Entire Amber Archive: by thread

Re: Counterions Eberhard von Kitzing (Wed Mar 10 1999 - 05:24:04 PST)
Counterions Rebecca Perlow (Mon Mar 22 1999 - 16:42:06 PST)
Re: equilibration of water dek_at_cgl.ucsf.edu (Mon Mar 29 1999 - 08:31:55 PST)
Solvent - solute interactions reat valerie (Thu Apr 22 1999 - 09:44:21 PDT)
Re: Solvent - solute interactions ross_at_cgl.ucsf.EDU (Thu Apr 22 1999 - 11:45:26 PDT)
Re: Solvent equilibration problem Carlos Simmerling (Thu Apr 29 1999 - 10:29:02 PDT)
- Re: Solvent equilibration problem Thomas Cheatham (Thu Apr 29 1999 - 10:40:55 PDT)
Re: Viewing dynamic output ross_at_cgl.ucsf.EDU (Thu Apr 29 1999 - 14:13:05 PDT)
- Re: Viewing dynamic output Daniel Barsky (Thu Apr 29 1999 - 14:49:23 PDT)
Re: Viewing dynamic output Rik Deitsch (Thu Apr 29 1999 - 20:34:57 PDT)
- Re: Viewing dynamic output Carlos Simmerling (Fri Apr 30 1999 - 04:39:22 PDT)
parm98.dat Thomas E. Cheatham (Tue May 11 1999 - 08:20:48 PDT)
solvent diffusion problem solved Mathy Froeyen (Wed May 26 1999 - 02:05:23 PDT)
crown tutorial ross_at_cgl.ucsf.EDU (Sat May 29 1999 - 16:45:06 PDT)
Re: references for MD simulations of mutations Daniel Barsky (Wed Jun 09 1999 - 12:42:59 PDT)
- Re: references for MD simulations of mutations Marcela Madrid (Wed Jun 09 1999 - 12:47:10 PDT)
- Re: references for MD simulations of mutations Dr. Daniel Barsky (Thu Jul 08 1999 - 14:40:33 PDT)
Re: H2O to keep?.... (fwd) ross_at_cgl.ucsf.EDU (Tue Jun 29 1999 - 13:55:20 PDT)
output of xleap Thomas Connor Bishop (Wed Jun 30 1999 - 13:09:25 PDT)
AMBER FF in Gaussian98 James Duncan (Wed Jul 07 1999 - 21:43:45 PDT)
- Re: AMBER FF in Gaussian98 Eberhard von Kitzing (Wed Jul 07 1999 - 23:18:44 PDT)
- Re: references for MD simulations of mutations Marcela Madrid (Thu Jul 08 1999 - 14:31:30 PDT)
Re: charged solute ross_at_cgl.ucsf.EDU (Thu Jul 08 1999 - 17:39:38 PDT)
Re: Question on Ewald and Belly! Thomas A. Darden (Mon Jul 12 1999 - 07:25:54 PDT)
Re: Addtional impropers? (fwd) Ding Sun (Tue Jul 13 1999 - 12:30:09 PDT)
ANAL Questions! Dat H. Nguyen (Wed Jul 14 1999 - 14:09:01 PDT)
- Re: ANAL Questions! ross_at_cgl.ucsf.EDU (Wed Jul 14 1999 - 19:20:49 PDT)
  - Re: ANAL Questions! Yongxing Liu (Thu Jul 15 1999 - 07:17:27 PDT)
- residue (re)numbering in leap. Tom Bishop (Thu Jul 15 1999 - 07:16:00 PDT)
Re: RNA Sebastien Lemieux (Wed Jul 21 1999 - 10:47:25 PDT)
Re: RNA ross_at_cgl.ucsf.EDU (Wed Jul 21 1999 - 11:15:06 PDT)
(no subject) Rebecca Perlow (Thu Jul 22 1999 - 13:01:01 PDT)
- Re: (no subject) David A. Case (Tue Feb 18 2003 - 14:16:34 PST)
(no subject) ross_at_cgl.ucsf.EDU (Thu Jul 22 1999 - 14:35:12 PDT)
Re: Sander Omar Stradella (Wed Aug 11 1999 - 11:29:20 PDT)
Problem with bench test on PIII450 Claudio Chuaqui (Fri Aug 13 1999 - 10:33:54 PDT)
- Re: Problem with bench test on PIII450 David Case (Fri Aug 13 1999 - 11:54:48 PDT)
- Re: Problem with bench test on PIII450 ross_at_cgl.ucsf.EDU (Fri Aug 13 1999 - 12:55:32 PDT)
  - Re: Problem with bench test on PIII450 dek_at_cgl.ucsf.EDU (Fri Aug 13 1999 - 13:48:28 PDT)
  - high temperature MD Anton Guliaev (Fri Aug 20 1999 - 16:51:28 PDT)
  - Normal mode analysis - breathing motion? J.E. Maxwell (Tue Aug 24 1999 - 18:09:57 PDT)
Another BUG in ewald erfc (Was Re: erfc math library bug: gnu libm) Thomas Huber (Wed Aug 25 1999 - 05:52:21 PDT)
- Re: Another BUG in ewald erfc (Was Re: erfc math library bug: gnu libm) Thomas A. Darden (Wed Aug 25 1999 - 06:58:09 PDT)
- ANAL QUestion! Dat Nguyen (Wed Sep 01 1999 - 14:10:27 PDT)
- PMF calculations using Ewald Xavier Deupi (Thu Sep 23 1999 - 23:39:52 PDT)
- Interface CRAIG ANTHONY MARHEF (Mon Oct 18 1999 - 14:11:59 PDT)
  - Re: Interface David Pearlman (Mon Oct 18 1999 - 17:03:52 PDT)
re: pgc compilation error... ross_at_cgl.ucsf.EDU (Fri Oct 22 1999 - 02:44:40 PDT)
Solvated protein... Antonello Romani (Mon Oct 25 1999 - 05:06:24 PDT)
system translation in PBC Jianxin Guo (Mon Oct 25 1999 - 17:53:25 PDT)
Large RMS deviations samantha hughes (Tue Oct 26 1999 - 06:00:26 PDT)
more on RMS fits samantha hughes (Tue Oct 26 1999 - 06:26:31 PDT)
RMS fit summary samantha hughes (Wed Oct 27 1999 - 08:51:02 PDT)
- Re: RMS fit summary ross_at_cgl.ucsf.EDU (Wed Oct 27 1999 - 11:57:28 PDT)
- Re: RMS fit summary Carlos Simmerling (Wed Oct 27 1999 - 12:29:16 PDT)
- RMS Mihaly Mezei (Wed Oct 27 1999 - 13:36:09 PDT)
- About the nonbonded parameters Lu (Thu Oct 28 1999 - 10:20:59 PDT)
- H-bond monitor Carolyn A. Kanagy (Thu Oct 28 1999 - 10:35:56 PDT)
- About the 'mixing' rule of nonbonded parameters Lu (Fri Oct 29 1999 - 05:12:09 PDT)
- MACHINE file to use Marcela Madrid (Mon Nov 01 1999 - 08:25:13 PST)
- SPASM software... Antonello Romani (Tue Nov 02 1999 - 05:04:16 PST)
- File conversion: Amber 5.0 to 4.1 Peter M. Gannett (Tue Nov 02 1999 - 07:06:28 PST)
- dipolar coupling restraints Richard Stefl (Wed Nov 03 1999 - 06:13:57 PST)
  - Re: dipolar coupling restraints Vickie Tsui (Wed Nov 03 1999 - 09:48:37 PST)
- link user1 (Wed Nov 03 1999 - 07:51:20 PST)
  - Re: link jim caldwell (Wed Nov 03 1999 - 11:42:00 PST)
  - Re: link ross_at_cgl.ucsf.EDU (Wed Nov 03 1999 - 12:14:44 PST)
  - Request for the bugfixes R P Ojha c/o CHP (Wed Nov 03 1999 - 20:32:38 PST)
  - saving parameters in LEaP Nelson Teixeira Brito (Thu Nov 04 1999 - 03:38:53 PST)
  - creating a box of solvent Marcela Madrid (Thu Nov 04 1999 - 14:23:22 PST)
    - Re: creating a box of solvent ross_at_cgl.ucsf.EDU (Thu Nov 04 1999 - 17:55:40 PST)
    - Re: creating a box of solvent Dinesh Gupta (Fri Nov 05 1999 - 03:27:44 PST)
    - (no subject) Nicola Culeddu (Fri Nov 05 1999 - 00:33:57 PST)
Re: solvent box Bill Ross (Mon Nov 29 1999 - 15:20:36 PST)
energy decomposition Andrea Bernini (Wed Dec 01 1999 - 04:31:27 PST)
carnal Marcela Madrid (Wed Dec 01 1999 - 13:40:40 PST)
gibbs restraint ? Terreux Raphael (Fri Dec 03 1999 - 17:30:50 PST)
FORCE UNIT Fumiko ABOSHI (Sat Dec 04 1999 - 09:08:18 PST)
VDW parameters of Sulfone and sulfoxide Ting Wang (Mon Dec 06 1999 - 01:19:25 PST)
NADH r.wigglesworth_at_ic.ac.uk (Mon Dec 06 1999 - 02:44:34 PST)
Compiling Leap (Amber 5.0) under Linux Rohit Batra (Mon Dec 06 1999 - 07:59:14 PST)
Nucleic Acid Builder (NAB) Peter M. Gannett (Tue Dec 07 1999 - 10:01:50 PST)
atom types Jason McCary (Tue Dec 07 1999 - 12:16:33 PST)
Re: atom types Bill Ross (Tue Dec 07 1999 - 14:15:30 PST)
xleap problem Verschelde Jean-Luc (Wed Dec 08 1999 - 03:02:01 PST)
question Valeria Costa (Thu Dec 09 1999 - 10:02:17 PST)
- Re: question darden (Thu Dec 09 1999 - 12:32:18 PST)
- nmode memory? Jianxin Guo (Thu Dec 09 1999 - 15:21:40 PST)
- installing sander on T3E cecilia clementi (Fri Dec 10 1999 - 17:47:28 PST)
- multiplicity Jenny Viklund (Mon Dec 13 1999 - 04:07:04 PST)
- nmode in amber5 Scott E. Boesch (Tue Dec 14 1999 - 05:28:20 PST)
- AMBER version 6.0 Alain Porquet (Wed Dec 15 1999 - 00:45:05 PST)
  - Re: AMBER version 6.0 David Case (Wed Dec 15 1999 - 07:20:18 PST)
  - PME question francy_at_mvcch3.unica.it (Thu Dec 16 1999 - 04:45:08 PST)
  - PME question francy_at_mvcch3.unica.it (Thu Dec 16 1999 - 04:48:44 PST)
    - Re: PME question darden (Thu Dec 16 1999 - 15:09:27 PST)
    - parametrers.... Pascal Bonnet (Thu Dec 16 1999 - 19:33:44 PST)
    - MACHINE file Verschelde Jean-Luc (Fri Dec 17 1999 - 00:16:10 PST)
    - viewing md trajectory of a big system Terreux Raphael (Mon Dec 20 1999 - 18:12:39 PST)
    - Problems on Alpha: Too slow Martin Cernohorsky (Tue Dec 21 1999 - 12:48:21 PST)
    - Problems for Energy 1,4 Pascal Bonnet (Tue Dec 21 1999 - 16:45:22 PST)
    - [Newbie]MacOS X Server with Amber? Tsun-Mei Chang (Mon Dec 27 1999 - 11:16:29 PST)
    - Help on installing LEaP Jithesh P.V (Tue Dec 28 1999 - 05:23:48 PST)
    - Re: Help on installing LEaP dek_at_cgl.ucsf.edu (Tue Dec 28 1999 - 08:48:12 PST)
- Re: question David Case (Tue Nov 07 2000 - 11:55:47 PST)
- Re: question David A. Case (Fri Nov 15 2002 - 18:45:34 PST)
  - Re: question Ioana Cozmuta (Fri Nov 15 2002 - 19:22:13 PST)
    - RE: question Yong Duan (Fri Nov 15 2002 - 20:40:56 PST)
    - Re: question St�phane Teletch�a (Tue Nov 19 2002 - 04:43:04 PST)
    - limit of RMSD value Bimo Ario Tejo (Tue Nov 19 2002 - 05:57:40 PST)
    - Re: limit of RMSD value Thomas Cheatham (Tue Nov 19 2002 - 09:51:53 PST)
    - FEP/Gibbs question meiselba (Tue Nov 19 2002 - 07:29:07 PST)
    - Re: FEP/Gibbs question Lepsa (Tue Dec 10 2002 - 07:59:39 PST)
    - GIBBS - Error message. Miguel de Federico (Tue Nov 19 2002 - 08:00:25 PST)
    - Re: GIBBS - Error message. David A. Case (Tue Nov 19 2002 - 09:09:09 PST)
    - Conterions Monica (Sat Nov 16 2002 - 00:10:15 PST)
    - Re: Conterions David Case (Sat Nov 16 2002 - 11:45:01 PST)
    - Are posters to the Amber list being spammed? Nicholson, James D Mr ARO (Sun Nov 17 2002 - 17:48:15 PST)
    - choose dt in gibbs sxzheng (Sun Nov 17 2002 - 19:06:34 PST)
    - NATOM mismatch in coord and topology files. Narang Manpreet Kaur (Sun Nov 17 2002 - 22:49:46 PST)
    - creating a pdb trajectory with carnal Vlad Cojocaru (Mon Nov 18 2002 - 07:29:21 PST)
    - makeDIST_RST? Sichun Yang (Mon Nov 18 2002 - 15:44:09 PST)
    - Re: makeDIST_RST? David A. Case (Mon Nov 18 2002 - 16:15:35 PST)
    - (no subject) Narang Manpreet Kaur (Sat Nov 16 2002 - 02:17:02 PST)
    - Re: your mail David Case (Sat Nov 16 2002 - 07:43:29 PST)
Amber 6 - license agreement Peter M. Gannett (Tue Jan 04 2000 - 08:56:44 PST)
Surface accessible area and hydrogen bonds Koca, Jaroslav (Tue Jan 04 2000 - 09:24:42 PST)
AMBER 6 Bill Ross (Tue Jan 04 2000 - 11:46:01 PST)
problem of translation - rotation Emmanuel.Giudice_at_ibpc.fr (Tue Jan 11 2000 - 06:19:31 PST)
AMBER501 on linux Dr.Rajendra R. Joshi (Wed Jan 12 2000 - 04:43:00 PST)
Problem with AMBER installation Jithesh P.V (Wed Jan 12 2000 - 05:13:16 PST)
- Re: Problem with AMBER installation David Case (Wed Jan 12 2000 - 14:39:21 PST)
- compiling leap on a linux box Frank Yan (Wed Jan 12 2000 - 21:03:51 PST)
  - Re: compiling leap on a linux box Frank Yan (Thu Jan 13 2000 - 23:10:57 PST)
  - Amber on linux Dr.Rajendra R. Joshi (Thu Jan 13 2000 - 23:25:35 PST)
    - Re: Amber on linux dek_at_cgl.ucsf.edu (Thu Jan 13 2000 - 23:41:48 PST)
    - ewald and cutoff Frank Yan (Mon Jan 17 2000 - 19:54:07 PST)
    - Re: ewald and cutoff darden (Thu Jan 20 2000 - 08:31:52 PST)
    - adding counter ions Christopher Higgs (Fri Jan 21 2000 - 01:40:19 PST)
    - (no subject) Christopher Higgs (Fri Jan 21 2000 - 04:44:28 PST)
    - (no subject) Christopher Higgs (Fri Jan 21 2000 - 05:06:11 PST)
    - content of amber output:mden Thomas C. Bishop (Fri Jan 21 2000 - 09:01:55 PST)
    - carnal:TORSION phipsi BACKBONE error Thomas C. Bishop (Fri Jan 21 2000 - 10:16:11 PST)
    - (no subject) Frank Yan (Sun Jan 23 2000 - 12:37:06 PST)
    - DNA bending Anton Guliaev (Mon Jan 24 2000 - 16:52:28 PST)
    - Program to convert CHARMM force field file to AMBER format Kazuki Shinoda (Tue Jan 25 2000 - 01:23:05 PST)
    - SOS from Italy Giovanni Bottegoni (Tue Jan 25 2000 - 02:56:21 PST)
    - non-aqueous solvent; ethanediol Marcela Madrid (Tue Jan 25 2000 - 06:37:57 PST)
    - dimer Margaret Cheung (Tue Jan 25 2000 - 10:10:55 PST)
    - Amber2curves Anton Guliaev (Tue Jan 25 2000 - 13:59:00 PST)
    - imaging problem in moil-view Frank Yan (Tue Jan 25 2000 - 16:32:54 PST)
    - Amber paramters Christopher Higgs (Wed Jan 26 2000 - 04:40:53 PST)
    - 2parts ehanol, 1 part water Marcela Madrid (Wed Jan 26 2000 - 07:31:47 PST)
    - parameters for a tetrazole Christopher Higgs (Wed Jan 26 2000 - 08:45:19 PST)
    - message in minimisation Alexandre Gillet (Fri Jan 28 2000 - 11:13:59 PST)
    - RESP question CRAIG ANTHONY MARHEF (Fri Jan 28 2000 - 12:24:42 PST)
    - RE: RESP question Bayly, Chris (Fri Jan 28 2000 - 12:52:40 PST)
    - thanks Alexandre Gillet (Fri Jan 28 2000 - 17:38:12 PST)
    - Problem with Protonate Jithesh P.V (Sat Jan 29 2000 - 00:02:57 PST)
    - 6.0 shipping status Bill Ross (Mon Jan 31 2000 - 12:49:37 PST)
    - AMBER PC-linux/O2 SGI Fdo Danilo Gonzalez Nilo (Tue Feb 01 2000 - 12:20:33 PST)
    - Re: AMBER PC-linux/O2 SGI Mark Forster (Wed Feb 02 2000 - 02:00:15 PST)
    - VdW numbers in Amber Dow Hurst (Wed Feb 02 2000 - 09:27:15 PST)
    - amber6 CD's Bill Ross (Wed Feb 02 2000 - 11:04:36 PST)
    - GTP Parameters Kazuki Shinoda (Thu Feb 03 2000 - 03:33:12 PST)
    - library entry for amidated c-terminus Jessica Rogers (Thu Feb 03 2000 - 13:55:45 PST)
    - parallel computing of amber 6 Frank Yan (Thu Feb 03 2000 - 21:52:47 PST)
    - AMBER 5.0 MPI and IBM RS6000 John Trent (Fri Feb 04 2000 - 10:05:36 PST)
    - (no subject) Jithesh P.V (Fri Feb 04 2000 - 20:53:12 PST)
    - AMBER 5.0 on IBM SP2! Dat H. Nguyen (Sat Feb 05 2000 - 14:40:29 PST)
    - continue running Frank Yan (Sun Feb 06 2000 - 08:45:51 PST)
    - amber 6 note Bill Ross (Mon Feb 07 2000 - 13:39:57 PST)
    - Location of /doc directory? Marios Philippopoulos (Tue Feb 08 2000 - 08:40:03 PST)
    - Re: Location of /doc directory? Frank Yan (Tue Feb 08 2000 - 23:09:20 PST)
    - amber on alpha Tsun-Mei Chang (Tue Feb 08 2000 - 12:16:25 PST)
    - questions about AMBER_SERVER Sylvie Derreumaux (Tue Feb 08 2000 - 17:21:38 PST)
    - a question about compiling amber6 Frank Yan (Tue Feb 08 2000 - 23:02:07 PST)
    - urgent sohail qamar (Mon Jan 17 2000 - 22:31:33 PST)
    - make off file from minimized coordinate. Hyuk Soon Choi (Tue Jan 18 2000 - 17:31:24 PST)
    - Re: make off file from minimized coordinate. Hyuk Soon Choi (Tue Jan 18 2000 - 21:14:14 PST)
- List of force field parameters_II Fran�ois Yves Dupradeau (Thu Jan 13 2000 - 09:03:44 PST)
About periodic box & modification of sander(5.0) B (Wed Jan 19 2000 - 16:29:04 PST)
amber problem Alexandre Gillet (Wed Jan 19 2000 - 17:28:31 PST)
- Re: amber problem dek_at_cgl.ucsf.edu (Wed Jan 19 2000 - 09:12:05 PST)
- amber parameters request Alexandre Gillet (Wed Jan 19 2000 - 11:37:34 PST)
- Fw: amber problem Carlos Simmerling (Wed Aug 28 2002 - 10:10:26 PDT)
Re: a question about compiling amber6 (fwd) Nelson Teixeira Brito (Wed Feb 09 2000 - 08:07:34 PST)
first Amber 6 bug-fixes and manual updates are now available.... David Case (Wed Feb 09 2000 - 16:51:26 PST)
Compilation of AMBER 6.0 on Origin 2000 Marios Philippopoulos (Thu Feb 10 2000 - 08:00:03 PST)
- Re: Compilation of AMBER 6.0 on Origin 2000 Marios Philippopoulos (Thu Feb 10 2000 - 09:51:07 PST)
OWFEG and other AMBER 6.0 manual issues CRAIG ANTHONY MARHEF (Fri Feb 11 2000 - 08:00:20 PST)
- Re: OWFEG and other AMBER 6.0 manual issues David Pearlman (Fri Feb 11 2000 - 08:42:42 PST)
- PME on cluster on linux Kouji Hayama (Fri Feb 11 2000 - 09:20:36 PST)
  - Re: PME on cluster on linux Kouji Hayama (Fri Feb 11 2000 - 10:09:05 PST)
- Re: OWFEG and other AMBER 6.0 manual issues David Case (Fri Feb 11 2000 - 09:54:44 PST)
Solute temp Andrew A Petersen (Fri Feb 11 2000 - 08:42:32 PST)
unit Jin-Kee Hyun (Fri Feb 11 2000 - 11:09:13 PST)
is leap compatible? Frank Yan (Fri Feb 11 2000 - 14:02:40 PST)
- Re: is leap compatible? jim caldwell (Fri Feb 11 2000 - 14:18:40 PST)
Re: Is PME MPI-parallelized in v.6.0? Marios Philippopoulos (Tue Feb 15 2000 - 07:58:31 PST)
- Re: Is PME MPI-parallelized in v.6.0? Marios Philippopoulos (Wed Feb 16 2000 - 14:10:26 PST)
compilation problem Krzysztof Murzyn (Tue Feb 15 2000 - 09:19:10 PST)
AMBER6 on a CRAY SV1-B Didier Rognan (Wed Feb 16 2000 - 04:05:34 PST)
Leap compilation sami jabir (Wed Feb 16 2000 - 05:44:44 PST)
Missing opls_parm.dat Marios Philippopoulos (Thu Feb 17 2000 - 14:12:46 PST)
LAM Mpi not efficient for sander ? Xavier Deupi (Fri Feb 18 2000 - 02:11:06 PST)
compilation errors Giulio (Fri Feb 18 2000 - 02:46:31 PST)
(no subject) Sylvie Derreumaux (Fri Feb 18 2000 - 02:51:50 PST)
opls_parm.dat Marios Philippopoulos (Fri Feb 18 2000 - 12:21:34 PST)
parallel sander Frank Yan (Fri Feb 18 2000 - 14:42:26 PST)
- Re: parallel sander Jianxin Guo (Sat Feb 19 2000 - 11:58:57 PST)
- Re: parallel sander Yuguang Mu (Thu Jun 21 2001 - 23:43:07 PDT)
Can I use heme prameters with param94 ? Kazuki Shinoda (Mon Feb 21 2000 - 03:42:29 PST)
Merz-Kollman atomic radii for Cu and Fe Dmitry M. Medvedev (Tue Feb 22 2000 - 00:23:47 PST)
AMBER PBC images Alexander Issanin (Tue Feb 22 2000 - 05:45:28 PST)
- Re: AMBER PBC images David Case (Tue Feb 22 2000 - 07:43:57 PST)
- Moilview and Quicktime movies CRAIG ANTHONY MARHEF (Tue Feb 22 2000 - 12:55:27 PST)
- SGI+MPICH Krzysztof Murzyn (Wed Feb 23 2000 - 09:12:06 PST)
- the topology file in mutant MM-PBSA calculation? Jianxin Guo (Wed Feb 23 2000 - 10:03:07 PST)
- MOIL-View and Quicktime Recap CRAIG ANTHONY MARHEF (Wed Feb 23 2000 - 10:22:42 PST)
- Amber 6.0 build under Solaris 2.6 Thomas A. Spraggins (Wed Feb 23 2000 - 10:31:28 PST)
- problem of compilation of roar-cp mao xiang (Thu Feb 24 2000 - 01:47:34 PST)
- Molecular Modelling example Ulrich Essmann (Thu Feb 24 2000 - 07:57:36 PST)
- nmode out of memory Frank Yan (Thu Feb 24 2000 - 22:41:48 PST)
- ATP parameters for MD simulation Mary Kurnikova (Fri Feb 25 2000 - 13:47:39 PST)
- Problems using IBELLY in AMBER6 Marios Philippopoulos (Mon Feb 28 2000 - 11:53:51 PST)
  - Re: Problems using IBELLY in AMBER6 Marios Philippopoulos (Mon Feb 28 2000 - 15:24:22 PST)
  - Re: Problems using IBELLY in AMBER6 Marios Philippopoulos (Tue Feb 29 2000 - 07:43:04 PST)
  - Re: Problems using IBELLY in AMBER6 Marios Philippopoulos (Tue Feb 29 2000 - 10:25:36 PST)
Please tell me calcium parameter Kouji Hayama (Mon Feb 28 2000 - 21:38:43 PST)
parameter for mm_pbsa Frank Yan (Tue Feb 29 2000 - 16:39:44 PST)
problems with MD user1 (Wed Mar 01 2000 - 06:27:10 PST)
compile in linux Cui Guanglei (Wed Mar 01 2000 - 07:34:31 PST)
- Re: compile in linux Cui Guanglei (Wed Mar 01 2000 - 12:51:39 PST)
Testing problems with SGI Irix 6.5.5! James M. Funaoka (Wed Mar 01 2000 - 09:41:26 PST)
Issues with compiling AMBER6 (MPI) on Linux dek_at_nano.nmr.ucsf.edu (Wed Mar 01 2000 - 13:50:10 PST)
- Re: Issues with compiling AMBER6 (MPI) on Linux Guanglei Cui (Wed Mar 01 2000 - 19:03:51 PST)
- Compile problem Yanni Wang (Thu Mar 02 2000 - 03:34:52 PST)
- re Yanni Wang's compile problem Chuck Schneider (Thu Mar 02 2000 - 06:24:40 PST)
- compile on linux Guanglei Cui (Thu Mar 02 2000 - 19:11:59 PST)
- About PME neutralization B (Sun Mar 05 2000 - 18:42:19 PST)
  - Re: About PME neutralization darden (Wed Mar 08 2000 - 10:40:41 PST)
- compilation of sander Giulio (Mon Mar 06 2000 - 04:08:35 PST)
- parallel problem ? Alexandre Gillet (Mon Mar 06 2000 - 10:41:20 PST)
  - Re: parallel problem ? Alexandre Gillet (Mon Mar 06 2000 - 14:30:56 PST)
- Harmonic restraints on distances in sander Marios Philippopoulos (Mon Mar 06 2000 - 12:23:40 PST)
  - Re: Harmonic restraints on distances in sander Vickie Tsui (Mon Mar 06 2000 - 13:12:25 PST)
    - Re: Harmonic restraints on distances in sander Andrea Bernini (Wed Mar 08 2000 - 08:37:09 PST)
    - Re: Harmonic restraints on distances in sander Vickie Tsui (Wed Mar 08 2000 - 10:06:41 PST)
    - Re: Harmonic restraints on distances in sander Marios Philippopoulos (Wed Mar 08 2000 - 11:13:12 PST)
    - Re: Harmonic restraints on distances in sander Vickie Tsui (Wed Mar 08 2000 - 11:52:57 PST)
    - H-bond angles CRAIG ANTHONY MARHEF (Wed Mar 08 2000 - 12:28:37 PST)
    - Re: H-bond angles Cui Guanglei (Wed Mar 08 2000 - 12:56:29 PST)
    - Ewald parameters Alexander Issanin (Thu Mar 09 2000 - 04:26:40 PST)
    - Re: Ewald parameters darden (Thu Mar 09 2000 - 11:28:30 PST)
    - IBELLY Marios Philippopoulos (Thu Mar 09 2000 - 09:06:06 PST)
    - Re: IBELLY Jarrod Smith (Thu Mar 09 2000 - 10:07:13 PST)
    - Re: IBELLY Marios Philippopoulos (Thu Mar 09 2000 - 10:09:49 PST)
    - Re: IBELLY Carlos Simmerling (Thu Mar 09 2000 - 10:43:44 PST)
    - Re: IBELLY David Case (Thu Mar 09 2000 - 10:25:33 PST)
    - Re: IBELLY Jarrod Smith (Thu Mar 09 2000 - 10:41:53 PST)
    - Re: IBELLY darden (Thu Mar 09 2000 - 11:46:41 PST)
    - NRUN in input file David Bevan (Sun Mar 12 2000 - 12:36:03 PST)
    - Re: NRUN in input file jim caldwell (Sun Mar 12 2000 - 16:47:19 PST)
    - opls_parm.dat Elsa Sousa Henriques (Mon Mar 13 2000 - 07:34:23 PST)
    - OpenMP parallelization in AMBER6 Marios Philippopoulos (Mon Mar 13 2000 - 11:30:41 PST)
    - Re: OpenMP parallelization in AMBER6 Carlos Simmerling (Mon Mar 13 2000 - 12:04:44 PST)
    - Re: OpenMP parallelization in AMBER6 Yong Duan (Mon Mar 13 2000 - 12:21:07 PST)
    - problem with makeDIST_RST Lin Ivan (Mon Mar 13 2000 - 23:53:30 PST)
    - nmode-error message bernd wellenzohn (Wed Mar 15 2000 - 02:42:12 PST)
    - DHFR - MTX Eoin Galligan (Wed Mar 15 2000 - 07:17:45 PST)
    - estimate entropy of dna using nmode Frank Yan (Thu Mar 16 2000 - 07:43:50 PST)
    - Re: estimate entropy of dna using nmode David Case (Fri Mar 17 2000 - 08:21:15 PST)
    - Re: estimate entropy of dna using nmode Bill Ross (Fri Mar 17 2000 - 10:05:39 PST)
    - progesterone parameter Alexandre Gillet (Fri Mar 17 2000 - 14:07:03 PST)
    - protein capping Francois Dupradeau (Fri Mar 17 2000 - 16:35:29 PST)
    - Carnal NORM Pascal Bonnet (Mon Mar 20 2000 - 11:48:48 PST)
    - Error with GB Jarrod Smith (Tue Mar 21 2000 - 10:33:26 PST)
    - prep file Alexandre Gillet (Tue Mar 21 2000 - 14:45:09 PST)
    - CARNAL Code crwatts_at_creighton.edu (Tue Mar 21 2000 - 18:25:17 PST)
    - request Prem Raj Joseph (Wed Mar 08 2000 - 03:20:16 PST)
distance-dependent dielectric in nmode Frank Yan (Tue Mar 07 2000 - 10:55:36 PST)
About "Nukit"! James M. Funaoka (Tue Mar 07 2000 - 12:07:44 PST)
About "Nukit"! James M. Funaoka (Tue Mar 07 2000 - 12:07:44 PST)
About "Nukit"! James M. Funaoka (Tue Mar 07 2000 - 12:07:44 PST)
gibbs Giulio (Wed Mar 08 2000 - 01:17:31 PST)
- Re: gibbs Dr.Rajendra R. Joshi (Wed Mar 08 2000 - 01:38:02 PST)
perturbed topology file Terreux Raphael (Wed Mar 22 2000 - 16:26:07 PST)
- Re: perturbed topology file jim caldwell (Wed Mar 22 2000 - 08:24:23 PST)
- Re: perturbed topology file Bill Ross (Wed Mar 22 2000 - 09:07:51 PST)
- a question regarding ISCHARGE=1 Wu Tzu Hsien (Wed Mar 22 2000 - 18:36:01 PST)
  - Side chain mobility Aleksandras Gutmanas (Thu May 04 2000 - 08:28:13 PDT)
  - H+ parameters Pascal Bonnet (Thu May 04 2000 - 18:56:21 PDT)
  - pressureS Victor Pham (Fri May 05 2000 - 10:57:24 PDT)
  - problems in sander devi rvel (Sun May 07 2000 - 00:53:52 PDT)
    - Re: problems in sander Yong Duan (Sun May 07 2000 - 13:11:36 PDT)
    - (no subject) Michal Otyepka (Mon May 08 2000 - 02:02:31 PDT)
    - babel Fran�ois Yves Dupradeau (Mon May 08 2000 - 04:06:51 PDT)
    - Density value in sander output mariang98 (Mon May 08 2000 - 14:57:37 PDT)
    - protonated adenine and cytosine? Alan Cheng (Mon May 08 2000 - 20:09:40 PDT)
    - regarding edit option Prem Raj Joseph (Tue May 09 2000 - 11:19:30 PDT)
    - 6-12 nonbonded function Karl N. Kirschner (Tue May 09 2000 - 11:17:45 PDT)
    - AMBER 6 and residual dipolar coupling Fabio Arnesano (Wed May 10 2000 - 01:36:25 PDT)
    - Re: AMBER 6 and residual dipolar coupling Vickie Tsui (Wed May 10 2000 - 10:04:11 PDT)
    - Looking for a PREP input file Jose Ramon Blas (Thu May 11 2000 - 10:33:28 PDT)
    - carnal script Peter Gannett (Wed May 10 2000 - 06:37:37 PDT)
Re: how to get unusual topology in leap Bill Ross (Thu Mar 23 2000 - 11:25:00 PST)
Re: trouble with NTR=1 and NMROPT=1 Vickie Tsui (Sat Mar 25 2000 - 09:58:04 PST)
problem in AMBER Mao Xiang (Sun Mar 26 2000 - 02:18:00 PST)
problem in GIBBS Mao Xiang (Tue Mar 28 2000 - 23:54:11 PST)
parametrization Cristina Dezi (Thu Mar 30 2000 - 00:06:56 PST)
wcleap Nelson Teixeira Brito (Thu Mar 30 2000 - 02:07:38 PST)
- Re: wcleap Nelson Teixeira Brito (Mon Apr 03 2000 - 10:14:25 PDT)
entropy estimation from harmonic analysis Ann Hermone (Thu Mar 30 2000 - 17:29:38 PST)
Hi Mao Xiang (Thu Mar 30 2000 - 18:42:43 PST)
Empty gap in the watbox at the beginning of MD Francois Vanelle (Fri Mar 31 2000 - 01:28:15 PST)
- Re: Empty gap in the watbox at the beginning of MD David Case (Wed Apr 05 2000 - 08:36:29 PDT)
- Force field Yanni Wang (Wed Apr 05 2000 - 11:19:17 PDT)
- Protein and Ligand in Leap David Bevan (Thu Apr 06 2000 - 08:56:51 PDT)
- units of force constant Yasuyuki Fujii (Thu Apr 06 2000 - 20:23:37 PDT)
- Paramters for sulfate and methanol Oliver Zerbe (Fri Apr 07 2000 - 05:21:03 PDT)
- entropy estimation of dna with car. Frank Yan (Tue Apr 11 2000 - 10:42:28 PDT)
2 questions Fran�ois Yves Dupradeau (Fri Mar 31 2000 - 06:58:01 PST)
How to creat new force field parameter for Mg++? Minmin Wang (Tue Apr 04 2000 - 05:42:27 PDT)
Re: problems in sander Bill Ross (Sun May 07 2000 - 01:54:57 PDT)
Re: a6 sander gb breaks on smallmol Jarrod Smith (Thu May 11 2000 - 15:42:03 PDT)
pdb files Victor Pham (Thu May 11 2000 - 17:09:11 PDT)
d-uridine Friedrich A. Gollmick (Fri May 12 2000 - 03:17:41 PDT)
TAUP Surjit Dixit (Fri May 12 2000 - 12:18:35 PDT)
question about imaging rathinavelan thenmalarchelvi (Sat May 13 2000 - 14:45:30 PDT)
Amber6 documentation jim caldwell (Tue May 16 2000 - 11:37:49 PDT)
question on expanding nphb Margaret Cheung (Tue May 16 2000 - 18:27:31 PDT)
Hello Mao Xiang (Wed May 17 2000 - 01:13:42 PDT)
- Re: Hello David Case (Wed May 17 2000 - 07:43:47 PDT)
- [pavan.bnpi.com: 'Coordinate resetting in amber6'] David Case (Wed May 17 2000 - 15:08:18 PDT)
Re: [pavan.bnpi.com: 'Coordinate resetting in amber6'] Michael Crowley (Wed May 17 2000 - 16:08:26 PDT)
equilibration of CH2Cl2 box Jes�s G�mez (Thu May 18 2000 - 05:30:32 PDT)
gibbs in sodium Mao Xiang (Thu May 18 2000 - 19:06:48 PDT)
AMBER installation kian kani (Fri May 19 2000 - 10:27:37 PDT)
amber parameters Mao Xiang (Fri May 19 2000 - 21:07:56 PDT)
3-botton emulat Yunfeng Hu (Mon May 22 2000 - 13:10:23 PDT)
Compile Problem ptraj with PGI compiler Kouji Hauyama (Mon May 22 2000 - 19:45:10 PDT)
sander compile error with MPICH compiled by PGI compiler Kouji Hauyama (Tue May 23 2000 - 05:34:15 PDT)
Re: Crosslink in Leap Bill Ross (Tue May 23 2000 - 22:28:37 PDT)
Re: DOUBT IN PTRAJ DOCUMENTATION A.Madhumalar (Wed May 24 2000 - 00:05:12 PDT)
Re: DOUBT IN AMBER5 PTRAJ DOCUMENTATION (fwd) A.Madhumalar (Wed May 24 2000 - 03:53:32 PDT)
Re: Help with polynucleotide building David Case (Wed May 24 2000 - 15:53:24 PDT)
- Additional Water Potentials Garrett W Grahek (Wed Nov 29 2000 - 14:20:33 PST)
dummy atom as anchor in gibbs ? Terreux Raphael (Thu May 25 2000 - 14:53:43 PDT)
soft repulsion option Cristina Dezi (Fri May 26 2000 - 01:15:01 PDT)
4096wat running problem Kouji Hauyama (Fri May 26 2000 - 07:09:42 PDT)
- Re: 4096wat running problem David Konerding (Fri May 26 2000 - 08:02:18 PDT)
  - Re: 4096wat running problem Kouji Hayama (Fri May 26 2000 - 08:36:50 PDT)
  - Re: 4096wat running problem Michael Crowley (Fri May 26 2000 - 09:22:10 PDT)
Re: Periodic boundary condition jim caldwell (Fri May 26 2000 - 10:28:50 PDT)
Simulation of DNA Marcela Madrid (Fri May 26 2000 - 10:58:19 PDT)
Periodic boundary condition Prem Raj Joseph (Fri May 26 2000 - 11:36:41 PDT)
4096wat runnning problem Kouji Hauyama (Sat May 27 2000 - 05:41:24 PDT)
center of mass with gibbs ? Terreux Raphael (Mon May 29 2000 - 15:46:12 PDT)
AMBER 6.0 on parallel IBM SP system. Gerard GIL (Tue May 30 2000 - 07:09:07 PDT)
- Shake and a new computer system R. M. Fesinmeyer (Tue May 30 2000 - 10:50:25 PDT)
- improvements to force field Marcela Madrid (Tue May 30 2000 - 13:02:35 PDT)
- What does this mean? Renxiao Wang (Tue May 30 2000 - 16:46:03 PDT)
  - ROAR-CP calculation on axp machines HIRAO (Tue May 30 2000 - 19:23:02 PDT)
  - energy decomposition along MD trajectory Michal Otyepka (Wed May 31 2000 - 05:59:36 PDT)
  - md toolchest Cui Guanglei (Wed May 31 2000 - 10:16:32 PDT)
  - inquire about the cost of the license. Margaret Cheung (Wed May 31 2000 - 10:54:13 PDT)
  - rms in rdparm Frank Yan (Wed May 31 2000 - 15:38:51 PDT)
  - Visualization Garrett W Grahek (Wed May 31 2000 - 16:50:57 PDT)
    - Re: Visualization David Case (Thu Jun 01 2000 - 06:54:39 PDT)
  - RESP Pascal Bonnet (Wed May 31 2000 - 19:27:34 PDT)
  - Compiling AMBER in LINUX Antonio D�az (Thu Jun 01 2000 - 04:40:47 PDT)
    - Re: Compiling AMBER in LINUX Kouji Hayama (Thu Jun 01 2000 - 07:24:51 PDT)
    - amber on alpha Xiaolin Allen Zhao (Thu Jun 01 2000 - 23:00:00 PDT)
    - re: amber on alpha Chuck Schneider (Wed Feb 09 2000 - 05:19:45 PST)
    - Re: amber on alpha jim caldwell (Fri Jun 02 2000 - 12:08:56 PDT)
    - how to set up free energy perturbation Mao Xiang (Sun Jun 04 2000 - 02:23:40 PDT)
    - ANTECHAMBER Graham Russel (Tue Jun 06 2000 - 06:57:31 PDT)
    - Wee Problems. Mark Markson (Tue Jun 06 2000 - 07:10:35 PDT)
    - Benzamidine Osmar Norberto de Souza (Fri Jun 02 2000 - 04:37:50 PDT)
  - formamides r.wigglesworth_at_ic.ac.uk (Thu Jun 01 2000 - 06:34:05 PDT)
xleap EOIN GALLIGAN (Fri Jun 09 2000 - 09:51:07 PDT)
Re: xleap Bill Ross (Fri Jun 09 2000 - 11:28:28 PDT)
GB parameters Craig Marhefka (Sun Jun 11 2000 - 15:59:18 PDT)
- Re: GB parameters Vickie Tsui (Mon Jun 12 2000 - 10:05:46 PDT)
- Polarizabilities Olga Carvalho (Tue Jun 13 2000 - 04:19:01 PDT)
  - Re: Polarizabilities jim caldwell (Tue Jun 13 2000 - 13:09:46 PDT)
  - bond order EOIN GALLIGAN (Tue Jun 13 2000 - 08:44:09 PDT)
  - amber on AMDs cluster Xavier Deupi (Wed Jun 14 2000 - 05:35:41 PDT)
    - Re: amber on AMDs cluster Lawrence Tsang (Tue Jun 13 2000 - 08:55:47 PDT)
    - Re: amber on AMDs cluster Nelson Teixeira Brito (Tue Jun 13 2000 - 11:25:19 PDT)
    - Re: amber on AMDs cluster Cezary Czaplewski (Wed Jun 14 2000 - 09:33:39 PDT)
    - Re: amber on AMDs cluster David Konerding (Wed Jun 14 2000 - 10:18:16 PDT)
    - Re: amber on AMDs cluster Cezary Czaplewski (Wed Jun 14 2000 - 19:45:02 PDT)
    - AMBER performance with g77 David Konerding (Wed Jun 14 2000 - 20:53:54 PDT)
    - bond order Eoin Galligan (Thu Jun 15 2000 - 06:32:28 PDT)
    - Ibelly and sander6 Craig Marhefka (Thu Jun 15 2000 - 12:58:32 PDT)
    - CMC Craig Marhefka (Thu Jun 15 2000 - 13:01:02 PDT)
    - Re: CMC Jed Pitera (Thu Jun 22 2000 - 01:47:45 PDT)
    - force constants Roberta Spadaccini (Thu Jun 22 2000 - 08:49:04 PDT)
    - site mutation with xLeap Minmin Wang (Thu Jun 22 2000 - 09:04:46 PDT)
    - Compiling AMBER6 under OCTANE DUO Miguel Angel (Fri Jun 23 2000 - 08:45:25 PDT)
    - Re: Compiling AMBER6 under OCTANE DUO Nelson Teixeira Brito (Fri Jun 23 2000 - 09:18:13 PDT)
    - modify topology file Frank Yan (Fri Jun 23 2000 - 11:57:48 PDT)
    - Re: modify topology file Bill Ross (Fri Jun 23 2000 - 16:51:53 PDT)
    - SGI Grzegorz Jezierski (Fri Jun 16 2000 - 07:44:32 PDT)
    - ISTAR2 Craig A Marhefka (Fri Jun 16 2000 - 11:27:07 PDT)
    - pairlist Laila Abou Zeid (Sat Jun 17 2000 - 22:08:36 PDT)
    - Re: pairlist jim caldwell (Sun Jun 18 2000 - 07:19:43 PDT)
    - density decreases Michal Otyepka (Mon Jun 19 2000 - 01:30:32 PDT)
    - AMBER6.0 on t3e Grzegorz Jezierski (Mon Jun 19 2000 - 07:52:46 PDT)
    - Attachment Grzegorz Jezierski (Mon Jun 19 2000 - 07:53:50 PDT)
    - error message in compiling amber6 Margaret Cheung (Wed Jun 21 2000 - 13:05:06 PDT)
    - error message in compiling amber6 Margaret Cheung (Wed Jun 21 2000 - 13:05:06 PDT)
    - error message in compiling amber6 Margaret Cheung (Wed Jun 21 2000 - 13:05:06 PDT)
    - error message in compiling amber6 Margaret Cheung (Wed Jun 21 2000 - 13:05:06 PDT)
    - error message in compiling amber6 Margaret Cheung (Wed Jun 21 2000 - 13:05:06 PDT)
    - error message in compiling amber6 Margaret Cheung (Wed Jun 21 2000 - 13:05:06 PDT)
    - error message in compiling amber6 Margaret Cheung (Wed Jun 21 2000 - 13:05:06 PDT)
    - reading back into leap Marcela Madrid (Wed Jun 21 2000 - 13:50:00 PDT)
    - reading back into leap Marcela Madrid (Wed Jun 21 2000 - 13:50:00 PDT)
    - reading back into leap Marcela Madrid (Wed Jun 21 2000 - 13:50:00 PDT)
    - reading back into leap Marcela Madrid (Wed Jun 21 2000 - 13:50:00 PDT)
    - reading back into leap Marcela Madrid (Wed Jun 21 2000 - 13:50:00 PDT)
    - reading back into leap Marcela Madrid (Wed Jun 21 2000 - 13:50:00 PDT)
    - question in compiling amber6 on linux. Margaret Cheung (Wed Jun 21 2000 - 16:27:36 PDT)
    - question in compiling amber6 on linux. Margaret Cheung (Wed Jun 21 2000 - 16:27:36 PDT)
    - question in compiling amber6 on linux. Margaret Cheung (Wed Jun 21 2000 - 16:27:36 PDT)
    - A thought in the mind P.Kangueane (Wed Jun 14 2000 - 11:47:55 PDT)
    - amber ramon kleber da rocha (Wed Jun 14 2000 - 13:05:00 PDT)
    - (no subject) Peter Gannett (Wed Jun 14 2000 - 19:39:18 PDT)
    - (no subject) David Konerding (Wed Jun 14 2000 - 20:38:38 PDT)
ChemInt2000 - July 1 Early Registration Deadine Steve Heller (Mon Jun 12 2000 - 06:53:18 PDT)
Re: how to retrieve the average structure of MD? Ivan Bea i Bobet (Fri Jun 23 2000 - 16:58:03 PDT)
cion & LINMIN failure takahas_at_bio.nagoya-u.ac.jp (Sat Jun 24 2000 - 08:38:24 PDT)
- Re: cion & LINMIN failure takahas_at_bio.nagoya-u.ac.jp (Mon Jun 26 2000 - 02:24:01 PDT)
- Re: cion & LINMIN failure takahas_at_bio.nagoya-u.ac.jp (Mon Jun 26 2000 - 06:52:21 PDT)
partially solvate the protein Minmin Wang (Mon Jun 26 2000 - 13:10:32 PDT)
- Re: partially solvate the protein Minmin Wang (Mon Jun 26 2000 - 14:37:21 PDT)
- linmin failure? Margaret Cheung (Mon Jun 26 2000 - 14:55:32 PDT)
- Coord. reset. not accomp.: Set-up vs. Soft/Hardware issue? Robert Matthew Fesinmeyer (Mon Jun 26 2000 - 15:11:29 PDT)
  - Re: Coord. reset. not accomp.: Set-up vs. Soft/Hardware issue? David Konerding (Mon Jun 26 2000 - 15:55:05 PDT)
  - ambpdb problem r.wigglesworth_at_ic.ac.uk (Mon Jun 26 2000 - 23:55:44 PDT)
  - query Anat Zvi (Tue Jun 27 2000 - 07:20:22 PDT)
  - help! simulation of membrane protein Pornthep Sompornpisut (Tue Jun 27 2000 - 15:09:49 PDT)
  - NAN Laila Abou Zeid (Wed Jun 28 2000 - 03:14:39 PDT)
  - NAN ( Laila Abou Zeid (Wed Jun 28 2000 - 03:33:32 PDT)
  - unable to extract trajectory of MD simulation with sander_classic Minmin Wang (Wed Jun 28 2000 - 07:37:27 PDT)
    - Re: unable to extract trajectory of MD simulation with sander_classic David Konerding (Wed Jun 28 2000 - 08:57:48 PDT)
Re: amber6 and redhat 6.2 ( Margaret Cheung (Tue Jul 25 2000 - 11:48:21 PDT)
- Re: amber6 and redhat 6.2 (thank you all) Margaret Cheung (Tue Jul 25 2000 - 12:25:50 PDT)
- What can I get from docking? Lawrence Tsang (Tue Jul 25 2000 - 14:20:09 PDT)
- problem on launching xleap chinlin guo (Tue Jul 25 2000 - 17:52:33 PDT)
- Zinc potential? Hyuk Soon Choi (Thu Jul 27 2000 - 06:22:36 PDT)
- Periodic Boundary Condition Kouji Hayama (Sun Jul 30 2000 - 22:11:53 PDT)
  - Re: Periodic Boundary Condition Kouji Hayama (Thu Aug 24 2000 - 00:09:40 PDT)
- units Krzysztof Murzyn (Mon Jul 31 2000 - 05:06:29 PDT)
- Gibbs and PME simulation with DNA David Bosch (Mon Jul 31 2000 - 06:20:02 PDT)
- temperature and pressure control Marcela Madrid (Mon Jul 31 2000 - 07:35:16 PDT)
  - Re: temperature and pressure control jim caldwell (Mon Jul 31 2000 - 09:42:00 PDT)
  - Ca2+ parameters Jarrod Smith (Tue Aug 01 2000 - 16:44:44 PDT)
    - Re: Ca2+ parameters Kouji Hayama (Tue Aug 01 2000 - 23:20:06 PDT)
    - animation of normal modes Scott Boesch (Thu Aug 03 2000 - 13:26:34 PDT)
Re: How to make pdb"q" files easily? Bill Ross (Fri Aug 04 2000 - 10:33:58 PDT)
Profec wentaofu (Fri Aug 04 2000 - 11:17:56 PDT)
a question about the setting to contrain kinetic energy Margaret Cheung (Sat Aug 05 2000 - 23:04:43 PDT)
ChemInt2000 hotel rooms Steve Heller (Sun Aug 06 2000 - 14:59:49 PDT)
isoxazole force constants Eric Hu (Mon Aug 07 2000 - 12:30:11 PDT)
Did MM/PBSA runs on linux also? Lawrence Tsang (Mon Aug 07 2000 - 21:42:39 PDT)
Where to download mm5_car1.Z for example1 of mmpbsa? Lawrence Tsang (Mon Aug 07 2000 - 21:59:34 PDT)
Ph.D. thesis in Strasbourg-France Didier Rognan (Tue Aug 08 2000 - 02:11:10 PDT)
Myrinet + Beowulf for AMBER? Jarrod Smith (Tue Aug 08 2000 - 07:19:54 PDT)
- RE: Myrinet + Beowulf for AMBER? Kouji Hayama (Tue Aug 08 2000 - 22:11:41 PDT)
- Problem with PME test Jithesh P.V (Thu Aug 10 2000 - 05:01:55 PDT)
  - Re: Problem with PME test Jithesh P.V (Fri Aug 11 2000 - 09:04:02 PDT)
  - Re: Problem with PME test Michael Crowley (Fri Aug 11 2000 - 12:02:56 PDT)
  - compiling AMBER5.0 on Beowolf cluster Andrew Petersen (Fri Aug 11 2000 - 13:39:43 PDT)
    - Re: compiling AMBER5.0 on Beowolf cluster Juergen Suehnel (Sat Aug 12 2000 - 03:52:27 PDT)
    - MACHINE file for DEC Alpha! Jennifer Bui (Tue Aug 15 2000 - 00:40:55 PDT)
    - Re: MACHINE file for DEC Alpha! Thomas A. Spraggins (Tue Aug 15 2000 - 04:59:51 PDT)
    - Re: MACHINE file for DEC Alpha! jim caldwell (Tue Aug 15 2000 - 07:30:21 PDT)
    - PME with charged system Marcela Madrid (Tue Aug 15 2000 - 07:31:04 PDT)
    - Re: PME with charged system David Small (Tue Aug 15 2000 - 19:17:45 PDT)
    - AMBER installation Dayle Smith (Wed Aug 16 2000 - 11:55:27 PDT)
    - NAD parameters Raphael Buencamino (Wed Aug 16 2000 - 17:46:37 PDT)
    - cobalt DOIZI Denis 98775 (Thu Aug 17 2000 - 00:31:43 PDT)
    - dielectric constant David Small (Thu Aug 17 2000 - 12:10:25 PDT)
    - Re: dielectric constant Soaring Bear (Sat Aug 19 2000 - 08:03:43 PDT)
    - AMBER 5.01 on Linux Ramon Garduno (Fri Aug 18 2000 - 11:53:56 PDT)
    - Oct box and ptraj Robert Matthew Fesinmeyer (Mon Aug 21 2000 - 11:12:50 PDT)
    - Re: AMBER 5.01 on Linux Ramon Garduno (Thu Aug 24 2000 - 13:02:49 PDT)
    - absoft and AMBER6 Jarrod Smith (Thu Aug 24 2000 - 19:33:00 PDT)
    - minimization from the average structure of MD simulation Minmin Wang (Tue Aug 29 2000 - 09:25:01 PDT)
    - Re: PME with charged system darden (Fri Aug 18 2000 - 21:52:26 PDT)
    - need help nurindah wulandari (Tue Aug 15 2000 - 07:43:48 PDT)
  - analysis tool for water and stacking? Frank Yan (Fri Aug 11 2000 - 15:40:32 PDT)
- MM-PBSA trajectory file samantha hughes (Fri Aug 11 2000 - 07:28:48 PDT)
- reassigning temp. during MD Raik Gruenberg (Fri Aug 11 2000 - 08:03:06 PDT)
  - Re: reassigning temp. during MD Robert Matthew Fesinmeyer (Mon Aug 21 2000 - 15:20:53 PDT)
    - Re: reassigning temp. during MD Carlos Simmerling (Wed Aug 23 2000 - 09:41:17 PDT)
  - processing of carnal output Michal Otyepka (Tue Aug 22 2000 - 03:23:06 PDT)
  - how to justify the size of a periodic box. Margaret Cheung (Tue Aug 22 2000 - 16:47:41 PDT)
  - MDEN output file format Fabrice YERLY (Wed Aug 23 2000 - 03:14:01 PDT)
    - Calcium bonds schayg_at_puskin-a206.sote.hu (Thu Sep 07 2000 - 04:24:10 PDT)
    - Amber6 environment error kian kani (Thu Sep 07 2000 - 10:24:57 PDT)
    - Re: Amber6 environment error Thomas A. Spraggins (Thu Sep 07 2000 - 11:24:07 PDT)
    - Re: Amber6 environment error schayg_at_puskin-a206.sote.hu (Thu Sep 07 2000 - 13:44:11 PDT)
    - partial solvation EOIN GALLIGAN (Thu Sep 07 2000 - 07:53:10 PDT)
    - partial solvation EOIN GALLIGAN (Fri Sep 08 2000 - 03:56:30 PDT)
    - radius of gyration Peter Gannett (Mon Sep 11 2000 - 10:24:10 PDT)
  - sysdir Nelson Teixeira Brito (Wed Aug 23 2000 - 08:20:00 PDT)
    - Re: sysdir jim caldwell (Wed Aug 23 2000 - 10:30:22 PDT)
    - Re: sysdir Chuck Schneider (Wed Aug 23 2000 - 11:01:07 PDT)
    - shared mem David Small (Wed Aug 23 2000 - 15:03:40 PDT)
    - Parm99 Jie Guo (Thu Aug 24 2000 - 09:03:21 PDT)
    - Bang for the Buck Robert Matthew Fesinmeyer (Fri Feb 09 2001 - 13:50:57 PST)
    - Re: Bang for the Buck mite51 (Fri Feb 09 2001 - 14:33:44 PST)
    - Re: Bang for the Buck David Konerding (Fri Feb 09 2001 - 14:54:13 PST)
    - Re: Bang for the Buck Jarrod Smith (Fri Feb 09 2001 - 18:55:10 PST)
    - Re: Bang for the Buck David Pearlman (Fri Feb 09 2001 - 15:19:12 PST)
    - Re: Bang for the Buck Bill Ross (Fri Feb 09 2001 - 15:51:42 PST)
    - Re: Bang for the Buck David Pearlman (Fri Feb 09 2001 - 17:16:42 PST)
    - Re: Bang for the Buck Jarrod Smith (Fri Feb 09 2001 - 18:13:31 PST)
    - Re: Bang for the Buck Carlos Simmerling (Fri Feb 09 2001 - 19:59:16 PST)
    - Re: Bang for the Buck R. M. Fesinmeyer (Sat Feb 10 2001 - 03:10:46 PST)
    - Regarding MD dynamic group (Sat Feb 10 2001 - 01:29:42 PST)
    - Re: Regarding MD Andreas Svrcek-Seiler (Sun Feb 11 2001 - 23:26:12 PST)
    - Regarding the construction of gris in insightII dynamic group (Mon Feb 12 2001 - 01:43:19 PST)
    - batch mode Fernanda Camarinha (Mon Feb 12 2001 - 09:29:07 PST)
    - Re: batch mode Jake Isaacs (Mon Feb 12 2001 - 10:18:28 PST)
    - a few more questions Jake Isaacs (Mon Feb 12 2001 - 10:37:16 PST)
    - Gibbs Ann Hermone (Mon Feb 12 2001 - 12:17:51 PST)
    - Re: Bang for the Buck Margaret Cheung (Sat Feb 10 2001 - 23:20:46 PST)
    - (no subject) noor gaffoor (Sun Feb 11 2001 - 21:08:17 PST)
    - Re: sysdir Nelson Teixeira Brito (Thu Aug 24 2000 - 02:05:02 PDT)
urgent sohail qamar (Tue Aug 08 2000 - 07:21:16 PDT)
charges for new compound Marcela Madrid (Tue Aug 08 2000 - 08:03:54 PDT)
Re: Amber6 on a ES40/4CPUs jim caldwell (Tue Aug 08 2000 - 08:20:49 PDT)
Re: two questions: (1)dihedral, (2) movies Carlos Simmerling (Tue Aug 15 2000 - 08:15:45 PDT)
- Re: two questions: (1)dihedral, (2) movies Frank Yan (Tue Aug 15 2000 - 08:47:59 PDT)
- Re: two questions: (1)dihedral, (2) movies samantha hughes (Tue Aug 15 2000 - 09:12:41 PDT)
vdw parameter Todd J. Minehardt (Tue Aug 15 2000 - 09:44:50 PDT)
Annealing with rigid body Pornthep Sompornpisut (Tue Aug 15 2000 - 12:29:34 PDT)
anal.in format J. Bryan Buckalew (Thu Aug 24 2000 - 08:52:21 PDT)
Re: Questions on the definition of parameters jim caldwell (Tue Aug 29 2000 - 12:57:57 PDT)
Brief courses on AMBER 6 Michael Cooney (Wed Aug 30 2000 - 08:54:37 PDT)
- Re: Brief courses on AMBER 6 David Case (Wed Aug 30 2000 - 09:48:16 PDT)
  - Re: Brief courses on AMBER 6 Jarrod Smith (Wed Aug 30 2000 - 10:24:20 PDT)
    - Re: Brief courses on AMBER 6 Jarrod Smith (Fri Sep 01 2000 - 10:12:42 PDT)
    - Can I create a prmtop file without unwanted H atoms? Margaret Cheung (Fri Sep 01 2000 - 17:48:20 PDT)
    - NATOMS > 99999 for sander 6.0 Todd J. Minehardt (Mon Sep 04 2000 - 07:25:27 PDT)
    - last message continued Todd J. Minehardt (Mon Sep 04 2000 - 07:27:52 PDT)
    - NATOMS > 99999 David Konerding (Mon Sep 04 2000 - 09:03:55 PDT)
    - Gibbs / Torcon problem Terreux Raphael (Mon Sep 04 2000 - 10:53:58 PDT)
    - ambpdb input format Garrett W Grahek (Mon Sep 04 2000 - 13:58:29 PDT)
    - Leap problems with Zn, DNA Michael Cooney (Tue Sep 05 2000 - 14:59:54 PDT)
    - sander_pme.MC examples leila ayadi (Wed Sep 06 2000 - 07:13:05 PDT)
    - RAdius of Gyration Dat H. Nguyen (Wed Sep 06 2000 - 13:05:50 PDT)
    - ..and also getcor.f.... Todd J. Minehardt (Mon Sep 04 2000 - 07:42:52 PDT)
    - DFT parital charges Riccardo Nifosi (Mon Sep 04 2000 - 07:47:24 PDT)
  - "Protonate" errors Michael Cooney (Wed Aug 30 2000 - 11:40:53 PDT)
  - Benchmarking AMD CPUS Yongxing Liu (Thu Aug 31 2000 - 03:14:36 PDT)
  - rdparm/ptraj Tuomo Laitinen (Thu Aug 31 2000 - 05:50:59 PDT)
    - Re: rdparm/ptraj Thomas E. Cheatham, III (Thu Aug 31 2000 - 11:03:07 PDT)
manganese ions Natasja Brooijmans (Thu Aug 31 2000 - 15:23:24 PDT)
question about 2DRMSd made by rdparm. Margaret Cheung (Fri Sep 01 2000 - 03:34:47 PDT)
Re: RAdius of Gyration Bill Ross (Wed Sep 06 2000 - 15:11:16 PDT)
Re: Calcium bonds Bill Ross (Thu Sep 07 2000 - 11:50:47 PDT)
Re: radius of gyration Bill Ross (Mon Sep 11 2000 - 12:41:00 PDT)
NAMOT J. Bryan Buckalew (Mon Sep 11 2000 - 13:18:49 PDT)
Machine file for SV1 Matthew Lee (Mon Sep 11 2000 - 14:23:52 PDT)
Adding divalent metal ions to libraries Michael Cooney (Tue Sep 12 2000 - 14:31:06 PDT)
Ewald bomb ? Terreux Raphael (Tue Sep 12 2000 - 15:51:01 PDT)
compiling problems Paolo Dapporto (Wed Sep 13 2000 - 01:01:04 PDT)
- Re: compiling problems Todd J. Minehardt (Wed Sep 13 2000 - 08:02:24 PDT)
- compile on ibm Todd J. Minehardt (Wed Sep 13 2000 - 08:23:55 PDT)
- IBM SP Matthew Lee (Wed Sep 13 2000 - 10:27:32 PDT)
GB/SA question Andreas Svrcek-Seiler (Wed Sep 13 2000 - 07:47:11 PDT)
- EWALD parameter range problem schayg_at_puskin-a206.sote.hu (Wed Sep 13 2000 - 11:48:24 PDT)
  - Re: EWALD parameter range problem darden (Wed Sep 13 2000 - 15:29:16 PDT)
  - NMODE Tuomo Laitinen (Wed Sep 13 2000 - 23:36:43 PDT)
    - Re: NMODE Todd J. Minehardt (Thu Sep 14 2000 - 07:13:49 PDT)
  - VRAND Craig Marhefka (Thu Sep 14 2000 - 06:48:49 PDT)
Re: problem with leap Bill Ross (Thu Sep 14 2000 - 10:52:17 PDT)
problem with leap Prem Raj Joseph (Thu Sep 14 2000 - 22:31:57 PDT)
RE:pdb_MD Krishna Bisetty (Fri Sep 15 2000 - 05:18:53 PDT)
delphi Pascal Bonnet (Fri Sep 15 2000 - 06:29:43 PDT)
ANAL J. Bryan Buckalew (Fri Sep 15 2000 - 07:48:08 PDT)
C=C gail louise dempsey (Fri Sep 15 2000 - 09:25:34 PDT)
Call for Papers - ACS Symposium: "Artificial Intelligence in Computational Chemistry" Curt M. Breneman (Fri Sep 15 2000 - 10:23:31 PDT)
edit.out David Small (Fri Sep 15 2000 - 13:19:07 PDT)
Amber6/Compaq jim caldwell (Fri Sep 15 2000 - 14:27:16 PDT)
Re: Can amber6.0 do the implicit sovation model? Vickie Tsui (Sun Sep 17 2000 - 23:36:35 PDT)
erfcfun.c for Alpha Yasuyuki Fujii (Tue Sep 19 2000 - 22:55:10 PDT)
- Re: erfcfun.c for Alpha Chuck Schneider (Wed Sep 20 2000 - 04:46:43 PDT)
- GB source code question samantha hughes (Wed Sep 20 2000 - 07:12:03 PDT)
- Loading CRD or RST files into Leap Michael Cooney (Wed Sep 20 2000 - 08:55:17 PDT)
  - RE: Loading CRD or RST files into Leap Halima Amer (Wed Sep 20 2000 - 09:57:47 PDT)
Re: Loading CRD or RST files into Leap Bill Ross (Wed Sep 20 2000 - 12:39:11 PDT)
To Cray t3e users Grzegorz Jezierski (Thu Sep 21 2000 - 03:21:08 PDT)
interaction energy Christopher Higgs (Thu Sep 21 2000 - 03:42:00 PDT)
- Re: interaction energy Michal Otyepka (Thu Sep 21 2000 - 07:02:16 PDT)
- about constraints Hyuk Soon Choi (Thu Sep 21 2000 - 07:22:08 PDT)
Re: interaction energy Bill Ross (Thu Sep 21 2000 - 08:23:00 PDT)
Re: Too many atoms Bill Ross (Sat Sep 23 2000 - 12:55:06 PDT)
AMBER data file for program DOT J�rgen J. M�ller (Mon Sep 25 2000 - 10:12:56 PDT)
- (no subject) Christian Pilger (Tue Oct 10 2000 - 08:26:05 PDT)
  - Re: your mail schayg_at_puskin-a206.sote.hu (Thu Oct 12 2000 - 02:41:46 PDT)
  - HBOND analysis after CARNAL samantha hughes (Thu Oct 12 2000 - 05:31:11 PDT)
  - LGFIL and other outputs for OWFEG calcs Craig Marhefka (Thu Oct 12 2000 - 08:43:01 PDT)
  - Field delegate for MidasPlus Craig Marhefka (Thu Oct 12 2000 - 08:44:55 PDT)
  - Cysteine with negative charge Jennifer Ludington (Thu Oct 12 2000 - 10:16:52 PDT)
  - improper density in constant pressure md Scott A. Showalter (Thu Oct 12 2000 - 11:18:51 PDT)
    - (no subject) Christian Pilger (Mon Oct 16 2000 - 10:20:20 PDT)
    - (no subject) Christian Pilger (Mon Oct 16 2000 - 10:20:20 PDT)
    - Forwarded mail.... Christian Pilger (Tue Oct 17 2000 - 07:38:44 PDT)
    - Linux Giulio Rastelli (Tue Oct 17 2000 - 07:59:45 PDT)
  - amber6 Scott E. Boesch (Thu Oct 12 2000 - 12:28:15 PDT)
    - Re: amber6 jim caldwell (Thu Oct 12 2000 - 13:46:24 PDT)
    - correlation matrix Michal Otyepka (Fri Oct 13 2000 - 02:01:30 PDT)
    - Free Energy Calculation with Potential of Mean Force Nori (Fri Oct 13 2000 - 07:49:55 PDT)
- CYM residue Jennifer Ludington (Tue Oct 10 2000 - 12:54:11 PDT)
- gibbs output Marcela Madrid (Tue Oct 10 2000 - 14:35:22 PDT)
  - Re: gibbs output jim caldwell (Tue Oct 10 2000 - 15:37:28 PDT)
  - namelist Eoin Galligan (Wed Oct 11 2000 - 07:11:07 PDT)
  - MD namelist error with new Sander Michael Cooney (Wed Oct 11 2000 - 09:39:22 PDT)
TIP3P water in Amber6 Michael Cooney (Mon Sep 25 2000 - 10:47:19 PDT)
Re: TIP3P water in Amber6 Bill Ross (Mon Sep 25 2000 - 12:00:25 PDT)
vdW parameter for S atom Francois Dupradeau (Mon Sep 25 2000 - 17:07:06 PDT)
AMBER data file for program DOT J�rgen J. M�ller (Mon Sep 25 2000 - 22:26:27 PDT)
REPEATED LINMIN FAILURE Mao Xiang (Tue Sep 26 2000 - 03:12:57 PDT)
Re: excluded atoms in prmtop files Bill Ross (Wed Sep 27 2000 - 09:06:57 PDT)
Re: leap problem about periodic boundary box Bill Ross (Wed Sep 27 2000 - 20:54:04 PDT)
nmode out of memory schayg_at_puskin-a206.sote.hu (Thu Sep 28 2000 - 05:35:46 PDT)
- Re: nmode out of memory David Case (Thu Sep 28 2000 - 08:09:53 PDT)
- MPI gibbs Jarrod Smith (Thu Sep 28 2000 - 08:26:45 PDT)
- movie file Pascal Bonnet (Fri Sep 29 2000 - 02:56:16 PDT)
  - Re: movie file terreux_at_taloa.unice.fr (Fri Sep 29 2000 - 12:24:26 PDT)
  - help with amber 41 on linux redhat 6.2 Margaret Cheung (Sat Sep 30 2000 - 00:49:35 PDT)
    - Re: help with amber 41 on linux redhat 6.2 David Konerding (Sat Sep 30 2000 - 18:07:53 PDT)
    - xleap Marcela Madrid (Mon Oct 02 2000 - 09:10:45 PDT)
    - Re: xleap schayg_at_puskin-a206.sote.hu (Wed Oct 04 2000 - 11:12:33 PDT)
    - CATFEE Announcement CATFEE (Wed Oct 04 2000 - 19:17:29 PDT)
    - Ewald Bomb Luis Gracia (Mon Oct 02 2000 - 09:30:10 PDT)
    - docking Michal Otyepka (Mon Oct 02 2000 - 10:15:21 PDT)
    - Re: docking Andreas Svrcek-Seiler (Thu Oct 05 2000 - 09:48:46 PDT)
    - SGI_MP and sander 6 Jarrod Smith (Mon Oct 02 2000 - 14:37:45 PDT)
    - Re: SGI_MP and sander 6 Nathalie Godbout (Tue Oct 03 2000 - 11:24:52 PDT)
    - Organic solvents with Leap Jose Ramon Blas (Tue Oct 03 2000 - 17:20:58 PDT)
    - [Fwd: Re: SGI_MP and sander 6] input files Nathalie Godbout (Wed Oct 04 2000 - 08:09:53 PDT)
- repeated linmin failures Michael Cooney (Fri Sep 29 2000 - 07:49:07 PDT)
- (no subject) Yanni Wang (Fri Sep 29 2000 - 08:42:48 PDT)
  - Re: problem with Interface script David Pearlman (Fri Sep 29 2000 - 10:07:44 PDT)
Re: movie file Bill Ross (Fri Sep 29 2000 - 10:15:15 PDT)
HEllo! Dat H. Nguyen (Fri Sep 29 2000 - 11:49:54 PDT)
- Re: HEllo! Thomas E. Cheatham, III (Sat Sep 30 2000 - 09:36:51 PDT)
Re: HEllo! Bill Ross (Fri Sep 29 2000 - 12:57:22 PDT)
perturbing charge Marcela Madrid (Fri Sep 29 2000 - 16:02:41 PDT)
Re: perturbing charge Bill Ross (Fri Sep 29 2000 - 16:55:00 PDT)
automatic/semi-automatic type assignments Thomas C. Bishop (Sat Sep 30 2000 - 14:37:29 PDT)
Sander error solved Bhupesh Taneja (Fri Oct 06 2000 - 15:52:03 PDT)
Re: amber6 on HP N-4000 Complex Scott Boesch (Fri Oct 13 2000 - 10:07:43 PDT)
water density around the molecule Shixiang Yan (Fri Oct 13 2000 - 21:01:26 PDT)
water density around the molecule Shixiang Yan (Fri Oct 13 2000 - 21:01:26 PDT)
showing density map? Jianxin Guo (Sun Oct 15 2000 - 13:48:48 PDT)
showing density map? Jianxin Guo (Sun Oct 15 2000 - 13:48:48 PDT)
- Re: showing density map? Bill Ross (Sun Oct 15 2000 - 19:43:07 PDT)
- Re: showing density map? Bill Ross (Sun Oct 15 2000 - 19:43:07 PDT)
Re: missing parameters Jie Lu (Fri Oct 20 2000 - 15:22:24 PDT)
- Re: missing parameters Jie Lu (Wed Oct 25 2000 - 16:38:31 PDT)
shared memory sander Shixiang Yan (Fri Oct 20 2000 - 16:00:14 PDT)
self diffusion of water at equilibrium T=300K P=1atm gail louise dempsey (Fri Oct 20 2000 - 18:55:38 PDT)
calculation time Andrew Aird (Mon Oct 23 2000 - 03:49:27 PDT)
Z-dna J. Bryan Buckalew (Mon Oct 23 2000 - 10:55:48 PDT)
Re: Plotting Hbond info from Carnal samantha hughes (Mon Oct 23 2000 - 11:41:10 PDT)
Adding metal parameter kiyean.nam_at_pharma.Novartis.com (Mon Oct 23 2000 - 15:53:27 PDT)
- Re: Adding metal parameter Michael Cooney (Tue Oct 24 2000 - 11:37:55 PDT)
- How to M'Halla Jalel (Tue Oct 24 2000 - 11:57:03 PDT)
carnal Eoin Galligan (Tue Oct 24 2000 - 04:24:55 PDT)
Cl and NO2 Oscar Rey (Tue Oct 24 2000 - 07:25:28 PDT)
addition to prev. mail Eoin Galligan (Tue Oct 24 2000 - 07:44:44 PDT)
Xtal Waters and SolvateBox Javier De Las Rivas (Tue Oct 24 2000 - 08:04:46 PDT)
- Re: Xtal Waters and SolvateBox Michael Cooney (Mon Oct 30 2000 - 11:52:32 PST)
- POL3 Bill Ross (Mon Oct 30 2000 - 13:09:40 PST)
  - Re: POL3 Bill Ross (Mon Oct 30 2000 - 14:25:06 PST)
  - (no subject) Alessandra Ricca (Mon Oct 30 2000 - 16:19:55 PST)
  - (no subject) Alessandra Ricca (Mon Oct 30 2000 - 16:23:12 PST)
Re: How to Bill Ross (Tue Oct 24 2000 - 12:47:44 PDT)
Re: Xtal Waters and SolvateBox Bill Ross (Tue Oct 24 2000 - 13:58:17 PDT)
sander on sgi O2/R5k--workaround Nathalie Godbout (Tue Oct 24 2000 - 14:46:58 PDT)
ntwxm,ntwvm,ntwem gail louise dempsey (Tue Oct 24 2000 - 15:47:45 PDT)
(no subject) gail louise dempsey (Tue Oct 24 2000 - 15:54:32 PDT)
ENTER to WIN a beautiful 1969 Z/28 Camaro for $1.00 Shannon (Tue Oct 24 2000 - 21:40:21 PDT)
MM_GBSA and DNA methylation Sylvie Derreumaux (Wed Oct 25 2000 - 07:06:17 PDT)
gibbs ile->val energies Steve Edmondson (Wed Oct 25 2000 - 07:26:45 PDT)
min error Eoin Galligan (Wed Oct 25 2000 - 11:22:00 PDT)
- Re: min error jim caldwell (Wed Oct 25 2000 - 12:40:02 PDT)
nonbonded pairlist update Andrew Aird (Thu Oct 26 2000 - 05:55:48 PDT)
- Re: nonbonded pairlist update Andrew Aird (Thu Oct 26 2000 - 14:38:28 PDT)
LGFIL and other outputs for OWFEG calcs Craig Marhefka (Thu Oct 26 2000 - 11:40:31 PDT)
Sander_classic to Sander switch Michael Cooney (Thu Oct 26 2000 - 13:10:59 PDT)
information d'Alessio, Paola (Fri Oct 27 2000 - 08:42:36 PDT)
(no subject) Alessandra Ricca (Mon Oct 30 2000 - 09:08:30 PST)
A problem with "inhomogeneous' Wen Li (Mon Oct 30 2000 - 11:11:22 PST)
sodium_gibbs_pme test Marcela Madrid (Mon Oct 30 2000 - 11:19:19 PST)
Protein-Protein docking Sam Andersen (Mon Oct 30 2000 - 11:51:40 PST)
- Re: Protein-Protein docking Simon Cross (Tue Oct 31 2000 - 02:02:19 PST)
- PME Andrew Aird (Tue Oct 31 2000 - 04:34:16 PST)
  - Re: PME David Case (Tue Oct 31 2000 - 10:55:15 PST)
- Sander compilation problem on HP Scott Boesch (Tue Oct 31 2000 - 07:57:48 PST)
  - Re: Sander compilation problem on HP jim caldwell (Tue Oct 31 2000 - 11:04:56 PST)
- Running tests on SP2 machine ramon kleber da rocha (Tue Oct 31 2000 - 10:01:16 PST)
re: frcmod polar Bill Ross (Tue Oct 31 2000 - 00:06:56 PST)
Re: Element Bill Ross (Tue Oct 31 2000 - 11:26:30 PST)
(no subject) Alessandra Ricca (Tue Oct 31 2000 - 13:41:44 PST)
- Re: your mail jim caldwell (Wed Nov 01 2000 - 07:56:51 PST)
amber6.0 timing Andrew Petersen (Wed Nov 01 2000 - 06:36:31 PST)
- Re: amber6.0 timing jim caldwell (Wed Nov 01 2000 - 13:13:59 PST)
- Problems with memory for large systems Grzegorz Jezierski (Thu Nov 02 2000 - 01:14:36 PST)
- belly Andrew Aird (Thu Nov 02 2000 - 08:04:42 PST)
- shake/potential function Andrew Aird (Thu Nov 02 2000 - 08:08:23 PST)
  - re: shake/potential function Bill Ross (Thu Nov 02 2000 - 10:21:26 PST)
RE: Elements Bayly, Chris (Wed Nov 01 2000 - 09:05:36 PST)
(no subject) Alessandra Ricca (Wed Nov 01 2000 - 09:17:57 PST)
- Re: your mail jim caldwell (Wed Nov 01 2000 - 11:17:25 PST)
- make install Margaret Doll (Wed Nov 01 2000 - 13:11:06 PST)
Re: make install Bill Ross (Thu Nov 02 2000 - 09:12:11 PST)
(no subject) Alessandra Ricca (Thu Nov 02 2000 - 09:35:49 PST)
Re: Using CARNAL to compute per-residue RMSD between PDB files Bill Ross (Thu Nov 02 2000 - 13:35:08 PST)
Re: finding average Thomas Cheatham (Fri Nov 03 2000 - 08:54:19 PST)
Sander/MPI/redimension Mihaly Mezei (Fri Nov 03 2000 - 10:28:27 PST)
Restraints in Amber6 Troy Bothwell (Fri Nov 03 2000 - 10:35:31 PST)
- RE: Restraints in Amber6 Troy Bothwell (Fri Nov 03 2000 - 11:33:45 PST)
- RE: Restraints in Amber6 Troy Bothwell (Fri Nov 03 2000 - 11:36:52 PST)
Re: Sander/MPI/redimension Michael Crowley (Fri Nov 03 2000 - 13:28:51 PST)
(no subject) Alessandra Ricca (Fri Nov 03 2000 - 16:23:45 PST)
(no subject) Bill Ross (Fri Nov 03 2000 - 17:56:12 PST)
Md at NVE A.Madhumalar (Sun Nov 05 2000 - 04:29:40 PST)
Re: Improper Dihedrals Bill Ross (Mon Nov 06 2000 - 15:54:20 PST)
(no subject) Alessandra Ricca (Mon Nov 06 2000 - 16:22:02 PST)
Re: leap problems Bill Ross (Mon Nov 06 2000 - 23:27:32 PST)
carbohydrate minimisation Mark Forster (Tue Nov 07 2000 - 09:06:33 PST)
Trying to compile Amber 6 on Intel/linux Leila Ayadi (Tue Nov 07 2000 - 09:25:40 PST)
- Re: Trying to compile Amber 6 on Intel/linux jim caldwell (Tue Nov 07 2000 - 11:33:17 PST)
OWFEG documentation Craig Marhefka (Tue Nov 07 2000 - 13:31:37 PST)
leap Nelson Brito (Wed Nov 08 2000 - 02:57:09 PST)
RE: Profect visualization jim caldwell (Wed Nov 08 2000 - 11:26:54 PST)
Re: Amber on Linux schayg_at_puskin-a206.sote.hu (Fri Nov 10 2000 - 05:33:47 PST)
Re: Cannoct connect to Amber Home Page Michael Cooney (Fri Nov 10 2000 - 09:44:54 PST)
PME group decomposition Andrew Petersen (Fri Nov 10 2000 - 09:46:19 PST)
PMF and PME with DNA David Bosch (Mon Nov 13 2000 - 01:51:47 PST)
- GB vs. GB/SA Andreas Svrcek-Seiler (Mon Nov 20 2000 - 06:09:08 PST)
  - Re: GB vs. GB/SA David Case (Tue Nov 21 2000 - 10:15:42 PST)
  - how to turn off self repulsion Marcela Madrid (Tue Nov 21 2000 - 11:39:45 PST)
  - Performance of Compaq ES vs IBM or ORIGIN servers Sam Andersen (Tue Nov 21 2000 - 18:54:39 PST)
    - Re: CCL:Performance of Compaq ES vs IBM or ORIGIN servers Nathalie Godbout (Tue Nov 28 2000 - 14:09:51 PST)
    - purine partial charges Andrew Petersen (Tue Nov 28 2000 - 14:40:07 PST)
    - missing parameters Andrew Aird (Wed Nov 29 2000 - 02:31:55 PST)
    - MM-PBSA miyasaki_at_haystack.lclark.edu (Wed Nov 29 2000 - 07:07:56 PST)
    - Re: MM-PBSA samantha hughes (Thu Nov 30 2000 - 00:05:22 PST)
    - PME GIOVA (Thu Nov 30 2000 - 06:01:11 PST)
    - Re: PME Michael Cooney (Wed Jan 31 2001 - 13:13:47 PST)
    - SUMMARY for GAMESS/GAUSSIAN MEP Francois Dupradeau (Wed Jan 31 2001 - 23:37:36 PST)
    - I'm upset ! Stephane (Thu Feb 01 2001 - 01:55:15 PST)
    - Re: I'm upset ! Nelson Brito (Thu Feb 01 2001 - 02:51:49 PST)
    - Re: I'm upset ! samantha hughes (Thu Feb 01 2001 - 02:17:16 PST)
    - NSCM in periodic simulations Peter Varnai (Thu Feb 01 2001 - 07:24:55 PST)
    - Re: I'm upset ! Dow Hurst (Thu Feb 01 2001 - 07:40:12 PST)
    - sense of justice Nelson Teixeira Brito (Thu Feb 01 2001 - 09:53:36 PST)
    - Nonbonded Pair List Troy Bothwell (Fri Feb 02 2001 - 11:18:16 PST)
    - how do I turn on the verbose option? Marcela Madrid (Fri Feb 02 2001 - 12:01:46 PST)
    - error msg Eoin Galligan (Mon Feb 05 2001 - 04:44:59 PST)
    - error msg Eoin Galligan (Mon Feb 05 2001 - 04:44:59 PST)
    - parm96 Giulio Rastelli (Tue Feb 06 2001 - 09:18:25 PST)
    - ptraj Troy Bothwell (Tue Feb 06 2001 - 10:36:20 PST)
    - AMBER parameter for HCOO(-) and NCHCHNHC Yinghong Sheng (Tue Feb 06 2001 - 15:18:00 PST)
    - not using SHAKE Eoin Galligan (Wed Feb 07 2001 - 05:27:24 PST)
    - Re: not using SHAKE Michael Cooney (Wed Feb 07 2001 - 08:32:51 PST)
    - Lone Pairs. Fred P. Arnold (Wed Feb 07 2001 - 14:19:32 PST)
    - RE: Lone Pairs. Bayly, Christopher (Thu Feb 08 2001 - 08:39:39 PST)
    - TIP4P water Maria Kurnikova (Thu Nov 30 2000 - 07:36:25 PST)
    - missing angle parameters Andrew Aird (Thu Nov 30 2000 - 09:38:22 PST)
    - Acetonitrile Jose Ramon Blas (Thu Nov 30 2000 - 20:38:32 PST)
    - Discover to AMBER trajectory utilities Mark Forster (Fri Dec 01 2000 - 02:30:31 PST)
    - libcss for SP2 Sanjeev B.S. (Mon Dec 04 2000 - 04:38:56 PST)
    - AMBER6 RESP arubin_at_unmc.edu (Mon Dec 04 2000 - 11:26:30 PST)
    - sander compilers Andrew Petersen (Mon Apr 09 2001 - 07:21:55 PDT)
    - Re: sander compilers David Konerding (Mon Apr 09 2001 - 09:13:23 PDT)
    - internal variables in ptraj Therese Malliavin (Tue Apr 10 2001 - 01:29:44 PDT)
    - TIP3P/SPC VdW radius artem (Tue Apr 10 2001 - 09:00:18 PDT)
    - Re: TIP3P/SPC VdW radius Thomas Huber (Tue Apr 10 2001 - 13:02:43 PDT)
    - Re: TIP3P/SPC VdW radius Jung-Hsing Lin (Tue Apr 10 2001 - 13:43:52 PDT)
    - Re: TIP3P/SPC VdW radius Mihaly Mezei (Tue Apr 10 2001 - 14:01:35 PDT)
    - water density and rdf calculations thenmalar rathinavelan (Wed Apr 11 2001 - 03:02:59 PDT)
    - N-terminal and C-terminal hydrogens Troy Bothwell (Thu Apr 12 2001 - 11:10:16 PDT)
    - Re: N-terminal and C-terminal hydrogens Michael Cooney (Thu Apr 12 2001 - 13:55:06 PDT)
    - odd display of ambpdb generated files Jake Isaacs (Fri Apr 13 2001 - 13:20:39 PDT)
    - RE: odd display of ambpdb generated files Troy Bothwell (Fri Apr 13 2001 - 17:02:26 PDT)
    - isotropic scaling of coordinates during MD Giulio Rastelli (Sat Apr 14 2001 - 04:35:48 PDT)
    - Compilation problem of AMBER6.0! Ireena Bagai (Mon Apr 16 2001 - 05:24:25 PDT)
    - Re: Compilation problem of AMBER6.0! Carlos Simmerling (Mon Apr 16 2001 - 07:01:06 PDT)
    - Re: Compilation problem of AMBER6.0! Stephane (Tue Apr 17 2001 - 02:46:44 PDT)
    - Re: odd display of ambpdb generated files Elsa Sousa Henriques (Mon Apr 16 2001 - 10:49:03 PDT)
    - Windows version of AMBER? Stan (Mon Apr 16 2001 - 23:59:44 PDT)
    - RE: Windows version of AMBER? Ostlund, Neil S. (Tue Apr 17 2001 - 10:04:04 PDT)
    - Re: odd display of ambpdb generated files Richard W Dixon (Tue Apr 17 2001 - 06:26:45 PDT)
    - Re: odd display of ambpdb generated files Mark Forster (Tue Apr 17 2001 - 08:58:49 PDT)
    - Re: odd display of ambpdb generated files David Case (Tue Apr 17 2001 - 09:27:19 PDT)
    - atom types for xleap Marcela Madrid (Tue Apr 17 2001 - 09:08:59 PDT)
    - Re: odd display of ambpdb generated files Bill Ross (Tue Apr 17 2001 - 08:42:26 PDT)
    - Re: odd display of ambpdb generated files Michael Cooney (Tue Apr 17 2001 - 09:56:36 PDT)
    - Re: odd display of ambpdb generated files Bill Ross (Tue Apr 17 2001 - 11:20:18 PDT)
    - Re: odd display of ambpdb generated files Mihaly Mezei (Tue Apr 17 2001 - 12:18:03 PDT)
    - Re: odd display of ambpdb generated files David Case (Tue Apr 17 2001 - 12:33:16 PDT)
    - 1-4 nonbonded interactions David L. Bostick (Wed Apr 18 2001 - 11:37:12 PDT)
    - ISTAR2 and 64-bit sander Jarrod Smith (Wed Apr 18 2001 - 12:20:05 PDT)
    - Re: ISTAR2 and 64-bit sander jim caldwell (Wed Apr 18 2001 - 13:26:42 PDT)
    - Problem in adding solvent other than water ... Mausumi Mazumdar (Wed Apr 18 2001 - 21:56:42 PDT)
    - Amber 6 on parallel SUN Christian Pilger (Thu Apr 19 2001 - 02:47:02 PDT)
    - Test run for gb_rna on AMBER6 (IBM SP3) Sanjeev B.S. (Thu Apr 19 2001 - 12:54:57 PDT)
    - Where to Start working in AMBER from? Ireena Bagai (Fri Apr 20 2001 - 06:07:23 PDT)
    - tleap but no xleap on IBM SP3 Sanjeev B.S. (Fri Apr 20 2001 - 07:44:04 PDT)
    - ptraj correlation command Troy Bothwell (Sat Apr 21 2001 - 07:23:40 PDT)
    - test run Sanjeev B.S. (Sat Apr 21 2001 - 14:24:25 PDT)
    - amber-request.cgl.ucsf.edu k. vengadesan (Sat Apr 21 2001 - 19:57:24 PDT)
    - Model(l)ing 2001 in Erlangen/Germany: Speaker list Harald Lanig (Mon Apr 23 2001 - 05:59:29 PDT)
    - problem with carnal on linux Riccardo Nifosi (Mon Apr 23 2001 - 08:03:40 PDT)
    - Problem, setting up AMBERHOME! Ireena Bagai (Tue Apr 24 2001 - 03:42:04 PDT)
    - RE: Problem, setting up AMBERHOME! Thomas A. Spraggins (Tue Apr 24 2001 - 05:23:48 PDT)
    - Re: Problem, setting up AMBERHOME! Andrea Bernini (Tue Apr 24 2001 - 07:08:08 PDT)
    - Re: Problem, setting up AMBERHOME! jim caldwell (Tue Apr 24 2001 - 08:04:42 PDT)
    - How to let IBELLY and NTR both on? Hai Long (Tue Apr 24 2001 - 09:10:49 PDT)
    - Re: How to let IBELLY and NTR both on? Svetlana Nolde (Wed Apr 25 2001 - 02:55:32 PDT)
    - special belly minimization Didier Rognan (Wed Apr 25 2001 - 03:40:51 PDT)
    - AMBER on LINUX Osvaldo Andrade Santos Filho (Wed Apr 25 2001 - 12:30:05 PDT)
    - Essential dynamics David Bevan (Thu Apr 26 2001 - 04:18:25 PDT)
    - create a parm.top file Pascal Bonnet (Tue Apr 24 2001 - 10:18:51 PDT)
    - Request. hparikh (Tue Apr 24 2001 - 14:12:52 PDT)
    - sander on SP3 Sanjeev B.S. (Tue Apr 24 2001 - 14:59:16 PDT)
    - Sander minimization kian kani (Tue Apr 24 2001 - 18:50:44 PDT)
    - Re: odd display of ambpdb generated files Bill Ross (Tue Apr 17 2001 - 12:22:19 PDT)
    - minimization Andrew Aird (Tue Apr 10 2001 - 09:05:27 PDT)
    - Delphi Calculations Guanglei Cui (Tue Apr 10 2001 - 12:15:01 PDT)
    - electrostatic point charge Olga Carvalho (Mon Apr 09 2001 - 07:45:19 PDT)
    - Question about TEMP and PRESS on Sander AMBER 5.1 Ramon Garduno (Mon Dec 04 2000 - 19:39:24 PST)
    - Small Molecule Paramaterisation Simon Cross (Fri Dec 01 2000 - 02:46:28 PST)
    - question about using SUN machine for amber? wentaofu (Fri Dec 01 2000 - 07:06:00 PST)
    - modeling GPCRs Giulio Rastelli (Wed Nov 29 2000 - 09:49:14 PST)
    - Parameter-Web Page Christian Pilger (Wed Nov 29 2000 - 12:10:19 PST)
  - Amber5 RESP (fwd) Simon Cross (Wed Nov 22 2000 - 05:55:10 PST)
- (no subject) Raja Swamynathan (Mon Nov 20 2000 - 07:30:03 PST)
- announcing mdxvu MD aanalysis code Mark Forster (Mon Nov 20 2000 - 08:30:58 PST)
- (no subject) Alessandra Ricca (Mon Nov 20 2000 - 14:14:44 PST)
- normal modes hermone_at_pegasus.arc.nasa.gov (Mon Nov 20 2000 - 15:51:55 PST)
- about PMF Kazunori Yamanaka (Mon Nov 20 2000 - 23:56:27 PST)
- error 76 Sara Madail (Tue Nov 21 2000 - 02:30:50 PST)
  - Re: error 76 Chuck Schneider (Tue Nov 21 2000 - 04:37:18 PST)
  - server down Michael Cooney (Tue Nov 21 2000 - 08:42:19 PST)
  - (no subject) robert (Tue Nov 21 2000 - 09:02:46 PST)
Question on Parallel Sander AMBER 6.0 Jennifer Bui (Mon Nov 13 2000 - 09:56:50 PST)
Re: Question on Parallel Sander AMBER 6.0 Michael Crowley (Mon Nov 13 2000 - 11:23:28 PST)
About Retinal K. Watanabe. (Mon Nov 13 2000 - 17:16:34 PST)
(no subject) Alessandra Ricca (Tue Nov 14 2000 - 15:12:00 PST)
- Re: your mail jim caldwell (Tue Nov 14 2000 - 16:29:29 PST)
- 2 questions mkf7_at_cornell.edu (Wed Nov 15 2000 - 15:00:54 PST)
  - Re: 2 questions David Case (Thu Nov 16 2000 - 07:55:35 PST)
    - Issues with Trunc. Oct. Robert Matthew Fesinmeyer (Thu Nov 16 2000 - 15:44:31 PST)
    - Re: Issues with Trunc. Oct. Pascal Bonnet (Fri Nov 17 2000 - 10:12:30 PST)
    - Re: 2 questions Simon Cross (Fri Nov 17 2000 - 01:40:57 PST)
  - (no subject) Joseph Nachman (Thu Nov 16 2000 - 08:13:48 PST)
    - Re: your mail Michael Cooney (Fri Nov 17 2000 - 08:56:30 PST)
    - (no subject) Joseph Nachman (Fri Nov 17 2000 - 08:59:23 PST)
Re: 2 questions Bill Ross (Wed Nov 15 2000 - 19:48:17 PST)
DNA dissociation in Ewald simulation Michael Cooney (Fri Nov 17 2000 - 13:39:05 PST)
Re: dynamics with different pH conditions David Case (Thu Nov 23 2000 - 12:02:46 PST)
Re: doubt in constant pressure simulations jim caldwell (Sat Nov 25 2000 - 10:15:15 PST)
File /usr/lib/libI77_mp.a Sanjeev B.S. (Sun Nov 26 2000 - 05:42:47 PST)
Re: Additional Water Potentials Bill Ross (Wed Nov 29 2000 - 16:47:37 PST)
Re: minimization of many structures jim caldwell (Tue Dec 05 2000 - 06:55:07 PST)
Re: minimization of many structures Bill Ross (Tue Dec 05 2000 - 08:47:16 PST)
Re: MPI Sander on a 5 node SMP cluster David Konerding (Tue Dec 05 2000 - 12:52:36 PST)
intprt on gibbs Marcela Madrid (Tue Dec 05 2000 - 13:19:52 PST)
Re: filter? jim caldwell (Wed Dec 06 2000 - 09:09:06 PST)
Monte-Carlo Andrew Aird (Wed Dec 06 2000 - 09:12:08 PST)
- Re: Monte-Carlo Jed Pitera (Thu Dec 07 2000 - 09:50:02 PST)
- Parm File MBDXISN2 (Thu Dec 07 2000 - 03:38:41 PST)
  - Re: Parm File jim caldwell (Thu Dec 07 2000 - 07:40:53 PST)
- run sander on shared memory sgi Shixiang Yan (Thu Dec 07 2000 - 11:48:41 PST)
- DEVIATION IS TOO LARGE Shixiang Yan (Fri Dec 08 2000 - 10:42:37 PST)
- QUESTION ABOUT SANDER Ramon Garduno (Fri Dec 08 2000 - 21:13:31 PST)
- sulfur parameters Cristina Dezi (Mon Dec 11 2000 - 12:39:16 PST)
- DNA flexibility Jithesh P.V (Mon Dec 11 2000 - 20:33:08 PST)
  - Re: DNA flexibility Filip Lankas (Tue Dec 12 2000 - 03:04:45 PST)
  - crd file input for ptraj Michael Cooney (Tue Dec 12 2000 - 09:02:37 PST)
  - frcmod file format in amber 6.0 Mathy Froeyen (Wed Dec 13 2000 - 01:01:04 PST)
- (no subject) danilosili (Tue Dec 12 2000 - 01:27:51 PST)
- (no subject) danilosili (Tue Dec 12 2000 - 01:27:57 PST)
Re: INTERNATIONAL PIANO MASTER CLASS 2001 Nelson Brito (Wed Dec 13 2000 - 02:17:35 PST)
reading in residues Eoin Galligan (Wed Dec 13 2000 - 09:12:51 PST)
Re: frcmod file format in amber 6.0 Bill Ross (Wed Dec 13 2000 - 09:57:27 PST)
Review a sample issue of the Journal of Applied Spectroscopy (eu20) Steve C. Franklin (Wed Dec 13 2000 - 18:31:17 PST)
Can I...? Tim Astley (Wed Dec 13 2000 - 20:38:31 PST)
MPI on SUN Sanjeev B.S. (Thu Dec 14 2000 - 04:00:29 PST)
Machine file.... Lalith Perera (Thu Dec 14 2000 - 06:27:31 PST)
where to specify parm98.dat + has AMBER been compiled on HP N-4000 complex Jake Isaacs (Thu Dec 14 2000 - 09:20:28 PST)
omit non-bonded energy in Amber 6 Pornthep Sompornpisut (Thu Dec 14 2000 - 13:12:55 PST)
- Re: omit non-bonded energy in Amber 6 Laurent Chiche (Fri Dec 15 2000 - 00:27:07 PST)
- sizes.h for sander Sanjeev B.S. (Sat Dec 16 2000 - 11:56:44 PST)
- EWALD BOMB Grzegorz Jezierski (Mon Dec 18 2000 - 07:53:12 PST)
  - Re: EWALD BOMB darden (Mon Dec 18 2000 - 15:20:43 PST)
    - One question about praj ZhiYong Zhang (Mon Dec 18 2000 - 19:59:14 PST)
    - Re: One question about praj Pascal Bonnet (Tue Dec 19 2000 - 09:32:32 PST)
    - one question Zhangxd (Tue Dec 19 2000 - 07:44:47 PST)
    - pdbgen Olga Carvalho (Tue Dec 19 2000 - 02:52:52 PST)
    - Re: pdbgen Achintya Das (Tue Dec 19 2000 - 06:21:11 PST)
    - restraints + potential Eoin Galligan (Tue Dec 19 2000 - 04:22:35 PST)
- initial density generated by solvatebox Jake Isaacs (Mon Dec 18 2000 - 08:42:23 PST)
Re: initial density generated by solvatebox Bill Ross (Mon Dec 18 2000 - 09:23:04 PST)
1-4 interactions Andrew Petersen (Mon Dec 18 2000 - 12:33:24 PST)
RST file for non-standard residue arubin_at_unmc.edu (Mon Dec 18 2000 - 14:08:40 PST)
PostDoc Position available Ronald Kuehne (Wed Dec 20 2000 - 00:57:15 PST)
water and ions Prem Raj Joseph (Thu Dec 21 2000 - 08:12:53 PST)
- hi Zhangxd (Thu Dec 21 2000 - 13:22:50 PST)
Brazilian Symposium on Medicinal Chemistry Carlos Montanari (Thu Dec 21 2000 - 09:01:05 PST)
Re: Saving coordinates with sander_classic Michael Cooney (Thu Dec 21 2000 - 13:34:34 PST)
ibelly Joseph Nachman (Thu Dec 21 2000 - 14:37:25 PST)
- froce field parameters Christian Pilger (Fri Dec 22 2000 - 09:31:16 PST)
  - Re: CCL:froce field parameters xin_hu (Fri Dec 22 2000 - 10:05:09 PST)
    - question Zhangxd (Fri Dec 22 2000 - 12:16:15 PST)
    - compile error Margaret Cheung (Sun Dec 24 2000 - 02:23:50 PST)
    - about defining disulfide bond shuji ichikawa (Tue Dec 26 2000 - 06:10:24 PST)
    - about temperture Zhangxd (Thu Dec 28 2000 - 11:52:13 PST)
    - software Zhangxd (Thu Jan 04 2001 - 10:30:53 PST)
    - MD with 'Solvated Ions' Andreas Svrcek-Seiler (Mon Jan 15 2001 - 06:19:30 PST)
    - (no subject) Zhangxd (Mon Jan 15 2001 - 07:46:08 PST)
    - Sander sara nu�ez (Mon Jan 15 2001 - 07:55:29 PST)
    - i need help! dwang (Mon Jan 15 2001 - 08:58:46 PST)
    - Request for using AMBER server deborah buam (Tue Dec 26 2000 - 09:15:32 PST)
Configuring AMBER program deborah buam (Fri Dec 22 2000 - 08:41:15 PST)
Re: CCL:AMBER6 and MPICH David Case (Fri Dec 29 2000 - 09:56:24 PST)
- Re: CCL:AMBER6 and MPICH David Konerding (Sat Dec 30 2000 - 21:44:00 PST)
references Mark Forster (Tue Jan 02 2001 - 06:39:38 PST)
- RE: references Halima Amer (Tue Jan 02 2001 - 07:29:16 PST)
  - RE: references jim caldwell (Tue Jan 02 2001 - 08:54:17 PST)
Re: velocity-output Michael Cooney (Fri Jan 12 2001 - 16:34:33 PST)
Re: MD with 'Solvated Ions' Bill Ross (Mon Jan 15 2001 - 11:19:15 PST)
Gibbs with Linux RH 7.0 GUILBAUD Philippe 153683 (Tue Jan 16 2001 - 06:12:46 PST)
- Re: Gibbs with Linux RH 7.0 jim caldwell (Tue Jan 16 2001 - 08:28:00 PST)
- "Goodness" of Trajectory Troy Bothwell (Tue Jan 16 2001 - 13:28:03 PST)
  - Re: "Goodness" of Trajectory Michael Cooney (Thu Jan 18 2001 - 11:29:25 PST)
  - solvate cap Eoin Galligan (Fri Jan 19 2001 - 06:33:37 PST)
  - Measuring rigid-body rotation with AMBER samantha hughes (Fri Jan 19 2001 - 07:23:24 PST)
- Re: Gibbs with Linux RH 7.0 Etienne ENGLER (Wed Jan 17 2001 - 01:43:47 PST)
- EWALD Zhangxd (Wed Jan 17 2001 - 11:13:44 PST)
- Post-doctoral position Chris Chipot (Wed Jan 17 2001 - 11:58:19 PST)
Constant Pressure vs. Constant Volume Troy Bothwell (Tue Jan 16 2001 - 13:28:04 PST)
Re: solvate cap Bill Ross (Fri Jan 19 2001 - 09:06:26 PST)
Parmscan and iron parameters Erlend Moldrheim (Fri Jan 19 2001 - 09:13:38 PST)
Ewald sum oppie1_at_excite.co.jp (Sat Jan 20 2001 - 06:30:20 PST)
octahedral box in AMBER6 Peter Varnai (Mon Jan 22 2001 - 04:32:17 PST)
Trouble compiling amber on an Indy, R4400, running IRIX 6.5.10 Margaret Doll (Mon Jan 22 2001 - 07:52:32 PST)
- Re: Trouble compiling amber on an Indy, R4400, running IRIX 6.5.10 Nathalie Godbout (Mon Jan 22 2001 - 13:31:45 PST)
- Freze solute molecules in AMBER Assoc.Prof.Dr.Kritsana Sagarik (Tue Jan 23 2001 - 04:58:34 PST)
  - Re: Freze solute molecules in AMBER jim caldwell (Tue Jan 23 2001 - 08:26:56 PST)
  - sader-classic Joseph Nachman (Tue Jan 23 2001 - 08:32:21 PST)
    - Re: sader-classic Nathalie Godbout (Tue Jan 23 2001 - 11:10:54 PST)
- AMBER on alpha Alan Todd (Tue Jan 23 2001 - 05:34:23 PST)
  - Re: AMBER on alpha jim caldwell (Tue Jan 23 2001 - 14:54:18 PST)
- Re: Trouble compiling amber on an Indy, R4400, running IRIX 6.5.10 Gota Kawai (Tue Jan 23 2001 - 15:36:02 PST)
- Re: Trouble compiling amber on an Indy, R4400, running IRIX 6.5.10 Gota Kawai (Tue Jan 23 2001 - 19:30:29 PST)
- pressure regulation Andrew Aird (Wed Jan 24 2001 - 10:51:37 PST)
  - Re: pressure regulation jim caldwell (Wed Jan 24 2001 - 11:47:48 PST)
  - Re: pressure regulation darden (Thu Jan 25 2001 - 08:50:13 PST)
  - Incomplete coord file after crash Michael Cooney (Thu Jan 25 2001 - 11:09:47 PST)
question Zhangxd (Mon Jan 22 2001 - 10:24:48 PST)
Phosphorylated residues. Andrew Hoofnagle (Mon Jan 22 2001 - 12:33:16 PST)
question about RESP calculation xin hu (Mon Jan 22 2001 - 16:45:37 PST)
Re: Incomplete coord file after crash Bill Ross (Thu Jan 25 2001 - 12:47:26 PST)
- Re: Incomplete coord file after crash Michael Cooney (Thu Jan 25 2001 - 13:24:46 PST)
- X-ray vs. MD Anton Guliaev (Thu Jan 25 2001 - 14:28:34 PST)
- [Amber]: Peptide torsions in Parm99.dat Warren DeLano (Thu Jan 25 2001 - 14:53:15 PST)
  - Re: [Amber]: Peptide torsions in Parm99.dat Warren DeLano (Thu Jan 25 2001 - 17:06:04 PST)
    - Typo's in the Parm99.dat Craig Marhefka (Fri Jan 26 2001 - 12:19:45 PST)
    - (no subject) Pierre Tran (Wed Jan 31 2001 - 08:58:40 PST)
  - MEP with GAMESS or GAUSSIAN Francois Dupradeau (Fri Jan 26 2001 - 04:16:55 PST)
    - Re: CCL:MEP with GAMESS or GAUSSIAN Curt M. Breneman (Fri Jan 26 2001 - 09:32:44 PST)
    - (no subject) Jose Ramon Blas (Fri Jan 26 2001 - 10:18:20 PST)
  - 2-Amino Purine Parameters Scott A. Showalter (Fri Jan 26 2001 - 07:43:29 PST)
Re: Serious Problem with parm99.dat jim caldwell (Fri Jan 26 2001 - 12:18:51 PST)
Re: Measuring rigid-body rotation with AMBER Bill Ross (Fri Jan 26 2001 - 13:33:25 PST)
Info Abdo MALAC (Mon Jan 29 2001 - 08:39:58 PST)
GAMESS and RESP. Andrew Hoofnagle (Mon Jan 29 2001 - 14:51:56 PST)
Cavity solvation Anton Guliaev (Mon Jan 29 2001 - 15:45:15 PST)
ester Okimasa Okada (Mon Jan 29 2001 - 16:47:29 PST)
Re: Cavity solvation Bill Ross (Mon Jan 29 2001 - 16:54:04 PST)
Postdoctoral position Chris Chipot (Tue Jan 30 2001 - 11:48:16 PST)
Gibbs/non-bonded pairs Scott Boesch (Tue Jan 30 2001 - 12:50:17 PST)
(no subject) lkirnars_at_unmc.edu (Tue Jan 30 2001 - 13:25:54 PST)
process problem Eoin Galligan (Wed Jan 31 2001 - 07:54:11 PST)
- Re: process problem jim caldwell (Wed Jan 31 2001 - 08:51:42 PST)
  - Re: process problem David Konerding (Wed Jan 31 2001 - 09:48:08 PST)
  - Belly option in sander Florian Barth (Wed Jan 31 2001 - 10:17:51 PST)
    - Re: Belly option in sander David Case (Wed Jan 31 2001 - 11:28:43 PST)
    - (no subject) Andrew Aird (Wed Jan 31 2001 - 11:46:10 PST)
    - xleap silly thing Jose Ramon Blas (Wed Jan 31 2001 - 12:32:20 PST)
Re: Ionic solutions Bill Ross (Mon Feb 12 2001 - 14:52:07 PST)
- Re: Ionic solutions Elsa Sousa Henriques (Tue Feb 13 2001 - 10:01:08 PST)
- Re: Ionic solutions Thomas Cheatham (Tue Feb 13 2001 - 10:22:54 PST)
  - RE: Ionic solutions Yong Duan (Tue Feb 13 2001 - 12:49:58 PST)
- Re: Ionic solutions Elsa Sousa Henriques (Tue Feb 13 2001 - 13:56:18 PST)
- Re: Ionic solutions Mihaly Mezei (Tue Feb 20 2001 - 14:18:45 PST)
One article Zhiyong Zhang (Tue Feb 13 2001 - 03:46:42 PST)
DMSO ? Yuguang Mu (Tue Feb 13 2001 - 08:22:42 PST)
- (no subject) Christian Pilger (Tue Feb 13 2001 - 11:33:31 PST)
  - (no subject) Lynn Amon (Tue Feb 13 2001 - 11:39:20 PST)
generating parameters for a small molecule ligand Jake Isaacs (Tue Feb 13 2001 - 08:48:03 PST)
- Re: generating parameters for a small molecule ligand Simon Cross (Wed Feb 14 2001 - 04:40:15 PST)
Minor correction (I think) on RESP input Fred P. Arnold (Tue Feb 13 2001 - 09:23:22 PST)
Belly Atonms Mark Markson (Tue Feb 13 2001 - 12:52:53 PST)
Dual Origin vs dual Alfa Anton Guliaev (Tue Feb 13 2001 - 16:06:37 PST)
- Re: Dual Origin vs dual Alfa Nathalie Godbout (Wed Feb 14 2001 - 08:18:23 PST)
  - Athlon 1GHz (was: Dual Origin vs dual Alfa) Tru Huynh (Wed Feb 14 2001 - 09:29:53 PST)
    - Re: Athlon 1GHz (was: Dual Origin vs dual Alfa) R. M. Fesinmeyer (Wed Feb 14 2001 - 11:02:11 PST)
    - Re: Athlon 1GHz (was: Dual Origin vs dual Alfa) Nathalie Godbout (Wed Feb 14 2001 - 12:00:25 PST)
    - Re: Athlon 1GHz (was: Dual Origin vs dual Alfa) R. M. Fesinmeyer (Wed Feb 14 2001 - 12:16:51 PST)
    - REMD Michal Otyepka (Wed Feb 14 2001 - 11:30:06 PST)
  - (no subject) Yinghong Sheng (Wed Feb 14 2001 - 09:45:43 PST)
(no subject) robert (Tue Feb 13 2001 - 16:35:21 PST)
- Re: LES analysis Carlos Simmerling (Tue Feb 13 2001 - 10:39:47 PST)
- dynamic memory allocation Bill Ross (Tue Feb 13 2001 - 11:30:28 PST)
  - Re: dynamic memory allocation Chuck Schneider (Wed Feb 14 2001 - 08:20:02 PST)
  - Re: dynamic memory allocation Christian Pilger (Wed Feb 14 2001 - 08:24:47 PST)
  - Implicit solvent MD with small RNA's Andreas Svrcek-Seiler (Wed Feb 14 2001 - 08:52:56 PST)
  - Re: dynamic memory allocation Bill Ross (Wed Feb 14 2001 - 10:21:22 PST)
    - trajectory-problem Christian Pilger (Wed Feb 14 2001 - 17:14:25 PST)
    - Re: trajectory-problem Miyashita, Osamu (Thu Feb 15 2001 - 09:14:02 PST)
    - disk file larger than 2 GB Yuguang Mu (Wed Feb 14 2001 - 23:12:47 PST)
    - Re: disk file larger than 2 GB Mite51_at_hotmail.com (Wed Feb 14 2001 - 23:59:25 PST)
Amber Parameters Antonio Entrena Guadix (Wed Feb 14 2001 - 03:04:54 PST)
- Re: Amber Parameters Christian Pilger (Wed Feb 14 2001 - 05:05:55 PST)
- how to handle a metal ion Jake Isaacs (Wed Feb 14 2001 - 07:43:14 PST)
  - Re: how to handle a metal ion Mark Forster (Thu Feb 15 2001 - 02:11:24 PST)
RE: periodic box size Guanglei Cui (Fri Feb 16 2001 - 10:30:27 PST)
Roar Yanni Wang (Wed Feb 21 2001 - 01:34:47 PST)
Re: belly run Bill Ross (Wed Feb 21 2001 - 10:37:03 PST)
running Amber on dual processor machine HAllawi_at_TWT.com (Wed Feb 21 2001 - 11:24:07 PST)
(no subject) Michal Otyepka (Wed Feb 21 2001 - 12:23:01 PST)
- Re: your mail Krzysztof Murzyn (Thu Feb 22 2001 - 02:45:36 PST)
- modified aminoacids using Leap Giulio Rastelli (Thu Feb 22 2001 - 03:14:00 PST)
Fe4S4 cluster Agnes Hahn (Thu Feb 22 2001 - 08:06:09 PST)
Re: modified aminoacids using Leap Bill Ross (Thu Feb 22 2001 - 09:03:16 PST)
shake comparison Xiaoliang Qian (Fri Feb 23 2001 - 09:13:07 PST)
Can't run sander_classic with parallel machine Khatcharin Siriwong (Fri Feb 23 2001 - 09:31:16 PST)
- Re: Can't run sander_classic with parallel machine Miyashita, Osamu (Fri Feb 23 2001 - 09:58:47 PST)
- consult ZHANG RB (Sun Feb 25 2001 - 03:50:11 PST)
- consult ZHANG RB (Sun Feb 25 2001 - 03:50:47 PST)
- parm94.dat vs parm99.dat Andreas Svrcek-Seiler (Mon Feb 26 2001 - 00:24:00 PST)
- leap and SP2 nitrogen Mark Forster (Mon Feb 26 2001 - 04:07:27 PST)
  - Re: leap and SP2 nitrogen Andrew Gordon Purkiss (Mon Feb 26 2001 - 05:07:26 PST)
  - QM/MM in roar Yanni Wang (Mon Feb 26 2001 - 10:04:03 PST)
  - params - ADP, neutral ARG Heather A.Carlson (Mon Feb 26 2001 - 10:58:17 PST)
db4 with amber5.0 Daniel GENEST (Fri Feb 23 2001 - 09:44:56 PST)
RE: Linux 6.2 install problems Ross Walker (Mon Feb 26 2001 - 13:39:02 PST)
Re: Linux 6.2 install problems Bill Ross (Mon Feb 26 2001 - 14:01:24 PST)
- Re: Linux 6.2 install problems David Konerding (Mon Feb 26 2001 - 15:32:07 PST)
- MD without SHAKE Dayle Smith (Mon Feb 26 2001 - 17:06:33 PST)
Re: MD without SHAKE Bill Ross (Mon Feb 26 2001 - 17:51:25 PST)
- Re: MD without SHAKE jim caldwell (Tue Feb 27 2001 - 07:04:25 PST)
- Re: MD without SHAKE Bill Ross (Tue Feb 27 2001 - 08:40:48 PST)
  - Re: MD without SHAKE Troy Wymore (Wed Feb 28 2001 - 10:59:51 PST)
- Re: MD without SHAKE Bill Ross (Wed Feb 28 2001 - 11:25:50 PST)
porphyrin parameters Kristin Maher (Mon Feb 26 2001 - 22:28:43 PST)
- LEAP and crystal waters Michal Otyepka (Mon Feb 26 2001 - 23:35:42 PST)
Re: porphyrin parameters Bill Ross (Tue Feb 27 2001 - 00:50:34 PST)
Gibbs input Kiyean Nam (Tue Feb 27 2001 - 20:24:44 PST)
8-Oxo-G Eva Darian (Wed Feb 28 2001 - 10:00:18 PST)
Re: Sander parallel compilation David Case (Wed Feb 28 2001 - 10:27:40 PST)
- Re: Sander parallel compilation David Case (Wed Feb 28 2001 - 10:46:04 PST)
PBC box problems Michael Ford (Wed Feb 28 2001 - 14:34:36 PST)
Re: PBC box problems Bill Ross (Wed Feb 28 2001 - 15:50:16 PST)
Fluorescent dyes Troy Bothwell (Wed Feb 28 2001 - 20:01:47 PST)
Parm98 for amino acids? Sanjeev B.S. (Wed Feb 28 2001 - 22:09:16 PST)
GIBBS Andrea Bernini (Thu Mar 01 2001 - 03:20:07 PST)
about prep input Zhangxd (Thu Mar 01 2001 - 05:40:23 PST)
Dummy Atoms Matthew Davies (Thu Mar 01 2001 - 05:58:14 PST)
Pentium IV compiler in MD Jose Ramon Blas (Thu Mar 01 2001 - 13:11:08 PST)
PROFEC Anna Ferrari (Fri Mar 02 2001 - 02:57:28 PST)
imaging in amber6 Riccardo Nifosi (Fri Mar 02 2001 - 07:52:15 PST)
- Re: imaging in amber6 David Case (Fri Mar 02 2001 - 09:05:39 PST)
- compilation problems Christian Pilger (Sun Mar 04 2001 - 07:03:34 PST)
  - Re: compilation problems Chuck Schneider (Mon Mar 05 2001 - 05:20:18 PST)
  - Interface Svetlana Nolde (Mon Mar 05 2001 - 06:59:02 PST)
  - leap adding terminal phosphates Michael Cooney (Mon Mar 05 2001 - 10:20:00 PST)
    - re: leap adding terminal phosphates Bill Ross (Mon Mar 05 2001 - 12:27:27 PST)
  - Pentium 4 Robert Matthew Fesinmeyer (Mon Mar 05 2001 - 11:01:26 PST)
    - Re: Pentium 4 David Konerding (Mon Mar 05 2001 - 11:57:04 PST)
    - RE: Pentium 4 Heirich, Alan (Mon Mar 05 2001 - 12:47:08 PST)
    - recommended vs. default values Jake Isaacs (Mon Mar 05 2001 - 13:22:43 PST)
    - Amber Website - UK Mirror Ross Walker (Tue Mar 06 2001 - 02:47:28 PST)
    - (no subject) Yongxing Liu (Tue Mar 06 2001 - 09:42:54 PST)
  - Q about RESP Ramon Garduno (Mon Mar 05 2001 - 11:35:47 PST)
- curves Troy Bothwell (Sun Mar 04 2001 - 15:27:05 PST)
  - RE: curves Wing Lok Abe Kurtz (Sun Mar 04 2001 - 16:46:54 PST)
  - anal ouput Francois Dupradeau (Mon Mar 05 2001 - 00:40:14 PST)
Re: lipid bilayer MD simulations Bill Ross (Tue Mar 06 2001 - 11:06:44 PST)
- Re: lipid bilayer MD simulations Bill Ross (Tue Mar 06 2001 - 11:48:02 PST)
Re: SHAKE David Case (Thu Mar 08 2001 - 09:28:28 PST)
- Re: SHAKE Michael Cooney (Thu Mar 08 2001 - 09:39:51 PST)
sander VS sander_classic Khatcharin Siriwong (Thu Mar 08 2001 - 10:18:44 PST)
- Re: sander VS sander_classic David Case (Thu Mar 08 2001 - 10:53:51 PST)
- Re: sander VS sander_classic Jarrod Smith (Thu Mar 08 2001 - 11:03:59 PST)
Re: SHAKE Bill Ross (Thu Mar 08 2001 - 11:22:13 PST)
Re: using "radial" in PTRAJ Pascal Bonnet (Fri Mar 09 2001 - 09:26:17 PST)
Principal component analysis Andreas Svrcek-Seiler (Fri Mar 09 2001 - 11:11:21 PST)
variable NTWXM in Sander Michael Cooney (Fri Mar 09 2001 - 14:54:23 PST)
Again Gibbs... yu kaneko (Sat Mar 10 2001 - 00:12:10 PST)
Generating C-DNA using nucgen! A.Madhumalar (Sun Mar 11 2001 - 00:31:16 PST)
MM-PBSA Eoin Galligan (Mon Mar 12 2001 - 07:34:20 PST)
AMBER6 on IBMSP3 Sanjeev B.S. (Tue Mar 13 2001 - 03:59:55 PST)
- Re: AMBER6 on IBMSP3 David Skinner (Tue Mar 13 2001 - 08:18:19 PST)
  - Re: AMBER6 on IBMSP3 Sanjeev B.S. (Fri Mar 16 2001 - 10:03:22 PST)
  - carnal problem Joseph Nachman (Fri Mar 16 2001 - 11:58:45 PST)
  - AMBER6 on IBMSP3 Installation Sanjeev B.S. (Tue Mar 20 2001 - 06:07:05 PST)
    - RE: AMBER6 on IBMSP3 Installation Thomas A. Spraggins (Tue Mar 20 2001 - 05:09:27 PST)
    - RE: AMBER6 on IBMSP3 Installation Sanjeev B.S. (Tue Mar 20 2001 - 11:53:07 PST)
    - RE: AMBER6 on IBMSP3 Installation Thomas Cheatham (Tue Mar 20 2001 - 10:45:40 PST)
    - amber6 compilation failure (fwd) Jamal G. Musaev (Tue Mar 20 2001 - 12:29:55 PST)
    - Re: amber6 compilation failure (fwd) David Skinner (Tue Mar 20 2001 - 13:09:49 PST)
  - PME with octahedral box Ann Hermone (Tue Mar 20 2001 - 10:01:05 PST)
    - Re: PME with octahedral box David Konerding (Tue Mar 20 2001 - 10:43:11 PST)
ptraj image for octahedral box Peter Varnai (Tue Mar 13 2001 - 07:47:28 PST)
- Re: ptraj image for octahedral box Pascal Bonnet (Tue Mar 13 2001 - 17:28:47 PST)
ATP+Mg, P-tyrosine a P-threonine Michal Otyepka (Wed Mar 14 2001 - 02:35:53 PST)
How to calculate energy from mdcrd output file Khatcharin Siriwong (Wed Mar 14 2001 - 06:23:47 PST)
Re: why the slowdown? Bill Ross (Wed Mar 14 2001 - 13:34:10 PST)
Re: Selection Bill Ross (Wed Mar 14 2001 - 14:11:32 PST)
ptraj resolved; irest=1? Peter Varnai (Thu Mar 15 2001 - 07:29:54 PST)
- RE: ptraj resolved; irest=1? Guanglei Cui (Thu Mar 15 2001 - 08:08:01 PST)
  - Re: PBC box problems Michael Ford (Tue Mar 20 2001 - 10:10:17 PST)
- LEAP kiyean.nam_at_pharma.Novartis.com (Thu Mar 15 2001 - 15:01:43 PST)
- (no subject) chomsri upkaew (Fri Mar 16 2001 - 01:36:38 PST)
  - (no subject) David Konerding (Fri Mar 16 2001 - 09:28:06 PST)
- Can't compile sander witk parallel on Linux cluster chomsri upkaew (Fri Mar 16 2001 - 03:54:27 PST)
  - Re: Can't compile sander witk parallel on Linux cluster Tru Huynh (Fri Mar 16 2001 - 04:14:14 PST)
  - RE: Can't compile sander witk parallel on Linux cluster Ross Walker (Fri Mar 16 2001 - 04:54:07 PST)
- summary: lipid bilayer MD simulations Xavier Deupi (Fri Mar 16 2001 - 04:01:46 PST)
RE: Can't compile Sander with parallel on Linux cluster Ross Walker (Fri Mar 16 2001 - 07:05:49 PST)
- RE: Can't compile Sander with parallel on Linux cluster Thomas A. Spraggins (Fri Mar 16 2001 - 09:37:24 PST)
- Re: Can't compile Sander with parallel on Linux cluster David Konerding (Fri Mar 16 2001 - 09:54:10 PST)
Re: carnal problem Bill Ross (Fri Mar 16 2001 - 14:09:56 PST)
DNA out of a box Xiaolin Chuang (Sat Mar 17 2001 - 05:08:56 PST)
- Re: DNA out of a box Michael Cooney (Wed Mar 21 2001 - 09:43:18 PST)
- SP3 name list Sanjeev B.S. (Wed Mar 21 2001 - 11:10:13 PST)
  - Correction: SP3 name list Sanjeev B.S. (Wed Mar 21 2001 - 22:47:53 PST)
  - Amber 6.0 Benchmarks Florian Barth (Thu Mar 22 2001 - 02:54:18 PST)
    - Re: Amber 6.0 Benchmarks Tru Huynh (Thu Mar 22 2001 - 05:26:10 PST)
  - (no subject) txyang (Thu Mar 22 2001 - 04:54:18 PST)
  - Re: SP3 name list David Case (Thu Mar 22 2001 - 07:43:37 PST)
  - (no subject) Bill Ross (Thu Mar 22 2001 - 09:44:16 PST)
- GIBBS error kiyean.nam_at_pharma.Novartis.com (Wed Mar 21 2001 - 14:02:35 PST)
[charmm-bbs] Post-doctoral position available Chris Chipot (Sat Mar 17 2001 - 10:21:59 PST)
Post-doctoral position available Chris Chipot (Sat Mar 17 2001 - 10:21:59 PST)
Problem of running sander on Linux cluster chomsri upkaew (Mon Mar 19 2001 - 07:24:59 PST)
- Re: Problem of running sander on Linux cluster David Konerding (Mon Mar 19 2001 - 08:22:31 PST)
- RE: Problem of running sander on Linux cluster Thomas A. Spraggins (Mon Mar 19 2001 - 08:23:12 PST)
  - Re: Problem of running sander on Linux cluster Carlos Simmerling (Mon Mar 19 2001 - 09:03:02 PST)
    - RE: Problem of running sander on Linux cluster Thomas A. Spraggins (Mon Mar 19 2001 - 10:54:49 PST)
    - (no subject) Yongxing Liu (Mon Mar 19 2001 - 10:58:49 PST)
    - PME with octahedral box Ann Hermone (Mon Mar 19 2001 - 13:31:16 PST)
    - Test Group - swarm.ca Mite51_at_hotmail.com (Mon Mar 19 2001 - 14:56:09 PST)
Re: amber6 compilation failure (fwd) Bill Ross (Tue Mar 20 2001 - 13:40:51 PST)
Question about installing AMBER jllo (Tue Mar 20 2001 - 19:46:40 PST)
- Re: Question about installing AMBER Andreas Svrcek-Seiler (Wed Mar 21 2001 - 02:31:22 PST)
- error in sander rathinavelan thenmalarchelvi (Wed Mar 21 2001 - 04:12:23 PST)
Re: GIBBS error Bill Ross (Wed Mar 21 2001 - 16:07:56 PST)
GIBSS pertType yu kaneko (Thu Mar 22 2001 - 04:58:28 PST)
Re: Correction: SP3 name list Michael Crowley (Thu Mar 22 2001 - 09:46:21 PST)
- Re: Correction: SP3 name list Michael Crowley (Thu Mar 22 2001 - 09:49:43 PST)
parallel load difference under linux (long) Tru Huynh (Thu Mar 22 2001 - 12:01:47 PST)
- Re: parallel load difference under linux (long) David Konerding (Thu Mar 22 2001 - 12:58:23 PST)
  - RE: parallel load difference under linux (long) Yong Duan (Thu Mar 22 2001 - 14:51:05 PST)
- Re: parallel load difference under linux (long) Michael Crowley (Thu Mar 22 2001 - 13:31:08 PST)
  - Re: parallel load difference under linux (long) Tru Huynh (Fri Mar 23 2001 - 03:43:28 PST)
Re: How tleap does not add missing H atoms? Bill Ross (Mon Mar 26 2001 - 09:54:34 PST)
periodic box size Jake Isaacs (Mon Mar 26 2001 - 10:40:49 PST)
- Re: periodic box size Jake Isaacs (Fri Feb 16 2001 - 10:54:25 PST)
  - RE: periodic box size Guanglei Cui (Fri Feb 16 2001 - 11:48:50 PST)
- Re: periodic box size Bill Ross (Fri Feb 16 2001 - 12:35:36 PST)
- Compilation of Amber6 in linux machine A.Madhumalar (Sun Feb 18 2001 - 00:08:48 PST)
  - RE: Compilation of Amber6 in linux machine Thomas A. Spraggins (Sun Feb 18 2001 - 11:06:14 PST)
  - Re: Compilation of Amber6 in linux machine David Konerding (Mon Feb 19 2001 - 07:46:55 PST)
  - GB protein simulation Guanglei Cui (Mon Feb 19 2001 - 08:58:23 PST)
  - Nucleic acid notation within Toolchest Rebecca Ann Perlow (Mon Feb 19 2001 - 13:59:59 PST)
  - AMBER on SUN Craig Marhefka (Tue Feb 20 2001 - 06:43:33 PST)
    - RE: AMBER on SUN Yong Duan (Tue Feb 20 2001 - 10:29:41 PST)
    - RE: AMBER on SUN Bill Ross (Tue Feb 20 2001 - 11:17:50 PST)
- Re: periodic box size Michael Crowley (Sun Feb 18 2001 - 22:48:05 PST)
Re: periodic box size Bill Ross (Mon Mar 26 2001 - 12:06:08 PST)
Re: Combining trajectories Bill Ross (Tue Mar 27 2001 - 08:53:58 PST)
nstlim in sander Michael Cooney (Tue Mar 27 2001 - 10:12:08 PST)
PMF input file c724128 (Tue Mar 27 2001 - 11:14:18 PST)
Re: PMF input file Bill Ross (Tue Mar 27 2001 - 11:18:18 PST)
Compilation of LEaP on SP3 Sanjeev B.S. (Wed Mar 28 2001 - 00:02:02 PST)
Resp Yanni Wang (Wed Mar 28 2001 - 05:24:04 PST)
- Re: Resp Elsa Sousa Henriques (Wed Mar 28 2001 - 17:25:53 PST)
- LEaP compilation Sanjeev B.S. (Wed Mar 28 2001 - 22:00:27 PST)
- How to remove CIO from prmtop & crd Jithesh P.V (Thu Mar 29 2001 - 01:21:25 PST)
- Average structure Khatcharin Siriwong (Thu Mar 29 2001 - 07:07:11 PST)
  - RE: Average structure Guanglei Cui (Thu Mar 29 2001 - 07:42:38 PST)
    - Re: Average structure Laurent Chiche (Thu Mar 29 2001 - 08:01:32 PST)
    - Re: Average structure David Konerding (Thu Mar 29 2001 - 08:27:08 PST)
    - Re: Average structure Carlos Simmerling (Thu Mar 29 2001 - 09:55:55 PST)
    - RE: Average structure Yongxing Liu (Thu Mar 29 2001 - 11:51:05 PST)
    - parameters for NADH marin (Thu Mar 29 2001 - 13:28:25 PST)
    - problem with Leap xin hu (Fri Mar 30 2001 - 05:08:41 PST)
    - how to get dials_and_windows thenmalar rathinavelan (Fri Mar 30 2001 - 00:23:41 PST)
    - Membrane Yanni Wang (Fri Mar 30 2001 - 00:31:34 PST)
    - helix analyse Yuguang Mu (Fri Mar 30 2001 - 09:20:21 PST)
    - Ca2+ parameters and how ? ... A. Ababou (Sat Mar 31 2001 - 07:07:39 PST)
    - Missing "ASH" parameters Jake Isaacs (Thu Mar 29 2001 - 10:09:01 PST)
Re: loading prmtop and inpcrd into leap Bill Ross (Wed Mar 28 2001 - 10:37:38 PST)
parm warnings Troy Bothwell (Wed Mar 28 2001 - 10:48:50 PST)
Minimization and NSNB Lillian Chong (Wed Mar 28 2001 - 10:59:15 PST)
Re: parm warnings Bill Ross (Wed Mar 28 2001 - 11:58:17 PST)
[charmm-bbs] Post-doctoral position available Heather A.Carlson (Wed Mar 28 2001 - 14:51:37 PST)
Post-doctoral position available Heather A.Carlson (Wed Mar 28 2001 - 14:51:37 PST)
[charmm-bbs] Post-doctoral Position Ronald Kuehne (Wed Mar 28 2001 - 16:51:26 PST)
Post-doctoral Position Ronald Kuehne (Wed Mar 28 2001 - 16:51:26 PST)
Re: LEaP adding an extra hydrogen to N-terminus Jake Isaacs (Thu Mar 29 2001 - 07:31:04 PST)
RE: LEaP adding an extra hydrogen to N-terminus Guanglei Cui (Thu Mar 29 2001 - 07:48:05 PST)
FW: about Owfeg in Amber 6.0 Craig Marhefka (Mon Apr 02 2001 - 06:19:18 PDT)
pressure with polarizable potentials Pavel Jungwirth (Mon Apr 02 2001 - 07:21:26 PDT)
- (no subject) Michal Otyepka (Mon Apr 02 2001 - 02:33:38 PDT)
- about OWFEG nicolas baurin (Mon Apr 02 2001 - 02:36:11 PDT)
- about dials_and_windows thenmalar rathinavelan (Mon Apr 02 2001 - 05:13:41 PDT)
  - RE: about dials_and_windows Guanglei Cui (Mon Apr 02 2001 - 06:34:24 PDT)
  - terminal base pair opening 2 Peter Varnai (Mon Apr 02 2001 - 06:46:06 PDT)
  - setting random velocities Svetlana Nolde (Mon Apr 02 2001 - 09:17:01 PDT)
  - (no subject) Bill Ross (Mon Apr 02 2001 - 09:51:45 PDT)
- about dials_and_windows thenmalar rathinavelan (Mon Apr 02 2001 - 05:13:41 PDT)
- terminal base pair opening Peter Varnai (Mon Apr 02 2001 - 05:19:54 PDT)
  - RE: terminal base pair opening Guanglei Cui (Mon Apr 02 2001 - 06:27:19 PDT)
  - RE: terminal base pair opening Bill Ross (Mon Apr 02 2001 - 10:18:38 PDT)
  - Ca2+ parameters and how ? ... A. Ababou (Mon Apr 02 2001 - 12:46:27 PDT)
  - saving a trajectory as individual pdb files Jake Isaacs (Mon Apr 02 2001 - 14:42:38 PDT)
    - RE: saving a trajectory as individual pdb files Guanglei Cui (Mon Apr 02 2001 - 15:23:51 PDT)
    - Re: saving a trajectory as individual pdb files Jarrod Smith (Mon Apr 02 2001 - 15:39:15 PDT)
- Re: pressure with polarizable potentials jim caldwell (Mon Apr 02 2001 - 14:51:10 PDT)
Re: saving a trajectory as individual pdb files Bill Ross (Mon Apr 02 2001 - 15:29:07 PDT)
Re: Ca2+ parameters and how ? ... Bill Ross (Mon Apr 02 2001 - 15:54:54 PDT)
producing a post-ptraj prmtop R. M. Fesinmeyer (Tue Apr 03 2001 - 17:20:41 PDT)
- RE: producing a post-ptraj prmtop Guanglei Cui (Tue Apr 03 2001 - 18:13:27 PDT)
- Pairlist error Troy Bothwell (Tue Apr 03 2001 - 20:20:35 PDT)
  - Re: Pairlist error jim caldwell (Tue Apr 03 2001 - 21:44:54 PDT)
- Re: producing a post-ptraj prmtop Peter Varnai (Wed Apr 04 2001 - 01:44:26 PDT)
- OCCO in parm99 Peter Varnai (Wed Apr 04 2001 - 01:52:32 PDT)
- creating a restrt file from frames of mdcrd and mdvel Jake Isaacs (Wed Apr 04 2001 - 07:31:35 PDT)
- sander_classic: bellyrun with constraints nicolas baurin (Wed Apr 04 2001 - 11:13:21 PDT)
  - Re: sander_classic: bellyrun with constraints nicolas baurin (Thu Apr 05 2001 - 00:12:51 PDT)
  - structure verification Christian Pilger (Thu Apr 05 2001 - 06:22:29 PDT)
  - RDF figure txyang (Fri Apr 06 2001 - 00:19:20 PDT)
  - AMBER6/PME on Origin 2000 Didier Rognan (Fri Apr 06 2001 - 04:43:43 PDT)
  - AMBER 6 on PME Didier Rognan (Fri Apr 06 2001 - 09:41:19 PDT)
    - Re: AMBER 6 on PME Jarrod Smith (Fri Apr 06 2001 - 11:07:57 PDT)
- Following Coordinates Troy Bothwell (Wed Apr 04 2001 - 16:23:16 PDT)
  - Re: Following Coordinates Bill Ross (Wed Apr 04 2001 - 17:24:54 PDT)
  - Box info after minimization Troy Bothwell (Wed Apr 04 2001 - 20:38:58 PDT)
  - Blowup problem txyang (Thu Apr 05 2001 - 00:12:45 PDT)
Re: Pairlist error Bill Ross (Tue Apr 03 2001 - 21:23:29 PDT)
Re: opinions on supercomputer platforms Nathalie Godbout (Fri Apr 06 2001 - 12:57:37 PDT)
ask help Yang Tom (Sun Apr 08 2001 - 00:40:01 PDT)
GB and Ions Andreas Svrcek-Seiler (Mon Apr 09 2001 - 03:21:06 PDT)
Re: odd display of ambpdb generated files Bill Ross (Fri Apr 13 2001 - 15:12:45 PDT)
Re: atom types for xleap Bill Ross (Tue Apr 17 2001 - 11:23:37 PDT)
Re: 1-4 nonbonded interactions Bill Ross (Wed Apr 18 2001 - 12:58:59 PDT)
Re: applying atom types Bill Ross (Fri Apr 27 2001 - 10:24:19 PDT)
about plevel in sander 6 Shixiang Yan (Fri Apr 27 2001 - 15:32:48 PDT)
AMBER6 on Alphas40 Sanjeev B.S. (Sat Apr 28 2001 - 01:06:22 PDT)
Re: AMBER6 on Alphas40 (fwd) Sanjeev B.S. (Mon Apr 30 2001 - 00:31:14 PDT)
- Re: AMBER6 on Alphas40 (fwd) Jarrod Smith (Mon Apr 30 2001 - 09:11:34 PDT)
- Re: AMBER6 on Alphas40 (fwd) Michael Crowley (Mon Apr 30 2001 - 09:35:36 PDT)
- Re: AMBER6 on Alphas40 (fwd) Thomas Cheatham (Mon Apr 30 2001 - 10:05:37 PDT)
- AMBER parameters Andreas Svrcek-Seiler (Tue May 01 2001 - 06:58:13 PDT)
- Wallclock on Intel/Linux sander Jarrod Smith (Tue May 01 2001 - 12:48:36 PDT)
- ANAL (Amber6.0) Aldo Jongejan (Wed May 02 2001 - 06:01:31 PDT)
- Important Address change jim caldwell (Wed May 02 2001 - 11:42:04 PDT)
  - question about mm-pbsa Zhangxd (Wed May 02 2001 - 13:02:50 PDT)
  - Why does water leak!? Sanjeev B.S. (Thu May 03 2001 - 02:07:51 PDT)
  - sander6/Linux compiled with pgf77 + mpipro Jarrod Smith (Thu May 03 2001 - 08:11:16 PDT)
    - Re: sander6/Linux compiled with pgf77 + mpipro Jarrod Smith (Thu May 03 2001 - 12:41:06 PDT)
sander crash / linux cluster C. Klein (Mon Apr 30 2001 - 08:06:58 PDT)
Re: addions in leap Bill Ross (Fri May 04 2001 - 07:23:44 PDT)
Ewalb bomb on SP3 Sanjeev B.S. (Sat May 05 2001 - 12:38:23 PDT)
- question about mm-pbsa Zhangxd (Mon May 07 2001 - 05:32:26 PDT)
- peek_ewald_inpcrd Andrew Aird (Mon May 07 2001 - 09:48:59 PDT)
  - Re: peek_ewald_inpcrd darden (Mon May 07 2001 - 14:01:08 PDT)
  - sander_classic: bond energy problem Miyashita, Osamu (Mon May 07 2001 - 14:28:03 PDT)
  - parameters forms Yuguang Mu (Tue May 08 2001 - 01:13:32 PDT)
- parameters Adrian E. Roitberg (Mon May 07 2001 - 11:00:55 PDT)
Re: topology description Andreas Svrcek-Seiler (Tue May 08 2001 - 08:18:12 PDT)
- Re: topology description Bill Ross (Wed May 09 2001 - 15:27:01 PDT)
escaping atoms.... Amesh Patel (Wed May 09 2001 - 07:36:30 PDT)
- DNA strand flying Stephane (Thu May 10 2001 - 08:48:17 PDT)
- Minimization inputs in AMBER6!! A.Madhumalar (Thu May 10 2001 - 10:09:27 PDT)
- sorry for the virus. Guo, Jianxin (Thu May 10 2001 - 11:52:55 PDT)
- ptraj Vector command Troy Bothwell (Thu May 10 2001 - 15:36:04 PDT)
- tree names in group spec. Artem Mamonov (Thu May 10 2001 - 16:49:02 PDT)
Resp liz (Wed May 09 2001 - 12:14:32 PDT)
Re: escaping atoms.... Bill Ross (Wed May 09 2001 - 15:34:27 PDT)
Diffusion constant Yanni Wang (Thu May 10 2001 - 02:14:34 PDT)
Re: tree names in group spec. Bill Ross (Thu May 10 2001 - 18:37:01 PDT)
carnal error with crd files stripped of waters Michael Cooney (Fri May 11 2001 - 13:52:47 PDT)
- Re: carnal error with crd files stripped of waters samantha hughes (Mon May 14 2001 - 01:20:17 PDT)
Re: Residue wise RMSD using carnal Bill Ross (Sun May 13 2001 - 10:28:05 PDT)
Amber 6.0 on LINUX with absoft Soonmin Jang (Mon May 14 2001 - 00:43:16 PDT)
- Re: Amber 6.0 on LINUX with absoft Jarrod Smith (Mon May 14 2001 - 07:22:42 PDT)
  - the program and references Zhangxd (Tue May 15 2001 - 08:33:01 PDT)
  - phosphotyrosine Fabrizio Giordanetto (Tue May 15 2001 - 08:34:51 PDT)
  - AMBER enquiry Marjoribanks, Andrew G (Tue May 15 2001 - 10:21:03 PDT)
  - RMSD calculation arubin_at_unmc.edu (Tue May 15 2001 - 12:43:46 PDT)
Re: RMSD calculation Bill Ross (Tue May 15 2001 - 14:49:39 PDT)
- Re: RMSD calculation Carlos Simmerling (Tue May 15 2001 - 16:13:47 PDT)
- ewald bomb Martin Crnugelj (Wed May 16 2001 - 00:43:13 PDT)
- average structure Krishna Bisetty (Wed May 16 2001 - 03:33:41 PDT)
- (no subject) Rino Ragno (Wed May 16 2001 - 04:47:15 PDT)
- PSC BIOMEDICAL WORKSHOPS 2001 Troy Wymore (Wed May 16 2001 - 10:27:50 PDT)
Re: CCL:Date: Wed, 16 May 2001 13:47:15 +0200 Bill Ross (Wed May 16 2001 - 12:59:11 PDT)
box of water Marcela Madrid (Wed May 16 2001 - 15:04:01 PDT)
Re: Residence time Nada Spackova (Thu May 17 2001 - 06:24:07 PDT)
Query Monica (Sat May 19 2001 - 05:09:24 PDT)
GDP/GTP Nathalie Duclert (Mon May 21 2001 - 06:02:12 PDT)
matrix diagonalizing subroutines Haitao Dong (Mon May 21 2001 - 11:15:16 PDT)
matrix diagonalizing subroutines Haitao Dong (Mon May 21 2001 - 11:45:03 PDT)
f2c.h Osmar Norberto de Souza (Mon May 21 2001 - 13:20:38 PDT)
Re: Ewald error estimation darden (Mon May 21 2001 - 13:58:17 PDT)
Re: f2c.h Bill Ross (Mon May 21 2001 - 15:10:56 PDT)
CUT in AMBER6 arubin_at_unmc.edu (Mon May 21 2001 - 15:53:41 PDT)
AMBER compilation woes Elizabeth K. White (Mon May 21 2001 - 22:12:04 PDT)
Re: AMBER compilation woes Bill Ross (Tue May 22 2001 - 00:01:52 PDT)
Re: problem in xleap Bill Ross (Wed May 30 2001 - 09:50:17 PDT)
Re: add counterions Bill Ross (Wed May 30 2001 - 09:58:53 PDT)
Peter Kollman memorial jim caldwell (Wed May 30 2001 - 16:25:17 PDT)
(no subject) Sarah Tschampel (Thu May 31 2001 - 09:01:09 PDT)
make test.all crashes in AMBER Elizabeth K. White (Thu May 31 2001 - 14:48:12 PDT)
- Re: make test.all crashes in AMBER jim caldwell (Thu May 31 2001 - 15:29:52 PDT)
- machine/OS on which make test.all crashes in AMBER Elizabeth K. White (Thu May 31 2001 - 17:51:22 PDT)
- sander 6 warming up Shixiang Yan (Thu May 31 2001 - 19:06:20 PDT)
  - Re: sander 6 warming up Andreas Svrcek-Seiler (Fri Jun 01 2001 - 06:53:35 PDT)
  - sander_classic no mdcrd Daniel Flint (Fri Jun 01 2001 - 07:06:10 PDT)
    - Re: sander_classic no mdcrd Christoph Sotriffer (Fri Jun 01 2001 - 06:53:27 PDT)
  - sander_classic no mdcrd Daniel Flint (Fri Jun 01 2001 - 07:06:10 PDT)
    - Re: sander_classic no mdcrd Richard W Dixon (Fri Jun 01 2001 - 08:41:10 PDT)
    - Re: sander_classic no mdcrd Richard W Dixon (Fri Jun 01 2001 - 08:41:10 PDT)
  - ice cube flying through space Marcela Madrid (Fri Jun 01 2001 - 08:10:53 PDT)
    - Re: ice cube flying through space Andreas Svrcek-Seiler (Sat Jun 02 2001 - 05:54:55 PDT)
    - Adding crystal water using tleap. Sanjeev B.S. (Sun Jun 03 2001 - 08:04:51 PDT)
    - compiling amber6 in linux clusters A.Madhumalar (Sun Jun 03 2001 - 09:35:16 PDT)
    - How to minimization of Average structure? Xiaolin Chuang (Sun Jun 03 2001 - 09:57:48 PDT)
  - ice cube flying through space Marcela Madrid (Fri Jun 01 2001 - 08:10:53 PDT)
Re: Adding crystal water using tleap. Bill Ross (Sun Jun 03 2001 - 10:19:32 PDT)
Re: How to minimization of Average structure? Bill Ross (Sun Jun 03 2001 - 11:24:15 PDT)
dsp3 hybrid for P ? Todd J. Minehardt (Sun Jun 03 2001 - 12:47:41 PDT)
90 degree phase offset in AMBER? Kristin Lynne Meagher (Mon Jun 04 2001 - 10:14:27 PDT)
informations Osvaldo A. Santos-Filho (Mon Jun 04 2001 - 13:31:11 PDT)
- Re: informations schayg_at_puskin-a206.sote.hu (Tue Jun 05 2001 - 08:39:03 PDT)
- Error in Gibbs Kian Kani (Tue Jun 05 2001 - 09:42:48 PDT)
- number of atoms for large system Shixiang Yan (Tue Jun 05 2001 - 12:36:50 PDT)
- free energy method Eoin Galligan (Wed Jun 06 2001 - 02:34:53 PDT)
- reflector limitations jim caldwell (Wed Jun 06 2001 - 07:51:05 PDT)
- error msg in leap Eoin Galligan (Wed Jun 06 2001 - 10:30:43 PDT)
  - Re: error msg in leap schayg_at_puskin-a206.sote.hu (Wed Jun 06 2001 - 12:27:49 PDT)
  - LIE method Katherine Wallis Abold (Wed Jun 06 2001 - 14:14:10 PDT)
    - Re: LIE method Wei Wang (Wed Jun 06 2001 - 20:24:26 PDT)
    - leap not reaing torsion from frcmod file Eoin Galligan (Thu Jun 07 2001 - 06:45:22 PDT)
    - AMBER on Hitachi SR8000 Florian Barth (Thu Jun 07 2001 - 13:22:32 PDT)
    - Re: AMBER on Hitachi SR8000 Noriyuki Yamaotsu (Thu Jun 07 2001 - 19:19:09 PDT)
    - error message. Margaret Cheung (Fri Jun 08 2001 - 00:24:07 PDT)
    - Re: error message. Andreas Svrcek-Seiler (Fri Jun 08 2001 - 04:36:41 PDT)
    - a correction, sorry Andreas Svrcek-Seiler (Fri Jun 08 2001 - 06:43:39 PDT)
    - summary of Zn+2 van der Waals radii responses Katherine Wallis Abold (Fri Jun 08 2001 - 07:43:03 PDT)
    - igb=1 error message: Unable to find bonded partner for atom 239 Guanglei Cui (Sat Jun 09 2001 - 13:46:03 PDT)
  - make test.all Elizabeth K. White (Wed Jun 06 2001 - 14:22:46 PDT)
  - 2'-deoxy-uracil Anton B. Guliaev (Wed Jun 06 2001 - 15:36:01 PDT)
benchmark on X-86 Sanjeev B.S. (Tue Jun 05 2001 - 01:23:37 PDT)
Re: AMBER on Hitachi SR8000 Bill Ross (Thu Jun 07 2001 - 14:43:48 PDT)
Zn+2 van der Waals radii Katherine Wallis Abold (Thu Jun 07 2001 - 15:16:14 PDT)
Re: atom coordinates Bill Ross (Mon Jun 11 2001 - 16:29:39 PDT)
Dual-processor performance. Sanjeev B.S. (Mon Jun 11 2001 - 23:45:24 PDT)
Re: Non-standard DNA bases Bill Ross (Tue Jun 12 2001 - 14:39:05 PDT)
Non-standard DNA bases J Suggs (Tue Jun 12 2001 - 16:32:21 PDT)
- Re: Non-standard DNA bases Bill Ross (Tue Jun 12 2001 - 22:29:40 PDT)
  - Re: Non-standard DNA bases David Konerding (Wed Jun 13 2001 - 07:41:09 PDT)
  - GFP chromophore force field parameters Dr Chris L. Brown (Wed Jun 13 2001 - 18:31:56 PDT)
Re: mm_pbsa samantha hughes (Thu Jun 14 2001 - 00:06:47 PDT)
- Re: mm_pbsa Wei Wang (Mon Nov 19 2001 - 17:27:10 PST)
Problem in MD! PRADIPTA Bandyopadhyay (Thu Jun 14 2001 - 10:16:59 PDT)
Is there a potential for speedup in the GB-code ? Andreas Svrcek-Seiler (Fri Jun 15 2001 - 08:05:36 PDT)
coordinate blowup in sander Michael Cooney (Fri Jun 15 2001 - 09:29:05 PDT)
- Re: coordinate blowup in sander jim caldwell (Fri Jun 15 2001 - 10:54:53 PDT)
  - Re: coordinate blowup in sander Carlos Simmerling (Fri Jun 15 2001 - 11:46:36 PDT)
  - An Invitation From The Middle East Chemical Industry iec_at_emirates.net.ae (Sat Jun 16 2001 - 12:34:21 PDT)
  - RESP X GAMESS Dummie Question Jones de Andrade (Mon Jun 18 2001 - 10:22:11 PDT)
  - WHY NOT TRY IT? go5612gwe_at_arabia.com (Mon Jun 18 2001 - 12:02:17 PDT)
  - water parameters+TIP3 water model Satyavani Vemparala (Mon Jun 18 2001 - 13:00:00 PDT)
    - Re: water parameters+TIP3 water model jim caldwell (Tue Jun 19 2001 - 11:52:04 PDT)
    - Linux stability Stephane (Fri Jun 22 2001 - 15:05:29 PDT)
    - (no subject) bxiong (Fri Jun 22 2001 - 19:11:09 PDT)
    - AMBER Phil Cunningham (Tue Jun 19 2001 - 13:53:11 PDT)
    - Re: AMBER jim caldwell (Tue Jun 19 2001 - 15:30:17 PDT)
    - parallel sander Yuguang Mu (Wed Jun 20 2001 - 07:58:39 PDT)
    - Re: parallel sander Sanjeev B.S. (Wed Jun 20 2001 - 10:39:23 PDT)
    - equilibrating water in sander Elizabeth K. White (Wed Jun 20 2001 - 16:00:00 PDT)
    - Re: equilibrating water in sander Yong Duan (Wed Jun 20 2001 - 21:27:02 PDT)
  - PMF calculations Eoin Galligan (Tue Jun 19 2001 - 03:58:26 PDT)
emin after molecular dynamics Nicole Silvester (Fri Jun 22 2001 - 00:41:06 PDT)
gb with explicit water molecules Guanglei Cui (Fri Jun 22 2001 - 09:05:52 PDT)
- PDB old to new Jithesh P.V. (Tue Jun 26 2001 - 23:48:06 PDT)
iwrap & TIP3P model water Xiaolin Chuang (Fri Jun 22 2001 - 09:20:06 PDT)
- Re: iwrap & TIP3P model water Jung-Hsing Lin (Fri Jun 22 2001 - 09:53:00 PDT)
Re: Linux stability Bill Ross (Fri Jun 22 2001 - 13:51:17 PDT)
Re: CCl4 charge problem... jim caldwell (Fri Jun 22 2001 - 14:03:13 PDT)
Re: Wrong compilation artifacts on ES40s? Bill Ross (Sun Jun 24 2001 - 10:59:27 PDT)
- Re: Wrong compilation artifacts on ES40s? Bill Ross (Sun Jun 24 2001 - 12:58:33 PDT)
- Re: Wrong compilation artifacts on ES40s? Sanjeev B.S. (Sun Jun 24 2001 - 13:17:48 PDT)
- AmberFFC version 1.2 Francois Dupradeau (Sun Jun 24 2001 - 13:49:29 PDT)
Wrong compilation artifacts on ES40s? Sanjeev B.S. (Sun Jun 24 2001 - 11:43:11 PDT)
- Re: Wrong compilation artifacts on ES40s? Bill Ross (Sun Jun 24 2001 - 23:51:20 PDT)
- gradual warming + partial solvation Eoin Galligan (Mon Jun 25 2001 - 07:59:44 PDT)
- My input problem in amber6 ! A. Ababou (Mon Jun 25 2001 - 08:54:18 PDT)
- Charges for a 2-iodine-phenol stefania_at_mail.unimo.it (Mon Jun 25 2001 - 09:29:27 PDT)
- Machine file for sgi kian kani (Mon Jun 25 2001 - 10:25:21 PDT)
- Best Topolgy for Linux Cluster Sanjeev B.S. (Tue Jun 26 2001 - 05:17:51 PDT)
- Energy calculation Prem Raj Joseph (Tue Jun 26 2001 - 09:34:38 PDT)
- begginer's question about RESP and GAMESS Jones de Andrade (Tue Jun 26 2001 - 10:44:02 PDT)
Re: begginer's question. jim caldwell (Tue Jun 26 2001 - 12:20:32 PDT)
Resp input confusion. jim caldwell (Tue Jun 26 2001 - 14:55:07 PDT)
RE: CCl4 charge problem... Thomas.Fox_at_bc.boehringer-ingelheim.com (Wed Jun 27 2001 - 01:16:19 PDT)
RE: CCl4 charge problem... (part II) Thomas.Fox_at_bc.boehringer-ingelheim.com (Wed Jun 27 2001 - 03:04:17 PDT)
tleap input format A.Madhumalar (Wed Jun 27 2001 - 06:20:02 PDT)
AMBER on mpi Marco Punta (Wed Jun 27 2001 - 10:39:46 PDT)
resp charges: ccl4 jag vs. g98 jim caldwell (Wed Jun 27 2001 - 15:51:49 PDT)
Parameter for abasic nucleotide Numan Oezguen (Wed Jun 27 2001 - 19:48:58 PDT)
re: Amber compiling on Alpha Clusters Redhat Linux Chuck Schneider (Thu Jun 28 2001 - 05:08:41 PDT)
folding simulations Elizabeth K. White (Thu Jun 28 2001 - 14:52:19 PDT)
- Re: folding simulations David Case (Thu Jun 28 2001 - 17:27:00 PDT)
- Problems with AMBER John Finke (Thu Jun 28 2001 - 18:04:52 PDT)
Re: Problems with AMBER Bill Ross (Thu Jun 28 2001 - 19:49:52 PDT)
- Re: Problems with AMBER Bill Ross (Thu Jun 28 2001 - 19:49:52 PDT)
- Re: Problems with AMBER John Finke (Fri Jun 29 2001 - 15:55:06 PDT)
- Re: Problems with AMBER Bill Ross (Fri Jun 29 2001 - 16:23:06 PDT)
- Creating capped peptides with AMBER John Finke (Tue Jul 10 2001 - 17:41:28 PDT)
- problem in xleap Monica (Tue Jul 10 2001 - 20:51:18 PDT)
  - Re: problem in xleap schayg_at_puskin-a206.sote.hu (Wed Jul 11 2001 - 15:25:18 PDT)
  - Re: problem in xleap schayg_at_puskin-a206.sote.hu (Wed Jul 11 2001 - 15:25:18 PDT)
- problem in xleap Monica (Tue Jul 10 2001 - 20:51:18 PDT)
  - Re:problem in xleap Harshit Patel (Wed Jul 11 2001 - 08:13:56 PDT)
  - Re:problem in xleap Bill Ross (Wed Jul 11 2001 - 09:30:08 PDT)
  - Request r ojha (Wed Jul 11 2001 - 11:06:23 PDT)
  - Internal Restraints in Sander Problem Manoj Cheriyan (Wed Jul 11 2001 - 15:19:31 PDT)
- about ion concentration in protein simulation Shixiang Yan (Wed Jul 11 2001 - 06:48:16 PDT)
TIP3P Guanglei Cui (Thu Jun 28 2001 - 22:22:57 PDT)
torsion parameters needed Guanglei Cui (Thu Jun 28 2001 - 22:40:06 PDT)
Re: TIP3P Bill Ross (Thu Jun 28 2001 - 23:34:47 PDT)
AMBER parameter database Dr Richard Bryce (Fri Jun 29 2001 - 09:47:18 PDT)
gibbs_restrt Olga Carvalho (Mon Jul 02 2001 - 05:21:00 PDT)
- Re: gibbs_restrt jim caldwell (Mon Jul 02 2001 - 10:02:22 PDT)
  - limit the distance Zhangxd (Mon Jul 02 2001 - 13:13:08 PDT)
  - C DNA MONOMER UNITS A.Madhumalar (Tue Jul 03 2001 - 00:38:11 PDT)
- vdw parameters for:THR-HG1, TYR-HH Omer Katzenelson (Mon Jul 02 2001 - 18:49:27 PDT)
high density spot Guanglei Cui (Mon Jul 02 2001 - 07:49:30 PDT)
Hritz Jozef Hritz (Tue Jul 03 2001 - 04:58:18 PDT)
Re: CCl4 ESP Grid problem with jaguar | 010628a (fwd) jim caldwell (Tue Jul 03 2001 - 12:38:21 PDT)
addles Eoin Galligan (Wed Jul 04 2001 - 06:18:59 PDT)
- RE: addles Guanglei Cui (Wed Jul 04 2001 - 07:11:51 PDT)
- amber5 and 77000 atoms ... A. Ababou (Wed Jul 04 2001 - 08:36:16 PDT)
- Re: addles Carlos Simmerling (Thu Jul 05 2001 - 04:38:25 PDT)
- nucgen Xiaolin Chuang (Thu Jul 05 2001 - 05:06:39 PDT)
- gamess X resp : Conclusions. (fwd) jim caldwell (Thu Jul 05 2001 - 10:17:50 PDT)
  - Structure with coordinates of C-alpha atoms only Jung-Hsing Lin (Thu Jul 05 2001 - 19:23:48 PDT)
RE: CCl4 ESP Grid problem with jaguar | 010628a (fwd) Bayly, Christopher (Wed Jul 04 2001 - 08:50:19 PDT)
(no subject) Michal Otyepka (Wed Jul 04 2001 - 10:20:54 PDT)
amber5 and 77000 atoms ... A. Ababou (Wed Jul 04 2001 - 11:20:38 PDT)
RE: CCl4 ESP Grid problem with jaguar GUILBAUD Philippe 153683 (Thu Jul 05 2001 - 02:09:07 PDT)
Re: amber5/6 Bill Ross (Fri Jul 06 2001 - 13:18:23 PDT)
problem in xleap Monica (Sun Jul 08 2001 - 23:47:48 PDT)
Re: stop COM motions in AMBER 5.0.1 question David Case (Mon Jul 09 2001 - 08:06:21 PDT)
Help with Leap! Dat H. Nguyen (Mon Jul 09 2001 - 17:17:58 PDT)
Re: Help with Leap! Bill Ross (Mon Jul 09 2001 - 17:34:52 PDT)
Re: Internal Restraints in Sander Problem Bill Ross (Wed Jul 11 2001 - 15:40:55 PDT)
Re: about ion concentration in protein simulation Bill Ross (Wed Jul 11 2001 - 15:49:27 PDT)
Parameters for phosphonate available? Gudrun Schuerer (Thu Jul 12 2001 - 06:27:46 PDT)
histidines normal-modes Jones de Andrade (Thu Jul 12 2001 - 07:04:23 PDT)
ptraj diffusion dkon_at_email.arizona.edu (Thu Jul 12 2001 - 11:32:38 PDT)
- Re: ptraj diffusion Thomas Cheatham (Thu Jul 12 2001 - 12:15:46 PDT)
- addions tianxiao young (Thu Jul 12 2001 - 19:55:38 PDT)
- parm94 eric arnoult (Fri Jul 13 2001 - 05:40:20 PDT)
- ewald bomb in amber 6 Todd J. Minehardt (Fri Jul 13 2001 - 07:21:50 PDT)
  - Re: ewald bomb in amber 6 David Konerding (Fri Jul 13 2001 - 07:28:30 PDT)
    - Re: ewald bomb in amber 6 Thomas Cheatham (Fri Jul 13 2001 - 14:51:42 PDT)
    - Re: ewald bomb in amber 6 David Konerding (Fri Jul 13 2001 - 15:07:41 PDT)
    - ADDING IONS USING EDIT A.Madhumalar (Sat Jul 14 2001 - 10:54:31 PDT)
    - Essential Dynamics Sanjeev B.S. (Sun Jul 15 2001 - 08:48:12 PDT)
    - dipolar couplings Richard Stefl (Mon Jul 16 2001 - 05:30:07 PDT)
    - sander minimization problems with igb=3, ntb =0 Todd J. Minehardt (Mon Jul 16 2001 - 06:28:46 PDT)
    - installing amber6 UMEMOTO, Kimiko (Tue Jul 17 2001 - 01:37:13 PDT)
  - Re: ewald bomb in amber 6 Sanjeev B.S. (Fri Jul 13 2001 - 11:30:38 PDT)
  - Re: ewald bomb in amber 6 Michael Crowley (Fri Jul 13 2001 - 11:38:23 PDT)
Re: installing amber6 Bill Ross (Tue Jul 17 2001 - 11:18:06 PDT)
potentials tianxiao young (Tue Jul 17 2001 - 19:58:28 PDT)
ptraj: principal axes Thomas C. Bishop (Wed Jul 18 2001 - 06:23:30 PDT)
Announcing PyMOL v0.56 (+ Windows Installer) DeLano, Warren (Wed Jul 18 2001 - 12:14:45 PDT)
AMBER box dkon_at_email.arizona.edu (Wed Jul 18 2001 - 16:20:00 PDT)
- Re: AMBER box Carlos Simmerling (Thu Jul 19 2001 - 04:24:35 PDT)
- question Zhangxd (Thu Jul 19 2001 - 07:05:18 PDT)
- Amber installation Miguel Cabrera Fuentes (Fri Jul 20 2001 - 11:47:35 PDT)
  - Amber installation on linux Miguel Cabrera Fuentes (Sat Jul 21 2001 - 16:13:59 PDT)
  - constraining hydrogen bonds A.Madhumalar (Sun Jul 22 2001 - 08:19:02 PDT)
    - RE: constraining hydrogen bonds Guanglei Cui (Sun Jul 22 2001 - 09:02:45 PDT)
- dissociation of protein from DNA in MD Michael Cooney (Sat Jul 21 2001 - 12:50:27 PDT)
  - Re: dissociation of protein from DNA in MD David Case (Sat Jul 21 2001 - 13:15:13 PDT)
equilibriating LES Eoin Galligan (Thu Jul 19 2001 - 03:27:55 PDT)
- Re: equilibriating LES Carlos Simmerling (Thu Jul 19 2001 - 04:22:54 PDT)
parm99 Giulio Rastelli (Thu Jul 19 2001 - 04:01:41 PDT)
Re: constraining hydrogen bonds Bill Ross (Sun Jul 22 2001 - 15:50:24 PDT)
Intprt in PMF calculations Ulf Ryde (Mon Jul 23 2001 - 04:18:57 PDT)
rigid body motion dkon_at_email.arizona.edu (Mon Jul 23 2001 - 10:20:27 PDT)
- Re: rigid body motion Sanjeev B.S. (Wed Jul 25 2001 - 09:00:00 PDT)
Npairs Exceeds Max Anton B. Guliaev (Mon Jul 23 2001 - 10:37:48 PDT)
[charmm-bbs] Post-doctoral position available Chris Chipot (Mon Jul 23 2001 - 16:32:19 PDT)
Post-doctoral position available Chris Chipot (Mon Jul 23 2001 - 16:32:19 PDT)
Question... backy_at_ibms.sinica.edu.tw (Mon Jul 23 2001 - 22:57:56 PDT)
A request regarding AMBER postings with attached files Anita Ilze Zvaigzne (Tue Jul 24 2001 - 03:18:42 PDT)
Windows Virus Markus Drumm (Tue Jul 24 2001 - 03:42:07 PDT)
Re: A request regarding AMBER postings with attached files (fwd) Andrew Gordon Purkiss (Tue Jul 24 2001 - 04:14:29 PDT)
block attachments? Jake Isaacs (Tue Jul 24 2001 - 06:22:46 PDT)
- Re: block attachments? Anita Ilze Zvaigzne (Tue Jul 24 2001 - 08:06:07 PDT)
- trajectory analysis dkon_at_email.arizona.edu (Tue Jul 24 2001 - 11:15:31 PDT)
  - Re: trajectory analysis Andreas Svrcek-Seiler (Tue Jul 24 2001 - 12:00:59 PDT)
  - Re: trajectory analysis Carlos Simmerling (Tue Jul 24 2001 - 12:22:24 PDT)
  - spam jim caldwell (Tue Jul 24 2001 - 14:11:45 PDT)
  - water cap Guanglei Cui (Tue Jul 24 2001 - 21:29:45 PDT)
    - Re: water cap Michael Cooney (Wed Jul 25 2001 - 10:27:54 PDT)
    - DelPhi's manual Xiaolin Chuang (Wed Jul 25 2001 - 10:37:04 PDT)
    - Re: DelPhi's manual Andreas Svrcek-Seiler (Thu Jul 26 2001 - 04:55:11 PDT)
    - ptraj to re-associate protein+DNA Michael Cooney (Wed Jul 25 2001 - 14:34:29 PDT)
    - About Delphi... backy_at_ibms.sinica.edu.tw (Wed Jul 25 2001 - 20:42:10 PDT)
  - Trosion parameters Eric ARNOULT (Wed Jul 25 2001 - 01:34:25 PDT)
hybridization tianxiao young (Tue Jul 24 2001 - 07:10:55 PDT)
Re: trajectory analysis Bill Ross (Tue Jul 24 2001 - 11:48:54 PDT)
- Re: trajectory analysis Bill Ross (Sat Oct 13 2001 - 12:50:04 PDT)
Re: Adding ions in xleap Yuguang Mu (Thu Jul 26 2001 - 23:25:38 PDT)
MD run with constantly decreasing total energy (fwd) jim caldwell (Sun Jul 29 2001 - 19:28:36 PDT)
- Re: MD run with constantly decreasing total energy (fwd) Andreas Svrcek-Seiler (Mon Jul 30 2001 - 02:06:55 PDT)
- simulating membranes with AMBER (fwd) jim caldwell (Mon Jul 30 2001 - 08:16:06 PDT)
- beginners problem (fwd) jim caldwell (Mon Jul 30 2001 - 08:16:28 PDT)
- vdW parameters for our friend, vanadium (fwd) jim caldwell (Mon Jul 30 2001 - 11:54:33 PDT)
- problem with xleap and sander! (fwd) jim caldwell (Mon Jul 30 2001 - 11:56:23 PDT)
- is parm98 the same as parm99? (fwd) jim caldwell (Tue Jul 31 2001 - 07:59:54 PDT)
- restarting gibbs (fwd) jim caldwell (Tue Jul 31 2001 - 08:00:25 PDT)
- box information Giulio Rastelli (Tue Jul 31 2001 - 10:39:29 PDT)
Re: simulating membranes with AMBER Thomas Huber (Tue Jul 31 2001 - 11:54:38 PDT)
Problem with Dat H. Nguyen (Tue Jul 31 2001 - 16:22:21 PDT)
questions for group specification... backy_at_ibms.sinica.edu.tw (Wed Aug 01 2001 - 02:11:59 PDT)
Gibbs and cutoff! PRADIPTA Bandyopadhyay (Sat Aug 04 2001 - 15:23:30 PDT)
varying cartesian restraint Raik Grunberg (Sun Aug 05 2001 - 02:48:28 PDT)
Model(l)ing 2001 in Erlangen/Germany: Bursaries and Awards available! Harald Lanig (Mon Aug 06 2001 - 06:04:51 PDT)
water molecules in a periodic box Giulio Rastelli (Mon Aug 06 2001 - 10:03:41 PDT)
Leap and parm/pert! PRADIPTA Bandyopadhyay (Mon Aug 06 2001 - 16:45:00 PDT)
Can amber calculate the gibbs perturb energy when a ligand added a group sxzheng (Mon Aug 06 2001 - 20:26:13 PDT)
reflector back on. jim caldwell (Tue Aug 14 2001 - 12:30:19 PDT)
Linux-cluster performance Florian Barth (Wed Aug 15 2001 - 06:07:51 PDT)
- Re: Linux-cluster performance Jarrod Smith (Wed Aug 15 2001 - 10:23:09 PDT)
- box size tianxiao young (Wed Aug 15 2001 - 21:31:40 PDT)
- Protonated Water Dr. Andrea Cavalli (Thu Aug 16 2001 - 00:37:33 PDT)
- dual K7 (was Re: Linux-cluster performance) Tru Huynh (Mon Aug 20 2001 - 12:09:18 PDT)
- changing the g77 optimization for compiling sander_classic Margaret Cheung (Mon Aug 20 2001 - 13:08:30 PDT)
- adding atoms and amino acid residues Marcela Madrid (Mon Aug 20 2001 - 14:52:31 PDT)
  - Re: adding atoms and amino acid residues Omer Katzenelson (Tue Aug 21 2001 - 14:25:31 PDT)
  - CARNAL Omer Katzenelson (Tue Aug 21 2001 - 18:27:54 PDT)
  - Utilizing Amber6 on Linux Cluster Scott E. Boesch (Wed Aug 22 2001 - 07:24:42 PDT)
    - Re: Utilizing Amber6 on Linux Cluster David Konerding (Wed Aug 22 2001 - 08:31:56 PDT)
    - Re: Utilizing Amber6 on Linux Cluster Margaret Cheung (Wed Aug 22 2001 - 10:23:40 PDT)
    - Re: Utilizing Amber6 on Linux Cluster Jung-Hsing Lin (Wed Aug 22 2001 - 10:49:25 PDT)
    - Re: Utilizing Amber6 on Linux Cluster David Konerding (Wed Aug 22 2001 - 12:41:13 PDT)
    - Analysising the results Rozita Dara (Wed Aug 22 2001 - 13:03:28 PDT)
    - defining states in Gibbs Sophia Kondratova (Wed Aug 22 2001 - 12:39:35 PDT)
    - problem using xleap and tleap Rozita Dara (Wed Aug 22 2001 - 10:13:08 PDT)
    - Re: Utilizing Amber6 on Linux Cluster Sanjeev B.S. (Wed Aug 22 2001 - 22:31:58 PDT)
    - ptraj Troy Wymore (Thu Aug 23 2001 - 08:30:23 PDT)
    - Re: ptraj Thomas Cheatham (Thu Aug 23 2001 - 09:36:51 PDT)
    - Error message Rozita Dara (Thu Aug 23 2001 - 10:46:12 PDT)
    - Re: Error message Jung-Hsing Lin (Thu Aug 23 2001 - 10:54:27 PDT)
    - ... error message Rozita Dara (Thu Aug 23 2001 - 12:14:07 PDT)
    - summary: AMBER6 on IBMSP3 Xavier Deupi (Fri Aug 24 2001 - 00:04:19 PDT)
    - How to deal with the little molcule? sxzheng (Fri Aug 24 2001 - 07:48:22 PDT)
    - Error message Rozita Dara (Thu Aug 23 2001 - 08:59:57 PDT)
    - (no subject) Xiaolin Chuang (Thu Aug 23 2001 - 09:00:49 PDT)
    - Re:Re: (to "Xiaolin Chuang") Elsa de Sousa Henriques (Fri Aug 24 2001 - 11:38:05 PDT)
    - ntc in sander6 Xavier Deupi (Sat Aug 25 2001 - 05:08:12 PDT)
    - Mystery protons! Sanjeev B.S. (Sun Aug 26 2001 - 05:03:11 PDT)
    - coordinate resetting ? Guido Hansen (Mon Aug 27 2001 - 01:46:51 PDT)
    - Re: coordinate resetting ? A.Madhumalar (Mon Aug 27 2001 - 05:50:59 PDT)
    - computing order parameters from an MD trajectory Jake Isaacs (Mon Aug 27 2001 - 07:45:58 PDT)
    - L-J mixing rules? Kevin Van Workum (Mon Aug 27 2001 - 09:10:24 PDT)
    - Program versoins Stephane (Wed Sep 05 2001 - 03:05:58 PDT)
    - shake tricks? Peter Varnai (Thu Aug 30 2001 - 06:57:00 PDT)
    - residue numbering in dimers and trimers Joseph Nachman (Thu Aug 30 2001 - 09:41:48 PDT)
    - RE: residue numbering in dimers and trimers Bayly, Christopher (Thu Aug 30 2001 - 11:30:47 PDT)
    - Re: residue numbering in dimers and trimers samantha hughes (Fri Aug 31 2001 - 00:43:55 PDT)
    - NPT restart problem Sanjeev B.S. (Fri Aug 31 2001 - 03:16:37 PDT)
    - movie for subset of atoms Anton B. Guliaev (Thu Aug 30 2001 - 13:42:14 PDT)
    - Re: movie for subset of atoms Florian Barth (Thu Aug 30 2001 - 14:16:00 PDT)
    - RE: movie for subset of atoms DeLano, Warren (Thu Aug 30 2001 - 14:32:53 PDT)
    - Newton-Raphson minimization! Dat H. Nguyen (Thu Aug 30 2001 - 16:20:56 PDT)
    - torsional profile Giulio Rastelli (Thu Aug 30 2001 - 17:02:39 PDT)
- changing the g77 optimization for compiling sander_classic Margaret Cheung (Mon Aug 20 2001 - 17:25:41 PDT)
Combination of two solvents Alexander Steudle (Wed Aug 15 2001 - 07:58:15 PDT)
charge on protein Giulio Rastelli (Wed Aug 15 2001 - 10:08:43 PDT)
Re: adding atoms and amino acid residues Bill Ross (Mon Aug 20 2001 - 18:10:48 PDT)
- Re: adding atoms and amino acid residues Raik Grunberg (Tue Aug 21 2001 - 01:20:50 PDT)
- density in equilibration? Shixiang Yan (Tue Aug 21 2001 - 09:38:35 PDT)
Re: problem using xleap and tleap Bill Ross (Wed Aug 22 2001 - 10:23:27 PDT)
Re: residue numbering in dimers and trimers Bill Ross (Thu Aug 30 2001 - 10:00:44 PDT)
question Jie Guo (Thu Aug 30 2001 - 10:58:37 PDT)
NPT restart problem Sanjeev B.S. (Fri Aug 31 2001 - 06:19:48 PDT)
SPC water Jerry wu (Fri Aug 31 2001 - 07:01:32 PDT)
COORDINATE RESETTING Sanjeev B.S. (Sun Sep 02 2001 - 05:56:12 PDT)
error message Guanglei Cui (Mon Sep 03 2001 - 08:12:17 PDT)
peek_ewad_inpcrd Lakshmi P. Kotra (Mon Sep 03 2001 - 10:57:31 PDT)
- Re: peek_ewad_inpcrd schayg_at_puskin-a206.sote.hu (Tue Sep 04 2001 - 14:13:22 PDT)
  - Re: peek_ewad_inpcrd Sanjeev B.S. (Wed Sep 05 2001 - 00:07:10 PDT)
Dist restraints + Belly Dyn Sanjeev B.S. (Thu Sep 06 2001 - 05:05:41 PDT)
library files in leap Michael G Cooney (Thu Sep 06 2001 - 12:35:15 PDT)
Unit of force constant Chigusa Kobayashi (Thu Sep 06 2001 - 13:23:14 PDT)
xleap crashing on sgi's Michael G Cooney (Thu Sep 06 2001 - 13:36:46 PDT)
Re: library files in leap Bill Ross (Thu Sep 06 2001 - 15:11:06 PDT)
Belly+Restraints Sanjeev B.S. (Fri Sep 07 2001 - 03:32:16 PDT)
Strange density behavior with tr. octahedral box and constant pressure Michael Jakusch (Fri Sep 07 2001 - 06:24:53 PDT)
ESS Workshop - Flexibility and Function of Proteins ess-ws_at_iwr.uni-heidelberg.de (Fri Sep 07 2001 - 07:04:57 PDT)
generalized born model on protein or peptide liz (Fri Sep 07 2001 - 09:43:02 PDT)
- Re: generalized born model on protein or peptide Andreas Svrcek-Seiler (Fri Sep 07 2001 - 12:39:27 PDT)
- parameter regarding S-O Shixiang Yan (Fri Sep 07 2001 - 14:32:25 PDT)
- hydorgen bond life time thenmalar rathinavelan (Fri Sep 07 2001 - 21:14:18 PDT)
- Result: Dist restraints + Belly Sanjeev B.S. (Sat Sep 08 2001 - 04:24:37 PDT)
- MD run with constantly decreasing total energy Sue Heavner (Sat Sep 08 2001 - 15:00:25 PDT)
- partial solvation using delphi Shixiang Yan (Sun Sep 09 2001 - 11:10:32 PDT)
- input parameter for amber5 Hungie Hungie (Mon Sep 10 2001 - 05:03:26 PDT)
  - Re: input parameter for amber5 Stephane (Mon Sep 10 2001 - 05:17:45 PDT)
  - Add electric field Long Hai (Mon Sep 10 2001 - 11:41:12 PDT)
    - how to write out ... Michal Otyepka (Thu Sep 13 2001 - 05:07:39 PDT)
  - a funny problem about output for sander_classic Shixiang Yan (Tue Sep 11 2001 - 14:12:13 PDT)
    - Problem with carnal ... Stephane (Thu Sep 13 2001 - 09:25:38 PDT)
    - Re: Problem with carnal ... Sanjeev B.S. (Thu Sep 13 2001 - 09:43:56 PDT)
    - Problem minimizing on SGI (SHOULD NOT BE HERE). Andrew Hoofnagle (Thu Sep 13 2001 - 10:37:05 PDT)
    - Re: Problem minimizing on SGI (SHOULD NOT BE HERE). Andrew Hoofnagle (Thu Sep 13 2001 - 13:39:29 PDT)
    - Problem with compilation of AMBER on IBM Power3 SP Eric Aubanel (Thu Sep 13 2001 - 13:05:50 PDT)
    - Re: Problem with compilation of AMBER on IBM Power3 SP Sanjeev B.S. (Thu Sep 13 2001 - 21:00:36 PDT)
    - Re: Problem with compilation of AMBER on IBM Power3 SP Nicolas Grima (Fri Sep 14 2001 - 02:20:27 PDT)
    - error Rozita Dara (Fri Sep 14 2001 - 09:07:07 PDT)
  - trajectory analysis Eoin Galligan (Wed Sep 12 2001 - 09:21:16 PDT)
  - energies for part of the protein Elizabeth K. White (Wed Sep 12 2001 - 15:21:10 PDT)
    - Re: energies for part of the protein jim caldwell (Wed Sep 12 2001 - 15:33:59 PDT)
- Re: generalized born model on protein or peptide Raik Grunberg (Mon Sep 10 2001 - 05:14:58 PDT)
problem with anal arnaud (Fri Sep 07 2001 - 09:47:24 PDT)
Re: energies for part of the protein Bill Ross (Wed Sep 12 2001 - 17:07:32 PDT)
Re: how to write out... F. Ryjacek (Fri Sep 14 2001 - 10:23:20 PDT)
(no subject) F. Ryjacek (Fri Sep 14 2001 - 10:34:41 PDT)
- analysis of the results Rozita Dara (Tue Sep 18 2001 - 08:56:07 PDT)
- esp with gamess-usB Uwe Richter (Wed Sep 19 2001 - 06:05:26 PDT)
- another error Rozita Dara (Wed Sep 19 2001 - 08:01:11 PDT)
- Gibbs, PME, DynModW, ISDX0, etc. Michael Jakusch (Thu Sep 20 2001 - 05:39:47 PDT)
  - Dual Athlon Stephane (Thu Sep 27 2001 - 01:38:09 PDT)
    - Re: Dual Athlon Chuck Schneider (Thu Sep 27 2001 - 04:12:06 PDT)
    - about pressure Nikolai Smolin (Thu Sep 27 2001 - 06:33:56 PDT)
    - (no subject) xin hu (Thu Sep 27 2001 - 21:27:27 PDT)
    - (no subject) Stephane (Fri Sep 28 2001 - 01:18:21 PDT)
    - P-N-parameters Christine Bathelt (Fri Sep 28 2001 - 06:15:36 PDT)
- Problem in GIBBS! PRADIPTA Bandyopadhyay (Thu Sep 20 2001 - 11:38:05 PDT)
- Segmentation fault (core dumped) Rozita Dara (Tue Sep 25 2001 - 19:31:30 PDT)
  - problem with xleap Rozita Dara (Wed Sep 26 2001 - 15:22:29 PDT)
    - problem with ambpdb Rozita Dara (Sun Sep 30 2001 - 09:16:24 PDT)
    - Re: problem with ambpdb Bill Ross (Wed Oct 03 2001 - 01:16:23 PDT)
    - Temperature and pressure couplings Filip Lankas (Wed Oct 03 2001 - 08:38:56 PDT)
    - Re: Temperature and pressure couplings David Case (Wed Oct 03 2001 - 08:57:33 PDT)
    - NAN errors during production runs Oliver Zerbe (Wed Oct 03 2001 - 09:45:10 PDT)
    - ?s: Xeon vs. Athlon, latency R. M. Fesinmeyer (Wed Oct 03 2001 - 20:36:38 PDT)
    - RE: Xeon vs. Athlon, latency Yong Duan (Thu Oct 04 2001 - 10:19:29 PDT)
    - Re: ?s: Xeon vs. Athlon, latency Stephane (Fri Oct 05 2001 - 01:34:15 PDT)
    - post-processing of energy analysis Katherine Wallis Abold (Sun Oct 07 2001 - 13:58:30 PDT)
    - [Fwd: ?s: Xeon vs. Athlon, latency] Stephane (Mon Oct 08 2001 - 00:43:24 PDT)
    - NPSCAL parameter Nikolai Smolin (Mon Oct 08 2001 - 04:20:24 PDT)
    - Amber 6 MDCRD Files > 2GB in 32 bit Linux. Ross Walker (Mon Oct 08 2001 - 04:49:14 PDT)
    - analysis problem Eoin Galligan (Mon Oct 08 2001 - 06:12:22 PDT)
    - Re: ?s: Xeon vs. Athlon, latency R. M. Fesinmeyer (Mon Oct 08 2001 - 10:15:39 PDT)
  - CMC/MD wentaofu (Wed Sep 26 2001 - 16:03:37 PDT)
- Perturbed internal coordinate parameters Michael Jakusch (Wed Sep 26 2001 - 12:40:36 PDT)
LAPACK required by Amber Eric Aubanel (Fri Sep 14 2001 - 11:49:46 PDT)
parameters Marcela Madrid (Fri Sep 14 2001 - 12:50:26 PDT)
- Re: parameters jim caldwell (Fri Sep 14 2001 - 14:35:10 PDT)
- compile leap nepenthes_at_vplaces.net (Mon Sep 17 2001 - 00:16:51 PDT)
Re: compile leap Bill Ross (Mon Sep 17 2001 - 00:28:12 PDT)
about radius of gyration Nikolai Smolin (Mon Sep 17 2001 - 07:49:10 PDT)
Re: about radius of gyration Bill Ross (Mon Sep 17 2001 - 09:14:53 PDT)
Ewald Bomb Marcela Madrid (Tue Sep 18 2001 - 06:29:23 PDT)
Re: restraints and type Bill Ross (Fri Sep 21 2001 - 08:41:15 PDT)
restraints and type Christine Bathelt (Fri Sep 21 2001 - 09:24:57 PDT)
limit in xleap Anton B. Guliaev (Fri Sep 21 2001 - 15:13:03 PDT)
Info about LEaP Paolo Daniele (Mon Sep 24 2001 - 08:21:39 PDT)
- Re: Info about LEaP David Konerding (Mon Sep 24 2001 - 08:29:16 PDT)
Re: starting MD from t=0 Sanjeev B.S. (Mon Sep 24 2001 - 09:30:07 PDT)
water model Jerry wu (Mon Sep 24 2001 - 17:23:33 PDT)
Re: water model Bill Ross (Mon Sep 24 2001 - 23:21:44 PDT)
chlorine parameters M ESTA Laurent (Tue Sep 25 2001 - 01:06:31 PDT)
(no subject) A.Madhumalar (Tue Sep 25 2001 - 03:36:46 PDT)
RESP demo files Michael G Cooney (Tue Sep 25 2001 - 09:05:09 PDT)
Re: Velocity information in CARNAL generated restart files Bill Ross (Tue Sep 25 2001 - 12:32:51 PDT)
Re: CMC/MD Bill Ross (Wed Sep 26 2001 - 17:34:45 PDT)
Re: LINMIN Failure Michael Jakusch (Mon Oct 01 2001 - 08:17:17 PDT)
Possible error in AMBER parm94 file? John D. Chodera (Mon Oct 01 2001 - 17:01:37 PDT)
GB and Ions, 2nd try Andreas Svrcek-Seiler (Tue Oct 02 2001 - 08:43:39 PDT)
prowat test difficulties C. Singer (Tue Oct 02 2001 - 11:37:39 PDT)
RE: Binary mdcrd Halima Amer (Tue Oct 02 2001 - 23:43:41 PDT)
Re: NPSCAL parameter Bill Ross (Mon Oct 08 2001 - 08:36:10 PDT)
RESP charges Eva Darian (Mon Oct 08 2001 - 14:44:16 PDT)
- Re: RESP charges Lepsa (Tue Oct 09 2001 - 00:56:49 PDT)
  - RESP charges (correction) Eva Darian (Tue Oct 09 2001 - 08:54:49 PDT)
    - Re: RESP charges (correction) Lepsa (Wed Oct 10 2001 - 00:15:53 PDT)
    - MM-PBSA; E(internal) Michal Otyepka (Wed Oct 10 2001 - 09:58:19 PDT)
    - P4 benchmarks posted Robert Matthew Fesinmeyer (Thu Oct 11 2001 - 13:10:14 PDT)
    - 5-methyl deoxycytosine parameters Jake Isaacs (Fri Oct 12 2001 - 06:13:59 PDT)
    - parameters Didier Rognan (Fri Oct 12 2001 - 09:12:37 PDT)
    - energy decomposition Elizabeth K. White (Sat Oct 13 2001 - 06:51:40 PDT)
    - re: energy decomposition Bill Ross (Sat Oct 13 2001 - 12:10:18 PDT)
    - trajectory analysis Sue Heavner (Sat Oct 13 2001 - 12:26:41 PDT)
    - Re: RESP charges (correction) Lepsa (Wed Oct 31 2001 - 08:01:30 PST)
  - ISTAR option and performance Anton B. Guliaev (Tue Oct 09 2001 - 10:39:10 PDT)
    - Re: ISTAR option and performance Jarrod Smith (Tue Oct 09 2001 - 11:30:22 PDT)
- RE: RESP charges Ross Walker (Wed Apr 17 2002 - 08:28:58 PDT)
Code modification. John Finke (Mon Oct 08 2001 - 16:16:44 PDT)
adding water Rozita Dara (Sat Oct 13 2001 - 19:40:22 PDT)
Re: adding water Bill Ross (Sat Oct 13 2001 - 21:44:47 PDT)
Re: Can amber calculate the gibbs perturb energy when a ligand added a group Bill Ross (Sat Oct 13 2001 - 21:50:14 PDT)
torsional profile with MD Giulio Rastelli (Mon Oct 15 2001 - 09:17:34 PDT)
- Re: torsional profile with MD Bill Ross (Mon Oct 15 2001 - 10:17:12 PDT)
- ANAL Elizabeth K. White (Mon Oct 15 2001 - 10:45:18 PDT)
Re: torsional profile with MD Bill Ross (Mon Oct 15 2001 - 10:12:21 PDT)
Re: ANAL Bill Ross (Mon Oct 15 2001 - 11:17:23 PDT)
problem in a short MD with protein fixed dwang (Tue Oct 16 2001 - 18:00:26 PDT)
- Re: problem in a short MD with protein fixed Michael G Cooney (Wed Oct 17 2001 - 11:52:30 PDT)
- possible bug in carnal in AMBER5 Michael G Cooney (Wed Oct 17 2001 - 14:00:01 PDT)
Amber6 on SuSE Linux Toshikazu Matsuoka (Wed Oct 17 2001 - 01:56:49 PDT)
- Re: Amber6 on SuSE Linux jim caldwell (Wed Oct 17 2001 - 10:00:06 PDT)
distribution of Na+ around DNA Xiaolin Chuang (Wed Oct 17 2001 - 05:04:54 PDT)
image command of ptraj Xiaolin Chuang (Wed Oct 17 2001 - 05:22:20 PDT)
iwrap Xiaolin Chuang (Wed Oct 17 2001 - 05:27:39 PDT)
help seema namboori (Wed Oct 17 2001 - 06:50:53 PDT)
Re: distribution of Na+ around DNA Bill Ross (Wed Oct 17 2001 - 07:32:02 PDT)
Re: possible bug in carnal in AMBER5 Bill Ross (Wed Oct 17 2001 - 14:09:00 PDT)
Drivers to support Stereo Viewing in VMD etc using Standard GeForce Cards Ross Walker (Thu Oct 18 2001 - 07:00:48 PDT)
- torsional profile Giulio Rastelli (Thu Oct 18 2001 - 08:29:12 PDT)
- Re: Drivers to support Stereo Viewing in VMD etc using Standard GeForce Cards David Konerding (Thu Oct 18 2001 - 08:30:38 PDT)
  - RE: Drivers to support Stereo Viewing in VMD etc using Standard GeForce Cards Ross Walker (Thu Oct 18 2001 - 12:29:56 PDT)
  - Interface program installation Sophia Kondratova (Fri Oct 19 2001 - 10:25:19 PDT)
    - Re: Interface program installation David Pearlman (Fri Oct 19 2001 - 14:22:45 PDT)
  - Problem in GIBBS! PRADIPTA Bandyopadhyay (Fri Oct 19 2001 - 13:43:41 PDT)
- RE: Drivers to support Stereo Viewing in VMD etc using Standard GeForce Cards DeLano, Warren (Thu Oct 18 2001 - 09:48:53 PDT)
Re: Aqvist LJ parameters Samantha (Thu Oct 18 2001 - 11:34:46 PDT)
Re: generation of small organic molecules on xleap Bill Ross (Sun Oct 21 2001 - 21:48:53 PDT)
xleap: japanese keyboad Toshikazu Matsuoka (Sun Oct 21 2001 - 22:41:02 PDT)
Err in equilibration run A.Madhumalar (Sun Oct 21 2001 - 23:22:09 PDT)
Re: Err in equilibration run Bill Ross (Mon Oct 22 2001 - 00:03:38 PDT)
DNA strands separated... Jithesh P.V. (Mon Oct 22 2001 - 00:07:09 PDT)
question about implicit solvation model with AMBER Howard Feldman (Tue Oct 23 2001 - 07:55:36 PDT)
substracting of MM nonbondeb potential from QM curve Michal Otyepka (Tue Oct 23 2001 - 10:24:44 PDT)
Define flexible residues during MD simulation wentaofu (Tue Oct 23 2001 - 14:59:59 PDT)
- Re: Define flexible residues during MD simulation Bill Ross (Tue Oct 23 2001 - 21:14:35 PDT)
- Methane minimization using Interface Sophia Kondratova (Wed Oct 24 2001 - 07:17:36 PDT)
- param CT-CT-CT-OH Michal Otyepka (Wed Oct 24 2001 - 11:54:56 PDT)
- roar-cp crashed Yuguang Mu (Wed Oct 24 2001 - 14:25:38 PDT)
- how to add Zn Ca parameters Xin Hu (Wed Oct 24 2001 - 16:08:51 PDT)
Re: how to add Zn Ca parameters Bill Ross (Wed Oct 24 2001 - 17:04:58 PDT)
- Re: how to add Zn Ca parameters Eva Darian (Thu Oct 25 2001 - 14:29:50 PDT)
- Need some help with Amber/Linux John Nicholas (Thu Oct 25 2001 - 14:42:52 PDT)
  - Re: Need some help with Amber/Linux David Pearlman (Thu Oct 25 2001 - 18:04:23 PDT)
    - Re: Need some help with Amber/Linux John Nicholas (Fri Oct 26 2001 - 09:19:11 PDT)
NSCM setting to remove center of mass motion Michael G Cooney (Thu Oct 25 2001 - 09:52:09 PDT)
- Re: NSCM setting to remove center of mass motion Sanjeev B.S. (Thu Oct 25 2001 - 20:44:41 PDT)
- unusual parameters pascal bonnet (Fri Oct 26 2001 - 01:06:26 PDT)
Maxwell-Boltzmann distribution of velocities Marcela Madrid (Thu Oct 25 2001 - 12:23:08 PDT)
- Re: Maxwell-Boltzmann distribution of velocities Andreas Svrcek-Seiler (Fri Oct 26 2001 - 03:46:36 PDT)
- Xleap, PDB file format Sophia Kondratova (Fri Oct 26 2001 - 08:00:26 PDT)
  - Re: Xleap, PDB file format Jarrod Smith (Fri Oct 26 2001 - 08:12:49 PDT)
  - Re: Xleap, PDB file format David Case (Fri Oct 26 2001 - 08:59:14 PDT)
  - Re: Xleap, PDB file format Bill Ross (Fri Oct 26 2001 - 09:31:16 PDT)
  - MAX_RSTACK Dr David R V Buckley (Fri Oct 26 2001 - 10:44:02 PDT)
  - RESP charges! PRADIPTA Bandyopadhyay (Fri Oct 26 2001 - 13:24:45 PDT)
belly with GB term Tomoshi Kameda (Thu Oct 25 2001 - 12:54:22 PDT)
Re: (no subject) Bill Ross (Fri Oct 26 2001 - 15:51:36 PDT)
help for restrained minimization xin.hu_at_ndsu.nodak.edu (Fri Oct 26 2001 - 21:10:19 PDT)
- Re: help for restrained minimization Stephane (Mon Oct 29 2001 - 00:39:21 PST)
- Re: help for restrained minimization Bill Ross (Mon Oct 29 2001 - 01:32:16 PST)
- Interface and Sander_classic Sophia Kondratova (Tue Oct 30 2001 - 05:06:03 PST)
  - Re: Interface and Sander_classic David Pearlman (Tue Oct 30 2001 - 10:34:31 PST)
  - IMPORTANT Amber mail list announcement jim caldwell (Tue Oct 30 2001 - 11:44:48 PST)
  - Re: Interface and Sander_classic David Pearlman (Tue Oct 30 2001 - 12:13:42 PST)
- NFFT Hungie Hungie (Tue Oct 30 2001 - 06:43:48 PST)
  - Re: NFFT darden (Tue Oct 30 2001 - 10:03:22 PST)
- How to turn off PME? Hungie Hungie (Tue Oct 30 2001 - 07:49:45 PST)
Err in equilibration run A.Madhumalar (Sun Oct 28 2001 - 02:02:55 PST)
Re: NFFT Michael Crowley (Tue Oct 30 2001 - 08:24:38 PST)
what should change in the parameter? backy_at_ibms.sinica.edu.tw (Wed Oct 31 2001 - 01:52:10 PST)
NPT to NVE ensemble Hungie Hungie (Wed Oct 31 2001 - 05:31:20 PST)
charges for non-standard AAs Uwe Richter (Wed Oct 31 2001 - 05:46:15 PST)
sander_classic wentaofu (Wed Oct 31 2001 - 11:57:07 PST)
- Re: sander_classic Carlos Simmerling (Wed Oct 31 2001 - 12:57:43 PST)
- charge fitting Uwe Richter (Thu Nov 01 2001 - 04:36:35 PST)
- query Monica (Thu Nov 01 2001 - 06:14:02 PST)
- restraint Xin Hu (Thu Nov 01 2001 - 14:48:29 PST)
Re: restraint Bill Ross (Thu Nov 01 2001 - 15:04:13 PST)
equilibration Amesh Patel (Thu Nov 01 2001 - 21:09:57 PST)
New product creates custom e-mail lists! paopao1188_at_hotmail.com (Fri Nov 02 2001 - 07:10:35 PST)
query (fwd) Monica (Fri Nov 02 2001 - 20:56:30 PST)
help seema namboori (Sat Nov 03 2001 - 09:05:40 PST)
help seema namboori (Sat Nov 03 2001 - 09:06:29 PST)
- Re: help Elsa de Sousa Henriques (Mon Nov 05 2001 - 09:42:39 PST)
- MD in vacuo Lepsa (Mon Nov 05 2001 - 10:52:08 PST)
  - Re: MD in vacuo Carlos Simmerling (Mon Nov 05 2001 - 12:27:23 PST)
  - New product creates custom e-mail lists! paopao1188_at_hotmail.com (Tue Nov 06 2001 - 04:18:24 PST)
  - Parameters for DMSO solvent Salinthip Thipayang (Tue Nov 06 2001 - 10:26:48 PST)
  - Gaussian 98 to RESP Sophia Kondratova (Tue Nov 06 2001 - 11:04:59 PST)
  - PARMSCAN Michal Otyepka (Tue Nov 06 2001 - 12:59:42 PST)
  - AMBER Compile Question C. Singer (Tue Nov 06 2001 - 18:07:31 PST)
    - Re: AMBER Compile Question David Case (Tue Nov 06 2001 - 18:22:34 PST)
    - how to pay Koji YOSHIDA (Tue Nov 06 2001 - 19:53:18 PST)
    - Question Irina Tikhonova (Thu Nov 08 2001 - 10:26:11 PST)
E is not constant in NVE Hungie Hungie (Mon Nov 05 2001 - 01:03:10 PST)
Prep.in Tikhonova Irina (Thu Nov 08 2001 - 13:44:49 PST)
Amber 6.0 on Intel IA-64 Server EPD-BLRSJP-PEG (Thu Nov 08 2001 - 19:08:51 PST)
RESP fit: ivary -1 ? nanook1000_at_web.de (Sat Nov 10 2001 - 03:47:39 PST)
Amber 6.0 on Linux Cluster C. Singer (Sat Nov 10 2001 - 09:34:27 PST)
- Re: Amber 6.0 on Linux Cluster Tru (Mon Nov 12 2001 - 02:17:19 PST)
  - Parallel Amber on Solaris 2.6 Thomas A. Spraggins (Mon Jun 03 2002 - 07:49:45 PDT)
    - Re: Parallel Amber on Solaris 2.6 William Gropp (Mon Jun 03 2002 - 12:20:26 PDT)
- how to form ljp-files for PROFEC ? Irina Tikhonova (Tue Nov 13 2001 - 08:23:37 PST)
- AMBER 6 on Linux - help C. Singer (Tue Nov 13 2001 - 09:26:26 PST)
- mm_pbsa on single structure Raik Grunberg (Wed Nov 14 2001 - 06:45:38 PST)
- parameters for 5'-phosphate GUA Linjing Yang (Wed Nov 14 2001 - 12:22:47 PST)
- An Amber question Fabio Schoen (Thu Nov 15 2001 - 00:11:06 PST)
- pyridoxal phosphate parameters Andrea Bernini (Thu Nov 15 2001 - 01:43:33 PST)
- RMS matrix with CARNAL Margit Mollhoff (Fri Nov 16 2001 - 11:09:22 PST)
- What do the exit codes mean? Andrew Hoofnagle (Fri Nov 16 2001 - 15:09:58 PST)
- fatal error during equilibration of solvated system Amesh Patel (Mon Nov 19 2001 - 06:31:39 PST)
- mm_pbsa wentaofu (Mon Nov 19 2001 - 15:32:14 PST)
opinion about buying linux clusters. Margaret Cheung (Sat Nov 10 2001 - 12:00:46 PST)
PME model Jerry wu (Sat Nov 10 2001 - 23:01:40 PST)
GIBBS on Cray Alexander Issanin (Mon Nov 19 2001 - 23:24:31 PST)
DNA force field Marcela Madrid (Tue Nov 20 2001 - 13:57:59 PST)
supercritical water Jerry wu (Tue Nov 20 2001 - 18:28:46 PST)
RMS calculations Nikolai Smolin (Wed Nov 21 2001 - 05:34:54 PST)
- Re: RMS calculations Pascal Bonnet (Wed Nov 21 2001 - 15:16:47 PST)
  - Constraining backbone dihedrals Eva Darian (Wed Nov 28 2001 - 10:14:38 PST)
- solvatebox Jerry wu (Wed Nov 21 2001 - 21:40:24 PST)
Linux 2.2.19 Compil. Amber 4.1 with gcc 2.95.4 Fabrice YERLY (Wed Nov 21 2001 - 08:18:59 PST)
- Re: Linux 2.2.19 Compil. Amber 4.1 with gcc 2.95.4 jim caldwell (Wed Nov 21 2001 - 09:02:48 PST)
Re: Gaussian to Amber David Case (Wed Nov 21 2001 - 10:39:43 PST)
- Re: Gaussian to Amber jim caldwell (Wed Nov 21 2001 - 11:47:05 PST)
  - Re: Gaussian to Amber Filip Ryjacek (Thu Nov 22 2001 - 02:03:06 PST)
  - no. of processors decrease Hungie Hungie (Thu Nov 22 2001 - 05:25:10 PST)
  - Amber & F90 Pricl Sabrina (Fri Nov 23 2001 - 05:22:20 PST)
    - Re: Amber & F90 Tru (Mon Nov 26 2001 - 03:28:22 PST)
    - parallel gibbs Sophia Kondratova (Mon Nov 26 2001 - 06:02:59 PST)
    - re: parallel gibbs Sophia Kondratova (Mon Nov 26 2001 - 11:54:00 PST)
    - TIP4P L. Renee Olano (Mon Nov 26 2001 - 06:59:53 PST)
  - Methane in water box FEP Sophia Kondratova (Fri Nov 23 2001 - 11:33:25 PST)
  - C8-methyl-guanine Sue Heavner (Sun Nov 25 2001 - 09:58:51 PST)
    - O6-methyl-guanine parameters Mahadevan Seetharaman (Mon Nov 26 2001 - 14:50:50 PST)
    - plotting MD results for DNA Jake Isaacs (Tue Nov 27 2001 - 09:56:00 PST)
    - RE: plotting MD results for DNA Guanglei Cui (Tue Nov 27 2001 - 10:11:09 PST)
    - (no subject) hathaimard pongkasem (Tue Nov 27 2001 - 17:40:33 PST)
    - benchmarks Giulio Rastelli (Wed Nov 28 2001 - 07:41:33 PST)
    - Not able to do parallel run St�phane (Fri Nov 30 2001 - 07:36:37 PST)
    - MPI version of Gibbs ramon kleber da rocha (Mon Dec 03 2001 - 09:18:04 PST)
    - running Sander in 4 CPUs Rozita Dara (Mon Dec 03 2001 - 09:31:17 PST)
    - the molecule rotates during the MD run Soonmin Jang (Tue Dec 04 2001 - 00:46:42 PST)
    - Informations Paolo Daniele (Wed Dec 05 2001 - 07:54:24 PST)
    - Problems with analin Irina Tikhonova (Wed Dec 05 2001 - 10:50:43 PST)
    - Amber6 on AMD Athlon Peter Varnai (Thu Dec 06 2001 - 06:06:47 PST)
    - MD of DNA Marcela Madrid (Thu Dec 06 2001 - 12:38:04 PST)
    - Re: MD of DNA Michael G Cooney (Thu Dec 06 2001 - 13:05:14 PST)
    - General install questions Paul A Wilson (Wed Nov 28 2001 - 09:48:06 PST)
    - protonate database Jerry Greenberg (Wed Nov 28 2001 - 10:08:19 PST)
Re: (fwd) amber mail account (Thu Dec 20 2001 - 12:36:43 PST)
Re: Cl and H-bonding (fwd) amber mail account (Thu Dec 20 2001 - 12:36:58 PST)
Re: how to create a bond (fwd) amber mail account (Thu Dec 20 2001 - 12:37:11 PST)
linux? Shixiang Yan (Thu Jan 03 2002 - 18:17:46 PST)
- Re: linux? Carlos Simmerling (Fri Jan 04 2002 - 05:55:15 PST)
- pairlist limit Laila Abou Zeid (Fri Jan 04 2002 - 06:32:57 PST)
  - Re: pairlist limit Guanglei Cui (Fri Jan 04 2002 - 20:56:39 PST)
  - MPI (parallel) version of GIBBS Etienne ENGLER (Mon Jan 07 2002 - 04:13:45 PST)
- xleap sara nunez (Fri Jan 04 2002 - 15:28:14 PST)
Re: Not able to do parallel run (again) St�phane Teletch�a (Mon Jan 07 2002 - 09:08:17 PST)
- Re: Not able to do parallel run (again) St�phane Teletch�a (Tue Jan 08 2002 - 08:21:07 PST)
- questions about resp X. Tan (Tue Jan 08 2002 - 08:31:55 PST)
  - Re: questions about resp X. Tan (Tue Mar 12 2002 - 13:02:22 PST)
- Amber on Tru64 Sebastian Jayaraj (Tue Jan 08 2002 - 11:22:43 PST)
  - Re: Amber on Tru64 jim caldwell (Tue Jan 08 2002 - 11:51:06 PST)
average position of water Hungie Hungie (Tue Jan 08 2002 - 04:28:00 PST)
- Re: average position of water Elsa de Sousa Henriques (Tue Jan 08 2002 - 14:15:44 PST)
- adiabatic map franck chevalier (Wed Jan 09 2002 - 04:41:57 PST)
- SCEE parameter Sophia Kondratova (Wed Jan 09 2002 - 08:49:36 PST)
- removing rotational motion in MD Michael G Cooney (Wed Jan 09 2002 - 09:41:26 PST)
  - Re: removing rotational motion in MD St�phane Teletch�a (Wed Jan 09 2002 - 10:04:30 PST)
    - Re: removing rotational motion in MD Sanjeev B.S. (Wed Jan 09 2002 - 10:54:55 PST)
    - Re: removing rotational motion in MD St�phane Teletch�a (Thu Jan 10 2002 - 00:35:54 PST)
    - (no subject) amutha ramaswamy (Thu Jan 10 2002 - 02:11:15 PST)
    - inquiry regarding AMBER xz27 (Thu Jan 10 2002 - 13:24:08 PST)
    - Re: inquiry regarding AMBER David Case (Thu Jan 10 2002 - 14:51:54 PST)
    - seperate_solute_output Mirjam Lerch (Fri Jan 11 2002 - 01:02:31 PST)
    - Amber 6 on IA64 Karen Haskell (Wed Jan 09 2002 - 13:35:02 PST)
- question: velocity units Martina Roeselova (Wed Jan 09 2002 - 09:46:00 PST)
  - Re: question: velocity units Pascal Bonnet (Wed Jan 09 2002 - 09:57:58 PST)
Re: Re:ERROR TERMINATION DUE TO SHAKE OR TORCON sxzheng (Fri Jan 11 2002 - 19:21:30 PST)
multiple improper torsion terms Thijs Beuming (Fri Jan 11 2002 - 19:37:58 PST)
pukering of DNA bases? A.Madhumalar (Sat Jan 12 2002 - 21:03:50 PST)
ptraj cannot use compressed files? Michael G Cooney (Mon Jan 14 2002 - 08:17:03 PST)
ptraj and compressed files Michael G Cooney (Mon Jan 14 2002 - 08:48:40 PST)
(no subject) Sophia Kondratova (Mon Jan 14 2002 - 10:28:01 PST)
- Re: your mail jim caldwell (Mon Jan 14 2002 - 11:01:44 PST)
- how to neutralise the system? X. Tan (Mon Jan 14 2002 - 11:18:14 PST)
  - Re: how to neutralise the system? David Case (Mon Jan 14 2002 - 11:35:00 PST)
  - resizing and recompiling sander UMEMOTO kimiko (Mon Jan 14 2002 - 17:12:02 PST)
  - temperature control Jerry wu (Mon Jan 14 2002 - 19:55:16 PST)
    - Re: temperature control Michael G Cooney (Tue Feb 05 2002 - 11:15:58 PST)
    - quasih Sue Heavner (Wed Feb 06 2002 - 07:16:25 PST)
    - Re: quasih CUI, Guanglei (Wed Feb 06 2002 - 07:53:55 PST)
    - ImagingAtom eric ARNOULT (Wed Feb 06 2002 - 08:07:04 PST)
    - Re: ImagingAtom Bill Ross (Thu Feb 07 2002 - 02:41:57 PST)
    - compile AMBER on cygwin? quch quch (Thu Feb 07 2002 - 11:46:43 PST)
    - frcmod file format Sophia Kondratova (Mon Feb 11 2002 - 10:16:23 PST)
    - Re: frcmod file format CUI, Guanglei (Mon Feb 11 2002 - 10:38:37 PST)
    - Re: frcmod file format Lepsa (Mon Feb 11 2002 - 23:05:54 PST)
    - parm94.dat file x357l (Tue Feb 12 2002 - 10:21:44 PST)
    - Lipid simulation, DMPC Samantha (Wed Feb 13 2002 - 08:24:20 PST)
    - Linking to its own image Miguel Angel Rodriguez Carvajal (Thu Feb 14 2002 - 06:15:52 PST)
    - RESP Crash Mike Keller (Thu Feb 14 2002 - 07:24:51 PST)
    - IFTRES option in sander and gibbs Alexander Issanin (Tue Feb 12 2002 - 13:09:52 PST)
    - belly input Prabal Maiti (Tue Feb 12 2002 - 14:26:21 PST)
  - azobenzene parameters Uwe Richter (Tue Jan 15 2002 - 02:18:03 PST)
  - minimising WATBOX216 sara nunez (Tue Jan 15 2002 - 11:11:04 PST)
    - Re: minimising WATBOX216 Michael G Cooney (Tue Jan 15 2002 - 13:38:58 PST)
    - I can not see text in xleap ! S. Jang (Tue Jan 15 2002 - 22:56:04 PST)
    - Amber 6.0 purchasing!! hathaimard pongkasem (Wed Jan 16 2002 - 00:14:48 PST)
    - Amber 6.0 purchasing!! hathaimard pongkasem (Wed Jan 16 2002 - 00:15:03 PST)
    - sander (Amber5) vs sander_classic (Amber6) Uwe Richter (Wed Jan 16 2002 - 03:33:32 PST)
    - unsuscribe Ivan Be� (Wed Jan 16 2002 - 07:25:38 PST)
    - Open position: Postdoctoral Scientist Joachim Reichelt (Wed Jan 16 2002 - 07:57:07 PST)
    - Parameters Marta Murcia (Wed Jan 16 2002 - 07:59:26 PST)
    - Stretching Constants Daniel Flint (Thu Jan 17 2002 - 03:21:52 PST)
    - Maxwell Boltzmann Distribution St�phane Teletch�a (Thu Jan 17 2002 - 06:48:02 PST)
    - Amino acid unit "NHE" problem ? S. Jang (Thu Jan 17 2002 - 04:27:19 PST)
    - Re: Amino acid unit "NHE" problem ? Michael Jakusch (Thu Jan 17 2002 - 06:32:28 PST)
    - Re: Amino acid unit "NHE" problem ? Raik Grunberg (Thu Jan 17 2002 - 07:23:30 PST)
    - Re: Amino acid unit "NHE" problem ? David Case (Thu Jan 17 2002 - 08:37:55 PST)
    - NAD parameters Andy Purkiss (Thu Jan 17 2002 - 11:42:21 PST)
    - nmode memory requirements Michael Jakusch (Fri Jan 18 2002 - 08:15:52 PST)
    - Re: nmode memory requirements David Case (Fri Jan 18 2002 - 09:50:29 PST)
    - Amber6 + IBM SP3 Sanjeev B.S. (Sat Jan 19 2002 - 06:59:58 PST)
    - Latest parm + getting parm98 as default in LEaP Sanjeev B.S. (Sun Jan 20 2002 - 22:43:42 PST)
    - Re: Latest parm + getting parm98 as default in LEaP Andreas Svrcek-Seiler (Mon Jan 21 2002 - 02:01:49 PST)
    - Re: Latest parm + getting parm98 as default in LEaP Lepsa (Mon Jan 21 2002 - 22:39:59 PST)
    - Re: Latest parm + getting parm98 as default in LEaP David Case (Tue Jan 22 2002 - 08:14:55 PST)
    - timescale of deoxyribose ring repuckering Jake Isaacs (Tue Jan 22 2002 - 08:43:40 PST)
    - nmode vectors Thijs Beuming (Mon Jan 21 2002 - 04:24:48 PST)
    - triNAG parameters?4 Andrea Bernini (Mon Jan 21 2002 - 07:13:26 PST)
    - Re: triNAG parameters?4 Michael Ford (Tue Jan 22 2002 - 09:19:21 PST)
    - "flags" in .lib files Sue Heavner (Wed Jan 23 2002 - 08:22:08 PST)
    - Re: "flags" in .lib files Bill Ross (Wed Jan 23 2002 - 11:39:45 PST)
    - Re:Latest parm + getting parm98 as default in LEaP Bill Ross (Mon Jan 21 2002 - 23:07:39 PST)
DOCK Peter Gannett (Thu Jan 24 2002 - 06:48:52 PST)
MP_Lite St�phane Teletch�a (Thu Jan 24 2002 - 09:44:40 PST)
torsional fit Fabrizio Giordanetto (Fri Jan 25 2002 - 02:34:55 PST)
group input in ANAL Elizabeth K. White (Fri Jan 25 2002 - 14:11:13 PST)
- Re: group input in ANAL Mite51 (Sat Jan 26 2002 - 13:09:46 PST)
- xleap and PDB file Prabal Maiti (Mon Jan 28 2002 - 23:28:23 PST)
- restart md simulation Uwe Richter (Tue Jan 29 2002 - 01:35:50 PST)
  - Re: restart md simulation Michael G Cooney (Tue Jan 29 2002 - 08:44:03 PST)
  - B-factor Michal Otyepka (Thu Jan 31 2002 - 02:45:50 PST)
  - LIMIN Faliure/Energies per residue for B-DNA etc. Prabal Maiti (Thu Jan 31 2002 - 11:49:00 PST)
    - Re: LIMIN Faliure/Energies per residue for B-DNA etc. darden (Thu Jan 31 2002 - 13:11:19 PST)
    - question regarding ntwv. Margaret Cheung (Thu Jan 31 2002 - 17:55:58 PST)
    - Re: question regarding ntwv. David Case (Thu Jan 31 2002 - 22:43:51 PST)
- box_size Susanna Monti (Tue Jan 29 2002 - 02:34:22 PST)
  - Re: box_size darden (Tue Jan 29 2002 - 07:38:55 PST)
  - Re: box_size jim caldwell (Tue Jan 29 2002 - 07:56:23 PST)
  - MacOS X David Bevan (Tue Jan 29 2002 - 08:15:12 PST)
help on parameters. X. Tan (Mon Feb 04 2002 - 17:40:52 PST)
Re: problem in running MM-PBSA script David Case (Thu Feb 14 2002 - 08:42:52 PST)
residual dipolar coupling restraints Jake Isaacs (Thu Feb 14 2002 - 11:37:42 PST)
memory problem on gibbs X. Tan (Thu Feb 14 2002 - 16:24:55 PST)
flying monomers... Margaret Cheung (Fri Feb 15 2002 - 15:58:39 PST)
MPICH/LAM on sparc Sanjeev B.S. (Sat Feb 16 2002 - 04:23:26 PST)
Power Point slides Krishna Bisetty (Sun Feb 17 2002 - 23:11:22 PST)
.OFF file format Dr Jan Rosenzweig (Mon Feb 18 2002 - 10:14:27 PST)
- Re: .OFF file format Bill Ross (Mon Feb 18 2002 - 12:26:16 PST)
- Gibbs Question Bernd Wellenzohn (Mon Feb 18 2002 - 12:47:15 PST)
- removing rotational motion John Finke (Tue Feb 19 2002 - 01:44:08 PST)
  - Re: removing rotational motion Andreas Svrcek-Seiler (Tue Feb 19 2002 - 04:27:18 PST)
  - Re: removing rotational motion Raik Grunberg (Tue Feb 19 2002 - 04:30:00 PST)
    - Re: removing rotational motion St�phane Teletch�a (Tue Feb 19 2002 - 05:15:10 PST)
    - restrt problem Sanjeev B.S. (Tue Feb 19 2002 - 05:50:41 PST)
    - Xleap x357l (Tue Feb 19 2002 - 08:03:11 PST)
    - The link is out St�phane Teletch�a (Tue Feb 19 2002 - 08:58:44 PST)
    - Re: The link is out Carlos Simmerling (Tue Feb 19 2002 - 12:53:45 PST)
    - ERROR from RESNBA X. Tan (Tue Feb 19 2002 - 17:39:21 PST)
    - AMBER logo citation FyD (Tue Feb 19 2002 - 23:53:18 PST)
    - Re: AMBER logo citation Lepsa (Wed Feb 20 2002 - 01:02:15 PST)
    - Re: AMBER logo citation Pascal Bonnet (Wed Feb 20 2002 - 00:17:39 PST)
    - Re: AMBER logo citation David Case (Wed Feb 20 2002 - 09:11:41 PST)
    - Re: The link is out David Case (Wed Feb 20 2002 - 09:20:00 PST)
  - Re: removing rotational motion Raik Grunberg (Tue Feb 19 2002 - 04:30:00 PST)
  - Re: removing rotational motion Jianxin Guo (Fri Feb 22 2002 - 14:32:48 PST)
  - anal input Prabal Maiti (Fri Feb 22 2002 - 16:31:58 PST)
rms and watershell (in ptraj) dkon_at_email.arizona.edu (Wed Feb 20 2002 - 16:54:58 PST)
MPI sander Uwe Richter (Thu Feb 21 2002 - 05:13:52 PST)
vlimit exceed Prabal Maiti (Thu Feb 21 2002 - 19:23:39 PST)
- Re: vlimit exceed Yuguang Mu (Thu Feb 21 2002 - 23:44:53 PST)
- MD with simulated annealing Giulio Rastelli (Fri Feb 22 2002 - 10:39:56 PST)
- Re: vlimit exceed David Case (Sat Feb 23 2002 - 22:03:24 PST)
- recursively calling sander? Jeff Ames (Mon Feb 25 2002 - 08:32:54 PST)
  - Re: recursively calling sander? David Pearlman (Mon Feb 25 2002 - 19:10:22 PST)
  - (no subject) deepak rangaswamy (Tue Feb 26 2002 - 03:28:18 PST)
  - leap:segmentation fault Sanjeev B.S. (Tue Feb 26 2002 - 08:30:45 PST)
  - xleap and carbohydrates and stuff Amesh Patel (Wed Feb 27 2002 - 06:43:23 PST)
  - (no subject) Ian Bates (Wed Feb 27 2002 - 13:23:17 PST)
  - visualizaion program for NMODE! Pradipta Bandyopadhyay (Wed Feb 27 2002 - 14:48:30 PST)
    - Re: visualizaion program for NMODE! Yuguang Mu (Thu Feb 28 2002 - 00:56:44 PST)
  - correlated motions in a protein! Pradipta Bandyopadhyay (Wed Feb 27 2002 - 15:52:55 PST)
- redius of B-DNA duplex Hungie Hungie (Mon Feb 25 2002 - 08:49:26 PST)
  - Re: redius of B-DNA duplex A.Madhumalar (Mon Feb 25 2002 - 09:41:42 PST)
  - Carnal coordinate averaging Michael G Cooney (Mon Feb 25 2002 - 14:01:26 PST)
    - Re: Carnal coordinate averaging Bill Ross (Mon Feb 25 2002 - 14:44:17 PST)
Re: Cholesterol PREP file St�phane Teletch�a (Thu Feb 28 2002 - 01:48:16 PST)
Persistence length Bernd Wellenzohn (Thu Feb 28 2002 - 07:39:11 PST)
AMBER 99 John Finke (Thu Feb 28 2002 - 16:22:55 PST)
- Re: AMBER 99 Felipe Pineda (Fri Mar 01 2002 - 00:25:27 PST)
(no subject) deepak rangaswamy (Fri Mar 01 2002 - 03:00:51 PST)
Release of Amber, version 7 (fwd) amber mail account (Sun Mar 03 2002 - 15:13:26 PST)
- Re: Release of Amber, version 7 (fwd) SPEROLEEM_at_aol.com (Tue Mar 05 2002 - 14:16:27 PST)
- a question about .in files Vlad Cojocaru (Wed Mar 06 2002 - 07:00:02 PST)
  - Re: a question about .in files Bill Ross (Wed Mar 06 2002 - 11:16:53 PST)
- leap calculation Itziar Maestre Asenjo (Wed Mar 06 2002 - 09:43:44 PST)
- bug in .../sander/egb.f ? Thomas A. Spraggins (Thu Jun 20 2002 - 10:45:28 PDT)
  - Re: bug in .../sander/egb.f ? Sanjeev B.S. (Mon Jul 08 2002 - 12:08:09 PDT)
- RESP Multiconformer Fitting Miguel de Federico (Thu Jun 20 2002 - 16:05:11 PDT)
- van der Waals explosion Arvid Soederhaell (Fri Jun 21 2002 - 01:54:05 PDT)
  - Re: van der Waals explosion David A. Case (Fri Jun 21 2002 - 07:55:26 PDT)
    - taupt: time constant for heat bath coupling for the SOLUTE Qing Zhang (Fri Jun 21 2002 - 16:44:55 PDT)
    - Re: taupt: time constant for heat bath coupling for the SOLUTE David A. Case (Fri Jun 21 2002 - 17:28:38 PDT)
    - SHAKE... Arvid Soederhaell (Mon Jun 24 2002 - 04:25:05 PDT)
  - Compilation ov Amber 7 Dov Barak (Fri Jun 21 2002 - 09:40:58 PDT)
    - Re: Compilation ov Amber 7 Sanjeev B.S. (Sun Jun 30 2002 - 10:42:28 PDT)
- more van der Waals explosion Arvid Soederhaell (Fri Jun 21 2002 - 02:00:59 PDT)
- even more van der Waals explosion Arvid Soederhaell (Fri Jun 21 2002 - 02:23:17 PDT)
- j3 coupling Yuguang Mu (Fri Jun 21 2002 - 03:38:31 PDT)
  - Re: j3 coupling David A. Case (Fri Jun 21 2002 - 07:49:40 PDT)
- Re: amber-request.cgl.ucsf.edu Mihaly Mezei (Mon Jul 29 2002 - 11:42:22 PDT)
concentrated system Jerry wu (Mon Mar 04 2002 - 00:36:21 PST)
carnal and union Pascal Bonnet (Mon Mar 04 2002 - 01:00:20 PST)
carnal and union: solution Pascal Bonnet (Mon Mar 04 2002 - 04:33:17 PST)
Re: leap calculation (loadamberprep) Bill Ross (Wed Mar 06 2002 - 11:22:33 PST)
Are the programs sander and gibbs in Amber 7 parallel? ramon kleber da rocha (Wed Mar 06 2002 - 11:28:01 PST)
converting some files Vlad Cojocaru (Thu Mar 07 2002 - 03:00:00 PST)
- Re: converting some files Lepsa (Fri Dec 07 2001 - 03:36:22 PST)
- amber6 in SGI Origin 2000 Marcela Madrid (Fri Dec 07 2001 - 13:15:56 PST)
- about ion-amino group non-bonded distance thenmalar rathinavelan (Fri Dec 07 2001 - 21:30:00 PST)
- secondary structure Nikolai Smolin (Mon Dec 10 2001 - 10:20:34 PST)
- NRUN in AMBER 6 Jithesh P.V. (Mon Dec 10 2001 - 22:27:07 PST)
  - Re: NRUN in AMBER 6 Raik Grunberg (Tue Dec 11 2001 - 02:53:00 PST)
  - software to build molecules Marcela Madrid (Tue Dec 11 2001 - 08:17:30 PST)
    - RE: software to build molecules DeLano, Warren (Tue Dec 11 2001 - 09:02:44 PST)
    - Re: software to build molecules Andreas Svrcek-Seiler (Tue Dec 11 2001 - 10:44:58 PST)
    - Amber for SP asit_at_frontierdomain.com (Tue Dec 11 2001 - 19:54:48 PST)
    - (no subject) Thijs Beuming (Wed Dec 12 2001 - 05:39:57 PST)
    - program req ponmalai kolandaivel (Wed Dec 12 2001 - 05:52:08 PST)
    - Help with new residue Penny Govender (Thu Dec 13 2001 - 23:15:33 PST)
    - Re: Help with new residue Pascal Bonnet (Fri Dec 14 2001 - 01:18:56 PST)
    - problem in Leap Walker, Jerrylaine (Fri Dec 14 2001 - 06:51:03 PST)
    - quasih dkon_at_email.arizona.edu (Sun Dec 16 2001 - 17:50:44 PST)
    - nmode analysis Ms. Parul Kalra (Sun Dec 16 2001 - 22:30:11 PST)
    - (no subject) Wenguang Zhu (Mon Dec 17 2001 - 20:13:32 PST)
    - leap compile on alpha linux Wenguang Zhu (Mon Dec 17 2001 - 20:17:09 PST)
    - floating overflow in alpha Redhat 7.1 Wenguang Zhu (Tue Dec 18 2001 - 01:16:25 PST)
    - idsx0 parameter Sophia Kondratova (Tue Dec 18 2001 - 10:23:15 PST)
    - quasih again dkon_at_email.arizona.edu (Tue Dec 18 2001 - 11:30:05 PST)
    - sander_classic NPAIRS limit Andrea Bernini (Fri Dec 14 2001 - 01:12:56 PST)
  - problem processing stripped RST/CRD files Michael G Cooney (Tue Dec 11 2001 - 08:25:20 PST)
- (no subject) Fumihito Mohri (Mon Dec 10 2001 - 22:34:09 PST)
  - (no subject) Elsa de Sousa Henriques (Tue Dec 11 2001 - 10:34:24 PST)
dG of wild type/mutant FyD (Thu Mar 07 2002 - 03:26:31 PST)
- Re: dG of wild type/mutant Lepsa (Wed Dec 19 2001 - 06:43:25 PST)
- Cl and H-bonding M ESTA Laurent (Wed Dec 19 2001 - 09:42:48 PST)
- xleap for windows 98? Marcela Madrid (Wed Dec 19 2001 - 17:14:47 PST)
- File format convert yu kaneko (Thu Dec 20 2001 - 04:19:01 PST)
  - Re: File format convert Andreas Svrcek-Seiler (Thu Dec 20 2001 - 04:58:53 PST)
  - C-terminal amide Romina Oliva (Thu Dec 20 2001 - 09:40:36 PST)
  - TOPOLOGY FILE PROCESSING Carles Ferrer (Thu Dec 20 2001 - 10:01:04 PST)
  - how to create a bond Marcela Madrid (Thu Dec 20 2001 - 11:15:36 PST)
  - list filter jim caldwell (Thu Dec 20 2001 - 12:12:43 PST)
    - Re: list filter Thomas Huber (Thu Dec 20 2001 - 13:42:19 PST)
    - Nitro group Lorenzo Gontrani (Fri Dec 21 2001 - 01:47:48 PST)
statistical analysis of MD trajectories Jake Isaacs (Thu Mar 07 2002 - 09:24:03 PST)
parameter estimation Vlad Cojocaru (Thu Mar 07 2002 - 10:32:25 PST)
- Fw: parameter estimation Lepsa (Fri Mar 08 2002 - 01:52:50 PST)
- new units Vlad Cojocaru (Fri Mar 08 2002 - 06:35:46 PST)
  - rdparm error message Rukman Hertadi (Sun Mar 10 2002 - 00:46:53 PST)
  - Europium force field parms Peter Gannett (Sun Mar 10 2002 - 12:07:44 PST)
  - Re Europium force field parms Fabrice Yerly (Sun Mar 10 2002 - 23:32:59 PST)
    - scaleCharges Vojta Klusak (Mon Mar 11 2002 - 01:45:54 PST)
    - Re: scaleCharges David Case (Mon Mar 11 2002 - 09:37:51 PST)
    - limit of written files with ptraj Carles Ferrer (Mon Mar 11 2002 - 12:54:16 PST)
    - combining trajectory file Rukman Hertadi (Tue Mar 12 2002 - 01:48:49 PST)
    - Re: combining trajectory file Natasja Brooijmans (Tue Mar 12 2002 - 08:00:38 PST)
    - Re: combining trajectory file CUI, Guanglei (Tue Mar 12 2002 - 08:24:44 PST)
    - Re: combining trajectory file Thomas Cheatham (Tue Mar 12 2002 - 10:30:51 PST)
    - Re Europium force field parms Marc Baaden (Mon Mar 11 2002 - 03:52:40 PST)
choosing a forcefield nepenthes_at_vplaces.net (Thu Mar 07 2002 - 19:51:25 PST)
high electrostatic energy thenmalar rathinavelan (Thu Mar 07 2002 - 21:13:40 PST)
question on Gibbs calculation X. Tan (Tue Mar 12 2002 - 13:50:24 PST)
help please :) Richard Kho (Fri Mar 15 2002 - 16:59:23 PST)
Post-doctoral position Wolfe, Jennifer (Mon Mar 18 2002 - 08:33:11 PST)
Dual AMD motherboards jim caldwell (Mon Mar 18 2002 - 15:47:12 PST)
- RE: Dual AMD motherboards Demchuk, Eugene (Mon Mar 18 2002 - 16:52:55 PST)
  - RE: Dual AMD motherboards jim caldwell (Mon Mar 18 2002 - 18:04:24 PST)
  - Dual AMD ASUS A7M266-D Solved jim caldwell (Mon Mar 18 2002 - 18:37:19 PST)
- RE: Dual AMD motherboards Contractor-SIMTECH (Fri Jul 12 2002 - 08:33:54 PDT)
  - Re: Dual AMD motherboards Pietro Amodeo (Mon Jul 15 2002 - 01:36:34 PDT)
    - RE: Dual AMD motherboards Ross Walker (Tue Jul 16 2002 - 00:31:56 PDT)
    - Problem with LEAP Miguel de Federico (Tue Jul 16 2002 - 03:53:37 PDT)
    - Re: Problem with LEAP David A. Case (Tue Jul 16 2002 - 08:19:24 PDT)
    - antechamber created prep file--Problem in xleap Sarangan Ravichandran (Tue Jul 16 2002 - 06:54:45 PDT)
    - antechamber created prep file--Problem in xleap--additional info Sarangan Ravichandran (Tue Jul 16 2002 - 07:06:31 PDT)
    - Minimization in GB-SA-E-Spikes, LINMIN Sarangan Ravichandran (Tue Jul 16 2002 - 08:02:58 PDT)
    - Re: Minimization in GB-SA-E-Spikes, LINMIN Andreas Svrcek-Seiler (Tue Jul 16 2002 - 09:00:55 PDT)
    - Re: Minimization in GB-SA-E-Spikes, LINMIN Sarangan Ravichandran (Tue Jul 16 2002 - 10:11:27 PDT)
    - PME in gibbs module X. Tan (Tue Jul 16 2002 - 13:29:27 PDT)
    - water molecules diffuse during equilibration Qing Zhang (Tue Jul 16 2002 - 16:56:53 PDT)
    - Re: water molecules diffuse during equilibration David A. Case (Tue Jul 16 2002 - 18:31:12 PDT)
    - PTRAJ: radial distribution function A. Hungie (Wed Jul 17 2002 - 08:58:14 PDT)
    - Re: PTRAJ: radial distribution function Thomas Cheatham (Wed Jul 17 2002 - 14:47:24 PDT)
    - building general solvent boxes with leap Xavier Deupi (Wed Jul 17 2002 - 10:19:28 PDT)
    - Re: building general solvent boxes with leap David A. Case (Wed Jul 17 2002 - 13:14:40 PDT)
    - Re: building general solvent boxes with leap Xavier Deupi (Thu Jul 18 2002 - 16:16:17 PDT)
    - Re: The 216 water box Mihaly Mezei (Thu Jul 18 2002 - 15:48:12 PDT)
    - prmtop file question. Carlos Andres Ramirez-Mondragon (Wed Jul 17 2002 - 14:15:59 PDT)
    - Re: prmtop file question. David A. Case (Wed Jul 17 2002 - 17:08:28 PDT)
    - Re: building general solvent boxes with leap Bill Ross (Thu Jul 18 2002 - 12:18:57 PDT)
    - Defining Restraints in Sander Asif Rahaman (Thu Jul 18 2002 - 13:21:59 PDT)
    - Re: Defining Restraints in Sander Carlos Simmerling (Thu Jul 18 2002 - 14:29:22 PDT)
    - Re: Defining Restraints in Sander John Bushnell (Thu Jul 18 2002 - 17:44:16 PDT)
    - Re: building general solvent boxes with leap Elsa de Sousa Henriques (Thu Jul 18 2002 - 20:41:25 PDT)
    - about solvateOct Nikolai Smolin (Fri Jul 19 2002 - 01:22:20 PDT)
    - correction about solvateOct Nikolai Smolin (Fri Jul 19 2002 - 02:09:58 PDT)
    - Re: correction about solvateOct Michael Jakusch (Fri Jul 19 2002 - 02:49:48 PDT)
    - Re: correction about solvateOct Michael Crowley (Fri Jul 19 2002 - 09:37:10 PDT)
    - Questions about xleap and mm_pbsa] Salinthip Thipayang (Fri Jul 19 2002 - 10:49:08 PDT)
    - Re: Questions about xleap and mm_pbsa] David A. Case (Fri Jul 19 2002 - 11:59:24 PDT)
    - Questions about xleap and mm_pbsa(cont.) Salinthip Thipayang (Tue Jul 23 2002 - 07:46:20 PDT)
    - Re: Questions about xleap and mm_pbsa(cont.) David A. Case (Tue Jul 23 2002 - 10:18:44 PDT)
    - Questions about xleap and mm_pbsa (cont.2) Salinthip Thipayang (Tue Jul 23 2002 - 08:21:23 PDT)
    - problem compiling roar (mop7mm) on alpha hagop demirdjian (Tue Jul 23 2002 - 08:35:11 PDT)
    - Re: problem compiling roar (mop7mm) on alpha Tru (Tue Jul 23 2002 - 10:05:08 PDT)
    - Re: problem compiling roar (mop7mm) on alpha Chuck Schneider (Tue Jul 23 2002 - 10:09:37 PDT)
    - CA-OS parameter Bimo Ario Tejo (Tue Jul 23 2002 - 09:07:19 PDT)
    - "crd" file created with VMD Soonmin Jang (Tue Jul 23 2002 - 09:23:56 PDT)
    - AMBER7 and Movie Y Fang (Fri Jul 19 2002 - 14:03:22 PDT)
    - water box size eric hu (Fri Jul 19 2002 - 15:09:25 PDT)
    - Re: water box size Shixiang Yan (Fri Jul 19 2002 - 16:02:32 PDT)
    - Including explicit waters in GB dynamics Kristina Furse (Sat Jul 20 2002 - 17:30:43 PDT)
    - Re: water box size eric hu (Thu Jul 25 2002 - 12:21:24 PDT)
    - New Promotion Products at American Disc Corporation Service (Thu Jul 25 2002 - 12:56:47 PDT)
    - Water molecule numbering Masaki Tomimoto (Thu Jul 25 2002 - 15:28:25 PDT)
    - Re: Water molecule numbering Shixiang Yan (Thu Jul 25 2002 - 16:25:08 PDT)
    - RE: Water molecule numbering Masaki Tomimoto (Thu Jul 25 2002 - 17:04:01 PDT)
    - RE: Water molecule numbering Shixiang Yan (Thu Jul 25 2002 - 19:28:02 PDT)
    - RE: Water molecule numbering Masaki Tomimoto (Thu Jul 25 2002 - 17:32:19 PDT)
    - RE: AMBER7 and Movie Snyder, James (Fri Jul 19 2002 - 15:25:37 PDT)
    - Re: AMBER7 and Movie Pascal Bonnet (Mon Jul 22 2002 - 01:36:50 PDT)
    - Re: AMBER7 and Movie Carlos Simmerling (Mon Jul 22 2002 - 09:56:52 PDT)
    - Re: AMBER7 and Movie Y Fang (Mon Jul 22 2002 - 13:58:23 PDT)
    - Summary: make_crd_hp, mm_pbsa Jianhui Wu (Mon Jul 22 2002 - 14:45:32 PDT)
    - (no subject) deepak rangaswamy (Tue Jul 23 2002 - 00:01:41 PDT)
    - (no subject) Carlos Simmerling (Tue Jul 23 2002 - 04:48:48 PDT)
    - C sp2 connected to OS Bimo Ario Tejo (Mon Jul 22 2002 - 10:37:27 PDT)
    - Re: C sp2 connected to OS Bimo Ario Tejo (Tue Jul 23 2002 - 01:23:03 PDT)
    - problem with make_crd_hg, mm_pbsa Jianhui Wu (Mon Jul 22 2002 - 11:28:29 PDT)
    - electrostatics truncation in AMBER Therese Malliavin (Fri Jul 19 2002 - 06:21:59 PDT)
    - Re: electrostatics truncation in AMBER David A. Case (Fri Jul 19 2002 - 08:26:20 PDT)
    - RE: correction about solvateOct William Wei (Fri Jul 19 2002 - 08:18:53 PDT)
    - Re: Minimization in GB-SA-E-Spikes, LINMIN David A. Case (Wed Jul 17 2002 - 17:43:57 PDT)
    - GENERALIZED BORN model on a protein with Fe Mahadevan Seetharaman (Thu Jul 18 2002 - 07:55:01 PDT)
    - Re: GENERALIZED BORN model on a protein with Fe David A. Case (Thu Jul 18 2002 - 10:41:53 PDT)
  - Decrease the solvated system by removing the outside crystal water Ling Zhang (Mon Jul 15 2002 - 09:58:34 PDT)
Re: polarizabilities Lepsa (Tue Mar 26 2002 - 01:12:09 PST)
- Polarizabilities, charge scaling and ions Michal Otyepka (Wed Mar 27 2002 - 01:42:29 PST)
- s-matrix format and ftnmr Shixiang Yan (Wed Mar 27 2002 - 13:49:50 PST)
- What is the atoms limit for Amber 7? William Wei (Wed Mar 27 2002 - 14:19:34 PST)
  - Re: What is the atoms limit for Amber 7? David Case (Wed Mar 27 2002 - 15:45:44 PST)
  - sulfate and sulfamate parameters jeff dyason (Wed Mar 27 2002 - 20:28:55 PST)
  - AMBER 5 Monica (Wed Mar 27 2002 - 20:29:12 PST)
  - change topology Michal Otyepka (Thu Mar 28 2002 - 00:44:38 PST)
    - Re: change topology Bill Ross (Thu Mar 28 2002 - 01:45:49 PST)
    - Magnesium as a DNA counterion in AMBER 6.0 Mike Keller (Thu Mar 28 2002 - 07:31:29 PST)
    - Amber6, GB (Memory, MATOM, nmr.h)/Folding (mutation) IAF (Thu Mar 28 2002 - 09:56:04 PST)
    - Re: Amber6, GB (Memory, MATOM, nmr.h)/Folding (mutation) David Case (Thu Mar 28 2002 - 10:40:16 PST)
    - a little bit confused with leap-frog algorithm... Margaret Cheung (Thu Mar 28 2002 - 13:08:40 PST)
    - Re: a little bit confused with leap-frog algorithm... David Case (Thu Mar 28 2002 - 17:52:38 PST)
    - Re: a little bit confused with leap-frog algorithm... Margaret Cheung (Sat Mar 30 2002 - 19:35:36 PST)
    - compiling error. Margaret Cheung (Sat Mar 30 2002 - 23:26:53 PST)
    - Re: compiling error. Carlos Simmerling (Sun Mar 31 2002 - 07:24:19 PST)
    - Re: compiling error. Margaret Cheung (Sun Mar 31 2002 - 20:44:07 PST)
    - Re: compiling error. Bill Ross (Sun Mar 31 2002 - 23:30:24 PST)
    - does PME function without charge neutralization? Ian R Bates (Tue Apr 02 2002 - 10:30:41 PST)
    - Re: does PME function without charge neutralization? darden (Tue Apr 02 2002 - 14:23:02 PST)
    - (no subject) deepak rangaswamy (Tue Apr 02 2002 - 20:52:55 PST)
    - input files Monica (Wed Apr 03 2002 - 05:00:42 PST)
    - Re: input files Carlos Simmerling (Wed Apr 03 2002 - 05:40:30 PST)
    - Initial Amber 7 benchmark timings David Case (Wed Apr 03 2002 - 18:33:14 PST)
    - Re: Initial Amber 7 benchmark timings St�phane Teletch�a (Thu Apr 04 2002 - 01:36:23 PST)
    - amber7, PME and anisotrop press. Arvid Soederhaell (Thu Apr 04 2002 - 01:46:58 PST)
    - new residues Vlad Cojocaru (Thu Apr 04 2002 - 05:03:37 PST)
    - About the sander_classic calculation Alan Leo (Thu Apr 04 2002 - 13:32:34 PST)
    - Re: About the sander_classic calculation John Bushnell (Thu Apr 04 2002 - 14:31:11 PST)
    - convergence of MD simulations Sue Heavner (Thu Apr 04 2002 - 14:24:05 PST)
    - Re: convergence of MD simulations Andreas Svrcek-Seiler (Fri Apr 05 2002 - 02:12:11 PST)
    - Sander-Gibbs Kidley N J (Mon Apr 08 2002 - 08:34:49 PDT)
    - PDB file with CONECT record Prabal Maiti (Mon Apr 08 2002 - 12:06:21 PDT)
    - Re:PDB file with CONECT record Bill Ross (Mon Apr 08 2002 - 13:02:21 PDT)
    - Re: PDB file with CONECT record Bill Ross (Tue Apr 09 2002 - 23:09:36 PDT)
    - Re: PDB file with CONECT record Prabal Maiti (Thu Apr 11 2002 - 23:27:15 PDT)
    - Re: PDB file with CONECT record Bill Ross (Fri Apr 12 2002 - 00:27:37 PDT)
    - Re: PDB file with CONECT record Miguel Angel (Fri Apr 12 2002 - 03:03:09 PDT)
    - order parameters? Arvid Soederhaell (Fri Apr 12 2002 - 05:55:33 PDT)
    - Re: PDB file with CONECT record Prabal Maiti (Mon Apr 15 2002 - 22:48:00 PDT)
    - compiling amber 6.0 in a Sun starfire ENT10000 ramon kleber da rocha (Tue Apr 16 2002 - 12:08:54 PDT)
    - 4 Medicinal and Computational Chemistry Candidates medicinal and Compuatational Chemistry Resumes and Jobs (Tue Apr 16 2002 - 14:55:48 PDT)
    - Recalculating energies John Finke (Tue Apr 16 2002 - 17:45:23 PDT)
    - Re: Recalculating energies Carlos Simmerling (Wed Apr 17 2002 - 04:39:27 PDT)
    - RESP charges Vlad Cojocaru (Wed Apr 17 2002 - 03:53:27 PDT)
    - Re: RESP charges Lepsa (Wed Apr 17 2002 - 05:26:27 PDT)
    - (no subject) Filip Ryjacek (Wed Apr 17 2002 - 09:01:48 PDT)
    - (no subject) Lepsa (Wed Apr 17 2002 - 07:38:47 PDT)
    - Minimization of pentane holding a plane of carbon atoms Hungie Hungie (Wed Apr 17 2002 - 10:32:28 PDT)
    - again...Minimization of pentane holding a plane of carbon atoms Hungie Hungie (Wed Apr 17 2002 - 11:03:23 PDT)
    - mm pbsa: generate snapshots Mark Hsieh (Wed Apr 17 2002 - 14:52:41 PDT)
    - Re: mm pbsa: generate snapshots Mathy Froeyen (Thu Apr 18 2002 - 00:19:35 PDT)
    - pentane minimization Hungie Hungie (Thu Apr 18 2002 - 02:15:33 PDT)
    - pentane minimization Hungie Hungie (Thu Apr 18 2002 - 02:16:46 PDT)
    - DNA shifts during MD; C.O.M. removing and ptraj doesn't help... Filip Ryjacek (Thu Apr 18 2002 - 08:17:12 PDT)
    - RESP cfrenz_at_aecom.yu.edu (Thu Apr 18 2002 - 08:55:55 PDT)
    - pentane minimization...again Hungie Hungie (Thu Apr 18 2002 - 09:30:15 PDT)
    - MPICH and AMBER 7 Mark Hsieh (Thu Apr 18 2002 - 16:12:58 PDT)
    - RESP-ivary Vlad Cojocaru (Fri Apr 19 2002 - 04:26:22 PDT)
    - Re: RESP-ivary Qing Zhang (Fri Apr 19 2002 - 09:15:27 PDT)
    - RE: RESP-ivary John Bushnell (Fri Apr 19 2002 - 11:16:40 PDT)
    - amber7 compilation on a beowulf cluster Peter Gannett (Fri Apr 19 2002 - 12:59:56 PDT)
    - RE: amber7 compilation on a beowulf cluster John Bushnell (Fri Apr 19 2002 - 14:48:00 PDT)
    - RE: amber7 compilation on a beowulf cluster Bill Ross (Fri Apr 19 2002 - 15:26:19 PDT)
    - mm_pbsa for uhbd Mark Hsieh (Fri Apr 19 2002 - 18:56:18 PDT)
    - Re: amber7 compilation on a beowulf cluster David Case (Fri Apr 19 2002 - 18:56:50 PDT)
    - (no subject) deepak rangaswamy (Fri Apr 19 2002 - 22:22:54 PDT)
    - Re: your mail David Case (Sat Apr 20 2002 - 09:06:32 PDT)
    - Re: your mail deepak rangaswamy (Tue Apr 30 2002 - 05:06:06 PDT)
    - valine to alanine example Sophia Kondratova (Tue Apr 30 2002 - 08:23:21 PDT)
    - heterochirical peptides ? Yuguang Mu (Tue Apr 30 2002 - 08:43:39 PDT)
    - Re: heterochirical peptides ? David Case (Tue Apr 30 2002 - 11:21:38 PDT)
    - dummy atoms. Yongjun Jiang (Sat Apr 20 2002 - 20:20:44 PDT)
    - leap bugfix Bill Ross (Sun Apr 21 2002 - 14:55:34 PDT)
    - RESP Vlad Cojocaru (Mon Apr 22 2002 - 03:17:17 PDT)
    - Re: RESP jim caldwell (Mon Apr 22 2002 - 08:04:25 PDT)
    - a problem Vlad Cojocaru (Mon Apr 22 2002 - 08:56:48 PDT)
    - RE: a problem John Bushnell (Wed Apr 24 2002 - 14:02:31 PDT)
    - (no subject) SPEROLEEM_at_aol.com (Mon Apr 22 2002 - 11:47:28 PDT)
    - a more general question Vlad Cojocaru (Tue Apr 23 2002 - 07:20:34 PDT)
    - DME and Carnal with AMBER6 Katherine W. Abold (Tue Apr 23 2002 - 07:48:04 PDT)
    - RESP tutorial Michael G Cooney (Tue Apr 23 2002 - 10:15:51 PDT)
    - Re: RESP tutorial David Case (Tue Apr 23 2002 - 17:41:49 PDT)
    - RESP on Deoxy-ADE Qing Zhang (Tue Apr 23 2002 - 18:34:23 PDT)
    - RESP on Deoxy-ADE Qing Zhang (Tue Apr 23 2002 - 18:34:23 PDT)
    - sander & prmtop file generated from antechamber input ? jeff dyason (Tue Apr 23 2002 - 20:33:58 PDT)
    - Re: sander & prmtop file generated from antechamber input ? David Case (Wed Apr 24 2002 - 08:59:14 PDT)
    - Re: sander & prmtop file generated from antechamber input ? sychen (Sun Apr 06 2003 - 09:12:44 PDT)
    - Re: sander & prmtop file generated from antechamber input ? David A. Case (Sun Apr 06 2003 - 22:28:58 PDT)
    - INTPRT and PMF Sophia Kondratova (Tue Apr 23 2002 - 11:23:36 PDT)
    - Re: INTPRT and PMF David Pearlman (Tue Apr 23 2002 - 13:05:12 PDT)
    - generating left-handed A-DNA Marcela Madrid (Tue Apr 23 2002 - 17:41:08 PDT)
    - Re: generating left-handed A-DNA David Case (Wed Apr 24 2002 - 09:09:07 PDT)
    - (no subject) Bill Ross (Tue Apr 23 2002 - 12:30:58 PDT)
    - parallel sander? Mark Hsieh (Tue Apr 23 2002 - 12:31:55 PDT)
    - RE: parallel sander? Mark Hsieh (Tue Apr 23 2002 - 12:35:44 PDT)
    - amber6 with parallel Khatcharin Siriwong (Mon Apr 22 2002 - 05:48:24 PDT)
    - Re: amber7 compilation on a beowulf cluster Peter Gannett (Sat Apr 20 2002 - 05:14:01 PDT)
    - To PROFEC users Salinthip Thipayang (Fri Apr 19 2002 - 07:13:11 PDT)
    - RESP charges Vlad Cojocaru (Wed Apr 17 2002 - 05:36:43 PDT)
    - RE: RESP charges Ross Walker (Wed Apr 17 2002 - 06:21:37 PDT)
    - Re: RESP charges jim caldwell (Wed Apr 17 2002 - 07:22:04 PDT)
    - Thanks FyD (Fri Apr 12 2002 - 00:04:53 PDT)
    - Amber7 and VMD Soonmin Jang (Wed Apr 10 2002 - 01:40:37 PDT)
    - Re: Amber7 and VMD Thomas Cheatham (Wed Apr 10 2002 - 06:55:46 PDT)
    - (no subject) Mark Hsieh (Wed Apr 10 2002 - 13:31:50 PDT)
    - (no subject) Carlos Simmerling (Sat Apr 13 2002 - 05:06:29 PDT)
    - Matching Patterns Tali (Wed Apr 10 2002 - 14:57:59 PDT)
    - DNA structure get distorted Monica (Thu Apr 11 2002 - 01:00:48 PDT)
    - Re: DNA structure get distorted David Case (Fri Apr 12 2002 - 09:27:10 PDT)
    - Compiling Amber7 on a Beowulf Cluster - Compiling Error Peter Gannett (Fri Apr 12 2002 - 16:59:38 PDT)
    - Re: Compiling Amber7 on a Beowulf Cluster - Compiling Error David Case (Fri Apr 12 2002 - 17:37:01 PDT)
    - Passing arguments with SP2 LoadLeveler Thomas A. Spraggins (Mon Jun 24 2002 - 07:41:26 PDT)
    - New Residue Monica (Mon Jun 24 2002 - 08:01:42 PDT)
    - ptraj problem Vlad Cojocaru (Mon Jun 24 2002 - 08:54:32 PDT)
    - Re: ptraj problem Thomas Cheatham (Mon Jun 24 2002 - 10:24:30 PDT)
    - help ..problem about antechamber Yi ming Cheng (Fri Apr 12 2002 - 22:30:26 PDT)
    - Re: Compiling Amber7 on a Beowulf Cluster - Compiling Error Peter Gannett (Sat Apr 13 2002 - 06:59:29 PDT)
    - Vulgar Models Do Everything And Love It!!! telesales (Mon Apr 15 2002 - 17:03:45 PDT)
    - noesy intensity input in DNA Monica (Thu Apr 11 2002 - 01:03:50 PDT)
    - Follow distances during MD Francois Dupradeau (Thu Apr 11 2002 - 03:19:02 PDT)
    - Re: Follow distances during MD Raik Grunberg (Thu Apr 11 2002 - 05:49:16 PDT)
    - (no subject) Mark Beardsell (Thu Apr 11 2002 - 06:36:29 PDT)
    - Re: your mail Andreas Svrcek-Seiler (Thu Apr 11 2002 - 07:33:22 PDT)
    - Save from LEaP to a PDBQ file ? jeff dyason (Thu Apr 11 2002 - 20:50:32 PDT)
    - Re: Save from LEaP to a PDBQ file ? Bill Ross (Thu Apr 11 2002 - 23:16:28 PDT)
    - Re: convergence of MD simulations darden (Mon Apr 08 2002 - 13:08:10 PDT)
    - PDB file with CONECT record (fwd) Prabal Maiti (Tue Apr 09 2002 - 18:04:50 PDT)
    - Re: PDB file with CONECT record (fwd) David Case (Tue Apr 09 2002 - 20:30:38 PDT)
    - Roar 2.1 with Amber7 Soonmin Jang (Tue Apr 09 2002 - 20:39:07 PDT)
    - RE: Roar 2.1 with Amber7 Ross Walker (Tue Apr 09 2002 - 22:48:43 PDT)
    - convergence of MD simulations Sue Heavner (Sat Mar 30 2002 - 15:02:16 PST)
    - Problem with atom type rhertadi_at_bio.titech.ac.jp (Thu Mar 28 2002 - 13:55:33 PST)
    - Re: Problem with atom type Bill Ross (Thu Mar 28 2002 - 16:14:16 PST)
Hydrogen bond energy using Anal A.Madhumalar (Tue Mar 26 2002 - 02:23:34 PST)
One question about how to use the amber Zhe SUN (Tue Mar 26 2002 - 04:49:35 PST)
secondary structure Ian R Bates (Tue Mar 26 2002 - 11:49:48 PST)
problems using Link John Finke (Tue Mar 26 2002 - 12:39:59 PST)
GB model and belly dkon_at_email.arizona.edu (Tue Mar 26 2002 - 13:46:40 PST)
- Re: GB model and belly David Case (Tue Mar 26 2002 - 15:07:33 PST)
More GB/Belly dkon_at_email.arizona.edu (Tue Mar 26 2002 - 14:00:23 PST)
Re: Help! Sander run error: Bus error David Case (Mon Apr 15 2002 - 22:32:16 PDT)
Amber in a distributed environment Peter Gannett (Wed Apr 17 2002 - 05:07:56 PDT)
- Re: Amber in a distributed environment Sudhakar Pamidighantam (Wed Apr 17 2002 - 06:55:34 PDT)
Re: amber7 and tip5p David Case (Wed Apr 24 2002 - 14:04:05 PDT)
Number of WATBOX yuann (Wed Apr 24 2002 - 22:54:02 PDT)
- Re: Number of WATBOX David Smith (Thu Apr 25 2002 - 06:25:40 PDT)
- PMF calculations Sophia Kondratova (Thu Apr 25 2002 - 06:30:11 PDT)
  - Re: PMF calculations David Smith (Thu Apr 25 2002 - 08:13:23 PDT)
    - Re: PMF calculations David Pearlman (Thu Apr 25 2002 - 11:36:41 PDT)
    - sander mpich hangs Mark Hsieh (Thu Apr 25 2002 - 15:01:26 PDT)
    - Re: sander mpich hangs St�phane Teletch�a (Fri Apr 26 2002 - 04:54:01 PDT)
    - RE: sander mpich hangs Mark Hsieh (Fri Apr 26 2002 - 12:08:48 PDT)
    - max_rstack requested Albert Codony (Sun Apr 28 2002 - 15:39:58 PDT)
    - parmjoin Vlad Cojocaru (Mon Apr 29 2002 - 09:53:01 PDT)
    - Re: parmjoin David Case (Mon Apr 29 2002 - 11:26:26 PDT)
    - Fail message:Segmantation fault and Bus error? William Wei (Mon Apr 29 2002 - 12:38:48 PDT)
    - NTT=5? Jung-Hsing Lin (Mon Apr 29 2002 - 16:10:30 PDT)
    - Re: NTT=5? David Case (Mon Apr 29 2002 - 22:32:20 PDT)
    - Re: NTT=5? Jung-Hsing Lin (Tue Apr 30 2002 - 09:10:46 PDT)
    - Re: NTT=5? David Case (Tue Apr 30 2002 - 11:16:04 PDT)
    - Re: NTT=5? Jung-Hsing Lin (Tue Apr 30 2002 - 13:36:45 PDT)
    - Re: NTT=5? Jake Isaacs (Wed May 01 2002 - 12:47:09 PDT)
    - Carnal BUG?? William Wei (Wed May 01 2002 - 20:19:03 PDT)
    - about ew_legal.h X. Tan (Tue Apr 30 2002 - 17:12:01 PDT)
    - IFBOX=0 error in amber7 Eva Darian (Tue Apr 30 2002 - 21:43:31 PDT)
    - Re: IFBOX=0 error in amber7 Bill Ross (Tue Apr 30 2002 - 22:15:05 PDT)
    - AMBER 7 - more problems with leap Mark Beardsell (Wed May 01 2002 - 05:17:46 PDT)
    - Re: about ew_legal.h David Case (Wed May 01 2002 - 09:10:36 PDT)
    - Amber7 nmode Sue Heavner (Wed May 01 2002 - 10:23:19 PDT)
    - Re: Amber7 nmode David Case (Wed May 01 2002 - 10:55:07 PDT)
    - Amber7 compilation on IBM sp3 machine Soonmin Jang (Tue Apr 30 2002 - 21:33:05 PDT)
    - install leap not working nepenthes_at_vplaces.net (Tue Apr 30 2002 - 00:52:07 PDT)
    - Re: install leap not working Bill Ross (Tue Apr 30 2002 - 12:21:01 PDT)
    - NaCl concentration Peter Gannett (Tue Apr 30 2002 - 12:34:38 PDT)
    - How to run the leap module param_at_ibab.ac.in (Tue Apr 30 2002 - 02:34:32 PDT)
    - Re: How to run the leap module Sanjeev B.S. (Tue Apr 30 2002 - 03:37:11 PDT)
    - Re: How to run the leap module John Bushnell (Tue Apr 30 2002 - 10:46:35 PDT)
    - TIP4P parameters Ge Zhou (Mon Apr 29 2002 - 19:03:54 PDT)
    - Re: TIP4P parameters David Case (Mon Apr 29 2002 - 22:17:49 PDT)
    - Problems with AMBER7 and Multiple Processors on SGI servers Vincent BOSQUIER (Fri Apr 26 2002 - 01:39:35 PDT)
    - Re: Problems with AMBER7 and Multiple Processors on SGI servers Carlos Simmerling (Fri Apr 26 2002 - 05:05:52 PDT)
    - Re: Problems with AMBER7 and Multiple Processors on SGI servers Ian bates (Fri Apr 26 2002 - 08:17:52 PDT)
    - RE: Problems with AMBER7 and Multiple Processors on SGI servers Vincent BOSQUIER (Tue Apr 30 2002 - 02:59:11 PDT)
    - Re: Problems with AMBER7 and Multiple Processors on SGI servers David Case (Tue Apr 30 2002 - 09:02:30 PDT)
    - RE: Problems with AMBER7 and Multiple Processors on SGI servers Vincent BOSQUIER (Thu May 02 2002 - 01:55:45 PDT)
  - About Group in Carnal William Wei (Thu Apr 25 2002 - 08:50:08 PDT)
  - Re: PMF calculations David Pearlman (Thu Apr 25 2002 - 11:30:24 PDT)
RE: Carnal BUG?? --- How can I get the correct residue number? William Wei (Thu May 02 2002 - 09:09:21 PDT)
- RE: Carnal BUG?? --- How can I get the correct residue number? William Wei (Thu May 02 2002 - 10:48:10 PDT)
Compilation on RedHat-7.2 with MPICH Vincent BOSQUIER (Thu May 02 2002 - 09:29:32 PDT)
new RNA residues Vlad Cojocaru (Thu May 02 2002 - 12:07:32 PDT)
Re: How can I get the correct residue number? Bill Ross (Thu May 02 2002 - 13:26:45 PDT)
Re: How can I get the correct residue number? Bill Ross (Thu May 02 2002 - 13:38:24 PDT)
Help/suggestions needed with PROFEC Salinthip Thipayang (Fri May 03 2002 - 07:40:41 PDT)
help/suggestions needed with PROFEC Salinthip Thipayang (Fri May 03 2002 - 08:03:47 PDT)
TI integration Joe Fernandez (Sat May 04 2002 - 06:59:57 PDT)
Thanks to all Albert Codony (Sat May 04 2002 - 08:38:12 PDT)
crdgrow Vlad Cojocaru (Sat May 04 2002 - 13:06:32 PDT)
missing residues Mark Hsieh (Sun May 05 2002 - 00:15:31 PDT)
topology file generation Sanjeev B.S. (Sun May 05 2002 - 22:36:36 PDT)
- Re: topology file generation Andreas Svrcek-Seiler (Mon May 06 2002 - 05:11:54 PDT)
  - Re: topology file generation Sanjeev B.S. (Mon May 06 2002 - 05:24:30 PDT)
- Re: topology file generation Carlos Simmerling (Mon May 06 2002 - 05:27:06 PDT)
- (no subject) Sophia Kondratova (Mon May 06 2002 - 06:13:53 PDT)
- TI using sander on cluster Joe Fernandez (Mon May 06 2002 - 07:52:50 PDT)
- "Unit 5 Error" with a Linux/MPICH Amber7 Vincent BOSQUIER (Mon May 06 2002 - 08:50:07 PDT)
  - Re: "Unit 5 Error" with a Linux/MPICH Amber7 David Case (Mon May 06 2002 - 09:18:24 PDT)
  - Re: "Unit 5 Error" with a Linux/MPICH Amber7 St�phane Teletch�a (Mon May 06 2002 - 09:22:42 PDT)
  - RE: "Unit 5 Error" with a Linux/MPICH Amber7 Vincent BOSQUIER (Mon May 06 2002 - 09:44:09 PDT)
Problems with parallel computing in Amber7 Vincent BOSQUIER (Tue May 14 2002 - 07:28:10 PDT)
NMR refinement Jake Isaacs (Tue May 14 2002 - 12:16:37 PDT)
- Re: NMR refinement David Case (Wed May 15 2002 - 10:09:27 PDT)
- Re: NMR refinement A. Hungie (Thu May 16 2002 - 08:02:17 PDT)
Topology file format in AMBER 7 Joffre Heredia (Tue May 14 2002 - 14:14:55 PDT)
- Re: Topology file format in AMBER 7 David Case (Tue May 14 2002 - 14:33:15 PDT)
- question Masamichi Fujinami 4029 (Tue May 14 2002 - 22:49:03 PDT)
- Energy problem during dynamics with amber 7 Florence CASSET (Wed May 15 2002 - 02:48:23 PDT)
  - Re: Energy problem during dynamics with amber 7 David Case (Wed May 15 2002 - 10:29:55 PDT)
  - Sander, Setup for Parallel SMP Linux Cluster Jianhui Wu (Wed May 15 2002 - 12:02:27 PDT)
    - Re: Sander, Setup for Parallel SMP Linux Cluster Tru (Wed May 15 2002 - 12:40:45 PDT)
    - Re: Sander, Setup for Parallel SMP Linux Cluster Joffre Heredia (Thu May 16 2002 - 11:01:16 PDT)
    - Mutations - Molecular Dynamics William Wei (Thu May 16 2002 - 16:11:36 PDT)
    - RE: Mutations - Molecular Dynamics William Wei (Mon May 27 2002 - 08:21:04 PDT)
    - igb=2,gbsa=1,antechamber,bad atom type Jianhui Wu (Fri May 17 2002 - 12:20:14 PDT)
RE: automated rescoring of ligands Vickie Tsui (Tue May 14 2002 - 14:23:29 PDT)
Re: help: nmode compile question!!! Andreas Svrcek-Seiler (Wed May 15 2002 - 04:30:12 PDT)
Re: About the box info read error Bill Ross (Fri May 17 2002 - 13:33:51 PDT)
Re: Anal in AMBER7 David Case (Sun May 19 2002 - 18:44:38 PDT)
- Re: Anal in AMBER7 Ting Wang (Tue May 21 2002 - 05:48:48 PDT)
- (no subject) Sophia Kondratova (Tue May 21 2002 - 11:37:24 PDT)
- ptraj problem Jake Isaacs (Tue May 21 2002 - 14:20:02 PDT)
  - Re: ptraj problem Prabal Maiti (Tue May 21 2002 - 16:51:22 PDT)
  - Re: Junmei et al. 1999 Michal Otyepka (Wed May 22 2002 - 00:57:11 PDT)
    - Re: Junmei et al. 1999 Lepsa (Wed May 22 2002 - 01:58:41 PDT)
    - Re: Junmei et al. 1999 Yuguang Mu (Wed May 22 2002 - 02:30:29 PDT)
    - Re: Junmei et al. 1999 David Case (Wed May 22 2002 - 08:05:23 PDT)
    - antechamber Giulio Rastelli (Wed May 22 2002 - 03:56:25 PDT)
    - Re: antechamber David Case (Wed May 22 2002 - 08:03:50 PDT)
- Re: Anal in AMBER7 Ting Wang (Mon Jul 22 2002 - 02:19:16 PDT)
vanadium Natasja Brooijmans (Sun May 19 2002 - 19:35:27 PDT)
about sander_classic AMBER6.0 Nikolai Smolin (Mon May 20 2002 - 06:08:14 PDT)
helix analysis Prabal Maiti (Mon May 20 2002 - 12:20:45 PDT)
mm_pbsa X. Tan (Mon May 20 2002 - 16:04:52 PDT)
Energy conservation in NVE simulation ? Soonmin Jang (Mon May 20 2002 - 22:42:40 PDT)
Re: Protonate doesn-t recognize my pdb input file St�phane Teletch�a (Wed May 22 2002 - 04:41:08 PDT)
again about sander_classic Amber 6.0 Nikolai Smolin (Wed May 22 2002 - 04:42:50 PDT)
- Re: again about sander_classic Amber 6.0 David Case (Wed May 22 2002 - 08:15:06 PDT)
- still having ptraj problems Jake Isaacs (Wed May 22 2002 - 08:19:06 PDT)
  - Re: still having ptraj problems Jake Isaacs (Wed May 22 2002 - 08:50:11 PDT)
this is a test of the amber reflector. Please ignore. Marcela Marcela Madrid (Wed May 22 2002 - 06:59:24 PDT)
Protonate doesn-t recognize by pdb input file David Case (Wed May 22 2002 - 09:20:20 PDT)
- Re: Protonate doesn-t recognize by pdb input file St�phane Teletch�a (Thu May 23 2002 - 05:23:31 PDT)
- charges Marcela Madrid (Thu May 23 2002 - 13:25:43 PDT)
  - Re: charges David Case (Thu May 23 2002 - 13:54:38 PDT)
  - helix analysis (fwd) Prabal Maiti (Thu May 23 2002 - 14:30:33 PDT)
    - Re: helix analysis (fwd) David Case (Thu May 23 2002 - 14:41:00 PDT)
TIP4P water with AMBER6 Noriaki Okimoto (Wed May 22 2002 - 11:01:35 PDT)
- Re: TIP4P water with AMBER6 jim caldwell (Wed May 22 2002 - 13:25:00 PDT)
- ambpdb in AMBER7 Matthew Lee (Wed May 22 2002 - 13:42:34 PDT)
  - Re: ambpdb in AMBER7 David Case (Wed May 22 2002 - 14:09:32 PDT)
  - this is a test for amber reflector - please ignore Asif Rahaman (Wed May 22 2002 - 15:17:29 PDT)
  - Problem with 2D Gibbs run Asif Rahaman (Wed May 22 2002 - 15:32:49 PDT)
  - This is a test for amber reflector - please ignore Lorenzo Gontrani (Thu May 23 2002 - 01:34:38 PDT)
  - CARNAL Vlad Cojocaru (Thu May 23 2002 - 03:35:29 PDT)
Re: compilation of sander on Alpha/Linux clusters jim caldwell (Fri May 24 2002 - 14:41:00 PDT)
PME & cutoff A. Hungie (Sat May 25 2002 - 06:12:48 PDT)
- Re: PME & cutoff darden (Sun May 26 2002 - 10:03:30 PDT)
- compilation for Hitachi SR8000 A. Hungie (Sun May 26 2002 - 10:25:17 PDT)
- Charge export from Leap is rounded off jeff dyason (Sun May 26 2002 - 17:06:36 PDT)
- Linux Parallel compilation Linux Mpich PGI Fabrice Yerly (Mon May 27 2002 - 05:31:09 PDT)
  - Re: Linux Parallel compilation Linux Mpich PGI Viktor Hornak (Mon May 27 2002 - 07:56:24 PDT)
parallel sander on T3E Peter Gannett (Sat May 25 2002 - 07:46:37 PDT)
- Re: parallel sander on T3E Natasja Brooijmans (Sat May 25 2002 - 08:44:34 PDT)
glucose Yuguang Mu (Tue May 28 2002 - 08:05:10 PDT)
- Re: glucose Carlos Simmerling (Tue May 28 2002 - 08:50:59 PDT)
- RESP charges for phosphorylated residues Uwe Richter (Tue May 28 2002 - 09:05:05 PDT)
- xleap Marcela Madrid (Tue May 28 2002 - 14:21:39 PDT)
- Cyclodextrin Toshikazu Matsuoka (Tue May 28 2002 - 23:48:19 PDT)
- minimization to fix up hydrogen positions yuann (Wed May 29 2002 - 00:33:23 PDT)
- SHAKE troubles Arvid Soederhaell (Wed May 29 2002 - 03:07:17 PDT)
  - Re: SHAKE troubles St�phane Teletch�a (Wed May 29 2002 - 03:50:12 PDT)
  - Re: SHAKE troubles Yong Duan (Wed May 29 2002 - 05:33:14 PDT)
  - MPich error Fabrice Yerly (Wed May 29 2002 - 05:46:29 PDT)
    - Re: MPich error St�phane Teletch�a (Wed May 29 2002 - 07:00:44 PDT)
  - Re: SHAKE troubles Lepsa (Wed May 29 2002 - 07:02:15 PDT)
  - xLeap problem Donald Thomas (Wed May 29 2002 - 21:42:04 PDT)
    - Re: xLeap problem John Bushnell (Wed May 29 2002 - 22:53:05 PDT)
    - sander_classic, erratic on IBM Giovanni Fossati (Wed May 29 2002 - 23:17:07 PDT)
    - Re: sander_classic, erratic on IBM David Case (Thu May 30 2002 - 07:13:44 PDT)
    - Re: sander_classic, erratic on IBM Giovanni Fossati (Thu May 30 2002 - 10:05:22 PDT)
    - (no subject) SPEROLEEM_at_aol.com (Thu May 30 2002 - 15:51:26 PDT)
    - GROUP Specification - Error decoding variable yuann (Thu May 30 2002 - 00:43:02 PDT)
    - Re: GROUP Specification - Error decoding variable Yongjun Jiang (Thu May 30 2002 - 01:23:57 PDT)
    - TIP4P SEKIJIMA Masakazu (Thu May 30 2002 - 01:43:14 PDT)
    - Re: TIP4P SEKIJIMA Masakazu (Fri May 31 2002 - 00:32:08 PDT)
    - Re: TIP4P David Case (Fri May 31 2002 - 07:44:19 PDT)
    - H-bond Dmitry Pavlov (Fri May 31 2002 - 01:01:42 PDT)
    - Intel ifc Compiler Joachim Reichelt (Thu May 30 2002 - 02:23:21 PDT)
    - Re: Intel ifc Compiler Robert Duke (Thu May 30 2002 - 06:13:59 PDT)
    - Comparing simulations using Amber 5 and Amber 6 Rebecca Perlow (Thu May 30 2002 - 07:18:36 PDT)
    - Re: Intel ifc Compiler David Case (Thu May 30 2002 - 07:00:55 PDT)
    - Re: Intel ifc Compiler David Case (Fri May 31 2002 - 07:51:21 PDT)
    - Re: Intel ifc Compiler Joachim Reichelt (Sun Jun 02 2002 - 23:51:54 PDT)
    - (no subject) Ishita sharma (Mon Jun 03 2002 - 04:07:38 PDT)
    - AMBER7 Michael Sattler (Thu May 30 2002 - 05:59:11 PDT)
  - Re: SHAKE troubles Arvid Soederhaell (Fri May 31 2002 - 01:50:01 PDT)
    - Re: SHAKE troubles St�phane Teletch�a (Fri May 31 2002 - 02:45:48 PDT)
    - Re: SHAKE troubles Arvid Soederhaell (Tue Jun 04 2002 - 01:22:40 PDT)
    - Amber PGF77 comilation error + MPICH problem Fabrice Yerly (Wed Jun 05 2002 - 01:31:26 PDT)
    - Parameters for hexachloroethane Bjorn-Olav Brandsdal (Wed Jun 05 2002 - 02:13:54 PDT)
    - Machine_file for Hitachi SR8000 A. Hungie (Wed Jun 05 2002 - 04:09:03 PDT)
    - PME box ? Yi ming Cheng (Wed Jun 05 2002 - 05:11:15 PDT)
    - Re: PME box ? David Smith (Wed Jun 05 2002 - 07:15:44 PDT)
    - Re: PME box ? Long Hai (Wed Jun 05 2002 - 09:07:29 PDT)
    - Amber7, sander, restart, blast up Jianhui Wu (Wed Jun 05 2002 - 10:07:51 PDT)
    - Running amber7 and nab on FreeBSD bdodson_at_scms.utmb.EDU (Wed Jun 05 2002 - 13:31:24 PDT)
    - cap water eric hu (Wed Jun 05 2002 - 17:14:10 PDT)
    - Re: cap water eric hu (Fri Jun 07 2002 - 11:39:22 PDT)
    - reference Marcela Madrid (Wed Jun 05 2002 - 08:48:55 PDT)
    - Question TL Poulos (Wed Jun 05 2002 - 08:49:10 PDT)
Fwd: NPT-MD Antonio J. D�az Quintana (Fri May 31 2002 - 02:17:55 PDT)
- Re: Fwd: NPT-MD David Case (Fri May 31 2002 - 07:56:43 PDT)
- Problem with Gibbs 2D run Asif Rahaman (Sun Jun 02 2002 - 20:29:38 PDT)
Re: mm_pbsa in parallel system David Case (Mon Jun 03 2002 - 07:49:08 PDT)
Re: mm_pbsa in parallel system (fwd) Jianhui Wu (Mon Jun 03 2002 - 09:03:12 PDT)
Clarification R.Sathyapriya (Tue Jun 04 2002 - 00:45:19 PDT)
Suggestion to Bill and Case William Wei (Fri Jun 07 2002 - 13:49:10 PDT)
- Re: Suggestion to Bill and Case Bill Ross (Fri Jun 07 2002 - 13:16:30 PDT)
- model molecules for getting charges of DNA Jiyoung Heo (Sat Jun 08 2002 - 17:20:10 PDT)
  - Re: model molecules for getting charges of DNA Qing Zhang (Sun Jun 09 2002 - 12:47:04 PDT)
  - C=C=C bending parameters Jones de Andrade (Sun Jun 09 2002 - 13:55:33 PDT)
  - cold belly run error eric hu (Sun Jun 09 2002 - 15:55:47 PDT)
    - Re: cold belly run error Asim Okur (Mon Jun 10 2002 - 21:58:30 PDT)
    - Re: cold belly run error eric hu (Tue Jun 11 2002 - 10:41:47 PDT)
    - Re: cold belly run error eric hu (Tue Jun 11 2002 - 12:42:19 PDT)
    - sander input for a newbie Randy M. Wadkins (Tue Jun 11 2002 - 16:21:22 PDT)
    - Re: sander input for a newbie Randy M. Wadkins (Wed Jun 12 2002 - 06:04:55 PDT)
    - Application of Amber Monica (Wed Jun 12 2002 - 08:24:49 PDT)
    - test of mm_pbsa Yongjun Jiang (Tue Jun 11 2002 - 20:08:23 PDT)
    - igb problem in sander Emma.Sigfridsson_at_astrazeneca.com (Wed Jun 12 2002 - 02:11:20 PDT)
    - vlimit exceeded A. Hungie (Wed Jun 12 2002 - 02:49:44 PDT)
    - Re: vlimit exceeded Carlos Simmerling (Wed Jun 12 2002 - 04:42:14 PDT)
    - Re: vlimit exceeded Thomas Cheatham (Wed Jun 12 2002 - 12:35:53 PDT)
    - sander parallel eric hu (Wed Jun 12 2002 - 14:11:24 PDT)
    - Re: sander parallel Joffre Heredia (Thu Jun 13 2002 - 10:39:55 PDT)
    - How to set the dielctric constant equals 1, when running MD simulations in real solvent water? Ling Zhang (Thu Jun 13 2002 - 13:54:53 PDT)
    - The atom number mismatch in coord and topology file. Ling Zhang (Thu Jun 13 2002 - 14:41:08 PDT)
    - Re: The atom number mismatch in coord and topology file. Carlos Simmerling (Thu Jun 13 2002 - 15:27:38 PDT)
    - Using TIP4P water S. Yamasaki (Thu Jun 13 2002 - 18:05:48 PDT)
    - (no subject) Christian.Pilger_at_bc.boehringer-ingelheim.com (Thu Jun 13 2002 - 22:30:15 PDT)
    - Re: sander parallel eric hu (Thu Jun 13 2002 - 15:05:13 PDT)
    - Re: sander parallel St�phane Teletch�a (Fri Jun 14 2002 - 01:58:53 PDT)
    - free energy for binding Qing Zhang (Fri Jun 14 2002 - 15:50:54 PDT)
    - how to keep aromatic ring flat Qing Zhang (Fri Jun 14 2002 - 16:00:51 PDT)
    - Re: how to keep aromatic ring flat Bill Ross (Fri Jun 14 2002 - 16:34:42 PDT)
    - remove COM velocity in Amber7 Peter VARNAI (Mon Jun 17 2002 - 05:16:27 PDT)
    - Re: remove COM velocity in Amber7 Peter VARNAI (Thu Jun 20 2002 - 05:03:07 PDT)
    - WG: Christian.Pilger_at_bc.boehringer-ingelheim.com (Mon Jun 17 2002 - 22:48:01 PDT)
    - question Craig A Bayse (Tue Jun 18 2002 - 15:04:47 PDT)
    - Re: question jim caldwell (Tue Jun 18 2002 - 15:52:19 PDT)
    - propeller twist of ideal B-DNA A. Hungie (Wed Jun 19 2002 - 09:37:29 PDT)
    - solvated time-averaged restraint refinement of DNA Jake Isaacs (Wed Jun 19 2002 - 09:52:35 PDT)
    - parameters for Zn2+ bond to CYS- X. Tan (Wed Jun 19 2002 - 17:23:16 PDT)
    - Amber tutorial rino ragno (Sat Jun 15 2002 - 02:53:53 PDT)
    - Mn parameters!!! navjot_at_bioinfo.ernet.in (Mon Jun 17 2002 - 02:19:12 PDT)
    - (no subject) Christian.Pilger_at_bc.boehringer-ingelheim.com (Mon Jun 17 2002 - 03:09:11 PDT)
    - Periodic water box Rudesh Toofanny (Fri Jun 14 2002 - 05:41:01 PDT)
    - Re: Periodic water box Thomas Cheatham (Wed Jun 19 2002 - 20:57:04 PDT)
    - The atom number mismatch in coord and topology file in AMBER6. Ling Zhang (Fri Jun 14 2002 - 07:58:45 PDT)
    - Re: The atom number mismatch in coord and topology file in AMBER6. Robert Duke (Fri Jun 14 2002 - 09:27:00 PDT)
    - tleap error for systems with 64-bit pointers Karen Haskell (Fri Jun 14 2002 - 12:55:16 PDT)
    - perturbed type DH not found Mao Xiang (Wed Jun 12 2002 - 03:47:19 PDT)
    - Protonated database Andrew Petersen (Tue Jun 11 2002 - 12:12:28 PDT)
  - (no subject) Snyder, James (Sun Jun 09 2002 - 17:45:03 PDT)
RE: xaLeap make fails on AIX Thomas A. Spraggins (Mon Jun 10 2002 - 09:13:01 PDT)
Re:xaLeap make fails on AIX Bill Ross (Mon Jun 10 2002 - 11:19:47 PDT)
entropy calculation X. Tan (Mon Jun 10 2002 - 16:42:59 PDT)
- RE: entropy calculation case (Tue Jun 11 2002 - 06:56:37 PDT)
Re: Floating Invalid Bill Ross (Mon Jun 10 2002 - 22:36:16 PDT)
- Re: Floating Invalid jim caldwell (Tue Jun 11 2002 - 07:43:49 PDT)
Reorder water in amber7 Peter Varnai (Tue Jun 11 2002 - 01:38:32 PDT)
- Re: Reorder water in amber7 Carlos Simmerling (Tue Jun 11 2002 - 04:36:04 PDT)
  - Re: Reorder water in amber7 Peter VARNAI (Tue Jun 11 2002 - 10:16:00 PDT)
- Amber protein-ion problem Emma.Sigfridsson_at_astrazeneca.com (Tue Jun 11 2002 - 04:41:29 PDT)
- RE: Reorder water in amber7 case (Tue Jun 11 2002 - 06:53:59 PDT)
minimization probs Amesh Patel (Tue Jun 11 2002 - 08:57:12 PDT)
- RE: minimization probs case (Tue Jun 11 2002 - 10:36:57 PDT)
RE: Floating Invalid lifang xu (Wed Jun 12 2002 - 20:02:21 PDT)
re: parameters for zn2+ bond to cys- lamon_at_lav.Boehringer-Ingelheim.com (Thu Jun 20 2002 - 06:17:38 PDT)
turning PME off in AMBER7 lamon_at_lav.Boehringer-Ingelheim.com (Thu Jun 20 2002 - 06:28:30 PDT)
- Re: turning PME off in AMBER7 Arvid Soederhaell (Thu Jun 20 2002 - 06:45:25 PDT)
- Re: turning PME off in AMBER7 David A. Case (Thu Jun 20 2002 - 06:49:33 PDT)
Re: SHAKE (actually: new atom types) Bill Ross (Mon Jun 24 2002 - 12:22:02 PDT)
antechamber charges don't sum up to zero Michael Jakusch (Mon Jun 24 2002 - 12:38:15 PDT)
partial charges Osvaldo Santos-Filho (Mon Jun 24 2002 - 17:33:15 PDT)
- Re: partial charges Carlos Simmerling (Mon Jun 24 2002 - 18:38:35 PDT)
- Re: partial charges David A. Case (Mon Jun 24 2002 - 18:52:47 PDT)
- Query regarding Gamess Nitin Kumar Singh (Tue Jun 25 2002 - 08:23:09 PDT)
- plep question FyD (Wed Jun 26 2002 - 00:28:23 PDT)
- minimum image cut-off Nikolai Smolin (Wed Jun 26 2002 - 04:05:08 PDT)
- transferring structures Matt Hartings (Wed Jun 26 2002 - 10:24:23 PDT)
  - Re: transferring structures Bill Ross (Wed Jun 26 2002 - 12:47:02 PDT)
  - Re: transferring structures Matt Hartings (Wed Jun 26 2002 - 13:58:11 PDT)
Using a trucated octahedral box in Amber6 Ling Zhang (Wed Jun 26 2002 - 18:28:46 PDT)
Problem in amber Monica (Wed Jun 26 2002 - 22:28:21 PDT)
- Re: Problem in amber David Case (Thu Jun 27 2002 - 07:38:30 PDT)
xleap problem FyD (Thu Jun 27 2002 - 01:20:53 PDT)
- Re: xleap problem David A. Case (Thu Jun 27 2002 - 08:33:16 PDT)
a problem with AMBER7 Vlad Cojocaru (Thu Jun 27 2002 - 03:12:58 PDT)
dummy torsional parameters Giulio Rastelli (Thu Jun 27 2002 - 03:31:50 PDT)
- Re: dummy torsional parameters David A. Case (Thu Jun 27 2002 - 08:38:49 PDT)
- problems compiling Amber 7 ramon kleber da rocha (Thu Jun 27 2002 - 10:18:50 PDT)
  - Re: problems compiling Amber 7 David A. Case (Thu Jun 27 2002 - 11:27:09 PDT)
  - Re: problems compiling Amber 7 ramon kleber da rocha (Tue Jul 02 2002 - 07:42:05 PDT)
    - problems compiling Amber 7 ramon kleber da rocha (Fri Jul 05 2002 - 10:52:45 PDT)
    - RE: problems compiling Amber 7 Thomas A. Spraggins (Fri Jul 05 2002 - 11:42:32 PDT)
    - anal in AMBER7 gives inconsistent results with itself Prabal Maiti (Fri Jul 05 2002 - 16:00:55 PDT)
    - Re: anal in AMBER7 gives inconsistent results with itself Prabal Maiti (Sun Jul 07 2002 - 22:46:31 PDT)
- mopac David.Rilett_at_astrazeneca.com (Thu Jun 27 2002 - 10:50:41 PDT)
  - Re: mopac David A. Case (Thu Jun 27 2002 - 11:34:34 PDT)
    - Re: mopac Pascal Bonnet (Fri Jun 28 2002 - 01:49:11 PDT)
    - van der Waals, hydrogen bond energy Qing Zhang (Fri Jun 28 2002 - 15:57:10 PDT)
    - Re: van der Waals, hydrogen bond energy Carlos Simmerling (Fri Jun 28 2002 - 16:41:11 PDT)
    - Re: van der Waals, hydrogen bond energy jim caldwell (Fri Jun 28 2002 - 17:24:21 PDT)
    - Re: van der Waals, hydrogen bond energy Andreas Svrcek-Seiler (Sat Jun 29 2002 - 05:29:38 PDT)
    - EWALD BOMB (The system has extended beyond ...) Michael Jakusch (Fri Jun 28 2002 - 02:17:20 PDT)
  - iwrap set in sander of Amber6 Ling Zhang (Thu Jun 27 2002 - 13:43:41 PDT)
Re: Fwd: Re: probelms in install of amber (fwd) Marcelo Roitburd (Thu Jun 27 2002 - 13:59:35 PDT)
- Re: Fwd: Re: probelms in install of amber (fwd) Marcelo Roitburd (Thu Jun 27 2002 - 15:23:29 PDT)
- Re: Fwd: Re: probelms in install of amber (fwd) Marcelo Roitburd (Thu Jun 27 2002 - 15:47:41 PDT)
xmkmf: not found Bill Ross (Thu Jun 27 2002 - 15:29:08 PDT)
box size & 1st equilibrium yuann (Thu Jun 27 2002 - 23:16:51 PDT)
- Re: box size & 1st equilibrium Carlos Simmerling (Fri Jun 28 2002 - 04:56:09 PDT)
installing MPICH for AMBER on Linux CLuster root (Mon Jul 08 2002 - 03:02:52 PDT)
- Re: installing MPICH for AMBER on Linux CLuster Walter Langel (Mon Jul 08 2002 - 05:26:36 PDT)
  - RE: installing MPICH for AMBER on Linux CLuster Thomas A. Spraggins (Mon Jul 08 2002 - 06:15:23 PDT)
    - Re: installing MPICH for AMBER on Linux CLuster update Thomas Steinbrecher (Mon Jul 08 2002 - 06:46:48 PDT)
  - md equilibration in chloroform Sophia Kondratova (Mon Jul 08 2002 - 06:38:27 PDT)
    - Re: md equilibration in chloroform David A. Case (Mon Jul 08 2002 - 08:42:24 PDT)
    - RE: md equilibration in chloroform Thomas.Fox_at_bc.boehringer-ingelheim.com (Thu Jul 11 2002 - 10:51:47 PDT)
    - China International Biology Projects Fair Genefax (Thu Jul 11 2002 - 22:40:19 PDT)
    - looking for frcmod in AMBER Tutorials yuann (Fri Jul 12 2002 - 02:19:45 PDT)
    - Question about error message about "lastist" and "virtual box" Masaki Tomimoto (Fri Jul 12 2002 - 08:19:12 PDT)
    - Re: Question about error message about "lastist" and "virtual box" David A. Case (Fri Jul 12 2002 - 08:55:51 PDT)
Re: amber on sp3 David A. Case (Wed Jul 17 2002 - 12:14:44 PDT)
Format in a trajectory files is suddenly changed Masaki Tomimoto (Mon Jul 22 2002 - 09:54:44 PDT)
Benchmark St�phane Teletch�a (Mon Jul 22 2002 - 09:55:14 PDT)
Re: Questions about xleap ... Bill Ross (Tue Jul 23 2002 - 12:03:52 PDT)
Segmentation fault Bimo Ario Tejo (Tue Jul 23 2002 - 12:44:58 PDT)
- Re: Segmentation fault David A. Case (Tue Jul 23 2002 - 15:44:02 PDT)
- Re: Segmentation fault Bimo Ario Tejo (Wed Jul 24 2002 - 02:42:26 PDT)
- Trajectory files Miguel de Federico (Wed Jul 24 2002 - 05:10:51 PDT)
  - Re: Trajectory files Natasja Brooijmans (Wed Jul 24 2002 - 07:34:28 PDT)
  - Re: Trajectory files David A. Case (Wed Jul 24 2002 - 08:15:55 PDT)
  - Re: Trajectory files Laurent Chiche (Wed Jul 24 2002 - 08:26:36 PDT)
  - CCL4 solvent box Bimo Ario Tejo (Wed Jul 24 2002 - 08:40:10 PDT)
  - Re: Trajectory files Carlos Simmerling (Wed Jul 24 2002 - 08:52:29 PDT)
  - am1-bcc charges, antechamber Sophia Kondratova (Wed Jul 24 2002 - 12:02:02 PDT)
    - Re: am1-bcc charges, antechamber David A. Case (Wed Jul 24 2002 - 12:58:25 PDT)
    - Re: am1-bcc charges, antechamber M. L. Dodson (Wed Jul 24 2002 - 13:24:23 PDT)
    - Re: am1-bcc charges, antechamber Laurent Chiche (Thu Jul 25 2002 - 02:17:58 PDT)
    - Re: am1-bcc charges, antechamber Giulio Rastelli (Thu Jul 25 2002 - 03:53:46 PDT)
    - Re: am1-bcc charges, antechamber M. L. Dodson (Thu Jul 25 2002 - 05:32:05 PDT)
    - creating a solvent box Bimo Ario Tejo (Thu Jul 25 2002 - 05:32:17 PDT)
    - Re: creating a solvent box CUI, Guanglei (Thu Jul 25 2002 - 06:33:01 PDT)
    - Re: creating a solvent box Laurent Chiche (Thu Jul 25 2002 - 07:46:47 PDT)
    - sulfonic group generated with antechamber Michael Jakusch (Thu Jul 25 2002 - 05:23:30 PDT)
    - Purine to Pyrimidine mutation Bernd Wellenzohn (Thu Jul 25 2002 - 05:29:27 PDT)
    - mol2 with antechamber Giulio Rastelli (Fri Jul 26 2002 - 03:57:22 PDT)
    - Re: mol2 with antechamber David A. Case (Fri Jul 26 2002 - 08:54:08 PDT)
    - increase lastist Marcela Madrid (Wed Jul 24 2002 - 13:41:45 PDT)
    - Re: increase lastist David A. Case (Wed Jul 24 2002 - 14:41:48 PDT)
    - Re: increase lastist jim caldwell (Wed Jul 24 2002 - 15:45:43 PDT)
    - Umbrella sampling in AMBER Pratul Agarwal (Wed Jul 24 2002 - 13:53:54 PDT)
    - Re: Umbrella sampling in AMBER David A. Case (Wed Jul 24 2002 - 14:44:35 PDT)
  - SS bond Masaki Tomimoto (Wed Jul 24 2002 - 12:04:21 PDT)
    - Re: SS bond David A. Case (Wed Jul 24 2002 - 13:00:44 PDT)
  - makeDIP_RST.dna McAteer, Kathleen (Wed Jul 24 2002 - 12:24:42 PDT)
    - Re: makeDIP_RST.dna Vickie Tsui (Wed Jul 24 2002 - 16:49:57 PDT)
    - Gibbs tutorial problem yuann (Wed Jul 24 2002 - 17:40:50 PDT)
    - Re: Gibbs tutorial problem David A. Case (Thu Jul 25 2002 - 12:03:17 PDT)
    - (no subject) deepak rangaswamy (Wed Jul 24 2002 - 20:57:14 PDT)
    - Re: trajectory problem? David Case (Wed Jul 24 2002 - 22:22:57 PDT)
    - Pressure probs in MD suvendu lomash (Thu Jul 25 2002 - 00:49:28 PDT)
    - Re: Pressure probs in MD jim caldwell (Thu Jul 25 2002 - 08:55:57 PDT)
    - "amber mail" jim caldwell (Thu Jul 25 2002 - 09:11:01 PDT)
    - acetyl groups on protein fragments Elizabeth K. White (Thu Jul 25 2002 - 11:55:04 PDT)
    - Re: acetyl groups on protein fragments Laurent Chiche (Fri Jul 26 2002 - 00:43:03 PDT)
    - Re: your mail CUI, Guanglei (Thu Jul 25 2002 - 06:30:30 PDT)
  - CCl4 solvent box Bimo Ario Tejo (Wed Jul 24 2002 - 12:55:04 PDT)
- gaff and parm99 Pascal Bonnet (Wed Jul 24 2002 - 06:11:36 PDT)
  - Re: gaff and parm99 David A. Case (Wed Jul 24 2002 - 08:13:48 PDT)
    - Re: gaff and parm99 Pascal Bonnet (Wed Jul 24 2002 - 08:51:30 PDT)
problemas running amber7 tests on a SP2 machine ramon kleber da rocha (Tue Jul 23 2002 - 13:33:28 PDT)
several questions David Keller (Tue Jul 23 2002 - 15:24:04 PDT)
- Re: several questions David A. Case (Tue Jul 23 2002 - 17:08:10 PDT)
  - Re: several questions Heather A Carlson (Tue Jul 23 2002 - 20:17:35 PDT)
- "crd" file created with VMD Soonmin Jang (Tue Jul 23 2002 - 17:47:04 PDT)
  - Re: "crd" file created with VMD Carlos Simmerling (Tue Jul 23 2002 - 18:42:15 PDT)
  - Re: "crd" file created with VMD Carlos Simmerling (Tue Jul 23 2002 - 20:02:50 PDT)
  - Re: "crd" file created with VMD David Case (Wed Jul 24 2002 - 00:04:02 PDT)
    - Re: "crd" file created with VMD Soonmin Jang (Wed Jul 24 2002 - 00:28:27 PDT)
Re: SANDER documentation for nmropt David A. Case (Mon Jul 29 2002 - 17:27:52 PDT)
a water jumps Masaki Tomimoto (Mon Jul 29 2002 - 20:47:21 PDT)
- Re: a water jumps David Case (Mon Jul 29 2002 - 22:13:16 PDT)
- NON-BONDED INTERACTION Rosalia Pascual (Tue Jul 30 2002 - 07:41:49 PDT)
  - Re: NON-BONDED INTERACTION David A. Case (Tue Oct 01 2002 - 08:28:00 PDT)
- sander mpirun hangs with 4 CPU, but not with 2 Thomas Steinbrecher (Tue Jul 30 2002 - 08:09:03 PDT)
  - RE: sander mpirun hangs with 4 CPU, but not with 2 lamon_at_lav.Boehringer-Ingelheim.com (Tue Jul 30 2002 - 10:06:05 PDT)
  - AM1-BCC sensitivity to AM1 charges Matthew Lee (Tue Jul 30 2002 - 10:31:43 PDT)
    - RE: AM1-BCC sensitivity to AM1 charges ajakalian_at_lav.Boehringer-Ingelheim.com (Tue Jul 30 2002 - 11:28:25 PDT)
    - 'triangular' bond or angle Mahadevan Seetharaman (Tue Jul 30 2002 - 13:53:20 PDT)
    - building ss DNA/RNA Cozmuta (Tue Jul 30 2002 - 14:47:45 PDT)
    - Re: building ss DNA/RNA David A. Case (Tue Jul 30 2002 - 15:29:19 PDT)
    - tests for amber Cozmuta (Tue Jul 30 2002 - 16:47:18 PDT)
    - Re: tests for amber jim caldwell (Tue Jul 30 2002 - 17:57:49 PDT)
    - structure Cozmuta (Tue Jul 30 2002 - 20:34:44 PDT)
    - Re: structure David Case (Tue Jul 30 2002 - 22:43:50 PDT)
- AMBER Machine Questions DTphonehome33_at_aol.com (Tue Jul 30 2002 - 10:00:33 PDT)
Re: "number of processors must be a power of two" Sanjeev B.S. (Tue Aug 06 2002 - 09:17:35 PDT)
- Re: "number of processors must be a power of two" David A. Case (Tue Aug 06 2002 - 09:40:33 PDT)
- Re: "number of processors must be a power of two" Michael Crowley (Tue Aug 06 2002 - 10:31:50 PDT)
creating a solvent box Bimo Ario Tejo (Tue Aug 06 2002 - 10:23:13 PDT)
- Re: creating a solvent box David A. Case (Tue Aug 06 2002 - 11:53:50 PDT)
- check-up question Cozmuta (Tue Aug 06 2002 - 12:13:31 PDT)
  - Re: check-up question David A. Case (Tue Aug 06 2002 - 14:14:56 PDT)
FW: Compiling on HP-UX 11.00 Hagedorn, Dan N (Fri Aug 09 2002 - 11:45:00 PDT)
Amber/Gentoo linux Jianhui Wu (Fri Aug 09 2002 - 12:53:16 PDT)
- RE: Amber/Gentoo linux Ross Walker (Sun Aug 11 2002 - 14:32:37 PDT)
  - RE: Amber/Gentoo linux Margaret Cheung (Sun Aug 11 2002 - 16:31:02 PDT)
  - Nanotubes with AMBER Stefan Andreev Andreev (Sun Aug 11 2002 - 16:59:26 PDT)
    - Re: Nanotubes with AMBER David Case (Sun Aug 11 2002 - 21:13:23 PDT)
    - literature for NVE Khatcharin Siriwong (Mon Aug 12 2002 - 02:07:05 PDT)
    - Re: literature for NVE David A. Case (Mon Aug 12 2002 - 08:38:45 PDT)
    - Re: literature for NVE Khatcharin Siriwong (Mon Aug 12 2002 - 09:19:03 PDT)
    - chesey.panther.gsu.edu Michael G Cooney (Mon Aug 12 2002 - 12:03:37 PDT)
    - misdirected message Michael G Cooney (Mon Aug 12 2002 - 12:35:35 PDT)
    - Format of prep input files dianah_at_unm.edu (Tue Aug 13 2002 - 10:42:11 PDT)
    - Re: Format of prep input files David A. Case (Tue Aug 13 2002 - 11:13:47 PDT)
    - sander minimizations failing John Bushnell (Tue Aug 13 2002 - 17:03:12 PDT)
    - minimization in amber7 for nonperiodic systems David Case (Tue Aug 13 2002 - 22:47:43 PDT)
    - Re: minimization in amber7 for nonperiodic systems Giulio Rastelli (Wed Aug 14 2002 - 08:03:11 PDT)
    - Re: minimization in amber7 for nonperiodic systems David A. Case (Wed Aug 14 2002 - 08:28:21 PDT)
    - dihedral parameter for conjugated double bonds in GAFF Giulio Rastelli (Wed Aug 14 2002 - 01:37:50 PDT)
    - GB in Amber7 Jithesh (Wed Aug 14 2002 - 01:37:54 PDT)
    - Re: GB in Amber7 David A. Case (Wed Aug 14 2002 - 08:33:57 PDT)
    - Running amber7 on Param10000 Sanjeev B.S. (Wed Aug 14 2002 - 08:38:34 PDT)
    - Re: Running amber7 on Param10000 Jithesh (Thu Aug 15 2002 - 00:35:46 PDT)
    - force field name A. Hungie (Thu Aug 15 2002 - 06:50:48 PDT)
    - RE: force field name Yong Duan (Thu Aug 15 2002 - 09:11:19 PDT)
    - sander on NEC-SX5 C. Klein (Thu Aug 15 2002 - 09:12:24 PDT)
    - RE: sander on NEC-SX5 Karen Haskell (Thu Aug 15 2002 - 09:38:57 PDT)
    - trajectory file limit??? Vlad Cojocaru (Thu Aug 15 2002 - 09:43:54 PDT)
    - Re: trajectory file limit??? David A. Case (Thu Aug 15 2002 - 10:26:34 PDT)
    - Re: trajectory file limit??? jim caldwell (Thu Aug 15 2002 - 12:26:13 PDT)
    - Order of a protein, bound waters and ligand in saveamberparm Masaki Tomimoto (Thu Aug 15 2002 - 13:25:45 PDT)
    - RE: Order of a protein, bound waters and ligand in saveamberparm Masaki Tomimoto (Thu Aug 15 2002 - 15:04:18 PDT)
    - Extra points Sarah Tschampel (Thu Aug 15 2002 - 13:25:45 PDT)
    - Re: Extra points jim caldwell (Thu Aug 15 2002 - 14:54:21 PDT)
    - Re: Extra points David A. Case (Thu Aug 15 2002 - 16:01:21 PDT)
    - Re: trajectory file limit??? Pratul Agarwal (Thu Aug 15 2002 - 14:12:35 PDT)
    - RE: trajectory file limit??? Ross Walker (Thu Aug 15 2002 - 14:48:30 PDT)
    - RE: force field name Peter Gannett (Thu Aug 15 2002 - 16:03:52 PDT)
    - GB in amber6 Prabal Maiti (Thu Aug 15 2002 - 17:26:22 PDT)
    - Re: GB in amber6 CUI, Guanglei (Thu Aug 15 2002 - 19:33:27 PDT)
    - Re: GB in amber6 David Case (Thu Aug 15 2002 - 22:23:23 PDT)
    - Re: GB in amber6 CUI, Guanglei (Fri Aug 16 2002 - 06:25:52 PDT)
    - dihedral parameter for conjugated double bonds in GAFF Giulio Rastelli (Fri Aug 16 2002 - 09:37:03 PDT)
    - Etot drops after restarting MD in sander Pratul Agarwal (Fri Aug 16 2002 - 11:18:58 PDT)
    - antechamber's prepc option Matthew Lee (Fri Aug 16 2002 - 12:20:59 PDT)
    - Re: antechamber's prepc option David A. Case (Fri Aug 16 2002 - 13:10:55 PDT)
    - mol2_to_off Matthew Randolph Lee, Ph.D. (Fri Aug 16 2002 - 15:15:41 PDT)
    - average of LES copies mer_at_chem.wayne.edu (Sun Aug 18 2002 - 18:00:22 PDT)
    - Antibody residue numbering Mark Hsieh (Mon Aug 19 2002 - 13:56:00 PDT)
    - Re: Antibody residue numbering David A. Case (Mon Aug 19 2002 - 14:15:45 PDT)
    - RE: Antibody residue numbering Mark Hsieh (Mon Aug 19 2002 - 18:00:03 PDT)
    - RE: Antibody residue numbering Mark Hsieh (Tue Aug 20 2002 - 09:52:24 PDT)
    - Im lost Sankha Subhra Som (Mon Aug 19 2002 - 22:16:00 PDT)
    - Re: Im lost David A. Case (Tue Aug 20 2002 - 08:15:29 PDT)
    - PC (principal component) analysis Soonmin Jang (Tue Aug 20 2002 - 01:02:24 PDT)
    - mail host switchover jim caldwell (Mon Aug 19 2002 - 14:58:11 PDT)
    - a couple missing gaff angle terms Matthew Lee (Fri Aug 16 2002 - 14:55:44 PDT)
    - follow-up post on missing gaff terms Matthew Randolph Lee, Ph.D. (Tue Aug 20 2002 - 10:21:50 PDT)
    - segmentation fault Vlad Cojocaru (Tue Aug 20 2002 - 14:21:30 PDT)
    - Nitro parameters Jerry Matthew Parks (Wed Aug 21 2002 - 14:28:48 PDT)
    - RMSD by residue (fwd) amber_at_heimdal.compchem.ucsf.edu (Mon Aug 26 2002 - 14:49:39 PDT)
    - Re: RMSD by residue (fwd) Holger Gohlke (Mon Aug 26 2002 - 18:08:35 PDT)
    - Re: RMSD by residue (fwd) Carlos Simmerling (Mon Aug 26 2002 - 18:10:41 PDT)
    - Perturbation with sander : trouble in keeping perturbed part bonded to unperturbed (fwd) amber_at_heimdal.compchem.ucsf.edu (Mon Aug 26 2002 - 14:50:02 PDT)
    - Re: Perturbation with sander : trouble in keeping perturbed part bonded to unperturbed (fwd) David A. Case (Mon Aug 26 2002 - 18:21:06 PDT)
    - adding_hydrogens_to_pdb (fwd) amber_at_heimdal.compchem.ucsf.edu (Mon Aug 26 2002 - 14:50:07 PDT)
    - Re: adding_hydrogens_to_pdb (fwd) David A. Case (Mon Aug 26 2002 - 17:34:36 PDT)
    - ewald bomb in md equilibration (fwd) amber_at_heimdal.compchem.ucsf.edu (Mon Aug 26 2002 - 14:50:14 PDT)
    - Re: ewald bomb in md equilibration (fwd) David A. Case (Mon Aug 26 2002 - 18:23:52 PDT)
    - why is mm_pbsa broken ? (fwd) amber_at_heimdal.compchem.ucsf.edu (Mon Aug 26 2002 - 14:50:27 PDT)
    - Re: why is mm_pbsa broken ? (fwd) Holger Gohlke (Tue Aug 27 2002 - 10:12:17 PDT)
    - restraints in parm in amber7 Sarah Tschampel (Tue Aug 27 2002 - 14:57:33 PDT)
    - Re: restraints in parm in amber7 Carlos Simmerling (Tue Aug 27 2002 - 18:38:59 PDT)
    - problem in MD Xiang Mao (Tue Aug 27 2002 - 17:05:11 PDT)
    - Re: problem in MD Carlos Simmerling (Tue Aug 27 2002 - 18:40:06 PDT)
    - ambpdb problem (fwd) amber_at_heimdal.compchem.ucsf.edu (Mon Aug 26 2002 - 14:50:32 PDT)
    - Re: ambpdb problem (fwd) David A. Case (Mon Aug 26 2002 - 18:27:08 PDT)
    - Gibbs (FEP) (fwd) amber_at_heimdal.compchem.ucsf.edu (Mon Aug 26 2002 - 14:50:36 PDT)
    - Re: Gibbs (FEP) (fwd) David A. Case (Mon Aug 26 2002 - 18:30:28 PDT)
    - QUICK HELP! Parameters for neutral amino acids (fwd) amber_at_heimdal.compchem.ucsf.edu (Mon Aug 26 2002 - 14:50:43 PDT)
    - Re: QUICK HELP! Parameters for neutral amino acids (fwd) David A. Case (Mon Aug 26 2002 - 18:32:50 PDT)
    - amber7, gaff and minimization (fwd) amber_at_heimdal.compchem.ucsf.edu (Mon Aug 26 2002 - 14:50:50 PDT)
    - Re: amber7, gaff and minimization (fwd) David A. Case (Mon Aug 26 2002 - 18:35:26 PDT)
    - Interface and Amber 7.0 Nigel D Priestley (Mon Aug 26 2002 - 19:45:55 PDT)
    - Re: Interface and Amber 7.0 David A. Case (Tue Aug 27 2002 - 04:53:45 PDT)
    - Re: Interface and Amber 7.0 David Pearlman (Tue Aug 27 2002 - 09:35:19 PDT)
    - amber7: ES40s Sanjeev B.S. (Tue Aug 27 2002 - 06:08:49 PDT)
    - difference 94 99 force field Vlad Cojocaru (Tue Aug 27 2002 - 06:34:11 PDT)
    - Re: difference 94 99 force field Carlos Simmerling (Tue Aug 27 2002 - 07:34:50 PDT)
    - question Sankha Subhra Som (Mon Aug 26 2002 - 23:24:32 PDT)
    - regarding RESP run from gamess output (fwd) amber_at_heimdal.compchem.ucsf.edu (Mon Aug 26 2002 - 14:50:55 PDT)
    - why is mm_pbsa broken ? (fwd) amber_at_heimdal.compchem.ucsf.edu (Mon Aug 26 2002 - 14:50:59 PDT)
    - add DUMMY atom into coordinate file yuann (Fri Aug 16 2002 - 02:12:04 PDT)
    - Re: add DUMMY atom into coordinate file Alan Leo (Fri Aug 16 2002 - 12:51:35 PDT)
    - Q: waters in NPT & periodic boundary condition Masaki Tomimoto (Wed Aug 14 2002 - 09:06:15 PDT)
    - Re: Q: waters in NPT & periodic boundary condition David A. Case (Wed Aug 14 2002 - 09:45:46 PDT)
    - E going up and down??? Jiyoung Heo (Wed Aug 14 2002 - 14:13:44 PDT)
    - Re: E going up and down??? David A. Case (Wed Aug 14 2002 - 15:16:05 PDT)
    - PMF with sander module mer_at_gordon.chem.wayne.edu (Wed Aug 14 2002 - 16:23:25 PDT)
    - Re: PMF with sander module Pratul Agarwal (Wed Aug 14 2002 - 20:49:34 PDT)
    - Re: PMF with sander module David A. Case (Fri Aug 16 2002 - 12:23:16 PDT)
    - problem with amber7 compiling on SGI Chris Switzer (Wed Aug 14 2002 - 18:26:54 PDT)
    - a question about carnal Vlad Cojocaru (Wed Aug 14 2002 - 09:39:36 PDT)
    - problem reading rstrnt file with pgf77 compiled sander Michael Petersen (Wed Aug 14 2002 - 03:13:24 PDT)
    - Carnal stream problem Vlad Cojocaru (Wed Aug 14 2002 - 07:45:04 PDT)
Re: Help needed about mm_pbsa Holger Gohlke (Thu Aug 15 2002 - 10:04:03 PDT)
- can carnal do the job as anal to break down the energy? Haizhen Zhong (Wed Aug 28 2002 - 11:02:48 PDT)
- [Re: can carnal do the job as anal to break down the energy?] Holger Gohlke (Wed Aug 28 2002 - 11:36:51 PDT)
  - IMIN=5 ? (Was: Re: [Re: can carnal do the job as anal ...) Michael Jakusch (Thu Aug 29 2002 - 00:36:57 PDT)
    - Re: IMIN=5 ? (Was: Re: [Re: can carnal do the job as anal ...) Carlos Simmerling (Thu Aug 29 2002 - 03:54:15 PDT)
    - Re: IMIN=5 ? (Was: Re: [Re: can carnal do the job as anal ...) Michael Jakusch (Thu Aug 29 2002 - 04:56:12 PDT)
    - MDaemon Warning - Virus Found postmaster_at_96com.com (Thu Aug 29 2002 - 05:20:52 PDT)
    - pbc in amber Xiang Mao (Thu Aug 29 2002 - 06:00:04 PDT)
  - MDaemon Warning - Virus Found postmaster_at_96com.com (Thu Aug 29 2002 - 03:14:06 PDT)
Re: problem reading rstrnt file with pgf77 Michael Petersen (Fri Aug 16 2002 - 06:23:48 PDT)
Re: Can we get trajectories coordinates after FIT in Carnal? (fwd) amber_at_heimdal.compchem.ucsf.edu (Mon Aug 26 2002 - 14:51:03 PDT)
How to make mpeg files from amber trajectories (fwd) amber_at_heimdal.compchem.ucsf.edu (Mon Aug 26 2002 - 14:51:07 PDT)
- Re: How to make mpeg files from amber trajectories (fwd) Jake Isaacs (Tue Aug 27 2002 - 06:48:24 PDT)
- Re: How to make mpeg files from amber trajectories (fwd) Michal Otyepka (Wed Aug 28 2002 - 00:22:54 PDT)
- What's this "interface" the tutorial talks about? Andreas Kerzmann (Wed Aug 28 2002 - 05:41:01 PDT)
  - Re: What's this "interface" the tutorial talks about? David Pearlman (Wed Aug 28 2002 - 12:49:57 PDT)
    - RE: What's this "interface" the tutorial talks about? priestle (Wed Aug 28 2002 - 12:02:52 PDT)
  - gibbs sara nunez (Wed Aug 28 2002 - 12:52:56 PDT)
  - [Re: can carnal do the job as anal to break down the energy?] Bill Ross (Wed Aug 28 2002 - 13:35:40 PDT)
  - a missing variable Vlad Cojocaru (Wed Aug 28 2002 - 13:43:04 PDT)
    - Re: a missing variable Matthew Randolph Lee, Ph.D. (Wed Aug 28 2002 - 15:27:12 PDT)
    - sorry!!!!maybe another stupid question Vlad Cojocaru (Wed Aug 28 2002 - 15:48:03 PDT)
    - Re: sorry!!!!maybe another stupid question Pratul Agarwal (Wed Aug 28 2002 - 18:45:28 PDT)
    - Tutorial Error Message Joel Konkle-Parker (Wed Aug 28 2002 - 16:19:48 PDT)
    - Re: Tutorial Error Message Holger Gohlke (Thu Aug 29 2002 - 08:22:25 PDT)
    - MDaemon Warning - Virus Found postmaster_at_96com.com (Thu Aug 29 2002 - 10:02:23 PDT)
    - image command Sophia Kondratova (Thu Aug 29 2002 - 10:46:01 PDT)
    - PyMOL + AMBER Trajectories DeLano, Warren (Thu Aug 29 2002 - 11:27:01 PDT)
    - RE: PyMOL + AMBER Trajectories DeLano, Warren (Tue Sep 03 2002 - 10:51:57 PDT)
    - MDaemon Warning - Virus Found postmaster_at_96com.com (Wed Sep 04 2002 - 03:40:26 PDT)
    - Escaping Atoms ch cureton (Wed Sep 04 2002 - 03:43:03 PDT)
    - RE: Escaping Atoms case (Thu Sep 05 2002 - 15:04:06 PDT)
    - bondbydistance eric hu (Thu Sep 05 2002 - 16:20:43 PDT)
    - RE: bondbydistance case (Fri Sep 06 2002 - 17:04:02 PDT)
    - RE: bondbydistance Nicholson, James D Mr ARO (Sat Sep 07 2002 - 17:16:28 PDT)
    - about amber and charmm, thanks Zhang Jian (Sun Sep 08 2002 - 02:10:57 PDT)
    - who to address this to?... Jessica Swanson (Sun Sep 08 2002 - 15:59:23 PDT)
    - Re: who to address this to?... Holger Gohlke (Mon Sep 09 2002 - 09:25:00 PDT)
    - Re: who to address this to?... Michael Crowley (Mon Sep 09 2002 - 10:41:16 PDT)
    - amber7 compilation on irix6.4 mp K.Seshadri (Mon Sep 09 2002 - 10:44:13 PDT)
    - How to check whether the trajectory file matches the coordinates file or not? Ling Zhang (Mon Sep 09 2002 - 11:31:13 PDT)
    - Re: How to check whether the trajectory file matches the coordinates file or not? Shixiang Yan (Mon Sep 09 2002 - 11:53:04 PDT)
    - RE: How to check whether the trajectory file matches the coordinates file or not? Kristina Furse (Mon Sep 09 2002 - 12:32:27 PDT)
    - why are the results so large difference calculating by mm_pbsa and mm_gbsa? Yongjun Jiang (Tue Sep 10 2002 - 00:18:46 PDT)
    - Re: why are the results so large difference calculating by mm_pbsa and mm_gbsa? Holger Gohlke (Tue Sep 10 2002 - 09:26:07 PDT)
    - Strange MD simulation results with GB solvation at high temp. Soonmin Jang (Tue Sep 10 2002 - 03:09:06 PDT)
    - Re: Strange MD simulation results with GB solvation at high temp. Carlos Simmerling (Tue Sep 10 2002 - 05:07:58 PDT)
    - Re: Strange MD simulation results with GB solvation at high temp. Soonmin Jang (Tue Sep 10 2002 - 08:56:53 PDT)
    - MDaemon Warning - Virus Found postmaster_at_96com.com (Tue Sep 10 2002 - 08:57:00 PDT)
    - nmode compile question? Yongjun Jiang (Tue Sep 10 2002 - 05:46:18 PDT)
    - Re: nmode compile question? Holger Gohlke (Tue Sep 10 2002 - 09:17:24 PDT)
    - Re: nmode compile question? James W. Caldwell (Tue Sep 10 2002 - 11:04:07 PDT)
    - rdparm Joffre Heredia (Tue Sep 10 2002 - 11:07:26 PDT)
    - loadpdb error messages Joel Konkle-Parker (Tue Sep 10 2002 - 15:58:07 PDT)
    - Re: loadpdb error messages James W. Caldwell (Tue Sep 10 2002 - 16:49:48 PDT)
    - Polarizability, a general question Michal Otyepka (Wed Sep 11 2002 - 01:56:32 PDT)
    - memory allocation in mm_pbsa Giulio Rastelli (Wed Sep 11 2002 - 03:41:04 PDT)
    - Re: memory allocation in mm_pbsa James W. Caldwell (Wed Sep 11 2002 - 08:26:19 PDT)
    - Re: memory allocation in mm_pbsa Holger Gohlke (Wed Sep 11 2002 - 08:55:07 PDT)
    - Problems during equilibration Pratul Agarwal (Wed Sep 11 2002 - 12:38:36 PDT)
    - Re: Problems during equilibration Pratul Agarwal (Wed Sep 11 2002 - 13:14:05 PDT)
    - Dual Processor AMD vs. Single Processor DeLano, Warren (Wed Sep 11 2002 - 17:34:47 PDT)
    - Re: Dual Processor AMD vs. Single Processor St�phane Teletch�a (Thu Sep 12 2002 - 01:09:58 PDT)
    - Qustion about calculation of pressure Nikolai Smolin (Thu Sep 12 2002 - 03:01:44 PDT)
    - Re: Qustion about calculation of pressure James W. Caldwell (Thu Sep 12 2002 - 09:43:25 PDT)
    - sorry this is just a test Vlad Cojocaru (Thu Sep 12 2002 - 08:23:24 PDT)
    - leap and topology file Marcela Madrid (Thu Sep 12 2002 - 09:12:20 PDT)
    - Re: leap and topology file Lepsa (Fri Sep 13 2002 - 07:39:45 PDT)
    - sander.LES questions Peter Varnai (Thu Sep 12 2002 - 09:27:12 PDT)
    - Re: sander.LES questions Carlos Simmerling (Thu Sep 12 2002 - 10:24:25 PDT)
    - large energy fluctration eric hu (Thu Sep 12 2002 - 11:05:10 PDT)
    - Re: large energy fluctration Carlos Simmerling (Thu Sep 12 2002 - 11:50:09 PDT)
    - Re: large energy fluctration eric hu (Fri Sep 20 2002 - 11:00:17 PDT)
    - the amino group of 2amino purine has strange behaviour Vlad Cojocaru (Thu Sep 12 2002 - 11:42:10 PDT)
    - Re: Problems during equilibration Pratul Agarwal (Wed Sep 11 2002 - 19:40:05 PDT)
    - just a test Vlad Cojocaru (Wed Sep 11 2002 - 06:39:59 PDT)
    - GBSA and surface crystal waters Raik Grunberg (Tue Sep 10 2002 - 07:44:20 PDT)
    - Re: Strange MD simulation results with GB solvation at high temp. David A. Case (Wed Sep 11 2002 - 18:20:17 PDT)
    - Re: Strange MD simulation results with GB solvation at high temp. Carlos Simmerling (Wed Sep 11 2002 - 19:04:44 PDT)
    - Re: Strange MD simulation results with GB solvation at high temp. Soonmin Jang (Thu Sep 12 2002 - 22:21:32 PDT)
    - Distace dependent dielectric constant Lorenzo Gontrani (Mon Sep 09 2002 - 01:33:43 PDT)
    - Re: Distace dependent dielectric constant David A. Case (Thu Sep 12 2002 - 15:39:35 PDT)
    - Changing MAXINT Joel Konkle-Parker (Thu Sep 12 2002 - 16:21:13 PDT)
    - Re: Changing MAXINT John Bushnell (Fri Sep 13 2002 - 15:38:52 PDT)
    - D-tryptophan Perdita Barran (Sat Sep 14 2002 - 07:16:45 PDT)
    - Re: D-tryptophan James W. Caldwell (Sat Sep 14 2002 - 08:21:42 PDT)
    - amber K.Veluraja (Sun Sep 15 2002 - 22:14:04 PDT)
    - amber question yao yong (Mon Sep 16 2002 - 04:03:16 PDT)
    - Re: amber question David A. Case (Mon Sep 16 2002 - 09:47:03 PDT)
    - Re: amber question James W. Caldwell (Mon Sep 16 2002 - 10:24:20 PDT)
    - SETVEL, incorrect number of arguments? Giovanni Fossati (Mon Sep 16 2002 - 15:43:30 PDT)
    - Re: SETVEL, incorrect number of arguments? David A. Case (Tue Sep 17 2002 - 12:18:38 PDT)
    - non-bonded metal ion in complex yuann (Mon Sep 16 2002 - 23:28:45 PDT)
    - Re: non-bonded metal ion in complex Pratul Agarwal (Tue Sep 17 2002 - 06:59:14 PDT)
    - question about nmode again. Yongjun Jiang (Tue Sep 17 2002 - 00:15:54 PDT)
    - Re: question about nmode again. David A. Case (Tue Sep 17 2002 - 07:40:00 PDT)
    - RE: Changing MAXINT Ross Walker (Mon Sep 16 2002 - 07:39:36 PDT)
    - binding site volume Shixiang Yan (Thu Sep 12 2002 - 16:38:41 PDT)
    - Re: binding site volume Michal Otyepka (Fri Sep 13 2002 - 00:13:08 PDT)
    - MDaemon Warning - Virus Found postmaster_at_96com.com (Fri Sep 13 2002 - 06:10:40 PDT)
    - MDaemon Warning - Virus Found postmaster_at_96com.com (Fri Sep 13 2002 - 06:13:22 PDT)
    - problems on IBM AIX Giovanni Fossati (Thu Sep 12 2002 - 18:43:52 PDT)
    - Re: problems on IBM AIX David A. Case (Fri Sep 13 2002 - 07:42:14 PDT)
    - Re: problems on IBM AIX Carlos P. Sosa (Fri Sep 13 2002 - 08:47:31 PDT)
    - Beowulf killing jobs Peter Gannett (Fri Sep 13 2002 - 14:03:19 PDT)
    - RE: Beowulf killing jobs Ross Walker (Mon Sep 16 2002 - 07:46:45 PDT)
    - example 1 problems Alicia Hopkins (Mon Sep 16 2002 - 08:57:23 PDT)
    - Re: example 1 problems David A. Case (Mon Sep 16 2002 - 09:25:54 PDT)
    - Re: example 1 problems Alicia Hopkins (Tue Sep 17 2002 - 05:03:53 PDT)
    - Re: example 1 problems James W. Caldwell (Tue Sep 17 2002 - 07:24:30 PDT)
    - Re: example 1 problems David A. Case (Tue Sep 17 2002 - 07:45:31 PDT)
    - mm_pbsa question. wentaofu (Tue Sep 17 2002 - 08:35:59 PDT)
    - Density during equilibration (sander) Pratul Agarwal (Tue Sep 17 2002 - 09:56:10 PDT)
    - Re: Density during equilibration (sander) David A. Case (Tue Sep 17 2002 - 12:21:49 PDT)
    - Re: Density during equilibration (sander) Marc Dobler (Tue Sep 17 2002 - 17:29:22 PDT)
    - Re: Density during equilibration (sander) Carlos Simmerling (Tue Sep 17 2002 - 18:44:13 PDT)
    - Re: Density during equilibration (sander) Marc Dobler (Wed Sep 18 2002 - 00:11:21 PDT)
    - Carnal+HBond confusion Sanjeev B.S. (Wed Sep 18 2002 - 21:18:36 PDT)
    - Re: Carnal+HBond confusion Sanjeev B.S. (Tue Sep 24 2002 - 05:13:05 PDT)
    - bug in New2oldparm Pascal Bonnet (Thu Sep 19 2002 - 03:35:46 PDT)
    - Re: bug in New2oldparm David A. Case (Thu Sep 19 2002 - 08:28:30 PDT)
    - offset of temperature when running MD with CAP and no periodic conditions Therese Malliavin (Thu Sep 19 2002 - 08:44:24 PDT)
    - Re: offset of temperature when running MD with CAP and no periodic conditions Andreas Svrcek-Seiler (Thu Sep 19 2002 - 10:11:31 PDT)
    - image X. Tan (Thu Sep 19 2002 - 10:32:15 PDT)
    - Re: image David A. Case (Thu Sep 19 2002 - 10:43:32 PDT)
    - Question about Counterions Markus Drumm (Thu Sep 19 2002 - 10:38:24 PDT)
    - new2oldparm format (2) Pascal Bonnet (Thu Sep 19 2002 - 03:43:39 PDT)
    - a freeware to display RMSD matrices Vlad Cojocaru (Thu Sep 19 2002 - 05:44:53 PDT)
    - Re: a freeware to display RMSD matrices CUI, Guanglei (Thu Sep 19 2002 - 06:42:29 PDT)
    - Re: Density during equilibration (sander) Pratul Agarwal (Tue Sep 17 2002 - 17:22:22 PDT)
    - Re: Density during equilibration (sander) Pratul Agarwal (Thu Sep 26 2002 - 07:09:02 PDT)
    - Re: example 1 problems Natasja Brooijmans (Mon Sep 16 2002 - 09:40:38 PDT)
    - assistance required amit kumar (Mon Sep 16 2002 - 09:25:05 PDT)
    - Help using moilview to make animations of trajectories Nicholson, James D Mr ARO (Fri Sep 13 2002 - 15:15:33 PDT)
    - parameterization of a new class of compounds (nucleic acid base analogues) Vlad Cojocaru (Mon Sep 09 2002 - 02:40:05 PDT)
    - MDaemon Warning - Virus Found postmaster_at_96com.com (Mon Sep 09 2002 - 04:04:45 PDT)
    - MDaemon Warning - Virus Found postmaster_at_96com.com (Fri Sep 06 2002 - 04:13:47 PDT)
    - group selection for all heavy atoms ? Raik Grunberg (Fri Sep 06 2002 - 09:23:33 PDT)
    - compiling amber on a linux box using DMEM-ALLOC ramon kleber da rocha (Fri Sep 06 2002 - 13:46:43 PDT)
    - Re: compiling amber on a linux box using DMEM-ALLOC Scott Brozell (Fri Sep 06 2002 - 15:01:27 PDT)
    - Re: compiling amber on a linux box using DMEM-ALLOC ramon kleber da rocha (Fri Sep 06 2002 - 16:11:55 PDT)
    - Re: compiling amber on a linux box using DMEM-ALLOC John Bushnell (Fri Sep 06 2002 - 16:43:12 PDT)
    - Re: compiling amber on a linux box using DMEM-ALLOC James W. Caldwell (Fri Sep 06 2002 - 17:56:42 PDT)
    - Re: compiling amber on a linux box using DMEM-ALLOC Scott Brozell (Fri Sep 06 2002 - 17:16:40 PDT)
    - Re: compiling amber on a linux box using DMEM-ALLOC Florian Barth (Fri Sep 06 2002 - 15:13:31 PDT)
    - cut-off question Cozmuta (Fri Sep 06 2002 - 15:49:21 PDT)
    - RE: cut-off question case (Fri Sep 06 2002 - 17:01:28 PDT)
    - old prmtop Thomas Steinbrecher (Wed Sep 04 2002 - 08:56:47 PDT)
    - Re: old prmtop C. Klein (Wed Sep 04 2002 - 09:21:18 PDT)
    - Re: old prmtop Holger Gohlke (Wed Sep 04 2002 - 09:21:32 PDT)
    - Re: old prmtop Peter Gannett (Wed Sep 04 2002 - 11:10:56 PDT)
    - how to detect bad contact? X. Tan (Wed Sep 04 2002 - 12:14:40 PDT)
    - cut-off question Ioana Cozmuta (Wed Sep 04 2002 - 12:43:38 PDT)
    - DNA Tutorial Script Joel Konkle-Parker (Wed Sep 04 2002 - 16:18:16 PDT)
    - Re: DNA Tutorial Script Holger Gohlke (Wed Sep 04 2002 - 20:29:23 PDT)
    - ES40 hangs amber7 jobs. Sanjeev B.S. (Thu Aug 29 2002 - 20:09:13 PDT)
    - Re: ES40 hangs amber7 jobs. James W. Caldwell (Fri Aug 30 2002 - 09:07:11 PDT)
    - Re: ES40 hangs amber7 jobs. Sanjeev B.S. (Mon Sep 02 2002 - 19:29:45 PDT)
    - dump coordinate into mdcrd A. Hungie (Fri Aug 30 2002 - 01:03:17 PDT)
    - MDaemon Warning - Virus Found postmaster_at_96com.com (Fri Aug 30 2002 - 03:08:15 PDT)
    - example gibbs file for the methane tutorial Andreas Kerzmann (Fri Aug 30 2002 - 03:18:06 PDT)
    - NTX value giudice (Fri Aug 30 2002 - 03:31:19 PDT)
    - Re: NTX value James W. Caldwell (Fri Aug 30 2002 - 09:10:10 PDT)
    - Re: NTX value James W. Caldwell (Fri Aug 30 2002 - 11:35:30 PDT)
    - Vanderbilt Biomolecular Modeling Symposium Jarrod Smith (Fri Aug 30 2002 - 11:00:40 PDT)
    - RE: Vanderbilt Biomolecular Modeling Symposium Douglas Kojetin (Fri Aug 30 2002 - 12:22:19 PDT)
    - Binding site volume/Sander MD Jianhui Wu (Fri Aug 30 2002 - 14:20:09 PDT)
    - GBSA with IGB=2, setting the PBradii bondi Sarangan Ravichandran (Fri Aug 30 2002 - 14:55:28 PDT)
    - Re: GBSA with IGB=2, setting the PBradii bondi David Case (Sat Aug 31 2002 - 10:58:35 PDT)
    - mpirun Ioana Cozmuta (Sun Sep 01 2002 - 11:32:08 PDT)
    - RE: mpirun Ross Walker (Sun Sep 01 2002 - 15:36:24 PDT)
    - additional info Ioana Cozmuta (Sun Sep 01 2002 - 11:44:32 PDT)
    - Re: NTX value David A. Case (Fri Aug 30 2002 - 12:07:44 PDT)
    - Re: NTX value giudice (Mon Sep 02 2002 - 00:05:45 PDT)
    - mm_pbsa positive binding energies Mathy Froeyen (Mon Sep 02 2002 - 02:11:34 PDT)
    - Re: mm_pbsa positive binding energies David A. Case (Mon Sep 02 2002 - 10:50:30 PDT)
    - MDaemon Warning - Virus Found postmaster_at_96com.com (Mon Sep 02 2002 - 03:12:42 PDT)
    - MDaemon Warning - Virus Found postmaster_at_96com.com (Mon Sep 02 2002 - 04:25:18 PDT)
    - carnal averaging Vlad Cojocaru (Mon Sep 02 2002 - 04:43:33 PDT)
    - Re: carnal averaging Holger Gohlke (Mon Sep 02 2002 - 13:43:52 PDT)
    - atoms coming too close during MD (with SHAKE on) Pratul Agarwal (Mon Sep 02 2002 - 18:01:18 PDT)
    - MDaemon Warning - Virus Found postmaster_at_96com.com (Fri Aug 30 2002 - 03:59:25 PDT)
    - sander7 on IBM 7040-681 under AIX 5.1 Peter Varnai (Fri Aug 30 2002 - 06:01:07 PDT)
    - ewald bomb Vlad Cojocaru (Fri Aug 30 2002 - 06:38:49 PDT)
    - Re: ewald bomb David A. Case (Fri Aug 30 2002 - 12:13:14 PDT)
- iwrap and image Sophia Kondratova (Wed Aug 28 2002 - 05:55:36 PDT)
  - Re: iwrap and image James W. Caldwell (Wed Aug 28 2002 - 07:35:50 PDT)
Carnal RMSDs (fwd) amber_at_heimdal.compchem.ucsf.edu (Mon Aug 26 2002 - 14:51:12 PDT)
Re: Etot drops after restarting MD in sander (fwd) amber_at_heimdal.compchem.ucsf.edu (Mon Aug 26 2002 - 14:51:16 PDT)
turning off ewald (fwd) amber_at_heimdal.compchem.ucsf.edu (Mon Aug 26 2002 - 14:51:21 PDT)
- Re: turning off ewald (fwd) David A. Case (Mon Aug 26 2002 - 18:12:29 PDT)
a more general question about ff (fwd) amber_at_heimdal.compchem.ucsf.edu (Mon Aug 26 2002 - 14:51:25 PDT)
leaprc file (fwd) amber_at_heimdal.compchem.ucsf.edu (Mon Aug 26 2002 - 14:51:29 PDT)
Torsion restraint between center of mass groups Pratul Agarwal (Mon Aug 26 2002 - 14:51:33 PDT)
a more general question (fwd) amber_at_heimdal.compchem.ucsf.edu (Mon Aug 26 2002 - 14:51:41 PDT)
leaprc file (fwd) amber_at_heimdal.compchem.ucsf.edu (Mon Aug 26 2002 - 14:51:44 PDT)
- Re: leaprc file (fwd) David A. Case (Mon Aug 26 2002 - 18:09:22 PDT)
Re: Extra points (fwd) amber_at_heimdal.compchem.ucsf.edu (Mon Aug 26 2002 - 14:51:49 PDT)
Scaling of Sander on Linux Clusters (fwd) amber_at_heimdal.compchem.ucsf.edu (Mon Aug 26 2002 - 14:51:57 PDT)
- Re: Scaling of Sander on Linux Clusters (fwd) Pratul Agarwal (Mon Aug 26 2002 - 17:32:24 PDT)
  - Re: Scaling of Sander on Linux Clusters (fwd) St�phane Teletch�a (Tue Aug 27 2002 - 01:41:06 PDT)
    - Re: Scaling of Sander on Linux Clusters (fwd) Sanjeev B.S. (Tue Aug 27 2002 - 01:56:15 PDT)
    - Re: Scaling of Sander on Linux Clusters (fwd) St�phane Teletch�a (Tue Aug 27 2002 - 02:31:16 PDT)
    - Re: Scaling of Sander on Linux Clusters (fwd) Sanjeev B.S. (Tue Aug 27 2002 - 10:59:51 PDT)
- Re: Scaling of Sander on Linux Clusters (fwd) Peter Gannett (Mon Aug 26 2002 - 17:56:06 PDT)
Re: "number of processors must be a power of two" (fwd) amber_at_heimdal.compchem.ucsf.edu (Mon Aug 26 2002 - 14:52:01 PDT)
Using GBSA for a DNA-PROTEIN complex (fwd) amber_at_heimdal.compchem.ucsf.edu (Mon Aug 26 2002 - 14:52:06 PDT)
test James W. Caldwell (Mon Aug 26 2002 - 15:04:35 PDT)
mail reflector James W. Caldwell (Mon Aug 26 2002 - 15:35:53 PDT)
ewald bomb in md equilibration Sophia Kondratova (Mon Aug 26 2002 - 15:54:37 PDT)
Re: Carnal RMSDs Bill Ross (Mon Aug 26 2002 - 16:56:50 PDT)
Re: how to make mpeg files from amber trajectories Anke Eisenmann (Tue Aug 27 2002 - 07:41:01 PDT)
question Ioana Cozmuta (Tue Sep 03 2002 - 10:46:04 PDT)
why are the results so large difference calculating by mm_pbsaandmm_gbsa? Yongjun Jiang (Thu Sep 12 2002 - 00:25:32 PDT)
Z DNA Sue Heavner (Tue Sep 17 2002 - 12:55:04 PDT)
RE: compiling without ISTAR2 Ross Walker (Thu Sep 19 2002 - 10:50:49 PDT)
BLOWUP after 100 ns??? Randy M. Wadkins (Thu Sep 19 2002 - 13:51:28 PDT)
- Re: BLOWUP after 100 ns??? Randy M. Wadkins (Thu Sep 19 2002 - 14:39:48 PDT)
- Re: BLOWUP after 100 ns??? David A. Case (Thu Sep 19 2002 - 17:29:58 PDT)
  - Re: BLOWUP after 100 ns??? Randy M. Wadkins (Thu Sep 19 2002 - 18:41:16 PDT)
  - Dynamic Movement of Molecule Yuuki Komata (Fri Sep 20 2002 - 01:03:48 PDT)
    - Re: Dynamic Movement of Molecule Thomas Cheatham (Fri Sep 20 2002 - 12:01:39 PDT)
    - ptraj rdf output Prabal Maiti (Fri Sep 20 2002 - 16:24:35 PDT)
    - Periodicity Question DeLano, Warren (Fri Sep 20 2002 - 17:29:49 PDT)
Re: Parameters for AMBER David A. Case (Fri Sep 20 2002 - 06:53:18 PDT)
mol2 file format in the future of amber M. L. Dodson (Fri Sep 20 2002 - 07:41:02 PDT)
- Re: mol2 file format in the future of amber David A. Case (Sun Sep 22 2002 - 08:10:42 PDT)
  - Re: mol2 file format in the future of amber M. L. Dodson (Sun Sep 22 2002 - 08:34:06 PDT)
Re: vlimit and vmax Thomas Cheatham (Fri Sep 20 2002 - 12:14:11 PDT)
- Re: vlimit and vmax darden (Fri Sep 20 2002 - 12:27:10 PDT)
mm_pbsa Sue Heavner (Fri Sep 20 2002 - 13:00:36 PDT)
- Re: mm_pbsa Holger Gohlke (Sun Sep 22 2002 - 14:01:22 PDT)
  - Re: mm_pbsa Mahadevan Seetharaman (Sun Sep 22 2002 - 19:07:27 PDT)
    - Re: mm_pbsa David A. Case (Mon Sep 23 2002 - 06:25:02 PDT)
  - ptraj-6.4/LES Peter Varnai (Mon Sep 23 2002 - 02:18:25 PDT)
Re: Do I have to rerun 1ns MD?? Holger Gohlke (Sun Sep 22 2002 - 12:30:40 PDT)
Re: betaP,SURFOFF inconsistency Holger Gohlke (Sun Sep 22 2002 - 13:20:03 PDT)
Fw: Do I have to rerun 1ns MD?? Lepsa (Mon Sep 23 2002 - 08:50:26 PDT)
mm_pbsa output error Michael Murray (Mon Sep 23 2002 - 10:26:11 PDT)
- Re: mm_pbsa output error Holger Gohlke (Mon Sep 23 2002 - 21:21:30 PDT)
- watershell in ptraj Michael Trieb (Tue Sep 24 2002 - 02:03:49 PDT)
  - expression of V(lambda) in GIBBS hagop demirdjian (Tue Sep 24 2002 - 05:44:02 PDT)
    - Re: expression of V(lambda) in GIBBS David A. Case (Tue Sep 24 2002 - 07:14:01 PDT)
  - Re: watershell in ptraj Thomas Cheatham (Tue Sep 24 2002 - 12:28:09 PDT)
  - ambpdb? Arvid Soederhaell (Wed Sep 25 2002 - 00:38:34 PDT)
    - Re: ambpdb? Lepsa (Wed Sep 25 2002 - 01:29:25 PDT)
    - ptraj - BONDS_WITHOUT_HYDROGEN Sophia Kondratova (Wed Sep 25 2002 - 09:54:48 PDT)
    - (no subject) Apostoluk, Wlodzimierz K (Wed Sep 25 2002 - 12:09:53 PDT)
    - Re: your mail David A. Case (Mon Sep 30 2002 - 09:35:06 PDT)
    - compiling amber 7 with Intel Fortran Compiler 6.0 ramon kleber da rocha (Wed Sep 25 2002 - 12:23:21 PDT)
    - Re: compiling amber 7 with Intel Fortran Compiler 6.0 Scott Brozell (Wed Sep 25 2002 - 13:05:45 PDT)
    - compiling amber 7 with Intel Fortran Compiler 6.0 (fwd) John Bushnell (Wed Sep 25 2002 - 13:10:50 PDT)
    - Re: compiling amber 7 with Intel Fortran Compiler 6.0 James W. Caldwell (Wed Sep 25 2002 - 13:16:48 PDT)
    - Re: compiling amber 7 with Intel Fortran Compiler 6.0 James W. Caldwell (Wed Sep 25 2002 - 13:58:04 PDT)
    - Question about Antechamber Masaki Tomimoto (Wed Sep 25 2002 - 14:37:55 PDT)
    - Re: Question about Antechamber David A. Case (Thu Sep 26 2002 - 08:28:51 PDT)
    - mm_pbsa and statistic program Pascal Bonnet (Thu Sep 26 2002 - 03:50:52 PDT)
    - Re: mm_pbsa and statistic program David A. Case (Thu Sep 26 2002 - 08:37:15 PDT)
    - Torsion driving ch cureton (Thu Sep 26 2002 - 09:00:34 PDT)
    - Question on Antechamber paper Nicholson, James D Mr ARO (Thu Sep 26 2002 - 10:18:17 PDT)
    - Amber Reflector James W. Caldwell (Thu Sep 26 2002 - 10:47:58 PDT)
    - Constant pressure equilibration in a system with a solvent cap dianah_at_unm.edu (Thu Sep 26 2002 - 18:04:38 PDT)
    - Re: Constant pressure equilibration in a system with a solvent cap James W. Caldwell (Fri Sep 27 2002 - 06:54:46 PDT)
    - nmanal help request Peter Fojan (Fri Sep 27 2002 - 06:59:11 PDT)
    - Re: nmanal help request David A. Case (Fri Sep 27 2002 - 08:38:23 PDT)
    - Re: Constant pressure equilibration in a system with a solvent cap David A. Case (Fri Sep 27 2002 - 08:26:09 PDT)
    - Re: Constant pressure equilibration in a system with a solvent cap David Smith (Fri Sep 27 2002 - 09:11:19 PDT)
    - MM-PBSA basics Michael Ford (Fri Sep 27 2002 - 12:53:01 PDT)
    - Re: MM-PBSA basics Holger Gohlke (Sun Sep 29 2002 - 19:44:52 PDT)
    - Re: MM-PBSA basics Lepsa (Mon Sep 30 2002 - 00:13:16 PDT)
    - groups in targeted md Christoph Brockmann (Mon Sep 30 2002 - 06:15:10 PDT)
    - Re: groups in targeted md Carlos Simmerling (Mon Sep 30 2002 - 07:04:26 PDT)
    - Re: groups in targeted md Christoph Brockmann (Mon Sep 30 2002 - 07:48:16 PDT)
    - Amber 7 and 6 topology files. Miguel de Federico (Mon Sep 30 2002 - 08:08:36 PDT)
    - Re: Amber 7 and 6 topology files. James W. Caldwell (Mon Sep 30 2002 - 08:41:25 PDT)
    - BondEn shoots in solvent minimization suvendu lomash (Mon Sep 30 2002 - 08:50:39 PDT)
    - write problem on IBM-AIX Giovanni Fossati (Mon Sep 30 2002 - 08:51:54 PDT)
    - Re: write problem on IBM-AIX Nicolas Grima (Tue Oct 01 2002 - 02:40:07 PDT)
    - Image charges with the solvate cap command dkeller_at_unm.edu (Mon Sep 30 2002 - 08:52:11 PDT)
    - Re: Image charges with the solvate cap command David A. Case (Mon Sep 30 2002 - 17:34:28 PDT)
    - MD Primers Joel Konkle-Parker (Fri Sep 27 2002 - 12:54:03 PDT)
    - Re: MD Primers Peter Gannett (Fri Sep 27 2002 - 16:34:40 PDT)
    - Request for help with Antechamber Nicholson, James D Mr ARO (Fri Sep 27 2002 - 16:58:58 PDT)
    - Re: Request for help with Antechamber David A. Case (Fri Sep 27 2002 - 17:54:21 PDT)
    - Re: Request for help with Antechamber James W. Caldwell (Fri Sep 27 2002 - 22:54:24 PDT)
    - question about using 10-12 in amber7/sander. Margaret Cheung (Sat Sep 28 2002 - 12:53:56 PDT)
    - Re: question about using 10-12 in amber7/sander. Margaret Cheung (Sat Sep 28 2002 - 13:35:48 PDT)
    - parameters for sugars A.Madhumalar (Sun Sep 29 2002 - 09:30:36 PDT)
    - Re: parameters for sugars Elsa de Sousa Henriques (Mon Sep 30 2002 - 09:42:24 PDT)
    - Problems with poly(A)-poly(T) tutorial... Andrei Leit�o (Mon Sep 30 2002 - 12:55:53 PDT)
    - Partial charge generation RESP/antechamber James W. Caldwell (Mon Sep 30 2002 - 15:27:37 PDT)
    - divalent cations parameters Apostoluk, Wlodzimierz K (Mon Sep 30 2002 - 15:38:11 PDT)
    - RE: Request for help with Antechamber Nicholson, James D Mr ARO (Fri Sep 27 2002 - 18:00:37 PDT)
    - Is H-bonding really there? suvendu lomash (Fri Sep 27 2002 - 12:59:48 PDT)
    - Re: Is H-bonding really there? Thomas Cheatham (Fri Sep 27 2002 - 13:53:24 PDT)
    - Re: Is H-bonding really there? Pratul Agarwal (Fri Sep 27 2002 - 13:58:25 PDT)
    - Re: Is H-bonding really there? Ioana Cozmuta (Fri Sep 27 2002 - 15:04:37 PDT)
    - Anal Error : Group Lifeng Tian (Fri Sep 27 2002 - 15:35:23 PDT)
    - Re: Is H-bonding really there? Ioana Cozmuta (Tue Oct 01 2002 - 14:44:55 PDT)
    - Questions on crosslinking residues Nicholson, James D Mr ARO (Tue Oct 01 2002 - 14:59:19 PDT)
    - Re: Questions on crosslinking residues David A. Case (Wed Oct 02 2002 - 16:34:47 PDT)
    - RE: Questions on crosslinking residues Nicholson, James D Mr ARO (Wed Oct 02 2002 - 18:03:47 PDT)
    - Re: Questions on crosslinking residues M. L. Dodson (Thu Oct 03 2002 - 05:42:08 PDT)
    - RESP gaussian job crashing Nicholson, James D Mr ARO (Wed Oct 02 2002 - 18:22:59 PDT)
    - Re: RESP gaussian job crashing James W. Caldwell (Thu Oct 03 2002 - 07:04:59 PDT)
    - RE: RESP gaussian job crashing Nicholson, James D Mr ARO (Thu Oct 03 2002 - 14:57:46 PDT)
    - Re: RESP gaussian job crashing Carlos P. Sosa (Thu Oct 03 2002 - 15:39:59 PDT)
    - compiling SGI/mpi Ioana Cozmuta (Thu Oct 03 2002 - 18:16:38 PDT)
    - Re: compiling SGI/mpi David A. Case (Thu Oct 03 2002 - 18:50:11 PDT)
    - Re: compiling SGI/mpi Ioana Cozmuta (Thu Oct 03 2002 - 20:09:02 PDT)
    - Re: compiling SGI/mpi David A. Case (Fri Oct 04 2002 - 08:07:23 PDT)
    - NTX / IREST inconsistency Bimo Ario Tejo (Fri Oct 04 2002 - 08:11:59 PDT)
    - Re: NTX / IREST inconsistency David A. Case (Fri Oct 04 2002 - 08:35:07 PDT)
    - RMSD calculation question Soonmin Jang (Fri Oct 04 2002 - 00:02:37 PDT)
    - Re: RESP gaussian job crashing David Smith (Fri Oct 04 2002 - 05:08:53 PDT)
    - Re: Questions on crosslinking residues David A. Case (Thu Oct 03 2002 - 08:04:18 PDT)
    - antechamber web page Ioana Cozmuta (Tue Oct 01 2002 - 15:33:36 PDT)
    - Re: antechamber web page David A. Case (Tue Oct 01 2002 - 16:00:33 PDT)
    - tutorial on plastocyanin Ioana Cozmuta (Tue Oct 01 2002 - 23:04:37 PDT)
    - Re: tutorial on plastocyanin David A. Case (Wed Oct 02 2002 - 07:48:27 PDT)
    - restart without velocities Michal Otyepka (Wed Oct 02 2002 - 00:39:02 PDT)
    - Re: restart without velocities Sanjeev B.S. (Wed Oct 02 2002 - 00:44:57 PDT)
    - different counterions for special type of DNA Vlad Cojocaru (Thu Sep 26 2002 - 05:59:31 PDT)
    - RMSD for heavy atoms only Pratul Agarwal (Wed Sep 25 2002 - 13:54:45 PDT)
    - sander_classic: Recompile without ISTAR2 Mahadevan Seetharaman (Wed Sep 25 2002 - 12:53:59 PDT)
    - ISTAR2 - oops, just found the answer... Mahadevan Seetharaman (Wed Sep 25 2002 - 12:55:46 PDT)
antechamber best practices/charge equivalence w/ AM1-BCC Tom Bishop (Mon Sep 23 2002 - 14:28:57 PDT)
- RE: antechamber best practices/charge equivalence w/ AM1-BCC Bayly, Christopher (Tue Sep 24 2002 - 07:49:56 PDT)
- Mopac509mn/linux James W. Caldwell (Tue Sep 24 2002 - 08:00:20 PDT)
Re: GB tutorial David A. Case (Thu Sep 26 2002 - 08:31:19 PDT)
RE:SAMUEL METU sam_008_at_www.com (Thu Oct 03 2002 - 18:46:50 PDT)
- RE:SAMUEL METU sam_008_at_www.com (Thu Oct 03 2002 - 18:46:51 PDT)
Re: About the Memory allocation in MM_PBSA and SANDER Alan Leo (Fri Oct 04 2002 - 05:46:15 PDT)
Different numbers on different architectures. David Smith (Fri Oct 04 2002 - 06:33:24 PDT)
- Re: Different numbers on different architectures. David A. Case (Fri Oct 04 2002 - 09:26:07 PDT)
solved: nmr and positional restraint in input Peter Varnai (Thu Oct 10 2002 - 08:26:27 PDT)
[Fwd: Re: trouble with snapshots GC option of MM_PBSA] Holger Gohlke (Thu Oct 10 2002 - 09:15:39 PDT)
IBELLY and NMROPT in sander Tom Bishop (Thu Oct 10 2002 - 09:54:43 PDT)
Dielectric constant for interior of proteins Pratul Agarwal (Thu Oct 10 2002 - 10:53:59 PDT)
- Re: Dielectric constant for interior of proteins David A. Case (Thu Oct 10 2002 - 11:33:19 PDT)
  - Re: Dielectric constant for interior of proteins Pratul Agarwal (Thu Oct 10 2002 - 12:25:51 PDT)
  - How to do 2dRMS in ptraj Ying Zhao (Thu Oct 10 2002 - 12:33:43 PDT)
  - question about antibodies Ioana Cozmuta (Thu Oct 10 2002 - 13:05:25 PDT)
  - Some error message on Leap Sichun Yang (Thu Oct 10 2002 - 13:15:43 PDT)
    - Re: Some error message on Leap Michael Ford (Thu Oct 10 2002 - 14:27:03 PDT)
    - Re: Some error message on Leap Ioana Cozmuta (Thu Oct 10 2002 - 15:22:51 PDT)
    - docking in amber? Sichun Yang (Thu Oct 10 2002 - 16:44:45 PDT)
    - problem in sander Ioana Cozmuta (Thu Oct 10 2002 - 19:11:06 PDT)
    - Re: problem in sander David A. Case (Fri Oct 11 2002 - 08:00:53 PDT)
    - volume of ucell too big!! sxzheng (Fri Oct 11 2002 - 08:06:52 PDT)
    - period boundary Shunzhou Wan (Fri Oct 11 2002 - 08:50:39 PDT)
    - DNA Tutorial: min_ntr.in Joel Konkle-Parker (Fri Oct 11 2002 - 15:28:47 PDT)
    - perturbation of gln to glu M. L. Dodson (Sun Oct 13 2002 - 17:02:00 PDT)
Re: reg: MAC OS David A. Case (Mon Oct 21 2002 - 09:11:56 PDT)
- Re: reg: MAC OS Mengjuei Hsieh (Mon Oct 21 2002 - 11:13:35 PDT)
- question on ouput of sander Sichun Yang (Mon Oct 21 2002 - 11:19:17 PDT)
  - Re: question on ouput of sander CUI, Guanglei (Mon Oct 21 2002 - 11:43:40 PDT)
  - Re: question on ouput of sander Sichun Yang (Mon Oct 21 2002 - 11:45:29 PDT)
  - Re: question on ouput of sander David A. Case (Mon Oct 21 2002 - 11:59:27 PDT)
  - sander7: MPI_COMM_RANK problem Matteo Dal Peraro (Mon Oct 21 2002 - 12:17:14 PDT)
    - systems.Re: sander7: MPI_COMM_RANK problem Carlos P. Sosa (Mon Oct 21 2002 - 12:44:56 PDT)
    - problem with gibbs !!!! Asif Rahaman (Mon Oct 21 2002 - 19:18:10 PDT)
    - Re: problem with gibbs !!!! James W. Caldwell (Tue Oct 22 2002 - 07:34:23 PDT)
    - MM-PGBSA Question!! Bernd Wellenzohn (Tue Oct 22 2002 - 05:46:29 PDT)
    - Re: MM-PGBSA Question!! Lepsa (Sat Dec 22 2001 - 06:46:53 PST)
    - About :ERROR TERMINATION DUE TO SHAKE OR TORCON sxzheng (Sun Dec 30 2001 - 19:24:17 PST)
    - Re: MM-PGBSA Question!! David A. Case (Tue Oct 22 2002 - 07:45:20 PDT)
    - Amber Crd format Tod Pascal (Tue Oct 22 2002 - 11:21:05 PDT)
    - Re: Amber Crd format Natasja Brooijmans (Tue Oct 22 2002 - 12:04:43 PDT)
    - mm_pbsa-amber7 Sue Heavner (Tue Oct 22 2002 - 12:06:01 PDT)
    - replacing fft routines Florian Barth (Tue Oct 22 2002 - 13:08:14 PDT)
    - Re: replacing fft routines David A. Case (Tue Oct 22 2002 - 15:58:34 PDT)
    - Dummy atoms... Miguel de Federico (Wed Oct 23 2002 - 00:44:34 PDT)
    - Re: Dummy atoms... David A. Case (Wed Oct 23 2002 - 09:35:31 PDT)
    - Amber6 and MPI Yu Chen (Wed Oct 23 2002 - 11:10:30 PDT)
    - Antechamber generating bad charges w/ gaussian 98. Nicholson, James D Mr ARO (Wed Oct 23 2002 - 14:50:56 PDT)
    - Re: Antechamber generating bad charges w/ gaussian 98. James W. Caldwell (Wed Oct 23 2002 - 16:16:05 PDT)
    - min output Ioana Cozmuta (Wed Oct 23 2002 - 16:26:44 PDT)
    - Re: min output David A. Case (Wed Oct 23 2002 - 16:51:06 PDT)
    - Re: min output James W. Caldwell (Thu Oct 24 2002 - 09:01:15 PDT)
    - RE: Antechamber generating bad charges w/ gaussian 98. Nicholson, James D Mr ARO (Wed Oct 23 2002 - 19:00:47 PDT)
    - Protein jump out, please help Lich Nguyen (Thu Oct 24 2002 - 02:45:45 PDT)
    - Re: Protein jump out, please help Michael G Cooney (Thu Oct 24 2002 - 11:51:52 PDT)
    - carnal output trajectory Vlad Cojocaru (Thu Oct 24 2002 - 13:07:35 PDT)
    - Re: carnal output trajectory Margaret Cheung (Thu Oct 24 2002 - 13:57:50 PDT)
    - residue cross-correlation Bimo Ario Tejo (Thu Oct 24 2002 - 14:15:50 PDT)
    - Re: Protein jump out, please help Lich Nguyen (Thu Oct 24 2002 - 20:21:40 PDT)
    - RE: Antechamber generating bad charges w/ gaussian 98. Nicholson, James D Mr ARO (Wed Oct 23 2002 - 19:12:32 PDT)
    - SDS forcefield? Arvid Soederhaell (Thu Oct 24 2002 - 02:25:58 PDT)
  - scaling of amber with number of atoms Marcela Madrid (Mon Oct 21 2002 - 12:23:59 PDT)
Re: Patching AMBER7 with #24 Lepsa (Wed Oct 23 2002 - 00:49:07 PDT)
- Re: Patching AMBER7 with #24 Lepsa (Wed Oct 23 2002 - 08:23:14 PDT)
Re: HIS residues Ioana Cozmuta (Thu Oct 24 2002 - 14:51:40 PDT)
- Re: HIS residues Natasja Brooijmans (Thu Oct 24 2002 - 16:09:55 PDT)
carnal output trajectory Vlad Cojocaru (Fri Oct 25 2002 - 02:50:55 PDT)
Re:SURFTEN for GB Lepsa (Fri Oct 25 2002 - 06:51:30 PDT)
- Fw: Re:SURFTEN for GB Lepsa (Fri Oct 25 2002 - 06:55:12 PDT)
- once again: residue cross-correlation Bimo Ario Tejo (Fri Oct 25 2002 - 07:39:40 PDT)
- time correlation function Bimo Ario Tejo (Fri Oct 25 2002 - 07:47:28 PDT)
  - Re: time correlation function David A. Case (Thu Oct 31 2002 - 07:21:28 PST)
  - *.top file: "PARM-F-UHOSED, try again" david (Thu Oct 31 2002 - 09:17:18 PST)
    - Re: *.top file: "PARM-F-UHOSED, try again" David A. Case (Thu Oct 31 2002 - 09:19:06 PST)
    - Re: *.top file: "PARM-F-UHOSED, try again" Michael Ford (Thu Oct 31 2002 - 09:43:10 PST)
    - carnal Ioana Cozmuta (Thu Oct 31 2002 - 10:30:35 PST)
    - Re: carnal St�phane Teletch�a (Mon Nov 04 2002 - 02:09:10 PST)
    - periodic box Craig A Bayse (Mon Nov 04 2002 - 08:49:53 PST)
    - Re: periodic box Peter Gannett (Sat Jul 27 2002 - 07:41:50 PDT)
    - sander crash K.Seshadri (Mon Jul 29 2002 - 01:40:57 PDT)
    - parallel jobs die with no error message from sander lamon_at_lav.Boehringer-Ingelheim.com (Mon Jul 29 2002 - 10:48:20 PDT)
    - Re: parallel jobs die with no error message from sander Scott Brozell (Mon Jul 29 2002 - 15:43:51 PDT)
    - Re: parallel jobs die with no error message from sander Joffre Heredia (Mon Jul 29 2002 - 21:06:33 PDT)
    - Re: parallel jobs die with no error message from sander jim caldwell (Mon Jul 29 2002 - 13:08:50 PDT)
    - Re: parallel jobs die with no error message from sander Joffre Heredia (Tue Jul 30 2002 - 10:46:37 PDT)
    - Error decoding variable Rukman Hertadi (Wed Jul 31 2002 - 03:52:02 PDT)
    - Re: Error decoding variable Carlos Simmerling (Wed Jul 31 2002 - 05:37:46 PDT)
    - Re: Error decoding variable jim caldwell (Wed Jul 31 2002 - 07:43:56 PDT)
    - Re: Error decoding variable Carlos Simmerling (Wed Jul 31 2002 - 08:41:04 PDT)
    - Re: Error decoding variable Rukman Hertadi (Wed Jul 31 2002 - 18:50:27 PDT)
    - problem with amber7 mpi Bimo Ario Tejo (Thu Aug 01 2002 - 03:50:32 PDT)
    - Re: problem with amber7 mpi Carlos Simmerling (Thu Aug 01 2002 - 05:34:43 PDT)
    - Re: problem with amber7 mpi Shixiang Yan (Thu Aug 01 2002 - 06:29:58 PDT)
    - Potential Energy and RMS-Deviation Issues mdk7p_at_cms.mail.virginia.edu (Thu Aug 01 2002 - 08:01:07 PDT)
    - Re: Potential Energy and RMS-Deviation Issues CUI, Guanglei (Thu Aug 01 2002 - 08:38:36 PDT)
    - Re: Potential Energy and RMS-Deviation Issues Thomas Cheatham (Thu Aug 01 2002 - 09:08:09 PDT)
    - Re: Potential Energy and RMS-Deviation Issues David A. Case (Thu Aug 01 2002 - 09:25:57 PDT)
    - file Cozmuta (Thu Aug 01 2002 - 10:24:13 PDT)
    - Re: file David A. Case (Thu Aug 01 2002 - 13:46:52 PDT)
    - proton_info/PS Cozmuta (Thu Aug 01 2002 - 10:29:02 PDT)
    - Using the new2oldparm command dianah_at_unm.edu (Thu Aug 01 2002 - 13:18:32 PDT)
    - Re: Using the new2oldparm command Holger Gohlke (Thu Aug 01 2002 - 13:52:23 PDT)
    - RE: Using the new2oldparm command Karen Haskell (Thu Aug 01 2002 - 13:55:28 PDT)
    - MD on cytochrome Mahadevan Seetharaman (Thu Aug 01 2002 - 14:15:52 PDT)
    - Solvated DNA using Amber 7 Nicholson, James D Mr ARO (Thu Aug 01 2002 - 14:32:13 PDT)
    - Re: Using the new2oldparm command Pascal Bonnet (Fri Aug 02 2002 - 01:17:54 PDT)
    - reorder water with nmropt Peter Varnai (Fri Aug 02 2002 - 05:24:59 PDT)
    - Re: reorder water with nmropt David A. Case (Fri Aug 02 2002 - 09:01:22 PDT)
    - look for benchmark with myrinet vs. 100-BT Jianhui Wu (Fri Aug 02 2002 - 10:15:29 PDT)
    - Re: look for benchmark with myrinet vs. 100-BT Margaret Cheung (Fri Aug 02 2002 - 11:20:22 PDT)
    - FWD: RE: Including explicit waters in GB dynamics Kristina Furse (Fri Aug 02 2002 - 13:32:52 PDT)
    - igb=2 in amber7 Randy M. Wadkins (Fri Aug 02 2002 - 15:28:48 PDT)
    - water box-nonperiodic Cozmuta (Fri Aug 02 2002 - 20:14:35 PDT)
    - Re: water box-nonperiodic David Case (Fri Aug 02 2002 - 22:16:18 PDT)
    - Benchmarks Sanjeev B.S. (Fri Aug 02 2002 - 22:48:09 PDT)
    - Please give me a hand on understanding AMBER/MPI and locmem. Margaret Cheung (Fri Aug 02 2002 - 23:49:46 PDT)
    - Re: Please give me a hand on understanding AMBER/MPI and locmem. David Case (Sat Aug 03 2002 - 13:02:42 PDT)
    - Re: Please give me a hand on understanding AMBER/MPI and locmem. Margaret Cheung (Sat Aug 03 2002 - 15:23:50 PDT)
    - Generalized Born and OPLS potential Soonmin Jang (Sat Aug 03 2002 - 01:05:27 PDT)
    - Re: Generalized Born and OPLS potential David A. Case (Mon Aug 05 2002 - 08:51:30 PDT)
    - Amber trajectory movies in Powerpoint mdk7p_at_cms.mail.virginia.edu (Tue Aug 06 2002 - 08:53:39 PDT)
    - Re: Amber trajectory movies in Powerpoint Cozmuta (Tue Aug 06 2002 - 11:25:31 PDT)
    - am1-bcc charges Sophia Kondratova (Tue Aug 06 2002 - 11:26:22 PDT)
    - Re: am1-bcc charges David A. Case (Tue Aug 06 2002 - 12:32:12 PDT)
    - Leap error: PDB file with more than 10000 residues Pratul Agarwal (Tue Aug 06 2002 - 12:50:04 PDT)
    - Re: Leap error: PDB file with more than 10000 residues David A. Case (Tue Aug 06 2002 - 14:13:30 PDT)
    - Re: Leap error: PDB file with more than 10000 residues Pratul Agarwal (Tue Aug 06 2002 - 14:47:00 PDT)
    - Re: Leap error: PDB file with more than 10000 residues jim caldwell (Tue Aug 06 2002 - 14:57:34 PDT)
    - charges Cozmuta (Tue Aug 06 2002 - 16:24:14 PDT)
    - Re: charges David A. Case (Wed Aug 07 2002 - 18:35:07 PDT)
    - Re: charges-again Cozmuta (Wed Aug 07 2002 - 18:47:14 PDT)
    - mpich, I/O, Master node, filesystem Jianhui Wu (Wed Aug 07 2002 - 21:24:13 PDT)
    - Re: mpich, I/O, Master node, filesystem David Case (Wed Aug 07 2002 - 22:14:25 PDT)
    - nmode segmentation fault zhongh_at_umich.edu (Thu Aug 08 2002 - 06:56:08 PDT)
    - Re: nmode segmentation fault Holger Gohlke (Thu Aug 08 2002 - 11:16:11 PDT)
    - Re: nmode segmentation fault Haizhen Zhong (Fri Aug 09 2002 - 06:46:19 PDT)
    - problems runing gibbs on a IBM SP2 machine ramon kleber da rocha (Fri Aug 09 2002 - 07:48:11 PDT)
    - Re: nmode segmentation fault jim caldwell (Thu Aug 08 2002 - 11:21:03 PDT)
    - Gentoo vs. Redhat Linux, shared/distributed filesystem Jianhui Wu (Thu Aug 08 2002 - 12:44:53 PDT)
    - protonation pH dependent Cozmuta (Thu Aug 08 2002 - 14:14:46 PDT)
    - Re: protonation pH dependent David A. Case (Thu Aug 08 2002 - 15:05:25 PDT)
    - LINMIN failure during minimization Giulio Rastelli (Fri Aug 09 2002 - 01:46:18 PDT)
    - Re: LINMIN failure during minimization David A. Case (Fri Aug 09 2002 - 09:09:09 PDT)
    - namelist error with sander Andreas Kerzmann (Fri Aug 09 2002 - 01:47:53 PDT)
    - Re: namelist error with sander David A. Case (Fri Aug 09 2002 - 08:50:27 PDT)
    - Re: namelist error with sander Andreas Kerzmann (Mon Aug 12 2002 - 05:40:12 PDT)
    - Constant pressure MD problems (sander) Pratul Agarwal (Mon Aug 12 2002 - 07:45:15 PDT)
    - Re: Constant pressure MD problems (sander) David A. Case (Mon Aug 12 2002 - 08:47:10 PDT)
    - Memory and swap in sander William Wei (Mon Aug 12 2002 - 08:11:35 PDT)
    - Re: Memory and swap in sander David A. Case (Mon Aug 12 2002 - 08:55:55 PDT)
    - Compiling Amber7 for a multiprocessor SUN Ultra-Sparc system. jeff dyason (Wed Aug 07 2002 - 21:45:49 PDT)
    - Re: Compiling Amber7 for a multiprocessor SUN Ultra-Sparc system. Sanjeev B.S. (Wed Aug 07 2002 - 21:46:08 PDT)
    - Re: Amber trajectory movies in Powerpoint Elsa de Sousa Henriques (Tue Aug 06 2002 - 18:58:15 PDT)
    - (no subject) Giulio Rastelli (Wed Aug 07 2002 - 02:07:21 PDT)
    - Re: your mail darden (Wed Aug 07 2002 - 04:58:17 PDT)
    - SHAKE problem Rosalia Pascual (Wed Aug 07 2002 - 08:13:12 PDT)
    - Re: SHAKE problem Pratul Agarwal (Wed Oct 09 2002 - 06:39:55 PDT)
    - nmr and positional restraint in input Peter Varnai (Wed Oct 09 2002 - 10:44:03 PDT)
    - Re: nmr and positional restraint in input Christoph Brockmann (Thu Oct 10 2002 - 02:12:49 PDT)
    - MM-PBSA tutorial Giulio Rastelli (Thu Oct 10 2002 - 07:22:59 PDT)
    - Re: MM-PBSA tutorial Holger Gohlke (Thu Oct 10 2002 - 11:57:41 PDT)
    - Re: MM-PBSA tutorial Lepsa (Mon Oct 14 2002 - 00:14:47 PDT)
    - MM-PBSA and Insight's version of Delphi Emma.Sigfridsson_at_astrazeneca.com (Mon Oct 14 2002 - 00:47:21 PDT)
    - pressure variation coupled with taup value Vlad Cojocaru (Mon Oct 14 2002 - 02:36:42 PDT)
    - loss of disulfide bonds Nicolas Le Novere (Mon Oct 14 2002 - 08:31:23 PDT)
    - Re: loss of disulfide bonds Holger Gohlke (Mon Oct 14 2002 - 08:51:01 PDT)
    - Re: loss of disulfide bonds David A. Case (Mon Oct 14 2002 - 09:04:30 PDT)
    - Re: loss of disulfide bonds Natasja Brooijmans (Mon Oct 14 2002 - 09:46:54 PDT)
    - Re: loss of disulfide bonds Carlos Simmerling (Mon Oct 14 2002 - 09:49:15 PDT)
    - Re: loss of disulfide bonds James W. Caldwell (Mon Oct 14 2002 - 10:28:15 PDT)
    - Re: loss of disulfide bonds Richard Henchman (Mon Oct 14 2002 - 10:44:30 PDT)
    - Re: loss of disulfide bonds David A. Case (Mon Oct 14 2002 - 11:10:50 PDT)
    - Potential bug in gbsa.h of sander-7 Vlad (Mon Oct 14 2002 - 17:35:58 PDT)
    - Compiler & Hardware requirement of AMBER7 ? yuann (Mon Oct 14 2002 - 21:08:12 PDT)
    - Re: Compiler & Hardware requirement of AMBER7 ? David Case (Mon Oct 14 2002 - 22:51:43 PDT)
    - Re: Compiler & Hardware requirement of AMBER7 ? yuann (Tue Oct 22 2002 - 07:30:34 PDT)
    - Computational alchemy Aldo Jongejan (Tue Oct 15 2002 - 03:52:12 PDT)
    - Dummy torsions Aldo Jongejan (Tue Oct 15 2002 - 06:33:02 PDT)
    - Re: Dummy torsions David A. Case (Tue Oct 15 2002 - 08:25:41 PDT)
    - bug fixes Filip Lankas (Thu Dec 05 2002 - 06:48:00 PST)
    - Re: bug fixes David A. Case (Thu Dec 05 2002 - 08:41:02 PST)
    - not compiled with -DHAS_10_12!! William Wei (Thu Dec 05 2002 - 08:29:22 PST)
    - Re: not compiled with -DHAS_10_12!! Sarah Tschampel (Thu Dec 05 2002 - 08:43:40 PST)
    - Re: not compiled with -DHAS_10_12!! Carlos Simmerling (Thu Dec 05 2002 - 09:03:08 PST)
    - md failure: deep energetics problem eric hu (Thu Dec 05 2002 - 10:42:42 PST)
    - Re: md failure: deep energetics problem David A. Case (Thu Dec 05 2002 - 11:55:40 PST)
    - ptraj rmsd calculation Thomas Steinbrecher (Thu Dec 05 2002 - 12:15:40 PST)
    - Overwrite files Joffre Heredia (Thu Dec 05 2002 - 12:25:33 PST)
    - Re: Overwrite files Long Hai (Thu Dec 05 2002 - 13:33:53 PST)
    - RE: Overwrite files Yong Duan (Thu Dec 05 2002 - 18:41:37 PST)
    - timings? Arvid Soederhaell (Fri Dec 06 2002 - 00:51:10 PST)
    - Re: timings? David A. Case (Fri Dec 06 2002 - 07:46:27 PST)
    - positional restraints Vlad Cojocaru (Fri Dec 06 2002 - 04:55:05 PST)
    - Re: positional restraints David A. Case (Fri Dec 06 2002 - 08:05:02 PST)
    - Re: Overwrite files Scott Brozell (Thu Dec 05 2002 - 13:39:23 PST)
    - About counterions Andrei Leit�o (Thu Dec 05 2002 - 11:10:30 PST)
    - Re: About counterions David A. Case (Thu Dec 05 2002 - 11:47:04 PST)
    - Cap-atom-pointer in GIBBS Jose Ramon Blas (Thu Dec 05 2002 - 11:50:45 PST)
    - Re: Cap-atom-pointer in GIBBS James W. Caldwell (Thu Dec 05 2002 - 11:23:45 PST)
    - Error in Antechamber program in ammber7 Narang Manpreet Kaur (Tue Oct 15 2002 - 07:49:52 PDT)
    - Re: Error in Antechamber program in ammber7 Lepsa (Tue Oct 15 2002 - 08:07:57 PDT)
    - Re: Error in Antechamber program in ammber7 David A. Case (Tue Oct 15 2002 - 08:33:09 PDT)
    - Re: Error in Antechamber program in ammber7 Narang Manpreet Kaur (Tue Oct 15 2002 - 22:01:45 PDT)
    - Re: Error in Antechamber program in ammber7 David A. Case (Wed Oct 16 2002 - 08:04:40 PDT)
    - dummy parameters Pierre Mignon (Wed Oct 16 2002 - 00:10:46 PDT)
    - How to specify the counterion positions using xleap? A.Madhumalar (Wed Oct 16 2002 - 05:54:41 PDT)
    - Re: How to specify the counterion positions using xleap? David A. Case (Wed Oct 16 2002 - 08:09:21 PDT)
    - Re: How to specify the counterion positions using xleap? M. L. Dodson (Wed Oct 16 2002 - 17:10:22 PDT)
    - Can I use belly and ntr at the same time? sxzheng (Wed Oct 16 2002 - 08:21:10 PDT)
    - Re: Can I use belly and ntr at the same time? David A. Case (Wed Oct 16 2002 - 08:45:49 PDT)
    - Molecular Dynamic procedure... Andrei Leit�o (Wed Oct 16 2002 - 08:48:10 PDT)
    - How to convert oldparmtop to newparmtop? A.Madhumalar (Wed Oct 16 2002 - 10:18:35 PDT)
    - Re: How to convert oldparmtop to newparmtop? David A. Case (Wed Oct 16 2002 - 11:04:59 PDT)
    - Re: How to convert oldparmtop to newparmtop? Michael Ford (Wed Oct 16 2002 - 12:47:57 PDT)
    - Re: How to convert oldparmtop to newparmtop? A.Madhumalar (Thu Oct 17 2002 - 10:05:29 PDT)
    - sander6 running and crashing at PSC? CUI, Guanglei (Thu Oct 17 2002 - 10:17:40 PDT)
    - IGB =4 with GAFF and bugfix24 incomplete? Tom Bishop (Wed Oct 16 2002 - 11:12:37 PDT)
    - Re: IGB =4 with GAFF and bugfix24 incomplete? David A. Case (Wed Oct 16 2002 - 11:55:24 PDT)
    - syntax Ioana Cozmuta (Wed Oct 16 2002 - 11:14:54 PDT)
    - Re: syntax David A. Case (Wed Oct 16 2002 - 11:57:44 PDT)
    - error message Vlad Cojocaru (Wed Oct 16 2002 - 10:25:01 PDT)
    - Re: error message Holger Gohlke (Wed Oct 16 2002 - 10:38:34 PDT)
    - Re: error message Natasja Brooijmans (Wed Oct 16 2002 - 10:48:41 PDT)
    - Re: error message Margaret Cheung (Wed Oct 16 2002 - 10:56:50 PDT)
    - Re: confusing error messages David A. Case (Wed Oct 16 2002 - 11:42:15 PDT)
    - restraining atoms Ioana Cozmuta (Wed Oct 16 2002 - 10:56:10 PDT)
    - Re: restraining atoms Lepsa (Wed Oct 16 2002 - 23:56:17 PDT)
    - Re: restraining atoms Ioana Cozmuta (Thu Oct 17 2002 - 10:54:37 PDT)
    - Solvent exposed surface area over a trajectory Rebecca Perlow (Thu Oct 17 2002 - 11:20:03 PDT)
    - Re: Solvent exposed surface area over a trajectory Michael Ford (Thu Oct 17 2002 - 12:09:17 PDT)
    - Re: Solvent exposed surface area over a trajectory Sanjeev B.S. (Thu Oct 17 2002 - 12:18:56 PDT)
    - Reference for GB model 2 Jianhui Wu (Thu Oct 17 2002 - 12:26:18 PDT)
    - Re: Reference for GB model 2 Andreas Svrcek-Seiler (Thu Oct 17 2002 - 13:34:40 PDT)
    - cutoffs in GB David A. Case (Thu Oct 17 2002 - 14:08:16 PDT)
    - Carnal table output Christoph Brockmann (Fri Oct 18 2002 - 01:48:37 PDT)
    - Re: Carnal table output Holger Gohlke (Fri Oct 18 2002 - 08:20:57 PDT)
    - targeted MD Giulio Rastelli (Fri Oct 18 2002 - 07:28:48 PDT)
    - Re: targeted MD David A. Case (Fri Oct 18 2002 - 08:32:14 PDT)
    - Re: targeted MD Carlos Simmerling (Fri Oct 18 2002 - 08:45:33 PDT)
    - Re: targeted MD Peter VARNAI (Sat Oct 19 2002 - 07:26:30 PDT)
    - number of H-bonds Bimo Ario Tejo (Sat Oct 19 2002 - 21:54:44 PDT)
    - Re: number of H-bonds Sanjeev B.S. (Sat Oct 19 2002 - 22:14:32 PDT)
    - How to define a sphere to minimize? Guillermo Mulliert Carl�n (Sun Oct 20 2002 - 23:46:57 PDT)
    - Re: How to define a sphere to minimize? David Smith (Mon Oct 21 2002 - 04:00:03 PDT)
    - Re: How to define a sphere to minimize? Bill Ross (Mon Oct 21 2002 - 08:11:19 PDT)
    - Not able to use xleap ... St�phane Teletch�a (Fri Oct 18 2002 - 08:58:21 PDT)
    - Re: Not able to use xleap ... CUI, Guanglei (Fri Oct 18 2002 - 09:26:47 PDT)
    - Re: Not able to use xleap ... David A. Case (Fri Oct 18 2002 - 09:38:23 PDT)
    - Re: Not able to use xleap ... CUI, Guanglei (Fri Oct 18 2002 - 10:14:24 PDT)
    - RE: Not able to use xleap ... Ross Walker (Sat Oct 19 2002 - 02:51:30 PDT)
    - Re: Not able to use xleap ... St�phane Teletch�a (Mon Oct 21 2002 - 00:08:12 PDT)
    - Re: Not able to use xleap ... CUI, Guanglei (Mon Oct 21 2002 - 06:43:51 PDT)
    - Re: Not able to use xleap ... St�phane Teletch�a (Mon Oct 21 2002 - 08:02:25 PDT)
    - Re: Not able to use xleap ... CUI, Guanglei (Mon Oct 21 2002 - 08:33:23 PDT)
    - Re: Not able to use xleap ... St�phane Teletch�a (Fri Oct 18 2002 - 10:24:38 PDT)
    - allocation memory error Ioana Cozmuta (Fri Oct 18 2002 - 12:50:22 PDT)
    - Re: allocation memory error Ioana Cozmuta (Tue Oct 22 2002 - 14:52:56 PDT)
    - Amber 4 question Tod Pascal (Fri Oct 18 2002 - 15:42:40 PDT)
    - Sander segmentation fault Joel Konkle-Parker (Thu Oct 17 2002 - 12:28:48 PDT)
    - Reference, GB 2, Amber7 Jianhui Wu (Thu Oct 17 2002 - 12:34:12 PDT)
    - Re: Solvent exposed surface area over a trajectory Natasja Brooijmans (Thu Oct 17 2002 - 12:35:34 PDT)
    - time averaged restraint parameters Jake Isaacs (Thu Oct 17 2002 - 13:09:59 PDT)
    - Sir, Venkanna Belde (Thu Oct 17 2002 - 02:33:18 PDT)
    - Imaging & fitting in carnal Sanjeev B.S. (Thu Oct 17 2002 - 04:01:55 PDT)
    - Truncated Octahedron Box giudice (Thu Oct 17 2002 - 06:06:28 PDT)
    - a leap question Vlad Cojocaru (Thu Oct 17 2002 - 06:20:23 PDT)
    - Re: a leap question CUI, Guanglei (Thu Oct 17 2002 - 06:43:24 PDT)
    - Re: a leap question David A. Case (Thu Oct 17 2002 - 08:35:01 PDT)
    - dummy torsional parameters again. X. Tan (Thu Oct 17 2002 - 09:52:05 PDT)
    - Re: dummy torsional parameters again. David A. Case (Thu Oct 17 2002 - 10:58:38 PDT)
    - Re: error message Andreas Svrcek-Seiler (Wed Oct 16 2002 - 10:58:18 PDT)
    - Re: error message Bill Ross (Wed Oct 16 2002 - 12:22:44 PDT)
    - more information about the previous email Vlad Cojocaru (Wed Oct 16 2002 - 10:26:43 PDT)
    - Re: How to specify the counterion positions using xleap? James W. Caldwell (Wed Oct 16 2002 - 08:28:06 PDT)
    - Re: How to specify the counterion positions using xleap? Ioana Cozmuta (Wed Oct 16 2002 - 10:45:06 PDT)
    - Bug in reading binary restart file with BOX parameters Vlad (Tue Oct 15 2002 - 19:58:54 PDT)
    - Re: Bug in reading binary restart file with BOX parameters David A. Case (Wed Oct 16 2002 - 08:27:51 PDT)
    - new telescopes-Maksutov-Cassegrain, reflector, refractor wang lan (Tue Oct 15 2002 - 04:13:49 PDT)
    - new telescopes-Maksutov-Cassegrain, reflector, refractor wang lan (Tue Oct 15 2002 - 04:42:50 PDT)
    - CH2Cl2 box Eric ARNOULT (Mon Oct 14 2002 - 10:51:21 PDT)
    - trouble with snapshots GC option of MM_PBSA Michael Ford (Thu Oct 10 2002 - 07:23:24 PDT)
    - Re: trouble with snapshots GC option of MM_PBSA Michael Ford (Thu Oct 10 2002 - 07:31:05 PDT)
    - Re: trouble with snapshots GC option of MM_PBSA - Now no output for lig and rec Michael Ford (Thu Oct 10 2002 - 08:10:35 PDT)
    - reaction field energy of a ligand in MM-PBSA Giulio Rastelli (Wed Oct 09 2002 - 11:04:10 PDT)
    - Re: reaction field energy of a ligand in MM-PBSA Lepsa (Wed Oct 09 2002 - 06:19:56 PDT)
    - about dummy parameter of multiplicity sxzheng (Thu Oct 10 2002 - 00:55:15 PDT)
    - Re: about dummy parameter of multiplicity David A. Case (Thu Oct 10 2002 - 11:37:40 PDT)
    - Amber+Mosix Jianhui Wu (Wed Aug 07 2002 - 13:40:15 PDT)
    - RE: Amber+Mosix Ross Walker (Sun Aug 11 2002 - 14:33:04 PDT)
    - using belly with GB David A. Case (Wed Aug 07 2002 - 18:36:18 PDT)
    - PROTON_INFO Cozmuta (Fri Aug 02 2002 - 20:25:37 PDT)
    - Re: PROTON_INFO Qing Zhang (Sat Aug 03 2002 - 18:12:24 PDT)
    - Re: look for benchmark with myrinet vs. 100-BT C. Klein (Sun Aug 04 2002 - 01:21:29 PDT)
    - problems with parallel sander on linux clusters? David Case (Sun Aug 04 2002 - 11:34:20 PDT)
    - (no subject) sepideh ameli (Sun Aug 04 2002 - 12:01:20 PDT)
    - Import of CHARMM force field and GB potential parameters into Amber7 Soonmin Jang (Sun Aug 04 2002 - 19:19:20 PDT)
    - Re: Import of CHARMM force field and GB potential parameters into Amber7 David Case (Sun Aug 04 2002 - 22:25:28 PDT)
    - MD in alcohol Marc DOBLER (Sun Aug 04 2002 - 19:33:52 PDT)
    - Re: MD in alcohol David Case (Sun Aug 04 2002 - 22:31:40 PDT)
    - Re: MD in alcohol Marc DOBLER (Mon Aug 05 2002 - 01:46:17 PDT)
    - Information request - where to buy software Claire Edmonds (Mon Aug 05 2002 - 06:23:59 PDT)
    - distance restraint stuff Layi Adekoya (Thu Aug 01 2002 - 08:24:50 PDT)
    - Re: distance restraint stuff CUI, Guanglei (Thu Aug 01 2002 - 08:44:25 PDT)
    - dielectric constant for partialy solvated MD Miyashita, Osamu (Wed Jul 31 2002 - 11:55:58 PDT)
    - Re: dielectric constant for partialy solvated MD Carlos Simmerling (Wed Jul 31 2002 - 13:54:12 PDT)
    - Energies/coordinate files from mm_pbsa problem Peter Gannett (Tue Jul 30 2002 - 11:25:29 PDT)
    - Re: periodic box Thomas E. Cheatham, III (Wed Jul 31 2002 - 07:26:49 PDT)
    - Re: periodic box David A. Case (Mon Nov 04 2002 - 10:32:11 PST)
    - Visualizing AMBER coordinates trajectory in VMD Pratul Agarwal (Mon Nov 04 2002 - 12:54:57 PST)
    - Re: Visualizing AMBER coordinates trajectory in VMD David A. Case (Mon Nov 04 2002 - 13:57:10 PST)
    - Re: Visualizing AMBER coordinates trajectory in VMD Tom Bishop (Tue Nov 05 2002 - 03:36:41 PST)
    - restart Ioana Cozmuta (Mon Nov 04 2002 - 12:57:16 PST)
    - Re: restart David A. Case (Mon Nov 04 2002 - 13:59:15 PST)
    - RUNMIN hung_at_atc.atccu.chula.ac.th (Mon Nov 04 2002 - 17:04:23 PST)
    - Re: RUNMIN Ioana Cozmuta (Mon Nov 04 2002 - 17:37:08 PST)
    - procheck hung_at_atc.atccu.chula.ac.th (Mon Nov 04 2002 - 22:53:56 PST)
    - Re: procheck David A. Case (Tue Nov 05 2002 - 08:31:31 PST)
    - pseudoatoms and NMR restraints david (Tue Nov 05 2002 - 01:46:42 PST)
    - Re: pseudoatoms and NMR restraints David A. Case (Tue Nov 05 2002 - 08:06:07 PST)
    - P4_GLOBMEMSIZE problem Jean-Christophe Ducom (Mon Nov 04 2002 - 09:33:19 PST)
    - RE: P4_GLOBMEMSIZE problem Ross Walker (Tue Nov 05 2002 - 09:16:55 PST)
    - Re: P4_GLOBMEMSIZE problem Jean-Christophe Ducom (Tue Nov 05 2002 - 09:53:11 PST)
    - RE: P4_GLOBMEMSIZE problem Ross Walker (Tue Nov 05 2002 - 15:04:03 PST)
    - entropy calcs in mm_pbsa giulio_at_unimo.it (Tue Nov 05 2002 - 12:21:00 PST)
    - Re: entropy calcs in mm_pbsa Holger Gohlke (Tue Nov 05 2002 - 13:27:39 PST)
    - xleap and modified sugar residues Michael Ford (Thu Oct 31 2002 - 11:22:17 PST)
    - Re: xleap and modified sugar residues Holger Gohlke (Thu Oct 31 2002 - 11:54:23 PST)
    - NAV detected a virus in a document YOU sent to webmaster.nctimes.com. Mercury (Thu Oct 31 2002 - 19:12:51 PST)
    - flag TREE_CHAIN_CLASSIFICATION in topology file from amber7 Pascal Bonnet (Fri Nov 01 2002 - 01:08:20 PST)
    - Re: flag TREE_CHAIN_CLASSIFICATION in topology file from amber7 David A. Case (Fri Nov 01 2002 - 05:51:26 PST)
    - CCl4 as solvent Aldo Jongejan (Tue Nov 05 2002 - 05:44:02 PST)
    - Snapshot stuff Layi Adekoya (Tue Nov 05 2002 - 06:32:11 PST)
    - molsurf reference Giulio Rastelli (Fri Nov 01 2002 - 04:17:35 PST)
    - Re: molsurf reference David A. Case (Fri Nov 01 2002 - 05:46:21 PST)
- specification for memory requirement yuann (Fri Oct 25 2002 - 17:37:13 PDT)
  - Re: specification for memory requirement Carlos Simmerling (Fri Oct 25 2002 - 18:55:42 PDT)
  - 2nd restart CUI, Guanglei (Sun Oct 27 2002 - 09:02:30 PST)
  - total energies during MM-PBSA Giulio Rastelli (Sun Oct 27 2002 - 10:20:19 PST)
    - Re: total energies during MM-PBSA Lepsa (Fri Nov 01 2002 - 09:29:33 PST)
    - problem about cut and cap sxzheng (Sun Nov 03 2002 - 04:40:25 PST)
  - Amber vijay dasa (Sun Oct 27 2002 - 22:51:02 PST)
    - Re: Amber shailendra singh (Mon Mar 18 2002 - 21:57:48 PST)
    - minimization problem Uwe Richter (Tue Mar 19 2002 - 04:22:06 PST)
    - Re: minimization problem Andreas Svrcek-Seiler (Tue Mar 19 2002 - 05:33:19 PST)
    - carnal RST output format Pascal Bonnet (Tue Mar 19 2002 - 06:12:31 PST)
    - Re: carnal RST output format Bill Ross (Tue Mar 19 2002 - 11:32:36 PST)
    - Re: carnal RST output format Andy Purkiss (Tue Mar 19 2002 - 12:45:00 PST)
    - Amber6 & ES40 incompatability Sanjeev B.S. (Tue Mar 19 2002 - 23:01:17 PST)
    - building bcyd with tleap Itziar Maestre Asenjo (Wed Mar 20 2002 - 02:51:47 PST)
    - MM-PBSA philosophy Michal Otyepka (Wed Mar 20 2002 - 04:34:24 PST)
    - Re: MM-PBSA philosophy Felipe Pineda (Wed Mar 20 2002 - 06:25:05 PST)
    - Re: MM-PBSA philosophy David Case (Wed Mar 20 2002 - 08:10:05 PST)
    - Internal dielectric in MM-GBSA Robert J. Woods (Mon Feb 10 2003 - 11:29:36 PST)
    - Re: Internal dielectric in MM-GBSA David A. Case (Mon Feb 10 2003 - 12:29:44 PST)
    - AMBER mail reflector archive Jarrod Smith (Mon Feb 10 2003 - 12:37:09 PST)
    - RE: AMBER mail reflector archive Jianxin Guo (Thu Feb 15 2001 - 15:13:09 PST)
    - RE: AMBER mail reflector archive Bill Ross (Thu Feb 15 2001 - 15:47:31 PST)
    - force field problem Bayly, Christopher (Mon Feb 10 2003 - 12:01:37 PST)
    - Question about obtaining amber! Peter Fojan (Thu Mar 21 2002 - 05:19:59 PST)
    - MS program ... A. Ababou (Sat Mar 23 2002 - 08:21:15 PST)
    - Re: MS program ... Samantha (Sat Mar 23 2002 - 09:09:14 PST)
    - nmropt problem in AMBER7 Rukman Hertadi (Mon Mar 25 2002 - 01:51:22 PST)
    - Resending: Medicinal and Computational Chemistry Job Market Computational Chemistry Job Market (Mon Mar 25 2002 - 12:05:03 PST)
    - mdcrd to arc Ian R Bates (Sat Mar 23 2002 - 08:46:21 PST)
    - atom connection, .off file problem Uwe Richter (Wed Mar 20 2002 - 05:48:07 PST)
    - Still no bench St�phane Teletch�a (Tue Mar 19 2002 - 07:17:45 PST)
    - creating a unit wth xleap Marcela Madrid (Tue Mar 19 2002 - 11:07:30 PST)
    - Re: creating a unit wth xleap Bill Ross (Tue Mar 19 2002 - 11:43:25 PST)
    - leap - sander information flow Wiktor Jurkowski (Mon Oct 28 2002 - 04:34:51 PST)
    - Re: leap - sander information flow David A. Case (Mon Oct 28 2002 - 13:44:28 PST)
    - quasih Pratul Agarwal (Mon Oct 28 2002 - 14:25:02 PST)
    - Targeted MD Giulio Rastelli (Mon Oct 28 2002 - 13:44:05 PST)
    - Re: Targeted MD Carlos Simmerling (Mon Oct 28 2002 - 15:09:19 PST)
    - 64-bit Compilation SUN's forte compiler Fernando Martin (Mon Oct 28 2002 - 15:15:52 PST)
    - Re: 64-bit Compilation SUN's forte compiler Ioana Cozmuta (Mon Oct 28 2002 - 15:33:49 PST)
    - Re: 64-bit Compilation SUN's forte compiler Scott Brozell (Mon Oct 28 2002 - 16:00:08 PST)
    - Re: 64-bit Compilation SUN's forte compiler David A. Case (Mon Oct 28 2002 - 19:41:15 PST)
    - LEaP: The parm and coord files disagree on the number of atoms Miguel de Federico (Tue Oct 29 2002 - 00:24:58 PST)
    - Re: LEaP: The parm and coord files disagree on the number of atoms James W. Caldwell (Tue Oct 29 2002 - 07:50:26 PST)
    - mm_pbsa curious output of coordinates and resulting errors... Michael Ford (Tue Oct 29 2002 - 14:01:43 PST)
    - mm_pbsa error message (warning?) Michael Ford (Tue Oct 29 2002 - 14:47:02 PST)
    - Problems with tes.antechamber Chen, Ya (Tue Oct 29 2002 - 17:21:59 PST)
    - Resp Multiconformational charge fitting! Marco Aur�lio Correia Preto (Wed Oct 30 2002 - 03:50:52 PST)
    - Re: Resp Multiconformational charge fitting! Pascal Bonnet (Wed Dec 18 2002 - 02:21:46 PST)
    - carnal output trajectory Vlad Cojocaru (Wed Oct 30 2002 - 05:25:36 PST)
    - Re: carnal output trajectory Bill Ross (Thu Oct 24 2002 - 14:26:15 PDT)
    - Re: carnal output trajectory St�phane Teletch�a (Wed Oct 30 2002 - 05:50:19 PST)
    - Re: carnal output trajectory Sanjeev B.S. (Wed Oct 30 2002 - 05:50:45 PST)
    - Re: carnal output trajectory Francesca Mocci (Fri Nov 01 2002 - 08:53:31 PST)
    - Sander Recompilation for the Biotin-Streptavidin Tutorial? Thomas Steinbrecher (Wed Oct 30 2002 - 07:46:30 PST)
    - Re: carnal output trajectory Bill Ross (Wed Oct 30 2002 - 08:37:00 PST)
    - Charges derivation question! Marco Aur�lio Correia Preto (Wed Oct 30 2002 - 08:39:24 PST)
    - Fw: Charges derivation question! Lepsa (Wed Dec 11 2002 - 08:21:23 PST)
    - Fw: Fw: Charges derivation question! Lepsa (Thu Dec 12 2002 - 01:55:17 PST)
    - FEP - ligand to nothing (or water)?? Aldo Jongejan (Tue Oct 29 2002 - 01:50:54 PST)
    - Re: FEP - ligand to nothing (or water)?? David A. Case (Tue Oct 29 2002 - 06:24:47 PST)
    - RE: 64-bit Compilation SUN's forte compiler Fernando Martin (Mon Oct 28 2002 - 16:24:21 PST)
  - Hello Amber, vijay dasa (Mon Oct 28 2002 - 02:20:24 PST)
Re: equilibrium problem about cut and belly David A. Case (Tue Nov 05 2002 - 08:14:51 PST)
- Re: equilibrium problem about cut and belly Thomas Steinbrecher (Tue Nov 05 2002 - 09:24:54 PST)
torsion restraints in GIBBS Jose Ramon Blas (Tue Nov 05 2002 - 16:35:44 PST)
- Re: torsion restraints in GIBBS David A. Case (Tue Nov 05 2002 - 08:20:57 PST)
Bugfixes William Wei (Wed Nov 06 2002 - 01:50:35 PST)
average and runningaverage in ptraj Vlad Cojocaru (Wed Nov 06 2002 - 07:40:51 PST)
- Re: average and runningaverage in ptraj Holger Gohlke (Wed Nov 06 2002 - 08:56:23 PST)
- Re: average and runningaverage in ptraj Thomas Cheatham (Wed Nov 06 2002 - 09:36:56 PST)
- time-averaged restraint developer Jake Isaacs (Wed Nov 06 2002 - 14:20:11 PST)
- restrt format problem Marcela Madrid (Wed Nov 06 2002 - 14:48:02 PST)
- nbflag Ioana Cozmuta (Wed Nov 06 2002 - 19:19:26 PST)
- nbflag Ioana Cozmuta (Wed Nov 06 2002 - 19:45:02 PST)
surface Ioana Cozmuta (Thu Nov 07 2002 - 13:03:56 PST)
Re: amber on RH8 Scott Brozell (Thu Nov 07 2002 - 13:13:14 PST)
averaging with ptraj and carnal Vlad Cojocaru (Fri Nov 08 2002 - 04:31:03 PST)
ramdomized start velocities Arvid Soederhaell (Fri Nov 08 2002 - 04:35:23 PST)
- Re: ramdomized start velocities David A. Case (Fri Nov 08 2002 - 11:20:54 PST)
- Re: ramdomized start velocities Andy Purkiss (Fri Nov 08 2002 - 11:28:46 PST)
- Re: ramdomized start velocities James W. Caldwell (Fri Nov 08 2002 - 12:35:39 PST)
Sander: check COM velocity, temp: 0.000000 0.00(Removed) Miguel de Federico de la R�a (Fri Nov 08 2002 - 06:08:38 PST)
- Re: Sander: check COM velocity, temp: 0.000000 0.00(Removed) Thomas Cheatham (Fri Nov 08 2002 - 21:49:21 PST)
- MEP g98_option FyD (Fri Nov 08 2002 - 22:35:22 PST)
  - Re: MEP g98_option Pascal Bonnet (Mon Nov 11 2002 - 03:05:55 PST)
  - nonpeoridic boundary + mm/gbsa Yongjun Jiang (Mon Nov 11 2002 - 04:49:03 PST)
    - Re: nonpeoridic boundary + mm/gbsa Holger Gohlke (Mon Nov 11 2002 - 08:59:27 PST)
    - saveAmberParm of leap Sichun Yang (Mon Nov 11 2002 - 11:27:16 PST)
    - Re: saveAmberParm of leap David A. Case (Mon Nov 11 2002 - 16:05:15 PST)
- Re: Sander: check COM velocity, temp: 0.000000 0.00(Removed) David Case (Fri Nov 08 2002 - 23:17:18 PST)
more about averaging Vlad Cojocaru (Fri Nov 08 2002 - 06:12:00 PST)
- Re: more about averaging Bill Ross (Fri Nov 08 2002 - 13:21:39 PST)
- Problem in run Monica (Fri Nov 08 2002 - 20:41:52 PST)
  - Re: Problem in run David Case (Fri Nov 08 2002 - 23:33:27 PST)
    - Re: Problem in run Monica Jain (Fri Nov 08 2002 - 22:52:46 PST)
  - Forwarded mail.... Narang Manpreet Kaur (Sat Nov 09 2002 - 01:56:37 PST)
    - Re: Forwarded mail.... David A. Case (Sun Nov 10 2002 - 14:40:19 PST)
  - drifting from average structure Vlad Cojocaru (Sat Nov 09 2002 - 08:17:38 PST)
  - carnal7 produces memory fault and a core Giulio Rastelli (Sat Nov 09 2002 - 08:21:10 PST)
  - belly and EWALD in amber7 Zhang Jian (Sat Nov 09 2002 - 19:04:14 PST)
    - Re: belly and EWALD in amber7 darden (Sun Nov 10 2002 - 14:25:31 PST)
    - Re: belly and EWALD in amber7 Zhang Jian (Sun Nov 10 2002 - 17:36:25 PST)
    - .top files read into xLeap? Arvid Soederhaell (Mon Nov 11 2002 - 02:24:00 PST)
    - Re: .top files read into xLeap? David A. Case (Mon Nov 11 2002 - 18:20:41 PST)
residue cross-correlation Bimo Ario Tejo (Fri Nov 08 2002 - 07:00:01 PST)
- Re: residue cross-correlation St�phane Teletch�a (Tue Nov 12 2002 - 02:57:10 PST)
- problem in PME Monica (Tue Nov 12 2002 - 05:42:21 PST)
  - Re: problem in PME David A. Case (Tue Nov 12 2002 - 06:06:47 PST)
  - RE: problem in PME Kristina Furse (Tue Nov 12 2002 - 08:43:03 PST)
    - Re: problem in PME David A. Case (Tue Nov 12 2002 - 15:16:52 PST)
Roar capabilities M. L. Dodson (Fri Nov 08 2002 - 09:37:48 PST)
residue cross-correlation Bimo Ario Tejo (Fri Nov 08 2002 - 10:57:48 PST)
- Re: residue cross-correlation Andreas Svrcek-Seiler (Fri Nov 08 2002 - 12:16:59 PST)
- Re: residue cross-correlation Thomas Cheatham (Fri Nov 08 2002 - 12:50:42 PST)
Re: belly and ivcap conflict in gibbs David A. Case (Sun Nov 10 2002 - 14:35:16 PST)
re: the removal of global motion Shixiang Yan (Tue Nov 12 2002 - 08:44:38 PST)
- Re: the removal of global motion David A. Case (Tue Nov 12 2002 - 15:25:09 PST)
  - Re: the removal of global motion Ioana Cozmuta (Tue Nov 12 2002 - 15:52:41 PST)
    - Re: the removal of global motion David A. Case (Tue Nov 12 2002 - 16:18:31 PST)
    - help! Non bond list overflow! Zhang Jian (Wed Nov 13 2002 - 02:56:39 PST)
    - Re: help! Non bond list overflow! David A. Case (Wed Nov 13 2002 - 16:51:07 PST)
    - Re: help! Non bond list overflow! Zhang Jian (Wed Nov 13 2002 - 18:10:02 PST)
    - Re: help! Non bond list overflow! Jian Zhang (Wed Nov 13 2002 - 18:32:01 PST)
    - input format for gibbs restraints Jose Ramon Blas (Wed Nov 13 2002 - 18:59:43 PST)
    - Re: input format for gibbs restraints David A. Case (Wed Nov 13 2002 - 17:53:27 PST)
    - (no subject) Monica (Wed Nov 13 2002 - 22:26:57 PST)
    - Re: your mail David A. Case (Thu Nov 14 2002 - 08:00:48 PST)
    - Linmin question... Andrei Leit�o (Thu Nov 14 2002 - 10:10:21 PST)
    - Re: Linmin question... David A. Case (Fri Nov 15 2002 - 00:12:20 PST)
    - simulating dna Tod Pascal (Fri Nov 15 2002 - 17:23:54 PST)
    - Re: simulating dna David A. Case (Mon Nov 18 2002 - 16:29:22 PST)
    - polarizabitlity X. Tan (Fri Nov 15 2002 - 17:41:37 PST)
    - Re: polarizabitlity David A. Case (Mon Nov 18 2002 - 16:44:10 PST)
    - Re: polarizabitlity X. Tan (Tue Nov 19 2002 - 10:08:31 PST)
    - Frictional forces in gB Kristina Furse (Tue Nov 19 2002 - 15:41:32 PST)
    - Nz-Acetyllysine parameters Luis Gracia (Tue Nov 19 2002 - 16:08:13 PST)
    - intdiel & extdiel Fredrick Robin Devadoss (Wed Nov 20 2002 - 03:23:59 PST)
    - Re: intdiel & extdiel David A. Case (Wed Nov 20 2002 - 07:51:44 PST)
    - Re: intdiel & extdiel Fredrick Robin Devadoss (Wed Nov 20 2002 - 20:28:35 PST)
    - Re: intdiel & extdiel Holger Gohlke (Thu Nov 21 2002 - 07:55:15 PST)
    - P.3 in antechamber Giulio Rastelli (Thu Nov 21 2002 - 03:02:16 PST)
    - PARMSET sara nunez (Thu Nov 21 2002 - 06:08:12 PST)
    - RE: PARMSET Ross Walker (Thu Nov 21 2002 - 06:30:36 PST)
    - Re: PARMSET David A. Case (Thu Nov 21 2002 - 08:13:38 PST)
    - ion distances Marcela Madrid (Thu Nov 21 2002 - 12:59:12 PST)
    - Re: ion distances 남기엽 (Thu Nov 21 2002 - 14:52:55 PST)
    - Restraint Ambiguities Neema Salimi (Thu Nov 21 2002 - 14:56:44 PST)
    - Re: Restraint Ambiguities David A. Case (Thu Nov 21 2002 - 18:08:04 PST)
    - Re: Restraint Ambiguities Neema Salimi (Thu Nov 21 2002 - 20:37:13 PST)
    - Re: Restraint Ambiguities David A. Case (Fri Nov 22 2002 - 08:33:34 PST)
    - problem in restrt Marcela Madrid (Fri Nov 22 2002 - 08:37:53 PST)
    - Re: problem in restrt Thomas Cheatham (Fri Nov 22 2002 - 09:55:27 PST)
    - restarting simulation Marcela Madrid (Fri Nov 22 2002 - 12:06:42 PST)
    - Re: restarting simulation Carlos Simmerling (Fri Nov 22 2002 - 12:56:24 PST)
    - solvateOct Kristina Furse (Fri Nov 22 2002 - 13:36:33 PST)
    - Re: solvateOct David A. Case (Fri Nov 22 2002 - 18:31:03 PST)
    - RE: solvateOct Kristina Furse (Tue Nov 26 2002 - 14:51:52 PST)
    - Re: solvateOct David A. Case (Tue Nov 26 2002 - 15:51:31 PST)
    - RE: solvateOct Kristina Furse (Sun Dec 01 2002 - 13:57:13 PST)
    - Re: solvateOct David A. Case (Mon Dec 02 2002 - 07:40:02 PST)
    - err in specifying disulphide bridge using xleap! A.Madhumalar (Mon Dec 02 2002 - 08:25:30 PST)
    - Re: err in specifying disulphide bridge using xleap! David A. Case (Mon Dec 02 2002 - 09:05:01 PST)
    - penalty function in NMR refinement Mahadevan Seetharaman (Mon Dec 02 2002 - 09:09:05 PST)
    - Re: err in specifying disulphide bridge using xleap! James W. Caldwell (Mon Dec 02 2002 - 11:07:07 PST)
    - LEAP - Introducing dummy atoms Miguel de Federico (Mon Dec 02 2002 - 08:42:49 PST)
    - Re: LEAP - Introducing dummy atoms James W. Caldwell (Mon Dec 02 2002 - 11:11:27 PST)
    - Biphasic box (fwd) amber_at_heimdal.compchem.ucsf.edu (Tue Dec 03 2002 - 14:13:10 PST)
    - Re: Biphasic box David A. Case (Tue Dec 03 2002 - 15:09:50 PST)
    - Re: Biphasic box Gemma Kinsella (Wed Dec 04 2002 - 00:15:53 PST)
    - Re: Biphasic box (fwd) James W. Caldwell (Tue Dec 03 2002 - 15:15:50 PST)
    - test mail Jim Caldwell (Tue Dec 03 2002 - 14:48:07 PST)
    - freeware for RNA modeling on Linux (fwd) amber_at_heimdal.compchem.ucsf.edu (Tue Dec 03 2002 - 14:57:10 PST)
    - Re: freeware for RNA modeling on Linux (fwd) David A. Case (Tue Dec 03 2002 - 15:11:48 PST)
    - Re: freeware for RNA modeling on Linux (fwd) Joerg-Gerald Siebers (Mon Dec 16 2002 - 18:43:05 PST)
    - Re: freeware for RNA modeling on Linux (fwd) James W. Caldwell (Tue Dec 17 2002 - 11:09:37 PST)
    - Chains, LEaP and ambpdb Luis Gracia (Tue Dec 17 2002 - 11:47:59 PST)
    - Re: Chains, LEaP and ambpdb Ioana Cozmuta (Tue Dec 17 2002 - 13:07:24 PST)
    - Re: Chains, LEaP and ambpdb David A. Case (Tue Dec 17 2002 - 13:09:48 PST)
    - Re: Chains, LEaP and ambpdb Luis Gracia (Tue Dec 17 2002 - 13:23:55 PST)
    - Re: Chains, LEaP and ambpdb David A. Case (Tue Dec 17 2002 - 19:28:21 PST)
    - Studying in Australia John Pritchard (Tue Dec 17 2002 - 22:36:07 PST)
    - amber trajectory Ioana Cozmuta (Tue Dec 17 2002 - 21:16:14 PST)
    - SUMMARY: solvating a protein with large cavity Tom Bishop (Wed Dec 18 2002 - 07:03:27 PST)
    - Re: SUMMARY: solvating a protein with large cavity Richard Henchman (Wed Dec 18 2002 - 11:56:20 PST)
    - roar-cp problems M. L. Dodson (Wed Dec 18 2002 - 13:00:37 PST)
    - Re: SUMMARY: solvating a protein with large cavity Ioana Cozmuta (Wed Dec 18 2002 - 17:21:23 PST)
    - MPI_BCAST error Nathan A. Baker (Wed Dec 18 2002 - 07:51:02 PST)
    - Re: MPI_BCAST error Scott Brozell (Wed Dec 18 2002 - 13:24:55 PST)
    - Re: MPI_BCAST error Nathan A. Baker (Wed Dec 18 2002 - 17:31:47 PST)
    - water/nonTIP3P Ioana Cozmuta (Wed Dec 18 2002 - 17:33:23 PST)
    - Re: water/nonTIP3P Ioana Cozmuta (Wed Dec 18 2002 - 18:17:24 PST)
    - ntwv saves v(t) or v(t+dt/2) ? hagop demirdjian (Thu Dec 19 2002 - 08:04:55 PST)
    - Re: ntwv saves v(t) or v(t+dt/2) ? David A. Case (Thu Dec 19 2002 - 09:24:33 PST)
    - antechamber Carsten Detering (Wed Dec 18 2002 - 14:32:44 PST)
    - message during minimization Ioana Cozmuta (Tue Dec 17 2002 - 21:31:52 PST)
    - Re: message during minimization darden (Wed Dec 18 2002 - 08:24:48 PST)
    - Re: message during minimization Ioana Cozmuta (Wed Dec 18 2002 - 15:09:05 PST)
    - Re: message during minimization darden (Wed Dec 18 2002 - 16:32:21 PST)
    - Re: message during minimization Ioana Cozmuta (Wed Dec 18 2002 - 18:02:26 PST)
    - Re: message during minimization David A. Case (Thu Dec 19 2002 - 08:05:00 PST)
    - chirality.c failure - diagnosis, but no cure... Michael Ford (Thu Dec 19 2002 - 10:07:07 PST)
    - Re: chirality.c failure - diagnosis, but no cure... Michael Ford (Thu Dec 19 2002 - 15:25:21 PST)
    - selection of residues Ioana Cozmuta (Fri Dec 20 2002 - 16:51:52 PST)
    - cap option Ioana Cozmuta (Sun Dec 22 2002 - 17:21:01 PST)
    - beginners question dynamic group (Sun Dec 22 2002 - 21:17:52 PST)
    - targeted MD sample eric hu (Thu Dec 26 2002 - 12:25:36 PST)
    - Molecular dynamic protocol... Andrei Leit�o (Fri Dec 27 2002 - 10:40:26 PST)
    - Re: Molecular dynamic protocol... David A. Case (Fri Dec 27 2002 - 11:25:51 PST)
    - cannot deal with large trajectory? yuann (Sat Dec 28 2002 - 19:17:23 PST)
    - Re: cannot deal with large trajectory? yuann (Mon Dec 30 2002 - 18:55:41 PST)
    - Trajectory file converted in pdb file Yongjun Jiang (Sun Dec 29 2002 - 17:13:38 PST)
    - Sander rfree error kxg2248_at_njit.edu (Mon Dec 30 2002 - 14:58:19 PST)
    - Re: Sander rfree error James Caldwell (Mon Dec 30 2002 - 16:36:45 PST)
    - sander (CAP) chokes on efc (Itanium2/Linux) Tadashi Takemori (Mon Dec 16 2002 - 23:11:14 PST)
    - RE: sander (CAP) chokes on efc (Itanium2/Linux) Karen Haskell (Tue Dec 17 2002 - 14:05:31 PST)
    - Re: sander (CAP) chokes on efc (Itanium2/Linux) Tadashi Takemori (Wed Dec 18 2002 - 01:38:25 PST)
    - water box, Ioana Cozmuta (Tue Dec 17 2002 - 15:18:31 PST)
    - Re: water box, Carlos Simmerling (Wed Dec 18 2002 - 05:18:18 PST)
    - Re: water box, darden (Wed Dec 18 2002 - 08:33:07 PST)
    - Re: water box, Ioana Cozmuta (Wed Dec 18 2002 - 15:37:41 PST)
    - Re: water box, David A. Case (Wed Dec 18 2002 - 16:17:31 PST)
    - Re: water box, darden (Wed Dec 18 2002 - 16:45:55 PST)
    - off-to-mol2 Anke Eisenmann (Wed Dec 18 2002 - 08:49:22 PST)
    - Re: off-to-mol2 David A. Case (Wed Dec 18 2002 - 10:03:48 PST)
    - About heating... Andrei Leit�o (Wed Dec 18 2002 - 10:23:43 PST)
    - Re: About heating... David A. Case (Wed Dec 18 2002 - 11:42:51 PST)
    - antechamber Carsten Detering (Wed Dec 18 2002 - 11:38:16 PST)
    - mm_pbsa error message! William Wei (Wed Dec 18 2002 - 09:17:16 PST)
    - Re: mm_pbsa error message! Michael Ford (Wed Dec 18 2002 - 09:37:57 PST)
    - solvatebox Luis Gracia (Tue Dec 17 2002 - 16:52:07 PST)
    - Re: solvatebox Luis Gracia (Wed Dec 18 2002 - 07:58:47 PST)
    - RST file for nonstandard residue vannajan_at_chiangmai.ac.th (Tue Dec 17 2002 - 01:07:04 PST)
    - GIBBS - Routine TORCON (internal constraints) failed Miguel de Federico (Tue Dec 17 2002 - 07:29:04 PST)
    - carnal amber 7.0 Vlad Cojocaru (Mon Dec 02 2002 - 00:35:34 PST)
    - combinig two trajectory files. Yongjun Jiang (Mon Dec 02 2002 - 04:18:29 PST)
    - Re: combinig two trajectory files. Carlos Simmerling (Mon Dec 02 2002 - 04:49:21 PST)
    - Re: combinig two trajectory files. Pascal Bonnet (Mon Dec 02 2002 - 04:50:26 PST)
    - Re: restarting simulation Marcela Madrid (Fri Nov 22 2002 - 14:07:47 PST)
    - Equilibration output Amber7 Fredrick Robin Devadoss (Fri Nov 22 2002 - 01:42:32 PST)
    - Re: Equilibration output Amber7 Thomas Cheatham (Fri Nov 22 2002 - 09:49:55 PST)
    - Error running AMBER6 on Beowulf cluster arubin_at_unmc.edu (Thu Nov 21 2002 - 15:10:39 PST)
    - Re: Error running AMBER6 on Beowulf cluster David A. Case (Thu Nov 21 2002 - 17:31:47 PST)
    - Re: Error running AMBER6 on Beowulf cluster arubin_at_unmc.edu (Fri Nov 22 2002 - 13:38:12 PST)
    - Re: Error running AMBER6 on Beowulf cluster Carlos Simmerling (Fri Nov 22 2002 - 15:33:49 PST)
    - ntx=7, irest=0 Marcela Madrid (Fri Nov 22 2002 - 15:56:00 PST)
    - Re: ntx=7, irest=0 David A. Case (Fri Nov 22 2002 - 18:36:28 PST)
    - Re: ntx=7, irest=0, redux David Case (Fri Nov 22 2002 - 22:53:37 PST)
    - (no subject) Narang Manpreet Kaur (Sat Nov 23 2002 - 02:40:12 PST)
    - Re: your mail darden (Sun Nov 24 2002 - 14:46:35 PST)
    - Hydrophobic protein in water Luo Liu (Sun Nov 24 2002 - 14:52:20 PST)
    - atom type not recognized by GB eric hu (Sun Nov 24 2002 - 17:05:59 PST)
    - Re: atom type not recognized by GB David A. Case (Sun Nov 24 2002 - 17:50:01 PST)
    - Re: atom type not recognized by GB eric hu (Sun Nov 24 2002 - 18:30:17 PST)
    - Inquiry software_at_kagaku.com (Sun Nov 24 2002 - 19:44:51 PST)
    - (no subject) CHAUMONT Alain (Mon Nov 25 2002 - 07:32:50 PST)
    - using SHAKE for solvent only hagop demirdjian (Mon Nov 25 2002 - 07:42:57 PST)
    - Re: using SHAKE for solvent only David A. Case (Mon Nov 25 2002 - 10:17:54 PST)
    - external electric field Ioana Cozmuta (Mon Nov 25 2002 - 15:18:38 PST)
    - a second question Ioana Cozmuta (Mon Nov 25 2002 - 16:20:52 PST)
    - Please help. Energy suddenly increase. Protein jump out Lich Nguyen (Tue Nov 26 2002 - 23:42:29 PST)
    - Re: Please help. Energy suddenly increase. Protein jump out David A. Case (Wed Nov 27 2002 - 08:26:55 PST)
    - RE: Please help. Energy suddenly increase. Protein jump out Yong Duan (Wed Nov 27 2002 - 10:42:39 PST)
    - Re: Please help. Energy suddenly increase. Protein jump out Carlos Simmerling (Wed Nov 27 2002 - 13:35:15 PST)
    - RE: Please help. Energy suddenly increase. Protein jump out Yong Duan (Wed Nov 27 2002 - 14:52:54 PST)
    - esp.sh problem FyD (Wed Nov 27 2002 - 09:17:40 PST)
    - Re: esp.sh problem David Smith (Wed Nov 27 2002 - 10:13:09 PST)
    - Re: esp.sh problem David A. Case (Wed Nov 27 2002 - 11:12:54 PST)
    - Re: esp.sh problem FyD (Thu Nov 28 2002 - 00:03:33 PST)
    - C60 parameter vannajan_at_chiangmai.ac.th (Thu Nov 28 2002 - 00:47:47 PST)
    - Re: C60 parameter Pascal Bonnet (Thu Nov 28 2002 - 04:12:19 PST)
    - Problem Monica (Thu Nov 28 2002 - 22:35:19 PST)
    - Re: Problem David Case (Fri Nov 29 2002 - 11:49:20 PST)
    - parmchk -p option Thomas.Fox_at_bc.boehringer-ingelheim.com (Fri Nov 29 2002 - 02:09:09 PST)
    - parameters for cyclic nucleotides Thomas.Fox_at_bc.boehringer-ingelheim.com (Fri Nov 29 2002 - 02:11:43 PST)
    - (no subject) Narang Manpreet Kaur (Fri Nov 29 2002 - 02:54:03 PST)
    - Re: your mail David Case (Fri Nov 29 2002 - 12:07:19 PST)
    - Break down energy contributions Numan Oezguen (Fri Nov 29 2002 - 13:06:36 PST)
    - How Amber calculates electrostatic energy? Daniel Svozil (Wed Nov 27 2002 - 06:47:11 PST)
    - Calculating atomic charges for AMBER with Gaussian98W Thomas Steinbrecher (Sat Nov 23 2002 - 05:52:47 PST)
    - Re: Calculating atomic charges for AMBER with Gaussian98W M. L. Dodson (Sat Nov 23 2002 - 07:36:27 PST)
    - pdb file Ioana Cozmuta (Fri Nov 22 2002 - 16:41:01 PST)
    - Re: pdb file Ioana Cozmuta (Fri Nov 22 2002 - 17:44:22 PST)
    - Re: ion distances Thomas E. Cheatham, III (Thu Nov 21 2002 - 15:54:46 PST)
    - Re: ion distances Bill Ross (Mon Nov 25 2002 - 16:51:46 PST)
    - GIBBS - ERROR: Restraint read error from RSTIN; Check format: Miguel de Federico (Tue Nov 26 2002 - 01:14:19 PST)
    - Re: GIBBS - ERROR: Restraint read error from RSTIN; Check format: David A. Case (Tue Nov 26 2002 - 15:30:52 PST)
    - restrain a residue as center of mass eric hu (Tue Nov 26 2002 - 15:36:19 PST)
    - Re: restrain a residue as center of mass Carlos Simmerling (Tue Nov 26 2002 - 16:17:58 PST)
    - Re: restrain a residue as center of mass eric hu (Wed Nov 27 2002 - 10:42:36 PST)
    - Re: restrain a residue as center of mass Carlos Simmerling (Wed Nov 27 2002 - 13:34:00 PST)
    - Re: restrain a residue as center of mass Carlos Simmerling (Wed Nov 27 2002 - 13:38:57 PST)
    - external electric field/another try Ioana Cozmuta (Wed Nov 27 2002 - 14:13:08 PST)
    - Re: external electric field/another try darden (Wed Nov 27 2002 - 15:27:32 PST)
    - Re: external electric field/another try James W. Caldwell (Wed Nov 27 2002 - 15:31:24 PST)
    - the tree name? Sichun Yang (Tue Nov 26 2002 - 19:29:27 PST)
    - Re: the tree name? David A. Case (Wed Nov 27 2002 - 14:44:17 PST)
    - Error in Equilibration Fredrick Robin Devadoss (Tue Nov 26 2002 - 02:14:12 PST)
    - targeted MD for more than 2 groups Sichun Yang (Thu Nov 21 2002 - 13:20:44 PST)
    - Re: targeted MD for more than 2 groups Carlos Simmerling (Thu Nov 21 2002 - 15:54:53 PST)
    - Re: PARMSET John Bushnell (Thu Nov 21 2002 - 14:32:25 PST)
    - Bulk Email Sending & Bullet Proof Web Hosting pposton (Wed Nov 20 2002 - 14:25:53 PST)
    - defining groups on dif. sets in carnal Vlad Cojocaru (Tue Nov 19 2002 - 02:59:06 PST)
    - Linmin question... Andrei Leit�o (Thu Nov 14 2002 - 10:13:01 PST)
    - Amber Perl module Tod Pascal (Thu Nov 14 2002 - 13:33:01 PST)
    - Re: Amber Perl module Luis Gracia (Thu Nov 14 2002 - 13:55:25 PST)
    - Re: Amber Perl module Michael Ford (Thu Nov 14 2002 - 15:26:24 PST)
    - non-zero 10-12 coefficient Anonymous (Thu Nov 14 2002 - 16:18:34 PST)
    - restart mm_pbsa Layi Adekoya (Thu Nov 14 2002 - 05:02:51 PST)
    - Re: restart mm_pbsa Lepsa (Thu Nov 14 2002 - 05:52:22 PST)
    - Re: restart mm_pbsa Pascal Bonnet (Thu Nov 14 2002 - 07:13:06 PST)
    - Amber on PC-Linux Philippe Aplincourt (Thu Nov 14 2002 - 07:22:20 PST)
    - error in reading .crd file with GIBBS hagop demirdjian (Thu Nov 14 2002 - 07:40:32 PST)
    - help on VMD movie Zhang Jian (Wed Nov 13 2002 - 04:44:36 PST)
    - Re: help on VMD movie St�phane Teletch�a (Wed Nov 13 2002 - 05:12:58 PST)
    - Re: help on VMD movie Francesca Mocci (Wed Nov 13 2002 - 06:28:06 PST)
    - Ewald Monica (Wed Nov 13 2002 - 07:20:23 PST)
    - Re: Ewald David A. Case (Wed Nov 13 2002 - 08:09:08 PST)
    - CMM method Ioana Cozmuta (Wed Nov 13 2002 - 14:57:10 PST)
    - Re: CMM method David A. Case (Wed Nov 13 2002 - 16:42:26 PST)
    - Re: help on VMD movie Zhang Jian (Wed Nov 13 2002 - 07:21:30 PST)
    - Re: help on VMD movie Zhang Jian (Wed Nov 13 2002 - 17:40:14 PST)
NMR restraints on a 10-mer DNA in Sander Jo.Vinje_at_kj.uib.no (Tue Nov 12 2002 - 09:34:55 PST)
- Re: NMR restraints on a 10-mer DNA in Sander Michael G Cooney (Tue Nov 12 2002 - 12:16:32 PST)
- Amber7/CYGWIN compiling James W. Caldwell (Tue Nov 12 2002 - 13:09:33 PST)
- Re: NMR restraints on a 10-mer DNA in Sander David A. Case (Tue Nov 12 2002 - 15:30:52 PST)
Re: EWALD crash David A. Case (Mon Nov 18 2002 - 16:27:37 PST)
leap for peptide Sichun Yang (Fri Nov 22 2002 - 14:33:51 PST)
Re: CCL:freeware for RNA modeling on Linux (fwd) amber_at_heimdal.compchem.ucsf.edu (Tue Dec 03 2002 - 14:57:21 PST)
Constraints in Amber (fwd) amber_at_heimdal.compchem.ucsf.edu (Tue Dec 03 2002 - 14:57:30 PST)
- Re: Constraints in Amber David A. Case (Tue Dec 03 2002 - 15:16:02 PST)
gB vs. explicit (fwd) amber_at_heimdal.compchem.ucsf.edu (Tue Dec 03 2002 - 14:57:53 PST)
- Re: gB vs. explicit David A. Case (Wed Dec 04 2002 - 08:28:43 PST)
Amber Trajectories + VMD (fwd) amber_at_heimdal.compchem.ucsf.edu (Tue Dec 03 2002 - 14:58:00 PST)
- RE: Amber Trajectories + VMD (fwd) Nicholson, James D Mr ARO (Tue Dec 03 2002 - 15:35:09 PST)
Energy decomposition with ANAL (fwd) amber_at_heimdal.compchem.ucsf.edu (Tue Dec 03 2002 - 14:58:05 PST)
- Re: Energy decomposition with ANAL (fwd) David A. Case (Wed Dec 04 2002 - 08:31:52 PST)
- restrained MD Vlad Cojocaru (Wed Dec 04 2002 - 10:18:54 PST)
- DIANA like files Vlad Cojocaru (Wed Dec 04 2002 - 12:24:12 PST)
- Amber 7 bugfix 27 !! urgent William Wei (Wed Dec 04 2002 - 12:45:13 PST)
  - Re: Amber 7 bugfix 27 !! urgent Holger Gohlke (Wed Dec 04 2002 - 13:18:48 PST)
  - MDaemon Warning - Virus Found postmaster_at_bydnet.com.pl (Wed Dec 04 2002 - 19:49:28 PST)
Reflector problems amber_at_heimdal.compchem.ucsf.edu (Tue Dec 03 2002 - 15:05:02 PST)
Re: corrupted trajectory Shixiang Yan (Tue Dec 03 2002 - 15:36:37 PST)
increasing the number of processors Ioana Cozmuta (Tue Dec 03 2002 - 16:17:58 PST)
increasing the number of processors (fwd) Ioana Cozmuta (Tue Dec 03 2002 - 16:19:24 PST)
Re: corrupted trajectory CUI, Guanglei (Tue Dec 03 2002 - 18:04:13 PST)
Re: Energy decomposition with ANAL Numan Oezguen (Fri Dec 06 2002 - 09:08:20 PST)
- Re: Energy decomposition with ANAL Natasja Brooijmans (Fri Dec 06 2002 - 09:24:21 PST)
- default GB radii Robert G. Endres (Fri Dec 06 2002 - 13:00:31 PST)
  - Re: default GB radii David A. Case (Fri Dec 06 2002 - 13:11:13 PST)
  - carnal Ioana Cozmuta (Fri Dec 06 2002 - 15:47:56 PST)
    - Re: carnal Bill Ross (Fri Dec 06 2002 - 17:16:59 PST)
  - Re: default GB radii Andreas Svrcek-Seiler (Sat Dec 07 2002 - 04:02:09 PST)
    - dual H-bonding of bridging waters - CARNAL Michael Ford (Tue Dec 10 2002 - 16:16:24 PST)
    - bad protein structure eric hu (Tue Dec 10 2002 - 17:30:52 PST)
  - (no subject) Jennifer Hawkings (Sat Dec 07 2002 - 14:48:46 PST)
  - CHARMm NPT input files Mahadevan Seetharaman (Sat Dec 07 2002 - 15:39:07 PST)
  - NMR restrains Marcela Madrid (Mon Dec 09 2002 - 12:33:31 PST)
  - running sander_classic for amber6 using different version of mpi Asif Rahaman (Mon Dec 09 2002 - 15:01:35 PST)
  - difference in energy in amber6 and amber7 Prabal Maiti (Mon Dec 09 2002 - 18:07:15 PST)
    - Re: difference in energy in amber6 and amber7 David A. Case (Wed Dec 11 2002 - 07:40:48 PST)
  - Question to perturbation charge meiselba (Tue Dec 10 2002 - 05:35:38 PST)
- Re: Energy decomposition with ANAL Numan Oezguen (Mon Dec 16 2002 - 07:49:08 PST)
Re: CCL:Amber7 and partial charges David Case (Wed Dec 11 2002 - 10:07:10 PST)
- Amber 7 MM-PBSA for Amber 6 trajectories Qing Zhang (Thu Dec 12 2002 - 11:52:23 PST)
  - Re: Amber 7 MM-PBSA for Amber 6 trajectories David A. Case (Sat Dec 14 2002 - 11:26:01 PST)
  - a question about force field in AMBER jzhou (Sat Dec 14 2002 - 17:55:15 PST)
    - Re: a question about force field in AMBER sychen (Sat Dec 14 2002 - 21:17:59 PST)
    - Re: a question about force field in AMBER David A. Case (Mon Dec 16 2002 - 17:56:29 PST)
- ambpdb Vlad Cojocaru (Thu Dec 12 2002 - 14:01:23 PST)
  - Re: ambpdb Holger Gohlke (Thu Dec 12 2002 - 16:44:44 PST)
  - Business Cooperation (Inheritance Claim) Mr. Daniel Osondu (Fri Dec 13 2002 - 01:50:38 PST)
  - GIBBS - end-of-file during read Miguel de Federico (Fri Dec 13 2002 - 02:12:48 PST)
  - plotting electrostatic potential surface Ioana Cozmuta (Fri Dec 13 2002 - 15:18:17 PST)
  - Re: ambpdb David A. Case (Fri Dec 13 2002 - 20:46:12 PST)
  - solvating a protein with large cavity Tom Bishop (Sat Dec 14 2002 - 07:42:38 PST)
    - Re: solvating a protein with large cavity M. L. Dodson (Sat Dec 14 2002 - 08:23:15 PST)
    - FEP/Gibbs question to valine alanine tutorial meiselba (Sat Dec 14 2002 - 08:58:12 PST)
MM-PBSA: .crg file for Delphi Thomas Steinbrecher (Wed Dec 11 2002 - 10:08:40 PST)
- Re: MM-PBSA: .crg file for Delphi Holger Gohlke (Wed Dec 11 2002 - 10:31:07 PST)
- Question on 2 stage RESP fit Ambarish Nag (Wed Dec 11 2002 - 22:39:08 PST)
  - Re: Question on 2 stage RESP fit M. L. Dodson (Thu Dec 12 2002 - 05:05:15 PST)
  - Business Cooperation (Inheritance Claim) Mr. Daniel Osondu (Thu Dec 12 2002 - 10:10:29 PST)
disulfide bond link between two chains pu xuemei (Mon Dec 16 2002 - 04:50:35 PST)
- Re: disulfide bond link between two chains Natasja Brooijmans (Mon Dec 16 2002 - 05:49:46 PST)
Fw: Valine to alanine Gibbs tutorial Lepsa (Mon Dec 16 2002 - 05:20:26 PST)
atomicfluct in ptraj Kristina Furse (Wed Dec 18 2002 - 15:16:29 PST)
- Re: atomicfluct in ptraj David A. Case (Thu Dec 19 2002 - 09:28:43 PST)
- RE: atomicfluct in ptraj Kristina Furse (Thu Dec 19 2002 - 11:28:16 PST)
- RESTARTED DUE TO LINMIN FAILURE William Wei (Thu Dec 19 2002 - 11:33:07 PST)
  - Re: RESTARTED DUE TO LINMIN FAILURE Natasja Brooijmans (Thu Dec 19 2002 - 13:16:44 PST)
- Nmode Pratul Agarwal (Thu Dec 19 2002 - 13:07:47 PST)
  - Re: Nmode James Caldwell (Thu Dec 19 2002 - 13:17:31 PST)
new on the Amber web pages... David A. Case (Tue Dec 31 2002 - 13:51:31 PST)
Sander box error and thanks on previous mdin error kxg2248_at_njit.edu (Thu Jan 02 2003 - 19:41:49 PST)
- Re: Sander box error and thanks on previous mdin error David A. Case (Fri Jan 03 2003 - 07:40:07 PST)
  - Re: Sander box error and thanks on previous mdin error kxg2248_at_njit.edu (Fri Jan 03 2003 - 09:37:05 PST)
- JACS 125th and PAK Carlos Simmerling (Fri Jan 03 2003 - 09:02:12 PST)
  - Re: JACS 125th and PAK David A. Case (Fri Jan 03 2003 - 10:36:47 PST)
  - Linux cluster Amber7 sander mpi error -- Null communicator, IOT Trap Chris Switzer (Fri Jan 03 2003 - 19:18:11 PST)
    - Re: Linux cluster Amber7 sander mpi error -- Null communicator, IOT Trap David Case (Fri Jan 03 2003 - 21:46:00 PST)
    - Re: Linux cluster Amber7 sander mpi error -- Null communicator, IOT Trap Florian Barth (Fri Jan 03 2003 - 22:36:27 PST)
    - looking for 'pdb_to_mass' yuann (Mon Jan 06 2003 - 22:54:32 PST)
    - Re: looking for 'pdb_to_mass' CUI, Guanglei (Tue Jan 07 2003 - 06:06:05 PST)
    - Small organic molecules Dvira Segal (Tue Jan 07 2003 - 07:55:31 PST)
    - Re: Small organic molecules David A. Case (Tue Jan 07 2003 - 08:16:48 PST)
    - water reordering in sander Michael Trieb (Tue Jan 07 2003 - 05:43:38 PST)
    - Re: water reordering in sander David A. Case (Tue Jan 07 2003 - 08:03:58 PST)
    - reducing restrains Luis Gracia (Tue Jan 07 2003 - 08:14:43 PST)
    - Re: reducing restrains David A. Case (Tue Jan 07 2003 - 09:08:24 PST)
    - Re: Linux cluster Amber7 sander mpi error -- Null communicator, IOT Trap Jim Newhouse (Tue Jan 07 2003 - 11:07:32 PST)
    - virtual box eric hu (Tue Jan 07 2003 - 15:26:15 PST)
    - Re: virtual box David A. Case (Tue Jan 07 2003 - 15:56:29 PST)
    - Re: virtual box eric hu (Tue Jan 07 2003 - 23:35:09 PST)
    - Re: virtual box eric hu (Tue Jan 07 2003 - 23:35:21 PST)
    - building molecules by script files for leap Dvira Segal (Wed Jan 08 2003 - 08:07:57 PST)
    - Re: building molecules by script files for leap David A. Case (Wed Jan 08 2003 - 09:27:13 PST)
    - mm_gbsa error message Mahadevan Seetharaman (Wed Jan 08 2003 - 10:17:23 PST)
    - Re: mm_gbsa error message Holger Gohlke (Wed Jan 08 2003 - 13:52:31 PST)
    - Predefined Water_cap with xleap Jose Ramon Blas (Wed Jan 08 2003 - 10:42:16 PST)
    - mm_pbsa question wentaofu (Tue Jan 07 2003 - 16:17:08 PST)
    - Re: mm_pbsa question Holger Gohlke (Tue Jan 07 2003 - 16:41:30 PST)
    - the unit of velocity Jian Zhang (Tue Jan 07 2003 - 20:36:58 PST)
    - Re: the unit of velocity David A. Case (Wed Jan 08 2003 - 08:09:43 PST)
    - Re: the unit of velocity Jian Zhang (Wed Jan 08 2003 - 18:12:15 PST)
    - GIBBS - Routine TORCON failed. Required change is too large. Miguel de Federico (Thu Jan 09 2003 - 02:11:41 PST)
    - nmanal & quasih question yuann (Tue Jan 07 2003 - 23:16:56 PST)
    - Re: nmanal & quasih question yuann (Thu Jan 09 2003 - 08:13:30 PST)
    - Re: nmanal & quasih question David A. Case (Thu Jan 09 2003 - 09:16:11 PST)
    - MM_pbsa prmtop file wentaofu (Thu Jan 09 2003 - 15:29:38 PST)
    - Re: MM_pbsa prmtop file David A. Case (Thu Jan 09 2003 - 15:53:53 PST)
    - free energy perturbation (Gibbs/Amber 5)? meiselba (Thu Jan 09 2003 - 08:49:09 PST)
    - Re: free energy perturbation (Gibbs/Amber 5)? Lepsa (Fri Jan 10 2003 - 01:56:50 PST)
    - xleap crashes Layi Adekoya (Fri Jan 10 2003 - 04:16:26 PST)
    - Re: xleap crashes David Case (Fri Jan 10 2003 - 22:05:45 PST)
    - electrostatic potential calculations Vlad Cojocaru (Sat Jan 11 2003 - 08:05:07 PST)
    - Re: electrostatic potential calculations Andreas Svrcek-Seiler (Sat Jan 11 2003 - 08:43:33 PST)
    - Re: CCL:electrostatic potential calculations Nathan A. Baker (Mon Jan 13 2003 - 14:27:00 PST)
    - xleap crashes Layi Adekoya (Tue Jan 14 2003 - 00:46:49 PST)
    - Dummy atoms in free energy calculation Lepsa (Sat Jan 11 2003 - 10:18:44 PST)
    - Re: Dummy atoms in free energy calculation David A. Case (Sun Jan 12 2003 - 23:37:35 PST)
    - xleap crashes Layi Adekoya (Sun Jan 12 2003 - 23:54:20 PST)
    - Re: xleap crashes David A. Case (Mon Jan 13 2003 - 09:08:15 PST)
    - coordinates for quasih Jake Isaacs (Mon Jan 13 2003 - 06:43:54 PST)
    - Re: coordinates for quasih Pratul Agarwal (Mon Jan 13 2003 - 07:48:17 PST)
    - problem with antechamber Craig A Bayse (Sun Jan 12 2003 - 10:54:05 PST)
    - Re: problem with antechamber David A. Case (Sun Jan 12 2003 - 14:01:06 PST)
    - Re: electrostatic potential calculations Peter Gannett (Mon Jan 13 2003 - 09:32:19 PST)
    - IDSX0 in free energy calculations Lepsa (Fri Jan 10 2003 - 05:29:04 PST)
    - (no subject) amkumar_at_post.its.mcw.edu (Fri Jan 10 2003 - 09:35:12 PST)
    - errors in MD trajectories Vlad Cojocaru (Fri Jan 10 2003 - 10:13:03 PST)
    - pdb_to_mass Jake Isaacs (Fri Jan 10 2003 - 12:42:35 PST)
    - Re: pdb_to_mass sychen (Fri Jan 10 2003 - 17:53:37 PST)
    - Force Fields Colin Connelly (Fri Jan 10 2003 - 21:44:35 PST)
Amber parameters for Netropsin Manuel Rueda (Wed Jan 08 2003 - 15:48:12 PST)
Summary: mm_pbsa -- COMPT must be specified (correctly) William Wei (Tue Jan 14 2003 - 07:31:07 PST)
Re: how to stop mapping of N- and C-terminal residues in xleap (The RTFM solution) Michael Ford (Wed Jan 15 2003 - 10:02:52 PST)
octahedral volume Peter Varnai (Fri Jan 17 2003 - 02:26:58 PST)
- Re: octahedral volume David A. Case (Tue Jan 21 2003 - 09:03:23 PST)
mm_pbsa Stop at statistics William Wei (Fri Jan 17 2003 - 10:52:48 PST)
UCSF Network changes to affect Amber Web site. caldwell_at_heimdal.compchem.ucsf.edu (Fri Jan 17 2003 - 11:41:19 PST)
- RE: UCSF Network changes to affect Amber Web site. Ross Walker (Fri Jan 17 2003 - 12:07:29 PST)
- Re: UCSF Network changes to affect Amber Web site. David A. Case (Fri Jan 17 2003 - 12:14:59 PST)
- nucleic acid structures Ioana Cozmuta (Fri Jan 17 2003 - 17:12:35 PST)
- Bug found in sander - incorrect conversion factor causes randomized velocities to be too cold John D. Chodera (Sat Jan 18 2003 - 01:26:12 PST)
  - Re: Bug found in sander - incorrect conversion factor causes randomized velocities to be too cold David A. Case (Sat Jan 18 2003 - 10:53:54 PST)
  - High temperature MD A.Madhumalar (Sun Jan 19 2003 - 08:02:41 PST)
    - Re: High temperature MD Lepsa (Wed Jan 29 2003 - 23:27:19 PST)
  - Re: Bug found in sander - incorrect conversion factor causes randomized velocities to be too cold David A. Case (Sun Jan 19 2003 - 23:26:16 PST)
equilibrated solvent box pu xuemei (Mon Jan 20 2003 - 00:54:33 PST)
- Re: equilibrated solvent box David A. Case (Wed Jan 22 2003 - 08:48:12 PST)
equilibrated solvent box pu xuemei (Mon Jan 20 2003 - 00:55:26 PST)
Has anyone ever used MEAD? Vlad Cojocaru (Mon Jan 20 2003 - 05:58:30 PST)
CARNAL Lepsa (Mon Jan 20 2003 - 07:22:22 PST)
Ewald error Miguel de Federico (Mon Jan 20 2003 - 07:32:21 PST)
- Re: Ewald error David A. Case (Mon Jan 20 2003 - 09:31:49 PST)
- scripts for compiling UHBD/MEAD with amber 7.0 eric hu (Mon Jan 20 2003 - 09:54:37 PST)
morse potential hagop demirdjian (Mon Jan 20 2003 - 08:22:03 PST)
- Re: morse potential David A. Case (Mon Jan 20 2003 - 09:29:59 PST)
script for Potential/kinectic energy Layi Adekoya (Mon Jan 20 2003 - 08:30:09 PST)
- Re: script for Potential/kinectic energy Holger Gohlke (Mon Jan 20 2003 - 08:44:13 PST)
- Re: script for Potential/kinectic energy Luis Gracia (Mon Jan 20 2003 - 10:16:52 PST)
- SASA and H-bond over trajectories Bimo Ario Tejo (Mon Jan 20 2003 - 20:59:12 PST)
Amber tutorial crown-ether Dvira Segal (Tue Jan 21 2003 - 06:06:55 PST)
- Re: Amber tutorial crown-ether David A. Case (Tue Jan 21 2003 - 08:48:47 PST)
(no subject) Anke Eisenmann (Tue Jan 21 2003 - 06:07:25 PST)
- Re: your mail David A. Case (Tue Jan 21 2003 - 08:35:52 PST)
'hot-solvent' and 'cold solute' problem Stefan Jungblut (Tue Jan 21 2003 - 07:36:37 PST)
- Re: 'hot-solvent' and 'cold solute' problem David A. Case (Tue Jan 21 2003 - 08:38:14 PST)
reduce the disk space eric hu (Tue Jan 21 2003 - 10:48:14 PST)
average structure generated by carnal eric hu (Tue Jan 21 2003 - 10:53:49 PST)
- Re: average structure generated by carnal Peter Gannett (Tue Jan 21 2003 - 12:14:38 PST)
  - Re: average structure generated by carnal Andreas Svrcek-Seiler (Wed Jan 22 2003 - 07:16:53 PST)
- Re: average structure generated by carnal eric hu (Tue Jan 21 2003 - 13:02:34 PST)
- RE: average structure generated by carnal Kristina Furse (Tue Jan 21 2003 - 17:55:46 PST)
- How to control box size pu xuemei (Wed Jan 22 2003 - 04:58:53 PST)
  - Re: How to control box size David A. Case (Wed Jan 22 2003 - 08:53:02 PST)
shake and belly GUILLERMINA L ESTIU (Tue Jan 21 2003 - 13:38:59 PST)
- Re: shake and belly David A. Case (Wed Jan 22 2003 - 10:17:22 PST)
- Re: shake and belly GUILLERMINA L ESTIU (Wed Jan 22 2003 - 10:47:30 PST)
- SCSL Joffre Heredia (Wed Jan 22 2003 - 12:23:12 PST)
  - Re: SCSL David A. Case (Wed Jan 22 2003 - 08:37:33 PST)
    - Re: SCSL Roberto Gomperts (Thu Jan 23 2003 - 07:52:06 PST)
    - Proper torsion parameters missing? Heike Meiselbach (Thu Jan 23 2003 - 11:05:05 PST)
    - Re: Proper torsion parameters missing? Miguel de Federico (Fri Jan 24 2003 - 01:27:21 PST)
    - Shake problem in organic solvent yuan bo (Fri Jan 24 2003 - 04:03:48 PST)
    - Re: Shake problem in organic solvent David A. Case (Fri Jan 24 2003 - 13:43:20 PST)
    - RESP-group constraint Artur Galstyan (Fri Jan 24 2003 - 06:38:53 PST)
    - Re: RESP-group constraint Marco Preto (Wed Oct 30 2002 - 08:50:21 PST)
    - IDECOMP Mark Hsieh (Wed Oct 30 2002 - 10:11:02 PST)
    - Re: IDECOMP Holger Gohlke (Wed Oct 30 2002 - 12:11:13 PST)
    - question on belly and restraint Sichun Yang (Wed Oct 30 2002 - 12:54:37 PST)
    - How to choose the box and cap size sxzheng (Wed Oct 30 2002 - 22:42:27 PST)
    - Nmode query kinsellg (Fri Jan 24 2003 - 07:00:40 PST)
    - Amber Web page. caldwell_at_heimdal.compchem.ucsf.edu (Fri Jan 24 2003 - 08:45:00 PST)
    - Zn2+ parameters Xiang, Tian-Xiang (Fri Jan 24 2003 - 13:42:07 PST)
    - Re: Zn2+ parameters Robert G. Endres (Sat Jan 25 2003 - 12:25:36 PST)
    - posphinic acid parameters Alfonso Garcia Sosa (Sun Jan 26 2003 - 08:28:11 PST)
    - polarization + ewald GUILBAUD Philippe 153683 (Mon Jan 27 2003 - 03:21:44 PST)
    - Re: polarization + ewald darden (Mon Jan 27 2003 - 16:58:10 PST)
    - structure image Xiang, Tian-Xiang (Mon Jan 27 2003 - 07:31:46 PST)
    - RE: structure image Xiang, Tian-Xiang (Mon Jan 27 2003 - 08:25:34 PST)
    - gibbs run Xiang, Tian-Xiang (Mon Jan 27 2003 - 09:05:06 PST)
    - Re: gibbs run David A. Case (Mon Jan 27 2003 - 10:38:13 PST)
    - crystal structure of DNA/RNA homopolymers Ioana Cozmuta (Mon Jan 27 2003 - 11:34:13 PST)
    - Re: crystal structure of DNA/RNA homopolymers David A. Case (Mon Jan 27 2003 - 11:48:35 PST)
    - Re: crystal structure of DNA/RNA homopolymers Ioana Cozmuta (Mon Jan 27 2003 - 11:54:18 PST)
    - compiling amber on myrinet Scott E. Boesch (Mon Jan 27 2003 - 12:12:31 PST)
    - freeware to visualize RMSD matrices creatde with Carnal Vlad Cojocaru (Mon Jan 27 2003 - 14:41:00 PST)
    - xleap in Amber7 arubin_at_unmc.edu (Mon Jan 27 2003 - 16:54:46 PST)
    - xleap in Amber7 arubin_at_unmc.edu (Mon Jan 27 2003 - 16:56:16 PST)
    - lastrst Steve Seibold (Mon Jan 27 2003 - 09:46:57 PST)
    - Re: lastrst David A. Case (Mon Jan 27 2003 - 10:33:12 PST)
    - Re: structure image A.Madhumalar (Mon Jan 27 2003 - 17:51:35 PST)
    - Question: about restarting Energy vannajan_at_chiangmai.ac.th (Mon Jan 27 2003 - 17:53:30 PST)
    - Re: Question: about restarting Energy David A. Case (Mon Jan 27 2003 - 18:33:14 PST)
    - single point mutations to investigate the conformational change Sichun Yang (Mon Jan 27 2003 - 19:43:29 PST)
    - Intramolecular H-bonds in charge fitting Lepsa (Tue Jan 28 2003 - 01:05:58 PST)
    - RE: Intramolecular H-bonds in charge fitting Bayly, Christopher (Tue Jan 28 2003 - 07:35:14 PST)
    - one question Fan Gao (Tue Jan 28 2003 - 08:14:56 PST)
    - Re: one question Lepsa (Tue Jan 28 2003 - 08:16:05 PST)
    - Re: one question Holger Gohlke (Tue Jan 28 2003 - 08:17:02 PST)
    - script for H-bonds extracting Bimo Ario Tejo (Tue Jan 28 2003 - 02:00:52 PST)
    - RE: script for H-bonds extracting Bayly, Christopher (Tue Jan 28 2003 - 10:40:53 PST)
    - gibbs calculation Xiang, Tian-Xiang (Tue Jan 28 2003 - 11:03:44 PST)
    - Re: gibbs calculation David A. Case (Tue Jan 28 2003 - 12:03:37 PST)
    - MM_PBSA Lepsa (Wed Jan 29 2003 - 05:12:34 PST)
    - Re: MM_PBSA Holger Gohlke (Wed Jan 29 2003 - 07:24:58 PST)
    - antechamber and gamess David A. Case (Wed Jan 29 2003 - 08:16:03 PST)
    - mm_pbsa and ALA scan Ahammadunny Pathiaseril (Wed Jan 29 2003 - 08:24:06 PST)
    - Re: mm_pbsa and ALA scan Lepsa (Wed Jan 29 2003 - 08:31:41 PST)
    - Polymers Ndubuisi Emmanuel Okoro (Wed Jan 29 2003 - 13:40:53 PST)
    - Request johneluwa_at_eircom.net (Wed Jan 29 2003 - 18:42:28 PST)
    - naphthalene, anthracene force field yuann (Wed Jan 29 2003 - 06:58:47 PST)
    - antechamber and gamess Arvid Soederhaell (Wed Jan 29 2003 - 07:08:00 PST)
    - 2drms command in ptraj Vlad Cojocaru (Tue Jan 28 2003 - 04:52:17 PST)
    - mm-pbsa error message Thomas Steinbrecher (Tue Jan 28 2003 - 07:02:04 PST)
- Gibbs tutorial question Patricia Burgess (Wed Jan 22 2003 - 12:27:34 PST)
  - Re: Gibbs tutorial question David A. Case (Wed Jan 22 2003 - 13:54:10 PST)
  - MM_PBSA for Linux Ram�n Gardu�o-Ju�rez (Wed Jan 22 2003 - 16:53:55 PST)
  - LAM-MPI, Oscar and Amber compile Machine.g77_lam-mpi Dr Chris L. Brown (Wed Jan 22 2003 - 19:10:34 PST)
    - Re: LAM-MPI, Oscar and Amber compile Machine.g77_lam-mpi Chuck Schneider (Thu Jan 23 2003 - 04:52:41 PST)
    - conformational sampling Robert G. Endres (Thu Jan 23 2003 - 06:17:57 PST)
    - Re: conformational sampling Carlos Simmerling (Thu Jan 23 2003 - 15:45:58 PST)
    - Polymers Ndubuisi Emmanuel Okoro (Thu Jan 23 2003 - 19:12:10 PST)
    - Chloroform Parameters N. Jiten Singh (Thu Jan 23 2003 - 21:27:24 PST)
    - How much is minimum distance pu xuemei (Thu Jan 23 2003 - 23:11:29 PST)
  - Dummy-parameters in Amber? meiselba (Thu Jan 23 2003 - 02:39:17 PST)
    - Re: Dummy-parameters in Amber? Miguel de Federico (Thu Jan 23 2003 - 03:07:14 PST)
- question on ptraj Ioana Cozmuta (Wed Jan 22 2003 - 13:01:26 PST)
problems in equilibrating NaCl solution Seongeun Yang (Tue Jan 21 2003 - 14:48:04 PST)
- Re: problems in equilibrating NaCl solution David A. Case (Fri Jan 24 2003 - 14:20:12 PST)
  - Re: problems in equilibrating NaCl solution Seongeun Yang (Fri Jan 24 2003 - 16:13:41 PST)
- terminal phosphate group in RNA David A. Case (Fri Jan 24 2003 - 16:03:06 PST)
new amino acid residues Nick Polfer (Thu Jan 30 2003 - 04:58:41 PST)
- Re: new amino acid residues David A. Case (Thu Jan 30 2003 - 09:46:35 PST)
- Quasi-harmonic analysis Pratul Agarwal (Thu Jan 30 2003 - 15:48:22 PST)
  - Re: Quasi-harmonic analysis David A. Case (Thu Jan 30 2003 - 17:58:32 PST)
    - ptraj distanse question Sichun Yang (Thu Jan 30 2003 - 20:16:06 PST)
    - Re: ptraj distanse question Lepsa (Fri Jan 31 2003 - 04:16:25 PST)
    - AMBER7 & mpich FyD (Fri Jan 31 2003 - 06:05:41 PST)
    - ptraj on Methane in water box Dvira Segal (Fri Jan 31 2003 - 02:45:03 PST)
    - Re: Quasi-harmonic analysis Miyashita, Osamu (Fri Jan 31 2003 - 10:25:23 PST)
mm-pbsa problem & possible solution Thomas Steinbrecher (Thu Jan 30 2003 - 07:51:57 PST)
- Re: mm-pbsa problem & possible solution Holger Gohlke (Thu Jan 30 2003 - 09:22:39 PST)
roar-cp : input for QM part ; output for CM2 charges hagop demirdjian (Fri Jan 31 2003 - 07:38:29 PST)
Domain/Helix movement/MD Jianhui Wu (Fri Jan 31 2003 - 08:35:18 PST)
- Re: Domain/Helix movement/MD Lepsa (Fri Jan 31 2003 - 08:52:59 PST)
- Re: Domain/Helix movement/MD Pratul Agarwal (Fri Jan 31 2003 - 13:00:54 PST)
Re: acetonitrile parameters Jose Ramon Blas (Tue Feb 04 2003 - 11:21:39 PST)
about Mg++ Lishan Yao (Wed Feb 05 2003 - 09:17:12 PST)
noninteger charge eric hu (Wed Feb 05 2003 - 10:03:08 PST)
- Re: noninteger charge David A. Case (Wed Feb 05 2003 - 10:59:32 PST)
URGENT UPDATE . frankikpendu_at_hknetmail.com (Mon Feb 17 2003 - 13:02:33 PST)
Final energy minimization step Andrei Leit�o (Tue Feb 18 2003 - 12:30:08 PST)
- Re: Final energy minimization step David A. Case (Tue Feb 18 2003 - 14:25:05 PST)
restrained atoms NTR Sichun Yang (Tue Feb 18 2003 - 13:45:33 PST)
- Re: restrained atoms NTR David A. Case (Tue Feb 18 2003 - 20:16:50 PST)
  - Re: restrained atoms NTR Sichun Yang (Wed Feb 19 2003 - 09:27:18 PST)
  - no statistics.out in mm_pbsa binding energy calculations eric hu (Wed Feb 19 2003 - 10:27:10 PST)
    - Re: no statistics.out in mm_pbsa binding energy calculations Holger Gohlke (Wed Feb 19 2003 - 10:48:59 PST)
File in the tutorial Alexei Valiaev (Tue Feb 18 2003 - 15:18:05 PST)
- Re: File in the tutorial David A. Case (Tue Feb 18 2003 - 14:19:24 PST)
antechamber and its prepin files Steve Seibold (Wed Feb 19 2003 - 11:11:23 PST)
- Re: antechamber and its prepin files David A. Case (Wed Feb 19 2003 - 13:08:55 PST)
  - Energy calculation Sichun Yang (Wed Feb 19 2003 - 14:25:45 PST)
    - Re: Energy calculation Holger Gohlke (Wed Feb 19 2003 - 14:54:30 PST)
    - Re: Energy calculation Sichun Yang (Wed Feb 19 2003 - 18:51:11 PST)
Web site problems. caldwell.heimdal.compchem.ucsf.edu (Wed Feb 19 2003 - 13:47:11 PST)
Minimization after dynamic? Andrei Leitão (Wed Feb 19 2003 - 16:13:31 PST)
Nmode thenmalar rathinavelan (Wed Feb 19 2003 - 22:21:03 PST)
- Re: Nmode Holger Gohlke (Thu Feb 20 2003 - 10:35:57 PST)
probelms with antechamber Yongmei Wang (Thu Feb 20 2003 - 12:09:44 PST)
- Re: probelms with antechamber David A. Case (Thu Feb 20 2003 - 17:19:24 PST)
AMBER6 problem in Solaris 8 S.Swaminathan (Fri Feb 21 2003 - 11:18:19 PST)
- Re: AMBER6 problem in Solaris 8 David A. Case (Thu Feb 20 2003 - 23:56:21 PST)
  - Re: AMBER6 problem in Solaris 8 S.Swaminathan (Wed Feb 26 2003 - 10:10:56 PST)
    - Re: AMBER6 problem in Solaris 8 Sanjeev B.S. (Tue Feb 25 2003 - 21:03:55 PST)
about urea and glycerol Nikolai Smolin (Fri Feb 21 2003 - 03:04:33 PST)
minimization with fixed UC dimensions Ioana Cozmuta (Fri Feb 21 2003 - 11:38:01 PST)
- Re: minimization with fixed UC dimensions David A. Case (Fri Feb 21 2003 - 12:00:09 PST)
  - Re: minimization with fixed UC dimensions Ioana Cozmuta (Fri Feb 21 2003 - 17:24:32 PST)
failure of minimization Ioana Cozmuta (Fri Feb 21 2003 - 17:10:37 PST)
- RE: failure of minimization Yong Duan (Fri Feb 21 2003 - 18:34:04 PST)
  - RE: failure of minimization Ioana Cozmuta (Mon Feb 24 2003 - 11:33:58 PST)
    - RE: failure of minimization Ioana Cozmuta (Mon Feb 24 2003 - 15:11:23 PST)
    - RE: failure of minimization Yong Duan (Mon Feb 24 2003 - 17:42:14 PST)
new-style prmtop file chernhoe (Sun Feb 23 2003 - 19:45:46 PST)
- Re: new-style prmtop file David A. Case (Sun Feb 23 2003 - 21:38:29 PST)
  - Re: new-style prmtop file chernhoe (Sun Feb 23 2003 - 22:48:47 PST)
Binary output switch (IOUTFM=1) broken in sander? (AMBER7) John D. Chodera (Sun Feb 23 2003 - 20:49:56 PST)
GB/SA Franck Chevalier (Mon Feb 24 2003 - 01:04:22 PST)
- Re: GB/SA David A. Case (Fri Feb 28 2003 - 18:29:29 PST)
Force field ? Subba.Raju (Mon Feb 24 2003 - 02:17:54 PST)
adjust virial Ioana Cozmuta (Tue Feb 25 2003 - 00:15:45 PST)
problem patch files chernhoe (Tue Feb 25 2003 - 00:15:44 PST)
ptraj residue number out of range Giulio Rastelli (Tue Feb 25 2003 - 09:20:30 PST)
- Re: ptraj residue number out of range Holger Gohlke (Tue Feb 25 2003 - 08:24:00 PST)
- Re: ptraj residue number out of range Giulio Rastelli (Tue Feb 25 2003 - 15:35:24 PST)
- Re: ptraj residue number out of range Holger Gohlke (Tue Feb 25 2003 - 09:31:14 PST)
Compilation error of Amber 7 using pgi and mpich on Linux Cluster Fabrice Yerly (Tue Feb 25 2003 - 05:02:00 PST)
- Re: Compilation error of Amber 7 using pgi and mpich on Linux Cluster Tormod Skauge (Tue Feb 25 2003 - 07:00:19 PST)
Info request: Amber on 64-bit CPUs Daniel Svozil (Tue Feb 25 2003 - 05:34:57 PST)
- Re: Info request: Amber on 64-bit CPUs Chuck Schneider (Tue Feb 25 2003 - 07:02:49 PST)
- Re: Info request: Amber on 64-bit CPUs Carlos P. Sosa (Tue Feb 25 2003 - 09:43:23 PST)
(no subject) Robert Cave (Tue Feb 25 2003 - 11:55:51 PST)
- Re: Amber under Linux Scott Brozell (Tue Feb 25 2003 - 13:13:11 PST)
EXTRA_PTS: frtype 2 Should not be here Artem Mamonov (Tue Feb 25 2003 - 14:09:56 PST)
- Re: EXTRA_PTS: frtype 2 Should not be here Artem Mamonov (Tue Feb 25 2003 - 15:49:42 PST)
mm_pbsa Layi Adekoya (Wed Feb 26 2003 - 02:05:35 PST)
- Fw: mm_pbsa Lepsa (Fri May 24 2002 - 07:27:21 PDT)
- subdomain moving as a rigid unit during MD Marcela Madrid (Fri May 24 2002 - 08:59:40 PDT)
- Re: mm_pbsa Lepsa (Wed Feb 26 2003 - 04:41:47 PST)
Analysis of close waters Markus Drumm (Wed Feb 26 2003 - 04:23:25 PST)
Namelist READ error Thomas Steinbrecher (Wed Feb 26 2003 - 04:54:46 PST)
Re: Namelist READ error - solved Thomas Steinbrecher (Wed Feb 26 2003 - 06:54:54 PST)
nmode on Linux : another memory question E.S. (Thu Feb 27 2003 - 14:42:15 PST)
Beyond 1,000,000 atoms... Vlad (Thu Feb 27 2003 - 17:45:14 PST)
seperate one trajectory file into two eric hu (Thu Feb 27 2003 - 19:02:58 PST)
- Re: seperate one trajectory file into two Holger Gohlke (Thu Feb 27 2003 - 19:45:50 PST)
protein dna simulation chernhoe (Thu Feb 27 2003 - 20:13:58 PST)
how to validate ff parameters obtained from antechamber Jiyoung Heo (Thu Feb 27 2003 - 21:27:54 PST)
- Why the NMA discrepancies? Jones de Andrade (Sun Mar 16 2003 - 17:09:16 PST)
  - RE: Why the NMA discrepancies? Yong Duan (Sun Mar 16 2003 - 19:46:57 PST)
    - RE: Why the NMA discrepancies? Jones de Andrade (Mon Mar 17 2003 - 06:35:05 PST)
Protein Reorientation Gemma Kinsella (Mon Mar 03 2003 - 05:54:48 PST)
- Re: Protein Reorientation samantha hughes (Mon Mar 03 2003 - 06:02:11 PST)
- Re: Protein Reorientation Carlos Simmerling (Mon Mar 03 2003 - 07:39:19 PST)
parameters GB/SA Franck Chevalier (Mon Mar 03 2003 - 07:41:52 PST)
GIBBS - Non periodic simulations. Miguel de Federico (Mon Mar 03 2003 - 10:08:03 PST)
tautp in gibbs Sophia Kondratova (Mon Mar 03 2003 - 12:57:03 PST)
- Re: tautp in gibbs David A. Case (Mon Mar 03 2003 - 13:59:35 PST)
Leap to prep Dominico J Vigil (Mon Mar 03 2003 - 14:26:45 PST)
- Re: Leap to prep caldwell.heimdal.compchem.ucsf.edu (Mon Mar 03 2003 - 15:03:25 PST)
Forwarded mail.... amber.heimdal.compchem.ucsf.edu (Wed Mar 05 2003 - 10:05:51 PST)
- :trouble shooting in amber amit kumar (Thu Oct 19 2000 - 14:39:41 PDT)
- sander test /Amber6 Giulio Rastelli (Fri Oct 20 2000 - 01:29:03 PDT)
  - Re: sander test /Amber6 Nathalie Godbout (Fri Oct 20 2000 - 06:14:50 PDT)
  - missing parameters Jie Lu (Fri Oct 20 2000 - 11:25:28 PDT)
- Parm98 parameters Simon Cross (Fri Oct 20 2000 - 01:57:10 PDT)
- teleap Carlos Simmerling (Wed Mar 05 2003 - 10:38:42 PST)
- Re: Forwarded mail.... Natasja Brooijmans (Wed Mar 05 2003 - 11:02:42 PST)
pressure variation control (fwd) amber.heimdal.compchem.ucsf.edu (Wed Mar 05 2003 - 10:05:29 PST)
Max residues (fwd) amber.heimdal.compchem.ucsf.edu (Wed Mar 05 2003 - 10:05:20 PST)
- Re: Max residues (fwd) amber.heimdal.compchem.ucsf.edu (Fri Mar 07 2003 - 09:12:29 PST)
- Re: Max residues (fwd) amber.heimdal.compchem.ucsf.edu (Fri Mar 07 2003 - 09:12:54 PST)
Re: Protein Reorientation (fwd) amber.heimdal.compchem.ucsf.edu (Wed Mar 05 2003 - 10:05:11 PST)
nasty npt md problem (fwd) amber.heimdal.compchem.ucsf.edu (Wed Mar 05 2003 - 10:05:58 PST)
- Re: nasty npt md problem (fwd) David A. Case (Sun Mar 09 2003 - 21:58:58 PST)
install amber7 on Linux (fwd) amber.heimdal.compchem.ucsf.edu (Fri Mar 07 2003 - 09:13:40 PST)
- Re: install amber7 on Linux (fwd) David A. Case (Fri Mar 07 2003 - 09:51:55 PST)
Re: Forwarded mail.... (fwd) amber.heimdal.compchem.ucsf.edu (Fri Mar 07 2003 - 09:12:19 PST)
- Re: Forwarded mail.... (fwd) amber.heimdal.compchem.ucsf.edu (Fri Mar 07 2003 - 09:12:49 PST)
intra-perturbed group (fwd) amber.heimdal.compchem.ucsf.edu (Fri Mar 07 2003 - 09:13:57 PST)
- Re: intra-perturbed group (fwd) David A. Case (Fri Mar 07 2003 - 09:55:29 PST)
amber installation problems (fwd) amber.heimdal.compchem.ucsf.edu (Fri Mar 07 2003 - 09:12:44 PST)
Notes: Compiling Amber 7 on Mac OS X (fwd) amber.heimdal.compchem.ucsf.edu (Fri Mar 07 2003 - 09:13:28 PST)
GB simulation on protein (fwd) amber.heimdal.compchem.ucsf.edu (Fri Mar 07 2003 - 09:13:34 PST)
- Re: GB simulation on protein (fwd) David A. Case (Fri Mar 07 2003 - 10:02:13 PST)
lanes when solvating in LEAP (fwd) amber.heimdal.compchem.ucsf.edu (Fri Mar 07 2003 - 09:14:24 PST)
- Re: lanes when solvating in LEAP (fwd) David A. Case (Fri Mar 07 2003 - 09:56:39 PST)
  - Water density and force output questions dianah.unm.edu (Fri Mar 07 2003 - 15:36:41 PST)
    - Re: Water density and force output questions David A. Case (Fri Mar 07 2003 - 16:15:38 PST)
Notes: Compiling Amber 7 on Mac OS X (fwd) amber.heimdal.compchem.ucsf.edu (Fri Mar 07 2003 - 09:13:10 PST)
amber7 & mpich on sgi (fwd) amber.heimdal.compchem.ucsf.edu (Fri Mar 07 2003 - 09:13:22 PST)
- Re: amber7 & mpich on sgi (fwd) David A. Case (Fri Mar 07 2003 - 11:24:00 PST)
question about dummy atoms? (fwd) amber.heimdal.compchem.ucsf.edu (Fri Mar 07 2003 - 09:14:06 PST)
GRASP (fwd) amber.heimdal.compchem.ucsf.edu (Fri Mar 07 2003 - 09:13:49 PST)
- Re: GRASP (fwd) Peter Gannett (Fri Mar 07 2003 - 10:50:01 PST)
pressure variation control (fwd) amber.heimdal.compchem.ucsf.edu (Fri Mar 07 2003 - 09:13:16 PST)
- Re: pressure variation control (fwd) amber.heimdal.compchem.ucsf.edu (Fri Mar 07 2003 - 09:12:35 PST)
about maxium number of residues read by xleap (fwd) amber.heimdal.compchem.ucsf.edu (Fri Mar 07 2003 - 09:13:03 PST)
three digits in the charges of extPDB Giulio Rastelli (Fri Mar 07 2003 - 16:27:48 PST)
- Re: three digits in the charges of extPDB David A. Case (Fri Mar 07 2003 - 13:21:39 PST)
Re: pressure variation control Vlad Cojocaru (Fri Mar 07 2003 - 10:20:38 PST)
surface accesible area Yongmei Wang (Fri Mar 07 2003 - 15:22:22 PST)
- Re: surface accesible area David A. Case (Fri Mar 07 2003 - 16:11:02 PST)
(no subject) Steve Seibold (Sat Mar 08 2003 - 11:51:35 PST)
how to convert the amber force field files to any proper format that can be used by gaussian98 Ye Mei (Sat Mar 08 2003 - 19:06:10 PST)
- RE: how to convert the amber force field files to any proper format that can be used by gaussian98 Yong Duan (Sun Mar 09 2003 - 20:17:33 PST)
EWALD Yuguang Mu (Sun Mar 09 2003 - 08:46:16 PST)
- Re: EWALD David A. Case (Sun Mar 09 2003 - 14:10:40 PST)
  - Re: EWALD caldwell.heimdal.compchem.ucsf.edu (Sun Mar 09 2003 - 15:41:02 PST)
    - Re: EWALD caldwell.heimdal.compchem.ucsf.edu (Sun Mar 09 2003 - 19:11:51 PST)
  - Re: EWALD Yuguang Mu (Sun Mar 09 2003 - 23:13:31 PST)
question about mm_pbsa Lishan Yao (Sun Mar 09 2003 - 18:26:47 PST)
- Re: question about mm_pbsa Holger Gohlke (Sun Mar 09 2003 - 19:31:10 PST)
  - Re: question about mm_pbsa Joachim Reichelt (Mon Mar 10 2003 - 04:43:58 PST)
barium Patrizia Rossi (Sun Mar 09 2003 - 23:38:13 PST)
velocities sara nunez (Mon Mar 10 2003 - 02:30:09 PST)
- Re: velocities David A. Case (Mon Mar 10 2003 - 08:04:58 PST)
- Re: velocities Bill Ross (Mon Mar 10 2003 - 13:14:57 PST)
Fourth European Workshop in Drug Design Andrea Tafi (Mon Mar 10 2003 - 06:12:40 PST)
profec Michael Trieb (Mon Mar 10 2003 - 06:46:40 PST)
Parameters: additive, lone pair William Wei (Mon Mar 10 2003 - 06:57:35 PST)
- Re: Parameters: additive, lone pair David A. Case (Mon Mar 10 2003 - 08:11:35 PST)
question about mm_pbsa? Lishan Yao (Mon Mar 10 2003 - 08:04:17 PST)
Barium Holger Gohlke (Mon Mar 10 2003 - 08:21:20 PST)
Parameters for Hyddantoin derivatives? William Wei (Mon Mar 10 2003 - 10:13:48 PST)
installing AMBER 7 Mauro Carlos Costa Ribeiro (Mon Mar 10 2003 - 11:11:46 PST)
- Re: installing AMBER 7 Scott Brozell (Mon Mar 10 2003 - 11:42:23 PST)
- Re: installing AMBER 7 Chuck Schneider (Mon Mar 10 2003 - 12:05:37 PST)
Machine for IBM Horizon Sichun Yang (Mon Mar 10 2003 - 14:23:35 PST)
- Re: Machine for IBM Horizon David A. Case (Mon Mar 10 2003 - 15:04:09 PST)
- Re: Machine for IBM Horizon Carlos P. Sosa (Mon Mar 10 2003 - 15:13:49 PST)
subscribe Xiaodong ZHANG (Mon Mar 10 2003 - 14:46:24 PST)
using xleap Mauro Carlos Costa Ribeiro (Tue Mar 11 2003 - 10:33:47 PST)
- Re: using xleap David A. Case (Tue Mar 11 2003 - 11:05:56 PST)
- Re: using xleap caldwell.heimdal.compchem.ucsf.edu (Tue Mar 11 2003 - 11:31:47 PST)
- Re: using xleap Mauro Carlos Costa Ribeiro (Wed Mar 12 2003 - 09:29:23 PST)
Analysis of Curves program output Andrei Leitão (Tue Mar 11 2003 - 11:34:13 PST)
Solaris Benchmark for Amber7 Jeffrey Dyason (Tue Mar 11 2003 - 17:04:53 PST)
sequence Ioana Cozmuta (Tue Mar 11 2003 - 17:23:02 PST)
- Re: sequence CUI, Guanglei (Tue Mar 11 2003 - 20:50:59 PST)
Regarding the quotation for AMBER 7 Programme Prof.S.B.Rai (Wed Mar 12 2003 - 08:53:00 PST)
atom type Emmanuel Giudice (Wed Mar 12 2003 - 09:21:18 PST)
intel ifc amber5 and mpich-1.2.5 Karl N. Kirschner (Wed Mar 12 2003 - 13:25:46 PST)
- Re: intel ifc amber5 and mpich-1.2.5 Scott Brozell (Wed Mar 12 2003 - 14:09:21 PST)
Amber Web page caldwell.heimdal.compchem.ucsf.edu (Wed Mar 12 2003 - 13:48:04 PST)
Amber web page caldwell.heimdal.compchem.ucsf.edu (Wed Mar 12 2003 - 14:28:20 PST)
problem of mass center yuan bo (Wed Mar 12 2003 - 19:06:32 PST)
- Re: problem of mass center David A. Case (Wed Mar 12 2003 - 21:02:10 PST)
The gblambda parameter Thomas Steinbrecher (Thu Mar 13 2003 - 06:29:03 PST)
- Re: The gblambda parameter David A. Case (Thu Mar 13 2003 - 08:34:08 PST)
tip5p water model Marvin Rich (Thu Mar 13 2003 - 09:44:04 PST)
- Re: tip5p water model Carlos Simmerling (Thu Mar 13 2003 - 09:58:31 PST)
  - Re: tip5p water model Marvin Rich (Thu Mar 13 2003 - 10:35:22 PST)
    - Re: tip5p water model David A. Case (Thu Mar 13 2003 - 11:53:26 PST)
[Fwd: MPI problem in modi4.ncsa.uiuc.edu] Eddy (Thu Mar 13 2003 - 21:57:23 PST)
- Re: [Fwd: MPI problem in modi4.ncsa.uiuc.edu] David A. Case (Fri Mar 14 2003 - 08:30:48 PST)
Algorithm for the motion equations? Marco Aurelio Correia Preto (Fri Mar 14 2003 - 04:20:41 PST)
- Re: Algorithm for the motion equations? Andreas Svrcek-Seiler (Fri Mar 14 2003 - 05:11:07 PST)
AMBER/FEP: RESP charges Ghislain Deslongchamps (Fri Mar 14 2003 - 05:37:13 PST)
- Re: AMBER/FEP: RESP charges caldwell.heimdal.compchem.ucsf.edu (Fri Mar 14 2003 - 07:32:48 PST)
Compiling Amber7 for linux Miguel de Federico (Fri Mar 14 2003 - 08:49:06 PST)
- Re: Compiling Amber7 for linux caldwell.heimdal.compchem.ucsf.edu (Fri Mar 14 2003 - 08:59:07 PST)
CMC/MD Andrew Petersen (Fri Mar 14 2003 - 11:31:29 PST)
- Re: CMC/MD David A. Case (Fri Mar 14 2003 - 13:01:57 PST)
leap remove command CUI, Guanglei (Fri Mar 14 2003 - 14:19:12 PST)
- Re: leap remove command darden (Sun Mar 16 2003 - 13:26:02 PST)
  - RE: leap remove command Yong Duan (Sun Mar 16 2003 - 19:31:12 PST)
- RE: leap remove command CUI, Guanglei (Sun Mar 16 2003 - 21:30:44 PST)
  - RE: leap remove command Yong Duan (Mon Mar 17 2003 - 04:32:21 PST)
Preparation of RESP input from GAUSSIAN output Martin Klvana (Mon Mar 17 2003 - 04:55:24 PST)
- Re: Preparation of RESP input from GAUSSIAN output Lepsa (Mon Mar 17 2003 - 05:11:41 PST)
Mg2+ ion parameters Arpita Mitra (Mon Mar 17 2003 - 16:09:52 PST)
Resp Charges for large ligand. Bengt Svensson (Mon Mar 17 2003 - 16:11:42 PST)
- Re: Resp Charges for large ligand. John Bushnell (Mon Mar 17 2003 - 16:47:33 PST)
Lipids Gemma Kinsella (Tue Mar 18 2003 - 00:43:16 PST)
- Re: Lipids Arvid Soederhaell (Tue Mar 18 2003 - 02:33:15 PST)
namelist read: variable not in namelist Majid moghaddam (Tue Mar 18 2003 - 02:18:46 PST)
Diferences in gibbs Miguel de Federico (Tue Mar 18 2003 - 01:37:21 PST)
- Re: Diferences in gibbs David A. Case (Tue Mar 18 2003 - 07:43:10 PST)
PBC without solvent Franck Chevalier (Tue Mar 18 2003 - 02:37:55 PST)
- Re: PBC without solvent CUI, Guanglei (Tue Mar 18 2003 - 06:58:41 PST)
- Re: PBC without solvent David A. Case (Tue Mar 18 2003 - 07:38:04 PST)
- Re: PBC without solvent caldwell.heimdal.compchem.ucsf.edu (Tue Mar 18 2003 - 08:21:40 PST)
hydrogen bonding seraphimo.gmx.de (Tue Mar 18 2003 - 07:51:48 PST)
using antechamber Mauro Carlos Costa Ribeiro (Tue Mar 18 2003 - 08:39:44 PST)
- Re: using antechamber Pascal Bonnet (Tue Mar 18 2003 - 08:36:23 PST)
- Re: using antechamber David A. Case (Tue Mar 18 2003 - 08:54:49 PST)
Question about mm_pbsa? Lishan Yao (Tue Mar 18 2003 - 08:43:51 PST)
- Re: Question about mm_pbsa? Holger Gohlke (Tue Mar 18 2003 - 09:06:20 PST)
Maximum molecular size for Amber? Wen Li (Tue Mar 18 2003 - 11:21:16 PST)
question about mm_pbsa? Lishan Yao (Tue Mar 18 2003 - 12:00:46 PST)
- Re: question about mm_pbsa? Holger Gohlke (Tue Mar 18 2003 - 13:05:29 PST)
DelphiLinux V. 4 Segmentation Fault Thomas Steinbrecher (Wed Mar 19 2003 - 05:10:16 PST)
a perl question for Hbond occupancies analysis Vlad Cojocaru (Wed Mar 19 2003 - 05:43:30 PST)
NTX / INIT inconsistency Sichun Yang (Wed Mar 19 2003 - 14:31:36 PST)
- Re: NTX / INIT inconsistency caldwell.heimdal.compchem.ucsf.edu (Wed Mar 19 2003 - 15:13:15 PST)
Carnal processing of binary mdcrd files (IOUTFM=1) Sander 7 Chris Switzer (Wed Mar 19 2003 - 19:14:01 PST)
Polarization simulation Lepsa (Thu Mar 20 2003 - 01:55:33 PST)
AMBER6 in Solaris 8 S.Swaminathan (Thu Mar 20 2003 - 16:28:11 PST)
- Re: AMBER6 in Solaris 8 S.Swaminathan (Fri Mar 21 2003 - 10:37:45 PST)
- Re: AMBER6 in Solaris 8 Sanjeev B.S. (Fri Mar 21 2003 - 01:44:37 PST)
GB vs. explicit solvent calculations Thomas Steinbrecher (Thu Mar 20 2003 - 05:53:44 PST)
- Re: GB vs. explicit solvent calculations Carlos Simmerling (Thu Mar 20 2003 - 06:25:12 PST)
- RE: GB vs. explicit solvent calculations Yong Duan (Thu Mar 20 2003 - 06:48:30 PST)
- Re: GB vs. explicit solvent calculations David A. Case (Thu Mar 20 2003 - 07:46:53 PST)
  - Install Amber7 in linux cluster Wen Li (Mon Jun 02 2003 - 07:20:51 PDT)
    - Re: Install Amber7 in linux cluster Viktor Hornak (Mon Jun 02 2003 - 08:11:10 PDT)
mpirun problem! William Wei (Thu Mar 20 2003 - 08:21:17 PST)
Move the atom with specific velosity Alexei Valiaev (Thu Mar 20 2003 - 12:28:19 PST)
a question about simulation at high temperature Xiaoqin Huang (Thu Mar 20 2003 - 05:38:24 PST)
- Re: a question about simulation at high temperature Carlos Simmerling (Thu Mar 20 2003 - 11:25:19 PST)
a question about simulation at high temperature Xiaoqin Huang (Thu Mar 20 2003 - 09:24:18 PST)
doubts thenmalar rathinavelan (Thu Mar 20 2003 - 20:26:50 PST)
- RE: doubts Yong Duan (Fri Mar 21 2003 - 06:30:59 PST)
- Re: doubts David A. Case (Sat Mar 22 2003 - 08:56:11 PST)
reg. problem with SM and ICE libraries S.Swaminathan (Fri Mar 21 2003 - 12:56:59 PST)
MM-PBSA results Thomas Steinbrecher (Fri Mar 21 2003 - 05:15:25 PST)
Script and MPICH FyD (Fri Mar 21 2003 - 06:01:40 PST)
amber7 on sgi Wiktor Jurkowski (Fri Mar 21 2003 - 06:26:54 PST)
MM_PBSA (Amber7) and delphi Sue Heavner (Fri Mar 21 2003 - 06:27:00 PST)
- Re: MM_PBSA (Amber7) and delphi CUI, Guanglei (Fri Mar 21 2003 - 07:04:04 PST)
ptraj html documentation still available? Vlad Cojocaru (Fri Mar 21 2003 - 06:39:08 PST)
Hbond analysis with Carnal Vlad Cojocaru (Fri Mar 21 2003 - 06:50:36 PST)
Helical Drift Gemma Kinsella (Fri Mar 21 2003 - 08:55:17 PST)
waterbox GUILLERMINA L ESTIU (Fri Mar 21 2003 - 14:22:41 PST)
- Re: waterbox caldwell.heimdal.compchem.ucsf.edu (Fri Mar 21 2003 - 14:31:07 PST)
- Re: waterbox caldwell.heimdal.compchem.ucsf.edu (Fri Mar 21 2003 - 15:33:31 PST)
writing mol2 files using antechamber Giulio Rastelli (Sat Mar 22 2003 - 15:41:41 PST)
- Re: writing mol2 files using antechamber David A. Case (Sat Mar 22 2003 - 10:08:29 PST)
format of 'mask' in ptraj Jiyoung Heo (Sun Mar 23 2003 - 22:46:18 PST)
- Re: format of 'mask' in ptraj Jose Ramon Blas (Mon Mar 24 2003 - 08:14:33 PST)
RMS in carnal Shunzhou Wan (Mon Mar 24 2003 - 03:12:53 PST)
Protein-Inhibitor binding afinity William Wei (Mon Mar 24 2003 - 10:02:04 PST)
- Summary: Protein-Inhibitor binding affinity William Wei (Fri Mar 28 2003 - 06:51:30 PST)
improper torsion for X -CB-CB-X yuann (Mon Mar 24 2003 - 19:23:33 PST)
- Re: improper torsion for X -CB-CB-X Scott Brozell (Mon Mar 24 2003 - 20:16:13 PST)
  - Re: improper torsion for X -CB-CB-X sychen (Mon Mar 24 2003 - 21:16:17 PST)
abt. Plastocyanin tutorial S.Swaminathan (Tue Mar 25 2003 - 10:51:50 PST)
problem with "Example 3" tutorials S.Swaminathan (Tue Mar 25 2003 - 14:39:23 PST)
- Re: problem with "Example 3" tutorials S.Swaminathan (Fri Mar 28 2003 - 11:41:20 PST)
Antechamber atom types Simon Lenzen (Tue Mar 25 2003 - 02:41:30 PST)
antechamber -rn keyword Giulio Rastelli (Tue Mar 25 2003 - 15:06:48 PST)
- Re: antechamber -rn keyword David A. Case (Fri Mar 28 2003 - 11:54:46 PST)
unit of energy Monica (Thu Mar 27 2003 - 00:01:56 PST)
- Re: unit of energy Holger Gohlke (Fri Mar 28 2003 - 16:36:02 PST)
Re: Extracting structures Jose Ramon Blas (Thu Mar 27 2003 - 08:18:31 PST)
how to generate FF of DNA complex? tang kwa (Thu Mar 27 2003 - 07:43:47 PST)
Install Amber 7 Wen Li (Thu Mar 27 2003 - 08:01:10 PST)
Install Amber 7 Wen Li (Thu Mar 27 2003 - 08:05:53 PST)
Disulphide bridges Vlad Cojocaru (Thu Mar 27 2003 - 09:10:24 PST)
- Re: Disulphide bridges caldwell.heimdal.compchem.ucsf.edu (Thu Mar 27 2003 - 10:05:06 PST)
CHARMm force field for AMBER kbyun.wesleyan.edu (Thu Mar 27 2003 - 09:18:17 PST)
Re: tleap in large systems David A. Case (Thu Mar 27 2003 - 12:43:01 PST)
- Re: tleap in large systems GUILLERMINA L ESTIU (Thu Mar 27 2003 - 12:57:21 PST)
Re: SANDER vs GIBBS equilibration David A. Case (Thu Mar 27 2003 - 12:44:08 PST)
- Re: SANDER vs GIBBS equilibration Carlos Simmerling (Thu Mar 27 2003 - 12:58:58 PST)
Antechamber questions Scott Shandler (Thu Mar 27 2003 - 17:35:32 PST)
- Re: Antechamber questions David A. Case (Fri Mar 28 2003 - 11:58:00 PST)
  - Re: Antechamber questions Scott Shandler (Mon Mar 31 2003 - 15:42:35 PST)
  - atom position restraints Yuuki Komata (Tue Apr 29 2003 - 05:44:25 PDT)
sander outputs S.Swaminathan (Fri Mar 28 2003 - 11:47:18 PST)
- Re: sander outputs Holger Gohlke (Fri Mar 28 2003 - 16:26:10 PST)
Parameters for Cy3 and Fluorescein Vlad Cojocaru (Fri Mar 28 2003 - 04:27:14 PST)
ambpdb GUILLERMINA L ESTIU (Fri Mar 28 2003 - 09:05:09 PST)
- Re: ambpdb David A. Case (Fri Mar 28 2003 - 10:42:34 PST)
Antechamber Manual Nicholson, James D Mr ARO (Fri Mar 28 2003 - 12:17:12 PST)
Examples for Energy Minimisation methods S.Swaminathan (Tue Apr 01 2003 - 12:35:41 PST)
- Re: Examples for Energy Minimisation methods Carlos P. Sosa (Tue Apr 01 2003 - 10:08:27 PST)
Polarizable simulation2 Lepsa (Tue Apr 01 2003 - 04:25:22 PST)
- Re: Polarizable simulation2 David A. Case (Tue Apr 01 2003 - 13:49:39 PST)
Problem of Hbond in CARNAL yuann (Tue Apr 01 2003 - 04:08:59 PST)
- Re: Problem of Hbond in CARNAL sychen (Tue Apr 01 2003 - 06:23:11 PST)
size of a simulation system Wen Li (Tue Apr 01 2003 - 07:49:42 PST)
- Re: size of a simulation system David A. Case (Tue Apr 01 2003 - 13:44:14 PST)
- RE: size of a simulation system Kristina Furse (Tue Apr 01 2003 - 14:36:01 PST)
- Re: size of a simulation system Pratul Agarwal (Wed Apr 02 2003 - 06:32:44 PST)
  - Re: size of a simulation system Ioana Cozmuta (Wed Apr 02 2003 - 10:37:40 PST)
    - Re: size of a simulation system Pratul Agarwal (Wed Apr 02 2003 - 12:02:29 PST)
AMBER pdb help - lost atoms kxg2248.njit.edu (Tue Apr 01 2003 - 11:39:27 PST)
- Re: AMBER pdb help - lost atoms David A. Case (Tue Apr 01 2003 - 12:19:35 PST)
  - Re: AMBER pdb help - lost atoms Ioana Cozmuta (Tue Apr 01 2003 - 14:21:46 PST)
    - Re: AMBER pdb help - lost atoms David A. Case (Tue Apr 01 2003 - 18:17:41 PST)
A weird antechamber error Yuhui Cheng (Tue Apr 01 2003 - 20:21:46 PST)
- Re: A weird antechamber error David A. Case (Wed Apr 02 2003 - 07:24:12 PST)
About electrostatic force calculations Soonmin Jang (Tue Apr 01 2003 - 21:58:38 PST)
old prmtop format in AMBER 6 differs from what is presented in AMBER 7 manual Filip Ryj�cek (Wed Apr 02 2003 - 04:29:07 PST)
Using MPI, PBS Venkata S Koppuravuri (Wed Apr 02 2003 - 10:58:23 PST)
- Re: Using MPI, PBS Ioana Cozmuta (Wed Apr 02 2003 - 11:13:01 PST)
  - Re: Using MPI, PBS Carlos Simmerling (Wed Apr 02 2003 - 11:29:41 PST)
(no subject) dicksmit.umich.edu (Wed Apr 02 2003 - 11:32:37 PST)
Beyond 1,000,000 atoms Vlad (Wed Apr 02 2003 - 14:45:21 PST)
- New Machine.sgi_mpi file Roberto Gomperts (Thu Apr 03 2003 - 10:33:35 PST)
Side-chain/main-chain decomposition in MM-GBSA Lepsa (Thu Apr 03 2003 - 00:24:35 PST)
- Re: Side-chain/main-chain decomposition in MM-GBSA Holger Gohlke (Thu Apr 03 2003 - 14:46:52 PST)
Hydrogen bond energy Dr.K.Veluraja (Thu Apr 03 2003 - 02:37:02 PST)
- Re: Hydrogen bond energy David A. Case (Thu Apr 03 2003 - 09:26:04 PST)
Unit of velocity A. Hungie (Thu Apr 03 2003 - 05:38:59 PST)
- Re: Unit of velocity David A. Case (Thu Apr 03 2003 - 09:18:11 PST)
- Re: Unit of velocity A. Hungie (Thu Apr 03 2003 - 09:46:18 PST)
Re: AMBER pdb help - lost atoms - Part 2 David A. Case (Thu Apr 03 2003 - 09:23:41 PST)
- Re: AMBER pdb help - lost atoms - Part 2 kxg2248.njit.edu (Thu Apr 03 2003 - 09:50:29 PST)
frcmod file Wen Li (Thu Apr 03 2003 - 12:04:34 PST)
anal question Hai-Long Wang (Thu Apr 03 2003 - 13:48:11 PST)
general minimisation methods S.Swaminathan (Fri Apr 04 2003 - 16:26:48 PST)
ptraj problem Sophia Kondratova (Fri Apr 04 2003 - 06:00:46 PST)
frcmod file for Free energy perturbation tutorial of valine to alanine dicksmit.umich.edu (Fri Apr 04 2003 - 10:06:37 PST)
free energy calculations Joseph Fernandez (Fri Apr 04 2003 - 13:18:25 PST)
please kindly help S.Swaminathan (Mon Apr 07 2003 - 19:03:34 PDT)
- Re: please kindly help David A. Case (Mon Apr 07 2003 - 08:34:21 PDT)
(no subject) Carolina Salvador-Morales (Mon Apr 07 2003 - 06:22:27 PDT)
growing side chains Robert G. Endres (Mon Apr 07 2003 - 11:37:30 PDT)
Nitro group introduction in tyrosine residue chandran karunakaran (Mon Apr 07 2003 - 12:23:33 PDT)
a-Helix direction? William Wei (Mon Apr 07 2003 - 13:26:40 PDT)
Trouble with AMBER 7 Shafinaz (Mon Apr 07 2003 - 13:59:52 PDT)
protonate S.Swaminathan (Tue Apr 08 2003 - 12:14:50 PDT)
- Re: protonate David A. Case (Tue Apr 08 2003 - 09:06:21 PDT)
- Re: protonate David A. Case (Tue Jul 01 2003 - 10:29:54 PDT)
problem with tleap S.Swaminathan (Tue Apr 08 2003 - 18:56:44 PDT)
- Re: problem with tleap David A. Case (Tue Apr 08 2003 - 09:12:34 PDT)
addles Samy Name_removed_after_user_request (Tue Apr 08 2003 - 09:56:44 PDT)
- Re: addles Carlos Simmerling (Mon Apr 14 2003 - 09:22:29 PDT)
very important Shafinaz (Tue Apr 08 2003 - 07:19:18 PDT)
- Re: very important CUI, Guanglei (Tue Apr 08 2003 - 07:47:55 PDT)
mm_pbsa & nmode FyD (Tue Apr 08 2003 - 08:04:38 PDT)
mutating residues Craig A Bayse (Tue Apr 08 2003 - 09:09:38 PDT)
The error in the trajectory file Ling Zhang (Tue Apr 08 2003 - 09:37:58 PDT)
question about MM-PBSA? Lishan Yao (Tue Apr 08 2003 - 10:21:20 PDT)
- Re: question about MM-PBSA? Lepsa (Mon Apr 21 2003 - 23:50:42 PDT)
characteristics of nucleic acids homopolymers Ioana Cozmuta (Tue Apr 08 2003 - 11:33:03 PDT)
Groups defenition Javier Cuervo (Tue Apr 08 2003 - 13:31:27 PDT)
- Re: Groups defenition David A. Case (Wed Apr 09 2003 - 08:59:11 PDT)
  - GB/SA Robert G. Endres (Wed Apr 23 2003 - 09:26:14 PDT)
    - Re: GB/SA David A. Case (Wed Apr 23 2003 - 12:36:56 PDT)
    - Re: GB/SA Robert G. Endres (Mon Apr 28 2003 - 11:10:56 PDT)
    - Re: GB/SA Robert G. Endres (Wed Apr 30 2003 - 12:57:31 PDT)
Periodic Boundary Condition in AMBER7 (the sander module)! Dat H. Nguyen (Tue Apr 08 2003 - 14:44:37 PDT)
- Re: Periodic Boundary Condition in AMBER7 (the sander module)! David A. Case (Tue Apr 08 2003 - 15:25:53 PDT)
  - Tleap chandran karunakaran (Tue Apr 08 2003 - 16:01:21 PDT)
    - Re: Tleap David A. Case (Tue Apr 08 2003 - 18:09:46 PDT)
    - Re: Tleap-metalloprotein chandran karunakaran (Thu Apr 10 2003 - 18:20:40 PDT)
    - RE: Tleap-metalloprotein Yong Duan (Thu Apr 10 2003 - 19:42:53 PDT)
nmode for S calculation wentaofu (Tue Apr 08 2003 - 16:22:47 PDT)
Trying to understand parm99.dat Sichun Yang (Tue Apr 08 2003 - 17:44:32 PDT)
- RE: Trying to understand parm99.dat Yong Duan (Tue Apr 08 2003 - 18:48:48 PDT)
SANDER Source Code Documentation Jones, Garth A (Thu Apr 10 2003 - 00:07:13 PDT)
Amber7 and mpirun on Linux Wen Li (Thu Apr 10 2003 - 11:14:59 PDT)
- Re: Amber7 and mpirun on Linux Scott Brozell (Thu Apr 10 2003 - 12:28:00 PDT)
  - RE: Amber7 and mpirun on Linux Francesc Corcho (Fri Apr 11 2003 - 04:28:32 PDT)
    - RE: Amber7 and mpirun on Linux Scott Brozell (Fri Apr 11 2003 - 12:40:38 PDT)
free energy in sander Joseph Fernandez (Thu Apr 10 2003 - 14:32:52 PDT)
- Re: free energy in sander David A. Case (Thu Apr 10 2003 - 15:45:05 PDT)
  - Re: free energy in sander Joseph Fernandez (Thu Apr 10 2003 - 19:58:30 PDT)
Usubscribe Miguel de Federico (Fri Apr 11 2003 - 01:17:04 PDT)
Bugfixes Francesc Corcho (Fri Apr 11 2003 - 04:40:08 PDT)
- Re: Bugfixes Natasja Brooijmans (Fri Apr 11 2003 - 09:49:59 PDT)
SSBonds and charge problems Steve Seibold (Fri Apr 11 2003 - 12:54:23 PDT)
- Re: SSBonds and charge problems caldwell.heimdal.compchem.ucsf.edu (Fri Apr 11 2003 - 12:50:04 PDT)
- Re: SSBonds and charge problems David A. Case (Fri Apr 11 2003 - 22:29:53 PDT)
Amber on Linux Wen Li (Sat Apr 12 2003 - 10:00:46 PDT)
- Re: Amber on Linux Viktor Hornak (Sat Apr 12 2003 - 16:41:41 PDT)
  - Re: Amber on Linux Wen Li (Sun Apr 13 2003 - 08:06:52 PDT)
    - ALA-scan problem with mm_pbsa.pl Natasja Brooijmans (Sun Apr 13 2003 - 15:21:03 PDT)
    - Re: ALA-scan problem with mm_pbsa.pl Holger Gohlke (Wed Apr 16 2003 - 10:40:44 PDT)
    - Re: ALA-scan problem with mm_pbsa.pl Natasja Brooijmans (Wed Apr 16 2003 - 11:14:55 PDT)
diffusion coefficients yuan bo (Sun Apr 13 2003 - 19:34:25 PDT)
- RE: diffusion coefficients Yong Duan (Sun Apr 13 2003 - 20:50:48 PDT)
- Re: diffusion coefficients David A. Case (Sun Apr 13 2003 - 23:03:15 PDT)
  - Metalloprotein chandran karunakaran (Mon Apr 14 2003 - 18:18:39 PDT)
- Re: diffusion coefficients Thomas Cheatham (Mon Apr 14 2003 - 14:34:39 PDT)
  - phi and psi angles analysis Xiao Jian Tan (Tue Apr 29 2003 - 16:27:17 PDT)
    - Re: phi and psi angles analysis Holger Gohlke (Tue Apr 29 2003 - 16:48:50 PDT)
    - Re: phi and psi angles analysis Guanglei Cui (Tue Apr 29 2003 - 20:31:11 PDT)
To: amber as a Nicer Person Dr. Carter, President (Mon Apr 14 2003 - 01:16:06 PDT)
A problem in Sander production dynamics yuann (Mon Apr 14 2003 - 01:37:50 PDT)
- Re: A problem in Sander production dynamics Carlos Simmerling (Mon Apr 14 2003 - 04:21:04 PDT)
- Re: A problem in Sander production dynamics Thomas Cheatham (Mon Apr 14 2003 - 14:24:31 PDT)
id_torus(): Could not find torus for atoms 1878 and 1894 Yunfeng Hu (Mon Apr 14 2003 - 15:26:18 PDT)
A problem in opening the file Khanh.Dao.iac.uib.no (Mon Apr 14 2003 - 22:01:11 PDT)
- Re: A problem in opening the file David A. Case (Mon Apr 14 2003 - 23:50:04 PDT)
  - Re: A problem in opening the file Khanh.Dao.iac.uib.no (Tue Apr 15 2003 - 00:19:58 PDT)
PME box information Khanh.Dao.iac.uib.no (Tue Apr 15 2003 - 02:56:38 PDT)
solvents aren't loading Mac Brown (Tue Apr 15 2003 - 13:20:15 PDT)
Proper Restraint usage Steve Seibold (Tue Apr 15 2003 - 13:42:59 PDT)
- Re: Proper Restraint usage David A. Case (Tue Apr 15 2003 - 14:04:50 PDT)
- Re: Proper Restraint usage CUI, Guanglei (Tue Apr 15 2003 - 14:30:22 PDT)
ibelly and ntr Youyi Peng (Tue Apr 15 2003 - 14:59:59 PDT)
- Re: ibelly and ntr David A. Case (Tue Apr 15 2003 - 16:13:11 PDT)
  - Re: ibelly and ntr sychen (Tue Apr 15 2003 - 20:03:57 PDT)
- RE: ibelly and ntr Kristina Furse (Wed Apr 16 2003 - 12:51:43 PDT)
AMBER chandran karunakaran (Tue Apr 15 2003 - 16:55:16 PDT)
- Re: AMBER CUI, Guanglei (Tue Apr 15 2003 - 17:32:12 PDT)
- Re: AMBER David A. Case (Tue Apr 15 2003 - 17:38:59 PDT)
  - Re: AMBER chandran karunakaran (Tue Apr 15 2003 - 18:25:08 PDT)
ambpdb Youyi Peng (Tue Apr 15 2003 - 18:32:22 PDT)
- Re: ambpdb Luis Gracia (Tue Apr 15 2003 - 21:40:57 PDT)
- Re: ambpdb Florian Barth (Wed Apr 16 2003 - 04:59:42 PDT)
- Re: ambpdb Venkata S Koppuravuri (Fri Apr 18 2003 - 09:14:34 PDT)
No statistical output for MM-PBSA? Lishan Yao (Tue Apr 15 2003 - 19:25:22 PDT)
- Re: No statistical output for MM-PBSA? Holger Gohlke (Wed Apr 16 2003 - 11:05:38 PDT)
CYS and HIS Youyi Peng (Wed Apr 16 2003 - 07:20:40 PDT)
- Re: CYS and HIS caldwell.heimdal.compchem.ucsf.edu (Wed Apr 16 2003 - 07:55:55 PDT)
MPI run problem William Wei (Wed Apr 16 2003 - 09:36:31 PDT)
- Re: CCL:MPI run problem Carlos Simmerling (Wed Apr 16 2003 - 13:26:42 PDT)
velocity auto-correlation function A. Hungie (Wed Apr 16 2003 - 09:25:32 PDT)
Adding ACE to chopped protein Karl N. Kirschner (Wed Apr 16 2003 - 13:08:45 PDT)
makeDIST_RST Youyi Peng (Wed Apr 16 2003 - 19:24:19 PDT)
- Re: makeDIST_RST David A. Case (Thu Apr 17 2003 - 09:50:14 PDT)
ambpdb and protonate in AMBER7 Francisco Blanco (Thu Apr 17 2003 - 04:38:29 PDT)
Organic solvents Carlos P. Sosa (Thu Apr 17 2003 - 08:17:54 PDT)
quasih cailliez (Thu Apr 17 2003 - 08:35:26 PDT)
unsubscribe from the mail list Xiaoqin Huang (Thu Apr 17 2003 - 05:15:11 PDT)
question about MM-PBSA? Lishan Yao (Thu Apr 17 2003 - 12:15:38 PDT)
- Re: question about MM-PBSA? Holger Gohlke (Thu Apr 17 2003 - 18:31:31 PDT)
  - Re: question about MM-PBSA? Lishan Yao (Fri Apr 18 2003 - 07:10:24 PDT)
topology file in large systems GUILLERMINA L ESTIU (Thu Apr 17 2003 - 14:58:35 PDT)
- Re: topology file in large systems caldwell.heimdal.compchem.ucsf.edu (Thu Apr 17 2003 - 15:25:49 PDT)
MD went crazy Youyi Peng (Fri Apr 18 2003 - 08:20:25 PDT)
- Re: MD went crazy Carlos Simmerling (Fri Apr 18 2003 - 08:20:07 PDT)
- Re: MD went crazy Youyi Peng (Fri Apr 18 2003 - 09:17:24 PDT)
- Re: MD went crazy Carlos Simmerling (Fri Apr 18 2003 - 09:17:11 PDT)
- Re: MD went crazy Youyi Peng (Fri Apr 18 2003 - 10:36:35 PDT)
  - Re: MD went crazy Michael Crowley (Fri Apr 18 2003 - 10:30:53 PDT)
- Re: MD went crazy Carlos Simmerling (Fri Apr 18 2003 - 10:31:41 PDT)
- Re: MD went crazy Youyi Peng (Fri Apr 18 2003 - 11:33:26 PDT)
- Re: MD went crazy Youyi Peng (Fri Apr 18 2003 - 11:55:51 PDT)
- Re: MD went crazy Carlos Simmerling (Fri Apr 18 2003 - 12:04:49 PDT)
- Re: MD went crazy Youyi Peng (Fri Apr 18 2003 - 12:28:14 PDT)
MM-GBSA question Javier Cuervo (Fri Apr 18 2003 - 13:39:23 PDT)
debug leap vze6jslz.verizon.net (Sat Apr 19 2003 - 11:52:40 PDT)
- Re: debug leap Scott Brozell (Sat Apr 19 2003 - 16:40:03 PDT)
AMBER chandran karunakaran (Sun Apr 20 2003 - 18:13:32 PDT)
(no subject) Khanh.Dao.iac.uib.no (Mon Apr 21 2003 - 09:35:02 PDT)
trouble with OFF files Mac Brown (Mon Apr 21 2003 - 12:07:32 PDT)
- Re: trouble with OFF files M. L. Dodson (Mon Apr 21 2003 - 13:13:24 PDT)
Problem Finishing Tutorial Derek Smith (Mon Apr 21 2003 - 16:31:00 PDT)
- Re: Problem Finishing Tutorial Ioana Cozmuta (Mon Apr 21 2003 - 16:41:13 PDT)
Re: Fwd: Re: Request for Amber7 (fwd) Rajendra P. OJHA (Tue Apr 22 2003 - 02:53:12 PDT)
Organic Solvents Petrodler.aol.com (Tue Apr 22 2003 - 03:57:11 PDT)
- Re: Organic Solvents Jose Ramon Blas (Tue Apr 22 2003 - 15:00:58 PDT)
How to use GLYCAM force field in AMBER Peng Tao (Tue Apr 22 2003 - 08:08:06 PDT)
- Re: How to use GLYCAM force field in AMBER David A. Case (Wed Apr 23 2003 - 14:51:30 PDT)
mm_pbsa_statistics.pm kbyun.wesleyan.edu (Tue Apr 22 2003 - 09:40:10 PDT)
Re: Request for Amber7 (xleap problem) John Bushnell (Tue Apr 22 2003 - 15:30:41 PDT)
converting amber to gromos format Jake Isaacs (Wed Apr 23 2003 - 06:59:19 PDT)
mm_pbsa nmode calculation kbyun.wesleyan.edu (Wed Apr 23 2003 - 11:33:17 PDT)
- Re: mm_pbsa nmode calculation Holger Gohlke (Wed Apr 23 2003 - 12:12:51 PDT)
  - Re: mm_pbsa nmode calculation kbyun.wesleyan.edu (Wed Apr 23 2003 - 13:33:55 PDT)
anyone have AMBER benchmarks with gigabit ethernet? Carlos Simmerling (Wed Apr 23 2003 - 11:37:07 PDT)
- RE: anyone have AMBER benchmarks with gigabit ethernet? Ross Walker (Thu Apr 24 2003 - 02:42:57 PDT)
- RE: anyone have AMBER benchmarks with gigabit ethernet? Ross Walker (Thu Apr 24 2003 - 06:20:07 PDT)
leap problem yuan bo (Wed Apr 23 2003 - 20:49:36 PDT)
Problem_to_open_PROTON_INFO_file Khanh.Dao.iac.uib.no (Thu Apr 24 2003 - 01:46:10 PDT)
- Re: Problem_to_open_PROTON_INFO_file David A. Case (Thu Apr 24 2003 - 08:30:32 PDT)
- Re: Problem_to_open_PROTON_INFO_file Venkata S Koppuravuri (Thu Apr 24 2003 - 12:43:59 PDT)
non bonded pair list Jean-François Taly (Thu Apr 24 2003 - 09:22:08 PDT)
- Re: non bonded pair list David A. Case (Thu Apr 24 2003 - 16:24:37 PDT)
Question: Nmode with counter ions. Masaki Tomimoto (Thu Apr 24 2003 - 10:09:02 PDT)
- Re: Question: Nmode with counter ions. David A. Case (Thu Apr 24 2003 - 16:16:22 PDT)
PSC Summer Workshop: Modeling from Protein Sequence to Structure Troy Wymore (Thu Apr 24 2003 - 10:33:39 PDT)
job stopped Youyi Peng (Thu Apr 24 2003 - 10:52:12 PDT)
- Re: job stopped CUI, Guanglei (Thu Apr 24 2003 - 11:06:25 PDT)
  - Re: job stopped Youyi Peng (Thu Apr 24 2003 - 11:49:47 PDT)
    - Re: job stopped Natasja Brooijmans (Thu Apr 24 2003 - 11:55:06 PDT)
- Re: job stopped Youyi Peng (Thu Apr 24 2003 - 13:33:37 PDT)
  - Re: job stopped CUI, Guanglei (Thu Apr 24 2003 - 13:32:29 PDT)
Future of structural biology conference David Cowburn (Thu Apr 24 2003 - 11:58:23 PDT)
Annealing blown up Nick Polfer (Thu Apr 24 2003 - 12:02:38 PDT)
- Re: Annealing blown up David A. Case (Thu Apr 24 2003 - 16:21:53 PDT)
question about H-bond in carnal? Lishan Yao (Fri Apr 25 2003 - 07:44:55 PDT)
- Re: question about H-bond in carnal? Sanjeev B.S. (Fri Apr 25 2003 - 08:35:58 PDT)
  - Re: question about H-bond in carnal? Lishan Yao (Fri Apr 25 2003 - 08:24:56 PDT)
    - Re: question about H-bond in carnal? Sanjeev B.S. (Fri Apr 25 2003 - 08:53:35 PDT)
    - Re: question about H-bond in carnal? Lishan Yao (Sun Apr 27 2003 - 17:37:13 PDT)
    - Re: question about H-bond in carnal? Sanjeev B.S. (Mon Apr 28 2003 - 23:59:15 PDT)
- Re: question about H-bond in carnal? Bill Ross (Fri Apr 25 2003 - 11:57:20 PDT)
nmode and mm_pbsa questions? wentaofu (Fri Apr 25 2003 - 13:47:48 PDT)
- Re: nmode and mm_pbsa questions? Holger Gohlke (Fri Apr 25 2003 - 15:21:05 PDT)
troubles on RS6000 Wayne Dawson (Mon Apr 28 2003 - 02:37:50 PDT)
how to restrain base pair Shuang Ding (Mon Apr 28 2003 - 11:59:58 PDT)
- Re: how to restrain base pair David A. Case (Mon Apr 28 2003 - 12:14:49 PDT)
Amber on Parallel Sun? Bengt Svensson (Mon Apr 28 2003 - 14:59:14 PDT)
Protein - DNA complex simulation - protocol Harikrishnan (Mon Apr 28 2003 - 21:40:39 PDT)
- Re: Protein - DNA complex simulation - protocol Andreas Svrcek-Seiler (Tue Apr 29 2003 - 01:50:22 PDT)
  - Re: Protein - DNA complex simulation - protocol Harikrishnan (Tue Apr 29 2003 - 06:16:25 PDT)
    - Re: Protein - DNA complex simulation - protocol Pratul Agarwal (Tue Apr 29 2003 - 07:39:18 PDT)
problem_namelist_reading Khanh.Dao.iac.uib.no (Mon Apr 28 2003 - 23:19:46 PDT)
- Re: problem_namelist_reading David A. Case (Tue Apr 29 2003 - 08:12:01 PDT)
  - Re: problem_namelist_reading Khanh.Dao.iac.uib.no (Tue Apr 29 2003 - 22:26:58 PDT)
test Dr.Rajendra Joshi (Mon Apr 28 2003 - 18:58:57 PDT)
any one has references to parallelization aspects of AMBER Satish Kumar (Tue Apr 29 2003 - 02:59:05 PDT)
- Re: any one has references to parallelization aspects of AMBER Harikrishnan (Tue Apr 29 2003 - 04:54:51 PDT)
force field parameters for phosphoserine Christoph Kluck (Tue Apr 29 2003 - 07:07:59 PDT)
- Re: force field parameters for phosphoserine David A. Case (Tue Apr 29 2003 - 07:56:48 PDT)
Description of ATOM type in GLYCAM Peng Tao (Tue Apr 29 2003 - 12:14:52 PDT)
- Re: Description of ATOM type in GLYCAM FyD (Tue Apr 29 2003 - 14:07:35 PDT)
Future of Structural Biology Conference, 2003, http://futurestructuralbiology.org David Cowburn (Tue Apr 29 2003 - 13:04:27 PDT)
about molecular dynamics ronnie (Tue Apr 29 2003 - 18:09:25 PDT)
- Re: about molecular dynamics Carlos Simmerling (Tue Apr 29 2003 - 18:14:39 PDT)
- Re: about molecular dynamics Carlos Simmerling (Tue Apr 29 2003 - 20:30:06 PDT)
atom position restraints Yuuki Komata (Tue Apr 29 2003 - 18:34:06 PDT)
Residual dipolar couplings McAteer, Kathleen (Wed Apr 30 2003 - 10:56:34 PDT)
problem about virtual box? Youyi Peng (Thu May 01 2003 - 08:49:00 PDT)
- Re: problem about virtual box? Carlos Simmerling (Thu May 01 2003 - 08:46:05 PDT)
- Re: problem about virtual box? pengyo.rwja.umdnj.edu (Thu May 01 2003 - 09:20:10 PDT)
- Re: problem about virtual box? Thomas Cheatham (Thu May 01 2003 - 10:07:52 PDT)
- Re: problem about virtual box? Youyi Peng (Thu May 01 2003 - 10:42:47 PDT)
  - Re: problem about virtual box? Thomas E. Cheatham, III (Thu May 01 2003 - 10:33:49 PDT)
Ewald: coeff, error estimate Paula Petrone (Thu May 01 2003 - 09:05:28 PDT)
- Re: Ewald: coeff, error estimate darden (Thu May 01 2003 - 14:30:48 PDT)
Simple math of memory calculation for nmode Masaki Tomimoto (Thu May 01 2003 - 11:26:08 PDT)
- Re: Simple math of memory calculation for nmode David A. Case (Thu May 01 2003 - 17:23:06 PDT)
problem on MD simulation of damage DNA Shuang Ding (Thu May 01 2003 - 13:11:04 PDT)
- Re: problem on MD simulation of damage DNA Carlos Simmerling (Thu May 01 2003 - 13:20:02 PDT)
carnal hbond Hai-Long Wang (Wed Apr 30 2003 - 11:03:39 PDT)
Questoin about temperature Maverick (Thu May 01 2003 - 22:27:29 PDT)
initial velocity Youyi Peng (Fri May 02 2003 - 07:22:52 PDT)
- Re: initial velocity Natasja Brooijmans (Fri May 02 2003 - 07:18:26 PDT)
- Re: initial velocity Carlos Simmerling (Fri May 02 2003 - 07:20:09 PDT)
Question about BELLY NMODE Masaki Tomimoto (Fri May 02 2003 - 08:30:36 PDT)
- RE: Question about BELLY NMODE Masaki Tomimoto (Fri May 02 2003 - 08:46:36 PDT)
Help with Sander test output error Donald Keidel (Fri May 02 2003 - 10:38:11 PDT)
multiple timesteps Ioana Cozmuta (Fri May 02 2003 - 15:41:51 PDT)
upper limited of memory for nmode wentaofu (Fri May 02 2003 - 17:06:06 PDT)
(no subject) Narang Manpreet Kaur (Fri May 02 2003 - 22:02:20 PDT)
(no subject) smolnar.jadeinc.com (Sat May 03 2003 - 11:19:25 PDT)
Latest Leap Compile Errors smolnar.jadeinc.com (Sun May 04 2003 - 04:44:50 PDT)
- Re: Latest Leap Compile Errors David A. Case (Sun May 04 2003 - 14:02:05 PDT)
  - Re: Latest Leap Compile Errors Stephen P. Molnar, Ph.D. (Mon May 05 2003 - 06:18:35 PDT)
SPC/E water model Ioana Cozmuta (Sun May 04 2003 - 14:38:06 PDT)
- Re: SPC/E water model Holger Gohlke (Sun May 04 2003 - 16:27:01 PDT)
  - Re: SPC/E water model Ioana Cozmuta (Wed May 07 2003 - 01:53:43 PDT)
SPC/E model -LJ parameters Ioana Cozmuta (Sun May 04 2003 - 14:55:53 PDT)
can not minimize tang kwa (Mon May 05 2003 - 04:57:42 PDT)
- Re: can not minimize Carlos Simmerling (Mon May 05 2003 - 05:00:04 PDT)
  - Re: can not minimize tang kwa (Mon May 05 2003 - 06:49:31 PDT)
- Re: can not minimize Guanglei Cui (Mon May 05 2003 - 06:42:37 PDT)
  - Re: can not minimize tang kwa (Mon May 05 2003 - 06:57:40 PDT)
    - Re: can not minimize Guanglei Cui (Mon May 05 2003 - 07:07:39 PDT)
    - Re: can not minimize tang kwa (Mon May 05 2003 - 07:45:24 PDT)
    - minimizaiton in vacuum David A. Case (Mon May 05 2003 - 09:01:16 PDT)
    - Re: minimizaiton in vacuum tang kwa (Tue May 06 2003 - 05:17:03 PDT)
how to set up a carbon nanotube pdb file zhaoxc.puccini.che.pitt.edu (Mon May 05 2003 - 14:24:10 PDT)
ANAL in AMBER A.Madhumalar (Tue May 06 2003 - 00:25:05 PDT)
- Re: ANAL in AMBER David A. Case (Fri May 09 2003 - 09:11:33 PDT)
saveAmberParm problems in xleap Wayne Dawson (Tue May 06 2003 - 01:14:58 PDT)
- Re: saveAmberParm problems in xleap caldwell.heimdal.compchem.ucsf.edu (Tue May 06 2003 - 05:45:36 PDT)
- Re: saveAmberParm problems in xleap Guanglei Cui (Tue May 06 2003 - 06:42:13 PDT)
  - Re: saveAmberParm problems in xleap Ioana Cozmuta (Tue May 06 2003 - 13:54:49 PDT)
- Re: saveAmberParm problems in xleap Wayne Dawson (Tue May 06 2003 - 10:04:19 PDT)
- Re: saveAmberParm problems in xleap Wayne Dawson (Thu May 08 2003 - 02:02:45 PDT)
minimization with restraints A. Hungie (Tue May 06 2003 - 05:57:22 PDT)
- Re: minimization with restraints Carlos Simmerling (Tue May 20 2003 - 06:42:43 PDT)
Pi-Pi stacking Fernando Martin (Tue May 06 2003 - 10:35:45 PDT)
non bonded pairlist? Arvid Soederhaell (Wed May 07 2003 - 00:34:27 PDT)
MD steps limit in sander (Amber 6) Marco Preto (Wed Oct 30 2002 - 18:09:14 PST)
- Re: MD steps limit in sander (Amber 6) Carlos Simmerling (Wed May 07 2003 - 08:51:01 PDT)
- Re: MD steps limit in sander (Amber 6) Marco Preto (Wed Oct 30 2002 - 19:41:01 PST)
help me switching from amber5 to amber6 Asif Rahaman (Wed May 07 2003 - 17:18:01 PDT)
- Re: help me switching from amber5 to amber6 David A. Case (Wed May 07 2003 - 17:59:54 PDT)
Phosphotyrosine parametrization Obdulia Rabal (Thu May 08 2003 - 00:51:19 PDT)
current AMBER citation? Jake Isaacs (Thu May 08 2003 - 07:08:38 PDT)
- Re: current AMBER citation? David A. Case (Thu May 08 2003 - 08:16:13 PDT)
RMSD fluctuation too much Youyi Peng (Thu May 08 2003 - 08:02:43 PDT)
- Re: RMSD fluctuation too much Carlos Simmerling (Thu May 08 2003 - 08:26:41 PDT)
Use of Mg2+ in AMBER 7 Peter Anderson (Thu May 08 2003 - 11:55:06 PDT)
2 questions FyD (Fri May 09 2003 - 03:02:41 PDT)
- Re: 2 questions Carlos Simmerling (Fri May 09 2003 - 04:08:51 PDT)
- Re: 2 questions David A. Case (Fri May 09 2003 - 08:54:41 PDT)
Etot is not constant in NVE ensemble A. Hungie (Fri May 09 2003 - 06:46:43 PDT)
- Re: Etot is not constant in NVE ensemble darden (Fri May 09 2003 - 07:38:53 PDT)
  - Re: Etot is not constant in NVE ensemble Thomas Cheatham (Fri May 09 2003 - 08:49:18 PDT)
- RE: Etot is not constant in NVE ensemble Yong Duan (Fri May 09 2003 - 07:58:25 PDT)
- Re: Etot is not constant in NVE ensemble A. Hungie (Fri May 09 2003 - 09:08:56 PDT)
  - Re: Etot is not constant in NVE ensemble darden (Fri May 09 2003 - 16:20:24 PDT)
- Re: Etot is not constant in NVE ensemble bishop (Fri May 09 2003 - 12:41:34 PDT)
What kind of interactions are ignored for end group interactions Huang Zunnan (Fri May 09 2003 - 13:41:10 PDT)
- Re: What kind of interactions are ignored for end group interactions Carlos Simmerling (Fri May 09 2003 - 14:07:26 PDT)
10-12 H-bond terms Ioana Cozmuta (Fri May 09 2003 - 15:27:53 PDT)
- Re: 10-12 H-bond terms Andreas Svrcek-Seiler (Sat May 10 2003 - 16:13:08 PDT)
  - Re: 10-12 H-bond terms Ioana Cozmuta (Mon May 12 2003 - 12:50:40 PDT)
    - Re: 10-12 H-bond terms David A. Case (Mon May 12 2003 - 14:58:52 PDT)
    - Re: 10-12 H-bond terms Ioana Cozmuta (Mon May 12 2003 - 16:32:19 PDT)
RMSF problem yuan bo (Sat May 10 2003 - 02:31:27 PDT)
a question about scale factor Ye Mei (Sat May 10 2003 - 19:53:45 PDT)
- Re: a question about scale factor Carlos Simmerling (Sat May 10 2003 - 21:00:24 PDT)
difference between iwrap and image? yuann (Sat May 10 2003 - 22:47:23 PDT)
Minimisation - peek_ewald_inpcrd: SHOULD NOT BE HERE Omar Wahab (Mon May 12 2003 - 02:49:52 PDT)
unit of vlimit? Fabian Boes (Mon May 12 2003 - 07:36:25 PDT)
Heat of Vaporization Karl N. Kirschner (Mon May 12 2003 - 07:46:17 PDT)
- Re: Heat of Vaporization David A. Case (Tue May 13 2003 - 08:12:41 PDT)
School Amber Study Treakle, Kirk (Mon May 12 2003 - 10:00:33 PDT)
no MD output Youyi Peng (Mon May 12 2003 - 12:01:47 PDT)
- Re: no MD output Marco Preto (Wed Oct 30 2002 - 10:33:30 PST)
Simple question about sander parameter set Peng Tao (Tue May 13 2003 - 07:44:40 PDT)
- Re: Simple question about sander parameter set David A. Case (Tue May 13 2003 - 08:00:22 PDT)
- Re: Simple question about sander parameter set Peng Tao (Tue May 13 2003 - 08:19:50 PDT)
re: parameters for nitro group Shixiang Yan (Tue May 13 2003 - 08:30:49 PDT)
- Re: parameters for nitro group David A. Case (Tue May 13 2003 - 09:45:02 PDT)
water residence time analysis Mahadevan Seetharaman (Tue May 13 2003 - 10:18:14 PDT)
Increase lastist in the &cntrl namelist GUILLERMINA L ESTIU (Tue May 13 2003 - 11:16:09 PDT)
- Re: Increase lastist in the &cntrl namelist GUILLERMINA L ESTIU (Tue May 13 2003 - 11:37:24 PDT)
- Re: Increase lastist in the &cntrl namelist Ioana Cozmuta (Tue May 13 2003 - 11:58:09 PDT)
  - Re: Increase lastist in the &cntrl namelist Dodi Heryadi (Tue May 13 2003 - 13:14:25 PDT)
    - Re: Increase lastist in the &cntrl namelist Ioana Cozmuta (Tue May 13 2003 - 13:26:48 PDT)
H-O-H angle Ioana Cozmuta (Tue May 13 2003 - 13:17:54 PDT)
- Re: H-O-H angle Luis Gracia (Tue May 13 2003 - 14:46:05 PDT)
  - Re: H-O-H angle Ioana Cozmuta (Tue May 13 2003 - 21:32:17 PDT)
Sander help tianxiao yang (Tue May 13 2003 - 16:47:17 PDT)
- Re: Sander help David A. Case (Tue May 13 2003 - 17:51:12 PDT)
  - ptraj rdf help tianxiao yang (Wed May 21 2003 - 15:28:26 PDT)
    - Re: ptraj rdf help Thomas Cheatham (Wed May 21 2003 - 21:12:57 PDT)
  - Re: ptraj and rdf help tianxiao yang (Wed May 21 2003 - 15:54:59 PDT)
A question about AMBER, leaprc.ff02EP yuming chen (Tue May 13 2003 - 22:17:47 PDT)
- Re: A question about AMBER, leaprc.ff02EP David A. Case (Tue May 13 2003 - 23:26:56 PDT)
- Re: A question about AMBER, leaprc.ff02EP yuming chen (Wed May 14 2003 - 03:45:11 PDT)
mm_pbsa and B/Z DNA relative stabilities Peter Gannett (Wed May 14 2003 - 04:54:47 PDT)
- Re: mm_pbsa and B/Z DNA relative stabilities Robert G. Endres (Wed May 14 2003 - 06:36:14 PDT)
serine/tyrosine in charged states Layi Adekoya (Wed May 14 2003 - 05:26:55 PDT)
protonate problem Venkata S Koppuravuri (Wed May 14 2003 - 10:17:39 PDT)
- Re: protonate problem David A. Case (Wed May 14 2003 - 11:36:04 PDT)
Using GLYCAM in sander with a non-zero 10-12 coefficient Peng Tao (Wed May 14 2003 - 11:54:32 PDT)
Newton-Raphson minimization for large systems Qing Zhang (Wed May 14 2003 - 16:09:07 PDT)
Simulation under physiological conditions Michal Otyepka (Thu May 15 2003 - 08:02:34 PDT)
- Re: Simulation under physiological conditions Michal Otyepka (Thu May 15 2003 - 08:50:44 PDT)
- Re: Simulation under physiological conditions Andreas Svrcek-Seiler (Thu May 15 2003 - 09:11:13 PDT)
atomic positional fluctuation pengyo.rwja.umdnj.edu (Thu May 15 2003 - 11:22:25 PDT)
- Re: atomic positional fluctuation Holger Gohlke (Thu May 15 2003 - 13:38:07 PDT)
nucgen.dat Maria Zavodszky (Thu May 15 2003 - 11:37:14 PDT)
- Re: nucgen.dat Ioana Cozmuta (Thu May 15 2003 - 13:08:50 PDT)
using distance restraints in Sander (AIX 4.3 RS6000) Wayne Dawson (Fri May 16 2003 - 01:33:02 PDT)
- Re: using distance restraints in Sander (AIX 4.3 RS6000) David A. Case (Fri May 16 2003 - 13:42:18 PDT)
ptraj generated PDB files Fabian Boes (Fri May 16 2003 - 07:01:38 PDT)
- Re: ptraj generated PDB files caldwell.heimdal.compchem.ucsf.edu (Fri May 16 2003 - 06:07:57 PDT)
- Re: ptraj generated PDB files David A. Case (Fri May 16 2003 - 08:43:34 PDT)
mm_pbsa with PBCAL = 0 wentaofu (Fri May 16 2003 - 12:14:42 PDT)
- Re: mm_pbsa with PBCAL = 0 Holger Gohlke (Fri May 16 2003 - 14:34:41 PDT)
anal, amber7 and resnum 0 Sanjeev B.S. (Fri May 16 2003 - 15:15:19 PDT)
- Re: anal, amber7 and resnum 0 Sanjeev B.S. (Fri May 16 2003 - 15:23:04 PDT)
- Re: anal, amber7 and resnum 0 David A. Case (Fri May 16 2003 - 14:57:33 PDT)
DNA base-step distortion kbyun.wesleyan.edu (Sun May 18 2003 - 12:37:12 PDT)
Re: DNA base-step distortion kbyun.wesleyan.edu (Sun May 18 2003 - 16:43:59 PDT)
- Re: DNA base-step distortion Jiri Sponer (Mon May 19 2003 - 02:56:00 PDT)
RESP, constraining Dipole Moment Artur Galstyan (Mon May 19 2003 - 03:06:51 PDT)
Mainchain.dat tang kwa (Mon May 19 2003 - 09:16:12 PDT)
- Re: Mainchain.dat Lepsa (Tue May 20 2003 - 06:34:36 PDT)
force field parameters for torsions cailliez (Mon May 19 2003 - 08:19:36 PDT)
- Re: force field parameters for torsions David A. Case (Mon May 19 2003 - 10:44:27 PDT)
Re: force field parameters for torsions (I am away) Charles Laughton (Mon May 19 2003 - 10:49:32 PDT)
Fluorine atom type in mm_pbsa? Lishan Yao (Mon May 19 2003 - 14:00:09 PDT)
- Re: Fluorine atom type in mm_pbsa? Lishan Yao (Tue May 20 2003 - 06:12:04 PDT)
- Re: Fluorine atom type in mm_pbsa? David A. Case (Tue May 20 2003 - 07:30:53 PDT)
Calcium in proteins Javier Cuervo (Mon May 19 2003 - 17:11:54 PDT)
- Re: Calcium in proteins David A. Case (Tue May 20 2003 - 07:40:06 PDT)
  - Q) vdw radii & GBSA error Sukjoon Yoon (Fri Jun 06 2003 - 09:58:03 PDT)
off-diagonal VDW term Jiyoung Heo (Mon May 19 2003 - 18:01:13 PDT)
- Re: off-diagonal VDW term Ioana Cozmuta (Mon May 19 2003 - 18:24:34 PDT)
  - RE: off-diagonal VDW term Yong Duan (Tue May 20 2003 - 00:24:25 PDT)
- Re: off-diagonal VDW term David A. Case (Tue May 20 2003 - 07:43:33 PDT)
parm99 cailliez (Tue May 20 2003 - 05:55:17 PDT)
- Re: parm99 David A. Case (Tue May 20 2003 - 15:37:32 PDT)
  - Re: parm99 Junmei Wang (Wed May 21 2003 - 11:30:18 PDT)
- RE: parm99 Bayly, Christopher (Thu May 22 2003 - 06:36:18 PDT)
Xleap adding torsions Andrew Petersen (Tue May 20 2003 - 08:32:40 PDT)
Problem with CMC/MD Sameer P. Kawatkar (Tue May 20 2003 - 08:35:16 PDT)
a question about constructing a periodic box by PLEP. Margaret Shun Cheung (Tue May 20 2003 - 08:48:56 PDT)
Re: From Dr. Ekaterina Nikitina caldwell.heimdal.compchem.ucsf.edu (Tue May 20 2003 - 09:27:04 PDT)
- Re: From Dr. Ekaterina Nikitina David A. Case (Thu May 22 2003 - 10:16:58 PDT)
  - Re: From Dr. Ekaterina Nikitina Nikitina Ekaterina (Sun May 25 2003 - 03:26:09 PDT)
Amber 7.xx installation on FreeBSD Joseph Maxwell (Tue May 20 2003 - 13:27:11 PDT)
- Re: Amber 7.xx installation on FreeBSD M. L. Dodson (Tue May 20 2003 - 14:19:21 PDT)
Residual dipolar couplings McAteer, Kathleen (Tue May 20 2003 - 14:03:58 PDT)
- Re: Residual dipolar couplings David A. Case (Fri May 02 2003 - 10:21:53 PDT)
- RE: Residual dipolar couplings McAteer, Kathleen (Wed May 21 2003 - 10:49:18 PDT)
Hybdrogen bonds and LJ 10-12 Michal Otyepka (Wed May 21 2003 - 02:49:47 PDT)
- Re: Hybdrogen bonds and LJ 10-12 David A. Case (Thu May 22 2003 - 10:21:18 PDT)
  - charge fitting for c-term homocysteine. X. Tan (Thu May 22 2003 - 19:25:19 PDT)
  - best force field for Protein+DNA Robert G. Endres (Fri May 23 2003 - 08:14:51 PDT)
bad atom type f(fluorine) in MM-PBSA? Lishan Yao (Wed May 21 2003 - 06:29:01 PDT)
- Re: bad atom type f(fluorine) in MM-PBSA? Holger Gohlke (Wed May 21 2003 - 08:49:20 PDT)
- Re: bad atom type f(fluorine) in MM-PBSA? Lishan Yao (Wed May 21 2003 - 10:12:17 PDT)
I still have problems with parm99.dat cailliez (Wed May 21 2003 - 06:37:19 PDT)
non-periodic system Ioana Cozmuta (Wed May 21 2003 - 15:50:18 PDT)
- Re: non-periodic system Michael Crowley (Wed May 21 2003 - 16:27:03 PDT)
  - Re: non-periodic system Ioana Cozmuta (Wed May 21 2003 - 19:47:34 PDT)
  - RE: non-periodic system Yong Duan (Wed May 21 2003 - 20:17:03 PDT)
  - RE: non-periodic system Yong Duan (Wed May 21 2003 - 20:24:01 PDT)
Xleap: 'triangular' and 'square' bond Christian Gossens (Thu May 22 2003 - 03:58:51 PDT)
- Re: Xleap: 'triangular' and 'square' bond Andreas Svrcek-Seiler (Thu May 22 2003 - 06:00:58 PDT)
leap complains! Layi Adekoya (Thu May 22 2003 - 04:56:11 PDT)
- Re: leap complains! Jose Ramon Blas (Thu May 22 2003 - 15:03:02 PDT)
- RE: leap complains! Kristina Furse (Thu May 22 2003 - 16:17:16 PDT)
rotational and translational motion Jean-François Taly (Thu May 22 2003 - 05:45:18 PDT)
- Re: rotational and translational motion Carlos Simmerling (Thu May 22 2003 - 05:54:51 PDT)
translational and rotational motion (more information) Jean-François Taly (Thu May 22 2003 - 06:25:49 PDT)
- Re: translational and rotational motion (more information) Carlos Simmerling (Thu May 22 2003 - 06:35:13 PDT)
Minimization problem w/ counter-ion ! Marco Preto (Wed Oct 30 2002 - 18:54:27 PST)
- Re: Minimization problem w/ counter-ion ! David A. Case (Thu May 22 2003 - 09:51:28 PDT)
- Re: Minimization problem w/ counter-ion ! Marco Preto (Wed Oct 30 2002 - 11:11:58 PST)
Questions about statistics output of mm_pbsa? Lishan Yao (Thu May 22 2003 - 14:04:04 PDT)
- Re: Questions about statistics output of mm_pbsa? Holger Gohlke (Thu May 22 2003 - 14:41:32 PDT)
- Re: Questions about statistics output of mm_pbsa? David A. Case (Thu May 22 2003 - 17:32:15 PDT)
  - Re: Questions about statistics output of mm_pbsa? Lishan Yao (Fri May 23 2003 - 06:22:07 PDT)
  - Re: Questions about statistics output of mm_pbsa? Lishan Yao (Fri May 23 2003 - 06:31:44 PDT)
Please help on xleap: FATAL ERROR Margaret Shun Cheung (Thu May 22 2003 - 15:20:42 PDT)
- Re: Please help on xleap: FATAL ERROR David A. Case (Thu May 22 2003 - 17:25:07 PDT)
  - Re: Please help on xleap: FATAL ERROR Margaret Shun Cheung (Fri May 23 2003 - 07:06:10 PDT)
- Re: Please help on xleap: FATAL ERROR John Bushnell (Thu May 22 2003 - 19:04:15 PDT)
A question of how to choose a appropriate box size for imposing periodic boundary conditions in the simulations. Margaret Shun Cheung (Fri May 23 2003 - 08:18:39 PDT)
distance-dependent dielectric function Robert G. Endres (Fri May 23 2003 - 08:44:27 PDT)
- Re: distance-dependent dielectric function Shixiang Yan (Fri May 23 2003 - 09:39:04 PDT)
water box distortion GUILLERMINA L ESTIU (Fri May 23 2003 - 13:36:17 PDT)
- Re: water box distortion caldwell.heimdal.compchem.ucsf.edu (Fri May 23 2003 - 14:21:33 PDT)
- Re: water box distortion David A. Case (Fri May 23 2003 - 16:13:40 PDT)
- Re: water box distortion GUILLERMINA L ESTIU (Sat May 24 2003 - 08:34:11 PDT)
  - Re: water box distortion Holger Gohlke (Sat May 24 2003 - 18:26:21 PDT)
center command Ioana Cozmuta (Fri May 23 2003 - 14:40:50 PDT)
problems with anal in amber7 Liliana Wroblewska (Fri May 23 2003 - 14:53:28 PDT)
MD input file for MM-PBSA calculations Thomas Steinbrecher (Sat May 24 2003 - 05:36:43 PDT)
- Re: MD input file for MM-PBSA calculations Natasja Brooijmans (Sat May 24 2003 - 09:28:39 PDT)
- Re: MD input file for MM-PBSA calculations Lepsa (Mon May 26 2003 - 02:03:02 PDT)
IR6 and makeDIST-RST Francisco Blanco (Sat May 24 2003 - 12:15:29 PDT)
- Re: IR6 and makeDIST-RST David A. Case (Sun Jun 01 2003 - 17:14:04 PDT)
HBOND energies in sander Francisco Blanco (Sun May 25 2003 - 04:37:52 PDT)
- Re: HBOND energies in sander Holger Gohlke (Mon May 26 2003 - 10:24:01 PDT)
EWALD BOMB tang kwa (Mon May 26 2003 - 07:27:07 PDT)
- Re: EWALD BOMB Holger Gohlke (Mon May 26 2003 - 12:58:00 PDT)
  - RE: EWALD BOMB Yong Duan (Mon May 26 2003 - 16:51:22 PDT)
  - Re: EWALD BOMB tang kwa (Tue May 27 2003 - 08:38:31 PDT)
    - Re: EWALD BOMB Michael Crowley (Tue May 27 2003 - 08:45:22 PDT)
Order parameters cailliez (Tue May 27 2003 - 01:25:30 PDT)
- Re: Order parameters Holger Gohlke (Tue May 27 2003 - 12:15:15 PDT)
Amber on SGI with Itanium compilers for linux (fwd) Sanjeev B.S. (Tue May 27 2003 - 05:21:20 PDT)
Re: Amber on SGI with Itanium compilers for linux Sanjeev B.S. (Tue May 27 2003 - 06:58:17 PDT)
NOTIFICATION CLARK WOOD (Tue May 27 2003 - 06:16:49 PDT)
NOTIFICATION CLARK WOOD (Tue May 27 2003 - 06:40:26 PDT)
- Re: NOTIFICATION Joseph Maxwell (Tue May 27 2003 - 09:11:36 PDT)
  - Re: NOTIFICATION Jiten (Tue May 27 2003 - 17:31:10 PDT)
AMD opteron Hai-Long Wang (Tue May 27 2003 - 08:57:39 PDT)
- Re: AMD opteron Tru Huynh (Wed May 28 2003 - 06:08:51 PDT)
  - Re: AMD opteron Tru Huynh (Wed May 28 2003 - 09:52:18 PDT)
mm_gbsa question Javier Cuervo (Tue May 27 2003 - 17:49:18 PDT)
- Re: mm_gbsa question Holger Gohlke (Tue May 27 2003 - 18:40:36 PDT)
Does Leap has a problem with Isoleucines? Frederico.Miranda.ibmb.uib.no (Tue May 27 2003 - 23:28:21 PDT)
- Re: Does Leap has a problem with Isoleucines? Holger Gohlke (Wed May 28 2003 - 09:14:47 PDT)
about the dielectric Ye Mei (Wed May 28 2003 - 00:42:22 PDT)
- RE: about the dielectric Yong Duan (Wed May 28 2003 - 02:24:58 PDT)
about the dielectric Ye Mei (Wed May 28 2003 - 00:57:49 PDT)
NVT system implosion!!! Marco Preto (Wed Oct 30 2002 - 16:29:24 PST)
- Re: NVT system implosion!!! Marco Preto (Wed Oct 30 2002 - 10:46:07 PST)
CFP: Informatics Approaches in Structural Genomics at PSB 2004 Sean Mooney (Wed May 28 2003 - 08:46:17 PDT)
Does Anyone Have a Working MACHINE File for Solaris/SPARC? Chen, Ya (Wed May 28 2003 - 10:30:53 PDT)
LES analysis tool other than Moil-view Sameer P. Kawatkar (Wed May 28 2003 - 11:21:38 PDT)
clustering trajectories chernhoe (Wed May 28 2003 - 20:19:41 PDT)
coordinate files from carnal jaw3.cec.wustl.edu (Thu May 29 2003 - 07:13:25 PDT)
antechamber read gaussian file quch quch (Thu May 29 2003 - 13:32:14 PDT)
antechamber read gaussian file quch quch (Thu May 29 2003 - 13:32:10 PDT)
- Re: antechamber read gaussian file David A. Case (Sun Jun 01 2003 - 17:18:54 PDT)
MD problem Shuang Ding (Thu May 29 2003 - 13:47:20 PDT)
- Re: MD problem Carlos Simmerling (Thu May 29 2003 - 13:56:27 PDT)
- Re: MD problem Shuang Ding (Thu May 29 2003 - 14:04:22 PDT)
- Re: MD problem Guanglei Cui (Thu May 29 2003 - 14:14:14 PDT)
- Re: MD problem Shuang Ding (Thu May 29 2003 - 14:30:54 PDT)
  - Re: MD problem Guanglei Cui (Thu May 29 2003 - 14:28:07 PDT)
    - RE: MD problem Yong Duan (Thu May 29 2003 - 17:58:21 PDT)
information aram joel panay (Thu May 29 2003 - 20:45:48 PDT)
- Re: information David A. Case (Sun Jun 01 2003 - 17:14:29 PDT)
(no subject) 你的朋友 (Thu May 29 2003 - 23:15:53 PDT)
Phosphorylated Serine Library Frederico.Miranda.ibmb.uib.no (Fri May 30 2003 - 01:01:31 PDT)
A simple question about offset, want to make sure Huang Zunnan (Sat May 31 2003 - 09:44:46 PDT)
HGH, IGF-1 Supply fsdjklfdsf.ddhdf.com (Sun Jun 01 2003 - 18:09:08 PDT)
HGH, IGF-1 Supply fsdjklfdsf.ddhdf.com (Sun Jun 01 2003 - 23:20:52 PDT)
EGB problem in MMPBSA Obdulia Rabal (Mon Jun 02 2003 - 04:11:45 PDT)
Need help recompiling Peter Anderson (Mon Jun 02 2003 - 07:23:11 PDT)
- Re: Need help recompiling caldwell.heimdal.compchem.ucsf.edu (Mon Jun 02 2003 - 08:14:06 PDT)
run sander? quch quch (Mon Jun 02 2003 - 09:22:35 PDT)
- Re: run sander? David A. Case (Mon Jun 02 2003 - 10:52:00 PDT)
  - Re: run sander? quch quch (Mon Jun 02 2003 - 11:52:22 PDT)
    - Re: run sander? Michael Crowley (Tue Jun 03 2003 - 05:42:53 PDT)
pol_h Giulio Rastelli (Tue Jun 03 2003 - 09:34:23 PDT)
- Re: pol_h David A. Case (Tue Jun 03 2003 - 09:26:41 PDT)
MGB RADII PARAMETRIZATION Obdulia Rabal (Tue Jun 03 2003 - 04:08:15 PDT)
Mg++ polarizability Robert Duke (Tue Jun 03 2003 - 04:39:25 PDT)
Nancy's leaving caldwell.heimdal.compchem.ucsf.edu (Tue Jun 03 2003 - 19:42:00 PDT)
solventbox at constant pressure Petrodler.aol.com (Wed Jun 04 2003 - 00:19:05 PDT)
- Re: solventbox at constant pressure David A. Case (Wed Jun 04 2003 - 08:13:37 PDT)
angle violation in SANDER simulation XU Xingfu (Wed Jun 04 2003 - 02:11:24 PDT)
- Re: angle violation in SANDER simulation David A. Case (Wed Jun 04 2003 - 08:17:32 PDT)
keeping pdb residues numbers ? GUILBAUD Philippe 153683 (Wed Jun 04 2003 - 05:48:50 PDT)
- Re: keeping pdb residues numbers ? David A. Case (Wed Jun 04 2003 - 10:40:08 PDT)
belly vs. position restraints Peter Anderson (Wed Jun 04 2003 - 07:17:05 PDT)
- Re: belly vs. position restraints David A. Case (Wed Jun 04 2003 - 08:57:02 PDT)
RDPARM problems (ptraj) Sophia Kondratova (Thu Jun 05 2003 - 10:13:35 PDT)
PROBLEM WITH LIBRARY Frederico.Miranda.ibmb.uib.no (Thu Jun 05 2003 - 13:06:27 PDT)
constant volume Shuang Ding (Thu Jun 05 2003 - 15:26:39 PDT)
- Re: constant volume David A. Case (Fri Jun 06 2003 - 15:48:16 PDT)
unit of output velocity Yuguang Mu (Fri Jun 06 2003 - 08:33:01 PDT)
- Re: unit of output velocity Holger Gohlke (Fri Jun 06 2003 - 08:46:38 PDT)
- Re: unit of output velocity Satish Kumar (Fri Jun 06 2003 - 09:25:58 PDT)
- Re: unit of output velocity Satish Mummadi (Fri Jun 06 2003 - 09:39:45 PDT)
- Re: unit of output velocity Andreas Svrcek-Seiler (Fri Jun 06 2003 - 09:49:32 PDT)
how to use profec??? sxzheng (Sun Jun 08 2003 - 01:04:09 PDT)
mm_pbsa error message chernhoe (Sun Jun 08 2003 - 02:48:02 PDT)
- Re: mm_pbsa error message Holger Gohlke (Sun Jun 08 2003 - 09:19:24 PDT)
Amber Installation on Octane Joseph Maxwell (Sun Jun 08 2003 - 14:55:55 PDT)
VdW in FEP ENikitina (Mon Jun 09 2003 - 00:06:49 PDT)
- Re: VdW in FEP David A. Case (Mon Jun 09 2003 - 08:05:58 PDT)
  - Re: VdW in FEP ENikitina (Tue Jun 10 2003 - 04:56:23 PDT)
  - VdW in FEP ENikitina (Wed Jun 18 2003 - 07:02:14 PDT)
  - Ar as a solvent ENikitina (Wed Jul 09 2003 - 04:42:47 PDT)
May I get you help from new user of amber? Wu Yingliang (Mon Jun 09 2003 - 07:21:49 PDT)
- Re: May I get you help from new user of amber? Guanglei Cui (Mon Jun 09 2003 - 07:41:07 PDT)
- RE: May I get you help from new user of amber? Yong Duan (Mon Jun 09 2003 - 08:12:41 PDT)
- Re: May I get you help from new user of amber? Satish Mummadi (Mon Jun 09 2003 - 08:28:54 PDT)
- Re: May I get you help from new user of amber?(xmkmf) Satish Kumar (Mon Jun 09 2003 - 08:46:53 PDT)
saving trajectory of solute only Peter Anderson (Mon Jun 09 2003 - 09:01:53 PDT)
- Re: saving trajectory of solute only Carlos Simmerling (Mon Jun 09 2003 - 09:06:01 PDT)
- Re: saving trajectory of solute only David A. Case (Mon Jun 09 2003 - 09:24:03 PDT)
shake problem? Shuang Ding (Mon Jun 09 2003 - 11:33:50 PDT)
helix movement Bimo Ario Tejo (Tue Jun 10 2003 - 03:10:29 PDT)
- Re: helix movement Yuguang Mu (Tue Jun 10 2003 - 03:47:42 PDT)
- Re: helix movement Bimo Ario Tejo (Tue Jun 10 2003 - 04:19:05 PDT)
  - PME Yuguang Mu (Tue Jun 10 2003 - 05:04:08 PDT)
    - Re: PME darden (Wed Jun 11 2003 - 08:21:25 PDT)
- Re: helix movement Andreas Svrcek-Seiler (Tue Jun 10 2003 - 05:07:49 PDT)
- Re: helix movement Bimo Ario Tejo (Tue Jun 10 2003 - 05:18:14 PDT)
  - Re: helix movement Yuguang Mu (Wed Jun 11 2003 - 05:47:34 PDT)
helix axis for A-RNA Vlad Cojocaru (Tue Jun 10 2003 - 05:25:09 PDT)
- Re: helix axis for A-RNA M. L. Dodson (Tue Jun 10 2003 - 06:36:44 PDT)
Superimposed trajectory Filip Razga (Tue Jun 10 2003 - 06:59:06 PDT)
- Re: Superimposed trajectory David A. Case (Tue Jun 10 2003 - 07:53:42 PDT)
Problem in separating LES copies into different trajectory Sameer P. Kawatkar (Tue Jun 10 2003 - 08:15:18 PDT)
- Re: Problem in separating LES copies into different trajectory Viktor Hornak (Tue Jun 10 2003 - 08:50:36 PDT)
A question of time Darren Davies (Tue Jun 10 2003 - 08:52:31 PDT)
- Re: A question of time David A. Case (Tue Jun 10 2003 - 09:34:19 PDT)
restart MD Shuang Ding (Tue Jun 10 2003 - 11:12:08 PDT)
GB model MF Yang (Tue Jun 10 2003 - 12:54:33 PDT)
Minimization does not converge. Javier Cuervo (Tue Jun 10 2003 - 20:14:43 PDT)
- Re: Minimization does not converge. David A. Case (Tue Jun 10 2003 - 22:52:29 PDT)
Re: any tool to know what functions are being called while sander is being run?? Satish Mummadi (Tue Jun 10 2003 - 22:32:11 PDT)
New location for the Amber web site David A. Case (Tue Jun 10 2003 - 23:04:54 PDT)
- PME Yuguang Mu (Wed Jun 11 2003 - 01:33:29 PDT)
  - RE: PME crowley (Tue Oct 31 2000 - 10:03:42 PST)
  - Re: PME darden (Wed Jun 11 2003 - 07:33:12 PDT)
delphi on linux chernhoe (Wed Jun 11 2003 - 02:03:13 PDT)
vlimit exceeded when sander calculate free energies using TI zsx (Wed Jun 11 2003 - 04:51:09 PDT)
- Re: vlimit exceeded when sander calculate free energies using TI David A. Case (Wed Jun 11 2003 - 08:21:31 PDT)
any tool to know what functions are being called while sander is being run?? Satish Mummadi (Wed Jun 11 2003 - 06:42:58 PDT)
- Re: any tool to know what functions are being called while sander is being run?? Guanglei Cui (Wed Jun 11 2003 - 06:53:45 PDT)
quasih problem Yang, Mingfeng (Wed Jun 11 2003 - 07:10:30 PDT)
- Re: quasih problem David A. Case (Wed Jun 11 2003 - 08:12:54 PDT)
calculated b-factor higher than x-ray Bimo Ario Tejo (Wed Jun 11 2003 - 11:23:03 PDT)
which AMBER program to use to get the e-density output? salinthip thipayang (Wed Jun 11 2003 - 12:24:40 PDT)
bugfix ptraj-6.4 (need to confirm) Bimo Ario Tejo (Thu Jun 12 2003 - 05:51:27 PDT)
jarrod Jarrod Wesley Barnes (Thu Jun 12 2003 - 07:51:33 PDT)
- Re: jarrod Holger Gohlke (Thu Jun 12 2003 - 08:18:43 PDT)
- Re: jarrod Matheus Froeyen (Fri Jun 13 2003 - 00:36:14 PDT)
install problem Dave S Walker (Thu Jun 12 2003 - 14:18:02 PDT)
- Re: install problem David A. Case (Thu Jun 12 2003 - 15:26:56 PDT)
  - Re: install problem Dave S Walker (Thu Jun 12 2003 - 17:03:21 PDT)
glycam force field with amber PSR04996.mailstudenti.unimi.it (Fri Jun 13 2003 - 04:28:07 PDT)
- Re: glycam force field with amber David A. Case (Fri Jun 13 2003 - 09:42:31 PDT)
Problem with a library Frederico.Miranda.ibmb.uib.no (Fri Jun 13 2003 - 13:27:36 PDT)
- Re: Problem with a library David A. Case (Fri Jun 13 2003 - 14:07:37 PDT)
parallel sander jobs die with error: "MPI_COMM_RANK : Null communicator" chris switzer (Sat Jun 14 2003 - 19:00:51 PDT)
can you give me more advice about: vlimit exceeded when sander calculate free energies using TI sxzheng (Mon Jun 16 2003 - 05:47:53 PDT)
- Re: can you give me more advice about: vlimit exceeded when sander calculate free energies using TI David A. Case (Mon Jun 16 2003 - 08:12:05 PDT)
Medical Imaging Risk & Reward -- Medical Imaging Consultant Radiation Aware (Mon Jun 16 2003 - 20:17:03 PDT)
LEAP compiling problem yuann (Tue Jun 17 2003 - 03:14:23 PDT)
- Re: LEAP compiling problem David A. Case (Tue Jun 17 2003 - 08:51:21 PDT)
  - Re: LEAP compiling problem David A. Case (Tue Jun 17 2003 - 09:09:26 PDT)
    - Re: LEAP compiling problem yuann (Tue Jun 17 2003 - 18:17:56 PDT)
CCL: Amber free energy equation Daquan Gao (Tue Jun 17 2003 - 09:33:39 PDT)
AMBER7 on linux cluster Venkata S Koppuravuri (Tue Jun 17 2003 - 09:49:06 PDT)
- Re: AMBER7 on linux cluster Carlos Simmerling (Tue Jun 17 2003 - 09:54:28 PDT)
  - Re: AMBER7 on linux cluster Venkata S Koppuravuri (Fri Jun 20 2003 - 07:53:17 PDT)
    - Re: AMBER7 on linux cluster Carlos Simmerling (Fri Jun 20 2003 - 07:55:10 PDT)
    - RE: AMBER7 on linux cluster Yong Duan (Fri Jun 20 2003 - 18:35:04 PDT)
new tutorial available: introduction to ptraj David A. Case (Tue Jun 17 2003 - 11:03:54 PDT)
Sander error Yuhui Cheng (Tue Jun 17 2003 - 11:37:21 PDT)
- Re: Sander error Natasja Brooijmans (Tue Jun 17 2003 - 11:44:53 PDT)
Error in minimization using sander_classic of AMBER6 dicksmit.umich.edu (Tue Jun 17 2003 - 13:20:03 PDT)
- Re: Error in minimization using sander_classic of AMBER6 David A. Case (Tue Jun 17 2003 - 13:53:49 PDT)
web link for PLEP is not available. Margaret Shun Cheung (Tue Jun 17 2003 - 13:28:40 PDT)
Problem with LES topology file Courtney Stanton (Tue Jun 17 2003 - 15:28:10 PDT)
- Re: Problem with LES topology file Carlos Simmerling (Tue Jun 17 2003 - 15:42:07 PDT)
Flag for antechamber Nick Polfer (Wed Jun 18 2003 - 01:59:01 PDT)
mpirun problem: no rsh Peter Anderson (Wed Jun 18 2003 - 10:50:26 PDT)
- Re: mpirun problem: no rsh Carlos Simmerling (Wed Jun 18 2003 - 10:56:48 PDT)
- Re: mpirun problem: no rsh Michael Crowley (Wed Jun 18 2003 - 12:04:52 PDT)
help on solvatecap Mao Xiang (Wed Jun 18 2003 - 18:47:36 PDT)
debug sander Andrew Petersen (Wed Jun 18 2003 - 23:40:04 PDT)
- Re: debug sander Satish Mummadi (Thu Jun 19 2003 - 01:32:02 PDT)
- RE: debug sander Yong Duan (Thu Jun 19 2003 - 02:21:27 PDT)
constraint + restraint Jose Ramon Blas (Thu Jun 19 2003 - 16:58:41 PDT)
- Re: constraint + restraint David A. Case (Thu Jun 19 2003 - 08:39:44 PDT)
- constraint + restraint tang kwa (Tue Jul 08 2003 - 00:05:11 PDT)
  - Re: constraint + restraint David A. Case (Tue Jul 08 2003 - 10:33:35 PDT)
NOESY restraints Teletchéa Stéphane (Fri Jun 20 2003 - 04:28:03 PDT)
- Re: NOESY restraints David A. Case (Fri Jun 20 2003 - 17:49:00 PDT)
  - Re: NOESY restraints Steph (Sat Jun 21 2003 - 03:27:35 PDT)
AMBER question David (Fri Jun 20 2003 - 09:31:55 PDT)
- Re: AMBER question David A. Case (Fri Jun 20 2003 - 17:59:04 PDT)
perl question Ioana Cozmuta (Fri Jun 20 2003 - 15:28:57 PDT)
mm_pbsa problem Peter Anderson (Fri Jun 20 2003 - 15:31:17 PDT)
- Re: mm_pbsa problem Holger Gohlke (Fri Jun 20 2003 - 18:47:21 PDT)
Question about defining force field FUNG WAI KEUNG (Fri Jun 20 2003 - 20:12:59 PDT)
Problem with XLEaP in Mandrake 9.1 Karthikeyan Pasupathy (Sun Jun 22 2003 - 10:08:23 PDT)
- RE: Problem with XLEaP in Mandrake 9.1 Ross Walker (Sun Jun 22 2003 - 10:31:02 PDT)
- Re: Problem with XLEaP in Mandrake 9.1 CUI, Guanglei (Sun Jun 22 2003 - 10:44:51 PDT)
- Re: Problem with XLEaP in Mandrake 9.1 John Bushnell (Sun Jun 22 2003 - 18:04:43 PDT)
1-4 vdw term in Glycam2000 yuann (Sun Jun 22 2003 - 21:24:16 PDT)
viewing movie with VMD Layi Adekoya (Mon Jun 23 2003 - 01:00:51 PDT)
- Re: viewing movie with VMD Lepsa (Mon Jun 23 2003 - 01:09:29 PDT)
- RE: viewing movie with VMD Ross Walker (Mon Jun 23 2003 - 15:36:30 PDT)
Running MD Balvinder Singh (Mon Jun 23 2003 - 10:33:56 PDT)
- Re: Running MD Carlos Simmerling (Mon Jun 23 2003 - 05:10:23 PDT)
  - Re: Running MD Balvinder Singh (Mon Jun 23 2003 - 11:02:33 PDT)
    - Re: Running MD Carlos Simmerling (Mon Jun 23 2003 - 05:40:24 PDT)
how to restrain water Mao Xiang (Mon Jun 23 2003 - 07:59:23 PDT)
- Re: how to restrain water Alfonso Garcia Sosa (Mon Jun 23 2003 - 08:14:02 PDT)
  - Re: how to restrain water Alfonso Garcia Sosa (Mon Jun 23 2003 - 08:42:42 PDT)
AMBER parameters D Fernandez (Mon Jun 23 2003 - 22:26:09 PDT)
- Re: AMBER parameters David A. Case (Tue Jun 24 2003 - 08:25:35 PDT)
ptraj question Ioana Cozmuta (Tue Jun 24 2003 - 00:59:48 PDT)
- Re: ptraj question Thomas Cheatham (Tue Jun 24 2003 - 13:56:51 PDT)
Another mm_pbsa problem Peter Anderson (Tue Jun 24 2003 - 09:47:58 PDT)
- Re: Another mm_pbsa problem Holger Gohlke (Tue Jun 24 2003 - 10:08:25 PDT)
GAFF in GUI MD apps Thomas (Tue Jun 24 2003 - 12:07:54 PDT)
- Re: GAFF in GUI MD apps FyD (Tue Jun 24 2003 - 22:50:58 PDT)
electrostatic interaction energ. /delphi Tommi Kajander (Tue Jun 24 2003 - 12:39:51 PDT)
- Re: electrostatic interaction energ. /delphi Natasja Brooijmans (Tue Jun 24 2003 - 12:45:22 PDT)
RE: Software Sales Pete Koladich (Tue Jun 24 2003 - 13:41:53 PDT)
Memory problem Frederico.Miranda.ibmb.uib.no (Tue Jun 24 2003 - 17:17:40 PDT)
T in MD vs. T in wet experiments Jianhui Wu (Tue Jun 24 2003 - 18:34:31 PDT)
Sander problem Yuhui Cheng (Tue Jun 24 2003 - 19:31:28 PDT)
- Re: Sander problem David A. Case (Wed Jun 25 2003 - 15:30:21 PDT)
Question about defining force field (followup) FUNG WAI KEUNG (Tue Jun 24 2003 - 21:14:10 PDT)
unifying trajectory files Peter Anderson (Wed Jun 25 2003 - 08:57:42 PDT)
- Re: unifying trajectory files Carlos Simmerling (Wed Jun 25 2003 - 09:05:57 PDT)
- Re: unifying trajectory files Natasja Brooijmans (Wed Jun 25 2003 - 09:25:41 PDT)
  - Re: unifying trajectory files Ioana Cozmuta (Wed Jun 25 2003 - 12:58:39 PDT)
Antechamber Shweta Sikri (Wed Jun 25 2003 - 09:47:52 PDT)
- Re: Antechamber David A. Case (Wed Jun 25 2003 - 10:31:31 PDT)
  - Re: Antechamber Shweta Sikri (Wed Jun 25 2003 - 12:26:31 PDT)
pyroglutamic acid (PCA) Javier Cuervo (Wed Jun 25 2003 - 18:16:44 PDT)
- Re: pyroglutamic acid (PCA) David A. Case (Thu Jun 26 2003 - 10:34:25 PDT)
Amber6 on RH 9 Yichen Cao (Thu Jun 26 2003 - 08:37:09 PDT)
- Re: Amber6 on RH 9 David A. Case (Thu Jun 26 2003 - 10:31:56 PDT)
Problem with Snader Frederico.Miranda.ibmb.uib.no (Sat Jun 28 2003 - 06:17:12 PDT)
- Re: Problem with Snader Guanglei Cui (Sat Jun 28 2003 - 07:53:59 PDT)
protonate Giulio Rastelli (Sun Jun 29 2003 - 14:31:20 PDT)
Nmode recompilation Thomas Steinbrecher (Tue Jul 01 2003 - 01:41:33 PDT)
- g77 on 32 bits cpu (was Re: Nmode recompilation) Tru Huynh (Tue Jul 01 2003 - 02:48:15 PDT)
Re: AMBER Cutoff Darren Davies (Tue Jul 01 2003 - 03:45:05 PDT)
- Re: AMBER Cutoff David A. Case (Tue Jul 01 2003 - 08:00:00 PDT)
parallel version amber installation problem Raja Swaminathan (Tue Jul 01 2003 - 04:09:43 PDT)
- Re: parallel version amber installation problem David A. Case (Tue Jul 01 2003 - 10:43:03 PDT)
parallel version amber installation problem Raja Swaminathan (Tue Jul 01 2003 - 04:12:41 PDT)
(no subject) Lifang Xu (Tue Jul 01 2003 - 07:22:43 PDT)
- Re: your mail (IBM runtime problem) Thomas Cheatham (Tue Jul 01 2003 - 09:58:00 PDT)
Re: Questions about output archive and micromolecules David A. Case (Tue Jul 01 2003 - 10:39:33 PDT)
input problem Herbert Georg (Tue Jul 01 2003 - 12:12:23 PDT)
- Re: input problem David A. Case (Tue Jul 01 2003 - 12:24:42 PDT)
Nmode doesn't work ? Gus Carri (Tue Jul 01 2003 - 14:09:11 PDT)
about the read error Zhi Qiang ZHOU (Tue Jul 01 2003 - 19:35:41 PDT)
PMF X. Tan (Wed Jul 02 2003 - 12:02:53 PDT)
Nmanal Gus Carri (Wed Jul 02 2003 - 14:26:50 PDT)
Antechamber Shweta Sikri (Thu Jul 03 2003 - 09:29:03 PDT)
- Re: Antechamber David A. Case (Thu Jul 03 2003 - 09:59:12 PDT)
  - Re: Antechamber Shweta Sikri (Thu Jul 03 2003 - 10:18:58 PDT)
    - Re: Antechamber David A. Case (Thu Jul 03 2003 - 10:36:47 PDT)
sander,ntt=5 Monika Fuxreiter (Fri Jul 04 2003 - 04:17:33 PDT)
- Re: sander,ntt=5 David A. Case (Fri Jul 04 2003 - 10:13:21 PDT)
How to do a rigid solvent model? Marco Aurelio Correia Preto (Fri Jul 04 2003 - 07:30:00 PDT)
- Re: How to do a rigid solvent model? David A. Case (Fri Jul 04 2003 - 10:16:51 PDT)
- Re: How to do a rigid solvent model? Carlos Simmerling (Fri Jul 04 2003 - 10:25:21 PDT)
  - RE: How to do a rigid solvent model? Yong Duan (Sat Jul 05 2003 - 11:48:01 PDT)
    - Re: How to do a rigid solvent model? Carlos Simmerling (Sat Jul 05 2003 - 13:06:39 PDT)
    - RE: How to do a rigid solvent model? Yong Duan (Sun Jul 06 2003 - 12:59:23 PDT)
- RE: How to do a rigid solvent model? Marco Aurelio Correia Preto (Mon Jul 07 2003 - 01:25:27 PDT)
Machine file available for ICC compiler ? Teletchéa Stéphane (Fri Jul 04 2003 - 10:08:30 PDT)
- Re: Machine file available for ICC compiler ? David A. Case (Fri Jul 04 2003 - 12:14:00 PDT)
vlimit exceeded Peter Anderson (Sat Jul 05 2003 - 09:39:01 PDT)
parallelisation gold gunaseelan (Mon Jul 07 2003 - 06:32:00 PDT)
- Re: parallelisation Carlos Simmerling (Mon Jul 07 2003 - 06:38:32 PDT)
ALAscan of Proline Martin Lepsik (Mon Jul 07 2003 - 14:14:09 PDT)
Valdiation of Latest Amber parameters Sia Meshkat (Mon Jul 07 2003 - 09:35:57 PDT)
- Re: Valdiation of Latest Amber parameters David A. Case (Mon Jul 07 2003 - 14:23:48 PDT)
  - RE: Valdiation of Latest Amber parameters Sia Meshkat (Mon Jul 07 2003 - 14:48:41 PDT)
    - RE: Valdiation of Latest Amber parameters caldwell.heimdal.compchem.ucsf.edu (Mon Jul 07 2003 - 14:44:53 PDT)
    - Re: Valdiation of Latest Amber parameters David A. Case (Mon Jul 07 2003 - 15:04:01 PDT)
    - RE: Valdiation of Latest Amber parameters Sia Meshkat (Mon Jul 07 2003 - 15:19:04 PDT)
  - RE: Valdiation of Latest Amber parameters Yong Duan (Mon Jul 07 2003 - 16:28:41 PDT)
    - Re: Valdiation of Latest Amber parameters Carlos Simmerling (Mon Jul 07 2003 - 17:50:14 PDT)
    - RE: Valdiation of Latest Amber parameters Sia Meshkat (Mon Jul 07 2003 - 18:40:52 PDT)
    - RE: Valdiation of Latest Amber parameters Yong Duan (Tue Jul 08 2003 - 20:12:27 PDT)
    - Re: Valdiation of Latest Amber parameters Jiri Sponer (Wed Jul 09 2003 - 10:03:53 PDT)
    - RE: Valdiation of Latest Amber parameters Yong Duan (Wed Jul 09 2003 - 22:25:33 PDT)
ptraj Ioana Cozmuta (Mon Jul 07 2003 - 12:06:13 PDT)
- RE: ptraj Kristina Furse (Fri Jul 26 2002 - 11:32:38 PDT)
  - RE: ptraj Thomas Cheatham (Fri Jul 26 2002 - 12:15:04 PDT)
  - ptraj Joseph Nachman (Fri Jul 26 2002 - 12:43:36 PDT)
    - Re: ptraj David A. Case (Fri Jul 26 2002 - 12:08:54 PDT)
  - RE: ptraj Joseph Nachman (Fri Jul 26 2002 - 13:14:53 PDT)
  - periodic box Jiyoung Heo (Fri Jul 26 2002 - 15:00:28 PDT)
New program available: PMEMD (Particle Mesh Ewald Molecular Dynamics) David A. Case (Mon Jul 07 2003 - 14:13:33 PDT)
correction to location of the PMEMD program David A. Case (Mon Jul 07 2003 - 14:17:44 PDT)
diffusion in ptraj Ioana Cozmuta (Mon Jul 07 2003 - 14:56:56 PDT)
Distribution Min with truncated octahedron box Ling Zhang (Tue Jul 08 2003 - 10:24:47 PDT)
- Re: Distribution Min with truncated octahedron box Bill Ross (Tue Jul 08 2003 - 11:24:09 PDT)
  - Re: Distribution Min with truncated octahedron box Ling Zhang (Tue Jul 08 2003 - 11:31:42 PDT)
carnal in big systems GUILLERMINA L ESTIU (Tue Jul 08 2003 - 11:44:21 PDT)
- Re: carnal in big systems Bill Ross (Tue Jul 08 2003 - 12:22:09 PDT)
Lennard-Jones A and B coefficients Gus Carri (Tue Jul 08 2003 - 15:53:56 PDT)
memory shortage with mm_pbsa Peter Anderson (Tue Jul 08 2003 - 17:36:09 PDT)
- Re: memory shortage with mm_pbsa David A. Case (Tue Jul 08 2003 - 18:47:55 PDT)
- Re: memory shortage with mm_pbsa - some more thoughts Joffre Heredia (Sat Jul 12 2003 - 03:26:39 PDT)
  - AMBER: Re: memory shortage with mm_pbsa - some more thoughts Qing Zhang (Mon Jul 14 2003 - 16:10:26 PDT)
May I get your help? Wu Yingliang (Wed Jul 09 2003 - 05:39:05 PDT)
- Re: May I get your help? David A. Case (Thu Jul 10 2003 - 20:05:21 PDT)
- RE: May I get your help? Zhijun Li (Fri Jul 11 2003 - 08:22:30 PDT)
memory problem zhaoxc.puccini.che.pitt.edu (Wed Jul 09 2003 - 06:34:09 PDT)
- Re: memory problem David A. Case (Thu Jul 10 2003 - 20:03:14 PDT)
Refining a docked protein complex Wu Yingliang (Wed Jul 09 2003 - 06:59:26 PDT)
(no subject) Richard Dayton Smith (Wed Jul 09 2003 - 10:23:38 PDT)
- Re: your mail David A. Case (Thu Jul 10 2003 - 20:01:51 PDT)
Adding missing parameters Peter Anderson (Wed Jul 09 2003 - 11:18:33 PDT)
- Re: Adding missing parameters David A. Case (Thu Jul 10 2003 - 19:58:21 PDT)
npscal Shuang Ding (Wed Jul 09 2003 - 13:12:04 PDT)
- Re: npscal David A. Case (Wed Jul 09 2003 - 13:53:54 PDT)
Temperature control Andrei Leitão (Wed Jul 09 2003 - 13:25:12 PDT)
- Re: Temperature control Carlos Simmerling (Wed Jul 09 2003 - 13:38:26 PDT)
- Re: Temperature control David A. Case (Wed Jul 09 2003 - 13:53:10 PDT)
- Re: Temperature control Carlos Simmerling (Wed Jul 09 2003 - 14:15:29 PDT)
van der Waals term David (Wed Jul 09 2003 - 23:47:34 PDT)
AMBER question David (Wed Jul 09 2003 - 23:51:31 PDT)
Amber7 on Opteron Florian Barth (Thu Jul 10 2003 - 03:46:32 PDT)
- RE: Amber7 on Opteron Ross Walker (Thu Jul 10 2003 - 04:58:08 PDT)
3 simultaneous simulations in one computer ptolonen.cc.joensuu.fi (Thu Jul 10 2003 - 04:20:15 PDT)
- RE: 3 simultaneous simulations in one computer Ross Walker (Thu Jul 10 2003 - 05:01:57 PDT)
nab compilation Vlad Cojocaru (Thu Jul 10 2003 - 05:02:04 PDT)
Opteron Experience ian r gould (Thu Jul 10 2003 - 06:29:38 PDT)
effect of forcing neutrality zhaoxc.puccini.che.pitt.edu (Thu Jul 10 2003 - 12:56:00 PDT)
- Re: effect of forcing neutrality David A. Case (Mon Jul 14 2003 - 08:49:57 PDT)
  - Re: effect of forcing neutrality zhaoxc.puccini.che.pitt.edu (Mon Jul 14 2003 - 09:17:24 PDT)
resp for charged molecule? quch quch (Thu Jul 10 2003 - 14:09:08 PDT)
Comparative MD FyD (Fri Jul 11 2003 - 06:29:02 PDT)
- Re: Comparative MD Thomas Cheatham (Fri Jul 11 2003 - 12:32:35 PDT)
  - AMBER: about the npscal, box size changes and rms Haizhen Zhong (Thu Aug 07 2003 - 07:05:08 PDT)
    - AMBER: one more line about the npscal, box size changes and rms Haizhen Zhong (Thu Aug 07 2003 - 07:58:31 PDT)
    - Re: AMBER: one more line about the npscal, box size changes and rms Andy Purkiss (Thu Aug 07 2003 - 08:30:25 PDT)
    - a bug? Re: AMBER: one more line about the npscal, box size changes and rms Dr. Yong Duan (Thu Aug 07 2003 - 08:49:10 PDT)
    - Re: a bug? Re: AMBER: one more line about the npscal, box size changes and rms Haizhen Zhong (Thu Aug 07 2003 - 10:54:17 PDT)
    - Re: a bug? Re: AMBER: one more line about the npscal, box size changes and rms David A. Case (Thu Aug 07 2003 - 11:35:46 PDT)
    - AMBER: more than 100,000 atoms ? David Smith (Thu Aug 07 2003 - 12:44:23 PDT)
    - Re: AMBER: more than 100,000 atoms ? Robert Duke (Thu Aug 07 2003 - 13:33:36 PDT)
    - Re: AMBER: more than 100,000 atoms ? David Smith (Fri Aug 08 2003 - 08:17:39 PDT)
    - Re: AMBER: more than 100,000 atoms ? darden (Thu Aug 07 2003 - 14:23:25 PDT)
    - RE: AMBER: more than 100,000 atoms ? Kristina Furse (Fri Aug 08 2003 - 11:14:10 PDT)
    - RE: a bug? Re: AMBER: one more line about the npscal, box size changes and rms Yong Duan (Thu Aug 07 2003 - 11:49:39 PDT)
AMBER question David (Fri Jul 11 2003 - 06:42:12 PDT)
- RE: AMBER question Marco Aurelio Correia Preto (Thu Jul 10 2003 - 01:04:08 PDT)
- RE: AMBER question Marco Aurelio Correia Preto (Fri Jul 11 2003 - 07:29:11 PDT)
  - Re: AMBER question Carlos Simmerling (Fri Jul 11 2003 - 08:24:30 PDT)
parallelisation gold gunaseelan (Fri Jul 11 2003 - 08:06:43 PDT)
delphi with amber 7 Noriaki Okimoto (Fri Jul 11 2003 - 11:34:34 PDT)
- Re: delphi with amber 7 Guanglei Cui (Fri Jul 11 2003 - 13:44:09 PDT)
- Re: delphi with amber 7 Nori (Fri Jul 11 2003 - 19:15:30 PDT)
ntx in sander dvira (Sat Jul 12 2003 - 06:00:57 PDT)
Strange F.E.P. behavior Peter Anderson (Sun Jul 13 2003 - 06:15:49 PDT)
- Bad atom type: f Sukjoon Yoon (Mon Jul 14 2003 - 08:28:58 PDT)
methylphosphonate A. Hungie (Mon Jul 14 2003 - 06:20:52 PDT)
- AMBER: Re: methylphosphonate David A. Case (Mon Jul 14 2003 - 17:22:28 PDT)
  - Re: AMBER: Re: methylphosphonate Piotr Cieplak (Mon Jul 14 2003 - 17:43:14 PDT)
    - AMBER: Re: methylphosphonate Thomas E. Cheatham, III (Mon Jul 14 2003 - 19:46:06 PDT)
    - AMBER: variable not in namelist for Sander input Haizhen Zhong (Mon Jul 21 2003 - 07:16:40 PDT)
    - RE: AMBER: variable not in namelist for Sander input Yong Duan (Mon Jul 21 2003 - 07:49:07 PDT)
    - RE: AMBER: variable not in namelist for Sander input Haizhen Zhong (Mon Jul 21 2003 - 09:25:38 PDT)
    - Re: AMBER: variable not in namelist for Sander input Angela Pantelogianis (Mon Jul 21 2003 - 07:59:24 PDT)
    - Re: AMBER: variable not in namelist for Sander input Vlad Cojocaru (Mon Jul 21 2003 - 08:16:22 PDT)
    - Re: AMBER: variable not in namelist for Sander input Teletchéa Stéphane (Mon Jul 21 2003 - 09:35:46 PDT)
    - Re: AMBER: variable not in namelist for Sander input Thomas E. Cheatham, III (Mon Jul 21 2003 - 09:40:29 PDT)
    - Re: AMBER: variable not in namelist for Sander input Haizhen Zhong (Mon Jul 21 2003 - 11:08:39 PDT)
    - Re: AMBER: variable not in namelist for Sander input Thomas E. Cheatham, III (Mon Jul 21 2003 - 11:18:50 PDT)
    - RE: AMBER: variable not in namelist for Sander input Yong Duan (Mon Jul 21 2003 - 11:51:30 PDT)
  - AMBER: Questions about mm_pbsa and alanine scanning Haizhen Zhong (Tue Jul 15 2003 - 13:34:32 PDT)
    - Re: AMBER: Questions about mm_pbsa and alanine scanning Natasja Brooijmans (Tue Jul 15 2003 - 13:42:40 PDT)
    - Re: AMBER: Questions about mm_pbsa and alanine scanning Haizhen Zhong (Tue Jul 15 2003 - 14:01:47 PDT)
    - Re: AMBER: Questions about mm_pbsa and alanine scanning Haizhen Zhong (Wed Jul 16 2003 - 06:04:30 PDT)
parallelisation gold gunaseelan (Mon Jul 14 2003 - 08:48:56 PDT)
- Re: parallelisation Carlos P. Sosa (Mon Jul 14 2003 - 09:19:00 PDT)
- Re: parallelisation David A. Case (Mon Jul 14 2003 - 15:24:34 PDT)
Sander_classic output: NAN pantelo.okstate.edu (Mon Jul 14 2003 - 09:07:19 PDT)
- Re: Sander_classic output: NAN David A. Case (Mon Jul 14 2003 - 15:27:17 PDT)
big changes coming caldwell.heimdal.compchem.ucsf.edu (Mon Jul 14 2003 - 08:27:11 PDT)
mail reflector address is changing David A. Case (Mon Jul 14 2003 - 14:56:21 PDT)
- AMBER: increase size of NATOM or NRES for "ambpdb" Wen Li (Mon Sep 22 2003 - 12:14:36 PDT)
  - Re: AMBER: increase size of NATOM or NRES for "ambpdb" David A. Case (Mon Sep 22 2003 - 12:24:12 PDT)
- AMBER: prep file for zinc finger Wen Li (Wed Jan 21 2004 - 14:02:54 PST)
- AMBER: rdparm: a parameter array overflowed Wen Li (Wed Apr 21 2004 - 09:04:17 PDT)
  - Re: AMBER: rdparm: a parameter array overflowed David A. Case (Wed Apr 21 2004 - 10:15:16 PDT)
Welcome to amber Majordomo.scripps.edu (Mon Jul 14 2003 - 15:12:03 PDT)
AMBER: question on LJ parameters for molecules Ioana Cozmuta (Mon Jul 14 2003 - 17:38:58 PDT)
- RE: AMBER: question on LJ parameters for molecules Yong Duan (Mon Jul 14 2003 - 20:52:27 PDT)
Re: AMBER: Re: methylphosphonate Piotr Cieplak (Mon Jul 14 2003 - 22:01:59 PDT)
AMBER: Re: methylphosphonate A. Hungie (Tue Jul 15 2003 - 01:31:52 PDT)
AMBER: PMF X. Tan (Tue Jul 15 2003 - 10:02:47 PDT)
- Re: AMBER: PMF David Smith (Wed Jul 16 2003 - 02:37:56 PDT)
AMBER: Coordinate resetting (SHAKE) cannot be accomplished Anton B. Guliaev (Tue Jul 15 2003 - 14:35:59 PDT)
- Re: AMBER: Coordinate resetting (SHAKE) cannot be accomplished David A. Case (Tue Jul 15 2003 - 18:25:26 PDT)
- Re: AMBER: Coordinate resetting (SHAKE) cannot be accomplished Bill Ross (Wed Jul 16 2003 - 12:46:44 PDT)
AMBER: neutral N- and C- termini ! Xavier Periole (Wed Jul 16 2003 - 11:52:29 PDT)
- Re: AMBER: neutral N- and C- termini ! David A. Case (Thu Jul 17 2003 - 09:05:00 PDT)
AMBER: curves nomenclature Sue Heavner (Wed Jul 16 2003 - 12:34:13 PDT)
- Re: AMBER: curves nomenclature David A. Case (Wed Jul 16 2003 - 15:29:01 PDT)
AMBER: N/C termini Xavier Periole (Wed Jul 16 2003 - 15:24:19 PDT)
AMBER: PMEMD and sander from AMBER6 performances Teletchéa Stéphane (Wed Jul 16 2003 - 16:37:34 PDT)
- Re: AMBER: PMEMD and sander from AMBER6 performances Robert Duke (Wed Jul 16 2003 - 20:11:55 PDT)
  - Re: AMBER: PMEMD and sander from AMBER6 performances Teletchéa Stéphane (Thu Aug 07 2003 - 09:55:03 PDT)
  - AMBER: PMEMD and myrinet trouble Chris Moth (Wed Mar 24 2004 - 13:25:57 PST)
    - Re: AMBER: PMEMD and myrinet trouble Robert Duke (Wed Mar 24 2004 - 13:56:10 PST)
    - AMBER: PMEMD and myrinet trouble Chris Moth (Mon Mar 29 2004 - 11:05:07 PST)
    - Re: AMBER: PMEMD and myrinet trouble Robert Duke (Mon Mar 29 2004 - 11:16:36 PST)
- Re: AMBER: PMEMD and sander from AMBER6 performances Robert Duke (Thu Aug 07 2003 - 12:01:39 PDT)
AMBER: RADII in DELPHI Obdulia Rabal (Thu Jul 17 2003 - 01:58:57 PDT)
- Re: AMBER: RADII in DELPHI David A. Case (Thu Jul 17 2003 - 09:03:29 PDT)
- AMBER: FILE UNITIO.C Obdulia Rabal (Tue Jul 22 2003 - 11:15:48 PDT)
  - Re: AMBER: FILE UNITIO.C David A. Case (Tue Jul 22 2003 - 11:54:14 PDT)
    - RE: AMBER: FILE UNITIO.C Obdulia Rabal (Wed Jul 23 2003 - 00:51:22 PDT)
    - Re: AMBER: FILE UNITIO.C David A. Case (Wed Jul 23 2003 - 08:04:54 PDT)
AMBER: Big system in Gibbs ENikitina (Wed Jul 16 2003 - 23:01:23 PDT)
- Re: AMBER: Big system in Gibbs David A. Case (Thu Jul 17 2003 - 09:00:57 PDT)
  - Re: AMBER: Big system in Gibbs ENikitina (Tue Jul 22 2003 - 08:40:07 PDT)
AMBER: question about quasih? Lishan Yao (Fri Jul 18 2003 - 15:15:32 PDT)
- Re: AMBER: question about quasih? Thomas E. Cheatham, III (Fri Jul 18 2003 - 15:39:15 PDT)
AMBER: Fwd: Minimizing after solvation Angela Pantelogianis (Fri Jul 18 2003 - 15:34:30 PDT)
- Re: AMBER: Fwd: Minimizing after solvation David A. Case (Sat Jul 19 2003 - 21:34:53 PDT)
- Re: AMBER: Fwd: Minimizing after solvation Angela Pantelogianis (Mon Jul 21 2003 - 08:26:30 PDT)
  - Re: AMBER: Fwd: Minimizing after solvation Dr. Yong Duan (Mon Jul 21 2003 - 08:48:00 PDT)
  - Re: AMBER: Fwd: Minimizing after solvation David A. Case (Mon Jul 21 2003 - 08:50:35 PDT)
Returned mail: see transcript for details Mail Delivery Subsystem (Sun Jul 20 2003 - 12:22:37 PDT)
Returned mail: see transcript for details Mail Delivery Subsystem (Mon Jul 21 2003 - 03:31:44 PDT)
AMBER: dielectric in sander Michele Lunelli (Mon Jul 21 2003 - 08:36:19 PDT)
- Re: AMBER: dielectric in sander David A. Case (Mon Jul 21 2003 - 08:52:57 PDT)
AMBER: Odd Problem with PMEMD Chen, Ya (Mon Jul 21 2003 - 20:35:23 PDT)
- Re: AMBER: Odd Problem with PMEMD Johannes Zuegg (Mon Jul 21 2003 - 21:12:37 PDT)
  - Re: AMBER: Odd Problem with PMEMD Robert Duke (Tue Jul 22 2003 - 04:17:25 PDT)
AMBER: (no subject) ENikitina (Tue Jul 22 2003 - 08:53:56 PDT)
- Re: AMBER: (no subject) David A. Case (Tue Jul 22 2003 - 09:30:00 PDT)
- RE: AMBER: (no subject) Ross Walker (Wed Jul 14 2004 - 11:33:38 PDT)
  - RE: AMBER: (no subject) FyD (Wed Jul 14 2004 - 12:30:04 PDT)
  - AMBER: ptraj Wen Li (Wed Jul 14 2004 - 14:07:11 PDT)
- Re: AMBER: (no subject) David A. Case (Fri Jul 30 2004 - 13:42:15 PDT)
AMBER: Non-standard Residue Ran Ye (Tue Jul 22 2003 - 12:34:06 PDT)
- Re: AMBER: Non-standard Residue David A. Case (Tue Jul 22 2003 - 14:06:50 PDT)
  - Re: AMBER: Non-standard Residue Ran Ye (Wed Jul 23 2003 - 09:08:03 PDT)
    - Re: AMBER: Non-standard Residue David A. Case (Wed Jul 23 2003 - 11:31:44 PDT)
AMBER: HB dynamics in water and Ion solvation free energies Ioana Cozmuta (Tue Jul 22 2003 - 15:09:41 PDT)
- Re: AMBER: HB dynamics in water and Ion solvation free energies David A. Case (Tue Jul 22 2003 - 19:18:51 PDT)
AMBER: strange problem with a small system GUILLERMINA L ESTIU (Wed Jul 23 2003 - 10:22:34 PDT)
- Re: AMBER: strange problem with a small system David A. Case (Wed Jul 23 2003 - 11:51:59 PDT)
- Re: AMBER: strange problem with a small system GUILLERMINA L ESTIU (Wed Jul 23 2003 - 12:13:47 PDT)
  - Re: AMBER: strange problem with a small system David A. Case (Thu Jul 24 2003 - 21:51:04 PDT)
- Re: AMBER: strange problem with a small system GUILLERMINA L ESTIU (Mon Jul 28 2003 - 09:00:55 PDT)
  - Re: AMBER: strange problem with a small system David A. Case (Mon Jul 28 2003 - 10:12:30 PDT)
- AMBER: Antechamber problem Shafinaz (Mon Sep 22 2003 - 09:33:58 PDT)
  - Re: AMBER: Antechamber problem David A. Case (Tue Sep 23 2003 - 08:19:54 PDT)
AMBER: addition to: problem with a small system GUILLERMINA L ESTIU (Wed Jul 23 2003 - 11:36:03 PDT)
AMBER: /exe/teLeap does not exist Mizuguchi Mineyuki (Thu Jul 24 2003 - 00:23:55 PDT)
- Re: AMBER: /exe/teLeap does not exist David A. Case (Thu Jul 24 2003 - 17:50:17 PDT)
AMBER: water box problem Omar Wahab (Thu Jul 24 2003 - 01:32:35 PDT)
- Re: AMBER: water box problem Carlos Simmerling (Thu Jul 24 2003 - 04:36:29 PDT)
AMBER: (no subject) Narang Manpreet Kaur (Thu Jul 24 2003 - 04:57:36 PDT)
- Re: AMBER: (no subject) Holger Gohlke (Thu Jul 24 2003 - 08:38:15 PDT)
  - Re: AMBER: (no subject) Thomas E. Cheatham, III (Thu Jul 24 2003 - 09:32:28 PDT)
    - Re: AMBER: (no subject) Narang Manpreet Kaur (Thu Jul 24 2003 - 21:36:54 PDT)
AMBER: question about ptraj? Lishan Yao (Thu Jul 24 2003 - 09:18:20 PDT)
- Re: AMBER: question about ptraj? Thomas E. Cheatham, III (Thu Jul 24 2003 - 09:40:50 PDT)
  - Re: AMBER: question about ptraj? rluo.uci.edu (Thu Jul 24 2003 - 09:48:54 PDT)
AMBER: running AMBER on an IBM P690 cluster Vlad Cojocaru (Thu Jul 24 2003 - 10:46:30 PDT)
AMBER: TEMP is not reaching 300K sd233.georgetown.edu (Thu Jul 24 2003 - 10:06:49 PDT)
- Re: AMBER: TEMP is not reaching 300K Carlos Simmerling (Thu Jul 24 2003 - 10:35:03 PDT)
- Re: AMBER: TEMP is not reaching 300K Vlad Cojocaru (Thu Jul 24 2003 - 10:35:21 PDT)
- Re: AMBER: TEMP is not reaching 300K Michele Lunelli (Fri Jul 25 2003 - 08:27:09 PDT)
AMBER: PMF calculation Lishan Yao (Thu Jul 24 2003 - 12:25:48 PDT)
- Re: AMBER: PMF calculation Carlos Simmerling (Mon Jul 28 2003 - 08:09:45 PDT)
AMBER: MOPAC509mn test jobs on linux takanori.kanazawa.pharma.novartis.com (Thu Jul 24 2003 - 16:54:39 PDT)
AMBER: Dynamics and Simulated Annealing Narang Manpreet Kaur (Fri Jul 25 2003 - 06:03:52 PDT)
- Re: AMBER: Dynamics and Simulated Annealing Carlos Simmerling (Fri Jul 25 2003 - 09:53:38 PDT)
- Re: AMBER: Dynamics and Simulated Annealing Teletchéa Stéphane (Fri Jul 25 2003 - 09:57:53 PDT)
AMBER: Taisung Lee/San Diego/Accelrys is out of the office. Taisung Lee (Fri Jul 25 2003 - 10:02:29 PDT)
AMBER: monitor vdw along time Ling Zhang (Fri Jul 25 2003 - 10:48:26 PDT)
- Re: AMBER: monitor vdw along time Holger Gohlke (Fri Jul 25 2003 - 11:56:28 PDT)
AMBER: DYNAMICS RUN sd233.georgetown.edu (Fri Jul 25 2003 - 10:47:44 PDT)
Re: AMBER: monitor vdw along time Suse Broyde (Fri Jul 25 2003 - 12:57:06 PDT)
AMBER: a note on problems with MPI and sander David A. Case (Sat Jul 26 2003 - 11:50:37 PDT)
AMBER: AMBER and NAMD Vlad Cojocaru (Sun Jul 27 2003 - 06:57:24 PDT)
- Re: AMBER: AMBER and NAMD Andreas Svrcek-Seiler (Sun Jul 27 2003 - 09:10:10 PDT)
  - Re: AMBER: AMBER and NAMD Vlad Cojocaru (Sun Jul 27 2003 - 10:45:40 PDT)
AMBER: Impropers from Amber parm files to NAMD Vlad Cojocaru (Sun Jul 27 2003 - 10:56:47 PDT)
AMBER: please let me know if this is correct Vlad Cojocaru (Mon Jul 28 2003 - 06:58:55 PDT)
- Re: AMBER: please let me know if this is correct Andreas Svrcek-Seiler (Mon Jul 28 2003 - 09:07:28 PDT)
- Re: AMBER: please let me know if this is correct David A. Case (Mon Jul 28 2003 - 09:55:28 PDT)
AMBER: Question about quasih analysis Lishan Yao (Mon Jul 28 2003 - 07:04:26 PDT)
- Re: AMBER: Question about quasih analysis David A. Case (Mon Jul 28 2003 - 09:16:13 PDT)
  - Re: AMBER: Question about quasih analysis Lishan Yao (Mon Jul 28 2003 - 10:30:26 PDT)
    - Re: AMBER: Question about quasih analysis David A. Case (Mon Jul 28 2003 - 11:37:20 PDT)
    - Re: AMBER: Question about quasih analysis Lishan Yao (Mon Jul 28 2003 - 13:24:19 PDT)
    - Re: AMBER: Question about quasih analysis David A. Case (Mon Jul 28 2003 - 14:40:48 PDT)
AMBER: ambpdb and residue number Vlad Cojocaru (Mon Jul 28 2003 - 12:47:26 PDT)
AMBER: H-O-H angle in TIP3P water model during minimization Vlad Cojocaru (Mon Jul 28 2003 - 17:42:10 PDT)
- RE: AMBER: H-O-H angle in TIP3P water model during minimization Yong Duan (Mon Jul 28 2003 - 17:54:28 PDT)
AMBER: chemical potential Petrodler.aol.com (Mon Jul 28 2003 - 23:28:57 PDT)
- Re: AMBER: chemical potential David A. Case (Tue Jul 29 2003 - 07:50:23 PDT)
- Re: AMBER: chemical potential Petrodler.aol.com (Wed Jul 30 2003 - 00:50:05 PDT)
  - Re: AMBER: chemical potential David A. Case (Wed Jul 30 2003 - 09:31:34 PDT)
AMBER: dynamics of isolated system Herbert Georg (Tue Jul 29 2003 - 11:19:18 PDT)
- Re: AMBER: dynamics of isolated system Vlad Cojocaru (Tue Jul 29 2003 - 11:50:52 PDT)
- Re: AMBER: dynamics of isolated system Dr. Yong Duan (Tue Jul 29 2003 - 12:04:42 PDT)
  - Re: AMBER: dynamics of isolated system Herbert Georg (Tue Jul 29 2003 - 12:27:15 PDT)
    - Re: AMBER: dynamics of isolated system Dr. Yong Duan (Tue Jul 29 2003 - 13:16:35 PDT)
- Re: AMBER: dynamics of isolated system Herbert Georg (Tue Jul 29 2003 - 12:05:45 PDT)
- Re: AMBER: dynamics of isolated system David A. Case (Tue Jul 29 2003 - 17:35:03 PDT)
AMBER: combine prep files Mi-Kyung Seo (Tue Jul 29 2003 - 14:14:52 PDT)
- Re: AMBER: combine prep files David A. Case (Tue Jul 29 2003 - 17:27:57 PDT)
AMBER: Ewald_Bomb Susanna Monti (Wed Jul 30 2003 - 06:37:40 PDT)
- Re: AMBER: Ewald_Bomb David A. Case (Wed Jul 30 2003 - 09:30:13 PDT)
AMBER: Ewald problem Shuang Ding (Wed Jul 30 2003 - 09:08:55 PDT)
- Re: AMBER: Ewald problem David A. Case (Wed Jul 30 2003 - 10:01:49 PDT)
- Re: AMBER: Ewald problem Shuang Ding (Wed Jul 30 2003 - 10:28:31 PDT)
AMBER: (no subject) Mi-Kyung Seo (Wed Jul 30 2003 - 12:00:49 PDT)
- Re: AMBER: (no subject) Junmei Wang (Wed Jul 30 2003 - 12:34:54 PDT)
AMBER: compile problem Shuang Ding (Wed Jul 30 2003 - 13:59:08 PDT)
- Re: AMBER: compile problem David A. Case (Wed Jul 30 2003 - 14:56:58 PDT)
- Re: AMBER: compile problem Scott Brozell (Wed Jul 30 2003 - 14:58:55 PDT)
AMBER: Aki Hoji (Wed Jul 30 2003 - 14:19:02 PDT)
- Re: AMBER: charris5 (Tue Jan 13 2004 - 11:07:33 PST)
- Re: AMBER: Michael George Lerner (Tue Jan 13 2004 - 11:18:57 PST)
AMBER: frequency analysis Lishan Yao (Wed Jul 30 2003 - 14:43:16 PDT)
- Re: AMBER: frequency analysis Piotr Cieplak (Wed Jul 30 2003 - 14:49:08 PDT)
  - RE: AMBER: frequency analysis Yong Duan (Wed Jul 30 2003 - 16:04:00 PDT)
AMBER: question about ptraj Ioana Cozmuta (Wed Jul 30 2003 - 15:07:21 PDT)
- Re: AMBER: question about ptraj Thomas E. Cheatham, III (Wed Jul 30 2003 - 15:38:52 PDT)
AMBER: parallelisation gold gunaseelan (Thu Jul 31 2003 - 05:42:25 PDT)
AMBER: parallelisation gold gunaseelan (Thu Jul 31 2003 - 05:42:32 PDT)
AMBER: Running Amber on MacOSX(XDarwin) Aki Hoji (Thu Jul 31 2003 - 07:10:16 PDT)
AMBER: add Ran Ye (Thu Jul 31 2003 - 13:08:30 PDT)
- Re: AMBER: add Scott Brozell (Thu Jul 31 2003 - 14:51:46 PDT)
  - Re: AMBER: add Ran Ye (Thu Jul 31 2003 - 15:03:43 PDT)
    - Re: AMBER: add Scott Brozell (Thu Jul 31 2003 - 16:45:54 PDT)
AMBER: chage WATBOX216 Ioana Cozmuta (Thu Jul 31 2003 - 14:10:44 PDT)
AMBER: parallelisation gold gunaseelan (Thu Jul 31 2003 - 23:13:21 PDT)
AMBER: parallelisation gold gunaseelan (Thu Jul 31 2003 - 23:12:33 PDT)
- RE: AMBER: parallelisation Yong Duan (Fri Aug 01 2003 - 05:21:36 PDT)
AMBER: Amber parallelisation arun prasad (Fri Aug 01 2003 - 02:15:05 PDT)
- RE: AMBER: Amber parallelisation Yong Duan (Fri Aug 01 2003 - 05:28:31 PDT)
- Re: AMBER: Amber parallelisation David A. Case (Fri Aug 01 2003 - 08:18:17 PDT)
AMBER: Problem generating .tpp and .rst files for a complex Yogesh Sabnis (Fri Aug 01 2003 - 03:57:07 PDT)
- Re: AMBER: Problem generating .tpp and .rst files for a complex David A. Case (Fri Aug 01 2003 - 08:32:24 PDT)
AMBER: Restrain of dihedral angle! Marco Aurelio Correia Preto (Fri Aug 01 2003 - 03:59:08 PDT)
- AMBER: RE: Restrain of dihedral angle! Yong Duan (Fri Aug 01 2003 - 06:27:04 PDT)
- Re: AMBER: Restrain of dihedral angle! Luis Gracia (Fri Aug 01 2003 - 09:14:21 PDT)
- RE: AMBER: Restrain of dihedral angle! Marco Aurelio Correia Preto (Mon Aug 04 2003 - 02:15:22 PDT)
AMBER: AMBER7 & mpich takanori.kanazawa.pharma.novartis.com (Sat Aug 02 2003 - 05:17:52 PDT)
- Re: AMBER: AMBER7 & mpich Carlos Simmerling (Sat Aug 02 2003 - 05:53:26 PDT)
AMBER: AMBER7 & mpich : (no-attachment version) takanori.kanazawa.pharma.novartis.com (Sat Aug 02 2003 - 06:03:06 PDT)
- Re: AMBER: AMBER7 & mpich : (no-attachment version) Natasja Brooijmans (Sat Aug 02 2003 - 11:24:59 PDT)
- Re: AMBER: AMBER7 & mpich : (no-attachment version) David A. Case (Sat Aug 02 2003 - 13:30:00 PDT)
AMBER: xplor2amber Mahadevan Seetharaman (Sat Aug 02 2003 - 19:35:48 PDT)
AMBER: xplor2amber Mahadevan Seetharaman (Sat Aug 02 2003 - 19:34:24 PDT)
AMBER: charge method of antechamber Helios Chen (Sun Aug 03 2003 - 21:00:35 PDT)
- Re: AMBER: charge method of antechamber Junmei Wang (Mon Aug 04 2003 - 07:39:58 PDT)
- Re: AMBER: charge method of antechamber David A. Case (Mon Aug 04 2003 - 22:24:00 PDT)
- Re: AMBER: charge method of antechamber Helios Chen (Mon Aug 18 2003 - 05:39:18 PDT)
AMBER: sanderparallel gold gunaseelan (Mon Aug 04 2003 - 00:32:48 PDT)
AMBER: sanderparallel gold gunaseelan (Mon Aug 04 2003 - 00:34:25 PDT)
AMBER: sanderparallel gold gunaseelan (Mon Aug 04 2003 - 00:32:43 PDT)
AMBER: sanderparallel gold gunaseelan (Mon Aug 04 2003 - 00:33:14 PDT)
AMBER: sanderparallel gold gunaseelan (Mon Aug 04 2003 - 00:40:10 PDT)
AMBER: sanderparallel gold gunaseelan (Mon Aug 04 2003 - 00:39:29 PDT)
AMBER: sanderparallel gold gunaseelan (Mon Aug 04 2003 - 00:41:13 PDT)
AMBER: sanderparallel gold gunaseelan (Mon Aug 04 2003 - 00:41:03 PDT)
AMBER: sanderparallel gold gunaseelan (Mon Aug 04 2003 - 00:40:29 PDT)
AMBER: sanderparallel gold gunaseelan (Mon Aug 04 2003 - 00:42:22 PDT)
AMBER: sanderparallel gold gunaseelan (Mon Aug 04 2003 - 00:41:35 PDT)
AMBER: sanderparallel gold gunaseelan (Mon Aug 04 2003 - 00:41:44 PDT)
AMBER: separate thermostats for different molecules Arvid Soederhaell (Mon Aug 04 2003 - 06:13:11 PDT)
- Re: AMBER: separate thermostats for different molecules David A. Case (Mon Aug 04 2003 - 22:19:02 PDT)
AMBER: normal mode analysis Marcela Madrid (Mon Aug 04 2003 - 11:03:23 PDT)
- Re: AMBER: normal mode analysis David A. Case (Mon Aug 04 2003 - 22:12:36 PDT)
AMBER: Re: AMBER7 & mpich : (no-attachment version) takanori.kanazawa.pharma.novartis.com (Mon Aug 04 2003 - 16:51:17 PDT)
- Re: AMBER: Re: AMBER7 & mpich : (no-attachment version) takanori.kanazawa.pharma.novartis.com (Wed Aug 06 2003 - 21:11:30 PDT)
  - Re: AMBER: Re: AMBER7 & mpich : (no-attachment version) Scott Brozell (Thu Aug 07 2003 - 00:40:06 PDT)
AMBER: (no subject) Narang Manpreet Kaur (Tue Aug 05 2003 - 06:55:57 PDT)
- Re: AMBER: (no subject) David A. Case (Tue Aug 05 2003 - 12:32:56 PDT)
AMBER: parallelisation gold gunaseelan (Tue Aug 05 2003 - 06:55:31 PDT)
- Re: AMBER: parallelisation Jian Zhang (Wed Aug 06 2003 - 05:39:22 PDT)
AMBER: zero free energy change for nonbond leg of electrst. decoupling Alfonso Garcia Sosa (Tue Aug 05 2003 - 07:03:59 PDT)
- Re: AMBER: zero free energy change for nonbond leg of electrst. decoupling David A. Case (Tue Aug 05 2003 - 12:39:22 PDT)
  - Re: AMBER: zero free energy change for nonbond leg of electrst. decoupling Alfonso Garcia Sosa (Tue Aug 05 2003 - 14:12:10 PDT)
AMBER: compile problem? Shuang Ding (Tue Aug 05 2003 - 13:51:25 PDT)
AMBER: Comparing PE of different conformations Pratul K. Agarwal (Wed Aug 06 2003 - 09:14:03 PDT)
- Re: AMBER: Comparing PE of different conformations Carlos Simmerling (Wed Aug 06 2003 - 09:33:42 PDT)
  - Re: AMBER: Comparing PE of different conformations Pratul K. Agarwal (Wed Aug 06 2003 - 09:40:16 PDT)
    - Re: AMBER: Comparing PE of different conformations Carlos Simmerling (Wed Aug 06 2003 - 09:45:53 PDT)
  - Re: AMBER: Comparing PE of different conformations Pratul K. Agarwal (Thu Aug 07 2003 - 11:21:07 PDT)
    - Re: AMBER: Comparing PE of different conformations Carlos Simmerling (Thu Aug 07 2003 - 12:57:11 PDT)
AMBER: problem regarding surface Vikas Varshney (Wed Aug 06 2003 - 10:00:09 PDT)
AMBER: anal - memory problem sd233.georgetown.edu (Wed Aug 06 2003 - 10:02:44 PDT)
- Re: AMBER: anal - memory problem David A. Case (Wed Aug 06 2003 - 12:00:32 PDT)
AMBER: SHAKE Problem Richard Smith (Wed Aug 06 2003 - 13:02:30 PDT)
- Re: AMBER: SHAKE Problem Xavier Periole (Wed Aug 06 2003 - 13:26:05 PDT)
- Re: AMBER: SHAKE Problem David A. Case (Wed Aug 06 2003 - 14:52:21 PDT)
  - RE: AMBER: SHAKE Problem Richard Smith (Thu Aug 07 2003 - 07:42:56 PDT)
AMBER: Re: dynamics of isolated system (fwd) David A. Case (Wed Aug 06 2003 - 14:43:29 PDT)
AMBER: references about AMBER MD simulations sd233.georgetown.edu (Wed Aug 06 2003 - 22:23:35 PDT)
- Re: AMBER: references about AMBER MD simulations David A. Case (Wed Aug 06 2003 - 23:21:05 PDT)
- Re: AMBER: references about AMBER MD simulations sd233.georgetown.edu (Thu Aug 07 2003 - 08:04:39 PDT)
AMBER: 2D periodic box Vikas Varshney (Thu Aug 07 2003 - 07:50:20 PDT)
- Re: AMBER: 2D periodic box David A. Case (Thu Aug 07 2003 - 09:28:09 PDT)
- Re: AMBER: 2D periodic box Teletchéa Stéphane (Thu Aug 07 2003 - 09:52:01 PDT)
- Re: AMBER: 2D periodic box Ioana Cozmuta (Thu Aug 07 2003 - 10:00:22 PDT)
AMBER: mpi in mm-pbsa Shuang Ding (Thu Aug 07 2003 - 10:57:03 PDT)
- Re: AMBER: mpi in mm-pbsa Holger Gohlke (Thu Aug 07 2003 - 12:22:53 PDT)
- Re: AMBER: mpi in mm-pbsa Shuang Ding (Thu Aug 07 2003 - 13:14:53 PDT)
AMBER: import pdb file in xleap Mi-Kyung Seo (Thu Aug 07 2003 - 12:07:17 PDT)
- Re: AMBER: import pdb file in xleap Vikas Varshney (Thu Aug 07 2003 - 12:21:32 PDT)
  - Re: AMBER: import pdb file in xleap Scott Brozell (Thu Aug 07 2003 - 16:25:18 PDT)
- Re: AMBER: import pdb file in xleap David A. Case (Thu Aug 07 2003 - 14:30:51 PDT)
AMBER: PMEMD and EAMBER Kristina Furse (Thu Aug 07 2003 - 13:32:45 PDT)
- Re: AMBER: PMEMD and EAMBER Robert Duke (Thu Aug 07 2003 - 14:06:11 PDT)
- RE: AMBER: PMEMD and EAMBER Kristina Furse (Fri Aug 08 2003 - 11:33:28 PDT)
- Re: Fw: AMBER: PMEMD and EAMBER Robert Duke (Mon Aug 11 2003 - 06:49:36 PDT)
AMBER: About the limitation of characters on one line in carnal input fi le Ming Lei (Thu Aug 07 2003 - 14:16:26 PDT)
Re: AMBER: About the limitation of characters on one line in carnal input fi le Bill Ross (Thu Aug 07 2003 - 14:31:39 PDT)
- Re: AMBER: About the limitation of characters on one line in carnal input fi le Bill Ross (Thu Aug 07 2003 - 15:01:40 PDT)
AMBER: Insight pdb file in xleap Mi-Kyung Seo (Thu Aug 07 2003 - 16:09:47 PDT)
- Re: AMBER: Insight pdb file in xleap Rhonda Torres (Thu Aug 07 2003 - 16:29:47 PDT)
- RE: AMBER: Insight pdb file in xleap Yong Duan (Thu Aug 07 2003 - 16:35:03 PDT)
- AMBER: Insight pdb file in xleap Wayne Dawson (Thu Aug 07 2003 - 19:33:26 PDT)
- Re: AMBER: Insight pdb file in xleap Gaurav Sahni (Thu Aug 07 2003 - 23:25:42 PDT)
AMBER: saveamberprep in xLeap Mi-Kyung Seo (Thu Aug 07 2003 - 20:38:24 PDT)
- Re: AMBER: saveamberprep in xLeap David A. Case (Fri Aug 08 2003 - 09:38:34 PDT)
AMBER: derive corresponding torsional parameters yuann (Fri Aug 08 2003 - 03:25:31 PDT)
- Re: AMBER: derive corresponding torsional parameters David Smith (Fri Aug 08 2003 - 06:39:57 PDT)
  - Re[2]: AMBER: derive corresponding torsional parameters sychen (Fri Aug 08 2003 - 08:43:43 PDT)
    - Re: Re[2]: AMBER: derive corresponding torsional parameters David Smith (Fri Aug 08 2003 - 09:20:32 PDT)
AMBER: Reference for Amber7 heme parameters Ross Walker (Fri Aug 08 2003 - 04:41:30 PDT)
- Re: AMBER: Reference for Amber7 heme parameters David A. Case (Fri Aug 08 2003 - 08:23:46 PDT)
AMBER: water model tianxiao yang (Fri Aug 08 2003 - 08:10:04 PDT)
AMBER: saveamberprep and saveoff in xLeap Mi-Kyung Seo (Fri Aug 08 2003 - 10:39:37 PDT)
AMBER: PMEMD NMR Restraints fix Robert Duke (Fri Aug 08 2003 - 15:13:08 PDT)
AMBER: MD simulation with ATP and MG Thomas Steinbrecher (Mon Aug 11 2003 - 02:45:08 PDT)
- Re: AMBER: MD simulation with ATP and MG Heather A.Carlson (Mon Aug 11 2003 - 05:11:27 PDT)
AMBER: Takanori Kanazawa is out of the office. takanori.kanazawa.pharma.novartis.com (Mon Aug 11 2003 - 03:28:02 PDT)
AMBER: Takanori Kanazawa is out of the office. takanori.kanazawa.pharma.novartis.com (Mon Aug 11 2003 - 04:27:56 PDT)
AMBER: Takanori Kanazawa is out of the office. takanori.kanazawa.pharma.novartis.com (Mon Aug 11 2003 - 05:28:55 PDT)
AMBER: Takanori Kanazawa is out of the office. takanori.kanazawa.pharma.novartis.com (Mon Aug 11 2003 - 06:29:55 PDT)
AMBER: Takanori Kanazawa is out of the office. takanori.kanazawa.pharma.novartis.com (Mon Aug 11 2003 - 07:29:55 PDT)
AMBER: machine dependent? Shuang Ding (Mon Aug 11 2003 - 11:39:10 PDT)
- Re: AMBER: machine dependent? David A. Case (Mon Aug 11 2003 - 13:46:14 PDT)
- Re: AMBER: machine dependent? Shuang Ding (Mon Aug 11 2003 - 15:01:38 PDT)
  - Re: AMBER: machine dependent? Michael Crowley (Tue Aug 12 2003 - 07:24:58 PDT)
    - AMBER: secondary structure Yuguang Mu (Wed Aug 13 2003 - 05:37:08 PDT)
    - Re: AMBER: secondary structure Holger Gohlke (Wed Aug 13 2003 - 07:55:22 PDT)
- Re: AMBER: machine dependent? Shuang Ding (Tue Aug 12 2003 - 11:48:00 PDT)
AMBER: GLYCAM Herbert Georg (Mon Aug 11 2003 - 13:57:37 PDT)
AMBER: How to develop parameters for metallic atoms Gustavo A. Carri (Mon Aug 11 2003 - 14:11:19 PDT)
AMBER: "irstrnt=1"in input file for RESP Mi-Kyung Seo (Mon Aug 11 2003 - 15:26:30 PDT)
Instantaneously Dig Up Free Money! Spomer Hooker (Tue Aug 12 2003 - 09:27:34 PDT)
AMBER: question to calculate diffusion coefficient under periodic boundary conditions. Margaret S. Cheung (Tue Aug 12 2003 - 11:56:47 PDT)
- Re: AMBER: question to calculate diffusion coefficient under periodic boundary conditions. David A. Case (Tue Aug 12 2003 - 12:23:55 PDT)
  - Re: AMBER: question to calculate diffusion coefficient under periodic boundary conditions. Margaret S. Cheung (Tue Aug 12 2003 - 12:46:24 PDT)
- Re: AMBER: question to calculate diffusion coefficient under periodic boundary conditions. Thomas E. Cheatham, III (Tue Aug 12 2003 - 12:32:36 PDT)
  - Re: AMBER: question to calculate diffusion coefficient under periodic boundary conditions. Ioana Cozmuta (Sun Aug 17 2003 - 20:08:00 PDT)
AMBER: constant energy simulation Lishan Yao (Tue Aug 12 2003 - 12:38:49 PDT)
- Re: AMBER: constant energy simulation Xavier Periole (Tue Aug 12 2003 - 12:51:24 PDT)
  - Re: AMBER: constant energy simulation Lishan Yao (Tue Aug 12 2003 - 15:25:37 PDT)
- Re: AMBER: constant energy simulation Xavier Periole (Tue Aug 12 2003 - 15:39:29 PDT)
  - Re: AMBER: constant energy simulation Lishan Yao (Wed Aug 13 2003 - 06:00:20 PDT)
- Re: AMBER: constant energy simulation Andreas Svrcek-Seiler (Wed Aug 13 2003 - 06:50:32 PDT)
  - Re: AMBER: constant energy simulation Lishan Yao (Wed Aug 13 2003 - 08:07:29 PDT)
- Re: AMBER: constant energy simulation David A. Case (Wed Aug 13 2003 - 08:46:52 PDT)
  - Re: AMBER: constant energy simulation Lishan Yao (Wed Aug 13 2003 - 09:09:14 PDT)
    - Re: AMBER: constant energy simulation David A. Case (Wed Aug 13 2003 - 15:52:56 PDT)
    - Re: AMBER: constant energy simulation Lishan Yao (Thu Aug 14 2003 - 08:53:13 PDT)
AMBER: Antechamber functionality, MOL2 files bigbrainstorm (Tue Aug 12 2003 - 19:50:40 PDT)
- Re: AMBER: Antechamber functionality, MOL2 files Junmei Wang (Wed Aug 13 2003 - 08:06:47 PDT)
  - Re: AMBER: Antechamber functionality, MOL2 files bigbrainstorm (Wed Aug 13 2003 - 09:20:09 PDT)
    - Re: AMBER: Antechamber functionality, MOL2 files Junmei Wang (Wed Aug 13 2003 - 09:28:03 PDT)
AMBER: amber-on-cheetah-question Endres, Robert G. (Wed Aug 13 2003 - 12:20:10 PDT)
AMBER: ANAL component sd233.georgetown.edu (Wed Aug 13 2003 - 14:36:56 PDT)
- Re: AMBER: ANAL component David A. Case (Wed Aug 13 2003 - 15:45:36 PDT)
AMBER: Atom type in prepin file Yong-Liang Zhu (Wed Aug 13 2003 - 15:21:28 PDT)
Re: AMBER: Atom type in prepin file Rhonda Torres (Wed Aug 13 2003 - 15:38:26 PDT)
AMBER: complete pdb structure Mi-Kyung Seo (Wed Aug 13 2003 - 15:41:52 PDT)
- Re: AMBER: complete pdb structure David A. Case (Wed Aug 13 2003 - 22:30:08 PDT)
RE: AMBER: Atom type in prepin file - new problem Yong-Liang Zhu (Wed Aug 13 2003 - 16:05:01 PDT)
- RE: AMBER: Atom type in prepin file - new problem John Bushnell (Wed Aug 13 2003 - 17:01:21 PDT)
AMBER: modelling a Ca binding site Karsten Suhre (Thu Aug 14 2003 - 02:36:53 PDT)
- Re: AMBER: modelling a Ca binding site Xavier Periole (Thu Aug 14 2003 - 10:07:26 PDT)
  - Re: AMBER: modelling a Ca binding site Karsten Suhre (Fri Aug 15 2003 - 02:44:09 PDT)
AMBER: simulating a crystal using the unit cell Sarah Wittkopp (Thu Aug 14 2003 - 04:09:07 PDT)
- Re: AMBER: simulating a crystal using the unit cell David A. Case (Thu Aug 14 2003 - 08:40:42 PDT)
  - AMBER: Problems with extra points on parralellized linux and sgi machine Sarah Wittkopp (Fri Aug 15 2003 - 00:07:11 PDT)
    - Re: AMBER: Problems with extra points on parralellized linux and sgi machine David A. Case (Fri Aug 15 2003 - 09:17:15 PDT)
    - Re: AMBER: Problems with extra points on parralellized linux and sgi machine Sarah Wittkopp (Mon Aug 18 2003 - 00:33:36 PDT)
    - Re: AMBER: Problems with extra points on parralellized linux and sgi machine David A. Case (Mon Aug 18 2003 - 08:08:57 PDT)
- Re: AMBER: simulating a crystal using the unit cell Joseph Nachman (Thu Aug 14 2003 - 09:01:34 PDT)
AMBER: minimization error Venkata S Koppuravuri (Thu Aug 14 2003 - 11:23:39 PDT)
- Re: AMBER: minimization error Xavier Periole (Thu Aug 14 2003 - 11:38:39 PDT)
- Re: AMBER: minimization error David A. Case (Thu Aug 14 2003 - 11:41:43 PDT)
  - RE: AMBER: minimization error Yong Duan (Thu Aug 14 2003 - 13:56:54 PDT)
AMBER: How to add new atom type. Yong-Liang Zhu (Thu Aug 14 2003 - 12:49:49 PDT)
AMBER: Hydrogen bond plot from carnal Layi Adekoya (Fri Aug 15 2003 - 03:16:02 PDT)
AMBER: Gibbs pmf calculation Lishan Yao (Fri Aug 15 2003 - 08:35:51 PDT)
- Re: AMBER: Gibbs pmf calculation David A. Case (Fri Aug 15 2003 - 09:51:07 PDT)
AMBER: protonation states of small molecules Lee, Matthew (Fri Aug 15 2003 - 11:33:40 PDT)
AMBER: NTX 5 or 7 after equilibration in constant pressure? Majid moghaddam (Sat Aug 16 2003 - 00:08:38 PDT)
- Re: AMBER: NTX 5 or 7 after equilibration in constant pressure? David A. Case (Sat Aug 16 2003 - 17:04:18 PDT)
AMBER: Is NTC=2 correct for minimization when hydrogens are added? Majid moghaddam (Sat Aug 16 2003 - 01:00:04 PDT)
- Re: AMBER: Is NTC=2 correct for minimization when hydrogens are added? Alexey Onufriev (Sat Aug 16 2003 - 09:37:35 PDT)
AMBER: minimum image convention mystery Martin Mucha (Sat Aug 16 2003 - 13:42:37 PDT)
- Re: AMBER: minimum image convention mystery David A. Case (Sat Aug 16 2003 - 17:02:03 PDT)
AMBER: large changes in xyz coordinates Sivakolundu, Sivashankar (Sat Aug 16 2003 - 18:06:14 PDT)
- Re: AMBER: large changes in xyz coordinates David A. Case (Sat Aug 16 2003 - 21:07:25 PDT)
- RE: AMBER: large changes in xyz coordinates Sivakolundu, Sivashankar (Mon Aug 18 2003 - 10:51:49 PDT)
- RE: AMBER: large changes in xyz coordinates Kristina Furse (Mon Aug 18 2003 - 11:26:27 PDT)
  - RE: AMBER: large changes in xyz coordinates james tomomi macdonald (Mon Aug 18 2003 - 11:35:18 PDT)
AMBER: AMBER 7_make install Krishna Bisetty (Mon Aug 18 2003 - 00:36:37 PDT)
- Re: AMBER: AMBER 7_make install David A. Case (Mon Aug 18 2003 - 08:16:20 PDT)
AMBER: Hydrogen bond plot from carnal Layi Adekoya (Mon Aug 18 2003 - 00:51:51 PDT)
AMBER: united atom weiner force field sohail qamar (Mon Aug 18 2003 - 03:46:18 PDT)
- Re: AMBER: united atom weiner force field David A. Case (Mon Aug 18 2003 - 08:21:03 PDT)
AMBER: MM-GB/PBSA:Main-chain/side-chain decomposition in ligands Martin Lepsik (Mon Aug 18 2003 - 06:12:51 PDT)
- Re: AMBER: MM-GB/PBSA:Main-chain/side-chain decomposition in ligands Holger Gohlke (Mon Aug 18 2003 - 08:50:49 PDT)
Re: AMBER: charge method of antechamber(it's ok) Helios Chen (Mon Aug 18 2003 - 06:15:28 PDT)
- Re: AMBER: charge method of antechamber(it's ok) Junmei Wang (Mon Aug 18 2003 - 07:26:41 PDT)
AMBER: pmemd james tomomi macdonald (Mon Aug 18 2003 - 08:18:47 PDT)
- Re: AMBER: pmemd Robert Duke (Mon Aug 18 2003 - 08:45:47 PDT)
  - Re: AMBER: pmemd james tomomi macdonald (Mon Aug 18 2003 - 09:05:20 PDT)
    - Re: AMBER: pmemd Robert Duke (Mon Aug 18 2003 - 09:51:16 PDT)
    - Re: AMBER: pmemd james tomomi macdonald (Mon Aug 18 2003 - 12:52:32 PDT)
Re: AMBER: united atom weiner force field Bill Ross (Mon Aug 18 2003 - 09:12:49 PDT)
AMBER: tleap under amber6 Qiang Lu (Mon Aug 18 2003 - 10:32:05 PDT)
- Re: AMBER: tleap under amber6 David A. Case (Mon Aug 18 2003 - 11:48:19 PDT)
AMBER: nmanal in amber7 Qiang Lu (Mon Aug 18 2003 - 10:41:42 PDT)
- Re: AMBER: nmanal in amber7 David A. Case (Mon Aug 18 2003 - 11:44:20 PDT)
  - Re[2]: AMBER: nmanal in amber7 Qiang Lu (Mon Aug 18 2003 - 12:17:30 PDT)
    - Re: AMBER: nmanal in amber7 David A. Case (Mon Aug 18 2003 - 12:54:04 PDT)
AMBER: ptraj problem Lishan Yao (Mon Aug 18 2003 - 11:22:43 PDT)
- Re: AMBER: ptraj problem Thomas E. Cheatham, III (Wed Aug 20 2003 - 12:00:57 PDT)
  - Re: AMBER: ptraj problem Lishan Yao (Mon Aug 25 2003 - 06:23:10 PDT)
Returned mail Norton_AntiVirus_Gateways.cemi.rssi.ru (Mon Aug 18 2003 - 13:41:55 PDT)
AMBER: overlap problem Ioana Cozmuta (Mon Aug 18 2003 - 14:26:57 PDT)
- Re: AMBER: overlap problem Xavier Periole (Tue Aug 19 2003 - 09:23:45 PDT)
AMBER: nmanal's error message Qiang Lu (Mon Aug 18 2003 - 15:23:20 PDT)
- Re: AMBER: nmanal's error message David Case (Mon Aug 18 2003 - 16:24:11 PDT)
  - Re[2]: AMBER: nmanal's error message Qiang Lu (Mon Aug 18 2003 - 17:10:29 PDT)
AMBER: prepin file Helios Chen (Mon Aug 18 2003 - 23:53:27 PDT)
- Re: AMBER: prepin file David A. Case (Tue Aug 19 2003 - 08:45:30 PDT)
AMBER: temperature does not reach to temp0 Majid moghaddam (Tue Aug 19 2003 - 05:32:43 PDT)
- Re: AMBER: temperature does not reach to temp0 David A. Case (Tue Aug 19 2003 - 08:47:15 PDT)
AMBER: minimization termination sd233.georgetown.edu (Tue Aug 19 2003 - 10:40:53 PDT)
AMBER: ptraj problem Lishan Yao (Tue Aug 19 2003 - 14:08:02 PDT)
AMBER: nmanal's rvec file Qiang Lu (Tue Aug 19 2003 - 16:19:27 PDT)
- Re: AMBER: nmanal's rvec file David A. Case (Tue Aug 19 2003 - 19:00:19 PDT)
AMBER: PARMSET problem Yichen Cao (Wed Aug 20 2003 - 10:07:29 PDT)
- Re: AMBER: PARMSET problem Junmei Wang (Wed Aug 20 2003 - 11:06:00 PDT)
AMBER: PMEMD 3.01 Update available Robert Duke (Wed Aug 20 2003 - 11:36:56 PDT)
AMBER: antechamber problem Qiang Lu (Wed Aug 20 2003 - 11:56:14 PDT)
- Re: AMBER: antechamber problem David A. Case (Wed Aug 20 2003 - 15:07:30 PDT)
  - Re[2]: AMBER: antechamber problem Qiang Lu (Wed Aug 20 2003 - 15:17:30 PDT)
    - Re[2]: AMBER: antechamber problem Natasja Brooijmans (Wed Aug 20 2003 - 15:26:58 PDT)
    - Re: Re[2]: AMBER: antechamber problem Junmei Wang (Thu Aug 21 2003 - 13:16:02 PDT)
    - Re: Re[2]: AMBER: antechamber problem David A. Case (Thu Aug 21 2003 - 16:34:17 PDT)
    - Re: Re[2]: AMBER: antechamber problem Junmei Wang (Fri Aug 22 2003 - 08:03:23 PDT)
    - AMBER: problems with pmemd james tomomi macdonald (Fri Aug 22 2003 - 08:37:34 PDT)
    - Re: AMBER: problems with pmemd Robert Duke (Fri Aug 22 2003 - 09:45:47 PDT)
AMBER: gibbs pmf calculation Lishan Yao (Wed Aug 20 2003 - 12:24:29 PDT)
- Re: AMBER: gibbs pmf calculation David A. Case (Wed Aug 20 2003 - 15:13:23 PDT)
  - Re: AMBER: gibbs pmf calculation Lishan Yao (Mon Aug 25 2003 - 06:16:03 PDT)
    - Re: AMBER: gibbs pmf calculation David A. Case (Mon Aug 25 2003 - 08:25:27 PDT)
    - Re: AMBER: gibbs pmf calculation Lishan Yao (Mon Aug 25 2003 - 14:06:29 PDT)
    - Re: AMBER: gibbs pmf calculation David A. Case (Mon Aug 25 2003 - 16:07:16 PDT)
    - Re: AMBER: gibbs pmf calculation Lishan Yao (Wed Aug 27 2003 - 08:34:02 PDT)
    - AMBER: RESP calculation Yuhui Cheng (Wed Aug 27 2003 - 19:04:57 PDT)
AMBER: NTT Herbert Georg (Thu Aug 21 2003 - 09:31:06 PDT)
- Re: AMBER: NTT Herbert Georg (Thu Aug 21 2003 - 12:48:17 PDT)
AMBER: The FCAP parameter in amber7 Thomas Steinbrecher (Fri Aug 22 2003 - 02:21:35 PDT)
- Re: AMBER: The FCAP parameter in amber7 David A. Case (Mon Aug 25 2003 - 16:59:45 PDT)
AMBER: PMEMD BUG ALERT!!! Robert Duke (Fri Aug 22 2003 - 13:50:02 PDT)
AMBER: Spartan and AMBER7 Peter Oelschlaeger (Fri Aug 22 2003 - 19:52:21 PDT)
AMBER: Questions on Phi, Psi angles produced by pmemd/sander7 Chen, Ya (Fri Aug 22 2003 - 21:47:21 PDT)
- Re: AMBER: Questions on Phi, Psi angles produced by pmemd/sander7 Robert Duke (Sat Aug 23 2003 - 05:41:49 PDT)
- Re: AMBER: Questions on Phi, Psi angles produced by pmemd/sander7 Robert Duke (Sat Aug 23 2003 - 07:41:42 PDT)
- Fw: AMBER: Questions on Phi, Psi angles produced by pmemd/sander7 Robert Duke (Sat Aug 23 2003 - 20:44:06 PDT)
- Re: AMBER: Questions on Phi, Psi angles produced by pmemd/sander7 Robert Duke (Mon Aug 25 2003 - 14:33:38 PDT)
AMBER: temperature problem Lishan Yao (Mon Aug 25 2003 - 06:37:01 PDT)
AMBER: CARNAL Wen Li (Mon Aug 25 2003 - 07:30:19 PDT)
- RE: AMBER: CARNAL Ming Lei (Mon Aug 25 2003 - 12:27:42 PDT)
- RE: AMBER: CARNAL Bill Ross (Mon Aug 25 2003 - 12:40:29 PDT)
- RE: AMBER: CARNAL Ming Lei (Mon Aug 25 2003 - 13:12:50 PDT)
- RE: AMBER: CARNAL Bill Ross (Mon Aug 25 2003 - 13:45:13 PDT)
Re: AMBER: CARNAL Bill Ross (Mon Aug 25 2003 - 12:04:56 PDT)
AMBER: Re: apparent PMEMD bug -- NTWPRT > 0 & IWRAP = 1 Robert Duke (Mon Aug 25 2003 - 12:20:48 PDT)
AMBER: Apparent PMEMD bug -- NTWPRT > 0 & IWRAP = 1 Robert Duke (Mon Aug 25 2003 - 13:41:08 PDT)
AMBER: Antechamber formal charges with Gasteiger method Lee, Matthew (Tue Aug 26 2003 - 11:07:14 PDT)
- Re: AMBER: Antechamber formal charges with Gasteiger method Junmei Wang (Tue Aug 26 2003 - 12:55:14 PDT)
  - Re: AMBER: Antechamber formal charges with Gasteiger method Scott Brozell (Thu Aug 02 2007 - 18:44:28 PDT)
    - Re: AMBER: Antechamber formal charges with Gasteiger method David A. Case (Fri Aug 03 2007 - 13:17:11 PDT)
    - Re: AMBER: Antechamber formal charges with Gasteiger method Scott Brozell (Sat Aug 04 2007 - 12:42:43 PDT)
AMBER: mpprun: exec of '/usr/local/bin/sander7.0' failed: Not enough space zhaoxc.puccini.che.pitt.edu (Tue Aug 26 2003 - 16:17:00 PDT)
- Re: AMBER: mpprun: exec of '/usr/local/bin/sander7.0' failed: Not enough space David A. Case (Tue Aug 26 2003 - 18:32:20 PDT)
  - AMBER: Antechamber Problem Yuhui Cheng (Wed Aug 27 2003 - 09:31:43 PDT)
    - Re: AMBER: Antechamber Problem Junmei Wang (Thu Aug 28 2003 - 10:16:24 PDT)
- Re: AMBER: mpprun: exec of '/usr/local/bin/sander7.0' failed: Not enough space Robert Duke (Tue Aug 26 2003 - 18:53:06 PDT)
AMBER: xleap memory issue Terry Downing (Tue Aug 26 2003 - 17:30:06 PDT)
- Re: AMBER: xleap memory issue David A. Case (Tue Aug 26 2003 - 18:25:29 PDT)
Re: AMBER: xleap memory issue Bill Ross (Tue Aug 26 2003 - 17:52:40 PDT)
AMBER: LEaP not compiling Niko Jukarainen (Wed Aug 27 2003 - 07:50:01 PDT)
- Re: AMBER: LEaP not compiling David A. Case (Wed Aug 27 2003 - 08:42:49 PDT)
  - RE: AMBER: LEaP not compiling Niko Jukarainen (Wed Aug 27 2003 - 08:58:52 PDT)
    - RE: AMBER: LEaP not compiling John Bushnell (Wed Aug 27 2003 - 14:56:32 PDT)
    - RE: AMBER: LEaP not compiling Niko Jukarainen (Wed Aug 27 2003 - 21:58:24 PDT)
AMBER: target MD simulation Lishan Yao (Wed Aug 27 2003 - 11:01:46 PDT)
- Re: AMBER: target MD simulation Carlos Simmerling (Wed Aug 27 2003 - 12:59:09 PDT)
- Re: AMBER: target MD simulation David A. Case (Wed Aug 27 2003 - 13:39:31 PDT)
AMBER: PMF calculation with gibbs Xiao Jian Tan (Wed Aug 27 2003 - 15:34:16 PDT)
AMBER: "ATTN, need revision" atobak.eden.rutgers.edu (Thu Aug 28 2003 - 09:31:05 PDT)
- Re: AMBER: "ATTN, need revision" Junmei Wang (Thu Aug 28 2003 - 10:06:46 PDT)
AMBER: forces estimation Ioana Cozmuta (Thu Aug 28 2003 - 11:54:52 PDT)
AMBER: what can't I use ibelly? nie beining (Thu Aug 28 2003 - 12:30:23 PDT)
- Re: AMBER: what can't I use ibelly? David A. Case (Thu Aug 28 2003 - 12:40:55 PDT)
  - AMBER: Could you please give me an example? Thanks! nie beining (Thu Aug 28 2003 - 13:04:00 PDT)
  - title card? Re: AMBER: what can't I use ibelly? nie beining (Mon Sep 01 2003 - 19:39:06 PDT)
    - Re: title card? Re: AMBER: what can't I use ibelly? David A. Case (Mon Sep 01 2003 - 21:18:12 PDT)
    - AMBER: error message is the same after I added a title nie beining (Tue Sep 02 2003 - 08:20:11 PDT)
AMBER: Fxnal form of NMR-style restraints Kristina Furse (Thu Aug 28 2003 - 14:41:56 PDT)
- Re: AMBER: Fxnal form of NMR-style restraints Holger Gohlke (Thu Aug 28 2003 - 15:41:04 PDT)
AMBER: usability of mm_pbsa with ligand - membrane protein - complex Frank Boeckler (Thu Aug 28 2003 - 15:20:09 PDT)
- Re: AMBER: usability of mm_pbsa with ligand - membrane protein - complex Holger Gohlke (Thu Aug 28 2003 - 16:01:11 PDT)
AMBER: AmberFFC v1.3 released FyD (Fri Aug 29 2003 - 09:35:12 PDT)
AMBER: sander minimization atobak.eden.rutgers.edu (Fri Aug 29 2003 - 13:39:58 PDT)
- Re: AMBER: sander minimization Qiang Lu (Fri Aug 29 2003 - 14:13:53 PDT)
- Re: AMBER: sander minimization David A. Case (Fri Aug 29 2003 - 14:32:55 PDT)
AMBER: processors Herbert Georg (Mon Sep 01 2003 - 12:30:04 PDT)
- Re: AMBER: processors Scott Brozell (Thu Sep 04 2003 - 09:50:10 PDT)
AMBER: MIPS R14000 and Machine-file Antonio J.Díaz Quintana (Tue Sep 02 2003 - 01:14:33 PDT)
AMBER: MIPS R14000 and Machine-file Antonio J.Díaz Quintana (Tue Sep 02 2003 - 04:49:37 PDT)
- Re: AMBER: MIPS R14000 and Machine-file Sanjeev B.S. (Tue Sep 02 2003 - 05:48:33 PDT)
- Re: AMBER: MIPS R14000 and Machine-file David A. Case (Tue Sep 02 2003 - 07:56:26 PDT)
AMBER: PMF ethane example: Can someone correct the INPUT? Thanks. Christophe L M J Verlinde (Tue Sep 02 2003 - 10:57:52 PDT)
- Re: AMBER: PMF ethane example: Can someone correct the INPUT? Thanks. David A. Case (Wed Sep 03 2003 - 08:38:56 PDT)
AMBER: GLYCAM/AMBER Configurator ayongye.sunchem.chem.uga.edu (Tue Sep 02 2003 - 11:36:51 PDT)
AMBER: surften value in mm_gbsa/mm_pbsa calculations Sergio E. Wong (Tue Sep 02 2003 - 12:34:22 PDT)
- Re: AMBER: surften value in mm_gbsa/mm_pbsa calculations Holger Gohlke (Tue Sep 02 2003 - 13:30:15 PDT)
  - AMBER: mm_pbsa - ?small bugs? Chris Moth (Wed Sep 24 2003 - 10:37:37 PDT)
    - AMBER: ?small bugs? - 2nd suggestion Chris Moth (Wed Sep 24 2003 - 13:23:41 PDT)
AMBER: atomic clash or structure size? atobak.eden.rutgers.edu (Tue Sep 02 2003 - 14:08:51 PDT)
- Re: AMBER: atomic clash or structure size? Qiang Lu (Tue Sep 02 2003 - 14:20:32 PDT)
- Re: AMBER: atomic clash or structure size? David A. Case (Wed Sep 03 2003 - 08:32:42 PDT)
AMBER: charge of IRON in HEME!! Pradipta Bandyopadhyay (Thu Sep 04 2003 - 17:28:11 PDT)
- Re: AMBER: charge of IRON in HEME!! Qiang Lu (Thu Sep 04 2003 - 17:40:48 PDT)
- RE: AMBER: charge of IRON in HEME!! Ming Lei (Fri Sep 05 2003 - 11:15:32 PDT)
AMBER: problems with periodic boundary conditions Monika Fuxreiter (Fri Sep 05 2003 - 02:17:40 PDT)
- Re: AMBER: problems with periodic boundary conditions Michael Crowley (Fri Sep 05 2003 - 07:32:29 PDT)
- Re: AMBER: problems with periodic boundary conditions David A. Case (Fri Sep 05 2003 - 07:43:29 PDT)
AMBER: DNA helix is not in z-direction A. Hungie (Fri Sep 05 2003 - 02:35:50 PDT)
- AMBER: IG value SEKIJIMA Masakazu (Fri Sep 05 2003 - 04:50:05 PDT)
  - Re: AMBER: IG value Carlos Simmerling (Fri Sep 05 2003 - 04:57:07 PDT)
  - Re: AMBER: IG value David A. Case (Fri Sep 05 2003 - 07:46:58 PDT)
    - AMBER: Accuracy of PB solvation energy Qing Zhang (Fri Sep 05 2003 - 10:15:15 PDT)
    - Re: AMBER: Accuracy of PB solvation energy Jiri Sponer (Fri Sep 05 2003 - 10:46:04 PDT)
- Re: AMBER: DNA helix is not in z-direction David A. Case (Fri Sep 05 2003 - 17:37:20 PDT)
AMBER: Using NWCHEM for esp? David E. Konerding DSD Staff (Fri Sep 05 2003 - 10:59:45 PDT)
- Re: AMBER: Using NWCHEM for esp? Peter Oelschlaeger (Fri Sep 05 2003 - 21:03:29 PDT)
  - Re: AMBER: Using NWCHEM for esp? FyD (Sun Sep 07 2003 - 14:19:33 PDT)
AMBER: 'ho' vDW parameters Lee, Matthew (Fri Sep 05 2003 - 15:33:12 PDT)
- Re: AMBER: 'ho' vDW parameters Junmei Wang (Mon Sep 08 2003 - 13:01:25 PDT)
  - Re: AMBER: 'ho' vDW parameters Carlos Simmerling (Mon Sep 08 2003 - 13:10:13 PDT)
  - RE: AMBER: 'ho' vDW parameters Yong Duan (Mon Sep 08 2003 - 13:27:48 PDT)
    - AMBER: Compiling 64-bit version on AIX Pratul K. Agarwal (Mon Sep 08 2003 - 19:00:55 PDT)
    - Re: AMBER: Compiling 64-bit version on AIX Nicolas Grima (Tue Sep 09 2003 - 00:11:03 PDT)
    - Re: AMBER: Compiling 64-bit version on AIX Pratul K. Agarwal (Tue Sep 09 2003 - 08:45:58 PDT)
    - Re: AMBER: Compiling 64-bit version on AIX Carlos P. Sosa (Tue Sep 09 2003 - 09:06:39 PDT)
    - Re: AMBER: Compiling 64-bit version on AIX David A. Case (Tue Sep 09 2003 - 09:36:12 PDT)
    - Re: AMBER: Compiling 64-bit version on AIX Pratul K. Agarwal (Tue Sep 09 2003 - 10:01:13 PDT)
AMBER: solvatebox-solvateshell Majid moghaddam (Sat Sep 06 2003 - 04:42:55 PDT)
- Re: AMBER: solvatebox-solvateshell David A. Case (Sat Sep 06 2003 - 12:56:39 PDT)
- Re: AMBER: solvatebox-solvateshell Thomas E. Cheatham, III (Sat Sep 06 2003 - 13:16:38 PDT)
- Re: AMBER: solvatebox-solvateshell Xavier Periole (Mon Sep 08 2003 - 14:46:00 PDT)
AMBER: charge definition Khanh KIm Dao (Sat Sep 06 2003 - 11:40:31 PDT)
- Re: AMBER: charge definition Holger Gohlke (Sat Sep 06 2003 - 12:00:01 PDT)
AMBER: update to answer about solvateShell David A. Case (Sat Sep 06 2003 - 13:00:50 PDT)
AMBER: dielectric constant for blends Taner E. Dirama (Mon Sep 08 2003 - 07:21:11 PDT)
- Re: AMBER: dielectric constant for blends David A. Case (Mon Sep 08 2003 - 08:23:34 PDT)
AMBER: parm. and top. for sugars, charmm? Endres, Robert G. (Mon Sep 08 2003 - 09:05:00 PDT)
- Re: AMBER: parm. and top. for sugars, charmm? Itziar Maestre Asenjo (Mon Sep 08 2003 - 22:57:27 PDT)
AMBER: radial distribution-function by Ptraj Petrodler.aol.com (Tue Sep 09 2003 - 02:15:10 PDT)
AMBER: reporting atoms clashed during simple energy minimization jackie.ibms.sinica.edu.tw (Tue Sep 09 2003 - 03:19:36 PDT)
- Re: AMBER: reporting atoms clashed during simple energy minimization Dr. Yong Duan (Tue Sep 09 2003 - 05:18:44 PDT)
- Re: AMBER: reporting atoms clashed during simple energy minimization David A. Case (Tue Sep 09 2003 - 08:36:29 PDT)
AMBER: SHAKE poblem with dummy atoms Itziar Maestre Asenjo (Tue Sep 09 2003 - 03:06:57 PDT)
- Re: AMBER: SHAKE poblem with dummy atoms David A. Case (Tue Sep 09 2003 - 08:38:49 PDT)
AMBER: PMF calculations Sébastien Canneaux (Tue Sep 09 2003 - 05:29:36 PDT)
AMBER: TIP5P Ulf Johansson (Tue Sep 09 2003 - 06:27:27 PDT)
- Re: AMBER: TIP5P David A. Case (Tue Sep 09 2003 - 08:32:58 PDT)
- Re: AMBER: TIP5P Ulf Johansson (Wed Sep 10 2003 - 00:37:36 PDT)
  - Re: AMBER: TIP5P David A. Case (Wed Sep 10 2003 - 08:14:18 PDT)
AMBER: Re: torsional energy David A. Case (Wed Sep 10 2003 - 15:15:34 PDT)
AMBER: altering mass in .top file hagop demirdjian (Thu Sep 11 2003 - 02:07:02 PDT)
- Re: AMBER: altering mass in .top file Pascal Bonnet (Thu Sep 11 2003 - 03:05:15 PDT)
AMBER: EWALD BOMB and solvent density problem northrop.chem.ucla.edu (Thu Sep 11 2003 - 11:28:51 PDT)
AMBER: ptraj question Lishan Yao (Thu Sep 11 2003 - 12:48:08 PDT)
AMBER: gaff parameters astrid.maass (Fri Sep 12 2003 - 02:10:32 PDT)
- Re: AMBER: gaff parameters Kazuo Koyano (Fri Sep 12 2003 - 03:31:33 PDT)
- Re: AMBER: gaff parameters Junmei Wang (Fri Sep 12 2003 - 14:46:24 PDT)
AMBER: DMSO box Dalmaris, John (Fri Sep 12 2003 - 02:25:21 PDT)
- Re: AMBER: DMSO box Jiten (Fri Sep 12 2003 - 18:05:46 PDT)
AMBER: FF parameters for BOC - group Balvinder Singh (Fri Sep 12 2003 - 10:38:34 PDT)
- Re: AMBER: FF parameters for BOC - group Martin Lepsik (Fri Sep 12 2003 - 07:57:24 PDT)
AMBER: minimization error Venkata S Koppuravuri (Fri Sep 12 2003 - 12:00:05 PDT)
- Re: AMBER: minimization error Scott Brozell (Fri Sep 12 2003 - 12:24:37 PDT)
- Re: AMBER: minimization error David A. Case (Fri Sep 12 2003 - 14:19:48 PDT)
AMBER: AMBER on LINUX ?? (fwd) sangeeta.bioinfo.ernet.in (Sun Sep 14 2003 - 23:57:20 PDT)
- Re: AMBER: AMBER on LINUX ?? (fwd) Sanjeev B.S. (Mon Sep 15 2003 - 02:17:01 PDT)
- Re: AMBER: AMBER on LINUX ?? (fwd) David A. Case (Mon Sep 15 2003 - 13:08:56 PDT)
  - AMBER: MD simulations on small molecules immersed in sparse water shell Junmei Wang (Tue Sep 16 2003 - 09:42:56 PDT)
    - Re: AMBER: MD simulations on small molecules immersed in sparse water shell Alfonso Garcia Sosa (Tue Sep 16 2003 - 10:08:24 PDT)
    - Re: AMBER: MD simulations on small molecules immersed in sparse water shell rluo.uci.edu (Tue Sep 16 2003 - 11:16:41 PDT)
    - Re: AMBER: MD simulations on small molecules immersed in sparse water shell Carlos Simmerling (Tue Sep 16 2003 - 11:23:53 PDT)
    - Re: AMBER: MD simulations on small molecules immersed in sparse water shell rluo.uci.edu (Tue Sep 16 2003 - 12:07:03 PDT)
    - Re: AMBER: MD simulations on small molecules immersed in sparse water shell Carlos Simmerling (Tue Sep 16 2003 - 12:21:18 PDT)
AMBER: AMBER error in CHALANGE sd233.georgetown.edu (Mon Sep 15 2003 - 08:58:31 PDT)
- Re: AMBER: AMBER error in CHALANGE Carlos Simmerling (Mon Sep 15 2003 - 09:04:26 PDT)
- Re: AMBER: AMBER error in CHALANGE David A. Case (Mon Sep 15 2003 - 13:06:21 PDT)
AMBER: sander on cygwin Lee, Matthew (Mon Sep 15 2003 - 11:14:40 PDT)
- Re: AMBER: sander on cygwin David E. Konerding DSD Staff (Mon Sep 15 2003 - 11:24:29 PDT)
  - Re: AMBER: sander on cygwin David A. Case (Mon Sep 15 2003 - 13:03:23 PDT)
    - Re: AMBER: sander on cygwin David E. Konerding DSD Staff (Mon Sep 15 2003 - 14:21:57 PDT)
    - AMBER: PMEMD: dual XEON vs SGI cluster Chris Moth (Tue Sep 16 2003 - 14:46:45 PDT)
    - Re: AMBER: PMEMD: dual XEON vs SGI cluster Robert Duke (Mon Sep 15 2003 - 15:55:28 PDT)
    - Re: AMBER: PMEMD: dual XEON vs SGI cluster Johannes Zuegg (Mon Sep 15 2003 - 16:45:27 PDT)
    - RE: AMBER: PMEMD: dual XEON vs SGI cluster Chris Moth (Mon Sep 15 2003 - 18:55:46 PDT)
AMBER: performance vs number of processors GUILLERMINA L ESTIU (Mon Sep 15 2003 - 11:58:37 PDT)
- Re: AMBER: performance vs number of processors zhaoxc.puccini.che.pitt.edu (Mon Sep 15 2003 - 12:41:20 PDT)
  - AMBER: Compiling sander with single precision rluo.uci.edu (Tue Sep 16 2003 - 18:37:01 PDT)
    - Re: AMBER: Compiling sander with single precision Scott Brozell (Tue Sep 16 2003 - 18:59:25 PDT)
    - Re: AMBER: Compiling sander with single precision Mengjuei Hsieh (Wed Sep 17 2003 - 14:56:34 PDT)
- Re: AMBER: performance vs number of processors David A. Case (Mon Sep 15 2003 - 12:53:32 PDT)
- AMBER: leap/frcmod problem Joseph Nachman (Wed Sep 17 2003 - 13:08:37 PDT)
  - Re: AMBER: leap/frcmod problem David A. Case (Wed Sep 17 2003 - 13:57:18 PDT)
AMBER: Benchmark of AMBER on Apple G5 machine Mengjuei Hsieh (Mon Sep 15 2003 - 13:56:43 PDT)
AMBER: MD problem! Pradipta Bandyopadhyay (Tue Sep 16 2003 - 17:33:17 PDT)
- Re: AMBER: MD problem! darden (Wed Sep 17 2003 - 08:29:50 PDT)
AMBER: mfef90 - installation problem Joseph Maxwell (Wed Sep 17 2003 - 09:34:18 PDT)
- Re: AMBER: mfef90 - installation problem Michael Crowley (Wed Sep 17 2003 - 10:28:19 PDT)
  - Re: AMBER: mfef90 - installation problem Joseph Maxwell (Wed Sep 17 2003 - 11:11:58 PDT)
AMBER: Scyld cluster amber 7 compile problems Bengt Svensson (Wed Sep 17 2003 - 18:11:04 PDT)
- Re: AMBER: Scyld cluster amber 7 compile problems Scott Brozell (Thu Sep 18 2003 - 10:50:08 PDT)
AMBER: Amber 7 - bugfix 42 problem. Bengt Svensson (Wed Sep 17 2003 - 18:21:08 PDT)
- Re: AMBER: Amber 7 - bugfix 42 problem. David A. Case (Fri Sep 19 2003 - 11:17:10 PDT)
AMBER: Suggestion regarding long simulation. uddhavesh bhaskar sonavane (Wed Sep 17 2003 - 23:50:37 PDT)
- Re: AMBER: Suggestion regarding long simulation. Johannes Zuegg (Thu Sep 18 2003 - 15:56:39 PDT)
  - RE: AMBER: Suggestion regarding long simulation. Yong Duan (Thu Sep 18 2003 - 17:33:30 PDT)
    - Re: AMBER: Suggestion regarding long simulation. Carlos Simmerling (Thu Sep 18 2003 - 19:12:20 PDT)
- Re: AMBER: Suggestion regarding long simulation. Carlos Simmerling (Fri Sep 19 2003 - 05:05:58 PDT)
AMBER: Calculating solvation energies for MM-PBSA use Thomas Steinbrecher (Thu Sep 18 2003 - 05:43:37 PDT)
- Re: AMBER: Calculating solvation energies for MM-PBSA use samantha hughes (Thu Sep 18 2003 - 06:13:04 PDT)
AMBER: FEP problem Itziar Maestre Asenjo (Thu Sep 18 2003 - 05:35:37 PDT)
- Re: AMBER: FEP problem David A. Case (Thu Sep 18 2003 - 08:08:18 PDT)
AMBER: re: MD problem!! Pradipta Bandyopadhyay (Thu Sep 18 2003 - 10:36:59 PDT)
- RE: AMBER: re: MD problem!! Yong Duan (Thu Sep 18 2003 - 12:32:49 PDT)
AMBER: Generalized Born parameters Peter VARNAI (Thu Sep 18 2003 - 11:51:24 PDT)
AMBER: MD problem!! Pradipta Bandyopadhyay (Thu Sep 18 2003 - 13:35:36 PDT)
- Re: AMBER: MD problem!! yduan.udel.edu (Thu Sep 18 2003 - 14:21:22 PDT)
AMBER: no defined type for atom N atom Wu Yingliang (Fri Sep 19 2003 - 05:57:12 PDT)
AMBER: no defined type for atom N atom Wu Yingliang (Fri Sep 19 2003 - 06:02:31 PDT)
- Re: AMBER: no defined type for atom N atom David A. Case (Fri Sep 19 2003 - 10:01:29 PDT)
AMBER: xLEAP Problem Stephen P. Molnar, Ph.D. (Fri Sep 19 2003 - 13:07:14 PDT)
- RE: AMBER: xLEAP Problem Niko Jukarainen (Fri Sep 19 2003 - 14:18:30 PDT)
- Re: AMBER: xLEAP Problem Kazuo Koyano (Sun Sep 21 2003 - 19:18:49 PDT)
- Re: AMBER: xLEAP Problem Donald Thomas (Sun Sep 21 2003 - 19:37:23 PDT)
- AMBER: Re: xLEAP Problem Stephen P. Molnar, Ph.D. (Mon Sep 22 2003 - 09:36:48 PDT)
AMBER: 'high' temp. simulation!! Pradipta Bandyopadhyay (Fri Sep 19 2003 - 13:09:05 PDT)
AMBER: double bonds in prmtop Herbert Georg (Fri Sep 19 2003 - 13:09:16 PDT)
- Re: AMBER: double bonds in prmtop Ioana Cozmuta (Fri Sep 19 2003 - 13:24:18 PDT)
- Re: AMBER: double bonds in prmtop Herbert Georg (Fri Sep 19 2003 - 14:27:53 PDT)
  - Re: AMBER: double bonds in prmtop David A. Case (Fri Sep 19 2003 - 15:42:23 PDT)
    - AMBER: C-alpha RMS Do Anh Tuan (Fri Sep 19 2003 - 23:39:42 PDT)
    - Re: AMBER: C-alpha RMS Kun Song (Mon Sep 22 2003 - 06:45:20 PDT)
AMBER: AMBER Carnal files Frederico.Miranda.ibmb.uib.no (Sat Sep 20 2003 - 15:24:12 PDT)
- RE: AMBER: AMBER Carnal files Yong Duan (Sat Sep 20 2003 - 15:44:44 PDT)
  - RE: AMBER: AMBER Carnal files Frederico.Miranda.ibmb.uib.no (Sun Sep 21 2003 - 17:09:01 PDT)
    - RE: AMBER: AMBER Carnal files Yong Duan (Sun Sep 21 2003 - 19:02:40 PDT)
AMBER: slow simulation nie beining (Sun Sep 21 2003 - 23:46:21 PDT)
- Re: AMBER: slow simulation David A. Case (Mon Sep 22 2003 - 07:54:46 PDT)
AMBER: plane angle. Pascal Bonnet (Mon Sep 22 2003 - 08:14:44 PDT)
AMBER: slower simulation nie beining (Mon Sep 22 2003 - 08:43:24 PDT)
- Re: AMBER: slower simulation Carlos Simmerling (Mon Sep 22 2003 - 08:59:02 PDT)
AMBER: Slower simulation and pair-range cutoff? nie beining (Mon Sep 22 2003 - 10:11:11 PDT)
Re: AMBER: plane angle. Bill Ross (Mon Sep 22 2003 - 11:42:40 PDT)
AMBER: Carnal Input file Frederico.Miranda.ibmb.uib.no (Mon Sep 22 2003 - 16:06:55 PDT)
- RE: AMBER: Carnal Input file Ming Lei (Mon Sep 22 2003 - 20:34:05 PDT)
Re: AMBER: Carnal Input file Bill Ross (Mon Sep 22 2003 - 16:23:27 PDT)
AMBER: How can I set ntx=7, but exclude the velocity? Margaret S. Cheung (Tue Sep 23 2003 - 08:30:28 PDT)
- Re: AMBER: How can I set ntx=7, but exclude the velocity? Carlos Simmerling (Tue Sep 23 2003 - 08:35:28 PDT)
AMBER: pair-cutoff nie beining (Tue Sep 23 2003 - 08:40:32 PDT)
- Re: AMBER: pair-cutoff David A. Case (Tue Sep 23 2003 - 08:59:01 PDT)
AMBER: GROUP Atchara Wijitkosoom (Tue Sep 23 2003 - 13:04:20 PDT)
AMBER: residues and molecules GUILLERMINA L ESTIU (Tue Sep 23 2003 - 14:56:01 PDT)
- Re: AMBER: residues and molecules David A. Case (Wed Sep 24 2003 - 11:45:40 PDT)
- Re: AMBER: residues and molecules Robert Duke (Wed Sep 24 2003 - 12:53:20 PDT)
AMBER: PMEMD 3.03 Update available Robert Duke (Tue Sep 23 2003 - 19:13:57 PDT)
AMBER: cd-c-os and c3-cd-c angle parameters Vikas Varshney (Wed Sep 24 2003 - 08:10:09 PDT)
- Re: AMBER: cd-c-os and c3-cd-c angle parameters Junmei Wang (Wed Sep 24 2003 - 11:16:18 PDT)
  - AMBER: problem with file format Shafinaz (Wed Sep 24 2003 - 12:05:23 PDT)
    - Re: AMBER: problem with file format David A. Case (Wed Sep 24 2003 - 12:28:22 PDT)
    - RE: AMBER: problem with file format Shafinaz (Wed Sep 24 2003 - 13:29:10 PDT)
    - RE: AMBER: problem with file format Junmei Wang (Wed Sep 24 2003 - 13:34:14 PDT)
AMBER: NaCl ion pairs in TIP3P water box Nathan A. Baker (Wed Sep 24 2003 - 13:13:11 PDT)
- Re: AMBER: NaCl ion pairs in TIP3P water box David A. Case (Wed Sep 24 2003 - 14:09:06 PDT)
- Re: AMBER: NaCl ion pairs in TIP3P water box Jiri Sponer (Wed Sep 24 2003 - 14:41:27 PDT)
- Re: AMBER: NaCl ion pairs in TIP3P water box Bill Ross (Wed Sep 24 2003 - 15:13:47 PDT)
  - Re: AMBER: NaCl ion pairs in TIP3P water box Ioana Cozmuta (Wed Sep 24 2003 - 15:30:26 PDT)
    - Re: AMBER: NaCl ion pairs in TIP3P water box M. L. Dodson (Wed Sep 24 2003 - 16:53:22 PDT)
    - Re: AMBER: NaCl ion pairs in TIP3P water box Nathan A. Baker (Wed Sep 24 2003 - 18:14:47 PDT)
    - Re: AMBER: NaCl ion pairs in TIP3P water box Jiri Sponer (Thu Sep 25 2003 - 04:59:51 PDT)
    - Re: AMBER: NaCl ion pairs in TIP3P water box Pascal Auffinger (Thu Sep 25 2003 - 06:30:08 PDT)
Re: AMBER: NaCl ion pairs in TIP3P water box Bill Ross (Wed Sep 24 2003 - 13:53:39 PDT)
AMBER: MM_PBSA(GBSA) Examples Kazuo Koyano (Thu Sep 25 2003 - 03:35:50 PDT)
AMBER: MM_PBSA(GBSA) Examples Chris Moth (Thu Sep 25 2003 - 08:56:23 PDT)
- Re: AMBER: MM_PBSA(GBSA) Examples Kazuo Koyano (Fri Sep 26 2003 - 03:37:40 PDT)
AMBER: Online model of 2C9 Peter Gannett (Thu Sep 25 2003 - 12:23:22 PDT)
- AMBER: about the mopac7 installation. Yong Wang (Fri Sep 26 2003 - 00:07:16 PDT)
AMBER: MeCNBOX northrop.chem.ucla.edu (Thu Sep 25 2003 - 12:35:03 PDT)
- Re: AMBER: MeCNBOX David A. Case (Thu Sep 25 2003 - 13:25:23 PDT)
  - Re: AMBER: MeCNBOX northrop.chem.ucla.edu (Thu Sep 25 2003 - 13:40:37 PDT)
  - Re: AMBER: MeCNBOX northrop.chem.ucla.edu (Thu Sep 25 2003 - 13:47:03 PDT)
    - Re: AMBER: MeCNBOX James W. Caldwell (Thu Sep 25 2003 - 14:04:03 PDT)
- Re: AMBER: MeCNBOX Pascal Bonnet (Fri Sep 26 2003 - 01:38:03 PDT)
AMBER: Re:MeCNBOX Pradipta Bandyopadhyay (Thu Sep 25 2003 - 14:23:09 PDT)
AMBER: Zn in antechamber Lishan Yao (Fri Sep 26 2003 - 06:48:44 PDT)
- Re: AMBER: Zn in antechamber Junmei Wang (Fri Sep 26 2003 - 07:47:45 PDT)
  - Re: AMBER: Zn in antechamber Lishan Yao (Fri Sep 26 2003 - 08:01:41 PDT)
    - Re: AMBER: Zn in antechamber Junmei Wang (Fri Sep 26 2003 - 10:00:11 PDT)
    - Re: AMBER: Zn in antechamber Lishan Yao (Fri Sep 26 2003 - 12:15:21 PDT)
    - Re: AMBER: Zn in antechamber Junmei Wang (Fri Sep 26 2003 - 13:24:46 PDT)
    - Re: AMBER: Zn in antechamber Lishan Yao (Mon Sep 29 2003 - 08:13:42 PDT)
    - Re: AMBER: Zn in antechamber Junmei Wang (Mon Sep 29 2003 - 08:32:52 PDT)
    - Re: AMBER: Zn in antechamber Lishan Yao (Mon Sep 29 2003 - 08:59:09 PDT)
    - Re: AMBER: Zn in antechamber Junmei Wang (Mon Sep 29 2003 - 09:38:09 PDT)
    - Re: AMBER: Zn in antechamber Lishan Yao (Mon Sep 29 2003 - 13:15:04 PDT)
- Re: AMBER: Zn in antechamber Rhonda Torres (Fri Sep 26 2003 - 10:24:16 PDT)
AMBER: non-bonded cutoffs Michael Dolan (Fri Sep 26 2003 - 08:17:16 PDT)
- Re: AMBER: non-bonded cutoffs David A. Case (Fri Sep 26 2003 - 08:32:09 PDT)
- Re: AMBER: non-bonded cutoffs Michael Dolan (Fri Sep 26 2003 - 08:39:34 PDT)
AMBER: Phase for torsion angle different of 0 or 180 ? Teletchéa Stéphane (Fri Sep 26 2003 - 09:27:34 PDT)
- Re: AMBER: Phase for torsion angle different of 0 or 180 ? David A. Case (Fri Sep 26 2003 - 13:41:35 PDT)
  - AMBER: polarizability and PME Martin Mucha (Sat Sep 27 2003 - 07:46:08 PDT)
    - Re: AMBER: polarizability and PME David A. Case (Sat Sep 27 2003 - 09:17:46 PDT)
AMBER: FW: Residual dipolar couplings McAteer, Kathleen (Fri Sep 26 2003 - 12:44:57 PDT)
- Re: AMBER: FW: Residual dipolar couplings David A. Case (Fri Sep 26 2003 - 13:36:25 PDT)
AMBER: AMBER quasih question(s) Rachel Ward (Mon Sep 29 2003 - 12:39:17 PDT)
- Re: AMBER: AMBER quasih question(s) David Case (Thu Oct 02 2003 - 04:34:18 PDT)
AMBER: nstlim Amber Administration (Mon Sep 29 2003 - 16:55:42 PDT)
- Re: AMBER: nstlim Robert Duke (Mon Sep 29 2003 - 18:40:24 PDT)
  - Re: Re: AMBER: nstlim uddhavesh bhaskar sonavane (Wed Oct 01 2003 - 08:32:27 PDT)
    - Re: Re: AMBER: nstlim Robert Duke (Wed Oct 01 2003 - 09:32:48 PDT)
AMBER: A problem about xleap Jiang Pengju (Mon Sep 29 2003 - 19:04:14 PDT)
- Re: AMBER: A problem about xleap John Bushnell (Tue Sep 30 2003 - 10:13:06 PDT)
AMBER: density equilibrium & harmonic restrain yuann (Mon Sep 29 2003 - 19:59:50 PDT)
- Re: AMBER: density equilibrium & harmonic restrain David Case (Thu Oct 02 2003 - 04:39:05 PDT)
AMBER: iam a newbie !!! Karthikeyan Pasupathy (Mon Sep 29 2003 - 21:25:05 PDT)
- Re: AMBER: iam a newbie !!! Vlad Cojocaru (Tue Sep 30 2003 - 02:12:43 PDT)
AMBER: following salt and waterbridges during a simulation Karsten Suhre (Mon Sep 29 2003 - 23:33:31 PDT)
AMBER: TTF parameters northrop.chem.ucla.edu (Mon Sep 29 2003 - 23:49:20 PDT)
Re: AMBER: improper Bill Ross (Tue Sep 30 2003 - 13:15:28 PDT)
- Re: AMBER: improper ya ya (Wed Oct 01 2003 - 07:59:16 PDT)
- Re: AMBER: improper Bill Ross (Wed Oct 01 2003 - 10:21:03 PDT)
- Re: AMBER: improper Bill Ross (Wed Oct 01 2003 - 10:38:08 PDT)
AMBER: improper Li Ying (Tue Sep 30 2003 - 13:08:11 PDT)
AMBER: Added water and mm_pbsa Yong-Liang Zhu (Wed Oct 01 2003 - 10:29:37 PDT)
AMBER: addions/xleap question FyD (Wed Oct 01 2003 - 13:39:47 PDT)
Re: AMBER: addions/xleap question Rhonda Torres (Wed Oct 01 2003 - 14:10:00 PDT)
- Re: AMBER: addions/xleap question Bill Ross (Wed Oct 01 2003 - 14:10:44 PDT)
  - Re: AMBER: addions/xleap question FyD (Wed Oct 01 2003 - 14:24:38 PDT)
AMBER: constant pressure in GB aini.UMDNJ.EDU (Wed Oct 01 2003 - 18:19:12 PDT)
- RE: AMBER: constant pressure in GB Yong Duan (Wed Oct 01 2003 - 18:45:04 PDT)
- Re: AMBER: constant pressure in GB David Case (Thu Oct 02 2003 - 04:53:32 PDT)
AMBER: regarding trajectory input and output with ptraj or Carnal Vlad Cojocaru (Thu Oct 02 2003 - 05:37:19 PDT)
- Re: AMBER: regarding trajectory input and output with ptraj or Carnal David Case (Thu Oct 02 2003 - 05:54:11 PDT)
AMBER: calculation of LJ 12-6 from .dat file (fwd) Michal Otyepka (Thu Oct 02 2003 - 07:53:27 PDT)
- Re: AMBER: calculation of LJ 12-6 from .dat file (fwd) Martin Lepsik (Fri Oct 03 2003 - 02:53:50 PDT)
- Re: AMBER: calculation of LJ 12-6 from .dat file (fwd)-CORRECTION!!! Martin Lepsik (Fri Oct 03 2003 - 02:56:07 PDT)
Re: AMBER: regarding trajectory input and output with ptraj or Carnal Bill Ross (Thu Oct 02 2003 - 09:28:41 PDT)
AMBER: SHAKE for TIP4P! Pradipta Bandyopadhyay (Thu Oct 02 2003 - 16:25:49 PDT)
- Re: AMBER: SHAKE for TIP4P! David Case (Fri Oct 03 2003 - 00:43:43 PDT)
AMBER: Compiling antechamber on amber 8 Mengjuei Hsieh (Fri Oct 03 2003 - 03:10:35 PDT)
- Re: AMBER: Compiling antechamber on amber 8 Junmei Wang (Fri Oct 03 2003 - 07:50:01 PDT)
  - Re: AMBER: Compiling antechamber on amber 8 Mengjuei Hsieh (Fri Oct 03 2003 - 17:42:32 PDT)
AMBER: H-bond analysis RAJA SWAMINATHAN (Fri Oct 03 2003 - 09:11:17 PDT)
- RE: AMBER: H-bond analysis myang (Fri Oct 03 2003 - 11:08:49 PDT)
AMBER: ibelly Amber Administration (Fri Oct 03 2003 - 11:55:02 PDT)
AMBER: surface code in Amber John Lee (Sun Oct 05 2003 - 14:13:43 PDT)
- Re: AMBER: surface code in Amber Alexey Onufriev (Fri Oct 10 2003 - 16:25:45 PDT)
  - Re[2]: AMBER: surface code in Amber John Lee (Sun Oct 26 2003 - 18:06:56 PST)
    - Re: AMBER: surface code in Amber David A. Case (Sun Oct 26 2003 - 22:45:18 PST)
    - Re[2]: AMBER: surface code in Amber John Lee (Mon Oct 27 2003 - 22:53:49 PST)
    - Re[2]: AMBER: surface code in Amber Dr. Yong Duan (Tue Oct 28 2003 - 06:46:32 PST)
    - Re: AMBER: surface code in Amber David E. Konerding (Tue Oct 28 2003 - 08:38:56 PST)
    - RE: AMBER: surface code in Amber Yong Duan (Tue Oct 28 2003 - 09:01:33 PST)
    - Re: AMBER: surface code in Amber David A. Case (Tue Oct 28 2003 - 16:15:33 PST)
    - Re: AMBER: surface code in Amber David E. Konerding (Mon Oct 27 2003 - 07:32:41 PST)
AMBER: output frequency GUILLERMINA L ESTIU (Mon Oct 06 2003 - 06:43:26 PDT)
- RE: AMBER: output frequency Yong Duan (Mon Oct 06 2003 - 07:08:21 PDT)
AMBER: mgbjsb Radii in GBSA Giulio Rastelli (Tue Oct 07 2003 - 07:42:34 PDT)
AMBER: Atomic charges and internal H-bond Martin Lepsik (Tue Oct 07 2003 - 04:41:19 PDT)
- Re: AMBER: Atomic charges and internal H-bond Jiri Sponer (Tue Oct 07 2003 - 07:12:27 PDT)
- Re: AMBER: Atomic charges and internal H-bond Martin Lepsik (Wed Oct 08 2003 - 01:44:21 PDT)
Re: AMBER: Atomic charges and internal H-bond Piotr Cieplak (Tue Oct 07 2003 - 10:41:49 PDT)
AMBER: Re:atomic charges and internal H-bond Pradipta Bandyopadhyay (Tue Oct 07 2003 - 11:24:18 PDT)
- Re: AMBER: Re:atomic charges and internal H-bond Jiri Sponer (Tue Oct 07 2003 - 13:48:00 PDT)
- Re: AMBER: Re:atomic charges and internal H-bond Piotr Cieplak (Tue Oct 07 2003 - 14:36:10 PDT)
  - Re: AMBER: Re:atomic charges and internal H-bond Jiri Sponer (Tue Oct 07 2003 - 15:08:09 PDT)
AMBER: Resp Problem Vikas Varshney (Tue Oct 07 2003 - 08:18:39 PDT)
AMBER: Addles Mark K. Dean (Wed Oct 08 2003 - 07:46:41 PDT)
- Re: AMBER: Addles xiaolin cheng (Wed Oct 08 2003 - 08:56:18 PDT)
AMBER: mopac lil.umbi.umd.edu (Wed Oct 08 2003 - 09:19:18 PDT)
- Re: AMBER: mopac Junmei Wang (Wed Oct 08 2003 - 10:15:18 PDT)
AMBER: Compiling AMBER franck (Thu Oct 09 2003 - 07:16:17 PDT)
- Re: AMBER: Compiling AMBER, ie, number of atoms limit Scott Brozell (Thu Oct 09 2003 - 14:30:02 PDT)
  - Re: AMBER: Compiling AMBER, ie, number of atoms limit Robert Duke (Thu Oct 09 2003 - 15:18:27 PDT)
AMBER: question about ewald Lishan Yao (Thu Oct 09 2003 - 09:03:44 PDT)
- Re: AMBER: question about ewald Scott Brozell (Thu Oct 09 2003 - 11:11:21 PDT)
- Re: AMBER: question about ewald darden (Thu Oct 09 2003 - 13:38:10 PDT)
AMBER: mm_pbsa example Jory Zmuda (Thu Oct 09 2003 - 13:35:21 PDT)
Re: AMBER: mm_pbsa example Rhonda Torres (Thu Oct 09 2003 - 14:09:33 PDT)
AMBER: Not getting restrt file on running sanders Vikas Varshney (Thu Oct 09 2003 - 14:40:15 PDT)
- RE: AMBER: Not getting restrt file on running sanders Asim Okur (Thu Oct 09 2003 - 14:53:37 PDT)
  - RE: AMBER: Not getting restrt file on running sanders Scott Brozell (Thu Oct 09 2003 - 16:25:11 PDT)
AMBER: Freezing the residues Vikas Varshney (Thu Oct 09 2003 - 20:37:11 PDT)
- Re: AMBER: Freezing the residues zhaoxc.puccini.che.pitt.edu (Fri Oct 10 2003 - 05:30:38 PDT)
  - Re: AMBER: Freezing the residues Scott Brozell (Fri Oct 10 2003 - 12:25:04 PDT)
- AMBER: is there a good program to quantitatively analyze hydration effect? zhaoxc.puccini.che.pitt.edu (Fri Oct 10 2003 - 05:36:08 PDT)
- Re: AMBER: Freezing the residues Bill Ross (Fri Oct 10 2003 - 12:43:38 PDT)
AMBER: monte carlo Vlad Cojocaru (Fri Oct 10 2003 - 06:40:11 PDT)
- Re: AMBER: monte carlo Andreas Svrcek-Seiler (Fri Oct 10 2003 - 07:19:41 PDT)
  - AMBER: force field for hybrid systems Ioana Cozmuta (Sun Oct 12 2003 - 10:58:41 PDT)
AMBER: input/output error Dalmaris, John (Fri Oct 10 2003 - 09:32:15 PDT)
- Re: AMBER: input/output error Scott Brozell (Fri Oct 10 2003 - 15:10:08 PDT)
AMBER: nmanal projection Qiang Lu (Fri Oct 10 2003 - 15:22:48 PDT)
- Re: AMBER: nmanal projection David A. Case (Tue Oct 14 2003 - 15:11:29 PDT)
AMBER: MeCNBOX & EWALD bomb northrop.chem.ucla.edu (Fri Oct 10 2003 - 17:31:46 PDT)
- Re: AMBER: MeCNBOX & EWALD bomb Jiten (Fri Oct 10 2003 - 20:29:04 PDT)
- AMBER: Re:mm_pbsa problem Itziar Maestre Asenjo (Mon Oct 13 2003 - 02:18:38 PDT)
- Re: AMBER: MeCNBOX & EWALD bomb David A. Case (Tue Oct 14 2003 - 15:12:42 PDT)
AMBER: Water as part of protein in mm_pbsa calculation Yong-Liang Zhu (Sat Oct 11 2003 - 20:20:12 PDT)
AMBER: problem with pdb files Mithun Mitra (Sun Oct 12 2003 - 13:12:45 PDT)
- Re: AMBER: problem with pdb files Vlad Cojocaru (Mon Oct 13 2003 - 01:35:04 PDT)
- Re: AMBER: problem with pdb files Bill Ross (Mon Oct 13 2003 - 10:12:41 PDT)
AMBER: sander: vlimit problem Vikas Varshney (Sun Oct 12 2003 - 19:19:41 PDT)
- Re: AMBER: sander: vlimit problem David A. Case (Tue Oct 14 2003 - 15:15:02 PDT)
- Re: AMBER: sander: vlimit problem Bill Ross (Tue Oct 14 2003 - 15:23:59 PDT)
AMBER: Reverse TI run Martin Lepsik (Mon Oct 13 2003 - 09:55:03 PDT)
- Re: AMBER: Reverse TI run Martin Lepsik (Tue Oct 14 2003 - 06:02:22 PDT)
  - Re: AMBER: Reverse TI run Michael Crowley (Wed Oct 15 2003 - 02:55:39 PDT)
AMBER: mm_pbsa crg file kbyun.wesleyan.edu (Mon Oct 13 2003 - 10:24:15 PDT)
- Re: AMBER: mm_pbsa crg file kbyun.wesleyan.edu (Tue Oct 14 2003 - 07:09:35 PDT)
AMBER: mm_pbsa rna/dna charges kbyun.wesleyan.edu (Mon Oct 13 2003 - 13:45:37 PDT)
AMBER: antechamber lil.umbi.umd.edu (Mon Oct 13 2003 - 16:30:25 PDT)
- Re: AMBER: antechamber Xin Hu (Thu Jul 15 2004 - 19:51:26 PDT)
  - Re: AMBER: antechamber David A. Case (Fri Jul 16 2004 - 09:16:14 PDT)
Re: AMBER: antechamber Bill Ross (Mon Oct 13 2003 - 17:38:24 PDT)
AMBER: Amber charge problem Yuhui Cheng (Mon Oct 13 2003 - 17:25:58 PDT)
Re: AMBER: Amber charge problem Bill Ross (Mon Oct 13 2003 - 18:21:00 PDT)
AMBER: running sander_classic on multiple processors Richard Smith (Tue Oct 14 2003 - 06:48:23 PDT)
- RE: AMBER: running sander_classic on multiple processors Richard Smith (Wed Oct 15 2003 - 12:09:57 PDT)
AMBER: mm_pbsa with amber7 Itziar Maestre Asenjo (Tue Oct 14 2003 - 09:22:18 PDT)
AMBER: infinitely long DNA & moil-view? Endres, Robert G. (Tue Oct 14 2003 - 11:57:43 PDT)
- Re: AMBER: infinitely long DNA & moil-view? Carlos Simmerling (Tue Oct 14 2003 - 12:18:30 PDT)
  - RE: AMBER: infinitely long DNA & moil-view? Yong Duan (Tue Oct 14 2003 - 13:15:29 PDT)
- Re: AMBER: infinitely long DNA & moil-view? bishop (Tue Oct 14 2003 - 12:24:52 PDT)
- RE: AMBER: infinitely long DNA & moil-view? Bill Ross (Tue Oct 14 2003 - 13:36:56 PDT)
AMBER: 'vlimit exceeded' Vikas Varshney (Tue Oct 14 2003 - 12:36:19 PDT)
AMBER: tru64 alpha Mu Yuguang (Dr) (Tue Oct 14 2003 - 18:19:06 PDT)
- RE: AMBER: tru64 alpha Mu Yuguang (Dr) (Wed Oct 15 2003 - 00:07:45 PDT)
  - Re: AMBER: tru64 alpha David A. Case (Wed Oct 15 2003 - 07:25:03 PDT)
- RE: AMBER: tru64 alpha Bill Ross (Wed Oct 15 2003 - 07:38:45 PDT)
- Re: AMBER: tru64 alpha Robert Duke (Wed Oct 15 2003 - 19:51:20 PDT)
- RE: AMBER: tru64 alpha Mu Yuguang (Dr) (Wed Oct 15 2003 - 19:59:29 PDT)
  - Re: AMBER: tru64 alpha Robert Duke (Wed Oct 15 2003 - 20:41:57 PDT)
- Re: AMBER: tru64 alpha Robert Duke (Thu Oct 16 2003 - 07:17:00 PDT)
- RE: AMBER: tru64 alpha Mu Yuguang (Dr) (Thu Oct 16 2003 - 17:40:56 PDT)
  - Re: AMBER: tru64 alpha Robert Duke (Thu Oct 16 2003 - 18:18:41 PDT)
  - Re: AMBER: tru64 alpha Robert Duke (Thu Oct 16 2003 - 18:27:27 PDT)
  - RE: AMBER: tru64 alpha Yong Duan (Thu Oct 16 2003 - 19:00:04 PDT)
- RE: AMBER: tru64 alpha Mu Yuguang (Dr) (Thu Oct 16 2003 - 18:52:41 PDT)
  - Re: AMBER: tru64 alpha Robert Duke (Thu Oct 16 2003 - 19:50:08 PDT)
- RE: AMBER: tru64 alpha Mu Yuguang (Dr) (Thu Oct 16 2003 - 19:08:14 PDT)
  - RE: AMBER: tru64 alpha Yong Duan (Fri Oct 17 2003 - 04:53:39 PDT)
AMBER: Restraints to maintain base pair planarity Mahadevan Seetharaman (Tue Oct 14 2003 - 20:10:29 PDT)
- Re: AMBER: Restraints to maintain base pair planarity David A. Case (Wed Oct 15 2003 - 07:18:10 PDT)
- Re: AMBER: Restraints to maintain base pair planarity Andreas Svrcek-Seiler (Wed Oct 15 2003 - 09:51:12 PDT)
AMBER: a problem with xleap Ye Mei (Wed Oct 15 2003 - 01:03:36 PDT)
- Re: AMBER: a problem with xleap David A. Case (Wed Oct 15 2003 - 07:31:06 PDT)
AMBER: STREAM problems : segmentation fault with CARNAL Jean-François Taly (Wed Oct 15 2003 - 03:03:35 PDT)
AMBER: charmm force field in amber Hyonseok Hwang (Thu Oct 16 2003 - 11:05:36 PDT)
- RE: AMBER: charmm force field in amber myang (Thu Oct 16 2003 - 13:57:47 PDT)
Re: AMBER: a problem with xleap Bill Ross (Thu Oct 16 2003 - 11:22:42 PDT)
AMBER: problem in tleap aini.UMDNJ.EDU (Fri Oct 17 2003 - 08:41:27 PDT)
- Re: AMBER: problem in tleap David A. Case (Fri Oct 17 2003 - 08:59:27 PDT)
  - Re: AMBER: problem in tleap aini.UMDNJ.EDU (Fri Oct 24 2003 - 12:23:33 PDT)
    - Re: AMBER: problem in tleap Scott Brozell (Fri Oct 24 2003 - 19:05:33 PDT)
    - Re: AMBER: problem in tleap David A. Case (Sat Oct 25 2003 - 20:56:29 PDT)
AMBER: Implicit precision in sander vs architecture Teletchéa Stéphane (Fri Oct 17 2003 - 08:42:41 PDT)
- Re: AMBER: Implicit precision in sander vs architecture David A. Case (Fri Oct 17 2003 - 09:05:15 PDT)
  - Re: AMBER: Implicit precision in sander vs architecture Teletchéa Stéphane (Fri Oct 17 2003 - 09:15:13 PDT)
- RE: AMBER: Implicit precision in sander vs architecture Yong Duan (Fri Oct 17 2003 - 09:30:31 PDT)
  - Re: AMBER: Implicit precision in sander vs architecture David E. Konerding (Fri Oct 17 2003 - 10:05:14 PDT)
    - Re: AMBER: Implicit precision in sander vs architecture Teletchéa Stéphane (Mon Oct 20 2003 - 01:45:04 PDT)
    - Re: AMBER: Implicit precision in sander vs architecture David A. Case (Mon Oct 20 2003 - 17:13:15 PDT)
- Re: AMBER: Implicit precision in sander vs architecture Bill Ross (Fri Oct 17 2003 - 11:10:46 PDT)
- Re: AMBER: Implicit precision in sander vs architecture Robert Duke (Mon Oct 20 2003 - 06:01:47 PDT)
  - AMBER: ECC vs non-ECC (non-amber issue) Yong Duan (Mon Oct 20 2003 - 19:04:37 PDT)
    - Re: AMBER: ECC vs non-ECC (non-amber issue) Robert Duke (Mon Oct 20 2003 - 19:40:24 PDT)
- Re: AMBER: Implicit precision in sander vs architecture Amber Administration (Mon Oct 20 2003 - 16:18:02 PDT)
  - Re: AMBER: Implicit precision in sander vs architecture Robert Duke (Mon Oct 20 2003 - 18:06:22 PDT)
  - Re: AMBER: Implicit precision in sander vs architecture Teletchéa Stéphane (Tue Oct 21 2003 - 01:42:54 PDT)
AMBER: a question Pingna Xu (Fri Oct 17 2003 - 14:01:12 PDT)
- AMBER: ibelly in AMBER 6 Qing Zhang (Fri Oct 17 2003 - 15:32:21 PDT)
  - Re: AMBER: ibelly in AMBER 6 David A. Case (Fri Oct 17 2003 - 17:51:29 PDT)
  - Re: AMBER: ibelly in AMBER 6 David A. Case (Sat Oct 18 2003 - 09:48:16 PDT)
    - AMBER: torsional restraints for groups of atoms Samy Name_removed_after_user_request (Sun Oct 19 2003 - 10:42:59 PDT)
    - Re: AMBER: torsional restraints for groups of atoms David A. Case (Wed Oct 22 2003 - 17:00:16 PDT)
    - Re: AMBER: torsional restraints for groups of atoms xiaolin cheng (Wed Oct 22 2003 - 17:30:33 PDT)
    - AMBER: absolute vs. relative binding free energy Qing Zhang (Wed Nov 05 2003 - 16:24:45 PST)
    - Re: AMBER: absolute vs. relative binding free energy David A. Case (Wed Nov 05 2003 - 17:45:54 PST)
- Re: AMBER: a question David A. Case (Fri Oct 17 2003 - 15:36:08 PDT)
AMBER: one more question Pingna Xu (Sat Oct 18 2003 - 11:01:32 PDT)
- RE: AMBER: one more question myang (Sat Oct 18 2003 - 11:51:33 PDT)
AMBER: carnal Frederico.Miranda.ibmb.uib.no (Sun Oct 19 2003 - 12:48:06 PDT)
- RE: AMBER: carnal Yong Duan (Sun Oct 19 2003 - 13:00:11 PDT)
AMBER: more questions about igb Pingna Xu (Sun Oct 19 2003 - 20:54:49 PDT)
- AMBER: stable protein Do Anh Tuan (Mon Oct 20 2003 - 10:30:45 PDT)
  - Re: AMBER: stable protein Carlos Simmerling (Mon Oct 20 2003 - 10:48:03 PDT)
- Re: AMBER: more questions about igb David A. Case (Mon Oct 20 2003 - 16:47:35 PDT)
  - AMBER: what is the unit for the energy calculated from MM_PBSA? zhaoxc.puccini.che.pitt.edu (Mon Oct 20 2003 - 18:08:51 PDT)
    - RE: AMBER: what is the unit for the energy calculated from MM_PBSA? Rhonda Torres (Mon Oct 20 2003 - 18:19:09 PDT)
AMBER: memory SC45 Mu Yuguang (Dr) (Mon Oct 20 2003 - 19:39:29 PDT)
- Re: AMBER: memory SC45 Robert Duke (Mon Oct 20 2003 - 20:17:25 PDT)
- RE: AMBER: memory SC45 Mu Yuguang (Dr) (Mon Oct 20 2003 - 20:46:50 PDT)
  - Re: AMBER: memory SC45 Robert Duke (Tue Oct 21 2003 - 05:55:22 PDT)
- RE: AMBER: memory SC45 Bill Ross (Mon Oct 20 2003 - 21:09:01 PDT)
- Re: AMBER: memory SC45 Robert Duke (Tue Oct 21 2003 - 06:20:59 PDT)
- RE: AMBER: memory SC45 Mu Yuguang (Dr) (Tue Oct 21 2003 - 18:19:45 PDT)
  - Re: AMBER: memory SC45 Robert Duke (Tue Oct 21 2003 - 19:12:31 PDT)
Re: AMBER: memory SC45 Bill Ross (Mon Oct 20 2003 - 20:19:37 PDT)
AMBER: how to mend the peptide with missing residues? Ye Mei (Tue Oct 21 2003 - 08:07:14 PDT)
- RE: AMBER: how to mend the peptide with missing residues? Yong Duan (Tue Oct 21 2003 - 08:15:53 PDT)
AMBER: frozen x unfrozen Herbert Georg (Tue Oct 21 2003 - 12:04:44 PDT)
- Re: AMBER: frozen x unfrozen David A. Case (Wed Oct 22 2003 - 16:58:41 PDT)
  - Re: AMBER: frozen x unfrozen Herbert Georg (Thu Oct 23 2003 - 07:25:20 PDT)
    - AMBER: frozen x unfrozen and the gibbs tragedy David Smith (Thu Oct 23 2003 - 08:56:00 PDT)
Re: AMBER: frozen x unfrozen Bill Ross (Tue Oct 21 2003 - 12:52:55 PDT)
AMBER: antechamber and bond type Herbert Georg (Wed Oct 22 2003 - 05:56:15 PDT)
- Re: AMBER: antechamber and bond type David A. Case (Sat Oct 25 2003 - 19:49:05 PDT)
AMBER: Simulation of small protein Endres, Robert G. (Thu Oct 23 2003 - 08:52:52 PDT)
- Re: AMBER: Simulation of small protein Carlos Simmerling (Thu Oct 23 2003 - 09:13:09 PDT)
- RE: AMBER: Simulation of small protein Endres, Robert G. (Thu Oct 23 2003 - 10:27:45 PDT)
  - AMBER: Simulation of small protein (MD Display tips) Chris Moth (Fri Oct 24 2003 - 11:56:38 PDT)
  - Re: AMBER: Simulation of small protein Carlos Simmerling (Thu Oct 23 2003 - 15:59:58 PDT)
    - RE: AMBER: Simulation of small protein Yong Duan (Thu Oct 23 2003 - 18:11:02 PDT)
- RE: AMBER: Simulation of small protein Endres, Robert G. (Thu Oct 23 2003 - 18:28:21 PDT)
  - RE: AMBER: Simulation of small protein Yong Duan (Thu Oct 23 2003 - 18:51:12 PDT)
AMBER: correlated motion Jory L. Zmuda (Thu Oct 23 2003 - 11:17:01 PDT)
AMBER: mddisplay Samy Name_removed_after_user_request (Thu Oct 23 2003 - 13:57:37 PDT)
- AMBER: mddisplay Chris Moth (Fri Oct 24 2003 - 14:22:18 PDT)
AMBER: SHAKE question Herbert Georg (Thu Oct 23 2003 - 15:17:45 PDT)
Re: AMBER: SHAKE question Bill Ross (Thu Oct 23 2003 - 15:24:20 PDT)
AMBER: carnal iteration deviation from original crd file Dalmaris, John (Fri Oct 24 2003 - 04:11:36 PDT)
- Re: AMBER: carnal iteration deviation from original crd file Vlad Cojocaru (Fri Oct 24 2003 - 04:32:17 PDT)
- RE: AMBER: carnal iteration deviation from original crd file Dalmaris, John (Fri Oct 24 2003 - 05:29:28 PDT)
  - Re: AMBER: carnal iteration deviation from original crd file Vlad Cojocaru (Fri Oct 24 2003 - 05:42:24 PDT)
    - Re: AMBER: carnal iteration deviation from original crd file aini.UMDNJ.EDU (Fri Oct 24 2003 - 06:11:30 PDT)
- RE: AMBER: carnal iteration deviation from original crd file Bill Ross (Fri Oct 24 2003 - 08:35:53 PDT)
AMBER: prmtop file format Herbert Georg (Fri Oct 24 2003 - 07:37:42 PDT)
- RE: AMBER: prmtop file format Yong Duan (Fri Oct 24 2003 - 08:05:35 PDT)
  - Re: AMBER: prmtop file format Herbert Georg (Fri Oct 24 2003 - 11:51:50 PDT)
    - RE: AMBER: prmtop file format Yong Duan (Fri Oct 24 2003 - 12:19:16 PDT)
Re: AMBER: carnal iteration deviation from original crd file Bill Ross (Fri Oct 24 2003 - 08:31:17 PDT)
- RE: AMBER: carnal iteration deviation from original crd file John (Mon Oct 27 2003 - 17:05:28 PST)
AMBER: Pressure in NVT ensemble Shiang-Tai Lin (Fri Oct 24 2003 - 10:44:21 PDT)
- Re: AMBER: Pressure in NVT ensemble David A. Case (Sat Oct 25 2003 - 20:16:37 PDT)
  - Re: AMBER: Pressure in NVT ensemble Shiang-Tai Lin (Mon Oct 27 2003 - 09:48:48 PST)
AMBER: RMSD and Radius of Gyration Endres, Robert G. (Sat Oct 25 2003 - 15:24:07 PDT)
- Re: AMBER: RMSD and Radius of Gyration Carlos Simmerling (Sat Oct 25 2003 - 16:28:28 PDT)
  - RE: AMBER: RMSD and Radius of Gyration Yong Duan (Sat Oct 25 2003 - 18:40:07 PDT)
  - AMBER: MD simulation: enzyme and its substrate Do Anh Tuan (Sat Oct 25 2003 - 21:51:20 PDT)
AMBER: comparing versions 6.0 and 7.0 of AMBER Therese Malliavin (Mon Oct 27 2003 - 01:30:21 PST)
AMBER: amber 7 for industrial application Jose Gallego (Mon Oct 27 2003 - 05:18:16 PST)
- Re: AMBER: amber 7 for industrial application David A. Case (Mon Oct 27 2003 - 22:21:35 PST)
- RE: AMBER: amber 7 for industrial application Jose Gallego (Tue Oct 28 2003 - 06:45:19 PST)
  - RE: AMBER: amber 7 for industrial application Junmei Wang (Tue Oct 28 2003 - 07:58:43 PST)
- RE: AMBER: amber 7 for industrial application Bayly, Christopher (Wed Oct 29 2003 - 08:45:27 PST)
AMBER: solute images Sandro Fornili (Mon Oct 27 2003 - 07:28:34 PST)
- Re: AMBER: solute images Scott Brozell (Mon Oct 27 2003 - 12:39:21 PST)
AMBER: Implicit MD simulations in Amber7 Joey Harriman (Mon Oct 27 2003 - 10:53:01 PST)
- Re: AMBER: Implicit MD simulations in Amber7 Scott Brozell (Mon Oct 27 2003 - 12:20:14 PST)
AMBER: Removal of Rotational and Translational Motion in AMBER6 Richard Smith (Mon Oct 27 2003 - 12:51:59 PST)
AMBER: aminoacid mutation Ioana Cozmuta (Mon Oct 27 2003 - 16:46:13 PST)
- RE: AMBER: aminoacid mutation Yong Duan (Mon Oct 27 2003 - 18:09:02 PST)
  - RE: AMBER: aminoacid mutation Ioana Cozmuta (Tue Oct 28 2003 - 12:25:53 PST)
- AMBER: aminoacid mutation Wayne Dawson (Mon Oct 27 2003 - 21:47:25 PST)
  - RE: AMBER: aminoacid mutation Endres, Robert G. (Mon Oct 27 2003 - 19:02:15 PST)
  - RE: AMBER: aminoacid mutation Bill Ross (Mon Oct 27 2003 - 21:09:23 PST)
  - RE: AMBER: aminoacid mutation Sivakolundu, Sivashankar (Tue Oct 28 2003 - 07:43:38 PST)
  - Re: AMBER: aminoacid mutation Amber Administration (Tue Oct 28 2003 - 14:34:47 PST)
- Re: AMBER: aminoacid mutation Osmar Norberto de Souza (Tue Oct 28 2003 - 12:38:00 PST)
AMBER: SC45 Mu Yuguang (Dr) (Mon Oct 27 2003 - 17:12:29 PST)
AMBER: Radius of Gyration and RMSD Jagannadh B (Tue Oct 28 2003 - 01:36:55 PST)
- RE: AMBER: Radius of Gyration and RMSD Endres, Robert G. (Tue Oct 28 2003 - 06:36:27 PST)
- RE: AMBER: Radius of Gyration and RMSD Bill Ross (Tue Oct 28 2003 - 09:21:10 PST)
AMBER: how to measure the minor groove widths of a DNA? zhaoxc.puccini.che.pitt.edu (Tue Oct 28 2003 - 09:16:06 PST)
- Re: AMBER: how to measure the minor groove widths of a DNA? Peter Gannett (Tue Oct 28 2003 - 11:43:22 PST)
- Re: AMBER: how to measure the minor groove widths of a DNA? Thomas E. Cheatham, III (Wed Oct 29 2003 - 09:31:09 PST)
  - AMBER: atomtypenumber Rajendra P. OJHA (Tue Nov 04 2003 - 13:07:20 PST)
AMBER: ibelly problem Vikas Varshney (Tue Oct 28 2003 - 11:34:00 PST)
- Re: AMBER: ibelly problem Thomas E. Cheatham, III (Wed Oct 29 2003 - 09:23:12 PST)
AMBER: Installation Problem, xleap can't load pdb files Jonathan Neidigh (Tue Oct 28 2003 - 15:19:59 PST)
- Re: AMBER: Installation Problem, xleap can't load pdb files Jonathan Neidigh (Wed Oct 29 2003 - 07:54:18 PST)
AMBER: mddisplay Samy Name_removed_after_user_request (Tue Oct 28 2003 - 16:21:04 PST)
- AMBER: mddisplay Chris Moth (Thu Oct 30 2003 - 10:29:12 PST)
  - RE: AMBER: mddisplay Kristina Furse (Tue Oct 28 2003 - 16:48:30 PST)
AMBER: reduce box and delete excess solvent Endres, Robert G. (Wed Oct 29 2003 - 11:31:52 PST)
AMBER: MD simulation: enzyme and its substrate Do Anh Tuan (Wed Oct 29 2003 - 11:52:24 PST)
Re: AMBER: MD simulation: enzyme and its substrate!! Pradipta Bandyopadhyay (Wed Oct 29 2003 - 12:26:17 PST)
AMBER: JAC on NCSA titan (Itanium 2 833MHZ) Qiang Lu (Wed Oct 29 2003 - 14:09:56 PST)
AMBER: wangf2 (Thu Oct 30 2003 - 08:00:15 PST)
- Re: AMBER: David A. Case (Thu Oct 30 2003 - 09:23:12 PST)
AMBER: minimize a covalently bounded protein-ligand complex Eric Hu (Thu Oct 30 2003 - 15:36:53 PST)
- Re: AMBER: minimize a covalently bounded protein-ligand complex David A. Case (Thu Oct 30 2003 - 15:50:11 PST)
AMBER: PMEMD 3.1 Release - High Scalability Update to PMEMD Robert Duke (Fri Oct 31 2003 - 07:40:37 PST)
- Re: AMBER: PMEMD 3.1 Release - High Scalability Update to PMEMD David E. Konerding (Mon Nov 03 2003 - 10:41:08 PST)
- Re: AMBER: PMEMD 3.1 Release - High Scalability Update to PMEMD Robert Duke (Mon Nov 03 2003 - 11:31:34 PST)
AMBER: What does this error message mean? nie beining (Fri Oct 31 2003 - 07:34:40 PST)
- Re: AMBER: What does this error message mean? Ioana Cozmuta (Fri Oct 31 2003 - 07:46:46 PST)
- Re: AMBER: What does this error message mean? Jose Ramon Blas (Fri Oct 31 2003 - 16:29:19 PST)
AMBER: Freezing of water with TIP3P potential. Mahesh Chandran (Mon Nov 03 2003 - 03:41:21 PST)
AMBER: question about input files for small molecule with fluorine aini.rwja.umdnj.edu (Mon Nov 03 2003 - 07:45:10 PST)
- Re: AMBER: question about input files for small molecule with fluorine Carlos Simmerling (Mon Nov 03 2003 - 07:53:49 PST)
AMBER: large file for carnal volodya (Sat Oct 04 2003 - 10:12:37 PDT)
- Re: AMBER: large file for carnal volodya (Sun Oct 05 2003 - 04:23:44 PDT)
- Re: AMBER: large file for carnal Bill Ross (Tue Nov 04 2003 - 09:03:44 PST)
- Re: AMBER: large file for carnal Bill Ross (Tue Nov 04 2003 - 12:19:19 PST)
  - Re: AMBER: large file for carnal volodya (Tue Oct 07 2003 - 05:52:04 PDT)
AMBER: distrance restraints for alpha carbons Sheldon Holder (Mon Nov 03 2003 - 11:27:48 PST)
- Re: AMBER: distrance restraints for alpha carbons Sheldon Holder (Mon Nov 03 2003 - 11:56:49 PST)
- Re: AMBER: distrance restraints for alpha carbons David A. Case (Mon Nov 03 2003 - 15:06:57 PST)
AMBER: Restart a simulation Frederico.Miranda.ibmb.uib.no (Tue Nov 04 2003 - 11:21:03 PST)
AMBER: MD Equil Chenglong Li (Mon Nov 03 2003 - 15:07:56 PST)
- Re: AMBER: MD Equil David A. Case (Mon Nov 03 2003 - 16:55:59 PST)
AMBER: make clean doesn't clean leap Karen Haskell (Mon Nov 03 2003 - 14:47:22 PST)
- RE: AMBER: make clean doesn't clean leap Ming Lei (Tue Nov 04 2003 - 08:01:26 PST)
- Re: AMBER: make clean doesn't clean leap David A. Case (Mon Nov 03 2003 - 14:58:38 PST)
  - Re: AMBER: make clean doesn't clean leap Karen Haskell (Mon Nov 03 2003 - 15:19:23 PST)
AMBER: RESP fitting limit? yuann (Tue Nov 04 2003 - 20:46:10 PST)
AMBER: How to estimate SD of the delta delta G between two mm_pbsa runs Zheng Suxin (Wed Nov 05 2003 - 05:41:34 PST)
- Re: AMBER: How to estimate SD of the delta delta G between two mm_pbsa runs Holger Gohlke (Wed Nov 05 2003 - 23:24:42 PST)
AMBER: shake constraint on all bonds Jian Zhang, Dr (Wed Nov 05 2003 - 19:34:24 PST)
- RE: AMBER: shake constraint on all bonds Yong Duan (Wed Nov 05 2003 - 20:08:44 PST)
AMBER: RMSd per residue volodya (Tue Oct 07 2003 - 05:58:20 PDT)
AMBER: parmchk on MAC Kaushik Raha (Thu Nov 06 2003 - 08:19:52 PST)
AMBER: handling non neutral systems hagop demirdjian (Thu Nov 06 2003 - 07:31:19 PST)
AMBER: Restraints Steve Seibold (Thu Nov 06 2003 - 12:28:09 PST)
- Re: AMBER: Restraints David A. Case (Thu Nov 06 2003 - 15:26:47 PST)
AMBER: Can use mm_pbsa_statistics.pl to calculate each snapshot's Delta Delta G, then give the SD Zheng Suxin (Thu Nov 06 2003 - 19:41:12 PST)
- Re: AMBER: Can use mm_pbsa_statistics.pl to calculate each snapshot's Delta Delta G, then give the SD Holger Gohlke (Fri Nov 07 2003 - 00:23:29 PST)
AMBER: fix some area Helios Chen (Fri Nov 07 2003 - 01:06:06 PST)
- Re: AMBER: fix some area Carlos Simmerling (Fri Nov 07 2003 - 04:27:38 PST)
- Re: AMBER: fix some area Helios Chen (Sun Nov 09 2003 - 17:21:42 PST)
- Re: AMBER: fix some area Carlos Simmerling (Sun Nov 09 2003 - 17:50:17 PST)
AMBER: restrain Vlad Cojocaru (Fri Nov 07 2003 - 07:53:52 PST)
- Re: AMBER: restrain David A. Case (Fri Nov 07 2003 - 08:34:21 PST)
RE: AMBER: infinitely long DNA (to Yong Duan) Endres, Robert G. (Fri Nov 07 2003 - 12:50:17 PST)
- Re: AMBER: infinitely long DNA (to Yong Duan) bishop (Fri Nov 07 2003 - 13:59:46 PST)
- RE: AMBER: infinitely long DNA (to Yong Duan) Yong Duan (Fri Nov 07 2003 - 14:24:41 PST)
AMBER: mpich problem Qiang Lu (Sat Nov 08 2003 - 00:25:08 PST)
- Re[3]: AMBER: mpich problem Qiang Lu (Sun Nov 09 2003 - 16:28:37 PST)
AMBER: mpich problem Qiang Lu (Sat Nov 08 2003 - 00:23:50 PST)
- Re: AMBER: mpich problem David E. Konerding (Sat Nov 08 2003 - 09:15:34 PST)
  - Re[2]: AMBER: mpich problem Qiang Lu (Sun Nov 09 2003 - 14:27:47 PST)
  - RE: AMBER: mpich problem Yong Duan (Sun Nov 09 2003 - 16:13:13 PST)
    - Re[2]: AMBER: mpich problem Qiang Lu (Sun Nov 09 2003 - 18:24:20 PST)
- Re: AMBER: mpich problem Viktor Hornak (Sun Nov 09 2003 - 16:06:53 PST)
  - Re[2]: AMBER: mpich problem Qiang Lu (Sun Nov 09 2003 - 18:27:09 PST)
  - Re[2]: AMBER: mpich problem Qiang Lu (Mon Nov 10 2003 - 16:07:06 PST)
AMBER: a problem with antechamber and leap Ye Mei (Sun Nov 09 2003 - 21:02:04 PST)
- Re: AMBER: a problem with antechamber and leap David A. Case (Sun Nov 09 2003 - 23:24:41 PST)
  - Re: Re: AMBER: a problem with antechamber and leap Ye Mei (Mon Nov 10 2003 - 01:15:06 PST)
    - Re: Re: AMBER: a problem with antechamber and leap Junmei Wang (Tue Nov 11 2003 - 14:33:02 PST)
    - Re: Re: AMBER: a problem with antechamber and leap David A. Case (Tue Nov 11 2003 - 17:01:39 PST)
    - Re: Re: AMBER: a problem with antechamber and leap Junmei Wang (Wed Nov 12 2003 - 12:46:02 PST)
    - Re: Re: Re: AMBER: a problem with antechamber and leap Ye Mei (Wed Nov 12 2003 - 00:48:06 PST)
    - Re: Re: Re: AMBER: a problem with antechamber and leap Junmei Wang (Wed Nov 12 2003 - 12:51:05 PST)
    - Re: Re: Re: Re: AMBER: a problem with antechamber and leap Ye Mei (Wed Nov 12 2003 - 22:52:38 PST)
    - Re: Re: AMBER: a problem with antechamber and leap Junmei Wang (Tue Nov 11 2003 - 14:38:32 PST)
AMBER: mgbjsb radii in GBSA Giulio Rastelli (Mon Nov 10 2003 - 08:39:18 PST)
- Re: AMBER: mgbjsb radii in GBSA David A. Case (Mon Nov 10 2003 - 08:10:17 PST)
  - Re: AMBER: mgbjsb radii in GBSA Giulio Rastelli (Mon Nov 10 2003 - 15:02:00 PST)
- Re: AMBER: mgbjsb radii in GBSA Junmei Wang (Tue Nov 11 2003 - 14:12:08 PST)
  - Re: AMBER: mgbjsb radii in GBSA Giulio Rastelli (Sat Nov 15 2003 - 09:05:49 PST)
    - Re: AMBER: mgbjsb radii in GBSA David A. Case (Sat Nov 15 2003 - 09:58:35 PST)
AMBER: AM1-BCC in Amber7 Joey Harriman (Mon Nov 10 2003 - 04:56:23 PST)
- Re: AMBER: AM1-BCC in Amber7 Ye Mei (Mon Nov 10 2003 - 05:37:05 PST)
  - Re: AMBER: AM1-BCC in Amber7 Joey Harriman (Mon Nov 10 2003 - 06:15:25 PST)
    - Re: AMBER: AM1-BCC in Amber7 Junmei Wang (Tue Nov 11 2003 - 13:49:31 PST)
- Re: AMBER: AM1-BCC in Amber7 David A. Case (Mon Nov 10 2003 - 08:12:07 PST)
AMBER: change force constants Obdulia Rabal (Mon Nov 10 2003 - 09:27:23 PST)
- Re: AMBER: change force constants David A. Case (Mon Nov 10 2003 - 15:56:59 PST)
AMBER: Re: AM1-BCC in Amber7 Rhonda Torres (Mon Nov 10 2003 - 10:22:19 PST)
AMBER: restraints and reordering water Vlad Cojocaru (Tue Nov 11 2003 - 01:42:04 PST)
- Re: AMBER: restraints and reordering water David A. Case (Tue Nov 11 2003 - 09:21:10 PST)
AMBER: Protein Rotation Frederico.Miranda.ibmb.uib.no (Tue Nov 11 2003 - 04:47:44 PST)
- Re: AMBER: Protein Rotation Carlos Simmerling (Tue Nov 11 2003 - 05:02:32 PST)
  - Re: AMBER: Protein Rotation Frederico.Miranda.ibmb.uib.no (Tue Nov 11 2003 - 06:52:44 PST)
- Re: AMBER: Protein Rotation volodya (Sun Oct 12 2003 - 06:40:07 PDT)
- Re: AMBER: Protein Rotation Carlos Simmerling (Tue Nov 11 2003 - 07:11:40 PST)
Re: AMBER: Protein Rotation Bill Ross (Tue Nov 11 2003 - 08:06:33 PST)
- Re: AMBER: Protein Rotation Bill Ross (Tue Nov 11 2003 - 08:35:08 PST)
Re: AMBER: RMSd per residue Bill Ross (Tue Nov 11 2003 - 08:20:20 PST)
AMBER: GB/SA Yichen Cao (Tue Nov 11 2003 - 11:02:41 PST)
- Re: AMBER: GB/SA Chris Moth (Wed Nov 12 2003 - 12:30:33 PST)
  - Re: AMBER: GB/SA Holger Gohlke (Tue Nov 11 2003 - 12:47:59 PST)
AMBER: Separation of a Water molecules nabe (Tue Nov 11 2003 - 16:59:22 PST)
- Re: AMBER: Separation of a Water molecules Carlos Simmerling (Tue Nov 11 2003 - 18:15:53 PST)
- Re: AMBER: Separation of a Water molecules Thomas E. Cheatham, III (Tue Nov 11 2003 - 20:13:41 PST)
  - Re: AMBER: Separation of a Water molecules nabe (Wed Nov 12 2003 - 00:43:59 PST)
- Re: AMBER: Separation of a Water molecules Carlos Simmerling (Wed Nov 12 2003 - 04:47:20 PST)
- Re: AMBER: Separation of a Water molecules nabe (Wed Nov 12 2003 - 18:32:45 PST)
  - Re: AMBER: Separation of a Water molecules Thomas E. Cheatham, III (Wed Nov 12 2003 - 20:16:38 PST)
  - Re: AMBER: Separation of a Water molecules Dr. Yong Duan (Wed Nov 12 2003 - 21:43:26 PST)
- Re: AMBER: Separation of a Water molecules Carlos Simmerling (Thu Nov 13 2003 - 05:48:28 PST)
Re: AMBER: Correction [Separation of a Water molecules] nabe (Wed Nov 12 2003 - 00:53:49 PST)
AMBER: antechamber mopac7 parameters Joey Harriman (Wed Nov 12 2003 - 07:06:41 PST)
AMBER: average coordinates Frederico.Miranda.ibmb.uib.no (Wed Nov 12 2003 - 09:47:33 PST)
Re: AMBER: average coordinates Bill Ross (Wed Nov 12 2003 - 10:12:20 PST)
- Re: AMBER: average coordinates Bill Ross (Wed Nov 12 2003 - 10:24:18 PST)
AMBER: about some of the cards in Sander 7 Pingna Xu (Wed Nov 12 2003 - 12:09:12 PST)
- Re: AMBER: about some of the cards in Sander 7 Vlad Cojocaru (Wed Nov 12 2003 - 12:38:39 PST)
Re: AMBER: about some of the cards in Sander 7 Rhonda Torres (Wed Nov 12 2003 - 12:35:43 PST)
- AMBER: ndfmin in belly runs John (Thu Nov 13 2003 - 02:50:52 PST)
  - Re: AMBER: ndfmin in belly runs David A. Case (Thu Nov 13 2003 - 08:07:14 PST)
AMBER: atmtypenumbers for halogens Thomas.Fox.bc.boehringer-ingelheim.com (Thu Nov 13 2003 - 00:53:38 PST)
- Re: AMBER: atmtypenumbers for halogens Giulio Rastelli (Fri Nov 14 2003 - 07:00:41 PST)
AMBER: RNA and Protein questions (also some general questions) a b (Thu Nov 13 2003 - 02:55:07 PST)
- Re: AMBER: RNA and Protein questions (also some general questions) Balvinder Singh (Thu Nov 13 2003 - 09:21:49 PST)
- Re: AMBER: RNA and Protein questions (also some general questions) Dr. Yong Duan (Thu Nov 13 2003 - 07:57:41 PST)
  - AMBER: high temperature, 498K, unfolding simulations james tomomi macdonald (Thu Nov 13 2003 - 08:19:05 PST)
    - Re: AMBER: high temperature, 498K, unfolding simulations Andreas Svrcek-Seiler (Thu Nov 13 2003 - 09:05:46 PST)
- Re: AMBER: RNA and Protein questions (also some general questions) FyD (Thu Nov 13 2003 - 08:45:33 PST)
AMBER: GIBBS - PMF problem: Lambda has not changed Jiri Matousek (Thu Nov 13 2003 - 04:32:01 PST)
- Re: AMBER: GIBBS - PMF problem: Lambda has not changed David Smith (Thu Nov 13 2003 - 06:00:48 PST)
  - Re: AMBER: GIBBS - PMF problem: Lambda has not changed Jiri Matousek (Thu Nov 13 2003 - 09:09:49 PST)
- Re: AMBER: GIBBS - PMF problem: Lambda has not changed David Smith (Fri Nov 14 2003 - 02:50:01 PST)
AMBER: Nmode Problem Yuqin Cai (Thu Nov 13 2003 - 08:26:25 PST)
- Re: AMBER: Nmode Problem Holger Gohlke (Thu Nov 13 2003 - 11:13:45 PST)
Re: AMBER: RNA and Protein questions (also some general questions) Piotr Cieplak (Thu Nov 13 2003 - 09:37:14 PST)
AMBER: water prep file needed Youyi Peng (Thu Nov 13 2003 - 13:37:36 PST)
- Re: AMBER: water prep file needed David A. Case (Thu Nov 13 2003 - 13:36:38 PST)
AMBER: Any correct way to image a molecule ? Teletchéa Stéphane (Thu Nov 13 2003 - 13:37:40 PST)
- Re: AMBER: Any correct way to image a molecule ? Thomas E. Cheatham, III (Thu Nov 13 2003 - 13:58:38 PST)
  - Re: AMBER: Any correct way to image a molecule ? Teletchéa Stéphane (Thu Nov 13 2003 - 14:46:48 PST)
- Re: AMBER: Any correct way to image a molecule ? Carlos Simmerling (Thu Nov 13 2003 - 16:35:19 PST)
  - Re: AMBER: Any correct way to image a molecule ? Teletchéa Stéphane (Fri Nov 14 2003 - 01:55:36 PST)
- Re: AMBER: Any correct way to image a molecule ? Carlos Simmerling (Fri Nov 14 2003 - 02:27:18 PST)
AMBER: Problems restarting with sander raist.mmb.pcb.ub.es (Fri Nov 14 2003 - 13:26:07 PST)
- Re: AMBER: Problems restarting with sander David A. Case (Fri Nov 14 2003 - 08:31:12 PST)
  - Re: AMBER: Problems restarting with sander raist.mmb.pcb.ub.es (Fri Nov 14 2003 - 17:14:42 PST)
AMBER: rotation removal in sander GB Mu Yuguang (Dr) (Fri Nov 14 2003 - 07:40:56 PST)
- Re: AMBER: rotation removal in sander GB David A. Case (Fri Nov 14 2003 - 08:34:06 PST)
AMBER: update of BOX dim. Endres, Robert G. (Fri Nov 14 2003 - 11:53:21 PST)
- RE: AMBER: update of BOX dim. Endres, Robert G. (Fri Nov 14 2003 - 12:23:14 PST)
AMBER: sander lastist Frederico.Miranda.ibmb.uib.no (Sat Nov 15 2003 - 02:01:57 PST)
- Re: AMBER: sander lastist David A. Case (Sat Nov 15 2003 - 09:40:13 PST)
AMBER: Diffusion constant franck (Sat Nov 15 2003 - 11:00:56 PST)
- Re: AMBER: Diffusion constant David A. Case (Sat Nov 15 2003 - 12:45:56 PST)
AMBER: a problem with memory size Ye Mei (Sun Nov 16 2003 - 07:45:39 PST)
- Re: AMBER: a problem with memory size David A. Case (Sun Nov 16 2003 - 14:49:30 PST)
AMBER: MM_pbsa Rajendra P. OJHA (Sun Nov 16 2003 - 09:35:23 PST)
AMBER: dual processor Rajendra P. OJHA (Sun Nov 16 2003 - 09:45:40 PST)
AMBER: Pressure during MD João Barroso (Sun Nov 16 2003 - 10:12:18 PST)
- Re: AMBER: Pressure during MD David A. Case (Sun Nov 16 2003 - 14:52:36 PST)
  - Re: AMBER: Pressure during MD João Barroso (Mon Nov 17 2003 - 01:36:41 PST)
    - Re: AMBER: Pressure during MD David A. Case (Mon Nov 17 2003 - 19:03:47 PST)
AMBER: Restarting MD amber7 raist.mmb.pcb.ub.es (Mon Nov 17 2003 - 10:54:32 PST)
- Re: AMBER: Restarting MD amber7 Carlos Simmerling (Sun Nov 16 2003 - 06:39:03 PST)
AMBER: RESP charge Youyi Peng (Mon Nov 17 2003 - 06:46:32 PST)
- Re: AMBER: RESP charge FyD (Mon Nov 17 2003 - 14:27:25 PST)
AMBER: ptraj and charmm files Endres, Robert G. (Mon Nov 17 2003 - 07:25:04 PST)
- Re: AMBER: ptraj and charmm files Thomas E. Cheatham, III (Mon Nov 17 2003 - 07:50:22 PST)
AMBER: Lone pairs and resp Perdita Barran (Mon Nov 17 2003 - 08:49:35 PST)
AMBER: Lone pairs and resp Perdita Barran (Mon Nov 17 2003 - 08:55:05 PST)
- Re: AMBER: Lone pairs and resp FyD (Mon Nov 17 2003 - 18:06:57 PST)
AMBER: antechamber test failure Meg McCarrick (Mon Nov 17 2003 - 12:39:58 PST)
- Re: AMBER: antechamber test failure David A. Case (Mon Nov 17 2003 - 19:03:56 PST)
AMBER: amber on mac cluster yu275197.yorku.ca (Mon Nov 17 2003 - 17:58:34 PST)
AMBER: Compiling AMBER7 on Suse Herbert Georg (Tue Nov 18 2003 - 05:08:06 PST)
- Re: AMBER: Compiling AMBER7 on Suse Andreas Svrcek-Seiler (Tue Nov 18 2003 - 05:41:47 PST)
AMBER: Zinc parameters Annette Höglund (Tue Nov 18 2003 - 05:19:28 PST)
- RE: AMBER: Zinc parameters Ross Walker (Tue Nov 18 2003 - 13:26:49 PST)
AMBER: Problem with MPI_Finalize Thomas.Fox.bc.boehringer-ingelheim.com (Tue Nov 18 2003 - 06:10:02 PST)
- Re: AMBER: Problem with MPI_Finalize Robert Duke (Tue Nov 18 2003 - 06:54:36 PST)
AW: AMBER: Problem with MPI_Finalize Thomas.Fox.bc.boehringer-ingelheim.com (Tue Nov 18 2003 - 07:34:36 PST)
Re: AMBER: Problem with MPI_Finalize Bill Ross (Tue Nov 18 2003 - 10:06:13 PST)
Re: AMBER: Compiling AMBER7 on Suse Bill Ross (Tue Nov 18 2003 - 10:27:25 PST)
AMBER: molsuf failure with too many intersecting cusps Lee, Matthew (Tue Nov 18 2003 - 12:24:29 PST)
AMBER: Cutress %cmass error Jory Zmuda (Wed Nov 19 2003 - 07:17:08 PST)
AMBER: MM_PB/GB/SA Chenglong Li (Wed Nov 19 2003 - 10:44:19 PST)
- Re: AMBER: MM_PB/GB/SA Holger Gohlke (Thu Nov 20 2003 - 04:36:30 PST)
Re: AMBER: Cutress %cmass error Bill Ross (Wed Nov 19 2003 - 11:51:04 PST)
[Fwd: AMBER: MM_PB/GB/SA] Chenglong Li (Thu Nov 20 2003 - 10:07:19 PST)
AMBER: missing of VdW Parameters for N3 Nikolai Smolin (Fri Nov 21 2003 - 01:45:09 PST)
- Re: AMBER: missing of VdW Parameters for N3 David A. Case (Fri Nov 21 2003 - 08:08:07 PST)
- Re: AMBER: missing of VdW Parameters for N3 Piotr Cieplak (Fri Nov 21 2003 - 10:56:53 PST)
- Re: AMBER: missing of VdW Parameters for N3 wendy.cornell.pharma.novartis.com (Wed Dec 03 2003 - 07:18:23 PST)
AMBER: Why I get the same TSTRA for different strucutures from Nmode calculation? Yuqin Cai (Fri Nov 21 2003 - 12:54:54 PST)
- Re: AMBER: Why I get the same TSTRA for different strucutures from Nmode calculation? David A. Case (Fri Nov 21 2003 - 15:33:38 PST)
AMBER: Compaq Tru64 Unix Herbert de Castro Georg (Fri Nov 21 2003 - 13:37:07 PST)
- Re: AMBER: Compaq Tru64 Unix David A. Case (Fri Nov 21 2003 - 15:34:43 PST)
AMBER: mm_pbsa and antechamber Rajendra P. OJHA (Sat Nov 22 2003 - 11:03:34 PST)
- Re: AMBER: mm_pbsa and antechamber Holger Gohlke (Mon Nov 24 2003 - 11:37:02 PST)
AMBER: structure refinement using CNS vs. AMBER a b (Sat Nov 22 2003 - 13:27:06 PST)
AMBER: Fluorine in GBSA aini.UMDNJ.EDU (Mon Nov 24 2003 - 06:38:38 PST)
- Re: AMBER: Fluorine in GBSA Alexey Onufriev (Tue Nov 25 2003 - 13:33:43 PST)
AMBER: protein MD - problem RAJA SWAMINATHAN (Mon Nov 24 2003 - 06:47:53 PST)
- Re: AMBER: protein MD - problem Carlos Simmerling (Mon Nov 24 2003 - 06:52:53 PST)
- Re: AMBER: protein MD - problem David A. Case (Mon Nov 24 2003 - 08:27:08 PST)
AMBER: water mediated contacts Vlad Cojocaru (Mon Nov 24 2003 - 08:42:12 PST)
AMBER: Re: AMBER water mediated contacts Rhonda Torres (Mon Nov 24 2003 - 09:51:31 PST)
AMBER: torsion problems of dummy atoms Difei Wang (Mon Nov 24 2003 - 12:24:11 PST)
Re: AMBER: torsion problems of dummy atoms Bill Ross (Mon Nov 24 2003 - 15:58:21 PST)
AMBER: saveamberparm Atchara Wijitkosoom (Mon Nov 24 2003 - 17:20:36 PST)
- Re: AMBER: saveamberparm David A. Case (Mon Nov 24 2003 - 17:32:22 PST)
Re: AMBER: saveamberparm Bill Ross (Mon Nov 24 2003 - 17:31:51 PST)
AMBER: charge fitting Itziar Maestre Asenjo (Tue Nov 25 2003 - 00:28:05 PST)
- Re: AMBER: charge fitting FyD (Tue Nov 25 2003 - 08:42:56 PST)
AMBER: 1 fs timestep for GB? Peter VARNAI (Tue Nov 25 2003 - 09:48:35 PST)
- Re: AMBER: 1 fs timestep for GB? Andreas Svrcek-Seiler (Tue Nov 25 2003 - 10:32:15 PST)
  - Re: AMBER: 1 fs timestep for GB? Alexey Onufriev (Tue Nov 25 2003 - 13:19:04 PST)
Re: AMBER: charge fitting Piotr Cieplak (Tue Nov 25 2003 - 09:59:59 PST)
- Re: AMBER: charge fitting Itziar Maestre Asenjo (Thu Nov 27 2003 - 01:00:58 PST)
  - Re: AMBER: charge fitting FyD (Fri Nov 28 2003 - 10:45:21 PST)
AMBER: image question Li Ying (Tue Nov 25 2003 - 10:13:21 PST)
- RE: AMBER: image question Rhonda Torres (Tue Nov 25 2003 - 10:50:36 PST)
AMBER: intermolecular force Dave S Walker (Tue Nov 25 2003 - 15:19:15 PST)
AMBER: gaff errors? Difei Wang (Tue Nov 25 2003 - 16:53:43 PST)
- Re: AMBER: gaff errors? David A. Case (Wed Nov 26 2003 - 08:40:37 PST)
  - AMBER: restart MD program Do Anh Tuan (Wed Nov 26 2003 - 09:12:50 PST)
    - Re: AMBER: restart MD program Carlos Simmerling (Wed Nov 26 2003 - 09:23:06 PST)
    - AMBER: restarted MD and ptraj Frederico.Miranda.ibmb.uib.no (Wed Nov 26 2003 - 17:35:35 PST)
AMBER: compiling amber using gcc on SGI Unix machines Wayne Dawson (Wed Nov 26 2003 - 05:15:57 PST)
AMBER: Nmode problem Wu Yingliang (Fri Nov 28 2003 - 05:52:31 PST)
- Re: AMBER: Nmode problem Holger Gohlke (Fri Nov 28 2003 - 07:11:49 PST)
AMBER: Hello Rajendra P. OJHA (Sat Nov 29 2003 - 07:51:21 PST)
AMBER: Pseudouridine force field parameters Peter Gannett (Sat Nov 29 2003 - 16:27:38 PST)
- Re: AMBER: Pseudouridine force field parameters David A. Case (Sat Nov 29 2003 - 16:48:59 PST)
- Re: AMBER: Pseudouridine force field parameters Pascal Auffinger (Sun Nov 30 2003 - 07:58:30 PST)
- Re: AMBER: Pseudouridine force field parameters Peter Gannett (Sun Nov 30 2003 - 07:56:28 PST)
- Re: AMBER: Pseudouridine force field parameters Peter Gannett (Tue Dec 02 2003 - 04:45:01 PST)
AMBER: Re: Nmode problem Wu Yingliang (Sat Nov 29 2003 - 19:52:15 PST)
- AMBER: Re: Nmode problem Holger Gohlke (Sun Nov 30 2003 - 07:24:50 PST)
  - Re: AMBER: Re: Nmode problem Wu Yingliang (Mon Dec 01 2003 - 05:34:40 PST)
    - Re: AMBER: Re: Nmode problem Holger Gohlke (Mon Dec 01 2003 - 06:17:37 PST)
AMBER: NAD+ and NADH amber parameters Jiten (Mon Dec 01 2003 - 06:01:17 PST)
- Re: AMBER: NAD+ and NADH amber parameters David A. Case (Mon Dec 01 2003 - 08:35:56 PST)
- RE: AMBER: NAD+ and NADH amber parameters Ross Walker (Mon Dec 01 2003 - 09:07:40 PST)
- Re: AMBER: NAD+ and NADH amber parameters Ulf Ryde (Tue Dec 02 2003 - 05:20:26 PST)
- Re: AMBER: NAD+ and NADH amber parameters Jiten (Sun Dec 07 2003 - 20:17:53 PST)
  - Re: AMBER: NAD+ and NADH amber parameters Ulf Ryde (Mon Dec 08 2003 - 03:05:25 PST)
  - AMBER: Temperature dependent properties of TIP4P and TIP5P rluo.uci.edu (Mon Dec 08 2003 - 09:00:21 PST)
- Re: AMBER: NAD+ and NADH amber parameters Ross Walker (Sun Dec 07 2003 - 22:22:56 PST)
AMBER: partial charge Li Ying (Mon Dec 01 2003 - 09:31:56 PST)
- Re: AMBER: partial charge David A. Case (Mon Dec 01 2003 - 22:46:04 PST)
  - Re: AMBER: partial charge Li Ying (Tue Dec 02 2003 - 11:19:22 PST)
    - Re: AMBER: partial charge David A. Case (Tue Dec 02 2003 - 12:06:02 PST)
    - Re: AMBER: partial charge Li Ying (Wed Dec 03 2003 - 10:08:14 PST)
AMBER: Compiling on Suse 9 Pro with ifc... Herbert Georg (Mon Dec 01 2003 - 11:17:15 PST)
- Re: AMBER: Compiling on Suse 9 Pro with ifc... David A. Case (Mon Dec 01 2003 - 12:49:33 PST)
  - Re: AMBER: Compiling on Suse 9 Pro with ifc... Herbert Georg (Wed Dec 03 2003 - 05:26:07 PST)
  - Re: AMBER: Compiling on Suse 9 Pro with ifc... Herbert Georg (Wed Dec 03 2003 - 06:04:30 PST)
    - Re: AMBER: Compiling on Suse 9 Pro with ifc... David A. Case (Thu Dec 04 2003 - 08:42:15 PST)
    - Re: Re: AMBER: Compiling on Suse 9 Pro with ifc... Ye Mei (Fri Dec 05 2003 - 20:44:49 PST)
  - Re: AMBER: Compiling on Suse 9 Pro with ifc... Herbert Georg (Wed Dec 03 2003 - 11:13:42 PST)
  - Re: AMBER: Compiling on Suse 9 Pro with ifc... Herbert Georg (Thu Dec 04 2003 - 04:56:55 PST)
AMBER: Sander / Anal Emmanuel Giudice (Mon Dec 01 2003 - 12:06:00 PST)
- Re: AMBER: Sander / Anal David A. Case (Mon Dec 01 2003 - 12:58:32 PST)
- Re: AMBER: Sander / Anal Emmanuel Giudice (Fri Dec 05 2003 - 09:54:20 PST)
AMBER: basic questions Wei Wang (Mon Dec 01 2003 - 15:02:52 PST)
- Re: AMBER: basic questions David A. Case (Mon Dec 01 2003 - 22:37:59 PST)
- Re: AMBER: basic questions Wei Wang (Tue Dec 02 2003 - 08:23:13 PST)
  - Re: AMBER: basic questions David A. Case (Tue Dec 02 2003 - 08:37:42 PST)
AMBER: sander output Dave S Walker (Mon Dec 01 2003 - 18:04:31 PST)
- Re: AMBER: sander output Carlos Simmerling (Mon Dec 01 2003 - 18:37:06 PST)
  - Re: AMBER: sander output Dave S Walker (Thu Dec 04 2003 - 16:41:05 PST)
    - Re: AMBER: sander output David A. Case (Thu Dec 04 2003 - 16:51:03 PST)
    - Re: AMBER: sander output Dave S Walker (Thu Feb 19 2004 - 15:55:59 PST)
    - Re: AMBER: sander output David A. Case (Thu Feb 19 2004 - 21:54:32 PST)
    - Re: AMBER: sander output Dave S Walker (Fri Feb 20 2004 - 13:47:24 PST)
AMBER: about H-bond definition for TIP3P Nikolai Smolin (Tue Dec 02 2003 - 05:44:19 PST)
AMBER: Ptraj-HBOND Taner E. Dirama (Tue Dec 02 2003 - 10:42:58 PST)
AMBER: Anal/MMPBSA Wu Yingliang (Tue Dec 02 2003 - 17:16:02 PST)
- Re: AMBER: Anal/MMPBSA David A. Case (Tue Dec 02 2003 - 17:29:46 PST)
  - AMBER: segmentation fault Do Anh Tuan (Tue Dec 02 2003 - 20:56:32 PST)
    - Re: AMBER: segmentation fault David A. Case (Wed Dec 03 2003 - 09:46:46 PST)
AMBER: GIBBS - PMFquestion Jiri Matousek (Wed Dec 03 2003 - 02:47:41 PST)
AMBER: how to calculate vibration frequency? A. Hungie (Wed Dec 03 2003 - 06:46:26 PST)
- Re: AMBER: how to calculate vibration frequency? David A. Case (Wed Dec 03 2003 - 08:59:41 PST)
AMBER: MM-PBSA question Giovanni (Wed Dec 03 2003 - 10:10:10 PST)
- Re: AMBER: MM-PBSA question Holger Gohlke (Wed Dec 03 2003 - 10:58:23 PST)
AMBER: Resp Esp charge Derive (RED v-1.0) release FyD (Wed Dec 03 2003 - 11:09:39 PST)
AMBER: Paramters for beta and gamma peptides Jagannadh B (Thu Dec 04 2003 - 04:34:43 PST)
AMBER: NO2-TYR arubin.unmc.edu (Thu Dec 04 2003 - 09:30:24 PST)
AMBER: Amber - compiler help Malone, Scott (Thu Dec 04 2003 - 14:11:53 PST)
- RE: AMBER: Amber - compiler help Chris Moth (Thu Dec 04 2003 - 14:45:10 PST)
- Re: AMBER: Amber - compiler help David A. Case (Thu Dec 04 2003 - 16:54:07 PST)
AMBER: initial structures Raghunadha Reddy Burri (Mon Dec 08 2003 - 07:21:28 PST)
- Re: AMBER: initial structures Carlos Simmerling (Mon Dec 08 2003 - 07:51:04 PST)
  - AMBER: Re: initial structures Raghunadha Reddy Burri (Mon Dec 08 2003 - 09:19:10 PST)
    - Re: AMBER: Re: initial structures David A. Case (Mon Dec 08 2003 - 09:30:57 PST)
AMBER: MD L Jin (Mon Dec 08 2003 - 09:45:01 PST)
- AMBER: gaff atom types for phosphor compouds astrid.maass (Tue Dec 09 2003 - 05:51:33 PST)
  - Re: AMBER: gaff atom types for phosphor compouds Junmei Wang (Tue Dec 09 2003 - 07:28:08 PST)
AMBER: Small problems L Jin (Mon Dec 08 2003 - 09:47:47 PST)
AMBER: Mg2+ parameters for RNA usage Vlad Cojocaru (Wed Dec 10 2003 - 05:38:59 PST)
- Re: AMBER: Mg2+ parameters for RNA usage Jiri Sponer (Wed Dec 10 2003 - 06:21:24 PST)
- Re: AMBER: Mg2+ parameters for RNA usage Pascal Auffinger (Wed Dec 10 2003 - 07:30:47 PST)
  - Re: AMBER: Mg2+ parameters for RNA usage Peter VARNAI (Wed Dec 10 2003 - 08:06:30 PST)
  - Re: AMBER: Mg2+ parameters for RNA usage Jiri Sponer (Wed Dec 10 2003 - 11:32:57 PST)
- Re: AMBER: Mg2+ parameters for RNA usage Bill Ross (Wed Dec 10 2003 - 10:07:49 PST)
AMBER: RESP charges Youyi Peng (Wed Dec 10 2003 - 06:34:58 PST)
- Re: AMBER: RESP charges David A. Case (Wed Dec 10 2003 - 08:31:38 PST)
- Re: AMBER: RESP charges Youyi Peng (Wed Dec 10 2003 - 09:28:40 PST)
  - Re: AMBER: RESP charges Joey Harriman (Wed Dec 10 2003 - 10:05:44 PST)
  - Re: AMBER: RESP charges David A. Case (Wed Dec 10 2003 - 10:28:00 PST)
    - Re: AMBER: RESP charges Junmei Wang (Wed Dec 10 2003 - 10:38:15 PST)
- Re: AMBER: RESP charges Jiten (Wed Dec 10 2003 - 09:55:51 PST)
- Re: AMBER: RESP charges Youyi Peng (Wed Dec 10 2003 - 12:57:56 PST)
  - Re: AMBER: RESP charges Junmei Wang (Wed Dec 10 2003 - 13:07:24 PST)
- Re: AMBER: RESP charges Youyi Peng (Wed Dec 10 2003 - 14:48:05 PST)
  - Re: AMBER: RESP charges Junmei Wang (Wed Dec 10 2003 - 15:29:19 PST)
- Re: AMBER: RESP charges Youyi Peng (Wed Dec 10 2003 - 14:50:46 PST)
- Re: AMBER: RESP charges Youyi Peng (Thu Dec 11 2003 - 08:41:45 PST)
  - Re: AMBER: RESP charges Junmei Wang (Thu Dec 11 2003 - 08:55:21 PST)
- Re: AMBER: RESP charges Youyi Peng (Thu Dec 18 2003 - 07:20:43 PST)
  - Re: AMBER: RESP charges Junmei Wang (Thu Dec 18 2003 - 13:17:28 PST)
- Re: AMBER: RESP charges Youyi Peng (Thu Dec 18 2003 - 15:31:51 PST)
  - Re: AMBER: RESP charges Junmei Wang (Thu Dec 18 2003 - 18:29:45 PST)
AMBER: About Temperature Regulation L Jin (Wed Dec 10 2003 - 07:09:00 PST)
- Re: AMBER: About Temperature Regulation David A. Case (Wed Dec 10 2003 - 08:30:24 PST)
  - Re: AMBER: About Temperature Regulation L Jin (Wed Dec 10 2003 - 09:06:25 PST)
AMBER: Antechamber & Ptraj/Rdparm L Jin (Wed Dec 10 2003 - 07:07:25 PST)
- Re: AMBER: Antechamber & Ptraj/Rdparm Bill Ross (Thu Jan 01 2004 - 14:26:55 PST)
  - AMBER: Molecular Frame Byungchan Kim (Thu Jan 01 2004 - 19:46:14 PST)
    - Re: AMBER: Molecular Frame David A. Case (Fri Jan 02 2004 - 08:22:10 PST)
    - Re: AMBER: Molecular Frame Byungchan Kim (Fri Jan 02 2004 - 15:03:36 PST)
    - Re: AMBER: Molecular Frame David A. Case (Sat Jan 03 2004 - 07:51:13 PST)
    - Re: AMBER: Molecular Frame Bill Ross (Fri Jan 02 2004 - 15:40:54 PST)
    - Re: AMBER: Molecular Frame Byungchan Kim (Sat Jan 03 2004 - 11:00:20 PST)
AMBER: Nitrated Tyr arubin.unmc.edu (Wed Dec 10 2003 - 08:36:45 PST)
AMBER: MOPAC from antechamber Beale, John (Wed Dec 10 2003 - 09:46:02 PST)
- Re: AMBER: MOPAC from antechamber Joey Harriman (Wed Dec 10 2003 - 10:08:13 PST)
Re: AMBER: Antechamber & Ptraj/Rdparm Bill Ross (Wed Dec 10 2003 - 10:17:37 PST)
- Re: AMBER: Antechamber & Ptraj/Rdparm L Jin (Fri Dec 12 2003 - 03:35:46 PST)
- Re: AMBER: Antechamber & Ptraj/Rdparm L Jin (Wed Dec 31 2003 - 03:44:00 PST)
  - Re: AMBER: Antechamber & Ptraj/Rdparm David A. Case (Wed Dec 31 2003 - 07:47:46 PST)
    - Re: AMBER: Antechamber & Ptraj/Rdparm L Jin (Thu Jan 01 2004 - 02:47:18 PST)
    - Re: AMBER: Antechamber & Ptraj/Rdparm zhaoxc.puccini.che.pitt.edu (Thu Jan 01 2004 - 07:05:31 PST)
AMBER: a simple question about HBond energy... Florent Barbault (Thu Dec 11 2003 - 00:04:27 PST)
- Re: AMBER: a simple question about HBond energy... David A. Case (Fri Dec 12 2003 - 13:57:47 PST)
- Re: AMBER: a simple question about HBond energy... Bill Ross (Fri Dec 12 2003 - 14:16:42 PST)
AMBER: Carbohydrate connectivity Bimo Ario Tejo (Thu Dec 11 2003 - 07:14:05 PST)
- Re: AMBER: Carbohydrate connectivity Jiten (Thu Dec 11 2003 - 08:04:44 PST)
- Re: AMBER: Carbohydrate connectivity David A. Case (Thu Dec 11 2003 - 08:09:08 PST)
AMBER: GBSA problem northrop.chem.ucla.edu (Thu Dec 11 2003 - 15:28:27 PST)
- Re: AMBER: GBSA problem Wu Yingliang (Thu Dec 11 2003 - 20:20:05 PST)
AMBER: lifetime in ptraj hbond Fajar Rakhman Wibowo (Fri Dec 12 2003 - 01:28:45 PST)
- Re: AMBER: lifetime in ptraj hbond Martin Lepsik (Fri Dec 12 2003 - 05:29:28 PST)
AMBER: ambpdb L Jin (Fri Dec 12 2003 - 02:43:36 PST)
- Re: AMBER: ambpdb ch cureton (Fri Dec 12 2003 - 02:47:06 PST)
  - Re: AMBER: ambpdb L Jin (Fri Dec 12 2003 - 03:24:42 PST)
    - Re: AMBER: ambpdb ch cureton (Fri Dec 12 2003 - 03:53:17 PST)
AMBER: adding extra salt Vlad Cojocaru (Fri Dec 12 2003 - 05:34:55 PST)
AMBER: Antechamber:charges missing L Jin (Fri Dec 12 2003 - 07:45:35 PST)
Re: AMBER: adding extra salt Bill Ross (Fri Dec 12 2003 - 08:44:07 PST)
- AMBER: order parameter myang (Fri Dec 12 2003 - 12:25:17 PST)
  - Re: AMBER: order parameter David A. Case (Fri Dec 12 2003 - 13:29:26 PST)
AMBER: nmode, trajectory kbyun.wesleyan.edu (Fri Dec 12 2003 - 09:05:08 PST)
- Re: AMBER: nmode, trajectory Holger Gohlke (Sat Dec 13 2003 - 07:42:39 PST)
AMBER: parmscan Jessica Swanson (Fri Dec 12 2003 - 10:39:19 PST)
AMBER: non-zero 10-12 coefficient Bimo Ario Tejo (Sat Dec 13 2003 - 06:44:49 PST)
- Re: AMBER: non-zero 10-12 coefficient David A. Case (Sat Dec 13 2003 - 12:48:12 PST)
AMBER: How to use quasih? A. Hungie (Thu Dec 11 2003 - 08:12:23 PST)
- Re: AMBER: How to use quasih? David A. Case (Thu Dec 11 2003 - 08:34:39 PST)
AMBER: Heme and Zn parameters Vema Aparna (Sun Dec 14 2003 - 06:04:43 PST)
AMBER: Energy map L Jin (Mon Dec 15 2003 - 06:42:52 PST)
- Re: AMBER: Energy map Tammy Smith (Mon Dec 15 2003 - 06:57:29 PST)
  - Re: AMBER: Energy map Tammy Smith (Mon Dec 15 2003 - 07:17:31 PST)
    - Re: AMBER: Energy map Tammy Smith (Mon Dec 15 2003 - 07:37:30 PST)
    - Re: AMBER: Energy map Tammy Smith (Mon Dec 15 2003 - 07:57:31 PST)
    - Re: AMBER: Energy map Tammy Smith (Mon Dec 15 2003 - 08:27:32 PST)
    - Re: AMBER: Energy map Tammy Smith (Mon Dec 15 2003 - 08:57:31 PST)
    - Re: AMBER: Energy map Tammy Smith (Mon Dec 15 2003 - 09:17:32 PST)
    - Re: AMBER: Energy map Tammy Smith (Mon Dec 15 2003 - 09:37:32 PST)
    - Re: AMBER: Energy map Tammy Smith (Mon Dec 15 2003 - 09:57:32 PST)
    - Re: AMBER: Energy map Tammy Smith (Mon Dec 15 2003 - 10:17:33 PST)
    - Re: AMBER: Energy map Tammy Smith (Mon Dec 15 2003 - 10:37:33 PST)
AMBER: Message removed at request of author Name Removed (Mon Dec 15 2003 - 07:29:55 PST)
- Re: AMBER: water neighborhood of amide hydrogens Tammy Smith (Mon Dec 15 2003 - 07:37:30 PST)
  - Re: AMBER: water neighborhood of amide hydrogens Tammy Smith (Mon Dec 15 2003 - 07:57:31 PST)
    - Re: AMBER: water neighborhood of amide hydrogens Tammy Smith (Mon Dec 15 2003 - 08:27:32 PST)
    - Re: AMBER: water neighborhood of amide hydrogens Tammy Smith (Mon Dec 15 2003 - 08:47:32 PST)
    - Re: AMBER: water neighborhood of amide hydrogens Tammy Smith (Mon Dec 15 2003 - 09:17:32 PST)
    - Re: AMBER: water neighborhood of amide hydrogens Tammy Smith (Mon Dec 15 2003 - 09:37:32 PST)
    - Re: AMBER: water neighborhood of amide hydrogens Tammy Smith (Mon Dec 15 2003 - 09:57:32 PST)
    - Re: AMBER: water neighborhood of amide hydrogens Tammy Smith (Mon Dec 15 2003 - 10:27:33 PST)
    - Re: AMBER: water neighborhood of amide hydrogens Tammy Smith (Mon Dec 15 2003 - 10:47:34 PST)
  - Re: AMBER: water neighborhood of amide hydrogens Bill Ross (Mon Dec 15 2003 - 11:26:29 PST)
- Re: AMBER: water neighborhood of amide hydrogens Thomas E. Cheatham, III (Mon Dec 15 2003 - 09:29:00 PST)
  - Re: AMBER: water neighborhood of amide hydrogens Tammy Smith (Mon Dec 15 2003 - 09:47:32 PST)
    - Re: AMBER: water neighborhood of amide hydrogens Tammy Smith (Mon Dec 15 2003 - 10:07:32 PST)
    - Re: AMBER: water neighborhood of amide hydrogens Tammy Smith (Mon Dec 15 2003 - 10:27:33 PST)
    - Re: AMBER: water neighborhood of amide hydrogens Tammy Smith (Mon Dec 15 2003 - 10:47:34 PST)
AMBER: length of deltaG calcs Heather A.Carlson (Mon Dec 15 2003 - 07:32:48 PST)
- Re: AMBER: length of deltaG calcs Tammy Smith (Mon Dec 15 2003 - 07:37:30 PST)
  - Re: AMBER: length of deltaG calcs Tammy Smith (Mon Dec 15 2003 - 07:57:31 PST)
    - Re: AMBER: length of deltaG calcs Tammy Smith (Mon Dec 15 2003 - 08:27:32 PST)
    - Re: AMBER: length of deltaG calcs Tammy Smith (Mon Dec 15 2003 - 08:47:32 PST)
    - Re: AMBER: length of deltaG calcs Tammy Smith (Mon Dec 15 2003 - 09:07:32 PST)
    - Re: AMBER: length of deltaG calcs Tammy Smith (Mon Dec 15 2003 - 09:37:32 PST)
    - Re: AMBER: length of deltaG calcs Tammy Smith (Mon Dec 15 2003 - 09:57:32 PST)
    - Re: AMBER: length of deltaG calcs Tammy Smith (Mon Dec 15 2003 - 10:17:33 PST)
    - Re: AMBER: length of deltaG calcs Tammy Smith (Mon Dec 15 2003 - 10:37:33 PST)
- Re: AMBER: length of deltaG calcs David Smith (Mon Dec 15 2003 - 08:16:26 PST)
  - Re: AMBER: length of deltaG calcs Tammy Smith (Mon Dec 15 2003 - 08:37:31 PST)
    - Re: AMBER: length of deltaG calcs Tammy Smith (Mon Dec 15 2003 - 08:57:31 PST)
    - Re: AMBER: length of deltaG calcs Tammy Smith (Mon Dec 15 2003 - 09:17:32 PST)
    - Re: AMBER: length of deltaG calcs Tammy Smith (Mon Dec 15 2003 - 09:37:32 PST)
    - Re: AMBER: length of deltaG calcs Tammy Smith (Mon Dec 15 2003 - 09:57:33 PST)
    - Re: AMBER: length of deltaG calcs Tammy Smith (Mon Dec 15 2003 - 10:17:33 PST)
    - Re: AMBER: length of deltaG calcs Tammy Smith (Mon Dec 15 2003 - 10:37:33 PST)
AMBER: question about namelist aini.UMDNJ.EDU (Mon Dec 15 2003 - 07:42:04 PST)
- Re: AMBER: question about namelist Tammy Smith (Mon Dec 15 2003 - 07:47:30 PST)
  - Re: AMBER: question about namelist Tammy Smith (Mon Dec 15 2003 - 08:07:31 PST)
    - Re: AMBER: question about namelist Tammy Smith (Mon Dec 15 2003 - 08:27:32 PST)
    - Re: AMBER: question about namelist Tammy Smith (Mon Dec 15 2003 - 08:47:32 PST)
    - Re: AMBER: question about namelist Tammy Smith (Mon Dec 15 2003 - 09:07:32 PST)
    - Re: AMBER: question about namelist Tammy Smith (Mon Dec 15 2003 - 09:27:32 PST)
    - Re: AMBER: question about namelist Tammy Smith (Mon Dec 15 2003 - 09:47:32 PST)
    - Re: AMBER: question about namelist Tammy Smith (Mon Dec 15 2003 - 10:07:32 PST)
    - Re: AMBER: question about namelist Tammy Smith (Mon Dec 15 2003 - 10:27:33 PST)
    - Re: AMBER: question about namelist Tammy Smith (Mon Dec 15 2003 - 10:47:34 PST)
- Re: AMBER: question about namelist Holger Gohlke (Mon Dec 15 2003 - 08:10:05 PST)
  - Re: AMBER: question about namelist Tammy Smith (Mon Dec 15 2003 - 08:27:32 PST)
    - Re: AMBER: question about namelist Tammy Smith (Mon Dec 15 2003 - 08:47:32 PST)
    - Re: AMBER: question about namelist Tammy Smith (Mon Dec 15 2003 - 09:07:32 PST)
    - Re: AMBER: question about namelist Tammy Smith (Mon Dec 15 2003 - 09:27:32 PST)
    - Re: AMBER: question about namelist Tammy Smith (Mon Dec 15 2003 - 09:47:32 PST)
    - Re: AMBER: question about namelist Tammy Smith (Mon Dec 15 2003 - 10:07:32 PST)
    - Re: AMBER: question about namelist Tammy Smith (Mon Dec 15 2003 - 10:27:33 PST)
    - Re: AMBER: question about namelist Tammy Smith (Mon Dec 15 2003 - 10:47:34 PST)
- Re: AMBER: question about namelist Suse Broyde (Mon Dec 15 2003 - 09:37:58 PST)
  - Re: AMBER: question about namelist Ioana Cozmuta (Mon Dec 15 2003 - 11:14:40 PST)
- Re: AMBER: question about namelist Piotr Cieplak (Mon Dec 15 2003 - 14:02:33 PST)
AMBER: minimization on sander Herbert Georg (Mon Dec 15 2003 - 12:05:25 PST)
Re: AMBER: minimization on sander Bill Ross (Mon Dec 15 2003 - 12:32:39 PST)
- Re: AMBER: minimization on sander Herbert Georg (Mon Dec 15 2003 - 13:21:13 PST)
AMBER: no "Input orientation" in g98 log Lee, Matt (Mon Dec 15 2003 - 15:13:10 PST)
AMBER: Ibelly and Ewald error message when ewald should be off Ben Cossins (Tue Dec 16 2003 - 15:01:52 PST)
- Re: AMBER: Ibelly and Ewald error message when ewald should be off Scott Brozell (Wed Jan 28 2004 - 21:57:06 PST)
AMBER: Nmode analysis ptn-ligand complex Jory Zmuda (Tue Dec 16 2003 - 15:11:13 PST)
AMBER: nmode statistics kbyun.wesleyan.edu (Wed Dec 17 2003 - 11:52:51 PST)
- Re: AMBER: nmode statistics Holger Gohlke (Wed Dec 17 2003 - 23:09:05 PST)
AMBER: PMEMD Performance on Beowulf systems Stephen.Titmuss.csiro.au (Thu Dec 18 2003 - 19:19:59 PST)
- Re: AMBER: PMEMD Performance on Beowulf systems Robert Duke (Thu Dec 18 2003 - 20:35:40 PST)
- Re: AMBER: PMEMD Performance on Beowulf systems Carlos Simmerling (Fri Dec 19 2003 - 06:53:12 PST)
- RE: RE: AMBER: PMEMD Performance on Beowulf systems Aldo Jongejan (Sun Dec 21 2003 - 23:27:41 PST)
  - Re: AMBER: PMEMD Performance on Beowulf systems Viktor Hornak (Mon Dec 22 2003 - 05:47:42 PST)
    - Re: AMBER: PMEMD Performance on Beowulf systems David E. Konerding (Mon Dec 22 2003 - 07:53:20 PST)
- Re: AMBER: PMEMD Performance on Beowulf systems Carlos Simmerling (Mon Dec 22 2003 - 08:12:37 PST)
  - Re: AMBER: PMEMD Performance on Beowulf systems David E. Konerding (Mon Dec 22 2003 - 08:57:23 PST)
  - AMBER: HT vs no HT John Mongan (Mon Dec 22 2003 - 11:18:31 PST)
- Re: AMBER: PMEMD Performance on Beowulf systems Robert Duke (Mon Dec 22 2003 - 08:44:47 PST)
  - Re: AMBER: PMEMD Performance on Beowulf systems David E. Konerding (Mon Dec 22 2003 - 09:04:03 PST)
- Re: AMBER: PMEMD Performance on Beowulf systems Carlos Simmerling (Mon Dec 22 2003 - 09:06:39 PST)
AMBER: MD: restrt L Jin (Fri Dec 19 2003 - 02:47:55 PST)
AMBER: special gaff atom types available? astrid.maass (Fri Dec 19 2003 - 03:58:30 PST)
- Re: AMBER: special gaff atom types available? David A. Case (Sat Dec 20 2003 - 08:25:14 PST)
AMBER: Ewald in Amber 7 Ben Cossins (Fri Dec 19 2003 - 07:49:11 PST)
- Re: AMBER: Ewald in Amber 7 David A. Case (Fri Dec 19 2003 - 09:30:23 PST)
AMBER: Vibration frequency of nucleobases A. Hungie (Fri Dec 19 2003 - 09:48:03 PST)
AMBER: Toolchest Shuang Ding (Fri Dec 19 2003 - 12:45:08 PST)
AMBER: initial velocity Fan Gao (Fri Dec 19 2003 - 16:56:16 PST)
- Re: AMBER: initial velocity Peter Oelschlaeger (Fri Dec 19 2003 - 18:08:43 PST)
AMBER: Curves parameters UU and PP Peter Gannett (Fri Dec 19 2003 - 20:08:02 PST)
- Re: AMBER: Curves parameters UU and PP Surjit Dixit (Sat Dec 20 2003 - 07:45:28 PST)
AMBER: vlimit? Ran Ye (Sun Dec 21 2003 - 14:15:57 PST)
- Re: AMBER: vlimit? David A. Case (Mon Dec 22 2003 - 09:24:18 PST)
  - Re: AMBER: vlimit? Ryan Ye (Tue Dec 23 2003 - 20:04:45 PST)
    - Re: AMBER: vlimit? David A. Case (Fri Dec 26 2003 - 10:18:16 PST)
Re: AMBER: vlimit? Bill Ross (Sun Dec 21 2003 - 20:04:40 PST)
AMBER: using sander without SHAKE Wayne Dawson (Sun Dec 21 2003 - 22:38:14 PST)
- Re: AMBER: using sander without SHAKE David A. Case (Mon Dec 22 2003 - 09:22:09 PST)
  - Re: AMBER: using sander without SHAKE Wayne Dawson (Wed Dec 24 2003 - 08:39:43 PST)
    - Re: AMBER: using sander without SHAKE David A. Case (Wed Dec 24 2003 - 10:06:40 PST)
- Re: AMBER: using sander without SHAKE Bill Ross (Wed Dec 24 2003 - 11:03:43 PST)
AMBER: GIBBS - PMF question: How to get <dV/d_lam> during TI calculations? Jiri Matousek (Mon Dec 22 2003 - 01:51:25 PST)
- Re: AMBER: GIBBS - PMF question: How to get <dV/d_lam> during TI calculations? David A. Case (Tue Dec 23 2003 - 11:18:39 PST)
AMBER: RESP charge redistribution Youyi Peng (Mon Dec 22 2003 - 13:27:13 PST)
AMBER: umbrella sampling with AMBER Mey Khalili (Mon Dec 22 2003 - 15:14:24 PST)
- Re: AMBER: umbrella sampling with AMBER David A. Case (Mon Dec 22 2003 - 17:48:30 PST)
2 FREE Worldwide Airline Tickets Worth $1600 for just $189! Bette Pagan (Mon Dec 22 2003 - 19:05:04 PST)
AMBER: MSMS Salma B. Rafi (Tue Dec 23 2003 - 10:36:18 PST)
- Re: AMBER: MSMS David A. Case (Tue Dec 23 2003 - 10:56:32 PST)
AMBER: PMEMD Performance on IBM SP David Skinner (Tue Dec 23 2003 - 12:00:45 PST)
AMBER: Basic potential question: a b (Wed Dec 24 2003 - 01:29:56 PST)
- AMBER: Basic potential question: Wayne Dawson (Wed Dec 24 2003 - 07:56:37 PST)
  - Re: AMBER: Basic potential question: FyD (Wed Dec 24 2003 - 10:35:22 PST)
  - Re: AMBER: Basic potential question: Piotr Cieplak (Wed Dec 24 2003 - 10:47:57 PST)
    - Re: AMBER: Basic potential question: Wayne Dawson (Thu Dec 25 2003 - 19:04:37 PST)
AMBER: MSE Wen Li (Wed Dec 24 2003 - 08:25:33 PST)
- Re: AMBER: MSE David A. Case (Wed Dec 24 2003 - 10:08:59 PST)
AMBER: Constant temperature L Jin (Sat Dec 27 2003 - 03:29:13 PST)
- Re: AMBER: Constant temperature David A. Case (Sat Dec 27 2003 - 22:46:46 PST)
Re: AMBER: Constant temperature Bill Ross (Sat Dec 27 2003 - 09:14:00 PST)
AMBER: roar topology and coordinate files PSR04996.mailstudenti.unimi.it (Mon Dec 29 2003 - 01:11:28 PST)
- Re: AMBER: roar topology and coordinate files M. L. Dodson (Mon Dec 29 2003 - 05:35:42 PST)
  - Re: AMBER: roar topology and coordinate files M. L. Dodson (Mon Dec 29 2003 - 12:15:57 PST)
- Re: AMBER: roar topology and coordinate files Bill Ross (Mon Dec 29 2003 - 16:14:53 PST)
  - Re: AMBER: roar topology and coordinate files M. L. Dodson (Mon Dec 29 2003 - 16:42:49 PST)
AMBER: The restart file generated by Ptraj Ling Zhang (Mon Dec 29 2003 - 12:49:52 PST)
AMBER: The lost velocities in the restart file generated by Ptraj Ling Zhang (Mon Dec 29 2003 - 13:12:47 PST)
Re: AMBER: The lost velocities in the restart file generated by Ptraj Bill Ross (Mon Dec 29 2003 - 16:11:54 PST)
AMBER: problems with pressure control Endres, Robert G. (Tue Dec 30 2003 - 06:38:02 PST)
- Re: AMBER: problems with pressure control David A. Case (Tue Dec 30 2003 - 10:03:06 PST)
AMBER: algorithm used in AMBER A. Hungie (Fri Jan 02 2004 - 02:07:11 PST)
- RE: AMBER: algorithm used in AMBER Ross Walker (Fri Jan 02 2004 - 05:05:13 PST)
AMBER: force field A. Hungie (Fri Jan 02 2004 - 04:28:59 PST)
- RE: AMBER: force field Ross Walker (Fri Jan 02 2004 - 04:55:24 PST)
AMBER: rms in ptraj L Jin (Mon Jan 05 2004 - 06:49:47 PST)
- Re: AMBER: rms in ptraj Thomas E. Cheatham, III (Mon Jan 05 2004 - 08:04:20 PST)
AMBER: File format generated by respgen Lishan Yao (Mon Jan 05 2004 - 08:50:38 PST)
AMBER: prep file Youyi Peng (Mon Jan 05 2004 - 15:40:07 PST)
- Re: AMBER: prep file James W. Caldwell (Mon Jan 05 2004 - 16:01:20 PST)
Re: AMBER: prep file Bill Ross (Mon Jan 05 2004 - 15:49:14 PST)
AMBER: Radius of gyration Bimo Ario Tejo (Mon Jan 05 2004 - 22:14:37 PST)
- Re: AMBER: Radius of gyration Alexey Onufriev (Tue Jan 06 2004 - 10:59:24 PST)
AMBER: Parameters for deuterium Charlie Laughton (Tue Jan 06 2004 - 07:17:46 PST)
- Re: AMBER: Parameters for deuterium David A. Case (Tue Jan 06 2004 - 08:32:14 PST)
AMBER: Intel Fortran Compiler 8.0 / pmemd 3.1 warning Robert Duke (Tue Jan 06 2004 - 12:20:44 PST)
- Re: AMBER: Intel Fortran Compiler 8.0 / pmemd 3.1 warning Andreas Svrcek-Seiler (Wed Jan 07 2004 - 04:12:30 PST)
  - Re: AMBER: Intel Fortran Compiler 8.0 / pmemd 3.1 warning Viktor Hornak (Wed Jan 07 2004 - 05:46:28 PST)
  - Re: AMBER: Intel Fortran Compiler 8.0 / pmemd 3.1 warning Robert Duke (Wed Jan 07 2004 - 06:17:27 PST)
    - Re: AMBER: Intel Fortran Compiler 8.0 / pmemd 3.1 warning David E. Konerding (Wed Jan 07 2004 - 08:16:49 PST)
- Re: AMBER: Intel Fortran Compiler 8.0 / pmemd 3.1 warning Robert Duke (Wed Jan 07 2004 - 06:31:19 PST)
AMBER: Atom type L Jin (Wed Jan 07 2004 - 03:26:25 PST)
AMBER: strange output of MD L Jin (Wed Jan 07 2004 - 08:42:49 PST)
Re: AMBER: strange output of MD Rhonda Torres (Wed Jan 07 2004 - 09:48:54 PST)
- Re: AMBER: strange output of MD Bill Ross (Wed Jan 07 2004 - 09:57:13 PST)
  - Re: AMBER: strange output of MD L Jin (Wed Jan 07 2004 - 10:21:03 PST)
- Re: AMBER: strange output of MD Bill Ross (Wed Jan 07 2004 - 10:39:35 PST)
Re: AMBER: Atom type Rhonda Torres (Wed Jan 07 2004 - 10:09:17 PST)
- Re: AMBER: Atom type Rhonda Torres (Wed Jan 07 2004 - 10:55:40 PST)
AMBER: .crg file for Delphi a b (Wed Jan 07 2004 - 10:22:34 PST)
AMBER: modeling GPCR in lipid environment Giulio Rastelli (Thu Jan 08 2004 - 08:49:53 PST)
- Re: AMBER: modeling GPCR in lipid environment Alexey Onufriev (Thu Jan 08 2004 - 11:08:01 PST)
AMBER: Minimiation (AMBER5/AMBER7) does not reach the tageted rmsd Anna Schrey (Thu Jan 08 2004 - 02:30:37 PST)
- Re: AMBER: Minimiation (AMBER5/AMBER7) does not reach the tageted rmsd David A. Case (Thu Jan 08 2004 - 16:15:12 PST)
- Re: AMBER: Minimiation (AMBER5/AMBER7) does not reach the tageted rmsd Anna Schrey (Fri Jan 23 2004 - 02:39:47 PST)
AMBER: Vlimit problem Yuqin Cai (Thu Jan 08 2004 - 10:15:38 PST)
- Re: AMBER: Vlimit problem David A. Case (Thu Jan 08 2004 - 16:31:00 PST)
- Re: AMBER: Vlimit problem Thomas E. Cheatham, III (Fri Jan 09 2004 - 13:53:10 PST)
AMBER: running on Itanium machines northrop.chem.ucla.edu (Thu Jan 08 2004 - 11:14:52 PST)
- Re: AMBER: running on Itanium machines David A. Case (Fri Jan 09 2004 - 08:43:48 PST)
  - Re: AMBER: running on Itanium machines northrop.chem.ucla.edu (Fri Jan 09 2004 - 11:28:56 PST)
AMBER: Amber compilation in IBM-SP4 Jiten (Sat Jan 10 2004 - 00:28:12 PST)
- Re: AMBER: Amber compilation in IBM-SP4 David A. Case (Sat Jan 10 2004 - 10:43:06 PST)
AMBER: references? a b (Sun Jan 11 2004 - 06:40:50 PST)
- Re: AMBER: references? Martin Lepsik (Thu Jan 29 2004 - 07:32:23 PST)
AMBER: Improper dihedral Herbert Georg (Mon Jan 12 2004 - 06:23:22 PST)
- Re: AMBER: Improper dihedral Bill Ross (Mon Jan 12 2004 - 11:23:44 PST)
  - Re: AMBER: Improper dihedral Herbert Georg (Mon Jan 12 2004 - 11:39:12 PST)
- Re: AMBER: Improper dihedral Bill Ross (Mon Jan 12 2004 - 11:52:53 PST)
  - Re: AMBER: Improper dihedral Herbert Georg (Mon Jan 12 2004 - 12:21:39 PST)
- Re: AMBER: Improper dihedral David A. Case (Mon Jan 12 2004 - 12:14:22 PST)
  - Re: AMBER: Improper dihedral Herbert Georg (Tue Jan 13 2004 - 07:36:29 PST)
Re: AMBER: Improper dihedral Bill Ross (Mon Jan 12 2004 - 10:21:03 PST)
- Re: AMBER: Improper dihedral Herbert Georg (Mon Jan 12 2004 - 10:57:39 PST)
AMBER: disulfide bonds Wen Li (Mon Jan 12 2004 - 13:56:26 PST)
- Re: AMBER: disulfide bonds David A. Case (Mon Jan 12 2004 - 17:54:48 PST)
  - Re: AMBER: disulfide bonds Wen Li (Tue Jan 13 2004 - 10:13:50 PST)
    - Re: AMBER: disulfide bonds David A. Case (Tue Jan 13 2004 - 10:57:25 PST)
Re: AMBER: disulfide bonds/ Engineered bishop (Tue Jan 13 2004 - 06:20:19 PST)
AMBER: error in minimization Itziar Maestre Asenjo (Tue Jan 13 2004 - 07:12:22 PST)
- Re: AMBER: error in minimization David A. Case (Tue Jan 13 2004 - 08:48:50 PST)
- Re: AMBER: error in minimization Itziar Maestre Asenjo (Wed Jan 14 2004 - 22:58:46 PST)
AMBER: LEAP - Error loading units Miguel de Federico (Wed Jan 14 2004 - 09:12:29 PST)
AMBER: DMF box Stefano.Pieraccini.unimi.it (Wed Jan 14 2004 - 08:42:02 PST)
Re: AMBER: LEAP - Error loading units Bill Ross (Wed Jan 14 2004 - 11:45:19 PST)
AMBER: "ATTN, need revision" klamothe.uiuc.edu (Wed Jan 14 2004 - 12:07:56 PST)
- Re: AMBER: "ATTN, need revision" Junmei Wang (Wed Jan 14 2004 - 12:39:47 PST)
AMBER: free energy profile calculation Martina Roeselova (Wed Jan 14 2004 - 13:14:48 PST)
- Re: AMBER: free energy profile calculation David Smith (Thu Jan 15 2004 - 06:37:27 PST)
  - Re: AMBER: free energy profile calculation David A. Case (Thu Jan 15 2004 - 08:32:17 PST)
AMBER: NTF L Jin (Fri Jan 16 2004 - 03:15:16 PST)
- Re: AMBER: NTF David A. Case (Fri Jan 16 2004 - 08:09:27 PST)
AMBER: atom type CM Kristina Furse (Fri Jan 16 2004 - 12:37:38 PST)
- Re: AMBER: atom type CM Junmei Wang (Fri Jan 16 2004 - 13:13:19 PST)
- RE: AMBER: atom type CM Kristina Furse (Fri Jan 16 2004 - 13:56:47 PST)
  - RE: AMBER: atom type CM Junmei Wang (Tue Jan 20 2004 - 08:43:23 PST)
Re: AMBER: atom type CM Bill Ross (Fri Jan 16 2004 - 13:17:29 PST)
AMBER: GB and Atom Type Steve Seibold (Tue Jan 20 2004 - 07:34:45 PST)
- Re: AMBER: GB and Atom Type David A. Case (Tue Jan 20 2004 - 15:03:52 PST)
AMBER: Question for PMEMD users Robert Duke (Tue Jan 20 2004 - 08:05:38 PST)
AMBER: restraint tang kwa (Tue Jan 20 2004 - 08:10:39 PST)
- Re: AMBER: restraint David A. Case (Tue Jan 20 2004 - 15:05:59 PST)
AMBER: Parm98 Vs 02 A.Madhumalar (Tue Jan 20 2004 - 08:27:03 PST)
- Re: AMBER: Parm98 Vs 02 David A. Case (Tue Jan 20 2004 - 15:08:57 PST)
  - Re: AMBER: Parm98 Vs 02 A.Madhumalar (Wed Jan 21 2004 - 09:01:31 PST)
AMBER: PDB files Beale, John (Tue Jan 20 2004 - 08:43:36 PST)
- Re: AMBER: PDB files David A. Case (Tue Jan 20 2004 - 15:12:04 PST)
AMBER: Do I need to repeat MD simulation? aini.UMDNJ.EDU (Tue Jan 20 2004 - 15:43:00 PST)
- Re: AMBER: Do I need to repeat MD simulation? Andreas Svrcek-Seiler (Wed Jan 21 2004 - 02:40:17 PST)
  - Re: AMBER: Do I need to repeat MD simulation? Robert Duke (Wed Jan 21 2004 - 05:44:22 PST)
- Re: AMBER: Do I need to repeat MD simulation? bishop (Wed Jan 21 2004 - 07:14:45 PST)
- Re: AMBER: Do I need to repeat MD simulation? Bill Ross (Wed Jan 21 2004 - 08:01:54 PST)
  - Re: AMBER: Do I need to repeat MD simulation? aini.UMDNJ.EDU (Wed Jan 21 2004 - 10:42:30 PST)
AMBER: segmentation fault in Leap Ioana Cozmuta (Tue Jan 20 2004 - 20:39:28 PST)
Re: AMBER: segmentation fault in Leap Bill Ross (Wed Jan 21 2004 - 01:47:58 PST)
- Re: AMBER: segmentation fault in Leap Ioana Cozmuta (Wed Jan 21 2004 - 21:56:10 PST)
  - Re: AMBER: segmentation fault in Leap David E. Konerding (Thu Jan 22 2004 - 07:22:47 PST)
- Re: AMBER: segmentation fault in Leap Bill Ross (Thu Jan 22 2004 - 09:37:09 PST)
  - Re: AMBER: segmentation fault in Leap Ioana Cozmuta (Thu Jan 22 2004 - 23:26:41 PST)
AMBER: Errors in MM-PBSA??? ML (Wed Jan 21 2004 - 03:46:35 PST)
- Re: AMBER: Errors in MM-PBSA??? Holger Gohlke (Wed Jan 21 2004 - 04:37:39 PST)
AMBER: NMODE via MM-PBSA ML (Wed Jan 21 2004 - 04:03:31 PST)
- Re: AMBER: NMODE via MM-PBSA Holger Gohlke (Wed Jan 21 2004 - 04:49:48 PST)
  - Re: AMBER: NMODE via MM-PBSA ML (Wed Jan 21 2004 - 05:42:29 PST)
  - AMBER: NMODE for protein via MM-PBSA-cntd ML (Wed Feb 04 2004 - 08:09:57 PST)
    - Re: AMBER: NMODE for protein via MM-PBSA-cntd David A. Case (Wed Feb 04 2004 - 08:32:37 PST)
    - Re: AMBER: NMODE for protein via MM-PBSA-cntd ML (Wed Feb 04 2004 - 09:18:12 PST)
AMBER: antechamber and mopac5010mn S. Frank Yan (Wed Jan 21 2004 - 07:37:25 PST)
- Re: AMBER: antechamber and mopac5010mn David A. Case (Wed Jan 21 2004 - 08:41:53 PST)
AMBER: crystal lattice determination Scott Brozell (Wed Jan 21 2004 - 08:51:37 PST)
- Re: AMBER: crystal lattice determination David A. Case (Thu Jan 22 2004 - 17:20:42 PST)
AMBER: oxs g5 machine file Knut Langsetmo (Wed Jan 21 2004 - 12:10:33 PST)
AMBER: crosslink a residue with a small molecule Eric Hu (Wed Jan 21 2004 - 13:41:08 PST)
AMBER: remove rotational motion Itziar Maestre Asenjo (Wed Jan 21 2004 - 23:39:15 PST)
- Re: AMBER: remove rotational motion David A. Case (Thu Jan 22 2004 - 17:21:03 PST)
AMBER: How does LEaP place Na+ ions? tang kwa (Thu Jan 22 2004 - 02:10:16 PST)
- Re: AMBER: How does LEaP place Na+ ions? Jose Ramon Blas (Thu Jan 22 2004 - 13:38:03 PST)
- Re: AMBER: How does LEaP place Na+ ions? Bill Ross (Thu Jan 22 2004 - 09:17:32 PST)
- Re: AMBER: How does LEaP place Na+ ions? Jiten (Sun Jan 25 2004 - 17:44:36 PST)
AMBER: restrt L Jin (Thu Jan 22 2004 - 03:03:51 PST)
- Re: AMBER: restrt Dr. Yong Duan (Thu Jan 22 2004 - 05:24:40 PST)
  - Re: AMBER: restrt L Jin (Thu Jan 22 2004 - 06:05:03 PST)
    - Re: AMBER: restrt Dr. Yong Duan (Thu Jan 22 2004 - 18:27:05 PST)
- Re: AMBER: restrt Bill Ross (Thu Jan 22 2004 - 09:15:58 PST)
Re: AMBER: How does LEaP place Na+ ions? Bill Ross (Thu Jan 22 2004 - 09:12:07 PST)
AMBER: Segmentation fault (core dumped) error of antechamber program S. Frank Yan (Thu Jan 22 2004 - 11:36:54 PST)
- Re: AMBER: Segmentation fault (core dumped) error of antechamber program David A. Case (Thu Jan 22 2004 - 17:21:40 PST)
AMBER: oxygen positions around a DNA Ioana Cozmuta (Thu Jan 22 2004 - 18:19:51 PST)
AMBER: Problem using GLYCAM with sander Itziar Maestre Asenjo (Fri Jan 23 2004 - 09:05:52 PST)
- Re: AMBER: Problem using GLYCAM with sander David A. Case (Fri Jan 23 2004 - 13:41:22 PST)
- Re: AMBER: Problem using GLYCAM with sander Bimo Ario Tejo (Sat Jan 24 2004 - 07:28:15 PST)
AMBER: Which program to use to visualize the RESP Outputs derived by AMBER 7 Ilyas Yildirim (Fri Jan 23 2004 - 10:18:23 PST)
- Re: AMBER: Which program to use to visualize the RESP Outputs derived by AMBER 7 Joey Harriman (Fri Jan 23 2004 - 10:43:43 PST)
- Re: AMBER: Which program to use to visualize the RESP Outputs derived by AMBER 7 FyD (Fri Jan 23 2004 - 11:52:28 PST)
Re: AMBER: Which program to use to visualize the RESP Outputs derived by AMBER 7 Bill Ross (Fri Jan 23 2004 - 11:26:15 PST)
AMBER: phosphothreonine Youyi Peng (Fri Jan 23 2004 - 14:57:06 PST)
AMBER: Fwd: NVE & polarizable force field] Martina Roeselova (Fri Jan 23 2004 - 18:16:32 PST)
- Re: AMBER: Fwd: NVE & polarizable force field] Byungchan Kim (Fri Jan 23 2004 - 18:58:04 PST)
- Re: AMBER: Fwd: NVE & polarizable force field] darden (Sat Jan 24 2004 - 13:14:55 PST)
  - Re: AMBER: Fwd: NVE & polarizable force field] David A. Case (Sat Jan 24 2004 - 17:18:45 PST)
AMBER: Memory for AMBER 6 simulation Sergey (Sat Jan 24 2004 - 01:22:56 PST)
- Re: AMBER: Memory for AMBER 6 simulation Bimo Ario Tejo (Mon Jan 26 2004 - 02:39:25 PST)
AMBER: NTR force constant for restraint !! Jiten (Sat Jan 24 2004 - 23:37:09 PST)
AMBER: Cartitian Restraint Error Jiten (Sun Jan 25 2004 - 06:17:11 PST)
- Re: AMBER: Cartitian Restraint Error Jiten (Sun Jan 25 2004 - 06:26:31 PST)
Re: AMBER: Cartitian Restraint Error Bill Ross (Sun Jan 25 2004 - 11:39:58 PST)
- Re: AMBER: Cartitian Restraint Error Jiten (Sun Jan 25 2004 - 17:36:24 PST)
Re: AMBER: how to correctly change frcmod? David A. Case (Sun Jan 25 2004 - 17:17:47 PST)
AMBER: mopac.sh Beale, John (Mon Jan 26 2004 - 06:31:46 PST)
- Re: AMBER: mopac.sh Joey Harriman (Mon Jan 26 2004 - 06:46:31 PST)
AMBER: B factors from simulation and from cryst Vlad Cojocaru (Mon Jan 26 2004 - 08:21:50 PST)
- Re: AMBER: B factors from simulation and from cryst Joseph Nachman (Mon Jan 26 2004 - 13:23:49 PST)
AMBER: B factors --- one more explanation Vlad Cojocaru (Mon Jan 26 2004 - 08:25:47 PST)
Re: AMBER: ambpdb in AMBER7 Bill Ross (Mon Jan 26 2004 - 14:40:12 PST)
- RE: AMBER: ambpdb in AMBER7 Yong Duan (Mon Jan 26 2004 - 15:34:41 PST)
AMBER: Lattice structures in xleap Brandon Tefft (Mon Jan 26 2004 - 21:11:46 PST)
Re: AMBER: Lattice structures in xleap Bill Ross (Mon Jan 26 2004 - 23:52:38 PST)
- AMBER: trajectory file corruption John (Tue Jan 27 2004 - 03:11:54 PST)
  - Re: AMBER: trajectory file corruption Peter Oelschlaeger (Tue Jan 27 2004 - 10:27:44 PST)
  - Re: AMBER: trajectory file corruption James W. Caldwell (Tue Jan 27 2004 - 10:30:20 PST)
  - Re: AMBER: trajectory file corruption Bill Ross (Tue Jan 27 2004 - 10:54:30 PST)
    - AMBER: dielectric constant John (Wed Jan 28 2004 - 06:20:16 PST)
    - Re: AMBER: dielectric constant Martin Lepsik (Wed Jan 28 2004 - 07:42:05 PST)
Re: AMBER: Which program to use to visualize the RESP Outputs FyD (Tue Jan 27 2004 - 08:59:51 PST)
- Re: AMBER: Which program to use to visualize the RESP Outputs Ilyas Yildirim (Tue Jan 27 2004 - 10:49:01 PST)
Re: AMBER: ambpdb in AMBER7 xhu1.memphis.edu (Tue Jan 27 2004 - 09:48:37 PST)
AMBER: compilation under fedora core 1 Carsten Detering (Tue Jan 27 2004 - 10:51:26 PST)
- Re: AMBER: compilation under fedora core 1 James W. Caldwell (Tue Jan 27 2004 - 10:40:48 PST)
- AMBER: Error message in antechamber Ilyas Yildirim (Tue Jan 27 2004 - 10:44:26 PST)
AMBER: A few questions in the protein unfolding simulations using GB model Jiayun Pang (Tue Jan 27 2004 - 12:33:15 PST)
- Re: AMBER: A few questions in the protein unfolding simulations using GB model Bill Ross (Wed Jan 28 2004 - 10:21:10 PST)
  - Re: AMBER: A few questions in the protein unfolding simulations using GB model Carlos Simmerling (Wed Jan 28 2004 - 10:26:31 PST)
- RE: AMBER: A few questions in the protein unfolding simulations using GB model Bill Ross (Wed Jan 28 2004 - 10:22:55 PST)
- Re: AMBER: A few questions in the protein unfolding simulations using GB model Jiayun Pang (Thu Jan 29 2004 - 02:47:52 PST)
  - Re: AMBER: A few questions in the protein unfolding simulations using GB model Andy Purkiss (Thu Jan 29 2004 - 06:19:22 PST)
  - Re: AMBER: A few questions in the protein unfolding simulations using GB model David A. Case (Thu Jan 29 2004 - 19:59:24 PST)
Re: AMBER: A few questions in the protein unfolding simulations using GB model Bill Ross (Tue Jan 27 2004 - 13:19:10 PST)
- Re: AMBER: A few questions in the protein unfolding simulations using GB model Jiayun Pang (Wed Jan 28 2004 - 04:20:48 PST)
  - RE: AMBER: A few questions in the protein unfolding simulations using GB model florent.barbault (Wed Jan 28 2004 - 04:38:13 PST)
AMBER: SANDER - Abnormal high velocities Miguel de Federico (Wed Jan 28 2004 - 03:16:45 PST)
- Re: AMBER: SANDER - Abnormal high velocities David A. Case (Wed Jan 28 2004 - 08:31:18 PST)
- Re: AMBER: SANDER - Abnormal high velocities Carlos Simmerling (Wed Jan 28 2004 - 08:36:45 PST)
AMBER: Normal modes of protein-ligand Martin Lepsik (Wed Jan 28 2004 - 05:43:12 PST)
- Re: AMBER: Normal modes of protein-ligand bishop (Wed Jan 28 2004 - 06:44:20 PST)
- Re: AMBER: Normal modes of protein-ligand Holger Gohlke (Wed Jan 28 2004 - 11:32:49 PST)
  - Re: AMBER: Normal modes of protein-ligand Martin Lepsik (Thu Jan 29 2004 - 01:47:22 PST)
- Re: AMBER: Normal modes of protein-ligand Holger Gohlke (Wed Jan 28 2004 - 11:38:57 PST)
AMBER: LES question Lishan Yao (Wed Jan 28 2004 - 10:52:58 PST)
- Re: AMBER: LES question Carlos Simmerling (Wed Jan 28 2004 - 11:03:04 PST)
- Re: AMBER: LES question Lishan Yao (Thu Jan 29 2004 - 06:46:22 PST)
- Re: AMBER: LES question Carlos Simmerling (Thu Jan 29 2004 - 08:36:04 PST)
- Re: AMBER: LES question xiaolin cheng (Tue Feb 10 2004 - 16:14:31 PST)
- Re: AMBER: LES question Carlos Simmerling (Wed Feb 11 2004 - 05:48:48 PST)
  - Re: AMBER: LES question Lishan Yao (Wed Feb 11 2004 - 06:16:01 PST)
- Re: AMBER: LES question Carlos Simmerling (Wed Feb 11 2004 - 09:55:27 PST)
  - Re: AMBER: LES question Lishan Yao (Wed Feb 11 2004 - 11:20:54 PST)
  - Re: AMBER: LES question Lishan Yao (Wed Feb 11 2004 - 11:52:09 PST)
- Re: AMBER: LES question Carlos Simmerling (Wed Feb 11 2004 - 11:43:58 PST)
- Re: AMBER: LES question Carlos Simmerling (Wed Feb 11 2004 - 12:03:44 PST)
  - Re: AMBER: LES question Lishan Yao (Thu Feb 12 2004 - 05:59:02 PST)
AMBER: sander and mpich Thomas Exner (Thu Jan 29 2004 - 00:26:55 PST)
AMBER: CYS, CYX and CYM Nikolai Smolin (Thu Jan 29 2004 - 01:56:09 PST)
AMBER: conversion of amber trajectories to gromos /(xtc) Karin Schleinkofer (Thu Jan 29 2004 - 05:10:28 PST)
- Re: AMBER: conversion of amber trajectories to gromos /(xtc) Luis Gracia (Thu Jan 29 2004 - 12:27:48 PST)
- Re: AMBER: conversion of amber trajectories to gromos /(xtc) Bill Ross (Thu Jan 29 2004 - 12:43:45 PST)
AMBER: XLEAP L Jin (Thu Jan 29 2004 - 06:40:28 PST)
- Re: AMBER: XLEAP Martin Lepsik (Thu Jan 29 2004 - 07:43:18 PST)
- Re: AMBER: XLEAP A.B.S.M Osman gani (Thu Jan 29 2004 - 07:19:04 PST)
AMBER: Moil View on Linux Vlad Cojocaru (Thu Jan 29 2004 - 09:13:57 PST)
- Re: AMBER: Moil View on Linux Carlos Simmerling (Thu Jan 29 2004 - 09:21:20 PST)
AMBER: LES Simulations Vlad Cojocaru (Thu Jan 29 2004 - 09:18:14 PST)
- Re: AMBER: LES Simulations Carlos Simmerling (Thu Jan 29 2004 - 09:20:45 PST)
AMBER: question about LES simulation Vlad Cojocaru (Thu Jan 29 2004 - 08:43:25 PST)
AMBER: LES error Vlad Cojocaru (Thu Jan 29 2004 - 12:49:49 PST)
- Re: AMBER: LES error Carlos Simmerling (Thu Jan 29 2004 - 12:51:28 PST)
AMBER: (No subject) opitz.che.udel.edu (Thu Jan 29 2004 - 14:09:47 PST)
- Re: AMBER: (No subject) David A. Case (Thu Jan 29 2004 - 20:20:43 PST)
  - Re: AMBER: (No subject) Junmei Wang (Fri Jan 30 2004 - 07:02:50 PST)
- Re: AMBER: (No subject) opitz.che.udel.edu (Fri Jan 30 2004 - 08:21:30 PST)
  - Re: AMBER: (No subject) Vlad Cojocaru (Fri Jan 30 2004 - 08:31:10 PST)
- Re: AMBER: (No subject) opitz.che.udel.edu (Fri Jan 30 2004 - 13:32:01 PST)
  - Re: AMBER: (No subject) Junmei Wang (Fri Jan 30 2004 - 13:37:46 PST)
AMBER: test Vlad Cojocaru (Fri Jan 30 2004 - 05:39:14 PST)
Re: AMBER: sander and mpich (which compilers/mpich work) Jerry Grooms (Fri Jan 30 2004 - 15:00:22 PST)
- Re: AMBER: sander and mpich (which compilers/mpich work) Carlos Simmerling (Fri Jan 30 2004 - 15:09:09 PST)
- Re: AMBER: sander and mpich (which compilers/mpich work) Viktor Hornak (Fri Jan 30 2004 - 17:23:21 PST)
  - AMBER: Nose Hoover chain thermostat Byungchan Kim (Fri Jan 30 2004 - 17:35:08 PST)
  - Re: AMBER: sander and mpich (which compilers/mpich work) Jerry Grooms (Sat Jan 31 2004 - 12:44:30 PST)
    - Re: AMBER: sander and mpich (which compilers/mpich work) Viktor Hornak (Wed Feb 04 2004 - 11:13:13 PST)
  - Re: AMBER: sander and mpich (which compilers/mpich work) Jerry Grooms (Sat Jan 31 2004 - 15:08:57 PST)
AMBER: sander.LES on IBM SP cluster Vlad Cojocaru (Sat Jan 31 2004 - 02:40:56 PST)
- Re: AMBER: sander.LES on IBM SP cluster Carlos Simmerling (Sat Jan 31 2004 - 06:27:30 PST)
  - Re: AMBER: sander.LES on IBM SP cluster Vlad Cojocaru (Sat Jan 31 2004 - 09:18:56 PST)
    - AMBER: Installing Amber on IBM AIX cluster Vlad Cojocaru (Sat Jan 31 2004 - 10:50:30 PST)
    - AMBER: Installing Amber on IBM AIX cluster Wayne Dawson (Mon Feb 02 2004 - 22:11:49 PST)
    - Re: AMBER: sander.LES on IBM SP cluster David A. Case (Sat Jan 31 2004 - 11:02:01 PST)
    - AMBER: AMBER on IBM SP cluster Vlad Cojocaru (Sat Jan 31 2004 - 11:07:29 PST)
- Re: AMBER: sander.LES on IBM SP cluster Carlos Simmerling (Sat Jan 31 2004 - 11:07:50 PST)
  - Re: AMBER: sander.LES on IBM SP cluster Vlad Cojocaru (Sat Jan 31 2004 - 11:20:56 PST)
- Re: AMBER: sander.LES on IBM SP cluster Carlos Simmerling (Sat Jan 31 2004 - 11:29:23 PST)
AMBER: Unknown Amber Nomeclature Andrew M K Law (Sat Jan 31 2004 - 14:17:47 PST)
AMBER: DNA Beale, John (Mon Feb 02 2004 - 05:31:51 PST)
- Re: AMBER: DNA David A. Case (Mon Feb 02 2004 - 08:58:26 PST)
AMBER: convert restart to mdcrd? Karin Schleinkofer (Mon Feb 02 2004 - 06:39:40 PST)
- Re: AMBER: convert restart to mdcrd? Dr. Yong Duan (Mon Feb 02 2004 - 08:48:55 PST)
  - Re: AMBER: convert restart to mdcrd? Vlad Cojocaru (Mon Feb 02 2004 - 08:07:12 PST)
  - Re: AMBER: convert restart to mdcrd? Vlad Cojocaru (Mon Feb 02 2004 - 08:07:49 PST)
    - Re: AMBER: convert restart to mdcrd? Dr. Yong Duan (Mon Feb 02 2004 - 09:27:41 PST)
- Re: AMBER: convert restart to mdcrd? Vlad Cojocaru (Mon Feb 02 2004 - 07:33:35 PST)
- Re: AMBER: convert restart to mdcrd? Teletchéa Stéphane (Mon Feb 02 2004 - 08:17:30 PST)
AMBER: ptraj & LES Vlad Cojocaru (Mon Feb 02 2004 - 08:46:08 PST)
- Re: AMBER: ptraj & LES Michael Trieb (Mon Feb 02 2004 - 09:11:08 PST)
  - Re: AMBER: ptraj & LES Vlad Cojocaru (Mon Feb 02 2004 - 09:22:09 PST)
AMBER: LEaP- Error reading frcmod parameters. Miguel de Federico (Mon Feb 02 2004 - 10:03:00 PST)
- Re: AMBER: LEaP- Error reading frcmod parameters. David A. Case (Mon Feb 02 2004 - 10:20:43 PST)
Re: AMBER: NVE&polarizable force field Martina Roeselova (Mon Feb 02 2004 - 09:33:17 PST)
- AMBER: cell dimensions Dave S Walker (Mon Feb 02 2004 - 13:46:54 PST)
  - Re: AMBER: cell dimensions David A. Case (Thu Feb 05 2004 - 10:00:41 PST)
- Re: AMBER: NVE&polarizable force field Byungchan Kim (Tue Feb 03 2004 - 09:54:55 PST)
Re: AMBER: ANAL problem. David A. Case (Mon Feb 02 2004 - 10:51:02 PST)
AMBER: TI, angle parameters for nitrogen, frcmod Carsten Detering (Mon Feb 02 2004 - 12:38:59 PST)
- Re: AMBER: TI, angle parameters for nitrogen, frcmod David A. Case (Thu Feb 05 2004 - 09:51:39 PST)
AMBER: nucleic acid bases nonplanar during LES sim Vlad Cojocaru (Mon Feb 02 2004 - 13:17:09 PST)
- Re: AMBER: nucleic acid bases nonplanar during LES sim Carlos Simmerling (Mon Feb 02 2004 - 13:56:00 PST)
  - AMBER: temperature in DelPhi for MM-PBSA calculation Qing Zhang (Mon Feb 02 2004 - 14:54:05 PST)
    - RE: AMBER: temperature in DelPhi for MM-PBSA calculation S. Frank Yan (Mon Feb 02 2004 - 15:18:22 PST)
    - RE: AMBER: temperature in DelPhi for MM-PBSA calculation Qing Zhang (Mon Feb 02 2004 - 16:58:54 PST)
    - Re: AMBER: temperature in DelPhi for MM-PBSA calculation rluo.uci.edu (Mon Feb 02 2004 - 18:45:52 PST)
AMBER: leap - orientation of sequenced residues Sarah Wittkopp (Mon Feb 02 2004 - 17:58:33 PST)
- Re: AMBER: leap - orientation of sequenced residues David A. Case (Tue Feb 03 2004 - 09:44:50 PST)
AMBER: xleap & antechamber L Jin (Tue Feb 03 2004 - 01:46:54 PST)
- Re: AMBER: xleap & antechamber David A. Case (Thu Feb 05 2004 - 09:46:02 PST)
AMBER: protonation Nikolai Smolin (Tue Feb 03 2004 - 01:50:23 PST)
AMBER: the uses for Amber FFs a b (Tue Feb 03 2004 - 06:48:24 PST)
- Re: AMBER: the uses for Amber FFs Vlad Cojocaru (Tue Feb 03 2004 - 06:56:26 PST)
AMBER: What does this error message mean? nie beining (Tue Feb 03 2004 - 07:58:41 PST)
- Re: AMBER: What does this error message mean? nie beining (Fri Oct 31 2003 - 09:41:27 PST)
- Re: AMBER: What does this error message mean? David A. Case (Tue Feb 03 2004 - 08:12:48 PST)
- Re: AMBER: What does this error message mean? Carlos Simmerling (Tue Feb 03 2004 - 08:30:56 PST)
- Re: AMBER: What does this error message mean? Martina Roeselova (Tue Feb 03 2004 - 11:55:22 PST)
AMBER: Carnal Herbert Georg (Tue Feb 03 2004 - 08:11:28 PST)
Re: AMBER: Carnal Bill Ross (Tue Feb 03 2004 - 10:14:02 PST)
- Re: AMBER: Carnal Herbert Georg (Tue Feb 03 2004 - 11:30:33 PST)
AMBER: Amber on Redhat Enterprise Mingfeng Yang (Tue Feb 03 2004 - 10:23:44 PST)
Re: AMBER: What does this error message mean? Bill Ross (Tue Feb 03 2004 - 10:40:15 PST)
AMBER: A general question aini.UMDNJ.EDU (Tue Feb 03 2004 - 15:49:06 PST)
- Re: AMBER: A general question Carlos Simmerling (Tue Feb 03 2004 - 16:13:09 PST)
  - Re: AMBER: A general question aini.UMDNJ.EDU (Tue Feb 03 2004 - 17:39:44 PST)
    - Re: AMBER: questions parm94/99 ff secondary structure Wayne Dawson (Thu Feb 05 2004 - 23:50:07 PST)
    - Re: AMBER: questions parm94/99 ff secondary structure Carlos Simmerling (Fri Feb 06 2004 - 04:58:45 PST)
AMBER: rstdip Martina Roeselova (Wed Feb 04 2004 - 09:57:18 PST)
- Re: AMBER: rstdip Scott Brozell (Wed Feb 04 2004 - 10:19:45 PST)
AMBER: carnal Herbert Georg (Wed Feb 04 2004 - 11:18:37 PST)
Re: AMBER: carnal Bill Ross (Wed Feb 04 2004 - 11:40:31 PST)
- AMBER: How to remove Cl- ions Do Anh Tuan (Fri Feb 06 2004 - 02:38:41 PST)
  - Re: AMBER: How to remove Cl- ions Itziar Maestre Asenjo (Fri Feb 06 2004 - 02:58:05 PST)
  - Re: AMBER: How to remove Cl- ions Vlad Cojocaru (Fri Feb 06 2004 - 03:09:52 PST)
  - AMBER: How to remove Cl- ions Wayne Dawson (Fri Feb 06 2004 - 03:19:33 PST)
- Re: AMBER: carnal Bill Ross (Mon Feb 16 2004 - 10:37:54 PST)
- Re: AMBER: carnal Bill Ross (Tue Feb 24 2004 - 09:49:16 PST)
AMBER: antechamber + mopac error Carsten Detering (Wed Feb 04 2004 - 18:57:48 PST)
- RE: AMBER: antechamber + mopac error Meg McCarrick (Thu Feb 05 2004 - 09:12:42 PST)
- Re: AMBER: antechamber + mopac error David A. Case (Thu Feb 05 2004 - 09:21:11 PST)
AMBER: ptraj Julien Pecher (Thu Feb 05 2004 - 00:46:09 PST)
- Re: AMBER: ptraj xueping (Fri Mar 11 2005 - 23:08:37 PST)
Re: AMBER: ptraj Bill Ross (Thu Feb 05 2004 - 01:43:59 PST)
AMBER: PMEMD and nmropt=1 aldo jongejan (Thu Feb 05 2004 - 03:52:29 PST)
- Re: AMBER: PMEMD and nmropt=1 Robert Duke (Thu Feb 05 2004 - 04:39:58 PST)
- RE: AMBER: PMEMD and nmropt=1 Kristina Furse (Thu Feb 05 2004 - 13:19:52 PST)
  - Re: AMBER: PMEMD and nmropt=1 Robert Duke (Thu Feb 05 2004 - 13:45:07 PST)
  - Re: AMBER: PMEMD and nmropt=1 David A. Case (Thu Feb 05 2004 - 17:29:41 PST)
Re: AMBER: Re: ANAL problem David A. Case (Thu Feb 05 2004 - 09:36:05 PST)
- Re: AMBER: Re: ANAL problem Bill Ross (Thu Feb 05 2004 - 10:07:58 PST)
AMBER: antechamber error in test / differences in prmtop files Carsten Detering (Thu Feb 05 2004 - 12:07:07 PST)
- Re: AMBER: antechamber error in test / differences in prmtop files David A. Case (Thu Feb 05 2004 - 13:11:53 PST)
AMBER: ptraj and dipoles Herbert Georg (Thu Feb 05 2004 - 13:40:24 PST)
- Re: AMBER: ptraj and dipoles David A. Case (Thu Feb 05 2004 - 23:11:50 PST)
  - Re: AMBER: ptraj and dipoles Herbert Georg (Fri Feb 06 2004 - 03:47:12 PST)
    - AMBER: ptraj and dipoles.... Herbert Georg (Fri Feb 06 2004 - 13:12:10 PST)
AMBER: MCSS Chen, Ya (Thu Feb 05 2004 - 20:33:48 PST)
- Re: AMBER: MCSS David A. Case (Thu Feb 05 2004 - 23:12:47 PST)
AMBER: water as a "ligand" in GBSA and MM-PBSA? Giulio Rastelli (Fri Feb 06 2004 - 09:41:50 PST)
AMBER: How to remove Cl- ions Do Anh Tuan (Fri Feb 06 2004 - 05:24:10 PST)
Re: AMBER: How to remove Cl- ions Bill Ross (Fri Feb 06 2004 - 08:35:27 PST)
AMBER: off-subject ROCKS/Qbank James W. Caldwell (Fri Feb 06 2004 - 12:03:09 PST)
Fwd: Re: AMBER: Lattice structures in xleap Brandon Tefft (Fri Feb 06 2004 - 13:27:50 PST)
- Re: Fwd: Re: AMBER: Lattice structures in xleap David A. Case (Fri Feb 06 2004 - 13:54:07 PST)
- Re: Fwd: Re: AMBER: Lattice structures in xleap Bill Ross (Fri Feb 06 2004 - 14:21:12 PST)
AMBER: antechamber + mopac +scf failed Carsten Detering (Fri Feb 06 2004 - 16:11:22 PST)
AMBER: antechamber + mopac + MAXIMUM NUMBER OF ATOMIC ORBITALS EXCEEDED Carsten Detering (Fri Feb 06 2004 - 17:50:46 PST)
- Re: AMBER: antechamber + mopac + MAXIMUM NUMBER OF ATOMIC ORBITALS EXCEEDED David A. Case (Sat Feb 07 2004 - 08:33:48 PST)
AMBER: adding ions to nucleic acids a b (Sun Feb 08 2004 - 02:47:19 PST)
- Re: AMBER: adding ions to nucleic acids Vlad Cojocaru (Sun Feb 08 2004 - 04:25:55 PST)
AMBER: question about the average structure from ptraj aini.UMDNJ.EDU (Sun Feb 08 2004 - 11:33:23 PST)
- Re: AMBER: question about the average structure from ptraj Thomas E. Cheatham, III (Sun Feb 08 2004 - 11:49:23 PST)
Re: AMBER: adding ions to nucleic acids Bill Ross (Sun Feb 08 2004 - 11:40:50 PST)
- Re: AMBER: adding ions to nucleic acids Dr. Yong Duan (Tue Feb 10 2004 - 21:54:58 PST)
Re: AMBER: question about the average structure from ptraj Bill Ross (Sun Feb 08 2004 - 11:47:11 PST)
AMBER: dipole moment in ptraj Herbert Georg (Sun Feb 08 2004 - 10:42:07 PST)
- Re: AMBER: dipole moment in ptraj Thomas E. Cheatham, III (Sun Feb 08 2004 - 15:00:55 PST)
AMBER: Aldo's PMEMD bug Robert Duke (Mon Feb 09 2004 - 05:53:43 PST)
- Re: AMBER: Aldo's PMEMD bug aldo jongejan (Mon Feb 09 2004 - 07:44:39 PST)
AMBER: antechamber error jwfang (Mon Feb 09 2004 - 07:50:17 PST)
- Re: AMBER: antechamber error David A. Case (Mon Feb 09 2004 - 08:22:07 PST)
- Re: AMBER: antechamber error Carsten Detering (Mon Feb 09 2004 - 09:38:41 PST)
AMBER: antechamber + FAILED TO ACHIEVE SCF Carsten Detering (Mon Feb 09 2004 - 11:17:41 PST)
- Re: AMBER: antechamber + FAILED TO ACHIEVE SCF Junmei Wang (Mon Feb 09 2004 - 11:27:02 PST)
  - Re: AMBER: antechamber + FAILED TO ACHIEVE SCF Carsten Detering (Mon Feb 09 2004 - 14:02:10 PST)
  - Re: AMBER: antechamber + FAILED TO ACHIEVE SCF David A. Case (Mon Feb 09 2004 - 14:17:49 PST)
AMBER: Nmode convergence ML (Mon Feb 09 2004 - 23:36:27 PST)
- Re: AMBER: Nmode convergence ML (Tue Feb 10 2004 - 07:26:12 PST)
- Re: AMBER: Nmode convergence David A. Case (Tue Feb 10 2004 - 08:34:17 PST)
  - Re: AMBER: Nmode convergence ML (Wed Feb 11 2004 - 00:14:31 PST)
AMBER: Temperature in Nmode ML (Tue Feb 10 2004 - 07:25:12 PST)
- Re: AMBER: Temperature in Nmode David A. Case (Tue Feb 10 2004 - 08:42:06 PST)
  - Re: AMBER: Temperature in Nmode ML (Tue Feb 10 2004 - 12:46:19 PST)
AMBER: minimization output L Jin (Tue Feb 10 2004 - 08:36:25 PST)
- Re: AMBER: minimization output David A. Case (Tue Feb 10 2004 - 13:05:59 PST)
  - Re: AMBER: minimization output L Jin (Fri Feb 13 2004 - 01:49:52 PST)
- Re: AMBER: minimization output Anna Schrey (Fri Feb 20 2004 - 01:07:40 PST)
  - Re: AMBER: minimization output L Jin (Fri Feb 20 2004 - 02:36:35 PST)
AMBER: LES question Lishan Yao (Tue Feb 10 2004 - 12:47:20 PST)
- Re: AMBER: LES question Vlad Cojocaru (Tue Feb 10 2004 - 13:01:12 PST)
  - Re: AMBER: LES question Lishan Yao (Tue Feb 10 2004 - 13:02:18 PST)
AMBER: Nitrogen vdw type Terry Downing (Tue Feb 10 2004 - 14:56:37 PST)
AMBER: Installing AMBER on SGI Octane 2-CPU - erfcfun.c compile prob. Joseph E. Maxwell (Tue Feb 10 2004 - 15:36:26 PST)
- Re: AMBER: Installing AMBER on SGI Octane 2-CPU - erfcfun.c compile prob. David A. Case (Tue Feb 10 2004 - 15:54:45 PST)
AMBER: Box of mixed solvant FyD (Tue Feb 10 2004 - 20:18:42 PST)
- Re: AMBER: Box of mixed solvant Dr. Yong Duan (Tue Feb 10 2004 - 22:09:28 PST)
AMBER: atom type for GBSA aini.UMDNJ.EDU (Wed Feb 11 2004 - 07:13:04 PST)
- Re: AMBER: atom type for GBSA David A. Case (Wed Feb 11 2004 - 09:33:04 PST)
AMBER: GBSA frequency update Sergio E. Wong (Wed Feb 11 2004 - 15:29:10 PST)
- Re: AMBER: GBSA frequency update David A. Case (Wed Feb 11 2004 - 22:09:34 PST)
AMBER: Run calculations for protein in Amber Małgorzata Jarończyk (Thu Feb 12 2004 - 01:18:20 PST)
- Re: AMBER: Run calculations for protein in Amber Carlos Simmerling (Thu Feb 12 2004 - 05:18:32 PST)
AMBER: ptraj Karin Schleinkofer (Thu Feb 12 2004 - 02:57:47 PST)
- Re: AMBER: ptraj Vlad Cojocaru (Thu Feb 12 2004 - 03:45:55 PST)
- Re: AMBER: ptraj Thomas E. Cheatham, III (Thu Feb 12 2004 - 10:03:36 PST)
Re: AMBER: Run calculations for protein in Amber-distance dependent dielectric function Małgorzata Jarończyk (Thu Feb 12 2004 - 06:28:59 PST)
- Re: AMBER: Run calculations for protein in Amber-distance dependent dielectric function Vlad Cojocaru (Thu Feb 12 2004 - 06:34:31 PST)
- Re: AMBER: Run calculations for protein in Amber-distance dependent dielectric function David A. Case (Thu Feb 12 2004 - 08:41:16 PST)
AMBER: TER in amber Lishan Yao (Thu Feb 12 2004 - 07:04:03 PST)
- Re: AMBER: TER in amber Vlad Cojocaru (Thu Feb 12 2004 - 07:56:04 PST)
  - Re: AMBER: TER in amber Lishan Yao (Thu Feb 12 2004 - 08:17:02 PST)
    - Re: AMBER: TER in amber Vlad Cojocaru (Fri Feb 13 2004 - 00:35:41 PST)
- Re: AMBER: TER in amber David A. Case (Thu Feb 12 2004 - 08:56:45 PST)
  - Re: AMBER: TER in amber Lishan Yao (Thu Feb 12 2004 - 10:08:29 PST)
  - Re: AMBER: TER in amber Lishan Yao (Thu Feb 12 2004 - 09:12:45 PST)
AMBER: MM-PBSA: molecular charges and active site water Anselm Horn (Thu Feb 12 2004 - 07:23:05 PST)
- Re: AMBER: MM-PBSA: molecular charges and active site water David A. Case (Thu Feb 12 2004 - 20:06:56 PST)
  - Re: AMBER: MM-PBSA: molecular charges and active site water ML (Thu Feb 12 2004 - 23:30:23 PST)
AMBER: center of mass in CARNAL Herbert Georg (Thu Feb 12 2004 - 08:15:17 PST)
AMBER: neutrality of charge in AMBER 7 Sichun Yang (Thu Feb 12 2004 - 12:51:51 PST)
- Re: AMBER: neutrality of charge in AMBER 7 David A. Case (Sat Feb 14 2004 - 12:10:22 PST)
AMBER: Re: To David Case Małgorzata Jarończyk (Fri Feb 13 2004 - 03:25:52 PST)
AMBER: minimizating complex-protein with AMBER susan.costantini.unina2.it (Sun Feb 15 2004 - 01:27:00 PST)
- Re: AMBER: minimizating complex-protein with AMBER David A. Case (Sun Feb 15 2004 - 21:14:02 PST)
AMBER: problem with tleap in Amber donna j (Sun Feb 15 2004 - 18:44:25 PST)
- Re: AMBER: problem with tleap in Amber David A. Case (Sun Feb 15 2004 - 21:10:31 PST)
AMBER: MM-PBSA:??Decomposition of receptor energies?? ML (Mon Feb 16 2004 - 01:18:17 PST)
- Re: AMBER: MM-PBSA:??Decomposition of receptor energies?? Holger Gohlke (Mon Feb 16 2004 - 02:09:07 PST)
  - AMBER: SIGSEGV John (Mon Feb 16 2004 - 02:43:36 PST)
    - Re: AMBER: SIGSEGV David A. Case (Mon Feb 16 2004 - 08:30:18 PST)
    - AMBER: John (Tue Feb 17 2004 - 02:05:22 PST)
  - Re: AMBER: MM-PBSA:??Decomposition of receptor energies?? ML (Mon Feb 16 2004 - 07:59:04 PST)
- Re: AMBER: MM-PBSA:??Decomposition of receptor energies?? Holger Gohlke (Mon Feb 16 2004 - 23:24:25 PST)
AMBER: TIP4P Nikolai Smolin (Mon Feb 16 2004 - 02:58:56 PST)
- Re: AMBER: TIP4P David A. Case (Mon Feb 16 2004 - 08:36:37 PST)
AMBER: IFC COMPILER Obdulia Rabal (Mon Feb 16 2004 - 04:54:00 PST)
- Re: AMBER: IFC COMPILER Robert Duke (Mon Feb 16 2004 - 05:18:03 PST)
AMBER: carnal Julien Pecher (Mon Feb 16 2004 - 05:17:33 PST)
AMBER: DIELC L Jin (Mon Feb 16 2004 - 05:51:35 PST)
AMBER: bad crd file John (Mon Feb 16 2004 - 07:30:26 PST)
AMBER: image in ptraj Lishan Yao (Mon Feb 16 2004 - 08:11:25 PST)
AMBER: TIP4P extended Nikolai Smolin (Mon Feb 16 2004 - 09:06:30 PST)
- Re: AMBER: TIP4P extended Sarah Wittkopp (Mon Feb 16 2004 - 09:21:15 PST)
- Re: AMBER: TIP4P extended David A. Case (Mon Feb 16 2004 - 09:37:32 PST)
AMBER: TIP4P extended Nikolai Smolin (Mon Feb 16 2004 - 09:10:19 PST)
Re: AMBER: bad crd file Bill Ross (Mon Feb 16 2004 - 10:51:57 PST)
AMBER: problem with tleap in Amber donna j (Sun Feb 15 2004 - 19:01:27 PST)
AMBER: saveamberparm warning in leap? opitz.che.udel.edu (Mon Feb 16 2004 - 13:24:45 PST)
- Re: AMBER: saveamberparm warning in leap? David A. Case (Mon Feb 16 2004 - 17:04:17 PST)
AMBER: multiple messages on the amber reflector David A. Case (Mon Feb 16 2004 - 15:33:40 PST)
AMBER: moil-view question S. Frank Yan (Mon Feb 16 2004 - 18:43:57 PST)
- Re: AMBER: moil-view question Carlos Simmerling (Tue Feb 17 2004 - 05:38:59 PST)
- Re: AMBER: moil-view question Teletchéa Stéphane (Tue Feb 17 2004 - 05:49:31 PST)
AMBER: flexible water potential Herbert Georg (Tue Feb 17 2004 - 03:22:12 PST)
AMBER: Close contact warnings L Jin (Tue Feb 17 2004 - 06:29:57 PST)
- Re: AMBER: Close contact warnings David A. Case (Tue Feb 17 2004 - 08:39:22 PST)
  - Re: AMBER: Close contact warnings L Jin (Tue Feb 17 2004 - 10:14:37 PST)
    - Re: AMBER: Close contact warnings David A. Case (Tue Feb 17 2004 - 10:37:06 PST)
    - Re: AMBER: Close contact warnings L Jin (Wed Feb 18 2004 - 02:14:55 PST)
    - Re: AMBER: Close contact warnings Michael George Lerner (Wed Feb 18 2004 - 05:58:50 PST)
    - Re: AMBER: Close contact warnings L Jin (Wed Feb 18 2004 - 08:55:55 PST)
    - Re: AMBER: Close contact warnings David A. Case (Wed Feb 18 2004 - 11:34:24 PST)
- Re: AMBER: Close contact warnings Bill Ross (Wed Feb 18 2004 - 10:20:38 PST)
  - Re: AMBER: Close contact warnings L Jin (Wed Feb 18 2004 - 10:56:49 PST)
    - RE: AMBER: Close contact warnings Yong Duan (Wed Feb 18 2004 - 11:07:36 PST)
    - RE: AMBER: Close contact warnings L Jin (Thu Feb 19 2004 - 07:11:54 PST)
    - Re: AMBER: Close contact warnings David A. Case (Thu Feb 19 2004 - 08:30:15 PST)
    - AMBER: prep files for modified bases Wen Li (Thu Feb 19 2004 - 08:58:01 PST)
    - Re: AMBER: prep files for modified bases David A. Case (Thu Feb 19 2004 - 12:23:41 PST)
- Re: AMBER: Close contact warnings Bill Ross (Wed Feb 18 2004 - 11:29:19 PST)
- RE: AMBER: Close contact warnings Bill Ross (Thu Feb 19 2004 - 11:25:33 PST)
  - AMBER: Build a H+ ion in Leap? Xin Chen (Thu Feb 19 2004 - 11:40:40 PST)
AMBER: RESP charges for protein fragment Tom Turner (Tue Feb 17 2004 - 08:20:15 PST)
AMBER: How to add H+ ion in leap? xinchen (Tue Feb 17 2004 - 11:46:10 PST)
Re: AMBER: center of mass in CARNAL Bill Ross (Tue Feb 17 2004 - 12:25:43 PST)
Re: AMBER: How to add H+ ion in leap? Bill Ross (Tue Feb 17 2004 - 12:29:17 PST)
- Re: AMBER: How to add H+ ion in leap? xinchen (Tue Feb 17 2004 - 12:43:18 PST)
- Re: AMBER: How to add H+ ion in leap? Bill Ross (Tue Feb 17 2004 - 13:09:01 PST)
AMBER: (no subject) ThuZar Lwin (Tue Feb 17 2004 - 12:52:40 PST)
Re: AMBER: (no subject) Bill Ross (Tue Feb 17 2004 - 13:17:39 PST)
- Re: AMBER: (no subject) ThuZar Lwin (Tue Feb 17 2004 - 13:33:30 PST)
AMBER: multiple messages on the amber reflector Amber Administration (Tue Feb 17 2004 - 14:27:52 PST)
AMBER: contributed parameters (modified base - PSU) Shau Grossman (Tue Feb 17 2004 - 18:14:16 PST)
- RE: AMBER: contributed parameters (modified base - PSU) S. Frank Yan (Tue Feb 17 2004 - 18:32:56 PST)
- Re: AMBER: contributed parameters FyD (Wed Feb 18 2004 - 09:12:04 PST)
  - Re: AMBER: contributed parameters Shau Grossman (Thu Feb 19 2004 - 18:55:46 PST)
    - AMBER: ions94.lib file Wen Li (Fri Feb 20 2004 - 09:10:06 PST)
    - Re: AMBER: contributed parameters FyD (Fri Feb 20 2004 - 09:08:34 PST)
    - Re: AMBER: contributed parameters Shau Grossman (Fri Feb 20 2004 - 13:46:04 PST)
    - Re: AMBER: contributed parameters FyD (Fri Feb 20 2004 - 16:05:48 PST)
    - AMBER: R.E.D. Shau Grossman (Mon Feb 23 2004 - 17:20:44 PST)
    - Re: AMBER: R.E.D. FyD (Mon Feb 23 2004 - 17:42:13 PST)
    - Re: AMBER: R.E.D. Shau Grossman (Mon Feb 23 2004 - 18:13:43 PST)
    - Re: AMBER: R.E.D. FyD (Tue Feb 24 2004 - 08:16:57 PST)
AMBER: Segmentation fault in SaveAmberParm xinchen (Tue Feb 17 2004 - 19:31:35 PST)
- Re: AMBER: Segmentation fault in SaveAmberParm Xin Chen (Wed Feb 18 2004 - 11:12:53 PST)
AMBER: histidine and its various forms Stern, Julie (Wed Feb 18 2004 - 06:38:31 PST)
- Re: AMBER: histidine and its various forms David A. Case (Wed Feb 18 2004 - 07:58:44 PST)
- Re: AMBER: histidine and its various forms Peter Oelschlaeger (Wed Feb 18 2004 - 10:10:49 PST)
AMBER: sander + ewald bomb Carsten Detering (Wed Feb 18 2004 - 11:20:51 PST)
- Re: AMBER: sander + ewald bomb Michael Crowley (Wed Feb 18 2004 - 13:13:42 PST)
- Re: AMBER: sander + ewald bomb David A. Case (Wed Feb 18 2004 - 14:00:40 PST)
AMBER: GLYCAM web site Scott Brozell (Wed Feb 18 2004 - 12:00:39 PST)
AMBER: MD simulations with 2 molecules Joey Harriman (Wed Feb 18 2004 - 12:32:47 PST)
- Re: AMBER: MD simulations with 2 molecules David A. Case (Wed Feb 18 2004 - 14:15:04 PST)
AMBER: check unit + saveamberparm Carsten Detering (Wed Feb 18 2004 - 18:21:58 PST)
- re: AMBER: check unit + saveamberparm S. Frank Yan (Fri Feb 20 2004 - 16:17:41 PST)
AMBER: tmd question hj zou (Wed Feb 18 2004 - 18:58:45 PST)
- Re: AMBER: tmd question Carlos Simmerling (Thu Feb 19 2004 - 08:17:51 PST)
AMBER: mm_pbsa question hj zou (Wed Feb 18 2004 - 19:22:00 PST)
AMBER: pmf calculation using gibbs. Myunggi Yi (Wed Feb 18 2004 - 21:22:46 PST)
- Re: AMBER: pmf calculation using gibbs. David A. Case (Wed Feb 18 2004 - 20:45:57 PST)
  - Re: AMBER: pmf calculation using gibbs. Myunggi Yi (Thu Feb 19 2004 - 07:13:30 PST)
    - Re: AMBER: pmf calculation using gibbs. David A. Case (Thu Feb 19 2004 - 08:27:33 PST)
Re: AMBER: compiling software(RESP) on MAC G5 Scott Brozell (Wed Feb 18 2004 - 21:36:06 PST)
- Re: AMBER: compiling software(RESP) on MAC G5 FyD (Thu Feb 19 2004 - 08:27:54 PST)
- Re: AMBER: compiling software(RESP) on MAC G5 James W. Caldwell (Thu Feb 19 2004 - 10:50:28 PST)
- Re: AMBER: compiling software(RESP) on MAC G5 David A. Case (Thu Feb 19 2004 - 12:21:39 PST)
  - AMBER: how to add force field parameters Ioana Cozmuta (Thu Feb 19 2004 - 12:27:02 PST)
  - Re: AMBER: compiling software(RESP) on MAC G5 Lifeng Tian.PantherServer (Thu Feb 19 2004 - 12:41:05 PST)
- AMBER: compiling xleap on MAC OS X.3 Yunfeng Hu (Wed Mar 03 2004 - 14:19:57 PST)
  - Re: AMBER: compiling xleap on MAC OS X.3 Bill Ross (Wed Mar 03 2004 - 15:16:53 PST)
AMBER: LCPO parameters in gbsa Giulio Rastelli (Thu Feb 19 2004 - 08:53:56 PST)
- Re: AMBER: LCPO parameters in gbsa David A. Case (Mon Feb 23 2004 - 10:51:46 PST)
AMBER: distance-aromatic ring John (Thu Feb 19 2004 - 03:03:56 PST)
AMBER: LES Petr Jeřábek (Thu Feb 19 2004 - 10:10:50 PST)
- Re: AMBER: LES Carlos Simmerling (Thu Feb 19 2004 - 12:26:21 PST)
- Re: AMBER: LES Petr Jeřábek (Thu Feb 19 2004 - 13:08:38 PST)
  - Re: AMBER: LES Viktor Hornak (Thu Feb 19 2004 - 13:30:32 PST)
- Re: AMBER: LES Carlos Simmerling (Thu Feb 19 2004 - 13:11:58 PST)
- Re: AMBER: LES Petr Jeřábek (Thu Feb 19 2004 - 14:10:00 PST)
- Re: AMBER: LES Carlos Simmerling (Thu Feb 19 2004 - 14:13:07 PST)
Re: AMBER: distance-aromatic ring Bill Ross (Thu Feb 19 2004 - 11:41:32 PST)
Re: AMBER: Build a H+ ion in Leap? Bill Ross (Thu Feb 19 2004 - 12:00:38 PST)
- Re: AMBER: Build a H+ ion in Leap? xinchen (Thu Feb 19 2004 - 12:19:20 PST)
- Re: AMBER: Build a H+ ion in Leap? Bill Ross (Thu Feb 19 2004 - 13:22:08 PST)
AMBER: The charge given by xleap from amber 5 Ben Cossins (Fri Feb 20 2004 - 04:25:55 PST)
AMBER: LES methodology question Vlad Cojocaru (Fri Feb 20 2004 - 04:12:14 PST)
- Re: AMBER: LES methodology question Carlos Simmerling (Fri Feb 20 2004 - 05:01:06 PST)
AMBER: Defining residues opitz.che.udel.edu (Sat Feb 21 2004 - 20:34:56 PST)
- Re: AMBER: Defining residues David A. Case (Mon Feb 23 2004 - 08:49:58 PST)
- Re: AMBER: Defining residues Bill Ross (Mon Feb 23 2004 - 10:04:33 PST)
- Re: AMBER: Defining residues opitz.che.udel.edu (Mon Feb 23 2004 - 11:02:58 PST)
  - Re: AMBER: Defining residues John Bushnell (Mon Feb 23 2004 - 12:44:44 PST)
- Re: AMBER: Defining residues Bill Ross (Mon Feb 23 2004 - 12:14:46 PST)
- Re: AMBER: Defining residues opitz.che.udel.edu (Mon Feb 23 2004 - 13:35:44 PST)
  - Re: AMBER: Defining residues John Bushnell (Mon Feb 23 2004 - 14:19:48 PST)
- Re: AMBER: Defining residues opitz.che.udel.edu (Mon Feb 23 2004 - 13:47:51 PST)
- Re: AMBER: Defining residues Bill Ross (Mon Feb 23 2004 - 14:39:48 PST)
  - Re: AMBER: Defining residues John Bushnell (Mon Feb 23 2004 - 15:39:46 PST)
AMBER: xleap don't recognize my residue/atom scopio (Sun Feb 22 2004 - 03:18:42 PST)
- Re: AMBER: xleap don't recognize my residue/atom Rhonda Torres (Sun Feb 22 2004 - 14:23:59 PST)
  - Re: AMBER: xleap don't recognize my residue/atom scopio (Tue Mar 02 2004 - 00:00:31 PST)
    - RE: AMBER: xleap don't recognize my residue/atom Ross Walker (Tue Mar 02 2004 - 09:44:13 PST)
    - RE: AMBER: xleap don't recognize my residue/atom Rhonda Torres (Tue Mar 02 2004 - 10:11:07 PST)
AMBER: Can anybody help me with CHARMM Gabbar Daaku (Sun Feb 22 2004 - 19:13:09 PST)
- Re: AMBER: Can anybody help me with CHARMM Tru Huynh (Wed Feb 25 2004 - 05:36:18 PST)
Re: AMBER: Can anybody help me with CHARMM Piotr Cieplak (Sun Feb 22 2004 - 19:49:21 PST)
AMBER: How to add ACE and NME groups? Małgorzata Jarończyk (Mon Feb 23 2004 - 01:47:00 PST)
- Re: AMBER: How to add ACE and NME groups? David A. Case (Mon Feb 23 2004 - 08:47:05 PST)
- Re: AMBER: How to add ACE and NME groups? Ben Cossins (Tue Feb 24 2004 - 08:47:43 PST)
AMBER: protein - fractional native contacts uddhavesh bhaskar sonavane (Mon Feb 23 2004 - 03:50:06 PST)
AMBER: pka calculation hj zou (Mon Feb 23 2004 - 05:33:00 PST)
AMBER: Thermostat comparison ? MD Tyka, Biochemistry (Mon Feb 23 2004 - 09:41:56 PST)
AMBER: how to use prep file Fang, Jianwen (Mon Feb 23 2004 - 11:15:19 PST)
- RE: AMBER: how to use prep file Kristina Furse (Mon Feb 23 2004 - 12:14:20 PST)
- Re: AMBER: how to use prep file David A. Case (Mon Feb 23 2004 - 12:19:30 PST)
- RE: AMBER: how to use prep file Bill Ross (Mon Feb 23 2004 - 12:30:37 PST)
AMBER: problem with frcmod file donna j (Mon Feb 23 2004 - 13:47:12 PST)
- Re: AMBER: problem with frcmod file David A. Case (Mon Feb 23 2004 - 14:43:59 PST)
- Re: AMBER: problem with frcmod file donna j (Thu Feb 26 2004 - 10:23:25 PST)
  - Re: AMBER: problem with frcmod file James W. Caldwell (Thu Feb 26 2004 - 10:45:44 PST)
    - Re: AMBER: problem with frcmod file donna j (Sun Feb 29 2004 - 11:43:24 PST)
Re: AMBER: problem with frcmod file Bill Ross (Mon Feb 23 2004 - 14:44:08 PST)
AMBER: Can you write me how can I add the ACE and NMe groups in the Xleap? Małgorzata Jarończyk (Tue Feb 24 2004 - 06:59:46 PST)
AMBER: carnal Youyi Peng (Tue Feb 24 2004 - 08:36:11 PST)
AMBER: add Na+ L Jin (Tue Feb 24 2004 - 10:23:55 PST)
- RE: AMBER: add Na+ Ross Walker (Tue Feb 24 2004 - 10:42:28 PST)
  - RE: AMBER: add Na+ L Jin (Tue Feb 24 2004 - 11:29:36 PST)
    - Re: AMBER: add Na+ David A. Case (Tue Feb 24 2004 - 11:35:06 PST)
- RE: AMBER: add Na+ Bill Ross (Tue Feb 24 2004 - 11:07:07 PST)
- RE: AMBER: add Na+ Bill Ross (Tue Feb 24 2004 - 11:33:34 PST)
  - RE: AMBER: add Na+ L Jin (Wed Feb 25 2004 - 02:33:02 PST)
- RE: AMBER: add Na+ Bill Ross (Wed Feb 25 2004 - 10:31:43 PST)
AMBER: Star like (branching) molecule opitz.che.udel.edu (Tue Feb 24 2004 - 14:54:45 PST)
- Re: AMBER: Star like (branching) molecule John Bushnell (Tue Feb 24 2004 - 15:33:45 PST)
Re: AMBER: Star like (branching) molecule Bill Ross (Tue Feb 24 2004 - 15:40:13 PST)
- Re: AMBER: Star like (branching) molecule Bill Ross (Tue Feb 24 2004 - 15:51:10 PST)
AMBER: PGA Beale, John (Wed Feb 25 2004 - 05:09:46 PST)
AMBER: NMR restraints-Floating point exception John (Wed Feb 25 2004 - 06:44:52 PST)
- Re: AMBER: NMR restraints-Floating point exception David A. Case (Wed Feb 25 2004 - 08:17:46 PST)
- RE: AMBER: NMR restraints-Floating point exception John (Wed Feb 25 2004 - 10:19:25 PST)
AMBER: pmf calculation using gibbs Myunggi Yi (Wed Feb 25 2004 - 08:47:25 PST)
- Re: AMBER: pmf calculation using gibbs David Smith (Thu Feb 26 2004 - 00:57:02 PST)
AMBER: Errors when running tleap Ann P (Wed Feb 25 2004 - 13:13:53 PST)
- RE: AMBER: Errors when running tleap Ann P (Thu Feb 26 2004 - 11:21:03 PST)
- RE: AMBER: Errors when running tleap Bill Ross (Thu Feb 26 2004 - 11:47:05 PST)
Re: AMBER: Errors when running tleap Bill Ross (Wed Feb 25 2004 - 13:31:54 PST)
AMBER: averaged structure with unknown elements Youyi Peng (Wed Feb 25 2004 - 13:32:54 PST)
- Re: AMBER: averaged structure with unknown elements David A. Case (Wed Feb 25 2004 - 14:15:25 PST)
Re: AMBER: averaged structure with unknown elements Bill Ross (Wed Feb 25 2004 - 13:49:40 PST)
AMBER: mmpbsa qustion hj zou (Wed Feb 25 2004 - 17:23:37 PST)
- Re: AMBER: mmpbsa qustion Holger Gohlke (Wed Feb 25 2004 - 23:29:06 PST)
  - Re: AMBER: mmpbsa qustion James W. Caldwell (Thu Feb 26 2004 - 10:06:13 PST)
AMBER: size.h error Emmanuel Giudice (Thu Feb 26 2004 - 13:15:20 PST)
- Re: AMBER: size.h error Surjit Dixit (Thu Feb 26 2004 - 13:53:20 PST)
- Re: AMBER: size.h error David A. Case (Thu Feb 26 2004 - 14:48:29 PST)
AMBER: sander + vlimit exceed... Carsten Detering (Thu Feb 26 2004 - 15:16:31 PST)
- Re: AMBER: sander + vlimit exceed... David A. Case (Mon Mar 01 2004 - 06:50:23 PST)
AMBER: pka calculation hj zou (Fri Feb 27 2004 - 18:42:34 PST)
- Re: AMBER: pka calculation Florian Barth (Sat Feb 28 2004 - 07:46:04 PST)
AMBER: PB in mm-pbsa Sue Heavner (Sat Feb 28 2004 - 08:30:05 PST)
- Re: AMBER: PB in mm-pbsa Holger Gohlke (Sun Feb 29 2004 - 06:02:29 PST)
AMBER: Jiten (Mon Mar 01 2004 - 06:04:17 PST)
- Re: AMBER: ML (Mon Mar 01 2004 - 06:49:18 PST)
(no subject) Job Success (Mon Mar 01 2004 - 06:17:29 PST)
AMBER: GIBBS + vlimit exceeded Miguel de Federico (Mon Mar 01 2004 - 09:17:44 PST)
AMBER: ptraj Carsten Detering (Mon Mar 01 2004 - 09:23:26 PST)
- RE: AMBER: ptraj Ross Walker (Mon Mar 01 2004 - 15:25:41 PST)
  - Re: AMBER: ptraj Carsten Detering (Tue Mar 02 2004 - 10:48:35 PST)
Re: AMBER: Piotr Cieplak (Mon Mar 01 2004 - 09:38:49 PST)
- Re: AMBER: Jiten (Mon Mar 01 2004 - 16:14:13 PST)
  - AMBER: NMODE COMPILATION Obdulia Rabal (Mon Mar 15 2004 - 02:58:11 PST)
    - Re: AMBER: NMODE COMPILATION Anselm Horn (Mon Mar 15 2004 - 03:34:50 PST)
- Re: AMBER: Bill Ross (Mon Aug 30 2004 - 14:33:38 PDT)
AMBER: production input file Ryan Ye (Mon Mar 01 2004 - 10:58:48 PST)
- Re: AMBER: production input file darden (Mon Mar 01 2004 - 14:32:35 PST)
AMBER: Problems with xleap Javier Perez Miron (Thu Feb 26 2004 - 17:18:11 PST)
- RE: AMBER: Problems with xleap Ross Walker (Mon Mar 01 2004 - 15:25:23 PST)
- Re: AMBER: Problems with xleap Rhonda Torres (Mon Mar 01 2004 - 16:02:23 PST)
AMBER: error in minimization atchara.mercury.hec.utah.edu (Tue Mar 02 2004 - 09:47:14 PST)
- Re: AMBER: error in minimization David A. Case (Tue Mar 02 2004 - 11:41:36 PST)
AMBER: A question about RMSD calculation yonchen (Tue Mar 02 2004 - 11:05:13 PST)
- Re: AMBER: A question about RMSD calculation David A. Case (Tue Mar 02 2004 - 11:52:05 PST)
AMBER: How to use tleap convert *.pdb file to *.crd and *.top files yonchen (Tue Mar 02 2004 - 11:08:55 PST)
- Re: AMBER: How to use tleap convert *.pdb file to *.crd and *.top files Carsten Detering (Tue Mar 02 2004 - 11:18:42 PST)
- Re: AMBER: How to use tleap convert *.pdb file to *.crd and *.top files David A. Case (Tue Mar 02 2004 - 11:53:31 PST)
Re: AMBER: A question about RMSD calculation Bill Ross (Tue Mar 02 2004 - 11:53:11 PST)
- RE: AMBER: A question about RMSD calculation Obdulia Rabal (Thu Mar 11 2004 - 10:09:25 PST)
AMBER: diffusion coefficient with external applied electric field Ioana Cozmuta (Tue Mar 02 2004 - 12:36:35 PST)
AMBER: General Questions Sekwan Oh (Tue Mar 02 2004 - 16:07:08 PST)
- Re: AMBER: General Questions David A. Case (Wed Mar 03 2004 - 05:22:14 PST)
AMBER: HIV-RT Nevirapin Annette Höglund (Wed Mar 03 2004 - 07:37:40 PST)
AMBER: torsion term Guanglei Cui (Wed Mar 03 2004 - 08:48:36 PST)
AMBER: questions about mmpbsa xhu1.memphis.edu (Wed Mar 03 2004 - 11:48:12 PST)
- Re: AMBER: questions about mmpbsa Holger Gohlke (Thu Mar 04 2004 - 23:35:57 PST)
AMBER: pls forget my first question in my last email xhu1.memphis.edu (Wed Mar 03 2004 - 12:02:06 PST)
Re: AMBER: compiling xleap on MAC OS X.3 Bill Ross (Wed Mar 03 2004 - 14:37:50 PST)
- Re: AMBER: compiling xleap on MAC OS X.3 Yunfeng Hu (Wed Mar 03 2004 - 14:43:53 PST)
AMBER: Use tleap convert *.pdb file to *.top and *.crd file yonchen (Wed Mar 03 2004 - 20:01:04 PST)
- Re: AMBER: Use tleap convert *.pdb file to *.top and *.crd file David A. Case (Thu Mar 04 2004 - 08:47:10 PST)
- Re: AMBER: Use tleap convert *.pdb file to *.top and *.crd file Carsten Detering (Fri Mar 05 2004 - 10:19:18 PST)
AMBER: Question about RMSD calculation yonchen (Wed Mar 03 2004 - 20:25:01 PST)
Re: AMBER: Question about RMSD calculation Carlos Simmerling (Wed Mar 03 2004 - 20:43:58 PST)
AMBER: Leap atom removal bug? david.evans.ulsop.ac.uk (Thu Mar 04 2004 - 02:30:01 PST)
- Re: AMBER: Leap atom removal bug? david.evans.ulsop.ac.uk (Thu Mar 04 2004 - 03:30:00 PST)
- Re: AMBER: Leap atom removal bug? Bill Ross (Thu Mar 04 2004 - 05:06:44 PST)
- Re: AMBER: Leap atom removal bug? David A. Case (Thu Mar 04 2004 - 08:00:08 PST)
  - AMBER: Glycam_04.prep Karl N. Kirschner (Thu Mar 04 2004 - 08:20:24 PST)
  - AMBER: Sorry about that... Karl N. Kirschner (Thu Mar 04 2004 - 08:22:53 PST)
- Re: AMBER: Leap atom removal bug? Scott Brozell (Fri Mar 05 2004 - 18:34:16 PST)
Re: AMBER: Use tleap convert *.pdb file to *.top and *.crd file Bill Ross (Thu Mar 04 2004 - 05:11:45 PST)
AMBER: conversion of Amber 7 .pdb file to .bgf file Peter Oelschlaeger (Thu Mar 04 2004 - 14:31:43 PST)
- Re: AMBER: conversion of Amber 7 .pdb file to .bgf file David A. Case (Thu Mar 04 2004 - 14:59:21 PST)
  - Re: AMBER: conversion of Amber 7 .pdb file to .bgf file Peter Oelschlaeger (Thu Mar 04 2004 - 18:00:34 PST)
    - Re: AMBER: conversion of Amber 7 .pdb file to .bgf file David A. Case (Fri Mar 05 2004 - 08:16:19 PST)
    - Re: AMBER: conversion of Amber 7 .pdb file to .bgf file Peter Oelschlaeger (Fri Mar 05 2004 - 12:47:59 PST)
  - AMBER: recovering total force array Dave S Walker (Thu Mar 11 2004 - 18:20:57 PST)
    - Re: AMBER: recovering total force array David A. Case (Fri Mar 12 2004 - 09:13:57 PST)
    - Re: AMBER: recovering total force array Dave S Walker (Tue Mar 30 2004 - 17:51:41 PST)
    - Re: AMBER: recovering total force array Carlos Simmerling (Tue Mar 30 2004 - 18:11:28 PST)
    - Re: AMBER: recovering total force array Dave S Walker (Wed Mar 31 2004 - 13:29:13 PST)
    - Re: AMBER: recovering total force array Carlos Simmerling (Wed Mar 31 2004 - 13:39:18 PST)
    - Re: AMBER: recovering total force array Dave S Walker (Tue Oct 19 2004 - 12:04:16 PDT)
    - Re: AMBER: recovering total force array David A. Case (Tue Oct 19 2004 - 14:26:31 PDT)
    - Re: AMBER: recovering total force array Dave S Walker (Tue Oct 19 2004 - 16:59:00 PDT)
AMBER: PKA calculation hj zou (Thu Mar 04 2004 - 22:34:21 PST)
AMBER: positive binding free energy hj zou (Thu Mar 04 2004 - 22:53:18 PST)
- Re: AMBER: positive binding free energy Holger Gohlke (Fri Mar 05 2004 - 00:30:35 PST)
AMBER: MD at different pH !! Jiten (Thu Mar 04 2004 - 22:30:30 PST)
- Re: AMBER: MD at different pH !! David A. Case (Fri Mar 05 2004 - 08:23:27 PST)
  - AMBER: Ewald calculation using PME for charged system Byungchan Kim (Fri Mar 05 2004 - 10:13:43 PST)
    - AMBER: Ewald calculation using PME for charged system Byungchan Kim (Tue Mar 09 2004 - 13:04:31 PST)
    - Re: AMBER: Ewald calculation using PME for charged system David A. Case (Tue Mar 09 2004 - 14:58:29 PST)
    - Re: AMBER: Ewald calculation using PME for charged system Byungchan Kim (Tue Mar 09 2004 - 15:09:18 PST)
    - Re: AMBER: Ewald calculation using PME for charged system Wayne Dawson (Tue Mar 09 2004 - 19:28:36 PST)
    - Re: AMBER: Ewald calculation using PME for charged system David A. Case (Wed Mar 10 2004 - 00:11:54 PST)
- Re: AMBER: MD at different pH !! Xin Chen (Fri Mar 05 2004 - 12:04:46 PST)
  - Re: AMBER: MD at different pH !! David A. Case (Fri Mar 05 2004 - 17:43:19 PST)
- Re: AMBER: MD at different pH !! Do Anh Tuan (Fri Mar 05 2004 - 13:11:25 PST)
  - Re: AMBER: MD at different pH !! Bimo Ario Tejo (Fri Mar 05 2004 - 18:43:36 PST)
    - Re: AMBER: MD at different pH !! Do Anh Tuan (Fri Mar 05 2004 - 20:20:04 PST)
    - Re: AMBER: MD at different pH !! Bimo Ario Tejo (Fri Mar 05 2004 - 20:58:39 PST)
- Re: AMBER: MD at different pH !! Jiten (Fri Mar 05 2004 - 23:37:27 PST)
  - Re: AMBER: MD at different pH !! Bimo Ario Tejo (Sat Mar 06 2004 - 04:18:15 PST)
AMBER: AMBER7 sander compiled on SGI R10000 fails to complete test suite james.m.woolven.gsk.com (Fri Mar 05 2004 - 04:40:31 PST)
- Re: AMBER: AMBER7 sander compiled on SGI R10000 fails to complete test suite David A. Case (Fri Mar 05 2004 - 10:20:26 PST)
AMBER: Sander problem with different CPU yuann (Fri Mar 05 2004 - 04:29:49 PST)
- Re: AMBER: Sander problem with different CPU Carlos Simmerling (Fri Mar 05 2004 - 05:27:22 PST)
- Re: AMBER: Sander problem with different CPU Robert Duke (Fri Mar 05 2004 - 05:39:37 PST)
  - Re: AMBER: Sander problem with different CPU sychen (Sat Mar 06 2004 - 17:40:25 PST)
- Re: AMBER: Sander problem with different CPU Carlos Simmerling (Mon Mar 08 2004 - 06:45:19 PST)
AMBER: Unbinding with different pH Volodymyr Nechiporuk-Zloy (Fri Mar 05 2004 - 06:10:23 PST)
AMBER: A Question about RESP ::忠誠:: (Sat Mar 06 2004 - 04:39:22 PST)
- Re: AMBER: A Question about RESP Bimo Ario Tejo (Sat Mar 06 2004 - 05:31:51 PST)
- Re: AMBER: A Question about RESP Ming-Hsun Ho (Sat Mar 06 2004 - 05:58:44 PST)
  - Re: AMBER: A Question about RESP Jiten (Sat Mar 06 2004 - 06:42:01 PST)
  - Re: AMBER: A Question about RESP Jiten (Sat Mar 06 2004 - 06:41:15 PST)
- Re: AMBER: A Question about RESP Ming-Hsun Ho (Sat Mar 06 2004 - 07:28:25 PST)
  - Re: AMBER: A Question about RESP Jiten (Sat Mar 06 2004 - 18:54:52 PST)
    - RE: AMBER: A Question about RESP William Wei (Mon Mar 15 2004 - 07:23:57 PST)
    - AMBER: understanding SANDER source code myang (Sat Mar 20 2004 - 07:33:33 PST)
    - Re: AMBER: understanding SANDER source code Scott Brozell (Sun Mar 21 2004 - 11:47:40 PST)
    - RE: AMBER: understanding SANDER source code Yong Duan (Sun Mar 21 2004 - 18:32:03 PST)
    - Re: AMBER: understanding SANDER source code Andreas Svrcek-Seiler (Mon Mar 22 2004 - 04:15:42 PST)
    - Re: AMBER: understanding SANDER source code David E. Konerding (Mon Mar 22 2004 - 08:15:49 PST)
- Re: AMBER: A Question about RESP Ming-Hsun Ho (Sat Mar 06 2004 - 07:58:38 PST)
- Re: AMBER: A Question about RESP Ming-Hsun Ho (Sat Mar 06 2004 - 22:15:16 PST)
AMBER: pka questions hj zou (Sat Mar 06 2004 - 19:22:54 PST)
AMBER: antechamber prepin Guanglei Cui (Sun Mar 07 2004 - 11:03:22 PST)
- Re: AMBER: antechamber prepin David A. Case (Sun Mar 07 2004 - 22:49:48 PST)
  - Re: AMBER: antechamber prepin Guanglei Cui (Mon Mar 08 2004 - 08:22:40 PST)
AMBER: factor used in b-factor calculation Fabian Boes (Tue Mar 09 2004 - 00:12:11 PST)
- Re: AMBER: factor used in b-factor calculation ML (Tue Mar 09 2004 - 02:36:57 PST)
- Re: AMBER: factor used in b-factor calculation Bimo Ario Tejo (Wed Mar 10 2004 - 03:02:46 PST)
AMBER: a problem about alanine scan of proline luocheng (Tue Mar 09 2004 - 01:00:27 PST)
AMBER: Amber on RedHat 3.0 madeleine.richard.bull.net (Tue Mar 09 2004 - 01:39:47 PST)
AMBER: MD simulation of a DNA decamer Thomas Steinbrecher (Tue Mar 09 2004 - 02:10:15 PST)
- Re: AMBER: MD simulation of a DNA decamer Vlad Cojocaru (Tue Mar 09 2004 - 02:35:25 PST)
- RE: AMBER: MD simulation of a DNA decamer Ross Walker (Tue Mar 09 2004 - 10:07:35 PST)
AMBER: what's the meaning of parameter NRUN scopio (Tue Mar 09 2004 - 05:40:51 PST)
- Re: AMBER: what's the meaning of parameter NRUN Carlos Simmerling (Tue Mar 09 2004 - 06:04:29 PST)
  - Re: AMBER: what's the meaning of parameter NRUN scopio (Tue Mar 09 2004 - 17:25:07 PST)
    - Re: AMBER: what's the meaning of parameter NRUN David A. Case (Tue Mar 09 2004 - 22:31:33 PST)
- Re: AMBER: what's the meaning of parameter NRUN David A. Case (Tue Mar 09 2004 - 07:23:56 PST)
AMBER: NMR restraint in sander Lishan Yao (Tue Mar 09 2004 - 06:19:30 PST)
- Re: AMBER: NMR restraint in sander Guanglei Cui (Tue Mar 09 2004 - 06:55:15 PST)
AMBER: Residue question opitz.che.udel.edu (Tue Mar 09 2004 - 08:29:22 PST)
- Re: AMBER: Residue question David A. Case (Wed Mar 10 2004 - 08:10:11 PST)
AMBER: mol2 vs. prepin opitz.che.udel.edu (Tue Mar 09 2004 - 08:53:46 PST)
- Re: AMBER: mol2 vs. prepin Guanglei Cui (Tue Mar 09 2004 - 09:05:22 PST)
AMBER: sander + child process died Carsten Detering (Tue Mar 09 2004 - 18:18:21 PST)
AMBER: positive binding free energy hj zou (Tue Mar 09 2004 - 22:43:58 PST)
- RE: AMBER: positive binding free energy Yong Duan (Wed Mar 10 2004 - 07:47:37 PST)
AMBER: Some questions in building a new residue Chung-Chien Wei (Wed Mar 10 2004 - 09:16:37 PST)
- Re: AMBER: Some questions in building a new residue Vlad Cojocaru (Wed Mar 10 2004 - 09:28:55 PST)
- Re: AMBER: Some questions in building a new residue Ilyas Yildirim (Wed Mar 10 2004 - 10:57:11 PST)
  - Re: AMBER: Some questions in building a new residue Chung-Chien Wei (Wed Mar 10 2004 - 11:49:33 PST)
    - Re: AMBER: Some questions in building a new residue FyD (Wed Mar 10 2004 - 12:31:25 PST)
AMBER: residue insertion Yunfeng Hu (Wed Mar 10 2004 - 16:24:52 PST)
- Re: AMBER: residue insertion David A. Case (Wed Mar 10 2004 - 23:00:39 PST)
  - Re: AMBER: residue insertion Scott Brozell (Fri Mar 19 2004 - 15:01:02 PST)
AMBER: positive binding free energy hj zou (Thu Mar 11 2004 - 05:59:09 PST)
- Re: AMBER: positive binding free energy Natasja Brooijmans (Thu Mar 11 2004 - 08:10:41 PST)
- Re: AMBER: positive binding free energy Jiri Sponer (Thu Mar 11 2004 - 09:02:18 PST)
AMBER: PMEMD COMPILATION REDHAT Obdulia Rabal (Thu Mar 11 2004 - 10:36:45 PST)
- Re: AMBER: PMEMD COMPILATION REDHAT Robert Duke (Thu Mar 11 2004 - 10:57:45 PST)
  - Re: AMBER: PMEMD COMPILATION REDHAT David Smith (Fri Mar 12 2004 - 05:55:13 PST)
AMBER: Atomic Charge in Residue opitz.che.udel.edu (Thu Mar 11 2004 - 11:29:21 PST)
AMBER: compiling on SGI Beale, John (Thu Mar 11 2004 - 13:26:22 PST)
- Re: AMBER: compiling on SGI Scott Brozell (Thu Mar 11 2004 - 14:24:36 PST)
AMBER: Resizing sizes.h and recompiling problem! Marco Aurelio Correia Preto (Sat Mar 13 2004 - 06:38:56 PST)
- Re: AMBER: Resizing sizes.h and recompiling problem! David A. Case (Sat Mar 13 2004 - 10:03:39 PST)
- Re: AMBER: Resizing sizes.h and recompiling problem! Stefano.Pieraccini.unimi.it (Sat Mar 13 2004 - 10:03:07 PST)
  - Re: AMBER: Resizing sizes.h and recompiling problem! Carlos Simmerling (Sat Mar 13 2004 - 11:24:44 PST)
AMBER: Anal module on PDBs Sanjeev B.S. (Sat Mar 13 2004 - 07:35:31 PST)
- RE: AMBER: Anal module on PDBs Sanjeev B.S. (Sat Mar 13 2004 - 11:25:07 PST)
Re: AMBER: Anal module on PDBs Bill Ross (Sat Mar 13 2004 - 16:17:25 PST)
AMBER: xleap couldn't display any word scopio (Sun Mar 14 2004 - 18:45:42 PST)
- Re: AMBER: xleap couldn't display any word John Bushnell (Mon Mar 15 2004 - 11:46:50 PST)
  - Re: AMBER: xleap couldn't display any word scopio (Mon Mar 15 2004 - 17:44:47 PST)
    - AMBER: About RESP Calculation Ilyas Yildirim (Thu Mar 18 2004 - 23:20:16 PST)
    - Re: AMBER: About RESP Calculation David A. Case (Fri Mar 19 2004 - 08:14:29 PST)
    - Re: AMBER: About RESP Calculation Ilyas Yildirim (Fri Mar 19 2004 - 11:50:13 PST)
    - Re: AMBER: About RESP Calculation FyD (Fri Mar 19 2004 - 12:10:19 PST)
    - Re: AMBER: About RESP Calculation David A. Case (Fri Mar 19 2004 - 12:15:39 PST)
    - Re: AMBER: About RESP Calculation FyD (Fri Mar 19 2004 - 12:30:00 PST)
    - Re: AMBER: About RESP Calculation Qing Zhang (Fri Mar 19 2004 - 22:43:03 PST)
    - Re: AMBER: About RESP Calculation FyD (Sat Mar 20 2004 - 23:30:41 PST)
    - Re: AMBER: About RESP Calculation FyD (Fri Mar 19 2004 - 09:45:22 PST)
AMBER: Release announcement for Amber 8 David A. Case (Sun Mar 14 2004 - 22:39:25 PST)
AMBER: new wed site for amber tutorials Juan Fernandez-Carmona (Mon Mar 15 2004 - 00:57:29 PST)
- Re: AMBER: new wed site for amber tutorials scopio (Mon Mar 15 2004 - 00:17:19 PST)
  - AMBER: Hydrogen Bond-statistics John (Mon Mar 15 2004 - 08:56:53 PST)
- Re: AMBER: new wed site for amber tutorials David A. Case (Mon Mar 15 2004 - 07:35:16 PST)
AMBER: How to convert charmm parameters to amber scopio (Mon Mar 15 2004 - 01:55:11 PST)
AMBER: [Fwd: No timings from jac test on opteron quad] Arvid Soderhall (Mon Mar 15 2004 - 05:28:02 PST)
AMBER: antechamber/mopac question opitz.che.udel.edu (Mon Mar 15 2004 - 12:20:24 PST)
- Re: AMBER: antechamber/mopac question David A. Case (Mon Mar 15 2004 - 17:56:51 PST)
AMBER: rdparm/ptraj writeparm david.evans.ulsop.ac.uk (Tue Mar 16 2004 - 00:57:16 PST)
- Re: AMBER: rdparm/ptraj writeparm Thomas E. Cheatham, III (Tue Mar 16 2004 - 09:04:47 PST)
  - Re: AMBER: rdparm/ptraj writeparm + leap problem david.evans.ulsop.ac.uk (Wed Mar 17 2004 - 01:36:51 PST)
    - Re: AMBER: rdparm/ptraj writeparm + leap problem David A. Case (Wed Mar 17 2004 - 08:33:34 PST)
    - Re: AMBER: rdparm/ptraj writeparm + leap problem david.evans.ulsop.ac.uk (Wed Mar 17 2004 - 08:50:16 PST)
AMBER: re:can i get help from you? hj zou (Tue Mar 16 2004 - 05:53:48 PST)
AMBER: literature question/residue charges opitz.che.udel.edu (Tue Mar 16 2004 - 12:09:43 PST)
- AMBER: AMBER6 manual Joseph Nachman (Tue Mar 16 2004 - 13:09:53 PST)
  - Re: AMBER: AMBER6 manual David A. Case (Tue Mar 16 2004 - 13:30:52 PST)
- AMBER: trajectory file Joseph Nachman (Tue Mar 16 2004 - 13:11:58 PST)
Re: AMBER: trajectory file Bill Ross (Tue Mar 16 2004 - 12:54:10 PST)
- Re: AMBER: trajectory file Joseph Nachman (Tue Mar 23 2004 - 14:38:28 PST)
- Re: AMBER: trajectory file Bill Ross (Tue Mar 23 2004 - 14:20:31 PST)
- Re: AMBER: trajectory file Joseph Nachman (Mon Mar 29 2004 - 09:16:58 PST)
  - Re: AMBER: trajectory file Andy Purkiss (Mon Mar 29 2004 - 08:54:24 PST)
  - Re: AMBER: trajectory file Rhonda Torres (Mon Mar 29 2004 - 10:03:03 PST)
Re: AMBER: literature question/residue charges Piotr Cieplak (Tue Mar 16 2004 - 14:07:21 PST)
AMBER: How to use these parameters? scopio (Tue Mar 16 2004 - 17:15:15 PST)
- Re: AMBER: How to use these parameters? Juan Fernandez-Carmona (Wed Mar 17 2004 - 00:41:39 PST)
  - Re: AMBER: How to use these parameters? scopio (Wed Mar 17 2004 - 01:31:28 PST)
AMBER: description of toplogy file format? Oliver Hucke (Tue Mar 16 2004 - 17:44:10 PST)
- Re: AMBER: description of toplogy file format? David A. Case (Tue Mar 16 2004 - 17:57:26 PST)
AMBER: segmentation fault with sander Carsten Detering (Tue Mar 16 2004 - 18:29:55 PST)
AMBER: MD problem. Osman Gani (Wed Mar 17 2004 - 03:07:47 PST)
- Re: AMBER: MD problem. David A. Case (Wed Mar 17 2004 - 08:36:04 PST)
AMBER: amber98 with amberffc+INSIGHT II a b (Wed Mar 17 2004 - 06:28:58 PST)
- Re: AMBER: amber98 with amberffc+INSIGHT II FyD (Wed Mar 17 2004 - 07:50:28 PST)
AMBER: protein-protein interaction Oscar Rey i Puiggròs (Wed Mar 17 2004 - 06:50:06 PST)
- Re: AMBER: protein-protein interaction David A. Case (Wed Mar 17 2004 - 08:37:40 PST)
AMBER: Preparing complex in Xleap for Amber calculations warka.il.waw.pl (Wed Mar 17 2004 - 08:02:38 PST)
- Re: AMBER: Preparing complex in Xleap for Amber calculations David A. Case (Wed Mar 17 2004 - 08:39:27 PST)
AMBER: using LJ 10-12 non bonded potential for glycoproteins in Amber8 Tom Turner (Wed Mar 17 2004 - 10:49:18 PST)
- Re: AMBER: using LJ 10-12 non bonded potential for glycoproteins in Amber8 David A. Case (Wed Mar 17 2004 - 11:26:00 PST)
AMBER: segmentation fault Hailong Lin (Thu Mar 18 2004 - 04:48:24 PST)
- Re: AMBER: segmentation fault David A. Case (Thu Mar 18 2004 - 08:19:04 PST)
AMBER: segmentation fault when convert pdb to mol2 Ye Mei (Thu Mar 18 2004 - 05:02:44 PST)
- Re: AMBER: segmentation fault when convert pdb to mol2 David A. Case (Thu Mar 18 2004 - 08:13:42 PST)
  - Re: Re: AMBER: segmentation fault when convert pdb to mol2 Ye Mei (Thu Mar 18 2004 - 16:38:21 PST)
Re: AMBER: segmentation fault Bill Ross (Thu Mar 18 2004 - 10:22:24 PST)
- Re: AMBER: segmentation fault Hailong Lin (Fri Mar 19 2004 - 04:41:50 PST)
  - Re: AMBER: segmentation fault Scott Brozell (Mon Mar 22 2004 - 18:10:27 PST)
  - Re: AMBER: segmentation fault Scott Brozell (Thu Mar 25 2004 - 14:33:32 PST)
AMBER: alignment problem using carnal xhu1.memphis.edu (Thu Mar 18 2004 - 11:48:55 PST)
AMBER: About RESP Calculation Chris Moth (Fri Mar 19 2004 - 13:38:40 PST)
- Re: AMBER: About RESP Calculation Piotr Cieplak (Fri Mar 19 2004 - 12:20:42 PST)
AMBER: EWALD BOMB? Ryan Ye (Sat Mar 20 2004 - 11:28:01 PST)
- Re: AMBER: EWALD BOMB? Martina Roeselova (Mon Mar 22 2004 - 11:42:01 PST)
- Re: AMBER: EWALD BOMB? scott.brown.abbott.com (Mon Mar 22 2004 - 12:21:21 PST)
- Re: AMBER: EWALD BOMB? Scott Brozell (Mon Mar 22 2004 - 12:44:51 PST)
AMBER: langevin dynamics Wei Fu (Sun Mar 21 2004 - 19:22:27 PST)
- Re: AMBER: langevin dynamics David A. Case (Tue Mar 23 2004 - 14:33:01 PST)
  - Re: AMBER: langevin dynamics Wei Fu (Tue Mar 23 2004 - 18:39:44 PST)
AMBER: Compilation problem in SUN OS 5.7! Pradipta Bandyopadhyay (Mon Mar 22 2004 - 00:48:59 PST)
- Re: AMBER: Compilation problem in SUN OS 5.7! Scott Brozell (Mon Mar 22 2004 - 13:57:03 PST)
AMBER: Assignment of parameters, missing parameters Julien Michel (Mon Mar 22 2004 - 07:47:15 PST)
- Re: AMBER: Assignment of parameters, missing parameters David A. Case (Tue Mar 23 2004 - 14:28:59 PST)
AMBER: gibbs dynamic memory error jwfang (Mon Mar 22 2004 - 08:43:46 PST)
AMBER: Re: About RESP Calculation FyD (Mon Mar 22 2004 - 09:09:00 PST)
AMBER: SANDER general questions. Osman Gani (Mon Mar 22 2004 - 09:37:18 PST)
- Re: AMBER: SANDER general questions. Scott Brozell (Mon Mar 22 2004 - 13:26:55 PST)
AMBER: [Fwd: KLAMBDA in amber7] Ahammadunny Pathiaseril (Mon Mar 22 2004 - 10:44:11 PST)
- Re: AMBER: [Fwd: KLAMBDA in amber7] David A. Case (Wed Mar 24 2004 - 17:38:10 PST)
AMBER: downloading antechamber astrid.maass (Mon Mar 22 2004 - 23:53:56 PST)
- Re: AMBER: downloading antechamber David A. Case (Tue Mar 23 2004 - 14:20:34 PST)
AMBER: M7G parameters Vlad Cojocaru (Tue Mar 23 2004 - 04:43:55 PST)
- Re: AMBER: M7G parameters David A. Case (Tue Mar 23 2004 - 14:16:24 PST)
AMBER: Residue Charges opitz.che.udel.edu (Tue Mar 23 2004 - 07:17:38 PST)
- Re: AMBER: Residue Charges Rhonda Torres (Tue Mar 23 2004 - 09:51:55 PST)
AMBER: About glycam2004 Javier Perez Miron (Wed Mar 17 2004 - 19:02:47 PST)
- RE: AMBER: About glycam2004 Ross Walker (Tue Mar 23 2004 - 10:11:01 PST)
AMBER: gibbs error Fang, Jianwen (Tue Mar 23 2004 - 08:27:22 PST)
AMBER: How to make leap recognise inosine? arvind.mbu.iisc.ernet.in (Tue Mar 23 2004 - 09:33:40 PST)
- Re: AMBER: How to make leap recognise inosine? Rhonda Torres (Tue Mar 23 2004 - 09:54:49 PST)
Re: AMBER: How to make leap recognise inosine? Bill Ross (Tue Mar 23 2004 - 09:57:27 PST)
AMBER: residence time Ioana Cozmuta (Tue Mar 23 2004 - 19:51:10 PST)
AMBER: fluorine in mmpbsa ferranna.unimore.it (Wed Mar 24 2004 - 01:49:27 PST)
AMBER: Amber: Equilibrated DMSO solvent box Marco Aurelio Correia Preto (Wed Mar 24 2004 - 03:32:31 PST)
- Re: AMBER: Amber: Equilibrated DMSO solvent box Jiten (Wed Mar 24 2004 - 05:37:30 PST)
AMBER: non-isotropic pressure scaling Lubos Vrbka (Wed Mar 24 2004 - 04:38:08 PST)
- Re: AMBER: non-isotropic pressure scaling Robert Duke (Wed Mar 24 2004 - 05:44:35 PST)
  - Re: AMBER: non-isotropic pressure scaling Lubos Vrbka (Wed Mar 24 2004 - 06:33:20 PST)
  - Re: AMBER: non-isotropic pressure scaling Lubos Vrbka (Wed Mar 31 2004 - 11:44:19 PST)
- Re: AMBER: non-isotropic pressure scaling Robert Duke (Wed Mar 31 2004 - 12:35:14 PST)
  - Re: AMBER: non-isotropic pressure scaling Lubos Vrbka (Wed Apr 14 2004 - 05:48:59 PDT)
    - Re: AMBER: non-isotropic pressure scaling David A. Case (Wed Apr 14 2004 - 08:36:52 PDT)
    - Re: AMBER: non-isotropic pressure scaling Lubos Vrbka (Wed Apr 14 2004 - 09:18:22 PDT)
    - Re: AMBER: non-isotropic pressure scaling David A. Case (Wed Apr 14 2004 - 09:56:52 PDT)
    - Re: AMBER: non-isotropic pressure scaling Lubos Vrbka (Wed Apr 14 2004 - 12:21:54 PDT)
    - AMBER: ntwprt feature in AMBER7 Dave S Walker (Thu May 06 2004 - 19:26:51 PDT)
- Re: AMBER: non-isotropic pressure scaling Robert Duke (Sun Apr 18 2004 - 06:44:09 PDT)
AMBER: Cadmium Beale, John (Wed Mar 24 2004 - 05:10:36 PST)
AMBER: make sure of the Magnesium parameters sychen (Wed Mar 24 2004 - 10:15:25 PST)
- Re: AMBER: make sure of the Magnesium parameters Rhonda Torres (Wed Mar 24 2004 - 10:53:55 PST)
  - AMBER: INtel Fortran 90 compiler Carsten Detering (Wed Mar 24 2004 - 11:03:17 PST)
    - Re: AMBER: INtel Fortran 90 compiler Robert Duke (Wed Mar 24 2004 - 12:36:35 PST)
    - Re: AMBER: INtel Fortran 90 compiler Scott Brozell (Wed Mar 24 2004 - 13:37:37 PST)
    - Re: AMBER: INtel Fortran 90 compiler Bill Ross (Wed Mar 24 2004 - 13:41:30 PST)
    - Re: AMBER: INtel Fortran 90 compiler Robert Duke (Wed Mar 24 2004 - 14:01:54 PST)
    - Re: AMBER: INtel Fortran 90 compiler Robert Duke (Wed Mar 24 2004 - 14:54:01 PST)
AMBER: vlimit and vmax problem Venkata S Koppuravuri (Wed Mar 24 2004 - 10:25:31 PST)
- Re: AMBER: vlimit and vmax problem Rhonda Torres (Wed Mar 24 2004 - 13:05:20 PST)
- Re: AMBER: vlimit and vmax problem Bill Ross (Wed Mar 24 2004 - 13:17:32 PST)
AMBER: Glycam04 Karl N. Kirschner (Wed Mar 24 2004 - 11:37:56 PST)
AMBER: antechamber download files should now be available David A. Case (Wed Mar 24 2004 - 15:05:19 PST)
- AMBER: Antechamber license ? Julien Michel (Thu Mar 25 2004 - 02:24:30 PST)
AMBER: RE: Amber: Equilibrated DMSO solvent box Marco Aurelio Correia Preto (Thu Mar 25 2004 - 01:26:41 PST)
AMBER: MM_PBSA GB parameters david.evans.ulsop.ac.uk (Thu Mar 25 2004 - 02:54:59 PST)
- Re: AMBER: MM_PBSA GB parameters david.evans.ulsop.ac.uk (Thu Mar 25 2004 - 08:25:56 PST)
AMBER: phosphorylated serin / histidin Nadine Homeyer (Thu Mar 25 2004 - 05:04:38 PST)
AMBER: FW: Problems with antechamber innstallation Osman Gani (Thu Mar 25 2004 - 07:12:20 PST)
AMBER: Antechamber MOPAC Beale, John (Thu Mar 25 2004 - 07:24:56 PST)
- Re: AMBER: Antechamber MOPAC David A. Case (Thu Mar 25 2004 - 16:34:53 PST)
AMBER: hbond analysis in ptraj(%occupied>1) Lishan Yao (Thu Mar 25 2004 - 07:19:01 PST)
- Re: AMBER: hbond analysis in ptraj(%occupied>1) Thomas E. Cheatham, III (Thu Mar 25 2004 - 10:26:50 PST)
  - Re: AMBER: hbond analysis in ptraj(%occupied>1) Sichun Yang (Thu Mar 25 2004 - 10:46:01 PST)
  - Re: AMBER: hbond analysis in ptraj(%occupied>1) Lishan Yao (Thu Mar 25 2004 - 10:54:59 PST)
    - AMBER: GIBBS: FEP and TI Miguel de Federico (Mon Mar 29 2004 - 09:03:53 PST)
    - Re: AMBER: GIBBS: FEP and TI David A. Case (Wed Mar 31 2004 - 11:07:17 PST)
AMBER: undefined loops and protonate Stern, Julie (Thu Mar 25 2004 - 09:52:41 PST)
- Re: AMBER: undefined loops and protonate David A. Case (Thu Mar 25 2004 - 16:37:47 PST)
AMBER: eedmeth atchara.mercury.hec.utah.edu (Thu Mar 25 2004 - 10:53:23 PST)
- Re: AMBER: eedmeth David A. Case (Thu Mar 25 2004 - 16:46:44 PST)
AMBER: Error while protonating a PDB file Mike (Thu Mar 25 2004 - 15:47:54 PST)
- Re: AMBER: Error while protonating a PDB file David A. Case (Thu Mar 25 2004 - 17:34:43 PST)
  - Re: AMBER: Error while protonating a PDB file Madan (Thu Mar 25 2004 - 21:03:56 PST)
    - Re: AMBER: Error while protonating a PDB file David A. Case (Sat Mar 27 2004 - 14:46:43 PST)
AMBER: Pang-model of Zn2+ Oliver Hucke (Thu Mar 25 2004 - 17:04:48 PST)
- Re: AMBER: Pang-model of Zn2+ Peter Oelschlaeger (Thu Mar 25 2004 - 17:44:01 PST)
  - Re: AMBER: Pang-model of Zn2+ Kennie Merz (Fri Mar 26 2004 - 05:52:43 PST)
AMBER: Pang Zn2+ model - correction Oliver Hucke (Thu Mar 25 2004 - 17:32:30 PST)
AMBER: a question about anal Xiao He (Thu Mar 25 2004 - 19:06:10 PST)
- RE: AMBER: a question about anal Chris Moth (Thu Mar 25 2004 - 19:54:51 PST)
AMBER: nmanal - segmentation fault Sivakolundu, Sivashankar (Thu Mar 25 2004 - 22:11:16 PST)
AMBER: tleap error and warnings Mike (Thu Mar 25 2004 - 23:06:38 PST)
- RE: AMBER: tleap error and warnings Chris Moth (Fri Mar 26 2004 - 07:34:08 PST)
AMBER: How to compile antechamber? scopio (Thu Mar 25 2004 - 23:17:54 PST)
- Re: AMBER: How to compile antechamber? Julien Michel (Fri Mar 26 2004 - 02:35:11 PST)
  - Re: AMBER: How to compile antechamber? David A. Case (Fri Mar 26 2004 - 09:56:10 PST)
AMBER: Problem solved Xiao He (Fri Mar 26 2004 - 07:35:01 PST)
Be Smart job Access (Fri Mar 26 2004 - 09:26:13 PST)
AMBER: Xiaowei Li (Fri Mar 26 2004 - 12:21:08 PST)
- Re: AMBER: David A. Case (Fri Mar 26 2004 - 13:41:32 PST)
  - Re: AMBER: Xiaowei Li (Fri Mar 26 2004 - 19:53:54 PST)
- AMBER: CARNAL RMS Wen Li (Mon Jun 07 2004 - 08:25:28 PDT)
Re: Fwd: Re: AMBER: Pang-model of Zn2+ Oliver Hucke (Fri Mar 26 2004 - 13:29:24 PST)
- Re: Fwd: Re: AMBER: Pang-model of Zn2+ David A. Case (Fri Mar 26 2004 - 14:18:35 PST)
AMBER: questions for PNA parameters Suwipa saen-oon (Fri Mar 26 2004 - 19:36:56 PST)
AMBER: erreo in sander Anshul Awasthi (Sat Mar 27 2004 - 05:15:54 PST)
- Re: AMBER: erreo in sander David A. Case (Sat Mar 27 2004 - 01:13:20 PST)
AMBER: solvation energy hj zou (Sun Mar 28 2004 - 09:36:31 PST)
- Re: AMBER: solvation energy David A. Case (Sun Mar 28 2004 - 21:15:25 PST)
AMBER: fix two groups Helios Chen (Sun Mar 28 2004 - 19:07:07 PST)
- Re: AMBER: fix two groups Carlos Simmerling (Sun Mar 28 2004 - 19:16:17 PST)
- Re: AMBER: fix two groups Helios Chen (Sun Mar 28 2004 - 20:54:58 PST)
- Re: AMBER: fix two groups Bill Ross (Sun Mar 28 2004 - 21:35:00 PST)
- Re: AMBER: fix two groups Joseph Nachman (Mon Mar 29 2004 - 08:14:33 PST)
AMBER: pmemd machinefiles Lubos Vrbka (Mon Mar 29 2004 - 02:38:13 PST)
- Re: AMBER: pmemd machinefiles Robert Duke (Mon Mar 29 2004 - 04:51:56 PST)
  - Re: AMBER: pmemd machinefiles Lubos Vrbka (Mon Mar 29 2004 - 05:34:50 PST)
- Re: AMBER: pmemd machinefiles Robert Duke (Mon Mar 29 2004 - 06:27:17 PST)
- AMBER: HBOND calculation John (Mon Mar 29 2004 - 09:40:26 PST)
  - Re: AMBER: HBOND calculation Rhonda Torres (Mon Mar 29 2004 - 10:28:19 PST)
AMBER: radial distribution franck (Mon Mar 29 2004 - 05:20:48 PST)
Re: AMBER: HBOND calculation Bill Ross (Mon Mar 29 2004 - 10:24:59 PST)
AMBER: segmentation fault of minimization scopio (Mon Mar 29 2004 - 18:57:39 PST)
- Re: AMBER: segmentation fault of minimization Thomas E. Cheatham, III (Mon Mar 29 2004 - 19:42:01 PST)
AMBER: gaff: hydrogen atom types astrid.maass (Mon Mar 29 2004 - 23:37:58 PST)
AMBER: segmentation fault when running parmchk Ye Mei (Tue Mar 30 2004 - 01:52:14 PST)
- Re: AMBER: segmentation fault when running parmchk David A. Case (Wed Mar 31 2004 - 09:50:54 PST)
- Re: AMBER: segmentation fault when running parmchk Chutintorn Punwong (Mon May 24 2004 - 15:34:11 PDT)
  - Re: AMBER: segmentation fault when running parmchk David A. Case (Mon May 24 2004 - 21:41:14 PDT)
- Re: AMBER: segmentation fault when running parmchk Chutintorn Punwong (Thu May 27 2004 - 11:01:16 PDT)
  - Re: AMBER: segmentation fault when running parmchk David A. Case (Thu May 27 2004 - 11:24:27 PDT)
- Re: AMBER: segmentation fault when running parmchk Chutintorn Punwong (Thu May 27 2004 - 11:37:09 PDT)
  - Re: AMBER: segmentation fault when running parmchk David A. Case (Thu May 27 2004 - 16:47:49 PDT)
- Re: AMBER: segmentation fault when running parmchk Chutintorn Punwong (Fri May 28 2004 - 13:08:56 PDT)
- Re: AMBER: segmentation fault when running parmchk Chutintorn Punwong (Wed Jun 02 2004 - 10:57:06 PDT)
  - Re: AMBER: segmentation fault when running parmchk David A. Case (Wed Jun 02 2004 - 11:41:56 PDT)
- Re: AMBER: segmentation fault when running parmchk Chutintorn Punwong (Wed Jun 02 2004 - 12:11:22 PDT)
- Re: AMBER: segmentation fault when running parmchk Chutintorn Punwong (Tue Jun 08 2004 - 11:07:45 PDT)
  - Re: AMBER: segmentation fault when running parmchk David A. Case (Fri Jun 11 2004 - 08:00:13 PDT)
- Re: AMBER: segmentation fault when running parmchk Bill Ross (Tue Jun 08 2004 - 11:16:35 PDT)
AMBER: Bad atom symbol, K+ and IB in vacuum Skauge Tormod (Tue Mar 30 2004 - 04:50:42 PST)
- Re: AMBER: Bad atom symbol, K+ and IB in vacuum Rhonda Torres (Tue Mar 30 2004 - 10:30:23 PST)
  - Re: AMBER: Bad atom symbol, K+ and IB in vacuum Skauge Tormod (Wed Mar 31 2004 - 04:20:30 PST)
- Re: AMBER: Bad atom symbol, K+ and IB in vacuum David A. Case (Wed Mar 31 2004 - 10:38:47 PST)
AMBER: solvation energy hj zou (Tue Mar 30 2004 - 04:55:20 PST)
- AMBER: NMR refinement John (Tue Mar 30 2004 - 06:32:55 PST)
AMBER: pmemd speedup and interactions Lubos Vrbka (Wed Mar 31 2004 - 01:27:21 PST)
- RE: AMBER: pmemd speedup and interactions Ross Walker (Wed Mar 31 2004 - 09:42:32 PST)
AMBER: pmemd speedup and interactions Lubos Vrbka (Wed Mar 31 2004 - 01:55:14 PST)
- Re: AMBER: pmemd speedup and interactions Robert Duke (Wed Mar 31 2004 - 12:03:39 PST)
AMBER: Pasrameters for MAI Anshul Awasthi (Wed Mar 31 2004 - 13:46:18 PST)
AMBER: test output of amber8 Oliver Hucke (Wed Mar 31 2004 - 15:54:38 PST)
- Re: AMBER: test output of amber8 David A. Case (Wed Mar 31 2004 - 17:37:50 PST)
AMBER: about glycam 04 Javier Perez Miron (Mon Mar 29 2004 - 09:40:18 PST)
AMBER: Question on Amber7... Pmartin (Thu Apr 01 2004 - 15:31:49 PST)
- Re: AMBER: Question on Amber7... David A. Case (Thu Apr 01 2004 - 17:33:30 PST)
  - Re: AMBER: Question on Amber7... Pmartin (Tue Apr 06 2004 - 14:44:34 PDT)
    - Re: AMBER: Question on Amber7... David A. Case (Tue Apr 06 2004 - 17:25:37 PDT)
AMBER: Mac OSX xleap compilation Sergio Pantano (Thu Apr 01 2004 - 22:32:07 PST)
- Re: AMBER: Mac OSX xleap compilation Mengjuei Hsieh (Thu Apr 01 2004 - 23:19:30 PST)
  - Re: AMBER: Mac OSX xleap compilation Yusuf Abdulghani (Fri Apr 02 2004 - 11:16:14 PST)
    - Re: AMBER: Mac OSX xleap compilation Mengjuei Hsieh (Fri Apr 02 2004 - 11:46:14 PST)
AMBER: PERT.charge problem in xleap Helios Chen (Fri Apr 02 2004 - 04:10:54 PST)
AMBER: Alignment tensor for Sander RDCs tim (Fri Apr 02 2004 - 06:47:47 PST)
- Re: AMBER: Alignment tensor for Sander RDCs David A. Case (Fri Apr 02 2004 - 09:46:24 PST)
AMBER: Parameters for ions? nie beining (Fri Apr 02 2004 - 10:15:51 PST)
AMBER: installing amber8 on a dual processor single box Carsten Detering (Fri Apr 02 2004 - 10:37:46 PST)
- Re: AMBER: installing amber8 on a dual processor single box Robert Duke (Fri Apr 02 2004 - 10:58:35 PST)
- Re: AMBER: installing amber8 on a dual processor single box David A. Case (Fri Apr 02 2004 - 11:39:24 PST)
AMBER: Intel fortran compiler and -static switch in older pmemd releases Robert Duke (Fri Apr 02 2004 - 13:10:49 PST)
- Re: AMBER: Intel fortran compiler and -static switch in older pmemd releases David E. Konerding DSD Staff (Fri Apr 02 2004 - 13:21:11 PST)
- Re: AMBER: Intel fortran compiler and -static switch in older pmemd releases Robert Duke (Fri Apr 02 2004 - 13:35:45 PST)
AMBER: question about image Youyi Peng (Fri Apr 02 2004 - 14:41:36 PST)
- AMBER: AMBER 7 Installation Ilyas Yildirim (Fri Apr 02 2004 - 15:17:09 PST)
  - Re: AMBER: AMBER 7 Installation David A. Case (Fri Apr 02 2004 - 17:37:57 PST)
- Re: AMBER: question about image Thomas E. Cheatham, III (Fri Apr 02 2004 - 15:51:01 PST)
  - Re: AMBER: question about image pengyo.UMDNJ.EDU (Fri Apr 02 2004 - 19:35:06 PST)
    - Re: AMBER: question about image Thomas E. Cheatham, III (Mon Apr 05 2004 - 09:37:00 PDT)
AMBER: sander + ew_legal.h Carsten Detering (Fri Apr 02 2004 - 17:08:07 PST)
- Re: AMBER: sander + ew_legal.h David A. Case (Fri Apr 02 2004 - 17:34:32 PST)
AMBER: question about image - truncated octahedron Chris Moth (Sat Apr 03 2004 - 07:22:14 PST)
- Re: AMBER: question about image - truncated octahedron Thomas E. Cheatham, III (Mon Apr 05 2004 - 14:21:36 PDT)
AMBER: amber8 tutorial Patil, Sachin (Sun Apr 04 2004 - 17:03:20 PDT)
- Re: AMBER: amber8 tutorial Viktor Hornak (Sun Apr 04 2004 - 19:03:56 PDT)
- RE: AMBER: amber8 tutorial Ross Walker (Sun Apr 04 2004 - 19:45:52 PDT)
AMBER: Error in building a molecule anshul.imtech.res.in (Mon Apr 05 2004 - 15:01:54 PDT)
AMBER: minimization of GLH Hailong Lin (Mon Apr 05 2004 - 04:57:31 PDT)
- Re: AMBER: minimization of GLH David A. Case (Mon Apr 05 2004 - 08:26:27 PDT)
- Re: AMBER: minimization of GLH Hailong Lin (Mon Apr 05 2004 - 08:51:47 PDT)
  - Re: AMBER: minimization of GLH David A. Case (Mon Apr 05 2004 - 10:06:39 PDT)
AMBER: Antechamber compilation error Arvind (Mon Apr 05 2004 - 09:22:21 PDT)
- Re: AMBER: Antechamber compilation error David A. Case (Mon Apr 05 2004 - 10:12:05 PDT)
- AMBER: PMEMD Problems... Jon Gray (Mon Apr 05 2004 - 13:38:23 PDT)
  - Re: AMBER: PMEMD Problems... Robert Duke (Mon Apr 05 2004 - 14:13:24 PDT)
    - Re: AMBER: PMEMD Problems... Jon Gray (Mon Apr 05 2004 - 20:56:47 PDT)
  - Re: AMBER: PMEMD Problems... Robert Duke (Mon Apr 05 2004 - 21:38:58 PDT)
AMBER: antechamber: frcmod parameter need revision atchara.mercury.hec.utah.edu (Mon Apr 05 2004 - 14:11:12 PDT)
AMBER: which parameters for Ca2+ ? cailliez (Tue Apr 06 2004 - 00:50:03 PDT)
AMBER: anshul.imtech.res.in (Tue Apr 06 2004 - 14:58:07 PDT)
AMBER: free energy perturbation Herbert Georg (Tue Apr 06 2004 - 08:21:55 PDT)
- Re: AMBER: free energy perturbation David Smith (Tue Apr 06 2004 - 08:45:06 PDT)
- RE: AMBER: free energy perturbation Kristina Furse (Tue Apr 06 2004 - 09:53:39 PDT)
  - Re: AMBER: free energy perturbation Herbert Georg (Tue Apr 06 2004 - 10:03:51 PDT)
- Re: AMBER: free energy perturbation David A. Case (Tue Apr 06 2004 - 18:26:37 PDT)
AMBER: which atoms are H's for SHAKE? Oliver Hucke (Tue Apr 06 2004 - 10:32:12 PDT)
AMBER: gibbs calculation Carsten Detering (Tue Apr 06 2004 - 11:11:55 PDT)
AMBER: new leap with old gibbs Carsten Detering (Tue Apr 06 2004 - 12:16:01 PDT)
- Re: AMBER: new leap with old gibbs David A. Case (Tue Apr 06 2004 - 14:31:10 PDT)
- Re: AMBER: new leap with old gibbs Carsten Detering (Tue Apr 06 2004 - 14:48:26 PDT)
  - Re: AMBER: new leap with old gibbs David A. Case (Tue Apr 06 2004 - 17:13:57 PDT)
  - AMBER: MOPAC 7 - How to modift the mopac.sh file to run antechamber properly? Ilyas Yildirim (Tue Apr 06 2004 - 17:27:31 PDT)
    - Re: AMBER: MOPAC 7 - How to modift the mopac.sh file to run antechamber properly? Ilyas Yildirim (Tue Apr 06 2004 - 18:25:46 PDT)
    - Re: AMBER: MOPAC 7 - How to modift the mopac.sh file to run antechamber properly? David A. Case (Wed Apr 07 2004 - 08:19:27 PDT)
Re: AMBER: which atoms are H's for SHAKE? Bill Ross (Tue Apr 06 2004 - 13:11:41 PDT)
AMBER: more vlimit exceeded problems... Linda Prengaman (Tue Apr 06 2004 - 19:22:44 PDT)
- Re: AMBER: more vlimit exceeded problems... David A. Case (Wed Apr 07 2004 - 08:06:31 PDT)
AMBER: Amber 8 ptraj segmentation fault Sivakolundu, Sivashankar (Tue Apr 06 2004 - 22:49:08 PDT)
- AMBER: ptraj parser Thomas C. Bishop (Wed Apr 07 2004 - 08:01:15 PDT)
  - Re: AMBER: ptraj parser Viktor Hornak (Wed Apr 07 2004 - 09:20:40 PDT)
AMBER: riccardodesantis.fastwebnet.it (Tue Apr 06 2004 - 23:02:57 PDT)
AMBER: ANAL: how can i buld the anal.in file? riccardodesantis.fastwebnet.it (Tue Apr 06 2004 - 23:14:49 PDT)
- Re: AMBER: ANAL: how can i buld the anal.in file? David A. Case (Wed Apr 07 2004 - 08:21:53 PDT)
AMBER: Error message while testing Alessio Comisso (Wed Apr 07 2004 - 04:53:24 PDT)
- Re: AMBER: Error message while testing Scott Brozell (Mon Apr 12 2004 - 18:10:30 PDT)
AMBER: error in antechamber anshul.imtech.res.in (Wed Apr 07 2004 - 15:49:47 PDT)
- Re: AMBER: error in antechamber Ilyas Yildirim (Wed Apr 07 2004 - 06:30:55 PDT)
  - Re: AMBER: error in antechamber David A. Case (Wed Apr 07 2004 - 08:27:43 PDT)
    - Re: AMBER: error in antechamber anshul.imtech.res.in (Thu Apr 08 2004 - 10:36:57 PDT)
    - Re: AMBER: error in antechamber David A. Case (Thu Apr 08 2004 - 07:58:42 PDT)
AMBER: unique atom names anshul.imtech.res.in (Wed Apr 07 2004 - 16:00:31 PDT)
AMBER: unique atom names Chris Moth (Wed Apr 07 2004 - 07:20:11 PDT)
- RE: AMBER: unique atom names Chris Moth (Wed Apr 07 2004 - 07:21:50 PDT)
AMBER: Ti of CH3 -> NH2 Carsten Detering (Wed Apr 07 2004 - 15:14:11 PDT)
- AMBER: respgen Ilyas Yildirim (Wed Apr 07 2004 - 15:45:33 PDT)
  - Re: AMBER: respgen David A. Case (Wed Apr 07 2004 - 18:20:36 PDT)
    - AMBER: Gaussian 98 Installation Ilyas Yildirim (Thu Apr 08 2004 - 13:52:05 PDT)
- Re: AMBER: Ti of CH3 -> NH2 David A. Case (Wed Apr 07 2004 - 18:17:30 PDT)
AMBER: bug of leap? Ye Mei (Wed Apr 07 2004 - 19:27:11 PDT)
AMBER: bug of leap? Ye Mei (Wed Apr 07 2004 - 19:29:07 PDT)
- Re: AMBER: bug of leap? Ye Mei (Wed Apr 07 2004 - 19:40:29 PDT)
  - Re: AMBER: bug of leap? Chris Moth (Thu Apr 08 2004 - 09:10:06 PDT)
AMBER: Carnal in Amber7 Sichun Yang (Wed Apr 07 2004 - 21:03:35 PDT)
AMBER: warning about improper dihedral in leap!! Pradipta Bandyopadhyay (Thu Apr 08 2004 - 04:50:18 PDT)
- Re: AMBER: warning about improper dihedral in leap!! David A. Case (Thu Apr 08 2004 - 08:09:11 PDT)
AMBER: Beale, John (Thu Apr 08 2004 - 06:04:04 PDT)
- Re: AMBER: Holger Gohlke (Thu Apr 08 2004 - 07:20:51 PDT)
Re: AMBER: Carnal in Amber7 Bill Ross (Thu Apr 08 2004 - 11:16:02 PDT)
AMBER: Dipole moment changes during MD Jiten (Thu Apr 08 2004 - 18:31:17 PDT)
- RE: AMBER: Dipole moment changes during MD Ross Walker (Fri Apr 09 2004 - 09:48:29 PDT)
  - Re: AMBER: Dipole moment changes during MD Jiten (Fri Apr 09 2004 - 11:05:01 PDT)
    - RE: AMBER: Dipole moment changes during MD Ross Walker (Fri Apr 09 2004 - 14:56:48 PDT)
    - Re: AMBER: Dipole moment changes during MD Jiten (Fri Apr 09 2004 - 17:48:03 PDT)
AMBER: script on tutorial page Ioana Cozmuta (Thu Apr 08 2004 - 19:25:50 PDT)
- RE: AMBER: script on tutorial page Ross Walker (Thu Apr 08 2004 - 21:21:44 PDT)
  - RE: AMBER: script on tutorial page Ioana Cozmuta (Fri Apr 09 2004 - 15:03:57 PDT)
    - RE: AMBER: script on tutorial page Thomas E. Cheatham, III (Sat Apr 10 2004 - 13:31:51 PDT)
AMBER: NMODE xiaowei li (Fri Apr 09 2004 - 13:20:23 PDT)
- Re: AMBER: NMODE David A. Case (Fri Apr 09 2004 - 15:46:35 PDT)
AMBER: Suggestions for newer pentium chips and hyperthreading with PMEMD Robert Duke (Fri Apr 09 2004 - 14:13:59 PDT)
- RE: AMBER: Suggestions for newer pentium chips and hyperthreading with PMEMD Ross Walker (Fri Apr 09 2004 - 14:38:18 PDT)
  - Re: AMBER: Suggestions for newer pentium chips and hyperthreading with PMEMD David E. Konerding DSD Staff (Fri Apr 09 2004 - 15:41:57 PDT)
AMBER: equilibration does not start with SHAKE Oliver Hucke (Fri Apr 09 2004 - 15:30:55 PDT)
- Re: AMBER: equilibration does not start with SHAKE David A. Case (Fri Apr 09 2004 - 16:16:09 PDT)
AMBER: amber/pmemd with mpiexec Lubos Vrbka (Sat Apr 10 2004 - 09:50:30 PDT)
- Re: AMBER: amber/pmemd with mpiexec Robert Duke (Sat Apr 10 2004 - 10:21:15 PDT)
  - Re: AMBER: amber/pmemd with mpiexec Lubos Vrbka (Sun Apr 11 2004 - 07:00:36 PDT)
- Re: AMBER: amber/pmemd with mpiexec Robert Duke (Mon Apr 12 2004 - 07:41:22 PDT)
Returned mail: see transcript for details Mail Delivery Subsystem (Sat Apr 10 2004 - 13:42:30 PDT)
AMBER: Antechamber compilation: leap error Arvind (Mon Apr 12 2004 - 04:05:58 PDT)
- Re: AMBER: Antechamber compilation: leap error Ye Mei (Mon Apr 12 2004 - 04:55:11 PDT)
AMBER: XLeap: head/tail and frcmod L Jin (Mon Apr 12 2004 - 04:35:47 PDT)
- Re: AMBER: XLeap: head/tail and frcmod David A. Case (Mon Apr 12 2004 - 08:15:29 PDT)
AMBER: Compiling Amber 8 Beale, John (Mon Apr 12 2004 - 06:44:25 PDT)
- Re: AMBER: Compiling Amber 8 Viktor Hornak (Mon Apr 12 2004 - 06:53:29 PDT)
- Re: AMBER: Compiling Amber 8 Robert Duke (Mon Apr 12 2004 - 07:22:27 PDT)
- Re: AMBER: Compiling Amber 8 Andreas Svrcek-Seiler (Tue Apr 13 2004 - 02:57:29 PDT)
- Re: AMBER: Compiling Amber 8 Bill Ross (Tue Apr 13 2004 - 09:38:58 PDT)
AMBER: Group in sander xiaowei li (Mon Apr 12 2004 - 12:05:29 PDT)
- Re: AMBER: Group in sander Viktor Hornak (Mon Apr 12 2004 - 12:13:15 PDT)
- Re: AMBER: Group in sander Thomas E. Cheatham, III (Mon Apr 12 2004 - 12:30:46 PDT)
- AMBER: Group in sander Chris Moth (Mon Apr 12 2004 - 12:20:37 PDT)
AMBER: scali amber8 Guanglei Cui (Mon Apr 12 2004 - 13:02:11 PDT)
- Re: AMBER: scali amber8 Scott Brozell (Mon Apr 12 2004 - 15:54:42 PDT)
AMBER: ptraj pengyo.UMDNJ.EDU (Mon Apr 12 2004 - 13:09:22 PDT)
- Re: AMBER: ptraj Thomas E. Cheatham, III (Mon Apr 12 2004 - 13:23:12 PDT)
  - Re: AMBER: ptraj pengyo.UMDNJ.EDU (Mon Apr 12 2004 - 14:22:26 PDT)
    - Re: AMBER: ptraj ayongye.sunchem.chem.uga.edu (Tue Apr 13 2004 - 08:48:54 PDT)
AMBER: water hole Holly Freedman (Mon Apr 12 2004 - 14:43:32 PDT)
- Re: AMBER: water hole Carlos Simmerling (Mon Apr 12 2004 - 15:40:13 PDT)
  - Re: AMBER: water hole Andreas Svrcek-Seiler (Tue Apr 13 2004 - 03:02:12 PDT)
- Re: AMBER: water hole David A. Case (Mon Apr 12 2004 - 17:13:37 PDT)
  - Re: AMBER: water hole Holly Freedman (Mon Apr 12 2004 - 17:39:19 PDT)
- Re: AMBER: water hole Bill Ross (Mon Apr 12 2004 - 18:58:47 PDT)
- Re: AMBER: water hole Amber Administration (Wed Apr 14 2004 - 16:59:31 PDT)
  - Re: AMBER: water hole Holly Freedman (Wed Apr 14 2004 - 17:32:06 PDT)
- Re: AMBER: water hole Bill Ross (Thu Apr 15 2004 - 11:49:02 PDT)
AMBER: how to use mm_pbsa_statistics.pl independently Jufang Shan (Mon Apr 12 2004 - 19:23:36 PDT)
- RE: AMBER: how to use mm_pbsa_statistics.pl independently Chris Moth (Tue Apr 13 2004 - 08:34:26 PDT)
- Re: AMBER: how to use mm_pbsa_statistics.pl independently Holger Gohlke (Tue Apr 13 2004 - 10:06:43 PDT)
AMBER: Re: a new question Viktor Hornak (Mon Apr 12 2004 - 20:02:35 PDT)
AMBER: WHICH LINUX Raj Badhan (Tue Apr 13 2004 - 07:50:52 PDT)
- Re: AMBER: WHICH LINUX Marc Baaden (Tue Apr 13 2004 - 08:20:35 PDT)
- Re: AMBER: WHICH LINUX Andreas Svrcek-Seiler (Tue Apr 13 2004 - 08:30:20 PDT)
AMBER: how to check metal ion bonding ? Venkata S Koppuravuri (Tue Apr 13 2004 - 12:13:52 PDT)
- Re: AMBER: how to check metal ion bonding ? Oliver Hucke (Tue Apr 13 2004 - 13:28:09 PDT)
Re: AMBER: how to check metal ion bonding ? Bill Ross (Tue Apr 13 2004 - 14:34:52 PDT)
AMBER: Amber 7 on SGI: Sander MPI problem Rohn Wood (Tue Apr 13 2004 - 15:34:12 PDT)
- Re: AMBER: Amber 7 on SGI: Sander MPI problem David A. Case (Tue Apr 13 2004 - 17:37:04 PDT)
  - Re: AMBER: Amber 7 on SGI: Sander MPI problem Rohn Wood (Wed Apr 14 2004 - 10:28:17 PDT)
    - Re: AMBER: Amber 7 on SGI: Sander MPI problem Rohn Wood (Wed Apr 14 2004 - 16:48:58 PDT)
- Re: AMBER: Amber 7 on SGI: Sander MPI problem Tru Huynh (Wed Apr 14 2004 - 05:45:08 PDT)
Out of Office AutoReply: Boost your sex life Bernor, Sandie L (Tue Apr 13 2004 - 17:34:52 PDT)
AMBER: Creating Parmtop files for NAMD Edward Patrick Obrien (Tue Apr 13 2004 - 17:37:52 PDT)
- Re: AMBER: Creating Parmtop files for NAMD M. L. Dodson (Tue Apr 13 2004 - 18:39:26 PDT)
- Re: AMBER: Creating Parmtop files for NAMD Thomas C. Bishop (Wed Apr 14 2004 - 06:49:23 PDT)
AMBER: Amber and Linux compilation Raj Badhan (Wed Apr 14 2004 - 04:26:36 PDT)
- Re: AMBER: Amber and Linux compilation Ye Mei (Wed Apr 14 2004 - 04:52:55 PDT)
  - Re: AMBER: Amber and Linux compilation Raj Badhan (Wed Apr 14 2004 - 04:59:34 PDT)
  - Re: AMBER: Amber and Linux compilation Raj Badhan (Wed Apr 14 2004 - 05:54:54 PDT)
    - Re: Re: AMBER: Amber and Linux compilation Ye Mei (Wed Apr 14 2004 - 06:26:40 PDT)
    - Re: Re: AMBER: Amber and Linux compilation Raj Badhan (Wed Apr 14 2004 - 07:17:18 PDT)
    - Re: Re: AMBER: Amber and Linux compilation Andreas Svrcek-Seiler (Wed Apr 14 2004 - 07:44:21 PDT)
    - Re: Re: AMBER: Amber and Linux compilation Teletchéa Stéphane (Wed Apr 14 2004 - 08:08:29 PDT)
AMBER: salt concentration cailliez (Wed Apr 14 2004 - 07:45:44 PDT)
- Re: AMBER: salt concentration tim (Wed Apr 14 2004 - 04:56:52 PDT)
AMBER: atomicfluct in ptraj Qiang Lu (Wed Apr 14 2004 - 11:12:06 PDT)
- Re: AMBER: atomicfluct in ptraj Holger Gohlke (Wed Apr 14 2004 - 12:14:47 PDT)
- Re[2]: AMBER: atomicfluct in ptraj Qiang Lu (Wed Apr 14 2004 - 15:06:32 PDT)
AMBER: Time to minimize the energy by NMODE xiaowei li (Wed Apr 14 2004 - 11:23:02 PDT)
- Re: AMBER: Time to minimize the energy by NMODE Holger Gohlke (Wed Apr 14 2004 - 12:40:28 PDT)
- Re: AMBER: Time to minimize the energy by NMODE David A. Case (Wed Apr 14 2004 - 15:54:10 PDT)
AMBER: gibbs termination Carsten Detering (Wed Apr 14 2004 - 12:17:29 PDT)
- Re: AMBER: gibbs termination David A. Case (Wed Apr 14 2004 - 18:24:10 PDT)
Re: AMBER: gibbs termination Bill Ross (Wed Apr 14 2004 - 13:16:50 PDT)
AMBER: xleap bug? Carsten Detering (Wed Apr 14 2004 - 15:28:07 PDT)
- RE: AMBER: xleap bug? Ross Walker (Wed Apr 14 2004 - 15:48:18 PDT)
AMBER: Problem in loading a PDB file in Leap - Please help me Mike (Wed Apr 14 2004 - 23:25:07 PDT)
- Re: AMBER: Problem in loading a PDB file in Leap - Please help me tim (Wed Apr 14 2004 - 22:53:41 PDT)
  - Re: AMBER: Problem in loading a PDB file in Leap - Please help me Mike (Fri Apr 16 2004 - 22:19:02 PDT)
- Re: AMBER: Problem in loading a PDB file in Leap - Please help me Bill Ross (Fri Apr 16 2004 - 22:55:43 PDT)
  - Re: AMBER: Problem in loading a PDB file in Leap - Please help me Mike (Sat Apr 17 2004 - 10:35:22 PDT)
- Re: AMBER: Problem in loading a PDB file in Leap - Please help me Bill Ross (Sat Apr 17 2004 - 12:40:06 PDT)
AMBER: ptraj-6.5 cailliez (Thu Apr 15 2004 - 02:42:36 PDT)
AMBER: pbsa Chenglong Li (Thu Apr 15 2004 - 10:26:51 PDT)
- Re: AMBER: pbsa rluo.uci.edu (Thu Apr 15 2004 - 11:14:34 PDT)
AMBER: distance measurement in carnal and ptraj anshul.imtech.res.in (Fri Apr 16 2004 - 13:56:33 PDT)
- Re: AMBER: distance measurement in carnal and ptraj David A. Case (Fri Apr 16 2004 - 08:46:04 PDT)
AMBER: new atom and increase the number of bonds Tomas Hrobarik (Fri Apr 16 2004 - 07:01:56 PDT)
Re: AMBER: distance measurement in carnal and ptraj Bill Ross (Fri Apr 16 2004 - 11:32:07 PDT)
AMBER: compiling Amber 8 Beale, John (Fri Apr 16 2004 - 10:23:23 PDT)
- RE: AMBER: compiling Amber 8 Ross Walker (Fri Apr 16 2004 - 11:47:36 PDT)
  - AMBER: Do we have to optimize the structure in order to do MEP Calculations? Ilyas Yildirim (Mon Apr 19 2004 - 13:35:45 PDT)
    - Re: AMBER: Do we have to optimize the structure in order to do MEP Calculations? David A. Case (Mon Apr 19 2004 - 14:45:34 PDT)
    - Re: AMBER: Do we have to optimize the structure in order to do MEP Calculations? Ilyas Yildirim (Tue Apr 20 2004 - 13:13:09 PDT)
    - Re: AMBER: Do we have to optimize the structure in order to do MEP Calculations? David A. Case (Tue Apr 20 2004 - 13:29:47 PDT)
    - Re: AMBER: Do we have to optimize the structure in order to do MEP Calculations? Ilyas Yildirim (Tue Apr 20 2004 - 13:51:55 PDT)
    - Re: AMBER: Do we have to optimize the structure in order to do MEP Calculations? David A. Case (Tue Apr 20 2004 - 14:50:42 PDT)
    - Re: AMBER: Do we have to optimize the structure in order to do MEP Calculations? Ilyas Yildirim (Tue Apr 20 2004 - 16:42:34 PDT)
    - AMBER: What kind of informations are needed in a .pdb file in order to start using antechamber? Ilyas Yildirim (Wed Apr 21 2004 - 21:51:40 PDT)
    - RE: AMBER: What kind of informations are needed in a .pdb file in order to start using antechamber? Chris Moth (Thu Apr 22 2004 - 05:02:30 PDT)
    - Re: AMBER: Do we have to optimize the structure in order to do MEP Calculations? Ilyas Yildirim (Tue Apr 20 2004 - 13:28:13 PDT)
- RE: AMBER: compiling Amber 8 Bill Ross (Fri Apr 16 2004 - 12:36:44 PDT)
- RE: AMBER: compiling Amber 8 Bill Ross (Fri Apr 16 2004 - 12:45:06 PDT)
AMBER: free energy perturbation questions hj zou (Sat Apr 17 2004 - 07:38:28 PDT)
AMBER: loading PDB problem in leap Suwipa saen-oon (Sun Apr 18 2004 - 02:35:35 PDT)
- Re: AMBER: loading PDB problem in leap Jiten (Sun Apr 18 2004 - 20:57:16 PDT)
AMBER: xleap console message Guanglei Cui (Mon Apr 19 2004 - 08:06:05 PDT)
- Re: AMBER: xleap console message David A. Case (Mon Apr 19 2004 - 09:40:46 PDT)
  - Re: AMBER: xleap console message Guanglei Cui (Mon Apr 19 2004 - 10:11:11 PDT)
- Re: AMBER: xleap console message Bill Ross (Mon Apr 19 2004 - 10:28:17 PDT)
  - Re: AMBER: xleap console message Guanglei Cui (Mon Apr 19 2004 - 13:48:28 PDT)
- Re: AMBER: xleap console message Bill Ross (Mon Apr 19 2004 - 13:58:05 PDT)
AMBER: Intel Fortran Compiler, 7.1 status Robert Duke (Mon Apr 19 2004 - 08:32:49 PDT)
AMBER: ptraj projections help Thomas C. Bishop (Mon Apr 19 2004 - 10:41:08 PDT)
AMBER: memory problem in NMODE xhu1.memphis.edu (Mon Apr 19 2004 - 13:06:46 PDT)
- Re: AMBER: memory problem in NMODE David A. Case (Mon Apr 19 2004 - 14:54:34 PDT)
- Re: AMBER: memory problem in NMODE xhu1.memphis.edu (Mon Apr 19 2004 - 16:43:47 PDT)
  - Re: AMBER: memory problem in NMODE David A. Case (Mon Apr 19 2004 - 17:56:44 PDT)
AMBER: nucgen generated RNA duplex: leap problems Arvind (Tue Apr 20 2004 - 04:44:37 PDT)
- Re: AMBER: nucgen generated RNA duplex: leap problems Skauge Tormod (Tue Apr 20 2004 - 08:03:09 PDT)
- Re: AMBER: nucgen generated RNA duplex: leap problems David A. Case (Tue Apr 20 2004 - 11:26:17 PDT)
AMBER: Simulation of lipid bilayers Greg Jezierski (Tue Apr 20 2004 - 07:41:50 PDT)
AMBER: "No radius found for F" error and vdw radii for F in MMPBSA Ming Lei (Tue Apr 20 2004 - 08:47:40 PDT)
AMBER: instalation of amber7 on SUN anshul.imtech.res.in (Tue Apr 20 2004 - 19:53:20 PDT)
- Re: AMBER: instalation of amber7 on SUN David A. Case (Tue Apr 20 2004 - 11:14:58 PDT)
  - Re: AMBER: instalation of amber7 on SUN anshul.imtech.res.in (Thu Apr 22 2004 - 09:35:37 PDT)
    - Re: AMBER: instalation of amber7 on SUN David A. Case (Sat Apr 24 2004 - 11:00:40 PDT)
AMBER: Using pbsa Thomas Steinbrecher (Tue Apr 20 2004 - 16:16:37 PDT)
- Re: AMBER: Using pbsa Chenglong Li (Tue Apr 20 2004 - 16:47:34 PDT)
  - Re: AMBER: Using pbsa David A. Case (Tue Apr 20 2004 - 18:26:08 PDT)
AMBER: distance dependent dielectric anshul.imtech.res.in (Wed Apr 21 2004 - 08:30:49 PDT)
- Re: AMBER: distance dependent dielectric Viktor Hornak (Wed Apr 21 2004 - 05:23:31 PDT)
AMBER: Question about compiling PMEMD Tod Pascal (Wed Apr 21 2004 - 00:21:40 PDT)
- Re: AMBER: Question about compiling PMEMD Robert Duke (Wed Apr 21 2004 - 05:27:02 PDT)
  - RE: AMBER: Question about compiling PMEMD Tod Pascal (Wed Apr 21 2004 - 23:29:55 PDT)
    - Re: AMBER: Question about compiling PMEMD Robert Duke (Thu Apr 22 2004 - 04:35:45 PDT)
    - Re: AMBER: Question about compiling PMEMD Robert Duke (Thu Apr 22 2004 - 05:10:47 PDT)
AMBER: Turning off non-bond interactions david.evans.ulsop.ac.uk (Wed Apr 21 2004 - 01:22:21 PDT)
- RE: AMBER: Turning off non-bond interactions Chris Moth (Wed Apr 21 2004 - 08:00:14 PDT)
- RE: AMBER: Turning off non-bond interactions Chris Moth (Wed Apr 21 2004 - 08:58:07 PDT)
  - RE: AMBER: Turning off non-bond interactions david.evans.ulsop.ac.uk (Wed Apr 21 2004 - 09:09:26 PDT)
  - Re: AMBER: Turning off non-bond interactions Robert Duke (Wed Apr 21 2004 - 09:12:11 PDT)
- Re: AMBER: Turning off non-bond interactions David A. Case (Wed Apr 21 2004 - 08:54:54 PDT)
- RE: AMBER: Turning off non-bond interactions Bill Ross (Wed Apr 21 2004 - 11:09:44 PDT)
AMBER: How to solve these warnings? Xiao He (Wed Apr 21 2004 - 01:37:40 PDT)
- Re: AMBER: How to solve these warnings? Jiten (Wed Apr 21 2004 - 05:06:41 PDT)
- RE: AMBER: How to solve these warnings? Kristina Furse (Wed Apr 21 2004 - 13:35:57 PDT)
AMBER: Why are there LENNARD_JONES_COEF A,B zero Xiao He (Wed Apr 21 2004 - 01:46:29 PDT)
- Re: AMBER: Why are there LENNARD_JONES_COEF A,B zero Dr. Yong Duan (Wed Apr 21 2004 - 05:56:19 PDT)
- Re: AMBER: Why are there LENNARD_JONES_COEF A,B zero David A. Case (Wed Apr 21 2004 - 08:57:26 PDT)
  - Re: Re: AMBER: Why are there LENNARD_JONES_COEF A,B zero Xiao He (Wed Apr 21 2004 - 06:05:49 PDT)
    - Re: Re: AMBER: Why are there LENNARD_JONES_COEF A,B zero Jiten (Wed Apr 21 2004 - 06:28:26 PDT)
    - Re: Re: AMBER: Why are there LENNARD_JONES_COEF A,B zero Dr. Yong Duan (Wed Apr 21 2004 - 07:41:59 PDT)
    - Re: Re: Re: AMBER: Why are there LENNARD_JONES_COEF A,B zero Xiao He (Wed Apr 21 2004 - 06:48:06 PDT)
    - Re: Re: Re: AMBER: Why are there LENNARD_JONES_COEF A,B zero Dr. Yong Duan (Wed Apr 21 2004 - 08:59:58 PDT)
AMBER: non-periodic simulation and box information !! Pradipta Bandyopadhyay (Wed Apr 21 2004 - 08:56:31 PDT)
- Re: AMBER: non-periodic simulation and box information !! Robert Duke (Wed Apr 21 2004 - 09:04:54 PDT)
- Re: AMBER: non-periodic simulation and box information !! Michael Crowley (Wed Apr 21 2004 - 10:32:58 PDT)
Re: AMBER: How to solve these warnings? Bill Ross (Wed Apr 21 2004 - 11:21:30 PDT)
Re: AMBER: nucgen generated RNA duplex: leap problems Bill Ross (Wed Apr 21 2004 - 11:33:00 PDT)
- Re: AMBER: nucgen generated RNA duplex: leap problems Arvind (Wed Apr 21 2004 - 13:23:28 PDT)
- Re: AMBER: nucgen generated RNA duplex: leap problems Bill Ross (Wed Apr 21 2004 - 13:34:40 PDT)
AMBER: gaff "ha" atom type Oliver Hucke (Wed Apr 21 2004 - 13:38:20 PDT)
AMBER: restraintmask and ambmask Oliver Hucke (Wed Apr 21 2004 - 17:17:24 PDT)
- Re: AMBER: restraintmask and ambmask Viktor Hornak (Thu Apr 22 2004 - 05:27:38 PDT)
AMBER: Bond type in leap anshul.imtech.res.in (Thu Apr 22 2004 - 12:22:31 PDT)
AMBER: mm_pbsa examples; delphi in mm_pbsa Kazuo Koyano (Thu Apr 22 2004 - 01:34:03 PDT)
- Re: AMBER: mm_pbsa examples; delphi in mm_pbsa Holger Gohlke (Mon Apr 26 2004 - 06:11:28 PDT)
- Re: AMBER: mm_pbsa examples; delphi in mm_pbsa Kazuo Koyano (Fri May 14 2004 - 02:35:36 PDT)
  - AMBER: time-averaged restraints John (Fri May 14 2004 - 10:04:49 PDT)
AMBER: antechamber bcctype.c typo Chris Moth (Thu Apr 22 2004 - 05:07:32 PDT)
- Re: AMBER: antechamber bcctype.c typo David A. Case (Wed Apr 28 2004 - 14:42:11 PDT)
AMBER: Euclidean distances Wen Li (Thu Apr 22 2004 - 07:49:45 PDT)
Re: AMBER: Euclidean distances Bill Ross (Thu Apr 22 2004 - 09:34:37 PDT)
Re: AMBER: Bond type in leap Bill Ross (Thu Apr 22 2004 - 09:53:33 PDT)
AMBER: MD for protein-carbohydrate complex Mikyung Seo (Thu Apr 22 2004 - 13:03:33 PDT)
Re: AMBER: MD for protein-carbohydrate complex Bill Ross (Thu Apr 22 2004 - 13:03:54 PDT)
AMBER: protein-carbohydrate complex Mikyung Seo (Thu Apr 22 2004 - 15:27:31 PDT)
Re: AMBER: protein-carbohydrate complex Bill Ross (Thu Apr 22 2004 - 15:39:16 PDT)
AMBER: solvateCap warning Helios Chen (Fri Apr 23 2004 - 02:47:25 PDT)
- Re: AMBER: solvateCap warning Guanglei Cui (Fri Apr 23 2004 - 06:47:49 PDT)
- Re: AMBER: solvateCap warning Chenglong Li (Fri Apr 23 2004 - 10:44:14 PDT)
AMBER: partition error in shake Guanglei Cui (Fri Apr 23 2004 - 08:18:19 PDT)
- Re: AMBER: partition error in shake Scott Brozell (Tue Apr 27 2004 - 15:26:44 PDT)
AMBER: pmemd and mpich - myrinet Lubos Vrbka (Fri Apr 23 2004 - 08:59:31 PDT)
- Re: AMBER: pmemd and mpich - myrinet Robert Duke (Fri Apr 23 2004 - 09:23:37 PDT)
  - Re: AMBER: pmemd and mpich - myrinet Lubos Vrbka (Fri Apr 23 2004 - 10:33:32 PDT)
  - Re: AMBER: pmemd and mpich - myrinet Lubos Vrbka (Sat Apr 24 2004 - 03:50:02 PDT)
- Re: AMBER: pmemd and mpich - myrinet Robert Duke (Fri Apr 23 2004 - 10:57:48 PDT)
  - Re: AMBER: pmemd and mpich - myrinet Lubos Vrbka (Fri Apr 23 2004 - 11:18:36 PDT)
- Re: AMBER: pmemd and mpich - myrinet Robert Duke (Sat Apr 24 2004 - 05:31:59 PDT)
  - Re: AMBER: pmemd and mpich - myrinet Lubos Vrbka (Sat Apr 24 2004 - 14:18:11 PDT)
    - AMBER: Optimizing a structure and the interpretation of it Ilyas Yildirim (Sat Apr 24 2004 - 16:08:14 PDT)
    - Re: AMBER: Optimizing a structure and the interpretation of it Kazuo Koyano (Sun Apr 25 2004 - 22:14:25 PDT)
  - AMBER: PMEMD scaling Lubos Vrbka (Sun Apr 25 2004 - 07:07:43 PDT)
    - Re: AMBER: PMEMD scaling Robert Duke (Sun Apr 25 2004 - 08:24:11 PDT)
  - Re: AMBER: pmemd and mpich - myrinet Lubos Vrbka (Tue Apr 27 2004 - 07:58:25 PDT)
AMBER: Parameters for nonpolar contribution to solvation Thomas Steinbrecher (Fri Apr 23 2004 - 10:48:42 PDT)
- Re: AMBER: Parameters for nonpolar contribution to solvation Holger Gohlke (Sat Apr 24 2004 - 05:06:34 PDT)
AMBER: parameters for neutral Arg Mikyung Seo (Fri Apr 23 2004 - 13:51:14 PDT)
- Re: AMBER: parameters for neutral Arg Adrian E. Roitberg (Fri Apr 23 2004 - 14:05:03 PDT)
AMBER: compile amber8 in linux with ifort quch quch (Fri Apr 23 2004 - 14:08:05 PDT)
- RE: AMBER: compile amber8 in linux with ifort Ross Walker (Fri Apr 23 2004 - 14:23:21 PDT)
- RE: AMBER: compile amber8 in linux with ifort Ross Walker (Fri Apr 23 2004 - 14:42:39 PDT)
  - RE: AMBER: compile amber8 in linux with ifort quch quch (Fri Apr 23 2004 - 14:50:52 PDT)
- Re: AMBER: compile amber8 in linux with ifort Viktor Hornak (Fri Apr 23 2004 - 14:49:49 PDT)
AMBER: Antechamber: problems with bcc correction Oliver Hucke (Fri Apr 23 2004 - 15:08:47 PDT)
- Re: AMBER: Antechamber: problems with bcc correction David A. Case (Sun Apr 25 2004 - 00:26:59 PDT)
AMBER: "matrix" in ptraj Sichun Yang (Fri Apr 23 2004 - 18:19:28 PDT)
- Re: AMBER: "matrix" in ptraj Holger Gohlke (Sat Apr 24 2004 - 04:47:41 PDT)
  - Re: AMBER: "matrix" in ptraj Sichun Yang (Sat Apr 24 2004 - 16:20:50 PDT)
    - Re: AMBER: "matrix" in ptraj Thomas E. Cheatham, III (Sat Apr 24 2004 - 17:30:34 PDT)
AMBER: NSNB parameter Helios Chen (Fri Apr 23 2004 - 20:45:42 PDT)
- Re: AMBER: NSNB parameter Chris Moth (Sat Apr 24 2004 - 05:31:55 PDT)
- Re: AMBER: NSNB parameter Robert Duke (Sat Apr 24 2004 - 07:05:05 PDT)
  - Re: AMBER: NSNB parameter David A. Case (Sat Apr 24 2004 - 13:13:11 PDT)
- Re: AMBER: NSNB parameter Robert Duke (Sat Apr 24 2004 - 20:05:51 PDT)
AMBER: tutorial of Biotin/Streptavidin Helios Chen (Sat Apr 24 2004 - 06:37:43 PDT)
- Re: AMBER: tutorial of Biotin/Streptavidin David A. Case (Sat Apr 24 2004 - 13:08:00 PDT)
AMBER: overlap between HE and OE in GLH Hailong Lin (Mon Apr 26 2004 - 08:49:36 PDT)
- Re: AMBER: overlap between HE and OE in GLH tim (Mon Apr 26 2004 - 07:11:08 PDT)
- RE: AMBER: overlap between HE and OE in GLH Yong Duan (Mon Apr 26 2004 - 10:17:00 PDT)
- RE: AMBER: overlap between HE and OE in GLH Yong Duan (Mon Apr 26 2004 - 10:24:32 PDT)
  - Re: AMBER: overlap between HE and OE in GLH Hailong Lin (Tue Apr 27 2004 - 07:32:47 PDT)
AMBER: neutral residues Mikyung Seo (Mon Apr 26 2004 - 09:33:04 PDT)
- Re: AMBER: neutral residues tim (Mon Apr 26 2004 - 07:26:09 PDT)
- RE: AMBER: neutral residues Yong Duan (Mon Apr 26 2004 - 10:25:46 PDT)
AMBER: PARMSCAN Sergio Emanuel Galembeck (Mon Apr 26 2004 - 11:29:05 PDT)
AMBER: universal recognition of chemicals Ioana Cozmuta (Mon Apr 26 2004 - 15:15:55 PDT)
- RE: AMBER: universal recognition of chemicals Ross Walker (Mon Apr 26 2004 - 15:35:41 PDT)
AMBER: Titratable amino acid termini Sarah Harris (Tue Apr 27 2004 - 02:43:16 PDT)
- Re: AMBER: Titratable amino acid termini John Mongan (Tue Apr 27 2004 - 16:28:15 PDT)
Ready and (0nline) amber preview.jpg Date Chatters (Tue Apr 27 2004 - 07:14:24 PDT)
Ready and (0nline) amber preview.jpg Date Chatters (Tue Apr 27 2004 - 07:14:28 PDT)
AMBER: xleap don't recognize formaldehyde? scopio (Tue Apr 27 2004 - 07:53:00 PDT)
- Re: AMBER: xleap don't recognize formaldehyde? David A. Case (Tue Apr 27 2004 - 11:56:30 PDT)
  - Re: AMBER: xleap don't recognize formaldehyde? anshul.imtech.res.in (Sat May 08 2004 - 12:44:33 PDT)
AMBER: AMBER Gibbs Memory problem Jiten (Tue Apr 27 2004 - 09:01:09 PDT)
- Re: AMBER: AMBER Gibbs Memory problem David A. Case (Tue Apr 27 2004 - 12:04:15 PDT)
AMBER: amber8 performance on linux cluster quch quch (Tue Apr 27 2004 - 10:05:45 PDT)
- Re: AMBER: amber8 performance on linux cluster Lubos Vrbka (Tue Apr 27 2004 - 10:26:14 PDT)
- RE: AMBER: amber8 performance on linux cluster Yong Duan (Tue Apr 27 2004 - 10:47:21 PDT)
AMBER: PMEMD and ifort 8 update Robert Duke (Tue Apr 27 2004 - 11:08:05 PDT)
- Re: AMBER: PMEMD and ifort 8 update David A. Case (Tue Apr 27 2004 - 11:52:02 PDT)
AMBER: Additional note on ld.so.conf vs. LD_LIBRARY_PATH Robert Duke (Tue Apr 27 2004 - 11:29:35 PDT)
- Re: AMBER: Additional note on ld.so.conf vs. LD_LIBRARY_PATH David E. Konerding DSD Staff (Tue Apr 27 2004 - 15:11:33 PDT)
- Re: AMBER: Additional note on ld.so.conf vs. LD_LIBRARY_PATH Robert Duke (Tue Apr 27 2004 - 15:36:51 PDT)
AMBER: %GIBBS-F-MISMATCH, The parm and coord files disagree on the number of atoms Jiten (Tue Apr 27 2004 - 19:29:25 PDT)
- Re: AMBER: %GIBBS-F-MISMATCH, The parm and coord files disagree on the number of atoms David A. Case (Wed Apr 28 2004 - 10:56:10 PDT)
AMBER: question on simulated annealing Venkata S Koppuravuri (Wed Apr 28 2004 - 09:00:39 PDT)
- Re: AMBER: question on simulated annealing David A. Case (Wed Apr 28 2004 - 09:24:59 PDT)
AMBER: questions about NMODE xhu1.memphis.edu (Wed Apr 28 2004 - 10:43:34 PDT)
- Re: AMBER: questions about NMODE David A. Case (Wed Apr 28 2004 - 12:06:01 PDT)
- Re: AMBER: questions about NMODE xhu1.memphis.edu (Wed Apr 28 2004 - 14:47:18 PDT)
  - Re: AMBER: questions about NMODE David A. Case (Wed Apr 28 2004 - 15:24:34 PDT)
- Re: AMBER: questions about NMODE xhu1.memphis.edu (Wed Apr 28 2004 - 16:04:04 PDT)
  - Re: AMBER: questions about NMODE David A. Case (Wed Apr 28 2004 - 17:21:41 PDT)
- Re: AMBER: questions about NMODE xhu1.memphis.edu (Thu Apr 29 2004 - 11:11:41 PDT)
  - Re: AMBER: questions about NMODE David A. Case (Thu Apr 29 2004 - 12:03:54 PDT)
- Re: AMBER: questions about NMODE xhu1.memphis.edu (Thu Apr 29 2004 - 16:34:08 PDT)
AMBER: a general question about the mmpbsa method a b (Wed Apr 28 2004 - 20:51:00 PDT)
AMBER: mm_pbsa question: MAXAT=10000 exceeded Fang, Jianwen (Wed Apr 28 2004 - 21:48:09 PDT)
- Re: AMBER: mm_pbsa question: MAXAT=10000 exceeded Holger Gohlke (Wed Apr 28 2004 - 23:42:27 PDT)
AMBER: VS: mmpbsa question Olayiwola Adekoya (Thu Apr 29 2004 - 02:32:32 PDT)
- Re: AMBER: VS: mmpbsa question Holger Gohlke (Fri Apr 30 2004 - 00:47:32 PDT)
AMBER: Redhat install Helios Chen (Thu Apr 29 2004 - 07:24:17 PDT)
- Re: AMBER: Redhat install David A. Case (Thu Apr 29 2004 - 10:32:33 PDT)
- Re: AMBER: Redhat install scopio (Thu Apr 29 2004 - 17:32:26 PDT)
- Re: AMBER: Redhat install Mengjuei Hsieh (Thu Apr 29 2004 - 21:44:12 PDT)
AMBER: CHARMM PSF to PRMTOP Gabbar Daaku (Thu Apr 29 2004 - 14:42:33 PDT)
AMBER: Angle Restraining Pooja Narang (Fri Apr 30 2004 - 00:17:30 PDT)
- Re: AMBER: Angle Restraining David A. Case (Fri Apr 30 2004 - 08:39:27 PDT)
AMBER: just sander not run Helios Chen (Fri Apr 30 2004 - 02:27:45 PDT)
- Re: AMBER: just sander not run David A. Case (Fri Apr 30 2004 - 08:34:47 PDT)
AMBER: energy criteria. anshul.imtech.res.in (Fri Apr 30 2004 - 13:51:04 PDT)
- Re: AMBER: energy criteria. David A. Case (Fri Apr 30 2004 - 08:36:13 PDT)
- Re: AMBER: energy criteria. Chris Moth (Fri Apr 30 2004 - 11:03:39 PDT)
AMBER: Amber8 compilation error Arvind (Fri Apr 30 2004 - 10:04:02 PDT)
- Re: AMBER: Amber8 compilation error David A. Case (Fri Apr 30 2004 - 11:31:57 PDT)
  - Re: AMBER: Amber8 compilation error Arvind (Fri Apr 30 2004 - 12:50:38 PDT)
AMBER: esp or resp for all_amino94.lib Mikyung Seo (Fri Apr 30 2004 - 16:06:54 PDT)
- Re: AMBER: esp or resp for all_amino94.lib FyD (Fri Apr 30 2004 - 16:28:57 PDT)
AMBER: problem for compiling amber7 by ifc8 scopio (Sat May 01 2004 - 05:26:57 PDT)
- Re: AMBER: problem for compiling amber7 by ifc8 Viktor Hornak (Sat May 01 2004 - 07:11:49 PDT)
  - Re: AMBER: problem for compiling amber7 by ifc8 scopio (Sun May 02 2004 - 17:15:58 PDT)
  - Re: AMBER: problem for compiling amber7 by ifc8 scopio (Sun May 02 2004 - 21:18:31 PDT)
AMBER: Gibbs and solvent caps Sébastien Osborne (Sat May 01 2004 - 11:59:07 PDT)
- Re: AMBER: Gibbs and solvent caps Miguel de Federico (Mon May 03 2004 - 03:28:47 PDT)
AMBER: ptraj: radius of gyration Sichun Yang (Sat May 01 2004 - 19:50:37 PDT)
- Re: AMBER: ptraj: radius of gyration Scott Brozell (Sun May 02 2004 - 01:09:12 PDT)
- Re: AMBER: ptraj: radius of gyration Bill Ross (Sun May 02 2004 - 13:12:23 PDT)
AMBER: xleap problem hj zou (Sun May 02 2004 - 06:49:40 PDT)
- Re: AMBER: xleap problem David A. Case (Sun May 02 2004 - 14:07:20 PDT)
- Re: AMBER: xleap problem Oliver Hucke (Sun May 02 2004 - 15:53:42 PDT)
AMBER: nmode analysis sebnem (Sun May 02 2004 - 17:52:12 PDT)
- Re: AMBER: nmode analysis David A. Case (Mon May 03 2004 - 08:50:44 PDT)
  - Re: AMBER: nmode analysis sebnem.mercury.chem.pitt.edu (Mon May 03 2004 - 09:31:18 PDT)
    - Re: AMBER: nmode analysis David A. Case (Mon May 03 2004 - 10:14:19 PDT)
AMBER: any program or tool Helios Chen (Mon May 03 2004 - 03:16:15 PDT)
- Re: AMBER: any program or tool Andreas Svrcek-Seiler (Mon May 03 2004 - 05:11:50 PDT)
- Re: AMBER: any program or tool Viktor Hornak (Mon May 03 2004 - 05:18:56 PDT)
AMBER: some bugfixes David A. Case (Mon May 03 2004 - 11:10:47 PDT)
- Re: AMBER: some bugfixes Sébastien Osborne (Mon May 03 2004 - 11:14:33 PDT)
  - Re: AMBER: some bugfixes David A. Case (Mon May 10 2004 - 16:10:08 PDT)
- Re: AMBER: some bugfixes Oliver Hucke (Tue May 04 2004 - 11:12:53 PDT)
  - Re: AMBER: some bugfixes Junmei Wang (Tue May 04 2004 - 12:23:55 PDT)
AMBER: resp demo files Kristy Mardis (Mon May 03 2004 - 12:29:45 PDT)
- Re: AMBER: resp demo files FyD (Mon May 03 2004 - 14:40:15 PDT)
AMBER: why delete water molecule Helios Chen (Mon May 03 2004 - 21:18:49 PDT)
- Re: AMBER: why delete water molecule Dr. Yong Duan (Tue May 04 2004 - 07:40:57 PDT)
  - Re: AMBER: why delete water molecule Oliver Hucke (Tue May 04 2004 - 09:23:01 PDT)
AMBER: separate the longitudinal and transverse vibrations frequencies xiaowei li (Mon May 03 2004 - 21:33:11 PDT)
- Re: AMBER: separate the longitudinal and transverse vibrations frequencies David A. Case (Tue May 04 2004 - 11:15:38 PDT)
AMBER: Troubles in the NTP simulation: "vlimit exceeded". Ülo Lille (Tue May 04 2004 - 03:16:24 PDT)
- Re: AMBER: Troubles in the NTP simulation: "vlimit exceeded". Jiten (Tue May 04 2004 - 03:58:20 PDT)
- Re: AMBER: Troubles in the NTP simulation: "vlimit exceeded". David A. Case (Tue May 04 2004 - 08:10:36 PDT)
AMBER: PMF correction factor Harvey, David Richard (Tue May 04 2004 - 06:35:13 PDT)
- Re: AMBER: PMF correction factor David A. Case (Tue May 04 2004 - 11:01:18 PDT)
AMBER: How to choose force constant? tomjas.poczta.onet.pl (Tue May 04 2004 - 06:48:44 PDT)
- Re: AMBER: How to choose force constant? David A. Case (Wed May 05 2004 - 15:00:14 PDT)
AMBER: Normal Mode Analysis possibility myang (Tue May 04 2004 - 08:52:05 PDT)
- Re: AMBER: Normal Mode Analysis possibility David A. Case (Tue May 04 2004 - 11:25:27 PDT)
Re: AMBER: Troubles in the NTP simulation: "vlimit exceeded". Bill Ross (Tue May 04 2004 - 09:44:16 PDT)
AMBER: reproduction of RESP charges for Gly Mikyung Seo (Tue May 04 2004 - 10:51:01 PDT)
- Re: AMBER: reproduction of RESP charges for Gly FyD (Tue May 04 2004 - 13:16:00 PDT)
- Re: AMBER: reproduction of RESP charges for Gly Bill Ross (Tue May 04 2004 - 13:24:41 PDT)
- Re: AMBER: reproduction of RESP charges for Gly Bill Ross (Tue May 04 2004 - 13:35:49 PDT)
  - Re: AMBER: reproduction of RESP charges for Gly FyD (Tue May 04 2004 - 13:48:43 PDT)
AMBER: problem with MM/PBSA Itziar Maestre Asenjo (Tue May 04 2004 - 09:38:32 PDT)
- Re: AMBER: problem with MM/PBSA Holger Gohlke (Wed May 05 2004 - 03:14:47 PDT)
AMBER: antechamber Guanglei Cui (Tue May 04 2004 - 19:49:28 PDT)
AMBER: methane box anshul.imtech.res.in (Wed May 05 2004 - 11:57:16 PDT)
- Re: AMBER: methane box FyD (Wed May 05 2004 - 08:36:08 PDT)
AMBER: ptraj analyze matrix entropy Marcin Krol (Wed May 05 2004 - 02:19:32 PDT)
- Re: AMBER: ptraj analyze matrix entropy Holger Gohlke (Wed May 05 2004 - 03:28:57 PDT)
  - Re: AMBER: ptraj analyze matrix entropy Marcin Krol (Wed May 05 2004 - 08:07:05 PDT)
- Re: AMBER: ptraj analyze matrix entropy Holger Gohlke (Wed May 05 2004 - 09:32:23 PDT)
- Re: AMBER: ptraj analyze matrix entropy Marcin Krol (Thu May 06 2004 - 06:48:02 PDT)
  - Re: AMBER: ptraj analyze matrix entropy David A. Case (Thu May 06 2004 - 08:29:30 PDT)
- Re: AMBER: ptraj analyze matrix entropy Holger Gohlke (Mon May 17 2004 - 11:05:57 PDT)
  - Re: AMBER: ptraj analyze matrix entropy David A. Case (Mon May 17 2004 - 12:36:41 PDT)
  - AMBER: Nonplanar ring systems in nucleic acid Ilyas Yildirim (Wed May 19 2004 - 13:14:14 PDT)
    - Re: AMBER: Nonplanar ring systems in nucleic acid darden (Wed May 19 2004 - 14:05:59 PDT)
    - Re: AMBER: Nonplanar ring systems in nucleic acid Jiri Sponer (Thu May 20 2004 - 05:42:16 PDT)
    - Re: AMBER: Nonplanar ring systems in nucleic acid Jiri Sponer (Thu May 20 2004 - 04:46:41 PDT)
AMBER: H Bonds anshul.imtech.res.in (Wed May 05 2004 - 13:07:01 PDT)
- Re: AMBER: H Bonds David A. Case (Wed May 05 2004 - 09:20:26 PDT)
  - Re: AMBER: H Bonds anshul.imtech.res.in (Thu May 06 2004 - 16:01:33 PDT)
- Re: AMBER: H Bonds Bill Ross (Thu May 06 2004 - 11:16:11 PDT)
  - Re: AMBER: H Bonds Sanjeev B.S. (Fri May 07 2004 - 01:38:24 PDT)
AMBER: Implicit solvents anshul.imtech.res.in (Wed May 05 2004 - 13:10:20 PDT)
- Re: AMBER: Implicit solvents David A. Case (Wed May 05 2004 - 08:54:56 PDT)
AMBER: reorientation in R.E.D Mikyung Seo (Wed May 05 2004 - 09:38:01 PDT)
- Re: AMBER: reorientation in R.E.D FyD (Wed May 05 2004 - 10:55:51 PDT)
AMBER: antechamber gives GDP 0 charge Raik Grünberg (Wed May 05 2004 - 13:17:53 PDT)
- Re: AMBER: antechamber gives GDP 0 charge Oliver Hucke (Wed May 05 2004 - 13:46:06 PDT)
Re: AMBER: H Bonds Bill Ross (Wed May 05 2004 - 14:18:22 PDT)
- Re: AMBER: H Bonds Sanjeev B.S. (Wed May 05 2004 - 22:09:06 PDT)
- Re: AMBER: H Bonds anshul.imtech.res.in (Thu May 06 2004 - 15:51:32 PDT)
AMBER: Solvent accessible surface area(LCPO) computation Sunil_Koovakkat.berlex.com (Wed May 05 2004 - 14:51:59 PDT)
- Re: AMBER: Solvent accessible surface area(LCPO) computation David A. Case (Fri May 07 2004 - 08:23:33 PDT)
AMBER: Sander klambda question Linda Prengaman (Wed May 05 2004 - 15:14:22 PDT)
- Re: AMBER: Sander klambda question David A. Case (Wed May 05 2004 - 16:43:44 PDT)
AMBER: simulated anealing ...vlimit exceed anshul.imtech.res.in (Thu May 06 2004 - 14:50:35 PDT)
- Re: AMBER: simulated anealing ...vlimit exceed Carlos Simmerling (Thu May 06 2004 - 04:47:48 PDT)
  - Re: AMBER: simulated anealing ...vlimit exceed anshul.imtech.res.in (Thu May 06 2004 - 16:14:53 PDT)
    - Re: AMBER: simulated anealing ...vlimit exceed Carlos Simmerling (Thu May 06 2004 - 06:24:02 PDT)
    - AMBER: simulated anealing ...vlimit exceed Michele Porro (Tue May 11 2004 - 00:24:56 PDT)
AMBER: Possible amber8 antechamber PDB parsing bug Mark Williamson (Thu May 06 2004 - 08:16:19 PDT)
AMBER: ions in mm_pbsa Fang, Jianwen (Thu May 06 2004 - 08:30:12 PDT)
- FW: AMBER: ions in mm_pbsa S. Frank Yan (Thu May 06 2004 - 10:23:55 PDT)
- Re: AMBER: ions in mm_pbsa Thomas E. Cheatham, III (Thu May 06 2004 - 12:07:42 PDT)
  - AMBER: reference with ptraj John (Thu May 06 2004 - 12:50:48 PDT)
    - Re: AMBER: reference with ptraj Thomas E. Cheatham, III (Thu May 06 2004 - 13:11:58 PDT)
    - Re: AMBER: reference with ptraj Bill Ross (Thu May 06 2004 - 15:05:55 PDT)
    - Re: AMBER: reference with ptraj Thomas E. Cheatham, III (Thu May 06 2004 - 15:12:18 PDT)
    - Re: AMBER: reference with ptraj Fernandez-Carmona Juan (Thu May 06 2004 - 23:27:53 PDT)
AMBER: Ligand from CCDC. Osman Gani (Thu May 06 2004 - 08:38:16 PDT)
AMBER: Possible amber8 antechamber PDB parsing bug Junmei Wang (Thu May 06 2004 - 10:09:30 PDT)
AMBER: Computing psec/day using Amber 8 Craig TOEPFER (Thu May 06 2004 - 11:21:53 PDT)
- Re: AMBER: Computing psec/day using Amber 8 David A. Case (Thu May 06 2004 - 11:42:37 PDT)
- Re: AMBER: Computing psec/day using Amber 8 Craig TOEPFER (Thu May 06 2004 - 12:19:01 PDT)
  - Re: AMBER: Computing psec/day using Amber 8 David A. Case (Thu May 06 2004 - 12:27:10 PDT)
AMBER: Opteron PMEMD Gary Waters (Thu May 06 2004 - 11:29:56 PDT)
- Re: AMBER: Opteron PMEMD Robert Duke (Thu May 06 2004 - 13:31:46 PDT)
  - Re: AMBER: Opteron PMEMD David A. Case (Thu May 06 2004 - 15:09:47 PDT)
AMBER: cap waters always flexible? Oliver Hucke (Thu May 06 2004 - 13:41:19 PDT)
AMBER: choosing 3 atoms for reorientaion in R.E.D Mikyung Seo (Thu May 06 2004 - 14:38:19 PDT)
- Re: AMBER: choosing 3 atoms for reorientaion in R.E.D FyD (Thu May 06 2004 - 15:00:44 PDT)
AMBER: solvent cap and eedmeth Oliver Hucke (Thu May 06 2004 - 16:31:42 PDT)
- Re: AMBER: solvent cap and eedmeth David A. Case (Fri May 07 2004 - 08:20:18 PDT)
AMBER: ptraj analyze matrix entropy Marcin Krol (Fri May 07 2004 - 01:01:23 PDT)
- Re: AMBER: ptraj analyze matrix entropy Holger Gohlke (Fri May 07 2004 - 05:48:51 PDT)
AMBER: hbond in ptraj Qiang Lu (Fri May 07 2004 - 11:43:33 PDT)
- Re: AMBER: hbond in ptraj Thomas E. Cheatham, III (Fri May 07 2004 - 12:15:15 PDT)
AMBER: Charges and atom type anshul.imtech.res.in (Sat May 08 2004 - 14:06:25 PDT)
AMBER: what is its file format ? scopio (Sat May 08 2004 - 07:13:21 PDT)
AMBER: ligand minimization atobak.eden.rutgers.edu (Sat May 08 2004 - 14:13:21 PDT)
AMBER: MD with NTR + NMROPT Martin Fabani (Mon May 10 2004 - 01:56:28 PDT)
- Re: AMBER: MD with NTR + NMROPT David A. Case (Mon May 10 2004 - 08:46:06 PDT)
  - Re: AMBER: MD with NTR + NMROPT anshul.imtech.res.in (Wed May 12 2004 - 08:07:49 PDT)
    - Re: AMBER: MD with NTR + NMROPT David A. Case (Wed May 12 2004 - 12:09:24 PDT)
AMBER: HIS protonation Stefano.Pieraccini.unimi.it (Mon May 10 2004 - 02:50:40 PDT)
- Re: AMBER: HIS protonation scopio (Mon May 10 2004 - 04:00:19 PDT)
AMBER: ptraj read in matrix Marcin Krol (Mon May 10 2004 - 04:57:25 PDT)
- Re: AMBER: ptraj read in matrix Holger Gohlke (Tue May 11 2004 - 07:45:11 PDT)
AMBER: A parm file suit for half beta and half alpha structure Qiang Lu (Mon May 10 2004 - 11:51:57 PDT)
AMBER: question about mm-pbsa aini.UMDNJ.EDU (Mon May 10 2004 - 17:10:05 PDT)
- Re: AMBER: question about mm-pbsa Thomas Steinbrecher (Mon May 10 2004 - 18:10:09 PDT)
AMBER: what does EAMBER stand for? scopio (Mon May 10 2004 - 18:08:35 PDT)
- Re: AMBER: what does EAMBER stand for? David A. Case (Tue May 11 2004 - 10:30:56 PDT)
- Re: AMBER: what does EAMBER stand for? Scott Brozell (Tue May 11 2004 - 10:45:09 PDT)
AMBER: mm-pbsa:- atom charges and radii ? Jeffrey Dyason (Tue May 11 2004 - 01:07:12 PDT)
- Re: AMBER: mm-pbsa:- atom charges and radii ? Thomas E. Cheatham, III (Tue May 11 2004 - 07:24:17 PDT)
  - Re: AMBER: mm-pbsa:- atom charges and radii ? Ray Luo (Mon May 10 2004 - 23:21:06 PDT)
- Re: AMBER: mm-pbsa:- atom charges and radii ? Holger Gohlke (Tue May 11 2004 - 23:40:52 PDT)
AMBER: gaussian03 output in antechamber Stefano.Pieraccini.unimi.it (Tue May 11 2004 - 02:27:46 PDT)
AMBER: PMEMD Built ? Wont run.. Gary Waters (Tue May 11 2004 - 09:00:33 PDT)
- Re: AMBER: PMEMD Built ? Wont run.. david.evans.ulsop.ac.uk (Tue May 11 2004 - 09:32:18 PDT)
  - Re: AMBER: PMEMD Built ? Wont run.. Gary Waters (Tue May 11 2004 - 09:55:14 PDT)
- Re: AMBER: PMEMD Built ? Wont run.. Amber admin (Tue May 11 2004 - 10:25:03 PDT)
  - Re: AMBER: PMEMD Built ? Wont run.. Gary Waters (Tue May 11 2004 - 10:36:16 PDT)
    - Re: AMBER: PMEMD Built ? Wont run.. Scott Brozell (Tue May 11 2004 - 12:41:15 PDT)
    - Re: AMBER: PMEMD Built ? Wont run.. Gary Waters (Tue May 11 2004 - 13:08:49 PDT)
- Re: AMBER: PMEMD Built ? Wont run.. Amber Administration (Tue May 11 2004 - 14:15:14 PDT)
AMBER: ptraj and LES Guanglei Cui (Tue May 11 2004 - 14:00:12 PDT)
- Re: AMBER: ptraj and LES David A. Case (Wed May 12 2004 - 08:19:00 PDT)
  - Re: AMBER: ptraj and LES Guanglei Cui (Wed May 12 2004 - 12:34:31 PDT)
AMBER: AMBER charges(Cornell et al JACS, 1995) and R.E.D Mikyung Seo (Tue May 11 2004 - 15:51:01 PDT)
- Re: AMBER: AMBER charges(Cornell et al JACS, 1995) and R.E.D FyD (Wed May 12 2004 - 09:42:31 PDT)
- RE: AMBER: AMBER charges(Cornell et al JACS, 1995) and R.E.D FyD (Wed May 12 2004 - 11:01:31 PDT)
- Re: AMBER: AMBER charges(Cornell et al JACS, 1995) and R.E.D Piotr Cieplak (Wed May 12 2004 - 11:57:20 PDT)
AMBER: dummy atom other than H Carsten Detering (Tue May 11 2004 - 18:12:22 PDT)
- Re: AMBER: dummy atom other than H David A. Case (Wed May 12 2004 - 12:30:26 PDT)
- Re: AMBER: dummy atom other than H Carsten Detering (Wed May 12 2004 - 14:18:23 PDT)
AMBER: Problem : antechamber produces no output Marc Perea (Tue May 11 2004 - 03:19:52 PDT)
- Re: AMBER: Problem : antechamber produces no output Junmei Wang (Wed May 12 2004 - 07:40:00 PDT)
AMBER: gaussian03 output in antechamber Stefano.Pieraccini.unimi.it (Wed May 12 2004 - 01:46:17 PDT)
AMBER: shake option in sander Lishan Yao (Wed May 12 2004 - 06:32:48 PDT)
- Re: AMBER: shake option in sander David A. Case (Wed May 12 2004 - 12:11:53 PDT)
AMBER: dihedral driver Beale, John (Wed May 12 2004 - 06:58:35 PDT)
AMBER: performance of periodic vs. non-periodic simulation Oliver Hucke (Wed May 12 2004 - 12:08:18 PDT)
- Re: AMBER: performance of periodic vs. non-periodic simulation Thomas E. Cheatham, III (Wed May 12 2004 - 13:17:33 PDT)
- Re: AMBER: performance of periodic vs. non-periodic simulation Oliver Hucke (Wed May 12 2004 - 13:42:50 PDT)
- Re: AMBER: performance of periodic vs. non-periodic simulation Ben Cossins (Thu May 13 2004 - 02:22:21 PDT)
- Re: AMBER: performance of periodic vs. non-periodic simulation Oliver Hucke (Thu May 13 2004 - 09:14:08 PDT)
AMBER: tmd questions hj zou (Wed May 12 2004 - 19:07:36 PDT)
- Re: AMBER: tmd questions Carlos Simmerling (Thu May 13 2004 - 04:41:31 PDT)
  - Re: AMBER: tmd questions Viktor Hornak (Thu May 13 2004 - 05:16:36 PDT)
- AMBER: Atom type with/without POL Jiten (Thu May 13 2004 - 07:01:38 PDT)
AMBER: antechamber/Mopac: strange GTP charges Raik Grünberg (Thu May 13 2004 - 10:57:06 PDT)
- Re: AMBER: antechamber/Mopac: strange GTP charges carlsonh.umich.edu (Thu May 13 2004 - 11:40:03 PDT)
- Re: AMBER: antechamber/Mopac: strange GTP charges David A. Case (Thu May 13 2004 - 11:41:18 PDT)
  - Re: AMBER: antechamber/Mopac: strange GTP charges Raik Grünberg (Fri May 14 2004 - 03:35:13 PDT)
    - Re: AMBER: antechamber/Mopac: strange GTP charges David A. Case (Fri May 14 2004 - 12:20:24 PDT)
    - Re: AMBER: antechamber/Mopac: strange GTP charges Raik Grünberg (Mon May 17 2004 - 08:38:17 PDT)
    - Re: AMBER: antechamber/Mopac: strange GTP charges David A. Case (Mon May 17 2004 - 12:31:38 PDT)
AMBER: sander_classic for cap simulations? Oliver Hucke (Thu May 13 2004 - 15:43:36 PDT)
- Re: AMBER: sander_classic for cap simulations? David A. Case (Mon May 17 2004 - 13:18:41 PDT)
AMBER: Decomposition in MMPBSA Thomas Steinbrecher (Thu May 13 2004 - 17:15:03 PDT)
AMBER: FAD cofactor. Osman Gani (Fri May 14 2004 - 02:34:28 PDT)
AMBER: Converting ORAC's topology file to AMBER's prepi file scopio (Fri May 14 2004 - 05:30:32 PDT)
AMBER: Simulated annealing ...vlimit problem Venkata S Koppuravuri (Fri May 14 2004 - 07:22:44 PDT)
- Re: AMBER: Simulated annealing ...vlimit problem David A. Case (Sat May 15 2004 - 09:14:06 PDT)
  - AMBER: Program error in testing of Amber8 Do Anh Tuan (Sat May 15 2004 - 21:16:44 PDT)
    - Re: AMBER: Program error in testing of Amber8 Scott Brozell (Sun May 16 2004 - 16:17:44 PDT)
  - Re: AMBER: Simulated annealing ...vlimit problem Venkata S Koppuravuri (Mon May 17 2004 - 10:00:44 PDT)
    - Re: AMBER: Simulated annealing ...vlimit problem Carlos Simmerling (Mon May 17 2004 - 10:08:56 PDT)
    - Re: AMBER: Simulated annealing ...vlimit problem David A. Case (Mon May 17 2004 - 12:27:30 PDT)
    - Re: AMBER: Simulated annealing ...vlimit problem Narang Manpreet Kaur (Tue May 18 2004 - 07:09:31 PDT)
- Re: AMBER: Simulated annealing ...vlimit problem anshul.imtech.res.in (Sun May 16 2004 - 13:01:55 PDT)
AMBER: questions on mm_pbsa Fang, Jianwen (Fri May 14 2004 - 11:49:54 PDT)
- Re: AMBER: questions on mm_pbsa Holger Gohlke (Tue May 18 2004 - 08:18:24 PDT)
AMBER: solvents reference. Herbert Georg (Fri May 14 2004 - 12:56:38 PDT)
- Re: AMBER: solvents reference. David A. Case (Fri May 14 2004 - 13:16:06 PDT)
Five Fingered F'in amber Unreal Photos Fist Action (Fri May 14 2004 - 23:23:15 PDT)
Five Fingered F'in amber Unreal Photos Fist Action (Fri May 14 2004 - 23:23:18 PDT)
AMBER: antechamber anshul.imtech.res.in (Sat May 15 2004 - 09:43:48 PDT)
- Re: AMBER: antechamber David A. Case (Sat May 15 2004 - 09:02:30 PDT)
AMBER: install RESP Gustavo Pierdominici Sottile (Sat May 15 2004 - 04:54:41 PDT)
- Re: AMBER: install RESP David A. Case (Sat May 15 2004 - 09:03:57 PDT)
AMBER: installing RESP Gustavo Pierdominici Sottile (Sat May 15 2004 - 04:52:59 PDT)
AMBER: energy conservation with GB !! Pradipta Bandyopadhyay (Sat May 15 2004 - 23:27:01 PDT)
- Re: AMBER: energy conservation with GB !! Dr. Yong Duan (Sat May 15 2004 - 23:58:25 PDT)
AMBER: parametrizacion partial charges Gustavo Pierdominici Sottile (Mon May 17 2004 - 06:45:58 PDT)
- Re: AMBER: parametrizacion partial charges FyD (Mon May 17 2004 - 08:37:02 PDT)
AMBER: why EGB = nan Fang, Jianwen (Mon May 17 2004 - 07:54:44 PDT)
AMBER: Gustavo Pierdominici Sottile (Mon May 17 2004 - 11:38:53 PDT)
- Re: AMBER: David A. Case (Thu May 20 2004 - 10:14:13 PDT)
AMBER: Treating atom type LP the same as EP Sarah Wittkopp (Mon May 17 2004 - 12:16:20 PDT)
AMBER: thermodynamic integration of ring opening Carsten Detering (Mon May 17 2004 - 13:37:42 PDT)
- Re: AMBER: thermodynamic integration of ring opening David A. Case (Mon May 17 2004 - 16:21:15 PDT)
  - AMBER: CG maxitn exceeded Obdulia Rabal (Tue May 18 2004 - 09:29:53 PDT)
    - Re: AMBER: CG maxitn exceeded Ray Luo (Mon May 17 2004 - 12:10:29 PDT)
- Re: AMBER: thermodynamic integration of ring opening Bill Ross (Mon May 17 2004 - 17:10:36 PDT)
  - Re: AMBER: thermodynamic integration of ring opening M. L. Dodson (Tue May 18 2004 - 05:33:28 PDT)
- Re: AMBER: thermodynamic integration of ring opening Bill Ross (Tue May 18 2004 - 12:08:13 PDT)
Re: AMBER: thermodynamic integration of ring opening Bill Ross (Mon May 17 2004 - 15:47:24 PDT)
- Re: AMBER: thermodynamic integration of ring opening Bill Ross (Mon May 17 2004 - 16:42:25 PDT)
- Re: AMBER: thermodynamic integration of ring opening M. L. Dodson (Mon May 17 2004 - 16:46:29 PDT)
AMBER: single amino acid energy Helios Chen (Tue May 18 2004 - 01:15:02 PDT)
- Re: AMBER: single amino acid energy Holger Gohlke (Tue May 18 2004 - 08:23:26 PDT)
AMBER: PCA prep file Majid moghaddam (Tue May 18 2004 - 01:19:26 PDT)
AMBER: CAP PROTOCOL SIMULATION Obdulia Rabal (Tue May 18 2004 - 02:32:29 PDT)
- Re: AMBER: CAP PROTOCOL SIMULATION Andreas Svrcek-Seiler (Tue May 18 2004 - 05:13:56 PDT)
  - Re: AMBER: CAP PROTOCOL SIMULATION Ray Luo (Mon May 17 2004 - 14:43:55 PDT)
- Re: AMBER: CAP PROTOCOL SIMULATION Oliver Hucke (Tue May 18 2004 - 14:07:45 PDT)
  - Re: AMBER: CAP PROTOCOL SIMULATION Ray Luo (Mon May 17 2004 - 16:07:17 PDT)
    - Re: AMBER: CAP PROTOCOL SIMULATION David A. Case (Tue May 18 2004 - 15:47:26 PDT)
AMBER: Clean in RESP Gustavo Pierdominici Sottile (Tue May 18 2004 - 04:46:38 PDT)
- Re: AMBER: Clean in RESP David A. Case (Tue May 18 2004 - 07:55:42 PDT)
AMBER: DEBUG and GB Jones, Garth A (Tue May 18 2004 - 05:02:32 PDT)
- Re: AMBER: DEBUG and GB David A. Case (Thu May 20 2004 - 11:34:38 PDT)
AMBER: NTT=4 Joachim Reichelt (Tue May 18 2004 - 07:30:33 PDT)
- Re: AMBER: NTT=4 David A. Case (Tue May 18 2004 - 07:57:19 PDT)
  - Re: AMBER: NTT=4 Joachim Reichelt (Tue May 18 2004 - 10:01:50 PDT)
AMBER: IGR1/grnam1 problem Marcin Krol (Tue May 18 2004 - 10:40:58 PDT)
- Re: AMBER: IGR1/grnam1 problem David A. Case (Sat May 22 2004 - 21:03:16 PDT)
AMBER: PB bomb in pb_saarc S. Frank Yan (Tue May 18 2004 - 13:41:41 PDT)
- Re: AMBER: PB bomb in pb_saarc Ray Luo (Mon May 17 2004 - 15:58:21 PDT)
AMBER: average structure from traj Holly Freedman (Tue May 18 2004 - 14:30:07 PDT)
AMBER: Removal of rotation: Flying ice cube koby levy (Tue May 18 2004 - 17:23:54 PDT)
- Re: AMBER: Removal of rotation: Flying ice cube Carlos Simmerling (Tue May 18 2004 - 17:39:59 PDT)
AMBER: rmsd over residues using ptraj Qiang Lu (Tue May 18 2004 - 17:41:16 PDT)
- RE: AMBER: rmsd over residues using ptraj Ty Curtis (Wed May 19 2004 - 09:23:50 PDT)
  - Re[2]: AMBER: rmsd over residues using ptraj Qiang Lu (Wed May 19 2004 - 10:19:38 PDT)
Re: AMBER: rmsd over residues using ptraj Bill Ross (Tue May 18 2004 - 17:57:54 PDT)
AMBER: Does this warning matter? (about improper torsion parameters) J. Zhang, Dr (Tue May 18 2004 - 20:04:32 PDT)
- Re: AMBER: Does this warning matter? (about improper torsion parameters) David A. Case (Wed May 19 2004 - 08:00:59 PDT)
  - Re: Re: AMBER: Does this warning matter? (about improper torsion parameters) J. Zhang, Dr (Wed May 19 2004 - 18:57:35 PDT)
AMBER: Reproducing the energy during restart in MD! Pradipta Bandyopadhyay (Tue May 18 2004 - 23:33:27 PDT)
- Re: AMBER: Reproducing the energy during restart in MD! Carlos Simmerling (Wed May 19 2004 - 06:41:17 PDT)
AMBER: problem in antechamber Suwipa saen-oon (Wed May 19 2004 - 01:27:24 PDT)
- Re: AMBER: problem in antechamber Junmei Wang (Wed May 19 2004 - 15:21:43 PDT)
AMBER: ptraj bug? Ian Withers (Wed May 19 2004 - 07:33:38 PDT)
- Re: AMBER: ptraj bug? Holger Gohlke (Wed May 19 2004 - 08:31:12 PDT)
Extreme Privacy Violation 4896 Deanna Yarbro (Wed May 19 2004 - 09:48:11 PDT)
AMBER: address error Carsten Detering (Wed May 19 2004 - 10:09:12 PDT)
Re: Re[2]: AMBER: rmsd over residues using ptraj Bill Ross (Wed May 19 2004 - 11:34:08 PDT)
- Re[4]: AMBER: rmsd over residues using ptraj Qiang Lu (Wed May 19 2004 - 12:19:33 PDT)
Re: Re[4]: AMBER: rmsd over residues using ptraj Bill Ross (Wed May 19 2004 - 14:15:01 PDT)
AMBER: parallel installation problem Oliver Hucke (Wed May 19 2004 - 15:17:08 PDT)
- Re: AMBER: parallel installation problem Guanglei Cui (Wed May 19 2004 - 18:54:21 PDT)
- Re: AMBER: parallel installation problem Oliver Hucke (Mon May 24 2004 - 16:57:01 PDT)
AMBER: amber7, namelist, xlf and osx Knut Langsetmo (Wed May 19 2004 - 15:47:26 PDT)
- Re: AMBER: amber7, namelist, xlf and osx Mengjuei Hsieh (Wed May 19 2004 - 17:56:23 PDT)
- Re: AMBER: amber7, namelist, xlf and osx Knut Langsetmo (Tue May 25 2004 - 06:17:26 PDT)
AMBER: Amber8 on Tru64 UNIX on Alpha systems Jiten (Wed May 19 2004 - 18:28:50 PDT)
- Re: AMBER: Amber8 on Tru64 UNIX on Alpha systems David A. Case (Thu May 20 2004 - 08:22:26 PDT)
- Re: AMBER: Amber8 on Tru64 UNIX on Alpha systems Jiten (Thu May 20 2004 - 17:49:42 PDT)
  - Re: AMBER: Amber8 on Tru64 UNIX on Alpha systems David A. Case (Thu May 20 2004 - 18:33:14 PDT)
    - Re: AMBER: Amber8 on Tru64 UNIX on Alpha systems James W. Caldwell (Thu May 20 2004 - 20:02:01 PDT)
- Re: AMBER: Amber8 on Tru64 UNIX on Alpha systems Jiten (Mon May 24 2004 - 20:54:40 PDT)
AMBER: instalation of RES anshul.imtech.res.in (Thu May 20 2004 - 11:22:08 PDT)
- Re: AMBER: instalation of RES David A. Case (Thu May 20 2004 - 10:15:35 PDT)
AMBER: SHAKE in thermodynamic integration by way of riccardo nifosi (Thu May 20 2004 - 03:38:21 PDT)
- Re: AMBER: SHAKE in thermodynamic integration David A. Case (Thu May 20 2004 - 11:01:17 PDT)
AMBER: pbsa calculation on part of the molecule S. Frank Yan (Thu May 20 2004 - 13:25:46 PDT)
- Re: AMBER: pbsa calculation on part of the molecule Ray Luo (Wed May 19 2004 - 13:31:50 PDT)
AMBER: Ammonia Lishan Yao (Thu May 20 2004 - 14:11:43 PDT)
AMBER: PF6- force field parameters Jiten (Thu May 20 2004 - 17:32:29 PDT)
RE: AMBER: pbsa calculation on part of the molecule & nmode analysis S. Frank Yan (Thu May 20 2004 - 18:06:11 PDT)
- Re: AMBER: pbsa calculation on part of the molecule & nmode analysis David A. Case (Thu May 20 2004 - 18:40:10 PDT)
AMBER: Problem compiling amber7 Miguel (Fri May 21 2004 - 02:15:10 PDT)
- Re: AMBER: Problem compiling amber7 David A. Case (Fri May 21 2004 - 08:23:09 PDT)
- Re: AMBER: Problem compiling amber7 Viktor Hornak (Mon May 24 2004 - 08:19:04 PDT)
  - Re: AMBER: Problem compiling amber7 Miguel (Tue May 25 2004 - 02:54:55 PDT)
    - Re: AMBER: Problem compiling amber7 scopio (Tue May 25 2004 - 05:15:28 PDT)
    - Re: AMBER: Problem compiling amber7 Andreas Svrcek-Seiler (Tue May 25 2004 - 05:21:40 PDT)
    - Re: AMBER: Problem compiling amber7 Viktor Hornak (Tue May 25 2004 - 05:20:40 PDT)
    - Re: AMBER: Problem compiling amber7 Joachim Reichelt (Tue May 25 2004 - 05:27:59 PDT)
Request to mailing list Ahmadis rejected ahmadis-bounces.imperial.ac.uk (Fri May 21 2004 - 05:31:19 PDT)
AMBER: NHE problem Ryan Ye (Fri May 21 2004 - 22:36:44 PDT)
- Re: AMBER: NHE problem David A. Case (Sat May 22 2004 - 16:55:52 PDT)
  - Re: AMBER: NHE problem Ryan Ye (Sun May 23 2004 - 08:19:56 PDT)
    - Re: AMBER: NHE problem David A. Case (Sun May 23 2004 - 09:14:34 PDT)
- Re: AMBER: NHE problem Mengjuei Hsieh (Sat May 22 2004 - 17:30:07 PDT)
AMBER: a question about Van der waals radius Xiao He (Sat May 22 2004 - 05:07:05 PDT)
- Re: AMBER: a question about Van der waals radius Jiri Sponer (Sat May 22 2004 - 05:41:12 PDT)
  - Re: Re: AMBER: a question about Van der waals radius Xiao He (Sat May 22 2004 - 06:55:05 PDT)
    - Re: Re: AMBER: a question about Van der waals radius Jiri Sponer (Sat May 22 2004 - 07:09:46 PDT)
    - Re: Re: Re: AMBER: a question about Van der waals radius Xiao He (Sat May 22 2004 - 07:29:56 PDT)
    - Re: Re: Re: AMBER: a question about Van der waals radius Jiri Sponer (Sat May 22 2004 - 07:42:27 PDT)
    - Re: Re: Re: Re: AMBER: a question about Van der waals radius Xiao He (Sat May 22 2004 - 08:01:28 PDT)
    - Re: Re: Re: Re: Re: AMBER: a question about Van der waals radius Ye Mei (Sun May 23 2004 - 23:54:30 PDT)
AMBER: parallel installation problem Oliver Hucke (Sat May 22 2004 - 17:40:17 PDT)
- Re: AMBER: parallel installation problem Viktor Hornak (Mon May 24 2004 - 07:38:50 PDT)
AMBER: h bond Ye Mei (Sun May 23 2004 - 23:27:37 PDT)
AMBER: performance of amber7/xlf/macosX 10.3 with JAC on xserve g5.2.0GHz Tru Huynh (Mon May 24 2004 - 00:45:39 PDT)
- Re: AMBER: performance of amber7/xlf/macosX 10.3 with JAC on xserve g5.2.0GHz David A. Case (Mon May 24 2004 - 08:37:29 PDT)
- Re: AMBER: performance of amber7/xlf/macosX 10.3 with JAC on xserve g5@2.0GHz Mengjuei Hsieh (Mon May 24 2004 - 12:12:39 PDT)
  - Re: AMBER: performance of amber7/xlf/macosX 10.3 with JAC on xserve g5.2.0GHz Tru Huynh (Tue May 25 2004 - 07:31:34 PDT)
AMBER: Free energies using Sander in Amber8 Jiten (Mon May 24 2004 - 19:52:52 PDT)
- Re: AMBER: Free energies using Sander in Amber8 David A. Case (Mon May 24 2004 - 21:36:22 PDT)
AMBER: IOUTFM and binary/unformatted files error Martin Mucha (Tue May 25 2004 - 00:18:44 PDT)
- Re: AMBER: IOUTFM and binary/unformatted files error David A. Case (Tue May 25 2004 - 08:01:28 PDT)
AMBER: Installation AMber 8: "cannot find -lU77" A. Hungie (Tue May 25 2004 - 06:21:09 PDT)
AMBER: mm_pbsa energy decomposition error Fang, Jianwen (Tue May 25 2004 - 07:40:32 PDT)
- Re: AMBER: mm_pbsa energy decomposition error David A. Case (Tue May 25 2004 - 08:20:13 PDT)
AMBER: Compiling AMBER MPI program using GCC/G77 compiler and MPICH on AMD OPTERON 64 Ming Lei (Tue May 25 2004 - 08:27:49 PDT)
- Re: AMBER: Compiling AMBER MPI program using GCC/G77 compiler and MPICH on AMD OPTERON 64 Scott Brozell (Tue May 25 2004 - 12:24:23 PDT)
AMBER: Scaling nb between groups Marcin Krol (Tue May 25 2004 - 08:34:00 PDT)
- Re: AMBER: Scaling nb between groups David A. Case (Tue May 25 2004 - 13:52:30 PDT)
  - AMBER: Surface E&S Potential Mapping Ilyas Yildirim (Tue May 25 2004 - 14:14:45 PDT)
AMBER: ptraj Holly Freedman (Tue May 25 2004 - 09:16:42 PDT)
- RE: AMBER: ptraj Ross Walker (Tue May 25 2004 - 10:35:39 PDT)
  - Re: AMBER: ptraj Holly Freedman (Tue May 25 2004 - 17:45:24 PDT)
- AMBER: Bug in babel conversion (while following the RED manual in pp.15) Ilyas Yildirim (Tue May 25 2004 - 11:00:39 PDT)
  - Re: AMBER: Bug in babel conversion FyD (Tue May 25 2004 - 11:14:55 PDT)
- Re: AMBER: ptraj scopio (Tue May 25 2004 - 16:49:47 PDT)
  - Re: AMBER: ptraj Holly Freedman (Wed May 26 2004 - 10:30:07 PDT)
AMBER: A problem for compiling amber8 parallel version Chen Yongzhi (Tue May 25 2004 - 13:58:37 PDT)
- Re: AMBER: A problem for compiling amber8 parallel version David A. Case (Wed May 26 2004 - 10:08:43 PDT)
AMBER: protein is out of the water box Feng, Hanqiao (NIH/NCI) (Tue May 25 2004 - 15:35:01 PDT)
- Re: AMBER: protein is out of the water box David A. Case (Wed May 26 2004 - 09:17:00 PDT)
AMBER: Cannot read in sander bybaker.itsa.ucsf.edu (Tue May 25 2004 - 15:51:48 PDT)
- Re: AMBER: Cannot read in sander David A. Case (Wed May 26 2004 - 09:14:52 PDT)
- Re: AMBER: Cannot read in sander bybaker.itsa.ucsf.edu (Wed May 26 2004 - 17:47:30 PDT)
  - RE: AMBER: Cannot read in sander Ross Walker (Wed May 26 2004 - 18:08:48 PDT)
  - Re: AMBER: Cannot read in sander David A. Case (Thu May 27 2004 - 08:11:03 PDT)
    - AMBER: fit a 3D line to points myang (Thu May 27 2004 - 14:11:08 PDT)
- Re: AMBER: Cannot read in sander bybaker.itsa.ucsf.edu (Thu May 27 2004 - 13:56:12 PDT)
  - RE: AMBER: Cannot read in sander Ross Walker (Thu May 27 2004 - 15:36:10 PDT)
Re: AMBER: Compiling AMBER MPI program using GCC/G77 compiler andMPICH on AMD OPTERON 64 Jyh-Shyong Ho (Tue May 25 2004 - 17:07:34 PDT)
AMBER: Amber 8 compilation A. Hungie (Wed May 26 2004 - 09:23:07 PDT)
- Re: AMBER: Amber 8 compilation Viktor Hornak (Wed May 26 2004 - 10:08:08 PDT)
AMBER: types of water atom Gustavo Pierdominici Sottile (Wed May 26 2004 - 10:06:16 PDT)
Re: AMBER: types of water atom Piotr Cieplak (Wed May 26 2004 - 10:28:17 PDT)
- Re: AMBER: types of water atom Gustavo Pierdominici Sottile (Thu May 27 2004 - 12:28:27 PDT)
  - Re: AMBER: types of water atom David A. Case (Thu May 27 2004 - 13:34:59 PDT)
    - Re: AMBER: types of water atom Gustavo Pierdominici Sottile (Fri May 28 2004 - 11:25:45 PDT)
AMBER: amber 8 under windows XP Adrian E. Roitberg (Wed May 26 2004 - 11:50:02 PDT)
- RE: AMBER: amber 8 under windows XP Ross Walker (Wed May 26 2004 - 12:03:54 PDT)
- Re: AMBER: amber 8 under windows XP David A. Case (Wed May 26 2004 - 13:07:05 PDT)
- Re: AMBER: amber 8 under windows XP Adrian E. Roitberg (Thu May 27 2004 - 06:09:51 PDT)
  - Re: AMBER: amber 8 under windows XP David A. Case (Thu May 27 2004 - 08:34:50 PDT)
Re: AMBER: amber 8 under windows XP Piotr Cieplak (Wed May 26 2004 - 15:08:38 PDT)
AMBER: xleap solvatebox problem Tomas Kubar (Thu May 27 2004 - 05:33:44 PDT)
- Re: AMBER: xleap solvatebox problem David A. Case (Thu May 27 2004 - 08:42:48 PDT)
  - Re: AMBER: xleap solvatebox problem Tomas Kubar (Thu Jun 10 2004 - 01:58:51 PDT)
- Re: AMBER: xleap solvatebox problem James W. Caldwell (Wed Jun 09 2004 - 15:49:07 PDT)
AMBER: antechamber: atomtype assignment of cc/cd etc pairs in GAFF / creating atom type definition file Kamp, Marc vander (Thu May 27 2004 - 06:01:13 PDT)
- Re: AMBER: antechamber: atomtype assignment of cc/cd etc pairs in GAFF / creating atom type definition file David A. Case (Fri May 28 2004 - 14:34:45 PDT)
AMBER: pdb in RED Gustavo Pierdominici Sottile (Thu May 27 2004 - 10:29:44 PDT)
- Re: AMBER: pdb in RED FyD (Thu May 27 2004 - 12:16:59 PDT)
AMBER: Amber 7 (sander) use of PME Linda Prengaman (Thu May 27 2004 - 12:42:13 PDT)
- Re: AMBER: Amber 7 (sander) use of PME Carlos Simmerling (Thu May 27 2004 - 12:47:50 PDT)
Re: AMBER: Cannot read in sander-again bybaker.itsa.ucsf.edu (Thu May 27 2004 - 14:22:00 PDT)
- Re: AMBER: Cannot read in sander-again Bill Ross (Thu May 27 2004 - 14:28:27 PDT)
- Re: AMBER: Cannot read in sander-again Guanglei Cui (Thu May 27 2004 - 14:28:39 PDT)
- Re: AMBER: Cannot read in sander-again bybaker.itsa.ucsf.edu (Thu May 27 2004 - 15:05:22 PDT)
- Re: AMBER: Cannot read in sander-again Bill Ross (Thu May 27 2004 - 15:16:56 PDT)
- Re: AMBER: Cannot read in sander-again David A. Case (Thu May 27 2004 - 16:15:37 PDT)
AMBER: Re: CCL:Helical parameters extraction from trajectory Peter Gannett (Fri May 28 2004 - 04:47:08 PDT)
AMBER: problems with mpich Amber admin (Fri May 28 2004 - 07:55:25 PDT)
- Re: AMBER: problems with mpich David A. Case (Fri May 28 2004 - 09:52:56 PDT)
- Re: AMBER: problems with mpich Chen Yongzhi (Fri May 28 2004 - 11:23:48 PDT)
  - Re: AMBER: problems with mpich David A. Case (Fri May 28 2004 - 11:43:23 PDT)
    - Re: AMBER: problems with mpich Viktor Hornak (Fri May 28 2004 - 12:00:15 PDT)
AMBER: amber on AMD 64 xhu1.memphis.edu (Fri May 28 2004 - 11:56:02 PDT)
AMBER: Use of RED Gustavo Pierdominici Sottile (Fri May 28 2004 - 11:44:26 PDT)
- Re: AMBER: Use of RED FyD (Fri May 28 2004 - 13:20:42 PDT)
AMBER: torsion angles John (Fri May 28 2004 - 16:02:04 PDT)
AMBER: Sander went through bybaker.itsa.ucsf.edu (Fri May 28 2004 - 17:19:02 PDT)
- Re: AMBER: Sander went through Rhonda Torres (Fri May 28 2004 - 17:49:44 PDT)
- Re: AMBER: Sander went through bybaker.itsa.ucsf.edu (Sat May 29 2004 - 04:51:26 PDT)
AMBER: about amber8, replica exchange J. Zhang, Dr (Fri May 28 2004 - 20:45:49 PDT)
- Re: AMBER: about amber8, replica exchange Guanglei Cui (Fri May 28 2004 - 21:04:33 PDT)
- Re: AMBER: about amber8, replica exchange Carlos Simmerling (Fri May 28 2004 - 20:55:34 PDT)
  - Re: Re: AMBER: about amber8, replica exchange J. Zhang, Dr (Sun May 30 2004 - 17:09:24 PDT)
AMBER: Low frequency in quasi-harmonic analysis!! Pradipta Bandyopadhyay (Sun May 30 2004 - 02:23:50 PDT)
AMBER: MMPBSA problem Dalmaris, John (Sun May 30 2004 - 06:22:55 PDT)
AMBER: question about NMODE for RNA xhu1.memphis.edu (Sun May 30 2004 - 15:32:22 PDT)
- Re: AMBER: question about NMODE for RNA David A. Case (Sun May 30 2004 - 16:14:33 PDT)
- Re: AMBER: question about NMODE for RNA xhu1.memphis.edu (Sun May 30 2004 - 18:53:58 PDT)
AMBER: program compatibility hj zou (Sun May 30 2004 - 19:07:39 PDT)
- Re: AMBER: program compatibility David A. Case (Sun May 30 2004 - 22:05:15 PDT)
AMBER: FEP error/early termination - why? Annette Höglund (Mon May 31 2004 - 06:23:27 PDT)
- Re: AMBER: FEP error/early termination - why? David A. Case (Mon May 31 2004 - 10:33:08 PDT)
  - Re: AMBER: FEP error/early termination - why? Sébastien Osborne (Mon May 31 2004 - 10:51:15 PDT)
- Re: AMBER: FEP error/early termination - why? Carlos Simmerling (Mon May 31 2004 - 10:56:24 PDT)
  - Re: AMBER: FEP error/early termination - why? Sébastien Osborne (Mon May 31 2004 - 11:12:54 PDT)
- Re: AMBER: FEP error/early termination - why? Carlos Simmerling (Mon May 31 2004 - 11:21:41 PDT)
- Re: AMBER: FEP error/early termination - why? Annette Höglund (Tue Jun 01 2004 - 07:34:53 PDT)
AMBER: Install Amber8 under cygwin Seonah Kim (Mon May 31 2004 - 18:35:16 PDT)
- Re: AMBER: Install Amber8 under cygwin Scott Brozell (Tue Jun 01 2004 - 00:22:14 PDT)
AMBER: Software to visualize normal modes! Pradipta Bandyopadhyay (Mon May 31 2004 - 21:42:39 PDT)
- Re: AMBER: Software to visualize normal modes! John Mongan (Tue Jun 01 2004 - 16:20:38 PDT)
AMBER: Periodic boundary simulation Soon (Tue Jun 01 2004 - 02:08:31 PDT)
- Re: AMBER: Periodic boundary simulation Jiten (Tue Jun 01 2004 - 03:14:59 PDT)
  - Re: AMBER: Periodic boundary simulation Miguel (Tue Jun 01 2004 - 04:14:34 PDT)
- Re: AMBER: Periodic boundary simulation darden (Tue Jun 01 2004 - 06:11:54 PDT)
AMBER: Free energy in Amber8 Jiten (Tue Jun 01 2004 - 03:11:54 PDT)
- Re: AMBER: Free energy in Amber8 Miguel (Tue Jun 01 2004 - 04:11:39 PDT)
- Re: AMBER: Free energy in Amber8 David A. Case (Tue Jun 01 2004 - 12:17:34 PDT)
- Re: AMBER: Free energy in Amber8 Jiten (Tue Jun 01 2004 - 18:02:40 PDT)
  - Re: AMBER: Free energy in Amber8 David A. Case (Wed Jun 02 2004 - 07:35:24 PDT)
AMBER: Heme parameters Gustavo Pierdominici Sottile (Tue Jun 01 2004 - 08:32:06 PDT)
- Re: AMBER: Heme parameters David A. Case (Tue Jun 01 2004 - 12:20:56 PDT)
AMBER: Amber force field for protein-DNA system jz7.duke.edu (Tue Jun 01 2004 - 09:14:16 PDT)
- Re: AMBER: Amber force field for protein-DNA system Rhonda Torres (Tue Jun 01 2004 - 10:24:57 PDT)
- RE: AMBER: Amber force field for protein-DNA system Ross Walker (Tue Jun 01 2004 - 11:09:37 PDT)
- RE: AMBER: Amber force field for protein-DNA system Bill Ross (Tue Jun 01 2004 - 11:32:52 PDT)
- Re: AMBER: Amber force field for protein-DNA system David A. Case (Tue Jun 01 2004 - 11:40:15 PDT)
- AMBER: Amber force field for protein-DNA system (again) jz7.duke.edu (Tue Jun 01 2004 - 12:51:59 PDT)
AMBER: sander8 performance Oliver Hucke (Tue Jun 01 2004 - 10:53:46 PDT)
- Re: AMBER: sander8 performance David A. Case (Tue Jun 01 2004 - 12:22:29 PDT)
- Re: AMBER: sander8 performance Oliver Hucke (Tue Jun 01 2004 - 12:46:06 PDT)
  - Re: AMBER: sander8 performance David A. Case (Tue Jun 01 2004 - 13:15:50 PDT)
AMBER: Amber7: pdb format file vidit kumar (Tue Jun 01 2004 - 11:13:03 PDT)
- Re: AMBER: Amber7: pdb format file Peter Gannett (Tue Jun 01 2004 - 11:22:32 PDT)
- RE: AMBER: Amber7: pdb format file Ross Walker (Tue Jun 01 2004 - 11:49:31 PDT)
  - AMBER: Re: AMBER vidit kumar (Wed Jun 02 2004 - 18:19:08 PDT)
    - Re: AMBER: Re: AMBER Jiten (Wed Jun 02 2004 - 18:48:37 PDT)
- Re: AMBER: Amber7: pdb format file David A. Case (Tue Jun 01 2004 - 12:23:47 PDT)
AMBER: sander of AMBER 8 doesn't work Feng, Hanqiao (NIH/NCI) (Tue Jun 01 2004 - 11:39:56 PDT)
- RE: AMBER: sander of AMBER 8 doesn't work Ross Walker (Tue Jun 01 2004 - 11:56:29 PDT)
- RE: AMBER: sander of AMBER 8 doesn't work Feng, Hanqiao (NIH/NCI) (Wed Jun 02 2004 - 05:45:01 PDT)
  - Re: AMBER: sander of AMBER 8 doesn't work David A. Case (Wed Jun 02 2004 - 07:47:20 PDT)
AMBER: RED Xin Hu (Tue Jun 01 2004 - 16:02:37 PDT)
Re: [pradipta_b.mail.jnu.ac.in: AMBER: Software to visualize normal modes!] David A. Case (Tue Jun 01 2004 - 16:24:54 PDT)
AMBER: Add Hydrogen bond through xLeap? Nan Lin (Tue Jun 01 2004 - 23:25:18 PDT)
- Re: AMBER: Add Hydrogen bond through xLeap? Guanglei Cui (Wed Jun 02 2004 - 07:06:47 PDT)
AMBER: question about replica exchange in amber8 J. Zhang, Dr (Wed Jun 02 2004 - 02:24:24 PDT)
- Re: AMBER: question about replica exchange in amber8 apw397.soton.ac.uk (Wed Jun 02 2004 - 02:43:21 PDT)
- Re: AMBER: question about replica exchange in amber8 Guanglei Cui (Wed Jun 02 2004 - 06:58:32 PDT)
- Re: AMBER: question about replica exchange in amber8 xiaolin cheng (Wed Jun 02 2004 - 07:23:30 PDT)
- Re: AMBER: question about replica exchange in amber8 J. Zhang, Dr (Wed Jun 02 2004 - 19:16:19 PDT)
AMBER: Gaussian Interface ? Jiten (Wed Jun 02 2004 - 08:06:12 PDT)
- AMBER: mm_pbsa test problem Difei Wang (Wed Jun 02 2004 - 08:54:40 PDT)
AMBER: Amber force field for protein-DNA system (again) jz7.duke.edu (Wed Jun 02 2004 - 10:31:56 PDT)
- AMBER: question about xleap jz7.duke.edu (Thu Jun 03 2004 - 10:19:27 PDT)
  - Re: AMBER: question about xleap Viktor Hornak (Thu Jun 03 2004 - 10:31:23 PDT)
    - Re: AMBER: question about xleap jz7.duke.edu (Thu Jun 03 2004 - 11:34:03 PDT)
    - RE: AMBER: question about xleap Ross Walker (Thu Jun 03 2004 - 12:19:55 PDT)
    - RE: AMBER: question about xleap jz7.duke.edu (Thu Jun 03 2004 - 12:40:10 PDT)
  - RE: AMBER: question about xleap Ross Walker (Thu Jun 03 2004 - 11:03:04 PDT)
AMBER: confusion about epsilon=4r for nmode calclation of nucleic acid xiaowei li (Wed Jun 02 2004 - 20:15:29 PDT)
- Re: AMBER: confusion about epsilon=4r for nmode calclation of nucleic acid David A. Case (Thu Jun 03 2004 - 19:31:06 PDT)
  - Re: AMBER: confusion about epsilon=4r for nmode calclation of nucleic acid xiaowei li (Thu Jun 03 2004 - 19:52:16 PDT)
AMBER: simulated anealling anshul.imtech.res.in (Thu Jun 03 2004 - 07:12:55 PDT)
- Re: AMBER: simulated anealling Jiten (Wed Jun 02 2004 - 21:02:00 PDT)
  - AMBER: About DelPhi and GRASP Ilyas Yildirim (Wed Jun 02 2004 - 21:10:07 PDT)
  - Re: AMBER: simulated anealling anshul.imtech.res.in (Thu Jun 03 2004 - 09:56:58 PDT)
- Re: AMBER: simulated anealling Rhonda Torres (Thu Jun 03 2004 - 11:05:58 PDT)
AMBER: Simulated anealling anshul.imtech.res.in (Thu Jun 03 2004 - 07:30:42 PDT)
- Re: AMBER: Simulated anealling David A. Case (Thu Jun 03 2004 - 19:34:17 PDT)
  - Re: AMBER: Simulated anealling anshul.imtech.res.in (Fri Jun 04 2004 - 13:56:50 PDT)
    - Re: AMBER: Simulated anealling anshul.imtech.res.in (Wed Jun 09 2004 - 07:41:56 PDT)
AMBER: parallel Sander (amber8): run-time error under Irix Karol Miaskiewicz (Thu Jun 03 2004 - 07:42:25 PDT)
- Re: AMBER: parallel Sander (amber8): run-time error under Irix Carlos Simmerling (Thu Jun 03 2004 - 08:03:43 PDT)
  - Re: AMBER: parallel Sander (amber8): run-time error under Irix Karol Miaskiewicz (Thu Jun 03 2004 - 08:29:06 PDT)
- Re: AMBER: parallel Sander (amber8): run-time error under Irix Viktor Hornak (Thu Jun 03 2004 - 12:01:40 PDT)
  - Re: AMBER: parallel Sander (amber8): run-time error under Irix Karol Miaskiewicz (Thu Jun 03 2004 - 12:15:05 PDT)
- AMBER: Re: parallel Sander (amber8): run-time error under Irix Karol Miaskiewicz (Tue Jun 08 2004 - 13:04:14 PDT)
  - AMBER: Re: parallel Sander (amber8): run-time error under Irix Karol Miaskiewicz (Tue Jun 08 2004 - 13:30:38 PDT)
AMBER: amber8 compile on Lemieux Guanglei Cui (Thu Jun 03 2004 - 08:06:21 PDT)
- Re: AMBER: amber8 compile on Lemieux David A. Case (Thu Jun 03 2004 - 19:39:58 PDT)
  - Re: AMBER: amber8 compile on Lemieux Guanglei Cui (Thu Jun 03 2004 - 20:56:13 PDT)
AMBER: MMPBSA problem John (Thu Jun 03 2004 - 09:09:05 PDT)
AMBER: Loading mol2 Files in XLEaP Robyn Ayscue (Thu Jun 03 2004 - 09:14:00 PDT)
- Re: AMBER: Loading mol2 Files in XLEaP FyD (Thu Jun 03 2004 - 09:26:38 PDT)
  - Re: AMBER: Loading mol2 Files in XLEaP Robyn Ayscue (Thu Jun 03 2004 - 11:39:37 PDT)
    - Re: AMBER: Loading mol2 Files in XLEaP FyD (Thu Jun 03 2004 - 12:18:26 PDT)
    - Re: AMBER: Loading mol2 Files in XLEaP Robyn Ayscue (Fri Jun 04 2004 - 11:24:05 PDT)
    - Re: AMBER: Loading mol2 Files in XLEaP Guanglei Cui (Thu Jun 03 2004 - 12:20:26 PDT)
    - AMBER: Amber7: Vidit Kumar (Thu Jun 03 2004 - 12:55:21 PDT)
    - Re: AMBER: Amber7: FyD (Thu Jun 03 2004 - 13:11:28 PDT)
    - AMBER: CARNAL- movement of an axis Wen Li (Thu Jun 03 2004 - 13:34:11 PDT)
    - Re: AMBER: Loading mol2 Files in XLEaP Scott Brozell (Thu Jun 03 2004 - 14:49:13 PDT)
- Re: AMBER: Loading mol2 Files in XLEaP Bill Ross (Thu Jun 03 2004 - 13:44:39 PDT)
- Re: AMBER: Loading mol2 Files in XLEaP David A. Case (Thu Jun 03 2004 - 15:02:07 PDT)
AMBER: Loading mol2 files in XLEaP Robyn Ayscue (Thu Jun 03 2004 - 09:17:54 PDT)
AMBER: Sander & fix atoms bybaker.itsa.ucsf.edu (Thu Jun 03 2004 - 09:48:40 PDT)
- Re: AMBER: Sander & fix atoms Viktor Hornak (Thu Jun 03 2004 - 10:22:55 PDT)
- Re: AMBER: Sander & fix atoms bybaker.itsa.ucsf.edu (Thu Jun 03 2004 - 13:54:55 PDT)
- Re: AMBER: Sander & fix atoms bybaker.itsa.ucsf.edu (Thu Jun 03 2004 - 13:59:50 PDT)
  - Re: AMBER: Sander & fix atoms Viktor Hornak (Thu Jun 03 2004 - 14:14:10 PDT)
- Re: AMBER: Sander & fix atoms Bill Ross (Thu Jun 03 2004 - 14:06:04 PDT)
- Re: AMBER: Sander & fix atoms bybaker.itsa.ucsf.edu (Thu Jun 03 2004 - 15:32:53 PDT)
- Re: AMBER: Sander & fix atoms bybaker.itsa.ucsf.edu (Thu Jun 03 2004 - 15:36:24 PDT)
AMBER: mm_pbsa.pl question Fang, Jianwen (Thu Jun 03 2004 - 10:14:29 PDT)
AMBER: sander7 on quad opteron Tru Huynh (Thu Jun 03 2004 - 11:13:39 PDT)
Re: AMBER: CARNAL- movement of an axis Bill Ross (Thu Jun 03 2004 - 13:53:47 PDT)
AMBER: information PROTON_INFO Ye Mei (Thu Jun 03 2004 - 20:33:30 PDT)
AMBER: why the enegy of native state of protein is high in GBSA calculation? J. Zhang, Dr (Fri Jun 04 2004 - 02:21:20 PDT)
- Re: AMBER: why the enegy of native state of protein is high in GBSA calculation? Carlos Simmerling (Fri Jun 04 2004 - 04:52:40 PDT)
  - Re: AMBER: why the enegy of native state of protein is high in GBSA calculation? Andreas Svrcek-Seiler (Fri Jun 04 2004 - 08:15:03 PDT)
    - Re: Re: AMBER: why the enegy of native state of protein is high in GBSA calculation? J. Zhang, Dr (Sat Jun 05 2004 - 18:25:20 PDT)
- Re: AMBER: why the enegy of native state of protein is high in GBSA calculation? David A. Case (Fri Jun 04 2004 - 06:00:47 PDT)
AMBER: gibbs in amber8 A. Hungie (Fri Jun 04 2004 - 10:13:12 PDT)
- Re: AMBER: gibbs in amber8 David A. Case (Sat Jun 05 2004 - 20:33:37 PDT)
AMBER: free energy A. Hungie (Fri Jun 04 2004 - 10:21:59 PDT)
- Re: AMBER: free energy Oliver Hucke (Fri Jun 04 2004 - 12:19:25 PDT)
- Re: AMBER: free energy Kazuo Koyano (Mon Jun 28 2004 - 01:45:41 PDT)
- Re: AMBER: free energy Carlos Simmerling (Mon Jun 28 2004 - 06:06:43 PDT)
AMBER: water BOX Xioling Chuang (Mon Jun 07 2004 - 07:09:33 PDT)
AMBER: question about building initial structure xhu1.memphis.edu (Mon Jun 07 2004 - 10:19:13 PDT)
Re: AMBER: Bad contacts Bill Ross (Mon Jun 07 2004 - 18:37:16 PDT)
AMBER: Partial Charge on ligand for MD & MM/PBSA Nan Lin (Mon Jun 07 2004 - 19:11:25 PDT)
AMBER: bug in leap? Carsten Detering (Mon Jun 07 2004 - 16:14:30 PDT)
- RE: AMBER: bug in leap? Ross Walker (Mon Jun 07 2004 - 16:50:10 PDT)
  - Re: AMBER: bug in leap? Tomas Kubar (Tue Jun 08 2004 - 00:27:30 PDT)
    - Re: AMBER: bug in leap? Scott Brozell (Thu Jun 10 2004 - 21:32:24 PDT)
AMBER: Bad contacts bybaker.itsa.ucsf.edu (Mon Jun 07 2004 - 17:44:37 PDT)
- Re: AMBER: Bad contacts Carlos Simmerling (Mon Jun 07 2004 - 18:26:19 PDT)
- Re: AMBER: Bad contacts bybaker.itsa.ucsf.edu (Wed Jun 09 2004 - 10:02:01 PDT)
  - Re: AMBER: Bad contacts Carlos Simmerling (Wed Jun 09 2004 - 11:56:09 PDT)
    - AMBER: Trajectory file Joseph Nachman (Wed Jun 09 2004 - 12:22:45 PDT)
    - Re: AMBER: Trajectory file Guanglei Cui (Wed Jun 09 2004 - 13:27:16 PDT)
- Re: AMBER: Bad contacts bybaker.itsa.ucsf.edu (Wed Jun 09 2004 - 13:30:38 PDT)
AMBER: paramitrization problem lei jia (Mon Jun 07 2004 - 15:12:37 PDT)
- RE: AMBER: paramitrization problem Ross Walker (Mon Jun 07 2004 - 15:24:15 PDT)
- RE: AMBER: paramitrization problem lei jia (Tue Jun 08 2004 - 08:00:11 PDT)
  - RE: AMBER: paramitrization problem Ross Walker (Tue Jun 08 2004 - 10:31:10 PDT)
    - Re: AMBER: paramitrization problem lei jia (Tue Jun 08 2004 - 10:45:02 PDT)
AMBER: unnatural base - RESP charges in ANTECHAMBER Dr. Rainer Glaser (Mon Jun 07 2004 - 17:12:56 PDT)
- AMBER: old trajectory file (amber6) to new trajectory file ? Difei Wang (Mon Jun 07 2004 - 19:55:39 PDT)
  - Re: AMBER: old trajectory file (amber6) to new trajectory file ? Carlos Simmerling (Tue Jun 08 2004 - 04:37:48 PDT)
  - Re: AMBER: old trajectory file (amber6) to new trajectory file ? David A. Case (Wed Jun 09 2004 - 19:16:26 PDT)
- Re: AMBER: unnatural base - RESP charges in ANTECHAMBER Junmei Wang (Mon Jun 07 2004 - 18:22:31 PDT)
- Re: AMBER: unnatural base - RESP charges in ANTECHAMBER FyD (Tue Jun 08 2004 - 09:23:46 PDT)
AMBER: Constant Pressure Problem of MD Nan Lin (Mon Jun 07 2004 - 19:04:23 PDT)
- Re: AMBER: Constant Pressure Problem of MD SIVA (Mon Jun 07 2004 - 20:53:39 PDT)
- Re: AMBER: Constant Pressure Problem of MD David A. Case (Mon Jun 07 2004 - 19:12:41 PDT)
AMBER: Calcium and GB cailliez (Tue Jun 08 2004 - 04:38:58 PDT)
- Re: AMBER: Calcium and GB David A. Case (Wed Jun 09 2004 - 19:10:26 PDT)
AMBER: Compile xleap (amber8) in linux Red Hat 8.0 Xiaobing Tian (Tue Jun 08 2004 - 09:00:06 PDT)
- Re: AMBER: Compile xleap (amber8) in linux Red Hat 8.0 Viktor Hornak (Tue Jun 08 2004 - 10:35:51 PDT)
  - Re: AMBER: Compile xleap (amber8) in linux Red Hat 8.0 Scott Brozell (Tue Jun 08 2004 - 11:11:15 PDT)
    - Re: AMBER: Compile xleap (amber8) in linux Red Hat 8.0 Viktor Hornak (Tue Jun 08 2004 - 11:29:29 PDT)
- Re: AMBER: Compile xleap (amber8) in linux Red Hat 8.0 Scott Brozell (Tue Jun 08 2004 - 10:53:34 PDT)
- Re: AMBER: Compile xleap (amber8) in linux Red Hat 8.0 Xiaobing Tian (Tue Jun 08 2004 - 11:33:43 PDT)
  - Re: AMBER: Compile xleap (amber8) in linux Red Hat 8.0 Guanglei Cui (Tue Jun 08 2004 - 11:30:05 PDT)
- Re: AMBER: Compile xleap (amber8) in linux Red Hat 8.0 Xiaobing Tian (Tue Jun 08 2004 - 12:21:39 PDT)
  - Re: AMBER: Compile xleap (amber8) in linux Red Hat 8.0 Viktor Hornak (Tue Jun 08 2004 - 12:30:38 PDT)
  - Re: AMBER: Compile xleap (amber8) in linux Red Hat 8.0 Guanglei Cui (Tue Jun 08 2004 - 12:45:56 PDT)
AMBER: antechamber Matheus Froeyen (Wed Jun 09 2004 - 00:39:26 PDT)
- Re: AMBER: antechamber Guanglei Cui (Wed Jun 09 2004 - 07:05:02 PDT)
AMBER: cluster analysis Stefano.Pieraccini.unimi.it (Wed Jun 09 2004 - 04:19:40 PDT)
- Re: AMBER: cluster analysis Tim Meyer (Wed Jun 09 2004 - 06:28:15 PDT)
AMBER: How to neutralize system? scopio (Wed Jun 09 2004 - 07:47:44 PDT)
- Re: AMBER: How to neutralize system? Marcin Krol (Wed Jun 09 2004 - 07:57:11 PDT)
- Re: AMBER: How to neutralize system? Guanglei Cui (Wed Jun 09 2004 - 07:58:37 PDT)
AMBER: Amber Transition State Output Johnson Agbo (Wed Jun 09 2004 - 12:46:03 PDT)
- Re: AMBER: Amber Transition State Output David A. Case (Wed Jun 09 2004 - 15:55:14 PDT)
  - Re: AMBER: Amber Transition State Output Johnson Agbo (Wed Jun 09 2004 - 17:33:58 PDT)
    - Re: AMBER: Amber Transition State Output David A. Case (Wed Jun 09 2004 - 18:54:23 PDT)
    - Re: AMBER: Amber Transition State Output Johnson Agbo (Thu Jun 10 2004 - 22:28:05 PDT)
Re: AMBER: Trajectory file Bill Ross (Wed Jun 09 2004 - 14:19:36 PDT)
AMBER: xleap solvatebox problem Shan, Jufang (Wed Jun 09 2004 - 15:17:59 PDT)
- RE: AMBER: xleap solvatebox problem Ross Walker (Wed Jun 09 2004 - 15:48:12 PDT)
- Re: AMBER: xleap solvatebox problem David A. Case (Wed Jun 09 2004 - 15:51:06 PDT)
AMBER: antechamber/parmchk ATTN: needs revision Nan Lin (Wed Jun 09 2004 - 11:48:55 PDT)
AMBER: Amber & mutation bybaker.itsa.ucsf.edu (Wed Jun 09 2004 - 17:53:58 PDT)
- Re: AMBER: Amber & mutation Tim Meyer (Wed Jun 09 2004 - 22:14:11 PDT)
- Re: AMBER: Amber & mutation bybaker.itsa.ucsf.edu (Thu Jun 10 2004 - 09:24:24 PDT)
AMBER: nmode with mm/pbsa Nan Lin (Wed Jun 09 2004 - 18:18:15 PDT)
- Re: AMBER: nmode with mm/pbsa Rhonda Torres (Thu Jun 10 2004 - 11:33:40 PDT)
AMBER: LINMIN failure Mizuguchi Mineyuki (Wed Jun 09 2004 - 19:40:16 PDT)
- Re: AMBER: LINMIN failure Robyn Ayscue (Thu Jun 10 2004 - 04:52:07 PDT)
  - Re: AMBER: LINMIN failure Mizuguchi Mineyuki (Thu Jun 10 2004 - 19:58:24 PDT)
    - RE: AMBER: LINMIN failure Ross Walker (Thu Jun 10 2004 - 23:10:23 PDT)
- RE: AMBER: LINMIN failure Ross Walker (Thu Jun 10 2004 - 10:10:08 PDT)
  - AMBER: cluster MD conformations from sander Wen Li (Thu Jun 10 2004 - 12:13:14 PDT)
    - Re: AMBER: cluster MD conformations from sander aldo jongejan (Fri Jun 11 2004 - 01:22:40 PDT)
- Re: AMBER: LINMIN failure Linda Prengaman (Thu Jun 10 2004 - 14:41:46 PDT)
AMBER: Xleap YangPeng (Thu Jun 10 2004 - 01:49:02 PDT)
- Re: AMBER: Xleap Scott Brozell (Thu Jun 10 2004 - 13:36:25 PDT)
AMBER: Compiling Amber8 on Mac OS X Robyn Ayscue (Thu Jun 10 2004 - 05:25:40 PDT)
- Re: AMBER: Compiling Amber8 on Mac OS X Mengjuei Hsieh (Thu Jun 10 2004 - 14:11:24 PDT)
  - Re: AMBER: Compiling Amber8 on Mac OS X Yusuf Abdulghani (Fri Jun 11 2004 - 15:14:12 PDT)
    - Re: AMBER: Compiling Amber8 on Mac OS X Mengjuei Hsieh (Fri Jun 11 2004 - 15:59:14 PDT)
    - Re: AMBER: Compiling Amber8 on Mac OS X Robyn Ayscue (Mon Jun 14 2004 - 11:41:15 PDT)
  - Re: AMBER: Compiling Amber8 on Mac OS X Robyn Ayscue (Mon Jun 14 2004 - 11:39:27 PDT)
AMBER: parmcal problem scopio (Thu Jun 10 2004 - 07:46:11 PDT)
- Re: AMBER: parmcal problem scopio (Thu Jun 10 2004 - 17:21:30 PDT)
- Re: AMBER: parmcal problem David A. Case (Fri Jun 11 2004 - 15:37:53 PDT)
AMBER: xleap solvatebox problem Shan, Jufang (Thu Jun 10 2004 - 07:49:25 PDT)
AMBER: PARSE radius for P david.evans.ulsop.ac.uk (Thu Jun 10 2004 - 10:59:30 PDT)
Re: AMBER: Thank you Xiaobing Tian (Thu Jun 10 2004 - 12:37:37 PDT)
AMBER: Core Dump ERROR When Using TIP4P Dat H. Nguyen (Thu Jun 10 2004 - 18:12:06 PDT)
- Re: AMBER: Core Dump ERROR When Using TIP4P David A. Case (Fri Jun 11 2004 - 07:08:18 PDT)
  - Re: AMBER: Core Dump ERROR When Using TIP4P Dat H. Nguyen (Tue Jun 15 2004 - 14:21:28 PDT)
    - Re: AMBER: Core Dump ERROR When Using TIP4P David A. Case (Tue Jun 15 2004 - 15:28:36 PDT)
AMBER: Checking Results? Linda Prengaman (Thu Jun 10 2004 - 18:49:33 PDT)
AMBER: ifort -parallel Joachim Reichelt (Fri Jun 11 2004 - 02:15:58 PDT)
- Re: AMBER: ifort -parallel Scott Brozell (Fri Jun 11 2004 - 08:36:36 PDT)
AMBER: savepdb vs ambpdb Golebiowski Jerome (Fri Jun 11 2004 - 08:17:40 PDT)
AMBER: PBCAL in mm-pbsa calculation nlxc (Fri Jun 11 2004 - 10:26:21 PDT)
- Re: AMBER: PBCAL in mm-pbsa calculation Thomas Steinbrecher (Fri Jun 11 2004 - 11:00:17 PDT)
- Re: AMBER: PBCAL in mm-pbsa calculation Thomas Steinbrecher (Fri Jun 11 2004 - 12:53:21 PDT)
  - Re: AMBER: PBCAL in mm-pbsa calculation Kazuo Koyano (Sun Jun 20 2004 - 23:14:56 PDT)
AMBER: Suface area parameter for fluorine in MM/PBSA nlxc (Fri Jun 11 2004 - 16:38:30 PDT)
- Re: AMBER: Suface area parameter for fluorine in MM/PBSA Scott Brozell (Sun Jun 13 2004 - 01:05:02 PDT)
AMBER: POPE membrane, How to obtain prep and parm files? Marek Dynowski (Sat Jun 12 2004 - 10:07:08 PDT)
AMBER: question about force field scopio (Mon Jun 14 2004 - 08:05:57 PDT)
- Re: AMBER: question about force field Carlos Simmerling (Mon Jun 14 2004 - 09:14:18 PDT)
  - AMBER: GBSA and thermodynamic ensemble Osmar Norberto de Souza (Mon Jun 13 2005 - 11:29:18 PDT)
    - Re: AMBER: GBSA and thermodynamic ensemble Julien Michel (Mon Jun 13 2005 - 12:51:23 PDT)
    - Re: AMBER: GBSA and thermodynamic ensemble David A. Case (Mon Jun 13 2005 - 13:13:14 PDT)
AMBER: Improper Torsional Parameters Johnson Agbo (Mon Jun 14 2004 - 13:41:12 PDT)
- Re: AMBER: Improper Torsional Parameters David A. Case (Mon Jun 14 2004 - 14:20:21 PDT)
  - Re: AMBER: Improper Torsional Parameters Johnson Agbo (Thu Jun 17 2004 - 13:57:08 PDT)
- Re: AMBER: Improper Torsional Parameters Carlos Simmerling (Mon Jun 14 2004 - 14:54:57 PDT)
  - AMBER: MOIL-View question Joseph Nachman (Tue Jun 15 2004 - 11:11:30 PDT)
    - Re: AMBER: MOIL-View question Carlos Simmerling (Wed Jun 16 2004 - 04:57:27 PDT)
    - Re: AMBER: MOIL-View question Joseph Nachman (Wed Jun 16 2004 - 12:35:17 PDT)
    - Re: AMBER: MOIL-View question Carlos Simmerling (Wed Jun 16 2004 - 13:25:45 PDT)
    - Re: AMBER: MOIL-View question Joseph Nachman (Wed Jun 16 2004 - 13:22:07 PDT)
    - Re: AMBER: MOIL-View question David E. Konerding DSD Staff (Wed Jun 16 2004 - 15:30:47 PDT)
    - AMBER: newer OPLS/AA? Sichun Yang (Mon Jun 21 2004 - 16:23:03 PDT)
  - AMBER: RMSD calculations in ptraj and Carnal Joseph Nachman (Tue Jun 15 2004 - 11:24:38 PDT)
AMBER: Config file for installing Amber 8 on PC with Windows XP fangyu liang (Mon Jun 14 2004 - 16:21:07 PDT)
- Re: AMBER: Config file for installing Amber 8 on PC with Windows XP David A. Case (Mon Jun 14 2004 - 18:01:57 PDT)
AMBER: About umbrella sampling in Amber 8 Yuhui Cheng (Mon Jun 14 2004 - 18:45:44 PDT)
- Re: AMBER: About umbrella sampling in Amber 8 David A. Case (Tue Jun 15 2004 - 09:05:59 PDT)
  - AMBER: The parallel problem for umbrella sampling in Amber 8 Yuhui Cheng (Tue Jun 15 2004 - 14:14:07 PDT)
    - Re: AMBER: The parallel problem for umbrella sampling in Amber 8 David A. Case (Tue Jun 15 2004 - 15:55:20 PDT)
AMBER: DENSITY in constant pressure MD nlxc (Tue Jun 15 2004 - 11:17:41 PDT)
- Re: AMBER: DENSITY in constant pressure MD David A. Case (Tue Jun 15 2004 - 15:50:57 PDT)
Re: AMBER: RMSD calculations in ptraj and Carnal Bill Ross (Tue Jun 15 2004 - 12:23:40 PDT)
- Re: AMBER: RMSD calculations in ptraj and Carnal Joseph Nachman (Tue Jun 15 2004 - 12:37:18 PDT)
- Re: AMBER: RMSD calculations in ptraj and Carnal Thomas E. Cheatham, III (Tue Jun 15 2004 - 13:06:38 PDT)
  - Re: AMBER: RMSD calculations in ptraj and Carnal Joseph Nachman (Mon Jun 21 2004 - 08:07:57 PDT)
- Re: AMBER: RMSD calculations in ptraj and Carnal Bill Ross (Tue Jun 15 2004 - 13:55:31 PDT)
  - Re: AMBER: RMSD calculations in ptraj and Carnal Joseph Nachman (Wed Jun 16 2004 - 13:16:52 PDT)
  - Re: AMBER: RMSD calculations in ptraj and Carnal Luis Gracia (Tue Jun 15 2004 - 17:19:53 PDT)
AMBER: binary files richard dimelow (Wed Jun 16 2004 - 06:29:48 PDT)
- Re: AMBER: binary files David A. Case (Wed Jun 16 2004 - 07:44:39 PDT)
AMBER: Trouble running molecular dynamics with an increase in temp in Sander Robyn Ayscue (Wed Jun 16 2004 - 06:43:05 PDT)
- Re: AMBER: Trouble running molecular dynamics with an increase in temp in Sander David A. Case (Wed Jun 16 2004 - 07:40:32 PDT)
- Re: AMBER: Trouble running molecular dynamics with an increase in temp in Sander Carlos Simmerling (Wed Jun 16 2004 - 07:42:33 PDT)
- Re: AMBER: Trouble running molecular dynamics with an increase in temp in Sander Andreas Svrcek-Seiler (Wed Jun 16 2004 - 07:58:33 PDT)
  - Re: AMBER: Trouble running molecular dynamics with an increase in temp in Sander Carlos Simmerling (Wed Jun 16 2004 - 08:15:20 PDT)
    - Re: AMBER: Trouble running molecular dynamics with an increase in temp in Sander Robyn Ayscue (Thu Jun 17 2004 - 08:35:34 PDT)
AMBER: problems with extra points German Sciaini (Wed Jun 16 2004 - 09:29:45 PDT)
- Re: AMBER: problems with extra points David A. Case (Wed Jun 16 2004 - 11:50:05 PDT)
  - Re: AMBER: problems with extra points German Sciaini (Fri Jun 18 2004 - 04:08:18 PDT)
AMBER: Nmode sebnem (Wed Jun 16 2004 - 16:47:18 PDT)
- Re: AMBER: Nmode David A. Case (Wed Jun 16 2004 - 21:20:10 PDT)
  - Re: AMBER: Nmode sebnem (Wed Jun 16 2004 - 22:30:54 PDT)
    - Re: AMBER: Nmode David A. Case (Thu Jun 17 2004 - 08:14:26 PDT)
AMBER: Z-DNA xiaowei li (Thu Jun 17 2004 - 11:43:13 PDT)
Re: AMBER: Z-DNA Bill Ross (Thu Jun 17 2004 - 13:00:55 PDT)
AMBER: Using gibbs to calculate free energy Xioling Chuang (Fri Jun 18 2004 - 06:15:31 PDT)
- Re: AMBER: Using gibbs to calculate free energy David A. Case (Fri Jun 18 2004 - 08:14:55 PDT)
AMBER: Deeper problem with the energetics of the system nlxc (Fri Jun 18 2004 - 10:56:52 PDT)
- Re: AMBER: Deeper problem with the energetics of the system David A. Case (Fri Jun 18 2004 - 11:20:20 PDT)
- Re: AMBER: all_amino03.in discrepancy Vojtech Klusak (Mon Jun 21 2004 - 02:36:09 PDT)
  - Re: AMBER: all_amino03.in discrepancy Dr. Yong Duan (Mon Jun 21 2004 - 09:41:03 PDT)
AMBER: The first and second derivatives Johnson Agbo (Fri Jun 18 2004 - 11:08:49 PDT)
- Re: AMBER: The first and second derivatives David A. Case (Fri Jun 18 2004 - 11:18:34 PDT)
  - Re: AMBER: The first and second derivatives Johnson Agbo (Fri Jun 18 2004 - 12:05:25 PDT)
    - Re: AMBER: The first and second derivatives David A. Case (Fri Jun 18 2004 - 13:25:29 PDT)
- Re: AMBER: The first and second derivatives Bill Ross (Fri Jun 18 2004 - 14:02:22 PDT)
  - Re: AMBER: The first and second derivatives Johnson Agbo (Fri Jun 18 2004 - 14:31:15 PDT)
AMBER: Could not assign parameters Sivanesan Dakshanamurthy (Fri Jun 18 2004 - 11:52:18 PDT)
- Re: AMBER: Could not assign parameters David A. Case (Fri Jun 18 2004 - 12:04:57 PDT)
- Re: AMBER: Could not assign parameters Sivanesan Dakshanamurthy (Fri Jun 18 2004 - 12:35:32 PDT)
AMBER: Changing MAXPR in Amber 8? Robyn Ayscue (Fri Jun 18 2004 - 12:08:13 PDT)
- RE: AMBER: Changing MAXPR in Amber 8? Ross Walker (Fri Jun 18 2004 - 12:23:33 PDT)
  - RE: AMBER: Changing MAXPR in Amber 8? Robyn Ayscue (Fri Jun 18 2004 - 13:03:06 PDT)
- Re: AMBER: Changing MAXPR in Amber 8? David A. Case (Fri Jun 18 2004 - 13:34:43 PDT)
AMBER: leap.log warnings scopio (Sun Jun 20 2004 - 18:18:40 PDT)
- Re: AMBER: leap.log warnings Bill Ross (Mon Jun 21 2004 - 10:40:13 PDT)
- Re: AMBER: leap.log warnings Bill Ross (Mon Jun 21 2004 - 12:25:35 PDT)
- Re: AMBER: leap.log warnings German Sciaini (Tue Jun 22 2004 - 03:50:01 PDT)
  - Re: AMBER: leap.log warnings scopio (Tue Jun 22 2004 - 17:54:37 PDT)
Re: AMBER: leap.log warnings Bill Ross (Sun Jun 20 2004 - 19:52:17 PDT)
- Re: AMBER: leap.log warnings David A. Case (Mon Jun 21 2004 - 08:43:07 PDT)
AMBER: solvate proteins in xleap/amber8 Ting Wang (Mon Jun 21 2004 - 06:20:03 PDT)
- Re: AMBER: solvate proteins in xleap/amber8 David A. Case (Mon Jun 21 2004 - 08:42:47 PDT)
  - Re: AMBER: solvate proteins in xleap/amber8 Tomas Kubar (Tue Jun 22 2004 - 00:44:54 PDT)
- Re: AMBER: solvate proteins in xleap/amber8 Ting Wang (Tue Jul 13 2004 - 05:23:51 PDT)
AMBER: TOP file in AMBER7/8 Ting Wang (Mon Jun 21 2004 - 06:32:25 PDT)
- Re: AMBER: TOP file in AMBER7/8 Carlos Simmerling (Mon Jun 21 2004 - 06:52:38 PDT)
AMBER: nmanal problem Ben Cossins (Mon Jun 21 2004 - 08:45:20 PDT)
- Re: AMBER: nmanal problem David A. Case (Mon Jun 21 2004 - 08:51:59 PDT)
  - Re: AMBER: nmanal problem Ben Cossins (Mon Jun 21 2004 - 09:40:50 PDT)
AMBER: Opteron-64bit work station sachin patil (Mon Jun 21 2004 - 09:18:16 PDT)
- Re: AMBER: Opteron-64bit work station ian gould (Mon Jun 21 2004 - 09:34:33 PDT)
AMBER: High B-factor!! Pradipta Bandyopadhyay (Tue Jun 22 2004 - 05:13:09 PDT)
- Re: AMBER: High B-factor!! Bimo Ario Tejo (Tue Jun 22 2004 - 07:25:36 PDT)
Re: AMBER: MD & running time Linda Prengaman (Tue Jun 22 2004 - 12:12:00 PDT)
- Re: AMBER: MD & running time bybaker.itsa.ucsf.edu (Tue Jun 22 2004 - 21:29:58 PDT)
- Re: AMBER: MD & running time Robert Duke (Wed Jun 23 2004 - 15:25:27 PDT)
AMBER: problems to run ptraj German Sciaini (Tue Jun 22 2004 - 15:29:36 PDT)
AMBER: Problems in Amber MPI version (64 bits machine) Haijun Yang (Tue Jun 22 2004 - 14:57:07 PDT)
- Re: AMBER: Problems in Amber MPI version (64 bits machine) David A. Case (Tue Jun 22 2004 - 17:31:25 PDT)
- Re: AMBER: Problems in Amber MPI version (64 bits machine) Haijun Yang (Wed Jun 23 2004 - 10:33:49 PDT)
  - Re: AMBER: Problems in Amber MPI version (64 bits machine) David A. Case (Wed Jun 23 2004 - 10:58:07 PDT)
Thanks - Re: AMBER: MD & running time bybaker.itsa.ucsf.edu (Tue Jun 22 2004 - 16:29:09 PDT)
Re: AMBER: MD & running time Bill Ross (Tue Jun 22 2004 - 18:48:03 PDT)
- RE: AMBER: MD & running time Ross Walker (Tue Jun 22 2004 - 20:51:28 PDT)
  - RE: AMBER: MD & running time Kristina Furse (Wed Jun 23 2004 - 12:53:13 PDT)
    - Re: AMBER: MD & running time David A. Case (Wed Jun 23 2004 - 14:02:45 PDT)
AMBER: GB parameters for Calcium cailliez (Wed Jun 23 2004 - 05:39:38 PDT)
- Re: AMBER: GB parameters for Calcium David A. Case (Wed Jun 23 2004 - 11:10:23 PDT)
AMBER: Box range in vacuum when restart MD scopio (Wed Jun 23 2004 - 06:22:31 PDT)
- Re: AMBER: Box range in vacuum when restart MD David A. Case (Wed Jun 23 2004 - 09:06:29 PDT)
AMBER: a question on MM-PBSA and Delphi Jiayun (Wed Jun 23 2004 - 06:34:31 PDT)
- Re: AMBER: a question on MM-PBSA and Delphi Thomas Steinbrecher (Wed Jun 23 2004 - 08:13:48 PDT)
- RE: AMBER: a question on MM-PBSA and Delphi Jiayun (Wed Jun 23 2004 - 11:00:17 PDT)
  - RE: AMBER: a question on MM-PBSA and Delphi Thomas Steinbrecher (Wed Jun 23 2004 - 11:09:16 PDT)
- RE: AMBER: a question on MM-PBSA and Delphi Jiayun (Tue Jun 29 2004 - 02:54:46 PDT)
AMBER: amber8 parallel jobs spookie (Wed Jun 23 2004 - 21:50:48 PDT)
- Re: AMBER: amber8 parallel jobs Carlos Simmerling (Thu Jun 24 2004 - 05:17:05 PDT)
- Re: AMBER: amber8 parallel jobs spookie (Fri Jun 25 2004 - 06:42:09 PDT)
- Re: AMBER: amber8 parallel jobs spookie (Fri Jun 25 2004 - 11:05:23 PDT)
AMBER: AMBER7 : update force field gaff.dat and parm99.dat Guillaume Bollot (Thu Jun 24 2004 - 05:48:39 PDT)
AMBER: AMBER7 update force field Guillaume Bollot (Thu Jun 24 2004 - 06:23:44 PDT)
AMBER: Restrain or freeze molecule question? Guillaume Bollot (Thu Jun 24 2004 - 03:48:33 PDT)
- Re: AMBER: Restrain or freeze molecule question? David A. Case (Thu Jun 24 2004 - 08:24:37 PDT)
- Re: AMBER: Restrain or freeze molecule question? Carlos Simmerling (Thu Jun 24 2004 - 08:39:58 PDT)
- RE: AMBER: Restrain or freeze molecule question? Junmei Wang (Thu Jun 24 2004 - 10:44:03 PDT)
AMBER: A problem about a sander parallel run Yongzhi Chen (Thu Jun 24 2004 - 11:40:37 PDT)
AMBER: Units of Charges on Atoms Johnson Agbo (Thu Jun 24 2004 - 12:22:49 PDT)
- Re: AMBER: Units of Charges on Atoms Tomas Kubar (Thu Jun 24 2004 - 12:48:36 PDT)
- Re: AMBER: Units of Charges on Atoms Carlos Simmerling (Thu Jun 24 2004 - 12:49:43 PDT)
AMBER: Amber 8 installation fangyu liang (Thu Jun 24 2004 - 15:24:43 PDT)
- RE: AMBER: Amber 8 installation Ross Walker (Thu Jun 24 2004 - 15:38:57 PDT)
- Re: AMBER: Amber 8 installation spookie (Thu Jun 24 2004 - 15:42:40 PDT)
- RE: AMBER: Amber 8 installation fangyu liang (Fri Jun 25 2004 - 11:03:06 PDT)
  - RE: AMBER: Amber 8 installation spookie (Fri Jun 25 2004 - 11:08:21 PDT)
    - Re: RE: AMBER: Amber 8 installation fangyu liang (Fri Jun 25 2004 - 00:34:45 PDT)
    - Re: RE: AMBER: Amber 8 installation David A. Case (Fri Jun 25 2004 - 08:33:30 PDT)
    - RE: RE: AMBER: Amber 8 installation Ross Walker (Fri Jun 25 2004 - 10:27:23 PDT)
  - Re: AMBER: Amber 8 installation David A. Case (Fri Jun 25 2004 - 12:15:50 PDT)
AMBER: Born radii Marcin Krol (Fri Jun 25 2004 - 04:24:48 PDT)
- Re: AMBER: Born radii David A. Case (Fri Jun 25 2004 - 08:36:20 PDT)
AMBER: sander in parallel, amber8 spookie (Fri Jun 25 2004 - 01:49:30 PDT)
- Re: AMBER: sander in parallel, amber8 Stef (Fri Jun 25 2004 - 11:11:09 PDT)
  - Re: AMBER: sander in parallel, amber8 spookie (Fri Jun 25 2004 - 11:26:58 PDT)
AMBER: Problems with X.R.E.D. Scott (Fri Jun 25 2004 - 08:49:24 PDT)
- Re: AMBER: Problems with X.R.E.D. FyD (Fri Jun 25 2004 - 10:20:30 PDT)
AMBER: restraints error Venkata S Koppuravuri (Fri Jun 25 2004 - 10:10:35 PDT)
- Re: AMBER: restraints error Carlos Simmerling (Fri Jun 25 2004 - 10:23:26 PDT)
- Re: AMBER: restraints error David A. Case (Fri Jun 25 2004 - 10:32:48 PDT)
  - Re: AMBER: restraints error Venkata S Koppuravuri (Fri Jun 25 2004 - 11:11:20 PDT)
    - Re: AMBER: restraints error Carlos Simmerling (Fri Jun 25 2004 - 11:19:34 PDT)
    - Re: AMBER: restraints error David A. Case (Fri Jun 25 2004 - 12:26:56 PDT)
AMBER: PBCAL in MM/PBSA nlxc (Fri Jun 25 2004 - 12:09:19 PDT)
- Re: AMBER: PBCAL in MM/PBSA Thomas Steinbrecher (Fri Jun 25 2004 - 12:37:07 PDT)
AMBER: octavalent metal Brent Krueger (Fri Jun 25 2004 - 14:17:01 PDT)
AMBER: Problem with menu bar in LEAP Cenk Andac (Fri Jun 25 2004 - 14:54:47 PDT)
- Re: AMBER: Problem with menu bar in LEAP Dat H. Nguyen (Fri Jun 25 2004 - 15:09:00 PDT)
- RE: AMBER: Problem with menu bar in LEAP Ross Walker (Fri Jun 25 2004 - 15:12:13 PDT)
- AMBER: AMBPDB command requires libcxa.so.5 Cenk Andac (Sat Jun 26 2004 - 08:16:52 PDT)
  - Re: AMBER: AMBPDB command requires libcxa.so.5 David A. Case (Sat Jun 26 2004 - 11:56:09 PDT)
  - Re: AMBER: AMBPDB command requires libcxa.so.5 Amber admin (Mon Jun 28 2004 - 08:12:45 PDT)
  - AMBER: Problems with processing SYBYL-Tripos pdb files in LEAP Cenk Andac (Wed Jun 30 2004 - 08:12:10 PDT)
  - AMBER: Problems with processing SYBYL-Tripos pdb files in LEAP Cenk Andac (Wed Jun 30 2004 - 08:14:18 PDT)
    - Re: AMBER: Problems with processing SYBYL-Tripos pdb files in LEAP David A. Case (Wed Jun 30 2004 - 10:50:41 PDT)
    - Re: AMBER: Problems with processing SYBYL-Tripos pdb files in LEAP Cenk Andac (Wed Jun 30 2004 - 22:02:17 PDT)
- Re: AMBER: Problem with menu bar in LEAP sachin patil (Sun Jun 27 2004 - 10:01:30 PDT)
AMBER: -p4pg problem spookie (Sat Jun 26 2004 - 01:34:40 PDT)
- Re: AMBER: -p4pg problem Lubos Vrbka (Sat Jun 26 2004 - 03:59:53 PDT)
  - Re: AMBER: -p4pg problem spookie (Sat Jun 26 2004 - 07:00:48 PDT)
    - Re: AMBER: -p4pg problem Lubos Vrbka (Sat Jun 26 2004 - 07:42:55 PDT)
- Re: AMBER: -p4pg problem David A. Case (Sat Jun 26 2004 - 11:54:03 PDT)
  - Re: AMBER: -p4pg problem spookie (Sat Jun 26 2004 - 22:19:33 PDT)
AMBER: "Total vdw box size" information is gone Helios Chen (Sun Jun 27 2004 - 00:57:50 PDT)
- Re: AMBER: "Total vdw box size" information is gone David A. Case (Sun Jun 27 2004 - 14:03:39 PDT)
- Re: AMBER: "Total vdw box size" information is gone Jiten (Mon Jun 28 2004 - 07:45:39 PDT)
AMBER: (no subject) Andrew Box (Sun Jun 27 2004 - 20:29:34 PDT)
- Re: AMBER: (no subject) David A. Case (Sun Jun 27 2004 - 23:12:26 PDT)
AMBER: problem not with sander, but with mpich spookie (Mon Jun 28 2004 - 02:08:37 PDT)
- Re: AMBER: problem not with sander, but with mpich Viktor Hornak (Mon Jun 28 2004 - 05:48:51 PDT)
AMBER: Amber8 compilation in IBM-AIX Jiten (Mon Jun 28 2004 - 02:19:42 PDT)
- Re: AMBER: Amber8 compilation in IBM-AIX Nicolas Grima (Mon Jun 28 2004 - 03:55:59 PDT)
  - Re: AMBER: Amber8 compilation in IBM-AIX David A. Case (Mon Jun 28 2004 - 08:42:20 PDT)
- Re: AMBER: Amber8 compilation in IBM-AIX Jiten (Mon Jun 28 2004 - 07:39:02 PDT)
  - Re: AMBER: Amber8 compilation in IBM-AIX Nicolas Grima (Mon Jun 28 2004 - 08:13:32 PDT)
- Re: AMBER: Amber8 compilation in IBM-AIX Jiten (Mon Jun 28 2004 - 17:48:25 PDT)
AMBER: NEC and Regatta Filip Lankas (Mon Jun 28 2004 - 04:47:26 PDT)
- Re: AMBER: NEC and Regatta Robert Duke (Mon Jun 28 2004 - 05:18:24 PDT)
- Re: AMBER: NEC and Regatta Robert Duke (Mon Jun 28 2004 - 05:38:27 PDT)
AMBER: jump in temperature + problem in trajectory files cailliez (Mon Jun 28 2004 - 07:11:14 PDT)
AMBER: question about building prmtop and inpcrd files in xleap jz7.duke.edu (Mon Jun 28 2004 - 07:49:39 PDT)
- Re: AMBER: question about building prmtop and inpcrd files in xleap David A. Case (Mon Jun 28 2004 - 09:02:37 PDT)
  - AMBER: question about water molecule jz7.duke.edu (Mon Jun 28 2004 - 10:34:19 PDT)
    - Re: AMBER: question about water molecule Carlos Simmerling (Mon Jun 28 2004 - 10:48:11 PDT)
AMBER: Octahedron Box Seonah Kim (Mon Jun 28 2004 - 08:30:34 PDT)
- Re: AMBER: Octahedron Box Carlos Simmerling (Mon Jun 28 2004 - 08:43:21 PDT)
AMBER: About TI with sander Chunhu Tan (Mon Jun 28 2004 - 12:35:54 PDT)
- Re: AMBER: About TI with sander Guanglei Cui (Mon Jun 28 2004 - 12:46:52 PDT)
- Re: AMBER: About TI with sander David A. Case (Tue Jun 29 2004 - 09:45:52 PDT)
  - AMBER: Question about dummy atoms Sébastien Osborne (Tue Jun 29 2004 - 10:16:30 PDT)
    - Re: AMBER: Question about dummy atoms David A. Case (Tue Jun 29 2004 - 10:24:56 PDT)
    - AMBER: mmpbsa question Sébastien Osborne (Thu Aug 19 2004 - 12:58:42 PDT)
- Re: AMBER: About TI with sander Chunhu Tan (Sun Jul 04 2004 - 18:18:48 PDT)
  - Re: AMBER: About TI with sander David A. Case (Mon Jul 05 2004 - 08:31:23 PDT)
AMBER: Amber 8 installation error fangyu liang (Tue Jun 29 2004 - 00:00:32 PDT)
- Re: AMBER: Amber 8 installation error David A. Case (Tue Jun 29 2004 - 07:56:53 PDT)
- Re: AMBER: Amber 8 installation error fangyu liang (Tue Jun 29 2004 - 15:31:28 PDT)
  - Re: AMBER: Amber 8 installation error David A. Case (Tue Jun 29 2004 - 16:55:18 PDT)
- Re: AMBER: Amber 8 installation error fangyu liang (Tue Jun 29 2004 - 15:52:29 PDT)
  - RE: AMBER: Amber 8 installation error Ross Walker (Tue Jun 29 2004 - 16:08:21 PDT)
- Re: AMBER: Amber 8 installation error fangyu liang (Thu Jul 01 2004 - 00:53:21 PDT)
AMBER: Test run error in amber8 : IBM-AIX Jiten (Tue Jun 29 2004 - 05:16:48 PDT)
- Re: AMBER: Test run error in amber8 : IBM-AIX David A. Case (Tue Jun 29 2004 - 08:00:58 PDT)
- Re: AMBER: Test run error in amber8 : IBM-AIX Jiten (Tue Jun 29 2004 - 18:19:43 PDT)
AMBER: image and restart problems Steve Seibold (Tue Jun 29 2004 - 05:56:52 PDT)
- Re: AMBER: image and restart problems Andy Purkiss (Tue Jun 29 2004 - 06:05:48 PDT)
- Re: AMBER: image and restart problems Carlos Simmerling (Tue Jun 29 2004 - 07:57:42 PDT)
AMBER: PBCAL in mmpbsa nlxc (Tue Jun 29 2004 - 11:17:25 PDT)
- Re: AMBER: PBCAL in mmpbsa Thomas Steinbrecher (Tue Jun 29 2004 - 13:50:43 PDT)
  - Re: AMBER: PBCAL in mmpbsa nlxc (Tue Jun 29 2004 - 17:29:51 PDT)
AMBER: Atom Labels Karl N. Kirschner (Tue Jun 29 2004 - 13:36:22 PDT)
- Re: AMBER: Atom Labels Viktor Hornak (Tue Jun 29 2004 - 13:53:41 PDT)
- Re: AMBER: Atom Labels David A. Case (Tue Jun 29 2004 - 13:54:37 PDT)
- Re: AMBER: Atom Labels German Sciaini (Wed Jun 30 2004 - 04:36:14 PDT)
AMBER: Amber8 compilation problems on AIX Gabbar Daaku (Tue Jun 29 2004 - 19:50:13 PDT)
- Re: AMBER: Amber8 compilation problems on AIX Nicolas Grima (Wed Jun 30 2004 - 00:12:19 PDT)
AMBER: GB+LES Marcin Krol (Wed Jun 30 2004 - 02:43:27 PDT)
- Re: AMBER: GB+LES Carlos Simmerling (Wed Jun 30 2004 - 04:26:59 PDT)
AMBER: About Hbond calculations using ptraj javier perez (Mon Jun 28 2004 - 10:43:37 PDT)
- Re: AMBER: About Hbond calculations using ptraj Thomas E. Cheatham, III (Wed Jun 30 2004 - 11:11:05 PDT)
  - AMBER: ptraj and clustering Fabian Boes (Fri Oct 15 2004 - 01:15:51 PDT)
Re: AMBER: problems in using glycam David A. Case (Wed Jun 30 2004 - 08:03:07 PDT)
- Re: AMBER: problems in using glycam Karl N. Kirschner (Wed Jun 30 2004 - 08:29:37 PDT)
  - Re: AMBER: problems in using glycam Wen-Chi Tseng (Thu Jul 01 2004 - 05:44:27 PDT)
AMBER: traj. analysis Grace Li (Wed Jun 30 2004 - 12:05:07 PDT)
- Re: AMBER: traj. analysis Carlos Simmerling (Wed Jun 30 2004 - 12:08:50 PDT)
- Re: AMBER: traj. analysis Joseph Nachman (Wed Jun 30 2004 - 14:44:43 PDT)
AMBER: N-terminal Arg charges in ff99 not 1.00 Michael Dolan (Wed Jun 30 2004 - 14:08:15 PDT)
- Re: AMBER: N-terminal Arg charges in ff99 not 1.00 Guanglei Cui (Wed Jun 30 2004 - 14:13:55 PDT)
- RE: AMBER: N-terminal Arg charges in ff99 not 1.00 Ross Walker (Wed Jun 30 2004 - 14:26:22 PDT)
- Re: AMBER: N-terminal Arg charges in ff99 not 1.00 Michael Dolan (Thu Jul 01 2004 - 12:00:45 PDT)
  - RE: AMBER: N-terminal Arg charges in ff99 not 1.00 Ross Walker (Thu Jul 01 2004 - 12:17:02 PDT)
- Re: AMBER: N-terminal Arg charges in ff99 not 1.00 Michael Dolan (Thu Jul 01 2004 - 12:04:37 PDT)
  - Re: AMBER: N-terminal Arg charges in ff99 not 1.00 David A. Case (Thu Jul 01 2004 - 12:17:52 PDT)
- Re: AMBER: N-terminal Arg charges in ff99 not 1.00 Michael Dolan (Thu Jul 01 2004 - 12:57:37 PDT)
  - RE: AMBER: N-terminal Arg charges in ff99 not 1.00 Ross Walker (Thu Jul 01 2004 - 13:13:00 PDT)
AMBER: Questions about pert.charge and atom type change. Chunhu Tan (Wed Jun 30 2004 - 17:20:38 PDT)
- Re: AMBER: Questions about pert.charge and atom type change. Guanglei Cui (Wed Jun 30 2004 - 17:54:28 PDT)
- Re: AMBER: Questions about pert.charge and atom type change. David A. Case (Wed Jun 30 2004 - 18:10:02 PDT)
Re: AMBER: Implicit MD simulation Carlos Simmerling (Thu Jul 01 2004 - 05:07:52 PDT)
AMBER: average structure using ptraj NI AI (Thu Jul 01 2004 - 09:18:34 PDT)
- Re: AMBER: average structure using ptraj Thomas E. Cheatham, III (Thu Jul 01 2004 - 10:40:25 PDT)
  - Re: AMBER: average structure using ptraj NI AI (Fri Jul 02 2004 - 08:15:53 PDT)
  - AMBER: average using ptraj Holly Freedman (Thu Jul 08 2004 - 12:13:58 PDT)
    - RE: AMBER: average using ptraj Ross Walker (Thu Jul 08 2004 - 13:18:58 PDT)
- Re: AMBER: average structure using ptraj Chris Moth (Fri Jul 02 2004 - 10:11:42 PDT)
AMBER: no 'water.lib' in /amber8/dat/leap/ fangyu liang (Thu Jul 01 2004 - 13:21:50 PDT)
- Re: AMBER: no 'water.lib' in /amber8/dat/leap/ Rhonda Torres (Thu Jul 01 2004 - 13:25:15 PDT)
- RE: AMBER: no 'water.lib' in /amber8/dat/leap/ Ross Walker (Thu Jul 01 2004 - 13:30:25 PDT)
AMBER: MAXRMSPT error in MOIL-view Robyn Ayscue (Thu Jul 01 2004 - 15:19:23 PDT)
- Re: AMBER: MAXRMSPT error in MOIL-view Carlos Simmerling (Thu Jul 01 2004 - 15:26:53 PDT)
AMBER: tleap input file error fangyu liang (Thu Jul 01 2004 - 16:26:18 PDT)
- Re: AMBER: tleap input file error David A. Case (Thu Jul 01 2004 - 17:06:18 PDT)
AMBER: peptide-DNA crosslink modeling M. L. Dodson (Thu Jul 01 2004 - 14:51:24 PDT)
- Re: AMBER: peptide-DNA crosslink modeling Carlos Simmerling (Thu Jul 01 2004 - 18:42:48 PDT)
- Re: AMBER: peptide-DNA crosslink modeling David A. Case (Thu Jul 01 2004 - 22:01:40 PDT)
  - Re: AMBER: peptide-DNA crosslink modeling M. L. Dodson (Fri Jul 02 2004 - 11:06:39 PDT)
AMBER: mm_pbsa problem steven.j.enoch.gsk.com (Fri Jul 02 2004 - 03:29:57 PDT)
- Re: AMBER: mm_pbsa problem david.evans.ulsop.ac.uk (Fri Jul 02 2004 - 03:53:23 PDT)
- Re: AMBER: mm_pbsa problem David A. Case (Fri Jul 02 2004 - 07:52:46 PDT)
AMBER: question about antechamber program Sivanesan Dakshanamurthy (Fri Jul 02 2004 - 11:42:07 PDT)
- Re: AMBER: question about antechamber program David A. Case (Fri Jul 02 2004 - 13:26:12 PDT)
AMBER: best PC laptop system to run Amber 8 fangyu liang (Sat Jul 03 2004 - 14:05:35 PDT)
- Re: AMBER: best PC laptop system to run Amber 8 Andreas Svrcek-Seiler (Sun Jul 04 2004 - 05:24:07 PDT)
- Re: AMBER: best PC laptop system to run Amber 8 fangyu liang (Sun Jul 04 2004 - 22:04:41 PDT)
AMBER: Problem to converge minimization Guillaume Bollot (Mon Jul 05 2004 - 01:41:06 PDT)
- Re: AMBER: Problem to converge minimization Jiten (Mon Jul 05 2004 - 05:38:26 PDT)
- Re: AMBER: Problem to converge minimization David A. Case (Mon Jul 05 2004 - 08:22:01 PDT)
- AMBER: "closestwater" algorithm Grace Li (Mon Jul 05 2004 - 15:42:08 PDT)
AMBER: Namelist problem Vlad Cojocaru (Mon Jul 05 2004 - 02:25:07 PDT)
- Re: AMBER: Namelist problem Guanglei Cui (Mon Jul 05 2004 - 05:56:10 PDT)
  - Re: AMBER: Namelist problem Vlad Cojocaru (Mon Jul 05 2004 - 06:10:51 PDT)
- Re: AMBER: Namelist problem Viktor Hornak (Mon Jul 05 2004 - 07:07:36 PDT)
- Re: AMBER: Namelist problem David A. Case (Mon Jul 05 2004 - 08:21:12 PDT)
AMBER: details for Namelist problem Vlad Cojocaru (Mon Jul 05 2004 - 02:48:40 PDT)
AMBER: combination rules German Sciaini (Mon Jul 05 2004 - 05:31:43 PDT)
- Re: AMBER: combination rules David A. Case (Mon Jul 05 2004 - 10:29:04 PDT)
AMBER: details for Namelist problem Vlad Cojocaru (Mon Jul 05 2004 - 06:22:33 PDT)
AMBER: leap problem in AMBER7 (residue insertion) Kuhn, Bernd {PRBD~Basel} (Mon Jul 05 2004 - 04:26:34 PDT)
- Re: AMBER: leap problem in AMBER7 (residue insertion) David A. Case (Mon Jul 05 2004 - 10:21:50 PDT)
- Re: AMBER: leap problem in AMBER7 (residue insertion) Kuhn, Bernd {PRBD~Basel} (Wed Jul 14 2004 - 04:44:00 PDT)
AMBER: Amber8 on Digital UNIX Guillermo Mulliert Carlín (Mon Jul 05 2004 - 08:30:15 PDT)
- Re: AMBER: Amber8 on Digital UNIX David A. Case (Mon Jul 05 2004 - 09:55:20 PDT)
  - Re: AMBER: Amber8 on Digital UNIX Guillermo Mulliert Carlín (Wed Jul 07 2004 - 02:41:53 PDT)
AMBER: multiple heat bath GB+LES Marcin Krol (Mon Jul 05 2004 - 09:53:31 PDT)
AMBER: How to make leap recognise Zn2+? Yongzhi Chen (Mon Jul 05 2004 - 18:41:26 PDT)
- Re: AMBER: How to make leap recognise Zn2+? Guanglei Cui (Tue Jul 06 2004 - 06:58:27 PDT)
  - Re: AMBER: How to make leap recognise Zn2+? Yongzhi Chen (Tue Jul 06 2004 - 09:00:26 PDT)
AMBER: sander on multiprocessors cailliez (Tue Jul 06 2004 - 00:38:39 PDT)
- Re: AMBER: sander on multiprocessors Stef (Tue Jul 06 2004 - 01:42:36 PDT)
- Re: AMBER: sander on multiprocessors Andreas Svrcek-Seiler (Tue Jul 06 2004 - 04:15:48 PDT)
AMBER: idecomp Marcela Madrid (Tue Jul 06 2004 - 08:42:20 PDT)
- Re: AMBER: idecomp David A. Case (Tue Jul 06 2004 - 09:37:42 PDT)
- Re: AMBER: idecomp Marcela Madrid (Thu Jul 08 2004 - 12:35:57 PDT)
AMBER: running MD simulatons sachin patil (Tue Jul 06 2004 - 09:52:58 PDT)
- Re: AMBER: running MD simulatons David A. Case (Tue Jul 06 2004 - 11:40:50 PDT)
AMBER: Amber7 bugfix1 sachin patil (Tue Jul 06 2004 - 10:47:38 PDT)
- RE: AMBER: Amber7 bugfix1 Ross Walker (Tue Jul 06 2004 - 11:17:49 PDT)
- Re: AMBER: Amber7 bugfix1 David A. Case (Tue Jul 06 2004 - 11:37:04 PDT)
AMBER: parameter development for nucleotide analogues Vlad Cojocaru (Wed Jul 07 2004 - 03:37:50 PDT)
- RE: AMBER: parameter development for nucleotide analogues Ross Walker (Thu Jul 08 2004 - 10:49:33 PDT)
AMBER: name error Prashansa Agrawal (Wed Jul 07 2004 - 15:57:53 PDT)
- RE: AMBER: name error Ross Walker (Thu Jul 08 2004 - 10:35:46 PDT)
- Re: AMBER: name error David A. Case (Thu Jul 08 2004 - 13:54:48 PDT)
AMBER: Namelist problem solved Vlad Cojocaru (Wed Jul 07 2004 - 04:09:16 PDT)
AMBER: Molecular dynamic bybaker.itsa.ucsf.edu (Wed Jul 07 2004 - 14:12:33 PDT)
- RE: AMBER: Molecular dynamic Ross Walker (Thu Jul 08 2004 - 10:24:21 PDT)
- Re: AMBER: Molecular dynamic bybaker.itsa.ucsf.edu (Fri Jul 09 2004 - 15:54:38 PDT)
  - RE: AMBER: Molecular dynamic Ross Walker (Mon Jul 12 2004 - 11:12:53 PDT)
    - RE: AMBER: Molecular dynamic Andy Purkiss (Tue Jul 13 2004 - 02:21:02 PDT)
    - RE: AMBER: Molecular dynamic Joseph Nachman (Tue Jul 13 2004 - 08:21:09 PDT)
AMBER: My strange result of TI. Chunhu Tan (Wed Jul 07 2004 - 16:35:19 PDT)
AMBER: correlation in Amber 8 Bimo Ario Tejo (Thu Jul 08 2004 - 01:14:34 PDT)
AMBER: segmentation fault in leap anshul.imtech.res.in (Thu Jul 08 2004 - 14:40:42 PDT)
- Re: AMBER: segmentation fault in leap Guillermo Mulliert Carlín (Thu Jul 08 2004 - 05:02:05 PDT)
  - Re: AMBER: segmentation fault in leap anshul.imtech.res.in (Thu Jul 08 2004 - 18:17:40 PDT)
    - AMBER: ptraj Wen Li (Thu Jul 08 2004 - 09:06:01 PDT)
    - RE: AMBER: ptraj Ross Walker (Thu Jul 08 2004 - 10:01:43 PDT)
    - AMBER: ptraj-closestwaters command Grace Li (Sat Jul 10 2004 - 09:14:34 PDT)
    - Re: AMBER: ptraj-closestwaters command Thomas E. Cheatham, III (Mon Jul 12 2004 - 13:38:41 PDT)
- RE: AMBER: segmentation fault in leap Ross Walker (Thu Jul 08 2004 - 10:07:28 PDT)
AMBER: question about Ptraj jz7.duke.edu (Thu Jul 08 2004 - 09:32:07 PDT)
- RE: AMBER: question about Ptraj Ross Walker (Thu Jul 08 2004 - 09:47:28 PDT)
- Re: AMBER: question about Ptraj Thomas E. Cheatham, III (Thu Jul 08 2004 - 09:56:04 PDT)
  - AMBER: question about Ptraj - AND OR james tomomi macdonald (Mon Jul 12 2004 - 08:06:59 PDT)
    - Re: AMBER: question about Ptraj - AND OR Thomas E. Cheatham, III (Mon Jul 12 2004 - 08:15:13 PDT)
    - Re: AMBER: question about Ptraj - AND OR Herr/Señor/Monsieur/Mister Gregory (Mon Jul 12 2004 - 09:15:47 PDT)
AMBER: weird box expansion Herbert Georg (Thu Jul 08 2004 - 09:57:57 PDT)
- Re: AMBER: weird box expansion Thomas E. Cheatham, III (Thu Jul 08 2004 - 10:06:57 PDT)
  - Re: AMBER: weird box expansion Herbert Georg (Thu Jul 08 2004 - 10:38:01 PDT)
AMBER: problems with mdcrd Carsten Detering (Thu Jul 08 2004 - 10:16:04 PDT)
- RE: AMBER: problems with mdcrd Ross Walker (Thu Jul 08 2004 - 10:32:04 PDT)
- RE: AMBER: problems with mdcrd Ross Walker (Thu Jul 08 2004 - 12:54:08 PDT)
RE: AMBER: charge problem in minimization Ross Walker (Thu Jul 08 2004 - 10:40:56 PDT)
AMBER: parameter development for nucleotide analogues Vlad Cojocaru (Thu Jul 08 2004 - 10:49:42 PDT)
AMBER: namelist problem solved Vlad Cojocaru (Thu Jul 08 2004 - 10:50:10 PDT)
Re: AMBER: charge problem in minimization David A. Case (Thu Jul 08 2004 - 13:54:54 PDT)
AMBER: Problem with sander - Error on Open Mike (Thu Jul 08 2004 - 14:38:37 PDT)
- RE: AMBER: Problem with sander - Error on Open Ross Walker (Thu Jul 08 2004 - 15:15:04 PDT)
  - RE: AMBER: Problem with sander - Error on Open Mike (Thu Jul 08 2004 - 18:57:43 PDT)
    - RE: AMBER: Problem with sander - Error on Open Thomas E. Cheatham, III (Thu Jul 08 2004 - 19:18:10 PDT)
AMBER: how to calculate E-pot from restart file? J. Zhang, Dr (Thu Jul 08 2004 - 20:13:44 PDT)
- Re: AMBER: how to calculate E-pot from restart file? David A. Case (Thu Jul 08 2004 - 21:07:49 PDT)
AMBER: execution time cailliez (Fri Jul 09 2004 - 02:50:25 PDT)
- RE: AMBER: execution time Ross Walker (Fri Jul 09 2004 - 11:52:08 PDT)
AMBER: cys protecting group parameters Stefano.Pieraccini.unimi.it (Fri Jul 09 2004 - 06:48:36 PDT)
AMBER: cys protecting groups parameters Stefano.Pieraccini.unimi.it (Fri Jul 09 2004 - 05:41:20 PDT)
AMBER: Setup for parallel computing fangyu liang (Fri Jul 09 2004 - 10:00:32 PDT)
- Re: AMBER: Setup for parallel computing Stef (Sat Jul 10 2004 - 14:14:56 PDT)
- Re: AMBER: Setup for parallel computing fangyu liang (Sat Jul 10 2004 - 16:10:19 PDT)
  - AMBER: opteron 64 bit workstation sachin patil (Wed Aug 11 2004 - 11:59:33 PDT)
    - Re: AMBER: opteron 64 bit workstation David A. Case (Thu Aug 12 2004 - 12:55:13 PDT)
AMBER: Disulfide bond command bybaker.itsa.ucsf.edu (Fri Jul 09 2004 - 11:16:13 PDT)
- RE: AMBER: Disulfide bond command Ross Walker (Fri Jul 09 2004 - 11:27:13 PDT)
- Re: AMBER: Disulfide bond command bybaker.itsa.ucsf.edu (Fri Jul 09 2004 - 11:51:46 PDT)
AMBER: MD simulation : problem sachin patil (Fri Jul 09 2004 - 22:08:15 PDT)
- RE: AMBER: MD simulation : problem Ross Walker (Fri Jul 09 2004 - 22:35:14 PDT)
- RE: AMBER: MD simulation : problem sachin patil (Sun Jul 11 2004 - 08:08:13 PDT)
  - RE: AMBER: MD simulation : problem Ross Walker (Sun Jul 11 2004 - 17:41:11 PDT)
    - RE: AMBER: MD simulation : problem sachin patil (Sun Jul 11 2004 - 21:53:51 PDT)
    - RE: AMBER: MD simulation : problem Ross Walker (Mon Jul 12 2004 - 10:55:33 PDT)
    - RE: AMBER: MD simulation : problem :THANK YOU sachin patil (Tue Jul 13 2004 - 07:51:28 PDT)
AMBER: About the calculation of non-bond list Wu Lei (Sat Jul 10 2004 - 07:21:57 PDT)
AMBER: Problem amber8 compilation in Opteron(Linux) with PGI-workstation compiler Jiten (Sat Jul 10 2004 - 08:30:15 PDT)
- Re: AMBER: Problem amber8 compilation in Opteron(Linux) with PGI-workstation compiler Mark Williamson (Sat Jul 10 2004 - 10:54:56 PDT)
- Re: AMBER: Problem amber8 compilation in Opteron(Linux) with PGI-workstation compiler David A. Case (Sat Jul 10 2004 - 20:46:57 PDT)
- Re: AMBER: Problem amber8 compilation in Opteron(Linux) with PGI-workstation compiler Jiten (Sat Jul 10 2004 - 22:04:35 PDT)
  - RE: AMBER: Problem amber8 compilation in Opteron(Linux) with PGI-workstation compiler Ross Walker (Sun Jul 11 2004 - 11:38:49 PDT)
    - RE: AMBER: Problem amber8 compilation in Opteron(Linux) with PGI-workstation compiler Mark Williamson (Sun Jul 11 2004 - 13:52:45 PDT)
    - RE: AMBER: Problem amber8 compilation in Opteron(Linux) with PGI-workstation compiler Scott Brozell (Mon Jul 12 2004 - 11:30:39 PDT)
    - Re: AMBER: Problem amber8 compilation in Opteron(Linux) with PGI-workstation compiler Jiten (Mon Jul 12 2004 - 02:36:36 PDT)
- Re: AMBER: Problem amber8 compilation in Opteron(Linux) with PGI-workstation compiler Jiten (Sat Jul 10 2004 - 22:24:27 PDT)
- Re: AMBER: Problem amber8 compilation in Opteron(Linux) with PGI-workstation compiler Jiten (Tue Jul 13 2004 - 02:46:57 PDT)
- Re: AMBER: Problem amber8 compilation in Opteron(Linux) with PGI-workstation compiler Jiten (Tue Jul 13 2004 - 02:52:06 PDT)
AMBER: Rigid counteranion during MD !! Jiten (Sun Jul 11 2004 - 01:26:35 PDT)
- Re: AMBER: Rigid counteranion during MD !! Jiten (Sun Jul 11 2004 - 07:51:48 PDT)
AMBER: solvation free energy hj zou (Sat Jul 10 2004 - 23:16:19 PDT)
- Re: AMBER: solvation free energy Ray Luo (Sun Jul 11 2004 - 19:25:44 PDT)
AMBER: hj zou (Sat Jul 10 2004 - 23:16:17 PDT)
AMBER: solvation free energy hj zou (Fri Jul 09 2004 - 00:38:39 PDT)
- Re: AMBER: solvation free energy Qizhi Cui (Mon Jul 19 2004 - 10:32:17 PDT)
AMBER: Fe parameter hj zou (Mon Jul 12 2004 - 00:09:29 PDT)
- Re: AMBER: Fe parameter Wu Lei (Mon Jul 12 2004 - 00:51:18 PDT)
- Re: AMBER: Fe parameter scopio (Mon Jul 12 2004 - 07:18:52 PDT)
- RE: AMBER: Fe parameter Ross Walker (Mon Jul 12 2004 - 11:19:23 PDT)
AMBER: Problems with CPU scaling on cluster Your Name (Mon Jul 12 2004 - 01:12:48 PDT)
- RE: AMBER: Problems with CPU scaling on cluster Ross Walker (Mon Jul 12 2004 - 11:38:27 PDT)
- RE: AMBER: Problems with CPU scaling on cluster Ross Walker (Thu Jul 15 2004 - 11:48:15 PDT)
  - Re: AMBER: Problems with CPU scaling on cluster David E. Konerding (Fri Jul 16 2004 - 08:46:01 PDT)
AMBER: RNA sequence with DNA backbone? Arvind (Mon Jul 12 2004 - 04:26:36 PDT)
- Re: AMBER: RNA sequence with DNA backbone? David A. Case (Mon Jul 12 2004 - 13:35:43 PDT)
  - Re: AMBER: RNA sequence with DNA backbone? Arvind (Wed Jul 14 2004 - 03:50:29 PDT)
    - Re: AMBER: RNA sequence with DNA backbone? Vlad Cojocaru (Wed Jul 14 2004 - 04:09:13 PDT)
AMBER: what is averaged RMS fluctuation? jz7.duke.edu (Mon Jul 12 2004 - 09:17:30 PDT)
- RE: AMBER: what is averaged RMS fluctuation? Ross Walker (Mon Jul 12 2004 - 11:51:47 PDT)
  - RE: AMBER: what is averaged RMS fluctuation? jz7.duke.edu (Mon Jul 12 2004 - 12:59:26 PDT)
    - RE: AMBER: what is averaged RMS fluctuation? Thomas E. Cheatham, III (Mon Jul 12 2004 - 13:28:21 PDT)
    - RE: AMBER: what is averaged RMS fluctuation? Ross Walker (Mon Jul 12 2004 - 13:40:23 PDT)
    - AMBER: question about ptraj jz7.duke.edu (Wed Jul 21 2004 - 13:00:01 PDT)
    - Re: AMBER: question about ptraj Guanglei Cui (Wed Jul 21 2004 - 13:32:29 PDT)
    - AMBER: cut offs in amber? Grace Li (Wed Jul 21 2004 - 13:47:43 PDT)
    - RE: AMBER: cut offs in amber? Ross Walker (Wed Jul 21 2004 - 14:05:02 PDT)
    - RE: AMBER: cut offs in amber? Grace Li (Wed Jul 21 2004 - 14:20:40 PDT)
    - Re: AMBER: cut offs in amber? Carlos Simmerling (Wed Jul 21 2004 - 14:32:18 PDT)
    - RE: AMBER: cut offs in amber? Ross Walker (Wed Jul 21 2004 - 14:39:47 PDT)
    - RE: AMBER: cut offs in amber? Grace Li (Wed Jul 21 2004 - 15:03:05 PDT)
    - RE: AMBER: cut offs in amber? Ross Walker (Wed Jul 21 2004 - 15:10:09 PDT)
- Re: AMBER: what is averaged RMS fluctuation? Carlos Simmerling (Mon Jul 12 2004 - 13:37:13 PDT)
AMBER: About the free energy difference in vacuum with GIBBS. Chunhu Tan (Mon Jul 12 2004 - 15:34:35 PDT)
- Re: AMBER: About the free energy difference in vacuum with GIBBS. David A. Case (Wed Jul 14 2004 - 13:51:38 PDT)
AMBER: Jiten (Tue Jul 13 2004 - 02:25:53 PDT)
- Re: AMBER: Carlos Simmerling (Tue Jul 13 2004 - 04:59:08 PDT)
AMBER: Angle restraint during MD Jiten (Tue Jul 13 2004 - 02:28:14 PDT)
- Re: AMBER: Angle restraint during MD Carlos Simmerling (Tue Jul 13 2004 - 05:00:42 PDT)
- Re: AMBER: Angle restraint during MD Jiten (Tue Jul 13 2004 - 09:21:28 PDT)
- Re: AMBER: Angle restraint during MD Carlos Simmerling (Tue Jul 13 2004 - 10:47:16 PDT)
- Re: AMBER: Angle restraint during MD Jiten (Tue Jul 13 2004 - 22:51:42 PDT)
- Re: AMBER: Angle restraint during MD Carlos Simmerling (Wed Jul 14 2004 - 06:39:38 PDT)
AMBER: Use of ibelly with nmode analysis steven.j.enoch.gsk.com (Tue Jul 13 2004 - 06:30:30 PDT)
- Re: AMBER: Use of ibelly with nmode analysis David A. Case (Tue Jul 13 2004 - 09:24:27 PDT)
- Re: AMBER: Use of ibelly with nmode analysis marti (Thu Feb 24 2005 - 03:47:28 PST)
  - Re: AMBER: Use of ibelly with nmode analysis David A. Case (Thu Feb 24 2005 - 08:30:31 PST)
AMBER: torsion scan Guanglei Cui (Tue Jul 13 2004 - 08:18:32 PDT)
- Re: AMBER: torsion scan Furse, Kristina Elisabet (Tue Jul 13 2004 - 10:37:35 PDT)
- Re: AMBER: torsion scan David A. Case (Tue Jul 13 2004 - 13:47:00 PDT)
  - Re: AMBER: torsion scan Guanglei Cui (Tue Jul 13 2004 - 14:12:50 PDT)
AMBER: (no subject) anshul.imtech.res.in (Tue Jul 13 2004 - 20:40:08 PDT)
- RE: AMBER: (no subject) Ross Walker (Tue Jul 13 2004 - 10:32:22 PDT)
AMBER: Parameter generation from RESP charges anshul.imtech.res.in (Tue Jul 13 2004 - 21:02:07 PDT)
Re: AMBER: Molecular dynamic & Acknowledgement bybaker.itsa.ucsf.edu (Tue Jul 13 2004 - 11:20:50 PDT)
AMBER: anisotropic scaling Xiang, Tian-Xiang (Tue Jul 13 2004 - 12:12:32 PDT)
- RE: AMBER: anisotropic scaling Ross Walker (Tue Jul 13 2004 - 12:39:05 PDT)
- Re: AMBER: anisotropic scaling David A. Case (Tue Jul 13 2004 - 13:43:02 PDT)
Re: AMBER: Implicit MD problem Carlos Simmerling (Wed Jul 14 2004 - 06:42:18 PDT)
- Re: AMBER: Implicit MD problem David A. Case (Wed Jul 14 2004 - 09:29:47 PDT)
- Re: AMBER: Implicit MD problem Carlos Simmerling (Wed Jul 14 2004 - 09:53:31 PDT)
AMBER: Problem with divcon - increasing MXATTS? steven.j.enoch.gsk.com (Wed Jul 14 2004 - 08:33:38 PDT)
- Re: AMBER: Problem with divcon - increasing MXATTS? Kennie Merz (Wed Jul 14 2004 - 09:01:54 PDT)
  - Re: AMBER: Problem with divcon - increasing MXATTS? steven.j.enoch.gsk.com (Wed Jul 14 2004 - 09:45:54 PDT)
    - Re: AMBER: Problem with divcon - increasing MXATTS? Kennie Merz (Wed Jul 14 2004 - 10:03:32 PDT)
    - RE: AMBER: Problem with divcon - increasing MXATTS? Ross Walker (Wed Jul 14 2004 - 11:13:19 PDT)
Re: AMBER: Angle restraint during MD and namelist problem in amber8 Jiten (Wed Jul 14 2004 - 09:13:38 PDT)
- Re: AMBER: Angle restraint during MD and namelist problem in amber8 Thomas E. Cheatham, III (Wed Jul 14 2004 - 09:22:26 PDT)
AMBER: Enthalpy of solvent-solute vanderWaals Scott (Wed Jul 14 2004 - 12:56:45 PDT)
AMBER: tleap - FATAL error Sivanesan Dakshanamurthy (Wed Jul 14 2004 - 14:28:41 PDT)
- Re: AMBER: tleap - FATAL error Scott Brozell (Wed Jul 14 2004 - 14:44:41 PDT)
AMBER: Normal mode calculation with periodic boundary condition Johnson Agbo (Wed Jul 14 2004 - 22:15:09 PDT)
- Re: AMBER: Normal mode calculation with periodic boundary condition David A. Case (Thu Jul 15 2004 - 10:04:07 PDT)
AMBER: announcing normal mode analysis web server ElNemo Karsten Suhre (Thu Jul 15 2004 - 01:21:07 PDT)
AMBER: Correl in Amber8: Diagonal elements not 1? Bimo Ario Tejo (Thu Jul 15 2004 - 04:47:43 PDT)
Re: AMBER: xleap solvatebox/oct problem Jiten (Thu Jul 15 2004 - 08:18:59 PDT)
- Re: AMBER: xleap solvatebox/oct problem David A. Case (Thu Jul 15 2004 - 10:02:11 PDT)
- Re: AMBER: xleap solvatebox/oct problem Jiten (Fri Jul 16 2004 - 02:07:09 PDT)
  - AMBER: Leap & x86_64 / PGI (was: xleap solvatebox/oct problem) Hannes Barsch (Mon Nov 29 2004 - 09:02:15 PST)
    - Re: AMBER: Leap & x86_64 / PGI (was: xleap solvatebox/oct problem) David A. Case (Wed Dec 01 2004 - 09:44:12 PST)
    - (long) Re: AMBER: Leap & x86_64 / PGI (was: xleap solvatebox/oct problem) Tru Huynh (Thu Dec 02 2004 - 12:00:17 PST)
AMBER: Problems with amber8 and pgf90 Marc Perea (Thu Jul 15 2004 - 03:30:36 PDT)
- Re: AMBER: Problems with amber8 and pgf90 Scott Brozell (Thu Jul 15 2004 - 09:23:44 PDT)
AMBER: antechamber Xin Hu (Thu Jul 15 2004 - 11:03:44 PDT)
- RE: AMBER: antechamber Ross Walker (Thu Jul 15 2004 - 11:21:44 PDT)
  - Re: AMBER: antechamber Xin Hu (Thu Jul 15 2004 - 13:57:09 PDT)
    - Re: AMBER: antechamber David A. Case (Thu Jul 15 2004 - 16:30:26 PDT)
AMBER: pH effect on protein folding Rukman Hertadi (Thu Jul 15 2004 - 19:00:54 PDT)
- Re: AMBER: pH effect on protein folding Bimo Ario Tejo (Thu Jul 15 2004 - 20:34:39 PDT)
- Re: AMBER: pH effect on protein folding tri nam Vo (Fri Apr 06 2007 - 23:27:40 PDT)
AMBER: Amber8: Vlimit problem again Yuhui Cheng (Thu Jul 15 2004 - 19:34:58 PDT)
- Re: AMBER: Amber8: Vlimit problem again German Sciaini (Fri Jul 16 2004 - 06:12:59 PDT)
- Re: AMBER: Amber8: Vlimit problem again David A. Case (Fri Jul 16 2004 - 09:26:06 PDT)
  - Re: AMBER: Amber8: Vlimit problem again Yuhui Cheng (Wed Jul 21 2004 - 16:44:09 PDT)
    - RE: AMBER: Amber8: Vlimit problem again Ross Walker (Wed Jul 21 2004 - 16:55:59 PDT)
AMBER: Is it a bug?(in prep file opls_unict.in) Wu Lei (Thu Jul 15 2004 - 20:44:09 PDT)
- Re: AMBER: Is it a bug?(in prep file opls_unict.in) David A. Case (Fri Jul 16 2004 - 09:27:41 PDT)
- Re: AMBER: Is it a bug?(in prep file opls_unict.in) Wu Lei (Fri Jul 16 2004 - 22:15:16 PDT)
  - Re: AMBER: Is it a bug?(in prep file opls_unict.in) David A. Case (Wed Jul 21 2004 - 01:52:22 PDT)
AMBER: NB pairs exceeds? Chen (Fri Jul 16 2004 - 00:35:16 PDT)
- Re: AMBER: NB pairs exceeds? Wu Lei (Fri Jul 16 2004 - 01:07:56 PDT)
  - Re: Re: AMBER: NB pairs exceeds? Chen (Fri Jul 16 2004 - 01:40:42 PDT)
    - Re: Re: AMBER: NB pairs exceeds? David A. Case (Fri Jul 16 2004 - 09:23:22 PDT)
  - Re: Re: AMBER: NB pairs exceeds? csong.mail.sdu.edu.cn (Sat Jul 17 2004 - 03:10:23 PDT)
    - Re: Re: AMBER: NB pairs exceeds? David A. Case (Sat Jul 17 2004 - 18:09:22 PDT)
  - Re: Re: AMBER: NB pairs exceeds? csong.mail.sdu.edu.cn (Sun Jul 18 2004 - 01:28:27 PDT)
AMBER: X-CA-CT-X dih. FF param ? FyD (Fri Jul 16 2004 - 10:08:26 PDT)
- Re: AMBER: X-CA-CT-X dih. FF param ? Guanglei Cui (Fri Jul 16 2004 - 10:24:46 PDT)
AMBER: question about production runs opitz.che.udel.edu (Fri Jul 16 2004 - 12:42:06 PDT)
AMBER: RESP vs. AM1-BCC charges for isoprene Oliver Hucke (Fri Jul 16 2004 - 14:00:57 PDT)
- Re: AMBER: RESP vs. AM1-BCC charges for isoprene Rhonda Torres (Fri Jul 16 2004 - 14:20:42 PDT)
  - Re: AMBER: RESP vs. AM1-BCC charges for isoprene Oliver Hucke (Fri Jul 16 2004 - 15:49:00 PDT)
- Re: AMBER: RESP vs. AM1-BCC charges for isoprene Carsten Detering (Fri Jul 16 2004 - 14:33:51 PDT)
- Re: AMBER: RESP vs. AM1-BCC charges for isoprene Carsten Detering (Fri Jul 16 2004 - 14:37:22 PDT)
- Re: AMBER: RESP vs. AM1-BCC charges for isoprene Ilyas Yildirim (Fri Jul 16 2004 - 15:36:22 PDT)
- Re: AMBER: RESP vs. AM1-BCC charges for isoprene Joe Harriman (Sat Jul 17 2004 - 05:44:47 PDT)
- RE: AMBER: RESP vs. AM1-BCC charges for isoprene ajakalian.lav.Boehringer-Ingelheim.com (Thu Jul 22 2004 - 05:43:16 PDT)
  - Re: AMBER: RESP vs. AM1-BCC charges for isoprene Oliver Hucke (Fri Jul 23 2004 - 10:41:05 PDT)
- RE: AMBER: RESP vs. AM1-BCC charges for isoprene ajakalian.lav.Boehringer-Ingelheim.com (Mon Jul 26 2004 - 08:09:31 PDT)
AMBER: Cubic Ice Johnson Agbo (Fri Jul 16 2004 - 18:08:14 PDT)
AMBER: Amber7 (8):FLUSH--FAILED:: Resource temporarily unavailable Jean-Christophe Ducom (Sat Jul 17 2004 - 13:01:47 PDT)
AMBER: Re: Results from RED-II beta FyD (Sun Jul 18 2004 - 09:11:41 PDT)
AMBER: vdw energy in minimization anshul.imtech.res.in (Mon Jul 19 2004 - 08:11:17 PDT)
- Re: AMBER: vdw energy in minimization carlos (Mon Jul 19 2004 - 05:13:30 PDT)
  - Re: AMBER: vdw energy in minimization anshul.imtech.res.in (Mon Jul 19 2004 - 20:44:30 PDT)
    - Re: AMBER: vdw energy in minimization Carlos Simmerling (Mon Jul 19 2004 - 11:47:21 PDT)
AMBER: Weird compiling problem in Amber 8 echanco.uci.edu (Sun Jul 18 2004 - 22:51:29 PDT)
- Re: AMBER: Weird compiling problem in Amber 8 fangyu liang (Sun Jul 18 2004 - 23:30:22 PDT)
- Re: AMBER: Weird compiling problem in Amber 8 Scott Brozell (Mon Jul 19 2004 - 10:08:54 PDT)
  - Re: AMBER: Weird compiling problem in Amber 8 Ray Luo (Sun Jul 18 2004 - 22:34:03 PDT)
AMBER: .lib file error in tleap anita pachaimuthu (Mon Jul 19 2004 - 10:19:19 PDT)
- Re: AMBER: .lib file error in tleap Sébastien Osborne (Mon Jul 19 2004 - 11:15:11 PDT)
- AMBER: antechamber - missing improper torsions O. Hucke (Mon Jul 19 2004 - 11:58:39 PDT)
  - Re: AMBER: antechamber - missing improper torsions German Sciaini (Tue Jul 20 2004 - 06:04:17 PDT)
  - RE: AMBER: antechamber - missing improper torsions Junmei Wang (Wed Jul 21 2004 - 09:11:04 PDT)
AMBER: A problem regarding constant pH calculation in Amber 8 Yongzhi Chen (Mon Jul 19 2004 - 18:54:43 PDT)
AMBER: PB Bomb in pb_reslist(): maxnbr too small steven.j.enoch.gsk.com (Tue Jul 20 2004 - 06:00:59 PDT)
- Re: AMBER: PB Bomb in pb_reslist(): maxnbr too small Ray Luo (Mon Jul 19 2004 - 05:22:26 PDT)
AMBER: antechamber - improper torsions Oliver Hucke (Tue Jul 20 2004 - 09:23:02 PDT)
AMBER: FW: missing bondi radii of Br and F for surface area calculation S. Frank Yan (Tue Jul 20 2004 - 10:30:13 PDT)
AMBER: about GLYCAM prep files in AMBER Ozlem Demir (Tue Jul 20 2004 - 10:34:07 PDT)
AMBER: Problem with sander tutorial. tarek mahfouz (Tue Jul 20 2004 - 12:09:44 PDT)
- RE: AMBER: Problem with sander tutorial. Ross Walker (Tue Jul 20 2004 - 13:16:28 PDT)
  - RE: AMBER: Problem with sander tutorial. tarek mahfouz (Thu Jul 22 2004 - 09:59:42 PDT)
    - RE: AMBER: Problem with sander tutorial. Ross Walker (Thu Jul 22 2004 - 13:57:20 PDT)
    - RE: AMBER: Problem with sander tutorial. Scott (Thu Jul 22 2004 - 19:08:19 PDT)
AMBER: Bondi radii for BR and F in mm_pbsa calculation S. Frank Yan (Tue Jul 20 2004 - 16:01:03 PDT)
- Re: AMBER: Bondi radii for BR and F in mm_pbsa calculation Rhonda Torres (Tue Jul 20 2004 - 17:23:10 PDT)
AMBER: Leap could not find atom type CK 吴磊 (Tue Jul 20 2004 - 21:35:54 PDT)
AMBER: Re: Re: AMBER: Is it a bug?(in prep file opls_unict.in) 吴磊 (Wed Jul 21 2004 - 03:59:13 PDT)
- Re: AMBER: Re: Re: AMBER: Is it a bug?(in prep file opls_unict.in) David A. Case (Wed Jul 21 2004 - 06:32:44 PDT)
AMBER: atom out of bounds Venkata S Koppuravuri (Wed Jul 21 2004 - 06:25:25 PDT)
AMBER: Co-ordination error while running tleap anita pachaimuthu (Wed Jul 21 2004 - 08:12:12 PDT)
AMBER: What happen when sander reads charge increments from cpin file? Yongzhi Chen (Wed Jul 21 2004 - 13:24:51 PDT)
- RE: AMBER: What happen when sander reads charge increments from cpin file? Ross Walker (Wed Jul 21 2004 - 13:41:45 PDT)
  - RE: AMBER: What happen when sander reads charge increments from cpin file? Yongzhi Chen (Wed Jul 21 2004 - 14:59:40 PDT)
AMBER: amparm Vincent Bisetty (Wed Jul 21 2004 - 13:37:39 PDT)
- RE: AMBER: amparm Ross Walker (Wed Jul 21 2004 - 14:11:29 PDT)
AMBER: sander tutorial mathew k varghese (Thu Jul 22 2004 - 05:16:33 PDT)
- Re: AMBER: sander tutorial Carlos Simmerling (Thu Jul 22 2004 - 05:33:08 PDT)
AMBER: mutation of atoms Nelson Fonseca (Thu Jul 22 2004 - 05:41:22 PDT)
AMBER: found unknown atflg PB Scott (Thu Jul 22 2004 - 06:38:33 PDT)
- Re: AMBER: found unknown atflg PB Holger Gohlke (Thu Jul 22 2004 - 07:56:38 PDT)
AMBER: Xleap crash, problem with residue bonding opitz.che.udel.edu (Thu Jul 22 2004 - 07:24:35 PDT)
- RE: AMBER: Xleap crash, problem with residue bonding Ross Walker (Thu Jul 22 2004 - 14:31:22 PDT)
- RE: AMBER: Xleap crash, problem with residue bonding Bill Ross (Thu Jul 22 2004 - 14:55:58 PDT)
- Re: AMBER: Xleap crash, problem with residue bonding opitz.che.udel.edu (Mon Jul 26 2004 - 08:39:51 PDT)
AMBER: user force Myunggi Yi (Thu Jul 22 2004 - 10:00:16 PDT)
- Re: AMBER: user force Furse, Kristina Elisabet (Thu Jul 22 2004 - 14:07:46 PDT)
  - Re: AMBER: user force myunggi.csit.fsu.edu (Thu Jul 22 2004 - 14:48:28 PDT)
    - RE: AMBER: user force Ross Walker (Thu Jul 22 2004 - 15:08:04 PDT)
    - RE: AMBER: user force myunggi.csit.fsu.edu (Thu Jul 22 2004 - 15:25:50 PDT)
    - Re: AMBER: user force Carlos Simmerling (Thu Jul 22 2004 - 15:28:42 PDT)
    - RE: AMBER: user force Ross Walker (Thu Jul 22 2004 - 15:40:16 PDT)
    - RE: AMBER: user force myunggi.csit.fsu.edu (Thu Jul 22 2004 - 16:26:14 PDT)
    - Re: AMBER: user force Carlos Simmerling (Fri Jul 23 2004 - 04:47:17 PDT)
- Re: AMBER: user force Bill Ross (Thu Jul 22 2004 - 14:57:24 PDT)
AMBER: (no subject) myunggi.csit.fsu.edu (Thu Jul 22 2004 - 10:10:09 PDT)
AMBER: atom out of bounds (fwd) Venkata S Koppuravuri (Thu Jul 22 2004 - 12:52:13 PDT)
- RE: AMBER: atom out of bounds (fwd) Ross Walker (Thu Jul 22 2004 - 13:54:52 PDT)
AMBER: Ewald parameter range Johnson Agbo (Thu Jul 22 2004 - 17:16:08 PDT)
- Re: AMBER: Ewald parameter range David A. Case (Fri Jul 23 2004 - 01:53:50 PDT)
  - Re: AMBER: Ewald parameter range Johnson Agbo (Fri Jul 23 2004 - 11:00:12 PDT)
AMBER: sander : constraints to conserve hydrogen bonds sachin patil (Thu Jul 22 2004 - 21:15:04 PDT)
- Re: AMBER: sander : constraints to conserve hydrogen bonds Jiten (Thu Jul 22 2004 - 22:58:15 PDT)
  - Re: AMBER: sander : constraints to conserve hydrogen bonds Carlos Simmerling (Fri Jul 23 2004 - 05:08:43 PDT)
AMBER: pmemd. Osman Gani (Fri Jul 23 2004 - 10:09:55 PDT)
- Re: AMBER: pmemd. Robert Duke (Fri Jul 23 2004 - 10:46:48 PDT)
- RE: AMBER: pmemd. Osman Gani (Mon Aug 16 2004 - 06:03:15 PDT)
  - Re: AMBER: pmemd. Robert Duke (Mon Aug 16 2004 - 07:33:21 PDT)
    - Re: AMBER: pmemd. David E. Konerding (Mon Aug 16 2004 - 09:27:02 PDT)
AMBER: parametrization problem Carsten Detering (Fri Jul 23 2004 - 11:16:13 PDT)
- RE: AMBER: parametrization problem Ross Walker (Fri Jul 23 2004 - 12:32:15 PDT)
  - AMBER: about RDF calculation in action.c Grace Li (Fri Jul 23 2004 - 13:39:07 PDT)
  - Re: AMBER: parametrization problem Carsten Detering (Fri Jul 23 2004 - 13:38:59 PDT)
  - Re: AMBER: parametrization problem Carsten Detering (Fri Jul 23 2004 - 13:33:01 PDT)
- FW: AMBER: parametrization problem Ross Walker (Fri Jan 14 2005 - 14:39:12 PST)
  - RE: FW: AMBER: parametrization problem Vineet Pande (Sat Jan 15 2005 - 03:15:39 PST)
AMBER: atoms not in residue templates anshul.imtech.res.in (Sat Jul 24 2004 - 08:19:42 PDT)
- RE: AMBER: atoms not in residue templates Ross Walker (Sat Jul 24 2004 - 08:05:36 PDT)
AMBER: erroe in installing amber8 anshul.imtech.res.in (Sat Jul 24 2004 - 10:11:02 PDT)
- Re: AMBER: erroe in installing amber8 David A. Case (Sat Jul 24 2004 - 01:40:06 PDT)
  - Re: AMBER: erroe in installing amber8 Scott Brozell (Sun Jul 25 2004 - 17:58:58 PDT)
AMBER: about the parameter of the cystein pair in MD simulation Yuhui Cheng (Sun Jul 25 2004 - 19:01:13 PDT)
- Re: AMBER: about the parameter of the cystein pair in MD simulation Thomas E. Cheatham, III (Sun Jul 25 2004 - 20:07:44 PDT)
AMBER: about running ptraj in amber8 jz7.duke.edu (Mon Jul 26 2004 - 07:04:33 PDT)
- RE: AMBER: about running ptraj in amber8 Ross Walker (Mon Jul 26 2004 - 09:22:36 PDT)
  - RE: AMBER: about running ptraj in amber8 jz7.duke.edu (Mon Jul 26 2004 - 09:30:42 PDT)
    - AMBER: about running ptraj in ambber8 (re-post) jz7.duke.edu (Mon Jul 26 2004 - 13:47:52 PDT)
AMBER: amber compilation Livadaru, Lucian (Mon Jul 26 2004 - 13:15:50 PDT)
- Re: AMBER: amber compilation Viktor Hornak (Mon Jul 26 2004 - 13:47:33 PDT)
AMBER: Temperature Regulation Johnson Agbo (Mon Jul 26 2004 - 21:40:44 PDT)
- Re: AMBER: Temperature Regulation Andreas Svrcek-Seiler (Tue Jul 27 2004 - 07:09:51 PDT)
- Re: AMBER: Temperature Regulation David A. Case (Tue Jul 27 2004 - 08:24:31 PDT)
AMBER: mm_pbsa Abmer8 example John (Tue Jul 27 2004 - 03:38:50 PDT)
- Re: AMBER: mm_pbsa Abmer8 example Holger Gohlke (Mon Aug 02 2004 - 23:39:06 PDT)
AMBER: question on simulated annealing Venkata S Koppuravuri (Tue Jul 27 2004 - 11:21:52 PDT)
- Re: AMBER: question on simulated annealing Carlos Simmerling (Tue Jul 27 2004 - 11:28:27 PDT)
- Re: AMBER: question on simulated annealing David A. Case (Tue Jul 27 2004 - 12:26:06 PDT)
AMBER: Question on Clustering Analysis Chen, Ya (Tue Jul 27 2004 - 11:26:30 PDT)
AMBER: using ptraj Carsten Detering (Tue Jul 27 2004 - 14:10:02 PDT)
- Re: AMBER: using ptraj Scott (Thu Jul 29 2004 - 14:15:17 PDT)
  - Re: AMBER: using ptraj Carsten Detering (Thu Jul 29 2004 - 15:11:11 PDT)
    - Re: AMBER: using ptraj Scott (Thu Jul 29 2004 - 15:48:19 PDT)
AMBER: about correlation calculation in ptraj jz7.duke.edu (Tue Jul 27 2004 - 14:20:53 PDT)
AMBER: animation? S. Frank Yan (Tue Jul 27 2004 - 23:29:51 PDT)
- Re: AMBER: animation? Guanglei Cui (Wed Jul 28 2004 - 06:20:12 PDT)
- Re: AMBER: animation? aldo jongejan (Wed Jul 28 2004 - 05:36:21 PDT)
AMBER: PB bomb in pb_saarc steven.j.enoch.gsk.com (Wed Jul 28 2004 - 01:26:38 PDT)
- RE: AMBER: PB bomb in pb_saarc S. Frank Yan (Tue May 18 2004 - 16:14:36 PDT)
  - Re: AMBER: PB bomb in pb_saarc Ray Luo (Tue May 18 2004 - 17:54:21 PDT)
- Re: AMBER: PB bomb in pb_saarc steven.j.enoch.gsk.com (Wed Jul 28 2004 - 01:49:20 PDT)
Re: AMBER: simulated annealing Carlos Simmerling (Wed Jul 28 2004 - 05:17:55 PDT)
- Re: AMBER: simulated annealing nurul bahiyah (Sun Aug 15 2004 - 05:42:53 PDT)
AMBER: simulated annealing.. Abd Ghani Bin Abd Aziz (Wed Jul 28 2004 - 06:45:55 PDT)
- Re: AMBER: simulated annealing.. Carlos Simmerling (Wed Jul 28 2004 - 07:06:01 PDT)
AMBER: tleap: automatically identify and connect disulfide bonds? Raik Grünberg (Wed Jul 28 2004 - 10:27:31 PDT)
- Re: AMBER: tleap: automatically identify and connect disulfide bonds? Scott Brozell (Wed Jul 28 2004 - 13:22:52 PDT)
  - AMBER: ptraj: load crd without hydrogen (i.e. missing parm file) Raik Grünberg (Thu Jul 29 2004 - 03:34:44 PDT)
    - Re: AMBER: ptraj: load crd without hydrogen (i.e. missing parm file) Raik Grünberg (Mon Aug 02 2004 - 02:30:56 PDT)
  - Re: AMBER: tleap: automatically identify and connect disulfide bonds? Austin B. Yongye (Thu Jul 29 2004 - 06:13:46 PDT)
    - Re: AMBER: tleap: automatically identify and connect disulfide bonds? Raik Grünberg (Mon Aug 02 2004 - 02:15:34 PDT)
AMBER: Re: AMBER: Temperature Regulation Dawsonzhu.aol.com (Wed Jul 28 2004 - 17:44:56 PDT)
AMBER: NSPSOL in parm file Sichun Yang (Wed Jul 28 2004 - 21:14:01 PDT)
- Re: AMBER: NSPSOL in parm file David A. Case (Thu Jul 29 2004 - 08:07:54 PDT)
AMBER: umbrella sampling tang kwa (Thu Jul 29 2004 - 10:25:00 PDT)
- Re: AMBER: umbrella sampling David A. Case (Thu Jul 29 2004 - 11:19:13 PDT)
AMBER: Re: constant pH calculation in Amber8 John Mongan (Thu Jul 29 2004 - 14:40:36 PDT)
AMBER: csong.mail.sdu.edu.cn (Fri Jul 30 2004 - 02:08:40 PDT)
- Re: AMBER: Guanglei Cui (Fri Jul 30 2004 - 06:39:51 PDT)
- Re: AMBER: David A. Case (Fri Jul 30 2004 - 08:06:56 PDT)
- RE: AMBER: Ross Walker (Fri Jul 30 2004 - 08:46:52 PDT)
AMBER: (no subject) HL Eastwood (Fri Jul 30 2004 - 08:47:18 PDT)
- RE: AMBER: (no subject) Ross Walker (Fri Jul 30 2004 - 09:21:33 PDT)
  - RE: AMBER: (no subject) HL Eastwood (Fri Jul 30 2004 - 11:12:34 PDT)
    - RE: AMBER: (no subject) Ross Walker (Fri Jul 30 2004 - 14:09:25 PDT)
    - AMBER: xleap problem fixed! HL Eastwood (Tue Aug 03 2004 - 10:20:21 PDT)
AMBER: WHAM program tang kwa (Fri Jul 30 2004 - 09:09:02 PDT)
- Re: AMBER: WHAM program David A. Case (Fri Jul 30 2004 - 10:16:02 PDT)
AMBER: AMBER 6 compilation problems! Grace Li (Fri Jul 30 2004 - 10:17:39 PDT)
- Re: AMBER: AMBER 6 compilation problems! Carlos Simmerling (Fri Jul 30 2004 - 10:26:59 PDT)
- RE: AMBER: AMBER 6 compilation problems! Ross Walker (Fri Jul 30 2004 - 10:30:54 PDT)
  - RE: AMBER: AMBER 6 compilation problems! Grace Li (Fri Jul 30 2004 - 11:52:15 PDT)
    - Re: AMBER: AMBER 6 compilation problems! Carlos Simmerling (Fri Jul 30 2004 - 12:03:31 PDT)
    - Re: AMBER: AMBER 6 compilation problems! Grace Li (Fri Jul 30 2004 - 13:42:03 PDT)
AMBER: Imaging problem Steve Seibold (Fri Jul 30 2004 - 12:05:12 PDT)
- Re: AMBER: Imaging problem Thomas E. Cheatham, III (Fri Jul 30 2004 - 13:41:45 PDT)
Re: AMBER: lib file David A. Case (Fri Jul 30 2004 - 13:48:50 PDT)
- Re: AMBER: lib file Ilyas Yildirim (Thu Feb 02 2006 - 12:18:28 PST)
  - Re: AMBER: lib file snoze pa (Fri Feb 03 2006 - 11:32:39 PST)
    - Re: AMBER: lib file Ilyas Yildirim (Fri Feb 03 2006 - 17:11:36 PST)
AMBER: FW: Imaging problem Steve Seibold (Mon Aug 02 2004 - 13:32:37 PDT)
AMBER: recompiling amber8 Carsten Detering (Mon Aug 02 2004 - 17:57:19 PDT)
- Re: AMBER: recompiling amber8 Robert Duke (Mon Aug 02 2004 - 18:12:52 PDT)
- Re: AMBER: recompiling amber8 David A. Case (Mon Aug 02 2004 - 18:18:25 PDT)
  - AMBER: Minimum imaging Grace Li (Mon Aug 02 2004 - 20:21:50 PDT)
    - Re: AMBER: Minimum imaging David A. Case (Tue Aug 03 2004 - 07:25:47 PDT)
    - Re: AMBER: Minimum imaging Joseph Nachman (Tue Aug 03 2004 - 22:01:54 PDT)
  - Re: AMBER: recompiling amber8 Carsten Detering (Tue Aug 03 2004 - 08:55:04 PDT)
    - Re: AMBER: recompiling amber8 Xiao Jian Tan (Tue Aug 03 2004 - 11:02:12 PDT)
    - Re: AMBER: recompiling amber8 Viktor Hornak (Tue Aug 03 2004 - 13:31:00 PDT)
- Re: AMBER: recompiling amber8 Robert Duke (Tue Aug 03 2004 - 09:30:41 PDT)
AMBER: charge not zero anshul.imtech.res.in (Tue Aug 03 2004 - 10:29:12 PDT)
- AMBER: cpinutil.pl error Rukman Hertadi (Tue Aug 03 2004 - 04:22:59 PDT)
  - Re: AMBER: cpinutil.pl error John Mongan (Tue Aug 03 2004 - 11:03:40 PDT)
- Re: AMBER: charge not zero FyD (Tue Aug 03 2004 - 07:46:54 PDT)
  - Re: AMBER: charge not zero anshul.imtech.res.in (Wed Aug 04 2004 - 20:48:11 PDT)
    - Re: AMBER: charge not zero FyD (Wed Aug 04 2004 - 11:23:13 PDT)
    - Re: AMBER: charge not zero FyD (Wed Aug 04 2004 - 12:57:51 PDT)
AMBER: mm_pbsa problem Carsten Detering (Tue Aug 03 2004 - 13:49:34 PDT)
- Re: AMBER: mm_pbsa problem Ray Luo (Tue Aug 03 2004 - 16:18:48 PDT)
AMBER: Problem: Installing Amber8 on PC with Windows XP Nhat-hang Duong (Tue Aug 03 2004 - 13:38:55 PDT)
- Re: AMBER: Problem: Installing Amber8 on PC with Windows XP fangyu liang (Tue Aug 03 2004 - 14:47:08 PDT)
- Re: AMBER: Problem: Installing Amber8 on PC with Windows XP David A. Case (Tue Aug 03 2004 - 15:28:25 PDT)
AMBER: Re: Phosphoserine residue in AMBER David A. Case (Tue Aug 03 2004 - 14:23:20 PDT)
AMBER: Bug and Patch in ANAL Andy Purkiss (Wed Aug 04 2004 - 08:38:30 PDT)
- Re: AMBER: Bug and Patch in ANAL David A. Case (Thu Aug 05 2004 - 08:44:38 PDT)
AMBER: RMSD result from GB model Yongzhi Chen (Wed Aug 04 2004 - 10:35:03 PDT)
- RE: AMBER: RMSD result from GB model Ross Walker (Wed Aug 04 2004 - 11:06:50 PDT)
- Re: AMBER: RMSD result from GB model Marcin Krol (Thu Aug 05 2004 - 01:32:36 PDT)
AMBER: atoms not in residue templates Yongzhi Chen (Wed Aug 04 2004 - 10:53:08 PDT)
- RE: AMBER: atoms not in residue templates Ross Walker (Wed Aug 04 2004 - 11:26:55 PDT)
AMBER: intense and spectrum Yaroslava Yingling (Wed Aug 04 2004 - 11:15:28 PDT)
- Re: AMBER: intense and spectrum David A. Case (Wed Aug 04 2004 - 16:41:13 PDT)
AMBER: RE: Hello Sir, Ross Walker (Wed Aug 04 2004 - 11:32:28 PDT)
AMBER: sander.QMMM: CHARGE keyword in divcon.in file M. L. Dodson (Wed Aug 04 2004 - 12:23:29 PDT)
- RE: AMBER: sander.QMMM: CHARGE keyword in divcon.in file Ross Walker (Wed Aug 04 2004 - 13:48:08 PDT)
  - Re: AMBER: sander.QMMM: CHARGE keyword in divcon.in file M. L. Dodson (Wed Aug 04 2004 - 17:08:07 PDT)
    - Re: AMBER: sander.QMMM: CHARGE keyword in divcon.in file M. L. Dodson (Thu Aug 05 2004 - 15:30:20 PDT)
AMBER: A question about pheTI in AMBER8 test. Chunhu Tan (Wed Aug 04 2004 - 14:35:48 PDT)
- Re: AMBER: A question about pheTI in AMBER8 test. David A. Case (Wed Aug 04 2004 - 16:38:52 PDT)
- Re: AMBER: A question about pheTI in AMBER8 test. Chunhu Tan (Thu Aug 05 2004 - 15:56:56 PDT)
  - Re: AMBER: A question about pheTI in AMBER8 test. David A. Case (Thu Aug 05 2004 - 17:39:06 PDT)
AMBER: Angle parameters in phosphate groups Seongeun Yang (Thu Aug 05 2004 - 05:17:44 PDT)
- Re: AMBER: Angle parameters in phosphate groups Seongeun Yang (Sat Aug 14 2004 - 02:58:07 PDT)
  - Re: AMBER: Angle parameters in phosphate groups Guanglei Cui (Sun Aug 15 2004 - 07:08:29 PDT)
  - Re: AMBER: Angle parameters in phosphate groups David A. Case (Sun Aug 15 2004 - 15:59:51 PDT)
- Re: AMBER: Angle parameters in phosphate groups Seongeun Yang (Sun Aug 15 2004 - 23:04:16 PDT)
AMBER: How to covalently bind a ligand to a residue? Ozlem Demir (Thu Aug 05 2004 - 08:54:19 PDT)
- Re: AMBER: How to covalently bind a ligand to a residue? Bimo Ario Tejo (Thu Aug 05 2004 - 22:06:02 PDT)
  - AMBER: AMBER7 plastocyanin tutorial problem. tarek mahfouz (Fri Aug 06 2004 - 10:40:33 PDT)
    - Re: AMBER: AMBER7 plastocyanin tutorial problem. Rhonda Torres (Fri Aug 06 2004 - 10:57:42 PDT)
    - Re: AMBER: AMBER7 plastocyanin tutorial problem. David A. Case (Fri Aug 06 2004 - 12:09:34 PDT)
- Re: AMBER: How to covalently bind a ligand to a residue? david.evans.ulsop.ac.uk (Fri Aug 06 2004 - 01:11:39 PDT)
- Re: AMBER: How to covalently bind a ligand to a residue? david.evans.ulsop.ac.uk (Fri Aug 06 2004 - 01:22:17 PDT)
AMBER: Using TIP4P water in free energy calculation Lijiang Yang (Thu Aug 05 2004 - 15:03:36 PDT)
- Re: AMBER: Using TIP4P water in free energy calculation David A. Case (Thu Aug 05 2004 - 15:35:22 PDT)
- Re: AMBER: Using TIP4P water in free energy calculation Lijiang Yang (Fri Aug 06 2004 - 11:42:06 PDT)
AMBER: sander error Rukman Hertadi (Thu Aug 05 2004 - 21:33:41 PDT)
- RE: AMBER: sander error Ross Walker (Thu Aug 05 2004 - 21:50:09 PDT)
- Re: AMBER: Using TIP4P water in free energy calculation Lijiang Yang (Thu Aug 05 2004 - 22:04:07 PDT)
  - Re: AMBER: Using TIP4P water in free energy calculation David A. Case (Fri Aug 06 2004 - 08:56:46 PDT)
- Re: AMBER: sander error Robert Duke (Tue Oct 18 2005 - 08:18:05 PDT)
  - Re: Re: AMBER: sander error Xiao He (Sat Oct 30 2004 - 01:19:15 PDT)
AMBER: another cpinutil.pl error Rukman Hertadi (Thu Aug 05 2004 - 22:35:09 PDT)
- Re: AMBER: another cpinutil.pl error David A. Case (Fri Aug 06 2004 - 08:58:46 PDT)
AMBER: RE: about PME in Amber6 Ross Walker (Fri Aug 06 2004 - 11:37:06 PDT)
AMBER: atomic positional fluctuation RAJA SWAMINATHAN (Sat Aug 07 2004 - 00:18:32 PDT)
AMBER: antechamber test mathew k varghese (Sun Aug 08 2004 - 05:31:22 PDT)
- Re: AMBER: antechamber test David A. Case (Sun Aug 08 2004 - 09:40:34 PDT)
AMBER: Problems with Carnal coordinate average HL Eastwood (Mon Aug 09 2004 - 04:35:37 PDT)
AMBER: error while loading shared libraries: libcxa.so.5 Madalin Giambasu (Mon Aug 09 2004 - 06:54:00 PDT)
- Re: AMBER: error while loading shared libraries: libcxa.so.5 Guanglei Cui (Mon Aug 09 2004 - 07:24:06 PDT)
- Re: AMBER: error while loading shared libraries: libcxa.so.5 Mark Williamson (Mon Aug 09 2004 - 07:42:16 PDT)
AMBER: trival question about format of pev file and covariance matrix jz7.duke.edu (Mon Aug 09 2004 - 08:52:03 PDT)
AMBER: Sander sachin patil (Mon Aug 09 2004 - 09:24:59 PDT)
- Re: AMBER: Sander David A. Case (Mon Aug 09 2004 - 09:57:40 PDT)
  - Re: AMBER: Sander sachin patil (Mon Aug 09 2004 - 11:26:20 PDT)
    - Re: AMBER: Sander David A. Case (Mon Aug 09 2004 - 15:21:12 PDT)
Re: AMBER: Problems with Carnal coordinate average Bill Ross (Mon Aug 09 2004 - 10:12:04 PDT)
Re: AMBER: Adding residues tarek mahfouz (Mon Aug 09 2004 - 11:51:26 PDT)
- Re: AMBER: Adding residues Rhonda Torres (Mon Aug 09 2004 - 12:00:50 PDT)
- Re: AMBER: Adding residues Bill Ross (Mon Aug 09 2004 - 12:23:08 PDT)
RE: AMBER: Adding residues Ross Walker (Mon Aug 09 2004 - 11:50:59 PDT)
AMBER: question about covariance matrix from ptraj jz7.duke.edu (Mon Aug 09 2004 - 12:25:10 PDT)
- Re: AMBER: question about covariance matrix from ptraj Elijah Gregory (Mon Aug 09 2004 - 13:00:06 PDT)
AMBER: resp charge calculation for Fe+3 heme Sebastian Fernandez Alberti (Mon Aug 09 2004 - 12:45:18 PDT)
- Re: AMBER: resp charge calculation for Fe+3 heme James W. Caldwell (Mon Aug 09 2004 - 13:18:46 PDT)
AMBER: rdparm problem Lijiang Yang (Mon Aug 09 2004 - 15:43:10 PDT)
AMBER: perturb a water to a dummy water with shake Dr. Turgut Bastug (Mon Aug 09 2004 - 17:24:25 PDT)
AMBER: how to correct the charge of oligosaccharides Wen-Chi Tseng (Mon Aug 09 2004 - 19:28:25 PDT)
- Re: AMBER: how to correct the charge of oligosaccharides David A. Case (Tue Aug 10 2004 - 07:31:40 PDT)
- Re: AMBER: how to correct the charge of oligosaccharides Karl N. Kirschner (Tue Aug 10 2004 - 07:53:29 PDT)
  - Re: AMBER: how to correct the charge of oligosaccharides Wen-Chi Tseng (Thu Aug 12 2004 - 02:16:38 PDT)
AMBER: pb_bomb in setgrd() steven.j.enoch.gsk.com (Tue Aug 10 2004 - 03:34:42 PDT)
- Re: AMBER: pb_bomb in setgrd() Ray Luo (Tue Aug 10 2004 - 09:29:13 PDT)
AMBER: Amber8 - LAM MPI Compilation problems Thomas Steinbrecher (Tue Aug 10 2004 - 09:16:38 PDT)
- RE: AMBER: Amber8 - LAM MPI Compilation problems Ross Walker (Tue Aug 10 2004 - 09:59:33 PDT)
AMBER: RESP partial charge calculation Sebastian Fernandez Alberti (Tue Aug 10 2004 - 09:21:06 PDT)
- Re: AMBER: RESP partial charge calculation James W. Caldwell (Tue Aug 10 2004 - 10:25:55 PDT)
- Re: AMBER: RESP partial charge calculation FyD (Tue Aug 10 2004 - 10:46:16 PDT)
AMBER: unknown residue: ABA Guowen Han (Tue Aug 10 2004 - 11:31:25 PDT)
- RE: AMBER: unknown residue: ABA Ross Walker (Tue Aug 10 2004 - 11:46:14 PDT)
  - RE: AMBER: unknown residue: ABA Lao_3 (Wed Aug 11 2004 - 08:45:44 PDT)
AMBER: Re: RED II and changepot FyD (Tue Aug 10 2004 - 11:35:05 PDT)
Re: AMBER: unknown residue: ABA Bill Ross (Tue Aug 10 2004 - 12:20:36 PDT)
- Re: AMBER: unknown residue: ABA Lao_3 (Tue Aug 10 2004 - 14:45:27 PDT)
AMBER: Membrane protein simulation Gabbar Daaku (Tue Aug 10 2004 - 13:37:22 PDT)
- Re: AMBER: Membrane protein simulation David A. Case (Tue Aug 10 2004 - 18:06:57 PDT)
AMBER: bugfix.all Lihua Wang (Tue Aug 10 2004 - 13:48:51 PDT)
- RE: AMBER: bugfix.all Ross Walker (Tue Aug 10 2004 - 17:54:25 PDT)
AMBER: Atomic charges in Lactose Johnson Agbo (Tue Aug 10 2004 - 17:23:53 PDT)
- Re: AMBER: Atomic charges in Lactose Karl N. Kirschner (Wed Aug 11 2004 - 05:47:46 PDT)
  - Re: AMBER: Atomic charges in Lactose Johnson Agbo (Fri Aug 20 2004 - 12:35:48 PDT)
AMBER: installing amber 8 on 64 bit amd opteron Dr Gavin Seddon (Tue Aug 10 2004 - 22:55:05 PDT)
- AMBER: different cooling schedules for simulated annealing Madalin Giambasu (Wed Aug 11 2004 - 04:51:09 PDT)
  - Re: AMBER: different cooling schedules for simulated annealing David A. Case (Wed Aug 11 2004 - 07:41:50 PDT)
    - Re: AMBER: different cooling schedules for simulated annealing Madalin Giambasu (Wed Aug 11 2004 - 09:23:08 PDT)
    - Re: AMBER: different cooling schedules for simulated annealing David A. Case (Thu Aug 12 2004 - 07:55:45 PDT)
AMBER: units Gustavo Pierdominici Sottile (Wed Aug 11 2004 - 08:03:38 PDT)
- Re: AMBER: units David A. Case (Thu Aug 12 2004 - 07:56:09 PDT)
AMBER: RESP charge derivation Vlad Cojocaru (Wed Aug 11 2004 - 09:10:19 PDT)
- AMBER: How to test the used parameters. tarek mahfouz (Wed Aug 11 2004 - 09:56:08 PDT)
  - RE: AMBER: How to test the used parameters. Ross Walker (Wed Aug 11 2004 - 10:33:56 PDT)
- Re: AMBER: RESP charge derivation FyD (Wed Aug 11 2004 - 09:55:57 PDT)
Re: AMBER: How to test the used parameters. Bill Ross (Wed Aug 11 2004 - 10:31:28 PDT)
AMBER: parameter Gustavo Pierdominici Sottile (Wed Aug 11 2004 - 13:45:02 PDT)
- Re: AMBER: parameter Guanglei Cui (Wed Aug 11 2004 - 14:07:18 PDT)
  - AMBER: Amber 8 Installation - C compiler? Nhat-hang Duong (Wed Aug 11 2004 - 14:51:51 PDT)
    - Re: AMBER: Amber 8 Installation - C compiler? fangyu liang (Wed Aug 11 2004 - 17:23:03 PDT)
    - RE: AMBER: Amber 8 Installation - C compiler? Ross Walker (Wed Aug 11 2004 - 17:37:45 PDT)
    - Re: AMBER: Amber 8 Installation - C compiler? Do Anh Tuan (Wed Aug 11 2004 - 22:28:37 PDT)
AMBER: Gaussian in RED Vlad Cojocaru (Thu Aug 12 2004 - 05:37:05 PDT)
- AMBER: Antechamber and dummy atoms Perdita Barran (Fri Aug 13 2004 - 06:03:44 PDT)
  - Re: AMBER: Antechamber and dummy atoms David A. Case (Fri Aug 13 2004 - 07:49:49 PDT)
  - Re: AMBER: Antechamber and dummy atoms Oliver Hucke (Fri Aug 13 2004 - 10:55:57 PDT)
- Re: AMBER: Gaussian in RED FyD (Fri Aug 13 2004 - 22:16:30 PDT)
AMBER: Angle parameters in phosphate groups Seongeun Yang (Thu Aug 12 2004 - 06:29:02 PDT)
- Re: AMBER: Angle parameters in phosphate groups Guanglei Cui (Thu Aug 12 2004 - 07:18:06 PDT)
AMBER: ptraj -- velocities set to zero? Gabbar Daaku (Thu Aug 12 2004 - 08:53:04 PDT)
AMBER: minimization output file format Marsita M (Thu Aug 12 2004 - 10:51:35 PDT)
- RE: AMBER: minimization output file format Ross Walker (Thu Aug 12 2004 - 12:43:02 PDT)
AMBER: bending Gustavo Pierdominici Sottile (Thu Aug 12 2004 - 12:28:42 PDT)
- Re: AMBER: bending David A. Case (Thu Aug 12 2004 - 12:48:30 PDT)
AMBER: bending Gustavo Pierdominici Sottile (Thu Aug 12 2004 - 13:47:16 PDT)
AMBER: question about compilation of AMBER8 on MANDRAKE9.2 Madalin Giambasu (Fri Aug 13 2004 - 03:02:57 PDT)
- RE: AMBER: question about compilation of AMBER8 on MANDRAKE9.2 Niko Jukarainen (Fri Aug 13 2004 - 03:09:10 PDT)
- Re: AMBER: question about compilation of AMBER8 on MANDRAKE9.2 Sarah Rankin (Mon Aug 16 2004 - 10:14:38 PDT)
  - RE: AMBER: question about compilation of AMBER8 on MANDRAKE9.2 Ross Walker (Mon Aug 16 2004 - 11:13:09 PDT)
    - Re: AMBER: question about compilation of AMBER8 on MANDRAKE9.2 Sarah Rankin (Tue Aug 17 2004 - 01:18:30 PDT)
AMBER: RED fails to read g94 output Vlad Cojocaru (Fri Aug 13 2004 - 03:35:20 PDT)
- Re: AMBER: RED fails to read g94 output FyD (Fri Aug 13 2004 - 22:34:21 PDT)
- Re: AMBER: RED fails to read g94 output FyD (Sat Aug 14 2004 - 01:26:33 PDT)
AMBER: Amber: xleap crash Helios (Fri Aug 13 2004 - 05:00:30 PDT)
- RE: AMBER: Amber: xleap crash Ross Walker (Fri Aug 13 2004 - 09:23:50 PDT)
AMBER: RED BUG!!!!...perhaps I fixed it Vlad Cojocaru (Fri Aug 13 2004 - 05:34:50 PDT)
AMBER: RED BUG!!! Vlad Cojocaru (Fri Aug 13 2004 - 05:56:25 PDT)
- AMBER: pmemd config.h request for athlon Madalin Giambasu (Fri Aug 13 2004 - 10:47:53 PDT)
  - RE: AMBER: pmemd config.h request for athlon Ross Walker (Fri Aug 13 2004 - 11:09:15 PDT)
  - Re: AMBER: pmemd config.h request for athlon Robert Duke (Fri Aug 13 2004 - 11:40:05 PDT)
  - Re: AMBER: pmemd config.h request for athlon Robert Duke (Fri Aug 13 2004 - 11:42:42 PDT)
AMBER: Temp control ding (Fri Aug 13 2004 - 11:46:20 PDT)
- Re: AMBER: Temp control David A. Case (Fri Aug 13 2004 - 13:13:20 PDT)
AMBER: pmemd problems Florian Barth (Fri Aug 13 2004 - 11:52:22 PDT)
- Re: AMBER: pmemd problems Robert Duke (Fri Aug 13 2004 - 12:14:39 PDT)
AMBER: Moil-view, prmtop, inpcrd question opitz.che.udel.edu (Fri Aug 13 2004 - 13:08:33 PDT)
- Re: AMBER: Moil-view, prmtop, inpcrd question Viktor Hornak (Fri Aug 13 2004 - 13:20:14 PDT)
- Re: AMBER: Moil-view, prmtop, inpcrd question opitz.che.udel.edu (Fri Aug 13 2004 - 13:28:26 PDT)
  - Re: AMBER: Moil-view, prmtop, inpcrd question Viktor Hornak (Fri Aug 13 2004 - 13:41:27 PDT)
- Re: AMBER: Moil-view, prmtop, inpcrd question opitz.che.udel.edu (Fri Aug 13 2004 - 14:08:27 PDT)
  - Re: AMBER: Moil-view, prmtop, inpcrd question Viktor Hornak (Fri Aug 13 2004 - 14:22:30 PDT)
  - Re: AMBER: Moil-view, prmtop, inpcrd question David A. Case (Fri Aug 13 2004 - 15:07:42 PDT)
- Re: AMBER: Moil-view, prmtop, inpcrd question Carlos Simmerling (Sat Aug 14 2004 - 05:13:23 PDT)
- Re: AMBER: Moil-view, prmtop, inpcrd question opitz.che.udel.edu (Mon Aug 16 2004 - 11:17:35 PDT)
  - Re: AMBER: Moil-view, prmtop, inpcrd question Viktor Hornak (Mon Aug 16 2004 - 11:45:08 PDT)
- Re: AMBER: Moil-view, prmtop, inpcrd question opitz.che.udel.edu (Mon Aug 16 2004 - 12:18:50 PDT)
  - Re: AMBER: Moil-view, prmtop, inpcrd question Viktor Hornak (Mon Aug 16 2004 - 12:26:27 PDT)
- Re: AMBER: Moil-view, prmtop, inpcrd question opitz.che.udel.edu (Mon Aug 16 2004 - 12:51:30 PDT)
AMBER: Bug: ptraj adds spurious box information Don Bashford (Fri Aug 13 2004 - 13:27:54 PDT)
- Re: AMBER: Bug: ptraj adds spurious box information David A. Case (Fri Aug 13 2004 - 15:13:33 PDT)
AMBER: simulated annealing Lee SL (Sat Aug 14 2004 - 02:51:14 PDT)
- Re: AMBER: simulated annealing Carlos Simmerling (Sat Aug 14 2004 - 05:20:12 PDT)
AMBER: residue database Lihua Wang (Sat Aug 14 2004 - 14:55:59 PDT)
AMBER: About the Amber constraint constant Yuhui Cheng (Sun Aug 15 2004 - 01:12:50 PDT)
- Re: AMBER: About the Amber constraint constant David A. Case (Sun Aug 15 2004 - 16:07:11 PDT)
  - Re: AMBER: About the Amber constraint constant Yuhui Cheng (Mon Aug 16 2004 - 23:34:24 PDT)
    - Re: AMBER: About the Amber constraint constant David A. Case (Tue Aug 17 2004 - 08:08:04 PDT)
AMBER: installing amber8 Dr Gavin Seddon (Mon Aug 16 2004 - 02:20:20 PDT)
AMBER: ANAL memory problem. Osman Gani (Mon Aug 16 2004 - 06:16:15 PDT)
- Re: AMBER: ANAL memory problem. David A. Case (Mon Aug 16 2004 - 18:34:22 PDT)
- RE: AMBER: ANAL memory problem. Osman Gani (Tue Aug 17 2004 - 03:38:42 PDT)
  - Re: AMBER: ANAL memory problem. David A. Case (Tue Aug 17 2004 - 09:33:03 PDT)
Re: AMBER: pmemd. - OOPS!!! Robert Duke (Mon Aug 16 2004 - 07:45:03 PDT)
AMBER: temperature control in coupled potential runs M. L. Dodson (Mon Aug 16 2004 - 12:05:49 PDT)
AMBER: Improving PMEMD performance on gigabit ethernet Linux clusters Robert Duke (Mon Aug 16 2004 - 14:17:45 PDT)
AMBER: Amber: Anal program format Helios (Mon Aug 16 2004 - 23:15:57 PDT)
- Re: AMBER: Amber: Anal program format David A. Case (Tue Aug 17 2004 - 09:14:31 PDT)
AMBER: peoblemwith RED II anshul.imtech.res.in (Tue Aug 17 2004 - 12:15:30 PDT)
- Re: AMBER: peoblemwith RED II FyD (Thu Aug 26 2004 - 08:44:16 PDT)
- Re: AMBER: peoblemwith RED II FyD (Fri Aug 27 2004 - 03:02:37 PDT)
- Re: AMBER: peoblemwith RED II FyD (Sat Aug 28 2004 - 02:52:20 PDT)
AMBER: Improving PMEMD Performance on gigabit ethernet - CORRECTION Robert Duke (Tue Aug 17 2004 - 05:42:33 PDT)
AMBER: leap: impose Guanglei Cui (Tue Aug 17 2004 - 11:44:04 PDT)
- Re: AMBER: leap: impose Guanglei Cui (Tue Aug 17 2004 - 12:23:27 PDT)
- Re: AMBER: leap: impose Guanglei Cui (Tue Aug 17 2004 - 13:15:27 PDT)
AMBER: RESP calculation with different multiplicities Sebastian Fernandez Alberti (Tue Aug 17 2004 - 13:44:54 PDT)
- Re: AMBER: RESP calculation with different multiplicities FyD (Thu Aug 26 2004 - 11:09:18 PDT)
AMBER: turning off HB interactions Taner E. Dirama (Tue Aug 17 2004 - 13:12:34 PDT)
AMBER: Dr. Herman Von Grafenstein Harsh Parikh (Tue Aug 17 2004 - 16:43:06 PDT)
AMBER: mm-gbsa Oliver Hucke (Tue Aug 17 2004 - 16:59:21 PDT)
AMBER: intrinsic born radius of Br Oliver Hucke (Tue Aug 17 2004 - 18:33:18 PDT)
AMBER: thermal ellipsoid-DNA RAJA SWAMINATHAN (Thu Aug 19 2004 - 02:29:34 PDT)
AMBER: angle bending Gustavo Pierdominici Sottile (Thu Aug 19 2004 - 05:31:21 PDT)
- RE: AMBER: angle bending Ross Walker (Thu Aug 19 2004 - 10:09:52 PDT)
AMBER: metal atoms in Xleap Atilio Anzellotti (Thu Aug 19 2004 - 08:05:23 PDT)
- Re: AMBER: metal atoms in Xleap Rhonda Torres (Thu Aug 19 2004 - 09:57:04 PDT)
  - Re: AMBER: metal atoms in Xleap Atilio Anzellotti (Fri Aug 20 2004 - 11:43:51 PDT)
    - Re: AMBER: metal atoms in Xleap Jiri Sponer (Fri Aug 20 2004 - 12:04:32 PDT)
    - Re: AMBER: metal atoms in Xleap Atilio Anzellotti (Fri Aug 20 2004 - 13:25:47 PDT)
- RE: AMBER: metal atoms in Xleap Ross Walker (Thu Aug 19 2004 - 09:59:28 PDT)
AMBER: how to read in CHARMM or AMBER binary trajectories Grace Li (Thu Aug 19 2004 - 11:19:48 PDT)
- RE: AMBER: how to read in CHARMM or AMBER binary trajectories Ross Walker (Thu Aug 19 2004 - 11:30:59 PDT)
  - AMBER: can MM-PBSA be applied to Charmm format trajectory file? jz7.duke.edu (Thu Aug 19 2004 - 11:55:06 PDT)
    - RE: AMBER: can MM-PBSA be applied to Charmm format trajectory file? Ross Walker (Thu Aug 19 2004 - 12:02:50 PDT)
AMBER: born radius and screening parameter for Br Oliver Hucke (Thu Aug 19 2004 - 15:58:44 PDT)
AMBER: questions on mm_pbsa cailliez (Fri Aug 20 2004 - 05:13:51 PDT)
- RE: AMBER: questions on mm_pbsa Fang, Jianwen (Fri Jun 11 2004 - 07:59:18 PDT)
- Re: AMBER: questions on mm_pbsa Thomas Steinbrecher (Sat Aug 21 2004 - 04:59:46 PDT)
AMBER: Updating Amber 7 Johnson Agbo (Fri Aug 20 2004 - 11:52:23 PDT)
- Re: AMBER: Updating Amber 7 David A. Case (Tue Aug 31 2004 - 21:00:46 PDT)
AMBER: mm_pbsa.pl in Amber8 Shan, Jufang (Fri Aug 20 2004 - 12:13:54 PDT)
- Re: AMBER: mm_pbsa.pl in Amber8 Sarah Rankin (Mon Aug 23 2004 - 03:00:21 PDT)
AMBER: Minimization error opitz.che.udel.edu (Fri Aug 20 2004 - 12:43:31 PDT)
- RE: AMBER: Minimization error Ross Walker (Fri Aug 20 2004 - 15:48:27 PDT)
- Re: AMBER: Minimization error opitz.che.udel.edu (Tue Aug 24 2004 - 14:09:15 PDT)
  - RE: AMBER: Minimization error Ross Walker (Wed Aug 25 2004 - 10:23:13 PDT)
- Re: AMBER: Minimization error opitz.che.udel.edu (Wed Aug 25 2004 - 13:55:24 PDT)
  - RE: AMBER: Minimization error Ross Walker (Wed Aug 25 2004 - 15:35:18 PDT)
- Re: AMBER: Minimization error opitz.che.udel.edu (Fri Aug 27 2004 - 13:56:46 PDT)
  - RE: AMBER: Minimization error Ross Walker (Sat Aug 28 2004 - 12:34:31 PDT)
AMBER: Increasing MAXATOM in antechamber Niko Jukarainen (Sat Aug 21 2004 - 02:45:08 PDT)
- Re: AMBER: Increasing MAXATOM in antechamber Guanglei Cui (Sat Aug 21 2004 - 08:07:10 PDT)
  - Re: AMBER: Increasing MAXATOM in antechamber Niko Jukarainen (Sat Aug 21 2004 - 09:13:56 PDT)
AMBER: Sander : Vrand flag sachin patil (Mon Aug 23 2004 - 10:59:30 PDT)
- RE: AMBER: Sander : Vrand flag Ross Walker (Mon Aug 23 2004 - 11:20:15 PDT)
  - RE: AMBER: Sander : Vrand flag sachin patil (Mon Aug 23 2004 - 12:07:32 PDT)
    - RE: AMBER: Sander : Vrand flag Ross Walker (Mon Aug 23 2004 - 12:29:06 PDT)
    - RE: AMBER: Sander : Vrand flag sachin patil (Mon Aug 23 2004 - 12:54:52 PDT)
    - RE: AMBER: Sander : Vrand flag Ross Walker (Mon Aug 23 2004 - 13:58:15 PDT)
- RE: AMBER: Sander : Vrand flag Furse, Kristina Elisabet (Tue Aug 24 2004 - 11:47:38 PDT)
  - RE: AMBER: Sander : Vrand flag sachin patil (Tue Aug 31 2004 - 07:15:37 PDT)
AMBER: error estimates in AMBER Grace Li (Mon Aug 23 2004 - 13:43:14 PDT)
AMBER: NTT=0 and TAUTP Gabbar Daaku (Mon Aug 23 2004 - 15:25:26 PDT)
- RE: AMBER: NTT=0 and TAUTP Ross Walker (Mon Aug 23 2004 - 16:03:30 PDT)
AMBER: how to deal with the initial structure? hj zou (Mon Aug 23 2004 - 18:48:22 PDT)
- RE: AMBER: how to deal with the initial structure? Ross Walker (Mon Aug 23 2004 - 19:19:23 PDT)
- Re: AMBER: how to deal with the initial structure? Furse, Kristina Elisabet (Tue Aug 24 2004 - 12:29:39 PDT)
  - AMBER: Trajectory file conversion between Amber & Charmm CK Sim (Tue Aug 24 2004 - 13:42:19 PDT)
    - RE: AMBER: Trajectory file conversion between Amber & Charmm Ross Walker (Tue Aug 24 2004 - 16:51:17 PDT)
    - AMBER: Amber 8 - Energy Minimization Parameters Nhat-hang Duong (Wed Aug 25 2004 - 08:34:28 PDT)
    - RE: AMBER: Amber 8 - Energy Minimization Parameters Ross Walker (Wed Aug 25 2004 - 09:02:31 PDT)
    - RE: AMBER: Amber 8 - Energy Minimization Parameters Nhat-hang Duong (Wed Aug 25 2004 - 13:26:56 PDT)
    - AMBER: Amber8 - Floating point Nhat-hang Duong (Thu Aug 26 2004 - 06:28:24 PDT)
    - Re: AMBER: Amber8 - Floating point Carlos Simmerling (Thu Aug 26 2004 - 07:00:52 PDT)
    - Re: AMBER: Amber8 - Floating point Nhat-hang Duong (Thu Aug 26 2004 - 07:15:00 PDT)
    - Re: AMBER: Amber8 - Floating point Carlos Simmerling (Thu Aug 26 2004 - 07:25:31 PDT)
    - Re: AMBER: Amber8 - Floating point Michael Crowley (Thu Aug 26 2004 - 08:56:06 PDT)
    - Re: AMBER: Amber8 - Floating point Nhat-hang Duong (Thu Aug 26 2004 - 09:51:28 PDT)
    - RE: AMBER: Trajectory file conversion between Amber & Charmm CK Sim (Mon Sep 20 2004 - 10:45:09 PDT)
    - Re: AMBER: Trajectory file conversion between Amber & Charmm Carlos Simmerling (Mon Sep 20 2004 - 10:59:41 PDT)
    - RE: AMBER: Trajectory file conversion between Amber & Charmm Thomas E. Cheatham, III (Mon Sep 20 2004 - 11:18:46 PDT)
AMBER: problem loading pdb in leap. anshul.imtech.res.in (Tue Aug 24 2004 - 07:52:05 PDT)
- RE: AMBER: problem loading pdb in leap. Ross Walker (Mon Aug 23 2004 - 21:53:49 PDT)
  - RE: AMBER: problem loading pdb in leap. anshul.imtech.res.in (Tue Aug 24 2004 - 09:34:58 PDT)
    - RE: AMBER: problem loading pdb in leap. Ross Walker (Tue Aug 24 2004 - 10:35:08 PDT)
- RE: AMBER: problem loading pdb in leap. Andrew Box (Mon Aug 23 2004 - 23:30:46 PDT)
  - AMBER: freezing atoms in impliciti solvent Sergio E. Wong (Tue Aug 24 2004 - 10:27:32 PDT)
    - Re: AMBER: freezing atoms in impliciti solvent Carlos Simmerling (Tue Aug 24 2004 - 10:54:58 PDT)
AMBER: mutation of Tyr to Leu with TI Oliver Hucke (Tue Aug 24 2004 - 16:56:47 PDT)
- Re: AMBER: mutation of Tyr to Leu with TI Thomas Steinbrecher (Wed Aug 25 2004 - 00:17:34 PDT)
AMBER: density calculation in AMBER output Grace Li (Wed Aug 25 2004 - 06:51:47 PDT)
- RE: AMBER: density calculation in AMBER output Ross Walker (Wed Aug 25 2004 - 10:11:02 PDT)
AMBER: restart a MD after replacing molecules cailliez (Wed Aug 25 2004 - 07:03:41 PDT)
- RE: AMBER: restart a MD after replacing molecules Ross Walker (Wed Aug 25 2004 - 10:29:13 PDT)
  - Re: AMBER: restart a MD after replacing molecules cailliez (Thu Aug 26 2004 - 01:38:55 PDT)
AMBER: Lennard-Jones particle simulation Guanglei Cui (Wed Aug 25 2004 - 12:38:57 PDT)
- Re: AMBER: Lennard-Jones particle simulation Thomas E. Cheatham, III (Wed Aug 25 2004 - 13:05:58 PDT)
  - Re: AMBER: Lennard-Jones particle simulation Carlos Simmerling (Wed Aug 25 2004 - 13:06:47 PDT)
  - Re: AMBER: Lennard-Jones particle simulation Guanglei Cui (Wed Aug 25 2004 - 14:11:37 PDT)
- Re: AMBER: Lennard-Jones particle simulation darden (Wed Aug 25 2004 - 13:57:15 PDT)
- Re: AMBER: Lennard-Jones particle simulation Piotr Cieplak (Wed Aug 25 2004 - 15:31:37 PDT)
AMBER: About tree structure of TRP residue Yuhui Cheng (Wed Aug 25 2004 - 16:46:36 PDT)
- Re: AMBER: About tree structure of TRP residue Lihua Wang (Wed Aug 25 2004 - 17:16:46 PDT)
  - Re: AMBER: About tree structure of TRP residue Yuhui Cheng (Wed Aug 25 2004 - 17:35:13 PDT)
  - AMBER: One more question about the tree structure of looping residues Yuhui Cheng (Wed Aug 25 2004 - 20:11:36 PDT)
  - Re: AMBER: About tree structure of TRP residue David A. Case (Wed Sep 01 2004 - 10:48:34 PDT)
- Re: AMBER: About tree structure of TRP residue Bill Ross (Wed Aug 25 2004 - 17:56:13 PDT)
AMBER: ptraj and hbond Nelson Fonseca (Thu Aug 26 2004 - 02:50:39 PDT)
AMBER: problem loading molecule in leap anshul.imtech.res.in (Thu Aug 26 2004 - 13:38:44 PDT)
AMBER: question on minimization Venkata S Koppuravuri (Thu Aug 26 2004 - 08:41:48 PDT)
AMBER: RESP charges in Fe+3 heme system Sebastian Fernandez Alberti (Thu Aug 26 2004 - 10:43:08 PDT)
- Re: AMBER: RESP charges in Fe+3 heme system FyD (Thu Aug 26 2004 - 11:33:09 PDT)
Re: AMBER: One more question about the tree structure of looping residues Bill Ross (Thu Aug 26 2004 - 11:31:23 PDT)
AMBER: charge perturbation - xleap question Oliver Hucke (Thu Aug 26 2004 - 11:57:43 PDT)
- Re: AMBER: charge perturbation - xleap question Thomas Steinbrecher (Fri Aug 27 2004 - 00:19:25 PDT)
AMBER: Biotin/streptavidin tutorial. Osman Gani (Fri Aug 27 2004 - 02:57:51 PDT)
AMBER: error for performing MD tang kwa (Fri Aug 27 2004 - 04:51:00 PDT)
AMBER: snapshots of MD trajectory Xin Hu (Fri Aug 27 2004 - 08:23:08 PDT)
- Re: AMBER: snapshots of MD trajectory Guanglei Cui (Fri Aug 27 2004 - 08:27:20 PDT)
- Re: AMBER: snapshots of MD trajectory Carlos Simmerling (Fri Aug 27 2004 - 08:36:38 PDT)
- Re: AMBER: snapshots of MD trajectory Peter Gannett (Fri Aug 27 2004 - 08:43:33 PDT)
- Re: AMBER: snapshots of MD trajectory Xin Hu (Fri Aug 27 2004 - 09:36:06 PDT)
  - Re: AMBER: snapshots of MD trajectory Guanglei Cui (Fri Aug 27 2004 - 12:38:44 PDT)
    - Re: AMBER: snapshots of MD trajectory Carlos Simmerling (Fri Aug 27 2004 - 12:44:36 PDT)
- Re: AMBER: snapshots of MD trajectory Xin Hu (Fri Aug 27 2004 - 14:15:27 PDT)
  - AMBER: Neutral C and N termini. tarek mahfouz (Fri Aug 27 2004 - 15:58:18 PDT)
    - AMBER: Neutral C and N termini. tarek mahfouz (Sun Aug 29 2004 - 16:37:19 PDT)
    - Re: AMBER: Neutral C and N termini. M. L. Dodson (Sun Aug 29 2004 - 19:14:10 PDT)
AMBER: error of performing simulation tang kwa (Fri Aug 27 2004 - 10:07:21 PDT)
Re: AMBER: Biotin/streptavidin tutorial. Bill Ross (Fri Aug 27 2004 - 10:57:47 PDT)
AMBER: nonpalar energy contribution-DMSO Dalmaris, John (Sat Aug 28 2004 - 07:11:43 PDT)
AMBER: MD & net charge bybaker.itsa.ucsf.edu (Sat Aug 28 2004 - 23:19:18 PDT)
- Re: AMBER: MD & net charge Carlos Simmerling (Mon Aug 30 2004 - 06:23:20 PDT)
  - Re: AMBER: MD & net charge Chris Harrison (Mon Aug 30 2004 - 06:28:46 PDT)
    - Re: AMBER: MD & net charge Carlos Simmerling (Mon Aug 30 2004 - 06:41:21 PDT)
- Re: AMBER: MD & net charge bybaker.itsa.ucsf.edu (Mon Aug 30 2004 - 13:48:00 PDT)
  - Re: AMBER: MD & net charge Carlos Simmerling (Mon Aug 30 2004 - 13:57:50 PDT)
- Re: AMBER: MD & net charge bybaker.itsa.ucsf.edu (Mon Aug 30 2004 - 15:02:53 PDT)
AMBER: temperature scaling with ntt=3(Langevin thermostat) Madalin Giambasu (Mon Aug 30 2004 - 01:01:05 PDT)
- Re: AMBER: temperature scaling with ntt=3(Langevin thermostat) Carlos Simmerling (Mon Aug 30 2004 - 06:21:36 PDT)
  - Re: AMBER: temperature scaling with ntt=3(Langevin thermostat) Madalin Giambasu (Mon Aug 30 2004 - 06:51:35 PDT)
    - Re: AMBER: temperature scaling with ntt=3(Langevin thermostat) Carlos Simmerling (Mon Aug 30 2004 - 06:51:28 PDT)
    - Re: AMBER: temperature scaling with ntt=3(Langevin thermostat) Madalin Giambasu (Mon Aug 30 2004 - 07:47:55 PDT)
- Re: AMBER: temperature scaling with ntt=3(Langevin thermostat) David A. Case (Tue Aug 31 2004 - 21:43:01 PDT)
AMBER: Amber 03 Forcefield discrepancy MD Tyka, Biochemistry (Mon Aug 30 2004 - 07:36:18 PDT)
- Re: AMBER: Amber 03 Forcefield discrepancy Yong Duan (Mon Aug 30 2004 - 11:16:21 PDT)
AMBER: Differences in RESP charges for G in RG and DG residues Vlad Cojocaru (Mon Aug 30 2004 - 08:59:35 PDT)
- Re: AMBER: Differences in RESP charges for G in RG and DG residues FyD (Sat Sep 04 2004 - 03:12:33 PDT)
AMBER: jwcraft.uh.edu (Mon Aug 30 2004 - 12:54:46 PDT)
- Re: AMBER: David A. Case (Tue Aug 31 2004 - 20:56:27 PDT)
AMBER: Glycam-04 Parameters in Amber 7 Johnson Agbo (Mon Aug 30 2004 - 18:12:17 PDT)
AMBER: parm94 bybaker.itsa.ucsf.edu (Mon Aug 30 2004 - 23:50:09 PDT)
- Re: AMBER: parm94 Asim Okur (Tue Aug 31 2004 - 06:12:58 PDT)
- Re: AMBER: parm94 bybaker.itsa.ucsf.edu (Tue Aug 31 2004 - 09:21:00 PDT)
- Re: AMBER: parm94 bybaker.itsa.ucsf.edu (Tue Aug 31 2004 - 15:15:04 PDT)
  - Re: AMBER: parm94 Lihua Wang (Tue Aug 31 2004 - 15:22:29 PDT)
- Re: AMBER: parm94 bybaker.itsa.ucsf.edu (Tue Aug 31 2004 - 18:57:39 PDT)
AMBER: Using AMBER to simulate carbon nanotubes? Chen Song (Tue Aug 31 2004 - 03:54:26 PDT)
- Re: AMBER: Using AMBER to simulate carbon nanotubes? darden (Tue Aug 31 2004 - 08:43:56 PDT)
AMBER: Increase lastrst in the &cntrl namelist Sichun Yang (Tue Aug 31 2004 - 09:06:46 PDT)
- Re: AMBER: Increase lastrst in the &cntrl namelist David A. Case (Tue Aug 31 2004 - 21:53:20 PDT)
  - Re: AMBER: Increase lastrst in the &cntrl namelist Sichun Yang (Tue Aug 31 2004 - 23:29:27 PDT)
- RE: AMBER: Increase lastrst in the &cntrl namelist Osman Gani (Tue Aug 31 2004 - 23:51:32 PDT)
  - RE: AMBER: Increase lastrst in the &cntrl namelist Sichun Yang (Wed Sep 01 2004 - 10:19:18 PDT)
    - Re: AMBER: Increase lastrst in the &cntrl namelist Carlos Simmerling (Wed Sep 01 2004 - 10:54:37 PDT)
    - Re: AMBER: Increase lastrst in the &cntrl namelist David A. Case (Wed Sep 01 2004 - 11:22:07 PDT)
AMBER: PBC in sander Mingfeng Yang (Tue Aug 31 2004 - 13:27:26 PDT)
- AMBER: Pulling versus Distance Restraints Nhat-hang Duong (Tue Aug 31 2004 - 14:16:15 PDT)
  - Re: AMBER: Pulling versus Distance Restraints Furse, Kristina Elisabet (Wed Sep 01 2004 - 10:08:49 PDT)
- Re: AMBER: PBC in sander David A. Case (Tue Aug 31 2004 - 20:57:49 PDT)
AMBER: question on mm-pbsa cailliez (Wed Sep 01 2004 - 02:48:54 PDT)
- Re: AMBER: question on mm-pbsa Holger Gohlke (Wed Sep 01 2004 - 11:55:50 PDT)
AMBER: [0] MPI Abort by user Aborting program ! tang kwa (Wed Sep 01 2004 - 05:07:51 PDT)
- Re: AMBER: [0] MPI Abort by user Aborting program ! Melinda Layten (Wed Sep 01 2004 - 08:04:15 PDT)
AMBER: Setting up thermodynamic integration david.evans.ulsop.ac.uk (Wed Sep 01 2004 - 07:31:10 PDT)
- Re: AMBER: Setting up thermodynamic integration david.evans.ulsop.ac.uk (Wed Sep 01 2004 - 10:24:40 PDT)
AMBER: Re. HSG Convention jwcraft.uh.edu (Wed Sep 01 2004 - 08:48:41 PDT)
- Re: AMBER: Re. HSG Convention David A. Case (Wed Sep 01 2004 - 09:01:44 PDT)
AMBER: parameters-DGnp John (Wed Sep 01 2004 - 17:25:03 PDT)
AMBER: error in installing amber8 anshul.imtech.res.in (Thu Sep 02 2004 - 15:37:12 PDT)
- Re: AMBER: error in installing amber8 David A. Case (Thu Sep 02 2004 - 08:31:02 PDT)
- Re: AMBER: error in installing amber8 Scott Brozell (Thu Sep 02 2004 - 08:56:50 PDT)
  - Re: AMBER: error in installing amber8 anshul.imtech.res.in (Wed Sep 08 2004 - 14:39:27 PDT)
    - Re: AMBER: error in installing amber8 David A. Case (Wed Sep 08 2004 - 09:23:04 PDT)
- Re: AMBER: error in installing amber8 Bill Ross (Wed Sep 08 2004 - 07:49:11 PDT)
AMBER: loading frcmod.mod_phipsi.1 bybaker.itsa.ucsf.edu (Thu Sep 02 2004 - 14:12:04 PDT)
AMBER: Water Box & MD bybaker.itsa.ucsf.edu (Thu Sep 02 2004 - 14:48:00 PDT)
Re: AMBER: loading frcmod.mod_phipsi.1 Bill Ross (Thu Sep 02 2004 - 15:07:44 PDT)
- Re: AMBER: loading frcmod.mod_phipsi.1 bybaker.itsa.ucsf.edu (Thu Sep 02 2004 - 15:18:07 PDT)
AMBER: Amber7 tleap problem Ed Pate (Sat Sep 04 2004 - 12:03:47 PDT)
- Re: AMBER: Amber7 tleap problem David A. Case (Sat Sep 04 2004 - 13:11:39 PDT)
AMBER: general questions Marsita M (Mon Sep 06 2004 - 08:58:34 PDT)
- Re: AMBER: general questions Stefano.Pieraccini.unimi.it (Tue Sep 07 2004 - 04:11:01 PDT)
AMBER: Electrostatic potential from the trajectory ! Pradipta Bandyopadhyay (Tue Sep 07 2004 - 04:40:09 PDT)
- RE: AMBER: Electrostatic potential from the trajectory ! Ross Walker (Wed Sep 08 2004 - 04:32:58 PDT)
AMBER: is it a bug in mmpbsa Shan, Jufang (Tue Sep 07 2004 - 07:29:27 PDT)
AMBER: xLeap menus not working properly Hannes Barsch (Wed Sep 08 2004 - 01:14:38 PDT)
- Re: AMBER: xLeap menus not working properly Heike.Meiselbach.chemie.uni-erlangen.de (Wed Sep 08 2004 - 02:19:13 PDT)
AMBER: Amber: BOMB Helios (Wed Sep 08 2004 - 05:18:11 PDT)
- RE: AMBER: Amber: BOMB Ross Walker (Wed Sep 08 2004 - 07:42:53 PDT)
- Re: AMBER: Amber: BOMB David A. Case (Wed Sep 08 2004 - 07:55:04 PDT)
AMBER: Spike in energy and RMS Balvinder Singh (Wed Sep 08 2004 - 15:49:04 PDT)
- RE: AMBER: Spike in energy and RMS Ross Walker (Wed Sep 08 2004 - 07:37:26 PDT)
- Re: AMBER: Spike in energy and RMS Andreas Svrcek-Seiler (Thu Sep 09 2004 - 02:37:57 PDT)
AMBER: REST Yanze Zhang (Wed Sep 08 2004 - 13:09:31 PDT)
- Re: AMBER: REST Melinda Layten (Wed Sep 08 2004 - 13:51:30 PDT)
AMBER: Nucgen and PNA? opitz.che.udel.edu (Wed Sep 08 2004 - 14:14:42 PDT)
- Re: AMBER: Nucgen and PNA? Rhonda Torres (Wed Sep 08 2004 - 14:22:30 PDT)
- Re: AMBER: Nucgen and PNA? opitz.che.udel.edu (Thu Sep 09 2004 - 06:36:25 PDT)
AMBER: Antechamber Failure Johnson Agbo (Wed Sep 08 2004 - 14:56:58 PDT)
- Re: AMBER: Antechamber Failure David A. Case (Wed Sep 08 2004 - 15:48:41 PDT)
AMBER: Amber:how to increase the memory allocation? Helios (Wed Sep 08 2004 - 20:35:14 PDT)
- Re: AMBER: Amber:how to increase the memory allocation? David A. Case (Thu Sep 09 2004 - 08:38:12 PDT)
AMBER: REM make test Sergio E. Wong (Thu Sep 09 2004 - 15:50:50 PDT)
- Re: AMBER: REM make test David A. Case (Thu Sep 09 2004 - 16:40:13 PDT)
  - Re: AMBER: REM make test Sergio E. Wong (Thu Sep 09 2004 - 17:55:49 PDT)
  - AMBER: GB and langevin dynamics Sergio E. Wong (Thu Sep 09 2004 - 22:41:18 PDT)
    - Re: AMBER: GB and langevin dynamics David A. Case (Mon Sep 13 2004 - 12:59:31 PDT)
    - Re: AMBER: GB and langevin dynamics Sergio E. Wong (Wed Sep 15 2004 - 12:38:43 PDT)
    - Re: AMBER: GB and langevin dynamics David A. Case (Wed Sep 15 2004 - 15:01:31 PDT)
    - AMBER: amber8 performance problem on Itanium II's Sergio E. Wong (Thu Sep 16 2004 - 21:18:47 PDT)
    - Re: AMBER: amber8 performance problem on Itanium II's Andreas Svrcek-Seiler (Fri Sep 17 2004 - 01:52:53 PDT)
    - Re: AMBER: amber8 performance problem on Itanium II's Sergio E. Wong (Fri Sep 17 2004 - 11:23:18 PDT)
- Re: AMBER: REM make test Carlos Simmerling (Fri Sep 10 2004 - 06:35:18 PDT)
AMBER: MAC Based Beowulf Cluster Peter Gannett (Thu Sep 09 2004 - 16:17:14 PDT)
AMBER: How many ions? Volodymyr Zloy (Fri Sep 10 2004 - 04:23:38 PDT)
AMBER: make install error Abd Ghani Bin Abd Aziz (Fri Sep 10 2004 - 04:21:15 PDT)
- RE: AMBER: make install error Ross Walker (Fri Sep 10 2004 - 15:41:02 PDT)
AMBER: Monte Carlo simulation tang kwa (Fri Sep 10 2004 - 05:15:35 PDT)
- Re: AMBER: Monte Carlo simulation David A. Case (Fri Sep 10 2004 - 14:56:20 PDT)
AMBER: MPICH problem Abd Ghani Bin Abd Aziz (Fri Sep 10 2004 - 05:33:45 PDT)
- RE: AMBER: MPICH problem Ross Walker (Sun Sep 12 2004 - 03:12:05 PDT)
AMBER: Test Calculation of atomic charges (RESP) for RNA bases Vlad Cojocaru (Fri Sep 10 2004 - 06:41:26 PDT)
- Re: AMBER: Test Calculation of atomic charges (RESP) for RNA bases FyD (Fri Sep 10 2004 - 17:35:09 PDT)
AMBER: re:your message to amber... hj zou (Fri Sep 10 2004 - 06:46:58 PDT)
AMBER: Amber7 - mm_pbsa/molsurf Nadine Homeyer (Fri Sep 10 2004 - 05:25:20 PDT)
- Re: AMBER: Amber7 - mm_pbsa/molsurf Oliver Hucke (Fri Sep 10 2004 - 11:03:57 PDT)
Re: AMBER: Test Calculation of atomic charges (RESP) for RNA bases Piotr Cieplak (Fri Sep 10 2004 - 10:28:25 PDT)
- Re: AMBER: Test Calculation of atomic charges (RESP) for RNA bases Vlad Cojocaru (Mon Sep 13 2004 - 03:10:48 PDT)
  - Re: AMBER: Test Calculation of atomic charges (RESP) for RNA bases FyD (Mon Sep 13 2004 - 14:59:11 PDT)
AMBER: An question about PTRAJ b86203054.ntu.edu.tw (Fri Sep 10 2004 - 18:29:17 PDT)
- Re: AMBER: An question about PTRAJ Stef (Sat Sep 11 2004 - 01:01:52 PDT)
  - Re: AMBER: An question about PTRAJ b86203054.ntu.edu.tw (Mon Sep 13 2004 - 10:37:00 PDT)
- Re: AMBER: An question about PTRAJ Thomas E. Cheatham, III (Sat Sep 11 2004 - 12:06:05 PDT)
  - Re: AMBER: An question about PTRAJ b86203054.ntu.edu.tw (Mon Sep 13 2004 - 10:35:51 PDT)
AMBER: make install error Abd Ghani Bin Abd Aziz (Sat Sep 11 2004 - 02:56:40 PDT)
- RE: AMBER: make install error Ross Walker (Sun Sep 12 2004 - 03:15:03 PDT)
- RE: AMBER: make install error Abd Ghani Bin Abd Aziz (Sun Sep 12 2004 - 04:25:19 PDT)
  - Re: AMBER: make install error Robert Duke (Sun Sep 12 2004 - 04:52:48 PDT)
- Re: AMBER: make install error Abd Ghani Bin Abd Aziz (Sun Sep 12 2004 - 05:40:42 PDT)
  - Re: AMBER: make install error Robert Duke (Sun Sep 12 2004 - 05:46:30 PDT)
- Re: AMBER: make install error Abd Ghani Bin Abd Aziz (Sun Sep 12 2004 - 05:53:52 PDT)
- Re: AMBER: make install error Abd Ghani Bin Abd Aziz (Tue Sep 14 2004 - 08:23:37 PDT)
AMBER: mmpbsa: can not generate coordinates/snapshots Magne Olufsen (Mon Sep 13 2004 - 03:37:54 PDT)
AMBER: AMBER7 : update gaff and parm99 force field Guillaume Bollot (Mon Sep 13 2004 - 06:35:01 PDT)
- Re: AMBER: AMBER7 : update gaff and parm99 force field David A. Case (Mon Sep 13 2004 - 12:59:12 PDT)
AMBER: Compilation Problem in Amber 7 Stephen P. Molnar, Ph.D. (Mon Sep 13 2004 - 08:54:27 PDT)
- RE: AMBER: Compilation Problem in Amber 7 Ross Walker (Mon Sep 13 2004 - 21:05:35 PDT)
AMBER: AMBER7 : Hybrid macromolecule Guillaume Bollot (Mon Sep 13 2004 - 08:54:28 PDT)
- Re: AMBER: AMBER7 : Hybrid macromolecule david.evans.ulsop.ac.uk (Mon Sep 13 2004 - 09:30:43 PDT)
AMBER: target rmsd William Andrew McLaughlin (Mon Sep 13 2004 - 13:35:51 PDT)
- Re: AMBER: target rmsd Carlos Simmerling (Mon Sep 13 2004 - 13:49:30 PDT)
  - Re: AMBER: target rmsd Viktor Hornak (Mon Sep 13 2004 - 13:57:07 PDT)
    - Re: AMBER: target rmsd William Andrew McLaughlin (Mon Sep 13 2004 - 14:40:24 PDT)
    - Re: AMBER: target rmsd Viktor Hornak (Mon Sep 13 2004 - 15:15:56 PDT)
AMBER: bond between two polypeptides Jagdish Rai (Tue Sep 14 2004 - 01:19:48 PDT)
- Re: AMBER: bond between two polypeptides David A. Case (Tue Sep 14 2004 - 09:20:23 PDT)
AMBER: mm_pbsa for Delphi Helios Chen (Tue Sep 14 2004 - 02:28:28 PDT)
AMBER: Re: to Francois Vlad Cojocaru (Tue Sep 14 2004 - 04:35:13 PDT)
- Re: AMBER: R.E.D. II to Vlad FyD (Wed Sep 15 2004 - 09:25:44 PDT)
AMBER: MM binding energy with ANAL Ben Cossins (Tue Sep 14 2004 - 05:56:37 PDT)
- Re: AMBER: MM binding energy with ANAL David A. Case (Tue Sep 14 2004 - 15:32:48 PDT)
AMBER: amber 8 Abd Ghani Bin Abd Aziz (Tue Sep 14 2004 - 06:17:56 PDT)
- RE: AMBER: amber 8 Ross Walker (Tue Sep 14 2004 - 08:09:31 PDT)
- RE: AMBER: amber 8 Abd Ghani Bin Abd Aziz (Tue Sep 14 2004 - 08:28:47 PDT)
  - RE: AMBER: amber 8 Ross Walker (Tue Sep 14 2004 - 08:40:26 PDT)
AMBER: want to generate ammonium ion..where to start? Grace Li (Tue Sep 14 2004 - 09:48:20 PDT)
AMBER: TI with sander Oliver Hucke (Tue Sep 14 2004 - 11:58:01 PDT)
- Re: AMBER: TI with sander David A. Case (Tue Sep 14 2004 - 12:20:49 PDT)
AMBER: Restraints in sander.QMMM Joseph Fernandez (Tue Sep 14 2004 - 13:54:07 PDT)
- Re: AMBER: Restraints in sander.QMMM David A. Case (Tue Sep 14 2004 - 15:21:07 PDT)
AMBER: restrain on the distance between two molecules. Qiang Lu (Tue Sep 14 2004 - 14:18:00 PDT)
- Re: AMBER: restrain on the distance between two molecules. Nhat-hang Duong (Tue Sep 14 2004 - 14:34:49 PDT)
AMBER: nmode Carsten Detering (Tue Sep 14 2004 - 15:29:49 PDT)
- Re: AMBER: nmode David A. Case (Tue Sep 14 2004 - 16:13:14 PDT)
  - AMBER: trajectory Wen Li (Thu Sep 23 2004 - 06:35:21 PDT)
AMBER: Intel Fortran Compiler Problem Stephen P. Molnar, Ph.D. (Wed Sep 15 2004 - 07:52:55 PDT)
- Re: AMBER: Intel Fortran Compiler Problem Viktor Hornak (Wed Sep 15 2004 - 07:33:44 PDT)
  - Re: AMBER: Intel Fortran Compiler Problem Stephen P. Molnar, Ph.D. (Wed Sep 15 2004 - 08:13:49 PDT)
- Re: AMBER: Intel Fortran Compiler Problem Robert Duke (Wed Sep 15 2004 - 07:52:50 PDT)
  - Re: AMBER: Intel Fortran Compiler Problem Viktor Hornak (Wed Sep 15 2004 - 07:52:04 PDT)
  - Re: AMBER: Intel Fortran Compiler Problem Stephen P. Molnar, Ph.D. (Wed Sep 15 2004 - 08:38:11 PDT)
    - Re: AMBER: Intel Fortran Compiler Problem Viktor Hornak (Wed Sep 15 2004 - 08:18:01 PDT)
- Re: AMBER: Intel Fortran Compiler Problem Robert Duke (Wed Sep 15 2004 - 08:30:11 PDT)
  - Re: AMBER: Intel Fortran Compiler Problem Stephen P. Molnar, Ph.D. (Wed Sep 15 2004 - 09:23:30 PDT)
    - Re: AMBER: Intel Fortran Compiler Problem David A. Case (Wed Sep 15 2004 - 09:08:04 PDT)
- Re: AMBER: Intel Fortran Compiler Problem Robert Duke (Wed Sep 15 2004 - 08:38:03 PDT)
- Re: AMBER: Intel Fortran Compiler Problem Robert Duke (Wed Sep 15 2004 - 09:12:46 PDT)
- RE: AMBER: Intel Fortran Compiler Problem Ross Walker (Thu Sep 16 2004 - 21:00:30 PDT)
AMBER: F90 compiler for linux ppc64 Guanglei Cui (Wed Sep 15 2004 - 07:42:12 PDT)
- Re: AMBER: F90 compiler for linux ppc64 Carlos P. Sosa (Wed Sep 15 2004 - 08:10:32 PDT)
  - Re: AMBER: F90 compiler for linux ppc64 Guanglei Cui (Wed Sep 15 2004 - 08:28:17 PDT)
AMBER: principal axis Alberto Perez (Wed Sep 15 2004 - 06:36:37 PDT)
- Re: AMBER: principal axis Thomas E. Cheatham, III (Wed Sep 15 2004 - 08:41:37 PDT)
AMBER: bond constraints in nmode richard dimelow (Wed Sep 15 2004 - 08:15:05 PDT)
- Re: AMBER: bond constraints in nmode David A. Case (Wed Sep 15 2004 - 09:03:09 PDT)
AMBER: md problem Volodymyr Zloy (Wed Sep 15 2004 - 09:03:29 PDT)
- Re: AMBER: md problem Furse, Kristina Elisabet (Wed Sep 15 2004 - 12:53:23 PDT)
- RE: AMBER: md problem Ross Walker (Thu Sep 16 2004 - 07:43:19 PDT)
  - RE: AMBER: md problem Volodymyr Zloy (Mon Sep 20 2004 - 11:05:25 PDT)
AMBER: A tool for building coordinates of huge macromolecules Hwankyu Lee (Wed Sep 15 2004 - 09:28:19 PDT)
- Re: AMBER: A tool for building coordinates of huge macromolecules Joachim Reichelt (Wed Sep 15 2004 - 09:37:05 PDT)
AMBER: back interpret Joshua Hicks (Wed Sep 15 2004 - 14:49:57 PDT)
- Re: AMBER: back interpret Carlos Simmerling (Wed Sep 15 2004 - 15:08:40 PDT)
- Re: AMBER: back interpret David A. Case (Wed Sep 15 2004 - 15:23:18 PDT)
AMBER: Sander TI with NTR = 1. Chunhu Tan (Wed Sep 15 2004 - 16:33:47 PDT)
- Re: AMBER: Sander TI with NTR = 1. David A. Case (Thu Sep 16 2004 - 07:56:48 PDT)
AMBER: VDWAALS error during minimisation anita pachaimuthu (Thu Sep 16 2004 - 07:42:34 PDT)
- RE: AMBER: VDWAALS error during minimisation Ross Walker (Thu Sep 16 2004 - 08:20:34 PDT)
AMBER: extra points richard dimelow (Thu Sep 16 2004 - 09:21:05 PDT)
- Re: AMBER: extra points David A. Case (Thu Sep 16 2004 - 10:26:09 PDT)
AMBER: restraining internal coordinates Taner E. Dirama (Thu Sep 16 2004 - 09:53:51 PDT)
- Re: AMBER: restraining internal coordinates Carlos Simmerling (Thu Sep 16 2004 - 10:04:14 PDT)
AMBER: Force Compiling AMBER8 for an SGI O2 Justin Sanders (Thu Sep 16 2004 - 11:34:12 PDT)
AMBER: Amber 7 Compiling Problem Stephen P. Molnar, Ph.D. (Fri Sep 17 2004 - 08:33:15 PDT)
- Re: AMBER: Amber 7 Compiling Problem David A. Case (Fri Sep 17 2004 - 09:29:58 PDT)
  - Re: AMBER: Amber 7 Compiling Problem Stephen P. Molnar, Ph.D. (Fri Sep 17 2004 - 10:33:47 PDT)
    - Re: AMBER: Amber 7 Compiling Problem David A. Case (Fri Sep 17 2004 - 10:23:23 PDT)
    - Re: AMBER: Amber 7 Compiling Problem Stephen P. Molnar, Ph.D. (Fri Sep 17 2004 - 11:24:52 PDT)
    - Re: AMBER: Amber 7 Compiling Problem Stephen P. Molnar, Ph.D. (Fri Sep 17 2004 - 11:32:02 PDT)
AMBER: Problem with MacroMolecule to AMBER7 Guillaume Bollot (Fri Sep 17 2004 - 08:56:22 PDT)
- Re: AMBER: Problem with MacroMolecule to AMBER7 Sébastien Osborne (Fri Sep 17 2004 - 09:04:48 PDT)
AMBER: PMEMD Greg Kellogg (Fri Sep 17 2004 - 09:20:00 PDT)
- Re: AMBER: PMEMD Robert Duke (Fri Sep 17 2004 - 09:56:01 PDT)
AMBER: Moil-view & Amber trajectory opitz.che.udel.edu (Fri Sep 17 2004 - 13:41:42 PDT)
- Re: AMBER: Moil-view & Amber trajectory Carlos Simmerling (Fri Sep 17 2004 - 14:01:37 PDT)
- Re: AMBER: Moil-view & Amber trajectory Thomas E. Cheatham, III (Fri Sep 17 2004 - 14:23:14 PDT)
- Re: AMBER: Moil-view & Amber trajectory opitz.che.udel.edu (Mon Sep 20 2004 - 14:59:39 PDT)
  - Re: AMBER: Moil-view & Amber trajectory Carlos Simmerling (Tue Sep 21 2004 - 09:17:59 PDT)
AMBER: mm_pbsa nmode problem Fang, Jianwen (Fri Sep 17 2004 - 15:28:47 PDT)
AMBER: Re: Delphi PATH question hj zou (Fri Sep 17 2004 - 23:22:08 PDT)
AMBER: about PARALLEL run on SGI. Ji Changge (Fri Sep 17 2004 - 23:47:38 PDT)
- Re: AMBER: about PARALLEL run on SGI. David A. Case (Sun Sep 19 2004 - 17:49:30 PDT)
Re: AMBER: About binding energy Oliver Hucke (Sat Sep 18 2004 - 21:53:36 PDT)
AMBER: More details about free energy Xiao He (Sun Sep 19 2004 - 01:02:53 PDT)
AMBER: ifort installation mathew k varghese (Sun Sep 19 2004 - 01:46:57 PDT)
- Re: AMBER: ifort installation Nhat-hang Duong (Sun Sep 19 2004 - 12:03:32 PDT)
AMBER: Questions on simulating dendrimer in AMBER. Hwankyu Lee (Sun Sep 19 2004 - 20:21:03 PDT)
AMBER: The question about SAS calculation in MM_PBSA Jack Lei (Mon Sep 20 2004 - 10:19:29 PDT)
- Re: AMBER: The question about SAS calculation in MM_PBSA David A. Case (Wed Sep 22 2004 - 11:29:52 PDT)
AMBER: RESP problem... FyD (Mon Sep 20 2004 - 12:59:04 PDT)
AMBER: sander8 compile: myrinet and mpigm Guanglei Cui (Mon Sep 20 2004 - 13:42:14 PDT)
AMBER: about MM-PBSA Xiao He (Mon Sep 20 2004 - 22:40:16 PDT)
- RE: AMBER: about MM-PBSA S. Frank Yan (Mon Sep 20 2004 - 22:59:02 PDT)
  - Re: RE: AMBER: about MM-PBSA Xiao He (Tue Sep 21 2004 - 00:49:24 PDT)
    - Re: AMBER: about MM-PBSA Ray Luo (Mon Sep 20 2004 - 19:26:52 PDT)
    - Re: Re: AMBER: about MM-PBSA Xiao He (Tue Sep 21 2004 - 20:44:51 PDT)
    - AMBER: compressed files Jessica Koplin (Wed Sep 22 2004 - 09:56:27 PDT)
    - RE: AMBER: compressed files Ross Walker (Wed Sep 22 2004 - 10:20:18 PDT)
AMBER: Ptraj data Steve Seibold (Tue Sep 21 2004 - 11:13:49 PDT)
- Re: AMBER: Ptraj data Viktor Hornak (Tue Sep 21 2004 - 11:43:44 PDT)
- Re: AMBER: Ptraj data Thomas E. Cheatham, III (Tue Sep 21 2004 - 11:59:58 PDT)
  - Re: AMBER: Ptraj data Elijah Gregory (Tue Sep 21 2004 - 15:04:45 PDT)
AMBER: MAXRING Antechamber problem Karl N. Kirschner (Tue Sep 21 2004 - 12:37:44 PDT)
- RE: AMBER: MAXRING Antechamber problem Ross Walker (Tue Sep 21 2004 - 12:49:51 PDT)
  - RE: AMBER: MAXRING Antechamber problem Karl N. Kirschner (Wed Sep 22 2004 - 13:17:31 PDT)
AMBER: Question about Parallel Compilation David LeBard (Tue Sep 21 2004 - 16:12:54 PDT)
- Re: AMBER: Question about Parallel Compilation David A. Case (Wed Sep 22 2004 - 09:49:02 PDT)
  - Re: AMBER: Question about Parallel Compilation David LeBard (Wed Sep 22 2004 - 19:49:47 PDT)
AMBER: amber8 installation mathew k varghese (Wed Sep 22 2004 - 00:07:50 PDT)
- Re: AMBER: amber8 installation Andreas Svrcek-Seiler (Wed Sep 22 2004 - 04:05:02 PDT)
AMBER: all_nucleic02 and all_nucleic94 Vlad Cojocaru (Wed Sep 22 2004 - 03:40:10 PDT)
- Re: AMBER: all_nucleic02 and all_nucleic94 David A. Case (Wed Sep 22 2004 - 09:59:01 PDT)
AMBER: Re: Re: Delphi PATH question hj zou (Wed Sep 22 2004 - 06:40:23 PDT)
- Re: AMBER: Re: Re: Delphi PATH question Xiao He (Wed Sep 22 2004 - 08:47:47 PDT)
AMBER: amber8 tests mathew k varghese (Wed Sep 22 2004 - 07:30:09 PDT)
- Re: AMBER: amber8 tests David A. Case (Wed Sep 22 2004 - 11:28:34 PDT)
AMBER: all_nucleic94 versus all_nucleic02 Vlad Cojocaru (Wed Sep 22 2004 - 08:15:12 PDT)
- Re: AMBER: all_nucleic94 versus all_nucleic02 Jiten (Wed Sep 22 2004 - 08:45:36 PDT)
- RE: AMBER: all_nucleic94 versus all_nucleic02 Ross Walker (Wed Sep 22 2004 - 08:53:49 PDT)
- RE: AMBER: all_nucleic94 versus all_nucleic02 Ross Walker (Wed Sep 22 2004 - 10:11:21 PDT)
AMBER: building parameters with Amber Amber admin (Wed Sep 22 2004 - 09:41:38 PDT)
- Re: AMBER: building parameters with Amber Furse, Kristina Elisabet (Wed Sep 22 2004 - 11:36:41 PDT)
AMBER: mm_pbsa.pl nmode entropy estimating problem jwfang (Wed Sep 22 2004 - 12:30:21 PDT)
- Re: AMBER: mm_pbsa.pl nmode entropy estimating problem David A. Case (Wed Sep 22 2004 - 13:29:04 PDT)
AMBER: RESTARTED DUE TO LINMIN FAILURE ... ying xiong (Thu Sep 23 2004 - 01:24:13 PDT)
- Re: AMBER: RESTARTED DUE TO LINMIN FAILURE ... cailliez (Thu Sep 23 2004 - 01:42:31 PDT)
AMBER: Jiten (Thu Sep 23 2004 - 01:44:49 PDT)
- RE: AMBER: Ross Walker (Thu Sep 23 2004 - 10:36:45 PDT)
AMBER: replica exchange with thermodynamic integration david.evans.ulsop.ac.uk (Thu Sep 23 2004 - 04:18:44 PDT)
- Re: AMBER: replica exchange with thermodynamic integration David A. Case (Fri Sep 24 2004 - 08:44:01 PDT)
AMBER: question about J. Am. Chem. Soc. 2001, 123, 5221 paper jwfang (Thu Sep 23 2004 - 08:15:36 PDT)
AMBER: Amber job submission using PBS Jiten (Thu Sep 23 2004 - 08:44:39 PDT)
- Re: AMBER: Amber job submission using PBS Guanglei Cui (Thu Sep 23 2004 - 08:52:01 PDT)
- Re: AMBER: Amber job submission using PBS Jiten (Thu Sep 23 2004 - 09:11:41 PDT)
  - Re: AMBER: Amber job submission using PBS Guanglei Cui (Thu Sep 23 2004 - 09:20:30 PDT)
- Re: AMBER: Amber job submission using PBS Jiten (Thu Sep 23 2004 - 09:57:35 PDT)
- Re: AMBER: Amber job submission using PBS Jiten (Thu Sep 23 2004 - 10:04:36 PDT)
  - Re: AMBER: Amber job submission using PBS Guanglei Cui (Thu Sep 23 2004 - 10:49:35 PDT)
    - Re: AMBER: Amber job submission using PBS Thomas E. Cheatham, III (Thu Sep 23 2004 - 10:59:00 PDT)
- RE: AMBER: Amber job submission using PBS Ross Walker (Thu Sep 23 2004 - 10:44:04 PDT)
- RE: AMBER: Amber job submission using PBS Bill Ross (Thu Sep 23 2004 - 12:18:37 PDT)
- Re: AMBER: Amber job submission using PBS Jiten (Thu Sep 23 2004 - 21:05:39 PDT)
- Re: AMBER: Amber job submission using PBS Jiten (Thu Sep 23 2004 - 21:09:06 PDT)
- Re: AMBER: Amber job submission using PBS Jiten (Thu Sep 23 2004 - 23:21:27 PDT)
AMBER: Amber 8 installation error on Xeon 2-CPU Kei ODAI (Thu Sep 23 2004 - 16:11:15 PDT)
- RE: AMBER: Amber 8 installation error on Xeon 2-CPU Ross Walker (Thu Sep 23 2004 - 16:32:49 PDT)
AMBER: ptraj problem Marsita M (Thu Sep 23 2004 - 16:53:53 PDT)
Re: AMBER: Amber 8 installation error on Xeon 2-CPU Bill Ross (Thu Sep 23 2004 - 17:17:17 PDT)
AMBER: about mm_pbsa parameter Xiao He (Thu Sep 23 2004 - 20:56:04 PDT)
- Re: AMBER: about mm_pbsa parameter Oliver Hucke (Fri Sep 24 2004 - 08:49:22 PDT)
AMBER: nbflag cailliez (Thu Sep 23 2004 - 23:44:22 PDT)
- Re: AMBER: nbflag David A. Case (Fri Sep 24 2004 - 08:15:20 PDT)
  - AMBER: hydrogen bonds Jessica Koplin (Fri Oct 01 2004 - 09:24:29 PDT)
    - Re: AMBER: hydrogen bonds Tim Meyer (Tue Oct 05 2004 - 04:11:09 PDT)
- Re: AMBER: nbflag cailliez (Fri Sep 24 2004 - 08:20:13 PDT)
AMBER: phosphoserine library component jwcraft.uh.edu (Fri Sep 24 2004 - 07:01:28 PDT)
- Re: AMBER: phosphoserine library component Jiten (Fri Sep 24 2004 - 07:25:24 PDT)
- Re: AMBER: phosphoserine library component David A. Case (Fri Sep 24 2004 - 08:25:10 PDT)
- Re: AMBER: phosphoserine library component FyD (Fri Sep 24 2004 - 10:10:40 PDT)
AMBER: regular ewald sum in Amber8 Jianwen Jiang (Fri Sep 24 2004 - 09:15:34 PDT)
- Re: AMBER: regular ewald sum in Amber8 David A. Case (Fri Sep 24 2004 - 12:12:30 PDT)
AMBER: Parameters for Inosine yuqin cai (Fri Sep 24 2004 - 11:51:40 PDT)
- Re: AMBER: Parameters for Inosine Jiri Sponer (Fri Sep 24 2004 - 13:02:59 PDT)
AMBER: Question Amber8 install errer with Windows Amber admin (Fri Sep 24 2004 - 12:46:06 PDT)
- Re: AMBER: Question Amber8 install errer with Windows David A. Case (Fri Sep 24 2004 - 13:41:18 PDT)
AMBER: nmode error Xiao He (Fri Sep 24 2004 - 19:17:24 PDT)
- Re: AMBER: nmode error David A. Case (Sat Sep 25 2004 - 11:44:37 PDT)
AMBER: Analysis mm_pbsa result Xiao He (Fri Sep 24 2004 - 19:53:08 PDT)
AMBER: output of mm_pbsa.log Xiao He (Sat Sep 25 2004 - 02:30:16 PDT)
AMBER: minimization problem hj zou (Sat Sep 25 2004 - 02:30:11 PDT)
- Re: AMBER: minimization problem David A. Case (Sat Sep 25 2004 - 11:43:49 PDT)
AMBER: Abd Ghani Bin Abd Aziz (Sat Sep 25 2004 - 03:16:39 PDT)
AMBER: radius of gyration Marsita M (Sat Sep 25 2004 - 19:13:25 PDT)
- Re: AMBER: radius of gyration Sanjeev B.S. (Sat Sep 25 2004 - 20:28:32 PDT)
AMBER: amber 8 error on installation Abd Ghani Bin Abd Aziz (Sun Sep 26 2004 - 05:55:07 PDT)
- Re: AMBER: amber 8 error on installation Carlos Simmerling (Sun Sep 26 2004 - 06:24:08 PDT)
- Re: AMBER: amber 8 error on installation Abd Ghani Bin Abd Aziz (Sun Sep 26 2004 - 06:47:04 PDT)
AMBER: dihedral hj zou (Sun Sep 26 2004 - 18:08:20 PDT)
- Re: AMBER: dihedral Thomas E. Cheatham, III (Sun Sep 26 2004 - 19:13:42 PDT)
AMBER: Atom distance bybaker.itsa.ucsf.edu (Sun Sep 26 2004 - 23:59:05 PDT)
- Re: AMBER: Atom distance Tomas Linhart (Mon Sep 27 2004 - 00:12:59 PDT)
  - AMBER: Box information from Amber Priti Hansia (Sat Oct 09 2004 - 04:19:46 PDT)
    - Re: AMBER: Box information from Amber Carlos Simmerling (Sat Oct 09 2004 - 05:10:56 PDT)
    - Re: AMBER: Box information from Amber Priti Hansia (Sat Oct 09 2004 - 10:51:16 PDT)
    - Re: AMBER: Box information from Amber Carlos Simmerling (Sat Oct 09 2004 - 11:00:43 PDT)
- Re: AMBER: Atom distance bybaker.itsa.ucsf.edu (Mon Sep 27 2004 - 13:39:49 PDT)
  - Re: AMBER: Atom distance Thomas E. Cheatham, III (Mon Sep 27 2004 - 13:48:11 PDT)
AMBER: Principal Component Analysis Vlad Cojocaru (Mon Sep 27 2004 - 05:09:50 PDT)
AMBER: unformatted md problem richard dimelow (Mon Sep 27 2004 - 06:13:40 PDT)
- Re: AMBER: unformatted md problem David A. Case (Mon Sep 27 2004 - 08:06:05 PDT)
AMBER: Great help:Analysis mm_pbsa result Xiao He (Mon Sep 27 2004 - 07:44:03 PDT)
AMBER: how to visualize modes from PCA Vlad Cojocaru (Mon Sep 27 2004 - 09:05:35 PDT)
- Re: AMBER: how to visualize modes from PCA Carlos Simmerling (Mon Sep 27 2004 - 09:13:10 PDT)
AMBER: Amber-7:Bugfix.47 sachin patil (Mon Sep 27 2004 - 12:32:21 PDT)
- Re: AMBER: Amber-7:Bugfix.47 David A. Case (Mon Sep 27 2004 - 13:20:20 PDT)
- RE: AMBER: Amber-7:Bugfix.47 Ross Walker (Mon Sep 27 2004 - 13:34:36 PDT)
AMBER: intramolecular energies Guanglei Cui (Mon Sep 27 2004 - 14:17:11 PDT)
- Re: AMBER: intramolecular energies David A. Case (Mon Sep 27 2004 - 16:27:25 PDT)
  - Re: AMBER: intramolecular energies Guanglei Cui (Mon Sep 27 2004 - 18:55:41 PDT)
    - Re: AMBER: intramolecular energies David A. Case (Tue Sep 28 2004 - 08:43:11 PDT)
    - Re: AMBER: intramolecular energies Guanglei Cui (Tue Sep 28 2004 - 09:11:10 PDT)
    - Re: AMBER: intramolecular energies David A. Case (Tue Sep 28 2004 - 10:11:57 PDT)
    - Re: AMBER: intramolecular energies Guanglei Cui (Tue Sep 28 2004 - 10:38:16 PDT)
AMBER: Re: Atom distance bybaker.itsa.ucsf.edu (Mon Sep 27 2004 - 18:21:20 PDT)
AMBER: question about delphi and UHBD xhu1.memphis.edu (Tue Sep 28 2004 - 09:19:32 PDT)
- Re: AMBER: question about delphi and UHBD Ray Luo (Tue Sep 28 2004 - 10:58:11 PDT)
  - Re: AMBER: question about delphi and UHBD Thomas E. Cheatham, III (Tue Sep 28 2004 - 12:34:59 PDT)
- Re: AMBER: question about delphi and UHBD xhu1.memphis.edu (Tue Sep 28 2004 - 13:32:51 PDT)
  - Re: AMBER: question about delphi and UHBD Carlos Simmerling (Tue Sep 28 2004 - 13:46:43 PDT)
- Re: AMBER: question about delphi and UHBD xhu1.memphis.edu (Tue Sep 28 2004 - 15:06:12 PDT)
  - Re: AMBER: question about delphi and UHBD Ray Luo (Tue Sep 28 2004 - 15:19:59 PDT)
- Re: AMBER: question about delphi and UHBD xhu1.memphis.edu (Wed Sep 29 2004 - 12:11:47 PDT)
- Re: AMBER: question about delphi and UHBD xhu1.memphis.edu (Thu Sep 30 2004 - 09:52:01 PDT)
AMBER: Ahammadunny Pathiaseril (Tue Sep 28 2004 - 11:05:44 PDT)
- Re: AMBER: Ray Luo (Tue Sep 28 2004 - 11:30:10 PDT)
AMBER: The convergence of energy minimisation Binbin Liu (Tue Sep 28 2004 - 12:10:56 PDT)
AMBER: Amber bybaker.itsa.ucsf.edu (Tue Sep 28 2004 - 12:28:32 PDT)
- Re: AMBER: Amber Thomas E. Cheatham, III (Tue Sep 28 2004 - 12:37:25 PDT)
- Re: AMBER: Amber Tomas Linhart (Tue Sep 28 2004 - 12:50:28 PDT)
AMBER: Phosphoserine parameters Venkata S Koppuravuri (Tue Sep 28 2004 - 13:41:23 PDT)
- Re: AMBER: Phosphoserine parameters Oliver Hucke (Tue Sep 28 2004 - 16:53:27 PDT)
- Re: AMBER: Phosphoserine parameters Joseph Nachman (Wed Sep 29 2004 - 08:50:24 PDT)
AMBER: Re: Amber bybaker.itsa.ucsf.edu (Tue Sep 28 2004 - 14:35:01 PDT)
AMBER: scaling 1-4 NB interaction for rings j-shimada.az.jp.nec.com (Wed Sep 29 2004 - 07:16:38 PDT)
- Re: AMBER: scaling 1-4 NB interaction for rings David A. Case (Wed Sep 29 2004 - 08:11:02 PDT)
AMBER: (no subject) Rasha Radwan (Wed Sep 29 2004 - 07:24:25 PDT)
- Re: AMBER: (no subject) Jiten (Wed Sep 29 2004 - 08:23:55 PDT)
- Re: AMBER: (no subject) M. L. Dodson (Wed Sep 29 2004 - 08:39:12 PDT)
- Re: AMBER: (no subject) David A. Case (Wed Sep 29 2004 - 08:39:43 PDT)
- Re: AMBER: (no subject) Anselm Horn (Wed Sep 29 2004 - 08:00:43 PDT)
AMBER: impose: Illegal angle internal definition Madalin Giambasu (Wed Sep 29 2004 - 09:34:18 PDT)
- Re: AMBER: impose: Illegal angle internal definition David A. Case (Wed Sep 29 2004 - 12:13:36 PDT)
AMBER: resp error message Andre Farias de Moura (Wed Sep 29 2004 - 09:25:07 PDT)
- Re: AMBER: resp error message FyD (Wed Sep 29 2004 - 12:55:26 PDT)
  - Re: AMBER: resp error message Andre Farias de Moura (Wed Sep 29 2004 - 10:41:05 PDT)
    - Re: AMBER: resp error message FyD (Wed Sep 29 2004 - 13:54:12 PDT)
    - Re: AMBER: resp error message Andre Farias de Moura (Thu Sep 30 2004 - 06:58:38 PDT)
    - Re: AMBER: resp error message FyD (Thu Sep 30 2004 - 09:54:33 PDT)
AMBER: Compiling AMBER8 Justin Sanders (Thu Sep 30 2004 - 07:54:05 PDT)
- Re: AMBER: Compiling AMBER8 David A. Case (Thu Sep 30 2004 - 08:59:42 PDT)
AMBER: Testing Delphi for mm_pbsa Scott Pendley (Thu Sep 30 2004 - 10:20:15 PDT)
AMBER: anal error Guanglei Cui (Thu Sep 30 2004 - 13:28:35 PDT)
AMBER: (no subject) Rasha Radwan (Fri Oct 01 2004 - 07:30:53 PDT)
AMBER: frcmod_dmso Vincent Bisetty (Fri Oct 01 2004 - 14:21:42 PDT)
- RE: AMBER: frcmod_dmso Ross Walker (Fri Oct 01 2004 - 15:05:05 PDT)
- RE: AMBER: frcmod_dmso Ross Walker (Tue Oct 05 2004 - 13:10:41 PDT)
AMBER: amber 8 error Abd Ghani Bin Abd Aziz (Sat Oct 02 2004 - 00:25:30 PDT)
- Re: AMBER: amber 8 error Tomas Linhart (Sat Oct 02 2004 - 01:04:43 PDT)
AMBER: small molecule simulation hj zou (Sat Oct 02 2004 - 22:59:55 PDT)
- Re: AMBER: small molecule simulation Carlos Simmerling (Sun Oct 03 2004 - 05:54:40 PDT)
AMBER: antechamber, mopac RESTART opitz.che.udel.edu (Sun Oct 03 2004 - 11:41:24 PDT)
AMBER: Running on MPI wish_71 (Sun Oct 03 2004 - 18:59:58 PDT)
- Re: AMBER: Running on MPI Jiten (Sun Oct 03 2004 - 20:08:54 PDT)
- Re: AMBER: Running on MPI Carlos Simmerling (Mon Oct 04 2004 - 04:37:18 PDT)
- Re: AMBER: Running on MPI wish_71 (Tue Oct 05 2004 - 03:17:55 PDT)
  - Re: AMBER: Running on MPI Carlos Simmerling (Tue Oct 05 2004 - 05:16:59 PDT)
- Re: AMBER: Running on MPI wish_71 (Tue Oct 05 2004 - 19:43:16 PDT)
  - Re: AMBER: Running on MPI Carlos Simmerling (Wed Oct 06 2004 - 07:33:19 PDT)
AMBER: mdinfo on amber6 Abd Ghani Bin Abd Aziz (Sun Oct 03 2004 - 22:26:41 PDT)
- Re: AMBER: mdinfo on amber6 Tomas Linhart (Mon Oct 04 2004 - 00:49:29 PDT)
- Re: AMBER: mdinfo on amber6 Carlos Simmerling (Mon Oct 04 2004 - 04:40:03 PDT)
AMBER: neutral Arg, charged Tyr ?? Peter Trodler (Mon Oct 04 2004 - 00:25:49 PDT)
AMBER: amber with MPI Stefano.Pieraccini.unimi.it (Mon Oct 04 2004 - 07:40:16 PDT)
AMBER: Phosphoserine Venkata S Koppuravuri (Mon Oct 04 2004 - 12:26:28 PDT)
AMBER: Is AME equal to NME? myang.vitamin.uni.cc (Mon Oct 04 2004 - 12:15:46 PDT)
- Re: AMBER: Is AME equal to NME? myang.vitamin.uni.cc (Mon Oct 04 2004 - 13:07:12 PDT)
AMBER: building a small molecule mathew k varghese (Tue Oct 05 2004 - 02:01:09 PDT)
- Re: AMBER: building a small molecule Oliver Hucke (Tue Oct 05 2004 - 10:15:00 PDT)
AMBER: Parameters for phosphorylated aminoacids Nadine Homeyer (Tue Oct 05 2004 - 08:21:31 PDT)
- Re: AMBER: Parameters for phosphorylated aminoacids Carlos Simmerling (Tue Oct 05 2004 - 08:58:07 PDT)
  - Re: AMBER: Parameters for phosphorylated aminoacids Nadine Homeyer (Wed Oct 06 2004 - 03:57:14 PDT)
AMBER: parameter error for a ligand Sivanesan Dakshanamurthy (Tue Oct 05 2004 - 09:59:54 PDT)
- Re: AMBER: parameter error for a ligand David A. Case (Tue Oct 05 2004 - 13:23:01 PDT)
- Re: AMBER: parameter error for a ligand Sivanesan Dakshanamurthy (Tue Oct 05 2004 - 14:45:51 PDT)
AMBER: problem with protonate Richard Stefl (Tue Oct 05 2004 - 10:44:05 PDT)
- Re: AMBER: problem with protonate myang.vitamin.uni.cc (Tue Oct 05 2004 - 13:36:36 PDT)
- Re: AMBER: problem with protonate David A. Case (Tue Oct 05 2004 - 14:31:12 PDT)
AMBER: question about nmode xiaowei li (Tue Oct 05 2004 - 11:09:15 PDT)
- Re: AMBER: question about nmode David A. Case (Tue Oct 05 2004 - 12:03:52 PDT)
AMBER: Note to all concerning filtering of messages posted to the amber list. Ross Walker (Tue Oct 05 2004 - 12:51:34 PDT)
- Re: AMBER: Note to all concerning filtering of messages posted to the amber list. Stef (Wed Oct 06 2004 - 01:33:17 PDT)
AMBER: Compiling using pgf90 David Lomelin (Tue Oct 05 2004 - 18:33:22 PDT)
- Re: AMBER: Compiling using pgf90 Craig TOEPFER (Wed Oct 06 2004 - 09:52:06 PDT)
  - Re: AMBER: Compiling using pgf90 David Lomelin (Wed Oct 06 2004 - 13:30:34 PDT)
AMBER: Comparison of simulation results on amber7 and amber 8 anshul.imtech.res.in (Wed Oct 06 2004 - 13:28:04 PDT)
- Re: AMBER: Comparison of simulation results on amber7 and amber 8 Carlos Simmerling (Wed Oct 06 2004 - 06:36:03 PDT)
  - Re: AMBER: Comparison of simulation results on amber7 and amber 8 Sergio E. Wong (Wed Oct 06 2004 - 09:54:44 PDT)
    - Re: AMBER: Comparison of simulation results on amber7 and amber 8 Carlos Simmerling (Wed Oct 06 2004 - 10:21:54 PDT)
    - AMBER: atoms out of bounds Balvinder Singh (Thu Oct 07 2004 - 14:27:45 PDT)
    - Re: AMBER: atoms out of bounds Carlos Simmerling (Thu Oct 07 2004 - 05:17:15 PDT)
AMBER: ptraj and PCA J Pang (Wed Oct 06 2004 - 03:54:17 PDT)
AMBER: Antechamber on cluster with queue? opitz.che.udel.edu (Wed Oct 06 2004 - 08:08:25 PDT)
- Re: AMBER: Antechamber on cluster with queue? David A. Case (Wed Oct 06 2004 - 08:24:17 PDT)
- Re: AMBER: Antechamber on cluster with queue? opitz.che.udel.edu (Wed Oct 06 2004 - 09:06:43 PDT)
  - Re: AMBER: Antechamber on cluster with queue? David A. Case (Wed Oct 06 2004 - 09:31:53 PDT)
AMBER: GIbbs : failure to start sachin patil (Wed Oct 06 2004 - 11:01:23 PDT)
AMBER: AddIons Vincent Bisetty (Thu Oct 07 2004 - 05:15:03 PDT)
AMBER: ptraj analyze modes question Vlad Cojocaru (Thu Oct 07 2004 - 06:17:02 PDT)
AMBER: rms fluctuation units from ptraj Vlad Cojocaru (Thu Oct 07 2004 - 06:36:03 PDT)
Re: AMBER: AddIons Bill Ross (Thu Oct 07 2004 - 12:36:24 PDT)
AMBER: solute leaving PBC box opitz.che.udel.edu (Thu Oct 07 2004 - 14:24:47 PDT)
- Re: AMBER: solute leaving PBC box Carlos Simmerling (Thu Oct 07 2004 - 14:48:12 PDT)
- Re: AMBER: solute leaving PBC box myang.vitamin.uni.cc (Thu Oct 07 2004 - 15:00:09 PDT)
- Re: AMBER: solute leaving PBC box opitz.che.udel.edu (Thu Oct 07 2004 - 15:01:19 PDT)
  - Re: AMBER: solute leaving PBC box Carlos Simmerling (Thu Oct 07 2004 - 15:43:49 PDT)
- Re: AMBER: solute leaving PBC box opitz.che.udel.edu (Fri Oct 08 2004 - 06:43:06 PDT)
  - Re: AMBER: solute leaving PBC box Carlos Simmerling (Fri Oct 08 2004 - 07:02:42 PDT)
AMBER: Problem with AMBER/ANAL Daniel Wetzler (Fri Oct 08 2004 - 01:31:29 PDT)
- Re: AMBER: Problem with AMBER/ANAL David A. Case (Fri Oct 08 2004 - 09:15:12 PDT)
AMBER: MAXATOM failure in ANTECHAMBER Cenk Andac (Fri Oct 08 2004 - 02:31:18 PDT)
- Re: AMBER: MAXATOM failure in ANTECHAMBER david.evans.ulsop.ac.uk (Fri Oct 08 2004 - 03:09:18 PDT)
AMBER: problems with dihedrals Petr Kulhanek (Fri Oct 08 2004 - 05:53:03 PDT)
- Re: AMBER: problems with dihedrals Carlos Simmerling (Fri Oct 08 2004 - 06:27:44 PDT)
AMBER: generalized Born parameters Peter Varnai (Fri Oct 08 2004 - 07:16:08 PDT)
- Re: AMBER: generalized Born parameters David A. Case (Fri Oct 08 2004 - 09:08:02 PDT)
AMBER: sander8 Vincent Bisetty (Fri Oct 08 2004 - 07:59:01 PDT)
- Re: AMBER: sander8 Carlos Simmerling (Fri Oct 08 2004 - 08:07:23 PDT)
- Re: AMBER: sander8 Vincent Bisetty (Sat Oct 09 2004 - 09:13:55 PDT)
  - Re: AMBER: sander8 Carlos Simmerling (Sat Oct 09 2004 - 10:39:34 PDT)
AMBER: A torsion parameter in AMBER2003 force field Scott E. Boesch (Fri Oct 08 2004 - 09:23:41 PDT)
- Re: AMBER: A torsion parameter in AMBER2003 force field David A. Case (Fri Oct 08 2004 - 09:53:21 PDT)
- RE: AMBER: A torsion parameter in AMBER2003 force field Yong Duan (Fri Oct 08 2004 - 10:41:41 PDT)
AMBER: restrain one tosion angle Yaroslava Yingling (Fri Oct 08 2004 - 12:02:01 PDT)
- Re: AMBER: restrain one tosion angle Carlos Simmerling (Fri Oct 08 2004 - 12:10:16 PDT)
  - Re: AMBER: restrain one tosion angle Yaroslava Yingling (Fri Oct 08 2004 - 12:20:09 PDT)
    - Re: AMBER: restrain one tosion angle Carlos Simmerling (Fri Oct 08 2004 - 13:50:34 PDT)
AMBER: about antechamber MURAT CETINKAYA (Sat Oct 09 2004 - 18:48:52 PDT)
- Re: AMBER: about antechamber David A. Case (Mon Oct 11 2004 - 09:13:05 PDT)
AMBER: Amber8 compilation in Dec-Alpha Jiten (Sun Oct 10 2004 - 09:22:01 PDT)
- RE: AMBER: Amber8 compilation in Dec-Alpha Ross Walker (Mon Oct 11 2004 - 10:09:40 PDT)
AMBER: exclusion list Guanglei Cui (Sun Oct 10 2004 - 09:34:38 PDT)
- Re: AMBER: exclusion list Guanglei Cui (Mon Oct 11 2004 - 08:26:20 PDT)
AMBER: nmode error Xiao He (Mon Oct 11 2004 - 00:10:22 PDT)
- Re: AMBER: nmode error David A. Case (Mon Oct 11 2004 - 08:09:18 PDT)
AMBER: question about mm_pbsa and nmode Xiao He (Mon Oct 11 2004 - 00:43:53 PDT)
AMBER: AMBER 8 installation trouble Atro Tossavainen (Mon Oct 11 2004 - 01:36:44 PDT)
- Re: AMBER: AMBER 8 installation trouble David A. Case (Mon Oct 11 2004 - 08:43:44 PDT)
  - Re: AMBER: AMBER 8 installation trouble Atro Tossavainen (Tue Oct 12 2004 - 00:29:23 PDT)
    - Re: AMBER: AMBER 8 installation trouble David A. Case (Tue Oct 12 2004 - 10:28:14 PDT)
    - Re: AMBER: AMBER 8 installation trouble Atro Tossavainen (Tue Oct 12 2004 - 23:56:19 PDT)
  - Re: AMBER: AMBER 8 installation trouble Atro Tossavainen (Fri Oct 15 2004 - 00:20:54 PDT)
    - Re: AMBER: AMBER 8 installation trouble David A. Case (Fri Oct 15 2004 - 07:51:59 PDT)
AMBER: AMBER 8 installation - continued Atro Tossavainen (Mon Oct 11 2004 - 01:57:45 PDT)
- RE: AMBER: AMBER 8 installation - continued Ross Walker (Mon Oct 11 2004 - 10:17:50 PDT)
  - Re: AMBER: AMBER 8 installation - continued Atro Tossavainen (Tue Oct 12 2004 - 00:37:24 PDT)
  - AMBER: order parameter Jessica Koplin (Sun Oct 17 2004 - 03:30:44 PDT)
    - Re: AMBER: order parameter Carlos Simmerling (Sun Oct 17 2004 - 06:14:43 PDT)
AMBER: Hot solvent/cold solute reference Stef (Mon Oct 11 2004 - 03:56:30 PDT)
- Re: AMBER: Hot solvent/cold solute reference Andreas Svrcek-Seiler (Mon Oct 11 2004 - 06:16:18 PDT)
  - Re: AMBER: Hot solvent/cold solute reference Stef (Mon Oct 11 2004 - 09:41:10 PDT)
AMBER: Distance Restraints Nelson Fonseca (Mon Oct 11 2004 - 05:56:23 PDT)
- Re: AMBER: Distance Restraints David A. Case (Mon Oct 11 2004 - 08:17:39 PDT)
AMBER: Question about restart MD Xin Hu (Mon Oct 11 2004 - 11:38:38 PDT)
- Re: AMBER: Question about restart MD Carlos Simmerling (Mon Oct 11 2004 - 11:55:39 PDT)
- Re: AMBER: Question about restart MD myang.vitamin.uni.cc (Mon Oct 11 2004 - 12:05:04 PDT)
- RE: AMBER: Question about restart MD Ross Walker (Mon Oct 11 2004 - 12:06:09 PDT)
  - AMBER: Questions about MD sampling Xin Hu (Tue Oct 12 2004 - 08:03:06 PDT)
    - Re: AMBER: Questions about MD sampling Thomas E. Cheatham, III (Tue Oct 12 2004 - 09:12:18 PDT)
    - RE: AMBER: Questions about MD sampling Ross Walker (Tue Oct 12 2004 - 10:25:30 PDT)
    - RE: AMBER: Questions about MD sampling Ross Walker (Tue Oct 12 2004 - 10:31:12 PDT)
AMBER: how to set up more than 3 groups constrain 卢强 (Mon Oct 11 2004 - 11:33:51 PDT)
Re: AMBER: About missing residues FyD (Mon Oct 11 2004 - 22:27:58 PDT)
AMBER: process_mdout.perl bybaker.itsa.ucsf.edu (Mon Oct 11 2004 - 23:08:06 PDT)
- Re: AMBER: process_mdout.perl Donald Thomas (Mon Oct 11 2004 - 23:23:13 PDT)
- Re: AMBER: process_mdout.perl Tomas Linhart (Tue Oct 12 2004 - 00:43:28 PDT)
AMBER: RE:sander8 Vincent Bisetty (Tue Oct 12 2004 - 00:19:35 PDT)
- Re: AMBER: RE:sander8 Carlos Simmerling (Tue Oct 12 2004 - 04:21:02 PDT)
AMBER: More installation problems on Solaris 8 Atro Tossavainen (Tue Oct 12 2004 - 00:44:01 PDT)
AMBER: Parameter for chlorophyll Fajar Rakhman Wibowo (Tue Oct 12 2004 - 03:46:27 PDT)
AMBER: rms fluct and displacement in modes analysis Vlad Cojocaru (Tue Oct 12 2004 - 03:47:34 PDT)
- Re: AMBER: rms fluct and displacement in modes analysis David A. Case (Tue Oct 12 2004 - 09:19:48 PDT)
AMBER: klambdas and Weights for Gaussian Quadrature Nelson Fonseca (Tue Oct 12 2004 - 10:01:33 PDT)
- Re: AMBER: klambdas and Weights for Gaussian Quadrature David A. Case (Tue Oct 12 2004 - 16:37:11 PDT)
AMBER: Re: rms fluct and displacement in modes analysis Vlad Cojocaru (Tue Oct 12 2004 - 10:39:33 PDT)
AMBER: Carnal & Radius of gyration opitz.che.udel.edu (Tue Oct 12 2004 - 14:29:26 PDT)
Re: AMBER: Carnal & Radius of gyration Bill Ross (Tue Oct 12 2004 - 14:51:30 PDT)
AMBER: PBSA parameter question (Radii and Charges) Marc Baaden (Tue Oct 12 2004 - 17:01:19 PDT)
- Re: AMBER: PBSA parameter question (Radii and Charges) Ray Luo (Wed Oct 13 2004 - 09:38:38 PDT)
AMBER: process_mdout.perl: work now bybaker.itsa.ucsf.edu (Tue Oct 12 2004 - 18:32:49 PDT)
AMBER: Re: process_mdout.perl bybaker.itsa.ucsf.edu (Tue Oct 12 2004 - 18:36:45 PDT)
AMBER: A question on AMBER8 installation Hwankyu Lee (Tue Oct 12 2004 - 21:39:33 PDT)
- RE: AMBER: A question on AMBER8 installation Ross Walker (Tue Oct 12 2004 - 22:43:49 PDT)
- Re: AMBER: A question on AMBER8 installation David A. Case (Wed Oct 13 2004 - 07:58:58 PDT)
- RE: AMBER: A question on AMBER8 installation Bill Ross (Wed Oct 13 2004 - 10:13:48 PDT)
- Re: AMBER: A question on AMBER8 installation Scott Brozell (Wed Oct 13 2004 - 10:24:51 PDT)
  - Re: AMBER: A question on AMBER8 installation Hwankyu Lee (Wed Oct 13 2004 - 10:53:30 PDT)
- RE: AMBER: A question on AMBER8 installation Ross Walker (Wed Oct 13 2004 - 13:21:27 PDT)
  - RE: AMBER: A question on AMBER8 installation Hwankyu Lee (Thu Oct 14 2004 - 09:04:18 PDT)
    - Re: AMBER: A question on AMBER8 installation David A. Case (Thu Oct 14 2004 - 09:45:30 PDT)
    - RE: AMBER: A question on AMBER8 installation Ross Walker (Thu Oct 14 2004 - 09:50:25 PDT)
    - RE: AMBER: A question on AMBER8 installation Hwankyu Lee (Thu Oct 14 2004 - 10:57:45 PDT)
    - RE: AMBER: A question on AMBER8 installation Hwankyu Lee (Thu Oct 14 2004 - 11:13:33 PDT)
    - Re: AMBER: A question on AMBER8 installation David A. Case (Thu Oct 14 2004 - 11:22:14 PDT)
    - Re: AMBER: A question on AMBER8 installation M. L. Dodson (Thu Oct 14 2004 - 11:41:15 PDT)
    - Re: AMBER: A question on AMBER8 installation Hwankyu Lee (Thu Oct 14 2004 - 20:01:05 PDT)
    - Re: AMBER: A question on AMBER8 installation David A. Case (Fri Oct 15 2004 - 07:58:29 PDT)
    - Re: AMBER: A question on AMBER8 installation Hwankyu Lee (Tue Oct 19 2004 - 13:43:48 PDT)
    - Re: AMBER: A question on AMBER8 installation David A. Case (Tue Oct 19 2004 - 16:27:08 PDT)
    - Re: AMBER: A question on AMBER8 installation Hwankyu Lee (Tue Oct 19 2004 - 21:12:20 PDT)
    - Re: AMBER: A question on AMBER8 installation David A. Case (Tue Oct 19 2004 - 22:04:36 PDT)
- Re: AMBER: A question on AMBER8 installation Robert Duke (Wed Oct 20 2004 - 05:35:00 PDT)
AMBER: Plot B-factor extracted from PDB file Xin Hu (Wed Oct 13 2004 - 07:41:29 PDT)
AMBER: MMPBSA PB parameters - PARSE implementation in Amber Marc Baaden (Wed Oct 13 2004 - 10:42:34 PDT)
AMBER: Question about Amino acid mutations sachin patil (Wed Oct 13 2004 - 16:03:22 PDT)
AMBER: errors in SGI Xiao He (Thu Oct 14 2004 - 00:08:42 PDT)
- AMBER: Problem with EDIT (AMBER 5) Daniel Wetzler (Thu Oct 14 2004 - 04:53:45 PDT)
  - Re: AMBER: Problem with EDIT (AMBER 5) Daniel Wetzler (Thu Oct 14 2004 - 05:23:32 PDT)
- Re: AMBER: errors in SGI David A. Case (Thu Oct 14 2004 - 08:04:24 PDT)
  - AMBER: Amber8 - Energy Calculations Nhat-hang Duong (Thu Oct 14 2004 - 08:53:29 PDT)
    - Re: AMBER: Amber8 - Energy Calculations David A. Case (Thu Oct 14 2004 - 10:55:38 PDT)
  - Re: Re: AMBER: errors in SGI Xiao He (Thu Oct 14 2004 - 09:09:40 PDT)
    - Re: Re: AMBER: errors in SGI David A. Case (Thu Oct 14 2004 - 09:33:32 PDT)
    - RE: Re: AMBER: errors in SGI Ross Walker (Thu Oct 14 2004 - 09:34:46 PDT)
AMBER: modes analysis in ptraj Vlad Cojocaru (Thu Oct 14 2004 - 05:13:14 PDT)
- Re: AMBER: modes analysis in ptraj David A. Case (Fri Oct 15 2004 - 08:18:50 PDT)
AMBER: distance between images riccardo nifosi (Thu Oct 14 2004 - 07:56:40 PDT)
- Re: AMBER: distance between images Thomas E. Cheatham, III (Thu Oct 14 2004 - 08:51:33 PDT)
AMBER: mm-pbsa problem Dawei Zhang (Thu Oct 14 2004 - 07:36:03 PDT)
AMBER: amber8 compilation on AIX (regatta) SEKIJIMA Masakazu (Thu Oct 14 2004 - 06:41:40 PDT)
- Re: AMBER: amber8 compilation on AIX (regatta) David A. Case (Thu Oct 14 2004 - 10:36:28 PDT)
Re: AMBER: distance between images Bill Ross (Thu Oct 14 2004 - 08:09:11 PDT)
AMBER: (no subject) HL Eastwood (Thu Oct 14 2004 - 09:33:34 PDT)
AMBER: Problem with installing Amber8: Where are the MK libraries? HL Eastwood (Thu Oct 14 2004 - 09:34:54 PDT)
- RE: AMBER: Problem with installing Amber8: Where are the MK libraries? Ross Walker (Thu Oct 14 2004 - 10:00:02 PDT)
  - RE: AMBER: Problem with installing Amber8: Where are the MK libraries? HL Eastwood (Thu Oct 14 2004 - 10:42:54 PDT)
    - RE: AMBER: Problem with installing Amber8: Where are the MK libraries? Ross Walker (Thu Oct 14 2004 - 11:06:52 PDT)
    - Re: AMBER: Problem with installing Amber8: Where are the MK libraries? Atro Tossavainen (Thu Oct 14 2004 - 23:24:13 PDT)
    - Re: AMBER: Problem with installing Amber8: Where are the MK libraries? Atro Tossavainen (Fri Oct 15 2004 - 00:13:55 PDT)
    - RE: AMBER: Problem with installing Amber8: Where are the MK libraries? Ross Walker (Fri Oct 15 2004 - 00:29:47 PDT)
    - RE: AMBER: Problem with installing Amber8: Where are the MK libraries? Ross Walker (Fri Oct 15 2004 - 00:26:32 PDT)
    - Re: AMBER: Problem with installing Amber8: Where are the MK libraries? Atro Tossavainen (Fri Oct 15 2004 - 02:59:29 PDT)
    - Re: AMBER: Amber8: ifort 8.0.046 Woo hoo! HL Eastwood (Fri Oct 15 2004 - 03:36:57 PDT)
    - Re: AMBER: Amber8: ifort 8.0.046 Woo hoo! Atro Tossavainen (Fri Oct 15 2004 - 03:55:27 PDT)
    - Re: AMBER: Amber8: ifort 8.0.046 Woo hoo! Atro Tossavainen (Fri Oct 15 2004 - 05:38:59 PDT)
    - AMBER: pmemd and ifort 8.1 Niko Jukarainen (Fri Oct 15 2004 - 06:14:03 PDT)
    - Re: AMBER: pmemd and ifort 8.1 Robert Duke (Fri Oct 15 2004 - 10:10:08 PDT)
- Re: AMBER: Problem with installing Amber8: Where are the MK libraries? Andreas Svrcek-Seiler (Thu Oct 14 2004 - 10:42:35 PDT)
AMBER: Use of intel compilers v8.1 for Amber 8. Ross Walker (Thu Oct 14 2004 - 11:13:15 PDT)
AMBER: normal mode analysis after energy minimizaiton using sander xiaowei li (Thu Oct 14 2004 - 14:57:30 PDT)
- Re: AMBER: normal mode analysis after energy minimizaiton using sander David A. Case (Thu Oct 14 2004 - 16:35:01 PDT)
AMBER: Curves 5.3 Mu Yuguang $Dr$ (Thu Oct 14 2004 - 19:57:57 PDT)
AMBER: Amber 8 - OS support. Poh-Guan Khoo (Thu Oct 14 2004 - 22:54:27 PDT)
AMBER: question about molsurf Xiao He (Fri Oct 15 2004 - 01:13:05 PDT)
- Re: AMBER: question about molsurf David A. Case (Fri Oct 15 2004 - 08:28:10 PDT)
- Re: AMBER: question about molsurf Chris Page (Thu Nov 25 2004 - 10:45:28 PST)
AMBER: difference in GBSOL in amber7 and amber8 Xiao He (Fri Oct 15 2004 - 04:11:11 PDT)
- Re: AMBER: difference in GBSOL in amber7 and amber8 David A. Case (Fri Oct 15 2004 - 08:07:04 PDT)
AMBER: Trajectory corruption Steve Seibold (Fri Oct 15 2004 - 06:48:50 PDT)
- Re: AMBER: Trajectory corruption Carlos Simmerling (Fri Oct 15 2004 - 07:54:14 PDT)
- Re: AMBER: Trajectory corruption Adrian E. Roitberg (Fri Oct 15 2004 - 10:06:23 PDT)
Re: AMBER: Trajectory corruption Bill Ross (Fri Oct 15 2004 - 11:00:59 PDT)
AMBER: from gaussian to antechamber Cai, Yufeng (Fri Oct 15 2004 - 11:14:48 PDT)
- Re: AMBER: from gaussian to antechamber Robyn Ayscue (Fri Oct 15 2004 - 11:41:56 PDT)
AMBER: changepot Cai, Yufeng (Fri Oct 15 2004 - 11:33:08 PDT)
- Re: AMBER: changepot & mol2 file FyD (Fri Oct 15 2004 - 11:59:46 PDT)
AMBER: H bond calculation of CHARMM trajactory using PTRAJ anshul.imtech.res.in (Fri Oct 15 2004 - 21:59:33 PDT)
- Re: AMBER: H bond calculation of CHARMM trajactory using PTRAJ Thomas E. Cheatham, III (Wed Oct 20 2004 - 07:16:50 PDT)
AMBER: error in mm_pbsa Xiao He (Sat Oct 16 2004 - 02:12:41 PDT)
- Re: AMBER: error in mm_pbsa Wu Yingliang (Sat Oct 16 2004 - 02:52:47 PDT)
- Re: AMBER: error in mm_pbsa Holger Gohlke (Sat Oct 16 2004 - 06:53:36 PDT)
  - Re: Re: AMBER: error in mm_pbsa Xiao He (Sat Oct 16 2004 - 08:40:17 PDT)
AMBER: amber 8 error Abd Ghani Abd Aziz (Sat Oct 16 2004 - 02:19:38 PDT)
- RE: AMBER: amber 8 error Ross Walker (Sat Oct 16 2004 - 22:20:34 PDT)
AMBER: amber 8 parallel problem Abd Ghani Abd Aziz (Sat Oct 16 2004 - 03:47:44 PDT)
- RE: AMBER: amber 8 parallel problem Ross Walker (Sat Oct 16 2004 - 22:28:51 PDT)
- RE: AMBER: amber 8 parallel problem Ross Walker (Sun Oct 17 2004 - 11:05:33 PDT)
Re: AMBER: problems with dihedrals - extended information Petr Kulhanek (Sun Oct 17 2004 - 08:39:31 PDT)
- Re: AMBER: problems with dihedrals - extended information David A. Case (Mon Oct 18 2004 - 10:42:50 PDT)
- Re: AMBER: problems with dihedrals - extended information Bill Ross (Mon Oct 18 2004 - 11:04:33 PDT)
AMBER: problem with antechamber Cai, Yufeng (Sun Oct 17 2004 - 19:04:28 PDT)
- Re: AMBER: problem with antechamber David A. Case (Mon Oct 18 2004 - 13:14:29 PDT)
AMBER: More AMBER 8 compilation problems on OSF1 4.0F Atro Tossavainen (Mon Oct 18 2004 - 01:08:30 PDT)
- Re: AMBER: More AMBER 8 compilation problems on OSF1 4.0F David A. Case (Mon Oct 18 2004 - 08:59:58 PDT)
  - Re: AMBER: More AMBER 8 compilation problems on OSF1 4.0F Atro Tossavainen (Mon Oct 18 2004 - 23:21:57 PDT)
    - Re: AMBER: More AMBER 8 compilation problems on OSF1 4.0F M. L. Dodson (Tue Oct 19 2004 - 05:22:32 PDT)
    - Re: AMBER: More AMBER 8 compilation problems on OSF1 4.0F Atro Tossavainen (Tue Oct 19 2004 - 05:39:21 PDT)
    - Re: AMBER: More AMBER 8 compilation problems on OSF1 4.0F David A. Case (Tue Oct 19 2004 - 07:48:52 PDT)
    - AMBER: Sander-7 for Win32 Vlad (Tue Oct 19 2004 - 16:11:38 PDT)
    - Re: AMBER: Sander-7 for Win32 David A. Case (Wed Oct 20 2004 - 16:03:49 PDT)
Re: AMBER: about AM1-BCC charge method Natasja Brooijmans (Mon Oct 18 2004 - 06:38:11 PDT)
- Re: Re: AMBER: about AM1-BCC charge method Xiao He (Mon Oct 18 2004 - 06:59:43 PDT)
AMBER: Calculating H-Bond networks using ptraj Thomas Steinbrecher (Mon Oct 18 2004 - 07:12:05 PDT)
AMBER: file corruption with ptraj Steve Seibold (Mon Oct 18 2004 - 08:10:51 PDT)
- Re: AMBER: file corruption with ptraj Thomas E. Cheatham, III (Mon Oct 18 2004 - 08:42:02 PDT)
- Re: AMBER: file corruption with ptraj cailliez (Mon Oct 18 2004 - 08:32:32 PDT)
AMBER: const-P MD at high T MURAT CETINKAYA (Mon Oct 18 2004 - 08:27:49 PDT)
- Re: AMBER: const-P MD at high T Carlos Simmerling (Mon Oct 18 2004 - 09:25:52 PDT)
- Re: AMBER: const-P MD at high T MURAT CETINKAYA (Mon Oct 18 2004 - 09:52:11 PDT)
  - Re: AMBER: const-P MD at high T Carlos Simmerling (Mon Oct 18 2004 - 10:22:48 PDT)
- Re: AMBER: const-P MD at high T Bill Ross (Mon Oct 18 2004 - 12:16:26 PDT)
Re: AMBER: const-P MD at high T Bill Ross (Mon Oct 18 2004 - 10:47:58 PDT)
- Re: AMBER: const-P MD at high T MURAT CETINKAYA (Mon Oct 18 2004 - 11:13:07 PDT)
  - Re: AMBER: const-P MD at high T Carlos Simmerling (Mon Oct 18 2004 - 11:29:35 PDT)
- Re: AMBER: const-P MD at high T Bill Ross (Mon Oct 18 2004 - 11:26:26 PDT)
AMBER: question on NAB ioana.pegasus.arc.nasa.gov (Mon Oct 18 2004 - 14:18:19 PDT)
- Re: AMBER: question on NAB David A. Case (Tue Oct 19 2004 - 08:06:50 PDT)
AMBER: question on NMR restrain 卢强 (Mon Oct 18 2004 - 15:55:54 PDT)
- Re: AMBER: question on NMR restrain David A. Case (Mon Oct 18 2004 - 18:30:30 PDT)
AMBER: error in using AM1-BCC charge by antechamber Xiao He (Mon Oct 18 2004 - 21:22:04 PDT)
AMBER: BOND energy during minimisation cailliez (Tue Oct 19 2004 - 00:53:47 PDT)
- Re: AMBER: BOND energy during minimisation Stef (Tue Oct 19 2004 - 01:35:05 PDT)
- Re: AMBER: BOND energy during minimisation Carlos Simmerling (Tue Oct 19 2004 - 04:21:28 PDT)
- Re: AMBER: BOND energy during minimisation David A. Case (Tue Oct 19 2004 - 07:59:46 PDT)
- Re: AMBER: BOND energy during minimisation cailliez (Tue Oct 19 2004 - 09:12:55 PDT)
  - Re: AMBER: BOND energy during minimisation Carlos Simmerling (Tue Oct 19 2004 - 10:33:52 PDT)
- Re: AMBER: BOND energy during minimisation cailliez (Wed Oct 20 2004 - 00:16:26 PDT)
AMBER: amber 8 error Abd Ghani Abd Aziz (Tue Oct 19 2004 - 01:14:24 PDT)
- Re: AMBER: amber 8 error Abd Ghani Bin Abd Aziz (Sat Oct 02 2004 - 02:26:10 PDT)
- Re: AMBER: amber 8 error Andreas Svrcek-Seiler (Tue Oct 19 2004 - 02:00:59 PDT)
  - Re: AMBER: amber 8 error Atro Tossavainen (Tue Oct 19 2004 - 03:23:23 PDT)
- Re: AMBER: amber 8 error Carlos Simmerling (Tue Oct 19 2004 - 04:22:37 PDT)
AMBER: MAXMASK problem Qiang Lu (Tue Oct 19 2004 - 10:19:54 PDT)
- Re: AMBER: MAXMASK problem David A. Case (Tue Oct 19 2004 - 14:10:29 PDT)
  - Re: AMBER: MAXMASK problem Qiang Lu (Tue Oct 19 2004 - 15:25:03 PDT)
AMBER: About STD in NMODE Xiao He (Wed Oct 20 2004 - 09:06:15 PDT)
AMBER: International PhD Symppozium "DECODING NATURE: HIERARCHY OF INTERACTIONS" Vlad Cojocaru (Wed Oct 20 2004 - 09:10:43 PDT)
AMBER: Question about Xleap David LeBard (Wed Oct 20 2004 - 15:28:28 PDT)
- RE: AMBER: Question about Xleap Ross Walker (Fri Oct 22 2004 - 06:31:58 PDT)
AMBER: Wich CPU? Joachim Reichelt (Thu Oct 21 2004 - 02:34:26 PDT)
- Re: AMBER: Wich CPU? Robert Duke (Thu Oct 21 2004 - 06:23:48 PDT)
AMBER: add charge error message: Number of electrons is odd berry1027 Eric (Fri Oct 22 2004 - 01:45:30 PDT)
- Re: AMBER: add charge error message: Number of electrons is odd David A. Case (Fri Oct 22 2004 - 14:12:00 PDT)
AMBER: Jiten (Fri Oct 22 2004 - 08:17:15 PDT)
- AMBER: MD problem (very long parhabs endless runtime) Daniel Wetzler (Sat Oct 23 2004 - 06:05:49 PDT)
  - RE: AMBER: MD problem (very long parhabs endless runtime) Ross Walker (Sat Oct 23 2004 - 09:57:39 PDT)
    - Re: AMBER: MD problem (very long parhabs endless runtime) Daniel Wetzler (Sat Oct 23 2004 - 11:16:12 PDT)
    - Re: AMBER: MD problem (very long parhabs endless runtime) myang.vitamin.uni.cc (Sat Oct 23 2004 - 11:35:59 PDT)
    - RE: AMBER: MD problem (very long parhabs endless runtime) Ross Walker (Sat Oct 23 2004 - 11:53:22 PDT)
    - Re: AMBER: MD problem (very long parhabs endless runtime) Daniel Wetzler (Sun Oct 24 2004 - 02:40:09 PDT)
AMBER: No radius for F atom in MM_PBSA Xiao He (Sun Oct 24 2004 - 06:30:48 PDT)
Re: AMBER: Amber: what different? David A. Case (Sun Oct 24 2004 - 07:17:47 PDT)
AMBER: continue for No radius for F atom in MM_PBSA Xiao He (Sun Oct 24 2004 - 07:40:21 PDT)
- Re: AMBER: continue for No radius for F atom in MM_PBSA Holger Gohlke (Sun Oct 24 2004 - 13:06:15 PDT)
AMBER: parallel of sander_classic Xioling Chuang (Sun Oct 24 2004 - 22:57:16 PDT)
- Re: AMBER: parallel of sander_classic David A. Case (Mon Oct 25 2004 - 06:17:44 PDT)
- RE: AMBER: parallel of sander_classic Ross Walker (Mon Oct 25 2004 - 06:15:58 PDT)
- Re: AMBER: parallel of sander_classic Michael Crowley (Tue Oct 26 2004 - 13:03:36 PDT)
AMBER: PMF tang kwa (Mon Oct 25 2004 - 04:59:22 PDT)
- Re: AMBER: PMF Carlos Simmerling (Mon Oct 25 2004 - 05:14:19 PDT)
AMBER: long minimization in sander MURAT CETINKAYA (Mon Oct 25 2004 - 07:53:14 PDT)
- RE: AMBER: long minimization in sander Ross Walker (Mon Oct 25 2004 - 08:11:29 PDT)
Re: AMBER: long minimization in sander Bill Ross (Mon Oct 25 2004 - 08:09:49 PDT)
- Re: AMBER: long minimization in sander MURAT CETINKAYA (Mon Oct 25 2004 - 08:32:10 PDT)
  - RE: AMBER: long minimization in sander Ross Walker (Mon Oct 25 2004 - 17:03:19 PDT)
- Re: AMBER: long minimization in sander Bill Ross (Mon Oct 25 2004 - 13:30:32 PDT)
AMBER: MM_PBSA reproduction of literature values and accuracy Karl N. Kirschner (Mon Oct 25 2004 - 10:41:34 PDT)
- Re: AMBER: MM_PBSA reproduction of literature values and accuracy Carlos Simmerling (Mon Oct 25 2004 - 10:53:50 PDT)
  - Re: AMBER: MM_PBSA reproduction of literature values and accuracy Karl N. Kirschner (Tue Oct 26 2004 - 15:35:19 PDT)
    - Re: AMBER: MM_PBSA reproduction of literature values and accuracy Carlos Simmerling (Tue Oct 26 2004 - 15:51:16 PDT)
- Re: AMBER: MM_PBSA reproduction of literature values and accuracy Thomas Steinbrecher (Tue Oct 26 2004 - 00:05:51 PDT)
AMBER: pure aromatic? Cai, Yufeng (Mon Oct 25 2004 - 14:16:06 PDT)
AMBER: No skew or curtosis when zero variance in moment Xiao He (Mon Oct 25 2004 - 21:55:08 PDT)
AMBER: Continued:No skew or curtosis when zero variance in moment Xiao He (Mon Oct 25 2004 - 22:02:31 PDT)
- Re: AMBER: Continued:No skew or curtosis when zero variance in moment Elijah Gregory (Tue Oct 26 2004 - 06:48:55 PDT)
AMBER: AMBER 8 default is now HIS->HIE and not HIS->HID - typo? Chris Moth (Tue Oct 26 2004 - 13:24:05 PDT)
- Re: AMBER: AMBER 8 default is now HIS->HIE and not HIS->HID - typo? David A. Case (Thu Oct 28 2004 - 09:50:34 PDT)
AMBER: AM1-BCC charges Xin Hu (Tue Oct 26 2004 - 17:19:04 PDT)
- Re: AMBER: AM1-BCC charges Oliver Hucke (Tue Oct 26 2004 - 18:29:02 PDT)
AMBER: how to neutralize the peptide Ye Mei (Tue Oct 26 2004 - 19:10:23 PDT)
- Re: AMBER: how to neutralize the peptide Joseph Nachman (Wed Oct 27 2004 - 10:04:50 PDT)
- Re: AMBER: how to neutralize the peptide Chris Moth (Wed Oct 27 2004 - 09:57:23 PDT)
AMBER: questions regarding JTREE Annette Höglund (Wed Oct 27 2004 - 08:37:06 PDT)
Re: AMBER: questions regarding JTREE Bill Ross (Wed Oct 27 2004 - 10:53:39 PDT)
AMBER: getting new box info Vincent Bisetty (Thu Oct 28 2004 - 07:25:51 PDT)
- Re: AMBER: getting new box info David A. Case (Thu Oct 28 2004 - 07:39:07 PDT)
  - Re: AMBER: getting new box info Melinda Layten (Thu Oct 28 2004 - 08:46:57 PDT)
AMBER: a question on ntwx and ntwr scopio (Thu Oct 28 2004 - 07:42:14 PDT)
- Re: AMBER: a question on ntwx and ntwr Carlos Simmerling (Thu Oct 28 2004 - 08:50:10 PDT)
AMBER: solvation free energies using mmpbsa Karl N. Kirschner (Thu Oct 28 2004 - 10:15:38 PDT)
- Re: AMBER: solvation free energies using mmpbsa FyD (Thu Oct 28 2004 - 10:33:34 PDT)
- Re: AMBER: solvation free energies using mmpbsa Ray Luo (Wed Oct 27 2004 - 21:06:07 PDT)
AMBER: icc 8.0 built antechamber Scott Brozell (Thu Oct 28 2004 - 10:24:02 PDT)
AMBER: trajectory file question? opitz.che.udel.edu (Thu Oct 28 2004 - 11:15:12 PDT)
- Re: AMBER: trajectory file question? Melinda Layten (Thu Oct 28 2004 - 12:35:17 PDT)
AMBER: question about ptraj's Mask Kun Song (Thu Oct 28 2004 - 13:52:08 PDT)
- Re: AMBER: question about ptraj's Mask Viktor Hornak (Thu Oct 28 2004 - 14:03:45 PDT)
  - Re: AMBER: question about ptraj's Mask Kun Song (Thu Oct 28 2004 - 14:10:34 PDT)
AMBER: sander gets stuck MURAT CETINKAYA (Fri Oct 29 2004 - 07:32:22 PDT)
- RE: AMBER: sander gets stuck Ross Walker (Fri Oct 29 2004 - 07:52:43 PDT)
- RE: AMBER: sander gets stuck MURAT CETINKAYA (Fri Oct 29 2004 - 08:11:15 PDT)
AMBER: Settings about frozen atoms in sander Xiao He (Fri Oct 29 2004 - 08:17:07 PDT)
- Re: AMBER: Settings about frozen atoms in sander Oliver Hucke (Fri Oct 29 2004 - 09:54:10 PDT)
- Re: AMBER: Settings about frozen atoms in sander Jiten (Fri Oct 29 2004 - 09:05:36 PDT)
AMBER: amber7 test on osx Knut Langsetmo (Fri Oct 29 2004 - 11:03:25 PDT)
- Re: AMBER: amber7 test on osx Michael Crowley (Fri Oct 29 2004 - 11:31:09 PDT)
- RE: AMBER: amber7 test on osx Ross Walker (Fri Oct 29 2004 - 11:38:31 PDT)
Re: AMBER: Settings about frozen atoms in sander Bill Ross (Fri Oct 29 2004 - 11:44:41 PDT)
AMBER: RSM fluctuation & residues bybaker.itsa.ucsf.edu (Fri Oct 29 2004 - 13:21:42 PDT)
AMBER: sander error Xiao He (Fri Oct 29 2004 - 23:49:17 PDT)
- Re: AMBER: sander error Jiten (Sat Oct 30 2004 - 00:58:33 PDT)
AMBER: MD after partially solvated Xiao He (Sat Oct 30 2004 - 19:52:51 PDT)
- Re: AMBER: MD after partially solvated Carlos Simmerling (Sat Oct 30 2004 - 20:11:27 PDT)
AMBER: RSM & ptraj bybaker.itsa.ucsf.edu (Sat Oct 30 2004 - 23:13:10 PDT)
- Re: AMBER: RSM & ptraj Carlos Simmerling (Sat Oct 30 2004 - 23:25:14 PDT)
- Re: AMBER: RSM & ptraj Elijah Gregory (Sat Oct 30 2004 - 23:29:23 PDT)
AMBER: RSM fluctuation by residues bybaker.itsa.ucsf.edu (Sat Oct 30 2004 - 23:22:53 PDT)
AMBER: ptraj questions Amber admin (Sun Oct 31 2004 - 06:59:51 PST)
- Re: AMBER: ptraj questions Carlos Simmerling (Sun Oct 31 2004 - 07:45:21 PST)
- Re: AMBER: ptraj questions Oliver Hucke (Mon Nov 01 2004 - 09:59:06 PST)
  - Re: AMBER: ptraj questions Carlos Simmerling (Sun Oct 31 2004 - 09:06:54 PST)
  - Re: AMBER: ptraj questions Viktor Hornak (Sun Oct 31 2004 - 11:39:48 PST)
  - AMBER: Building the parallel version in AMBER 8 and GIBBS Ilyas Yildirim (Tue Nov 09 2004 - 19:03:54 PST)
    - Re: AMBER: Building the parallel version in AMBER 8 and GIBBS David A. Case (Tue Nov 09 2004 - 21:07:05 PST)
AMBER: Re: RSM & ptraj bybaker.itsa.ucsf.edu (Sun Oct 31 2004 - 10:43:41 PST)
AMBER: Amber7 installation error on Solaris 9 Joe Nolan (Mon Nov 01 2004 - 12:03:25 PST)
- Re: AMBER: Amber7 installation error on Solaris 9 David A. Case (Mon Nov 01 2004 - 13:11:24 PST)
AMBER: MD & folding bybaker.itsa.ucsf.edu (Mon Nov 01 2004 - 23:03:42 PST)
- Re: AMBER: MD & folding Bimo Ario Tejo (Mon Nov 01 2004 - 23:26:09 PST)
AMBER: about FEP Xiao He (Tue Nov 02 2004 - 00:29:43 PST)
- Re: AMBER: about FEP Annette Ho (Tue Nov 02 2004 - 02:44:03 PST)
  - Re: AMBER: about FEP david.evans.ulsop.ac.uk (Tue Nov 02 2004 - 03:28:44 PST)
    - Re: AMBER: about FEP Annette Höglund (Tue Nov 02 2004 - 03:58:27 PST)
    - Re: AMBER: about FEP david.evans.ulsop.ac.uk (Tue Nov 02 2004 - 04:42:25 PST)
    - Re: AMBER: about FEP Ray Luo (Tue Nov 02 2004 - 06:05:41 PST)
    - Re: Re: AMBER: about FEP Xiao He (Tue Nov 02 2004 - 19:18:22 PST)
    - Re: Re: AMBER: about FEP Thomas Steinbrecher (Wed Nov 03 2004 - 00:07:51 PST)
    - AMBER: FEP and charges Annette Höglund (Wed Nov 03 2004 - 03:59:16 PST)
    - Re: AMBER: FEP and charges Chunhu Tan (Thu Nov 04 2004 - 14:23:16 PST)
  - Re: AMBER: about FEP David A. Case (Tue Nov 02 2004 - 08:19:27 PST)
AMBER: ESP fitting from Gaussian03 cube files Ye Mei (Tue Nov 02 2004 - 01:01:40 PST)
AMBER: MD & folding bybaker.itsa.ucsf.edu (Tue Nov 02 2004 - 13:31:31 PST)
- Re: AMBER: MD & folding Carlos Simmerling (Tue Nov 02 2004 - 15:03:41 PST)
AMBER: MD & folding bybaker.itsa.ucsf.edu (Tue Nov 02 2004 - 16:05:00 PST)
AMBER: Clustering in PTRAJ Stephen.Titmuss.csiro.au (Tue Nov 02 2004 - 17:38:31 PST)
AMBER: SANDER BOMB in subroutine nonbond_list Marc Perea (Tue Nov 02 2004 - 04:45:34 PST)
- Re: AMBER: SANDER BOMB in subroutine nonbond_list David A. Case (Wed Nov 03 2004 - 10:05:15 PST)
AMBER: basis set Yanze Zhang (Tue Nov 02 2004 - 21:57:19 PST)
- Re: AMBER: basis set FyD (Fri Nov 05 2004 - 11:55:06 PST)
: AMBER: basis set ying xiong (Tue Nov 02 2004 - 22:43:52 PST)
AMBER: ESPGEN problems to read G03 output files Hernán Alonso (Tue Nov 02 2004 - 23:03:12 PST)
- Re: AMBER: ESPGEN problems to read G03 output files Jiten (Wed Nov 03 2004 - 00:33:04 PST)
- Re: AMBER: ESPGEN problems to read G03 output files FyD (Fri Nov 05 2004 - 11:56:52 PST)
AMBER: Extracting torsional angles for specific conformation Darian, Eva (Wed Nov 03 2004 - 10:12:33 PST)
AMBER: gaff parameter ambiguities Anthony Fejes (Wed Nov 03 2004 - 15:16:07 PST)
AMBER: MD simulation at pH=1 Kijeong Kwac (Wed Nov 03 2004 - 20:20:01 PST)
AMBER: Fluctuation in temperature anshul.imtech.res.in (Thu Nov 04 2004 - 14:09:58 PST)
- Re: AMBER: Fluctuation in temperature Oliver Hucke (Thu Nov 04 2004 - 10:14:36 PST)
- RE: AMBER: Fluctuation in temperature Ross Walker (Thu Nov 04 2004 - 12:05:57 PST)
AMBER: H-bonded waters selection pl (Thu Nov 04 2004 - 04:41:32 PST)
- Re: AMBER: H-bonded waters selection Thomas E. Cheatham, III (Thu Nov 04 2004 - 21:05:24 PST)
  - Re: AMBER: H-bonded waters selection pl (Fri Nov 05 2004 - 02:42:01 PST)
AMBER: gaussian command line Yanze Zhang (Thu Nov 04 2004 - 11:40:27 PST)
- Re: AMBER: gaussian command line FyD (Fri Nov 05 2004 - 12:02:45 PST)
AMBER: Kara Wald (Thu Nov 04 2004 - 13:05:42 PST)
AMBER: Re: Antechamber Kara Wald (Thu Nov 04 2004 - 13:13:28 PST)
- RE: AMBER: Re: Antechamber Ross Walker (Thu Nov 04 2004 - 13:31:48 PST)
  - Re: AMBER: Re: Antechamber Kara Wald (Mon Nov 08 2004 - 13:49:13 PST)
AMBER: ptraj problem Abd Ghani Abd Aziz (Thu Nov 04 2004 - 17:53:39 PST)
- Re: AMBER: ptraj problem Thomas E. Cheatham, III (Thu Nov 04 2004 - 18:13:51 PST)
  - Re: AMBER: ptraj problem Abd Ghani Abd Aziz (Thu Nov 04 2004 - 18:39:37 PST)
AMBER: constructing a small colecule mathew k varghese (Thu Nov 04 2004 - 20:41:58 PST)
- Re: AMBER: constructing a small colecule david.evans.ulsop.ac.uk (Fri Nov 05 2004 - 01:53:07 PST)
AMBER: translational and rotational entropy hj zou (Thu Nov 04 2004 - 22:48:22 PST)
- Re: AMBER: translational and rotational entropy Andreas Svrcek-Seiler (Thu Nov 04 2004 - 23:43:00 PST)
AMBER: end point contribution in MCTI Cai, Yufeng (Fri Nov 05 2004 - 06:12:11 PST)
- Re: AMBER: end point contribution in MCTI David A. Case (Fri Nov 05 2004 - 08:36:31 PST)
AMBER: Amber7 compilation error Joe Nolan (Fri Nov 05 2004 - 07:17:39 PST)
- Re: AMBER: Amber7 compilation error David A. Case (Fri Nov 05 2004 - 08:50:01 PST)
AMBER: Problems using mm_pbsa.perl Daniel Wetzler (Fri Nov 05 2004 - 08:28:15 PST)
- Re: AMBER: Problems using mm_pbsa.perl Holger Gohlke (Fri Nov 05 2004 - 08:41:39 PST)
AMBER: ptraj radial Sandro Fornili (Fri Nov 05 2004 - 08:28:57 PST)
AMBER: Minimization failure: 1cbn Harianto (Fri Nov 05 2004 - 09:16:30 PST)
- Re: AMBER: Minimization failure: 1cbn Bimo Ario Tejo (Fri Nov 05 2004 - 14:12:03 PST)
- Re: AMBER: Minimization failure: 1cbn Bill Ross (Fri Nov 05 2004 - 14:32:41 PST)
AMBER: where is the VDW radius? Cai, Yufeng (Sat Nov 06 2004 - 07:42:29 PST)
- Re: AMBER: where is the VDW radius? Oliver Hucke (Sat Nov 06 2004 - 11:16:00 PST)
AMBER: positive VDWAALS John (Sun Nov 07 2004 - 10:11:13 PST)
- Re: AMBER: positive VDWAALS Michael Crowley (Sun Nov 07 2004 - 13:51:26 PST)
AMBER: mm_PBSA: problems calculating molecular surface for some snapshots Magne Olufsen (Mon Nov 08 2004 - 01:50:39 PST)
AMBER: time-averaged restraints John (Mon Nov 08 2004 - 12:21:51 PST)
AMBER: amber 7 nmode on osx Knut Langsetmo (Mon Nov 08 2004 - 15:26:26 PST)
AMBER: salt bridge detection Ye Mei (Mon Nov 08 2004 - 18:33:21 PST)
AMBER: error message about the input file of sander Ru-Zhen Li (Mon Nov 08 2004 - 18:23:23 PST)
- Re: AMBER: error message about the input file of sander Michael Crowley (Mon Nov 08 2004 - 22:48:03 PST)
  - Re: AMBER: error message about the input file of sander Ru-Zhen Li (Tue Nov 09 2004 - 04:20:40 PST)
  - Re: AMBER: error message about the input file of sander Ru-Zhen Li (Tue Nov 09 2004 - 04:49:26 PST)
    - RE: AMBER: error message about the input file of sander Ross Walker (Tue Nov 09 2004 - 09:44:31 PST)
    - Re: AMBER: error message about the input file of sander Ru-Zhen Li (Tue Nov 09 2004 - 12:33:57 PST)
AMBER: Problem with Water solute during MD Daniel Wetzler (Tue Nov 09 2004 - 05:20:13 PST)
- Re: AMBER: Problem with Water solute during MD David A. Case (Tue Nov 09 2004 - 08:06:31 PST)
  - Re: AMBER: Problem with Water solute during MD Daniel Wetzler (Wed Nov 10 2004 - 02:19:11 PST)
    - Re: AMBER: Problem with Water solute during MD David A. Case (Wed Nov 10 2004 - 07:42:50 PST)
- Re: AMBER: Problem with Water solute during MD Bill Ross (Wed Nov 10 2004 - 07:20:23 PST)
AMBER: Leap Greg Kellogg (Tue Nov 09 2004 - 08:24:43 PST)
- Re: AMBER: Leap David A. Case (Tue Nov 09 2004 - 09:00:38 PST)
Re: AMBER: Problem with Water solute during MD Bill Ross (Tue Nov 09 2004 - 09:36:22 PST)
AMBER: IBELLY Harianto (Tue Nov 09 2004 - 12:40:58 PST)
AMBER: Solaris f77 Machine file for Amber7? Joe Nolan (Tue Nov 09 2004 - 14:13:58 PST)
- Re: AMBER: Solaris f77 Machine file for Amber7? David A. Case (Tue Nov 09 2004 - 16:57:24 PST)
- Re: AMBER: Solaris f77 Machine file for Amber7? Joe Nolan (Wed Nov 10 2004 - 08:45:50 PST)
  - Re: AMBER: Solaris f77 Machine file for Amber7? David A. Case (Wed Nov 10 2004 - 09:07:13 PST)
- Re: AMBER: Solaris f77 Machine file for Amber7? Joe Nolan (Wed Nov 10 2004 - 13:11:44 PST)
  - Re: AMBER: Solaris f77 Machine file for Amber7? David A. Case (Wed Nov 10 2004 - 13:49:47 PST)
- Re: AMBER: Solaris f77 Machine file for Amber7? Joe Nolan (Wed Nov 10 2004 - 14:43:54 PST)
  - Re: AMBER: Solaris f77 Machine file for Amber7? David A. Case (Wed Nov 10 2004 - 16:15:32 PST)
- Re: AMBER: Solaris f77 Machine file for Amber7? Joe Nolan (Thu Nov 11 2004 - 10:50:06 PST)
- Re: AMBER: Solaris f77 Machine file for Amber7? Joe Nolan (Thu Nov 11 2004 - 14:00:33 PST)
AMBER: single strand simulation ding (Tue Nov 09 2004 - 16:12:17 PST)
- Re: AMBER: single strand simulation Thomas E. Cheatham, III (Tue Nov 09 2004 - 16:32:58 PST)
AMBER: AMBER Parameter Database Yanze Zhang (Wed Nov 10 2004 - 07:35:32 PST)
AMBER: parameter set Yanze Zhang (Wed Nov 10 2004 - 11:56:54 PST)
- Re: AMBER: parameter set David A. Case (Wed Nov 10 2004 - 12:10:40 PST)
Re: AMBER: parameter set Bill Ross (Wed Nov 10 2004 - 12:17:25 PST)
- AMBER: About the parameter names Ilyas Yildirim (Wed Nov 10 2004 - 13:20:31 PST)
  - Re: AMBER: About the parameter names David A. Case (Wed Nov 10 2004 - 13:50:58 PST)
RE: AMBER: Can parallel simulation have a nonperiodic boundary condition? Ross Walker (Wed Nov 10 2004 - 16:26:27 PST)
AMBER: ptraj MURAT CETINKAYA (Thu Nov 11 2004 - 13:19:45 PST)
AMBER: Solvation free energy of a charged molecule. Chunhu Tan (Thu Nov 11 2004 - 17:53:58 PST)
- Re: AMBER: Solvation free energy of a charged molecule. David A. Case (Fri Nov 12 2004 - 08:11:15 PST)
- Re: AMBER: Solvation free energy of a charged molecule. Chunhu Tan (Fri Nov 12 2004 - 10:43:32 PST)
AMBER: glibc version Ye Mei (Thu Nov 11 2004 - 22:04:00 PST)
- Re: AMBER: glibc version David A. Case (Fri Nov 12 2004 - 14:17:53 PST)
AMBER: AMBER 4 Manual? Ru-Zhen Li (Fri Nov 12 2004 - 09:02:16 PST)
- Re: AMBER: AMBER 4 Manual? David A. Case (Fri Nov 12 2004 - 14:10:42 PST)
AMBER: Energy change for isomerization reaction of cyclic peptide nlxc (Fri Nov 12 2004 - 10:03:00 PST)
- Re: AMBER: Energy change for isomerization reaction of cyclic peptide David A. Case (Fri Nov 12 2004 - 14:02:10 PST)
AMBER: a quick question about carnal Haijun Yang (Fri Nov 12 2004 - 12:51:17 PST)
Re: AMBER: a quick question about carnal Bill Ross (Fri Nov 12 2004 - 13:53:41 PST)
- Re: AMBER: a quick question about carnal Haijun Yang (Mon Nov 15 2004 - 09:31:53 PST)
AMBER: the energy difference between sander and nmode xiaowei li (Fri Nov 12 2004 - 13:52:57 PST)
- Re: AMBER: the energy difference between sander and nmode David A. Case (Fri Nov 12 2004 - 14:43:28 PST)
AMBER: xleap problems Kepa Koldo Burusco Goñi (Fri Nov 12 2004 - 11:33:42 PST)
- Re: AMBER: xleap problems Mark Williamson (Fri Nov 12 2004 - 15:58:05 PST)
- Re: AMBER: xleap problems Ilyas Yildirim (Fri Nov 12 2004 - 15:58:21 PST)
AMBER: Parameters for new residue? Satpal Virdee (Sat Nov 13 2004 - 11:34:27 PST)
- Re: AMBER: Parameters for new residue? David A. Case (Sat Nov 13 2004 - 17:30:39 PST)
AMBER: convert .pdb to .mol2 bybaker.itsa.ucsf.edu (Sat Nov 13 2004 - 20:35:45 PST)
- Re: AMBER: convert .pdb to .mol2 Ye Mei (Sat Nov 13 2004 - 20:57:32 PST)
AMBER: Babel bybaker.itsa.ucsf.edu (Sat Nov 13 2004 - 23:29:40 PST)
- Re: AMBER: Babel Carlos Simmerling (Sun Nov 14 2004 - 06:02:17 PST)
- Re: AMBER: Babel FyD (Mon Nov 15 2004 - 15:07:11 PST)
AMBER: nmode:Number of atoms in -p and -c files do not agree! myang.vitamin.uni.cc (Sun Nov 14 2004 - 18:20:25 PST)
- Re: AMBER: nmode:Number of atoms in -p and -c files do not agree! David A. Case (Mon Nov 15 2004 - 08:10:43 PST)
  - Re: AMBER: nmode:Number of atoms in -p and -c files do not agree! myang.vitamin.uni.cc (Mon Nov 15 2004 - 11:58:58 PST)
    - Re: AMBER: nmode:Number of atoms in -p and -c files do not agree! David A. Case (Mon Nov 15 2004 - 13:43:15 PST)
    - AMBER: ifort 8.0 Ilyas Yildirim (Mon Nov 15 2004 - 14:41:28 PST)
    - Re: AMBER: ifort 8.0 Jack Lei (Mon Nov 15 2004 - 14:46:01 PST)
    - RE: AMBER: ifort 8.0 Ross Walker (Wed Nov 17 2004 - 10:39:49 PST)
    - Re: AMBER: nmode:Number of atoms in -p and -c files do not agree! myang.vitamin.uni.cc (Mon Nov 15 2004 - 17:26:17 PST)
AMBER: restraintmask problem in ptraj Takanori TANAKA (Mon Nov 15 2004 - 03:06:23 PST)
- Re: AMBER: restraintmask problem in ptraj Viktor Hornak (Mon Nov 15 2004 - 05:37:24 PST)
AMBER: gibbs compilation error Nelson Fonseca (Mon Nov 15 2004 - 09:41:27 PST)
- Re: AMBER: gibbs compilation error David A. Case (Mon Nov 15 2004 - 10:18:12 PST)
AMBER: AMBER8 parallel job Emmanuel Giudice (Sun Nov 14 2004 - 23:39:50 PST)
AMBER: Re: Amber Re: Antechamber problems Kara Wald (Mon Nov 15 2004 - 13:05:19 PST)
AMBER: Can xleap to handle homology model altogether X-ray structure? Jack Lei (Mon Nov 15 2004 - 14:39:55 PST)
- AMBER: Can xleap handle homology model altogether with X-ray structure? Jack Lei (Mon Nov 15 2004 - 15:08:44 PST)
- Re: AMBER: Can xleap to handle homology model altogether X-ray structure? David A. Case (Tue Nov 16 2004 - 08:13:11 PST)
  - Re: AMBER: Can xleap to handle homology model altogether X-ray structure? Joachim Reichelt (Tue Nov 16 2004 - 09:42:02 PST)
    - AMBER: Problem with a single aminoacid as inhibitor Daniel Wetzler (Wed Nov 17 2004 - 03:54:04 PST)
    - Re: AMBER: Problem with a single aminoacid as inhibitor Carlos Simmerling (Wed Nov 17 2004 - 04:43:08 PST)
AMBER: AMBER8 compiling error under Itanium 2. qlu.notes.cc.sunysb.edu (Mon Nov 15 2004 - 16:39:36 PST)
- Re: AMBER: AMBER8 compiling error under Itanium 2. Ye Mei (Mon Nov 15 2004 - 17:46:52 PST)
  - Re: AMBER: AMBER8 compiling error under Itanium 2. Jack Lei (Tue Nov 16 2004 - 09:32:23 PST)
AMBER: constant pH simulations reference Sergio E. Wong (Mon Nov 15 2004 - 17:50:16 PST)
- Re: AMBER: constant pH simulations reference David A. Case (Mon Nov 15 2004 - 18:23:42 PST)
AMBER: ambpdb segmentation fault justin litchfield (Mon Nov 15 2004 - 18:57:14 PST)
- RE: AMBER: ambpdb segmentation fault Ross Walker (Wed Nov 17 2004 - 13:35:40 PST)
  - Re: AMBER: ambpdb segmentation fault justin litchfield (Wed Nov 17 2004 - 14:46:01 PST)
    - Re: AMBER: ambpdb segmentation fault justin litchfield (Sun Nov 21 2004 - 21:09:25 PST)
- Re: AMBER: ambpdb segmentation fault Bill Ross (Sun Nov 21 2004 - 21:34:13 PST)
FWD: RE: AMBER: xleap problems Kepa Koldo Burusco Goñi (Tue Nov 16 2004 - 02:56:40 PST)
- AMBER: SUSE 9.1 and AMBER 8 Ilyas Yildirim (Tue Nov 16 2004 - 03:12:16 PST)
  - Re: AMBER: SUSE 9.1 and AMBER 8 Andreas Svrcek-Seiler (Tue Nov 16 2004 - 05:10:44 PST)
  - INSTALLATION GUIDE FOR IFORT AND AMBER8 IN LINUX SUSE 9.1 ....Re: AMBER: SUSE 9.1 and AMBER 8 Cenk Andac (Tue Nov 16 2004 - 06:19:03 PST)
    - AMBER: Re: INSTALLATION GUIDE FOR IFORT AND AMBER8 IN LINUX SUSE 9.1 ....Re: AMBER: SUSE 9.1 and AMBER 8 Ilyas Yildirim (Wed Dec 01 2004 - 13:12:49 PST)
    - Re: AMBER: Re: INSTALLATION GUIDE FOR IFORT AND AMBER8 IN LINUX SUSE 9.1 ....Re: AMBER: SUSE 9.1 and AMBER 8 Cenk Andac (Wed Dec 01 2004 - 19:04:31 PST)
AMBER: How to compile the downloadable RESP in UNIX Yanze Zhang (Tue Nov 16 2004 - 07:33:03 PST)
- Re: AMBER: How to compile the downloadable RESP in UNIX Satpal Virdee (Tue Nov 16 2004 - 07:58:41 PST)
  - Re: AMBER: How to compile the downloadable RESP in UNIX Yanze Zhang (Wed Nov 17 2004 - 15:04:57 PST)
    - Re: AMBER: How to compile the downloadable RESP in UNIX Satpal Virdee (Thu Nov 18 2004 - 04:36:07 PST)
    - Re: AMBER: How to compile the downloadable RESP in UNIX Yanze Zhang (Thu Nov 18 2004 - 12:10:13 PST)
AMBER: restrained options Toshifumi Yui (Tue Nov 16 2004 - 08:42:22 PST)
AMBER: <dV/dL> fluctuations in TI Nelson Fonseca (Wed Nov 17 2004 - 03:39:01 PST)
- Re: AMBER: <dV/dL> fluctuations in TI Thomas Steinbrecher (Wed Nov 17 2004 - 05:06:40 PST)
- Re: AMBER: <dV/dL> fluctuations in TI Chunhu Tan (Thu Nov 18 2004 - 14:57:05 PST)
- Re: AMBER: <dV/dL> fluctuations in TI Chunhu Tan (Fri Nov 19 2004 - 11:07:03 PST)
AMBER: Problem with a single aminoacid as inhibitor Daniel Wetzler (Wed Nov 17 2004 - 03:59:12 PST)
- Re: AMBER: Problem with a single aminoacid as inhibitor david.evans.ulsop.ac.uk (Wed Nov 17 2004 - 04:55:58 PST)
  - Re: AMBER: Problem with a single aminoacid as inhibitor M. L. Dodson (Wed Nov 17 2004 - 07:29:26 PST)
    - Re: AMBER: Problem with a single aminoacid as inhibitor Daniel Wetzler (Wed Nov 17 2004 - 08:13:50 PST)
AMBER: Problem to update antechamber package. Guillaume Bollot (Wed Nov 17 2004 - 05:50:49 PST)
AMBER: RMS of energy in Minimization using SANDER Jack Lei (Wed Nov 17 2004 - 10:15:31 PST)
- RE: AMBER: RMS of energy in Minimization using SANDER Ross Walker (Wed Nov 17 2004 - 10:36:25 PST)
AMBER: Fifth European Workshop in Drug Design Andrea Tafi (Thu Nov 18 2004 - 04:35:02 PST)
AMBER: Diastereoisomers of ATP William Boxford (Thu Nov 18 2004 - 07:18:42 PST)
AMBER: calcium van der Waals parameters cailliez (Thu Nov 18 2004 - 08:53:23 PST)
- Re: AMBER: calcium van der Waals parameters Bill Ross (Mon Nov 22 2004 - 10:57:09 PST)
- Re: AMBER: calcium van der Waals parameters Piotr Cieplak (Mon Nov 22 2004 - 11:03:57 PST)
Re: AMBER: calcium van der Waals parameters Bill Ross (Thu Nov 18 2004 - 10:25:49 PST)
- Re: AMBER: calcium van der Waals parameters cailliez (Mon Nov 22 2004 - 09:10:30 PST)
AMBER: Problem with carnal on linux Sébastien Fiorucci (Fri Nov 19 2004 - 06:13:26 PST)
- RE: AMBER: Problem with carnal on linux Ross Walker (Fri Nov 19 2004 - 09:36:08 PST)
AMBER: SHAKE probelm Huang, Hai (Fri Nov 19 2004 - 08:25:24 PST)
- RE: AMBER: SHAKE probelm Ross Walker (Fri Nov 19 2004 - 09:35:18 PST)
- RE: AMBER: SHAKE probelm Huang, Hai (Fri Nov 19 2004 - 14:56:54 PST)
  - RE: AMBER: SHAKE probelm Ross Walker (Fri Nov 19 2004 - 15:09:05 PST)
- RE: AMBER: SHAKE probelm Huang, Hai (Tue Nov 23 2004 - 14:01:25 PST)
AMBER: amber8 compilation lucian livadaru (Fri Nov 19 2004 - 10:51:00 PST)
- RE: AMBER: amber8 compilation Ross Walker (Fri Nov 19 2004 - 11:20:00 PST)
  - RE: AMBER: amber8 compilation lucian livadaru (Mon Nov 22 2004 - 14:22:43 PST)
    - RE: AMBER: amber8 compilation Ross Walker (Mon Nov 22 2004 - 14:48:03 PST)
AMBER: leap compiling problem on a 64-bit machine xhu1.memphis.edu (Fri Nov 19 2004 - 11:13:22 PST)
- RE: AMBER: leap compiling problem on a 64-bit machine Ross Walker (Fri Nov 19 2004 - 11:32:01 PST)
  - Re: RE: AMBER: leap compiling problem on a 64-bit machine xhu1.memphis.edu (Fri Nov 19 2004 - 15:51:58 PST)
    - Re: RE: AMBER: leap compiling problem on a 64-bit machine Tomas Linhart (Fri Nov 19 2004 - 17:14:51 PST)
  - Re: RE: AMBER: leap compiling problem on a 64-bit machine xhu1.memphis.edu (Sat Nov 20 2004 - 12:19:27 PST)
    - Re: RE: AMBER: leap compiling problem on a 64-bit machine Tomas Linhart (Sat Nov 20 2004 - 14:15:44 PST)
  - Re: RE: AMBER: leap compiling problem on a 64-bit machine xhu1.memphis.edu (Sun Nov 21 2004 - 14:52:02 PST)
    - Re: RE: AMBER: leap compiling problem on a 64-bit machine Tomas Linhart (Sun Nov 21 2004 - 15:22:25 PST)
  - Re: RE: AMBER: leap compiling problem on a 64-bit machine xhu1.memphis.edu (Sun Nov 21 2004 - 19:31:53 PST)
AMBER: Electrolyte concentrations in MD arubin.unmc.edu (Fri Nov 19 2004 - 12:56:09 PST)
Re: AMBER: leap compiling problem on a 64-bit machine Bill Ross (Fri Nov 19 2004 - 13:14:07 PST)
AMBER: calculation of pKa values Peter Trodler (Mon Nov 22 2004 - 00:32:25 PST)
AMBER: sander, MD problems Kepa Koldo Burusco Goñi (Mon Nov 22 2004 - 04:00:37 PST)
- Re: AMBER: sander, MD problems Carlos Simmerling (Mon Nov 22 2004 - 04:53:29 PST)
AMBER: problem solved: leap compiling problem on a 64-bit machine xhu1.memphis.edu (Mon Nov 22 2004 - 12:51:28 PST)
AMBER: New problem on our 64bit box: xleap Segmentation fault xhu1.memphis.edu (Mon Nov 22 2004 - 13:03:48 PST)
- RE: AMBER: New problem on our 64bit box: xleap Segmentation fault Ross Walker (Mon Nov 22 2004 - 13:29:13 PST)
  - Re: RE: AMBER: New problem on our 64bit box: xleap Segmentation fault xhu1.memphis.edu (Mon Nov 22 2004 - 14:37:03 PST)
AMBER: LEaP compilation error on Solaris 9 Joe Nolan (Mon Nov 22 2004 - 13:21:41 PST)
- Re: AMBER: LEaP compilation error on Solaris 9 David A. Case (Mon Nov 22 2004 - 14:02:35 PST)
- Re: AMBER: LEaP compilation error on Solaris 9 Bill Ross (Mon Nov 22 2004 - 14:16:10 PST)
Re: AMBER: New problem on our 64bit box: xleap Segmentation fault Bill Ross (Mon Nov 22 2004 - 13:27:21 PST)
- Re: AMBER: New problem on our 64bit box: xleap Segmentation fault xhu1.memphis.edu (Mon Nov 22 2004 - 14:38:37 PST)
AMBER: generating parmfile containing topology and parameter information Nitin Bhardwaj (Mon Nov 22 2004 - 13:29:00 PST)
- RE: AMBER: generating parmfile containing topology and parameter information Ross Walker (Mon Nov 22 2004 - 13:46:30 PST)
  - RE: AMBER: generating parmfile containing topology and parameter information Nitin Bhardwaj (Mon Nov 22 2004 - 15:53:07 PST)
    - Re: AMBER: generating parmfile containing topology and parameter information David A. Case (Mon Nov 22 2004 - 16:12:20 PST)
AMBER: questions on dummy atom types in FEP setup Eric Hu (Mon Nov 22 2004 - 13:37:54 PST)
- Re: AMBER: questions on dummy atom types in FEP setup Chunhu Tan (Mon Nov 22 2004 - 15:37:57 PST)
  - Re: AMBER: questions on dummy atom types in FEP setup Eric Hu (Mon Nov 22 2004 - 18:22:45 PST)
AMBER: mm_pbsa +fillratio Carsten Detering (Mon Nov 22 2004 - 15:14:55 PST)
- Re: AMBER: mm_pbsa +fillratio David A. Case (Mon Nov 22 2004 - 15:20:03 PST)
  - Re: AMBER: mm_pbsa +fillratio Carsten Detering (Mon Nov 22 2004 - 16:38:13 PST)
Re: AMBER: problem solved: leap compiling problem on a 64-bit machine Bill Ross (Mon Nov 22 2004 - 14:37:58 PST)
- Re: AMBER: problem solved: leap compiling problem on a 64-bit machine xhu1.memphis.edu (Mon Nov 22 2004 - 15:48:43 PST)
AMBER: Problem with converting AMBER PREP to MOL2 Cenk Andac (Mon Nov 22 2004 - 16:13:39 PST)
- Re: AMBER: Problem with converting AMBER PREP to MOL2 David A. Case (Tue Nov 23 2004 - 08:12:06 PST)
  - Re: AMBER: Problem with converting AMBER PREP to MOL2 david.evans.ulsop.ac.uk (Tue Nov 23 2004 - 09:06:22 PST)
- Re: AMBER: Problem with converting AMBER PREP to MOL2 Bill Ross (Tue Nov 23 2004 - 10:00:31 PST)
AMBER: mm_pbsa + vertex atom mismatch Carsten Detering (Mon Nov 22 2004 - 19:01:28 PST)
AMBER: Resend: Problem with converting AMBER8 PREP to MOL2 Cenk Andac (Tue Nov 23 2004 - 00:57:55 PST)
AMBER: langevin dynamic in sander Stefano.Pieraccini.unimi.it (Tue Nov 23 2004 - 01:33:08 PST)
- Re: AMBER: langevin dynamic in sander David A. Case (Tue Nov 23 2004 - 08:21:30 PST)
AMBER: TI with electrostatic decoupling Nelson Fonseca (Tue Nov 23 2004 - 01:56:44 PST)
- AMBER: Problem with minimisation of an protein-inhibitor complex Daniel Wetzler (Tue Nov 23 2004 - 02:31:33 PST)
- Re: AMBER: TI with electrostatic decoupling David A. Case (Tue Nov 23 2004 - 08:42:16 PST)
- Re: AMBER: TI with electrostatic decoupling Chunhu Tan (Tue Nov 23 2004 - 11:01:48 PST)
AMBER: restart calculation tang kwa (Tue Nov 23 2004 - 02:31:22 PST)
- Re: AMBER: restart calculation Tomas Linhart (Tue Nov 23 2004 - 02:53:29 PST)
  - Re: AMBER: restart calculation tang kwa (Tue Nov 23 2004 - 03:44:45 PST)
    - Re: AMBER: restart calculation David A. Case (Tue Nov 23 2004 - 08:39:37 PST)
- Re: AMBER: restart calculation Carlos Simmerling (Tue Nov 23 2004 - 04:45:28 PST)
- RE: AMBER: restart calculation Ross Walker (Tue Nov 23 2004 - 10:02:12 PST)
AMBER: Problem with minimisation of an protein-inhibitor complex Daniel Wetzler (Tue Nov 23 2004 - 04:31:38 PST)
- RE: AMBER: Problem with minimisation of an protein-inhibitor complex Ross Walker (Tue Nov 23 2004 - 10:16:04 PST)
AMBER: add dummy atoms tang kwa (Tue Nov 23 2004 - 06:27:05 PST)
- Re: AMBER: add dummy atoms David A. Case (Tue Nov 23 2004 - 08:27:48 PST)
AMBER: Antechamber problems Kara Wald (Tue Nov 23 2004 - 10:49:43 PST)
AMBER: md.out & plot bybaker.itsa.ucsf.edu (Tue Nov 23 2004 - 14:23:41 PST)
- Re: AMBER: md.out & plot Luis Gracia (Tue Nov 23 2004 - 14:43:33 PST)
- RE: AMBER: md.out & plot Ross Walker (Tue Nov 23 2004 - 14:59:58 PST)
AMBER: cannot load frcmod file properly Eric Hu (Tue Nov 23 2004 - 15:10:17 PST)
- Re: AMBER: cannot load frcmod file properly Chunhu Tan (Tue Nov 23 2004 - 18:12:42 PST)
  - Re: AMBER: cannot load frcmod file properly Eric Hu (Wed Nov 24 2004 - 10:28:02 PST)
    - Re: AMBER: cannot load frcmod file properly Chunhu Tan (Wed Nov 24 2004 - 12:37:46 PST)
AMBER: Re: md.out & plot bybaker.itsa.ucsf.edu (Tue Nov 23 2004 - 17:26:36 PST)
- Re: AMBER: Re: md.out & plot Furse, Kristina Elisabet (Tue Nov 23 2004 - 20:29:37 PST)
- Re: AMBER: Re: md.out & plot Furse, Kristina Elisabet (Tue Nov 23 2004 - 20:37:21 PST)
AMBER: build a cyclic peptide Eric Hu (Tue Nov 23 2004 - 17:34:13 PST)
- Re: AMBER: build a cyclic peptide Carlos Simmerling (Tue Nov 23 2004 - 18:43:13 PST)
  - Re: AMBER: build a cyclic peptide Eric Hu (Wed Nov 24 2004 - 10:26:44 PST)
    - Re: AMBER: build a cyclic peptide Carlos Simmerling (Wed Nov 24 2004 - 10:56:57 PST)
    - Re: AMBER: build a cyclic peptide Eric Hu (Wed Nov 24 2004 - 12:11:18 PST)
    - Re: AMBER: build a cyclic peptide Carlos Simmerling (Wed Nov 24 2004 - 12:33:10 PST)
- Re: AMBER: build a cyclic peptide Bill Ross (Wed Nov 24 2004 - 10:39:15 PST)
- Re: AMBER: build a cyclic peptide Bill Ross (Wed Nov 24 2004 - 13:56:44 PST)
Re: AMBER: build a cyclic peptide Bill Ross (Tue Nov 23 2004 - 18:33:04 PST)
AMBER: Installation of AMBER8 on AMD cluster using pgf90 Hwankyu Lee (Tue Nov 23 2004 - 18:41:13 PST)
- Re: AMBER: Installation of AMBER8 on AMD cluster using pgf90 David A. Case (Tue Nov 23 2004 - 23:03:55 PST)
  - Re: AMBER: Installation of AMBER8 on AMD cluster using pgf90 Hwankyu Lee (Wed Nov 24 2004 - 06:03:28 PST)
AMBER: Re: md.out & plot bybaker.itsa.ucsf.edu (Tue Nov 23 2004 - 22:21:10 PST)
AMBER: missing XaLeap_wcl file Nitin Bhardwaj (Wed Nov 24 2004 - 10:22:04 PST)
AMBER: extracting energy from trajector? MURAT CETINKAYA (Wed Nov 24 2004 - 10:33:04 PST)
- Re: AMBER: extracting energy from trajector? Carlos Simmerling (Wed Nov 24 2004 - 10:55:49 PST)
- Re: AMBER: extracting energy from trajector? Bill Ross (Wed Nov 24 2004 - 11:33:29 PST)
- Re: AMBER: extracting energy from trajector? David Smith (Wed Nov 24 2004 - 11:29:34 PST)
- Re: AMBER: extracting energy from trajector? MURAT CETINKAYA (Sun Nov 28 2004 - 16:59:27 PST)
  - Re: AMBER: extracting energy from trajector? David Smith (Mon Nov 29 2004 - 04:37:41 PST)
  - Re: AMBER: extracting energy from trajector? David Smith (Mon Nov 29 2004 - 05:04:52 PST)
- Re: AMBER: extracting energy from trajector? MURAT CETINKAYA (Mon Nov 29 2004 - 07:31:14 PST)
  - Re: AMBER: extracting energy from trajector? David Smith (Mon Nov 29 2004 - 08:54:53 PST)
- Re: AMBER: extracting energy from trajector? MURAT CETINKAYA (Mon Nov 29 2004 - 09:20:12 PST)
  - Re: AMBER: extracting energy from trajector? David Smith (Mon Nov 29 2004 - 09:39:30 PST)
- Re: AMBER: extracting energy from trajector? MURAT CETINKAYA (Thu Dec 02 2004 - 12:56:47 PST)
  - Re: AMBER: extracting energy from trajector? David Smith (Thu Dec 02 2004 - 13:30:59 PST)
Re: AMBER: extracting energy from trajector? Bill Ross (Wed Nov 24 2004 - 10:50:30 PST)
- Re: AMBER: extracting energy from trajector? Carlos Simmerling (Wed Nov 24 2004 - 11:07:12 PST)
AMBER: nucgen problem opitz.che.udel.edu (Wed Nov 24 2004 - 14:08:52 PST)
- Re: AMBER: nucgen problem david.evans.ulsop.ac.uk (Thu Nov 25 2004 - 01:04:28 PST)
AMBER: Regarding Dielectric Constant in AMBER8 pande.vineet.fc.up.pt (Thu Nov 25 2004 - 07:22:41 PST)
- Re: AMBER: Regarding Dielectric Constant in AMBER8 Carlos Simmerling (Thu Nov 25 2004 - 07:50:12 PST)
  - Re: AMBER: Regarding Dielectric Constant in AMBER8 pande.vineet.fc.up.pt (Thu Nov 25 2004 - 08:03:27 PST)
    - Re: AMBER: Regarding Dielectric Constant in AMBER8 Carlos Simmerling (Thu Nov 25 2004 - 08:45:34 PST)
    - Re: AMBER: Regarding Dielectric Constant in AMBER8 pande.vineet.fc.up.pt (Fri Nov 26 2004 - 00:45:50 PST)
    - Re: AMBER: Regarding Dielectric Constant in AMBER8 Carlos Simmerling (Fri Nov 26 2004 - 06:02:56 PST)
    - Re: AMBER: Regarding Dielectric Constant in AMBER8 pande.vineet.fc.up.pt (Fri Nov 26 2004 - 08:35:43 PST)
    - Re: AMBER: Regarding Dielectric Constant in AMBER8 pande.vineet.fc.up.pt (Fri Nov 26 2004 - 08:45:47 PST)
    - Re: AMBER: Regarding Dielectric Constant in AMBER8 Carlos Simmerling (Fri Nov 26 2004 - 08:55:48 PST)
    - Re: AMBER: Regarding Dielectric Constant in AMBER8 pande.vineet.fc.up.pt (Fri Nov 26 2004 - 10:59:19 PST)
    - Re: AMBER: Regarding Dielectric Constant in AMBER8 Carlos Simmerling (Fri Nov 26 2004 - 11:24:59 PST)
AMBER: combine crd files bybaker.itsa.ucsf.edu (Fri Nov 26 2004 - 14:54:43 PST)
- Re: AMBER: combine crd files Furse, Kristina Elisabet (Fri Nov 26 2004 - 15:42:09 PST)
- Re: AMBER: combine crd files Carlos Simmerling (Fri Nov 26 2004 - 16:03:28 PST)
AMBER: sander.QMMM on Mac justin litchfield (Fri Nov 26 2004 - 15:17:35 PST)
- RE: AMBER: sander.QMMM on Mac Ross Walker (Fri Nov 26 2004 - 17:56:56 PST)
  - Re: AMBER: sander.QMMM on Mac justin litchfield (Sat Nov 27 2004 - 00:29:26 PST)
AMBER: Protein with maximum hydrogen bonds anshul.imtech.res.in (Sat Nov 27 2004 - 09:23:43 PST)
- RE: AMBER: Protein with maximum hydrogen bonds Ross Walker (Fri Nov 26 2004 - 23:15:34 PST)
- Re: AMBER: Protein with maximum hydrogen bonds pande.vineet.fc.up.pt (Sat Nov 27 2004 - 06:13:58 PST)
- Re: AMBER: Protein with maximum hydrogen bonds Sanjeev B.S. (Sat Nov 27 2004 - 07:14:01 PST)
AMBER: About Disulfer bond Xiao He (Sat Nov 27 2004 - 00:11:00 PST)
- Re: AMBER: About Disulfer bond David A. Case (Sat Nov 27 2004 - 10:05:28 PST)
Fwd: Re: AMBER: Protein with maximum hydrogen bonds pande.vineet.fc.up.pt (Sat Nov 27 2004 - 06:19:31 PST)
AMBER: xfl90 and xlc "C" compiler Dr. Noah Allen (Sat Nov 27 2004 - 12:05:28 PST)
- Re: AMBER: xfl90 and xlc "C" compiler justin litchfield (Sat Nov 27 2004 - 12:42:22 PST)
AMBER: GO lie Amber simulation Alena Shmygelska (Sat Nov 27 2004 - 13:48:53 PST)
- Re: AMBER: GO lie Amber simulation David A. Case (Sat Nov 27 2004 - 15:37:45 PST)
AMBER: saving trajectory parameters Ed Pate (Sat Nov 27 2004 - 16:17:40 PST)
- RE: AMBER: saving trajectory parameters Ross Walker (Sat Nov 27 2004 - 16:52:03 PST)
AMBER: MD run: frozen bybaker.itsa.ucsf.edu (Sat Nov 27 2004 - 22:17:36 PST)
- RE: AMBER: MD run: frozen Ross Walker (Sat Nov 27 2004 - 23:00:37 PST)
- Re: AMBER: MD run: frozen Carlos Simmerling (Sun Nov 28 2004 - 07:32:25 PST)
- Re: AMBER: MD run: frozen bybaker.itsa.ucsf.edu (Sun Nov 28 2004 - 16:39:30 PST)
AMBER: FEP - GIBBS of charged sidechains using IELPER Annette Höglund (Sun Nov 28 2004 - 09:26:06 PST)
- Re: AMBER: FEP - GIBBS of charged sidechains using IELPER David A. Case (Sun Nov 28 2004 - 15:28:43 PST)
AMBER: question! Marsita M (Sun Nov 28 2004 - 19:01:41 PST)
AMBER: problem in quasih.f diagonalising matrix Phineus Markwick (Mon Nov 29 2004 - 05:14:35 PST)
- Re: AMBER: problem in quasih.f diagonalising matrix David A. Case (Mon Nov 29 2004 - 08:38:46 PST)
AMBER: Restrained minimization problem opitz.che.udel.edu (Mon Nov 29 2004 - 14:11:56 PST)
- Re: AMBER: Restrained minimization problem Bill Ross (Mon Nov 29 2004 - 14:31:54 PST)
- Re: AMBER: Restrained minimization problem opitz.che.udel.edu (Mon Nov 29 2004 - 14:50:14 PST)
- Re: AMBER: Restrained minimization problem opitz.che.udel.edu (Mon Nov 29 2004 - 14:56:47 PST)
  - Re: AMBER: Restrained minimization problem David A. Case (Mon Nov 29 2004 - 15:27:41 PST)
    - AMBER: increasing the maximum value of NPHB parameter Alena Shmygelska (Mon Nov 29 2004 - 21:05:08 PST)
    - Re: AMBER: increasing the maximum value of NPHB parameter David A. Case (Tue Nov 30 2004 - 17:58:59 PST)
    - Re: AMBER: increasing the maximum value of NPHB parameter Alena Shmygelska (Wed Dec 01 2004 - 23:42:44 PST)
- Re: AMBER: Restrained minimization problem Thomas E. Cheatham, III (Mon Nov 29 2004 - 15:02:44 PST)
- Re: AMBER: Restrained minimization problem Bill Ross (Mon Nov 29 2004 - 15:25:58 PST)
- Re: AMBER: Restrained minimization problem Furse, Kristina Elisabet (Mon Nov 29 2004 - 15:32:28 PST)
AMBER: Slowly releasing restraints Marcin Krol (Tue Nov 30 2004 - 03:12:37 PST)
- Re: AMBER: Slowly releasing restraints David A. Case (Tue Nov 30 2004 - 11:55:40 PST)
AMBER: amber8 parallel installation with mpich cailliez (Tue Nov 30 2004 - 04:24:41 PST)
- Re: AMBER: amber8 parallel installation with mpich Marc Baaden (Tue Nov 30 2004 - 04:00:26 PST)
- Re: AMBER: amber8 parallel installation with mpich Marc Baaden (Tue Nov 30 2004 - 04:27:18 PST)
AMBER: problem loading mdcrd to VMD Ru-Zhen Li (Tue Nov 30 2004 - 04:59:40 PST)
- Re: AMBER: problem loading mdcrd to VMD Stefano.Pieraccini.unimi.it (Tue Nov 30 2004 - 06:04:07 PST)
- Re: AMBER: problem loading mdcrd to VMD David Smith (Tue Nov 30 2004 - 06:19:24 PST)
  - AMBER: memory prolem of the nmode calculation Xiao Jian Tan (Tue Nov 30 2004 - 15:24:18 PST)
    - Re: AMBER: memory prolem of the nmode calculation David A. Case (Tue Nov 30 2004 - 17:40:29 PST)
- Re: AMBER: problem loading mdcrd to VMD David E. Konerding (Tue Nov 30 2004 - 07:45:59 PST)
- Re: AMBER: problem loading mdcrd to VMD Ru-Zhen Li (Tue Nov 30 2004 - 09:05:57 PST)
  - Re: AMBER: problem loading mdcrd to VMD David Smith (Tue Nov 30 2004 - 09:44:16 PST)
  - Re: AMBER: problem loading mdcrd to VMD myang.vitamin.uni.cc (Tue Nov 30 2004 - 10:48:43 PST)
- Re: AMBER: problem loading mdcrd to VMD John Bushnell (Tue Nov 30 2004 - 14:41:14 PST)
- Re: AMBER: problem loading mdcrd to VMD Ru-Zhen Li (Tue Nov 30 2004 - 15:17:08 PST)
AMBER: Implicit 4r md yen li (Tue Nov 30 2004 - 08:58:34 PST)
- Re: AMBER: Implicit 4r md Stefano.Pieraccini.unimi.it (Wed Dec 01 2004 - 00:52:27 PST)
  - Re: AMBER: Implicit 4r md yen li (Thu Dec 02 2004 - 21:14:06 PST)
    - Re: AMBER: Implicit 4r md David A. Case (Fri Dec 03 2004 - 08:48:00 PST)
AMBER: Re: AMBER: problem loading mdcrd to VMD Dawsonzhu.aol.com (Tue Nov 30 2004 - 15:03:46 PST)
AMBER: FEP along a reaction coordinate in sander Tomasz Borowski (Wed Dec 01 2004 - 00:46:54 PST)
- Re: AMBER: FEP along a reaction coordinate in sander Masataka Nagaoka (Wed Dec 01 2004 - 04:05:01 PST)
- Re: AMBER: FEP along a reaction coordinate in sander David A. Case (Wed Dec 01 2004 - 09:38:45 PST)
AMBER: question about parallel simulation qlu.notes.cc.sunysb.edu (Wed Dec 01 2004 - 11:17:43 PST)
- RE: AMBER: question about parallel simulation Ross Walker (Wed Dec 01 2004 - 12:40:19 PST)
- RE: AMBER: question about parallel simulation qlu.notes.cc.sunysb.edu (Wed Dec 01 2004 - 15:38:01 PST)
  - RE: AMBER: question about parallel simulation Ross Walker (Wed Dec 01 2004 - 17:00:33 PST)
- RE: AMBER: question about parallel simulation qlu.notes.cc.sunysb.edu (Thu Dec 02 2004 - 12:30:28 PST)
- RE: AMBER: question about parallel simulation qlu.notes.cc.sunysb.edu (Thu Dec 02 2004 - 13:28:43 PST)
  - RE: AMBER: question about parallel simulation Ross Walker (Thu Dec 02 2004 - 14:37:12 PST)
AMBER: ntt parameter tang kwa (Wed Dec 01 2004 - 13:32:22 PST)
- Re: AMBER: ntt parameter David A. Case (Wed Dec 01 2004 - 16:14:30 PST)
  - Re: AMBER: ntt parameter David Smith (Thu Dec 02 2004 - 02:30:01 PST)
    - Re: AMBER: ntt parameter Ross Walker (Thu Dec 02 2004 - 23:11:31 PST)
AMBER: restrainted torsion tang kwa (Thu Dec 02 2004 - 05:18:43 PST)
- Re: AMBER: restrainted torsion David A. Case (Thu Dec 02 2004 - 11:12:19 PST)
AMBER: nmode & mm-pbsa Shekter, Lee (Thu Dec 02 2004 - 18:50:45 PST)
AMBER: Residue Loading Problem Garhan Attebury (Thu Dec 02 2004 - 22:20:51 PST)
- Re: AMBER: Residue Loading Problem Furse, Kristina Elisabet (Thu Dec 02 2004 - 23:23:05 PST)
  - Re: AMBER: Residue Loading Problem david.evans.ulsop.ac.uk (Fri Dec 03 2004 - 01:41:13 PST)
- Re: AMBER: Residue Loading Problem David A. Case (Thu Dec 16 2004 - 18:10:43 PST)
AMBER: Dielectric Constant Marsita M (Sat Dec 04 2004 - 03:42:36 PST)
- Re: AMBER: Dielectric Constant David A. Case (Sat Dec 04 2004 - 15:15:10 PST)
Re: AMBER: Dielectric Constant Bill Ross (Sat Dec 04 2004 - 12:22:33 PST)
AMBER: one question about dielectric dependent model Xiaowei (David) Li (Sun Dec 05 2004 - 09:42:56 PST)
AMBER: Compiling Antechamber/Amber8 with ia64_ifort Toru Yagi (Sun Dec 05 2004 - 22:25:02 PST)
- Re: AMBER: Compiling Antechamber/Amber8 with ia64_ifort Andreas Svrcek-Seiler (Mon Dec 06 2004 - 00:56:34 PST)
  - Re: AMBER: Compiling Antechamber/Amber8 with ia64_ifort Jack Lei (Mon Dec 06 2004 - 07:11:05 PST)
AMBER: strange bond energies Magne Olufsen (Mon Dec 06 2004 - 05:42:16 PST)
- Re: AMBER: strange bond energies Carlos Simmerling (Mon Dec 06 2004 - 06:22:10 PST)
AMBER: Wanxin Sun (Mon Dec 06 2004 - 07:06:25 PST)
- Re: AMBER: David A. Case (Wed Dec 08 2004 - 11:49:41 PST)
AMBER: md's yen li (Mon Dec 06 2004 - 08:08:07 PST)
AMBER: cut-off & MD bybaker.itsa.ucsf.edu (Mon Dec 06 2004 - 12:49:04 PST)
- RE: AMBER: cut-off & MD Ross Walker (Mon Dec 06 2004 - 13:17:30 PST)
AMBER: converting from NAMD trajectory format Stern, Julie (Mon Dec 06 2004 - 15:02:49 PST)
- Re: AMBER: converting from NAMD trajectory format Thomas E. Cheatham, III (Wed Dec 08 2004 - 16:53:50 PST)
AMBER: FW: two processor amd 64 bit pc Spero Manolatos (Mon Dec 06 2004 - 17:36:33 PST)
- RE: AMBER: FW: two processor amd 64 bit pc Ross Walker (Mon Dec 06 2004 - 19:17:41 PST)
AMBER: (no subject) Andrew Box (Mon Dec 06 2004 - 19:32:52 PST)
- Re: AMBER: (no subject) David A. Case (Tue Dec 07 2004 - 05:00:49 PST)
AMBER: install problem Kevin Murphy (Tue Dec 07 2004 - 02:23:11 PST)
- Re: AMBER: install problem David A. Case (Tue Dec 07 2004 - 05:03:12 PST)
AMBER: Gigabit Ethernet Switch/Opteron 246 jianhui wu (Tue Dec 07 2004 - 09:09:11 PST)
- RE: AMBER: Gigabit Ethernet Switch/Opteron 246 Ross Walker (Tue Dec 07 2004 - 10:11:24 PST)
AMBER: 1-4 EEL tang kwa (Tue Dec 07 2004 - 09:12:54 PST)
- Re: AMBER: 1-4 EEL David A. Case (Wed Dec 08 2004 - 10:13:08 PST)
AMBER: imin=5 in sander MURAT CETINKAYA (Tue Dec 07 2004 - 11:07:34 PST)
- Re: AMBER: imin=5 in sander Carlos Simmerling (Mon Dec 06 2004 - 17:52:14 PST)
- Re: AMBER: imin=5 in sander Asim Okur (Tue Dec 07 2004 - 12:44:52 PST)
- Re: AMBER: imin=5 in sander Asim Okur (Tue Dec 07 2004 - 12:47:38 PST)
AMBER: question about mmpbsa xhu1.memphis.edu (Tue Dec 07 2004 - 17:20:19 PST)
- Re: AMBER: question about mmpbsa cailliez (Wed Dec 08 2004 - 10:23:01 PST)
AMBER: NMR constraint problem Andrew Box (Tue Dec 07 2004 - 19:06:02 PST)
- Re: AMBER: NMR constraint problem David A. Case (Wed Dec 08 2004 - 10:08:11 PST)
- Re: AMBER: NMR constraint problem John Bushnell (Wed Dec 08 2004 - 12:39:32 PST)
AMBER: Why the surface calculations sometimes fail? hj zou (Tue Dec 07 2004 - 22:53:09 PST)
- Re: AMBER: Why the surface calculations sometimes fail? David A. Case (Wed Dec 08 2004 - 11:52:29 PST)
  - Re: Re: AMBER: Why the surface calculations sometimes fail? hj zou (Wed Dec 08 2004 - 17:58:19 PST)
    - Re: Re: AMBER: Why the surface calculations sometimes fail? David A. Case (Mon Dec 13 2004 - 18:29:17 PST)
    - Re: Re: Re: AMBER: Why the surface calculations sometimes fail? hj zou (Wed Dec 15 2004 - 20:12:59 PST)
    - Re: Re: Re: AMBER: Why the surface calculations sometimes fail? David A. Case (Thu Dec 16 2004 - 09:32:29 PST)
AMBER: some questions.... Germán Sciaini (Wed Dec 08 2004 - 08:49:55 PST)
- Re: AMBER: some questions.... David A. Case (Wed Dec 08 2004 - 10:04:13 PST)
AMBER: calculate ligand's rmsd Yong Xu (Wed Dec 08 2004 - 22:11:15 PST)
- RE: AMBER: calculate ligand's rmsd Ross Walker (Wed Dec 08 2004 - 22:00:30 PST)
AMBER: Implicit Solvent Models Nelson Fonseca (Thu Dec 09 2004 - 04:02:10 PST)
- Re: AMBER: Implicit Solvent Models David A. Case (Fri Dec 10 2004 - 08:51:12 PST)
AMBER: pbsa error in mm_pbsa amber 8 Ben Cossins (Thu Dec 09 2004 - 06:58:19 PST)
- Re: AMBER: pbsa error in mm_pbsa amber 8 Ben Cossins (Thu Dec 09 2004 - 07:19:20 PST)
  - Re: AMBER: pbsa error in mm_pbsa amber 8 david.evans.ulsop.ac.uk (Thu Dec 09 2004 - 08:15:52 PST)
    - Re: AMBER: pbsa error in mm_pbsa amber 8 Ben Cossins (Fri Dec 10 2004 - 05:05:33 PST)
    - Re: AMBER: pbsa error in mm_pbsa amber 8 Ray Luo (Fri Dec 10 2004 - 13:36:53 PST)
    - Re: AMBER: pbsa error in mm_pbsa amber 8 Ben Cossins (Tue Dec 14 2004 - 05:41:08 PST)
    - Re: AMBER: pbsa error in mm_pbsa amber 8 david.evans.ulsop.ac.uk (Tue Dec 14 2004 - 07:28:24 PST)
    - Re: AMBER: pbsa error in mm_pbsa amber 8 Ray Luo (Tue Dec 14 2004 - 22:17:01 PST)
    - Re: AMBER: pbsa error in mm_pbsa amber 8 Ben Cossins (Wed Dec 15 2004 - 04:04:50 PST)
    - Re: AMBER: pbsa error in mm_pbsa amber 8 Ray Luo (Thu Dec 16 2004 - 15:58:29 PST)
- Re: AMBER: pbsa error in mm_pbsa amber 8 Ray Luo (Fri Dec 10 2004 - 10:17:07 PST)
AMBER: No radius found for 2412 Zn Zn Yong Xu (Thu Dec 09 2004 - 23:13:37 PST)
- Re: AMBER: No radius found for 2412 Zn Zn Holger Gohlke (Fri Dec 10 2004 - 00:21:45 PST)
- Re: AMBER: No radius found for 2412 Zn Zn Jack Lei (Fri Dec 10 2004 - 06:49:53 PST)
  - Re: Re: AMBER: No radius found for 2412 Zn Zn Yong Xu (Fri Dec 10 2004 - 01:15:14 PST)
    - Re: AMBER: No radius found for 2412 Zn Zn Holger Gohlke (Fri Dec 10 2004 - 02:22:19 PST)
  - Re: Re: AMBER: No radius found for 2412 Zn Zn Yong Xu (Fri Dec 10 2004 - 21:53:18 PST)
AMBER: how to prepare Zn.lib Yong Xu (Thu Dec 09 2004 - 23:50:16 PST)
- RE: AMBER: how to prepare Zn.lib Ross Walker (Fri Dec 10 2004 - 10:29:24 PST)
AMBER: question about md's yen li (Fri Dec 10 2004 - 07:27:39 PST)
AMBER: question about MGB and PB xhu1.memphis.edu (Fri Dec 10 2004 - 14:12:30 PST)
- AMBER: Workshop 2004, Tutorial #6, QMMM MD Simulation Ilyas Yildirim (Mon Dec 13 2004 - 20:34:34 PST)
  - RE: AMBER: Workshop 2004, Tutorial #6, QMMM MD Simulation Ross Walker (Tue Dec 14 2004 - 09:53:58 PST)
    - RE: AMBER: Workshop 2004, Tutorial #6, QMMM MD Simulation Ilyas Yildirim (Wed Dec 15 2004 - 16:47:05 PST)
    - AMBER: Free Energy Perturbation using Sander (TI Method) Ilyas Yildirim (Wed Dec 15 2004 - 18:43:09 PST)
    - AMBER: General Question about AMBER's Free Energy Perturbation Method Ilyas Yildirim (Wed Dec 15 2004 - 20:13:07 PST)
    - Re: AMBER: General Question about AMBER's Free Energy Perturbation Method David A. Case (Wed Dec 15 2004 - 23:03:18 PST)
    - Re: AMBER: General Question about AMBER's Free Energy Perturbation Method Ilyas Yildirim (Fri Dec 17 2004 - 13:53:07 PST)
    - Re: AMBER: General Question about AMBER's Free Energy Perturbation Method David A. Case (Fri Dec 17 2004 - 15:26:34 PST)
AMBER: Why the charge is not an integer? mmv (Sun Dec 12 2004 - 01:44:36 PST)
- Re: AMBER: Why the charge is not an integer? Guanglei Cui (Sun Dec 12 2004 - 08:21:32 PST)
- Re: AMBER: Why the charge is not an integer? FyD (Sun Dec 12 2004 - 11:47:02 PST)
- Re: AMBER: Why the charge is not an integer? David A. Case (Sun Dec 12 2004 - 13:05:57 PST)
- RE: AMBER: Why the charge is not an integer? Ross Walker (Mon Dec 13 2004 - 10:15:13 PST)
  - AMBER: Why the charge is not an integer? Annette Höglund (Mon Dec 13 2004 - 23:39:11 PST)
    - Re: AMBER: Why the charge is not an integer? John Mongan (Tue Dec 14 2004 - 19:10:49 PST)
AMBER: Binding free energy from separate/single trajectory yuann (Sun Dec 12 2004 - 21:01:17 PST)
AMBER: ptraj hbond memory allocation on opteron Fabian Boes (Mon Dec 13 2004 - 04:07:11 PST)
- Re: AMBER: ptraj hbond memory allocation on opteron Andreas Svrcek-Seiler (Mon Dec 13 2004 - 08:07:25 PST)
  - Re: AMBER: ptraj hbond memory allocation on opteron Fabian Boes (Tue Dec 14 2004 - 06:33:42 PST)
AMBER: cobalt parameters Peter Gannett (Mon Dec 13 2004 - 17:21:50 PST)
AMBER: entropy implementation in ptraj Raik Grünberg (Tue Dec 14 2004 - 09:37:18 PST)
- Re: AMBER: entropy implementation in ptraj David A. Case (Wed Dec 15 2004 - 10:07:50 PST)
  - Re: AMBER: entropy implementation in ptraj Raik Grünberg (Fri Dec 17 2004 - 06:44:13 PST)
    - Re: AMBER: entropy implementation in ptraj David A. Case (Fri Dec 17 2004 - 08:11:29 PST)
AMBER: Compiling question Yanze Zhang (Tue Dec 14 2004 - 11:27:53 PST)
- Re: AMBER: Compiling question David A. Case (Tue Dec 14 2004 - 11:33:34 PST)
  - Re: AMBER: Compiling question James W. Caldwell (Tue Dec 14 2004 - 12:10:19 PST)
- RE: AMBER: Compiling question Ross Walker (Tue Dec 14 2004 - 11:44:27 PST)
- Re: AMBER: Compiling question Robert Duke (Tue Dec 14 2004 - 11:51:20 PST)
  - Re: AMBER: Compiling question Yanze Zhang (Tue Dec 14 2004 - 12:11:07 PST)
AMBER: Ewald tang kwa (Wed Dec 15 2004 - 08:31:41 PST)
- Re: AMBER: Ewald David A. Case (Wed Dec 15 2004 - 10:17:04 PST)
AMBER: unknown elements Youyi Peng (Wed Dec 15 2004 - 08:33:54 PST)
- Re: AMBER: unknown elements David A. Case (Wed Dec 15 2004 - 10:00:32 PST)
AMBER: mm_pbsa Carsten Detering (Wed Dec 15 2004 - 13:57:13 PST)
AMBER: About MM/PBSA, PB Calculation nlxc (Wed Dec 15 2004 - 15:11:29 PST)
- Re: AMBER: About MM/PBSA, PB Calculation David A. Case (Thu Dec 16 2004 - 09:38:32 PST)
  - Re: AMBER: About MM/PBSA, PB Calculation nlxc (Thu Dec 16 2004 - 14:31:13 PST)
AMBER: sander imin=5 MURAT CETINKAYA (Thu Dec 16 2004 - 00:01:45 PST)
AMBER: nmode problem Yong Xu (Thu Dec 16 2004 - 20:16:23 PST)
AMBER: Question concerning ANAL total energy calculation Daniel Wetzler (Fri Dec 17 2004 - 04:04:05 PST)
- Re: AMBER: Question concerning ANAL total energy calculation David A. Case (Fri Dec 17 2004 - 07:58:49 PST)
  - Re: AMBER: Question concerning ANAL total energy calculation Daniel Wetzler (Sat Dec 18 2004 - 01:33:26 PST)
    - Re: AMBER: Question concerning ANAL total energy calculation David A. Case (Sat Dec 18 2004 - 08:50:01 PST)
  - Re: AMBER: Question concerning ANAL total energy calculation Daniel Wetzler (Mon Dec 20 2004 - 13:15:12 PST)
    - Re: AMBER: Question concerning ANAL total energy calculation David A. Case (Mon Dec 20 2004 - 14:10:08 PST)
AMBER: MD: Water network analysis + visualization Sanjeev B.S. (Fri Dec 17 2004 - 10:23:22 PST)
- Re: AMBER: MD: Water network analysis + visualization sanjeev.mbu.iisc.ernet.in (Tue Mar 22 2005 - 05:58:24 PST)
AMBER: nanotube parameters MURAT CETINKAYA (Fri Dec 17 2004 - 12:28:24 PST)
- Re: AMBER: nanotube parameters David A. Case (Fri Dec 17 2004 - 15:34:31 PST)
- Re: AMBER: nanotube parameters Andreas Svrcek-Seiler (Mon Dec 20 2004 - 02:02:56 PST)
Re: AMBER: nanotube parameters Bill Ross (Fri Dec 17 2004 - 13:52:13 PST)
AMBER: Kinetics energy Germán Sciaini (Sat Dec 18 2004 - 09:54:04 PST)
- Re: AMBER: Kinetics energy Carlos Simmerling (Sat Dec 18 2004 - 11:07:11 PST)
- Re: AMBER: Kinetics energy Andreas Svrcek-Seiler (Mon Dec 20 2004 - 02:11:10 PST)
AMBER: Question on tleap of amber8 Okimoto Noriaki (Mon Dec 20 2004 - 01:00:38 PST)
- Re: AMBER: Question on tleap of amber8 David A. Case (Mon Dec 20 2004 - 09:27:07 PST)
AMBER: constraints on atoms cailliez (Mon Dec 20 2004 - 03:06:19 PST)
- Re: AMBER: constraints on atoms David A. Case (Tue Dec 21 2004 - 09:12:55 PST)
  - AMBER: Ideal bonds and angles Nhat-hang Duong (Tue Dec 21 2004 - 09:49:38 PST)
    - Re: AMBER: Ideal bonds and angles David A. Case (Tue Dec 21 2004 - 10:52:15 PST)
AMBER: Sander TI Cai, Yufeng (Mon Dec 20 2004 - 10:11:29 PST)
- Re: AMBER: Sander TI David A. Case (Tue Dec 21 2004 - 08:15:50 PST)
AMBER: parameter development Sebastian Fernandez Alberti (Mon Dec 20 2004 - 11:34:42 PST)
- Re: AMBER: parameter development David A. Case (Tue Dec 21 2004 - 08:53:19 PST)
AMBER: use leap to build top & crd files for a pdb file with crytalline water molecules Jianwen Jiang (Mon Dec 20 2004 - 16:18:52 PST)
- Re: AMBER: use leap to build top & crd files for a pdb file with crytalline water molecules Ilyas Yildirim (Mon Dec 20 2004 - 16:42:29 PST)
- RE: AMBER: use leap to build top & crd files for a pdb file with crytalline water molecules Ross Walker (Mon Dec 20 2004 - 16:55:17 PST)
  - Re: AMBER: use leap to build top & crd files for a pdb file with crytalline water molecules Jianwen Jiang (Tue Dec 21 2004 - 14:30:47 PST)
    - RE: AMBER: use leap to build top & crd files for a pdb file with crytalline water molecules Ross Walker (Tue Dec 21 2004 - 21:26:48 PST)
    - Re: AMBER: use leap to build top & crd files for a pdb file with crytalline water molecules Jianwen Jiang (Wed Dec 22 2004 - 12:01:40 PST)
    - Re: AMBER: use leap to build top & crd files for a pdb file with crytalline water molecules David A. Case (Wed Dec 22 2004 - 13:50:00 PST)
    - Re: AMBER: use leap to build top & crd files for a pdb file with crytalline water molecules Jianwen Jiang (Wed Dec 22 2004 - 13:59:47 PST)
    - Re: AMBER: use leap to build top & crd files for a pdb file with crytalline water molecules David A. Case (Wed Dec 22 2004 - 16:39:57 PST)
- Re: AMBER: use leap to build top & crd files for a pdb file with crytalline water molecules Bill Ross (Tue Dec 21 2004 - 14:57:13 PST)
  - Re: AMBER: use leap to build top & crd files for a pdb file with crytalline water molecules Jianwen Jiang (Tue Dec 21 2004 - 18:22:00 PST)
AMBER: cluster analysis with ptraj in amber 8.0 Eric Hu (Mon Dec 20 2004 - 18:01:26 PST)
- Re: AMBER: cluster analysis with ptraj in amber 8.0 David Smith (Tue Dec 21 2004 - 00:47:46 PST)
AMBER: Dummy torsion paramters for thermodynamic integration Thomas Steinbrecher (Tue Dec 21 2004 - 00:25:31 PST)
- Re: AMBER: Dummy torsion paramters for thermodynamic integration David A. Case (Tue Dec 21 2004 - 07:49:29 PST)
AMBER: a question Germán Sciaini (Tue Dec 21 2004 - 06:10:14 PST)
- Re: AMBER: a question David A. Case (Tue Dec 21 2004 - 14:07:51 PST)
AMBER: nrespa=2 Marsita M (Tue Dec 21 2004 - 07:19:58 PST)
- Re: AMBER: nrespa=2 David A. Case (Tue Dec 21 2004 - 07:52:53 PST)
- Re: AMBER: nrespa=2 Carlos Simmerling (Tue Dec 21 2004 - 07:54:15 PST)
AMBER: TFE parameters Adrian E. Roitberg (Tue Dec 21 2004 - 12:34:29 PST)
AMBER: Output of sander Harianto (Wed Dec 22 2004 - 08:09:37 PST)
- Re: AMBER: Output of sander David A. Case (Wed Dec 22 2004 - 09:35:27 PST)
- Re: AMBER: Output of sander Harianto (Thu Dec 23 2004 - 12:36:27 PST)
  - Re: AMBER: Output of sander David A. Case (Thu Dec 23 2004 - 13:35:49 PST)
AMBER: energy unit Chen Song (Wed Dec 22 2004 - 21:20:00 PST)
- Re: AMBER: energy unit Harianto (Thu Dec 23 2004 - 08:25:32 PST)
AMBER: amber7 on digital unix anshul.imtech.res.in (Thu Dec 23 2004 - 14:23:15 PST)
- Re: AMBER: amber7 on digital unix David A. Case (Thu Dec 23 2004 - 08:18:46 PST)
  - Re: AMBER: amber7 on digital unix anshul.imtech.res.in (Thu Dec 23 2004 - 19:15:47 PST)
    - Re: AMBER: amber7 on digital unix David A. Case (Thu Dec 23 2004 - 10:26:55 PST)
AMBER: Molecular modelling. Osman Gani (Thu Dec 23 2004 - 06:44:05 PST)
- Re: AMBER: Molecular modelling. David A. Case (Thu Dec 23 2004 - 18:03:50 PST)
AMBER: RMSD of ligand Yong Xu (Thu Dec 23 2004 - 16:26:14 PST)
AMBER: mm_gbsa results for charged ligands Cenk Andac (Fri Dec 24 2004 - 01:50:10 PST)
- Re: AMBER: mm_gbsa results for charged ligands Holger Gohlke (Fri Dec 24 2004 - 02:31:22 PST)
AMBER: Problem with computing Resp charges using RED Cenk Andac (Sat Dec 25 2004 - 07:54:54 PST)
- Re: AMBER: Problem with computing Resp charges using RED FyD (Wed Dec 29 2004 - 12:54:05 PST)
  - Re: AMBER: Problem with computing Resp charges using RED Cenk Andac (Thu Dec 30 2004 - 09:30:34 PST)
    - AMBER: Dummy Atoms: How to create them? Ilyas Yildirim (Thu Dec 30 2004 - 17:23:02 PST)
    - Re: AMBER: Dummy Atoms: How to create them? David A. Case (Thu Dec 30 2004 - 19:55:59 PST)
    - Re: AMBER: Dummy Atoms: How to create them? Ilyas Yildirim (Tue Jan 04 2005 - 19:25:24 PST)
    - Re: AMBER: Dummy Atoms: How to create them? David A. Case (Wed Jan 05 2005 - 09:40:11 PST)
    - Re: AMBER: Dummy Atoms: How to create them? Ilyas Yildirim (Wed Jan 05 2005 - 13:05:22 PST)
    - Re: AMBER: Dummy Atoms: How to create them? David A. Case (Tue Jan 11 2005 - 21:54:02 PST)
    - Re: AMBER: Problem with computing Resp charges using RED Cenk Andac (Sat Jan 01 2005 - 06:08:24 PST)
    - Re: AMBER: Problem with computing Resp charges using RED FyD (Sat Jan 01 2005 - 11:51:12 PST)
AMBER: input conversion error [Amber8] Bimo Ario Tejo (Tue Dec 28 2004 - 21:15:58 PST)
AMBER: NSCM Alberto p (Wed Dec 29 2004 - 04:07:48 PST)
- Re: AMBER: NSCM David A. Case (Sun Jan 02 2005 - 14:35:54 PST)
AMBER: MM_PBSA calculations Jiten (Wed Dec 29 2004 - 23:22:25 PST)
AMBER: MM_PBSA calculation error Jiten (Thu Dec 30 2004 - 02:57:30 PST)
AMBER: MD simulations on heparin and heparin sulfate Harald Lanig (Thu Dec 30 2004 - 08:23:24 PST)
AMBER: How is optimization done during energy minimization of the force field? fangyu liang (Thu Dec 30 2004 - 21:11:28 PST)
- Re: AMBER: How is optimization done during energy minimization of the force field? myang (Fri Dec 31 2004 - 08:49:58 PST)
AMBER: mm_pbsa +fillratio Jiten (Fri Dec 31 2004 - 01:31:57 PST)
AMBER: Sander and NMODE energy minimization fangyu liang (Sat Jan 01 2005 - 21:53:49 PST)
- Re: AMBER: Sander and NMODE energy minimization David A. Case (Sun Jan 02 2005 - 14:47:28 PST)
AMBER: How can i use AMBER with CHARMM forcefield parameter? 王小清 (Sun Jan 02 2005 - 19:54:25 PST)
- Re: AMBER: How can i use AMBER with CHARMM forcefield parameter? David A. Case (Thu Jan 06 2005 - 06:23:44 PST)
AMBER: MM_PBSA fillratio error Jiten (Mon Jan 03 2005 - 01:36:30 PST)
- Re: AMBER: MM_PBSA fillratio error Ray Luo (Mon Jan 03 2005 - 14:28:46 PST)
- Re: AMBER: MM_PBSA fillratio error Jiten (Tue Jan 04 2005 - 22:54:35 PST)
AMBER: Hbonds restraints OK but Dihedral restraints not applied pl (Mon Jan 03 2005 - 06:06:48 PST)
- Re: AMBER: Hbonds restraints OK but Dihedral restraints not applied David A. Case (Mon Jan 03 2005 - 08:34:09 PST)
  - Re: AMBER: Hbonds restraints OK but Dihedral restraints not applied pl (Tue Jan 04 2005 - 03:27:07 PST)
    - Re: AMBER: Hbonds restraints OK but Dihedral restraints not applied Carlos Simmerling (Tue Jan 04 2005 - 04:47:03 PST)
    - Re: AMBER: Hbonds restraints OK but Dihedral restraints not applied pl (Tue Jan 04 2005 - 05:25:39 PST)
  - AMBER: Weighting of different restraint types? pl (Fri Jan 07 2005 - 05:03:15 PST)
    - Re: AMBER: Weighting of different restraint types? David A. Case (Fri Jan 07 2005 - 16:06:37 PST)
    - Re: AMBER: Weighting of different restraint types? pl (Mon Jan 10 2005 - 01:27:19 PST)
- Re: AMBER: Hbonds restraints OK but Dihedral restraints not applied Bill Ross (Tue Jan 04 2005 - 10:07:49 PST)
AMBER: AMBER related employment Anthony Fejes (Mon Jan 03 2005 - 17:43:24 PST)
AMBER: lipid bilayer membrane force field parameter Xiaoqing,Wang (Tue Jan 04 2005 - 01:51:47 PST)
AMBER: Steered Molecular Dynamics with AMBER? Rino Ragno (Tue Jan 04 2005 - 14:33:09 PST)
- Re: AMBER: Steered Molecular Dynamics with AMBER? Carlos Simmerling (Tue Jan 04 2005 - 14:47:38 PST)
- Re: AMBER: Steered Molecular Dynamics with AMBER? David E. Konerding (Tue Jan 04 2005 - 20:44:15 PST)
  - Re: AMBER: Steered Molecular Dynamics with AMBER? Anthony Fejes (Wed Jan 05 2005 - 08:26:05 PST)
- Re: AMBER: Steered Molecular Dynamics with AMBER? Piotr Cieplak (Tue Jan 04 2005 - 23:29:41 PST)
  - Re: AMBER: Steered Molecular Dynamics with AMBER? aldo jongejan (Tue Jan 04 2005 - 23:46:44 PST)
  - Re: AMBER: Steered Molecular Dynamics with AMBER? Adrian E. Roitberg (Wed Jan 05 2005 - 06:13:10 PST)
AMBER: lipid parameter file Xiaoqing,Wang (Wed Jan 05 2005 - 00:23:07 PST)
AMBER: distance between images cailliez (Wed Jan 05 2005 - 02:34:46 PST)
- Re: AMBER: distance between images Thomas E. Cheatham, III (Wed Jan 05 2005 - 09:29:19 PST)
AMBER: MM_PBSA arguments for MM calculations Nelson Fonseca (Wed Jan 05 2005 - 03:54:30 PST)
AMBER: Floating Exception in sander anshul.imtech.res.in (Wed Jan 05 2005 - 15:26:20 PST)
- Re: AMBER: Floating Exception in sander Robert Duke (Wed Jan 05 2005 - 05:55:22 PST)
  - Re: AMBER: Floating Exception in sander anshul.imtech.res.in (Fri Jan 07 2005 - 06:14:12 PST)
- Re: AMBER: Floating Exception in sander Robert Duke (Fri Jan 07 2005 - 05:15:44 PST)
AMBER: General Question about AMBER's Free Energy Perturbation Method Chris Moth (Wed Jan 05 2005 - 14:06:33 PST)
AMBER: about install amber8 on windows xiaowen (Thu Jan 06 2005 - 14:56:53 PST)
- Re: AMBER: about install amber8 on windows David A. Case (Fri Jan 07 2005 - 10:59:27 PST)
AMBER: recompiling problem on IBM aix Yuuki A. Komata (Thu Jan 06 2005 - 18:35:46 PST)
- Re: AMBER: recompiling problem on IBM aix David A. Case (Fri Jan 07 2005 - 11:03:30 PST)
AMBER: Questions about sander.QMMM Cenk Andac (Fri Jan 07 2005 - 07:51:56 PST)
- Re: AMBER: Questions about sander.QMMM M. L. Dodson (Fri Jan 07 2005 - 08:26:25 PST)
  - Re: AMBER: Questions about sander.QMMM M. L. Dodson (Fri Jan 07 2005 - 08:45:45 PST)
- RE: AMBER: Questions about sander.QMMM Ross Walker (Fri Jan 07 2005 - 11:38:29 PST)
  - RE: AMBER: Questions about sander.QMMM Cenk Andac (Sat Jan 08 2005 - 01:57:22 PST)
AMBER: dynamics Germán Sciaini (Sat Jan 08 2005 - 11:51:30 PST)
- Re: AMBER: dynamics David A. Case (Sat Jan 08 2005 - 13:05:53 PST)
AMBER: Floating Exception and installation on Digital Unix. anshul.imtech.res.in (Sun Jan 09 2005 - 19:32:11 PST)
- Re: AMBER: Floating Exception and installation on Digital Unix. Robert Duke (Sun Jan 09 2005 - 09:54:16 PST)
  - Re: AMBER: Floating Exception and installation on Digital Unix. anshul.imtech.res.in (Tue Jan 11 2005 - 07:17:32 PST)
- Re: AMBER: Floating Exception and installation on Digital Unix. Robert Duke (Tue Jan 11 2005 - 05:18:20 PST)
  - Re: AMBER: Floating Exception and installation on Digital Unix. M. L. Dodson (Tue Jan 11 2005 - 07:46:45 PST)
AMBER: error in parallel gsmith.ibab.ac.in (Mon Jan 10 2005 - 00:18:51 PST)
- AMBER: .dat and frcmod files Ilyas Yildirim (Mon Jan 10 2005 - 14:10:36 PST)
  - Re: AMBER: .dat and frcmod files Anthony Fejes (Mon Jan 10 2005 - 14:47:12 PST)
  - Re: AMBER: .dat and frcmod files Germán Sciaini (Tue Jan 11 2005 - 02:46:03 PST)
    - AMBER: pmemd and restraints Filip Lankas (Wed Jan 26 2005 - 09:01:50 PST)
    - Re: AMBER: pmemd and restraints Robert Duke (Wed Jan 26 2005 - 09:45:01 PST)
    - Re: AMBER: pmemd and restraints Fabien Cailliez (Thu Jan 27 2005 - 01:01:31 PST)
    - Re: AMBER: pmemd and restraints Robert Duke (Thu Jan 27 2005 - 05:15:00 PST)
AMBER: istart2 gsmith.ibab.ac.in (Mon Jan 10 2005 - 05:14:15 PST)
- RE: AMBER: istart2 Ross Walker (Mon Jan 10 2005 - 09:18:32 PST)
AMBER: guanidinium chloride Monica Civera (Mon Jan 10 2005 - 07:27:38 PST)
- RE: AMBER: guanidinium chloride Nagy, Peter I. (Mon Jan 10 2005 - 09:15:41 PST)
AMBER: Copper library? Cenk Andac (Mon Jan 10 2005 - 10:31:51 PST)
- Re: AMBER: Copper library? Germán Sciaini (Tue Jan 11 2005 - 02:40:55 PST)
AMBER: the DNA conformation after engery minimization using NMODE Xiaowei (David) Li (Mon Jan 10 2005 - 11:32:26 PST)
AMBER: AMBER tutorial ambpdb question Kara Wald (Mon Jan 10 2005 - 17:33:44 PST)
- RE: AMBER: AMBER tutorial ambpdb question Ross Walker (Mon Jan 10 2005 - 18:14:49 PST)
- Re: AMBER: AMBER tutorial ambpdb question David A. Case (Mon Jan 10 2005 - 19:16:10 PST)
Re: AMBER: the DNA conformation after engery minimization using NMODE Bill Ross (Mon Jan 10 2005 - 19:56:25 PST)
AMBER: parallel run gsmith.ibab.ac.in (Tue Jan 11 2005 - 02:27:20 PST)
AMBER: QM/MM with pmemd Ping Lin (Tue Jan 11 2005 - 11:08:45 PST)
AMBER: sander free energy calculation Cai, Yufeng (Tue Jan 11 2005 - 11:47:03 PST)
AMBER: PB dynamics Nelson Fonseca (Wed Jan 12 2005 - 02:06:33 PST)
- AMBER: van der waals parameters Monica Civera (Wed Jan 12 2005 - 03:42:53 PST)
  - Re: AMBER: van der waals parameters Carlos Simmerling (Wed Jan 12 2005 - 04:41:31 PST)
- Re: AMBER: PB dynamics David A. Case (Wed Jan 12 2005 - 09:26:19 PST)
AMBER: amber8 parallel sander yen li (Wed Jan 12 2005 - 02:57:19 PST)
- Re: AMBER: amber8 parallel sander Carlos Simmerling (Wed Jan 12 2005 - 04:38:30 PST)
- Re: AMBER: amber8 parallel sander Robert Duke (Wed Jan 12 2005 - 05:03:05 PST)
  - Re: AMBER: amber8 parallel sander yen li (Wed Jan 12 2005 - 05:54:48 PST)
    - Re: AMBER: amber8 parallel sander Carlos Simmerling (Wed Jan 12 2005 - 06:03:32 PST)
    - Re: AMBER: amber8 parallel sander Robert Duke (Wed Jan 12 2005 - 07:20:40 PST)
- Re: AMBER: amber8 parallel sander Carlos Simmerling (Wed Jan 12 2005 - 07:30:22 PST)
- Re: AMBER: amber8 parallel sander Bill Ross (Wed Jan 12 2005 - 12:12:18 PST)
- Re: AMBER: amber8 parallel sander yen li (Mon Jan 17 2005 - 09:55:26 PST)
  - Re: AMBER: amber8 parallel sander Robert Duke (Mon Jan 17 2005 - 10:13:10 PST)
- Re: AMBER: amber8 parallel sander Kathleen Erickson (Thu Sep 22 2005 - 09:44:39 PDT)
  - Re: AMBER: amber8 parallel sander Robert Duke (Thu Sep 22 2005 - 09:57:53 PDT)
  - Re: AMBER: amber8 parallel sander Carlos P. Sosa (Fri Sep 23 2005 - 05:02:26 PDT)
- Re: AMBER: amber8 parallel sander Peter Gannett (Thu Sep 22 2005 - 14:18:22 PDT)
  - Re: AMBER: amber8 parallel sander Carlos Simmerling (Thu Sep 22 2005 - 15:25:07 PDT)
- Re: AMBER: amber8 parallel sander Peter Gannett (Thu Sep 22 2005 - 14:15:12 PDT)
  - Re: AMBER: amber8 parallel sander Robert Duke (Thu Sep 22 2005 - 14:47:10 PDT)
- Re: AMBER: amber8 parallel sander Kathleen Erickson (Mon Oct 03 2005 - 13:37:47 PDT)
- Re: AMBER: amber8 parallel sander MURAT CETINKAYA (Mon Oct 03 2005 - 19:04:04 PDT)
  - Re: AMBER: amber8 parallel sander Robert Duke (Mon Oct 03 2005 - 22:26:28 PDT)
AMBER: units Monica Civera (Wed Jan 12 2005 - 07:12:19 PST)
- Re: AMBER: units David A. Case (Wed Jan 12 2005 - 09:22:03 PST)
- Re: AMBER: units Germán Sciaini (Thu Jan 13 2005 - 03:33:16 PST)
- Re: AMBER: units Germán Sciaini (Thu Jan 13 2005 - 03:35:07 PST)
AMBER: Problem with restart file Azira Muhamad (Wed Jan 12 2005 - 23:45:30 PST)
- Re: AMBER: Problem with restart file Melinda Layten (Thu Jan 13 2005 - 06:53:42 PST)
- Re: AMBER: Problem with restart file Guanglei Cui (Thu Jan 13 2005 - 07:40:14 PST)
AMBER: PBCAL=0. Problems in MM/PBSA Javier Perez Miron (Thu Jan 13 2005 - 12:41:29 PST)
- Re: AMBER: PBCAL=0. Problems in MM/PBSA Holger Gohlke (Thu Jan 13 2005 - 23:31:45 PST)
- AMBER: problem runing parallel (REM) on tru64 Sergio E. Wong (Fri Jan 21 2005 - 16:22:26 PST)
  - Re: AMBER: problem runing parallel (REM) on tru64 David A. Case (Sat Jan 22 2005 - 10:25:55 PST)
    - Re: AMBER: problem runing parallel (REM) on tru64 Sergio E. Wong (Sat Jan 22 2005 - 12:44:23 PST)
    - AMBER: amber 8 benchmarks dec alpha Sergio E. Wong (Mon Jan 24 2005 - 14:08:14 PST)
    - Re: AMBER: amber 8 benchmarks dec alpha Robert Duke (Mon Jan 24 2005 - 14:27:50 PST)
    - Re: AMBER: amber 8 benchmarks dec alpha Sergio E. Wong (Mon Jan 24 2005 - 15:54:41 PST)
AMBER: last call for early registrations for "Horizons2005" Vlad Cojocaru (Fri Jan 14 2005 - 05:19:00 PST)
AMBER: protonate Gustavo Pierdominici Sottile (Fri Jan 14 2005 - 10:05:49 PST)
- Re: AMBER: protonate David A. Case (Fri Jan 14 2005 - 10:36:35 PST)
  - Re: AMBER: protonate myang (Tue Jan 18 2005 - 08:07:12 PST)
AMBER: Coordinate Superimposition in PTRAJ Vineet Pande (Sun Jan 16 2005 - 03:42:09 PST)
- Re: AMBER: Coordinate Superimposition in PTRAJ Carlos Simmerling (Sun Jan 16 2005 - 06:56:30 PST)
- RE: AMBER: Coordinate Superimposition in PTRAJ Ross Walker (Sun Jan 16 2005 - 10:59:48 PST)
  - RE: AMBER: Coordinate Superimposition in PTRAJ Vineet Pande (Mon Jan 17 2005 - 01:45:20 PST)
AMBER: How to set AMBER parameter files for lipid? Xiaoqing Wang (Sun Jan 16 2005 - 17:38:49 PST)
AMBER: Sander Replica Exchange exits with unit 6 error] Jordi Rodrigo (Mon Jan 17 2005 - 00:02:51 PST)
- Re: AMBER: Sander Replica Exchange exits with unit 6 error] Carlos Simmerling (Mon Jan 17 2005 - 05:58:20 PST)
AMBER: distance restraint and file fort.35 Fabien Cailliez (Mon Jan 17 2005 - 03:34:00 PST)
- Re: AMBER: distance restraint and file fort.35 Robert Duke (Mon Jan 17 2005 - 06:48:57 PST)
  - Re: AMBER: distance restraint and file fort.35 Fabien Cailliez (Mon Jan 17 2005 - 07:58:03 PST)
AMBER: RMS fluctuations along modes obtained from PCA Majid moghaddam (Mon Jan 17 2005 - 05:47:56 PST)
- Re: AMBER: RMS fluctuations along modes obtained from PCA Holger Gohlke (Wed Jan 19 2005 - 06:51:10 PST)
AMBER: Sander Replica Exchange exits with unit 6 error Jordi Rodrigo (Mon Jan 17 2005 - 04:37:00 PST)
- Re: AMBER: Sander Replica Exchange exits with unit 6 error Carlos Simmerling (Mon Jan 17 2005 - 06:45:56 PST)
- Re: AMBER: Sander Replica Exchange exits with unit 6 error Guanglei Cui (Mon Jan 17 2005 - 08:09:03 PST)
AMBER: Sander Replica Exchange exits with unit 6 error Jordi Rodrigo (Mon Jan 17 2005 - 05:25:14 PST)
AMBER: new aminoacid Gustavo Pierdominici Sottile (Mon Jan 17 2005 - 08:26:32 PST)
- Re: AMBER: new aminoacid David A. Case (Mon Jan 17 2005 - 09:56:34 PST)
- RE: AMBER: new aminoacid Ross Walker (Mon Jan 17 2005 - 10:34:05 PST)
AMBER: Sander Replica Exchange exits with unit 6 error Jordi Rodrigo (Mon Jan 17 2005 - 06:57:53 PST)
- Re: AMBER: Sander Replica Exchange exits with unit 6 error Carlos Simmerling (Mon Jan 17 2005 - 09:17:56 PST)
- Re: AMBER: Sander Replica Exchange exits with unit 6 error Guanglei Cui (Mon Jan 17 2005 - 11:31:07 PST)
AMBER: Compiling AMBER 8 for Mac OSX (Parallel) nallen.unca.edu (Mon Jan 17 2005 - 09:41:06 PST)
- Re: AMBER: Compiling AMBER 8 for Mac OSX (Parallel) Emmanuel Giudice (Mon Jan 17 2005 - 22:09:47 PST)
  - RE: AMBER: Compiling AMBER 8 for Mac OSX (Parallel) Ross Walker (Wed Jan 19 2005 - 10:23:40 PST)
- AMBER: stereo Filip Lankas (Wed Feb 09 2005 - 09:53:45 PST)
  - RE: AMBER: stereo Vineet Pande (Wed Feb 09 2005 - 10:51:06 PST)
  - Re: AMBER: stereo Chris Moth (Wed Feb 09 2005 - 12:02:13 PST)
AMBER: H-atom types attached to a carbon atom next to carbonyl group Takashi Nakamura (Mon Jan 17 2005 - 09:52:56 PST)
- RE: AMBER: H-atom types attached to a carbon atom next to carbonyl group Vineet Pande (Mon Jan 17 2005 - 12:32:37 PST)
AMBER: SO4 prep file Jagdish Rai (Tue Jan 18 2005 - 04:36:42 PST)
- Re: AMBER: SO4 prep file scopio (Tue Jan 18 2005 - 04:57:29 PST)
AMBER: details of new aminoacid Gustavo Pierdominici Sottile (Tue Jan 18 2005 - 05:01:15 PST)
- Re: AMBER: details of new aminoacid David A. Case (Tue Jan 18 2005 - 08:01:20 PST)
AMBER: GB differences between AMBER7 and AMBER8 Fabien Cailliez (Tue Jan 18 2005 - 05:53:04 PST)
- Re: AMBER: GB differences between AMBER7 and AMBER8 Carlos Simmerling (Tue Jan 18 2005 - 06:08:20 PST)
AMBER: problem with position restraints (refc file) pl (Tue Jan 18 2005 - 07:25:27 PST)
- Re: AMBER: problem with position restraints (refc file) Carlos Simmerling (Tue Jan 18 2005 - 08:03:03 PST)
  - Re: AMBER: problem with position restraints (refc file) pl (Tue Jan 18 2005 - 09:13:17 PST)
    - Re: AMBER: problem with position restraints (refc file) Carlos Simmerling (Tue Jan 18 2005 - 09:36:55 PST)
    - Re: AMBER: problem with position restraints (refc file) pl (Wed Jan 19 2005 - 03:47:18 PST)
AMBER: Amber8 installation problems on Sparc/Solaris9 Joe Nolan (Tue Jan 18 2005 - 08:17:35 PST)
- Re: AMBER: Amber8 installation problems on Sparc/Solaris9 David A. Case (Tue Jan 18 2005 - 08:48:33 PST)
AMBER: Sander Replica Exchange exits with unit 6 error Jordi Rodrigo (Tue Jan 18 2005 - 06:46:27 PST)
AMBER: Converting prmtop and inpcrd files Andrew Box (Tue Jan 18 2005 - 15:02:02 PST)
Re: AMBER: Converting prmtop and inpcrd files Bill Ross (Tue Jan 18 2005 - 15:43:04 PST)
AMBER: Scaling of charges in a polarizable simulation ! Pradipta Bandyopadhyay (Wed Jan 19 2005 - 08:02:37 PST)
- Re: AMBER: Scaling of charges in a polarizable simulation ! David A. Case (Wed Jan 19 2005 - 12:11:08 PST)
  - Re: AMBER: Scaling of charges in a polarizable simulation ! Pradipta Bandyopadhyay (Wed Jan 19 2005 - 20:54:13 PST)
- Re: AMBER: Scaling of charges in a polarizable simulation ! Piotr Cieplak (Wed Jan 19 2005 - 22:56:04 PST)
AMBER: IGB parameter Javier Perez Miron (Wed Jan 19 2005 - 09:09:38 PST)
- Re: AMBER: IGB parameter Furse, Kristina Elisabet (Wed Jan 19 2005 - 11:33:13 PST)
AMBER: enhanced sampling methods Vlad Cojocaru (Wed Jan 19 2005 - 10:13:58 PST)
- Re: AMBER: enhanced sampling methods David A. Case (Wed Jan 19 2005 - 12:34:24 PST)
  - AMBER: AMBER8: compiling under cygwin using lahey fortran Rino Ragno (Wed Jan 19 2005 - 14:13:07 PST)
Re: AMBER: Scaling of charges in a polarizable simulation ! Piotr Cieplak (Wed Jan 19 2005 - 10:14:05 PST)
AMBER: ptraj analysis Thomas E. Cheatham, III (Wed Jan 19 2005 - 10:16:17 PST)
- Re: AMBER: ptraj analysis David A. Case (Wed Jan 19 2005 - 12:24:58 PST)
- Re: AMBER: ptraj analysis Holger Gohlke (Wed Jan 19 2005 - 23:28:27 PST)
AMBER:Hydroxy Proline S.Sundar Raman (Thu Jan 20 2005 - 01:19:42 PST)
AMBER: pmemd and distance restraint Fabien Cailliez (Thu Jan 20 2005 - 02:39:20 PST)
- Re: AMBER: pmemd and distance restraint Robert Duke (Thu Jan 20 2005 - 04:41:30 PST)
- Re: AMBER: pmemd and distance restraint Robert Duke (Thu Jan 20 2005 - 19:12:17 PST)
AMBER: some question about MM-PBSA scopio (Thu Jan 20 2005 - 07:10:39 PST)
AMBER: Cutoff for anal Harianto (Thu Jan 20 2005 - 09:50:14 PST)
- Re: AMBER: Cutoff for anal David A. Case (Thu Jan 20 2005 - 11:17:31 PST)
AMBER: new tutorial available David A. Case (Thu Jan 20 2005 - 11:06:30 PST)
- Re: AMBER: new tutorial available Ilyas Yildirim (Wed Jan 26 2005 - 03:59:16 PST)
  - Re: AMBER: new tutorial available Julien Michel (Wed Jan 26 2005 - 05:48:55 PST)
  - Re: AMBER: new tutorial available David A. Case (Wed Jan 26 2005 - 09:27:58 PST)
- Re: AMBER: new tutorial available Difei Wang (Fri Jan 28 2005 - 16:08:59 PST)
  - Re: AMBER: new tutorial available David A. Case (Fri Jan 28 2005 - 16:57:28 PST)
AMBER: Can someone recommend a tutorial? Kara Wald (Thu Jan 20 2005 - 12:28:46 PST)
- RE: AMBER: Can someone recommend a tutorial? Ross Walker (Thu Jan 20 2005 - 12:37:22 PST)
AMBER: sander failure ygao.phase1.unl.edu (Thu Jan 20 2005 - 13:46:56 PST)
- RE: AMBER: sander failure Ross Walker (Thu Jan 20 2005 - 14:04:32 PST)
  - RE: AMBER: sander failure ygao.phase1.unl.edu (Thu Jan 20 2005 - 14:09:56 PST)
    - Re: AMBER: sander failure Carlos Simmerling (Thu Jan 20 2005 - 14:20:00 PST)
    - RE: AMBER: sander failure Ross Walker (Thu Jan 20 2005 - 14:26:58 PST)
    - RE: AMBER: sander failure ygao.phase1.unl.edu (Thu Jan 20 2005 - 14:31:37 PST)
    - RE: AMBER: sander failure Ross Walker (Thu Jan 20 2005 - 14:47:34 PST)
    - Re: AMBER: sander failure Asim Okur (Thu Jan 20 2005 - 14:50:25 PST)
AMBER: Suspended (tty input) ygao.phase1.unl.edu (Thu Jan 20 2005 - 15:39:48 PST)
- RE: AMBER: Suspended (tty input) Ross Walker (Thu Jan 20 2005 - 15:58:13 PST)
- Re: AMBER: Suspended (tty input) Thomas E. Cheatham, III (Thu Jan 20 2005 - 16:09:16 PST)
AMBER: &dipoles in sander Cenk Andac (Fri Jan 21 2005 - 03:59:47 PST)
- RE: AMBER: &dipoles in sander Ross Walker (Fri Jan 21 2005 - 10:26:24 PST)
  - RE: AMBER: &dipoles in sander Cenk Andac (Sat Jan 22 2005 - 01:47:50 PST)
    - RE: AMBER: &dipoles in sander Ross Walker (Sat Jan 22 2005 - 11:11:54 PST)
    - RE: AMBER: &dipoles in sander Cenk Andac (Fri Jan 28 2005 - 02:04:21 PST)
    - RE: AMBER: &dipoles in sander Ross Walker (Fri Jan 28 2005 - 10:10:21 PST)
    - Re: AMBER: &dipoles in sander David A. Case (Fri Jan 28 2005 - 10:21:59 PST)
    - Re: AMBER: &dipoles in sander Cenk Andac (Fri Jan 28 2005 - 11:25:36 PST)
AMBER: mm_pbsa example doesn't run Yuuki Komata (Fri Jan 21 2005 - 04:10:48 PST)
AMBER: amber 8 installation Stern, Julie (Fri Jan 21 2005 - 09:28:17 PST)
- Re: AMBER: amber 8 installation David A. Case (Fri Jan 21 2005 - 09:55:50 PST)
- Re: AMBER: amber 8 installation Robert Duke (Fri Jan 21 2005 - 10:03:42 PST)
AMBER: Andersen thermostat: target T? Arantxa Sanz (Fri Jan 21 2005 - 11:06:01 PST)
- Re: AMBER: Andersen thermostat: target T? David A. Case (Fri Jan 21 2005 - 16:23:17 PST)
  - RE: AMBER: Andersen thermostat: target T? Arantxa Sanz (Mon Jan 24 2005 - 02:18:05 PST)
AMBER: carnal - water-mediated HBond Sichun Yang (Fri Jan 21 2005 - 14:36:52 PST)
AMBER: eedmeth=5 Lihua Wang (Fri Jan 21 2005 - 16:20:59 PST)
- Re: AMBER: eedmeth=5 David A. Case (Sat Jan 22 2005 - 10:20:22 PST)
- RE: AMBER: eedmeth=5 Vineet Pande (Sun Jan 23 2005 - 03:46:23 PST)
AMBER: nmode calculation mingche Pan (Fri Jan 21 2005 - 17:43:32 PST)
Re: AMBER: carnal - water-mediated HBond Bill Ross (Sat Jan 22 2005 - 20:49:09 PST)
- Re: AMBER: carnal - water-mediated HBond Jiri Sponer (Sun Jan 23 2005 - 06:52:55 PST)
AMBER: Question about TI integral method tanc.uci.edu (Sun Jan 23 2005 - 02:01:33 PST)
- Re: AMBER: Question about TI integral method David A. Case (Sun Jan 23 2005 - 22:41:26 PST)
AMBER: D-amino acid prep-files(simple method) Jagdish Rai (Sun Jan 23 2005 - 06:18:45 PST)
- Re: AMBER: D-amino acid prep-files(simple method) FyD (Sun Jan 23 2005 - 12:05:38 PST)
AMBER: system size limit Guanglei Cui (Sun Jan 23 2005 - 21:54:06 PST)
- Re: AMBER: system size limit David A. Case (Sun Jan 23 2005 - 22:56:30 PST)
AMBER: What does a crash mean while running a md simulation? shuli kang (Sun Jan 23 2005 - 21:56:00 PST)
- RE: AMBER: What does a crash mean while running a md simulation? Ross Walker (Mon Jan 24 2005 - 11:19:48 PST)
  - Re: AMBER: What does a crash mean while running a md simulation? shuli kang (Mon Jan 24 2005 - 21:58:54 PST)
    - RE: AMBER: What does a crash mean while running a md simulation? Ross Walker (Mon Jan 24 2005 - 22:28:32 PST)
    - Re: AMBER: What does a crash mean while running a md simulation? shuli kang (Mon Jan 24 2005 - 23:35:45 PST)
    - Re[2]: AMBER: What does a crash mean while running a md simulation? sychen (Tue Dec 06 2005 - 04:16:49 PST)
    - RE: Re[2]: AMBER: What does a crash mean while running a md simulation? Ross Walker (Tue Dec 06 2005 - 08:54:11 PST)
AMBER: FW: amber 8 problem Vojtěch Klusák (Mon Jan 24 2005 - 00:13:47 PST)
- Re: AMBER: FW: amber 8 problem David A. Case (Mon Jan 31 2005 - 10:37:08 PST)
AMBER: nmode calculation mingche Pan (Mon Jan 24 2005 - 07:34:18 PST)
- RE: AMBER: nmode calculation Ross Walker (Mon Jan 24 2005 - 11:13:59 PST)
  - RE: AMBER: nmode calculation mingche Pan (Mon Jan 24 2005 - 14:12:13 PST)
  - AMBER: error in pbsa calculation mingche Pan (Tue Apr 26 2005 - 14:15:13 PDT)
    - Re: AMBER: error in pbsa calculation Ray Luo (Tue Apr 26 2005 - 14:39:50 PDT)
    - Re: AMBER: error in pbsa calculation mingche Pan (Wed Apr 27 2005 - 09:20:10 PDT)
    - Re: AMBER: error in pbsa calculation Ray Luo (Wed Apr 27 2005 - 10:03:33 PDT)
  - AMBER: molsurf error mingche Pan (Tue May 17 2005 - 09:52:57 PDT)
AMBER: AMBER 8: Freeze AND restrain questions Guillaume Bollot (Mon Jan 24 2005 - 08:19:11 PST)
- Re: AMBER: AMBER 8: Freeze AND restrain questions Viktor Hornak (Mon Jan 24 2005 - 10:02:53 PST)
AMBER: test suite possible failures Stern, Julie (Mon Jan 24 2005 - 11:39:42 PST)
- Re: AMBER: test suite possible failures David A. Case (Mon Jan 24 2005 - 14:38:21 PST)
AMBER: How to make PDB file by myself Mayumi Haga (Mon Jan 24 2005 - 20:23:32 PST)
- RE: AMBER: How to make PDB file by myself Vineet Pande (Tue Jan 25 2005 - 03:06:42 PST)
- Re: AMBER: How to make PDB file by myself David A. Case (Tue Jan 25 2005 - 08:40:21 PST)
AMBER: TI with electrostatic decoupling at sander yipinl.umich.edu (Mon Jan 24 2005 - 21:15:43 PST)
- Re: AMBER: TI with electrostatic decoupling at sander David A. Case (Tue Jan 25 2005 - 08:41:36 PST)
  - Re: AMBER: TI with electrostatic decoupling at sander yipinl.umich.edu (Wed Jan 26 2005 - 09:19:43 PST)
    - Re: AMBER: TI with electrostatic decoupling at sander David A. Case (Wed Jan 26 2005 - 21:51:32 PST)
    - Re: AMBER: TI with electrostatic decoupling at sander yipinl.umich.edu (Thu Jan 27 2005 - 09:39:46 PST)
    - Re: AMBER: TI with electrostatic decoupling at sander David A. Case (Thu Jan 27 2005 - 17:27:10 PST)
AMBER: calculating electrostatic potential Vlad Cojocaru (Tue Jan 25 2005 - 02:59:48 PST)
- Re: AMBER: calculating electrostatic potential david.evans.ulsop.ac.uk (Tue Jan 25 2005 - 03:24:52 PST)
  - AMBER: Error while running resp. praveena moldy (Tue Jan 25 2005 - 06:24:01 PST)
    - Re: AMBER: Error while running resp. David A. Case (Tue Jan 25 2005 - 08:43:32 PST)
  - AMBER: Error while running resp. praveena moldy (Tue Jan 25 2005 - 06:28:55 PST)
- Re: AMBER: calculating electrostatic potential Ilyas Yildirim (Tue Jan 25 2005 - 10:26:32 PST)
AMBER: PBSA residual and pairwise decompostion Jiten (Tue Jan 25 2005 - 05:43:38 PST)
AMBER: LEAP heddi (Tue Jan 25 2005 - 05:42:36 PST)
AMBER: Sander Replica Exchange exits with unit 6 error Jordi Rodrigo (Tue Jan 25 2005 - 06:28:13 PST)
AMBER: gold atoms Stern, Julie (Tue Jan 25 2005 - 08:53:09 PST)
AMBER: collision frequency in GBSA dynamics Giulio Rastelli (Tue Jan 25 2005 - 10:33:33 PST)
- Re: AMBER: collision frequency in GBSA dynamics David A. Case (Tue Jan 25 2005 - 14:23:34 PST)
AMBER: NAN errors Venkata S Koppuravuri (Tue Jan 25 2005 - 13:39:45 PST)
- RE: AMBER: NAN errors Ross Walker (Tue Jan 25 2005 - 13:56:33 PST)
- Re: AMBER: NAN errors David A. Case (Tue Jan 25 2005 - 14:09:11 PST)
AMBER: ANTECHAMBER & DIVCON Vineet Pande (Wed Jan 26 2005 - 02:18:17 PST)
- Re: AMBER: ANTECHAMBER & DIVCON Julien Michel (Wed Jan 26 2005 - 03:09:05 PST)
- Re: AMBER: ANTECHAMBER & DIVCON David A. Case (Thu Jan 27 2005 - 17:12:23 PST)
AMBER: how to solvate in TIP5P box ygao.phase1.unl.edu (Wed Jan 26 2005 - 07:59:43 PST)
- RE: AMBER: how to solvate in TIP5P box Ross Walker (Wed Jan 26 2005 - 10:26:22 PST)
AMBER: Increasing Volume with ntb=1 Harianto (Wed Jan 26 2005 - 12:12:29 PST)
- RE: AMBER: Increasing Volume with ntb=1 Ross Walker (Wed Jan 26 2005 - 12:42:13 PST)
  - Re: AMBER: Increasing Volume with ntb=1 Harianto (Wed Jan 26 2005 - 15:19:59 PST)
    - RE: AMBER: Increasing Volume with ntb=1 Ross Walker (Wed Jan 26 2005 - 14:59:57 PST)
    - Re: AMBER: Increasing Volume with ntb=1 Harianto (Thu Jan 27 2005 - 09:49:52 PST)
    - RE: AMBER: Increasing Volume with ntb=1 Ross Walker (Thu Jan 27 2005 - 10:13:27 PST)
AMBER:idecomp 小杉貴洋 (Thu Jan 27 2005 - 03:22:37 PST)
AMBER: replica exchange trouble with unit 6 Yuuki Komata (Thu Jan 27 2005 - 06:39:03 PST)
- Re: AMBER: replica exchange trouble with unit 6 Carlos Simmerling (Thu Jan 27 2005 - 07:10:20 PST)
  - Re: AMBER: replica exchange trouble with unit 6 Yuuki Komata (Thu Jan 27 2005 - 17:27:50 PST)
AMBER: antechamber error message Yanze Zhang (Thu Jan 27 2005 - 07:02:46 PST)
- Re: AMBER: antechamber error message David A. Case (Fri Jan 28 2005 - 14:00:22 PST)
AMBER: problem with pressure equilibration Cenk Andac (Thu Jan 27 2005 - 14:23:59 PST)
- RE: AMBER: problem with pressure equilibration Ross Walker (Thu Jan 27 2005 - 14:45:20 PST)
  - RE: AMBER: problem with pressure equilibration Cenk Andac (Fri Jan 28 2005 - 11:18:02 PST)
AMBER: question about xwin load pdb file xiaowen (Thu Jan 27 2005 - 21:04:57 PST)
- RE: AMBER: question about xwin load pdb file Ross Walker (Thu Jan 27 2005 - 21:38:30 PST)
AMBER: sugar pucker with Carnal and ptraj Vlad Cojocaru (Fri Jan 28 2005 - 06:56:23 PST)
AMBER: pucker: deatails about pucker calculation Vlad Cojocaru (Fri Jan 28 2005 - 07:13:13 PST)
AMBER: question about xwin load pdb file xiaowen (Fri Jan 28 2005 - 08:48:28 PST)
- RE: AMBER: question about xwin load pdb file Ross Walker (Fri Jan 28 2005 - 10:20:18 PST)
AMBER: plane definition in ptraj Vlad Cojocaru (Fri Jan 28 2005 - 10:00:23 PST)
AMBER: Problems with xLEaP Kara Di Giorgio (Fri Jan 28 2005 - 14:04:14 PST)
- RE: AMBER: Problems with xLEaP Ross Walker (Fri Jan 28 2005 - 14:19:52 PST)
  - Re: AMBER: Problems with xLEaP Kara Di Giorgio (Fri Jan 28 2005 - 16:14:02 PST)
    - Re: AMBER: Problems with xLEaP Kara Di Giorgio (Fri Jan 28 2005 - 16:48:52 PST)
Re: AMBER: Problems with xLEaP Bill Ross (Fri Jan 28 2005 - 14:26:12 PST)
- Re: AMBER: Problems with xLEaP Kara Di Giorgio (Fri Jan 28 2005 - 16:18:44 PST)
  - RE: AMBER: Problems with xLEaP Ross Walker (Fri Jan 28 2005 - 16:29:10 PST)
AMBER: NCOPY definition Kenley Barrett (Fri Jan 28 2005 - 14:59:14 PST)
- RE: AMBER: NCOPY definition Ross Walker (Fri Jan 28 2005 - 15:18:05 PST)
AMBER: Problem in ptraj anshul.imtech.res.in (Mon Jan 31 2005 - 14:23:30 PST)
- Re: AMBER: Problem in ptraj Furse, Kristina Elisabet (Mon Jan 31 2005 - 09:22:21 PST)
  - Re: AMBER: Problem in ptraj anshul.imtech.res.in (Tue Feb 01 2005 - 14:26:48 PST)
- Re: AMBER: Problem in ptraj Furse, Kristina Elisabet (Tue Feb 01 2005 - 11:30:53 PST)
  - Re: AMBER: Problem in ptraj anshul.imtech.res.in (Wed Feb 02 2005 - 14:04:28 PST)
    - Re: AMBER: Problem in ptraj Thomas E. Cheatham, III (Wed Feb 02 2005 - 10:34:01 PST)
- Re: AMBER: Problem in ptraj Furse, Kristina Elisabet (Wed Feb 02 2005 - 10:16:03 PST)
AMBER: amber 8 problem Vojtěch Klusák (Mon Jan 31 2005 - 05:01:35 PST)
AMBER: gaussian output file Yanze Zhang (Mon Jan 31 2005 - 09:09:40 PST)
- RE: AMBER: gaussian output file Junmei Wang (Tue Feb 01 2005 - 15:03:22 PST)
AMBER: skip snapshots with ptraj in amber 8.0 Eric Hu (Mon Jan 31 2005 - 11:30:58 PST)
- Re: AMBER: skip snapshots with ptraj in amber 8.0 Guanglei Cui (Mon Jan 31 2005 - 14:19:27 PST)
  - Re: AMBER: skip snapshots with ptraj in amber 8.0 Eric Hu (Mon Jan 31 2005 - 17:08:26 PST)
AMBER: Manuals need update: protonate -b and -c options gone in Amber 7 and 8 Chris Moth (Mon Jan 31 2005 - 13:39:56 PST)
- Re: AMBER: Manuals need update: protonate -b and -c options gone in Amber 7 and 8 David A. Case (Mon Jan 31 2005 - 14:56:21 PST)
AMBER: amber8 in IBM-SP4 Jiten (Mon Jan 31 2005 - 19:32:28 PST)
AMBER: N Metyl amino acids Andrew Box (Mon Jan 31 2005 - 21:14:47 PST)
- Re: AMBER: N Metyl amino acids Carlos Simmerling (Tue Feb 01 2005 - 04:47:30 PST)
AMBER: vacuum bubbles in system equilibration Marie-Pierre Durrieu (Tue Feb 01 2005 - 02:56:21 PST)
AMBER: Carnal in Amber8 Vlad Cojocaru (Tue Feb 01 2005 - 08:11:09 PST)
- Re: AMBER: Carnal in Amber8 David A. Case (Tue Feb 01 2005 - 09:27:25 PST)
- Re: AMBER: Carnal in Amber8 Bill Ross (Tue Feb 01 2005 - 11:57:19 PST)
AMBER: Multiple dihedral restraints Joseph Fernandez (Tue Feb 01 2005 - 09:29:40 PST)
- Re: AMBER: Multiple dihedral restraints David A. Case (Tue Feb 01 2005 - 14:54:49 PST)
  - AMBER: Multiple dihedral restraints (follow up) Joseph Fernandez (Wed Feb 02 2005 - 10:11:01 PST)
    - Re: AMBER: Multiple dihedral restraints (follow up) David A. Case (Wed Feb 02 2005 - 11:04:47 PST)
    - AMBER: non-periodic condition gsciaini (Thu Feb 03 2005 - 08:40:46 PST)
    - RE: AMBER: non-periodic condition Ross Walker (Thu Feb 03 2005 - 10:27:30 PST)
    - RE: AMBER: non-periodic condition Germán Sciaini (Thu Feb 03 2005 - 12:42:34 PST)
    - AMBER: dppsv returns error code: 29 Xiaowei (David) Li (Fri Feb 04 2005 - 09:58:56 PST)
    - Re: AMBER: dppsv returns error code: 29 David A. Case (Fri Feb 04 2005 - 14:48:38 PST)
    - Re: AMBER: Multiple dihedral restraints (follow up) M. L. Dodson (Thu Feb 03 2005 - 12:07:11 PST)
AMBER: Redhat Enterprise Linux Beale, John (Tue Feb 01 2005 - 09:49:20 PST)
- RE: AMBER: Redhat Enterprise Linux S. Frank Yan (Tue Feb 01 2005 - 09:57:00 PST)
- RE: AMBER: Redhat Enterprise Linux Andrew Box (Tue Feb 01 2005 - 15:37:55 PST)
- RE: AMBER: Redhat Enterprise Linux Beale, John (Wed Feb 02 2005 - 10:01:53 PST)
Re: AMBER: Carnal in Amber8 Bill Ross (Tue Feb 01 2005 - 11:47:15 PST)
AMBER: doubts with a new aminoacid Gustavo Pierdominici Sottile (Tue Feb 01 2005 - 12:28:52 PST)
- Re: AMBER: doubts with a new aminoacid David A. Case (Tue Feb 01 2005 - 15:35:36 PST)
- Re: AMBER: doubts with a new aminoacid Bill Ross (Tue Feb 01 2005 - 16:36:38 PST)
AMBER: External Electric Field Brandon Tefft (Tue Feb 01 2005 - 13:30:22 PST)
- Re: AMBER: External Electric Field David A. Case (Wed Feb 02 2005 - 10:08:59 PST)
AMBER: sander segmentation fault Xin Wang (Tue Feb 01 2005 - 14:15:12 PST)
- Re: AMBER: sander segmentation fault David A. Case (Wed Feb 02 2005 - 11:28:37 PST)
  - Re: AMBER: sander segmentation fault Xin Wang (Wed Feb 02 2005 - 13:36:25 PST)
    - Re: AMBER: sander segmentation fault David A. Case (Wed Feb 02 2005 - 14:39:06 PST)
- Re: AMBER: sander segmentation fault Furse, Kristina Elisabet (Wed Feb 02 2005 - 15:32:25 PST)
  - Re: AMBER: sander segmentation fault Thomas E. Cheatham, III (Wed Feb 02 2005 - 15:59:13 PST)
  - RE: AMBER: sander segmentation fault Ross Walker (Wed Feb 02 2005 - 18:05:41 PST)
AMBER: xleap: different distance results from "check" command in xleap Woojin Lee (Tue Feb 01 2005 - 21:54:14 PST)
AMBER: Compilation problem at dual processor linux ! Pradipta Bandyopadhyay (Wed Feb 02 2005 - 04:32:52 PST)
- RE: AMBER: Compilation problem at dual processor linux ! Ross Walker (Wed Feb 02 2005 - 09:52:10 PST)
AMBER: change of prmtop file Gustavo Pierdominici Sottile (Wed Feb 02 2005 - 07:43:34 PST)
- Re: AMBER: change of prmtop file Guanglei Cui (Wed Feb 02 2005 - 10:03:53 PST)
- Re: AMBER: change of prmtop file David A. Case (Wed Feb 02 2005 - 10:21:34 PST)
AMBER: xleap MOVE and .lib file Stern, Julie (Wed Feb 02 2005 - 09:01:55 PST)
AMBER: amber 8 system requirements dkohen.carleton.edu (Wed Feb 02 2005 - 10:28:48 PST)
- RE: AMBER: amber 8 system requirements Ross Walker (Wed Feb 02 2005 - 10:47:55 PST)
AMBER: gaff frcmod file for TI calculation Eric Hu (Wed Feb 02 2005 - 15:50:00 PST)
- Re: AMBER: gaff frcmod file for TI calculation David A. Case (Wed Feb 02 2005 - 16:44:13 PST)
  - Re: AMBER: gaff frcmod file for TI calculation Eric Hu (Wed Feb 02 2005 - 17:47:32 PST)
AMBER: question about tleap load pdb file xiaowen (Wed Feb 02 2005 - 19:19:19 PST)
AMBER: protonate and input conversion error Stern, Julie (Thu Feb 03 2005 - 08:48:20 PST)
- Re: AMBER: protonate and input conversion error David A. Case (Thu Feb 03 2005 - 10:09:31 PST)
AMBER: DNA melting free energy calculation lei jia (Thu Feb 03 2005 - 16:39:57 PST)
AMBER: unnatural ligand Eric Hu (Thu Feb 03 2005 - 19:37:41 PST)
- Re: AMBER: unnatural ligand David A. Case (Fri Feb 04 2005 - 14:54:06 PST)
  - Re: AMBER: unnatural ligand Eric Hu (Mon Feb 07 2005 - 10:28:14 PST)
    - AMBER: Creating an input file for GRASP using AMBER 8 Ilyas Yildirim (Mon Feb 07 2005 - 11:07:29 PST)
    - Re: AMBER: Creating an input file for GRASP using AMBER 8 FyD (Mon Feb 07 2005 - 11:52:42 PST)
AMBER: clusters Germán Sciaini (Fri Feb 04 2005 - 04:36:48 PST)
AMBER: tleap load pdb file xiaowen (Fri Feb 04 2005 - 07:44:17 PST)
- Re: AMBER: tleap load pdb file David A. Case (Fri Feb 04 2005 - 08:35:49 PST)
AMBER: tleap load pdb file xiaowen (Fri Feb 04 2005 - 13:18:09 PST)
- Re: AMBER: tleap load pdb file David A. Case (Fri Feb 04 2005 - 14:45:50 PST)
- Re: AMBER: tleap load pdb file xiaowen (Sat Feb 05 2005 - 09:20:12 PST)
- RE: AMBER: tleap load pdb file Ross Walker (Sun Feb 06 2005 - 10:50:29 PST)
- RE: AMBER: tleap load pdb file xiaowen (Mon Feb 07 2005 - 12:58:39 PST)
- RE: AMBER: tleap load pdb file xiaowen (Mon Feb 07 2005 - 19:52:36 PST)
  - Re: AMBER: tleap load pdb file David A. Case (Tue Feb 08 2005 - 11:50:08 PST)
- Re: AMBER: tleap load pdb file xiaowen (Wed Feb 09 2005 - 10:51:44 PST)
  - RE: AMBER: tleap load pdb file Ross Walker (Wed Feb 09 2005 - 11:18:31 PST)
AMBER: Antechamber/formatting question Kara Di Giorgio (Fri Feb 04 2005 - 15:05:18 PST)
- Re: AMBER: Antechamber/formatting question David A. Case (Sat Feb 05 2005 - 11:17:24 PST)
  - Re: AMBER: Antechamber/formatting question Kara Di Giorgio (Fri Feb 18 2005 - 10:20:40 PST)
    - Re: AMBER: Antechamber/formatting question YoungJin Cho (Mon Feb 21 2005 - 08:15:32 PST)
    - Re: AMBER: Antechamber/formatting question Kara Di Giorgio (Fri Feb 25 2005 - 16:43:36 PST)
    - Re: AMBER: Antechamber/formatting question Ilyas Yildirim (Fri Feb 25 2005 - 17:31:46 PST)
    - Re: AMBER: Antechamber/formatting question Kara Di Giorgio (Fri Feb 25 2005 - 18:02:40 PST)
    - RE: AMBER: Antechamber/formatting question Ross Walker (Sun Feb 27 2005 - 11:56:18 PST)
    - Re: AMBER: Antechamber/formatting question Kara Di Giorgio (Sun Feb 27 2005 - 17:13:19 PST)
    - Re: AMBER: Antechamber/formatting question FyD (Sun Feb 27 2005 - 20:12:37 PST)
    - Re: AMBER: Antechamber/formatting question FyD (Sun Feb 27 2005 - 20:43:23 PST)
    - AMBER: vlimit problem Ilyas Yildirim (Fri Feb 25 2005 - 17:45:03 PST)
    - Re: AMBER: vlimit problem David A. Case (Mon Feb 28 2005 - 09:40:26 PST)
- AMBER: Dynamics error S.Sundar Raman (Tue Feb 08 2005 - 03:25:07 PST)
  - Re: AMBER: Dynamics error Carlos Simmerling (Tue Feb 08 2005 - 04:59:04 PST)
    - Re: AMBER: Dynamics error S.Sundar Raman (Tue Feb 08 2005 - 06:09:04 PST)
AMBER: huge bond distances in new residue Stern, Julie (Fri Feb 04 2005 - 15:48:14 PST)
- Re: AMBER: huge bond distances in new residue David A. Case (Sat Feb 05 2005 - 10:57:37 PST)
AMBER: trajectory of minimization Stern, Julie (Fri Feb 04 2005 - 15:49:17 PST)
- Re: AMBER: trajectory of minimization David A. Case (Sat Feb 05 2005 - 10:54:39 PST)
- RE: AMBER: trajectory of minimization Ross Walker (Sun Feb 06 2005 - 10:36:29 PST)
AMBER: Is droplet boundary condition option possible ? Soo (Fri Feb 04 2005 - 22:18:36 PST)
- Re: AMBER: Is droplet boundary condition option possible ? David A. Case (Sat Feb 05 2005 - 10:53:53 PST)
AMBER: loading pdb in leap to create parmeter files mrbroad.ilstu.edu (Sat Feb 05 2005 - 13:24:04 PST)
- Re: AMBER: loading pdb in leap to create parmeter files David A. Case (Sat Feb 05 2005 - 14:29:13 PST)
AMBER: Tutorial Request Kara Di Giorgio (Sun Feb 06 2005 - 09:01:15 PST)
- Re: AMBER: Tutorial Request David A. Case (Sun Feb 06 2005 - 09:40:28 PST)
AMBER: inconsistent ordering in an improper dihedral of TRP Sanghyun Park (Sun Feb 06 2005 - 20:38:03 PST)
- Re: AMBER: inconsistent ordering in an improper dihedral of TRP David A. Case (Fri Feb 11 2005 - 14:19:03 PST)
  - Re: AMBER: inconsistent ordering in an improper dihedral of TRP Carlos Simmerling (Fri Feb 11 2005 - 15:41:26 PST)
    - AMBER: nucgen problem Ilyas Yildirim (Fri Feb 11 2005 - 16:56:41 PST)
    - Re: AMBER: nucgen problem David A. Case (Fri Feb 11 2005 - 17:37:32 PST)
- Re: AMBER: inconsistent ordering in an improper dihedral of TRP Bill Ross (Fri Feb 11 2005 - 17:56:10 PST)
- AMBER: Re: inconsistent ordering in an improper dihedral of TRP Sanghyun Park (Thu Mar 10 2005 - 19:08:25 PST)
AMBER: correlation along PCA modes Vlad Cojocaru (Mon Feb 07 2005 - 03:35:44 PST)
Re: AMBER: Creating an input file for GRASP using AMBER 8 Bill Ross (Mon Feb 07 2005 - 11:40:33 PST)
- Re: AMBER: Creating an input file for GRASP using AMBER 8 Ilyas Yildirim (Mon Feb 07 2005 - 14:24:24 PST)
  - Re: AMBER: Creating an input file for GRASP using AMBER 8 FyD (Mon Feb 07 2005 - 14:45:05 PST)
AMBER: problem in writing Gustavo Pierdominici Sottile (Mon Feb 07 2005 - 11:59:49 PST)
- Re: AMBER: problem in writing David A. Case (Mon Feb 07 2005 - 15:22:05 PST)
AMBER: How to calculate RESTRAINT value Mayumi Haga (Mon Feb 07 2005 - 20:09:25 PST)
- Re: AMBER: How to calculate RESTRAINT value Carlos Simmerling (Tue Feb 08 2005 - 05:01:46 PST)
AMBER: dynamics error S.Sundar Raman (Tue Feb 08 2005 - 03:10:19 PST)
AMBER: MMGBSA and dielectric constant with AMBER8 - dielc and intdiel Fabien Cailliez (Tue Feb 08 2005 - 09:16:51 PST)
- Re: AMBER: MMGBSA and dielectric constant with AMBER8 - dielc and intdiel David A. Case (Tue Feb 08 2005 - 11:28:23 PST)
AMBER: problem in minimization Gustavo Pierdominici Sottile (Tue Feb 08 2005 - 10:31:17 PST)
- Re: AMBER: problem in minimization David A. Case (Tue Feb 08 2005 - 11:51:42 PST)
  - Re: AMBER: problem in minimization Natasja Brooijmans (Tue Feb 08 2005 - 11:56:22 PST)
AMBER: Minimization Beale, John (Tue Feb 08 2005 - 11:30:52 PST)
AMBER: Linux Enterprise Beale, John (Tue Feb 08 2005 - 11:39:54 PST)
- RE: AMBER: Linux Enterprise S. Frank Yan (Tue Feb 08 2005 - 11:45:40 PST)
- Re: AMBER: Linux Enterprise David A. Case (Tue Feb 08 2005 - 11:59:15 PST)
- RE: AMBER: Linux Enterprise Ross Walker (Tue Feb 08 2005 - 11:59:43 PST)
AMBER: Amber8 installation test possible failures Joe Nolan (Tue Feb 08 2005 - 11:55:39 PST)
- Re: AMBER: Amber8 installation test possible failures David A. Case (Tue Feb 08 2005 - 12:02:54 PST)
- RE: AMBER: Amber8 installation test possible failures Ross Walker (Tue Feb 08 2005 - 12:17:40 PST)
AMBER: leap bond angle building Stern, Julie (Tue Feb 08 2005 - 15:44:39 PST)
Re: AMBER: leap bond angle building Bill Ross (Tue Feb 08 2005 - 16:00:12 PST)
AMBER: minimize a ptraj average pdb structure Eric Hu (Tue Feb 08 2005 - 17:48:26 PST)
- RE: AMBER: minimize a ptraj average pdb structure Vineet Pande (Wed Feb 09 2005 - 02:05:14 PST)
- RE: AMBER: minimize a ptraj average pdb structure Bill Ross (Wed Feb 09 2005 - 11:39:27 PST)
AMBER: energy plot in minimization Gustavo Pierdominici Sottile (Wed Feb 09 2005 - 09:36:25 PST)
- RE: AMBER: energy plot in minimization Ross Walker (Wed Feb 09 2005 - 10:10:13 PST)
AMBER: question about mm_gbsa output file michael chen (Wed Feb 09 2005 - 10:10:06 PST)
AMBER: Convert to Pdb Beale, John (Wed Feb 09 2005 - 11:03:27 PST)
- Re: AMBER: Convert to Pdb Peter Gannett (Wed Feb 09 2005 - 11:07:07 PST)
- RE: AMBER: Convert to Pdb Ross Walker (Wed Feb 09 2005 - 11:19:15 PST)
- Re: AMBER: Convert to Pdb M. L. Dodson (Wed Feb 09 2005 - 11:28:22 PST)
AMBER: minimization.out Gustavo Pierdominici Sottile (Wed Feb 09 2005 - 11:32:01 PST)
- Re: AMBER: minimization.out David A. Case (Wed Feb 09 2005 - 11:53:41 PST)
AMBER: DIVCON optimization Kara Di Giorgio (Wed Feb 09 2005 - 11:46:03 PST)
- Re: AMBER: DIVCON optimization David A. Case (Wed Feb 09 2005 - 12:22:59 PST)
  - Re: AMBER: DIVCON optimization Kara Wald (Wed Feb 09 2005 - 15:30:07 PST)
    - Re: AMBER: DIVCON optimization David A. Case (Wed Feb 09 2005 - 18:22:07 PST)
AMBER: Can REM be used as multiple normal sander jobs on parallel machine qlu.notes.cc.sunysb.edu (Wed Feb 09 2005 - 15:15:59 PST)
- Re: AMBER: Can REM be used as multiple normal sander jobs on parallel machine Carlos Simmerling (Wed Feb 09 2005 - 16:03:55 PST)
AMBER: desc NEWRES and blank unit type Stern, Julie (Wed Feb 09 2005 - 18:07:00 PST)
- Re: AMBER: desc NEWRES and blank unit type David A. Case (Fri Feb 11 2005 - 14:24:25 PST)
AMBER: question about surface area to GBsurf calculation michael chen (Wed Feb 09 2005 - 22:20:58 PST)
- Re: AMBER: question about surface area to GBsurf calculation David A. Case (Thu Feb 10 2005 - 07:55:33 PST)
AMBER: Another question about surface area calculation michael chen (Wed Feb 09 2005 - 22:26:00 PST)
AMBER: Poisson Boltzmann dynamics error Rachel Burdge (Thu Feb 10 2005 - 08:04:55 PST)
- Re: AMBER: Poisson Boltzmann dynamics error David A. Case (Thu Feb 10 2005 - 08:57:51 PST)
- RE: AMBER: Poisson Boltzmann dynamics error Ross Walker (Thu Feb 10 2005 - 09:03:46 PST)
- Re: AMBER: Poisson Boltzmann dynamics error Ray Luo (Tue Feb 08 2005 - 04:13:58 PST)
  - Re: AMBER: Poisson Boltzmann dynamics error Rachel Burdge (Thu Feb 10 2005 - 10:51:05 PST)
AMBER: Protonate state of ARG and LYS. Liu, Jingyuan (Thu Feb 10 2005 - 13:56:39 PST)
AMBER: How to converts a binary mdcrd file thanyarat Udom (Thu Feb 10 2005 - 23:02:21 PST)
AMBER: How to converts a binary mdcrd file thanyarat Udom (Fri Feb 11 2005 - 00:00:10 PST)
AMBER: Cu++ and RED Cenk Andac (Fri Feb 11 2005 - 01:46:13 PST)
- Re: AMBER: Cu++ and RED FyD (Fri Feb 11 2005 - 09:23:53 PST)
  - Re: AMBER: Cu++ and RED Cenk Andac (Mon Feb 14 2005 - 21:30:47 PST)
    - Re: AMBER: Cu++ and RED FyD (Tue Feb 15 2005 - 10:19:16 PST)
- Re: AMBER: Cu++ and RED Cenk Andac (Sat Mar 12 2005 - 04:28:34 PST)
  - Re: AMBER: Cu++ and RED FyD (Sat Mar 12 2005 - 09:35:53 PST)
    - Modification of GAMESS outputs for resp jobs Re: AMBER: Cu++ and RED Cenk Andac (Sat Oct 22 2005 - 11:02:00 PDT)
    - AMBER: Problem with the QMMM example in AMBER 2004 tutorial Cenk Andac (Sun Oct 23 2005 - 09:31:45 PDT)
    - RE: AMBER: Problem with the QMMM example in AMBER 2004 tutorial Ross Walker (Sun Oct 23 2005 - 10:02:55 PDT)
    - Re: Modification of GAMESS outputs for resp jobs Re: AMBER: Cu++ and RED FyD (Mon Oct 24 2005 - 01:44:31 PDT)
    - Re: Modification of GAMESS outputs for resp jobs Re: AMBER: Cu++ and RED Cenk Andac (Mon Oct 24 2005 - 09:12:30 PDT)
    - Re: Modification of GAMESS outputs for resp jobs Re: AMBER: Cu++ and RED Cenk Andac (Mon Oct 24 2005 - 09:43:36 PDT)
    - Re: Modification of GAMESS outputs for resp jobs Re: AMBER: Cu++ and RED FyD (Mon Oct 24 2005 - 22:58:56 PDT)
- Re:Re: AMBER: Cu++ and RED Cenk Andac (Sat Mar 12 2005 - 10:39:10 PST)
  - Re: AMBER: Cu++ and RED FyD (Sat Mar 12 2005 - 14:00:56 PST)
AMBER: too much vacuum in the box created by Leap Marie-Pierre Durrieu (Fri Feb 11 2005 - 04:53:35 PST)
- Re: AMBER: too much vacuum in the box created by Leap Carlos Simmerling (Fri Feb 11 2005 - 05:21:23 PST)
- Re: AMBER: too much vacuum in the box created by Leap David A. Case (Fri Feb 11 2005 - 08:21:29 PST)
AMBER: ptraj error and min problems Gustavo Pierdominici Sottile (Fri Feb 11 2005 - 06:54:23 PST)
- Re: AMBER: ptraj error and min problems David A. Case (Fri Feb 11 2005 - 08:29:42 PST)
AMBER: archive Gustavo Pierdominici Sottile (Fri Feb 11 2005 - 06:58:33 PST)
AMBER: reverse TI charge perturbation Eric Hu (Fri Feb 11 2005 - 17:59:10 PST)
- Re: AMBER: reverse TI charge perturbation David A. Case (Sat Feb 12 2005 - 16:14:58 PST)
  - Re: AMBER: reverse TI charge perturbation Eric Hu (Mon Feb 14 2005 - 16:42:14 PST)
AMBER: S.Sundar Raman (Mon Feb 14 2005 - 01:03:27 PST)
- RE: AMBER: Ross Walker (Mon Feb 14 2005 - 09:03:52 PST)
AMBER:how to analyse trajectory files S.Sundar Raman (Mon Feb 14 2005 - 01:17:39 PST)
- RE: AMBER:how to analyse trajectory files Vineet Pande (Mon Feb 14 2005 - 03:07:21 PST)
  - Re: AMBER:how to analyse trajectory files S.Sundar Raman (Mon Feb 14 2005 - 20:58:19 PST)
AMBER: vlimit Gustavo Pierdominici Sottile (Mon Feb 14 2005 - 04:23:31 PST)
- RE: AMBER: vlimit Ross Walker (Mon Feb 14 2005 - 09:14:56 PST)
AMBER: AMBER 8 : Water cap problem Guillaume Bollot (Mon Feb 14 2005 - 05:14:20 PST)
- RE: AMBER: AMBER 8 : Water cap problem Ross Walker (Mon Feb 14 2005 - 09:07:21 PST)
AMBER: constrains Gustavo Pierdominici Sottile (Mon Feb 14 2005 - 06:53:18 PST)
- RE: AMBER: constrains Vineet Pande (Mon Feb 14 2005 - 07:48:39 PST)
- RE: AMBER: constrains Ross Walker (Mon Feb 14 2005 - 09:10:42 PST)
AMBER: Restart Problem opitz.che.udel.edu (Mon Feb 14 2005 - 11:12:54 PST)
- RE: AMBER: Restart Problem Ross Walker (Mon Feb 14 2005 - 12:01:16 PST)
AMBER: Mainchain example needed Kara Wald (Mon Feb 14 2005 - 13:43:06 PST)
AMBER: running shell scripts in tleap? Cenk Andac (Mon Feb 14 2005 - 14:23:44 PST)
- Re: AMBER: running shell scripts in tleap? Lihua Wang (Mon Feb 14 2005 - 15:26:31 PST)
- RE: AMBER: running shell scripts in tleap? Ross Walker (Mon Feb 14 2005 - 15:31:03 PST)
  - RE: AMBER: running shell scripts in tleap? Cenk Andac (Mon Feb 14 2005 - 21:24:44 PST)
- Re: AMBER: running shell scripts in tleap? John Bushnell (Mon Feb 14 2005 - 15:32:32 PST)
- AMBER: Dummy Atom Types on both states Ilyas Yildirim (Mon Feb 14 2005 - 18:29:03 PST)
  - Re: AMBER: Dummy Atom Types on both states Thomas Steinbrecher (Tue Feb 15 2005 - 01:04:06 PST)
    - Re: AMBER: Dummy Atom Types on both states yipinl.umich.edu (Tue Feb 15 2005 - 07:31:56 PST)
    - Re: AMBER: Dummy Atom Types on both states Julien Michel (Tue Feb 15 2005 - 08:10:34 PST)
    - Re: AMBER: Dummy Atom Types on both states david.evans.ulsop.ac.uk (Tue Feb 15 2005 - 09:29:39 PST)
    - Re: AMBER: Dummy Atom Types on both states david.evans.ulsop.ac.uk (Tue Feb 15 2005 - 10:13:57 PST)
    - Re: AMBER: Dummy Atom Types on both states David A. Case (Tue Feb 15 2005 - 14:26:21 PST)
    - AMBER: soft-cores and Amber David A. Case (Tue Feb 15 2005 - 14:55:30 PST)
    - Re: AMBER: soft-cores and Amber Carlos Simmerling (Tue Feb 15 2005 - 15:11:14 PST)
AMBER: Topology Format Amber 8 Stuart Murdock (Tue Feb 15 2005 - 04:00:56 PST)
- Re: AMBER: Topology Format Amber 8 Carlos Simmerling (Tue Feb 15 2005 - 04:42:29 PST)
- Re: AMBER: Topology Format Amber 8 Ian Withers (Tue Feb 15 2005 - 05:33:15 PST)
AMBER: problems with running sander in parallel on linux Piotr Cieplak (Tue Feb 15 2005 - 10:28:02 PST)
- RE: AMBER: problems with running sander in parallel on linux Ross Walker (Tue Feb 15 2005 - 10:50:53 PST)
  - Re: AMBER: problems with running sander in parallel on linux Robert Duke (Tue Feb 15 2005 - 11:43:37 PST)
    - Re: AMBER: problems with running sander in parallel on linux Scott Brozell (Tue Feb 15 2005 - 13:01:21 PST)
    - Re: AMBER: problems with running sander in parallel on linux Piotr Cieplak (Tue Feb 15 2005 - 13:58:09 PST)
- RE: AMBER: problems with running sander in parallel on linux Piotr Cieplak (Tue Feb 15 2005 - 11:01:15 PST)
- Re: AMBER: problems with running sander in parallel on linux Scott Brozell (Tue Feb 15 2005 - 11:42:45 PST)
  - Re: AMBER: problems with running sander in parallel on linux Piotr Cieplak (Tue Feb 15 2005 - 12:55:59 PST)
- Re: AMBER: problems with running sander in parallel on linux David E. Konerding DSD staff (Tue Feb 15 2005 - 12:48:50 PST)
- Re: AMBER: problems with running sander in parallel on linux Robert Duke (Tue Feb 15 2005 - 13:25:52 PST)
  - Re: AMBER: problems with running sander in parallel on linux Scott Brozell (Tue Feb 15 2005 - 14:02:56 PST)
AMBER: blows up Gustavo Pierdominici Sottile (Tue Feb 15 2005 - 11:11:43 PST)
AMBER: check in leap Gustavo Pierdominici Sottile (Tue Feb 15 2005 - 11:34:21 PST)
- Re: AMBER: check in leap David A. Case (Tue Feb 15 2005 - 13:17:07 PST)
AMBER: Cyclic peptide arubin.unmc.edu (Tue Feb 15 2005 - 13:12:28 PST)
- Re: AMBER: Cyclic peptide Stefano Federico Massimiliano Pieraccini (Stefano.Pieraccini) (Wed Feb 16 2005 - 01:48:19 PST)
  - Re: AMBER: Cyclic peptide Carlos Simmerling (Wed Feb 16 2005 - 05:00:29 PST)
AMBER: PDB conversion to gzmat using antechamber Scott Pendley (Tue Feb 15 2005 - 15:32:21 PST)
- Re: AMBER: PDB conversion to gzmat using antechamber David A. Case (Mon Feb 28 2005 - 10:02:58 PST)
AMBER: EWALD and belly not strictly correct Stern, Julie (Tue Feb 15 2005 - 21:41:49 PST)
- Re: AMBER: EWALD and belly not strictly correct darden (Wed Feb 16 2005 - 09:08:31 PST)
- Re: AMBER: EWALD and belly not strictly correct David A. Case (Wed Feb 16 2005 - 08:52:20 PST)
AMBER: Why I couldnt used carnal for analyzed RMSD ? thanyarat Udom (Wed Feb 16 2005 - 01:28:17 PST)
AMBER: Gustavo Pierdominici Sottile (Wed Feb 16 2005 - 04:22:59 PST)
- Re: AMBER: Carlos Simmerling (Wed Feb 16 2005 - 04:55:57 PST)
AMBER: rms Gustavo Pierdominici Sottile (Wed Feb 16 2005 - 05:14:50 PST)
- Re: AMBER: rms Carlos Simmerling (Wed Feb 16 2005 - 05:59:43 PST)
AMBER: Beale, John (Wed Feb 16 2005 - 05:42:26 PST)
- Re: AMBER: David A. Case (Wed Feb 16 2005 - 08:49:18 PST)
AMBER: Phi-Psi-Energy plot L Jin (Wed Feb 16 2005 - 07:45:18 PST)
AMBER: generate charmm paramater file from amber parm file HL Eastwood (Wed Feb 16 2005 - 09:19:56 PST)
- Re: AMBER: generate charmm paramater file from amber parm file david.evans.ulsop.ac.uk (Wed Feb 16 2005 - 10:02:07 PST)
- Re: AMBER: generate charmm paramater file from amber parm file David E. Konerding DSD staff (Wed Feb 16 2005 - 10:13:23 PST)
Re: AMBER: Why I couldnt used carnal for analyzed RMSD ? Bill Ross (Wed Feb 16 2005 - 10:19:30 PST)
AMBER: Amber7 nmropt Markus W. Germann (Wed Feb 16 2005 - 13:09:08 PST)
- RE: AMBER: Amber7 nmropt Ross Walker (Wed Feb 16 2005 - 13:32:05 PST)
  - Re: AMBER: Amber7 nmropt Markus W. Germann (Wed Feb 16 2005 - 13:40:46 PST)
    - RE: AMBER: Amber7 nmropt Ross Walker (Wed Feb 16 2005 - 13:55:40 PST)
- Re: AMBER: Amber7 nmropt David A. Case (Wed Feb 16 2005 - 13:53:19 PST)
- Re: AMBER: Amber7 nmropt Robert Duke (Wed Feb 16 2005 - 15:05:37 PST)
AMBER: installation of amber 8 on windows anshul.imtech.res.in (Thu Feb 17 2005 - 12:17:11 PST)
- Re: AMBER: installation of amber 8 on windows David Mathews (Thu Feb 17 2005 - 08:42:05 PST)
  - Re: AMBER: installation of amber 8 on windows anshul.imtech.res.in (Fri Feb 18 2005 - 06:33:40 PST)
- Re: AMBER: installation of amber 8 on windows David Mathews (Sat Feb 19 2005 - 08:01:54 PST)
AMBER: Re: pmemd problems Robert Duke (Thu Feb 17 2005 - 07:15:33 PST)
AMBER: rotameric populations? Cenk Andac (Thu Feb 17 2005 - 07:15:05 PST)
AMBER: moil-view Beale, John (Thu Feb 17 2005 - 07:56:30 PST)
- Re: AMBER: moil-view Carlos Simmerling (Thu Feb 17 2005 - 08:28:15 PST)
AMBER: Antechamber help needed Kara Di Giorgio (Thu Feb 17 2005 - 09:24:34 PST)
AMBER: Moil view trajectory clusters Austin B. Yongye (Thu Feb 17 2005 - 09:36:15 PST)
- Re: AMBER: Moil view trajectory clusters Carlos Simmerling (Thu Feb 17 2005 - 10:19:50 PST)
  - Re: AMBER: Moil view trajectory clusters Austin B. Yongye (Thu Feb 17 2005 - 13:31:37 PST)
AMBER: problem with ptraj and randomizeions Fabien Cailliez (Thu Feb 17 2005 - 09:56:24 PST)
- Re: AMBER: problem with ptraj and randomizeions Thomas E. Cheatham, III (Thu Feb 17 2005 - 10:57:23 PST)
  - Re: AMBER: problem with ptraj and randomizeions Fabien Cailliez (Fri Feb 18 2005 - 00:50:00 PST)
    - Re: AMBER: problem with ptraj and randomizeions Filip Lankas (Fri Feb 18 2005 - 04:19:10 PST)
- Re: AMBER: problem with ptraj and randomizeions Marie-Pierre Durrieu (Fri Feb 18 2005 - 01:49:16 PST)
  - Re: AMBER: problem with ptraj and randomizeions Marie-Pierre Durrieu (Fri Feb 18 2005 - 02:19:06 PST)
AMBER: PSC Summer Workshop: Modeling Proteins and Nucleic Acids with AMBER, VMD and the MMTSB Toolkit Troy Wymore (Thu Feb 17 2005 - 11:00:36 PST)
AMBER: amber8 and moil-view Lihua Wang (Thu Feb 17 2005 - 11:26:32 PST)
- Re: AMBER: amber8 and moil-view Carlos Simmerling (Thu Feb 17 2005 - 11:42:13 PST)
  - Re: AMBER: amber8 and moil-view Lihua Wang (Thu Feb 17 2005 - 11:52:08 PST)
    - Re: AMBER: amber8 and moil-view Carlos Simmerling (Thu Feb 17 2005 - 12:06:42 PST)
    - Re: AMBER: amber8 and moil-view Lihua Wang (Thu Feb 17 2005 - 12:14:04 PST)
    - Re: AMBER: amber8 and moil-view Carlos Simmerling (Fri Feb 18 2005 - 12:13:03 PST)
AMBER: Amber8 Solaris installation failure Joe Nolan (Thu Feb 17 2005 - 12:27:12 PST)
- Re: AMBER: Amber8 Solaris installation failure David A. Case (Thu Feb 17 2005 - 18:31:00 PST)
  - Re: AMBER: Amber8 Solaris installation failure Joe Nolan (Tue Feb 22 2005 - 12:12:02 PST)
    - Re: AMBER: Amber8 Solaris installation failure Atro Tossavainen (Tue Feb 22 2005 - 12:19:31 PST)
    - Re: AMBER: Amber8 Solaris installation failure Joe Nolan (Tue Feb 22 2005 - 15:34:50 PST)
    - RE: AMBER: Amber8 Solaris installation failure Ross Walker (Tue Feb 22 2005 - 15:55:17 PST)
    - Re: AMBER: Amber8 Solaris installation failure David A. Case (Tue Feb 22 2005 - 16:52:13 PST)
    - Re: AMBER: Amber8 Solaris installation failure M. L. Dodson (Tue Feb 22 2005 - 18:33:31 PST)
    - Re: AMBER: Amber8 Solaris installation failure Joe Nolan (Mon Feb 28 2005 - 12:24:28 PST)
    - Re: AMBER: Amber8 Solaris installation failure M. L. Dodson (Mon Feb 28 2005 - 12:55:47 PST)
    - Re: AMBER: Amber8 Solaris installation failure David A. Case (Mon Feb 28 2005 - 14:42:21 PST)
    - Re: AMBER: Amber8 Solaris installation failure Joe Nolan (Tue Mar 01 2005 - 07:23:06 PST)
- RE: AMBER: Amber8 Solaris installation failure Bill Ross (Tue Feb 22 2005 - 16:08:37 PST)
AMBER: sander errors with atom restraints on ia64 Rachel Burdge (Thu Feb 17 2005 - 13:46:04 PST)
- Re: AMBER: sander errors with atom restraints on ia64 Viktor Hornak (Thu Feb 17 2005 - 14:46:26 PST)
  - Re: AMBER: sander errors with atom restraints on ia64 Rachel Burdge (Fri Feb 18 2005 - 08:04:17 PST)
AMBER: leap saveamberparm chain types response Stern, Julie (Thu Feb 17 2005 - 15:16:50 PST)
AMBER: Compiling/Runing on BSD - emulation and/or gfortran (Linux and BSD) Greg Recine (Thu Feb 17 2005 - 16:23:01 PST)
- Re: AMBER: Compiling/Runing on BSD - emulation and/or gfortran (Linux and BSD) M. L. Dodson (Thu Feb 17 2005 - 18:21:29 PST)
- Re: AMBER: Compiling/Runing on BSD - emulation and/or gfortran (Linux and BSD) David A. Case (Thu Feb 17 2005 - 23:41:23 PST)
  - Re: AMBER: Compiling/Runing on BSD - emulation and/or gfortran (Linux and BSD) David A. Case (Thu Feb 17 2005 - 23:56:20 PST)
Re: AMBER: leap saveamberparm chain types response Bill Ross (Thu Feb 17 2005 - 17:15:20 PST)
AMBER: GB solvation and "boxed" environment simulation Soo (Thu Feb 17 2005 - 21:32:38 PST)
AMBER: molecule blowing apart during equilibration Stern, Julie (Thu Feb 17 2005 - 23:12:16 PST)
- RE: AMBER: molecule blowing apart during equilibration Ross Walker (Fri Feb 18 2005 - 08:56:30 PST)
- Re: AMBER: molecule blowing apart during equilibration Carlos Simmerling (Fri Feb 18 2005 - 12:11:49 PST)
AMBER: ptraj Gustavo Pierdominici Sottile (Fri Feb 18 2005 - 06:58:37 PST)
AMBER: XMGR Beale, John (Fri Feb 18 2005 - 10:20:44 PST)
- Re: AMBER: XMGR Andreas Svrcek-Seiler (Fri Feb 18 2005 - 12:31:15 PST)
AMBER: DNA Tutorial Dwayne Hoobler (Fri Feb 18 2005 - 15:07:34 PST)
- RE: AMBER: DNA Tutorial Ross Walker (Fri Feb 18 2005 - 17:15:31 PST)
  - RE: AMBER: DNA Tutorial Dwayne Hoobler (Mon Feb 21 2005 - 12:26:37 PST)
    - Re: AMBER: DNA Tutorial David A. Case (Mon Feb 21 2005 - 15:52:21 PST)
AMBER: Amber: sander error segmentation fault. S.Sundar Raman (Fri Feb 18 2005 - 22:03:50 PST)
- RE: AMBER: Amber: sander error segmentation fault. Ross Walker (Fri Feb 18 2005 - 22:34:22 PST)
AMBER: ptraj for RDF calculations Javier Perez Miron (Sat Feb 19 2005 - 08:47:02 PST)
AMBER: simulation with explicit water molecules Ye MEI (Sat Feb 19 2005 - 19:24:48 PST)
AMBER: (no subject) yen li (Sun Feb 20 2005 - 10:16:32 PST)
AMBER: AIX problem Mayumi Haga (Sun Feb 20 2005 - 21:17:29 PST)
- Re: AMBER: AIX problem David A. Case (Mon Feb 21 2005 - 16:05:40 PST)
  - RE: AMBER: AIX problem Mayumi Haga (Mon Feb 21 2005 - 16:45:33 PST)
AMBER: ptraj for RDF calculations Javier Perez Miron (Mon Feb 21 2005 - 00:42:33 PST)
- Re: AMBER: ptraj for RDF calculations Carlos Jaime (Mon Feb 21 2005 - 01:11:22 PST)
AMBER: Amber 8 with lam compilation problem m m (Mon Feb 21 2005 - 00:55:49 PST)
- RE: AMBER: Amber 8 with lam compilation problem Ross Walker (Mon Feb 21 2005 - 01:20:21 PST)
AMBER: problem with protein minimization yen li (Mon Feb 21 2005 - 01:12:02 PST)
- Re: AMBER: problem with protein minimization David A. Case (Mon Feb 21 2005 - 16:11:37 PST)
  - Re: AMBER: problem with protein minimization yen li (Tue Feb 22 2005 - 01:26:37 PST)
    - RE: AMBER: problem with protein minimization Ross Walker (Tue Feb 22 2005 - 08:47:56 PST)
    - Re: AMBER: problem with protein minimization Robert Duke (Tue Feb 22 2005 - 09:10:51 PST)
AMBER: separate solvent-solvent and solvent-solute interaction Ye MEI (Mon Feb 21 2005 - 04:44:22 PST)
- Re: AMBER: separate solvent-solvent and solvent-solute interaction David A. Case (Mon Feb 21 2005 - 09:07:24 PST)
  - Re: Re: AMBER: separate solvent-solvent and solvent-solute interaction Ye MEI (Mon Feb 21 2005 - 19:21:48 PST)
AMBER: Formatting Questions Kara Di Giorgio (Mon Feb 21 2005 - 11:09:44 PST)
- Re: AMBER: Formatting Questions David A. Case (Mon Feb 21 2005 - 17:33:34 PST)
  - Re: AMBER: Formatting Questions Kara Di Giorgio (Mon Feb 21 2005 - 18:03:37 PST)
  - Re: AMBER: Formatting Questions Kara Di Giorgio (Tue Feb 22 2005 - 13:48:46 PST)
- Re: AMBER: Formatting Questions Bill Ross (Tue Feb 22 2005 - 16:03:26 PST)
AMBER: Free energy extimate for the same structure but different conformers claudio (Mon Feb 21 2005 - 12:56:10 PST)
- Re: AMBER: Free energy extimate for the same structure but different conformers David A. Case (Mon Feb 21 2005 - 16:00:39 PST)
AMBER: ptraj problem Mayumi Haga (Tue Feb 22 2005 - 01:38:43 PST)
- Re: AMBER: ptraj problem scopio (Tue Feb 22 2005 - 02:08:28 PST)
AMBER: restraint only for Z cartegian coordinate? Jaroslav Hanus (Tue Feb 22 2005 - 07:40:58 PST)
- Re: AMBER: restraint only for Z cartegian coordinate? Carlos Simmerling (Tue Feb 22 2005 - 08:02:31 PST)
- Re: AMBER: restraint only for Z cartegian coordinate? Jaroslav Hanus (Fri Feb 25 2005 - 03:12:48 PST)
AMBER: Restraint of atoms during minimization L Jin (Tue Feb 22 2005 - 08:17:05 PST)
- Re: AMBER: Restraint of atoms during minimization Carlos Simmerling (Tue Feb 22 2005 - 08:34:06 PST)
  - Re: AMBER: Restraint of atoms during minimization L Jin (Tue Feb 22 2005 - 09:12:13 PST)
    - Re: AMBER: Restraint of atoms during minimization David A. Case (Tue Feb 22 2005 - 09:19:17 PST)
    - Re: AMBER: Restraint of atoms during minimization Carlos Simmerling (Tue Feb 22 2005 - 09:28:01 PST)
    - Re: AMBER: Restraint of atoms during minimization Thomas E. Cheatham, III (Tue Feb 22 2005 - 09:36:42 PST)
AMBER: dihedral driver? Beale, John (Tue Feb 22 2005 - 08:26:26 PST)
AMBER: vlimit exceeded and temperature blow up Stern, Julie (Tue Feb 22 2005 - 08:36:05 PST)
- Re: AMBER: vlimit exceeded and temperature blow up Carlos Simmerling (Tue Feb 22 2005 - 08:46:21 PST)
AMBER: MPI for sander8 S. Frank Yan (Tue Feb 22 2005 - 09:04:56 PST)
- Re: AMBER: MPI for sander8 Viktor Hornak (Tue Feb 22 2005 - 09:13:46 PST)
- Re: AMBER: MPI for sander8 Thomas E. Cheatham, III (Tue Feb 22 2005 - 09:22:18 PST)
- RE: AMBER: MPI for sander8 Ross Walker (Tue Feb 22 2005 - 09:54:37 PST)
  - RE: AMBER: MPI for sander8 James W. Caldwell (Tue Feb 22 2005 - 11:52:56 PST)
AMBER: ptraj8: trajectory windows Anselm Horn (Tue Feb 22 2005 - 09:16:13 PST)
AMBER: lastrst Stern, Julie (Tue Feb 22 2005 - 15:06:24 PST)
- Re: AMBER: lastrst David A. Case (Tue Feb 22 2005 - 21:53:28 PST)
AMBER: lastrst Stern, Julie (Tue Feb 22 2005 - 17:21:00 PST)
- Re: AMBER: lastrst Carlos Simmerling (Tue Feb 22 2005 - 17:39:37 PST)
- Re: AMBER: lastrst Ilyas Yildirim (Tue Feb 22 2005 - 18:36:00 PST)
AMBER: minimizing structures before MM-PBSA? scopio (Tue Feb 22 2005 - 17:23:37 PST)
- Re: AMBER: minimizing structures before MM-PBSA? Carlos Simmerling (Tue Feb 22 2005 - 17:37:18 PST)
AMBER: convert one functional group to another with TI Eric Hu (Tue Feb 22 2005 - 17:29:42 PST)
- Re: AMBER: convert one functional group to another with TI David A. Case (Tue Feb 22 2005 - 21:44:41 PST)
  - Re: AMBER: convert one functional group to another with TI Eric Hu (Tue Feb 22 2005 - 22:36:03 PST)
    - Re: AMBER: convert one functional group to another with TI David A. Case (Wed Feb 23 2005 - 14:46:55 PST)
    - Re: AMBER: convert one functional group to another with TI David A. Case (Wed Feb 23 2005 - 15:01:42 PST)
    - AMBER: Does delta.charge mean "final charge" for a dummy atom? Eric Hu (Thu Feb 24 2005 - 17:22:23 PST)
    - Re: AMBER: Does delta.charge mean "final charge" for a dummy atom? David A. Case (Thu Feb 24 2005 - 18:31:04 PST)
    - Re: AMBER: Does delta.charge mean "final charge" for a dummy atom? Eric Hu (Fri Feb 25 2005 - 16:38:05 PST)
    - Re: AMBER: convert one functional group to another with TI Eric Hu (Wed Feb 23 2005 - 15:18:29 PST)
AMBER: total energy of solvation Holly Freedman (Tue Feb 22 2005 - 20:05:36 PST)
- Re: AMBER: total energy of solvation David A. Case (Tue Feb 22 2005 - 21:40:47 PST)
AMBER: size of solventbox mathew k varghese (Tue Feb 22 2005 - 20:07:00 PST)
- AMBER: parallel AMBER/pmemd installation problem on Opteron Jyh-Shyong Ho (Tue Feb 22 2005 - 21:08:22 PST)
  - Re: AMBER: parallel AMBER/pmemd installation problem on Opteron Robert Duke (Wed Feb 23 2005 - 05:17:54 PST)
    - Re: AMBER: parallel AMBER/pmemd installation problem on Opteron Lars Packschies (Wed Feb 23 2005 - 08:22:59 PST)
  - Re: AMBER: parallel AMBER/pmemd installation problem on Opteron Robert Duke (Wed Feb 23 2005 - 09:27:13 PST)
  - Re: AMBER: parallel AMBER/pmemd installation problem on Opteron Lars Packschies (Thu Feb 24 2005 - 15:58:25 PST)
    - Re: AMBER: parallel AMBER/pmemd installation problem on Opteron Robert Duke (Thu Feb 24 2005 - 20:06:54 PST)
- RE: AMBER: size of solventbox Ross Walker (Tue Feb 22 2005 - 21:22:03 PST)
  - AMBER: RE:Amber 8 with lam compilation problem Maciej KA (Tue Feb 22 2005 - 23:08:16 PST)
    - RE: AMBER: RE:Amber 8 with lam compilation problem Ross Walker (Tue Feb 22 2005 - 23:20:54 PST)
    - Re: AMBER: RE:Amber 8 with lam compilation problem Robert Duke (Thu Feb 24 2005 - 05:54:08 PST)
  - Re: AMBER: size of solventbox Brent Krueger (Wed Feb 23 2005 - 12:54:35 PST)
- Re: AMBER: size of solventbox Germán Sciaini (Wed Feb 23 2005 - 02:50:39 PST)
  - Re: AMBER: size of solventbox Fabien Cailliez (Wed Feb 23 2005 - 03:21:52 PST)
AMBER: mpirun sander8 problem S. Frank Yan (Tue Feb 22 2005 - 23:13:34 PST)
- Re: AMBER: mpirun sander8 problem Carlos Simmerling (Wed Feb 23 2005 - 05:05:01 PST)
- RE: AMBER: mpirun sander8 problem S. Frank Yan (Wed Feb 23 2005 - 08:58:08 PST)
- FW: AMBER: mpirun sander8 problem S. Frank Yan (Thu Feb 24 2005 - 00:41:14 PST)
  - Re: FW: AMBER: mpirun sander8 problem Guanglei Cui (Thu Feb 24 2005 - 07:46:05 PST)
- Re: AMBER: mpirun sander8 problem S. Frank Yan (Thu Feb 24 2005 - 08:30:23 PST)
AMBER: RE:Amber 8 with lam compilation problem Maciej KA (Wed Feb 23 2005 - 00:07:37 PST)
- RE: AMBER: RE:Amber 8 with lam compilation problem Ross Walker (Wed Feb 23 2005 - 10:02:47 PST)
Re: AMBER: lastrst Stern, Julie (Wed Feb 23 2005 - 13:03:57 PST)
- Re: AMBER: lastrst Furse, Kristina Elisabet (Wed Feb 23 2005 - 13:36:08 PST)
AMBER: classes Gustavo Pierdominici Sottile (Wed Feb 23 2005 - 13:00:47 PST)
- RE: AMBER: classes Vineet Pande (Thu Feb 24 2005 - 06:29:19 PST)
AMBER: solvateOct method Cameron Mura (Wed Feb 23 2005 - 18:26:19 PST)
- Re: AMBER: solvateOct method David A. Case (Fri Feb 25 2005 - 08:53:19 PST)
AMBER: How to build dynamics input for guanine with tleap ? Maciej (Thu Feb 24 2005 - 05:44:37 PST)
- RE: AMBER: How to build dynamics input for guanine with tleap ? Vineet Pande (Thu Feb 24 2005 - 06:35:23 PST)
AMBER: Joining residues/units Bogos Agianian (Thu Feb 24 2005 - 06:58:55 PST)
- Re: AMBER: Joining residues/units David A. Case (Thu Feb 24 2005 - 12:54:37 PST)
  - Re: AMBER: Joining residues/units Bogos Agianian (Thu Feb 24 2005 - 13:22:07 PST)
- Re: AMBER: Joining residues/units FyD (Fri Feb 25 2005 - 09:13:29 PST)
AMBER: cross-correlation Xin Hu (Thu Feb 24 2005 - 08:40:54 PST)
AMBER: ambpdb radii Harianto (Thu Feb 24 2005 - 11:24:39 PST)
- Re: AMBER: ambpdb radii David A. Case (Thu Feb 24 2005 - 16:56:40 PST)
- Re: AMBER: ambpdb radii Harianto (Fri Feb 25 2005 - 08:20:31 PST)
  - Re: AMBER: ambpdb radii David A. Case (Fri Feb 25 2005 - 08:09:53 PST)
- Re: AMBER: ambpdb radii Harianto (Fri Feb 25 2005 - 10:41:59 PST)
  - Re: AMBER: ambpdb radii David A. Case (Fri Feb 25 2005 - 10:15:57 PST)
AMBER: units describing projection onto modes Vlad Cojocaru (Thu Feb 24 2005 - 10:40:18 PST)
AMBER: correlation Gustavo Pierdominici Sottile (Thu Feb 24 2005 - 11:48:50 PST)
- Re: AMBER: correlation David A. Case (Mon Feb 28 2005 - 09:32:54 PST)
- AMBER: MM_PBSA error Xin Hu (Mon Apr 11 2005 - 11:46:30 PDT)
  - Re: AMBER: MM_PBSA error Holger Gohlke (Mon Apr 11 2005 - 13:49:37 PDT)
  - Re: AMBER: MM_PBSA error Xin Hu (Mon Apr 11 2005 - 15:33:51 PDT)
  - Re: AMBER: MM_PBSA error Holger Gohlke (Mon Apr 11 2005 - 23:30:24 PDT)
AMBER: pmemd + pgi 5.1 + ntr = 1 Peter Varnai (Thu Feb 24 2005 - 14:25:04 PST)
- Re: AMBER: pmemd + pgi 5.1 + ntr = 1 Robert Duke (Thu Feb 24 2005 - 14:38:02 PST)
  - Re: AMBER: pmemd + pgi 5.1 + ntr = 1 Peter Varnai (Thu Feb 24 2005 - 14:59:16 PST)
- Re: AMBER: pmemd + pgi 5.1 + ntr = 1 Robert Duke (Thu Feb 24 2005 - 15:22:37 PST)
AMBER: My last posting Robert Duke (Thu Feb 24 2005 - 20:15:08 PST)
AMBER: compile amber8 on RHEL4 HuiZhe Li (Thu Feb 24 2005 - 23:59:02 PST)
- Re: AMBER: compile amber8 on RHEL4 Ye MEI (Fri Feb 25 2005 - 04:01:17 PST)
- Re: AMBER: compile amber8 on RHEL4 Tru Huynh (Fri Feb 25 2005 - 05:09:33 PST)
AMBER: nmode entropy calculations in MMPBSA Fabien Cailliez (Fri Feb 25 2005 - 02:20:23 PST)
- Re: AMBER: nmode entropy calculations in MMPBSA david.evans.ulsop.ac.uk (Fri Feb 25 2005 - 06:14:55 PST)
AMBER: vlimit Gustavo Pierdominici Sottile (Fri Feb 25 2005 - 04:45:35 PST)
AMBER: make test.lmod error yuann (Fri Feb 25 2005 - 08:45:11 PST)
- Re: AMBER: make test.lmod error David A. Case (Fri Feb 25 2005 - 09:41:32 PST)
AMBER: setBox buffer in leap Stern, Julie (Fri Feb 25 2005 - 10:43:19 PST)
AMBER: problem with solvateBox ReichertD.mir.wustl.edu (Fri Feb 25 2005 - 12:38:51 PST)
- Re: AMBER: problem with solvateBox David A. Case (Fri Feb 25 2005 - 13:41:38 PST)
AMBER: Austin B. Yongye (Fri Feb 25 2005 - 13:43:56 PST)
- AMBER: Pyranose pucker parameters Austin B. Yongye (Fri Feb 25 2005 - 21:10:06 PST)
  - RE: AMBER: Pyranose pucker parameters Ross Walker (Sun Feb 27 2005 - 11:58:30 PST)
    - RE: AMBER: Pyranose pucker parameters Austin B. Yongye (Sun Feb 27 2005 - 19:08:52 PST)
  - Re: AMBER: Pyranose pucker parameters Thomas E. Cheatham, III (Wed Apr 27 2005 - 20:57:26 PDT)
AMBER: ico(i)=-1? Xiao He (Fri Feb 25 2005 - 19:49:46 PST)
- Re: AMBER: ico(i)=-1? Guanglei Cui (Sat Feb 26 2005 - 07:42:08 PST)
AMBER: Amber Poisson-Boltzmann MD :Equilibration Problem praveena moldy (Sun Feb 27 2005 - 21:36:36 PST)
- Re: AMBER: Amber Poisson-Boltzmann MD :Equilibration Problem David A. Case (Tue Mar 01 2005 - 08:41:08 PST)
AMBER: GBSA calculation Stefano Federico Massimiliano Pieraccini (Stefano.Pieraccini) (Mon Feb 28 2005 - 02:59:23 PST)
- Re: AMBER: GBSA calculation David A. Case (Mon Feb 28 2005 - 09:48:24 PST)
AMBER: creating a new residue Amber admin (Mon Feb 28 2005 - 08:44:59 PST)
- Re: AMBER: creating a new residue YoungJin Cho (Tue Mar 01 2005 - 07:18:16 PST)
AMBER: Controlling number of water residues... Pavan G (Mon Feb 28 2005 - 23:14:51 PST)
- Re: AMBER: Controlling number of water residues... Guanglei Cui (Tue Mar 01 2005 - 07:49:57 PST)
- Re: AMBER: Controlling number of water residues... David A. Case (Tue Mar 01 2005 - 08:25:14 PST)
AMBER: An error during minimization using RED tomjas.poczta.onet.pl (Mon Feb 28 2005 - 23:18:55 PST)
- Re: AMBER: An error during minimization using RED FyD (Tue Mar 01 2005 - 13:44:33 PST)
  - Re: Re: AMBER: An error during minimization using RED tomjas.poczta.onet.pl (Wed Mar 02 2005 - 01:15:15 PST)
  - Re: Re: AMBER: An error during minimization using RED tomjas.poczta.onet.pl (Wed Mar 02 2005 - 05:18:00 PST)
AMBER: problem with MD simulation Ye Mei (Tue Mar 01 2005 - 00:00:31 PST)
- RE: AMBER: problem with MD simulation Ross Walker (Tue Mar 01 2005 - 08:51:40 PST)
  - Re: RE: AMBER: problem with MD simulation Ye Mei (Fri Mar 04 2005 - 17:46:24 PST)
AMBER: NaNQ ilaria massarelli (Tue Mar 01 2005 - 00:45:10 PST)
- RE: AMBER: NaNQ Ross Walker (Tue Mar 01 2005 - 08:46:08 PST)
  - RE: AMBER: NaNQ ilaria massarelli (Wed Mar 02 2005 - 07:01:33 PST)
    - AMBER: across-correlation in ptraj Xin Hu (Wed Mar 02 2005 - 08:20:09 PST)
AMBER: Dihedral Energy calculation yen li (Tue Mar 01 2005 - 10:12:56 PST)
- RE: AMBER: Dihedral Energy calculation Junmei Wang (Tue Mar 01 2005 - 10:57:49 PST)
  - RE: AMBER: Dihedral Energy calculation yen li (Wed Mar 02 2005 - 04:37:01 PST)
    - RE: AMBER: Dihedral Energy calculation Ross Walker (Wed Mar 02 2005 - 08:48:56 PST)
    - RE: AMBER: Dihedral Energy calculation yen li (Wed Mar 02 2005 - 10:03:24 PST)
    - RE: AMBER: Dihedral Energy calculation Ross Walker (Wed Mar 02 2005 - 14:37:20 PST)
- AMBER: MM-GBSA Alessio Coi (Wed Mar 02 2005 - 02:00:52 PST)
  - Re: AMBER: MM-GBSA David A. Case (Wed Mar 02 2005 - 07:44:15 PST)
- RE: AMBER: Dihedral Energy calculation yen li (Fri Mar 04 2005 - 13:29:08 PST)
AMBER: PMEMD on Opterons; building/benchmarks/recommendations Robert Duke (Tue Mar 01 2005 - 11:14:56 PST)
AMBER: Xleap execution problems on Solaris Joe Nolan (Tue Mar 01 2005 - 12:51:26 PST)
- Re: AMBER: Xleap execution problems on Solaris Scott Brozell (Tue Mar 01 2005 - 19:36:56 PST)
AMBER: RESP of negatively charged molecule Rhoad, Jonathan S. (Tue Mar 01 2005 - 13:39:05 PST)
AMBER: Sample more conformational space Bogos Agianian (Wed Mar 02 2005 - 04:52:49 PST)
- Re: AMBER: Sample more conformational space Marc Baaden (Wed Mar 02 2005 - 05:03:02 PST)
- Re: AMBER: Sample more conformational space Carlos Simmerling (Wed Mar 02 2005 - 08:35:18 PST)
AMBER: bond type for a virtual bond in a biomolecular transition state Eric Hu (Wed Mar 02 2005 - 14:54:45 PST)
- Re: AMBER: bond type for a virtual bond in a biomolecular transition state David A. Case (Wed Mar 02 2005 - 15:08:38 PST)
AMBER: Installation problem S.Sundar Raman (Wed Mar 02 2005 - 22:28:29 PST)
- Re: AMBER: Installation problem Maciej (Thu Mar 03 2005 - 01:26:30 PST)
- Re: AMBER: Installation problem David A. Case (Thu Mar 03 2005 - 08:18:47 PST)
AMBER: Amber 8 on cygwin install problem Maciej (Thu Mar 03 2005 - 02:49:17 PST)
- Re: AMBER: Amber 8 on cygwin install problem David A. Case (Thu Mar 03 2005 - 08:07:52 PST)
- Re: AMBER: Amber 8 on cygwin install problem Maciej (Thu Mar 03 2005 - 22:51:32 PST)
  - Re: AMBER: Amber 8 on cygwin install problem David A. Case (Sun Mar 06 2005 - 11:23:52 PST)
AMBER: phosphorylated DNA not recognized Annette Höglund (Thu Mar 03 2005 - 06:55:18 PST)
- Re: AMBER: phosphorylated DNA not recognized FyD (Thu Mar 03 2005 - 10:59:27 PST)
AMBER: bond connectivity among dummy atoms Eric Hu (Thu Mar 03 2005 - 10:56:32 PST)
- Re: AMBER: bond connectivity among dummy atoms Ilyas Yildirim (Thu Mar 03 2005 - 11:57:48 PST)
  - Re: AMBER: bond connectivity among dummy atoms Eric Hu (Thu Mar 03 2005 - 13:25:19 PST)
    - Re: AMBER: bond connectivity among dummy atoms Ilyas Yildirim (Thu Mar 03 2005 - 13:58:38 PST)
    - Re: AMBER: bond connectivity among dummy atoms Eric Hu (Thu Mar 03 2005 - 14:12:26 PST)
AMBER: A problem about Gaussian Yanze Zhang (Thu Mar 03 2005 - 14:38:59 PST)
- Re: AMBER: A problem about Gaussian FyD (Thu Mar 03 2005 - 15:27:23 PST)
  - AMBER: Dummy atoms: Changing the source code Ilyas Yildirim (Thu Mar 03 2005 - 16:24:03 PST)
    - Re: AMBER: Dummy atoms: Changing the source code Julien Michel (Fri Mar 04 2005 - 01:44:31 PST)
    - Re: AMBER: Dummy atoms: Changing the source code Ilyas Yildirim (Fri Mar 04 2005 - 18:56:34 PST)
    - Re: AMBER: Dummy atoms: Changing the source code David A. Case (Tue Mar 08 2005 - 11:50:58 PST)
    - Re: AMBER: Dummy atoms: Changing the source code Ilyas Yildirim (Tue Mar 08 2005 - 12:56:48 PST)
- Re: AMBER: A problem about Gaussian David A. Case (Thu Mar 03 2005 - 16:55:35 PST)
AMBER: Antechamber/Divcon assigned charges Marc Christensen (Thu Mar 03 2005 - 19:38:10 PST)
- Re: AMBER: Antechamber/Divcon assigned charges David A. Case (Thu Mar 03 2005 - 21:17:13 PST)
- RE: AMBER: Antechamber/Divcon assigned charges Junmei Wang (Thu Mar 03 2005 - 21:20:38 PST)
AMBER: atom type designation Lihua Wang (Fri Mar 04 2005 - 16:05:10 PST)
AMBER: R.E.D Wai Keat Yam (Sat Mar 05 2005 - 21:14:49 PST)
- Re: AMBER: R.E.D FyD (Sun Mar 06 2005 - 17:42:20 PST)
  - Re: AMBER: R.E.D Wai Keat Yam (Sun Mar 06 2005 - 18:31:57 PST)
Re: AMBER: R.E.D Piotr Cieplak (Sun Mar 06 2005 - 16:20:42 PST)
AMBER: Citing Generalized Born Implicit solvent Model (igb=5) Cenk Andac (Sun Mar 06 2005 - 16:57:21 PST)
- Re: AMBER: Citing Generalized Born Implicit solvent Model (igb=5) Yuuki Komata (Sun Mar 06 2005 - 17:14:18 PST)
- Re: AMBER: Citing Generalized Born Implicit solvent Model (igb=5) David A. Case (Sun Mar 06 2005 - 17:14:35 PST)
AMBER: AMBER8 Compile Error on Dual Opteron Thomas Patko (Sun Mar 06 2005 - 17:53:46 PST)
- Re: AMBER: AMBER8 Compile Error on Dual Opteron David A. Case (Sun Mar 06 2005 - 20:24:27 PST)
AMBER: amber with mpich-G2 putra abdullah (Sun Mar 06 2005 - 18:55:44 PST)
- Re: AMBER: amber with mpich-G2 Robert Duke (Sun Mar 06 2005 - 20:07:21 PST)
AMBER: A problem about removing waters and counterions by ptraj scopio (Mon Mar 07 2005 - 04:28:19 PST)
- Re: AMBER: A problem about removing waters and counterions by ptraj Carlos Simmerling (Mon Mar 07 2005 - 05:29:14 PST)
  - Re: AMBER: A problem about removing waters and counterions by ptraj scopio (Mon Mar 07 2005 - 05:48:40 PST)
AMBER: New pmemd build utility; pathscale vs. pgi vs. ifort em64 opteron benchmarks Robert Duke (Mon Mar 07 2005 - 08:47:02 PST)
- Re: AMBER: New pmemd build utility; pathscale vs. pgi vs. ifort em64 opteron benchmarks David A. Case (Mon Mar 07 2005 - 10:36:40 PST)
AMBER: What PRESS is? hj zou (Mon Mar 07 2005 - 19:08:39 PST)
- Re: AMBER: What PRESS is? Mingyue Zheng (Mon Mar 07 2005 - 19:26:01 PST)
- RE: AMBER: What PRESS is? Ross Walker (Mon Mar 07 2005 - 20:07:37 PST)
AMBER: global pH variation in AMBER. Osman Gani (Tue Mar 08 2005 - 02:56:06 PST)
- Re: AMBER: global pH variation in AMBER. David A. Case (Tue Mar 08 2005 - 11:38:30 PST)
AMBER: Error limits of TI and MM_PBSA methods Nelson Fonseca (Tue Mar 08 2005 - 08:54:42 PST)
AMBER: Energy fluctuations David.LeBard.asu.edu (Tue Mar 08 2005 - 09:40:46 PST)
- Re: AMBER: Energy fluctuations David A. Case (Tue Mar 08 2005 - 11:36:14 PST)
AMBER: radii "leap" from which file xhu1.memphis.edu (Tue Mar 08 2005 - 11:34:48 PST)
- Re: AMBER: radii "leap" from which file David A. Case (Wed Mar 09 2005 - 17:02:43 PST)
AMBER: Sander questions on dual-processor Sun with MPICH Joe Nolan (Tue Mar 08 2005 - 12:37:50 PST)
- RE: AMBER: Sander questions on dual-processor Sun with MPICH Ross Walker (Tue Mar 08 2005 - 17:50:55 PST)
- Re: AMBER: Sander questions on dual-processor Sun with MPICH Robert Duke (Wed Mar 09 2005 - 05:41:08 PST)
- Re: AMBER: Sander questions on dual-processor Sun with MPICH Joe Nolan (Thu Mar 10 2005 - 08:46:23 PST)
AMBER: X Windows for LEaP on SGI Akshay Patny (Tue Mar 08 2005 - 13:07:44 PST)
- RE: AMBER: X Windows for LEaP on SGI Ross Walker (Tue Mar 08 2005 - 18:05:01 PST)
  - Re: AMBER: X Windows for LEaP on SGI Thomas Patko (Tue Mar 08 2005 - 21:44:26 PST)
AMBER: capping? Hui-Hsu Tsai (Tue Mar 08 2005 - 13:34:59 PST)
- RE: AMBER: capping? Ross Walker (Tue Mar 08 2005 - 18:09:44 PST)
  - RE: AMBER: capping? FyD (Wed Mar 09 2005 - 08:51:32 PST)
    - Re: AMBER: capping? Heiko Meyer (Wed Mar 09 2005 - 09:17:01 PST)
Re: AMBER: radii "leap" from which file Bill Ross (Tue Mar 08 2005 - 13:43:18 PST)
- Re: AMBER: radii "leap" from which file xhu1.memphis.edu (Tue Mar 08 2005 - 19:06:22 PST)
AMBER: heating Gustavo Pierdominici Sottile (Tue Mar 08 2005 - 14:20:34 PST)
- Re: AMBER: heating Ilyas Yildirim (Tue Mar 08 2005 - 15:02:17 PST)
  - AMBER: Compiling just sander Ilyas Yildirim (Thu Mar 10 2005 - 19:07:31 PST)
    - Re: AMBER: Compiling just sander david.evans.ulsop.ac.uk (Fri Mar 11 2005 - 01:24:24 PST)
  - AMBER: "The system has extended beyond" error Ilyas Yildirim (Tue Mar 29 2005 - 14:28:35 PST)
    - Re: AMBER: "The system has extended beyond" error David A. Case (Wed Mar 30 2005 - 07:08:07 PST)
    - Re: AMBER: "The system has extended beyond" error Ilyas Yildirim (Thu Mar 31 2005 - 04:26:21 PST)
Re: AMBER: heating Bill Ross (Tue Mar 08 2005 - 14:55:47 PST)
AMBER: The pressure bybaker.itsa.ucsf.edu (Tue Mar 08 2005 - 17:54:44 PST)
- RE: AMBER: The pressure Ross Walker (Tue Mar 08 2005 - 18:20:44 PST)
- Re: AMBER: The pressure bybaker.itsa.ucsf.edu (Tue Mar 08 2005 - 22:38:14 PST)
  - AMBER: Priti Hansia (Tue Mar 08 2005 - 23:38:59 PST)
    - Re: AMBER: David A. Case (Fri Mar 11 2005 - 11:02:40 PST)
    - RE: AMBER: Ross Walker (Sun Mar 13 2005 - 16:29:08 PST)
    - AMBER: carnal problem Priti Hansia (Thu Sep 08 2005 - 02:25:53 PDT)
AMBER: how can I deal with the puzzle? hj zou (Tue Mar 08 2005 - 19:36:39 PST)
- Re: AMBER: how can I deal with the puzzle? Thomas E. Cheatham, III (Tue Mar 08 2005 - 19:53:48 PST)
  - Re: Re: AMBER: how can I deal with the puzzle? ZhangJian (Tue Mar 08 2005 - 23:59:42 PST)
AMBER: Problems Binding Protein to DNA Pieter Smith (Tue Mar 08 2005 - 21:21:30 PST)
- RE: AMBER: Problems Binding Protein to DNA Vineet Pande (Wed Mar 09 2005 - 03:16:44 PST)
AMBER: amber on sgi mathew k varghese (Wed Mar 09 2005 - 03:23:12 PST)
- Re: AMBER: amber on sgi Robert Duke (Wed Mar 09 2005 - 05:32:29 PST)
- Re: AMBER: amber on sgi Karol Miaskiewicz (Wed Mar 09 2005 - 05:37:31 PST)
- Re: AMBER: amber on sgi Bill Ross (Wed Mar 09 2005 - 07:35:21 PST)
  - Re: AMBER: amber on sgi Melinda Layten (Wed Mar 09 2005 - 08:52:28 PST)
AMBER: For further question about Targeted MD ZhangJian (Wed Mar 09 2005 - 04:48:44 PST)
- AMBER: problem with running AMBER with lam-mpi though PBS script Ru-Zhen Li (Wed Mar 09 2005 - 06:01:24 PST)
  - Re: AMBER: problem with running AMBER with lam-mpi though PBS script Karol Miaskiewicz (Wed Mar 09 2005 - 05:57:46 PST)
  - Re: AMBER: problem with running AMBER with lam-mpi though PBS script Ru-Zhen Li (Wed Mar 09 2005 - 17:48:56 PST)
AMBER: vlimit in heating Gustavo Pierdominici Sottile (Wed Mar 09 2005 - 06:13:20 PST)
- Re: AMBER: vlimit in heating David A. Case (Wed Mar 09 2005 - 08:10:42 PST)
Re: AMBER: vlimit in heating Bill Ross (Wed Mar 09 2005 - 07:44:06 PST)
AMBER: solvatebox problem in the antechamber tutorial Heiko Meyer (Wed Mar 09 2005 - 08:29:00 PST)
- Re: AMBER: solvatebox problem in the antechamber tutorial David A. Case (Wed Mar 09 2005 - 16:18:19 PST)
AMBER: vlimit heat Gustavo Pierdominici Sottile (Wed Mar 09 2005 - 09:36:30 PST)
AMBER: Re: Amber 8 dual-Xeon compile problem keiodai.shohoku.ac.jp (Wed Mar 09 2005 - 20:14:33 PST)
AMBER: how to excite a single residue ? Priti Hansia (Wed Mar 09 2005 - 20:28:24 PST)
- Re: AMBER: how to excite a single residue ? Pradipta Bandyopadhyay (Wed Mar 09 2005 - 21:24:34 PST)
AMBER: PTRAJ $ Antechamber Andrew Box (Wed Mar 09 2005 - 22:47:29 PST)
- Re: AMBER: PTRAJ $ Antechamber David A. Case (Sat Mar 12 2005 - 14:17:49 PST)
AMBER: Sander error Vojtěch Klusák (Thu Mar 10 2005 - 04:03:21 PST)
- Re: AMBER: Sander error Viktor Hornak (Fri Mar 11 2005 - 08:36:38 PST)
Re: AMBER: PTRAJ $ Antechamber Bill Ross (Thu Mar 10 2005 - 09:22:39 PST)
AMBER: expected error in mean (Amber 8 TI tutorial) Eric Hu (Thu Mar 10 2005 - 15:38:13 PST)
- Re: AMBER: expected error in mean (Amber 8 TI tutorial) David A. Case (Sat Mar 12 2005 - 14:18:40 PST)
AMBER: IDIEL in sander sebnem (Thu Mar 10 2005 - 23:14:50 PST)
- Re: AMBER: IDIEL in sander David A. Case (Sat Mar 12 2005 - 14:10:09 PST)
AMBER: vlimit Gustavo Pierdominici Sottile (Fri Mar 11 2005 - 04:33:36 PST)
AMBER: Holes in water Lukasz Bielecki (Fri Mar 11 2005 - 06:13:40 PST)
- Re :AMBER: Holes in water Pascal Auffinger (Fri Mar 11 2005 - 07:26:31 PST)
  - Re: Re :AMBER: Holes in water Bill Ross (Sat Mar 12 2005 - 11:15:43 PST)
- AMBER: My model loses its motion in MD Lukasz Bielecki (Thu Nov 24 2005 - 07:06:14 PST)
  - Re: AMBER: My model loses its motion in MD Thomas Cheatham (Thu Nov 24 2005 - 08:03:07 PST)
  - Re: AMBER: My model loses its motion in MD Andreas Svrcek-Seiler (Thu Nov 24 2005 - 08:07:42 PST)
AMBER: problem with nmode using ntrun=5 Phineus Markwick (Fri Mar 11 2005 - 06:38:34 PST)
Re: AMBER: Re: inconsistent ordering in an improper dihedral of TRP Bill Ross (Fri Mar 11 2005 - 07:46:40 PST)
Re: Re :AMBER: Holes in water Bill Ross (Fri Mar 11 2005 - 07:59:03 PST)
- Re: Re :AMBER: Holes in water Lukasz Bielecki (Sat Mar 12 2005 - 08:52:31 PST)
  - Re: Re :AMBER: Holes in water Carlos Simmerling (Sat Mar 12 2005 - 10:32:06 PST)
- Re: Re :AMBER: Holes in water Bill Ross (Sat Mar 12 2005 - 10:13:06 PST)
  - Re: Re :AMBER: Holes in water Carlos Simmerling (Sat Mar 12 2005 - 10:46:24 PST)
    - Re: Re :AMBER: Holes in water Thomas E. Cheatham, III (Sat Mar 12 2005 - 14:20:32 PST)
AMBER: problem with nmode using ntrun=5 (2) Phineus Markwick (Fri Mar 11 2005 - 08:39:43 PST)
AMBER: ptraj xueping (Fri Mar 11 2005 - 20:56:29 PST)
- Re: AMBER: ptraj scopio (Fri Mar 11 2005 - 21:44:04 PST)
AMBER: Amber PBMD:Energy fluctuation Praveena Gopal (Sat Mar 12 2005 - 01:48:03 PST)
AMBER: spherical boundary condition Hui-Hsu Tsai (Sat Mar 12 2005 - 11:05:52 PST)
- Re: AMBER: spherical boundary condition David A. Case (Sat Mar 12 2005 - 18:51:58 PST)
- Re: AMBER: spherical boundary condition protege.snu.ac.kr (Mon Mar 14 2005 - 09:43:14 PST)
- Re: AMBER: spherical boundary condition protege.snu.ac.kr (Mon Mar 14 2005 - 09:43:14 PST)
  - Re: AMBER: spherical boundary condition Andreas Svrcek-Seiler (Mon Mar 14 2005 - 10:36:06 PST)
    - Re: AMBER: spherical boundary condition Hui-Hsu Tsai (Mon Mar 14 2005 - 10:59:01 PST)
AMBER: mesure dihedral angle during MD julien (Sun Mar 13 2005 - 08:52:01 PST)
- Re: AMBER: mesure dihedral angle during MD Guanglei Cui (Sun Mar 13 2005 - 10:10:46 PST)
AMBER: gyration radius julien (Sun Mar 13 2005 - 08:49:50 PST)
- Re: AMBER: gyration radius Guanglei Cui (Sun Mar 13 2005 - 10:18:18 PST)
Re: AMBER: gyration radius Bill Ross (Sun Mar 13 2005 - 11:36:15 PST)
AMBER: leap warnings mathew k varghese (Sun Mar 13 2005 - 22:34:32 PST)
- RE: AMBER: leap warnings Ross Walker (Sun Mar 13 2005 - 22:56:17 PST)
AMBER: surfen and surfoff Giulio Rastelli (Mon Mar 14 2005 - 08:21:22 PST)
AMBER: RDF input preparation problem Maciej (Sun Mar 13 2005 - 20:12:22 PST)
AMBER: Xserve and amber Markus W. Germann (Mon Mar 14 2005 - 08:55:53 PST)
- Re: AMBER: Xserve and amber Mengjuei Hsieh (Mon Mar 14 2005 - 17:51:12 PST)
AMBER: Geometrical distortion because of charge? peng79.email.unc.edu (Mon Mar 14 2005 - 10:21:28 PST)
AMBER: Question about radial command in ptraj opitz.che.udel.edu (Mon Mar 14 2005 - 11:19:11 PST)
Re: AMBER: Question about radial command in ptraj Bill Ross (Mon Mar 14 2005 - 11:48:17 PST)
- Re: AMBER: Question about radial command in ptraj opitz.che.udel.edu (Mon Mar 14 2005 - 12:04:55 PST)
- Re: AMBER: Question about radial command in ptraj Bill Ross (Mon Mar 14 2005 - 13:09:08 PST)
AMBER: antechamber and multiplicity Cenk Andac (Mon Mar 14 2005 - 11:57:27 PST)
AMBER: determining solvent/ion densities Joseph W.Toporowski (Mon Mar 14 2005 - 15:35:25 PST)
AMBER: Hydrogen bonding question opitz.che.udel.edu (Tue Mar 15 2005 - 06:57:45 PST)
- Re: AMBER: Hydrogen bonding question Carlos Simmerling (Tue Mar 15 2005 - 07:21:37 PST)
- Re: AMBER: Hydrogen bonding question David A. Case (Tue Mar 15 2005 - 07:23:30 PST)
- Re: AMBER: Hydrogen bonding question opitz.che.udel.edu (Tue Mar 15 2005 - 07:34:53 PST)
  - Re: AMBER: Hydrogen bonding question Carlos Simmerling (Tue Mar 15 2005 - 07:48:41 PST)
  - Re: AMBER: Hydrogen bonding question Thomas E. Cheatham, III (Tue Mar 15 2005 - 07:59:00 PST)
AMBER: Problem saving file in xleap aanzellotti.mail2.vcu.edu (Tue Mar 15 2005 - 09:03:12 PST)
- RE: AMBER: Problem saving file in xleap Ross Walker (Tue Mar 15 2005 - 10:02:32 PST)
  - RE: AMBER: Problem saving file in xleap aanzellotti.mail2.vcu.edu (Thu Mar 17 2005 - 08:45:07 PST)
AMBER: Sander: idecomp lei jia (Tue Mar 15 2005 - 11:45:47 PST)
- Re: AMBER: Sander: idecomp Jack Lei (Tue Mar 15 2005 - 15:57:21 PST)
- Re: AMBER: Sander: idecomp lei jia (Tue Mar 15 2005 - 18:25:24 PST)
  - Re: Re: AMBER: Sander: idecomp Xiao He (Mon Mar 28 2005 - 05:44:53 PST)
AMBER: frcmod.mod_phipsi.2 bybaker.itsa.ucsf.edu (Tue Mar 15 2005 - 12:04:31 PST)
- RE: AMBER: frcmod.mod_phipsi.2 Junmei Wang (Tue Mar 15 2005 - 12:22:29 PST)
- Re: AMBER: frcmod.mod_phipsi.2 Carlos Simmerling (Tue Mar 15 2005 - 14:52:53 PST)
AMBER: in vacuo parameters Stern, Julie (Tue Mar 15 2005 - 15:14:44 PST)
- Re: AMBER: in vacuo parameters Carlos Simmerling (Tue Mar 15 2005 - 15:29:31 PST)
AMBER: restraintmask dimension Piero Altoè (Wed Mar 16 2005 - 03:42:12 PST)
- Re: AMBER: restraintmask dimension Viktor Hornak (Wed Mar 16 2005 - 05:46:27 PST)
AMBER: Bio-Image summer school in Paris this year Marc Baaden (Wed Mar 16 2005 - 03:44:47 PST)
AMBER: Velocity Info Vineet Pande (Wed Mar 16 2005 - 06:08:42 PST)
- Re: AMBER: Velocity Info Guanglei Cui (Wed Mar 16 2005 - 06:55:07 PST)
  - Re: AMBER: Velocity Info Vineet Pande (Wed Mar 16 2005 - 08:02:04 PST)
    - Re: AMBER: Velocity Info Guanglei Cui (Wed Mar 16 2005 - 08:29:35 PST)
AMBER: "personality" of Amber force field Hui-Hsu Tsai (Wed Mar 16 2005 - 08:01:00 PST)
- Re:AMBER: "personality" of Amber force field Asim Okur (Fri Mar 18 2005 - 13:01:19 PST)
  - Re:AMBER: "personality" of Amber force field Hui-Hsu Tsai (Fri Mar 18 2005 - 13:22:11 PST)
    - Re: AMBER: "personality" of Amber force field Adrian E. Roitberg (Fri Mar 18 2005 - 13:24:50 PST)
    - Re: AMBER: "personality" of Amber force field Hui-Hsu Tsai (Fri Mar 18 2005 - 15:05:07 PST)
    - Re: AMBER: "personality" of Amber force field Ray Luo (Thu Mar 17 2005 - 14:17:03 PST)
AMBER: question about amber parameter file format etc. jz7.duke.edu (Wed Mar 16 2005 - 09:37:29 PST)
- RE: AMBER: question about amber parameter file format etc. Vineet Pande (Wed Mar 16 2005 - 10:06:53 PST)
AMBER: periodicity problem Stern, Julie (Wed Mar 16 2005 - 13:02:28 PST)
- Re: AMBER: periodicity problem Ilyas Yildirim (Wed Mar 16 2005 - 13:25:39 PST)
AMBER: Zn complex parametrization question Ashutosh Suhas Jogalekar (Wed Mar 16 2005 - 13:27:38 PST)
Re: AMBER: periodicity problem Bill Ross (Wed Mar 16 2005 - 14:23:03 PST)
AMBER: sander.QMMM and fcap Claudio Morgado (Thu Mar 17 2005 - 05:56:34 PST)
- Re: AMBER: sander.QMMM and fcap David A. Case (Thu Mar 17 2005 - 08:00:04 PST)
AMBER: van der Waals interactions (PTRAJ) Vineet Pande (Thu Mar 17 2005 - 06:07:12 PST)
AMBER: Minimization of avg structure-SANDER Bomb Vineet Pande (Thu Mar 17 2005 - 06:50:03 PST)
- Re: AMBER: Minimization of avg structure-SANDER Bomb David A. Case (Thu Mar 17 2005 - 08:51:59 PST)
  - Re: AMBER: Minimization of avg structure-SANDER Bomb Vineet Pande (Thu Mar 17 2005 - 10:45:01 PST)
    - Re: AMBER: Minimization of avg structure-SANDER Bomb David A. Case (Thu Mar 17 2005 - 10:54:18 PST)
    - Re: AMBER: Minimization of avg structure-SANDER Bomb Vineet Pande (Thu Mar 17 2005 - 12:11:10 PST)
- Re: AMBER: Minimization of avg structure-SANDER Bomb Thomas E. Cheatham, III (Thu Mar 17 2005 - 11:01:33 PST)
AMBER: Bus error - ambpdb David C. Chan (Thu Mar 17 2005 - 06:54:17 PST)
- Re: AMBER: Bus error - ambpdb David A. Case (Thu Mar 17 2005 - 08:54:28 PST)
AMBER: compiler for amber8 on opteron Marc Petitmermet (Thu Mar 17 2005 - 07:56:37 PST)
- Re: AMBER: compiler for amber8 on opteron Noriyuki Yamaotsu (Thu Mar 17 2005 - 17:50:24 PST)
  - Re: AMBER: compiler for amber8 on opteron Marc Petitmermet (Fri Mar 18 2005 - 00:22:42 PST)
- Re: AMBER: compiler for amber8 on opteron Robert Duke (Fri Mar 18 2005 - 05:11:22 PST)
AMBER: Making topology files of big moleucles in antechamber Hwankyu Lee (Thu Mar 17 2005 - 08:09:06 PST)
- Re: AMBER: Making topology files of big moleucles in antechamber Melinda Layten (Thu Mar 17 2005 - 11:48:39 PST)
  - Re: AMBER: Making topology files of big moleucles in antechamber Hwankyu Lee (Fri Mar 18 2005 - 08:48:02 PST)
AMBER: add waters to a system + leap problem with solvateOct command Fabien Cailliez (Thu Mar 17 2005 - 10:30:24 PST)
AMBER: Trajectory problems Steve Seibold (Thu Mar 17 2005 - 11:21:37 PST)
- Re: AMBER: Trajectory problems Melinda Layten (Thu Mar 17 2005 - 11:34:50 PST)
AMBER: building helix bundle Yanze Zhang (Thu Mar 17 2005 - 13:30:54 PST)
AMBER: Trajectory problems Steve Seibold (Thu Mar 17 2005 - 13:44:23 PST)
- Re: AMBER: Trajectory problems Asim Okur (Thu Mar 17 2005 - 15:14:28 PST)
AMBER: Separating solvent and solute energy in the microcanonical mode Mey Khalili (Thu Mar 17 2005 - 14:50:09 PST)
- Re: AMBER: Separating solvent and solute energy in the microcanonical mode Carlos Simmerling (Thu Mar 17 2005 - 15:05:17 PST)
  - Re: AMBER: Separating solvent and solute energy in the microcanonical mode Mey Khalili (Thu Mar 17 2005 - 15:11:48 PST)
    - Re: AMBER: Separating solvent and solute energy in the microcanonical mode Carlos Simmerling (Thu Mar 17 2005 - 15:33:43 PST)
AMBER: ptraj: determining solvent/ion densities Joseph W.Toporowski (Thu Mar 17 2005 - 17:40:38 PST)
AMBER: re Updating Tutorials Vidana.Epa.csiro.au (Thu Mar 17 2005 - 19:17:50 PST)
AMBER: Replica Exchange crashing Hayden Eastwood (Fri Mar 18 2005 - 04:39:48 PST)
- Re: AMBER: Replica Exchange crashing Viktor Hornak (Fri Mar 18 2005 - 04:51:48 PST)
- Re: AMBER: Replica Exchange crashing Carlos Simmerling (Fri Mar 18 2005 - 05:11:13 PST)
AMBER: layer Gustavo Pierdominici Sottile (Fri Mar 18 2005 - 06:42:53 PST)
- Re: AMBER: layer Guanglei Cui (Fri Mar 18 2005 - 07:13:32 PST)
- Re: AMBER: layer Carlos Simmerling (Fri Mar 18 2005 - 08:01:45 PST)
AMBER: lmanal input file problem Phineus Markwick (Fri Mar 18 2005 - 08:00:18 PST)
- Re: AMBER: lmanal input file problem David A. Case (Fri Mar 18 2005 - 12:10:00 PST)
AMBER: parameter meaning Wei Wang (Fri Mar 18 2005 - 10:33:15 PST)
AMBER: Problems with Iodine David.Maxwell.di.mdacc.tmc.edu (Fri Mar 18 2005 - 13:03:38 PST)
- Re: AMBER: Problems with Iodine Carlos Simmerling (Fri Mar 18 2005 - 13:22:47 PST)
AMBER: question about periodicity of torsion parameter jz7.duke.edu (Fri Mar 18 2005 - 14:08:50 PST)
- Re: AMBER: question about periodicity of torsion parameter Carlos Simmerling (Fri Mar 18 2005 - 14:51:40 PST)
AMBER: PMEMD with big systems Florian Barth (Fri Mar 18 2005 - 15:25:41 PST)
- Re: AMBER: PMEMD with big systems Robert Duke (Fri Mar 18 2005 - 16:12:24 PST)
  - Re: AMBER: PMEMD with big systems Florian Barth (Wed Mar 23 2005 - 12:48:10 PST)
AMBER: substrate exit from protein in Amber 8.0 TI vdw simulation Eric Hu (Fri Mar 18 2005 - 15:35:39 PST)
- Re: AMBER: substrate exit from protein in Amber 8.0 TI vdw simulation David A. Case (Mon Mar 21 2005 - 10:27:40 PST)
AMBER: igb=10 some vdW terms disappear? Wells, David H (Sun Mar 20 2005 - 23:54:23 PST)
- Re: AMBER: igb=10 some vdW terms disappear? Ray Luo (Mon Mar 21 2005 - 09:15:24 PST)
- Re: AMBER: igb=10 some vdW terms disappear? Ray Luo (Tue Mar 22 2005 - 13:54:57 PST)
  - Re: AMBER: igb=10 some vdW terms disappear? Ray Luo (Tue Mar 22 2005 - 14:59:00 PST)
- Re: AMBER: igb=10 some vdW terms disappear? Wells, David H (Wed Mar 23 2005 - 10:40:53 PST)
AMBER: Making prepin file for individual residues of huge molecule. Hwankyu Lee (Mon Mar 21 2005 - 07:00:11 PST)
- Re: AMBER: Making prepin file for individual residues of huge molecule. David A. Case (Mon Mar 21 2005 - 08:27:23 PST)
AMBER: mm-pbsa with multiple-processors Eric Hu (Mon Mar 21 2005 - 14:21:16 PST)
- Re: AMBER: mm-pbsa with multiple-processors FyD (Mon Mar 21 2005 - 14:39:54 PST)
- Re: AMBER: mm-pbsa with multiple-processors Piotr Cieplak (Mon Mar 21 2005 - 16:17:30 PST)
AMBER: Dual Xeon EM64T Intel Fortran Compile Problem Shekter, Lee (Mon Mar 21 2005 - 16:12:26 PST)
- RE: AMBER: Dual Xeon EM64T Intel Fortran Compile Problem Ross Walker (Mon Mar 21 2005 - 16:54:52 PST)
- RE: AMBER: Dual Xeon EM64T Intel Fortran Compile Problem Shekter, Lee (Mon Mar 21 2005 - 19:39:42 PST)
  - RE: AMBER: Dual Xeon EM64T Intel Fortran Compile Problem Ross Walker (Tue Mar 22 2005 - 10:05:15 PST)
- RE: AMBER: Dual Xeon EM64T Intel Fortran Compile Problem Shekter, Lee (Wed Mar 23 2005 - 08:29:57 PST)
AMBER: TMD force constant Phineus Markwick (Tue Mar 22 2005 - 05:14:53 PST)
- Re: AMBER: TMD force constant Viktor Hornak (Tue Mar 22 2005 - 05:42:37 PST)
- Re: AMBER: TMD force constant Carlos Simmerling (Tue Mar 22 2005 - 05:57:01 PST)
AMBER: nonbonded interaction Svetlana Kirillova (Tue Mar 22 2005 - 08:37:54 PST)
- Re: AMBER: nonbonded interaction David A. Case (Tue Mar 22 2005 - 21:38:08 PST)
  - AMBER: align snapshots to a reference Wen Li (Tue Mar 29 2005 - 13:38:36 PST)
    - Re: AMBER: align snapshots to a reference Carlos Simmerling (Tue Mar 29 2005 - 14:15:29 PST)
    - Re: AMBER: align snapshots to a reference Wen Li (Wed Mar 30 2005 - 07:43:21 PST)
    - Re: AMBER: align snapshots to a reference Carlos Simmerling (Wed Mar 30 2005 - 08:08:01 PST)
    - Re: AMBER: align snapshots to a reference Wen Li (Wed Mar 30 2005 - 08:14:44 PST)
    - Re: AMBER: align snapshots to a reference Thomas E. Cheatham, III (Wed Mar 30 2005 - 08:23:21 PST)
    - Re: AMBER: align snapshots to a reference Wen Li (Wed Mar 30 2005 - 11:52:34 PST)
    - Re: AMBER: align snapshots to a reference Carlos Simmerling (Wed Mar 30 2005 - 08:28:13 PST)
AMBER: ANAL module/AMBER8 Vineet Pande (Tue Mar 22 2005 - 09:32:06 PST)
- RE: AMBER: ANAL module/AMBER8 Vineet Pande (Tue Mar 22 2005 - 10:11:22 PST)
AMBER: Amber8 Parallel installation troubles Joe Nolan (Tue Mar 22 2005 - 11:03:05 PST)
- RE: AMBER: Amber8 Parallel installation troubles Ross Walker (Tue Mar 22 2005 - 11:20:22 PST)
  - Re: AMBER: Amber8 Parallel installation troubles Atro Tossavainen (Tue Mar 22 2005 - 23:43:18 PST)
- Re: AMBER: Amber8 Parallel installation troubles Wei Zhang (Tue Mar 22 2005 - 15:39:06 PST)
AMBER: wierd behavior of addions jz7.duke.edu (Tue Mar 22 2005 - 11:22:54 PST)
- RE: AMBER: wierd behavior of addions Ross Walker (Tue Mar 22 2005 - 11:45:32 PST)
- RE: AMBER: wierd behavior of addions Bill Ross (Tue Mar 22 2005 - 13:23:52 PST)
AMBER: Methionine with both C-ter and N-ter jz7.duke.edu (Tue Mar 22 2005 - 14:17:18 PST)
- Re: AMBER: Methionine with both C-ter and N-ter FyD (Tue Mar 22 2005 - 16:26:35 PST)
AMBER: AMBER 8 installation problem -- undefined reference to `EXIT' luckyang.gmail.com (Tue Mar 22 2005 - 15:34:05 PST)
- Re: AMBER: AMBER 8 installation problem -- undefined reference to `EXIT' Wei Zhang (Tue Mar 22 2005 - 16:29:26 PST)
  - Re: AMBER: AMBER 8 installation problem -- undefined reference to `EXIT' luckyang.gmail.com (Tue Mar 22 2005 - 16:46:26 PST)
- Re: AMBER: AMBER 8 installation problem -- undefined reference to `EXIT' Wei Zhang (Tue Mar 22 2005 - 17:34:26 PST)
  - Re: AMBER: AMBER 8 installation problem -- undefined reference to `EXIT' luckyang.gmail.com (Wed Mar 23 2005 - 14:18:45 PST)
    - Re: AMBER: AMBER 8 installation problem -- undefined reference to `EXIT' luckyang.gmail.com (Wed Mar 23 2005 - 15:01:49 PST)
- Re: AMBER: AMBER 8 installation problem -- undefined reference to `EXIT' Wei Zhang (Wed Mar 23 2005 - 16:49:14 PST)
AMBER: "ERROR TERMINATION DUE TO SHAKE OR TORCON" in Gibbs tanc.uci.edu (Tue Mar 22 2005 - 21:11:41 PST)
Re: AMBER: nonbonded interactions Svetlana Kirillova (Wed Mar 23 2005 - 01:23:47 PST)
AMBER: warning in PBSA Fabien Cailliez (Wed Mar 23 2005 - 05:39:00 PST)
- Re: AMBER: warning in PBSA Ray Luo (Wed Mar 23 2005 - 09:42:34 PST)
AMBER: Could not open file (trajin) with mode (r) Maciej (Wed Mar 23 2005 - 05:52:20 PST)
- RE: AMBER: Could not open file (trajin) with mode (r) Vineet Pande (Wed Mar 23 2005 - 08:26:06 PST)
- RE: AMBER: Could not open file (trajin) with mode (r) Ross Walker (Wed Mar 23 2005 - 10:13:56 PST)
AMBER: antechamber availability dmitri.mikhailov.novartis.com (Wed Mar 23 2005 - 12:40:47 PST)
- Re: AMBER: antechamber availability Guanglei Cui (Wed Mar 23 2005 - 15:21:23 PST)
- Re: AMBER: antechamber availability David A. Case (Thu Mar 24 2005 - 10:42:49 PST)
AMBER: A few question about RDF input preparation Maciej (Thu Mar 24 2005 - 03:13:10 PST)
- Re: AMBER: A few question about RDF input preparation Wei Zhang (Thu Mar 24 2005 - 03:58:47 PST)
AMBER: Make test error Amber (Thu Mar 24 2005 - 13:10:53 PST)
AMBER: question about placing a substrate in a protein pocket Kara Di Giorgio (Thu Mar 24 2005 - 20:33:26 PST)
- RE: AMBER: question about placing a substrate in a protein pocket Vineet Pande (Fri Mar 25 2005 - 01:41:18 PST)
AMBER: Re: ask for your help: parallel on mm_pbsa FyD (Sat Mar 26 2005 - 09:09:23 PST)
AMBER: PTRAJ:"hbond" doubts Vineet Pande (Sun Mar 27 2005 - 05:55:24 PST)
AMBER: missing residue xueping (Sun Mar 27 2005 - 23:34:17 PST)
- RE: AMBER: missing residue Ross Walker (Mon Mar 28 2005 - 08:23:47 PST)
AMBER: ptraj analysis Tatyana B Mamonova (Mon Mar 28 2005 - 09:24:55 PST)
AMBER: Parameter files for general lipids Nitin Bhardwaj (Mon Mar 28 2005 - 16:57:46 PST)
- RE: AMBER: Parameter files for general lipids Vineet Pande (Mon Mar 28 2005 - 23:28:48 PST)
AMBER: REM mdinfo file Sergio E. Wong (Mon Mar 28 2005 - 17:51:45 PST)
- Re: AMBER: REM mdinfo file Guanglei Cui (Tue Mar 29 2005 - 10:00:10 PST)
AMBER: vlimit exceeded in thermalization Holly Freedman (Mon Mar 28 2005 - 20:16:12 PST)
- Re: AMBER: vlimit exceeded in thermalization David A. Case (Tue Mar 29 2005 - 09:22:20 PST)
AMBER: Are the constant pH simulations with explicit water possible? Kateryna Miroshnychenko (Tue Mar 29 2005 - 05:54:14 PST)
- Re: AMBER: Are the constant pH simulations with explicit water possible? David A. Case (Tue Mar 29 2005 - 09:37:27 PST)
AMBER: protonated aspartic acid Adrian E. Roitberg (Tue Mar 29 2005 - 12:14:35 PST)
AMBER: tleap,xleap bond order for triple bonds Stern, Julie (Tue Mar 29 2005 - 14:49:38 PST)
- RE: AMBER: tleap,xleap bond order for triple bonds Ross Walker (Tue Mar 29 2005 - 15:58:51 PST)
  - Re: AMBER: tleap,xleap bond order for triple bonds David A. Case (Tue Mar 29 2005 - 20:43:39 PST)
AMBER: Minimization failure S.Sundar Raman (Tue Mar 29 2005 - 20:47:22 PST)
AMBER: how to cap regions S.Sundar Raman (Tue Mar 29 2005 - 21:00:12 PST)
- Re: AMBER: how to cap regions David A. Case (Thu Mar 31 2005 - 07:45:26 PST)
AMBER: Amber Performance in Parallel on Itanium Robert J. Woods (Wed Mar 30 2005 - 07:32:10 PST)
- RE: AMBER: Amber Performance in Parallel on Itanium Ross Walker (Wed Mar 30 2005 - 08:20:14 PST)
  - Re: AMBER: Amber Performance in Parallel on Itanium Robert J. Woods (Wed Mar 30 2005 - 08:47:25 PST)
AMBER: PTRAJ:"hbond" analysis Vineet Pande (Wed Mar 30 2005 - 09:15:30 PST)
- Re: AMBER: PTRAJ:"hbond" analysis Thomas E. Cheatham, III (Wed Mar 30 2005 - 09:40:16 PST)
  - Re: AMBER: PTRAJ:"hbond" analysis Vineet Pande (Thu Mar 31 2005 - 01:17:57 PST)
AMBER: OH- dynamics Eric Hu (Wed Mar 30 2005 - 09:55:19 PST)
- Re: AMBER: OH- dynamics Carlos Simmerling (Wed Mar 30 2005 - 11:14:07 PST)
  - Re: AMBER: OH- dynamics Eric Hu (Wed Mar 30 2005 - 14:03:53 PST)
    - Re: AMBER: OH- dynamics Carlos Simmerling (Wed Mar 30 2005 - 14:32:09 PST)
    - Re: AMBER: OH- dynamics Eric Hu (Wed Mar 30 2005 - 14:50:03 PST)
    - Re: AMBER: OH- dynamics Carlos Simmerling (Wed Mar 30 2005 - 15:37:26 PST)
    - Re: AMBER: OH- dynamics Eric Hu (Wed Mar 30 2005 - 16:23:32 PST)
AMBER: igb10 vlimit exceeded Wells, David H (Thu Mar 31 2005 - 01:08:55 PST)
- Re: AMBER: igb10 vlimit exceeded Ray Luo (Thu Mar 31 2005 - 08:52:50 PST)
AMBER: All the tests passed except prmtop and prepin... mmv.whu.edu.cn (Thu Mar 31 2005 - 01:59:26 PST)
- Re: AMBER: All the tests passed except prmtop and prepin... David A. Case (Thu Mar 31 2005 - 07:40:18 PST)
  - Re: AMBER: All the tests passed except prmtop and prepin... shuli (Sun Apr 03 2005 - 08:24:47 PDT)
  - Re: AMBER: All the tests passed except prmtop and prepin... shuli (Mon Apr 04 2005 - 07:56:23 PDT)
AMBER: AMBER under MOSIX? Atro Tossavainen (Thu Mar 31 2005 - 03:47:47 PST)
AMBER: Compiling on dual-opteron with pathscale 2.1 on RHEL 4 AS Marc Petitmermet (Thu Mar 31 2005 - 07:32:31 PST)
- Re: AMBER: Compiling on dual-opteron with pathscale 2.1 on RHEL 4 AS Robert Duke (Sat Apr 02 2005 - 16:42:47 PST)
AMBER: What does this mean .. ? Pavan Ghatty (Thu Mar 31 2005 - 11:14:53 PST)
- Re: AMBER: What does this mean .. ? Carlos Simmerling (Thu Mar 31 2005 - 11:33:25 PST)
AMBER: leap bond error Stern, Julie (Thu Mar 31 2005 - 17:11:29 PST)
AMBER: Target MD and nmode test hang Mingfeng Yang (Thu Mar 31 2005 - 18:08:13 PST)
AMBER: GB dynamics mathew k varghese (Thu Mar 31 2005 - 20:01:30 PST)
- Re: AMBER: GB dynamics David A. Case (Fri Apr 01 2005 - 08:16:46 PST)
  - AMBER: trajectory alignment using ptraj Wen Li (Fri Apr 01 2005 - 09:38:02 PST)
    - Re: AMBER: trajectory alignment using ptraj Thomas E. Cheatham, III (Fri Apr 01 2005 - 09:47:30 PST)
    - Re: AMBER: trajectory alignment using ptraj Wen Li (Fri Apr 01 2005 - 10:42:36 PST)
    - Re: AMBER: trajectory alignment using ptraj Wen Li (Fri Apr 01 2005 - 12:12:34 PST)
    - Re: AMBER: trajectory alignment using ptraj Thomas E. Cheatham, III (Fri Apr 01 2005 - 12:39:07 PST)
    - Re: AMBER: trajectory alignment using ptraj Wen Li (Fri Apr 01 2005 - 13:23:14 PST)
    - Re: AMBER: trajectory alignment using ptraj Thomas E. Cheatham, III (Fri Apr 01 2005 - 13:38:50 PST)
    - Re: AMBER: trajectory alignment using ptraj Wen Li (Fri Apr 01 2005 - 18:42:43 PST)
    - Re: AMBER: trajectory alignment using ptraj Wen Li (Fri Apr 01 2005 - 13:37:57 PST)
AMBER: solvateoct mymolecule CHCL3BOX 10 PROBLEM!!! chaiann ng (Thu Mar 31 2005 - 20:30:40 PST)
- Re: AMBER: solvateoct mymolecule CHCL3BOX 10 PROBLEM!!! Jiri Matousek (Thu Mar 31 2005 - 23:37:39 PST)
AMBER: How to fix the torsion angles during energy minimization Ananda Rama Krishnan Selvaraj (Thu Mar 31 2005 - 22:42:27 PST)
- Re: AMBER: How to fix the torsion angles during energy minimization Ananda Rama Krishnan Selvaraj (Fri Apr 01 2005 - 04:54:18 PST)
- Re: AMBER: How to fix the torsion angles during energy minimization David A. Case (Fri Apr 01 2005 - 09:24:37 PST)
AMBER: scaleCharges with polarisable force fields Phineus Markwick (Fri Apr 01 2005 - 04:57:43 PST)
- Re: AMBER: scaleCharges with polarisable force fields David A. Case (Fri Apr 01 2005 - 08:31:22 PST)
AMBER: Problems with protonate on Linux Atro Tossavainen (Fri Apr 01 2005 - 05:09:32 PST)
- Re: AMBER: Problems with protonate on Linux David A. Case (Fri Apr 01 2005 - 09:34:17 PST)
  - Re: AMBER: Problems with protonate on Linux Atro Tossavainen (Tue Apr 05 2005 - 23:46:34 PDT)
    - Re: AMBER: Problems with protonate on Linux David A. Case (Wed Apr 06 2005 - 09:19:11 PDT)
AMBER: reference of Targeted MD xhu1.memphis.edu (Fri Apr 01 2005 - 13:52:59 PST)
Re: AMBER: GB dynamics Bill Ross (Fri Apr 01 2005 - 13:55:07 PST)
AMBER: oxo-heme Peter Gannett (Fri Apr 01 2005 - 14:32:47 PST)
AMBER: problem with input files when using ff02EP + pol3 Phineus Markwick (Sun Apr 03 2005 - 05:35:28 PDT)
- Re: AMBER: problem with input files when using ff02EP + pol3 David A. Case (Sun Apr 03 2005 - 22:18:29 PDT)
AMBER: helical parameters obtaining Kateryna Miroshnychenko (Sat Apr 02 2005 - 03:08:17 PST)
AMBER: surface area John (Mon Apr 04 2005 - 03:35:58 PDT)
- Re: AMBER: surface area Tim Meyer (Mon Apr 04 2005 - 08:38:12 PDT)
AMBER: Sander minimization & dynamic question chaiann ng (Mon Apr 04 2005 - 03:45:48 PDT)
- Re: AMBER: Sander minimization & dynamic question Carlos Simmerling (Mon Apr 04 2005 - 04:48:26 PDT)
- Re: AMBER: Sander minimization & dynamic question Andreas Svrcek-Seiler (Mon Apr 04 2005 - 05:01:32 PDT)
AMBER: ff02EP + pol3 (2) Phineus Markwick (Mon Apr 04 2005 - 05:06:36 PDT)
- Re: AMBER: ff02EP + pol3 (2) David A. Case (Mon Apr 04 2005 - 23:28:22 PDT)
AMBER: emilia wu (Mon Apr 04 2005 - 07:11:48 PDT)
- Re: AMBER: David A. Case (Mon Apr 04 2005 - 23:06:34 PDT)
AMBER: single-stranded poly(rC) simulation Kateryna Miroshnychenko (Mon Apr 04 2005 - 06:49:39 PDT)
- Re: AMBER: single-stranded poly(rC) simulation David A. Case (Mon Apr 04 2005 - 23:31:35 PDT)
AMBER: force constant Unit used in TMD xhu1.memphis.edu (Mon Apr 04 2005 - 08:05:30 PDT)
- Re: AMBER: force constant Unit used in TMD Carlos Simmerling (Mon Apr 04 2005 - 09:06:45 PDT)
- Re: AMBER: force constant Unit used in TMD xhu1.memphis.edu (Mon Apr 04 2005 - 09:33:01 PDT)
  - Re: AMBER: force constant Unit used in TMD Viktor Hornak (Mon Apr 04 2005 - 09:53:23 PDT)
    - Re: AMBER: force constant Unit used in TMD Asim Okur (Mon Apr 04 2005 - 10:36:08 PDT)
- Re: AMBER: force constant Unit used in TMD xhu1.memphis.edu (Mon Apr 04 2005 - 10:28:36 PDT)
- Re: AMBER: force constant Unit used in TMD xhu1.memphis.edu (Mon Apr 04 2005 - 10:59:02 PDT)
AMBER: Compile Error on Running Amber on AMD opterons in the Linux-based clusters Wu Yingliang (Mon Apr 04 2005 - 23:18:11 PDT)
- Re: AMBER: Compile Error on Running Amber on AMD opterons in the Linux-based clusters Wei Zhang (Tue Apr 05 2005 - 00:49:38 PDT)
- Re: AMBER: Compile Error on Running Amber on AMD opterons in the Linux-based clusters David A. Case (Tue Apr 05 2005 - 08:31:15 PDT)
- Re: AMBER: Compile Error on Running Amber on AMD opterons in the Linux-based clusters Bill Ross (Tue Apr 05 2005 - 09:26:34 PDT)
AMBER: AMBER 8.0 problems with impose (tleap) on linux Guillermo Mulliert Carlín (Mon Apr 04 2005 - 23:35:17 PDT)
- Re: AMBER: AMBER 8.0 problems with impose (tleap) on linux David A. Case (Tue Apr 05 2005 - 21:48:14 PDT)
AMBER: how to make a nonsymmetric box around the solute Lina Nilsson (Tue Apr 05 2005 - 00:56:44 PDT)
AMBER: doble C and N terminal Stefano Federico Massimiliano Pieraccini (Stefano.Pieraccini) (Tue Apr 05 2005 - 02:45:58 PDT)
- Re: AMBER: doble C and N terminal David A. Case (Tue Apr 05 2005 - 14:25:10 PDT)
AMBER: GB with Langevin dynamics problem Peter Varnai (Tue Apr 05 2005 - 09:04:15 PDT)
- Re: AMBER: GB with Langevin dynamics problem Carlos Simmerling (Tue Apr 05 2005 - 09:17:24 PDT)
- Re: AMBER: GB with Langevin dynamics problem Andreas Svrcek-Seiler (Tue Apr 05 2005 - 10:04:08 PDT)
AMBER: Re:Re:single-stranded poly(rC) simulation Kateryna Miroshnychenko (Tue Apr 05 2005 - 10:37:54 PDT)
- Re: AMBER: Re:Re:single-stranded poly(rC) simulation Thomas E. Cheatham, III (Tue Apr 05 2005 - 11:32:15 PDT)
AMBER: Protein with structural ions Kara Wald (Tue Apr 05 2005 - 14:29:46 PDT)
- Re: AMBER: Protein with structural ions Oliver Hucke (Tue Apr 05 2005 - 14:42:29 PDT)
- RE: AMBER: Protein with structural ions Kara Di Giorgio (Tue Apr 12 2005 - 08:51:32 PDT)
  - Re: AMBER: Protein with structural ions Carlos Simmerling (Tue Apr 12 2005 - 09:09:48 PDT)
    - Re: AMBER: Protein with structural ions Kara Di Giorgio (Tue Apr 12 2005 - 09:59:40 PDT)
    - Re: Re: AMBER: Protein with structural ions Yong Xu (Tue Apr 05 2005 - 21:34:55 PDT)
    - Re: AMBER: Protein with structural ions Tim Meyer (Thu Apr 07 2005 - 07:05:15 PDT)
    - Re: AMBER: Protein with structural ions Kara Di Giorgio (Thu Apr 07 2005 - 22:29:26 PDT)
    - Re: AMBER: Protein with structural ions David A. Case (Fri Apr 08 2005 - 08:41:22 PDT)
    - Re: AMBER: Protein with structural ions Kara Di Giorgio (Fri Apr 08 2005 - 09:30:26 PDT)
    - Re: AMBER: Protein with structural ions David A. Case (Fri Apr 08 2005 - 10:29:44 PDT)
    - Re: AMBER: Protein with structural ions Kara Di Giorgio (Fri Apr 08 2005 - 11:55:41 PDT)
    - Re: AMBER: Protein with structural ions Kara Di Giorgio (Sun Apr 10 2005 - 20:05:08 PDT)
    - Re: AMBER: Protein with structural ions David A. Case (Sun Apr 10 2005 - 21:04:52 PDT)
    - Re: AMBER: Protein with structural ions Kara Di Giorgio (Sun Apr 10 2005 - 21:47:29 PDT)
    - Re: AMBER: Protein with structural ions David A. Case (Mon Apr 11 2005 - 07:50:28 PDT)
    - Re: AMBER: Protein with structural ions Kara Di Giorgio (Mon Apr 11 2005 - 08:40:45 PDT)
    - Re: Re: AMBER: Protein with structural ions Y. Xu (Thu Apr 07 2005 - 23:39:45 PDT)
AMBER: FW: Amber installation Eric Mullins (Wed Apr 06 2005 - 08:36:20 PDT)
- Re: AMBER: FW: Amber installation David A. Case (Wed Apr 06 2005 - 14:39:42 PDT)
AMBER: a bimolecular reaction Eric Hu (Wed Apr 06 2005 - 10:14:23 PDT)
- Re: AMBER: a bimolecular reaction David A. Case (Tue Apr 12 2005 - 09:59:07 PDT)
  - Re: AMBER: a bimolecular reaction duan_list.albert.genomecenter.ucdavis.edu (Tue Apr 12 2005 - 11:00:14 PDT)
    - Re: AMBER: a bimolecular reaction Eric Hu (Tue Apr 12 2005 - 16:50:58 PDT)
    - Re: AMBER: a bimolecular reaction Yong Duan (Tue Apr 12 2005 - 17:22:51 PDT)
    - Re: AMBER: a bimolecular reaction Eric Hu (Wed Apr 13 2005 - 11:08:03 PDT)
    - RE: AMBER: a bimolecular reaction Yong Duan (Wed Apr 13 2005 - 12:51:08 PDT)
  - Re: AMBER: a bimolecular reaction Yong Duan (Fri Jul 22 2005 - 10:44:23 PDT)
    - RE: AMBER: a bimolecular reaction Yong Duan (Fri Jul 22 2005 - 12:25:09 PDT)
AMBER: About Gaussian Key Words Katagiri Daisuke (Wed Apr 06 2005 - 20:10:12 PDT)
- RE: AMBER: About Gaussian Key Words Vineet Pande (Thu Apr 07 2005 - 01:36:04 PDT)
AMBER: value of SALTCON mathew k varghese (Wed Apr 06 2005 - 21:29:01 PDT)
- Re: AMBER: value of SALTCON David A. Case (Thu Apr 07 2005 - 11:25:50 PDT)
AMBER: combine mdcrd using ptraj xueping (Wed Apr 06 2005 - 21:41:48 PDT)
- Re: AMBER: combine mdcrd using ptraj Asim Okur (Wed Apr 06 2005 - 22:17:57 PDT)
- Re: AMBER: combine mdcrd using ptraj xueping (Wed Apr 06 2005 - 23:59:54 PDT)
  - Re: AMBER: combine mdcrd using ptraj Lihua Wang (Thu Apr 07 2005 - 00:45:18 PDT)
- Re: AMBER: combine mdcrd using ptraj xueping (Thu Apr 07 2005 - 02:13:59 PDT)
AMBER: RADIOPT=1 Fabien Cailliez (Thu Apr 07 2005 - 06:19:09 PDT)
AMBER: RE: system comparison for amber Ross Walker (Thu Apr 07 2005 - 09:41:06 PDT)
- Re: AMBER: RE: system comparison for amber Carlos Simmerling (Thu Apr 07 2005 - 10:00:18 PDT)
AMBER: leap single precision Guanglei Cui (Thu Apr 07 2005 - 11:04:20 PDT)
- Re: AMBER: leap single precision Scott Brozell (Fri Apr 08 2005 - 00:07:31 PDT)
  - Re: AMBER: leap single precision Guanglei Cui (Fri Apr 08 2005 - 09:19:38 PDT)
    - Re: AMBER: leap single precision David A. Case (Sat Apr 09 2005 - 22:27:52 PDT)
Re: AMBER: About Gaussian Key Words (fwd) duan_list.albert.genomecenter.ucdavis.edu (Thu Apr 07 2005 - 16:09:25 PDT)
- Re: AMBER: About Gaussian Key Words (fwd) Daisuke Katagiri (Mon Apr 11 2005 - 17:03:36 PDT)
AMBER: makeDIST_RST ERROR Y. Xu (Thu Apr 07 2005 - 19:14:19 PDT)
- Re: AMBER: makeDIST_RST ERROR David A. Case (Fri Apr 08 2005 - 08:36:30 PDT)
AMBER: problems with "protonate" Kenley Barrett (Thu Apr 07 2005 - 19:27:07 PDT)
- Re: AMBER: problems with "protonate" David A. Case (Fri Apr 08 2005 - 08:49:29 PDT)
  - Re: AMBER: problems with "protonate" Kenley Barrett (Mon Apr 11 2005 - 14:20:47 PDT)
    - Re: AMBER: problems with "protonate" David A. Case (Mon Apr 11 2005 - 18:45:47 PDT)
- Re: AMBER: problems with "protonate" Bill Ross (Mon Apr 11 2005 - 15:33:17 PDT)
- Re: AMBER: problems with "protonate" Bill Ross (Tue Apr 12 2005 - 09:14:27 PDT)
AMBER: how to get the parameters for modified amino acid residue? ying xiong (Thu Apr 07 2005 - 20:31:14 PDT)
- Re: AMBER: how to get the parameters for modified amino acid residue? FyD (Fri Apr 08 2005 - 09:03:34 PDT)
- Re: AMBER: how to get the parameters for modified amino acid residue? David A. Case (Sat Apr 09 2005 - 22:29:09 PDT)
AMBER: linit in mm-pbsa Fabien Cailliez (Fri Apr 08 2005 - 02:08:52 PDT)
- Re: AMBER: linit in mm-pbsa Arantxa Sanz (Fri Apr 08 2005 - 02:43:22 PDT)
  - Re: AMBER: linit in mm-pbsa Ray Luo (Thu Apr 07 2005 - 21:30:06 PDT)
AMBER: Disulfide bond michael chen (Fri Apr 08 2005 - 07:36:41 PDT)
- Re: AMBER: Disulfide bond Carlos Simmerling (Fri Apr 08 2005 - 07:54:46 PDT)
- Re: AMBER: Disulfide bond FyD (Fri Apr 08 2005 - 09:09:03 PDT)
AMBER: GB with Langevin dynamics problem 2 Peter Varnai (Fri Apr 08 2005 - 09:29:08 PDT)
- Re: AMBER: GB with Langevin dynamics problem 2 David A. Case (Fri Apr 08 2005 - 10:48:27 PDT)
  - AMBER: GB with Langevin dynamics - solution Peter Varnai (Mon Apr 11 2005 - 10:18:13 PDT)
    - Re: AMBER: GB with Langevin dynamics - solution David A. Case (Tue Apr 12 2005 - 09:56:34 PDT)
    - Re: AMBER: GB with Langevin dynamics - solution Peter Varnai (Tue Apr 12 2005 - 10:39:54 PDT)
- Re: AMBER: GB with Langevin dynamics problem 2 Andreas Svrcek-Seiler (Fri Apr 08 2005 - 10:55:48 PDT)
  - Re: AMBER: GB with Langevin dynamics problem 2 David A. Case (Sat Apr 09 2005 - 22:34:48 PDT)
- Re: AMBER: GB with Langevin dynamics problem 2 Carlos Simmerling (Fri Apr 08 2005 - 12:03:14 PDT)
AMBER: Announcment: Nucleic Acid Builder (NAB) version 5 is released David A. Case (Fri Apr 08 2005 - 09:52:54 PDT)
AMBER: question about TGMD: vlimit exceeded for step xhu1.memphis.edu (Fri Apr 08 2005 - 13:31:10 PDT)
- Re: AMBER: question about TGMD: vlimit exceeded for step Viktor Hornak (Fri Apr 08 2005 - 13:47:40 PDT)
- Re: AMBER: question about TGMD: vlimit exceeded for step xhu1.memphis.edu (Fri Apr 08 2005 - 14:55:05 PDT)
  - Re: AMBER: question about TGMD: vlimit exceeded for step Viktor Hornak (Fri Apr 08 2005 - 15:24:13 PDT)
- Re: AMBER: question about TGMD: vlimit exceeded for step xhu1.memphis.edu (Fri Apr 08 2005 - 16:04:17 PDT)
AMBER: average structure-ptraj xueping (Sat Apr 09 2005 - 01:23:23 PDT)
- Re: AMBER: average structure-ptraj Carlos Simmerling (Sat Apr 09 2005 - 08:02:02 PDT)
- Re: AMBER: average structure-ptraj xueping (Sun Apr 10 2005 - 01:50:19 PDT)
- Re: AMBER: average structure-ptraj xueping (Sun Apr 10 2005 - 02:10:55 PDT)
AMBER: A question on connecting residues in xleap Hwankyu Lee (Sun Apr 10 2005 - 09:54:55 PDT)
- RE: AMBER: A question on connecting residues in xleap Ross Walker (Sun Apr 10 2005 - 11:25:16 PDT)
  - Re: AMBER: A question on connecting residues in xleap Hwankyu Lee (Sun Apr 10 2005 - 14:22:16 PDT)
    - RE: AMBER: A question on connecting residues in xleap Ross Walker (Sun Apr 10 2005 - 22:00:34 PDT)
    - Re: AMBER: A question on connecting residues in xleap Hwankyu Lee (Mon Apr 11 2005 - 07:49:47 PDT)
    - RE: AMBER: A question on connecting residues in xleap Ross Walker (Mon Apr 11 2005 - 10:13:15 PDT)
AMBER: Warnings as a file Pavan Ghatty (Sun Apr 10 2005 - 21:37:21 PDT)
- Re: AMBER: Warnings as a file scopio (Sun Apr 10 2005 - 22:03:39 PDT)
AMBER: Two question about dielectric constant 烨武 (Mon Apr 11 2005 - 01:02:10 PDT)
- Re: AMBER: Two question about dielectric constant Carlos Simmerling (Mon Apr 11 2005 - 06:18:07 PDT)
  - Re: AMBER: Two question about dielectric constant Lihua Wang (Mon Apr 11 2005 - 10:04:24 PDT)
AMBER: rst file problems mathew k varghese (Mon Apr 11 2005 - 03:03:41 PDT)
- Re: AMBER: rst file problems Carlos Simmerling (Mon Apr 11 2005 - 06:22:41 PDT)
- Re: AMBER: rst file problems mathew k varghese (Mon Apr 11 2005 - 20:13:21 PDT)
  - Re: AMBER: rst file problems Carlos Simmerling (Tue Apr 12 2005 - 06:39:02 PDT)
    - AMBER: rdparm Tim Meyer (Tue Apr 12 2005 - 07:23:55 PDT)
    - AMBER: nscm Ilyas Yildirim (Tue Apr 12 2005 - 07:55:50 PDT)
    - Re: AMBER: nscm David A. Case (Tue Apr 12 2005 - 08:55:58 PDT)
    - Re: AMBER: nscm duan_list.albert.genomecenter.ucdavis.edu (Tue Apr 12 2005 - 09:45:49 PDT)
- Re: AMBER: rst file problems Furse, Kristina Elisabet (Tue Apr 12 2005 - 13:39:35 PDT)
AMBER:FAD can't be minimized. zhli_2000.126.com (Mon Apr 11 2005 - 05:48:15 PDT)
- Re: AMBER:FAD can't be minimized. David A. Case (Mon Apr 11 2005 - 07:58:45 PDT)
AMBER: breaking symmetry in minimization Stern, Julie (Mon Apr 11 2005 - 13:58:53 PDT)
Re: AMBER: breaking symmetry in minimization Bill Ross (Mon Apr 11 2005 - 15:25:25 PDT)
AMBER: Fail to load the trajectory file. Jinzhi Lei (Mon Apr 11 2005 - 17:36:34 PDT)
- Re: AMBER: Fail to load the trajectory file. Thomas E. Cheatham, III (Mon Apr 11 2005 - 19:08:11 PDT)
  - Re: Re: AMBER: Fail to load the trajectory file. Jinzhi Lei (Tue Apr 12 2005 - 13:54:52 PDT)
Re: AMBER: Fail to load the trajectory file. Bill Ross (Mon Apr 11 2005 - 17:41:52 PDT)
- Re: Re: AMBER: Fail to load the trajectory file. Jinzhi Lei (Mon Apr 11 2005 - 18:00:14 PDT)
- Re: Re: AMBER: Fail to load the trajectory file. Bill Ross (Mon Apr 11 2005 - 18:11:19 PDT)
  - Re: Re: Re: AMBER: Fail to load the trajectory file. Jinzhi Lei (Mon Apr 11 2005 - 18:53:50 PDT)
AMBER: peptide side chain modification with LEAP Hannes Barsch (Tue Apr 12 2005 - 07:19:53 PDT)
- RE: AMBER: peptide side chain modification with LEAP Ross Walker (Tue Apr 12 2005 - 08:45:23 PDT)
AMBER: implementing AMBER in NAMD Lina Nilsson (Thu Apr 28 2005 - 07:23:16 PDT)
- AMBER: The effect appling paches Yagi Toru (Tue Apr 19 2005 - 06:11:54 PDT)
  - Re: AMBER: The effect appling paches David A. Case (Tue Apr 19 2005 - 08:01:58 PDT)
AMBER: Does anybody know the experimental solvation free energies of Efavirenz and some other DPC drugs Ye MEI (Tue Apr 12 2005 - 08:19:37 PDT)
AMBER: MM_PBSA problem Xin Hu (Tue Apr 12 2005 - 09:09:36 PDT)
- Re: AMBER: MM_PBSA problem Nelson Fonseca (Tue Apr 12 2005 - 09:20:53 PDT)
- Re: AMBER: MM_PBSA problem Fabien Cailliez (Tue Apr 12 2005 - 09:50:14 PDT)
- Re: AMBER: MM_PBSA problem Xin Hu (Tue Apr 12 2005 - 12:31:45 PDT)
- Re: AMBER: MM_PBSA problem Xin Hu (Tue Apr 12 2005 - 12:36:07 PDT)
  - Re: AMBER: MM_PBSA problem Nelson Fonseca (Tue Apr 12 2005 - 14:15:00 PDT)
    - Re: AMBER: MM_PBSA problem David A. Case (Wed Apr 13 2005 - 08:23:17 PDT)
- Re: AMBER: MM_PBSA problem Xin Hu (Wed Apr 13 2005 - 08:28:17 PDT)
- Re: AMBER: MM_PBSA problem Xin Hu (Wed Apr 13 2005 - 10:49:05 PDT)
- Re: AMBER: MM_PBSA problem Magne Olufsen (Thu Nov 03 2005 - 23:50:30 PST)
  - Re: AMBER: MM_PBSA problem haixiao jin (Fri Nov 04 2005 - 00:58:14 PST)
    - Re: AMBER: MM_PBSA problem Scott Pendley (Fri Nov 04 2005 - 10:18:17 PST)
    - Re: AMBER: MM_PBSA problem haixiao jin (Mon Nov 07 2005 - 00:59:27 PST)
Re: AMBER: peptide side chain modification with LEAP Bill Ross (Tue Apr 12 2005 - 09:22:40 PDT)
AMBER: Silicon related parameters luckyang.gmail.com (Tue Apr 12 2005 - 09:38:35 PDT)
AMBER: ibelly not working Stern, Julie (Tue Apr 12 2005 - 09:52:56 PDT)
AMBER: vdw or center box dimensions, periodicity, and the jagged edge Stern, Julie (Tue Apr 12 2005 - 10:30:38 PDT)
AMBER: Protein With Structural Ions Kara Di Giorgio (Tue Apr 12 2005 - 10:47:52 PDT)
AMBER: No. of Snapshots in MM/GB/SA Sagar D Khare (Tue Apr 12 2005 - 10:48:44 PDT)
- Re: AMBER: No. of Snapshots in MM/GB/SA Guangyu Sun (Tue Apr 12 2005 - 11:17:35 PDT)
Re: AMBER: ibelly not working Bill Ross (Tue Apr 12 2005 - 11:11:28 PDT)
AMBER: ptraj, hbond problem Joseph W.Toporowski (Tue Apr 12 2005 - 17:07:35 PDT)
AMBER: MM-PBSA in protein-Zn-ligand system Yong Xu (Tue Apr 12 2005 - 18:37:55 PDT)
- Re: AMBER: MM-PBSA in protein-Zn-ligand system Kara Di Giorgio (Tue Apr 12 2005 - 19:50:20 PDT)
  - Re: Re: AMBER: MM-PBSA in protein-Zn-ligand system Yong Xu (Tue Apr 12 2005 - 20:17:00 PDT)
AMBER: freee energy calculation without minimised structure S.Sundar Raman (Wed Apr 13 2005 - 00:00:08 PDT)
- RE: AMBER: freee energy calculation without minimised structure Yong Duan (Wed Apr 13 2005 - 00:40:26 PDT)
AMBER: Watson-Crick restraints YoungJin Cho (Wed Apr 13 2005 - 07:43:22 PDT)
- Re: AMBER: Watson-Crick restraints David A. Case (Wed Apr 13 2005 - 22:37:16 PDT)
AMBER: what is wrong with my amber job or installation? Amber (Wed Apr 13 2005 - 11:57:56 PDT)
- RE: AMBER: what is wrong with my amber job or installation? Ross Walker (Wed Apr 13 2005 - 13:46:01 PDT)
  - AMBER: About NAB Ilyas Yildirim (Wed Apr 13 2005 - 17:19:32 PDT)
    - Re: AMBER: About NAB David A. Case (Wed Apr 13 2005 - 22:10:51 PDT)
    - Re: AMBER: About NAB Ilyas Yildirim (Thu Apr 14 2005 - 17:19:14 PDT)
    - Re: AMBER: About NAB David A. Case (Thu Apr 14 2005 - 18:33:26 PDT)
    - Re: AMBER: About NAB Andreas Svrcek-Seiler (Thu Apr 14 2005 - 10:03:49 PDT)
AMBER: Formatting a restraint file Kara Wald (Wed Apr 13 2005 - 13:57:24 PDT)
- Re: AMBER: Formatting a restraint file Carlos Simmerling (Wed Apr 13 2005 - 14:18:54 PDT)
  - Re: AMBER: Formatting a restraint file Kara Di Giorgio (Wed Apr 13 2005 - 17:31:25 PDT)
- Re: AMBER: Formatting a restraint file Furse, Kristina Elisabet (Wed Apr 13 2005 - 22:06:49 PDT)
  - Re: AMBER: Formatting a restraint file Kara Di Giorgio (Thu Apr 14 2005 - 08:26:17 PDT)
    - Re: AMBER: Formatting a restraint file Carlos Simmerling (Thu Apr 14 2005 - 09:13:49 PDT)
    - Re: AMBER: Formatting a restraint file Kara Di Giorgio (Thu Apr 14 2005 - 09:25:18 PDT)
    - Re: AMBER: Formatting a restraint file David A. Case (Thu Apr 14 2005 - 09:28:23 PDT)
- Re: AMBER: Formatting a restraint file Furse, Kristina Elisabet (Thu Apr 14 2005 - 13:02:20 PDT)
AMBER: xleap, lib file question opitz.che.udel.edu (Wed Apr 13 2005 - 14:36:51 PDT)
- RE: AMBER: xleap, lib file question Ross Walker (Wed Apr 13 2005 - 15:07:04 PDT)
AMBER: solvate water box bybaker.itsa.ucsf.edu (Wed Apr 13 2005 - 23:42:21 PDT)
- Re: AMBER: solvate water box David A. Case (Thu Apr 14 2005 - 09:30:11 PDT)
AMBER: Antechamber -reorders atom sequence Austin B. Yongye (Thu Apr 14 2005 - 05:05:09 PDT)
- Re: AMBER: Antechamber -reorders atom sequence David A. Case (Thu Apr 14 2005 - 07:53:17 PDT)
- Re: AMBER: Antechamber -reorders atom sequence FyD (Fri Apr 15 2005 - 09:10:27 PDT)
  - Re: AMBER: Antechamber -reorders atom sequence Austin B. Yongye (Fri Apr 15 2005 - 13:12:40 PDT)
AMBER: Warning: Error opening "New" file from subroutine OPNMRG in pmemd Fabien Cailliez (Thu Apr 14 2005 - 06:05:32 PDT)
AMBER: periodic boundaries and repeating structure Stern, Julie (Thu Apr 14 2005 - 10:55:09 PDT)
AMBER: antechamber for cyano group nlxc (Thu Apr 14 2005 - 11:03:35 PDT)
- RE: AMBER: antechamber for cyano group Junmei Wang (Tue Apr 19 2005 - 09:28:59 PDT)
Re: AMBER: periodic boundaries and repeating structure Bill Ross (Thu Apr 14 2005 - 11:13:48 PDT)
AMBER: Sander/Mpich2 error with mpd_singinit Joe Nolan (Thu Apr 14 2005 - 13:00:09 PDT)
- Re: AMBER: Sander/Mpich2 error with mpd_singinit David LeBard (Thu Apr 14 2005 - 13:17:54 PDT)
AMBER: small target pressure in constant pressure dynamics Eric Hu (Thu Apr 14 2005 - 14:37:49 PDT)
- Re: AMBER: small target pressure in constant pressure dynamics Thomas E. Cheatham, III (Thu Apr 14 2005 - 15:09:18 PDT)
  - Re: AMBER: small target pressure in constant pressure dynamics Eric Hu (Thu Apr 14 2005 - 15:26:23 PDT)
- RE: AMBER: small target pressure in constant pressure dynamics Yong Duan (Thu Apr 14 2005 - 16:30:09 PDT)
AMBER: big fluctuation in MM-PBSA/GA Eric Hu (Thu Apr 14 2005 - 15:54:05 PDT)
- Re: AMBER: big fluctuation in MM-PBSA/GA David A. Case (Thu Apr 14 2005 - 16:33:00 PDT)
  - Re: AMBER: big fluctuation in MM-PBSA/GA Eric Hu (Thu Apr 14 2005 - 17:21:40 PDT)
- Re: AMBER: big fluctuation in MM-PBSA/GA Thomas E. Cheatham, III (Thu Apr 14 2005 - 16:53:48 PDT)
- Re: AMBER: big fluctuation in MM-PBSA/GA Xin Hu (Fri Apr 15 2005 - 11:17:28 PDT)
  - Re: AMBER: big fluctuation in MM-PBSA/GA Eric Hu (Fri Apr 15 2005 - 11:59:09 PDT)
- Re: AMBER: big fluctuation in MM-PBSA/GA Xin Hu (Fri Apr 15 2005 - 13:53:02 PDT)
  - Re: AMBER: big fluctuation in MM-PBSA/GA Eric Hu (Fri Apr 15 2005 - 14:42:45 PDT)
AMBER: parameters in gaff.dat Lihua Wang (Thu Apr 14 2005 - 22:21:29 PDT)
- Re: AMBER: parameters in gaff.dat David A. Case (Thu Apr 14 2005 - 23:02:48 PDT)
  - Re: AMBER: parameters in gaff.dat Lihua Wang (Fri Apr 15 2005 - 11:50:04 PDT)
    - Re: AMBER: parameters in gaff.dat David A. Case (Fri Apr 15 2005 - 13:31:56 PDT)
AMBER: how to make the prepin file for dimer and clusters of organic molecule in Amber7 Ananda Rama Krishnan Selvaraj (Fri Apr 15 2005 - 01:11:27 PDT)
- Re: AMBER: how to make the prepin file for dimer and clusters of organic molecule in Amber7 David A. Case (Fri Apr 15 2005 - 08:25:56 PDT)
AMBER: carnal problem Ed Pate (Fri Apr 15 2005 - 09:15:54 PDT)
AMBER: SollvateBox with ethanol Huaer XC (Fri Apr 15 2005 - 09:21:01 PDT)
- Re: AMBER: SollvateBox with ethanol Guanglei Cui (Fri Apr 15 2005 - 10:50:20 PDT)
  - AMBER: Solvate with mixture of ethanol and water(Newbie question) Huaer XC (Tue Apr 26 2005 - 22:41:00 PDT)
AMBER: gaff atom types Claudio Morgado (Fri Apr 15 2005 - 10:11:18 PDT)
- RE: AMBER: gaff atom types Junmei Wang (Tue Apr 19 2005 - 09:18:44 PDT)
Re: AMBER: carnal problem Bill Ross (Fri Apr 15 2005 - 10:32:02 PDT)
- Re: AMBER: carnal problem Ed Pate (Fri Apr 15 2005 - 11:10:37 PDT)
- Re: AMBER: carnal problem Bill Ross (Fri Apr 15 2005 - 11:42:16 PDT)
  - Re: AMBER: carnal problem Ed Pate (Fri Apr 15 2005 - 11:53:37 PDT)
- Re: AMBER: carnal problem Bill Ross (Fri Apr 15 2005 - 12:20:03 PDT)
  - Re: AMBER: carnal problem Ed Pate (Fri Apr 15 2005 - 12:30:26 PDT)
- Re: AMBER: carnal problem Bill Ross (Thu Sep 08 2005 - 08:51:34 PDT)
  - Ptraj question -- Re: AMBER: carnal problem Joseph Fernandez (Thu Sep 08 2005 - 10:04:14 PDT)
AMBER: RESP charges with Gaussian03 and Amber Delon Wilson (Fri Apr 15 2005 - 13:57:19 PDT)
- Re: AMBER: RESP charges with Gaussian03 and Amber FyD (Fri Apr 15 2005 - 15:16:05 PDT)
- AMBER: RESP charges with Gaussian03 and Amber Delon Wilson (Mon Apr 18 2005 - 06:19:16 PDT)
AMBER: the restart of replica exchange method (REM) simulations in AMBER8 Scott E. Boesch (Fri Apr 15 2005 - 14:24:24 PDT)
- Re: AMBER: the restart of replica exchange method (REM) simulations in AMBER8 Carlos Simmerling (Sat Apr 16 2005 - 05:42:37 PDT)
AMBER: amber8/antechamber installation problem Xin Hu (Sat Apr 16 2005 - 18:39:07 PDT)
- Re: AMBER: amber8/antechamber installation problem David A. Case (Sun Apr 17 2005 - 14:38:51 PDT)
- Re: AMBER: amber8/antechamber installation problem Xin Hu (Tue Apr 19 2005 - 07:14:41 PDT)
AMBER: about equilibration dynamics S.Sundar Raman (Mon Apr 18 2005 - 00:18:10 PDT)
AMBER: ATTN REVISION 吕海婷 (Mon Apr 18 2005 - 01:19:46 PDT)
- Re: AMBER: ATTN REVISION David A. Case (Mon Apr 18 2005 - 07:57:58 PDT)
- RE: AMBER: ATTN REVISION Junmei Wang (Wed Apr 20 2005 - 07:31:47 PDT)
AMBER: dielectric constant Nina Fischer (Mon Apr 18 2005 - 01:22:34 PDT)
- Re: AMBER: dielectric constant David A. Case (Mon Apr 18 2005 - 08:00:41 PDT)
AMBER:Bond lengths aren't reasonable after minimisation. zhli_2000.126.com (Mon Apr 18 2005 - 03:39:22 PDT)
- RE: AMBER:Bond lengths aren't reasonable after minimisation. Ross Walker (Mon Apr 18 2005 - 09:55:54 PDT)
AMBER: Rep Exch. suggestion Brent Krueger (Mon Apr 18 2005 - 04:56:33 PDT)
- Re: AMBER: Rep Exch. suggestion Guanglei Cui (Mon Apr 18 2005 - 06:37:37 PDT)
AMBER: langevin, GB and simulated annealing? pascal.baillod.epfl.ch (Mon Apr 18 2005 - 08:14:08 PDT)
- Re: AMBER: langevin, GB and simulated annealing? Adrian E. Roitberg (Mon Apr 18 2005 - 08:21:04 PDT)
- Re: AMBER: langevin, GB and simulated annealing? Carlos Simmerling (Mon Apr 18 2005 - 08:36:19 PDT)
  - AMBER: langevin, GB and simulated annealing - 2 pascal.baillod.epfl.ch (Tue Apr 19 2005 - 14:07:23 PDT)
    - Re: AMBER: langevin, GB and simulated annealing - 2 David A. Case (Tue Apr 19 2005 - 17:04:56 PDT)
    - Re: AMBER: langevin, GB and simulated annealing - 2 Andreas Svrcek-Seiler (Wed Apr 20 2005 - 01:03:56 PDT)
AMBER: Dual Xeon EM64T Intel Fortran Compiler Shekter, Lee (Mon Apr 18 2005 - 11:17:58 PDT)
AMBER: local dielectric constant Xavier Deupi (Mon Apr 18 2005 - 18:17:40 PDT)
AMBER: Re: Re: AMBER: ATTN REVISION 吕海婷 (Mon Apr 18 2005 - 18:38:02 PDT)
- Re: AMBER: Re: Re: AMBER: ATTN REVISION David A. Case (Mon Apr 18 2005 - 21:37:13 PDT)
- RE: AMBER: Re: Re: AMBER: ATTN REVISION Junmei Wang (Tue Apr 19 2005 - 09:08:58 PDT)
  - Re: AMBER: ATTN REVISION lv haiting (Tue Apr 19 2005 - 19:08:14 PDT)
AMBER: RESP charges - multiple conformations Austin B. Yongye (Mon Apr 18 2005 - 19:54:20 PDT)
- Re: AMBER: RESP charges - multiple conformations FyD (Mon Apr 18 2005 - 22:44:04 PDT)
  - Re: AMBER: RESP charges - multiple conformations Austin B. Yongye (Tue Apr 19 2005 - 05:43:45 PDT)
    - Re: AMBER: RESP charges - multiple conformations FyD (Tue Apr 19 2005 - 07:26:48 PDT)
AMBER: New parametrs Maciej (Mon Apr 18 2005 - 22:38:51 PDT)
AMBER: GAFF: H type on carbon bearing a cyano group Claudio Morgado (Tue Apr 19 2005 - 01:34:12 PDT)
AMBER: Gibbs compilation problem Maciej (Tue Apr 19 2005 - 04:36:52 PDT)
- Re: AMBER: Gibbs compilation problem David A. Case (Tue Apr 19 2005 - 07:50:12 PDT)
AMBER: solvent accessible surface area John (Tue Apr 19 2005 - 03:45:40 PDT)
- RE: AMBER: solvent accessible surface area John (Tue Apr 19 2005 - 05:22:04 PDT)
  - Re: AMBER: solvent accessible surface area David A. Case (Tue Apr 19 2005 - 07:43:24 PDT)
  - Re: AMBER: solvent accessible surface area Ray Luo (Mon Apr 18 2005 - 19:12:54 PDT)
AMBER: Amber8 installation on IBM (power4) with SUSE 9.1 Linux (IBM XLF compiler) Soo Joo (Tue Apr 19 2005 - 02:36:26 PDT)
- Re: AMBER: Amber8 installation on IBM (power4) with SUSE 9.1 Linux (IBM XLF compiler) David A. Case (Tue Apr 19 2005 - 07:40:30 PDT)
AMBER: a problem with mm_pbsa Ye MEI (Tue Apr 19 2005 - 07:23:01 PDT)
- Re: AMBER: a problem with mm_pbsa Xin Hu (Tue Apr 19 2005 - 07:44:35 PDT)
AMBER: Amber compilation problem David A. Case (Tue Apr 19 2005 - 07:59:27 PDT)
AMBER: Non-Bonded Cutoff vs PME Vineet Pande (Tue Apr 19 2005 - 09:13:26 PDT)
- Re: AMBER: Non-Bonded Cutoff vs PME David A. Case (Tue Apr 19 2005 - 14:35:51 PDT)
  - Re: AMBER: Non-Bonded Cutoff vs PME Thomas E. Cheatham, III (Tue Apr 19 2005 - 16:47:10 PDT)
    - Re: AMBER: Non-Bonded Cutoff vs PME Vineet Pande (Wed Apr 20 2005 - 02:17:20 PDT)
    - Re: AMBER: Non-Bonded Cutoff vs PME Thomas E. Cheatham, III (Wed Apr 20 2005 - 07:53:38 PDT)
AMBER: Yong Xu (Tue Apr 19 2005 - 19:57:44 PDT)
AMBER: tleap and water thenmalar (Wed Apr 20 2005 - 01:13:58 PDT)
- Re: AMBER: tleap and water Thomas E. Cheatham, III (Wed Apr 20 2005 - 07:28:33 PDT)
AMBER: GB and mm_pbsa.pl Nelson Fonseca (Wed Apr 20 2005 - 04:48:48 PDT)
- Re: AMBER: GB and mm_pbsa.pl David A. Case (Wed Apr 20 2005 - 08:12:56 PDT)
  - Re: AMBER: GB and mm_pbsa.pl Nelson Fonseca (Wed Apr 20 2005 - 09:05:12 PDT)
    - Re: AMBER: GB and mm_pbsa.pl David A. Case (Wed Apr 20 2005 - 10:18:35 PDT)
AMBER: interaction between residues Stefano Federico Massimiliano Pieraccini (Stefano.Pieraccini) (Wed Apr 20 2005 - 07:27:31 PDT)
AMBER: Re: RE: AMBER:Bond lengths aren't reasonable after minimisation. zhli_2000 (Wed Apr 20 2005 - 06:52:18 PDT)
- Large files to AMBER, RE: AMBER: Re: RE: AMBER:Bond lengths aren't reasonable after minimisation. Yong Duan (Wed Apr 20 2005 - 08:16:55 PDT)
AMBER: Re: RE: AMBER:Bond lengths aren't reasonable after minimisation. Ross Walker (Wed Apr 20 2005 - 10:04:03 PDT)
AMBER: ibelly not working Stern, Julie (Wed Apr 20 2005 - 12:40:28 PDT)
- Re: AMBER: ibelly not working David A. Case (Thu Apr 21 2005 - 08:36:40 PDT)
AMBER: intramolecular nonbonded interactions in AMBER force field John Silvio Vieceli (Wed Apr 20 2005 - 15:06:48 PDT)
- Re: AMBER: intramolecular nonbonded interactions in AMBER force field Carlos Simmerling (Wed Apr 20 2005 - 15:28:08 PDT)
  - Re: AMBER: intramolecular nonbonded interactions in AMBER force field Vineet Pande (Thu Apr 21 2005 - 01:33:19 PDT)
    - Re: AMBER: intramolecular nonbonded interactions in AMBER force field Carlos Simmerling (Thu Apr 21 2005 - 05:50:46 PDT)
    - Re: AMBER: intramolecular nonbonded interactions in AMBER force field Vineet Pande (Thu Apr 21 2005 - 06:26:30 PDT)
    - Re: AMBER: intramolecular nonbonded interactions in AMBER force field Thomas E. Cheatham, III (Thu Apr 21 2005 - 07:50:24 PDT)
    - Re: AMBER: intramolecular nonbonded interactions in AMBER force field David A. Case (Thu Apr 21 2005 - 08:42:10 PDT)
    - Re: AMBER: intramolecular nonbonded interactions in AMBER force field Guanglei Cui (Fri Apr 22 2005 - 06:52:53 PDT)
- RE: AMBER: intramolecular nonbonded interactions in AMBER force field Ross Walker (Wed Apr 20 2005 - 15:33:41 PDT)
AMBER: about run time in GB and PB Yong Xu (Thu Apr 21 2005 - 01:06:27 PDT)
- Re: AMBER: about run time in GB and PB Phineus Markwick (Thu Apr 21 2005 - 01:26:26 PDT)
  - RE: AMBER: about run time in GB and PB Yong Duan (Thu Apr 21 2005 - 01:57:32 PDT)
    - Re: RE: AMBER: about run time in GB and PB Yong Xu (Thu Apr 21 2005 - 06:17:19 PDT)
    - Re: AMBER: about run time in GB and PB Phineus Markwick (Thu Apr 21 2005 - 07:10:20 PDT)
    - Re: AMBER: about run time in GB and PB Yong Xu (Fri Apr 22 2005 - 01:19:05 PDT)
    - Re: Re: AMBER: about run time in GB and PB Yong Xu (Thu Apr 21 2005 - 01:55:41 PDT)
    - Re: AMBER: about run time in GB and PB Phineus Markwick (Thu Apr 21 2005 - 03:15:57 PDT)
AMBER: On the role of neutralizing ions in GB-MD and GBSA Wu Yingliang (Thu Apr 21 2005 - 03:26:05 PDT)
AMBER: On the role of neutralizing ions in GB-MD and GBSA Wu Yingliang (Thu Apr 21 2005 - 03:16:29 PDT)
- Re: AMBER: On the role of neutralizing ions in GB-MD and GBSA David A. Case (Thu Apr 21 2005 - 08:22:37 PDT)
  - Re: Re: AMBER: On the role of neutralizing ions in GB-MD and GBSA Wu Yingliang (Thu Apr 21 2005 - 19:50:09 PDT)
AMBER: Nose-Hoover thermostat Sam Moors (Thu Apr 21 2005 - 05:40:44 PDT)
- Re: AMBER: Nose-Hoover thermostat David A. Case (Thu Apr 21 2005 - 08:44:13 PDT)
AMBER: re: about run time in GB and PB Phineus Markwick (Thu Apr 21 2005 - 07:29:33 PDT)
AMBER: Moil-view and Quicktime movie Steve Seibold (Thu Apr 21 2005 - 07:55:01 PDT)
AMBER: Sander bomb - atom out of bounds Joe Nolan (Thu Apr 21 2005 - 10:46:01 PDT)
- RE: AMBER: Sander bomb - atom out of bounds Ross Walker (Thu Apr 21 2005 - 11:02:18 PDT)
AMBER: problem with belly calculation restart Ed Pate (Thu Apr 21 2005 - 17:28:59 PDT)
AMBER: mean structure calculation mmv (Fri Apr 22 2005 - 02:17:20 PDT)
AMBER: PB Bomb in circle(): Stored surface points over limit Nelson Fonseca (Fri Apr 22 2005 - 05:56:57 PDT)
AMBER: writing MASKs Sagar D Khare (Fri Apr 22 2005 - 07:58:24 PDT)
- RE: AMBER: writing MASKs Vineet Pande (Fri Apr 22 2005 - 08:45:43 PDT)
AMBER: strange VDWAALS and EEL energies calculated by pbsa Fabien Cailliez (Fri Apr 22 2005 - 08:56:41 PDT)
- Re: AMBER: strange VDWAALS and EEL energies calculated by pbsa Carlos Simmerling (Fri Apr 22 2005 - 09:05:42 PDT)
- Re: AMBER: strange VDWAALS and EEL energies calculated by pbsa David A. Case (Fri Apr 22 2005 - 09:12:15 PDT)
- Re: AMBER: strange VDWAALS and EEL energies calculated by pbsa Ray Luo (Thu Apr 21 2005 - 05:18:17 PDT)
AMBER: Induced dipole in AMBER8 Cenk Andac (Fri Apr 22 2005 - 09:57:56 PDT)
- Re: AMBER: Induced dipole in AMBER8 David A. Case (Fri Apr 22 2005 - 18:23:41 PDT)
- Re: AMBER: Induced dipole in AMBER8 Cenk Andac (Mon Apr 25 2005 - 12:00:17 PDT)
  - AMBER: atommask error Sergio E. Wong (Thu Apr 28 2005 - 23:02:05 PDT)
    - Re: AMBER: atommask error hornak.csb.sunysb.edu (Fri Apr 29 2005 - 00:41:09 PDT)
    - Re: AMBER: atommask error Sergio E. Wong (Fri Apr 29 2005 - 10:19:25 PDT)
AMBER: Amber Installation pmullins (Fri Apr 22 2005 - 11:28:34 PDT)
- Re: AMBER: Amber Installation David A. Case (Fri Apr 22 2005 - 12:14:01 PDT)
AMBER: Calculate vdw parameters for alkaline earth metal ions Kenley Barrett (Fri Apr 22 2005 - 15:19:23 PDT)
Re: AMBER: Calculate vdw parameters for alkaline earth metal ions Bill Ross (Fri Apr 22 2005 - 15:48:15 PDT)
AMBER: Problem when converting AMBER trajectories to CHARMM format Chen Hu (Sat Apr 23 2005 - 15:20:56 PDT)
- Re: AMBER: Problem when converting AMBER trajectories to CHARMM format Thomas E. Cheatham, III (Sat Apr 23 2005 - 16:33:48 PDT)
AMBER: serial and parallel Aknb (Sun Apr 24 2005 - 04:35:37 PDT)
- RE: AMBER: serial and parallel Ross Walker (Sun Apr 24 2005 - 11:49:38 PDT)
AMBER: coordinates translation Ye MEI (Sun Apr 24 2005 - 09:26:39 PDT)
- Re: AMBER: coordinates translation Jack Lei (Sun Apr 24 2005 - 16:51:16 PDT)
AMBER: AMBER Test Error tpatko (Sun Apr 24 2005 - 17:31:42 PDT)
- AMBER: Re: AMBER Test Error (Follow Up) tpatko (Sun Apr 24 2005 - 17:55:18 PDT)
AMBER: How to deal with the Non-standard residue lv haiting (Mon Apr 25 2005 - 01:18:08 PDT)
- Re: AMBER: How to deal with the Non-standard residue FyD (Mon Apr 25 2005 - 13:07:33 PDT)
AMBER: the restarting error zhli_2000.126.com (Mon Apr 25 2005 - 07:08:02 PDT)
- Re: AMBER: the restarting error Guanglei Cui (Mon Apr 25 2005 - 07:37:50 PDT)
  - Re: AMBER: the restarting error zhli_2000.126.com (Tue Apr 26 2005 - 03:54:44 PDT)
AMBER: Free energy pertubation (thermodynamic intergration) mrbroad.ilstu.edu (Mon Apr 25 2005 - 09:20:35 PDT)
- Re: AMBER: Free energy pertubation (thermodynamic intergration) Sichun Yang (Mon Apr 25 2005 - 09:55:16 PDT)
- Re: AMBER: Free energy pertubation (thermodynamic intergration) Ilyas Yildirim (Mon Apr 25 2005 - 13:43:36 PDT)
AMBER: radius parameter for F atom Ye MEI (Mon Apr 25 2005 - 10:05:06 PDT)
- Re: AMBER: radius parameter for F atom scopio (Mon Apr 25 2005 - 18:36:16 PDT)
- Re: AMBER: radius parameter for F atom Scott Pendley (Tue May 10 2005 - 12:49:21 PDT)
  - Re: Re: AMBER: radius parameter for F atom Ye MEI (Tue Apr 26 2005 - 06:30:07 PDT)
AMBER: mm_pbsa problem Husni Fattayer (Mon Apr 25 2005 - 13:59:22 PDT)
- Re: AMBER: mm_pbsa problem Husni Fattayer (Wed Apr 27 2005 - 08:09:40 PDT)
AMBER: A problem in TI approach - test case: meth2eth and eth2meth Ilyas Yildirim (Mon Apr 25 2005 - 18:47:19 PDT)
- Re: AMBER: A problem in TI approach - test case: meth2eth and eth2meth Thomas Steinbrecher (Tue Apr 26 2005 - 01:37:01 PDT)
  - Re: AMBER: A problem in TI approach - test case: meth2eth and eth2meth Ilyas Yildirim (Wed Apr 27 2005 - 21:34:32 PDT)
    - Re: AMBER: A problem in TI approach - test case: meth2eth and eth2meth Petr Kulhanek (Thu Apr 28 2005 - 00:02:47 PDT)
    - Re: AMBER: A problem in TI approach - test case: meth2eth and eth2meth Ilyas Yildirim (Thu Apr 28 2005 - 16:34:48 PDT)
    - Re: AMBER: A problem in TI approach - test case: meth2eth and eth2meth David Case (Thu Apr 28 2005 - 06:03:00 PDT)
    - Re: AMBER: A problem in TI approach - test case: meth2eth and eth2meth Ilyas Yildirim (Thu Apr 28 2005 - 17:00:11 PDT)
    - AMBER: Representation of cations in MD Thomas Steinbrecher (Fri May 20 2005 - 02:30:24 PDT)
    - Re: AMBER: Representation of cations in MD David A. Case (Fri May 20 2005 - 08:16:15 PDT)
AMBER: Free energy Maciej (Tue Apr 26 2005 - 00:01:16 PDT)
AMBER: Re:Gibbs compilation problem Maciej (Tue Apr 26 2005 - 00:05:31 PDT)
AMBER: langevin, GB and simulated annealing - 3 pascal.baillod.epfl.ch (Tue Apr 26 2005 - 03:37:16 PDT)
- Re: AMBER: langevin, GB and simulated annealing - 3 David Case (Tue Apr 26 2005 - 07:06:08 PDT)
  - AMBER: langevin, GB and simulated annealing - 4 pascal.baillod.epfl.ch (Tue Apr 26 2005 - 08:23:20 PDT)
    - Re: AMBER: langevin, GB and simulated annealing - 4 David Case (Tue Apr 26 2005 - 08:44:32 PDT)
AMBER: AMBER Test Anthony Cruz (Tue Apr 26 2005 - 03:36:27 PDT)
- Re: AMBER: AMBER Test David Case (Tue Apr 26 2005 - 07:12:05 PDT)
AMBER: How to restart MM_PBSA or doing the statistics only Xin Hu (Tue Apr 26 2005 - 09:00:05 PDT)
AMBER: doesn't work in pmemd, and no output in parallel simulations Hwankyu Lee (Tue Apr 26 2005 - 13:35:26 PDT)
- Re: AMBER: doesn't work in pmemd, and no output in parallel simulations Robert Duke (Tue Apr 26 2005 - 14:24:04 PDT)
  - Re: AMBER: doesn't work in pmemd, and no output in parallel simulations Hwankyu Lee (Tue Apr 26 2005 - 19:46:09 PDT)
- Re: AMBER: doesn't work in pmemd, and no output in parallel simulations Robert Duke (Wed Apr 27 2005 - 05:06:46 PDT)
AMBER: capping amit.mbu.iisc.ernet.in (Wed Apr 27 2005 - 00:30:37 PDT)
- Re: AMBER: capping FyD (Wed Apr 27 2005 - 09:40:36 PDT)
- Re: AMBER: capping John Mongan (Wed Apr 27 2005 - 09:50:43 PDT)
- Re: AMBER: capping Bill Ross (Wed Apr 27 2005 - 14:00:50 PDT)
  - Re: AMBER: capping amit.mbu.iisc.ernet.in (Wed Apr 27 2005 - 23:15:19 PDT)
    - Re: AMBER: capping FyD (Thu Apr 28 2005 - 09:21:03 PDT)
- Re: AMBER: capping Bill Ross (Wed Apr 27 2005 - 23:41:48 PDT)
AMBER: emilia wu (Wed Apr 27 2005 - 19:35:59 PDT)
AMBER: mixture solvent model Huaer XC (Wed Apr 27 2005 - 21:13:11 PDT)
AMBER: distance restraints mathew k varghese (Thu Apr 28 2005 - 00:00:16 PDT)
AMBER: Problem with "Thermodynamic integration calculations" tutorial ,unsuspected error Maciej (Thu Apr 28 2005 - 00:41:21 PDT)
AMBER: false bond created upon coordinate retrieval Stern, Julie (Thu Apr 28 2005 - 14:29:38 PDT)
Re: AMBER: false bond created upon coordinate retrieval Bill Ross (Thu Apr 28 2005 - 15:00:38 PDT)
AMBER: segmentation problem aanzellotti.mail2.vcu.edu (Thu Apr 28 2005 - 16:46:36 PDT)
AMBER: Re: R.E.D. question FyD (Fri Apr 29 2005 - 13:21:34 PDT)
- Re: AMBER: Re: R.E.D. question Yanze Zhang (Mon May 02 2005 - 12:19:14 PDT)
  - Re: AMBER: Re: R.E.D. question FyD (Mon May 02 2005 - 12:53:35 PDT)
- AMBER: molsurf error in MM/PBSA calculation JunJun Liu (Tue Jul 12 2005 - 06:43:55 PDT)
  - Re: AMBER: molsurf error in MM/PBSA calculation David A. Case (Tue Jul 12 2005 - 15:03:23 PDT)
  - Re: AMBER: molsurf error in MM/PBSA calculation David A. Case (Tue Jul 12 2005 - 18:23:50 PDT)
  - RE: AMBER: molsurf error in MM/PBSA calculation Paul Beroza (Thu Jul 14 2005 - 16:01:08 PDT)
AMBER: Odd Antechamber Behavior Kara Di Giorgio (Fri Apr 29 2005 - 21:48:01 PDT)
AMBER: ipol=1 & use_pme= ?? Cenk Andac (Sat Apr 30 2005 - 06:26:57 PDT)
- Re: AMBER: ipol=1 & use_pme= ?? David A. Case (Mon May 02 2005 - 09:44:47 PDT)
AMBER: Identifying water molecules with ptraj Joseph Fernandez (Sun May 01 2005 - 14:00:59 PDT)
AMBER: fast 1/r methods Brent Krueger (Mon May 02 2005 - 04:51:56 PDT)
- Re: AMBER: fast 1/r methods fangyu liang (Mon May 02 2005 - 07:17:32 PDT)
- Re: AMBER: fast 1/r methods Andreas Svrcek-Seiler (Mon May 02 2005 - 07:18:22 PDT)
AMBER: How to fix the atom in NPT case? george Chen (Mon May 02 2005 - 11:19:54 PDT)
- Re: AMBER: How to fix the atom in NPT case? David A. Case (Mon May 02 2005 - 11:31:26 PDT)
  - Re: AMBER: How to fix the atom in NPT case? george Chen (Mon May 02 2005 - 12:35:42 PDT)
    - AMBER: problem with prepfile Shafinaz (Wed May 24 2006 - 12:50:21 PDT)
    - Re: AMBER: problem with prepfile David A. Case (Wed May 24 2006 - 13:56:08 PDT)
    - RE: AMBER: problem with prepfile Junmei Wang (Thu May 25 2006 - 09:24:51 PDT)
  - Re: AMBER: How to fix the atom in NPT case? george Chen (Tue May 03 2005 - 13:50:59 PDT)
    - Re: AMBER: How to fix the atom in NPT case? David A. Case (Tue May 03 2005 - 17:16:33 PDT)
AMBER: sander run YoungJin Cho (Mon May 02 2005 - 13:45:01 PDT)
AMBER: GB with dipoles ! Pradipta Bandyopadhyay (Tue May 03 2005 - 04:54:44 PDT)
Fwd: Re: AMBER: AMBER Test Anthony Cruz (Tue May 03 2005 - 05:25:46 PDT)
AMBER: Can I add iodide anione? Myunggi Yi (Tue May 03 2005 - 10:36:07 PDT)
AMBER: rborn(i) in egb.f Harianto Tjong (Tue May 03 2005 - 12:04:39 PDT)
- Re: AMBER: rborn(i) in egb.f John Mongan (Tue May 03 2005 - 11:26:15 PDT)
- Re: AMBER: rborn(i) in egb.f Harianto Tjong (Tue May 03 2005 - 13:31:43 PDT)
  - Re: AMBER: rborn(i) in egb.f David A. Case (Tue May 03 2005 - 13:23:14 PDT)
- Re: AMBER: rborn(i) in egb.f Harianto Tjong (Tue May 03 2005 - 15:13:16 PDT)
  - Re: AMBER: rborn(i) in egb.f David A. Case (Tue May 03 2005 - 15:59:23 PDT)
AMBER: NOE constraints Hui-Hsu Tsai (Tue May 03 2005 - 12:18:27 PDT)
- Re: AMBER: NOE constraints David A. Case (Tue May 03 2005 - 13:25:44 PDT)
AMBER: Relative stability with MMPBSA Angelo Pugliese (Wed May 04 2005 - 09:09:27 PDT)
AMBER: Bromelain PDF xleap load error Thomas Patko (Wed May 04 2005 - 10:13:35 PDT)
- Re: AMBER: Bromelain PDF xleap load error (Proton Problems?) Thomas Patko (Thu May 05 2005 - 15:02:40 PDT)
  - Re: AMBER: Bromelain PDF xleap load error (Proton Problems?) JunJun Liu (Thu May 05 2005 - 17:37:36 PDT)
  - Re: AMBER: Bromelain PDF xleap load error (Proton Problems?) Andy Purkiss (Fri May 06 2005 - 04:05:36 PDT)
    - Re: AMBER: Bromelain PDF xleap load error (Proton Problems?) Thomas Patko (Wed May 11 2005 - 00:10:53 PDT)
AMBER: mm/pbsa error Eric Hu (Wed May 04 2005 - 11:06:34 PDT)
- Re: AMBER: mm/pbsa error Scott Pendley (Tue May 10 2005 - 12:56:52 PDT)
  - Re: AMBER: mm/pbsa error Eric Hu (Wed Jun 01 2005 - 10:23:53 PDT)
AMBER: Meaning of induced dipole moments for atom pairs? Cenk Andac (Wed May 04 2005 - 13:52:06 PDT)
- Re: AMBER: Meaning of induced dipole moments for atom pairs? David A. Case (Wed May 04 2005 - 15:13:14 PDT)
- Re: AMBER: Meaning of induced dipole moments for atom pairs? Cenk Andac (Thu May 05 2005 - 17:28:49 PDT)
  - AMBER: keeping two domains closed together during a simulation Sergio E. Wong (Thu May 05 2005 - 17:44:45 PDT)
AMBER: How can I read parm99.dat file? Myunggi Yi (Wed May 04 2005 - 16:08:49 PDT)
- Re: AMBER: How can I read parm99.dat file? David A. Case (Thu May 05 2005 - 08:10:59 PDT)
- Re: AMBER: How can I read parm99.dat file? Myunggi Yi (Fri May 06 2005 - 06:18:47 PDT)
- Re: AMBER: How can I read parm99.dat file? Bill Ross (Fri May 06 2005 - 13:08:59 PDT)
Re: AMBER: How can I read parm99.dat file? Bill Ross (Wed May 04 2005 - 17:12:08 PDT)
- Re: AMBER: How can I read parm99.dat file? Vineet Pande (Thu May 05 2005 - 02:12:09 PDT)
- Re: AMBER: How can I read parm99.dat file? Myunggi Yi (Fri May 06 2005 - 07:14:04 PDT)
- Re: AMBER: How can I read parm99.dat file? Myunggi Yi (Fri May 06 2005 - 07:14:15 PDT)
AMBER: ibelly in nmode Dawei Zhang (Thu May 05 2005 - 12:23:13 PDT)
- Re: AMBER: ibelly in nmode David A. Case (Sat May 07 2005 - 09:44:21 PDT)
AMBER: problem with gb md emilia wu (Thu May 05 2005 - 19:05:00 PDT)
- RE: AMBER: problem with gb md Ross Walker (Thu May 05 2005 - 21:47:40 PDT)
  - Re: RE: AMBER: problem with gb md emilia wu (Thu May 05 2005 - 23:29:33 PDT)
    - Re: RE: AMBER: problem with gb md Andreas Svrcek-Seiler (Fri May 06 2005 - 02:19:00 PDT)
AMBER: No vdW parameters for HO.. Vineet Pande (Fri May 06 2005 - 03:20:02 PDT)
- Re: AMBER: No vdW parameters for HO.. David A. Case (Fri May 06 2005 - 07:38:16 PDT)
  - Re: AMBER: No vdW parameters for HO.. Vineet Pande (Fri May 06 2005 - 08:40:09 PDT)
    - Re: AMBER: No vdW parameters for HO.. Yong Duan (Fri May 06 2005 - 09:28:25 PDT)
AMBER: a nomenclature question Kenley Barrett (Fri May 06 2005 - 09:11:24 PDT)
- Re: AMBER: a nomenclature question David A. Case (Thu May 12 2005 - 15:18:20 PDT)
AMBER: Dr. Cornell's calculation of Sulfur vdw epsilon value in parm94.dat? Chris Moth (Fri May 06 2005 - 12:32:23 PDT)
AMBER: langevin, GB and simulated annealing - 5 pascal.baillod.epfl.ch (Mon May 09 2005 - 09:25:12 PDT)
- Re: AMBER: langevin, GB and simulated annealing - 5 Carlos Simmerling (Mon May 09 2005 - 12:58:57 PDT)
  - Re: AMBER: langevin, GB and simulated annealing - 5 Carlos Simmerling (Tue May 10 2005 - 04:58:42 PDT)
  - AMBER: Problem with xleap Ilyas Yildirim (Wed May 11 2005 - 18:45:50 PDT)
    - Re: AMBER: Problem with xleap FyD (Wed May 11 2005 - 19:21:12 PDT)
    - Re: AMBER: Problem with xleap Ilyas Yildirim (Thu May 12 2005 - 16:14:38 PDT)
    - Re: AMBER: Problem with xleap JunJun Liu (Thu May 12 2005 - 00:19:24 PDT)
- Re: AMBER: langevin, GB and simulated annealing - 5 David A. Case (Mon May 09 2005 - 16:18:04 PDT)
AMBER: radial distribution function Myunggi Yi (Mon May 09 2005 - 11:36:43 PDT)
AMBER: parameter for sulfur in thio-octyl-glucopyranoside Vijay Manickam Achari (Mon May 09 2005 - 20:23:07 PDT)
- RE: AMBER: parameter for sulfur in thio-octyl-glucopyranoside Spero Manolatos (Thu May 12 2005 - 15:08:49 PDT)
AMBER: AMBER8 Build on Linux x64 running Opterons Thomas Patko (Wed May 11 2005 - 00:10:14 PDT)
- Re: AMBER: AMBER8 Build on Linux x64 running Opterons Mark Rance (Wed May 11 2005 - 08:02:05 PDT)
  - Re: AMBER: AMBER8 Build on Linux x64 running Opterons David A. Case (Thu May 12 2005 - 09:58:19 PDT)
- Re: AMBER: AMBER8 Build on Linux x64 running Opterons Robert Duke (Wed May 11 2005 - 08:14:50 PDT)
- Re: AMBER: AMBER8 Build on Linux x64 running Opterons Robert Duke (Wed May 11 2005 - 08:18:12 PDT)
  - Re: AMBER: AMBER8 Build on Linux x64 running Opterons Thomas Patko (Wed May 11 2005 - 08:34:18 PDT)
- Re: AMBER: AMBER8 Build on Linux x64 running Opterons Bill Ross (Thu May 12 2005 - 13:08:34 PDT)
AMBER: Trouble with example tutorial Maciej (Wed May 11 2005 - 04:08:02 PDT)
- Re: AMBER: Trouble with example tutorial David A. Case (Thu May 12 2005 - 10:04:51 PDT)
AMBER: Parameter for alpha-lactose Sagarika Dev (Wed May 11 2005 - 07:48:21 PDT)
- Re: AMBER: Parameter for alpha-lactose David A. Case (Thu May 12 2005 - 08:29:08 PDT)
AMBER: Asking how to creat alanine "dipeptide" in amber8 Li Su (Wed May 11 2005 - 08:37:07 PDT)
- Re: AMBER: Asking how to creat alanine "dipeptide" in amber8 Thomas E. Cheatham, III (Wed May 11 2005 - 08:38:54 PDT)
- Re: AMBER: Asking how to creat alanine "dipeptide" in amber8 FyD (Wed May 11 2005 - 09:06:27 PDT)
- RE: AMBER: Asking how to creat alanine "dipeptide" in amber8 Ross Walker (Wed May 11 2005 - 10:13:30 PDT)
Fwd: Re: AMBER: AMBER Test Anthony Cruz (Wed May 11 2005 - 08:49:38 PDT)
- Re: Fwd: Re: AMBER: AMBER Test David A. Case (Thu May 12 2005 - 08:33:15 PDT)
AMBER: SANDER BOMB: volume of ucell too big Stern, Julie (Wed May 11 2005 - 09:07:38 PDT)
- Re: AMBER: SANDER BOMB: volume of ucell too big Michael Crowley (Thu May 12 2005 - 10:10:20 PDT)
- RE: AMBER: SANDER BOMB: volume of ucell too big Stern, Julie (Thu May 12 2005 - 12:34:55 PDT)
  - Re: AMBER: SANDER BOMB: volume of ucell too big David A. Case (Thu May 12 2005 - 13:27:50 PDT)
- Re: AMBER: SANDER BOMB: volume of ucell too big Robert Duke (Thu May 12 2005 - 13:44:11 PDT)
AMBER: maximum number of processors MURAT CETINKAYA (Wed May 11 2005 - 20:53:44 PDT)
- Re: AMBER: maximum number of processors Asim Okur (Thu May 12 2005 - 08:41:25 PDT)
- Re: AMBER: maximum number of processors Michael Crowley (Thu May 12 2005 - 10:00:09 PDT)
- Re: AMBER: maximum number of processors Abd Ghani Abd Aziz (Fri May 13 2005 - 23:42:49 PDT)
  - Re: AMBER: maximum number of processors C J Kenneth Tan -- OptimaNumerics (Sat May 14 2005 - 07:57:22 PDT)
AMBER: RESP charge fitting for N-methylguanine cation Grzegorz Jezierski (Thu May 12 2005 - 09:50:17 PDT)
- Re: AMBER: RESP charge fitting for N-methylguanine cation Kara Di Giorgio (Thu May 12 2005 - 19:40:17 PDT)
- Re: AMBER: RESP charge fitting for N-methylguanine cation FyD (Fri May 13 2005 - 08:33:05 PDT)
AMBER: Tutorial #1 ptraj/sander problem Daniela Kohen (Thu May 12 2005 - 15:03:07 PDT)
- RE: AMBER: Tutorial #1 ptraj/sander problem Ross Walker (Thu May 12 2005 - 15:33:44 PDT)
AMBER: the restraint MD fail with amber8,but success with amber7 Shulin Zhuang (Thu May 12 2005 - 18:44:04 PDT)
- Re: AMBER: the restraint MD fail with amber8,but success with amber7 Carlos Simmerling (Fri May 13 2005 - 03:50:10 PDT)
  - Re: AMBER: the restraint MD fail with amber8,but success with amber7 Shulin Zhuang (Fri May 13 2005 - 04:19:20 PDT)
    - Re: AMBER: the restraint MD fail with amber8,but success with amber7 Shulin Zhuang (Fri May 13 2005 - 04:21:28 PDT)
AMBER: amber8 test error Cordova, Luis E. (Thu May 12 2005 - 20:26:00 PDT)
- Re: AMBER: amber8 test error David A. Case (Fri May 13 2005 - 10:11:27 PDT)
AMBER: creating residues - charge assign problems Hayden Eastwood (Fri May 13 2005 - 04:06:06 PDT)
- Re: AMBER: creating residues - charge assign problems FyD (Fri May 13 2005 - 08:25:48 PDT)
- Re: AMBER: creating residues - charge assign problems David A. Case (Fri May 13 2005 - 09:43:41 PDT)
AMBER: platinum atom in Xleap Chen Chengwen (Fri May 13 2005 - 19:11:12 PDT)
AMBER: How to create a parallel job for amber 8? 易虹 (Sat May 14 2005 - 04:20:15 PDT)
- Re: AMBER: How to create a parallel job for amber 8? Shulin Zhuang (Sat May 14 2005 - 06:45:54 PDT)
AMBER: Which source file determine the initial value of IX XX arrray in AMBER8? caoch.cherry.bio.titech.ac.jp (Sat May 14 2005 - 10:17:17 PDT)
- Re: AMBER: Which source file determine the initial value of IX XX arrray in AMBER8? Carlos Simmerling (Sat May 14 2005 - 10:52:56 PDT)
- RE: AMBER: Which source file determine the initial value of IX XX arrray in AMBER8? ross.rosswalker.co.uk (Sat May 14 2005 - 12:43:46 PDT)
  - AMBER: amber 8 REM possible test problem Sergio E. Wong (Tue May 17 2005 - 14:51:04 PDT)
AMBER: Calculating of radius of gyration in Carnal Hwankyu Lee (Sat May 14 2005 - 11:36:37 PDT)
Re: AMBER: Calculating of radius of gyration in Carnal Bill Ross (Sat May 14 2005 - 15:26:43 PDT)
AMBER: how to reduce box size and delete excess solvent hj zou (Sun May 15 2005 - 04:51:32 PDT)
AMBER: How to set constraint Li Su (Sun May 15 2005 - 11:58:51 PDT)
- Re: AMBER: How to set constraint David A. Case (Mon May 16 2005 - 08:42:27 PDT)
Re: AMBER: how to reduce box size and delete excess solvent Bill Ross (Sun May 15 2005 - 12:50:01 PDT)
- Re: Re: AMBER: how to reduce box size and delete excess solvent hj zou (Wed Jul 27 2005 - 06:36:40 PDT)
AMBER: strange mm_pbsa.pl bug Nelson Fonseca (Mon May 16 2005 - 08:39:21 PDT)
AMBER: How to set up dihedral constraints in amber Li Su (Mon May 16 2005 - 08:39:50 PDT)
AMBER: generating over 16 bps of DNA in nucgen Hwankyu Lee (Mon May 16 2005 - 08:33:04 PDT)
- Re: AMBER: generating over 16 bps of DNA in nucgen Garhan Attebury (Tue May 17 2005 - 08:27:13 PDT)
  - Re: AMBER: generating over 16 bps of DNA in nucgen aanzellotti.mail2.vcu.edu (Tue May 17 2005 - 08:57:45 PDT)
AMBER: output of force field info Stern, Julie (Mon May 16 2005 - 12:24:37 PDT)
- Re: AMBER: output of force field info David A. Case (Mon May 16 2005 - 17:16:55 PDT)
- Re: AMBER: output of force field info Thomas E. Cheatham, III (Mon May 16 2005 - 18:21:51 PDT)
  - AMBER: ATOM TYPE Ilyas Yildirim (Mon May 16 2005 - 19:10:48 PDT)
AMBER: nmode in mmpbsa Joseph Fernandez (Mon May 16 2005 - 16:36:28 PDT)
- AMBER: *** Proper torsion parameters missing *** Ilyas Yildirim (Mon May 16 2005 - 17:19:04 PDT)
  - AMBER: gaff: ca-ca-c -o torsion parameter Oliver Hucke (Tue May 17 2005 - 13:54:24 PDT)
    - Re: AMBER: gaff: ca-ca-c -o torsion parameter David A. Case (Tue May 17 2005 - 23:38:33 PDT)
- Re: AMBER: nmode in mmpbsa Holger Gohlke (Mon May 16 2005 - 23:44:17 PDT)
AMBER: MMPBSA calculations on Highly charged systems Vitor Manuel Sousa F?x (Tue May 17 2005 - 04:01:21 PDT)
- Re: AMBER: MMPBSA calculations on Highly charged systems Nelson Fonseca (Tue May 17 2005 - 05:36:16 PDT)
AMBER: Message in .out file Atilio Anzellotti (Tue May 17 2005 - 05:31:36 PDT)
- Re: AMBER: Message in .out file David A. Case (Tue May 17 2005 - 23:38:40 PDT)
AMBER: GAFF angle parameters Monica Civera (Tue May 17 2005 - 09:11:46 PDT)
- RE: AMBER: GAFF angle parameters Junmei Wang (Tue May 17 2005 - 15:08:47 PDT)
AMBER: compiling pmemd on dual xeon Tiziano Tuccinardi (Tue May 17 2005 - 10:28:31 PDT)
- Re: AMBER: compiling pmemd on dual xeon Robert Duke (Tue May 17 2005 - 10:49:48 PDT)
  - Re: AMBER: compiling pmemd on dual xeon Tiziano Tuccinardi (Tue May 17 2005 - 11:05:49 PDT)
AMBER: ERROR in readParm: ...failed to find ANGLES_INC_HYDROGEN Rajeev Ranjan Singh (Tue May 17 2005 - 13:15:33 PDT)
AMBER: RE: Tutorial#1 ptraj/sander problem Ross Walker (Tue May 17 2005 - 15:56:59 PDT)
AMBER: MD on surface Yanze Zhang (Tue May 17 2005 - 16:58:29 PDT)
AMBER: error with ptraj Xiaowei (David) Li (Tue May 17 2005 - 21:27:33 PDT)
- Re: AMBER: error with ptraj David A. Case (Tue May 17 2005 - 23:38:22 PDT)
AMBER: loading pdb cbala.igib.res.in (Tue May 17 2005 - 22:56:13 PDT)
- Re: AMBER: loading pdb David A. Case (Tue May 17 2005 - 23:38:27 PDT)
- Re: AMBER: loading pdb Rajeev Ranjan Singh (Wed May 18 2005 - 07:01:34 PDT)
- Re: AMBER: loading pdb Ilyas Yildirim (Wed May 18 2005 - 13:21:24 PDT)
AMBER: Using AMBER for Carbon nanotubes Zhang Yingyan (Wed May 18 2005 - 01:21:42 PDT)
- RE: AMBER: Using AMBER for Carbon nanotubes Ross Walker (Wed May 18 2005 - 10:12:29 PDT)
AMBER: error during MD run cbala.igib.res.in (Wed May 18 2005 - 11:39:25 PDT)
- Re: AMBER: error during MD run Thomas E. Cheatham, III (Wed May 18 2005 - 11:10:36 PDT)
- Re: AMBER: error during MD run Rajeev Ranjan Singh (Wed May 18 2005 - 11:16:12 PDT)
AMBER: frcmod info for Nickel Kara Di Giorgio (Wed May 18 2005 - 12:04:44 PDT)
AMBER: parameter for sulfur in thio-glucoside residue Vijay Manickam Achari (Wed May 18 2005 - 18:58:57 PDT)
- Re: AMBER: parameter for sulfur in thio-glucoside residue Ilyas Yildirim (Wed May 18 2005 - 19:11:34 PDT)
AMBER: Can we load prmtop and inpcrd files into xleap? Ilyas Yildirim (Wed May 18 2005 - 19:16:35 PDT)
- Re: AMBER: Can we load prmtop and inpcrd files into xleap? Kara Di Giorgio (Wed May 18 2005 - 19:45:43 PDT)
  - Re: AMBER: Can we load prmtop and inpcrd files into xleap? Ilyas Yildirim (Wed May 18 2005 - 21:00:07 PDT)
    - Re: AMBER: Can we load prmtop and inpcrd files into xleap? Kara Di Giorgio (Wed May 18 2005 - 21:10:36 PDT)
    - Re: AMBER: Can we load prmtop and inpcrd files into xleap? Ilyas Yildirim (Wed May 18 2005 - 21:47:49 PDT)
- Re: AMBER: Can we load prmtop and inpcrd files into xleap? Bill Ross (Wed May 18 2005 - 21:49:04 PDT)
AMBER: Amber 8 and LAM compilation problem Glen Otero (Wed May 18 2005 - 22:52:00 PDT)
- Re: AMBER: Amber 8 and LAM compilation problem Robert Duke (Thu May 19 2005 - 05:05:48 PDT)
AMBER: the out put I get... parameter for sulfur in thio-glucoside residue Vijay Manickam Achari (Wed May 18 2005 - 23:55:21 PDT)
- RE: AMBER: the out put I get... parameter for sulfur in thio-glucoside residue Ross Walker (Thu May 19 2005 - 00:16:41 PDT)
- Re: AMBER: the out put I get... parameter for sulfur in thio-glucoside residue Ilyas Yildirim (Thu May 19 2005 - 00:37:22 PDT)
- Re: AMBER: the out put I get... parameter for sulfur in thio-glucoside residue Cenk Andac (Thu May 19 2005 - 10:03:43 PDT)
  - AMBER: Re: antechamber not working .. for thio residue.. Vijay Manickam Achari (Fri May 20 2005 - 02:32:19 PDT)
    - Re: AMBER: Re: antechamber not working .. for thio residue.. Shulin Zhuang (Fri May 20 2005 - 03:22:39 PDT)
AMBER: GB - igb=1 versus dielc=? milion.c-box.cz (Thu May 19 2005 - 09:53:00 PDT)
- Re: AMBER: GB - igb=1 versus dielc=? David A. Case (Thu May 19 2005 - 09:09:47 PDT)
AMBER: write format of restart crd in sander/pmemd Peter Varnai (Thu May 19 2005 - 05:12:22 PDT)
AMBER: Using amber4 generated prep files in amber8? Simon Whitehead (Thu May 19 2005 - 05:51:00 PDT)
- Re: AMBER: Using amber4 generated prep files in amber8? David A. Case (Thu May 19 2005 - 08:31:54 PDT)
AMBER: read pdb back to xleap after solvation of chloroform chaiann ng (Thu May 19 2005 - 18:19:04 PDT)
- Re: AMBER: read pdb back to xleap after solvation of chloroform David A. Case (Thu May 19 2005 - 18:38:49 PDT)
  - Re: AMBER: read pdb back to xleap after solvation of chloroform chaiann ng (Thu May 19 2005 - 18:59:47 PDT)
- RE: AMBER: read pdb back to xleap after solvation of chloroform Ross Walker (Thu May 19 2005 - 18:41:31 PDT)
  - RE: AMBER: read pdb back to xleap after solvation of chloroform chaiann ng (Thu May 19 2005 - 19:05:27 PDT)
- RE: AMBER: read pdb back to xleap after solvation of chloroform Bill Ross (Thu May 19 2005 - 19:16:22 PDT)
  - RE: AMBER: read pdb back to xleap after solvation of chloroform chaiann ng (Thu May 19 2005 - 19:55:23 PDT)
- RE: AMBER: read pdb back to xleap after solvation of chloroform Bill Ross (Thu May 19 2005 - 20:56:58 PDT)
- Re: AMBER: read pdb back to xleap after solvation of chloroform Furse, Kristina Elisabet (Fri May 20 2005 - 14:20:55 PDT)
AMBER: MM_PBSA for NMR restrained structures Cenk Andac (Fri May 20 2005 - 01:36:10 PDT)
AMBER: leap problem: savepdb Hannes Barsch (Fri May 20 2005 - 02:30:29 PDT)
- Re: AMBER: leap problem: savepdb David A. Case (Fri May 20 2005 - 08:21:13 PDT)
AMBER: how to creat leaprc.gaff Vijay Manickam Achari (Fri May 20 2005 - 02:36:25 PDT)
- Re: AMBER: how to creat leaprc.gaff Ilyas Yildirim (Fri May 20 2005 - 02:48:14 PDT)
AMBER: Error in minimization Priti Hansia (Fri May 20 2005 - 03:58:36 PDT)
- Re: AMBER: Error in minimization Carlos Simmerling (Fri May 20 2005 - 05:57:37 PDT)
AMBER: Steve Seibold (Fri May 20 2005 - 10:45:24 PDT)
- Re: AMBER: luckyang.gmail.com (Fri May 20 2005 - 11:28:17 PDT)
- Re: AMBER: JunJun Liu (Fri May 20 2005 - 19:41:24 PDT)
AMBER: crashing xleap Kenley Barrett (Fri May 20 2005 - 11:48:13 PDT)
- Re: AMBER: crashing xleap Scott Brozell (Fri May 20 2005 - 13:03:40 PDT)
  - Re: AMBER: crashing xleap Kenley Barrett (Fri May 20 2005 - 13:57:00 PDT)
    - Re: AMBER: crashing xleap Ilyas Yildirim (Fri May 20 2005 - 14:47:09 PDT)
- Re: AMBER: crashing xleap Furse, Kristina Elisabet (Fri May 20 2005 - 15:28:05 PDT)
  - Re: AMBER: crashing xleap; bugfix.44 Scott Brozell (Mon May 23 2005 - 10:22:51 PDT)
AMBER: 1-4 scaling factors Stern, Julie (Fri May 20 2005 - 12:13:22 PDT)
- Re: AMBER: 1-4 scaling factors Thomas E. Cheatham, III (Fri May 20 2005 - 12:43:34 PDT)
Re: AMBER: crashing xleap Bill Ross (Fri May 20 2005 - 12:55:15 PDT)
AMBER: Unexpected stop of Sander run Grzegorz Jezierski (Sun May 22 2005 - 12:44:55 PDT)
- Re: AMBER: Unexpected stop of Sander run Grzegorz Jezierski (Mon May 23 2005 - 00:14:54 PDT)
- Re: AMBER: Unexpected stop of Sander run Carlos Simmerling (Mon May 23 2005 - 04:15:34 PDT)
  - Re: AMBER: Unexpected stop of Sander run Grzegorz Jezierski (Mon May 23 2005 - 06:43:51 PDT)
    - Re: AMBER: Unexpected stop of Sander run Carlos Simmerling (Mon May 23 2005 - 06:57:00 PDT)
    - Re: AMBER: Unexpected stop of Sander run Grzegorz Jezierski (Mon May 23 2005 - 07:38:58 PDT)
- Re: AMBER: Unexpected stop of Sander run David A. Case (Mon May 23 2005 - 08:00:46 PDT)
AMBER: Copyright for PBSA Cenk Andac (Sat May 21 2005 - 01:32:00 PDT)
- Re: AMBER: Copyright for PBSA David A. Case (Sat May 21 2005 - 20:37:45 PDT)
AMBER: Citing the PBSA module of AMBER8 Cenk Andac (Fri May 20 2005 - 14:27:03 PDT)
AMBER: rotating and repositioning molecules in xleap Hwankyu Lee (Fri May 20 2005 - 23:09:45 PDT)
- Re: AMBER: rotating and repositioning molecules in xleap Angelo Pugliese (Sun May 22 2005 - 02:37:44 PDT)
  - Re: AMBER: rotating and repositioning molecules in xleap Hwankyu Lee (Sun May 22 2005 - 06:03:40 PDT)
- Re: AMBER: rotating and repositioning molecules in xleap Bill Ross (Sun May 22 2005 - 08:36:16 PDT)
AMBER: modeller Zhang Bing (Fri May 20 2005 - 21:53:13 PDT)
Re: AMBER: Unexpected stop of Sander run Bill Ross (Sun May 22 2005 - 13:18:16 PDT)
- Re: AMBER: Unexpected stop of Sander run Carlos Simmerling (Sun May 22 2005 - 13:22:11 PDT)
AMBER: Error in sander: stack trace terminated abnormally. Hwankyu Lee (Sun May 22 2005 - 14:05:31 PDT)
- RE: AMBER: Error in sander: stack trace terminated abnormally. Ross Walker (Sun May 22 2005 - 14:53:36 PDT)
AMBER: antechamber not working .. for thio residue.. Vijay Manickam Achari (Sun May 22 2005 - 19:15:20 PDT)
- Re: AMBER: antechamber not working .. for thio residue.. Shulin Zhuang (Sun May 22 2005 - 19:31:27 PDT)
AMBER: Setting Amber force field parameters Chen Chengwen (Mon May 23 2005 - 00:55:38 PDT)
AMBER: using antechamber ... to get prepin file Vijay Manickam Achari (Mon May 23 2005 - 01:59:16 PDT)
- RE: AMBER: using antechamber ... to get prepin file Vineet Pande (Mon May 23 2005 - 05:02:26 PDT)
AMBER: Connecting two molecules Hwankyu Lee (Mon May 23 2005 - 08:13:00 PDT)
- Re: AMBER: Connecting two molecules David A. Case (Mon May 23 2005 - 08:23:51 PDT)
  - Re: AMBER: Connecting two molecules Hwankyu Lee (Mon May 23 2005 - 09:51:20 PDT)
    - AMBER: hbond detailed analysis over time? pascal.baillod.epfl.ch (Mon May 23 2005 - 11:04:10 PDT)
AMBER: how to generate frcmod file for using prepin file.. Vijay Manickam Achari (Mon May 23 2005 - 19:52:18 PDT)
- RE: AMBER: how to generate frcmod file for using prepin file.. chaiann ng (Mon May 23 2005 - 20:03:55 PDT)
AMBER: my frcmod file created using parmchk Vijay Manickam Achari (Mon May 23 2005 - 20:44:21 PDT)
- Re: AMBER: my frcmod file created using parmchk Ilyas Yildirim (Mon May 23 2005 - 21:03:42 PDT)
AMBER: my prepin file in lowe-case Vijay Manickam Achari (Tue May 24 2005 - 00:51:55 PDT)
AMBER: Which forcefield? Simon Whitehead (Tue May 24 2005 - 01:13:01 PDT)
- Re: AMBER: Which forcefield? David A. Case (Tue May 24 2005 - 22:32:09 PDT)
AMBER: conformational sampling of a peptide Hannes Barsch (Tue May 24 2005 - 01:58:04 PDT)
- Re: AMBER: conformational sampling of a peptide Joseph Nachman (Tue May 24 2005 - 08:26:52 PDT)
AMBER: amber code Juan Fernandez Carmona (Tue May 24 2005 - 03:08:00 PDT)
- Re: AMBER: amber code Andreas Svrcek-Seiler (Tue May 24 2005 - 07:18:11 PDT)
Re: AMBER: conformational sampling of a peptide Carlos Simmerling (Tue May 24 2005 - 06:11:53 PDT)
AMBER: Fw: Installing PMEMD on IBM machine (CPU power4) running SUSE_9.1 Robert Duke (Tue May 24 2005 - 07:42:15 PDT)
AMBER: Amber 8 : installation problems : undefined reference to `mpi_allreduce_' René Ranzinger (Tue May 24 2005 - 08:04:42 PDT)
- RE: AMBER: Amber 8 : installation problems : undefined reference to `mpi_allreduce_' Ross Walker (Tue May 24 2005 - 08:43:37 PDT)
AMBER: Sander Restart Problem Garhan Attebury (Tue May 24 2005 - 08:07:49 PDT)
AMBER: How to fix certain bond angles Li Su (Tue May 24 2005 - 08:27:14 PDT)
- Re: AMBER: How to fix certain bond angles Guanglei Cui (Tue May 24 2005 - 08:40:00 PDT)
AMBER: Error: vlimit exceeded for step Hwankyu Lee (Tue May 24 2005 - 10:20:10 PDT)
- Re: AMBER: Error: vlimit exceeded for step Carlos Simmerling (Tue May 24 2005 - 10:51:14 PDT)
  - Re: AMBER: Error: vlimit exceeded for step Hwankyu Lee (Tue May 24 2005 - 11:07:41 PDT)
    - Re: AMBER: Error: vlimit exceeded for step Thomas E. Cheatham, III (Tue May 24 2005 - 11:12:58 PDT)
    - Re: AMBER: Error: vlimit exceeded for step Hwankyu Lee (Tue May 24 2005 - 11:34:34 PDT)
    - Re: AMBER: Error: vlimit exceeded for step David Mobley (Tue May 24 2005 - 12:27:23 PDT)
    - AMBER: Error: vlimit exceeded for step Hwankyu Lee (Mon Jun 06 2005 - 06:55:57 PDT)
    - RE: AMBER: Error: vlimit exceeded for step Ross Walker (Mon Jun 06 2005 - 10:19:04 PDT)
    - Re: AMBER: Error: vlimit exceeded for step Hwankyu Lee (Mon Jun 06 2005 - 15:47:29 PDT)
    - RE: AMBER: Error: vlimit exceeded for step Ross Walker (Mon Jun 06 2005 - 16:24:21 PDT)
    - Re: AMBER: Error: vlimit exceeded for step Hwankyu Lee (Mon Jun 06 2005 - 16:48:56 PDT)
    - RE: AMBER: Error: vlimit exceeded for step Ross Walker (Mon Jun 06 2005 - 20:49:05 PDT)
    - Re: AMBER: Error: vlimit exceeded for step Hwankyu Lee (Mon Jun 06 2005 - 16:26:16 PDT)
    - Re: AMBER: Error: vlimit exceeded for step Bill Ross (Mon Jun 06 2005 - 17:03:38 PDT)
Solute-solvent boundary in pbsa ..Re: AMBER: Copyright for PBSA Cenk Andac (Tue May 24 2005 - 11:48:26 PDT)
- Re: AMBER: Solute-solvent boundary in pbsa Ray Luo (Tue May 24 2005 - 01:48:10 PDT)
  - Re: AMBER: Solute-solvent boundary in pbsa Cenk Andac (Wed May 25 2005 - 09:21:52 PDT)
    - Re: AMBER: Solute-solvent boundary in pbsa Ray Luo (Tue May 24 2005 - 22:54:50 PDT)
  - Re:Re: AMBER: Solute-solvent boundary in pbsa Cenk Andac (Thu May 26 2005 - 13:58:55 PDT)
    - Re: AMBER: Solute-solvent boundary in pbsa Ray Luo (Wed May 25 2005 - 18:40:39 PDT)
AMBER: Is Amber able to constrain(not restrain) certain angles at certain values? Li Su (Tue May 24 2005 - 12:14:09 PDT)
- Re: AMBER: Is Amber able to constrain(not restrain) certain angles at certain values? Petr Kulhanek (Wed May 25 2005 - 04:56:34 PDT)
  - Re: AMBER: Is Amber able to constrain(not restrain) certain angles at certain values? Guanglei Cui (Wed May 25 2005 - 06:55:23 PDT)
    - Re: AMBER: Is Amber able to constrain(not restrain) certain angles at certain values? Petr Kulhanek (Thu May 26 2005 - 03:44:37 PDT)
AMBER: charges difference of atom in xleap and prmtop chaiann ng (Tue May 24 2005 - 21:02:33 PDT)
- Re: AMBER: charges difference of atom in xleap and prmtop David A. Case (Tue May 24 2005 - 22:27:51 PDT)
AMBER: PARMSCAN program Philippe ARNAUD (Wed May 25 2005 - 00:28:31 PDT)
AMBER: average structure after MD kuljeets.igib.res.in (Wed May 25 2005 - 02:14:19 PDT)
- Re: AMBER: average structure after MD kuljeets.igib.res.in (Wed May 25 2005 - 22:42:32 PDT)
AMBER: quadrupole in resp riccardo nifosi (Wed May 25 2005 - 03:44:20 PDT)
- Re: AMBER: quadrupole in resp David A. Case (Tue Jun 07 2005 - 10:30:12 PDT)
AMBER: error in chirality.c? Kenley Barrett (Wed May 25 2005 - 07:27:07 PDT)
- Re: AMBER: error in chirality.c? David A. Case (Wed May 25 2005 - 08:21:48 PDT)
Re#2:Re: AMBER: Solute-solvent boundary in pbsa Cenk Andac (Wed May 25 2005 - 13:03:47 PDT)
- Re: Re#2:Re: AMBER: Solute-solvent boundary in pbsa Ray Luo (Tue May 24 2005 - 22:56:08 PDT)
AMBER: dissolving micelle structure in water.. amber7 Vijay Manickam Achari (Wed May 25 2005 - 20:59:22 PDT)
- Re: AMBER: dissolving micelle structure in water.. amber7 David A. Case (Thu May 26 2005 - 09:30:17 PDT)
- Re: AMBER: dissolving micelle structure in water.. amber7 Bill Ross (Thu May 26 2005 - 09:50:23 PDT)
- Re: AMBER: dissolving micelle structure in water.. amber7 Vijay Manickam Achari (Thu May 26 2005 - 18:19:57 PDT)
AMBER: distance restraints between two centers of mass JAVIER PEREZ (Thu May 26 2005 - 01:37:30 PDT)
- Re: AMBER: distance restraints between two centers of mass Fabien Cailliez (Thu May 26 2005 - 02:01:08 PDT)
AMBER: Is the MD simulation normal Shulin Zhuang (Thu May 26 2005 - 08:30:48 PDT)
- RE: AMBER: Is the MD simulation normal Yong Duan (Thu May 26 2005 - 10:05:14 PDT)
- Re: AMBER: Is the MD simulation normal Thomas E. Cheatham, III (Thu May 26 2005 - 10:41:03 PDT)
  - Re: AMBER: Is the MD simulation normal Shulin Zhuang (Thu May 26 2005 - 21:23:37 PDT)
    - RE: AMBER: Is the MD simulation normal Yong Duan (Thu May 26 2005 - 23:17:00 PDT)
    - Re: AMBER: Is the MD simulation normal Shulin Zhuang (Fri May 27 2005 - 00:38:05 PDT)
    - RE: AMBER: Is the MD simulation normal Yong Duan (Fri May 27 2005 - 09:31:27 PDT)
- Re: AMBER: Is the MD simulation normal Bill Ross (Fri May 27 2005 - 11:14:30 PDT)
  - Re: AMBER: Is the MD simulation normal Shulin Zhuang (Sat May 28 2005 - 06:02:05 PDT)
- Re: AMBER: Is the MD simulation normal Bill Ross (Sat May 28 2005 - 10:00:42 PDT)
  - Re: AMBER: Is the MD simulation normal Shulin Zhuang (Sun May 29 2005 - 07:53:35 PDT)
    - RE: AMBER: Is the MD simulation normal Yong Duan (Sun May 29 2005 - 09:46:44 PDT)
- Re: AMBER: Is the MD simulation normal Bill Ross (Sun May 29 2005 - 08:33:13 PDT)
- RE: AMBER: Is the MD simulation normal Bill Ross (Sun May 29 2005 - 10:04:01 PDT)
  - Re: AMBER: Is the MD simulation normal Shulin Zhuang (Mon May 30 2005 - 07:39:50 PDT)
- Re: AMBER: Is the MD simulation normal Bill Ross (Mon May 30 2005 - 09:49:32 PDT)
  - Re: AMBER: Is the MD simulation normal JunJun Liu (Tue May 31 2005 - 19:01:07 PDT)
- Re: AMBER: Is the MD simulation normal Bill Ross (Tue May 31 2005 - 20:41:42 PDT)
- Re: AMBER: Is the MD simulation normal Shulin Zhuang (Wed Jun 29 2005 - 03:11:53 PDT)
  - Re: AMBER: Is the MD simulation normal Shulin Zhuang (Wed Jun 29 2005 - 08:03:20 PDT)
  - RE: AMBER: Is the MD simulation normal Ross Walker (Wed Jun 29 2005 - 09:09:13 PDT)
    - Re: AMBER: Is the MD simulation normal Shulin Zhuang (Thu Jun 30 2005 - 07:52:03 PDT)
    - Re: AMBER: Is the MD simulation normal Shulin Zhuang (Thu Jun 30 2005 - 08:00:11 PDT)
AMBER: setting up Parallel processing mathew k varghese (Thu May 26 2005 - 08:39:00 PDT)
- Re: AMBER: setting up Parallel processing Robert Duke (Thu May 26 2005 - 09:15:30 PDT)
- RE: AMBER: setting up Parallel processing 'Ross Walker' (Thu May 26 2005 - 11:14:18 PDT)
AMBER: hbond analysis in ptaj/carnal Jana Precechtelova (Thu May 26 2005 - 09:25:20 PDT)
- Re: AMBER: hbond analysis in ptaj/carnal Thomas E. Cheatham, III (Thu May 26 2005 - 10:05:00 PDT)
Re: AMBER: hbond analysis in ptaj/carnal Bill Ross (Thu May 26 2005 - 09:44:13 PDT)
AMBER: why is snaupe.f is empty? Cordova, Luis E. (Thu May 26 2005 - 10:06:24 PDT)
- RE: AMBER: why is snaupe.f is empty? 'Ross Walker' (Thu May 26 2005 - 11:14:34 PDT)
AMBER: ptraj - hbond detailed analysis over time? pascal.baillod.epfl.ch (Thu May 26 2005 - 10:38:38 PDT)
AMBER: Mol2 to prepin file conversion Andrew Box (Thu May 26 2005 - 17:08:22 PDT)
- Re: AMBER: Mol2 to prepin file conversion David A. Case (Thu May 26 2005 - 17:44:36 PDT)
AMBER: question about loadiing pdb file of a molecule complex gtg549i.mail.gatech.edu (Fri May 27 2005 - 14:39:28 PDT)
- Re: AMBER: question about loadiing pdb file of a molecule complex Chutintorn Punwong (Fri May 27 2005 - 15:07:52 PDT)
- Re: AMBER: question about loadiing pdb file of a molecule complex David A. Case (Sat May 28 2005 - 22:29:53 PDT)
  - AMBER: Reference (?) for normal-mode analysis in nmode Cenk Andac (Mon May 30 2005 - 02:18:59 PDT)
    - Re: AMBER: Reference (?) for normal-mode analysis in nmode David A. Case (Tue May 31 2005 - 08:30:10 PDT)
  - Re: AMBER: question about loadiing pdb file of a molecule complex gtg549i.mail.gatech.edu (Mon May 30 2005 - 08:56:09 PDT)
    - Re: AMBER: question about loadiing pdb file of a molecule complex David A. Case (Tue May 31 2005 - 11:00:59 PDT)
    - Re: AMBER: question about loadiing pdb file of a molecule complex gtg549i.mail.gatech.edu (Tue May 31 2005 - 12:12:39 PDT)
AMBER: Workshop Tutorials Downtime this weekend. Ross Walker (Fri May 27 2005 - 14:49:05 PDT)
AMBER: Antechamber RESP failed for large organic molecule junwang (Sun May 29 2005 - 12:57:59 PDT)
- Re: AMBER: Antechamber RESP failed for large organic molecule David A. Case (Mon May 30 2005 - 09:09:27 PDT)
- RE: AMBER: Antechamber RESP failed for large organic molecule Junmei Wang (Tue May 31 2005 - 07:37:35 PDT)
  - Re: RE: AMBER: Antechamber RESP failed for large organic molecule junwang (Tue May 31 2005 - 09:58:33 PDT)
  - RE: RE: AMBER: Antechamber RESP failed for large organic molecule Junmei Wang (Wed Jun 01 2005 - 09:54:42 PDT)
    - Re: RE: RE: AMBER: Antechamber RESP failed for large organic molecule junwang (Wed Jun 01 2005 - 14:18:05 PDT)
AMBER: question about initial conditions for amber Ed Pate (Sun May 29 2005 - 19:42:21 PDT)
- Re: AMBER: question about initial conditions for amber Stefano Federico Pieraccini (Mon May 30 2005 - 04:44:54 PDT)
- Re: AMBER: question about initial conditions for amber Stefano Federico Massimiliano Pieraccini (Stefano.Pieraccini) (Mon May 30 2005 - 04:40:59 PDT)
AMBER: density profiles in ptraj or carnal Hwankyu Lee (Sun May 29 2005 - 20:27:37 PDT)
AMBER: pairwise energy decomposition using MM-PBSA Xin Hu (Sun May 29 2005 - 20:38:30 PDT)
AMBER: Force field modification problem yuann (Mon May 30 2005 - 04:16:27 PDT)
- Re: AMBER: Force field modification problem David A. Case (Mon May 30 2005 - 09:21:00 PDT)
  - Re[2]: AMBER: Force field modification problem sychen (Mon May 30 2005 - 17:05:45 PDT)
    - Re: AMBER: Force field modification problem David A. Case (Mon May 30 2005 - 22:17:06 PDT)
AMBER: Bond angle restraints setting files Li Su (Mon May 30 2005 - 09:05:15 PDT)
Re: AMBER: density profiles in ptraj or carnal Bill Ross (Mon May 30 2005 - 10:00:08 PDT)
- Re: AMBER: density profiles in ptraj or carnal Hwankyu Lee (Mon May 30 2005 - 15:58:54 PDT)
  - Re: AMBER: density profiles in ptraj or carnal Hwankyu Lee (Mon May 30 2005 - 21:13:26 PDT)
- Re: AMBER: density profiles in ptraj or carnal Bill Ross (Tue May 31 2005 - 09:13:28 PDT)
AMBER: density problem cristian obiol (Tue May 31 2005 - 02:17:46 PDT)
- RE: AMBER: density problem Ross Walker (Tue May 31 2005 - 08:33:39 PDT)
  - Re: AMBER: density problem Shulin Zhuang (Tue May 31 2005 - 18:49:47 PDT)
    - RE: AMBER: density problem Ross Walker (Wed Jun 01 2005 - 09:21:33 PDT)
- RE:AMBER: density problem cristian obiol (Thu Jun 02 2005 - 01:14:21 PDT)
- RE:AMBER: density problem cristian obiol (Wed Jun 08 2005 - 01:56:23 PDT)
AMBER: stack terminated abnormally drugdesign (Tue May 31 2005 - 03:20:33 PDT)
- RE: AMBER: stack terminated abnormally Ross Walker (Tue May 31 2005 - 08:35:15 PDT)
AMBER: if setting ntf=4, will it cause someproblem? Li Su (Tue May 31 2005 - 07:55:03 PDT)
- Re: AMBER: if setting ntf=4, will it cause someproblem? Carlos Simmerling (Tue May 31 2005 - 08:12:30 PDT)
  - Re: AMBER: if setting ntf=4, will it cause someproblem? Li Su (Tue May 31 2005 - 14:07:25 PDT)
AMBER: Error on restrained MD equilibration (AMBER 7) L Jin (Tue May 31 2005 - 08:23:51 PDT)
- Re: AMBER: Error on restrained MD equilibration (AMBER 7) David A. Case (Tue May 31 2005 - 08:45:01 PDT)
- Re: AMBER: Error on restrained MD equilibration (AMBER 7) Viktor Hornak (Tue May 31 2005 - 08:52:48 PDT)
- Re: AMBER: Error on restrained MD equilibration (AMBER 7) L Jin (Tue May 31 2005 - 09:21:55 PDT)
  - RE: AMBER: Error on restrained MD equilibration (AMBER 7) Ross Walker (Tue May 31 2005 - 09:45:19 PDT)
    - RE: AMBER: Error on restrained MD equilibration (AMBER 7) L Jin (Wed Jun 01 2005 - 03:20:40 PDT)
    - Re: AMBER: Error on restrained MD equilibration (AMBER 7) Petr Kulhanek (Wed Jun 01 2005 - 04:03:21 PDT)
    - Re: AMBER: Error on restrained MD equilibration (AMBER 7) L Jin (Wed Jun 01 2005 - 08:05:12 PDT)
  - AMBER: runtime error in sander? Dave S Walker (Tue May 31 2005 - 10:07:13 PDT)
    - RE: AMBER: runtime error in sander? Ross Walker (Tue May 31 2005 - 10:34:51 PDT)
    - RE: AMBER: runtime error in sander? Dave S Walker (Mon Jun 20 2005 - 11:02:16 PDT)
  - Re: AMBER: Error on restrained MD equilibration (AMBER 7) Guanglei Cui (Tue May 31 2005 - 12:02:46 PDT)
    - Re: AMBER: Error on restrained MD equilibration (AMBER 7) Shulin Zhuang (Tue May 31 2005 - 18:36:32 PDT)
    - Re: AMBER: Error on restrained MD equilibration (AMBER 7) L Jin (Wed Jun 01 2005 - 03:24:12 PDT)
    - Re: AMBER: Error on restrained MD equilibration (AMBER 7) Guanglei Cui (Wed Jun 01 2005 - 07:18:37 PDT)
AMBER: DNA base-flipping: TI vs PMF Lauren O'Neil (Tue May 31 2005 - 08:40:45 PDT)
- Re: AMBER: DNA base-flipping: TI vs PMF Peter Varnai (Thu Jun 02 2005 - 10:21:56 PDT)
AMBER: Failure of Periodic Boundary Conditions using LEAP in AMBER8 with "OldPrmtopFormat on" Grzegorz Jezierski (Tue May 31 2005 - 09:04:20 PDT)
- RE: AMBER: Failure of Periodic Boundary Conditions using LEAP in AMBER8 with "OldPrmtopFormat on" Ross Walker (Tue May 31 2005 - 09:09:20 PDT)
- Re: AMBER: Failure of Periodic Boundary Conditions using LEAP in AMBER8 with "OldPrmtopFormat on" Marcin Krol (Tue May 31 2005 - 09:17:30 PDT)
AMBER: MM-PBSA calculation masi.nmr.mpibpc.mpg.de (Tue May 31 2005 - 09:37:40 PDT)
- AMBER: Loading pdb-residue (re)numbering in leap gtg549i.mail.gatech.edu (Tue May 31 2005 - 10:48:13 PDT)
- Re: AMBER: MM-PBSA calculation Scott Pendley (Wed Jun 01 2005 - 16:44:05 PDT)
AMBER: STOP 0 masi.nmr.mpibpc.mpg.de (Tue May 31 2005 - 09:40:25 PDT)
- RE: AMBER: STOP 0 Ross Walker (Tue May 31 2005 - 09:47:20 PDT)
AMBER:Sander errors: Unit 6 Error on OPEN: mdout Douali, Latifa (Tue May 31 2005 - 10:34:41 PDT)
- RE: AMBER:Sander errors: Unit 6 Error on OPEN: mdout Ross Walker (Tue May 31 2005 - 10:45:53 PDT)
- RE: AMBER:Sander errors: Unit 6 Error on OPEN: mdout Bill Ross (Tue May 31 2005 - 11:42:50 PDT)
Re: AMBER: STOP 0 Bill Ross (Tue May 31 2005 - 10:43:32 PDT)
AMBER: meaningful tax for sander question Cordova, Luis E. (Tue May 31 2005 - 12:19:30 PDT)
- RE: AMBER: meaningful tax for sander question Ross Walker (Tue May 31 2005 - 12:55:14 PDT)
- Re: AMBER: meaningful tax for sander question David A. Case (Tue May 31 2005 - 12:59:20 PDT)
- RE: AMBER: meaningful tax for sander question Cordova, Luis E. (Tue May 31 2005 - 13:03:59 PDT)
- RE: AMBER: meaningful tax for sander question Ross Walker (Tue May 31 2005 - 13:12:10 PDT)
AMBER: double counting of potentials Stern, Julie (Tue May 31 2005 - 16:04:43 PDT)
- RE: AMBER: double counting of potentials Ross Walker (Tue May 31 2005 - 16:21:43 PDT)
AMBER: Working with a nickel-organometallic compound Kara Di Giorgio (Tue May 31 2005 - 16:36:30 PDT)
AMBER: External Field in AMBER? junwang (Tue May 31 2005 - 19:19:38 PDT)
AMBER: problem in minimization Ananda Rama Krishnan Selvaraj (Wed Jun 01 2005 - 01:48:46 PDT)
- Re: AMBER: problem in minimization Bill Ross (Tue Feb 08 2005 - 12:16:18 PST)
  - Re: AMBER: problem in minimization Carlos Simmerling (Tue Feb 08 2005 - 13:47:30 PST)
    - Re: AMBER: problem in minimization David A. Case (Tue Feb 08 2005 - 14:23:51 PST)
- Re: AMBER: problem in minimization Bill Ross (Tue Feb 08 2005 - 14:16:47 PST)
- RE: AMBER: problem in minimization Ross Walker (Wed Jun 01 2005 - 09:56:46 PDT)
  - Re: RE: AMBER: problem in minimization Ananda Rama Krishnan Selvaraj (Thu Jun 02 2005 - 00:39:36 PDT)
AMBER: Saturated DNA bases L.C. Heady (Wed Jun 01 2005 - 01:55:54 PDT)
AMBER: eigenvalues in vector of ptraj Hwankyu Lee (Wed Jun 01 2005 - 05:53:51 PDT)
AMBER: stripwater Lukasz Bielecki (Wed Jun 01 2005 - 07:16:05 PDT)
AMBER: Build of AMBER for YDL ? Gert Kiss (Wed Jun 01 2005 - 16:15:57 PDT)
- RE: AMBER: Build of AMBER for YDL ? Ross Walker (Wed Jun 01 2005 - 16:29:49 PDT)
AMBER: gaff.dat typo Brent Krueger (Wed Jun 01 2005 - 18:35:58 PDT)
- Re: AMBER: gaff.dat typo David A. Case (Thu Jun 02 2005 - 08:01:58 PDT)
AMBER: amber question about leap du yongchun (Wed Jun 01 2005 - 22:12:12 PDT)
- Re: AMBER: amber question about leap David A. Case (Thu Jun 02 2005 - 08:05:12 PDT)
AMBER: amber8 installation problems Zhang Bing (Wed Jun 01 2005 - 23:44:47 PDT)
AMBER: amber8 installation problems Zhang Bing (Wed Jun 01 2005 - 23:55:48 PDT)
- Re: AMBER: amber8 installation problems David A. Case (Thu Jun 02 2005 - 08:07:19 PDT)
AMBER: question whem using leap du yongchun (Thu Jun 02 2005 - 00:25:16 PDT)
- Re: AMBER: question whem using leap Carlos Simmerling (Thu Jun 02 2005 - 04:45:53 PDT)
AMBER: Argon Box Biswaroop Mukherjee (Thu Jun 02 2005 - 01:44:46 PDT)
AMBER: center-of-mass distance restraints JAVIER PEREZ (Thu Jun 02 2005 - 04:14:15 PDT)
AMBER: Simon Whitehead (Thu Jun 02 2005 - 05:44:03 PDT)
- RE: AMBER: Ross Walker (Fri Jun 03 2005 - 09:51:48 PDT)
AMBER: Protein ions? Anthony Cruz (Thu Jun 02 2005 - 07:12:56 PDT)
- Re: AMBER: Protein ions? Stefano Federico Massimiliano Pieraccini (Stefano.Pieraccini) (Thu Jun 02 2005 - 07:57:02 PDT)
  - Re: AMBER: Protein ions? Anthony Cruz (Thu Jun 02 2005 - 09:45:34 PDT)
- Re: AMBER: Protein ions? David A. Case (Thu Jun 02 2005 - 08:25:07 PDT)
AMBER: How does Amber8 implemnet ntf=4? Li Su (Thu Jun 02 2005 - 08:32:30 PDT)
- Re: AMBER: How does Amber8 implemnet ntf=4? David A. Case (Thu Jun 02 2005 - 08:52:10 PDT)
- Re: AMBER: How does Amber8 implemnet ntf=4? Carlos Simmerling (Thu Jun 02 2005 - 08:53:36 PDT)
AMBER: checkoverlap Gustavo Pierdominici Sottile (Thu Jun 02 2005 - 10:45:19 PDT)
AMBER: pressure output Germán Sciaini (Thu Jun 02 2005 - 15:27:13 PDT)
- Re: AMBER: pressure output David A. Case (Fri Jun 03 2005 - 08:05:59 PDT)
AMBER: advice needed for minimization and dynamic protocol chaiann ng (Thu Jun 02 2005 - 18:33:44 PDT)
AMBER: New problem of parallel sander Zhang Bing (Thu Jun 02 2005 - 19:46:13 PDT)
- Re: AMBER: New problem of parallel sander David A. Case (Fri Jun 03 2005 - 08:00:30 PDT)
- RE: AMBER: New problem of parallel sander Ross Walker (Fri Jun 03 2005 - 09:53:55 PDT)
AMBER: TI in Amber8 建平胡 (Fri Jun 03 2005 - 02:49:02 PDT)
- Re: AMBER: TI in Amber8 David A. Case (Fri Jun 03 2005 - 08:04:45 PDT)
AMBER: Nmode with residues excluded Martin Sippel (Fri Jun 03 2005 - 09:56:42 PDT)
AMBER: Nmode calculations Martin Sippel (Fri Jun 03 2005 - 10:17:48 PDT)
AMBER: radius parameter for Mg2+ in mm_pbsa calculation Ye Mei (Sat Jun 04 2005 - 07:37:04 PDT)
- Re: AMBER: radius parameter for Mg2+ in mm_pbsa calculation Guanglei Cui (Sat Jun 04 2005 - 08:17:11 PDT)
  - Re: AMBER: radius parameter for Mg2+ in mm_pbsa calculation Thomas Steinbrecher (Mon Jun 06 2005 - 00:23:16 PDT)
AMBER: SHAKE in md with partial solvation Ye Mei (Sun Jun 05 2005 - 00:30:00 PDT)
- Re: AMBER: SHAKE in md with partial solvation Ye Mei (Sun Jun 05 2005 - 04:19:45 PDT)
- Re: AMBER: SHAKE in md with partial solvation Germán Sciaini (Mon Jun 06 2005 - 03:34:09 PDT)
- RE: AMBER: SHAKE in md with partial solvation Ross Walker (Mon Jun 06 2005 - 10:12:20 PDT)
  - Re: RE: AMBER: SHAKE in md with partial solvation Ye Mei (Tue Jun 07 2005 - 06:46:49 PDT)
AMBER: fail of minimization in sander wendy (Sun Jun 05 2005 - 20:01:25 PDT)
- Re: AMBER: fail of minimization in sander wendy (Mon Jun 06 2005 - 03:06:01 PDT)
  - Re: AMBER: fail of minimization in sander Carlos Simmerling (Mon Jun 06 2005 - 04:24:25 PDT)
- Re: AMBER: fail of minimization in sander Bill Ross (Mon Jun 06 2005 - 07:34:39 PDT)
  - Re: AMBER: fail of minimization in sander wendy (Mon Jun 06 2005 - 09:13:10 PDT)
    - RE: AMBER: fail of minimization in sander Ross Walker (Mon Jun 06 2005 - 10:25:26 PDT)
    - Re: AMBER: fail of minimization in sander wendy (Wed Jun 15 2005 - 00:54:59 PDT)
    - Re: AMBER: fail of minimization in sander Carlos Simmerling (Wed Jun 15 2005 - 04:24:04 PDT)
- Re: AMBER: fail of minimization in sander wendy (Mon Jun 06 2005 - 08:57:08 PDT)
  - Re: AMBER: fail of minimization in sander Carlos Simmerling (Mon Jun 06 2005 - 09:12:38 PDT)
- Re: AMBER: fail of minimization in sander Bill Ross (Mon Jun 06 2005 - 10:58:54 PDT)
  - Re: AMBER: fail of minimization in sander Andy Purkiss (Tue Jun 07 2005 - 05:17:24 PDT)
- Re: AMBER: fail of minimization in sander Stefano Federico Massimiliano Pieraccini (Stefano.Pieraccini) (Wed Jun 15 2005 - 04:05:25 PDT)
- Re: AMBER: fail of minimization in sander wendy (Thu Jun 16 2005 - 01:19:15 PDT)
  - Re: AMBER: fail of minimization in sander Carlos Simmerling (Thu Jun 16 2005 - 04:06:42 PDT)
  - Re: AMBER: fail of minimization in sander David A. Case (Thu Jun 16 2005 - 07:44:21 PDT)
- Re: AMBER: fail of minimization in sander wendy (Thu Jun 16 2005 - 19:43:11 PDT)
Re: AMBER: fail of minimization in sander Bill Ross (Sun Jun 05 2005 - 20:50:48 PDT)
- Re: AMBER: fail of minimization in sander wendy (Sun Jun 05 2005 - 21:59:15 PDT)
AMBER: nmode with ibelly Martin Sippel (Mon Jun 06 2005 - 02:38:42 PDT)
- Re: AMBER: nmode with ibelly David A. Case (Mon Jun 06 2005 - 13:09:08 PDT)
- Re: AMBER: nmode with ibelly Martin Sippel (Tue Jun 07 2005 - 03:11:44 PDT)
  - Re: AMBER: nmode with ibelly David A. Case (Tue Jun 07 2005 - 07:41:41 PDT)
- Re: AMBER: nmode with ibelly Martin Sippel (Wed Jun 08 2005 - 10:48:04 PDT)
  - Re: AMBER: nmode with ibelly David A. Case (Wed Jun 08 2005 - 21:30:01 PDT)
AMBER: Solvate question? Anthony Cruz (Mon Jun 06 2005 - 03:30:44 PDT)
- Re: AMBER: Solvate question? Carlos Simmerling (Mon Jun 06 2005 - 04:26:53 PDT)
  - Re: AMBER: Solvate question? Anthony Cruz (Mon Jun 06 2005 - 08:59:06 PDT)
    - Re: AMBER: Solvate question? Carlos Simmerling (Mon Jun 06 2005 - 09:13:37 PDT)
    - Re: AMBER: Solvate question? Anthony Cruz (Tue Jun 07 2005 - 05:31:30 PDT)
AMBER: Re: Re: AMBER: SHAKE in md with partial solvation Ye Mei (Mon Jun 06 2005 - 03:49:44 PDT)
AMBER: Compile question?? Anthony Cruz (Mon Jun 06 2005 - 04:59:13 PDT)
- Re: AMBER: Compile question?? Robert Duke (Mon Jun 06 2005 - 05:38:02 PDT)
  - Re: AMBER: Compile question?? Anthony Cruz (Mon Jun 06 2005 - 06:24:40 PDT)
- Re: AMBER: Compile question?? Robert Duke (Mon Jun 06 2005 - 07:17:48 PDT)
- Re: AMBER: Compile question?? Robert Duke (Mon Jun 06 2005 - 07:32:06 PDT)
AMBER: Solvents Anthony Cruz (Mon Jun 06 2005 - 09:00:07 PDT)
AMBER: GB/SA/LD parallel sander Lwin, ThuZar (Mon Jun 06 2005 - 09:48:27 PDT)
AMBER: eelnb Stern, Julie (Mon Jun 06 2005 - 13:16:31 PDT)
AMBER: Protein dynamics. Laurence Lavelle (Mon Jun 06 2005 - 14:43:50 PDT)
- Re: AMBER: Protein dynamics. David A. Case (Mon Jun 06 2005 - 15:37:10 PDT)
AMBER: segmentation fault in sander Kenley Barrett (Mon Jun 06 2005 - 15:07:59 PDT)
- Re: AMBER: segmentation fault in sander Bill Ross (Tue Jun 07 2005 - 09:35:27 PDT)
Re: AMBER: segmentation fault in sander Bill Ross (Mon Jun 06 2005 - 15:18:45 PDT)
- Re: AMBER: segmentation fault in sander Kenley Barrett (Tue Jun 07 2005 - 08:36:44 PDT)
AMBER: Gibbs perturb DNA strands separate ivan.mmb.pcb.ub.es (Tue Jun 07 2005 - 04:16:41 PDT)
AMBER: nucgen problem cbala.igib.res.in (Tue Jun 07 2005 - 06:41:27 PDT)
- Re: AMBER: nucgen problem Bill Ross (Thu Nov 25 2004 - 09:08:14 PST)
- Re: AMBER: nucgen problem David A. Case (Tue Jun 07 2005 - 07:38:15 PDT)
  - Re: AMBER: nucgen problem cbala.igib.res.in (Tue Jun 07 2005 - 12:48:13 PDT)
    - Re: AMBER: nucgen problem Carlos Simmerling (Tue Jun 07 2005 - 12:34:17 PDT)
    - Re: AMBER: nucgen problem David A. Case (Tue Jun 07 2005 - 13:17:12 PDT)
- Re: AMBER: nucgen problem Bill Ross (Tue Jun 07 2005 - 12:27:14 PDT)
AMBER: Question about tutorial-9 Varsha Goyal (Tue Jun 07 2005 - 09:27:57 PDT)
Re: AMBER: nucgen problem Bill Ross (Tue Jun 07 2005 - 09:47:42 PDT)
AMBER: AMBER frcmod+off input vs. prep input K. Yarem (Tue Jun 07 2005 - 09:57:19 PDT)
Re: AMBER: AMBER frcmod+off input vs. prep input Bill Ross (Tue Jun 07 2005 - 10:58:06 PDT)
AMBER: TI calculation using sander Latifa Douali (Tue Jun 07 2005 - 17:10:54 PDT)
- Re: AMBER: TI calculation using sander David A. Case (Tue Jun 07 2005 - 18:32:34 PDT)
AMBER: How to run amber more efficiently? alice (Tue Jun 07 2005 - 19:59:26 PDT)
AMBER: Protein dynamics. Laurence Lavelle (Tue Jun 07 2005 - 22:52:00 PDT)
- Re: AMBER: Protein dynamics. Yong Duan (Wed Jun 08 2005 - 10:24:02 PDT)
AMBER: Sander is changing directories Andreas Kerzmann (Wed Jun 08 2005 - 02:39:23 PDT)
AMBER: Sander is changing directories Andreas Kerzmann (Wed Jun 08 2005 - 02:37:58 PDT)
AMBER: total energy leaps cristian obiol (Wed Jun 08 2005 - 03:44:18 PDT)
- Re: AMBER: total energy leaps Carlos Simmerling (Wed Jun 08 2005 - 04:22:06 PDT)
AMBER: TI tutorial in Amber 8 huhu (Wed Jun 08 2005 - 02:52:24 PDT)
- Re: AMBER: TI tutorial in Amber 8 David A. Case (Wed Jun 08 2005 - 21:27:42 PDT)
AMBER: (no subject) Mohammed Mayeed (Wed Jun 08 2005 - 10:26:15 PDT)
AMBER: Protein-surface interaction Mohammed Mayeed (Wed Jun 08 2005 - 11:37:30 PDT)
AMBER: GB/SA/LD parallel sander Lwin, ThuZar (Wed Jun 08 2005 - 12:36:41 PDT)
- Re: AMBER: GB/SA/LD parallel sander Carlos Simmerling (Wed Jun 08 2005 - 13:09:59 PDT)
AMBER: Compile Problems of Parallel Amber8 on Mac G5 Suxin Zheng (Wed Jun 08 2005 - 16:02:23 PDT)
AMBER: precision switch from 64 to 32 bit (double from single precision) Cordova, Luis E. (Wed Jun 08 2005 - 22:39:59 PDT)
- Re: AMBER: precision switch from 64 to 32 bit (double from single precision) Robert Duke (Thu Jun 09 2005 - 05:20:52 PDT)
AMBER: normal mode mm/pbsa interupted Eric Hu (Thu Jun 09 2005 - 11:46:04 PDT)
AMBER: setting up restraint with ntr option Lwin, ThuZar (Thu Jun 09 2005 - 14:49:04 PDT)
- AMBER: transfer data from Linux to windows gtg549i.mail.gatech.edu (Thu Jun 09 2005 - 15:24:05 PDT)
  - Re: AMBER: transfer data from Linux to windows Lihua Wang (Thu Jun 09 2005 - 15:32:14 PDT)
  - Re: AMBER: transfer data from Linux to windows Carlos Simmerling (Thu Jun 09 2005 - 15:41:26 PDT)
    - Re: AMBER: transfer data from Linux to windows Fajar Rakhman Wibowo (Thu Jun 09 2005 - 16:11:33 PDT)
  - Re: AMBER: transfer data from Linux to windows Thomas Patko (Thu Jun 09 2005 - 15:49:02 PDT)
  - AMBER: Make Distance restraints for non-standard residues gtg549i.mail.gatech.edu (Fri Jun 10 2005 - 08:47:41 PDT)
    - Re: AMBER: Make Distance restraints for non-standard residues David A. Case (Fri Jun 10 2005 - 12:59:13 PDT)
    - Re: AMBER: Make Distance restraints for non-standard residues gtg549i.mail.gatech.edu (Fri Jun 10 2005 - 13:45:00 PDT)
- Re: AMBER: setting up restraint with ntr option Viktor Hornak (Thu Jun 09 2005 - 16:53:05 PDT)
AMBER: atom type for -CH=CH- Qizhi Cui (Thu Jun 09 2005 - 18:46:13 PDT)
- Re: AMBER: atom type for -CH=CH- Guanglei Cui (Fri Jun 10 2005 - 06:56:52 PDT)
AMBER: substitute missing residues? Wai Keat Yam (Fri Jun 10 2005 - 01:20:29 PDT)
AMBER: Vibrational spectrum? milion.c-box.cz (Fri Jun 10 2005 - 09:53:01 PDT)
- Re: AMBER: Vibrational spectrum? [SOLUTION] Mark Williamson (Fri Jun 10 2005 - 03:33:51 PDT)
AMBER: SOURCE3 in gaff.dat Stern, Julie (Fri Jun 10 2005 - 02:40:20 PDT)
AMBER: vdw for terminal phosphate Rhoad, Jonathan S. (Fri Jun 10 2005 - 09:16:47 PDT)
- RE: AMBER: vdw for terminal phosphate Rhoad, Jonathan S. (Mon Jun 13 2005 - 09:21:49 PDT)
- RE: AMBER: vdw for terminal phosphate Bill Ross (Mon Jun 13 2005 - 13:22:47 PDT)
Re: AMBER: vdw for terminal phosphate Bill Ross (Fri Jun 10 2005 - 11:10:32 PDT)
AMBER: Can constant pH be used for minimization? Kenley Barrett (Fri Jun 10 2005 - 14:34:41 PDT)
- Re: AMBER: Can constant pH be used for minimization? David A. Case (Sat Jun 11 2005 - 05:42:51 PDT)
- Re: AMBER: Can constant pH be used for minimization? John Mongan (Tue Jun 14 2005 - 17:03:38 PDT)
AMBER: inpcrd file Douali, Latifa (Fri Jun 10 2005 - 16:04:24 PDT)
AMBER: Installation problem Sukjoon Yoon (Sun Jun 12 2005 - 02:21:50 PDT)
- Re: AMBER: Installation problem Chris Harrison (Sun Jun 12 2005 - 16:04:22 PDT)
  - RE: AMBER: Installation problem Sukjoon Yoon (Sun Jun 12 2005 - 19:35:37 PDT)
  - AMBER: Installation problem Sukjoon Yoon (Sun Jun 12 2005 - 21:07:26 PDT)
    - Re: AMBER: Installation problem Chris Harrison (Mon Jun 13 2005 - 17:33:13 PDT)
- Re: AMBER: Installation problem. . Don.Bashford.stjude.org (Mon Jun 13 2005 - 10:56:46 PDT)
  - AMBER: Installation problem. . Sukjoon Yoon (Tue Jun 14 2005 - 23:08:51 PDT)
    - Re: AMBER: Installation problem. . Andreas Svrcek-Seiler (Wed Jun 15 2005 - 05:31:46 PDT)
    - RE: AMBER: Installation problem. . Ross Walker (Wed Jun 15 2005 - 09:46:25 PDT)
    - AMBER: Installation problem. . Sukjoon Yoon (Thu Jun 16 2005 - 07:49:19 PDT)
    - Re: AMBER: Installation problem. . Mark Williamson (Thu Jun 16 2005 - 08:06:57 PDT)
    - Re: AMBER: Installation problem. . Mark Williamson (Thu Jun 16 2005 - 08:15:58 PDT)
    - Re: AMBER: Installation problem. . Andreas Svrcek-Seiler (Thu Jun 16 2005 - 21:54:42 PDT)
    - RE: AMBER: Installation problem. . Ross Walker (Fri Jun 17 2005 - 09:33:42 PDT)
    - RE: AMBER: Installation problem. . Andreas Svrcek-Seiler (Fri Jun 17 2005 - 10:12:10 PDT)
    - RE: AMBER: Installation problem - wrong address Andreas Svrcek-Seiler (Fri Jun 17 2005 - 10:28:43 PDT)
    - RE: AMBER: Installation problem. . Ross Walker (Fri Jun 17 2005 - 10:39:15 PDT)
    - AMBER: nonbond_list question . caoch.cherry.bio.titech.ac.jp (Fri Jun 17 2005 - 18:38:27 PDT)
    - Re: AMBER: nonbond_list question . Michael Crowley (Sat Jun 18 2005 - 12:51:01 PDT)
    - Re: AMBER: nonbond_list question . Robert Duke (Sat Jun 18 2005 - 20:03:07 PDT)
    - Re: AMBER: nonbond_list question . Petr Kulhanek (Sun Jun 19 2005 - 03:06:31 PDT)
    - Re: AMBER: nonbond_list question . Robert Duke (Sun Jun 19 2005 - 07:25:37 PDT)
AMBER: no corrected reaction field energy in *.out files after running mm_pbsa haixiao jin (Sun Jun 12 2005 - 19:04:40 PDT)
AMBER: how to pull out frames Vijay Manickam Achari (Sun Jun 12 2005 - 22:23:51 PDT)
- Re: AMBER: how to pull out frames Husni Fattayer (Mon Jun 13 2005 - 04:22:40 PDT)
  - Re: AMBER: how to pull out frames Vijay Manickam Achari (Mon Jun 13 2005 - 21:04:42 PDT)
AMBER: leap issues on a powerbook justin litchfield (Sun Jun 12 2005 - 16:21:02 PDT)
AMBER: Need help in charge fitting through RESP S.Sundar Raman (Mon Jun 13 2005 - 06:55:29 PDT)
- Re: AMBER: Need help in charge fitting through RESP Shulin Zhuang (Mon Jun 13 2005 - 07:29:02 PDT)
  - Re: AMBER: Need help in charge fitting through RESP FyD (Mon Jun 13 2005 - 09:15:42 PDT)
- Re: AMBER: Need help in charge fitting through RESP Nadine Homeyer (Mon Jun 13 2005 - 09:20:49 PDT)
- Re: AMBER: Need help in charge fitting through RESP junwang (Mon Jun 13 2005 - 10:51:41 PDT)
AMBER: Announcing the LMOD website Istvan Kolossvary (Mon Jun 13 2005 - 11:18:52 PDT)
AMBER: atom type question opitz.che.udel.edu (Mon Jun 13 2005 - 12:41:30 PDT)
- Re: AMBER: atom type question David A. Case (Mon Jun 13 2005 - 13:05:44 PDT)
- Re: AMBER: atom type question opitz.che.udel.edu (Mon Jun 13 2005 - 13:46:18 PDT)
  - Re: AMBER: atom type question David A. Case (Wed Jun 15 2005 - 08:18:18 PDT)
AMBER: why the dipeptide always moving out the virtual box Li Su (Mon Jun 13 2005 - 14:40:47 PDT)
- Re: AMBER: why the dipeptide always moving out the virtual box David A. Case (Mon Jun 13 2005 - 15:55:19 PDT)
  - Re: AMBER: why the dipeptide always moving out the virtual box Li Su (Tue Jun 14 2005 - 14:11:41 PDT)
    - Re: AMBER: why the dipeptide always moving out the virtual box David A. Case (Tue Jun 14 2005 - 15:50:03 PDT)
AMBER: Restrained-MD Ananda Rama Krishnan Selvaraj (Mon Jun 13 2005 - 16:04:14 PDT)
- Re: AMBER: Restrained-MD David A. Case (Mon Jun 13 2005 - 16:10:00 PDT)
AMBER: compiler Zhang Bing (Tue Jun 14 2005 - 01:14:08 PDT)
- RE: AMBER: compiler Ross Walker (Tue Jun 14 2005 - 10:43:58 PDT)
AMBER: nmropt =1 AND ntr=1 in pmemd Christoph Brockmann (Tue Jun 14 2005 - 02:33:39 PDT)
- Re: AMBER: nmropt =1 AND ntr=1 in pmemd Robert Duke (Tue Jun 14 2005 - 05:18:20 PDT)
- Re: AMBER: nmropt =1 AND ntr=1 in pmemd Furse, Kristina Elisabet (Fri Jun 17 2005 - 12:16:13 PDT)
  - Re: AMBER: nmropt =1 AND ntr=1 in pmemd Robert Duke (Fri Jun 17 2005 - 14:58:44 PDT)
AMBER: creating pdb file.... Vijay Manickam Achari (Tue Jun 14 2005 - 03:49:09 PDT)
- Re: AMBER: creating pdb file.... Angelo Pugliese (Tue Jun 14 2005 - 04:11:41 PDT)
- RE: AMBER: creating pdb file.... Ross Walker (Tue Jun 14 2005 - 10:51:21 PDT)
AMBER: compiler Zhang Bing (Tue Jun 14 2005 - 04:13:19 PDT)
- Re: AMBER: compiler David LeBard (Tue Jun 14 2005 - 10:45:27 PDT)
  - Re: AMBER: compiler David A. Case (Tue Jun 14 2005 - 11:40:16 PDT)
AMBER: time and lifetime in hbond analysis (ptraj) Giulio Rastelli (Tue Jun 14 2005 - 07:23:50 PDT)
- Re: AMBER: time and lifetime in hbond analysis (ptraj) Angelo Pugliese (Tue Jun 14 2005 - 07:57:56 PDT)
AMBER: Request for g98 (IOP...) Paramasivam Manikandan (Tue Jun 14 2005 - 08:04:30 PDT)
- Re: AMBER: Request for g98 (IOP...) FyD (Tue Jun 14 2005 - 08:55:27 PDT)
- Re: AMBER: Request for g98 (IOP...) Oliver Hucke (Tue Jun 14 2005 - 09:20:51 PDT)
AMBER: sp2 carbon atom parametrization Gustavo Pierdominici Sottile (Tue Jun 14 2005 - 09:30:16 PDT)
AMBER: Extended bonds-MD Ananda Rama Krishnan Selvaraj (Tue Jun 14 2005 - 09:29:29 PDT)
- RE: AMBER: Extended bonds-MD Ross Walker (Tue Jun 14 2005 - 10:28:43 PDT)
AMBER: Free Energy Calculation torsion missing mrbroad.ilstu.edu (Tue Jun 14 2005 - 11:21:54 PDT)
AMBER: puzzling gaff parameter Oliver Hucke (Tue Jun 14 2005 - 18:16:35 PDT)
AMBER: Thanks Zhang Bing (Tue Jun 14 2005 - 19:26:23 PDT)
AMBER: solutions of amber installation problems Zhang Bing (Tue Jun 14 2005 - 19:42:13 PDT)
- RE: AMBER: solutions of amber installation problems Ross Walker (Tue Jun 14 2005 - 21:55:20 PDT)
AMBER: Extended bonds-MD Ananda Rama Krishnan Selvaraj (Wed Jun 15 2005 - 00:02:25 PDT)
- Re: AMBER: Extended bonds-MD Carlos Simmerling (Wed Jun 15 2005 - 04:22:29 PDT)
- Re: AMBER: Extended bonds-MD Ananda Rama Krishnan Selvaraj (Wed Jun 15 2005 - 05:55:41 PDT)
AMBER: bad atom type: H alice (Wed Jun 15 2005 - 03:53:50 PDT)
- Re: AMBER: bad atom type: H David A. Case (Wed Jun 15 2005 - 08:09:17 PDT)
  - Re: Re: AMBER: bad atom type: H alice (Wed Jun 15 2005 - 18:35:00 PDT)
AMBER: Question about "quasih" Yen-Ting Lai (Wed Jun 15 2005 - 09:46:22 PDT)
- Re: AMBER: Question about "quasih" David A. Case (Wed Jun 15 2005 - 10:43:47 PDT)
- Re: AMBER: Question about "quasih" Yen-Ting Lai (Wed Jun 15 2005 - 12:25:57 PDT)
  - Re: AMBER: Question about "quasih" David A. Case (Wed Jun 15 2005 - 14:01:33 PDT)
AMBER: position of protonation info from constant pH run Kenley Barrett (Wed Jun 15 2005 - 18:27:44 PDT)
AMBER: Cut pdb files Yogesh Sabnis (Thu Jun 16 2005 - 00:57:18 PDT)
AMBER: adenine test for LMOD in amber8 Giulio Rastelli (Thu Jun 16 2005 - 02:57:16 PDT)
- Re: AMBER: adenine test for LMOD in amber8 Istvan Kolossvary (Thu Jun 16 2005 - 06:16:22 PDT)
- AMBER: Apologies - LMOD website down Istvan Kolossvary (Thu Jul 14 2005 - 07:39:54 PDT)
AMBER: How to modify force constants and equalibrium values for standard residues Li Su (Thu Jun 16 2005 - 06:30:41 PDT)
- Re: AMBER: How to modify force constants and equalibrium values for standard residues David A. Case (Thu Jun 16 2005 - 07:41:18 PDT)
- RE: AMBER: How to modify force constants and equalibrium values for standard residues Ross Walker (Thu Jun 16 2005 - 14:05:33 PDT)
- Re: AMBER: How to modify force constants and equalibrium values for standard residues gsciaini (Fri Jun 17 2005 - 06:41:44 PDT)
AMBER: Question about GAFF atom types Herbert Georg (Thu Jun 16 2005 - 12:18:50 PDT)
- Re: AMBER: Question about GAFF atom types Herbert Georg (Fri Jun 17 2005 - 12:49:53 PDT)
  - Re: AMBER: Question about GAFF atom types Ilyas Yildirim (Fri Jun 17 2005 - 13:42:18 PDT)
    - Re: AMBER: Question about GAFF atom types Herbert Georg (Fri Jun 17 2005 - 15:31:52 PDT)
    - Re: AMBER: Question about GAFF atom types Ilyas Yildirim (Fri Jun 17 2005 - 18:29:24 PDT)
    - Re: AMBER: Question about GAFF atom types Herbert Georg (Mon Jun 20 2005 - 09:47:38 PDT)
    - Re: AMBER: Question about GAFF atom types Ilyas Yildirim (Mon Jun 20 2005 - 12:51:59 PDT)
    - AMBER: PBSA error: PB bomb in pd_aaradi Xin Hu (Wed Jun 22 2005 - 07:34:13 PDT)
    - Re: AMBER: PBSA error: PB bomb in pd_aaradi JunJun Liu (Wed Jun 22 2005 - 08:17:43 PDT)
AMBER: For calculating the energy rised from deviation of equalibrium values of bond angles does amber use degree or radians Li Su (Thu Jun 16 2005 - 14:19:36 PDT)
- RE: AMBER: For calculating the energy rised from deviation of equalibrium values of bond angles does amber use degree or radians Ross Walker (Thu Jun 16 2005 - 15:00:41 PDT)
  - Re: AMBER: For calculating the energy rised from deviation of equalibrium values of bond angles does amber use degree or radians Li Su (Thu Jun 16 2005 - 16:17:46 PDT)
AMBER: antechamber problems hj zou (Fri Jun 17 2005 - 06:32:27 PDT)
AMBER: RE: AMBER :LINMIN problem Ross Walker (Fri Jun 17 2005 - 11:27:25 PDT)
AMBER: Analysing my simulation data.. Vijay Manickam Achari (Sat Jun 18 2005 - 01:32:13 PDT)
- Re: AMBER: Analysing my simulation data.. Varsha Goyal (Sat Jun 18 2005 - 09:21:28 PDT)
  - Re: AMBER: Analysing my simulation data.. Ilyas Yildirim (Sat Jun 18 2005 - 09:47:06 PDT)
AMBER: antechamber problems hj zou (Sun Jun 19 2005 - 06:50:08 PDT)
AMBER: average structure emilia wu (Sun Jun 19 2005 - 17:15:53 PDT)
- RE: AMBER: average structure Ross Walker (Sun Jun 19 2005 - 17:41:07 PDT)
AMBER: How to set the virtual box size for a calculation run in vacuum Li Su (Mon Jun 20 2005 - 06:27:33 PDT)
- AMBER: RMS Wen Li (Mon Apr 03 2006 - 14:03:29 PDT)
  - Re: AMBER: RMS carlos (Mon Apr 03 2006 - 14:18:24 PDT)
    - Re: AMBER: RMS Wen Li (Tue Apr 04 2006 - 06:59:04 PDT)
AMBER: How to turn off pme when using periodic box Li Su (Mon Jun 20 2005 - 11:31:09 PDT)
- RE: AMBER: How to turn off pme when using periodic box Ross Walker (Mon Jun 20 2005 - 13:31:04 PDT)
AMBER: RESP charges of RNA nucleotides with 3' and 5' ends Ilyas Yildirim (Mon Jun 20 2005 - 18:51:11 PDT)
- Re: AMBER: RESP charges of RNA nucleotides with 3' and 5' ends FyD (Wed Jun 22 2005 - 14:56:30 PDT)
  - Re: AMBER: RESP charges of RNA nucleotides with 3' and 5' ends Ilyas Yildirim (Wed Jun 22 2005 - 15:13:19 PDT)
  - Re: AMBER: RESP charges of RNA nucleotides with 3' and 5' ends Ilyas Yildirim (Wed Jul 06 2005 - 15:24:45 PDT)
    - Re: AMBER: RESP charges of RNA nucleotides with 3' and 5' ends Ilyas Yildirim (Wed Jul 06 2005 - 20:18:46 PDT)
    - Re: AMBER: RESP charges of RNA nucleotides with 3' and 5' ends Qing Zhang (Thu Jul 07 2005 - 01:30:14 PDT)
    - Re: AMBER: RESP charges of RNA nucleotides with 3' and 5' ends Ilyas Yildirim (Thu Jul 07 2005 - 14:56:14 PDT)
    - Re: AMBER: RESP charges of RNA nucleotides with 3' and 5' ends Qing Zhang (Thu Jul 07 2005 - 17:48:40 PDT)
    - Re: AMBER: RESP charges of RNA nucleotides with 3' and 5' ends Ilyas Yildirim (Mon Jul 11 2005 - 18:25:00 PDT)
    - Re: AMBER: RESP charges of RNA nucleotides with 3' and 5' ends Qing Zhang (Tue Jul 12 2005 - 12:59:01 PDT)
    - Re: AMBER: RESP charges of RNA nucleotides with 3' and 5' ends FyD (Thu Jul 07 2005 - 08:54:00 PDT)
AMBER: large std error in entropy estimation Ye Mei (Tue Jun 21 2005 - 19:51:43 PDT)
- Re: AMBER: large std error in entropy estimation David A. Case (Thu Jun 23 2005 - 11:25:03 PDT)
AMBER: a question about varying positions of dihedral restraints with step number Li Su (Wed Jun 22 2005 - 12:42:02 PDT)
- Re: AMBER: a question about varying positions of dihedral restraints with step number David A. Case (Fri Jun 24 2005 - 08:09:21 PDT)
AMBER: question about Carnal opitz.che.udel.edu (Wed Jun 22 2005 - 13:03:45 PDT)
Re: AMBER: question about Carnal Bill Ross (Wed Jun 22 2005 - 13:51:34 PDT)
AMBER: RE: tutorial 8 Ross Walker (Wed Jun 22 2005 - 14:15:33 PDT)
AMBER: software for real polymer MD simulation xhu1.memphis.edu (Wed Jun 22 2005 - 14:31:51 PDT)
AMBER: how the phosphated threonine to be recognized in leap haixiao jin (Thu Jun 23 2005 - 02:03:26 PDT)
AMBER: Parameters for phosphorylated amino acids Nadine Homeyer (Thu Jun 23 2005 - 06:54:22 PDT)
AMBER: Parameters for phosphorylated amino acids Nadine Homeyer (Thu Jun 23 2005 - 07:24:08 PDT)
- AMBER: Searching for NAD parameter files / Problems with parameter file creation Daniel Wetzler (Thu Jun 23 2005 - 07:43:29 PDT)
  - RE: AMBER: Searching for NAD parameter files / Problems with parameter file creation Rhoad, Jonathan S. (Thu Jun 23 2005 - 08:08:01 PDT)
  - RE: AMBER: Searching for NAD parameter files / Problems with parameter file creation Ross Walker (Thu Jun 23 2005 - 09:26:56 PDT)
- Re: AMBER: Parameters for phosphorylated amino acids Suxin Zheng (Thu Jun 23 2005 - 15:41:30 PDT)
AMBER: GCC for AMBER on 64 bit machine mfyang (Thu Jun 23 2005 - 10:55:01 PDT)
- Re: AMBER: GCC for AMBER on 64 bit machine Andreas Svrcek-Seiler (Thu Jun 23 2005 - 11:44:44 PDT)
AMBER: using xmgrace.... Vijay Manickam Achari (Thu Jun 23 2005 - 19:51:37 PDT)
AMBER: Have the parameters for dUMP been calculated by somebody? Suxin Zheng (Fri Jun 24 2005 - 18:30:12 PDT)
AMBER: TI-FEP for ALA --> GLY Jiten (Fri Jun 24 2005 - 22:07:03 PDT)
- Re: AMBER: TI-FEP for ALA --> GLY Ilyas Yildirim (Fri Jun 24 2005 - 23:48:36 PDT)
  - Re: AMBER: TI-FEP for VAL --> ALA Jiten (Sat Jun 25 2005 - 09:13:44 PDT)
    - Re: AMBER: TI-FEP for VAL --> ALA Ilyas Yildirim (Sat Jun 25 2005 - 16:39:11 PDT)
    - Re: AMBER: TI-FEP for VAL --> ALA Jiten (Sun Jun 26 2005 - 19:11:03 PDT)
    - Re: AMBER: TI-FEP for VAL --> ALA Ilyas Yildirim (Mon Jun 27 2005 - 16:43:16 PDT)
    - Re: AMBER: TI-FEP for ALA --> GLY Jiten (Mon Jun 27 2005 - 19:24:56 PDT)
    - Re: AMBER: TI-FEP for ALA --> GLY Ilyas Yildirim (Mon Jun 27 2005 - 22:46:17 PDT)
    - AMBER: Re: TI tutorial Jiten (Tue Jun 28 2005 - 07:17:39 PDT)
    - Re: AMBER: Re: TI tutorial David A. Case (Tue Jun 28 2005 - 08:49:53 PDT)
    - Re: AMBER: Re: TI tutorial Jiten (Tue Jun 28 2005 - 09:36:59 PDT)
    - Re: AMBER: Re: TI tutorial David A. Case (Tue Jun 28 2005 - 18:09:44 PDT)
    - Re: AMBER: Re: TI tutorial Jiten (Tue Jun 28 2005 - 20:46:17 PDT)
    - Re: AMBER: Re: TI tutorial David A. Case (Wed Jun 29 2005 - 07:30:31 PDT)
    - Re: AMBER: Re: TI tutorial Jiten (Wed Jun 29 2005 - 09:22:04 PDT)
    - Re: AMBER: Re: TI tutorial David A. Case (Wed Jun 29 2005 - 10:01:23 PDT)
    - Re: AMBER: Re: TI tutorial Jiten (Wed Jun 29 2005 - 10:24:19 PDT)
AMBER: RED question Kara Di Giorgio (Sat Jun 25 2005 - 15:44:23 PDT)
- Re: AMBER: RED question FyD (Sun Jun 26 2005 - 20:37:59 PDT)
  - Re: AMBER: RED question Kara Di Giorgio (Sun Jun 26 2005 - 22:13:13 PDT)
- Re: AMBER: RED question FyD (Wed Jun 29 2005 - 09:34:16 PDT)
AMBER: MM_PBSA ! Pradipta Bandyopadhyay (Sun Jun 26 2005 - 05:43:18 PDT)
- Re: AMBER: MM_PBSA ! Jiten (Sun Jun 26 2005 - 17:43:13 PDT)
AMBER: Hbond analysis xueping (Sun Jun 26 2005 - 18:27:48 PDT)
- Re: AMBER: Hbond analysis Fabian Boes (Mon Jun 27 2005 - 06:12:34 PDT)
AMBER: mm_pbsa script ! Pradipta Bandyopadhyay (Sun Jun 26 2005 - 23:43:53 PDT)
AMBER: Request for calculating free energy using AMBER6 S.Sundar Raman (Mon Jun 27 2005 - 04:59:00 PDT)
AMBER: parallel error Zhang Bing (Mon Jun 27 2005 - 05:36:14 PDT)
- Re: AMBER: parallel error Peter Varnai (Fri Jul 01 2005 - 08:51:18 PDT)
AMBER: INTRA molecular hbonds Giulio Rastelli (Mon Jun 27 2005 - 07:09:23 PDT)
- Re: AMBER: INTRA molecular hbonds Fabian Boes (Mon Jun 27 2005 - 07:45:13 PDT)
AMBER: pb_pgb test fail acb15885.uprm.edu (Mon Jun 27 2005 - 11:17:48 PDT)
- Re: AMBER: pb_pgb test fail David A. Case (Mon Jun 27 2005 - 11:48:32 PDT)
AMBER: script for calculating hydrogen bond Vijay Manickam Achari (Mon Jun 27 2005 - 19:57:30 PDT)
- RE: AMBER: script for calculating hydrogen bond Ross Walker (Mon Jun 27 2005 - 20:04:43 PDT)
AMBER: questions about RNA xinhuang.indiana.edu (Mon Jun 27 2005 - 20:19:58 PDT)
AMBER: calculating torsion angles Vijay Manickam Achari (Tue Jun 28 2005 - 01:59:02 PDT)
AMBER: dielectric constant Germán Sciaini (Wed Jun 29 2005 - 04:02:24 PDT)
- Re: AMBER: dielectric constant David LeBard (Tue Jun 28 2005 - 13:01:30 PDT)
AMBER: compiler error, SGI Octane Peter Gannett (Tue Jun 28 2005 - 05:54:35 PDT)
AMBER: amber 8 leap topology file dihedral term problem Angela Liu (Tue Jun 28 2005 - 06:59:57 PDT)
AMBER: Fw: TI tutorial --> ALA --> GLY TI calculation Jiten (Tue Jun 28 2005 - 08:02:42 PDT)
AMBER: calculating hydrogen bonds Vijay Manickam Achari (Tue Jun 28 2005 - 19:50:36 PDT)
AMBER: How to read unformatted restart file in PTRAJ ? JunJun Liu (Tue Jun 28 2005 - 23:20:57 PDT)
Re: [pgannett.hsc.wvu.edu: AMBER: compiler error, SGI Octane] Roberto Gomperts (Wed Jun 29 2005 - 08:01:00 PDT)
AMBER: error - compiling antechamber Peter Gannett (Wed Jun 29 2005 - 12:30:20 PDT)
- Re: AMBER: error - compiling antechamber Roberto Gomperts (Wed Jun 29 2005 - 14:11:41 PDT)
AMBER: Free energy calculation for protein-protein complex using MM_PBSA Zhiguo Liu (Wed Jun 29 2005 - 18:59:01 PDT)
- Re: AMBER: Free energy calculation for protein-protein complex using MM_PBSA Thomas Steinbrecher (Thu Jun 30 2005 - 00:14:01 PDT)
AMBER: acceptor and donor in hbond calculation Vijay Manickam Achari (Wed Jun 29 2005 - 22:01:58 PDT)
AMBER: example script for hbond calculation Vijay Manickam Achari (Wed Jun 29 2005 - 23:27:15 PDT)
- Re: AMBER: example script for hbond calculation Thomas E. Cheatham, III (Fri Jul 01 2005 - 09:10:07 PDT)
AMBER: 10-12 potential and create atom type Fabien CAILLIEZ (Thu Jun 30 2005 - 10:19:41 PDT)
- Re: AMBER: 10-12 potential and create atom type David A. Case (Tue Jul 05 2005 - 15:03:09 PDT)
AMBER: antechamber error Peter Gannett (Thu Jun 30 2005 - 12:05:25 PDT)
- Re: AMBER: antechamber error David A. Case (Thu Jun 30 2005 - 14:38:11 PDT)
  - Re: AMBER: antechamber error -> metals Scott Brozell (Sun Aug 13 2006 - 14:58:14 PDT)
AMBER: Create new Unit Douali, Latifa (Thu Jun 30 2005 - 16:45:37 PDT)
- Re: AMBER: Create new Unit FyD (Thu Jun 30 2005 - 17:25:02 PDT)
- Re: AMBER: Create new Unit David A. Case (Thu Jun 30 2005 - 18:38:42 PDT)
AMBER: least square fit of snapshots in md trajectory to a reference frame Ye Mei (Thu Jun 30 2005 - 19:56:08 PDT)
- Re: AMBER: least square fit of snapshots in md trajectory to a reference frame David A. Case (Fri Jul 01 2005 - 08:51:21 PDT)
AMBER: question about spline in sander -- array size of eed_cub Cordova, Luis E. (Thu Jun 30 2005 - 21:33:25 PDT)
AMBER: question about leaprc.gaff and xxx.top Vijay Manickam Achari (Thu Jun 30 2005 - 22:52:15 PDT)
AMBER: how to make cluster files? Ananda Rama Krishnan Selvaraj (Fri Jul 01 2005 - 00:10:05 PDT)
AMBER: Stacking energy Angelo Pugliese (Fri Jul 01 2005 - 01:32:34 PDT)
- Re: AMBER: Stacking energy ivan.mmb.pcb.ub.es (Fri Jul 01 2005 - 01:44:57 PDT)
  - Re: AMBER: Stacking energy Jiri Sponer (Fri Jul 01 2005 - 02:52:45 PDT)
    - Re: AMBER: Stacking energy Angelo Pugliese (Fri Jul 01 2005 - 03:42:28 PDT)
    - Re: AMBER: Stacking energy Jiri Sponer (Fri Jul 01 2005 - 07:01:24 PDT)
    - Re: AMBER: Stacking energy Angelo Pugliese (Fri Jul 01 2005 - 07:38:37 PDT)
    - Re: AMBER: Stacking energy Jiri Sponer (Fri Jul 01 2005 - 08:00:03 PDT)
AMBER: molecular dynamics simulation of protein containing Mg2+ cation Ye Mei (Fri Jul 01 2005 - 02:33:31 PDT)
- Re: AMBER: molecular dynamics simulation of protein containing Mg2+ cation David A. Case (Sun Jul 03 2005 - 16:34:14 PDT)
AMBER: cavity volume Anthony Cruz (Fri Jul 01 2005 - 05:46:24 PDT)
- Re: AMBER: cavity volume Germán Sciaini (Mon Jul 04 2005 - 03:29:59 PDT)
AMBER: Replica exchange Anthony Cruz (Fri Jul 01 2005 - 07:33:46 PDT)
AMBER: Temperature varible in MMPBSA script JunJun Liu (Fri Jul 01 2005 - 06:59:05 PDT)
AMBER: please help us on partial charge calculation of PT complex using RESP peng79.email.unc.edu (Fri Jul 01 2005 - 08:10:31 PDT)
- Re: AMBER: please help us on partial charge calculation of PT complex using RESP FyD (Fri Jul 01 2005 - 09:07:40 PDT)
AMBER: questions about topology file Fabien CAILLIEZ (Fri Jul 01 2005 - 08:49:20 PDT)
- Re: AMBER: questions about topology file David A. Case (Fri Jul 01 2005 - 13:24:02 PDT)
AMBER: (no subject) Varsha Goyal (Fri Jul 01 2005 - 14:46:55 PDT)
- Re: AMBER: (no subject) S.Sundar Raman (Sat Jul 02 2005 - 05:58:59 PDT)
  - Re: AMBER: (no subject) Varsha Goyal (Sat Jul 02 2005 - 09:10:49 PDT)
AMBER: loading DNA-RNA hybrid in xleap cbala.igib.res.in (Sat Jul 02 2005 - 08:36:59 PDT)
- Re: AMBER: loading DNA-RNA hybrid in xleap David A. Case (Sat Jul 02 2005 - 10:30:58 PDT)
  - Re: AMBER: loading DNA-RNA hybrid in xleap cbala.igib.res.in (Sat Jul 02 2005 - 12:57:33 PDT)
    - Re: AMBER: loading DNA-RNA hybrid in xleap Ilyas Yildirim (Sun Jul 03 2005 - 04:23:56 PDT)
AMBER: Question about Lennard-Jones Parameters in Topology file Linda Prengaman (Sat Jul 02 2005 - 11:15:51 PDT)
- Re: AMBER: Question about Lennard-Jones Parameters in Topology file Germán Sciaini (Mon Jul 04 2005 - 03:46:00 PDT)
  - Re: AMBER: Question about Lennard-Jones Parameters in Topology file Linda Prengaman (Tue Jul 05 2005 - 10:40:44 PDT)
AMBER: MM-PBSA-big energies John (Sun Jul 03 2005 - 14:31:56 PDT)
- Re: AMBER: MM-PBSA-big energies Carlos Simmerling (Sun Jul 03 2005 - 15:13:48 PDT)
- AMBER: Problems with parameter lib and prep püarameter files Daniel Wetzler (Mon Jul 04 2005 - 02:14:56 PDT)
  - RE: AMBER: Problems with parameter lib and prep püarameter files Ross Walker (Tue Jul 05 2005 - 08:47:22 PDT)
    - AMBER: Re: AMBER: Problems with parameter lib and prep püarameter files Daniel Wetzler (Wed Jul 06 2005 - 03:40:53 PDT)
AMBER: estimation of interface size Ye Mei (Sun Jul 03 2005 - 19:19:55 PDT)
- Re: AMBER: estimation of interface size Carlos Simmerling (Mon Jul 04 2005 - 04:39:11 PDT)
AMBER: Loading a macmodel file complex Yogesh Sabnis (Mon Jul 04 2005 - 08:02:49 PDT)
- RE: AMBER: Loading a macmodel file complex Ross Walker (Tue Jul 05 2005 - 08:54:57 PDT)
AMBER: pmemd - bug report Petr Kulhanek (Mon Jul 04 2005 - 09:33:05 PDT)
- Re: AMBER: pmemd - bug report Robert Duke (Mon Jul 04 2005 - 13:30:54 PDT)
- Re: AMBER: pmemd - bug report Robert Duke (Mon Jul 04 2005 - 14:40:18 PDT)
- Re: AMBER: pmemd - bug report Robert Duke (Mon Jul 04 2005 - 20:58:14 PDT)
  - Re: AMBER: pmemd - bug report Petr Kulhanek (Tue Jul 05 2005 - 03:31:14 PDT)
    - Re: AMBER: pmemd - bug report Petr Kulhanek (Tue Jul 05 2005 - 09:29:54 PDT)
    - Re: AMBER: pmemd - bug report David A. Case (Tue Jul 05 2005 - 10:38:09 PDT)
    - Re: AMBER: pmemd - bug report David A. Case (Tue Jul 05 2005 - 10:43:18 PDT)
- Re: AMBER: pmemd - bug report Robert Duke (Tue Jul 05 2005 - 09:47:19 PDT)
AMBER: nucgen and nukit dthomas.chem.uwa.edu.au (Tue Jul 05 2005 - 07:55:44 PDT)
Re: AMBER: nucgen and nukit Bill Ross (Tue Jul 05 2005 - 09:33:04 PDT)
AMBER: restart file Harianto Tjong (Tue Jul 05 2005 - 11:49:20 PDT)
- RE: AMBER: restart file Ross Walker (Tue Jul 05 2005 - 12:29:27 PDT)
  - Re: AMBER: restart file Harianto Tjong (Tue Jul 05 2005 - 13:49:16 PDT)
    - RE: AMBER: restart file Ross Walker (Tue Jul 05 2005 - 14:15:49 PDT)
    - Re: AMBER: restart file Carlos Simmerling (Tue Jul 05 2005 - 14:22:16 PDT)
- Re: AMBER: restart file Carlos Simmerling (Tue Jul 05 2005 - 12:36:43 PDT)
AMBER: DNA strands separate ivan.mmb.pcb.ub.es (Wed Jul 06 2005 - 03:39:24 PDT)
- Re: AMBER: DNA strands separate Angelo Pugliese (Wed Jul 06 2005 - 05:46:05 PDT)
  - Re: AMBER: DNA strands separate ivan.mmb.pcb.ub.es (Wed Jul 06 2005 - 06:40:18 PDT)
    - Re: AMBER: DNA strands separate Angelo Pugliese (Wed Jul 06 2005 - 07:04:36 PDT)
    - Re: AMBER: DNA strands separate ivan.mmb.pcb.ub.es (Wed Jul 06 2005 - 07:39:04 PDT)
    - Re: AMBER: DNA strands separate Angelo Pugliese (Wed Jul 06 2005 - 08:00:00 PDT)
AMBER: how to average the structure along md trajectory Ye Mei (Wed Jul 06 2005 - 06:51:56 PDT)
- Re: AMBER: how to average the structure along md trajectory Angelo Pugliese (Wed Jul 06 2005 - 08:02:48 PDT)
AMBER: AMBER on Mac OS X Varsha Goyal (Wed Jul 06 2005 - 07:55:12 PDT)
- Re: AMBER: AMBER on Mac OS X David A. Case (Wed Jul 06 2005 - 08:36:08 PDT)
- Re: AMBER: AMBER on Mac OS X Kara Di Giorgio (Wed Jul 06 2005 - 09:46:11 PDT)
AMBER: box size in explicit water Lwin, ThuZar (Wed Jul 06 2005 - 09:39:47 PDT)
- Re: AMBER: box size in explicit water Melinda Layten (Wed Jul 06 2005 - 09:52:55 PDT)
- Re: AMBER: box size in explicit water David A. Case (Wed Jul 06 2005 - 10:30:59 PDT)
AMBER: sander problem Anthony Cruz (Wed Jul 06 2005 - 16:05:44 PDT)
- RE: AMBER: sander problem Ross Walker (Wed Jul 06 2005 - 14:19:34 PDT)
- Re: AMBER: sander problem David A. Case (Wed Jul 06 2005 - 15:30:59 PDT)
  - Re: AMBER: sander problem Anthony Cruz (Thu Jul 07 2005 - 08:25:29 PDT)
AMBER: problem with addIons Lwin, ThuZar (Wed Jul 06 2005 - 14:41:25 PDT)
- Re: AMBER: problem with addIons David LeBard (Wed Jul 06 2005 - 15:08:35 PDT)
- Re: AMBER: problem with addIons David A. Case (Wed Jul 06 2005 - 15:41:21 PDT)
AMBER: question about sander minimization error drugdesign (Thu Jul 07 2005 - 01:37:51 PDT)
- Re: AMBER: question about sander minimization error Ilyas Yildirim (Thu Jul 07 2005 - 01:59:13 PDT)
AMBER: Replica Exchange Anthony Cruz (Thu Jul 07 2005 - 08:27:51 PDT)
- Re: AMBER: Replica Exchange Carlos Simmerling (Thu Jul 07 2005 - 06:43:17 PDT)
AMBER: tyrosyl charges Ozlem Demir (Thu Jul 07 2005 - 10:07:24 PDT)
- Re: AMBER: tyrosyl charges Ilyas Yildirim (Thu Jul 07 2005 - 15:30:20 PDT)
AMBER: Release of R.E.D-II FyD (Thu Jul 07 2005 - 10:58:54 PDT)
AMBER: problems with bonds in sander Fabien CAILLIEZ (Thu Jul 07 2005 - 11:18:19 PDT)
AMBER: how is truncated octahedron box calculated Lwin, ThuZar (Thu Jul 07 2005 - 13:38:05 PDT)
- Re: AMBER: how is truncated octahedron box calculated Chris Moth (Thu Jul 07 2005 - 14:50:24 PDT)
AMBER: building nucleic acids mathew k varghese (Thu Jul 07 2005 - 21:07:03 PDT)
- AMBER: Problem with building AMBER7 on SUSE Linux 9.2 Daniel Wetzler (Fri Jul 08 2005 - 04:18:09 PDT)
  - Re: AMBER: Problem with building AMBER7 on SUSE Linux 9.2 Daniel Wetzler (Tue Jul 12 2005 - 00:53:40 PDT)
Re: AMBER: building nucleic acids Bill Ross (Fri Jul 08 2005 - 12:05:15 PDT)
- Re: AMBER: building nucleic acids mathew k varghese (Fri Jul 08 2005 - 22:55:00 PDT)
  - Re: AMBER: building nucleic acids David A. Case (Sun Jul 10 2005 - 21:51:46 PDT)
AMBER: LCPO SASA parameters for other elements when using gbsa=1 option David.Maxwell.di.mdacc.tmc.edu (Fri Jul 08 2005 - 13:10:00 PDT)
AMBER: infinite DNA Stern, Julie (Fri Jul 08 2005 - 14:44:25 PDT)
- Re: AMBER: infinite DNA Carlos Simmerling (Fri Jul 08 2005 - 16:33:59 PDT)
  - Re: AMBER: infinite DNA David A. Case (Fri Jul 08 2005 - 17:26:04 PDT)
AMBER: Water simulation David LeBard (Fri Jul 08 2005 - 16:44:12 PDT)
- Re: AMBER: Water simulation David A. Case (Fri Jul 08 2005 - 17:13:37 PDT)
  - Re: AMBER: Water simulation David LeBard (Sat Jul 09 2005 - 17:30:55 PDT)
AMBER: glc0358.vip.sina.com (Fri Jul 08 2005 - 23:22:45 PDT)
AMBER: simulation with Mg2+ ions and counter ions Ye Mei (Fri Jul 08 2005 - 23:54:16 PDT)
- Re: AMBER: simulation with Mg2+ ions and counter ions Lihua Wang (Sat Jul 09 2005 - 01:11:42 PDT)
  - Re: AMBER: simulation with Mg2+ ions and counter ions Jiri Sponer (Sat Jul 09 2005 - 01:50:10 PDT)
AMBER: glc0358.vip.sina.com (Sat Jul 09 2005 - 00:03:23 PDT)
AMBER: how to see the box lines Ananda Rama Krishnan Selvaraj (Sat Jul 09 2005 - 11:10:50 PDT)
AMBER: molecular dynamics Vijay Manickam Achari (Sat Jul 09 2005 - 19:55:55 PDT)
- RE: AMBER: molecular dynamics Ross Walker (Sat Jul 09 2005 - 20:42:06 PDT)
- Re: AMBER: molecular dynamics course Ilan Samish (Sat Jul 09 2005 - 23:23:05 PDT)
AMBER: Leap compilation issues justin litchfield (Sun Jul 10 2005 - 18:41:50 PDT)
- Re: AMBER: Leap compilation issues David A. Case (Sun Jul 10 2005 - 22:13:04 PDT)
  - Re: AMBER: Leap compilation issues justin litchfield (Sun Jul 10 2005 - 23:49:33 PDT)
    - RE: AMBER: Leap compilation issues Ross Walker (Mon Jul 11 2005 - 10:05:25 PDT)
    - Re: AMBER: Leap compilation issues justin litchfield (Mon Jul 11 2005 - 18:25:10 PDT)
    - RE: AMBER: Leap compilation issues Ross Walker (Tue Jul 12 2005 - 09:47:05 PDT)
  - Re: AMBER: Leap compilation issues Andreas Svrcek-Seiler (Mon Jul 11 2005 - 03:43:39 PDT)
- Re: AMBER: Leap compilation issues Bill Ross (Mon Jul 11 2005 - 18:34:35 PDT)
  - Re: AMBER: Leap compilation issues justin litchfield (Mon Jul 11 2005 - 18:55:54 PDT)
- Re: AMBER: Leap compilation issues Jiten (Tue Jan 10 2006 - 19:19:14 PST)
Re: AMBER: Leap compilation issues Bill Ross (Sun Jul 10 2005 - 19:11:43 PDT)
AMBER: Critical PMEMD 8 Bugfix Robert Duke (Mon Jul 11 2005 - 05:38:59 PDT)
AMBER: Question about "nmanal" Yen-Ting Lai (Mon Jul 11 2005 - 07:11:25 PDT)
- Re: AMBER: Question about "nmanal" David A. Case (Mon Jul 11 2005 - 09:15:32 PDT)
- Re: AMBER: Question about "nmanal" Yen-Ting Lai (Tue Jul 12 2005 - 03:09:24 PDT)
- Re: AMBER: Question about "nmanal" Yen-Ting Lai (Tue Jul 12 2005 - 06:36:25 PDT)
  - Re: AMBER: Question about "nmanal" David A. Case (Tue Jul 12 2005 - 09:29:46 PDT)
AMBER: MM_PBSA help, please opitz.che.udel.edu (Mon Jul 11 2005 - 08:55:47 PDT)
- Re: AMBER: MM_PBSA help, please Scott Pendley (Mon Jul 11 2005 - 11:30:34 PDT)
- Re: AMBER: MM_PBSA help, please opitz.che.udel.edu (Mon Jul 11 2005 - 14:15:19 PDT)
  - Re: AMBER: MM_PBSA help, please Scott Pendley (Mon Jul 11 2005 - 14:37:50 PDT)
- Re: AMBER: MM_PBSA help, please opitz.che.udel.edu (Tue Jul 12 2005 - 07:19:05 PDT)
  - Re: AMBER: MM_PBSA help, please David A. Case (Tue Jul 12 2005 - 09:34:56 PDT)
- Re: AMBER: MM_PBSA help, please opitz.che.udel.edu (Tue Jul 12 2005 - 10:29:19 PDT)
  - Re: AMBER: MM_PBSA help, please Scott Pendley (Tue Jul 12 2005 - 14:57:08 PDT)
- Re: AMBER: MM_PBSA help, please opitz.che.udel.edu (Tue Jul 12 2005 - 15:18:50 PDT)
AMBER: Ptraj and order of operations Furse, Kristina Elisabet (Mon Jul 11 2005 - 17:26:09 PDT)
- Re: AMBER: Ptraj and order of operations Scott Pendley (Tue Jul 12 2005 - 16:22:29 PDT)
- Re: AMBER: Ptraj and order of operations Furse, Kristina Elisabet (Tue Jul 12 2005 - 18:07:04 PDT)
  - Re: AMBER: Ptraj and order of operations Petr Kulhanek (Wed Jul 13 2005 - 00:21:48 PDT)
- Re: AMBER: Ptraj and order of operations Furse, Kristina Elisabet (Wed Jul 13 2005 - 11:55:02 PDT)
  - AMBER: pdb files from traj file YoungJin Cho (Wed Jul 13 2005 - 14:06:30 PDT)
    - Re: AMBER: pdb files from traj file Carlos Simmerling (Wed Jul 13 2005 - 14:16:52 PDT)
    - RE: AMBER: pdb files from traj file Rhoad, Jonathan S. (Wed Jul 13 2005 - 14:22:56 PDT)
    - Re: AMBER: pdb files from traj file David LeBard (Wed Jul 13 2005 - 14:30:07 PDT)
    - RE: AMBER: pdb files from traj file Ross Walker (Wed Jul 13 2005 - 14:37:05 PDT)
AMBER: MD simulation on a protein solvated by a combination of some water models ? 荒牧武志 (Mon Jul 11 2005 - 21:10:12 PDT)
- RE: AMBER: MD simulation on a protein solvated by a combination of some water models ? Ross Walker (Tue Jul 12 2005 - 09:41:44 PDT)
AMBER: doubt on the value of Pressure on MD run Ananda Rama Krishnan Selvaraj (Tue Jul 12 2005 - 01:21:07 PDT)
- Re: AMBER: doubt on the value of Pressure on MD run Carlos Simmerling (Tue Jul 12 2005 - 04:07:08 PDT)
AMBER: Anal - problems with energy analysis Yogesh Sabnis (Tue Jul 12 2005 - 01:33:30 PDT)
- Re: AMBER: Anal - problems with energy analysis David A. Case (Tue Jul 12 2005 - 15:00:45 PDT)
AMBER: TI - frcmod file Oliver Hucke (Tue Jul 12 2005 - 12:21:44 PDT)
- Re: AMBER: TI - frcmod file Ilyas Yildirim (Tue Jul 12 2005 - 15:06:53 PDT)
  - Re: AMBER: TI - frcmod file Oliver Hucke (Tue Jul 12 2005 - 16:54:11 PDT)
    - Re: AMBER: TI - frcmod file Ilyas Yildirim (Wed Jul 13 2005 - 13:42:49 PDT)
    - Re: AMBER: TI - frcmod file David A. Case (Wed Jul 13 2005 - 14:10:56 PDT)
    - Re: AMBER: TI - frcmod file Ilyas Yildirim (Wed Jul 13 2005 - 14:32:41 PDT)
    - Re: AMBER: TI - frcmod file Oliver Hucke (Wed Jul 13 2005 - 14:18:08 PDT)
- FW: AMBER: TI - frcmod file Douali, Latifa (Wed Jul 13 2005 - 08:38:25 PDT)
  - Re: FW: AMBER: TI - frcmod file Ilyas Yildirim (Wed Jul 13 2005 - 13:51:00 PDT)
- RE: AMBER: TI - frcmod file Rhoad, Jonathan S. (Wed Jul 13 2005 - 14:03:17 PDT)
AMBER: question replica exchange acceptance ratio Zhuang (Tue Jul 12 2005 - 14:01:19 PDT)
- Re: AMBER: question replica exchange acceptance ratio Carlos Simmerling (Tue Jul 12 2005 - 14:42:55 PDT)
  - Re: AMBER: question replica exchange acceptance ratio Zhuang (Tue Jul 12 2005 - 15:39:47 PDT)
    - Re: AMBER: question replica exchange acceptance ratio Carlos Simmerling (Tue Jul 12 2005 - 16:43:01 PDT)
AMBER: Comparison of AMBER against DL-POLY Devashish Kumar (Tue Jul 12 2005 - 15:32:03 PDT)
AMBER: Amber 8: create topology for solvent - PBC box size problem Angela Liu (Wed Jul 13 2005 - 11:41:04 PDT)
AMBER: Amber 8: heterogeneous multiple copy LES method Angela Liu (Wed Jul 13 2005 - 11:47:08 PDT)
- Re: AMBER: Amber 8: heterogeneous multiple copy LES method Carlos Simmerling (Thu Jul 14 2005 - 14:17:07 PDT)
  - Re: AMBER: Amber 8: heterogeneous multiple copy LES method Angela Liu (Fri Jul 15 2005 - 07:16:23 PDT)
AMBER: lib file for nonstandard residue Eric Hu (Wed Jul 13 2005 - 16:52:19 PDT)
- Re: AMBER: lib file for nonstandard residue Bill Ross (Thu Jul 14 2005 - 15:20:25 PDT)
AMBER: units of mwcovar matrix befor conversion Kateryna Miroshnychenko (Thu Jul 14 2005 - 01:18:28 PDT)
- AMBER: units of mwcovar matrix befor conversion Chris Moth (Thu Feb 22 2007 - 15:01:57 PST)
Re:AMBER: MD simulation on a protein solvated by a combination of some water mod 荒牧武志 (Thu Jul 14 2005 - 02:56:39 PDT)
- Re: AMBER: MD simulation on a protein solvated by a combination of some water mod David A. Case (Thu Jul 14 2005 - 08:29:20 PDT)
AMBER: Modeling of a radical L Jin (Thu Jul 14 2005 - 03:46:20 PDT)
- Re: AMBER: Modeling of a radical David A. Case (Thu Jul 14 2005 - 08:48:54 PDT)
- Re: AMBER: Modeling of a radical L Jin (Mon Aug 01 2005 - 06:50:55 PDT)
AMBER: Leap question Kara Di Giorgio (Thu Jul 14 2005 - 08:10:12 PDT)
- Re: AMBER: Leap question David A. Case (Thu Jul 14 2005 - 08:39:59 PDT)
Re: AMBER: lib file for nonstandard residue Bill Ross (Thu Jul 14 2005 - 12:08:03 PDT)
- Re: AMBER: lib file for nonstandard residue Bill Ross (Thu Jul 14 2005 - 12:37:01 PDT)
  - Re: AMBER: lib file for nonstandard residue Eric Hu (Thu Jul 14 2005 - 15:02:35 PDT)
    - Re: AMBER: lib file for nonstandard residue David A. Case (Thu Jul 14 2005 - 15:35:47 PDT)
AMBER: Leap problem Kara Di Giorgio (Thu Jul 14 2005 - 17:06:50 PDT)
- Re: AMBER: Leap problem Furse, Kristina Elisabet (Thu Jul 14 2005 - 17:31:40 PDT)
  - Re: AMBER: Leap problem Kara Di Giorgio (Thu Jul 14 2005 - 18:19:00 PDT)
- Re: AMBER: Leap problem Oliver Hucke (Thu Jul 14 2005 - 18:48:52 PDT)
  - Re: AMBER: Leap problem Kara Di Giorgio (Fri Jul 15 2005 - 06:59:47 PDT)
AMBER: Can GB and MS work correctly together in mmpbsa? zhli_2000.126.com (Thu Jul 14 2005 - 19:38:08 PDT)
- Re: AMBER: Can GB and MS work correctly together in mmpbsa? Holger Gohlke (Thu Jul 14 2005 - 22:39:21 PDT)
  - Re: AMBER: Can GB and MS work correctly together in mmpbsa? zhli_2000.126.com (Fri Jul 15 2005 - 00:10:41 PDT)
    - Re: AMBER: Can GB and MS work correctly together in mmpbsa? Scott Pendley (Fri Jul 15 2005 - 10:46:46 PDT)
    - Re: AMBER: Can GB and MS work correctly together in mmpbsa? Scott Pendley (Fri Jul 15 2005 - 13:08:43 PDT)
    - Re: AMBER: Can GB and MS work correctly together in mmpbsa? zhli_2000.126.com (Sat Jul 16 2005 - 20:30:47 PDT)
    - Re: AMBER: Can GB and MS work correctly together in mmpbsa? Scott Pendley (Mon Jul 18 2005 - 10:31:29 PDT)
    - Re: AMBER: Can GB and MS work correctly together in mmpbsa? Alfonso Garcia-Sosa (Mon Jul 18 2005 - 12:16:21 PDT)
    - AMBER: Re: (瑞星提示-此邮件可能是垃圾邮件)Re: AMBER: Can GB and MS work correctly together in mmpbsa? zhli_2000.126.com (Mon Jul 18 2005 - 18:09:23 PDT)
    - AMBER: Re: (瑞星提示-此邮件可能是垃圾邮件)Re: AMBER: Can GB and MS work correctly together in mmpbsa? zhli_2000.126.com (Mon Jul 18 2005 - 18:23:39 PDT)
AMBER: Energy decomposition parameters Angelo Pugliese (Fri Jul 15 2005 - 01:57:21 PDT)
AMBER: P4 EM64T Intel Fortran Compile Problem Dawei Zhang (Fri Jul 15 2005 - 10:04:49 PDT)
- RE: AMBER: P4 EM64T Intel Fortran Compile Problem Ross Walker (Fri Jul 15 2005 - 10:26:36 PDT)
  - Re: AMBER: P4 EM64T Intel Fortran Compile Problem Dawei Zhang (Fri Jul 15 2005 - 13:54:39 PDT)
- Re: AMBER: P4 EM64T Intel Fortran Compile Problem Andreas Svrcek-Seiler (Fri Jul 15 2005 - 10:49:47 PDT)
AMBER: Re: Problems with ptraj/rdparm Thomas E. Cheatham, III (Fri Jul 15 2005 - 12:22:28 PDT)
AMBER: problem with protein ligand complex Claire Zerafa (Sat Jul 16 2005 - 09:31:56 PDT)
- Re: AMBER: problem with protein ligand complex David A. Case (Sat Jul 16 2005 - 12:05:02 PDT)
AMBER: random-coil polymer Varsha Goyal (Sat Jul 16 2005 - 15:35:19 PDT)
AMBER: AMBER-process_mdout.perl Praveena Gopal (Mon Jul 18 2005 - 00:26:19 PDT)
- Re: AMBER: AMBER-process_mdout.perl julien (Mon Jul 18 2005 - 00:48:01 PDT)
- Re: AMBER: AMBER-process_mdout.perl mathew k varghese (Mon Jul 18 2005 - 04:22:56 PDT)
- RE: AMBER: AMBER-process_mdout.perl Ross Walker (Mon Jul 18 2005 - 08:24:18 PDT)
AMBER: PMF calculations with TI using the sander Vitor Manuel Sousa F?x (Mon Jul 18 2005 - 00:30:59 PDT)
- Re: AMBER: PMF calculations with TI using the sander David A. Case (Mon Jul 18 2005 - 09:03:47 PDT)
AMBER: cap simulations questions Fabien CAILLIEZ (Mon Jul 18 2005 - 07:50:32 PDT)
- Re: AMBER: cap simulations questions David A. Case (Mon Jul 18 2005 - 09:01:34 PDT)
AMBER: segmentation fault in radial ptraj Kateryna Miroshnychenko (Mon Jul 18 2005 - 09:55:08 PDT)
AMBER: Using Antechamber with Gamess and other molecular manipulations Charles Karney (Mon Jul 18 2005 - 10:28:20 PDT)
AMBER: comparing md trajectories ayongye.chem.uga.edu (Mon Jul 18 2005 - 18:12:15 PDT)
- Re: AMBER: comparing md trajectories Carlos Simmerling (Tue Jul 19 2005 - 05:58:44 PDT)
  - Re: AMBER: comparing md trajectories Austin B. Yongye (Wed Aug 10 2005 - 14:16:08 PDT)
AMBER: mm_pbsa question Matthew Davies (Tue Jul 19 2005 - 03:07:51 PDT)
AMBER: pdb file and xleap Wai Keat Yam (Tue Jul 19 2005 - 03:06:50 PDT)
- RE: AMBER: pdb file and xleap Ross Walker (Tue Jul 19 2005 - 08:33:44 PDT)
  - RE: AMBER: pdb file and xleap Wai Keat Yam (Wed Jul 20 2005 - 23:01:07 PDT)
- AMBER: problem with xleap Alessio Coi (Fri Jul 22 2005 - 06:47:23 PDT)
  - Re: AMBER: problem with xleap David A. Case (Fri Jul 22 2005 - 08:59:24 PDT)
AMBER: Amber 7 Compiler Error Stephen P. Molnar, Ph.D. (Tue Jul 19 2005 - 05:26:14 PDT)
- RE: AMBER: Amber 7 Compiler Error Ross Walker (Tue Jul 19 2005 - 08:36:03 PDT)
  - Re: AMBER: Amber 7 Compiler Error Daniel Wetzler (Wed Jul 20 2005 - 02:38:25 PDT)
AMBER: Trouble with Amber8 Dustin (Tue Jul 19 2005 - 13:16:10 PDT)
- RE: AMBER: Trouble with Amber8 Ross Walker (Tue Jul 19 2005 - 13:41:27 PDT)
AMBER: Compiling Amber7 wint Intel Fortran v8 Compiler Stephen P. Molnar, Ph.D. (Tue Jul 19 2005 - 13:14:30 PDT)
AMBER: cap and ptraj Fabien CAILLIEZ (Tue Jul 19 2005 - 15:14:50 PDT)
AMBER: FW: Andrew Box (Tue Jul 19 2005 - 19:07:44 PDT)
- Re: AMBER: FW: David A. Case (Tue Jul 19 2005 - 19:46:48 PDT)
AMBER: P4 EM64T Intel Fortran Compile Problem Zhang Bing (Wed Jul 20 2005 - 19:24:20 PDT)
AMBER: Atom type :Si Ananda Rama Krishnan Selvaraj (Thu Jul 21 2005 - 12:02:23 PDT)
- Re: AMBER: Atom type :Si Stefano.Pieraccini.unimi.it (Fri Jul 22 2005 - 01:37:50 PDT)
- Re: AMBER: Atom type :Si Ananda Rama Krishnan Selvaraj (Fri Jul 22 2005 - 12:45:30 PDT)
AMBER: [OT] A nab programming question M. L. Dodson (Thu Jul 21 2005 - 13:07:09 PDT)
- Re: AMBER: [OT] A nab programming question David A. Case (Mon Jul 25 2005 - 14:35:49 PDT)
  - Re: AMBER: [OT] A nab programming question M. L. Dodson (Tue Jul 26 2005 - 07:32:47 PDT)
AMBER: Question about Prep file opitz.che.udel.edu (Thu Jul 21 2005 - 13:52:41 PDT)
- AMBER: Carbonane Kara Di Giorgio (Thu Jul 21 2005 - 17:55:26 PDT)
- Re: AMBER: Question about Prep file Marc Baaden (Thu Jul 21 2005 - 23:38:42 PDT)
  - Re: AMBER: Question about Prep file David A. Case (Fri Jul 22 2005 - 11:34:57 PDT)
- Re: AMBER: Question about Prep file opitz.che.udel.edu (Fri Jul 22 2005 - 12:21:20 PDT)
AMBER: Error in MD mathew k varghese (Thu Jul 21 2005 - 20:53:08 PDT)
- Re: AMBER: Error in MD Guanglei Cui (Thu Jul 21 2005 - 21:08:56 PDT)
AMBER: Lipid bilayer parameters nag raj (Fri Jul 22 2005 - 00:18:24 PDT)
AMBER: An atom name with 4 characters is not compatible with Leap ? Arnoult, Eric [PRDFR] (Fri Jul 22 2005 - 00:53:24 PDT)
- Re: AMBER: An atom name with 4 characters is not compatible with Leap ? ivan.mmb.pcb.ub.es (Fri Jul 22 2005 - 01:16:52 PDT)
- Re: AMBER: An atom name with 4 characters is not compatible with Leap ? Tim Meyer (Fri Jul 22 2005 - 08:06:52 PDT)
  - Re: AMBER: An atom name with 4 characters is not compatible with Leap ? David A. Case (Fri Jul 22 2005 - 10:27:31 PDT)
- Re: AMBER: An atom name with 4 characters is not compatible with Leap ? David A. Case (Fri Jul 22 2005 - 10:24:58 PDT)
AMBER: SHAKE error Agata Jurkiewicz (Fri Jul 22 2005 - 07:09:34 PDT)
- Re: AMBER: SHAKE error Carlos Simmerling (Fri Jul 22 2005 - 07:56:53 PDT)
- Re: AMBER: SHAKE error David A. Case (Fri Jul 22 2005 - 09:04:15 PDT)
  - Re: AMBER: SHAKE error Agata Jurkiewicz (Fri Jul 22 2005 - 10:01:16 PDT)
    - Re: AMBER: SHAKE error Carlos Simmerling (Fri Jul 22 2005 - 10:24:46 PDT)
    - Re: AMBER: SHAKE error Agata Jurkiewicz (Fri Jul 22 2005 - 12:12:10 PDT)
    - Re: AMBER: SHAKE error Ilyas Yildirim (Fri Jul 22 2005 - 12:23:06 PDT)
    - Re: AMBER: SHAKE error Carlos Simmerling (Fri Jul 22 2005 - 12:26:36 PDT)
    - Re: AMBER: SHAKE error David A. Case (Fri Jul 22 2005 - 13:46:42 PDT)
    - Re: AMBER: SHAKE error Agata Jurkiewicz (Fri Jul 22 2005 - 15:06:49 PDT)
    - Re: AMBER: SHAKE error David A. Case (Mon Jul 25 2005 - 16:57:02 PDT)
AMBER: nucgen bdna types Stern, Julie (Fri Jul 22 2005 - 18:01:20 PDT)
- Re: AMBER: nucgen bdna types David A. Case (Sun Jul 24 2005 - 16:42:44 PDT)
AMBER: mmpbsa test problem Suxin Zheng (Fri Jul 22 2005 - 18:41:11 PDT)
AMBER: Lipid bilayer parameters and charmm force field parameters nag raj (Fri Jul 22 2005 - 20:15:35 PDT)
Re: AMBER: Modeling of a radical Peter Gannett (Sat Jul 23 2005 - 07:21:25 PDT)
AMBER: Adding residues to a DNA sequence Kara Di Giorgio (Sun Jul 24 2005 - 18:50:45 PDT)
- Re: AMBER: Adding residues to a DNA sequence David A. Case (Mon Jul 25 2005 - 14:39:23 PDT)
  - Re: AMBER: Adding residues to a DNA sequence Kara Di Giorgio (Mon Jul 25 2005 - 19:20:53 PDT)
    - Re: AMBER: Adding residues to a DNA sequence David A. Case (Wed Jul 27 2005 - 14:31:16 PDT)
    - Re: AMBER: Adding residues to a DNA sequence Kara Di Giorgio (Fri Jul 29 2005 - 09:39:43 PDT)
AMBER: fit Yong Xu (Mon Jul 25 2005 - 02:04:57 PDT)
- Re: AMBER: fit Kateryna Miroshnychenko (Mon Jul 25 2005 - 03:11:11 PDT)
- AMBER: NTWPRY problem wenfei Li (Mon Jul 25 2005 - 08:44:31 PDT)
  - Re: AMBER: NTWPRY problem David A. Case (Mon Jul 25 2005 - 16:54:25 PDT)
  - Re: AMBER: NTWPRY problem wenfei Li (Mon Jul 25 2005 - 18:39:21 PDT)
  - Re: AMBER: NTWPRY problem wenfei Li (Mon Jul 25 2005 - 18:42:16 PDT)
  - Re: AMBER: NTWPRY problem wenfei Li (Mon Jul 25 2005 - 18:51:09 PDT)
AMBER: ptraj-acceptor mask format Peter Gannett (Mon Jul 25 2005 - 12:10:47 PDT)
- Re: AMBER: ptraj-acceptor mask format Thomas E. Cheatham, III (Tue Jul 26 2005 - 13:06:08 PDT)
- Re: AMBER: ptraj-acceptor mask format Peter Gannett (Wed Jul 27 2005 - 13:54:50 PDT)
AMBER: antechamber Dustin (Mon Jul 25 2005 - 13:30:40 PDT)
- Re: AMBER: antechamber David A. Case (Mon Jul 25 2005 - 16:42:32 PDT)
AMBER: nucgen H5T H3T Stern, Julie (Mon Jul 25 2005 - 18:55:52 PDT)
- Re: AMBER: nucgen H5T H3T David A. Case (Tue Jul 26 2005 - 07:54:32 PDT)
AMBER: potential of mean force calculation along reaction coordinates Ye Mei (Tue Jul 26 2005 - 00:04:00 PDT)
AMBER: Lipid parameters nag raj (Tue Jul 26 2005 - 03:55:22 PDT)
AMBER: Periodic box imaging using ptraj Grzegorz Jezierski (Tue Jul 26 2005 - 06:25:53 PDT)
- Re: AMBER: Periodic box imaging using ptraj Thomas E. Cheatham, III (Tue Jul 26 2005 - 13:11:39 PDT)
  - Re: AMBER: Periodic box imaging using ptraj Grzegorz Jezierski (Wed Jul 27 2005 - 02:27:24 PDT)
    - Re: AMBER: Periodic box imaging using ptraj Grzegorz Jezierski (Wed Jul 27 2005 - 04:28:29 PDT)
- RE: AMBER: Periodic box imaging using ptraj Ross Walker (Wed Jul 27 2005 - 09:28:05 PDT)
AMBER: why not minimize snapshots before MM/PBSA calculations JunJun Liu (Tue Jul 26 2005 - 08:02:00 PDT)
- RE: AMBER: why not minimize snapshots before MM/PBSA calculations Arnoult, Eric [PRDFR] (Wed Jul 27 2005 - 00:21:30 PDT)
RE: AMBER: Tutoial 8 (Case Study) Ross Walker (Tue Jul 26 2005 - 10:03:37 PDT)
AMBER: Thermodynamic Integration for conformational changes? Grzegorz Jezierski (Tue Jul 26 2005 - 10:33:00 PDT)
- Re: AMBER: Thermodynamic Integration for conformational changes? Carlos Simmerling (Tue Jul 26 2005 - 11:02:57 PDT)
- Re: AMBER: Thermodynamic Integration for conformational changes? David A. Case (Tue Jul 26 2005 - 11:42:54 PDT)
- AMBER: Format of atom specifiication after FIND Joseph Nachman (Tue Aug 16 2005 - 12:02:55 PDT)
AMBER: new residue Douali, Latifa (Tue Jul 26 2005 - 17:50:51 PDT)
- Re: AMBER: new residue Furse, Kristina Elisabet (Tue Jul 26 2005 - 18:40:51 PDT)
- RE: AMBER: new residue Douali, Latifa (Wed Jul 27 2005 - 09:09:01 PDT)
  - RE: AMBER: new residue Ross Walker (Wed Jul 27 2005 - 09:54:14 PDT)
  - Re: AMBER: new residue David A. Case (Wed Jul 27 2005 - 10:20:42 PDT)
- RE: AMBER: new residue Douali, Latifa (Wed Jul 27 2005 - 13:45:17 PDT)
  - Re: AMBER: new residue David A. Case (Wed Jul 27 2005 - 14:13:32 PDT)
- RE: AMBER: new residue Douali, Latifa (Wed Jul 27 2005 - 14:36:27 PDT)
RE: AMBER: An atom name with 4 characters is not compatible with Leap ? Arnoult, Eric [PRDFR] (Wed Jul 27 2005 - 00:20:27 PDT)
- Re: AMBER: An atom name with 4 characters is not compatible with Leap ? David A. Case (Wed Jul 27 2005 - 08:08:11 PDT)
- RE: AMBER: An atom name with 4 characters is not compatible with Leap ? Arnoult, Eric [PRDFR] (Wed Jul 27 2005 - 08:59:43 PDT)
  - Re: AMBER: An atom name with 4 characters is not compatible with Leap ? David A. Case (Wed Jul 27 2005 - 10:39:08 PDT)
AMBER: cutoff in ANAL Madjid Taghdir (Wed Jul 27 2005 - 01:06:54 PDT)
- Re: AMBER: cutoff in ANAL David A. Case (Thu Jul 28 2005 - 09:26:40 PDT)
AMBER: prepi format and question about it Ilyas Yildirim (Wed Jul 27 2005 - 02:20:00 PDT)
- Re: AMBER: prepi format and question about it David A. Case (Wed Jul 27 2005 - 07:57:30 PDT)
  - Re: AMBER: prepi format and question about it Ilyas Yildirim (Wed Jul 27 2005 - 22:10:36 PDT)
AMBER: Protein residue numbering Sukjoon Yoon (Wed Jul 27 2005 - 04:52:42 PDT)
AMBER: [FWD] water minimalization problems blakrose.gazeta.pl (Wed Jul 27 2005 - 08:46:47 PDT)
AMBER: How to insert a protein in lipid bilayer nag raj (Wed Jul 27 2005 - 09:56:07 PDT)
- Re: AMBER: How to insert a protein in lipid bilayer Yong Xu (Wed Jul 27 2005 - 18:47:22 PDT)
AMBER: pbsa problem Suxin Zheng (Wed Jul 27 2005 - 12:47:29 PDT)
AMBER: convert_trajectory Wei Chen (Wed Jul 27 2005 - 13:58:36 PDT)
- Re: AMBER: convert_trajectory Thomas E. Cheatham, III (Wed Jul 27 2005 - 14:27:57 PDT)
  - Re: AMBER: convert_trajectory Wei Chen (Wed Jul 27 2005 - 16:07:55 PDT)
    - Re: AMBER: convert_trajectory Thomas E. Cheatham, III (Wed Jul 27 2005 - 16:45:34 PDT)
    - Re: AMBER: convert_trajectory Wei Chen (Wed Jul 27 2005 - 19:06:28 PDT)
AMBER: Minimized structure Yam (Wed Jul 27 2005 - 20:02:03 PDT)
- Re: AMBER: Minimized structure Thomas E. Cheatham, III (Wed Jul 27 2005 - 20:47:28 PDT)
  - Re: AMBER: Minimized structure Yam (Thu Jul 28 2005 - 19:25:29 PDT)
    - Re: AMBER: Minimized structure Thomas E. Cheatham, III (Thu Jul 28 2005 - 20:09:55 PDT)
    - Re: AMBER: Minimized structure Yam (Thu Jul 28 2005 - 21:03:40 PDT)
    - RE: Re: AMBER: Minimized structure Linchen Gong (Wed Jul 27 2005 - 23:55:05 PDT)
    - Re: AMBER: Minimized structure Carlos Simmerling (Thu Jul 28 2005 - 03:53:45 PDT)
    - Re: AMBER: Minimized structure Vitor Manuel Sousa F?x (Thu Jul 28 2005 - 04:07:09 PDT)
AMBER: nucgen error (U not generated) mathew k varghese (Wed Jul 27 2005 - 20:28:51 PDT)
- Re: AMBER: nucgen error (U not generated) Thomas E. Cheatham, III (Wed Jul 27 2005 - 20:49:33 PDT)
AMBER: dihedral term in prmtop file Ye Mei (Thu Jul 28 2005 - 07:38:55 PDT)
- Re: AMBER: dihedral term in prmtop file Carlos Simmerling (Thu Jul 28 2005 - 07:59:36 PDT)
AMBER: Division by zero in sander Caleb S Howe (cshowe.Princeton.EDU) (Thu Jul 28 2005 - 07:57:00 PDT)
AMBER: Fatal Error on loading a pdb in xLeap Kara Di Giorgio (Thu Jul 28 2005 - 08:10:45 PDT)
- Re: AMBER: Fatal Error on loading a pdb in xLeap David A. Case (Thu Jul 28 2005 - 15:17:14 PDT)
- Re: AMBER: Fatal Error on loading a pdb in xLeap Ilyas Yildirim (Thu Jul 28 2005 - 20:56:32 PDT)
AMBER: ambpdb core dump Peter Gannett (Fri Jul 29 2005 - 04:27:46 PDT)
- Re: AMBER: ambpdb core dump David A. Case (Fri Jul 29 2005 - 07:40:03 PDT)
  - Re: AMBER: ambpdb core dump David A. Case (Fri Jul 29 2005 - 07:56:42 PDT)
AMBER: ptraj output missing opitz.che.udel.edu (Fri Jul 29 2005 - 08:05:19 PDT)
AMBER: temperature keep increasing in high temp. Hwankyu Lee (Fri Jul 29 2005 - 14:27:04 PDT)
- Re: AMBER: temperature keep increasing in high temp. Carlos Simmerling (Fri Jul 29 2005 - 17:28:42 PDT)
- RE: AMBER: temperature keep increasing in high temp. Yong Duan (Fri Jul 29 2005 - 20:43:52 PDT)
AMBER: mm_pbsa Wei Chen (Fri Jul 29 2005 - 17:10:46 PDT)
- Re: AMBER: mm_pbsa Suxin Zheng (Fri Jul 29 2005 - 17:39:15 PDT)
  - Re: AMBER: mm_pbsa Wei Chen (Fri Jul 29 2005 - 17:55:07 PDT)
    - Re: AMBER: mm_pbsa JunJun Liu (Fri Jul 29 2005 - 17:58:53 PDT)
    - Re: AMBER: mm_pbsa Wei Chen (Fri Jul 29 2005 - 18:09:13 PDT)
    - Re: AMBER: mm_pbsa JunJun Liu (Fri Jul 29 2005 - 19:22:20 PDT)
    - Re: AMBER: mm_pbsa Wei Chen (Fri Jul 29 2005 - 20:53:36 PDT)
AMBER: Failed sander runs for large systems Pratul K. Agarwal (Fri Jul 29 2005 - 19:41:44 PDT)
- Re: AMBER: Failed sander runs for large systems Guanglei Cui (Fri Jul 29 2005 - 21:33:27 PDT)
  - Re: AMBER: Failed sander runs for large systems David A. Case (Sat Jul 30 2005 - 09:57:14 PDT)
AMBER: Amber parameters for ADP zgleo (Fri Jul 29 2005 - 22:22:19 PDT)
- Re: AMBER: Amber parameters for ADP David A. Case (Sat Jul 30 2005 - 10:08:08 PDT)
AMBER: RESTARTED DUE TO LINMIN FAILURE Sukjoon Yoon (Fri Jul 29 2005 - 23:00:24 PDT)
- Re: AMBER: RESTARTED DUE TO LINMIN FAILURE David A. Case (Sat Jul 30 2005 - 09:59:19 PDT)
AMBER: questions about MG ions JIANING WANG (Sun Jul 31 2005 - 16:12:36 PDT)
- Re: AMBER: questions about MG ions Kara Di Giorgio (Sun Jul 31 2005 - 21:55:46 PDT)
- Re: AMBER: questions about MG ions JIANING WANG (Mon Aug 01 2005 - 07:27:45 PDT)
AMBER: AMBER8 crashes machine(nodes) under IBM compiler, Suse Linux, amd IBM loadleveler Soo (Sun Jul 31 2005 - 19:45:01 PDT)
AMBER: coordinated water molecules deleted when addions Ye Mei (Mon Aug 01 2005 - 02:20:11 PDT)
- Re: AMBER: coordinated water molecules deleted when addions David A. Case (Mon Aug 01 2005 - 06:39:39 PDT)
- RE: AMBER: coordinated water molecules deleted when addions Ross Walker (Mon Aug 01 2005 - 10:09:17 PDT)
AMBER: ptraj help, how to enable disabled ptraj routine? opitz.che.udel.edu (Mon Aug 01 2005 - 08:19:20 PDT)
- Re: AMBER: ptraj help, how to enable disabled ptraj routine? Thomas E. Cheatham, III (Mon Aug 01 2005 - 13:51:27 PDT)
AMBER: antechamber problem using RESP luckyang.gmail.com (Mon Aug 01 2005 - 18:29:26 PDT)
AMBER: AMBER8 limitation of memory in QM/MM calculation nadtanet nunthaboot (Mon Aug 01 2005 - 19:21:59 PDT)
- RE: AMBER: AMBER8 limitation of memory in QM/MM calculation Ross Walker (Mon Aug 01 2005 - 19:52:32 PDT)
- RE: AMBER: AMBER8 limitation of memory in QM/MM calculation Ross Walker (Mon Aug 01 2005 - 19:52:29 PDT)
AMBER: strange minimalization output blakrose.gazeta.pl (Tue Aug 02 2005 - 07:56:38 PDT)
- RE: AMBER: strange minimalization output Ross Walker (Tue Aug 02 2005 - 08:47:59 PDT)
AMBER: Leap set head/tail question Kara Di Giorgio (Tue Aug 02 2005 - 11:01:08 PDT)
- RE: AMBER: Leap set head/tail question Rhoad, Jonathan S. (Tue Aug 02 2005 - 11:10:42 PDT)
- RE: AMBER: Leap set head/tail question Ross Walker (Tue Aug 02 2005 - 11:28:03 PDT)
  - RE: AMBER: Leap set head/tail question Ilyas Yildirim (Wed Aug 03 2005 - 14:40:23 PDT)
AMBER: Boron and Amber Kara Di Giorgio (Tue Aug 02 2005 - 13:18:46 PDT)
AMBER: bond breaking/ energetic ion vannajan.chiangmai.ac.th (Tue Aug 02 2005 - 19:11:16 PDT)
- RE: AMBER: bond breaking/ energetic ion Ross Walker (Tue Aug 02 2005 - 19:26:02 PDT)
AMBER: power supply crash==>boot problems Kristof Stevens (Wed Aug 03 2005 - 01:20:08 PDT)
- Re: AMBER: power supply crash==>boot problems David LeBard (Wed Aug 03 2005 - 10:20:30 PDT)
AMBER: bond parameters Gustavo Pierdominici Sottile (Wed Aug 03 2005 - 07:39:34 PDT)
- Re: AMBER: bond parameters ivan.mmb.pcb.ub.es (Wed Aug 03 2005 - 07:54:29 PDT)
- RE: AMBER: bond parameters Ross Walker (Wed Aug 03 2005 - 09:11:00 PDT)
AMBER: installing amber7 on 64bit cluster MURAT CETINKAYA (Wed Aug 03 2005 - 08:46:20 PDT)
- RE: AMBER: installing amber7 on 64bit cluster Zhang Bing (Wed Aug 03 2005 - 18:33:55 PDT)
- RE: AMBER: installing amber7 on 64bit cluster Ross Walker (Wed Aug 03 2005 - 23:39:22 PDT)
- RE: AMBER: installing amber7 on 64bit cluster MURAT CETINKAYA (Thu Aug 04 2005 - 08:04:47 PDT)
AMBER: Strange difference in speed between Altix (Itanium2) and Tezro (MIPS) SGI for small GB/SA run David.Maxwell.di.mdacc.tmc.edu (Wed Aug 03 2005 - 10:39:43 PDT)
- Re: AMBER: Strange difference in speed between Altix (Itanium2) and Tezro (MIPS) SGI for small GB/SA run Roberto Gomperts (Thu Aug 04 2005 - 04:57:12 PDT)
Re: AMBER: bond breaking/ energetic ion Bill Ross (Wed Aug 03 2005 - 10:41:36 PDT)
AMBER: Error with antechamber Joseph Fernandez (Wed Aug 03 2005 - 12:45:29 PDT)
- Re: AMBER: Error with antechamber David A. Case (Fri Aug 05 2005 - 05:26:36 PDT)
AMBER: a trivial question Linchen Gong (Thu Aug 04 2005 - 02:14:04 PDT)
- Re: AMBER: a trivial question Carlos Simmerling (Thu Aug 04 2005 - 04:28:36 PDT)
  - RE: Re: AMBER: a trivial question Linchen Gong (Fri Aug 05 2005 - 08:26:25 PDT)
    - RE: Re: AMBER: a trivial question David LeBard (Fri Aug 05 2005 - 09:32:47 PDT)
    - RE: RE: Re: AMBER: a trivial question Linchen Gong (Fri Aug 05 2005 - 19:52:39 PDT)
AMBER: nmode Wei Chen (Thu Aug 04 2005 - 11:04:17 PDT)
- RE: AMBER: nmode Yong Duan (Thu Aug 04 2005 - 17:03:26 PDT)
  - RE: AMBER: nmode Wei Chen (Thu Aug 04 2005 - 20:07:43 PDT)
AMBER: Incorrect imaging when using Periodic Boundary Conditions in NAMD with AMBER parameters Grzegorz Jezierski (Thu Aug 04 2005 - 11:24:42 PDT)
AMBER: about salt bridges xueping (Thu Aug 04 2005 - 23:34:18 PDT)
- Re: AMBER: about salt bridges Carlos Simmerling (Fri Aug 05 2005 - 04:53:06 PDT)
AMBER: Conformational energy (QM) for parameterization yuann (Fri Aug 05 2005 - 03:09:14 PDT)
AMBER: leap question Kara Di Giorgio (Fri Aug 05 2005 - 09:38:47 PDT)
- Re: AMBER: leap question David A. Case (Fri Aug 05 2005 - 15:34:39 PDT)
  - Re: AMBER: leap question Kara Di Giorgio (Fri Aug 05 2005 - 18:56:40 PDT)
    - Re: AMBER: leap question David A. Case (Sat Aug 06 2005 - 04:33:44 PDT)
    - Re: AMBER: leap question Kara Di Giorgio (Sat Aug 06 2005 - 20:02:45 PDT)
AMBER: NMR refinement Lei Jia (Fri Aug 05 2005 - 12:50:29 PDT)
AMBER: Convert .prmtop (AMBER7/8) to old format (AMBER6) Hwankyu Lee (Fri Aug 05 2005 - 20:44:07 PDT)
- Re: AMBER: Convert .prmtop (AMBER7/8) to old format (AMBER6) David A. Case (Sat Aug 06 2005 - 04:26:14 PDT)
- RE: AMBER: Convert .prmtop (AMBER7/8) to old format (AMBER6) Ross Walker (Sat Aug 06 2005 - 11:47:26 PDT)
AMBER: is calculated B-factors always smaller than experimental ones? haixiao jin (Sun Aug 07 2005 - 07:57:54 PDT)
- Re: AMBER: is calculated B-factors always smaller than experimental ones? Carlos Simmerling (Sun Aug 07 2005 - 08:23:42 PDT)
  - Re: AMBER: is calculated B-factors always smaller than experimental ones? haixiao jin (Sun Aug 07 2005 - 22:33:48 PDT)
AMBER: How to calculate hydrogen bond involved with water molecules quickly? haixiao jin (Sun Aug 07 2005 - 22:07:48 PDT)
AMBER: Zymeworks job posting John Vieceli (Mon Aug 08 2005 - 10:11:42 PDT)
AMBER: RE: is calculated B-factors always smaller than experimental ones? Yong Duan (Mon Aug 08 2005 - 11:24:26 PDT)
- Re: AMBER: RE: is calculated B-factors always smaller than experimental ones? haixiao jin (Mon Aug 08 2005 - 22:47:19 PDT)
AMBER: Tutorial question and some more... blakrose.gazeta.pl (Mon Aug 08 2005 - 23:49:45 PDT)
- RE: AMBER: Tutorial question and some more... Ross Walker (Tue Aug 09 2005 - 12:03:01 PDT)
- Re: AMBER: Tutorial question and some more... blakrose.gazeta.pl (Tue Aug 09 2005 - 14:00:20 PDT)
  - Re: AMBER: Tutorial question and some more... Yam (Wed Aug 10 2005 - 00:50:54 PDT)
Re: AMBER: Tutorial question and some more... Bill Ross (Tue Aug 09 2005 - 11:30:46 PDT)
AMBER: The “crystallographic” waters should be retained or deleted? haixiao jin (Wed Aug 10 2005 - 05:35:34 PDT)
AMBER: Creating protonated cytidine residue Peter Cornish (Wed Aug 10 2005 - 07:57:17 PDT)
AMBER: replica exchange Anthony Cruz (Wed Aug 10 2005 - 11:13:41 PDT)
AMBER: ptraj command inputs opitz.che.udel.edu (Wed Aug 10 2005 - 15:29:34 PDT)
- Re: AMBER: ptraj command inputs Thomas E. Cheatham, III (Wed Aug 10 2005 - 15:43:31 PDT)
AMBER: group-based cutoff John Vieceli (Wed Aug 10 2005 - 17:44:56 PDT)
- RE: AMBER: group-based cutoff Ross Walker (Wed Aug 10 2005 - 18:57:35 PDT)
- Re: AMBER: group-based cutoff Thomas E. Cheatham, III (Wed Aug 10 2005 - 19:53:38 PDT)
AMBER: solvent problem blakrose.gazeta.pl (Thu Aug 11 2005 - 00:14:17 PDT)
AMBER: Atom type problem nag raj (Thu Aug 11 2005 - 07:18:31 PDT)
- Re: AMBER: Atom type problem Ilyas Yildirim (Thu Aug 11 2005 - 08:15:28 PDT)
- Re: AMBER: Atom type problem Ilyas Yildirim (Thu Aug 11 2005 - 09:40:12 PDT)
AMBER: molsurf: problem with calculate surface area Magne Olufsen (Fri Aug 12 2005 - 01:06:45 PDT)
AMBER: How is the origin of the grid defined?(PBSA question) JunJun Liu (Sun Aug 14 2005 - 09:35:46 PDT)
- Re: AMBER: How is the origin of the grid defined?(PBSA question) Ray Luo (Sat Aug 13 2005 - 12:40:54 PDT)
  - Re: AMBER: How is the origin of the grid defined?(PBSA question) Suxin Zheng (Tue Aug 16 2005 - 13:54:27 PDT)
    - Re: AMBER: How is the origin of the grid defined?(PBSA question) Ray Luo (Tue Aug 16 2005 - 06:46:01 PDT)
- Re: AMBER: How is the origin of the grid defined?(PBSA question) JunJun Liu (Tue Aug 23 2005 - 01:46:03 PDT)
  - Re: AMBER: How is the origin of the grid defined?(PBSA question) Ray Luo (Mon Aug 22 2005 - 18:15:48 PDT)
AMBER: wtmol and resp Guanglei Cui (Mon Aug 15 2005 - 07:59:42 PDT)
AMBER: difference of energy in sander and nmode in amber 7 sebnem (Mon Aug 15 2005 - 14:55:24 PDT)
- Re: AMBER: difference of energy in sander and nmode in amber 7 sebnem (Wed Aug 17 2005 - 08:39:02 PDT)
- Re: AMBER: difference of energy in sander and nmode in amber 7 David A. Case (Wed Aug 17 2005 - 09:36:11 PDT)
  - Re: AMBER: difference of energy in sander and nmode in amber 7 sebnem (Wed Aug 17 2005 - 10:51:15 PDT)
    - Re: AMBER: difference of energy in sander and nmode in amber 7 David A. Case (Thu Aug 18 2005 - 07:39:55 PDT)
AMBER: AMBER on g5 10.4 w/g95 or gfortran Rachel Burdge (Tue Aug 16 2005 - 08:12:40 PDT)
- Re: AMBER: AMBER on g5 10.4 w/g95 or gfortran justin litchfield (Tue Aug 16 2005 - 09:27:26 PDT)
AMBER: min problem Gustavo Pierdominici Sottile (Tue Aug 16 2005 - 16:05:56 PDT)
- RE: AMBER: min problem Ross Walker (Fri Aug 19 2005 - 11:52:36 PDT)
AMBER: Solution for those who have mpich problem while building the parallel version of AMBER 8 Ilyas Yildirim (Tue Aug 16 2005 - 18:40:11 PDT)
- Re: AMBER: Solution for those who have mpich problem while building the parallel version of AMBER 8 S. Teletchéa (Wed Aug 17 2005 - 16:22:43 PDT)
  - Re: AMBER: Solution for those who have mpich problem while building the parallel version of AMBER 8 Ilyas Yildirim (Wed Aug 17 2005 - 17:04:37 PDT)
AMBER: QM/MM jojartb.pharm.u-szeged.hu (Wed Aug 17 2005 - 04:42:06 PDT)
- RE: AMBER: QM/MM Ross Walker (Fri Aug 19 2005 - 11:27:44 PDT)
AMBER: glycan Wei Chen (Wed Aug 17 2005 - 11:25:27 PDT)
- Re: AMBER: glycan kkirschn.hamilton.edu (Wed Aug 17 2005 - 12:55:35 PDT)
  - Re: AMBER: glycan Wei Chen (Wed Aug 17 2005 - 15:29:52 PDT)
AMBER: residence time of electrons/holes in DNA ioana.pegasus.arc.nasa.gov (Wed Aug 17 2005 - 14:48:43 PDT)
- Re: AMBER: residence time of electrons/holes in DNA David LeBard (Wed Aug 17 2005 - 16:43:47 PDT)
AMBER: Energy Comparisons Kara Di Giorgio (Wed Aug 17 2005 - 15:00:44 PDT)
- Re: AMBER: Energy Comparisons Wei Chen (Wed Aug 17 2005 - 15:24:08 PDT)
AMBER: Amber 8: all_nucleic94.lib nucleotide geometry Angela Liu (Wed Aug 17 2005 - 15:42:03 PDT)
Re: AMBER: Amber 8: all_nucleic94.lib nucleotide geometry Bill Ross (Wed Aug 17 2005 - 16:04:49 PDT)
AMBER: ew_bspline.h error khn _ (Wed Aug 17 2005 - 20:33:08 PDT)
- Re: AMBER: ew_bspline.h error Michael Crowley (Fri Aug 19 2005 - 08:54:39 PDT)
- RE: AMBER: ew_bspline.h error Ross Walker (Fri Aug 19 2005 - 11:33:57 PDT)
- RE: AMBER: ew_bspline.h error Ross Walker (Fri Aug 26 2005 - 08:03:29 PDT)
AMBER: mm_pbsa amit.mbu.iisc.ernet.in (Thu Aug 18 2005 - 14:04:40 PDT)
- Re: AMBER: mm_pbsa Ray Luo (Thu Aug 18 2005 - 14:43:51 PDT)
  - Re: AMBER: mm_pbsa amit.mbu.iisc.ernet.in (Sat Aug 20 2005 - 00:46:24 PDT)
    - Re: AMBER: mm_pbsa Ray Luo (Sun Aug 21 2005 - 11:29:41 PDT)
AMBER: parm99.dat non-bonded parameters Angela Liu (Thu Aug 18 2005 - 15:00:45 PDT)
- Re: AMBER: parm99.dat non-bonded parameters Anthony Fejes (Fri Aug 19 2005 - 09:35:36 PDT)
  - Re: AMBER: parm99.dat non-bonded parameters Angela Liu (Fri Aug 19 2005 - 10:44:03 PDT)
    - Re: AMBER: parm99.dat non-bonded parameters Anthony Fejes (Fri Aug 19 2005 - 11:18:36 PDT)
AMBER: parallel amber8 with mpi through qsnet Ye Mei (Thu Aug 18 2005 - 19:11:55 PDT)
- RE: AMBER: parallel amber8 with mpi through qsnet Ross Walker (Fri Aug 19 2005 - 11:42:40 PDT)
AMBER: How to construct a lipid bilayer nag raj (Thu Aug 18 2005 - 22:01:06 PDT)
AMBER: ptraj correlation facility Simon Whitehead (Fri Aug 19 2005 - 02:15:41 PDT)
AMBER: amber8installation cbala.igib.res.in (Fri Aug 19 2005 - 05:53:03 PDT)
- Re: AMBER: amber8installation Carlos Simmerling (Fri Aug 19 2005 - 05:13:24 PDT)
  - Re: AMBER: amber8installation cbala.igib.res.in (Fri Aug 19 2005 - 08:33:44 PDT)
AMBER: shake Gustavo Pierdominici Sottile (Fri Aug 19 2005 - 09:37:46 PDT)
- Re: AMBER: shake Carlos Simmerling (Fri Aug 19 2005 - 09:45:16 PDT)
AMBER: structures extracted from mmpbsa Lwin, ThuZar (Fri Aug 19 2005 - 16:25:44 PDT)
AMBER: minimization stuck problem blakrose.gazeta.pl (Sat Aug 20 2005 - 04:46:07 PDT)
- Re: AMBER: minimization stuck problem Carlos Simmerling (Sat Aug 20 2005 - 05:10:45 PDT)
  - RE: AMBER: minimization stuck problem Yong Duan (Sat Aug 20 2005 - 06:05:03 PDT)
- RE: AMBER: minimization stuck problem Ross Walker (Sat Aug 20 2005 - 11:00:11 PDT)
AMBER: minimization stuck problem blakrose.gazeta.pl (Sat Aug 20 2005 - 05:32:31 PDT)
AMBER: AMBER topology file format santanu chatterjee (Mon Aug 22 2005 - 02:18:18 PDT)
AMBER: Restraints kanon gemini (Mon Aug 22 2005 - 03:58:25 PDT)
Re: AMBER: Restraints Carlos Simmerling (Mon Aug 22 2005 - 05:12:26 PDT)
AMBER: minimization stuck problem blakrose.gazeta.pl (Mon Aug 22 2005 - 08:17:29 PDT)
- Re: AMBER: minimization stuck problem blakrose.gazeta.pl (Sat Aug 20 2005 - 14:11:54 PDT)
  - RE: AMBER: minimization stuck problem Ross Walker (Sun Aug 21 2005 - 13:02:09 PDT)
    - Re: AMBER: minimization stuck problem Adrian Roitberg (Sun Aug 21 2005 - 14:29:53 PDT)
- RE: AMBER: minimization stuck problem Ross Walker (Tue Aug 23 2005 - 08:22:53 PDT)
AMBER: How to deal with the problem that a molecule go out the virtual box in vaccum Li Su (Tue Aug 23 2005 - 10:37:38 PDT)
- RE: AMBER: How to deal with the problem that a molecule go out the virtual box in vaccum Ross Walker (Tue Aug 23 2005 - 21:42:52 PDT)
AMBER: mm_pbsa energy decomposition error amit.mbu.iisc.ernet.in (Wed Aug 24 2005 - 05:06:34 PDT)
- Re: AMBER: mm_pbsa energy decomposition error David A. Case (Wed Aug 24 2005 - 06:26:49 PDT)
  - Re: AMBER: mm_pbsa energy decomposition error amit.mbu.iisc.ernet.in (Thu Aug 25 2005 - 04:57:18 PDT)
AMBER: essential dynamics Anthony Cruz (Wed Aug 24 2005 - 10:50:03 PDT)
- Re: AMBER: essential dynamics John Mongan (Wed Aug 24 2005 - 09:27:46 PDT)
AMBER: Replica exchange Anthony Cruz (Wed Aug 24 2005 - 10:57:42 PDT)
AMBER: a problem encountered when trying to equalibrate alanine dipeptide in explicit water Li Su (Wed Aug 24 2005 - 10:36:06 PDT)
- RE: AMBER: a problem encountered when trying to equalibrate alanine dipeptide in explicit water Ross Walker (Wed Aug 24 2005 - 10:45:59 PDT)
AMBER: ptraj efficiency justin litchfield (Wed Aug 24 2005 - 11:13:03 PDT)
- RE: AMBER: ptraj efficiency Ross Walker (Wed Aug 24 2005 - 11:29:36 PDT)
AMBER: RED II and Gaussian Raviprasad Aduri (Wed Aug 24 2005 - 19:01:46 PDT)
- Re: AMBER: RED II and Gaussian FyD (Sat Aug 27 2005 - 08:02:09 PDT)
  - Re: AMBER: RED II and Gaussian rpaduri.chem.wayne.edu (Sat Aug 27 2005 - 15:40:53 PDT)
AMBER: Antechamber error "Cannot successfully assign bond type for this molecule" Whitney Allen (Thu Aug 25 2005 - 09:13:11 PDT)
- RE: AMBER: Antechamber error "Cannot successfully assign bond type for this molecule" Junmei Wang (Fri Sep 02 2005 - 13:30:29 PDT)
AMBER: PLease remove my post rpaduri.chem.wayne.edu (Thu Aug 25 2005 - 09:08:38 PDT)
AMBER: Add constraints over time Andrew Box (Thu Aug 25 2005 - 22:51:49 PDT)
- RE: AMBER: Add constraints over time Ross Walker (Fri Aug 26 2005 - 09:41:04 PDT)
AMBER: minimization blakrose.gazeta.pl (Fri Aug 26 2005 - 05:20:25 PDT)
- RE: AMBER: minimization Ross Walker (Fri Aug 26 2005 - 08:07:59 PDT)
AMBER: replica exchange Anthony Cruz (Fri Aug 26 2005 - 09:53:48 PDT)
Re: AMBER: replica exchange Carlos Simmerling (Fri Aug 26 2005 - 08:16:51 PDT)
- Re: AMBER: replica exchange Anthony Cruz (Fri Aug 26 2005 - 11:14:47 PDT)
  - AMBER: NRESPA Sergio E. Wong (Sat Aug 27 2005 - 12:12:29 PDT)
AMBER: compilation problem (Mac OS X.4) Mark H. Schofield (Fri Aug 26 2005 - 09:07:05 PDT)
Re: AMBER: Replica exchange Carlos Simmerling (Sun Aug 28 2005 - 06:16:46 PDT)
- Re: AMBER: Replica exchange Anthony Cruz (Mon Aug 29 2005 - 05:46:52 PDT)
AMBER: can I setup a simulation with restrain the COM of a group to a reference structure? bzlu.ucsd.edu (Sun Aug 28 2005 - 13:32:33 PDT)
AMBER: Temperature equilibration Anthony Cruz (Mon Aug 29 2005 - 05:44:04 PDT)
- RE: AMBER: Temperature equilibration Ross Walker (Mon Aug 29 2005 - 08:44:08 PDT)
  - Re: AMBER: Temperature equilibration Anthony Cruz (Mon Aug 29 2005 - 12:47:36 PDT)
AMBER: params for cofactors Michael Dolan (Mon Aug 29 2005 - 12:54:41 PDT)
- RE: AMBER: params for cofactors Ross Walker (Mon Aug 29 2005 - 13:10:55 PDT)
- Re: AMBER: params for cofactors Michael Dolan (Mon Aug 29 2005 - 13:23:10 PDT)
AMBER: anwar.cdfd.org.in (Mon Aug 29 2005 - 20:59:49 PDT)
AMBER: floating point exception anwar.cdfd.org.in (Mon Aug 29 2005 - 21:00:31 PDT)
- AMBER: floating point exception anwar.cdfd.org.in (Tue Aug 30 2005 - 19:27:47 PDT)
  - RE: AMBER: floating point exception Ross Walker (Wed Aug 31 2005 - 09:51:27 PDT)
AMBER: in vacuo? Yam (Tue Aug 30 2005 - 02:53:07 PDT)
- Re: AMBER: in vacuo? blakrose.gazeta.pl (Wed Aug 31 2005 - 02:44:00 PDT)
  - AMBER: MM-PBSA and 1-4 nonbonded interactions Nelson Fonseca (Wed Aug 31 2005 - 07:55:31 PDT)
AMBER: nmode minimization and normal mode calculation Bing Xiong (Tue Aug 30 2005 - 06:53:11 PDT)
- Re: AMBER: nmode minimization and normal mode calculation David A. Case (Tue Aug 30 2005 - 07:38:14 PDT)
AMBER: Temperature regulation Monica Civera (Tue Aug 30 2005 - 07:43:26 PDT)
- Re: AMBER: Temperature regulation David A. Case (Tue Aug 30 2005 - 15:45:13 PDT)
AMBER: Lennard-Jones coeff... Pavan G (Tue Aug 30 2005 - 13:26:49 PDT)
AMBER: Re:Antechamber Raviprasad Aduri (Tue Aug 30 2005 - 16:34:33 PDT)
AMBER: disulfide bonds by "bond" or "edit -> draw" ? Benjamin Juhl (Wed Aug 31 2005 - 09:23:45 PDT)
- RE: AMBER: disulfide bonds by "bond" or "edit -> draw" ? Ross Walker (Wed Aug 31 2005 - 09:48:39 PDT)
Re: AMBER: disulfide bonds by "bond" or "edit -> draw" ? Bill Ross (Wed Aug 31 2005 - 09:57:23 PDT)
AMBER: Interpreting Amber8 Benchmark Results Nikhil Kelshikar $nkelshik$ (Wed Aug 31 2005 - 10:07:24 PDT)
- RE: AMBER: Interpreting Amber8 Benchmark Results Ross Walker (Wed Aug 31 2005 - 13:09:20 PDT)
  - Re: AMBER: Interpreting Amber8 Benchmark Results Robert Duke (Wed Aug 31 2005 - 13:34:42 PDT)
- RE: AMBER: Interpreting Amber8 Benchmark Results Bill Ross (Wed Aug 31 2005 - 13:44:55 PDT)
  - RE: AMBER: Interpreting Amber8 Benchmark Results Ross Walker (Wed Aug 31 2005 - 14:00:55 PDT)
- RE: AMBER: Interpreting Amber8 Benchmark Results Bill Ross (Wed Aug 31 2005 - 14:29:58 PDT)
  - Re: AMBER: Interpreting Amber8 Benchmark Results Robert Duke (Wed Aug 31 2005 - 14:37:53 PDT)
AMBER: Why are some of the Lennard-Jones coeffs 0 ? Pavan G (Wed Aug 31 2005 - 10:18:28 PDT)
- Re: AMBER: Why are some of the Lennard-Jones coeffs 0 ? Thomas E. Cheatham, III (Wed Aug 31 2005 - 10:53:38 PDT)
AMBER: addles question Kevin Murphy (Wed Aug 31 2005 - 14:46:00 PDT)
- AMBER: broblem of replica exchange MD with polarizable force field wenfei Li (Wed Aug 31 2005 - 17:51:32 PDT)
  - Re: AMBER: broblem of replica exchange MD with polarizable force field Guanglei Cui (Thu Sep 01 2005 - 08:01:46 PDT)
    - AMBER: unstable MD velocities hayden (Thu Sep 01 2005 - 10:38:11 PDT)
    - RE: AMBER: unstable MD velocities Ross Walker (Thu Sep 01 2005 - 11:06:08 PDT)
- Re: AMBER: addles question Carlos Simmerling (Fri Sep 02 2005 - 12:07:30 PDT)
  - AMBER: RED-II failure to recognize GAMESS output Cenk Andac (Fri Sep 02 2005 - 13:47:07 PDT)
    - Re: AMBER: RED-II failure to recognize GAMESS output FyD (Sat Sep 03 2005 - 00:33:38 PDT)
    - Re: AMBER: RED-II failure to recognize GAMESS output Cenk Andac (Tue Sep 06 2005 - 01:30:19 PDT)
    - Re: AMBER: RED-II failure to recognize GAMESS output FyD (Tue Sep 06 2005 - 01:48:41 PDT)
AMBER: Opinion needed-Solvents chaiann ng (Wed Aug 31 2005 - 18:59:00 PDT)
AMBER: ptraj problem Zhang Bing (Thu Sep 01 2005 - 00:01:20 PDT)
- Re: AMBER: ptraj problem Bill Ross (Mon Aug 25 2003 - 12:14:23 PDT)
- Re: AMBER: ptraj problem Thomas E. Cheatham, III (Thu Sep 01 2005 - 13:54:24 PDT)
AMBER: H-bond energy Sebastian Fernandez Alberti (Thu Sep 01 2005 - 06:16:14 PDT)
AMBER: Tyrosine CZ Parameterization Bug continues in Amber 8 Chris Moth (Thu Sep 01 2005 - 15:04:21 PDT)
AMBER: Error in MD run! Ananda Rama Krishnan Selvaraj (Fri Sep 02 2005 - 03:42:54 PDT)
- Re: AMBER: Error in MD run! David A. Case (Fri Sep 02 2005 - 09:27:33 PDT)
AMBER: Equilibration MD mathew k varghese (Fri Sep 02 2005 - 22:55:22 PDT)
AMBER: fixing protein for minimisation of solvent Simon Whitehead (Sat Sep 03 2005 - 03:56:55 PDT)
Re: AMBER: fixing protein for minimisation of solvent Bill Ross (Sat Sep 03 2005 - 09:49:18 PDT)
Re: AMBER: Equilibration MD Bill Ross (Sat Sep 03 2005 - 09:53:17 PDT)
AMBER: STARTING WHERE I LEFT OFF Claire Zerafa (Sat Sep 03 2005 - 10:13:59 PDT)
- Re: AMBER: STARTING WHERE I LEFT OFF Bill Ross (Sat Sep 03 2005 - 11:12:40 PDT)
  - Re: AMBER: STARTING WHERE I LEFT OFF Carlos Simmerling (Sat Sep 03 2005 - 11:28:27 PDT)
- Re: AMBER: STARTING WHERE I LEFT OFF Bill Ross (Sat Sep 03 2005 - 15:55:19 PDT)
Re: AMBER: STARTING WHERE I LEFT OFF Bill Ross (Sat Sep 03 2005 - 10:36:23 PDT)
- Re: AMBER: STARTING WHERE I LEFT OFF Claire Zerafa (Sat Sep 03 2005 - 10:49:31 PDT)
- Re: AMBER: STARTING WHERE I LEFT OFF Carlos Simmerling (Sat Sep 03 2005 - 10:58:29 PDT)
AMBER: MM-PBSA error MURAT CETINKAYA (Mon Sep 05 2005 - 09:00:13 PDT)
AMBER: RED and Multi-Orientation Raviprasad Aduri (Mon Sep 05 2005 - 19:34:56 PDT)
- Re: AMBER: RED and Multi-Orientation FyD (Tue Sep 06 2005 - 00:35:58 PDT)
  - Re: AMBER: RED and Multi-Orientation Raviprasad Aduri (Tue Sep 06 2005 - 18:24:29 PDT)
    - Re: AMBER: RED and Multi-Orientation FyD (Wed Sep 07 2005 - 04:29:54 PDT)
AMBER: How to get PDB structures optimized for RED-II Cenk Andac (Tue Sep 06 2005 - 01:49:13 PDT)
- Re: AMBER: How to get PDB structures optimized for RED-II FyD (Tue Sep 06 2005 - 02:36:51 PDT)
- Re: AMBER: How to get PDB structures optimized for RED-II FyD (Wed Sep 07 2005 - 05:40:25 PDT)
  - Re: AMBER: How to get PDB structures optimized for RED-II Cenk Andac (Sat Oct 08 2005 - 06:34:42 PDT)
    - Re: AMBER: How to get PDB structures optimized for RED-II Cenk Andac (Fri Oct 14 2005 - 10:14:02 PDT)
  - Problem solved! Re: AMBER: How to get PDB structures optimized for RED-II Cenk Andac (Sat Oct 22 2005 - 10:38:58 PDT)
    - Re: Problem solved! Re: AMBER: How to get PDB structures optimized for RED-II FyD (Mon Oct 24 2005 - 01:27:07 PDT)
AMBER: masks in ptraj - Hbond analysis Fabien Cailliez (Tue Sep 06 2005 - 04:38:11 PDT)
- RE: AMBER: masks in ptraj - Hbond analysis Ross Walker (Tue Sep 06 2005 - 13:13:50 PDT)
AMBER: generation of conformations for multi-conf. RESP fitting Kateryna Miroshnychenko (Tue Sep 06 2005 - 07:29:40 PDT)
- Re: AMBER: generation of conformations for multi-conf. RESP fitting FyD (Tue Sep 06 2005 - 09:20:52 PDT)
AMBER: AMBER antechamber; dimenion size Toshifumi Yui (Tue Sep 06 2005 - 20:22:17 PDT)
- RE: AMBER: AMBER antechamber; dimenion size Junmei Wang (Wed Sep 07 2005 - 09:02:24 PDT)
AMBER: solvation energy Madjid Taghdir (Wed Sep 07 2005 - 03:08:31 PDT)
- Re: AMBER: solvation energy Peter Gannett (Wed Sep 07 2005 - 06:10:45 PDT)
  - Re: AMBER: solvation energy Wei Chen (Wed Sep 07 2005 - 09:19:47 PDT)
AMBER: Quick question about xLeap Kara Di Giorgio (Thu Sep 08 2005 - 07:31:59 PDT)
- Re: AMBER: Quick question about xLeap FyD (Thu Sep 08 2005 - 07:54:12 PDT)
  - Re: AMBER: Quick question about xLeap S.Sundar Raman (Thu Sep 08 2005 - 08:33:36 PDT)
AMBER: Amber 8 and PATH buffer overflow Amber Correspondece (Thu Sep 08 2005 - 10:01:45 PDT)
- RE: AMBER: Amber 8 and PATH buffer overflow Ross Walker (Thu Sep 08 2005 - 10:22:23 PDT)
- RE: AMBER: Amber 8 and PATH buffer overflow Ross Walker (Thu Sep 08 2005 - 10:26:52 PDT)
- RE: AMBER: Amber 8 and PATH buffer overflow Bill Ross (Thu Sep 08 2005 - 10:57:42 PDT)
AMBER: Amber8 compilation error Joe Nolan (Thu Sep 08 2005 - 12:47:08 PDT)
- Re: AMBER: Amber8 compilation error Bill Ross (Fri Apr 30 2004 - 13:50:28 PDT)
- Re: AMBER: Amber8 compilation error Scott Brozell (Thu Sep 08 2005 - 23:55:23 PDT)
AMBER: Equillibration run mathew k varghese (Thu Sep 08 2005 - 23:40:08 PDT)
- Re: AMBER: Equillibration run Carlos Simmerling (Fri Sep 09 2005 - 04:16:55 PDT)
  - Re: AMBER: Equillibration run mathew k varghese (Fri Sep 09 2005 - 06:16:24 PDT)
- Re: AMBER: Equillibration run Bill Ross (Fri Sep 09 2005 - 07:30:40 PDT)
AMBER: mm_pbsa example number 3 Thomas Whitington (Fri Sep 09 2005 - 01:14:19 PDT)
- Re: AMBER: mm_pbsa example number 3 Carlos Simmerling (Fri Sep 09 2005 - 04:19:59 PDT)
  - Re: AMBER: mm_pbsa example number 3 Thomas Whitington (Sat Sep 10 2005 - 19:32:58 PDT)
    - Re: AMBER: mm_pbsa example number 3 Carlos Simmerling (Sun Sep 11 2005 - 06:12:17 PDT)
AMBER: leap segmentation fault-bugfix1 didn't work Kateryna Miroshnychenko (Fri Sep 09 2005 - 06:28:43 PDT)
- Re: AMBER: leap segmentation fault-bugfix1 didn't work Kateryna Miroshnychenko (Tue Sep 13 2005 - 01:06:45 PDT)
AMBER: amber compilation on SGI ALTIX 350 (TEST FAILD) Anthony Cruz (Fri Sep 09 2005 - 12:19:12 PDT)
- RE: AMBER: amber compilation on SGI ALTIX 350 (TEST FAILD) Ross Walker (Fri Sep 09 2005 - 10:37:30 PDT)
- AMBER: antechamber dimesion size, again Toshifumi Yui (Thu Oct 06 2005 - 02:44:29 PDT)
  - RE: AMBER: antechamber dimesion size, again Junmei Wang (Thu Oct 06 2005 - 12:29:04 PDT)
    - Re: AMBER: antechamber dimesion size, again Toshifumi Yui (Thu Oct 06 2005 - 19:14:47 PDT)
AMBER: parralel test Anthony Cruz (Fri Sep 09 2005 - 13:41:44 PDT)
- Re: AMBER: parralel test David A. Case (Fri Sep 09 2005 - 12:07:16 PDT)
AMBER: AMBBER: ptraj question Douali, Latifa (Fri Sep 09 2005 - 13:49:24 PDT)
AMBER: Amber 8: questions about free energy perturbation Angela Liu (Sun Sep 11 2005 - 17:43:41 PDT)
- RE: AMBER: Amber 8: questions about free energy perturbation case (Mon Sep 12 2005 - 00:29:15 PDT)
  - RE: AMBER: Amber 8: questions about free energy perturbation Angela Liu (Mon Sep 12 2005 - 03:37:30 PDT)
    - Re: AMBER: Amber 8: questions about free energy perturbation David A. Case (Fri Sep 16 2005 - 02:00:13 PDT)
    - Re: AMBER: Amber 8: questions about free energy perturbation Angela Liu (Fri Sep 16 2005 - 08:15:26 PDT)
    - Re: AMBER: Amber 8: questions about free energy perturbation David Mobley (Fri Sep 23 2005 - 12:40:03 PDT)
  - AMBER: How to build a crystal structure from a unit cell pdb? Chunhu Tan (Tue Sep 20 2005 - 11:55:06 PDT)
- AMBER: umbrella sampling output question caoch.cherry.bio.titech.ac.jp (Mon Sep 12 2005 - 00:50:32 PDT)
  - Re: AMBER: umbrella sampling output question Guanglei Cui (Mon Sep 12 2005 - 06:06:31 PDT)
- Re: AMBER: Amber 8: questions about free energy perturbation Angela Liu (Mon Sep 12 2005 - 03:40:34 PDT)
  - Re: AMBER: Amber 8: questions about free energy perturbation Angela Liu (Mon Sep 12 2005 - 05:28:49 PDT)
- Re: AMBER: Amber 8: questions about free energy perturbation Angela Liu (Tue Sep 13 2005 - 06:34:25 PDT)
  - AMBER: How to split LES trajectory using TRAJ Xin Hu (Tue Sep 13 2005 - 08:03:20 PDT)
    - Re: AMBER: How to split LES trajectory using TRAJ Carlos Simmerling (Mon Sep 19 2005 - 10:40:47 PDT)
    - Re: AMBER: How to split LES trajectory using TRAJ Xin Hu (Mon Sep 19 2005 - 13:49:47 PDT)
    - Re: AMBER: How to split LES trajectory using TRAJ Melinda Layten (Wed Sep 21 2005 - 13:09:29 PDT)
  - Re: AMBER: Amber 8: questions about free energy perturbation darden (Tue Sep 13 2005 - 08:13:14 PDT)
    - Re: AMBER: Amber 8: questions about free energy perturbation Angela Liu (Tue Sep 13 2005 - 09:06:18 PDT)
  - AMBER: How does leap choose params ? ivan.mmb.pcb.ub.es (Wed Sep 14 2005 - 07:47:14 PDT)
AMBER: Fail to run parallel Anthony Cruz (Mon Sep 12 2005 - 05:52:29 PDT)
- Re: AMBER: Fail to run parallel Anthony Cruz (Mon Sep 12 2005 - 06:27:50 PDT)
AMBER: ibelly and free energy calculations David Mobley (Mon Sep 12 2005 - 14:36:25 PDT)
AMBER: REM error Anthony Cruz (Mon Sep 12 2005 - 17:06:05 PDT)
- Re: AMBER: REM error Guanglei Cui (Mon Sep 12 2005 - 18:04:33 PDT)
  - Re: AMBER: REM error Anthony Cruz (Tue Sep 13 2005 - 05:37:13 PDT)
    - Re: AMBER: REM error Carlos Simmerling (Tue Sep 13 2005 - 04:25:11 PDT)
    - Re: AMBER: REM error Anthony Cruz (Tue Sep 13 2005 - 11:37:19 PDT)
    - Re: AMBER: REM error Carlos Simmerling (Tue Sep 13 2005 - 10:40:20 PDT)
    - Re: AMBER: REM error Anthony Cruz (Tue Sep 13 2005 - 14:36:21 PDT)
AMBER: Can I get each corresponding sanpshots' delta delta energy term from mm_pbsa Suxin Zheng (Mon Sep 12 2005 - 15:43:13 PDT)
- Re: AMBER: Can I get each corresponding sanpshots' delta delta energy term from mm_pbsa JunJun Liu (Mon Sep 19 2005 - 19:51:32 PDT)
AMBER: improper torsion parameters Simon Whitehead (Tue Sep 13 2005 - 10:23:13 PDT)
AMBER: about the %occupied of hydrogen bond haixiao jin (Tue Sep 13 2005 - 22:39:05 PDT)
- Re: AMBER: about the %occupied of hydrogen bond Thomas E. Cheatham, III (Fri Sep 16 2005 - 07:30:58 PDT)
  - Re: AMBER: about the %occupied of hydrogen bond Carlos Simmerling (Fri Sep 16 2005 - 07:49:04 PDT)
    - Re: AMBER: about the %occupied of hydrogen bond haixiao jin (Sun Sep 18 2005 - 21:44:07 PDT)
    - Re: AMBER: about the %occupied of hydrogen bond Carlos Simmerling (Mon Sep 19 2005 - 06:04:14 PDT)
    - Re: AMBER: about the %occupied of hydrogen bond haixiao jin (Mon Sep 19 2005 - 07:12:42 PDT)
    - Re: AMBER: about the %occupied of hydrogen bond Carlos Simmerling (Mon Sep 19 2005 - 07:28:19 PDT)
    - Re: AMBER: about the %occupied of hydrogen bond haixiao jin (Mon Sep 19 2005 - 08:17:31 PDT)
AMBER: New information about AmberFFC FyD (Wed Sep 14 2005 - 03:18:36 PDT)
AMBER: Glycam-parameters and antechamber Michele Porro (Wed Sep 14 2005 - 09:06:42 PDT)
- Re: AMBER: Glycam-parameters and antechamber kkirschn.hamilton.edu (Tue Sep 20 2005 - 13:37:16 PDT)
AMBER: Error in "restrt" output file Alexander Rubinstein (Wed Sep 14 2005 - 14:30:49 PDT)
- Re: AMBER: Error in "restrt" output file Thomas E. Cheatham, III (Wed Sep 14 2005 - 14:41:41 PDT)
- RE: AMBER: Error in "restrt" output file Ross Walker (Wed Sep 14 2005 - 14:46:40 PDT)
AMBER: strange case quch 2004 (Wed Sep 14 2005 - 14:57:28 PDT)
AMBER: about radius of Br in MMPBSA calculation Yong Xu (Wed Sep 14 2005 - 19:36:35 PDT)
- RE: AMBER: about radius of Br in MMPBSA calculation Shan Jufang (Thu Sep 15 2005 - 15:00:56 PDT)
  - Re: RE: AMBER: about radius of Br in MMPBSA calculation Yong Xu (Fri Sep 16 2005 - 01:41:30 PDT)
    - Re: RE: AMBER: about radius of Br in MMPBSA calculation Shan Jufang (Wed Sep 21 2005 - 08:05:54 PDT)
AMBER: mm_pbsa: problems with dielec constant when using Magne Olufsen (Thu Sep 15 2005 - 04:02:35 PDT)
AMBER: Problem with installation AMBER8 on Solaris 8 using original SUN compilers Daniel Wetzler (Thu Sep 15 2005 - 04:46:14 PDT)
- RE: AMBER: Problem with installation AMBER8 on Solaris 8 using original SUN compilers Ross Walker (Thu Sep 15 2005 - 10:05:36 PDT)
- RE: AMBER: Problem with installation AMBER8 on Solaris 8 using original SUN compilers Ross Walker (Thu Sep 15 2005 - 13:48:38 PDT)
- RE: AMBER: Problem with installation AMBER8 on Solaris 8 using original SUN compilers Ross Walker (Thu Sep 15 2005 - 17:36:49 PDT)
AMBER: antechamber + mopac failure Nitin Bhardwaj (Thu Sep 15 2005 - 12:59:27 PDT)
- AMBER: antechamber + mopac failure Nitin Bhardwaj (Mon Sep 19 2005 - 09:36:30 PDT)
AMBER: creating a respgen file without Gaussian. Nitin Bhardwaj (Thu Sep 15 2005 - 13:08:36 PDT)
- AMBER: creating a resp input file without Gaussian. Nitin Bhardwaj (Mon Sep 19 2005 - 09:37:29 PDT)
  - Re: AMBER: creating a resp input file without Gaussian. Kenley Barrett (Mon Sep 19 2005 - 12:08:25 PDT)
  - Re: AMBER: creating a resp input file without Gaussian. FyD (Mon Sep 19 2005 - 23:47:20 PDT)
AMBER: roar question Lishan Yao (Thu Sep 15 2005 - 18:08:37 PDT)
AMBER: sander prob cbala.igib.res.in (Fri Sep 16 2005 - 01:18:42 PDT)
- Re: AMBER: sander prob Carlos Simmerling (Fri Sep 16 2005 - 04:03:03 PDT)
  - Re: AMBER: sander prob cbala.igib.res.in (Sat Sep 17 2005 - 03:28:51 PDT)
    - RE: AMBER: sander prob Ross Walker (Sat Sep 17 2005 - 09:23:27 PDT)
    - RE: AMBER: sander prob cbala.igib.res.in (Mon Sep 19 2005 - 08:57:58 PDT)
AMBER: charges jojartb.pharm.u-szeged.hu (Fri Sep 16 2005 - 00:33:00 PDT)
AMBER: GB refinement of CYANA structures Eugene DeRose (Fri Sep 16 2005 - 06:25:52 PDT)
- Re: AMBER: GB refinement of CYANA structures David A. Case (Fri Sep 16 2005 - 14:40:37 PDT)
AMBER: using SALTCON for human cell cytoplasm Kenley Barrett (Sun Sep 18 2005 - 09:45:42 PDT)
- Re: AMBER: using SALTCON for human cell cytoplasm Carlos Simmerling (Sun Sep 18 2005 - 10:11:29 PDT)
AMBER: Could not open file (Melb.mdcrd) with mode (r) Varsha Goyal (Mon Sep 19 2005 - 09:50:42 PDT)
- Re: AMBER: Could not open file (Melb.mdcrd) with mode (r) Melinda Layten (Mon Sep 19 2005 - 10:00:51 PDT)
- RE: AMBER: Could not open file (Melb.mdcrd) with mode (r) Ross Walker (Mon Sep 19 2005 - 10:17:29 PDT)
  - RE: AMBER: Could not open file (Melb.mdcrd) with mode (r) Varsha Goyal (Tue Sep 20 2005 - 14:25:45 PDT)
    - RE: AMBER: Could not open file (Melb.mdcrd) with mode (r) Ross Walker (Tue Sep 20 2005 - 14:39:20 PDT)
    - Re: AMBER: Could not open file (Melb.mdcrd) with mode (r) Brent Krueger (Tue Sep 20 2005 - 17:13:32 PDT)
AMBER: Xleap menu bar problems Steve Seibold (Mon Sep 19 2005 - 12:29:09 PDT)
- RE: AMBER: Xleap menu bar problems Ross Walker (Mon Sep 19 2005 - 12:44:11 PDT)
- RE: AMBER: Xleap menu bar problems Steve Seibold (Mon Sep 19 2005 - 13:44:52 PDT)
AMBER: building monosaccharides with glycam force field Lina Nilsson (Tue Sep 20 2005 - 09:09:41 PDT)
- Re: AMBER: building monosaccharides with glycam force field kkirschn.hamilton.edu (Tue Sep 20 2005 - 12:12:33 PDT)
AMBER: D-enantiomers M. Scott Shell (Tue Sep 20 2005 - 11:43:03 PDT)
- Re: AMBER: D-enantiomers David A. Case (Tue Sep 20 2005 - 16:07:53 PDT)
- Re: AMBER: D-enantiomers Thomas E. Cheatham, III (Tue Sep 20 2005 - 19:36:34 PDT)
  - Re: AMBER: D-enantiomers FyD (Tue Sep 20 2005 - 23:53:49 PDT)
    - Re: AMBER: D-enantiomers justin litchfield (Wed Sep 21 2005 - 00:50:36 PDT)
    - Re: AMBER: D-enantiomers Piotr Cieplak (Wed Sep 21 2005 - 01:13:26 PDT)
    - Re: AMBER: D-enantiomers FyD (Thu Sep 22 2005 - 00:03:55 PDT)
    - Re: AMBER: D-enantiomers Carlos Simmerling (Thu Sep 22 2005 - 04:35:06 PDT)
- Re: AMBER: D-enantiomers FyD (Thu Sep 22 2005 - 05:15:49 PDT)
- Re: AMBER: D-enantiomers Piotr Cieplak (Thu Sep 22 2005 - 10:41:24 PDT)
  - Re: AMBER: D-enantiomers FyD (Fri Sep 23 2005 - 00:12:36 PDT)
AMBER: antechamber problem bybaker.itsa.ucsf.edu (Tue Sep 20 2005 - 15:20:59 PDT)
AMBER: Linear Interaction Energy Daniel Oehme (Tue Sep 20 2005 - 18:39:53 PDT)
AMBER: Build an acetone Box gtg549i.mail.gatech.edu (Wed Sep 21 2005 - 00:18:49 PDT)
AMBER: Leap compilation with pgf77 under 64bit platform Mingfeng Yang (Wed Sep 21 2005 - 14:09:39 PDT)
AMBER: highly fluctuating reaction field energies in MM/PBSA Ulf Ryde (Thu Sep 22 2005 - 03:32:05 PDT)
AMBER: AMBER7 xleap problem Kristof Stevens (Thu Sep 22 2005 - 04:00:54 PDT)
- Re: AMBER: AMBER7 xleap problem Andreas Svrcek-Seiler (Thu Sep 22 2005 - 05:28:31 PDT)
AMBER: clustering julien (Thu Sep 22 2005 - 05:10:00 PDT)
AMBER: Problem finding transition state using NMODE Peter Anderson (Thu Sep 22 2005 - 05:36:00 PDT)
- Re: AMBER: Problem finding transition state using NMODE David A. Case (Thu Sep 22 2005 - 07:56:59 PDT)
- RE: AMBER: Problem finding transition state using NMODE Zhang Bing (Thu Sep 22 2005 - 08:27:45 PDT)
AMBER: Query: Problem during Production jpragati.ibab.ac.in (Thu Sep 22 2005 - 06:52:05 PDT)
AMBER: How to split LES trajectory using TRAJ Xin Hu (Thu Sep 22 2005 - 08:12:51 PDT)
AMBER: no statistics part Zhang Bing (Thu Sep 22 2005 - 08:23:30 PDT)
AMBER: no statistics part Zhang Bing (Thu Sep 22 2005 - 08:29:52 PDT)
AMBER: atommask question Istvan Kolossvary (Fri Sep 23 2005 - 08:57:44 PDT)
- Re: AMBER: atommask question Viktor Hornak (Fri Sep 23 2005 - 09:46:39 PDT)
AMBER: Problem during Production jpragati.ibab.ac.in (Sat Sep 24 2005 - 07:04:10 PDT)
- RE: AMBER: Problem during Production Ross Walker (Sat Sep 24 2005 - 08:54:38 PDT)
AMBER: Unformatted restart file cannot be read by sander when PME in use (AMBER8) John D. Chodera (Sun Sep 25 2005 - 18:08:37 PDT)
AMBER: Modified RNA Bases Raviprasad Aduri (Mon Sep 26 2005 - 19:41:12 PDT)
- Re: AMBER: Modified RNA Bases FyD (Mon Sep 26 2005 - 22:45:17 PDT)
  - Re: AMBER: Modified RNA Bases Raviprasad Aduri (Tue Sep 27 2005 - 10:22:45 PDT)
AMBER: Mg2+ radius in my_parse_delphi.siz JunJun Liu (Mon Sep 26 2005 - 20:30:14 PDT)
- Re: AMBER: Mg2+ radius in my_parse_delphi.siz Thomas Steinbrecher (Mon Sep 26 2005 - 23:49:05 PDT)
  - Re: AMBER: Mg2+ radius in my_parse_delphi.siz JunJun Liu (Tue Sep 27 2005 - 00:11:45 PDT)
AMBER: (no subject) Andrew Box (Mon Sep 26 2005 - 21:40:51 PDT)
- Re: AMBER: (no subject) Carlos Simmerling (Tue Sep 27 2005 - 04:06:16 PDT)
AMBER: Trajectory Problem Anthony Cruz (Thu Sep 22 2005 - 13:24:10 PDT)
- Re: AMBER: Trajectory Problem Wei Zhang (Tue Sep 27 2005 - 09:40:45 PDT)
  - Re: AMBER: Trajectory Problem Thomas E. Cheatham, III (Tue Sep 27 2005 - 09:59:50 PDT)
RE: AMBER: number of processors Douali, Latifa (Wed Sep 28 2005 - 10:41:21 PDT)
- Re: AMBER: number of processors Carlos Simmerling (Wed Sep 28 2005 - 11:01:04 PDT)
AMBER: Invalid Digit "*" Gert Kiss (Wed Sep 28 2005 - 11:18:04 PDT)
- Re: AMBER: Invalid Digit "*" Melinda Layten (Wed Sep 28 2005 - 12:17:29 PDT)
- RE: AMBER: Invalid Digit "*" Yong Duan (Wed Sep 28 2005 - 13:50:21 PDT)
AMBER: antechamber -- missing improper torsions David Mobley (Wed Sep 28 2005 - 15:35:25 PDT)
AMBER: Making prep file of sugar derivative Toshifumi Yui (Thu Sep 29 2005 - 05:02:12 PDT)
FW: AMBER: number of processors Douali, Latifa (Thu Sep 29 2005 - 13:49:29 PDT)
- Re: FW: AMBER: number of processors Carlos Simmerling (Thu Sep 29 2005 - 14:44:26 PDT)
AMBER: Minimization in sander and nmode Mingfeng Yang (Thu Sep 29 2005 - 16:01:24 PDT)
- Re: AMBER: Minimization in sander and nmode David A. Case (Thu Oct 06 2005 - 03:06:33 PDT)
AMBER: MM_PB/GBSA Zhang Bing (Thu Sep 29 2005 - 20:13:05 PDT)
- Re: AMBER: MM_PB/GBSA Thomas E. Cheatham, III (Thu Sep 29 2005 - 21:04:46 PDT)
AMBER: Amber compilation on opteron with PGI compiler Mingfeng Yang (Fri Sep 30 2005 - 06:15:43 PDT)
- Re: AMBER: Amber compilation on opteron with PGI compiler Robert Duke (Fri Sep 30 2005 - 06:53:58 PDT)
AMBER: Error check COM velocity!! jpragati.ibab.ac.in (Mon Oct 03 2005 - 04:58:01 PDT)
AMBER: cut-offs in non-periodic simulations Fabien Cailliez (Mon Oct 03 2005 - 09:31:26 PDT)
- Re: AMBER: cut-offs in non-periodic simulations Andreas Svrcek-Seiler (Mon Oct 03 2005 - 12:15:19 PDT)
AMBER: question temperature coupling tautp value for RNA Zhuang (Mon Oct 03 2005 - 15:40:23 PDT)
AMBER: question temperature coupling tautp value for RNA Zhuang (Mon Oct 03 2005 - 15:40:09 PDT)
- RE: AMBER: question temperature coupling tautp value for RNA Ross Walker (Mon Oct 03 2005 - 15:50:47 PDT)
  - Re: AMBER: question temperature coupling tautp value for RNA Carlos Simmerling (Tue Oct 04 2005 - 05:42:07 PDT)
AMBER: Problem during production!! jpragati.ibab.ac.in (Tue Oct 04 2005 - 01:33:48 PDT)
AMBER: Can I trust ANAL result? Madjid Taghdir (Tue Oct 04 2005 - 03:55:51 PDT)
AMBER: Manganese ion parameter nadtanet (Tue Oct 04 2005 - 04:55:59 PDT)
AMBER: Energy output problem! Pradipta Bandyopadhyay (Tue Oct 04 2005 - 05:08:04 PDT)
AMBER: The default of HIS in leaprc : HID or HIE ? Jiten (Tue Oct 04 2005 - 09:21:52 PDT)
AMBER: Fw: The default of HIS in leaprc : HID or HIE ? Jiten (Tue Oct 04 2005 - 09:34:54 PDT)
AMBER: Installation error - icc: command not found Sukjoon Yoon (Tue Oct 04 2005 - 18:13:11 PDT)
- AMBER: AMBER compilation - RH Enterprise 4, Xeon EM64T Sukjoon Yoon (Tue Oct 04 2005 - 22:55:07 PDT)
- Re: AMBER: Installation error - icc: command not found Andreas Svrcek-Seiler (Wed Oct 05 2005 - 02:47:31 PDT)
- Re: AMBER: Installation error - icc: command not found Mingfeng Yang (Wed Oct 05 2005 - 07:14:16 PDT)
AMBER: Is AMBER package suitable for simulating multiple molecule in solvent? wulei (Wed Oct 05 2005 - 02:26:00 PDT)
AMBER: question about grid in ptraj Linchen Gong (Thu Oct 06 2005 - 06:03:00 PDT)
- Re: AMBER: question about grid in ptraj Angelo Pugliese (Fri Oct 07 2005 - 02:23:17 PDT)
AMBER: R factors in NMR intensity refinement Yuqin Cai (Thu Oct 06 2005 - 09:29:31 PDT)
- Re: AMBER: R factors in NMR intensity refinement YoungJin Cho (Thu Oct 06 2005 - 09:56:02 PDT)
AMBER: AMBER compilation error Sukjoon Yoon (Thu Oct 06 2005 - 19:32:36 PDT)
- Re: AMBER: AMBER compilation error Andreas Svrcek-Seiler (Fri Oct 07 2005 - 02:46:24 PDT)
AMBER: QMMM question xiaoqin huang (Thu Oct 06 2005 - 21:09:53 PDT)
- Re: AMBER: QMMM question Guanglei Cui (Mon Oct 10 2005 - 07:14:20 PDT)
- RE: AMBER: QMMM question Ross Walker (Mon Oct 10 2005 - 07:38:50 PDT)
- Re: AMBER: QMMM question xiaoqin huang (Mon Oct 10 2005 - 11:59:55 PDT)
AMBER: parameters for pyridoxal phosphate Anna Feldman-Salit (Fri Oct 07 2005 - 06:46:29 PDT)
AMBER: problem with temperature weights Manish Datt (Fri Oct 07 2005 - 08:43:52 PDT)
- Re: AMBER: problem with temperature weights Carlos Simmerling (Fri Oct 07 2005 - 09:55:12 PDT)
  - Re: AMBER: problem with temperature weights Manish Datt (Fri Oct 07 2005 - 21:50:07 PDT)
    - Re: AMBER: problem with temperature weights Carlos Simmerling (Sat Oct 08 2005 - 04:03:41 PDT)
AMBER: sander error Yam (Sun Oct 09 2005 - 19:04:20 PDT)
- Re: AMBER: sander error Guanglei Cui (Mon Oct 10 2005 - 06:52:29 PDT)
- RE: AMBER: sander error Ross Walker (Mon Oct 10 2005 - 07:13:35 PDT)
  - RE: AMBER: sander error Yam (Tue Oct 11 2005 - 02:21:08 PDT)
    - Re: AMBER: sander error David A. Case (Tue Oct 11 2005 - 07:27:20 PDT)
    - AMBER: sander error Yam (Mon Oct 17 2005 - 19:10:50 PDT)
    - RE: AMBER: sander error Ross Walker (Tue Oct 18 2005 - 07:23:18 PDT)
    - Re: AMBER: sander error Robert Duke (Tue Oct 18 2005 - 07:49:05 PDT)
    - Re: AMBER: sander error David A. Case (Tue Oct 18 2005 - 07:59:39 PDT)
AMBER: Parameters and topology for Diacylglycerol (DAG) Nitin Bhardwaj (Mon Oct 10 2005 - 11:02:14 PDT)
AMBER: how to constitute T-phosphotyrosine group? luaj.sohu.com (Tue Oct 11 2005 - 05:28:38 PDT)
AMBER: PCA Claire Zerafa (Tue Oct 11 2005 - 06:33:49 PDT)
- Re: AMBER: PCA David A. Case (Tue Oct 11 2005 - 07:32:36 PDT)
AMBER: how can I constitute T-phosphotyrosine group ? luaj.sohu.com (Tue Oct 11 2005 - 07:25:02 PDT)
AMBER: maxgrp error Javier Pérez Mirón (Tue Oct 11 2005 - 12:55:46 PDT)
AMBER: warning in leap Marcela Madrid (Tue Oct 11 2005 - 14:26:42 PDT)
- Re: AMBER: warning in leap David A. Case (Tue Oct 11 2005 - 15:17:20 PDT)
AMBER: How to simulate a crystal structure? Chunhu Tan (Tue Oct 11 2005 - 16:22:39 PDT)
- Re: AMBER: How to simulate a crystal structure? David A. Case (Wed Oct 12 2005 - 08:17:35 PDT)
  - Re: AMBER: How to simulate a crystal structure? Joseph Nachman (Wed Oct 12 2005 - 09:57:56 PDT)
AMBER: F,Cl,Br,I in MMPBSA Yong Xu (Wed Oct 12 2005 - 01:58:53 PDT)
- Re: AMBER: F,Cl,Br,I in MMPBSA David A. Case (Mon Oct 17 2005 - 08:10:17 PDT)
  - Re: Re: AMBER: F,Cl,Br,I in MMPBSA Yong Xu (Thu Oct 20 2005 - 18:12:15 PDT)
AMBER: troubleshooting replica exchange Zhuang (Wed Oct 12 2005 - 16:46:08 PDT)
- Re: AMBER: troubleshooting replica exchange Sergio E. Wong (Wed Oct 12 2005 - 17:48:45 PDT)
- Re: AMBER: troubleshooting replica exchange Peter Varnai (Thu Oct 13 2005 - 00:44:59 PDT)
AMBER: how can I constitute T-phosphotyrosine group ? luaj.sohu.com (Wed Oct 12 2005 - 21:50:16 PDT)
AMBER: AMBER goes in a Loop Imran Khan (Thu Oct 13 2005 - 10:05:40 PDT)
- Re: AMBER: AMBER goes in a Loop David A. Case (Fri Oct 14 2005 - 08:05:41 PDT)
  - Re: AMBER: AMBER goes in a Loop Imran Khan (Fri Oct 14 2005 - 09:37:44 PDT)
- Re: AMBER: AMBER goes in a Loop Robert Duke (Fri Oct 14 2005 - 10:58:50 PDT)
AMBER: Scaling factor of NMR restraint FyD (Fri Oct 14 2005 - 07:28:24 PDT)
- RE: AMBER: Scaling factor of NMR restraint Ross Walker (Fri Oct 14 2005 - 07:55:44 PDT)
  - RE: AMBER: Scaling factor of NMR restraint FyD (Fri Oct 14 2005 - 23:34:58 PDT)
- Re: AMBER: Scaling factor of NMR restraint David A. Case (Fri Oct 14 2005 - 08:00:01 PDT)
AMBER: oxidised methionine residue Megan G (Fri Oct 14 2005 - 08:45:21 PDT)
AMBER: again: F, Cl, Br, I in MMPBSA Yong Xu (Fri Oct 14 2005 - 20:07:59 PDT)
AMBER: GNU Autotool integration for Amber8! mk mk (Sun Oct 16 2005 - 00:06:11 PDT)
- Re: AMBER: GNU Autotool integration for Amber8! David A. Case (Tue Oct 18 2005 - 09:54:37 PDT)
  - Re: AMBER: GNU Autotool integration for Amber8! Xuebin Qiao (Wed Oct 19 2005 - 08:17:54 PDT)
    - Re: AMBER: GNU Autotool integration for Amber8! David A. Case (Wed Oct 19 2005 - 16:41:32 PDT)
    - Re: AMBER: GNU Autotool integration for Amber8! Xuebin Qiao (Thu Oct 20 2005 - 06:55:10 PDT)
AMBER: Free energy for L and D amino acids S.Sundar Raman (Sun Oct 16 2005 - 08:40:24 PDT)
- Re: AMBER: Free energy for L and D amino acids Carlos Simmerling (Sun Oct 16 2005 - 09:05:03 PDT)
AMBER: Cyclohexane solvent Box chaiann ng (Sun Oct 16 2005 - 21:43:21 PDT)
- RE: AMBER: Cyclohexane solvent Box Ross Walker (Mon Oct 17 2005 - 07:03:54 PDT)
  - Re: AMBER: Cyclohexane solvent Box chai ann ng (Mon Oct 17 2005 - 07:27:13 PDT)
AMBER: antechamber -- missing improper torsions David Mobley (Mon Oct 17 2005 - 11:33:43 PDT)
- RE: AMBER: antechamber -- missing improper torsions Ross Walker (Mon Oct 17 2005 - 15:04:23 PDT)
  - Re: AMBER: antechamber -- missing improper torsions David Mobley (Tue Oct 18 2005 - 12:21:39 PDT)
    - RE: AMBER: antechamber -- missing improper torsions Ross Walker (Tue Oct 18 2005 - 20:33:13 PDT)
    - Re: AMBER: antechamber -- missing improper torsions David Mobley (Fri Oct 21 2005 - 10:21:01 PDT)
    - Re: AMBER: antechamber -- missing improper torsions David A. Case (Fri Oct 21 2005 - 10:57:31 PDT)
AMBER: pca with ptraj Claire Zerafa (Mon Oct 17 2005 - 16:11:21 PDT)
- AMBER: Question about NVE simulation. tanc.uci.edu (Mon Oct 17 2005 - 22:45:51 PDT)
  - Re: AMBER: Question about NVE simulation. Carlos Simmerling (Tue Oct 18 2005 - 05:02:39 PDT)
  - Re: AMBER: Question about NVE simulation. Chunhu Tan (Tue Oct 18 2005 - 12:39:43 PDT)
    - Re: AMBER: Question about NVE simulation. Carlos Simmerling (Tue Oct 18 2005 - 13:23:02 PDT)
AMBER: program to visualize crystal symmetries Hannes Loeffler (Tue Oct 18 2005 - 01:36:31 PDT)
- Re: AMBER: program to visualize crystal symmetries Karsten Suhre (Tue Oct 18 2005 - 02:13:23 PDT)
- Re: AMBER: program to visualize crystal symmetries Joseph Nachman (Tue Oct 18 2005 - 09:21:22 PDT)
AMBER: problem with xleap Vlad Cojocaru (Tue Oct 18 2005 - 06:56:38 PDT)
- Re: AMBER: problem with xleap Mark Williamson (Tue Oct 18 2005 - 07:04:43 PDT)
- Re: AMBER: problem with xleap Heike.Meiselbach.chemie.uni-erlangen.de (Tue Oct 18 2005 - 07:07:02 PDT)
AMBER: Simple 3D Molecule Visualization Alec M. Resnick (Tue Oct 18 2005 - 09:29:43 PDT)
- Re: AMBER: Simple 3D Molecule Visualization Joachim Reichelt (Tue Oct 18 2005 - 09:45:42 PDT)
- Re: AMBER: Simple 3D Molecule Visualization Karsten Suhre (Tue Oct 18 2005 - 09:45:36 PDT)
- Re: AMBER: Simple 3D Molecule Visualization Mark Williamson (Tue Oct 18 2005 - 09:50:07 PDT)
- Re: AMBER: Simple 3D Molecule Visualization FyD (Tue Oct 18 2005 - 12:16:19 PDT)
- Re: AMBER: Simple 3D Molecule Visualization Furse, Kristina Elisabet (Tue Oct 18 2005 - 15:10:54 PDT)
  - Re: AMBER: Simple 3D Molecule Visualization Mingfeng Yang (Wed Oct 19 2005 - 11:19:01 PDT)
  - Re: AMBER: Simple 3D Molecule Visualization Mingfeng Yang (Wed Oct 19 2005 - 11:19:18 PDT)
AMBER: Neutral C-terminal residue Sébastien Fiorucci (Wed Oct 19 2005 - 03:12:44 PDT)
- Re: AMBER: Neutral C-terminal residue Carlos Simmerling (Wed Oct 19 2005 - 04:40:10 PDT)
- Re: AMBER: Neutral C-terminal residue FyD (Wed Oct 19 2005 - 05:17:12 PDT)
AMBER: Fw: pca with ptraj Claire Zerafa (Wed Oct 19 2005 - 05:02:08 PDT)
AMBER: ptraj hbond analysis S.Sundar Raman (Wed Oct 19 2005 - 06:28:09 PDT)
- Re: AMBER: ptraj hbond analysis haixiao jin (Thu Oct 20 2005 - 04:07:30 PDT)
- Re: AMBER: ptraj hbond analysis Thomas Cheatham (Thu Oct 20 2005 - 19:03:36 PDT)
AMBER: amber file formats. Shishir (Wed Oct 19 2005 - 13:16:04 PDT)
- Re: AMBER: amber file formats. David A. Case (Thu Oct 20 2005 - 09:20:36 PDT)
  - Re: AMBER: amber file formats. Shishir (Thu Oct 20 2005 - 13:37:16 PDT)
    - Re: AMBER: amber file formats. David A. Case (Thu Oct 20 2005 - 14:32:29 PDT)
AMBER: (no subject) mathew k varghese (Wed Oct 19 2005 - 22:19:06 PDT)
- Re: AMBER: (no subject) Yam (Thu Oct 20 2005 - 00:31:37 PDT)
  - Re: AMBER: (no subject) mathew k varghese (Thu Oct 20 2005 - 01:31:21 PDT)
AMBER: porblem in ptraj julien (Thu Oct 20 2005 - 02:19:47 PDT)
- AMBER: Simulating transition metals in amber Thomas Steinbrecher (Thu Oct 20 2005 - 02:32:58 PDT)
  - Re: AMBER: Simulating transition metals in amber FyD (Mon Oct 24 2005 - 01:21:52 PDT)
AMBER: trouble in calculating the distance between O atom of water molecule and atom of residue haixiao jin (Thu Oct 20 2005 - 03:49:29 PDT)
- Re: AMBER: trouble in calculating the distance between O atom of water molecule and atom of residue Thomas Cheatham (Thu Oct 20 2005 - 18:50:43 PDT)
  - Re: AMBER: trouble in calculating the distance between O atom of water molecule and atom of residue haixiao jin (Thu Oct 20 2005 - 19:03:43 PDT)
AMBER: REMD error!!! Anthony Cruz (Thu Oct 20 2005 - 06:53:18 PDT)
- Re: AMBER: REMD error!!! Carlos Simmerling (Thu Oct 20 2005 - 05:05:41 PDT)
  - Re: AMBER: REMD error!!! Anthony Cruz (Thu Oct 20 2005 - 07:45:32 PDT)
    - Re: AMBER: REMD error!!! Carlos Simmerling (Thu Oct 20 2005 - 06:35:13 PDT)
    - Re: AMBER: REMD error!!! Anthony Cruz (Thu Oct 20 2005 - 09:48:12 PDT)
    - Re: AMBER: REMD error!!! Carlos Simmerling (Thu Oct 20 2005 - 08:00:22 PDT)
    - Re: AMBER: REMD error!!! Guanglei Cui (Thu Oct 20 2005 - 08:51:21 PDT)
    - Re: AMBER: REMD error!!! Carlos Simmerling (Thu Oct 20 2005 - 09:14:25 PDT)
- Re: AMBER: REMD error!!! Wei Zhang (Thu Oct 20 2005 - 09:15:51 PDT)
  - Re: AMBER: REMD error!!! Carlos Simmerling (Thu Oct 20 2005 - 09:28:15 PDT)
    - Re: AMBER: REMD error!!! Anthony Cruz (Thu Oct 20 2005 - 12:13:20 PDT)
    - Re: AMBER: REMD error!!! Carlos Simmerling (Thu Oct 20 2005 - 10:30:13 PDT)
    - Fwd: Re: AMBER: REMD error!!! Anthony Cruz (Fri Oct 28 2005 - 06:06:39 PDT)
    - Re: Re: AMBER: REMD error!!! Melinda Layten (Fri Oct 28 2005 - 08:26:46 PDT)
    - Re: Fwd: Re: AMBER: REMD error!!! Carlos Simmerling (Fri Oct 28 2005 - 07:38:48 PDT)
    - AMBER: REMD trajectory error!!! Anthony Cruz (Fri Oct 28 2005 - 11:10:18 PDT)
    - Re: AMBER: REMD trajectory error!!! Carlos Simmerling (Fri Oct 28 2005 - 10:06:44 PDT)
AMBER: delphi and surface in MMPBSA Yong Xu (Thu Oct 20 2005 - 07:07:17 PDT)
- Re: AMBER: delphi and surface in MMPBSA David A. Case (Thu Oct 20 2005 - 09:06:15 PDT)
  - Re: Re: AMBER: delphi and surface in MMPBSA Yong Xu (Thu Oct 20 2005 - 18:09:07 PDT)
    - Re: Re: AMBER: delphi and surface in MMPBSA David A. Case (Sat Oct 22 2005 - 09:44:37 PDT)
AMBER: Targeted MD Whitney Allen (Thu Oct 20 2005 - 11:04:31 PDT)
- Re: AMBER: Targeted MD Carlos Simmerling (Thu Oct 20 2005 - 11:31:21 PDT)
AMBER: xleap with modified residue Whitney Allen (Thu Oct 20 2005 - 11:12:42 PDT)
- Re: AMBER: xleap with modified residue Kenley Barrett (Thu Oct 20 2005 - 11:25:41 PDT)
- RE: AMBER: xleap with modified residue Ross Walker (Thu Oct 20 2005 - 11:58:53 PDT)
- RE: AMBER: xleap with modified residue Whitney Allen (Mon Oct 24 2005 - 09:24:25 PDT)
  - Re: AMBER: xleap with modified residue David A. Case (Mon Oct 24 2005 - 10:36:40 PDT)
Re: (2) Re: AMBER: F,Cl,Br,I in MMPBSA Yong Xu (Thu Oct 20 2005 - 18:21:33 PDT)
- Re: (2) Re: AMBER: F,Cl,Br,I in MMPBSA David A. Case (Fri Oct 21 2005 - 08:31:06 PDT)
AMBER: Dipolar coupling refinement s0344557.sms.ed.ac.uk (Fri Oct 21 2005 - 06:04:39 PDT)
- Re: AMBER: Dipolar coupling refinement David A. Case (Fri Oct 21 2005 - 18:03:43 PDT)
AMBER: using position restraints in target MD? Ben-Zhuo Lu (Fri Oct 21 2005 - 11:58:05 PDT)
- Re: AMBER: using position restraints in target MD? Viktor Hornak (Fri Oct 21 2005 - 13:14:42 PDT)
AMBER: Hi..I am new to AMBER.(compilation with MPICH-G2 libraries)... konnipati murali (Sat Oct 22 2005 - 23:38:28 PDT)
AMBER: rdparm: a parameter array overflowed ying xiong (Mon Oct 24 2005 - 02:17:33 PDT)
- Re: AMBER: rdparm: a parameter array overflowed David A. Case (Mon Oct 24 2005 - 09:00:50 PDT)
  - Re: Re: AMBER: rdparm: a parameter array overflowed ying xiong (Mon Oct 24 2005 - 23:03:27 PDT)
AMBER: compiling amber with pgi 5.2.4 Hannes Barsch (Mon Oct 24 2005 - 05:21:11 PDT)
- Re: AMBER: compiling amber with pgi 5.2.4 Robert Duke (Mon Oct 24 2005 - 05:44:42 PDT)
  - AW: AMBER: compiling amber with pgi 5.2.4 Hannes Barsch (Tue Oct 25 2005 - 08:42:53 PDT)
- Re: AMBER: compiling amber with pgi 5.2.4 Xuebin Qiao (Mon Oct 24 2005 - 08:20:08 PDT)
AMBER: error in safe Claire Zerafa (Mon Oct 24 2005 - 06:18:50 PDT)
- RE: AMBER: error in safe Ross Walker (Mon Oct 24 2005 - 07:25:38 PDT)
- Re: AMBER: error in safe Xuebin Qiao (Mon Oct 24 2005 - 08:26:41 PDT)
AMBER: Is MM-PBSA doable for transition metals ? Cenk Andac (Mon Oct 24 2005 - 09:55:27 PDT)
- AMBER: QMMM for copper complexes! Cenk Andac (Mon Oct 24 2005 - 10:12:22 PDT)
Re: AMBER: Is MM-PBSA doable for transition metals ? Bill Ross (Mon Oct 24 2005 - 10:10:44 PDT)
AMBER: atmtypenumbers Yong Xu (Mon Oct 24 2005 - 20:25:00 PDT)
AMBER: How to calculate binding free energy of ligand bound to complex with two active-site water molecules? haixiao jin (Tue Oct 25 2005 - 00:55:46 PDT)
AMBER: Using RED to calculate partial charges of new amino acid Donald Thomas (Tue Oct 25 2005 - 07:50:40 PDT)
- Re: AMBER: Using RED to calculate partial charges of new amino acid FyD (Wed Oct 26 2005 - 03:36:21 PDT)
AMBER: I am looking forward to hearing from you. Mehdi Davari (Tue Oct 25 2005 - 11:38:28 PDT)
- Re: AMBER: I am looking forward to hearing from you. Majid moghaddam (Wed Oct 26 2005 - 03:18:58 PDT)
AMBER: parmchk error : Cannot open CONNECT.TPL, exit Nitin Bhardwaj (Tue Oct 25 2005 - 14:08:02 PDT)
- Re: AMBER: parmchk error : Cannot open CONNECT.TPL, exit David A. Case (Tue Oct 25 2005 - 14:16:35 PDT)
  - Re: AMBER: parmchk error : Cannot open CONNECT.TPL, exit Nitin Bhardwaj (Tue Oct 25 2005 - 14:52:32 PDT)
AMBER: Antechamber error Nitin Bhardwaj (Tue Oct 25 2005 - 16:27:39 PDT)
- Re: AMBER: Antechamber error Nitin Bhardwaj (Tue Oct 25 2005 - 17:16:20 PDT)
- Re: AMBER: Antechamber error David A. Case (Thu Nov 03 2005 - 15:06:35 PST)
AMBER: AMBER tests (x86-64, PGI / Intel) Hannes Barsch (Wed Oct 26 2005 - 00:54:36 PDT)
- Re: AMBER: AMBER tests (x86-64, PGI / Intel) Scott Brozell (Thu Oct 27 2005 - 17:42:37 PDT)
AMBER: Increase the runtime of Amber benchmarks Imran Khan (Wed Oct 26 2005 - 02:23:10 PDT)
- Re: AMBER: Increase the runtime of Amber benchmarks Carlos Simmerling (Wed Oct 26 2005 - 04:30:37 PDT)
AMBER: seg fault error in resp Kateryna Miroshnychenko (Wed Oct 26 2005 - 06:24:37 PDT)
- Re: AMBER: seg fault error in resp FyD (Wed Oct 26 2005 - 07:06:40 PDT)
- Re: AMBER: seg fault error in resp Kateryna Miroshnychenko (Wed Oct 26 2005 - 08:26:37 PDT)
  - Re: AMBER: seg fault error in resp FyD (Wed Oct 26 2005 - 09:13:05 PDT)
- Re: AMBER: seg fault error in resp Bill Ross (Wed Oct 26 2005 - 09:35:38 PDT)
- Re: AMBER: seg fault error in resp Kateryna Miroshnychenko (Thu Oct 27 2005 - 07:14:24 PDT)
  - Re: AMBER: seg fault error in resp FyD (Thu Oct 27 2005 - 07:39:44 PDT)
- Re: AMBER: seg fault error in resp Bill Ross (Thu Oct 27 2005 - 11:40:47 PDT)
AMBER: xleap, opteron, pgi and segmentation fault. Lars Packschies (Wed Oct 26 2005 - 06:57:40 PDT)
AMBER: using constraints with QM/MM Jakub Kostal (Wed Oct 26 2005 - 11:58:40 PDT)
AMBER: Re: restraints xiaoqin huang (Wed Oct 26 2005 - 14:25:03 PDT)
AMBER: some questions when using ATP du yongchun (Wed Oct 26 2005 - 19:28:44 PDT)
AMBER: restart file and crd file Lishan Yao (Thu Oct 27 2005 - 06:37:29 PDT)
- Re: AMBER: restart file and crd file Mingfeng Yang (Thu Oct 27 2005 - 09:11:16 PDT)
  - Re: AMBER: restart file and crd file Lishan Yao (Thu Oct 27 2005 - 08:50:15 PDT)
    - Re: AMBER: restart file and crd file Melinda Layten (Thu Oct 27 2005 - 11:35:54 PDT)
    - Re: AMBER: restart file and crd file Lishan Yao (Thu Oct 27 2005 - 10:03:58 PDT)
- Re: AMBER: restart file and crd file Carlos Simmerling (Thu Oct 27 2005 - 09:18:18 PDT)
  - Re: AMBER: restart file and crd file Lishan Yao (Thu Oct 27 2005 - 08:33:20 PDT)
    - Re: AMBER: restart file and crd file Carlos Simmerling (Thu Oct 27 2005 - 12:03:13 PDT)
    - Re: AMBER: restart file and crd file Lishan Yao (Thu Oct 27 2005 - 10:54:26 PDT)
    - Re: AMBER: restart file and crd file Mingfeng Yang (Thu Oct 27 2005 - 12:40:51 PDT)
    - Re: AMBER: restart file and crd file Lishan Yao (Thu Oct 27 2005 - 11:59:29 PDT)
    - Re: AMBER: restart file and crd file Carlos Simmerling (Thu Oct 27 2005 - 13:03:20 PDT)
    - AMBER: Cluster analysis by MMTSB or ptraj Shuting Wei (Fri Oct 28 2005 - 08:30:49 PDT)
    - Re: AMBER: restart file and crd file Heiko Meyer (Fri Nov 04 2005 - 04:56:41 PST)
    - Re: AMBER: restart file and crd file Heiko Meyer (Fri Nov 04 2005 - 07:49:18 PST)
    - RE: AMBER: restart file and crd file Ross Walker (Fri Nov 04 2005 - 08:22:41 PST)
AMBER: problems installing amber 7 on a RH Linux 8 machine Marios Constantinou (Thu Oct 27 2005 - 08:28:00 PDT)
- Re: AMBER: problems installing amber 7 on a RH Linux 8 machine David A. Case (Thu Oct 27 2005 - 12:33:33 PDT)
- Re: AMBER: problems installing amber 7 on a RH Linux 8 machine Andreas Svrcek-Seiler (Fri Oct 28 2005 - 00:44:20 PDT)
AMBER: Unknown atomtypes in amber Nitin Bhardwaj (Thu Oct 27 2005 - 10:26:49 PDT)
- Re: AMBER: Unknown atomtypes in amber David A. Case (Sat Oct 29 2005 - 10:06:20 PDT)
  - Re: AMBER: Unknown atomtypes in amber Nitin Bhardwaj (Sat Oct 29 2005 - 12:24:04 PDT)
AMBER: Metals with Amber Anton B. Guliaev (Fri Oct 28 2005 - 10:09:07 PDT)
- Re: AMBER: Metals with Amber Marc Baaden (Thu Nov 03 2005 - 04:33:34 PST)
AMBER: vdw of h atoms Gustavo Pierdominici Sottile (Fri Oct 28 2005 - 12:16:10 PDT)
- Re: AMBER: vdw of h atoms Jiri Sponer (Fri Oct 28 2005 - 13:00:19 PDT)
- RE: AMBER: vdw of h atoms Rhoad, Jonathan S. (Fri Oct 28 2005 - 16:56:24 PDT)
- RE: AMBER: vdw of h atoms Bill Ross (Fri Oct 28 2005 - 17:21:56 PDT)
Re: AMBER: Metals with Amber Bill Ross (Fri Oct 28 2005 - 13:56:50 PDT)
Re: AMBER: vdw of h atoms Bill Ross (Fri Oct 28 2005 - 15:13:59 PDT)
AMBER: Improper Torsional Parameters Ilyas Yildirim (Fri Oct 28 2005 - 17:59:35 PDT)
- Re: AMBER: Improper Torsional Parameters David A. Case (Wed Nov 02 2005 - 08:47:34 PST)
  - Re: AMBER: Improper Torsional Parameters Ilyas Yildirim (Wed Nov 02 2005 - 10:00:50 PST)
    - RE: AMBER: Improper Torsional Parameters Ross Walker (Wed Nov 02 2005 - 20:06:28 PST)
    - Re: AMBER: Improper Torsional Parameters David A. Case (Thu Nov 03 2005 - 16:41:53 PST)
AMBER: rounding in xleap when using saveoff command... Ilyas Yildirim (Fri Oct 28 2005 - 18:26:22 PDT)
- Re: AMBER: rounding in xleap when using saveoff command... David A. Case (Wed Nov 02 2005 - 08:50:41 PST)
- Re: AMBER: rounding in xleap when using saveoff command... Wei Zhang (Wed Nov 02 2005 - 11:34:10 PST)
  - Re: AMBER: rounding in xleap when using saveoff command... Ilyas Yildirim (Wed Nov 02 2005 - 17:15:36 PST)
AMBER: amber7.0: F,Br,radius in MMPBSA Yong Xu (Sat Oct 29 2005 - 07:46:00 PDT)
AMBER: amber7.0: F,Br,radius in MMPBSA Yong Xu (Sat Oct 29 2005 - 07:47:21 PDT)
AMBER: with two water molecules in active site, how to calculate the free energy of ligand bound to complex? haixiao jin (Sun Oct 30 2005 - 22:27:08 PST)
AMBER: GBSA simulation problem Guillaume Bollot (Mon Oct 31 2005 - 00:23:26 PST)
- Re: AMBER: GBSA simulation problem Carlos Simmerling (Mon Oct 31 2005 - 04:25:22 PST)
AMBER: tkbc2 Mingfeng Yang (Mon Oct 31 2005 - 14:59:17 PST)
- Re: AMBER: tkbc2 David A. Case (Tue Nov 08 2005 - 08:50:51 PST)
AMBER: mm_pbsa problem emilia wu (Mon Oct 31 2005 - 18:53:51 PST)
- Re: AMBER: mm_pbsa problem Cenk Andac (Tue Nov 01 2005 - 00:15:23 PST)
  - Re: AMBER: mm_pbsa problem Scott Pendley (Tue Nov 01 2005 - 14:36:48 PST)
AMBER: About WHAM program Atsutoshi Okabe (Tue Nov 01 2005 - 19:29:14 PST)
- Re: AMBER: About WHAM program Guanglei Cui (Wed Nov 02 2005 - 05:47:01 PST)
AMBER: fedora installation problem Simon Whitehead (Wed Nov 02 2005 - 08:11:26 PST)
- RE: AMBER: fedora installation problem Ross Walker (Wed Nov 02 2005 - 08:50:03 PST)
  - RE: AMBER: fedora installation problem Scott Brozell (Wed Nov 02 2005 - 19:35:16 PST)
    - Re: AMBER: fedora installation problem David A. Case (Thu Nov 03 2005 - 10:50:42 PST)
- Re: AMBER: fedora installation problem caoch.cherry.bio.titech.ac.jp (Thu Nov 03 2005 - 05:17:32 PST)
AMBER: ptraj distance mask Peter Gannett (Wed Nov 02 2005 - 09:04:48 PST)
- Re: AMBER: ptraj distance mask Thomas E. Cheatham, III (Wed Nov 02 2005 - 09:32:09 PST)
AMBER: Leap error: Could not find atom type: CE Vlad Cojocaru (Wed Nov 02 2005 - 10:08:33 PST)
- Re: AMBER: Leap error: Could not find atom type: CE Ilyas Yildirim (Wed Nov 02 2005 - 10:31:23 PST)
- Re: AMBER: Leap error: Could not find atom type: CE David A. Case (Wed Nov 02 2005 - 10:57:59 PST)
AMBER: Density of Cyclohexane box chaiann ng (Wed Nov 02 2005 - 19:57:49 PST)
- RE: AMBER: Density of Cyclohexane box Ross Walker (Wed Nov 02 2005 - 20:52:32 PST)
  - RE: AMBER: Density of Cyclohexane box chaiann ng (Thu Nov 03 2005 - 19:10:50 PST)
- Re: AMBER: Density of Cyclohexane box FyD (Wed Nov 02 2005 - 23:47:41 PST)
AMBER: EEL and EAMBER values Andrew Box (Wed Nov 02 2005 - 20:19:14 PST)
- RE: AMBER: EEL and EAMBER values Ross Walker (Wed Nov 02 2005 - 21:02:44 PST)
AMBER: REM difficulties Peter Varnai (Thu Nov 03 2005 - 10:15:01 PST)
- Re: AMBER: REM difficulties Carlos Simmerling (Thu Nov 03 2005 - 10:38:23 PST)
  - Re: AMBER: REM difficulties Peter Varnai (Thu Nov 03 2005 - 11:26:11 PST)
    - Re: AMBER: REM difficulties Carlos Simmerling (Thu Nov 03 2005 - 11:41:05 PST)
- Re: AMBER: REM difficulties David A. Case (Thu Nov 03 2005 - 10:41:40 PST)
AMBER: Ask for helpf to get examples for MM-PBSA with AMBER8 Peng Tao (Thu Nov 03 2005 - 11:45:39 PST)
- Re: AMBER: Ask for helpf to get examples for MM-PBSA with AMBER8 Wei Chen (Thu Nov 03 2005 - 12:07:25 PST)
AMBER: How to generate a RMSd-residue number graph using AMBER8 ptraj? Jiapu.Zhang.csiro.au (Thu Nov 03 2005 - 17:16:17 PST)
- Re: AMBER: How to generate a RMSd-residue number graph using AMBER8 ptraj? Carlos Simmerling (Thu Nov 03 2005 - 17:31:39 PST)
AMBER: MM_PBSA problem haixiao jin (Thu Nov 03 2005 - 22:43:49 PST)
AMBER: Leap task Vlad Cojocaru (Fri Nov 04 2005 - 03:44:39 PST)
AMBER: just one more try:) xleap, opteron, pgi and segmentation fault. (fwd) Lars Packschies (Fri Nov 04 2005 - 04:09:40 PST)
AMBER: PMEMD limitation on NFFT Chng Choon-Peng (Fri Nov 04 2005 - 16:38:38 PST)
- Re: AMBER: PMEMD limitation on NFFT Robert Duke (Fri Nov 04 2005 - 19:29:17 PST)
  - Re: AMBER: PMEMD limitation on NFFT Chng Choon-Peng (Fri Nov 04 2005 - 19:44:58 PST)
AMBER: About WHAM program Atsutoshi Okabe (Sat Nov 05 2005 - 20:16:43 PST)
AMBER: bug report Ye Mei (Sat Nov 05 2005 - 22:21:50 PST)
- Re: AMBER: bug report David A. Case (Mon Nov 07 2005 - 08:36:29 PST)
  - Re: Re: AMBER: bug report Ye Mei (Tue Nov 08 2005 - 17:30:35 PST)
AMBER: bugfix 49 Lihua Wang (Sun Nov 06 2005 - 15:05:20 PST)
AMBER: rluo.uci.edu (Sun Nov 06 2005 - 16:42:30 PST)
AMBER: DNA simulations Andrew Box (Sun Nov 06 2005 - 21:15:15 PST)
AMBER: AMBER 8 compilation with lahey F95 ! Pradipta Bandyopadhyay (Mon Nov 07 2005 - 02:13:57 PST)
- Re: AMBER: AMBER 8 compilation with lahey F95 ! Amber admin (Mon Nov 07 2005 - 11:08:03 PST)
AMBER: addition to the last mail (lahey F95) ! Pradipta Bandyopadhyay (Mon Nov 07 2005 - 02:20:06 PST)
AMBER: XRED II error while initializing tomjas.poczta.onet.pl (Mon Nov 07 2005 - 04:17:12 PST)
- Re: AMBER: XRED II error while initializing FyD (Mon Nov 07 2005 - 05:03:05 PST)
  - Re: AMBER: XRED II error while initializing tomjas (Tue Nov 08 2005 - 22:38:40 PST)
    - Re: AMBER: XRED II error while initializing FyD (Wed Nov 09 2005 - 00:06:58 PST)
AMBER: tRNA's modified bases in the Amber parameters database Whitney Allen (Mon Nov 07 2005 - 06:52:45 PST)
- Re: AMBER: tRNA's modified bases in the Amber parameters database David A. Case (Mon Nov 07 2005 - 08:26:41 PST)
AMBER: Making movie from AMBER trajectory Varsha Goyal (Mon Nov 07 2005 - 08:03:01 PST)
- Re: AMBER: Making movie from AMBER trajectory Carlos Simmerling (Mon Nov 07 2005 - 08:28:26 PST)
  - Re: AMBER: Making movie from AMBER trajectory Varsha Goyal (Mon Nov 07 2005 - 09:23:50 PST)
    - Re: AMBER: Making movie from AMBER trajectory Carlos Simmerling (Mon Nov 07 2005 - 09:45:27 PST)
    - Re: AMBER: Making movie from AMBER trajectory Varsha Goyal (Mon Nov 07 2005 - 10:13:09 PST)
    - Re: AMBER: Making movie from AMBER trajectory Carlos Simmerling (Mon Nov 07 2005 - 10:28:20 PST)
    - Re: AMBER: Making movie from AMBER trajectory David Bevan (Mon Nov 07 2005 - 10:50:19 PST)
    - Re: AMBER: Making movie from AMBER trajectory Knut Langsetmo (Mon Nov 07 2005 - 10:42:08 PST)
    - Re: AMBER: Making movie from AMBER trajectory caoch.cherry.bio.titech.ac.jp (Mon Nov 07 2005 - 18:09:16 PST)
    - Re: AMBER: Making movie from AMBER trajectory Carlos Simmerling (Tue Nov 08 2005 - 04:44:38 PST)
    - Re: AMBER: Making movie from AMBER trajectory YoungJin Cho (Tue Nov 08 2005 - 07:00:07 PST)
    - Re: AMBER: Making movie from AMBER trajectory Mingfeng Yang (Tue Nov 08 2005 - 08:01:52 PST)
    - Re: AMBER: Making movie from AMBER trajectory David E. Konerding (Tue Nov 08 2005 - 10:56:55 PST)
    - Re: AMBER: Making movie from AMBER trajectory David E. Konerding (Tue Nov 08 2005 - 15:01:13 PST)
    - Re: AMBER: Making movie from AMBER trajectory using UCSF Chimera David E. Konerding (Wed Nov 09 2005 - 08:21:29 PST)
- RE: AMBER: Making movie from AMBER trajectory Ross Walker (Mon Nov 07 2005 - 08:55:48 PST)
  - RE: AMBER: Making movie from AMBER trajectory Varsha Goyal (Mon Nov 07 2005 - 09:25:41 PST)
AMBER: calculating time correlation functions with ptraj John S Zintsmaster (Mon Nov 07 2005 - 08:39:38 PST)
- AMBER: Time Correlation Functions with Amber John S Zintsmaster (Tue Nov 08 2005 - 08:15:45 PST)
  - Re: AMBER: Time Correlation Functions with Amber David A. Case (Tue Nov 08 2005 - 08:25:50 PST)
    - Re: AMBER: Time Correlation Functions with Amber John S Zintsmaster (Tue Nov 08 2005 - 09:57:26 PST)
    - Re: AMBER: Time Correlation Functions with Amber David A. Case (Tue Nov 08 2005 - 10:43:55 PST)
    - Re: AMBER: Time Correlation Functions with Amber John S. Zintsmaster (Tue Nov 08 2005 - 11:56:54 PST)
AMBER: mm_pbsa Wei Chen (Wed Nov 09 2005 - 11:51:01 PST)
- Re: AMBER: mm_pbsa Ray Luo (Tue Nov 08 2005 - 21:26:52 PST)
  - Re: AMBER: mm_pbsa Wei Chen (Fri Nov 11 2005 - 09:21:32 PST)
    - Re: AMBER: mm_pbsa Ray Luo (Fri Nov 11 2005 - 15:57:04 PST)
    - Re: AMBER: mm_pbsa Wei Chen (Sat Nov 12 2005 - 20:45:14 PST)
    - Re: AMBER: mm_pbsa Ray Luo (Sat Nov 12 2005 - 00:09:13 PST)
    - Re: AMBER: mm_pbsa Wei Chen (Mon Nov 14 2005 - 14:06:44 PST)
    - Re: Re: AMBER: mm_pbsa zgleo (Sun Jul 31 2005 - 08:26:02 PDT)
    - AMBER: memory_mm_pbsa Wei Chen (Mon Aug 01 2005 - 20:00:34 PDT)
    - RE: AMBER: memory_mm_pbsa Ross Walker (Mon Aug 01 2005 - 20:14:47 PDT)
    - RE: AMBER: memory_mm_pbsa Wei Chen (Mon Aug 01 2005 - 21:03:34 PDT)
- Re: AMBER: mm_pbsa Cenk Andac (Thu Nov 10 2005 - 06:08:24 PST)
  - Re: AMBER: mm_pbsa Wei Chen (Fri Nov 11 2005 - 09:05:40 PST)
  - CORRENDUM: Re: AMBER: mm_pbsa Cenk Andac (Sat Nov 12 2005 - 00:31:27 PST)
AMBER: Resp install problem Jianzhong Liu (Wed Nov 09 2005 - 15:21:09 PST)
- Re: AMBER: Resp install problem David A. Case (Wed Nov 09 2005 - 15:51:10 PST)
AMBER: LoadPdb Error: In file [chirality.c], line 121 Message: Atom C67 is not in the first list Nitin Bhardwaj (Wed Nov 09 2005 - 16:55:41 PST)
- Re: AMBER: LoadPdb Error: In file [chirality.c], line 121 Message: Atom C67 is not in the first list Ilyas Yildirim (Wed Nov 09 2005 - 19:56:24 PST)
  - Re: AMBER: LoadPdb Error: In file [chirality.c], line 121 Message: Atom C67 is not in the first list Nitin Bhardwaj (Thu Nov 10 2005 - 08:40:21 PST)
    - Re: AMBER: LoadPdb Error: In file [chirality.c], line 121 Message: Atom C67 is not in the first list David A. Case (Thu Nov 10 2005 - 09:00:12 PST)
    - Re: AMBER: LoadPdb Error: In file [chirality.c], line 121 Message: Atom C67 is not in the first list Nitin Bhardwaj (Thu Nov 10 2005 - 09:13:33 PST)
    - Re: AMBER: LoadPdb Error: In file [chirality.c], line 121 Message: Atom C67 is not in the first list David A. Case (Fri Nov 11 2005 - 18:58:21 PST)
    - Re: AMBER: LoadPdb Error: In file [chirality.c], line 121 Message: Atom C67 is not in the first list Ilyas Yildirim (Thu Nov 10 2005 - 18:58:23 PST)
    - Re: AMBER: LoadPdb Error: In file [chirality.c], line 121 Message: Atom C67 is not in the first list Nitin Bhardwaj (Fri Nov 11 2005 - 08:25:52 PST)
    - Re: AMBER: LoadPdb Error: In file [chirality.c], line 121 Message: Atom C67 is not in the first list David A. Case (Mon Nov 14 2005 - 09:01:25 PST)
    - Re: AMBER: LoadPdb Error: In file [chirality.c], line 121 Message: Atom C67 is not in the first list Nitin Bhardwaj (Tue Nov 15 2005 - 16:11:31 PST)
    - Re: AMBER: LoadPdb Error: In file [chirality.c], line 121 Message: Atom C67 is not in the first list Ilyas Yildirim (Tue Nov 15 2005 - 20:43:09 PST)
    - Re: AMBER: LoadPdb Error: In file [chirality.c], line 121 Message: Atom C67 is not in the first list David A. Case (Wed Nov 16 2005 - 08:56:44 PST)
Re: AMBER: LoadPdb Error: In file [chirality.c], line 121 Message: Atom C67 is not in the first list Bill Ross (Wed Nov 09 2005 - 17:40:41 PST)
AMBER: ESP exceeds the MAXESP(20000), nag raj (Thu Nov 10 2005 - 02:36:37 PST)
- RE: AMBER: ESP exceeds the MAXESP(20000), Junmei Wang (Thu Nov 10 2005 - 07:37:05 PST)
AMBER: restart coordinate file s0344557.sms.ed.ac.uk (Thu Nov 10 2005 - 05:55:43 PST)
- Re: AMBER: restart coordinate file Carlos Simmerling (Thu Nov 10 2005 - 07:31:18 PST)
Re: AMBER: restart coordinate file Bill Ross (Thu Nov 10 2005 - 07:42:53 PST)
- Re: AMBER: restart coordinate file s0344557.sms.ed.ac.uk (Thu Nov 10 2005 - 08:11:49 PST)
AMBER: Resp install problem, again Jianzhong Liu (Thu Nov 10 2005 - 08:03:24 PST)
- Re: AMBER: Resp install problem, again David A. Case (Thu Nov 10 2005 - 09:39:49 PST)
- Re: AMBER: Resp install problem, again FyD (Thu Nov 10 2005 - 13:49:21 PST)
- Re: AMBER: Resp install problem, again Jianzhong Liu (Wed Nov 16 2005 - 10:14:51 PST)
  - Re: AMBER: Resp install problem, again David A. Case (Wed Nov 16 2005 - 10:43:13 PST)
- Re: AMBER: Resp install problem, again Jianzhong Liu (Wed Nov 16 2005 - 10:55:06 PST)
  - Re: AMBER: Resp install problem, again David A. Case (Wed Nov 16 2005 - 13:53:27 PST)
AMBER: Error message Sukjoon Yoon (Mon Nov 14 2005 - 00:14:07 PST)
- RE: AMBER: Error message Ross Walker (Mon Nov 14 2005 - 07:04:04 PST)
AMBER: RESP problem RESP laura zan (Mon Nov 14 2005 - 05:54:28 PST)
- Re: AMBER: RESP problem RESP FyD (Mon Nov 14 2005 - 06:59:12 PST)
AMBER: iwork array for nmr Peter Varnai (Mon Nov 14 2005 - 12:20:38 PST)
- Re: AMBER: iwork array for nmr Guanglei Cui (Mon Nov 14 2005 - 15:17:31 PST)
AMBER: Antechamber/Leap, problem with Improper angles Christophe Guilbert (Mon Nov 14 2005 - 18:06:28 PST)
- Re: AMBER: Antechamber/Leap, problem with Improper angles David A. Case (Tue Nov 15 2005 - 13:03:11 PST)
AMBER: ew_legal.h Yam (Mon Nov 14 2005 - 18:54:03 PST)
- RE: AMBER: ew_legal.h Ross Walker (Mon Nov 14 2005 - 19:22:31 PST)
  - RE: AMBER: ew_legal.h Yam (Mon Nov 14 2005 - 20:40:37 PST)
- Re: AMBER: ew_legal.h David A. Case (Mon Nov 14 2005 - 21:41:54 PST)
- Re: AMBER: ew_legal.h Yam (Mon Nov 14 2005 - 23:10:18 PST)
  - Re: AMBER: ew_legal.h darden (Tue Nov 15 2005 - 05:44:26 PST)
AMBER: calculating end-end distance C Balasubramanian (Tue Nov 15 2005 - 02:24:21 PST)
- Re: AMBER: calculating end-end distance David A. Case (Tue Nov 15 2005 - 08:24:01 PST)
AMBER: recent Chimera MD enhancements Eric Pettersen (Tue Nov 15 2005 - 12:59:16 PST)
- Re: AMBER: recent Chimera MD enhancements Eric Pettersen (Tue Nov 15 2005 - 13:09:21 PST)
AMBER: pH=1 MD simulation Harianto Tjong (Tue Nov 15 2005 - 14:16:12 PST)
AMBER: Quantifying DNA perterbation Kara Di Giorgio (Tue Nov 15 2005 - 17:44:03 PST)
- Re: AMBER: Quantifying DNA perterbation Thomas Cheatham (Tue Nov 15 2005 - 21:55:55 PST)
- Re: AMBER: Quantifying DNA perterbation Carlos Simmerling (Wed Nov 16 2005 - 03:08:41 PST)
AMBER: anal and periodic boundary conditions Rachel Burdge (Wed Nov 16 2005 - 08:18:34 PST)
Re: AMBER: anal and periodic boundary conditions Bill Ross (Wed Nov 16 2005 - 09:32:57 PST)
AMBER: using periodic boundary conditions to create infinite double helix Kenley Barrett (Wed Nov 16 2005 - 09:32:39 PST)
- Re: AMBER: using periodic boundary conditions to create infinite double helix David A. Case (Wed Nov 16 2005 - 16:10:17 PST)
- Re: AMBER: using periodic boundary conditions to create infinite double helix Bill Ross (Wed Nov 16 2005 - 16:34:53 PST)
AMBER: ptraj Hbond analysis mathew k varghese (Wed Nov 16 2005 - 20:28:52 PST)
- Re: AMBER: ptraj Hbond analysis Thomas Cheatham (Wed Nov 16 2005 - 21:28:42 PST)
  - Re: AMBER: ptraj Hbond analysis mathew k varghese (Thu Nov 17 2005 - 20:09:14 PST)
    - Re: AMBER: ptraj Hbond analysis Thomas Cheatham (Thu Nov 17 2005 - 21:20:00 PST)
    - Re: AMBER: ptraj Hbond analysis mathew k varghese (Sat Nov 19 2005 - 03:36:12 PST)
    - Re: AMBER: ptraj Hbond analysis Thomas Cheatham (Sun Nov 20 2005 - 15:13:44 PST)
AMBER: FATAL error with ATP, MG2 residue Michael Mazanetz (Thu Nov 17 2005 - 01:41:12 PST)
AMBER: need clarification on EWALD BOMB error S.Sundar Raman (Thu Nov 17 2005 - 02:03:22 PST)
- RE: AMBER: need clarification on EWALD BOMB error Ross Walker (Thu Nov 17 2005 - 08:20:02 PST)
  - Re: AMBER: need clarification on EWALD BOMB error S.Sundar Raman (Thu Nov 17 2005 - 19:38:43 PST)
- Re: AMBER: need clarification on EWALD BOMB error Thomas Cheatham (Thu Nov 17 2005 - 09:45:28 PST)
  - AMBER: Question about using MM_PBSA gtg549i.mail.gatech.edu (Thu Nov 17 2005 - 13:28:19 PST)
    - Re: AMBER: Question about using MM_PBSA Wei Chen (Thu Nov 17 2005 - 15:50:05 PST)
AMBER: FATAL error with ATP and MG2 - fixed Michael Mazanetz (Thu Nov 17 2005 - 04:45:27 PST)
AMBER: RED and EP from GAMESS Vlad Cojocaru (Fri Nov 18 2005 - 02:12:49 PST)
AMBER: Polarization & energy analysis GUILBAUD Philippe 153683 (Fri Nov 18 2005 - 02:52:26 PST)
- Re: AMBER: Polarization & energy analysis David A. Case (Fri Nov 18 2005 - 09:05:43 PST)
AMBER: RED and EP from GAMESS FyD (Fri Nov 18 2005 - 04:04:47 PST)
- AMBER: Question about PDB format FyD (Sat Nov 19 2005 - 00:11:23 PST)
  - RE: AMBER: Question about PDB format Ross Walker (Sat Nov 19 2005 - 08:55:11 PST)
  - Re: AMBER: Question about PDB format David A. Case (Sat Nov 19 2005 - 10:47:45 PST)
  - Re: AMBER: Question about PDB format Andy Purkiss (Sat Nov 19 2005 - 11:19:00 PST)
    - Re: AMBER: Question about PDB format FyD (Sun Nov 20 2005 - 06:21:22 PST)
AMBER: RED&GAMESS: sorry ... my mistake Vlad Cojocaru (Fri Nov 18 2005 - 04:28:31 PST)
AMBER: MM/PBSA basic questions Peng Tao (Fri Nov 18 2005 - 07:41:26 PST)
- Re: AMBER: MM/PBSA basic questions Wei Chen (Fri Nov 18 2005 - 09:06:04 PST)
- Re: AMBER: MM/PBSA basic questions David A. Case (Fri Nov 18 2005 - 09:09:05 PST)
  - Re: AMBER: MM/PBSA basic questions Peng Tao (Fri Nov 18 2005 - 10:59:39 PST)
AMBER: RED: extra variable definition Vlad Cojocaru (Sun Nov 20 2005 - 06:48:32 PST)
- Re: AMBER: RED: extra variable definition FyD (Mon Nov 21 2005 - 06:58:17 PST)
- Re: AMBER: RED: extra variable definition Vlad Cojocaru (Tue Nov 22 2005 - 01:08:32 PST)
  - Re: AMBER: RED: extra variable definition FyD (Tue Nov 22 2005 - 01:34:33 PST)
  - Re: AMBER: RED: extra variable definition FyD (Tue Nov 22 2005 - 01:40:09 PST)
    - Re: AMBER: RED: extra variable definition Vlad Cojocaru (Tue Nov 22 2005 - 06:26:49 PST)
AMBER: How to use XLEAP to link one atom in a monomer to another atom in another monomer? (where both the 2 monomers are in a same pdb file) Jiapu.Zhang.csiro.au (Sun Nov 20 2005 - 17:35:57 PST)
- RE: AMBER: How to use XLEAP to link one atom in a monomer to another atom in another monomer? (where both the 2 monomers are in a same pdb file) Ross Walker (Sun Nov 20 2005 - 21:59:18 PST)
- RE: AMBER: How to use XLEAP to link one atom in a monomer to another atom in another monomer? (where both the 2 monomers are in a same pdb file) Ross Walker (Mon Nov 21 2005 - 08:33:44 PST)
- RE: AMBER: How to use XLEAP to link one atom in a monomer to another atom in ano Andrew Box (Mon Nov 21 2005 - 14:48:34 PST)
  - AMBER: how to extract the residues of first solvation shell from the simulated system after the production? gtg549i.mail.gatech.edu (Mon Nov 21 2005 - 15:46:04 PST)
    - Re: AMBER: how to extract the residues of first solvation shell from the simulated system after the production? Thomas Cheatham (Mon Nov 21 2005 - 19:50:09 PST)
    - Re: AMBER: how to extract the residues of first solvation shell from the simulated system after the production? gtg549i.mail.gatech.edu (Tue Nov 22 2005 - 07:13:49 PST)
    - Re: AMBER: how to extract the residues of first solvation shell from the simulated system after the production? gtg549i.mail.gatech.edu (Tue Nov 22 2005 - 13:28:36 PST)
    - Re: AMBER: how to extract the residues of first solvation shell from the simulated system after the production? Thomas Cheatham (Tue Nov 22 2005 - 20:35:11 PST)
AMBER: Will Amber 9 available? Xioling Chuang (Sun Nov 20 2005 - 17:54:55 PST)
- Re: AMBER: Will Amber 9 available? David A. Case (Sun Nov 20 2005 - 18:16:09 PST)
  - Re: AMBER: Will Amber 9 available? bmbbjm.bmb.leeds.ac.uk (Mon Nov 21 2005 - 01:54:45 PST)
    - Re: AMBER: Will Amber 9 available? David A. Case (Mon Nov 21 2005 - 08:28:34 PST)
  - Re: AMBER: Will Amber 9 available? Barbault Florent (Mon Nov 21 2005 - 02:25:04 PST)
AMBER: temprature and restraint in constant volumm MD tonglei (Mon Nov 21 2005 - 00:55:40 PST)
- Re: AMBER: temprature and restraint in constant volumm MD Carlos Simmerling (Mon Nov 21 2005 - 05:00:08 PST)
  - Re: AMBER: temprature and restraint in constant volumm MD tonglei (Mon Nov 21 2005 - 05:56:12 PST)
AMBER: average struct without solvent C Balasubramanian (Mon Nov 21 2005 - 05:51:26 PST)
- Re: AMBER: average struct without solvent mcpreto.fc.up.pt (Mon Nov 21 2005 - 06:20:39 PST)
- RE: AMBER: average struct without solvent Ross Walker (Mon Nov 21 2005 - 08:28:23 PST)
- Re: AMBER: average struct without solvent Thomas Cheatham (Mon Nov 21 2005 - 08:34:23 PST)
AMBER: ANAL problem Sébastien Fiorucci (Mon Nov 21 2005 - 09:18:07 PST)
- Re: AMBER: ANAL problem David A. Case (Mon Nov 21 2005 - 16:17:14 PST)
AMBER: Question about PB bomb zgleo (Mon Nov 21 2005 - 18:11:08 PST)
AMBER: Question of PB bomb zgleo (Mon Nov 21 2005 - 20:59:54 PST)
AMBER: sp0 console message after using addAtomTypes Lorna Stimson (Tue Nov 22 2005 - 00:44:19 PST)
- Re: AMBER: sp0 console message after using addAtomTypes David A. Case (Tue Nov 22 2005 - 08:44:30 PST)
  - Re: AMBER: sp0 console message after using addAtomTypes Lorna Stimson (Tue Nov 22 2005 - 09:04:07 PST)
AMBER: Leap handling crystallographic waters Vlad Cojocaru (Tue Nov 22 2005 - 05:44:57 PST)
- Re: AMBER: Leap handling crystallographic waters Andy Purkiss (Tue Nov 22 2005 - 06:31:07 PST)
- Re: AMBER: Leap handling crystallographic waters Furse, Kristina Elisabet (Tue Nov 22 2005 - 09:13:57 PST)
  - RE: AMBER: Leap handling crystallographic waters Ross Walker (Tue Nov 22 2005 - 09:46:38 PST)
- RE: AMBER: Leap handling crystallographic waters Furse, Kristina Elisabet (Tue Nov 22 2005 - 11:18:34 PST)
  - RE: AMBER: Leap handling crystallographic waters Ross Walker (Tue Nov 22 2005 - 12:09:27 PST)
  - Re: AMBER: Leap handling crystallographic waters David A. Case (Tue Nov 22 2005 - 12:08:39 PST)
- AMBER: RE: gaff sugar residue instability hayden (Tue Nov 22 2005 - 11:32:14 PST)
  - Re: AMBER: RE: gaff sugar residue instability David A. Case (Tue Nov 22 2005 - 11:40:18 PST)
  - AMBER: gaff sugar residue instability hayden (Thu Nov 24 2005 - 06:43:03 PST)
    - Re: AMBER: gaff sugar residue instability David A. Case (Thu Nov 24 2005 - 10:28:23 PST)
    - Re: AMBER: gaff sugar residue instability Bill Ross (Thu Nov 24 2005 - 10:45:16 PST)
AMBER: GRID program used to add ions and solvate AMBER minimized structures Vlad Cojocaru (Tue Nov 22 2005 - 06:53:55 PST)
AMBER: MM_PBSA problem Zhang Bing (Tue Nov 22 2005 - 07:37:32 PST)
- Re: AMBER: MM_PBSA problem David A. Case (Tue Nov 22 2005 - 08:49:59 PST)
AMBER: Using OPLS atom types Lorna Stimson (Tue Nov 22 2005 - 08:18:48 PST)
- Re: AMBER: Using OPLS atom types Furse, Kristina Elisabet (Tue Nov 22 2005 - 09:10:06 PST)
- Re: AMBER: Using OPLS atom types David A. Case (Fri Dec 02 2005 - 20:01:17 PST)
- Re: AMBER: Using OPLS atom types Bill Ross (Sat Dec 03 2005 - 10:15:53 PST)
Re: AMBER: Using OPLS atom types Bill Ross (Tue Nov 22 2005 - 09:44:16 PST)
AMBER: MM_PBSA problem---Illegal division by zero at ... Zhang Bing (Tue Nov 22 2005 - 16:15:40 PST)
AMBER: cluster analysis mathew k varghese (Tue Nov 22 2005 - 23:03:27 PST)
- Re: AMBER: cluster analysis Sue Heavner (Thu Jun 10 2004 - 03:40:56 PDT)
- RE: AMBER: cluster analysis Ross Walker (Wed Nov 23 2005 - 08:15:53 PST)
  - AMBER: MM_PBSA_parameter Wei Chen (Wed Nov 23 2005 - 11:48:12 PST)
    - Re: AMBER: MM_PBSA_parameter Ray Luo (Wed Nov 23 2005 - 13:48:17 PST)
    - Re: AMBER: MM_PBSA_parameter Wei Chen (Wed Nov 23 2005 - 14:51:16 PST)
    - Re: AMBER: MM_PBSA_parameter Ray Luo (Wed Nov 23 2005 - 15:23:33 PST)
AMBER: MM_PBSA question Tiziano Tuccinardi (Thu Nov 24 2005 - 01:01:53 PST)
- Re: AMBER: MM_PBSA question David A. Case (Thu Nov 24 2005 - 10:25:56 PST)
AMBER: Parameters for S-substituted nucleic acids E.A.Moore (Thu Nov 24 2005 - 01:29:18 PST)
Re: AMBER: gaff sugar residue instability Bill Ross (Thu Nov 24 2005 - 10:48:02 PST)
AMBER: aloks.mbu.iisc.ernet.in (Fri Nov 25 2005 - 04:11:01 PST)
AMBER: PARM-99 Angelo Pugliese (Fri Nov 25 2005 - 06:03:23 PST)
- Re: AMBER: PARM-99 Carlos Simmerling (Fri Nov 25 2005 - 08:36:45 PST)
- Re: AMBER: PARM-99 Claire Zerafa (Sat Nov 26 2005 - 01:24:25 PST)
AMBER: reordering atoms after antechamber Vlad Cojocaru (Fri Nov 25 2005 - 09:02:38 PST)
- Re: AMBER: reordering atoms after antechamber David A. Case (Fri Nov 25 2005 - 09:19:28 PST)
- Re: AMBER: reordering atoms after antechamber FyD (Mon Nov 28 2005 - 07:10:17 PST)
Re: AMBER: PARM-99 Piotr Cieplak (Fri Nov 25 2005 - 17:46:31 PST)
AMBER: How to wrap a truncated octahedron water box into the primary box? Xioling Chuang (Sat Nov 26 2005 - 02:19:44 PST)
AMBER: input for mm_pbsa Xioling Chuang (Sat Nov 26 2005 - 22:31:09 PST)
AMBER: Comparing EELEC from amber and that calculated in the trivial fashion. Pavan G (Sun Nov 27 2005 - 19:14:48 PST)
- Re: AMBER: Comparing EELEC from amber and that calculated in the trivial fashion. David A. Case (Sun Nov 27 2005 - 22:12:55 PST)
- Re: AMBER: Comparing EELEC from amber and that calculated in the trivial fashion. Carlos Simmerling (Mon Nov 28 2005 - 04:41:30 PST)
AMBER: How to check for water mediated hydrogen bonds? Hannes Loeffler (Sun Nov 27 2005 - 20:52:44 PST)
AMBER: Cluster - input files Ananda Rama Krishnan Selvaraj (Mon Nov 28 2005 - 02:37:22 PST)
- Re: AMBER: Cluster - input files David A. Case (Mon Nov 28 2005 - 10:47:12 PST)
- Re: AMBER: Cluster - input files Ananda Rama Krishnan Selvaraj (Mon Nov 28 2005 - 12:39:44 PST)
  - Re: AMBER: Cluster - input files David A. Case (Mon Nov 28 2005 - 13:28:14 PST)
- Re: AMBER: Cluster - input files Bill Ross (Mon Nov 28 2005 - 13:51:04 PST)
AMBER: CD spectrum Anthony Cruz (Mon Nov 28 2005 - 09:58:34 PST)
- Re: AMBER: CD spectrum Adrian Roitberg (Mon Nov 28 2005 - 07:10:15 PST)
AMBER: antechamber charge methods Sagar S. Rane (Mon Nov 28 2005 - 08:20:45 PST)
AMBER: MM_PBSA stopped at some snapshot Xioling Chuang (Mon Nov 28 2005 - 21:57:54 PST)
- Re: AMBER: MM_PBSA stopped at some snapshot Ray Luo (Sun Nov 27 2005 - 18:37:12 PST)
- Re: AMBER: MM_PBSA stopped at some snapshot Ray Luo (Tue Nov 29 2005 - 18:55:41 PST)
AMBER: AMBER compilation with -DREM Sergey Krishtal (Tue Nov 29 2005 - 04:45:46 PST)
- Re: AMBER: AMBER compilation with -DREM David A. Case (Tue Nov 29 2005 - 09:40:18 PST)
- Re[2]: AMBER: AMBER compilation with -DREM Sergey Krishtal (Wed Nov 30 2005 - 03:38:17 PST)
  - RE: Re[2]: AMBER: AMBER compilation with -DREM Ross Walker (Wed Nov 30 2005 - 08:26:29 PST)
AMBER: some problems with Antechamber David Mobley (Tue Nov 29 2005 - 08:39:26 PST)
- Re: AMBER: some problems with Antechamber Wei Zhang (Tue Nov 29 2005 - 09:14:53 PST)
  - Re: AMBER: some problems with Antechamber David Mobley (Tue Nov 29 2005 - 11:08:00 PST)
AMBER: constant pressure vs. constant volume heating Vlad Cojocaru (Tue Nov 29 2005 - 10:50:39 PST)
- Re: AMBER: constant pressure vs. constant volume heating David Mobley (Tue Nov 29 2005 - 11:20:46 PST)
- RE: AMBER: constant pressure vs. constant volume heating Ross Walker (Tue Nov 29 2005 - 11:20:38 PST)
Re: AMBER: constant pressure vs. constant volume heating Bill Ross (Tue Nov 29 2005 - 11:51:12 PST)
AMBER: Solvation in trifluoroethanol Ann Vilan Tran (Tue Nov 29 2005 - 11:57:17 PST)
AMBER: rdparm bug David Mobley (Tue Nov 29 2005 - 18:40:02 PST)
AMBER: question convert crd files to pdb files Zhuang (Tue Nov 29 2005 - 20:02:08 PST)
- RE: AMBER: question convert crd files to pdb files Ross Walker (Tue Nov 29 2005 - 20:27:02 PST)
AMBER: parmchk segfaulting David A. Case (Tue Nov 29 2005 - 20:06:03 PST)
AMBER: more data points on the parmchk problem David A. Case (Wed Nov 30 2005 - 07:30:12 PST)
- Re: AMBER: more data points on the parmchk problem David Mobley (Wed Nov 30 2005 - 09:04:01 PST)
- Re: AMBER: more data points on the parmchk problem John Mongan (Wed Nov 30 2005 - 13:01:35 PST)
AMBER: ifort compiling problem Simon Whitehead (Wed Nov 30 2005 - 07:27:48 PST)
- Re: AMBER: ifort compiling problem Andy Purkiss (Wed Nov 30 2005 - 07:39:48 PST)
AMBER: Targeted MD Whitney Allen (Wed Nov 30 2005 - 08:20:10 PST)
- Re: AMBER: Targeted MD Viktor Hornak (Wed Nov 30 2005 - 09:46:55 PST)
- Re: AMBER: Targeted MD Carlos Simmerling (Wed Nov 30 2005 - 09:51:47 PST)
AMBER: Fluorine in MM-PBSA (AMBER8) yuann.bioinfo.ndhu.edu.tw (Wed Nov 30 2005 - 08:30:36 PST)
- Re: AMBER: Fluorine in MM-PBSA (AMBER8) sychen (Wed Nov 30 2005 - 21:43:55 PST)
AMBER: Residual Dipolar Refinement RadhaKumari Yadav (Wed Nov 30 2005 - 09:16:23 PST)
- Re: AMBER: Residual Dipolar Refinement David A. Case (Thu Dec 01 2005 - 06:22:11 PST)
AMBER: MM-PBSA: plot the "Ggas+Gsol" vs time Lihong Song (Wed Nov 30 2005 - 10:15:28 PST)
- Re: AMBER: MM-PBSA: plot the "Ggas+Gsol" vs time Nelson Fonseca (Wed Nov 30 2005 - 13:33:09 PST)
  - Re: AMBER: MM-PBSA: plot the "Ggas+Gsol" vs time Holger Gohlke (Wed Nov 30 2005 - 23:06:49 PST)
AMBER: Any way to get different charge on same type atom Jianzhong Liu (Wed Nov 30 2005 - 15:07:28 PST)
- Re: AMBER: Any way to get different charge on same type atom rpaduri.chem.wayne.edu (Wed Nov 30 2005 - 16:37:13 PST)
AMBER: Creating an Ester with Antechamber/Gaff John O'Mahony (Thu Dec 01 2005 - 01:46:40 PST)
- Re: AMBER: Creating an Ester with Antechamber/Gaff David A. Case (Fri Dec 02 2005 - 20:05:16 PST)
AMBER: regarding ambpdb S.Sundar Raman (Thu Dec 01 2005 - 02:40:58 PST)
- Re: AMBER: regarding ambpdb Ilyas Yildirim (Thu Dec 01 2005 - 02:54:03 PST)
  - Re: AMBER: regarding ambpdb S.Sundar Raman (Thu Dec 01 2005 - 05:39:31 PST)
    - Re: AMBER: regarding ambpdb Carlos Simmerling (Thu Dec 01 2005 - 05:57:39 PST)
AMBER: MD without a thermostat Vlad Cojocaru (Thu Dec 01 2005 - 07:32:57 PST)
- Re: AMBER: MD without a thermostat David A. Case (Thu Dec 01 2005 - 11:42:51 PST)
AMBER: no thermostat versus very weak thermostat Vlad Cojocaru (Thu Dec 01 2005 - 07:57:15 PST)
AMBER: Some explanations of MM_PBSA .DECOMP OUTPUT file? Peng Tao (Thu Dec 01 2005 - 08:35:09 PST)
AMBER: Mg2+ issues of using MM-PB/GBSA mingche Pan (Thu Dec 01 2005 - 11:01:24 PST)
- Re: AMBER: Mg2+ issues of using MM-PB/GBSA Carlos Simmerling (Thu Dec 01 2005 - 11:26:11 PST)
- Re: AMBER: Mg2+ issues of using MM-PB/GBSA Ray Luo (Wed Nov 30 2005 - 08:46:56 PST)
- Re: AMBER: Mg2+ issues of using MM-PB/GBSA David A. Case (Thu Dec 01 2005 - 11:47:20 PST)
- Re: AMBER: Mg2+ issues of using MM-PB/GBSA Thomas Cheatham (Thu Dec 01 2005 - 21:27:21 PST)
- Re: AMBER: Mg2+ issues of using MM-PB/GBSA mingche Pan (Fri Dec 02 2005 - 08:32:15 PST)
- Re: AMBER: Mg2+ issues of using MM-PB/GBSA mingche Pan (Fri Dec 02 2005 - 10:09:28 PST)
  - Re: AMBER: Mg2+ issues of using MM-PB/GBSA Ray Luo (Wed Nov 30 2005 - 18:04:55 PST)
    - Re: AMBER: Mg2+ issues of using MM-PB/GBSA mingche Pan (Fri Dec 02 2005 - 11:36:53 PST)
    - Re: AMBER: Mg2+ issues of using MM-PB/GBSA Ray Luo (Wed Nov 30 2005 - 20:31:29 PST)
- Re: AMBER: Mg2+ issues of using MM-PB/GBSA. . Don.Bashford.stjude.org (Mon Dec 05 2005 - 10:09:20 PST)
  - AMBER: Installation of AMBER8 on a PC with a Pentium EE type CPU Cenk Andac (Sat Dec 31 2005 - 10:24:30 PST)
    - Re: AMBER: Installation of AMBER8 on a PC with a Pentium EE type CPU David Mathews (Sun Jan 01 2006 - 15:08:17 PST)
    - Re: AMBER: Installation of AMBER8 on a PC with a Pentium EE type CPU David Mathews (Sun Jan 01 2006 - 15:29:40 PST)
AMBER: Radial Distribution functions by ptraj Priti Hansia (Thu Dec 01 2005 - 11:44:02 PST)
AMBER: Position restraints and Models Steve Seibold (Thu Dec 01 2005 - 12:54:06 PST)
AMBER: Questions about MM-PBSA in Amber8 zgleo (Thu Dec 01 2005 - 21:04:26 PST)
- Re: AMBER: Questions about MM-PBSA in Amber8 Ray Luo (Wed Nov 30 2005 - 16:39:50 PST)
AMBER: Problem in running AMBER 7 in solaris ! Pradipta Bandyopadhyay (Fri Dec 02 2005 - 01:17:19 PST)
- Re: AMBER: Problem in running AMBER 7 in solaris ! Atro Tossavainen (Fri Dec 02 2005 - 04:14:42 PST)
AMBER: Problem with sander test suites in solaris ! Pradipta Bandyopadhyay (Fri Dec 02 2005 - 06:26:05 PST)
AMBER: ptraj crash error Simon Whitehead (Fri Dec 02 2005 - 09:51:47 PST)
- Re: AMBER: ptraj crash error David E. Konerding (Fri Dec 02 2005 - 10:24:35 PST)
AMBER: rotational motion in periodic simulation Douali, Latifa (Fri Dec 02 2005 - 10:50:28 PST)
- Re: AMBER: rotational motion in periodic simulation David A. Case (Fri Dec 02 2005 - 15:06:22 PST)
AMBER: Replica-Exchange MD from AMBER8! Peng Tao (Fri Dec 02 2005 - 14:28:27 PST)
- Re: AMBER: Replica-Exchange MD from AMBER8! Carlos Simmerling (Fri Dec 02 2005 - 14:49:25 PST)
  - Re: AMBER: Replica-Exchange MD from AMBER8! Peng Tao (Sat Dec 03 2005 - 09:13:15 PST)
  - Re: AMBER: Replica-Exchange MD from AMBER8! Peng Tao (Sat Dec 03 2005 - 12:19:12 PST)
    - Re: AMBER: Replica-Exchange MD from AMBER8! Carlos Simmerling (Sat Dec 03 2005 - 13:11:07 PST)
AMBER: ERROR in readParm: ...failed to find BONDS_WITHOUT_HYDROGEN Rhoad, Jonathan S. (Fri Dec 02 2005 - 15:02:36 PST)
AMBER: parmchk bug fix David A. Case (Fri Dec 02 2005 - 20:22:21 PST)
AMBER: parmchk bug fix, with attachment David A. Case (Fri Dec 02 2005 - 20:33:20 PST)
AMBER: Alignment tensor and Interia tensor RadhaKumari Yadav (Sat Dec 03 2005 - 08:58:01 PST)
- Re: AMBER: Alignment tensor and Interia tensor David A. Case (Sat Dec 03 2005 - 11:05:30 PST)
AMBER: The error during calculating PB with pbsa zhli_2000.126.com (Sun Dec 04 2005 - 20:39:19 PST)
- Re: AMBER: The error during calculating PB with pbsa Ray Luo (Sun Dec 04 2005 - 18:16:09 PST)
AMBER: RMSD Calculations Kara Di Giorgio (Mon Dec 05 2005 - 07:22:03 PST)
- Re: AMBER: RMSD Calculations Carlos Simmerling (Mon Dec 05 2005 - 08:00:23 PST)
  - Re: AMBER: RMSD Calculations Kara Wald (Mon Dec 05 2005 - 08:39:44 PST)
    - Re: AMBER: RMSD Calculations Carlos Simmerling (Mon Dec 05 2005 - 08:56:36 PST)
- Re: AMBER: RMSD Calculations kkirschn.hamilton.edu (Mon Dec 05 2005 - 08:29:23 PST)
- Re: AMBER: RMSD Calculations Thomas Cheatham (Mon Dec 05 2005 - 14:50:36 PST)
  - AMBER: AMBER vs QM: base pairing and stacking Jiri Sponer (Wed Dec 07 2005 - 10:22:02 PST)
  - AMBER: distance restraint simulation Ed Pate (Tue Dec 27 2005 - 10:36:44 PST)
    - Re: AMBER: distance restraint simulation David A. Case (Tue Dec 27 2005 - 12:31:03 PST)
AMBER: RESP: Question Carlos Jaime (Mon Dec 05 2005 - 09:43:16 PST)
- Re: AMBER: RESP: Question Piotr Cieplak (Mon Dec 05 2005 - 10:00:37 PST)
- Re: AMBER: RESP: Question FyD (Mon Dec 05 2005 - 13:31:32 PST)
- Re: AMBER: RESP: Question FyD (Tue Dec 06 2005 - 05:13:49 PST)
AMBER: 6-thioguanine E.A.Moore (Tue Dec 06 2005 - 06:31:59 PST)
AMBER: MM_PBSA parameters Nelson Fonseca (Tue Dec 06 2005 - 07:26:55 PST)
AMBER: hi Germán Sciaini (Wed Dec 07 2005 - 02:51:06 PST)
- Re: AMBER: hi David A. Case (Wed Dec 07 2005 - 12:01:52 PST)
AMBER: about resp JAVIER PEREZ (Wed Dec 07 2005 - 04:12:48 PST)
- Re:AMBER: about resp Kateryna Miroshnychenko (Wed Dec 07 2005 - 05:50:07 PST)
AMBER: Relax in tLEaP ? FyD (Wed Dec 07 2005 - 06:00:38 PST)
- Re: AMBER: Relax in tLEaP ? David A. Case (Wed Dec 07 2005 - 11:58:43 PST)
AMBER: Clustering - MMTSB Toolkit kclust kkirschn.hamilton.edu (Wed Dec 07 2005 - 10:43:52 PST)
- Re: AMBER: Clustering - MMTSB Toolkit kclust Adrian Roitberg (Wed Dec 07 2005 - 12:46:50 PST)
AMBER: Adding/recognizing calcium atoms Nitin Bhardwaj (Wed Dec 07 2005 - 13:24:38 PST)
Re: AMBER: Adding/recognizing calcium atoms Bill Ross (Wed Dec 07 2005 - 13:32:05 PST)
AMBER: error about using ambmask zhli_2000.126.com (Thu Dec 08 2005 - 05:40:34 PST)
- Re: AMBER: error about using ambmask Viktor Hornak (Thu Dec 08 2005 - 05:53:22 PST)
AMBER: Question on makeing up of missing atoms Benjamin Juhl (Fri Dec 09 2005 - 04:30:57 PST)
- Re: AMBER: Question on makeing up of missing atoms Carlos Simmerling (Fri Dec 09 2005 - 04:57:06 PST)
AMBER: reading frcmod torsional parameters ivan.mmb.pcb.ub.es (Mon Dec 12 2005 - 05:44:36 PST)
- Re: AMBER: reading frcmod torsional parameters David A. Case (Mon Dec 12 2005 - 08:56:02 PST)
  - Re: AMBER: reading frcmod torsional parameters ivan.mmb.pcb.ub.es (Tue Dec 13 2005 - 07:42:37 PST)
AMBER: question about mmpbsa cui wei (Mon Dec 12 2005 - 23:33:08 PST)
- Re: AMBER: question about mmpbsa xhu1.memphis.edu (Wed Dec 08 2004 - 14:23:27 PST)
- Re: AMBER: question about mmpbsa Ray Luo (Mon Dec 12 2005 - 19:34:13 PST)
  - Re: AMBER: question about mmpbsa cui wei (Tue Dec 13 2005 - 17:09:29 PST)
    - Re: AMBER: question about mmpbsa Ray Luo (Thu Dec 15 2005 - 10:08:55 PST)
  - AMBER: E of amber calculations YoungJin Cho (Wed Dec 14 2005 - 09:34:47 PST)
    - Re: AMBER: E of amber calculations Carlos Simmerling (Thu Dec 15 2005 - 04:30:08 PST)
    - RE: AMBER: E of amber calculations Ross Walker (Thu Dec 15 2005 - 08:23:46 PST)
AMBER: How to add water to calculate MMPBSA Kitiyaporn Wittayanarakul (Wed Dec 14 2005 - 10:06:53 PST)
- Re: AMBER: How to add water to calculate MMPBSA David A. Case (Wed Dec 14 2005 - 15:50:13 PST)
  - Re: AMBER: How to add water to calculate MMPBSA. . Don.Bashford.stjude.org (Thu Dec 15 2005 - 09:13:30 PST)
    - Re: AMBER: How to add water to calculate MMPBSA. . Thomas Cheatham (Thu Dec 15 2005 - 10:09:47 PST)
AMBER: nmode error: GNORM is greater than the requested maximum zhli_2000.126.com (Wed Dec 14 2005 - 18:16:07 PST)
- Re: AMBER: nmode error: GNORM is greater than the requested maximum David A. Case (Fri Dec 16 2005 - 14:08:21 PST)
AMBER: error with compiling amber8 with lam on intel pc clusters Ye Mei (Wed Dec 14 2005 - 19:36:54 PST)
- Re: AMBER: error with compiling amber8 with lam on intel pc clusters Xuebin Qiao (Wed Dec 14 2005 - 23:57:24 PST)
- RE: AMBER: error with compiling amber8 with lam on intel pc clusters Ross Walker (Thu Dec 15 2005 - 08:11:05 PST)
AMBER: about antechamber(amber8) linfu (Wed Dec 14 2005 - 23:51:16 PST)
- Re: AMBER: about antechamber(amber8) Carlos Simmerling (Thu Dec 15 2005 - 04:45:59 PST)
- RE: AMBER: about antechamber(amber8) Junmei Wang (Thu Dec 15 2005 - 07:54:40 PST)
AMBER: aniso and iso Yam (Thu Dec 15 2005 - 02:11:45 PST)
- Re: AMBER: aniso and iso David A. Case (Thu Dec 15 2005 - 08:28:28 PST)
- Re: AMBER: aniso and iso Yam (Mon Dec 19 2005 - 00:17:43 PST)
  - Re: AMBER: aniso and iso Carlos Simmerling (Mon Dec 19 2005 - 04:26:37 PST)
AMBER: parameters for fluorine atom Morena Spreafico (Thu Dec 15 2005 - 04:33:52 PST)
- Re: AMBER: parameters for fluorine atom Carlos Simmerling (Thu Dec 15 2005 - 04:47:20 PST)
AMBER: Build for single precision David Caliga (Thu Dec 15 2005 - 07:31:02 PST)
- Re: AMBER: Build for single precision Robert Duke (Thu Dec 15 2005 - 08:23:49 PST)
- RE: AMBER: Build for single precision Ross Walker (Thu Dec 15 2005 - 08:29:35 PST)
AMBER: parallel AMBER on cluster Kateryna Miroshnychenko (Thu Dec 15 2005 - 10:16:17 PST)
- Re: AMBER: parallel AMBER on cluster Robert Duke (Thu Dec 15 2005 - 10:37:22 PST)
- RE: AMBER: parallel AMBER on cluster Ross Walker (Thu Dec 15 2005 - 10:38:57 PST)
Re: AMBER: parallel AMBER on cluster Carlos Simmerling (Thu Dec 15 2005 - 10:55:55 PST)
AMBER: | ERROR: Could not read coords from rst file Jiapu.Zhang.csiro.au (Thu Dec 15 2005 - 18:26:46 PST)
- Re: AMBER: | ERROR: Could not read coords from rst file Robert Duke (Thu Dec 15 2005 - 19:14:35 PST)
AMBER: installation on a dual core Barbault Florent (Fri Dec 16 2005 - 06:00:08 PST)
- Re: AMBER: installation on a dual core Nelson Fonseca (Fri Dec 16 2005 - 06:14:22 PST)
AMBER: About Salt concentration Varsha Goyal (Fri Dec 16 2005 - 16:03:05 PST)
- Re: AMBER: About Salt concentration Jiri Sponer (Fri Dec 16 2005 - 17:05:13 PST)
  - Re: AMBER: About Salt concentration Varsha Goyal (Fri Dec 16 2005 - 17:37:45 PST)
- RE: AMBER: About Salt concentration David Cowburn (Wed Dec 21 2005 - 13:33:15 PST)
AMBER: distance restraints Ed Pate (Sat Dec 17 2005 - 14:43:32 PST)
- Re: AMBER: distance restraints Carlos Simmerling (Sat Dec 17 2005 - 15:08:28 PST)
AMBER: | ERROR: Could not read coords from *.rst Jiapu.Zhang.csiro.au (Sat Dec 17 2005 - 15:59:22 PST)
AMBER: No exchange among replicas in REMD! Peng Tao (Sun Dec 18 2005 - 14:01:28 PST)
- Re: AMBER: No exchange among replicas in REMD! Carlos Simmerling (Sun Dec 18 2005 - 14:26:42 PST)
  - Re: AMBER: No exchange among replicas in REMD! Peng Tao (Sun Dec 18 2005 - 17:45:03 PST)
    - Re: AMBER: No exchange among replicas in REMD! Carlos Simmerling (Sun Dec 18 2005 - 18:23:14 PST)
    - Re: AMBER: No exchange among replicas in REMD! Peng Tao (Mon Dec 19 2005 - 06:57:30 PST)
    - Re: AMBER: No exchange among replicas in REMD! Carlos Simmerling (Mon Dec 19 2005 - 08:35:30 PST)
    - Re: AMBER: No exchange among replicas in REMD! Peng Tao (Mon Dec 19 2005 - 10:35:24 PST)
AMBER: No exchange among replicas in REMD! Peng Tao (Sun Dec 18 2005 - 14:11:06 PST)
- Re: AMBER: No exchange among replicas in REMD! Carlos Simmerling (Sun Dec 18 2005 - 14:27:25 PST)
- Re: AMBER: No exchange among replicas in REMD! Adrian E. Roitberg (Sun Dec 18 2005 - 15:16:22 PST)
  - Re: AMBER: No exchange among replicas in REMD! Carlos Simmerling (Sun Dec 18 2005 - 18:22:48 PST)
AMBER: a quistion about compile cui wei (Mon Dec 19 2005 - 04:10:07 PST)
- Re: AMBER: a quistion about compile David A. Case (Mon Dec 19 2005 - 08:22:58 PST)
  - Re: AMBER: a quistion about compile cui wei (Mon Dec 19 2005 - 17:00:20 PST)
  - Re: AMBER: a quistion about compile snowyowls (Tue Dec 20 2005 - 05:30:07 PST)
    - Re: AMBER: a quistion about compile David A. Case (Tue Dec 20 2005 - 08:56:58 PST)
    - Re: AMBER: a quistion about compile snowyowls (Wed Dec 21 2005 - 06:53:21 PST)
    - Re: AMBER: a quistion about compile David A. Case (Wed Dec 21 2005 - 13:01:52 PST)
    - Re: AMBER: a quistion about compile snowyowls (Fri Dec 23 2005 - 04:32:52 PST)
- Re: AMBER: a quistion about compile Wei Zhang (Mon Dec 19 2005 - 09:01:22 PST)
  - Re: AMBER: a quistion about compile cui wei (Mon Dec 19 2005 - 17:03:46 PST)
    - Re: AMBER: a quistion about compile Wei Zhang (Tue Dec 20 2005 - 08:35:34 PST)
AMBER: MD problems (SHAKE) blakrose.gazeta.pl (Mon Dec 19 2005 - 04:49:41 PST)
AMBER: Atoms restrain Angelo Pugliese (Mon Dec 19 2005 - 05:09:35 PST)
- Re: AMBER: Atoms restrain David A. Case (Mon Dec 19 2005 - 08:20:25 PST)
AMBER: compiling leap with Xeon EM64 (suse linux 9.2) HL Eastwood (Mon Dec 19 2005 - 07:17:08 PST)
AMBER: re: leap compilation problems xeon EM64 processor HL Eastwood (Mon Dec 19 2005 - 07:30:57 PST)
AMBER: MD problems/shake blakrose.gazeta.pl (Mon Dec 19 2005 - 12:34:52 PST)
- Re: AMBER: MD problems/shake Thomas E. Cheatham, III (Mon Dec 19 2005 - 12:53:40 PST)
- Re: AMBER: MD problems/shake Bill Ross (Mon Dec 19 2005 - 12:59:04 PST)
- Re: AMBER: MD problems/shake blakrose.gazeta.pl (Mon Dec 19 2005 - 14:45:43 PST)
  - Re: AMBER: MD problems/shake Thomas E. Cheatham, III (Mon Dec 19 2005 - 15:40:40 PST)
    - Re: AMBER: MD problems/shake Thomas E. Cheatham, III (Tue Dec 20 2005 - 11:20:26 PST)
- Re: AMBER: MD problems/shake Bill Ross (Mon Dec 19 2005 - 15:14:10 PST)
- Re: AMBER: MD problems/shake blakrose.gazeta.pl (Mon Dec 19 2005 - 15:33:12 PST)
- Re: AMBER: MD problems/shake blakrose.gazeta.pl (Mon Dec 19 2005 - 15:44:59 PST)
- Re: AMBER: MD problems/shake Bill Ross (Mon Dec 19 2005 - 15:50:33 PST)
- Re: AMBER: MD problems/shake Bill Ross (Mon Dec 19 2005 - 15:54:01 PST)
- Re: AMBER: MD problems/shake blakrose.gazeta.pl (Mon Dec 19 2005 - 16:03:08 PST)
- Re: AMBER: MD problems/shake blakrose.gazeta.pl (Mon Dec 19 2005 - 16:07:44 PST)
- Re: AMBER: MD problems/shake blakrose.gazeta.pl (Tue Dec 20 2005 - 15:17:45 PST)
AMBER: rdc multiple tensors dmcelh.uchicago.edu (Mon Dec 19 2005 - 15:01:13 PST)
AMBER: Ligand problem bybaker.itsa.ucsf.edu (Mon Dec 19 2005 - 16:40:22 PST)
- Re: AMBER: Ligand problem blakrose.gazeta.pl (Mon Dec 19 2005 - 17:02:54 PST)
- Re: AMBER: Ligand problem Suxin Zheng (Mon Dec 19 2005 - 17:05:13 PST)
AMBER: Sander.LES questions Bing Liu (Tue Dec 20 2005 - 06:51:09 PST)
- Re: AMBER: Sander.LES questions Carlos Simmerling (Tue Dec 20 2005 - 07:07:12 PST)
AMBER: rmsd Anthony Cruz (Tue Dec 20 2005 - 11:17:51 PST)
Fwd: AMBER: rdc multiple tensors dmcelh.uchicago.edu (Tue Dec 20 2005 - 09:55:51 PST)
AMBER: Re: Ligand problem bybaker.itsa.ucsf.edu (Tue Dec 20 2005 - 10:50:03 PST)
- Re: AMBER: Re: Ligand problem Ilyas Yildirim (Tue Dec 20 2005 - 16:39:02 PST)
Re: AMBER: MD problems/shake-many thanks blakrose.gazeta.pl (Tue Dec 20 2005 - 15:04:24 PST)
AMBER: some questions about nmode zhli_2000.126.com (Tue Dec 20 2005 - 18:30:22 PST)
AMBER: No skew or curtosis when zero variance in moment Ye Mei (Wed Dec 21 2005 - 07:56:43 PST)
- Re: AMBER: No skew or curtosis when zero variance in moment David A. Case (Thu Dec 22 2005 - 10:14:25 PST)
AMBER: lib-4324 : UNRECOVERABLE library error lv haiting (Wed Dec 21 2005 - 18:31:46 PST)
- Re: AMBER: lib-4324 : UNRECOVERABLE library error Thomas Cheatham (Wed Dec 21 2005 - 19:16:22 PST)
- Re: AMBER: lib-4324 : UNRECOVERABLE library error lv haiting (Wed Dec 21 2005 - 20:21:50 PST)
AMBER: Amber crashes at simulation in the NVT ensemble with the periodic box equiilbrated in the NPT ensemble. Sergey Krishtal (Wed Dec 21 2005 - 22:15:14 PST)
- Re: AMBER: Amber crashes at simulation in the NVT ensemble with the periodic box equiilbrated in the NPT ensemble. David A. Case (Thu Dec 22 2005 - 11:56:36 PST)
AMBER: Merry Xmas Angelo Pugliese (Thu Dec 22 2005 - 03:43:14 PST)
AMBER: increase the limit of restraintmask Sichun Yang (Thu Dec 22 2005 - 10:58:14 PST)
AMBER: does the result of H bond is consistent with the ∆Eele of MM_PBSA? haixiao jin (Thu Dec 22 2005 - 20:12:46 PST)
- RE: AMBER: does the result of H bond is consistent with the ?Eele of MM_PBSA? Yong Duan (Thu Dec 22 2005 - 22:43:53 PST)
  - Re: AMBER: does the result of H bond is consistent with the ?Eele of MM_PBSA? cristian obiol (Fri Dec 23 2005 - 03:01:42 PST)
AMBER: ERROR in readParm: ...failed to find ANGLES_INC_HYDROGEN Priti Hansia (Fri Dec 23 2005 - 03:28:57 PST)
- Re: AMBER: ERROR in readParm: ...failed to find ANGLES_INC_HYDROGEN David A. Case (Tue Dec 27 2005 - 08:17:49 PST)
  - Re: AMBER: ERROR in readParm: ...failed to find ANGLES_INC_HYDROGEN Priti Hansia (Tue Dec 27 2005 - 09:35:41 PST)
    - Re: AMBER: ERROR in readParm: ...failed to find ANGLES_INC_HYDROGEN David A. Case (Tue Dec 27 2005 - 11:18:06 PST)
    - Re: AMBER: ERROR in readParm: ...failed to find ANGLES_INC_HYDROGEN Priti Hansia (Wed Dec 28 2005 - 05:05:56 PST)
AMBER: the averaged structure VS the specific snapshot haixiao jin (Thu Dec 22 2005 - 20:24:04 PST)
- RE: AMBER: the averaged structure VS the specific snapshot Yong Duan (Thu Dec 22 2005 - 22:38:00 PST)
AMBER: ambpdb TER problems Sam (Fri Dec 23 2005 - 08:23:26 PST)
- Re: AMBER: ambpdb TER problems David A. Case (Fri Dec 23 2005 - 17:53:50 PST)
- Re: AMBER: ambpdb TER problems samuel.arey.epfl.ch (Mon Dec 26 2005 - 11:26:27 PST)
  - Re: AMBER: ambpdb TER problems David A. Case (Mon Dec 26 2005 - 18:08:26 PST)
    - Re: AMBER: ambpdb TER problems Sam (Tue Dec 27 2005 - 08:23:39 PST)
    - Re: AMBER: ambpdb TER problems David A. Case (Tue Dec 27 2005 - 12:30:48 PST)
    - Re: AMBER: ambpdb TER problems Sam (Wed Dec 28 2005 - 09:17:14 PST)
    - Re: AMBER: ambpdb TER problems David A. Case (Fri Dec 30 2005 - 10:05:10 PST)
- Re: AMBER: ambpdb TER problems Bill Ross (Mon Dec 26 2005 - 13:27:07 PST)
AMBER: To post or mail to the list (subscribers only) ping jiang (Fri Dec 23 2005 - 12:07:45 PST)
AMBER: (no subject) ping jiang (Fri Dec 23 2005 - 12:46:58 PST)
- Re: AMBER: (no subject) Thomas Cheatham (Fri Dec 23 2005 - 13:37:57 PST)
- Re: AMBER: (no subject) David A. Case (Fri Dec 23 2005 - 17:43:28 PST)
  - Re: AMBER: (no subject) ping jiang (Fri Dec 23 2005 - 18:25:19 PST)
AMBER: problem with improper torsions in parmchk Kateryna Miroshnychenko (Mon Dec 26 2005 - 08:55:54 PST)
AMBER: building amino acid based surfactants? Eugene Billiot (Mon Dec 26 2005 - 13:25:33 PST)
- Re: AMBER: building amino acid based surfactants? David A. Case (Mon Dec 26 2005 - 17:53:19 PST)
AMBER: problem with ssh and xleap A D (Tue Dec 27 2005 - 12:12:51 PST)
- Re: AMBER: problem with ssh and xleap Scott Brozell (Wed Dec 28 2005 - 14:02:48 PST)
  - Re: AMBER: problem with ssh and xleap A D (Fri Dec 30 2005 - 19:06:15 PST)
- Re: AMBER: problem with ssh and xleap Peter Gannett (Mon Jan 02 2006 - 08:26:18 PST)
  - Re: AMBER: problem with ssh and xleap Robyn Ayscue (Mon Jan 02 2006 - 18:33:13 PST)
AMBER: problem of calculate the charge ping jiang (Tue Dec 27 2005 - 16:47:16 PST)
- Re: AMBER: problem of calculate the charge David A. Case (Fri Dec 30 2005 - 09:58:47 PST)
  - Re: AMBER: problem of calculate the charge ping jiang (Fri Dec 30 2005 - 10:48:41 PST)
AMBER: problem of calculate the charge2 ping jiang (Tue Dec 27 2005 - 18:17:05 PST)
AMBER: Question about partial charge for ligand molecules Woojin Lee (Wed Dec 28 2005 - 18:37:47 PST)
AMBER: non bond over flow S.Sundar Raman (Wed Dec 28 2005 - 19:50:27 PST)
- RE: AMBER: non bond over flow Ross Walker (Thu Dec 29 2005 - 08:15:35 PST)
AMBER:how to deal with metal ion? snowyowls (Thu Dec 29 2005 - 22:24:58 PST)
- Re: AMBER:how to deal with metal ion? samuel.arey.epfl.ch (Fri Dec 30 2005 - 02:56:08 PST)
- Re: AMBER:how to deal with metal ion? samuel.arey.epfl.ch (Fri Dec 30 2005 - 03:05:39 PST)
- Re: AMBER:how to deal with metal ion? Tim Meyer (Fri Dec 30 2005 - 08:05:06 PST)
- Re: AMBER:how to deal with metal ion? Tim Meyer (Fri Dec 30 2005 - 08:09:07 PST)
AMBER: water molecules with in 3 angstroms to the solute nag raj (Mon Jan 02 2006 - 20:47:06 PST)
- Re: AMBER: water molecules with in 3 angstroms to the solute Ilyas Yildirim (Tue Jan 03 2006 - 01:05:24 PST)
- Re: AMBER: water molecules with in 3 angstroms to the solute Ilyas Yildirim (Tue Jan 03 2006 - 16:40:07 PST)
AMBER: requirement of delphi for mm_pbsa Manish Datt (Tue Jan 03 2006 - 10:46:53 PST)
- Re: AMBER: requirement of delphi for mm_pbsa David A. Case (Wed Jan 04 2006 - 08:22:53 PST)
  - Re: AMBER: requirement of delphi for mm_pbsa Holger Gohlke (Wed Jan 04 2006 - 09:09:46 PST)
AMBER: How to run mm_pbsa_statistics.pl? Peng Tao (Wed Jan 04 2006 - 05:51:55 PST)
- Re: AMBER: How to run mm_pbsa_statistics.pl? Holger Gohlke (Wed Jan 04 2006 - 09:27:05 PST)
  - Re: AMBER: How to run mm_pbsa_statistics.pl? Peng Tao (Thu Jan 05 2006 - 05:39:19 PST)
  - Re: AMBER: How to run mm_pbsa_statistics.pl? Peng Tao (Thu Jan 05 2006 - 15:11:42 PST)
  - Re: AMBER: How to run mm_pbsa_statistics.pl? Peng Tao (Tue Jan 10 2006 - 07:49:00 PST)
AMBER: minimalization prior to nmode analysis, is it necessary? Magne Olufsen (Wed Jan 04 2006 - 09:42:21 PST)
- Re: AMBER: minimalization prior to nmode analysis, is it necessary? David A. Case (Thu Jan 05 2006 - 17:56:26 PST)
  - Re: AMBER: minimalization prior to nmode analysis, is it necessary? Adrian Roitberg (Thu Jan 05 2006 - 18:38:51 PST)
AMBER: Ligand charge bybaker.itsa.ucsf.edu (Wed Jan 04 2006 - 10:51:57 PST)
- Re: AMBER: Ligand charge David Mobley (Wed Jan 04 2006 - 11:43:54 PST)
- Re: AMBER: Ligand charge Ilyas Yildirim (Wed Jan 04 2006 - 22:02:42 PST)
- Re: AMBER: Ligand charge Bill Ross (Thu Jan 05 2006 - 10:24:18 PST)
AMBER: Leap Joseph Fernandez (Wed Jan 04 2006 - 13:36:13 PST)
Re: AMBER: Leap Bill Ross (Wed Jan 04 2006 - 14:02:20 PST)
AMBER: Q: results from PB solver in example no.3 Tomimoto_Masaki.takeda.co.jp (Wed Jan 04 2006 - 15:09:42 PST)
- Re: AMBER: Q: results from PB solver in example no.3 Ray Luo (Wed Jan 04 2006 - 18:45:28 PST)
AMBER: Where to modify the atom type in sander? zhli_2000.126.com (Thu Jan 05 2006 - 01:21:20 PST)
- RE: AMBER: Where to modify the atom type in sander? Ross Walker (Thu Jan 05 2006 - 08:12:34 PST)
AMBER: creating a RST file from specific set of binpos/crd file Baird, Jamie $bairdje$ (Fri Jan 06 2006 - 09:33:00 PST)
- Re: AMBER: creating a RST file from specific set of binpos/crd file Thomas E. Cheatham, III (Fri Jan 06 2006 - 09:53:51 PST)
- RE: AMBER: creating a RST file from specific set of binpos/crd file Ross Walker (Fri Jan 06 2006 - 10:01:39 PST)
Re: AMBER: Installation of AMBER8 on a PC with a Pentium EE type Amber admin (Fri Jan 06 2006 - 13:36:19 PST)
AMBER: SHAKE - ntc = 3 Jennie Thomas (Fri Jan 06 2006 - 17:05:09 PST)
- Re: AMBER: SHAKE - ntc = 3 David A. Case (Fri Jan 06 2006 - 17:26:55 PST)
  - Re: AMBER: SHAKE - ntc = 3 Jennie Thomas (Mon Jan 09 2006 - 14:38:24 PST)
    - RE: AMBER: SHAKE - ntc = 3 Ross Walker (Mon Jan 09 2006 - 14:51:01 PST)
    - Re: AMBER: SHAKE - ntc = 3 David A. Case (Mon Jan 09 2006 - 14:59:46 PST)
    - Re: AMBER: SHAKE - ntc = 3 Jennie Thomas (Mon Jan 09 2006 - 16:07:47 PST)
- Re: AMBER: SHAKE - ntc = 3 Bill Ross (Mon Jan 09 2006 - 16:39:12 PST)
  - Re: AMBER: SHAKE - ntc = 3 Jennie Thomas (Mon Jan 09 2006 - 17:54:09 PST)
AMBER: Could you help me about mmpbsa! thank you! linfu (Sun Jan 08 2006 - 01:28:13 PST)
AMBER: amber alexandratm.sapo.pt (Mon Jan 09 2006 - 03:31:56 PST)
AMBER: parameters for C=S alexandra.marques.fc.up.pt (Mon Jan 09 2006 - 06:53:30 PST)
- Re: AMBER: parameters for C=S David A. Case (Mon Jan 09 2006 - 15:04:52 PST)
- AMBER: NAD parameters alexandra.marques.fc.up.pt (Mon Jan 30 2006 - 08:04:43 PST)
  - Re: AMBER: NAD parameters ivan.mmb.pcb.ub.es (Mon Jan 30 2006 - 08:20:19 PST)
  - RE: AMBER: NAD parameters Ross Walker (Mon Jan 30 2006 - 08:34:20 PST)
    - AMBER: parallel compile problems on amber8 hayden (Tue Jan 31 2006 - 10:55:34 PST)
    - RE: AMBER: parallel compile problems on amber8 Ross Walker (Tue Jan 31 2006 - 14:04:52 PST)
    - RE: AMBER: parallel compile problems on amber8 Ross Walker (Tue Jan 31 2006 - 14:03:31 PST)
AMBER: about mmpbsa linfu (Mon Jan 09 2006 - 17:17:15 PST)
AMBER: problem with the output file for free energy perturbation calculation brmeher.iitg.ernet.in (Mon Jan 09 2006 - 21:15:30 PST)
AMBER: strange result of mm/pbsa snowyowls (Mon Jan 09 2006 - 20:43:11 PST)
- AMBER: PTRAJ generating wrong dihedral angles hayden (Tue Jan 10 2006 - 03:40:05 PST)
  - Re: AMBER: PTRAJ generating wrong dihedral angles Thomas E. Cheatham, III (Tue Jan 10 2006 - 11:42:42 PST)
AMBER: regarding Hydrogen bond analysis S.Sundar Raman (Mon Jan 09 2006 - 19:19:15 PST)
- Re: AMBER: regarding Hydrogen bond analysis David A. Case (Tue Jan 10 2006 - 00:45:50 PST)
AMBER: How to use PTRAJ to analyze the CA RMS diveations as a function of residue number? tonglei (Sun Jan 08 2006 - 18:36:30 PST)
AMBER: Problem in Antechamber Sai Kumar Ramadugu (Tue Jan 10 2006 - 03:17:53 PST)
- Re: AMBER: Problem in Antechamber David A. Case (Thu Jan 12 2006 - 17:40:50 PST)
  - Re: AMBER: Problem in Antechamber Sai Kumar Ramadugu (Thu Jan 12 2006 - 22:01:46 PST)
- RE: AMBER: Problem in Antechamber Junmei Wang (Thu Jan 19 2006 - 15:02:39 PST)
  - Re: AMBER: Problem in Antechamber Sai Kumar Ramadugu (Thu Jan 26 2006 - 20:46:42 PST)
AMBER: mpich Amber7 problem Jan Dohnalek (Tue Jan 10 2006 - 06:31:38 PST)
- Re: AMBER: mpich Amber7 problem Petr Kulhanek (Wed Jan 11 2006 - 01:27:01 PST)
- Re: AMBER: mpich Amber7 problem linfu (Wed Jan 11 2006 - 01:27:57 PST)
  - Re: AMBER: mpich Amber7 problem Jan Dohnalek (Wed Jan 11 2006 - 02:32:18 PST)
AMBER: ptraj distance matrix Holly Freedman (Tue Jan 10 2006 - 14:03:36 PST)
- Re: AMBER: ptraj distance matrix Holger Gohlke (Wed Jan 11 2006 - 00:09:33 PST)
AMBER: Gibbs pmf calculation Atsutoshi Okabe (Wed Jan 11 2006 - 02:14:30 PST)
AMBER: Workshops a a (Wed Jan 11 2006 - 06:27:59 PST)
AMBER: GLUTATHIONE Joachim Reichelt (Wed Jan 11 2006 - 06:40:30 PST)
- Re: AMBER: GLUTATHIONE Ilyas Yildirim (Wed Jan 11 2006 - 07:38:56 PST)
  - AMBER: amber atom type -> length of name Tim Meyer (Wed Jan 11 2006 - 11:22:22 PST)
    - Re: AMBER: amber atom type -> length of name David A. Case (Wed Jan 11 2006 - 23:59:48 PST)
- Re: AMBER: GLUTATHIONE Tim Meyer (Wed Jan 11 2006 - 11:13:11 PST)
AMBER: About preparing Zn.lib Varsha Goyal (Wed Jan 11 2006 - 17:21:26 PST)
- Re: AMBER: About preparing Zn.lib Ilyas Yildirim (Wed Jan 11 2006 - 23:46:03 PST)
AMBER: EEL and 1-4 EEL; VDWAALS and 1-4 VDWAALS Ilyas Yildirim (Wed Jan 11 2006 - 23:43:06 PST)
- Re: AMBER: EEL and 1-4 EEL; VDWAALS and 1-4 VDWAALS Carlos Simmerling (Thu Jan 12 2006 - 05:04:46 PST)
  - Re: AMBER: EEL and 1-4 EEL; VDWAALS and 1-4 VDWAALS Ilyas Yildirim (Thu Jan 12 2006 - 14:00:24 PST)
    - Re: AMBER: EEL and 1-4 EEL; VDWAALS and 1-4 VDWAALS Carlos Simmerling (Thu Jan 12 2006 - 14:10:58 PST)
AMBER: ptraj mask question Vlad Cojocaru (Thu Jan 12 2006 - 02:50:37 PST)
AMBER: stripping trajectories: ptraj versus Carnal Vlad Cojocaru (Thu Jan 12 2006 - 06:19:17 PST)
- Re: AMBER: stripping trajectories: ptraj versus Carnal Andy Purkiss (Thu Jan 12 2006 - 06:52:14 PST)
  - Re: AMBER: stripping trajectories: ptraj versus Carnal Andy Purkiss (Thu Jan 12 2006 - 07:01:09 PST)
  - Re: AMBER: stripping trajectories: ptraj versus Carnal Carlos Simmerling (Thu Jan 12 2006 - 07:04:45 PST)
    - Re: AMBER: stripping trajectories: ptraj versus Carnal Vlad Cojocaru (Thu Jan 12 2006 - 07:42:41 PST)
    - Re: AMBER: stripping trajectories: ptraj versus Carnal Vlad Cojocaru (Thu Jan 12 2006 - 07:51:57 PST)
    - Re: AMBER: stripping trajectories: ptraj versus Carnal Thomas E. Cheatham, III (Thu Jan 12 2006 - 08:59:35 PST)
    - Re: AMBER: stripping trajectories: ptraj versus Carnal Vlad Cojocaru (Thu Jan 12 2006 - 09:13:58 PST)
    - Re: AMBER: stripping trajectories: ptraj versus Carnal Vlad Cojocaru (Thu Jan 12 2006 - 09:25:56 PST)
AMBER: ATCOR.dat format Kateryna Miroshnychenko (Thu Jan 12 2006 - 08:43:05 PST)
AMBER: Na+ with GB/SA? Steve Gwaltney (Thu Jan 12 2006 - 09:59:22 PST)
- Re: AMBER: Na+ with GB/SA? David A. Case (Thu Jan 12 2006 - 14:24:17 PST)
AMBER: About tleap Varsha Goyal (Thu Jan 12 2006 - 10:28:04 PST)
- RE: AMBER: About tleap Ross Walker (Thu Jan 12 2006 - 12:08:14 PST)
AMBER: problem in saving parameter file for non-standard residue Priti Hansia (Fri Jan 13 2006 - 01:58:04 PST)
- Re: AMBER: problem in saving parameter file for non-standard residue Ilyas Yildirim (Fri Jan 13 2006 - 02:40:56 PST)
- RE: AMBER: problem in saving parameter file for non-standard residue Ross Walker (Fri Jan 13 2006 - 08:49:17 PST)
  - AMBER: Trimming ptraj output Andy Purkiss (Fri Jan 13 2006 - 09:29:00 PST)
    - Re: AMBER: Trimming ptraj output Thomas E. Cheatham, III (Fri Jan 13 2006 - 09:37:45 PST)
    - Re: AMBER: Trimming ptraj output Andy Purkiss (Fri Jan 13 2006 - 10:03:54 PST)
Re: AMBER: problem in saving parameter file for non-standard residue Priti Hansia (Fri Jan 13 2006 - 02:51:13 PST)
- Re: AMBER: problem in saving parameter file for non-standard residue Ilyas Yildirim (Fri Jan 13 2006 - 03:10:52 PST)
- RE: AMBER: problem in saving parameter file for non-standard residue Ross Walker (Fri Jan 13 2006 - 08:44:12 PST)
Re: AMBER: problem in saving parameter file for non-standard residue Priti Hansia (Fri Jan 13 2006 - 03:50:36 PST)
AMBER: analysing water behavior during MD Vlad Cojocaru (Fri Jan 13 2006 - 07:17:06 PST)
- Re: AMBER: analysing water behavior during MD Fabian Boes (Fri Jan 13 2006 - 08:22:01 PST)
AMBER: base-base interaction Douali, Latifa (Fri Jan 13 2006 - 09:54:32 PST)
- Re: AMBER: base-base interaction Carlos Simmerling (Fri Jan 13 2006 - 10:07:57 PST)
RE: AMBER: problem in saving parameter file for non-standard residue Priti Hansia (Fri Jan 13 2006 - 20:29:03 PST)
- RE: AMBER: problem in saving parameter file for non-standard residue Ross Walker (Mon Jan 16 2006 - 08:44:11 PST)
  - Re: AMBER: problem in saving parameter file for non-standard residue David A. Case (Mon Jan 16 2006 - 11:44:22 PST)
AMBER: heme improper torsions nkyx.sohu.com (Mon Jan 16 2006 - 00:55:38 PST)
- Re: AMBER: heme improper torsions Vlad Cojocaru (Mon Jan 16 2006 - 01:50:50 PST)
- Re: AMBER: heme improper torsions David A. Case (Mon Jan 16 2006 - 08:46:47 PST)
AMBER: the problem of mdcrd xiphias xie (Mon Jan 16 2006 - 01:16:09 PST)
- Re: AMBER: the problem of mdcrd Vlad Cojocaru (Mon Jan 16 2006 - 01:55:45 PST)
  - 回复： Re: AMBER: the problem of mdcrd xiphias xie (Mon Jan 16 2006 - 18:23:00 PST)
- RE: AMBER: the problem of mdcrd Ross Walker (Mon Jan 16 2006 - 08:44:11 PST)
  - 回复： RE: AMBER: the problem of mdcrd xiphias xie (Mon Jan 16 2006 - 18:13:53 PST)
  - RE：AMBER: the problem of mdcrd xiphias xie (Mon Jan 16 2006 - 23:52:03 PST)
    - AMBER: Re: RE：AMBER: the problem of mdcrd Vlad Cojocaru (Tue Jan 17 2006 - 04:40:41 PST)
    - RE：AMBER: the problem of mdcrd xiphias xie (Wed Jan 18 2006 - 00:54:18 PST)
    - AMBER: Re: RE：AMBER: the problem of mdcrd Vlad Cojocaru (Wed Jan 18 2006 - 01:48:36 PST)
    - AMBER: Re: RE：AMBER: the problem of mdcrd Carlos Simmerling (Tue Jan 17 2006 - 04:56:58 PST)
AMBER: MPICH on OpenMosix Jan Dohnalek (Mon Jan 16 2006 - 05:21:04 PST)
AMBER: ACTIVE SITE Claire Zerafa (Mon Jan 16 2006 - 06:06:52 PST)
AMBER: Release of RESP ESP charge DDatabase FyD (Mon Jan 16 2006 - 08:04:47 PST)
AMBER: About the unit of the projection onto eigenvectors zgleo (Tue Jan 17 2006 - 01:58:39 PST)
- Re: AMBER: About the unit of the projection onto eigenvectors David A. Case (Fri Jan 27 2006 - 14:20:17 PST)
AMBER: nmode calculations error Jiten (Tue Jan 17 2006 - 05:58:53 PST)
AMBER: rms in principal component analysis Lydia (Tue Jan 17 2006 - 12:54:32 PST)
- Re: AMBER: rms in principal component analysis David A. Case (Wed Jan 18 2006 - 08:30:51 PST)
  - Re: AMBER: rms in principal component analysis Lydia (Wed Jan 18 2006 - 09:43:03 PST)
    - Re: AMBER: rms in principal component analysis David A. Case (Wed Jan 18 2006 - 10:52:51 PST)
AMBER: Amber 8 install problem Andrew Box (Tue Jan 17 2006 - 20:50:21 PST)
- Re: AMBER: Amber 8 install problem Andreas Svrcek-Seiler (Wed Jan 18 2006 - 03:10:38 PST)
AMBER: bugfix for impropers in parmchk Kateryna Miroshnychenko (Wed Jan 18 2006 - 06:48:55 PST)
- Re: AMBER: bugfix for impropers in parmchk David A. Case (Wed Jan 18 2006 - 18:04:36 PST)
  - Re: AMBER: bugfix for impropers in parmchk David Mobley (Fri Jan 20 2006 - 10:23:39 PST)
- Re: AMBER: bugfix for impropers in parmchk David Mobley (Fri Jan 20 2006 - 10:21:49 PST)
- Re: AMBER: bugfix for impropers in parmchk David A. Case (Sat Feb 04 2006 - 10:50:15 PST)
- Re: AMBER: bugfix for impropers in parmchk Kateryna Miroshnychenko (Mon Feb 06 2006 - 07:09:06 PST)
- Re: AMBER: bugfix for impropers in parmchk Jiten (Wed Aug 01 2007 - 21:02:24 PDT)
  - Re: AMBER: bugfix for impropers in parmchk David A. Case (Wed Aug 01 2007 - 22:04:20 PDT)
- Re: AMBER: bugfix for impropers in parmchk Jiten (Wed Aug 01 2007 - 23:23:20 PDT)
AMBER: IGB=10 Ahammadunny Pathiaseril (Wed Jan 18 2006 - 07:53:25 PST)
AMBER: A few problems on the parameterisation of a Glutamine residue Jason K (Wed Jan 18 2006 - 10:12:16 PST)
- RE: AMBER: A few problems on the parameterisation of a Glutamine residue Ross Walker (Wed Jan 18 2006 - 10:32:25 PST)
AMBER: is there any relationship between RMSD and B-factor? haixiao jin (Wed Jan 18 2006 - 19:30:33 PST)
- Re: AMBER: is there any relationship between RMSD and B-factor? Carlos Simmerling (Wed Jan 18 2006 - 19:53:26 PST)
  - Re: AMBER: is there any relationship between RMSD and B-factor? haixiao jin (Wed Jan 18 2006 - 20:58:28 PST)
    - Re: AMBER: is there any relationship between RMSD and B-factor? Carlos Simmerling (Thu Jan 19 2006 - 04:59:39 PST)
    - Re: AMBER: is there any relationship between RMSD and B-factor? Andy Purkiss (Thu Jan 19 2006 - 05:19:06 PST)
AMBER: ptraj grid output Vlad Cojocaru (Thu Jan 19 2006 - 10:25:49 PST)
- Re: AMBER: ptraj grid output Thomas E. Cheatham, III (Thu Jan 19 2006 - 10:47:05 PST)
AMBER: ptraj PCA Marcela Madrid (Thu Jan 19 2006 - 17:04:46 PST)
AMBER: amber: problem in center command xiphias xie (Thu Jan 19 2006 - 18:36:27 PST)
- Re: AMBER: amber: problem in center command Vlad Cojocaru (Fri Jan 20 2006 - 01:48:42 PST)
  - Re: AMBER: problem in center command xiphias xie (Fri Jan 20 2006 - 17:30:44 PST)
    - Re: AMBER: problem in center command Bill Ross (Fri Jan 20 2006 - 17:40:51 PST)
    - Re: AMBER: problem in center command Thomas Cheatham (Fri Jan 20 2006 - 19:37:49 PST)
    - AMBER: Charges from NMR spin densities David LeBard (Thu Jan 26 2006 - 15:33:50 PST)
    - Re: AMBER: Charges from NMR spin densities David A. Case (Fri Jan 27 2006 - 08:57:32 PST)
AMBER: partial charge glycam Kevin Murphy (Fri Jan 20 2006 - 03:28:27 PST)
- Re: AMBER: partial charge glycam kkirschn.hamilton.edu (Fri Jan 20 2006 - 07:39:14 PST)
- Re: AMBER: partial charge glycam FyD (Fri Jan 20 2006 - 23:30:37 PST)
- RE: AMBER: partial charge glycam Kevin Murphy (Tue Jan 24 2006 - 04:18:05 PST)
  - RE: AMBER: partial charge glycam FyD (Wed Jan 25 2006 - 01:23:06 PST)
    - Re: AMBER: partial charge glycam kkirschn.hamilton.edu (Thu Jan 26 2006 - 06:49:35 PST)
AMBER: ptraj PCA Vlad Cojocaru (Tue Jan 24 2006 - 08:02:20 PST)
AMBER: AMBER 8.0 : Octane Implicit Solvent? Guillaume Bollot (Tue Jan 24 2006 - 08:25:42 PST)
- Re: AMBER: AMBER 8.0 : Octane Implicit Solvent? David A. Case (Tue Jan 24 2006 - 11:09:32 PST)
AMBER: monosaccharide residues Fren T (Tue Jan 24 2006 - 14:20:03 PST)
AMBER: Charges of enantiomers for Amber8 lily ferreira (Wed Jan 25 2006 - 00:01:24 PST)
- Re: AMBER: Charges of enantiomers for Amber8 FyD (Wed Jan 25 2006 - 01:38:36 PST)
  - Re: AMBER: Charges of enantiomers for Amber8 lily ferreira (Wed Jan 25 2006 - 22:46:53 PST)
    - Re: AMBER: Charges of enantiomers for Amber8 FyD (Wed Jan 25 2006 - 23:53:43 PST)
- Re: AMBER: Charges of enantiomers for Amber8 FyD (Wed Jan 25 2006 - 03:41:47 PST)
AMBER: ptraj PCA: projection mask bug?? Vlad Cojocaru (Wed Jan 25 2006 - 05:28:42 PST)
AMBER: MM-PBSA Douali, Latifa (Wed Jan 25 2006 - 15:03:06 PST)
- Re: AMBER: MM-PBSA Jianyin Shao (Tue Jan 31 2006 - 09:08:09 PST)
- Re: AMBER: MM-PBSA David A. Case (Thu Feb 02 2006 - 11:00:23 PST)
AMBER: AMBER 7 and restrained bonds. Toomas Kaevand (Thu Jan 26 2006 - 07:27:28 PST)
- Re: AMBER: AMBER 7 and restrained bonds. David A. Case (Thu Jan 26 2006 - 08:26:42 PST)
AMBER: antechamber ping jiang (Thu Jan 26 2006 - 15:18:29 PST)
- Re: AMBER: antechamber David Case (Thu Jan 26 2006 - 15:48:55 PST)
AMBER: h-bond Gustavo Pierdominici Sottile (Fri Jan 27 2006 - 06:59:07 PST)
AMBER: atom type "O3" not recognized by XLeap Kenley Barrett (Fri Jan 27 2006 - 09:32:48 PST)
- Re: AMBER: atom type "O3" not recognized by XLeap David A. Case (Fri Jan 27 2006 - 14:01:43 PST)
AMBER: anal vs sander Piotr Cieplak (Fri Jan 27 2006 - 12:58:39 PST)
- Re: AMBER: anal vs sander David A. Case (Fri Jan 27 2006 - 13:33:57 PST)
  - Re: AMBER: anal vs sander Piotr Cieplak (Fri Jan 27 2006 - 14:59:13 PST)
    - Re: AMBER: anal vs sander David A. Case (Fri Jan 27 2006 - 15:28:51 PST)
AMBER: lifetimes Gustavo Pierdominici Sottile (Mon Jan 30 2006 - 07:15:55 PST)
- Re: AMBER: lifetimes David A. Case (Wed Feb 01 2006 - 08:20:56 PST)
AMBER: Problem in compiling sander with MMTSB luckyang.gmail.com (Mon Jan 30 2006 - 18:06:32 PST)
- Re: AMBER: Problem in compiling sander with MMTSB Scott Brozell (Mon Jan 30 2006 - 19:44:06 PST)
  - Re: AMBER: Problem in compiling sander with MMTSB luckyang.gmail.com (Mon Jan 30 2006 - 22:10:15 PST)
    - Re: AMBER: Problem in compiling sander with MMTSB Scott Brozell (Tue Jan 31 2006 - 21:54:56 PST)
    - Re: AMBER: Problem in compiling sander with MMTSB luckyang.gmail.com (Wed Feb 01 2006 - 11:39:04 PST)
    - Re: AMBER: Problem in compiling sander with MMTSB David A. Case (Wed Feb 01 2006 - 16:05:58 PST)
    - Re: AMBER: Problem in compiling sander with MMTSB luckyang.gmail.com (Wed Feb 01 2006 - 19:26:55 PST)
    - Re: AMBER: Problem in compiling sander with MMTSB David A. Case (Fri Feb 03 2006 - 16:31:32 PST)
    - Re: AMBER: Problem in compiling sander with MMTSB luckyang.gmail.com (Fri Feb 03 2006 - 17:21:51 PST)
AMBER: Decomposed GB energy in idecomp=3 option Sukjoon Yoon (Mon Jan 30 2006 - 18:13:27 PST)
AMBER: About placing counter ions Varsha Goyal (Tue Jan 31 2006 - 10:23:03 PST)
AMBER: Problem in compiling AMBER8 parallel version luckyang.gmail.com (Tue Jan 31 2006 - 15:09:09 PST)
- Re: AMBER: Problem in compiling AMBER8 parallel version David LeBard (Tue Jan 31 2006 - 15:23:16 PST)
  - Re: AMBER: Problem in compiling AMBER8 parallel version luckyang.gmail.com (Tue Jan 31 2006 - 15:51:06 PST)
AMBER: Values of Spring Constants Sai Kumar Ramadugu (Tue Jan 31 2006 - 23:18:44 PST)
- Re: AMBER: Values of Spring Constants Carlos Simmerling (Wed Feb 01 2006 - 04:52:50 PST)
  - Re: AMBER: Values of Spring Constants Sai Kumar Ramadugu (Wed Feb 01 2006 - 07:43:05 PST)
    - Re: AMBER: Values of Spring Constants David A. Case (Wed Feb 01 2006 - 08:38:13 PST)
    - Re: AMBER: Values of Spring Constants Sai Kumar Ramadugu (Wed Feb 01 2006 - 21:00:56 PST)
    - Re: AMBER: Values of Spring Constants Carlos Simmerling (Thu Feb 02 2006 - 03:34:30 PST)
    - Re: AMBER: Values of Spring Constants Sai Kumar Ramadugu (Thu Feb 02 2006 - 20:01:44 PST)
    - Re: AMBER: Values of Spring Constants David A. Case (Fri Feb 03 2006 - 15:51:22 PST)
- Re: AMBER: Values of Spring Constants Adrian Roitberg (Wed Feb 01 2006 - 05:05:14 PST)
AMBER: Gibbs PMF Calculation Atsutoshi Okabe (Wed Feb 01 2006 - 04:31:12 PST)
- Re: AMBER: Gibbs PMF Calculation Carlos Simmerling (Wed Feb 01 2006 - 04:54:33 PST)
AMBER: prepi definitions Michael Mazanetz (Wed Feb 01 2006 - 07:56:25 PST)
- Re: AMBER: prepi definitions ivan.mmb.pcb.ub.es (Wed Feb 01 2006 - 08:33:42 PST)
AMBER: protein ligand complex snoze pa (Wed Feb 01 2006 - 09:21:21 PST)
- Re: AMBER: protein ligand complex Carlos Simmerling (Wed Feb 01 2006 - 09:53:06 PST)
  - Re: AMBER: protein ligand complex snoze pa (Wed Feb 01 2006 - 10:06:39 PST)
    - Re: AMBER: protein ligand complex Carlos Simmerling (Wed Feb 01 2006 - 10:26:10 PST)
- Re: AMBER: protein ligand complex snoze pa (Wed Feb 01 2006 - 11:42:11 PST)
AMBER: Cannot successfully assign bond type for this molecule? snoze pa (Wed Feb 01 2006 - 12:43:53 PST)
- Re: AMBER: Cannot successfully assign bond type for this molecule? David Case (Wed Feb 01 2006 - 13:49:55 PST)
  - Re: AMBER: Cannot successfully assign bond type for this molecule? snoze pa (Wed Feb 01 2006 - 15:00:40 PST)
AMBER: basic minimize question A D (Wed Feb 01 2006 - 14:50:53 PST)
- RE: AMBER: basic minimize question Ross Walker (Wed Feb 01 2006 - 15:06:07 PST)
  - Re: AMBER: basic minimize question A D (Wed Feb 01 2006 - 15:35:38 PST)
    - Re: AMBER: basic minimize question David A. Case (Wed Feb 01 2006 - 16:09:11 PST)
    - RE: AMBER: basic minimize question Ross Walker (Wed Feb 01 2006 - 16:17:57 PST)
AMBER: Charges on atoms in protein :AMBER Varsha Goyal (Wed Feb 01 2006 - 19:00:09 PST)
- RE: AMBER: Charges on atoms in protein :AMBER Ross Walker (Wed Feb 01 2006 - 20:17:24 PST)
  - RE: AMBER: Charges on atoms in protein :AMBER Varsha Goyal (Thu Feb 02 2006 - 11:20:59 PST)
    - Re: AMBER: Charges on atoms in protein :AMBER Adrian Roitberg (Thu Feb 02 2006 - 11:50:54 PST)
    - RE: AMBER: Charges on atoms in protein :AMBER Ilyas Yildirim (Thu Feb 02 2006 - 12:14:53 PST)
- RE: AMBER: Charges on atoms in protein :AMBER Bill Ross (Thu Feb 02 2006 - 10:43:23 PST)
- RE: AMBER: Charges on atoms in protein :AMBER Bill Ross (Thu Feb 02 2006 - 11:31:28 PST)
AMBER: positional restraints & constant pressure Kateryna Miroshnychenko (Thu Feb 02 2006 - 07:40:30 PST)
- Re: AMBER: positional restraints & constant pressure David A. Case (Fri Feb 03 2006 - 08:40:53 PST)
AMBER: lib file snoze pa (Thu Feb 02 2006 - 08:55:33 PST)
- Re: AMBER: lib file Furse, Kristina Elisabet (Fri Jul 30 2004 - 14:38:37 PDT)
- Re: AMBER: lib file Ilyas Yildirim (Thu Feb 02 2006 - 11:08:12 PST)
AMBER: Amber8 parallel compilation problems on EM64T system HL Eastwood (Thu Feb 02 2006 - 11:32:32 PST)
- Re: AMBER: Amber8 parallel compilation problems on EM64T system David A. Case (Thu Feb 02 2006 - 12:28:27 PST)
  - AMBER: Amber8 parallel compilation problems on an OSCAR Cluster Aaron J. Greenwood (Thu Feb 02 2006 - 14:18:59 PST)
    - Re: AMBER: Amber8 parallel compilation problems on an OSCAR Cluster David A. Case (Thu Feb 02 2006 - 17:49:39 PST)
    - Re: AMBER: Amber8 parallel compilation problems on an OSCAR Cluster Aaron J. Greenwood (Fri Feb 03 2006 - 07:57:30 PST)
AMBER: parameter loading problem Lihua Wang (Thu Feb 02 2006 - 13:01:51 PST)
AMBER: MD of oligomer sequences Atilio I Anzellotti/O/VCU (Thu Feb 02 2006 - 14:53:28 PST)
- Re: AMBER: MD of oligomer sequences David A. Case (Thu Feb 02 2006 - 18:08:42 PST)
AMBER: simulated annealing run--temp won't rise Kenley Barrett (Thu Feb 02 2006 - 19:26:52 PST)
- Re: AMBER: simulated annealing run--temp won't rise David Case (Thu Feb 02 2006 - 22:46:00 PST)
AMBER: Re: Force Decomposition for MTS in AMBER 8. David Case (Thu Feb 02 2006 - 22:34:23 PST)
AMBER: Gibbs PMF Calculation Atsutoshi Okabe (Fri Feb 03 2006 - 00:38:55 PST)
- Re: AMBER: Gibbs PMF Calculation Carlos Simmerling (Fri Feb 03 2006 - 03:52:56 PST)
AMBER: MPICH-1.2.7 compilation problem ! Pradipta Bandyopadhyay (Fri Feb 03 2006 - 05:49:31 PST)
AMBER: AMBER 7 and cutoff's Toomas Kaevand (Fri Feb 03 2006 - 09:58:53 PST)
- Re: AMBER: AMBER 7 and cutoff's Carlos Simmerling (Fri Feb 03 2006 - 11:20:30 PST)
AMBER: Rhoad, Jonathan S. (Fri Feb 03 2006 - 11:56:37 PST)
- Re: AMBER: David A. Case (Fri Feb 03 2006 - 15:46:28 PST)
AMBER: MMPBSA: magnitude of PB calculation sishi.tang.utoronto.ca (Fri Feb 03 2006 - 15:34:10 PST)
- Re: AMBER: MMPBSA: magnitude of PB calculation Ray Luo (Thu Feb 02 2006 - 23:49:07 PST)
  - Re: AMBER: MMPBSA: magnitude of PB calculation sishi.tang.utoronto.ca (Sat Feb 04 2006 - 08:47:21 PST)
    - Re: AMBER: MMPBSA: magnitude of PB calculation Thomas Steinbrecher (Mon Feb 06 2006 - 00:54:01 PST)
    - Re: AMBER: MMPBSA: magnitude of PB calculation Natasja Brooijmans (Mon Feb 06 2006 - 04:52:36 PST)
AMBER: Paweł Gruszczyński (Sat Feb 04 2006 - 01:16:10 PST)
- Re: AMBER: David Mobley (Sat Feb 04 2006 - 10:06:23 PST)
AMBER: Strange minimization output problem andy ng (Sat Feb 04 2006 - 04:39:31 PST)
- Re: AMBER: Strange minimization output problem Ananda Rama Krishnan Selvaraj (Sat Feb 04 2006 - 08:12:19 PST)
- Re: AMBER: Strange minimization output problem David A. Case (Sat Feb 04 2006 - 12:20:17 PST)
- Re: AMBER: Strange minimization output problem Andreas Svrcek-Seiler (Sun Feb 05 2006 - 07:23:03 PST)
AMBER: dihedral parameters richard dimelow (Sat Feb 04 2006 - 08:06:41 PST)
- Re: AMBER: dihedral parameters Carlos Simmerling (Sat Feb 04 2006 - 09:30:27 PST)
- Re: AMBER: dihedral parameters richard dimelow (Mon Feb 06 2006 - 02:22:08 PST)
  - Re: AMBER: dihedral parameters Carlos Simmerling (Mon Feb 06 2006 - 04:22:03 PST)
AMBER: What Viewer is best Brian Stupi (Sat Feb 04 2006 - 21:59:29 PST)
- Re: AMBER: What Viewer is best Vlad Cojocaru (Sun Feb 05 2006 - 09:01:11 PST)
  - AMBER: Error when installing Brian Stupi (Mon Feb 13 2006 - 12:19:19 PST)
    - Re: AMBER: Error when installing Brian Stupi (Mon Feb 13 2006 - 12:40:46 PST)
    - RE: AMBER: Error when installing Ross Walker (Tue Feb 14 2006 - 10:30:29 PST)
AMBER: could amber calculte the binding free energy ofonly two small ligands (no big molecules) ? linfu (Sun Feb 05 2006 - 08:49:32 PST)
AMBER: Hessian matrix Marie Brut (Mon Feb 06 2006 - 04:12:53 PST)
- Re: AMBER: Hessian matrix David A. Case (Tue Feb 07 2006 - 08:40:37 PST)
  - Re: AMBER: Hessian matrix mbrut.laas.fr (Tue Feb 07 2006 - 09:55:17 PST)
AMBER: helix content during my simulation julien (Mon Feb 06 2006 - 05:09:38 PST)
- Re: AMBER: helix content during my simulation Mingfeng Yang (Mon Feb 06 2006 - 06:03:32 PST)
  - Re: AMBER: helix content during my simulation julien (Mon Feb 06 2006 - 07:04:51 PST)
    - Re: AMBER: helix content during my simulation Mingfeng Yang (Mon Feb 06 2006 - 07:39:59 PST)
AMBER: Parallel version of Amber: error message snoze pa (Mon Feb 06 2006 - 10:55:39 PST)
- Re: AMBER: Parallel version of Amber: error message Carlos Simmerling (Mon Feb 06 2006 - 11:21:31 PST)
  - Re: AMBER: Parallel version of Amber: error message snoze pa (Mon Feb 06 2006 - 11:45:48 PST)
    - Re: AMBER: Parallel version of Amber: error message David LeBard (Mon Feb 06 2006 - 12:10:29 PST)
    - Re: AMBER: Parallel version of Amber: error message Mingfeng Yang (Mon Feb 06 2006 - 12:29:38 PST)
    - Re: AMBER: Parallel version of Amber: error message Mark Williamson (Mon Feb 06 2006 - 13:00:09 PST)
- Re: AMBER: Parallel version of Amber: error message Lihua Wang (Mon Feb 06 2006 - 12:27:40 PST)
AMBER: Parallel error in Amber 8 snoze pa (Mon Feb 06 2006 - 14:47:19 PST)
- Re: AMBER: Parallel error in Amber 8 snoze pa (Mon Feb 06 2006 - 15:02:22 PST)
- Re: AMBER: Parallel error in Amber 8 Wei Zhang (Mon Feb 06 2006 - 15:06:07 PST)
  - Re: AMBER: Parallel error in Amber 8 snoze pa (Mon Feb 06 2006 - 15:18:16 PST)
- Re: AMBER: Parallel error in Amber 8 David A. Case (Mon Feb 06 2006 - 15:37:56 PST)
  - Re: AMBER: Parallel error in Amber 8 snoze pa (Mon Feb 06 2006 - 16:16:20 PST)
AMBER: soft-core potential in amber? Lydia (Mon Feb 06 2006 - 16:13:14 PST)
- Re: AMBER: soft-core potential in amber? David Mobley (Tue Feb 07 2006 - 06:54:33 PST)
AMBER: non bond list overflow Kenley Barrett (Mon Feb 06 2006 - 19:43:06 PST)
- Re: AMBER: non bond list overflow David A. Case (Mon Feb 06 2006 - 22:37:59 PST)
  - Re: AMBER: non bond list overflow Kenley Barrett (Tue Feb 07 2006 - 08:32:18 PST)
    - Re: AMBER: non bond list overflow David A. Case (Tue Feb 07 2006 - 11:00:54 PST)
AMBER: format of qusaiharmonic eigenvector file in AMBER7 Phineus Markwick (Tue Feb 07 2006 - 03:10:44 PST)
- Re: AMBER: format of qusaiharmonic eigenvector file in AMBER7 Chris Moth (Tue Feb 07 2006 - 06:10:07 PST)
AMBER: Ask for your help to install Amber8 software Cao Tran (Wed Feb 08 2006 - 05:53:11 PST)
- Re: AMBER: Ask for your help to install Amber8 software Cenk Andac (Wed Feb 08 2006 - 06:44:30 PST)
  - RE: AMBER: Ask for your help to install Amber8 software CaoTran (Wed Feb 08 2006 - 07:03:51 PST)
  - RE: AMBER: Ask for your help to install Amber8 software Cao Tran (Fri Feb 10 2006 - 01:01:38 PST)
    - RE: AMBER: Ask for your help to install Amber8 software Cenk Andac (Fri Feb 10 2006 - 02:46:12 PST)
- RE: AMBER: Ask for your help to install Amber8 software Lei Wang (Wed Feb 08 2006 - 07:16:32 PST)
AMBER: DNA tutorial xleap help Amanda Jonsson (Wed Feb 08 2006 - 10:56:32 PST)
- Re: AMBER: DNA tutorial xleap help Wei Zhang (Wed Feb 08 2006 - 11:42:32 PST)
AMBER: desc related issue snoze pa (Wed Feb 08 2006 - 11:15:19 PST)
Re: AMBER: DNA tutorial xleap help Bill Ross (Wed Feb 08 2006 - 11:56:25 PST)
AMBER: PMED in AMBER snoze pa (Wed Feb 08 2006 - 17:07:40 PST)
AMBER: Acetyl CoA Satyan Sharma (Thu Feb 09 2006 - 09:55:19 PST)
AMBER: Distortion in parallelploied Varsha Goyal (Thu Feb 09 2006 - 17:39:06 PST)
- Re: AMBER: Distortion in parallelploied David A. Case (Fri Feb 10 2006 - 09:04:13 PST)
- Re: AMBER: Distortion in parallelploied Angelo Pugliese (Mon Feb 13 2006 - 07:40:40 PST)
AMBER: EAMBER Mingfeng Yang (Thu Feb 09 2006 - 19:56:04 PST)
- Re: AMBER: EAMBER Carlos Simmerling (Thu Feb 09 2006 - 20:15:21 PST)
AMBER: PMEMD MPI_Finalize() error Mingfeng Yang (Fri Feb 10 2006 - 06:50:59 PST)
- Re: AMBER: PMEMD MPI_Finalize() error Robert Duke (Fri Feb 10 2006 - 07:15:29 PST)
  - Re: AMBER: PMEMD MPI_Finalize() error Mingfeng Yang (Fri Feb 10 2006 - 08:07:53 PST)
AMBER: minization: outputing intermediate snapshots Vlad Cojocaru (Fri Feb 10 2006 - 03:49:04 PST)
- RE: AMBER: minization: outputing intermediate snapshots Ross Walker (Tue Feb 14 2006 - 10:34:30 PST)
AMBER: minization: outputing intermediate snapshots Vlad Cojocaru (Fri Feb 10 2006 - 07:05:59 PST)
AMBER: Problem in running umbrella sampling Sai Kumar Ramadugu (Sun Feb 12 2006 - 20:28:09 PST)
- Re: AMBER: Problem in running umbrella sampling David A. Case (Sun Feb 12 2006 - 21:11:48 PST)
  - Re: AMBER: Problem in running umbrella sampling Sai Kumar Ramadugu (Sun Feb 12 2006 - 21:22:49 PST)
AMBER: shuli kang (Mon Feb 13 2006 - 04:26:07 PST)
- Re: AMBER: Scott Pendley (Mon Feb 13 2006 - 13:00:15 PST)
AMBER: MM_PBSA problem (No values for MM_GAS ) Bing Liu (Mon Feb 13 2006 - 06:40:47 PST)
- Re: AMBER: MM_PBSA problem (No values for MM_GAS ) Scott Pendley (Mon Feb 13 2006 - 12:57:27 PST)
AMBER: 2D-topology Baldoni Hector Armando (Mon Feb 13 2006 - 13:50:11 PST)
- Re: AMBER: 2D-topology David A. Case (Tue Feb 14 2006 - 13:57:45 PST)
AMBER: mm_pbsa output lucas luquitas (Mon Feb 13 2006 - 15:40:28 PST)
AMBER: script advice A D (Mon Feb 13 2006 - 18:35:35 PST)
- Re: AMBER: script advice JunJun Liu (Wed Feb 15 2006 - 07:35:44 PST)
AMBER: double stranded polyribocytidylic acid Kateryna Miroshnychenko (Tue Feb 14 2006 - 01:44:01 PST)
- Re: AMBER: double stranded polyribocytidylic acid Jiri Sponer (Tue Feb 14 2006 - 02:54:05 PST)
- Re: AMBER: double stranded polyribocytidylic acid Kateryna Miroshnychenko (Tue Feb 14 2006 - 04:09:36 PST)
  - Re: AMBER: double stranded polyribocytidylic acid Jiri Sponer (Tue Feb 14 2006 - 04:56:07 PST)
- Re: AMBER: double stranded polyribocytidylic acid Bill Ross (Tue Feb 14 2006 - 12:35:19 PST)
  - Re: AMBER: double stranded polyribocytidylic acid Jiri Sponer (Wed Feb 15 2006 - 05:16:46 PST)
- Re: AMBER: double stranded polyribocytidylic acid Bill Ross (Wed Feb 15 2006 - 09:25:21 PST)
  - Re: AMBER: double stranded polyribocytidylic acid Jiri Sponer (Wed Feb 15 2006 - 09:46:27 PST)
- Re: AMBER: double stranded polyribocytidylic acid Kateryna Miroshnychenko (Thu Feb 16 2006 - 02:41:52 PST)
- Re: AMBER: double stranded polyribocytidylic acid Bill Ross (Thu Feb 16 2006 - 10:49:20 PST)
- Re: AMBER: double stranded polyribocytidylic acid Bill Ross (Thu Feb 16 2006 - 10:53:10 PST)
AMBER: Istallation AMBER8 Dr.Rudolf Friedemann (Tue Feb 14 2006 - 02:41:39 PST)
- Re: AMBER: Istallation AMBER8 David A. Case (Tue Feb 14 2006 - 22:57:13 PST)
AMBER: paralelization and sander problems cristian obiol (Tue Feb 14 2006 - 02:24:18 PST)
- Re: AMBER: paralelization and sander problems Carlos Simmerling (Tue Feb 14 2006 - 05:59:43 PST)
  - Re: AMBER: paralelization and sander problems David A. Case (Tue Feb 14 2006 - 08:32:59 PST)
  - Re: AMBER: paralelization and sander problems cristian obiol (Fri Feb 17 2006 - 02:07:37 PST)
    - Re: AMBER: paralelization and sander problems Carlos Simmerling (Fri Feb 17 2006 - 03:59:44 PST)
    - Re: AMBER: paralelization and sander problems cristian obiol (Mon Feb 20 2006 - 04:13:58 PST)
    - Re: AMBER: paralelization and sander problems Carlos Simmerling (Tue Feb 21 2006 - 04:57:10 PST)
- RE: AMBER: paralelization and sander problems Ross Walker (Tue Feb 14 2006 - 09:48:06 PST)
AMBER: Organic molecules Marie Brut (Tue Feb 14 2006 - 08:42:23 PST)
- RE: AMBER: Organic molecules Ross Walker (Tue Feb 14 2006 - 09:44:25 PST)
AMBER: Xleap crash Scott Pendley (Tue Feb 14 2006 - 08:55:12 PST)
- Re: AMBER: Xleap crash David A. Case (Tue Feb 14 2006 - 09:36:21 PST)
  - Re: AMBER: Xleap crash Scott Pendley (Tue Feb 14 2006 - 09:53:37 PST)
    - Re: AMBER: Xleap crash Scott Pendley (Tue Feb 14 2006 - 10:08:59 PST)
    - Re: AMBER: Xleap crash David A. Case (Tue Feb 14 2006 - 11:51:53 PST)
AMBER: Absoft Pro Fortran and AMBER 8 on MacOS X 10.4.4 Jingyuan Luke (Tue Feb 14 2006 - 17:35:37 PST)
- Re: AMBER: Absoft Pro Fortran and AMBER 8 on MacOS X 10.4.4 David A. Case (Tue Feb 14 2006 - 22:12:42 PST)
AMBER: negative T_solv values Markus O Kaukonen (Wed Feb 15 2006 - 00:25:40 PST)
- Re: AMBER: negative T_solv values David A. Case (Wed Feb 15 2006 - 08:18:25 PST)
AMBER: m4 error with Amber8 on SUN Amber admin (Wed Feb 15 2006 - 14:51:38 PST)
- Re: AMBER: m4 error with Amber8 on SUN David A. Case (Wed Feb 15 2006 - 15:56:06 PST)
AMBER: Charge of the phosphorylated Ser/Thr in MM_PBSA calculation zgleo (Wed Feb 15 2006 - 22:04:47 PST)
- Re: AMBER: Charge of the phosphorylated Ser/Thr in MM_PBSA calculation german (Thu Feb 16 2006 - 04:04:39 PST)
AMBER: sander problem bala (Thu Feb 16 2006 - 07:57:43 PST)
- Re: AMBER: sander problem snoze pa (Thu Feb 16 2006 - 08:13:22 PST)
- Re: AMBER: sander problem Carlos Simmerling (Thu Feb 16 2006 - 08:25:20 PST)
- Re: AMBER: sander problem JunJun Liu (Thu Feb 16 2006 - 08:16:34 PST)
- RE: AMBER: sander problem Ross Walker (Thu Feb 16 2006 - 08:51:24 PST)
  - RE: AMBER: sander problem Brian Stupi (Thu Feb 16 2006 - 12:44:11 PST)
    - RE: AMBER: sander problem Thomas E. Cheatham, III (Thu Feb 16 2006 - 13:12:39 PST)
    - RE: AMBER: sander problem Ross Walker (Thu Feb 16 2006 - 13:20:45 PST)
    - AMBER: process_mdout.perl Brian Stupi (Thu Feb 16 2006 - 14:02:06 PST)
AMBER: Torsional restraints for groups of atoms Supat Jiranusornkul (Fri Feb 17 2006 - 04:14:12 PST)
AMBER: Question about renaming a residue Kara Di Giorgio (Fri Feb 17 2006 - 15:28:26 PST)
- Re: AMBER: Question about renaming a residue Thomas E. Cheatham, III (Fri Feb 17 2006 - 15:46:27 PST)
- Re: AMBER: Question about renaming a residue Ilyas Yildirim (Fri Feb 17 2006 - 18:05:37 PST)
AMBER: mm_pbsa problem in IBM-aix Jiten (Fri Feb 17 2006 - 23:36:52 PST)
- Re: AMBER: mm_pbsa problem in IBM-aix Ray Luo (Sun Feb 19 2006 - 12:22:01 PST)
AMBER: instructions for making a library file for an unusual residue? Kenley Barrett (Sat Feb 18 2006 - 14:02:42 PST)
- Re: AMBER: instructions for making a library file for an unusual residue? FyD (Sun Feb 19 2006 - 09:14:10 PST)
  - Re: AMBER: instructions for making a library file for an unusual residue? Kenley Barrett (Mon Feb 20 2006 - 16:22:22 PST)
    - Re: AMBER: instructions for making a library file for an unusual residue? Ilyas Yildirim (Mon Feb 20 2006 - 22:28:49 PST)
    - Re: AMBER: instructions for making a library file for an unusual residue? FyD (Tue Feb 21 2006 - 05:17:48 PST)
AMBER: antechamber for a database of organic molecules Yogesh Sabnis (Sun Feb 19 2006 - 07:16:23 PST)
- Re: AMBER: antechamber for a database of organic molecules FyD (Sun Feb 19 2006 - 07:51:52 PST)
- RE: AMBER: antechamber for a database of organic molecules Junmei Wang (Sun Feb 19 2006 - 19:32:22 PST)
AMBER: Phosphorylated amino acid andy ng (Sun Feb 19 2006 - 15:51:41 PST)
- Re: AMBER: Phosphorylated amino acid Tim Meyer (Mon Feb 20 2006 - 00:56:36 PST)
  - Re: AMBER: Phosphorylated amino acid andy ng (Mon Feb 20 2006 - 21:55:55 PST)
AMBER: parallel problem of amber8 linfu (Mon Feb 20 2006 - 05:01:02 PST)
- RE: AMBER: parallel problem of amber8 Ross Walker (Mon Feb 20 2006 - 09:00:26 PST)
  - AMBER: Problem with file size of sander outputs Cenk Andac (Tue Feb 21 2006 - 23:54:24 PST)
    - Re: AMBER: Problem with file size of sander outputs shuli kang (Wed Feb 22 2006 - 00:45:21 PST)
    - Re: AMBER: Problem with file size of sander outputs german (Wed Feb 22 2006 - 02:49:49 PST)
    - AMBER: Free energy perturbation Angelo Pugliese (Wed Feb 22 2006 - 08:42:06 PST)
    - Re: AMBER: Problem with file size of sander outputs JunJun Liu (Wed Feb 22 2006 - 12:58:00 PST)
    - RE: AMBER: Problem with file size of sander outputs Ross Walker (Wed Feb 22 2006 - 13:16:30 PST)
    - RE: AMBER: Problem with file size of sander outputs Cenk Andac (Wed Feb 22 2006 - 23:23:02 PST)
    - RE: AMBER: Problem with file size of sander outputs Feng X Zhou (Thu Feb 23 2006 - 09:42:22 PST)
    - RE: AMBER: Problem with file size of sander outputs Ross Walker (Thu Feb 23 2006 - 10:06:30 PST)
AMBER: charge redistribution in .prep files Stefano Federico Massimiliano Pieraccini (Stefano.Pieraccini) (Mon Feb 20 2006 - 04:37:54 PST)
- Re: AMBER: charge redistribution in .prep files David A. Case (Mon Feb 20 2006 - 08:29:41 PST)
AMBER: Truncated octahedral box as triclinic lattice vectors Markus O Kaukonen (Mon Feb 20 2006 - 06:42:45 PST)
AMBER: amber 8 problem Abd Ghani Abd Aziz (Mon Feb 20 2006 - 07:08:12 PST)
- Re: AMBER: amber 8 problem JunJun Liu (Mon Feb 20 2006 - 08:05:53 PST)
  - Re: AMBER: amber 8 problem Abd Ghani Abd Aziz (Mon Feb 20 2006 - 08:17:37 PST)
- Re: AMBER: amber 8 problem Andreas Svrcek-Seiler (Mon Feb 20 2006 - 08:20:28 PST)
- Re: AMBER: amber 8 problem David A. Case (Mon Feb 20 2006 - 08:33:01 PST)
- RE: AMBER: amber 8 problem Ross Walker (Mon Feb 20 2006 - 09:05:57 PST)
  - AMBER: Ti calculations in dmso solvent Vitor Manuel Sousa F?x (Mon Feb 20 2006 - 09:55:32 PST)
    - Re: AMBER: Ti calculations in dmso solvent David Mobley (Thu Feb 23 2006 - 08:58:17 PST)
    - Re: AMBER: Ti calculations in dmso solvent David A. Case (Thu Feb 23 2006 - 10:01:26 PST)
    - Re: AMBER: Ti calculations in dmso solvent David Mobley (Thu Feb 23 2006 - 12:06:43 PST)
  - RE: AMBER: amber 8 problem Abd Ghani Abd Aziz (Mon Feb 20 2006 - 20:55:27 PST)
AMBER: Error in RST files in long simulations! lucas luquitas (Mon Feb 20 2006 - 11:59:35 PST)
- Re: AMBER: Error in RST files in long simulations! Carlos Simmerling (Mon Feb 20 2006 - 12:32:13 PST)
  - Re: AMBER: Error in RST files in long simulations! lucas luquitas (Mon Feb 20 2006 - 15:08:38 PST)
    - Re: AMBER: Error in RST files in long simulations! Carlos Simmerling (Tue Feb 21 2006 - 05:02:58 PST)
AMBER: NMR restraints and LES Sivakolundu, Sivashankar (Mon Feb 20 2006 - 17:43:38 PST)
- Re: AMBER: NMR restraints and LES David A. Case (Mon Feb 20 2006 - 18:26:17 PST)
AMBER: About WHAM Atsutoshi Okabe (Mon Feb 20 2006 - 22:22:01 PST)
AMBER: does anyone have library file for methylated histidine, 2003 ff? Kenley Barrett (Tue Feb 21 2006 - 08:27:13 PST)
AMBER: CARNAL: H-BOND Specifying side chains only Kay Kunes (Tue Feb 21 2006 - 12:47:14 PST)
Re: AMBER: CARNAL: H-BOND Specifying side chains only Bill Ross (Tue Feb 21 2006 - 13:41:25 PST)
AMBER: AMBER force field with namd Fabien Cailliez (Wed Feb 22 2006 - 09:54:23 PST)
- Re: AMBER: AMBER force field with namd Vlad Cojocaru (Thu Feb 23 2006 - 02:11:17 PST)
  - Re: AMBER: AMBER force field with namd Carlos Simmerling (Thu Feb 23 2006 - 05:41:31 PST)
    - Re: AMBER: AMBER force field with namd Vlad Cojocaru (Thu Feb 23 2006 - 06:04:51 PST)
AMBER: generating parameters for the NADH analogue H4NAD Simon Whitehead (Thu Feb 23 2006 - 10:31:02 PST)
- Re: AMBER: generating parameters for the NADH analogue H4NAD Vlad Cojocaru (Thu Feb 23 2006 - 10:53:30 PST)
- RE: AMBER: generating parameters for the NADH analogue H4NAD Ross Walker (Thu Feb 23 2006 - 11:00:30 PST)
- RE: AMBER: generating parameters for the NADH analogue H4NAD Simon Whitehead (Thu Mar 02 2006 - 15:17:50 PST)
  - RE: AMBER: generating parameters for the NADH analogue H4NAD Ross Walker (Thu Mar 02 2006 - 15:32:27 PST)
AMBER: TI cal Steve Seibold (Thu Feb 23 2006 - 11:02:45 PST)
- RE: AMBER: TI cal Ross Walker (Thu Feb 23 2006 - 11:25:57 PST)
- RE: AMBER: TI cal Steve Seibold (Thu Feb 23 2006 - 12:08:20 PST)
AMBER: A problem with Amber force field new parameter derivation Vidana.Epa.csiro.au (Thu Feb 23 2006 - 22:16:04 PST)
- Re: AMBER: A problem with Amber force field new parameter derivation FyD (Thu Feb 23 2006 - 22:27:31 PST)
AMBER: entropic energy Nina Fischer (Fri Feb 24 2006 - 04:15:17 PST)
- Re: AMBER: entropic energy David A. Case (Fri Feb 24 2006 - 08:36:49 PST)
AMBER: Antechamber Package Announcement Junmei Wang (Fri Feb 24 2006 - 08:26:52 PST)
- AMBER: from Wei Zhang: flight information Wei Zhang (Fri Mar 03 2006 - 10:45:59 PST)
AMBER: Constant pressure - restart - Amber8 Jennie Thomas (Fri Feb 24 2006 - 08:59:34 PST)
- Re: AMBER: Constant pressure - restart - Amber8 David A. Case (Fri Feb 24 2006 - 09:34:46 PST)
  - Re: AMBER: Constant pressure - restart - Amber8 Jennie Thomas (Fri Feb 24 2006 - 12:18:56 PST)
    - Re: AMBER: Constant pressure - restart - Amber8 David A. Case (Fri Feb 24 2006 - 13:18:58 PST)
    - AMBER: dynamic memory allocation problem in nmode Cenk Andac (Sun Feb 26 2006 - 00:58:14 PST)
    - Re: AMBER: dynamic memory allocation problem in nmode Cenk Andac (Sun Feb 26 2006 - 01:26:23 PST)
    - Re: AMBER: dynamic memory allocation problem in nmode Jiten (Sun Feb 26 2006 - 07:07:23 PST)
    - Re: AMBER: dynamic memory allocation problem in nmode Cenk Andac (Sun Mar 19 2006 - 01:10:22 PST)
    - Re: AMBER: dynamic memory allocation problem in nmode David A. Case (Sun Feb 26 2006 - 20:21:02 PST)
    - Re: AMBER: Constant pressure - restart - Amber8 Jennie Thomas (Sun Feb 26 2006 - 17:56:59 PST)
AMBER: specifying RSOLV when calculating 2003 force field charges Kenley Barrett (Fri Feb 24 2006 - 12:50:07 PST)
AMBER: How to explain the meaning of the mmpbsa/DC result? zhli_2000.126.com (Sat Feb 25 2006 - 23:01:04 PST)
AMBER: ptraj atomicfluct: is it possible to calculate atomic fluctations from a reference structure Magne Olufsen (Sun Feb 26 2006 - 11:00:23 PST)
AMBER: Sulfonamides and GAFF Varsha Goyal (Sun Feb 26 2006 - 17:16:18 PST)
AMBER: ptraj warning while loading reference Vlad Cojocaru (Mon Feb 27 2006 - 04:45:28 PST)
- Re: AMBER: ptraj warning while loading reference David A. Case (Mon Feb 27 2006 - 08:44:52 PST)
  - Re: AMBER: ptraj warning while loading reference Vlad Cojocaru (Mon Feb 27 2006 - 09:00:43 PST)
AMBER: MD job stopped without any error information? ying xiong (Mon Feb 27 2006 - 00:29:50 PST)
- Re: AMBER: MD job stopped without any error information? Melinda Layten (Mon Feb 27 2006 - 07:18:09 PST)
- Re: AMBER: MD job stopped without any error information? Guanglei Cui (Mon Feb 27 2006 - 07:55:47 PST)
- RE: AMBER: MD job stopped without any error information? Ross Walker (Mon Feb 27 2006 - 08:22:25 PST)
AMBER: RE: about compiling errors for Leap Ross Walker (Mon Feb 27 2006 - 08:17:27 PST)
AMBER: sander testing problem mdione.fcq.unc.edu.ar (Mon Feb 27 2006 - 13:53:23 PST)
AMBER: mask issues Claire Zerafa (Tue Feb 28 2006 - 04:46:12 PST)
- Re: AMBER: mask issues Vlad Cojocaru (Tue Feb 28 2006 - 05:03:16 PST)
AMBER: failed to save prm and xyz using ff96 Abd Ghani Abd Aziz (Tue Feb 28 2006 - 07:32:49 PST)
- RE: AMBER: failed to save prm and xyz using ff96 Ross Walker (Tue Feb 28 2006 - 08:31:41 PST)
  - Re: AMBER: failed to save prm and xyz using ff96 Carlos Simmerling (Tue Feb 28 2006 - 09:24:23 PST)
    - Re: AMBER: failed to save prm and xyz using ff96 Abd Ghani Abd Aziz (Tue Feb 28 2006 - 23:49:57 PST)
    - Re: AMBER: failed to save prm and xyz using ff96 Joseph Nachman (Wed Mar 01 2006 - 12:51:09 PST)
    - Re: AMBER: failed to save prm and xyz using ff96 Viktor Hornak (Wed Mar 01 2006 - 13:16:13 PST)
    - Re: AMBER: failed to save prm and xyz using ff96 Joseph Nachman (Wed Mar 01 2006 - 15:29:18 PST)
  - AMBER: How to develop charge for my deprotonated glycine Jianzhong Liu (Tue Feb 28 2006 - 11:58:31 PST)
    - Re: AMBER: How to develop charge for my deprotonated glycine FyD (Tue Feb 28 2006 - 21:00:37 PST)
    - Re: AMBER: How to develop charge for my deprotonated glycine Jianzhong Liu (Fri Mar 03 2006 - 11:05:41 PST)
    - Re: AMBER: How to develop charge for my deprotonated glycine FyD (Sat Mar 04 2006 - 01:26:13 PST)
    - Re: AMBER: How to develop charge for my deprotonated glycine Jianzhong Liu (Sat Mar 04 2006 - 19:05:12 PST)
AMBER: Compiling the parallel version of amber 8 in a beowulf linux cluster Carlos Silva Lopez (Tue Feb 28 2006 - 09:30:42 PST)
- Re: AMBER: Compiling the parallel version of amber 8 in a beowulf linux cluster Wei Zhang (Tue Feb 28 2006 - 10:01:34 PST)
  - Re: AMBER: Compiling the parallel version of amber 8 in a beowulf linux cluster Carlos Silva Lopez (Tue Feb 28 2006 - 14:27:07 PST)
AMBER: Angle restraint venditti2.unisi.it (Tue Feb 28 2006 - 12:00:48 PST)
- Re: AMBER: Angle restraint David A. Case (Tue Feb 28 2006 - 15:54:40 PST)
AMBER: install error biolabadmin.ibt.lt (Wed Mar 01 2006 - 03:13:12 PST)
- RE: AMBER: install error Ross Walker (Wed Mar 01 2006 - 08:08:24 PST)
  - Re: AMBER: install error biolabadmin.ibt.lt (Thu Mar 02 2006 - 04:48:17 PST)
    - AMBER: transition metals and the parmcal of the antechamber module Cenk Andac (Thu Mar 02 2006 - 03:09:44 PST)
    - Re: AMBER: install error Mark Williamson (Thu Mar 02 2006 - 03:13:40 PST)
    - Re: AMBER: install error biolabadmin.ibt.lt (Fri Mar 03 2006 - 01:47:11 PST)
AMBER: Nmode vs QM Freq Calculation Mark Williamson (Wed Mar 01 2006 - 03:28:57 PST)
- Re: AMBER: Nmode vs QM Freq Calculation David A. Case (Wed Mar 01 2006 - 10:54:12 PST)
AMBER: leap: syntax error when use source command Dmitry Osolodkin (Wed Mar 01 2006 - 04:27:47 PST)
- RE:AMBER: leap: syntax error when use source command Kateryna Miroshnychenko (Wed Mar 01 2006 - 04:58:22 PST)
AMBER: replica exchange hangs Peter Varnai (Wed Mar 01 2006 - 09:29:34 PST)
- Re: AMBER: replica exchange hangs Sergey Krishtal (Wed Mar 01 2006 - 10:15:46 PST)
  - Re: AMBER: replica exchange hangs Carlos Simmerling (Wed Mar 01 2006 - 10:37:04 PST)
    - Re: AMBER: replica exchange hangs Peter Varnai (Wed Mar 01 2006 - 10:56:21 PST)
- Re: AMBER: replica exchange hangs Carlos Simmerling (Wed Mar 01 2006 - 10:37:40 PST)
AMBER: GAFF + AM1BCC & small-molecule aggregation Scott P Brown (Wed Mar 01 2006 - 12:00:33 PST)
- Re: AMBER: GAFF + AM1BCC & small-molecule aggregation Thomas E. Cheatham, III (Wed Mar 01 2006 - 13:17:35 PST)
  - Re: AMBER: GAFF + AM1BCC & small-molecule aggregation Carlos Simmerling (Wed Mar 01 2006 - 13:34:06 PST)
    - Re: AMBER: GAFF + AM1BCC & small-molecule aggregation Carlos Simmerling (Wed Mar 01 2006 - 14:00:40 PST)
AMBER: N-H and C-H Residual Dipolar Coupling thenmalar (Wed Mar 01 2006 - 14:01:52 PST)
- Re: AMBER: N-H and C-H Residual Dipolar Coupling David A. Case (Wed Mar 01 2006 - 14:38:09 PST)
  - Re: AMBER: N-H and C-H Residual Dipolar Coupling thenmalar (Wed Mar 01 2006 - 16:59:34 PST)
AMBER: Amber 9. Sergey Krishtal (Wed Mar 01 2006 - 19:37:02 PST)
- AMBER: G95, SGI and Amber8 Cenk Andac (Thu Mar 02 2006 - 23:30:44 PST)
- Re: AMBER: Amber 9. David A. Case (Fri Mar 03 2006 - 09:29:25 PST)
AMBER: Which PTRAJ distribution to use? Chng Choon-Peng (Wed Mar 01 2006 - 23:30:49 PST)
- Re: AMBER: Which PTRAJ distribution to use? Thomas Cheatham (Thu Mar 02 2006 - 15:47:51 PST)
  - Re: AMBER: Which PTRAJ distribution to use? Chng Choon-Peng (Thu Mar 02 2006 - 16:27:15 PST)
AMBER: amber8 and gfortran 4.1.0 Tru Huynh (Thu Mar 02 2006 - 08:00:00 PST)
- RE: AMBER: amber8 and gfortran 4.1.0 Ross Walker (Thu Mar 02 2006 - 08:17:49 PST)
  - Re: AMBER: amber8 and gfortran 4.1.0 Tru Huynh (Thu Mar 02 2006 - 09:57:59 PST)
    - Re: AMBER: amber8 and gfortran 4.1.0 David A. Case (Thu Mar 02 2006 - 10:07:05 PST)
- Re: AMBER: amber8 and gfortran 4.1.0 Andreas Svrcek-Seiler (Thu Mar 02 2006 - 08:35:16 PST)
  - Re: AMBER: amber8 and gfortran 4.1.0 Tru Huynh (Thu Mar 02 2006 - 09:55:10 PST)
AMBER: AMBER 8 VS AMBER 7 venditti2.unisi.it (Thu Mar 02 2006 - 11:54:47 PST)
- Re: AMBER: AMBER 8 VS AMBER 7 David A. Case (Thu Mar 02 2006 - 12:42:39 PST)
  - Re: AMBER: AMBER 8 VS AMBER 7 Carlos Simmerling (Thu Mar 02 2006 - 13:04:09 PST)
AMBER: about Br- parameters JAVIER PEREZ (Fri Mar 03 2006 - 02:18:23 PST)
- Re: AMBER: about Br- parameters Vitor Manuel Sousa F?x (Fri Mar 03 2006 - 02:28:40 PST)
  - Re: AMBER: about Br- parameters Shulin Zhuang (Fri Mar 03 2006 - 03:04:27 PST)
  - Re: AMBER: about Br- parameters Mathy Froeyen (Fri Mar 03 2006 - 06:38:42 PST)
    - Re: AMBER: about Br- parameters Vitor Manuel Sousa F?x (Fri Mar 03 2006 - 06:48:24 PST)
- Re: AMBER: about Br- parameters german (Fri Mar 03 2006 - 02:52:50 PST)
AMBER: sander restart problem Vlad Cojocaru (Sun Mar 05 2006 - 05:31:30 PST)
- Re: AMBER: sander restart problem Melinda Layten (Mon Mar 06 2006 - 09:35:01 PST)
AMBER: charge neutralization with GB Manish Datt (Sun Mar 05 2006 - 09:27:34 PST)
AMBER: ptraj:hbond question Yam (Sun Mar 05 2006 - 19:09:39 PST)
AMBER: how to calculate the RMSD and B-factor for all atoms of residue haixiao jin (Mon Mar 06 2006 - 00:13:04 PST)
- Re: AMBER: how to calculate the RMSD and B-factor for all atoms of residue Chng Choon-Peng (Mon Mar 06 2006 - 00:51:13 PST)
  - Re: AMBER: how to calculate the RMSD and B-factor for all atoms of residue haixiao jin (Tue Mar 07 2006 - 00:10:02 PST)
AMBER: the total energy is not converge as the cutoff increase thanyarat Udom (Mon Mar 06 2006 - 00:51:46 PST)
- Re: AMBER: the total energy is not converge as the cutoff increase Stefano Federico Massimiliano Pieraccini (Stefano.Pieraccini) (Mon Mar 06 2006 - 01:28:52 PST)
- Re: AMBER: the total energy is not converge as the cutoff increase Cenk Andac (Mon Mar 06 2006 - 05:28:04 PST)
- RE: AMBER: the total energy is not converge as the cutoff increase Ross Walker (Mon Mar 06 2006 - 07:39:51 PST)
  - RE: AMBER: the total energy is not converge as the cutoff increase thanyarat Udom (Mon Mar 06 2006 - 23:17:23 PST)
AMBER: How to patch the configure script (macosx) K. Yarem (Mon Mar 06 2006 - 07:40:58 PST)
- Re: AMBER: How to patch the configure script (macosx) David A. Case (Mon Mar 06 2006 - 10:25:16 PST)
  - AMBER: Problem taking the PDB to the Amber coordinates for calculations Brian Stupi (Mon Mar 06 2006 - 15:17:22 PST)
    - Re: AMBER: Problem taking the PDB to the Amber coordinates for calculations Ilyas Yildirim (Mon Mar 06 2006 - 15:42:29 PST)
    - Re: AMBER: Problem taking the PDB to the Amber coordinates for calculations Thomas Cheatham (Mon Mar 06 2006 - 15:51:08 PST)
    - Re: AMBER: Problem taking the PDB to the Amber coordinates for calculations Brian Stupi (Tue Mar 07 2006 - 11:30:59 PST)
    - Re: AMBER: Problem taking the PDB to the Amber coordinates for calculations David A. Case (Tue Mar 07 2006 - 11:47:30 PST)
    - Re: AMBER: Problem taking the PDB to the Amber coordinates for calculations Brian Stupi (Tue Mar 07 2006 - 11:55:13 PST)
AMBER: Different results between serial and parallel runs in AMBER 8 Ilyas Yildirim (Mon Mar 06 2006 - 16:28:14 PST)
- Re: AMBER: Different results between serial and parallel runs in AMBER 8 Carlos Simmerling (Mon Mar 06 2006 - 16:33:14 PST)
  - Re: AMBER: Different results between serial and parallel runs in AMBER 8 Ilyas Yildirim (Tue Mar 07 2006 - 05:45:01 PST)
    - Re: AMBER: Different results between serial and parallel runs in AMBER 8 David A. Case (Tue Mar 07 2006 - 08:26:23 PST)
    - AMBER: MD and MMPBSA alexandra.marques.fc.up.pt (Wed Mar 08 2006 - 20:29:23 PST)
    - RE: AMBER: MD and MMPBSA Ross Walker (Wed Mar 08 2006 - 21:26:34 PST)
- Re: AMBER: Different results between serial and parallel runs in AMBER 8 David A. Case (Mon Mar 06 2006 - 18:05:31 PST)
  - Re: AMBER: Different results between serial and parallel runs in AMBER 8 Ilyas Yildirim (Tue Mar 07 2006 - 04:51:14 PST)
    - Re: AMBER: Different results between serial and parallel runs in AMBER 8 David A. Case (Tue Mar 07 2006 - 08:23:21 PST)
AMBER: rms processing A D (Mon Mar 06 2006 - 16:21:01 PST)
- Re: AMBER: rms processing Ilyas Yildirim (Mon Mar 06 2006 - 16:41:37 PST)
- Re: AMBER: rms processing Jianyin Shao (Mon Mar 20 2006 - 14:19:25 PST)
AMBER: h bond analysis Claire Zerafa (Mon Mar 06 2006 - 21:39:52 PST)
AMBER: Amber 8 under Solaris 9 compilation failed Dror (Mon Mar 06 2006 - 23:12:19 PST)
- Re: AMBER: Amber 8 under Solaris 9 compilation failed Scott Brozell (Sun Mar 26 2006 - 23:16:27 PST)
AMBER: Amber 8 under Solaris 9 compilation failed Dror (Mon Mar 06 2006 - 23:03:03 PST)
- Re: AMBER: Amber 8 under Solaris 9 compilation failed David A. Case (Tue Mar 07 2006 - 08:35:35 PST)
AMBER: ptraj: hbond analysis Yam (Tue Mar 07 2006 - 00:03:08 PST)
AMBER: Trouble with combining a non-standard residue with a protein of standard residue Nitin Bhardwaj (Tue Mar 07 2006 - 13:21:44 PST)
- Re: AMBER: Trouble with combining a non-standard residue with a protein of standard residue FyD (Wed Mar 08 2006 - 21:37:07 PST)
AMBER: question about solvatecap commander aini.umdnj.edu (Tue Mar 07 2006 - 18:46:41 PST)
- Re: AMBER: question about solvatecap commander mfyang (Tue Mar 07 2006 - 19:07:08 PST)
- Re: AMBER: question about solvatecap commander David A. Case (Tue Mar 07 2006 - 19:32:12 PST)
AMBER:molsurf: molsurf.c:1057: is_buried: Assertion `sarg1 >= 0.0' failed snowyowls (Tue Mar 07 2006 - 23:18:02 PST)
- Re: AMBER:molsurf: molsurf.c:1057: is_buried: Assertion `sarg1 >= 0.0' failed David A. Case (Wed Mar 08 2006 - 08:46:55 PST)
AMBER: NADP(H) parameters Simon Whitehead (Wed Mar 08 2006 - 02:06:45 PST)
- Re: AMBER: NADP(H) parameters David A. Case (Wed Mar 08 2006 - 08:26:04 PST)
AMBER: Dror (Wed Mar 08 2006 - 02:09:28 PST)
AMBER: converting .lib files Simon Whitehead (Wed Mar 08 2006 - 02:51:25 PST)
- Re: AMBER: converting .lib files David A. Case (Wed Mar 08 2006 - 08:06:38 PST)
AMBER: Cosine content calculation matteo filandri (Wed Mar 08 2006 - 07:59:58 PST)
- Re: AMBER: Cosine content calculation David A. Case (Wed Mar 08 2006 - 12:09:54 PST)
- Re: AMBER: Cosine content calculation matteo filandri (Thu Mar 09 2006 - 02:01:20 PST)
  - Re: AMBER: Cosine content calculation David A. Case (Thu Mar 09 2006 - 08:33:53 PST)
  - Re: AMBER: Cosine content calculation Hannes Loeffler (Thu Mar 09 2006 - 17:02:48 PST)
Re: AMBER: converting .lib files Bill Ross (Wed Mar 08 2006 - 08:30:17 PST)
AMBER: modeling a non-standard molecule. Nitin Bhardwaj (Wed Mar 08 2006 - 13:02:50 PST)
- Re: AMBER: modeling a non-standard molecule. Bill Ross (Wed Mar 08 2006 - 13:47:50 PST)
Re: AMBER: modeling a non-standard molecule. Bill Ross (Wed Mar 08 2006 - 13:19:21 PST)
- Re: AMBER: modeling a non-standard molecule. Nitin Bhardwaj (Wed Mar 08 2006 - 13:27:10 PST)
AMBER: aligning polymer with Z-axis of periodic box Kenley Barrett (Wed Mar 08 2006 - 13:59:18 PST)
- Re: AMBER: aligning polymer with Z-axis of periodic box Ilyas Yildirim (Wed Mar 08 2006 - 14:54:22 PST)
  - Re: AMBER: aligning polymer with Z-axis of periodic box Kenley Barrett (Wed Mar 08 2006 - 17:26:12 PST)
AMBER: bond parameters for positively charged guanidine group Ye Mei (Wed Mar 08 2006 - 18:54:15 PST)
- Re: AMBER: bond parameters for positively charged guanidine group Ilyas Yildirim (Wed Mar 08 2006 - 22:18:29 PST)
  - Re: Re: AMBER: bond parameters for positively charged guanidine group Ye Mei (Wed Mar 08 2006 - 22:35:51 PST)
    - Re: Re: AMBER: bond parameters for positively charged guanidine group Ilyas Yildirim (Wed Mar 08 2006 - 23:22:17 PST)
    - Re: Re: AMBER: bond parameters for positively charged guanidine group FyD (Thu Mar 09 2006 - 00:22:05 PST)
    - Re: Re: Re: AMBER: bond parameters for positively charged guanidine group Ye Mei (Thu Mar 09 2006 - 00:40:14 PST)
    - Re: Re: Re: AMBER: bond parameters for positively charged guanidine group Bill Ross (Thu Mar 09 2006 - 11:24:57 PST)
    - Re: Re: Re: Re: AMBER: bond parameters for positively charged guanidine group Ye Mei (Sat Mar 11 2006 - 09:01:53 PST)
    - Re: Re: Re: Re: AMBER: bond parameters for positively charged guanidine group Bill Ross (Sat Mar 11 2006 - 10:37:16 PST)
AMBER: prepin format nkyx.sohu.com (Wed Mar 08 2006 - 19:18:15 PST)
- Re: AMBER: prepin format David A. Case (Thu Mar 09 2006 - 22:49:22 PST)
AMBER: CPU utilization with Parallel Sander Jingyuan Luke (Thu Mar 09 2006 - 04:14:01 PST)
- RE: AMBER: CPU utilization with Parallel Sander Ross Walker (Thu Mar 09 2006 - 08:23:08 PST)
- AMBER: Power Mac G5 Shuting Wei (Thu Mar 09 2006 - 15:32:44 PST)
  - Re: AMBER: Power Mac G5 David A. Case (Thu Mar 09 2006 - 16:14:54 PST)
AMBER: RE: hi & question Ross Walker (Thu Mar 09 2006 - 14:14:02 PST)
AMBER: Antechamber calculations Varsha Goyal (Fri Mar 10 2006 - 11:26:08 PST)
- Re: AMBER: Antechamber calculations Vitor Manuel Sousa F?x (Fri Mar 10 2006 - 12:03:53 PST)
  - Re: AMBER: Antechamber calculations Varsha Goyal (Fri Mar 10 2006 - 15:47:41 PST)
AMBER: error while running sander snoze pa (Fri Mar 10 2006 - 20:23:54 PST)
- Re: AMBER: error while running sander Thomas Cheatham (Fri Mar 10 2006 - 20:41:16 PST)
AMBER: Input conversion error. Sergey Krishtal (Sat Mar 11 2006 - 05:46:47 PST)
- Re: AMBER: Input conversion error. Carlos Simmerling (Sat Mar 11 2006 - 11:23:29 PST)
  - Re[2]: AMBER: Input conversion error. Sergey Krishtal (Mon Mar 13 2006 - 06:52:23 PST)
AMBER: divalent ions Ioana Cozmuta (Sat Mar 11 2006 - 11:04:00 PST)
AMBER: using MM_PBSA just for binding site, feasible ??? tonglei (Sat Mar 11 2006 - 22:53:44 PST)
AMBER: Suitable water box simon whitehead (Mon Mar 13 2006 - 04:07:48 PST)
- Re: AMBER: Suitable water box Jianzhong Liu (Mon Mar 13 2006 - 08:20:52 PST)
AMBER: amber 8 install problem qiwenpeng.sinap.ac.cn (Mon Mar 13 2006 - 05:22:01 PST)
- Re: AMBER: amber 8 install problem David A. Case (Mon Mar 13 2006 - 10:44:40 PST)
- Re: AMBER: amber 8 install problem qiwenpeng.sinap.ac.cn (Wed Mar 15 2006 - 06:27:00 PST)
  - Re: AMBER: amber 8 install problem David A. Case (Wed Mar 15 2006 - 12:33:08 PST)
    - Re: AMBER: amber 8 install problem David A. Case (Wed Mar 15 2006 - 14:00:08 PST)
AMBER: Steve Seibold (Mon Mar 13 2006 - 06:17:41 PST)
- Re: AMBER: David A. Case (Mon Mar 13 2006 - 10:40:19 PST)
- Re: AMBER: Ilyas Yildirim (Mon Mar 13 2006 - 13:35:30 PST)
AMBER: NTT for production run snoze pa (Mon Mar 13 2006 - 10:03:32 PST)
- Re: AMBER: NTT for production run Vlad Cojocaru (Tue Mar 14 2006 - 00:44:35 PST)
  - AMBER: Xleap 64 bit installation problem Cenk Andac (Tue Mar 14 2006 - 03:37:18 PST)
    - Re: AMBER: Xleap 64 bit installation problem Andreas Svrcek-Seiler (Tue Mar 14 2006 - 04:16:47 PST)
    - Re: AMBER: Xleap 64 bit installation problem David A. Case (Tue Mar 14 2006 - 18:06:30 PST)
  - Re: AMBER: NTT for production run David A. Case (Tue Mar 14 2006 - 17:49:46 PST)
    - Re: AMBER: NTT for production run Vlad Cojocaru (Wed Mar 15 2006 - 00:53:46 PST)
    - RE: AMBER: NTT for production run Ross Walker (Wed Mar 15 2006 - 08:21:50 PST)
    - Re: AMBER: NTT for production run snoze pa (Wed Mar 15 2006 - 09:03:22 PST)
    - AMBER: Zoom Angelo (Thu Mar 16 2006 - 02:24:39 PST)
    - Re: AMBER: Zoom Laurent Chiche (Thu Mar 16 2006 - 07:37:38 PST)
    - Re: AMBER: Zoom Angelo (Thu Mar 16 2006 - 07:57:32 PST)
    - Re: AMBER: Zoom Laurent Chiche (Thu Mar 16 2006 - 08:40:42 PST)
    - Re: AMBER: Zoom Angelo (Thu Mar 16 2006 - 09:04:05 PST)
    - Re: AMBER: Zoom Ilyas Yildirim (Thu Mar 16 2006 - 11:50:12 PST)
    - Re: AMBER: NTT for production run David A. Case (Wed Mar 15 2006 - 12:21:52 PST)
    - Re: AMBER: NTT for production run Vlad Cojocaru (Thu Mar 16 2006 - 01:56:46 PST)
    - Re: AMBER: NTT for production run David A. Case (Thu Mar 16 2006 - 10:00:54 PST)
    - Re: AMBER: NTT for production run Vlad Cojocaru (Fri Mar 17 2006 - 01:16:36 PST)
AMBER: nucgen error bala (Tue Mar 14 2006 - 07:35:11 PST)
Re: AMBER: nucgen error Bill Ross (Tue Mar 14 2006 - 09:06:16 PST)
AMBER: divalent ions Ioana Cozmuta (Tue Mar 14 2006 - 11:54:49 PST)
- Re: AMBER: divalent ions Thomas E. Cheatham, III (Tue Mar 14 2006 - 14:10:19 PST)
AMBER: quistions about pbsa cacultaion snowyowls (Tue Mar 14 2006 - 17:26:12 PST)
- Re: AMBER: quistions about pbsa cacultaion Ray Luo (Sun Mar 12 2006 - 23:26:53 PST)
  - Re: AMBER: quistions about pbsa cacultaion snowyowls (Tue Mar 14 2006 - 18:43:46 PST)
    - Re: AMBER: quistions about pbsa cacultaion Ray Luo (Wed Mar 15 2006 - 09:36:56 PST)
AMBER: k-space cutoff with standard Ewald Guowen (Wed Mar 15 2006 - 08:29:33 PST)
AMBER: mm-pbsa vorasit vongsutilers (Thu Mar 16 2006 - 07:34:33 PST)
- Re: AMBER: mm-pbsa Holger Gohlke (Thu Mar 16 2006 - 09:33:20 PST)
  - Re: AMBER: mm-pbsa vorasit vongsutilers (Fri Mar 17 2006 - 06:03:15 PST)
    - Re: AMBER: mm-pbsa Scott Pendley (Fri Mar 17 2006 - 15:41:30 PST)
    - Re: AMBER: mm-pbsa vorasit vongsutilers (Sun Mar 19 2006 - 09:45:15 PST)
    - Re: AMBER: mm-pbsa Scott Pendley (Mon Mar 20 2006 - 10:06:38 PST)
AMBER: faulty ambpdb compilation? Benjamin Juhl (Thu Mar 16 2006 - 10:16:12 PST)
- RE: AMBER: faulty ambpdb compilation? Ross Walker (Thu Mar 16 2006 - 10:44:23 PST)
  - Re: AMBER: faulty ambpdb compilation? Benjamin Juhl (Thu Mar 16 2006 - 10:51:47 PST)
AMBER: constant pH simulation Abhilash Mohan (Thu Mar 16 2006 - 11:14:47 PST)
- Re: AMBER: constant pH simulation John Mongan (Tue Mar 21 2006 - 15:51:53 PST)
AMBER: prep files for L-sugar residues Qizhi Cui (Fri Mar 17 2006 - 18:42:56 PST)
- AMBER: Ewald and ibelly Austin B. Yongye (Sun Mar 19 2006 - 08:36:53 PST)
  - Re: AMBER: Ewald and ibelly David A. Case (Sun Mar 19 2006 - 22:26:17 PST)
AMBER: emilia wu (Mon Mar 20 2006 - 04:38:17 PST)
- Re: AMBER: David A. Case (Mon Mar 20 2006 - 22:36:09 PST)
  - AMBER: MMPBSA alexandra.marques.fc.up.pt (Tue Mar 21 2006 - 01:58:35 PST)
AMBER: energy conservation in NVE ensemble (ntt=0, ntb=1) Vlad Cojocaru (Mon Mar 20 2006 - 08:40:37 PST)
AMBER: a challenge: a periodic box that cuts through a monomer Kenley Barrett (Mon Mar 20 2006 - 14:06:49 PST)
- Re: AMBER: a challenge: a periodic box that cuts through a monomer David A. Case (Mon Mar 20 2006 - 22:29:33 PST)
AMBER: anal: dihedral error renyanliang (Mon Mar 20 2006 - 17:27:39 PST)
- Re: AMBER: anal: dihedral error David A. Case (Sat Mar 25 2006 - 12:48:36 PST)
AMBER: heating system snoze pa (Tue Mar 21 2006 - 13:58:25 PST)
- RE: AMBER: heating system Ross Walker (Tue Mar 21 2006 - 15:09:28 PST)
  - Re: AMBER: heating system snoze pa (Tue Mar 21 2006 - 15:39:15 PST)
- RE: AMBER: heating system Ross Walker (Wed Mar 22 2006 - 08:58:12 PST)
- RE: AMBER: heating system Ross Walker (Fri Mar 24 2006 - 09:29:32 PST)
AMBER: About statistics results in MMPBSA_DC pair 莉张 (Wed Mar 22 2006 - 07:22:17 PST)
AMBER: Related to RESTRAINT_WT snoze pa (Wed Mar 22 2006 - 14:06:04 PST)
- Re: AMBER: Related to RESTRAINT_WT David A. Case (Wed Mar 22 2006 - 16:15:29 PST)
- Re: AMBER: Related to RESTRAINT_WT Chng Choon-Peng (Wed Mar 22 2006 - 16:16:13 PST)
AMBER: Solvating the system with specific number of water molecules... Ilyas Yildirim (Wed Mar 22 2006 - 21:50:25 PST)
AMBER: about atomic fluctuation & RMSF xueping (Thu Mar 23 2006 - 02:05:03 PST)
- Re: AMBER: about atomic fluctuation & RMSF Holger Gohlke (Thu Mar 23 2006 - 05:01:14 PST)
  - Re: AMBER: about atomic fluctuation & RMSF xueping (Sun Mar 26 2006 - 18:39:45 PST)
    - AMBER: PCA venditti2.unisi.it (Thu Apr 06 2006 - 13:27:20 PDT)
    - Re: AMBER: PCA Holger Gohlke (Sun Apr 09 2006 - 11:09:06 PDT)
    - Re: AMBER: PCA venditti2.unisi.it (Mon Apr 10 2006 - 07:57:41 PDT)
    - Re: AMBER: PCA Holger Gohlke (Tue Apr 11 2006 - 05:27:26 PDT)
AMBER: question capping helix ends Zhuang (Thu Mar 23 2006 - 02:35:21 PST)
- Re: AMBER: question capping helix ends Vlad Cojocaru (Thu Mar 23 2006 - 02:48:14 PST)
AMBER: what is unit of the out put of mmpbsa caculation snowyowls (Thu Mar 23 2006 - 04:47:52 PST)
- Re: AMBER: what is unit of the out put of mmpbsa caculation Holger Gohlke (Thu Mar 23 2006 - 04:53:51 PST)
AMBER: Average pdb Claire Zerafa (Thu Mar 23 2006 - 13:17:33 PST)
- RE: AMBER: Average pdb John Jett (Thu Mar 23 2006 - 14:32:00 PST)
AMBER: question capping helix ends Zhuang (Thu Mar 23 2006 - 16:21:06 PST)
- Re: AMBER: question capping helix ends Cenk Andac (Fri Mar 24 2006 - 01:09:11 PST)
  - Re: AMBER: question capping helix ends Vlad Cojocaru (Fri Mar 24 2006 - 02:51:24 PST)
AMBER: Parmtop file: ANGLE_EQUIL_VALUE actually in radians? amanda.mccook.gatech.edu (Thu Mar 23 2006 - 20:32:39 PST)
- RE: AMBER: Parmtop file: ANGLE_EQUIL_VALUE actually in radians? Ross Walker (Thu Mar 23 2006 - 21:38:24 PST)
AMBER: negative values of PBSOL and PBCAL in mm_pbsa result tonglei (Sun Mar 26 2006 - 18:07:47 PST)
AMBER: temp control snoze pa (Sun Mar 26 2006 - 19:16:20 PST)
To dac --AMBER: anal: dihedral error 莉张 (Sun Mar 26 2006 - 22:43:22 PST)
AMBER: OSX 10.4 G4 xlf90 compilation errors K. Yarem (Mon Mar 27 2006 - 12:06:59 PST)
- Re: AMBER: OSX 10.4 G4 xlf90 compilation errors David Case (Mon Mar 27 2006 - 12:18:27 PST)
AMBER: How to give the specific pressure parameter for NTP=2 hbluo (Tue Mar 28 2006 - 09:29:48 PST)
AMBER: united atoms nadiav.soton.ac.uk (Tue Mar 28 2006 - 03:04:53 PST)
AMBER: amber8 error installation Abd Ghani Abd Aziz (Tue Mar 28 2006 - 07:14:59 PST)
- Re: AMBER: amber8 error installation Mark Williamson (Tue Mar 28 2006 - 07:23:28 PST)
  - Re: AMBER: amber8 error installation Abd Ghani Abd Aziz (Tue Mar 28 2006 - 07:44:42 PST)
    - Re: AMBER: amber8 error installation Mark Williamson (Tue Mar 28 2006 - 08:08:46 PST)
    - Re: AMBER: amber8 error installation Abd Ghani Abd Aziz (Tue Mar 28 2006 - 08:27:37 PST)
    - RE: AMBER: amber8 error installation Ross Walker (Tue Mar 28 2006 - 08:37:34 PST)
    - RE: AMBER: amber8 error installation John Bushnell (Tue Mar 28 2006 - 18:20:42 PST)
    - RE: AMBER: amber8 error installation Ross Walker (Tue Mar 28 2006 - 20:35:03 PST)
Re: AMBER: united atoms Bill Ross (Tue Mar 28 2006 - 09:02:01 PST)
AMBER: hessian calculation sebnem (Tue Mar 28 2006 - 13:48:19 PST)
- Re: AMBER: hessian calculation David A. Case (Tue Mar 28 2006 - 15:52:14 PST)
  - Re: AMBER: hessian calculation sebnem.mercury.chem.pitt.edu (Tue Mar 28 2006 - 16:20:18 PST)
    - Re: AMBER: hessian calculation David A. Case (Tue Mar 28 2006 - 18:15:58 PST)
    - Re: AMBER: hessian calculation sebnem (Tue Mar 28 2006 - 18:41:52 PST)
    - Re: AMBER: hessian calculation sebnem (Tue Mar 28 2006 - 18:53:59 PST)
    - Re: AMBER: hessian calculation sebnem.mercury.chem.pitt.edu (Wed Mar 29 2006 - 13:48:38 PST)
    - Re: AMBER: hessian calculation David A. Case (Wed Mar 29 2006 - 16:08:34 PST)
    - Re: AMBER: hessian calculation sebnem (Thu Mar 30 2006 - 08:22:23 PST)
AMBER: AMBER : About the kinetic energy and temperature (GBSA model) James W (Tue Mar 28 2006 - 18:00:46 PST)
- Re: AMBER: AMBER : About the kinetic energy and temperature (GBSA model) David A. Case (Tue Mar 28 2006 - 18:13:44 PST)
- Fw: AMBER: AMBER : About the kinetic energy and temperature (GBSA model) James W (Tue Mar 28 2006 - 19:44:42 PST)
  - Re: Fw: AMBER: AMBER : About the kinetic energy and temperature (GBSA model) Thomas Cheatham (Tue Mar 28 2006 - 20:32:37 PST)
  - RE: AMBER: AMBER : About the kinetic energy and temperature (GBSA model) Ross Walker (Tue Mar 28 2006 - 20:35:03 PST)
AMBER: installation problem r. a. (Tue Mar 28 2006 - 19:21:50 PST)
- Re: AMBER: installation problem Mark Williamson (Tue Mar 28 2006 - 19:40:27 PST)
- Re: AMBER: installation problem Abd Ghani Abd Aziz (Tue Mar 28 2006 - 19:50:08 PST)
AMBER: Impropers definition egorov (Tue Mar 28 2006 - 22:06:40 PST)
- Re: AMBER: Impropers definition David A. Case (Wed Mar 29 2006 - 09:10:27 PST)
AMBER: Simulating a periodic crystal Jiang Jianwen (Wed Mar 29 2006 - 07:01:26 PST)
- Re: AMBER: Simulating a periodic crystal Thomas Cheatham (Wed Mar 29 2006 - 07:57:10 PST)
- RE: AMBER: Simulating a periodic crystal Jiang Jianwen (Fri Mar 31 2006 - 03:31:47 PST)
AMBER: Announcement: Amber 9 is now available David A. Case (Wed Mar 29 2006 - 08:43:59 PST)
- Re: AMBER: Announcement: Amber 9 is now available David E. Konerding (Fri Mar 31 2006 - 08:38:06 PST)
  - Re: AMBER: Announcement: Amber 9 is now available David A. Case (Fri Mar 31 2006 - 08:56:48 PST)
    - Re: AMBER: Announcement: Amber 9 is now available David A. Case (Fri Mar 31 2006 - 09:29:54 PST)
- Re: AMBER: Announcement: Amber 9 is now available Thomas Patko (CSULB) (Sat Apr 01 2006 - 08:29:26 PST)
  - Re: AMBER: Announcement: Amber 9 is now available David A. Case (Sat Apr 01 2006 - 09:21:52 PST)
- Re: AMBER: Announcement: Amber 9 is now available Feng X Zhou (Mon Apr 03 2006 - 08:28:48 PDT)
  - Re: AMBER: Announcement: Amber 9 is now available FyD (Mon Apr 03 2006 - 11:00:44 PDT)
  - AMBER: Using XML for Amber files David A. Case (Tue Apr 04 2006 - 15:42:35 PDT)
    - RE: AMBER: Using XML for Amber files Feng X Zhou (Wed Apr 05 2006 - 08:21:35 PDT)
    - Re: AMBER: Using XML for Amber files Xuebin Qiao (Fri Apr 07 2006 - 10:52:08 PDT)
    - Re: AMBER: Using XML for Amber files Feng X Zhou (Fri Apr 07 2006 - 11:54:59 PDT)
    - AMBER: Umbrella sampling venditti2.unisi.it (Fri Apr 07 2006 - 13:04:55 PDT)
    - Re: AMBER: Umbrella sampling David A. Case (Fri Apr 07 2006 - 13:56:48 PDT)
    - Re: AMBER: Using XML for Amber files Xuebin Qiao (Mon Apr 24 2006 - 20:57:47 PDT)
    - Re: AMBER: Using XML for Amber files Feng X Zhou (Tue Apr 25 2006 - 08:07:39 PDT)
- AMBER: Question about interpretation of sander.QMMM results Cenk Andac (Thu Apr 06 2006 - 12:10:09 PDT)
AMBER: Dimer Image Wrapping Melinda Layten (Wed Mar 29 2006 - 15:12:00 PST)
- Re: AMBER: Dimer Image Wrapping Scott Pendley (Thu Mar 30 2006 - 09:29:23 PST)
  - Re: AMBER: Dimer Image Wrapping Melinda Layten (Thu Mar 30 2006 - 10:16:06 PST)
AMBER: post-processing replica exchange trajectory Zhuang (Wed Mar 29 2006 - 15:57:43 PST)
AMBER: Problem with setbox command... Ilyas Yildirim (Wed Mar 29 2006 - 23:44:37 PST)
- Re: AMBER: Problem with setbox command... David A. Case (Thu Mar 30 2006 - 08:06:04 PST)
  - Re: AMBER: Problem with setbox command... Ilyas Yildirim (Fri Mar 31 2006 - 04:34:33 PST)
AMBER: charge constraints in resp Kenley Barrett (Thu Mar 30 2006 - 08:22:36 PST)
- Re: AMBER: charge constraints in resp Ilyas Yildirim (Thu Mar 30 2006 - 09:03:43 PST)
  - Re: AMBER: charge constraints in resp Kenley Barrett (Thu Mar 30 2006 - 11:46:49 PST)
    - Re: AMBER: charge constraints in resp Ilyas Yildirim (Thu Mar 30 2006 - 16:05:35 PST)
AMBER: Gromos to Amber Ann Vilan Tran (Thu Mar 30 2006 - 11:29:07 PST)
AMBER: LES error Claudia Steinert (Thu Mar 30 2006 - 23:59:36 PST)
- Re: AMBER: LES error carlos (Sat Apr 01 2006 - 10:04:46 PST)
AMBER: Ptraj & pca Claire Zerafa (Fri Mar 31 2006 - 06:23:05 PST)
AMBER: MMPBSA & PBCAL Rabal Gracia María Obdulia (Fri Mar 31 2006 - 07:37:57 PST)
AMBER: ptraj help - ERROR in readParm: ... failed to find CHARGE fine wu (Fri Mar 31 2006 - 14:09:36 PST)
- Re: AMBER: ptraj help - ERROR in readParm: ... failed to find CHARGE Thomas E. Cheatham, III (Fri Mar 31 2006 - 14:18:57 PST)
- Re: AMBER: ptraj help - ERROR in readParm: ... failed to find CHARGE Ilyas Yildirim (Fri Mar 31 2006 - 16:46:03 PST)
AMBER: chirality.c error in xleap Kenley Barrett (Fri Mar 31 2006 - 14:43:33 PST)
- Re: AMBER: chirality.c error in xleap David A. Case (Fri Mar 31 2006 - 17:41:53 PST)
AMBER: what is the integration scheme for langevin dynamic used in amber8 Li Su (Sat Apr 01 2006 - 05:17:02 PST)
- Re: AMBER: what is the integration scheme for langevin dynamic used in amber8 David A. Case (Sat Apr 01 2006 - 09:18:57 PST)
AMBER: Different result for serial and parallel sander with IREST=1 (AMBER 8) ! Pradipta Bandyopadhyay (Sun Apr 02 2006 - 22:23:26 PDT)
- Re: AMBER: Different result for serial and parallel sander with IREST=1 (AMBER 8) ! David A. Case (Mon Apr 03 2006 - 07:57:36 PDT)
AMBER: Semi-empirical parameterization -- van der Waals and H-bonding? Evan Kelly (Mon Apr 03 2006 - 15:28:27 PDT)
- RE: AMBER: Semi-empirical parameterization -- van der Waals and H-bonding? Ross Walker (Mon Apr 03 2006 - 16:53:06 PDT)
AMBER: Entropy calculations with Nmode and ptraj Daniel Oehme (Tue Apr 04 2006 - 00:24:39 PDT)
- Re: AMBER: Entropy calculations with Nmode and ptraj David A. Case (Tue Apr 04 2006 - 15:50:55 PDT)
  - AMBER: POPC parameters xiaoqin huang (Thu Apr 06 2006 - 20:18:10 PDT)
    - Re: AMBER: POPC parameters David A. Case (Fri Apr 07 2006 - 09:14:53 PDT)
    - AMBER: angle between planes John (Fri Apr 07 2006 - 09:48:38 PDT)
AMBER: how to restrain the intramolecular hydrogen bond Ye Mei (Tue Apr 04 2006 - 02:35:42 PDT)
- Re: AMBER: how to restrain the intramolecular hydrogen bond David A. Case (Tue Apr 04 2006 - 15:52:52 PDT)
  - AMBER: Obtaining an average structure from a trajectory Alfredo Quevedo (Tue Apr 04 2006 - 16:11:02 PDT)
    - RE: AMBER: Obtaining an average structure from a trajectory Ross Walker (Tue Apr 04 2006 - 17:07:18 PDT)
AMBER: errors in mm_pbsa.in in AMBER 8 mannul ? tonglei (Tue Apr 04 2006 - 06:10:59 PDT)
- Re: AMBER: errors in mm_pbsa.in in AMBER 8 mannul ? David A. Case (Tue Apr 04 2006 - 15:11:51 PDT)
Re: AMBER: RMS (fwd) Wen Li (Tue Apr 04 2006 - 08:02:02 PDT)
- Re: AMBER: RMS (fwd) Wen Li (Tue Apr 04 2006 - 08:17:14 PDT)
  - AMBER: Any difference about RESP or ESP with Chelpg or MK Jianzhong Liu (Tue Apr 04 2006 - 08:51:36 PDT)
    - Re: AMBER: Any difference about RESP or ESP with Chelpg or MK FyD (Tue Apr 04 2006 - 10:01:40 PDT)
    - Re: AMBER: Any difference about RESP or ESP with Chelpg or MK David Mobley (Tue Apr 04 2006 - 15:13:30 PDT)
AMBER: molsurf or LCPO method in MM_GB/SA? tonglei (Tue Apr 04 2006 - 18:25:37 PDT)
AMBER: one question about mm_pbsa 杜永春 (Tue Apr 04 2006 - 23:47:06 PDT)
- Re: AMBER: one question about mm_pbsa JunJun Liu (Thu Apr 06 2006 - 14:48:20 PDT)
AMBER: nmode different units cristian obiol (Wed Apr 05 2006 - 03:47:04 PDT)
AMBER: Claire Zerafa (Wed Apr 05 2006 - 06:33:39 PDT)
- Re: AMBER: David A. Case (Wed Apr 05 2006 - 07:46:18 PDT)
AMBER: Restarting constant pressure sims with restraints Don.Bashford.stjude.org (Wed Apr 05 2006 - 11:08:41 PDT)
- Re: AMBER: Restarting constant pressure sims with restraints David A. Case (Wed Apr 05 2006 - 11:24:38 PDT)
- Re: AMBER: Restarting constant pressure sims with restraints Robert Duke (Wed Apr 05 2006 - 11:30:05 PDT)
AMBER: MM-GBSA decomposition sishi.tang.utoronto.ca (Thu Apr 06 2006 - 13:20:36 PDT)
- Re: AMBER: MM-GBSA decomposition Holger Gohlke (Sun Apr 09 2006 - 11:13:41 PDT)
  - Re: AMBER: MM-GBSA decomposition sishi.tang.utoronto.ca (Sat Apr 15 2006 - 10:54:34 PDT)
AMBER: organic molecule - from newbie :) Raffaella D'Auria (Thu Apr 06 2006 - 18:55:02 PDT)
- RE: AMBER: organic molecule - from newbie :) Ross Walker (Thu Apr 06 2006 - 19:13:46 PDT)
  - RE: AMBER: organic molecule - from newbie :) Raffaella D'Auria (Mon Apr 10 2006 - 15:12:44 PDT)
    - RE: AMBER: organic molecule - from newbie :) Ross Walker (Mon Apr 10 2006 - 15:41:56 PDT)
AMBER: NGL error when creating snapshots for MM/PB(GB)SA andy ng (Thu Apr 06 2006 - 23:05:50 PDT)
- Re: AMBER: NGL error when creating snapshots for MM/PB(GB)SA andy ng (Thu Apr 06 2006 - 23:20:16 PDT)
AMBER: angle between planes John (Fri Apr 07 2006 - 09:55:59 PDT)
- Re: AMBER: angle between planes Chris Moth (Fri Apr 07 2006 - 14:19:26 PDT)
AMBER: mm-pbsa: distant-dependent dielectric constant lhsong (Sat Apr 08 2006 - 11:30:56 PDT)
- Re: AMBER: mm-pbsa: distant-dependent dielectric constant David A. Case (Sat Apr 08 2006 - 22:23:15 PDT)
  - Re: AMBER: mm-pbsa: distant-dependent dielectric constant David A. Case (Sat Apr 08 2006 - 23:11:49 PDT)
AMBER: "average" command in ptraj Arjen-Joachim Jakobi (Mon Apr 10 2006 - 05:15:16 PDT)
- Re: AMBER: "average" command in ptraj Thomas E. Cheatham, III (Mon Apr 10 2006 - 11:06:20 PDT)
- Re: AMBER: "average" command in ptraj Arjen-Joachim Jakobi (Mon Apr 10 2006 - 11:50:34 PDT)
AMBER: PB bomb in pb_atmlist(): MAXNEI too short snowyowls (Mon Apr 10 2006 - 05:55:12 PDT)
- Re: AMBER: PB bomb in pb_atmlist(): MAXNEI too short Scott Brozell (Mon Apr 10 2006 - 07:59:46 PDT)
  - Re: AMBER: PB bomb in pb_atmlist(): MAXNEI too short snowyowls (Mon Apr 10 2006 - 20:07:40 PDT)
- Re: AMBER: PB bomb in pb_atmlist(): MAXNEI too short Ray Luo (Sun Apr 09 2006 - 19:44:44 PDT)
  - Re: AMBER: PB bomb in pb_atmlist(): MAXNEI too short snowyowls (Mon Apr 10 2006 - 20:09:35 PDT)
AMBER: printing Amber VdW radii as separate column in pdb files Vlad Cojocaru (Mon Apr 10 2006 - 07:41:51 PDT)
- Re: AMBER: printing Amber VdW radii as separate column in pdb files harianto (Mon Apr 10 2006 - 08:12:39 PDT)
  - Re: AMBER: printing Amber VdW radii as separate column in pdb files Vlad Cojocaru (Mon Apr 10 2006 - 08:43:18 PDT)
    - RE: AMBER: printing Amber VdW radii as separate column in pdb files Ross Walker (Mon Apr 10 2006 - 09:03:18 PDT)
AMBER: VdW radii in the topology file Vlad Cojocaru (Mon Apr 10 2006 - 09:14:16 PDT)
- Re: AMBER: VdW radii in the topology file harianto (Mon Apr 10 2006 - 09:51:55 PDT)
  - Re: AMBER: VdW radii in the topology file Vlad Cojocaru (Mon Apr 10 2006 - 10:01:33 PDT)
AMBER: reconstructing PMF Ioana Cozmuta (Mon Apr 10 2006 - 11:15:20 PDT)
AMBER: "vector" command in ptraj Lishan Yao (Mon Apr 10 2006 - 11:20:56 PDT)
AMBER: protocols for NMR protein refinement with AMBER ohucke.lav.boehringer-ingelheim.com (Mon Apr 10 2006 - 13:43:44 PDT)
- Re: AMBER: protocols for NMR protein refinement with AMBER David A. Case (Mon Apr 10 2006 - 13:55:43 PDT)
AMBER: the best force field for DNA Chengwen Chen (Mon Apr 10 2006 - 21:15:25 PDT)
AMBER: RESP problem Simon Whitehead (Tue Apr 11 2006 - 06:44:00 PDT)
- RE: AMBER: RESP problem Ross Walker (Tue Apr 11 2006 - 08:08:25 PDT)
  - AMBER: experiments with amber9 and fortran nag f95 on mac os x 10.4.3 Mathy Froeyen (Tue Apr 11 2006 - 10:44:40 PDT)
    - Re: AMBER: experiments with amber9 and fortran nag f95 on mac os x 10.4.3 David A. Case (Tue Apr 11 2006 - 11:19:59 PDT)
- Re: AMBER: RESP problem FyD (Tue Apr 11 2006 - 09:31:12 PDT)
  - AMBER: How to evaluate the binding energy of a ligand? Alfredo Quevedo (Tue Apr 11 2006 - 10:53:50 PDT)
    - Re: AMBER: How to evaluate the binding energy of a ligand? David Mobley (Tue Apr 11 2006 - 12:27:13 PDT)
AMBER: An issue with the "multimolecule and multiconformational" resp fit Jason K (Tue Apr 11 2006 - 11:16:57 PDT)
- Re: AMBER: An issue with the "multimolecule and multiconformational" resp fit FyD (Tue Apr 11 2006 - 12:39:40 PDT)
AMBER: Nmode memory allocation error ? Junmei Wang (Tue Apr 11 2006 - 11:47:46 PDT)
- Re: AMBER: Nmode memory allocation error ? David A. Case (Tue Apr 11 2006 - 12:09:26 PDT)
AMBER: Constant P for non-orthorhombic cells Jennie Thomas (Tue Apr 11 2006 - 21:40:00 PDT)
- Re: AMBER: Constant P for non-orthorhombic cells darden (Wed Apr 12 2006 - 05:41:14 PDT)
- Re: AMBER: Constant P for non-orthorhombic cells Michael Crowley (Wed Apr 12 2006 - 11:24:05 PDT)
  - Re: AMBER: Constant P for non-orthorhombic cells Jennie Thomas (Wed Apr 12 2006 - 11:36:47 PDT)
AMBER: Mass wieghted Covariance Matrix Daniel Oehme (Wed Apr 12 2006 - 00:16:32 PDT)
- Re: AMBER: Mass wieghted Covariance Matrix Holger Gohlke (Wed Apr 12 2006 - 00:46:19 PDT)
AMBER: deviations from idealized geometry Maarit Hellman (Wed Apr 12 2006 - 02:02:33 PDT)
AMBER: saltcon with explicit water? Kenley Barrett (Wed Apr 12 2006 - 09:36:20 PDT)
- Re: AMBER: saltcon with explicit water? David A. Case (Wed Apr 12 2006 - 12:25:38 PDT)
  - Re: AMBER: saltcon with explicit water? Kenley Barrett (Wed Apr 12 2006 - 16:07:44 PDT)
- Re: AMBER: saltcon with explicit water? Bill Ross (Wed Apr 12 2006 - 16:26:05 PDT)
AMBER: Which one is the best force field for DNA? Chengwen Chen (Wed Apr 12 2006 - 20:11:14 PDT)
- Re: AMBER: Which one is the best force field for DNA? Vlad Cojocaru (Thu Apr 13 2006 - 01:11:33 PDT)
  - Re: AMBER: Which one is the best force field for DNA? David A. Case (Thu Apr 13 2006 - 14:41:03 PDT)
    - Re: AMBER: Which one is the best force field for DNA? Vlad Cojocaru (Fri Apr 14 2006 - 02:57:33 PDT)
    - Re: AMBER: Which one is the best force field for DNA? Jiri Sponer (Fri Apr 14 2006 - 03:31:24 PDT)
    - Re: AMBER: Which one is the best force field for DNA? David A. Case (Fri Apr 14 2006 - 08:27:52 PDT)
    - Re: AMBER: Which one is the best force field for DNA? Jiri Sponer (Fri Apr 14 2006 - 09:59:00 PDT)
    - Re: AMBER: Which one is the best force field for DNA? Thomas E. Cheatham, III (Fri Apr 14 2006 - 09:01:50 PDT)
    - Re: AMBER: Which one is the best force field for DNA? Vlad Cojocaru (Fri Apr 14 2006 - 09:30:23 PDT)
    - Re: AMBER: Which one is the best force field for DNA? Carlos Simmerling (Fri Apr 14 2006 - 09:41:04 PDT)
    - Re: AMBER: Which one is the best force field for DNA? Jiri Sponer (Fri Apr 14 2006 - 09:49:58 PDT)
    - Re: AMBER: Which one is the best force field for DNA? Vlad Cojocaru (Fri Apr 14 2006 - 10:01:27 PDT)
    - Re: AMBER: Which one is the best force field for DNA? Jiri Sponer (Fri Apr 14 2006 - 10:08:34 PDT)
    - Re: AMBER: Which one is the best force field for DNA? Thomas Cheatham (Fri Apr 14 2006 - 10:20:14 PDT)
    - Re: AMBER: Which one is the best force field for DNA? David A. Case (Fri Apr 14 2006 - 10:53:50 PDT)
    - Re: AMBER: Which one is the best force field for DNA? Carlos Simmerling (Fri Apr 14 2006 - 11:28:42 PDT)
    - AMBER: Force field for DNA Osmar Norberto de Souza (Mon Apr 17 2006 - 03:50:31 PDT)
AMBER:a problem in parallel compiler snowyowls (Wed Apr 12 2006 - 21:27:10 PDT)
- AMBER:a problem in parallel compiler snowyowls (Thu Apr 13 2006 - 01:15:09 PDT)
  - RE: AMBER:a problem in parallel compiler Ross Walker (Thu Apr 13 2006 - 08:54:43 PDT)
AMBER: Dual Xeon mpich compilation error Simon Whitehead (Thu Apr 13 2006 - 00:56:47 PDT)
AMBER: one question about mm_pbsa 杜永春 (Thu Apr 13 2006 - 01:37:50 PDT)
- Re: AMBER: one question about mm_pbsa Ray Luo (Thu Apr 13 2006 - 08:39:53 PDT)
- Re: AMBER: one question about mm_pbsa 杜永春 (Thu Apr 13 2006 - 19:26:49 PDT)
AMBER: dual xeon mpich compilation problem: sorted Simon Whitehead (Thu Apr 13 2006 - 05:16:53 PDT)
AMBER: passwordless ssh stopped working Jan Dohnalek (Thu Apr 13 2006 - 08:51:50 PDT)
AMBER: Respgen segemtation fault Simon Whitehead (Thu Apr 13 2006 - 09:38:41 PDT)
- Re: AMBER: Respgen segemtation fault David A. Case (Thu Apr 13 2006 - 11:46:55 PDT)
AMBER: separating LES copies in moil view Amber admin (Thu Apr 13 2006 - 10:28:02 PDT)
- Re: AMBER: separating LES copies in moil view Carlos Simmerling (Thu Apr 13 2006 - 16:45:35 PDT)
AMBER: Saving single coordinate set from Amber trajectory file as a restrt file. Sergey Krishtal (Thu Apr 13 2006 - 20:05:45 PDT)
- Re: AMBER: Saving single coordinate set from Amber trajectory file as a restrt file. Vlad Cojocaru (Fri Apr 14 2006 - 02:18:41 PDT)
AMBER: MM-PBSA problem Miguel Ferreira (Fri Apr 14 2006 - 08:27:43 PDT)
- Re: AMBER: MM-PBSA problem Ray Luo (Fri Apr 14 2006 - 09:57:52 PDT)
  - Re: AMBER: MM-PBSA problem Miguel Ferreira (Fri Apr 14 2006 - 14:07:20 PDT)
    - Re: AMBER: MM-PBSA problem Ray Luo (Fri Apr 14 2006 - 14:40:45 PDT)
AMBER: DNA tutorial, in vacuo minimization amanda.mccook.gatech.edu (Fri Apr 14 2006 - 12:15:31 PDT)
- RE: AMBER: DNA tutorial, in vacuo minimization Ross Walker (Fri Apr 14 2006 - 12:34:32 PDT)
AMBER: compile error: can't locate file for: -lcrt1.o xyu3 (Fri Apr 14 2006 - 15:37:50 PDT)
- Re: AMBER: compile error: can't locate file for: -lcrt1.o David A. Case (Fri Apr 14 2006 - 15:58:33 PDT)
AMBER: amber memory usage Ed Pate (Fri Apr 14 2006 - 15:45:59 PDT)
- Re: AMBER: amber memory usage Robert Duke (Fri Apr 14 2006 - 15:56:12 PDT)
- RE: AMBER: amber memory usage Ross Walker (Fri Apr 14 2006 - 17:28:31 PDT)
- Re: AMBER: amber memory usage David A. Case (Fri Apr 14 2006 - 17:30:44 PDT)
AMBER: How I wasted a rainy Friday in San Diego David A. Case (Fri Apr 14 2006 - 17:24:00 PDT)
AMBER: Calculation of g(r) from PTRAJ Ananda Rama Krishnan Selvaraj (Sun Apr 16 2006 - 03:33:25 PDT)
- Re: AMBER: Calculation of g(r) from PTRAJ David A. Case (Mon Apr 17 2006 - 09:45:27 PDT)
- Re: AMBER: Calculation of g(r) from PTRAJ Ananda Rama Krishnan Selvaraj (Mon Apr 17 2006 - 10:45:39 PDT)
AMBER: amber7 compiling error linfu (Sun Apr 16 2006 - 08:26:17 PDT)
- Re: AMBER: amber7 compiling error Scott Brozell (Sun Apr 16 2006 - 12:30:23 PDT)
AMBER: Could not find atom type. Sergey Krishtal (Mon Apr 17 2006 - 02:08:19 PDT)
- Re: AMBER: Could not find atom type. David A. Case (Mon Apr 17 2006 - 09:40:05 PDT)
- RE: AMBER: Could not find atom type. Yong Duan (Mon Apr 17 2006 - 09:45:10 PDT)
- Re[2]: AMBER: Could not find atom type. Sergey Krishtal (Tue Apr 18 2006 - 03:48:07 PDT)
  - Re: AMBER: Could not find atom type. David A. Case (Tue Apr 18 2006 - 16:06:21 PDT)
    - Re[2]: AMBER: Could not find atom type. Sergey Krishtal (Tue Apr 18 2006 - 19:56:30 PDT)
    - Re: AMBER: Could not find atom type. David A. Case (Wed Apr 19 2006 - 12:37:33 PDT)
AMBER: ambpdb and original PDB snoze pa (Mon Apr 17 2006 - 11:20:05 PDT)
- RE: AMBER: ambpdb and original PDB Ross Walker (Mon Apr 17 2006 - 11:28:18 PDT)
  - Re: AMBER: ambpdb and original PDB snoze pa (Mon Apr 17 2006 - 11:48:55 PDT)
    - Re: AMBER: ambpdb and original PDB Mingfeng Yang (Mon Apr 17 2006 - 13:00:53 PDT)
    - Re: AMBER: ambpdb and original PDB Mingfeng Yang (Mon Apr 17 2006 - 13:05:43 PDT)
Re: AMBER: ambpdb and original PDB Bill Ross (Mon Apr 17 2006 - 11:38:17 PDT)
AMBER: probable bug in antechamber David Mobley (Mon Apr 17 2006 - 16:08:06 PDT)
- Re: AMBER: probable bug in antechamber David A. Case (Mon Apr 17 2006 - 17:33:35 PDT)
  - Re: AMBER: probable bug in antechamber David Mobley (Tue Apr 18 2006 - 06:52:13 PDT)
AMBER: ibelly & fix atom rdauria.uci.edu (Mon Apr 17 2006 - 20:41:28 PDT)
- Re: AMBER: ibelly & fix atom rdauria.uci.edu (Mon Apr 17 2006 - 20:59:56 PDT)
- RE: AMBER: ibelly & fix atom Ross Walker (Mon Apr 17 2006 - 21:08:42 PDT)
  - RE: AMBER: ibelly & fix atom rdauria.uci.edu (Mon Apr 17 2006 - 21:22:16 PDT)
AMBER: Error in the MD run Ananda Rama Krishnan Selvaraj (Mon Apr 17 2006 - 23:13:04 PDT)
- RE: AMBER: Error in the MD run Ross Walker (Tue Apr 18 2006 - 08:35:41 PDT)
AMBER: RE: about the fix_numbering_pdb.csh in Amber Tutorial_eight Ross Walker (Tue Apr 18 2006 - 08:42:41 PDT)
- Re: AMBER: RE: about the fix_numbering_pdb.csh in Amber Tutorial_eight Shulin Zhuang (Tue Apr 18 2006 - 22:58:06 PDT)
  - RE: AMBER: RE: about the fix_numbering_pdb.csh in Amber Tutorial_eight Ross Walker (Wed Apr 19 2006 - 08:16:51 PDT)
AMBER: RE: Respgen segemtation fault Simon Whitehead (Wed Apr 19 2006 - 10:10:11 PDT)
- AMBER: Installing Delphi to perform mm_pbsa analysis? Alfredo Quevedo (Wed Apr 19 2006 - 10:39:13 PDT)
  - Re: AMBER: Installing Delphi to perform mm_pbsa analysis? David A. Case (Wed Apr 19 2006 - 12:43:46 PDT)
- Re: AMBER: RE: Respgen segemtation fault David A. Case (Thu Apr 20 2006 - 04:49:34 PDT)
- Re: AMBER: RE: Respgen segemtation fault Simon Whitehead (Thu Apr 20 2006 - 05:30:48 PDT)
- AMBER: Antechamber & atom types FyD (Thu Apr 20 2006 - 10:04:17 PDT)
  - Re: AMBER: Antechamber & atom types David A. Case (Fri Apr 21 2006 - 08:22:45 PDT)
AMBER: timing estimates Ed Pate (Wed Apr 19 2006 - 16:10:30 PDT)
- Re: AMBER: timing estimates Robert Duke (Wed Apr 19 2006 - 17:06:59 PDT)
RE: AMBER: RE: Respgen segemtation fault - debug attempt Simon Whitehead (Thu Apr 20 2006 - 05:48:07 PDT)
- Re: AMBER: RE: Respgen segemtation fault - debug attempt Mark Williamson (Thu Apr 20 2006 - 06:23:55 PDT)
- RE: AMBER: RE: Respgen segemtation fault - debug attempt Simon Whitehead (Thu Apr 20 2006 - 09:30:51 PDT)
  - Re: AMBER: RE: Respgen segemtation fault - debug attempt Mark Williamson (Thu Apr 20 2006 - 09:56:55 PDT)
AMBER: about the decomposition energies using mm/pbsa litong (Thu Apr 20 2006 - 06:34:11 PDT)
- Re: AMBER: about the decomposition energies using mm/pbsa Holger Gohlke (Fri Apr 21 2006 - 00:25:44 PDT)
AMBER: Non-periodic simulations: How is the system kept together? pascal.baillod.epfl.ch (Thu Apr 20 2006 - 09:13:04 PDT)
- RE: AMBER: Non-periodic simulations: How is the system kept together? Ross Walker (Thu Apr 20 2006 - 09:35:26 PDT)
AMBER: a question about "solvateoct" in AMBER 8 Chengwen Chen (Thu Apr 20 2006 - 23:48:14 PDT)
AMBER: Error when compiling amber9 ptraj Thomas Steinbrecher (Fri Apr 21 2006 - 01:19:54 PDT)
- Re: AMBER: Error when compiling amber9 ptraj David A. Case (Fri Apr 21 2006 - 05:08:15 PDT)
AMBER: a question german (Fri Apr 21 2006 - 04:04:54 PDT)
- RE: AMBER: a question Ross Walker (Fri Apr 21 2006 - 13:35:51 PDT)
  - Re: AMBER: a question Robert Duke (Mon Apr 24 2006 - 11:21:34 PDT)
AMBER: problems with saveamberprep command JAVIER PEREZ (Fri Apr 21 2006 - 04:33:48 PDT)
AMBER: mm_pbsa: "Missing values for MM ..." Sam (Fri Apr 21 2006 - 06:39:19 PDT)
AMBER: Problems compiling amber9 Thomas Steinbrecher (Fri Apr 21 2006 - 07:27:51 PDT)
- Re: AMBER: Problems compiling amber9 David A. Case (Fri Apr 21 2006 - 08:03:37 PDT)
- Re: AMBER: Problems compiling amber9 Don Harden (Mon May 22 2006 - 10:10:15 PDT)
  - Re: AMBER: Problems compiling amber9 David A. Case (Mon May 22 2006 - 11:46:09 PDT)
    - Re: AMBER: Problems compiling amber9 Don Harden (Tue May 23 2006 - 12:45:02 PDT)
  - Re: AMBER: Problems compiling amber9 Andreas Svrcek-Seiler (Mon May 22 2006 - 12:01:09 PDT)
AMBER: Fujitsu frt compiler Evan Kelly (Fri Apr 21 2006 - 07:53:40 PDT)
Re: AMBER: a question about "solvateoct" in AMBER 8 Bill Ross (Fri Apr 21 2006 - 11:48:01 PDT)
- Re: AMBER: a question about "solvateoct" in AMBER 8 Michael Crowley (Fri Apr 21 2006 - 12:50:52 PDT)
  - Re: AMBER: a question about "solvateoct" in AMBER 8 Chengwen Chen (Sun Apr 23 2006 - 21:13:30 PDT)
AMBER: amber9 compilation error on SGI altix Lihua Wang (Sat Apr 22 2006 - 10:58:26 PDT)
- RE: AMBER: amber9 compilation error on SGI altix Ross Walker (Sat Apr 22 2006 - 12:21:24 PDT)
  - RE: AMBER: amber9 compilation error on SGI altix Lihua Wang (Sat Apr 22 2006 - 15:48:40 PDT)
AMBER: increase in computational time with LES Kenley Barrett (Sun Apr 23 2006 - 14:53:29 PDT)
- Re: AMBER: increase in computational time with LES Adrian Roitberg (Sun Apr 23 2006 - 15:26:20 PDT)
  - Re: AMBER: increase in computational time with LES Kenley Barrett (Sun Apr 23 2006 - 15:46:56 PDT)
    - Re: AMBER: increase in computational time with LES Carlos Simmerling (Sun Apr 23 2006 - 16:00:20 PDT)
AMBER: LES copies Claudia Steinert (Mon Apr 24 2006 - 01:28:06 PDT)
- Re: AMBER: LES copies Carlos Simmerling (Mon Apr 24 2006 - 04:14:20 PDT)
AMBER: a quetion german (Mon Apr 24 2006 - 04:17:34 PDT)
- Re: AMBER: a quetion Mingfeng Yang (Mon Apr 24 2006 - 06:07:30 PDT)
- RE: AMBER: a quetion Ross Walker (Mon Apr 24 2006 - 07:52:59 PDT)
- Re: AMBER: a quetion darden (Mon Apr 24 2006 - 07:57:59 PDT)
AMBER: modeling zinc binding site Jan Kosinski (Mon Apr 24 2006 - 05:28:55 PDT)
AMBER: MM_PBSA: “Found unknown atflag DELPHI” haixiao jin (Mon Apr 24 2006 - 08:23:23 PDT)
- Re: AMBER: MM_PBSA: “Found unknown atflag DELPHI” Ray Luo (Mon Apr 24 2006 - 11:40:28 PDT)
- Re: AMBER: MM_PBSA: “Found unknown atflag DELPHI” Scott Pendley (Wed Apr 26 2006 - 15:54:53 PDT)
AMBER: rmsd value for organic molecule Varsha Goyal (Mon Apr 24 2006 - 12:00:20 PDT)
- RE: AMBER: rmsd value for organic molecule Ross Walker (Mon Apr 24 2006 - 12:25:23 PDT)
  - RE: AMBER: rmsd value for organic molecule Varsha Goyal (Mon Apr 24 2006 - 13:48:59 PDT)
AMBER: compiling errors Alex Tzanov (Mon Apr 24 2006 - 17:17:50 PDT)
- RE: AMBER: compiling errors Ross Walker (Mon Apr 24 2006 - 17:58:52 PDT)
  - Re: AMBER: compiling errors Alex Tzanov (Mon Apr 24 2006 - 19:04:10 PDT)
  - Re: AMBER: compiling errors Atro Tossavainen (Wed Apr 26 2006 - 00:49:23 PDT)
AMBER: Born igb =2 harianto (Mon Apr 24 2006 - 18:27:24 PDT)
- Re: AMBER: Born igb =2 John Mongan (Tue Apr 25 2006 - 10:30:22 PDT)
AMBER: Test Failure during amber9 serial compilation Thomas Steinbrecher (Tue Apr 25 2006 - 07:17:29 PDT)
- Re: AMBER: Test Failure during amber9 serial compilation Ray Luo (Tue Apr 25 2006 - 11:01:49 PDT)
- RE: AMBER: Test Failure during amber9 serial compilation Ross Walker (Tue Apr 25 2006 - 12:30:19 PDT)
  - RE: AMBER: Test Failure during amber9 serial compilation Thomas Steinbrecher (Wed Apr 26 2006 - 02:23:24 PDT)
    - Re: AMBER: Test Failure during amber9 serial compilation Ray Luo (Wed Apr 26 2006 - 11:29:11 PDT)
    - RE: AMBER: Test Failure during amber9 serial compilation Ross Walker (Wed Apr 26 2006 - 11:49:06 PDT)
AMBER: DNA structure Ioana Cozmuta (Tue Apr 25 2006 - 13:17:12 PDT)
- Re: AMBER: DNA structure Ioana Cozmuta (Wed Apr 26 2006 - 12:06:22 PDT)
AMBER: error propagation in MM-PBSA binding free energy calculation lhsong (Tue Apr 25 2006 - 20:22:41 PDT)
- Re: AMBER: error propagation in MM-PBSA binding free energy calculation Jianyin Shao (Wed Apr 26 2006 - 17:13:48 PDT)
- Re: AMBER: error propagation in MM-PBSA binding free energy calculation lhsong (Fri Apr 28 2006 - 15:37:42 PDT)
  - Re: AMBER: error propagation in MM-PBSA binding free energy calculation Jianyin Shao (Mon May 01 2006 - 10:17:04 PDT)
AMBER: two references Ioana Cozmuta (Wed Apr 26 2006 - 13:18:28 PDT)
AMBER: two references- I got them, thank you! Ioana Cozmuta (Wed Apr 26 2006 - 14:15:11 PDT)
AMBER: internal coordinates Ioana Cozmuta (Wed Apr 26 2006 - 14:56:20 PDT)
- Re: AMBER: internal coordinates David A. Case (Sun Apr 30 2006 - 09:09:52 PDT)
- Re: AMBER: internal coordinates David A. Case (Mon May 01 2006 - 13:50:10 PDT)
  - Re: AMBER: internal coordinates Ioana Cozmuta (Tue May 02 2006 - 11:01:45 PDT)
AMBER: questions about mm_pbsa Weihua Li (Wed Apr 26 2006 - 20:09:45 PDT)
- Re: AMBER: questions about mm_pbsa Ray Luo (Wed Apr 26 2006 - 18:03:13 PDT)
AMBER: Force Field Question Ilyas Yildirim (Thu Apr 27 2006 - 14:57:58 PDT)
AMBER: distance restraints for umbrella sampling mkseo (Thu Apr 27 2006 - 15:21:16 PDT)
AMBER: heating process r. a. (Thu Apr 27 2006 - 22:56:06 PDT)
- Re: AMBER: heating process Carlos Simmerling (Fri Apr 28 2006 - 04:06:03 PDT)
  - AMBER: Langevin mode error?? Cenk Andac (Fri Apr 28 2006 - 04:52:02 PDT)
    - Re: AMBER: Langevin mode error?? David A. Case (Fri Apr 28 2006 - 13:13:31 PDT)
AMBER: how to perform parallel MD on a linux cluster with Platform LSF product Yu Zh.H. (Fri Apr 28 2006 - 03:31:08 PDT)
- Re: AMBER: how to perform parallel MD on a linux cluster with Platform LSF product Hector A. Baldoni (Sat Apr 29 2006 - 17:08:30 PDT)
AMBER: 7-Methylguanine force field parameters Supat Jiranusornkul (Fri Apr 28 2006 - 07:03:22 PDT)
AMBER: 7-Methylguanine force field parameters Supat Jiranusornkul (Fri Apr 28 2006 - 07:13:55 PDT)
AMBER: Performing Simulated Annealing? alfredoq.fcq.unc.edu.ar (Fri Apr 28 2006 - 09:58:31 PDT)
- RE: AMBER: Performing Simulated Annealing? Ross Walker (Fri Apr 28 2006 - 10:13:56 PDT)
- Re: AMBER: Performing Simulated Annealing? Carlos Simmerling (Fri Apr 28 2006 - 10:16:43 PDT)
AMBER: How to build 1,4-dimethyl benzene with amber9 martin peters (Fri Apr 28 2006 - 14:27:09 PDT)
- RE: AMBER: How to build 1,4-dimethyl benzene with amber9 Ross Walker (Fri Apr 28 2006 - 15:10:56 PDT)
  - Re: AMBER: How to build 1,4-dimethyl benzene with amber9 martin peters (Fri Apr 28 2006 - 16:00:29 PDT)
    - RE: AMBER: How to build 1,4-dimethyl benzene with amber9 Ross Walker (Fri Apr 28 2006 - 16:46:23 PDT)
AMBER: Setting box dimensions in leap Jennie Thomas (Fri Apr 28 2006 - 15:42:38 PDT)
- Re: AMBER: Setting box dimensions in leap David A. Case (Sat Apr 29 2006 - 22:42:48 PDT)
AMBER: about the execuation of REMD with sander of amber9 pang zhao (Fri Apr 28 2006 - 20:08:41 PDT)
- Re: AMBER: about the execuation of REMD with sander of amber9 pang zhao (Fri Apr 28 2006 - 22:12:22 PDT)
  - Re: AMBER: about the execuation of REMD with sander of amber9 Carlos Simmerling (Sat Apr 29 2006 - 06:45:24 PDT)
    - Re: AMBER: about the execuation of REMD with sander of amber9 pang zhao (Sun Apr 30 2006 - 01:58:06 PDT)
- Re: AMBER: about the execuation of REMD with sander of amber9 Carlos Simmerling (Sat Apr 29 2006 - 06:43:46 PDT)
AMBER: about the shake with self-guide LD pang zhao (Sat Apr 29 2006 - 03:44:39 PDT)
AMBER: AMBER9: MacG5 parallel sander.MPI In Hee Park (Sat Apr 29 2006 - 13:59:28 PDT)
- Re: AMBER: AMBER9: MacG5 parallel sander.MPI Gert Kiss (Sat Apr 29 2006 - 15:29:51 PDT)
- Re: AMBER: AMBER9: MacG5 parallel sander.MPI Mengjuei Hsieh (Wed May 03 2006 - 17:32:14 PDT)
- Re: AMBER: AMBER9: MacG5 parallel sander.MPI Mengjuei Hsieh (Sun May 07 2006 - 07:33:01 PDT)
AMBER: Did these differences come from so-called "different machines" ? Zhihong Yu (Sun Apr 30 2006 - 01:47:28 PDT)
- Re: AMBER: Did these differences come from so-called "different machines" ? David A. Case (Sun Apr 30 2006 - 21:09:35 PDT)
AMBER: Amber 9, sander imin = 5, -y flag z3020110.student.unsw.edu.au (Sun Apr 30 2006 - 18:08:44 PDT)
- Re: AMBER: Amber 9, sander imin = 5, -y flag David A. Case (Sun Apr 30 2006 - 21:08:24 PDT)
- Re: AMBER: Amber 9, sander imin = 5, -y flag Carlos Simmerling (Mon May 01 2006 - 06:35:56 PDT)
  - Re: AMBER: Amber 9, sander imin = 5, -y flag S.Sundar Raman (Wed Mar 07 2007 - 10:05:19 PST)
    - Re: AMBER: Amber 9, sander imin = 5, -y flag Carlos Simmerling (Wed Mar 07 2007 - 11:15:22 PST)
    - AMBER: netcdf support needed (Amber 9, sander imin = 5, -y flag) Chris Moth (Fri Apr 06 2007 - 11:50:29 PDT)
    - Re: AMBER: netcdf support needed (Amber 9, sander imin = 5, -y flag) Geoff Wood (Mon Jul 23 2007 - 10:23:46 PDT)
AMBER: sequential execution of number of parallel jobs In Hee Park (Mon May 01 2006 - 13:13:23 PDT)
- Re: AMBER: sequential execution of number of parallel jobs Petr Kulhanek (Tue May 02 2006 - 01:20:51 PDT)
AMBER: distance restraints mkseo (Mon May 01 2006 - 14:49:21 PDT)
AMBER: some new tutorials David A. Case (Mon May 01 2006 - 16:55:19 PDT)
AMBER: How does amber calculate HB? Li Su (Mon May 01 2006 - 18:01:05 PDT)
- Re: AMBER: How does amber calculate HB? David A. Case (Mon May 01 2006 - 23:20:31 PDT)
AMBER: AMBER Workshops, London UK 26th - 30th June 2006 Ross Walker (Tue May 02 2006 - 08:45:33 PDT)
AMBER: Simulation of crystal - problem with excluded atom list Jennie Thomas (Tue May 02 2006 - 10:07:20 PDT)
AMBER: MPI parallel problem in AMBER 8.0 mkseo (Tue May 02 2006 - 14:21:50 PDT)
- RE: AMBER: MPI parallel problem in AMBER 8.0 Ross Walker (Tue May 02 2006 - 14:42:33 PDT)
  - Re: AMBER: MPI parallel problem in AMBER 8.0 mkseo (Tue May 02 2006 - 15:14:16 PDT)
    - RE: AMBER: MPI parallel problem in AMBER 8.0 Ross Walker (Tue May 02 2006 - 15:40:37 PDT)
AMBER: Shared libraries error Andrew Box (Tue May 02 2006 - 20:14:38 PDT)
- RE: AMBER: Shared libraries error Ross Walker (Wed May 03 2006 - 08:13:32 PDT)
- Re: AMBER: Shared libraries error Viktor Hornak (Thu May 04 2006 - 11:54:26 PDT)
AMBER: proper restart procedure? John J. Love (Tue May 02 2006 - 20:33:57 PDT)
- Re: AMBER: proper restart procedure? Carlos Simmerling (Wed May 03 2006 - 04:48:25 PDT)
  - Re: AMBER: proper restart procedure? David A. Case (Wed May 03 2006 - 08:18:43 PDT)
AMBER: Question bonds and angles in frcmod and lib files Jennie Thomas (Wed May 03 2006 - 01:02:55 PDT)
- Re: AMBER: Question bonds and angles in frcmod and lib files David A. Case (Wed May 03 2006 - 08:23:12 PDT)
  - Re: AMBER: Question bonds and angles in frcmod and lib files Jennie Thomas (Wed May 03 2006 - 08:54:43 PDT)
- Re: AMBER: Question bonds and angles in frcmod and lib files Bill Ross (Wed May 03 2006 - 09:28:08 PDT)
  - Re: AMBER: Question bonds and angles in frcmod and lib files Jennie Thomas (Wed May 03 2006 - 10:26:55 PDT)
AMBER: Error while running test.serial in Amber9 Priti Hansia (Wed May 03 2006 - 04:03:27 PDT)
- Re: AMBER: Error while running test.serial in Amber9 Carlos Simmerling (Wed May 03 2006 - 04:50:37 PDT)
  - Re: AMBER: Error while running test.serial in Amber9 Priti Hansia (Wed May 03 2006 - 05:02:04 PDT)
    - RE: AMBER: Error while running test.serial in Amber9 Ross Walker (Wed May 03 2006 - 08:21:42 PDT)
    - RE: AMBER: Error while running test.serial in Amber9 Priti Hansia (Wed May 03 2006 - 22:08:02 PDT)
    - Re: AMBER: Error while running test.serial in Amber9 David A. Case (Wed May 03 2006 - 23:13:06 PDT)
    - Re: AMBER: Error while running test.serial in Amber9 Priti Hansia (Thu May 04 2006 - 08:48:36 PDT)
AMBER: cluster architecture for the best amber performance Kateryna Miroshnychenko (Wed May 03 2006 - 05:54:58 PDT)
- RE: AMBER: cluster architecture for the best amber performance Ross Walker (Wed May 03 2006 - 08:42:19 PDT)
  - Re: AMBER: cluster architecture for the best amber performance Robert Duke (Wed May 03 2006 - 10:05:57 PDT)
AMBER: concatenating .mdcrd files Kenley Barrett (Wed May 03 2006 - 09:31:59 PDT)
- RE: AMBER: concatenating .mdcrd files Ross Walker (Wed May 03 2006 - 09:39:11 PDT)
AMBER: question about group format Holly Freedman (Wed May 03 2006 - 12:18:36 PDT)
- Re: AMBER: question about group format Viktor Hornak (Thu May 04 2006 - 11:49:20 PDT)
  - Re: AMBER: question about group format Holly Freedman (Thu May 04 2006 - 16:16:22 PDT)
[Fwd: Re: AMBER: Question bonds and angles in frcmod and lib files] Jennie Thomas (Wed May 03 2006 - 14:49:19 PDT)
Re: [Fwd: Re: AMBER: Question bonds and angles in frcmod and lib files] Bill Ross (Wed May 03 2006 - 15:00:58 PDT)
- Re: [Fwd: Re: AMBER: Question bonds and angles in frcmod and lib files] Jennie Thomas (Thu May 04 2006 - 15:45:21 PDT)
AMBER: Amber install on RedHat Linux a a (Wed May 03 2006 - 19:17:14 PDT)
- RE: AMBER: Amber install on RedHat Linux Ross Walker (Wed May 03 2006 - 19:36:45 PDT)
  - RE: AMBER: Amber install on RedHat Linux a a (Thu May 04 2006 - 00:37:34 PDT)
    - Re: AMBER: Amber install on RedHat Linux David A. Case (Thu May 04 2006 - 08:17:08 PDT)
    - RE: AMBER: Amber install on RedHat Linux Ross Walker (Thu May 04 2006 - 08:31:56 PDT)
    - AMBER: Tutorial one : libsvml.so error a a (Tue May 16 2006 - 23:01:26 PDT)
    - Re: AMBER: Tutorial one : libsvml.so error Mark Williamson (Wed May 17 2006 - 00:27:05 PDT)
    - AMBER: Tutorial one : xaLeap command not found. a a (Wed May 17 2006 - 03:12:53 PDT)
    - RE: AMBER: Tutorial one : xaLeap command not found. Ross Walker (Wed May 17 2006 - 08:40:12 PDT)
    - AMBER: process_mdout.perl error a a (Fri May 19 2006 - 02:35:20 PDT)
    - RE: AMBER: process_mdout.perl error Ross Walker (Fri May 19 2006 - 07:43:25 PDT)
    - AMBER: trajin and rms a a (Sun May 21 2006 - 21:18:37 PDT)
    - RE: AMBER: trajin and rms Ross Walker (Sun May 21 2006 - 21:43:09 PDT)
    - RE: AMBER: trajin and rms a a (Mon May 22 2006 - 01:55:03 PDT)
    - Re: AMBER: trajin and rms Carlos Simmerling (Mon May 22 2006 - 04:58:04 PDT)
    - RE: AMBER: trajin and rms a a (Wed May 24 2006 - 03:49:05 PDT)
    - AMBER: xmgr error a a (Fri May 19 2006 - 02:50:25 PDT)
    - Re: AMBER: xmgr error mathew k varghese (Fri May 19 2006 - 03:54:00 PDT)
    - RE: AMBER: xmgr error Douali, Latifa (Fri May 19 2006 - 10:07:01 PDT)
AMBER: carnal prob bala (Thu May 04 2006 - 00:44:53 PDT)
- Re: AMBER: carnal prob Stefano Federico Massimiliano Pieraccini (Stefano.Pieraccini) (Thu May 04 2006 - 00:58:18 PDT)
AMBER: conflicting types for XawScrolledTableSetLocation K. Yarem (Thu May 04 2006 - 08:43:57 PDT)
- Re: AMBER: conflicting types for XawScrolledTableSetLocation Wei Zhang (Thu May 04 2006 - 10:17:40 PDT)
AMBER: molsurf.c error Miguel Ferreira (Thu May 04 2006 - 09:00:31 PDT)
- RE: AMBER: molsurf.c error Ross Walker (Thu May 04 2006 - 09:28:49 PDT)
  - RE: AMBER: molsurf.c error Miguel Ferreira (Thu May 04 2006 - 12:43:41 PDT)
    - Re: AMBER: molsurf.c error David A. Case (Thu May 04 2006 - 13:21:28 PDT)
- Re: AMBER: molsurf.c error Miguel Ferreira (Fri May 05 2006 - 04:46:24 PDT)
  - Re: AMBER: molsurf.c error David A. Case (Fri May 05 2006 - 10:34:32 PDT)
AMBER: amber9 serial compilation error Arvind Marathe (Thu May 04 2006 - 09:55:39 PDT)
- AMBER: Trouble with ptraj closestwater in Amber8 Kerry P Donny-Clark (Thu May 04 2006 - 10:29:23 PDT)
- Re: AMBER: amber9 serial compilation error David A. Case (Thu May 04 2006 - 10:36:53 PDT)
Re: AMBER: carnal prob Bill Ross (Thu May 04 2006 - 10:31:22 PDT)
AMBER: lipid bi-layer system Lwin, ThuZar (Thu May 04 2006 - 10:41:11 PDT)
AMBER: restraintmask Joseph Fernandez (Thu May 04 2006 - 11:22:21 PDT)
- Re: AMBER: restraintmask Viktor Hornak (Thu May 04 2006 - 11:41:37 PDT)
AMBER: Problem with shared libraries: libimf.so Priti Hansia (Fri May 05 2006 - 10:55:39 PDT)
- RE: AMBER: Problem with shared libraries: libimf.so Ross Walker (Fri May 05 2006 - 11:04:10 PDT)
  - RE: AMBER: Problem with shared libraries: libimf.so Priti Hansia (Fri May 05 2006 - 11:39:50 PDT)
    - RE: AMBER: Problem with shared libraries: libimf.so Ross Walker (Fri May 05 2006 - 14:08:31 PDT)
    - RE: AMBER: Problem with shared libraries: libimf.so Priti Hansia (Sat May 06 2006 - 00:01:51 PDT)
    - Re: AMBER: Problem with shared libraries: libimf.so David A. Case (Sat May 06 2006 - 14:17:51 PDT)
    - Re: AMBER: Problem with shared libraries: libimf.so Priti Hansia (Sat May 06 2006 - 22:40:49 PDT)
    - RE: AMBER: Problem with shared libraries: libimf.so Ross Walker (Sun May 07 2006 - 09:10:54 PDT)
AMBER: experiences with compiling amber9 for FreeBSD M. L. Dodson (Fri May 05 2006 - 11:37:19 PDT)
- Re: AMBER: experiences with compiling amber9 for FreeBSD David A. Case (Fri May 05 2006 - 11:46:29 PDT)
  - Re: AMBER: experiences with compiling amber9 for FreeBSD M. L. Dodson (Fri May 05 2006 - 11:59:48 PDT)
    - Re: AMBER: experiences with compiling amber9 for FreeBSD David A. Case (Fri May 05 2006 - 12:19:31 PDT)
- RE: AMBER: experiences with compiling amber9 for FreeBSD Ross Walker (Fri May 05 2006 - 14:10:51 PDT)
  - Re: AMBER: experiences with compiling amber9 for FreeBSD M. L. Dodson (Fri May 05 2006 - 15:00:10 PDT)
    - Re: AMBER: experiences with compiling amber9 for FreeBSD Mengjuei Hsieh (Fri May 05 2006 - 17:30:16 PDT)
    - Re: AMBER: experiences with compiling amber9 for FreeBSD David A. Case (Fri May 05 2006 - 18:31:13 PDT)
    - Re: AMBER: experiences with compiling amber9 for FreeBSD Mengjuei Hsieh (Fri May 05 2006 - 19:05:41 PDT)
    - Re: AMBER: experiences with compiling amber9 for FreeBSD M. L. Dodson (Fri May 05 2006 - 19:34:07 PDT)
- Re: AMBER: experiences with compiling amber9 for FreeBSD Mengjuei Hsieh (Fri May 05 2006 - 17:24:30 PDT)
- Re: AMBER: experiences with compiling amber9 for FreeBSD Xuebin Qiao (Fri May 05 2006 - 23:31:06 PDT)
AMBER: xleap on iMac G5 Evan Kelly (Fri May 05 2006 - 21:01:53 PDT)
- Re: AMBER: xleap on iMac G5 Mengjuei Hsieh (Fri May 05 2006 - 22:44:00 PDT)
AMBER: AMBER9 INSTALLATION problem on O2 sgi system S.Sundar Raman (Sun May 07 2006 - 00:10:15 PDT)
- Re: AMBER: AMBER9 INSTALLATION problem on O2 sgi system David A. Case (Sun May 07 2006 - 07:27:56 PDT)
  - Re: AMBER: AMBER9 INSTALLATION problem on O2 sgi system S.Sundar Raman (Mon May 08 2006 - 04:33:58 PDT)
    - Re: AMBER: AMBER9 INSTALLATION problem on O2 sgi system Atro Tossavainen (Mon May 08 2006 - 04:48:29 PDT)
    - RE: AMBER: AMBER9 INSTALLATION problem on O2 sgi system Ross Walker (Mon May 08 2006 - 08:17:55 PDT)
AMBER: xleap not recognizing residue Kenley Barrett (Sun May 07 2006 - 17:13:13 PDT)
- Re: AMBER: xleap not recognizing residue David A. Case (Sun May 07 2006 - 18:50:06 PDT)
  - Re: AMBER: xleap not recognizing residue Kenley Barrett (Mon May 08 2006 - 10:04:37 PDT)
    - Re: AMBER: xleap not recognizing residue David A. Case (Tue May 09 2006 - 15:42:14 PDT)
AMBER: question on distance calculation bala (Mon May 08 2006 - 03:09:23 PDT)
AMBER: Amber9 test error on SGI Altix amit.mbu.iisc.ernet.in (Mon May 08 2006 - 10:14:19 PDT)
- Re: AMBER: Amber9 test error on SGI Altix David A. Case (Mon May 08 2006 - 11:07:17 PDT)
  - Re: AMBER: Amber9 test error on SGI Altix David A. Case (Mon May 08 2006 - 11:45:30 PDT)
- Re: AMBER: Amber9 test error on SGI Altix Ray Luo (Tue May 09 2006 - 05:57:57 PDT)
AMBER: Problem with impose in lep Osmar Norberto de Souza (Mon May 08 2006 - 10:31:16 PDT)
AMBER: IA64 / Altix Amber 9 Intel Compiler Problems. l_fc_c_9.0.031 Ross Walker (Mon May 08 2006 - 11:13:11 PDT)
- AMBER: Re: IA64 / Altix Amber 9 Intel Compiler Problems. l_fc_c_9.0.031 amit.mbu.iisc.ernet.in (Tue May 09 2006 - 11:32:52 PDT)
  - RE: AMBER: Re: IA64 / Altix Amber 9 Intel Compiler Problems. l_fc_c_9.0.031 Ross Walker (Tue May 09 2006 - 12:12:09 PDT)
    - RE: AMBER: Re: IA64 / Altix Amber 9 Intel Compiler Problems. l_fc_c_9.0.031 amit.mbu.iisc.ernet.in (Wed May 10 2006 - 00:06:46 PDT)
    - RE: AMBER: Re: IA64 / Altix Amber 9 Intel Compiler Problems. l_fc_c_9.0.031 Ross Walker (Tue Oct 02 2007 - 19:00:07 PDT)
  - Re: AMBER: Re: IA64 / Altix Amber 9 Intel Compiler Problems. l_fc_c_9.0.031 David A. Case (Tue May 09 2006 - 13:16:30 PDT)
AMBER: Intel compiler version 9.0.033 Ross Walker (Mon May 08 2006 - 12:40:23 PDT)
- Re: AMBER: Intel compiler version 9.0.033 Priti Hansia (Mon May 08 2006 - 12:55:37 PDT)
AMBER: PMEMD compilation error Joseph Fernandez (Mon May 08 2006 - 12:37:03 PDT)
- Re: AMBER: PMEMD compilation error Robert Duke (Mon May 08 2006 - 13:18:05 PDT)
AMBER: About the Amber trajectories converted to XPLOR ( = DCD) format wang (Mon May 08 2006 - 23:25:47 PDT)
AMBER: San Fransisco Amber users homeira amirkhani (Tue May 09 2006 - 04:38:06 PDT)
AMBER: Amber9 test error on SGI Altix Priti Hansia (Tue May 09 2006 - 08:18:02 PDT)
- Re: AMBER: Amber9 test error on SGI Altix Robert Duke (Tue May 09 2006 - 09:06:19 PDT)
AMBER: RE: Intel Compiler. Ross Walker (Tue May 09 2006 - 09:05:28 PDT)
- AMBER: Compiler with AMD 64 bit support alfredoq.fcq.unc.edu.ar (Tue May 09 2006 - 10:10:30 PDT)
  - RE: AMBER: Compiler with AMD 64 bit support Ross Walker (Tue May 09 2006 - 10:19:18 PDT)
- AMBER: RE: Intel Compiler. Priti Hansia (Tue May 09 2006 - 10:12:18 PDT)
  - RE: AMBER: RE: Intel Compiler. Ross Walker (Tue May 09 2006 - 10:21:43 PDT)
    - RE: AMBER: RE: Intel Compiler. Priti Hansia (Wed May 10 2006 - 08:39:04 PDT)
AMBER: problem with prep file Simon Whitehead (Wed May 10 2006 - 03:52:32 PDT)
- Re: AMBER: problem with prep file David A. Case (Wed May 10 2006 - 09:12:59 PDT)
- RE: AMBER: problem with prep file Junmei Wang (Mon May 15 2006 - 14:10:53 PDT)
AMBER: bug in ambpdb (AMBER8) Petr Kulhanek (Wed May 10 2006 - 03:54:55 PDT)
- Re: AMBER: bug in ambpdb (AMBER8) David A. Case (Wed May 10 2006 - 08:10:08 PDT)
AMBER: Hexahydrated Counterions Mahalakshmi Sahasranaman (Wed May 10 2006 - 06:22:02 PDT)
- Re: AMBER: Hexahydrated Counterions David A. Case (Wed May 10 2006 - 08:32:31 PDT)
[Fwd: AMBER: Problem with impose in lep] Osmar Norberto de Souza (Wed May 10 2006 - 10:09:48 PDT)
Re: AMBER: xleap not recognizing residue--I fixed it, but I'm not sure why Kenley Barrett (Wed May 10 2006 - 12:54:46 PDT)
- Re: AMBER: xleap not recognizing residue--I fixed it, but I'm not sure why David A. Case (Wed May 10 2006 - 13:12:52 PDT)
AMBER: I'm very sorry, please disregard previous e-mail--problem seems to be fixed Kenley Barrett (Wed May 10 2006 - 13:04:16 PDT)
AMBER: which patch for ioutfm = 1 in Amber8? Hannes Loeffler (Wed May 10 2006 - 22:21:25 PDT)
AMBER: why the drms from sander minimization is not consistent with that from nmode ntrun=1? Pan, Yongmei (Thu May 11 2006 - 07:13:02 PDT)
- Re: AMBER: why the drms from sander minimization is not consistent with that from nmode ntrun=1? David A. Case (Thu May 11 2006 - 07:43:28 PDT)
AMBER: bond information in amber snoze pa (Thu May 11 2006 - 09:48:58 PDT)
- Re: AMBER: bond information in amber Navnit Kumar Mishra (Thu May 11 2006 - 10:25:10 PDT)
  - Re: AMBER: bond information in amber snoze pa (Thu May 11 2006 - 11:36:18 PDT)
    - Re: AMBER: bond information in amber snoze pa (Thu May 11 2006 - 11:41:00 PDT)
    - AMBER: About mm_pbsa calculation setting up alfredoq.fcq.unc.edu.ar (Thu May 11 2006 - 19:19:03 PDT)
    - Re: AMBER: bond information in amber Navnit Kumar Mishra (Thu May 11 2006 - 23:28:00 PDT)
  - AMBER: Opteron vs. Xeon performance Jim Paugh (Thu May 11 2006 - 11:47:42 PDT)
    - RE: AMBER: Opteron vs. Xeon performance Ross Walker (Thu May 11 2006 - 16:17:12 PDT)
    - Re: AMBER: Opteron vs. Xeon performance Robert Duke (Thu May 11 2006 - 19:02:10 PDT)
    - Re: AMBER: Opteron vs. Xeon performance ian gould (Fri May 12 2006 - 00:35:12 PDT)
    - Re: AMBER: Opteron vs. Xeon performance Robert Duke (Fri May 12 2006 - 05:29:14 PDT)
    - RE: AMBER: Opteron vs. Xeon performance Ross Walker (Fri May 12 2006 - 08:13:48 PDT)
    - Re: AMBER: Opteron vs. Xeon performance Robert Duke (Fri May 12 2006 - 08:24:43 PDT)
    - Re: Re: AMBER: Opteron vs. Xeon performance Ye Mei (Fri May 12 2006 - 06:23:00 PDT)
    - Re: AMBER: Opteron vs. Xeon performance Ye Mei (Fri May 12 2006 - 01:04:45 PDT)
    - Re: AMBER: Opteron vs. Xeon performance Robert Duke (Fri May 12 2006 - 05:46:08 PDT)
    - RE: AMBER: Opteron vs. Xeon performance Yong Duan (Sun May 14 2006 - 17:53:55 PDT)
- Re: AMBER: bond information in amber snoze pa (Thu May 11 2006 - 12:16:56 PDT)
AMBER: why the perturbation from PHE to ALA is not stable with gibbs, amber 7 Pan, Yongmei (Thu May 11 2006 - 11:50:36 PDT)
- Re: AMBER: why the perturbation from PHE to ALA is not stable with gibbs, amber 7 David Mobley (Fri May 12 2006 - 10:22:41 PDT)
AMBER: Amber9/mpich2 performance Joseph Fernandez (Thu May 11 2006 - 15:30:03 PDT)
- RE: AMBER: Amber9/mpich2 performance Ross Walker (Thu May 11 2006 - 16:07:21 PDT)
  - RE: AMBER: Amber9/mpich2 performance Joseph Fernandez (Fri May 12 2006 - 18:09:20 PDT)
AMBER: question about REDII Raffaella D'Auria (Thu May 11 2006 - 19:04:51 PDT)
- Re: AMBER: question about REDII FyD (Thu May 11 2006 - 23:34:48 PDT)
  - Re: AMBER: question about REDII Raffaella D'Auria (Fri May 12 2006 - 12:12:41 PDT)
AMBER: AMBER 8 - dihedral angles when clambda=1 Ilyas Yildirim (Thu May 11 2006 - 21:57:37 PDT)
AMBER: Xleap compilation problem Sergio Dall'Angelo (Fri May 12 2006 - 02:49:16 PDT)
- Re: AMBER: Xleap compilation problem Sergio Dall'Angelo (Fri May 12 2006 - 08:21:02 PDT)
AMBER: Xleap compilation problem Sergio Dall'Angelo (Fri May 12 2006 - 03:19:48 PDT)
AMBER: RMSD calculation between ligands Stefan Henrich (Fri May 12 2006 - 05:09:15 PDT)
AMBER: another question: is rms 2E-2 good for nmode ntrun=1? Pan, Yongmei (Fri May 12 2006 - 08:22:00 PDT)
- Re: AMBER: another question: is rms 2E-2 good for nmode ntrun=1? David A. Case (Fri May 12 2006 - 08:39:37 PDT)
  - Re: AMBER: another question: is rms 2E-2 good for nmode ntrun=1? nadiav.soton.ac.uk (Fri May 12 2006 - 09:00:21 PDT)
    - Re: AMBER: another question: is rms 2E-2 good for nmode ntrun=1? David A. Case (Fri May 12 2006 - 10:01:05 PDT)
AMBER: binpos file Varsha Goyal (Fri May 12 2006 - 13:46:24 PDT)
AMBER: strange mm_pbsa output alfredoq.fcq.unc.edu.ar (Sat May 13 2006 - 08:44:58 PDT)
- Re: AMBER: strange mm_pbsa output Ray Luo (Fri May 12 2006 - 17:22:57 PDT)
  - Re: AMBER: strange mm_pbsa output alfredoq.fcq.unc.edu.ar (Sat May 13 2006 - 13:43:53 PDT)
    - Re: AMBER: strange mm_pbsa output David A. Case (Sat May 13 2006 - 15:44:14 PDT)
    - Re: AMBER: strange mm_pbsa output alfredoq.fcq.unc.edu.ar (Sun May 14 2006 - 07:22:14 PDT)
AMBER: Compilers and libraries for AMBER in HPC! Pradipta Bandyopadhyay (Sun May 14 2006 - 06:25:07 PDT)
AMBER: PBS script for lemieux Stern, Julie (Sun May 14 2006 - 16:09:30 PDT)
AMBER: the parallel efficiency of my sander and pmemd descended rapidly with increasing CPUs Zhihong Yu (Sun May 14 2006 - 20:55:51 PDT)
- RE: AMBER: the parallel efficiency of my sander and pmemd descended rapidly with increasing CPUs Ross Walker (Sun May 14 2006 - 22:13:01 PDT)
- RE: AMBER: the parallel efficiency of my sander and pmemd descended rapidly with increasing CPUs Zhihong Yu (Mon May 15 2006 - 02:00:03 PDT)
AMBER: AMBER9 compilation error on IBM Cluster amit.mbu.iisc.ernet.in (Mon May 15 2006 - 04:11:50 PDT)
- RE: AMBER: AMBER9 compilation error on IBM Cluster Ross Walker (Mon May 15 2006 - 20:28:12 PDT)
AMBER: Problem with "impose" in leap Osmar Norberto de Souza (Mon May 15 2006 - 04:27:13 PDT)
AMBER: fail to execute addles pang zhao (Mon May 15 2006 - 04:59:10 PDT)
- Re: AMBER: fail to execute addles Carlos Simmerling (Mon May 15 2006 - 05:43:31 PDT)
  - Re: AMBER: fail to execute addles pang zhao (Mon May 15 2006 - 07:31:19 PDT)
    - Re: AMBER: fail to execute addles David A. Case (Mon May 15 2006 - 09:46:28 PDT)
    - Re: AMBER: fail to execute addles Carlos Simmerling (Mon May 15 2006 - 09:59:29 PDT)
    - Re: AMBER: fail to execute addles pang zhao (Mon May 15 2006 - 23:13:21 PDT)
    - Re: AMBER: fail to execute addles pang zhao (Mon May 15 2006 - 23:17:05 PDT)
    - Re: AMBER: fail to execute addles pang zhao (Mon May 15 2006 - 23:39:28 PDT)
    - Re: AMBER: fail to execute addles Carlos Simmerling (Tue May 16 2006 - 06:47:37 PDT)
    - Re: AMBER: fail to execute addles pang zhao (Tue May 16 2006 - 07:42:36 PDT)
AMBER: ff02 + POL3 problem ! Pradipta Bandyopadhyay (Mon May 15 2006 - 06:53:20 PDT)
- RE: AMBER: ff02 + POL3 problem ! Yong Duan (Mon May 15 2006 - 09:15:02 PDT)
  - RE: AMBER: ff02 + POL3 problem ! Pradipta Bandyopadhyay (Tue May 16 2006 - 07:08:03 PDT)
    - RE: AMBER: ff02 + POL3 problem ! Yong Duan (Tue May 16 2006 - 13:06:54 PDT)
AMBER: installation problem Mahalakshmi Sahasranaman (Mon May 15 2006 - 11:12:51 PDT)
- Re: AMBER: installation problem Robert Duke (Mon May 15 2006 - 11:25:53 PDT)
AMBER: density mathew k varghese (Mon May 15 2006 - 21:02:51 PDT)
- RE: AMBER: density Yong Duan (Mon May 15 2006 - 22:37:28 PDT)
  - RE: AMBER: density mathew k varghese (Tue May 16 2006 - 21:09:17 PDT)
    - RE: AMBER: density Ross Walker (Wed May 17 2006 - 08:31:20 PDT)
    - RE: AMBER: density mathew k varghese (Wed May 17 2006 - 20:24:07 PDT)
    - RE: AMBER: density Ross Walker (Wed May 17 2006 - 21:11:11 PDT)
AMBER: amber8 compiled erro on opteron with 64 bit renyanliang (Tue May 16 2006 - 02:15:24 PDT)
- Re: AMBER: amber8 compiled erro on opteron with 64 bit Andreas Svrcek-Seiler (Tue May 16 2006 - 03:53:14 PDT)
AMBER: trouble stripping waters with ptraj Adam Pelzer (Tue May 16 2006 - 13:09:30 PDT)
- Re: AMBER: trouble stripping waters with ptraj Asim Okur (Tue May 16 2006 - 13:17:32 PDT)
AMBER: amber compilation on Red Hat 8 with MPICH kawamura_hiro.riken.jp (Tue May 16 2006 - 22:38:35 PDT)
- Re: AMBER: amber compilation on Red Hat 8 with MPICH David A. Case (Wed May 17 2006 - 04:52:55 PDT)
- RE: AMBER: amber compilation on Red Hat 8 with MPICH Ross Walker (Wed May 17 2006 - 08:35:00 PDT)
AMBER: "atom number exceeds the MAXATOM" BAUVAIS.itodys.jussieu.fr (Tue May 16 2006 - 22:54:24 PDT)
- Re: AMBER: "atom number exceeds the MAXATOM" David A. Case (Wed May 17 2006 - 04:53:58 PDT)
AMBER: distance dependent dielectric constant Mahalakshmi Sahasranaman (Wed May 17 2006 - 03:36:55 PDT)
- Re: AMBER: distance dependent dielectric constant David A. Case (Wed May 17 2006 - 04:59:41 PDT)
AMBER: "The system has extended beyond" error message Atsutoshi Okabe (Wed May 17 2006 - 22:04:31 PDT)
- Re: AMBER: "The system has extended beyond" error message german (Thu May 18 2006 - 05:27:42 PDT)
- Re: AMBER: "The system has extended beyond" error message David A. Case (Thu May 18 2006 - 05:38:58 PDT)
AMBER: Correlation matrix used in quasih (Amber 7) Craig Gough (Thu May 18 2006 - 00:06:03 PDT)
- Re: AMBER: Correlation matrix used in quasih (Amber 7) David A. Case (Thu May 18 2006 - 05:31:00 PDT)
AMBER: AMBER9 installation error on Compaq machine. Soonmin Jang (Thu May 18 2006 - 00:11:46 PDT)
- RE: AMBER: AMBER9 installation error on Compaq machine. Ross Walker (Thu May 18 2006 - 15:32:57 PDT)
AMBER: vlimit exceeded aixiaoli (Thu May 18 2006 - 01:14:29 PDT)
- Re: AMBER: vlimit exceeded David A. Case (Thu May 18 2006 - 05:24:49 PDT)
AMBER: problem with installation, or bug? Kenley Barrett (Thu May 18 2006 - 03:09:10 PDT)
AMBER: force field parameters Douali, Latifa (Thu May 18 2006 - 10:33:35 PDT)
- Re: AMBER: force field parameters Navnit Kumar Mishra (Thu May 18 2006 - 11:21:59 PDT)
- RE: AMBER: force field parameters Douali, Latifa (Thu May 18 2006 - 11:40:53 PDT)
  - Re: AMBER: force field parameters Navnit Kumar Mishra (Fri May 19 2006 - 04:01:59 PDT)
AMBER: RMSd calculations Claire Zerafa (Thu May 18 2006 - 12:25:57 PDT)
AMBER: OT: software to support AMBER? Steve Gwaltney (Thu May 18 2006 - 11:37:06 PDT)
AMBER: Compiling parallel Amber 9 on Red-Hat Enterprise 64 problem Hall, Spencer (Thu May 18 2006 - 15:44:14 PDT)
- RE: AMBER: Compiling parallel Amber 9 on Red-Hat Enterprise 64 problem Ross Walker (Thu May 18 2006 - 16:37:30 PDT)
- Re: AMBER: Compiling parallel Amber 9 on Red-Hat Enterprise 64 problem Michael Crowley (Mon May 22 2006 - 11:28:58 PDT)
- RE: AMBER: Compiling parallel Amber 9 on Red-Hat Enterprise 64 problem Hall, Spencer (Tue May 23 2006 - 14:15:08 PDT)
- RE: AMBER: Compiling parallel Amber 9 on Red-Hat Enterprise 64 problem Hall, Spencer (Tue May 23 2006 - 14:15:12 PDT)
AMBER: Intel fortran compiler 7? Simon Whitehead (Fri May 19 2006 - 02:47:55 PDT)
- Re: AMBER: Intel fortran compiler 7? Robert Duke (Fri May 19 2006 - 04:59:43 PDT)
AMBER: Fw: RMSd calculations Claire Zerafa (Fri May 19 2006 - 05:07:30 PDT)
- Re: AMBER: Fw: RMSd calculations Carlos Simmerling (Fri May 19 2006 - 06:00:50 PDT)
AMBER: problem loading forcefield leaprc.ff86 Mahalakshmi Sahasranaman (Fri May 19 2006 - 07:27:38 PDT)
- Re: AMBER: problem loading forcefield leaprc.ff86 David A. Case (Fri May 19 2006 - 08:45:33 PDT)
AMBER: RE: PMEMD compilation problems Simon Whitehead (Fri May 19 2006 - 08:37:46 PDT)
- Re: AMBER: RE: PMEMD compilation problems Robert Duke (Fri May 19 2006 - 09:20:52 PDT)
AMBER: amber .off file format question Ilyas Yildirim (Fri May 19 2006 - 19:30:55 PDT)
- Re: AMBER: amber .off file format question Ilyas Yildirim (Mon May 22 2006 - 02:16:39 PDT)
  - Re: AMBER: amber .off file format question Wei Zhang (Mon May 22 2006 - 11:13:12 PDT)
    - Re: AMBER: amber .off file format question Ilyas Yildirim (Mon May 22 2006 - 22:53:19 PDT)
    - Re: AMBER: amber .off file format question David A. Case (Mon May 22 2006 - 23:21:33 PDT)
- Re: AMBER: amber .off file format question Bill Ross (Mon May 22 2006 - 11:17:26 PDT)
AMBER: RE: trouble stripping waters with ptraj Adam Pelzer (Sat May 20 2006 - 09:00:12 PDT)
- Re: AMBER: RE: trouble stripping waters with ptraj Carlos Simmerling (Sat May 20 2006 - 10:10:24 PDT)
- Re: AMBER: RE: trouble stripping waters with ptraj Asim Okur (Mon May 22 2006 - 09:49:46 PDT)
AMBER: Problem with running xleap remotely heaton.chem.utah.edu (Sat May 20 2006 - 12:20:27 PDT)
- RE: AMBER: Problem with running xleap remotely Ross Walker (Sat May 20 2006 - 12:37:35 PDT)
  - RE: AMBER: Problem with running xleap remotely heaton.chem.utah.edu (Sat May 20 2006 - 13:43:53 PDT)
AMBER: RMSd error Claire Zerafa (Mon May 22 2006 - 01:52:34 PDT)
- Re: AMBER: RMSd error Carlos Simmerling (Mon May 22 2006 - 05:02:02 PDT)
- Re: AMBER: RMSd error Claire Zerafa (Fri May 26 2006 - 05:26:06 PDT)
  - Re: AMBER: RMSd error Carlos Simmerling (Fri May 26 2006 - 05:58:42 PDT)
- Re: AMBER: RMSd error Claire Zerafa (Fri May 26 2006 - 06:30:57 PDT)
- Re: AMBER: RMSd error Claire Zerafa (Sun May 28 2006 - 09:26:14 PDT)
AMBER: Water density output Navnit Kumar Mishra (Mon May 22 2006 - 04:02:48 PDT)
AMBER: A dummy atom on the center of solute molecule Atsutoshi Okabe (Mon May 22 2006 - 04:49:23 PDT)
- Re: AMBER: A dummy atom on the center of solute molecule Ilyas Yildirim (Mon May 22 2006 - 04:58:24 PDT)
  - RE: AMBER: A dummy atom on the center of solute molecule Atsutoshi Okabe (Tue May 23 2006 - 18:46:35 PDT)
    - RE: AMBER: A dummy atom on the center of solute molecule Ilyas Yildirim (Tue May 23 2006 - 19:49:00 PDT)
- RE: AMBER: A dummy atom on the center of solute molecule Ilyas Yildirim (Sun May 28 2006 - 21:26:33 PDT)
  - RE: AMBER: A dummy atom on the center of solute molecule Atsutoshi Okabe (Sun May 28 2006 - 22:51:49 PDT)
    - RE: AMBER: A dummy atom on the center of solute molecule Ilyas Yildirim (Tue May 30 2006 - 16:06:54 PDT)
AMBER: Macromodel Amber* vs. Amber7 opitz.che.udel.edu (Mon May 22 2006 - 05:56:54 PDT)
AMBER: More Amber 9 Benchmarks available Robert Duke (Mon May 22 2006 - 07:23:15 PDT)
AMBER: Again SASA lucas luquitas (Mon May 22 2006 - 12:51:22 PDT)
AMBER: 3Dsig: Struct Bioinfo & Comp Biophysics Meeting, 4-5 Aug. Brazil 3Dsig06 (Mon May 22 2006 - 15:03:45 PDT)
AMBER: error in AMBER 9.0 mkseo (Tue May 23 2006 - 14:43:28 PDT)
- Re: AMBER: error in AMBER 9.0 David A. Case (Tue May 23 2006 - 22:19:47 PDT)
AMBER: amber8 bugfix effects kawamura_hiro.riken.jp (Wed May 24 2006 - 01:17:32 PDT)
- Re: AMBER: amber8 bugfix effects David A. Case (Wed May 24 2006 - 07:38:39 PDT)
AMBER: simulate proteins with non-standard residues Hui Lei (Wed May 24 2006 - 10:10:08 PDT)
AMBER: freeze interval vibrations Eric Hu (Wed May 24 2006 - 10:52:47 PDT)
- Re: AMBER: freeze interval vibrations David A. Case (Wed May 24 2006 - 12:00:35 PDT)
AMBER: use_pme=0 problem luckyang.gmail.com (Wed May 24 2006 - 16:18:47 PDT)
- Re: AMBER: use_pme=0 problem David A. Case (Wed May 24 2006 - 16:50:56 PDT)
  - Re: AMBER: use_pme=0 problem luckyang.gmail.com (Wed May 24 2006 - 17:20:35 PDT)
    - Re: AMBER: use_pme=0 problem David A. Case (Wed May 24 2006 - 17:33:53 PDT)
    - Re: AMBER: use_pme=0 problem luckyang.gmail.com (Wed May 24 2006 - 17:51:10 PDT)
    - Re: AMBER: use_pme=0 problem luckyang.gmail.com (Thu May 25 2006 - 10:09:59 PDT)
    - Re: AMBER: use_pme=0 problem David A. Case (Thu May 25 2006 - 10:56:56 PDT)
    - Re: AMBER: use_pme=0 problem luckyang.gmail.com (Thu May 25 2006 - 18:56:30 PDT)
    - Re: AMBER: use_pme=0 problem David A. Case (Fri May 26 2006 - 10:34:39 PDT)
    - Re: AMBER: use_pme=0 problem luckyang.gmail.com (Fri May 26 2006 - 12:10:19 PDT)
    - Re: AMBER: use_pme=0 problem David A. Case (Fri May 26 2006 - 12:30:01 PDT)
    - Re: AMBER: use_pme=0 problem luckyang.gmail.com (Fri May 26 2006 - 13:19:11 PDT)
- Re: AMBER: use_pme=0 problem Bill Ross (Fri May 26 2006 - 13:32:35 PDT)
AMBER: output of first stage RESP calculation JunJun Liu (Wed May 24 2006 - 15:23:55 PDT)
- Re: AMBER: output of first stage RESP calculation FyD (Thu May 25 2006 - 01:12:12 PDT)
AMBER: How to built the deprotonated form of lysine and tyrosine jitrayut jitonnom (Wed May 24 2006 - 19:49:04 PDT)
AMBER: Fwd: RESP for deprotonated tyrosine and lysine jitrayut jitonnom (Wed May 24 2006 - 19:57:45 PDT)
- Re: AMBER: Fwd: RESP for deprotonated tyrosine and lysine FyD (Thu May 25 2006 - 01:26:15 PDT)
AMBER: Qestion about input for RESP program JunJun Liu (Wed May 24 2006 - 19:44:41 PDT)
- Re: AMBER: Qestion about input for RESP program Ilyas Yildirim (Wed May 24 2006 - 21:49:11 PDT)
- Re: AMBER: Qestion about input for RESP program FyD (Thu May 25 2006 - 01:22:13 PDT)
  - Re: AMBER: Qestion about input for RESP program JunJun Liu (Thu May 25 2006 - 07:01:41 PDT)
    - Re: AMBER: Qestion about input for RESP program FyD (Thu May 25 2006 - 08:53:28 PDT)
AMBER: How to build NH2 of amino acid in amber jitrayut jitonnom (Wed May 24 2006 - 20:52:25 PDT)
AMBER: question about QM/MM in amber9 aixiaoli (Thu May 25 2006 - 01:37:10 PDT)
- Re: AMBER: question about QM/MM in amber9 Adrian Roitberg (Thu May 25 2006 - 03:57:25 PDT)
- RE: AMBER: question about QM/MM in amber9 Ross Walker (Thu May 25 2006 - 08:33:17 PDT)
AMBER: New united atom force field and GB solvation model in amber9 (leaprc.ff03ua) Soonmin Jang (Thu May 25 2006 - 03:51:02 PDT)
- Re: AMBER: New united atom force field and GB solvation model in amber9 (leaprc.ff03ua) Ray Luo (Wed May 24 2006 - 16:14:33 PDT)
  - Re: AMBER: New united atom force field and GB solvation model in amber9 (leaprc.ff03ua) David A. Case (Thu May 25 2006 - 13:33:33 PDT)
AMBER: 1st 2 lines of restart files hayden (Thu May 25 2006 - 04:40:03 PDT)
- Re: AMBER: 1st 2 lines of restart files Steven Winfield (Thu May 25 2006 - 04:50:18 PDT)
AMBER: alpha helix preference problem harianto (Thu May 25 2006 - 14:16:23 PDT)
- Re: AMBER: alpha helix preference problem Carlos Simmerling (Thu May 25 2006 - 18:35:10 PDT)
  - Re: AMBER: alpha helix preference problem harianto (Fri May 26 2006 - 07:04:30 PDT)
    - RE: AMBER: alpha helix preference problem Ross Walker (Fri May 26 2006 - 08:23:27 PDT)
AMBER: RMSd error Claire Zerafa (Thu May 25 2006 - 21:37:54 PDT)
- Re: AMBER: RMSd error Carlos Simmerling (Fri May 26 2006 - 04:27:18 PDT)
- Re: AMBER: RMSd error Thomas Cheatham (Fri May 26 2006 - 08:59:34 PDT)
AMBER: RE: trouble stripping waters with ptraj Adam Pelzer (Thu May 25 2006 - 21:50:53 PDT)
- Re: AMBER: RE: trouble stripping waters with ptraj Carlos Simmerling (Fri May 26 2006 - 04:28:35 PDT)
- Re: [UCE]AMBER: RE: trouble stripping waters with ptraj Thomas Cheatham (Fri May 26 2006 - 09:04:22 PDT)
  - AMBER: RE: trouble stripping waters with ptraj Adam Pelzer (Mon May 29 2006 - 15:20:23 PDT)
    - Re: [UCE]AMBER: RE: trouble stripping waters with ptraj Thomas Cheatham (Tue May 30 2006 - 10:17:31 PDT)
AMBER: ptraj: calculating distances between atoms in charges residues Magne Olufsen (Fri May 26 2006 - 00:13:48 PDT)
- Re: AMBER: ptraj: calculating distances between atoms in charges residues Thomas Cheatham (Fri May 26 2006 - 09:12:40 PDT)
AMBER: Question about .off file Sergey Krishtal (Fri May 26 2006 - 01:15:06 PDT)
- Re: AMBER: Question about .off file Ilyas Yildirim (Fri May 26 2006 - 01:58:19 PDT)
AMBER: different TI calculations starting from the same state Andrea Bortolato (Fri May 26 2006 - 06:56:47 PDT)
AMBER: different TI calculations starting from the same state Andrea Bortolato (Fri May 26 2006 - 03:12:12 PDT)
- Re: AMBER: different TI calculations starting from the same state David A. Case (Fri May 26 2006 - 08:16:19 PDT)
AMBER: Saving RMSD values in VMD nag raj (Fri May 26 2006 - 07:33:00 PDT)
- RE: AMBER: Saving RMSD values in VMD Ross Walker (Fri May 26 2006 - 08:27:08 PDT)
  - Re: AMBER: Saving RMSD values in VMD Carlos Simmerling (Fri May 26 2006 - 08:45:17 PDT)
  - AMBER: Pt containing complex: xleap a a (Sun May 28 2006 - 20:30:48 PDT)
    - Re: AMBER: Pt containing complex: xleap Ilyas Yildirim (Sun May 28 2006 - 21:00:08 PDT)
AMBER: check as error: load prepin in tleap jitrayut jitonnom (Fri May 26 2006 - 10:13:41 PDT)
AMBER: Please reply Shafinaz (Fri May 26 2006 - 12:19:42 PDT)
- Re: AMBER: Please reply Ananda Rama Krishnan Selvaraj (Fri May 26 2006 - 12:36:26 PDT)
- Re: AMBER: Please reply David A. Case (Fri May 26 2006 - 12:39:02 PDT)
AMBER: Installing / Compiling Question Seth Lilavivat (Fri May 26 2006 - 20:29:06 PDT)
- Re: AMBER: Installing / Compiling Question David A. Case (Sat May 27 2006 - 21:50:54 PDT)
  - RE: AMBER: Installing / Compiling Question Ross Walker (Sat May 27 2006 - 22:12:46 PDT)
    - AMBER: Pt containing complex: antechamber a a (Sun May 28 2006 - 20:42:31 PDT)
    - Re: AMBER: Pt containing complex: antechamber David A. Case (Tue May 30 2006 - 10:39:20 PDT)
    - AMBER: Antechamber : +ve charge species a a (Tue May 30 2006 - 03:04:05 PDT)
    - RE: AMBER: Antechamber : +ve charge species Junmei Wang (Tue May 30 2006 - 08:31:07 PDT)
    - AMBER: ESP calculations. a a (Tue May 30 2006 - 03:10:41 PDT)
    - Re: AMBER: ESP calculations. FyD (Tue May 30 2006 - 04:15:31 PDT)
    - Re: AMBER: ESP calculations. Ken Merz (Tue May 30 2006 - 04:55:24 PDT)
    - Re: AMBER: ESP calculations. Ken Merz (Tue May 30 2006 - 04:59:38 PDT)
AMBER: md error : sander jitrayut jitonnom (Sun May 28 2006 - 11:11:45 PDT)
- Re: AMBER: md error : sander Carlos Simmerling (Sun May 28 2006 - 13:06:21 PDT)
AMBER: which time should I use to calculate the number of "ps/Day" Zhihong Yu (Mon May 29 2006 - 02:32:26 PDT)
- Re: AMBER: which time should I use to calculate the number of "ps/Day" Carlos Simmerling (Mon May 29 2006 - 02:50:31 PDT)
- Re: AMBER: which time should I use to calculate the number of "ps/Day" Robert Duke (Mon May 29 2006 - 06:10:04 PDT)
  - AMBER: Thermodynamic integration using the amber 9 Vitor Manuel Sousa F?x (Mon May 29 2006 - 06:41:14 PDT)
    - Re: AMBER: Thermodynamic integration using the amber 9 Ilyas Yildirim (Mon May 29 2006 - 07:25:21 PDT)
    - Re: AMBER: Thermodynamic integration using the amber 9 Ilyas Yildirim (Fri Jun 02 2006 - 13:12:18 PDT)
- Re: AMBER: which time should I use to calculate the number of "ps/Day" Zhihong Yu (Mon May 29 2006 - 17:42:01 PDT)
AMBER: antechamber help needed for FAD pkb bioinfo (Mon May 29 2006 - 02:38:48 PDT)
AMBER: Difference in results for TI calculation brmeher.iitg.ernet.in (Mon May 29 2006 - 06:53:41 PDT)
- Re: AMBER: Difference in results for TI calculation David A. Case (Tue May 30 2006 - 11:01:49 PDT)
AMBER: Difference in results for TI calculation brmeher.iitg.ernet.in (Mon May 29 2006 - 07:23:45 PDT)
AMBER: problems with antechamber JAVIER PEREZ (Mon May 29 2006 - 08:04:52 PDT)
- Re: AMBER: problems with antechamber linfu (Tue May 30 2006 - 05:01:59 PDT)
- RE: AMBER: problems with antechamber Junmei Wang (Tue May 30 2006 - 08:20:33 PDT)
AMBER: energy terms JAVIER PEREZ (Mon May 29 2006 - 08:25:31 PDT)
AMBER: SAVEPDB in Xleap could not save 4 character atom names Jiayun Pang (Mon May 29 2006 - 09:38:22 PDT)
- Re: AMBER: SAVEPDB in Xleap could not save 4 character atom names David A. Case (Tue May 30 2006 - 10:36:37 PDT)
  - Re: AMBER: SAVEPDB in Xleap could not save 4 character atom names Andy Purkiss (Tue May 30 2006 - 11:18:58 PDT)
Re: AMBER: SAVEPDB in Xleap could not save 4 character atom names Bill Ross (Mon May 29 2006 - 13:26:56 PDT)
AMBER: Different results for TI calculation Biswa Ranjan Meher (Wed May 31 2006 - 00:25:13 PDT)
- Re: AMBER: Different results for TI calculation David A. Case (Thu Jun 01 2006 - 07:33:32 PDT)
  - AMBER: Amber 8 QMMM tests fail on AIX Shan-ho Tsai (Thu Jun 01 2006 - 08:08:26 PDT)
    - RE: AMBER: Amber 8 QMMM tests fail on AIX Ross Walker (Thu Jun 01 2006 - 09:27:24 PDT)
    - RE: AMBER: Amber 8 QMMM tests fail on AIX Shan-ho Tsai (Thu Jun 01 2006 - 10:31:08 PDT)
AMBER: Replica exchage: about exchange interval Atsutoshi Okabe (Wed May 31 2006 - 05:36:27 PDT)
- Re: AMBER: Replica exchage: about exchange interval Carlos Simmerling (Wed May 31 2006 - 06:02:32 PDT)
AMBER: Force units in forcedump.dat Steven Winfield (Wed May 31 2006 - 06:41:43 PDT)
- Re: AMBER: Force units in forcedump.dat darden (Wed May 31 2006 - 10:53:34 PDT)
AMBER: Namelists in input files Steven Winfield (Wed May 31 2006 - 09:42:05 PDT)
- Re: AMBER: Namelists in input files David A. Case (Fri Jun 02 2006 - 13:48:42 PDT)
AMBER: SHAKE, TIP3P and 2fs Timesteps Mark Williamson (Wed May 31 2006 - 10:32:56 PDT)
- RE: AMBER: SHAKE, TIP3P and 2fs Timesteps Ross Walker (Wed May 31 2006 - 10:56:31 PDT)
  - RE: AMBER: SHAKE, TIP3P and 2fs Timesteps Andreas Svrcek-Seiler (Wed May 31 2006 - 11:38:29 PDT)
AMBER: xleap problem and answer Thomas Pochapsky (Wed May 31 2006 - 11:32:32 PDT)
AMBER: AMBER mdcrd file bigger than 2GB snoze pa (Wed May 31 2006 - 14:57:22 PDT)
- Re: AMBER: AMBER mdcrd file bigger than 2GB snoze pa (Wed May 31 2006 - 16:04:53 PDT)
- Re: AMBER: AMBER mdcrd file bigger than 2GB Thomas Cheatham (Wed May 31 2006 - 16:27:16 PDT)
  - Re: AMBER: AMBER mdcrd file bigger than 2GB snoze pa (Thu Jun 01 2006 - 08:41:02 PDT)
    - Re: AMBER: AMBER mdcrd file bigger than 2GB Thomas Cheatham (Thu Jun 01 2006 - 09:25:19 PDT)
AMBER: Installation of Amber8 on Fedora Core 5 DAVID P. RANGEL (Wed May 31 2006 - 15:48:11 PDT)
- Re: AMBER: Installation of Amber8 on Fedora Core 5. . Don.Bashford.stjude.org (Thu Jun 01 2006 - 09:23:11 PDT)
  - Re: AMBER: Installation of Amber8 on Fedora Core 5. . David A. Case (Fri Jun 02 2006 - 12:27:59 PDT)
AMBER: offset? Tonda March (Wed May 31 2006 - 23:12:19 PDT)
- Re: AMBER: offset? Angelo (Thu Jun 01 2006 - 02:39:20 PDT)
AMBER: Bond Force Conctants in Amber Force Fields Егоров Д.А. (Wed May 31 2006 - 22:22:01 PDT)
AMBER: Another Installation Problem Seth Lilavivat (Thu Jun 01 2006 - 16:01:13 PDT)
- RE: AMBER: Another Installation Problem Ross Walker (Thu Jun 01 2006 - 22:02:03 PDT)
  - Re: AMBER: Another Installation Problem Scott Pendley (Fri Jun 02 2006 - 09:21:09 PDT)
AMBER: compile error with pgf90 Evan Kelly (Thu Jun 01 2006 - 22:33:21 PDT)
- RE: AMBER: compile error with pgf90 Ross Walker (Fri Jun 02 2006 - 08:15:01 PDT)
AMBER: some questions and problems about antechamber and divcon Zhihong Yu (Fri Jun 02 2006 - 00:11:22 PDT)
- Re: AMBER: some questions and problems about antechamber and divcon Martin Peters (Fri Jun 02 2006 - 06:07:03 PDT)
- Re: AMBER: some questions and problems about antechamber and divcon David A. Case (Fri Jun 02 2006 - 17:12:42 PDT)
AMBER: How to analyze the trajectory generated by LES simulation pang zhao (Fri Jun 02 2006 - 00:08:03 PDT)
- Re: AMBER: How to analyze the trajectory generated by LES simulation Vlad Cojocaru (Fri Jun 02 2006 - 02:54:20 PDT)
AMBER: attachments for my last mail Zhihong Yu (Fri Jun 02 2006 - 00:30:30 PDT)
AMBER: Programes to calculate ligand RMSD nag raj (Fri Jun 02 2006 - 03:59:04 PDT)
- Re: AMBER: Programes to calculate ligand RMSD Carlos Simmerling (Fri Jun 02 2006 - 04:45:17 PDT)
AMBER: individual torsion/bond energies from a minimization Thomas Pochapsky (Fri Jun 02 2006 - 06:25:33 PDT)
- Re: AMBER: individual torsion/bond energies from a minimization David A. Case (Mon Jun 05 2006 - 07:21:40 PDT)
AMBER: distance restraints Myunggi Yi (Fri Jun 02 2006 - 08:06:38 PDT)
AMBER: bugfix for frcmod.ff03 in Amber 9 David A. Case (Fri Jun 02 2006 - 09:45:29 PDT)
AMBER: NMR restraint Myunggi Yi (Fri Jun 02 2006 - 11:11:51 PDT)
- Re: AMBER: NMR restraint Myunggi Yi (Fri Jun 02 2006 - 12:15:41 PDT)
  - Re: AMBER: NMR restraint Myunggi Yi (Fri Jun 02 2006 - 12:23:28 PDT)
  - Re: AMBER: NMR restraint David A. Case (Fri Jun 02 2006 - 17:28:16 PDT)
    - Re: AMBER: NMR restraint Myunggi Yi (Sat Jun 03 2006 - 06:25:26 PDT)
AMBER: trouble adding mdcrd files together Adam Pelzer (Fri Jun 02 2006 - 15:22:46 PDT)
- Re: AMBER: trouble adding mdcrd files together Carlos Simmerling (Fri Jun 02 2006 - 15:37:54 PDT)
  - AMBER: Calculating energy for specific part of system Adam Pelzer (Tue Jul 18 2006 - 15:32:34 PDT)
- Re: AMBER: trouble adding mdcrd files together David A. Case (Fri Jun 02 2006 - 16:30:20 PDT)
  - Re: AMBER: trouble adding mdcrd files together Carlos Simmerling (Fri Jun 02 2006 - 16:45:16 PDT)
- Re: AMBER: trouble adding mdcrd files together Adam Pelzer (Sat Jun 03 2006 - 17:40:28 PDT)
AMBER: manual docking mathew k varghese (Fri Jun 02 2006 - 20:39:13 PDT)
AMBER: manual docking mathew k varghese (Fri Jun 02 2006 - 20:50:03 PDT)
- Re: AMBER: manual docking linfu (Sat Jun 03 2006 - 00:39:44 PDT)
  - Re: AMBER: manual docking snoze pa (Sun Jun 04 2006 - 21:46:05 PDT)
AMBER: How to use the prmtop and inpcrd files of ligand in a complex system? Zhihong Yu (Sat Jun 03 2006 - 00:00:23 PDT)
- Re: AMBER: How to use the prmtop and inpcrd files of ligand in a complex system? Navnit Kumar Mishra (Mon Jun 05 2006 - 01:08:12 PDT)
Re: AMBER: How to use the prmtop and inpcrd files of ligand in acomplex system? Zhihong Yu (Mon Jun 05 2006 - 01:57:44 PDT)
- Re: AMBER: How to use the prmtop and inpcrd files of ligand in acomplex system? Navnit Kumar Mishra (Mon Jun 05 2006 - 02:22:33 PDT)
AMBER: MM-PBSA and first solvation shell Andrea Bortolato (Mon Jun 05 2006 - 02:42:39 PDT)
- Re: AMBER: MM-PBSA and first solvation shell Thomas Cheatham (Mon Jun 05 2006 - 10:23:58 PDT)
AMBER: process_mdout Navnit Kumar Mishra (Mon Jun 05 2006 - 05:00:40 PDT)
- RE: AMBER: process_mdout Ross Walker (Mon Jun 05 2006 - 08:19:47 PDT)
AMBER: Amber: Segfault while running sander sethl.gatech.edu (Mon Jun 05 2006 - 11:19:33 PDT)
- RE: AMBER: Amber: Segfault while running sander Ross Walker (Mon Jun 05 2006 - 11:31:35 PDT)
  - AMBER: Amber: Can't get sander to run sethl.gatech.edu (Tue Jun 06 2006 - 11:15:14 PDT)
    - Re: AMBER: Amber: Can't get sander to run David A. Case (Tue Jun 06 2006 - 13:31:56 PDT)
AMBER: does the Amber8 or Amber9 contains Br,I and Sulfur parameter for MM-PBSA or MM-GBSA. linfu (Mon Jun 05 2006 - 19:24:17 PDT)
- Re: AMBER: does the Amber8 or Amber9 contains Br,I and Sulfur parameter for MM-PBSA or MM-GBSA. David A. Case (Wed Jun 07 2006 - 15:22:41 PDT)
AMBER: How to submit a job in cluster pkb bioinfo (Tue Jun 06 2006 - 01:46:21 PDT)
AMBER: calculating box dimensions during MD Vlad Cojocaru (Tue Jun 06 2006 - 07:13:14 PDT)
- Re: AMBER: calculating box dimensions during MD Ananda Rama Krishnan Selvaraj (Tue Jun 06 2006 - 07:31:32 PDT)
AMBER: antechamber and FMN David Mobley (Tue Jun 06 2006 - 10:47:03 PDT)
AMBER: xleap problem Hashem Taha (Tue Jun 06 2006 - 11:29:31 PDT)
- Re: AMBER: xleap problem Myunggi Yi (Tue Jun 06 2006 - 16:32:16 PDT)
  - Re: AMBER: xleap problem Myunggi Yi (Tue Jun 06 2006 - 16:42:34 PDT)
  - Re: AMBER: xleap problem Ilyas Yildirim (Tue Jun 06 2006 - 23:49:04 PDT)
    - Re: AMBER: xleap problem Myunggi Yi (Wed Jun 07 2006 - 07:22:12 PDT)
AMBER: compiler error for Amber9 Weihua Li (Wed Jun 07 2006 - 07:34:49 PDT)
- Re: AMBER: compiler error for Amber9 Robert Duke (Wed Jun 07 2006 - 08:03:15 PDT)
- RE: AMBER: compiler error for Amber9 Ross Walker (Wed Jun 07 2006 - 08:34:20 PDT)
- Re: AMBER: compiler error for Amber9 David A. Case (Wed Jun 07 2006 - 08:52:14 PDT)
AMBER: antechamber Steve Seibold (Wed Jun 07 2006 - 09:16:47 PDT)
- Re: AMBER: antechamber Myunggi Yi (Wed Jun 07 2006 - 09:31:46 PDT)
- RE: AMBER: antechamber Ross Walker (Wed Jun 07 2006 - 09:56:01 PDT)
AMBER: RE: antechamber and FMN Junmei Wang (Wed Jun 07 2006 - 13:39:48 PDT)
AMBER: pmemd_parallel_ins_prob pkmukher (Wed Jun 07 2006 - 14:00:20 PDT)
- Re: AMBER: pmemd_parallel_ins_prob Robert Duke (Wed Jun 07 2006 - 14:21:28 PDT)
- Re: AMBER: pmemd_parallel_ins_prob pkmukher (Thu Jun 08 2006 - 11:09:00 PDT)
- Re: AMBER: pmemd_parallel_ins_prob Amber admin (Thu Jun 15 2006 - 12:08:46 PDT)
AMBER: problem with amber 9 and igb=5 M. Scott Shell (Wed Jun 07 2006 - 18:06:02 PDT)
- Re: AMBER: problem with amber 9 and igb=5 Carlos Simmerling (Wed Jun 07 2006 - 19:02:34 PDT)
  - Re: AMBER: problem with amber 9 and igb=5 M. Scott Shell (Thu Jun 08 2006 - 09:05:10 PDT)
    - AMBER: GB and protein backbone parameters Carlos Simmerling (Thu Jun 08 2006 - 09:27:47 PDT)
- Re: AMBER: problem with amber 9 and igb=5 John Mongan (Wed Jun 07 2006 - 19:04:59 PDT)
  - Re: AMBER: problem with amber 9 and igb=5 M. Scott Shell (Thu Jun 08 2006 - 08:55:36 PDT)
    - Re: AMBER: problem with amber 9 and igb=5 M. Scott Shell (Thu Jun 08 2006 - 22:15:56 PDT)
    - Re: AMBER: problem with amber 9 and igb=5 David A. Case (Fri Jun 09 2006 - 14:58:02 PDT)
    - Re: AMBER: problem with amber 9 and igb=5 M. Scott Shell (Sat Jun 10 2006 - 11:40:05 PDT)
    - RE: AMBER: problem with amber 9 and igb=5 Ross Walker (Sat Jun 10 2006 - 12:31:26 PDT)
AMBER: How to build N-terminal of alanine : NH2 jitrayut jitonnom (Thu Jun 08 2006 - 00:59:34 PDT)
- Re: AMBER: How to build N-terminal of alanine : NH2 FyD (Thu Jun 08 2006 - 01:27:58 PDT)
  - Fwd: AMBER: How to build N-terminal of alanine : NH2 jitrayut jitonnom (Thu Jun 08 2006 - 05:32:22 PDT)
    - Re: Fwd: AMBER: How to build N-terminal of alanine : NH2 FyD (Thu Jun 08 2006 - 23:45:27 PDT)
AMBER: save coordinates during SANDER minimisation Hannes Barsch (Thu Jun 08 2006 - 02:34:51 PDT)
- Re: AMBER: save coordinates during SANDER minimisation Ilyas Yildirim (Thu Jun 08 2006 - 03:22:24 PDT)
- Re: AMBER: save coordinates during SANDER minimisation David A. Case (Thu Jun 08 2006 - 15:39:01 PDT)
AMBER: Ask for help in pbsa error in AMBER9 Cheng Luo, Ph.D. (Thu Jun 08 2006 - 09:08:10 PDT)
- Re: AMBER: Ask for help in pbsa error in AMBER9 Ray Luo (Thu Jun 08 2006 - 12:01:06 PDT)
AMBER: software to visualize normal modes Douali, Latifa (Thu Jun 08 2006 - 10:03:26 PDT)
- RE: AMBER: software to visualize normal modes Ross Walker (Thu Jun 08 2006 - 10:07:41 PDT)
  - Re: AMBER: software to visualize normal modes David A. Case (Thu Jun 08 2006 - 10:46:38 PDT)
AMBER: AMD 64 Installation / configuration clarification sethl.gatech.edu (Thu Jun 08 2006 - 12:09:50 PDT)
- Re: AMBER: AMD 64 Installation / configuration clarification David LeBard (Thu Jun 08 2006 - 12:57:18 PDT)
  - Re: AMBER: AMD 64 Installation / configuration clarification sethl.gatech.edu (Thu Jun 08 2006 - 13:23:51 PDT)
    - Re: AMBER: AMD 64 Installation / configuration clarification David LeBard (Thu Jun 08 2006 - 16:52:57 PDT)
AMBER: COM khn _ (Thu Jun 08 2006 - 17:13:27 PDT)
- Re: AMBER: COM Thomas Cheatham (Thu Jun 08 2006 - 17:34:03 PDT)
AMBER: charmm force field in amber9 soo (Thu Jun 08 2006 - 21:23:26 PDT)
- Re: AMBER: charmm force field in amber9 David A. Case (Fri Jun 09 2006 - 07:02:03 PDT)
AMBER: Problem with Leap jitrayut jitonnom (Thu Jun 08 2006 - 21:40:52 PDT)
AMBER: use ptraj and two differenct prmtop file to analyze LES trajectory pang zhao (Fri Jun 09 2006 - 01:56:57 PDT)
AMBER: MMPBSA problem jitrayut jitonnom (Fri Jun 09 2006 - 02:48:50 PDT)
- Re: AMBER: MMPBSA problem Thomas Steinbrecher (Fri Jun 09 2006 - 08:06:34 PDT)
AMBER: ptraj Marcela Madrid (Fri Jun 09 2006 - 14:19:54 PDT)
AMBER: Why the result from sander minimization (epsilon=4r) is not same with that from nmode, when restraint is applied? Yongmei Pan (Fri Jun 09 2006 - 20:03:26 PDT)
AMBER: Why the energy from sander minimization (epsilon=4r) is not same with that from nmode, when restraint is applied? Yongmei Pan (Fri Jun 09 2006 - 19:57:42 PDT)
- Re: AMBER: Why the energy from sander minimization (epsilon=4r) is not same with that from nmode, when restraint is applied? David A. Case (Sat Jun 10 2006 - 10:06:49 PDT)
AMBER: is seems that The SAS in MMPBSA is SES , not SAS. ???? linfu (Fri Jun 09 2006 - 20:25:24 PDT)
- Re: AMBER: is seems that The SAS in MMPBSA is SES , not SAS. ???? Ray Luo (Sat Jun 10 2006 - 10:45:17 PDT)
- Re: AMBER: is seems that The SAS in MMPBSA is SES , not SAS. ???? David A. Case (Sat Jun 10 2006 - 11:24:29 PDT)
AMBER: MD stopped Miguel Ferreira (Sat Jun 10 2006 - 02:33:05 PDT)
- RE: AMBER: MD stopped Ross Walker (Mon Jun 12 2006 - 08:50:34 PDT)
AMBER: Umbrella sampling Atsutoshi Okabe (Sat Jun 10 2006 - 03:42:34 PDT)
- Re: AMBER: Umbrella sampling Ilyas Yildirim (Sat Jun 10 2006 - 07:53:41 PDT)
  - RE: AMBER: Umbrella sampling Atsutoshi Okabe (Sun Jun 18 2006 - 03:14:10 PDT)
    - RE: AMBER: Umbrella sampling Ilyas Yildirim (Sun Jun 18 2006 - 09:57:09 PDT)
AMBER: parmchk error Evan Kelly (Sat Jun 10 2006 - 20:30:11 PDT)
- RE: AMBER: parmchk error Ross Walker (Mon Jun 12 2006 - 08:31:59 PDT)
  - Re: AMBER: parmchk error Evan Kelly (Mon Jun 12 2006 - 22:42:16 PDT)
    - Re: AMBER: parmchk error David A. Case (Wed Jun 14 2006 - 20:28:20 PDT)
- RE: AMBER: parmchk error Junmei Wang (Thu Jun 15 2006 - 08:16:10 PDT)
Re: Re: AMBER:it seems that The SAS in MMPBSA is SES , not SAS. ???? linfu (Sat Jun 10 2006 - 20:27:20 PDT)
AMBER: mm_pbsa calculation for calcium Navnit Kumar Mishra (Sun Jun 11 2006 - 22:59:06 PDT)
- Re: AMBER: mm_pbsa calculation for calcium Scott Pendley (Mon Jun 12 2006 - 14:42:59 PDT)
  - Re: AMBER: mm_pbsa calculation for calcium Navnit Kumar Mishra (Tue Jun 13 2006 - 00:45:32 PDT)
    - Re: AMBER: mm_pbsa calculation for calcium Scott Pendley (Tue Jun 13 2006 - 09:20:42 PDT)
    - Re: AMBER: mm_pbsa calculation for calcium Navnit Kumar Mishra (Tue Jun 13 2006 - 10:26:56 PDT)
    - Re: AMBER: mm_pbsa calculation for calcium Scott Pendley (Tue Jun 13 2006 - 13:03:17 PDT)
AMBER: switching function for electrostatic interactions Fabien Cailliez (Mon Jun 12 2006 - 04:38:22 PDT)
- RE: AMBER: switching function for electrostatic interactions Ross Walker (Mon Jun 12 2006 - 08:28:19 PDT)
- Re: AMBER: switching function for electrostatic interactions Thomas Cheatham (Mon Jun 12 2006 - 09:12:28 PDT)
AMBER: How to calculate the mmpbsa for explicit MD ? jitrayut jitonnom (Mon Jun 12 2006 - 09:41:52 PDT)
- Re: AMBER: How to calculate the mmpbsa for explicit MD ? Thomas Steinbrecher (Mon Jun 12 2006 - 09:58:33 PDT)
  - Fwd: AMBER: How to calculate the mmpbsa for explicit MD ? jitrayut jitonnom (Mon Jun 12 2006 - 11:37:49 PDT)
    - Re: Fwd: AMBER: How to calculate the mmpbsa for explicit MD ? Thomas Steinbrecher (Mon Jun 12 2006 - 11:50:30 PDT)
    - Fwd: Fwd: AMBER: How to calculate the mmpbsa for explicit MD ? jitrayut jitonnom (Mon Jun 12 2006 - 12:15:06 PDT)
- Re: AMBER: How to calculate the mmpbsa for explicit MD ? Chris Moth (Mon Jun 12 2006 - 12:23:01 PDT)
AMBER: How to strip waters in trajectorie ? jitrayut jitonnom (Mon Jun 12 2006 - 12:50:02 PDT)
- Re: AMBER: How to strip waters in trajectorie ? Gustavo Seabra (Mon Jun 12 2006 - 12:57:30 PDT)
- Re: AMBER: How to strip waters in trajectorie ? David A. Case (Mon Jun 12 2006 - 13:06:19 PDT)
- Re: AMBER: How to strip waters in trajectorie ? simon whitehead (Tue Jun 13 2006 - 01:24:37 PDT)
AMBER: Nmode memory allocation problem JunJun Liu (Mon Jun 12 2006 - 16:45:14 PDT)
- RE: AMBER: Nmode memory allocation problem Ross Walker (Mon Jun 12 2006 - 18:34:24 PDT)
  - Re: AMBER: Nmode memory allocation problem JunJun Liu (Tue Jun 13 2006 - 08:08:25 PDT)
AMBER: SGI compiler problems Peter Gannett (Tue Jun 13 2006 - 05:46:18 PDT)
- Re: AMBER: SGI compiler problems Atro Tossavainen (Wed Jun 21 2006 - 04:30:00 PDT)
  - Re: AMBER: SGI compiler problems Roberto Gomperts (Wed Jun 21 2006 - 08:09:54 PDT)
AMBER: MMPBSA error jitrayut jitonnom (Tue Jun 13 2006 - 07:52:08 PDT)
- Re: AMBER: MMPBSA error Heike.Meiselbach.chemie.uni-erlangen.de (Tue Jun 13 2006 - 08:27:22 PDT)
  - Fwd: AMBER: MMPBSA error jitrayut jitonnom (Tue Jun 13 2006 - 09:28:43 PDT)
    - Re: Fwd: AMBER: MMPBSA error JunJun Liu (Tue Jun 13 2006 - 08:51:58 PDT)
AMBER: Difficulty loading a pdb file Kara Di Giorgio (Tue Jun 13 2006 - 11:20:41 PDT)
- Re: AMBER: Difficulty loading a pdb file Ilyas Yildirim (Tue Jun 13 2006 - 14:25:27 PDT)
- RE: AMBER: Difficulty loading a pdb file Ross Walker (Wed Jun 14 2006 - 07:05:34 PDT)
AMBER: LEaP Warning ... when do NH2-neutral fragment jitrayut jitonnom (Tue Jun 13 2006 - 11:40:47 PDT)
- Re: AMBER: LEaP Warning ... when do NH2-neutral fragment FyD (Tue Jun 13 2006 - 12:20:52 PDT)
- Re: AMBER: LEaP Warning ... when do NH2-neutral fragment Ilyas Yildirim (Tue Jun 13 2006 - 14:23:18 PDT)
  - AMBER: Problem of Ptraj in AMBER9 Chunhu Tan (Tue Jun 13 2006 - 15:24:26 PDT)
AMBER: compiler requirement for SGI Fuel To install AMBER9 S.Sundar Raman (Tue Jun 13 2006 - 23:45:40 PDT)
AMBER: How to simplify this big system rationally to perform MD studies Zhihong Yu (Wed Jun 14 2006 - 03:43:59 PDT)
Fwd: Fwd: AMBER: MMPBSA error jitrayut jitonnom (Wed Jun 14 2006 - 04:27:51 PDT)
AMBER: problems on mm_pbsa Giovanni (Wed Jun 14 2006 - 05:05:03 PDT)
- Re: AMBER: problems on mm_pbsa Ray Luo (Tue Jun 13 2006 - 22:04:28 PDT)
  - AMBER: Review. Chunhu Tan (Mon Jun 26 2006 - 12:37:22 PDT)
AMBER: saveamberparams error in Amber9 Weihua Li (Wed Jun 14 2006 - 06:28:43 PDT)
- Re: AMBER: saveamberparams error in Amber9 Thomas Steinbrecher (Wed Jun 14 2006 - 08:07:28 PDT)
  - Re: AMBER: saveamberparams error in Amber9 Weihua Li (Wed Jun 14 2006 - 19:15:03 PDT)
- Re: AMBER: saveamberparams error in Amber9 David A. Case (Wed Jun 14 2006 - 20:15:05 PDT)
  - Re: AMBER: saveamberparams error in Amber9 Weihua Li (Wed Jun 14 2006 - 23:48:52 PDT)
AMBER: ptraj: rms per residue simon whitehead (Wed Jun 14 2006 - 07:14:28 PDT)
- Re: AMBER: ptraj: rms per residue Mingfeng Yang (Wed Jun 14 2006 - 13:28:07 PDT)
AMBER: Fully QM periodic runs Steven Winfield (Wed Jun 14 2006 - 09:03:43 PDT)
- RE: AMBER: Fully QM periodic runs Ross Walker (Wed Jun 14 2006 - 09:41:58 PDT)
  - Re: AMBER: Fully QM periodic runs Wei Zhang (Wed Jun 14 2006 - 09:58:51 PDT)
    - Re: AMBER: Fully QM periodic runs Gustavo Seabra (Wed Jun 14 2006 - 10:44:37 PDT)
- Re: AMBER: Fully QM periodic runs Ken Merz (Thu Jun 15 2006 - 07:10:13 PDT)
- RE: AMBER: Fully QM periodic runs hfox1.nd.edu (Mon Nov 24 2008 - 13:28:36 PST)
  - Re: AMBER: Fully QM periodic runs David A. Case (Tue Nov 25 2008 - 03:56:51 PST)
  - RE: AMBER: Fully QM periodic runs Ross Walker (Tue Nov 25 2008 - 08:54:24 PST)
Re: AMBER: Difficulty loading a pdb file (Modified by Kara Di Giorgio) Kara Di Giorgio (Wed Jun 14 2006 - 10:20:40 PDT)
- Re: AMBER: Difficulty loading a pdb file (Modified by Kara Di Giorgio) Ilyas Yildirim (Wed Jun 14 2006 - 11:46:22 PDT)
  - Re: AMBER: Difficulty loading a pdb file (Modified by Kara Di Giorgio) Knut Langsetmo (Wed Jun 14 2006 - 12:55:56 PDT)
    - RE: AMBER: Difficulty loading a pdb file (Modified by Kara Di Giorgio) Ross Walker (Wed Jun 14 2006 - 13:06:49 PDT)
    - Re: AMBER: Difficulty loading a pdb file (Modified by Kara Di Giorgio) Kara Di Giorgio (Thu Jun 15 2006 - 09:27:45 PDT)
- Re: AMBER: Difficulty loading a pdb file (Modified by Kara Di Giorgio) Mengjuei Hsieh (Sun Jun 25 2006 - 21:15:26 PDT)
AMBER: best way to customize linkages sethl.gatech.edu (Wed Jun 14 2006 - 13:25:07 PDT)
AMBER: Re: Problem in compiling sander with MMTSB Scott Brozell (Wed Jun 14 2006 - 20:29:57 PDT)
AMBER: RMS FLUCTUATIONS Jiang Jianwen (Thu Jun 15 2006 - 04:37:24 PDT)
- RE: AMBER: RMS FLUCTUATIONS Yong Duan (Thu Jun 15 2006 - 07:49:16 PDT)
  - RE: AMBER: RMS FLUCTUATIONS Jiang Jianwen (Fri Jun 16 2006 - 00:01:10 PDT)
- Re: AMBER: RMS FLUCTUATIONS David A. Case (Thu Jun 15 2006 - 21:09:53 PDT)
AMBER: GBSA of nonstandard cations Martin LEPSIK (Thu Jun 15 2006 - 15:46:16 PDT)
AMBER: Re: Problem in compiling sander with MMTSB Scott Brozell (Thu Jun 15 2006 - 16:28:27 PDT)
AMBER: repeat use of a trimer lib file Eric Hu (Thu Jun 15 2006 - 16:35:39 PDT)
AMBER: MPICH and Sander Andrew Box (Thu Jun 15 2006 - 19:07:11 PDT)
- Re: AMBER: MPICH and Sander David A. Case (Thu Jun 15 2006 - 20:47:36 PDT)
AMBER: LEaP error : unbalanced charge jitrayut jitonnom (Fri Jun 16 2006 - 06:52:33 PDT)
- Re: AMBER: LEaP error : unbalanced charge Thomas Steinbrecher (Fri Jun 16 2006 - 07:59:50 PDT)
  - Fwd: AMBER: LEaP error : unbalanced charge jitrayut jitonnom (Fri Jun 16 2006 - 09:34:42 PDT)
- Re: AMBER: LEaP error : unbalanced charge FyD (Mon Jun 19 2006 - 00:03:38 PDT)
Fwd: Fwd: AMBER: LEaP error : unbalanced charge jitrayut jitonnom (Fri Jun 16 2006 - 10:28:08 PDT)
- Fwd: Fwd: AMBER: LEaP error : unbalanced charge jitrayut jitonnom (Sat Jun 17 2006 - 13:37:46 PDT)
  - Re: Fwd: Fwd: AMBER: LEaP error : unbalanced charge Ilyas Yildirim (Sun Jun 18 2006 - 00:53:58 PDT)
    - Fwd: Fwd: Fwd: AMBER: LEaP error : unbalanced charge jitrayut jitonnom (Sun Jun 18 2006 - 06:17:57 PDT)
AMBER: Antechamber - NH2 and C not planar when it should be on one of my ligand Christophe Guilbert (Fri Jun 16 2006 - 21:32:12 PDT)
- Re: AMBER: Antechamber - NH2 and C not planar when it should be on one of my ligand Ilyas Yildirim (Sat Jun 17 2006 - 01:28:55 PDT)
AMBER: Problems with restart file from pmemd sim. anna.schrey.gmx.de (Sat Jun 17 2006 - 05:30:56 PDT)
- Re: AMBER: Problems with restart file from pmemd sim. Robert Duke (Sat Jun 17 2006 - 06:10:24 PDT)
AMBER: charge in LEaP step jitrayut jitonnom (Sat Jun 17 2006 - 11:14:24 PDT)
AMBER: Non bond list overflow in amber8.0 program. nag raj (Sun Jun 18 2006 - 21:54:04 PDT)
AMBER: Post-MD minimization sangeeta.bioinfo.ernet.in (Mon Jun 19 2006 - 04:33:58 PDT)
- Re: AMBER: Post-MD minimization Carlos Simmerling (Mon Jun 19 2006 - 07:27:37 PDT)
- RE: AMBER: Post-MD minimization Ross Walker (Mon Jun 19 2006 - 08:20:25 PDT)
  - RE: AMBER: checkoverlap doubt [was: Post-MD minimization] sangeeta.bioinfo.ernet.in (Tue Jun 20 2006 - 06:21:11 PDT)
    - RE: AMBER: checkoverlap doubt [was: Post-MD minimization] Thomas Cheatham (Tue Jun 20 2006 - 15:28:36 PDT)
  - RE: AMBER: Post-MD minimization sangeeta.bioinfo.ernet.in (Thu Jun 22 2006 - 23:09:31 PDT)
    - RE: AMBER: Post-MD minimization Ross Walker (Fri Jun 23 2006 - 05:19:14 PDT)
    - AMBER: Can we submit jobs in sequences to amber? a a (Mon Jun 26 2006 - 00:14:05 PDT)
    - Re: AMBER: Can we submit jobs in sequences to amber? Ilyas Yildirim (Mon Jun 26 2006 - 00:22:00 PDT)
    - AMBER: Minizsation strange error message! Please help. a a (Mon Jun 26 2006 - 03:38:35 PDT)
    - Re: AMBER: Can we submit jobs in sequences to amber? Roberto Gomperts (Mon Jun 26 2006 - 03:25:03 PDT)
AMBER: Amber7-CHARMM22-TRIPOS force fields opitz.che.udel.edu (Mon Jun 19 2006 - 08:37:24 PDT)
AMBER: help with custom RNA molecule sethl.gatech.edu (Mon Jun 19 2006 - 11:55:59 PDT)
AMBER: Antechamber poorly define atom angles of a five ring system which causes NH2 and C not to be planar as expected Christophe Guilbert (Mon Jun 19 2006 - 18:00:29 PDT)
AMBER: ions+proteins Hannes Loeffler (Mon Jun 19 2006 - 18:45:57 PDT)
AMBER: RE: Antechamber poorly define atom angles of a five ring system whichcauses NH2 and C not to be planar as expected Junmei Wang (Mon Jun 19 2006 - 20:08:56 PDT)
AMBER: second derivative matrix Marie Brut (Tue Jun 20 2006 - 05:28:02 PDT)
- Re: AMBER: second derivative matrix David A. Case (Tue Jun 20 2006 - 14:37:01 PDT)
  - AMBER: Tutorial 2: Production MD. a a (Wed Jun 21 2006 - 03:19:05 PDT)
    - Re: AMBER: Tutorial 2: Production MD. Thomas Steinbrecher (Wed Jun 21 2006 - 08:37:51 PDT)
    - AMBER: kill job command? a a (Thu Jun 22 2006 - 00:47:51 PDT)
    - Re: AMBER: kill job command? JunJun Liu (Thu Jun 22 2006 - 06:13:04 PDT)
    - AMBER: Tutorial 2: Minimise and equlibrium error NaN a a (Fri Jun 23 2006 - 03:05:05 PDT)
    - RE: AMBER: Tutorial 2: Minimise and equlibrium error NaN Ross Walker (Fri Jun 23 2006 - 04:28:17 PDT)
- AMBER: SURFTEN in GB (mm_pbsa calculations) Shuting Wei (Thu Aug 03 2006 - 12:18:10 PDT)
  - Re: AMBER: SURFTEN in GB (mm_pbsa calculations) Carlos Simmerling (Thu Aug 03 2006 - 12:38:59 PDT)
AMBER: why has "ELE " a large fluctuation in MMP BSA? yxiong99 (Tue Jun 20 2006 - 06:47:44 PDT)
- Re: AMBER: why has "ELE " a large fluctuation in MMP BSA? JunJun Liu (Tue Jun 20 2006 - 14:37:52 PDT)
  - Re: AMBER: why has "ELE " a large fluctuation in MMP BSA? Carlos Simmerling (Tue Jun 20 2006 - 16:10:48 PDT)
    - Re: AMBER: why has "ELE " a large fluctuation in MMP BSA? Thomas Cheatham (Tue Jun 20 2006 - 16:48:54 PDT)
    - Re: AMBER: why has "ELE " a large fluctuation in MMP BSA? JunJun Liu (Tue Jun 20 2006 - 15:55:09 PDT)
    - Re: AMBER: why has "ELE " a large fluctuation in MMP BSA? Carlos Simmerling (Tue Jun 20 2006 - 17:18:21 PDT)
    - Re: AMBER: why has "ELE " a large fluctuation in MMP BSA? Carlos Simmerling (Tue Jun 20 2006 - 17:19:10 PDT)
    - Re: AMBER: why has "ELE " a large fluctuation in MMP BSA? JunJun Liu (Tue Jun 20 2006 - 16:45:52 PDT)
    - Re: AMBER: why has "ELE " a large fluctuation in MMP BSA? Carlos Simmerling (Tue Jun 20 2006 - 18:54:51 PDT)
    - Re: AMBER: why has "ELE " a large fluctuation in MMP BSA? JunJun Liu (Tue Jun 20 2006 - 18:08:32 PDT)
AMBER: why has "ELE " a large fluctuation in MMPBSA? JunJun Liu (Tue Jun 20 2006 - 06:56:25 PDT)
AMBER: ptraj vector Myunggi Yi (Tue Jun 20 2006 - 09:13:54 PDT)
- Re: AMBER: ptraj vector Myunggi Yi (Tue Jun 20 2006 - 11:20:53 PDT)
- Re: AMBER: ptraj vector Thomas Cheatham (Tue Jun 20 2006 - 12:32:17 PDT)
  - Re: AMBER: ptraj vector Myunggi Yi (Tue Jun 20 2006 - 13:07:36 PDT)
    - Re: AMBER: ptraj vector David A. Case (Tue Jun 20 2006 - 14:36:49 PDT)
    - Re: AMBER: ptraj vector Myunggi Yi (Tue Jun 20 2006 - 14:55:05 PDT)
    - Re: AMBER: ptraj vector Thomas Cheatham (Tue Jun 20 2006 - 15:13:06 PDT)
    - Re: AMBER: ptraj vector Thomas Cheatham (Tue Jun 20 2006 - 14:59:50 PDT)
AMBER: amber9 hostfile snoze pa (Tue Jun 20 2006 - 17:12:50 PDT)
AMBER: Amber9 under SGI Prism (Altix) with Intel 8.0 error in pbpgb test David McGiven (Wed Jun 21 2006 - 03:46:40 PDT)
- Re: AMBER: Amber9 under SGI Prism (Altix) with Intel 8.0 error in pbpgb test Roberto Gomperts (Wed Jun 21 2006 - 07:10:44 PDT)
  - Re: AMBER: Amber9 under SGI Prism (Altix) with Intel 8.0 error in pbpgb test David McGiven (Wed Jun 21 2006 - 08:54:44 PDT)
AMBER: MMTSB: phi-pdi-based clustering sangeeta.bioinfo.ernet.in (Wed Jun 21 2006 - 05:37:39 PDT)
AMBER: terms in mm-pbsa Lwin, ThuZar (Wed Jun 21 2006 - 08:48:37 PDT)
AMBER: openmpi snoze pa (Wed Jun 21 2006 - 10:28:28 PDT)
AMBER: problems with cpinutil.pl Abhilash Mohan (Wed Jun 21 2006 - 14:06:05 PDT)
AMBER: What's the meaning of NTYPES? JunJun Liu (Wed Jun 21 2006 - 13:27:51 PDT)
- Re: AMBER: What's the meaning of NTYPES? JunJun Liu (Wed Jun 21 2006 - 13:59:23 PDT)
  - Re: AMBER: What's the meaning of NTYPES? Wei Zhang (Thu Jun 22 2006 - 09:18:38 PDT)
AMBER: problems about compiling a parallel version of AMBER 9 Chengwen Chen (Thu Jun 22 2006 - 00:25:11 PDT)
- Re: AMBER: problems about compiling a parallel version of AMBER 9 Wei Zhang (Thu Jun 22 2006 - 09:21:32 PDT)
  - Re: AMBER: problems about compiling a parallel version of AMBER 9 Chengwen Chen (Mon Jun 26 2006 - 21:41:05 PDT)
- Re: AMBER: problems about compiling a parallel version of AMBER 9 Kateryna Miroshnychenko (Tue Jun 27 2006 - 01:41:21 PDT)
  - Re: AMBER: problems about compiling a parallel version of AMBER 9 Chengwen Chen (Tue Jul 04 2006 - 21:29:38 PDT)
    - Re: AMBER: problems about compiling a parallel version of AMBER 9 David A. Case (Wed Jul 05 2006 - 11:06:08 PDT)
AMBER: Restraint internal coordinates in Amber 8.0 Guillaume Bollot (Thu Jun 22 2006 - 02:00:03 PDT)
AMBER: average struct.problem bala (Thu Jun 22 2006 - 02:11:15 PDT)
- Re: AMBER: average struct.problem Thomas Cheatham (Thu Jun 22 2006 - 07:35:45 PDT)
AMBER: can i use unusual amino acid priya priya (Thu Jun 22 2006 - 02:15:55 PDT)
- AMBER: RESP charge fitting problems with capping group hayden (Thu Jun 22 2006 - 02:51:52 PDT)
  - Re: AMBER: RESP charge fitting problems with capping group FyD (Thu Jun 22 2006 - 11:51:13 PDT)
AMBER: help creating RNA sethl.gatech.edu (Thu Jun 22 2006 - 12:14:06 PDT)
- Re: AMBER: help creating RNA Ilyas Yildirim (Thu Jun 22 2006 - 12:29:49 PDT)
- Re: AMBER: help creating RNA David A. Case (Thu Jun 22 2006 - 14:08:45 PDT)
  - Re: AMBER: help creating RNA sethl.gatech.edu (Mon Jun 26 2006 - 08:42:00 PDT)
- Re: AMBER: help creating RNA Vlad Cojocaru (Fri Jun 23 2006 - 01:14:24 PDT)
AMBER: ANN: APBS/Amber interface released Robert Konecny (Thu Jun 22 2006 - 23:23:35 PDT)
AMBER: Ptraj reimage truncated octahedral box simulation with AMBER8 Ricardo J. F. Branco (Fri Jun 23 2006 - 00:36:44 PDT)
- RE: AMBER: Ptraj reimage truncated octahedral box simulation with AMBER8 Ross Walker (Fri Jun 23 2006 - 04:34:47 PDT)
AMBER: references simon whitehead (Fri Jun 23 2006 - 03:35:56 PDT)
- Re: AMBER: references Ricardo J. F. Branco (Fri Jun 23 2006 - 03:47:50 PDT)
  - Re: AMBER: references simon whitehead (Fri Jun 23 2006 - 04:46:22 PDT)
- RE: AMBER: references Ross Walker (Fri Jun 23 2006 - 04:32:57 PDT)
AMBER: constant pressure equillibration simon whitehead (Fri Jun 23 2006 - 02:17:35 PDT)
- RE: AMBER: constant pressure equillibration Ross Walker (Fri Jun 23 2006 - 08:53:17 PDT)
AMBER: Implicit solvent question Anthony Cruz (Fri Jun 23 2006 - 06:49:22 PDT)
- Re: AMBER: Implicit solvent question John Mongan (Fri Jun 23 2006 - 09:09:49 PDT)
  - Re: AMBER: Implicit solvent question Anthony Cruz (Thu Jun 29 2006 - 09:44:54 PDT)
AMBER: problems with cpinutil.pl Abhilash Mohan (Fri Jun 23 2006 - 10:00:36 PDT)
AMBER: how to create 2'-5' RNA sethl.gatech.edu (Fri Jun 23 2006 - 14:13:57 PDT)
- Re: AMBER: how to create 2'-5' RNA FyD (Fri Jun 23 2006 - 23:29:43 PDT)
- Re: AMBER: how to create 2'-5' RNA Ilyas Yildirim (Mon Jun 26 2006 - 15:52:10 PDT)
AMBER: Second derivative matrix mbrut.laas.fr (Sat Jun 24 2006 - 04:21:27 PDT)
- Re: AMBER: Second derivative matrix David A. Case (Tue Jun 27 2006 - 01:36:57 PDT)
AMBER: about GBSA sishi.tang.utoronto.ca (Sun Jun 25 2006 - 11:45:11 PDT)
AMBER: periodic boundary condition in the X and Y dimensions only hbluo (Mon Jun 26 2006 - 14:58:00 PDT)
AMBER: periodic boundary condition in the X and Y dimensions only hbluo (Mon Jun 26 2006 - 15:15:51 PDT)
AMBER:Checkoverlap query sangeeta.bioinfo.ernet.in (Mon Jun 26 2006 - 05:12:56 PDT)
AMBER: Amber minimization with multiple restraints Qingning Shu (Mon Jun 26 2006 - 10:23:33 PDT)
- Re: AMBER: Amber minimization with multiple restraints Myunggi Yi (Wed Jun 28 2006 - 12:53:12 PDT)
  - Re: AMBER: Amber minimization with multiple restraints Myunggi Yi (Wed Jun 28 2006 - 12:56:49 PDT)
AMBER: Curves and Average Structures Lauren O'Neil (Mon Jun 26 2006 - 10:26:46 PDT)
- Re: AMBER: Curves and Average Structures David E. Konerding (Mon Jun 26 2006 - 12:42:05 PDT)
  - Re: AMBER: Curves and Average Structures Angelo (Tue Jun 27 2006 - 01:57:47 PDT)
AMBER: manual/prmtop/missing bonds section David Mobley (Mon Jun 26 2006 - 13:27:39 PDT)
- Re: AMBER: manual/prmtop/missing bonds section David A. Case (Wed Jul 05 2006 - 09:09:06 PDT)
AMBER: creating RNA, nucgen / leap sethl.gatech.edu (Mon Jun 26 2006 - 13:59:46 PDT)
AMBER: MM-PBSA and gaff atom types anna ferrari (Tue Jun 27 2006 - 02:28:03 PDT)
- Re: AMBER: MM-PBSA and gaff atom types Ray Luo (Tue Jun 27 2006 - 19:47:51 PDT)
  - Re: AMBER: MM-PBSA and gaff atom types anna ferrari (Wed Jun 28 2006 - 09:43:41 PDT)
AMBER: Leap: neutralising the charge Miguel Ferreira (Tue Jun 27 2006 - 02:49:36 PDT)
- Re: AMBER: Leap: neutralising the charge FyD (Tue Jun 27 2006 - 04:19:08 PDT)
AMBER: rgbmax--something wrong with my input file? Kenley Barrett (Tue Jun 27 2006 - 14:10:27 PDT)
- RE: AMBER: rgbmax--something wrong with my input file? Ross Walker (Tue Jun 27 2006 - 15:52:06 PDT)
- Re: AMBER: rgbmax--something wrong with my input file? tmarch.coin.org (Wed Jun 28 2006 - 14:37:19 PDT)
AMBER: Question about ptraj setup for phase angles (P) of ribose sugar puckering Cenk Andac (Wed Jun 28 2006 - 03:46:49 PDT)
- Re: AMBER: Question about ptraj setup for phase angles (P) of ribose sugar puckering Thomas Cheatham (Wed Jun 28 2006 - 09:22:42 PDT)
  - AMBER: Amber 9 installation problem Cenk Andac (Thu Oct 19 2006 - 08:43:02 PDT)
    - Re: AMBER: Amber 9 installation problem Mark Williamson (Thu Oct 19 2006 - 09:12:01 PDT)
    - Re: AMBER: Amber 9 installation problem Cenk Andac (Thu Oct 19 2006 - 10:55:54 PDT)
    - Re: AMBER: Amber 9 installation problem David A. Case (Thu Oct 19 2006 - 11:43:35 PDT)
    - Re: AMBER: Amber 9 installation problem Cenk Andac (Thu Oct 19 2006 - 12:13:58 PDT)
AMBER: REM test failures on IA-64 architecture Glass, Kevin A (Wed Jun 28 2006 - 08:28:07 PDT)
- Re: AMBER: REM test failures on IA-64 architecture Asim Okur (Wed Jun 28 2006 - 13:09:08 PDT)
AMBER: remlog option changed in amber9? Alik Widge (Wed Jun 28 2006 - 12:36:47 PDT)
- Re: AMBER: remlog option changed in amber9? Carlos Simmerling (Wed Jun 28 2006 - 14:11:22 PDT)
  - Re: AMBER: remlog option changed in amber9? Alik Widge (Wed Jun 28 2006 - 14:24:07 PDT)
    - Re: AMBER: remlog option changed in amber9? Carlos Simmerling (Wed Jun 28 2006 - 14:37:54 PDT)
AMBER: problem with pattern searching in mm_pbsa_calceneent.pm, Amber8, when salt>0 using delphi version 4 Lwin, ThuZar (Wed Jun 28 2006 - 17:58:14 PDT)
- AMBER: MM-PBSA questions Miguel Ferreira (Wed Jun 28 2006 - 18:26:14 PDT)
  - Re: AMBER: MM-PBSA questions Ray Luo (Thu Jun 29 2006 - 22:56:42 PDT)
AMBER: How to calculate binding free energy using MM-PBSA Xioling Chuang (Thu Jun 29 2006 - 02:38:58 PDT)
- Re: AMBER: How to calculate binding free energy using MM-PBSA Cenk Andac (Thu Jun 29 2006 - 03:38:11 PDT)
  - Re: AMBER: How to calculate binding free energy using MM-PBSA Xioling Chuang (Thu Jun 29 2006 - 21:16:48 PDT)
    - Re: AMBER: How to calculate binding free energy using MM-PBSA Cenk Andac (Fri Jun 30 2006 - 05:22:08 PDT)
    - Re: AMBER: How to calculate binding free energy using MM-PBSA Xioling Chuang (Fri Jun 30 2006 - 21:39:09 PDT)
AMBER: Strange problems with PMEMD on Intel Xeons with Infiniband Fabian Boes (Thu Jun 29 2006 - 08:58:26 PDT)
- Re: AMBER: Strange problems with PMEMD on Intel Xeons with Infiniband Robert Duke (Thu Jun 29 2006 - 09:37:53 PDT)
  - Re: AMBER: Strange problems with PMEMD on Intel Xeons with Infiniband Fabian Boes (Thu Jun 29 2006 - 10:53:23 PDT)
- Re: AMBER: Strange problems with PMEMD on Intel Xeons with Infiniband Robert Duke (Thu Jun 29 2006 - 11:24:14 PDT)
- AMBER: Re: Strange problems with PMEMD on Intel Xeons with Infiniband Fabian Boes (Thu Jul 06 2006 - 01:29:35 PDT)
  - Re: AMBER: Re: Strange problems with PMEMD on Intel Xeons with Infiniband Robert Duke (Thu Jul 06 2006 - 05:43:24 PDT)
AMBER: Having trouble getting Iron parameters for QM/MM zachary hartman (Thu Jun 29 2006 - 12:23:06 PDT)
- Re: AMBER: Having trouble getting Iron parameters for QM/MM Ken Merz (Thu Jun 29 2006 - 12:54:45 PDT)
  - Re: AMBER: Having trouble getting Iron parameters for QM/MM FyD (Thu Jun 29 2006 - 13:55:14 PDT)
  - RE: AMBER: Having trouble getting Iron parameters for QM/MM Ross Walker (Fri Jun 30 2006 - 01:54:28 PDT)
AMBER: inconsistence in MM_PBSA between mm_pbsa .pl and mm_pbsa_statistics.pl yxiong99 (Thu Jun 29 2006 - 13:49:50 PDT)
- Re: AMBER: inconsistence in MM_PBSA between mm_pbsa .pl and mm_pbsa_statistics.pl Ray Luo (Thu Jun 29 2006 - 17:47:13 PDT)
  - Re: AMBER: inconsistence in MM_PBSA between mm_pbsa .pl and mm_pbsa_statistics.pl JunJun Liu (Thu Jun 29 2006 - 16:56:34 PDT)
AMBER: RDII and epsilon of ho and hw wrong in gaff.dat ??!!! Christophe Guilbert (Thu Jun 29 2006 - 14:48:31 PDT)
- Re: AMBER: RDII and epsilon of ho and hw wrong in gaff.dat ??!!! Bill Ross (Fri Jun 30 2006 - 11:42:53 PDT)
Re: AMBER: RDII and epsilon of ho and hw wrong in gaff.dat ??!!! Bill Ross (Thu Jun 29 2006 - 16:46:17 PDT)
- Re: AMBER: RDII and epsilon of ho and hw wrong in gaff.dat ??!!! Christophe Guilbert (Thu Jun 29 2006 - 18:06:29 PDT)
AMBER: general question about hydrogen bond energy vs electrostatic energy Eric Hu (Thu Jun 29 2006 - 17:58:24 PDT)
AMBER: tleap BUG to write a pdb file if atom name contains 4 chars. Christophe Guilbert (Thu Jun 29 2006 - 18:28:31 PDT)
- Re: AMBER: tleap BUG to write a pdb file if atom name contains 4 chars. David A. Case (Wed Jul 05 2006 - 14:31:14 PDT)
  - Re: AMBER: tleap BUG to write a pdb file if atom name contains 4 chars. Christophe Guilbert (Wed Jul 05 2006 - 16:55:49 PDT)
    - Re: AMBER: tleap BUG to write a pdb file if atom name contains 4 chars. David A. Case (Wed Jul 05 2006 - 18:54:38 PDT)
    - Re: AMBER: tleap BUG to write a pdb file if atom name contains 4 chars. Christophe Guilbert (Wed Jul 05 2006 - 19:50:24 PDT)
AMBER: GB simulation problem Anthony Cruz (Fri Jun 30 2006 - 09:49:53 PDT)
AMBER: NAMOT sethl.gatech.edu (Fri Jun 30 2006 - 12:17:46 PDT)
- Re: AMBER: NAMOT Andreas Svrcek-Seiler (Mon Jul 03 2006 - 04:02:57 PDT)
AMBER: pmemd9 issue Brent Krueger (Sat Jul 01 2006 - 20:45:11 PDT)
- Re: AMBER: pmemd9 issue Robert Duke (Sun Jul 02 2006 - 04:12:11 PDT)
- Re: AMBER: pmemd9 issue Robert Duke (Sun Jul 02 2006 - 04:46:21 PDT)
AMBER: R.E.D II Franck_Vendeix.ncsu.edu (Sun Jul 02 2006 - 19:11:39 PDT)
- Re: AMBER: R.E.D II FyD (Sun Jul 02 2006 - 23:39:20 PDT)
  - Re: AMBER: R.E.D II a a (Mon Jul 03 2006 - 02:35:35 PDT)
    - Re: AMBER: R.E.D II FyD (Mon Jul 03 2006 - 03:03:19 PDT)
  - AMBER: Tutorial 4-section 4 (plc.frcmod) a a (Mon Jul 03 2006 - 02:41:44 PDT)
    - AMBER: Tutorial 4-section 4 - VDW parameters a a (Mon Jul 03 2006 - 02:49:31 PDT)
    - Re: AMBER: Tutorial 4-section 4 (plc.frcmod) Mark Williamson (Mon Jul 03 2006 - 05:46:08 PDT)
    - AMBER: Tutorial 4-section 4 DIHE in frcmod file. a a (Mon Jul 03 2006 - 19:13:04 PDT)
    - Re: AMBER: Tutorial 4-section 4 DIHE in frcmod file. Ilyas Yildirim (Mon Jul 03 2006 - 20:47:22 PDT)
  - Re: AMBER: R.E.D II Franck_Vendeix.ncsu.edu (Mon Jul 03 2006 - 23:23:22 PDT)
    - Re: AMBER: R.E.D II FyD (Tue Jul 04 2006 - 00:47:51 PDT)
    - Re: AMBER: R.E.D II Franck_Vendeix.ncsu.edu (Tue Jul 04 2006 - 07:29:59 PDT)
    - Re: AMBER: R.E.D II FyD (Tue Jul 04 2006 - 09:33:46 PDT)
    - Re: AMBER: R.E.D II Franck_Vendeix.ncsu.edu (Tue Jul 04 2006 - 21:33:21 PDT)
    - Re: AMBER: R.E.D II FyD (Tue Jul 04 2006 - 23:55:13 PDT)
    - Re: AMBER: R.E.D II Franck Vendeix (Wed Jul 05 2006 - 07:56:24 PDT)
AMBER: compiling amber9 nadiav.soton.ac.uk (Mon Jul 03 2006 - 01:50:44 PDT)
- RE: AMBER: compiling amber9 Ross Walker (Mon Jul 03 2006 - 03:48:10 PDT)
  - RE: AMBER: compiling amber9 nadiav.soton.ac.uk (Tue Jul 04 2006 - 07:31:02 PDT)
AMBER: fixing residues Prabhakar. G. (Mon Jul 03 2006 - 05:16:46 PDT)
- RE: AMBER: fixing residues a a (Mon Jul 03 2006 - 19:47:08 PDT)
  - Re: AMBER: fixing residues Prabhakar. G. (Wed Jul 05 2006 - 20:57:38 PDT)
AMBER: 2-D free energy surface using WHAM Atsutoshi Okabe (Mon Jul 03 2006 - 05:08:01 PDT)
- Re: AMBER: 2-D free energy surface using WHAM David Mobley (Mon Jul 03 2006 - 07:33:24 PDT)
AMBER: multiple "restraint_wt" in sander kanazta1.yahoo.co.jp (Mon Jul 03 2006 - 07:12:21 PDT)
- Re: AMBER: multiple "restraint_wt" in sander Viktor Hornak (Mon Jul 03 2006 - 07:43:44 PDT)
AMBER: compilation of amber8 on Xeon x86_64 x86_64 x86_64 GNU/Linux frustrated modeller (Mon Jul 03 2006 - 10:51:13 PDT)
- Re: AMBER: compilation of amber8 on Xeon x86_64 x86_64 x86_64 GNU/Linux David LeBard (Mon Jul 03 2006 - 11:15:50 PDT)
  - Re: AMBER: compilation of amber8 on Xeon x86_64 x86_64 x86_64 GNU/Linux frustrated modeller (Mon Jul 03 2006 - 11:40:50 PDT)
- Re: AMBER: compilation of amber8 on Xeon x86_64 x86_64 x86_64 GNU/Linux David A. Case (Wed Jul 05 2006 - 15:22:42 PDT)
  - Re: AMBER: compilation of amber8 on Xeon x86_64 x86_64 x86_64 GNU/Linux frustrated modeller (Wed Jul 05 2006 - 17:29:52 PDT)
    - Re: AMBER: compilation of amber8 on Xeon x86_64 x86_64 x86_64 GNU/Linux David A. Case (Thu Jul 06 2006 - 09:43:36 PDT)
  - AMBER: FIX conformation of a ligand a a (Wed Jul 05 2006 - 19:17:23 PDT)
    - Re: AMBER: FIX conformation of a ligand David A. Case (Thu Jul 06 2006 - 07:30:01 PDT)
  - AMBER: amber9 compilation problems on EM64T xeon system hayden (Thu Jul 06 2006 - 11:11:04 PDT)
    - RE: AMBER: amber9 compilation problems on EM64T xeon system Yong Duan (Thu Jul 06 2006 - 12:38:05 PDT)
    - RE: AMBER: amber9 compilation problems on EM64T xeon system Ross Walker (Thu Jul 06 2006 - 20:06:15 PDT)
    - RE: AMBER: amber9 compilation problems on EM64T xeon system hayden (Mon Jul 10 2006 - 09:57:44 PDT)
RE: AMBER: compilation of amber8 on Xeon x86_64 x86_64 x86_64 GNU/Linux. . Lwin, ThuZar (Mon Jul 03 2006 - 12:02:31 PDT)
- RE: AMBER: compilation of amber8 on Xeon x86_64 x86_64 x86_64 GNU/Linux. . hayden (Mon Jul 03 2006 - 17:28:37 PDT)
AMBER: hbond analysis Claire Zerafa (Mon Jul 03 2006 - 14:06:22 PDT)
- Re: AMBER: hbond analysis Thomas Cheatham (Mon Jul 03 2006 - 12:19:57 PDT)
AMBER: Dihedral analysis Claire Zerafa (Mon Jul 03 2006 - 14:25:33 PDT)
- Re: AMBER: Dihedral analysis Thomas Cheatham (Mon Jul 03 2006 - 12:47:42 PDT)
AMBER: MM-PBSA: Problem when Generating Snapshots Zu Thur Yew (Tue Jul 04 2006 - 00:20:39 PDT)
AMBER: Constant pH simulation : LYS residue Guillaume Bollot (Tue Jul 04 2006 - 04:13:00 PDT)
AMBER: hbond analysis2 Claire Zerafa (Tue Jul 04 2006 - 07:00:35 PDT)
AMBER: Can you use VMD to measure bond angles/lengths sethl.gatech.edu (Tue Jul 04 2006 - 08:24:49 PDT)
- Re: AMBER: Can you use VMD to measure bond angles/lengths Andreas Svrcek-Seiler (Tue Jul 04 2006 - 09:09:21 PDT)
- Re: AMBER: Can you use VMD to measure bond angles/lengths Mark Williamson (Tue Jul 04 2006 - 09:06:59 PDT)
AMBER: error on running parallel sander on remote node- amber9 Chengwen Chen (Wed Jul 05 2006 - 00:46:11 PDT)
AMBER: problem with saving the parameters file amere swathi (Wed Jul 05 2006 - 01:50:40 PDT)
- Re: AMBER: problem with saving the parameters file David A. Case (Wed Jul 05 2006 - 11:09:12 PDT)
AMBER: analysis of atoms in a range during simulation pkb bioinfo (Wed Jul 05 2006 - 05:41:58 PDT)
AMBER: Question about Energy calculation using MM-PBSA scripts & Imaging Zu Thur Yew (Wed Jul 05 2006 - 10:03:13 PDT)
- Re: AMBER: Question about Energy calculation using MM-PBSA scripts & Imaging David A. Case (Wed Jul 05 2006 - 10:50:52 PDT)
AMBER: Namot on AMD 64 possible sethl.gatech.edu (Wed Jul 05 2006 - 10:05:26 PDT)
- Re: AMBER: Namot on AMD 64 possible Andreas Svrcek-Seiler (Wed Jul 05 2006 - 11:08:44 PDT)
AMBER: New united atom force field and GB solvation model in amber9 (leaprc.ff03ua) Ray Luo (Wed Jul 05 2006 - 10:45:49 PDT)
Re: AMBER: problem with saving the parameters file Bill Ross (Wed Jul 05 2006 - 11:23:05 PDT)
AMBER: igb=2 and "bad atom type" conflict Evan Kelly (Wed Jul 05 2006 - 12:25:16 PDT)
- Re: AMBER: igb=2 and "bad atom type" conflict Scott Pendley (Wed Jul 05 2006 - 13:22:43 PDT)
  - Re: AMBER: igb=2 and "bad atom type" conflict Evan Kelly (Thu Jul 06 2006 - 08:45:10 PDT)
- Re: AMBER: igb=2 and "bad atom type" conflict Evan Kelly (Thu Jul 06 2006 - 09:21:06 PDT)
- Re: AMBER: igb=2 and "bad atom type" conflict Evan Kelly (Thu Jul 06 2006 - 15:01:39 PDT)
  - Re: AMBER: igb=2 and "bad atom type" conflict David A. Case (Fri Jul 07 2006 - 14:42:09 PDT)
AMBER: Addendum: igb=2 and "bad atom type" conflict Evan Kelly (Wed Jul 05 2006 - 12:29:10 PDT)
AMBER: change atom in a DNA double strand Carra, Claudio $JSC-SK$[USRA] (Wed Jul 05 2006 - 14:09:23 PDT)
- Re: AMBER: change atom in a DNA double strand David A. Case (Thu Jul 06 2006 - 09:57:12 PDT)
- RE: AMBER: change atom in a DNA double strand Carra, Claudio $JSC-SK$[USRA] (Mon Jul 10 2006 - 12:24:02 PDT)
AMBER: PTRAJ OUTPUT Cporteli (Wed Jul 05 2006 - 16:02:47 PDT)
RE: AMBER: compilation of amber8 on Xeon x86_64 x86_64 x86_64 GNU/Linux. .. . Lwin, ThuZar (Wed Jul 05 2006 - 16:01:25 PDT)
- RE: AMBER: compilation of amber8 on Xeon x86_64 x86_64 x86_64 GNU/Linux. .. . hayden (Thu Jul 06 2006 - 05:02:13 PDT)
Re: AMBER: PTRAJ OUTPUT Bill Ross (Wed Jul 05 2006 - 16:43:57 PDT)
AMBER: Units for Leonard-Jones potential parameters Vanessa Oklejas (Wed Jul 05 2006 - 20:02:59 PDT)
- Re: AMBER: Units for Leonard-Jones potential parameters David A. Case (Thu Jul 06 2006 - 09:45:00 PDT)
AMBER: analysis of ATOMs in ´certain range distance during simulation pkb bioinfo (Wed Jul 05 2006 - 20:37:46 PDT)
- Re: AMBER: analysis of ATOMs in ´certain range distance during simulation Scott Pendley (Thu Jul 06 2006 - 14:47:57 PDT)
  - Re: AMBER: analysis of ATOMs in ´certain range distance during simulation Myunggi Yi (Thu Jul 06 2006 - 15:03:12 PDT)
AMBER: Compiling AMBER 9 on windows XP using cygwin Gobind Bisht (Wed Jul 05 2006 - 22:17:54 PDT)
- Re: AMBER: Compiling AMBER 9 on windows XP using cygwin Emilio Xavier Esposito (Thu Jul 06 2006 - 06:40:39 PDT)
  - Re: AMBER: Compiling AMBER 9 on windows XP using cygwin Gobind Bisht (Thu Jul 06 2006 - 08:36:28 PDT)
    - Re: AMBER: Compiling AMBER 9 on windows XP using cygwin Gustavo Seabra (Thu Jul 06 2006 - 08:50:05 PDT)
    - Re: AMBER: Compiling AMBER 9 on windows XP using cygwin Emilio Xavier Esposito (Thu Jul 06 2006 - 09:08:34 PDT)
    - Re: AMBER: Compiling AMBER 9 on windows XP using cygwin Gobind Bisht (Fri Jul 07 2006 - 07:13:37 PDT)
    - Re: AMBER: Compiling AMBER 9 on windows XP using cygwin Gustavo Seabra (Fri Jul 07 2006 - 07:36:50 PDT)
    - Re: AMBER: Compiling AMBER 9 on windows XP using cygwin Gobind Bisht (Fri Jul 07 2006 - 08:48:35 PDT)
    - Re: AMBER: Compiling AMBER 9 on windows XP using cygwin Gustavo Seabra (Fri Jul 07 2006 - 09:00:36 PDT)
    - Re: AMBER: Compiling AMBER 9 on windows XP using cygwin Emilio Xavier Esposito (Fri Jul 07 2006 - 09:13:40 PDT)
    - Re: AMBER: Compiling AMBER 9 on windows XP using cygwin Gobind Bisht (Fri Jul 07 2006 - 09:39:31 PDT)
- Re: AMBER: Compiling AMBER 9 on windows XP using cygwin David A. Case (Thu Jul 06 2006 - 08:16:11 PDT)
AMBER: working with large strained system Tanya Johannsen (Wed Jul 05 2006 - 19:29:58 PDT)
- Re: AMBER: working with large strained system Carlos Simmerling (Thu Jul 06 2006 - 06:41:39 PDT)
- Re: AMBER: working with large strained system Robert Duke (Thu Jul 06 2006 - 07:06:48 PDT)
AMBER: Problem with bcc flag of antechamber Gobind Bisht (Thu Jul 06 2006 - 10:00:49 PDT)
- RE: AMBER: Problem with bcc flag of antechamber Junmei Wang (Thu Jul 06 2006 - 10:53:37 PDT)
Re: AMBER: working with large strained system Bill Ross (Thu Jul 06 2006 - 10:06:57 PDT)
AMBER: Problem with bcc flag of antechamber..continued Gobind Bisht (Thu Jul 06 2006 - 10:08:45 PDT)
- Re: AMBER: Problem with bcc flag of antechamber..continued amit.mbu.iisc.ernet.in (Fri Jul 07 2006 - 03:09:32 PDT)
AMBER: Problem with donor/acceptor specification in ptraj hbonding facilities Thomas Steinbrecher (Thu Jul 06 2006 - 16:02:19 PDT)
AMBER: Sander NOE violations Andrew Box (Thu Jul 06 2006 - 16:55:59 PDT)
- Re: AMBER: Sander NOE violations David A. Case (Thu Jul 06 2006 - 18:01:19 PDT)
  - Re: AMBER: Sander NOE violations Andrew Box (Thu Jul 06 2006 - 18:32:21 PDT)
    - Re: AMBER: Sander NOE violations David A. Case (Thu Jul 06 2006 - 18:41:28 PDT)
AMBER: Why "ho" and "hw" VDW's radius are set to 0 in "gaff.dat" ? Christophe Guilbert (Thu Jul 06 2006 - 17:51:49 PDT)
- Re: AMBER: Why "ho" and "hw" VDW's radius are set to 0 in "gaff.dat" ? David A. Case (Thu Jul 06 2006 - 18:48:12 PDT)
- Re: AMBER: Why "ho" and "hw" VDW's radius are set to 0 in "gaff.dat" ? Carlos Simmerling (Thu Jul 06 2006 - 18:51:58 PDT)
AMBER: Amber8.0 predictied pKa problem for a Lysine! Guillaume Bollot (Fri Jul 07 2006 - 02:38:08 PDT)
- Re: AMBER: Amber8.0 predictied pKa problem for a Lysine! Myunggi Yi (Fri Jul 07 2006 - 09:14:42 PDT)
AMBER: calculating dihedral angles, radius of gyration madhumalar.bii-sg.org (Fri Jul 07 2006 - 02:57:14 PDT)
AMBER: Antechamber RESP charges do not sum to zero even with -nc 0 flag Bob Johnson (Fri Jul 07 2006 - 07:55:32 PDT)
- RE: AMBER: Antechamber RESP charges do not sum to zero even with -nc 0 flag Junmei Wang (Fri Jul 07 2006 - 10:04:00 PDT)
  - RE: AMBER: Antechamber RESP charges do not sum to zero even with -nc 0 flag Bob Johnson (Fri Jul 07 2006 - 10:35:59 PDT)
    - Re: AMBER: Antechamber RESP charges do not sum to zero even with -nc 0 flag David A. Case (Fri Jul 07 2006 - 14:06:34 PDT)
AMBER: script to extract data from minimization .out file Tanya Johannsen (Fri Jul 07 2006 - 09:55:44 PDT)
- Re: AMBER: script to extract data from minimization .out file Gustavo Seabra (Fri Jul 07 2006 - 10:35:32 PDT)
- Re: AMBER: script to extract data from minimization .out file sangeeta.bioinfo.ernet.in (Sat Jul 08 2006 - 03:23:52 PDT)
  - Re: AMBER: script to extract data from minimization .out file sangeeta.bioinfo.ernet.in (Sat Jul 08 2006 - 03:41:44 PDT)
- RE: AMBER: script to extract data from minimization .out file Ross Walker (Sat Jul 08 2006 - 08:47:17 PDT)
AMBER: Error in loading molecule in tleap Gobind Bisht (Fri Jul 07 2006 - 11:01:45 PDT)
- Re: AMBER: Error in loading molecule in tleap David A. Case (Fri Jul 07 2006 - 14:11:15 PDT)
  - Re: AMBER: Error in loading molecule in tleap Gobind Bisht (Fri Jul 07 2006 - 14:18:08 PDT)
AMBER: AMBER 8: Problem with MPI_Finalize jrd (Fri Jul 07 2006 - 11:24:08 PDT)
- Re: AMBER: AMBER 8: Problem with MPI_Finalize David A. Case (Fri Jul 07 2006 - 14:29:10 PDT)
AMBER: convert chemical structure to pdb file Baker, Bo-Yang (Fri Jul 07 2006 - 11:44:25 PDT)
- Re: AMBER: convert chemical structure to pdb file Gustavo Seabra (Fri Jul 07 2006 - 11:56:37 PDT)
AMBER: MM/PBSA Wei Chen (Fri Jul 07 2006 - 14:20:47 PDT)
- Re: AMBER: MM/PBSA Ray Luo (Fri Jul 07 2006 - 17:26:28 PDT)
  - Re: AMBER: MM/PBSA Wei Chen (Sat Jul 08 2006 - 11:29:06 PDT)
AMBER: Error in running MD in sander Gobind Bisht (Sat Jul 08 2006 - 10:20:10 PDT)
- RE: AMBER: Error in running MD in sander Ross Walker (Sat Jul 08 2006 - 10:38:15 PDT)
AMBER: peptide simulation before docking jitrayut jitonnom (Sat Jul 08 2006 - 13:45:28 PDT)
AMBER: Fwd: ADL: peptide simulation before docking jitrayut jitonnom (Sun Jul 09 2006 - 02:26:59 PDT)
AMBER: (no subject) Andrew Box (Sun Jul 09 2006 - 15:49:02 PDT)
- Re: [UCE]AMBER: (no subject) Thomas Cheatham (Sun Jul 09 2006 - 16:18:49 PDT)
- Re: AMBER: (no subject) David A. Case (Sun Jul 09 2006 - 16:20:30 PDT)
AMBER: Replica exchange Atsutoshi Okabe (Mon Jul 10 2006 - 04:38:17 PDT)
- Re: AMBER: Replica exchange Carlos Simmerling (Mon Jul 10 2006 - 05:13:48 PDT)
  - RE: AMBER: Replica exchange Atsutoshi Okabe (Mon Jul 10 2006 - 19:43:17 PDT)
    - Re: AMBER: Replica exchange Carlos Simmerling (Tue Jul 11 2006 - 05:49:20 PDT)
    - RE: AMBER: Replica exchange Atsutoshi Okabe (Tue Jul 11 2006 - 21:13:38 PDT)
    - Re: AMBER: Replica exchange Carlos Simmerling (Wed Jul 12 2006 - 07:25:14 PDT)
AMBER: residue and atom number Andrea Bortolato (Mon Jul 10 2006 - 05:57:05 PDT)
- Re: AMBER: residue and atom number David A. Case (Mon Jul 10 2006 - 08:09:29 PDT)
AMBER: about restraint format. Qingning Shu (Mon Jul 10 2006 - 06:11:16 PDT)
- Re: AMBER: about restraint format. David A. Case (Mon Jul 10 2006 - 08:10:11 PDT)
AMBER: small bug in ambmask (amber9) Kateryna Miroshnychenko (Mon Jul 10 2006 - 07:53:02 PDT)
- Re: AMBER: small bug in ambmask (amber9) David A. Case (Mon Jul 10 2006 - 08:39:38 PDT)
AMBER: program to calculate net charge of a ligand for Antechamber Christophe Guilbert (Mon Jul 10 2006 - 18:30:39 PDT)
- Re: AMBER: program to calculate net charge of a ligand for Antechamber David Mobley (Mon Jul 10 2006 - 21:18:36 PDT)
AMBER: Question about NSCM Xiaowei (David) Li (Tue Jul 11 2006 - 01:25:48 PDT)
- Re: AMBER: Question about NSCM David A. Case (Tue Jul 11 2006 - 08:02:11 PDT)
AMBER: Amber 8.0 no numerical value and offset for the predicted pKa of many titrable residue!! Guillaume Bollot (Tue Jul 11 2006 - 04:19:29 PDT)
- Re: AMBER: Amber 8.0 no numerical value and offset for the predicted pKa of many titrable residue!! Myunggi Yi (Tue Jul 11 2006 - 09:00:58 PDT)
AMBER: Amber crashed due to power surge and giving problems.. Gobind Bisht (Tue Jul 11 2006 - 07:46:54 PDT)
- Re: AMBER: Amber crashed due to power surge and giving problems.. Carlos Simmerling (Tue Jul 11 2006 - 08:09:21 PDT)
  - Re: AMBER: Amber crashed due to power surge and giving problems.. Gobind Bisht (Tue Jul 11 2006 - 10:13:36 PDT)
    - Re: AMBER: Amber crashed due to power surge and giving problems.. David A. Case (Tue Jul 11 2006 - 11:55:16 PDT)
    - Re: AMBER: Amber crashed due to power surge and giving problems.. Carlos Simmerling (Tue Jul 11 2006 - 12:05:48 PDT)
    - Re: AMBER: Amber crashed due to power surge and giving problems.. Gobind Bisht (Tue Jul 11 2006 - 12:17:46 PDT)
AMBER: Ptraj: Hbond time series Zu Thur Yew (Tue Jul 11 2006 - 08:19:34 PDT)
- Re: AMBER: Ptraj: Hbond time series Chng Choon-Peng (Tue Jul 11 2006 - 16:56:20 PDT)
AMBER: applying restraints on pre-defined planes Vlad Cojocaru (Tue Jul 11 2006 - 08:34:07 PDT)
- Re: AMBER: applying restraints on pre-defined planes David A. Case (Tue Jul 11 2006 - 16:34:52 PDT)
AMBER: problem about Distance Restraints. Qingning Shu (Tue Jul 11 2006 - 20:38:48 PDT)
- Re: AMBER: problem about Distance Restraints. David A. Case (Wed Jul 12 2006 - 16:33:54 PDT)
AMBER: iso command and a cubic box Patricia Hunt (Wed Jul 12 2006 - 00:03:03 PDT)
- Re: AMBER: iso command and a cubic box David A. Case (Wed Jul 12 2006 - 12:00:25 PDT)
AMBER: Where is the repulsion energy ( part of nonpolar solvation energy) in MM_PBSA ? Changge Ji (Tue Jul 11 2006 - 23:03:30 PDT)
- Re: AMBER: Where is the repulsion energy ( part of nonpolar solvation energy) in MM_PBSA ? Ray Luo (Thu Jul 13 2006 - 14:21:30 PDT)
AMBER: simulate a self-assemble process in vacuum Eric Hu (Wed Jul 12 2006 - 16:22:58 PDT)
- Re: AMBER: simulate a self-assemble process in vacuum Gustavo Seabra (Thu Jul 13 2006 - 06:22:15 PDT)
  - Re: AMBER: simulate a self-assemble process in vacuum Eric Hu (Thu Jul 20 2006 - 14:43:35 PDT)
AMBER: Antechamber 1.26 is released Junmei Wang (Wed Jul 12 2006 - 16:42:32 PDT)
AMBER: Etot has downward drift in 'NVE' ensemble John S. Zintsmaster (Wed Jul 12 2006 - 19:01:08 PDT)
- Re: AMBER: Etot has downward drift in 'NVE' ensemble Thomas Cheatham (Wed Jul 12 2006 - 19:43:11 PDT)
AMBER: Free energy calculated from mm_pbsa gtg549i.mail.gatech.edu (Thu Jul 13 2006 - 00:26:44 PDT)
AMBER: New (small) Topology without solvent from previous one (big) with solvent j j (Thu Jul 13 2006 - 03:50:55 PDT)
- Re: AMBER: New (small) Topology without solvent from previous one (big) with solvent Thomas Cheatham (Thu Jul 13 2006 - 09:34:00 PDT)
  - Re: AMBER: New (small) Topology without solvent from previous one (big) with solvent j j (Thu Jul 13 2006 - 10:59:00 PDT)
    - Re: AMBER: New (small) Topology without solvent from previous one (big) with solvent David A. Case (Thu Jul 13 2006 - 11:14:20 PDT)
    - Re: AMBER: New (small) Topology without solvent from previous one (big) with solvent j j (Fri Jul 14 2006 - 01:40:10 PDT)
- Re: AMBER: New (small) Topology without solvent from previous one (big) with solvent Petr Kulhanek (Fri Jul 14 2006 - 00:44:09 PDT)
  - Re: AMBER: New (small) Topology without solvent from previous one (big) with solvent j j (Fri Jul 14 2006 - 01:48:33 PDT)
    - Re: AMBER: New (small) Topology without solvent from previous one (big) with solvent Petr Kulhanek (Fri Jul 14 2006 - 02:24:26 PDT)
AMBER: New (small) Topology without solvent from previous one (big) with solvent j j (Thu Jul 13 2006 - 03:47:15 PDT)
AMBER: Ringof dna Flora Mactavish (Thu Jul 13 2006 - 06:14:22 PDT)
- Re: AMBER: Ringof dna David A. Case (Thu Jul 13 2006 - 09:54:07 PDT)
  - Re: AMBER: Ringof dna f m (Thu Jul 13 2006 - 10:00:48 PDT)
    - Re: AMBER: Ring of dna f m (Fri Jul 14 2006 - 06:27:03 PDT)
    - Re: AMBER: Ring of dna j j (Fri Jul 14 2006 - 07:25:59 PDT)
    - Re: AMBER: Ring of dna Bill Ross (Fri Jul 14 2006 - 10:23:07 PDT)
    - Re: AMBER: Ring of dna f m (Sat Jul 15 2006 - 09:37:59 PDT)
    - Re: AMBER: Ring of dna Bill Ross (Sat Jul 15 2006 - 10:55:07 PDT)
    - Re: AMBER: Ring of dna f m (Mon Jul 17 2006 - 04:32:01 PDT)
    - Re: AMBER: Ring of dna f m (Mon Jul 17 2006 - 06:48:33 PDT)
    - Re: AMBER: Ring of dna M. L. Dodson (Mon Jul 17 2006 - 07:56:03 PDT)
    - Re: AMBER: Ring of dna Bill Ross (Mon Jul 17 2006 - 12:15:10 PDT)
    - Re: AMBER: Ring of dna f m (Tue Jul 18 2006 - 07:30:03 PDT)
    - Re: AMBER: Ring of dna Bill Ross (Mon Jul 17 2006 - 12:19:49 PDT)
AMBER: center molecule using iwrap=1? Gustavo Seabra (Thu Jul 13 2006 - 11:21:17 PDT)
- Re: AMBER: center molecule using iwrap=1? Carlos Simmerling (Thu Jul 13 2006 - 12:00:59 PDT)
  - Re: AMBER: center molecule using iwrap=1? Gustavo Seabra (Thu Jul 13 2006 - 12:07:40 PDT)
    - Re: AMBER: center molecule using iwrap=1? Carlos Simmerling (Thu Jul 13 2006 - 12:43:37 PDT)
    - Re: AMBER: center molecule using iwrap=1? Gustavo Seabra (Thu Jul 13 2006 - 12:49:39 PDT)
AMBER: QMMM simulation amit.mbu.iisc.ernet.in (Thu Jul 13 2006 - 11:38:48 PDT)
AMBER: Compiling / Installing Amber 8 on SUSE 10.1 Seth Lilavivat (Tue Jun 13 2006 - 20:23:25 PDT)
- RE: AMBER: Compiling / Installing Amber 8 on SUSE 10.1 hayden (Fri Jul 14 2006 - 03:27:54 PDT)
- Re: AMBER: Compiling / Installing Amber 8 on SUSE 10.1 Andreas Svrcek-Seiler (Fri Jul 14 2006 - 03:38:10 PDT)
- Re: AMBER: Compiling / Installing Amber 8 on SUSE 10.1 David A. Case (Mon Jul 17 2006 - 20:00:36 PDT)
AMBER: Replica exchange with Amber9 Atsutoshi Okabe (Thu Jul 13 2006 - 23:20:21 PDT)
- Re: AMBER: Replica exchange with Amber9 Adrian Roitberg (Fri Jul 14 2006 - 06:00:14 PDT)
  - RE: AMBER: Replica exchange with Amber9 Atsutoshi Okabe (Mon Jul 17 2006 - 01:20:25 PDT)
  - RE: AMBER: Replica exchange with Amber9 Atsutoshi Okabe (Wed Jul 19 2006 - 09:22:49 PDT)
AMBER: Amber 8 on Rocks 4, Opteron, PGI 6.1 Lars Packschies (Fri Jul 14 2006 - 03:18:08 PDT)
- Re: AMBER: Amber 8 on Rocks 4, Opteron, PGI 6.1 David A. Case (Fri Jul 14 2006 - 08:00:26 PDT)
AMBER: Compiling Leap problem sethl.gatech.edu (Fri Jul 14 2006 - 14:36:38 PDT)
- Re: AMBER: Compiling Leap problem David A. Case (Fri Jul 14 2006 - 15:57:31 PDT)
AMBER: amber9 Piotr Cieplak (Fri Jul 14 2006 - 15:02:36 PDT)
- Re: AMBER: amber9 Thomas Steinbrecher (Fri Jul 14 2006 - 15:12:13 PDT)
- RE: AMBER: amber9 Ross Walker (Fri Jul 14 2006 - 15:37:19 PDT)
  - RE: AMBER: amber9 Piotr Cieplak (Fri Jul 14 2006 - 16:33:00 PDT)
AMBER: Amber 9 installation issues Glass, Kevin A (Fri Jul 14 2006 - 16:18:36 PDT)
AMBER: "noimage" option for radial distribution functions Ozlem Demir (Sun Jul 16 2006 - 14:14:31 PDT)
AMBER: Amber 8.0 MM_PBSA Stability : question about methodology Guillaume Bollot (Mon Jul 17 2006 - 05:18:41 PDT)
- Re: AMBER: Amber 8.0 MM_PBSA Stability : question about methodology David A. Case (Mon Jul 24 2006 - 12:36:30 PDT)
AMBER: Replica exchange Austin B. Yongye (Mon Jul 17 2006 - 05:31:09 PDT)
- Re: AMBER: Replica exchange Guanglei Cui (Mon Jul 17 2006 - 07:18:57 PDT)
  - Re: AMBER: Replica exchange Carlos Simmerling (Mon Jul 17 2006 - 07:44:55 PDT)
    - Re: AMBER: Replica exchange Austin B. Yongye (Mon Jul 17 2006 - 15:22:51 PDT)
    - AMBER: temperature regulation Stefano Federico Massimiliano Pieraccini (Stefano.Pieraccini) (Tue Jul 18 2006 - 01:31:04 PDT)
    - Re: AMBER: temperature regulation Carlos Simmerling (Tue Jul 18 2006 - 04:41:18 PDT)
AMBER: RMS & PCA Zu Thur Yew (Mon Jul 17 2006 - 07:55:12 PDT)
- Re: AMBER: RMS & PCA Guanglei Cui (Mon Jul 17 2006 - 11:22:56 PDT)
  - Re: AMBER: RMS & PCA Zu Thur Yew (Mon Jul 17 2006 - 22:12:35 PDT)
AMBER: Obtaining LCPO parameters for F and Fe zachary hartman (Mon Jul 17 2006 - 11:16:54 PDT)
AMBER: Creating an Intercalation site Seth Lilavivat (Sat Jun 17 2006 - 12:25:59 PDT)
- Re: AMBER: Creating an Intercalation site Thomas Cheatham (Mon Jul 17 2006 - 13:13:54 PDT)
Re: AMBER: Creating an Intercalation site Bill Ross (Mon Jul 17 2006 - 12:49:20 PDT)
AMBER: PMEMD with NMR restraint and position restraint Ting Wang (Mon Jul 17 2006 - 16:18:31 PDT)
- Re: AMBER: PMEMD with NMR restraint and position restraint Robert Duke (Mon Jul 17 2006 - 20:03:29 PDT)
- Re: AMBER: PMEMD with NMR restraint and position restraint Ting Wang (Tue Jul 18 2006 - 13:12:41 PDT)
  - Re: AMBER: PMEMD with NMR restraint and position restraint Robert Duke (Tue Jul 18 2006 - 13:49:05 PDT)
- Re: AMBER: PMEMD with NMR restraint and position restraint Robert Duke (Tue Jul 18 2006 - 19:03:42 PDT)
- Re: AMBER: PMEMD with NMR restraint and position restraint Robert Duke (Tue Jul 18 2006 - 21:34:35 PDT)
AMBER: Dynamics and Restraint problem Andrew Box (Mon Jul 17 2006 - 16:49:51 PDT)
- Re: AMBER: Dynamics and Restraint problem David A. Case (Thu Jul 27 2006 - 16:08:16 PDT)
AMBER: water diffusion Sergei Smirnov (Mon Jul 17 2006 - 17:48:59 PDT)
- Re: AMBER: water diffusion Thomas Cheatham (Mon Jul 17 2006 - 23:36:36 PDT)
AMBER: PhosphoThreonine Parms for use with ff03 Zu Thur Yew (Mon Jul 17 2006 - 22:19:15 PDT)
- Re: AMBER: PhosphoThreonine Parms for use with ff03 FyD (Tue Jul 18 2006 - 00:57:24 PDT)
- Re: AMBER: PhosphoThreonine Parms for use with ff03 Carlos Simmerling (Tue Jul 18 2006 - 04:28:20 PDT)
  - Re: AMBER: PhosphoThreonine Parms for use with ff03 Vlad Cojocaru (Thu Aug 03 2006 - 03:07:48 PDT)
    - AMBER: ff03 and ff99SB force fields Carlos Simmerling (Thu Aug 03 2006 - 03:59:11 PDT)
    - RE: AMBER: ff03 and ff99SB force fields Yong Duan (Thu Aug 03 2006 - 12:29:51 PDT)
    - Re: AMBER: ff03 and ff99SB force fields Ray Luo (Thu Aug 03 2006 - 05:21:03 PDT)
    - Re: AMBER: ff03 and ff99SB force fields Vlad Cojocaru (Fri Aug 04 2006 - 01:17:59 PDT)
    - RE: AMBER: ff03 and ff99SB force fields Yong Duan (Fri Aug 04 2006 - 04:58:51 PDT)
AMBER: Replica exchange Austin B. Yongye (Wed Jul 19 2006 - 08:04:44 PDT)
- Re: AMBER: Replica exchange Carlos Simmerling (Wed Jul 19 2006 - 09:29:33 PDT)
  - Re: AMBER: Replica exchange Austin B. Yongye (Wed Jul 19 2006 - 10:23:47 PDT)
    - Re: AMBER: Replica exchange Carlos Simmerling (Thu Jul 20 2006 - 05:32:07 PDT)
- Re: AMBER: Replica exchange Guanglei Cui (Wed Jul 19 2006 - 11:24:55 PDT)
AMBER: Long line of input Myunggi Yi (Wed Jul 19 2006 - 13:13:26 PDT)
- Re: AMBER: Long line of input hornak.csb.sunysb.edu (Wed Jul 19 2006 - 13:37:29 PDT)
  - Re: AMBER: Long line of input Myunggi Yi (Wed Jul 19 2006 - 19:03:11 PDT)
- Re: AMBER: Long line of input David A. Case (Mon Jul 24 2006 - 12:37:20 PDT)
AMBER: difficulties with antechamber: tests dont even run frustrated modeller (Wed Jul 19 2006 - 16:06:36 PDT)
- AMBER: Fwd: difficulties with antechamber: tests dont even run frustrated modeller (Wed Jul 19 2006 - 16:30:07 PDT)
  - Re: AMBER: Fwd: difficulties with antechamber: tests dont even run David A. Case (Tue Jul 25 2006 - 08:11:22 PDT)
  - RE: AMBER: Fwd: difficulties with antechamber: tests dont even run Junmei Wang (Tue Jul 25 2006 - 16:00:04 PDT)
AMBER: Myrinet or Gigabit ethernet? Mingfeng Yang (Thu Jul 20 2006 - 06:35:08 PDT)
- Re: AMBER: Myrinet or Gigabit ethernet? Robert Duke (Thu Jul 20 2006 - 07:45:45 PDT)
AMBER: Failure of iwrap in PMEMD Myunggi Yi (Thu Jul 20 2006 - 07:01:07 PDT)
- Re: AMBER: Failure of iwrap in PMEMD darden (Thu Jul 20 2006 - 07:34:47 PDT)
- Re: AMBER: Failure of iwrap in PMEMD Robert Duke (Thu Jul 20 2006 - 07:40:48 PDT)
  - Re: AMBER: Failure of iwrap in PMEMD Myunggi Yi (Thu Jul 20 2006 - 08:04:31 PDT)
- Re: AMBER: Failure of iwrap in PMEMD Robert Duke (Thu Jul 20 2006 - 14:35:58 PDT)
  - Re: AMBER: Failure of iwrap in PMEMD Myunggi Yi (Thu Jul 20 2006 - 17:24:34 PDT)
- Re: AMBER: Failure of iwrap in PMEMD Robert Duke (Fri Jul 21 2006 - 06:34:02 PDT)
  - Re: AMBER: Failure of iwrap in PMEMD Myunggi Yi (Fri Jul 21 2006 - 06:57:03 PDT)
    - RE: AMBER: Failure of iwrap in PMEMD Ross Walker (Fri Jul 21 2006 - 08:33:53 PDT)
AMBER: Gb Na+ ions DNA Conn O'Rourke (Thu Jul 20 2006 - 08:16:05 PDT)
- Re: AMBER: Gb Na+ ions DNA Andreas Svrcek-Seiler (Fri Jul 21 2006 - 02:22:21 PDT)
Re: AMBER: ptraj help - amber7 failed, amber8 read prmtop file incorrectly... fine wu (Thu Jul 20 2006 - 08:55:55 PDT)
AMBER: saltcon variable Stefano Federico Massimiliano Pieraccini (Stefano.Pieraccini) (Thu Jul 20 2006 - 12:00:01 PDT)
- Re: AMBER: saltcon variable David A. Case (Mon Jul 24 2006 - 12:38:53 PDT)
AMBER: PDB from .rst? Evan Kelly (Thu Jul 20 2006 - 13:51:09 PDT)
- Re: AMBER: PDB from .rst? Wei Zhang (Thu Jul 20 2006 - 14:04:58 PDT)
- Re: AMBER: PDB from .rst? Ilyas Yildirim (Thu Jul 20 2006 - 14:08:20 PDT)
- Re: AMBER: PDB from .rst? priya priya (Thu Jul 20 2006 - 20:24:08 PDT)
AMBER: Replica Exchange Austin B. Yongye (Thu Jul 20 2006 - 19:07:46 PDT)
- Re: AMBER: Replica Exchange Carlos Simmerling (Thu Jul 20 2006 - 19:51:19 PDT)
  - Re: AMBER: Replica Exchange Austin B. Yongye (Fri Jul 21 2006 - 06:29:08 PDT)
    - Re: AMBER: Replica Exchange Adrian Roitberg (Fri Jul 21 2006 - 06:37:26 PDT)
AMBER: Modelling dsDNA less than 10bp Lena Dolghih (Fri Jul 21 2006 - 06:15:16 PDT)
AMBER: combining different versions of AMBER Melissa Foley (Fri Jul 21 2006 - 12:25:35 PDT)
- RE: AMBER: combining different versions of AMBER Ross Walker (Fri Jul 21 2006 - 13:11:44 PDT)
  - AMBER: converting from parm to parm7 Raffaella D'Auria (Fri Jul 21 2006 - 18:26:55 PDT)
    - Re: AMBER: converting from parm to parm7 Carlos Simmerling (Sat Jul 22 2006 - 04:27:10 PDT)
    - Re: AMBER: converting from parm to parm7 & L-J coeff A and B Raffaella D'Auria (Sat Jul 22 2006 - 08:55:56 PDT)
    - Re: AMBER: converting from parm to parm7 David A. Case (Sun Jul 23 2006 - 07:47:05 PDT)
    - Re: AMBER: converting from parm to parm7 Raffaella D'Auria (Tue Jul 25 2006 - 09:00:50 PDT)
  - Re: AMBER: combining different versions of AMBER Atro Tossavainen (Sun Jul 23 2006 - 22:44:10 PDT)
AMBER: Silicon related parameters hbluo (Sat Jul 22 2006 - 10:52:17 PDT)
AMBER: Simulating an "average" DNA sequence S. Jamal Rahi (Fri Jul 21 2006 - 20:20:36 PDT)
- Re: AMBER: Simulating an "average" DNA sequence David A. Case (Sun Jul 23 2006 - 07:47:15 PDT)
AMBER: problems of running sander.MPI of amber9 on remote node Chengwen Chen (Sun Jul 23 2006 - 23:29:20 PDT)
AMBER: AMBER9 netcdf trajectory with VMD 1.8.4 Fabian Boes (Mon Jul 24 2006 - 01:01:46 PDT)
AMBER: How to resume remaining simulation pkb bioinfo (Mon Jul 24 2006 - 03:05:23 PDT)
- Re: AMBER: How to resume remaining simulation Guanglei Cui (Mon Jul 24 2006 - 08:19:56 PDT)
AMBER: Minimization problem: coordinates out of virtual box Zu Thur Yew (Mon Jul 24 2006 - 05:53:19 PDT)
AMBER: Tutorial 8, section 6: best fit before clustering sangeeta (Mon Jul 24 2006 - 06:18:05 PDT)
- RE: AMBER: Tutorial 8, section 6: best fit before clustering Ross Walker (Mon Jul 24 2006 - 07:45:59 PDT)
  - RE: AMBER: Tutorial 8, section 6: best fit before clustering sangeeta (Wed Jul 26 2006 - 06:42:47 PDT)
AMBER: library for 8oxoguanine Carra, Claudio $JSC-SK$[USRA] (Mon Jul 24 2006 - 12:50:59 PDT)
- Re: AMBER: library for 8oxoguanine M. L. Dodson (Mon Jul 24 2006 - 13:07:17 PDT)
  - Re: AMBER: library for 8oxoguanine Carlos Simmerling (Mon Jul 24 2006 - 14:12:38 PDT)
- Re: AMBER: library for 8oxoguanine FyD (Tue Jul 25 2006 - 05:39:27 PDT)
AMBER: Building an RNA - Proflavin Complex sethl.gatech.edu (Mon Jul 24 2006 - 13:05:49 PDT)
AMBER: Confusion re AMBER SMD output Alik Widge (Mon Jul 24 2006 - 13:31:34 PDT)
- AMBER: Re: Confusion re AMBER SMD output Alik Widge (Mon Jul 31 2006 - 15:54:59 PDT)
  - Re: AMBER: Re: Confusion re AMBER SMD output Adrian Roitberg (Tue Aug 01 2006 - 04:07:03 PDT)
AMBER: process_mdout.perl's output is empty Prashanth Athri (Mon Jul 24 2006 - 13:53:04 PDT)
- Re: AMBER: process_mdout.perl's output is empty Chng Choon-Peng (Mon Jul 24 2006 - 18:02:57 PDT)
  - Re: AMBER: process_mdout.perl's output is empty Alik Widge (Tue Jul 25 2006 - 08:19:44 PDT)
Re: [Fwd: AMBER: Long line of input] Myunggi Yi (Tue Jul 25 2006 - 09:08:27 PDT)
AMBER: Hybridization in leap opitz.che.udel.edu (Tue Jul 25 2006 - 11:23:12 PDT)
- Re: AMBER: Hybridization in leap David A. Case (Tue Jul 25 2006 - 13:37:30 PDT)
AMBER: how to mutate in amber 8 for thermodynamic integration without using xleap Lwin, ThuZar (Tue Jul 25 2006 - 17:39:32 PDT)
- Re: AMBER: how to mutate in amber 8 for thermodynamic integration without using xleap David A. Case (Wed Jul 26 2006 - 10:44:58 PDT)
AMBER: parallel installation of amber8 on HP cluster Manish Datt (Wed Jul 26 2006 - 03:00:30 PDT)
- Re: AMBER: parallel installation of amber8 on HP cluster michael crowley (Wed Jul 26 2006 - 07:42:19 PDT)
- Re: AMBER: parallel installation of amber8 on HP cluster David A. Case (Wed Jul 26 2006 - 08:00:53 PDT)
  - Re: AMBER: parallel installation of amber8 on HP cluster Manish Datt (Wed Jul 26 2006 - 10:54:51 PDT)
    - Re: AMBER: parallel installation of amber8 on HP cluster Michael Crowley (Wed Jul 26 2006 - 11:52:09 PDT)
    - Re: AMBER: parallel installation of amber8 on HP cluster David A. Case (Thu Jul 27 2006 - 08:57:41 PDT)
AMBER: leap error AYTUG TUNCEL (Wed Jul 26 2006 - 16:29:35 PDT)
- Re: AMBER: leap error David A. Case (Thu Jul 27 2006 - 07:34:17 PDT)
AMBER: Harmonic restraint along z-axis Myunggi Yi (Wed Jul 26 2006 - 17:26:02 PDT)
- Re: AMBER: Harmonic restraint along z-axis David A. Case (Thu Jul 27 2006 - 07:32:52 PDT)
- Re: AMBER: Harmonic restraint along z-axis Carlos Simmerling (Thu Jul 27 2006 - 09:15:18 PDT)
AMBER: dummy atoms in MMPBSA Andrea Bortolato (Thu Jul 27 2006 - 01:10:50 PDT)
- Re: AMBER: dummy atoms in MMPBSA Ilyas Yildirim (Thu Jul 27 2006 - 05:18:01 PDT)
AMBER: xleap Md Jahidul Islam (Thu Jul 27 2006 - 02:49:36 PDT)
- Re: AMBER: xleap Chng Choon-Peng (Thu Jul 27 2006 - 03:14:58 PDT)
AMBER: Can't open xleap Jahidul Islam (Thu Jul 27 2006 - 03:16:08 PDT)
- Re: AMBER: Can't open xleap Chng Choon-Peng (Thu Jul 27 2006 - 03:45:58 PDT)
  - Re: AMBER: Can't open xleap Jahidul Islam (Thu Jul 27 2006 - 04:57:30 PDT)
    - Re: AMBER: Can't open xleap David A. Case (Thu Jul 27 2006 - 06:53:16 PDT)
- Re: AMBER: Can't open xleap Bill Ross (Thu Jul 27 2006 - 10:21:39 PDT)
AMBER: Zinc parameters Nitin Bhardwaj (Thu Jul 27 2006 - 09:35:57 PDT)
- RE: AMBER: Zinc parameters Ross Walker (Thu Jul 27 2006 - 10:26:29 PDT)
AMBER: Correction on Zinc parameters Nitin Bhardwaj (Thu Jul 27 2006 - 09:38:00 PDT)
AMBER: Zinc-coordinating histidine protonation state Nitin Bhardwaj (Thu Jul 27 2006 - 13:01:16 PDT)
- Re: AMBER: Zinc-coordinating histidine protonation state David A. Case (Mon Jul 31 2006 - 08:50:16 PDT)
AMBER: Zinc coordinating CYS Nitin Bhardwaj (Thu Jul 27 2006 - 14:30:45 PDT)
- Re: AMBER: Zinc coordinating CYS madhumalar.bii-sg.org (Thu Jul 27 2006 - 17:37:12 PDT)
  - Re: AMBER: Zinc coordinating CYS Nitin Bhardwaj (Thu Jul 27 2006 - 21:00:45 PDT)
    - Re: AMBER: Zinc coordinating CYS madhumalar.bii-sg.org (Fri Jul 28 2006 - 02:17:36 PDT)
RE: AMBER: how to mutate in amber 8 for thermodynamic integration without using xleap. . Lwin, ThuZar (Thu Jul 27 2006 - 18:35:19 PDT)
- Re: AMBER: how to mutate in amber 8 for thermodynamic integration without using xleap. . David A. Case (Fri Jul 28 2006 - 07:27:44 PDT)
AMBER: Ken Merz (Sat Jul 29 2006 - 08:28:53 PDT)
AMBER: Having trouble with Nucgen for generating pdb more than 16 bps amit.mbu.iisc.ernet.in (Sun Jul 30 2006 - 11:51:05 PDT)
Re: AMBER: Having trouble with Nucgen for generating pdb more than 16 bps Bill Ross (Mon Jul 31 2006 - 11:53:11 PDT)
AMBER: loading torsion parameters Nitin Bhardwaj (Mon Jul 31 2006 - 12:47:19 PDT)
- Re: AMBER: loading torsion parameters Wei Zhang (Mon Jul 31 2006 - 13:13:57 PDT)
- RE: AMBER: loading torsion parameters Ross Walker (Mon Jul 31 2006 - 13:25:08 PDT)
  - Re: AMBER: loading torsion parameters Nitin Bhardwaj (Mon Jul 31 2006 - 13:35:18 PDT)
  - AMBER: GB tutorials and disulphide bonds Abhilash (Mon Jul 31 2006 - 13:41:30 PDT)
    - Re: AMBER: GB tutorials and disulphide bonds David A. Case (Tue Aug 01 2006 - 10:14:20 PDT)
Re: AMBER: loading torsion parameters Bill Ross (Mon Jul 31 2006 - 13:49:38 PDT)
AMBER: For different ligand conformation pkb bioinfo (Mon Jul 31 2006 - 06:53:45 PDT)
- Re: AMBER: For different ligand conformation David Mobley (Mon Jul 31 2006 - 15:29:40 PDT)
AMBER: Using a trajectory and some PDB files as input for PCA Zu Thur Yew (Mon Jul 31 2006 - 03:20:42 PDT)
- Re: AMBER: Using a trajectory and some PDB files as input for PCA David A. Case (Tue Aug 01 2006 - 10:10:29 PDT)
AMBER: Distance between two regions Baker, Bo-Yang (Mon Jul 31 2006 - 17:16:02 PDT)
- Re: AMBER: Distance between two regions Guanglei Cui (Tue Aug 01 2006 - 08:35:54 PDT)
AMBER: from traj to crd Fabián Alejandro Rodríguez (Mon Jul 31 2006 - 17:58:19 PDT)
- AMBER: Xmgr in Windows Jahidul Islam (Mon Jul 31 2006 - 20:24:19 PDT)
  - Re: AMBER: Xmgr in Windows Ilyas Yildirim (Mon Jul 31 2006 - 22:33:38 PDT)
  - Re: AMBER: Xmgr in Windows Fabián Alejandro Rodríguez (Tue Aug 01 2006 - 04:39:19 PDT)
  - Re: AMBER: Xmgr in Windows Florian Haberl (Tue Aug 01 2006 - 05:11:44 PDT)
- Re: AMBER: from traj to crd Guanglei Cui (Tue Aug 01 2006 - 08:30:59 PDT)
  - Re: AMBER: from traj to crd Fabián Alejandro Rodríguez (Tue Aug 01 2006 - 08:41:22 PDT)
AMBER: How to set Bondi Radii using xleap Ilyas Yildirim (Mon Jul 31 2006 - 22:40:15 PDT)
- Re: AMBER: How to set Bondi Radii using xleap David A. Case (Tue Aug 01 2006 - 10:17:38 PDT)
  - Re: AMBER: How to set Bondi Radii using xleap Carlos Simmerling (Tue Aug 01 2006 - 10:43:04 PDT)
- Re: AMBER: How to set Bondi Radii using xleap. . Don.Bashford.stjude.org (Tue Aug 01 2006 - 10:23:51 PDT)
AMBER: regarding diffusion command output Arvind Marathe (Tue Aug 01 2006 - 03:45:21 PDT)
AMBER: Ignoring every other frame in a .crd trajectory in Ptraj Xiaojian Deng (Tue Aug 01 2006 - 10:55:31 PDT)
- Re: AMBER: Ignoring every other frame in a .crd trajectory in Ptraj Xiaojian Deng (Tue Aug 01 2006 - 11:02:22 PDT)
- Re: AMBER: Ignoring every other frame in a .crd trajectory in Ptraj Carlos Simmerling (Tue Aug 01 2006 - 11:13:07 PDT)
AMBER: pdb error AYTUG TUNCEL (Tue Aug 01 2006 - 12:36:39 PDT)
- Re: AMBER: pdb error Ilyas Yildirim (Tue Aug 01 2006 - 12:23:30 PDT)
AMBER: any work-around for 80 character mask string limit? Tanya Johannsen (Tue Aug 01 2006 - 13:12:22 PDT)
- Re: AMBER: any work-around for 80 character mask string limit? David A. Case (Tue Aug 01 2006 - 14:37:36 PDT)
AMBER: brookhaven to amber pdb format AYTUG TUNCEL (Wed Aug 02 2006 - 02:08:50 PDT)
- Re: AMBER: brookhaven to amber pdb format David A. Case (Wed Aug 02 2006 - 07:48:23 PDT)
- Re: AMBER: brookhaven to amber pdb format Ilyas Yildirim (Wed Aug 02 2006 - 11:55:38 PDT)
AMBER: mm_pbsa.pl fails to start in linux cluster pkb bioinfo (Wed Aug 02 2006 - 05:07:22 PDT)
- Re: AMBER: mm_pbsa.pl fails to start in linux cluster pkb bioinfo (Wed Aug 02 2006 - 06:58:48 PDT)
AMBER: neutral N-terminal amino-acid parameters for ff03 Vlad Cojocaru (Wed Aug 02 2006 - 07:21:31 PDT)
- Re: AMBER: neutral N-terminal amino-acid parameters for ff03 FyD (Sat Aug 05 2006 - 01:16:23 PDT)
AMBER: Bugfixes available for pmemd iwrap problem Robert Duke (Wed Aug 02 2006 - 10:05:32 PDT)
AMBER: where can I find the force field paramete r for Silica yxiong99 (Wed Aug 02 2006 - 12:53:33 PDT)
AMBER: Maximum system size in simulated annealing Juraj Kotulic Bunta (Wed Aug 02 2006 - 19:03:11 PDT)
- Re: AMBER: Maximum system size in simulated annealing Andreas Svrcek-Seiler (Thu Aug 03 2006 - 02:23:13 PDT)
- Re: AMBER: Maximum system size in simulated annealing Carlos Simmerling (Thu Aug 03 2006 - 03:26:58 PDT)
AMBER: TI-FEP for ILE--->VAL. Biswa Ranjan Meher (Wed Aug 02 2006 - 22:26:22 PDT)
- Re: AMBER: TI-FEP for ILE--->VAL. Ilyas Yildirim (Wed Aug 02 2006 - 23:15:10 PDT)
- Re: AMBER: TI-FEP for ILE--->VAL. David A. Case (Thu Aug 03 2006 - 09:43:44 PDT)
AMBER: problems with ptraj anna.schrey.gmx.de (Thu Aug 03 2006 - 07:49:39 PDT)
- Re: AMBER: problems with ptraj David A. Case (Thu Aug 03 2006 - 09:46:19 PDT)
- Re: AMBER: problems with ptraj Thomas Cheatham (Thu Aug 10 2006 - 12:25:18 PDT)
AMBER: Need to know meaning of numbers in parm99.dat file to be able to write frcmod file for dummy atoms Lwin, ThuZar (Thu Aug 03 2006 - 08:14:28 PDT)
- Re: AMBER: Need to know meaning of numbers in parm99.dat file to be able to write frcmod file for dummy atoms Carlos Simmerling (Thu Aug 03 2006 - 08:33:34 PDT)
AMBER: about Silica's polarizability yxiong99 (Thu Aug 03 2006 - 08:20:19 PDT)
- Re: AMBER: about Silica's polarizability David A. Case (Thu Aug 03 2006 - 09:16:40 PDT)
AMBER: question on chargning free energy in solvent vs vacuum Lwin, ThuZar (Thu Aug 03 2006 - 10:08:07 PDT)
- Re: AMBER: question on chargning free energy in solvent vs vacuum David A. Case (Fri Aug 04 2006 - 09:18:53 PDT)
AMBER: restraint=0.0000 during minimization? Evan Kelly (Thu Aug 03 2006 - 10:48:17 PDT)
AMBER: Please DISREGARD previous message (restraint=0.0000) Evan Kelly (Thu Aug 03 2006 - 10:57:46 PDT)
AMBER: HBOND ANALYSIS Claire Zerafa (Fri Aug 04 2006 - 07:35:50 PDT)
- Fw: AMBER: HBOND ANALYSIS Claire Zerafa (Sat Aug 05 2006 - 12:45:10 PDT)
- Re: AMBER: HBOND ANALYSIS Thomas Cheatham (Thu Aug 10 2006 - 16:57:34 PDT)
  - AMBER: klambda Vitor Manuel Sousa F?x (Mon Aug 14 2006 - 03:45:10 PDT)
    - Re: AMBER: klambda David A. Case (Mon Aug 14 2006 - 09:48:30 PDT)
    - Re: AMBER: klambda Ilyas Yildirim (Mon Aug 14 2006 - 10:31:24 PDT)
AMBER: H-bonds of peptide with water sangeeta (Fri Aug 04 2006 - 06:20:13 PDT)
- Re: AMBER: H-bonds of peptide with water Scott Pendley (Mon Aug 07 2006 - 12:56:04 PDT)
AMBER: Residue connection points on prep.in Gloria T. Anderle (Fri Aug 04 2006 - 09:10:53 PDT)
AMBER: parameter for Cd2+? JunJun Liu (Fri Aug 04 2006 - 08:50:46 PDT)
AMBER: to do tutorial 4 using tleap Come On (Fri Aug 04 2006 - 09:50:53 PDT)
AMBER: how to take care of toluene system neutrality Lwin, ThuZar (Fri Aug 04 2006 - 11:27:39 PDT)
AMBER: how to take care of toluene system neutrality Lwin, ThuZar (Fri Aug 04 2006 - 11:31:53 PDT)
RE: AMBER: question on chargning free energy in solvent vs vacuum. . Lwin, ThuZar (Fri Aug 04 2006 - 12:02:10 PDT)
AMBER: Amber Installation Help Kirk Hevener (Mon Aug 07 2006 - 05:43:25 PDT)
- Re: AMBER: Amber Installation Help David A. Case (Tue Aug 08 2006 - 08:25:49 PDT)
  - Re: AMBER: Amber Installation Help; link woes Scott Brozell (Tue Aug 08 2006 - 12:36:32 PDT)
AMBER: Info regarding reduced cysteines Rafi Ahmad (Mon Aug 07 2006 - 07:06:40 PDT)
- Re: AMBER: Info regarding reduced cysteines David A. Case (Mon Aug 07 2006 - 08:02:57 PDT)
AMBER: transition state John Chuang莊曜遠老師 (Mon Aug 07 2006 - 09:06:50 PDT)
- Re: AMBER: transition state Eric Hu (Wed Aug 09 2006 - 12:05:14 PDT)
  - Re: AMBER: transition state John Chuang莊曜遠老師 (Mon Aug 14 2006 - 15:20:20 PDT)
    - Re: AMBER: transition state Eric Hu (Mon Aug 21 2006 - 17:06:22 PDT)
AMBER: Glass, Kevin A (Mon Aug 07 2006 - 13:09:02 PDT)
- Re: AMBER: Scott Brozell (Mon Aug 07 2006 - 17:37:19 PDT)
AMBER: antechamber bond typing questions David Mobley (Mon Aug 07 2006 - 13:14:42 PDT)
AMBER: RE: antechamber bond typing questions Junmei Wang (Mon Aug 07 2006 - 18:43:05 PDT)
AMBER: Problem with restarting MD simulation Gobind Bisht (Mon Aug 07 2006 - 22:02:56 PDT)
- Re: AMBER: Problem with restarting MD simulation Carlos Simmerling (Tue Aug 08 2006 - 04:08:27 PDT)
AMBER: cutting the box after "solvatebox" Vlad Cojocaru (Tue Aug 08 2006 - 05:12:37 PDT)
- Re: AMBER: cutting the box after "solvatebox" Carlos Simmerling (Tue Aug 08 2006 - 05:43:47 PDT)
  - Re: AMBER: cutting the box after "solvatebox" Vlad Cojocaru (Tue Aug 08 2006 - 05:52:39 PDT)
- Re: AMBER: cutting the box after "solvatebox" Guanglei Cui (Tue Aug 08 2006 - 07:38:06 PDT)
  - Re: AMBER: cutting the box after "solvatebox" Ilyas Yildirim (Thu Aug 17 2006 - 12:28:55 PDT)
AMBER: PCA: can't complete projection Zu Thur Yew (Tue Aug 08 2006 - 07:17:31 PDT)
- Re: AMBER: PCA: can't complete projection Vlad Cojocaru (Tue Aug 08 2006 - 07:56:49 PDT)
  - AMBER: ptraj: nofit option for rmsd Joseph Nachman (Tue Aug 08 2006 - 08:27:41 PDT)
  - Re: AMBER: PCA: can't complete projection Zu Thur Yew (Tue Aug 08 2006 - 09:42:04 PDT)
AMBER: GAFF parameters: DPPC Bilayer Akshay Patny (Tue Aug 08 2006 - 12:53:49 PDT)
- Re: AMBER: GAFF parameters: DPPC Bilayer Nitin Bhardwaj (Tue Aug 08 2006 - 12:58:59 PDT)
  - RE: AMBER: GAFF parameters: DPPC Bilayer Yong Duan (Tue Aug 08 2006 - 13:42:50 PDT)
    - RE: AMBER: GAFF parameters: DPPC Bilayer Akshay Patny (Wed Aug 09 2006 - 14:08:00 PDT)
AMBER: Format of mdcrd files Gobind Bisht (Wed Aug 09 2006 - 06:56:18 PDT)
- Re: AMBER: Format of mdcrd files Carlos Simmerling (Wed Aug 09 2006 - 07:24:35 PDT)
- Re: AMBER: Format of mdcrd files Mark Williamson (Wed Aug 09 2006 - 07:32:06 PDT)
AMBER: Energy differecnes as using igb=1 and igb=0 backy (Wed Aug 09 2006 - 07:46:56 PDT)
- Re: AMBER: Energy differecnes as using igb=1 and igb=0 Carlos Simmerling (Wed Aug 09 2006 - 08:01:27 PDT)
- Re: AMBER: Energy differecnes as using igb=1 and igb=0 backy (Wed Aug 09 2006 - 23:47:37 PDT)
  - Re: AMBER: Energy differecnes as using igb=1 and igb=0 Carlos Simmerling (Thu Aug 10 2006 - 03:09:23 PDT)
AMBER: build box info for acetonitrile in the simulation with periodic boundary condition Eric Hu (Wed Aug 09 2006 - 11:06:30 PDT)
- Re: AMBER: build box info for acetonitrile in the simulation with periodic boundary condition David A. Case (Wed Aug 09 2006 - 13:45:42 PDT)
  - Re: AMBER: build box info for acetonitrile in the simulation with periodic boundary condition Eric Hu (Wed Aug 09 2006 - 14:30:04 PDT)
AMBER: how to reassign charges Lwin, ThuZar (Wed Aug 09 2006 - 11:16:01 PDT)
- Re: AMBER: how to reassign charges David Mobley (Wed Aug 09 2006 - 13:03:10 PDT)
  - RE: AMBER: how to reassign charges Yong Duan (Wed Aug 09 2006 - 14:26:10 PDT)
- Re: AMBER: how to reassign charges David A. Case (Wed Aug 09 2006 - 13:43:07 PDT)
  - AMBER: PO2 in a DNA fragement, not a type in xleap? What can I do next? a a (Thu Aug 10 2006 - 02:26:01 PDT)
    - Re: AMBER: PO2 in a DNA fragement, not a type in xleap? What can I do next? Thomas Cheatham (Thu Aug 10 2006 - 15:18:00 PDT)
    - Re: AMBER: PO2 in a DNA fragement, not a type in xleap? What can I do next? a a (Thu Aug 10 2006 - 19:39:54 PDT)
    - AMBER: Restart problem on PMEMD with position restraint. Chunhu Tan (Mon Sep 18 2006 - 10:46:35 PDT)
    - Re: AMBER: Restart problem on PMEMD with position restraint. Robert Duke (Mon Sep 18 2006 - 11:20:27 PDT)
    - RE: AMBER: Restart problem on PMEMD with position restraint. Ross Walker (Mon Sep 18 2006 - 11:32:05 PDT)
    - Re: AMBER: Restart problem on PMEMD with position restraint. David A. Case (Mon Sep 18 2006 - 12:09:46 PDT)
    - RE: AMBER: Restart problem on PMEMD with position restraint. Chunhu Tan (Mon Sep 18 2006 - 14:10:44 PDT)
    - RE: AMBER: Restart problem on PMEMD with position restraint. Ross Walker (Mon Sep 18 2006 - 14:57:58 PDT)
    - Re: AMBER: PO2 in a DNA fragement, not a type in xleap? What can I do next? FyD (Sat Aug 12 2006 - 12:09:29 PDT)
    - Re: AMBER: PO2 in a DNA fragement, not a type in xleap? What canI do next? a a (Sun Aug 13 2006 - 21:29:59 PDT)
  - AMBER: Phosphated Tyrosine, not a type (xleap)? a a (Thu Aug 10 2006 - 02:22:27 PDT)
    - Re: AMBER: Phosphated Tyrosine, not a type (xleap)? David A. Case (Thu Aug 10 2006 - 09:07:09 PDT)
    - Re: AMBER: Phosphated Tyrosine, not a type (xleap)? a a (Thu Aug 10 2006 - 19:38:47 PDT)
AMBER: Heme parameters Marcelo Puiatti (Wed Aug 09 2006 - 15:58:35 PDT)
- Re: AMBER: Heme parameters Weihua Li (Wed Aug 09 2006 - 19:44:15 PDT)
AMBER: Re: Simulated annealing Carlos Simmerling (Thu Aug 10 2006 - 04:40:24 PDT)
AMBER: Leap adds hydrogens but cannot resolve their type. Paul R Brenner (Thu Aug 10 2006 - 12:23:55 PDT)
- Re: AMBER: Leap adds hydrogens but cannot resolve their type. David A. Case (Thu Aug 10 2006 - 13:15:16 PDT)
  - Re: AMBER: Leap adds hydrogens but cannot resolve their type. Paul R Brenner (Tue Aug 15 2006 - 08:39:08 PDT)
AMBER: zero entry in LENNARD_JONES_ACOEF of prmtop files Jing Huang (Fri Aug 11 2006 - 06:35:12 PDT)
- Re: AMBER: zero entry in LENNARD_JONES_ACOEF of prmtop files Guanglei Cui (Fri Aug 11 2006 - 06:57:46 PDT)
AMBER: Could mm_pbsa decompose energy only for the receptor ? backy (Fri Aug 11 2006 - 07:10:52 PDT)
AMBER: ptraj quasiharmonic analysis question Shawn yy (Fri Aug 11 2006 - 07:45:21 PDT)
AMBER: how to do a molecular dynamic study on a trimer Abhilash (Fri Aug 11 2006 - 08:05:44 PDT)
- Re: AMBER: how to do a molecular dynamic study on a trimer David A. Case (Fri Aug 11 2006 - 09:05:12 PDT)
  - Re: AMBER: how to do a molecular dynamic study on a trimer Gobind Bisht (Sat Aug 12 2006 - 10:05:29 PDT)
    - Re: AMBER: how to do a molecular dynamic study on a trimer David A. Case (Sun Aug 13 2006 - 09:37:03 PDT)
    - AMBER: AMBER Tutorial 2 section 6, rmsd calculation: rmsd for residues number? a a (Mon Aug 14 2006 - 04:25:31 PDT)
AMBER: AMBER8 - RDF bug Petr Kulhanek (Fri Aug 11 2006 - 09:00:57 PDT)
AMBER: Nature of QM scanning protocol for parameter development Isherwood, James (Fri Aug 11 2006 - 09:17:01 PDT)
AMBER: Middlebury College Cluster and Amber 8 Lubans, Peter S (Fri Aug 11 2006 - 09:55:19 PDT)
- Re: AMBER: Middlebury College Cluster and Amber 8 Robert Duke (Fri Aug 11 2006 - 10:33:13 PDT)
- Re: AMBER: Middlebury College Cluster and Amber 8 David A. Case (Fri Aug 11 2006 - 11:30:46 PDT)
AMBER: Problem: Flag "SOLVENT_POINTERS" not found in PARM file Jianhui (Fri Aug 11 2006 - 11:50:54 PDT)
- Re: AMBER: Problem: Flag "SOLVENT_POINTERS" not found in PARM file David A. Case (Sun Aug 13 2006 - 09:49:27 PDT)
AMBER: Where can I find the SMD parameter file (or simple turtorial) in AMBER9 Cheng Luo, Ph.D. (Fri Aug 11 2006 - 13:41:32 PDT)
- Re: AMBER: Where can I find the SMD parameter file (or simple turtorial) in AMBER9 Adrian Roitberg (Fri Aug 11 2006 - 13:23:10 PDT)
AMBER: impose command in leap problem Piotr Cieplak (Fri Aug 11 2006 - 17:56:40 PDT)
- Re: AMBER: impose command in leap problem Scott Brozell (Fri Aug 11 2006 - 18:57:21 PDT)
  - Re: AMBER: impose command in leap problem Piotr Cieplak (Mon Aug 14 2006 - 13:44:02 PDT)
AMBER: DIELC? backy (Sat Aug 12 2006 - 05:16:47 PDT)
- Re: AMBER: DIELC? David A. Case (Sun Aug 13 2006 - 09:43:58 PDT)
- Re: AMBER: DIELC? backy (Sat Aug 19 2006 - 01:04:14 PDT)
AMBER: parallel pmemd with intel 9 fc bala (Sat Aug 12 2006 - 08:56:15 PDT)
- Re: AMBER: parallel pmemd with intel 9 fc Robert Duke (Sat Aug 12 2006 - 11:58:59 PDT)
AMBER: Problem with sander in Linux Wimal (Mon Aug 14 2006 - 01:14:00 PDT)
- Re: AMBER: Problem with sander in Linux David A. Case (Mon Aug 14 2006 - 09:49:53 PDT)
AMBER: RE: AMBER Tutorial 2 section 6, rmsd calculation: rmsd for residues number? Kateryna Miroshnychenko (Mon Aug 14 2006 - 06:19:46 PDT)
- RE: AMBER: RE: AMBER Tutorial 2 section 6, rmsd calculation: rmsd for residues number? a a (Mon Aug 14 2006 - 22:48:49 PDT)
  - AMBER: (no subject) a a (Tue Aug 15 2006 - 03:13:49 PDT)
    - Re: AMBER: (no subject) Navnit Kumar Mishra (Tue Aug 15 2006 - 05:51:49 PDT)
AMBER: problem imposing arbitrary peptide bonds through leap Amarda Shehu (Mon Aug 14 2006 - 09:27:24 PDT)
- Re: AMBER: problem imposing arbitrary peptide bonds through leap David A. Case (Mon Aug 14 2006 - 09:45:48 PDT)
  - Re: ***SPAM*** Re: AMBER: problem imposing arbitrary peptide bonds through leap Amarda Shehu (Mon Aug 14 2006 - 09:56:31 PDT)
AMBER: source code Yannick Bomble (Mon Aug 14 2006 - 11:09:31 PDT)
- Re: AMBER: source code Thomas Cheatham (Mon Aug 14 2006 - 11:31:08 PDT)
AMBER: Modify charges to increase/decrease hydrogen bond interaction Mingfeng Yang (Mon Aug 14 2006 - 11:25:19 PDT)
- Re: AMBER: Modify charges to increase/decrease hydrogen bond interaction Thomas Cheatham (Mon Aug 14 2006 - 11:42:52 PDT)
  - Re: AMBER: Modify charges to increase/decrease hydrogen bond interaction Mingfeng Yang (Mon Aug 14 2006 - 12:06:56 PDT)
AMBER: Advice on linux cluster sought Feng X Zhou (Mon Aug 14 2006 - 11:34:16 PDT)
AMBER: amber9 Test Failer kawamura_hiro.riken.jp (Tue Aug 15 2006 - 05:21:49 PDT)
- Re: AMBER: amber9 Test Failer David A. Case (Tue Aug 15 2006 - 08:05:54 PDT)
AMBER: amber 9 intel 9.1 ia64 Tim Robinson (Tue Aug 15 2006 - 06:45:16 PDT)
- Re: AMBER: amber 9 intel 9.1 ia64 Fabian Boes (Tue Aug 15 2006 - 06:59:39 PDT)
AMBER: Question about using antechamber with G03 Gustavo Seabra (Tue Aug 15 2006 - 08:58:40 PDT)
- Re: AMBER: Question about using antechamber with G03 David A. Case (Tue Aug 15 2006 - 14:15:26 PDT)
  - Re: AMBER: Question about using antechamber with G03 Gustavo Seabra (Wed Aug 16 2006 - 06:49:42 PDT)
AMBER: DOTA-Lanthanide complexes in Amber opitz.che.udel.edu (Tue Aug 15 2006 - 10:48:23 PDT)
- Re: AMBER: DOTA-Lanthanide complexes in Amber David A. Case (Wed Aug 16 2006 - 09:59:22 PDT)
- Re: AMBER: DOTA-Lanthanide complexes in Amber opitz.che.udel.edu (Wed Aug 16 2006 - 10:27:23 PDT)
  - Re: AMBER: DOTA-Lanthanide complexes in Amber Brent Krueger (Wed Aug 16 2006 - 13:08:57 PDT)
AMBER: (Another) Question about using antechamber with G03 Gustavo Seabra (Tue Aug 15 2006 - 10:51:16 PDT)
- Re: AMBER: (Another) Question about using antechamber with G03 David A. Case (Tue Aug 15 2006 - 16:09:56 PDT)
AMBER: antechamber failure on FMN David Mobley (Tue Aug 15 2006 - 11:04:42 PDT)
- Re: AMBER: antechamber failure on FMN David Mobley (Tue Aug 15 2006 - 11:16:47 PDT)
  - Re: AMBER: antechamber failure on FMN David A. Case (Tue Aug 15 2006 - 16:14:41 PDT)
AMBER: input conversion error mm_pbsa AYTUG TUNCEL (Tue Aug 15 2006 - 15:23:28 PDT)
- Re: AMBER: input conversion error mm_pbsa David A. Case (Tue Aug 15 2006 - 15:47:19 PDT)
AMBER: TI tutorial Mingfeng Yang (Tue Aug 15 2006 - 15:22:10 PDT)
- Re: AMBER: TI tutorial David A. Case (Tue Aug 15 2006 - 16:34:58 PDT)
AMBER: MM_PBSA : Question about Stability? Guillaume Bollot (Wed Aug 16 2006 - 00:00:15 PDT)
- Re: AMBER: MM_PBSA : Question about Stability? David A. Case (Wed Aug 16 2006 - 09:24:48 PDT)
AMBER: MMPBSA: positive energies during nmode Zu Thur Yew (Wed Aug 16 2006 - 07:15:11 PDT)
- Re: AMBER: MMPBSA: positive energies during nmode David A. Case (Wed Aug 16 2006 - 09:10:29 PDT)
AMBER: reading ff file into XLeap Petr Jerabek (Wed Aug 16 2006 - 09:21:00 PDT)
- Re: AMBER: reading ff file into XLeap David A. Case (Wed Aug 16 2006 - 10:21:47 PDT)
AMBER: Ptraj selecting specific atoms in specific residues Steve Seibold (Wed Aug 16 2006 - 10:05:16 PDT)
- Re: AMBER: Ptraj selecting specific atoms in specific residues Scott Pendley (Wed Aug 16 2006 - 10:19:31 PDT)
  - RE: AMBER: Ptraj selecting specific atoms in specific residues Steve Seibold (Wed Aug 16 2006 - 10:50:16 PDT)
- Re: AMBER: Ptraj selecting specific atoms in specific residues Thomas Cheatham (Wed Aug 16 2006 - 10:32:24 PDT)
AMBER: checkmask Steve Seibold (Wed Aug 16 2006 - 11:14:29 PDT)
AMBER: The PB GB energy from mm_pbsa will be positive on high charged system Suxin Zheng (Wed Aug 16 2006 - 11:23:44 PDT)
- Re: AMBER: The PB GB energy from mm_pbsa will be positive on high charged system David A. Case (Fri Aug 18 2006 - 10:50:32 PDT)
  - Re: AMBER: The PB GB energy from mm_pbsa will be positive on high charged system Suxin Zheng (Fri Aug 18 2006 - 11:23:17 PDT)
    - Re: AMBER: The PB GB energy from mm_pbsa will be positive on high charged system David A. Case (Fri Aug 18 2006 - 11:35:04 PDT)
AMBER: pmf input files Lauren O'Neil (Wed Aug 16 2006 - 10:20:45 PDT)
- AMBER: 答复: AMBER: pmf input files Chunhu Tan (Thu Aug 17 2006 - 09:36:30 PDT)
AMBER: generate "template" frcmod from standard residues? mernst.tricity.wsu.edu (Wed Aug 16 2006 - 11:41:02 PDT)
- Re: AMBER: generate "template" frcmod from standard residues? David Mobley (Wed Aug 16 2006 - 14:51:47 PDT)
- Re: AMBER: generate "template" frcmod from standard residues? David A. Case (Thu Aug 17 2006 - 09:04:22 PDT)
  - Re: AMBER: generate "template" frcmod from standard residues? mernst.tricity.wsu.edu (Thu Aug 17 2006 - 10:06:07 PDT)
    - Re: AMBER: generate "template" frcmod from standard residues? David A. Case (Thu Aug 17 2006 - 11:01:45 PDT)
    - Re: AMBER: generate "template" frcmod from standard residues? David Mobley (Fri Aug 18 2006 - 09:13:08 PDT)
AMBER: help with leap sethl.gatech.edu (Wed Aug 16 2006 - 16:24:42 PDT)
- Re: AMBER: help with leap Franck_Vendeix.ncsu.edu (Thu Aug 17 2006 - 07:46:07 PDT)
Re: AMBER: help with leap Bill Ross (Wed Aug 16 2006 - 17:51:56 PDT)
RE: AMBER: antechamber error -> metals Junmei Wang (Wed Aug 16 2006 - 19:29:46 PDT)
AMBER: RE: antechamber failure on FMN Junmei Wang (Thu Aug 17 2006 - 16:14:47 PDT)
- AMBER: Re: antechamber failure on FMN David Mobley (Fri Aug 18 2006 - 11:46:58 PDT)
AMBER: Execution time discrepancies Glass, Kevin A (Thu Aug 17 2006 - 17:18:20 PDT)
- RE: AMBER: Execution time discrepancies Ross Walker (Thu Aug 17 2006 - 20:00:29 PDT)
Re: AMBER: Execution time discrepancies Bill Ross (Thu Aug 17 2006 - 18:24:13 PDT)
AMBER: identical high energies Tanya Johannsen (Thu Aug 17 2006 - 19:22:40 PDT)
- RE: AMBER: identical high energies Ross Walker (Thu Aug 17 2006 - 19:52:38 PDT)
- Re: AMBER: identical high energies Thomas Cheatham (Thu Aug 17 2006 - 19:57:23 PDT)
AMBER: GBSA EGB = NaN William Lianhu Wei (Thu Aug 17 2006 - 19:30:50 PDT)
- RE: AMBER: GBSA EGB = NaN Ross Walker (Thu Aug 17 2006 - 19:57:29 PDT)
  - Re: AMBER: GBSA EGB = NaN William Wei (Fri Aug 18 2006 - 08:12:10 PDT)
    - RE: AMBER: GBSA EGB = NaN Ross Walker (Fri Aug 18 2006 - 15:11:52 PDT)
    - Re: AMBER: GBSA EGB = NaN William Wei (Mon Aug 21 2006 - 09:04:36 PDT)
    - Re: AMBER: GBSA EGB = NaN William Wei (Mon Aug 21 2006 - 09:04:26 PDT)
    - Re: AMBER: GBSA EGB = NaN Ilyas Yildirim (Mon Aug 21 2006 - 09:14:54 PDT)
    - Re: AMBER: GBSA EGB = NaN William Wei (Mon Aug 21 2006 - 09:37:47 PDT)
    - Re: AMBER: GBSA EGB = NaN David A. Case (Mon Aug 21 2006 - 10:10:24 PDT)
- Re: AMBER: GBSA EGB = NaN William Wei (Mon Aug 21 2006 - 11:00:21 PDT)
  - Re: AMBER: GBSA EGB = NaN David A. Case (Mon Aug 21 2006 - 11:21:10 PDT)
AMBER: amidine group/ gaff parameters Prashanth Athri (Fri Aug 18 2006 - 12:00:17 PDT)
AMBER: ptraj script Jardas sucuriba (Fri Aug 18 2006 - 13:08:31 PDT)
- AMBER: missing values in md.out Jardas sucuriba (Thu Aug 24 2006 - 09:15:40 PDT)
  - Re: AMBER: missing values in md.out Carlos Simmerling (Thu Aug 24 2006 - 09:24:28 PDT)
    - Re: AMBER: missing values in md.out Jardas sucuriba (Fri Aug 25 2006 - 05:36:45 PDT)
    - Re: AMBER: missing values in md.out Carlos Simmerling (Fri Aug 25 2006 - 05:53:26 PDT)
AMBER: Details about Gaussian basis set for Cobalt complex S.Sundar Raman (Sun Aug 20 2006 - 07:07:57 PDT)
- Re: AMBER: Details about Gaussian basis set for Cobalt complex FyD (Mon Aug 21 2006 - 05:28:49 PDT)
- Re: AMBER: Details about Gaussian basis set for Cobalt complex Thomas Cheatham (Fri Aug 25 2006 - 11:21:07 PDT)
  - Re: AMBER: Details about Gaussian basis set for Cobalt complex S.Sundar Raman (Sat Aug 26 2006 - 03:51:04 PDT)
    - AMBER: waters closest to specific residues Jardas sucuriba (Sat Aug 26 2006 - 08:39:35 PDT)
    - AMBER: RDF output Jardas sucuriba (Tue Aug 29 2006 - 07:48:29 PDT)
    - RE: AMBER: RDF output Jardas sucuriba (Wed Aug 30 2006 - 14:31:08 PDT)
    - Re: AMBER: RDF output Thomas Cheatham (Wed Aug 30 2006 - 15:18:29 PDT)
AMBER: Calculate interaction energy between small organic molecules Björn C-G. Karlsson (Sun Aug 20 2006 - 23:37:24 PDT)
- Re: AMBER: Calculate interaction energy between small organic molecules David Mobley (Mon Aug 21 2006 - 07:20:42 PDT)
- Re: AMBER: Calculate interaction energy between small organic molecules David A. Case (Mon Aug 21 2006 - 23:14:15 PDT)
AMBER: problem relating all atom structure prediction and folding simulations on AMBER8 priya priya (Mon Aug 21 2006 - 00:46:29 PDT)
- Re: AMBER: problem relating all atom structure prediction and folding simulations on AMBER8 Carlos Simmerling (Mon Aug 21 2006 - 07:19:10 PDT)
- RE: AMBER: problem relating all atom structure prediction and folding simulations on AMBER8 Ross Walker (Mon Aug 21 2006 - 08:48:00 PDT)
  - RE: AMBER: problem relating all atom structure prediction and folding simulations on AMBER8 priya priya (Tue Aug 22 2006 - 21:16:42 PDT)
    - Re: AMBER: problem relating all atom structure prediction and folding simulations on AMBER8 Carlos Simmerling (Wed Aug 23 2006 - 05:18:03 PDT)
    - AMBER: building AMBER9 with gfortran/cygwin Jyh-Shyong Ho (Thu Aug 24 2006 - 19:30:02 PDT)
    - Re: AMBER: building AMBER9 with gfortran/cygwin Andreas Svrcek-Seiler (Fri Aug 25 2006 - 03:39:08 PDT)
    - Re: AMBER: building AMBER9 with gfortran/cygwin David A. Case (Fri Aug 25 2006 - 09:39:40 PDT)
    - Re: AMBER: building AMBER9 with gfortran/cygwin David A. Case (Fri Aug 25 2006 - 08:41:49 PDT)
AMBER: mm_pbsa calculation allocation error AYTUG TUNCEL (Mon Aug 21 2006 - 06:15:31 PDT)
- Re: AMBER: mm_pbsa calculation allocation error Ray Luo (Mon Aug 21 2006 - 09:37:14 PDT)
AMBER: amber naming conventions for structure files sethl.gatech.edu (Tue Aug 22 2006 - 14:36:56 PDT)
Re: AMBER: amber naming conventions for structure files Bill Ross (Tue Aug 22 2006 - 15:00:10 PDT)
AMBER: holding a pair of residues fixed during minimization Seth Lilavivat (Tue Aug 22 2006 - 20:22:06 PDT)
- Re: AMBER: holding a pair of residues fixed during minimization David A. Case (Wed Aug 23 2006 - 13:05:25 PDT)
  - AMBER: Carnal: Internal error: stream file name 2 out of range Shuting Wei (Wed Aug 23 2006 - 13:43:31 PDT)
- Re: AMBER: holding a pair of residues fixed during minimization Bill Ross (Wed Aug 23 2006 - 13:45:13 PDT)
AMBER: compiling parallel amber 9 in linux Amber admin (Wed Aug 23 2006 - 12:00:08 PDT)
- RE: AMBER: compiling parallel amber 9 in linux Ross Walker (Wed Aug 23 2006 - 12:54:39 PDT)
- Re: AMBER: compiling parallel amber 9 in linux David A. Case (Wed Aug 23 2006 - 13:01:35 PDT)
- RE: AMBER: compiling parallel amber 9 in linux Amber admin (Thu Aug 24 2006 - 17:10:57 PDT)
Re: AMBER: Carnal: Internal error: stream file name 2 out of range Bill Ross (Wed Aug 23 2006 - 14:16:16 PDT)
AMBER: 0 steps the same as 1 step? S. Jamal Rahi (Wed Aug 23 2006 - 14:25:44 PDT)
- Re: AMBER: 0 steps the same as 1 step? David A. Case (Wed Aug 23 2006 - 18:14:53 PDT)
  - AMBER: Can I run RED/RESP for Platinum Complexes? a a (Thu Aug 24 2006 - 02:50:42 PDT)
    - AMBER: nmode memory problem William Wei (Thu Aug 24 2006 - 08:29:13 PDT)
    - Re: AMBER: nmode memory problem Knut Langsestmo (Thu Aug 24 2006 - 09:17:04 PDT)
    - Re: AMBER: nmode memory problem William Wei (Thu Aug 24 2006 - 10:04:59 PDT)
    - RE: AMBER: nmode memory problem Ross Walker (Thu Aug 24 2006 - 10:57:12 PDT)
    - Re: AMBER: nmode memory problem William Wei (Thu Aug 24 2006 - 14:05:55 PDT)
    - Re: AMBER: nmode memory problem Atro Tossavainen (Fri Aug 25 2006 - 03:10:50 PDT)
AMBER: antechamber charge calculation very sensitive to conformations ? Christophe Guilbert (Wed Aug 23 2006 - 18:59:08 PDT)
- RE: AMBER: antechamber charge calculation very sensitive to conformations ? Junmei Wang (Thu Aug 24 2006 - 19:51:07 PDT)
  - Re: AMBER: antechamber charge calculation very sensitive to conformations ? David Mobley (Fri Aug 25 2006 - 08:08:44 PDT)
AMBER: Calculate interaction energy between small organic molecules Björn C-G. Karlsson (Wed Aug 23 2006 - 23:17:56 PDT)
- Re: AMBER: Calculate interaction energy between small organic molecules David Mobley (Thu Aug 24 2006 - 13:07:57 PDT)
  - Re: AMBER: Calculate interaction energy between small organic molecules David LeBard (Thu Aug 24 2006 - 14:01:16 PDT)
AMBER: ptraj dumpq feature/bug Markus Kaukonen (Thu Aug 24 2006 - 01:31:51 PDT)
- Re: AMBER: ptraj dumpq feature/bug Thomas Cheatham (Thu Aug 24 2006 - 13:16:23 PDT)
AMBER: Backbone & Sidechain atoms: Definition Zu Thur Yew (Thu Aug 24 2006 - 06:13:14 PDT)
- Re: AMBER: Backbone & Sidechain atoms: Definition David A. Case (Thu Aug 24 2006 - 08:15:44 PDT)
  - Re: AMBER: Backbone & Sidechain atoms: Definition Zu Thur Yew (Thu Aug 24 2006 - 10:32:14 PDT)
AMBER: TI vlimit exceeded Andrea Bortolato (Thu Aug 24 2006 - 06:42:21 PDT)
- Re: AMBER: TI vlimit exceeded David A. Case (Sat Aug 26 2006 - 10:38:58 PDT)
AMBER: increase force constants Mahalakshmi Sahasranaman (Thu Aug 24 2006 - 06:45:28 PDT)
- Re: AMBER: increase force constants David A. Case (Thu Aug 24 2006 - 15:56:33 PDT)
- Re: AMBER: increase force constants Amber admin (Thu Aug 24 2006 - 17:15:24 PDT)
AMBER: Installation amber 9 on IBM SP4 Myunggi Yi (Thu Aug 24 2006 - 09:05:50 PDT)
- RE: AMBER: Installation amber 9 on IBM SP4 Ross Walker (Thu Aug 24 2006 - 10:23:02 PDT)
  - Re: AMBER: Installation amber 9 on IBM SP4 Myunggi Yi (Thu Aug 24 2006 - 12:00:04 PDT)
    - RE: AMBER: Installation amber 9 on IBM SP4 Ross Walker (Thu Aug 24 2006 - 15:08:03 PDT)
    - Re: AMBER: Installation amber 9 on IBM SP4 Myunggi Yi (Thu Aug 24 2006 - 18:29:58 PDT)
    - Re: AMBER: Installation amber 9 on IBM SP4 Scott Brozell (Thu Aug 24 2006 - 18:50:31 PDT)
    - Re: AMBER: Installation amber 9 on IBM SP4 Myunggi Yi (Thu Aug 24 2006 - 19:39:43 PDT)
    - Re: AMBER: Installation amber 9 on IBM SP4 Myunggi Yi (Thu Aug 24 2006 - 19:48:07 PDT)
    - Re: AMBER: Installation amber 9 on IBM SP4 Myunggi Yi (Thu Aug 24 2006 - 19:59:09 PDT)
    - Re: AMBER: Installation amber 9 on IBM SP4 Myunggi Yi (Thu Aug 24 2006 - 20:09:29 PDT)
    - Re: AMBER: Installation amber 9 on IBM SP4 Myunggi Yi (Thu Aug 24 2006 - 20:20:12 PDT)
    - Re: AMBER: Installation amber 9 on IBM SP4 Scott Brozell (Thu Aug 24 2006 - 23:28:35 PDT)
    - Re: AMBER: Installation amber 9 on IBM SP4 Scott Brozell (Thu Aug 24 2006 - 23:45:09 PDT)
    - Re: AMBER: Installation amber 9 on IBM SP4 Scott Brozell (Fri Oct 06 2006 - 10:13:15 PDT)
    - Re: AMBER: Installation amber 9 on IBM SP4; bugfix 12 Scott Brozell (Thu Aug 24 2006 - 19:57:03 PDT)
    - Re: AMBER: Installation amber 9 on IBM SP4 Scott Brozell (Thu Aug 24 2006 - 19:58:20 PDT)
    - Re: AMBER: Installation amber 9 on IBM SP4 David A. Case (Fri Aug 25 2006 - 08:03:10 PDT)
    - RE: AMBER: Installation amber 9 on IBM SP4 Ross Walker (Fri Aug 25 2006 - 09:16:13 PDT)
    - Re: AMBER: Installation amber 9 on IBM SP4 Myunggi Yi (Fri Aug 25 2006 - 18:20:47 PDT)
    - Re: AMBER: Installation amber 9 on IBM SP4 Jyh-Shyong Ho (Fri Aug 25 2006 - 19:11:21 PDT)
    - Re: AMBER: Installation amber 9 on IBM SP4 Myunggi Yi (Fri Aug 25 2006 - 19:41:46 PDT)
AMBER: how to use AddPdbAtomMap sethl.gatech.edu (Thu Aug 24 2006 - 13:03:59 PDT)
- Re: AMBER: how to use AddPdbAtomMap Ilyas Yildirim (Thu Aug 24 2006 - 13:27:41 PDT)
- Re: AMBER: how to use AddPdbAtomMap David A. Case (Thu Aug 24 2006 - 15:47:50 PDT)
AMBER: atomifluct Miguel Ferreira (Fri Aug 25 2006 - 04:09:03 PDT)
AMBER: How to create a modified NA in leap sethl.gatech.edu (Fri Aug 25 2006 - 13:20:35 PDT)
Re: AMBER: How to create a modified NA in leap Bill Ross (Fri Aug 25 2006 - 14:52:40 PDT)
- Re: AMBER: How to create a modified NA in leap sethl.gatech.edu (Sat Aug 26 2006 - 13:13:10 PDT)
- Re: AMBER: How to create a modified NA in leap Bill Ross (Sat Aug 26 2006 - 17:21:41 PDT)
AMBER: Error in compliling AMBER 9 on Fedora 5 linux machine Gobind Bisht (Sat Aug 26 2006 - 22:24:12 PDT)
- Re: AMBER: Error in compliling AMBER 9 on Fedora 5 linux machine David A. Case (Sun Aug 27 2006 - 09:03:54 PDT)
AMBER: Temperature fluctuation with Langevin Temperature control Gobind Singh Bisht (Sun Aug 27 2006 - 12:06:49 PDT)
- Re: AMBER: Temperature fluctuation with Langevin Temperature control Adrian Roitberg (Sun Aug 27 2006 - 14:07:07 PDT)
  - Re: AMBER: Temperature fluctuation with Langevin Temperature control David A. Case (Mon Aug 28 2006 - 10:32:08 PDT)
    - AMBER: Tutorial 2 - Section 4: Summary.density and summary.temp a a (Tue Aug 29 2006 - 03:15:07 PDT)
    - RE: AMBER: Tutorial 2 - Section 4: Summary.density and summary.temp Ross Walker (Wed Aug 30 2006 - 19:04:36 PDT)
AMBER: TI, mutation eric.henon.univ-reims.fr (Mon Aug 28 2006 - 05:39:48 PDT)
- Re: AMBER: TI, mutation Carlos Simmerling (Mon Aug 28 2006 - 05:18:56 PDT)
- Re: AMBER: TI, mutation Pradipta Bandyopadhyay (Mon Aug 28 2006 - 05:46:43 PDT)
- Re: AMBER: TI, mutation eric.henon.univ-reims.fr (Tue Aug 29 2006 - 01:43:04 PDT)
AMBER: preparing ligand/rna structure for MD sethl.gatech.edu (Mon Aug 28 2006 - 11:45:17 PDT)
- Re: AMBER: preparing ligand/rna structure for MD David A. Case (Mon Aug 28 2006 - 17:11:34 PDT)
AMBER: Periodic boundary condition (PBC) Rahaman, Asif (Mon Aug 28 2006 - 13:24:19 PDT)
- Re: AMBER: Periodic boundary condition (PBC) Carlos Simmerling (Mon Aug 28 2006 - 13:40:05 PDT)
- Re: AMBER: Periodic boundary condition (PBC) Bill Ross (Mon Aug 28 2006 - 16:21:57 PDT)
- Re: AMBER: Periodic boundary condition (PBC) David A. Case (Mon Aug 28 2006 - 17:17:42 PDT)
AMBER: nmode: number of atoms limitation AYTUG TUNCEL (Mon Aug 28 2006 - 16:15:04 PDT)
- Re: AMBER: nmode: number of atoms limitation David A. Case (Mon Aug 28 2006 - 22:55:53 PDT)
- Re: AMBER: nmode: number of atoms limitation Cenk Andac (Wed Aug 30 2006 - 06:01:58 PDT)
  - Re: Re: AMBER: nmode: number of atoms limitation Changge Ji (Mon Aug 28 2006 - 23:33:27 PDT)
AMBER: how to limit the simulation space Eric Hu (Mon Aug 28 2006 - 17:55:11 PDT)
Re: AMBER: how to limit the simulation space Bill Ross (Mon Aug 28 2006 - 18:04:39 PDT)
AMBER: counterions and particle-mesh-ewald cristian obiol (Tue Aug 29 2006 - 01:06:20 PDT)
- Re: AMBER: counterions and particle-mesh-ewald David A. Case (Wed Aug 30 2006 - 13:14:40 PDT)
  - Re: AMBER: counterions and particle-mesh-ewald darden (Wed Aug 30 2006 - 15:59:32 PDT)
AMBER: Qingning Shu (Tue Aug 29 2006 - 06:01:58 PDT)
- Re: AMBER: David A. Case (Tue Aug 29 2006 - 08:09:23 PDT)
  - AMBER: Missing LES reference in Amber 9 manual Chris Moth (Tue Aug 29 2006 - 11:43:12 PDT)
    - Re: AMBER: Missing LES reference in Amber 9 manual David A. Case (Wed Aug 30 2006 - 09:03:34 PDT)
AMBER: REMD: Hybrid topology file Austin B. Yongye (Wed Aug 30 2006 - 07:30:34 PDT)
- Re: AMBER: REMD: Hybrid topology file Carlos Simmerling (Wed Aug 30 2006 - 07:48:20 PDT)
AMBER: 1-4 interaction in AMBER8 Jianhui (Wed Aug 30 2006 - 12:08:09 PDT)
- Re: AMBER: 1-4 interaction in AMBER8 Carlos Simmerling (Wed Aug 30 2006 - 12:22:13 PDT)
- Re: AMBER: 1-4 interaction in AMBER8 Jianhui (Wed Aug 30 2006 - 12:48:28 PDT)
  - Re: AMBER: 1-4 interaction in AMBER8 Carlos Simmerling (Wed Aug 30 2006 - 14:23:26 PDT)
- Re: AMBER: 1-4 interaction in AMBER8 Bill Ross (Wed Aug 30 2006 - 14:05:27 PDT)
  - Re: AMBER: 1-4 interaction in AMBER8 Carlos Simmerling (Wed Aug 30 2006 - 14:15:23 PDT)
- Re: AMBER: 1-4 interaction in AMBER8 Bill Ross (Wed Aug 30 2006 - 14:17:10 PDT)
AMBER: reference of ff99 Myunggi Yi (Thu Aug 31 2006 - 08:59:51 PDT)
- Re: AMBER: reference of ff99 Carlos Simmerling (Thu Aug 31 2006 - 09:18:09 PDT)
- Re: AMBER: reference of ff99 Myunggi Yi (Thu Aug 31 2006 - 09:21:59 PDT)
  - Re: AMBER: reference of ff99 Myunggi Yi (Thu Aug 31 2006 - 09:26:09 PDT)
- Re: AMBER: reference of ff99 David A. Case (Thu Aug 31 2006 - 09:43:50 PDT)
AMBER: Question about free energy with mm_pbsa William Wei (Thu Aug 31 2006 - 11:50:11 PDT)
- Re: AMBER: Question about free energy with mm_pbsa David A. Case (Thu Aug 31 2006 - 22:32:54 PDT)
- Re: AMBER: Question about free energy with mm_pbsa Thomas Cheatham (Thu Aug 31 2006 - 23:23:59 PDT)
- Re: AMBER: Question about free energy with mm_pbsa William Wei (Fri Sep 01 2006 - 06:32:29 PDT)
RE: AMBER: Periodic boundary condition (PBC) > Problem now with ptraj Rahaman, Asif (Thu Aug 31 2006 - 13:24:43 PDT)
- RE: AMBER: Periodic boundary condition (PBC) > Problem now with ptraj Thomas Cheatham (Thu Aug 31 2006 - 13:49:42 PDT)
- RE: AMBER: Periodic boundary condition (PBC) > Problem now with ptraj Rahaman, Asif (Thu Aug 31 2006 - 14:34:50 PDT)
  - RE: AMBER: Periodic boundary condition (PBC) > Problem now with ptraj Thomas Cheatham (Thu Aug 31 2006 - 14:50:33 PDT)
- RE: AMBER: Periodic boundary condition (PBC) > Problem now with ptraj Rahaman, Asif (Thu Aug 31 2006 - 15:29:25 PDT)
  - RE: AMBER: Periodic boundary condition (PBC) > Problem now with ptraj Thomas Cheatham (Thu Aug 31 2006 - 21:38:02 PDT)
AMBER: minimization with my own charges Myunggi Yi (Thu Aug 31 2006 - 15:01:24 PDT)
- Re: AMBER: minimization with my own charges Ilyas Yildirim (Thu Aug 31 2006 - 15:12:24 PDT)
  - Re: AMBER: minimization with my own charges Myunggi Yi (Thu Aug 31 2006 - 15:22:08 PDT)
    - Re: AMBER: minimization with my own charges Ilyas Yildirim (Thu Aug 31 2006 - 15:50:26 PDT)
    - Re: AMBER: minimization with my own charges Myunggi Yi (Thu Aug 31 2006 - 16:13:29 PDT)
    - Re: AMBER: minimization with my own charges Ilyas Yildirim (Thu Aug 31 2006 - 16:47:54 PDT)
    - Re: AMBER: minimization with my own charges Myunggi Yi (Thu Aug 31 2006 - 18:16:49 PDT)
    - Re: AMBER: minimization with my own charges Ilyas Yildirim (Thu Aug 31 2006 - 20:37:18 PDT)
    - Re: AMBER: minimization with my own charges Thomas Cheatham (Thu Aug 31 2006 - 21:07:40 PDT)
    - AMBER: equilibration in explicit solvent Amarda Shehu (Sun Feb 04 2007 - 09:40:12 PST)
    - Re: AMBER: equilibration in explicit solvent David A. Case (Sun Feb 04 2007 - 10:21:18 PST)
    - Re: AMBER: equilibration in explicit solvent Amarda Shehu (Sun Feb 04 2007 - 10:32:05 PST)
    - Re: AMBER: equilibration in explicit solvent David A. Case (Sun Feb 04 2007 - 21:27:44 PST)
    - Re: AMBER: equilibration in explicit solvent Amarda Shehu (Thu Feb 08 2007 - 09:37:39 PST)
    - Re: AMBER: equilibration in explicit solvent Amarda Shehu (Thu Feb 08 2007 - 11:48:23 PST)
    - Re: AMBER: equilibration in explicit solvent Ilyas Yildirim (Thu Feb 08 2007 - 12:16:10 PST)
    - Re: AMBER: equilibration in explicit solvent Carlos Simmerling (Mon Feb 05 2007 - 10:35:30 PST)
    - RE: AMBER: equilibration in explicit solvent Yong Duan (Sun Feb 04 2007 - 11:07:30 PST)
    - Re: AMBER: equilibration in explicit solvent Ilyas Yildirim (Sun Feb 04 2007 - 21:13:48 PST)
AMBER: Error: cannot run "$AMBERHOME/exe/divcon" of bcc() in charge.c Jiten (Thu Aug 31 2006 - 23:55:21 PDT)
- Re: AMBER: Error: cannot run "$AMBERHOME/exe/divcon" of bcc() in charge.c David A. Case (Fri Sep 01 2006 - 07:34:10 PDT)
AMBER: force fields for proflavine molecule sethl.gatech.edu (Fri Sep 01 2006 - 10:49:00 PDT)
AMBER: output file not generated bala (Fri Sep 01 2006 - 08:35:40 PDT)
AMBER: Gaussian, antechamber, RESP Ed Pate (Sat Sep 02 2006 - 14:42:11 PDT)
- Re: AMBER: Gaussian, antechamber, RESP Stefano Federico Massimiliano Pieraccini (Stefano.Pieraccini) (Sun Sep 03 2006 - 05:57:57 PDT)
AMBER: Question about LEAP and twisting a dihedral angle Ilyas Yildirim (Sat Sep 02 2006 - 18:52:45 PDT)
- Re: AMBER: Question about LEAP and twisting a dihedral angle David A. Case (Sat Sep 02 2006 - 22:06:04 PDT)
  - Re: AMBER: Question about LEAP and twisting a dihedral angle Ilyas Yildirim (Sat Sep 02 2006 - 23:20:27 PDT)
    - Re: AMBER: Question about LEAP and twisting a dihedral angle David A. Case (Sun Sep 03 2006 - 08:55:16 PDT)
    - Re: AMBER: Question about LEAP and twisting a dihedral angle Ilyas Yildirim (Wed Sep 06 2006 - 01:46:57 PDT)
AMBER: Amber9: Free Energy Franck_Vendeix.ncsu.edu (Sun Sep 03 2006 - 16:11:44 PDT)
- Re: AMBER: Amber9: Free Energy David A. Case (Sun Sep 03 2006 - 18:57:50 PDT)
  - Re: AMBER: Amber9: Free Energy Franck_Vendeix.ncsu.edu (Sun Sep 03 2006 - 19:27:13 PDT)
AMBER: ligand file Fenghui Fan (Mon Sep 04 2006 - 11:20:27 PDT)
- Re: AMBER: ligand file David A. Case (Mon Sep 04 2006 - 12:02:34 PDT)
AMBER: cAMP ligand file Fenghui Fan (Mon Sep 04 2006 - 13:00:47 PDT)
AMBER: Implicit Water - Force field parameters Ramdas Pophale (Tue Sep 05 2006 - 12:22:49 PDT)
- Re: AMBER: Implicit Water - Force field parameters Fenghui Fan (Tue Sep 05 2006 - 13:16:37 PDT)
- Re: AMBER: Implicit Water - Force field parameters Ilyas Yildirim (Tue Sep 05 2006 - 13:22:13 PDT)
- Re: AMBER: Implicit Water - Force field parameters David A. Case (Wed Sep 06 2006 - 08:54:15 PDT)
AMBER: a ligand file Fenghui Fan (Tue Sep 05 2006 - 13:18:51 PDT)
- Re: AMBER: a ligand file David A. Case (Tue Sep 05 2006 - 13:55:26 PDT)
  - Re: AMBER: a ligand file Fenghui Fan (Wed Sep 06 2006 - 14:16:58 PDT)
    - Re: AMBER: a ligand file David A. Case (Wed Sep 06 2006 - 14:40:30 PDT)
AMBER: help with antechamber - creating ligand sethl.gatech.edu (Tue Sep 05 2006 - 14:10:08 PDT)
- Re: AMBER: help with antechamber - creating ligand Ilyas Yildirim (Tue Sep 05 2006 - 14:26:11 PDT)
- Re: AMBER: help with antechamber - creating ligand David A. Case (Tue Sep 05 2006 - 19:11:52 PDT)
AMBER: Amber parallel version Franck_Vendeix.ncsu.edu (Tue Sep 05 2006 - 23:05:20 PDT)
- Re: AMBER: Amber parallel version Jyh-Shyong Ho (Tue Sep 05 2006 - 23:43:08 PDT)
  - Re: AMBER: Amber parallel version Franck_Vendeix.ncsu.edu (Thu Sep 07 2006 - 11:45:47 PDT)
AMBER: PARAMETERISATION PROBLEM Claire Zerafa (Wed Sep 06 2006 - 07:12:04 PDT)
- Re: AMBER: PARAMETERISATION PROBLEM David A. Case (Wed Sep 06 2006 - 08:20:43 PDT)
AMBER: Question about using PMEMD and GB H W (Wed Sep 06 2006 - 10:41:12 PDT)
- Re: AMBER: Question about using PMEMD and GB David A. Case (Wed Sep 06 2006 - 10:58:59 PDT)
  - Re: AMBER: Question about using PMEMD and GB H W (Wed Sep 06 2006 - 11:31:20 PDT)
AMBER: improper torsion angle problem Fabian Alejandro Rodriguez (Wed Sep 06 2006 - 14:52:40 PDT)
- Re: AMBER: improper torsion angle problem David A. Case (Sun Sep 17 2006 - 16:52:38 PDT)
AMBER: trajout Weihua Li (Wed Sep 06 2006 - 20:22:28 PDT)
- Re: AMBER: trajout Carlos Simmerling (Thu Sep 07 2006 - 04:04:02 PDT)
AMBER: Ca2+ polarizability Martin LEPSIK (Thu Sep 07 2006 - 02:02:38 PDT)
AMBER: mdcrd file Jianhui (Thu Sep 07 2006 - 07:15:45 PDT)
- Re: AMBER: mdcrd file Mark Williamson (Thu Sep 07 2006 - 10:39:12 PDT)
  - Re: AMBER: mdcrd file Brent Krueger (Thu Sep 07 2006 - 19:55:27 PDT)
    - Re: AMBER: mdcrd file David A. Case (Thu Sep 07 2006 - 22:27:54 PDT)
    - Re: AMBER: mdcrd file Joseph Nachman (Fri Sep 08 2006 - 10:36:42 PDT)
    - Re: AMBER: mdcrd file Carlos Simmerling (Fri Sep 08 2006 - 13:54:34 PDT)
    - Re: AMBER: mdcrd file Joseph Nachman (Mon Sep 11 2006 - 11:00:21 PDT)
- RE: AMBER: mdcrd file Ross Walker (Thu Sep 07 2006 - 15:52:28 PDT)
AMBER: leap - how to recognize my structure sethl.gatech.edu (Thu Sep 07 2006 - 15:16:06 PDT)
- Re: AMBER: leap - how to recognize my structure Carlos Simmerling (Thu Sep 07 2006 - 15:34:09 PDT)
AMBER: nmode memory allocation error AYTUG TUNCEL (Fri Sep 08 2006 - 01:41:35 PDT)
- Re: AMBER: nmode memory allocation error David A. Case (Sat Sep 09 2006 - 21:17:54 PDT)
- Re: AMBER: nmode memory allocation error Cenk Andac (Mon Sep 11 2006 - 02:48:30 PDT)
AMBER: hydronium ion parameters Myunggi Yi (Fri Sep 08 2006 - 07:15:32 PDT)
- Re: AMBER: hydronium ion parameters Myunggi Yi (Fri Sep 08 2006 - 07:31:33 PDT)
  - Re: AMBER: hydronium ion parameters Ilyas Yildirim (Fri Sep 08 2006 - 13:41:17 PDT)
- Re: AMBER: hydronium ion parameters Jiten (Fri Sep 08 2006 - 08:12:03 PDT)
  - Re: AMBER: hydronium ion parameters Myunggi Yi (Fri Sep 08 2006 - 09:09:55 PDT)
AMBER: Problem with ptraj Gobind Singh Bisht (Fri Sep 08 2006 - 14:00:19 PDT)
- Re: AMBER: Problem with ptraj Gobind Singh Bisht (Fri Sep 08 2006 - 21:35:28 PDT)
- Re: AMBER: Problem with ptraj Thomas Cheatham (Tue Sep 12 2006 - 19:47:46 PDT)
AMBER: LEAP - "could not find type: NH" sethl.gatech.edu (Fri Sep 08 2006 - 14:08:11 PDT)
- Re: AMBER: LEAP - "could not find type: NH" Ilyas Yildirim (Fri Sep 08 2006 - 15:42:46 PDT)
AMBER: seg fault during test.serial Lachele Foley (Lists) (Fri Sep 08 2006 - 13:45:05 PDT)
- Re: AMBER: seg fault during test.serial David A. Case (Fri Sep 08 2006 - 18:19:16 PDT)
  - AMBER: a ligand file Fenghui Fan (Fri Sep 08 2006 - 18:31:59 PDT)
    - Re: AMBER: a ligand file David A. Case (Fri Sep 08 2006 - 18:53:18 PDT)
    - Re: AMBER: a ligand file Fenghui Fan (Fri Sep 08 2006 - 20:06:49 PDT)
    - Re: AMBER: a ligand file Ilyas Yildirim (Fri Sep 08 2006 - 21:05:11 PDT)
    - Re: AMBER: a ligand file Ilyas Yildirim (Fri Sep 08 2006 - 19:23:48 PDT)
  - Re: AMBER: seg fault during test.serial Lachele Foley (Lists) (Mon Sep 11 2006 - 07:50:57 PDT)
    - Re: AMBER: seg fault during test.serial David A. Case (Mon Sep 11 2006 - 08:54:43 PDT)
AMBER: pmf with respect to a surface Rahaman, Asif (Fri Sep 08 2006 - 15:35:22 PDT)
- Re: AMBER: pmf with respect to a surface David A. Case (Sat Sep 09 2006 - 21:14:30 PDT)
AMBER: post nmanal 杉森正道 (Fri Sep 08 2006 - 23:03:47 PDT)
- Re: AMBER: post nmanal David A. Case (Sat Sep 09 2006 - 09:54:34 PDT)
  - Re: AMBER: post nmanal 杉森正道 (Sun Sep 10 2006 - 23:09:28 PDT)
AMBER: EGB term decomposition backy (Sat Sep 09 2006 - 02:00:08 PDT)
AMBER: EGB term decomposition backy (Sat Sep 09 2006 - 01:57:43 PDT)
AMBER: EGB term decomposition backy (Sat Sep 09 2006 - 02:01:34 PDT)
AMBER: protein-ligand interaction Fenghui Fan (Sat Sep 09 2006 - 09:59:51 PDT)
- Re: AMBER: protein-ligand interaction Ilyas Yildirim (Sat Sep 09 2006 - 14:58:10 PDT)
AMBER: resp Fenghui Fan (Sat Sep 09 2006 - 18:03:06 PDT)
AMBER: resp Fenghui Fan (Sat Sep 09 2006 - 18:07:48 PDT)
- Re: AMBER: resp FyD (Sun Sep 10 2006 - 00:46:11 PDT)
AMBER: Parmchk problems (parm99.dat) Prashanth Athri (Sun Sep 10 2006 - 17:23:25 PDT)
- RE: AMBER: Parmchk problems (parm99.dat) Junmei Wang (Mon Sep 11 2006 - 13:48:51 PDT)
  - RE: AMBER: Parmchk problems (parm99.dat) Prashanth Athri (Tue Sep 12 2006 - 08:54:08 PDT)
    - RE: AMBER: Parmchk problems (parm99.dat) Prashanth Athri (Tue Sep 12 2006 - 10:10:55 PDT)
- RE: AMBER: Parmchk problems (parm99.dat) Junmei Wang (Tue Sep 12 2006 - 11:41:21 PDT)
  - RE: AMBER: Parmchk problems (parm99.dat) Prashanth Athri (Tue Sep 12 2006 - 12:30:02 PDT)
  - RE: AMBER: Parmchk problems (parm99.dat) Piotr Cieplak (Wed Sep 20 2006 - 20:46:19 PDT)
    - Re: AMBER: Parmchk problems (parm99.dat) David A. Case (Wed Sep 20 2006 - 21:22:56 PDT)
- RE: AMBER: Parmchk problems (parm99.dat) Junmei Wang (Tue Sep 12 2006 - 13:44:30 PDT)
AMBER: (no subject) Prashanth Athri (Sun Sep 10 2006 - 17:23:05 PDT)
AMBER: Oon Modeling the metalloprotein with GB model. wenfei Li (Mon Sep 11 2006 - 00:41:16 PDT)
- AMBER: mm_pbsa snapshots for "three-trajectory" In Hee Park (Thu Sep 14 2006 - 16:42:13 PDT)
AMBER: Error in Running Sander Jianhui Tian (Mon Sep 11 2006 - 06:52:39 PDT)
- Re: AMBER: Error in Running Sander David A. Case (Mon Sep 11 2006 - 08:59:45 PDT)
- Re: AMBER: Error in Running Sander Jianhui (Mon Sep 11 2006 - 10:10:55 PDT)
AMBER: set a trucated octahedron box in Leap Vlad Cojocaru (Mon Sep 11 2006 - 07:24:44 PDT)
- AMBER: How to get the ligand. ac file Fenghui Fan (Mon Sep 11 2006 - 07:46:54 PDT)
- Re: AMBER: set a trucated octahedron box in Leap David A. Case (Mon Sep 11 2006 - 08:56:59 PDT)
  - Re: AMBER: set a trucated octahedron box in Leap Vlad Cojocaru (Tue Sep 12 2006 - 01:30:06 PDT)
    - Re: AMBER: set a trucated octahedron box in Leap Ilyas Yildirim (Tue Sep 12 2006 - 01:48:56 PDT)
    - Re: AMBER: set a trucated octahedron box in Leap David A. Case (Tue Sep 12 2006 - 08:03:24 PDT)
AMBER: cAMP ligand charge Fenghui Fan (Mon Sep 11 2006 - 08:06:40 PDT)
- Re: AMBER: cAMP ligand charge David A. Case (Mon Sep 11 2006 - 08:35:53 PDT)
AMBER: Parallel compile: ld: cannot find -lfmpi Lachele Foley (Lists) (Mon Sep 11 2006 - 08:38:00 PDT)
- Re: AMBER: Parallel compile: ld: cannot find -lfmpi David A. Case (Mon Sep 11 2006 - 11:19:12 PDT)
  - Re: AMBER: Parallel compile: ld: cannot find -lfmpi Lachele Foley (Lists) (Mon Sep 11 2006 - 13:39:55 PDT)
AMBER: System in polarizable waters Martin LEPSIK (Mon Sep 11 2006 - 09:14:24 PDT)
- Re: AMBER: System in polarizable waters David A. Case (Mon Sep 11 2006 - 11:12:04 PDT)
AMBER: angle between helices 张勇 (Mon Sep 11 2006 - 19:05:51 PDT)
AMBER: Installing AMBER9 on cygwin (WinXP) HARADA Makoto (Tue Sep 12 2006 - 02:38:19 PDT)
- Re: AMBER: Installing AMBER9 on cygwin (WinXP) Gobind Singh Bisht (Tue Sep 12 2006 - 04:57:06 PDT)
- Re: AMBER: Installing AMBER9 on cygwin (WinXP) David A. Case (Tue Sep 12 2006 - 08:01:41 PDT)
AMBER: forrtl: severe (64): input conversion error, unit 9, file Ilyas Yildirim (Tue Sep 12 2006 - 14:09:34 PDT)
- RE: AMBER: forrtl: severe (64): input conversion error, unit 9, file Ross Walker (Tue Sep 12 2006 - 14:35:47 PDT)
  - RE: AMBER: forrtl: severe (64): input conversion error, unit 9, file Ilyas Yildirim (Tue Sep 12 2006 - 15:49:33 PDT)
AMBER: about ligand charge Fenghui Fan (Tue Sep 12 2006 - 20:16:27 PDT)
AMBER: how to feed dihedral angles of our choice to the linear sequence in amber8 priya priya (Wed Sep 13 2006 - 02:02:33 PDT)
- AW: AMBER: how to feed dihedral angles of our choice to the linear sequence in amber8 Hannes Barsch (Wed Sep 13 2006 - 06:54:54 PDT)
- Re: AMBER: how to feed dihedral angles of our choice to the linear sequence in amber8 Ilyas Yildirim (Wed Sep 13 2006 - 10:59:10 PDT)
AMBER: 'lastrst' error for amber8 Arvind Marathe (Wed Sep 13 2006 - 05:52:07 PDT)
- Re: AMBER: 'lastrst' error for amber8 michael crowley (Wed Sep 13 2006 - 08:14:08 PDT)
  - Re: AMBER: 'lastrst' error for amber8 Arvind Marathe (Thu Sep 14 2006 - 06:08:08 PDT)
    - Re: AMBER: 'lastrst' error for amber8 David A. Case (Thu Sep 14 2006 - 08:05:25 PDT)
    - Re: AMBER: 'lastrst' error for amber8 Arvind Marathe (Fri Sep 15 2006 - 13:01:43 PDT)
    - Re: AMBER: 'lastrst' error for amber8 David A. Case (Sat Sep 16 2006 - 09:50:31 PDT)
    - Re: AMBER: 'lastrst' error for amber8 Arvind Marathe (Sun Sep 17 2006 - 05:02:09 PDT)
    - Re: AMBER: 'lastrst' error for amber8 Arvind Marathe (Sun Sep 17 2006 - 23:50:41 PDT)
    - Re: AMBER: 'lastrst' error for amber8 David A. Case (Mon Sep 18 2006 - 08:44:49 PDT)
    - Re: AMBER: 'lastrst' error for amber8 Arvind Marathe (Mon Sep 18 2006 - 09:25:33 PDT)
    - Re: AMBER: 'lastrst' error for amber8 David A. Case (Mon Sep 18 2006 - 09:41:56 PDT)
    - Re: AMBER: 'lastrst' error for amber8 Arvind Marathe (Mon Sep 18 2006 - 10:44:11 PDT)
- Re: AMBER: 'lastrst' error for amber8 Robert Duke (Wed Sep 13 2006 - 08:28:16 PDT)
AMBER: "NO CONVERGENCE IN SCF CALCULATION" in divcon in Amber9 package Zhihong Yu (Wed Sep 13 2006 - 05:57:44 PDT)
- Re: AMBER: "NO CONVERGENCE IN SCF CALCULATION" in divcon in Amber9 package David A. Case (Wed Sep 13 2006 - 09:32:39 PDT)
- Re: AMBER: "NO CONVERGENCE IN SCF CALCULATION" in divcon in Amber9 package Zhihong Yu (Wed Sep 13 2006 - 20:21:07 PDT)
  - Re: AMBER: "NO CONVERGENCE IN SCF CALCULATION" in divcon in Amber9 package David A. Case (Wed Sep 13 2006 - 22:53:50 PDT)
- Re: AMBER: "NO CONVERGENCE IN SCF CALCULATION" in divcon in Amber9 package Zhihong Yu (Wed Sep 13 2006 - 23:47:07 PDT)
AMBER: On the temperature increasement in the restriction MD in the tutorial 2 section 5 Fenghui Fan (Wed Sep 13 2006 - 07:23:33 PDT)
- Re: AMBER: On the temperature increasement in the restriction MD in the tutorial 2 section 5 Thomas Cheatham (Wed Sep 13 2006 - 08:48:54 PDT)
AMBER: RDC refinement Young-Tae Lee (Wed Sep 13 2006 - 08:13:30 PDT)
- Re: AMBER: RDC refinement David A. Case (Wed Sep 13 2006 - 08:35:07 PDT)
AMBER: energy data for limited part of system Tanya Johannsen (Wed Sep 13 2006 - 10:57:15 PDT)
- Re: AMBER: energy data for limited part of system David A. Case (Sun Sep 17 2006 - 16:56:23 PDT)
  - AMBER: potential energy Fenghui Fan (Sun Sep 17 2006 - 17:38:44 PDT)
    - RE: AMBER: potential energy Ross Walker (Mon Sep 18 2006 - 08:52:23 PDT)
    - Re: RE: AMBER: potential energy linfu (Mon Sep 18 2006 - 18:44:18 PDT)
    - Re: [UCE]Re: RE: AMBER: potential energy Thomas Cheatham (Mon Sep 18 2006 - 19:16:20 PDT)
    - Re: [UCE]Re: RE: AMBER: potential energy Fenghui Fan (Mon Sep 18 2006 - 19:41:09 PDT)
    - RE: [UCE]Re: RE: AMBER: potential energy Ross Walker (Mon Sep 18 2006 - 21:01:04 PDT)
    - Re: RE: AMBER: potential energy Thomas Cheatham (Tue Sep 19 2006 - 09:57:47 PDT)
AMBER: residence time of water molecules venditti2.unisi.it (Wed Sep 13 2006 - 07:56:34 PDT)
- Re: AMBER: residence time of water molecules Angelo (Thu Sep 14 2006 - 01:57:38 PDT)
AMBER: the time length of the restricted MD Fenghui Fan (Wed Sep 13 2006 - 12:38:59 PDT)
AMBER: Mixed solvent? Mingfeng Yang (Wed Sep 13 2006 - 12:44:32 PDT)
AMBER: Error in reading RDC data Lee, Young-Tae (Wed Sep 13 2006 - 13:09:42 PDT)
- Re: AMBER: Error in reading RDC data David A. Case (Wed Sep 13 2006 - 14:44:14 PDT)
AMBER: MAXM in nmode William Wei (Wed Sep 13 2006 - 13:24:14 PDT)
- Re: AMBER: MAXM in nmode William Wei (Wed Sep 13 2006 - 14:07:52 PDT)
- Re: AMBER: MAXM in nmode David A. Case (Wed Sep 13 2006 - 14:17:29 PDT)
AMBER: LENNARD_JONES_ACOEF & BCOEF prmtop changes Michael Mazanetz (Wed Sep 13 2006 - 13:42:02 PDT)
- Re: AMBER: LENNARD_JONES_ACOEF & BCOEF prmtop changes Michael Mazanetz (Thu Sep 14 2006 - 01:15:43 PDT)
AMBER: pqr from constant pH MD harianto (Wed Sep 13 2006 - 14:43:13 PDT)
AMBER: MD on protein-ligand interaction Fenghui Fan (Thu Sep 14 2006 - 07:04:20 PDT)
- Re: AMBER: MD on protein-ligand interaction Ilyas Yildirim (Thu Sep 14 2006 - 12:09:14 PDT)
AMBER: potential energy in the MD result Fenghui Fan (Thu Sep 14 2006 - 07:39:12 PDT)
AMBER: pmemd error bala (Thu Sep 14 2006 - 08:34:12 PDT)
- Re: AMBER: pmemd error Robert Duke (Thu Sep 14 2006 - 09:46:40 PDT)
- Re: AMBER: pmemd error Robert Duke (Thu Sep 14 2006 - 09:46:30 PDT)
AMBER: addions default settings. asli ertekin (Thu Sep 14 2006 - 08:37:47 PDT)
Re: AMBER: addions default settings. Bill Ross (Thu Sep 14 2006 - 10:14:18 PDT)
AMBER: acidifying a water box Eric Shamay (Thu Sep 14 2006 - 11:36:11 PDT)
- Re: AMBER: acidifying a water box David A. Case (Thu Sep 14 2006 - 15:21:01 PDT)
- Re: AMBER: acidifying a water box Thomas Cheatham (Thu Sep 14 2006 - 15:56:32 PDT)
  - Re: AMBER: acidifying a water box Eric Shamay (Fri Sep 15 2006 - 01:49:15 PDT)
AMBER: DPPC Bilayer size Akshay Patny (Thu Sep 14 2006 - 11:47:45 PDT)
AMBER: Denaturing MD Fenghui Fan (Thu Sep 14 2006 - 15:58:35 PDT)
- Re: AMBER: Denaturing MD Thomas Cheatham (Thu Sep 14 2006 - 16:55:59 PDT)
AMBER: on the rst file of the current ruuning Fenghui Fan (Thu Sep 14 2006 - 20:33:50 PDT)
- RE: AMBER: on the rst file of the current ruuning Ross Walker (Mon Sep 18 2006 - 08:58:01 PDT)
AMBER: Temperature not rising enough during simulated annealing Adam Pelzer (Thu Sep 14 2006 - 20:30:12 PDT)
- Re: [UCE]AMBER: Temperature not rising enough during simulated annealing Thomas Cheatham (Thu Sep 14 2006 - 21:33:42 PDT)
AMBER: cyclic AMP off and frcmod files? Daniel Lee (Thu Sep 14 2006 - 20:52:33 PDT)
- Re: AMBER: cyclic AMP off and frcmod files? Fenghui Fan (Fri Sep 15 2006 - 06:44:49 PDT)
  - AMBER: have problems with restrained minimization Abhilash (Fri Sep 15 2006 - 11:10:50 PDT)
  - Re: AMBER: cyclic AMP off and frcmod files? Daniel Lee (Sun Sep 17 2006 - 19:10:28 PDT)
AMBER: restraints and constant pressure Joshua (Thu Sep 14 2006 - 22:44:09 PDT)
- Re: AMBER: restraints and constant pressure Thomas Cheatham (Thu Sep 14 2006 - 23:22:02 PDT)
- Re: AMBER: restraints and constant pressure Joshua (Fri Sep 15 2006 - 02:09:44 PDT)
  - Re: AMBER: restraints and constant pressure Myunggi Yi (Fri Sep 15 2006 - 12:52:21 PDT)
  - Re: AMBER: restraints and constant pressure Thomas Cheatham (Sat Sep 16 2006 - 21:38:06 PDT)
    - Re: AMBER: restraints and constant pressure Myunggi Yi (Sat Sep 16 2006 - 23:29:38 PDT)
    - Re: AMBER: restraints and constant pressure Carlos Simmerling (Sun Sep 17 2006 - 07:01:54 PDT)
    - Re: AMBER: restraints and constant pressure Myunggi Yi (Sun Sep 17 2006 - 07:23:33 PDT)
- Re: AMBER: restraints and constant pressure Joshua (Fri Oct 13 2006 - 15:46:26 PDT)
AMBER: About Lennard-Jones Parameters Jianhui (Fri Sep 15 2006 - 14:08:13 PDT)
- Re: AMBER: About Lennard-Jones Parameters David A. Case (Fri Sep 15 2006 - 17:07:35 PDT)
AMBER: distance between two atoms Fenghui Fan (Fri Sep 15 2006 - 13:49:11 PDT)
AMBER: Problems with a restrained minimization approach Abhilash (Fri Sep 15 2006 - 12:35:34 PDT)
- Re: AMBER: Problems with a restrained minimization approach David A. Case (Fri Sep 15 2006 - 17:41:04 PDT)
AMBER: new article on Amber force fields Carlos Simmerling (Fri Sep 15 2006 - 12:47:34 PDT)
AMBER: change mdcrd file to pdb file Fenghui Fan (Sat Sep 16 2006 - 22:02:54 PDT)
- Re: AMBER: change mdcrd file to pdb file Ilyas Yildirim (Sat Sep 16 2006 - 22:17:21 PDT)
- Re: AMBER: change mdcrd file to pdb file Jianhui (Sun Sep 17 2006 - 07:16:29 PDT)
  - Re: AMBER: change mdcrd file to pdb file Fenghui Fan (Sun Sep 17 2006 - 08:30:02 PDT)
    - Re: AMBER: change mdcrd file to pdb file Fabian Alejandro Rodriguez (Sun Sep 17 2006 - 09:04:22 PDT)
AMBER: lib-4324 : UNRECOVERABLE library error Vasu Chandrasekaran (Sun Sep 17 2006 - 00:36:26 PDT)
- Re: AMBER: lib-4324 : UNRECOVERABLE library error Robert Duke (Sun Sep 17 2006 - 05:30:08 PDT)
  - Re: AMBER: lib-4324 : UNRECOVERABLE library error Vasu Chandrasekaran (Sun Sep 17 2006 - 10:23:24 PDT)
AMBER: parameters for Nickel and iron Rachel (Mon Sep 18 2006 - 06:02:39 PDT)
- Re: AMBER: parameters for Nickel and iron Fenghui Fan (Mon Sep 18 2006 - 19:45:24 PDT)
  - Re: AMBER: parameters for Nickel and iron Rachel (Tue Sep 19 2006 - 09:00:45 PDT)
    - Re: AMBER: parameters for Nickel and iron Ken Merz (Tue Sep 19 2006 - 13:00:51 PDT)
    - Re: AMBER: parameters for Nickel and iron Rachel (Thu Sep 21 2006 - 04:50:23 PDT)
- RE: AMBER: parameters for Nickel and iron Junmei Wang (Tue Sep 19 2006 - 09:16:26 PDT)
- RE: AMBER: parameters for Nickel and iron Junmei Wang (Tue Sep 26 2006 - 14:38:08 PDT)
  - Re: AMBER: parameters for Nickel and iron Rachel (Wed Sep 27 2006 - 06:53:45 PDT)
    - AMBER: A script file for measuring the distance between 2 atoms during MD Fenghui Fan (Wed Sep 27 2006 - 08:14:23 PDT)
    - Re: AMBER: A script file for measuring the distance between 2 atoms during MD Fenghui Fan (Wed Sep 27 2006 - 10:49:53 PDT)
    - Re: AMBER: A script file for measuring the distance between 2 atoms during MD Carlos Simmerling (Wed Sep 27 2006 - 10:59:33 PDT)
    - Re: AMBER: A script file for measuring the distance between 2 atoms during MD Thomas Cheatham (Wed Sep 27 2006 - 11:05:25 PDT)
    - Re: AMBER: A script file for measuring the distance between 2 atoms during MD Carlos Simmerling (Wed Sep 27 2006 - 11:26:35 PDT)
    - AMBER: WHATIF Check after MD Fenghui Fan (Wed Sep 27 2006 - 19:24:39 PDT)
    - Re: AMBER: WHATIF Check after MD FyD (Wed Sep 27 2006 - 21:06:30 PDT)
    - Re: AMBER: A script file for measuring the distance between 2 atoms during MD Carlos Simmerling (Wed Sep 27 2006 - 11:33:01 PDT)
    - Re: AMBER: A script file for measuring the distance between 2 atoms during MD Fenghui Fan (Wed Sep 27 2006 - 12:44:08 PDT)
AMBER: Questions Joseph Fernandez (Mon Sep 18 2006 - 11:48:25 PDT)
- AMBER: coordinate files Ed Pate (Tue Sep 19 2006 - 13:17:26 PDT)
  - AMBER: the sequence command in leap Shuting Wei (Wed Sep 20 2006 - 08:32:17 PDT)
  - Re: AMBER: coordinate files David A. Case (Wed Sep 20 2006 - 18:22:47 PDT)
AMBER: ptraj RMSD vs. RMSF Steve Seibold (Mon Sep 18 2006 - 12:54:02 PDT)
AMBER: Question about Streptavidin/Biotin Tutorial. Qingning Shu (Mon Sep 18 2006 - 13:39:38 PDT)
- RE: AMBER: Question about Streptavidin/Biotin Tutorial. Ross Walker (Mon Sep 18 2006 - 15:10:39 PDT)
AMBER: A question about Dynamics. Qingning Shu (Mon Sep 18 2006 - 13:40:21 PDT)
- Re: AMBER: A question about Dynamics. David A. Case (Mon Sep 18 2006 - 13:55:47 PDT)
  - Re: AMBER: A question about Dynamics. Chunhu Tan (Mon Sep 18 2006 - 14:24:22 PDT)
    - Re: Re: AMBER: A question about Dynamics. Qingning Shu (Thu Sep 21 2006 - 07:38:47 PDT)
    - RE: Re: AMBER: A question about Dynamics. Ross Walker (Thu Sep 21 2006 - 08:58:08 PDT)
    - Re: RE: Re: AMBER: A question about Dynamics. Qingning Shu (Fri Sep 22 2006 - 15:28:54 PDT)
    - Re: RE: Re: AMBER: A question about Dynamics. David A. Case (Fri Sep 22 2006 - 17:57:46 PDT)
AMBER: A question about Dynamics. Qingning Shu (Mon Sep 18 2006 - 13:57:17 PDT)
AMBER: Can salt effect be determined in GB medel? Xioling Chuang (Mon Sep 18 2006 - 21:04:03 PDT)
- Re: AMBER: Can salt effect be determined in GB medel? linfu (Mon Sep 18 2006 - 23:32:16 PDT)
AMBER: implicit solovent model by adjusting the parameter EXTDIEL ? linfu (Mon Sep 18 2006 - 23:40:52 PDT)
- Re: AMBER: implicit solovent model by adjusting the parameter EXTDIEL ? David A. Case (Tue Sep 19 2006 - 10:29:51 PDT)
AMBER: resolving a bad initial model wang.cbs.cnrs.fr (Tue Sep 19 2006 - 07:42:11 PDT)
- Re: AMBER: resolving a bad initial model Andy Purkiss-Trew (Tue Sep 19 2006 - 07:51:01 PDT)
- Re: AMBER: resolving a bad initial model Carlos Simmerling (Tue Sep 19 2006 - 07:53:47 PDT)
- Re: AMBER: resolving a bad initial model Stefano Pieraccini (Tue Sep 19 2006 - 08:25:46 PDT)
AMBER: ACML and MASS/MASSV for sander and pmemd Nicolas Lux Fawzi (Tue Sep 19 2006 - 12:36:21 PDT)
- Re: AMBER: ACML and MASS/MASSV for sander and pmemd Robert Duke (Tue Sep 19 2006 - 13:03:00 PDT)
- RE: AMBER: ACML and MASS/MASSV for sander and pmemd Ross Walker (Tue Sep 19 2006 - 13:24:02 PDT)
  - Re: AMBER: ACML and MASS/MASSV for sander and pmemd Robert Duke (Tue Sep 19 2006 - 13:42:05 PDT)
AMBER: installation error for pmemd in Amber 9/Opteron Sergio Aragon (Tue Sep 19 2006 - 14:25:53 PDT)
- RE: AMBER: installation error for pmemd in Amber 9/Opteron Ross Walker (Tue Sep 19 2006 - 14:41:11 PDT)
  - AMBER: zzfft issue resolved -thanks! Sergio Aragon (Tue Sep 19 2006 - 16:09:25 PDT)
  - AMBER: zzfft error for pmemd in Amber 9/Opteron Sergio Aragon (Tue Sep 19 2006 - 15:53:10 PDT)
AMBER: Steve Seibold (Wed Sep 20 2006 - 09:56:00 PDT)
AMBER: GPCR-membrane issue Akshay Patny (Wed Sep 20 2006 - 10:30:24 PDT)
AMBER: Problems using rst distance constraints in Amber 8 Whitney Allen (Wed Sep 20 2006 - 11:30:05 PDT)
- Re: AMBER: Problems using rst distance constraints in Amber 8 David A. Case (Wed Sep 20 2006 - 12:12:20 PDT)
AMBER: Which POPC Bilayer to start? Akshay Patny (Wed Sep 20 2006 - 14:48:42 PDT)
AMBER: mm-pbsa output Stefano Pieraccini (Thu Sep 21 2006 - 01:51:28 PDT)
- Re: AMBER: mm-pbsa output alfredoq.fcq.unc.edu.ar (Thu Sep 21 2006 - 04:29:51 PDT)
AMBER: bad atom type: Li jitrayut jitonnom (Thu Sep 21 2006 - 03:30:24 PDT)
- Re: AMBER: bad atom type: Li David A. Case (Tue Sep 26 2006 - 23:03:56 PDT)
AMBER: proposed patch for ptraj/evec.c (Amber 9.0) Cameron Abrams (Thu Sep 21 2006 - 10:26:35 PDT)
- Re: AMBER: proposed patch for ptraj/evec.c (Amber 9.0) David A. Case (Mon Oct 02 2006 - 08:51:53 PDT)
AMBER: Temperature fluctuation BIG with ntt=3 Mingfeng Yang (Thu Sep 21 2006 - 16:14:24 PDT)
- Re: AMBER: Temperature fluctuation BIG with ntt=3 Carlos Simmerling (Thu Sep 21 2006 - 17:48:07 PDT)
- Re: AMBER: Temperature fluctuation BIG with ntt=3 David A. Case (Thu Sep 21 2006 - 18:39:46 PDT)
  - Re: AMBER: Temperature fluctuation BIG with ntt=3 Mingfeng Yang (Thu Sep 21 2006 - 21:59:54 PDT)
AMBER: Amber8: problem related to antechamber priya priya (Thu Sep 21 2006 - 21:11:23 PDT)
- Re: AMBER: Amber8: problem related to antechamber David A. Case (Fri Sep 22 2006 - 07:52:35 PDT)
AMBER: RMSd vs RMSf Steve Seibold (Fri Sep 22 2006 - 06:42:28 PDT)
AMBER: TI-FEP : strange result for different clambda values Biswa Ranjan Meher (Fri Sep 22 2006 - 08:26:30 PDT)
- Re: AMBER: TI-FEP : strange result for different clambda values Thomas Steinbrecher (Fri Sep 22 2006 - 08:38:10 PDT)
- Re: AMBER: TI-FEP : strange result for different clambda values David Mobley (Fri Sep 22 2006 - 09:38:19 PDT)
AMBER: center of mass dihedral restraints Lauren O'Neil (Fri Sep 22 2006 - 12:03:32 PDT)
- Re: AMBER: center of mass dihedral restraints Carlos Simmerling (Mon Sep 25 2006 - 04:43:49 PDT)
  - Re: AMBER: center of mass dihedral restraints Lauren O'Neil (Mon Sep 25 2006 - 08:39:19 PDT)
    - Re: AMBER: center of mass dihedral restraints venditti2.unisi.it (Mon Sep 25 2006 - 10:44:01 PDT)
AMBER: build a polymer with sequence command Shuting Wei (Fri Sep 22 2006 - 13:41:43 PDT)
- Re: AMBER: build a polymer with sequence command David A. Case (Fri Sep 22 2006 - 14:01:27 PDT)
  - Re: AMBER: build a polymer with sequence command Shuting Wei (Fri Sep 22 2006 - 14:42:04 PDT)
    - Re: AMBER: build a polymer with sequence command David A. Case (Fri Sep 22 2006 - 17:03:35 PDT)
    - Re: AMBER: build a polymer with sequence command Shuting Wei (Mon Sep 25 2006 - 10:15:10 PDT)
    - Re: AMBER: build a polymer with sequence command David A. Case (Mon Sep 25 2006 - 14:37:54 PDT)
AMBER: leap can't assign CALA Myunggi Yi (Fri Sep 22 2006 - 15:09:06 PDT)
- Re: AMBER: leap can't assign CALA David A. Case (Fri Sep 22 2006 - 17:53:29 PDT)
  - Re: AMBER: leap can't assign CALA Myunggi Yi (Sat Sep 23 2006 - 08:36:12 PDT)
AMBER: pbsa segmentation faults Thomas Steinbrecher (Fri Sep 22 2006 - 16:46:11 PDT)
- Re: AMBER: pbsa segmentation faults Ray Luo (Sat Sep 23 2006 - 23:40:58 PDT)
- AMBER: mm_pbsa segmentation faults Thomas Steinbrecher (Mon Sep 25 2006 - 11:24:17 PDT)
  - Re: AMBER: mm_pbsa segmentation faults linfu (Mon Sep 25 2006 - 17:56:08 PDT)
  - Re: AMBER: mm_pbsa segmentation faults Ray Luo (Mon Sep 25 2006 - 18:17:54 PDT)
  - Re: AMBER: mm_pbsa segmentation faults Ray Luo (Tue Sep 26 2006 - 09:29:26 PDT)
    - Re: AMBER: mm_pbsa segmentation faults Thomas Steinbrecher (Tue Sep 26 2006 - 10:31:34 PDT)
    - Re: AMBER: mm_pbsa segmentation faults Mark Williamson (Tue Sep 26 2006 - 14:41:06 PDT)
AMBER: Picking up water molecules around one molecule Atsutoshi Okabe (Sat Sep 23 2006 - 01:26:12 PDT)
AMBER: one question on MD Fenghui Fan (Sat Sep 23 2006 - 18:03:11 PDT)
- Re: AMBER: one question on MD Carlos Simmerling (Sat Sep 23 2006 - 18:32:46 PDT)
AMBER: the RMSD of MD Fenghui Fan (Sun Sep 24 2006 - 10:07:56 PDT)
- Re: AMBER: the RMSD of MD Adrian Roitberg (Sun Sep 24 2006 - 10:49:52 PDT)
AMBER: strange values of the energy of "1-4 EEL" , "EAMBER" and the RMS Zhihong Yu (Sun Sep 24 2006 - 20:03:28 PDT)
- Re: AMBER: strange values of the energy of "1-4 EEL" , "EAMBER" and the RMS Carlos Simmerling (Mon Sep 25 2006 - 04:30:57 PDT)
- Re: AMBER: strange values of the energy of "1-4 EEL" , "EAMBER" and the RMS JunJun Liu (Mon Sep 25 2006 - 12:28:55 PDT)
AMBER: polarizable ff for ligand bala (Mon Sep 25 2006 - 06:53:02 PDT)
AMBER: question on Lennard-Jones fitting in FF94 and 96 David Mobley (Mon Sep 25 2006 - 10:07:45 PDT)
Re: AMBER: strange values of the energy of "1-4 EEL" , "EAMBER" andthe RMS Zhihong Yu (Mon Sep 25 2006 - 18:20:14 PDT)
AMBER: from ADP-small protein complex to GTP-protein complex Fenghui Fan (Mon Sep 25 2006 - 21:00:53 PDT)
AMBER: lifetime and maxocc Sergey Samsonov (Tue Sep 26 2006 - 08:56:26 PDT)
AMBER: structure from MD Fenghui Fan (Tue Sep 26 2006 - 09:42:14 PDT)
- Re: AMBER: structure from MD Carlos Simmerling (Tue Sep 26 2006 - 09:43:58 PDT)
AMBER: chemical shift restrains Emilia Sikorska (Tue Sep 26 2006 - 11:22:05 PDT)
- Re: AMBER: chemical shift restrains David A. Case (Sun Oct 01 2006 - 06:35:01 PDT)
  - AMBER: polarization effects Vitor Manuel Sousa F?x (Sun Oct 01 2006 - 07:08:55 PDT)
AMBER: missing benchmark files Mark H. Schofield (Tue Sep 26 2006 - 15:32:38 PDT)
- Re: AMBER: missing benchmark files David A. Case (Tue Sep 26 2006 - 23:50:49 PDT)
AMBER: job crashes Xiaowei (David) Li (Tue Sep 26 2006 - 20:09:04 PDT)
- Re: AMBER: job crashes JunJun Liu (Tue Sep 26 2006 - 20:39:52 PDT)
  - Re: AMBER: job crashes Xiaowei (David) Li (Tue Sep 26 2006 - 20:57:18 PDT)
AMBER: RE: Amber8: problem related to antechamber priya priya (Wed Sep 27 2006 - 00:29:01 PDT)
- Re: AMBER: RE: Amber8: problem related to antechamber David A. Case (Sun Oct 01 2006 - 06:35:55 PDT)
AMBER: kclust Fabiana Caporuscio (Wed Sep 27 2006 - 01:32:51 PDT)
AMBER: Error in compiling Amber 8 parallel Jianhui Tian (Wed Sep 27 2006 - 13:28:48 PDT)
- AMBER: Multiple Timestep MD David LeBard (Wed Sep 27 2006 - 18:03:35 PDT)
  - Re: AMBER: Multiple Timestep MD David A. Case (Sun Oct 01 2006 - 06:35:25 PDT)
  - Re: AMBER: Multiple Timestep MD Robert Duke (Sun Oct 01 2006 - 07:22:34 PDT)
- RE: AMBER: Error in compiling Amber 8 parallel Ross Walker (Thu Sep 28 2006 - 08:36:25 PDT)
  - AMBER: running sander on several nodes Fenghui Fan (Thu Sep 28 2006 - 09:45:34 PDT)
    - Re: AMBER: running sander on several nodes Fenghui Fan (Thu Sep 28 2006 - 10:21:26 PDT)
    - RE: AMBER: running sander on several nodes Ross Walker (Thu Sep 28 2006 - 10:37:28 PDT)
AMBER: Questions/observations about Nudged Elastic Band (NEB) Pietro Amodeo (Thu Sep 28 2006 - 03:56:36 PDT)
- RE: AMBER: Questions/observations about Nudged Elastic Band (NEB) Ross Walker (Thu Sep 28 2006 - 08:29:29 PDT)
  - AMBER: Machine File for Intel Core 2 Duo E6400 Osmar Norberto de Souza (Thu Sep 28 2006 - 11:47:06 PDT)
    - RE: AMBER: Machine File for Intel Core 2 Duo E6400 Ross Walker (Thu Sep 28 2006 - 12:05:02 PDT)
    - Re: AMBER: Machine File for Intel Core 2 Duo E6400 Osmar Norberto de Souza (Thu Sep 28 2006 - 12:22:15 PDT)
  - RE: AMBER: Questions/observations about Nudged Elastic Band (NEB) Pietro Amodeo (Fri Sep 29 2006 - 02:21:43 PDT)
AMBER: NAD parameters Uni-Halle (Thu Sep 28 2006 - 06:06:06 PDT)
- Re: AMBER: NAD parameters cristian obiol (Thu Sep 28 2006 - 06:56:43 PDT)
- RE: AMBER: NAD parameters Ross Walker (Thu Sep 28 2006 - 08:32:48 PDT)
  - AMBER: Problem about installing amber9 on Mac OS X gtg549i.mail.gatech.edu (Thu Sep 28 2006 - 09:28:51 PDT)
    - RE: AMBER: Problem about installing amber9 on Mac OS X Ross Walker (Thu Sep 28 2006 - 10:40:26 PDT)
    - RE: AMBER: Problem about installing amber9 on Mac OS X gtg549i.mail.gatech.edu (Thu Sep 28 2006 - 11:32:18 PDT)
    - RE: AMBER: Problem about installing amber9 on Mac OS X Ross Walker (Thu Sep 28 2006 - 11:52:30 PDT)
    - RE: AMBER: Problem about installing amber9 on Mac OS X Shuting Wei (Fri Sep 29 2006 - 14:08:42 PDT)
AMBER: parm*.dat Ivelin Georgiev (Thu Sep 28 2006 - 09:39:23 PDT)
- Re: AMBER: parm*.dat Jianhui (Thu Sep 28 2006 - 14:24:49 PDT)
AMBER: Parameterization of ethidium - phenyl ring sethl.gatech.edu (Thu Sep 28 2006 - 13:02:08 PDT)
- AMBER: WHAT IF CHeck after MD Fenghui Fan (Thu Sep 28 2006 - 15:06:04 PDT)
  - Re: AMBER: WHAT IF CHeck after MD David Mobley (Thu Sep 28 2006 - 15:58:32 PDT)
AMBER: problem to center solvateshell Bonnet, Pascal [PRDBE] (Fri Sep 29 2006 - 02:30:49 PDT)
- Re: AMBER: problem to center solvateshell David A. Case (Mon Oct 02 2006 - 09:01:44 PDT)
  - AMBER: Pressure in MD Fenghui Fan (Mon Oct 02 2006 - 13:55:16 PDT)
    - Re: AMBER: Pressure in MD Thomas Steinbrecher (Mon Oct 02 2006 - 14:24:30 PDT)
- RE: AMBER: problem to center solvateshell Bonnet, Pascal [PRDBE] (Mon Oct 02 2006 - 23:30:53 PDT)
AMBER: Problem using antechamber Gustavo Seabra (Fri Sep 29 2006 - 09:19:12 PDT)
- RE: AMBER: Problem using antechamber Junmei Wang (Fri Sep 29 2006 - 11:17:37 PDT)
  - Re: AMBER: Problem using antechamber Gustavo Seabra (Fri Sep 29 2006 - 12:06:34 PDT)
AMBER: Electrostatic Energy Constant Ivelin Georgiev (Fri Sep 29 2006 - 10:50:03 PDT)
- Re: AMBER: Electrostatic Energy Constant Thomas Cheatham (Fri Sep 29 2006 - 11:19:00 PDT)
  - Re: AMBER: Electrostatic Energy Constant Fenghui Fan (Fri Sep 29 2006 - 12:23:03 PDT)
    - Re: AMBER: Electrostatic Energy Constant Thomas Cheatham (Fri Sep 29 2006 - 12:44:25 PDT)
- Re: AMBER: Electrostatic Energy Constant Carlos Simmerling (Fri Sep 29 2006 - 13:20:24 PDT)
AMBER: problem installing amber9 with g95 gcc on a fc5 m/c Sayandeep Purkayasth (Sun Oct 01 2006 - 19:15:54 PDT)
- Re: AMBER: problem installing amber9 with g95 gcc on a fc5 m/c David A. Case (Mon Oct 02 2006 - 08:28:25 PDT)
  - Re: AMBER: problem installing amber9 with g95 gcc on a fc5 m/c Sayandeep Purkayasth (Mon Oct 02 2006 - 17:30:40 PDT)
    - Re: AMBER: problem installing amber9 with g95 gcc on a fc5 m/c Sayandeep Purkayasth (Tue Oct 03 2006 - 22:14:06 PDT)
    - Re: AMBER: problem installing amber9 with g95 gcc on a fc5 m/c Scott Brozell (Wed Oct 04 2006 - 01:16:09 PDT)
    - Re: AMBER: problem installing amber9 with g95 gcc on a fc5 m/c Sayandeep Purkayasth (Mon Oct 09 2006 - 01:59:18 PDT)
    - Re: AMBER: problem installing amber9 with g95 gcc on a fc5 m/c Scott Brozell (Mon Oct 09 2006 - 18:14:54 PDT)
    - Re: AMBER: problem installing amber9 with g95 gcc on a fc5 m/c Sayandeep Purkayasth (Sun Oct 15 2006 - 23:32:04 PDT)
    - Re: AMBER: problem installing amber9 with g95 gcc on a fc5 m/c David A. Case (Mon Oct 16 2006 - 09:41:31 PDT)
    - Re: AMBER: problem installing amber9 with g95 gcc on a fc5 m/c Sayandeep Purkayasth (Fri Oct 27 2006 - 18:25:37 PDT)
    - Re: AMBER: problem installing amber9 with g95 gcc on a fc5 m/c David A. Case (Fri Oct 27 2006 - 21:42:08 PDT)
    - Re: AMBER: problem installing amber9 with g95 gcc on a fc5 m/c Sayandeep Purkayasth (Wed Nov 01 2006 - 22:48:03 PST)
AMBER: how to run a mm_pbsa on a minimized structure? Wang, Xuelin (Mon Oct 02 2006 - 14:50:02 PDT)
- AMBER: mdcrd file Fenghui Fan (Mon Oct 02 2006 - 17:09:37 PDT)
Re: AMBER: mdcrd file Bill Ross (Mon Oct 02 2006 - 17:23:18 PDT)
- Re: AMBER: mdcrd file Fenghui Fan (Mon Oct 02 2006 - 19:17:12 PDT)
  - RE: AMBER: mdcrd file Ross Walker (Mon Oct 02 2006 - 21:31:03 PDT)
    - AMBER: RMSD: is it related to flexibility? a a (Wed Oct 04 2006 - 02:42:12 PDT)
    - Re: AMBER: RMSD: is it related to flexibility? Carlos Simmerling (Wed Oct 04 2006 - 04:40:04 PDT)
    - AMBER: Distance between 2 atoms Fenghui Fan (Wed Oct 04 2006 - 06:52:16 PDT)
    - AMBER: on rst file Fenghui Fan (Wed Oct 04 2006 - 07:02:40 PDT)
    - Re: AMBER: RMSD: is it related to flexibility? David A. Case (Wed Oct 04 2006 - 08:08:32 PDT)
    - AMBER: atom nomination in the PDB file produced by Amber Fenghui Fan (Wed Oct 04 2006 - 08:37:45 PDT)
    - Re: AMBER: RMSD: is it related to flexibility? a a (Wed Oct 04 2006 - 21:15:20 PDT)
    - Re: AMBER: RMSD: is it related to flexibility? Gustavo Seabra (Thu Oct 05 2006 - 09:08:05 PDT)
    - Re: AMBER: RMSD: is it related to flexibility? a a (Thu Oct 05 2006 - 19:50:43 PDT)
    - Re: AMBER: RMSD: is it related to flexibility? Feng X Zhou (Fri Oct 06 2006 - 09:28:36 PDT)
    - AMBER: Potential of Mean Force calculation or Steered molecular dynamics a a (Sun Oct 08 2006 - 23:07:25 PDT)
    - AMBER: Steered molecular dynamics with Amber 8.0 a a (Tue Oct 10 2006 - 02:44:56 PDT)
    - AMBER: Ｆｅ complex Toshifumi Yui (Tue Oct 10 2006 - 18:09:36 PDT)
    - AMBER: Parameters for Nickel a a (Wed Oct 11 2006 - 02:05:15 PDT)
- Re: AMBER: mdcrd file Bill Ross (Mon Oct 02 2006 - 19:46:15 PDT)
AMBER: How to get the VDW contacts' messages from the mdcrd files Jiapu.Zhang.csiro.au (Mon Oct 02 2006 - 23:11:03 PDT)
AMBER: Pressure problem with restraint Jianhui (Tue Oct 03 2006 - 07:41:46 PDT)
- AMBER: mm_pbsa PBCAL William Wei (Tue Oct 03 2006 - 12:23:18 PDT)
- Re: AMBER: Pressure problem with restraint David A. Case (Wed Oct 04 2006 - 08:06:38 PDT)
- Re: AMBER: Pressure problem with restraint Jianhui (Wed Oct 04 2006 - 10:49:29 PDT)
  - Re: AMBER: Pressure problem with restraint David A. Case (Wed Oct 04 2006 - 11:03:45 PDT)
    - Re: Re: AMBER: Pressure problem with restraint Jianhui (Wed Oct 04 2006 - 12:24:35 PDT)
    - Re: Re: AMBER: Pressure problem with restraint David A. Case (Wed Oct 04 2006 - 15:19:50 PDT)
AMBER: hbond analysis Vlad Cojocaru (Tue Oct 03 2006 - 08:45:23 PDT)
- Re: AMBER: hbond analysis Thomas Cheatham (Tue Oct 03 2006 - 09:05:00 PDT)
  - Re: AMBER: hbond analysis Vlad Cojocaru (Tue Oct 03 2006 - 09:18:28 PDT)
    - Re: AMBER: hbond analysis Thomas Cheatham (Tue Oct 03 2006 - 09:27:56 PDT)
    - Re: AMBER: hbond analysis Vlad Cojocaru (Tue Oct 03 2006 - 09:35:32 PDT)
- Re: AMBER: hbond analysis Sergey Samsonov (Wed Oct 04 2006 - 07:49:35 PDT)
  - Re: AMBER: hbond analysis Vlad Cojocaru (Wed Oct 04 2006 - 08:26:32 PDT)
  - Re: AMBER: hbond analysis Thomas Cheatham (Wed Oct 04 2006 - 14:00:02 PDT)
    - Re: AMBER: hbond analysis Sergey Samsonov (Wed Oct 04 2006 - 23:40:59 PDT)
AMBER: MM_PBSA error Shozeb Haider (Tue Oct 03 2006 - 14:04:57 PDT)
- AMBER: Distance between two atoms Fenghui Fan (Tue Oct 03 2006 - 16:59:17 PDT)
AMBER: how to calculate rmsd for non hydrogen at oms? yxiong99 (Tue Oct 03 2006 - 09:43:49 PDT)
- Re: AMBER: how to calculate rmsd for non hydrogen at oms? Viktor Hornak (Tue Oct 03 2006 - 09:51:53 PDT)
  - Re: AMBER: how to calculate rmsd for non hydrogen at oms? JunJun Liu (Tue Oct 03 2006 - 12:10:25 PDT)
AMBER: Re: Distance between two atoms Fenghui Fan (Tue Oct 03 2006 - 23:12:06 PDT)
- Re: AMBER: Re: Distance between two atoms Fenghui Fan (Tue Oct 03 2006 - 23:41:27 PDT)
AMBER: Re: atom nomination in the PDB file produced by Amber Fenghui Fan (Wed Oct 04 2006 - 08:41:11 PDT)
AMBER: change from .rst file to .mdcrd file Wang, Xuelin (Wed Oct 04 2006 - 08:52:56 PDT)
- Re: AMBER: change from .rst file to .mdcrd file JunJun Liu (Wed Oct 04 2006 - 13:14:22 PDT)
Re: AMBER: on rst file Bill Ross (Wed Oct 04 2006 - 10:17:10 PDT)
AMBER: Is GB/SANDER slower than TIP3P/PMEMD b86203054.ntu.edu.tw (Wed Oct 04 2006 - 10:21:39 PDT)
- Re: AMBER: Is GB/SANDER slower than TIP3P/PMEMD Robert Duke (Wed Oct 04 2006 - 10:45:06 PDT)
- RE: AMBER: Is GB/SANDER slower than TIP3P/PMEMD Ross Walker (Wed Oct 04 2006 - 10:51:24 PDT)
AMBER: AMBER minimization vs. Gaussian optimization Ilyas Yildirim (Wed Oct 04 2006 - 13:27:48 PDT)
- Re: AMBER: AMBER minimization vs. Gaussian optimization Thomas Cheatham (Wed Oct 04 2006 - 13:45:59 PDT)
  - Re: AMBER: AMBER minimization vs. Gaussian optimization Ilyas Yildirim (Wed Oct 04 2006 - 15:17:51 PDT)
  - Re: AMBER: AMBER minimization vs. Gaussian optimization FyD (Wed Oct 04 2006 - 22:14:07 PDT)
AMBER: ptraj hbond analysis troubles Sayandeep Purkayasth (Wed Oct 04 2006 - 14:14:10 PDT)
- Re: AMBER: ptraj hbond analysis troubles Thomas Cheatham (Wed Oct 04 2006 - 14:36:49 PDT)
  - Re: AMBER: ptraj hbond analysis troubles Thomas Cheatham (Wed Oct 04 2006 - 15:41:55 PDT)
    - Re: AMBER: ptraj hbond analysis troubles Sayandeep Purkayasth (Thu Oct 05 2006 - 06:37:07 PDT)
    - Re: AMBER: ptraj hbond analysis troubles Thomas Cheatham (Thu Oct 05 2006 - 08:21:40 PDT)
    - Re: AMBER: ptraj hbond analysis troubles Reinhard Klement (Wed Oct 11 2006 - 01:25:27 PDT)
- Re: AMBER: ptraj hbond analysis troubles Robert Duke (Thu Oct 05 2006 - 06:58:50 PDT)
- Re: AMBER: ptraj hbond analysis troubles Robert Duke (Thu Oct 05 2006 - 11:35:20 PDT)
  - Re: AMBER: ptraj hbond analysis troubles Thomas Cheatham (Thu Oct 05 2006 - 12:43:37 PDT)
- Re: AMBER: ptraj hbond analysis troubles Robert Duke (Thu Oct 05 2006 - 18:55:42 PDT)
  - Re: AMBER: ptraj hbond analysis troubles Sayandeep Purkayasth (Mon Oct 09 2006 - 01:11:56 PDT)
AMBER: VMD PDB into LEAP Readable PDB Akshay Patny (Wed Oct 04 2006 - 18:07:11 PDT)
- Re: AMBER: VMD PDB into LEAP Readable PDB David A. Case (Thu Oct 05 2006 - 08:13:41 PDT)
AMBER: Missing values for MM VDW bala (Thu Oct 05 2006 - 04:33:14 PDT)
AMBER: PBSA calculation fail .... Changge Ji (Thu Oct 05 2006 - 06:42:39 PDT)
- Re: AMBER: PBSA calculation fail .... Ray Luo (Thu Oct 05 2006 - 09:36:32 PDT)
- AMBER: Building polymer with sequence command gtg549i.mail.gatech.edu (Thu Oct 05 2006 - 09:46:11 PDT)
  - Re: AMBER: Building polymer with sequence command David A. Case (Thu Oct 05 2006 - 17:31:36 PDT)
AMBER: generating resp input files with antechamber dhruva chakravorty (Thu Oct 05 2006 - 12:53:03 PDT)
AMBER: water prmtop/inpcrd problem Akshay Patny (Thu Oct 05 2006 - 18:08:59 PDT)
- Re: AMBER: water prmtop/inpcrd problem David A. Case (Thu Oct 05 2006 - 19:01:22 PDT)
- Re: AMBER: water prmtop/inpcrd problem Ilyas Yildirim (Fri Oct 06 2006 - 02:17:11 PDT)
  - RE: AMBER: water prmtop/inpcrd problem Akshay Patny (Fri Oct 06 2006 - 07:49:22 PDT)
AMBER: (no subject) Prashanth Athri (Thu Oct 05 2006 - 19:34:47 PDT)
- Re: AMBER: (no subject) David A. Case (Fri Oct 06 2006 - 09:20:03 PDT)
AMBER: Calculation of Dihedral constants Prashanth Athri (Thu Oct 05 2006 - 19:36:15 PDT)
AMBER: LEAP error Akshay Patny (Fri Oct 06 2006 - 09:49:42 PDT)
- Re: AMBER: LEAP error Scott Brozell (Fri Oct 06 2006 - 10:30:34 PDT)
- Re: AMBER: LEAP error Akshay Patny (Fri Oct 06 2006 - 16:17:05 PDT)
  - Re: AMBER: LEAP error Ilyas Yildirim (Fri Oct 06 2006 - 21:26:29 PDT)
  - Re: AMBER: LEAP error David A. Case (Sun Oct 08 2006 - 21:28:36 PDT)
    - RE: AMBER: LEAP error (Test Case) Akshay Patny (Mon Oct 09 2006 - 08:37:18 PDT)
AMBER: How to merge two molecules to one Myunggi Yi (Fri Oct 06 2006 - 11:51:19 PDT)
AMBER: MM_PBSA Rajendra P. OJHA (Sat Oct 07 2006 - 09:21:49 PDT)
AMBER: question about building molecules Rita Cassia (Sun Oct 08 2006 - 04:05:59 PDT)
- Re: AMBER: question about building molecules David A. Case (Sun Oct 08 2006 - 09:31:27 PDT)
  - Re: AMBER: question about building molecules Rita Cassia (Mon Oct 09 2006 - 08:49:10 PDT)
AMBER: some puzzles in equilibration MD Zhihong Yu (Mon Oct 09 2006 - 06:58:06 PDT)
- RE: AMBER: some puzzles in equilibration MD Ross Walker (Mon Oct 09 2006 - 07:53:20 PDT)
- RE: AMBER: some puzzles in equilibration MD Zhihong Yu (Mon Oct 09 2006 - 08:19:15 PDT)
  - RE: AMBER: some puzzles in equilibration MD Ross Walker (Mon Oct 09 2006 - 15:41:54 PDT)
- RE: AMBER: some puzzles in equilibration MD Bill Ross (Mon Oct 09 2006 - 20:14:39 PDT)
AMBER: Trouble with Leap Biswa Ranjan Meher (Mon Oct 09 2006 - 07:28:28 PDT)
- AMBER: how to combine NEB method with QM/MM approach caoch.cherry.bio.titech.ac.jp (Mon Oct 09 2006 - 09:23:07 PDT)
  - RE: AMBER: how to combine NEB method with QM/MM approach Ross Walker (Mon Oct 09 2006 - 15:33:00 PDT)
- Re: AMBER: Trouble with Leap Scott Brozell (Mon Oct 09 2006 - 18:42:38 PDT)
  - Re: AMBER: Trouble with Leap Biswa Ranjan Meher (Tue Oct 17 2006 - 22:35:48 PDT)
    - Re: AMBER: Trouble with Leap Biswa Ranjan Meher (Wed Oct 18 2006 - 22:28:46 PDT)
    - Re: AMBER: Trouble with Leap Ilyas Yildirim (Thu Oct 19 2006 - 01:04:59 PDT)
AMBER: MMPBSA vDW error Shozeb Haider (Mon Oct 09 2006 - 16:08:27 PDT)
AMBER: Announcement: Parameters for Modified Nucleosides in RNA Raviprasad Aduri (Mon Oct 09 2006 - 14:13:56 PDT)
AMBER: partial charges Fabian Alejandro Rodriguez (Tue Oct 10 2006 - 09:35:53 PDT)
- Re: AMBER: partial charges David A. Case (Wed Oct 11 2006 - 09:17:48 PDT)
AMBER: generalized born model for organic solvent Eric Hu (Tue Oct 10 2006 - 18:29:12 PDT)
- Re: AMBER: generalized born model for organic solvent David A. Case (Wed Oct 11 2006 - 09:16:23 PDT)
  - Re: AMBER: generalized born model for organic solvent Eric Hu (Wed Oct 11 2006 - 16:37:01 PDT)
    - Re: AMBER: generalized born model for organic solvent David A. Case (Wed Oct 11 2006 - 16:53:49 PDT)
    - Re: AMBER: generalized born model for organic solvent Adrian Roitberg (Wed Oct 11 2006 - 17:11:33 PDT)
    - Re: AMBER: generalized born model for organic solvent Eric Hu (Thu Oct 12 2006 - 10:47:44 PDT)
    - Re: AMBER: generalized born model for organic solvent David A. Case (Thu Oct 12 2006 - 11:00:00 PDT)
    - Re: AMBER: generalized born model for organic solvent Eric Hu (Thu Oct 12 2006 - 16:32:16 PDT)
AMBER: Re: AMBER: Ｆｅ complex　(correction) Toshifumi Yui (Tue Oct 10 2006 - 18:41:05 PDT)
AMBER: adding polar hydrogens Sean Rathlef (Tue Oct 10 2006 - 19:43:39 PDT)
- Re: AMBER: adding polar hydrogens David A. Case (Wed Oct 11 2006 - 09:14:29 PDT)
- Re: AMBER: adding polar hydrogens Sean Rathlef (Wed Oct 11 2006 - 11:02:28 PDT)
  - Re: AMBER: adding polar hydrogens David A. Case (Wed Oct 11 2006 - 11:28:11 PDT)
- Re: AMBER: adding polar hydrogens Sean Rathlef (Wed Oct 11 2006 - 11:35:47 PDT)
- Re: AMBER: adding polar hydrogens j j (Thu May 24 2007 - 04:09:04 PDT)
  - Re: AMBER: adding polar hydrogens j j (Thu May 24 2007 - 06:00:12 PDT)
AMBER: Reducind trajectory Sergey Samsonov (Wed Oct 11 2006 - 00:03:49 PDT)
- Re: AMBER: Reducing trajectory Sergey Samsonov (Wed Oct 11 2006 - 00:36:15 PDT)
AMBER: amber force field Noriaki Okimoto (Wed Oct 11 2006 - 11:21:03 PDT)
- Re: AMBER: amber force field Carlos Simmerling (Wed Oct 11 2006 - 11:33:36 PDT)
AMBER: problems for running sander.MPI Qizhi Cui (Wed Oct 11 2006 - 13:39:36 PDT)
- RE: AMBER: problems for running sander.MPI Ross Walker (Wed Oct 11 2006 - 15:18:14 PDT)
  - Re: AMBER: problems for running sander.MPI Christophe Deprez (Thu Oct 12 2006 - 06:54:41 PDT)
    - RE: AMBER: problems for running sander.MPI Ross Walker (Thu Oct 12 2006 - 10:41:19 PDT)
    - Re: AMBER: problems for running sander.MPI Christophe Deprez (Mon Oct 30 2006 - 10:27:12 PST)
    - RE: AMBER: problems for running sander.MPI Ross Walker (Mon Oct 30 2006 - 10:40:06 PST)
AMBER: puzzles about solvatoct or solvatebox Zhihong Yu (Thu Oct 12 2006 - 03:00:08 PDT)
AMBER: High Values in MMPBSA Shozeb Haider (Thu Oct 12 2006 - 09:55:15 PDT)
- Re: AMBER: High Values in MMPBSA Thomas Steinbrecher (Thu Oct 12 2006 - 08:36:31 PDT)
AMBER: angle between two vectors Lwin, ThuZar (Thu Oct 12 2006 - 09:51:15 PDT)
- Re: AMBER: angle between two vectors M. L. Dodson (Thu Oct 12 2006 - 10:40:35 PDT)
- Re: AMBER: angle between two vectors David A. Case (Thu Oct 12 2006 - 11:14:14 PDT)
  - Re: AMBER: angle between two vectors Myunggi Yi (Mon Oct 16 2006 - 09:15:59 PDT)
    - AMBER: Interbox interactions Austin B. Yongye (Mon Oct 16 2006 - 10:15:04 PDT)
    - Re: AMBER: Interbox interactions Thomas Cheatham (Tue Oct 17 2006 - 08:34:50 PDT)
    - Re: AMBER: Interbox interactions Austin B. Yongye (Tue Oct 17 2006 - 09:03:18 PDT)
Re: AMBER: puzzles about solvatoct or solvatebox Bill Ross (Thu Oct 12 2006 - 10:43:38 PDT)
- Re: AMBER: puzzles about solvatoct or solvatebox Zhihong Yu (Tue Oct 17 2006 - 07:42:54 PDT)
  - Re: AMBER: puzzles about solvatoct or solvatebox Thomas Cheatham (Tue Oct 17 2006 - 08:05:08 PDT)
- Re: AMBER: puzzles about solvatoct or solvatebox Bill Ross (Tue Oct 17 2006 - 09:13:58 PDT)
AMBER: Phenyl Ring atom types sethl.gatech.edu (Thu Oct 12 2006 - 11:59:24 PDT)
AMBER: Ptraj problems Charlisa Daniels (Thu Oct 12 2006 - 13:01:30 PDT)
AMBER: TFE parameters for Amber Mingfeng Yang (Thu Oct 12 2006 - 16:33:21 PDT)
AMBER: BioBlade Sean Rathlef (Thu Oct 12 2006 - 20:12:41 PDT)
AMBER: klambda Sergey Samsonov (Fri Oct 13 2006 - 07:49:05 PDT)
AMBER: Updated Tutorials Page Ross Walker (Fri Oct 13 2006 - 12:17:07 PDT)
AMBER: force fiels for a-rna asli ertekin (Fri Oct 13 2006 - 15:28:58 PDT)
- Re: AMBER: force fiels for a-rna Carlos Simmerling (Fri Oct 13 2006 - 15:41:21 PDT)
  - Re: AMBER: force fiels for a-rna asli ertekin (Fri Oct 13 2006 - 16:20:32 PDT)
- Re: AMBER: force fiels for a-rna Jiri Sponer (Sat Oct 14 2006 - 00:59:13 PDT)
AMBER: SURFTEN/SURFOFF values in amber9 ferranna.unimo.it (Sat Oct 14 2006 - 00:27:42 PDT)
AMBER: Grid command of ptraj Atsutoshi Okabe (Sat Oct 14 2006 - 00:31:01 PDT)
- Re: AMBER: Grid command of ptraj Sean Rathlef (Sat Oct 14 2006 - 03:25:59 PDT)
- RE: AMBER: Grid command of ptraj Atsutoshi Okabe (Mon Oct 16 2006 - 02:26:55 PDT)
  - RE: AMBER: Grid command of ptraj Thomas Cheatham (Tue Oct 17 2006 - 08:40:22 PDT)
    - RE: AMBER: Grid command of ptraj Atsutoshi Okabe (Tue Oct 17 2006 - 21:19:13 PDT)
    - RE: AMBER: Grid command of ptraj Thomas Cheatham (Mon Oct 23 2006 - 09:24:20 PDT)
    - AMBER: PKDIV lone pair dihedrals Lorenzo Gontrani (Mon Oct 23 2006 - 10:16:25 PDT)
    - Re: AMBER: PKDIV lone pair dihedrals David A. Case (Mon Oct 23 2006 - 13:26:58 PDT)
    - Re: AMBER: PKDIV lone pair dihedrals darden (Mon Oct 23 2006 - 14:05:37 PDT)
AMBER: How to calculate RDF based on the center of mass of specific solute atoms? Xioling Chuang (Sun Oct 15 2006 - 21:04:10 PDT)
- Re: AMBER: How to calculate RDF based on the center of mass of specific solute atoms? Fenghui Fan (Sun Oct 15 2006 - 21:36:25 PDT)
  - Re: AMBER: How to calculate RDF based on the center of mass of specific solute atoms? Xioling Chuang (Mon Oct 16 2006 - 01:48:04 PDT)
AMBER: simulation of protein in non-aq or organic solvent bath Smriti Sharma (Sun Oct 15 2006 - 21:06:53 PDT)
AMBER: Amber8: problem related to antechamber priya priya (Mon Oct 16 2006 - 00:00:38 PDT)
- RE: AMBER: Amber8: problem related to antechamber Junmei Wang (Tue Sep 26 2006 - 14:15:07 PDT)
  - AMBER: RE: Amber8: problem related to antechamber priya priya (Tue Sep 26 2006 - 20:49:34 PDT)
    - Re: AMBER: RE: Amber8: problem related to antechamber David A. Case (Sun Oct 01 2006 - 06:34:45 PDT)
- Re: AMBER: Amber8: problem related to antechamber David A. Case (Mon Oct 16 2006 - 08:29:19 PDT)
  - Re: AMBER: Amber8: problem related to antechamber priya priya (Mon Oct 16 2006 - 23:49:03 PDT)
    - Re: AMBER: Amber8: problem related to antechamber David A. Case (Tue Oct 17 2006 - 08:10:43 PDT)
- RE: AMBER: Amber8: problem related to antechamber Ross Walker (Mon Oct 16 2006 - 08:32:20 PDT)
AMBER: Amber8: how to do Simulated Annealing and Equilibration priya priya (Mon Oct 16 2006 - 01:32:18 PDT)
- RE: AMBER: Amber8: how to do Simulated Annealing and Equilibration Ross Walker (Mon Oct 16 2006 - 08:32:20 PDT)
  - RE: AMBER: Amber8: how to do Simulated Annealing and Equilibration priya priya (Mon Oct 16 2006 - 21:42:15 PDT)
AMBER: modeling of ligand concentrations Sean Rathlef (Mon Oct 16 2006 - 13:43:51 PDT)
- Re: AMBER: modeling of ligand concentrations David A. Case (Mon Oct 16 2006 - 15:24:34 PDT)
- Re: AMBER: modeling of ligand concentrations Sean Rathlef (Mon Oct 16 2006 - 15:48:16 PDT)
  - Re: AMBER: modeling of ligand concentrations David A. Case (Mon Oct 16 2006 - 17:33:54 PDT)
- Re: AMBER: modeling of ligand concentrations Sean Rathlef (Mon Oct 16 2006 - 18:37:25 PDT)
  - Re: AMBER: modeling of ligand concentrations David A. Case (Tue Oct 17 2006 - 08:38:07 PDT)
- Re: AMBER: modeling of ligand concentrations Sean Rathlef (Tue Oct 17 2006 - 09:07:18 PDT)
  - Re: AMBER: modeling of ligand concentrations David A. Case (Tue Oct 17 2006 - 09:41:24 PDT)
  - Re: AMBER: modeling of ligand concentrations Thomas Cheatham (Mon Oct 23 2006 - 09:38:55 PDT)
- Re: AMBER: modeling of ligand concentrations Sean Rathlef (Mon Oct 23 2006 - 15:19:18 PDT)
  - Re: AMBER: modeling of ligand concentrations Carlos Simmerling (Mon Oct 23 2006 - 15:38:22 PDT)
    - Re: AMBER: modeling of ligand concentrations Adrian Roitberg (Mon Oct 23 2006 - 16:44:46 PDT)
  - Re: AMBER: modeling of ligand concentrations Thomas Cheatham (Mon Oct 23 2006 - 15:51:28 PDT)
- Re: AMBER: modeling of ligand concentrations Sean Rathlef (Tue Oct 24 2006 - 16:47:03 PDT)
  - Re: AMBER: modeling of ligand concentrations Thomas Steinbrecher (Tue Oct 24 2006 - 18:11:05 PDT)
    - Re: AMBER: modeling of ligand concentrations David A. Case (Tue Oct 24 2006 - 18:56:14 PDT)
    - AMBER: Essential ions and water molecules in MMPBSA computations Cenk Andac (Mon Mar 12 2007 - 02:13:56 PDT)
    - Re: AMBER: Essential ions and water molecules in MMPBSA computations Jiri Sponer (Mon Mar 12 2007 - 06:05:49 PDT)
    - Re: AMBER: Essential ions and water molecules in MMPBSA computations Cenk Andac (Mon Mar 12 2007 - 07:03:03 PDT)
    - Re: AMBER: Essential ions and water molecules in MMPBSA computations Jiri Sponer (Mon Mar 12 2007 - 07:44:08 PDT)
    - Re: AMBER: Essential ions and water molecules in MMPBSA computations Cenk Andac (Mon Mar 19 2007 - 06:16:42 PDT)
    - Re: AMBER: Essential ions and water molecules in MMPBSA computations David A. Case (Mon Mar 19 2007 - 08:02:41 PDT)
    - Re: AMBER: Essential ions and water molecules in MMPBSA computations Cenk Andac (Mon Mar 19 2007 - 06:30:00 PDT)
- Re: AMBER: modeling of ligand concentrations Sean Rathlef (Tue Oct 24 2006 - 19:29:43 PDT)
- Re: AMBER: modeling of ligand concentrations Sean Rathlef (Tue Oct 24 2006 - 19:30:54 PDT)
AMBER: Density calculation Jianhui (Mon Oct 16 2006 - 14:12:24 PDT)
- Re: AMBER: Density calculation David A. Case (Mon Oct 16 2006 - 15:26:49 PDT)
RE: AMBER: angle between two vectors. . Lwin, ThuZar (Mon Oct 16 2006 - 13:51:28 PDT)
AMBER: How to find equillibration time for my system in a generalised born solvation model Gobind Singh Bisht (Mon Oct 16 2006 - 14:34:11 PDT)
- Re: AMBER: How to find equillibration time for my system in a generalised born solvation model David A. Case (Mon Oct 16 2006 - 15:33:14 PDT)
AMBER: regarding PBCAL in MM-PBSA Cenk Andac (Mon Oct 16 2006 - 16:11:33 PDT)
- Re: AMBER: regarding PBCAL in MM-PBSA Ray Luo (Mon Oct 16 2006 - 17:35:42 PDT)
  - Re: AMBER: regarding PBCAL in MM-PBSA Cenk Andac (Mon Oct 16 2006 - 18:15:20 PDT)
AMBER: General Coding Problem Elijah Gregory (Mon Oct 16 2006 - 16:53:27 PDT)
- Re: AMBER: General Coding Problem David A. Case (Mon Oct 16 2006 - 17:27:56 PDT)
Re: AMBER: General Coding Problem Bill Ross (Mon Oct 16 2006 - 17:56:37 PDT)
AMBER: Problem working with Antechamber nur avneet (Tue Oct 17 2006 - 00:44:54 PDT)
AMBER: RDF calculation Xioling Chuang (Tue Oct 17 2006 - 03:54:02 PDT)
- Re: AMBER: RDF calculation Thomas Cheatham (Tue Oct 17 2006 - 08:23:05 PDT)
AMBER: How did the coordinates change in xleap? Zhihong Yu (Tue Oct 17 2006 - 08:03:47 PDT)
- Re: AMBER: How did the coordinates change in xleap? David A. Case (Tue Oct 17 2006 - 08:28:52 PDT)
AMBER: Unstable RMS trajectory Dave, Sonya (Tue Oct 17 2006 - 09:03:59 PDT)
- Re: AMBER: Unstable RMS trajectory Carlos Simmerling (Tue Oct 17 2006 - 09:10:52 PDT)
  - Re: AMBER: Unstable RMS trajectory Gustavo Seabra (Tue Oct 17 2006 - 09:22:31 PDT)
    - Re: AMBER: Unstable RMS trajectory Carlos Simmerling (Tue Oct 17 2006 - 09:33:40 PDT)
    - Re: AMBER: Unstable RMS trajectory Gustavo Seabra (Tue Oct 17 2006 - 09:56:23 PDT)
    - Re: AMBER: Unstable RMS trajectory Adrian Roitberg (Tue Oct 17 2006 - 09:46:48 PDT)
- Re: AMBER: Unstable RMS trajectory Bill Ross (Tue Oct 17 2006 - 09:26:18 PDT)
- RE: AMBER: Unstable RMS trajectory Ross Walker (Tue Oct 17 2006 - 09:40:43 PDT)
  - RE: AMBER: Unstable RMS trajectory Dave, Sonya (Tue Oct 17 2006 - 10:10:03 PDT)
- RE: AMBER: Unstable RMS trajectory Dave, Sonya (Tue Oct 17 2006 - 10:17:59 PDT)
  - Re: AMBER: Unstable RMS trajectory Adrian Roitberg (Tue Oct 17 2006 - 10:41:31 PDT)
  - Re: AMBER: Unstable RMS trajectory Gustavo Seabra (Tue Oct 17 2006 - 10:41:43 PDT)
- RE: AMBER: Unstable RMS trajectory Dave, Sonya (Tue Oct 17 2006 - 11:14:44 PDT)
AMBER: sander/topology problem Lorenzo Gontrani (Tue Oct 17 2006 - 09:51:39 PDT)
- Re: AMBER: sander/topology problem David A. Case (Tue Oct 17 2006 - 10:31:25 PDT)
  - Re: AMBER: sander/topology problem Jin-Soo Kim (Fri Mar 23 2007 - 07:31:00 PDT)
    - Re: AMBER: sander/topology problem Gustavo Seabra (Fri Mar 23 2007 - 08:15:21 PDT)
    - Re: AMBER: sander/topology problem Jin-Soo Kim (Sat Mar 24 2007 - 04:17:51 PDT)
AMBER: question on mm_pbsa_statistics.pl Yongmei Pan (Tue Oct 17 2006 - 15:36:23 PDT)
AMBER: questions on mm_pbsa_statitistics.pl Yongmei Pan (Tue Oct 17 2006 - 15:57:59 PDT)
- Re: AMBER: questions on mm_pbsa_statitistics.pl Holger Gohlke (Wed Oct 18 2006 - 00:42:52 PDT)
AMBER: Problem loading peptoid residues with antechamber nur avneet (Tue Oct 17 2006 - 23:23:42 PDT)
- RE: AMBER: Problem loading peptoid residues with antechamber Junmei Wang (Wed Oct 18 2006 - 09:05:24 PDT)
  - RE: AMBER: Problem loading peptoid residues with antechamber nur avneet (Wed Oct 18 2006 - 21:05:15 PDT)
AMBER: To create methanol solvent box Atsutoshi Okabe (Tue Oct 17 2006 - 23:31:02 PDT)
- Re: AMBER: To create methanol solvent box Smriti Sharma (Wed Oct 18 2006 - 01:14:38 PDT)
AMBER: how to simulate water flow inside a channel? Gobind Singh Bisht (Wed Oct 18 2006 - 07:33:51 PDT)
AMBER: alanine scan (mm/pbsa) rob yang (Wed Oct 18 2006 - 07:46:47 PDT)
AMBER: ptraj atomicfluct Myunggi Yi (Wed Oct 18 2006 - 11:59:22 PDT)
- Re: AMBER: ptraj atomicfluct Myunggi Yi (Wed Oct 18 2006 - 12:13:36 PDT)
AMBER: charge models in antechamber Eric Hu (Wed Oct 18 2006 - 15:51:00 PDT)
- Re: AMBER: charge models in antechamber Sean Rathlef (Wed Oct 18 2006 - 16:29:02 PDT)
- Re: AMBER: charge models in antechamber Sean Rathlef (Wed Oct 18 2006 - 16:48:00 PDT)
- Re: AMBER: charge models in antechamber David Mobley (Thu Oct 19 2006 - 10:48:14 PDT)
AMBER: RESP charges of iron-porphyrin system Shin Tokumoto (Wed Oct 18 2006 - 19:50:26 PDT)
- Re: AMBER: RESP charges of iron-porphyrin system Gustavo Seabra (Thu Oct 19 2006 - 06:40:20 PDT)
  - Re: AMBER: RESP charges of iron-porphyrin system Shin Tokumoto (Thu Oct 19 2006 - 21:45:08 PDT)
    - Re: AMBER: RESP charges of iron-porphyrin system FyD (Thu Oct 19 2006 - 22:23:14 PDT)
- Re: AMBER: RESP charges of iron-porphyrin system Chris Moth (Thu Oct 19 2006 - 09:39:24 PDT)
- Re: AMBER: RESP charges of iron-porphyrin system Marcelo Puiatti (Wed Oct 25 2006 - 10:42:07 PDT)
- Re: AMBER: RESP charges of iron-porphyrin system Shin Tokumoto (Thu Dec 14 2006 - 01:31:13 PST)
AMBER: mmpbsa in parallell Olayiwola Adekoya (Thu Oct 19 2006 - 00:57:07 PDT)
AMBER: Free-energy using MM-PBSA mathew k varghese (Thu Oct 19 2006 - 01:05:45 PDT)
- Re: AMBER: Free-energy using MM-PBSA Yongmei Pan (Thu Oct 19 2006 - 06:20:07 PDT)
AMBER: Amber9 serial installation -tests- severe (174): SIGSEGV, segmentation fault occurred Maniopoulou, A $Mina$ (Thu Oct 19 2006 - 05:48:08 PDT)
- Re: AMBER: Amber9 serial installation -tests- severe (174): SIGSEGV, segmentation fault occurred David A. Case (Thu Oct 19 2006 - 12:22:47 PDT)
- RE: AMBER: Amber9 serial installation -tests- severe (174): SIGSEGV, segmentation fault occurred Ross Walker (Thu Oct 19 2006 - 12:24:43 PDT)
  - RE: AMBER: Amber9 serial installation -tests- severe (174): SIGSEGV, segmentation fault occurred Maniopoulou, A $Mina$ (Fri Oct 20 2006 - 03:27:29 PDT)
    - RE: AMBER: Amber9 serial installation -tests- severe (174): SIGSEGV, segmentation fault occurred Ross Walker (Fri Oct 20 2006 - 09:06:49 PDT)
    - RE: AMBER: Amber9 serial installation -tests- severe (174): SIGSEGV, segmentation fault occurred Maniopoulou, A $Mina$ (Tue Oct 24 2006 - 06:59:26 PDT)
    - RE: AMBER: Amber9 serial installation -tests- severe (174): SIGSEGV, segmentation fault occurred Ross Walker (Tue Oct 24 2006 - 08:33:45 PDT)
AMBER: Curve fitting during dihedral parameter calculation Prashanth Athri (Thu Oct 19 2006 - 12:15:21 PDT)
AMBER: Issue with installation of Amber v9.0 parallel compilation Pravin_Kumar.jubilantbiosys.com (Thu Oct 19 2006 - 21:02:42 PDT)
AMBER: Issue with installation of Amber v9.0 parallel compilation Pravin_Kumar.jubilantbiosys.com (Thu Oct 19 2006 - 21:17:51 PDT)
- RE: AMBER: Issue with installation of Amber v9.0 parallel compilation Ross Walker (Thu Oct 19 2006 - 21:55:00 PDT)
AMBER: Probelm with running Amber 9 parallelly Rafi Ahmad (Fri Oct 20 2006 - 07:29:14 PDT)
- Re: AMBER: Probelm with running Amber 9 parallelly David A. Case (Fri Oct 20 2006 - 08:24:16 PDT)
AMBER: rbornstat average and fluctuations incorrect when nrespa != nrespai Ingvar Lagerstedt (Fri Oct 20 2006 - 09:17:08 PDT)
- Re: AMBER: rbornstat average and fluctuations incorrect when nrespa != nrespai David A. Case (Fri Oct 20 2006 - 10:27:50 PDT)
AMBER: Question about sander code Kijeong Kwac (Fri Oct 20 2006 - 11:13:49 PDT)
- Re: AMBER: Question about sander code David A. Case (Fri Oct 20 2006 - 11:37:51 PDT)
  - RE: Re: AMBER: Question about sander code Kijeong Kwac (Fri Oct 20 2006 - 14:08:17 PDT)
    - Re: Re: AMBER: Question about sander code David A. Case (Fri Oct 20 2006 - 14:47:50 PDT)
    - RE: Re: Re: AMBER: Question about sander code Kijeong Kwac (Fri Oct 20 2006 - 15:32:00 PDT)
    - RE: RE: Re: Re: AMBER: Question about sander code Kijeong Kwac (Fri Oct 20 2006 - 15:48:07 PDT)
    - Re: Re: Re: AMBER: Question about sander code David A. Case (Fri Oct 20 2006 - 15:55:05 PDT)
AMBER: problem of installing carnal on macosx gtg549i.mail.gatech.edu (Fri Oct 20 2006 - 11:37:39 PDT)
Re: AMBER: problem of installing carnal on macosx Bill Ross (Fri Oct 20 2006 - 11:50:19 PDT)
- Re: AMBER: problem of installing carnal on macosx Shuting Wei (Fri Oct 20 2006 - 12:45:03 PDT)
AMBER: atom type nh vs. n2 sethl.gatech.edu (Fri Oct 20 2006 - 14:31:09 PDT)
AMBER: question on molsurf Yongmei Pan (Fri Oct 20 2006 - 15:38:38 PDT)
AMBER: HBON in frcmod file Ilyas Yildirim (Fri Oct 20 2006 - 22:46:31 PDT)
- Re: AMBER: HBON in frcmod file David A. Case (Sun Oct 22 2006 - 22:11:58 PDT)
Re: AMBER: HBON in frcmod file Bill Ross (Sat Oct 21 2006 - 00:41:55 PDT)
- Re: AMBER: HBON in frcmod file Ilyas Yildirim (Sat Oct 21 2006 - 01:24:42 PDT)
- Re: AMBER: HBON in frcmod file Bill Ross (Sat Oct 21 2006 - 12:57:48 PDT)
AMBER: single or dual topology for TI? Holly Freedman (Sat Oct 21 2006 - 11:20:51 PDT)
- Re: AMBER: single or dual topology for TI? David Mobley (Sat Oct 21 2006 - 12:17:50 PDT)
- Re: AMBER: single or dual topology for TI? Holly Freedman (Sat Oct 21 2006 - 13:32:42 PDT)
  - Re: AMBER: single or dual topology for TI? David Mobley (Sat Oct 21 2006 - 13:58:41 PDT)
AMBER: mmpbsa: fail to run heat in tutorial A3 jitrayut jitonnom (Sun Oct 22 2006 - 10:31:53 PDT)
- RE: AMBER: mmpbsa: fail to run heat in tutorial A3 Ross Walker (Mon Oct 23 2006 - 08:39:26 PDT)
AMBER: Virus? Peter Gannett (Mon Oct 23 2006 - 05:34:29 PDT)
AMBER: ff for drug-dna complex and drug atom types assignment Kateryna Miroshnychenko (Mon Oct 23 2006 - 09:08:59 PDT)
- Re: AMBER: ff for drug-dna complex and drug atom types assignment Barbault Florent (Mon Oct 23 2006 - 11:37:53 PDT)
AMBER: Using modified NA bases sethl.gatech.edu (Mon Oct 23 2006 - 12:59:15 PDT)
- Re: AMBER: Using modified NA bases Fabian Alejandro Rodriguez (Mon Oct 23 2006 - 16:17:41 PDT)
  - Re: AMBER: Using modified NA bases Franck_Vendeix.ncsu.edu (Tue Oct 24 2006 - 06:03:36 PDT)
- Re: AMBER: Using modified NA bases FyD (Tue Oct 24 2006 - 11:14:54 PDT)
  - Re: AMBER: Using modified NA bases Qizhi Cui (Wed Oct 25 2006 - 08:51:32 PDT)
AMBER: ptraj radial problem: Segmentation fault Jianhui Tian (Mon Oct 23 2006 - 14:48:43 PDT)
AMBER: splitting LES with ptraj in amber9 bala (Mon Oct 23 2006 - 22:18:16 PDT)
AMBER: DIST_RST Urszula Uciechowska (Tue Oct 24 2006 - 01:32:03 PDT)
- Re: AMBER: DIST_RST Cenk Andac (Tue Oct 24 2006 - 03:51:01 PDT)
AMBER: problem with calcpka.pl Benjamin Juhl (Tue Oct 24 2006 - 04:58:27 PDT)
- Re: AMBER: problem with calcpka.pl David A. Case (Sun Oct 29 2006 - 20:33:54 PST)
  - Re: AMBER: problem with calcpka.pl Benjamin Juhl (Mon Oct 30 2006 - 05:57:42 PST)
    - AMBER: periodic boundary condition question... HL Eastwood (Mon Oct 30 2006 - 06:42:53 PST)
    - Re: AMBER: periodic boundary condition question... Sergey Samsonov (Mon Oct 30 2006 - 07:04:12 PST)
    - Re: AMBER: periodic boundary condition question... HL Eastwood (Mon Oct 30 2006 - 07:19:16 PST)
    - Re: AMBER: periodic boundary condition question... Sergey Samsonov (Mon Oct 30 2006 - 07:36:29 PST)
    - RE: AMBER: periodic boundary condition question... Ross Walker (Mon Oct 30 2006 - 08:24:26 PST)
    - Re: AMBER: periodic boundary condition question... David A. Case (Mon Oct 30 2006 - 08:32:56 PST)
    - Re: AMBER: periodic boundary condition question... HL Eastwood (Mon Oct 30 2006 - 08:52:04 PST)
- Re: AMBER: problem with calcpka.pl Amber admin (Tue Oct 31 2006 - 16:33:09 PST)
AMBER: pmemd installation on linux_p3_athlon ifort gtg549i.mail.gatech.edu (Tue Oct 24 2006 - 09:20:30 PDT)
- Re: AMBER: pmemd installation on linux_p3_athlon ifort Robert Duke (Tue Oct 24 2006 - 10:08:58 PDT)
  - Re: AMBER: pmemd installation on linux_p3_athlon ifort Shuting Wei (Tue Oct 24 2006 - 12:19:31 PDT)
AMBER: load charges to antechamber calculations Wang, Xuelin (Tue Oct 24 2006 - 12:30:24 PDT)
- Re: AMBER: load charges to antechamber calculations David A. Case (Tue Oct 24 2006 - 15:55:29 PDT)
  - Re: AMBER:pls help load peptoid residues in antechamber nur avneet (Tue Oct 24 2006 - 22:29:55 PDT)
AMBER: Not getting proper structure after minimization Dave, Sonya (Tue Oct 24 2006 - 13:50:04 PDT)
- Re: AMBER: Not getting proper structure after minimization Carlos Simmerling (Tue Oct 24 2006 - 14:06:14 PDT)
- Re: AMBER: Not getting proper structure after minimization Gustavo Seabra (Tue Oct 24 2006 - 14:28:27 PDT)
  - Re: AMBER: Not getting proper structure after minimization Elijah Gregory (Tue Oct 24 2006 - 14:39:08 PDT)
- RE: AMBER: Not getting proper structure after minimization Dave, Sonya (Tue Oct 24 2006 - 15:46:45 PDT)
  - Re: AMBER: Not getting proper structure after minimization Elijah Gregory (Tue Oct 24 2006 - 16:12:35 PDT)
    - Re: AMBER: Not getting proper structure after minimization Elijah Gregory (Tue Oct 24 2006 - 16:17:14 PDT)
    - Re: AMBER: Not getting proper structure after minimization Carlos Simmerling (Wed Oct 25 2006 - 06:45:38 PDT)
    - Re: AMBER: Not getting proper structure after minimization Giulio Rastelli (Wed Oct 25 2006 - 06:52:48 PDT)
AMBER: md and implicit solvation Jardas sucuriba (Tue Oct 24 2006 - 16:57:24 PDT)
- Re: AMBER: md and implicit solvation Adrian Roitberg (Tue Oct 24 2006 - 17:19:34 PDT)
  - Re: AMBER: md and implicit solvation Jardas sucuriba (Tue Oct 24 2006 - 18:29:35 PDT)
    - Re: AMBER: md and implicit solvation David A. Case (Tue Oct 24 2006 - 18:47:18 PDT)
- Re: AMBER: md and implicit solvation David A. Case (Tue Oct 24 2006 - 18:26:15 PDT)
- Re: AMBER: md and implicit solvation Thomas Cheatham (Tue Oct 24 2006 - 18:50:43 PDT)
AMBER: error estimate for free energy perturbation calculation jz7.duke.edu (Tue Oct 24 2006 - 21:15:26 PDT)
- Re: AMBER: error estimate for free energy perturbation calculation Chris Moth (Wed Oct 25 2006 - 09:58:14 PDT)
  - Re: AMBER: error estimate for free energy perturbation calculation David A. Case (Wed Oct 25 2006 - 11:40:47 PDT)
    - Re: AMBER: error estimate for free energy perturbation calculation Fenghui Fan (Wed Oct 25 2006 - 13:34:42 PDT)
  - Re: AMBER: error estimate for free energy perturbation calculation Ilyas Yildirim (Wed Oct 25 2006 - 16:17:36 PDT)
AMBER: Question regarding lastrst and taup Priti Hansia (Tue Oct 24 2006 - 23:37:09 PDT)
- RE: AMBER: Question regarding lastrst and taup Ross Walker (Wed Oct 25 2006 - 08:46:52 PDT)
  - RE: AMBER: Question regarding lastrst and taup Priti Hansia (Wed Oct 25 2006 - 21:58:10 PDT)
AMBER: parameters !!?? Urszula Uciechowska (Wed Oct 25 2006 - 02:27:22 PDT)
- Re: AMBER: parameters !!?? cristian obiol (Wed Oct 25 2006 - 03:29:42 PDT)
- Re: AMBER: parameters !!?? Urszula Uciechowska (Wed Oct 25 2006 - 06:32:49 PDT)
  - RE: AMBER: parameters !!?? Ross Walker (Wed Oct 25 2006 - 08:53:01 PDT)
AMBER: Shake&Lone Pairs Lorenzo Gontrani (Wed Oct 25 2006 - 03:58:59 PDT)
- Re: AMBER: Shake&Lone Pairs David A. Case (Wed Oct 25 2006 - 11:21:02 PDT)
AMBER: amber9: SA Bomb in sa_arc Giulio Rastelli (Wed Oct 25 2006 - 04:03:54 PDT)
- Re: AMBER: amber9: SA Bomb in sa_arc Ray Luo (Tue Oct 24 2006 - 14:55:24 PDT)
  - Re: AMBER: amber9: SA Bomb in sa_arc Giulio Rastelli (Thu Oct 26 2006 - 03:56:43 PDT)
    - RE: AMBER: amber9: SA Bomb in sa_arc Ross Walker (Thu Oct 26 2006 - 08:38:05 PDT)
    - Re: AMBER: amber9: SA Bomb in sa_arc Giulio Rastelli (Thu Oct 26 2006 - 08:58:50 PDT)
    - RE: AMBER: amber9: SA Bomb in sa_arc Ross Walker (Thu Oct 26 2006 - 09:35:19 PDT)
    - Re: AMBER: amber9: SA Bomb in sa_arc Ray Luo (Wed Oct 25 2006 - 02:14:08 PDT)
- Re: AMBER: amber9: SA Bomb in sa_arc Ray Luo (Tue Oct 31 2006 - 00:29:27 PST)
AMBER: residence time& hydration density Andres Palencia (Wed Oct 25 2006 - 07:16:53 PDT)
- Re: AMBER: residence time& hydration density Myunggi Yi (Thu Oct 26 2006 - 08:27:26 PDT)
AMBER: reinstall amber8 Rachel (Wed Oct 25 2006 - 07:57:59 PDT)
- Re: AMBER: reinstall amber8 Wei Zhang (Wed Oct 25 2006 - 08:13:01 PDT)
AMBER: mm_pbsa: binding energy calculation Varsha Goyal (Wed Oct 25 2006 - 11:51:57 PDT)
- AMBER: Phosphorylated protein MD simulation Fenghui Fan (Wed Oct 25 2006 - 14:16:50 PDT)
  - Re: AMBER: Phosphorylated protein MD simulation Myunggi Yi (Thu Oct 26 2006 - 08:13:17 PDT)
    - Re: AMBER: Phosphorylated protein MD simulation Myunggi Yi (Thu Oct 26 2006 - 08:18:26 PDT)
- Re: AMBER: mm_pbsa: binding energy calculation Angelo (Thu Oct 26 2006 - 06:04:18 PDT)
  - Re: AMBER: mm_pbsa: binding energy calculation Varsha Goyal (Sat Oct 28 2006 - 14:41:02 PDT)
    - AMBER: imaging issue David Smith (Sun Oct 29 2006 - 08:26:07 PST)
    - Re: AMBER: imaging issue Kristina Furse (Mon Oct 30 2006 - 10:30:25 PST)
    - Re: AMBER: imaging issue Thomas Cheatham (Mon Oct 30 2006 - 12:54:20 PST)
    - Re: AMBER: mm_pbsa: binding energy calculation Angelo (Mon Oct 30 2006 - 01:36:25 PST)
AMBER: How do we simulate deletion mutations Dave, Sonya (Wed Oct 25 2006 - 11:47:38 PDT)
- Re: AMBER: How do we simulate deletion mutations Fenghui Fan (Wed Oct 25 2006 - 13:13:20 PDT)
  - RE: AMBER: How do we simulate deletion mutations Dave, Sonya (Wed Oct 25 2006 - 14:41:48 PDT)
    - AMBER: CARNAL: carnal source code Keerthi Gottipati (Wed Oct 25 2006 - 15:14:41 PDT)
    - Re: AMBER: CARNAL: carnal source code Carlos Simmerling (Wed Oct 25 2006 - 16:06:08 PDT)
    - Re: AMBER: CARNAL: carnal source code Keerthi Gottipati (Thu Oct 26 2006 - 05:41:21 PDT)
    - RE: AMBER: How do we simulate deletion mutations Fenghui Fan (Wed Oct 25 2006 - 15:43:49 PDT)
    - RE: AMBER: How do we simulate deletion mutations Dave, Sonya (Thu Oct 26 2006 - 11:05:01 PDT)
    - AMBER: Two different HIS ligands David LeBard (Thu Oct 26 2006 - 14:16:09 PDT)
    - Re: AMBER: Two different HIS ligands Kristina Furse (Thu Oct 26 2006 - 14:41:49 PDT)
    - Re: AMBER: Two different HIS ligands David LeBard (Thu Oct 26 2006 - 16:16:42 PDT)
AMBER: how to select the problematic residues(atoms) in VMD Rachel (Thu Oct 26 2006 - 04:00:21 PDT)
- Re: AMBER: how to select the problematic residues(atoms) in VMD Andres Palencia (Thu Oct 26 2006 - 04:56:31 PDT)
  - RE: AMBER: how to select the problematic residues(atoms) in VMD Ross Walker (Thu Oct 26 2006 - 08:26:22 PDT)
AMBER: MM-PBSA memory usage Stefano Pieraccini (Thu Oct 26 2006 - 05:33:41 PDT)
AMBER: Calculating native contacts for mdcrd files Anna Bowman (Thu Oct 26 2006 - 08:20:50 PDT)
AMBER: how to add hydrogen molecules in the protein Rachel (Thu Oct 26 2006 - 09:28:16 PDT)
- Re: AMBER: how to add hydrogen molecules in the protein David A. Case (Thu Oct 26 2006 - 17:57:22 PDT)
AMBER: error GRID command in ptraj Andres Palencia (Thu Oct 26 2006 - 10:39:19 PDT)
AMBER: parameters for fluoromolecules with more than one single carbon? Jones de Andrade (Thu Oct 26 2006 - 14:51:27 PDT)
AMBER: halogen bondi radii in mm_pbsa_calceneent.pm Giulio Rastelli (Fri Oct 27 2006 - 01:46:30 PDT)
- AMBER: mm_pbsa reference Angelo (Fri Oct 27 2006 - 05:47:07 PDT)
AMBER: Compile AMBER 8 Esther Brugger (Fri Oct 27 2006 - 08:44:51 PDT)
- Re: AMBER: Compile AMBER 8 Mark Williamson (Fri Oct 27 2006 - 09:03:07 PDT)
  - Re: AMBER: Compile AMBER 8 Esther Brugger (Fri Oct 27 2006 - 11:21:13 PDT)
    - Re: AMBER: Compile AMBER 8 David A. Case (Fri Oct 27 2006 - 12:12:35 PDT)
    - Re: AMBER: Compile AMBER 8 Esther Brugger (Fri Oct 27 2006 - 13:18:00 PDT)
    - Re: AMBER: Compile AMBER 8 David A. Case (Fri Oct 27 2006 - 13:46:07 PDT)
    - Re: AMBER: Compile AMBER 8 Esther Brugger (Mon Oct 30 2006 - 07:28:08 PST)
    - Re: AMBER: Compile AMBER 8 HL Eastwood (Mon Oct 30 2006 - 08:43:51 PST)
    - Re: AMBER: Compile AMBER 8 Esther Brugger (Mon Oct 30 2006 - 09:24:59 PST)
    - Re: AMBER: Compile AMBER 8 HL Eastwood (Mon Oct 30 2006 - 09:37:22 PST)
    - Re: AMBER: Compile AMBER 8 Esther Brugger (Mon Oct 30 2006 - 10:14:05 PST)
    - AMBER: NEWPDB.PDB from antechamber Esther Brugger (Wed Nov 01 2006 - 08:59:29 PST)
    - RE: AMBER: NEWPDB.PDB from antechamber Junmei Wang (Wed Nov 01 2006 - 09:19:27 PST)
    - RE: AMBER: NEWPDB.PDB from antechamber Esther Brugger (Wed Nov 01 2006 - 11:10:20 PST)
    - RE: AMBER: NEWPDB.PDB from antechamber Junmei Wang (Wed Nov 01 2006 - 11:42:42 PST)
- Re: AMBER: Compile AMBER 8 David A. Case (Fri Oct 27 2006 - 09:45:36 PDT)
AMBER: where to set bondi radii for halogens Giulio Rastelli (Fri Oct 27 2006 - 09:59:00 PDT)
- Re: AMBER: where to set bondi radii for halogens David A. Case (Fri Oct 27 2006 - 11:58:04 PDT)
  - Re: AMBER: where to set bondi radii for halogens Giulio Rastelli (Fri Oct 27 2006 - 14:10:32 PDT)
    - Re: AMBER: where to set bondi radii for halogens David A. Case (Fri Oct 27 2006 - 17:24:12 PDT)
AMBER: Amber: Parallel Installation Problems Maniopoulou, A $Mina$ (Fri Oct 27 2006 - 10:13:56 PDT)
- RE: AMBER: Amber: Parallel Installation Problems Ross Walker (Fri Oct 27 2006 - 10:53:10 PDT)
AMBER: Help with polarization force field norberto.ualberta.ca (Fri Oct 27 2006 - 16:20:09 PDT)
AMBER: RESP charge fitting Mingfeng Yang (Fri Oct 27 2006 - 17:35:37 PDT)
- Re: AMBER: RESP charge fitting FyD (Fri Oct 27 2006 - 23:37:59 PDT)
AMBER: solvation and His protonation Jardas sucuriba (Sat Oct 28 2006 - 07:00:44 PDT)
- Re: AMBER: solvation and His protonation David A. Case (Mon Oct 30 2006 - 16:34:05 PST)
  - Re: AMBER: solvation and His protonation Jardas sucuriba (Tue Oct 31 2006 - 05:07:24 PST)
    - Re: AMBER: solvation and His protonation David A. Case (Tue Oct 31 2006 - 07:57:53 PST)
    - AMBER: matrix correl Jardas sucuriba (Tue Nov 21 2006 - 05:05:41 PST)
    - Re: AMBER: matrix correl Lars Skjærven (Wed Feb 20 2008 - 09:35:30 PST)
    - RE: AMBER: matrix correl Ibrahim Moustafa (Wed Feb 20 2008 - 10:19:31 PST)
AMBER: ff02 force fields norberto.ualberta.ca (Sun Oct 29 2006 - 12:18:25 PST)
- Re: AMBER: ff02 force fields David A. Case (Sun Oct 29 2006 - 21:17:44 PST)
  - Re: AMBER: ff02 force fields norberto.ualberta.ca (Mon Oct 30 2006 - 10:37:57 PST)
AMBER: C -N -CT-CT torsion parameters John Vieceli (Sun Oct 29 2006 - 17:10:49 PST)
AMBER: Closest(closest water) Sergey Samsonov (Mon Oct 30 2006 - 04:58:11 PST)
- Re: AMBER: Closest(closest water) Adrian Roitberg (Mon Oct 30 2006 - 05:12:13 PST)
  - Re: AMBER: Closest(closest water) Sergey Samsonov (Mon Oct 30 2006 - 06:27:40 PST)
    - Re: AMBER: Closest(closest water) Mingfeng Yang (Mon Oct 30 2006 - 12:29:00 PST)
    - Re: AMBER: Closest(closest water) Sergey Samsonov (Wed Nov 01 2006 - 00:38:55 PST)
AMBER: how to restrain some residues in a NPT MD? Zhihong Yu (Mon Oct 30 2006 - 07:20:38 PST)
- RE: AMBER: how to restrain some residues in a NPT MD? Ross Walker (Mon Oct 30 2006 - 08:34:46 PST)
AMBER: ff99SB vs ff02 (ff02pol.rl) Nicolas Lux Fawzi (Mon Oct 30 2006 - 17:48:32 PST)
- Re: AMBER: ff99SB vs ff02 (ff02pol.rl) Thomas Cheatham (Mon Oct 30 2006 - 18:15:18 PST)
  - Re: AMBER: ff99SB vs ff02 (ff02pol.rl) David A. Case (Mon Oct 30 2006 - 18:57:48 PST)
    - Re: AMBER: ff99SB vs ff02 (ff02pol.rl) Thomas Cheatham (Mon Oct 30 2006 - 21:07:46 PST)
AMBER: Re: Problems installing antechamber 1.27 andrea carotti (Tue Oct 31 2006 - 00:17:49 PST)
AMBER: what is the RMS value in resp charge fitting ? jitrayut jitonnom (Tue Oct 31 2006 - 00:46:31 PST)
AMBER: MMPBSA entropy question Barbault Florent (Tue Oct 31 2006 - 01:08:55 PST)
- Re: AMBER: MMPBSA entropy question David A. Case (Tue Oct 31 2006 - 17:04:29 PST)
AMBER: Problems with carnal (Amber7) anna.schrey.gmx.de (Tue Oct 31 2006 - 07:24:29 PST)
Re: AMBER: Problems with carnal (Amber7) Bill Ross (Tue Oct 31 2006 - 09:09:57 PST)
AMBER: N1-protonated adenosine, N-terminal myristyl group Michael F. Summers (Tue Oct 31 2006 - 12:54:49 PST)
AMBER: mm_pbsa does not terminate Holly Freedman (Tue Oct 31 2006 - 16:51:19 PST)
- Re: AMBER: mm_pbsa does not terminate Holly Freedman (Wed Nov 01 2006 - 09:56:28 PST)
- Re: AMBER: mm_pbsa does not terminate Holly Freedman (Wed Nov 01 2006 - 11:34:17 PST)
AMBER: Mass weights Sergey Samsonov (Wed Nov 01 2006 - 00:41:33 PST)
- Re: AMBER: Mass weights Thomas Cheatham (Mon Nov 06 2006 - 20:58:54 PST)
  - Re: AMBER: Mass weights Sergey Samsonov (Tue Nov 07 2006 - 00:06:14 PST)
AMBER: How to start a Simulation of a peptide in bilayer nur avneet (Wed Nov 01 2006 - 01:28:31 PST)
AMBER: ab initio terminology query HL Eastwood (Wed Nov 01 2006 - 03:38:24 PST)
- Re: AMBER: ab initio terminology query Jiri Sponer (Wed Nov 01 2006 - 03:59:04 PST)
  - RE: AMBER: ab initio terminology query Ross Walker (Wed Nov 01 2006 - 08:44:22 PST)
    - Re: AMBER: ab initio terminology query Gustavo Seabra (Wed Nov 01 2006 - 08:50:27 PST)
    - Re: AMBER: ab initio terminology query David A. Case (Wed Nov 01 2006 - 09:30:50 PST)
    - Re: AMBER: ab initio terminology query Jiri Sponer (Wed Nov 01 2006 - 10:34:57 PST)
    - RE: AMBER: ab initio terminology query Hayden Eastwood (Wed Nov 01 2006 - 12:12:49 PST)
    - Re: AMBER: ab initio terminology query David A. Case (Wed Nov 01 2006 - 12:42:23 PST)
    - RE: AMBER: ab initio terminology query Ilyas Yildirim (Wed Nov 01 2006 - 12:38:58 PST)
    - RE: AMBER: ab initio terminology query Yong Duan (Wed Nov 01 2006 - 15:17:43 PST)
    - RE: AMBER: ab initio terminology query Ross Walker (Wed Nov 01 2006 - 12:51:43 PST)
    - Re: AMBER: ab initio terminology query Jiri Sponer (Wed Nov 01 2006 - 10:27:44 PST)
    - Re: AMBER: ab initio terminology query Adrian Roitberg (Wed Nov 01 2006 - 11:01:38 PST)
    - RE: AMBER: ab initio terminology query Yong Duan (Wed Nov 01 2006 - 10:53:39 PST)
    - Re: AMBER: ab initio terminology query Jiri Sponer (Wed Nov 01 2006 - 11:43:13 PST)
AMBER: PCA and projections Miguel Ferreira (Wed Nov 01 2006 - 06:11:57 PST)
AMBER: Amber 9 parallel test fail on 4096wat/Run.column_fft Yu Chen (Wed Nov 01 2006 - 08:22:54 PST)
- Re: AMBER: Amber 9 parallel test fail on 4096wat/Run.column_fft David A. Case (Wed Nov 01 2006 - 08:54:06 PST)
  - Re: AMBER: Amber 9 parallel test fail on 4096wat/Run.column_fft Yu Chen (Wed Nov 01 2006 - 09:02:26 PST)
- RE: AMBER: Amber 9 parallel test fail on 4096wat/Run.column_fft Ross Walker (Wed Nov 01 2006 - 09:21:02 PST)
  - Re: AMBER: Amber 9 parallel test fail on 4096wat/Run.column_fft Yu Chen (Fri Nov 03 2006 - 07:18:35 PST)
- Re: AMBER: Amber 9 parallel test fail on 4096wat/Run.column_fft Ross Walker (Fri Nov 03 2006 - 08:39:22 PST)
  - AMBER: Simulation a small chain of amino acids - error in MD simulation Dave, Sonya (Fri Nov 03 2006 - 09:54:06 PST)
    - Re: AMBER: Simulation a small chain of amino acids - error in MD simulation Carlos Simmerling (Fri Nov 03 2006 - 10:05:22 PST)
    - RE: AMBER: Simulation a small chain of amino acids - error in MD simulation Ross Walker (Fri Nov 03 2006 - 10:32:27 PST)
    - RE: AMBER: Simulation a small chain of amino acids - error in MD simulation Dave, Sonya (Fri Nov 03 2006 - 11:20:55 PST)
  - Re: AMBER: Amber 9 parallel test fail on 4096wat/Run.column_fft Yu Chen (Fri Nov 03 2006 - 11:05:55 PST)
AMBER: grid output Sergey Samsonov (Wed Nov 01 2006 - 08:31:34 PST)
- Re: AMBER: grid output Thomas Cheatham (Mon Nov 06 2006 - 20:30:25 PST)
  - Re: AMBER: grid output Sergey Samsonov (Tue Nov 07 2006 - 00:35:28 PST)
    - Re: AMBER: grid output Thomas Cheatham (Tue Nov 07 2006 - 08:25:39 PST)
    - Re: AMBER: grid output Sergey Samsonov (Tue Nov 07 2006 - 08:46:07 PST)
AMBER: GBSA implicit chloroform nadiav.soton.ac.uk (Wed Nov 01 2006 - 08:41:18 PST)
- Re: AMBER: GBSA implicit chloroform David A. Case (Wed Nov 01 2006 - 08:56:07 PST)
  - Re: AMBER: GBSA implicit chloroform nadiav.soton.ac.uk (Wed Nov 01 2006 - 09:13:22 PST)
- Re: AMBER: GBSA implicit chloroform Adrian Roitberg (Wed Nov 01 2006 - 09:22:14 PST)
- AMBER: leap - compilation error Tomas Kubar (Tue Nov 07 2006 - 01:47:33 PST)
  - Re: AMBER: leap - compilation error David A. Case (Tue Nov 07 2006 - 18:25:37 PST)
AMBER: too big EEL values in the minimisation output Rachel (Wed Nov 01 2006 - 09:01:17 PST)
- Re: AMBER: too big EEL values in the minimisation output darden (Wed Nov 01 2006 - 10:08:27 PST)
  - Re: AMBER: too big EEL values in the minimisation output Rachel (Thu Nov 02 2006 - 10:08:00 PST)
    - Re: AMBER: too big EEL values in the minimisation output darden (Thu Nov 02 2006 - 11:13:29 PST)
    - Re: AMBER: too big EEL values in the minimisation output Rachel (Fri Nov 03 2006 - 04:09:54 PST)
AMBER: Problem of QM/MM calculation with amber 9 parallel version Lee Kyung-koo (Wed Nov 01 2006 - 11:50:28 PST)
- RE: AMBER: Problem of QM/MM calculation with amber 9 parallel version Ross Walker (Wed Nov 01 2006 - 13:36:17 PST)
- RE: AMBER: Problem of QM/MM calculation with amber 9 parallel version Ross Walker (Wed Nov 01 2006 - 16:04:28 PST)
  - RE: AMBER: Problem of QM/MM calculation with amber 9 parallel version Rafi Ahmad (Thu Nov 02 2006 - 01:51:18 PST)
    - RE: AMBER: Problem of QM/MM calculation with amber 9 parallel version Ross Walker (Thu Nov 02 2006 - 09:17:42 PST)
- RE: AMBER: Problem of QM/MM calculation with amber 9 parallel version Ross Walker (Thu Nov 02 2006 - 09:05:38 PST)
AMBER: How the ensemble average calculated in Gibbs, AMBER7? Yongmei Pan (Wed Nov 01 2006 - 14:06:09 PST)
- Re: AMBER: How the ensemble average calculated in Gibbs, AMBER7? David A. Case (Sun Nov 05 2006 - 19:26:02 PST)
[RE]RE: AMBER: Problem of QM/MM calculation with amber 9 parallel version Lee Kyung-koo (Wed Nov 01 2006 - 15:25:25 PST)
[RE]RE: AMBER: Problem of QM/MM calculation with amber 9 parallel version Lee Kyung-koo (Thu Nov 02 2006 - 00:53:53 PST)
AMBER: leap usage Stefano Federico Massimiliano Pieraccini (Stefano.Pieraccini) (Thu Nov 02 2006 - 01:41:34 PST)
- AMBER: Can we use the distance restraint in Replica-exchange simulation with AMBER8 wenfei Li (Thu Nov 02 2006 - 04:44:18 PST)
  - Re: AMBER: Can we use the distance restraint in Replica-exchange simulation with AMBER8 Carlos Simmerling (Thu Nov 02 2006 - 12:28:33 PST)
- Re: AMBER: leap usage Mark Williamson (Thu Nov 02 2006 - 07:26:42 PST)
- Re: AMBER: leap usage Angelo (Thu Nov 02 2006 - 08:39:57 PST)
AMBER: Interaction Energy Calculation Varsha Goyal (Thu Nov 02 2006 - 13:34:28 PST)
- Re: AMBER: Interaction Energy Calculation Vitor Manuel Sousa F?x (Thu Nov 02 2006 - 14:08:01 PST)
  - Re: AMBER: Interaction Energy Calculation Varsha Goyal (Thu Nov 02 2006 - 15:04:12 PST)
AMBER: ntt=1 in simulated annealing Tanya Johannsen (Thu Nov 02 2006 - 19:44:19 PST)
- Re: AMBER: ntt=1 in simulated annealing Carlos Simmerling (Fri Nov 03 2006 - 03:48:06 PST)
  - Re: AMBER: ntt=1 in simulated annealing Tanya Johannsen (Fri Nov 03 2006 - 16:38:38 PST)
    - RE: AMBER: ntt=1 in simulated annealing Ross Walker (Fri Nov 03 2006 - 18:04:08 PST)
    - Re: AMBER: ntt=1 in simulated annealing Steven Winfield (Tue Nov 07 2006 - 03:26:28 PST)
    - Re: AMBER: ntt=1 in simulated annealing Tanya Johannsen (Tue Nov 14 2006 - 15:59:04 PST)
    - Re: AMBER: ntt=1 in simulated annealing Sergey Samsonov (Tue Nov 14 2006 - 23:09:15 PST)
    - Re: AMBER: ntt=1 in simulated annealing kepa koldo burusco (Wed Nov 15 2006 - 03:53:27 PST)
    - Re: AMBER: ntt=1 in simulated annealing David A. Case (Wed Nov 15 2006 - 08:46:58 PST)
AMBER: how to choose the parameter for the production/sampling run after the equilibration run hbluo (Fri Nov 03 2006 - 17:57:01 PST)
AMBER: Problems with equilibrating the starting density Markus Weingarth (Fri Nov 03 2006 - 09:32:20 PST)
- RE: AMBER: Problems with equilibrating the starting density Ross Walker (Fri Nov 03 2006 - 11:41:55 PST)
AMBER: pmemd installation problem Ed Pate (Fri Nov 03 2006 - 10:51:36 PST)
- Re: AMBER: pmemd installation problem Robert Duke (Fri Nov 03 2006 - 11:09:52 PST)
AMBER: Re: Fluorine and Bromine Parameters in Amber 9 Philip Cheung (Fri Nov 03 2006 - 11:56:52 PST)
AMBER: I got the error meassage in testcase of QMMM Lee Kyung-koo (Fri Nov 03 2006 - 21:33:44 PST)
AMBER: PTRAJ RMS: dumping RMSd vs time data r. a. (Sat Nov 04 2006 - 00:45:25 PST)
AMBER: PTRAJ RMS: dumping RMSd vs time data r. a. (Sat Nov 04 2006 - 00:58:25 PST)
- Re: AMBER: PTRAJ RMS: dumping RMSd vs time data Adrian Roitberg (Sat Nov 04 2006 - 05:00:40 PST)
  - Re: AMBER: PTRAJ RMS: dumping RMSd vs time data Fenghui Fan (Sat Nov 04 2006 - 22:31:25 PST)
- Re: AMBER: PTRAJ RMS: dumping RMSd vs time data Thomas Cheatham (Mon Nov 06 2006 - 20:18:20 PST)
  - Re: AMBER: PTRAJ RMS: dumping RMSd vs time data r. a. (Mon Nov 06 2006 - 22:44:35 PST)
    - Re: AMBER: PTRAJ RMS: dumping RMSd vs time data David A. Case (Mon Nov 06 2006 - 23:26:13 PST)
    - Re: AMBER: PTRAJ RMS: dumping RMSd vs time data r. a. (Mon Nov 06 2006 - 23:41:35 PST)
AMBER: Unable to find solution for an error - "cannot successfully assign bond type" Rama krishnan (Sat Nov 04 2006 - 02:06:51 PST)
AMBER: Ross Walker (Sat Nov 04 2006 - 09:35:43 PST)
AMBER: RE: I got the error meassage in testcase of QMMM Ross Walker (Sat Nov 04 2006 - 10:09:13 PST)
- AMBER: Amber: disufide bond Fenghui Fan (Sat Nov 04 2006 - 20:29:57 PST)
  - RE: AMBER: Amber: disufide bond hayden (Sun Nov 05 2006 - 05:03:23 PST)
    - RE: AMBER: Amber: disufide bond Fenghui Fan (Sun Nov 05 2006 - 06:02:48 PST)
    - AMBER: trajout script Fenghui Fan (Sun Nov 05 2006 - 08:23:57 PST)
    - Re: AMBER: trajout script Thomas Cheatham (Mon Nov 06 2006 - 12:39:04 PST)
AMBER: ACS Chicago potential symposia and OASYS abstracts Thomas Cheatham (Sat Nov 04 2006 - 13:04:47 PST)
AMBER: Combine amber-force field and gaff94 for one molecule? Michel Becker (Sun Nov 05 2006 - 09:45:05 PST)
- Re: AMBER: Combine amber-force field and gaff94 for one molecule? Fenghui Fan (Sun Nov 05 2006 - 10:30:27 PST)
- Re: AMBER: Combine amber-force field and gaff94 for one molecule? M. L. Dodson (Sun Nov 05 2006 - 11:35:34 PST)
  - Re: AMBER: Combine amber-force field and gaff94 for one molecule? Fenghui Fan (Sun Nov 05 2006 - 12:13:57 PST)
    - Re: AMBER: Combine amber-force field and gaff94 for one molecule? M. L. Dodson (Sun Nov 05 2006 - 12:47:22 PST)
  - Re: AMBER: Combine amber-force field and gaff94 for one molecule? Jiri Sponer (Sun Nov 05 2006 - 14:01:27 PST)
AMBER: no g77 in Fedora Core 5. how to get around with this problem in Fedora Core 5? Margaret S. Cheung (Sun Nov 05 2006 - 15:16:34 PST)
- Re: AMBER: no g77 in Fedora Core 5. how to get around with this problem in Fedora Core 5? Peter Gannett (Sun Nov 05 2006 - 15:40:18 PST)
  - Re: AMBER: no g77 in Fedora Core 5. how to get around with this problem in Fedora Core 5? Fenghui Fan (Sun Nov 05 2006 - 16:22:26 PST)
    - AMBER: Zn metal library Fenghui Fan (Sun Nov 05 2006 - 19:51:19 PST)
    - RE: AMBER: Zn metal library Ross Walker (Sun Nov 05 2006 - 22:08:20 PST)
    - Re: AMBER: Zn metal library Carlos Simmerling (Mon Nov 06 2006 - 04:26:52 PST)
    - Re: AMBER: no g77 in Fedora Core 5. how to get around with this problem in Fedora Core 5? Andreas Svrcek-Seiler (Mon Nov 06 2006 - 01:17:11 PST)
    - Re: AMBER: no g77 in Fedora Core 5. how to get around with this problem in Fedora Core 5? Margaret S. Cheung (Mon Nov 06 2006 - 07:23:29 PST)
    - AMBER: PCA results with explicit Vs Implicit solvation Keerthi Gottipati (Mon Nov 06 2006 - 08:32:16 PST)
    - Re: AMBER: PCA results with explicit Vs Implicit solvation Angelo (Mon Nov 06 2006 - 09:14:47 PST)
    - Re: AMBER: no g77 in Fedora Core 5. how to get around with this problem in Fedora Core 5? Andreas Svrcek-Seiler (Mon Nov 06 2006 - 09:13:37 PST)
    - Re: AMBER: no g77 in Fedora Core 5. how to get around with this problem in Fedora Core 5? Scott Pendley (Mon Nov 06 2006 - 09:20:43 PST)
    - Re: AMBER: no g77 in Fedora Core 5. how to get around with this problem in Fedora Core 5? Scott Pendley (Mon Nov 06 2006 - 09:28:48 PST)
AMBER: Mutual exclusion of atoms Nitin Bhardwaj (Sun Nov 05 2006 - 21:59:38 PST)
- AMBER: Mutual exclusion of atoms Nitin Bhardwaj (Mon Nov 06 2006 - 13:40:50 PST)
  - Re: AMBER: Mutual exclusion of atoms Thomas Steinbrecher (Mon Nov 06 2006 - 14:02:47 PST)
    - Re: AMBER: Mutual exclusion of atoms Nitin Bhardwaj (Mon Nov 06 2006 - 14:27:49 PST)
AMBER: Potential Energy Calculation sangeeta (Mon Nov 06 2006 - 04:11:30 PST)
- Re: AMBER: Potential Energy Calculation Carlos Simmerling (Mon Nov 06 2006 - 04:32:35 PST)
  - Re: AMBER: Potential Energy Calculation Mingfeng Yang (Mon Nov 06 2006 - 13:06:18 PST)
- RE: AMBER: Potential Energy Calculation Hayden Eastwood (Mon Nov 06 2006 - 04:47:00 PST)
AMBER: problem with NAD+ parameters Urszula Uciechowska (Mon Nov 06 2006 - 06:27:16 PST)
- Re: AMBER: problem with NAD+ parameters Cenk Andac (Mon Nov 06 2006 - 14:05:52 PST)
AMBER: top2mol2.c scanf format string bug Chris Moth (Mon Nov 06 2006 - 16:19:36 PST)
- Re: AMBER: top2mol2.c scanf format string bug David A. Case (Tue Nov 07 2006 - 08:18:43 PST)
AMBER: klambda for TI method. Biswa Ranjan Meher (Tue Nov 07 2006 - 04:59:15 PST)
- Re: AMBER: klambda for TI method. David A. Case (Tue Nov 07 2006 - 08:06:21 PST)
[RE]AMBER: RE: I got the error meassage in testcase of QMMM Lee Kyung-koo (Tue Nov 07 2006 - 08:46:25 PST)
AMBER: building a box kepa koldo burusco (Tue Nov 07 2006 - 08:52:28 PST)
- Re: AMBER: building a box Fenghui Fan (Tue Nov 07 2006 - 09:49:54 PST)
  - Re: AMBER: building a box kepa koldo burusco (Wed Nov 08 2006 - 04:08:32 PST)
[RE]AMBER: RE: I got the error meassage in testcase of QMMM Lee Kyung-koo (Tue Nov 07 2006 - 08:59:16 PST)
AMBER: error about the number of snapshots AYTUG TUNCEL (Tue Nov 07 2006 - 13:11:24 PST)
AMBER: Format of the prmtop file (NUMBER_EXCLUDED_ATOMS) & (EXCLUDED_ATOMS_LIST) Nitin Bhardwaj (Tue Nov 07 2006 - 13:08:42 PST)
- Re: AMBER: Format of the prmtop file (NUMBER_EXCLUDED_ATOMS) & (EXCLUDED_ATOMS_LIST) David A. Case (Tue Nov 07 2006 - 17:51:48 PST)
AMBER: Atom Exclusion Nitin Bhardwaj (Tue Nov 07 2006 - 21:44:30 PST)
AMBER: Re: Unit of force Kakali Sen (Tue Nov 07 2006 - 22:41:30 PST)
AMBER: question about the topology file J. Zhang (Wed Nov 08 2006 - 01:24:10 PST)
- Re: AMBER: question about the topology file Carlos Simmerling (Wed Nov 08 2006 - 04:18:58 PST)
  - Re: Re: AMBER: question about the topology file J. Zhang (Sun Nov 12 2006 - 17:42:20 PST)
    - AMBER: ZN-CYS prepin and frcmd file Fenghui Fan (Sun Nov 12 2006 - 18:16:37 PST)
    - AMBER: The plc.frcmod file in the old version tutorial Fenghui Fan (Sun Nov 12 2006 - 18:50:29 PST)
    - RE: AMBER: The plc.frcmod file in the old version tutorial Ross Walker (Mon Nov 13 2006 - 08:29:26 PST)
AMBER: Unit of force Kakali Sen (Wed Nov 08 2006 - 03:06:16 PST)
- Re: AMBER: Unit of force Adrian Roitberg (Wed Nov 08 2006 - 04:57:00 PST)
  - Re: AMBER: Unit of force Kakali Sen (Wed Nov 08 2006 - 05:12:41 PST)
AMBER: vlimit exceeded for step 0, vmax = infinity Rachel (Wed Nov 08 2006 - 04:59:00 PST)
- Re: AMBER: vlimit exceeded for step 0, vmax = infinity David A. Case (Wed Nov 08 2006 - 08:48:01 PST)
  - Re: AMBER: vlimit exceeded for step 0, vmax = infinity Rachel (Wed Nov 08 2006 - 09:31:12 PST)
    - Re: AMBER: vlimit exceeded for step 0, vmax = infinity Carlos Simmerling (Wed Nov 08 2006 - 09:46:27 PST)
    - Re: AMBER: vlimit exceeded for step 0, vmax = infinity David A. Case (Wed Nov 08 2006 - 13:35:10 PST)
    - Re: AMBER: vlimit exceeded for step 0, vmax = infinity Rachel (Fri Nov 10 2006 - 06:42:31 PST)
    - Re: AMBER: vlimit exceeded for step 0, vmax = infinity Carlos Simmerling (Fri Nov 10 2006 - 06:58:26 PST)
    - Re: AMBER: vlimit exceeded for step 0, vmax = infinity Rachel (Fri Nov 10 2006 - 07:54:26 PST)
    - Re: AMBER: vlimit exceeded for step 0, vmax = infinity David A. Case (Fri Nov 10 2006 - 08:34:45 PST)
    - RE: AMBER: vlimit exceeded for step 0, vmax = infinity Yong Duan (Fri Nov 10 2006 - 13:55:23 PST)
    - Re: AMBER: vlimit exceeded for step 0, vmax = infinity Rachel (Mon Nov 13 2006 - 09:09:22 PST)
    - RE: AMBER: vlimit exceeded for step 0, vmax = infinity Yong Duan (Mon Nov 13 2006 - 17:56:29 PST)
    - Re: AMBER: vlimit exceeded for step 0, vmax = infinity Rachel (Tue Nov 14 2006 - 14:44:44 PST)
    - RE: AMBER: vlimit exceeded for step 0, vmax = infinity Yong Duan (Tue Nov 14 2006 - 15:05:08 PST)
- Re: AMBER: vlimit exceeded for step 0, vmax = infinity Carlos Simmerling (Wed Nov 08 2006 - 10:35:21 PST)
AMBER: NAD ?? Urszula Uciechowska (Wed Nov 08 2006 - 05:40:15 PST)
- Re: AMBER: NAD ?? David A. Case (Wed Nov 08 2006 - 06:49:31 PST)
- Re: AMBER: NAD ?? Urszula Uciechowska (Fri Nov 10 2006 - 01:36:15 PST)
  - Re: AMBER: NAD ?? Cenk Andac (Fri Nov 10 2006 - 15:20:53 PST)
  - Re: AMBER: NAD ?? Cenk Andac (Fri Nov 10 2006 - 15:27:35 PST)
    - AMBER: bond command between Zn and a CYM residue in one chain of a protein complex Fenghui Fan (Fri Nov 10 2006 - 21:25:01 PST)
    - Re: AMBER: NAD ?? Urszula Uciechowska (Mon Nov 13 2006 - 01:08:45 PST)
    - Re: AMBER: NAD ?? Cenk Andac (Mon Nov 13 2006 - 06:46:47 PST)
AMBER: Flag for removal of translational and rotational center-of-mass (COM) motion Rajesh Murarka (Wed Nov 08 2006 - 07:59:36 PST)
- Re: AMBER: Flag for removal of translational and rotational center-of-mass (COM) motion David A. Case (Wed Nov 08 2006 - 08:35:24 PST)
AMBER: simulating a small chain protein in water box Dave, Sonya (Wed Nov 08 2006 - 08:03:46 PST)
- Re: AMBER: simulating a small chain protein in water box Carlos Simmerling (Wed Nov 08 2006 - 09:50:59 PST)
AMBER: Problems amber mask in distance? Sergey Samsonov (Wed Nov 08 2006 - 08:39:18 PST)
- Re: AMBER: Problems amber mask in distance? Viktor Hornak (Wed Nov 08 2006 - 08:50:59 PST)
  - Re: AMBER: Problems amber mask in distance? Sergey Samsonov (Wed Nov 08 2006 - 08:57:20 PST)
AMBER: big bond energy change from minimization and md (heating) Rachel (Wed Nov 08 2006 - 08:40:12 PST)
AMBER: problem in calculating EGB using sander for ligand containing F atom VANDANA KUMARI (Wed Nov 08 2006 - 19:36:52 PST)
- Re: AMBER: problem in calculating EGB using sander for ligand containing F atom David A. Case (Thu Nov 09 2006 - 08:14:06 PST)
  - AMBER: saltconc for explicit solvent calculation. a a (Thu Nov 09 2006 - 09:51:36 PST)
    - Re: AMBER: saltconc for explicit solvent calculation. David A. Case (Thu Nov 09 2006 - 10:13:05 PST)
    - Re: AMBER: saltconc for explicit solvent calculation. Carlos Simmerling (Thu Nov 09 2006 - 10:14:21 PST)
AMBER: Amber H-bond print? Andres Palencia (Thu Nov 09 2006 - 01:07:46 PST)
AMBER: Probelm with running Amber 9 parallelly Rafi Ahmad (Thu Nov 09 2006 - 04:59:56 PST)
- AMBER: Biomolecular Simulation 2007 Angelo (Thu Nov 09 2006 - 08:03:43 PST)
AMBER: Building Library Steve Seibold (Thu Nov 09 2006 - 08:52:08 PST)
- Re: AMBER: Building Library Fenghui Fan (Thu Nov 09 2006 - 10:21:57 PST)
AMBER: Steve Seibold (Thu Nov 09 2006 - 09:03:14 PST)
- Re: AMBER: David A. Case (Thu Nov 09 2006 - 10:11:55 PST)
AMBER: antechamber:tutorial Lwin, ThuZar (Thu Nov 09 2006 - 10:48:58 PST)
- Re: AMBER: antechamber:tutorial Mark Williamson (Thu Nov 09 2006 - 11:06:24 PST)
- Re: AMBER: antechamber:tutorial Fenghui Fan (Thu Nov 09 2006 - 11:10:17 PST)
AMBER: FW: antechamber:tutorial Lwin, ThuZar (Thu Nov 09 2006 - 11:03:46 PST)
AMBER: Building Library Steve Seibold (Thu Nov 09 2006 - 11:40:30 PST)
AMBER: strange temperature behavior when changing to constant pressure Joshua (Thu Nov 09 2006 - 11:52:33 PST)
RE: AMBER: antechamber:tutorial. . Lwin, ThuZar (Thu Nov 09 2006 - 12:02:28 PST)
AMBER: sander error: rst file crash jitrayut jitonnom (Fri Nov 10 2006 - 04:52:19 PST)
- Re: AMBER: sander error: rst file crash Carlos Simmerling (Fri Nov 10 2006 - 05:26:16 PST)
  - Fwd: AMBER: sander error: rst file crash jitrayut jitonnom (Fri Nov 10 2006 - 07:52:00 PST)
- Re: AMBER: sander error: rst file crash David A. Case (Fri Nov 10 2006 - 13:11:15 PST)
  - Fwd: AMBER: sander error: rst file crash jitrayut jitonnom (Sat Nov 11 2006 - 03:16:37 PST)
    - Re: Fwd: AMBER: sander error: rst file crash Carlos Simmerling (Sat Nov 11 2006 - 04:38:52 PST)
    - Re: AMBER: sander error: rst file crash jitrayut jitonnom (Sat Nov 11 2006 - 09:22:20 PST)
    - Re: Fwd: AMBER: sander error: rst file crash David A. Case (Sun Nov 12 2006 - 18:44:48 PST)
AMBER: PTRAJ: radius of gyration kepa koldo burusco (Fri Nov 10 2006 - 09:05:09 PST)
Re: AMBER: PTRAJ: radius of gyration Bill Ross (Fri Nov 10 2006 - 11:04:06 PST)
AMBER: <kein Betreff> Michel Becker (Mon Nov 13 2006 - 03:21:58 PST)
- RE: AMBER: <kein Betreff> Ross Walker (Mon Nov 13 2006 - 08:44:03 PST)
- Re: AMBER: <kein Betreff> Gustavo Seabra (Mon Nov 13 2006 - 09:52:55 PST)
AMBER: what to do with the counter ions when minimizing average structure of DNA? Chengwen Chen (Tue Nov 14 2006 - 03:09:25 PST)
AMBER: how to remove the rotation of system in periodic condition? 张勇 (Tue Nov 14 2006 - 04:10:22 PST)
- Re: AMBER: how to remove the rotation of system in periodic condition? David A. Case (Wed Nov 15 2006 - 08:34:01 PST)
- AMBER: reading psf file jojartb.pharm.u-szeged.hu (Fri Nov 17 2006 - 15:24:24 PST)
  - AMBER: Amber9 installation error Keerthi Gottipati (Fri Nov 17 2006 - 16:12:53 PST)
    - RE: AMBER: Amber9 installation error Ross Walker (Sat Nov 18 2006 - 09:20:39 PST)
  - Re: AMBER: reading psf file Thomas Cheatham (Fri Nov 17 2006 - 16:28:45 PST)
    - Re: AMBER: reading psf file jojartb.pharm.u-szeged.hu (Sat Nov 18 2006 - 00:38:26 PST)
    - Re: AMBER: reading psf file jojartb.pharm.u-szeged.hu (Sat Nov 18 2006 - 01:40:37 PST)
AMBER: gfortran/gcc versus ifort/icc Lachele Foley (Lists) (Tue Nov 14 2006 - 06:35:21 PST)
- Re: AMBER: gfortran/gcc versus ifort/icc Fenghui Fan (Tue Nov 14 2006 - 09:40:13 PST)
  - Re: AMBER: gfortran/gcc versus ifort/icc Lachele Foley (Lists) (Wed Nov 15 2006 - 07:37:27 PST)
    - RE: AMBER: gfortran/gcc versus ifort/icc Jordi Camps (Wed Nov 15 2006 - 09:50:54 PST)
    - Re: AMBER: gfortran/gcc versus ifort/icc Luis Gracia (Wed Nov 15 2006 - 10:34:36 PST)
    - RE: AMBER: gfortran/gcc versus ifort/icc Jordi Camps (Thu Nov 16 2006 - 08:22:55 PST)
    - Re: AMBER: gfortran/gcc versus ifort/icc Lachele Foley (Lists) (Thu Nov 16 2006 - 12:49:23 PST)
AMBER: Ptraj: radial distribution and correlation coefficient Austin B. Yongye (Tue Nov 14 2006 - 10:10:39 PST)
- Re: AMBER: Ptraj: radial distribution and correlation coefficient Thomas Cheatham (Tue Nov 14 2006 - 10:34:57 PST)
  - Re: AMBER: Ptraj: radial distribution and correlation coefficient Austin B. Yongye (Tue Nov 14 2006 - 10:50:01 PST)
  - Re: AMBER: Ptraj: radial distribution and correlation coefficient Austin B. Yongye (Tue Nov 14 2006 - 11:02:27 PST)
    - Re: AMBER: Ptraj: radial distribution and correlation coefficient Thomas Cheatham (Tue Nov 14 2006 - 11:17:40 PST)
    - Re: AMBER: Ptraj: radial distribution and correlation coefficient Andres Palencia (Tue Nov 14 2006 - 12:13:39 PST)
AMBER: Acetone box SERGIO MIGUEL FERNANDES DOS SANTOS (Tue Nov 14 2006 - 10:34:24 PST)
AMBER: Restraints of the strand-endings? Michel Becker (Tue Nov 14 2006 - 12:22:36 PST)
Re: AMBER: Restraints of the strand-endings? Bill Ross (Tue Nov 14 2006 - 14:19:06 PST)
AMBER: error in tleap test Christian Roth (Tue Nov 14 2006 - 16:40:24 PST)
- Re: AMBER: error in tleap test Scott Brozell (Wed Nov 15 2006 - 09:55:07 PST)
  - RE: AMBER: error in tleap test Christian Roth (Wed Nov 15 2006 - 10:18:07 PST)
AMBER: ptraj and mdvel question Jianhui (Wed Nov 15 2006 - 11:07:06 PST)
- Re: AMBER: ptraj and mdvel question Thomas Cheatham (Wed Nov 15 2006 - 15:37:13 PST)
AMBER: H-Bond Terms in amber force field Ilyas Yildirim (Wed Nov 15 2006 - 11:28:06 PST)
- Re: AMBER: H-Bond Terms in amber force field Jiri Sponer (Wed Nov 15 2006 - 15:20:18 PST)
  - Re: AMBER: H-Bond Terms in amber force field Ilyas Yildirim (Wed Nov 15 2006 - 16:05:13 PST)
    - Re: AMBER: H-Bond Terms in amber force field Jiri Sponer (Wed Nov 15 2006 - 16:30:48 PST)
- Re: AMBER: H-Bond Terms in amber force field Thomas Cheatham (Wed Nov 15 2006 - 15:51:36 PST)
AMBER: Error in compliling LEAP on Fedora 5 Pankaj Daga (Wed Nov 15 2006 - 14:56:58 PST)
- Re: AMBER: Error in compliling LEAP on Fedora 5 Steven Winfield (Wed Nov 15 2006 - 16:10:33 PST)
- Re: AMBER: Error in compliling LEAP on Fedora 5 David A. Case (Wed Nov 15 2006 - 17:24:34 PST)
AMBER: MM_PBSA Varsha Goyal (Wed Nov 15 2006 - 18:27:15 PST)
- Re: AMBER: MM_PBSA Thomas Steinbrecher (Thu Nov 16 2006 - 08:21:55 PST)
AMBER: erroneous placement of TER card Gregory Sandala (Thu Nov 16 2006 - 01:12:43 PST)
- Re: AMBER: erroneous placement of TER card Robert Duke (Thu Nov 16 2006 - 05:56:11 PST)
- Re: AMBER: erroneous placement of TER card David A. Case (Thu Nov 16 2006 - 08:20:32 PST)
- Re: AMBER: erroneous placement of TER card Robert Duke (Thu Nov 16 2006 - 08:47:23 PST)
- Re: AMBER: erroneous placement of TER card Bill Ross (Thu Nov 16 2006 - 10:54:50 PST)
  - Re: AMBER: erroneous placement of TER card David A. Case (Thu Nov 16 2006 - 10:59:28 PST)
- Re: AMBER: erroneous placement of TER card Bill Ross (Thu Nov 16 2006 - 11:06:25 PST)
AMBER: opls_aa in amber Vitor Manuel Sousa F?x (Thu Nov 16 2006 - 06:29:45 PST)
AMBER: pqr file Seth Lilavivat (Thu Nov 16 2006 - 08:43:55 PST)
- Re: AMBER: pqr file David A. Case (Thu Nov 16 2006 - 08:53:46 PST)
AMBER: GLYCAM and ff98 atom-types Gabbar S. Daaku (Thu Nov 16 2006 - 10:11:05 PST)
- Re: AMBER: GLYCAM and ff98 atom-types Fenghui Fan (Thu Nov 16 2006 - 11:16:34 PST)
AMBER: Xleap woes Shozeb Haider (Thu Nov 16 2006 - 15:07:01 PST)
- Re: AMBER: Xleap woes David A. Case (Thu Nov 16 2006 - 10:39:39 PST)
  - Re: AMBER: Xleap woes M. L. Dodson (Thu Nov 16 2006 - 12:14:07 PST)
- Re: AMBER: Xleap woes Fenghui Fan (Thu Nov 16 2006 - 11:22:59 PST)
AMBER: parameters for beta peptides yipinl.umich.edu (Thu Nov 16 2006 - 11:29:08 PST)
Re: AMBER: GLYCAM and ff98 atom-types] Austin B. Yongye (Thu Nov 16 2006 - 11:53:03 PST)
AMBER: optimatized structure is so much different from the original pdb structure emilia wu (Thu Nov 16 2006 - 21:38:18 PST)
- Re: AMBER: optimatized structure is so much different from the original pdb structure Gabbar S. Daaku (Fri Nov 17 2006 - 09:13:04 PST)
AMBER: Ethanol Rita Cassia (Fri Nov 17 2006 - 04:13:14 PST)
- Re: AMBER: Ethanol FyD (Fri Nov 17 2006 - 06:19:15 PST)
  - Re: AMBER: Ethanol Rita Cassia (Wed Nov 22 2006 - 01:33:24 PST)
    - Re: AMBER: Ethanol FyD (Wed Nov 22 2006 - 04:22:28 PST)
AMBER: dihedral angle equation Vitor Manuel Sousa F?x (Fri Nov 17 2006 - 04:41:25 PST)
- Re: AMBER: dihedral angle equation Igor Schapiro (Fri Nov 17 2006 - 06:15:47 PST)
- Re: AMBER: dihedral angle equation Igor Schapiro (Fri Nov 17 2006 - 06:24:29 PST)
AMBER: gfortran and amber9 success on FreeBSD M. L. Dodson (Sat Nov 18 2006 - 14:02:16 PST)
AMBER: parameters for silicon atom Chengwen Chen (Sun Nov 19 2006 - 23:45:07 PST)
- Re: AMBER: parameters for silicon atom Scott Brozell (Mon Feb 25 2008 - 18:24:03 PST)
  - Re: AMBER: parameters for silicon atom Scott Brozell (Fri Feb 29 2008 - 00:31:03 PST)
AMBER: problems with saving self-built molecules parameters Rachel (Mon Nov 20 2006 - 04:59:07 PST)
- Re: AMBER: problems with saving self-built molecules parameters Fenghui Fan (Mon Nov 20 2006 - 05:57:10 PST)
  - Re: AMBER: problems with saving self-built molecules parameters Rachel (Mon Nov 20 2006 - 06:23:30 PST)
    - Re: AMBER: problems with saving self-built molecules parameters Fenghui Fan (Mon Nov 20 2006 - 07:06:53 PST)
    - Re: AMBER: problems with saving self-built molecules parameters Rachel (Mon Nov 20 2006 - 09:18:00 PST)
    - Re: AMBER: problems with saving self-built molecules parameters David A. Case (Mon Nov 20 2006 - 09:33:25 PST)
    - Re: AMBER: problems with saving self-built molecules parameters Fenghui Fan (Mon Nov 20 2006 - 10:10:21 PST)
    - Re: AMBER: problems with saving self-built molecules parameters Rachel (Mon Nov 20 2006 - 10:42:10 PST)
- Re: AMBER: problems with saving self-built molecules parameters Bill Ross (Mon Nov 20 2006 - 10:55:00 PST)
AMBER: Combining Residues in LEaP for Lipid Bilayers Matthew Tessier (Mon Nov 20 2006 - 09:09:13 PST)
- Re: AMBER: Combining Residues in LEaP for Lipid Bilayers David A. Case (Mon Nov 20 2006 - 09:35:04 PST)
  - RE: AMBER: Combining Residues in LEaP for Lipid Bilayers Matthew Tessier (Mon Nov 20 2006 - 09:48:32 PST)
    - Re: AMBER: Combining Residues in LEaP for Lipid Bilayers David A. Case (Tue Nov 21 2006 - 08:16:06 PST)
- RE: AMBER: Combining Residues in LEaP for Lipid Bilayers Bill Ross (Mon Nov 20 2006 - 10:58:11 PST)
- RE: AMBER: Combining Residues in LEaP for Lipid Bilayers kepa koldo burusco (Fri Nov 24 2006 - 03:38:06 PST)
AMBER: the energy and temperature both increasing during the simulation with NTT=0 Xiaowei (David) Li (Mon Nov 20 2006 - 10:50:00 PST)
- Re: AMBER: the energy and temperature both increasing during the simulation with NTT=0 David A. Case (Mon Nov 20 2006 - 22:09:28 PST)
AMBER: Quantifying pi-pi interactions zachary hartman (Tue Nov 21 2006 - 07:51:30 PST)
- Re: AMBER: Quantifying pi-pi interactions Jiri Sponer (Tue Nov 21 2006 - 08:14:32 PST)
AMBER: ff03 GLY HAs atom type Sandro Fornili (Tue Nov 21 2006 - 08:21:01 PST)
- RE: AMBER: ff03 GLY HAs atom type Yong Duan (Tue Nov 21 2006 - 09:41:17 PST)
  - RE: AMBER: ff03 GLY HAs atom type mahdi fathi (Tue Nov 21 2006 - 21:46:22 PST)
    - AMBER: Re: installation instructions David A. Case (Wed Nov 22 2006 - 08:48:17 PST)
AMBER: compile amber8 on IBM-sp4 Rachel (Tue Nov 21 2006 - 09:56:13 PST)
- Re: AMBER: compile amber8 on IBM-sp4 Scott Brozell (Tue Nov 21 2006 - 10:38:49 PST)
  - Re: AMBER: compile amber8 on IBM-sp4 Rachel (Wed Nov 22 2006 - 02:08:42 PST)
    - RE: AMBER: compile amber8 on IBM-sp4 Ross Walker (Wed Nov 22 2006 - 09:55:45 PST)
    - Re: AMBER: compile amber8 on IBM-sp4 Rachel (Wed Nov 22 2006 - 10:34:19 PST)
    - Re: AMBER: compile amber8 on IBM-sp4 Xuebin Qiao (Wed Nov 22 2006 - 19:51:57 PST)
    - Re: AMBER: compile amber8 on IBM-sp4 Rachel (Thu Nov 23 2006 - 01:56:53 PST)
    - Re: AMBER: compile amber8 on IBM-sp4 Xuebin Qiao (Thu Nov 23 2006 - 04:21:07 PST)
    - Re: AMBER: compile amber8 on IBM-sp4 Xuebin Qiao (Thu Nov 23 2006 - 04:26:12 PST)
    - Re: AMBER: compile amber8 on IBM-sp4 Rachel (Thu Nov 23 2006 - 05:14:09 PST)
    - Re: AMBER: compile amber8 on IBM-sp4 Xuebin Qiao (Thu Nov 23 2006 - 06:23:36 PST)
    - Re: AMBER: compile amber8 on IBM-sp4 Rachel (Thu Nov 23 2006 - 08:37:18 PST)
    - Re: AMBER: compile amber8 on IBM-sp4 Martin Peters (Thu Nov 23 2006 - 09:22:06 PST)
    - Re: AMBER: compile amber8 on IBM-sp4 Rachel (Thu Nov 23 2006 - 09:45:04 PST)
AMBER: Ptraj: diffusion rate Austin B. Yongye (Tue Nov 21 2006 - 13:03:52 PST)
AMBER: Ptraj: correlation time Austin B. Yongye (Tue Nov 21 2006 - 13:05:52 PST)
AMBER: Some warning !!! during SANDER ? jitrayut jitonnom (Wed Nov 22 2006 - 00:20:36 PST)
- RE: AMBER: Some warning !!! during SANDER ? Ross Walker (Wed Nov 22 2006 - 08:48:55 PST)
AMBER: Ptraj syntax change Amber8->Amber9 ? Markus Kaukonen (Wed Nov 22 2006 - 02:35:26 PST)
- Re: AMBER: Ptraj syntax change Amber8->Amber9 ? David A. Case (Wed Nov 22 2006 - 13:22:37 PST)
AMBER: Radius of gyration r. a. (Wed Nov 22 2006 - 02:11:14 PST)
- RE: AMBER: Radius of gyration kepa koldo burusco (Fri Nov 24 2006 - 02:27:01 PST)
  - RE: AMBER: Radius of gyration Andy Purkiss-Trew (Fri Nov 24 2006 - 04:58:53 PST)
    - RE: AMBER: Radius of gyration kepa koldo burusco (Fri Nov 24 2006 - 09:45:55 PST)
    - RE: AMBER: Radius of gyration Andy Purkiss-Trew (Fri Nov 24 2006 - 11:34:52 PST)
    - Re: RE: AMBER: Radius of gyration Carles Jaime Cardiel (Fri Nov 24 2006 - 10:25:02 PST)
    - Re: RE: AMBER: Radius of gyration Andy Purkiss-Trew (Fri Nov 24 2006 - 11:38:28 PST)
    - Re: RE: AMBER: Radius of gyration Elijah Gregory (Fri Nov 24 2006 - 12:33:50 PST)
    - Re: RE: AMBER: Radius of gyration r. a. (Mon Nov 27 2006 - 20:20:32 PST)
AMBER: SHAKE problem after minimization Rachel (Wed Nov 22 2006 - 03:39:18 PST)
- Re: AMBER: SHAKE problem after minimization Rachel (Wed Nov 22 2006 - 07:42:34 PST)
- RE: AMBER: SHAKE problem after minimization Ross Walker (Wed Nov 22 2006 - 09:59:58 PST)
  - Re: AMBER: SHAKE problem after minimization Rachel (Wed Nov 22 2006 - 10:43:50 PST)
    - RE: AMBER: SHAKE problem after minimization Hayden Eastwood (Wed Nov 22 2006 - 11:13:24 PST)
    - Re: AMBER: SHAKE problem after minimization Rachel (Wed Nov 22 2006 - 11:37:15 PST)
    - RE: AMBER: SHAKE problem after minimization Hayden Eastwood (Wed Nov 22 2006 - 12:33:17 PST)
    - RE: AMBER: SHAKE problem after minimization Hayden Eastwood (Wed Nov 22 2006 - 12:47:09 PST)
    - Re: AMBER: SHAKE problem after minimization Steven Winfield (Wed Nov 22 2006 - 13:53:07 PST)
    - Re: AMBER: SHAKE problem after minimization David A. Case (Wed Nov 22 2006 - 14:24:44 PST)
    - Re: AMBER: SHAKE problem after minimization Rachel (Thu Nov 23 2006 - 10:37:24 PST)
AMBER: Problem with mask when using distance in ptraj Christopher Gaughan (Wed Nov 22 2006 - 11:36:23 PST)
- Re: AMBER: Problem with mask when using distance in ptraj David A. Case (Wed Nov 22 2006 - 13:07:29 PST)
  - Re: AMBER: Problem with mask when using distance in ptraj Thomas Cheatham (Wed Nov 22 2006 - 13:17:12 PST)
    - Re: AMBER: Problem with mask when using distance in ptraj Christopher Gaughan (Sun Nov 26 2006 - 06:28:29 PST)
AMBER: problem of the REMD with nmr constraints wenfei Li (Wed Nov 22 2006 - 17:57:32 PST)
- Re: AMBER: problem of the REMD with nmr constraints Carlos Simmerling (Fri Nov 24 2006 - 06:35:25 PST)
- Re: AMBER: problem of the REMD with nmr constraints wenfei Li (Sat Nov 25 2006 - 17:56:05 PST)
- Re: AMBER: problem of the REMD with nmr constraints wenfei Li (Thu Dec 07 2006 - 16:55:04 PST)
AMBER: ammonia parameters Peter Trodler (Thu Nov 23 2006 - 00:51:39 PST)
- Re: AMBER: ammonia parameters Fenghui Fan (Thu Nov 23 2006 - 07:40:05 PST)
AMBER: Restarting with new topology Sergey Samsonov (Thu Nov 23 2006 - 08:39:53 PST)
AMBER: Snapshots (pdbs) from a trajectory. Jordi Rodrigo De Losada (Thu Nov 23 2006 - 09:11:18 PST)
- Re: AMBER: Snapshots (pdbs) from a trajectory. Carlos Simmerling (Thu Nov 23 2006 - 09:25:31 PST)
- Re: AMBER: Snapshots (pdbs) from a trajectory. David A. Case (Thu Nov 23 2006 - 19:58:34 PST)
  - AMBER: NTR for implicit solvent? How to defin restrain for two disconnected sequences? a a (Thu Nov 23 2006 - 22:13:38 PST)
    - Re: AMBER: NTR for implicit solvent? How to defin restrain for two disconnected sequences? David A. Case (Thu Nov 23 2006 - 23:02:21 PST)
    - Re: AMBER: NTR for implicit solvent? How to defin restrain for two disconnected sequences? a a (Fri Nov 24 2006 - 01:29:26 PST)
    - Re: AMBER: NTR for implicit solvent? How to defin restrain for two disconnectedsequences? cristian obiol (Fri Nov 24 2006 - 02:24:28 PST)
    - Re: AMBER: NTR for implicit solvent? How to defin restrain for two disconnectedsequences? a a (Fri Nov 24 2006 - 18:27:26 PST)
    - Re: AMBER: NTR for implicit solvent? How to defin restrain for two disconnectedsequences? David A. Case (Sat Nov 25 2006 - 00:51:06 PST)
    - AMBER: Did Antechamber support tertiary amines? How can I get the prepin file for it? a a (Mon Nov 27 2006 - 00:50:12 PST)
    - Re: AMBER: NTR for implicit solvent? How to defin restrain for two disconnectedsequences? a a (Mon Nov 27 2006 - 02:29:42 PST)
AMBER: Unable to find mopac charges in divcon.out Rachel (Thu Nov 23 2006 - 11:31:55 PST)
- Re: AMBER: Unable to find mopac charges in divcon.out Mark Williamson (Thu Nov 23 2006 - 14:06:35 PST)
  - Re: AMBER: Unable to find mopac charges in divcon.out Rachel (Thu Nov 23 2006 - 15:22:06 PST)
    - Re: AMBER: Unable to find mopac charges in divcon.out Mark Williamson (Fri Nov 24 2006 - 05:54:34 PST)
AMBER: failure in testing amber8 parallel parts on IBM-SP4 machines Rachel (Fri Nov 24 2006 - 09:58:53 PST)
- Re: AMBER: failure in testing amber8 parallel parts on IBM-SP4 machines Nicolas Lux Fawzi (Fri Nov 24 2006 - 11:16:01 PST)
  - Re: AMBER: failure in testing amber8 parallel parts on IBM-SP4 machines Rachel (Fri Nov 24 2006 - 11:53:29 PST)
    - Re: AMBER: failure in testing amber8 parallel parts on IBM-SP4 machines Xuebin Qiao (Fri Nov 24 2006 - 20:55:14 PST)
AMBER: Antechamber and gaussian questions Fenghui Fan (Fri Nov 24 2006 - 14:04:40 PST)
AMBER: amber9 serial compile with pathscale on SuSe10.1/AMD64 In Hee Park (Fri Nov 24 2006 - 14:50:54 PST)
- Re: AMBER: amber9 serial compile with pathscale on SuSe10.1/AMD64 David A. Case (Fri Nov 24 2006 - 16:43:20 PST)
AMBER: bondtype problem Fenghui Fan (Fri Nov 24 2006 - 16:22:23 PST)
AMBER: respin file Fenghui Fan (Fri Nov 24 2006 - 23:06:49 PST)
- Re: AMBER: respin file M. L. Dodson (Sat Nov 25 2006 - 06:37:05 PST)
AMBER: resp Fenghui Fan (Sat Nov 25 2006 - 13:03:00 PST)
AMBER: respin file Fenghui Fan (Sat Nov 25 2006 - 14:23:46 PST)
- Re: AMBER: respin file Ilyas Yildirim (Sat Nov 25 2006 - 17:07:04 PST)
  - Re: AMBER: respin file Fenghui Fan (Sat Nov 25 2006 - 17:49:58 PST)
    - Re: AMBER: respin file Ilyas Yildirim (Sat Nov 25 2006 - 18:45:37 PST)
    - Re: AMBER: respin file Fenghui Fan (Sat Nov 25 2006 - 19:15:53 PST)
    - Re: AMBER: respin file Ilyas Yildirim (Sun Nov 26 2006 - 00:03:33 PST)
    - Re: AMBER: respin file Fenghui Fan (Sun Nov 26 2006 - 09:12:01 PST)
    - Re: AMBER: respin file Ilyas Yildirim (Sun Nov 26 2006 - 09:45:20 PST)
    - Re: AMBER: respin file Fenghui Fan (Sun Nov 26 2006 - 16:42:09 PST)
    - Re: AMBER: respin file M. L. Dodson (Sun Nov 26 2006 - 10:05:33 PST)
    - AMBER: how to get complete prepin file Fenghui Fan (Sat Nov 25 2006 - 21:02:20 PST)
AMBER: how can i treat with long "mask" in ptraj analysis. Changge Ji (Sun Nov 26 2006 - 08:22:00 PST)
AMBER: ZN prepin Fenghui Fan (Sun Nov 26 2006 - 14:29:31 PST)
AMBER: bond information Fenghui Fan (Sun Nov 26 2006 - 20:10:42 PST)
- RE: AMBER: bond information Junmei Wang (Tue Nov 28 2006 - 14:16:03 PST)
AMBER: ptraj grid Hannes Loeffler (Sun Nov 26 2006 - 20:05:05 PST)
AMBER: helices in GB simulations Marie-Pierre Durrieu (Mon Nov 27 2006 - 09:43:41 PST)
- Re: AMBER: helices in GB simulations Carlos Simmerling (Mon Nov 27 2006 - 10:12:02 PST)
- Re: AMBER: helices in GB simulations Ilyas Yildirim (Mon Nov 27 2006 - 14:09:04 PST)
AMBER: minimization of Hydrogens with xLeaP rebeca.mmb.pcb.ub.es (Mon Nov 27 2006 - 10:38:04 PST)
- Re: AMBER: minimization of Hydrogens with xLeaP David A. Case (Mon Nov 27 2006 - 18:19:48 PST)
AMBER: Problem Installing Amber in SGI Irix 6.5 trudy.uoguelph.ca (Mon Nov 27 2006 - 12:29:53 PST)
- Re: AMBER: Problem Installing Amber in SGI Irix 6.5 David A. Case (Mon Nov 27 2006 - 17:56:14 PST)
  - Re: AMBER: Problem Installing Amber in SGI Irix 6.5 trudy.uoguelph.ca (Tue Nov 28 2006 - 07:41:07 PST)
  - Re: AMBER: Problem Installing Amber in SGI Irix 6.5 Joe Nolan (Wed Nov 29 2006 - 04:40:58 PST)
    - Re: AMBER: Problem Installing Amber in SGI Irix 6.5 trudy.uoguelph.ca (Wed Nov 29 2006 - 06:50:51 PST)
- Re: AMBER: Problem Installing Amber in SGI Irix 6.5 trudy.uoguelph.ca (Thu Nov 30 2006 - 07:31:02 PST)
AMBER: phantom sander8 in dmesg Lachele Foley (Lists) (Mon Nov 27 2006 - 13:25:57 PST)
- Re: AMBER: phantom sander8 in dmesg Lachele Foley (Lists) (Mon Dec 04 2006 - 09:21:12 PST)
AMBER: prepin file nan Fenghui Fan (Mon Nov 27 2006 - 19:28:16 PST)
- Re: AMBER: prepin file nan linfu (Tue Nov 28 2006 - 01:00:30 PST)
  - Re: AMBER: prepin file nan Fenghui Fan (Tue Nov 28 2006 - 06:48:33 PST)
- RE: AMBER: prepin file nan Junmei Wang (Tue Nov 28 2006 - 13:47:03 PST)
AMBER: Problem about dummy atoms when running antechamber 한 민우 (Mon Nov 27 2006 - 19:30:27 PST)
- RE: AMBER: Problem about dummy atoms when running antechamber Junmei Wang (Tue Nov 28 2006 - 13:54:42 PST)
- RE: AMBER: Problem about dummy atoms when running antechamber Junmei Wang (Thu Dec 07 2006 - 09:14:58 PST)
AMBER: protonated phosphate Einar Uggerud (Mon Nov 27 2006 - 23:11:46 PST)
AMBER: NONB values adjusted? Dave S Walker (Mon Nov 27 2006 - 23:37:28 PST)
- Re: AMBER: NONB values adjusted? Thomas Steinbrecher (Tue Nov 28 2006 - 08:31:33 PST)
  - Re: AMBER: NONB values adjusted? Dave S Walker (Tue Nov 28 2006 - 11:48:36 PST)
AMBER: energy minimizations in amber8 vs. amber9 Seongeun Yang (Mon Nov 27 2006 - 23:43:35 PST)
AMBER: How to specify user defined force fields or its parameters in amber?? Gobind Singh Bisht (Tue Nov 28 2006 - 03:51:30 PST)
- Re: AMBER: How to specify user defined force fields or its parameters in amber?? Carlos Simmerling (Tue Nov 28 2006 - 04:11:51 PST)
  - Re: AMBER: How to specify user defined force fields or its parameters in amber?? Gobind Singh Bisht (Tue Nov 28 2006 - 05:56:10 PST)
    - Re: AMBER: How to specify user defined force fields or its parameters in amber?? Carlos Simmerling (Tue Nov 28 2006 - 06:07:18 PST)
    - Re: AMBER: How to specify user defined force fields or its parameters in amber?? Gobind Singh Bisht (Tue Nov 28 2006 - 06:34:36 PST)
    - Re: AMBER: How to specify user defined force fields or its parameters in amber?? Gustavo Seabra (Tue Nov 28 2006 - 07:18:49 PST)
    - Re: AMBER: How to specify user defined force fields or its parameters in amber?? Gobind Singh Bisht (Tue Nov 28 2006 - 08:40:53 PST)
    - Re: AMBER: How to specify user defined force fields or its parameters in amber?? Gustavo Seabra (Thu Nov 30 2006 - 07:46:42 PST)
AMBER: xleap Steve Seibold (Tue Nov 28 2006 - 06:33:48 PST)
- Re: AMBER: xleap David A. Case (Tue Nov 28 2006 - 08:02:13 PST)
AMBER: uccadco.ucl.ac.uk (Tue Nov 28 2006 - 06:48:08 PST)
- Re: AMBER: David A. Case (Tue Nov 28 2006 - 07:53:48 PST)
AMBER: Modifying a Force Field Seth Lilavivat (Tue Nov 28 2006 - 07:27:08 PST)
AMBER: nmode output with ptraj nadiav.soton.ac.uk (Tue Nov 28 2006 - 07:59:02 PST)
- Re: AMBER: nmode output with ptraj David A. Case (Tue Nov 28 2006 - 18:36:33 PST)
  - Re: AMBER: nmode output with ptraj a a (Tue Nov 28 2006 - 19:18:32 PST)
  - AMBER: DNA helix end stable? a a (Tue Nov 28 2006 - 19:35:11 PST)
    - Re: AMBER: DNA helix end stable? Carlos Simmerling (Wed Nov 29 2006 - 04:24:14 PST)
AMBER: Charge fitting in Amber Changge Ji (Tue Nov 28 2006 - 08:50:20 PST)
- Re: AMBER: Charge fitting in Amber FyD (Tue Nov 28 2006 - 23:16:38 PST)
AMBER: Amber9 patch bugfix.all issue on SunOS 5.1 Michael John Hanby (Tue Nov 28 2006 - 10:06:16 PST)
- RE: AMBER: Amber9 patch bugfix.all issue on SunOS 5.1 Michael John Hanby (Tue Nov 28 2006 - 12:59:48 PST)
- Re: AMBER: Amber9 patch bugfix.all issue on SunOS 5.1 Mark Williamson (Tue Nov 28 2006 - 13:04:06 PST)
- RE: AMBER: Amber9 patch bugfix.all issue on SunOS 5.1 Michael John Hanby (Tue Nov 28 2006 - 13:43:06 PST)
AMBER: ambpdb -pqr Seth Lilavivat (Tue Nov 28 2006 - 12:52:10 PST)
- Re: AMBER: ambpdb -pqr harianto (Tue Nov 28 2006 - 13:03:26 PST)
- Re: AMBER: ambpdb -pqr Carlos Simmerling (Tue Nov 28 2006 - 13:03:18 PST)
- Re: AMBER: ambpdb -pqr Ilyas Yildirim (Tue Nov 28 2006 - 13:02:39 PST)
AMBER: RE: Amber: ZN-complex file Junmei Wang (Tue Nov 28 2006 - 15:21:40 PST)
- Re: AMBER: RE: Amber: ZN-complex file Fenghui Fan (Tue Nov 28 2006 - 15:47:19 PST)
  - Re: AMBER: RE: Amber: ZN-complex file FyD (Tue Nov 28 2006 - 23:21:19 PST)
- RE: AMBER: RE: Amber: ZN-complex file Junmei Wang (Tue Nov 28 2006 - 15:54:56 PST)
AMBER: Periodic simulations with net charge Jennie Thomas (Tue Nov 28 2006 - 16:47:32 PST)
- Re: AMBER: Periodic simulations with net charge David A. Case (Tue Nov 28 2006 - 18:03:22 PST)
AMBER: How to apply a force to some atom in a residues? a a (Tue Nov 28 2006 - 19:36:15 PST)
- Re: AMBER: How to apply a force to some atom in a residues? Carlos Simmerling (Wed Nov 29 2006 - 04:26:19 PST)
  - Re: AMBER: How to apply a force to some atom in a residues? a a (Wed Nov 29 2006 - 22:45:04 PST)
    - Re: AMBER: How to apply a force to some atom in a residues? Carlos Simmerling (Thu Nov 30 2006 - 04:13:42 PST)
    - Re: AMBER: How to apply a force to some atom in a residues? a a (Fri Dec 01 2006 - 02:26:51 PST)
AMBER: Solvation Energies Ivelin Georgiev (Wed Nov 29 2006 - 06:31:13 PST)
AMBER: Confusion about PBC anna.schrey.gmx.de (Wed Nov 29 2006 - 08:26:04 PST)
- Re: AMBER: Confusion about PBC Thomas Steinbrecher (Wed Nov 29 2006 - 08:40:05 PST)
AMBER: Langevin temperature control vs berendson heat bath Hayden Eastwood (Wed Nov 29 2006 - 10:12:16 PST)
- Re: AMBER: Langevin temperature control vs berendson heat bath Carlos Simmerling (Wed Nov 29 2006 - 11:02:20 PST)
  - RE: AMBER: Langevin temperature control vs berendson heat bath Hayden Eastwood (Thu Nov 30 2006 - 03:23:37 PST)
    - Re: AMBER: Langevin temperature control vs berendson heat bath Carlos Simmerling (Thu Nov 30 2006 - 04:23:24 PST)
- Re: AMBER: Langevin temperature control vs berendson heat bath Andreas Svrcek-Seiler (Thu Nov 30 2006 - 04:06:22 PST)
AMBER: ptraj----radial output files Esther Brugger (Wed Nov 29 2006 - 12:03:20 PST)
AMBER: How to run MD simulation of a silicon containing complex with AMBER9? Chengwen Chen (Wed Nov 29 2006 - 23:06:54 PST)
AMBER: How to specify a box with few walls rigid and others with periodic boundary conditions and then apply a pressure gradient across it? Gobind Singh Bisht (Wed Nov 29 2006 - 23:34:28 PST)
AMBER: How to run QM/MM simulation of DNA duplex bound with platinum moietes Chengwen Chen (Thu Nov 30 2006 - 00:07:28 PST)
- Re: AMBER: How to run QM/MM simulation of DNA duplex bound with platinum moietes Gustavo Seabra (Thu Nov 30 2006 - 07:20:00 PST)
  - Re: AMBER: How to run QM/MM simulation of DNA duplex bound with platinum moietes Chengwen Chen (Tue Dec 12 2006 - 23:01:03 PST)
AMBER: Performing Interactive Essential Dynamics in Ptraj hbluo (Thu Nov 30 2006 - 16:58:11 PST)
AMBER: amber9 parralel compiling Nikola Trbovic (Thu Nov 30 2006 - 08:31:22 PST)
- Re: AMBER: amber9 parralel compiling David A. Case (Thu Nov 30 2006 - 08:50:47 PST)
  - Re: AMBER: amber9 parralel compiling Nikola Trbovic (Thu Nov 30 2006 - 09:06:12 PST)
    - Re: AMBER: amber9 parralel compiling David A. Case (Thu Nov 30 2006 - 15:54:08 PST)
    - Re: AMBER: amber9 parralel compiling Nikola Trbovic (Fri Dec 01 2006 - 08:46:33 PST)
    - Re: AMBER: amber9 parralel compiling Scott Brozell (Fri Dec 01 2006 - 11:40:54 PST)
- Re: AMBER: amber9 parralel compiling Seaclear Theory (Thu Jan 25 2007 - 18:15:05 PST)
  - Re: AMBER: amber9 parralel compiling Seaclear Theory (Fri Jan 26 2007 - 10:55:43 PST)
  - Re: AMBER: amber9 parralel compiling David A. Case (Fri Jan 26 2007 - 15:45:25 PST)
    - Re: AMBER: amber9 parralel compiling Seaclear Theory (Sat Jan 27 2007 - 10:59:23 PST)
    - Re: AMBER: amber9 parralel compiling David A. Case (Sat Jan 27 2007 - 11:28:27 PST)
    - Re: AMBER: amber9 parralel compiling Seaclear Theory (Sat Jan 27 2007 - 15:16:19 PST)
AMBER: How to recompile sander for single-processor use in AMBER 8? Peter Anderson (Thu Nov 30 2006 - 13:41:27 PST)
- Re: AMBER: How to recompile sander for single-processor use in AMBER 8? David A. Case (Thu Nov 30 2006 - 15:19:10 PST)
AMBER: watershell and image commands Esther Brugger (Thu Nov 30 2006 - 14:37:58 PST)
- Re: AMBER: watershell and image commands Thomas Cheatham (Thu Nov 30 2006 - 15:22:59 PST)
  - Re: AMBER: watershell and image commands Esther Brugger (Thu Nov 30 2006 - 16:04:04 PST)
AMBER: watershell command Esther Brugger (Thu Nov 30 2006 - 15:16:52 PST)
AMBER: H-bond analysis (Ptraj) Esther Brugger (Thu Nov 30 2006 - 17:28:10 PST)
- Re: AMBER: H-bond analysis (Ptraj) Thomas Cheatham (Fri Dec 01 2006 - 10:00:05 PST)
  - Re: AMBER: H-bond analysis (Ptraj) Esther Brugger (Fri Dec 01 2006 - 11:01:25 PST)
AMBER: MM-PBSA problem vanessa wai (Thu Nov 30 2006 - 17:27:06 PST)
- AMBER: How to keep an hydrogen bond during an implicit MD calculation? a a (Fri Dec 01 2006 - 02:35:31 PST)
  - Re: AMBER: How to keep an hydrogen bond during an implicit MD calculation? j j (Fri Dec 01 2006 - 02:59:59 PST)
- Re: AMBER: MM-PBSA problem Varsha Goyal (Fri Dec 01 2006 - 13:35:27 PST)
  - Re: AMBER: MM-PBSA problem vanessa wai (Sat Dec 02 2006 - 01:11:18 PST)
- RE: AMBER: MM-PBSA problem Ray Luo (Fri Dec 01 2006 - 13:51:52 PST)
  - Re: AMBER: MM-PBSA problem vanessa wai (Sat Dec 02 2006 - 01:08:15 PST)
    - RE: AMBER: MM-PBSA problem Ray Luo (Sat Dec 02 2006 - 07:55:46 PST)
    - Re: AMBER: MM-PBSA problem vanessa wai (Sun Dec 03 2006 - 17:52:25 PST)
    - RE: AMBER: MM-PBSA problem Ray Luo (Tue Dec 05 2006 - 11:16:32 PST)
    - Re: AMBER: MM-PBSA problem vanessa wai (Tue Dec 05 2006 - 17:33:35 PST)
AMBER: Ions analysis with hbond, How can I specify an input for hbond to probe ions interactions? j j (Fri Dec 01 2006 - 02:51:06 PST)
- Re: AMBER: Ions analysis with hbond, How can I specify an input for hbond to probe ions interactions? Thomas Cheatham (Fri Dec 01 2006 - 09:53:50 PST)
  - Re: AMBER: Ions analysis with hbond, How can I specify an input for hbond to probe ions interactions? j j (Fri Dec 01 2006 - 12:28:24 PST)
    - Re: AMBER: Ions analysis with hbond, How can I specify an input for hbond to probe ions interactions? Thomas Cheatham (Fri Dec 01 2006 - 14:01:35 PST)
    - Re: AMBER: Ions analysis with hbond, How can I specify an input for hbond to probe ions interactions? j j (Mon Dec 04 2006 - 04:56:54 PST)
AMBER: about the std of computational alanine scanning tongli (Fri Dec 01 2006 - 03:50:11 PST)
AMBER: question on protein folding simulation Noriaki Okimoto (Fri Dec 01 2006 - 04:01:27 PST)
- RE: AMBER: question on protein folding simulation Yong Duan (Fri Dec 01 2006 - 10:32:58 PST)
  - Re: AMBER: question on protein folding simulation Noriaki Okimoto (Sun Dec 03 2006 - 18:43:11 PST)
    - Re: AMBER: question on protein folding simulation Carlos Simmerling (Mon Dec 04 2006 - 04:32:16 PST)
    - Re: AMBER: question on protein folding simulation Gustavo Seabra (Mon Dec 04 2006 - 10:31:54 PST)
- Re: AMBER: question on protein folding simulation Fenghui Fan (Fri Dec 01 2006 - 11:56:06 PST)
  - Re: AMBER: question on protein folding simulation Noriaki Okimoto (Sun Dec 03 2006 - 18:51:17 PST)
    - Re: AMBER: question on protein folding simulation Fenghui Fan (Mon Dec 04 2006 - 16:47:32 PST)
    - RE: AMBER: question on protein folding simulation Yong Duan (Tue Dec 05 2006 - 11:57:45 PST)
    - Re: AMBER: question on protein folding simulation Noriaki Okimoto (Thu Dec 07 2006 - 04:25:51 PST)
AMBER: sander error about fortran Shuting Wei (Fri Dec 01 2006 - 07:58:25 PST)
- Re: AMBER: sander error about fortran Scott Brozell (Fri Dec 01 2006 - 23:10:03 PST)
  - Re: AMBER: sander error about fortran Shuting Wei (Mon Dec 04 2006 - 09:02:52 PST)
    - Re: AMBER: sander error about fortran Scott Brozell (Mon Dec 04 2006 - 13:26:52 PST)
AMBER: H-bond analysis (Ptraj) input file Esther Brugger (Fri Dec 01 2006 - 08:22:44 PST)
- Re: AMBER: H-bond analysis (Ptraj) input file Thomas Cheatham (Fri Dec 01 2006 - 09:56:57 PST)
AMBER: dihedral calculation problem Esther Brugger (Fri Dec 01 2006 - 13:39:23 PST)
AMBER: Making sure that Amber jobs use Infiniband? Michael John Hanby (Fri Dec 01 2006 - 14:13:05 PST)
- Re: AMBER: Making sure that Amber jobs use Infiniband? David A. Case (Fri Dec 01 2006 - 16:24:44 PST)
AMBER: LogP Cenk Andac (Sat Dec 02 2006 - 02:44:06 PST)
AMBER: problem at the start of heating up (using extra-point) Rachel (Sat Dec 02 2006 - 07:29:09 PST)
- Re: AMBER: problem at the start of heating up (using extra-point) Cenk Andac (Sat Dec 02 2006 - 09:32:50 PST)
- Re: AMBER: problem at the start of heating up (using extra-point) David A. Case (Sun Dec 03 2006 - 14:04:25 PST)
AMBER: LEaP not recognising Phosphate group in TYR bertrand russell (Sat Dec 02 2006 - 08:41:23 PST)
- Re: AMBER: LEaP not recognising Phosphate group in TYR David A. Case (Sat Dec 02 2006 - 09:52:44 PST)
  - AMBER: MD with restraint (nmropt=1) a a (Tue Dec 05 2006 - 00:11:38 PST)
    - Re: AMBER: MD with restraint (nmropt=1) David A. Case (Tue Dec 05 2006 - 13:24:37 PST)
    - Re: AMBER: MD with restraint (nmropt=1) a a (Tue Dec 05 2006 - 22:11:59 PST)
    - Re: AMBER: MD with restraint (nmropt=1) David A. Case (Wed Dec 06 2006 - 07:59:43 PST)
    - Re: AMBER: MD with restraint (nmropt=1) a a (Wed Dec 06 2006 - 20:48:32 PST)
    - Re: AMBER: MD with restraint (nmropt=1) Thomas Cheatham (Wed Dec 06 2006 - 21:14:56 PST)
  - Re: AMBER: LEaP not recognising Phosphate group in TYR bertrand russell (Thu Dec 07 2006 - 02:39:46 PST)
    - Re: AMBER: LEaP not recognising Phosphate group in TYR David A. Case (Thu Dec 07 2006 - 09:06:17 PST)
AMBER: Problem with specifying NOSHAKEMASK Gobind Singh Bisht (Sun Dec 03 2006 - 02:42:01 PST)
- Re: AMBER: Problem with specifying NOSHAKEMASK Carlos Simmerling (Sun Dec 03 2006 - 05:48:56 PST)
  - Re: AMBER: Problem with specifying NOSHAKEMASK Gobind Singh Bisht (Sun Dec 03 2006 - 07:26:27 PST)
- Re: AMBER: Problem with specifying NOSHAKEMASK David A. Case (Sun Dec 03 2006 - 14:06:10 PST)
  - Re: AMBER: Problem with specifying NOSHAKEMASK Gobind Singh Bisht (Sun Dec 03 2006 - 19:11:57 PST)
    - Re: AMBER: Problem with specifying NOSHAKEMASK David A. Case (Mon Dec 04 2006 - 08:33:02 PST)
    - Re: AMBER: Problem with specifying NOSHAKEMASK Gobind Singh Bisht (Mon Dec 04 2006 - 20:26:16 PST)
AMBER: bugfix mahdi fathi (Sun Dec 03 2006 - 07:17:42 PST)
- Re: AMBER: bugfix Ye Mei (Sun Dec 03 2006 - 07:38:40 PST)
AMBER: About the creation of 1-4 pairs in AMBER program J. Zhang (Sun Dec 03 2006 - 18:17:02 PST)
AMBER: The VDW correctioin J. Zhang (Sun Dec 03 2006 - 18:29:28 PST)
AMBER: xleap problems anna.schrey.gmx.de (Mon Dec 04 2006 - 03:45:07 PST)
- Re: AMBER: xleap problems Cenk Andac (Mon Dec 04 2006 - 07:46:34 PST)
- Re: AMBER: xleap problems David A. Case (Mon Dec 04 2006 - 08:26:20 PST)
AMBER: how to include EXTRA POINTS in AMBER8 Rachel (Mon Dec 04 2006 - 07:59:34 PST)
- Re: AMBER: how to include EXTRA POINTS in AMBER8 David A. Case (Mon Dec 04 2006 - 08:23:15 PST)
  - Re: AMBER: how to include EXTRA POINTS in AMBER8 Rachel (Mon Dec 04 2006 - 09:03:11 PST)
    - Re: AMBER: how to include EXTRA POINTS in AMBER8 Rachel (Mon Dec 04 2006 - 10:35:08 PST)
    - Re: AMBER: how to include EXTRA POINTS in AMBER8 David A. Case (Wed Dec 06 2006 - 22:14:44 PST)
    - AMBER: DRMS setting for Nmode calculation Shuting Wei (Thu Dec 07 2006 - 12:46:54 PST)
AMBER: Is there anyway to recover the LISTOUT obtained after running a md with nmr restrictions j j (Mon Dec 04 2006 - 09:10:26 PST)
- Re: AMBER: Is there anyway to recover the LISTOUT obtained after running a md with nmr restrictions David A. Case (Mon Dec 04 2006 - 09:45:11 PST)
  - Re: AMBER: Is there anyway to recover the LISTOUT obtained after running a md with nmr restrictions j j (Mon Dec 04 2006 - 14:28:14 PST)
AMBER: ptraj vector corrplane bug Myunggi Yi (Mon Dec 04 2006 - 12:49:46 PST)
AMBER: Zn2+ and Ca2+ ions explicitly treated in MMPB/GB/SA Piotr Cieplak (Mon Dec 04 2006 - 16:20:02 PST)
AMBER: AMBER parallel run bombs Rahaman, Asif (Mon Dec 04 2006 - 16:29:53 PST)
- Re: AMBER: AMBER parallel run bombs Michael Crowley (Mon Dec 04 2006 - 17:41:32 PST)
AMBER: A BUG report, "ptraj corrplane" Myunggi Yi (Tue Dec 05 2006 - 09:42:08 PST)
- Re: AMBER: A BUG report, "ptraj corrplane" Myunggi Yi (Sun Dec 10 2006 - 17:32:22 PST)
AMBER: nonplanarity of NH2 groups laura zanet (Wed Dec 06 2006 - 07:48:33 PST)
- Re: AMBER: nonplanarity of NH2 groups FyD (Thu Dec 07 2006 - 09:17:54 PST)
- Re: AMBER: nonplanarity of NH2 groups Jiri Sponer (Thu Dec 07 2006 - 09:37:52 PST)
AMBER: perturbed and unperturbed charges Rachel (Wed Dec 06 2006 - 09:24:24 PST)
- Re: AMBER: perturbed and unperturbed charges David A. Case (Wed Dec 06 2006 - 10:22:37 PST)
AMBER: parameter definitions Ed Pate (Wed Dec 06 2006 - 10:27:15 PST)
- Re: AMBER: parameter definitions David A. Case (Wed Dec 06 2006 - 11:00:34 PST)
AMBER: setBox with buffer in leap Steven Winfield (Wed Dec 06 2006 - 11:05:22 PST)
AMBER: Amber9 failure to compile parallel on Rocks 4.2.1 system Michael John Hanby (Wed Dec 06 2006 - 13:26:11 PST)
- RE: AMBER: Amber9 failure to compile parallel on Rocks 4.2.1 system Ross Walker (Wed Dec 06 2006 - 14:48:51 PST)
- AMBER: Amber9 Parallel compiled with -lam, how to run test.parallel? Michael John Hanby (Sun Dec 10 2006 - 12:09:34 PST)
  - Re: AMBER: Amber9 Parallel compiled with -lam, how to run test.parallel? David A. Case (Sun Dec 10 2006 - 16:34:15 PST)
  - RE: AMBER: Amber9 Parallel compiled with -lam, how to run test.parallel? Michael John Hanby (Sun Dec 10 2006 - 19:31:57 PST)
AMBER: ibelly not work JunJun Liu (Wed Dec 06 2006 - 15:22:34 PST)
- RE: AMBER: ibelly not work Ross Walker (Wed Dec 06 2006 - 16:07:45 PST)
  - RE: AMBER: ibelly not work Andy Purkiss-Trew (Thu Dec 07 2006 - 04:33:24 PST)
AMBER: setBox with buffer in leap Steven Winfield (Wed Dec 06 2006 - 16:43:58 PST)
- Re: AMBER: setBox with buffer in leap Scott Brozell (Mon Dec 11 2006 - 21:08:38 PST)
  - Re: AMBER: setBox with buffer in leap David A. Case (Tue Dec 12 2006 - 08:30:25 PST)
AMBER: How could I simulate lipid membrane with AMBER9.0? 曹冉 (Wed Dec 06 2006 - 17:02:55 PST)
- Re: AMBER: How could I simulate lipid membrane with AMBER9.0? Fenghui Fan (Wed Dec 06 2006 - 18:49:09 PST)
- Re: AMBER: How could I simulate lipid membrane with AMBER9.0? 曹冉 (Thu Dec 07 2006 - 17:46:44 PST)
AMBER: What's going wrong when I use antechamber dealing with lipid molecular? 曹冉 (Wed Dec 06 2006 - 17:05:55 PST)
- Re: AMBER: What's going wrong when I use antechamber dealing with lipid molecular? Fenghui Fan (Wed Dec 06 2006 - 18:51:41 PST)
AMBER: PMEMD scaling Tiziano Tuccinardi (Thu Dec 07 2006 - 00:46:49 PST)
- Re: AMBER: PMEMD scaling Robert Duke (Thu Dec 07 2006 - 06:17:46 PST)
AMBER: Installing Amber 9 on Mac Pro Burkhard Heil (Thu Dec 07 2006 - 02:54:00 PST)
- Re: AMBER: Installing Amber 9 on Mac Pro Mathy Froeyen (Thu Dec 07 2006 - 04:54:48 PST)
- Re: AMBER: Installing Amber 9 on Mac Pro Mengjuei Hsieh (Mon Dec 11 2006 - 17:52:07 PST)
AMBER: MD with positional and NMR restraints Mike Summers (Thu Dec 07 2006 - 12:46:26 PST)
- Re: AMBER: MD with positional and NMR restraints David A. Case (Thu Dec 07 2006 - 13:51:53 PST)
  - Re: AMBER: MD with positional and NMR restraints Mike Summers (Thu Dec 07 2006 - 15:34:07 PST)
    - Re: AMBER: MD with positional and NMR restraints David A. Case (Thu Dec 07 2006 - 15:54:33 PST)
  - AMBER: Problem with installation of the leap module of AMBER9 on Linux Suse 10.2 Cenk Andac (Tue Jan 23 2007 - 04:03:37 PST)
    - Re: AMBER: Problem with installation of the leap module of AMBER9 on Linux Suse 10.2 Steven Winfield (Tue Jan 23 2007 - 04:11:12 PST)
    - Re: AMBER: Problem with installation of the leap module of AMBER9 on Linux Suse 10.2 David A. Case (Wed Jan 24 2007 - 07:09:36 PST)
    - RE: AMBER: Problem with installation of the leap module of AMBER9 on Linux Suse 10.2 Ross Walker (Wed Jan 24 2007 - 09:49:20 PST)
AMBER: Simulating proteins with calcium ion Qing Zhang (Thu Dec 07 2006 - 16:15:42 PST)
- Re: AMBER: Simulating proteins with calcium ion Fenghui Fan (Thu Dec 07 2006 - 17:56:02 PST)
- Re: AMBER: Simulating proteins with calcium ion Thomas Cheatham (Thu Dec 07 2006 - 19:23:26 PST)
- Re: AMBER: Simulating proteins with calcium ion Qing Zhang (Fri Dec 08 2006 - 16:31:02 PST)
  - Re: AMBER: Simulating proteins with calcium ion Karen Callahan (Tue Dec 12 2006 - 11:19:49 PST)
- Re: AMBER: Simulating proteins with calcium ion Bill Ross (Tue Dec 12 2006 - 11:47:48 PST)
- Re: AMBER: Simulating proteins with calcium ion 张勇 (Tue Dec 12 2006 - 16:25:03 PST)
- Re: AMBER: Simulating proteins with calcium ion Qing Zhang (Fri Dec 22 2006 - 11:32:43 PST)
- Re: AMBER: Simulating proteins with calcium ion Bill Ross (Fri Dec 22 2006 - 11:51:07 PST)
- Re: AMBER: Simulating proteins with calcium ion Qing Zhang (Fri Dec 22 2006 - 12:22:53 PST)
- Re: AMBER: Simulating proteins with calcium ion Qing Zhang (Fri Dec 22 2006 - 12:17:05 PST)
- Re: AMBER: Simulating proteins with calcium ion Bill Ross (Fri Dec 22 2006 - 13:12:50 PST)
- Re: AMBER: Simulating proteins with calcium ion 张勇 (Fri Dec 22 2006 - 17:02:57 PST)
- Re: AMBER: Simulating proteins with calcium ion Qing Zhang (Fri Dec 22 2006 - 23:26:11 PST)
AMBER: Error message in methane solvent system Atsutoshi Okabe (Thu Dec 07 2006 - 19:19:04 PST)
- Re: AMBER: Error message in methane solvent system David A. Case (Fri Dec 08 2006 - 08:41:49 PST)
AMBER: atome type error Steve Seibold (Fri Dec 08 2006 - 07:08:35 PST)
- RE: AMBER: atome type error Ross Walker (Fri Dec 08 2006 - 07:51:29 PST)
AMBER: Atom Type problem Steve Seibold (Fri Dec 08 2006 - 08:01:23 PST)
- RE: AMBER: Atom Type problem Ross Walker (Fri Dec 08 2006 - 08:21:19 PST)
  - RE: AMBER: Atom Type problem Steve Seibold (Fri Dec 08 2006 - 10:09:05 PST)
AMBER: Atom Type problem Steve Seibold (Fri Dec 08 2006 - 08:04:29 PST)
AMBER: Compiling Amber 9 on SGI with gcc Shin, John Y CONTRACTOR WRAIR-Wash DC (Fri Dec 08 2006 - 10:46:32 PST)
- Re: AMBER: Compiling Amber 9 on SGI with gcc Scott Brozell (Fri Dec 08 2006 - 19:29:15 PST)
- Re: AMBER: Compiling Amber 9 on SGI with gcc David A. Case (Sat Dec 09 2006 - 08:55:20 PST)
AMBER: RDC refinement Lee, Young-Tae (Fri Dec 08 2006 - 12:50:42 PST)
- Re: AMBER: RDC refinement David A. Case (Fri Dec 08 2006 - 15:52:11 PST)
AMBER: description of prep file Piotr Cieplak (Fri Dec 08 2006 - 14:28:29 PST)
- Re: AMBER: description of prep file David A. Case (Fri Dec 08 2006 - 14:52:30 PST)
AMBER: dihedral angle problem Esther Brugger (Fri Dec 08 2006 - 14:53:32 PST)
- Re: AMBER: dihedral angle problem David A. Case (Fri Dec 08 2006 - 15:47:39 PST)
  - Re: AMBER: dihedral angle problem Esther Brugger (Fri Dec 08 2006 - 17:00:48 PST)
    - Re: AMBER: dihedral angle problem David A. Case (Fri Dec 08 2006 - 18:10:36 PST)
AMBER: General Question about Abmer Sanya Kryklia (Mon Dec 11 2006 - 06:23:11 PST)
- Re: AMBER: General Question about Abmer M. L. Dodson (Mon Dec 11 2006 - 06:34:45 PST)
AMBER: addition of subroutine in pmemd module kakali sen (Mon Dec 11 2006 - 10:52:37 PST)
AMBER: Atoms overlapping Nitin Bhardwaj (Mon Dec 11 2006 - 11:43:44 PST)
- Re: AMBER: Atoms overlapping David A. Case (Mon Dec 11 2006 - 12:08:58 PST)
  - Re: AMBER: Atoms overlapping Nitin Bhardwaj (Mon Dec 11 2006 - 12:48:53 PST)
    - Re: AMBER: Atoms overlapping Thomas Steinbrecher (Mon Dec 11 2006 - 14:11:47 PST)
AMBER: Building Parameters Steve Seibold (Mon Dec 11 2006 - 13:29:15 PST)
AMBER: Coodinates not being unique Nitin Bhardwaj (Mon Dec 11 2006 - 16:50:41 PST)
AMBER: QM/MD energy conservation Evan Kelly (Mon Dec 11 2006 - 19:17:59 PST)
- Re: AMBER: QM/MD energy conservation Gustavo Seabra (Tue Dec 12 2006 - 06:02:39 PST)
AMBER: LEaP problem bertrand russell (Mon Dec 11 2006 - 21:10:48 PST)
Re: AMBER: LEaP problem Bill Ross (Mon Dec 11 2006 - 22:24:33 PST)
- Re: AMBER: LEaP problem Fenghui Fan (Mon Dec 11 2006 - 22:32:06 PST)
AMBER: ERROR: The PDB file is not in the working directory saurabh agrawal (Tue Dec 12 2006 - 03:39:39 PST)
- Re: AMBER: ERROR: The PDB file is not in the working directory FyD (Tue Dec 12 2006 - 04:57:56 PST)
  - Re: AMBER: ERROR: The PDB file is not in the working directory saurabh agrawal (Wed Dec 13 2006 - 23:18:33 PST)
    - Re: AMBER: ERROR: The PDB file is not in the working directory saurabh agrawal (Thu Dec 14 2006 - 03:38:05 PST)
    - Re: AMBER: ERROR: The PDB file is not in the working directory FyD (Fri Dec 15 2006 - 00:21:21 PST)
AMBER: RDF problem Esther Brugger (Tue Dec 12 2006 - 11:45:14 PST)
AMBER: floating point assist faults on IA64 PMEMD 9 Jarrod Smith (Wed Dec 13 2006 - 10:42:06 PST)
- Re: AMBER: floating point assist faults on IA64 PMEMD 9 Robert Duke (Wed Dec 13 2006 - 12:22:23 PST)
  - Re: AMBER: floating point assist faults on IA64 PMEMD 9 Jarrod Smith (Wed Dec 13 2006 - 13:54:18 PST)
    - Re: AMBER: floating point assist faults on IA64 PMEMD 9 Jarrod Smith (Wed Dec 13 2006 - 14:13:29 PST)
- Re: AMBER: floating point assist faults on IA64 PMEMD 9 Robert Duke (Wed Dec 13 2006 - 14:41:52 PST)
  - Re: AMBER: floating point assist faults on IA64 PMEMD 9 Jarrod Smith (Wed Dec 13 2006 - 15:32:36 PST)
AMBER: Unit 5 Error on OPEN: md.in Rachel (Wed Dec 13 2006 - 11:55:58 PST)
- Re: AMBER: Unit 5 Error on OPEN: md.in Rachel (Sat Dec 16 2006 - 10:01:12 PST)
  - Re: AMBER: Unit 5 Error on OPEN: md.in Chris Moth (Sat Dec 16 2006 - 10:25:03 PST)
  - Re: AMBER: Unit 5 Error on OPEN: md.in Chris Moth (Sat Dec 16 2006 - 10:27:17 PST)
AMBER: amber 9 installation problem Ed Pate (Wed Dec 13 2006 - 16:34:19 PST)
AMBER: coordinate out of bounds Miguel Ferreira (Wed Dec 13 2006 - 17:09:57 PST)
- Re: AMBER: coordinate out of bounds j j (Thu Dec 14 2006 - 02:21:50 PST)
AMBER: ISTRNG or SALT in MM_PBSA Qizhi Cui (Wed Dec 13 2006 - 19:23:48 PST)
AMBER: Free energy perturbation in SANDER Yumi Nukusina (Thu Dec 14 2006 - 00:59:36 PST)
- Re: AMBER: Free energy perturbation in SANDER Sergey Samsonov (Thu Dec 14 2006 - 01:38:46 PST)
- AMBER: Free energy perturbation in SANDER Chris Moth (Thu Dec 14 2006 - 06:21:11 PST)
AMBER: parallel computation time vs serial computation time Cenk Andac (Thu Dec 14 2006 - 03:17:28 PST)
- Re: AMBER: parallel computation time vs serial computation time Robert Duke (Thu Dec 14 2006 - 06:16:22 PST)
AMBER: sander: cannot execute binary file Kailee (Thu Dec 14 2006 - 07:53:50 PST)
- RE: AMBER: sander: cannot execute binary file Michael John Hanby (Thu Dec 14 2006 - 13:52:23 PST)
- RE: AMBER: sander: cannot execute binary file Ross Walker (Thu Dec 14 2006 - 15:15:46 PST)
  - Re: AMBER: sander: cannot execute binary file Kailee (Fri Dec 15 2006 - 09:25:21 PST)
    - Re: AMBER: sander: cannot execute binary file David A. Case (Fri Dec 15 2006 - 09:48:49 PST)
    - Re: AMBER: sander: cannot execute binary file Kailee (Mon Dec 18 2006 - 08:41:11 PST)
    - Re: AMBER: sander: cannot execute binary file Kailee (Mon Dec 18 2006 - 09:06:36 PST)
    - RE: AMBER: sander: cannot execute binary file Ross Walker (Mon Dec 18 2006 - 11:52:05 PST)
    - Re: AMBER: sander: cannot execute binary file Kailee (Tue Dec 19 2006 - 08:13:48 PST)
AMBER: Test Message Please Ignore Ross Walker (Thu Dec 14 2006 - 13:01:07 PST)
AMBER: Test Message Please Ignore. Ross Walker (Thu Dec 14 2006 - 13:01:07 PST)
AMBER: Can't compile PMEMD Michael John Hanby (Thu Dec 14 2006 - 13:47:15 PST)
- Re: AMBER: Can't compile PMEMD Robert Duke (Thu Dec 14 2006 - 14:12:12 PST)
- RE: AMBER: Can't compile PMEMD Michael John Hanby (Thu Dec 14 2006 - 15:13:47 PST)
  - Re: AMBER: Can't compile PMEMD Robert Duke (Thu Dec 14 2006 - 15:42:02 PST)
AMBER: rdparm venditti2.unisi.it (Fri Dec 15 2006 - 08:08:17 PST)
- Re: AMBER: rdparm Thomas Cheatham (Sat Dec 16 2006 - 19:43:55 PST)
- Re: AMBER: rdparm Tim Meyer (Tue Dec 19 2006 - 07:22:45 PST)
AMBER: AMBER - leap - problems with impose command Piotr Cieplak (Fri Dec 15 2006 - 10:18:06 PST)
- Re: AMBER: AMBER - leap - problems with impose command FyD (Fri Dec 15 2006 - 22:22:36 PST)
  - Re: AMBER: AMBER - leap - problems with impose command Piotr Cieplak (Fri Dec 15 2006 - 23:04:05 PST)
    - Re: AMBER: AMBER - leap - problems with impose command Ilyas Yildirim (Sat Dec 16 2006 - 03:17:22 PST)
    - Re: AMBER: AMBER - leap - problems with impose command Piotr Cieplak (Sat Dec 16 2006 - 23:20:28 PST)
    - Re: AMBER: AMBER - leap - problems with impose command Ilyas Yildirim (Sun Dec 17 2006 - 00:45:13 PST)
AMBER: Is there a way to simulate a box of pure water with amber Li Su (Fri Dec 15 2006 - 10:28:12 PST)
- RE: AMBER: Is there a way to simulate a box of pure water with amber Ross Walker (Fri Dec 15 2006 - 10:52:53 PST)
- Re: AMBER: Is there a way to simulate a box of pure water with amber Sergey Samsonov (Sun Dec 17 2006 - 23:43:27 PST)
Re: AMBER: Is there a way to simulate a box of pure water with amber Bill Ross (Fri Dec 15 2006 - 11:06:49 PST)
AMBER: Solvating a bilayer Matthew Tessier (Fri Dec 15 2006 - 11:32:25 PST)
AMBER: Error in sysdepend.c? Shin, John Y CONTRACTOR WRAIR-Wash DC (Fri Dec 15 2006 - 11:44:50 PST)
- Re: AMBER: Error in sysdepend.c? David A. Case (Fri Dec 15 2006 - 15:24:00 PST)
  - RE: AMBER: Error in sysdepend.c? Shin, John Y CONTRACTOR WRAIR-Wash DC (Mon Dec 18 2006 - 12:27:24 PST)
    - RE: AMBER: Error in sysdepend.c? Scott Brozell (Tue Dec 19 2006 - 11:19:38 PST)
    - RE: AMBER: Error in sysdepend.c? Shin, John Y CONTRACTOR WRAIR-Wash DC (Tue Dec 19 2006 - 13:29:12 PST)
AMBER: Volume of ucell too big Atsutoshi Okabe (Sat Dec 16 2006 - 00:41:43 PST)
- Re: AMBER: Volume of ucell too big Nicolas Lux Fawzi (Sat Dec 16 2006 - 10:37:31 PST)
AMBER: How to make a movie with .crd files in VMD? bertrand russell (Sat Dec 16 2006 - 02:03:53 PST)
- Re: AMBER: How to make a movie with .crd files in VMD? Carlos Simmerling (Sat Dec 16 2006 - 05:22:04 PST)
  - Re: AMBER: How to make a movie with .crd files in VMD? bertrand russell (Sat Dec 16 2006 - 09:35:16 PST)
    - Re: AMBER: How to make a movie with .crd files in VMD? Chris Moth (Sat Dec 16 2006 - 10:35:13 PST)
    - Re: AMBER: How to make a movie with .crd files in VMD? Carlos Simmerling (Sat Dec 16 2006 - 10:54:37 PST)
- Re: AMBER: How to make a movie with .crd files in VMD? Nicolas Lux Fawzi (Sat Dec 16 2006 - 10:32:35 PST)
AMBER: Amber 9 Leap install error A Box (Sun Dec 17 2006 - 20:06:52 PST)
- Re: AMBER: Amber 9 Leap install error David A. Case (Sun Dec 17 2006 - 21:54:56 PST)
AMBER: (no subject) lily ferreira (Mon Dec 18 2006 - 00:14:44 PST)
- AMBER: Parallelization method Jordi Camps (Tue Dec 19 2006 - 10:19:40 PST)
  - Re: AMBER: Parallelization method Robert Duke (Tue Dec 19 2006 - 10:29:09 PST)
    - Re: AMBER: Parallelization method Scott Brozell (Tue Dec 19 2006 - 10:58:07 PST)
AMBER: MM-PBSA Shozeb Haider (Mon Dec 18 2006 - 09:57:17 PST)
- Re: AMBER: MM-PBSA Angelo (Mon Dec 18 2006 - 08:30:00 PST)
AMBER: RESP charge fitting for HFIP Mingfeng Yang (Mon Dec 18 2006 - 18:44:19 PST)
- Re: AMBER: RESP charge fitting for HFIP Raviprasad Aduri (Mon Dec 18 2006 - 19:46:05 PST)
  - Re: AMBER: RESP charge fitting for HFIP Mingfeng Yang (Mon Dec 18 2006 - 23:17:24 PST)
    - Re: AMBER: RESP charge fitting for HFIP FyD (Tue Dec 19 2006 - 23:21:42 PST)
    - Re: AMBER: RESP charge fitting for HFIP Mingfeng Yang (Wed Dec 20 2006 - 10:31:53 PST)
  - Re: AMBER: RESP charge fitting for HFIP FyD (Mon Dec 18 2006 - 23:44:05 PST)
AMBER: sander ntc=2 ntf=1 Nicolas Lux Fawzi (Mon Dec 18 2006 - 19:10:42 PST)
- Re: AMBER: sander ntc=2 ntf=1 Carlos Simmerling (Tue Dec 19 2006 - 03:39:38 PST)
AMBER: Frozen at Minimization Steve Seibold (Tue Dec 19 2006 - 06:18:21 PST)
- Re: AMBER: Frozen at Minimization Chris Moth (Tue Dec 19 2006 - 07:01:16 PST)
AMBER: Renumber residues in LEAP Akshay Patny (Tue Dec 19 2006 - 13:55:57 PST)
- Re: AMBER: Renumber residues in LEAP David A. Case (Mon Dec 25 2006 - 14:11:34 PST)
AMBER: charge problem in MM-PBSA linfu (Tue Dec 19 2006 - 17:53:52 PST)
AMBER: mixing GAFF and CHARMM Ravinder Abrol (Tue Dec 19 2006 - 23:09:08 PST)
- Re:AMBER: mixing GAFF and CHARMM 曹冉 (Wed Dec 20 2006 - 09:12:05 PST)
- Re: AMBER: mixing GAFF and CHARMM Ravinder Abrol (Wed Dec 20 2006 - 09:38:23 PST)
- RE: AMBER: mixing GAFF and CHARMM Akshay Patny (Wed Dec 20 2006 - 09:46:45 PST)
- Re: AMBER: mixing GAFF and CHARMM Christophe Guilbert (Wed Dec 20 2006 - 11:51:18 PST)
- Re: AMBER: mixing GAFF and CHARMM Ravinder Abrol (Wed Dec 20 2006 - 16:58:36 PST)
AMBER: Installation help - SGI Altix 350 bertrand russell (Wed Dec 20 2006 - 02:47:03 PST)
- Re: AMBER: Installation help - SGI Altix 350 Gustavo Seabra (Wed Dec 20 2006 - 07:31:01 PST)
- RE: AMBER: Installation help - SGI Altix 350 Ross Walker (Wed Dec 20 2006 - 08:38:16 PST)
  - Re: AMBER: Installation help - SGI Altix 350 bertrand russell (Wed Dec 20 2006 - 20:13:03 PST)
    - RE: AMBER: Installation help - SGI Altix 350 Ross Walker (Wed Dec 20 2006 - 20:36:10 PST)
    - Re: AMBER: Installation help - SGI Altix 350 bertrand russell (Wed Dec 20 2006 - 21:09:48 PST)
    - RE: AMBER: Installation help - SGI Altix 350 Ross Walker (Wed Dec 20 2006 - 21:30:53 PST)
    - Re: AMBER: Installation help - SGI Altix 350 bertrand russell (Thu Dec 21 2006 - 21:51:48 PST)
    - Re: AMBER: Installation help - SGI Altix 350 Gustavo Seabra (Fri Dec 22 2006 - 17:42:03 PST)
    - Re: AMBER: Installation help - SGI Altix 350 bertrand russell (Tue Dec 26 2006 - 00:25:10 PST)
    - Re: AMBER: Installation help - SGI Altix 350 David A. Case (Tue Dec 26 2006 - 13:45:54 PST)
    - Re: AMBER: Installation help - SGI Altix 350 bertrand russell (Mon Jan 08 2007 - 23:17:54 PST)
    - RE: AMBER: Installation help - SGI Altix 350 Ross Walker (Tue Jan 09 2007 - 08:18:55 PST)
    - Re: AMBER: Installation help - SGI Altix 350 Gustavo Seabra (Wed Jan 10 2007 - 08:07:26 PST)
AMBER: Amber9 - openmpi? bertrand russell (Wed Dec 20 2006 - 03:22:37 PST)
- Re: AMBER: Amber9 - openmpi? Robert Duke (Wed Dec 20 2006 - 05:23:10 PST)
- Re: AMBER: Amber9 - openmpi? Gustavo Seabra (Wed Dec 20 2006 - 07:34:53 PST)
  - Re: AMBER: Amber9 - openmpi? bertrand russell (Wed Dec 20 2006 - 20:16:22 PST)
AMBER: MM_PBSA lily ferreira (Wed Dec 20 2006 - 05:42:20 PST)
AMBER: MM_PBSA lily ferreira (Wed Dec 20 2006 - 05:46:00 PST)
- Re: AMBER: MM_PBSA David A. Case (Mon Dec 25 2006 - 14:15:26 PST)
AMBER: RED - help with installation / config Seth Lilavivat (Wed Dec 20 2006 - 07:18:49 PST)
- Re: AMBER: RED - help with installation / config FyD (Thu Dec 21 2006 - 01:24:50 PST)
  - AMBER: Amber Input file from "qout", "resp.dat" saurabh agrawal (Thu Dec 21 2006 - 01:41:47 PST)
    - Re: AMBER: Amber Input file from "qout", "resp.dat" FyD (Thu Dec 21 2006 - 02:23:09 PST)
AMBER: RESP procedure for DMPC monomer Akshay Patny (Wed Dec 20 2006 - 08:04:00 PST)
- Re: AMBER: RESP procedure for DMPC monomer linfu (Wed Dec 20 2006 - 16:54:43 PST)
AMBER: Replica exchange rate in REMD Seongeun Yang (Thu Dec 21 2006 - 03:42:59 PST)
AMBER: tetrolic acid Russell Glavey (Thu Dec 21 2006 - 04:29:35 PST)
AMBER: xleap, generating prep file Seth Lilavivat (Thu Dec 21 2006 - 08:49:56 PST)
AMBER: EXTRA_PTS: frtype 2 Should not be here Kailee (Thu Dec 21 2006 - 10:26:31 PST)
- Re: AMBER: EXTRA_PTS: frtype 2 Should not be here David A. Case (Mon Dec 25 2006 - 14:32:11 PST)
AMBER: Sander--NMR refinement Esther Brugger (Thu Dec 21 2006 - 20:39:48 PST)
- Re: AMBER: Sander--NMR refinement David A. Case (Tue Dec 26 2006 - 10:44:46 PST)
AMBER: Compiling Amber8 with Sun HPC ClusterTools 5 Software Muhammad Naim Mohmad Rouyan (Thu Dec 21 2006 - 23:40:32 PST)
- Re: AMBER: Compiling Amber8 with Sun HPC ClusterTools 5 Software David A. Case (Sat Dec 23 2006 - 18:58:29 PST)
AMBER: Nucgen Problem puneet kacker (Fri Dec 22 2006 - 00:06:41 PST)
- Re: AMBER: Nucgen Problem Navnit Kumar Mishra (Fri Dec 22 2006 - 01:55:26 PST)
Re: AMBER: Nucgen Problem Bill Ross (Fri Dec 22 2006 - 10:51:25 PST)
AMBER: Problem with LEaP FyD (Fri Dec 22 2006 - 11:42:13 PST)
AMBER: A problem with mm_pbsa vic.mail.nankai.edu.cn (Mon Dec 25 2006 - 17:41:41 PST)
AMBER: .crd file bertrand russell (Tue Dec 26 2006 - 01:16:53 PST)
- Re: AMBER: .crd file Fenghui Fan (Tue Dec 26 2006 - 08:17:33 PST)
AMBER: bad connectivity Seth Lilavivat (Tue Dec 26 2006 - 09:24:17 PST)
- Re: AMBER: bad connectivity Fenghui Fan (Tue Dec 26 2006 - 09:33:57 PST)
  - AMBER: bad connectivity - more detail Seth Lilavivat (Tue Dec 26 2006 - 10:02:27 PST)
    - Re: AMBER: bad connectivity - more detail Fenghui Fan (Tue Dec 26 2006 - 20:19:41 PST)
    - Re: AMBER: bad connectivity - more detail Fenghui Fan (Tue Dec 26 2006 - 22:25:41 PST)
    - Re: AMBER: bad connectivity - more detail Seth Lilavivat (Wed Dec 27 2006 - 08:26:14 PST)
    - Re: AMBER: bad connectivity - more detail David A. Case (Wed Dec 27 2006 - 08:52:41 PST)
    - Re: AMBER: bad connectivity - more detail Seth Lilavivat (Wed Dec 27 2006 - 09:44:29 PST)
    - Re: AMBER: bad connectivity - more detail David A. Case (Wed Dec 27 2006 - 10:31:58 PST)
    - Re: AMBER: bad connectivity - more detail Seth Lilavivat (Wed Dec 27 2006 - 11:42:42 PST)
    - Re: AMBER: bad connectivity - more detail David A. Case (Fri Dec 29 2006 - 00:15:16 PST)
AMBER: G5 OSX serial compile error Kevin Kelliher (Tue Dec 26 2006 - 13:18:56 PST)
- Re: AMBER: G5 OSX serial compile error Mathy Froeyen (Thu Dec 28 2006 - 03:12:13 PST)
- Re: AMBER: G5 OSX serial compile error Mengjuei Hsieh (Mon Jan 01 2007 - 02:16:12 PST)
- Re: AMBER: G5 OSX serial compile error Kevin Kelliher (Fri Jan 05 2007 - 10:58:56 PST)
  - Re: AMBER: G5 OSX serial compile error Mengjuei Hsieh (Mon Jan 08 2007 - 16:26:26 PST)
AMBER: Error compiling amber on parallel (MPICH) Muhammad Naim Mohmad Rouyan (Tue Dec 26 2006 - 22:35:47 PST)
- Re: AMBER: Error compiling amber on parallel (MPICH) David A. Case (Wed Dec 27 2006 - 08:41:21 PST)
AMBER: recompiling bondtype.C Seth Lilavivat (Wed Dec 27 2006 - 08:49:32 PST)
- Re: AMBER: recompiling bondtype.C David A. Case (Wed Dec 27 2006 - 10:30:10 PST)
AMBER: PMEMD and OpenMPI, anyone have config options? Michael John Hanby (Wed Dec 27 2006 - 12:04:50 PST)
AMBER: chirality.c line 121 Seth Lilavivat (Wed Dec 27 2006 - 13:43:56 PST)
- Re: AMBER: chirality.c line 121 David A. Case (Wed Dec 27 2006 - 14:46:21 PST)
AMBER: PCA analysis Jardas sucuriba (Wed Dec 27 2006 - 21:04:41 PST)
- AMBER: tree name generated by tleap is different from the input PREP parameter file xiaoqin huang (Thu Dec 28 2006 - 08:48:14 PST)
- AMBER: fluctuations Jardas sucuriba (Tue Jan 02 2007 - 07:21:22 PST)
AMBER: problems trying to modify Amber8 Ed Pate (Thu Dec 28 2006 - 14:41:33 PST)
- Re: AMBER: problems trying to modify Amber8 David A. Case (Tue Jan 02 2007 - 15:53:36 PST)
AMBER: problems with Calcium ions treatment in GB run Piotr Cieplak (Thu Dec 28 2006 - 15:44:23 PST)
- Re: AMBER: problems with Calcium ions treatment in GB run David A. Case (Thu Dec 28 2006 - 23:56:25 PST)
AMBER: tree name generated by tleap is different from the input PREP parameter file xiaoqin huang (Thu Dec 28 2006 - 16:53:39 PST)
AMBER: AMBER complile problem Chengwen Chen (Thu Dec 28 2006 - 23:41:21 PST)
- Re: AMBER: AMBER complile problem David A. Case (Thu Dec 28 2006 - 23:51:49 PST)
  - Re: AMBER: AMBER complile problem Chengwen Chen (Mon Jan 01 2007 - 19:19:08 PST)
AMBER: Simulated Annealing problem... sai vikram (Fri Dec 29 2006 - 02:33:50 PST)
- Re: AMBER: Simulated Annealing problem... David A. Case (Fri Dec 29 2006 - 08:56:06 PST)
  - Re: AMBER: Simulated Annealing problem... sai vikram (Sat Dec 30 2006 - 05:12:53 PST)
Re: AMBER: tree name generated by tleap is different from the input PREP parameter file Bill Ross (Fri Dec 29 2006 - 19:00:26 PST)
AMBER: RE: protein simulation using AMBER Ross Walker (Fri Dec 29 2006 - 22:51:09 PST)
AMBER: Deep energetics problem sai vikram (Tue Jan 02 2007 - 09:10:19 PST)
- RE: AMBER: Deep energetics problem Ross Walker (Tue Jan 02 2007 - 11:12:53 PST)
  - Re: AMBER: Deep energetics problem sai vikram (Wed Jan 03 2007 - 00:26:42 PST)
AMBER: Distance Restraints Problem Esther Brugger (Tue Jan 02 2007 - 14:00:16 PST)
- Re: AMBER: Distance Restraints Problem David A. Case (Tue Jan 02 2007 - 15:37:18 PST)
AMBER: assign atom hybrid xiaoqin huang (Tue Jan 02 2007 - 17:54:52 PST)
AMBER: amber9 installation error Seaclear Theory (Tue Jan 02 2007 - 18:10:12 PST)
- Re: AMBER: amber9 installation error David A. Case (Tue Jan 02 2007 - 23:00:50 PST)
  - Re: AMBER: amber9 installation error Seaclear Theory (Wed Jan 03 2007 - 07:55:51 PST)
    - Re: AMBER: amber9 installation error David A. Case (Wed Jan 03 2007 - 18:05:35 PST)
    - Re: AMBER: amber9 installation error Seaclear Theory (Wed Jan 03 2007 - 20:34:49 PST)
    - Re: AMBER: amber9 installation error Seaclear Theory (Thu Jan 04 2007 - 13:27:14 PST)
  - Re: AMBER: amber9 installation error Seaclear Theory (Wed Jan 03 2007 - 10:04:27 PST)
AMBER: Re:tree name generated by tleap is different from the input PREP parameter file xiaoqin huang (Tue Jan 02 2007 - 18:41:13 PST)
Re: AMBER: Re:tree name generated by tleap is different from the input PREP parameter file Bill Ross (Tue Jan 02 2007 - 20:26:14 PST)
- Re: AMBER: Re:tree name generated by tleap is different from the input PREP parameter file xiaoqin huang (Wed Jan 03 2007 - 07:05:18 PST)
AMBER: H-bond in ptraj nag raj (Wed Jan 03 2007 - 04:17:51 PST)
- Re: AMBER: H-bond in ptraj Jianyin Shao (Thu Jan 04 2007 - 11:49:38 PST)
  - Re: AMBER: H-bond in ptraj nag raj (Thu Jan 04 2007 - 20:34:59 PST)
    - Re: AMBER: H-bond in ptraj Barbault Florent (Fri Jan 05 2007 - 00:20:22 PST)
    - Re: AMBER: H-bond in ptraj nag raj (Fri Jan 05 2007 - 23:22:10 PST)
    - AMBER: H-bond in each fram nag raj (Sun Jan 07 2007 - 21:49:57 PST)
AMBER: torsion angle penalty calculation Mike Summers (Wed Jan 03 2007 - 07:18:34 PST)
- Re: AMBER: torsion angle penalty calculation David A. Case (Wed Jan 03 2007 - 08:54:33 PST)
  - Re: AMBER: torsion angle penalty calculationy Mike Summers (Wed Jan 03 2007 - 10:13:24 PST)
- AMBER: MPI is slower than single processor with water Mike Summers (Tue Jan 16 2007 - 08:30:18 PST)
  - RE: AMBER: MPI is slower than single processor with water Ross Walker (Tue Jan 16 2007 - 08:50:36 PST)
    - Re: AMBER: MPI is slower than single processor with water Mike Summers (Tue Jan 16 2007 - 09:32:53 PST)
    - RE: AMBER: MPI is slower than single processor with water Yu Chen (Tue Jan 16 2007 - 12:23:23 PST)
AMBER: installing amber 8 on 5 nodes cluster PC Syed Tarique Moin (Wed Jan 03 2007 - 08:44:54 PST)
- Re: AMBER: installing amber 8 on 5 nodes cluster PC David A. Case (Wed Jan 03 2007 - 09:26:17 PST)
  - Re: AMBER: installing amber 8 on 5 nodes cluster PC Syed Tarique Moin (Wed Jan 03 2007 - 10:25:45 PST)
- AMBER: mm_pbsa problems Jardas sucuriba (Tue Jan 30 2007 - 07:55:00 PST)
AMBER: How to get a periodic box of modified water molecules Li Su (Wed Jan 03 2007 - 09:25:11 PST)
- Re: AMBER: How to get a periodic box of modified water molecules David A. Case (Wed Jan 03 2007 - 22:04:10 PST)
  - AMBER: AMBER citation questions caoch.cherry.bio.titech.ac.jp (Thu Jan 04 2007 - 00:59:08 PST)
    - Re: AMBER: AMBER citation questions Carlos Simmerling (Thu Jan 04 2007 - 03:36:28 PST)
AMBER: Distance Restraints Esther Brugger (Wed Jan 03 2007 - 12:29:26 PST)
- Re: AMBER: Distance Restraints Esther Brugger (Wed Jan 03 2007 - 14:04:03 PST)
  - AMBER: Preprocessor Error: _qmmm_module.f "Extra Characters..." Mike Hanby (Wed Jan 03 2007 - 14:53:43 PST)
    - RE: AMBER: Preprocessor Error: _qmmm_module.f "Extra Characters..." Ross Walker (Wed Jan 03 2007 - 15:34:23 PST)
  - Re: AMBER: Distance Restraints Esther Brugger (Fri Jan 05 2007 - 07:17:38 PST)
AMBER: NH3 potential Jennie Thomas (Wed Jan 03 2007 - 13:00:28 PST)
AMBER: H-acceptors problem in ptraj nag raj (Wed Jan 03 2007 - 21:20:09 PST)
AMBER: The unperturbed charge of the unit: -20.999999 is not zero. saurabh agrawal (Wed Jan 03 2007 - 23:03:49 PST)
- Re: AMBER: The unperturbed charge of the unit: -20.999999 is not zero. Nitin Bhardwaj (Thu Jan 04 2007 - 07:54:39 PST)
  - Re: AMBER: The unperturbed charge of the unit: -20.999999 is not zero. Carlos Simmerling (Thu Jan 04 2007 - 11:31:29 PST)
    - AMBER: 22 improper torsions in old prep form saurabh agrawal (Thu Jan 04 2007 - 22:29:21 PST)
AMBER: intra-molecular h-bonds in ptraj lily ferreira (Thu Jan 04 2007 - 07:17:37 PST)
- Re: AMBER: intra-molecular h-bonds in ptraj Jianyin Shao (Thu Jan 04 2007 - 12:11:36 PST)
AMBER: enzyme kinetics in silico Sean Rathlef (Thu Jan 04 2007 - 09:24:46 PST)
- Re: AMBER: enzyme kinetics in silico Suxin Zheng (Thu Jan 04 2007 - 09:54:47 PST)
  - RE: AMBER: enzyme kinetics in silico Xu, Yong (Tue Apr 03 2007 - 12:26:45 PDT)
- Re: AMBER: enzyme kinetics in silico Fenghui Fan (Thu Jan 04 2007 - 13:34:41 PST)
- Re: AMBER: enzyme kinetics in silico Sean Rathlef (Tue Apr 03 2007 - 14:08:10 PDT)
Fwd: AMBER: Atoms overlapping Nitin Bhardwaj (Thu Jan 04 2007 - 16:58:26 PST)
Re : AMBER: intra-molecular h-bonds in ptraj lily ferreira (Fri Jan 05 2007 - 05:37:52 PST)
- Re: Re : AMBER: intra-molecular h-bonds in ptraj Esther Brugger (Fri Jan 05 2007 - 07:11:43 PST)
- Re: Re : AMBER: intra-molecular h-bonds in ptraj Thomas Cheatham (Sun Jan 07 2007 - 20:51:29 PST)
Re: AMBER: 22 improper torsions in old prep form Bill Ross (Fri Jan 05 2007 - 10:39:23 PST)
AMBER: How to change the force field equation in amber by programming... Gobind Singh Bisht (Fri Jan 05 2007 - 11:55:22 PST)
- Re: AMBER: How to change the force field equation in amber by programming... David A. Case (Fri Jan 05 2007 - 13:34:41 PST)
  - Re: AMBER: How to change the force field equation in amber by programming... Gobind Singh Bisht (Sun Jan 07 2007 - 06:06:06 PST)
    - Re: AMBER: How to change the force field equation in amber by programming... David A. Case (Mon Jan 08 2007 - 15:00:10 PST)
  - AMBER: unsubscribe Perdita Barran (Sun Jan 07 2007 - 10:13:40 PST)
AMBER: Hydrogen in a phosphate ion Nitin Bhardwaj (Fri Jan 05 2007 - 14:00:09 PST)
- Re: AMBER: Hydrogen in a phosphate ion David A. Case (Tue Jan 09 2007 - 11:46:43 PST)
AMBER: Simulation of a charged system Kijeong Kwac (Fri Jan 05 2007 - 15:08:42 PST)
- Re: AMBER: Simulation of a charged system Carlos Simmerling (Fri Jan 05 2007 - 15:41:02 PST)
AMBER: question about the testing of AMBER9 Shaoqing.Zhang.mail.uh.edu (Fri Jan 05 2007 - 18:25:16 PST)
- Re: AMBER: question about the testing of AMBER9 David A. Case (Fri Jan 05 2007 - 20:54:53 PST)
  - Re: AMBER: question about the testing of AMBER9 Shaoqing.Zhang.mail.uh.edu (Sat Jan 06 2007 - 15:07:04 PST)
    - RE: AMBER: question about the testing of AMBER9 Ross Walker (Sat Jan 06 2007 - 15:37:06 PST)
    - Re: RE: AMBER: question about the testing of AMBER9 Shaoqing.Zhang.mail.uh.edu (Sun Jan 07 2007 - 13:25:39 PST)
    - Re: AMBER: question about the testing of AMBER9 Mark Williamson (Sun Jan 07 2007 - 15:36:28 PST)
    - Re: AMBER: question about the testing of AMBER9 Shaoqing.Zhang.mail.uh.edu (Sun Jan 07 2007 - 17:18:05 PST)
    - Re: AMBER: question about the testing of AMBER9 Mark Williamson (Mon Jan 08 2007 - 01:36:55 PST)
    - Re: AMBER: question about the testing of AMBER9 Shaoqing.Zhang.mail.uh.edu (Mon Jan 08 2007 - 09:06:18 PST)
    - RE: AMBER: question about the testing of AMBER9 Ross Walker (Mon Jan 08 2007 - 11:52:55 PST)
    - Re: AMBER: question about the testing of AMBER9 Mark Williamson (Mon Jan 08 2007 - 13:10:53 PST)
    - Re: AMBER: question about the testing of AMBER9 Shaoqing.Zhang.mail.uh.edu (Mon Jan 08 2007 - 13:56:44 PST)
    - Re: AMBER: question about the testing of AMBER9 Andreas Svrcek-Seiler (Mon Jan 08 2007 - 03:15:58 PST)
- RE: AMBER: question about the testing of AMBER9 Bill Ross (Mon Jan 08 2007 - 12:05:19 PST)
AMBER: entropy units Giulio Rastelli (Mon Jan 08 2007 - 02:33:19 PST)
AMBER: How to do minimization.. sai vikram (Mon Jan 08 2007 - 07:30:59 PST)
- RE: AMBER: How to do minimization.. Ross Walker (Mon Jan 08 2007 - 08:32:09 PST)
AMBER: improper torsions Ed Pate (Mon Jan 08 2007 - 11:08:36 PST)
- Re: AMBER: improper torsions Fenghui Fan (Mon Jan 08 2007 - 11:45:09 PST)
Re: AMBER: improper torsions Bill Ross (Mon Jan 08 2007 - 12:00:06 PST)
AMBER: How many steps should be used for a MD calculation? Michel Becker (Tue Jan 09 2007 - 01:12:55 PST)
AMBER: image command venditti2.unisi.it (Tue Jan 09 2007 - 06:09:07 PST)
- Re: AMBER: image command Thomas Cheatham (Tue Jan 09 2007 - 22:25:48 PST)
  - Re: AMBER: image command Petr Kulhanek (Wed Jan 10 2007 - 00:45:45 PST)
AMBER: amber 9 Sophie Barbe (Tue Jan 09 2007 - 07:29:04 PST)
- RE: AMBER: amber 9 Ross Walker (Tue Jan 09 2007 - 08:31:36 PST)
  - RE: AMBER: amber 9 Sophie Barbe (Wed Jan 10 2007 - 09:54:36 PST)
    - RE: AMBER: amber 9 Ross Walker (Wed Jan 10 2007 - 10:11:44 PST)
    - RE: AMBER: amber 9 Sophie Barbe (Wed Jan 10 2007 - 10:28:51 PST)
    - Re: AMBER: amber 9 Chris Moth (Thu Jan 11 2007 - 11:43:27 PST)
    - Re: AMBER: amber 9 David A. Case (Thu Jan 11 2007 - 11:21:09 PST)
AMBER: explicit implicit solvent Ji-Lai Li (Wed Jan 10 2007 - 06:24:20 PST)
- Re: AMBER: explicit implicit solvent Carlos Simmerling (Wed Jan 10 2007 - 06:53:53 PST)
AMBER: experimental phi-values as restraints rebeca.mmb.pcb.ub.es (Wed Jan 10 2007 - 08:06:11 PST)
- Re: AMBER: experimental phi-values as restraints Vladimir Tchoupakhine (Wed Jan 10 2007 - 08:23:58 PST)
AMBER: Steve Seibold (Wed Jan 10 2007 - 08:46:28 PST)
- Re: AMBER: Vladimir Tchoupakhine (Wed Jan 10 2007 - 08:51:46 PST)
- RE: AMBER: Ross Walker (Wed Jan 10 2007 - 09:17:11 PST)
  - RE: AMBER: Steve Seibold (Wed Jan 10 2007 - 11:03:30 PST)
AMBER: Section missing from AMBER 9 manual? Steven Winfield (Wed Jan 10 2007 - 08:57:36 PST)
- Re: AMBER: Section missing from AMBER 9 manual? David A. Case (Wed Jan 10 2007 - 13:02:12 PST)
AMBER: test submission through PBS queue Evan Kelly (Wed Jan 10 2007 - 11:20:45 PST)
- Re: AMBER: test submission through PBS queue Scott Brozell (Wed Jan 10 2007 - 11:33:09 PST)
- RE: AMBER: test submission through PBS queue Ross Walker (Wed Jan 10 2007 - 11:35:27 PST)
AMBER: sander crashes during minimization Seth Lilavivat (Wed Jan 10 2007 - 11:29:15 PST)
- RE: AMBER: sander crashes during minimization Ross Walker (Wed Jan 10 2007 - 11:40:05 PST)
AMBER: perturbed atoms are not bonded on using TIP5P water sugino tatsuro (Thu Jan 11 2007 - 06:12:09 PST)
- Re: AMBER: perturbed atoms are not bonded on using TIP5P water David A. Case (Thu Jan 11 2007 - 14:12:23 PST)
  - RE: AMBER: perturbed atoms are not bonded on using TIP5P water sugino tatsuro (Fri Jan 12 2007 - 05:58:40 PST)
    - Re: AMBER: perturbed atoms are not bonded on using TIP5P water Steven Winfield (Fri Jan 12 2007 - 06:07:38 PST)
    - Re: AMBER: perturbed atoms are not bonded on using TIP5P water David A. Case (Sun Jan 14 2007 - 09:39:13 PST)
- Re: AMBER: perturbed atoms are not bonded on using TIP5P water sugino tatsuro (Mon Jan 15 2007 - 17:40:32 PST)
  - Re: AMBER: perturbed atoms are not bonded on using TIP5P water David A. Case (Mon Jan 15 2007 - 18:23:17 PST)
    - RE: AMBER: perturbed atoms are not bonded on using TIP5P water sugino tatsuro (Mon Jan 15 2007 - 19:33:18 PST)
- Re: AMBER: perturbed atoms are not bonded on using TIP5P water sugino tatsuro (Mon Jan 15 2007 - 19:19:59 PST)
- RE: AMBER: perturbed atoms are not bonded on using TIP5P water sugino tatsuro (Tue Jan 16 2007 - 09:35:22 PST)
AMBER: Simulations with GB models Wei Chen (Thu Jan 11 2007 - 08:23:15 PST)
- Re: AMBER: Simulations with GB models Carlos Simmerling (Thu Jan 11 2007 - 10:28:16 PST)
AMBER: Leap adding 3 extra atoms Akshay Patny (Thu Jan 11 2007 - 09:35:00 PST)
AMBER: CYX residue missing from Amber 9 ff03ua (?) Chris Moth (Thu Jan 11 2007 - 11:32:04 PST)
- RE: AMBER: CYX residue missing from Amber 9 ff03ua (?) Ray Luo (Thu Jan 11 2007 - 14:59:29 PST)
Re: AMBER: Leap adding 3 extra atoms Bill Ross (Thu Jan 11 2007 - 11:33:14 PST)
- RE: AMBER: Leap adding extra atoms Akshay Patny (Thu Jan 11 2007 - 13:38:37 PST)
  - RE: AMBER: Leap adding extra atoms Scott Brozell (Mon Jan 15 2007 - 12:39:49 PST)
  - RE: AMBER: Leap adding extra atoms Scott Brozell (Mon Jan 15 2007 - 13:30:00 PST)
AMBER: Amber 8.0 : how to represent EPS with VMD? Guillaume Bollot (Fri Jan 12 2007 - 06:49:28 PST)
AMBER: solvation of protein using TIP3PBOX in amber 8 Syed Tarique Moin (Sat Jan 13 2007 - 10:25:46 PST)
- Re: AMBER: solvation of protein using TIP3PBOX in amber 8 David A. Case (Sat Jan 13 2007 - 21:40:46 PST)
  - Re: AMBER: solvation of protein using TIP3PBOX in amber 8 Syed Tarique Moin (Sun Jan 14 2007 - 01:59:32 PST)
AMBER: output khn _ (Sat Jan 13 2007 - 20:24:11 PST)
- Re: AMBER: output David A. Case (Sat Jan 13 2007 - 21:38:24 PST)
- Re: AMBER: output Thaison Tran (Sat Jan 13 2007 - 23:59:56 PST)
AMBER: problems in energy minimization using TIP5P water model sugino tatsuro (Sun Jan 14 2007 - 08:35:11 PST)
AMBER: problem compiling Amber 7 Kevin Cahill (Sun Jan 14 2007 - 18:35:00 PST)
- Re: AMBER: problem compiling Amber 7 Scott Brozell (Mon Jan 15 2007 - 09:29:10 PST)
- Re: AMBER: problem compiling Amber 7 David A. Case (Mon Jan 15 2007 - 09:38:26 PST)
AMBER: About the problem of the PMEMD and cutoff 方磊 (Sun Jan 14 2007 - 19:56:17 PST)
- Re: AMBER: About the problem of the PMEMD and cutoff Robert Duke (Sun Jan 14 2007 - 20:20:22 PST)
  - Re: AMBER: About the problem of the PMEMD and cutoff 方磊 (Mon Jan 15 2007 - 04:45:29 PST)
- Re: AMBER: About the problem of the PMEMD and cutoff Robert Duke (Mon Jan 15 2007 - 05:19:26 PST)
Fwd: Re: AMBER: solvation of protein using TIP3PBOX in amber 8 Syed Tarique Moin (Mon Jan 15 2007 - 21:14:12 PST)
AMBER: convert pdb files to restart files khn _ (Tue Jan 16 2007 - 02:50:47 PST)
- Re: AMBER: convert pdb files to restart files Stefano Pieraccini (Tue Jan 16 2007 - 04:57:41 PST)
- RE: AMBER: convert pdb files to restart files Ross Walker (Tue Jan 16 2007 - 07:19:54 PST)
AMBER: mm_pbsa_statistics.pl Antonio Morreale (Tue Jan 16 2007 - 04:28:52 PST)
AMBER: RE: help Ross Walker (Tue Jan 16 2007 - 08:23:44 PST)
AMBER: Radii for water hydrogens are different Steve Spronk (Tue Jan 16 2007 - 12:29:45 PST)
- Re: AMBER: Radii for water hydrogens are different David A. Case (Fri Jan 19 2007 - 10:13:41 PST)
AMBER: RESP charges for charged species Michel Becker (Tue Jan 16 2007 - 13:44:26 PST)
- Re: AMBER: RESP charges for charged species FyD (Tue Jan 16 2007 - 21:13:51 PST)
AMBER: How are water molecules at cutoff being treated? Li Su (Tue Jan 16 2007 - 14:48:47 PST)
- Re: AMBER: How are water molecules at cutoff being treated? David A. Case (Tue Jan 16 2007 - 15:36:07 PST)
AMBER: mm_pbsa vertex atom mismatch AYTUG TUNCEL (Tue Jan 16 2007 - 15:10:35 PST)
AMBER: calcium parameter for GB Wei Chen (Tue Jan 16 2007 - 15:21:08 PST)
- Re: AMBER: calcium parameter for GB David A. Case (Tue Jan 16 2007 - 15:33:43 PST)
  - Re: AMBER: calcium parameter for GB Ji-Lai Li (Wed Jan 17 2007 - 00:19:09 PST)
    - Re: AMBER: calcium parameter for GB Wei Chen (Wed Jan 17 2007 - 08:25:47 PST)
- Re: AMBER: calcium parameter for GB Qing Zhang (Wed Jan 17 2007 - 09:06:36 PST)
  - Re: AMBER: calcium parameter for GB Ji-Lai Li (Wed Jan 17 2007 - 17:25:20 PST)
    - Re: AMBER: calcium parameter for GB Wei Chen (Thu Jan 18 2007 - 08:15:45 PST)
- Re: AMBER: calcium parameter for GB Bill Ross (Thu Jan 18 2007 - 10:36:01 PST)
- Re: AMBER: calcium parameter for GB Qing Zhang (Tue Jan 23 2007 - 10:49:54 PST)
  - Re: AMBER: calcium parameter for GB Ji-Lai Li (Tue Jan 23 2007 - 18:07:21 PST)
- Re: AMBER: calcium parameter for GB Qing Zhang (Wed Jan 24 2007 - 09:33:24 PST)
AMBER: DNA structure analysis Catein Catherine (Tue Jan 16 2007 - 19:12:42 PST)
- Re: AMBER: DNA structure analysis Jiri Sponer (Wed Jan 17 2007 - 02:39:36 PST)
  - Re: AMBER: DNA structure analysis Catein Catherine (Wed Jan 17 2007 - 08:23:08 PST)
- Re: AMBER: DNA structure analysis Fenghui Fan (Wed Jan 17 2007 - 07:31:00 PST)
  - Re: AMBER: DNA structure analysis Catein Catherine (Wed Jan 17 2007 - 08:24:16 PST)
RE: AMBER: perturbed atoms are not bonded on using TIP5P wate sugino tatsuro (Tue Jan 16 2007 - 21:47:51 PST)
- Re: AMBER: perturbed atoms are not bonded on using TIP5P wate David A. Case (Thu Jan 18 2007 - 09:40:37 PST)
AMBER: Drug bound to the protein Sophie Barbe (Wed Jan 17 2007 - 00:56:21 PST)
- Re: AMBER: Drug bound to the protein Guillermo Mulliert Carlín (Wed Jan 17 2007 - 07:27:45 PST)
- Re: AMBER: Drug bound to the protein David A. Case (Wed Jan 17 2007 - 08:57:02 PST)
AMBER: solaris 10 and compilers on X86_64 hardware M. L. Dodson (Wed Jan 17 2007 - 07:45:27 PST)
- Re: AMBER: solaris 10 and compilers on X86_64 hardware Knut Langsetmo (Wed Jan 17 2007 - 08:03:33 PST)
AMBER: vdW parameters for chlorine atom Austin B. Yongye (Wed Jan 17 2007 - 09:19:34 PST)
- Re: AMBER: vdW parameters for chlorine atom David A. Case (Wed Jan 17 2007 - 17:55:15 PST)
AMBER: (no subject) Yusheng Dou (Wed Jan 17 2007 - 09:29:10 PST)
Re: AMBER: Drug bound to the protein Bill Ross (Wed Jan 17 2007 - 11:28:15 PST)
AMBER: vertex atom mismatch saurabh agrawal (Wed Jan 17 2007 - 23:49:25 PST)
- AMBER: WARNING: Missing VDWNB for MM in 1 -> Taken from 0 saurabh agrawal (Thu Jan 18 2007 - 09:15:40 PST)
AMBER: (no subject) mahdi fathi (Thu Jan 18 2007 - 02:10:24 PST)
AMBER: sanger deepti nayar (Thu Jan 18 2007 - 03:29:19 PST)
- Re: AMBER: sanger Chupakhin Vladimir (Thu Jan 18 2007 - 06:05:01 PST)
  - Re: AMBER: sanger Carlos Simmerling (Thu Jan 18 2007 - 06:09:31 PST)
- Re: AMBER: sanger David A. Case (Thu Jan 18 2007 - 09:05:34 PST)
AMBER: issues with restrt file Amit Kumar (Thu Jan 18 2007 - 08:15:52 PST)
- Re: AMBER: issues with restrt file Carlos Simmerling (Thu Jan 18 2007 - 09:07:35 PST)
  - Re: AMBER: issues with restrt file Amit Kumar (Thu Jan 18 2007 - 09:59:40 PST)
    - Re: AMBER: issues with restrt file Carlos Simmerling (Thu Jan 18 2007 - 10:02:48 PST)
    - Re: AMBER: issues with restrt file Amit Kumar (Thu Jan 18 2007 - 10:27:12 PST)
    - Re: AMBER: issues with restrt file Carlos Simmerling (Thu Jan 18 2007 - 10:30:01 PST)
AMBER: error when using sander.LES: exceeded MAXLES Kailee (Thu Jan 18 2007 - 08:33:18 PST)
- Re: AMBER: error when using sander.LES: exceeded MAXLES Carlos Simmerling (Thu Jan 18 2007 - 09:03:08 PST)
- Re: AMBER: error when using sander.LES: exceeded MAXLES David A. Case (Thu Jan 18 2007 - 09:12:23 PST)
AMBER: mm-pbsa, long distance free energy calculation problem Bing Liu (Thu Jan 18 2007 - 09:06:53 PST)
- Re: AMBER: mm-pbsa, long distance free energy calculation problem Wei Chen (Thu Jan 18 2007 - 12:24:26 PST)
  - Re: AMBER: mm-pbsa, long distance free energy calculation problem Bing Liu (Thu Jan 18 2007 - 13:09:38 PST)
AMBER: HF/6-31G* ESP Charges do not match with ff02 charges Pavan G (Thu Jan 18 2007 - 22:19:19 PST)
- Re: AMBER: HF/6-31G* ESP Charges do not match with ff02 charges mernst.tricity.wsu.edu (Thu Jan 18 2007 - 23:02:10 PST)
  - Re: AMBER: HF/6-31G* ESP Charges do not match with ff02 charges FyD (Fri Jan 19 2007 - 00:31:46 PST)
- Re: AMBER: HF/6-31G* ESP Charges do not match with ff02 charges mernst.tricity.wsu.edu (Fri Jan 19 2007 - 10:59:52 PST)
  - Re: AMBER: HF/6-31G* ESP Charges do not match with ff02 charges FyD (Fri Jan 19 2007 - 12:30:43 PST)
  - Re: AMBER: HF/6-31G* ESP Charges do not match with ff02 charges Pavan G (Sun Jan 28 2007 - 07:45:32 PST)
AMBER: RESP Charges for Charged Carboxylate in Organic Ligand Akshay Patny (Fri Jan 19 2007 - 00:34:58 PST)
- Re: AMBER: RESP Charges for Charged Carboxylate in Organic Ligand FyD (Fri Jan 19 2007 - 05:19:17 PST)
  - AMBER: Dihedral FF parameters FyD (Fri Jan 19 2007 - 07:40:10 PST)
    - Re: AMBER: Dihedral FF parameters Ye Mei (Fri Jan 19 2007 - 07:44:14 PST)
- RE: AMBER: RESP Charges for Charged Carboxylate in Organic Ligand Akshay Patny (Mon Jan 29 2007 - 08:57:45 PST)
AMBER: The convergence criteria for the energy minimization of the DNA molecule (dodecmer duplux) Chengwen Chen (Fri Jan 19 2007 - 01:37:53 PST)
- Re: AMBER: The convergence criteria for the energy minimization of the DNA molecule (dodecmer duplux) David A. Case (Fri Jan 19 2007 - 08:36:34 PST)
  - Re: AMBER: The convergence criteria for the energy minimization of the DNA molecule (dodecmer duplux) Chengwen Chen (Sat Jan 20 2007 - 19:55:46 PST)
AMBER: PB Bomb in pb_aaradi(): No radius assigned for atom 4474 F3 f emilia wu (Fri Jan 19 2007 - 05:15:56 PST)
- RE: AMBER: PB Bomb in pb_aaradi(): No radius assigned for atom 4474 F3 f Ray Luo (Fri Jan 19 2007 - 09:50:19 PST)
  - Re: RE: AMBER: PB Bomb in pb_aaradi(): No radius assigned for atom 4474 F3 f emilia wu (Fri Jan 19 2007 - 17:54:27 PST)
    - RE: RE: AMBER: PB Bomb in pb_aaradi(): No radius assigned for atom 4474 F3 f Ray Luo (Sat Jan 20 2007 - 10:45:36 PST)
    - Re: RE: RE: AMBER: PB Bomb in pb_aaradi(): No radius assigned for atom 4474 F3 f emilia wu (Sun Jan 21 2007 - 17:42:18 PST)
    - Re: RE: RE: AMBER: PB Bomb in pb_aaradi(): No radius assigned for atom 4474 F3 f emilia wu (Mon Jan 22 2007 - 16:22:39 PST)
    - RE: RE: RE: AMBER: PB Bomb in pb_aaradi(): No radius assigned for atom 4474 F3 f Ray Luo (Mon Jan 22 2007 - 18:35:06 PST)
    - Re: RE: RE: RE: AMBER: PB Bomb in pb_aaradi(): No radius assigned for atom 4474 F3 f emilia wu (Mon Jan 22 2007 - 18:45:46 PST)
    - RE: AMBER: PB Bomb in pb_aaradi(): No radius assigned for atom 4474 F3 f Ray Luo (Tue Jan 23 2007 - 10:43:23 PST)
    - Re: AMBER: PB Bomb in pb_aaradi(): No radius assigned for atom 4474 F3 f David A. Case (Wed Jan 24 2007 - 07:14:24 PST)
AMBER: (no subject) Yusheng Dou (Fri Jan 19 2007 - 06:51:51 PST)
AMBER: Steve Seibold (Fri Jan 19 2007 - 11:53:47 PST)
- RE: AMBER: Ross Walker (Fri Jan 19 2007 - 12:47:24 PST)
AMBER: equilibration with amber5, production of MD with amber7 Carlos Javier Nuñez Aguero (Fri Jan 19 2007 - 12:47:05 PST)
- Re: AMBER: equilibration with amber5, production of MD with amber7 David A. Case (Sun Jan 21 2007 - 21:28:46 PST)
AMBER: a question about analysis of DNA duplex after MD simulation with curves wendy chen (Sat Jan 20 2007 - 19:28:19 PST)
AMBER: deformation of DNA duplex after MD simulation (AMBER9) Chengwen Chen (Sat Jan 20 2007 - 20:28:59 PST)
AMBER: Can't run Normal Mode Analysis !!! jitrayut jitonnom (Sun Jan 21 2007 - 21:09:48 PST)
- Fwd: AMBER: Can't run Normal Mode Analysis !!! jitrayut jitonnom (Mon Jan 22 2007 - 04:58:24 PST)
- Re: AMBER: Can't run Normal Mode Analysis !!! Scott Pendley (Mon Jan 22 2007 - 09:05:26 PST)
AMBER: MM-PBSA problem: Why jitrayut jitonnom (Sun Jan 21 2007 - 21:20:38 PST)
- Re: AMBER: MM-PBSA problem: Why vanessa wai (Mon Jan 22 2007 - 02:47:30 PST)
AMBER: Can't run decompose energy in MM-PBSA jitrayut jitonnom (Mon Jan 22 2007 - 06:20:51 PST)
- RE: AMBER: Can't run decompose energy in MM-PBSA Ray Luo (Mon Jan 22 2007 - 09:27:03 PST)
  - Re: AMBER: Can't run decompose energy in MM-PBSA vanessa wai (Mon Jan 22 2007 - 17:37:02 PST)
AMBER: problem with distance restraints Ed Pate (Mon Jan 22 2007 - 11:43:58 PST)
- Re: AMBER: problem with distance restraints David A. Case (Mon Jan 22 2007 - 12:10:12 PST)
  - Re: AMBER: problem with distance restraints Ed Pate (Mon Jan 22 2007 - 14:29:15 PST)
    - Re: AMBER: problem with distance restraints David A. Case (Mon Jan 22 2007 - 15:41:50 PST)
AMBER: united atom parameters for -NH2 and -OH groups emine cebe (Mon Jan 22 2007 - 11:47:12 PST)
AMBER: how much restraint ? AYTUG TUNCEL (Mon Jan 22 2007 - 14:09:12 PST)
AMBER: ADDIONS do not neutralize to ZERO Akshay Patny (Mon Jan 22 2007 - 17:19:20 PST)
- RE: AMBER: ADDIONS do not neutralize to ZERO Akshay Patny (Mon Jan 22 2007 - 18:10:47 PST)
- RE: AMBER: ADDIONS do not neutralize to ZERO Bill Ross (Tue Jan 23 2007 - 09:30:06 PST)
- RE: AMBER: ADDIONS do not neutralize to ZERO Akshay Patny (Fri Jan 26 2007 - 15:38:48 PST)
  - RE: AMBER: ADDIONS do not neutralize to ZERO Ross Walker (Sun Jan 28 2007 - 20:38:25 PST)
    - RE: AMBER: ADDIONS do not neutralize to ZERO Akshay Patny (Mon Jan 29 2007 - 09:04:58 PST)
    - Re: AMBER: ADDIONS do not neutralize to ZERO Chris Moth (Mon Jan 29 2007 - 13:30:20 PST)
- RE: AMBER: ADDIONS do not neutralize to ZERO Bill Ross (Sun Jan 28 2007 - 12:41:43 PST)
  - RE: AMBER: ADDIONS do not neutralize to ZERO saurabh agrawal (Sun Jan 28 2007 - 20:07:37 PST)
Re: AMBER: ADDIONS do not neutralize to ZERO Bill Ross (Mon Jan 22 2007 - 17:58:11 PST)
AMBER: Defining BOX INFO during TLEAP Akshay Patny (Mon Jan 22 2007 - 19:02:15 PST)
- Re: AMBER: Defining BOX INFO during TLEAP David A. Case (Wed Jan 24 2007 - 07:04:24 PST)
- RE: AMBER: Defining BOX INFO during TLEAP Akshay Patny (Wed Jan 24 2007 - 11:54:37 PST)
  - RE: AMBER: Defining BOX INFO during TLEAP Ross Walker (Wed Jan 24 2007 - 12:09:30 PST)
AMBER: Antechamber esp calculation mathew k varghese (Mon Jan 22 2007 - 20:44:42 PST)
- Re: AMBER: Antechamber esp calculation Ilyas Yildirim (Mon Jan 22 2007 - 22:07:31 PST)
- Re: AMBER: Antechamber esp calculation FyD (Mon Jan 22 2007 - 22:05:46 PST)
AMBER: pmemd install error Ji-Lai Li (Mon Jan 22 2007 - 22:59:27 PST)
- AMBER: Re: pmemd install error Ji-Lai Li (Mon Jan 22 2007 - 23:03:33 PST)
- Re: AMBER: pmemd install error Robert Duke (Tue Jan 23 2007 - 05:01:46 PST)
  - Re: AMBER: pmemd install error David A. Case (Fri Jan 26 2007 - 15:45:14 PST)
    - Re: AMBER: pmemd install error Ji-Lai Li (Sun Jan 28 2007 - 19:18:05 PST)
- Re: AMBER: pmemd install error Robert Duke (Tue Jan 30 2007 - 12:24:19 PST)
AMBER: nuc.in file deepti nayar (Tue Jan 23 2007 - 00:21:27 PST)
- Re: AMBER: nuc.in file David A. Case (Thu Jan 25 2007 - 11:59:12 PST)
AMBER: Fatal error: Command failed for target `test.sander.no_lmod' Muhammad Naim Mohmad Rouyan (Tue Jan 23 2007 - 01:50:58 PST)
- Re: AMBER: Fatal error: Command failed for target `test.sander.no_lmod' Gustavo Seabra (Tue Jan 23 2007 - 08:54:09 PST)
AMBER: Molecular dynamic issues Sophie Barbe (Tue Jan 23 2007 - 06:34:50 PST)
- Re: AMBER: Molecular dynamic issues Chupakhin Vladimir (Tue Jan 23 2007 - 06:50:56 PST)
  - Re: AMBER: Molecular dynamic issues Carlos Simmerling (Tue Jan 23 2007 - 06:54:24 PST)
    - Re: AMBER: Molecular dynamic issues Sophie Barbe (Wed Jan 24 2007 - 06:41:19 PST)
AMBER: coordinates ****** kepa koldo burusco (Tue Jan 23 2007 - 08:19:54 PST)
- Re: AMBER: coordinates ****** David A. Case (Thu Jan 25 2007 - 12:08:52 PST)
  - AMBER: about coordinates ****** and diffusion kepa koldo burusco (Sun Jan 28 2007 - 09:15:57 PST)
    - RE: AMBER: about coordinates ****** and diffusion Ross Walker (Sun Jan 28 2007 - 09:28:30 PST)
    - Re: AMBER: about coordinates ****** and diffusion Thomas Cheatham (Sun Jan 28 2007 - 13:09:00 PST)
Re: AMBER: nuc.in file Bill Ross (Tue Jan 23 2007 - 09:42:44 PST)
AMBER: dihedral angle by Ptraj Esther Brugger (Tue Jan 23 2007 - 10:24:42 PST)
- Re: AMBER: dihedral angle by Ptraj Thomas Cheatham III (Tue Jan 23 2007 - 10:41:22 PST)
  - Re: AMBER: dihedral angle by Ptraj Esther Brugger (Tue Jan 23 2007 - 15:02:00 PST)
    - Re: AMBER: dihedral angle by Ptraj Thomas Cheatham (Tue Jan 23 2007 - 19:57:47 PST)
    - Re: AMBER: dihedral angle by Ptraj Esther Brugger (Wed Jan 24 2007 - 08:02:38 PST)
    - Re: AMBER: dihedral angle by Ptraj Esther Brugger (Wed Jan 24 2007 - 09:08:15 PST)
Re: AMBER: coordinates ****** Bill Ross (Tue Jan 23 2007 - 13:20:10 PST)
AMBER: Does amber use water density around 1 at room temperature Li Su (Tue Jan 23 2007 - 14:07:20 PST)
- RE: AMBER: Does amber use water density around 1 at room temperature Ross Walker (Tue Jan 23 2007 - 15:11:41 PST)
  - Re: AMBER: Does amber use water density around 1 at room temperature Li Su (Wed Jan 24 2007 - 14:44:40 PST)
    - Re: AMBER: Does amber use water density around 1 at room temperature Thomas Steinbrecher (Wed Jan 24 2007 - 15:26:50 PST)
    - AMBER: mm_pbsa error Syed Tarique Moin (Wed Jan 24 2007 - 23:15:29 PST)
    - Re: AMBER: mm_pbsa error vanessa wai (Wed Jan 24 2007 - 23:24:43 PST)
    - Re: AMBER: mm_pbsa error Syed Tarique Moin (Thu Jan 25 2007 - 02:04:36 PST)
    - Re: AMBER: mm_pbsa error Varsha Goyal (Thu Jan 25 2007 - 08:16:31 PST)
    - Re: AMBER: mm_pbsa error vanessa wai (Thu Jan 25 2007 - 18:13:19 PST)
    - Re: AMBER: mm_pbsa error Syed Tarique Moin (Thu Jan 25 2007 - 22:04:22 PST)
    - Re: AMBER: mm_pbsa error vanessa wai (Sat Jan 27 2007 - 07:02:33 PST)
    - AMBER: mm_pbsa Array reference error Syed Tarique Moin (Thu Jan 25 2007 - 22:21:07 PST)
AMBER: Fatal error: Command failed for target `test.sander.no_lmod' Muhammad Naim Mohmad Rouyan (Tue Jan 23 2007 - 17:26:45 PST)
AMBER: minimization using fcap Syed Tarique Moin (Wed Jan 24 2007 - 01:08:40 PST)
- Re: AMBER: minimization using fcap David A. Case (Wed Jan 24 2007 - 07:05:20 PST)
AMBER: MM-PSBA decoupling Sergey Samsonov (Wed Jan 24 2007 - 05:03:24 PST)
AMBER: Unable to compile amber9 Vinh To (Wed Jan 24 2007 - 06:41:06 PST)
- RE: AMBER: Unable to compile amber9 Ross Walker (Wed Jan 24 2007 - 07:48:41 PST)
AMBER: (no subject) Sophie Barbe (Wed Jan 24 2007 - 09:26:20 PST)
AMBER: organic solvent : hexan octan Sophie Barbe (Wed Jan 24 2007 - 09:38:50 PST)
- Re: AMBER: organic solvent : hexan octan Cenk Andac (Wed Jan 24 2007 - 10:18:19 PST)
  - Re: AMBER: organic solvent : hexan octan Sophie Barbe (Wed Jan 24 2007 - 10:28:38 PST)
    - Re: AMBER: organic solvent : hexan octan Gustavo Seabra (Wed Jan 24 2007 - 11:12:40 PST)
    - Re: AMBER: organic solvent : hexan octan Cenk Andac (Wed Jan 24 2007 - 11:37:12 PST)
- Re: AMBER: organic solvent : hexan octan FyD (Wed Jan 24 2007 - 20:50:33 PST)
AMBER: RE: a request Ross Walker (Wed Jan 24 2007 - 09:57:32 PST)
AMBER: LJ potential Steve Seibold (Wed Jan 24 2007 - 11:44:58 PST)
- Re: AMBER: LJ potential David A. Case (Sat Jan 27 2007 - 10:03:15 PST)
AMBER: evaluate expression Ji-Lai Li (Wed Jan 24 2007 - 20:14:11 PST)
AMBER: Drug Leads interaction with ds and Triplex DNA puneet kacker (Wed Jan 24 2007 - 21:28:41 PST)
AMBER: Fwd: a request santanu roy (Thu Jan 25 2007 - 00:55:32 PST)
- Re: AMBER: Fwd: a request Gustavo Seabra (Thu Jan 25 2007 - 04:44:58 PST)
  - Re: AMBER: Fwd: a request santanu roy (Thu Jan 25 2007 - 05:15:08 PST)
    - Re: AMBER: Fwd: a request Gustavo Seabra (Thu Jan 25 2007 - 07:49:49 PST)
    - Re: AMBER: Fwd: a request santanu roy (Fri Jan 26 2007 - 22:34:15 PST)
    - Re: AMBER: Fwd: a request Gustavo Seabra (Sat Jan 27 2007 - 20:52:08 PST)
    - Re: AMBER: Fwd: a request santanu roy (Sun Jan 28 2007 - 22:43:53 PST)
    - Re: AMBER: Fwd: a request Gustavo Seabra (Mon Jan 29 2007 - 09:24:12 PST)
    - Re: AMBER: Fwd: a request santanu roy (Tue Jan 30 2007 - 02:04:46 PST)
    - Re: AMBER: Fwd: a request Gustavo Seabra (Tue Jan 30 2007 - 07:53:33 PST)
    - AMBER: Including Relevant Subject Lines Ross Walker (Tue Jan 30 2007 - 08:43:59 PST)
AMBER: error when compiling Moilview Kailee (Thu Jan 25 2007 - 03:31:24 PST)
- Re: AMBER: error when compiling Moilview Carlos Simmerling (Thu Jan 25 2007 - 04:24:53 PST)
  - Re: AMBER: error when compiling Moilview Kailee (Thu Jan 25 2007 - 05:03:07 PST)
    - Re: AMBER: error when compiling Moilview Gustavo Seabra (Thu Jan 25 2007 - 07:50:57 PST)
    - Re: AMBER: error when compiling Moilview Kailee (Thu Jan 25 2007 - 08:12:09 PST)
    - Re: AMBER: error when compiling Moilview Carlos Simmerling (Thu Jan 25 2007 - 09:34:26 PST)
AMBER: Gas-phase energies (and more) Jason K (Thu Jan 25 2007 - 15:04:16 PST)
- RE: AMBER: Gas-phase energies (and more) Yong Duan (Thu Jan 25 2007 - 15:58:48 PST)
  - Re: AMBER: Gas-phase energies (and more) Jason K (Fri Jan 26 2007 - 13:36:25 PST)
    - Re: AMBER: Gas-phase energies (and more) Carlos Simmerling (Sun Jan 28 2007 - 10:48:13 PST)
    - Re: AMBER: Gas-phase energies (and more) David A. Case (Sun Jan 28 2007 - 18:23:29 PST)
    - RE: AMBER: Gas-phase energies (and more) Yong Duan (Sun Jan 28 2007 - 19:43:56 PST)
- RE: AMBER: Gas-phase energies (and more) Yong Duan (Tue Jan 30 2007 - 12:32:39 PST)
AMBER: sander bug? Nursultan Bogatov (Thu Jan 25 2007 - 18:28:53 PST)
- RE: AMBER: sander bug? Ross Walker (Thu Jan 25 2007 - 23:26:55 PST)
AMBER: another sander bug? Nursultan Bogatov (Thu Jan 25 2007 - 22:43:13 PST)
- RE: AMBER: another sander bug? Ross Walker (Thu Jan 25 2007 - 23:50:39 PST)
AMBER: improper dihedral lishan yao (Fri Jan 26 2007 - 06:42:15 PST)
- Re: AMBER: improper dihedral David A. Case (Fri Jan 26 2007 - 08:09:55 PST)
AMBER: Regarding energy of decomposition tutorials zachary hartman (Fri Jan 26 2007 - 07:29:50 PST)
Fwd: AMBER: mm_pbsa Array reference error Syed Tarique Moin (Fri Jan 26 2007 - 10:54:56 PST)
AMBER: amber parallel compile error with g95 Seaclear Theory (Fri Jan 26 2007 - 11:00:52 PST)
AMBER: radius of gyration Esther Brugger (Fri Jan 26 2007 - 12:17:37 PST)
AMBER: Is there a pmemd machine file for OSX Intel Kevin Kelliher (Fri Jan 26 2007 - 13:50:29 PST)
AMBER: NVT/NPT equilibration issue in GPCR-membrane simulation Akshay Patny (Fri Jan 26 2007 - 14:23:46 PST)
- RE: AMBER: NVT/NPT equilibration issue in GPCR-membrane simulation Ross Walker (Fri Jan 26 2007 - 15:11:06 PST)
  - Re: AMBER: NVT/NPT equilibration issue in GPCR-membrane simulation David A. Case (Fri Jan 26 2007 - 17:45:51 PST)
  - AMBER: Amber/ANAL and psf files rebeca.mmb.pcb.ub.es (Wed Feb 21 2007 - 08:24:33 PST)
    - AMBER: contacts in ptraj (Amber 9) rebeca.mmb.pcb.ub.es (Wed Feb 21 2007 - 10:56:50 PST)
    - Re: AMBER: Amber/ANAL and psf files David A. Case (Wed Feb 21 2007 - 20:14:42 PST)
- RE: AMBER: NVT/NPT equilibration issue in GPCR-membrane simulation Akshay Patny (Fri Jan 26 2007 - 15:27:56 PST)
AMBER: Ligand-Protein Distance Restraints during MD Simulation Akshay Patny (Fri Jan 26 2007 - 16:06:26 PST)
- Re: AMBER: Ligand-Protein Distance Restraints during MD Simulation David Mobley (Tue Jan 30 2007 - 09:16:19 PST)
AMBER: mm_pbsa Array reference error Syed Tarique Moin (Sat Jan 27 2007 - 00:02:16 PST)
- Re: AMBER: mm_pbsa Array reference error Scott Pendley (Wed Jan 31 2007 - 09:48:36 PST)
  - Re: AMBER: mm_pbsa Array reference error Syed Tarique Moin (Wed Jan 31 2007 - 21:19:48 PST)
    - Re: AMBER: mm_pbsa Array reference error Scott Pendley (Thu Feb 01 2007 - 09:05:27 PST)
    - AMBER: workaround for ibm xlf90 powerpc FORTRAN compiler: -q64 and -O3 yield Run.dhfr.min failure Chris Moth (Thu Feb 01 2007 - 10:33:33 PST)
    - Re: AMBER: mm_pbsa Array reference error Syed Tarique Moin (Thu Feb 01 2007 - 20:43:50 PST)
    - Re: AMBER: mm_pbsa Array reference error Scott Pendley (Fri Feb 02 2007 - 09:09:50 PST)
    - Re: AMBER: mm_pbsa Array reference error Syed Tarique Moin (Sat Feb 03 2007 - 21:51:27 PST)
AMBER: yet another SANDER bug? Miyeegombo Enkhbold (Sat Jan 27 2007 - 19:11:22 PST)
- RE: AMBER: yet another SANDER bug? Ross Walker (Sat Jan 27 2007 - 20:18:24 PST)
AMBER: Improper angle by Antechamber Pavan G (Sun Jan 28 2007 - 09:28:29 PST)
- Re: AMBER: Improper angle by Antechamber David A. Case (Sun Jan 28 2007 - 18:20:26 PST)
Re: AMBER: radius of gyration Bill Ross (Sun Jan 28 2007 - 12:01:05 PST)
- Re: AMBER: radius of gyration Esther Brugger (Mon Jan 29 2007 - 07:51:26 PST)
- Re: AMBER: radius of gyration Bill Ross (Mon Jan 29 2007 - 11:51:39 PST)
  - Re: AMBER: radius of gyration Esther Brugger (Mon Jan 29 2007 - 13:06:00 PST)
    - Re: AMBER: radius of gyration Thomas Cheatham III (Mon Jan 29 2007 - 13:21:20 PST)
    - Re: AMBER: radius of gyration Esther Brugger (Mon Jan 29 2007 - 14:27:34 PST)
AMBER: Why there is a gap or jump if continue ntt=3 or ntt=1 Jiapu.Zhang.csiro.au (Sun Jan 28 2007 - 22:04:34 PST)
- RE: AMBER: Why there is a gap or jump if continue ntt=3 or ntt=1 Ross Walker (Sun Jan 28 2007 - 22:16:32 PST)
- RE: AMBER: Why there is a gap or jump if continue ntt=3 or ntt=1 Jiapu.Zhang.csiro.au (Mon Jan 29 2007 - 14:08:26 PST)
AMBER: gaussian output to prepin problem Rima Chaudhuri (Mon Jan 29 2007 - 09:14:31 PST)
- RE: AMBER: gaussian output to prepin problem Junmei Wang (Mon Jan 29 2007 - 18:43:56 PST)
AMBER: Antechamber Charge Calculation Method A Box (Mon Jan 29 2007 - 16:46:42 PST)
- RE: AMBER: Antechamber Charge Calculation Method Junmei Wang (Mon Jan 29 2007 - 18:48:17 PST)
AMBER: MM-PBSA doubt mathew k varghese (Mon Jan 29 2007 - 18:12:44 PST)
- RE: AMBER: MM-PBSA doubt Ray Luo (Mon Jan 29 2007 - 20:04:52 PST)
  - RE: AMBER: MM-PBSA doubt mathew k varghese (Mon Jan 29 2007 - 20:22:50 PST)
    - RE: AMBER: MM-PBSA doubt Ray Luo (Mon Jan 29 2007 - 21:29:01 PST)
AMBER: xleap deepti nayar (Tue Jan 30 2007 - 02:40:10 PST)
- Re: AMBER: xleap Chupakhin Vladimir (Tue Jan 30 2007 - 02:55:40 PST)
- Re: AMBER: xleap Navnit Kumar Mishra (Tue Jan 30 2007 - 03:53:11 PST)
- Re: AMBER: xleap Gustavo Seabra (Tue Jan 30 2007 - 07:57:11 PST)
AMBER: questions about analysing LES results Kailee (Tue Jan 30 2007 - 09:00:40 PST)
Fwd: AMBER: Improper angle by Antechamber Pavan G (Tue Jan 30 2007 - 10:46:34 PST)
AMBER: Charges in TI calculations and leap Austin B. Yongye (Tue Jan 30 2007 - 11:35:50 PST)
- Re: AMBER: Charges in TI calculations and leap Ilyas Yildirim (Tue Jan 30 2007 - 11:48:00 PST)
- Re: AMBER: Charges in TI calculations and leap Austin B. Yongye (Tue Jan 30 2007 - 12:10:54 PST)
  - Re: AMBER: Charges in TI calculations and leap David A. Case (Tue Jan 30 2007 - 13:24:33 PST)
AMBER: Ptraj: watershell and distance Esther Brugger (Tue Jan 30 2007 - 13:26:17 PST)
- Re: AMBER: Ptraj: watershell and distance Pavan G (Tue Jan 30 2007 - 14:01:07 PST)
- Re: AMBER: Ptraj: watershell and distance Thomas Cheatham III (Thu Feb 01 2007 - 10:46:04 PST)
AMBER: I need some constant pressure MD help David Cerutti (Tue Jan 30 2007 - 20:39:06 PST)
- RE: AMBER: I need some constant pressure MD help Ross Walker (Tue Jan 30 2007 - 21:47:38 PST)
AMBER: some questions about minimization and MD of DNA duplex with sander Chengwen Chen (Tue Jan 30 2007 - 23:44:13 PST)
- RE: AMBER: some questions about minimization and MD of DNA duplex with sander Ross Walker (Wed Jan 31 2007 - 08:36:27 PST)
  - Re: AMBER: some questions about minimization and MD of DNA duplex with sander Chengwen Chen (Thu Feb 01 2007 - 21:40:11 PST)
    - RE: AMBER: some questions about minimization and MD of DNA duplex with sander Ross Walker (Fri Feb 02 2007 - 09:23:02 PST)
    - Re: AMBER: some questions about minimization and MD of DNA duplex with sander Chengwen Chen (Mon Feb 05 2007 - 21:43:29 PST)
AMBER: mm_pbsa error Syed Tarique Moin (Wed Jan 31 2007 - 01:19:46 PST)
AMBER: mm_pbsa error Syed Tarique Moin (Wed Jan 31 2007 - 01:19:02 PST)
AMBER: ptraj khn _ (Wed Jan 31 2007 - 08:26:00 PST)
- Re: AMBER: ptraj Thomas Cheatham III (Wed Jan 31 2007 - 16:03:00 PST)
AMBER: nonpolar solvation energy khn _ (Wed Jan 31 2007 - 08:33:55 PST)
- RE: AMBER: nonpolar solvation energy Ray Luo (Wed Jan 31 2007 - 11:37:34 PST)
  - Re: AMBER: nonpolar solvation energy Carlos Simmerling (Wed Jan 31 2007 - 11:54:14 PST)
AMBER: format of .xyz files and pdb Gobind Singh Bisht (Wed Jan 31 2007 - 14:05:24 PST)
- Re: AMBER: format of .xyz files and pdb Steven Winfield (Wed Jan 31 2007 - 14:20:43 PST)
AMBER: Still puzzled about this virial computation David Cerutti (Thu Feb 01 2007 - 00:00:10 PST)
- Re: AMBER: Still puzzled about this virial computation Robert Duke (Thu Feb 01 2007 - 07:35:25 PST)
- Re: AMBER: Still puzzled about this virial computation Robert Duke (Thu Feb 01 2007 - 08:16:51 PST)
AMBER: xleap deepti nayar (Thu Feb 01 2007 - 00:04:09 PST)
- RE: AMBER: xleap Ross Walker (Thu Feb 01 2007 - 08:18:19 PST)
- Re: AMBER: xleap David A. Case (Thu Feb 01 2007 - 08:58:40 PST)
AMBER: subscribe amber Stéphane Téletchéa (Thu Feb 01 2007 - 07:11:25 PST)
AMBER: Example needed for addAtomType command Kara Di Giorgio (Thu Feb 01 2007 - 13:26:12 PST)
- Re: AMBER: Example needed for addAtomType command David A. Case (Thu Feb 01 2007 - 14:30:03 PST)
  - Re: AMBER: Example needed for addAtomType command Kara Di Giorgio (Thu Feb 01 2007 - 15:02:39 PST)
AMBER: ab initio modeling using Amber snoze pa (Thu Feb 01 2007 - 18:59:17 PST)
- Re: AMBER: ab initio modeling using Amber Gustavo Seabra (Thu Feb 01 2007 - 20:07:45 PST)
AMBER: Problem with paralell installation Martin Stennett (Fri Feb 02 2007 - 00:22:25 PST)
- RE: AMBER: Problem with paralell installation Ross Walker (Fri Feb 02 2007 - 07:21:16 PST)
AMBER: RESP Charges for Charged Carboxylate in Organic Ligand Akshay Patny (Fri Feb 02 2007 - 08:05:35 PST)
- Re: AMBER: RESP Charges for Charged Carboxylate in Organic Ligand HL Eastwood (Fri Feb 02 2007 - 09:40:10 PST)
- Re: AMBER: RESP Charges for Charged Carboxylate in Organic Ligand HL Eastwood (Fri Feb 02 2007 - 09:41:50 PST)
AMBER: iRED and corrired Francois Theillet (Fri Feb 02 2007 - 09:07:47 PST)
- Re: AMBER: iRED and corrired David A. Case (Fri Feb 02 2007 - 10:57:43 PST)
  - Re: AMBER: iRED and corrired Francois Theillet (Fri Feb 02 2007 - 13:05:41 PST)
  - Re: AMBER: iRED and corrired Gohlke.bioinformatik.uni-frankfurt.de (Sun Feb 04 2007 - 05:01:17 PST)
    - Re: AMBER: iRED and corrired Holger Gohlke (Mon Feb 05 2007 - 08:09:15 PST)
AMBER: calculating distance between two atoms bertrand russell (Fri Feb 02 2007 - 09:49:07 PST)
- Re: AMBER: calculating distance between two atoms Carlos Simmerling (Fri Feb 02 2007 - 13:42:41 PST)
  - Re: AMBER: calculating distance between two atoms bertrand russell (Mon Feb 05 2007 - 04:22:16 PST)
    - Re: AMBER: calculating distance between two atoms Carlos Simmerling (Mon Feb 05 2007 - 04:55:19 PST)
AMBER: How do I make and enter new ff parameters into AMBER MARY O'CONNOR (Fri Feb 02 2007 - 11:35:20 PST)
AMBER: How do I make and enter new ff parameters into AMBER HL Eastwood (Fri Feb 02 2007 - 13:26:46 PST)
AMBER: angle command in Ptraj Esther Brugger (Fri Feb 02 2007 - 16:20:34 PST)
- Re: AMBER: angle command in Ptraj Esther Brugger (Fri Feb 02 2007 - 16:36:01 PST)
  - Re: AMBER: angle command in Ptraj Carlos Simmerling (Sat Feb 03 2007 - 05:17:26 PST)
AMBER: addions Amit Kumar (Sat Feb 03 2007 - 05:17:57 PST)
- Re: AMBER: addions David A. Case (Sun Feb 04 2007 - 09:33:37 PST)
AMBER: ptraj hbond jacopo.sgrignani.unifi.it (Sat Feb 03 2007 - 08:28:20 PST)
AMBER: Calculate force constants Markus Weingarth (Sun Feb 04 2007 - 14:13:28 PST)
AMBER: force fields deepti nayar (Sun Feb 04 2007 - 23:05:09 PST)
- Re: AMBER: force fields Carlos Simmerling (Mon Feb 05 2007 - 04:49:29 PST)
- RE: AMBER: force fields Yong Duan (Mon Feb 05 2007 - 09:15:10 PST)
  - Re: AMBER: force fields deepti nayar (Mon Feb 05 2007 - 21:37:05 PST)
    - RE: AMBER: force fields Yong Duan (Mon Feb 05 2007 - 22:24:01 PST)
    - Re: AMBER: force fields deepti nayar (Tue Feb 06 2007 - 00:20:05 PST)
    - Re: AMBER: force fields deepti nayar (Tue Feb 06 2007 - 02:33:37 PST)
    - RE: AMBER: force fields Yong Duan (Tue Feb 06 2007 - 08:11:20 PST)
    - Re: AMBER: force fields Carlos Simmerling (Tue Feb 06 2007 - 04:50:42 PST)
- RE: AMBER: force fields Yong Duan (Tue Feb 06 2007 - 08:13:58 PST)
AMBER: replacement of mutated atoms in protein structure bertrand russell (Mon Feb 05 2007 - 02:42:37 PST)
AMBER: MAXGRP error message Alexander Steudle (Mon Feb 05 2007 - 06:03:45 PST)
- Re: AMBER: MAXGRP error message David A. Case (Wed Feb 07 2007 - 09:43:33 PST)
AMBER: problem in xleap WANG,YING (Mon Feb 05 2007 - 07:45:14 PST)
- Re: AMBER: problem in xleap Steven Winfield (Mon Feb 05 2007 - 08:06:12 PST)
- Re: AMBER: problem in xleap WANG,YING (Tue Feb 06 2007 - 15:36:29 PST)
  - Re: AMBER: problem in xleap Carlos Simmerling (Tue Feb 06 2007 - 15:46:29 PST)
- Re: AMBER: problem in xleap WANG,YING (Tue Feb 06 2007 - 17:12:54 PST)
AMBER: Force fields for iron MARY O'CONNOR (Mon Feb 05 2007 - 08:19:52 PST)
- AMBER: positive binding energy saurabh agrawal (Mon Feb 05 2007 - 09:30:46 PST)
AMBER: Tutorial for chemical shift calculation? Mike Summers (Mon Feb 05 2007 - 17:04:48 PST)
- Re: AMBER: Tutorial for chemical shift calculation? David A. Case (Tue Feb 06 2007 - 08:25:40 PST)
  - Re: AMBER: Tutorial for chemical shift calculation? Mike Summers (Tue Feb 06 2007 - 10:36:05 PST)
  - AMBER: Pseudo-CSA in Amber? Mike Summers (Mon Feb 19 2007 - 06:30:13 PST)
    - Re: AMBER: Pseudo-CSA in Amber? David A. Case (Wed Feb 21 2007 - 16:04:32 PST)
AMBER: Link to Modified NA bases files Seth Lilavivat (Mon Feb 05 2007 - 14:22:50 PST)
- Re: AMBER: Link to Modified NA bases files Ilyas Yildirim (Mon Feb 05 2007 - 20:05:21 PST)
AMBER: Glycam Beale, John (Tue Feb 06 2007 - 05:07:22 PST)
- Re: AMBER: Glycam David A. Case (Tue Feb 06 2007 - 08:04:21 PST)
- Re: AMBER: Glycam kkirschn.hamilton.edu (Tue Feb 06 2007 - 06:44:52 PST)
AMBER: MM-PBSA questions/clarifications Rima Chaudhuri (Tue Feb 06 2007 - 10:51:08 PST)
- Re: AMBER: MM-PBSA questions/clarifications vanessa wai (Tue Feb 13 2007 - 02:36:27 PST)
AMBER: Compile Amber9 for MVAPICH Mike Hanby (Tue Feb 06 2007 - 11:51:18 PST)
- Re: AMBER: Compile Amber9 for MVAPICH David A. Case (Tue Feb 06 2007 - 12:23:07 PST)
AMBER: compiling AMBER9 on Mac OS X Tiger (Intel) Nevin Gerek (Tue Feb 06 2007 - 15:08:08 PST)
- Re: AMBER: compiling AMBER9 on Mac OS X Tiger (Intel) David A. Case (Tue Feb 06 2007 - 16:22:03 PST)
  - Re: AMBER: compiling AMBER9 on Mac OS X Tiger (Intel) Z. Nevin Gerek (Wed Feb 07 2007 - 09:20:12 PST)
    - Re: AMBER: compiling AMBER9 on Mac OS X Tiger (Intel) Mark Williamson (Wed Feb 07 2007 - 09:45:29 PST)
    - Re: AMBER: compiling AMBER9 on Mac OS X Tiger (Intel) Z. Nevin Gerek (Wed Feb 07 2007 - 09:57:54 PST)
    - Re: AMBER: compiling AMBER9 on Mac OS X Tiger (Intel) Scott Brozell (Wed Feb 07 2007 - 09:59:41 PST)
- Re: AMBER: compiling AMBER9 on Mac OS X Tiger (Intel) Mike Summers (Tue Feb 06 2007 - 18:30:22 PST)
AMBER: Missing Value for MM ELE Rima Chaudhuri (Tue Feb 06 2007 - 15:26:08 PST)
AMBER: side chain orientation Esther Brugger (Tue Feb 06 2007 - 15:36:48 PST)
- Re: AMBER: side chain orientation Fenghui Fan (Tue Feb 06 2007 - 16:11:47 PST)
  - Re: AMBER: side chain orientation Esther Brugger (Wed Feb 07 2007 - 07:23:55 PST)
    - Re: AMBER: side chain orientation Ilyas Yildirim (Wed Feb 07 2007 - 10:00:37 PST)
AMBER: trajectory problem Miguel Ferreira (Tue Feb 06 2007 - 20:52:25 PST)
- Re: AMBER: trajectory problem David A. Case (Wed Feb 07 2007 - 09:52:59 PST)
AMBER: antechamber for topology file deepti nayar (Wed Feb 07 2007 - 02:42:51 PST)
- Re: AMBER: antechamber for topology file Carlos Simmerling (Wed Feb 07 2007 - 04:32:52 PST)
- Re: AMBER: antechamber for topology file FyD (Wed Feb 07 2007 - 05:28:58 PST)
  - Re: AMBER: antechamber for topology file deepti nayar (Wed Feb 07 2007 - 22:07:22 PST)
- RE: AMBER: antechamber for topology file Akshay Patny (Wed Feb 07 2007 - 22:28:50 PST)
  - Re: AMBER: antechamber for topology file deepti nayar (Wed Feb 07 2007 - 22:55:35 PST)
    - Re: AMBER: antechamber for topology file David A. Case (Wed Feb 07 2007 - 23:08:04 PST)
    - Re: AMBER: antechamber for topology file FyD (Thu Feb 08 2007 - 00:10:29 PST)
AMBER: Help!! I cannot perform the ambpdb WANG,YING (Wed Feb 07 2007 - 06:03:07 PST)
- Re: AMBER: Help!! I cannot perform the ambpdb Mark Williamson (Wed Feb 07 2007 - 08:08:41 PST)
- RE: AMBER: Help!! I cannot perform the ambpdb Ross Walker (Wed Feb 07 2007 - 07:21:13 PST)
- Re: AMBER: Help!! I cannot perform the ambpdb WANG,YING (Wed Feb 07 2007 - 11:49:46 PST)
  - Re: AMBER: Help!! I cannot perform the ambpdb Mark Williamson (Wed Feb 07 2007 - 12:25:19 PST)
- RE: AMBER: Help!! I cannot perform the ambpdb WANG,YING (Wed Feb 07 2007 - 12:19:29 PST)
- Re: AMBER: Help!! I cannot perform the ambpdb WANG,YING (Wed Feb 07 2007 - 13:23:16 PST)
AMBER: Strange behavior on g95 compile. Martin Stennett (Wed Feb 07 2007 - 08:00:23 PST)
- Re: AMBER: Strange behavior on g95 compile. Mark Williamson (Wed Feb 07 2007 - 08:18:16 PST)
- RE: AMBER: Strange behavior on g95 compile. Ross Walker (Wed Feb 07 2007 - 08:17:37 PST)
- Re: AMBER: Strange behavior on g95 compile. Seth Hayik (Wed Feb 07 2007 - 08:31:50 PST)
AMBER: problem with AMBER8 installation Subhasish Chatterjee (Wed Feb 07 2007 - 09:50:48 PST)
- RE: AMBER: problem with AMBER8 installation Ross Walker (Wed Feb 07 2007 - 10:06:42 PST)
- Re: AMBER: problem with AMBER8 installation David A. Case (Wed Feb 07 2007 - 10:10:51 PST)
AMBER: Compiling Amber 8 on SuSE 10.2 Seth Lilavivat (Wed Feb 07 2007 - 11:50:12 PST)
- Re: AMBER: Compiling Amber 8 on SuSE 10.2 Cenk Andac (Wed Feb 07 2007 - 12:02:17 PST)
  - Re: AMBER: Compiling Amber 8 on SuSE 10.2 Seth Lilavivat (Wed Feb 07 2007 - 14:35:27 PST)
AMBER: Membrane Simulation: NPT issues Akshay Patny (Wed Feb 07 2007 - 10:29:36 PST)
AMBER: Binding free energy calculation - MM-pbsa Rima Chaudhuri (Wed Feb 07 2007 - 12:55:26 PST)
AMBER: Membrane Simulation: NPT Issues Akshay Patny (Wed Feb 07 2007 - 09:28:05 PST)
- RE: AMBER: Membrane Simulation: NPT Issues Akshay Patny (Mon Feb 12 2007 - 07:33:40 PST)
  - Re: AMBER: Membrane Simulation: NPT Issues David A. Case (Wed Feb 14 2007 - 15:04:47 PST)
    - RE: AMBER: Membrane Simulation: NPT Issues Akshay Patny (Thu Feb 15 2007 - 08:54:02 PST)
AMBER: Missing values for MM ELE (MM-PBSA)..help!! Rima Chaudhuri (Wed Feb 07 2007 - 08:21:38 PST)
AMBER: Compiling Amber 7 David J. Powers (Thu Feb 08 2007 - 07:13:00 PST)
- RE: AMBER: Compiling Amber 7 Ross Walker (Thu Feb 08 2007 - 08:30:30 PST)
  - RE: AMBER: Compiling Amber 7 David J. Powers (Thu Feb 08 2007 - 11:27:41 PST)
  - RE: AMBER: Compiling Amber 7 David J. Powers (Sat Feb 10 2007 - 07:59:42 PST)
    - RE: AMBER: Compiling Amber 7 Ross Walker (Sat Feb 10 2007 - 09:11:54 PST)
AMBER: H-Bond Esther Brugger (Thu Feb 08 2007 - 09:06:57 PST)
AMBER: Protonation of Aspartate sai vikram (Thu Feb 08 2007 - 09:12:03 PST)
- Re: AMBER: Protonation of Aspartate Adrian Roitberg (Thu Feb 08 2007 - 09:17:11 PST)
AMBER: Calcium and peptides Beale, John (Thu Feb 08 2007 - 10:20:30 PST)
AMBER: Compiling AMBER 8 on RHEL4 AMD64 Seth Lilavivat (Thu Feb 08 2007 - 11:53:44 PST)
- Re: AMBER: Compiling AMBER 8 on RHEL4 AMD64 David A. Case (Thu Feb 08 2007 - 22:22:01 PST)
AMBER: Energy calculation by Anal Alexander Rubinstein (Thu Feb 08 2007 - 12:11:16 PST)
AMBER: phe-phe prep file deepti nayar (Thu Feb 08 2007 - 22:09:15 PST)
AMBER: assigning charges to a prepi file deepti nayar (Thu Feb 08 2007 - 22:38:27 PST)
- Re: AMBER: assigning charges to a prepi file David A. Case (Thu Feb 08 2007 - 22:58:08 PST)
AMBER: question about distance restraint on terminal WC of DNA duplex (AMBER9) Chengwen Chen (Fri Feb 09 2007 - 00:25:00 PST)
- Re: AMBER: question about distance restraint on terminal WC of DNA duplex (AMBER9) David A. Case (Sat Feb 10 2007 - 22:57:27 PST)
AMBER: Umbrella sampling Franck Vendeix (Fri Feb 09 2007 - 06:37:35 PST)
- Re: AMBER: Umbrella sampling Jerome.GOLEBIOWSKI.unice.fr (Mon Feb 12 2007 - 01:33:18 PST)
  - Re: AMBER: Umbrella sampling Franck Vendeix (Wed Feb 14 2007 - 19:13:31 PST)
AMBER: amber9 possible failure tgtmd jlalonde (Fri Feb 09 2007 - 08:19:19 PST)
- Re: AMBER: amber9 possible failure tgtmd David A. Case (Mon Feb 12 2007 - 21:58:15 PST)
AMBER: problem with sander Seth Lilavivat (Fri Feb 09 2007 - 09:43:14 PST)
- Re: AMBER: problem with sander David A. Case (Sat Feb 10 2007 - 02:08:01 PST)
  - Re: AMBER: problem with sander Seth Lilavivat (Fri Feb 09 2007 - 11:35:34 PST)
AMBER: ptraj dipole calculation in QMMM simulation Evan Kelly (Fri Feb 09 2007 - 10:36:30 PST)
- RE: AMBER: ptraj dipole calculation in QMMM simulation Ross Walker (Fri Feb 09 2007 - 10:53:30 PST)
- Re: AMBER: ptraj dipole calculation in QMMM simulation Gustavo Seabra (Fri Feb 09 2007 - 10:54:04 PST)
AMBER: Heating the system prior to production run Ilyas Yildirim (Fri Feb 09 2007 - 13:28:08 PST)
AMBER: Umbrella sampling - Tutorial bertrand russell (Fri Feb 09 2007 - 23:35:31 PST)
AMBER: extracting coordinates from crd file gurpreet singh (Sat Feb 10 2007 - 00:40:44 PST)
- Re: AMBER: extracting coordinates from crd file Ilyas Yildirim (Sat Feb 10 2007 - 00:59:04 PST)
AMBER: extracting coordinate from crd file gurpreet singh (Sat Feb 10 2007 - 02:05:20 PST)
- Re: AMBER: extracting coordinate from crd file Amit Kumar (Sat Feb 10 2007 - 07:31:35 PST)
- Re: AMBER: extracting coordinate from crd file David A. Case (Sat Feb 10 2007 - 08:08:28 PST)
  - AMBER: atomicfluct Catein Catherine (Sun Feb 11 2007 - 21:45:40 PST)
    - RE: AMBER: atomicfluct Rafi Ahmad (Mon Feb 12 2007 - 00:32:37 PST)
    - RE: AMBER: atomicfluct Catein Catherine (Tue Feb 13 2007 - 19:36:35 PST)
    - AMBER: Help: 1 ns for implicit solvent (GB) calculations, enough? Catein Catherine (Tue Feb 13 2007 - 20:18:23 PST)
    - Re: AMBER: Help: 1 ns for implicit solvent (GB) calculations, enough? Carlos Simmerling (Wed Feb 14 2007 - 04:26:31 PST)
AMBER: simulating part of a molecule with homology modeling Dave, Sonya (Sat Feb 10 2007 - 16:00:11 PST)
- Re: AMBER: simulating part of a molecule with homology modeling Fenghui Fan (Sat Feb 10 2007 - 20:26:41 PST)
  - RE: AMBER: simulating part of a molecule with homology modeling Dave, Sonya (Mon Feb 12 2007 - 08:50:36 PST)
AMBER: quasiharnomic analysis Hans Lee (Sun Feb 11 2007 - 13:12:52 PST)
- Re: AMBER: quasiharnomic analysis David A. Case (Mon Feb 12 2007 - 08:31:36 PST)
Re: AMBER: extracting coordinate from crd file Bill Ross (Sun Feb 11 2007 - 21:13:38 PST)
AMBER: connect atom deepti nayar (Mon Feb 12 2007 - 03:01:57 PST)
- Re: AMBER: connect atom David A. Case (Mon Feb 12 2007 - 08:28:57 PST)
AMBER: help me out... Anju Sharma (Mon Feb 12 2007 - 04:21:00 PST)
- AMBER: Fwd: help me out... Anju Sharma (Mon Feb 12 2007 - 04:22:57 PST)
  - Re: AMBER: Fwd: help me out... Chris Moth (Mon Feb 12 2007 - 07:08:24 PST)
- RE: AMBER: help me out... Ross Walker (Mon Feb 12 2007 - 07:11:03 PST)
AMBER: reporting EPtot and EKtot separately for two molecules Gabbar S. Daaku (Mon Feb 12 2007 - 08:15:09 PST)
- AMBER: Re: reporting EPtot and EKtot separately for two molecules Gabbar S. Daaku (Mon Feb 12 2007 - 08:16:45 PST)
- Re: AMBER: reporting EPtot and EKtot separately for two molecules David A. Case (Mon Feb 12 2007 - 08:25:55 PST)
AMBER: Lone Pairs Beale, John (Mon Feb 12 2007 - 10:52:48 PST)
- Re: AMBER: Lone Pairs David A. Case (Mon Feb 12 2007 - 13:24:48 PST)
  - RE: AMBER: Lone Pairs Beale, John (Tue Feb 13 2007 - 06:33:44 PST)
    - Re: AMBER: Lone Pairs David A. Case (Tue Feb 13 2007 - 08:00:21 PST)
AMBER: How precise is a MD simulation? Dave, Sonya (Mon Feb 12 2007 - 16:00:07 PST)
- Re: AMBER: How precise is a MD simulation? Fenghui Fan (Mon Feb 12 2007 - 17:47:09 PST)
  - Re: AMBER: How precise is a MD simulation? David Mobley (Tue Feb 13 2007 - 11:36:17 PST)
    - RE: AMBER: How precise is a MD simulation? Yong Duan (Tue Feb 13 2007 - 11:45:48 PST)
    - RE: AMBER: How precise is a MD simulation? Dave, Sonya (Tue Feb 13 2007 - 12:01:23 PST)
    - Re: AMBER: How precise is a MD simulation? David Mobley (Tue Feb 13 2007 - 12:19:13 PST)
    - AMBER: Best Force field for protein, DNA, and organic compounds? Catein Catherine (Tue Feb 13 2007 - 20:13:31 PST)
    - Re: AMBER: Best Force field for protein, DNA, and organic compounds? Carlos Simmerling (Wed Feb 14 2007 - 04:28:05 PST)
    - RE: AMBER: Best Force field for protein, DNA, and organic compounds? Rafi Ahmad (Wed Feb 14 2007 - 05:35:28 PST)
    - Re: AMBER: Best Force field for protein, DNA, and organic compounds? Carlos Simmerling (Wed Feb 14 2007 - 06:08:17 PST)
    - Re: AMBER: How precise is a MD simulation? Which strcutures should be reported? Catein Catherine (Tue Feb 13 2007 - 20:28:09 PST)
    - Re: AMBER: How precise is a MD simulation? Which strcutures should be reported? Carlos Simmerling (Wed Feb 14 2007 - 04:25:02 PST)
    - Re: AMBER: How precise is a MD simulation? David Mobley (Tue Feb 13 2007 - 12:11:17 PST)
    - RE: AMBER: How precise is a MD simulation? Dave, Sonya (Wed Feb 14 2007 - 10:35:16 PST)
AMBER: How to place torsion restraint Seth Lilavivat (Mon Feb 12 2007 - 17:24:40 PST)
- Re: AMBER: How to place torsion restraint Gustavo Seabra (Tue Feb 13 2007 - 08:48:08 PST)
AMBER: Modified nucleotides mathew k varghese (Mon Feb 12 2007 - 20:44:31 PST)
- Re: AMBER: Modified nucleotides Ilyas Yildirim (Mon Feb 12 2007 - 20:58:50 PST)
- RE: AMBER: Modified nucleotides Seth Lilavivat (Mon Feb 12 2007 - 20:59:37 PST)
- Re: AMBER: Modified nucleotides Thomas Cheatham (Mon Feb 12 2007 - 21:03:38 PST)
- Re: AMBER: Modified nucleotides Sean Rathlef (Mon Feb 12 2007 - 21:55:20 PST)
- Re: AMBER: Modified nucleotides Raviprasad Aduri (Tue Feb 13 2007 - 09:23:15 PST)
  - Re: AMBER: Modified nucleotides mathew k varghese (Tue Feb 13 2007 - 19:47:08 PST)
    - Re: AMBER: Modified nucleotides Ilyas Yildirim (Tue Feb 13 2007 - 20:05:25 PST)
    - Re: AMBER: Modified nucleotides FyD (Wed Feb 14 2007 - 04:30:50 PST)
    - Re: AMBER: Modified nucleotides Raviprasad Aduri (Wed Feb 14 2007 - 16:58:39 PST)
    - Re: AMBER: Modified nucleotides mathew k varghese (Wed Feb 14 2007 - 21:09:56 PST)
AMBER: hi Anju Sharma (Tue Feb 13 2007 - 02:08:01 PST)
- Re: AMBER: hi Steven Winfield (Tue Feb 13 2007 - 02:42:16 PST)
  - AMBER: Solvate box Sophie Barbe (Tue Feb 13 2007 - 05:21:28 PST)
    - RE: AMBER: Solvate box Ross Walker (Tue Feb 13 2007 - 08:26:51 PST)
    - Re: AMBER: Solvate box M. L. Dodson (Tue Feb 13 2007 - 19:33:49 PST)
  - Re: AMBER: hi Anju Sharma (Tue Feb 13 2007 - 20:44:45 PST)
    - Re: AMBER: hi Ilyas Yildirim (Wed Feb 14 2007 - 14:14:11 PST)
    - Re: AMBER: hi Steven Winfield (Wed Feb 14 2007 - 14:21:01 PST)
- RE: AMBER: hi Ross Walker (Tue Feb 13 2007 - 08:16:56 PST)
  - Re: AMBER: hi Anju Sharma (Tue Feb 13 2007 - 20:48:36 PST)
    - Re: AMBER: hi Anju Sharma (Tue Feb 13 2007 - 20:50:16 PST)
    - RE: AMBER: hi Ross Walker (Wed Feb 14 2007 - 08:15:50 PST)
AMBER: Constraint virial David Cerutti (Tue Feb 13 2007 - 02:22:20 PST)
AMBER: Box problems in vacuum minimization with sander.serial 8 j j (Tue Feb 13 2007 - 11:05:16 PST)
- Re: AMBER: Box problems in vacuum minimization with sander.serial 8 David A. Case (Tue Feb 13 2007 - 11:34:57 PST)
  - Re: AMBER: Box problems in vacuum minimization with sander.serial 8 j j (Tue Feb 13 2007 - 11:43:34 PST)
AMBER: How to parameterize frcmod for NA Seth Lilavivat (Tue Feb 13 2007 - 11:27:59 PST)
AMBER: Replica Exchange Christopher Gaughan (Tue Feb 13 2007 - 13:20:08 PST)
AMBER: Positive binding free energy! Rima Chaudhuri (Tue Feb 13 2007 - 14:53:05 PST)
- Re: AMBER: Positive binding free energy! David Cerutti (Tue Feb 13 2007 - 16:40:35 PST)
AMBER: SANDER bug Ichinkhorloo Erdenebaatar (Tue Feb 13 2007 - 17:19:21 PST)
- Re: AMBER: SANDER bug David A. Case (Wed Feb 14 2007 - 10:11:12 PST)
AMBER: LeaP: Mol2 files A Box (Tue Feb 13 2007 - 17:44:08 PST)
- Re: AMBER: LeaP: Mol2 files FyD (Wed Feb 14 2007 - 09:47:40 PST)
AMBER: Comparison of normal modes with ptraj? Harald Lanig (Wed Feb 14 2007 - 02:10:19 PST)
- Re: AMBER: Comparison of normal modes with ptraj? Gohlke.bioinformatik.uni-frankfurt.de (Wed Feb 14 2007 - 05:08:38 PST)
AMBER: NMR violations increase in explicite water Michel Becker (Wed Feb 14 2007 - 12:15:14 PST)
- Re: AMBER: NMR violations increase in explicite water David A. Case (Thu Feb 15 2007 - 08:40:12 PST)
AMBER: Deriving constraint forces on water molecules based on SETTLE moves David Cerutti (Wed Feb 14 2007 - 16:08:45 PST)
- Re: AMBER: Deriving constraint forces on water molecules based on SETTLE moves Steven Winfield (Thu Feb 15 2007 - 05:28:00 PST)
AMBER: Prepgen A Box (Wed Feb 14 2007 - 20:15:21 PST)
- Re: Re: AMBER: Prepgen yongleli (Thu May 15 2008 - 09:18:31 PDT)
AMBER: units in hessian matrix Marie Brut (Thu Feb 15 2007 - 08:52:01 PST)
- Re: AMBER: units in hessian matrix David A. Case (Thu Feb 15 2007 - 09:31:01 PST)
  - Re: AMBER: units in hessian matrix Adrian Roitberg (Thu Feb 15 2007 - 09:35:07 PST)
    - Re: AMBER: units in hessian matrix David A. Case (Thu Feb 15 2007 - 10:07:03 PST)
AMBER: Simulating a section of a molecule Dave, Sonya (Thu Feb 15 2007 - 08:59:53 PST)
- Re: AMBER: Simulating a section of a molecule Carlos Simmerling (Thu Feb 15 2007 - 10:06:50 PST)
- Re: AMBER: Simulating a section of a molecule Thomas Cheatham III (Thu Feb 15 2007 - 13:33:40 PST)
- RE: AMBER: Simulating a section of a molecule Dave, Sonya (Thu Feb 15 2007 - 15:10:06 PST)
AMBER: implicit solvent free energy calcs David Mobley (Thu Feb 15 2007 - 10:07:37 PST)
- Re: AMBER: implicit solvent free energy calcs David A. Case (Thu Feb 15 2007 - 12:19:53 PST)
AMBER: read the data Esther Brugger (Thu Feb 15 2007 - 11:53:45 PST)
- Re: AMBER: read the data Florian Haberl (Thu Feb 15 2007 - 12:11:16 PST)
  - Re: AMBER: read the data Esther Brugger (Fri Feb 16 2007 - 09:43:39 PST)
    - Re: AMBER: read the data David LeBard (Fri Feb 16 2007 - 10:31:13 PST)
    - Re: AMBER: read the data Esther Brugger (Fri Feb 16 2007 - 11:01:27 PST)
    - Re: AMBER: read the data David LeBard (Fri Feb 16 2007 - 11:22:12 PST)
    - Re: AMBER: read the data Ilyas Yildirim (Fri Feb 16 2007 - 15:05:31 PST)
    - Re: AMBER: question about ADDLES module Z. Nevin Gerek (Fri Feb 16 2007 - 17:33:58 PST)
    - Re: AMBER: question about ADDLES module Carlos Simmerling (Fri Feb 16 2007 - 17:48:27 PST)
    - Re: AMBER: read the data Esther Brugger (Sat Feb 17 2007 - 12:22:50 PST)
- Re: AMBER: read the data David LeBard (Thu Feb 15 2007 - 13:18:08 PST)
  - Re: AMBER: read the data Esther Brugger (Thu Feb 15 2007 - 15:00:39 PST)
  - Re: AMBER: read the data Esther Brugger (Fri Feb 16 2007 - 10:40:45 PST)
    - Re: AMBER: read the data David LeBard (Fri Feb 16 2007 - 11:00:10 PST)
- Re: AMBER: read the data Esther Brugger (Fri Feb 16 2007 - 08:54:06 PST)
AMBER: Density of a system in MD Akshay Patny (Thu Feb 15 2007 - 12:45:27 PST)
AMBER: How to modify the velocity of a water molecule? Ji-Lai Li (Thu Feb 15 2007 - 18:15:45 PST)
- Re: AMBER: How to modify the velocity of a water molecule? Carlos Simmerling (Thu Feb 15 2007 - 18:58:54 PST)
- Re: AMBER: How to modify the velocity of a water molecule? Thomas Cheatham (Thu Feb 15 2007 - 19:47:24 PST)
AMBER: Box dimensions Steve Seibold (Fri Feb 16 2007 - 07:13:45 PST)
- Re: AMBER: Box dimensions Gustavo Seabra (Fri Feb 16 2007 - 08:19:39 PST)
  - RE: AMBER: Box dimensions Akshay Patny (Fri Feb 16 2007 - 08:34:40 PST)
    - Re: AMBER: Box dimensions David A. Case (Fri Feb 16 2007 - 08:54:48 PST)
  - RE: AMBER: Box dimensions Steve Seibold (Fri Feb 16 2007 - 09:12:41 PST)
AMBER: H-bond ptraj dilemma Lorenzo Gontrani (Fri Feb 16 2007 - 07:46:54 PST)
AMBER: Problem with dacdif when using cygwin Steven Winfield (Fri Feb 16 2007 - 10:33:38 PST)
- Re: AMBER: Problem with dacdif when using cygwin Scott Brozell (Fri Feb 16 2007 - 11:32:06 PST)
- Re: AMBER: Problem with dacdif when using cygwin David A. Case (Fri Feb 16 2007 - 11:44:00 PST)
  - Re: AMBER: Problem with dacdif when using cygwin Steven Winfield (Fri Feb 16 2007 - 12:15:00 PST)
    - Re: AMBER: Problem with dacdif when using cygwin Scott Brozell (Fri Feb 16 2007 - 12:43:07 PST)
AMBER: HELP: Are there anybody have used AMBER to simulate glucose chain? WANG,YING (Fri Feb 16 2007 - 12:57:40 PST)
- Re: AMBER: HELP: Are there anybody have used AMBER to simulate glucose chain? Franck Vendeix (Fri Feb 16 2007 - 14:04:48 PST)
- Re: AMBER: HELP: Are there anybody have used AMBER to simulate glucose chain? WANG,YING (Fri Feb 16 2007 - 21:55:53 PST)
AMBER: Torsion Restraint on Glycosidic Bond Seth Lilavivat (Fri Feb 16 2007 - 13:13:52 PST)
- Re: AMBER: Torsion Restraint on Glycosidic Bond Thomas Cheatham III (Fri Feb 16 2007 - 13:32:30 PST)
- Re: AMBER: Torsion Restraint on Glycosidic Bond Carlos Simmerling (Fri Feb 16 2007 - 13:32:44 PST)
AMBER: High Standard Deviation for nmode (TSVIB) mm_pbsa Rima Chaudhuri (Fri Feb 16 2007 - 14:17:49 PST)
- Re: AMBER: High Standard Deviation for nmode (TSVIB) mm_pbsa David A. Case (Fri Feb 16 2007 - 17:22:05 PST)
  - Re: AMBER: High Standard Deviation for nmode (TSVIB) mm_pbsa Rima Chaudhuri (Sat Feb 17 2007 - 12:10:38 PST)
    - Re: AMBER: High Standard Deviation for nmode (TSVIB) mm_pbsa David A. Case (Sat Feb 17 2007 - 13:22:38 PST)
    - Re: AMBER: High Standard Deviation for nmode (TSVIB) mm_pbsa Rima Chaudhuri (Wed Feb 28 2007 - 14:25:54 PST)
AMBER: Installing AMBER v9 in Linux Syed Tarique Moin (Sat Feb 17 2007 - 08:12:28 PST)
- RE: AMBER: Installing AMBER v9 in Linux Ross Walker (Sat Feb 17 2007 - 08:52:00 PST)
  - RE: AMBER: Installing AMBER v9 in Linux Syed Tarique Moin (Sun Feb 18 2007 - 21:51:55 PST)
    - RE: AMBER: Installing AMBER v9 in Linux Ross Walker (Sun Feb 18 2007 - 22:53:45 PST)
    - RE: AMBER: Installing AMBER v9 in Linux Syed Tarique Moin (Sun Feb 18 2007 - 23:26:33 PST)
    - RE: AMBER: Installing AMBER v9 in Linux Ross Walker (Sun Feb 18 2007 - 23:39:05 PST)
    - RE: AMBER: Installing AMBER v9 in Linux Syed Tarique Moin (Mon Feb 19 2007 - 00:25:13 PST)
    - RE: AMBER: Installing AMBER v9 in Linux Ross Walker (Mon Feb 19 2007 - 01:44:15 PST)
    - RE: AMBER: Installing AMBER v9 in Linux Syed Tarique Moin (Mon Feb 19 2007 - 02:13:35 PST)
    - RE: AMBER: Installing AMBER v9 in Linux Ross Walker (Mon Feb 19 2007 - 10:03:12 PST)
    - RE: AMBER: Installing AMBER v9 in Linux Peter Gannett (Mon Feb 19 2007 - 04:27:44 PST)
AMBER: Installing AMBER v9 in Linux Syed Tarique Moin (Sat Feb 17 2007 - 08:15:31 PST)
- Re: AMBER: Installing AMBER v9 in Linux Ilyas Yildirim (Sat Feb 17 2007 - 23:30:34 PST)
AMBER: REMD error on first exchange Daniel Oehme (Sun Feb 18 2007 - 18:31:57 PST)
- Re: AMBER: REMD error on first exchange Carlos Simmerling (Mon Feb 19 2007 - 06:21:16 PST)
AMBER: Water density calculation mathew k varghese (Sun Feb 18 2007 - 22:51:57 PST)
AMBER: Residence time of WATER gurpreet singh (Mon Feb 19 2007 - 00:33:59 PST)
AMBER: MDGRAPE and AMBER Craig Gough (Mon Feb 19 2007 - 00:34:43 PST)
- Re: AMBER: MDGRAPE and AMBER Carlos Simmerling (Mon Feb 19 2007 - 06:23:58 PST)
AMBER: crd to pdb conversion AYTUG TUNCEL (Mon Feb 19 2007 - 05:27:34 PST)
- Re: AMBER: crd to pdb conversion Ilyas Yildirim (Mon Feb 19 2007 - 05:35:16 PST)
  - Re: Re: AMBER: crd to pdb conversion AYTUG TUNCEL (Mon Feb 19 2007 - 07:04:58 PST)
    - Re: Re: AMBER: crd to pdb conversion Ilyas Yildirim (Mon Feb 19 2007 - 09:12:43 PST)
AMBER: carbohydrate-peptide Beale, John (Mon Feb 19 2007 - 08:09:54 PST)
- Re: AMBER: carbohydrate-peptide David A. Case (Wed Feb 21 2007 - 16:04:59 PST)
AMBER: DNA and RNA computations Jiri Sponer (Mon Feb 19 2007 - 10:16:53 PST)
AMBER: problems with bonding disulfide linkages Beale, John (Mon Feb 19 2007 - 12:39:10 PST)
- Re: AMBER: problems with bonding disulfide linkages Carlos Simmerling (Mon Feb 19 2007 - 12:45:28 PST)
- Re: AMBER: problems with bonding disulfide linkages Pankaj R. Daga (Mon Feb 19 2007 - 14:54:24 PST)
AMBER: Error in running replica exchange MD Seongeun Yang (Tue Feb 20 2007 - 03:45:38 PST)
- Re: AMBER: Error in running replica exchange MD Carlos Simmerling (Tue Feb 20 2007 - 06:17:56 PST)
  - Re: AMBER: Error in running replica exchange MD Carlos Simmerling (Tue Feb 20 2007 - 06:26:24 PST)
AMBER: Beale, John (Tue Feb 20 2007 - 05:02:24 PST)
AMBER: oops Beale, John (Tue Feb 20 2007 - 05:35:19 PST)
AMBER: RE: about ANTECHAMBER Ross Walker (Tue Feb 20 2007 - 08:22:21 PST)
- AMBER: interior dielectric constant Miguel Ferreira (Tue Feb 20 2007 - 09:22:31 PST)
AMBER: AMBER ff in CHARMM format!! Swarup Gupta (Tue Feb 20 2007 - 19:26:38 PST)
AMBER: Nanopore simulation subhasish chatterjee (Tue Feb 20 2007 - 20:02:56 PST)
AMBER: Is this system too large? Hu, Shaowen $JSC-SK$[USRA] (Tue Feb 20 2007 - 20:17:41 PST)
- Re: AMBER: Is this system too large? Fenghui Fan (Tue Feb 20 2007 - 20:53:26 PST)
  - RE: AMBER: Is this system too large? Hu, Shaowen $JSC-SK$[USRA] (Wed Feb 21 2007 - 09:02:21 PST)
    - RE: AMBER: Is this system too large? Fenghui Fan (Wed Feb 21 2007 - 14:55:57 PST)
- Re: AMBER: Is this system too large? David A. Case (Wed Feb 21 2007 - 16:05:39 PST)
  - RE: AMBER: Is this system too large? Hu, Shaowen $JSC-SK$[USRA] (Thu Feb 22 2007 - 07:58:01 PST)
    - Re: AMBER: Is this system too large? David A. Case (Thu Feb 22 2007 - 18:01:52 PST)
    - RE: AMBER: Is this system too large? Hu, Shaowen $JSC-SK$[USRA] (Fri Feb 23 2007 - 08:10:09 PST)
AMBER: LEaP Problem Beale, John (Wed Feb 21 2007 - 05:11:13 PST)
- Re: AMBER: LEaP Problem David A. Case (Thu Feb 22 2007 - 18:02:11 PST)
AMBER: native contact analysis! r. a. (Wed Feb 21 2007 - 18:52:37 PST)
AMBER: atom types deepti nayar (Wed Feb 21 2007 - 21:43:38 PST)
AMBER: Errors in amber9 parallel installation Seongeun Yang (Thu Feb 22 2007 - 05:34:23 PST)
- RE: AMBER: Errors in amber9 parallel installation Ross Walker (Thu Feb 22 2007 - 05:52:16 PST)
AMBER: applying restraints Seth Lilavivat (Thu Feb 22 2007 - 08:40:59 PST)
AMBER: Sander slower on 16 processors than 8 Sontum, Steve (Thu Feb 22 2007 - 12:32:42 PST)
- Re: AMBER: Sander slower on 16 processors than 8 Martin Stennett (Thu Feb 22 2007 - 13:10:40 PST)
  - Re: AMBER: Sander slower on 16 processors than 8 Carlos Simmerling (Thu Feb 22 2007 - 13:19:18 PST)
  - Re: AMBER: Sander slower on 16 processors than 8 Adrian Roitberg (Thu Feb 22 2007 - 13:25:15 PST)
  - RE: AMBER: Sander slower on 16 processors than 8 Ross Walker (Thu Feb 22 2007 - 14:10:57 PST)
- Re: AMBER: Sander slower on 16 processors than 8 Martin Stennett (Thu Feb 22 2007 - 13:58:57 PST)
  - RE: AMBER: Sander slower on 16 processors than 8 Yong Duan (Thu Feb 22 2007 - 14:10:45 PST)
  - RE: AMBER: Sander slower on 16 processors than 8 Yong Duan (Thu Feb 22 2007 - 14:20:34 PST)
- RE: AMBER: Sander slower on 16 processors than 8 Ross Walker (Thu Feb 22 2007 - 14:15:07 PST)
  - RE: AMBER: Sander slower on 16 processors than 8 Yong Duan (Thu Feb 22 2007 - 14:25:13 PST)
    - RE: AMBER: Sander slower on 16 processors than 8 Ross Walker (Thu Feb 22 2007 - 17:47:55 PST)
- Re: AMBER: Sander slower on 16 processors than 8 Robert Duke (Thu Feb 22 2007 - 19:27:12 PST)
AMBER: ptraj bug? -- doesn't like restart files from REMD Nicolas Lux Fawzi (Thu Feb 22 2007 - 13:33:58 PST)
AMBER: Problems with QMMM tests on Altix Jarrod Smith (Thu Feb 22 2007 - 14:03:14 PST)
- Re: AMBER: Problems with QMMM tests on Altix Luis Gracia (Thu Feb 22 2007 - 14:35:14 PST)
- RE: AMBER: Problems with QMMM tests on Altix Ross Walker (Thu Feb 22 2007 - 18:12:55 PST)
  - RE: AMBER: Problems with QMMM tests on Altix Jarrod Smith (Fri Feb 23 2007 - 11:34:53 PST)
    - RE: AMBER: Problems with QMMM tests on Altix Ross Walker (Sat Feb 24 2007 - 10:02:24 PST)
    - Re: AMBER: Problems with QMMM tests on Altix Roberto Gomperts (Thu Mar 08 2007 - 15:39:14 PST)
AMBER: [rsachdeva.imtech.res.in: Pls help - REMD with torsional restraints] David A. Case (Thu Feb 22 2007 - 18:03:47 PST)
AMBER: Intel Fortran Compiler 9.1, MPICH, and AMBER 8 Craig Gough (Fri Feb 23 2007 - 00:47:36 PST)
- AMBER: AMBER question: Combining Gaff and ff99 forcefields for a single molecule Chris-Kriton Skylaris (Fri Feb 23 2007 - 01:54:00 PST)
- Re: AMBER: Intel Fortran Compiler 9.1, MPICH, and AMBER 8 Andreas Svrcek-Seiler (Fri Feb 23 2007 - 03:02:52 PST)
- Re: AMBER: Intel Fortran Compiler 9.1, MPICH, and AMBER 8 David A. Case (Fri Feb 23 2007 - 08:35:34 PST)
AMBER: SCF convergence issues Steven Winfield (Fri Feb 23 2007 - 03:27:38 PST)
- RE: AMBER: SCF convergence issues Ross Walker (Fri Feb 23 2007 - 11:00:21 PST)
  - Re: AMBER: SCF convergence issues Steven Winfield (Fri Feb 23 2007 - 11:13:33 PST)
    - RE: AMBER: SCF convergence issues Ross Walker (Fri Feb 23 2007 - 15:35:47 PST)
    - Re: AMBER: SCF convergence issues Steven Winfield (Fri Mar 02 2007 - 05:43:58 PST)
AMBER: Error in running Replica Exchange MD with amber9 Seongeun Yang (Fri Feb 23 2007 - 06:15:48 PST)
- Re: AMBER: Error in running Replica Exchange MD with amber9 Carlos Simmerling (Fri Feb 23 2007 - 07:16:59 PST)
- Re: AMBER: Error in running Replica Exchange MD with amber9 Seongeun Yang (Sat Feb 24 2007 - 00:49:49 PST)
  - Re: AMBER: Error in running Replica Exchange MD with amber9 Carlos Simmerling (Sat Feb 24 2007 - 12:27:01 PST)
AMBER: MD temperature and MM_pbsa temperature Rima Chaudhuri (Fri Feb 23 2007 - 13:22:30 PST)
AMBER: RESP calculation of modified nucleotides mathew k varghese (Fri Feb 23 2007 - 22:50:23 PST)
- Re: AMBER: RESP calculation of modified nucleotides rpaduri.chem.wayne.edu (Sat Feb 24 2007 - 13:49:10 PST)
  - Re: AMBER: RESP calculation of modified nucleotides FyD (Sun Feb 25 2007 - 09:49:55 PST)
  - Re: AMBER: RESP calculation of modified nucleotides mathew k varghese (Sun Feb 25 2007 - 19:17:34 PST)
    - Re: AMBER: RESP calculation of modified nucleotides Raviprasad Aduri (Mon Feb 26 2007 - 08:56:47 PST)
    - Re: AMBER: RESP calculation of modified nucleotides mathew k varghese (Wed Feb 28 2007 - 00:55:58 PST)
    - Re: AMBER: RESP calculation of modified nucleotides Raviprasad Aduri (Wed Feb 28 2007 - 13:11:34 PST)
    - Re: AMBER: RESP calculation of modified nucleotides mathew k varghese (Thu Mar 01 2007 - 06:33:00 PST)
    - Re: AMBER: RESP calculation of modified nucleotides Raviprasad Aduri (Thu Mar 01 2007 - 10:12:54 PST)
    - Re: AMBER: RESP calculation of modified nucleotides mathew k varghese (Thu Mar 01 2007 - 19:22:43 PST)
    - Re: AMBER: RESP calculation of modified nucleotides mathew k varghese (Fri Mar 02 2007 - 03:35:41 PST)
    - Re: AMBER: RESP calculation of modified nucleotides Raviprasad Aduri (Fri Mar 02 2007 - 09:16:39 PST)
AMBER: Best way to apply WC basepair restraints during MD Seth Lilavivat (Sun Feb 25 2007 - 12:24:40 PST)
AMBER: problem with atom restraints Ed Pate (Sun Feb 25 2007 - 20:53:31 PST)
- Re: AMBER: problem with atom restraints David A. Case (Wed Feb 28 2007 - 10:54:58 PST)
AMBER: getting same box dimension bertrand russell (Sun Feb 25 2007 - 21:27:40 PST)
- Re: AMBER: getting same box dimension David A. Case (Mon Feb 26 2007 - 18:10:30 PST)
AMBER: phe-phe molecule deepti nayar (Sun Feb 25 2007 - 22:01:26 PST)
- Re: AMBER: phe-phe molecule bertrand russell (Sun Feb 25 2007 - 22:08:42 PST)
  - Re: AMBER: phe-phe molecule deepti nayar (Sun Feb 25 2007 - 23:46:10 PST)
    - Re: AMBER: phe-phe molecule bertrand russell (Mon Feb 26 2007 - 00:03:27 PST)
    - Re: AMBER: phe-phe molecule deepti nayar (Mon Feb 26 2007 - 20:51:53 PST)
    - Re: AMBER: phe-phe molecule David A. Case (Wed Feb 28 2007 - 10:03:49 PST)
AMBER: Modified nucleotides-ATOM TYPES mathew k varghese (Mon Feb 26 2007 - 01:13:59 PST)
- Re: AMBER: Modified nucleotides-ATOM TYPES David A. Case (Mon Feb 26 2007 - 06:21:16 PST)
AMBER: PTRAJ problem Beale, John (Mon Feb 26 2007 - 10:26:21 PST)
AMBER: Re: REMD with torsional restraints- Temperature swapping not occuring David A. Case (Mon Feb 26 2007 - 15:01:41 PST)
AMBER: IFVARI parameter Ed Pate (Tue Feb 27 2007 - 13:22:43 PST)
- Re: AMBER: IFVARI parameter Kristina Furse (Tue Feb 27 2007 - 13:50:45 PST)
AMBER: abnormal high temperature during NPT ensembles MD ebright HMS (Tue Feb 27 2007 - 15:13:29 PST)
- Re: AMBER: abnormal high temperature during NPT ensembles MD Carlos Simmerling (Tue Feb 27 2007 - 18:36:01 PST)
  - Re: AMBER: abnormal high temperature during NPT ensembles MD ebright HMS (Wed Feb 28 2007 - 08:29:41 PST)
AMBER: AM1-bcc Evan Kelly (Tue Feb 27 2007 - 16:26:22 PST)
- RE: AMBER: AM1-bcc Junmei Wang (Tue Feb 27 2007 - 18:57:23 PST)
AMBER: Disulfide Bonds Beale, John (Wed Feb 28 2007 - 04:56:55 PST)
- Re: AMBER: Disulfide Bonds Jerome.GOLEBIOWSKI.unice.fr (Wed Feb 28 2007 - 05:27:23 PST)
  - RE: AMBER: Disulfide Bonds Beale, John (Wed Feb 28 2007 - 05:37:48 PST)
AMBER: LEaP crashes Beale, John (Wed Feb 28 2007 - 08:29:16 PST)
- Re: AMBER: LEaP crashes David A. Case (Wed Feb 28 2007 - 10:03:29 PST)
AMBER: solvent accessible surface area (SASA) Esther Brugger (Wed Feb 28 2007 - 10:38:55 PST)
- Re: AMBER: solvent accessible surface area (SASA) Carlos Simmerling (Wed Feb 28 2007 - 14:50:20 PST)
  - Re: AMBER: solvent accessible surface area (SASA) Esther Brugger (Wed Feb 28 2007 - 15:54:51 PST)
    - Re: AMBER: solvent accessible surface area (SASA) Carlos Simmerling (Thu Mar 01 2007 - 04:10:55 PST)
    - Re: AMBER: solvent accessible surface area (SASA) Esther Brugger (Thu Mar 01 2007 - 07:23:04 PST)
    - Re: AMBER: solvent accessible surface area (SASA) Carlos Simmerling (Thu Mar 01 2007 - 08:07:51 PST)
    - Re: AMBER: solvent accessible surface area (SASA) Esther Brugger (Thu Mar 01 2007 - 08:40:16 PST)
    - Re: AMBER: solvent accessible surface area (SASA) David A. Case (Thu Mar 01 2007 - 10:42:31 PST)
    - Re: AMBER: solvent accessible surface area (SASA) Esther Brugger (Thu Mar 01 2007 - 11:15:51 PST)
    - Re: AMBER: solvent accessible surface area (SASA) Carlos Simmerling (Thu Mar 01 2007 - 14:42:31 PST)
    - Re: AMBER: solvent accessible surface area (SASA) Esther Brugger (Thu Mar 01 2007 - 15:58:50 PST)
    - Re: AMBER: solvent accessible surface area (SASA) Carlos Simmerling (Fri Mar 02 2007 - 04:14:20 PST)
    - Re: AMBER: solvent accessible surface area (SASA) David A. Case (Thu Mar 01 2007 - 08:47:19 PST)
    - Re: AMBER: solvent accessible surface area (SASA) Esther Brugger (Thu Mar 01 2007 - 09:03:34 PST)
AMBER: Difference in Equilibration & Production MD in Amber Akshay Patny (Wed Feb 28 2007 - 12:33:56 PST)
- Re: AMBER: Difference in Equilibration & Production MD in Amber Gustavo Seabra (Wed Feb 28 2007 - 12:54:13 PST)
AMBER: momentum and periodic boundary condition Wei Chen (Wed Feb 28 2007 - 17:59:49 PST)
- Re: AMBER: momentum and periodic boundary condition David A. Case (Thu Mar 01 2007 - 08:52:00 PST)
AMBER: Disulfide Problem Beale, John (Thu Mar 01 2007 - 05:49:22 PST)
- Re: AMBER: Disulfide Problem Carlos Simmerling (Thu Mar 01 2007 - 06:15:22 PST)
  - RE: AMBER: Disulfide Problem Beale, John (Thu Mar 01 2007 - 06:45:24 PST)
    - RE: AMBER: Disulfide Problem Kristina Furse (Thu Mar 01 2007 - 08:19:17 PST)
    - Re: AMBER: Disulfide Problem David A. Case (Thu Mar 01 2007 - 09:00:31 PST)
    - AMBER: OpenMPI on MacBook Pro -- problems Mike Summers (Fri Mar 02 2007 - 08:48:49 PST)
    - Re: AMBER: OpenMPI on MacBook Pro -- problems David A. Case (Fri Mar 02 2007 - 09:36:28 PST)
    - Re: AMBER: OpenMPI on MacBook Pro -- problems Mike Summers (Fri Mar 02 2007 - 12:04:17 PST)
    - Re: AMBER: OpenMPI on MacBook Pro -- problems Mike Summers (Fri Mar 02 2007 - 12:36:07 PST)
    - Re: AMBER: OpenMPI on MacBook Pro -- problems Mike Summers (Sat Mar 03 2007 - 08:07:28 PST)
    - AMBER: coordinate changes using ptraj Mike Summers (Sat Mar 03 2007 - 16:34:24 PST)
    - Re: AMBER: coordinate changes using ptraj Carlos Simmerling (Sat Mar 03 2007 - 16:44:00 PST)
    - Re: AMBER: coordinate changes using ptraj Mike Summers (Sat Mar 03 2007 - 17:39:28 PST)
    - Re: AMBER: coordinate changes using ptraj Carlos Simmerling (Sun Mar 04 2007 - 06:19:33 PST)
    - Re: AMBER: coordinate changes using ptraj David A. Case (Mon Mar 05 2007 - 08:41:42 PST)
  - Re: AMBER: Disulfide Problem xiaoqin huang (Fri Mar 02 2007 - 06:48:14 PST)
    - Re: AMBER: Disulfide Problem Carlos Simmerling (Fri Mar 02 2007 - 06:54:42 PST)
AMBER: Restart from restart file obtained from ptraj with added velocities j j (Thu Mar 01 2007 - 08:17:41 PST)
- Re: AMBER: Restart from restart file obtained from ptraj with added velocities Thomas Cheatham III (Thu Mar 01 2007 - 08:51:28 PST)
  - Re: AMBER: Restart from restart file obtained from ptraj with added velocities j j (Thu Mar 01 2007 - 09:43:13 PST)
AMBER: [rsachdeva.imtech.res.in: A query] David A. Case (Thu Mar 01 2007 - 09:02:27 PST)
- Re: AMBER: [rsachdeva.imtech.res.in: A query] Viktor Hornak (Thu Mar 01 2007 - 10:56:40 PST)
AMBER: qm/mm ti Ben Sattelle (Fri Mar 02 2007 - 05:54:53 PST)
- Re: AMBER: qm/mm ti Adrian Roitberg (Fri Mar 02 2007 - 06:02:49 PST)
AMBER: Restart Files Steve Seibold (Fri Mar 02 2007 - 07:26:03 PST)
- Re: AMBER: Restart Files Carlos Simmerling (Fri Mar 02 2007 - 07:32:46 PST)
  - RE: AMBER: Restart Files Steve Seibold (Fri Mar 02 2007 - 09:01:19 PST)
    - Re: AMBER: Restart Files Gustavo Seabra (Fri Mar 02 2007 - 10:06:16 PST)
    - RE: AMBER: Restart Files Steve Seibold (Fri Mar 02 2007 - 11:52:39 PST)
    - Re: AMBER: Restart Files Gustavo Seabra (Fri Mar 02 2007 - 13:28:26 PST)
AMBER: restraints during MD Seth Lilavivat (Fri Mar 02 2007 - 08:16:05 PST)
- Re: AMBER: restraints during MD Carlos Simmerling (Fri Mar 02 2007 - 08:27:50 PST)
AMBER: reproducibility between software Stern, Julie (Fri Mar 02 2007 - 08:34:32 PST)
- Re: AMBER: reproducibility between software Carlos Simmerling (Fri Mar 02 2007 - 08:43:04 PST)
- Re: AMBER: reproducibility between software Thomas Cheatham III (Fri Mar 02 2007 - 09:32:35 PST)
- Re: AMBER: reproducibility between software Robert Duke (Fri Mar 02 2007 - 09:49:01 PST)
AMBER: Amber 9 make parallel fails with mpich Rene Salmon (Fri Mar 02 2007 - 09:45:37 PST)
- Re: AMBER: Amber 9 make parallel fails with mpich David A. Case (Fri Mar 02 2007 - 09:59:50 PST)
AMBER: ptraj average structure strip water Youyi Peng (Fri Mar 02 2007 - 11:52:02 PST)
AMBER: Calcium parameters Lei Jia (Fri Mar 02 2007 - 11:58:27 PST)
- Re: AMBER: Calcium parameters Qing Zhang (Fri Mar 02 2007 - 15:10:24 PST)
AMBER: Restraints on modified NA's Seth Lilavivat (Fri Mar 02 2007 - 13:56:07 PST)
- Re: AMBER: Restraints on modified NA's David A. Case (Mon Mar 05 2007 - 08:44:56 PST)
AMBER: calculate RMSD of only chain C 赵亚雪 (Fri Mar 02 2007 - 18:21:33 PST)
- Re: AMBER: calculate RMSD of only chain C Carlos Simmerling (Sat Mar 03 2007 - 06:51:34 PST)
AMBER: TI calculation: charge is not zero in the perturbed state brmeher.iitg.ernet.in (Sat Mar 03 2007 - 12:32:02 PST)
- Re: AMBER: TI calculation: charge is not zero in the perturbed state David A. Case (Sat Mar 03 2007 - 13:11:52 PST)
AMBER: denaturing salt conditions Sean Rathlef (Sat Mar 03 2007 - 14:35:45 PST)
- Re: AMBER: denaturing salt conditions Jiri Sponer (Sat Mar 03 2007 - 16:28:28 PST)
AMBER: Question about translational and rotational degree of freedom in MM-PBSA v9 computations Cenk Andac (Sun Mar 04 2007 - 04:06:22 PST)
AMBER: prep file limit exceeding gurpreet singh (Sun Mar 04 2007 - 23:52:49 PST)
- Re: AMBER: prep file limit exceeding David A. Case (Mon Mar 05 2007 - 21:25:20 PST)
AMBER: distance calculation! r. a. (Mon Mar 05 2007 - 00:43:45 PST)
AMBER: psi , phi angles deepti nayar (Mon Mar 05 2007 - 03:07:41 PST)
- Re: AMBER: psi , phi angles Carlos Simmerling (Mon Mar 05 2007 - 04:08:27 PST)
  - Re: AMBER: psi , phi angles Piotr Cieplak (Mon Mar 05 2007 - 09:29:30 PST)
    - Re: AMBER: psi , phi angles Carlos Simmerling (Mon Mar 05 2007 - 09:39:40 PST)
    - Re: AMBER: psi , phi angles M. L. Dodson (Mon Mar 05 2007 - 09:42:13 PST)
    - Re: AMBER: psi , phi angles Piotr Cieplak (Mon Mar 05 2007 - 10:30:46 PST)
    - Re: AMBER: psi , phi angles Carlos Simmerling (Mon Mar 05 2007 - 10:56:46 PST)
    - Re: AMBER: psi , phi angles Piotr Cieplak (Mon Mar 05 2007 - 11:27:13 PST)
    - Re: AMBER: psi , phi angles Ilyas Yildirim (Tue Mar 06 2007 - 04:10:32 PST)
AMBER: pbsa installation problem bala (Mon Mar 05 2007 - 04:34:32 PST)
- Re: AMBER: pbsa installation problem David A. Case (Mon Mar 05 2007 - 09:48:13 PST)
AMBER: Beale, John (Mon Mar 05 2007 - 09:50:26 PST)
AMBER: Beale, John (Mon Mar 05 2007 - 09:51:29 PST)
AMBER: constraint pdb file Stern, Julie (Mon Mar 05 2007 - 13:06:47 PST)
AMBER: mm_pbsa individual contributions of residues AYTUG TUNCEL (Mon Mar 05 2007 - 15:12:54 PST)
AMBER: how to incorporate ismem =1 into mm_pbsa AYTUG TUNCEL (Mon Mar 05 2007 - 15:32:19 PST)
AMBER: any general approach to create SiO2 wall Sisir Das (Mon Mar 05 2007 - 20:46:42 PST)
AMBER: Trimannoside Problem Sandeep Kaushik (Tue Mar 06 2007 - 04:44:20 PST)
- Re: AMBER: Trimannoside Problem kkirschn.hamilton.edu (Tue Mar 06 2007 - 10:13:43 PST)
  - Re: AMBER: Trimannoside Problem Sandeep Kaushik (Wed Mar 07 2007 - 23:02:02 PST)
    - Re: AMBER: Trimannoside Problem kkirschn.hamilton.edu (Thu Mar 08 2007 - 05:37:27 PST)
    - Re: AMBER: Trimannoside Problem Austin B. Yongye (Thu Mar 08 2007 - 06:09:48 PST)
    - Re: AMBER: Trimannoside Problem Sandeep Kaushik (Mon Mar 19 2007 - 00:02:54 PDT)
AMBER: how is the standard deviations calculated in mm-pbsa? Magne Olufsen (Tue Mar 06 2007 - 04:58:17 PST)
- Re: AMBER: how is the standard deviations calculated in mm-pbsa? David A. Case (Tue Mar 06 2007 - 17:13:55 PST)
AMBER: DHAS_10_12 compilation aborted for egb.f Jesus Angulo (Tue Mar 06 2007 - 06:31:28 PST)
- Re: AMBER: DHAS_10_12 compilation aborted for egb.f David A. Case (Tue Mar 06 2007 - 08:31:10 PST)
  - RE: AMBER: DHAS_10_12 compilation aborted for egb.f Jesus Angulo (Tue Mar 06 2007 - 09:41:37 PST)
    - Re: AMBER: DHAS_10_12 compilation aborted for egb.f David A. Case (Wed Mar 07 2007 - 10:11:21 PST)
AMBER: how to modify map.DG-AMBER file? Seth Lilavivat (Tue Mar 06 2007 - 12:55:40 PST)
- Re: AMBER: how to modify map.DG-AMBER file? David A. Case (Tue Mar 06 2007 - 17:06:57 PST)
- Re: AMBER: how to modify map.DG-AMBER file? A Box (Tue Apr 10 2007 - 16:56:21 PDT)
AMBER: addles segmentation fault deepti nayar (Tue Mar 06 2007 - 23:18:39 PST)
- Re: AMBER: addles segmentation fault David A. Case (Wed Mar 07 2007 - 09:23:21 PST)
  - AMBER: simulation of the phosphorylated protein Fenghui Fan (Wed Mar 07 2007 - 17:20:09 PST)
  - Re: AMBER: addles segmentation fault deepti nayar (Thu Mar 08 2007 - 01:35:43 PST)
AMBER: Topology file problem in TI ! Pradipta Bandyopadhyay (Wed Mar 07 2007 - 03:08:39 PST)
- Re: AMBER: Topology file problem in TI ! Thomas Steinbrecher (Wed Mar 07 2007 - 08:48:10 PST)
  - Re: AMBER: Topology file problem in TI ! Ilyas Yildirim (Wed Mar 07 2007 - 10:09:39 PST)
    - Re: AMBER: Topology file problem in TI ! Thomas Steinbrecher (Wed Mar 07 2007 - 11:35:29 PST)
  - Re: AMBER: Topology file problem in TI ! Pradipta Bandyopadhyay (Wed Mar 07 2007 - 21:55:26 PST)
    - Re: AMBER: Topology file problem in TI ! David A. Case (Thu Mar 08 2007 - 07:59:22 PST)
    - Re: AMBER: Topology file problem in TI ! Pradipta Bandyopadhyay (Thu Mar 08 2007 - 08:18:58 PST)
AMBER: van der Waals parameters and 6-12 potential parameters of NB in parm99.dat? Chengwen Chen (Fri Mar 09 2007 - 00:04:00 PST)
- Re: AMBER: van der Waals parameters and 6-12 potential parameters of NB in parm99.dat? Carlos Simmerling (Fri Mar 09 2007 - 04:07:48 PST)
  - Re: AMBER: van der Waals parameters and 6-12 potential parameters of NB in parm99.dat? Chengwen Chen (Fri Mar 09 2007 - 23:37:06 PST)
  - AMBER: Problem with PCSHIFT module Edoardo Saccenti (Fri Mar 30 2007 - 04:20:37 PDT)
    - Re: AMBER: Problem with PCSHIFT module David A. Case (Sat Mar 31 2007 - 21:13:12 PDT)
    - Re: AMBER: Problem with PCSHIFT module Edoardo Saccenti (Tue Apr 03 2007 - 01:08:38 PDT)
    - Re: AMBER: Problem with PCSHIFT module Edoardo Saccenti (Thu Apr 12 2007 - 05:40:55 PDT)
    - Re: AMBER: Problem with PCSHIFT module David A. Case (Sun Apr 15 2007 - 21:24:01 PDT)
AMBER: problem with ptraj with calculating auto time correlation functions Terry Lang (Fri Mar 09 2007 - 10:36:14 PST)
- Re: AMBER: problem with ptraj with calculating auto time correlation functions David A. Case (Fri Mar 09 2007 - 17:01:44 PST)
  - Re: AMBER: problem with ptraj with calculating auto time correlation functions Terry Lang (Sat Mar 10 2007 - 07:59:09 PST)
    - Re: AMBER: problem with ptraj with calculating auto time correlation functions David A. Case (Sat Mar 10 2007 - 09:34:32 PST)
AMBER: abnormal termination of tleap Pankaj R. Daga (Fri Mar 09 2007 - 14:24:37 PST)
AMBER: rmsd calculation in ptraj gurpreet singh (Sat Mar 10 2007 - 05:24:50 PST)
AMBER: rmsd calculation in ptraj gurpreet singh (Sat Mar 10 2007 - 05:38:28 PST)
- Re: AMBER: rmsd calculation in ptraj Carlos Simmerling (Sat Mar 10 2007 - 06:26:34 PST)
AMBER: rmsd calculation in ptraj II gurpreet singh (Sat Mar 10 2007 - 20:37:10 PST)
- Re: AMBER: rmsd calculation in ptraj II David A. Case (Sat Mar 10 2007 - 21:55:32 PST)
AMBER: unable to run test Anju Sharma (Sun Mar 11 2007 - 22:14:03 PDT)
- Re: AMBER: unable to run test David A. Case (Sun Mar 11 2007 - 23:54:34 PDT)
AMBER: addles deepti nayar (Sun Mar 11 2007 - 23:29:37 PDT)
- Re: AMBER: addles Carlos Simmerling (Mon Mar 12 2007 - 04:28:20 PDT)
  - Re: AMBER: addles deepti nayar (Mon Mar 12 2007 - 04:37:27 PDT)
AMBER: NEB tutorial deepti nayar (Mon Mar 12 2007 - 03:03:17 PDT)
AMBER: The parallel test fails while sander.MPI seems to be installed correctly Mostafa Sadighi (Mon Mar 12 2007 - 04:43:14 PDT)
- Re: AMBER: The parallel test fails while sander.MPI seems to be installed correctly Carlos Simmerling (Mon Mar 12 2007 - 04:51:38 PDT)
- Re: AMBER: The parallel test fails while sander.MPI seems to be installed correctly Gustavo Seabra (Mon Mar 12 2007 - 06:23:50 PDT)
AMBER: DNA Helicoïdal Plots over time Stéphane Téletchéa (Mon Mar 12 2007 - 05:31:02 PDT)
- Re: AMBER: DNA Helicoïdal Plots over time Vitor Felix (Mon Mar 12 2007 - 05:51:12 PDT)
- AMBER: dna forcefield: PARMBSC0 Alberto Perez (Wed Mar 14 2007 - 00:14:36 PDT)
AMBER: Can I measure improper torsion by ptarj? Chengwen Chen (Mon Mar 12 2007 - 09:21:55 PDT)
- Re: AMBER: Can I measure improper torsion by ptarj? David A. Case (Mon Mar 12 2007 - 09:36:07 PDT)
  - Re: AMBER: Can I measure improper torsion by ptarj? Chengwen Chen (Mon Mar 12 2007 - 21:18:24 PDT)
    - Re: AMBER: Can I measure improper torsion by ptarj? David A. Case (Tue Mar 13 2007 - 09:55:13 PDT)
- Re: AMBER: Can I measure improper torsion by ptarj? Bill Ross (Tue Mar 13 2007 - 10:23:24 PDT)
AMBER: hi.. Anju Sharma (Tue Mar 13 2007 - 04:59:24 PDT)
- Re: AMBER: hi.. Carlos Simmerling (Tue Mar 13 2007 - 05:08:47 PDT)
  - Re: AMBER: hi.. Anju Sharma (Tue Mar 13 2007 - 05:15:27 PDT)
    - Re: AMBER: hi.. Carlos Simmerling (Tue Mar 13 2007 - 05:20:40 PDT)
    - Re: AMBER: hi.. Anju Sharma (Tue Mar 13 2007 - 05:28:23 PDT)
    - Re: AMBER: hi.. Anju Sharma (Tue Mar 13 2007 - 05:29:28 PDT)
    - RE: AMBER: hi.. Rafi Ahmad (Tue Mar 13 2007 - 05:32:18 PDT)
    - RE: AMBER: hi.. Rafi Ahmad (Tue Mar 13 2007 - 05:20:28 PDT)
AMBER: problem with mm_pbsa Yves Boulard (Tue Mar 13 2007 - 07:21:22 PDT)
AMBER: poor performance of sander on a quad-core linux machine Lillian chong (Tue Mar 13 2007 - 10:27:31 PDT)
- Re: AMBER: poor performance of sander on a quad-core linux machine David A. Case (Tue Mar 13 2007 - 10:42:48 PDT)
AMBER: problem while running minimisation Anju Sharma (Tue Mar 13 2007 - 21:10:15 PDT)
- Re: AMBER: problem while running minimisation Anju Sharma (Tue Mar 13 2007 - 21:19:03 PDT)
AMBER: Problem Solved Anju Sharma (Tue Mar 13 2007 - 21:19:57 PDT)
AMBER: NEB tutorial and addles deepti nayar (Tue Mar 13 2007 - 21:28:20 PDT)
- RE: AMBER: NEB tutorial and addles Ross Walker (Thu Mar 15 2007 - 09:21:29 PDT)
AMBER: problem while analysing result Anju Sharma (Tue Mar 13 2007 - 22:38:37 PDT)
- Re: AMBER: problem while analysing result puneet kacker (Tue Mar 13 2007 - 22:59:20 PDT)
  - Re: AMBER: problem while analysing result Anju Sharma (Tue Mar 13 2007 - 23:27:20 PDT)
    - Re: AMBER: problem while analysing result Syed Tarique Moin (Tue Mar 13 2007 - 23:43:59 PDT)
    - Re: AMBER: problem while analysing result puneet kacker (Tue Mar 13 2007 - 23:46:22 PDT)
AMBER: Need help in Analysis Anju Sharma (Wed Mar 14 2007 - 02:13:03 PDT)
- Re: AMBER: Need help in Analysis Heike.Meiselbach.chemie.uni-erlangen.de (Wed Mar 14 2007 - 03:35:34 PDT)
- Re: AMBER: Need help in Analysis Gustavo Seabra (Wed Mar 14 2007 - 03:39:51 PDT)
- AMBER: AMBER hydrophobic Box : script Sophie Barbe (Wed Mar 14 2007 - 03:48:50 PDT)
  - Re: AMBER: AMBER hydrophobic Box : script David A. Case (Wed Mar 14 2007 - 08:29:47 PDT)
    - Re: AMBER: AMBER hydrophobic Box : script Sophie Barbe (Wed Mar 14 2007 - 09:00:30 PDT)
    - Re: AMBER: AMBER hydrophobic Box : script David A. Case (Wed Mar 14 2007 - 09:22:41 PDT)
    - AMBER: Lipid bilayer nag raj (Wed Mar 14 2007 - 20:51:19 PDT)
AMBER: torsion angle deepti nayar (Wed Mar 14 2007 - 05:03:08 PDT)
- Re: AMBER: torsion angle Carlos Simmerling (Wed Mar 14 2007 - 05:27:02 PDT)
  - Re: AMBER: torsion angle deepti nayar (Wed Mar 14 2007 - 23:13:43 PDT)
    - AMBER: problem decomposing energies (MMPBSA) Cyril Bauvais (Thu Mar 15 2007 - 02:27:57 PDT)
    - AMBER: problem decomposing energies (MMPBSA) Cyril Bauvais (Tue Mar 20 2007 - 04:15:29 PDT)
AMBER: Question about Boron Kara Di Giorgio (Wed Mar 14 2007 - 10:15:22 PDT)
AMBER: mmpbsa free energy pairwise decomposition Gianluca Degliesposti (Wed Mar 14 2007 - 11:54:32 PDT)
AMBER: Regarding counter ions Rafi Ahmad (Wed Mar 14 2007 - 13:00:59 PDT)
AMBER: Segmentation fault (iforrtoccurs during minimization (Amber 9) Eric Shamay (Wed Mar 14 2007 - 18:12:49 PDT)
- Re: AMBER: Segmentation fault (iforrtoccurs during minimization (Amber 9) Carlos Simmerling (Wed Mar 14 2007 - 18:47:23 PDT)
  - Re: AMBER: Segmentation fault (iforrtoccurs during minimization (Amber 9) Eric Shamay (Wed Mar 14 2007 - 19:18:55 PDT)
- Re: AMBER: Segmentation fault (iforrtoccurs during minimization (Amber 9) David A. Case (Fri Mar 16 2007 - 13:51:14 PDT)
AMBER: How to build organic compound in Amber Anju Sharma (Wed Mar 14 2007 - 21:24:09 PDT)
AMBER: hii Anju Sharma (Thu Mar 15 2007 - 02:28:47 PDT)
- Re: AMBER: hii Benjamin Juhl (Thu Mar 15 2007 - 02:44:18 PDT)
AMBER: Problem related simulation of dimer priya priya (Thu Mar 15 2007 - 04:23:31 PDT)
- Re: AMBER: Problem related simulation of dimer Carlos Simmerling (Thu Mar 15 2007 - 04:38:57 PDT)
  - Re: AMBER: Problem related simulation of dimer Abhilash (Thu Mar 15 2007 - 09:03:06 PDT)
    - Re: AMBER: Problem related simulation of dimer David A. Case (Thu Mar 15 2007 - 10:09:52 PDT)
    - Re: AMBER: Problem related simulation of dimer janavi raghavan (Thu Mar 15 2007 - 10:24:23 PDT)
    - Re: AMBER: Problem related simulation of dimer janavi raghavan (Thu Mar 15 2007 - 10:28:32 PDT)
- Re: AMBER: Problem related simulation of dimer Sandeep Kaushik (Fri Mar 16 2007 - 03:32:20 PDT)
  - Re: AMBER: Problem related simulation of dimer priya priya (Sun Mar 18 2007 - 22:35:42 PDT)
    - Re: AMBER: Problem related simulation of dimer Sandeep Kaushik (Mon Mar 19 2007 - 00:47:49 PDT)
    - Re: AMBER: Problem related simulation of dimer priya priya (Mon Mar 19 2007 - 03:38:59 PDT)
    - Re: AMBER: Problem related simulation of dimer Sandeep Kaushik (Mon Mar 19 2007 - 04:16:39 PDT)
AMBER: Dipolar and Inertia Moments kepa koldo burusco (Thu Mar 15 2007 - 04:46:17 PDT)
AMBER: solvate shell janavi raghavan (Thu Mar 15 2007 - 09:33:13 PDT)
- Re: AMBER: solvate shell Carlos Simmerling (Thu Mar 15 2007 - 09:36:52 PDT)
  - Re: AMBER: solvate shell janavi raghavan (Thu Mar 15 2007 - 10:27:42 PDT)
  - AMBER: Problem with anisotropic pressure scaling Linda Prengaman (Fri Mar 16 2007 - 07:23:30 PDT)
    - RE: AMBER: Problem with anisotropic pressure scaling Akshay Patny (Fri Mar 16 2007 - 09:37:22 PDT)
    - Re: AMBER: Problem with anisotropic pressure scaling Robert Duke (Fri Mar 16 2007 - 08:46:58 PDT)
    - Re: AMBER: Problem with anisotropic pressure scaling Andy Purkiss-Trew (Fri Mar 16 2007 - 08:47:19 PDT)
    - Re: AMBER: Problem with anisotropic pressure scaling David A. Case (Fri Mar 16 2007 - 08:55:51 PDT)
- Re: AMBER: solvate shell David A. Case (Thu Mar 15 2007 - 12:36:04 PDT)
AMBER: van der waals parameters. Stefano Tonzani (Thu Mar 15 2007 - 10:52:09 PDT)
- Re: AMBER: van der waals parameters. David A. Case (Thu Mar 15 2007 - 12:30:34 PDT)
AMBER: Segmentation Fault when saving prmtop and inpcrd files in xleap Laura McDriscoll (Thu Mar 15 2007 - 22:59:33 PDT)
- Re: AMBER: Segmentation Fault when saving prmtop and inpcrd files in xleap David A. Case (Fri Mar 16 2007 - 08:24:16 PDT)
AMBER: hi Anju Sharma (Fri Mar 16 2007 - 03:50:44 PDT)
- Re: AMBER: hi Carlos Simmerling (Fri Mar 16 2007 - 04:14:15 PDT)
AMBER: vlimit error Amit Kumar (Fri Mar 16 2007 - 16:10:06 PDT)
- Re: AMBER: vlimit error David A. Case (Mon Mar 19 2007 - 16:11:57 PDT)
AMBER: antechamber error Ilyas Yildirim (Fri Mar 16 2007 - 23:44:57 PDT)
- RE: AMBER: antechamber error Fang, Jianwen (Mon Feb 09 2004 - 10:00:28 PST)
AMBER: targeted MD problem gurpreet singh (Sat Mar 17 2007 - 05:17:27 PDT)
- Re: AMBER: targeted MD problem Carlos Simmerling (Sat Mar 17 2007 - 05:27:28 PDT)
- AMBER: MMPBSA with water molecule in active site saurabh agrawal (Sun Mar 18 2007 - 10:25:44 PDT)
  - Re: AMBER: MMPBSA with water molecule in active site Carlos Simmerling (Sun Mar 18 2007 - 10:43:44 PDT)
    - Re: AMBER: MMPBSA with water molecule in active site saurabh agrawal (Sun Mar 18 2007 - 11:03:21 PDT)
    - Re: AMBER: MMPBSA with water molecule in active site Carlos Simmerling (Sun Mar 18 2007 - 11:07:14 PDT)
    - Re: AMBER: MMPBSA with water molecule in active site saurabh agrawal (Sun Mar 18 2007 - 11:30:31 PDT)
    - Re: AMBER: MMPBSA with water molecule in active site Jiri Sponer (Sun Mar 18 2007 - 11:21:17 PDT)
AMBER: targetedMD problem gurpreet singh (Sun Mar 18 2007 - 06:32:40 PDT)
AMBER: antechamber Ilyas Yildirim (Sun Mar 18 2007 - 10:56:00 PDT)
- Re: AMBER: antechamber David A. Case (Sun Mar 18 2007 - 16:50:00 PDT)
AMBER: hi Anju Sharma (Sun Mar 18 2007 - 20:56:22 PDT)
- RE: AMBER: hi Ross Walker (Sun Mar 18 2007 - 22:09:56 PDT)
AMBER: Problem while creating structure in xLeap Anju Sharma (Sun Mar 18 2007 - 21:30:03 PDT)
- Re: AMBER: Problem while creating structure in xLeap Jin-Soo Kim (Sat Mar 24 2007 - 04:53:29 PDT)
AMBER: Problem!! Anju Sharma (Sun Mar 18 2007 - 23:38:15 PDT)
- RE: AMBER: Problem!! Ross Walker (Mon Mar 19 2007 - 08:23:40 PDT)
AMBER: MM-GBSA residues decomposition comparison Sergey Samsonov (Tue Mar 20 2007 - 07:17:26 PDT)
AMBER: basis set for RESP calculation Michel Becker (Tue Mar 20 2007 - 13:43:10 PDT)
- Re: AMBER: basis set for RESP calculation FyD (Wed Mar 21 2007 - 01:03:15 PDT)
- Re: AMBER: basis set for RESP calculation FyD (Wed Mar 21 2007 - 10:17:44 PDT)
- Re: AMBER: basis set for RESP calculation Mark Williamson (Wed Mar 21 2007 - 10:36:40 PDT)
AMBER: Problem while loading Pdb in xleap Anju Sharma (Tue Mar 20 2007 - 21:12:55 PDT)
- Re: AMBER: Problem while loading Pdb in xleap David A. Case (Tue Mar 20 2007 - 22:31:42 PDT)
- Re: AMBER: Problem while loading Pdb in xleap Sandeep Kaushik (Thu Mar 22 2007 - 03:07:13 PDT)
AMBER: Problem while running Antechamber Anju Sharma (Wed Mar 21 2007 - 02:35:28 PDT)
- Re:AMBER: Problem while running Antechamber Kateryna Miroshnychenko (Wed Mar 21 2007 - 04:06:15 PDT)
AMBER: Modified Nucleic Acid Problem SHARAD gupta (Wed Mar 21 2007 - 06:22:10 PDT)
- Re: AMBER: Modified Nucleic Acid Problem FyD (Wed Mar 21 2007 - 07:19:09 PDT)
- Re: AMBER: Modified Nucleic Acid Problem FyD (Wed Mar 21 2007 - 07:20:34 PDT)
AMBER: How to reimage the trajectories of LES calculations? Kailee (Wed Mar 21 2007 - 06:35:06 PDT)
- Re: AMBER: How to reimage the trajectories of LES calculations? Carlos Simmerling (Wed Mar 21 2007 - 10:04:03 PDT)
  - Re: AMBER: How to reimage the trajectories of LES calculations? Kailee (Wed Mar 21 2007 - 10:32:34 PDT)
AMBER: ntt=1 or ntt= 3? Therese Malliavin (Wed Mar 21 2007 - 10:32:07 PDT)
- Re: AMBER: ntt=1 or ntt= 3? Carlos Simmerling (Wed Mar 21 2007 - 10:40:20 PDT)
- RE: AMBER: ntt=1 or ntt= 3? Yong Duan (Wed Mar 21 2007 - 11:00:56 PDT)
- Re: AMBER: ntt=1 or ntt= 3? David A. Case (Wed Mar 21 2007 - 12:29:45 PDT)
  - RE: AMBER: ntt=1 or ntt= 3? Yong Duan (Thu Mar 22 2007 - 03:42:37 PDT)
  - RE: AMBER: ntt=1 or ntt= 3? Hu, Shaowen $JSC-SK$[USRA] (Thu Mar 22 2007 - 14:24:10 PDT)
    - Re: AMBER: ntt=1 or ntt= 3? Carlos Simmerling (Thu Mar 22 2007 - 14:30:05 PDT)
    - RE: AMBER: ntt=1 or ntt= 3? Hu, Shaowen $JSC-SK$[USRA] (Thu Mar 22 2007 - 14:40:09 PDT)
    - Re: AMBER: ntt=1 or ntt= 3? Carlos Simmerling (Thu Mar 22 2007 - 14:47:26 PDT)
AMBER: xLeAP: TI calculation: the perturbed charge is not integral Ignacio Faustino (Wed Mar 21 2007 - 12:17:12 PDT)
- Re: AMBER: xLeAP: TI calculation: the perturbed charge is not integral David A. Case (Wed Mar 21 2007 - 12:33:33 PDT)
  - AMBER: sander.MPI vs MPICH2 problem!!! Swarup Gupta (Fri Mar 23 2007 - 19:33:44 PDT)
AMBER: TI calculation: the perturbed charge is not integral Ignacio Faustino (Wed Mar 21 2007 - 12:21:52 PDT)
AMBER: restraint in minimization deepti nayar (Thu Mar 22 2007 - 01:21:32 PDT)
- Re: AMBER: restraint in minimization Carlos Simmerling (Thu Mar 22 2007 - 04:14:22 PDT)
  - Re: AMBER: restraint in minimization Sandeep Kaushik (Mon Mar 26 2007 - 02:21:27 PDT)
    - Re: AMBER: restraint in minimization Carlos Simmerling (Mon Mar 26 2007 - 05:19:13 PDT)
    - Re: AMBER: restraint in minimization deepti nayar (Mon Mar 26 2007 - 22:10:50 PDT)
AMBER: Holding NA Base syn during annealing Seth Lilavivat (Thu Mar 22 2007 - 08:23:20 PDT)
- Re: AMBER: Holding NA Base syn during annealing David A. Case (Thu Mar 22 2007 - 08:41:30 PDT)
AMBER: Generating structure of polyethylene glycol in AMBER Lili Peng (Thu Mar 22 2007 - 14:35:07 PDT)
- Re: AMBER: Generating structure of polyethylene glycol in AMBER FyD (Thu Mar 22 2007 - 15:11:07 PDT)
  - Re: AMBER: Generating structure of polyethylene glycol in AMBER Lili Peng (Thu Mar 22 2007 - 15:17:22 PDT)
    - Re: AMBER: Generating structure of polyethylene glycol in AMBER luckyang.gmail.com (Thu Mar 22 2007 - 15:38:02 PDT)
    - Re: AMBER: Generating structure of polyethylene glycol in AMBER FyD (Thu Mar 22 2007 - 15:57:55 PDT)
AMBER: anneal algorthm Seth Lilavivat (Fri Mar 23 2007 - 12:33:42 PDT)
AMBER: Error - must define AMBERHOME environment variable bertrand russell (Fri Mar 23 2007 - 13:05:47 PDT)
- Re: AMBER: Error - must define AMBERHOME environment variable Eric Shamay (Fri Mar 23 2007 - 15:26:02 PDT)
  - Re: AMBER: Error - must define AMBERHOME environment variable bertrand russell (Sat Mar 24 2007 - 13:18:55 PDT)
    - Re: AMBER: Error - must define AMBERHOME environment variable Eric Shamay (Sat Mar 24 2007 - 17:32:40 PDT)
- RE: AMBER: Error - must define AMBERHOME environment variable Ross Walker (Sat Mar 24 2007 - 21:06:23 PDT)
  - Re: AMBER: Error - must define AMBERHOME environment variable bertrand russell (Mon Mar 26 2007 - 01:56:06 PDT)
    - Re: AMBER: Error - must define AMBERHOME environment variable bertrand russell (Mon Mar 26 2007 - 02:03:56 PDT)
    - RE: AMBER: Error - must define AMBERHOME environment variable Ross Walker (Mon Mar 26 2007 - 09:31:08 PDT)
    - Re: AMBER: Error - must define AMBERHOME environment variable bertrand russell (Mon Mar 26 2007 - 10:10:12 PDT)
    - Re: AMBER: Error - must define AMBERHOME environment variable bertrand russell (Mon Mar 26 2007 - 10:12:57 PDT)
    - RE: AMBER: Error - must define AMBERHOME environment variable Ross Walker (Mon Mar 26 2007 - 10:56:25 PDT)
    - Re: AMBER: Error - must define AMBERHOME environment variable bertrand russell (Mon Mar 26 2007 - 22:57:31 PDT)
    - RE: AMBER: Error - must define AMBERHOME environment variable Ross Walker (Tue Mar 27 2007 - 08:31:26 PDT)
    - Re: AMBER: Error - must define AMBERHOME environment variable bertrand russell (Tue Mar 27 2007 - 11:39:28 PDT)
    - Re: AMBER: Error - must define AMBERHOME environment variable bertrand russell (Tue Mar 27 2007 - 11:42:57 PDT)
    - AMBER: SGI Altix Compilation Problems (Was: Error - must define AMBERHOME environment variable) Ross Walker (Tue Mar 27 2007 - 12:14:28 PDT)
    - Re: AMBER: SGI Altix Compilation Problems (Was: Error - must define AMBERHOME environment variable) bertrand russell (Tue Mar 27 2007 - 23:36:17 PDT)
    - Re: AMBER: SGI Altix Compilation Problems (Was: Error - must define AMBERHOME environment variable) bertrand russell (Thu Mar 29 2007 - 02:04:00 PDT)
    - RE: AMBER: SGI Altix Compilation Problems (Was: Error - must define AMBERHOME environment variable) Ross Walker (Thu Mar 29 2007 - 15:43:21 PDT)
AMBER: Combining RESP with AM1-BCC Ilyas Yildirim (Fri Mar 23 2007 - 14:41:04 PDT)
- Re: AMBER: Combining RESP with AM1-BCC David Mobley (Fri Mar 23 2007 - 16:17:50 PDT)
  - Re: AMBER: Combining RESP with AM1-BCC Ilyas Yildirim (Fri Mar 23 2007 - 17:27:07 PDT)
  - Re: AMBER: Combining RESP with AM1-BCC FyD (Sat Mar 24 2007 - 02:03:37 PDT)
AMBER: water density Esther Brugger (Fri Mar 23 2007 - 15:47:33 PDT)
- Re: AMBER: water density Cenk Andac (Fri Mar 23 2007 - 16:13:16 PDT)
AMBER: amber 9 - output of forces Eric Shamay (Fri Mar 23 2007 - 16:00:39 PDT)
- Re: AMBER: amber 9 - output of forces David A. Case (Fri Mar 23 2007 - 22:10:21 PDT)
  - Re: AMBER: amber 9 - output of forces Eric Shamay (Fri Mar 23 2007 - 23:27:41 PDT)
  - Re: AMBER: amber 9 - output of forces Eric Shamay (Mon Mar 26 2007 - 15:08:58 PDT)
    - Re: AMBER: amber 9 - output of forces Eric Shamay (Tue Mar 27 2007 - 13:36:34 PDT)
AMBER: Does Sander.MPI support coupling effect between different molecules at the same area at the same temperature in the mixture? Jin-Soo Kim (Sat Mar 24 2007 - 04:40:26 PDT)
AMBER: Please check the total charge and your -nc flag snoze pa (Sun Mar 25 2007 - 21:54:52 PDT)
- Re: AMBER: Please check the total charge and your -nc flag David A. Case (Tue Mar 27 2007 - 15:29:32 PDT)
AMBER: phe-phe simulation deepti nayar (Mon Mar 26 2007 - 00:25:19 PDT)
- Re: AMBER: phe-phe simulation Carlos Simmerling (Mon Mar 26 2007 - 05:20:52 PDT)
  - Re: AMBER: phe-phe simulation deepti nayar (Mon Mar 26 2007 - 22:12:03 PDT)
    - Re: AMBER: phe-phe simulation deepti nayar (Tue Mar 27 2007 - 05:48:01 PDT)
    - Re: AMBER: phe-phe simulation Carlos Simmerling (Tue Mar 27 2007 - 07:23:15 PDT)
    - Re: AMBER: phe-phe simulation deepti nayar (Wed Mar 28 2007 - 04:28:51 PDT)
AMBER: pmemd segmentation fault Vlad Cojocaru (Mon Mar 26 2007 - 02:14:50 PDT)
- Re: AMBER: pmemd segmentation fault Robert Duke (Mon Mar 26 2007 - 06:25:36 PDT)
  - Re: AMBER: pmemd segmentation fault Vlad Cojocaru (Mon Mar 26 2007 - 07:29:12 PDT)
- Re: AMBER: pmemd segmentation fault Robert Duke (Mon Mar 26 2007 - 08:26:22 PDT)
  - Re: AMBER: pmemd segmentation fault Vlad Cojocaru (Mon Mar 26 2007 - 09:43:52 PDT)
    - RE: AMBER: pmemd segmentation fault Ross Walker (Mon Mar 26 2007 - 10:46:48 PDT)
    - Re: AMBER: pmemd segmentation fault Vlad Cojocaru (Tue Mar 27 2007 - 05:25:26 PDT)
- Re: AMBER: pmemd segmentation fault Robert Duke (Mon Mar 26 2007 - 10:16:08 PDT)
AMBER: pdb file produced by vmd Rita Cassia (Mon Mar 26 2007 - 09:04:19 PDT)
AMBER: DNA Flat Angle Restraints Kyle L. Brown (Mon Mar 26 2007 - 10:04:09 PDT)
AMBER: distcovar in ptraj Zhenyu Lu (Mon Mar 26 2007 - 21:00:13 PDT)
AMBER: Parameter file for Dipeptide Neelanjana Sengupta (Mon Mar 26 2007 - 22:23:32 PDT)
- Re: AMBER: Parameter file for Dipeptide Carlos Simmerling (Tue Mar 27 2007 - 07:20:55 PDT)
AMBER: The ring number exceeds MAXRING, increase MAXRING and recompile the programs, exit j j (Tue Mar 27 2007 - 07:04:48 PDT)
- Re: AMBER: The ring number exceeds MAXRING, increase MAXRING and recompile the programs, exit j j (Tue Mar 27 2007 - 11:43:49 PDT)
AMBER: Question about loadMol2 David LeBard (Tue Mar 27 2007 - 11:31:56 PDT)
- Re: AMBER: Question about loadMol2 Scott Brozell (Tue Mar 27 2007 - 12:49:25 PDT)
- Re: AMBER: Question about loadMol2 David Mobley (Tue Mar 27 2007 - 13:15:26 PDT)
  - Re: AMBER: Question about loadMol2 Thomas Steinbrecher (Tue Mar 27 2007 - 13:24:55 PDT)
    - Re: AMBER: Question about loadMol2 David LeBard (Tue Mar 27 2007 - 13:49:10 PDT)
    - Re: AMBER: Question about loadMol2 Scott Brozell (Tue Mar 27 2007 - 15:11:02 PDT)
    - Re: AMBER: Question about loadMol2 David LeBard (Tue Mar 27 2007 - 15:53:21 PDT)
    - AMBER: Minimization Sophie Barbe (Wed Mar 28 2007 - 01:36:35 PDT)
    - Re: AMBER: Minimization Jerome.GOLEBIOWSKI.unice.fr (Wed Mar 28 2007 - 01:48:35 PDT)
    - Re: AMBER: Minimization Sophie Barbe (Wed Mar 28 2007 - 02:27:27 PDT)
AMBER: amber 9 install: patch reject Stern, Julie (Tue Mar 27 2007 - 11:50:33 PDT)
AMBER: amber 9: fortran/test failures Stern, Julie (Tue Mar 27 2007 - 11:55:43 PDT)
- Re: AMBER: amber 9: fortran/test failures David A. Case (Tue Mar 27 2007 - 15:15:50 PDT)
AMBER: residue types for GLY/high pH Stern, Julie (Tue Mar 27 2007 - 13:19:47 PDT)
AMBER: Amber 9 TI Details Lachele Foley (Lists) (Tue Mar 27 2007 - 14:03:20 PDT)
- Re: AMBER: Amber 9 TI Details Thomas Steinbrecher (Tue Mar 27 2007 - 14:58:55 PDT)
- Re: AMBER: Amber 9 TI Details David A. Case (Tue Mar 27 2007 - 15:23:34 PDT)
AMBER: specifying psi and phi for a dipeptide deepti nayar (Wed Mar 28 2007 - 04:50:28 PDT)
AMBER: DISAVE value1 Kyle L. Brown (Wed Mar 28 2007 - 14:42:16 PDT)
- Re: AMBER: DISAVE value1 David A. Case (Fri Mar 30 2007 - 08:24:27 PDT)
AMBER: rms and rmsf in ptraj Mingfeng Yang (Wed Mar 28 2007 - 14:06:02 PDT)
- Re: AMBER: rms and rmsf in ptraj Thomas Cheatham (Wed Mar 28 2007 - 17:01:13 PDT)
  - Re: AMBER: rms and rmsf in ptraj Scott Brozell (Thu Mar 29 2007 - 08:57:43 PDT)
AMBER: problem in implcit simulation gurpreet singh (Wed Mar 28 2007 - 21:25:53 PDT)
- RE: AMBER: problem in implcit simulation Ross Walker (Wed Mar 28 2007 - 22:02:28 PDT)
AMBER: benchmarking pmemd and sander (pmemd segmentation fault problem follow up) Vlad Cojocaru (Thu Mar 29 2007 - 02:50:29 PDT)
- Re: AMBER: benchmarking pmemd and sander (pmemd segmentation fault problem follow up) Robert Duke (Thu Mar 29 2007 - 06:57:26 PDT)
  - Re: AMBER: benchmarking pmemd and sander (pmemd segmentation fault problem follow up) Vlad Cojocaru (Thu Mar 29 2007 - 08:25:59 PDT)
- Re: AMBER: benchmarking pmemd and sander (pmemd segmentation fault problem follow up) Robert Duke (Thu Mar 29 2007 - 08:53:56 PDT)
AMBER: minimization not running deepti nayar (Thu Mar 29 2007 - 02:57:15 PDT)
- Re: AMBER: minimization not running Vlad Cojocaru (Thu Mar 29 2007 - 03:15:36 PDT)
  - Re: AMBER: minimization not running deepti nayar (Thu Mar 29 2007 - 03:51:26 PDT)
AMBER: minimization energy query deepti nayar (Thu Mar 29 2007 - 03:55:39 PDT)
- Re: AMBER: minimization energy query Vlad Cojocaru (Thu Mar 29 2007 - 04:00:02 PDT)
  - Re: AMBER: minimization energy query deepti nayar (Thu Mar 29 2007 - 04:35:45 PDT)
    - Re: AMBER: minimization energy query deepti nayar (Fri Mar 30 2007 - 00:50:56 PDT)
    - Re: AMBER: minimization energy query Vlad Cojocaru (Fri Mar 30 2007 - 01:28:03 PDT)
    - Re: AMBER: minimization energy query deepti nayar (Fri Mar 30 2007 - 02:03:24 PDT)
    - AMBER: PDB file with charge and size in mm_pbsa calculations Wang, Xuelin (Fri Mar 30 2007 - 08:13:58 PDT)
AMBER: is possible to compile pmemd using scali MPI? Andrea Bortolato (Thu Mar 29 2007 - 09:17:05 PDT)
- Re: AMBER: is possible to compile pmemd using scali MPI? Robert Duke (Thu Mar 29 2007 - 09:36:01 PDT)
  - Re: AMBER: is possible to compile pmemd using scali MPI? Andrea Bortolato (Fri Mar 30 2007 - 12:48:12 PDT)
    - Re: AMBER: is possible to compile pmemd using scali MPI? Gustavo Seabra (Fri Mar 30 2007 - 13:21:39 PDT)
    - Re: AMBER: is possible to compile pmemd using scali MPI? Andrea Bortolato (Mon Apr 23 2007 - 05:31:53 PDT)
AMBER: Amber9 Sander Error A Box (Thu Mar 29 2007 - 19:26:21 PDT)
- Re: AMBER: Amber9 Sander Error David A. Case (Fri Mar 30 2007 - 07:04:40 PDT)
AMBER: Sander error : Coordinate resetting (SHAKE) cannot be accomplished Pankaj R. Daga (Thu Mar 29 2007 - 20:59:08 PDT)
- RE: AMBER: Sander error : Coordinate resetting (SHAKE) cannot be accomplished Ross Walker (Thu Mar 29 2007 - 21:33:37 PDT)
AMBER: minimization + simulation deepti nayar (Fri Mar 30 2007 - 00:54:03 PDT)
- Re: AMBER: minimization + simulation Vlad Cojocaru (Fri Mar 30 2007 - 01:19:55 PDT)
AMBER: RST can not be opened deepti nayar (Fri Mar 30 2007 - 02:21:58 PDT)
- Re: AMBER: RST can not be opened Vlad Cojocaru (Fri Mar 30 2007 - 02:45:55 PDT)
- RE: AMBER: RST can not be opened Ross Walker (Fri Mar 30 2007 - 08:42:45 PDT)
  - AMBER: mm_pbsa error Wang, Xuelin (Fri Mar 30 2007 - 09:21:50 PDT)
AMBER: problem regarding water handling in explicit simu gurpreet singh (Fri Mar 30 2007 - 02:35:49 PDT)
- AMBER: Fwd: problem regarding water handling in explicit simu gurpreet singh (Fri Mar 30 2007 - 02:36:52 PDT)
- Re: AMBER: problem regarding water handling in explicit simu Mingfeng Yang (Fri Mar 30 2007 - 12:50:00 PDT)
AMBER: Some problems during the testing of Amber. Liang, Lei (Fri Mar 30 2007 - 11:12:50 PDT)
- Re: AMBER: Some problems during the testing of Amber. David A. Case (Sat Mar 31 2007 - 21:13:38 PDT)
AMBER: A question about biomineral simulation, help!! WANG,YING (Fri Mar 30 2007 - 14:36:02 PDT)
AMBER: Distance restraint to centre of mass Evan Kelly (Fri Mar 30 2007 - 15:41:32 PDT)
- Re: AMBER: Distance restraint to centre of mass David A. Case (Sat Mar 31 2007 - 21:13:48 PDT)
AMBER: phosphorylated residues yxamber (Sun Apr 01 2007 - 22:13:17 PDT)
- Re: AMBER: phosphorylated residues David A. Case (Mon Apr 02 2007 - 15:13:37 PDT)
  - undefinedRe: AMBER: phosphorylated residues yxamber (Tue Apr 03 2007 - 06:12:35 PDT)
AMBER: Error at Equilibration.... Sandeep Kaushik (Mon Apr 02 2007 - 00:14:17 PDT)
- Re: AMBER: Error at Equilibration.... David A. Case (Mon Apr 02 2007 - 08:45:57 PDT)
AMBER: Problem with sander.MPI Sandeep Kaushik (Mon Apr 02 2007 - 06:06:21 PDT)
AMBER: RE: dihedral term charge dependence Williamson, Mark (Mon Apr 02 2007 - 09:07:29 PDT)
- Re: AMBER: RE: dihedral term charge dependence Carlos Simmerling (Mon Apr 02 2007 - 09:14:15 PDT)
AMBER: restraint command not taken deepti nayar (Mon Apr 02 2007 - 02:25:12 PDT)
- AMBER: restraint command not taken deepti nayar (Mon Apr 02 2007 - 03:21:51 PDT)
  - Re: AMBER: restraint command not taken Vlad Cojocaru (Mon Apr 02 2007 - 09:16:16 PDT)
- AMBER: restraint command not taken deepti nayar (Mon Apr 02 2007 - 02:54:44 PDT)
- Re: AMBER: restraint command not taken Vlad Cojocaru (Mon Apr 02 2007 - 09:57:37 PDT)
AMBER: Xleap errors Beale, John (Mon Apr 02 2007 - 10:20:43 PDT)
- Re: AMBER: Xleap errors David A. Case (Mon Apr 02 2007 - 10:32:47 PDT)
AMBER: Cut off for cavities Sangwai, Ashishvikas (Mon Apr 02 2007 - 11:47:30 PDT)
AMBER: Extra Points... How to Deal with Them David Cerutti (Mon Apr 02 2007 - 23:39:23 PDT)
AMBER: Sander.... Rita Cassia (Tue Apr 03 2007 - 01:23:06 PDT)
- RE: AMBER: Sander.... Ross Walker (Tue Apr 03 2007 - 08:28:51 PDT)
AMBER: nmode Marie Brut (Tue Apr 03 2007 - 03:17:39 PDT)
- Re: AMBER: nmode David A. Case (Tue Apr 03 2007 - 08:25:52 PDT)
AMBER: Regarding Simulated Annealing Anju Sharma (Tue Apr 03 2007 - 05:27:18 PDT)
- RE: AMBER: Regarding Simulated Annealing Ross Walker (Tue Apr 03 2007 - 08:43:55 PDT)
AMBER: RE: dihedral term charge dependence Kateryna Miroshnychenko (Tue Apr 03 2007 - 06:59:08 PDT)
AMBER: sander bomb janavi raghavan (Tue Apr 03 2007 - 07:28:39 PDT)
- RE: AMBER: sander bomb Ross Walker (Tue Apr 03 2007 - 08:35:40 PDT)
AMBER: principal axis calculation in Ptraj Esther Brugger (Tue Apr 03 2007 - 14:05:44 PDT)
AMBER: Energy minimization problem Bo Baker (Tue Apr 03 2007 - 18:24:05 PDT)
- Re: AMBER: Energy minimization problem David A. Case (Tue Apr 03 2007 - 18:39:37 PDT)
- RE: AMBER: Energy minimization problem Bo Baker (Wed Apr 04 2007 - 17:02:42 PDT)
  - Re: AMBER: Energy minimization problem David A. Case (Wed Apr 04 2007 - 18:25:26 PDT)
- RE: AMBER: Energy minimization problem Bo Baker (Thu Apr 05 2007 - 03:14:31 PDT)
AMBER: about define improper torsion in .frcmod file Chengwen Chen (Wed Apr 04 2007 - 02:02:57 PDT)
- Re: AMBER: about define improper torsion in .frcmod file David A. Case (Wed Apr 04 2007 - 08:25:11 PDT)
AMBER: parse radii AYTUG TUNCEL (Wed Apr 04 2007 - 02:10:10 PDT)
- Re: AMBER: parse radii Holger Gohlke (Wed Apr 04 2007 - 02:24:17 PDT)
  - Re: Re: AMBER: parse radii AYTUG TUNCEL (Mon Apr 09 2007 - 01:02:59 PDT)
    - Re: Re: AMBER: parse radii Gohlke.bioinformatik.uni-frankfurt.de (Mon Apr 09 2007 - 02:35:06 PDT)
AMBER: FW: parameter Ross Walker (Wed Apr 04 2007 - 08:18:07 PDT)
AMBER: choice of alpha carbons vs side chains Christopher Gaughan (Wed Apr 04 2007 - 15:34:31 PDT)
Re: AMBER: choice of alpha carbons vs side chains Bill Ross (Wed Apr 04 2007 - 16:28:34 PDT)
AMBER: Charges in antechamber Beale, John (Thu Apr 05 2007 - 08:46:34 PDT)
- Re: AMBER: Charges in antechamber Scott Brozell (Thu Apr 05 2007 - 13:43:59 PDT)
AMBER: Problems during compilation and test. Liang, Lei (Thu Apr 05 2007 - 13:43:23 PDT)
- Re: AMBER: Problems during compilation and test. Scott Brozell (Thu Apr 05 2007 - 19:11:30 PDT)
  - Re: AMBER: Problems during compilation and test. Liang, Lei (Mon Apr 09 2007 - 10:21:39 PDT)
    - Re: AMBER: Problems during compilation and test. David A. Case (Tue Apr 10 2007 - 18:27:39 PDT)
AMBER: principal mask dorotation Esther Brugger (Thu Apr 05 2007 - 14:46:51 PDT)
AMBER: amber 9 installation: broken pipe Stern, Julie (Thu Apr 05 2007 - 16:54:16 PDT)
- Re: AMBER: amber 9 installation: broken pipe Scott Brozell (Thu Apr 05 2007 - 18:46:09 PDT)
AMBER: MD at constan pH tri nam Vo (Fri Apr 06 2007 - 07:10:18 PDT)
- Re: AMBER: MD at constan pH Scott Brozell (Fri Apr 06 2007 - 09:41:39 PDT)
  - Re: AMBER: MD at constan pH tri nam Vo (Fri Apr 06 2007 - 20:53:52 PDT)
    - Re: AMBER: MD at constan pH tri nam Vo (Fri Apr 06 2007 - 21:05:20 PDT)
AMBER: Blue Gene, compile Amber9? Mike Hanby (Fri Apr 06 2007 - 10:22:57 PDT)
- Re: AMBER: Blue Gene, compile Amber9? Carlos P. Sosa (Fri Apr 06 2007 - 11:55:28 PDT)
- RE: AMBER: Blue Gene, compile Amber9? Ross Walker (Fri Apr 06 2007 - 14:23:33 PDT)
  - RE: AMBER: Blue Gene, compile Amber9? Mike Hanby (Tue Apr 10 2007 - 07:04:13 PDT)
    - RE: AMBER: Blue Gene, compile Amber9? Mike Hanby (Tue Apr 10 2007 - 08:13:11 PDT)
    - AMBER: dihedral angles restraint for DNA Hu, Shaowen (JSC-SK)[USRA] (Tue Apr 10 2007 - 10:51:13 PDT)
- Re: AMBER: Blue Gene, compile Amber9? Robert Duke (Tue Apr 10 2007 - 08:42:11 PDT)
  - RE: AMBER: Blue Gene, compile Amber9? Mike Hanby (Thu Apr 19 2007 - 07:34:46 PDT)
    - Re: AMBER: Blue Gene, compile Amber9? David A. Case (Thu Apr 19 2007 - 14:31:25 PDT)
    - RE: AMBER: Blue Gene, compile Amber9? Mike Hanby (Fri Apr 20 2007 - 12:33:39 PDT)
AMBER: SANDER PMEMD ntpr ntwx discrepancy (?bug? report) Chris Moth (Fri Apr 06 2007 - 14:07:17 PDT)
- Re: AMBER: SANDER PMEMD ntpr ntwx discrepancy (?bug? report) David A. Case (Fri Apr 06 2007 - 15:37:46 PDT)
  - AMBER: SANDER PMEMD ntpr ntwx discrepancy (?bug? report) Chris Moth (Mon Apr 09 2007 - 10:32:35 PDT)
AMBER: PDB file format for AMBER Neelanjana Sengupta (Fri Apr 06 2007 - 19:41:43 PDT)
- Re: AMBER: PDB file format for AMBER David A. Case (Sat Apr 07 2007 - 08:56:18 PDT)
AMBER: Extra points... virial computation David Cerutti (Sat Apr 07 2007 - 23:48:11 PDT)
AMBER: ptraj:problems with time correlation calculation (comp. with NMR experiments) anna.schrey.gmx.de (Sun Apr 08 2007 - 05:21:38 PDT)
- Re: AMBER: ptraj:problems with time correlation calculation (comp. with NMR experiments) David A. Case (Mon Apr 09 2007 - 10:27:59 PDT)
AMBER: supplement ptraj:problems with time correlation calculation (comp. with NMR experiments) anna.schrey.gmx.de (Sun Apr 08 2007 - 07:15:22 PDT)
- Re: AMBER: supplement ptraj:problems with time correlation calculation (comp. with NMR experiments) David A. Case (Mon Apr 09 2007 - 07:56:56 PDT)
AMBER: ptraj hbond Evan Kelly (Sun Apr 08 2007 - 17:37:04 PDT)
- Re: AMBER: ptraj hbond Evan Kelly (Sun Apr 08 2007 - 19:00:29 PDT)
AMBER: Fails to load libraries present in /leap/lib/ Neelanjana Sengupta (Mon Apr 09 2007 - 02:33:29 PDT)
- Re: AMBER: Fails to load libraries present in /leap/lib/ David A. Case (Mon Apr 09 2007 - 10:25:41 PDT)
- RE: AMBER: Fails to load libraries present in /leap/lib/ Ross Walker (Tue Apr 10 2007 - 15:53:07 PDT)
AMBER: Vlad has Tagged you! :) Vlad Cojocaru (Mon Apr 09 2007 - 03:06:37 PDT)
AMBER: NTX=7 ?............lastist= ?...........lastrst= ????? Sandeep Kaushik (Mon Apr 09 2007 - 03:35:54 PDT)
- Re: AMBER: NTX=7 ?............lastist= ?...........lastrst= ????? j j (Mon Apr 09 2007 - 07:18:58 PDT)
- Re: AMBER: NTX=7 ?............lastist= ?...........lastrst= ????? David A. Case (Mon Apr 09 2007 - 10:21:21 PDT)
- RE: AMBER: NTX=7 ?............lastist= ?...........lastrst= ????? Ross Walker (Tue Apr 10 2007 - 15:53:19 PDT)
  - Re: AMBER: NTX=7 ?............lastist= ?...........lastrst= ????? Sandeep Kaushik (Wed Apr 11 2007 - 23:11:40 PDT)
AMBER: I'm sorry ... please ignore the junk !! Vlad Cojocaru (Mon Apr 09 2007 - 03:50:54 PDT)
AMBER: Question about MMPBSA v9 Cenk Andac (Mon Apr 09 2007 - 03:54:39 PDT)
- Re: AMBER: Question about MMPBSA v9 David A. Case (Tue Apr 10 2007 - 19:20:58 PDT)
  - Re: AMBER: Question about MMPBSA v9 Cenk Andac (Wed Apr 11 2007 - 03:38:12 PDT)
AMBER: Constant volume simulations Christopher Gaughan (Mon Apr 09 2007 - 11:59:26 PDT)
- Re: AMBER: Constant volume simulations David A. Case (Mon Apr 09 2007 - 13:24:09 PDT)
  - Re: AMBER: Constant volume simulations Christopher Gaughan (Tue Apr 10 2007 - 08:31:58 PDT)
    - Re: AMBER: Constant volume simulations Carlos Simmerling (Tue Apr 10 2007 - 08:35:14 PDT)
    - Re: AMBER: Constant volume simulations Vlad Cojocaru (Tue Apr 10 2007 - 08:39:45 PDT)
    - Re: AMBER: Constant volume simulations Christopher Gaughan (Tue Apr 10 2007 - 08:50:39 PDT)
    - Re: AMBER: Constant volume simulations Vlad Cojocaru (Tue Apr 10 2007 - 09:02:42 PDT)
    - Re: AMBER: Constant volume simulations Christopher Gaughan (Tue Apr 10 2007 - 10:12:14 PDT)
AMBER: Sander Bomb in subroutine nonbond_list Jingyuan Luke (Mon Apr 09 2007 - 19:34:51 PDT)
AMBER: Problem while using antechamber Anju Sharma (Mon Apr 09 2007 - 23:15:47 PDT)
- Re: AMBER: Problem while using antechamber Benjamin Juhl (Tue Apr 10 2007 - 00:12:13 PDT)
  - Re: AMBER: Problem while using antechamber Anju Sharma (Tue Apr 10 2007 - 02:18:07 PDT)
AMBER: problem related to visualizing of structure deepti nayar (Mon Apr 09 2007 - 23:33:40 PDT)
- Re: AMBER: problem related to visualizing of structure Vlad Cojocaru (Tue Apr 10 2007 - 01:25:06 PDT)
  - Re: AMBER: problem related to visualizing of structure deepti nayar (Tue Apr 10 2007 - 02:18:38 PDT)
    - Re: AMBER: problem related to visualizing of structure Vlad Cojocaru (Tue Apr 10 2007 - 02:32:01 PDT)
    - Re: AMBER: problem related to visualizing of structure deepti nayar (Tue Apr 10 2007 - 02:42:58 PDT)
AMBER: sander (AMBER 9) and -y flag -- not working? David Mobley (Tue Apr 10 2007 - 11:22:39 PDT)
- Re: AMBER: sander (AMBER 9) and -y flag -- not working? Chris Moth (Tue Apr 10 2007 - 11:36:22 PDT)
  - Re: AMBER: sander (AMBER 9) and -y flag -- not working? David Mobley (Tue Apr 10 2007 - 11:52:29 PDT)
    - Re: AMBER: sander (AMBER 9) and -y flag -- not working? David Mobley (Tue Apr 10 2007 - 12:04:52 PDT)
    - Re: AMBER: sander (AMBER 9) and -y flag -- not working? Carlos Simmerling (Tue Apr 10 2007 - 12:10:41 PDT)
    - Re: AMBER: sander (AMBER 9) and -y flag -- not working? David Mobley (Tue Apr 10 2007 - 12:31:56 PDT)
AMBER: amber9: running parallel error Khatcharin Siriwong (Wed Apr 11 2007 - 01:08:16 PDT)
- RE: AMBER: amber9: running parallel error Ross Walker (Wed Apr 11 2007 - 06:43:19 PDT)
  - RE: AMBER: amber9: running parallel error Khatcharin Siriwong (Wed Apr 11 2007 - 20:40:27 PDT)
    - Re: AMBER: amber9: running parallel error Benjamin Juhl (Thu Apr 12 2007 - 01:33:48 PDT)
    - Re: AMBER: amber9: running parallel error Khatcharin Siriwong (Wed Apr 18 2007 - 00:03:13 PDT)
  - RE: AMBER: amber9: running parallel error Khatcharin Siriwong (Wed Apr 18 2007 - 00:00:29 PDT)
AMBER: Prblm rgrdng Simulated Annealing Anju Sharma (Wed Apr 11 2007 - 03:06:08 PDT)
- Re: AMBER: Prblm rgrdng Simulated Annealing Carlos Simmerling (Wed Apr 11 2007 - 04:23:43 PDT)
  - Re: AMBER: Prblm rgrdng Simulated Annealing Anju Sharma (Wed Apr 11 2007 - 04:33:03 PDT)
    - Re: AMBER: Prblm rgrdng Simulated Annealing Carlos Simmerling (Wed Apr 11 2007 - 04:39:30 PDT)
    - Re: AMBER: Prblm rgrdng Simulated Annealing Anju Sharma (Wed Apr 11 2007 - 04:46:08 PDT)
AMBER: Problem with Sander restart file. Martin Stennett (Wed Apr 11 2007 - 03:56:37 PDT)
- Re: AMBER: Problem with Sander restart file. Navnit Kumar Mishra (Wed Apr 11 2007 - 04:19:20 PDT)
  - Re: AMBER: Problem with Sander restart file. Martin Stennett (Wed Apr 11 2007 - 04:45:03 PDT)
- Re: AMBER: Problem with Sander restart file. David A. Case (Wed Apr 11 2007 - 11:11:40 PDT)
AMBER: temperature artifacts with andersen and GB? David Mobley (Wed Apr 11 2007 - 09:50:17 PDT)
AMBER: working with Antechamber Atila Iamarino (Wed Apr 11 2007 - 10:45:20 PDT)
- Re: AMBER: working with Antechamber David Mobley (Wed Apr 11 2007 - 11:34:55 PDT)
  - Re: AMBER: working with Antechamber Atila Iamarino (Wed Apr 11 2007 - 11:59:03 PDT)
    - Re: AMBER: working with Antechamber David A. Case (Wed Apr 11 2007 - 12:56:00 PDT)
AMBER: CHARMM vs. AMBER ff literature Seth Lilavivat (Wed Apr 11 2007 - 08:21:07 PDT)
- Re: AMBER: CHARMM vs. AMBER ff literature Thomas Cheatham (Wed Apr 11 2007 - 14:21:14 PDT)
- Re: AMBER: CHARMM vs. AMBER ff literature Jiri Sponer (Thu Apr 12 2007 - 05:58:32 PDT)
  - AMBER: nscm in simulation annealing Hu, Shaowen (JSC-SK)[USRA] (Thu Apr 12 2007 - 07:38:09 PDT)
    - Re: AMBER: nscm in simulation annealing David A. Case (Thu Apr 12 2007 - 09:41:03 PDT)
    - RE: AMBER: nscm in simulation annealing Hu, Shaowen (JSC-SK)[USRA] (Thu Apr 12 2007 - 10:53:18 PDT)
    - Re: AMBER: nscm in simulation annealing David A. Case (Thu Apr 12 2007 - 17:05:01 PDT)
    - RE: AMBER: nscm in simulation annealing Hu, Shaowen (JSC-SK)[USRA] (Fri Apr 13 2007 - 08:32:26 PDT)
    - AMBER: Restraints and free energy Sophie Barbe (Fri Apr 13 2007 - 09:05:06 PDT)
    - Re: AMBER: Restraints and free energy David A. Case (Fri Apr 13 2007 - 10:22:49 PDT)
    - Re: AMBER: nscm in simulation annealing David A. Case (Fri Apr 13 2007 - 10:22:32 PDT)
    - AMBER: Explicit water opinion Hayden Eastwood (Fri Apr 13 2007 - 11:39:19 PDT)
    - Re: AMBER: Explicit water opinion David Cerutti (Fri Apr 13 2007 - 15:58:32 PDT)
    - RE: AMBER: nscm in simulation annealing Hu, Shaowen (JSC-SK)[USRA] (Fri Apr 13 2007 - 11:36:59 PDT)
    - Re: AMBER: nscm in simulation annealing David A. Case (Fri Apr 13 2007 - 12:48:13 PDT)
    - RE: AMBER: nscm in simulation annealing Hu, Shaowen (JSC-SK)[USRA] (Fri Apr 13 2007 - 13:13:07 PDT)
    - RE: AMBER: nscm in simulation annealing Hu, Shaowen (JSC-SK)[USRA] (Tue Apr 17 2007 - 08:25:05 PDT)
    - Re: AMBER: nscm in simulation annealing David A. Case (Tue Apr 17 2007 - 09:18:02 PDT)
    - RE: AMBER: nscm in simulation annealing Hu, Shaowen (JSC-SK)[USRA] (Tue Apr 17 2007 - 09:26:01 PDT)
    - RE: AMBER: nscm in simulation annealing Ross Walker (Tue Apr 17 2007 - 09:25:35 PDT)
    - RE: AMBER: nscm in simulation annealing Hu, Shaowen (JSC-SK)[USRA] (Tue Apr 17 2007 - 09:59:43 PDT)
AMBER: Attaching capping groups Neelanjana Sengupta (Wed Apr 11 2007 - 18:28:33 PDT)
- Re: AMBER: Attaching capping groups Kristina Furse (Wed Apr 11 2007 - 19:30:30 PDT)
- RE: AMBER: Attaching capping groups Ross Walker (Wed Apr 11 2007 - 20:49:36 PDT)
  - Re: AMBER: Attaching capping groups Neelanjana Sengupta (Thu Apr 12 2007 - 19:54:30 PDT)
    - RE: AMBER: Attaching capping groups Ross Walker (Sun Apr 15 2007 - 20:49:26 PDT)
AMBER: Needed help regardng Simulated Annealing Anju Sharma (Wed Apr 11 2007 - 22:07:14 PDT)
AMBER: How can I modify the frcmod file of ligand with a nonstandard guanidine tonglei (Thu Apr 12 2007 - 00:13:34 PDT)
AMBER: topology for postprocessed files? anna.schrey.gmx.de (Thu Apr 12 2007 - 02:57:28 PDT)
- Re: AMBER: topology for postprocessed files? Vlad Cojocaru (Thu Apr 12 2007 - 03:07:08 PDT)
  - Re: AMBER: topology for postprocessed files? anna.schrey.gmx.de (Thu Apr 12 2007 - 03:42:41 PDT)
  - Re: AMBER: topology for postprocessed files? anna.schrey.gmx.de (Wed Apr 18 2007 - 10:40:51 PDT)
AMBER: bad atom type errors in GB for halides? David Mobley (Thu Apr 12 2007 - 10:19:51 PDT)
- Re: AMBER: bad atom type errors in GB for halides? Ilyas Yildirim (Thu Apr 12 2007 - 12:57:13 PDT)
- Re: AMBER: bad atom type errors in GB for halides? David A. Case (Thu Apr 12 2007 - 17:04:55 PDT)
AMBER: Multiple Bonds to one Atom crowfoot.unr.nevada.edu (Thu Apr 12 2007 - 13:41:36 PDT)
AMBER: polarization and water density Thérèse Malliavin (Fri Apr 13 2007 - 02:36:44 PDT)
- Re: AMBER: polarization and water density David A. Case (Fri Apr 13 2007 - 12:53:42 PDT)
AMBER: AMBER9 installation error on dual core AMD Opteron(tm) processor 275 Arvind Marathe (Fri Apr 13 2007 - 03:23:38 PDT)
- Re: AMBER: AMBER9 installation error on dual core AMD Opteron(tm) processor 275 Mark Williamson (Fri Apr 13 2007 - 05:51:54 PDT)
  - Re: AMBER: AMBER9 installation error on dual core AMD Opteron(tm) processor 275 Arvind Marathe (Fri Apr 13 2007 - 08:59:35 PDT)
AMBER: Amber:PBSA&Extract_coords problem (Needed help) odde (Fri Apr 13 2007 - 12:06:42 PDT)
- Re: AMBER: Amber:PBSA&Extract_coords problem (Needed help) Jiten (Sat Apr 14 2007 - 06:51:58 PDT)
AMBER: QMMM with printcharges Kijeong Kwac (Fri Apr 13 2007 - 17:37:45 PDT)
- RE: AMBER: QMMM with printcharges Ross Walker (Tue Apr 17 2007 - 14:37:27 PDT)
- RE: AMBER: QMMM with printcharges Ross Walker (Thu Feb 07 2008 - 14:12:17 PST)
AMBER: mdfil.f Peljidiyn Genden (Sat Apr 14 2007 - 00:43:27 PDT)
- RE: AMBER: mdfil.f Ross Walker (Mon Apr 16 2007 - 09:43:01 PDT)
  - Re: AMBER: mdfil.f David A. Case (Mon Apr 16 2007 - 10:25:02 PDT)
- Re: AMBER: mdfil.f Robert Duke (Mon Apr 16 2007 - 10:02:28 PDT)
AMBER: Amber 8 support of CHARMM ff? Seth Lilavivat (Sat Apr 14 2007 - 11:36:35 PDT)
- Re: AMBER: Amber 8 support of CHARMM ff? David A. Case (Sat Apr 14 2007 - 12:21:23 PDT)
AMBER: Release of the R.E.D.-III tools FyD (Sun Apr 15 2007 - 03:10:25 PDT)
AMBER: membrane simulation Jojart Balazs (Sun Apr 15 2007 - 11:06:31 PDT)
- Re: AMBER: membrane simulation nag raj (Sun Apr 15 2007 - 22:29:32 PDT)
- Re: AMBER: membrane simulation Florian Haberl (Mon Apr 16 2007 - 07:04:04 PDT)
  - Re: AMBER: membrane simulation nag raj (Wed Apr 18 2007 - 19:53:27 PDT)
    - Re: AMBER: membrane simulation Vlad Cojocaru (Thu Apr 19 2007 - 02:07:52 PDT)
    - Re: AMBER: membrane simulation nag raj (Thu Apr 19 2007 - 05:51:56 PDT)
AMBER: H-bond analysis............acceptorH absent..!!! Sandeep Kaushik (Sun Apr 15 2007 - 23:32:28 PDT)
AMBER: Projecting trajectories onto normal modes Harald Lanig (Mon Apr 16 2007 - 07:50:38 PDT)
- Re: AMBER: Projecting trajectories onto normal modes M. L. Dodson (Mon Apr 16 2007 - 08:41:50 PDT)
AMBER: ptraj and quasi harmonic analysis Hans Lee (Mon Apr 16 2007 - 14:19:34 PDT)
- Re: AMBER: ptraj and quasi harmonic analysis Hans Lee (Wed Apr 18 2007 - 07:47:11 PDT)
  - Re: AMBER: ptraj and quasi harmonic analysis Myunggi Yi (Wed Apr 18 2007 - 09:46:22 PDT)
  - AMBER: ptraj and quasi harmonic analysis Chris Moth (Thu Apr 19 2007 - 12:58:52 PDT)
    - Re: AMBER: ptraj and quasi harmonic analysis Thomas Cheatham III (Thu Apr 19 2007 - 13:26:35 PDT)
    - Re: AMBER: ptraj and quasi harmonic analysis Hans Lee (Thu Apr 19 2007 - 18:46:38 PDT)
    - Re: AMBER: ptraj and quasi harmonic analysis David A. Case (Fri Apr 20 2007 - 08:23:34 PDT)
    - Re: AMBER: ptraj and quasi harmonic analysis Hans Lee (Fri Apr 20 2007 - 09:35:49 PDT)
    - Re: AMBER: ptraj and quasi harmonic analysis David A. Case (Fri Apr 20 2007 - 09:49:26 PDT)
AMBER: MM-PBSA_binding energy script error odde (Mon Apr 16 2007 - 16:33:14 PDT)
AMBER: Re: amber mm-pbsa problem Jiten (Mon Apr 16 2007 - 18:39:26 PDT)
- Re: AMBER: Re: amber mm-pbsa problem odde (Tue Apr 17 2007 - 06:57:37 PDT)
AMBER: problem with calculating RMSD tri nam Vo (Tue Apr 17 2007 - 00:01:35 PDT)
- Re: AMBER: problem with calculating RMSD Gustavo Seabra (Tue Apr 17 2007 - 05:41:26 PDT)
  - Re: AMBER: problem with calculating RMSD tri nam Vo (Wed Apr 18 2007 - 01:22:45 PDT)
    - Re: AMBER: problem with calculating RMSD Gustavo Seabra (Wed Apr 18 2007 - 07:50:21 PDT)
    - RE: AMBER: problem with calculating RMSD Ross Walker (Wed Apr 18 2007 - 09:03:37 PDT)
AMBER: vmd and amber deepti nayar (Tue Apr 17 2007 - 04:58:51 PDT)
- Re: AMBER: vmd and amber Gustavo Seabra (Tue Apr 17 2007 - 05:33:48 PDT)
AMBER: PDBs Beale, John (Tue Apr 17 2007 - 05:22:42 PDT)
- Re: AMBER: PDBs John E. Kerrigan (Tue Apr 17 2007 - 05:40:54 PDT)
AMBER: ptraj secstruct core dumped error vijayaraj.clri.info (Tue Apr 17 2007 - 06:45:04 PDT)
AMBER: Request for addition of a useful command in ptraj module of AMBER Cenk Andac (Tue Apr 17 2007 - 10:18:30 PDT)
AMBER: Request for addition of a useful command in ptraj module of AMBER #2 Cenk Andac (Tue Apr 17 2007 - 10:24:37 PDT)
- Re: AMBER: Request for addition of a useful command in ptraj module of AMBER #2 Melinda Layten (Mon Apr 23 2007 - 14:52:26 PDT)
  - Re: AMBER: Request for addition of a useful command in ptraj module of AMBER #2 Cenk Andac (Mon Apr 23 2007 - 15:35:36 PDT)
    - Re: AMBER: Request for addition of a useful command in ptraj module of AMBER #2 Vlad Cojocaru (Tue Apr 24 2007 - 01:30:40 PDT)
AMBER: Re: MM-PBSA amber script problem odde (Tue Apr 17 2007 - 11:45:06 PDT)
- Re: AMBER: Re: MM-PBSA amber script problem David A. Case (Tue Apr 17 2007 - 14:35:59 PDT)
AMBER: single solvated glycine simulation - zwitterion, cation, anion parameters? Nicolas Lux Fawzi (Tue Apr 17 2007 - 12:00:18 PDT)
AMBER: using glycam04 parameters Sara Alexandra Moura (Tue Apr 17 2007 - 12:17:44 PDT)
- Re: AMBER: using glycam04 parameters David A. Case (Tue Apr 17 2007 - 14:37:35 PDT)
  - Re: AMBER: using glycam04 parameters FyD (Wed Apr 18 2007 - 03:57:02 PDT)
    - Re: AMBER: using glycam04 parameters Austin B. Yongye (Wed Apr 18 2007 - 06:24:38 PDT)
    - Re: AMBER: using glycam04 parameters Sara Alexandra Moura (Wed Apr 18 2007 - 07:59:10 PDT)
    - Re: AMBER: using glycam04 parameters David A. Case (Wed Apr 18 2007 - 08:28:27 PDT)
    - Re: AMBER: using glycam04 parameters Sara Alexandra Moura (Thu Apr 19 2007 - 09:27:38 PDT)
    - Re: AMBER: using glycam04 parameters kkirschn.hamilton.edu (Thu Apr 19 2007 - 10:53:37 PDT)
    - Re: AMBER: using glycam04 parameters Sara Alexandra Moura (Thu Apr 19 2007 - 11:35:16 PDT)
    - RE: AMBER: using glycam04 parameters Ross Walker (Thu Apr 19 2007 - 12:00:01 PDT)
    - Re: AMBER: using glycam04 parameters kkirschn.hamilton.edu (Wed Apr 25 2007 - 13:02:49 PDT)
    - Re: AMBER: using glycam04 parameters Austin B. Yongye (Wed Apr 18 2007 - 09:03:35 PDT)
  - Re: AMBER: using glycam04 parameters Sara Alexandra Moura (Wed Apr 18 2007 - 08:10:35 PDT)
AMBER: single solvated glycine simulation - zwitterion, cation, anion parameters? 2nd try Nicolas Lux Fawzi (Tue Apr 17 2007 - 14:50:07 PDT)
- Re: AMBER: single solvated glycine simulation - zwitterion, cation, anion parameters? 2nd try Pradipta Bandyopadhyay (Tue Apr 17 2007 - 21:33:52 PDT)
AMBER: frcmod file deepti nayar (Tue Apr 17 2007 - 23:31:52 PDT)
- Re: AMBER: frcmod file David A. Case (Wed Apr 18 2007 - 08:22:01 PDT)
- RE: AMBER: frcmod file Ross Walker (Wed Apr 18 2007 - 08:51:20 PDT)
AMBER: printcharges option when using QM/MM simulation 한재범 (Tue Apr 17 2007 - 23:41:33 PDT)
- RE: AMBER: printcharges option when using QM/MM simulation Ross Walker (Wed Apr 18 2007 - 08:31:17 PDT)
AMBER: Protonation/deprotonation of terminal residues Jesper Soerensen (Wed Apr 18 2007 - 05:56:26 PDT)
- Re: AMBER: Protonation/deprotonation of terminal residues FyD (Wed Apr 18 2007 - 11:26:47 PDT)
AMBER: signal SIGSEGV(11) Pankaj R. Daga (Wed Apr 18 2007 - 08:25:55 PDT)
- Re: AMBER: signal SIGSEGV(11) David A. Case (Wed Apr 18 2007 - 08:49:24 PDT)
- RE: AMBER: signal SIGSEGV(11) Ross Walker (Wed Apr 18 2007 - 09:09:10 PDT)
- Re: AMBER: signal SIGSEGV(11) Pankaj R. Daga (Wed Apr 18 2007 - 12:16:48 PDT)
  - Re: AMBER: signal SIGSEGV(11) Chris Moth (Wed Apr 18 2007 - 13:22:58 PDT)
- Re: AMBER: signal SIGSEGV(11) Pankaj R. Daga (Tue Apr 24 2007 - 07:55:14 PDT)
  - RE: AMBER: signal SIGSEGV(11) Ross Walker (Tue Apr 24 2007 - 12:43:49 PDT)
AMBER: ff02 + POL3 - polar interactions !! Pradipta Bandyopadhyay (Wed Apr 18 2007 - 09:04:22 PDT)
AMBER: Antechamber Warning Beale, John (Wed Apr 18 2007 - 12:39:31 PDT)
AMBER: ptraj bug? Tamara Rogers (Wed Apr 18 2007 - 15:09:39 PDT)
AMBER: Sander BOMB.. simulation terminates by itself... Vijay Manickam Achari (Wed Apr 18 2007 - 18:24:28 PDT)
AMBER: Ewald BOMB....... what is this.. Vijay Manickam Achari (Wed Apr 18 2007 - 20:13:38 PDT)
- RE: AMBER: Ewald BOMB....... what is this.. Ross Walker (Sat Apr 21 2007 - 10:08:15 PDT)
AMBER: Antechamber Beale, John (Thu Apr 19 2007 - 06:51:03 PDT)
- RE: AMBER: Antechamber Junmei Wang (Thu Apr 19 2007 - 06:58:14 PDT)
AMBER: regarding frcmod file Santanu Roy (Thu Apr 19 2007 - 08:28:01 PDT)
- Re: AMBER: regarding frcmod file Gustavo Seabra (Thu Apr 19 2007 - 08:50:44 PDT)
- Re: AMBER: regarding frcmod file David A. Case (Thu Apr 19 2007 - 09:14:03 PDT)
AMBER: RE: RE: AMBER: QMMM with printcharges Kijeong Kwac (Thu Apr 19 2007 - 08:42:38 PDT)
- RE: AMBER: RE: RE: AMBER: QMMM with printcharges Ross Walker (Thu Apr 19 2007 - 09:42:15 PDT)
AMBER: Problems with Machine file for sander.MPI Terry Lang (Thu Apr 19 2007 - 13:15:45 PDT)
- RE: AMBER: Problems with Machine file for sander.MPI Ross Walker (Thu Apr 19 2007 - 14:02:24 PDT)
  - Re: AMBER: Problems with Machine file for sander.MPI Terry Lang (Tue Apr 24 2007 - 16:55:11 PDT)
AMBER: AIX 5 test failures: -NaNQ Patrick McCarren (Thu Apr 19 2007 - 16:30:35 PDT)
- Re: AMBER: AIX 5 test failures: -NaNQ Scott Brozell (Thu Apr 19 2007 - 17:13:54 PDT)
  - Re: AMBER: AIX 5 test failures: -NaNQ Patrick McCarren (Fri Apr 20 2007 - 16:01:53 PDT)
    - Re: AMBER: AIX 5 test failures: -NaNQ Scott Brozell (Mon Apr 23 2007 - 10:10:23 PDT)
    - Re: AMBER: AIX 5 test failures: -NaNQ Patrick McCarren (Mon Apr 23 2007 - 14:51:46 PDT)
    - RE: AMBER: AIX 5 test failures: -NaNQ Ross Walker (Mon Apr 23 2007 - 15:47:20 PDT)
    - Re: AMBER: AIX 5 test failures: -NaNQ Patrick McCarren (Wed Apr 25 2007 - 16:44:15 PDT)
- Re: AMBER: AIX 5 test failures: -NaNQ David A. Case (Thu Apr 19 2007 - 18:13:46 PDT)
- RE: AMBER: AIX 5 test failures: -NaNQ Ross Walker (Thu Apr 19 2007 - 18:20:46 PDT)
AMBER: QM/MM NPT Simulation Daniel Oehme (Thu Apr 19 2007 - 21:46:14 PDT)
- RE: AMBER: QM/MM NPT Simulation Ross Walker (Fri Apr 20 2007 - 08:22:25 PDT)
AMBER: A test email Ruchi Sachdeva (Thu Apr 19 2007 - 23:54:55 PDT)
AMBER: process and plot matrix data Vlad Cojocaru (Fri Apr 20 2007 - 02:28:12 PDT)
- Re: AMBER: process and plot matrix data Patrick McCarren (Fri Apr 20 2007 - 03:02:15 PDT)
  - Re: AMBER: process and plot matrix data Vlad Cojocaru (Fri Apr 20 2007 - 06:18:46 PDT)
AMBER: rigid epoxide substrate Dr M. Blomberg (Fri Apr 20 2007 - 04:24:13 PDT)
- Re: AMBER: rigid epoxide substrate David A. Case (Fri Apr 20 2007 - 08:30:42 PDT)
AMBER: restraint value: written but none specified Ben Sattelle (Fri Apr 20 2007 - 13:42:56 PDT)
- Re: AMBER: restraint value: written but none specified Chris Moth (Fri Apr 20 2007 - 14:16:52 PDT)
  - Re: AMBER: restraint value: written but none specified Ben Sattelle (Fri Apr 20 2007 - 14:51:30 PDT)
    - RE: AMBER: restraint value: written but none specified Ross Walker (Fri Apr 20 2007 - 15:37:01 PDT)
    - RE: AMBER: restraint value: written but none specified Ben Sattelle (Fri Apr 20 2007 - 16:05:47 PDT)
- Re: AMBER: restraint value: written but none specified David A. Case (Fri Apr 20 2007 - 14:15:05 PDT)
  - Re: AMBER: restraint value: written but none specified Ben Sattelle (Fri Apr 20 2007 - 15:08:55 PDT)
AMBER: Error: "Suspended (tty input)" & "Unit 6 Error on OPEN: md.out" Khatcharin Siriwong (Sat Apr 21 2007 - 00:42:14 PDT)
- Re: AMBER: Error: "Suspended (tty input)" & "Unit 6 Error on OPEN: md.out" David A. Case (Sat Apr 21 2007 - 12:04:23 PDT)
  - Re: AMBER: Error: "Suspended (tty input)" & "Unit 6 Error on OPEN: md.out" Khatcharin Siriwong (Sat Apr 21 2007 - 20:57:18 PDT)
  - AMBER: prep file new residue Dr M. Blomberg (Mon Apr 23 2007 - 01:48:27 PDT)
    - Re: AMBER: prep file new residue David A. Case (Tue Apr 24 2007 - 12:12:44 PDT)
AMBER: mol2 format Jardas sucuriba (Sun Apr 22 2007 - 15:57:12 PDT)
- Re: AMBER: mol2 format j j (Mon Apr 23 2007 - 02:04:53 PDT)
AMBER: .prmtop entries Neelanjana Sengupta (Sun Apr 22 2007 - 22:53:46 PDT)
- Re: AMBER: .prmtop entries Andy Purkiss-Trew (Mon Apr 23 2007 - 04:13:18 PDT)
AMBER: problem regarding implicit simulation gurpreet singh (Sun Apr 22 2007 - 23:16:35 PDT)
- Re: AMBER: problem regarding implicit simulation Carlos Simmerling (Mon Apr 23 2007 - 04:30:34 PDT)
  - Re: AMBER: problem regarding implicit simulation gurpreet singh (Tue Apr 24 2007 - 04:18:57 PDT)
    - Re: AMBER: problem regarding implicit simulation Carlos Simmerling (Tue Apr 24 2007 - 04:25:31 PDT)
AMBER: MM-PBSA: decompose energy error jitrayut jitonnom (Mon Apr 23 2007 - 04:31:43 PDT)
- Re: AMBER: MM-PBSA: decompose energy error Sergey Samsonov (Mon Apr 23 2007 - 04:56:30 PDT)
AMBER: MM-PBSA: Can't finish the binding energy process jitrayut jitonnom (Mon Apr 23 2007 - 05:34:48 PDT)
- Re: AMBER: MM-PBSA: Can't finish the binding energy process Navnit Kumar Mishra (Mon Apr 23 2007 - 07:04:12 PDT)
  - Fwd: AMBER: MM-PBSA: Can't finish the binding energy process jitrayut jitonnom (Wed May 09 2007 - 21:12:55 PDT)
AMBER: Problem using Ptraj alfredoq.fcq.unc.edu.ar (Mon Apr 23 2007 - 08:41:56 PDT)
- Re: AMBER: Problem using Ptraj j j (Mon Apr 23 2007 - 09:47:50 PDT)
- Re: AMBER: Problem using Ptraj Thomas Cheatham III (Mon Apr 23 2007 - 10:02:17 PDT)
AMBER: Problems with AMBER8 on 32-bit FC6 David LeBard (Mon Apr 23 2007 - 11:51:02 PDT)
- Re: AMBER: Problems with AMBER8 on 32-bit FC6 David A. Case (Mon Apr 23 2007 - 14:17:09 PDT)
  - AMBER: Extracting Coords&MMPBSA&ambpdb Srinivas Odde (Tue Apr 24 2007 - 08:51:48 PDT)
AMBER: Error on compile amber8 tri nam Vo (Mon Apr 23 2007 - 22:04:34 PDT)
- Re: AMBER: Error on compile amber8 David LeBard (Mon Apr 23 2007 - 22:45:45 PDT)
  - Re: AMBER: Error on compile amber8 tri nam Vo (Mon Apr 23 2007 - 23:47:27 PDT)
AMBER: QM/MM simulation with SCC-DFTB 한재범 (Tue Apr 24 2007 - 01:19:25 PDT)
- Re: AMBER: QM/MM simulation with SCC-DFTB Gustavo Seabra (Tue Apr 24 2007 - 03:48:11 PDT)
AMBER: amber equation of ff99 Chengwen Chen (Tue Apr 24 2007 - 09:13:54 PDT)
- Re: AMBER: amber equation of ff99 Carlos Simmerling (Tue Apr 24 2007 - 09:18:57 PDT)
  - Re: AMBER: amber equation of ff99 Chengwen Chen (Tue Apr 24 2007 - 19:19:15 PDT)
Re: AMBER:a question about RMSD Carlos Simmerling (Tue Apr 24 2007 - 06:06:40 PDT)
AMBER: NAD parameters Jardas sucuriba (Tue Apr 24 2007 - 11:02:56 PDT)
- RE: AMBER: NAD parameters Ross Walker (Tue Apr 24 2007 - 12:32:27 PDT)
  - RE: AMBER: NAD parameters Jardas sucuriba (Wed Apr 25 2007 - 15:46:17 PDT)
AMBER: mobile proton algorithm HL Eastwood (Tue Apr 24 2007 - 12:25:10 PDT)
AMBER: Error on compiling AMBER8 tri nam Vo (Tue Apr 24 2007 - 19:03:16 PDT)
- Re: AMBER: Error on compiling AMBER8 David A. Case (Tue Apr 24 2007 - 20:31:44 PDT)
  - Re: AMBER: Error on compiling AMBER8 tri nam Vo (Wed Apr 25 2007 - 09:35:31 PDT)
    - Re: AMBER: Error on compiling AMBER8 David A. Case (Wed Apr 25 2007 - 11:33:11 PDT)
AMBER: ptraj error- glibc detected free(): invalid pointer: 0x0812bb38 Ruchi Sachdeva (Tue Apr 24 2007 - 20:54:14 PDT)
- Re: AMBER: ptraj error- glibc detected free(): invalid pointer: 0x0812bb38 Scott Brozell (Fri Apr 27 2007 - 13:25:23 PDT)
- Re: AMBER: ptraj error- glibc detected free(): invalid pointer: 0x0812bb38 Bill Ross (Fri Apr 27 2007 - 13:41:20 PDT)
- Re: AMBER: ptraj error- glibc detected free(): invalid pointer: 0x0812bb38 Bill Ross (Fri Apr 27 2007 - 16:07:54 PDT)
AMBER: Work with constand pH tri nam Vo (Wed Apr 25 2007 - 01:13:05 PDT)
- Re: AMBER: Work with constand pH Myunggi Yi (Wed Apr 25 2007 - 06:49:59 PDT)
  - Re: AMBER: Work with constand pH tri nam Vo (Thu Apr 26 2007 - 20:37:53 PDT)
    - Re: AMBER: Work with constand pH Myunggi Yi (Fri Apr 27 2007 - 18:42:32 PDT)
AMBER: Employing SCC-DFTB with a periodic boundary condtion 한재범 (Wed Apr 25 2007 - 23:48:58 PDT)
- Re: AMBER: Employing SCC-DFTB with a periodic boundary condtion Gustavo Seabra (Thu Apr 26 2007 - 06:18:32 PDT)
AMBER: protein-rna interaction & mmpbsa Antonio Morreale (Thu Apr 26 2007 - 01:28:19 PDT)
AMBER: Problems installing Amber9 Ângela dos Reis (Fri Apr 27 2007 - 04:14:05 PDT)
- Re: AMBER: Problems installing Amber9 Andreas Svrcek-Seiler (Fri Apr 27 2007 - 05:52:05 PDT)
- RE: AMBER: Problems installing Amber9 Ross Walker (Fri Apr 27 2007 - 08:56:41 PDT)
  - Re: AMBER: Problems installing Amber9 Ângela dos Reis (Fri Apr 27 2007 - 10:34:38 PDT)
AMBER: Error in protonating Neelanjana Sengupta (Fri Apr 27 2007 - 04:31:52 PDT)
- RE: AMBER: Error in protonating Ross Walker (Fri Apr 27 2007 - 08:46:50 PDT)
- Re: AMBER: Error in protonating David A. Case (Sat Apr 28 2007 - 14:26:08 PDT)
AMBER: Print individual free energies in MD trajectories using MM_PBSA Giulio Rastelli (Fri Apr 27 2007 - 09:05:39 PDT)
AMBER: QM/MM Umbrella sampling Jason DeChancie (Fri Apr 27 2007 - 13:53:08 PDT)
- RE: AMBER: QM/MM Umbrella sampling Ross Walker (Fri Apr 27 2007 - 15:01:46 PDT)
- Re: AMBER: QM/MM Umbrella sampling Jerome.GOLEBIOWSKI.unice.fr (Sat Apr 28 2007 - 00:55:49 PDT)
AMBER: thermodynamic integration Servaas Michielssens (Sat Apr 28 2007 - 10:48:10 PDT)
- Re: AMBER: thermodynamic integration David A. Case (Sat Apr 28 2007 - 14:26:28 PDT)
AMBER: Binding free energy errors: Grid setting fail jitrayut jitonnom (Sun Apr 29 2007 - 06:48:17 PDT)
AMBER: a problem of surface area calulated by MM/PBSA Chengwen Chen (Mon Apr 30 2007 - 00:34:38 PDT)
- Re: AMBER: a problem of surface area calulated by MM/PBSA David A. Case (Mon Apr 30 2007 - 08:20:43 PDT)
AMBER: Problem with MM-PBSA statistics Henar Martínez García (Mon Apr 30 2007 - 02:53:38 PDT)
- AMBER: AMBER MINIMIZATION Sophie Barbe (Mon Apr 30 2007 - 06:55:53 PDT)
  - Re: AMBER: AMBER MINIMIZATION David A. Case (Mon Apr 30 2007 - 08:24:34 PDT)
    - Re: AMBER: AMBER MINIMIZATION Sophie Barbe (Mon Apr 30 2007 - 09:23:41 PDT)
  - Re: AMBER: AMBER MINIMIZATION gsciaini.qi.fcen.uba.ar (Mon Apr 30 2007 - 14:08:47 PDT)
AMBER: Problem with calcpka.pl and constant pH Hayden Eastwood (Mon Apr 30 2007 - 04:35:23 PDT)
AMBER: Problem with calcpka.pl and constant pH Hayden Eastwood (Mon Apr 30 2007 - 06:04:11 PDT)
- Re: AMBER: Problem with calcpka.pl and constant pH David A. Case (Thu May 03 2007 - 10:13:50 PDT)
AMBER: PDB files Beale, John (Mon Apr 30 2007 - 09:16:59 PDT)
- RE: AMBER: PDB files Hayden Eastwood (Mon Apr 30 2007 - 10:12:01 PDT)
- RE: AMBER: PDB files Hayden Eastwood (Mon Apr 30 2007 - 10:20:14 PDT)
- Re: AMBER: PDB files David A. Case (Mon Apr 30 2007 - 13:00:33 PDT)
AMBER: pressure tensor in a slab configuration rdauria.uci.edu (Mon Apr 30 2007 - 19:16:08 PDT)
- AMBER: mm-pbsa error with nm = 1 Hayden Eastwood (Tue May 01 2007 - 10:21:22 PDT)
  - Re: AMBER: mm-pbsa error with nm = 1 Urszula Uciechowska (Tue May 01 2007 - 10:43:28 PDT)
  - Re: AMBER: mm-pbsa error with nm = 1 Cenk Andac (Tue May 01 2007 - 16:58:17 PDT)
    - RE: AMBER: mm-pbsa error with nm = 1 Hayden Eastwood (Wed May 02 2007 - 03:36:55 PDT)
    - RE: AMBER: mm-pbsa error with nm = 1 Cenk Andac (Wed May 02 2007 - 03:50:47 PDT)
    - RE: AMBER: mm-pbsa error with nm = 1 Hayden Eastwood (Wed May 02 2007 - 04:10:10 PDT)
    - RE: AMBER: mm-pbsa error with nm = 1 Cenk Andac (Wed May 02 2007 - 05:55:55 PDT)
AMBER: Problem with SCC-DFTB parameter files 한재범 (Tue May 01 2007 - 21:55:03 PDT)
- Re: AMBER: Problem with SCC-DFTB parameter files Gustavo Seabra (Wed May 02 2007 - 04:46:58 PDT)
- RE: AMBER: Problem with SCC-DFTB parameter files Ross Walker (Wed May 02 2007 - 07:45:07 PDT)
- Re: AMBER: Problem with SCC-DFTB parameter files M. L. Dodson (Wed May 02 2007 - 07:59:02 PDT)
  - Re: AMBER: Problem with SCC-DFTB parameter files Gustavo Seabra (Wed May 02 2007 - 08:27:00 PDT)
AMBER: Steered MD & Jarzynski's equality James W (Tue May 01 2007 - 23:44:20 PDT)
- Re: AMBER: Steered MD & Jarzynski's equality Adrian Roitberg (Wed May 02 2007 - 00:26:30 PDT)
  - Re: AMBER: Steered MD & Jarzynski's equality James W (Wed May 02 2007 - 02:44:28 PDT)
    - Re: AMBER: Steered MD & Jarzynski's equality Gustavo Seabra (Wed May 02 2007 - 04:37:51 PDT)
    - Re: AMBER: Steered MD & Jarzynski's equality David Mobley (Wed May 02 2007 - 07:39:23 PDT)
    - Re: AMBER: Steered MD & Jarzynski's equality wang (Thu May 03 2007 - 01:06:43 PDT)
    - distance constraint [Was: Re: AMBER: Steered MD & Jarzynski's equality] Gustavo Seabra (Thu May 03 2007 - 04:53:33 PDT)
AMBER: Group declaration question cristian obiol (Wed May 02 2007 - 02:28:19 PDT)
Re: AMBER: Group declaration question Bill Ross (Wed May 02 2007 - 12:10:23 PDT)
AMBER: command line alternatives for teLeap Neelanjana Sengupta (Wed May 02 2007 - 21:21:07 PDT)
- Re: AMBER: command line alternatives for teLeap David A. Case (Thu May 03 2007 - 07:30:00 PDT)
  - AMBER: DivCon calculation in Amber9 Wang, Xuelin (Thu May 03 2007 - 12:51:35 PDT)
AMBER: md output file deepti nayar (Thu May 03 2007 - 02:06:24 PDT)
- Re: AMBER: md output file Gustavo Seabra (Thu May 03 2007 - 04:32:56 PDT)
AMBER: Potential of mean force, how to calculate rate of dissociation? Catein Catherine (Thu May 03 2007 - 02:46:27 PDT)
- Re: AMBER: Potential of mean force, how to calculate rate of dissociation? Jerome.GOLEBIOWSKI.unice.fr (Thu May 03 2007 - 06:57:32 PDT)
- Re: AMBER: Potential of mean force, how to calculate rate of dissociation? David Mobley (Thu May 03 2007 - 15:17:31 PDT)
  - Re: AMBER: Potential of mean force, how to calculate rate of dissociation? Catein Catherine (Thu May 03 2007 - 19:13:55 PDT)
    - Re: AMBER: Potential of mean force, how to calculate rate of dissociation? Jerome.GOLEBIOWSKI.unice.fr (Fri May 04 2007 - 01:06:17 PDT)
    - Re: AMBER: Potential of mean force, how to calculate rate of dissociation? Thomas Steinbrecher (Fri May 04 2007 - 08:49:03 PDT)
    - Re: AMBER: Potential of mean force, how to calculate rate of dissociation? David Mobley (Fri May 04 2007 - 10:39:34 PDT)
    - Re: AMBER: Potential of mean force, how to calculate rate of dissociation? Thomas Steinbrecher (Fri May 04 2007 - 11:05:09 PDT)
    - Re: AMBER: Potential of mean force, how to calculate rate of dissociation? David Mobley (Fri May 04 2007 - 14:09:36 PDT)
    - Re: AMBER: Potential of mean force, how to calculate rate of dissociation? Catein Catherine (Fri May 04 2007 - 18:55:26 PDT)
    - Re: AMBER: Potential of mean force, how to calculate rate of dissociation? wang (Sun May 06 2007 - 23:20:41 PDT)
    - Re: AMBER: Potential of mean force, how to calculate rate of dissociation? Gustavo Seabra (Mon May 07 2007 - 05:26:55 PDT)
AMBER: Chemical shift: simulation vs. experiment Mingfeng Yang (Thu May 03 2007 - 18:07:05 PDT)
- Re: AMBER: Chemical shift: simulation vs. experiment Mingfeng Yang (Thu May 03 2007 - 22:16:30 PDT)
  - Re: AMBER: Chemical shift: simulation vs. experiment Adrian Roitberg (Thu May 03 2007 - 23:42:55 PDT)
    - Re: AMBER: Chemical shift: simulation vs. experiment Mingfeng Yang (Fri May 04 2007 - 00:17:04 PDT)
    - Re: AMBER: Chemical shift: simulation vs. experiment Mingfeng Yang (Fri May 04 2007 - 00:52:48 PDT)
AMBER: Tutorial 3: MM-PBSA.....implicit solvent for MD calculations? Catein Catherine (Fri May 04 2007 - 01:13:44 PDT)
AMBER: Rate of Dissociation Catein Catherine (Fri May 04 2007 - 02:37:46 PDT)
- Re: AMBER: Rate of Dissociation David Mobley (Fri May 04 2007 - 10:41:51 PDT)
- Re: AMBER: Rate of Dissociation Sean Rathlef (Fri May 04 2007 - 12:15:03 PDT)
  - Re: AMBER: Rate of Dissociation Catein Catherine (Fri May 04 2007 - 19:10:02 PDT)
    - Re: AMBER: Rate of Dissociation wang (Sun May 06 2007 - 18:44:36 PDT)
AMBER: B or E Dihedral Labels in RDPARM output Mark Williamson (Fri May 04 2007 - 07:04:17 PDT)
- Re: AMBER: B or E Dihedral Labels in RDPARM output Thomas Cheatham III (Fri May 04 2007 - 08:24:07 PDT)
AMBER: Average PDB - Unusual Bonds Seth Lilavivat (Fri May 04 2007 - 07:12:25 PDT)
- RE: AMBER: Average PDB - Unusual Bonds Hayden Eastwood (Fri May 04 2007 - 07:45:01 PDT)
  - RE: AMBER: Average PDB - Unusual Bonds Ross Walker (Fri May 04 2007 - 08:29:36 PDT)
AMBER: Simulated Annealing - Best way to create randomness Seth Lilavivat (Fri May 04 2007 - 13:42:18 PDT)
AMBER: RE: RE: AMBER: Problem with SCC-DFTB parameter files 한재범 (Fri May 04 2007 - 21:25:29 PDT)
- AMBER: polarizable water models. Karen Callahan (Fri May 04 2007 - 23:38:34 PDT)
  - Re: AMBER: polarizable water models. David A. Case (Sun May 06 2007 - 14:31:50 PDT)
AMBER: FW: Query regarding using tleap for preparing carbohydrate molecule Ross Walker (Sun May 06 2007 - 18:31:24 PDT)
- Re: AMBER: FW: Query regarding using tleap for preparing carbohydrate molecule Gustavo Seabra (Mon May 07 2007 - 05:36:15 PDT)
  - RE: AMBER: FW: Query regarding using tleap for preparing carbohydrate molecule Ross Walker (Mon May 07 2007 - 08:11:12 PDT)
AMBER: REF file problem deepti nayar (Sun May 06 2007 - 23:49:53 PDT)
- Re: AMBER: REF file problem Gustavo Seabra (Mon May 07 2007 - 05:20:10 PDT)
- RE: AMBER: REF file problem Ross Walker (Mon May 07 2007 - 08:13:58 PDT)
AMBER: Atoms closer to 2 angstroms to each other Christopher Gaughan (Mon May 07 2007 - 07:38:06 PDT)
- Re: AMBER: Atoms closer to 2 angstroms to each other David A. Case (Mon May 07 2007 - 07:55:30 PDT)
- RE: AMBER: Atoms closer to 2 angstroms to each other Ross Walker (Mon May 07 2007 - 08:30:29 PDT)
AMBER: GB Energy Spreads for MD Structures adelene.Stanford.EDU (Mon May 07 2007 - 12:19:47 PDT)
- Re: AMBER: GB Energy Spreads for MD Structures David A. Case (Mon May 07 2007 - 14:13:41 PDT)
AMBER: Keq computations Sean Rathlef (Mon May 07 2007 - 16:10:09 PDT)
- Re: AMBER: Keq computations Carlos Simmerling (Mon May 07 2007 - 15:43:53 PDT)
  - AMBER: Is the simulation reasonable ? (SMD : dissocation antibody-antigen) wang (Wed May 16 2007 - 23:41:39 PDT)
    - Re: AMBER: Is the simulation reasonable ? (SMD : dissocation antibody-antigen) Adrian Roitberg (Thu May 17 2007 - 08:06:49 PDT)
AMBER: NAB MD Output adelene.Stanford.EDU (Mon May 07 2007 - 15:30:51 PDT)
- Re: AMBER: NAB MD Output Russell Brown (Mon May 07 2007 - 16:06:27 PDT)
- Re: AMBER: NAB MD Output Andreas Svrcek-Seiler (Tue May 08 2007 - 03:09:18 PDT)
AMBER: PME memory requirement Russell Brown (Mon May 07 2007 - 15:36:45 PDT)
- Re: AMBER: PME memory requirement Robert Duke (Mon May 07 2007 - 19:05:48 PDT)
AMBER: PMF define dehedral angel and distance restrainst for center of mass of domains. Catein Catherine (Mon May 07 2007 - 23:28:14 PDT)
- Re: AMBER: PMF define dehedral angel and distance restrainst for center of mass of domains. Carlos Simmerling (Tue May 08 2007 - 04:11:42 PDT)
AMBER: query regarding parameter files for manganese and mercuric ions neetu.imtech.res.in (Tue May 08 2007 - 04:40:56 PDT)
- AMBER: query regarding parameter files for manganese neetu.imtech.res.in (Thu May 10 2007 - 05:43:44 PDT)
AMBER: Complexes Beale, John (Tue May 08 2007 - 11:54:34 PDT)
- Re: AMBER: Complexes M. L. Dodson (Tue May 08 2007 - 12:14:59 PDT)
  - Re: AMBER: Complexes M. L. Dodson (Tue May 08 2007 - 12:26:11 PDT)
AMBER: simulations stops in half way Vijay Manickam Achari (Tue May 08 2007 - 22:01:21 PDT)
- Re: AMBER: simulations stops in half way Robert Duke (Wed May 09 2007 - 05:51:17 PDT)
AMBER: hybrid remd Geoff Wood (Wed May 09 2007 - 03:15:16 PDT)
- AMBER: hybrid remd Geoff Wood (Wed May 09 2007 - 04:22:09 PDT)
  - Re: AMBER: hybrid remd Asim Okur (Wed May 09 2007 - 12:07:59 PDT)
    - Re: AMBER: hybrid remd Geoff Wood (Wed May 09 2007 - 13:38:45 PDT)
    - Re: AMBER: hybrid remd Carlos Simmerling (Wed May 09 2007 - 13:52:03 PDT)
    - Re: AMBER: hybrid remd Geoff Wood (Wed May 09 2007 - 14:13:32 PDT)
    - Re: AMBER: hybrid remd Carlos Simmerling (Wed May 09 2007 - 14:18:05 PDT)
    - Re: AMBER: hybrid remd Geoff Wood (Wed May 09 2007 - 14:30:50 PDT)
    - Re: AMBER: hybrid remd Carlos Simmerling (Thu May 10 2007 - 04:20:14 PDT)
    - Re: AMBER: hybrid remd Geoff Wood (Thu May 10 2007 - 04:49:59 PDT)
    - Re: AMBER: hybrid remd Carlos Simmerling (Thu May 10 2007 - 06:39:43 PDT)
    - Re: AMBER: hybrid remd Geoff Wood (Thu May 10 2007 - 12:24:55 PDT)
AMBER: Compiling parallel Amber9 on Linux cluster Jesus Angulo (Wed May 09 2007 - 03:27:23 PDT)
- RE: AMBER: Compiling parallel Amber9 on Linux cluster Ross Walker (Wed May 09 2007 - 08:27:36 PDT)
AMBER: pmemd source issues Thomas Zeiser (Wed May 09 2007 - 04:33:11 PDT)
- Re: AMBER: pmemd source issues Robert Duke (Wed May 09 2007 - 06:37:59 PDT)
  - AMBER: Covert NOEs form Xplor to Amber saccenti.cerm.unifi.it (Wed May 09 2007 - 07:09:12 PDT)
  - Re: AMBER: pmemd source issues Thomas Zeiser (Wed May 09 2007 - 08:00:00 PDT)
- Re: AMBER: pmemd source issues Robert Duke (Wed May 09 2007 - 08:43:36 PDT)
  - Re: AMBER: pmemd source issues Thomas Zeiser (Thu May 10 2007 - 04:55:16 PDT)
AMBER: leap problem Achuth Prabhu (Wed May 09 2007 - 05:03:51 PDT)
- Re: AMBER: leap problem David A. Case (Thu May 10 2007 - 13:51:13 PDT)
AMBER: leap problem Achuth Prabhu (Wed May 09 2007 - 05:28:01 PDT)
AMBER: leap problem Achuth Prabhu (Wed May 09 2007 - 05:48:33 PDT)
AMBER: Amber 9 compile on OS X Knut Langsetmo (Wed May 09 2007 - 14:29:44 PDT)
- Re: AMBER: Amber 9 compile on OS X David A. Case (Thu May 10 2007 - 16:48:49 PDT)
AMBER: (no subject) Dingguo Xu (Wed May 09 2007 - 14:29:58 PDT)
- Re: AMBER: (no subject) David A. Case (Thu May 10 2007 - 13:37:21 PDT)
AMBER: Missing BELE for MM in 1 (residue 47) AYTUG TUNCEL (Thu May 10 2007 - 00:32:26 PDT)
AMBER: umbrella sampling: distance restraint Catein Catherine (Thu May 10 2007 - 03:25:46 PDT)
- Re: AMBER: umbrella sampling: distance restraint Jerome.GOLEBIOWSKI.unice.fr (Thu May 10 2007 - 05:19:35 PDT)
AMBER: restraint_wt and fixing chi deepti nayar (Thu May 10 2007 - 03:44:40 PDT)
- Re: AMBER: restraint_wt and fixing chi Thomas Cheatham III (Thu May 10 2007 - 10:09:59 PDT)
AMBER: use of pucker function in ptraj Ben Tan (Thu May 10 2007 - 04:00:41 PDT)
- Re: AMBER: use of pucker function in ptraj Thomas Cheatham III (Thu May 10 2007 - 09:48:58 PDT)
AMBER: Electrostatic Energy in MD Simulation (GB) adelene.Stanford.EDU (Thu May 10 2007 - 10:20:32 PDT)
- Re: AMBER: Electrostatic Energy in MD Simulation (GB) David A. Case (Thu May 10 2007 - 10:45:45 PDT)
AMBER: need help to calculate IR spectra from amber trajectory S.Sundar Raman (Thu May 10 2007 - 10:53:16 PDT)
- Re: AMBER: need help to calculate IR spectra from amber trajectory Adrian Roitberg (Thu May 10 2007 - 12:16:59 PDT)
AMBER: bug in reprocessing with PB? David Mobley (Thu May 10 2007 - 11:08:10 PDT)
- Re: AMBER: bug in reprocessing with PB? Carlos Simmerling (Thu May 10 2007 - 11:14:08 PDT)
- Re: AMBER: bug in reprocessing with PB? David A. Case (Thu May 10 2007 - 11:24:20 PDT)
  - RE: AMBER: bug in reprocessing with PB? Ray Luo (Thu May 10 2007 - 11:52:37 PDT)
    - Re: AMBER: bug in reprocessing with PB? David Mobley (Thu May 10 2007 - 12:20:26 PDT)
    - RE: AMBER: bug in reprocessing with PB? Ray Luo (Thu May 10 2007 - 14:04:42 PDT)
  - Re: AMBER: bug in reprocessing with PB? David Mobley (Thu May 10 2007 - 12:18:23 PDT)
AMBER: Sander (Amber 9) crash on cortex Evan Kelly (Thu May 10 2007 - 11:57:20 PDT)
- Re: AMBER: Sander (Amber 9) crash on cortex David A. Case (Thu May 10 2007 - 12:55:16 PDT)
- RE: AMBER: Sander (Amber 9) crash on cortex Ross Walker (Thu May 10 2007 - 13:09:19 PDT)
  - Re: AMBER: Sander (Amber 9) crash on cortex Evan Kelly (Thu May 10 2007 - 18:10:46 PDT)
    - Re: AMBER: Sander (Amber 9) crash on cortex Thomas Cheatham (Thu May 10 2007 - 19:56:19 PDT)
- Re: AMBER: Sander (Amber 9) crash on cortex Robert Duke (Thu May 10 2007 - 21:46:28 PDT)
  - AMBER: binding energy_decomposition per residue Srinivas Odde (Fri May 11 2007 - 14:39:50 PDT)
AMBER: single phospholipid molecule in vacuo Kliman, Michal (Thu May 10 2007 - 13:02:55 PDT)
- Re: AMBER: single phospholipid molecule in vacuo David A. Case (Thu May 10 2007 - 16:51:39 PDT)
AMBER: Rotations about center of mass of an isolated system Jennie Thomas (Thu May 10 2007 - 18:08:06 PDT)
- Re: AMBER: Rotations about center of mass of an isolated system David A. Case (Mon May 14 2007 - 09:19:20 PDT)
  - Re: AMBER: Rotations about center of mass of an isolated system Jennie Thomas (Mon May 14 2007 - 12:50:30 PDT)
    - Re: AMBER: Rotations about center of mass of an isolated system David A. Case (Mon May 14 2007 - 14:37:09 PDT)
    - Re: AMBER: Rotations about center of mass of an isolated system Jennie Thomas (Mon May 14 2007 - 16:55:44 PDT)
    - Re: AMBER: Rotations about center of mass of an isolated system David A. Case (Mon May 14 2007 - 17:06:24 PDT)
AMBER: how to solvate the protein with different solvents Rachel (Fri May 11 2007 - 06:01:07 PDT)
AMBER: antechamber Santanu Roy (Fri May 11 2007 - 06:40:24 PDT)
- Re: AMBER: antechamber Scott Brozell (Fri May 11 2007 - 15:46:24 PDT)
AMBER: correlation between PBTOT and GBTOT values in a MD trajectory Giulio Rastelli (Fri May 11 2007 - 07:47:39 PDT)
- RE: AMBER: correlation between PBTOT and GBTOT values in a MD trajectory Ray Luo (Fri May 11 2007 - 09:54:21 PDT)
AMBER: missing impropers for nitros? David Mobley (Fri May 11 2007 - 17:03:55 PDT)
- AMBER: Re: missing impropers for nitros? David Mobley (Fri May 11 2007 - 17:15:11 PDT)
- Re: AMBER: missing impropers for nitros? David A. Case (Sat May 12 2007 - 10:37:27 PDT)
  - Re: AMBER: missing impropers for nitros? David Mobley (Mon May 14 2007 - 06:28:34 PDT)
- Fwd: AMBER: missing impropers for nitros? David Mobley (Mon May 21 2007 - 08:47:04 PDT)
  - RE: AMBER: missing impropers for nitros? Junmei Wang (Mon May 21 2007 - 10:48:58 PDT)
AMBER: distance.restraint for two groups of atoms (center of mass) Catein Catherine (Fri May 11 2007 - 19:30:36 PDT)
- Re: AMBER: distance.restraint for two groups of atoms (center of mass) David A. Case (Sat May 12 2007 - 10:18:59 PDT)
AMBER: PMF for DG calculation. Catein Catherine (Fri May 11 2007 - 19:45:30 PDT)
- Re: AMBER: PMF for DG calculation. David Mobley (Mon May 14 2007 - 07:06:46 PDT)
  - Re: AMBER: PMF for DG calculation. David A. Case (Mon May 14 2007 - 08:01:41 PDT)
AMBER: PMF along 1D axis or every axis Catein Catherine (Fri May 11 2007 - 20:05:57 PDT)
AMBER: PMF: WHAM result Catein Catherine (Fri May 11 2007 - 20:28:30 PDT)
AMBER: antechamber Santanu Roy (Fri May 11 2007 - 22:50:13 PDT)
- Re: AMBER: antechamber David A. Case (Sat May 12 2007 - 10:13:39 PDT)
AMBER: PMEMD and restart files Austin B. Yongye (Sat May 12 2007 - 11:21:30 PDT)
- Re: AMBER: PMEMD and restart files Robert Duke (Sat May 12 2007 - 15:01:38 PDT)
AMBER: Small scale compute environments M. L. Dodson (Sat May 12 2007 - 12:13:59 PDT)
- Re: AMBER: Small scale compute environments Robert Duke (Mon May 14 2007 - 08:59:50 PDT)
  - Re: AMBER: Small scale compute environments M. L. Dodson (Mon May 14 2007 - 11:32:36 PDT)
AMBER: problem about the coordinates out the box Shaoqing.Zhang.mail.uh.edu (Sat May 12 2007 - 20:26:45 PDT)
AMBER: restraining atoms deepti nayar (Sun May 13 2007 - 21:39:15 PDT)
- Re: AMBER: restraining atoms Thomas Cheatham III (Mon May 14 2007 - 10:27:01 PDT)
AMBER: polymer Achuth Prabhu (Mon May 14 2007 - 05:55:12 PDT)
AMBER: Energy Spread using GB & Langevin Dynamics (NAB) adelene.Stanford.EDU (Mon May 14 2007 - 13:17:28 PDT)
- Re: AMBER: Energy Spread using GB & Langevin Dynamics (NAB) David A. Case (Mon May 14 2007 - 14:40:50 PDT)
- Re: AMBER: Energy Spread using GB & Langevin Dynamics (NAB) Andreas Svrcek-Seiler (Tue May 15 2007 - 02:20:16 PDT)
  - Re: AMBER: Energy Spread using GB & Langevin Dynamics (NAB) David A. Case (Tue May 15 2007 - 09:03:52 PDT)
AMBER: assigning of head atom as null. SHARAD gupta (Tue May 15 2007 - 00:26:23 PDT)
AMBER: Finding x-displacement Ben Tan (Tue May 15 2007 - 02:23:11 PDT)
AMBER: Heat of Vaporization Rita Cassia (Tue May 15 2007 - 05:35:49 PDT)
- Re: AMBER: Heat of Vaporization David A. Case (Tue May 15 2007 - 09:09:27 PDT)
  - Re: AMBER: Heat of Vaporization Thomas Cheatham III (Tue May 15 2007 - 09:37:01 PDT)
  - Re: AMBER: Heat of Vaporization David A. Case (Tue May 15 2007 - 09:51:36 PDT)
    - Re: AMBER: Heat of Vaporization Rita Cassia (Wed May 16 2007 - 04:55:49 PDT)
- RE: AMBER: Heat of Vaporization Falck da Silva Eirik (Tue May 15 2007 - 13:00:31 PDT)
  - Re: AMBER: Heat of Vaporization David A. Case (Tue May 15 2007 - 13:14:24 PDT)
    - AMBER: total energies during MM-PBSA Hu, Shaowen (JSC-SK)[USRA] (Tue May 15 2007 - 14:01:11 PDT)
    - AMBER: total energies during MM-PBSA Hu, Shaowen (JSC-SK)[USRA] (Wed May 16 2007 - 06:57:26 PDT)
AMBER: constant pH with 25 titrable sites tri nam Vo (Tue May 15 2007 - 10:44:22 PDT)
AMBER: Is there any way to extract one frame from a whole trajectory just saving one file by using ptraj j j (Tue May 15 2007 - 10:55:40 PDT)
- Re: AMBER: Is there any way to extract one frame from a whole trajectory just saving one file by using ptraj Carlos Simmerling (Tue May 15 2007 - 11:11:57 PDT)
  - Re: AMBER: Is there any way to extract one frame from a whole trajectory just saving one file by using ptraj j j (Tue May 15 2007 - 11:32:30 PDT)
- Re: AMBER: Is there any way to extract one frame from a whole trajectory just saving one file by using ptraj Gustavo Seabra (Tue May 15 2007 - 12:11:21 PDT)
  - Re: AMBER: Is there any way to extract one frame from a whole trajectory just saving one file by using ptraj Carlos Simmerling (Tue May 15 2007 - 12:55:54 PDT)
  - Re: AMBER: Is there any way to extract one frame from a whole trajectory just saving one file by using ptraj j j (Wed May 16 2007 - 02:01:24 PDT)
    - Re: AMBER: Is there any way to extract one frame from a whole trajectory just saving one file by using ptraj Carlos Simmerling (Wed May 16 2007 - 04:11:15 PDT)
    - Re: AMBER: Is there any way to extract one frame from a whole trajectory just saving one file by using ptraj j j (Wed May 16 2007 - 04:39:48 PDT)
  - Re: AMBER: Is there any way to extract one frame from a whole trajectory just saving one file by using ptraj j j (Wed May 16 2007 - 01:56:54 PDT)
    - Re: AMBER: Is there any way to extract one frame from a whole trajectory just saving one file by using ptraj Carlos Simmerling (Wed May 16 2007 - 04:09:01 PDT)
AMBER: AMBER8 compiler with intel 9.1 compiler Peter Z. Qin (Tue May 15 2007 - 18:37:22 PDT)
- Re: AMBER: AMBER8 compiler with intel 9.1 compiler Scott Brozell (Wed May 16 2007 - 11:42:06 PDT)
  - Re: AMBER: AMBER8 compiler with intel 9.1 compiler Mark Williamson (Fri May 18 2007 - 05:19:37 PDT)
- Re: AMBER: AMBER8 compiler with intel 9.1 compiler Peter Z. Qin (Wed May 16 2007 - 13:37:53 PDT)
  - Re: AMBER: AMBER8 compiler with intel 9.1 compiler David A. Case (Wed May 16 2007 - 14:01:21 PDT)
- Re: AMBER: AMBER8 compiler with intel 9.1 compiler Peter Z. Qin (Thu May 17 2007 - 15:49:39 PDT)
  - Re: AMBER: AMBER8 compiler with intel 9.1 compiler David A. Case (Thu May 17 2007 - 18:38:00 PDT)
- Re: AMBER: AMBER8 compiler with intel 9.1 compiler Peter Z. Qin (Thu May 17 2007 - 16:17:29 PDT)
  - Re: AMBER: AMBER8 compiler with intel 9.1 compiler David A. Case (Thu May 17 2007 - 18:32:55 PDT)
- Re: AMBER: AMBER8 compiler with intel 9.1 compiler Peter Z. Qin (Fri May 18 2007 - 17:53:29 PDT)
  - Re: AMBER: AMBER8 compiler with intel 9.1 compiler Scott Brozell (Tue May 22 2007 - 19:20:26 PDT)
- Re: AMBER: AMBER8 compiler with intel 9.1 compiler Peter Z. Qin (Tue May 22 2007 - 22:39:18 PDT)
  - Re: AMBER: AMBER8 compiler with intel 9.1 compiler Scott Brozell (Fri May 25 2007 - 10:45:55 PDT)
- Re: AMBER: AMBER8 compiler with intel 9.1 compiler Peter Z. Qin (Fri May 25 2007 - 09:49:13 PDT)
AMBER: Thermodynamic Integration (TI) error: "numgroup must be 2 if icfe is set" S. Jamal Rahi (Wed May 16 2007 - 06:22:47 PDT)
- Re: AMBER: Thermodynamic Integration (TI) error: "numgroup must be 2 if icfe is set" Carlos Simmerling (Wed May 16 2007 - 06:29:35 PDT)
- Re: AMBER: Thermodynamic Integration (TI) error: "numgroup must be 2 if icfe is set" Thomas Steinbrecher (Wed May 16 2007 - 08:48:20 PDT)
- Re: AMBER: Thermodynamic Integration (TI) error: "numgroup must be 2 if icfe is set" David A. Case (Wed May 16 2007 - 09:04:57 PDT)
AMBER: MM-PBSA calculation with GB dynamic Andrea - Tisacali (Wed May 16 2007 - 06:56:15 PDT)
- Re: AMBER: MM-PBSA calculation with GB dynamic Carlos Simmerling (Wed May 16 2007 - 07:03:01 PDT)
AMBER: protonate Christopher Gaughan (Wed May 16 2007 - 08:56:37 PDT)
- Re: AMBER: protonate saccenti.cerm.unifi.it (Wed May 16 2007 - 09:22:20 PDT)
  - AMBER: Minimization with heme group saccenti.cerm.unifi.it (Wed May 16 2007 - 09:25:23 PDT)
  - Re: AMBER: protonate David A. Case (Wed May 16 2007 - 09:33:20 PDT)
    - AMBER: Re: Minimization with heme group saccenti.cerm.unifi.it (Wed May 16 2007 - 10:11:43 PDT)
- AMBER: Ignore my reply to Amber protonate! saccenti.cerm.unifi.it (Wed May 16 2007 - 09:24:12 PDT)
- Re: AMBER: protonate David A. Case (Wed May 16 2007 - 09:32:37 PDT)
AMBER: work with constant pH on amber8 tri nam Vo (Wed May 16 2007 - 10:52:47 PDT)
- AMBER: work with constant pH on amber8 tri nam Vo (Wed May 16 2007 - 11:13:43 PDT)
- Re: AMBER: work with constant pH on amber8 David A. Case (Wed May 16 2007 - 11:40:42 PDT)
AMBER: NOC 3.0 is released mchen2.mailer.fsu.edu (Wed May 16 2007 - 13:03:30 PDT)
AMBER: hbond ptraj Catein Catherine (Wed May 16 2007 - 20:39:02 PDT)
- Re: AMBER: hbond ptraj Thomas Cheatham (Wed May 16 2007 - 20:57:46 PDT)
  - Re: AMBER: hbond ptraj Catein Catherine (Wed May 16 2007 - 23:33:31 PDT)
    - Re: AMBER: hbond ptraj Chris Moth (Thu May 17 2007 - 05:14:31 PDT)
    - Re: AMBER: hbond ptraj Thomas Cheatham (Thu May 17 2007 - 07:32:15 PDT)
AMBER: high energy with mm_gbsa igb=5 AYTUG TUNCEL (Thu May 17 2007 - 02:53:07 PDT)
AMBER: deeper problem with the energetics Pankaj R. Daga (Thu May 17 2007 - 06:46:33 PDT)
- Re: AMBER: deeper problem with the energetics Carlos Simmerling (Thu May 17 2007 - 06:56:43 PDT)
- Re: AMBER: deeper problem with the energetics Pankaj R. Daga (Thu May 17 2007 - 09:50:11 PDT)
  - Re: AMBER: deeper problem with the energetics Carlos Simmerling (Mon May 21 2007 - 07:11:58 PDT)
AMBER: Average structure Steve Seibold (Thu May 17 2007 - 07:33:41 PDT)
- Re: AMBER: Average structure Thomas Cheatham (Thu May 17 2007 - 07:57:12 PDT)
AMBER: multiple excecution of sander Achuth Prabhu (Thu May 17 2007 - 08:55:47 PDT)
- Re: AMBER: multiple excecution of sander Carlos Simmerling (Thu May 17 2007 - 09:03:23 PDT)
  - Re :Re: AMBER: multiple excecution of sander Achuth Prabhu (Thu May 17 2007 - 23:03:23 PDT)
    - Re: Re :Re: AMBER: multiple excecution of sander Carlos Simmerling (Mon May 21 2007 - 07:12:59 PDT)
AMBER: NAB Average Structure adelene.Stanford.EDU (Thu May 17 2007 - 09:12:47 PDT)
- Re: AMBER: NAB Average Structure David A. Case (Thu May 17 2007 - 09:32:59 PDT)
  - Re: AMBER: NAB Average Structure adelene.Stanford.EDU (Thu May 17 2007 - 11:59:42 PDT)
    - Re: AMBER: NAB Average Structure Andreas Svrcek-Seiler (Thu May 17 2007 - 12:40:26 PDT)
    - Re: AMBER: NAB Average Structure David A. Case (Thu May 17 2007 - 14:13:10 PDT)
AMBER: high energy with mm_gbsa igb=5 AYTUG TUNCEL (Thu May 17 2007 - 23:39:43 PDT)
AMBER: Some questions on mm_pbsa Hu, Shaowen (JSC-SK)[USRA] (Fri May 18 2007 - 07:53:35 PDT)
AMBER: Temperature Drift in MD (NAB) adelene.Stanford.EDU (Fri May 18 2007 - 15:49:25 PDT)
- Re: AMBER: Temperature Drift in MD (NAB) David A. Case (Fri May 18 2007 - 16:07:09 PDT)
  - Re: AMBER: Temperature Drift in MD (NAB) adelene.Stanford.EDU (Fri May 18 2007 - 16:56:39 PDT)
    - Re: AMBER: Temperature Drift in MD (NAB) David A. Case (Sat May 19 2007 - 21:03:24 PDT)
AMBER: Statictical significance of differences in energy mean values between different simulations Mostafa Sadighi (Sat May 19 2007 - 08:54:40 PDT)
AMBER: antechamber question Francesco Pietra (Sun May 20 2007 - 00:05:59 PDT)
- Re: AMBER: antechamber question David A. Case (Sun May 20 2007 - 07:44:18 PDT)
  - Re: AMBER: antechamber question Francesco Pietra (Sun May 20 2007 - 08:36:28 PDT)
AMBER: Langevin dynamics in NAB David A. Case (Sun May 20 2007 - 18:39:42 PDT)
AMBER: [AMBER] QM/MM-DFTB 박민희 (Sun May 20 2007 - 18:55:42 PDT)
AMBER: QM/MM-DRFTB 박민희 (Sun May 20 2007 - 18:57:56 PDT)
- AMBER: Docking with AMber Urszula Uciechowska (Mon May 21 2007 - 00:13:01 PDT)
  - Re: AMBER: Docking with AMber David A. Case (Mon May 21 2007 - 21:26:07 PDT)
    - AMBER: Regarding conversion of CHARMM force field parameters to AMBER parameters. nag raj (Wed Jun 13 2007 - 20:58:22 PDT)
- Re: AMBER: QM/MM-DRFTB Gustavo Seabra (Mon May 21 2007 - 08:43:43 PDT)
- Re: AMBER: QM/MM-DRFTB Gustavo Seabra (Mon May 21 2007 - 12:18:10 PDT)
  - AMBER: dielectric constant in GB/SA Shuting Wei (Mon May 21 2007 - 13:25:12 PDT)
AMBER: ambpdb gives empty cpin Achuth Prabhu (Mon May 21 2007 - 01:27:16 PDT)
- Re: AMBER: ambpdb gives empty cpin tri nam Vo (Tue May 22 2007 - 07:01:42 PDT)
AMBER: Pi-pi interactions Roberto Veiga (Mon May 21 2007 - 05:33:32 PDT)
- Re: AMBER: Pi-pi interactions Jiri Sponer (Mon May 21 2007 - 06:09:08 PDT)
  - Re: AMBER: Pi-pi interactions Roberto Veiga (Mon May 21 2007 - 08:03:16 PDT)
    - Re: AMBER: Pi-pi interactions Jiri Sponer (Mon May 21 2007 - 08:34:37 PDT)
    - Re: AMBER: Pi-pi interactions Roberto Veiga (Tue May 22 2007 - 02:27:22 PDT)
    - Re: AMBER: Pi-pi interactions Jiri Sponer (Tue May 22 2007 - 03:14:36 PDT)
- Re: AMBER: Pi-pi interactions David Cerutti (Mon May 21 2007 - 06:13:16 PDT)
  - Re: AMBER: Pi-pi interactions Jiri Sponer (Mon May 21 2007 - 06:28:22 PDT)
    - Re: AMBER: Pi-pi interactions Adrian Roitberg (Mon May 21 2007 - 06:56:51 PDT)
  - AMBER: LES problem Urszula Uciechowska (Mon Jun 04 2007 - 06:34:42 PDT)
    - Re: AMBER: LES problem Carlos Simmerling (Tue Jun 05 2007 - 05:14:15 PDT)
    - Re: AMBER: LES problem Vlad Cojocaru (Tue Jun 05 2007 - 05:41:19 PDT)
AMBER: REMD error Jason K (Mon May 21 2007 - 08:20:12 PDT)
- Re: AMBER: REMD error Carlos Simmerling (Mon May 21 2007 - 08:41:53 PDT)
  - Re: AMBER: REMD error Jason K (Tue May 22 2007 - 12:02:22 PDT)
    - AMBER: Les analyse Urszula Uciechowska (Tue May 29 2007 - 02:12:07 PDT)
    - Re: AMBER: Les analyse Carlos Simmerling (Tue May 29 2007 - 04:16:22 PDT)
    - Re: AMBER: Les analyse Wei Zhang (Tue May 29 2007 - 07:26:28 PDT)
- Re: AMBER: REMD error Carlos Simmerling (Tue May 22 2007 - 14:15:43 PDT)
  - Re: AMBER: REMD error Jason K (Thu May 24 2007 - 08:31:17 PDT)
    - Re: AMBER: REMD error Carlos Simmerling (Thu May 24 2007 - 08:41:04 PDT)
- Re: AMBER: REMD error Carlos Simmerling (Thu May 24 2007 - 10:23:02 PDT)
AMBER: antechamber question Yao Xin (Tue May 22 2007 - 06:39:41 PDT)
- RE: AMBER: antechamber question Junmei Wang (Tue May 22 2007 - 08:08:18 PDT)
AMBER: Ionic strength in pbsa Hu, Shaowen (JSC-SK)[USRA] (Tue May 22 2007 - 07:59:01 PDT)
- Re: AMBER: Ionic strength in pbsa Qizhi Cui (Tue May 22 2007 - 13:21:27 PDT)
  - RE: AMBER: Ionic strength in pbsa Hu, Shaowen (JSC-SK)[USRA] (Tue May 22 2007 - 13:29:02 PDT)
AMBER: Simulated Annealing - Start with Poor Structure Seth Lilavivat (Tue May 22 2007 - 12:28:54 PDT)
- Re: AMBER: Simulated Annealing - Start with Poor Structure Carlos Simmerling (Tue May 22 2007 - 14:08:28 PDT)
AMBER: hbond ptraj pls help. Catein Catherine (Tue May 22 2007 - 21:56:50 PDT)
- Re: AMBER: hbond ptraj pls help. Kateryna Miroshnychenko (Wed May 23 2007 - 02:01:03 PDT)
  - Re: AMBER: hbond ptraj pls help. Catein Catherine (Wed May 23 2007 - 03:17:27 PDT)
    - Re: AMBER: hbond ptraj pls help. Kateryna Miroshnychenko (Wed May 23 2007 - 04:22:18 PDT)
    - AMBER: Minimization increases energy Hayden Eastwood (Wed May 23 2007 - 09:21:35 PDT)
    - Re: AMBER: Minimization increases energy saccenti.cerm.unifi.it (Wed May 23 2007 - 10:22:33 PDT)
AMBER: (no subject) Catein Catherine (Tue May 22 2007 - 22:00:36 PDT)
AMBER: MM/GBSA error message Catein Catherine (Tue May 22 2007 - 22:09:51 PDT)
AMBER: Minimization increases energy Hayden Eastwood (Wed May 23 2007 - 09:24:15 PDT)
AMBER: inconsistency between PBSA and GBSA AYTUG TUNCEL (Wed May 23 2007 - 10:30:11 PDT)
AMBER: inconsistency between PBSA and GBSA AYTUG TUNCEL (Wed May 23 2007 - 06:26:32 PDT)
AMBER: thermodynamic integration Servaas Michielssens (Thu May 24 2007 - 08:50:48 PDT)
- Re: AMBER: thermodynamic integration David A. Case (Thu May 24 2007 - 21:14:43 PDT)
  - Re: AMBER: thermodynamic integration Servaas Michielssens (Fri May 25 2007 - 00:23:21 PDT)
AMBER: NAB normal mode output nadiav.soton.ac.uk (Thu May 24 2007 - 10:27:59 PDT)
- Re: AMBER: NAB normal mode output David A. Case (Thu May 24 2007 - 21:17:04 PDT)
  - Re: AMBER: NAB normal mode output Andreas Svrcek-Seiler (Fri May 25 2007 - 02:15:46 PDT)
    - AMBER: Less error Urszula Uciechowska (Fri May 25 2007 - 03:32:56 PDT)
    - Re: AMBER: Less error Carlos Simmerling (Fri May 25 2007 - 03:42:48 PDT)
AMBER: rfree: Error input file Steve Seibold (Thu May 24 2007 - 11:43:02 PDT)
- Re: AMBER: rfree: Error input file Carlos Simmerling (Thu May 24 2007 - 11:56:51 PDT)
  - RE: AMBER: rfree: Error input file Steve Seibold (Thu May 24 2007 - 12:22:39 PDT)
- AMBER: pi-pi interactions Sara Alexandra Moura (Fri May 25 2007 - 03:36:05 PDT)
AMBER: Steve Seibold (Thu May 24 2007 - 12:00:09 PDT)
AMBER: parameter file for Fe-S cluster devrani mitra (Thu May 24 2007 - 15:26:05 PDT)
AMBER: grid output: bulk water density mathew k varghese (Fri May 25 2007 - 03:19:30 PDT)
AMBER: software to extract data from the output file?? Avinash Kumar (Sat May 26 2007 - 01:49:37 PDT)
- Re: AMBER: software to extract data from the output file?? Steven Winfield (Sat May 26 2007 - 02:15:52 PDT)
- Re: AMBER: software to extract data from the output file?? Gustavo Seabra (Sat May 26 2007 - 07:09:08 PDT)
AMBER: inconsistency between PBSA and GBSA - help AYTUG TUNCEL (Sat May 26 2007 - 02:35:36 PDT)
AMBER: Question about determination of hydration points in binding sites Cenk Andac (Sun May 27 2007 - 01:51:27 PDT)
AMBER: Calculating RMS for each residue? tri nam Vo (Sun May 27 2007 - 09:01:38 PDT)
AMBER: Antechamber Catein Catherine (Sun May 27 2007 - 17:45:42 PDT)
- Re: AMBER: Antechamber Cenk Andac (Sun May 27 2007 - 23:56:57 PDT)
  - Re: AMBER: Antechamber Francesco Pietra (Mon May 28 2007 - 00:20:55 PDT)
AMBER: water count mathew k varghese (Sun May 27 2007 - 23:41:50 PDT)
- Re: AMBER: water count Carlos Simmerling (Mon May 28 2007 - 05:20:30 PDT)
AMBER: Amber 9 install on Debian Linux amd64 Francesco Pietra (Mon May 28 2007 - 00:14:49 PDT)
AMBER: divcon missing in Antechamber 1.27 Neelanjana Sengupta (Mon May 28 2007 - 17:54:18 PDT)
- AMBER: Re: divcon missing in Antechamber 1.27 Neelanjana Sengupta (Mon May 28 2007 - 17:56:55 PDT)
- Re: AMBER: divcon missing in Antechamber 1.27 David A. Case (Mon May 28 2007 - 18:33:52 PDT)
  - Re: AMBER: divcon missing in Antechamber 1.27 Neelanjana Sengupta (Mon May 28 2007 - 19:18:08 PDT)
    - Re: AMBER: divcon missing in Antechamber 1.27 David A. Case (Tue May 29 2007 - 07:24:20 PDT)
AMBER: 64-bit pgf90 revisited Ingvar Lagerstedt (Tue May 29 2007 - 01:39:07 PDT)
AMBER: error in running sander devrani mitra (Tue May 29 2007 - 13:22:35 PDT)
- Re: AMBER: error in running sander Carlos Simmerling (Tue May 29 2007 - 13:47:24 PDT)
  - Re: AMBER: error in running sander devrani mitra (Tue May 29 2007 - 14:27:09 PDT)
    - Re: AMBER: error in running sander Carlos Simmerling (Tue May 29 2007 - 14:33:42 PDT)
    - Re: AMBER: error in running sander devrani mitra (Tue May 29 2007 - 15:01:40 PDT)
    - Re: AMBER: error in running sander Carlos Simmerling (Tue May 29 2007 - 15:06:29 PDT)
    - RE: AMBER: error in running sander Ross Walker (Tue May 29 2007 - 15:08:30 PDT)
    - Re: AMBER: error in running sander devrani mitra (Tue May 29 2007 - 17:41:57 PDT)
    - Re: AMBER: error in running sander devrani mitra (Tue May 29 2007 - 18:12:59 PDT)
    - Re: AMBER: error in running sander Thomas Cheatham (Tue May 29 2007 - 20:03:36 PDT)
    - RE: AMBER: error in running sander Ross Walker (Tue May 29 2007 - 19:49:37 PDT)
    - Re: AMBER: error in running sander devrani mitra (Wed May 30 2007 - 16:34:41 PDT)
    - Re: AMBER: error in running sander devrani mitra (Wed May 30 2007 - 16:39:47 PDT)
AMBER: Hydration points Cenk Andac (Tue May 29 2007 - 14:31:24 PDT)
- Re: AMBER: Hydration points Carlos Simmerling (Tue May 29 2007 - 14:34:54 PDT)
  - Re: AMBER: Hydration points Cenk Andac (Wed May 30 2007 - 14:23:33 PDT)
AMBER: Umbrella Sampling for the twist angle of a DNA base pairs Catein Catherine (Wed May 30 2007 - 01:33:18 PDT)
- AMBER: electric field calculation lishan yao (Wed May 30 2007 - 05:25:16 PDT)
  - Re: AMBER: electric field calculation David A. Case (Wed May 30 2007 - 16:14:37 PDT)
  - Re: AMBER: electric field calculation lishan yao (Thu May 31 2007 - 06:33:20 PDT)
    - Re: AMBER: electric field calculation David A. Case (Thu May 31 2007 - 09:44:34 PDT)
- AMBER: Umbrella Sampling for the twist angle of a DNA base pairs Catein Catherine (Wed May 30 2007 - 08:11:36 PDT)
AMBER: Atomic positional Fluctuations Sandeep Kaushik (Wed May 30 2007 - 06:08:09 PDT)
AMBER: (no subject) Catein Catherine (Wed May 30 2007 - 08:16:19 PDT)
- Re: AMBER: (no subject) M. L. Dodson (Wed May 30 2007 - 10:54:04 PDT)
AMBER: Backbone stability problems with parm94, glycam04 and AMBER 8 Andrew Borgert (Wed May 30 2007 - 10:35:51 PDT)
- Re: AMBER: Backbone stability problems with parm94, glycam04 and AMBER 8 Carlos Simmerling (Wed May 30 2007 - 10:50:05 PDT)
- Re: AMBER: Backbone stability problems with parm94, glycam04 and AMBER 8 kkirschn.hamilton.edu (Wed May 30 2007 - 13:28:55 PDT)
AMBER: cutoff & speed-up of GBSA Wei Chen (Wed May 30 2007 - 13:27:53 PDT)
- Re: AMBER: cutoff & speed-up of GBSA Carlos Simmerling (Wed May 30 2007 - 14:59:41 PDT)
  - Re: AMBER: cutoff & speed-up of GBSA Wei Chen (Thu May 31 2007 - 13:18:09 PDT)
    - Re: AMBER: cutoff & speed-up of GBSA Carlos Simmerling (Thu May 31 2007 - 13:30:00 PDT)
    - Re: AMBER: cutoff & speed-up of GBSA David A. Case (Thu May 31 2007 - 13:31:42 PDT)
    - Re: AMBER: cutoff & speed-up of GBSA Wei Chen (Thu May 31 2007 - 13:50:54 PDT)
    - Re: AMBER: cutoff & speed-up of GBSA Julien Michel (Thu May 31 2007 - 14:24:11 PDT)
AMBER: junk in `Noshake mask` output section Ben Sattelle (Wed May 30 2007 - 14:23:49 PDT)
- Re: AMBER: junk in `Noshake mask` output section David A. Case (Wed May 30 2007 - 14:47:51 PDT)
  - Re: AMBER: junk in `Noshake mask` output section Ben Sattelle (Wed May 30 2007 - 15:05:20 PDT)
    - AMBER: LES Urszula Uciechowska (Thu May 31 2007 - 05:57:26 PDT)
    - Re: AMBER: LES Carlos Simmerling (Thu May 31 2007 - 06:17:02 PDT)
    - Re: AMBER: LES Urszula Uciechowska (Thu May 31 2007 - 06:29:27 PDT)
    - Re: AMBER: LES Carlos Simmerling (Thu May 31 2007 - 06:35:57 PDT)
AMBER: RESTRAINTMASK Roberto Veiga (Thu May 31 2007 - 07:29:26 PDT)
- Re: AMBER: RESTRAINTMASK David A. Case (Thu May 31 2007 - 08:59:42 PDT)
  - Re: AMBER: RESTRAINTMASK Sandeep Kaushik (Sun Jun 03 2007 - 22:38:21 PDT)
    - Re: AMBER: RESTRAINTMASK Roberto Veiga (Mon Jun 04 2007 - 13:09:23 PDT)
AMBER: Solvent models Francesco Pietra (Thu May 31 2007 - 08:23:56 PDT)
- Re: AMBER: Solvent models FyD (Thu May 31 2007 - 13:41:24 PDT)
  - Re: AMBER: Solvent models Francesco Pietra (Fri Jun 01 2007 - 00:00:36 PDT)
    - Re: AMBER: Solvent models FyD (Fri Jun 01 2007 - 01:14:20 PDT)
AMBER: Reg restraint value obtained during umbrella sampling D.Usharani (Thu May 31 2007 - 10:22:21 PDT)
- Re: AMBER: Reg restraint value obtained during umbrella sampling Jerome.GOLEBIOWSKI.unice.fr (Thu May 31 2007 - 11:02:45 PDT)
  - Re: AMBER: Reg restraint value obtained during umbrella sampling D.Usharani (Thu May 31 2007 - 11:28:50 PDT)
    - Re: AMBER: Reg restraint value obtained during umbrella sampling David A. Case (Thu May 31 2007 - 12:17:53 PDT)
- Re: AMBER: Reg restraint value obtained during umbrella sampling David A. Case (Thu May 31 2007 - 13:39:39 PDT)
  - Re: AMBER: Reg restraint value obtained during umbrella sampling D.Usharani (Fri Jun 01 2007 - 10:12:23 PDT)
    - Re: AMBER: Reg restraint value obtained during umbrella sampling David A. Case (Fri Jun 01 2007 - 18:19:35 PDT)
    - Re: AMBER: Reg restraint value obtained during umbrella sampling D.Usharani (Sat Jun 02 2007 - 04:07:43 PDT)
    - Re: AMBER: Reg restraint value obtained during umbrella sampling David A. Case (Sat Jun 02 2007 - 13:07:47 PDT)
    - Re: AMBER: Reg restraint value obtained during umbrella sampling D.Usharani (Thu Jun 07 2007 - 23:01:46 PDT)
AMBER: les/nudged elastic band Tamara Rogers (Thu May 31 2007 - 16:20:21 PDT)
- RE: AMBER: les/nudged elastic band Ross Walker (Thu May 31 2007 - 16:59:25 PDT)
AMBER: problem in installing amber9 Syed Tarique Moin (Fri Jun 01 2007 - 00:10:44 PDT)
- Re: AMBER: problem in installing amber9 David A. Case (Fri Jun 01 2007 - 18:12:56 PDT)
  - Re: AMBER: problem in installing amber9 Syed Tarique Moin (Tue Jun 12 2007 - 01:04:57 PDT)
    - Re: AMBER: problem in installing amber9 David A. Case (Tue Jun 12 2007 - 14:29:14 PDT)
    - RE: AMBER: problem in installing amber9 Ross Walker (Tue Jun 12 2007 - 20:44:16 PDT)
    - Re: AMBER: problem in installing amber9 Henk Meij (Wed Jun 13 2007 - 06:41:27 PDT)
    - RE: AMBER: problem in installing amber9 Ross Walker (Wed Jun 13 2007 - 08:25:19 PDT)
    - Re: AMBER: problem in installing amber9 Henk Meij (Wed Jun 13 2007 - 10:30:59 PDT)
    - RE: AMBER: problem in installing amber9 Ross Walker (Wed Jun 13 2007 - 11:29:04 PDT)
    - RE: AMBER: problem in installing amber9 Syed Tarique Moin (Fri Jul 20 2007 - 22:18:05 PDT)
- Re: AMBER: problem in installing amber9 Robert Duke (Wed Jun 13 2007 - 12:11:40 PDT)
  - Re: AMBER: problem in installing amber9 Henk Meij (Wed Jun 13 2007 - 13:32:18 PDT)
  - Re: AMBER: problem in installing amber9 SOLVED! Henk Meij (Wed Jun 13 2007 - 13:43:06 PDT)
AMBER: rms in nmode Marie Brut (Fri Jun 01 2007 - 00:22:22 PDT)
- Re: AMBER: rms in nmode cristian (Fri Jun 01 2007 - 00:59:18 PDT)
- Re: AMBER: rms in nmode David A. Case (Fri Jun 01 2007 - 08:50:27 PDT)
AMBER: Question about separating bonded force Shawn yy (Fri Jun 01 2007 - 08:31:04 PDT)
- Re: AMBER: Question about separating bonded force David A. Case (Fri Jun 01 2007 - 08:42:29 PDT)
AMBER: equilibrium constants via MMPBSA Sean Rathlef (Fri Jun 01 2007 - 09:57:46 PDT)
- Re: AMBER: equilibrium constants via MMPBSA Julien Michel (Fri Jun 01 2007 - 09:48:55 PDT)
- Re: AMBER: equilibrium constants via MMPBSA David Mobley (Mon Jun 04 2007 - 06:11:25 PDT)
  - AMBER: Installation Question Chrystal Bruce (Mon Jun 04 2007 - 07:53:46 PDT)
    - Re: AMBER: Installation Question Carlos Simmerling (Mon Jun 04 2007 - 07:16:30 PDT)
    - Re: AMBER: Installation Question Jianmin Feng (Mon Jun 04 2007 - 07:33:20 PDT)
AMBER: BUG? Does TLEAP understand SPC/E water? David Cerutti (Fri Jun 01 2007 - 10:35:02 PDT)
- RE: AMBER: BUG? Does TLEAP understand SPC/E water? Ross Walker (Fri Jun 01 2007 - 11:23:35 PDT)
- Re: AMBER: BUG? Does TLEAP understand SPC/E water? Thomas Steinbrecher (Fri Jun 01 2007 - 11:30:54 PDT)
- Re: AMBER: BUG? Does TLEAP understand SPC/E water? David A. Case (Fri Jun 01 2007 - 11:37:10 PDT)
- Re: AMBER: BUG? Does TLEAP understand SPC/E water? David A. Case (Fri Jun 01 2007 - 11:39:42 PDT)
AMBER: RE: process_mdout.perl Ross Walker (Fri Jun 01 2007 - 12:47:04 PDT)
AMBER: "distance" command in ptraj Roberto Veiga (Sat Jun 02 2007 - 04:19:42 PDT)
- Re: AMBER: "distance" command in ptraj Carlos Simmerling (Sat Jun 02 2007 - 04:56:15 PDT)
- Re: AMBER: "distance" command in ptraj Barbault Florent (Sat Jun 02 2007 - 08:28:44 PDT)
AMBER: pdb flie format Mr Defang Ouyang (Sun Jun 03 2007 - 05:53:08 PDT)
- Re: AMBER: pdb flie format Fenghui Fan (Sun Jun 03 2007 - 10:57:02 PDT)
- Re: AMBER: pdb flie format David A. Case (Sun Jun 03 2007 - 20:04:58 PDT)
  - Re: AMBER: pdb flie format j j (Mon Jun 04 2007 - 14:10:32 PDT)
AMBER: dihedral simulation lishan yao (Sun Jun 03 2007 - 08:49:33 PDT)
- Re: AMBER: dihedral simulation David A. Case (Sun Jun 03 2007 - 20:06:26 PDT)
AMBER: MM-GBSA: pairwise decompose energy calculation can't read snapshot_com.all.out jitrayut jitonnom (Sun Jun 03 2007 - 09:08:16 PDT)
AMBER: Once again, "distance" command in ptraj Roberto Veiga (Mon Jun 04 2007 - 07:06:19 PDT)
- Re: AMBER: Once again, "distance" command in ptraj Carlos Simmerling (Mon Jun 04 2007 - 07:15:22 PDT)
  - Re: AMBER: Once again, "distance" command in ptraj Roberto Veiga (Mon Jun 04 2007 - 07:20:34 PDT)
AMBER: Once again, "distance" command in ptraj Roberto Veiga (Mon Jun 04 2007 - 09:47:01 PDT)
- Re: AMBER: Once again, "distance" command in ptraj Thomas Cheatham (Mon Jun 04 2007 - 21:22:45 PDT)
  - Re: AMBER: Once again, "distance" command in ptraj Roberto Veiga (Tue Jun 05 2007 - 02:20:27 PDT)
AMBER: Amber9's sander.MPI on x86_64 kkirschn.hamilton.edu (Mon Jun 04 2007 - 10:13:51 PDT)
- Re: AMBER: Amber9's sander.MPI on x86_64 Thomas Steinbrecher (Mon Jun 04 2007 - 10:26:55 PDT)
- RE: AMBER: Amber9's sander.MPI on x86_64 Ross Walker (Mon Jun 04 2007 - 11:20:43 PDT)
- Re: AMBER: Amber9's sander.MPI on x86_64 Steve Young (Tue Jun 05 2007 - 10:23:43 PDT)
  - RE: AMBER: Amber9's sander.MPI on x86_64 Ross Walker (Wed Jun 06 2007 - 09:18:33 PDT)
AMBER: Problem about prepare the model when running antechamber Liang, Lei (Mon Jun 04 2007 - 13:04:36 PDT)
- RE: AMBER: Problem about prepare the model when running antechamber Ross Walker (Mon Jun 04 2007 - 13:47:24 PDT)
  - Re: AMBER: Problem about prepare the model when running antechamber Carlos Simmerling (Mon Jun 04 2007 - 13:52:23 PDT)
    - Re: AMBER: Problem about prepare the model when running antechamber Liang, Lei (Mon Jun 04 2007 - 14:03:45 PDT)
  - Re: AMBER: Problem about prepare the model when running antechamber Liang, Lei (Mon Jun 04 2007 - 14:02:04 PDT)
AMBER: Nucleic acid analyse : base pair parameters, backbone torsions... Sophie Barbe (Mon Jun 04 2007 - 14:16:48 PDT)
- Re: AMBER: Nucleic acid analyse : base pair parameters, backbone torsions... Cenk Andac (Mon Jun 04 2007 - 15:00:25 PDT)
- Re: AMBER: Nucleic acid analyse : base pair parameters, backbone torsions... Thomas Cheatham (Mon Jun 04 2007 - 22:04:34 PDT)
- Re: AMBER: Nucleic acid analyse : base pair parameters, backbone torsions... Stéphane Téletchéa (Tue Jun 05 2007 - 01:01:10 PDT)
AMBER: problem with starting REM on amber9 priya priya (Tue Jun 05 2007 - 06:32:50 PDT)
- Re: AMBER: problem with starting REM on amber9 Carlos Simmerling (Tue Jun 05 2007 - 06:42:29 PDT)
  - Re: AMBER: problem with starting REM on amber9 priya priya (Tue Jun 05 2007 - 07:21:12 PDT)
    - RE: AMBER: problem with starting REM on amber9 Ross Walker (Tue Jun 05 2007 - 08:36:07 PDT)
    - RE: AMBER: problem with starting REM on amber9 priya priya (Wed Jun 06 2007 - 00:07:14 PDT)
AMBER: Ptraj hbond analysis Achuth Prabhu (Tue Jun 05 2007 - 07:51:54 PDT)
AMBER: problem running parallel jobs Nikola Trbovic (Tue Jun 05 2007 - 13:43:02 PDT)
- Re: AMBER: problem running parallel jobs Robert Konecny (Tue Jun 05 2007 - 14:34:44 PDT)
  - RE: AMBER: problem running parallel jobs Nikola Trbovic (Wed Jun 06 2007 - 10:31:16 PDT)
    - Re: AMBER: problem running parallel jobs Robert Duke (Wed Jun 06 2007 - 11:03:19 PDT)
    - RE: AMBER: problem running parallel jobs Nikola Trbovic (Wed Jun 06 2007 - 11:43:14 PDT)
    - Re: AMBER: problem running parallel jobs Robert Duke (Wed Jun 06 2007 - 12:08:08 PDT)
    - RE: AMBER: problem running parallel jobs Andy Purkiss-Trew (Thu Jun 07 2007 - 02:53:34 PDT)
    - RE: AMBER: problem running parallel jobs Nikola Trbovic (Thu Jun 07 2007 - 07:58:47 PDT)
AMBER: REMD and mpiexec Steve Young (Tue Jun 05 2007 - 17:53:14 PDT)
- RE: AMBER: REMD and mpiexec Ross Walker (Wed Jun 06 2007 - 09:06:06 PDT)
  - RE: AMBER: REMD and mpiexec Steve Young (Thu Jun 07 2007 - 10:47:37 PDT)
AMBER: g(r) in mixtures? BJÖRN KARLSSON (Wed Jun 06 2007 - 00:56:05 PDT)
AMBER: Restraining valence angles Abi Ghanem josephine (Wed Jun 06 2007 - 01:35:12 PDT)
- Re: AMBER: Restraining valence angles David A. Case (Wed Jun 06 2007 - 07:49:08 PDT)
AMBER: Reg COM restraint to DNA D.Usharani (Wed Jun 06 2007 - 02:56:00 PDT)
AMBER: GB vs. Invacuo Energies Seth Lilavivat (Wed Jun 06 2007 - 07:38:32 PDT)
AMBER: Hardware recommendations please Jeremy Weedon (Wed Jun 06 2007 - 09:15:16 PDT)
- Re: AMBER: Hardware recommendations please Jeremy Weedon (Thu Jun 07 2007 - 08:24:54 PDT)
  - Re: AMBER: Hardware recommendations please David LeBard (Thu Jun 07 2007 - 11:31:21 PDT)
AMBER: Ptraj: reading PDB files Austin B. Yongye (Wed Jun 06 2007 - 14:37:31 PDT)
- Re: AMBER: Ptraj: reading PDB files Austin B. Yongye (Thu Jun 07 2007 - 07:16:10 PDT)
AMBER: How to fix two angle but do umberlla sampling for distance? Catein Catherine (Thu Jun 07 2007 - 08:14:30 PDT)
- Re: AMBER: How to fix two angle but do umberlla sampling for distance? Jerome.GOLEBIOWSKI.unice.fr (Thu Jun 07 2007 - 08:38:26 PDT)
  - AMBER: Potential of mean force. Catein Catherine (Fri Jun 08 2007 - 05:01:42 PDT)
    - Re: AMBER: Potential of mean force. Carlos Simmerling (Fri Jun 08 2007 - 05:08:06 PDT)
    - AMBER: Input files for the Potential of mean force. Catein Catherine (Sun Jun 10 2007 - 19:43:12 PDT)
AMBER: Should we just vary one parameter at a time only for PMF calculations? Catein Catherine (Thu Jun 07 2007 - 08:18:51 PDT)
- Re: AMBER: Should we just vary one parameter at a time only for PMF calculations? David A. Case (Fri Jun 08 2007 - 08:55:12 PDT)
  - AMBER: prepin for metal centre Mattias Blomberg (Mon Jun 25 2007 - 11:17:02 PDT)
    - Re: AMBER: prepin for metal centre David A. Case (Mon Jun 25 2007 - 17:43:26 PDT)
AMBER: extracting starting structures from equilibration trajectory Nikola Trbovic (Thu Jun 07 2007 - 11:06:15 PDT)
- Re: AMBER: extracting starting structures from equilibration trajectory Ilyas Yildirim (Thu Jun 07 2007 - 11:14:18 PDT)
  - RE: AMBER: extracting starting structures from equilibration trajectory Nikola Trbovic (Thu Jun 07 2007 - 12:33:35 PDT)
    - Re: AMBER: extracting starting structures from equilibration trajectory Carlos Simmerling (Thu Jun 07 2007 - 12:41:36 PDT)
    - RE: AMBER: extracting starting structures from equilibration trajectory Nikola Trbovic (Thu Jun 07 2007 - 12:54:35 PDT)
    - RE: AMBER: extracting starting structures from equilibration trajectory Ilyas Yildirim (Thu Jun 07 2007 - 12:54:06 PDT)
    - RE: AMBER: extracting starting structures from equilibration trajectory Ilyas Yildirim (Thu Jun 07 2007 - 12:58:19 PDT)
    - RE: AMBER: extracting starting structures from equilibration trajectory Nikola Trbovic (Thu Jun 07 2007 - 13:07:48 PDT)
AMBER: Dihedral driver Beale, John (Thu Jun 07 2007 - 13:08:35 PDT)
- Re: AMBER: Dihedral driver Ilyas Yildirim (Thu Jun 07 2007 - 13:16:15 PDT)
AMBER: amber94 parameters for cholesterol paula lario (Thu Jun 07 2007 - 15:57:38 PDT)
AMBER: Trouble on wiki about GAFF j j (Thu Jun 07 2007 - 16:29:37 PDT)
- Re: AMBER: Trouble on wiki about GAFF David A. Case (Thu Jun 07 2007 - 20:31:12 PDT)
  - Re: AMBER: Trouble on wiki about GAFF j j (Fri Jun 08 2007 - 00:14:13 PDT)
    - Re: AMBER: Trouble on wiki about GAFF David A. Case (Fri Jun 08 2007 - 09:11:17 PDT)
AMBER: mmpbsa decomposition error cristian (Fri Jun 08 2007 - 08:34:21 PDT)
AMBER: Compiling openmpi/icc/icpc Francesco Pietra (Fri Jun 08 2007 - 10:27:20 PDT)
- RE: AMBER: Compiling openmpi/icc/icpc Ross Walker (Fri Jun 08 2007 - 14:30:02 PDT)
  - RE: AMBER: Compiling openmpi/icc/icpc Francesco Pietra (Fri Jun 08 2007 - 23:04:45 PDT)
AMBER: Taryn Hartley (Fri Jun 08 2007 - 11:39:15 PDT)
- Re: AMBER: Carlos Simmerling (Fri Jun 08 2007 - 11:47:43 PDT)
AMBER: RE: Need your gudiance Ross Walker (Fri Jun 08 2007 - 14:18:23 PDT)
AMBER: RE: Need your gudiance Ross Walker (Fri Jun 08 2007 - 14:24:47 PDT)
AMBER: antechamber/charges/conformation Francesco Pietra (Sun Jun 10 2007 - 00:02:15 PDT)
- Re: AMBER: antechamber/charges/conformation FyD (Mon Jun 11 2007 - 01:40:11 PDT)
  - Re: AMBER: antechamber/charges/conformation Francesco Pietra (Mon Jun 11 2007 - 02:44:21 PDT)
AMBER: amber9 compile problem hmeij.wesleyan.edu (Sun Jun 10 2007 - 06:58:54 PDT)
- Re: AMBER: amber9 compile problem Mark Williamson (Sun Jun 10 2007 - 09:03:28 PDT)
  - Re: AMBER: amber9 compile problem Henk Meij (Mon Jun 11 2007 - 06:20:17 PDT)
    - Re: AMBER: amber9 compile problem Mark Williamson (Mon Jun 11 2007 - 06:28:30 PDT)
- RE: AMBER: amber9 compile problem Ross Walker (Sun Jun 10 2007 - 10:15:18 PDT)
  - Re: AMBER: amber9 compile problem Henk Meij (Mon Jun 11 2007 - 06:51:12 PDT)
    - RE: AMBER: amber9 compile problem Ross Walker (Mon Jun 11 2007 - 09:16:58 PDT)
    - Re: AMBER: amber9 compile problem Henk Meij (Mon Jun 11 2007 - 12:04:05 PDT)
    - RE: AMBER: amber9 compile problem Ross Walker (Mon Jun 11 2007 - 15:06:30 PDT)
    - Re: AMBER: amber9 compile problem Henk Meij (Tue Jun 12 2007 - 07:13:01 PDT)
    - RE: AMBER: amber9 compile problem Ross Walker (Tue Jun 12 2007 - 10:04:54 PDT)
    - Re: AMBER: amber9 compile problem Henk Meij (Tue Jun 12 2007 - 11:30:54 PDT)
    - AMBER: Problems simulating a big system Jordi Camps (Mon Jul 16 2007 - 04:55:55 PDT)
    - Re: AMBER: Problems simulating a big system David A. Case (Mon Jul 16 2007 - 18:44:09 PDT)
    - Re: AMBER: Problems simulating a big system Jordi Camps (Tue Jul 17 2007 - 02:57:13 PDT)
    - AMBER: configure question Steve Young (Thu Jun 28 2007 - 08:52:48 PDT)
    - Re: AMBER: configure question David A. Case (Thu Jun 28 2007 - 09:26:34 PDT)
    - Re: AMBER: configure question Andreas Svrcek-Seiler (Thu Jun 28 2007 - 09:49:38 PDT)
    - RE: AMBER: configure question Ross Walker (Thu Jun 28 2007 - 10:06:40 PDT)
    - RE: AMBER: configure question Steve Young (Fri Jun 29 2007 - 07:31:19 PDT)
    - Re: AMBER: configure question Robert Duke (Thu Jun 28 2007 - 15:18:53 PDT)
- Re: AMBER: amber9 compile problem Robert Duke (Wed Jun 13 2007 - 11:07:37 PDT)
AMBER: problem installing amber7 Saiful Islam (Sun Jun 10 2007 - 07:55:19 PDT)
- Re: AMBER: problem installing amber7 Carlos Simmerling (Sun Jun 10 2007 - 08:23:10 PDT)
- Re: AMBER: problem installing amber7 David A. Case (Sun Jun 10 2007 - 19:59:17 PDT)
AMBER: Rdf question BJÖRN KARLSSON (Sun Jun 10 2007 - 12:51:16 PDT)
AMBER: Installing on windows Colby C (Sun Jun 10 2007 - 16:42:25 PDT)
- Re: AMBER: Installing on windows Carlos Simmerling (Sun Jun 10 2007 - 16:54:04 PDT)
- Re: AMBER: Installing on windows Gustavo Seabra (Sun Jun 10 2007 - 17:28:01 PDT)
  - Re: AMBER: Installing on windows Colby C (Sun Jun 10 2007 - 18:48:30 PDT)
    - Re: AMBER: Installing on windows Gustavo Seabra (Sun Jun 10 2007 - 19:20:05 PDT)
    - Re: AMBER: Installing on windows Colby C (Sun Jun 10 2007 - 20:34:58 PDT)
    - Re: AMBER: Installing on windows David A. Case (Sun Jun 10 2007 - 21:25:28 PDT)
    - Re: AMBER: Installing on windows Colby C (Mon Jun 11 2007 - 05:56:39 PDT)
    - Re: AMBER: Installing on windows Gustavo Seabra (Mon Jun 11 2007 - 06:59:29 PDT)
    - Re: AMBER: Installing on windows Colby C (Mon Jun 11 2007 - 07:42:40 PDT)
    - Re: AMBER: Installing on windows Colby C (Mon Jun 11 2007 - 08:17:07 PDT)
    - Re: AMBER: Installing on windows Gustavo Seabra (Mon Jun 11 2007 - 08:41:05 PDT)
    - Re: AMBER: Installing on windows Colby C (Mon Jun 11 2007 - 10:14:33 PDT)
    - Re: AMBER: Installing on windows Gustavo Seabra (Mon Jun 11 2007 - 11:56:48 PDT)
- Re: AMBER: Installing on windows Bill Ross (Mon Jun 11 2007 - 12:01:06 PDT)
- Re: AMBER: Installing on windows Bill Ross (Mon Jun 11 2007 - 12:14:04 PDT)
AMBER: Steve Seibold (Mon Jun 11 2007 - 10:31:47 PDT)
AMBER: Question about MPI-IO David LeBard (Mon Jun 11 2007 - 13:58:54 PDT)
- Re: AMBER: Question about MPI-IO Thomas Cheatham III (Mon Jun 11 2007 - 14:40:08 PDT)
  - RE: AMBER: Question about MPI-IO Ross Walker (Mon Jun 11 2007 - 16:16:02 PDT)
    - Re: AMBER: Question about MPI-IO David LeBard (Mon Jun 11 2007 - 18:59:33 PDT)
- Re: AMBER: Question about MPI-IO Robert Duke (Mon Jun 11 2007 - 14:51:56 PDT)
AMBER: dihedral parameters Jardas sucuriba (Mon Jun 11 2007 - 15:13:36 PDT)
- Re: AMBER: dihedral parameters David A. Case (Tue Jun 12 2007 - 12:35:57 PDT)
- RE: AMBER: dihedral parameters Jardas sucuriba (Tue Jun 12 2007 - 19:18:12 PDT)
AMBER: Amber 9 on IRIX 6.5 Colby C (Mon Jun 11 2007 - 18:55:25 PDT)
AMBER: xleap on cygwin Colby C (Mon Jun 11 2007 - 18:59:17 PDT)
- Re: AMBER: xleap on cygwin Wei Chen (Tue Jun 12 2007 - 06:06:45 PDT)
  - Re: AMBER: xleap on cygwin Colby C (Tue Jun 12 2007 - 09:34:21 PDT)
    - Re: AMBER: xleap on cygwin Steven Winfield (Tue Jun 12 2007 - 09:45:09 PDT)
    - Re: AMBER: xleap on cygwin Colby C (Tue Jun 12 2007 - 17:42:52 PDT)
AMBER: NMR vs. X-ray structures Sally Pias (Mon Jun 11 2007 - 22:22:19 PDT)
- Re: AMBER: NMR vs. X-ray structures Marc Baaden (Mon Jun 11 2007 - 22:51:21 PDT)
- Re: AMBER: NMR vs. X-ray structures Carlos Simmerling (Tue Jun 12 2007 - 03:57:12 PDT)
AMBER: Amber: Number density profile, pucker..reg Praveena Gopal (Mon Jun 11 2007 - 23:17:37 PDT)
AMBER: building water box with desired number of molecules Vijay Manickam Achari (Tue Jun 12 2007 - 00:33:21 PDT)
- Re: AMBER: building water box with desired number of molecules gurpreet singh (Tue Jun 12 2007 - 02:09:10 PDT)
AMBER: Internal dielectric and MMPBSA Ileana Stoica (Tue Jun 12 2007 - 04:32:17 PDT)
AMBER: Metal ions in GBSA Wei Chen (Tue Jun 12 2007 - 06:13:36 PDT)
AMBER: Using position restraints during constant pressure equilibration priya priya (Tue Jun 12 2007 - 06:17:44 PDT)
AMBER: MM-PBSA calcuation for drug dna complex in 2:1 ratio saurabh agrawal (Tue Jun 12 2007 - 06:25:09 PDT)
AMBER: Steve Seibold (Tue Jun 12 2007 - 09:21:15 PDT)
- Re: AMBER: David A. Case (Tue Jun 12 2007 - 12:29:06 PDT)
RE: AMBER: Atom types Taryn Hartley (Tue Jun 12 2007 - 10:25:30 PDT)
- Re: AMBER: Atom types Melinda Layten (Tue Jun 12 2007 - 11:16:34 PDT)
AMBER: box size bomb in QMMM calculation M. L. Dodson (Tue Jun 12 2007 - 12:46:00 PDT)
- RE: AMBER: box size bomb in QMMM calculation Ross Walker (Tue Jun 12 2007 - 15:29:26 PDT)
  - Re: AMBER: box size bomb in QMMM calculation M. L. Dodson (Tue Jun 12 2007 - 16:23:50 PDT)
    - RE: AMBER: box size bomb in QMMM calculation Ross Walker (Tue Jun 12 2007 - 20:39:35 PDT)
    - Re: AMBER: box size bomb in QMMM calculation M. L. Dodson (Wed Jun 13 2007 - 02:43:52 PDT)
AMBER: frcmod Brooke Elizabeth Adams (Tue Jun 12 2007 - 13:38:50 PDT)
- Re: AMBER: frcmod David A. Case (Tue Jun 12 2007 - 14:34:35 PDT)
  - Re: AMBER: frcmod Brooke Elizabeth Adams (Fri Jun 15 2007 - 12:11:00 PDT)
    - Re: AMBER: frcmod David A. Case (Fri Jun 15 2007 - 14:43:48 PDT)
    - Re: AMBER: frcmod Brooke Elizabeth Adams (Mon Jun 18 2007 - 12:06:34 PDT)
    - Re: AMBER: frcmod David A. Case (Mon Jun 18 2007 - 12:37:52 PDT)
    - Re: AMBER: frcmod Brooke Elizabeth Adams (Mon Jun 18 2007 - 13:02:13 PDT)
AMBER: metal ions Wei Chen (Tue Jun 12 2007 - 14:20:26 PDT)
AMBER: Installing amber9 in IBM P5? Du, Shiyu (Tue Jun 12 2007 - 19:09:34 PDT)
- RE: AMBER: Installing amber9 in IBM P5? Ross Walker (Tue Jun 12 2007 - 20:34:33 PDT)
  - Re: AMBER: Installing amber9 in IBM P5? Du, Shiyu (Tue Jun 12 2007 - 22:01:56 PDT)
    - Re: AMBER: Installing amber9 in IBM P5? Jed W Pitera (Wed Jun 13 2007 - 08:04:31 PDT)
    - RE: AMBER: Installing amber9 in IBM P5? Ross Walker (Wed Jun 13 2007 - 08:17:45 PDT)
    - Re: AMBER: Installing amber9 in IBM P5? Du, Shiyu (Wed Jun 13 2007 - 10:52:11 PDT)
    - Re: AMBER: Installing amber9 in IBM P5? Du, Shiyu (Wed Jun 13 2007 - 14:20:37 PDT)
    - RE: AMBER: Installing amber9 in IBM P5? Ross Walker (Wed Jun 13 2007 - 16:39:11 PDT)
AMBER: hydrogen bond Guillaume Renvez (Wed Jun 13 2007 - 01:49:22 PDT)
AMBER: problems using TIP4PBOX john chen (Wed Jun 13 2007 - 03:53:30 PDT)
- Re: AMBER: problems using TIP4PBOX David A. Case (Wed Jun 13 2007 - 05:26:11 PDT)
- Re: AMBER: problems using TIP4PBOX Andy Purkiss-Trew (Wed Jun 13 2007 - 05:36:14 PDT)
AMBER: [Fwd: Tr: H bonds] Guillaume Renvez (Wed Jun 13 2007 - 05:37:20 PDT)
AMBER: Hbonds mbrut.laas.fr (Wed Jun 13 2007 - 05:54:52 PDT)
- Re: AMBER: Hbonds David A. Case (Wed Jun 13 2007 - 13:50:11 PDT)
  - AMBER: Running Amber8 - Sander tri nam Vo (Sun Nov 23 2008 - 22:28:31 PST)
    - Re: AMBER: Running Amber8 - Sander David A. Case (Mon Dec 01 2008 - 07:37:32 PST)
AMBER: S-nitrocysteine Anthony Cruz Balberdi (Wed Jun 13 2007 - 06:12:00 PDT)
- Re: AMBER: S-nitrocysteine FyD (Wed Jun 13 2007 - 14:44:59 PDT)
AMBER: g(r) khn _ (Wed Jun 13 2007 - 09:43:25 PDT)
AMBER: SANDER error: 'angles are not correct' Fred Baba (Wed Jun 13 2007 - 14:47:14 PDT)
THANKS -- Re: AMBER: NMR vs. X-ray structures Sally Pias (Wed Jun 13 2007 - 21:33:06 PDT)
AMBER: (no subject) Catein Catherine (Wed Jun 13 2007 - 22:54:28 PDT)
- AMBER: spring constant for restraint Catein Catherine (Thu Jun 14 2007 - 02:29:17 PDT)
- Re: AMBER: (no subject) Franck Vendeix (Thu Jun 14 2007 - 06:32:54 PDT)
AMBER: Hbonds mbrut.laas.fr (Thu Jun 14 2007 - 00:45:25 PDT)
- Re: AMBER: Hbonds David A. Case (Fri Jun 15 2007 - 11:06:26 PDT)
AMBER: ff99 vs ff99SB for RNA Brent Krueger (Thu Jun 14 2007 - 07:05:12 PDT)
- Re: AMBER: ff99 vs ff99SB for RNA Carlos Simmerling (Thu Jun 14 2007 - 07:57:02 PDT)
  - Re: AMBER: ff99 vs ff99SB for RNA j j (Thu Jun 14 2007 - 08:30:21 PDT)
    - Re: AMBER: ff99 vs ff99SB for RNA Carlos Simmerling (Thu Jun 14 2007 - 09:03:03 PDT)
- Re: AMBER: ff99 vs ff99SB for RNA Thomas Cheatham III (Thu Jun 14 2007 - 09:17:46 PDT)
AMBER: [ProblemSolved]Re: SANDER error: 'angles are not correct' Fred Baba (Thu Jun 14 2007 - 10:08:47 PDT)
AMBER: Compile openmpi Francesco Pietra (Thu Jun 14 2007 - 10:11:02 PDT)
AMBER: umbrella sampling dihedral restraint question Cen Gao (Thu Jun 14 2007 - 13:33:51 PDT)
- Re: AMBER: umbrella sampling dihedral restraint question David A. Case (Sun Jun 17 2007 - 22:46:16 PDT)
AMBER: pair distribution function khn _ (Thu Jun 14 2007 - 16:20:47 PDT)
- Re: AMBER: pair distribution function Thomas Cheatham III (Thu Jun 14 2007 - 16:41:51 PDT)
  - Re: AMBER: pair distribution function khn _ (Sun Jun 17 2007 - 01:25:56 PDT)
AMBER: isolated NTP Steve Seibold (Fri Jun 15 2007 - 07:07:16 PDT)
- Re: AMBER: isolated NTP David A. Case (Sun Jun 17 2007 - 22:40:29 PDT)
  - RE: AMBER: isolated NTP Steve Seibold (Mon Jun 18 2007 - 05:20:21 PDT)
    - Re: AMBER: isolated NTP David A. Case (Mon Jun 18 2007 - 08:39:06 PDT)
AMBER: Saving a structuring from trajectory Seth Lilavivat (Fri Jun 15 2007 - 11:42:12 PDT)
- Re: AMBER: Saving a structuring from trajectory Ilyas Yildirim (Fri Jun 15 2007 - 11:59:50 PDT)
Re: AMBER: Amber Installation Error David A. Case (Fri Jun 15 2007 - 11:56:29 PDT)
RE: AMBER: Amber Installation Error Ross Walker (Fri Jun 15 2007 - 12:25:28 PDT)
- RE: AMBER: Amber Installation Error Joe Nolan (Mon Jun 18 2007 - 07:34:12 PDT)
  - Re: AMBER: Amber Installation Error Mark Williamson (Mon Jun 18 2007 - 08:35:18 PDT)
    - Re: AMBER: Amber Installation Error Joe Nolan (Mon Jun 18 2007 - 08:52:16 PDT)
    - Re: AMBER: Amber Installation Error Mark Williamson (Mon Jun 18 2007 - 11:19:27 PDT)
    - Re: AMBER: Amber Installation Error Joe Nolan (Mon Jun 18 2007 - 12:08:48 PDT)
  - Re: AMBER: Amber Installation Error David A. Case (Mon Jun 18 2007 - 10:52:05 PDT)
AMBER: .lib files Taryn Hartley (Fri Jun 15 2007 - 12:42:16 PDT)
- Re: AMBER: .lib files Ilyas Yildirim (Fri Jun 15 2007 - 12:50:34 PDT)
AMBER: performance with implicit solvent Kijeong Kwac (Fri Jun 15 2007 - 13:02:49 PDT)
- Re: AMBER: performance with implicit solvent Carlos Simmerling (Fri Jun 15 2007 - 13:17:28 PDT)
- Re: AMBER: performance with implicit solvent David A. Case (Fri Jun 15 2007 - 13:18:31 PDT)
AMBER: PDB problems Taryn Hartley (Fri Jun 15 2007 - 13:17:13 PDT)
- Re: AMBER: PDB problems David A. Case (Fri Jun 15 2007 - 13:24:44 PDT)
- Re: AMBER: PDB problems Ilyas Yildirim (Fri Jun 15 2007 - 15:30:45 PDT)
Re: AMBER: Saving a structuring from trajectory Bill Ross (Fri Jun 15 2007 - 13:43:23 PDT)
AMBER: MMPBSA-nmode .top question Matthew Danielson (Fri Jun 15 2007 - 14:11:52 PDT)
- Re: AMBER: MMPBSA-nmode .top question David A. Case (Sun Jun 17 2007 - 22:35:39 PDT)
AMBER: Energy outputs in TI Approach Ilyas Yildirim (Fri Jun 15 2007 - 22:03:26 PDT)
- Re: AMBER: Energy outputs in TI Approach David A. Case (Sat Jun 16 2007 - 08:19:23 PDT)
AMBER: distance scan Miguel Ferreira (Sat Jun 16 2007 - 03:16:15 PDT)
- Re: AMBER: distance scan David A. Case (Sat Jun 16 2007 - 08:21:05 PDT)
AMBER: distance scan Miguel Ferreira (Sat Jun 16 2007 - 03:25:59 PDT)
AMBER: implementation of GB model in AMBER john chen (Sun Jun 17 2007 - 05:49:24 PDT)
- Re: AMBER: implementation of GB model in AMBER Carlos Simmerling (Sun Jun 17 2007 - 05:58:11 PDT)
  - AMBER: explanation to edit and use the script Syed Tarique Moin (Sun Jun 17 2007 - 21:26:38 PDT)
    - Re: AMBER: explanation to edit and use the script Syed Tarique Moin (Wed Jun 20 2007 - 02:33:15 PDT)
AMBER: error due to exceeding left-hand side digital numbers in restart output Cenk Andac (Mon Jun 18 2007 - 01:09:36 PDT)
- Re: AMBER: error due to exceeding left-hand side digital numbers in restart output David A. Case (Mon Jun 18 2007 - 11:06:16 PDT)
AMBER: problem with running rem on amber9 priya priya (Mon Jun 18 2007 - 05:41:02 PDT)
- Re: AMBER: problem with running rem on amber9 Carlos Simmerling (Mon Jun 18 2007 - 05:46:29 PDT)
  - Re: AMBER: problem with running rem on amber9 priya priya (Mon Jun 18 2007 - 05:59:38 PDT)
  - Re: AMBER: problem with running rem on amber9 priya priya (Mon Jun 18 2007 - 08:02:55 PDT)
    - Re: AMBER: problem with running rem on amber9 Carlos Simmerling (Mon Jun 18 2007 - 08:10:37 PDT)
    - Re: AMBER: problem with running rem on amber9 priya priya (Mon Jun 18 2007 - 08:25:37 PDT)
- Re: AMBER: problem with running rem on amber9 David A. Case (Mon Jun 18 2007 - 11:22:01 PDT)
AMBER: Charge not integral. Head-to-tail cyclic peptides Giacomo Bastianelli (Mon Jun 18 2007 - 06:55:46 PDT)
- Re: AMBER: Charge not integral. Head-to-tail cyclic peptides Melinda Layten (Mon Jun 18 2007 - 07:28:57 PDT)
- Re: AMBER: Charge not integral. Head-to-tail cyclic peptides Laurent Chiche (Mon Jun 18 2007 - 07:37:53 PDT)
Re: AMBER: problem with running rem on amber9 (NOT A REMD PROBLEM) Carlos Simmerling (Mon Jun 18 2007 - 08:31:19 PDT)
AMBER: shell model MD Stern, Julie (Mon Jun 18 2007 - 09:48:54 PDT)
- Re: AMBER: shell model MD Carlos Simmerling (Mon Jun 18 2007 - 09:53:56 PDT)
AMBER: Questions about how ptraj calculates solvent shells Roberto Veiga (Mon Jun 18 2007 - 11:46:59 PDT)
AMBER: unres Carra, Claudio (JSC-SK)[USRA] (Mon Jun 18 2007 - 13:55:20 PDT)
- Re: AMBER: unres Piotr Cieplak (Mon Jun 18 2007 - 17:00:47 PDT)
AMBER: H bond Guillaume Renvez (Tue Jun 19 2007 - 01:18:45 PDT)
- Re: AMBER: H bond Carlos Simmerling (Tue Jun 19 2007 - 04:24:27 PDT)
AMBER: Re: Strange shape in my MD simulations Pavan G (Tue Jun 19 2007 - 05:47:58 PDT)
- Re: AMBER: Re: Strange shape in my MD simulations Adrian Roitberg (Tue Jun 19 2007 - 05:57:07 PDT)
  - Re: AMBER: Re: Strange shape in my MD simulations Pavan G (Tue Jun 19 2007 - 07:09:48 PDT)
    - Re: AMBER: Re: Strange shape in my MD simulations Adrian Roitberg (Tue Jun 19 2007 - 07:16:17 PDT)
    - Re: AMBER: Re: Strange shape in my MD simulations Pavan G (Tue Jun 19 2007 - 07:34:45 PDT)
    - RE: AMBER: Re: Strange shape in my MD simulations Ross Walker (Tue Jun 19 2007 - 08:42:08 PDT)
    - Re: AMBER: Re: Strange shape in my MD simulations Pavan G (Tue Jun 19 2007 - 11:37:18 PDT)
- Re: AMBER: Re: Strange shape in my MD simulations gurpreet singh (Wed Jun 20 2007 - 00:58:03 PDT)
  - RE: AMBER: Re: Strange shape in my MD simulations Ross Walker (Wed Jun 20 2007 - 08:27:37 PDT)
AMBER: How to add semi-experience parameter in divcon? clarkzhy (Tue Jun 19 2007 - 07:23:04 PDT)
- RE: AMBER: How to add semi-experience parameter in divcon? Ross Walker (Tue Jun 19 2007 - 08:44:59 PDT)
- Re: AMBER: How to add semi-experience parameter in divcon? Seth Hayik (Tue Jun 19 2007 - 09:15:03 PDT)
AMBER: Reply regarding PCA with ptraj and IED Steve Spronk (Tue Jun 19 2007 - 14:00:37 PDT)
- Re: AMBER: Reply regarding PCA with ptraj and IED Hannes Loeffler (Tue Jun 19 2007 - 19:43:21 PDT)
AMBER: problems in adding ACE and NME group backy (Wed Jun 20 2007 - 02:09:26 PDT)
- Re: AMBER: problems in adding ACE and NME group Carlos Simmerling (Wed Jun 20 2007 - 04:28:46 PDT)
- Re: AMBER: problems in adding ACE and NME group backy (Wed Jun 20 2007 - 06:15:25 PDT)
  - Re: AMBER: problems in adding ACE and NME group Carlos Simmerling (Wed Jun 20 2007 - 08:37:45 PDT)
  - Re: AMBER: problems in adding ACE and NME group David A. Case (Wed Jun 20 2007 - 08:41:43 PDT)
- RE: AMBER: problems in adding ACE and NME group Gustavo Seabra (Wed Jun 20 2007 - 07:14:26 PDT)
- Re: AMBER: problems in adding ACE and NME group backy (Wed Jun 20 2007 - 20:54:47 PDT)
  - Re: AMBER: problems in adding ACE and NME group David A. Case (Wed Jun 20 2007 - 22:10:43 PDT)
- Re: AMBER: problems in adding ACE and NME group backy (Wed Jun 20 2007 - 21:00:39 PDT)
  - Re: AMBER: problems in adding ACE and NME group Carlos Simmerling (Wed Jun 20 2007 - 21:28:30 PDT)
- Re: AMBER: problems in adding ACE and NME group backy (Wed Jun 20 2007 - 22:00:12 PDT)
- Re: AMBER: problems in adding ACE and NME group backy (Wed Jun 20 2007 - 22:45:56 PDT)
- Re: AMBER: problems in adding ACE and NME group backy (Mon Jun 25 2007 - 06:21:47 PDT)
  - Re: AMBER: problems in adding ACE and NME group priya priya (Mon Jun 25 2007 - 07:01:52 PDT)
    - Re: AMBER: problems in adding ACE and NME group Melinda Layten (Tue Jun 26 2007 - 13:02:12 PDT)
- Re: AMBER: problems in adding ACE and NME group backy (Tue Jun 26 2007 - 23:55:47 PDT)
  - Re: AMBER: problems in adding ACE and NME group Melinda Layten (Wed Jun 27 2007 - 09:01:00 PDT)
  - RE: AMBER: problems in adding ACE and NME group Ross Walker (Wed Jun 27 2007 - 09:02:10 PDT)
  - Re: AMBER: problems in adding ACE and NME group David A. Case (Wed Jun 27 2007 - 09:19:51 PDT)
- Re: AMBER: problems in adding ACE and NME group backy (Wed Jun 27 2007 - 23:13:02 PDT)
  - Re: AMBER: problems in adding ACE and NME group David A. Case (Thu Jun 28 2007 - 09:04:52 PDT)
AMBER: Re: Fwd: joshua j j (Wed Jun 20 2007 - 04:27:43 PDT)
- Re: AMBER: Re: Fwd: joshua j j (Wed Jun 20 2007 - 06:01:00 PDT)
AMBER: 5 Ligands and 1 Protein Colby C (Wed Jun 20 2007 - 11:07:33 PDT)
- Re: AMBER: 5 Ligands and 1 Protein David A. Case (Wed Jun 20 2007 - 16:46:23 PDT)
  - Re: AMBER: 5 Ligands and 1 Protein Colby C (Wed Jun 20 2007 - 17:10:22 PDT)
    - Re: AMBER: 5 Ligands and 1 Protein David A. Case (Wed Jun 20 2007 - 17:16:27 PDT)
    - Re: AMBER: 5 Ligands and 1 Protein Colby C (Wed Jun 20 2007 - 19:01:40 PDT)
    - Re: AMBER: 5 Ligands and 1 Protein David A. Case (Wed Jun 20 2007 - 22:02:20 PDT)
    - Re: AMBER: 5 Ligands and 1 Protein Colby C (Thu Jun 21 2007 - 14:45:46 PDT)
    - Re: AMBER: 5 Ligands and 1 Protein David A. Case (Fri Jun 22 2007 - 08:05:28 PDT)
- Re: AMBER: 5 Ligands and 1 Protein Scott Brozell (Wed Jun 20 2007 - 17:25:05 PDT)
AMBER: Algorithm for integration of equations of motion Roberto Veiga (Wed Jun 20 2007 - 11:55:45 PDT)
- RE: AMBER: Algorithm for integration of equations of motion Ross Walker (Wed Jun 20 2007 - 12:38:36 PDT)
AMBER: sander core dumped during minimization zgleo (Wed Jun 20 2007 - 18:51:04 PDT)
- Re: AMBER: sander core dumped during minimization David A. Case (Wed Jun 20 2007 - 22:16:11 PDT)
AMBER: set up system solution with 3 different components, each with multiple copies Nicolas Lux Fawzi (Thu Jun 21 2007 - 08:56:57 PDT)
- Re: AMBER: set up system solution with 3 different components, each with multiple copies David A. Case (Tue Jun 26 2007 - 08:08:50 PDT)
  - Re: AMBER: set up system solution with 3 different components, each with multiple copies Nicolas Lux Fawzi (Tue Jun 26 2007 - 08:16:54 PDT)
    - Re: AMBER: set up system solution with 3 different components, each with multiple copies M. L. Dodson (Tue Jun 26 2007 - 08:27:41 PDT)
AMBER: ptray segfault: vector out Nicolas Lux Fawzi (Thu Jun 21 2007 - 12:19:49 PDT)
To Mr. Ross Walker Re: RE: AMBER: How to add semi-experience parameter in divcon? clarkzhy (Thu Jun 21 2007 - 18:19:23 PDT)
AMBER: testing protein stability Sally Pias (Thu Jun 21 2007 - 22:24:58 PDT)
- Re: AMBER: testing protein stability Carlos Simmerling (Fri Jun 22 2007 - 04:06:16 PDT)
  - Re: AMBER: testing protein stability Sally Pias (Fri Jun 22 2007 - 14:57:27 PDT)
AMBER: Limitation in number of atoms/residues Sascha Rehm (Fri Jun 22 2007 - 03:47:35 PDT)
- Re: AMBER: Limitation in number of atoms/residues Robert Duke (Fri Jun 22 2007 - 05:37:30 PDT)
  - Re: AMBER: Limitation in number of atoms/residues Sascha Rehm (Fri Jun 22 2007 - 06:46:05 PDT)
AMBER: radius of gyration priya priya (Fri Jun 22 2007 - 08:10:36 PDT)
- Re: AMBER: radius of gyration Marsita M (Sat Sep 25 2004 - 23:40:24 PDT)
  - Re: AMBER: radius of gyration Sanjeev B.S. (Sun Sep 26 2004 - 00:04:51 PDT)
- Re: AMBER: radius of gyration Bill Ross (Sun Sep 26 2004 - 20:41:58 PDT)
- Re: AMBER: radius of gyration Bill Ross (Sun Sep 26 2004 - 20:49:40 PDT)
- Re: AMBER: radius of gyration Carlos Simmerling (Fri Jun 22 2007 - 08:14:19 PDT)
  - Re: AMBER: radius of gyration priya priya (Fri Jun 22 2007 - 08:23:03 PDT)
    - Re: AMBER: radius of gyration Carlos Simmerling (Fri Jun 22 2007 - 08:40:27 PDT)
    - Re: AMBER: radius of gyration Thomas Cheatham III (Fri Jun 22 2007 - 09:30:01 PDT)
    - Re: AMBER: radius of gyration priya priya (Mon Jun 25 2007 - 05:59:39 PDT)
    - Re: AMBER: radius of gyration priya priya (Mon Jun 25 2007 - 05:57:39 PDT)
    - Re: AMBER: radius of gyration priya priya (Fri Jun 29 2007 - 02:16:24 PDT)
    - Re: AMBER: radius of gyration Carlos Simmerling (Fri Jun 29 2007 - 04:54:28 PDT)
    - Re: AMBER: radius of gyration priya priya (Fri Jun 29 2007 - 06:14:49 PDT)
AMBER: remd/rdc's McElheny, Dan (Fri Jun 22 2007 - 11:04:59 PDT)
- Re: AMBER: remd/rdc's Carlos Simmerling (Sat Jun 23 2007 - 05:43:21 PDT)
- Re: AMBER: remd/rdc's David A. Case (Sat Jun 23 2007 - 10:44:17 PDT)
  - Re: AMBER: remd/rdc's McElheny, Dan (Mon Jun 25 2007 - 09:12:20 PDT)
    - Re: AMBER: remd/rdc's David A. Case (Thu Jun 28 2007 - 08:37:44 PDT)
AMBER: radial distribution function in ptraj khn _ (Fri Jun 22 2007 - 18:25:05 PDT)
AMBER: SPCFW water: angle problems in leap Thomas Hofer (Sat Jun 23 2007 - 09:02:32 PDT)
- RE: AMBER: SPCFW water: angle problems in leap Ross Walker (Sat Jun 23 2007 - 09:47:25 PDT)
AMBER: Antechamber--Boron Parameters brmeher.iitg.ernet.in (Mon Jun 25 2007 - 03:04:30 PDT)
- Re: AMBER: Antechamber--Boron Parameters David A. Case (Mon Jun 25 2007 - 18:08:48 PDT)
AMBER: how to calculate energy of the peptide priya priya (Mon Jun 25 2007 - 06:56:54 PDT)
AMBER: environment variables Francesco Pietra (Mon Jun 25 2007 - 08:51:05 PDT)
- RE: AMBER: environment variables Ross Walker (Mon Jun 25 2007 - 12:43:39 PDT)
AMBER: RDF of pure chloroform BJÖRN KARLSSON (Mon Jun 25 2007 - 08:56:19 PDT)
AMBER: sander MPI fails included tests Sergio Wong (Mon Jun 25 2007 - 10:20:55 PDT)
- RE: AMBER: sander MPI fails included tests Ross Walker (Mon Jun 25 2007 - 11:17:34 PDT)
  - RE: AMBER: sander MPI fails included tests Sergio Wong (Mon Jun 25 2007 - 12:06:21 PDT)
    - RE: AMBER: sander MPI fails included tests Ross Walker (Mon Jun 25 2007 - 19:08:22 PDT)
    - RE: AMBER: sander MPI fails included tests Sergio Wong (Tue Jun 26 2007 - 13:58:04 PDT)
    - RE: AMBER: sander MPI fails included tests Ross Walker (Tue Jun 26 2007 - 15:06:30 PDT)
    - RE: AMBER: sander MPI fails included tests Sergio Wong (Thu Jun 28 2007 - 12:14:02 PDT)
    - RE: AMBER: sander MPI fails included tests Ross Walker (Thu Jun 28 2007 - 14:06:19 PDT)
    - RE: AMBER: sander MPI fails included tests Sergio Wong (Thu Jun 28 2007 - 17:05:08 PDT)
    - RE: AMBER: sander MPI fails included tests Ross Walker (Thu Jun 28 2007 - 21:17:50 PDT)
AMBER: Re: ff02 and ff03 parameters Pavan G (Mon Jun 25 2007 - 12:34:30 PDT)
- Re: AMBER: Re: ff02 and ff03 parameters Carlos Simmerling (Mon Jun 25 2007 - 16:28:02 PDT)
AMBER: PMF calculation Jena M (Mon Jun 25 2007 - 12:59:02 PDT)
- Re: AMBER: PMF calculation David A. Case (Mon Jun 25 2007 - 17:47:25 PDT)
AMBER: Simulated Annealing Joseph Maxwell (Mon Jun 25 2007 - 16:28:14 PDT)
- Re: AMBER: Simulated Annealing David A. Case (Mon Jun 25 2007 - 17:34:38 PDT)
- RE: AMBER: Simulated Annealing Hayden Eastwood (Tue Jun 26 2007 - 02:14:57 PDT)
  - Re: AMBER: Simulated Annealing Carlos Simmerling (Tue Jun 26 2007 - 04:16:25 PDT)
    - AMBER: Offending restraints???? saccenti.cerm.unifi.it (Tue Jun 26 2007 - 06:48:21 PDT)
    - Re: AMBER: Offending restraints???? Carlos Simmerling (Tue Jun 26 2007 - 06:59:24 PDT)
    - Re: AMBER: Offending restraints???? saccenti.cerm.unifi.it (Tue Jun 26 2007 - 07:34:05 PDT)
    - Re: AMBER: Offending restraints???? Carlos Simmerling (Tue Jun 26 2007 - 08:33:47 PDT)
    - Re: AMBER: Offending restraints???? saccenti.cerm.unifi.it (Tue Jun 26 2007 - 08:36:44 PDT)
    - RE: AMBER: Offending restraints???? Gustavo Seabra (Tue Jun 26 2007 - 07:09:18 PDT)
    - RE: AMBER: Offending restraints???? saccenti.cerm.unifi.it (Tue Jun 26 2007 - 07:23:45 PDT)
    - Re: AMBER: Offending restraints???? David A. Case (Tue Jun 26 2007 - 08:27:18 PDT)
    - Re: AMBER: Offending restraints???? saccenti.cerm.unifi.it (Tue Jun 26 2007 - 08:34:37 PDT)
    - Re: AMBER: Offending restraints???? David A. Case (Tue Jun 26 2007 - 09:37:21 PDT)
    - Re: AMBER: Offending restraints???? saccenti.cerm.unifi.it (Wed Jun 27 2007 - 02:33:16 PDT)
AMBER: PBSA Error Pankaj R. Daga (Tue Jun 26 2007 - 07:03:41 PDT)
AMBER: rst overflow for implicit REMD In Hee Park (Tue Jun 26 2007 - 07:37:45 PDT)
- Re: AMBER: rst overflow for implicit REMD David A. Case (Tue Jun 26 2007 - 08:28:28 PDT)
  - Re: AMBER: rst overflow for implicit REMD Carlos Simmerling (Tue Jun 26 2007 - 08:35:47 PDT)
AMBER: $AMBERHOME on PATH Francesco Pietra (Tue Jun 26 2007 - 10:38:35 PDT)
- Re: AMBER: $AMBERHOME on PATH David A. Case (Tue Jun 26 2007 - 11:01:02 PDT)
  - Re: AMBER: $AMBERHOME on PATH Francesco Pietra (Tue Jun 26 2007 - 13:15:11 PDT)
AMBER: "FATAL: Atom xxx does not have a type." Fred Baba (Tue Jun 26 2007 - 10:59:51 PDT)
- Re: AMBER: "FATAL: Atom xxx does not have a type." David A. Case (Tue Jun 26 2007 - 15:20:21 PDT)
AMBER: Unexpected Failure in XLeap Jason Brown (Tue Jun 26 2007 - 11:45:14 PDT)
- Re: AMBER: Unexpected Failure in XLeap David A. Case (Tue Jun 26 2007 - 13:47:30 PDT)
AMBER: Does Chimera support AMBER file formats? Ilyas Yildirim (Tue Jun 26 2007 - 16:58:56 PDT)
- Re: AMBER: Does Chimera support AMBER file formats? Mingfeng Yang (Tue Jun 26 2007 - 17:12:53 PDT)
Fwd: Re: AMBER: $AMBERHOME on PATH Francesco Pietra (Wed Jun 27 2007 - 07:30:09 PDT)
Fwd: Re: AMBER: $AMBERHOME on PATH Francesco Pietra (Wed Jun 27 2007 - 07:59:02 PDT)
- RE: Re: AMBER: $AMBERHOME on PATH Ross Walker (Wed Jun 27 2007 - 09:11:34 PDT)
  - RE: Re: AMBER: $AMBERHOME on PATH Francesco Pietra (Thu Jun 28 2007 - 07:40:09 PDT)
    - RE: Re: AMBER: $AMBERHOME on PATH Ross Walker (Thu Jun 28 2007 - 08:33:20 PDT)
    - Re: RE: Re: AMBER: $AMBERHOME on PATH Alexandar T Tzanov (Thu Jun 28 2007 - 08:39:57 PDT)
    - Re: RE: Re: AMBER: $AMBERHOME on PATH David A. Case (Thu Jun 28 2007 - 09:00:55 PDT)
    - RE: Problems with Ifort 9.1.047 on Altix (Was: RE: Re: AMBER: $AMBERHOME on PATH) Ross Walker (Thu Jun 28 2007 - 09:53:44 PDT)
    - AMBER: Re: RE: Problems with Ifort 9.1.047 on Altix (Was: RE: Re: AMBER: $AMBERHOME on PATH) Alexandar T Tzanov (Fri Jun 29 2007 - 07:48:13 PDT)
    - RE: Re: AMBER: $AMBERHOME on PATH Francesco Pietra (Thu Jun 28 2007 - 10:12:43 PDT)
    - RE: Re: AMBER: $AMBERHOME on PATH Ross Walker (Thu Jun 28 2007 - 10:58:09 PDT)
    - Re: Re: AMBER: $AMBERHOME on PATH David A. Case (Thu Jun 28 2007 - 11:37:58 PDT)
    - RE: Re: AMBER: $AMBERHOME on PATH Francesco Pietra (Thu Jun 28 2007 - 13:01:11 PDT)
    - RE: Re: AMBER: $AMBERHOME on PATH Francesco Pietra (Thu Jun 28 2007 - 13:55:53 PDT)
Fwd: Re: AMBER: $AMBERHOME on PATH & compilations Francesco Pietra (Wed Jun 27 2007 - 09:10:38 PDT)
- Re: Fwd: Re: AMBER: $AMBERHOME on PATH & compilations David A. Case (Wed Jun 27 2007 - 10:06:38 PDT)
AMBER: bugfix.all Francesco Pietra (Wed Jun 27 2007 - 13:26:15 PDT)
- Re: AMBER: bugfix.all M. L. Dodson (Wed Jun 27 2007 - 13:52:07 PDT)
  - Re: AMBER: bugfix.all Francesco Pietra (Wed Jun 27 2007 - 23:14:33 PDT)
- Re: AMBER: bugfix.all Carlos Simmerling (Wed Jun 27 2007 - 13:52:15 PDT)
- Re: AMBER: bugfix.all David A. Case (Wed Jun 27 2007 - 13:55:52 PDT)
- RE: AMBER: bugfix.all Ross Walker (Wed Jun 27 2007 - 14:19:32 PDT)
AMBER: how to stop ptraj atom renumbering Russell Green (Wed Jun 27 2007 - 13:25:53 PDT)
AMBER: Math libraries Francesco Pietra (Thu Jun 28 2007 - 02:56:45 PDT)
- Re: AMBER: Math libraries Robert Duke (Thu Jun 28 2007 - 05:15:07 PDT)
- Re: AMBER: Math libraries Andreas Svrcek-Seiler (Thu Jun 28 2007 - 09:27:28 PDT)
  - Re: AMBER: Math libraries Francesco Pietra (Thu Jun 28 2007 - 13:12:28 PDT)
AMBER: conversion of Macromodel substructure format to .frcmod file brmeher.iitg.ernet.in (Thu Jun 28 2007 - 03:24:24 PDT)
AMBER: Improving pmemd parallel scaling Alessandro Nascimento (Thu Jun 28 2007 - 09:07:15 PDT)
- Re: AMBER: Improving pmemd parallel scaling Mark Williamson (Thu Jun 28 2007 - 09:19:06 PDT)
- Re: AMBER: Improving pmemd parallel scaling Robert Duke (Thu Jun 28 2007 - 15:27:24 PDT)
AMBER: Problem with leaprc yen li (Thu Jun 28 2007 - 20:27:52 PDT)
- Re: AMBER: Problem with leaprc David A. Case (Fri Jun 29 2007 - 08:47:51 PDT)
  - Re: AMBER: Problem with leaprc yen li (Sat Jun 30 2007 - 07:11:47 PDT)
    - Re: AMBER: Problem with leaprc David A. Case (Sat Jun 30 2007 - 08:32:03 PDT)
    - Re: AMBER: Problem with leaprc Francesco Pietra (Sat Jun 30 2007 - 09:23:59 PDT)
    - Re: AMBER: Problem with leaprc yen li (Sun Jul 01 2007 - 06:10:09 PDT)
    - Re: AMBER: Problem with leaprc yen li (Sun Jul 01 2007 - 10:36:14 PDT)
    - Re: AMBER: Problem with leaprc David A. Case (Mon Jul 02 2007 - 07:44:59 PDT)
    - Re: AMBER: Problem with leaprc yen li (Wed Jul 04 2007 - 05:23:49 PDT)
    - Re: AMBER: Problem with leaprc David A. Case (Wed Jul 04 2007 - 09:15:39 PDT)
    - Re: AMBER: Problem with leaprc yen li (Wed Jul 04 2007 - 11:21:22 PDT)
    - Re: AMBER: Problem with leaprc David A. Case (Wed Jul 04 2007 - 13:31:29 PDT)
Fwd: RE: Re: AMBER: $AMBERHOME on PATH Francesco Pietra (Thu Jun 28 2007 - 22:58:19 PDT)
- Re: Fwd: RE: Re: AMBER: $AMBERHOME on PATH M. L. Dodson (Fri Jun 29 2007 - 06:34:08 PDT)
  - Re: Fwd: RE: Re: AMBER: $AMBERHOME on PATH Francesco Pietra (Sun Jul 01 2007 - 07:38:03 PDT)
    - Re: Fwd: RE: Re: AMBER: $AMBERHOME on PATH M. L. Dodson (Sun Jul 01 2007 - 08:57:05 PDT)
- Re: Fwd: RE: Re: AMBER: $AMBERHOME on PATH David A. Case (Fri Jun 29 2007 - 09:05:09 PDT)
  - AMBER: Serial "make" failure with xleap Francesco Pietra (Fri Jun 29 2007 - 10:17:39 PDT)
    - Re: AMBER: Serial "make" failure with xleap David A. Case (Fri Jun 29 2007 - 11:16:54 PDT)
    - Re: AMBER: Serial "make" failure with xleap Francesco Pietra (Fri Jun 29 2007 - 13:53:52 PDT)
AMBER: Sander Error Colby C (Fri Jun 29 2007 - 07:47:05 PDT)
- RE: AMBER: Sander Error Ross Walker (Fri Jun 29 2007 - 08:40:08 PDT)
- Re: AMBER: Sander Error Phineus Markwick (Fri Jun 29 2007 - 08:45:18 PDT)
- Re: AMBER: Sander Error Phineus Markwick (Fri Jun 29 2007 - 08:48:04 PDT)
  - RE: AMBER: Sander Error Ross Walker (Fri Jun 29 2007 - 09:28:44 PDT)
    - Re: AMBER: Sander Error Colby C (Fri Jun 29 2007 - 14:25:35 PDT)
    - Re: AMBER: Sander Error Carlos Simmerling (Fri Jun 29 2007 - 19:04:29 PDT)
    - RE: AMBER: Sander Error Ross Walker (Fri Jun 29 2007 - 20:42:50 PDT)
    - Re: AMBER: Sander Error Colby C (Tue Jul 03 2007 - 11:21:18 PDT)
    - Re: AMBER: Sander Error Colby C (Mon Jul 09 2007 - 08:39:50 PDT)
AMBER: Fwd: Serial "make" failure with xleap Francesco Pietra (Fri Jun 29 2007 - 10:26:54 PDT)
AMBER: Serial "make" failure Francesco Pietra (Fri Jun 29 2007 - 13:59:42 PDT)
AMBER: make serial failure for xleap Francesco Pietra (Fri Jun 29 2007 - 14:05:52 PDT)
- Re: AMBER: make serial failure for xleap M. L. Dodson (Fri Jun 29 2007 - 15:33:37 PDT)
  - Re: AMBER: make serial failure for xleap Francesco Pietra (Sat Jun 30 2007 - 01:39:32 PDT)
- Re: AMBER: make serial failure for xleap David A. Case (Fri Jun 29 2007 - 16:28:36 PDT)
Fwd: Re: AMBER: make serial failure for xleap Francesco Pietra (Sat Jun 30 2007 - 06:00:31 PDT)
AMBER: amber7 and xleap Saiful Islam (Sat Jun 30 2007 - 06:14:21 PDT)
- Re: AMBER: amber7 and xleap David A. Case (Sat Jun 30 2007 - 17:57:13 PDT)
  - Re: AMBER: amber7 and xleap Saiful Islam (Sat Jun 30 2007 - 20:37:00 PDT)
    - Re: AMBER: amber7 and xleap Saiful Islam (Sun Jul 01 2007 - 06:43:45 PDT)
    - RE: AMBER: amber7 and xleap Ross Walker (Sun Jul 01 2007 - 10:32:45 PDT)
Fwd: Re: AMBER: make test serial Francesco Pietra (Sat Jun 30 2007 - 06:42:56 PDT)
- Re: Fwd: Re: AMBER: make test serial David A. Case (Sat Jun 30 2007 - 08:28:01 PDT)
  - Re: Fwd: Re: AMBER: make test serial Francesco Pietra (Sat Jun 30 2007 - 09:18:38 PDT)
    - Re: Fwd: Re: AMBER: make test serial M. L. Dodson (Sat Jun 30 2007 - 09:30:05 PDT)
    - AMBER: bug in nonbond_list.f (nee ew_setup.f) Dan Kidger (Mon Jul 02 2007 - 02:42:58 PDT)
    - Re: AMBER: bug in nonbond_list.f (nee ew_setup.f) David A. Case (Fri Aug 03 2007 - 08:14:27 PDT)
    - Re: AMBER: bug in nonbond_list.f (nee ew_setup.f) neville forlemu (Wed Aug 08 2007 - 11:35:51 PDT)
    - RE: Fwd: Re: AMBER: make test serial Ross Walker (Sat Jun 30 2007 - 10:00:13 PDT)
AMBER: MM-PBSA POPC/TIP3P/GPCR/LIGAND Jojart Balazs (Sat Jun 30 2007 - 11:25:49 PDT)
AMBER: xleap and amber7 Saiful Islam (Sat Jun 30 2007 - 21:22:43 PDT)
- RE: AMBER: xleap and amber7 Ross Walker (Sun Jul 01 2007 - 10:33:15 PDT)
  - Re: AMBER: xleap and amber7 Saiful Islam (Mon Jul 02 2007 - 07:05:34 PDT)
    - Re: AMBER: xleap and amber7 Adrian Roitberg (Mon Jul 02 2007 - 07:20:28 PDT)
    - Re: AMBER: xleap and amber7 Saiful Islam (Wed Jul 04 2007 - 20:53:42 PDT)
    - Re: AMBER: xleap and amber7 Ilyas Yildirim (Wed Jul 04 2007 - 21:53:37 PDT)
    - Re: AMBER: xleap and amber7 Carlos Simmerling (Thu Jul 05 2007 - 05:23:44 PDT)
    - Re: AMBER: xleap and amber7 Saiful Islam (Fri Jul 06 2007 - 19:23:35 PDT)
    - Re: AMBER: xleap and amber7 Benjamin Juhl (Mon Jul 09 2007 - 00:08:57 PDT)
    - Re: AMBER: xleap and amber7 Saiful Islam (Tue Jul 10 2007 - 05:47:00 PDT)
AMBER: large RMS fluctuations in turning off VDW interactions by TI Holly Freedman (Sun Jul 01 2007 - 12:13:17 PDT)
- Re: AMBER: large RMS fluctuations in turning off VDW interactions by TI Holly Freedman (Sun Jul 01 2007 - 12:54:11 PDT)
- Re: AMBER: large RMS fluctuations in turning off VDW interactions by TI Julien Michel (Sun Jul 01 2007 - 15:42:53 PDT)
  - Re: AMBER: large RMS fluctuations in turning off VDW interactions by TI David Mobley (Mon Jul 02 2007 - 13:03:17 PDT)
    - Re: AMBER: large RMS fluctuations in turning off VDW interactions by TI David A. Case (Mon Jul 02 2007 - 13:20:27 PDT)
    - Re: AMBER: large RMS fluctuations in turning off VDW interactions by TI David Mobley (Tue Jul 03 2007 - 12:55:54 PDT)
    - Re: AMBER: large RMS fluctuations in turning off VDW interactions by TI steinbrt.scripps.edu (Wed Jul 04 2007 - 05:51:08 PDT)
- Re: AMBER: large RMS fluctuations in turning off VDW interactions by TI Holly Freedman (Mon Jul 02 2007 - 13:51:12 PDT)
  - Re: AMBER: large RMS fluctuations in turning off VDW interactions by TI David A. Case (Mon Jul 02 2007 - 23:34:13 PDT)
- Re: AMBER: large RMS fluctuations in turning off VDW interactions by TI Holly Freedman (Tue Jul 03 2007 - 10:14:29 PDT)
Fwd: Re: Fwd: RE: Re: AMBER: $AMBERHOME on PATH Francesco Pietra (Sun Jul 01 2007 - 13:50:39 PDT)
AMBER: Saving (.)prepin file Johnson Agbo (Mon Jul 02 2007 - 13:35:00 PDT)
- Re: AMBER: Saving (.)prepin file David A. Case (Mon Jul 02 2007 - 13:56:57 PDT)
Re: AMBER: Saving (.)prepin file Bill Ross (Mon Jul 02 2007 - 14:05:53 PDT)
AMBER: convergence criterion not reached Jena M (Mon Jul 02 2007 - 16:53:22 PDT)
- Re: AMBER: convergence criterion not reached David A. Case (Mon Jul 02 2007 - 18:14:53 PDT)
AMBER: Slow Processor Loads when Using PMEMD Jonathan Suever (Mon Jul 02 2007 - 17:28:48 PDT)
- RE: AMBER: Slow Processor Loads when Using PMEMD Ross Walker (Mon Jul 02 2007 - 18:42:01 PDT)
- Re: AMBER: Slow Processor Loads when Using PMEMD David A. Case (Mon Jul 02 2007 - 18:24:09 PDT)
AMBER: How to use antechamber properly? 한재범 (Mon Jul 02 2007 - 22:57:33 PDT)
AMBER: O-acetylated sugar Toshifumi Yui (Tue Jul 03 2007 - 05:26:12 PDT)
AMBER: About amber7 Saiful Islam (Tue Jul 03 2007 - 06:49:28 PDT)
- Re: AMBER: About amber7 Carlos Simmerling (Tue Jul 03 2007 - 06:57:14 PDT)
AMBER: ptraj: RMS per residues and per time Sascha Rehm (Tue Jul 03 2007 - 07:03:04 PDT)
- Re: AMBER: ptraj: RMS per residues and per time Jianyin Shao (Fri Jul 06 2007 - 00:54:06 PDT)
AMBER: Nucleic acid : nonplanarity Sophie Barbe (Tue Jul 03 2007 - 08:48:07 PDT)
AMBER: antechamber save prmtop inpcrd Francesco Pietra (Tue Jul 03 2007 - 10:55:11 PDT)
AMBER: Who has the structure file of beta-chitin? WANG,YING (Tue Jul 03 2007 - 11:19:11 PDT)
AMBER: Fwd: antechamber save prmtop inpcrd Francesco Pietra (Tue Jul 03 2007 - 23:14:23 PDT)
- Re: AMBER: Fwd: antechamber save prmtop inpcrd David A. Case (Wed Jul 04 2007 - 08:53:04 PDT)
  - Re: AMBER: Fwd: antechamber save prmtop inpcrd Francesco Pietra (Wed Jul 04 2007 - 09:54:08 PDT)
    - Re: AMBER: Fwd: antechamber save prmtop inpcrd David A. Case (Wed Jul 04 2007 - 13:15:21 PDT)
    - Re: AMBER: Fwd: antechamber save prmtop inpcrd Francesco Pietra (Wed Jul 04 2007 - 14:08:02 PDT)
AMBER: Simulated annealing - Nudget Elastic Band Francesco Pietra (Wed Jul 04 2007 - 00:01:58 PDT)
- Re: AMBER: Simulated annealing - Nudget Elastic Band Carlos Simmerling (Wed Jul 04 2007 - 03:39:10 PDT)
  - Re: AMBER: Simulated annealing - Nudget Elastic Band Francesco Pietra (Wed Jul 04 2007 - 06:13:41 PDT)
AMBER: Slight_error_on_Compiling_Replica_Exchange j j (Wed Jul 04 2007 - 01:57:28 PDT)
- Re: AMBER: Slight_error_on_Compiling_Replica_Exchange Ye Mei (Wed Jul 04 2007 - 02:30:09 PDT)
  - Re: AMBER: Slight_error_on_Compiling_Replica_Exchange j j (Wed Jul 04 2007 - 03:13:22 PDT)
AMBER: Generation of ESP(ind) within atomic charges derivation for polarizable force field Anela Ivanova (Wed Jul 04 2007 - 05:26:02 PDT)
AMBER: Nucleic acid : nonplanarity Sophie Barbe (Wed Jul 04 2007 - 05:37:26 PDT)
- Re: AMBER: Nucleic acid : nonplanarity Mathy Froeyen (Wed Jul 04 2007 - 06:57:08 PDT)
Re: AMBER: large RMS fluctuations in turning off VDW interactions by TI Holly Freedman (Wed Jul 04 2007 - 12:53:01 PDT)
- Re: AMBER: large RMS fluctuations in turning off VDW interactions by TI David Mobley (Thu Jul 05 2007 - 08:56:43 PDT)
  - Re: AMBER: large RMS fluctuations in turning off VDW interactions by TI Thomas Steinbrecher (Fri Jul 06 2007 - 10:55:32 PDT)
AMBER: antechamber: mopac charges Neelanjana Sengupta (Wed Jul 04 2007 - 16:21:02 PDT)
- Re: AMBER: antechamber: mopac charges David A. Case (Wed Jul 04 2007 - 16:27:02 PDT)
  - Re: AMBER: antechamber: mopac charges Neelanjana Sengupta (Thu Jul 05 2007 - 12:26:30 PDT)
    - Re: AMBER: antechamber: mopac charges David A. Case (Thu Jul 05 2007 - 13:24:09 PDT)
AMBER: testing amber9 for parallel use Sally Pias (Wed Jul 04 2007 - 23:47:22 PDT)
- Re: AMBER: testing amber9 for parallel use Carlos Simmerling (Thu Jul 05 2007 - 05:22:20 PDT)
AMBER: Convergence criteria in replica exchange simulations Seongeun Yang (Thu Jul 05 2007 - 04:18:17 PDT)
- Re: AMBER: Convergence criteria in replica exchange simulations Carlos Simmerling (Thu Jul 05 2007 - 05:26:26 PDT)
AMBER: How to extract energy of molecule from the system with explicit water molecules priya priya (Thu Jul 05 2007 - 07:31:03 PDT)
- Re: AMBER: How to extract energy of molecule from the system with explicit water molecules Carlos Simmerling (Thu Jul 05 2007 - 07:36:05 PDT)
  - Re: AMBER: How to extract energy of molecule from the system with explicit water molecules priya priya (Thu Jul 05 2007 - 08:10:23 PDT)
    - Re: AMBER: How to extract energy of molecule from the system with explicit water molecules Carlos Simmerling (Thu Jul 05 2007 - 08:25:42 PDT)
    - Re: AMBER: How to extract energy of molecule from the system with explicit water molecules priya priya (Thu Jul 05 2007 - 08:57:59 PDT)
    - Re: AMBER: How to extract energy of molecule from the system with explicit water molecules Carlos Simmerling (Thu Jul 05 2007 - 09:04:12 PDT)
    - Re: AMBER: How to extract energy of molecule from the system with explicit water molecules priya priya (Thu Jul 05 2007 - 09:40:41 PDT)
    - Re: AMBER: How to extract energy of molecule from the system with explicit water molecules Carlos Simmerling (Thu Jul 05 2007 - 09:45:14 PDT)
    - Re: AMBER: How to extract energy of molecule from the system with explicit water molecules priya priya (Thu Jul 05 2007 - 23:58:28 PDT)
    - Re: AMBER: How to extract energy of molecule from the system with explicit water molecules priya priya (Fri Jul 06 2007 - 03:39:58 PDT)
    - Re: AMBER: How to extract energy of molecule from the system with explicit water molecules priya priya (Fri Jul 06 2007 - 05:25:02 PDT)
AMBER: Nudget Elastic Band query Francesco Pietra (Thu Jul 05 2007 - 10:43:43 PDT)
- Re: AMBER: Nudget Elastic Band query Carlos Simmerling (Thu Jul 05 2007 - 10:53:53 PDT)
  - Re: AMBER: Nudget Elastic Band query Francesco Pietra (Thu Jul 05 2007 - 12:02:19 PDT)
    - Re: AMBER: Nudget Elastic Band query Carlos Simmerling (Thu Jul 05 2007 - 12:08:31 PDT)
    - Re: AMBER: Nudget Elastic Band query Francesco Pietra (Thu Jul 05 2007 - 13:28:31 PDT)
AMBER: QM/MM LJ parameters Evan Kelly (Thu Jul 05 2007 - 16:31:35 PDT)
- RE: AMBER: QM/MM LJ parameters Ross Walker (Thu Jul 05 2007 - 17:58:49 PDT)
AMBER: Stirp command in ptraj priya priya (Fri Jul 06 2007 - 05:33:11 PDT)
- Re: AMBER: Stirp command in ptraj Carlos Simmerling (Fri Jul 06 2007 - 05:35:33 PDT)
- Re: AMBER: Stirp command in ptraj Steven Winfield (Fri Jul 06 2007 - 05:36:06 PDT)
  - Re: AMBER: Stirp command in ptraj priya priya (Fri Jul 06 2007 - 05:41:22 PDT)
    - Re: AMBER: Stirp command in ptraj Carlos Simmerling (Fri Jul 06 2007 - 06:14:20 PDT)
    - Re: AMBER: Stirp command in ptraj priya priya (Fri Jul 06 2007 - 06:27:27 PDT)
    - Re: AMBER: Stirp command in ptraj Steven Winfield (Fri Jul 06 2007 - 06:32:07 PDT)
    - Re: AMBER: Stirp command in ptraj priya priya (Fri Jul 06 2007 - 06:43:13 PDT)
    - Re: AMBER: Stirp command in ptraj priya priya (Fri Jul 06 2007 - 09:41:05 PDT)
    - Re: AMBER: Stirp command in ptraj Carlos Simmerling (Fri Jul 06 2007 - 09:45:43 PDT)
AMBER: Substitute for GAFF Evan Kelly (Fri Jul 06 2007 - 10:32:50 PDT)
AMBER: Simulated Annealing - Best way to create randomness Francesco Pietra (Sat Jul 07 2007 - 07:56:41 PDT)
- Re: AMBER: Simulated Annealing - Best way to create randomness Seth Lilavivat (Mon Jul 09 2007 - 08:03:29 PDT)
AMBER: Problem with running Sander Lili Peng (Sat Jul 07 2007 - 16:10:06 PDT)
- Re: AMBER: Problem with running Sander David A. Case (Sat Jul 07 2007 - 21:59:05 PDT)
  - Re: AMBER: Problem with running Sander Carlos Simmerling (Sun Jul 08 2007 - 04:28:58 PDT)
  - Re: AMBER: Problem with running Sander Lili Peng (Tue Jul 10 2007 - 14:50:45 PDT)
    - Re: AMBER: Problem with running Sander David A. Case (Tue Jul 10 2007 - 15:39:31 PDT)
    - Re: AMBER: Problem with running Sander Lili Peng (Tue Jul 10 2007 - 15:58:22 PDT)
    - Re: AMBER: Problem with running Sander Lili Peng (Tue Jul 10 2007 - 16:01:11 PDT)
    - Re: AMBER: Problem with running Sander David A. Case (Tue Jul 10 2007 - 16:17:56 PDT)
    - RE: AMBER: Problem with running Sander Ross Walker (Tue Jul 10 2007 - 16:09:29 PDT)
AMBER: RESP charge generation Neelanjana Sengupta (Sat Jul 07 2007 - 16:08:07 PDT)
- Re: AMBER: RESP charge generation FyD (Sun Jul 08 2007 - 03:19:16 PDT)
AMBER: corrected reaction field energy and PBCAL AYTUG TUNCEL (Sun Jul 08 2007 - 17:40:53 PDT)
AMBER: program bug? M. Maeda (Sun Jul 08 2007 - 19:24:58 PDT)
- Re: AMBER: program bug? David A. Case (Mon Jul 09 2007 - 07:48:35 PDT)
- Re: AMBER: program bug? M. Maeda (Wed Jul 11 2007 - 21:47:19 PDT)
- Re: AMBER: program bug? M. Maeda (Wed Jul 11 2007 - 21:41:34 PDT)
  - Re: AMBER: program bug? Benjamin Juhl (Thu Jul 12 2007 - 00:17:31 PDT)
    - Re: AMBER: program bug? M. Maeda (Thu Jul 12 2007 - 04:29:03 PDT)
    - Re: AMBER: program bug? M. Maeda (Wed Aug 08 2007 - 19:37:13 PDT)
  - Re: AMBER: program bug? David A. Case (Thu Jul 12 2007 - 08:22:35 PDT)
    - Re: AMBER: program bug? Carlos Simmerling (Thu Jul 12 2007 - 08:32:54 PDT)
AMBER: adding water molecules in lipid bilayer model Vijay Manickam Achari (Sun Jul 08 2007 - 20:22:46 PDT)
- Re: AMBER: adding water molecules in lipid bilayer model M. L. Dodson (Mon Jul 09 2007 - 05:59:01 PDT)
  - Re: AMBER: adding water molecules in lipid bilayer model Vijay Manickam Achari (Tue Jul 10 2007 - 19:00:30 PDT)
- Re: AMBER: adding water molecules in lipid bilayer model Fenghui Fan (Mon Jul 09 2007 - 16:11:45 PDT)
  - AMBER: Question on TIP4P model Du, Shiyu (Mon Jul 09 2007 - 17:01:58 PDT)
AMBER: antechamber Marie Brut (Mon Jul 09 2007 - 04:56:19 PDT)
- Re: AMBER: antechamber David A. Case (Mon Jul 09 2007 - 07:41:23 PDT)
  - Re: AMBER: antechamber Francesco Pietra (Mon Jul 09 2007 - 14:57:45 PDT)
    - Re: AMBER: antechamber M. L. Dodson (Mon Jul 09 2007 - 17:08:27 PDT)
    - Re: AMBER: antechamber Francesco Pietra (Tue Jul 10 2007 - 00:04:39 PDT)
- Re: AMBER: antechamber Barbault Florent (Mon Jul 09 2007 - 07:59:03 PDT)
AMBER: Specific/Non-specific dihedral issue in Amber Narayanan Veeraraghavan (Mon Jul 09 2007 - 07:30:44 PDT)
- Re: AMBER: Specific/Non-specific dihedral issue in Amber David A. Case (Mon Jul 09 2007 - 07:58:51 PDT)
  - Re: AMBER: Specific/Non-specific dihedral issue in Amber Narayanan Veeraraghavan (Mon Jul 09 2007 - 11:02:38 PDT)
- Re: AMBER: Specific/Non-specific dihedral issue in Amber Bill Ross (Mon Jul 09 2007 - 11:48:28 PDT)
  - Re: AMBER: Specific/Non-specific dihedral issue in Amber Narayanan Veeraraghavan (Mon Jul 16 2007 - 14:35:53 PDT)
    - Re: AMBER: Specific/Non-specific dihedral issue in Amber David A. Case (Mon Jul 16 2007 - 17:13:45 PDT)
    - Re: AMBER: Specific/Non-specific dihedral issue in Amber Narayanan Veeraraghavan (Tue Jul 17 2007 - 15:01:10 PDT)
    - Re: AMBER: Specific/Non-specific dihedral issue in Amber David A. Case (Tue Jul 17 2007 - 16:15:59 PDT)
- Re: AMBER: Specific/Non-specific dihedral issue in Amber Bill Ross (Mon Jul 16 2007 - 16:38:26 PDT)
AMBER: Could not find cntrl namelist Francesco Pietra (Mon Jul 09 2007 - 09:56:58 PDT)
- Re: AMBER: Could not find cntrl namelist M. L. Dodson (Mon Jul 09 2007 - 10:10:58 PDT)
  - Re: AMBER: Could not find cntrl namelist Francesco Pietra (Mon Jul 09 2007 - 13:53:43 PDT)
    - Re: AMBER: Could not find cntrl namelist M. L. Dodson (Mon Jul 09 2007 - 14:09:06 PDT)
    - Re: AMBER: Could not find cntrl namelist Francesco Pietra (Mon Jul 09 2007 - 14:22:30 PDT)
    - Re: AMBER: Could not find cntrl namelist Thomas Cheatham III (Mon Jul 09 2007 - 14:17:23 PDT)
    - Re: AMBER: Could not find cntrl namelist Francesco Pietra (Mon Jul 09 2007 - 14:31:18 PDT)
    - RE: AMBER: Could not find cntrl namelist Ross Walker (Mon Jul 09 2007 - 14:38:01 PDT)
    - RE: AMBER: Could not find cntrl namelist Francesco Pietra (Mon Jul 09 2007 - 23:26:54 PDT)
    - Re: AMBER: Could not find cntrl namelist David A. Case (Tue Jul 10 2007 - 10:52:10 PDT)
    - RE: AMBER: Could not find cntrl namelist Ross Walker (Tue Jul 10 2007 - 11:21:12 PDT)
    - RE: AMBER: Could not find cntrl namelist Francesco Pietra (Tue Jul 10 2007 - 14:11:48 PDT)
    - Re: AMBER: Could not find cntrl namelist Robert Duke (Tue Jul 10 2007 - 14:57:54 PDT)
    - RE: AMBER: Could not find cntrl namelist Ross Walker (Tue Jul 10 2007 - 16:00:38 PDT)
    - Re: AMBER: Could not find cntrl namelist M. L. Dodson (Tue Jul 10 2007 - 15:25:17 PDT)
    - Re: AMBER: Could not find cntrl namelist Francesco Pietra (Wed Jul 11 2007 - 03:14:51 PDT)
    - Re: AMBER: Could not find cntrl namelist Robert Duke (Wed Jul 11 2007 - 06:07:36 PDT)
    - Re: AMBER: Could not find cntrl namelist Francesco Pietra (Wed Jul 11 2007 - 08:10:42 PDT)
    - Re: AMBER: Could not find cntrl namelist Robert Duke (Wed Jul 11 2007 - 10:47:57 PDT)
    - Re: AMBER: Could not find cntrl namelist Francesco Pietra (Wed Jul 11 2007 - 14:50:37 PDT)
    - Re: AMBER: Could not find cntrl namelist David A. Case (Tue Jul 10 2007 - 16:04:15 PDT)
    - Re: AMBER: Could not find cntrl namelist Francesco Pietra (Tue Jul 10 2007 - 23:48:41 PDT)
    - RE: AMBER: Could not find cntrl namelist Ross Walker (Tue Jul 10 2007 - 14:57:39 PDT)
    - RE: AMBER: Could not find cntrl namelist Francesco Pietra (Tue Jul 10 2007 - 23:48:59 PDT)
- RE: AMBER: Could not find cntrl namelist Ross Walker (Mon Jul 09 2007 - 10:26:29 PDT)
- Re: AMBER: Could not find cntrl namelist Robert Duke (Tue Jul 10 2007 - 19:21:07 PDT)
AMBER: TIP4P MD simulations Hashem Taha (Mon Jul 09 2007 - 10:53:28 PDT)
- Re: AMBER: TIP4P MD simulations Melinda Layten (Mon Jul 09 2007 - 11:05:39 PDT)
- Re: AMBER: TIP4P MD simulations David A. Case (Mon Jul 09 2007 - 11:31:15 PDT)
- Re: AMBER: TIP4P MD simulations Robert Duke (Mon Jul 09 2007 - 12:35:04 PDT)
AMBER: manganese ion Davide Moiani (Mon Jul 09 2007 - 14:02:31 PDT)
- Re: AMBER: manganese ion Guillermo Mulliert Carlín (Tue Jul 10 2007 - 01:39:40 PDT)
- Re: AMBER: manganese ion Davide Moiani (Tue Jul 10 2007 - 09:47:38 PDT)
  - Re: AMBER: manganese ion neetu.imtech.res.in (Tue Jul 10 2007 - 21:03:54 PDT)
- Re: AMBER: manganese ion Davide Moiani (Wed Jul 11 2007 - 14:47:18 PDT)
AMBER: surface area over the trajectory mkseo (Mon Jul 09 2007 - 14:52:32 PDT)
- Re: AMBER: surface area over the trajectory Carlos Simmerling (Mon Jul 09 2007 - 15:30:54 PDT)
  - Re: AMBER: surface area over the trajectory mkseo (Mon Jul 09 2007 - 15:55:18 PDT)
    - Re: AMBER: surface area over the trajectory Carlos Simmerling (Tue Jul 10 2007 - 03:33:44 PDT)
    - Re: AMBER: surface area over the trajectory Mikyung (Tue Jul 10 2007 - 09:20:12 PDT)
    - Re: AMBER: surface area over the trajectory Carlos Simmerling (Tue Jul 10 2007 - 12:09:51 PDT)
AMBER: tgtrmsmask and tgtfitmask Holly Freedman (Mon Jul 09 2007 - 19:03:39 PDT)
- Re: AMBER: tgtrmsmask and tgtfitmask Carlos Simmerling (Tue Jul 10 2007 - 04:26:08 PDT)
  - Re: AMBER: tgtrmsmask and tgtfitmask David A. Case (Tue Jul 10 2007 - 09:01:27 PDT)
AMBER: 来自pig5678的邮件 pig5678 (Mon Jul 09 2007 - 23:59:22 PDT)
- Re: AMBER: ????pig5678?????? David A. Case (Tue Jul 10 2007 - 08:14:45 PDT)
  - Re:Re: AMBER: ????pig5678?????? pig5678 (Tue Jul 10 2007 - 20:27:55 PDT)
  - Re:Re: AMBER: ????pig5678?????? pig5678 (Thu Jul 12 2007 - 18:36:10 PDT)
AMBER: Saving (.)prepin file Johnson Agbo (Mon Jul 09 2007 - 11:22:40 PDT)
- Re: AMBER: Saving (.)prepin file David A. Case (Tue Jul 10 2007 - 10:45:58 PDT)
AMBER: Input required for RESP Neelanjana Sengupta (Tue Jul 10 2007 - 11:03:54 PDT)
- Re: AMBER: Input required for RESP FyD (Tue Jul 10 2007 - 23:21:42 PDT)
AMBER: extract protein energy from MD trajectory Mikyung (Tue Jul 10 2007 - 14:47:53 PDT)
- Re: AMBER: extract protein energy from MD trajectory Carlos Simmerling (Tue Jul 10 2007 - 15:08:32 PDT)
  - Re: AMBER: extract protein energy from MD trajectory Mikyung (Tue Jul 10 2007 - 23:58:31 PDT)
    - Re: AMBER: extract protein energy from MD trajectory Carlos Simmerling (Wed Jul 11 2007 - 01:34:31 PDT)
AMBER: MPI Quiescence problem in REMD In Hee Park (Tue Jul 10 2007 - 21:03:08 PDT)
- Re: AMBER: MPI Quiescence problem in REMD Carlos Simmerling (Wed Jul 11 2007 - 02:28:56 PDT)
  - Re: AMBER: MPI Quiescence problem in REMD In Hee Park (Wed Jul 11 2007 - 09:41:47 PDT)
    - Re: AMBER: MPI Quiescence problem in REMD Carlos Simmerling (Wed Jul 11 2007 - 10:08:23 PDT)
    - Re: AMBER: MPI Quiescence problem in REMD In Hee Park (Thu Aug 16 2007 - 15:56:37 PDT)
AMBER: Question about NAB (Nucleic Acid Builder) Cenk Andac (Wed Jul 11 2007 - 01:30:18 PDT)
- Re: AMBER: Question about NAB (Nucleic Acid Builder) David A. Case (Wed Jul 11 2007 - 16:23:05 PDT)
AMBER: question about iwrap Kailee (Wed Jul 11 2007 - 06:17:29 PDT)
- Re: AMBER: question about iwrap David A. Case (Wed Jul 11 2007 - 16:24:11 PDT)
  - Re: AMBER: question about iwrap Kailee (Thu Jul 12 2007 - 03:55:28 PDT)
    - Re: AMBER: question about iwrap Carlos Simmerling (Thu Jul 12 2007 - 04:34:08 PDT)
    - Re: AMBER: question about iwrap Kailee (Thu Jul 12 2007 - 06:17:32 PDT)
    - Re: AMBER: question about iwrap Carlos Simmerling (Thu Jul 12 2007 - 06:28:29 PDT)
    - Re: AMBER: question about iwrap Kailee (Thu Jul 12 2007 - 06:55:06 PDT)
  - AMBER: dihedral angles Jardas sucuriba (Tue Oct 30 2007 - 17:43:10 PDT)
    - Re: AMBER: dihedral angles David A. Case (Wed Oct 31 2007 - 21:09:24 PDT)
AMBER: Basic AMBER question Lili Peng (Wed Jul 11 2007 - 12:15:48 PDT)
- Re: AMBER: Basic AMBER question Melinda Layten (Wed Jul 11 2007 - 13:05:11 PDT)
- RE: AMBER: Basic AMBER question Ross Walker (Wed Jul 11 2007 - 13:07:42 PDT)
AMBER: Belly Restraints and Distance Restraints Seth Lilavivat (Wed Jul 11 2007 - 12:13:04 PDT)
Fwd: Re: AMBER: Could not find cntrl namelist Francesco Pietra (Wed Jul 11 2007 - 14:52:25 PDT)
AMBER: computational Ala scan Sergio Wong (Wed Jul 11 2007 - 16:36:58 PDT)
AMBER: Amber9 analyze timecorr manual ambigous Nicolas Lux Fawzi (Thu Jul 12 2007 - 12:26:19 PDT)
- Re: AMBER: Amber9 analyze timecorr manual ambigous David A. Case (Thu Jul 12 2007 - 12:55:15 PDT)
  - Re: AMBER: Amber9 analyze timecorr manual ambigous Nicolas Lux Fawzi (Thu Jul 12 2007 - 15:11:30 PDT)
    - Re: AMBER: Amber9 analyze timecorr manual ambigous David A. Case (Thu Jul 12 2007 - 15:58:30 PDT)
AMBER: Molecular Dynamic Simulations using TIP4P water - Please Help Hashem Taha (Thu Jul 12 2007 - 13:31:59 PDT)
- Re: AMBER: Molecular Dynamic Simulations using TIP4P water - Please Help Robert Duke (Thu Jul 12 2007 - 13:55:15 PDT)
  - Re: AMBER: Molecular Dynamic Simulations using TIP4P water - Please Help Hashem Taha (Thu Jul 12 2007 - 14:45:50 PDT)
    - RE: AMBER: Molecular Dynamic Simulations using TIP4P water - Please Help Ross Walker (Thu Jul 12 2007 - 15:06:56 PDT)
    - Re: AMBER: Molecular Dynamic Simulations using TIP4P water - Please Help David A. Case (Thu Jul 12 2007 - 16:03:45 PDT)
AMBER: related to new amber force field snoze pa (Fri Jul 13 2007 - 08:57:38 PDT)
- Re: AMBER: related to new amber force field Carlos Simmerling (Fri Jul 13 2007 - 09:33:12 PDT)
AMBER: Multiple residues position snoze pa (Fri Jul 13 2007 - 09:04:59 PDT)
- Re: AMBER: Multiple residues position Carlos Simmerling (Fri Jul 13 2007 - 09:20:19 PDT)
AMBER: Cutoff list exceeds largest sphere in unit cell Andrew Borgert (Fri Jul 13 2007 - 09:18:05 PDT)
- Re: AMBER: Cutoff list exceeds largest sphere in unit cell Andrew Borgert (Fri Jul 13 2007 - 09:27:44 PDT)
- Re: AMBER: Cutoff list exceeds largest sphere in unit cell Robert Duke (Fri Jul 13 2007 - 09:30:40 PDT)
  - Re: AMBER: Cutoff list exceeds largest sphere in unit cell neville forlemu (Sat Jul 14 2007 - 19:09:36 PDT)
    - Re: AMBER: Non bond list overflow David A. Case (Sun Jul 15 2007 - 16:50:11 PDT)
- Re: AMBER: Cutoff list exceeds largest sphere in unit cell Barbault Florent (Fri Jul 13 2007 - 11:54:36 PDT)
AMBER: Ne van del waals potential Lishan Yao (Fri Jul 13 2007 - 09:09:37 PDT)
AMBER: MPI script Taryn Hartley (Fri Jul 13 2007 - 15:06:45 PDT)
- Re: AMBER: MPI script Carlos Simmerling (Fri Jul 13 2007 - 15:15:36 PDT)
- Re: AMBER: MPI script Thomas Cheatham III (Fri Jul 13 2007 - 15:19:37 PDT)
  - Re: AMBER: MPI script Hashem Taha (Tue Jul 17 2007 - 13:10:46 PDT)
AMBER: can open PDB file in xleap Vijay Manickam Achari (Sun Jul 15 2007 - 18:44:17 PDT)
AMBER: Can't open PDB file in xleap Vijay Manickam Achari (Mon Jul 16 2007 - 02:43:16 PDT)
- Re: AMBER: Can t open PDB file in xleap Benjamin Juhl (Mon Jul 16 2007 - 03:53:16 PDT)
AMBER: convergence in classical MD Seongeun Yang (Mon Jul 16 2007 - 04:23:01 PDT)
- Re: AMBER: convergence in classical MD Carlos Simmerling (Mon Jul 16 2007 - 04:37:09 PDT)
AMBER: Atoms in conatct to a specific atoms during MD Rafi Ahmad (Mon Jul 16 2007 - 06:23:38 PDT)
- AMBER: modelling substrate binding Mattias Blomberg (Mon Jul 16 2007 - 06:53:15 PDT)
- Re: AMBER: Atoms in contact to a specific atoms during MD Mark Williamson (Mon Jul 16 2007 - 07:52:39 PDT)
AMBER: Non-standard amino acid residue Sergey Samsonov (Mon Jul 16 2007 - 07:44:32 PDT)
- Re: AMBER: Non-standard amino acid residue FyD (Mon Jul 16 2007 - 09:45:07 PDT)
  - AMBER: Setting nonbonded cutoff to 1 Hayden Eastwood (Mon Jul 16 2007 - 10:27:45 PDT)
    - RE: AMBER: Setting nonbonded cutoff to 1 Ross Walker (Mon Jul 16 2007 - 10:43:28 PDT)
  - Re: AMBER: Non-standard amino acid residue Sergey Samsonov (Tue Jul 17 2007 - 05:30:14 PDT)
    - Re: AMBER: Non-standard amino acid residue FyD (Tue Jul 17 2007 - 06:41:57 PDT)
    - Re: AMBER: Non-standard amino acid residue Sergey Samsonov (Wed Jul 18 2007 - 07:19:42 PDT)
    - Re: AMBER: Non-standard amino acid residue FyD (Wed Jul 18 2007 - 07:50:55 PDT)
    - Re: AMBER: Non-standard amino acid residue Sergey Samsonov (Thu Jul 19 2007 - 02:45:52 PDT)
    - Re: AMBER: Non-standard amino acid residue FyD (Thu Jul 19 2007 - 04:26:39 PDT)
    - AMBER: Re: RED problem Sergey Samsonov (Mon Jul 23 2007 - 04:35:32 PDT)
    - Re: AMBER: Re: RED problem FyD (Mon Jul 23 2007 - 05:08:14 PDT)
    - Re: AMBER: Non-standard amino acid residue David A. Case (Tue Jul 17 2007 - 07:53:46 PDT)
    - Re: AMBER: Non-standard amino acid residue Sergey Samsonov (Tue Jul 17 2007 - 08:37:03 PDT)
SV: AMBER: Atoms in contact to a specific atoms during MD Rafi Ahmad (Mon Jul 16 2007 - 08:04:46 PDT)
- Re: SV: AMBER: Atoms in contact to a specific atoms during MD Mark Williamson (Mon Jul 16 2007 - 08:18:00 PDT)
AMBER: help with phosphotyrosine Samantha Kaye (Mon Jul 16 2007 - 08:45:36 PDT)
- Re: AMBER: help with phosphotyrosine David A. Case (Mon Jul 16 2007 - 11:11:51 PDT)
  - Re: AMBER: help with phosphotyrosine Samantha Kaye (Tue Jul 17 2007 - 06:00:23 PDT)
AMBER: Known residue, unknown error in teLeap Neelanjana Sengupta (Mon Jul 16 2007 - 12:19:07 PDT)
- Re: AMBER: Known residue, unknown error in teLeap David A. Case (Mon Jul 16 2007 - 18:32:16 PDT)
  - Re: AMBER: Known residue, unknown error in teLeap Neelanjana Sengupta (Tue Jul 17 2007 - 09:33:39 PDT)
    - Re: AMBER: Known residue, unknown error in teLeap David A. Case (Tue Jul 17 2007 - 09:49:41 PDT)
    - Re: AMBER: Known residue, unknown error in teLeap Neelanjana Sengupta (Tue Jul 17 2007 - 11:53:16 PDT)
    - Re: AMBER: Known residue, unknown error in teLeap Neelanjana Sengupta (Tue Jul 17 2007 - 11:58:12 PDT)
AMBER: RESP_compilation Karol Kaszuba (Mon Jul 16 2007 - 12:14:32 PDT)
- Re: AMBER: RESP_compilation FyD (Mon Jul 16 2007 - 15:55:20 PDT)
- Re: AMBER: RESP_compilation FyD (Mon Jul 16 2007 - 15:59:06 PDT)
  - Re: AMBER: RESP_compilation_IT_WORKS Karol Kaszuba (Tue Jul 17 2007 - 01:32:59 PDT)
  - AMBER: running_RED-III Karol Kaszuba (Wed Jul 18 2007 - 12:02:10 PDT)
    - Re: AMBER: running_RED-III FyD (Wed Jul 18 2007 - 18:33:20 PDT)
Re: SV: AMBER: Atoms in contact to a specific atoms during MD Bill Ross (Mon Jul 16 2007 - 12:49:45 PDT)
AMBER: refc error Lili Peng (Mon Jul 16 2007 - 16:56:11 PDT)
- Re: AMBER: refc error Davide Moiani (Mon Jul 16 2007 - 17:03:42 PDT)
  - Re: AMBER: refc error Lili Peng (Mon Jul 16 2007 - 17:08:18 PDT)
- Re: AMBER: refc error Davide Moiani (Mon Jul 16 2007 - 17:17:18 PDT)
  - Re: AMBER: refc error Lili Peng (Tue Jul 17 2007 - 11:35:06 PDT)
- Re: AMBER: refc error David A. Case (Mon Jul 16 2007 - 17:25:20 PDT)
- Re: AMBER: refc error Davide Moiani (Tue Jul 17 2007 - 14:00:20 PDT)
  - Re: AMBER: refc error Lili Peng (Tue Jul 17 2007 - 15:40:26 PDT)
AMBER: potential energy calculation Lili Peng (Mon Jul 16 2007 - 17:03:55 PDT)
- Re: AMBER: potential energy calculation Carlos Simmerling (Mon Jul 16 2007 - 18:34:01 PDT)
  - Re: AMBER: potential energy calculation Lili Peng (Tue Jul 17 2007 - 15:46:55 PDT)
    - Re: AMBER: potential energy calculation David A. Case (Tue Jul 17 2007 - 16:08:54 PDT)
    - Re: AMBER: potential energy calculation Rajendra P. OJHA (Tue Jul 17 2007 - 23:03:55 PDT)
    - Re: AMBER: potential energy calculation Lili Peng (Wed Jul 18 2007 - 13:47:57 PDT)
AMBER: Gaff Charge Colby C (Mon Jul 16 2007 - 20:39:15 PDT)
- Re: AMBER: Gaff Charge David A. Case (Mon Jul 16 2007 - 22:18:17 PDT)
AMBER: how to create an O linked N-acetylglucosamine in a protein ming hui (Mon Jul 16 2007 - 20:41:40 PDT)
- AMBER: Re: how to create an O linked N-acetylglucosamine in a protein ming hui (Mon Jul 16 2007 - 20:44:08 PDT)
  - Re: AMBER: Re: how to create an O linked N-acetylglucosamine in a Austin B. Yongye (Mon Jul 16 2007 - 23:22:12 PDT)
  - Re: AMBER: Re: how to create an O linked N-acetylglucosamine in a protein Karl Kirschner (Tue Jul 17 2007 - 06:39:43 PDT)
AMBER: General AMBER questions Lili Peng (Tue Jul 17 2007 - 15:51:32 PDT)
- Re: AMBER: General AMBER questions David A. Case (Wed Jul 18 2007 - 16:12:34 PDT)
AMBER: incoherent intermediate scattering function Jason Whitte (Tue Jul 17 2007 - 15:59:21 PDT)
AMBER: Problems during compilation Sébastien Kozlowskyj (Wed Jul 18 2007 - 02:26:06 PDT)
AMBER: bound magnesium ions in proteins with GBSA Wei Chen (Wed Jul 18 2007 - 09:01:26 PDT)
AMBER: Error during compilation on a SGI Irix machine Ruchi Sachdeva (Wed Jul 18 2007 - 09:47:30 PDT)
- Re: AMBER: Error during compilation on a SGI Irix machine Carlos Simmerling (Wed Jul 18 2007 - 09:57:27 PDT)
  - Re: AMBER: Error during compilation on a SGI Irix machine Ruchi Sachdeva (Wed Jul 18 2007 - 21:18:30 PDT)
    - Re: AMBER: Error during compilation on a SGI Irix machine David A. Case (Wed Jul 18 2007 - 21:34:18 PDT)
AMBER: Verifying Bond Angles Seth Lilavivat (Wed Jul 18 2007 - 14:32:30 PDT)
AMBER: (no subject) n.buis.soton.ac.uk (Thu Jul 19 2007 - 01:58:06 PDT)
AMBER: DNA RNA recognition problem Steve Seibold (Thu Jul 19 2007 - 06:51:43 PDT)
- Re: AMBER: DNA RNA recognition problem David A. Case (Thu Jul 19 2007 - 08:01:17 PDT)
AMBER: Re: amber-developers: -y option in sander Geoff Wood (Thu Jul 19 2007 - 06:54:47 PDT)
AMBER: secstruct command Anna Díaz Cirac (Thu Jul 19 2007 - 10:35:42 PDT)
- Re: AMBER: secstruct command Carlos Simmerling (Thu Jul 19 2007 - 10:46:30 PDT)
- Re: AMBER: secstruct command Holger Gohlke (Thu Jul 19 2007 - 11:22:37 PDT)
  - AMBER: ptraj error FyD (Fri Jul 20 2007 - 14:21:17 PDT)
- Re: AMBER: secstruct command Tim Meyer (Fri Jul 20 2007 - 06:55:47 PDT)
AMBER: temperature fluctuation in REMD priya priya (Fri Jul 20 2007 - 03:58:48 PDT)
- Re: AMBER: temperature fluctuation in REMD Carlos Simmerling (Fri Jul 20 2007 - 04:44:36 PDT)
  - Re: AMBER: temperature fluctuation in REMD priya priya (Fri Jul 20 2007 - 05:11:17 PDT)
    - Re: AMBER: temperature fluctuation in REMD Carlos Simmerling (Fri Jul 20 2007 - 05:34:03 PDT)
    - Re: AMBER: temperature fluctuation in REMD priya priya (Fri Jul 20 2007 - 06:36:12 PDT)
    - Re: AMBER: temperature fluctuation in REMD Carlos Simmerling (Fri Jul 20 2007 - 06:57:13 PDT)
    - Re: AMBER: temperature fluctuation in REMD priya priya (Fri Jul 20 2007 - 07:23:08 PDT)
    - Re: AMBER: temperature fluctuation in REMD Carlos Simmerling (Fri Jul 20 2007 - 07:34:35 PDT)
    - Re: AMBER: temperature fluctuation in REMD priya priya (Fri Jul 20 2007 - 08:00:30 PDT)
    - Re: AMBER: temperature fluctuation in REMD Adrian Roitberg (Fri Jul 20 2007 - 05:44:01 PDT)
    - Re: AMBER: temperature fluctuation in REMD priya priya (Fri Jul 20 2007 - 06:13:32 PDT)
- Re: AMBER: temperature fluctuation in REMD David A. Case (Fri Jul 20 2007 - 09:16:46 PDT)
AMBER: problem in compiling amber9 and running amber9 Prem Prakash Pathak (Sat Jul 21 2007 - 05:27:18 PDT)
- Re: AMBER: problem in compiling amber9 and running amber9 Mark Williamson (Sat Jul 21 2007 - 07:21:18 PDT)
AMBER: RE Amber: Simulated Annealing Francesco Pietra (Sat Jul 21 2007 - 08:13:11 PDT)
AMBER: GDP UNKNOWN ATOM TYPE: O3 warning j j (Sat Jul 21 2007 - 10:21:32 PDT)
AMBER: offending restraint Jena M (Sat Jul 21 2007 - 17:15:42 PDT)
- Re: AMBER: offending restraint David A. Case (Sat Jul 21 2007 - 18:35:51 PDT)
- Re: AMBER: offending restraint Carlos Simmerling (Sun Jul 22 2007 - 04:32:51 PDT)
AMBER: question about formatted mdrcrd files... Cenk Andac (Sun Jul 22 2007 - 09:47:45 PDT)
- Re: AMBER: question about formatted mdrcrd files... David A. Case (Sun Jul 22 2007 - 16:30:06 PDT)
  - Re: AMBER: question about formatted mdrcrd files... Cenk Andac (Sun Jul 22 2007 - 17:51:02 PDT)
  - Re: AMBER: question about formatted mdrcrd files... Cenk Andac (Sun Jul 22 2007 - 18:37:43 PDT)
AMBER: Truncated Octahedron box volume Ilyas Yildirim (Sun Jul 22 2007 - 19:52:16 PDT)
AMBER: using amber to minimize structure obatined from cyana Prem Prakash Pathak (Mon Jul 23 2007 - 00:27:26 PDT)
- Re: AMBER: using amber to minimize structure obatined from cyana David A. Case (Mon Jul 23 2007 - 07:52:00 PDT)
AMBER: parallel compilation Francesco Pietra (Mon Jul 23 2007 - 03:16:35 PDT)
- Re: AMBER: parallel compilation David A. Case (Mon Jul 23 2007 - 07:55:02 PDT)
  - Re: AMBER: parallel compilation Francesco Pietra (Mon Jul 23 2007 - 23:19:56 PDT)
    - Re: Re: AMBER: parallel compilation Ye Mei (Mon Jul 23 2007 - 23:44:43 PDT)
    - Re: Re: AMBER: parallel compilation Francesco Pietra (Tue Jul 24 2007 - 00:17:03 PDT)
AMBER: regarding distance restraints gurpreet singh (Mon Jul 23 2007 - 03:46:39 PDT)
- Re: AMBER: regarding distance restraints Carlos Simmerling (Mon Jul 23 2007 - 04:26:27 PDT)
- Re: AMBER: regarding distance restraints David A. Case (Mon Jul 23 2007 - 07:56:03 PDT)
AMBER: SHAKE failure in TI calculation of zero sum model system of "ethane-to-ethane" in water Ye Mei (Mon Jul 23 2007 - 06:00:34 PDT)
AMBER: RE: Query Ross Walker (Mon Jul 23 2007 - 08:13:13 PDT)
AMBER: problem in compiling amber with suse 9.1 i686, finally in leap Prem Prakash Pathak (Mon Jul 23 2007 - 08:39:21 PDT)
- Re: AMBER: problem in compiling amber with suse 9.1 i686, finally in leap Steven Winfield (Mon Jul 23 2007 - 08:43:17 PDT)
- RE: AMBER: problem in compiling amber with suse 9.1 i686, finally in leap Ross Walker (Mon Jul 23 2007 - 08:52:00 PDT)
  - Re: AMBER: problem in compiling amber with suse 9.1 i686, finally in leap Prem Prakash Pathak (Tue Jul 24 2007 - 05:30:31 PDT)
    - Re: AMBER: problem in compiling amber with suse 9.1 i686, finally in leap David A. Case (Tue Jul 24 2007 - 08:20:30 PDT)
    - Re: AMBER: problem in compiling amber with suse 9.1 i686, finally in leap Prem Prakash Pathak (Tue Jul 24 2007 - 21:12:48 PDT)
AMBER: md potential energy Francesco Pietra (Mon Jul 23 2007 - 09:14:48 PDT)
AMBER: MPI error message Taryn Hartley (Mon Jul 23 2007 - 10:39:27 PDT)
- RE: AMBER: MPI error message Ross Walker (Mon Jul 23 2007 - 10:56:35 PDT)
AMBER: DNA denatures during MD simulation Prashanth Athri (Mon Jul 23 2007 - 12:38:12 PDT)
- Re: AMBER: DNA denatures during MD simulation Carlos Simmerling (Mon Jul 23 2007 - 12:44:35 PDT)
- Re: AMBER: DNA denatures during MD simulation Thomas Cheatham (Mon Jul 23 2007 - 12:49:49 PDT)
  - Re: AMBER: DNA denatures during MD simulation Prashanth Athri (Mon Jul 23 2007 - 15:51:32 PDT)
AMBER: Bug report: a bug of xleap associated with NumLock Ye Mei (Mon Jul 23 2007 - 23:15:27 PDT)
- Re: AMBER: Bug report: a bug of xleap associated with NumLock David A. Case (Tue Jul 24 2007 - 08:16:07 PDT)
Fwd: Re: Re: AMBER: parallel compilation Francesco Pietra (Tue Jul 24 2007 - 00:19:58 PDT)
- Re: Fwd: Re: Re: AMBER: parallel compilation Ye Mei (Tue Jul 24 2007 - 03:07:31 PDT)
- Re: Fwd: Re: Re: AMBER: parallel compilation Ye Mei (Tue Jul 24 2007 - 03:15:28 PDT)
  - Re: Fwd: Re: Re: AMBER: parallel compilation Francesco Pietra (Tue Jul 24 2007 - 07:07:10 PDT)
    - Re: Re: Fwd: Re: Re: AMBER: parallel compilation Ye Mei (Tue Jul 24 2007 - 07:26:26 PDT)
    - Re: Re: Fwd: Re: Re: AMBER: parallel compilation Francesco Pietra (Tue Jul 24 2007 - 08:02:01 PDT)
    - Re: Re: Re: Fwd: Re: Re: AMBER: parallel compilation Ye Mei (Tue Jul 24 2007 - 19:27:04 PDT)
    - Re: Re: Re: Fwd: Re: Re: AMBER: parallel compilation Francesco Pietra (Tue Jul 24 2007 - 23:10:17 PDT)
AMBER: not getting topology and restraint file Prem Prakash Pathak (Tue Jul 24 2007 - 07:09:40 PDT)
- Re: AMBER: not getting topology and restraint file Carlos Simmerling (Tue Jul 24 2007 - 07:46:49 PDT)
  - Re: AMBER: not getting topology and restraint file Prem Prakash Pathak (Tue Jul 24 2007 - 21:11:00 PDT)
    - Re: AMBER: not getting topology and restraint file Carlos Simmerling (Wed Jul 25 2007 - 03:16:02 PDT)
    - Re: AMBER: not getting topology and restraint file Prem Prakash Pathak (Wed Jul 25 2007 - 06:45:57 PDT)
AMBER: FW: MPI error message Taryn Hartley (Tue Jul 24 2007 - 12:00:25 PDT)
- RE: AMBER: FW: MPI error message Gustavo Seabra (Tue Jul 24 2007 - 12:32:52 PDT)
- RE: AMBER: FW: MPI error message Ross Walker (Tue Jul 24 2007 - 14:31:12 PDT)
AMBER: MD simulation error Lili Peng (Tue Jul 24 2007 - 16:53:59 PDT)
- Re: AMBER: MD simulation error David A. Case (Tue Jul 24 2007 - 17:55:09 PDT)
- RE: AMBER: MD simulation error Ross Walker (Tue Jul 24 2007 - 18:01:13 PDT)
  - Re: AMBER: MD simulation error Lili Peng (Wed Jul 25 2007 - 10:38:10 PDT)
    - Re: AMBER: MD simulation error Carlos Simmerling (Wed Jul 25 2007 - 10:41:42 PDT)
    - RE: AMBER: MD simulation error Ross Walker (Wed Jul 25 2007 - 10:54:30 PDT)
    - Re: AMBER: MD simulation error Lili Peng (Wed Jul 25 2007 - 11:21:24 PDT)
AMBER: Amber9 parallel compilation openmpi issues Francesco Pietra (Tue Jul 24 2007 - 23:24:22 PDT)
- Re: AMBER: Amber9 parallel compilation openmpi issues Mark Williamson (Wed Jul 25 2007 - 06:33:35 PDT)
  - Re: AMBER: Amber9 parallel compilation openmpi issues Francesco Pietra (Wed Jul 25 2007 - 07:00:58 PDT)
    - Re: AMBER: Amber9 parallel compilation openmpi issues Benjamin Juhl (Wed Jul 25 2007 - 07:18:28 PDT)
    - Re: AMBER: Amber9 parallel compilation openmpi issues Francesco Pietra (Wed Jul 25 2007 - 07:44:46 PDT)
    - Re: AMBER: Amber9 parallel compilation openmpi issues Mark Williamson (Wed Jul 25 2007 - 08:28:06 PDT)
    - Re: AMBER: Amber9 parallel compilation openmpi issues David A. Case (Wed Jul 25 2007 - 09:09:18 PDT)
AMBER: Bad residue/molecule data in prmtop neva.mmb.pcb.ub.es (Wed Jul 25 2007 - 06:03:19 PDT)
- RE: AMBER: Bad residue/molecule data in prmtop Ross Walker (Wed Jul 25 2007 - 07:17:00 PDT)
AMBER: Fwd: Amber9 parallel compilation openmpi issues Francesco Pietra (Wed Jul 25 2007 - 06:24:10 PDT)
- RE: AMBER: Fwd: Amber9 parallel compilation openmpi issues Ross Walker (Wed Jul 25 2007 - 08:25:58 PDT)
  - RE: AMBER: Fwd: Amber9 parallel compilation openmpi issues Francesco Pietra (Wed Jul 25 2007 - 10:07:15 PDT)
- Re: AMBER: Fwd: Amber9 parallel compilation openmpi issues David A. Case (Wed Jul 25 2007 - 10:36:43 PDT)
  - Re: AMBER: Fwd: Amber9 parallel compilation openmpi issues Mark Williamson (Wed Jul 25 2007 - 12:19:29 PDT)
    - Re: AMBER: Fwd: Amber9 parallel compilation openmpi issues David A. Case (Wed Jul 25 2007 - 12:56:24 PDT)
    - Re: AMBER: Fwd: Amber9 parallel compilation openmpi issues Francesco Pietra (Wed Jul 25 2007 - 13:43:08 PDT)
    - Re: AMBER: Fwd: Amber9 parallel compilation openmpi issues David A. Case (Wed Jul 25 2007 - 14:32:32 PDT)
    - Re: AMBER: Fwd: Amber9 parallel compilation openmpi issues Mark Williamson (Wed Jul 25 2007 - 15:20:37 PDT)
    - Re: AMBER: Fwd: Amber9 parallel compilation openmpi issues David A. Case (Wed Jul 25 2007 - 15:48:55 PDT)
AMBER: crg file umbrita itl (Wed Jul 25 2007 - 07:43:17 PDT)
- RE: AMBER: crg file Ross Walker (Wed Jul 25 2007 - 08:26:28 PDT)
AMBER: RE: Contact TSRI: Ross Walker Ross Walker (Wed Jul 25 2007 - 08:31:53 PDT)
RE: AMBER:charge file umbrita itl (Wed Jul 25 2007 - 08:36:11 PDT)
Fwd: Re: AMBER: Fwd: Amber9 parallel compilation openmpi issues Francesco Pietra (Wed Jul 25 2007 - 15:01:40 PDT)
AMBER: rmsd residue wise ravishk kumar (Thu Jul 26 2007 - 06:02:20 PDT)
AMBER: methods to approach two atoms Jena M (Thu Jul 26 2007 - 06:53:09 PDT)
AMBER: RE: A little question Ross Walker (Thu Jul 26 2007 - 07:51:55 PDT)
AMBER: about wrap the trajectory Rachel (Thu Jul 26 2007 - 09:18:32 PDT)
- Re: AMBER: about wrap the trajectory Carlos Simmerling (Thu Jul 26 2007 - 09:28:33 PDT)
  - Re: AMBER: about wrap the trajectory Rachel (Thu Jul 26 2007 - 09:43:48 PDT)
    - Re: AMBER: about wrap the trajectory Carlos Simmerling (Fri Jul 27 2007 - 04:29:48 PDT)
    - Re: AMBER: about wrap the trajectory Rachel (Fri Jul 27 2007 - 07:08:23 PDT)
    - Re: AMBER: about wrap the trajectory Carlos Simmerling (Fri Jul 27 2007 - 07:23:30 PDT)
    - Re: AMBER: about wrap the trajectory Rachel (Fri Jul 27 2007 - 07:38:12 PDT)
    - Re: AMBER: about wrap the trajectory Carlos Simmerling (Fri Jul 27 2007 - 07:44:53 PDT)
    - Re: AMBER: about wrap the trajectory Rachel (Fri Jul 27 2007 - 07:52:50 PDT)
    - Re: AMBER: about wrap the trajectory Carlos Simmerling (Fri Jul 27 2007 - 09:10:49 PDT)
AMBER: adding organic molecule to polypeptide residue Lili Peng (Thu Jul 26 2007 - 15:36:29 PDT)
- Re: AMBER: adding organic molecule to polypeptide residue FyD (Sat Jul 28 2007 - 02:05:18 PDT)
AMBER: FLAG LENNARD_JONES_ACOEF NAN Greg Gannon (Fri Jul 27 2007 - 07:41:46 PDT)
- Re: AMBER: FLAG LENNARD_JONES_ACOEF NAN David A. Case (Fri Jul 27 2007 - 08:19:49 PDT)
  - Re: AMBER: FLAG LENNARD_JONES_ACOEF NAN Greg Gannon (Fri Jul 27 2007 - 08:55:52 PDT)
AMBER: RE: Query Ross Walker (Fri Jul 27 2007 - 08:24:56 PDT)
AMBER: errors in SHIFTS execution Tom Pochapsky (Sat Jul 28 2007 - 04:58:57 PDT)
- Re: AMBER: errors in SHIFTS execution David A. Case (Sun Jul 29 2007 - 08:44:05 PDT)
  - Re: AMBER: errors in SHIFTS execution Thomas Pochapsky (Mon Jul 30 2007 - 06:49:47 PDT)
  - Re: AMBER: errors in SHIFTS execution Thomas Pochapsky (Mon Jul 30 2007 - 07:06:19 PDT)
    - Re: AMBER: errors in SHIFTS execution David A. Case (Mon Jul 30 2007 - 08:37:26 PDT)
    - Re: AMBER: errors in SHIFTS execution Thomas Pochapsky (Mon Jul 30 2007 - 10:06:04 PDT)
AMBER: PCA with ptraj ravishk kumar (Sat Jul 28 2007 - 05:02:13 PDT)
- Re: AMBER: PCA with ptraj Chris Moth (Sun Jul 29 2007 - 05:27:32 PDT)
AMBER: thermodynamic data for conformers Francesco Pietra (Sun Jul 29 2007 - 10:11:11 PDT)
AMBER: what's the problem of "Missing BELE for MM in 1 (residue 246)" in MM-GBSA? tonglei (Sun Jul 29 2007 - 20:45:24 PDT)
AMBER: heme force field hadi behzadi (Mon Jul 30 2007 - 04:55:07 PDT)
- Re: AMBER: heme force field Marcelo Puiatti (Mon Jul 30 2007 - 06:08:52 PDT)
AMBER: QM-MM output interpretation Francesco Pietra (Mon Jul 30 2007 - 07:08:36 PDT)
- RE: AMBER: QM-MM output interpretation Ross Walker (Mon Jul 30 2007 - 08:51:36 PDT)
  - RE: AMBER: QM-MM output interpretation Francesco Pietra (Mon Jul 30 2007 - 10:59:13 PDT)
    - RE: AMBER: QM-MM output interpretation Ross Walker (Mon Jul 30 2007 - 21:11:50 PDT)
    - RE: AMBER: Average potential energies and conformer ratios Francesco Pietra (Mon Jul 30 2007 - 22:09:02 PDT)
AMBER: RE: Problem with sander.MPI Ross Walker (Mon Jul 30 2007 - 07:12:58 PDT)
AMBER: RE: help:- regarding "perl" in analyzing the simulation Ross Walker (Mon Jul 30 2007 - 09:38:33 PDT)
AMBER: QMMM to follow reaction involving water M. L. Dodson (Mon Jul 30 2007 - 11:23:14 PDT)
- RE: AMBER: QMMM to follow reaction involving water Gustavo Seabra (Mon Jul 30 2007 - 12:41:17 PDT)
- RE: AMBER: QMMM to follow reaction involving water Ross Walker (Mon Jul 30 2007 - 21:49:23 PDT)
  - Re: AMBER: QMMM to follow reaction involving water M. L. Dodson (Tue Jul 31 2007 - 08:14:57 PDT)
AMBER: Problem while saving .top and .crd files. Anju Sharma (Mon Jul 30 2007 - 20:47:39 PDT)
- RE: AMBER: Problem while saving .top and .crd files. Ross Walker (Mon Jul 30 2007 - 21:28:42 PDT)
  - Re: AMBER: Problem while saving .top and .crd files. Anju Sharma (Wed Aug 01 2007 - 22:25:19 PDT)
    - RE: AMBER: Problem while saving .top and .crd files. Ross Walker (Thu Aug 02 2007 - 07:54:21 PDT)
AMBER: Problem while creating input files in antechamber Anju Sharma (Mon Jul 30 2007 - 22:33:12 PDT)
- Re: AMBER: Problem while creating input files in antechamber Benjamin Juhl (Tue Jul 31 2007 - 00:08:35 PDT)
AMBER: Linux install Beale, John (Tue Jul 31 2007 - 04:55:34 PDT)
- Re: AMBER: Linux install David A. Case (Tue Jul 31 2007 - 08:35:37 PDT)
AMBER: Resp hadi behzadi (Tue Jul 31 2007 - 07:15:15 PDT)
AMBER: resp hadi behzadi (Tue Jul 31 2007 - 10:15:37 PDT)
AMBER: mm_pbsa and energy decomposition (missing BELE for MM in 1) Alessandro Nascimento (Tue Jul 31 2007 - 14:34:12 PDT)
AMBER: how to calculate the ps/day of md simulation using using my cluster system in amber7 Syed Tarique Moin (Wed Aug 01 2007 - 02:36:31 PDT)
AMBER: problem compiling Amber9 on 64-machine fatima.chami.durham.ac.uk (Wed Aug 01 2007 - 04:03:48 PDT)
- Re: AMBER: problem compiling Amber9 on 64-machine David A. Case (Wed Aug 01 2007 - 07:50:30 PDT)
  - Re: AMBER: problem compiling Amber9 on 64-machine S.Sundar Raman (Wed Aug 01 2007 - 08:46:10 PDT)
    - Re: AMBER: problem compiling Amber9 on 64-machine fatima.chami.durham.ac.uk (Wed Aug 01 2007 - 08:55:26 PDT)
    - RE: AMBER: problem compiling Amber9 on 64-machine Ross Walker (Wed Aug 01 2007 - 09:10:17 PDT)
    - Re: AMBER: problem compiling Amber9 on 64-machine David A. Case (Wed Aug 01 2007 - 09:43:21 PDT)
    - Re: AMBER: problem compiling Amber9 on 64-machine S.Sundar Raman (Wed Aug 01 2007 - 22:03:32 PDT)
  - Re: AMBER: problem compiling Amber9 on 64-machine fatima.chami.durham.ac.uk (Wed Aug 01 2007 - 08:52:13 PDT)
    - Re: AMBER: problem compiling Amber9 on 64-machine David A. Case (Wed Aug 01 2007 - 09:36:37 PDT)
Fwd: RE: AMBER: Average potential energies and conformer ratios Francesco Pietra (Wed Aug 01 2007 - 06:58:02 PDT)
AMBER: Problem with Antechamber and point charges anna duraj (Wed Aug 01 2007 - 12:40:44 PDT)
- Re: AMBER: Problem with Antechamber and point charges Carlos Simmerling (Wed Aug 01 2007 - 12:52:53 PDT)
  - Re: AMBER: Problem with Antechamber and point charges anna duraj (Fri Aug 03 2007 - 12:47:17 PDT)
    - Re: AMBER: Problem with Antechamber and point charges Carlos Simmerling (Fri Aug 03 2007 - 12:55:43 PDT)
AMBER: neutral terminals Jena M (Wed Aug 01 2007 - 17:15:46 PDT)
- Re: AMBER: neutral terminals Carlos Simmerling (Thu Aug 02 2007 - 05:04:15 PDT)
AMBER: Problem with antechamber Anju Sharma (Wed Aug 01 2007 - 23:34:39 PDT)
- Re: AMBER: Problem with antechamber gurpreet singh (Thu Aug 02 2007 - 01:24:18 PDT)
  - Re: AMBER: Problem with antechamber Anju Sharma (Thu Aug 02 2007 - 02:03:36 PDT)
    - Re: AMBER: Problem with antechamber David A. Case (Thu Aug 02 2007 - 08:07:30 PDT)
    - RE: AMBER: Problem with antechamber Ross Walker (Thu Aug 02 2007 - 08:22:52 PDT)
- Re: AMBER: Problem with antechamber Bill Ross (Thu Aug 02 2007 - 13:14:37 PDT)
AMBER: (no subject) Syed Tarique Moin (Wed Aug 01 2007 - 23:50:59 PDT)
- Re: AMBER: (no subject) gurpreet singh (Thu Aug 02 2007 - 01:39:07 PDT)
  - Re: AMBER: (no subject) Syed Tarique Moin (Thu Aug 02 2007 - 05:36:21 PDT)
    - Re: AMBER: (no subject) Carlos Simmerling (Thu Aug 02 2007 - 05:48:36 PDT)
    - RE: AMBER: (no subject) Gustavo Seabra (Thu Aug 02 2007 - 13:19:05 PDT)
    - RE: AMBER: (no subject) Syed Tarique Moin (Fri Aug 03 2007 - 23:11:51 PDT)
    - Re: AMBER: (no subject) Carlos Simmerling (Sat Aug 04 2007 - 03:55:29 PDT)
    - Re: AMBER: (no subject) Syed Tarique Moin (Sat Aug 04 2007 - 07:07:23 PDT)
    - RE: AMBER: (no subject) Ross Walker (Sat Aug 04 2007 - 08:30:36 PDT)
AMBER: planarity restraints for NA Seth Lilavivat (Thu Aug 02 2007 - 06:12:18 PDT)
- Re: AMBER: planarity restraints for NA Carlos Simmerling (Thu Aug 02 2007 - 06:17:56 PDT)
  - Re: AMBER: planarity restraints for NA Seth Lilavivat (Thu Aug 02 2007 - 07:07:23 PDT)
    - Re: AMBER: planarity restraints for NA Carlos Simmerling (Thu Aug 02 2007 - 07:17:32 PDT)
    - Re: AMBER: planarity restraints for NA Seth Lilavivat (Thu Aug 02 2007 - 10:01:39 PDT)
    - RE: AMBER: planarity restraints for NA Hu, Shaowen (JSC-SK)[USRA] (Thu Aug 02 2007 - 11:49:15 PDT)
    - Re: AMBER: planarity restraints for NA Seth Lilavivat (Thu Aug 02 2007 - 12:29:42 PDT)
AMBER: restrained md and mm pbsa Christopher Gaughan (Thu Aug 02 2007 - 07:15:17 PDT)
AMBER: vector corrplane Servaas Michielssens (Thu Aug 02 2007 - 08:25:45 PDT)
AMBER: Force Field Parameters Beale, John (Thu Aug 02 2007 - 09:46:16 PDT)
- Re: AMBER: Force Field Parameters Prashanth Athri (Thu Aug 02 2007 - 10:39:10 PDT)
- Re: AMBER: Force Field Parameters Raviprasad Aduri (Thu Aug 02 2007 - 12:49:37 PDT)
AMBER: Calculating cumulative average Francesco Pietra (Thu Aug 02 2007 - 10:00:10 PDT)
AMBER: edit.out amber version 9 Greg Gannon (Thu Aug 02 2007 - 11:21:31 PDT)
- Re: AMBER: edit.out amber version 9 David A. Case (Thu Aug 02 2007 - 12:00:22 PDT)
- Re: AMBER: edit.out amber version 9 WANG,YING (Thu Aug 02 2007 - 13:33:49 PDT)
AMBER: Problem generating .prepin file in Antechamber Lili Peng (Thu Aug 02 2007 - 12:07:11 PDT)
- Re: AMBER: Problem generating .prepin file in Antechamber Lili Peng (Thu Aug 02 2007 - 12:15:41 PDT)
- Re: AMBER: Problem generating .prepin file in Antechamber David A. Case (Thu Aug 02 2007 - 13:53:03 PDT)
AMBER: Any experience on Dell two quad core system? Ilyas Yildirim (Thu Aug 02 2007 - 17:33:40 PDT)
- Re: AMBER: Any experience on Dell two quad core system? Ye Mei (Thu Aug 02 2007 - 20:57:00 PDT)
  - Re: AMBER: Any experience on Dell two quad core system? Ilyas Yildirim (Thu Aug 02 2007 - 21:23:17 PDT)
    - RE: AMBER: Any experience on Dell two quad core system? Ross Walker (Fri Aug 03 2007 - 09:28:57 PDT)
    - RE: AMBER: Any experience on Dell two quad core system? Andreas Svrcek-Seiler (Mon Aug 13 2007 - 08:12:15 PDT)
    - Re: AMBER: Any experience on Dell two quad core system? M. L. Dodson (Mon Aug 13 2007 - 08:59:11 PDT)
    - Re: AMBER: Any experience on Dell two quad core system? Andreas Svrcek-Seiler (Mon Aug 13 2007 - 10:21:39 PDT)
    - Re: AMBER: Any experience on Dell two quad core system? M. L. Dodson (Mon Aug 13 2007 - 10:37:47 PDT)
    - RE: AMBER: Any experience on Dell two quad core system? Ilyas Yildirim (Mon Aug 13 2007 - 12:25:22 PDT)
    - RE: AMBER: Any experience on Dell two quad core system? Andreas Svrcek-Seiler (Mon Aug 13 2007 - 13:46:58 PDT)
- Re: AMBER: Any experience on Dell two quad core system? Andreas Svrcek-Seiler (Thu Aug 02 2007 - 21:18:42 PDT)
  - Re: AMBER: Any experience on Dell two quad core system? Ilyas Yildirim (Fri Aug 03 2007 - 09:35:26 PDT)
- Re: AMBER: Any experience on Dell two quad core system? David Cerutti (Mon Aug 13 2007 - 13:59:58 PDT)
  - Re: AMBER: Any experience on Dell two quad core system? Ilyas Yildirim (Mon Aug 13 2007 - 17:39:01 PDT)
    - Re: AMBER: Any experience on Dell two quad core system? David Cerutti (Tue Aug 14 2007 - 08:05:34 PDT)
- Re: AMBER: Any experience on Dell two quad core system? Robert Duke (Tue Aug 14 2007 - 09:13:07 PDT)
AMBER: Information about Amber 9 Lycourgos Chiniadis (Thu Aug 02 2007 - 22:11:17 PDT)
- Re: AMBER: Information about Amber 9 David A. Case (Fri Aug 03 2007 - 07:53:22 PDT)
AMBER: force field for hydrogels Prem Prakash Pathak (Thu Aug 02 2007 - 23:03:48 PDT)
AMBER: unable to save prmtop/inpcrd for chcl3box Francesco Pietra (Fri Aug 03 2007 - 03:09:03 PDT)
- Re: AMBER: unable to save prmtop/inpcrd for chcl3box David A. Case (Fri Aug 03 2007 - 07:58:03 PDT)
AMBER: Fwd: unable to save prmtop/inpcrd for chcl3box Francesco Pietra (Fri Aug 03 2007 - 05:24:24 PDT)
AMBER: Successful compile on Mac OSX + Intel compilers Viv Kendon (Fri Aug 03 2007 - 05:28:56 PDT)
- Re: AMBER: Successful compile on Mac OSX + Intel compilers Viv Kendon (Fri Aug 03 2007 - 09:00:57 PDT)
AMBER: Binary file curiosities David LeBard (Fri Aug 03 2007 - 15:59:45 PDT)
- Re: AMBER: Binary file curiosities David A. Case (Fri Aug 03 2007 - 16:21:25 PDT)
- Re: AMBER: Binary file curiosities Thomas Cheatham III (Fri Aug 03 2007 - 16:32:55 PDT)
  - Re: AMBER: Binary file curiosities David LeBard (Sat Aug 04 2007 - 14:34:23 PDT)
    - Re: AMBER: Binary file curiosities David A. Case (Mon Aug 06 2007 - 08:03:07 PDT)
AMBER: Fwd: QM region + cutoff larger that box Francesco Pietra (Sat Aug 04 2007 - 01:32:40 PDT)
- Re: AMBER: Fwd: QM region + cutoff larger that box M. L. Dodson (Sat Aug 04 2007 - 07:32:17 PDT)
  - Re: AMBER: Fwd: QM region + cutoff larger that box M. L. Dodson (Sat Aug 04 2007 - 07:51:22 PDT)
    - Re: AMBER: Fwd: QM region + cutoff larger that box Francesco Pietra (Sat Aug 04 2007 - 09:42:33 PDT)
- RE: AMBER: Fwd: QM region + cutoff larger that box Gustavo Seabra (Sat Aug 04 2007 - 08:33:12 PDT)
  - RE: AMBER: Fwd: QM region + cutoff larger that box Francesco Pietra (Sun Aug 05 2007 - 23:28:13 PDT)
    - Re: AMBER: Fwd: QM region + cutoff larger that box M. L. Dodson (Mon Aug 06 2007 - 05:58:56 PDT)
    - Re: AMBER: Fwd: QM region + cutoff larger that box Francesco Pietra (Mon Aug 06 2007 - 08:07:09 PDT)
    - Re: AMBER: Fwd: QM region + cutoff larger that box M. L. Dodson (Mon Aug 06 2007 - 08:29:43 PDT)
    - RE: AMBER: Fwd: QM region + cutoff larger that box Gustavo Seabra (Mon Aug 06 2007 - 08:38:19 PDT)
AMBER: nucleic acid electrostatic energy Tiago Sobreira (Sat Aug 04 2007 - 06:45:46 PDT)
- Re: AMBER: nucleic acid electrostatic energy David A. Case (Sat Aug 04 2007 - 08:28:36 PDT)
AMBER: Fwd: QM region + cutoff larger that box Francesco Pietra (Sat Aug 04 2007 - 07:33:35 PDT)
AMBER: GAFF atom typing for flavin Hans Martin Senn (Sat Aug 04 2007 - 09:15:30 PDT)
AMBER: force field for irregulate DNA ends Hu, Shaowen (JSC-SK)[USRA] (Sat Aug 04 2007 - 11:20:42 PDT)
AMBER: setting dimensions of truncated octahedron Lillian chong (Sat Aug 04 2007 - 13:34:59 PDT)
- Re: AMBER: setting dimensions of truncated octahedron Thomas Cheatham (Sat Aug 04 2007 - 15:38:15 PDT)
  - Re: AMBER: setting dimensions of truncated octahedron Lillian chong (Sun Aug 05 2007 - 06:25:01 PDT)
AMBER: RE: tutorial file polyAT_vac.prmtop Ross Walker (Sun Aug 05 2007 - 20:09:46 PDT)
AMBER: Problem while carrying out minimisation of drug molecule using sander Anju Sharma (Sun Aug 05 2007 - 20:51:11 PDT)
- Re: AMBER: Problem while carrying out minimisation of drug molecule using sander David A. Case (Mon Aug 06 2007 - 07:35:25 PDT)
  - Re: AMBER: Problem while carrying out minimisation of drug molecule using sander Anju Sharma (Mon Aug 06 2007 - 22:32:43 PDT)
    - Re: AMBER: Problem while carrying out minimisation of drug molecule using sander Carlos Simmerling (Tue Aug 07 2007 - 03:57:53 PDT)
AMBER: Specific heat graph is a straight line priya priya (Mon Aug 06 2007 - 06:33:52 PDT)
AMBER: Integrating the alpha-helix bias correction into ff94 Andrew Borgert (Mon Aug 06 2007 - 12:18:58 PDT)
- Re: AMBER: Integrating the alpha-helix bias correction into ff94 Carlos Simmerling (Mon Aug 06 2007 - 12:42:17 PDT)
AMBER: hybridization in Amber, pertaining to resonant structures, ions Karen Callahan (Mon Aug 06 2007 - 21:13:27 PDT)
- Re: AMBER: hybridization in Amber, pertaining to resonant structures, ions David A. Case (Sat Aug 11 2007 - 13:35:15 PDT)
AMBER: heical content in simulations priya priya (Tue Aug 07 2007 - 00:58:12 PDT)
- Re: AMBER: heical content in simulations Chng Choon-Peng (Tue Aug 07 2007 - 01:19:26 PDT)
  - Re: AMBER: heical content in simulations priya priya (Tue Aug 07 2007 - 01:41:16 PDT)
    - Re: AMBER: heical content in simulations Scott Pendley (Fri Nov 09 2007 - 12:25:18 PST)
AMBER: Problem with minimization Syed Tarique Moin (Tue Aug 07 2007 - 06:11:32 PDT)
- RE: AMBER: Problem with minimization Ross Walker (Tue Aug 07 2007 - 06:57:18 PDT)
AMBER: compile amber8 with mpich2 Kailee (Tue Aug 07 2007 - 06:18:14 PDT)
- Re: AMBER: compile amber8 with mpich2 Scott Brozell (Wed Aug 08 2007 - 19:46:22 PDT)
AMBER: Positive EPtot in QM-MM Francesco Pietra (Tue Aug 07 2007 - 07:34:35 PDT)
AMBER: about shake linfu (Tue Aug 07 2007 - 18:36:59 PDT)
- Re: AMBER: about shake Steven Winfield (Wed Aug 08 2007 - 08:59:45 PDT)
  - Re: Re: AMBER: about shake linfu (Wed Aug 08 2007 - 18:10:05 PDT)
AMBER: msubhamoy.ibab.ac.in (Wed Aug 08 2007 - 06:01:00 PDT)
AMBER: HOW TO CALCULATE FREE ENERGY OF A DNA DUPLEX USING MMPBSA msubhamoy.ibab.ac.in (Wed Aug 08 2007 - 06:08:04 PDT)
- RE: AMBER: HOW TO CALCULATE FREE ENERGY OF A DNA DUPLEX USING MMPBSA Ross Walker (Wed Aug 08 2007 - 07:49:11 PDT)
- Re: AMBER: HOW TO CALCULATE FREE ENERGY OF A DNA DUPLEX USING MMPBSA linfu (Wed Aug 08 2007 - 06:33:58 PDT)
AMBER: RE: TUTORIAL B1 file polyAT_vac.prmtop Ross Walker (Wed Aug 08 2007 - 07:52:39 PDT)
AMBER: RE: Problem loading pdf into tleap Ross Walker (Wed Aug 08 2007 - 10:29:19 PDT)
AMBER: Cygwin error Lili Peng (Wed Aug 08 2007 - 14:33:22 PDT)
- Re: AMBER: Cygwin error Bill Ross (Wed Aug 08 2007 - 15:29:24 PDT)
  - Re: AMBER: Cygwin error Lili Peng (Wed Aug 08 2007 - 16:04:31 PDT)
    - Re: AMBER: Cygwin error Gustavo Seabra (Wed Aug 08 2007 - 16:36:29 PDT)
    - Re: AMBER: Cygwin error Lili Peng (Thu Aug 09 2007 - 11:13:27 PDT)
    - RE: AMBER: Cygwin error Ross Walker (Thu Aug 09 2007 - 11:52:36 PDT)
    - Re: AMBER: Cygwin error Lili Peng (Thu Aug 09 2007 - 12:06:03 PDT)
    - Re: AMBER: Cygwin error Gustavo Seabra (Thu Aug 09 2007 - 13:30:19 PDT)
    - Re: AMBER: Cygwin error Gustavo Seabra (Thu Aug 09 2007 - 12:08:27 PDT)
    - Re: AMBER: Cygwin error Lili Peng (Thu Aug 09 2007 - 12:16:20 PDT)
- Re: AMBER: Cygwin error Bill Ross (Thu Aug 09 2007 - 13:42:48 PDT)
  - Re: AMBER: Cygwin error Gustavo Seabra (Thu Aug 09 2007 - 14:40:14 PDT)
Re: AMBER: Cygwin error Bill Ross (Wed Aug 08 2007 - 14:43:49 PDT)
- Re: AMBER: Cygwin error Lili Peng (Wed Aug 08 2007 - 14:56:00 PDT)
  - Re: AMBER: Cygwin error Mark Williamson (Wed Aug 08 2007 - 15:02:15 PDT)
    - Re: AMBER: Cygwin error Lili Peng (Wed Aug 08 2007 - 15:13:54 PDT)
    - Re: AMBER: Cygwin error Gustavo Seabra (Wed Aug 08 2007 - 15:21:01 PDT)
AMBER: how to combine two molecules Wenyong Tong (Wed Aug 08 2007 - 22:34:33 PDT)
- Re: AMBER: how to combine two molecules Benjamin Juhl (Fri Aug 10 2007 - 02:11:07 PDT)
  - Re: AMBER: how to combine two molecules Wenyong Tong (Sat Aug 11 2007 - 18:48:48 PDT)
    - Re: AMBER: how to combine two molecules David A. Case (Mon Aug 13 2007 - 09:43:57 PDT)
    - Re: AMBER: how to combine two molecules Wenyong Tong (Mon Aug 13 2007 - 16:14:49 PDT)
AMBER: NVE energy and temperature drift Nikola Trbovic (Thu Aug 09 2007 - 13:24:11 PDT)
- Re: AMBER: NVE energy and temperature drift Robert Duke (Thu Aug 09 2007 - 15:15:58 PDT)
  - Re: AMBER: NVE energy and temperature drift Nikola Trbovic (Thu Aug 09 2007 - 15:50:45 PDT)
- Re: AMBER: NVE energy and temperature drift Thomas Cheatham III (Thu Aug 09 2007 - 15:27:50 PDT)
- Re: AMBER: NVE energy and temperature drift Robert Duke (Thu Aug 09 2007 - 16:43:42 PDT)
  - RE: AMBER: NVE energy and temperature drift Nikola Trbovic (Thu Aug 09 2007 - 17:11:07 PDT)
    - Re: AMBER: NVE energy and temperature drift Robert Duke (Thu Aug 09 2007 - 19:15:19 PDT)
    - Re: AMBER: NVE energy and temperature drift Vlad Cojocaru (Fri Aug 10 2007 - 02:03:15 PDT)
    - Re: AMBER: NVE energy and temperature drift Vlad Cojocaru (Fri Aug 10 2007 - 02:10:51 PDT)
- Re: AMBER: NVE energy and temperature drift David A. Case (Sat Aug 11 2007 - 13:28:30 PDT)
  - Re: AMBER: NVE energy and temperature drift Nikola Trbovic (Sat Aug 11 2007 - 14:33:09 PDT)
AMBER: Implicit solvent simulation is too slow. SeungPyo Hong (Fri Aug 10 2007 - 05:42:11 PDT)
- Re: AMBER: Implicit solvent simulation is too slow. Carlos Simmerling (Fri Aug 10 2007 - 06:07:50 PDT)
  - Re: AMBER: Implicit solvent simulation is too slow. SeungPyo Hong (Fri Aug 10 2007 - 07:04:28 PDT)
- RE: AMBER: Implicit solvent simulation is too slow. Ross Walker (Fri Aug 10 2007 - 08:56:32 PDT)
AMBER: How to couple only one residue to the temperature bath? Michael Lerner (Fri Aug 10 2007 - 07:45:10 PDT)
- Re: AMBER: How to couple only one residue to the temperature bath? Carlos Simmerling (Fri Aug 10 2007 - 08:55:02 PDT)
  - Re: AMBER: How to couple only one residue to the temperature bath? Michael Lerner (Fri Aug 10 2007 - 14:35:38 PDT)
    - Re: AMBER: How to couple only one residue to the temperature bath? Carlos Simmerling (Fri Aug 10 2007 - 15:43:29 PDT)
AMBER: short 2'OH-OP contacts in RNA Jose Gallego (Fri Aug 10 2007 - 09:22:35 PDT)
AMBER: vlimit exceeded for the step Sudha Mani Karra (Fri Aug 10 2007 - 12:31:08 PDT)
- RE: AMBER: vlimit exceeded for the step Ross Walker (Fri Aug 10 2007 - 13:04:10 PDT)
AMBER: Steve Seibold (Fri Aug 10 2007 - 13:17:47 PDT)
- Re: AMBER: Thomas Pochapsky (Fri Aug 10 2007 - 13:34:32 PDT)
- Re: AMBER: David A. Case (Tue Aug 14 2007 - 08:27:48 PDT)
AMBER: Citation for Langevin thermostat? Marc Baaden (Sat Aug 11 2007 - 00:13:28 PDT)
- Re: AMBER: Citation for Langevin thermostat? David A. Case (Sat Aug 11 2007 - 12:47:59 PDT)
AMBER: Using charmm force field in amber Seongeun Yang (Sat Aug 11 2007 - 01:44:44 PDT)
AMBER: Failure to SCF convergence Francesco Pietra (Sat Aug 11 2007 - 09:56:53 PDT)
- RE: AMBER: Failure to SCF convergence Ross Walker (Sat Aug 11 2007 - 16:14:54 PDT)
  - RE: AMBER: Failure to SCF convergence & parallelization and memory Francesco Pietra (Sun Aug 12 2007 - 00:37:33 PDT)
    - AMBER: MM_PBSA No radius found for Br!! Urszula Uciechowska (Mon Aug 13 2007 - 02:52:34 PDT)
    - Re: AMBER: MM_PBSA No radius found for Br!! Antonio Morreale (Mon Aug 13 2007 - 04:39:52 PDT)
    - Re: AMBER: MM_PBSA No radius found for Br!! Urszula Uciechowska (Tue Aug 14 2007 - 06:49:06 PDT)
    - AMBER: MM_PBSA No radius found for Br!! Urszula Uciechowska (Tue Aug 14 2007 - 08:53:32 PDT)
    - Re: AMBER: MM_PBSA No radius found for Br!! Scott Brozell (Sun Aug 19 2007 - 10:40:20 PDT)
    - RE: AMBER: Failure to SCF convergence & parallelization and memory Ross Walker (Mon Aug 13 2007 - 10:16:25 PDT)
AMBER: imin=5 and inptraj Nikola Trbovic (Sat Aug 11 2007 - 13:11:08 PDT)
- Re: AMBER: imin=5 and inptraj Carlos Simmerling (Sat Aug 11 2007 - 14:23:29 PDT)
  - Re: AMBER: imin=5 and inptraj Nikola Trbovic (Sat Aug 11 2007 - 14:31:40 PDT)
- Re: AMBER: imin=5 and inptraj Chris Moth (Sat Aug 11 2007 - 14:37:11 PDT)
AMBER: Neutralize charges for simulated annealing? Francesco Pietra (Sat Aug 11 2007 - 15:35:30 PDT)
AMBER: setbox command error priya priya (Mon Aug 13 2007 - 09:18:16 PDT)
- Re: AMBER: setbox command error David A. Case (Mon Aug 13 2007 - 13:38:30 PDT)
  - Re: AMBER: setbox command error priya priya (Mon Aug 13 2007 - 23:42:45 PDT)
    - Re: AMBER: setbox command error Steven Winfield (Tue Aug 14 2007 - 00:45:08 PDT)
    - Re: AMBER: setbox command error priya priya (Tue Aug 14 2007 - 01:58:40 PDT)
    - Re: AMBER: setbox command error Steven Winfield (Tue Aug 14 2007 - 02:00:39 PDT)
AMBER: unsubscribe Pan, Yongmei (Mon Aug 13 2007 - 10:35:12 PDT)
AMBER: Using TLEAP to set up MD in the crystal lattice space? David Cerutti (Mon Aug 13 2007 - 14:09:51 PDT)
- Re: AMBER: Using TLEAP to set up MD in the crystal lattice space? David A. Case (Mon Aug 13 2007 - 18:26:24 PDT)
  - Re: AMBER: Using TLEAP to set up MD in the crystal lattice space? Thomas Cheatham (Mon Aug 13 2007 - 19:45:19 PDT)
AMBER: Normal Mode Analysis Kresimir Sikic (Mon Aug 13 2007 - 08:12:59 PDT)
- Re: AMBER: Normal Mode Analysis David A. Case (Wed Aug 15 2007 - 15:56:46 PDT)
AMBER: Machine environment to install AMBER 8 M. Maeda (Mon Aug 13 2007 - 23:03:07 PDT)
- Re: AMBER: Machine environment to install AMBER 8 Benjamin Juhl (Tue Aug 14 2007 - 01:28:09 PDT)
  - Re: AMBER: Machine environment to install AMBER 8 M. Maeda (Tue Aug 14 2007 - 01:54:03 PDT)
    - Re: AMBER: Machine environment to install AMBER 8 Benjamin Juhl (Tue Aug 14 2007 - 02:10:16 PDT)
  - Re: AMBER: Machine environment to install AMBER 8 M. Maeda (Tue Aug 14 2007 - 02:19:37 PDT)
    - Re: AMBER: Machine environment to install AMBER 8 Bertrand Russell (Tue Aug 14 2007 - 02:21:07 PDT)
- Re: AMBER: Machine environment to install AMBER 8 M. Maeda (Tue Aug 14 2007 - 02:45:53 PDT)
  - Re: AMBER: Machine environment to install AMBER 8 Bertrand Russell (Tue Aug 14 2007 - 02:50:07 PDT)
  - Re: AMBER: Machine environment to install AMBER 8 Benjamin Juhl (Tue Aug 14 2007 - 03:49:13 PDT)
- Re: AMBER: Machine environment to install AMBER 8 M. Maeda (Tue Aug 14 2007 - 22:17:03 PDT)
  - Re: AMBER: Machine environment to install AMBER 8 Bertrand Russell (Tue Aug 14 2007 - 23:34:02 PDT)
AMBER: regarding implicit simulation gurpreet singh (Mon Aug 13 2007 - 23:21:35 PDT)
- Re: AMBER: regarding implicit simulation Carlos Simmerling (Tue Aug 14 2007 - 04:22:24 PDT)
AMBER: MMPBSA NOT Getting results msubhamoy.ibab.ac.in (Tue Aug 14 2007 - 01:26:57 PDT)
- RE: AMBER: MMPBSA NOT Getting results Rafi Ahmad (Tue Aug 14 2007 - 01:34:35 PDT)
AMBER: How to carry out drug-dna complex simulations Anju Sharma (Tue Aug 14 2007 - 01:50:04 PDT)
- Re: AMBER: How to carry out drug-dna complex simulations David A. Case (Tue Aug 14 2007 - 08:18:47 PDT)
  - Re: AMBER: How to carry out drug-dna complex simulations Scott Brozell (Sun Aug 19 2007 - 11:06:22 PDT)
AMBER: Tutorial about SMD? Qiang Zhong (Tue Aug 14 2007 - 03:19:09 PDT)
AMBER: Parallelizin antechamber? Francesco Pietra (Tue Aug 14 2007 - 06:29:11 PDT)
- Re: AMBER: Parallelizin antechamber? M. L. Dodson (Tue Aug 14 2007 - 07:29:16 PDT)
  - Re: AMBER: Parallelizin antechamber? Junmei Wang (Wed Aug 15 2007 - 06:41:45 PDT)
AMBER: torsional restraints in a solvated MD simulation. Tom Pochapsky (Tue Aug 14 2007 - 13:31:34 PDT)
- Re: AMBER: torsional restraints in a solvated MD simulation. Carlos Simmerling (Tue Aug 14 2007 - 13:41:52 PDT)
  - Re: AMBER: torsional restraints in a solvated MD simulation. Tom Pochapsky (Tue Aug 14 2007 - 16:11:27 PDT)
- Re: AMBER: torsional restraints in a solvated MD simulation. David A. Case (Tue Aug 14 2007 - 13:50:31 PDT)
  - Re: AMBER: torsional restraints in a solvated MD simulation. Tom Pochapsky (Tue Aug 14 2007 - 16:15:06 PDT)
    - Re: AMBER: torsional restraints in a solvated MD simulation. Tom Pochapsky (Tue Aug 14 2007 - 18:04:24 PDT)
AMBER: antechamber, how does it work Francesco Pietra (Wed Aug 15 2007 - 01:43:45 PDT)
- Re: AMBER: antechamber, how does it work Junmei Wang (Wed Aug 15 2007 - 06:33:36 PDT)
  - Re: AMBER: antechamber, how does it work Francesco Pietra (Wed Aug 15 2007 - 07:25:12 PDT)
- Re: AMBER: antechamber, how does it work Gustavo Seabra (Wed Aug 15 2007 - 07:15:48 PDT)
  - Re: AMBER: antechamber, how does it work Francesco Pietra (Wed Aug 15 2007 - 08:05:31 PDT)
- Re: AMBER: antechamber, how does it work Seth Hayik (Wed Aug 15 2007 - 08:10:22 PDT)
  - Re: AMBER: antechamber, how does it work Francesco Pietra (Wed Aug 15 2007 - 09:08:37 PDT)
    - Re: AMBER: antechamber, how does it work David A. Case (Wed Aug 15 2007 - 10:07:22 PDT)
    - Re: AMBER: antechamber, how does it work Francesco Pietra (Wed Aug 15 2007 - 14:53:55 PDT)
    - Re: AMBER: antechamber, how does it work Thomas Cheatham III (Wed Aug 15 2007 - 16:02:07 PDT)
    - Re: AMBER: antechamber, how does it work Francesco Pietra (Wed Aug 15 2007 - 22:53:34 PDT)
    - Re: AMBER: antechamber, how does it work David A. Case (Thu Aug 16 2007 - 08:40:16 PDT)
    - Re: AMBER: antechamber, how does it work Francesco Pietra (Thu Aug 16 2007 - 10:25:35 PDT)
  - Re: AMBER: about parallelization in QM-MM Francesco Pietra (Thu Aug 16 2007 - 23:41:02 PDT)
    - RE: AMBER: about parallelization in QM-MM Ross Walker (Fri Aug 17 2007 - 09:58:54 PDT)
    - RE: AMBER: about parallelization in QM-MM Ross Walker (Fri Aug 17 2007 - 11:45:08 PDT)
AMBER: Building parallel Amber 9.0 Beale, John (Wed Aug 15 2007 - 05:21:56 PDT)
- Re: AMBER: Building parallel Amber 9.0 Gustavo Seabra (Wed Aug 15 2007 - 06:46:59 PDT)
- RE: AMBER: Building parallel Amber 9.0 Ross Walker (Wed Aug 15 2007 - 07:26:36 PDT)
  - RE: AMBER: Building parallel Amber 9.0 Rajendra P. OJHA (Wed Aug 15 2007 - 08:41:25 PDT)
    - RE: AMBER: Building parallel Amber 9.0 Balvinder Singh (Wed Aug 15 2007 - 20:53:44 PDT)
    - RE: AMBER: Building parallel Amber 9.0 Balvinder Singh (Wed Aug 15 2007 - 21:02:38 PDT)
  - RE: AMBER: Building parallel Amber 9.0 Rajendra P. OJHA (Wed Aug 15 2007 - 08:44:10 PDT)
    - RE: AMBER: Building parallel Amber 9.0 Ross Walker (Wed Aug 15 2007 - 10:43:28 PDT)
AMBER: Distance restraints between center of mass of two molecules Sudha Mani Karra (Wed Aug 15 2007 - 07:38:06 PDT)
- Re: AMBER: Distance restraints between center of mass of two molecules Carlos Simmerling (Wed Aug 15 2007 - 07:54:40 PDT)
  - Re: AMBER: Distance restraints between center of mass of two molecules Sudha Mani Karra (Wed Aug 15 2007 - 08:40:37 PDT)
    - Re: AMBER: Distance restraints between center of mass of two molecules Carlos Simmerling (Wed Aug 15 2007 - 08:52:27 PDT)
    - Re: AMBER: Distance restraints between center of mass of two molecules Sudha Mani Karra (Wed Aug 15 2007 - 14:02:55 PDT)
    - Re: AMBER: Distance restraints between center of mass of two molecules Carlos Simmerling (Wed Aug 15 2007 - 14:17:33 PDT)
AMBER: EXTRA_PTS: frtype 2 Should not be here Dilip Dagade (Wed Aug 15 2007 - 09:50:57 PDT)
- Re: AMBER: EXTRA_PTS: frtype 2 Should not be here David A. Case (Wed Aug 15 2007 - 10:34:49 PDT)
  - Re: AMBER: EXTRA_PTS: frtype 2 Should not be here Dilip Dagade (Wed Aug 15 2007 - 21:39:37 PDT)
    - Re: AMBER: EXTRA_PTS: frtype 2 Should not be here David A. Case (Thu Aug 16 2007 - 09:33:52 PDT)
    - Re: AMBER: EXTRA_PTS: frtype 2 Should not be here Dilip Dagade (Thu Aug 16 2007 - 09:52:56 PDT)
AMBER: docking ability anna duraj (Wed Aug 15 2007 - 10:34:37 PDT)
- Re: AMBER: docking ability Scott Brozell (Sun Aug 19 2007 - 11:19:08 PDT)
AMBER: Bug in ptraj mask processing? Steve Spronk (Wed Aug 15 2007 - 12:18:15 PDT)
AMBER: Missplaced TERs Steve Seibold (Thu Aug 16 2007 - 11:35:26 PDT)
- Re: AMBER: Missplaced TERs David A. Case (Thu Aug 16 2007 - 11:53:10 PDT)
  - RE: AMBER: Missplaced TERs Steve Seibold (Thu Aug 16 2007 - 12:47:38 PDT)
    - Re: AMBER: Missplaced TERs David A. Case (Mon Sep 10 2007 - 15:46:57 PDT)
AMBER: What is the best computer for running AMBER simulations? Lili Peng (Thu Aug 16 2007 - 14:37:03 PDT)
- Re: AMBER: What is the best computer for running AMBER simulations? David LeBard (Thu Aug 16 2007 - 15:17:42 PDT)
- Re: AMBER: What is the best computer for running AMBER simulations? Andreas Svrcek-Seiler (Thu Aug 16 2007 - 15:51:06 PDT)
  - Re: AMBER: What is the best computer for running AMBER simulations? David A. Case (Thu Aug 16 2007 - 16:42:54 PDT)
    - Re: AMBER: What is the best computer for running AMBER simulations? Yu Chen (Thu Aug 16 2007 - 20:44:49 PDT)
    - Re: AMBER: What is the best computer for running AMBER simulations? Lili Peng (Thu Aug 16 2007 - 21:50:42 PDT)
    - Re: AMBER: What is the best computer for running AMBER simulations? Prem Prakash Pathak (Sat Aug 18 2007 - 02:36:00 PDT)
    - AMBER: question about a 20 kDa protein David A. Case (Sat Aug 18 2007 - 09:07:09 PDT)
AMBER: NAN and vlimit exceeded errors in restrained MD.. using IBELLY Sandeep Kaushik (Thu Aug 16 2007 - 22:44:17 PDT)
AMBER: Thermodynamic Integration for a CHARGED molecule ming hui (Fri Aug 17 2007 - 02:12:38 PDT)
- Re: AMBER: Thermodynamic Integration for a CHARGED molecule David Mobley (Fri Aug 17 2007 - 06:56:33 PDT)
  - Re: AMBER: Thermodynamic Integration for a CHARGED molecule David A. Case (Fri Aug 17 2007 - 08:46:38 PDT)
AMBER: MPI Beale, John (Fri Aug 17 2007 - 05:00:33 PDT)
- Re: AMBER: MPI Mark Williamson (Fri Aug 17 2007 - 05:58:00 PDT)
AMBER: Molsurf error Pankaj R. Daga (Fri Aug 17 2007 - 10:46:54 PDT)
AMBER: ptraj hydrogen bonding defaults Michael Lerner (Fri Aug 17 2007 - 15:26:09 PDT)
- Re: AMBER: ptraj hydrogen bonding defaults Thomas Cheatham (Fri Aug 17 2007 - 19:33:55 PDT)
AMBER: DFTB email address Francesco Pietra (Sat Aug 18 2007 - 00:14:53 PDT)
- Re: AMBER: DFTB email address tomas.kubar.marge.uochb.cas.cz (Sun Aug 19 2007 - 13:27:48 PDT)
AMBER: charges in PBSA calculation Neha Gandhi (Sat Aug 18 2007 - 19:20:16 PDT)
- Re: AMBER: charges in PBSA calculation Ray Luo (Sun Aug 19 2007 - 06:32:19 PDT)
  - Re: AMBER: charges in PBSA calculation Neha Gandhi (Sun Aug 19 2007 - 16:01:47 PDT)
  - Re: AMBER: charges in PBSA calculation David A. Case (Sun Aug 19 2007 - 17:57:14 PDT)
AMBER: CRESP charges in antechamber prepin Francesco Pietra (Mon Aug 20 2007 - 00:23:24 PDT)
AMBER: mmpbsa calculation msubhamoy.ibab.ac.in (Mon Aug 20 2007 - 02:53:42 PDT)
AMBER: TEST_FAILURES Qiang Zhong (Mon Aug 20 2007 - 05:59:28 PDT)
- Re: AMBER: TEST_FAILURES Martin Stennett (Mon Aug 20 2007 - 05:56:36 PDT)
- Re: AMBER: TEST_FAILURES Qiang Zhong (Mon Aug 20 2007 - 17:43:23 PDT)
AMBER: Entropy in MM_PBSA Sergey Samsonov (Mon Aug 20 2007 - 08:01:37 PDT)
- Re: AMBER: Entropy in MM_PBSA David Mobley (Fri Aug 24 2007 - 09:31:28 PDT)
AMBER: Beale, John (Mon Aug 20 2007 - 08:41:06 PDT)
- Re: AMBER: David A. Case (Mon Aug 20 2007 - 17:31:21 PDT)
AMBER: $tleap is not normal Qiang Zhong (Mon Aug 20 2007 - 18:34:00 PDT)
- RE: AMBER: $tleap is not normal Ross Walker (Mon Aug 20 2007 - 19:51:16 PDT)
AMBER: Regarding free energy calculation and covalent bond nag raj (Mon Aug 20 2007 - 21:07:04 PDT)
- Re: AMBER: Regarding free energy calculation and covalent bond David A. Case (Thu Aug 23 2007 - 09:52:17 PDT)
AMBER: Error in MMPBSA Calculation msubhamoy.ibab.ac.in (Mon Aug 20 2007 - 22:53:17 PDT)
- Re: AMBER: Error in MMPBSA Calculation jitrayut jitonnom (Tue Aug 21 2007 - 00:11:52 PDT)
AMBER: command tleap is not normal Qiang Zhong (Tue Aug 21 2007 - 01:12:44 PDT)
- Re: AMBER: command tleap is not normal Ilyas Yildirim (Tue Aug 21 2007 - 01:50:35 PDT)
AMBER: how to include mpirun in this script Syed Tarique Moin (Tue Aug 21 2007 - 03:50:12 PDT)
- RE: AMBER: how to include mpirun in this script Ross Walker (Tue Aug 21 2007 - 11:45:23 PDT)
AMBER: How to use AMBER Parameter Database ? Qiang Zhong (Tue Aug 21 2007 - 05:36:46 PDT)
- Re: AMBER: How to use AMBER Parameter Database ? David A. Case (Thu Aug 23 2007 - 09:53:55 PDT)
AMBER: Thermodynamic Integration for conformational changes? Francesco Pietra (Tue Aug 21 2007 - 09:57:47 PDT)
- Re: AMBER: Thermodynamic Integration for conformational changes? Gustavo Seabra (Tue Aug 21 2007 - 20:33:36 PDT)
- Re: AMBER: Thermodynamic Integration for conformational changes? Gustavo Seabra (Tue Aug 21 2007 - 20:41:23 PDT)
  - Re: AMBER: Thermodynamic Integration for conformational changes? Francesco Pietra (Tue Aug 21 2007 - 23:53:15 PDT)
AMBER: xLeap "Could not find type" error Lili Peng (Tue Aug 21 2007 - 12:28:46 PDT)
- Re: AMBER: xLeap "Could not find type" error David A. Case (Tue Aug 21 2007 - 17:40:09 PDT)
  - Re: AMBER: xLeap "Could not find type" error Lili Peng (Tue Aug 21 2007 - 18:17:44 PDT)
    - Re: AMBER: xLeap "Could not find type" error David A. Case (Wed Aug 22 2007 - 08:15:25 PDT)
AMBER: Octahedral box orientation David Cerutti (Tue Aug 21 2007 - 06:08:38 PDT)
- Re: AMBER: Octahedral box orientation David Cerutti (Tue Aug 21 2007 - 17:07:32 PDT)
AMBER: Force field for RNA with U-turn motif Cenk Andac (Tue Aug 21 2007 - 06:52:48 PDT)
- Re: AMBER: Force field for RNA with U-turn motif Vlad Cojocaru (Wed Aug 22 2007 - 01:07:24 PDT)
  - Re: AMBER: Force field for RNA with U-turn motif Cenk Andac (Wed Aug 22 2007 - 09:08:29 PDT)
    - Re: AMBER: Force field for RNA with U-turn motif Jiri Sponer (Wed Aug 22 2007 - 09:33:46 PDT)
    - Re: AMBER: Force field for RNA with U-turn motif Cenk Andac (Wed Aug 22 2007 - 11:31:04 PDT)
AMBER: Tutorial of document about QM/MM in reaction pathways? Qiang Zhong (Tue Aug 21 2007 - 07:06:53 PDT)
AMBER: a question about xleap WANG,YING (Tue Aug 21 2007 - 12:16:48 PDT)
AMBER: How to use AMBER Parameter Database ? Qiang Zhong (Wed Aug 22 2007 - 01:53:04 PDT)
- AMBER: How to delete particular frame from mdcrd file (not with ptraj). saurabh agrawal (Wed Aug 22 2007 - 02:48:52 PDT)
  - Re: AMBER: How to delete particular frame from mdcrd file (not with ptraj). Steven Winfield (Wed Aug 22 2007 - 03:12:16 PDT)
    - Re: AMBER: How to delete particular frame from mdcrd file (not with ptraj). saurabh agrawal (Wed Aug 22 2007 - 03:25:53 PDT)
    - RE: AMBER: How to delete particular frame from mdcrd file (not with ptraj). Steve Spronk (Thu Aug 23 2007 - 06:25:50 PDT)
    - Re: AMBER: How to delete particular frame from mdcrd file (not with ptraj). Adrian Roitberg (Thu Aug 23 2007 - 06:32:28 PDT)
AMBER: MM-PBSA calculations of entropy within the sphere Sergey Samsonov (Wed Aug 22 2007 - 06:49:25 PDT)
AMBER: xLeap "Could not find type" error WANG,YING (Wed Aug 22 2007 - 07:04:37 PDT)
- Re: AMBER: xLeap "Could not find type" error Wei Zhang (Wed Aug 22 2007 - 08:18:11 PDT)
- Re: AMBER: xLeap "Could not find type" error WANG,YING (Wed Aug 22 2007 - 08:46:58 PDT)
- Re: AMBER: xLeap "Could not find type" error David A. Case (Wed Aug 22 2007 - 08:45:02 PDT)
AMBER: Running Gaussian to get .out files Lili Peng (Wed Aug 22 2007 - 13:27:25 PDT)
- RE: AMBER: Running Gaussian to get .out files Steve Spronk (Thu Aug 23 2007 - 06:05:25 PDT)
AMBER: Performance of polarizable model simulations Jones de Andrade (Wed Aug 22 2007 - 21:17:52 PDT)
AMBER: Parse charges for small molecules Neha Gandhi (Wed Aug 22 2007 - 21:50:38 PDT)
AMBER: Ca(2+) parameter Qiang Zhong (Thu Aug 23 2007 - 04:01:24 PDT)
- Re: AMBER: Ca(2+) parameter David A. Case (Thu Aug 23 2007 - 08:04:01 PDT)
[Fwd: Re: AMBER: How to delete particular frame from mdcrd file (not with ptraj).] Steven Winfield (Thu Aug 23 2007 - 06:31:49 PDT)
AMBER: Unable to open MDCRD file using vmd priya priya (Thu Aug 23 2007 - 08:04:19 PDT)
- RE: AMBER: Unable to open MDCRD file using vmd Ross Walker (Thu Aug 23 2007 - 13:40:27 PDT)
  - AMBER: ow to split MDCRD file using ptraj priya priya (Fri Aug 24 2007 - 00:34:27 PDT)
    - Re: AMBER: ow to split MDCRD file using ptraj Gustavo Seabra (Fri Aug 24 2007 - 19:17:27 PDT)
AMBER: How to perform MD simulation in NVT ensemble? WANG,YING (Thu Aug 23 2007 - 09:13:51 PDT)
- Re: AMBER: How to perform MD simulation in NVT ensemble? Chris Moth (Thu Aug 23 2007 - 10:07:30 PDT)
- Re: AMBER: How to perform MD simulation in NVT ensemble? WANG,YING (Thu Aug 23 2007 - 13:53:05 PDT)
  - Re: AMBER: How to perform MD simulation in NVT ensemble? Gustavo Seabra (Fri Aug 24 2007 - 19:21:59 PDT)
- Re: AMBER: How to perform MD simulation in NVT ensemble? WANG,YING (Wed Aug 29 2007 - 06:50:30 PDT)
  - Re: AMBER: How to perform MD simulation in NVT ensemble? Gustavo Seabra (Wed Aug 29 2007 - 07:53:11 PDT)
AMBER: Prepin error (?) in xleap Lili Peng (Thu Aug 23 2007 - 14:04:03 PDT)
- Re: AMBER: Prepin error (?) in xleap David A. Case (Thu Aug 23 2007 - 17:28:29 PDT)
  - Re: AMBER: Prepin error (?) in xleap Lili Peng (Fri Aug 24 2007 - 12:19:07 PDT)
    - Re: AMBER: Prepin error (?) in xleap Lili Peng (Fri Aug 24 2007 - 12:26:17 PDT)
    - Re: AMBER: Prepin error (?) in xleap David A. Case (Mon Aug 27 2007 - 08:58:20 PDT)
    - Re: AMBER: Prepin error (?) in xleap Lili Peng (Mon Aug 27 2007 - 14:38:30 PDT)
    - Re: AMBER: Prepin error (?) in xleap Junmei Wang (Mon Aug 27 2007 - 15:17:53 PDT)
    - Re: AMBER: Prepin error (?) in xleap David A. Case (Mon Aug 27 2007 - 15:29:49 PDT)
    - Re: AMBER: Prepin error (?) in xleap Lili Peng (Thu Aug 30 2007 - 13:48:34 PDT)
    - Re: AMBER: Prepin error (?) in xleap Junmei Wang (Fri Aug 31 2007 - 13:22:07 PDT)
    - Re: AMBER: Prepin error (?) in xleap Lili Peng (Thu Sep 06 2007 - 15:32:48 PDT)
    - Re: AMBER: Prepin error (?) in xleap David A. Case (Thu Sep 06 2007 - 21:38:27 PDT)
    - Re: AMBER: Prepin error (?) in xleap Junmei Wang (Thu Sep 06 2007 - 21:44:50 PDT)
    - Re: AMBER: Prepin error (?) in xleap Eduardo Mendez (Thu Sep 06 2007 - 22:56:00 PDT)
    - Re: AMBER: Prepin error (?) in xleap Lili Peng (Fri Sep 07 2007 - 14:22:42 PDT)
    - Re: AMBER: Prepin error (?) in xleap Lili Peng (Fri Sep 07 2007 - 14:54:23 PDT)
    - Re: AMBER: Prepin error (?) in xleap Ilyas Yildirim (Fri Sep 07 2007 - 15:21:55 PDT)
    - Re: AMBER: Prepin error (?) in xleap Lili Peng (Fri Sep 07 2007 - 16:33:24 PDT)
    - Re: AMBER: Prepin error (?) in xleap Ilyas Yildirim (Fri Sep 07 2007 - 17:39:04 PDT)
    - Re: AMBER: Prepin error (?) in xleap Lili Peng (Sat Sep 08 2007 - 14:54:15 PDT)
AMBER: protonation of His residue! Qiang Zhong (Thu Aug 23 2007 - 19:39:51 PDT)
- Re: AMBER: protonation of His residue! jitrayut jitonnom (Thu Aug 23 2007 - 20:52:51 PDT)
AMBER: QM/MM in reaction pathways? Qiang Zhong (Fri Aug 24 2007 - 01:00:50 PDT)
AMBER: solvateCap minin and mdin for qm-mm dftb Francesco Pietra (Fri Aug 24 2007 - 03:19:30 PDT)
- RE: AMBER: solvateCap minin and mdin for qm-mm dftb Ross Walker (Fri Aug 24 2007 - 06:10:54 PDT)
- Re: AMBER: solvateCap minin and mdin for qm-mm dftb M. L. Dodson (Fri Aug 24 2007 - 06:11:06 PDT)
  - Re: AMBER: solvateCap minin and mdin for qm-mm dftb Francesco Pietra (Fri Aug 24 2007 - 09:01:31 PDT)
    - Re: AMBER: solvateCap minin and mdin for qm-mm dftb M. L. Dodson (Fri Aug 24 2007 - 09:17:37 PDT)
    - RE: AMBER: solvateCap minin and mdin for qm-mm dftb Ross Walker (Fri Aug 24 2007 - 09:57:55 PDT)
    - RE: AMBER: solvateCap minin and mdin for qm-mm dftb Francesco Pietra (Fri Aug 24 2007 - 10:28:32 PDT)
    - Re: AMBER: solvateCap minin and mdin for qm-mm dftb Francesco Pietra (Fri Aug 24 2007 - 13:42:50 PDT)
    - Re: AMBER: solvateCap minin and mdin for qm-mm dftb M. L. Dodson (Fri Aug 24 2007 - 13:59:04 PDT)
    - RE: AMBER: solvateCap minin and mdin for qm-mm dftb Ross Walker (Fri Aug 24 2007 - 14:05:24 PDT)
    - RE: AMBER: solvateCap minin and mdin for qm-mm dftb Francesco Pietra (Fri Aug 24 2007 - 14:37:12 PDT)
AMBER: SMD simulation Qiang Zhong (Fri Aug 24 2007 - 03:33:41 PDT)
- Re: AMBER: SMD simulation Adrian Roitberg (Fri Aug 24 2007 - 05:43:35 PDT)
- RE: AMBER: SMD simulation Ross Walker (Fri Aug 24 2007 - 06:12:43 PDT)
- Re: AMBER: SMD simulation Qiang Zhong (Sat Aug 25 2007 - 02:49:09 PDT)
AMBER: NETCDF Geoff Wood (Fri Aug 24 2007 - 03:43:11 PDT)
- Re: AMBER: NETCDF Chris Moth (Fri Aug 24 2007 - 05:58:34 PDT)
- AMBER: NETCDF Chris Moth (Fri Aug 24 2007 - 06:03:37 PDT)
  - Re: AMBER: NETCDF Geoff Wood (Mon Aug 27 2007 - 00:18:48 PDT)
AMBER: articles Beale, John (Fri Aug 24 2007 - 06:02:05 PDT)
- Re: AMBER: articles Lili Peng (Fri Aug 24 2007 - 12:10:12 PDT)
AMBER: PM6? Thomas Patko (CSULB) (Fri Aug 24 2007 - 06:46:16 PDT)
- RE: AMBER: PM6? Ross Walker (Fri Aug 24 2007 - 09:36:26 PDT)
  - Re: AMBER: PM6? Thomas Patko (Fri Aug 24 2007 - 10:43:35 PDT)
    - RE: AMBER: PM6? Ross Walker (Fri Aug 24 2007 - 13:19:22 PDT)
AMBER: Running Gaussian to get .out files Steve Spronk (Fri Aug 24 2007 - 07:08:13 PDT)
AMBER: SCC convergence failure in QM-MM DFTB Francesco Pietra (Sat Aug 25 2007 - 10:54:12 PDT)
- Re: AMBER: SCC convergence failure in QM-MM DFTB Adrian Roitberg (Sat Aug 25 2007 - 11:10:35 PDT)
- Re: AMBER: SCC convergence failure in QM-MM DFTB Gustavo Seabra (Mon Aug 27 2007 - 10:20:37 PDT)
AMBER: Fwd: SCC convergence failure in QM-MM DFTB Francesco Pietra (Sun Aug 26 2007 - 00:26:42 PDT)
AMBER: personal computer configuration for parallel computing emine cebe (Sun Aug 26 2007 - 04:36:28 PDT)
AMBER: Fwd: SCC convergence failure in QM-MM DFTB Francesco Pietra (Sun Aug 26 2007 - 07:34:57 PDT)
- Re: AMBER: Fwd: SCC convergence failure in QM-MM DFTB M. L. Dodson (Sun Aug 26 2007 - 08:42:14 PDT)
  - Re: AMBER: Fwd: SCC convergence failure in QM-MM DFTB Francesco Pietra (Sun Aug 26 2007 - 09:28:14 PDT)
Fwd: Re: AMBER: Fwd: SCC convergence failure in QM-MM DFTB Francesco Pietra (Sun Aug 26 2007 - 23:24:33 PDT)
- Re: Re: AMBER: Fwd: SCC convergence failure in QM-MM DFTB Gustavo Seabra (Mon Aug 27 2007 - 12:12:23 PDT)
- Re: Re: AMBER: Fwd: SCC convergence failure in QM-MM DFTB Gustavo Seabra (Mon Aug 27 2007 - 13:50:40 PDT)
AMBER: metalloprotein dynamics Sally Pias (Mon Aug 27 2007 - 10:55:51 PDT)
AMBER: generating a .rst file from an .mdcrd file Thomas Pochapsky (Mon Aug 27 2007 - 11:41:56 PDT)
- Re: AMBER: generating a .rst file from an .mdcrd file Gustavo Seabra (Mon Aug 27 2007 - 12:15:23 PDT)
AMBER: Add hydrogen and charge calculation snoze pa (Mon Aug 27 2007 - 12:06:44 PDT)
- Re: AMBER: Add hydrogen and charge calculation Chris Moth (Mon Aug 27 2007 - 13:33:25 PDT)
  - Re: AMBER: Add hydrogen and charge calculation snoze pa (Mon Aug 27 2007 - 21:07:55 PDT)
AMBER: QM/MM in reaction pathways? Qiang Zhong (Tue Aug 28 2007 - 00:51:30 PDT)
- Re: AMBER: QM/MM in reaction pathways? Gustavo Seabra (Tue Aug 28 2007 - 07:55:20 PDT)
- RE: AMBER: QM/MM in reaction pathways? Ross Walker (Tue Aug 28 2007 - 08:21:40 PDT)
- RE: AMBER: QM/MM in reaction pathways? Qiang Zhong (Tue Aug 28 2007 - 17:52:21 PDT)
AMBER: protocols for high pressure simulation brmeher.iitg.ernet.in (Tue Aug 28 2007 - 08:23:00 PDT)
- Re: AMBER: protocols for high pressure simulation David A. Case (Tue Aug 28 2007 - 08:41:58 PDT)
AMBER: heating up system Francesco Pietra (Tue Aug 28 2007 - 09:16:57 PDT)
- Re: AMBER: heating up system Adrian Roitberg (Tue Aug 28 2007 - 11:45:26 PDT)
AMBER: energy minimization parameter Qiang Zhong (Wed Aug 29 2007 - 00:54:12 PDT)
- Re: AMBER: energy minimization parameter Lorenzo Gontrani (Wed Aug 29 2007 - 00:54:58 PDT)
AMBER: refinement of NMR struture using AMBER Prem Prakash Pathak (Wed Aug 29 2007 - 03:57:11 PDT)
- Re: AMBER: refinement of NMR struture using AMBER andy ng (Wed Sep 05 2007 - 02:59:00 PDT)
  - Re: AMBER: refinement of NMR struture using AMBER Prem Prakash Pathak (Wed Sep 05 2007 - 07:01:41 PDT)
    - Re: AMBER: refinement of NMR struture using AMBER Seth Lilavivat (Thu Sep 06 2007 - 12:20:52 PDT)
    - Re: AMBER: refinement of NMR struture using AMBER andy ng (Fri Sep 07 2007 - 06:42:44 PDT)
    - AMBER: for makeDIST_RST Wenyong Tong (Wed Sep 12 2007 - 14:30:29 PDT)
    - Re: AMBER: for makeDIST_RST David A. Case (Fri Sep 14 2007 - 08:10:28 PDT)
    - Re: AMBER: for makeDIST_RST Wenyong Tong (Fri Sep 14 2007 - 13:19:13 PDT)
    - Re: AMBER: for makeDIST_RST Wenyong Tong (Fri Sep 14 2007 - 15:15:56 PDT)
AMBER: Criteria for classical md being OK to move to QM-MM Francesco Pietra (Wed Aug 29 2007 - 09:51:15 PDT)
- Re: AMBER: Criteria for classical md being OK to move to QM-MM M. L. Dodson (Wed Aug 29 2007 - 10:11:29 PDT)
  - Re: AMBER: Criteria for classical md being OK to move to QM-MM Francesco Pietra (Wed Aug 29 2007 - 10:40:36 PDT)
    - Re: AMBER: Criteria for classical md being OK to move to QM-MM M. L. Dodson (Wed Aug 29 2007 - 11:24:43 PDT)
    - RE: AMBER: Criteria for classical md being OK to move to QM-MM Ross Walker (Wed Aug 29 2007 - 11:40:30 PDT)
- Re: AMBER: Criteria for classical md being OK to move to QM-MM Gustavo Seabra (Wed Aug 29 2007 - 11:13:05 PDT)
AMBER: Schedule for QM-MM with Amber9/Amber10 Francesco Pietra (Wed Aug 29 2007 - 23:30:10 PDT)
- AMBER: Dihedrals in Sander Martin Stennett (Thu Aug 30 2007 - 01:36:17 PDT)
  - RE: AMBER: Dihedrals in Sander Steve Spronk (Thu Sep 06 2007 - 12:37:24 PDT)
- Re: AMBER: Schedule for QM-MM with Amber9/Amber10 Gustavo Seabra (Fri Aug 31 2007 - 10:41:18 PDT)
AMBER: RDF unit cell volume BJÖRN KARLSSON (Thu Aug 30 2007 - 01:14:20 PDT)
AMBER: AMBER at WESTGRID Eduardo Mendez-Villuendas (Thu Aug 30 2007 - 04:49:07 PDT)
- Re: AMBER: AMBER at WESTGRID Gustavo Seabra (Thu Aug 30 2007 - 05:35:49 PDT)
AMBER: bad atom type:F Emilia Wu (Thu Aug 30 2007 - 05:36:14 PDT)
- Re: AMBER: bad atom type:F David A. Case (Thu Aug 30 2007 - 08:35:00 PDT)
AMBER: Beale, John (Thu Aug 30 2007 - 06:05:11 PDT)
- Re: AMBER: Melinda Layten (Fri Aug 31 2007 - 10:19:21 PDT)
AMBER: Fwd: Schedule for QM-MM with Amber9/Amber10 Francesco Pietra (Thu Aug 30 2007 - 06:17:41 PDT)
AMBER: Squished dimer during transition from NVT to NPT Katrina Lexa (Thu Aug 30 2007 - 14:02:20 PDT)
AMBER: Connecting two ethanes in LEaP Kliman, Michal (Thu Aug 30 2007 - 13:53:46 PDT)
- Re: AMBER: Connecting two ethanes in LEaP David A. Case (Fri Aug 31 2007 - 09:18:18 PDT)
AMBER: Scaling for octahedral versus rectilinear boxes David Cerutti (Thu Aug 30 2007 - 22:32:49 PDT)
- Re: AMBER: Scaling for octahedral versus rectilinear boxes Robert Duke (Fri Aug 31 2007 - 05:40:48 PDT)
  - Re: AMBER: Scaling for octahedral versus rectilinear boxes David Cerutti (Fri Aug 31 2007 - 06:27:38 PDT)
- Re: AMBER: Scaling for octahedral versus rectilinear boxes Robert Duke (Fri Aug 31 2007 - 07:23:11 PDT)
AMBER: Confusion about Langevin dymamics Hayden Eastwood (Fri Aug 31 2007 - 06:46:28 PDT)
- Re: AMBER: Confusion about Langevin dymamics Carlos Simmerling (Fri Aug 31 2007 - 06:52:02 PDT)
- Re: AMBER: Confusion about Langevin dymamics David A. Case (Fri Aug 31 2007 - 07:53:47 PDT)
  - Re: AMBER: Confusion about Langevin dymamics David Mobley (Fri Aug 31 2007 - 09:05:13 PDT)
AMBER: antechamber question Beale, John (Fri Aug 31 2007 - 07:07:56 PDT)
- Re: AMBER: antechamber question Junmei Wang (Fri Aug 31 2007 - 13:07:09 PDT)
AMBER: Converting AMBER-format force fields for tinker Aaron Virshup (Fri Aug 31 2007 - 12:04:12 PDT)
AMBER: Measuring Bond Angle over simulation Seth Lilavivat (Fri Aug 31 2007 - 12:25:20 PDT)
- Re: AMBER: Measuring Bond Angle over simulation Carlos Simmerling (Fri Aug 31 2007 - 12:34:13 PDT)
AMBER: modified leaprc for glycoproteins Irene Newhouse (Fri Aug 31 2007 - 13:53:05 PDT)
- Re: AMBER: modified leaprc for glycoproteins David A. Case (Fri Aug 31 2007 - 14:42:03 PDT)
  - RE: AMBER: modified leaprc for glycoproteins Irene Newhouse (Fri Aug 31 2007 - 18:14:32 PDT)
AMBER: Using ntr=1 in xleap Lili Peng (Fri Aug 31 2007 - 14:27:44 PDT)
- Re: AMBER: Using ntr=1 in xleap David A. Case (Fri Aug 31 2007 - 15:52:13 PDT)
- Re: AMBER: Using ntr=1 in xleap Carlos Simmerling (Fri Aug 31 2007 - 14:49:14 PDT)
  - Re: AMBER: Using ntr=1 in xleap Lili Peng (Tue Sep 04 2007 - 15:23:59 PDT)
AMBER: Solvent in closest contact with solute Francesco Pietra (Sat Sep 01 2007 - 07:15:11 PDT)
AMBER: ntt parameter in vacuum Age.Skjevik.student.uib.no (Mon Sep 03 2007 - 06:40:15 PDT)
- Re: AMBER: ntt parameter in vacuum Carlos Simmerling (Mon Sep 03 2007 - 06:53:16 PDT)
- Re: AMBER: ntt parameter in vacuum David A. Case (Mon Sep 03 2007 - 08:51:53 PDT)
AMBER: creating topology files for RNA DNA hybrid.molecule msubhamoy.ibab.ac.in (Mon Sep 03 2007 - 16:00:25 PDT)
- Re: AMBER: creating topology files for RNA DNA hybrid.molecule saurabh agrawal (Mon Sep 03 2007 - 21:21:56 PDT)
AMBER: installing LMOD error Xioling Chuang (Mon Sep 03 2007 - 22:52:56 PDT)
- Re: AMBER: installing LMOD error David A. Case (Tue Sep 04 2007 - 08:01:06 PDT)
  - Re: AMBER: installing LMOD error Xioling Chuang (Tue Sep 04 2007 - 19:04:17 PDT)
    - Re: AMBER: installing LMOD error David A. Case (Tue Sep 04 2007 - 22:35:24 PDT)
    - Re: AMBER: installing LMOD error Xioling Chuang (Thu Sep 06 2007 - 20:54:48 PDT)
AMBER: Catein Catherine (Mon Sep 03 2007 - 22:56:20 PDT)
AMBER: Running mpirun -np 1 on different processors Francesco Pietra (Tue Sep 04 2007 - 06:37:27 PDT)
- Re: AMBER: Running mpirun -np 1 on different processors Adrian Roitberg (Tue Sep 04 2007 - 06:45:11 PDT)
- Re: AMBER: Running mpirun -np 1 on different processors Carlos Simmerling (Tue Sep 04 2007 - 06:47:27 PDT)
  - Re: AMBER: Running mpirun -np 1 on different processors Francesco Pietra (Tue Sep 04 2007 - 07:39:40 PDT)
AMBER: decomposition energy Pankaj R. Daga (Tue Sep 04 2007 - 07:31:25 PDT)
- AMBER: PMF calculation - minimum conformer Catein Catherine (Wed Sep 05 2007 - 03:48:04 PDT)
- RE: AMBER: decomposition energy Catein Catherine (Wed Sep 05 2007 - 03:42:42 PDT)
AMBER: Problem compiling AMBER 9 on ppc64 Eric Shamay (Tue Sep 04 2007 - 09:14:07 PDT)
- Re: AMBER: Problem compiling AMBER 9 on ppc64 David A. Case (Tue Sep 04 2007 - 13:56:06 PDT)
AMBER: Problem with modelling ammonium ion? David Cerutti (Tue Sep 04 2007 - 18:26:22 PDT)
- Re: AMBER: Problem with modelling ammonium ion? David Cerutti (Tue Sep 04 2007 - 22:22:50 PDT)
AMBER: Comparing explicit solvent/vacuum qmmm Francesco Pietra (Wed Sep 05 2007 - 00:31:32 PDT)
AMBER: Fwd: Comparing explicit solvent/vacuum qmmm Francesco Pietra (Wed Sep 05 2007 - 04:05:07 PDT)
AMBER: amber md movie using Chimera Wang, Xuelin (Wed Sep 05 2007 - 10:42:08 PDT)
- Re: AMBER: amber md movie using Chimera Mingfeng Yang (Wed Sep 05 2007 - 11:04:57 PDT)
- Re: AMBER: amber md movie using Chimera David A. Case (Wed Sep 05 2007 - 11:12:27 PDT)
  - RE: AMBER: amber md movie using Chimera. . Wang, Xuelin (Wed Sep 05 2007 - 11:42:02 PDT)
- Re: AMBER: amber md movie using Chimera Bill Ross (Wed Sep 05 2007 - 14:38:32 PDT)
AMBER: chiral surfaces Hector A. Baldoni (Wed Sep 05 2007 - 16:35:42 PDT)
- Re: AMBER: chiral surfaces Carlos Simmerling (Wed Sep 05 2007 - 17:21:51 PDT)
AMBER: DelPhi Urszula Uciechowska (Thu Sep 06 2007 - 06:21:19 PDT)
AMBER: RE: Tutorial5 -- sustiva and xleap Ross Walker (Thu Sep 06 2007 - 06:20:08 PDT)
AMBER: electron density difference Ozlem Demir (Thu Sep 06 2007 - 06:36:29 PDT)
AMBER: Harmonic constraints Johan Qvist (Fri Sep 07 2007 - 07:43:57 PDT)
- Re: AMBER: Harmonic constraints Carlos Simmerling (Fri Sep 07 2007 - 08:31:46 PDT)
  - Re: AMBER: Harmonic constraints Ilyas Yildirim (Fri Sep 07 2007 - 10:13:55 PDT)
    - Re: AMBER: Harmonic constraints Carlos Simmerling (Fri Sep 07 2007 - 10:22:08 PDT)
    - Re: AMBER: Harmonic constraints Thomas Cheatham (Fri Sep 07 2007 - 11:52:48 PDT)
    - Re: AMBER: Harmonic constraints Carlos Simmerling (Fri Sep 07 2007 - 12:06:35 PDT)
    - Re: AMBER: Harmonic constraints Jiri Sponer (Fri Sep 07 2007 - 23:07:23 PDT)
    - Re: AMBER: Harmonic constraints Carlos Simmerling (Mon Sep 10 2007 - 07:14:54 PDT)
- AMBER: for NMR restrains files Wenyong Tong (Fri Sep 07 2007 - 10:26:09 PDT)
  - Re: AMBER: for NMR restrains files Prem Prakash Pathak (Fri Sep 07 2007 - 21:36:11 PDT)
- RE: AMBER: Harmonic constraints Hu, Shaowen (JSC-SK)[USRA] (Mon Sep 10 2007 - 07:05:18 PDT)
  - Re: AMBER: Harmonic constraints Carlos Simmerling (Mon Sep 10 2007 - 07:14:27 PDT)
AMBER: System extending beyond of (non existent) virtual box Francesco Pietra (Fri Sep 07 2007 - 10:17:36 PDT)
AMBER: Fwd: System extending beyond of (non existent) virtual box Francesco Pietra (Sat Sep 08 2007 - 01:33:34 PDT)
AMBER: solvent box pyridine Francesco Pietra (Sat Sep 08 2007 - 07:46:37 PDT)
AMBER: rms and rms nofit Alana Canfield (Sat Sep 08 2007 - 14:23:39 PDT)
AMBER: Targeted MD Beale, John (Sat Sep 08 2007 - 15:29:08 PDT)
- Re: AMBER: Targeted MD Adrian Roitberg (Sat Sep 08 2007 - 15:35:22 PDT)
  - AMBER: Explicit water in implicit enviornment? Hayden Eastwood (Sun Sep 09 2007 - 12:57:26 PDT)
    - Re: AMBER: Explicit water in implicit enviornment? Carlos Simmerling (Mon Sep 17 2007 - 08:35:58 PDT)
AMBER: RE: Asking for help Ross Walker (Mon Sep 10 2007 - 16:31:24 PDT)
AMBER: AMBER parametrization (??) for OAA and Mg++ Eduardo Mendez (Mon Sep 10 2007 - 21:39:43 PDT)
- Re:AMBER: AMBER parametrization (??) for OAA and Mg++ Qiang Zhong (Tue Sep 11 2007 - 00:32:17 PDT)
- Re: AMBER: AMBER parametrization (??) for OAA and Mg++ FyD (Tue Sep 11 2007 - 00:28:46 PDT)
AMBER: heme forcefield atom types john chen (Tue Sep 11 2007 - 07:09:45 PDT)
- Re: AMBER: heme forcefield atom types Vlad Cojocaru (Tue Sep 11 2007 - 08:05:46 PDT)
- Re: AMBER: heme forcefield atom types L. W. Yang (Wed Oct 24 2007 - 09:18:31 PDT)
- RE: AMBER: heme forcefield atom types Yang, Lee-Wei (Wed Oct 24 2007 - 11:41:29 PDT)
AMBER: heme force-field (2) john chen (Tue Sep 11 2007 - 08:08:05 PDT)
- Re: AMBER: heme force-field (2) Vlad Cojocaru (Tue Sep 11 2007 - 08:43:53 PDT)
AMBER: Tutorial protein-small-molecule-associates Francesco Pietra (Tue Sep 11 2007 - 09:26:01 PDT)
- Re: AMBER: Tutorial protein-small-molecule-associates Scott Brozell (Fri Sep 14 2007 - 08:50:09 PDT)
AMBER: PBradii Steve Seibold (Tue Sep 11 2007 - 11:40:00 PDT)
- Re: AMBER: PBradii Carlos Simmerling (Tue Sep 11 2007 - 12:06:32 PDT)
  - RE: AMBER: PBradii Steve Seibold (Tue Sep 11 2007 - 12:21:21 PDT)
AMBER: TIP5P questions Prashanth Athri (Tue Sep 11 2007 - 14:26:56 PDT)
- Re: AMBER: TIP5P questions Thomas Cheatham III (Thu Sep 13 2007 - 12:14:25 PDT)
- Re: AMBER: TIP5P questions David A. Case (Thu Sep 13 2007 - 17:17:12 PDT)
AMBER: Problems with Carbohydrate Non-standard Residue Moruz Luminita (Wed Sep 12 2007 - 03:30:09 PDT)
- Re: AMBER: Problems with Carbohydrate Non-standard Residue David A. Case (Wed Sep 12 2007 - 07:47:48 PDT)
  - AMBER: Complexe Energy Analysis saccenti.cerm.unifi.it (Wed Sep 12 2007 - 08:16:07 PDT)
- RE: AMBER: Problems with Carbohydrate Non-standard Residue Irene Newhouse (Wed Sep 12 2007 - 09:58:17 PDT)
AMBER: LINMIN Failure vs Parallelization Sandeep Kaushik (Thu Sep 13 2007 - 00:04:19 PDT)
- Re: AMBER: LINMIN Failure vs Parallelization linfu (Thu Sep 13 2007 - 03:24:10 PDT)
  - Re: AMBER: LINMIN Failure vs Parallelization Gustavo Seabra (Thu Sep 13 2007 - 06:26:45 PDT)
AMBER: Too big EEL energy in energy minimization Wang, Xuelin (Thu Sep 13 2007 - 07:34:27 PDT)
- RE: AMBER: Too big EEL energy in energy minimization Ross Walker (Thu Sep 13 2007 - 07:52:11 PDT)
  - RE: AMBER: Too big EEL energy in energy minimization. . Wang, Xuelin (Thu Sep 13 2007 - 09:00:17 PDT)
    - RE: AMBER: Too big EEL energy in energy minimization. . Ross Walker (Thu Sep 13 2007 - 09:25:07 PDT)
AMBER: Problem with Sander anna duraj (Thu Sep 13 2007 - 15:42:29 PDT)
- Re: AMBER: Problem with Sander Carlos Simmerling (Thu Sep 13 2007 - 16:38:06 PDT)
AMBER: FF02: sander problem with irstdip=1 Anselm Horn (Fri Sep 14 2007 - 03:31:19 PDT)
- Re: AMBER: FF02: sander problem with irstdip=1 David A. Case (Fri Sep 14 2007 - 07:59:26 PDT)
- RE: AMBER: FF02: sander problem with irstdip=1 Yong Duan (Fri Sep 14 2007 - 14:30:17 PDT)
AMBER: parallel implementation of Amber 9 Beale, John (Fri Sep 14 2007 - 05:40:03 PDT)
- Re: AMBER: parallel implementation of Amber 9 David A. Case (Fri Sep 14 2007 - 08:04:16 PDT)
AMBER: DNA base planarity restraint Hu, Shaowen (JSC-SK)[USRA] (Fri Sep 14 2007 - 08:29:46 PDT)
- Re: AMBER: DNA base planarity restraint Carlos Simmerling (Fri Sep 14 2007 - 09:00:22 PDT)
- RE: AMBER: DNA base planarity restraint Hu, Shaowen (JSC-SK)[USRA] (Fri Sep 14 2007 - 11:29:13 PDT)
  - Re: AMBER: DNA base planarity restraint Carlos Simmerling (Fri Sep 14 2007 - 12:43:03 PDT)
AMBER: calcium ion force-fields john chen (Fri Sep 14 2007 - 08:35:29 PDT)
AMBER: xleap question Anna Díaz Cirac (Fri Sep 14 2007 - 09:26:33 PDT)
- Re: AMBER: xleap question Carlos Simmerling (Fri Sep 14 2007 - 09:32:20 PDT)
AMBER: Torsion terms in xleap Lili Peng (Fri Sep 14 2007 - 15:35:23 PDT)
- Re: AMBER: Torsion terms in xleap Carlos Simmerling (Fri Sep 14 2007 - 15:42:52 PDT)
- Re: AMBER: Torsion terms in xleap Wenyong Tong (Fri Sep 14 2007 - 16:00:20 PDT)
- Re: AMBER: Torsion terms in xleap Davide Moiani (Fri Sep 14 2007 - 16:55:37 PDT)
- Re: AMBER: Torsion terms in xleap David A. Case (Fri Sep 14 2007 - 17:44:17 PDT)
  - Re: AMBER: Torsion terms in xleap Lili Peng (Mon Sep 17 2007 - 16:42:12 PDT)
    - Re: AMBER: Torsion terms in xleap David A. Case (Mon Sep 17 2007 - 19:35:24 PDT)
    - Re: AMBER: Torsion terms in xleap Lili Peng (Wed Sep 19 2007 - 11:41:14 PDT)
AMBER: AMBER sander Eduardo Mendez (Fri Sep 14 2007 - 16:42:38 PDT)
- Re: AMBER: AMBER sander David A. Case (Fri Sep 14 2007 - 17:50:47 PDT)
AMBER: Can I set harmonic constraints in SMD simulations ? James W (Fri Sep 14 2007 - 19:50:35 PDT)
- Re: AMBER: Can I set harmonic constraints in SMD simulations ? David A. Case (Sat Sep 15 2007 - 09:59:33 PDT)
AMBER: Problem encountered during thermodynamic integration ming hui (Sat Sep 15 2007 - 01:18:59 PDT)
- Re: AMBER: Problem encountered during thermodynamic integration David A. Case (Sat Sep 15 2007 - 10:02:39 PDT)
  - Re: AMBER: Problem encountered during thermodynamic integration ming hui (Wed Sep 19 2007 - 10:30:14 PDT)
AMBER: Problem with Getting SHAKE to work David Cerutti (Sat Sep 15 2007 - 11:04:14 PDT)
- Re: AMBER: Problem with Getting SHAKE to work David Cerutti (Sat Sep 15 2007 - 20:16:10 PDT)
- Re: AMBER: Problem with Getting SHAKE to work David A. Case (Sat Sep 15 2007 - 22:05:55 PDT)
  - Re: AMBER: Problem with Getting SHAKE to work David Cerutti (Sun Sep 16 2007 - 09:29:38 PDT)
    - Re: AMBER: Problem with Getting SHAKE to work David A. Case (Mon Sep 17 2007 - 09:38:26 PDT)
    - Re: AMBER: Problem with Getting SHAKE to work David Cerutti (Mon Sep 17 2007 - 13:36:59 PDT)
AMBER: replica exchange simulation Ji-Lai Li (Sat Sep 15 2007 - 17:58:06 PDT)
- Re: AMBER: replica exchange simulation Carlos Simmerling (Mon Sep 17 2007 - 07:04:46 PDT)
AMBER: Solvation net forces Tyler Luchko (Mon Sep 17 2007 - 09:23:03 PDT)
- Re: AMBER: Solvation net forces David A. Case (Tue Sep 18 2007 - 17:14:55 PDT)
  - Re: AMBER: Solvation net forces Tyler Luchko (Tue Sep 25 2007 - 12:21:24 PDT)
    - Re: AMBER: Solvation net forces Nicolas Lux Fawzi (Tue Sep 25 2007 - 14:24:05 PDT)
AMBER: CONFIGURATION FILE FOR OXALATE C2O4^2- Eduardo Mendez (Mon Sep 17 2007 - 19:32:22 PDT)
- Re: AMBER: CONFIGURATION FILE FOR OXALATE C2O4^2- Eduardo Mendez (Mon Sep 17 2007 - 20:16:02 PDT)
  - Re: AMBER: CONFIGURATION FILE FOR OXALATE C2O4^2- Ilyas Yildirim (Mon Sep 17 2007 - 21:38:58 PDT)
    - Re: AMBER: CONFIGURATION FILE FOR OXALATE C2O4^2- Jiri Sponer (Tue Sep 18 2007 - 01:11:19 PDT)
    - Re: AMBER: CONFIGURATION FILE FOR OXALATE C2O4^2- Eduardo Mendez (Tue Sep 18 2007 - 16:41:33 PDT)
- Re: AMBER: CONFIGURATION FILE FOR OXALATE C2O4^2- FyD (Tue Sep 18 2007 - 00:06:51 PDT)
  - AMBER: Potential of mean force: how to extract the min structure? Catein Catherine (Tue Sep 18 2007 - 00:39:12 PDT)
    - Re: AMBER: Potential of mean force: how to extract the min structure? Jerome.GOLEBIOWSKI.unice.fr (Tue Sep 18 2007 - 01:09:29 PDT)
  - AMBER: GBSA or PBSA: GPB or GGB are +ve or -ve? Catein Catherine (Tue Sep 18 2007 - 00:46:06 PDT)
  - Re: AMBER: CONFIGURATION FILE FOR OXALATE C2O4^2- Eduardo Mendez (Tue Sep 18 2007 - 16:52:18 PDT)
    - Re: AMBER: CONFIGURATION FILE FOR OXALATE C2O4^2- FyD (Tue Sep 18 2007 - 22:57:29 PDT)
    - Re: AMBER: CONFIGURATION FILE FOR OXALATE C2O4^2- Francesco Pietra (Tue Sep 18 2007 - 23:52:48 PDT)
    - Re: AMBER: CONFIGURATION FILE FOR OXALATE C2O4^2- FyD (Wed Sep 19 2007 - 00:50:14 PDT)
    - Re: AMBER: CONFIGURATION FILE FOR OXALATE C2O4^2- Eduardo Mendez (Wed Sep 19 2007 - 04:33:48 PDT)
    - Re: AMBER: CONFIGURATION FILE FOR OXALATE C2O4^2- FyD (Thu Sep 20 2007 - 01:37:30 PDT)
    - Re: AMBER: CONFIGURATION FILE FOR OXALATE C2O4^2- Eduardo Mendez (Thu Sep 20 2007 - 03:38:08 PDT)
    - Re: AMBER: CONFIGURATION FILE FOR OXALATE C2O4^2- FyD (Thu Sep 20 2007 - 04:54:23 PDT)
    - Re: AMBER: CONFIGURATION FILE FOR OXALATE C2O4^2- FyD (Thu Sep 20 2007 - 05:14:29 PDT)
AMBER: A question related with periodic boundary condition Jun Liu (Tue Sep 18 2007 - 18:48:22 PDT)
- Re: AMBER: A question related with periodic boundary condition Jun Liu (Wed Sep 19 2007 - 11:10:54 PDT)
AMBER: How to fix the distance between two atoms. nag raj (Tue Sep 18 2007 - 21:36:29 PDT)
AMBER: Targetted MD and ptraj analysis Ilyas Yildirim (Tue Sep 18 2007 - 22:47:19 PDT)
- RE: AMBER: Targetted MD and ptraj analysis Catein Catherine (Thu Sep 20 2007 - 19:11:30 PDT)
  - Re: AMBER: Targetted MD and ptraj analysis Carlos Simmerling (Fri Sep 21 2007 - 05:12:50 PDT)
    - Re: AMBER: Targetted MD and ptraj analysis Ilyas Yildirim (Fri Sep 21 2007 - 12:40:36 PDT)
AMBER: problem with Thermodynamic Integration Martin Stennett (Wed Sep 19 2007 - 04:46:30 PDT)
- Re: AMBER: problem with Thermodynamic Integration Ilyas Yildirim (Wed Sep 19 2007 - 09:45:47 PDT)
AMBER: problem compiling amber9 on IBM 64 bit machine with xlf90_suse compiler Hayden Eastwood (Wed Sep 19 2007 - 07:24:34 PDT)
- Re: AMBER: problem compiling amber9 on IBM 64 bit machine with xlf90_suse compiler Martin Klefas-Stennett (Wed Sep 19 2007 - 09:30:50 PDT)
  - RE: AMBER: problem compiling amber9 on IBM 64 bit machine with xlf90_suse compiler Hayden Eastwood (Wed Sep 19 2007 - 10:25:21 PDT)
    - Re: AMBER: problem compiling amber9 on IBM 64 bit machine with xlf90_suse compiler Martin Klefas-Stennett (Wed Sep 19 2007 - 11:16:49 PDT)
AMBER: A question related with periodic boundary condition Jun Liu (Wed Sep 19 2007 - 11:42:25 PDT)
AMBER: RE: AMBER9 Installation Help Ross Walker (Thu Sep 20 2007 - 07:48:12 PDT)
AMBER: Problems loading parameter file in tleap Eduardo Mendez (Fri Sep 21 2007 - 03:58:48 PDT)
- Re: AMBER: Problems loading parameter file in tleap Eddie Men (Fri Sep 21 2007 - 04:27:35 PDT)
- Re: AMBER: Problems loading parameter file in tleap FyD (Fri Sep 21 2007 - 04:55:39 PDT)
AMBER: MM_PBSA with complex plus Ion saccenti.cerm.unifi.it (Fri Sep 21 2007 - 07:26:58 PDT)
- Re: AMBER: MM_PBSA with complex plus Ion Pankaj Daga (Sun Sep 23 2007 - 08:50:21 PDT)
AMBER: kanon gemini (Fri Sep 21 2007 - 08:35:11 PDT)
- Re: AMBER: David A. Case (Sun Sep 23 2007 - 18:31:19 PDT)
AMBER: about restraining atoms san_amber roy (Fri Sep 21 2007 - 21:52:59 PDT)
- Re: AMBER: about restraining atoms Carlos Simmerling (Sat Sep 22 2007 - 06:32:52 PDT)
AMBER: TMD and "Current RMSD from reference" Ilyas Yildirim (Sat Sep 22 2007 - 03:40:05 PDT)
- Re: AMBER: TMD and "Current RMSD from reference" Carlos Simmerling (Sat Sep 22 2007 - 06:27:45 PDT)
  - Re: AMBER: TMD and "Current RMSD from reference" Ilyas Yildirim (Sat Sep 22 2007 - 13:49:26 PDT)
    - Re: AMBER: TMD and "Current RMSD from reference" Carlos Simmerling (Sat Sep 22 2007 - 15:40:08 PDT)
    - Re: AMBER: TMD and "Current RMSD from reference" Ilyas Yildirim (Sat Sep 22 2007 - 17:54:17 PDT)
    - Re: AMBER: TMD and "Current RMSD from reference" Carlos Simmerling (Sun Sep 23 2007 - 04:32:47 PDT)
    - Re: AMBER: TMD and "Current RMSD from reference" Ilyas Yildirim (Sun Sep 23 2007 - 11:14:48 PDT)
    - Re: AMBER: TMD and "Current RMSD from reference" Thomas Cheatham III (Sun Sep 23 2007 - 11:30:31 PDT)
AMBER: Water Question Eddie Men (Sun Sep 23 2007 - 01:09:21 PDT)
AMBER: about MD outputs saccenti.cerm.unifi.it (Sun Sep 23 2007 - 04:57:33 PDT)
- Re: AMBER: about MD outputs Carlos Simmerling (Sun Sep 23 2007 - 05:09:03 PDT)
  - Re: AMBER: about MD outputs saccenti.cerm.unifi.it (Sun Sep 23 2007 - 05:23:15 PDT)
    - Re: AMBER: about MD outputs Carlos Simmerling (Sun Sep 23 2007 - 05:31:06 PDT)
    - Re: AMBER: about MD outputs saccenti.cerm.unifi.it (Sun Sep 23 2007 - 05:34:00 PDT)
    - AMBER: Pribelm with Minimization & MD saccenti.cerm.unifi.it (Sun Sep 23 2007 - 11:27:20 PDT)
    - RE: AMBER: Pribelm with Minimization & MD Ross Walker (Mon Sep 24 2007 - 08:39:23 PDT)
AMBER: Water question Eddie Men (Sun Sep 23 2007 - 08:21:48 PDT)
- Re: AMBER: Water question David Cerutti (Sun Sep 23 2007 - 12:01:24 PDT)
AMBER: MAXPR san_amber roy (Sun Sep 23 2007 - 21:18:26 PDT)
- RE: AMBER: MAXPR Ross Walker (Mon Sep 24 2007 - 08:30:38 PDT)
  - Re: AMBER: MAXPR san_amber roy (Mon Oct 01 2007 - 01:10:35 PDT)
    - RE: AMBER: MAXPR Ross Walker (Mon Oct 01 2007 - 08:30:46 PDT)
    - Re: AMBER: MAXPR san_amber roy (Mon Oct 01 2007 - 23:58:03 PDT)
    - AMBER: How to get sane package caoch (Tue Oct 02 2007 - 03:09:26 PDT)
    - Re: AMBER: How to get sane package David A. Case (Wed Oct 31 2007 - 21:09:08 PDT)
AMBER: MacOSX installation help Quantum Mechanics (Mon Sep 24 2007 - 02:39:46 PDT)
- RE: AMBER: MacOSX installation help Ross Walker (Mon Sep 24 2007 - 07:26:35 PDT)
AMBER: Bertrand P. S. Russell (Mon Sep 24 2007 - 02:40:52 PDT)
AMBER: Statistical uncertainty estimation in Thermodynamic integration calculation.. cgji (Mon Sep 24 2007 - 06:13:36 PDT)
- AMBER: Help WARNING: The unperturbed charge of the unit saccenti.cerm.unifi.it (Mon Sep 24 2007 - 06:32:35 PDT)
  - Re: AMBER: Help WARNING: The unperturbed charge of the unit Ilyas Yildirim (Mon Sep 24 2007 - 14:53:40 PDT)
    - RE: AMBER: Help WARNING: The unperturbed charge of the unit Steve Spronk (Tue Sep 25 2007 - 05:08:21 PDT)
    - RE: AMBER: Help WARNING: The unperturbed charge of the unit saccenti.cerm.unifi.it (Tue Sep 25 2007 - 05:23:25 PDT)
    - RE: AMBER: Help WARNING: The unperturbed charge of the unit Ilyas Yildirim (Tue Sep 25 2007 - 11:56:19 PDT)
  - Re: AMBER: Help WARNING: The unperturbed charge of the unit saccenti.cerm.unifi.it (Tue Sep 25 2007 - 01:43:03 PDT)
AMBER: calcium parameters Mattia Mori - CERM (Mon Sep 24 2007 - 08:25:20 PDT)
- RE: AMBER: calcium parameters Ross Walker (Mon Sep 24 2007 - 09:04:08 PDT)
AMBER: RE: 回复： RE: Asking for help about heating Ross Walker (Mon Sep 24 2007 - 08:52:41 PDT)
AMBER: effective step period for constant pH simulations Lillian chong (Mon Sep 24 2007 - 11:22:50 PDT)
- Re: AMBER: effective step period for constant pH simulations Adrian Roitberg (Mon Sep 24 2007 - 11:31:05 PDT)
AMBER: problem with ptraj Terry Lang (Mon Sep 24 2007 - 15:55:29 PDT)
- Re: AMBER: problem with ptraj Carlos Simmerling (Mon Sep 24 2007 - 17:45:44 PDT)
AMBER: energy calculation gurpreet singh (Mon Sep 24 2007 - 22:54:16 PDT)
- AMBER: Copper and Chlorine parameters Syed Tarique Moin (Tue Sep 25 2007 - 03:39:16 PDT)
- Re: AMBER: energy calculation David A. Case (Tue Sep 25 2007 - 07:51:40 PDT)
AMBER: total energy in sander and nmode mbrut.laas.fr (Tue Sep 25 2007 - 05:55:48 PDT)
- Re: AMBER: total energy in sander and nmode David A. Case (Tue Sep 25 2007 - 07:56:49 PDT)
AMBER: atomicfluct Andres Palencia (Tue Sep 25 2007 - 10:45:50 PDT)
AMBER: Minimization and MD input files Su Nwe (Tue Sep 25 2007 - 11:23:49 PDT)
- Re: AMBER: Minimization and MD input files Carlos Simmerling (Tue Sep 25 2007 - 11:30:17 PDT)
  - Re: AMBER: Minimization and MD input files Su Nwe (Tue Sep 25 2007 - 11:55:07 PDT)
    - Re: AMBER: Minimization and MD input files Su Nwe (Tue Sep 25 2007 - 12:08:28 PDT)
    - RE: AMBER: Minimization and MD input files Ross Walker (Tue Sep 25 2007 - 12:23:53 PDT)
  - Re: AMBER: Minimization and MD input files Su Nwe (Tue Sep 25 2007 - 14:28:32 PDT)
    - Re: AMBER: Minimization and MD input files Carlos Simmerling (Tue Sep 25 2007 - 15:08:20 PDT)
- Re: AMBER: Minimization and MD input files David A. Case (Tue Sep 25 2007 - 12:27:37 PDT)
  - Re: AMBER: Minimization and MD input files Su Nwe (Tue Sep 25 2007 - 13:25:19 PDT)
    - Re: AMBER: Minimization and MD input files Carlos Simmerling (Tue Sep 25 2007 - 13:34:14 PDT)
    - Re: AMBER: Minimization and MD input files Su Nwe (Tue Sep 25 2007 - 13:47:19 PDT)
    - Re: AMBER: Minimization and MD input files Carlos Simmerling (Tue Sep 25 2007 - 14:27:49 PDT)
    - RE: AMBER: Minimization and MD input files Ross Walker (Tue Sep 25 2007 - 13:45:11 PDT)
AMBER: Re: using RESP Ilyas Yildirim (Tue Sep 25 2007 - 16:04:52 PDT)
- Re: AMBER: Re: using RESP FyD (Tue Sep 25 2007 - 23:14:58 PDT)
AMBER: regarding energy calculation gurpreet singh (Tue Sep 25 2007 - 22:16:41 PDT)
- Re: AMBER: regarding energy calculation Abi Ghanem josephine (Wed Sep 26 2007 - 02:13:38 PDT)
Fwd: AMBER: Copper and Chlorine parameters Syed Tarique Moin (Wed Sep 26 2007 - 00:41:59 PDT)
AMBER: Simulation continuation problem. Cant read restart file!!!!!! Anthony Cruz (Wed Sep 26 2007 - 07:55:45 PDT)
- Re: AMBER: Simulation continuation problem. Cant read restart file!!!!!! Carlos Simmerling (Wed Sep 26 2007 - 08:44:29 PDT)
  - Re: AMBER: Simulation continuation problem. Cant read restart file!!!!!! Anthony Cruz (Wed Sep 26 2007 - 09:03:41 PDT)
- RE: AMBER: Simulation continuation problem. Cant read restart file!!!!!! Ross Walker (Wed Sep 26 2007 - 08:51:10 PDT)
  - Re: AMBER: Simulation continuation problem. Cant read restart file!!!!!! Anthony Cruz (Fri Oct 05 2007 - 05:44:50 PDT)
    - Re: AMBER: Simulation continuation problem. Cant read restart file!!!!!! Gustavo Seabra (Fri Oct 05 2007 - 20:48:59 PDT)
- Re: AMBER: Simulation continuation problem. Cant read restart file!!!!!! Harianto Tjong (Wed Sep 26 2007 - 09:23:14 PDT)
  - AMBER: NMR refinement Wenyong Tong (Wed Sep 26 2007 - 14:38:46 PDT)
    - Re: AMBER: NMR refinement David A. Case (Wed Sep 26 2007 - 15:03:01 PDT)
    - Re: AMBER: NMR refinement Wenyong Tong (Fri Sep 28 2007 - 12:29:30 PDT)
    - AMBER: follow-up Wenyong Tong (Fri Sep 28 2007 - 12:55:39 PDT)
    - Re: AMBER: follow-up David A. Case (Fri Sep 28 2007 - 13:11:32 PDT)
    - Re: AMBER: follow-up Wenyong Tong (Fri Sep 28 2007 - 14:26:57 PDT)
    - Re: AMBER: follow-up Wenyong Tong (Tue Oct 09 2007 - 13:56:04 PDT)
    - RE: AMBER: follow-up Ross Walker (Tue Oct 09 2007 - 14:24:50 PDT)
AMBER: Solvation Issues Eddie Men (Wed Sep 26 2007 - 15:48:21 PDT)
- Re: AMBER: Solvation Issues David A. Case (Wed Sep 26 2007 - 16:16:58 PDT)
  - Re: AMBER: Solvation Issues David Cerutti (Wed Sep 26 2007 - 16:53:11 PDT)
    - Re: AMBER: Solvation Issues Eddie Men (Fri Sep 28 2007 - 23:31:26 PDT)
    - Re: AMBER: Solvation Issues David Cerutti (Sat Sep 29 2007 - 20:55:43 PDT)
AMBER: solvation issues Eddie Men (Wed Sep 26 2007 - 16:19:47 PDT)
Fwd: AMBER: Copper and Chlorine parameters Syed Tarique Moin (Wed Sep 26 2007 - 20:21:31 PDT)
AMBER: Reproducing constant pH results !! Pradipta Bandyopadhyay (Wed Sep 26 2007 - 22:16:49 PDT)
AMBER: force field question Eddie Men (Thu Sep 27 2007 - 00:31:42 PDT)
- Re: AMBER: force field question David A. Case (Thu Sep 27 2007 - 08:45:38 PDT)
AMBER: needing more detailed knowledge of tautp than the manual 宫维斌 (Thu Sep 27 2007 - 05:13:20 PDT)
- Re: AMBER: needing more detailed knowledge of tautp than the manual David A. Case (Thu Sep 27 2007 - 08:49:37 PDT)
AMBER: plotdat: Amber Data Plotting Program S. Ravichandran (Thu Sep 27 2007 - 07:33:37 PDT)
AMBER: restarting REMD simulations Austin B. Yongye (Thu Sep 27 2007 - 07:21:43 PDT)
- Re: AMBER: restarting REMD simulations Carlos Simmerling (Thu Sep 27 2007 - 09:48:45 PDT)
AMBER: step-by-ste weight changes of dwt -- patch? Douglas Kojetin (Thu Sep 27 2007 - 08:35:01 PDT)
- Re: AMBER: step-by-ste weight changes of dwt -- patch? David A. Case (Thu Sep 27 2007 - 12:04:20 PDT)
回复:Re: AMBER: needing more detailed knowledge of tautp than the manual 宫维斌 (Thu Sep 27 2007 - 19:07:09 PDT)
AMBER: implicit minimization Dr. Devanathan Raghunathan (Thu Sep 27 2007 - 19:21:14 PDT)
- Re: AMBER: implicit minimization David A. Case (Fri Sep 28 2007 - 08:17:16 PDT)
AMBER: the box vectors for a Leap generated truncated octahedron Vlad Cojocaru (Fri Sep 28 2007 - 01:48:33 PDT)
AMBER: cyclohexane and decalin on amber Jones de Andrade (Sat Sep 29 2007 - 08:26:02 PDT)
- Re: AMBER: cyclohexane and decalin on amber FyD (Sun Sep 30 2007 - 00:20:29 PDT)
  - Re: AMBER: cyclohexane and decalin on amber Jones de Andrade (Sun Sep 30 2007 - 22:46:44 PDT)
    - Re: AMBER: cyclohexane and decalin on amber FyD (Mon Oct 01 2007 - 00:20:29 PDT)
    - Re: AMBER: cyclohexane and decalin on amber Jones de Andrade (Tue Oct 02 2007 - 20:12:48 PDT)
AMBER: fragment parametrization tutorial? Miguel Ortiz-Lombardía (Sat Sep 29 2007 - 11:53:05 PDT)
- Re: AMBER: fragment parametrization tutorial? Carlos Simmerling (Sat Sep 29 2007 - 14:48:30 PDT)
  - Re: AMBER: fragment parametrization tutorial? David A. Case (Sat Sep 29 2007 - 22:04:16 PDT)
    - Re: AMBER: fragment parametrization tutorial? FyD (Sun Sep 30 2007 - 00:12:41 PDT)
    - Re: AMBER: fragment parametrization tutorial? Miguel Ortiz-Lombardía (Sun Sep 30 2007 - 03:37:56 PDT)
AMBER: regarding non bonded energy caculations gurpreet singh (Sun Sep 30 2007 - 22:41:47 PDT)
- Re: AMBER: regarding non bonded energy caculations David A. Case (Mon Oct 01 2007 - 07:46:00 PDT)
AMBER: atomicfluct Andres Palencia (Mon Oct 01 2007 - 11:12:20 PDT)
AMBER: dihedrals Ed Pate (Mon Oct 01 2007 - 16:07:47 PDT)
- Re: AMBER: dihedrals FyD (Mon Oct 01 2007 - 23:36:30 PDT)
- Re: AMBER: dihedrals Carlos Simmerling (Tue Oct 02 2007 - 03:13:12 PDT)
AMBER: constant pH Eddie Men (Tue Oct 02 2007 - 02:45:34 PDT)
AMBER: Constant pH Eddie Men (Tue Oct 02 2007 - 02:41:31 PDT)
AMBER: multichain simulations priya priya (Tue Oct 02 2007 - 02:31:26 PDT)
AMBER: Problems with cpin file Eddie Men (Tue Oct 02 2007 - 05:47:50 PDT)
- Re: AMBER: Problems with cpin file David A. Case (Tue Oct 02 2007 - 08:16:45 PDT)
  - Re: AMBER: Problems with cpin file Eddie Men (Wed Oct 03 2007 - 22:07:11 PDT)
  - Re: AMBER: Problems with cpin file Eddie Men (Thu Oct 04 2007 - 13:46:22 PDT)
    - Re: AMBER: Problems with cpin file Eduardo Mendez (Thu Oct 04 2007 - 14:11:06 PDT)
AMBER: parameterization for copper Syed Tarique Moin (Wed Oct 03 2007 - 03:45:33 PDT)
AMBER: 31 integers in the first section of a prmtop file David Cerutti (Wed Oct 03 2007 - 09:58:03 PDT)
- Re: AMBER: 31 integers in the first section of a prmtop file Carlos Simmerling (Wed Oct 03 2007 - 10:15:14 PDT)
- RE: AMBER: 31 integers in the first section of a prmtop file Ross Walker (Wed Oct 03 2007 - 10:32:12 PDT)
  - RE: AMBER: 31 integers in the first section of a prmtop file David Cerutti (Wed Oct 03 2007 - 11:47:42 PDT)
    - Re: AMBER: 31 integers in the first section of a prmtop file Carlos Simmerling (Wed Oct 03 2007 - 11:54:22 PDT)
    - Re: AMBER: 31 integers in the first section of a prmtop file David Cerutti (Wed Oct 03 2007 - 13:04:35 PDT)
AMBER: PBSA generate snapshots saccenti.cerm.unifi.it (Thu Oct 04 2007 - 02:17:04 PDT)
AMBER: multi chain simulations priya priya (Thu Oct 04 2007 - 03:30:27 PDT)
- Re: AMBER: multi chain simulations Carlos Simmerling (Thu Oct 04 2007 - 03:35:22 PDT)
  - Re: AMBER: multi chain simulations priya priya (Thu Oct 04 2007 - 04:07:44 PDT)
    - Re: AMBER: multi chain simulations Carlos Simmerling (Thu Oct 04 2007 - 04:28:46 PDT)
    - Re: AMBER: multi chain simulations priya priya (Thu Oct 04 2007 - 05:44:56 PDT)
    - Re: AMBER: multi chain simulations Carlos Simmerling (Thu Oct 04 2007 - 12:43:44 PDT)
AMBER: binary restart file Myunggi Yi (Thu Oct 04 2007 - 07:49:28 PDT)
- Re: AMBER: binary restart file Gustavo Seabra (Fri Oct 05 2007 - 20:56:02 PDT)
  - Re: AMBER: binary restart file Myunggi Yi (Sun Oct 07 2007 - 16:39:44 PDT)
AMBER: Problems with 'make' Hopkins, Robert (Thu Oct 04 2007 - 12:07:42 PDT)
- RE: AMBER: Problems with 'make' Ross Walker (Thu Oct 04 2007 - 13:55:25 PDT)
  - RE: AMBER: Problems with 'make' Hopkins, Robert (Fri Oct 05 2007 - 11:32:24 PDT)
    - RE: AMBER: Problems with 'make' Ross Walker (Fri Oct 05 2007 - 13:14:20 PDT)
AMBER: Applying bugfixes in Amber Lili Peng (Thu Oct 04 2007 - 14:28:29 PDT)
- RE: AMBER: Applying bugfixes in Amber Ross Walker (Thu Oct 04 2007 - 14:53:31 PDT)
AMBER: generating topology files for PBSA saccenti.cerm.unifi.it (Fri Oct 05 2007 - 02:46:14 PDT)
AMBER: PMEMD configuration and scaling Lars.Skjarven.biomed.uib.no (Sat Oct 06 2007 - 04:35:03 PDT)
- Re: AMBER: PMEMD configuration and scaling Robert Duke (Sat Oct 06 2007 - 06:20:16 PDT)
- RE: AMBER: PMEMD configuration and scaling Ross Walker (Sat Oct 06 2007 - 09:27:16 PDT)
AMBER: request for hardware recommendations Parish, Carol (Sat Oct 06 2007 - 08:59:01 PDT)
- Re: AMBER: request for hardware recommendations Carlos Simmerling (Sat Oct 06 2007 - 10:00:13 PDT)
  - RE: AMBER: request for hardware recommendations Parish, Carol (Sat Oct 06 2007 - 10:20:13 PDT)
    - RE: AMBER: request for hardware recommendations Ross Walker (Sat Oct 06 2007 - 18:45:14 PDT)
    - AMBER: PB Bomb Eddie Men (Sun Oct 07 2007 - 00:10:59 PDT)
    - Re: AMBER: PB Bomb Eddie Men (Sun Oct 07 2007 - 01:03:52 PDT)
    - AMBER: Transformation table Rajendra P. OJHA (Sun Oct 07 2007 - 03:12:37 PDT)
  - Re: AMBER: request for hardware recommendations Andy Purkiss (Sat Oct 06 2007 - 10:53:23 PDT)
AMBER: hey Eduardo Mendez (Sat Oct 06 2007 - 22:19:36 PDT)
AMBER: PMEMD configuration and scaling Lars.Skjarven.biomed.uib.no (Sun Oct 07 2007 - 03:40:00 PDT)
- Re: AMBER: PMEMD configuration and scaling Robert Duke (Sun Oct 07 2007 - 08:04:03 PDT)
AMBER: Resp: "Statistics of the Fitting" Jones de Andrade (Sun Oct 07 2007 - 11:40:04 PDT)
- Re: AMBER: Resp: "Statistics of the Fitting" FyD (Tue Oct 09 2007 - 21:53:05 PDT)
  - Re: AMBER: Resp: "Statistics of the Fitting" Jones de Andrade (Wed Oct 10 2007 - 09:05:09 PDT)
AMBER: regrading interaction energy calculations gurpreet singh (Sun Oct 07 2007 - 21:52:23 PDT)
AMBER: Problems compiling Amber9 on IBM-AIX Sampath Koppole (Mon Oct 08 2007 - 04:42:20 PDT)
- RE: AMBER: Problems compiling Amber9 on IBM-AIX Ross Walker (Mon Oct 08 2007 - 07:39:08 PDT)
AMBER: entropy with ptraj Marius Retegan (Mon Oct 08 2007 - 05:24:36 PDT)
- Re: AMBER: entropy with ptraj David A. Case (Mon Oct 08 2007 - 06:47:57 PDT)
AMBER: adding extra points to amber - how to? Jones de Andrade (Mon Oct 08 2007 - 09:44:42 PDT)
AMBER: RE: Amber query !! Ross Walker (Mon Oct 08 2007 - 10:02:36 PDT)
AMBER: Amber9 installation error on Mandriva 2007 linux Joe Nolan (Mon Oct 08 2007 - 10:07:58 PDT)
- Re: AMBER: Amber9 installation error on Mandriva 2007 linux Mark Williamson (Mon Oct 08 2007 - 10:31:39 PDT)
AMBER: Quick QUESTION Eddie Men (Mon Oct 08 2007 - 21:23:49 PDT)
- Re: AMBER: Quick QUESTION Eddie Men (Mon Oct 08 2007 - 22:02:10 PDT)
AMBER: Heat capacity, diffusivity way off in this simulation of SPC/E water? David Cerutti (Mon Oct 08 2007 - 22:25:43 PDT)
- Re: AMBER: Heat capacity, diffusivity way off in this simulation of SPC/E water? Steven Winfield (Tue Oct 09 2007 - 03:06:53 PDT)
- Re: AMBER: Heat capacity, diffusivity way off in this simulation of SPC/E water? David A. Case (Tue Oct 09 2007 - 07:09:02 PDT)
AMBER: PMEMD configuration and scaling Lars.Skjarven.biomed.uib.no (Tue Oct 09 2007 - 03:05:37 PDT)
- Re: AMBER: PMEMD configuration and scaling Robert Duke (Tue Oct 09 2007 - 06:15:34 PDT)
  - Re: AMBER: PMEMD configuration and scaling Lars Skjærven (Tue Oct 09 2007 - 06:56:09 PDT)
AMBER: RE: antechamber Ross Walker (Tue Oct 09 2007 - 09:51:57 PDT)
AMBER: interaction energy calculations gurpreet singh (Tue Oct 09 2007 - 10:06:24 PDT)
- Re: AMBER: interaction energy calculations Scott Pendley (Tue Oct 09 2007 - 13:51:25 PDT)
AMBER: neb for path between binding sites Holly Freedman (Tue Oct 09 2007 - 14:09:50 PDT)
- Re: AMBER: neb for path between binding sites Carlos Simmerling (Tue Oct 09 2007 - 14:25:27 PDT)
- Re: AMBER: neb for path between binding sites Holly Freedman (Tue Oct 09 2007 - 16:37:20 PDT)
- Re: AMBER: neb for path between binding sites Holly Freedman (Tue Oct 09 2007 - 16:35:19 PDT)
AMBER: Thermodynamic Integration with Explicit Solvent Scott Pendley (Tue Oct 09 2007 - 14:38:03 PDT)
- Re: AMBER: Thermodynamic Integration with Explicit Solvent Thomas Steinbrecher (Tue Oct 09 2007 - 17:12:13 PDT)
  - Re: AMBER: Thermodynamic Integration with Explicit Solvent Scott Pendley (Tue Oct 09 2007 - 18:09:14 PDT)
- Re: AMBER: Thermodynamic Integration with Explicit Solvent David A. Case (Tue Oct 09 2007 - 19:36:38 PDT)
  - Re: AMBER: Thermodynamic Integration with Explicit Solvent Scott Pendley (Wed Oct 10 2007 - 15:39:12 PDT)
- Re: AMBER: Thermodynamic Integration with Explicit Solvent Scott Pendley (Wed Oct 10 2007 - 15:38:20 PDT)
AMBER: error in modified PNA -DNA simulation.. Sharad gupta (Wed Oct 10 2007 - 03:39:07 PDT)
- Re: AMBER: error in modified PNA -DNA simulation.. Scott Brozell (Thu Oct 11 2007 - 17:26:11 PDT)
AMBER: ff99SB and the N- and C- charged terminal residues Nicolas Lux Fawzi (Wed Oct 10 2007 - 09:03:09 PDT)
- Re: AMBER: ff99SB and the N- and C- charged terminal residues Carlos Simmerling (Wed Oct 10 2007 - 10:37:13 PDT)
AMBER: Error- MM_PBSA calculation vikky 99 (Wed Oct 10 2007 - 10:44:53 PDT)
AMBER: constant-pH MD with replica exchange Maciej Dlugosz (Wed Oct 10 2007 - 23:38:49 PDT)
- Re: AMBER: constant-pH MD with replica exchange Adrian Roitberg (Thu Oct 11 2007 - 08:33:30 PDT)
  - Re: AMBER: constant-pH MD with replica exchange Carlos Simmerling (Thu Oct 11 2007 - 11:30:34 PDT)
    - Re: AMBER: constant-pH MD with replica exchange Adrian Roitberg (Thu Oct 11 2007 - 11:55:18 PDT)
AMBER: Error- MM_PBSA calculation vikky 99 (Thu Oct 11 2007 - 00:28:25 PDT)
AMBER: BOMB! Eddie Men (Thu Oct 11 2007 - 03:12:49 PDT)
- Re: AMBER: BOMB! Scott Brozell (Thu Oct 11 2007 - 16:59:50 PDT)
AMBER: lipid bilayer san_amber roy (Thu Oct 11 2007 - 04:52:42 PDT)
- Re: AMBER: lipid bilayer Vlad Cojocaru (Thu Oct 11 2007 - 05:09:23 PDT)
- Re: AMBER: lipid bilayer cgji (Thu Oct 11 2007 - 07:38:45 PDT)
AMBER: Error- MM_PBSA calculation vikky 99 (Thu Oct 11 2007 - 08:01:23 PDT)
- Re: AMBER: Error- MM_PBSA calculation Scott Pendley (Thu Oct 11 2007 - 14:56:43 PDT)
AMBER: Missing 'yacc' command Hopkins, Robert (Sat Oct 13 2007 - 15:00:00 PDT)
AMBER: Please Disregard My Last E-mail: Missing 'yacc' command Hopkins, Robert (Sat Oct 13 2007 - 16:04:11 PDT)
AMBER: error in modified PNA DNA simulation Sharad gupta (Sun Oct 14 2007 - 22:35:13 PDT)
AMBER: anal calculatons gurpreet singh (Mon Oct 15 2007 - 00:19:33 PDT)
- Re: AMBER: anal calculatons Eddie Men (Mon Oct 15 2007 - 00:43:02 PDT)
  - Re: AMBER: anal calculatons gurpreet singh (Mon Oct 15 2007 - 21:17:47 PDT)
- Re: Re: AMBER: anal calculatons cgji (Mon Oct 15 2007 - 22:48:09 PDT)
AMBER: RED III Age.Skjevik.student.uib.no (Mon Oct 15 2007 - 03:06:49 PDT)
- Re: AMBER: RED III FyD (Mon Oct 15 2007 - 03:20:47 PDT)
AMBER: using amber for cyclic peptides rebeca.mmb.pcb.ub.es (Mon Oct 15 2007 - 10:23:50 PDT)
- Re: AMBER: using amber for cyclic peptides FyD (Mon Oct 15 2007 - 10:53:54 PDT)
AMBER: Water cap MD error Rima Chaudhuri (Mon Oct 15 2007 - 15:17:07 PDT)
AMBER: MM_PBSA calcultion- help me varsha rani (Mon Oct 15 2007 - 22:53:14 PDT)
- Re: AMBER: MM_PBSA calcultion- help me S.Sundar Raman (Tue Oct 16 2007 - 06:58:50 PDT)
- Re: AMBER: MM_PBSA calcultion- help me Scott Pendley (Tue Oct 16 2007 - 10:24:34 PDT)
  - Re: AMBER: MM_PBSA calcultion- help me varsha rani (Tue Oct 16 2007 - 22:40:48 PDT)
    - AMBER: How to intergrate the area under a curve. Catein Catherine (Sun Oct 21 2007 - 23:34:16 PDT)
    - Re: AMBER: How to intergrate the area under a curve. Ilyas Yildirim (Mon Oct 22 2007 - 00:17:07 PDT)
AMBER: Test fails in Parallel version Amber9 gong wb (Mon Oct 15 2007 - 23:42:45 PDT)
- Re: AMBER: Test fails in Parallel version Amber9 Scott Brozell (Tue Oct 16 2007 - 11:35:24 PDT)
  - Re: AMBER: Test fails in Parallel version Amber9 gong wb (Wed Oct 17 2007 - 00:54:30 PDT)
  - Re: AMBER: Test fails in Parallel version Amber9 gong wb (Wed Oct 17 2007 - 01:04:13 PDT)
    - Re: AMBER: Test fails in Parallel version Amber9 gong wb (Thu Oct 18 2007 - 19:00:44 PDT)
    - RE: AMBER: Test fails in Parallel version Amber9 Ross Walker (Fri Oct 19 2007 - 07:24:47 PDT)
    - Re: AMBER: Test fails in Parallel version Amber9 gong wb (Sun Oct 21 2007 - 23:52:48 PDT)
    - Re: AMBER: Test fails in Parallel version Amber9 gong wb (Tue Oct 23 2007 - 18:37:20 PDT)
    - AMBER: An enquiry about "Dynamics of ligand escape from the heme pocket of myoglobin (JACS, 1988, 110, 7690 Catein Catherine (Wed Oct 24 2007 - 05:04:42 PDT)
    - Re: AMBER: An enquiry about "Dynamics of ligand escape from the heme pocket of myoglobin (JACS, 1988, 110, 7690 David Mobley (Wed Oct 24 2007 - 07:20:43 PDT)
    - Re: AMBER: An enquiry about "Dynamics of ligand escape from the heme pocket of myoglobin (JACS, 1988, 110, 7690 David A. Case (Wed Dec 26 2007 - 09:52:20 PST)
AMBER: amber9 installation problem Madjid Taghdir (Tue Oct 16 2007 - 01:46:05 PDT)
- Re: AMBER: amber9 installation problem Scott Brozell (Tue Oct 16 2007 - 10:15:04 PDT)
- Re: AMBER: amber9 installation problem Madjid Taghdir (Mon Nov 12 2007 - 00:38:57 PST)
AMBER: anal calculation error gurpreet singh (Tue Oct 16 2007 - 10:07:20 PDT)
AMBER: AMBER 9 - Force Field Options - Question dpandit.brandeis.edu (Tue Oct 16 2007 - 13:41:33 PDT)
- Re: AMBER: AMBER 9 - Force Field Options - Question Carlos Simmerling (Wed Oct 17 2007 - 06:54:51 PDT)
  - Re: AMBER: AMBER 9 - Force Field Options - Question dpandit.brandeis.edu (Wed Oct 17 2007 - 08:27:12 PDT)
  - AMBER: Polarizable Force Field: Ligand Parameterization et al. Anselm Horn (Thu Oct 25 2007 - 02:00:03 PDT)
    - RE: AMBER: Polarizable Force Field: Ligand Parameterization et al. Yong Duan (Thu Oct 25 2007 - 10:02:55 PDT)
    - RE: AMBER: Polarizable Force Field: Ligand Parameterization et al. Catein Catherine (Fri Oct 26 2007 - 00:17:16 PDT)
    - AMBER: How to calculate the time-dependent transmission coefficient for rate constant esimation from PMF ca Catein Catherine (Fri Oct 26 2007 - 00:28:57 PDT)
- Re: AMBER: AMBER 9 - Force Field Options - Question WANG,YING (Wed Oct 17 2007 - 08:47:05 PDT)
  - RE: AMBER: AMBER 9 - Force Field Options - Question Yong Duan (Wed Oct 17 2007 - 09:25:16 PDT)
    - Re: AMBER: AMBER 9 - Force Field Options - Question Adrian Roitberg (Wed Oct 17 2007 - 11:26:56 PDT)
    - RE: AMBER: AMBER 9 - Force Field Options - Question Yong Duan (Wed Oct 17 2007 - 13:47:55 PDT)
    - Re: AMBER: AMBER 9 - Force Field Options - Question Carlos Simmerling (Thu Oct 18 2007 - 03:06:44 PDT)
    - RE: AMBER: AMBER 9 - Force Field Options - Question Yong Duan (Thu Oct 18 2007 - 09:21:00 PDT)
    - Re: AMBER: AMBER 9 - Force Field Options - Question Adrian Roitberg (Thu Oct 18 2007 - 11:56:23 PDT)
    - RE: AMBER: AMBER 9 - Force Field Options - Question Yong Duan (Thu Oct 18 2007 - 12:18:01 PDT)
- RE: AMBER: AMBER 9 - Force Field Options - Question WANG,YING (Wed Oct 17 2007 - 12:11:19 PDT)
- Re: Re: AMBER: AMBER 9 - Force Field Options - Question cgji (Mon Nov 05 2007 - 09:19:58 PST)
  - Re: Re: AMBER: AMBER 9 - Force Field Options - Question Carlos Simmerling (Mon Nov 05 2007 - 09:39:01 PST)
AMBER: anal error gurpreet singh (Wed Oct 17 2007 - 11:14:52 PDT)
AMBER: error while Running TMD gurpreet singh (Wed Oct 17 2007 - 11:21:18 PDT)
- Re: AMBER: error while Running TMD Carlos Simmerling (Wed Oct 17 2007 - 11:50:45 PDT)
  - Re: AMBER: error while Running TMD gurpreet singh (Wed Oct 17 2007 - 21:19:54 PDT)
    - Re: AMBER: error while Running TMD Carlos Simmerling (Thu Oct 18 2007 - 03:01:07 PDT)
AMBER: Temperature fluctuation in NPT and NVE ensemble Lei Jia (Wed Oct 17 2007 - 16:46:29 PDT)
- Re: AMBER: Temperature fluctuation in NPT and NVE ensemble Robert Duke (Wed Oct 17 2007 - 18:44:47 PDT)
AMBER: anal gurpreet singh (Wed Oct 17 2007 - 21:35:23 PDT)
AMBER: how to simulate a ligand bound to a residue Jena M (Thu Oct 18 2007 - 06:49:55 PDT)
- Re: AMBER: how to simulate a ligand bound to a residue Thomas Steinbrecher (Thu Oct 18 2007 - 11:29:25 PDT)
- Re: AMBER: how to simulate a ligand bound to a residue FyD (Thu Oct 18 2007 - 14:02:13 PDT)
AMBER: Simulation died due to lack of disk space Samantha Kaye (Thu Oct 18 2007 - 06:57:57 PDT)
- RE: AMBER: Simulation died due to lack of disk space Ross Walker (Thu Oct 18 2007 - 07:53:50 PDT)
- RE: AMBER: Simulation died due to lack of disk space Bill Ross (Thu Oct 18 2007 - 12:00:33 PDT)
  - AMBER: Energy calculations. Karen Callahan (Thu Oct 18 2007 - 12:15:29 PDT)
  - Re: AMBER: Simulation died due to lack of disk space Samantha Kaye (Fri Oct 19 2007 - 02:23:33 PDT)
    - RE: AMBER: Simulation died due to lack of disk space Ross Walker (Fri Oct 19 2007 - 09:25:20 PDT)
- Re: AMBER: Simulation died due to lack of disk space Bill Ross (Fri Oct 19 2007 - 08:59:31 PDT)
- Re: AMBER: Simulation died due to lack of disk space Robert Duke (Fri Oct 19 2007 - 10:25:21 PDT)
AMBER: Backbone flexibility/entropy Seth Lilavivat (Thu Oct 18 2007 - 14:47:37 PDT)
AMBER: FORTRAN code for calculating ENERGY of all the four terms (bonds, angles, dihedrals, nonbanded pairs) of Amber8's sander Jiapu.Zhang.csiro.au (Thu Oct 18 2007 - 16:15:05 PDT)
- Re: AMBER: FORTRAN code for calculating ENERGY of all the four terms (bonds, angles, dihedrals, nonbanded pairs) of Amber8's sander Thomas Steinbrecher (Thu Oct 18 2007 - 16:43:47 PDT)
AMBER: subroutine ephi !! Sampath Koppole (Fri Oct 19 2007 - 01:08:26 PDT)
- Re: AMBER: subroutine ephi !! Tom Darden (Fri Oct 19 2007 - 05:06:33 PDT)
AMBER: mm_pbsa: missing values in ras-raf tutorials merc mertens (Fri Oct 19 2007 - 01:28:09 PDT)
AMBER: Abnormality in MM-PBSA result msubhamoy.ibab.ac.in (Fri Oct 19 2007 - 08:01:16 PDT)
- Re: AMBER: Abnormality in MM-PBSA result Thomas Cheatham III (Fri Oct 19 2007 - 08:56:36 PDT)
AMBER: How to use loadpdbusingseq command to load branched structure? Siang Yip (Fri Oct 19 2007 - 10:21:36 PDT)
AMBER: question about h bond WANG,YING (Fri Oct 19 2007 - 17:19:36 PDT)
- RE: AMBER: question about h bond Yong Duan (Fri Oct 19 2007 - 17:41:19 PDT)
- RE: AMBER: question about h bond WANG,YING (Fri Oct 19 2007 - 21:07:49 PDT)
AMBER: Heat capacity calculations not coming out right David Cerutti (Fri Oct 19 2007 - 19:37:38 PDT)
- AMBER: Addendum: Heat capacity calculations not coming out right David Cerutti (Fri Oct 19 2007 - 20:31:46 PDT)
  - Re: AMBER: Addendum: Heat capacity calculations not coming out right Robert Duke (Fri Oct 19 2007 - 21:24:30 PDT)
    - Re: AMBER: Addendum: Heat capacity calculations not coming out right David Cerutti (Sat Oct 20 2007 - 15:47:05 PDT)
  - AMBER: Solved: Heat capacity calculations not coming out right David Cerutti (Mon Oct 22 2007 - 11:01:32 PDT)
AMBER: Interactive Molecular Dynamics with Amber? Marc Baaden (Sat Oct 20 2007 - 15:10:23 PDT)
AMBER: EVB Calculations Jimmy Heimdal (Sun Oct 21 2007 - 23:30:48 PDT)
AMBER: Problems loading pdb file including Mg ions Idan Gabdank (Mon Oct 22 2007 - 08:53:12 PDT)
- Re: AMBER: Problems loading pdb file including Mg ions Peter Varnai (Tue Oct 23 2007 - 03:38:53 PDT)
  - Re: AMBER: Problems loading pdb file including Mg ions Idan Gabdank (Wed Oct 24 2007 - 06:05:46 PDT)
- Re: AMBER: Problems loading pdb file including Mg ions Bill Ross (Wed Oct 24 2007 - 10:21:43 PDT)
AMBER: results from TI Holly Freedman (Mon Oct 22 2007 - 09:42:26 PDT)
- Re: AMBER: results from TI Thomas Steinbrecher (Mon Oct 22 2007 - 10:35:15 PDT)
- Re: AMBER: results from TI Holly Freedman (Mon Oct 22 2007 - 12:03:20 PDT)
  - Re: AMBER: results from TI David Mobley (Tue Oct 23 2007 - 06:40:26 PDT)
- Re: AMBER: results from TI Holly Freedman (Tue Oct 23 2007 - 09:57:42 PDT)
  - Re: AMBER: results from TI David Mobley (Tue Oct 23 2007 - 10:09:31 PDT)
    - Re: AMBER: results from TI Thomas Steinbrecher (Tue Oct 23 2007 - 11:07:30 PDT)
- Re: AMBER: results from TI Holly Freedman (Tue Oct 23 2007 - 13:29:00 PDT)
  - Re: AMBER: results from TI Thomas Steinbrecher (Tue Oct 23 2007 - 14:25:24 PDT)
    - Re: AMBER: results from TI David Mobley (Wed Oct 24 2007 - 07:18:50 PDT)
AMBER: SASA per residue Evan Kelly (Mon Oct 22 2007 - 09:59:26 PDT)
AMBER: question about charge of prmtop file WANG,YING (Tue Oct 23 2007 - 07:11:22 PDT)
- Re: AMBER: question about charge of prmtop file Thomas Steinbrecher (Tue Oct 23 2007 - 08:41:09 PDT)
- Re: AMBER: question about charge of prmtop file WANG,YING (Tue Oct 23 2007 - 09:08:15 PDT)
  - RE: AMBER: question about charge of prmtop file Steve Spronk (Wed Oct 24 2007 - 07:21:25 PDT)
- RE: AMBER: question about charge of prmtop file WANG,YING (Wed Oct 24 2007 - 07:44:20 PDT)
AMBER: Beowulf cluster from PSSC Labs Aaron Greenwood (Tue Oct 23 2007 - 09:22:33 PDT)
- RE: AMBER: Beowulf cluster from PSSC Labs Ross Walker (Tue Oct 23 2007 - 10:28:29 PDT)
AMBER: Portland Group vs. Intel Compilers. Aaron Greenwood (Tue Oct 23 2007 - 10:03:43 PDT)
- Re: AMBER: Portland Group vs. Intel Compilers. Alexandar T Tzanov (Tue Oct 23 2007 - 10:11:46 PDT)
  - RE: AMBER: Portland Group vs. Intel Compilers. Ross Walker (Tue Oct 23 2007 - 10:35:45 PDT)
    - Re: RE: AMBER: Portland Group vs. Intel Compilers. Alexandar T Tzanov (Tue Oct 23 2007 - 11:35:25 PDT)
    - RE: RE: AMBER: Portland Group vs. Intel Compilers. Ross Walker (Tue Oct 23 2007 - 12:02:42 PDT)
- Re: AMBER: Portland Group vs. Intel Compilers. Robert Duke (Tue Oct 23 2007 - 10:46:52 PDT)
- Re: AMBER: Portland Group vs. Intel Compilers. Andreas Svrcek-Seiler (Tue Oct 23 2007 - 13:24:29 PDT)
AMBER: prepin file format description; pointers on parameterization David Mobley (Wed Oct 24 2007 - 10:52:24 PDT)
- Re: AMBER: prepin file format description; pointers on parameterization FyD (Wed Oct 24 2007 - 12:09:09 PDT)
  - Re: AMBER: prepin file format description; pointers on parameterization David Mobley (Wed Oct 24 2007 - 12:31:02 PDT)
    - Re: AMBER: prepin file format description; pointers on parameterization FyD (Wed Oct 24 2007 - 13:13:37 PDT)
    - Re: AMBER: prepin file format description; pointers on parameterization David Mobley (Wed Oct 24 2007 - 13:45:54 PDT)
    - Re: AMBER: prepin file format description; pointers on parameterization David Mobley (Wed Oct 24 2007 - 16:58:35 PDT)
    - Re: AMBER: prepin file format description; pointers on parameterization David A. Case (Wed Oct 24 2007 - 17:27:39 PDT)
    - Re: AMBER: prepin file format description; pointers on parameterization David Mobley (Wed Oct 24 2007 - 17:58:45 PDT)
    - Re: AMBER: prepin file format description; pointers on parameterization FyD (Wed Oct 24 2007 - 22:27:33 PDT)
    - Re: AMBER: prepin file format description; pointers on parameterization FyD (Wed Oct 24 2007 - 23:54:33 PDT)
    - Re: AMBER: prepin file format description; pointers on parameterization David Mobley (Thu Oct 25 2007 - 13:41:06 PDT)
  - Re: AMBER: prepin file format description; pointers on parameterization David Mobley (Wed Oct 24 2007 - 16:35:26 PDT)
    - Re: AMBER: prepin file format description; pointers on parameterization FyD (Wed Oct 24 2007 - 22:14:32 PDT)
    - Re: AMBER: prepin file format description; pointers on parameterization David Mobley (Thu Oct 25 2007 - 13:39:08 PDT)
    - Re: AMBER: prepin file format description; pointers on parameterization FyD (Thu Oct 25 2007 - 23:40:46 PDT)
    - AMBER: Average absolute value of cross velocity (Rate constant from PMF) Catein Catherine (Fri Oct 26 2007 - 00:26:58 PDT)
    - Re: AMBER: Average absolute value of cross velocity (Rate constant from PMF) David A. Case (Fri Oct 26 2007 - 08:22:40 PDT)
- Re: AMBER: prepin file format description; pointers on parameterization FyD (Thu Oct 25 2007 - 06:15:52 PDT)
- Re: AMBER: prepin file format description; pointers on parameterization FyD (Fri Oct 26 2007 - 05:45:10 PDT)
  - AMBER: Umbrella sampling Jena M (Fri Oct 26 2007 - 06:48:26 PDT)
    - Re: AMBER: Umbrella sampling Adrian Roitberg (Fri Oct 26 2007 - 07:11:14 PDT)
    - Re: AMBER: Umbrella sampling Jerome.GOLEBIOWSKI.unice.fr (Fri Oct 26 2007 - 10:08:09 PDT)
AMBER: regarding anal calculations gurpreet singh (Wed Oct 24 2007 - 11:50:49 PDT)
AMBER: hbond analysis output Claire Zerafa (Wed Oct 24 2007 - 12:21:02 PDT)
- RE: AMBER: hbond analysis output Steve Spronk (Thu Oct 25 2007 - 06:10:05 PDT)
AMBER: Pre-requisites for AMBER software Anamika Awasthi (Thu Oct 25 2007 - 05:05:19 PDT)
AMBER: &dipole input and some questions on using polarizable force fields Seongeun Yang (Thu Oct 25 2007 - 06:11:48 PDT)
- RE: AMBER: &dipole input and some questions on using polarizable force fields Ross Walker (Fri Oct 26 2007 - 09:28:57 PDT)
- Re: AMBER: &dipole input and some questions on using polarizable force fields Seongeun Yang (Fri Oct 26 2007 - 22:03:36 PDT)
  - RE: AMBER: &dipole input and some questions on using polarizable force fields Ross Walker (Mon Oct 29 2007 - 08:31:00 PDT)
- Re: AMBER: &dipole input and some questions on using polarizable force fields Seongeun Yang (Mon Oct 29 2007 - 23:14:13 PDT)
  - Re: AMBER: &dipole input and some questions on using polarizable force fields David A. Case (Tue Oct 30 2007 - 06:42:44 PDT)
- Re: AMBER: &dipole input and some questions on using polarizable force fields Seongeun Yang (Tue Oct 30 2007 - 08:19:32 PDT)
  - Re: AMBER: &dipole input and some questions on using polarizable force fields David A. Case (Tue Oct 30 2007 - 08:58:20 PDT)
- Re: AMBER: &dipole input and some questions on using polarizable force fields Seongeun Yang (Tue Oct 30 2007 - 20:52:45 PDT)
  - AMBER: Question about ptraj matrix correl command Catein Catherine (Wed Oct 31 2007 - 00:18:55 PDT)
  - Re: AMBER: &dipole input and some questions on using polarizable force fields David A. Case (Wed Oct 31 2007 - 07:38:34 PDT)
AMBER: problems compiling amber on mac OSX francesco zonta (Thu Oct 25 2007 - 06:50:04 PDT)
- Re: AMBER: problems compiling amber on mac OSX David A. Case (Fri Oct 26 2007 - 08:48:35 PDT)
- Re: AMBER: problems compiling amber on mac OSX Mengjuei Hsieh (Sat Oct 27 2007 - 02:31:04 PDT)
  - Re: AMBER: problems compiling amber on mac OSX francesco zonta (Sat Oct 27 2007 - 05:03:51 PDT)
    - Re: AMBER: problems compiling amber on mac OSX Mengjuei Hsieh (Sat Oct 27 2007 - 12:41:26 PDT)
AMBER: Including crystal water when using united-atom forcefield leaprc.ff03ua Yang, Lee-Wei (Thu Oct 25 2007 - 07:46:00 PDT)
- RE: AMBER: Including crystal water when using united-atom forcefield leaprc.ff03ua Ray Luo (Thu Oct 25 2007 - 11:20:14 PDT)
  - RE: AMBER: Including crystal water when using united-atom forcefield leaprc.ff03ua Yang, Lee-Wei (Thu Oct 25 2007 - 22:52:56 PDT)
    - Re: AMBER: Including crystal water when using united-atom forcefield leaprc.ff03ua Ray Luo (Fri Oct 26 2007 - 10:31:03 PDT)
AMBER: ANGVE/TORAVE Abi Ghanem josephine (Thu Oct 25 2007 - 08:58:11 PDT)
- Re: AMBER: ANGVE/TORAVE Kyle Brown (Thu Oct 25 2007 - 11:33:52 PDT)
AMBER: HG atoms in CYX residues francesco zonta (Fri Oct 26 2007 - 02:45:32 PDT)
- Re: AMBER: HG atoms in CYX residues Carlos Simmerling (Fri Oct 26 2007 - 03:20:05 PDT)
- Re: AMBER: HG atoms in CYX residues David A. Case (Fri Oct 26 2007 - 08:28:36 PDT)
AMBER: Heme and CYS !! Pradipta Bandyopadhyay (Fri Oct 26 2007 - 03:49:47 PDT)
AMBER: segmentation fault occured doing MD priya priya (Fri Oct 26 2007 - 04:51:31 PDT)
- Re: AMBER: segmentation fault occured doing MD David A. Case (Fri Oct 26 2007 - 08:32:07 PDT)
AMBER: RE: about deoxy- and oxy- heme Yang, Lee-Wei (Sun Oct 28 2007 - 01:52:58 PDT)
AMBER: How can i calculate generalized order parameters using ptraj. cgji (Sun Oct 28 2007 - 07:59:37 PDT)
- Re: AMBER: How can i calculate generalized order parameters using ptraj. David A. Case (Thu Nov 08 2007 - 18:23:34 PST)
AMBER: replica exchange Geoff Wood (Sun Oct 28 2007 - 09:29:42 PDT)
- Re: AMBER: replica exchange Carlos Simmerling (Sun Oct 28 2007 - 09:38:15 PDT)
- Re: AMBER: replica exchange Robert Duke (Sun Oct 28 2007 - 09:38:04 PDT)
AMBER: Amber FF parameters for the Zinc-hydroxammate interaction snoze pa (Sun Oct 28 2007 - 17:59:26 PDT)
AMBER: calculation of angle between helices Anupam Nath Jha (Sun Oct 28 2007 - 23:06:37 PDT)
AMBER: The number of the path atoms exceeds MAXPATHATOMNUM VANIA MARIA AMARO CALISTO (Mon Oct 29 2007 - 05:13:01 PDT)
AMBER: RED-vIII fails Jesper Soerensen (Mon Oct 29 2007 - 07:51:56 PDT)
- Re: AMBER: RED-vIII fails FyD (Mon Oct 29 2007 - 09:25:09 PDT)
  - Re: AMBER: RED-vIII fails Jesper Soerensen (Tue Oct 30 2007 - 02:16:36 PDT)
    - Re: AMBER: RED-vIII fails FyD (Tue Oct 30 2007 - 14:38:03 PDT)
    - Re: AMBER: RED-vIII fails Jesper Soerensen (Mon Nov 05 2007 - 08:01:21 PST)
    - Re: AMBER: RED-vIII fails FyD (Mon Nov 05 2007 - 10:27:33 PST)
AMBER: Getting prmtop and inpcrd Francesco Pietra (Mon Oct 29 2007 - 08:43:44 PDT)
- Re: AMBER: Getting prmtop and inpcrd Carlos Simmerling (Mon Oct 29 2007 - 08:47:33 PDT)
  - Re: AMBER: Getting prmtop and inpcrd Francesco Pietra (Mon Oct 29 2007 - 09:51:23 PDT)
AMBER: amber with periodic condition Mattia Mori - CERM (Mon Oct 29 2007 - 10:16:14 PDT)
Re: AMBER: Getting prmtop and inpcrd Bill Ross (Mon Oct 29 2007 - 12:26:16 PDT)
AMBER: mdfil: Error unknown flag: -p4pg Aaron Greenwood (Mon Oct 29 2007 - 12:38:44 PDT)
- Re: AMBER: mdfil: Error unknown flag: -p4pg David A. Case (Mon Oct 29 2007 - 19:46:01 PDT)
  - Re: AMBER: mdfil: Error unknown flag: -p4pg Aaron Greenwood (Tue Oct 30 2007 - 05:03:29 PDT)
AMBER: AMBER 8: QMMM - molecule fluctuates wildly Seth Lilavivat (Mon Oct 29 2007 - 13:40:06 PDT)
- RE: AMBER: AMBER 8: QMMM - molecule fluctuates wildly Ross Walker (Mon Oct 29 2007 - 14:06:45 PDT)
AMBER: Amber9 parallel installation error (with openMPI) Joe Nolan (Mon Oct 29 2007 - 14:02:10 PDT)
- Re: AMBER: Amber9 parallel installation error (with openMPI) Wei Zhang (Mon Oct 29 2007 - 14:16:45 PDT)
  - Re: AMBER: Amber9 parallel installation error (with openMPI) Joe Nolan (Mon Oct 29 2007 - 14:55:43 PDT)
    - Re: AMBER: Amber9 parallel installation error (with openMPI) Wei Zhang (Mon Oct 29 2007 - 15:16:49 PDT)
    - Re: AMBER: Amber9 parallel installation error (with openMPI) Joe Nolan (Mon Oct 29 2007 - 15:30:25 PDT)
AMBER: Amber 9 source code permissions (UNCLASSIFIED) Monaghan, Martin (Cont, ARL/CISD) (Mon Oct 29 2007 - 14:30:30 PDT)
- RE: AMBER: Amber 9 source code permissions (UNCLASSIFIED) Ross Walker (Mon Oct 29 2007 - 16:18:50 PDT)
AMBER: anal problem varsha rani (Tue Oct 30 2007 - 04:48:03 PDT)
AMBER: Amber9 parallel installation error (retry) Joe Nolan (Tue Oct 30 2007 - 11:25:35 PDT)
AMBER: antechamber fails with large molecules VANIA MARIA AMARO CALISTO (Wed Oct 31 2007 - 02:26:14 PDT)
- Re: AMBER: antechamber fails with large molecules FyD (Wed Oct 31 2007 - 07:02:36 PDT)
- Re: AMBER: antechamber fails with large molecules Junmei Wang (Wed Oct 31 2007 - 21:43:49 PDT)
  - Re: AMBER: antechamber fails with large molecules Francesco Pietra (Thu Nov 01 2007 - 01:29:26 PDT)
- Re: AMBER: antechamber fails with large molecules Junmei Wang (Thu Nov 01 2007 - 23:16:41 PDT)
  - Re: AMBER: antechamber fails with large molecules Ilyas Yildirim (Fri Nov 02 2007 - 01:24:26 PDT)
    - Re: AMBER: antechamber fails with large molecules Eddie Men (Fri Nov 02 2007 - 01:50:57 PDT)
    - Re: AMBER: antechamber fails with large molecules Ilyas Yildirim (Fri Nov 02 2007 - 02:10:33 PDT)
    - Re: AMBER: antechamber fails with large molecules Francesco Pietra (Fri Nov 02 2007 - 10:07:52 PDT)
    - Re: AMBER: antechamber fails with large molecules Ilyas Yildirim (Sat Nov 03 2007 - 01:38:03 PDT)
    - Re: AMBER: antechamber fails with large molecules Francesco Pietra (Sat Nov 03 2007 - 07:01:41 PDT)
    - Re: AMBER: antechamber fails with large molecules Ilyas Yildirim (Sat Nov 03 2007 - 09:47:49 PDT)
    - Re: AMBER: antechamber fails with large molecules FyD (Sun Nov 04 2007 - 04:29:09 PST)
AMBER: problems visualizing mdcrd in VMD Mattia Mori - CERM (Wed Oct 31 2007 - 04:17:21 PDT)
- Re: AMBER: problems visualizing mdcrd in VMD Vlad Cojocaru (Wed Oct 31 2007 - 04:33:37 PDT)
- Re: AMBER: problems visualizing mdcrd in VMD Vlad Cojocaru (Wed Oct 31 2007 - 05:41:42 PDT)
  - Re: AMBER: problems visualizing mdcrd in VMD Mattia Mori - CERM (Wed Oct 31 2007 - 05:59:24 PDT)
AMBER: gibbs problems JAVIER PEREZ (Wed Oct 31 2007 - 04:48:22 PDT)
- Re: AMBER: gibbs problems David A. Case (Wed Oct 31 2007 - 21:09:35 PDT)
AMBER: amber9 parallel compile problem Christopher Jones (Wed Oct 31 2007 - 10:09:32 PDT)
- RE: AMBER: amber9 parallel compile problem Ross Walker (Wed Oct 31 2007 - 10:36:00 PDT)
AMBER: Amber 9: Generating Input files for EVB simulations of the crosslinked structures (Hydrogels) sanket deshmukh (Wed Oct 31 2007 - 11:57:54 PDT)
- Re: AMBER: Amber 9: Generating Input files for EVB simulations of the crosslinked structures (Hydrogels) David A. Case (Wed Oct 31 2007 - 14:52:18 PDT)
  - Re: AMBER: Amber 9: Generating Input files for EVB simulations of the crosslinked structures (Hydrogels) sanket deshmukh (Thu Nov 08 2007 - 11:29:35 PST)
    - Re: AMBER: Amber 9: Generating Input files for EVB simulations of the crosslinked structures (Hydrogels) David A. Case (Thu Nov 08 2007 - 12:16:57 PST)
    - Re: AMBER: Amber 9: Generating Input files for EVB simulations of the crosslinked structures (Hydrogels) sanket deshmukh (Fri Nov 23 2007 - 15:30:11 PST)
    - AMBER: antechamber problem David A. Case (Fri Nov 23 2007 - 18:40:21 PST)
AMBER: &dipoles output in QM/MM simulations Seongeun Yang (Thu Nov 01 2007 - 03:43:54 PDT)
- RE: AMBER: &dipoles output in QM/MM simulations Ross Walker (Thu Nov 01 2007 - 10:12:52 PDT)
- Re: AMBER: &dipoles output in QM/MM simulations Seongeun Yang (Fri Nov 02 2007 - 02:07:04 PDT)
  - RE: AMBER: &dipoles output in QM/MM simulations Ross Walker (Fri Nov 02 2007 - 11:42:54 PDT)
- Re: AMBER: &dipoles output in QM/MM simulations Seongeun Yang (Fri Nov 02 2007 - 03:59:01 PDT)
  - Re: AMBER: &dipoles output in QM/MM simulations Eddie Men (Fri Nov 02 2007 - 05:01:10 PDT)
  - Re: AMBER: &dipoles output in QM/MM simulations Adrian Roitberg (Fri Nov 02 2007 - 06:06:28 PDT)
- Re: AMBER: &dipoles output in QM/MM simulations Seongeun Yang (Fri Nov 02 2007 - 23:33:58 PDT)
AMBER: Improper torsion terms Pavan G (Thu Nov 01 2007 - 17:24:46 PDT)
Re: AMBER:antechamber fails with large molecules Junmei Wang (Thu Nov 01 2007 - 23:29:11 PDT)
- AMBER: Failure to recompile antechamber Francesco Pietra (Fri Nov 02 2007 - 16:05:45 PDT)
- Re: AMBER:antechamber fails with large molecules Francesco Pietra (Sun Nov 11 2007 - 03:13:56 PST)
Re: AMBER: Improper torsion terms Bill Ross (Fri Nov 02 2007 - 09:41:00 PDT)
AMBER: Compiling single programs Francesco Pietra (Fri Nov 02 2007 - 10:44:09 PDT)
- Re: AMBER: Compiling single programs Mark Williamson (Fri Nov 02 2007 - 10:58:32 PDT)
- Re: AMBER: Compiling single programs Adrian Roitberg (Fri Nov 02 2007 - 11:08:44 PDT)
AMBER: error with amber9 production run. Vijay Singh (Sat Nov 03 2007 - 07:10:52 PDT)
AMBER: How to decide extra-helical or intra-helical bulge conformation by PTRAJ ? sychen (Sun Nov 04 2007 - 04:46:09 PST)
- Re: AMBER: How to decide extra-helical or intra-helical bulge conformation by PTRAJ ? Jiri Sponer (Sun Nov 04 2007 - 05:01:02 PST)
  - RE: AMBER: How to decide extra-helical or intra-helical bulge conformation by PTRAJ ? Catein Catherine (Sun Nov 04 2007 - 21:20:48 PST)
AMBER: dihedral driver fatima.chami.durham.ac.uk (Sun Nov 04 2007 - 04:51:22 PST)
AMBER: paper request Miguel Ortiz-Lombardía (Mon Nov 05 2007 - 01:01:08 PST)
- Re: AMBER: paper request FyD (Mon Nov 05 2007 - 01:13:38 PST)
- Re: AMBER: paper request Miguel Ortiz-Lombardía (Mon Nov 05 2007 - 02:14:09 PST)
AMBER: "Atom valence violated" from LEaP Francesco Pietra (Mon Nov 05 2007 - 03:00:28 PST)
AMBER: Fe bonds in HEME ! Pradipta Bandyopadhyay (Mon Nov 05 2007 - 03:50:58 PST)
AMBER: ptraj frames maximum Hannes Wallnoefer (Mon Nov 05 2007 - 06:19:25 PST)
- Re: AMBER: ptraj frames maximum David A. Case (Mon Nov 05 2007 - 07:34:20 PST)
  - Re: AMBER: ptraj frames maximum Hannes Wallnoefer (Mon Nov 05 2007 - 08:07:00 PST)
    - Re: AMBER: ptraj frames maximum David A. Case (Mon Nov 05 2007 - 08:37:11 PST)
- Re: AMBER: ptraj frames maximum Thomas Cheatham (Mon Nov 05 2007 - 15:54:37 PST)
AMBER: DUMBFREQ Steve Seibold (Mon Nov 05 2007 - 07:52:19 PST)
AMBER: ptraj hbond mask Lars Skjærven (Mon Nov 05 2007 - 08:00:03 PST)
- Re: AMBER: ptraj hbond mask Thomas Cheatham III (Wed Nov 07 2007 - 13:00:40 PST)
AMBER: umbrella sampling and WHAM Allen, Thomas W., Ph.D. [RO BIOCHM] (Mon Nov 05 2007 - 12:03:31 PST)
AMBER: Parallel test error with shared libraries Joe Nolan (Mon Nov 05 2007 - 13:05:27 PST)
AMBER: Request reg parameter for vitamin e Rama krishnan (Mon Nov 05 2007 - 23:13:51 PST)
AMBER: Request reg parameter for vitamin e Rama krishnan (Mon Nov 05 2007 - 23:11:47 PST)
AMBER: Can a simulation run on AMBER 9 be compared with another from AMBER 8? ming hui (Tue Nov 06 2007 - 00:30:17 PST)
- Re: AMBER: Can a simulation run on AMBER 9 be compared with another from AMBER 8? Carlos Simmerling (Tue Nov 06 2007 - 03:49:13 PST)
AMBER: Energy minimization problem of -SO3H group Takao Kobayashi (Tue Nov 06 2007 - 02:17:35 PST)
- Re: AMBER: Energy minimization problem of -SO3H group David A. Case (Tue Nov 06 2007 - 21:12:08 PST)
  - Re: AMBER: Energy minimization problem of -SO3H group Eddie Men (Tue Nov 06 2007 - 21:52:09 PST)
AMBER: Question dykyy (Tue Nov 06 2007 - 05:12:46 PST)
- Re: AMBER: Question David A. Case (Tue Nov 06 2007 - 21:18:33 PST)
AMBER: Minimum energy tolerance gradient setting for minimization Sandhya Tiwari (Tue Nov 06 2007 - 06:13:52 PST)
- Re: AMBER: Minimum energy tolerance gradient setting for minimization David A. Case (Tue Nov 06 2007 - 08:03:18 PST)
AMBER: Antechamber snoze pa (Tue Nov 06 2007 - 08:02:39 PST)
- Re: AMBER: Antechamber David Mobley (Tue Nov 06 2007 - 09:15:33 PST)
- Re: AMBER: Antechamber Ilyas Yildirim (Tue Nov 06 2007 - 09:36:35 PST)
  - Re: AMBER: Antechamber snoze pa (Tue Nov 06 2007 - 11:04:05 PST)
    - Re: AMBER: Antechamber David Mobley (Tue Nov 06 2007 - 12:41:17 PST)
    - Re: AMBER: Antechamber Ilyas Yildirim (Tue Nov 06 2007 - 13:03:13 PST)
AMBER: calculating charges to modified 4GA unit nag raj (Wed Nov 07 2007 - 03:26:51 PST)
- Re: AMBER: calculating charges to modified 4GA unit FyD (Wed Nov 07 2007 - 05:21:03 PST)
  - Re: AMBER: calculating charges to modified 4GA unit Austin B. Yongye (Wed Nov 07 2007 - 06:26:57 PST)
  - Re: AMBER: calculating charges to modified 4GA unit nag raj (Wed Nov 07 2007 - 19:04:53 PST)
  - Re: AMBER: calculating charges to modified 4GA unit nag raj (Wed Nov 07 2007 - 19:04:53 PST)
- Re: AMBER: calculating charges to modified 4GA unit Karl Kirschner (Wed Nov 07 2007 - 05:37:42 PST)
AMBER: AMBER 9 - visualization of MD trajectory by MOE dinko.x.ziher.gsk.com (Wed Nov 07 2007 - 04:45:41 PST)
AMBER: LEaP bond problem Beale, John (Wed Nov 07 2007 - 04:57:30 PST)
- Re: AMBER: LEaP bond problem David A. Case (Wed Nov 07 2007 - 08:39:49 PST)
AMBER: divcon on AIX using xlf 10.1 Joachim Hein (Wed Nov 07 2007 - 08:23:14 PST)
- AMBER: Re: divcon on AIX using xlf 10.1 Joachim Hein (Mon Dec 03 2007 - 08:43:19 PST)
AMBER: (no subject) Biman Jana (Wed Nov 07 2007 - 09:09:00 PST)
- Re: AMBER: (no subject) David A. Case (Wed Nov 07 2007 - 09:11:43 PST)
AMBER: TIP5P water Simulation Biman Jana (Wed Nov 07 2007 - 09:12:42 PST)
AMBER: MD simulations with Pt atom - how to keep square planar geometry? Pablo Englebienne (Wed Nov 07 2007 - 18:21:21 PST)
- Re: AMBER: MD simulations with Pt atom - how to keep square planar geometry? gsciaini.qi.fcen.uba.ar (Thu Nov 08 2007 - 08:09:31 PST)
- Re: AMBER: MD simulations with Pt atom - how to keep square planar geometry? Pablo Englebienne (Thu Nov 08 2007 - 09:44:43 PST)
AMBER: make test.parallel Francesco Pietra (Thu Nov 08 2007 - 00:33:21 PST)
- Re: AMBER: make test.parallel David A. Case (Thu Nov 08 2007 - 07:58:39 PST)
  - Re: AMBER: make test.parallel Francesco Pietra (Thu Nov 08 2007 - 09:30:36 PST)
    - Re: AMBER: make test.parallel Gustavo Seabra (Fri Nov 09 2007 - 08:28:23 PST)
AMBER: divcon san_amber roy (Thu Nov 08 2007 - 09:19:41 PST)
- Re: AMBER: divcon Pablo Englebienne (Thu Nov 08 2007 - 09:50:25 PST)
- Re: AMBER: divcon David A. Case (Thu Nov 08 2007 - 18:06:55 PST)
AMBER: xleap patch for xorg-7.3 ?? M. L. Dodson (Thu Nov 08 2007 - 11:04:05 PST)
- Re: AMBER: xleap patch for xorg-7.3 ?? David A. Case (Thu Nov 08 2007 - 18:03:39 PST)
  - Re: AMBER: xleap patch for xorg-7.3 ?? Xuebin Qiao (Fri Nov 09 2007 - 06:26:38 PST)
AMBER: thermodynamic integration Cooper, Matthew (Thu Nov 08 2007 - 13:14:25 PST)
- Re: AMBER: thermodynamic integration Ilyas Yildirim (Thu Nov 08 2007 - 14:42:04 PST)
  - RE: AMBER: thermodynamic integration Cooper, Matthew (Fri Nov 09 2007 - 06:32:52 PST)
- Re: AMBER: thermodynamic integration David A. Case (Thu Nov 08 2007 - 17:49:49 PST)
  - RE: AMBER: thermodynamic integration Cooper, Matthew (Fri Nov 09 2007 - 06:03:32 PST)
    - Re: AMBER: thermodynamic integration David A. Case (Fri Nov 09 2007 - 10:27:48 PST)
- Re: AMBER: thermodynamic integration Thomas Steinbrecher (Tue Nov 13 2007 - 08:36:15 PST)
AMBER: RESP question Eddie Men (Fri Nov 09 2007 - 16:33:16 PST)
- Re: AMBER: RESP question Gustavo Seabra (Fri Nov 09 2007 - 21:01:09 PST)
AMBER: TIP5P water simulation using AMBER7 Biman Jana (Sat Nov 10 2007 - 06:57:20 PST)
- Re: AMBER: TIP5P water simulation using AMBER7 Carlos Simmerling (Sat Nov 10 2007 - 07:00:36 PST)
  - Re: AMBER: TIP5P water simulation using AMBER7 Biman Jana (Sun Nov 11 2007 - 06:21:56 PST)
    - Re: AMBER: TIP5P water simulation using AMBER7 Carlos Simmerling (Sun Nov 11 2007 - 06:25:50 PST)
    - Re: AMBER: TIP5P water simulation using AMBER7 Adrian Roitberg (Sun Nov 11 2007 - 08:29:11 PST)
    - Re: AMBER: TIP5P water simulation using AMBER7 David A. Case (Sun Nov 11 2007 - 14:04:08 PST)
AMBER: addles Peter Varnai (Sat Nov 10 2007 - 08:40:21 PST)
- Re: AMBER: addles David A. Case (Wed Nov 28 2007 - 09:46:57 PST)
AMBER: replica exchange problems with ifort >10.0.023 Peter Varnai (Sat Nov 10 2007 - 08:44:30 PST)
AMBER: invalid digit '*' in the input file rebeca.mmb.pcb.ub.es (Mon Nov 12 2007 - 06:06:16 PST)
- Re: AMBER: invalid digit '*' in the input file Martin Klefas-Stennett (Mon Nov 12 2007 - 06:31:08 PST)
  - Re: AMBER: invalid digit '*' in the input file rebeca.mmb.pcb.ub.es (Mon Nov 12 2007 - 06:56:26 PST)
    - Re: AMBER: invalid digit '*' in the input file Adrian Roitberg (Mon Nov 12 2007 - 07:17:43 PST)
    - RE: AMBER: invalid digit '*' in the input file Yong Duan (Mon Nov 12 2007 - 17:07:26 PST)
- Re: AMBER: invalid digit '*' in the input file Chris Moth (Mon Nov 12 2007 - 06:40:26 PST)
- RE: AMBER: invalid digit '*' in the input file Hayden Eastwood (Mon Nov 12 2007 - 07:10:03 PST)
AMBER: restrain center of mass of one domain Wei Chen (Mon Nov 12 2007 - 15:14:11 PST)
AMBER: Installing Amber9 in a Cygwin environment on a MS-Windows XP machine Hopkins, Robert (Mon Nov 12 2007 - 15:32:20 PST)
- Re: AMBER: Installing Amber9 in a Cygwin environment on a MS-Windows XP machine David A. Case (Tue Nov 13 2007 - 07:54:38 PST)
  - RE: AMBER: Installing Amber9 in a Cygwin environment on a MS-Windows XP machine Hu, Shaowen (JSC-SK)[USRA] (Tue Nov 13 2007 - 08:13:18 PST)
    - Re: AMBER: Installing Amber9 in a Cygwin environment on a MS-Windows XP machine David A. Case (Tue Nov 13 2007 - 08:28:52 PST)
  - Re: AMBER: Installing Amber9 in a Cygwin environment on a MS-Windows XP machine Hopkins, Robert (Sun Dec 09 2007 - 13:44:34 PST)
- Re: AMBER: Installing Amber9 in a Cygwin environment on a MS-Windows XP machine Hopkins, Robert (Tue Dec 11 2007 - 15:50:17 PST)
  - Re: AMBER: Installing Amber9 in a Cygwin environment on a MS-Windows XP machine Gustavo Seabra (Tue Dec 11 2007 - 16:23:49 PST)
AMBER: Parallel scaling priya priya (Tue Nov 13 2007 - 02:35:20 PST)
- Re: AMBER: Parallel scaling Carlos Simmerling (Tue Nov 13 2007 - 03:07:53 PST)
  - Re: AMBER: Parallel scaling priya priya (Tue Nov 13 2007 - 03:26:23 PST)
AMBER: gb minimization using nab Guillaume Renvez (Tue Nov 13 2007 - 03:06:13 PST)
- Re: AMBER: gb minimization using nab Andreas Svrcek-Seiler (Tue Nov 13 2007 - 03:58:05 PST)
  - Re: AMBER: gb minimization using nab Guillaume Renvez (Tue Nov 13 2007 - 06:49:48 PST)
AMBER: Protein containing iron. Syed Tarique Moin (Tue Nov 13 2007 - 03:16:48 PST)
- RE: AMBER: Protein containing iron. Ross Walker (Tue Nov 13 2007 - 10:37:40 PST)
AMBER: Parallel Amber compilation problems !! Sampath Koppole (Tue Nov 13 2007 - 06:05:28 PST)
- AMBER: Problem with xLeap alfredoq.mail.fcq.unc.edu.ar (Tue Nov 13 2007 - 07:34:46 PST)
  - Re: AMBER: Problem with xLeap David A. Case (Tue Nov 13 2007 - 08:08:24 PST)
    - Re: AMBER: Problem with xLeap alfredoq.mail.fcq.unc.edu.ar (Tue Nov 13 2007 - 09:07:40 PST)
    - Re: AMBER: Problem with xLeap David A. Case (Tue Nov 13 2007 - 09:55:24 PST)
    - Re: AMBER: Problem with xLeap alfredoq.mail.fcq.unc.edu.ar (Tue Nov 13 2007 - 10:11:31 PST)
- RE: AMBER: Parallel Amber compilation problems !! Ross Walker (Tue Nov 13 2007 - 10:33:25 PST)
  - RE: AMBER: Parallel Amber compilation problems !! Sampath Koppole (Wed Nov 14 2007 - 01:22:15 PST)
AMBER: 2 double bond in AMBER ffield ABEL Stephane 984007 (Tue Nov 13 2007 - 09:00:08 PST)
AMBER: amber9 leap installation error on sgi_altix wei zhang (Tue Nov 13 2007 - 14:02:48 PST)
- RE: AMBER: amber9 leap installation error on sgi_altix Ross Walker (Tue Nov 13 2007 - 14:50:53 PST)
- Re: AMBER: amber9 leap installation error on sgi_altix David A. Case (Tue Nov 13 2007 - 15:27:55 PST)
  - Re: AMBER: amber9 leap installation error on sgi_altix wei zhang (Wed Nov 14 2007 - 08:05:26 PST)
[Fwd: Re: AMBER: xleap patch for xorg-7.3 ??] M. L. Dodson (Wed Nov 14 2007 - 10:51:35 PST)
- Re: [Fwd: Re: AMBER: xleap patch for xorg-7.3 ??] Xuebin Qiao (Wed Nov 14 2007 - 22:59:58 PST)
  - Re: [Fwd: Re: AMBER: xleap patch for xorg-7.3 ??] M. L. Dodson (Thu Nov 15 2007 - 09:28:28 PST)
    - Re: [Fwd: Re: AMBER: xleap patch for xorg-7.3 ??] Lili Peng (Thu Nov 15 2007 - 14:38:57 PST)
    - Re: [Fwd: Re: AMBER: xleap patch for xorg-7.3 ??] David A. Case (Thu Nov 15 2007 - 22:12:45 PST)
AMBER: Bug report: iwrap failure in PMEMD with netCDF Myunggi Yi (Wed Nov 14 2007 - 11:18:18 PST)
- Re: AMBER: Bug report: iwrap failure in PMEMD with netCDF Robert Duke (Wed Nov 14 2007 - 11:52:16 PST)
AMBER: Error when doing a TI simulation: "vlimit exceeded ming hui (Wed Nov 14 2007 - 17:10:07 PST)
- Re: AMBER: Error when doing a TI simulation: "vlimit exceeded Thomas Steinbrecher (Thu Nov 15 2007 - 09:06:03 PST)
  - Re: AMBER: Error when doing a TI simulation: "vlimit exceeded ming hui (Thu Nov 15 2007 - 16:48:05 PST)
    - Re: AMBER: Error when doing a TI simulation: "vlimit exceeded Thomas Steinbrecher (Thu Nov 15 2007 - 17:18:54 PST)
    - Re: AMBER: Error when doing a TI simulation: "vlimit exceeded ming hui (Thu Nov 15 2007 - 17:26:43 PST)
    - Re: AMBER: Error when doing a TI simulation: "vlimit exceeded Thomas Steinbrecher (Thu Nov 15 2007 - 17:52:47 PST)
AMBER: &shf setup McElheny, Dan (Thu Nov 15 2007 - 15:39:42 PST)
- Re: AMBER: &shf setup David A. Case (Fri Nov 16 2007 - 15:59:19 PST)
AMBER: Understading of mdcrd file and pdb file.. Vijay Manickam Achari (Thu Nov 15 2007 - 21:02:08 PST)
- Re: AMBER: Understading of mdcrd file and pdb file.. David A. Case (Thu Nov 15 2007 - 22:23:30 PST)
  - Re: AMBER: Understading of mdcrd file and pdb file.. Vijay Manickam Achari (Sun Nov 18 2007 - 21:27:19 PST)
AMBER: [chirality.c] Atom did not match Francesco Pietra (Fri Nov 16 2007 - 09:09:10 PST)
- Re: AMBER: [chirality.c] Atom did not match Jojart Balazs (Fri Nov 16 2007 - 09:48:51 PST)
  - Re: AMBER: [chirality.c] Atom did not match Francesco Pietra (Fri Nov 16 2007 - 11:38:20 PST)
AMBER: xleap heme iron coordination error Robyn Ayscue (Fri Nov 16 2007 - 11:33:35 PST)
- Re: AMBER: xleap heme iron coordination error David A. Case (Fri Nov 16 2007 - 11:47:53 PST)
AMBER: antechamber --> sander problem Yamada, Takahiro (Fri Nov 16 2007 - 12:18:18 PST)
- Re: AMBER: antechamber --> sander problem David A. Case (Fri Nov 16 2007 - 13:17:50 PST)
AMBER: chem shift format McElheny, Dan (Fri Nov 16 2007 - 13:46:57 PST)
- Re: AMBER: chem shift format David A. Case (Fri Nov 16 2007 - 16:00:27 PST)
AMBER: Fwd: [chirality.c] Atom did not match Francesco Pietra (Fri Nov 16 2007 - 13:59:40 PST)
- Re: AMBER: Fwd: [chirality.c] Atom did not match David A. Case (Fri Nov 16 2007 - 16:03:33 PST)
  - Re: AMBER: Fwd: [chirality.c] Atom did not match Francesco Pietra (Sat Nov 17 2007 - 02:56:01 PST)
    - Re: AMBER: Fwd: [chirality.c] Atom did not match David A. Case (Sat Nov 17 2007 - 08:53:01 PST)
AMBER: five-coordinated phosphorus Smooth Cutie (Fri Nov 16 2007 - 15:48:40 PST)
AMBER: How to calculate S2 from P2 using ptraj ? brmeher.iitg.ernet.in (Fri Nov 16 2007 - 22:34:11 PST)
- Re: AMBER: How to calculate S2 from P2 using ptraj ? David A. Case (Mon Nov 19 2007 - 10:04:48 PST)
AMBER: How to calculate S2 from P2 using ptraj ? brmeher.iitg.ernet.in (Fri Nov 16 2007 - 22:40:31 PST)
AMBER: five-coordinated phosphorus Yubo Fan (Sat Nov 17 2007 - 06:19:06 PST)
AMBER: question with ptraj loop Vijay Singh (Sat Nov 17 2007 - 08:06:53 PST)
Fwd: Re: AMBER: Fwd: [chirality.c] Atom did not match Francesco Pietra (Sat Nov 17 2007 - 08:16:09 PST)
- RE: Re: AMBER: Fwd: [chirality.c] Atom did not match Steve Spronk (Mon Nov 19 2007 - 05:28:07 PST)
- RE: Re: AMBER: Fwd: [chirality.c] Atom did not match Steve Spronk (Mon Nov 19 2007 - 05:31:42 PST)
AMBER: Puzzle with WAT Francesco Pietra (Sat Nov 17 2007 - 10:14:38 PST)
AMBER: EXCEEDED MAXLESADJ in sander.LES.MPI (amber9) Alessandro Nascimento (Sat Nov 17 2007 - 13:24:58 PST)
- Re: AMBER: EXCEEDED MAXLESADJ in sander.LES.MPI (amber9) Carlos Simmerling (Sat Nov 17 2007 - 13:51:09 PST)
Re: AMBER: Puzzle with WAT Bill Ross (Sat Nov 17 2007 - 16:00:06 PST)
- Re: AMBER: Puzzle with WAT Francesco Pietra (Sun Nov 18 2007 - 00:09:27 PST)
- Re: AMBER: Puzzle with WAT Bill Ross (Sun Nov 18 2007 - 10:55:15 PST)
AMBER: Atom types for polyunsaturated lipids ABEL Stephane 984007 (Sun Nov 18 2007 - 09:14:14 PST)
- RE : AMBER: Atom types for polyunsaturated lipids ABEL Stephane 984007 (Sun Nov 18 2007 - 11:40:24 PST)
AMBER: R.E.D.-III bug fixes FyD (Sun Nov 18 2007 - 09:22:47 PST)
- Re: AMBER: R.E.D.-III bug fixes snoze pa (Sat Dec 22 2007 - 11:14:44 PST)
AMBER: Missing BELE for MM in 1 backy (Mon Nov 19 2007 - 04:19:09 PST)
AMBER: Solvation free energy Mike Wykes (Mon Nov 19 2007 - 10:08:23 PST)
- Re: AMBER: Solvation free energy Thomas Steinbrecher (Mon Nov 19 2007 - 10:21:23 PST)
AMBER: pmemd with openmpi Myunggi Yi (Mon Nov 19 2007 - 11:25:48 PST)
- Re: AMBER: pmemd with openmpi Francesco Pietra (Mon Nov 19 2007 - 12:31:56 PST)
  - Re: AMBER: pmemd with openmpi Myunggi Yi (Mon Nov 19 2007 - 13:40:41 PST)
AMBER: newby question on converting xyz format to pdb format after energy minimization Mehmet Serkan Apaydin (Tue Nov 20 2007 - 13:02:42 PST)
- Re: AMBER: newby question on converting xyz format to pdb format after energy minimization Eddie Men (Tue Nov 20 2007 - 13:24:56 PST)
- Re: AMBER: newby question on converting xyz format to pdb format after energy minimization David A. Case (Tue Nov 20 2007 - 13:33:08 PST)
AMBER: Implicit/Explicit solvation Eddie Men (Tue Nov 20 2007 - 23:03:12 PST)
- RE: AMBER: Implicit/Explicit solvation Ross Walker (Wed Nov 21 2007 - 08:10:58 PST)
- Re: AMBER: Implicit/Explicit solvation David A. Case (Wed Nov 21 2007 - 08:46:19 PST)
AMBER: Zinc-Histidine force field Mattia Mori - CERM (Wed Nov 21 2007 - 08:54:02 PST)
- RE: AMBER: Zinc-Histidine force field Ray Luo (Wed Nov 21 2007 - 09:30:21 PST)
  - Re: AMBER: Zinc-Histidine force field Mattia Mori - CERM (Thu Nov 22 2007 - 04:06:20 PST)
    - RE: AMBER: Zinc-Histidine force field Ray Luo (Thu Nov 22 2007 - 11:01:30 PST)
    - Re: AMBER: Zinc-Histidine force field Mattia Mori - CERM (Thu Nov 22 2007 - 11:12:43 PST)
    - AMBER: BELLY Eddie Men (Thu Nov 22 2007 - 13:16:39 PST)
    - Re: AMBER: BELLY Eddie Men (Thu Nov 22 2007 - 14:30:38 PST)
AMBER:How to calculate the free energy of a series of conformations huzehan19870731.126.com (Mon Nov 19 2007 - 19:18:41 PST)
- Re: AMBER:How to calculate the free energy of a series of conformations David A. Case (Wed Nov 21 2007 - 11:42:09 PST)
  - Re: AMBER:How to calculate the free energy of a series of conformations Carlos Simmerling (Wed Nov 21 2007 - 15:04:03 PST)
AMBER: Problem with LEaP generating topology and coord files after double bond creation M. L. Dodson (Wed Nov 21 2007 - 12:45:17 PST)
- Re: AMBER: Problem with LEaP generating topology and coord files after double bond creation David A. Case (Wed Nov 21 2007 - 17:08:08 PST)
AMBER: modifications to force field for Fe4S4 cubane Boutheïna Kerkeni (Wed Nov 21 2007 - 13:41:45 PST)
- Re: AMBER: modifications to force field for Fe4S4 cubane David A. Case (Wed Nov 21 2007 - 14:30:30 PST)
 - Re: AMBER: modifications to force field for Fe4S4 cubane Boutheïna Kerkeni (Wed Nov 28 2007 - 07:36:38 PST)
 - Re: AMBER: modifications to force field for Fe4S4 cubane Boutheïna Kerkeni (Wed Nov 28 2007 - 13:31:02 PST)
 - Re: AMBER: modifications to force field for Fe4S4 cubane David A. Case (Tue Dec 04 2007 - 10:57:39 PST)
 - AMBER: FATAL: Atom .R<CYF 17>.A<N 1> does not have a type. Boutheina Kerkeni (Wed Dec 05 2007 - 15:28:41 PST)
 - Re: AMBER: FATAL: Atom .R<CYF 17>.A<N 1> does not have a type. David A. Case (Wed Dec 05 2007 - 16:41:32 PST)
AMBER: McElheny, Dan (Wed Nov 21 2007 - 14:04:26 PST)
AMBER: Atom type definition Xioling Chuang (Thu Nov 22 2007 - 01:03:29 PST)
AMBER: BELLY issues Eddie Men (Thu Nov 22 2007 - 02:03:52 PST)
AMBER: RE: FF94 or FF99? Patel, Bhavesh H (Thu Nov 22 2007 - 06:34:55 PST)
- Re: AMBER: RE: FF94 or FF99? Adrian Roitberg (Thu Nov 22 2007 - 07:20:22 PST)
  - Re: AMBER: RE: FF94 or FF99? Jerome.GOLEBIOWSKI.unice.fr (Thu Nov 22 2007 - 07:57:33 PST)
- Re: AMBER: RE: FF94 or FF99? Carlos Simmerling (Thu Nov 22 2007 - 16:13:16 PST)
  - Re: AMBER: RE: FF94 or FF99? Ilyas Yildirim (Thu Nov 22 2007 - 16:29:08 PST)
    - Re: AMBER: RE: FF94 or FF99? David A. Case (Fri Nov 23 2007 - 10:51:18 PST)
    - Re: AMBER: RE: FF94 or FF99? Ilyas Yildirim (Fri Nov 23 2007 - 15:29:15 PST)
    - Re: AMBER: RE: FF94 or FF99? Jiri Sponer (Sat Nov 24 2007 - 02:53:24 PST)
AMBER: Pressure Variation for NPT simulation of TIP5P water Biman Jana (Thu Nov 22 2007 - 06:50:16 PST)
- Re: AMBER: Pressure Variation for NPT simulation of TIP5P water David A. Case (Thu Nov 22 2007 - 09:34:34 PST)
AMBER: Pre-ABMER Installation Prob w/ MPICH2 Joseph Maxwell (Thu Nov 22 2007 - 11:55:18 PST)
- Re: AMBER: Pre-ABMER Installation Prob w/ MPICH2 jantonioms J. A. Mondragon S (Fri Nov 23 2007 - 09:36:12 PST)
AMBER: frcmod file and NONB for dummy atoms Ilyas Yildirim (Thu Nov 22 2007 - 16:48:31 PST)
- Re: AMBER: frcmod file and NONB for dummy atoms David A. Case (Fri Nov 23 2007 - 10:58:46 PST)
  - Re: AMBER: frcmod file and NONB for dummy atoms Ilyas Yildirim (Fri Nov 23 2007 - 18:26:37 PST)
AMBER: About TER records Francesco Pietra (Fri Nov 23 2007 - 00:15:05 PST)
- Re: AMBER: About TER records David A. Case (Fri Nov 23 2007 - 10:35:46 PST)
  - Re: AMBER: About TER records Francesco Pietra (Sat Nov 24 2007 - 13:34:59 PST)
AMBER: connecting a non standard residue to the rest of an enzyme Boutheïna Kerkeni (Fri Nov 23 2007 - 05:43:36 PST)
- Re: AMBER: connecting a non standard residue to the rest of an enzyme David A. Case (Fri Nov 23 2007 - 10:39:13 PST)
AMBER: Fwd: About TER records Francesco Pietra (Fri Nov 23 2007 - 07:23:41 PST)
- Re: AMBER: Fwd: About TER records Ilyas Yildirim (Fri Nov 23 2007 - 07:41:47 PST)
  - Re: AMBER: Fwd: About TER records Francesco Pietra (Sat Nov 24 2007 - 10:29:15 PST)
- Re: AMBER: Fwd: About TER records Francesco Pietra (Sat Nov 24 2007 - 13:27:11 PST)
AMBER: Hello Eddie Men (Fri Nov 23 2007 - 18:44:05 PST)
- Re: AMBER: Hello Carlos Simmerling (Fri Nov 23 2007 - 19:01:13 PST)
  - Re: AMBER: Hello Eddie Men (Sat Nov 24 2007 - 10:47:11 PST)
    - Re: AMBER: Hello Carlos Simmerling (Sat Nov 24 2007 - 10:55:46 PST)
    - Re: AMBER: Hello David A. Case (Sat Nov 24 2007 - 22:14:23 PST)
AMBER: Pressure Variation for NPT simulation of TIP5P water (fwd) Biman Jana (Sat Nov 24 2007 - 05:22:39 PST)
- Re: AMBER: Pressure Variation for NPT simulation of TIP5P water (fwd) David A. Case (Sat Nov 24 2007 - 09:36:44 PST)
AMBER: solvatebox vs solvateoct Francesco Pietra (Sun Nov 25 2007 - 10:27:06 PST)
AMBER: question about ntx=5 Wei Chen (Sun Nov 25 2007 - 11:21:44 PST)
- RE: AMBER: umbrella sampling Jardas sucuriba (Sun Nov 25 2007 - 11:32:28 PST)
  - Re: AMBER: umbrella sampling Carlos Simmerling (Sun Nov 25 2007 - 11:52:57 PST)
- Re: AMBER: question about ntx=5 David A. Case (Sun Nov 25 2007 - 16:27:30 PST)
  - Re: AMBER: question about ntx=5 Wei Chen (Sun Nov 25 2007 - 17:21:52 PST)
    - Re: AMBER: question about ntx=5 David A. Case (Tue Nov 27 2007 - 08:49:33 PST)
AMBER: Weird restart file with ioutfm=0, iwrap=1 and ntwprt >0 Hai Long (Mon Nov 26 2007 - 09:41:18 PST)
- Re: AMBER: Weird restart file with ioutfm=0, iwrap=1 and ntwprt >0 David A. Case (Wed Nov 28 2007 - 11:27:52 PST)
AMBER: LJ parameters for alkynes David Mobley (Mon Nov 26 2007 - 10:07:37 PST)
AMBER: Polarizable potentials Denis Courtier (Mon Nov 26 2007 - 10:49:33 PST)
- Re: AMBER: Polarizable potentials David A. Case (Mon Nov 26 2007 - 18:23:05 PST)
AMBER: Value of taup for bulk TIP5P water simulation(amber7) Biman Jana (Mon Nov 26 2007 - 11:25:37 PST)
AMBER: Restrained MD (amber9) Vincent Bisetty (Mon Nov 26 2007 - 14:52:28 PST)
- Re: AMBER: Restrained MD (amber9) David A. Case (Mon Nov 26 2007 - 15:49:43 PST)
AMBER: restraints to individual atoms Eddie Men (Mon Nov 26 2007 - 19:02:11 PST)
- Re: AMBER: restraints to individual atoms Gustavo Seabra (Tue Nov 27 2007 - 08:34:14 PST)
- RE: AMBER: restraints to individual atoms Ross Walker (Tue Nov 27 2007 - 09:05:44 PST)
  - Re: AMBER: restraints to individual atoms Eddie Men (Tue Nov 27 2007 - 19:54:30 PST)
AMBER: Extra-term to the Energy function !! Sampath Koppole (Tue Nov 27 2007 - 00:57:54 PST)
- Re: AMBER: Extra-term to the Energy function !! Carlos Simmerling (Tue Nov 27 2007 - 03:12:13 PST)
  - Re: AMBER: Extra-term to the Energy function !! Sampath Koppole (Tue Nov 27 2007 - 03:31:22 PST)
AMBER: modifications to force field for Fe4S4 cubane Boutheïna Kerkeni (Tue Nov 27 2007 - 03:26:22 PST)
- Re: AMBER: modifications to force field for Fe4S4 cubane Ilyas Yildirim (Tue Nov 27 2007 - 07:02:21 PST)
  - Re: AMBER: modifications to force field for Fe4S4 cubane Boutheïna Kerkeni (Tue Nov 27 2007 - 07:23:39 PST)
    - Re: AMBER: modifications to force field for Fe4S4 cubane Ilyas Yildirim (Tue Nov 27 2007 - 11:29:58 PST)
    - Re: AMBER: modifications to force field for Fe4S4 cubane David A. Case (Tue Nov 27 2007 - 13:10:40 PST)
AMBER: Xleap and Hydrogens Shozeb Haider (Tue Nov 27 2007 - 06:38:56 PST)
- Re: AMBER: Xleap and Hydrogens Ilyas Yildirim (Tue Nov 27 2007 - 07:08:29 PST)
  - Re: AMBER: Xleap and Hydrogens Marius Retegan (Tue Nov 27 2007 - 07:43:36 PST)
- Re: AMBER: Xleap and Hydrogens David A. Case (Tue Nov 27 2007 - 08:40:05 PST)
- Re: AMBER: Xleap and Hydrogens Bill Ross (Tue Nov 27 2007 - 09:11:35 PST)
AMBER: antechamber: read in charges fatima.chami.durham.ac.uk (Tue Nov 27 2007 - 07:40:13 PST)
- Re: AMBER: antechamber: read in charges Junmei Wang (Tue Nov 27 2007 - 09:50:11 PST)
  - Re: AMBER: antechamber: read in charges fatima.chami.durham.ac.uk (Wed Nov 28 2007 - 10:52:41 PST)
- Re: AMBER: antechamber: read in charges Junmei Wang (Wed Nov 28 2007 - 12:58:36 PST)
AMBER: predictive NOE generation Seth Lilavivat (Tue Nov 27 2007 - 09:41:08 PST)
- Re: AMBER: predictive NOE generation Nicolas Lux Fawzi (Tue Nov 27 2007 - 10:26:48 PST)
AMBER: Polarizable Potential Denis Courtier (Tue Nov 27 2007 - 09:40:34 PST)
AMBER: Re: antechamber problem Junmei Wang (Tue Nov 27 2007 - 09:38:17 PST)
- Re: AMBER: Re: antechamber problem sanket deshmukh (Wed Nov 28 2007 - 06:05:37 PST)
AMBER: RE: Amber9 compile problem Ross Walker (Tue Nov 27 2007 - 09:24:22 PST)
Re: AMBER: [SOLVED] Problem with LEaP generating topology and coord files after double bond creation M. L. Dodson (Tue Nov 27 2007 - 13:45:44 PST)
- Re: AMBER: [SOLVED] Problem with LEaP generating topology and coord files after double bond creation M. L. Dodson (Wed Nov 28 2007 - 10:33:38 PST)
AMBER: Would amber work with Linspire 6.0? Campbell, Patrick (Tue Nov 27 2007 - 15:01:02 PST)
- RE: AMBER: Would amber work with Linspire 6.0? Ross Walker (Tue Nov 27 2007 - 16:36:02 PST)
- Re: AMBER: Would amber work with Linspire 6.0? Peter Gannett (Tue Nov 27 2007 - 19:20:19 PST)
- Re: AMBER: Would amber work with Linspire 6.0? Christophe Guilbert (Tue Nov 27 2007 - 19:35:35 PST)
AMBER: QMMM simulations Pankaj R. Daga (Tue Nov 27 2007 - 15:20:51 PST)
- RE: AMBER: QMMM simulations Ross Walker (Tue Nov 27 2007 - 16:41:11 PST)
AMBER: bondi radii problems Eddie Men (Tue Nov 27 2007 - 19:31:19 PST)
- Re: AMBER: bondi radii problems David A. Case (Wed Nov 28 2007 - 08:32:21 PST)
  - Re: AMBER: bondi radii problems Eddie Men (Wed Nov 28 2007 - 10:45:34 PST)
AMBER: PB warning in pb_miccg(): CG maxitn exceeded! Eddie Men (Tue Nov 27 2007 - 20:35:17 PST)
AMBER: Error reading radii of Cu during ESP caculation. Syed Tarique Moin (Wed Nov 28 2007 - 03:27:53 PST)
- Re: AMBER: Error reading radii of Cu during ESP caculation. FyD (Wed Nov 28 2007 - 04:19:35 PST)
  - Re: AMBER: Error reading radii of Cu during ESP caculation. Syed Tarique Moin (Wed Nov 28 2007 - 22:26:39 PST)
    - Re: AMBER: Error reading radii of Cu during ESP caculation. FyD (Thu Nov 29 2007 - 00:07:07 PST)
AMBER: Polarizable potential Denis Courtier (Wed Nov 28 2007 - 06:32:49 PST)
- Re: AMBER: Polarizable potential David A. Case (Wed Nov 28 2007 - 08:19:06 PST)
AMBER: radial distribution by Ptraj Esther Brugger (Wed Nov 28 2007 - 06:35:49 PST)
AMBER: Equilibration of protein complex in POPC membrane, the whole TIP3 solvated Francesco Pietra (Wed Nov 28 2007 - 07:01:37 PST)
- Re: AMBER: Equilibration of protein complex in POPC membrane, the whole TIP3 solvated M. L. Dodson (Wed Nov 28 2007 - 09:31:04 PST)
- Re: AMBER: Equilibration of protein complex in POPC membrane, the whole TIP3 solvated Gustavo Seabra (Wed Nov 28 2007 - 13:04:32 PST)
- RE: AMBER: Equilibration of protein complex in POPC membrane, the whole TIP3 solvated Steve Spronk (Thu Nov 29 2007 - 06:44:33 PST)
  - RE: AMBER: Equilibration of protein complex in POPC membrane, the whole TIP3 solvated Francesco Pietra (Thu Nov 29 2007 - 07:44:33 PST)
AMBER: (no subject) Gabriele Viliani (Wed Nov 28 2007 - 08:56:32 PST)
- Re: AMBER: (no subject) David A. Case (Wed Nov 28 2007 - 09:09:04 PST)
AMBER: leaprc.ff02polEP.r1into xleap Denis Courtier (Wed Nov 28 2007 - 09:44:21 PST)
- RE: AMBER: leaprc.ff02polEP.r1into xleap Ross Walker (Wed Nov 28 2007 - 10:38:47 PST)
- Re: AMBER: leaprc.ff02polEP.r1into xleap David A. Case (Wed Nov 28 2007 - 10:58:30 PST)
  - Re: AMBER: leaprc.ff02polEP.r1into xleap Denis Courtier (Thu Nov 29 2007 - 03:01:38 PST)
    - Re: AMBER: leaprc.ff02polEP.r1into xleap David A. Case (Thu Nov 29 2007 - 07:40:04 PST)
    - RE: AMBER: leaprc.ff02polEP.r1into xleap Ross Walker (Thu Nov 29 2007 - 07:54:13 PST)
AMBER: [Fwd: Re: BOUNCE amber.scripps.edu: Non-member submission from [Taufik Al-Sarraj <taufik.alsarraj@utoronto.ca>]] Taufik Al-Sarraj (Wed Nov 28 2007 - 10:23:27 PST)
- AMBER: DNA on Si surface Taufik Al-Sarraj (Thu Nov 29 2007 - 15:20:12 PST)
AMBER: Calculating dipole moments Austin B. Yongye (Wed Nov 28 2007 - 11:33:41 PST)
- RE: AMBER: Calculating dipole moments Ross Walker (Wed Nov 28 2007 - 13:57:12 PST)
  - RE: AMBER: Calculating dipole moments Austin B. Yongye (Thu Nov 29 2007 - 07:40:51 PST)
    - RE: AMBER: Calculating dipole moments Ross Walker (Thu Nov 29 2007 - 08:08:50 PST)
AMBER: questions about smd of amber 9 WANG,YING (Wed Nov 28 2007 - 13:29:41 PST)
- Re: AMBER: questions about smd of amber 9 Wei Chen (Wed Nov 28 2007 - 14:35:10 PST)
- Re: AMBER: questions about smd of amber 9 WANG,YING (Wed Nov 28 2007 - 18:14:21 PST)
  - Re: AMBER: questions about smd of amber 9 Wei Chen (Thu Nov 29 2007 - 08:28:34 PST)
    - Re: AMBER: questions about smd of amber 9 Adrian Roitberg (Thu Nov 29 2007 - 08:56:15 PST)
- Re: AMBER: questions about smd of amber 9 Gustavo Seabra (Thu Nov 29 2007 - 06:53:24 PST)
AMBER: Error in installing amber8 on Ubuntu tri nam Vo (Wed Nov 28 2007 - 20:24:24 PST)
- RE: AMBER: Error in installing amber8 on Ubuntu Ross Walker (Thu Nov 29 2007 - 07:44:10 PST)
AMBER: About RAMD Francesco Pietra (Wed Nov 28 2007 - 23:26:45 PST)
- Re: AMBER: About RAMD Alessandro Nascimento (Thu Nov 29 2007 - 02:54:02 PST)
- Re: AMBER: About RAMD Robert Duke (Sat Jan 05 2008 - 09:05:55 PST)
  - Re: AMBER: About RAMD Adrian Roitberg (Sat Jan 05 2008 - 09:47:33 PST)
    - RE: AMBER: About RAMD Yong Duan (Sat Jan 05 2008 - 11:24:53 PST)
AMBER: ele vs van der Waals backy (Thu Nov 29 2007 - 01:14:19 PST)
AMBER: Error in reading number of frame in PTRAJ Vijay Manickam Achari (Thu Nov 29 2007 - 01:20:12 PST)
AMBER: vlimit exceeded, polarizable force field Denis Courtier (Thu Nov 29 2007 - 03:43:45 PST)
- Re: AMBER: vlimit exceeded, polarizable force field Denis Courtier (Thu Nov 29 2007 - 05:33:22 PST)
  - RE: AMBER: vlimit exceeded, polarizable force field Ross Walker (Thu Nov 29 2007 - 08:02:24 PST)
AMBER: problems with restart of smd simulation w/ jar=1 & nmr=1 Wei Chen (Thu Nov 29 2007 - 09:15:51 PST)
AMBER: Re: Calculating Energies with imin=5 Pavan G (Fri Nov 30 2007 - 04:24:18 PST)
- Re: AMBER: Re: Calculating Energies with imin=5 Carlos Simmerling (Fri Nov 30 2007 - 04:32:04 PST)
  - Re: AMBER: Re: Calculating Energies with imin=5 Pavan G (Fri Nov 30 2007 - 04:55:14 PST)
    - Re: AMBER: Re: Calculating Energies with imin=5 Chris Moth (Fri Nov 30 2007 - 06:11:40 PST)
    - Re: AMBER: Re: Calculating Energies with imin=5 Pavan G (Fri Nov 30 2007 - 08:35:02 PST)
    - Re: AMBER: Re: Calculating Energies with imin=5 Chris Moth (Fri Nov 30 2007 - 09:49:46 PST)
AMBER: angle between vectors Mag. rer. nat. Hannes Wallnöfer (Fri Nov 30 2007 - 04:45:02 PST)
- Re: AMBER: angle between vectors Ilyas Yildirim (Fri Nov 30 2007 - 09:28:59 PST)
  - Re: AMBER: angle between vectors Mag. rer. nat. Hannes Wallnöfer (Sun Dec 02 2007 - 23:55:51 PST)
    - Re: AMBER: angle between vectors Prem (Tue Dec 04 2007 - 13:59:29 PST)
AMBER: Group input for restrained atoms Francesco Pietra (Fri Nov 30 2007 - 08:28:50 PST)
- Re: AMBER: Group input for restrained atoms Pavan G (Fri Nov 30 2007 - 08:43:23 PST)
  - Re: AMBER: Group input for restrained atoms Francesco Pietra (Fri Nov 30 2007 - 13:12:42 PST)
AMBER: Minimization amber9 segmentation fault Francesco Pietra (Sat Dec 01 2007 - 07:46:23 PST)
- Re: AMBER: Minimization amber9 segmentation fault Adrian Roitberg (Sat Dec 01 2007 - 08:17:15 PST)
  - Re: AMBER: Minimization amber9 segmentation fault Francesco Pietra (Sat Dec 01 2007 - 10:48:01 PST)
    - Re: AMBER: Minimization amber9 segmentation fault Adrian Roitberg (Sat Dec 01 2007 - 11:44:16 PST)
    - Re: AMBER: Minimization amber9 segmentation fault Francesco Pietra (Sun Dec 02 2007 - 01:51:42 PST)
AMBER: mm_pbsa continue run Christopher Gaughan (Sun Dec 02 2007 - 10:46:42 PST)
AMBER: I need some help in PTRAJ Vijay Manickam Achari (Sun Dec 02 2007 - 22:49:29 PST)
- Re: AMBER: I need some help in PTRAJ Chris Moth (Mon Dec 03 2007 - 17:29:21 PST)
AMBER: sander and pmemd Nadia Vahdati (Mon Dec 03 2007 - 05:20:17 PST)
- Re: AMBER: sander and pmemd Robert Duke (Mon Dec 03 2007 - 06:19:24 PST)
Fwd: Re: AMBER: Minimization amber9 segmentation fault Francesco Pietra (Mon Dec 03 2007 - 08:30:11 PST)
- Re: Fwd: Re: AMBER: Minimization amber9 segmentation fault David A. Case (Mon Dec 03 2007 - 09:08:48 PST)
  - Re: Fwd: Re: AMBER: Minimization amber9 segmentation fault Francesco Pietra (Mon Dec 03 2007 - 13:45:14 PST)
- Re: Fwd: Re: AMBER: Minimization amber9 segmentation fault Francesco Pietra (Mon Dec 03 2007 - 14:18:01 PST)
  - Re: Fwd: Re: AMBER: Minimization amber9 segmentation fault Ilyas Yildirim (Mon Dec 03 2007 - 14:42:54 PST)
AMBER: Free energy for part of the system jialei (Mon Dec 03 2007 - 11:12:47 PST)
- Re: AMBER: Free energy for part of the system David A. Case (Mon Dec 03 2007 - 18:35:50 PST)
  - RE: AMBER: Free energy for part of the system jialei (Tue Dec 04 2007 - 10:21:03 PST)
    - Re: AMBER: Free energy for part of the system David A. Case (Tue Dec 04 2007 - 10:37:16 PST)
    - RE: AMBER: Free energy for part of the system jialei (Tue Dec 04 2007 - 17:10:18 PST)
AMBER: During the Sander process, does the pH of the solution change orr not Fenghui Fan (Mon Dec 03 2007 - 17:58:44 PST)
AMBER: Restraintmask syntax Francesco Pietra (Tue Dec 04 2007 - 07:30:50 PST)
- RE: AMBER: Restraintmask syntax Steve Spronk (Tue Dec 04 2007 - 08:49:36 PST)
  - RE: AMBER: Restraintmask syntax Francesco Pietra (Tue Dec 04 2007 - 09:44:01 PST)
    - RE: AMBER: Restraintmask syntax Andrew Purkiss-Trew (Wed Dec 05 2007 - 02:39:08 PST)
    - RE: AMBER: Restraintmask syntax Francesco Pietra (Wed Dec 05 2007 - 10:00:49 PST)
AMBER: Solution Structure Determination Protocols - Simulated Annealing Seth Lilavivat (Tue Dec 04 2007 - 09:23:16 PST)
AMBER: correlation time Tuncel, Aytug (Tue Dec 04 2007 - 10:22:55 PST)
- Re: AMBER: correlation time David A. Case (Tue Dec 04 2007 - 10:40:20 PST)
- RE: AMBER: correlation time Tuncel, Aytug (Thu Dec 06 2007 - 01:44:29 PST)
  - Re: AMBER: correlation time David A. Case (Thu Dec 06 2007 - 09:09:07 PST)
AMBER: POPS Lipid Bilayer: Full Parameter/Topology File Lalit Dubey (Tue Dec 04 2007 - 16:39:29 PST)
- Re: AMBER: POPS Lipid Bilayer: Full Parameter/Topology File David A. Case (Tue Dec 04 2007 - 17:11:53 PST)
  - Re: AMBER: POPS Lipid Bilayer: Full Parameter/Topology File Lalit Dubey (Thu Dec 06 2007 - 22:45:59 PST)
AMBER: phosphorylation bosco (Tue Dec 04 2007 - 17:36:27 PST)
- Re: AMBER: phosphorylation FyD (Thu Dec 06 2007 - 12:07:57 PST)
AMBER: (no subject) Madjid Taghdir (Wed Dec 05 2007 - 01:18:11 PST)
AMBER: nmode ntrun=2 JM Beames (Wed Dec 05 2007 - 02:03:24 PST)
- Re: AMBER: nmode ntrun=2 David A. Case (Wed Dec 05 2007 - 09:58:34 PST)
  - Re: AMBER: nmode ntrun=2 JM Beames (Thu Dec 06 2007 - 03:48:43 PST)
    - Re: AMBER: nmode ntrun=2 David A. Case (Thu Dec 06 2007 - 09:06:01 PST)
    - Re: AMBER: nmode ntrun=2 JM Beames (Thu Dec 13 2007 - 07:29:54 PST)
    - Re: AMBER: nmode ntrun=2 David A. Case (Fri Dec 14 2007 - 10:27:44 PST)
AMBER: leap restrainTorsion fatima.chami.durham.ac.uk (Wed Dec 05 2007 - 02:24:30 PST)
- Re: AMBER: leap restrainTorsion David A. Case (Wed Dec 05 2007 - 08:50:12 PST)
AMBER: calcium and zinc parameter Madjid Taghdir (Wed Dec 05 2007 - 03:07:17 PST)
- Re: AMBER: calcium and zinc parameter Mattia Mori - CERM (Wed Dec 05 2007 - 03:15:08 PST)
  - Re: AMBER: calcium and zinc parameter Taufik Al-Sarraj (Wed Dec 05 2007 - 10:43:45 PST)
    - Re: AMBER: calcium and zinc parameter Mattia Mori - CERM (Thu Dec 06 2007 - 05:21:10 PST)
- Re: AMBER: calcium and zinc parameter Madjid Taghdir (Mon Dec 10 2007 - 23:21:37 PST)
  - Re: AMBER: calcium and zinc parameter Mattia Mori - CERM (Tue Dec 11 2007 - 05:07:31 PST)
AMBER: THF parameters Yves Boulard (Wed Dec 05 2007 - 02:21:04 PST)
- Re: AMBER: THF parameters FyD (Wed Dec 05 2007 - 06:32:27 PST)
  - Re: AMBER: THF parameters David A. Case (Wed Dec 05 2007 - 09:56:18 PST)
    - Re: AMBER: THF parameters Piotr Cieplak (Wed Dec 05 2007 - 11:33:42 PST)
    - Re: AMBER: THF parameters FyD (Wed Dec 05 2007 - 12:42:29 PST)
AMBER: Amber 9 - bugfix.40 fails Kevin Davies (Wed Dec 05 2007 - 09:27:27 PST)
- Re: AMBER: Amber 9 - bugfix.40 fails Holger Gohlke (Wed Dec 05 2007 - 09:56:23 PST)
AMBER: Bulk water simulation with centre of mass position restrain Biman Jana (Wed Dec 05 2007 - 10:08:56 PST)
Fwd: Re: AMBER: leap restrainTorsion fatima.chami.durham.ac.uk (Wed Dec 05 2007 - 10:45:24 PST)
- Re: Fwd: Re: AMBER: leap restrainTorsion David A. Case (Wed Dec 05 2007 - 18:15:36 PST)
  - AMBER: Surface Taufik Al-Sarraj (Thu Dec 06 2007 - 11:11:21 PST)
    - Re: AMBER: Surface David A. Case (Thu Dec 06 2007 - 13:34:04 PST)
AMBER: How to apply psuedo-bonds for restraints Seth Lilavivat (Wed Dec 05 2007 - 11:28:37 PST)
- Re: AMBER: How to apply psuedo-bonds for restraints David A. Case (Wed Dec 05 2007 - 18:16:43 PST)
  - Re: AMBER: How to apply psuedo-bonds for restraints Seth Lilavivat (Thu Dec 06 2007 - 08:08:55 PST)
    - Re: AMBER: How to apply psuedo-bonds for restraints David A. Case (Thu Dec 06 2007 - 08:56:59 PST)
AMBER: amber on AMD opteron-250 servaas michielssens (Wed Dec 05 2007 - 12:10:22 PST)
- Re: AMBER: amber on AMD opteron-250 Robert Duke (Wed Dec 05 2007 - 12:35:04 PST)
- Re: AMBER: amber on AMD opteron-250 David LeBard (Wed Dec 05 2007 - 12:29:22 PST)
- Re: AMBER: amber on AMD opteron-250 Robert Duke (Wed Dec 05 2007 - 13:31:28 PST)
  - AMBER: PMEMD compilation problems !! Sampath Koppole (Thu Dec 06 2007 - 06:42:06 PST)
    - Re: AMBER: PMEMD compilation problems !! Robert Duke (Thu Dec 06 2007 - 06:56:04 PST)
    - Re: AMBER: PMEMD compilation problems !! Robert Duke (Thu Dec 06 2007 - 07:07:21 PST)
- Re: AMBER: amber on AMD opteron-250 servaas michielssens (Tue Dec 11 2007 - 01:35:08 PST)
  - RE: AMBER: amber on AMD opteron-250 Ross Walker (Tue Dec 11 2007 - 07:52:07 PST)
    - RE: AMBER: amber on AMD opteron-250 servaas michielssens (Tue Dec 11 2007 - 12:27:20 PST)
    - RE: AMBER: amber on AMD opteron-250 Ross Walker (Tue Dec 11 2007 - 13:20:11 PST)
    - RE: AMBER: amber on AMD opteron-250 Christopher Jones (Tue Dec 11 2007 - 14:08:31 PST)
AMBER: MD_model Urszula Uciechowska (Wed Dec 05 2007 - 15:05:45 PST)
- Re: AMBER: MD_model Thomas Steinbrecher (Wed Dec 05 2007 - 15:26:04 PST)
- Re: AMBER: MD_model Ilyas Yildirim (Wed Dec 05 2007 - 15:54:50 PST)
AMBER: Making movies in VMD Lili Peng (Wed Dec 05 2007 - 16:57:08 PST)
- Re: AMBER: Making movies in VMD Vijay Singh (Wed Dec 05 2007 - 17:25:26 PST)
- Re: AMBER: Making movies in VMD rdauria.uci.edu (Wed Dec 05 2007 - 21:20:12 PST)
AMBER: Problem in running CARNAL Vijay Manickam Achari (Thu Dec 06 2007 - 00:44:09 PST)
AMBER: Problem in running CARNAL Vijay Manickam Achari (Thu Dec 06 2007 - 00:45:35 PST)
AMBER: compilation error in SGI Altix 4700 with Intel Fortran 10.1.008 and IMKL 10.0.1.014 Ye Mei (Thu Dec 06 2007 - 04:20:56 PST)
- Re: AMBER: compilation error in SGI Altix 4700 with Intel Fortran 10.1.008 and IMKL 10.0.1.014 Andreas Svrcek-Seiler (Thu Dec 06 2007 - 07:49:34 PST)
AMBER: pmend vs sander.MPI Francesco Pietra (Thu Dec 06 2007 - 07:13:39 PST)
- Re: AMBER: pmend vs sander.MPI Robert Duke (Thu Dec 06 2007 - 07:18:20 PST)
  - Re: AMBER: pmend vs sander.MPI Francesco Pietra (Sun Dec 09 2007 - 09:35:48 PST)
Re: AMBER: Problem in running CARNAL Bill Ross (Thu Dec 06 2007 - 11:37:07 PST)
- Re: AMBER: Problem in running CARNAL Bill Ross (Fri Dec 07 2007 - 09:48:15 PST)
Re: Re: AMBER: compilation error in SGI Altix 4700 with Intel Fortran10.1.008 and IMKL 10.0.1.014 Ye Mei (Thu Dec 06 2007 - 19:23:11 PST)
AMBER: Problem in running CARNAL Vijay Manickam Achari (Thu Dec 06 2007 - 21:52:26 PST)
AMBER: Troubles installing amber Margaret Doll (Fri Dec 07 2007 - 11:47:26 PST)
- Re: AMBER: Troubles installing amber Wei Zhang (Fri Dec 07 2007 - 11:54:47 PST)
  - Re: AMBER: Troubles installing amber Margaret Doll (Fri Dec 07 2007 - 13:36:36 PST)
    - Re: AMBER: Troubles installing amber David A. Case (Fri Dec 07 2007 - 14:15:36 PST)
    - Re: AMBER: Troubles installing amber Margaret Doll (Fri Dec 07 2007 - 14:22:22 PST)
- Re: AMBER: Troubles installing amber Alessandro Nascimento (Fri Dec 07 2007 - 11:55:54 PST)
AMBER: ** No torsion terms for SNI-NI-SNI-CT Boutheina Kerkeni (Fri Dec 07 2007 - 14:13:19 PST)
- Re: AMBER: ** No torsion terms for SNI-NI-SNI-CT David A. Case (Fri Dec 07 2007 - 17:24:30 PST)
AMBER: ** No torsion terms for SNI-NI-SNI-CT Boutheina Kerkeni (Fri Dec 07 2007 - 14:17:07 PST)
Re: AMBER: ** No torsion terms for SNI-NI-SNI-CT Bill Ross (Fri Dec 07 2007 - 14:20:49 PST)
AMBER: running equilibration Boutheina Kerkeni (Fri Dec 07 2007 - 16:29:59 PST)
- RE: AMBER: running equilibration Ross Walker (Fri Dec 07 2007 - 17:00:15 PST)
Re: AMBER: running equilibration Bill Ross (Fri Dec 07 2007 - 17:11:02 PST)
AMBER: Continuing an amber 8 simulation with amber 9 ming hui (Fri Dec 07 2007 - 23:03:55 PST)
- Re: AMBER: Continuing an amber 8 simulation with amber 9 David A. Case (Sat Dec 08 2007 - 10:40:09 PST)
AMBER: protein_model Urszula Uciechowska (Sat Dec 08 2007 - 08:11:16 PST)
- Re: AMBER: protein_model steinbrt.scripps.edu (Sat Dec 08 2007 - 10:51:35 PST)
  - AMBER: AMBER7 Si atom type Taufik Al-Sarraj (Wed Dec 12 2007 - 09:30:49 PST)
AMBER: Backbone atoms Boutheina Kerkeni (Sat Dec 08 2007 - 14:42:20 PST)
- Re: AMBER: Backbone atoms David A. Case (Sat Dec 08 2007 - 14:58:30 PST)
AMBER: website problems Sally Pias (Sat Dec 08 2007 - 21:06:16 PST)
- Re: AMBER: website problems David A. Case (Sun Dec 09 2007 - 09:03:47 PST)
  - Re: AMBER: website problems Andreas Svrcek-Seiler (Sun Dec 09 2007 - 09:25:12 PST)
- RE: AMBER: website problems Ross Walker (Sun Dec 09 2007 - 09:52:42 PST)
  - Re: AMBER: website problems Sally Pias (Sun Dec 09 2007 - 10:45:51 PST)
  - RE: AMBER: website problems Ross Walker (Sun Dec 09 2007 - 11:06:00 PST)
AMBER: ptraj with protein-ligand Francesco Pietra (Sun Dec 09 2007 - 02:11:30 PST)
AMBER: Fwd: ptraj with protein-ligand Francesco Pietra (Sun Dec 09 2007 - 02:18:24 PST)
AMBER: Troubling with installing Amber8 #NGUYEN CONG TRI# (Sun Dec 09 2007 - 04:06:18 PST)
- Re: AMBER: Troubling with installing Amber8 David A. Case (Sun Dec 09 2007 - 09:18:29 PST)
- RE: AMBER: Troubling with installing Amber8 #NGUYEN CONG TRI# (Thu Dec 13 2007 - 06:19:47 PST)
  - Re: AMBER: Troubling with installing Amber8 David A. Case (Fri Dec 14 2007 - 08:39:58 PST)
AMBER: some input problem Urszula Uciechowska (Sun Dec 09 2007 - 07:25:52 PST)
- Re: AMBER: some input problem David A. Case (Sun Dec 09 2007 - 09:09:51 PST)
AMBER: Re: Amber_ifort_x86_64 test error Ilya Chorny (Sun Dec 09 2007 - 08:46:32 PST)
- Re: AMBER: Re: Amber_ifort_x86_64 test error David A. Case (Sun Dec 09 2007 - 09:13:00 PST)
  - Re: AMBER: Re: Amber_ifort_x86_64 test error Ilya Chorny (Sun Dec 09 2007 - 09:22:17 PST)
    - RE: AMBER: Re: Amber_ifort_x86_64 test error Ross Walker (Sun Dec 09 2007 - 10:01:57 PST)
    - Re: AMBER: Re: Amber_ifort_x86_64 test error Ilya Chorny (Sun Dec 09 2007 - 10:11:52 PST)
    - Re: AMBER: Re: Amber_ifort_x86_64 test error Ilya Chorny (Sun Dec 09 2007 - 10:12:57 PST)
    - RE: AMBER: Re: Amber_ifort_x86_64 test error Ross Walker (Sun Dec 09 2007 - 10:57:55 PST)
    - RE: AMBER: Re: Amber_ifort_x86_64 test error Ross Walker (Sun Dec 09 2007 - 11:54:44 PST)
    - RE: AMBER: Re: Amber_ifort_x86_64 test error Ilyas Yildirim (Sun Dec 09 2007 - 13:56:09 PST)
    - Re: AMBER: Re: Amber_ifort_x86_64 test error Ilya Chorny (Sun Dec 09 2007 - 18:42:45 PST)
AMBER: Ligand-Residue interaction tracking Evan Kelly (Mon Dec 10 2007 - 10:20:29 PST)
AMBER: TI Approach - mass perturbation Ilyas Yildirim (Mon Dec 10 2007 - 10:20:49 PST)
- Re: AMBER: TI Approach - mass perturbation David A. Case (Mon Dec 10 2007 - 23:13:08 PST)
  - Re: AMBER: TI Approach - mass perturbation Ilyas Yildirim (Mon Dec 10 2007 - 23:47:52 PST)
AMBER: implicit solvent simulations with calcium ion Akansha Saxena (Mon Dec 10 2007 - 13:19:01 PST)
AMBER: tleap crashing Ranjib Dey (Tue Dec 11 2007 - 11:12:20 PST)
- Re: AMBER: tleap crashing David A. Case (Tue Dec 11 2007 - 15:04:25 PST)
  - Re: AMBER: tleap crashing Ranjib Dey (Tue Dec 11 2007 - 23:04:55 PST)
AMBER: implicit solvent simulations WANG,YING (Tue Dec 11 2007 - 11:21:11 PST)
- Re: AMBER: implicit solvent simulations liu junjun (Tue Dec 11 2007 - 19:49:57 PST)
  - RE: AMBER: implicit solvent simulations Steve Spronk (Wed Dec 12 2007 - 05:00:01 PST)
- Re: AMBER: implicit solvent simulations WANG,YING (Tue Dec 11 2007 - 20:00:59 PST)
AMBER: amber 9 sander crashed with "forrtl: severe (174): SIGSEGV, segmentation fault occurred" Shuzhi Wang (Tue Dec 11 2007 - 13:07:25 PST)
- RE: AMBER: amber 9 sander crashed with "forrtl: severe (174): SIGSEGV, segmentation fault occurred" Ross Walker (Tue Dec 11 2007 - 13:32:43 PST)
  - Re: AMBER: amber 9 sander crashed with "forrtl: severe (174): SIGSEGV, segmentation fault occurred" Shuzhi Wang (Mon Dec 17 2007 - 14:49:57 PST)
    - RE: AMBER: amber 9 sander crashed with "forrtl: severe (174): SIGSEGV, segmentation fault occurred" Ross Walker (Mon Dec 17 2007 - 15:20:23 PST)
AMBER: equilibration Urszula Uciechowska (Wed Dec 12 2007 - 09:08:00 PST)
AMBER: Free Energy Calculations Mike Wykes (Wed Dec 12 2007 - 10:08:20 PST)
- Re: AMBER: Free Energy Calculations Thomas Steinbrecher (Wed Dec 12 2007 - 11:19:55 PST)
AMBER: New 2 the board Campbell, Patrick (Wed Dec 12 2007 - 13:12:30 PST)
- Re: AMBER: New 2 the board David A. Case (Wed Dec 12 2007 - 16:03:46 PST)
  - AMBER: loading a crystal PDB file Taufik Al-Sarraj (Wed Dec 12 2007 - 17:33:36 PST)
AMBER: make test.parallel not complete Prem Prakash Pathak (Thu Dec 13 2007 - 00:10:16 PST)
- RE: AMBER: make test.parallel not complete Ross Walker (Thu Dec 13 2007 - 06:19:42 PST)
  - Re: AMBER: make test.parallel not complete Prem Prakash Pathak (Thu Dec 20 2007 - 01:59:03 PST)
AMBER: MMPBSA Syed Tarique Moin (Thu Dec 13 2007 - 04:34:21 PST)
AMBER: protein-ligand binding affinity Francesco Pietra (Thu Dec 13 2007 - 06:00:17 PST)
AMBER: help in QM/MM simulation Pankaj R. Daga (Thu Dec 13 2007 - 13:02:17 PST)
- Re: AMBER: help in QM/MM simulation Gustavo Seabra (Wed Dec 19 2007 - 06:42:19 PST)
AMBER: PMEMD internals !! Sampath Koppole (Fri Dec 14 2007 - 01:13:49 PST)
- Re: AMBER: PMEMD internals !! Robert Duke (Fri Dec 14 2007 - 05:41:43 PST)
AMBER: replica exchange out files continually overwritten David Mobley (Fri Dec 14 2007 - 09:02:41 PST)
- Re: AMBER: replica exchange out files continually overwritten David A. Case (Fri Dec 14 2007 - 09:17:09 PST)
  - Re: AMBER: replica exchange out files continually overwritten David Mobley (Fri Dec 14 2007 - 10:47:27 PST)
    - Re: AMBER: replica exchange out files continually overwritten Carlos Simmerling (Fri Dec 14 2007 - 10:58:36 PST)
    - Re: AMBER: replica exchange out files continually overwritten David Mobley (Fri Dec 14 2007 - 11:18:21 PST)
    - Re: AMBER: replica exchange out files continually overwritten Carlos Simmerling (Fri Dec 14 2007 - 13:11:37 PST)
    - AMBER: xleap loading files Taufik Al-Sarraj (Fri Dec 14 2007 - 14:20:08 PST)
    - Re: AMBER: xleap loading files David A. Case (Fri Dec 14 2007 - 22:26:13 PST)
    - Re: AMBER: xleap loading files FyD (Sat Dec 15 2007 - 05:04:46 PST)
    - Re: AMBER: replica exchange out files continually overwritten David Mobley (Fri Dec 14 2007 - 15:04:50 PST)
- Re: AMBER: replica exchange out files continually overwritten Adrian Roitberg (Fri Dec 14 2007 - 10:33:23 PST)
AMBER: Time step & non-bonded interactions updating Francesco Pietra (Sat Dec 15 2007 - 10:39:48 PST)
- RE: AMBER: Time step & non-bonded interactions updating Ross Walker (Sat Dec 15 2007 - 17:32:08 PST)
  - RE: AMBER: Time step & non-bonded interactions updating Francesco Pietra (Sun Dec 16 2007 - 08:36:46 PST)
    - AMBER: pmemd: same rst, different result? Anselm Horn (Mon Dec 17 2007 - 01:54:20 PST)
    - Re: AMBER: pmemd: same rst, different result? Benjamin Juhl (Mon Dec 17 2007 - 02:25:04 PST)
    - Re: AMBER: pmemd: same rst, different result? Robert Duke (Mon Dec 17 2007 - 07:29:15 PST)
    - Re: AMBER: pmemd: same rst, different result? Anselm Horn (Tue Dec 18 2007 - 01:10:20 PST)
    - Re: AMBER: pmemd: same rst, different result? Robert Duke (Tue Dec 18 2007 - 05:51:04 PST)
    - Re: AMBER: pmemd: same rst, different result? David A. Case (Tue Dec 18 2007 - 07:46:56 PST)
    - RE: AMBER: pmemd: same rst, different result? Yong Duan (Tue Dec 18 2007 - 09:47:31 PST)
    - Re: AMBER: pmemd: same rst, different result? Robert Duke (Tue Dec 18 2007 - 18:26:34 PST)
    - Re: AMBER: pmemd: same rst, different result? Thomas Cheatham (Tue Dec 18 2007 - 22:39:50 PST)
    - Re: AMBER: pmemd: same rst, different result? Robert Duke (Wed Dec 19 2007 - 06:12:56 PST)
AMBER: MMTSB Toolset Urszula Uciechowska (Mon Dec 17 2007 - 04:19:34 PST)
- Re: AMBER: MMTSB Toolset Carlos Simmerling (Mon Dec 17 2007 - 04:26:27 PST)
AMBER: amber9/mmtsb Francesco Pietra (Tue Dec 18 2007 - 02:21:31 PST)
- Re: AMBER: amber9/mmtsb David A. Case (Tue Dec 18 2007 - 07:59:11 PST)
  - Re: AMBER: amber9/mmtsb Francesco Pietra (Tue Dec 18 2007 - 09:15:55 PST)
    - Re: AMBER: amber9/mmtsb David A. Case (Wed Dec 19 2007 - 08:19:47 PST)
AMBER: Scripts for md analysis Francesco Pietra (Tue Dec 18 2007 - 03:05:24 PST)
AMBER: PME and counter ions Lars Skjærven (Tue Dec 18 2007 - 08:04:12 PST)
Re: AMBER: PME and counter ions Bill Ross (Tue Dec 18 2007 - 10:36:38 PST)
- Re: AMBER: PME and counter ions Lars Skjærven (Tue Dec 18 2007 - 18:34:26 PST)
  - Re: AMBER: PME and counter ions Pablo Englebienne (Wed Dec 19 2007 - 11:05:30 PST)
    - Re: AMBER: PME and counter ions David A. Case (Wed Dec 19 2007 - 12:01:55 PST)
AMBER: closest water molecules with 8 angstroms nag raj (Tue Dec 18 2007 - 22:52:45 PST)
- Re: AMBER: closest water molecules with 8 angstroms Alessandro Nascimento (Wed Dec 19 2007 - 02:49:56 PST)
AMBER: Electron density profile Age.Skjevik.student.uib.no (Thu Dec 20 2007 - 04:13:56 PST)
AMBER: Use of Counter Ions in binding energy calculations Jonathan Suever (Thu Dec 20 2007 - 10:42:15 PST)
AMBER: Steered MD M kutty (Thu Dec 20 2007 - 22:03:29 PST)
- Re: AMBER: Steered MD M. L. Dodson (Fri Dec 21 2007 - 07:52:30 PST)
  - Re: AMBER: Steered MD M. L. Dodson (Fri Dec 21 2007 - 08:00:58 PST)
    - RE: AMBER: Steered MD M kutty (Sun Dec 23 2007 - 21:04:41 PST)
AMBER: No radius found for K+ (MM_PBSA) saurabh agrawal (Fri Dec 21 2007 - 06:45:01 PST)
- Re: AMBER: No radius found for K+ (MM_PBSA) Thomas Cheatham III (Fri Dec 21 2007 - 10:53:55 PST)
AMBER: About protein-ligand binding Francesco Pietra (Fri Dec 21 2007 - 06:52:00 PST)
AMBER: RESP using antechamber snoze pa (Sat Dec 22 2007 - 11:21:07 PST)
- Re: AMBER: RESP using antechamber Barbault Florent (Sat Dec 22 2007 - 12:13:31 PST)
AMBER: installation of amber9 on suse linux 10.3 s lal badshah (Sun Dec 23 2007 - 21:47:21 PST)
- Re: AMBER: installation of amber9 on suse linux 10.3 David A. Case (Sun Dec 23 2007 - 22:03:38 PST)
  - Re: AMBER: installation of amber9 on suse linux 10.3 s lal badshah (Wed Dec 26 2007 - 21:02:24 PST)
    - RE: AMBER: installation of amber9 on suse linux 10.3 Ross Walker (Wed Dec 26 2007 - 22:18:51 PST)
AMBER: installation s lal badshah (Wed Dec 26 2007 - 21:11:29 PST)
- Re: AMBER: installation Mark Williamson (Sat Dec 29 2007 - 09:23:15 PST)
AMBER: RESP charge fitting using antechamber Wei Chen (Sat Dec 29 2007 - 11:22:16 PST)
- Re: AMBER: RESP charge fitting using antechamber David A. Case (Sat Dec 29 2007 - 18:05:25 PST)
- Re: AMBER: RESP charge fitting using antechamber FyD (Sun Dec 30 2007 - 06:54:59 PST)
  - Re: AMBER: RESP charge fitting using antechamber Francesco Pietra (Sun Dec 30 2007 - 23:19:42 PST)
    - Re: AMBER: RESP charge fitting using antechamber FyD (Mon Dec 31 2007 - 07:40:11 PST)
- Re: AMBER: RESP charge fitting using antechamber FyD (Mon Dec 31 2007 - 06:06:34 PST)
AMBER: About RAMD Francesco Pietra (Mon Dec 31 2007 - 07:27:36 PST)
AMBER: a question of ptraj WANG,YING (Mon Dec 31 2007 - 11:39:03 PST)
- Re: AMBER: a question of ptraj Chris Moth (Mon Dec 31 2007 - 12:38:21 PST)
- Re: AMBER: a question of ptraj WANG,YING (Wed Jan 02 2008 - 10:04:24 PST)
AMBER: ff03-compatible parameters/charges for phosphothreonine and phosphotyrosine John Chodera (Tue Jan 01 2008 - 17:44:34 PST)
- Re: AMBER: ff03-compatible parameters/charges for phosphothreonine and phosphotyrosine FyD (Wed Jan 02 2008 - 00:52:15 PST)
- Re: AMBER: ff03-compatible parameters/charges for phosphothreonine and phosphotyrosine FyD (Fri Jan 04 2008 - 02:34:00 PST)
AMBER: Help reg. input file snoze pa (Wed Jan 02 2008 - 10:34:56 PST)
- Re: AMBER: Help reg. input file FyD (Wed Jan 02 2008 - 11:34:40 PST)
  - Re: AMBER: Help reg. input file snoze pa (Wed Jan 02 2008 - 11:50:50 PST)
    - Re: AMBER: Help reg. input file FyD (Wed Jan 02 2008 - 12:21:03 PST)
AMBER: AMBER-8 parallel installation - test run failure brmeher.iitg.ernet.in (Thu Jan 03 2008 - 02:10:58 PST)
- Re: AMBER: AMBER-8 parallel installation - test run failure Ming Lei (Thu Jan 03 2008 - 06:08:46 PST)
AMBER: question about antechamber Lynn (Thu Jan 03 2008 - 06:32:56 PST)
- Re: AMBER: question about antechamber Junmei Wang (Thu Jan 03 2008 - 07:18:34 PST)
AMBER: Thermodynamic integration with positional restraint? Cen Gao (Thu Jan 03 2008 - 08:43:32 PST)
- Re: AMBER: Thermodynamic integration with positional restraint? David A. Case (Thu Jan 03 2008 - 09:31:19 PST)
AMBER: Combine mdcrd files Francesco Pietra (Thu Jan 03 2008 - 15:01:47 PST)
- Re: AMBER: Combine mdcrd files Carlos Simmerling (Thu Jan 03 2008 - 15:09:23 PST)
- RE: AMBER: Combine mdcrd files Ross Walker (Fri Jan 04 2008 - 08:35:23 PST)
AMBER: MM-PBSA problem stephane acoca (Thu Jan 03 2008 - 19:45:10 PST)
- Re: AMBER: MM-PBSA problem Miguel Ferreira (Mon Apr 17 2006 - 10:24:05 PDT)
- Re: AMBER: MM-PBSA problem Jack Lei (Fri Jan 04 2008 - 17:31:05 PST)
  - Re: AMBER: MM-PBSA problem David A. Case (Fri Jan 04 2008 - 18:07:07 PST)
AMBER: check COM velocity Pankaj R. Daga (Fri Jan 04 2008 - 08:06:26 PST)
- Re: AMBER: check COM velocity David A. Case (Fri Jan 04 2008 - 08:29:09 PST)
- Re: AMBER: check COM velocity Lars Skjærven (Fri Jan 04 2008 - 08:36:53 PST)
AMBER: Combine mdcrd Francesco Pietra (Fri Jan 04 2008 - 08:37:07 PST)
- Re: AMBER: Combine mdcrd Carlos Simmerling (Fri Jan 04 2008 - 08:44:55 PST)
  - Re: AMBER: Combine mdcrd Francesco Pietra (Fri Jan 04 2008 - 09:07:15 PST)
AMBER: FW: AMBER vs Gaussian : zero VDW parameters? Ross Walker (Fri Jan 04 2008 - 09:01:14 PST)
Fwd: Re: AMBER: Combine mdcrd Francesco Pietra (Fri Jan 04 2008 - 09:23:45 PST)
- Re: Re: AMBER: Combine mdcrd Carlos Simmerling (Fri Jan 04 2008 - 09:30:31 PST)
Fwd: Re: AMBER: Combine mdcrd Francesco Pietra (Fri Jan 04 2008 - 09:36:49 PST)
- Re: Re: AMBER: Combine mdcrd Carlos Simmerling (Fri Jan 04 2008 - 09:56:04 PST)
  - Re: Re: AMBER: Combine mdcrd Francesco Pietra (Fri Jan 04 2008 - 13:26:32 PST)
AMBER: Combining multiple structures into single pdb Seth Lilavivat (Fri Jan 04 2008 - 12:21:58 PST)
AMBER: mm/pbsa and saltcon effect Christopher Gaughan (Fri Jan 04 2008 - 13:40:17 PST)
AMBER: amber :antechamber problem jani sahil (Fri Jan 04 2008 - 19:51:56 PST)
- Re: AMBER: amber :antechamber problem Wei Chen (Mon Jan 07 2008 - 08:14:53 PST)
- Re: AMBER: amber :antechamber problem Florian Haberl (Mon Jan 07 2008 - 08:33:02 PST)
  - AMBER: RESP Syed Tarique Moin (Tue Jan 08 2008 - 04:40:03 PST)
    - Re: AMBER: RESP FyD (Tue Jan 08 2008 - 11:49:31 PST)
    - Re: AMBER: RESP Syed Tarique Moin (Wed Jan 09 2008 - 22:36:05 PST)
    - Re: AMBER: RESP FyD (Wed Jan 09 2008 - 23:39:01 PST)
    - Re: AMBER: RESP Syed Tarique Moin (Thu Jan 10 2008 - 01:15:15 PST)
  - AMBER: RESP Syed Tarique Moin (Tue Jan 08 2008 - 04:41:06 PST)
  - AMBER: RESP Syed Tarique Moin (Tue Jan 08 2008 - 04:41:56 PST)
  - AMBER: RESP Syed Tarique Moin (Tue Jan 08 2008 - 04:40:21 PST)
AMBER: antechamber problems jani sahil (Fri Jan 04 2008 - 19:49:10 PST)
- RE: AMBER: antechamber problems Junmei Wang (Mon Jun 20 2005 - 09:35:12 PDT)
  - Re: AMBER: antechamber problems Shulin Zhuang (Mon Jun 20 2005 - 18:07:56 PDT)
- Re: AMBER: antechamber problems Junmei Wang (Sat Jan 05 2008 - 21:35:04 PST)
AMBER: About RAMD Francesco Pietra (Sat Jan 05 2008 - 02:39:44 PST)
- Re: AMBER: About RAMD Carlos Simmerling (Sat Jan 05 2008 - 08:12:40 PST)
  - Re: AMBER: About RAMD Francesco Pietra (Sat Jan 05 2008 - 08:26:01 PST)
    - Re: AMBER: About RAMD Carlos Simmerling (Sat Jan 05 2008 - 08:46:32 PST)
AMBER: NMROPT=1 in minimisation Binbin Liu (Sat Jan 05 2008 - 15:38:51 PST)
- Re: AMBER: NMROPT=1 in minimisation David A. Case (Sun Jan 06 2008 - 12:59:03 PST)
AMBER: temperature spikes Sally Pias (Sat Jan 05 2008 - 22:26:55 PST)
- Re: AMBER: temperature spikes Adrian Roitberg (Sun Jan 06 2008 - 08:41:50 PST)
AMBER: MD of protein-ligand comlex umbrita itl (Sun Jan 06 2008 - 12:54:47 PST)
- Re: AMBER: MD of protein-ligand comlex Syed Tarique Moin (Sun Jan 06 2008 - 22:18:20 PST)
- Re: AMBER: MD of protein-ligand comlex Chris Moth (Mon Jan 07 2008 - 04:10:23 PST)
AMBER: Cluster analysis Francesco Pietra (Mon Jan 07 2008 - 08:00:40 PST)
- Re: AMBER: Cluster analysis Carlos Simmerling (Mon Jan 07 2008 - 08:18:22 PST)
AMBER: Structure comparison-NMR and X-ray structure using AMBER9 Prem Prakash Pathak (Mon Jan 07 2008 - 08:11:22 PST)
- Re: AMBER: Structure comparison-NMR and X-ray structure using AMBER9 Carlos Simmerling (Mon Jan 07 2008 - 08:16:16 PST)
AMBER: offset residue numbering Brendan Duggan (Mon Jan 07 2008 - 12:14:30 PST)
- Re: AMBER: offset residue numbering David A. Case (Fri Jan 11 2008 - 23:10:08 PST)
AMBER: Torsional Forcing to generate PES? Praveena Gopal (Mon Jan 07 2008 - 20:42:04 PST)
- Re: AMBER: Torsional Forcing to generate PES? Chris Moth (Tue Jan 08 2008 - 09:08:12 PST)
AMBER: Nudged Elastic Band initial heating problem Mike Wykes (Tue Jan 08 2008 - 02:42:09 PST)
- Re: AMBER: Nudged Elastic Band initial heating problem Keith Van Nostrand (Tue Jan 08 2008 - 05:32:31 PST)
- RE: AMBER: Nudged Elastic Band initial heating problem Ross Walker (Tue Jan 08 2008 - 15:00:59 PST)
AMBER: solvateBox/solvateDontClip darkcz.tlen.pl (Tue Jan 08 2008 - 08:02:19 PST)
AMBER: Problem about antechamber 捞毛渔 (Tue Jan 08 2008 - 08:09:03 PST)
AMBER: A problem about antechamber 捞毛渔 (Tue Jan 08 2008 - 08:03:49 PST)
- Re: AMBER: A problem about antechamber Junmei Wang (Tue Jan 08 2008 - 14:19:15 PST)
AMBER: connectivity problem rams rams (Wed Jan 09 2008 - 06:53:55 PST)
- Re: AMBER: connectivity problem Junmei Wang (Wed Jan 09 2008 - 07:51:05 PST)
  - Re: AMBER: connectivity problem rams rams (Wed Jan 09 2008 - 21:04:41 PST)
    - Re: AMBER: connectivity problem Junmei Wang (Thu Jan 10 2008 - 07:27:07 PST)
AMBER: The energy minimization of SIngle RNA chain backy (Thu Jan 10 2008 - 00:33:20 PST)
AMBER: input options for replica exchange simulations rebeca.mmb.pcb.ub.es (Thu Jan 10 2008 - 08:46:42 PST)
- Re: AMBER: input options for replica exchange simulations Carlos Simmerling (Thu Jan 10 2008 - 08:57:12 PST)
  - Re: AMBER: input options for replica exchange simulations Adrian Roitberg (Thu Jan 10 2008 - 09:28:50 PST)
    - Re: AMBER: input options for replica exchange simulations rebeca.mmb.pcb.ub.es (Thu Jan 10 2008 - 10:00:10 PST)
    - Re: AMBER: input options for replica exchange simulations Carlos Simmerling (Thu Jan 10 2008 - 12:50:18 PST)
AMBER: using hydrogen bond facility to monitor ion pair interaction Zhenwei Lu (Thu Jan 10 2008 - 09:09:09 PST)
- Re: AMBER: using hydrogen bond facility to monitor ion pair interaction Thomas Cheatham III (Thu Jan 10 2008 - 09:21:10 PST)
  - Re: AMBER: using hydrogen bond facility to monitor ion pair interaction Zhenwei Lu (Thu Jan 10 2008 - 10:16:57 PST)
AMBER: antechamber problem gurpreet singh (Thu Jan 10 2008 - 09:49:15 PST)
- RE: AMBER: antechamber problem Junmei Wang (Tue Sep 20 2005 - 16:05:36 PDT)
- Re: AMBER: antechamber problem bybaker.itsa.ucsf.edu (Wed Sep 21 2005 - 17:55:45 PDT)
- Re: AMBER: antechamber problem bybaker.itsa.ucsf.edu (Wed Dec 21 2005 - 21:39:24 PST)
  - Re: AMBER: antechamber problem Ilyas Yildirim (Fri Dec 30 2005 - 16:25:38 PST)
- RE: AMBER: antechamber problem Baker, Bo-Yang (Mon Jan 02 2006 - 16:23:40 PST)
- Re: AMBER: antechamber problem Junmei Wang (Thu Jan 10 2008 - 10:29:23 PST)
  - Re: AMBER: antechamber problem gurpreet singh (Thu Jan 10 2008 - 20:05:38 PST)
AMBER: ANTECHAMBER NAMING Shozeb Haider (Thu Jan 10 2008 - 13:19:18 PST)
- Re: AMBER: ANTECHAMBER NAMING David A. Case (Thu Jan 10 2008 - 19:32:30 PST)
  - Re: AMBER: ANTECHAMBER NAMING FyD (Thu Jan 10 2008 - 23:53:04 PST)
AMBER: graphite Boutheina Kerkeni (Fri Jan 11 2008 - 03:26:58 PST)
AMBER: chromophore parameters for Molecular Dynamics Anthony Cruz (Fri Jan 11 2008 - 07:32:31 PST)
- Re: AMBER: chromophore parameters for Molecular Dynamics FyD (Fri Jan 11 2008 - 12:57:19 PST)
  - Re: AMBER: chromophore parameters for Molecular Dynamics Anthony Cruz (Wed Jan 16 2008 - 05:47:42 PST)
    - Re: AMBER: chromophore parameters for Molecular Dynamics FyD (Wed Jan 16 2008 - 06:59:31 PST)
AMBER: problems with restart of MD Vijay Singh (Fri Jan 11 2008 - 09:29:31 PST)
- Re: AMBER: problems with restart of MD Age.Skjevik.student.uib.no (Fri Jan 11 2008 - 10:16:00 PST)
- RE: AMBER: problems with restart of MD Pankaj R. Daga (Fri Jan 11 2008 - 10:34:13 PST)
- RE: AMBER: problems with restart of MD Ross Walker (Fri Jan 11 2008 - 11:56:16 PST)
  - Re: AMBER: problems with restart of MD Vijay Singh (Fri Jan 11 2008 - 12:04:39 PST)
    - Re: AMBER: problems with restart of MD Vijay Singh (Sat Jan 12 2008 - 01:48:39 PST)
    - RE: AMBER: problems with restart of MD Ross Walker (Sat Jan 12 2008 - 18:58:20 PST)
    - Re: AMBER: problems with restart of MD Vijay Singh (Sun Jan 13 2008 - 07:45:25 PST)
    - RE: AMBER: problems with restart of MD Yong Duan (Sun Jan 13 2008 - 10:08:52 PST)
    - Re: AMBER: problems with restart of MD Vijay Singh (Sun Jan 13 2008 - 11:53:11 PST)
    - RE: AMBER: problems with restart of MD Yong Duan (Mon Jan 14 2008 - 10:16:24 PST)
AMBER: Visualizing Electrostatic Potential Seth Lilavivat (Fri Jan 11 2008 - 11:57:31 PST)
AMBER: Amber DNA Model for X-ray Crystallography Hopkins, Robert (Fri Jan 11 2008 - 15:32:00 PST)
AMBER: Unable to create the top & crd files for a protein+ligand pdb structure abiram abiram (Fri Jan 11 2008 - 23:54:01 PST)
- Re: AMBER: Unable to create the top & crd files for a protein+ligand pdb structure Jiten (Sat Jan 12 2008 - 00:21:01 PST)
AMBER: connectivity lose during the minimizations rams rams (Sat Jan 12 2008 - 03:40:21 PST)
- Re: AMBER: connectivity lose during the minimizations David A. Case (Sat Jan 12 2008 - 12:28:37 PST)
AMBER: build RNA by nucgen 欧阳德方 (Sat Jan 12 2008 - 18:26:44 PST)
- Re: AMBER: build RNA by nucgen David A. Case (Sun Jan 13 2008 - 09:56:32 PST)
  - AMBER: Back on track Mike Summers (Mon Jan 28 2008 - 17:39:32 PST)
    - Re: AMBER: Back on track David A. Case (Wed Jan 30 2008 - 17:33:46 PST)
AMBER: problem:capping jani sahil (Sat Jan 12 2008 - 18:53:24 PST)
- Re: AMBER: problem:capping David A. Case (Sun Jan 13 2008 - 09:10:55 PST)
AMBER: problem in neturalization jani sahil (Sat Jan 12 2008 - 19:27:31 PST)
AMBER: Distorsion in protein and ligand during MD Francesco Pietra (Sun Jan 13 2008 - 01:46:23 PST)
AMBER: Fwd: Distorsion in protein and ligand during MD Francesco Pietra (Sun Jan 13 2008 - 01:57:43 PST)
AMBER: ELAN_EXCEPTION . --: 6 (Initialisation error) ELAN_EXCEPTION @ --: 6 (Initialisation error) Neko Maryam. (Sun Jan 13 2008 - 21:44:10 PST)
- Re: AMBER: ELAN_EXCEPTION . --: 6 (Initialisation error) ELAN_EXCEPTION @ --: 6 (Initialisation error) David A. Case (Sun Jan 13 2008 - 22:16:31 PST)
  - Re: AMBER: ELAN_EXCEPTION . --: 6 (Initialisation error) ELAN_EXCEPTION @ --: 6 (Initialisation error) Neko Maryam. (Sun Jan 13 2008 - 22:23:58 PST)
    - Re: AMBER: ELAN_EXCEPTION . --: 6 (Initialisation error) ELAN_EXCEPTION @ --: 6 (Initialisation error) Neko Maryam. (Sun Jan 13 2008 - 22:54:28 PST)
AMBER: Amber : neutralizing without adding ions jani sahil (Mon Jan 14 2008 - 03:43:01 PST)
- Re: AMBER: Amber : neutralizing without adding ions Lars Skjærven (Mon Jan 14 2008 - 07:41:55 PST)
AMBER: pmemd 9.0 compilation error Raphael Chaleil (Mon Jan 14 2008 - 06:38:12 PST)
- Re: AMBER: pmemd 9.0 compilation error Robert Duke (Mon Jan 14 2008 - 07:19:51 PST)
AMBER: QM/MM Heating Steven Winfield (Mon Jan 14 2008 - 07:22:27 PST)
- Re: AMBER: QM/MM Heating Steven Winfield (Mon Jan 21 2008 - 05:48:22 PST)
  - Re: AMBER: QM/MM Heating Adrian Roitberg (Mon Jan 21 2008 - 08:13:18 PST)
- RE: AMBER: QM/MM Heating Ross Walker (Mon Jan 21 2008 - 08:41:31 PST)
  - Re: AMBER: QM/MM Heating Steven Winfield (Wed Jan 23 2008 - 04:30:11 PST)
    - RE: AMBER: QM/MM Heating Ross Walker (Tue Jan 29 2008 - 06:49:48 PST)
AMBER: Disturb you for help! 捞毛渔 (Mon Jan 14 2008 - 08:16:37 PST)
- RE: AMBER: Disturb you for help! Yong Duan (Mon Jan 14 2008 - 12:06:11 PST)
  - 回复： RE: AMBER: Disturb you for help !?= 捞毛渔 (Mon Jan 14 2008 - 16:12:27 PST)
    - AMBER: RE: 回复： RE: AMBER: Disturb you for help !?= Yong Duan (Mon Jan 14 2008 - 20:14:26 PST)
    - 回复： AMBER: RE: 回复： RE: AMBER: Disturb you for help !?= 捞毛渔 (Mon Jan 14 2008 - 21:33:49 PST)
    - AMBER: RE: 回复： AMBER: RE: 回复： RE: AMBER: Disturb you for help !?= Yong Duan (Mon Jan 14 2008 - 23:40:39 PST)
    - 回复： AMBER: RE: 回复： AMBER: RE: 回复： RE: AMBER: Disturb you for help !?= 捞毛渔 (Tue Jan 15 2008 - 17:24:30 PST)
    - AMBER: RE: 回复： AMBER: RE: 回复： AMBER: RE: 回复： RE: AMBER: Disturb you for help !?= Yong Duan (Tue Jan 15 2008 - 20:16:10 PST)
    - 回复： AMBER: RE: 回复： AMBER(wrong string) �(wrong string) � RE: AMBER: Disturb you for help !?= 捞毛渔 (Wed Jan 16 2008 - 06:55:37 PST)
    - AMBER: RE: 回复： AMBER: RE: 回复： AMBER: RE: 回复： AMBER: RE: 回复： RE: AMBER: Disturb you for help !?= Yong Duan (Wed Jan 16 2008 - 08:13:15 PST)
    - 回复： AMBER: RE: 回复： AMBER(wrong string) �(wrong string) � AMBER: RE: �ظ�� RE: AMBER: Disturb you for help !?= 捞毛渔 (Thu Jan 17 2008 - 07:33:28 PST)
AMBER: running AMBER in NAMD Trucated Octahedron Seth Lilavivat (Mon Jan 14 2008 - 14:19:05 PST)
- Re: AMBER: running AMBER in NAMD Trucated Octahedron Jojart Balazs (Mon Jan 14 2008 - 14:31:05 PST)
AMBER: Using VMD to calculate end-to-end distance? Lili Peng (Mon Jan 14 2008 - 14:41:55 PST)
- Re: AMBER: Using VMD to calculate end-to-end distance? Keith Van Nostrand (Mon Jan 14 2008 - 19:35:42 PST)
AMBER: How to build a dimer using amber Reena ..... (Mon Jan 14 2008 - 23:19:45 PST)
- Re: AMBER: How to build a dimer using amber David A. Case (Mon Jan 14 2008 - 23:51:50 PST)
  - Re: AMBER: How to build a dimer using amber Reena ..... (Tue Jan 15 2008 - 01:29:03 PST)
    - Re: AMBER: How to build a dimer using amber Reena ..... (Tue Jan 15 2008 - 01:31:24 PST)
    - Re: AMBER: How to build a dimer using amber David A. Case (Tue Jan 15 2008 - 09:18:14 PST)
AMBER: NPT to NVT Age.Skjevik.student.uib.no (Tue Jan 15 2008 - 05:58:22 PST)
AMBER: Regarding neutral Arginine unit jani sahil (Tue Jan 15 2008 - 08:19:00 PST)
- Re: AMBER: Regarding neutral Arginine unit Carlos Simmerling (Tue Jan 15 2008 - 08:28:21 PST)
AMBER: Problem with: Increase lastrst in the &cntrl namelist rdauria.uci.edu (Tue Jan 15 2008 - 20:46:04 PST)
- Re: AMBER: Problem with: Increase lastrst in the &cntrl namelist David A. Case (Wed Jan 16 2008 - 08:46:35 PST)
  - Re: AMBER: Problem with: Increase lastrst in the &cntrl namelist rdauria.uci.edu (Wed Jan 16 2008 - 10:19:27 PST)
AMBER: DawsonSean (Wed Jan 16 2008 - 00:52:07 PST)
- Re: AMBER: Reena ..... (Wed Jan 16 2008 - 01:07:30 PST)
  - AMBER: Chris Moth (Wed Jan 16 2008 - 07:11:07 PST)
AMBER: Help in radii snoze pa (Wed Jan 16 2008 - 09:08:59 PST)
- Re: AMBER: Help in radii snoze pa (Wed Jan 16 2008 - 09:45:20 PST)
- Re: AMBER: Help in radii FyD (Wed Jan 16 2008 - 12:31:07 PST)
AMBER: diblock copolymer Z Insepov (Thu Jan 17 2008 - 07:27:47 PST)
- Re: AMBER: diblock copolymer Jed W Pitera (Tue Jan 22 2008 - 17:01:03 PST)
  - Re: AMBER: diblock copolymer Z Insepov (Tue Jan 22 2008 - 21:23:39 PST)
AMBER: Re: timestep problem Andrey Semichaevsky (Thu Jan 17 2008 - 10:24:00 PST)
- Re: AMBER: Re: timestep problem David A. Case (Thu Jan 17 2008 - 12:27:56 PST)
AMBER: PEO-PLA/PCE Z Insepov (Thu Jan 17 2008 - 12:19:47 PST)
- Re: AMBER: PEO-PLA/PCE FyD (Fri Jan 18 2008 - 12:42:06 PST)
AMBER: GAFF atom types for flavin (again) Hans Martin Senn (Thu Jan 17 2008 - 12:47:54 PST)
- Re: AMBER: GAFF atom types for flavin (again) Junmei Wang (Thu Jan 17 2008 - 21:21:21 PST)
AMBER: problems of antechamber liu junjun (Thu Jan 17 2008 - 18:15:54 PST)
- Re: AMBER: problems of antechamber Junmei Wang (Thu Jan 17 2008 - 21:24:52 PST)
  - Re: AMBER: problems of antechamber JunJun Liu (Tue Jan 22 2008 - 06:45:26 PST)
- Re: AMBER: problems of antechamber liu junjun (Sun Jan 20 2008 - 07:21:49 PST)
AMBER: NMR refinement Wenyong Tong (Thu Jan 17 2008 - 18:54:04 PST)
- Re: AMBER: NMR refinement David A. Case (Fri Jan 18 2008 - 09:11:54 PST)
  - Re: AMBER: NMR refinement David A. Case (Fri Jan 18 2008 - 09:35:37 PST)
AMBER: Tinker 4.3 Paulo Couto (Fri Jan 18 2008 - 07:22:25 PST)
- Re: AMBER: Tinker 4.3 David A. Case (Fri Jan 18 2008 - 09:07:50 PST)
AMBER: about AM1-BCC in antechamber Shun Zhu (Fri Jan 18 2008 - 14:06:30 PST)
- Re: AMBER: about AM1-BCC in antechamber David Mobley (Fri Jan 18 2008 - 14:21:44 PST)
  - Re: AMBER: about AM1-BCC in antechamber Junmei Wang (Fri Jan 18 2008 - 21:31:06 PST)
    - Re: AMBER: about AM1-BCC in antechamber Shun Zhu (Tue Jan 22 2008 - 09:38:01 PST)
    - Re: AMBER: about AM1-BCC in antechamber Junmei Wang (Tue Jan 22 2008 - 09:56:55 PST)
    - Re: AMBER: about AM1-BCC in antechamber Shun Zhu (Tue Jan 22 2008 - 10:09:49 PST)
AMBER: A problem to loadup the molecular in the xleap 捞毛渔 (Fri Jan 18 2008 - 21:28:02 PST)
- RE: AMBER: A problem to loadup the molecular in the xleap Yong Duan (Fri Jan 18 2008 - 22:17:35 PST)
  - 回复： RE: AMBER: A problem to loadup the molecular in the xleap 捞毛渔 (Sat Jan 19 2008 - 08:31:05 PST)
    - Re: ?????? RE: AMBER: A problem to loadup the molecular in the xleap David A. Case (Sat Jan 19 2008 - 10:17:16 PST)
    - AMBER: RE: 回复： RE: AMBER: A problem to loadup the molecular in the xleap Yong Duan (Sat Jan 19 2008 - 12:44:25 PST)
AMBER: RMSD calculation using AMBER7 Biman Jana (Sat Jan 19 2008 - 05:16:46 PST)
- Re: AMBER: RMSD calculation using AMBER7 Carlos Simmerling (Sat Jan 19 2008 - 06:19:45 PST)
  - AMBER: convergence of free energy calculations saurabh agrawal (Tue Jan 22 2008 - 03:54:28 PST)
    - Re: AMBER: convergence of free energy calculations David Mobley (Thu Jan 24 2008 - 10:20:35 PST)
AMBER: problem with group input Ed Pate (Sun Jan 20 2008 - 22:53:28 PST)
- Re: AMBER: problem with group input anna.schrey.gmx.de (Mon Jan 21 2008 - 06:22:48 PST)
AMBER: Atomic restraints Marie Brut (Mon Jan 21 2008 - 05:34:42 PST)
AMBER: BCC charges Thomas Exner (Tue Jan 22 2008 - 07:47:20 PST)
- RE: AMBER: BCC charges Ross Walker (Tue Jan 22 2008 - 09:16:05 PST)
  - Re: AMBER: BCC charges Thomas Exner (Wed Jan 23 2008 - 02:11:36 PST)
AMBER: Has anyone seen a protein fall apart due to PBCs? David Cerutti (Tue Jan 22 2008 - 08:10:10 PST)
- Re: AMBER: Has anyone seen a protein fall apart due to PBCs? Thomas Cheatham III (Tue Jan 22 2008 - 08:37:03 PST)
  - RE: AMBER: Has anyone seen a protein fall apart due to PBCs? Irene Newhouse (Tue Jan 22 2008 - 09:28:44 PST)
    - Re: AMBER: Has anyone seen a protein fall apart due to PBCs? Melinda Layten (Tue Jan 22 2008 - 10:43:23 PST)
    - Re: AMBER: Has anyone seen a protein fall apart due to PBCs? David Cerutti (Tue Jan 22 2008 - 11:13:42 PST)
    - RE: AMBER: Has anyone seen a protein fall apart due to PBCs? Yong Duan (Tue Jan 22 2008 - 19:20:41 PST)
AMBER: Systematic drift Francesco Pietra (Tue Jan 22 2008 - 14:06:46 PST)
AMBER: Installing OpenMPI Hopkins, Robert (Tue Jan 22 2008 - 15:57:49 PST)
- Re: AMBER: Installing OpenMPI David A. Case (Wed Jan 23 2008 - 09:07:46 PST)
  - Re: AMBER: Installing OpenMPI Francesco Pietra (Wed Jan 23 2008 - 10:18:44 PST)
    - Re: AMBER: Installing OpenMPI Hopkins, Robert (Wed Jan 23 2008 - 16:40:22 PST)
AMBER: collision with surface Z Insepov (Tue Jan 22 2008 - 16:25:55 PST)
AMBER: Re: Systematic drift Francesco Pietra (Tue Jan 22 2008 - 23:23:07 PST)
AMBER: Amber 9: Question regarding Test Failures and Compilers Jan Schulze (Wed Jan 23 2008 - 02:01:04 PST)
- Re: AMBER: Amber 9: Question regarding Test Failures and Compilers David A. Case (Wed Jan 23 2008 - 08:22:04 PST)
AMBER: distorted aromatic rings Marc Lindner (Wed Jan 23 2008 - 02:40:20 PST)
- Re: AMBER: distorted aromatic rings David A. Case (Wed Jan 23 2008 - 08:24:15 PST)
  - Re: AMBER: mmpbsa binding energy Marc Lindner (Thu Jan 24 2008 - 02:16:23 PST)
AMBER: vlimit exceeded error priya priya (Wed Jan 23 2008 - 03:27:37 PST)
- Re: AMBER: vlimit exceeded error David A. Case (Wed Jan 23 2008 - 08:29:18 PST)
AMBER: ptraj: new mask parser Vlad Cojocaru (Wed Jan 23 2008 - 03:59:24 PST)
- Re: AMBER: ptraj: new mask parser Jianyin Shao (Thu Jan 24 2008 - 09:23:53 PST)
  - Re: AMBER: ptraj: new mask parser Vlad Cojocaru (Thu Jan 24 2008 - 10:19:25 PST)
AMBER: regarding :scee jani sahil (Wed Jan 23 2008 - 07:50:45 PST)
- Re: AMBER: regarding :scee David A. Case (Wed Jan 23 2008 - 08:45:07 PST)
  - Re: AMBER: regarding :scee jani sahil (Wed Jan 23 2008 - 20:37:48 PST)
AMBER: tutorial_8_section_6 Urszula Uciechowska (Wed Jan 23 2008 - 09:04:38 PST)
AMBER: antechamber run on charged system san_amber roy (Wed Jan 23 2008 - 10:09:34 PST)
- Re: AMBER: antechamber run on charged system David A. Case (Wed Jan 23 2008 - 10:37:06 PST)
  - Re: AMBER: antechamber run on charged system snoze pa (Wed Jan 23 2008 - 11:34:04 PST)
AMBER: Units of atomicfluct Lili Peng (Wed Jan 23 2008 - 16:27:16 PST)
AMBER: Tough time with antechamber David Cerutti (Wed Jan 23 2008 - 23:29:38 PST)
- AMBER: Tough time with antechamber (UPDATE, still need help) David Cerutti (Thu Jan 24 2008 - 00:09:42 PST)
- Re: AMBER: Tough time with antechamber Junmei Wang (Thu Jan 24 2008 - 07:23:08 PST)
- Re: AMBER: Tough time with antechamber David Mobley (Thu Jan 24 2008 - 10:14:42 PST)
  - Re: AMBER: Tough time with antechamber David A. Case (Thu Jan 24 2008 - 10:42:56 PST)
    - Re: AMBER: Tough time with antechamber David Cerutti (Thu Jan 24 2008 - 10:55:48 PST)
    - Re: AMBER: Tough time with antechamber Junmei Wang (Thu Jan 24 2008 - 15:49:51 PST)
    - Re: AMBER: Tough time with antechamber David A. Case (Thu Jan 24 2008 - 18:25:33 PST)
AMBER: Problems in execution of Replica Exchange calculations Amber 9.0 rebeca.mmb.pcb.ub.es (Thu Jan 24 2008 - 08:50:22 PST)
- Re: AMBER: Problems in execution of Replica Exchange calculations Amber 9.0 David A. Case (Thu Jan 24 2008 - 09:25:09 PST)
AMBER: Help needed to analyze DNA Holliday Junction - Drug Binding MD simulations. Subramanian Arun Kumar (Thu Jan 24 2008 - 09:14:56 PST)
AMBER: NMR refinement Seth Lilavivat (Thu Jan 24 2008 - 09:39:08 PST)
- Re: AMBER: NMR refinement David A. Case (Thu Jan 24 2008 - 18:18:48 PST)
AMBER: QM/MM: input conversion error Pankaj R. Daga (Thu Jan 24 2008 - 10:11:36 PST)
- Re: AMBER: QM/MM: input conversion error M. L. Dodson (Thu Jan 24 2008 - 10:31:44 PST)
  - RE: AMBER: QM/MM: input conversion error Pankaj R. Daga (Thu Jan 24 2008 - 11:05:31 PST)
    - Re: AMBER: QM/MM: input conversion error M. L. Dodson (Thu Jan 24 2008 - 11:25:03 PST)
    - RE: AMBER: QM/MM: input conversion error Ross Walker (Thu Jan 24 2008 - 16:01:43 PST)
    - RE: AMBER: QM/MM: input conversion error Pankaj R. Daga (Fri Jan 25 2008 - 12:11:24 PST)
    - Re: AMBER: QM/MM: input conversion error M. L. Dodson (Fri Jan 25 2008 - 12:56:38 PST)
    - RE: AMBER: QM/MM: input conversion error Pankaj R. Daga (Fri Jan 25 2008 - 14:02:47 PST)
    - RE: AMBER: QM/MM: input conversion error Ross Walker (Fri Jan 25 2008 - 14:48:49 PST)
    - Re: AMBER: QM/MM: input conversion error David A. Case (Fri Jan 25 2008 - 14:59:35 PST)
AMBER: Number of Hydrogen Bonds? d90223013.ntu.edu.tw (Thu Jan 24 2008 - 17:07:39 PST)
- RE: AMBER: Number of Hydrogen Bonds? Jiapu.Zhang.csiro.au (Thu Jan 24 2008 - 17:35:04 PST)
  - Re: AMBER: Number of Hydrogen Bonds? Jack Lei (Fri Jan 25 2008 - 05:20:53 PST)
AMBER: flexible molecule parameterization Zhenwei Lu (Fri Jan 25 2008 - 07:36:46 PST)
- Re: AMBER: flexible molecule parameterization FyD (Sun Jan 27 2008 - 06:09:37 PST)
AMBER: AMBER installation problem Jun Liu (Fri Jan 25 2008 - 10:59:29 PST)
- Re: AMBER: AMBER installation problem Bertrand P. S. Russell (Sat Jan 26 2008 - 07:53:43 PST)
- Re: AMBER: AMBER installation problem Sampath Koppole (Mon Jan 28 2008 - 00:36:27 PST)
  - Re: AMBER: AMBER installation problem David A. Case (Mon Jan 28 2008 - 08:06:54 PST)
AMBER: Reg cysteine protonaitons states in pH constant MD D.Usharani (Sun Jan 27 2008 - 21:15:58 PST)
AMBER: Why LEap created a new H atom for CYM while generating TOPOLOGY file? Jack Lei (Mon Jan 28 2008 - 04:59:38 PST)
- RE: AMBER: Why LEap created a new H atom for CYM while generating TOPOLOGY file? Steve Spronk (Mon Jan 28 2008 - 05:47:39 PST)
  - Re: AMBER: Why LEap created a new H atom for CYM while generating TOPOLOGY file? Jack Lei (Mon Jan 28 2008 - 06:35:06 PST)
  - Re: AMBER: Why LEap created a new H atom for CYM while generating TOPOLOGY file? David A. Case (Mon Jan 28 2008 - 08:11:02 PST)
AMBER: Reference for rmsd Francesco Pietra (Mon Jan 28 2008 - 09:51:02 PST)
AMBER: How to determine the basic parameters of a Replica Exchange Molecular Dynamics(REMD? d90223013.ntu.edu.tw (Mon Jan 28 2008 - 23:35:08 PST)
- Re: AMBER: How to determine the basic parameters of a Replica Exchange Molecular Dynamics(REMD? Carlos Simmerling (Tue Jan 29 2008 - 04:21:37 PST)
AMBER: radial distribution function in ptraj Lili Peng (Tue Jan 29 2008 - 01:36:37 PST)
AMBER: Amber parallel version on CPU power of 2 only fatima.chami.durham.ac.uk (Tue Jan 29 2008 - 05:38:34 PST)
- RE: AMBER: Amber parallel version on CPU power of 2 only Ross Walker (Tue Jan 29 2008 - 06:39:21 PST)
  - RE: AMBER: Amber parallel version on CPU power of 2 only fatima.chami.durham.ac.uk (Tue Jan 29 2008 - 10:19:22 PST)
Re: AMBER: Amber parallel version on CPU power of 2 only Robert Duke (Tue Jan 29 2008 - 10:43:03 PST)
- Re: AMBER: Amber parallel version on CPU power of 2 only fatima.chami.durham.ac.uk (Tue Jan 29 2008 - 13:04:56 PST)
AMBER: problem to compile PMEMD? fatima.chami.durham.ac.uk (Tue Jan 29 2008 - 14:45:41 PST)
- Re: AMBER: problem to compile PMEMD? Robert Duke (Tue Jan 29 2008 - 15:09:05 PST)
  - Re: AMBER: problem to compile PMEMD? fatima.chami.durham.ac.uk (Tue Jan 29 2008 - 16:10:48 PST)
    - Re: AMBER: problem to compile PMEMD? Robert Duke (Tue Jan 29 2008 - 18:10:49 PST)
    - Re: AMBER: problem to compile PMEMD? Robert Duke (Tue Jan 29 2008 - 18:11:57 PST)
AMBER: Reg cysteine protonation states D.Usharani (Tue Jan 29 2008 - 19:58:22 PST)
AMBER: setting periodic box Vijay Manickam Achari (Tue Jan 29 2008 - 20:22:05 PST)
AMBER: Entropy calculation nag raj (Wed Jan 30 2008 - 01:51:26 PST)
AMBER: SANDER BOMB in subroutine nonbond_list Pankaj R. Daga (Wed Jan 30 2008 - 07:13:45 PST)
- RE: AMBER: SANDER BOMB in subroutine nonbond_list Ross Walker (Wed Jan 30 2008 - 08:20:51 PST)
AMBER: Amber9 fails test.parallel Marc Cozzi (Wed Jan 30 2008 - 10:58:41 PST)
- Re: AMBER: Amber9 fails test.parallel Mark Williamson (Wed Jan 30 2008 - 12:04:31 PST)
AMBER: (no subject) Syed Tarique Moin (Wed Jan 30 2008 - 21:31:24 PST)
- Re: AMBER: RESP FyD (Wed Jan 30 2008 - 21:47:38 PST)
AMBER: Entropy calculation nag raj (Thu Jan 31 2008 - 04:47:51 PST)
AMBER: LEAP: solute concentration fatima.chami.durham.ac.uk (Thu Jan 31 2008 - 07:12:24 PST)
AMBER: disulfide bridge with ff03ua FF Marcin Krol (Thu Jan 31 2008 - 10:30:56 PST)
- AMBER: disulfide bridge with ff03ua FF Marcin Krol (Thu Feb 07 2008 - 06:50:16 PST)
  - Re: AMBER: disulfide bridge with ff03ua FF raja pandian (Fri Feb 08 2008 - 08:17:50 PST)
    - Re: AMBER: disulfide bridge with ff03ua FF Marcin Krol (Fri Feb 08 2008 - 09:00:25 PST)
    - Re: AMBER: disulfide bridge with ff03ua FF raja pandian (Fri Feb 08 2008 - 20:17:48 PST)
    - Re: AMBER: disulfide bridge with ff03ua FF Marcin Krol (Mon Feb 11 2008 - 07:01:30 PST)
    - Re: AMBER: disulfide bridge with ff03ua FF Ray Luo (Tue Feb 12 2008 - 14:52:37 PST)
    - Re: AMBER: disulfide bridge with ff03ua FF Marcin Krol (Wed Feb 13 2008 - 07:32:18 PST)
AMBER: benchmark walltime to ps/day calculation Andrew Ring (Thu Jan 31 2008 - 12:11:05 PST)
- Re: AMBER: benchmark walltime to ps/day calculation Steven Winfield (Thu Jan 31 2008 - 12:34:49 PST)
  - Re: AMBER: benchmark walltime to ps/day calculation Andrew Ring (Thu Jan 31 2008 - 13:16:22 PST)
AMBER: hbonds in first solvation shells Ignacio J. General (Fri Feb 01 2008 - 11:02:30 PST)
AMBER: silica slab / FF Arturas Ziemys (Fri Feb 01 2008 - 13:42:13 PST)
AMBER: Entropy calculations using NMODE saurabh agrawal (Fri Feb 01 2008 - 23:18:24 PST)
- Re: AMBER: Entropy calculations using NMODE Eddie Mende (Sat Feb 02 2008 - 05:17:06 PST)
  - Re: AMBER: Entropy calculations using NMODE saurabh agrawal (Sat Feb 02 2008 - 05:50:13 PST)
AMBER: twin cut-off radii Sandeep Kaushik (Mon Feb 04 2008 - 01:17:57 PST)
- Re: AMBER: twin cut-off radii David A. Case (Mon Feb 04 2008 - 08:09:51 PST)
- Re: AMBER: twin cut-off radii Robert Duke (Mon Feb 04 2008 - 08:55:06 PST)
AMBER: principal component analysis rams rams (Mon Feb 04 2008 - 04:26:31 PST)
- Re: AMBER: principal component analysis Mark Williamson (Mon Feb 04 2008 - 04:55:47 PST)
  - Re: AMBER: principal component analysis rams rams (Mon Feb 04 2008 - 07:45:17 PST)
  - RE: AMBER: principal component analysis Marco A. Lopez (Mon Feb 04 2008 - 11:22:36 PST)
AMBER: (no subject) Syed Tarique Moin (Mon Feb 04 2008 - 06:07:26 PST)
AMBER: Re: bad atom type f(fluorine) in MM-PBSA kanazta1.yahoo.co.jp (Mon Feb 04 2008 - 09:32:51 PST)
AMBER: time autocorrelation: ?? fatima.chami.durham.ac.uk (Mon Feb 04 2008 - 10:05:47 PST)
AMBER: Using antechamber without AMBER program Surasak Chunsrivirot (Mon Feb 04 2008 - 12:58:59 PST)
- Re: AMBER: Using antechamber without AMBER program Scott Brozell (Mon Feb 04 2008 - 13:32:11 PST)
  - Re: AMBER: Using antechamber without AMBER program Surasak Chunsrivirot (Mon Feb 04 2008 - 16:38:07 PST)
    - Re: AMBER: Using antechamber without AMBER program David A. Case (Mon Feb 04 2008 - 17:55:47 PST)
- Re: AMBER: Using antechamber without AMBER program David A. Case (Mon Feb 04 2008 - 13:46:00 PST)
  - Re: AMBER: Using antechamber without AMBER program Surasak Chunsrivirot (Mon Feb 04 2008 - 16:22:38 PST)
- Re: AMBER: Using antechamber without AMBER program Junmei Wang (Fri Feb 08 2008 - 07:10:27 PST)
AMBER: VLIMIT units; TGTFITMASK Hopkins, Robert (Mon Feb 04 2008 - 14:55:03 PST)
- Re: AMBER: VLIMIT units; TGTFITMASK David A. Case (Mon Feb 04 2008 - 15:18:39 PST)
  - RE: AMBER: VLIMIT units; TGTFITMASK Hopkins, Robert (Tue Feb 05 2008 - 07:08:07 PST)
AMBER: mm_pbsa: vertex atom mismatch Marc Lindner (Tue Feb 05 2008 - 02:47:23 PST)
AMBER: infinite polymers in CHARMM David A. Case (Tue Feb 05 2008 - 08:39:45 PST)
AMBER: silica slab Arturas Ziemys (Tue Feb 05 2008 - 09:28:55 PST)
- Re: AMBER: silica slab David A. Case (Tue Feb 05 2008 - 10:00:33 PST)
  - Re: AMBER: silica slab Arturas Ziemys (Tue Feb 05 2008 - 10:35:03 PST)
    - RE: AMBER: silica slab Steve Spronk (Wed Feb 06 2008 - 11:01:22 PST)
    - Re: AMBER: silica slab Steven Winfield (Wed Feb 06 2008 - 15:48:59 PST)
    - AMBER: AMBER 9 testing Taufik Al-Sarraj (Fri Mar 28 2008 - 17:18:30 PDT)
    - Re: AMBER: AMBER 9 testing David A. Case (Fri Mar 28 2008 - 17:10:02 PDT)
    - Re: AMBER: AMBER 9 testing Taufik Al-Sarraj (Fri Mar 28 2008 - 21:13:31 PDT)
    - AMBER: Amber Workshop Chih-Ying Lin (Fri Mar 28 2008 - 22:58:14 PDT)
    - Re: AMBER: AMBER 9 testing David A. Case (Sun Mar 30 2008 - 09:23:15 PDT)
    - Re: AMBER: AMBER 9 testing Taufik Al-Sarraj (Wed Apr 02 2008 - 19:36:57 PDT)
AMBER: Problem with energy decomposition in MMPBSA alfredoq.mail.fcq.unc.edu.ar (Tue Feb 05 2008 - 13:32:05 PST)
AMBER: segmentation fault while generating the covariance matrix rams rams (Tue Feb 05 2008 - 21:12:29 PST)
AMBER: re MD simulations of NMR structures: minimized average structure vs. ensemble member Vidana.Epa.csiro.au (Tue Feb 05 2008 - 22:08:19 PST)
Fwd: AMBER: (no subject) Syed Tarique Moin (Wed Feb 06 2008 - 00:00:23 PST)
AMBER: Query related to implicit solvent EXTDIEL S.Sundar Raman (Wed Feb 06 2008 - 04:03:02 PST)
- Re: AMBER: Query related to implicit solvent EXTDIEL David A. Case (Wed Feb 06 2008 - 08:31:08 PST)
AMBER: Binary restart file !! Sampath Koppole (Wed Feb 06 2008 - 06:41:03 PST)
- Re: AMBER: Binary restart file !! David A. Case (Wed Feb 06 2008 - 08:35:42 PST)
  - Re: AMBER: Binary restart file !! Sampath Koppole (Wed Feb 06 2008 - 09:01:43 PST)
AMBER: using NAB to calculate entropy Wang, Xuelin (Wed Feb 06 2008 - 09:52:06 PST)
- Re: AMBER: using NAB to calculate entropy David A. Case (Wed Feb 06 2008 - 12:21:28 PST)
  - RE: AMBER: using NAB to calculate entropy. . Wang, Xuelin (Wed Feb 06 2008 - 13:00:46 PST)
    - Re: AMBER: using NAB to calculate entropy. . David A. Case (Wed Feb 06 2008 - 13:37:40 PST)
    - AMBER: using NAB to calculate normal modes Z. Nevin Gerek (Fri Feb 15 2008 - 12:24:50 PST)
    - Re: AMBER: using NAB to calculate normal modes David A. Case (Fri Feb 15 2008 - 14:17:23 PST)
    - RE: AMBER: using NAB to calculate normal modes. . Wang, Xuelin (Fri Feb 15 2008 - 14:29:55 PST)
    - Re: AMBER: using NAB to calculate normal modes. . David A. Case (Fri Feb 15 2008 - 15:54:46 PST)
    - Re: AMBER: using NAB to calculate normal modes Andreas Svrcek-Seiler (Fri Feb 15 2008 - 14:23:30 PST)
AMBER: Amber compilation with ifort Andrey Semichaevsky (Wed Feb 06 2008 - 13:23:26 PST)
- Re: AMBER: Amber compilation with ifort David A. Case (Wed Feb 06 2008 - 13:47:20 PST)
- RE: AMBER: Amber compilation with ifort Ross Walker (Wed Feb 06 2008 - 14:06:20 PST)
- Re: AMBER: Amber compilation with ifort Mark Williamson (Wed Feb 06 2008 - 14:24:16 PST)
- Re: AMBER: Amber compilation with ifort Atro Tossavainen (Wed Feb 06 2008 - 23:45:09 PST)
AMBER: Amber 8 Equivalent of the Amber 5 - Edit program Mohd Farid Ismail (Wed Feb 06 2008 - 14:07:55 PST)
- RE: AMBER: Amber 8 Equivalent of the Amber 5 - Edit program Ross Walker (Wed Feb 06 2008 - 16:35:33 PST)
Re: AMBER: Amber 8 Equivalent of the Amber 5 - Edit program Bill Ross (Wed Feb 06 2008 - 16:18:38 PST)
- RE: AMBER: Amber 8 Equivalent of the Amber 5 - Edit program Mohd Farid Ismail (Tue Mar 04 2008 - 17:09:52 PST)
AMBER: Problem:neturalization jani sahil (Wed Feb 06 2008 - 21:03:35 PST)
- Re: AMBER: Problem:neturalization David Cerutti (Wed Feb 06 2008 - 23:42:39 PST)
AMBER: A new program for doing RESP David Cerutti (Wed Feb 06 2008 - 22:56:04 PST)
AMBER: Deleting solute from box Kevin Davies (Thu Feb 07 2008 - 12:45:48 PST)
Re: AMBER: Deleting solute from box Bill Ross (Thu Feb 07 2008 - 13:37:27 PST)
- Re: AMBER: Deleting solute from box Kevin Davies (Thu Feb 07 2008 - 14:21:22 PST)
AMBER: Error while compiling Amber Lili Peng (Thu Feb 07 2008 - 17:14:42 PST)
- Re: AMBER: Error while compiling Amber David A. Case (Thu Feb 07 2008 - 17:42:31 PST)
  - Re: AMBER: Error while compiling Amber Lili Peng (Fri Feb 08 2008 - 17:51:55 PST)
    - RE: AMBER: Error while compiling Amber Ross Walker (Sat Feb 09 2008 - 09:58:59 PST)
    - Re: AMBER: Error while compiling Amber Lili Peng (Sat Feb 09 2008 - 11:11:39 PST)
    - RE: AMBER: Error while compiling Amber Ross Walker (Sat Feb 09 2008 - 11:40:41 PST)
    - Re: AMBER: Error while compiling Amber chen (Sat Feb 09 2008 - 16:00:09 PST)
    - Re: AMBER: Error while compiling Amber Lili Peng (Thu Feb 14 2008 - 01:09:22 PST)
    - Re: AMBER: Error while compiling Amber Jack Lei (Thu Feb 14 2008 - 04:50:57 PST)
    - Re: AMBER: Error while compiling Amber Lili Peng (Thu Feb 14 2008 - 09:41:18 PST)
    - Re: AMBER: Error while compiling Amber Junmei Wang (Thu Feb 14 2008 - 13:13:30 PST)
    - Re: AMBER: Error while compiling Amber Lili Peng (Thu Feb 14 2008 - 14:24:02 PST)
    - Re: AMBER: Error while compiling Amber Junmei Wang (Fri Feb 15 2008 - 09:16:47 PST)
AMBER: WARNING in readAmberTrajectory(): fsetpos() failed on when looking for box coordinates! rams rams (Thu Feb 07 2008 - 21:36:15 PST)
- RE: AMBER: WARNING in readAmberTrajectory(): fsetpos() failed on when looking for box coordinates! Ross Walker (Fri Feb 08 2008 - 08:40:25 PST)
  - Re: AMBER: WARNING in readAmberTrajectory(): fsetpos() failed on when looking for box coordinates! rams rams (Sun Feb 10 2008 - 21:32:01 PST)
AMBER: Which install compiler and flags? Sam Kaye (Fri Feb 08 2008 - 02:07:15 PST)
- RE: AMBER: Which install compiler and flags? Ross Walker (Fri Feb 08 2008 - 08:52:24 PST)
- Re: AMBER: Which install compiler and flags? David A. Case (Fri Feb 08 2008 - 09:04:55 PST)
AMBER: PB Bomb in pb_atmlist(): maxnba too short Eddie Mende (Fri Feb 08 2008 - 05:22:07 PST)
- RE: AMBER: PB Bomb in pb_atmlist(): maxnba too short Ross Walker (Fri Feb 08 2008 - 08:53:56 PST)
AMBER: Antechamber/mopac query Lynn F. Ten Eyck (Fri Feb 08 2008 - 17:15:12 PST)
AMBER: Input file for Minimization Campbell, Patrick (Sat Feb 09 2008 - 13:18:51 PST)
- RE: AMBER: Input file for Minimization Ross Walker (Sun Feb 10 2008 - 10:55:34 PST)
  - Re: AMBER: Input file for Minimization Carlos Simmerling (Mon Feb 11 2008 - 09:06:42 PST)
- RE: AMBER: Input file for Minimization Campbell, Patrick (Tue Feb 12 2008 - 09:43:34 PST)
  - Re: AMBER: Input file for Minimization Carlos Simmerling (Tue Feb 12 2008 - 09:55:18 PST)
AMBER: leaprc help snoze pa (Mon Feb 11 2008 - 09:50:30 PST)
- Re: AMBER: leaprc help Carlos Simmerling (Mon Feb 11 2008 - 09:56:38 PST)
  - Re: AMBER: leaprc help snoze pa (Mon Feb 11 2008 - 13:08:14 PST)
    - Re: AMBER: leaprc help Reena ..... (Mon Feb 11 2008 - 20:19:22 PST)
AMBER: mm_pbsa problem Badry Bursulaya (Mon Feb 11 2008 - 14:45:29 PST)
AMBER: Non-polar Parameters For MM_PBSA Calculation Neil Bruce (Tue Feb 12 2008 - 03:54:02 PST)
- RE: AMBER: Non-polar Parameters For MM_PBSA Calculation rluo.uci.edu (Tue Feb 12 2008 - 15:23:40 PST)
AMBER: PKa calculation Wang, Xuelin (Tue Feb 12 2008 - 08:45:16 PST)
- Re: AMBER: PKa calculation David A. Case (Tue Feb 12 2008 - 09:15:55 PST)
AMBER: RDCs in AMBER 10 Douglas Kojetin (Tue Feb 12 2008 - 15:39:37 PST)
- Re: AMBER: RDCs in AMBER 10 David A. Case (Tue Feb 12 2008 - 15:56:52 PST)
  - Re: AMBER: RDCs in AMBER 10 Douglas Kojetin (Tue Feb 12 2008 - 17:01:30 PST)
AMBER: (no subject) Syed Tarique Moin (Wed Feb 13 2008 - 02:55:02 PST)
- RE: AMBER: (no subject) Ross Walker (Wed Feb 13 2008 - 07:21:52 PST)
  - RE: AMBER: (no subject) Syed Tarique Moin (Wed Feb 13 2008 - 20:58:56 PST)
AMBER: AMBER 8 problems on RHEL4/Opteron/PGF 7.0-7 Atro Tossavainen (Wed Feb 13 2008 - 05:31:54 PST)
- RE: AMBER: AMBER 8 problems on RHEL4/Opteron/PGF 7.0-7 Ross Walker (Wed Feb 13 2008 - 07:20:07 PST)
  - Re: AMBER: AMBER 8 problems on RHEL4/Opteron/PGF 7.0-7 Atro Tossavainen (Wed Feb 13 2008 - 12:27:29 PST)
    - Re: AMBER: AMBER 8 problems on RHEL4/Opteron/PGF 7.0-7 Atro Tossavainen (Wed Feb 13 2008 - 12:49:57 PST)
    - Re: AMBER: AMBER 8 problems on RHEL4/Opteron/PGF 7.0-7 Atro Tossavainen (Wed Feb 13 2008 - 23:02:22 PST)
AMBER: Is boiling point a good way to validate solvent paramters? Mike Wykes (Wed Feb 13 2008 - 06:08:25 PST)
- Re: AMBER: Is boiling point a good way to validate solvent paramters? David A. Case (Wed Feb 13 2008 - 12:34:01 PST)
  - RE: AMBER: Is boiling point a good way to validate solvent paramters? Mike Wykes (Fri Feb 15 2008 - 07:27:35 PST)
    - Re: AMBER: Is boiling point a good way to validate solvent paramters? David A. Case (Fri Feb 15 2008 - 18:49:12 PST)
    - RE: AMBER: Is boiling point a good way to validate solvent paramters? FyD (Fri Feb 15 2008 - 23:31:14 PST)
AMBER: sander error on Make test.serial Evan Kelly (Wed Feb 13 2008 - 12:26:25 PST)
- Re: AMBER: sander error on Make test.serial Evan Kelly (Wed Feb 13 2008 - 13:03:58 PST)
- Re: AMBER: sander error on Make test.serial David A. Case (Wed Feb 13 2008 - 21:57:32 PST)
  - Re: AMBER: sander error on Make test.serial Evan Kelly (Thu Feb 14 2008 - 10:36:25 PST)
AMBER: ambmask problem Hopkins, Robert (Wed Feb 13 2008 - 16:42:53 PST)
- Re: AMBER: ambmask problem David A. Case (Fri Feb 15 2008 - 09:32:46 PST)
AMBER: AMBER parameters for Chlorophyll Sreeja Parameswaran (Wed Feb 13 2008 - 17:31:05 PST)
- Re: AMBER: AMBER parameters for Chlorophyll mathew k varghese (Sat Feb 16 2008 - 06:09:30 PST)
  - Re: AMBER: AMBER parameters for Chlorophyll Sreeja Parameswaran (Sat Feb 16 2008 - 06:45:32 PST)
    - Re: AMBER: AMBER parameters for Chlorophyll David LeBard (Sat Feb 16 2008 - 09:25:51 PST)
AMBER: xmgr graphics display program Hopkins, Robert (Wed Feb 13 2008 - 18:02:23 PST)
- Re: AMBER: xmgr graphics display program Gustavo Seabra (Wed Feb 13 2008 - 18:29:26 PST)
- Re: AMBER: xmgr graphics display program David A. Case (Wed Feb 13 2008 - 21:46:40 PST)
  - Re: AMBER: xmgr graphics display program Junmei Wang (Thu Feb 14 2008 - 12:04:16 PST)
- Re: AMBER: xmgr graphics display program Hopkins, Robert (Sun Feb 17 2008 - 12:38:41 PST)
AMBER: mpd error in submitting parallel job Lili Peng (Thu Feb 14 2008 - 01:11:25 PST)
- Re: AMBER: mpd error in submitting parallel job Gustavo Seabra (Thu Feb 14 2008 - 11:45:47 PST)
  - RE: AMBER: mpd error in submitting parallel job Ross Walker (Thu Feb 14 2008 - 20:11:23 PST)
AMBER: Distance restraints between com of two groups of residues Sudha Mani Karra (Thu Feb 14 2008 - 14:20:26 PST)
AMBER: print distance between atoms during simulation within sander itsself Vlad Cojocaru (Fri Feb 15 2008 - 06:06:24 PST)
AMBER: setbox for solvateoct model Wang, Xuelin (Fri Feb 15 2008 - 07:22:07 PST)
- Re: AMBER: setbox for solvateoct model David A. Case (Fri Feb 15 2008 - 18:52:14 PST)
AMBER: problem with ambmask David A. Case (Fri Feb 15 2008 - 10:07:54 PST)
- RE: AMBER: problem with ambmask Hopkins, Robert (Mon Feb 18 2008 - 13:57:07 PST)
AMBER: matrix correl David Beveridge (Sat Feb 16 2008 - 01:09:29 PST)
- Re: AMBER: matrix correl Holger Gohlke (Mon Feb 18 2008 - 04:56:07 PST)
- RE: AMBER: matrix correl Ibrahim Moustafa (Wed Feb 20 2008 - 09:22:53 PST)
AMBER: setting perioding box in AMBER Vijay Manickam Achari (Sun Feb 17 2008 - 17:47:17 PST)
- Re: AMBER: setting perioding box in AMBER David A. Case (Sun Feb 17 2008 - 18:14:31 PST)
  - Re: AMBER: setting perioding box in AMBER Vijay Manickam Achari (Mon Feb 18 2008 - 22:00:06 PST)
AMBER: TERs Steve Seibold (Mon Feb 18 2008 - 05:19:39 PST)
- Re: AMBER: TERs David A. Case (Mon Feb 18 2008 - 08:49:55 PST)
- Re: AMBER: TERs Thomas Cheatham (Mon Feb 18 2008 - 09:18:36 PST)
  - RE: AMBER: TERs Steve Seibold (Mon Feb 18 2008 - 09:51:51 PST)
AMBER: parameters of nonbonded potentials Alexander Klenner (Tue Feb 19 2008 - 02:43:27 PST)
- Re: AMBER: parameters of nonbonded potentials David A. Case (Tue Feb 19 2008 - 08:05:07 PST)
AMBER: Generating RESP charges Christopher Illingworth (Tue Feb 19 2008 - 03:39:22 PST)
- Re: AMBER: Generating RESP charges Junmei Wang (Tue Feb 19 2008 - 07:05:39 PST)
  - Re: AMBER: Generating RESP charges Christopher Illingworth (Tue Feb 19 2008 - 08:11:21 PST)
    - Re: AMBER: Generating RESP charges Junmei Wang (Tue Feb 19 2008 - 10:04:44 PST)
    - Re: AMBER: Generating RESP charges M. L. Dodson (Tue Feb 19 2008 - 10:38:22 PST)
    - Re: AMBER: Generating RESP charges Junmei Wang (Tue Feb 19 2008 - 11:22:59 PST)
AMBER: united atom force field: antechamber fatima.chami.durham.ac.uk (Tue Feb 19 2008 - 13:59:42 PST)
- Re: AMBER: united atom force field: antechamber David A. Case (Tue Feb 19 2008 - 15:33:32 PST)
AMBER: NAB to calcuate entropy Wang, Xuelin (Tue Feb 19 2008 - 15:58:15 PST)
- Re: AMBER: NAB to calcuate entropy David A. Case (Tue Feb 19 2008 - 17:33:59 PST)
  - Re: AMBER: NAB to calcuate entropy Z. Nevin Gerek (Wed Feb 20 2008 - 12:38:28 PST)
    - Re: AMBER: NAB to calcuate entropy David A. Case (Wed Feb 20 2008 - 13:36:15 PST)
    - RE: AMBER: NAB to calcuate entropy. . Wang, Xuelin (Wed Feb 20 2008 - 14:22:16 PST)
    - Re: AMBER: NAB to calcuate entropy. . David A. Case (Wed Feb 20 2008 - 15:18:32 PST)
    - RE: AMBER: NAB to calcuate entropy. . Wang, Xuelin (Wed Feb 20 2008 - 16:14:01 PST)
    - Re: AMBER: NAB to calcuate entropy. . David A. Case (Thu Feb 21 2008 - 09:10:16 PST)
    - RE: AMBER: NAB to calcuate entropy. . Wang, Xuelin (Thu Feb 21 2008 - 12:00:31 PST)
    - Re: AMBER: NAB to calcuate entropy. . David A. Case (Thu Feb 21 2008 - 12:26:06 PST)
    - Re: AMBER: NAB to calcuate entropy. . David A. Case (Thu Feb 21 2008 - 09:10:36 PST)
    - RE: AMBER: NAB to calcuate entropy. . Wang, Xuelin (Wed Feb 20 2008 - 13:21:15 PST)
    - Re: AMBER: NAB to calcuate entropy. . Z. Nevin Gerek (Wed Feb 20 2008 - 13:34:33 PST)
    - Re: AMBER: NAB to calcuate entropy. . David A. Case (Wed Feb 20 2008 - 15:16:14 PST)
AMBER: Regarding:PME and neturalization jani sahil (Tue Feb 19 2008 - 21:12:45 PST)
- Re: AMBER: Regarding:PME and neturalization Lars Skjærven (Wed Feb 20 2008 - 00:39:59 PST)
AMBER: is that possible fix box size in constant pressure MD Vijay Manickam Achari (Tue Feb 19 2008 - 21:39:46 PST)
AMBER: Dimension of the solvated box? abiram abiram (Wed Feb 20 2008 - 05:54:08 PST)
- Re: AMBER: Dimension of the solvated box? David A. Case (Wed Feb 20 2008 - 08:31:36 PST)
AMBER: saveAmberPrep in internal coordinates Xu, Huafeng (Wed Feb 20 2008 - 09:02:00 PST)
- Re: AMBER: saveAmberPrep in internal coordinates Junmei Wang (Wed Feb 20 2008 - 09:43:31 PST)
AMBER: Problem with "trajout pdb" Yi-Ming Cheng (Wed Feb 20 2008 - 08:53:32 PST)
- Re: AMBER: Problem with "trajout pdb" Yi-Ming Cheng (Sat Feb 23 2008 - 01:36:24 PST)
- Re: AMBER: Problem with "trajout pdb" Yi-Ming Cheng (Sat Feb 23 2008 - 02:15:29 PST)
AMBER: XLEaP Anamika Awasthi (Thu Feb 21 2008 - 01:36:20 PST)
- Re: AMBER: XLEaP David A. Case (Thu Feb 21 2008 - 08:45:08 PST)
AMBER: simulated annealing Holly Freedman (Thu Feb 21 2008 - 11:31:48 PST)
- Re: AMBER: simulated annealing Abd Ghani Bin Abd Aziz (Wed Jul 28 2004 - 06:22:37 PDT)
- RE: AMBER: simulated annealing Lee SL (Sat Aug 14 2004 - 03:40:54 PDT)
- Re: AMBER: simulated annealing David A. Case (Thu Feb 21 2008 - 12:04:26 PST)
- Re: AMBER: simulated annealing Holly Freedman (Thu Feb 21 2008 - 12:52:42 PST)
AMBER: Question: tweaking topology files to add SHAKE-constrained bonds David Cerutti (Thu Feb 21 2008 - 21:37:28 PST)
- AMBER: (no subject) Syed Tarique Moin (Thu Feb 21 2008 - 22:10:36 PST)
  - Re: AMBER: (no subject) Eddie Mende (Thu Feb 21 2008 - 22:31:01 PST)
  - Re: AMBER: (no subject) Eddie Mende (Thu Feb 21 2008 - 22:33:07 PST)
  - RE: AMBER: (no subject) Ibrahim Moustafa (Fri Feb 22 2008 - 08:29:59 PST)
- Re: AMBER: Question: tweaking topology files to add SHAKE-constrained bonds David A. Case (Fri Feb 22 2008 - 09:14:59 PST)
AMBER: problem bull linux compiling Yannick Monclin (Fri Feb 22 2008 - 03:22:49 PST)
- Re: AMBER: problem bull linux compiling Gustavo Seabra (Fri Feb 22 2008 - 07:56:25 PST)
  - Re: AMBER: problem bull linux compiling Yannick Monclin (Mon Feb 25 2008 - 05:16:06 PST)
    - Re: AMBER: problem bull linux compiling Gustavo Seabra (Tue Feb 26 2008 - 09:18:27 PST)
AMBER: gaff paramters servaas michielssens (Fri Feb 22 2008 - 09:38:53 PST)
- Re: AMBER: gaff paramters Servaas Michielssens (Fri Feb 22 2008 - 13:15:23 PST)
  - Re: AMBER: gaff paramters Servaas Michielssens (Fri Feb 22 2008 - 23:06:54 PST)
AMBER: More on tweaking a topology file David Cerutti (Fri Feb 22 2008 - 19:15:40 PST)
- Re: AMBER: More on tweaking a topology file Carlos Simmerling (Sat Feb 23 2008 - 04:08:30 PST)
Fwd: Re: AMBER: Problem with "trajout pdb" Yi-Ming Cheng (Sat Feb 23 2008 - 02:21:29 PST)
AMBER: dihedral energy in amber aneesh cna (Sat Feb 23 2008 - 02:32:08 PST)
- Re: AMBER: dihedral energy in amber David A. Case (Sat Feb 23 2008 - 08:37:09 PST)
AMBER: compiling PMEMD with MKL10.0 Alessandro Nascimento (Tue Feb 26 2008 - 02:20:47 PST)
- Re: AMBER: compiling PMEMD with MKL10.0 Francesco Pietra (Tue Feb 26 2008 - 03:00:32 PST)
  - Re: AMBER: compiling PMEMD with MKL10.0 Alessandro Nascimento (Tue Feb 26 2008 - 03:36:40 PST)
    - Re: AMBER: compiling PMEMD with MKL10.0 Gustavo Seabra (Tue Feb 26 2008 - 11:46:24 PST)
- Re: AMBER: compiling PMEMD with MKL10.0 Robert Duke (Tue Feb 26 2008 - 05:22:04 PST)
AMBER: Force fields oguz gurbulak (Tue Feb 26 2008 - 08:12:48 PST)
- Re: AMBER: Force fields David A. Case (Tue Feb 26 2008 - 09:31:19 PST)
AMBER: bond breaking in proteins Eddie Mende (Tue Feb 26 2008 - 08:16:21 PST)
- Re: AMBER: bond breaking in proteins David A. Case (Tue Feb 26 2008 - 09:16:46 PST)
- Re: AMBER: bond breaking in proteins Gustavo Seabra (Tue Feb 26 2008 - 11:58:22 PST)
  - Re: AMBER: bond breaking in proteins Eddie Mende (Tue Feb 26 2008 - 13:04:02 PST)
  - Re: AMBER: bond breaking in proteins Eddie Mende (Tue Feb 26 2008 - 12:49:04 PST)
AMBER: mol2 save snoze pa (Tue Feb 26 2008 - 09:09:18 PST)
- Re: AMBER: mol2 save Steven Winfield (Tue Feb 26 2008 - 09:13:23 PST)
- Re: AMBER: mol2 save FyD (Tue Feb 26 2008 - 09:38:40 PST)
- Re: AMBER: mol2 save David A. Case (Tue Feb 26 2008 - 09:51:19 PST)
AMBER: autodock pdb to obtain parm with tleap Henar Martínez (Tue Feb 26 2008 - 09:23:43 PST)
- Re: AMBER: autodock pdb to obtain parm with tleap David A. Case (Tue Feb 26 2008 - 13:34:07 PST)
  - Re: AMBER: autodock pdb to obtain parm with tleap Henar Martínez (Wed Feb 27 2008 - 02:58:09 PST)
    - Re: AMBER: autodock pdb to obtain parm with tleap David A. Case (Wed Feb 27 2008 - 10:25:02 PST)
    - Re: AMBER: autodock pdb to obtain parm with tleap Henar Martínez (Wed Feb 27 2008 - 10:30:33 PST)
  - Re: AMBER: autodock pdb to obtain parm with tleap Henar Martínez (Wed Feb 27 2008 - 03:14:58 PST)
    - Re: AMBER: autodock pdb to obtain parm with tleap Junmei Wang (Wed Feb 27 2008 - 09:42:52 PST)
    - Re: AMBER: autodock pdb to obtain parm with tleap Francesco Pietra (Wed Feb 27 2008 - 10:14:56 PST)
    - Re: AMBER: autodock pdb to obtain parm with tleap Henar Martínez (Wed Feb 27 2008 - 10:28:13 PST)
AMBER: bond breaking in proteins Eddie Mende (Tue Feb 26 2008 - 14:41:22 PST)
- AMBER: bond breaking in proteins Eddie Mende (Tue Feb 26 2008 - 15:40:03 PST)
  - Re: AMBER: bond breaking in proteins David A. Case (Tue Feb 26 2008 - 16:41:26 PST)
- Re: AMBER: bond breaking in proteins Gustavo Seabra (Wed Feb 27 2008 - 08:09:58 PST)
- Re: AMBER: bond breaking in proteins Eddie Mende (Tue Feb 26 2008 - 14:55:20 PST)
AMBER: Using restart files Lili Peng (Tue Feb 26 2008 - 15:36:50 PST)
- Re: AMBER: Using restart files David A. Case (Tue Feb 26 2008 - 16:45:34 PST)
AMBER: charge derivation for modified amino acids Denzil Bernard (Tue Feb 26 2008 - 17:14:44 PST)
- Re: AMBER: charge derivation for modified amino acids FyD (Tue Feb 26 2008 - 22:35:10 PST)
AMBER: "Assuming uniform neutralizing plasma" Evan Kelly (Tue Feb 26 2008 - 18:01:52 PST)
- Re: AMBER: "Assuming uniform neutralizing plasma" Thomas Cheatham (Tue Feb 26 2008 - 19:31:39 PST)
AMBER: stops writing trajectory Swarup Gupta (Wed Feb 27 2008 - 01:55:10 PST)
AMBER: initial command? Anamika Awasthi (Wed Feb 27 2008 - 04:01:51 PST)
- Re: AMBER: initial command? Carlos Simmerling (Wed Feb 27 2008 - 04:10:01 PST)
  - RE: AMBER: initial command? Steve Spronk (Wed Feb 27 2008 - 10:45:43 PST)
- RE: AMBER: initial command? Bill Ross (Wed Feb 27 2008 - 10:56:20 PST)
  - RE: AMBER: initial command? Steve Spronk (Fri Feb 29 2008 - 06:17:38 PST)
AMBER: Amber: shared memory vs cluster Francesco Pietra (Wed Feb 27 2008 - 10:08:19 PST)
- Re: AMBER: Amber: shared memory vs cluster Robert Duke (Wed Feb 27 2008 - 10:37:31 PST)
  - Re: AMBER: Amber: shared memory vs cluster Francesco Pietra (Wed Feb 27 2008 - 13:00:32 PST)
    - Re: AMBER: Amber: shared memory vs cluster Robert Duke (Wed Feb 27 2008 - 13:20:56 PST)
AMBER: Lennard-Jones parameters zhan chen (Wed Feb 27 2008 - 23:41:02 PST)
- Re: AMBER: Lennard-Jones parameters Klenner.bioinformatik.uni-frankfurt.de (Wed Feb 27 2008 - 14:11:50 PST)
  - Re: AMBER: Lennard-Jones parameters Bill Ross (Wed Feb 27 2008 - 16:09:10 PST)
    - Re: AMBER: Lennard-Jones parameters Zhan Chen (Wed Feb 27 2008 - 18:59:26 PST)
- Re: AMBER: Lennard-Jones parameters David A. Case (Wed Feb 27 2008 - 14:16:34 PST)
  - AMBER: change in secondary structure during MD Ibrahim Moustafa (Wed Feb 27 2008 - 17:45:21 PST)
    - RE: AMBER: change in secondary structure during MD Yong Duan (Wed Feb 27 2008 - 18:13:11 PST)
    - RE: AMBER: change in secondary structure during MD Ibrahim Moustafa (Thu Feb 28 2008 - 14:12:49 PST)
    - RE: AMBER: change in secondary structure during MD Fenghui Fan (Thu Feb 28 2008 - 14:48:53 PST)
    - Re: AMBER: change in secondary structure during MD Carlos Simmerling (Thu Feb 28 2008 - 04:15:58 PST)
- Re: AMBER: Lennard-Jones parameters Bill Ross (Thu Feb 28 2008 - 12:07:31 PST)
AMBER: DFTB/SCC-DFTB Eddie Mende (Wed Feb 27 2008 - 11:21:42 PST)
- Re: AMBER: DFTB/SCC-DFTB David A. Case (Wed Feb 27 2008 - 22:15:48 PST)
AMBER: varying restraint_wt with nmropt=1 Andrew Borgert (Wed Feb 27 2008 - 12:18:28 PST)
- Re: AMBER: varying restraint_wt with nmropt=1 Daniel Cappel (Wed Feb 27 2008 - 23:50:02 PST)
AMBER: problem with antechamber aneesh cna (Wed Feb 27 2008 - 21:55:53 PST)
- Re: AMBER: problem with antechamber Junmei Wang (Thu Feb 28 2008 - 07:06:31 PST)
AMBER: problems with Replica Exchange rebeca.mmb.pcb.ub.es (Thu Feb 28 2008 - 04:29:23 PST)
- Re: AMBER: problems with Replica Exchange Carlos Simmerling (Thu Feb 28 2008 - 04:46:57 PST)
  - Re: AMBER: problems with Replica Exchange rebeca.mmb.pcb.ub.es (Thu Feb 28 2008 - 07:16:27 PST)
    - Re: AMBER: problems with Replica Exchange Carlos Simmerling (Thu Feb 28 2008 - 08:14:14 PST)
- Re: AMBER: problems with Replica Exchange Carlos Simmerling (Fri Feb 29 2008 - 10:33:59 PST)
- AMBER: implicit energy calculations rebeca.mmb.pcb.ub.es (Thu Mar 13 2008 - 09:26:43 PDT)
  - Re: AMBER: implicit energy calculations Thomas Cheatham III (Thu Mar 13 2008 - 10:47:04 PDT)
AMBER: Plea for REMD tutorial tushar garud (Thu Feb 28 2008 - 05:56:42 PST)
- Re: AMBER: Plea for REMD tutorial Carlos Simmerling (Thu Feb 28 2008 - 06:08:26 PST)
  - AMBER: Molecular dynamics simulation of large-scale domainmovement in a protein Fenghui Fan (Thu Feb 28 2008 - 06:38:23 PST)
AMBER: Liquid/Gas Phase Rita Cassia (Thu Feb 28 2008 - 08:34:00 PST)
AMBER: problems with 10-12 potential in amber8 sander Amie Demmel (Thu Feb 28 2008 - 12:59:27 PST)
- Re: AMBER: problems with 10-12 potential in amber8 sander David A. Case (Thu Feb 28 2008 - 14:27:47 PST)
  - Re: AMBER: problems with 10-12 potential in amber8 sander Amie Demmel (Thu Feb 28 2008 - 14:53:15 PST)
    - Re: AMBER: problems with 10-12 potential in amber8 sander David A. Case (Thu Feb 28 2008 - 15:47:10 PST)
    - Re: AMBER: problems with 10-12 potential in amber8 sander Amie Demmel (Fri Feb 29 2008 - 08:23:15 PST)
  - Re: AMBER: problems with 10-12 potential in amber8 sander Lynn F. Ten Eyck (Thu Feb 28 2008 - 14:54:47 PST)
AMBER: Re: Force field parameter file for CNT Andrey Semichaevsky (Thu Feb 28 2008 - 13:34:01 PST)
- Re: AMBER: Re: Force field parameter file for CNT David A. Case (Fri Feb 29 2008 - 08:19:47 PST)
  - Re: AMBER: Re: Force field parameter file for CNT Andrey Semichaevsky (Fri Feb 29 2008 - 08:38:39 PST)
AMBER: for NMR refinement Wenyong Tong (Thu Feb 28 2008 - 18:20:08 PST)
- Re: AMBER: for NMR refinement David A. Case (Fri Feb 29 2008 - 10:53:59 PST)
AMBER: Visualizing Periodc box Vijay Manickam Achari (Thu Feb 28 2008 - 23:50:13 PST)
AMBER: Plea for REMD tutorial tushar garud (Fri Feb 29 2008 - 06:57:41 PST)
- Re: AMBER: Plea for REMD tutorial Carlos Simmerling (Fri Feb 29 2008 - 09:47:47 PST)
AMBER: Re: Amber Force field for CNT: leaprc.ff23 Andrey Semichaevsky (Fri Feb 29 2008 - 07:35:16 PST)
AMBER: Non aqueous implicit solvation Mike Wykes (Fri Feb 29 2008 - 10:56:01 PST)
AMBER: regarding:calculation of b factor using ptraj jani sahil (Sat Mar 01 2008 - 08:10:10 PST)
- Re: AMBER: regarding:calculation of b factor using ptraj gurpreet singh (Sun Mar 02 2008 - 09:24:29 PST)
AMBER: questions about run MD at different pH Kailee (Mon Mar 03 2008 - 06:51:40 PST)
- Re: AMBER: questions about run MD at different pH David A. Case (Mon Mar 03 2008 - 21:07:00 PST)
  - Re: AMBER: questions about run MD at different pH Kailee (Tue Mar 04 2008 - 03:40:30 PST)
    - Re: AMBER: questions about run MD at different pH David A. Case (Tue Mar 04 2008 - 17:59:49 PST)
  - Re: AMBER: questions about run MD at different pH Taufik Al-Sarraj (Tue Apr 15 2008 - 09:15:28 PDT)
    - Re: AMBER: questions about run MD at different pH David A. Case (Tue Apr 15 2008 - 10:19:11 PDT)
    - Re: AMBER: questions about run MD at different pH Taufik Al-Sarraj (Tue Apr 15 2008 - 13:06:39 PDT)
    - Re: AMBER: questions about run MD at different pH David A. Case (Tue Apr 15 2008 - 13:59:27 PDT)
    - Re: AMBER: questions about run MD at different pH Taufik Al-Sarraj (Tue Apr 15 2008 - 15:47:10 PDT)
AMBER: Writing pressure in md.out file in NVT simulation Sudha Mani Karra (Mon Mar 03 2008 - 10:58:46 PST)
- Re: AMBER: Writing pressure in md.out file in NVT simulation David A. Case (Mon Mar 03 2008 - 11:24:20 PST)
  - Re: AMBER: Writing pressure in md.out file in NVT simulation Sudha Mani Karra (Mon Mar 03 2008 - 12:56:13 PST)
- Re: AMBER: Writing pressure in md.out file in NVT simulation Vlad Cojocaru (Mon Mar 03 2008 - 11:26:50 PST)
AMBER: xleap screen output Francesco Pietra (Mon Mar 03 2008 - 13:02:54 PST)
- Re: AMBER: xleap screen output David A. Case (Mon Mar 03 2008 - 13:31:17 PST)
  - Re: AMBER: xleap screen output Francesco Pietra (Mon Mar 03 2008 - 13:48:59 PST)
- Re: AMBER: xleap screen output Bill Ross (Mon Mar 03 2008 - 14:08:17 PST)
  - Re: AMBER: xleap screen output Francesco Pietra (Tue Mar 04 2008 - 09:27:00 PST)
AMBER: ACS COMP Division awards- deadline this week Carlos Simmerling (Mon Mar 03 2008 - 16:14:03 PST)
AMBER: Problem running implicit minimization Lili Peng (Mon Mar 03 2008 - 21:10:52 PST)
- Re: AMBER: Problem running implicit minimization David A. Case (Mon Mar 03 2008 - 21:59:00 PST)
  - Re: AMBER: Problem running implicit minimization Lili Peng (Mon Mar 03 2008 - 22:17:27 PST)
    - Re: AMBER: Problem running implicit minimization Carlos Simmerling (Tue Mar 04 2008 - 03:04:38 PST)
    - Re: AMBER: Problem running implicit minimization Lili Peng (Tue Mar 04 2008 - 15:25:32 PST)
    - Re: AMBER: Problem running implicit minimization Carlos Simmerling (Tue Mar 04 2008 - 15:39:23 PST)
    - Re: AMBER: Problem running implicit minimization Lili Peng (Tue Mar 04 2008 - 17:29:36 PST)
    - Re: AMBER: Problem running implicit minimization Thomas Cheatham (Tue Mar 04 2008 - 15:47:50 PST)
AMBER: missing gaff parameters Samuele Giani (Tue Mar 04 2008 - 00:46:38 PST)
- Re: AMBER: missing gaff parameters Junmei Wang (Tue Mar 04 2008 - 06:53:39 PST)
- RE: AMBER: missing gaff parameters Ross Walker (Tue Mar 04 2008 - 07:39:03 PST)
  - Re: AMBER: missing gaff parameters Samuele Giani (Tue Mar 04 2008 - 08:42:03 PST)
    - AMBER: question on antechamber: jaguar ouput wei zhang (Tue Mar 11 2008 - 10:01:55 PDT)
    - Re: AMBER: question on antechamber: jaguar ouput Junmei Wang (Tue Mar 11 2008 - 11:22:52 PDT)
    - Re: AMBER: question on antechamber: jaguar ouput Marcelo Puiatti (Tue Mar 11 2008 - 11:35:10 PDT)
    - Re: AMBER: question on antechamber: jaguar ouput wei zhang (Wed Mar 12 2008 - 11:14:55 PDT)
Fwd: Re: AMBER: xleap screen output Francesco Pietra (Tue Mar 04 2008 - 09:33:34 PST)
Fwd: Re: AMBER: xleap screen output SOLVED Francesco Pietra (Tue Mar 04 2008 - 12:44:15 PST)
Re: Fwd: Re: AMBER: xleap screen output Bill Ross (Tue Mar 04 2008 - 09:59:58 PST)
AMBER: a question about parameter b in the hyperbolic form of penalty function for RESP fit Ye Mei (Wed Mar 05 2008 - 01:30:50 PST)
AMBER: Atom types/parameters for chromene anna.schrey.gmx.de (Wed Mar 05 2008 - 01:34:24 PST)
- Re: AMBER: Atom types/parameters for chromene Junmei Wang (Wed Mar 05 2008 - 08:23:19 PST)
  - Re: AMBER: Atom types/parameters for chromene Francesco Pietra (Wed Mar 05 2008 - 10:07:05 PST)
    - Re: AMBER: Atom types/parameters for chromene David A. Case (Wed Mar 05 2008 - 11:15:25 PST)
  - Re: AMBER: Atom types/parameters for chromene anna.schrey.gmx.de (Thu Mar 06 2008 - 05:35:06 PST)
AMBER: setBox command Vijay Manickam Achari (Wed Mar 05 2008 - 21:20:01 PST)
- Re: AMBER: setBox command Thomas Steinbrecher (Thu Mar 06 2008 - 10:06:32 PST)
AMBER: not equivalent oxygens in COO- / how to force order of atoms in IMPROPER? Edyta Malolepsza (Thu Mar 06 2008 - 04:23:06 PST)
- Re: AMBER: not equivalent oxygens in COO- / how to force order of atoms in IMPROPER? David A. Case (Wed Mar 19 2008 - 08:42:13 PDT)
  - Re: AMBER: not equivalent oxygens in COO- / how to force order of atoms in IMPROPER? Edyta Malolepsza (Wed Mar 19 2008 - 09:49:45 PDT)
    - Re: AMBER: not equivalent oxygens in COO- / how to force order of atoms in IMPROPER? Francesco Pietra (Wed Mar 19 2008 - 10:26:24 PDT)
    - Re: AMBER: not equivalent oxygens in COO- / how to force order of atoms in IMPROPER? David A. Case (Wed Mar 19 2008 - 15:54:24 PDT)
    - Re: AMBER: not equivalent oxygens in COO- / how to force order of atoms in IMPROPER? Edyta Malolepsza (Mon Mar 31 2008 - 06:05:42 PDT)
AMBER: Steve Seibold (Thu Mar 06 2008 - 10:04:01 PST)
- Re: AMBER: Thomas Steinbrecher (Thu Mar 06 2008 - 10:13:23 PST)
  - RE: AMBER: Steve Seibold (Thu Mar 06 2008 - 10:27:34 PST)
    - RE: AMBER: Ross Walker (Thu Mar 06 2008 - 10:37:16 PST)
    - Re: AMBER: Jianyin Shao (Thu Mar 06 2008 - 13:24:03 PST)
    - AMBER: XMGRACE on Linux 64 Bit dpandit.brandeis.edu (Thu Mar 06 2008 - 15:15:00 PST)
Re: AMBER: XMGRACE on Linux 64 Bit Bill Ross (Thu Mar 06 2008 - 16:12:51 PST)
- Re: AMBER: XMGRACE on Linux 64 Bit dpandit.brandeis.edu (Thu Mar 06 2008 - 17:50:55 PST)
  - RE: AMBER: XMGRACE on Linux 64 Bit Ross Walker (Thu Mar 06 2008 - 18:30:44 PST)
    - RE: AMBER: XMGRACE on Linux 64 Bit dpandit.brandeis.edu (Fri Mar 07 2008 - 10:40:19 PST)
    - Re: AMBER: XMGRACE on Linux 64 Bit David LeBard (Fri Mar 07 2008 - 10:53:47 PST)
AMBER: Microcannonical MD Reference priya priya (Fri Mar 07 2008 - 05:40:34 PST)
- Re: AMBER: Microcannonical MD Reference David A. Case (Fri Mar 07 2008 - 14:47:02 PST)
AMBER: NVE energy and temperature drift Lars Skjærven (Fri Mar 07 2008 - 07:36:48 PST)
- Re: AMBER: NVE energy and temperature drift David A. Case (Fri Mar 07 2008 - 08:32:51 PST)
  - Re: AMBER: NVE energy and temperature drift Lars Skjærven (Fri Mar 07 2008 - 09:34:33 PST)
AMBER: Fwd: positive potential energy and large 1-4 EEL Mey Khalili (Fri Mar 07 2008 - 08:54:28 PST)
- Re: AMBER: Fwd: positive potential energy and large 1-4 EEL David A. Case (Mon Mar 10 2008 - 17:19:51 PDT)
AMBER: Inquiry on nmode for alculate frequencies & thermodynamics analysis James Thomas (Fri Mar 07 2008 - 09:30:58 PST)
- Re: AMBER: Inquiry on nmode for alculate frequencies & thermodynamics analysis David A. Case (Fri Mar 07 2008 - 13:36:33 PST)
AMBER: RE: Request Ross Walker (Fri Mar 07 2008 - 12:38:25 PST)
AMBER: reg molecular dynamics Uma R (Fri Mar 07 2008 - 19:17:32 PST)
AMBER: Negative ligand (Peroxide) Syed Tarique Moin (Sat Mar 08 2008 - 03:36:56 PST)
AMBER: Compiler issues with Altix450 finke.oakland.edu (Sat Mar 08 2008 - 10:37:25 PST)
- Re: AMBER: Compiler issues with Altix450 Atro Tossavainen (Sat Mar 08 2008 - 14:19:36 PST)
- Re: AMBER: Compiler issues with Altix450 finke.oakland.edu (Mon Mar 10 2008 - 13:45:37 PDT)
  - Re: AMBER: Compiler issues with Altix450 Atro Tossavainen (Mon Mar 10 2008 - 16:13:45 PDT)
  - Re: AMBER: Compiler issues with Altix450 David A. Case (Mon Mar 10 2008 - 16:29:50 PDT)
AMBER: Clarification on error message Campbell, Patrick (Sat Mar 08 2008 - 12:09:23 PST)
- Re: AMBER: Clarification on error message Thomas Steinbrecher (Sat Mar 08 2008 - 12:17:35 PST)
  - RE: AMBER: Clarification on error message Campbell, Patrick (Sat Mar 08 2008 - 13:15:36 PST)
AMBER: mmpbsa INSTRNG error? Sergio Wong (Sat Mar 08 2008 - 22:06:44 PST)
- Re: AMBER: mmpbsa INSTRNG error? Gohlke.bioinformatik.uni-frankfurt.de (Sun Mar 09 2008 - 09:13:05 PDT)
AMBER: Timing analysis on Ranger David LeBard (Sun Mar 09 2008 - 13:06:18 PDT)
AMBER: Antechamber, net molecular charge gurpreet singh (Sun Mar 09 2008 - 21:51:58 PDT)
- Re: AMBER: Antechamber, net molecular charge Junmei Wang (Mon Mar 10 2008 - 07:39:08 PDT)
AMBER: Benchmarks on Fujitsu PrimePower 2500? Craig Gough (Sun Mar 09 2008 - 22:36:28 PDT)
- Re: AMBER: Benchmarks on Fujitsu PrimePower 2500? Atro Tossavainen (Mon Mar 10 2008 - 01:04:20 PDT)
  - Re: AMBER: Benchmarks on Fujitsu PrimePower 2500? Robert Duke (Mon Mar 10 2008 - 06:24:21 PDT)
    - Re: AMBER: Benchmarks on Fujitsu PrimePower 2500? Atro Tossavainen (Mon Mar 10 2008 - 06:24:33 PDT)
Fwd: AMBER: Negative ligand (Peroxide) Syed Tarique Moin (Sun Mar 09 2008 - 22:59:43 PDT)
AMBER: writing out a distance between two atoms in sander Vlad Cojocaru (Mon Mar 10 2008 - 06:33:55 PDT)
- Re: AMBER: writing out a distance between two atoms in sander Thomas Steinbrecher (Mon Mar 10 2008 - 10:17:35 PDT)
  - Re: AMBER: writing out a distance between two atoms in sander Vlad Cojocaru (Mon Mar 10 2008 - 10:35:58 PDT)
AMBER: problem with antech amber Madjid Taghdir (Mon Mar 10 2008 - 08:07:16 PDT)
- Re: AMBER: problem with antech amber David A. Case (Fri Mar 14 2008 - 22:09:00 PDT)
AMBER: output effective Born radii Holly Freedman (Mon Mar 10 2008 - 15:57:06 PDT)
- Re: AMBER: output effective Born radii David A. Case (Mon Mar 10 2008 - 17:07:39 PDT)
- Re: AMBER: output effective Born radii Holly Freedman (Mon Mar 10 2008 - 19:24:32 PDT)
AMBER: Re: Amber: parameters for Silicon Scott Brozell (Mon Mar 10 2008 - 16:57:29 PDT)
Re: AMBER: AMBER install problem David A. Case (Mon Mar 10 2008 - 17:50:30 PDT)
- Re: AMBER: AMBER install problem Atro Tossavainen (Mon Mar 10 2008 - 23:51:18 PDT)
  - Re: AMBER: AMBER install problem David A. Case (Tue Mar 11 2008 - 17:47:58 PDT)
    - AMBER: RE: Re: AMBER: AMBER install problem Kijeong Kwac (Thu Mar 13 2008 - 10:35:10 PDT)
AMBER: SMD using amber ChengZhong Zhang (Mon Mar 10 2008 - 18:54:23 PDT)
AMBER: convert AMBER format input files into DL_POLY format input files? Kefa Lu (Tue Mar 11 2008 - 01:27:23 PDT)
AMBER: solvate with methanol san_amber roy (Tue Mar 11 2008 - 02:23:40 PDT)
- Re: AMBER: solvate with methanol Rita Cassia (Tue Mar 11 2008 - 05:33:46 PDT)
AMBER: Adding New Parameters and Modifying Existing Parameters serhanyigen.mail.ege.edu.tr (Tue Mar 11 2008 - 04:51:18 PDT)
- Re: AMBER: Adding New Parameters and Modifying Existing Parameters Thomas Steinbrecher (Tue Mar 11 2008 - 09:46:33 PDT)
AMBER: SPARC benchmarks (was re Fujitsu PRIMEPOWER) Atro Tossavainen (Tue Mar 11 2008 - 07:33:33 PDT)
AMBER: Error during compilation of Amber8, /bin/sh: ./Makelist: not found, make[1]: *** [libobj] Error 127 David Rangel (Tue Mar 11 2008 - 20:30:14 PDT)
- Re: AMBER: Error during compilation of Amber8, /bin/sh: ./Makelist: not found, make[1]: *** [libobj] Error 127 David A. Case (Tue Mar 11 2008 - 22:43:26 PDT)
  - Re: AMBER: Error during compilation of Amber8, /bin/sh: ./Makelist: not found, make[1]: *** [libobj] Error 127 David Rangel (Wed Mar 12 2008 - 10:04:18 PDT)
AMBER: lastrst problem san_amber roy (Wed Mar 12 2008 - 08:07:23 PDT)
- Fwd: AMBER: lastrst problem san_amber roy (Wed Mar 12 2008 - 08:19:08 PDT)
  - Re: Fwd: AMBER: lastrst problem David A. Case (Tue Mar 18 2008 - 08:37:48 PDT)
    - Re: Fwd: AMBER: lastrst problem san_amber roy (Wed Mar 19 2008 - 09:07:26 PDT)
AMBER: ptraj and non-bonded contacts Samuel Genheden (a03samge) (Wed Mar 12 2008 - 09:34:44 PDT)
AMBER: study of protein stability in different ion using AMBER Prem Prakash Pathak (Wed Mar 12 2008 - 23:20:31 PDT)
- Re: AMBER: study of protein stability in different ion using AMBER David A. Case (Fri Mar 14 2008 - 22:48:13 PDT)
AMBER: distance restraint gurpreet singh (Thu Mar 13 2008 - 04:28:28 PDT)
- Re: AMBER: distance restraint David A. Case (Thu Mar 13 2008 - 13:40:07 PDT)
AMBER: [success] problem compiling Amber9 on Bull Linux Yannick Monclin (Thu Mar 13 2008 - 04:56:48 PDT)
AMBER: Energy calculation and replica exchange in Amber9 Li Dawei (Thu Mar 13 2008 - 06:50:49 PDT)
AMBER: can't make antechamber work for regular nucleotides Mey Khalili (Thu Mar 13 2008 - 07:03:45 PDT)
- Re: AMBER: can't make antechamber work for regular nucleotides Junmei Wang (Fri Mar 14 2008 - 19:10:41 PDT)
  - Re: AMBER: can't make antechamber work for regular nucleotides Mey Khalili (Mon Mar 17 2008 - 06:59:01 PDT)
    - Re: AMBER: can't make antechamber work for regular nucleotides Junmei Wang (Tue Mar 18 2008 - 14:08:46 PDT)
AMBER: ptraj, hbond and non-bonded contacts Samuel Genheden (a03samge) (Thu Mar 13 2008 - 07:54:03 PDT)
- Re: AMBER: ptraj, hbond and non-bonded contacts Thomas Cheatham III (Thu Mar 13 2008 - 10:49:14 PDT)
- Re: AMBER: ptraj, hbond and non-bonded contacts Jojart Balazs (Fri Mar 14 2008 - 01:19:37 PDT)
AMBER: Temperature Range For REMD tushar garud (Thu Mar 13 2008 - 08:20:02 PDT)
- Re: AMBER: Temperature Range For REMD Carlos Simmerling (Thu Mar 13 2008 - 08:26:44 PDT)
AMBER: force field oguz gurbulak (Thu Mar 13 2008 - 15:00:58 PDT)
AMBER: protonated histidine ( charges in parm file versus all_amino03.lib ) Lwin, ThuZar (Thu Mar 13 2008 - 17:13:57 PDT)
AMBER: How to calculate deformability by PTRAJ ? sychen (Thu Mar 13 2008 - 18:44:36 PDT)
AMBER: Torsion potential in GAFF / "statistic value of parm94" Alexander Metz (Fri Mar 14 2008 - 05:53:10 PDT)
- Re: AMBER: Torsion potential in GAFF / "statistic value of parm94" Junmei Wang (Fri Mar 14 2008 - 20:01:20 PDT)
AMBER: protonated histidine ( charges in parm file versus all_amino03.lib ). Lwin, ThuZar (Fri Mar 14 2008 - 08:32:25 PDT)
- RE: AMBER: protonated histidine ( charges in parm file versus all_amino03.lib ). Ross Walker (Fri Mar 14 2008 - 09:30:13 PDT)
  - RE: AMBER: protonated histidine ( charges in parm file versus all_a mino03.lib ). . . Lwin, ThuZar (Tue Mar 18 2008 - 09:45:49 PDT)
AMBER: Heating POL3 Box Troubles Paul Johns (Fri Mar 14 2008 - 11:44:44 PDT)
- Re: AMBER: Heating POL3 Box Troubles Thomas Steinbrecher (Fri Mar 14 2008 - 12:01:06 PDT)
  - Re: AMBER: Heating POL3 Box Troubles Paul Johns (Fri Mar 14 2008 - 12:13:02 PDT)
    - Re: AMBER: Heating POL3 Box Troubles Thomas Steinbrecher (Fri Mar 14 2008 - 12:31:03 PDT)
    - Re: AMBER: Heating POL3 Box Troubles Paul Johns (Fri Mar 14 2008 - 14:01:22 PDT)
    - Re: AMBER: Heating POL3 Box Troubles Thomas Steinbrecher (Fri Mar 14 2008 - 14:22:21 PDT)
- Re: AMBER: Heating POL3 Box Troubles David A. Case (Fri Mar 14 2008 - 20:40:35 PDT)
  - Re: AMBER: Heating POL3 Box Troubles David A. Case (Fri Mar 14 2008 - 21:41:09 PDT)
  - Re: AMBER: Heating POL3 Box Troubles Paul Johns (Mon Mar 17 2008 - 13:07:02 PDT)
    - Re: AMBER: Heating POL3 Box Troubles David A. Case (Mon Mar 17 2008 - 22:30:48 PDT)
    - Re: AMBER: Heating POL3 Box Troubles Paul Johns (Wed Mar 19 2008 - 12:22:50 PDT)
    - Re: AMBER: Heating POL3 Box Troubles David A. Case (Wed Mar 19 2008 - 14:57:54 PDT)
AMBER: Negative ligand Syed Tarique Moin (Sat Mar 15 2008 - 02:12:09 PDT)
SV: AMBER: ptraj, hbond and non-bonded contacts Samuel Genheden (a03samge) (Mon Mar 17 2008 - 03:43:21 PDT)
- Re: SV: AMBER: ptraj, hbond and non-bonded contacts Vlad Cojocaru (Mon Mar 17 2008 - 04:00:41 PDT)
- Re: SV: AMBER: ptraj, hbond and non-bonded contacts Thomas Cheatham III (Mon Mar 17 2008 - 09:51:54 PDT)
SV: AMBER: ptraj, hbond and non-bonded contacts Samuel Genheden (a03samge) (Mon Mar 17 2008 - 04:02:59 PDT)
SV: SV: AMBER: ptraj, hbond and non-bonded contacts Samuel Genheden (a03samge) (Mon Mar 17 2008 - 05:00:52 PDT)
AMBER: mm_pbsa positive ELE Qi Yan (Mon Mar 17 2008 - 11:20:21 PDT)
- Re: AMBER: mm_pbsa positive ELE Ray Luo (Mon Mar 17 2008 - 11:33:11 PDT)
- RE: AMBER: mm_pbsa positive ELE Qi Yan (Mon Mar 17 2008 - 12:23:52 PDT)
  - Re: AMBER: mm_pbsa positive ELE Ray Luo (Mon Mar 17 2008 - 13:14:57 PDT)
AMBER: compiling AMBER9 with bintraj option on AMD64 Vlad Cojocaru (Fri Mar 14 2008 - 10:44:56 PDT)
- Re: AMBER: compiling AMBER9 with bintraj option on AMD64 David A. Case (Mon Mar 17 2008 - 16:48:00 PDT)
  - Re: AMBER: compiling AMBER9 with bintraj option on AMD64 Vlad Cojocaru (Tue Mar 18 2008 - 02:32:13 PDT)
SV: SV: AMBER: ptraj, hbond and non-bonded contacts Samuel Genheden (a03samge) (Mon Mar 17 2008 - 13:41:31 PDT)
AMBER: What's making my system lose total energy? David Cerutti (Mon Mar 17 2008 - 17:20:30 PDT)
- RE: AMBER: What's making my system lose total energy? Ross Walker (Mon Mar 17 2008 - 19:54:19 PDT)
- Re: AMBER: What's making my system lose total energy? Thomas Cheatham (Mon Mar 17 2008 - 20:36:30 PDT)
  - Re: AMBER: What's making my system lose total energy? David Cerutti (Mon Mar 17 2008 - 20:52:10 PDT)
    - Re: AMBER: What's making my system lose total energy? David Cerutti (Tue Mar 18 2008 - 11:43:42 PDT)
    - Re: AMBER: What's making my system lose total energy? David A. Case (Wed Mar 19 2008 - 18:46:31 PDT)
AMBER: a minor bug in RESP Ye Mei (Tue Mar 18 2008 - 00:05:34 PDT)
AMBER: problem with distance restrain aneesh cna (Tue Mar 18 2008 - 03:16:09 PDT)
- Re: AMBER: problem with distance restrain David A. Case (Tue Mar 18 2008 - 12:00:11 PDT)
AMBER: replica exchange : problem with sander Guillaume Renvez (Tue Mar 18 2008 - 07:09:34 PDT)
- Re: AMBER: replica exchange : problem with sander Carlos Simmerling (Tue Mar 18 2008 - 07:29:38 PDT)
  - Re: AMBER: replica exchange : problem with sander Guillaume Renvez (Tue Mar 18 2008 - 08:29:39 PDT)
  - Re: AMBER: replica exchange : problem with sander Guillaume Renvez (Tue Mar 18 2008 - 09:21:21 PDT)
    - Re: AMBER: replica exchange : problem with sander Carlos Simmerling (Tue Mar 18 2008 - 09:39:01 PDT)
    - Re: AMBER: replica exchange : problem with sander Guillaume Renvez (Tue Mar 18 2008 - 10:07:54 PDT)
    - Re: AMBER: replica exchange : problem with sander Carlos Simmerling (Tue Mar 18 2008 - 10:12:03 PDT)
    - Re: AMBER: replica exchange : problem with sander Guillaume Renvez (Tue Mar 18 2008 - 10:24:10 PDT)
    - Re: AMBER: replica exchange : problem with sander Guillaume Renvez (Wed Mar 19 2008 - 05:14:38 PDT)
    - Re: AMBER: replica exchange : problem with sander Carlos Simmerling (Wed Mar 19 2008 - 05:47:04 PDT)
    - Re: AMBER: replica exchange : problem with sander Guillaume Renvez (Wed Mar 19 2008 - 06:13:01 PDT)
    - Re: AMBER: replica exchange : problem with sander Carlos Simmerling (Wed Mar 19 2008 - 06:25:11 PDT)
    - Re: AMBER: replica exchange : problem with sander Guillaume Renvez (Wed Mar 19 2008 - 06:35:55 PDT)
    - Re: AMBER: replica exchange : problem with sander Carlos Simmerling (Wed Mar 19 2008 - 06:49:23 PDT)
    - Re: AMBER: replica exchange : problem with sander Guillaume Renvez (Wed Mar 19 2008 - 06:57:55 PDT)
    - Re: AMBER: replica exchange : problem with sander Carlos Simmerling (Thu Mar 20 2008 - 07:47:32 PDT)
    - Re: AMBER: replica exchange : problem with sander Guillaume Renvez (Thu Mar 20 2008 - 08:02:29 PDT)
AMBER: Problems with neglected restaints anna.schrey.gmx.de (Tue Mar 18 2008 - 09:40:20 PDT)
- Re: AMBER: Problems with neglected restaints Carlos Simmerling (Tue Mar 18 2008 - 10:05:11 PDT)
- Re: AMBER: Problems with neglected restaints David A. Case (Tue Mar 18 2008 - 10:15:56 PDT)
  - Re: AMBER: Problems with neglected restaints anna.schrey.gmx.de (Thu Mar 20 2008 - 12:43:20 PDT)
AMBER: Inquiry on analyzing the amplitude from nmdout results James Thomas (Wed Mar 19 2008 - 09:09:05 PDT)
- Re: AMBER: Inquiry on analyzing the amplitude from nmdout results David A. Case (Wed Mar 19 2008 - 14:46:10 PDT)
  - Re: AMBER: Inquiry on analyzing the amplitude from nmdout results James Thomas (Wed Mar 19 2008 - 15:00:35 PDT)
    - Re: AMBER: Inquiry on analyzing the amplitude from nmdout results David A. Case (Wed Mar 19 2008 - 15:49:21 PDT)
AMBER: Amber9 Installation Problem trudy.uoguelph.ca (Wed Mar 19 2008 - 09:28:35 PDT)
- Re: AMBER: Amber9 Installation Problem Cenk Andac (Wed Mar 19 2008 - 13:25:25 PDT)
  - Re: AMBER: Amber9 Installation Problem Cenk Andac (Wed Mar 19 2008 - 13:43:50 PDT)
    - Re: AMBER: Amber9 Installation Problem Cenk Andac (Wed Mar 19 2008 - 13:55:23 PDT)
    - Re: AMBER: Amber9 Installation Problem trudy.uoguelph.ca (Thu Mar 20 2008 - 15:43:48 PDT)
- Re: AMBER: Amber9 Installation Problem David A. Case (Wed Mar 19 2008 - 18:37:57 PDT)
  - Re: AMBER: Amber9 Installation Problem trudy.uoguelph.ca (Thu Mar 20 2008 - 15:51:08 PDT)
    - Re: AMBER: Amber9 Installation Problem David A. Case (Thu Mar 20 2008 - 16:23:53 PDT)
AMBER: MNDO parameters for Mg+2 E.M. (Wed Mar 19 2008 - 10:28:09 PDT)
- RE: AMBER: MNDO parameters for Mg+2 Ross Walker (Wed Mar 19 2008 - 11:10:18 PDT)
AMBER: standard residues Holly Freedman (Wed Mar 19 2008 - 13:03:02 PDT)
- Re: AMBER: standard residues David A. Case (Sat Mar 22 2008 - 09:30:03 PDT)
- Re: AMBER: standard residues Holly Freedman (Sat Mar 22 2008 - 15:27:07 PDT)
AMBER: Water Topology Ivelin Georgiev (Wed Mar 19 2008 - 21:12:28 PDT)
- RE: AMBER: Water Topology Ross Walker (Wed Mar 19 2008 - 21:49:43 PDT)
  - Re: AMBER: Water Topology Ivelin Georgiev (Thu Mar 20 2008 - 06:44:51 PDT)
    - RE: AMBER: Water Topology Ross Walker (Thu Mar 20 2008 - 08:08:46 PDT)
    - AMBER: INPCRD error on open Campbell, Patrick (Thu Mar 20 2008 - 08:17:32 PDT)
    - Re: AMBER: INPCRD error on open Carlos Simmerling (Thu Mar 20 2008 - 08:22:56 PDT)
    - RE: AMBER: INPCRD error on open Campbell, Patrick (Thu Mar 20 2008 - 10:02:12 PDT)
    - Re: AMBER: INPCRD error on open Carlos Simmerling (Thu Mar 20 2008 - 10:10:23 PDT)
    - RE: AMBER: INPCRD error on open Campbell, Patrick (Thu Mar 20 2008 - 11:35:37 PDT)
    - Re: AMBER: INPCRD error on open Cyril Bauvais (Thu Mar 20 2008 - 09:04:31 PDT)
    - RE: AMBER: INPCRD error on open Campbell, Patrick (Thu Mar 20 2008 - 11:37:45 PDT)
AMBER: potential of mean force: Unit of PMF energies and min path Catein Catherine (Wed Mar 19 2008 - 22:26:43 PDT)
AMBER: Happy holi Bertrand P. S. Russell (Thu Mar 20 2008 - 02:03:22 PDT)
AMBER: problem with distance restraints aneesh cna (Thu Mar 20 2008 - 03:13:31 PDT)
- Re: AMBER: problem with distance restraints David A. Case (Fri Mar 21 2008 - 10:56:28 PDT)
AMBER: Charge scheme for simulating protonated adenine prateeksha s (Thu Mar 20 2008 - 23:58:19 PDT)
- Re: AMBER: Charge scheme for simulating protonated adenine FyD (Fri Mar 21 2008 - 00:43:51 PDT)
  - Re: AMBER: Charge scheme for simulating protonated adenine prateeksha s (Fri Mar 21 2008 - 09:32:06 PDT)
    - Re: AMBER: Charge scheme for simulating protonated adenine prateeksha s (Wed Apr 09 2008 - 23:11:35 PDT)
    - Re: AMBER: Charge scheme for simulating protonated adenine prateeksha s (Wed Apr 09 2008 - 23:19:40 PDT)
- Re: AMBER: Charge scheme for simulating protonated adenine rpaduri.chem.wayne.edu (Fri Mar 21 2008 - 08:29:18 PDT)
  - Re: AMBER: Charge scheme for simulating protonated adenine prateeksha s (Fri Mar 21 2008 - 09:32:14 PDT)
AMBER: equilibration of peptide tushar garud (Fri Mar 21 2008 - 21:02:25 PDT)
- Re: AMBER: equilibration of peptide David A. Case (Sat Mar 22 2008 - 10:51:47 PDT)
  - AMBER: addions and addions2 dpandit.brandeis.edu (Tue Mar 25 2008 - 07:38:22 PDT)
AMBER: cntrl namelist error Campbell, Patrick (Sat Mar 22 2008 - 08:40:16 PDT)
- RE: AMBER: cntrl namelist error Ross Walker (Sat Mar 22 2008 - 09:01:47 PDT)
  - RE: AMBER: cntrl namelist error Campbell, Patrick (Sat Mar 22 2008 - 09:11:39 PDT)
- Re: AMBER: cntrl namelist error David A. Case (Sat Mar 22 2008 - 09:11:52 PDT)
  - RE: AMBER: cntrl namelist error Campbell, Patrick (Sat Mar 22 2008 - 09:22:18 PDT)
AMBER: RE: Force Field Parameterizing Shultz, Jack (Mon Mar 24 2008 - 08:31:32 PDT)
- Re: AMBER: RE: Force Field Parameterizing David A. Case (Tue Mar 25 2008 - 08:23:34 PDT)
  - AMBER: RE: Force Field Parameterizing FyD (Tue Mar 25 2008 - 12:42:03 PDT)
AMBER: hybrid remd imaging Geoff Wood (Mon Mar 24 2008 - 08:51:51 PDT)
- Re: AMBER: hybrid remd imaging Carlos Simmerling (Mon Mar 24 2008 - 08:59:24 PDT)
  - Re: AMBER: hybrid remd imaging Geoff Wood (Mon Mar 24 2008 - 09:16:25 PDT)
  - Re: AMBER: hybrid remd imaging Geoff Wood (Mon Mar 24 2008 - 09:21:41 PDT)
    - Re: AMBER: hybrid remd imaging Geoff Wood (Thu Mar 27 2008 - 05:56:30 PDT)
AMBER: WARNING in readAmberTrajectory(): Set #7918 is corrupted (-) Qi Yan (Mon Mar 24 2008 - 13:01:35 PDT)
- Re: AMBER: WARNING in readAmberTrajectory(): Set #7918 is corrupted (-) Da-Wei Li (Mon Mar 24 2008 - 13:12:42 PDT)
- RE: AMBER: WARNING in readAmberTrajectory(): Set #7918 is corrupted (-) Qi Yan (Mon Mar 24 2008 - 13:50:40 PDT)
  - Re: AMBER: WARNING in readAmberTrajectory(): Set #7918 is corrupted (-) Andrew Borgert (Tue Mar 25 2008 - 08:11:20 PDT)
    - RE: AMBER: WARNING in readAmberTrajectory(): Set #7918 is corrupted (-) zachary hartman (Wed Apr 09 2008 - 07:00:45 PDT)
- RE: AMBER: WARNING in readAmberTrajectory(): Set #7918 is corrupted (-) Qi Yan (Tue Mar 25 2008 - 10:00:35 PDT)
  - Re: AMBER: WARNING in readAmberTrajectory(): Set #7918 is corrupted (-) Da-Wei Li (Tue Mar 25 2008 - 10:08:29 PDT)
- RE: AMBER: WARNING in readAmberTrajectory(): Set #7918 is corrupted (-) Qi Yan (Wed Mar 26 2008 - 07:42:54 PDT)
  - Re: AMBER: WARNING in readAmberTrajectory(): Set #7918 is corrupted (-) Steven Winfield (Wed Mar 26 2008 - 08:22:26 PDT)
  - RE: AMBER: WARNING in readAmberTrajectory(): Set #7918 is corrupted (-) Chris Moth (Wed Mar 26 2008 - 15:27:35 PDT)
AMBER: Nmode segmentation fault James Thomas (Tue Mar 25 2008 - 04:53:21 PDT)
- Re: AMBER: Nmode segmentation fault David A. Case (Tue Mar 25 2008 - 09:34:37 PDT)
  - Re: AMBER: Nmode segmentation fault James Thomas (Tue Mar 25 2008 - 10:22:43 PDT)
    - Re: AMBER: Nmode segmentation fault David A. Case (Tue Mar 25 2008 - 11:44:51 PDT)
    - Re: AMBER: Nmode segmentation fault James Thomas (Tue Mar 25 2008 - 12:00:44 PDT)
    - Re: AMBER: Nmode segmentation fault David A. Case (Wed Apr 02 2008 - 10:50:09 PDT)
AMBER: help regarding warning message snoze pa (Tue Mar 25 2008 - 09:17:43 PDT)
- Re: AMBER: help regarding warning message David A. Case (Tue Mar 25 2008 - 11:51:07 PDT)
  - Re: AMBER: help regarding warning message snoze pa (Tue Mar 25 2008 - 13:23:55 PDT)
AMBER: anion and cation simulaton gurpreet singh (Tue Mar 25 2008 - 09:22:29 PDT)
- Re: AMBER: anion and cation simulaton FyD (Tue Mar 25 2008 - 12:54:56 PDT)
Re: AMBER: addions and addions2 Bill Ross (Tue Mar 25 2008 - 10:34:52 PDT)
AMBER: Convert dcd to mdcrd Seth Lilavivat (Tue Mar 25 2008 - 11:13:22 PDT)
- Re: AMBER: Convert dcd to mdcrd Vlad Cojocaru (Wed Mar 26 2008 - 02:02:38 PDT)
  - AMBER: FAD and NAD parameters Thomas Leonard (Wed Mar 26 2008 - 02:26:52 PDT)
    - Re: AMBER: FAD and NAD parameters FyD (Wed Mar 26 2008 - 03:57:27 PDT)
    - Re: AMBER: FAD and NAD parameters Thomas Leonard (Wed Apr 09 2008 - 23:43:47 PDT)
AMBER: umbrella sampling for proton transfer cniu.ualberta.ca (Tue Mar 25 2008 - 17:30:33 PDT)
- Re: AMBER: umbrella sampling for proton transfer Thomas Steinbrecher (Tue Mar 25 2008 - 18:11:58 PDT)
AMBER: NTR Restraints Daniel Smith (Tue Mar 25 2008 - 18:17:27 PDT)
- Re: AMBER: NTR Restraints David A. Case (Thu Mar 27 2008 - 13:17:31 PDT)
  - AMBER: Questions toward Azobenzene Chih-Ying Lin (Thu Mar 27 2008 - 21:23:40 PDT)
AMBER: OPLS force field aneesh cna (Wed Mar 26 2008 - 08:48:19 PDT)
- Re: AMBER: OPLS force field David A. Case (Wed Mar 26 2008 - 09:08:57 PDT)
AMBER: mm-pbsa multiple trajectory approach? Seth Lilavivat (Wed Mar 26 2008 - 10:32:54 PDT)
- Re: AMBER: mm-pbsa multiple trajectory approach? Chris Moth (Wed Mar 26 2008 - 15:21:25 PDT)
  - Re: AMBER: mm-pbsa multiple trajectory approach? Seth Lilavivat (Fri Mar 28 2008 - 08:28:31 PDT)
    - Re: AMBER: mm-pbsa multiple trajectory approach? Chris Moth (Wed Apr 02 2008 - 14:18:06 PDT)
AMBER: residual dipolar couplings - alignment tensor energy Douglas Kojetin (Wed Mar 26 2008 - 12:46:48 PDT)
- Re: AMBER: residual dipolar couplings - alignment tensor energy Douglas Kojetin (Tue Apr 01 2008 - 08:23:59 PDT)
  - Re: AMBER: residual dipolar couplings - alignment tensor energy Douglas Kojetin (Tue Apr 01 2008 - 08:53:55 PDT)
- Re: AMBER: residual dipolar couplings - alignment tensor energy David A. Case (Wed Apr 02 2008 - 10:53:38 PDT)
AMBER: RMSD of two different molecules JunJun Liu (Wed Mar 26 2008 - 13:35:32 PDT)
- Re: AMBER: RMSD of two different molecules Da-Wei Li (Wed Mar 26 2008 - 13:39:19 PDT)
  - Re: AMBER: RMSD of two different molecules JunJun Liu (Wed Mar 26 2008 - 14:54:11 PDT)
AMBER: how to link two different atoms in xLeap snoze pa (Wed Mar 26 2008 - 13:56:12 PDT)
- Re: AMBER: how to link two different atoms in xLeap David A. Case (Wed Mar 26 2008 - 21:52:18 PDT)
AMBER: Error with a binary restart file Kijeong Kwac (Wed Mar 26 2008 - 16:07:51 PDT)
- Re: AMBER: Error with a binary restart file David A. Case (Wed Mar 26 2008 - 18:11:58 PDT)
AMBER: PF6 parameters aneesh cna (Wed Mar 26 2008 - 21:43:58 PDT)
- RE: AMBER: PF6 parameters caoch (Thu Mar 27 2008 - 21:28:03 PDT)
AMBER: Error- MM_PBSA calculation vikky 99 (Thu Mar 27 2008 - 01:47:53 PDT)
AMBER: FW: MD run time inquiry Campbell, Patrick (Thu Mar 27 2008 - 03:13:00 PDT)
- Re: AMBER: FW: MD run time inquiry Carlos Simmerling (Thu Mar 27 2008 - 03:41:02 PDT)
- FW: AMBER: FW: MD run time inquiry Campbell, Patrick (Thu Mar 27 2008 - 05:14:16 PDT)
  - Re: FW: AMBER: FW: MD run time inquiry Carlos Simmerling (Thu Mar 27 2008 - 06:15:09 PDT)
- FW: FW: AMBER: FW: MD run time inquiry Campbell, Patrick (Thu Mar 27 2008 - 06:55:28 PDT)
AMBER: Protein rotating out of box Lars Skjærven (Thu Mar 27 2008 - 14:34:48 PDT)
- RE: AMBER: Protein rotating out of box Steve Spronk (Tue Apr 01 2008 - 07:55:20 PDT)
  - Re: AMBER: Protein rotating out of box Lars Skjærven (Wed Apr 02 2008 - 05:36:20 PDT)
    - RE: AMBER: Protein rotating out of box Steve Spronk (Wed Apr 02 2008 - 06:13:12 PDT)
    - Re: AMBER: Protein rotating out of box Thomas Cheatham III (Wed Apr 02 2008 - 09:54:46 PDT)
- Re: AMBER: Protein rotating out of box Qiang Li (Wed Apr 02 2008 - 10:35:04 PDT)
  - Re: AMBER: Protein rotating out of box Lars Skjærven (Wed Apr 02 2008 - 12:17:23 PDT)
    - Re: AMBER: Protein rotating out of box Lars Skjærven (Wed Apr 02 2008 - 14:01:54 PDT)
    - Re: AMBER: Protein rotating out of box David A. Case (Tue Apr 08 2008 - 18:54:29 PDT)
AMBER: measuring contacts: error "glibc detected" rebeca.mmb.pcb.ub.es (Fri Mar 28 2008 - 05:26:42 PDT)
AMBER: GAFF Eric Germaneau (Fri Mar 28 2008 - 05:38:41 PDT)
AMBER: REMD simulation error Guillaume Renvez (Fri Mar 28 2008 - 07:01:20 PDT)
AMBER: problem with nmod yuri pomè (Fri Mar 28 2008 - 09:42:54 PDT)
- Re: AMBER: problem with nmod David A. Case (Fri Mar 28 2008 - 17:19:40 PDT)
AMBER: meet problem in adding ions and waterbox Qiang Li (Sat Mar 29 2008 - 22:43:54 PDT)
- Re: AMBER: meet problem in adding ions and waterbox Emilio Xavier Esposito (Sun Mar 30 2008 - 10:26:45 PDT)
AMBER: Regarding SHAKE gurpreet singh (Sun Mar 30 2008 - 03:38:48 PDT)
- Re: AMBER: Regarding SHAKE David A. Case (Wed Apr 02 2008 - 10:54:59 PDT)
AMBER: reproducing http://amber.scripps.edu/tutorials/advanced/tutorial6/index.htm with explicit water Markus Kaukonen (Sun Mar 30 2008 - 23:34:48 PDT)
- Re: AMBER: reproducing http://amber.scripps.edu/tutorials/advanced/tutorial6/index.htm with explicit water David A. Case (Mon Apr 07 2008 - 13:40:27 PDT)
  - AMBER: how to change the force field parameters inside the prmtop file? Chih-Ying Lin (Mon Apr 07 2008 - 14:24:17 PDT)
    - Re: AMBER: how to change the force field parameters inside the prmtop file? David A. Case (Mon Apr 07 2008 - 17:05:21 PDT)
    - Re: AMBER: how to change the force field parameters inside the prmtop file? Chih-Ying Lin (Mon Apr 07 2008 - 21:13:39 PDT)
    - Re: AMBER: how to change the force field parameters inside the prmtop file? David A. Case (Mon Apr 07 2008 - 21:58:53 PDT)
    - Re: AMBER: how to change the force field parameters inside the prmtop file? Chih-Ying Lin (Tue Apr 08 2008 - 14:41:38 PDT)
    - Re: AMBER: how to change the force field parameters inside the prmtop file? David A. Case (Tue Apr 08 2008 - 15:08:00 PDT)
    - Re: AMBER: how to change the force field parameters inside the prmtop file? Chih-Ying Lin (Tue Apr 08 2008 - 15:31:27 PDT)
    - Re: AMBER: how to change the force field parameters inside the prmtop file? Chih-Ying Lin (Tue Apr 08 2008 - 15:39:39 PDT)
    - AMBER: Should the two phenyl rings of the trans-azobenzene on the same plane after minimisation? Chih-Ying Lin (Tue Apr 08 2008 - 18:03:53 PDT)
AMBER: Free energy landscape? HOWTO? Yi-Ming Cheng (Mon Mar 31 2008 - 01:12:05 PDT)
AMBER: TI: perturbation method fatima.chami.durham.ac.uk (Mon Mar 31 2008 - 01:40:40 PDT)
- Re: AMBER: TI: perturbation method Thomas Steinbrecher (Mon Mar 31 2008 - 09:32:21 PDT)
AMBER: Select specific residues (leap) Marta Rossini (Mon Mar 31 2008 - 02:28:31 PDT)
- Re: AMBER: Select specific residues (leap) FyD (Mon Mar 31 2008 - 03:31:39 PDT)
  - RE: AMBER: Select specific residues (leap) Marta Rossini (Mon Mar 31 2008 - 04:00:52 PDT)
    - RE: AMBER: Select specific residues (leap) FyD (Mon Mar 31 2008 - 04:19:49 PDT)
    - RE: AMBER: Select specific residues (leap) Marta Rossini (Mon Mar 31 2008 - 05:57:04 PDT)
    - RE: AMBER: Select specific residues (leap) FyD (Mon Mar 31 2008 - 06:32:30 PDT)
AMBER: energy problems in simulation with restraints Daniel Cappel (Mon Mar 31 2008 - 02:39:13 PDT)
- Re: AMBER: energy problems in simulation with restraints David A. Case (Mon Mar 31 2008 - 08:35:58 PDT)
AMBER: installation amber9 Geoff Wood (Mon Mar 31 2008 - 04:02:01 PDT)
- Re: AMBER: installation amber9 David A. Case (Mon Mar 31 2008 - 10:51:45 PDT)
AMBER: multiple dihedral restraints using group mkseo (Mon Mar 31 2008 - 10:11:30 PDT)
- Re: AMBER: multiple dihedral restraints using group David A. Case (Wed Apr 02 2008 - 13:44:20 PDT)
AMBER: memory limitation of Amber 9 yavuzturkm.prc.boun.edu.tr (Mon Mar 31 2008 - 11:49:40 PDT)
- Re: AMBER: memory limitation of Amber 9 David A. Case (Mon Mar 31 2008 - 22:50:41 PDT)
AMBER: nmode James Thomas (Mon Mar 31 2008 - 11:48:43 PDT)
- Re: AMBER: nmode David A. Case (Mon Mar 31 2008 - 12:25:52 PDT)
AMBER: running minimisation on cis-azobenzene Chih-Ying Lin (Mon Mar 31 2008 - 12:45:20 PDT)
- Re: AMBER: running minimisation on cis-azobenzene Thomas Steinbrecher (Mon Mar 31 2008 - 13:14:17 PDT)
  - AMBER: Amber Workshop Chih-Ying Lin (Mon Mar 31 2008 - 13:40:52 PDT)
  - Re: AMBER: running minimisation on cis-azobenzene Chih-Ying Lin (Sat Apr 05 2008 - 06:33:46 PDT)
    - Re: AMBER: running minimisation on cis-azobenzene Chih-Ying Lin (Sun Apr 06 2008 - 17:33:11 PDT)
    - Re: AMBER: running minimisation on cis-azobenzene David A. Case (Mon Apr 07 2008 - 08:39:24 PDT)
    - Re: AMBER: running minimisation on cis-azobenzene Chih-Ying Lin (Mon Apr 07 2008 - 10:10:43 PDT)
  - AMBER: Minimisation: cis-azobenzene parameters Chih-Ying Lin (Sat Apr 05 2008 - 06:45:34 PDT)
    - Re: AMBER: Minimisation: cis-azobenzene parameters David A. Case (Sat Apr 05 2008 - 14:11:17 PDT)
  - Re: AMBER: running minimisation on cis-azobenzene Chih-Ying Lin (Mon Apr 07 2008 - 10:31:51 PDT)
    - Re: AMBER: running minimisation on cis-azobenzene Thomas Steinbrecher (Mon Apr 07 2008 - 10:39:18 PDT)
    - Re: AMBER: running minimisation on cis-azobenzene Chih-Ying Lin (Mon Apr 07 2008 - 11:03:18 PDT)
    - AMBER: Trans-azobenzene and cis-azobenzene Chih-Ying Lin (Mon Apr 07 2008 - 11:13:01 PDT)
    - Re: AMBER: running minimisation on cis-azobenzene Chih-Ying Lin (Mon Apr 07 2008 - 21:40:20 PDT)
    - Re: AMBER: running minimisation on cis-azobenzene Thomas Steinbrecher (Tue Apr 08 2008 - 13:37:39 PDT)
    - Re: AMBER: running minimisation on cis-azobenzene Junmei Wang (Tue Apr 08 2008 - 14:37:54 PDT)
    - Re: AMBER: running minimisation on cis-azobenzene----an electron-withdrew atom Chih-Ying Lin (Tue Apr 08 2008 - 14:45:51 PDT)
    - Re: AMBER: running minimisation on cis-azobenzene Chih-Ying Lin (Tue Apr 08 2008 - 14:51:51 PDT)
    - Re: AMBER: running minimisation on cis-azobenzene Junmei Wang (Tue Apr 08 2008 - 15:11:35 PDT)
    - Re: AMBER: running minimisation on cis-azobenzene Chih-Ying Lin (Tue Apr 08 2008 - 15:27:52 PDT)
    - AMBER: anything wrong with this script Chih-Ying Lin (Tue Apr 08 2008 - 17:27:50 PDT)
    - Re: AMBER: running minimisation on cis-azobenzene Chih-Ying Lin (Tue Apr 08 2008 - 15:00:20 PDT)
AMBER: Amber 8 on Redhat 4 X86_64 yavuzturkm.prc.boun.edu.tr (Mon Mar 31 2008 - 22:30:32 PDT)
AMBER: TIP5P water simulation with AMBER7 Biman Jana (Tue Apr 01 2008 - 00:14:54 PDT)
AMBER: hybrid remd imaging Geoff Wood (Tue Apr 01 2008 - 00:47:18 PDT)
AMBER: working with unformatted restart files in AMBER9 Vlad Cojocaru (Tue Apr 01 2008 - 06:35:57 PDT)
- Re: AMBER: working with unformatted restart files in AMBER9 Thomas Cheatham III (Wed Apr 02 2008 - 10:26:00 PDT)
AMBER: atomic posiltional fluctuation Furia Gargano (Tue Apr 01 2008 - 07:11:12 PDT)
- Re: AMBER: atomic posiltional fluctuation Thomas Cheatham III (Tue Apr 01 2008 - 09:50:43 PDT)
AMBER: Electric field on atoms in equallibrium Lishan Yao (Tue Apr 01 2008 - 09:55:39 PDT)
- Re: AMBER: Electric field on atoms in equallibrium Tom Darden (Tue Apr 01 2008 - 10:59:17 PDT)
- Re: AMBER: Electric field on atoms in equallibrium Lishan Yao (Tue Apr 01 2008 - 11:21:20 PDT)
  - Re: AMBER: Electric field on atoms in equallibrium Tom Darden (Tue Apr 01 2008 - 12:26:32 PDT)
AMBER: B-factor Furia Gargano (Tue Apr 01 2008 - 12:05:36 PDT)
- Re: AMBER: B-factor Thomas Cheatham III (Wed Apr 02 2008 - 10:18:18 PDT)
AMBER: Simulating DNA Backbone in NAB Adelene Sim (Tue Apr 01 2008 - 12:23:16 PDT)
- Re: AMBER: Simulating DNA Backbone in NAB David A. Case (Wed Apr 02 2008 - 13:24:25 PDT)
  - AMBER: PMF calculation for rate constant or binding constant? Catein Catherine (Tue Apr 15 2008 - 19:28:43 PDT)
AMBER: LEap error message for parmBSC0 force field Cenk Andac (Tue Apr 01 2008 - 16:31:17 PDT)
- Re: AMBER: LEap error message for parmBSC0 force field Thomas Cheatham III (Tue Apr 01 2008 - 16:55:38 PDT)
  - Re: AMBER: LEap error message for parmBSC0 force field Cenk Andac (Thu Apr 03 2008 - 05:52:37 PDT)
    - Re: AMBER: LEap error message for parmBSC0 force field Alberto Perez (Thu Apr 03 2008 - 07:00:09 PDT)
- Re: AMBER: LEap error message for parmBSC0 force field Bill Ross (Thu Apr 03 2008 - 10:28:51 PDT)
  - Re: AMBER: LEap error message for parmBSC0 force field Cenk Andac (Thu Apr 03 2008 - 11:08:58 PDT)
- Re: AMBER: LEap error message for parmBSC0 force field Bill Ross (Thu Apr 03 2008 - 13:12:12 PDT)
- Re: AMBER: LEap error message for parmBSC0 force field Bill Ross (Thu Apr 03 2008 - 13:16:27 PDT)
AMBER: meet problems in adding ions and waterbox Qiang Li (Tue Apr 01 2008 - 22:12:31 PDT)
- Re: AMBER: meet problems in adding ions and waterbox David A. Case (Tue Apr 01 2008 - 22:22:52 PDT)
- Re: AMBER: meet problems in adding ions and waterbox Qiang Li (Tue Apr 01 2008 - 23:12:13 PDT)
  - Re: AMBER: meet problems in adding ions and waterbox David A. Case (Wed Apr 02 2008 - 09:37:05 PDT)
AMBER: LJ parameters aneesh cna (Wed Apr 02 2008 - 04:46:22 PDT)
- Re: AMBER: LJ parameters Thomas Steinbrecher (Wed Apr 02 2008 - 10:31:57 PDT)
  - Re: AMBER: LJ parameters aneesh cna (Thu Apr 03 2008 - 04:30:39 PDT)
AMBER: REMD simulation error Guillaume Renvez (Wed Apr 02 2008 - 05:47:20 PDT)
AMBER: ANNOUNCE: Release of AmberTools, version 1.0 David A. Case (Wed Apr 02 2008 - 09:49:20 PDT)
AMBER: ptraj / covariance / quasiharmonic approximation / entropy Seth Lilavivat (Wed Apr 02 2008 - 12:18:55 PDT)
- Re: AMBER: ptraj / covariance / quasiharmonic approximation / entropy Chris Moth (Wed Apr 02 2008 - 14:09:14 PDT)
AMBER: NAD parameters Urszula Uciechowska (Thu Apr 03 2008 - 07:30:05 PDT)
- Re: AMBER: NAD parameters David A. Case (Thu Apr 03 2008 - 08:01:46 PDT)
- RE: AMBER: NAD parameters Ross Walker (Thu Apr 03 2008 - 07:56:45 PDT)
AMBER: dockmolecules in examples directory of AmberTools-1.0 M. L. Dodson (Thu Apr 03 2008 - 08:54:50 PDT)
AMBER: mm_pbsa error rams rams (Thu Apr 03 2008 - 09:28:56 PDT)
- Re: AMBER: mm_pbsa error stephane acoca (Thu Apr 03 2008 - 13:21:29 PDT)
  - Re: AMBER: mm_pbsa error Scott Pendley (Fri Apr 04 2008 - 09:29:16 PDT)
AMBER: MPI run problem Qi Yan (Thu Apr 03 2008 - 09:33:19 PDT)
- AMBER: Simple Minimization - Error dpandit.brandeis.edu (Thu Apr 03 2008 - 12:55:08 PDT)
  - Re: AMBER: Simple Minimization - Error David A. Case (Thu Apr 03 2008 - 13:11:13 PDT)
  - Re: AMBER: Simple Minimization - Error Daniel Smith (Thu Apr 03 2008 - 13:10:28 PDT)
- Re: AMBER: MPI run problem David A. Case (Thu Apr 03 2008 - 13:38:38 PDT)
- Re: AMBER: MPI run problem Robert Duke (Thu Apr 03 2008 - 13:57:33 PDT)
- RE: AMBER: MPI run problem Qi Yan (Thu Apr 03 2008 - 14:59:27 PDT)
AMBER: problem with Mg2+ during MD Zhenwei Lu (Thu Apr 03 2008 - 09:48:13 PDT)
AMBER: Using mdcrd files to look at minor charge changes Cooper, Matthew (Thu Apr 03 2008 - 11:45:12 PDT)
- Re: AMBER: Using mdcrd files to look at minor charge changes David A. Case (Thu Apr 03 2008 - 12:46:46 PDT)
AMBER: imem keyword using mmpbsa Sergio Wong (Thu Apr 03 2008 - 13:43:01 PDT)
- Re: AMBER: imem keyword using mmpbsa Sergio Wong (Thu Apr 03 2008 - 18:18:10 PDT)
- Re: AMBER: imem keyword using mmpbsa David A. Case (Thu Apr 03 2008 - 21:04:11 PDT)
  - AMBER: Restraintmask and Restraint_WT : Question dpandit.brandeis.edu (Fri Apr 04 2008 - 08:24:32 PDT)
    - Re: AMBER: Restraintmask and Restraint_WT : Question Thomas Steinbrecher (Fri Apr 04 2008 - 09:18:17 PDT)
AMBER: solvateOct produces strange residues compared to solvateCap Markus Kaukonen (Fri Apr 04 2008 - 01:08:53 PDT)
- Re: AMBER: solvateOct produces strange residues compared to solvateCap David A. Case (Thu Apr 10 2008 - 12:29:52 PDT)
AMBER: GAFF Eric Germaneau (Fri Apr 04 2008 - 01:18:03 PDT)
- Re: AMBER: GAFF Vlad Cojocaru (Fri Apr 04 2008 - 01:22:30 PDT)
  - Re: AMBER: GAFF Eric Germaneau (Fri Apr 04 2008 - 01:27:07 PDT)
    - Re: AMBER: GAFF Vlad Cojocaru (Fri Apr 04 2008 - 01:42:24 PDT)
    - Re: AMBER: GAFF Eric Germaneau (Fri Apr 04 2008 - 07:10:31 PDT)
    - Re: AMBER: GAFF David A. Case (Fri Apr 04 2008 - 08:59:08 PDT)
    - Re: AMBER: GAFF Eric Germaneau (Fri Apr 04 2008 - 10:49:40 PDT)
AMBER: ligand slips out of pocket Hannes Wallnoefer (Fri Apr 04 2008 - 00:58:29 PDT)
AMBER: sander.MPI setup with SGE Sasha Buzko (Fri Apr 04 2008 - 09:59:34 PDT)
- RE: AMBER: sander.MPI setup with SGE Ross Walker (Sat Apr 05 2008 - 09:18:45 PDT)
  - Re: AMBER: sander.MPI setup with SGE Sasha Buzko (Mon Apr 07 2008 - 13:51:20 PDT)
AMBER: artifacts in ptraj avg output stephane acoca (Sat Apr 05 2008 - 01:46:55 PDT)
- Re: AMBER: artifacts in ptraj avg output Barbault Florent (Sat Apr 05 2008 - 02:11:37 PDT)
  - Re: AMBER: artifacts in ptraj avg output stephane acoca (Sat Apr 05 2008 - 02:52:26 PDT)
AMBER: RE: amber help Ross Walker (Sat Apr 05 2008 - 20:25:19 PDT)
AMBER: NAB examples Hu, Shaowen (JSC-SK)[USRA] (Mon Apr 07 2008 - 07:32:07 PDT)
- Re: AMBER: NAB examples David A. Case (Mon Apr 07 2008 - 08:33:26 PDT)
  - RE: AMBER: NAB examples Hu, Shaowen (JSC-SK)[USRA] (Mon Apr 07 2008 - 09:09:44 PDT)
    - Re: AMBER: NAB examples David A. Case (Mon Apr 07 2008 - 09:26:58 PDT)
    - RE: AMBER: NAB examples Hu, Shaowen (JSC-SK)[USRA] (Mon Apr 07 2008 - 09:43:06 PDT)
    - Re: AMBER: NAB examples David A. Case (Mon Apr 07 2008 - 10:42:34 PDT)
    - AMBER: Build a MPI NAB Hu, Shaowen (JSC-SK)[USRA] (Mon Apr 07 2008 - 13:45:53 PDT)
    - Re: AMBER: Build a MPI NAB David A. Case (Mon Apr 07 2008 - 14:28:54 PDT)
    - RE: AMBER: Build a MPI NAB Hu, Shaowen (JSC-SK)[USRA] (Tue Apr 08 2008 - 13:19:22 PDT)
    - AMBER: Amber 9 run error Andrew Borgert (Tue Apr 08 2008 - 14:28:07 PDT)
    - RE: AMBER: Amber 9 run error Ross Walker (Tue Apr 08 2008 - 14:52:30 PDT)
    - Re: AMBER: Build a MPI NAB David A. Case (Tue Apr 08 2008 - 14:35:41 PDT)
    - RE: AMBER: Build a MPI NAB Hu, Shaowen (JSC-SK)[USRA] (Wed Apr 09 2008 - 07:12:57 PDT)
    - Re: AMBER: Build a MPI NAB David A. Case (Wed Apr 09 2008 - 09:27:28 PDT)
    - AMBER: Gbsa in NAB Hu, Shaowen (JSC-SK)[USRA] (Thu Apr 10 2008 - 10:04:14 PDT)
    - Re: AMBER: Gbsa in NAB David A. Case (Thu Apr 10 2008 - 10:24:17 PDT)
    - AMBER: xleap (draw using edit) Taufik Al-Sarraj (Wed May 07 2008 - 19:31:14 PDT)
    - AMBER: reset time and comments E.M. (Wed May 07 2008 - 21:13:02 PDT)
    - Re: AMBER: reset time and comments Benjamin Juhl (Thu May 08 2008 - 02:12:11 PDT)
    - RE: AMBER: reset time and comments Ross Walker (Thu May 08 2008 - 08:24:50 PDT)
    - Re: AMBER: xleap (draw using edit) David A. Case (Thu May 08 2008 - 11:02:58 PDT)
    - Re: AMBER: xleap (draw using edit) Taufik Al-Sarraj (Thu May 08 2008 - 13:58:24 PDT)
    - AMBER: Adjust Force Field parameters Chih-Ying Lin (Thu May 08 2008 - 16:46:21 PDT)
- Re: AMBER: NAB examples Andreas Svrcek-Seiler (Mon Apr 07 2008 - 09:46:34 PDT)
AMBER: restraint box dimension aneesh cna (Tue Apr 08 2008 - 03:45:20 PDT)
- Re: AMBER: restraint box dimension David A. Case (Tue Apr 08 2008 - 17:34:05 PDT)
  - Re: AMBER: restraint box dimension aneesh cna (Fri Apr 11 2008 - 02:56:17 PDT)
    - Re: AMBER: restraint box dimension Carlos Simmerling (Fri Apr 11 2008 - 03:22:38 PDT)
AMBER: Should the two phenyl rings of the trans-azobenzene on the same plane after minimisation? Chih-Ying Lin (Tue Apr 08 2008 - 18:09:24 PDT)
AMBER: converting from CNS file format Sally Pias (Tue Apr 08 2008 - 22:32:11 PDT)
- Re: AMBER: converting from CNS file format Sally Pias (Thu Apr 10 2008 - 22:04:55 PDT)
AMBER: Estimating dielectric constant Marcelo Puiatti (Wed Apr 09 2008 - 07:42:40 PDT)
AMBER: Collect dihedral angles Chih-Ying Lin (Wed Apr 09 2008 - 14:35:09 PDT)
- AMBER: Tutorial B3- Section6 Chih-Ying Lin (Wed Apr 09 2008 - 18:30:27 PDT)
  - Re: AMBER: Tutorial B3- Section6 David A. Case (Wed Apr 09 2008 - 18:46:16 PDT)
    - Re: AMBER: Tutorial B3- Section6 Chih-Ying Lin (Wed Apr 09 2008 - 19:13:32 PDT)
    - Re: AMBER: Tutorial B3- Section6 Chih-Ying Lin (Thu Apr 10 2008 - 16:50:14 PDT)
    - Re: AMBER: Tutorial B3- Section6 Carlos Simmerling (Fri Apr 11 2008 - 03:26:28 PDT)
AMBER: ASSERTion ' ier == 0 ' failed in nmode.f Qi Yan (Wed Apr 09 2008 - 16:24:08 PDT)
- Re: AMBER: ASSERTion ' ier == 0 ' failed in nmode.f David A. Case (Wed Apr 09 2008 - 22:03:14 PDT)
  - AMBER: Initial Equilibration dpandit.brandeis.edu (Thu Apr 10 2008 - 13:45:01 PDT)
    - RE: AMBER: Initial Equilibration Ross Walker (Thu Apr 10 2008 - 18:29:30 PDT)
- RE: AMBER: ASSERTion ' ier == 0 ' failed in nmode.f Qi Yan (Mon Apr 14 2008 - 14:50:27 PDT)
AMBER: Force field Parameters Chih-Ying Lin (Wed Apr 09 2008 - 19:17:51 PDT)
AMBER: tempi in Replica Exchange rebeca.mmb.pcb.ub.es (Thu Apr 10 2008 - 02:23:00 PDT)
- Re: AMBER: tempi in Replica Exchange Carlos Simmerling (Thu Apr 10 2008 - 08:37:46 PDT)
AMBER: WHAM: how frequently do I need data on the system coordinates? David Cerutti (Thu Apr 10 2008 - 09:14:23 PDT)
- Re: AMBER: WHAM: how frequently do I need data on the system coordinates? John Chodera (Thu Apr 10 2008 - 10:47:57 PDT)
AMBER: protein-ligand complex problem Lynn (Thu Apr 10 2008 - 15:51:32 PDT)
- RE: AMBER: protein-ligand complex problem Ross Walker (Thu Apr 10 2008 - 16:50:19 PDT)
- Re: AMBER: protein-ligand complex problem David A. Case (Thu Apr 10 2008 - 16:51:55 PDT)
AMBER: trans-azobenzene under minimisation Chih-Ying Lin (Thu Apr 10 2008 - 17:29:37 PDT)
AMBER: query about Generalized Born simulation gurvisha.leadinvent.com (Fri Apr 11 2008 - 06:42:23 PDT)
- Re: AMBER: query about Generalized Born simulation Carlos Simmerling (Fri Apr 11 2008 - 07:15:53 PDT)
- Re: AMBER: query about Generalized Born simulation rpaduri.chem.wayne.edu (Fri Apr 11 2008 - 07:31:21 PDT)
AMBER: Amber installation jacopo.sgrignani.unifi.it (Fri Apr 11 2008 - 06:23:24 PDT)
- RE: AMBER: Amber installation Ross Walker (Fri Apr 11 2008 - 11:09:14 PDT)
- Re: AMBER: Amber installation Mengjuei Hsieh (Fri Apr 11 2008 - 14:39:48 PDT)
- RE: AMBER: Amber installation Ross Walker (Fri Apr 11 2008 - 15:45:42 PDT)
AMBER: Imaging before HBond analysis? Evan Kelly (Fri Apr 11 2008 - 13:34:41 PDT)
- Re: AMBER: Imaging before HBond analysis? Thomas Cheatham III (Fri Apr 11 2008 - 15:24:29 PDT)
  - Re: AMBER: Imaging before HBond analysis? Evan Kelly (Fri Apr 11 2008 - 15:41:51 PDT)
    - Re: AMBER: Imaging before HBond analysis? Thomas Cheatham III (Fri Apr 11 2008 - 15:52:04 PDT)
    - Re: AMBER: Imaging before HBond analysis? Evan Kelly (Fri Apr 11 2008 - 16:09:32 PDT)
AMBER: installing pmemd with fftw YangMingjun (Sun Apr 13 2008 - 06:07:44 PDT)
- Re: AMBER: installing pmemd with fftw Robert Duke (Sun Apr 13 2008 - 06:57:36 PDT)
  - Re: Re: AMBER: installing pmemd with fftw YangMingjun (Sun Apr 13 2008 - 18:08:16 PDT)
AMBER: topology file Giuseppe De Marco (Mon Apr 14 2008 - 02:38:37 PDT)
- Re: AMBER: topology file David A. Case (Wed Apr 16 2008 - 10:45:52 PDT)
AMBER: Error: Bond: Maximum coordination exceeded -- setting atoms pert=true overrides default limits Ted Fischer (Mon Apr 14 2008 - 05:53:42 PDT)
- Re: AMBER: Error: Bond: Maximum coordination exceeded -- setting atoms pert=true overrides default limits David A. Case (Mon Apr 14 2008 - 22:26:45 PDT)
- Re: AMBER: Error: Bond: Maximum coordination exceeded -- setting atoms pert=true overrides default limits Ted Fischer (Tue Apr 15 2008 - 02:09:47 PDT)
  - Re: AMBER: Error: Bond: Maximum coordination exceeded -- setting atoms pert=true overrides default limits David A. Case (Fri Apr 18 2008 - 15:00:23 PDT)
AMBER: error in compilation elsize.cc snoze pa (Mon Apr 14 2008 - 09:38:07 PDT)
- Re: AMBER: error in compilation elsize.cc David A. Case (Mon Apr 14 2008 - 10:11:33 PDT)
  - Re: AMBER: error in compilation elsize.cc snoze pa (Mon Apr 14 2008 - 11:20:40 PDT)
- Re: AMBER: error in compilation elsize.cc Scott Brozell (Mon May 05 2008 - 11:55:49 PDT)
AMBER: ANNOUNCEMENT: release of Amber 10 David A. Case (Mon Apr 14 2008 - 10:18:40 PDT)
- AMBER: Prepgen does not give correct result? Rajendra P. OJHA (Fri May 09 2008 - 09:13:58 PDT)
AMBER: loadPdb returns extra atoms Seth Lilavivat (Mon Apr 14 2008 - 11:50:32 PDT)
- Re: AMBER: loadPdb returns extra atoms Thomas Cheatham III (Mon Apr 14 2008 - 12:19:03 PDT)
AMBER: Problems compiling Amber with MKL Sasha Buzko (Mon Apr 14 2008 - 12:13:23 PDT)
- RE: AMBER: Problems compiling Amber with MKL Ross Walker (Mon Apr 14 2008 - 14:32:49 PDT)
  - RE: AMBER: Problems compiling Amber with MKL Sasha Buzko (Mon Apr 14 2008 - 15:25:43 PDT)
    - RE: AMBER: Problems compiling Amber with MKL Sasha Buzko (Mon Apr 14 2008 - 16:24:05 PDT)
AMBER: JavaGenes Shultz, Jack (Mon Apr 14 2008 - 12:26:25 PDT)
- AMBER: Whole System Equilibration & Pressure dpandit.brandeis.edu (Mon Apr 14 2008 - 13:57:54 PDT)
  - RE: AMBER: Whole System Equilibration & Pressure Ross Walker (Mon Apr 14 2008 - 14:37:51 PDT)
    - RE: AMBER: Whole System Equilibration & Pressure dpandit.brandeis.edu (Tue Apr 15 2008 - 07:16:35 PDT)
AMBER: energy decomposition vs ala scan Sergio Wong (Mon Apr 14 2008 - 19:05:41 PDT)
AMBER: imaging problem Marcin Krol (Tue Apr 15 2008 - 04:54:30 PDT)
- Re: AMBER: imaging problem Carlos Simmerling (Tue Apr 15 2008 - 05:22:18 PDT)
  - Re: AMBER: imaging problem Marcin Krol (Tue Apr 15 2008 - 06:16:01 PDT)
    - Re: AMBER: imaging problem David Smith (Tue Apr 15 2008 - 06:30:48 PDT)
    - Re: AMBER: imaging problem Marcin Krol (Tue Apr 15 2008 - 06:38:07 PDT)
AMBER: mmpbsa with gromacs trajectory jacopo.sgrignani.unifi.it (Tue Apr 15 2008 - 07:10:21 PDT)
AMBER: loading pdb in leap to create parameter files Cristina Sisu (Tue Apr 15 2008 - 06:43:57 PDT)
- Re: AMBER: loading pdb in leap to create parameter files Da-Wei Li (Tue Apr 15 2008 - 06:53:06 PDT)
  - Re: AMBER: loading pdb in leap to create parameter files Cristina Sisu (Tue Apr 15 2008 - 07:50:12 PDT)
    - RE: AMBER: loading pdb in leap to create parameter files Steve Spronk (Mon Apr 21 2008 - 10:04:34 PDT)
AMBER: Is it possible to run PIMD simulation with QM/MM potential in Amber10? cgji (Tue Apr 15 2008 - 08:27:08 PDT)
- RE: AMBER: Is it possible to run PIMD simulation with QM/MM potential in Amber10? Ross Walker (Tue Apr 15 2008 - 08:47:53 PDT)
- Re: AMBER: Is it possible to run PIMD simulation with QM/MM potential in Amber10? David A. Case (Tue Apr 15 2008 - 14:01:15 PDT)
- Re: AMBER: Is it possible to run PIMD simulation with QM/MM potential in Amber10? cgji (Sat Sep 20 2008 - 09:22:07 PDT)
  - Re: AMBER: Is it possible to run PIMD simulation with QM/MM potential in Amber10? David A. Case (Mon Sep 22 2008 - 04:25:38 PDT)
AMBER: xleap segmentation fault on SaveAmberParm Brendan Duggan (Tue Apr 15 2008 - 12:15:46 PDT)
- Re: AMBER: xleap segmentation fault on SaveAmberParm Wei Zhang (Tue Apr 15 2008 - 12:32:32 PDT)
- Re: AMBER: xleap segmentation fault on SaveAmberParm David A. Case (Tue Apr 15 2008 - 14:00:47 PDT)
AMBER: Extracting the electric field (and its gradient) on particular solute atoms John Chodera (Tue Apr 15 2008 - 17:36:01 PDT)
- Re: AMBER: Extracting the electric field (and its gradient) on particular solute atoms Tom Darden (Wed Apr 16 2008 - 14:30:53 PDT)
  - Re: AMBER: Extracting the electric field (and its gradient) on particular solute atoms John Chodera (Wed Apr 16 2008 - 15:15:19 PDT)
AMBER: PMF calculation for binding constant or rate constant? Catein Catherine (Tue Apr 15 2008 - 19:26:46 PDT)
- Re: AMBER: PMF calculation for binding constant or rate constant? David A. Case (Wed Apr 16 2008 - 14:26:13 PDT)
AMBER: leap - using default radius 1.500000 for HO3 Nina Fischer (Wed Apr 16 2008 - 02:08:59 PDT)
- AMBER: vlimit-problems after image and restart Anselm Horn (Tue Apr 22 2008 - 02:04:46 PDT)
  - RE: AMBER: vlimit-problems after image and restart Ross Walker (Tue Apr 22 2008 - 21:45:29 PDT)
AMBER: Protonation states in Constant pH Simulations Neil Bruce (Wed Apr 16 2008 - 05:54:44 PDT)
AMBER: Distance in z dimension Age.Skjevik.student.uib.no (Wed Apr 16 2008 - 07:50:55 PDT)
AMBER: Amber9 with MPICH2 failure at runtime Sasha Buzko (Wed Apr 16 2008 - 14:43:07 PDT)
- RE: AMBER: Amber9 with MPICH2 failure at runtime Ross Walker (Wed Apr 16 2008 - 15:05:26 PDT)
  - RE: AMBER: Amber9 with MPICH2 failure at runtime Sasha Buzko (Wed Apr 16 2008 - 15:43:12 PDT)
    - RE: AMBER: Amber9 with MPICH2 failure at runtime Ross Walker (Wed Apr 16 2008 - 16:47:03 PDT)
    - RE: AMBER: Amber9 with MPICH2 failure at runtime Sasha Buzko (Wed Apr 16 2008 - 17:06:14 PDT)
    - Re: AMBER: Amber9 with MPICH2 failure at runtime David A. Case (Wed Apr 16 2008 - 17:26:05 PDT)
    - Re: AMBER: Amber9 with MPICH2 failure at runtime Sasha Buzko (Wed Apr 16 2008 - 17:40:09 PDT)
    - RE: AMBER: Amber9 with MPICH2 failure at runtime Ross Walker (Wed Apr 16 2008 - 21:25:19 PDT)
    - Re: AMBER: Amber9 with MPICH2 failure at runtime Sasha Buzko (Wed Apr 16 2008 - 21:49:01 PDT)
AMBER: xLeap unit editor "seg fault" inonshar.post.tau.ac.il (Wed Apr 16 2008 - 22:49:01 PDT)
- AMBER: Accessing Equilibration Results dpandit.brandeis.edu (Thu Apr 17 2008 - 06:29:35 PDT)
- Re: AMBER: xLeap unit editor "seg fault" David A. Case (Thu Apr 17 2008 - 17:53:29 PDT)
AMBER: Scale LJ parameters fatima.chami.durham.ac.uk (Thu Apr 17 2008 - 04:20:40 PDT)
- Re: AMBER: Scale LJ parameters David A. Case (Thu Apr 17 2008 - 17:54:43 PDT)
AMBER: uccabke.ucl.ac.uk (Thu Apr 17 2008 - 08:02:06 PDT)
- AMBER: H atom names in Amber David A. Case (Thu Apr 17 2008 - 08:16:19 PDT)
  - Re: AMBER: H atom names in Amber uccabke.ucl.ac.uk (Thu Apr 17 2008 - 08:49:57 PDT)
- Re: AMBER: Da-Wei Li (Thu Apr 17 2008 - 08:18:04 PDT)
- Re: AMBER: Florian Haberl (Thu Apr 17 2008 - 08:17:24 PDT)
AMBER: Performance issues on Ethernet clusters Sasha Buzko (Thu Apr 17 2008 - 11:20:52 PDT)
- Re: AMBER: Performance issues on Ethernet clusters David A. Case (Thu Apr 17 2008 - 12:02:45 PDT)
- Re: AMBER: Performance issues on Ethernet clusters Robert Duke (Thu Apr 17 2008 - 13:14:32 PDT)
  - Re: AMBER: Performance issues on Ethernet clusters Sasha Buzko (Thu Apr 17 2008 - 14:18:44 PDT)
    - AMBER: SiCortex as an alternative to Ethernet and infiniband clusters Kevin Abbey (Thu Apr 17 2008 - 14:37:23 PDT)
    - Re: AMBER: SiCortex as an alternative to Ethernet and infiniband clusters Sasha Buzko (Thu Apr 17 2008 - 15:39:46 PDT)
AMBER: Conformation search... Anthony Cruz (Thu Apr 17 2008 - 12:32:52 PDT)
AMBER: Short trajectory segments / frequent restarts causes explosion David Cerutti (Thu Apr 17 2008 - 14:04:14 PDT)
- Re: AMBER: Short trajectory segments / frequent restarts causes explosion Robert Duke (Thu Apr 17 2008 - 14:52:55 PDT)
AMBER: compile Amber9 on 64bit AMD Opteron Jeffrey (Fri Apr 18 2008 - 00:02:24 PDT)
- Re: AMBER: compile Amber9 on 64bit AMD Opteron David A. Case (Fri Apr 18 2008 - 08:23:48 PDT)
AMBER: nmode problem Hannes Wallnoefer (Fri Apr 18 2008 - 02:01:27 PDT)
- Re: AMBER: nmode problem Hannes Wallnoefer (Fri Apr 18 2008 - 02:44:38 PDT)
AMBER: AmberTools on OS X Leopard with Intel compilers Yu Chen (Fri Apr 18 2008 - 12:17:37 PDT)
- Re: AMBER: AmberTools on OS X Leopard with Intel compilers David A. Case (Fri Apr 18 2008 - 13:44:36 PDT)
  - Re: AMBER: AmberTools on OS X Leopard with Intel compilers David A. Case (Fri Apr 18 2008 - 14:17:32 PDT)
  - Re: AMBER: AmberTools on OS X Leopard with Intel compilers Yu Chen (Mon Apr 21 2008 - 07:30:10 PDT)
    - Re: AMBER: AmberTools on OS X Leopard with Intel compilers Yu Chen (Mon Apr 21 2008 - 11:47:06 PDT)
    - Re: AMBER: AmberTools on OS X Leopard with Intel compilers Scott Brozell (Mon Apr 21 2008 - 13:15:29 PDT)
    - Re: AMBER: AmberTools on OS X Leopard with Intel compilers Scott Brozell (Mon Apr 21 2008 - 13:33:49 PDT)
    - Re: AMBER: AmberTools on OS X Leopard with Intel compilers David A. Case (Mon Apr 21 2008 - 12:05:38 PDT)
    - Re: AMBER: AmberTools on OS X Leopard with Intel compilers Yu Chen (Mon Apr 21 2008 - 12:52:16 PDT)
    - Re: AMBER: AmberTools on OS X Leopard with Intel compilers David A. Case (Mon Apr 21 2008 - 13:55:26 PDT)
    - Re: AMBER: AmberTools on OS X Leopard with Intel compilers Yu Chen (Mon Apr 21 2008 - 20:21:34 PDT)
    - Re: AMBER: AmberTools on OS X Leopard with Intel compilers Mike Summers (Tue Apr 22 2008 - 05:03:53 PDT)
    - Re: AMBER: AmberTools on OS X Leopard with Intel compilers Mike Summers (Tue Apr 22 2008 - 05:22:18 PDT)
    - AMBER: RESP charges Jena M (Tue Apr 22 2008 - 05:31:54 PDT)
    - AMBER: RE: amber8 files in amber9 Jena M (Wed Apr 30 2008 - 08:55:45 PDT)
    - RE: AMBER: RE: amber8 files in amber9 Ross Walker (Wed Apr 30 2008 - 09:24:49 PDT)
    - Re: AMBER: AmberTools on OS X Leopard with Intel compilers David A. Case (Tue Apr 22 2008 - 08:13:38 PDT)
AMBER: hydrogens are flying in replica exchange simulations Ashish Sangwai (Fri Apr 18 2008 - 16:43:01 PDT)
- Re: AMBER: hydrogens are flying in replica exchange simulations Carlos Simmerling (Fri Apr 18 2008 - 17:02:39 PDT)
  - Re: AMBER: hydrogens are flying in replica exchange simulations Ashish Sangwai (Fri Apr 18 2008 - 17:18:32 PDT)
    - Re: AMBER: hydrogens are flying in replica exchange simulations Ashish Sangwai (Fri Apr 18 2008 - 17:28:02 PDT)
    - RE: AMBER: hydrogens are flying in replica exchange simulations Ross Walker (Fri Apr 18 2008 - 22:07:54 PDT)
    - Re: AMBER: hydrogens are flying in replica exchange simulations Carlos Simmerling (Sat Apr 19 2008 - 06:49:56 PDT)
    - Re: AMBER: hydrogens are flying in replica exchange simulations Ashish Sangwai (Sun Apr 20 2008 - 16:09:03 PDT)
    - Re: AMBER: hydrogens are flying in replica exchange simulations Adrian Roitberg (Mon Apr 21 2008 - 07:56:33 PDT)
    - Re: AMBER: hydrogens are flying in replica exchange simulations Carlos Simmerling (Mon Apr 21 2008 - 08:10:46 PDT)
    - Re: AMBER: hydrogens are flying in replica exchange simulations Adrian Roitberg (Mon Apr 21 2008 - 09:03:06 PDT)
    - Re: AMBER: hydrogens are flying in replica exchange simulations Carlos Simmerling (Mon Apr 21 2008 - 09:30:12 PDT)
    - Re: AMBER: hydrogens are flying in replica exchange simulations Ashish Sangwai (Mon Apr 21 2008 - 17:37:51 PDT)
    - Re: AMBER: hydrogens are flying in replica exchange simulations Carlos Simmerling (Tue Apr 22 2008 - 11:57:11 PDT)
    - Re: AMBER: hydrogens are flying in replica exchange simulations Karl Kirschner (kkirschn) (Mon Apr 21 2008 - 08:47:37 PDT)
AMBER: How to add radius of an atom saurabh agrawal (Sun Apr 20 2008 - 22:45:43 PDT)
AMBER: Average structure James Thomas (Mon Apr 21 2008 - 03:21:26 PDT)
- Re: AMBER: Average structure David Cerutti (Mon Apr 21 2008 - 09:12:30 PDT)
  - RE: AMBER: Average structure Ross Walker (Mon Apr 21 2008 - 19:27:08 PDT)
    - RE: AMBER: Average structure Francesco Pietra (Tue Apr 22 2008 - 00:02:23 PDT)
AMBER: nmode jacopo.sgrignani.unifi.it (Mon Apr 21 2008 - 10:38:44 PDT)
- Re: AMBER: nmode Marie Brut (Tue Apr 03 2007 - 08:42:17 PDT)
  - Re: AMBER: nmode David A. Case (Tue Apr 03 2007 - 09:31:54 PDT)
- Re: AMBER: nmode David A. Case (Mon Apr 21 2008 - 14:05:20 PDT)
AMBER: aromatic residues lost planarity during MD simulation cniu.ualberta.ca (Mon Apr 21 2008 - 13:18:26 PDT)
- Re: AMBER: aromatic residues lost planarity during MD simulation Carlos Simmerling (Mon Apr 21 2008 - 13:25:19 PDT)
AMBER: Can sander provide ESP with PBC? Khatcharin Siriwong (Mon Apr 21 2008 - 18:36:17 PDT)
- Re: AMBER: Can sander provide ESP with PBC? John Chodera (Mon Apr 21 2008 - 19:24:25 PDT)
  - Re: AMBER: Can sander provide ESP with PBC? Thomas Steinbrecher (Wed Apr 23 2008 - 11:39:10 PDT)
    - Re: AMBER: Can sander provide ESP with PBC? Khatcharin Siriwong (Wed Apr 23 2008 - 18:43:12 PDT)
AMBER: How to change default radius assigned to an atom saurabh agrawal (Mon Apr 21 2008 - 21:47:14 PDT)
- Re: AMBER: How to change default radius assigned to an atom David A. Case (Mon Apr 21 2008 - 22:36:16 PDT)
  - Re: AMBER: How to change default radius assigned to an atom Wei Zhang (Wed Apr 23 2008 - 08:29:03 PDT)
AMBER: pressure varies in constant pressure membrane simulation Vijay Manickam Achari (Mon Apr 21 2008 - 22:58:29 PDT)
- Re: AMBER: pressure varies in constant pressure membrane simulation David A. Case (Tue Apr 22 2008 - 11:31:53 PDT)
  - Re: AMBER: pressure varies in constant pressure membrane simulation Vijay Manickam Achari (Tue Apr 22 2008 - 21:10:54 PDT)
AMBER: matrxi dist command priya priya (Tue Apr 22 2008 - 04:37:50 PDT)
AMBER: minimization san_amber roy (Tue Apr 22 2008 - 07:01:52 PDT)
AMBER: refine cyana structures! Hongyan Li (Tue Apr 22 2008 - 18:33:08 PDT)
AMBER: RE: amber tutorial A3 Ross Walker (Tue Apr 22 2008 - 21:45:29 PDT)
AMBER: Topology file format for Amber9 Xioling Chuang (Tue Apr 22 2008 - 22:41:32 PDT)
- Re: AMBER: Topology file format for Amber9 David A. Case (Wed Apr 23 2008 - 09:01:13 PDT)
AMBER: cross time correlation function fatima.chami.durham.ac.uk (Wed Apr 23 2008 - 05:55:28 PDT)
- Re: AMBER: cross time correlation function David A. Case (Wed Apr 23 2008 - 08:55:07 PDT)
  - Re: AMBER: cross time correlation function fatima.chami.durham.ac.uk (Wed Apr 23 2008 - 10:00:43 PDT)
    - Re: AMBER: cross time correlation function David A. Case (Wed Apr 23 2008 - 10:10:46 PDT)
AMBER: ESP on atoms (2) Khatcharin Siriwong (Wed Apr 23 2008 - 07:29:04 PDT)
AMBER: 2D-RMSD Tom McGrory (Wed Apr 23 2008 - 08:00:57 PDT)
AMBER: Amber10 on Leopard with Intel compilers, "Undefined symbols" error Yu Chen (Wed Apr 23 2008 - 11:03:13 PDT)
- Re: AMBER: Amber10 on Leopard with Intel compilers, "Undefined symbols" error David A. Case (Wed Apr 23 2008 - 11:34:30 PDT)
  - Re: AMBER: Amber10 on Leopard with Intel compilers, "Undefined symbols" error Yu Chen (Wed Apr 23 2008 - 11:50:54 PDT)
  - AMBER: Tutorial B5 Chih-Ying Lin (Wed Apr 23 2008 - 15:13:56 PDT)
    - Re: AMBER: Tutorial B5 Alessandro Nascimento (Wed Apr 23 2008 - 17:25:12 PDT)
    - Re: AMBER: Tutorial B5 Chih-Ying Lin (Wed Apr 23 2008 - 18:09:23 PDT)
    - RE: AMBER: Tutorial B5 Ross Walker (Wed Apr 23 2008 - 19:06:42 PDT)
    - Re: RE: AMBER: Tutorial B5 Chih-Ying Lin (Wed Apr 23 2008 - 20:08:19 PDT)
    - AMBER: How to print out the improper dihedral angles/wilson angles? Chih-Ying Lin (Thu Apr 24 2008 - 17:23:51 PDT)
AMBER: saveamberparm taufik.alsarraj.utoronto.ca (Wed Apr 23 2008 - 17:34:02 PDT)
- Re: AMBER: saveamberparm David A. Case (Thu Apr 24 2008 - 07:58:20 PDT)
  - AMBER: Si parameters for MD (AMBER9) Taufik Al-Sarraj (Fri Apr 25 2008 - 15:08:44 PDT)
AMBER: saveamberparm taufik.alsarraj.utoronto.ca (Wed Apr 23 2008 - 17:38:16 PDT)
AMBER: sander & imin=5 Xioling Chuang (Thu Apr 24 2008 - 00:03:09 PDT)
- Re: AMBER: sander & imin=5 David A. Case (Fri Apr 25 2008 - 11:38:25 PDT)
AMBER: water in the binding site MMPBSA jacopo.sgrignani.unifi.it (Thu Apr 24 2008 - 06:51:43 PDT)
AMBER: pmemd: "undefined reference to `mpi_(name-varies)'" Lachele Foley (Lists) (Thu Apr 24 2008 - 07:22:42 PDT)
- Re: AMBER: pmemd: "undefined reference to `mpi_(name-varies)'" Robert Duke (Thu Apr 24 2008 - 08:04:31 PDT)
  - Re: AMBER: pmemd: "undefined reference to `mpi_(name-varies)'" Gustavo Seabra (Thu Apr 24 2008 - 10:51:10 PDT)
    - Re: AMBER: pmemd: "undefined reference to `mpi_(name-varies)'" Lachele Foley (Lists) (Thu Apr 24 2008 - 12:16:50 PDT)
- Re: AMBER: pmemd: "undefined reference to `mpi_(name-varies)'" Robert Duke (Thu Apr 24 2008 - 12:45:31 PDT)
AMBER: double strand DNA break up (imaging) Seth Lilavivat (Thu Apr 24 2008 - 11:53:44 PDT)
- Re: AMBER: double strand DNA break up (imaging) Thomas Cheatham III (Thu Apr 24 2008 - 12:43:36 PDT)
AMBER: nmode output jacopo.sgrignani.unifi.it (Fri Apr 25 2008 - 01:36:35 PDT)
- Re: AMBER: nmode output Lachele Foley (Lists) (Fri Apr 25 2008 - 07:09:37 PDT)
AMBER: query regarding loadpadb Anamika Awasthi (Fri Apr 25 2008 - 01:33:19 PDT)
- Re: AMBER: query regarding loadpadb Reena ..... (Fri Apr 25 2008 - 04:07:21 PDT)
AMBER: parallel error : undefined reference to `MAIN_' Arturas Ziemys (Fri Apr 25 2008 - 14:14:59 PDT)
AMBER: AMD Opteron: compiler recommendations? Sasha Buzko (Fri Apr 25 2008 - 14:54:57 PDT)
- Re: AMBER: AMD Opteron: compiler recommendations? Robert Duke (Fri Apr 25 2008 - 15:04:58 PDT)
  - Re: AMBER: AMD Opteron: compiler recommendations? Sasha Buzko (Fri Apr 25 2008 - 15:14:19 PDT)
  - Re: AMBER: AMD Opteron: compiler recommendations? Francesco Pietra (Sat Apr 26 2008 - 00:01:46 PDT)
    - Re: AMBER: AMD Opteron: compiler recommendations? Sasha Buzko (Sat Apr 26 2008 - 13:31:23 PDT)
    - Re: AMBER: AMD Opteron: compiler recommendations? Francesco Pietra (Sat Apr 26 2008 - 13:56:13 PDT)
    - Re: AMBER: AMD Opteron: compiler recommendations? Sasha Buzko (Sat Apr 26 2008 - 14:15:18 PDT)
    - Fw: Re: AMBER: AMD Opteron: compiler recommendations? Francesco Pietra (Sat Apr 26 2008 - 00:05:18 PDT)
AMBER: .... RESTARTED DUE TO LINMIN FAILURE ... saurabh agrawal (Sat Apr 26 2008 - 04:36:13 PDT)
- Re: AMBER: .... RESTARTED DUE TO LINMIN FAILURE ... Barbault Florent (Sat Apr 26 2008 - 06:13:47 PDT)
  - AMBER: Azobenzene: dihedral angle CCNN force field parameter Chih-Ying Lin (Sat Apr 26 2008 - 12:09:03 PDT)
    - Re: AMBER: Azobenzene: dihedral angle CCNN force field parameter Adrian Roitberg (Sat Apr 26 2008 - 14:10:25 PDT)
  - Re: AMBER: .... RESTARTED DUE TO LINMIN FAILURE ... saurabh agrawal (Sat Apr 26 2008 - 07:15:38 PDT)
    - Re: AMBER: .... RESTARTED DUE TO LINMIN FAILURE ... Barbault Florent (Tue Apr 29 2008 - 13:56:09 PDT)
    - RE: AMBER: .... RESTARTED DUE TO LINMIN FAILURE ... Ross Walker (Tue Apr 29 2008 - 13:57:21 PDT)
- RE: AMBER: .... RESTARTED DUE TO LINMIN FAILURE ... Ross Walker (Sat Apr 26 2008 - 22:59:57 PDT)
  - RE: AMBER: .... RESTARTED DUE TO LINMIN FAILURE ... saurabh agrawal (Sun Apr 27 2008 - 22:18:50 PDT)
AMBER: memory usage Ye Mei (Sat Apr 26 2008 - 06:57:44 PDT)
- RE: AMBER: memory usage Ross Walker (Sat Apr 26 2008 - 23:07:04 PDT)
- Re: RE: AMBER: memory usage Ye Mei (Sun Apr 27 2008 - 07:52:42 PDT)
  - RE: RE: AMBER: memory usage Ross Walker (Sun Apr 27 2008 - 09:45:16 PDT)
- Re: RE: RE: AMBER: memory usage Ye Mei (Mon Apr 28 2008 - 07:06:20 PDT)
  - Re: RE: RE: AMBER: memory usage David A. Case (Mon Apr 28 2008 - 10:26:22 PDT)
AMBER: NMR restraints Ilyas Yildirim (Sun Apr 27 2008 - 23:53:51 PDT)
- Re: AMBER: NMR restraints David A. Case (Mon Apr 28 2008 - 08:20:53 PDT)
AMBER: Read trajectories generated by CHARMM Jeffrey (Mon Apr 28 2008 - 06:06:17 PDT)
- Re: AMBER: Read trajectories generated by CHARMM David A. Case (Mon Apr 28 2008 - 08:25:13 PDT)
  - AMBER: Parrallel computing Chih-Ying Lin (Mon Apr 28 2008 - 17:14:10 PDT)
    - RE: AMBER: Parrallel computing Ross Walker (Mon Apr 28 2008 - 23:09:44 PDT)
  - Re: Re: AMBER: Read trajectories generated by CHARMM Jeffrey (Mon Apr 28 2008 - 17:58:36 PDT)
AMBER: query regarding energy minimization Anamika Awasthi (Mon Apr 28 2008 - 06:22:24 PDT)
- Re: AMBER: query regarding energy minimization rpaduri.chem.wayne.edu (Mon Apr 28 2008 - 07:26:25 PDT)
- Re: AMBER: query regarding energy minimization Deepangi Pandit (Mon Apr 28 2008 - 07:39:39 PDT)
- Re: AMBER: query regarding energy minimization D.Usharani (Mon Apr 28 2008 - 22:20:29 PDT)
- RE: AMBER: query regarding energy minimization Ross Walker (Mon Apr 28 2008 - 23:16:11 PDT)
AMBER: Charge derivation: RESP vs. antechamber Catein Catherine (Tue Apr 29 2008 - 03:21:54 PDT)
AMBER: Charge derivation: RESP vs. antechamber Catein Catherine (Tue Apr 29 2008 - 03:21:55 PDT)
- Re: AMBER: Charge derivation: RESP vs. antechamber David A. Case (Tue Apr 29 2008 - 16:40:40 PDT)
AMBER: segmentation fault in SANDER Anamika Awasthi (Tue Apr 29 2008 - 04:44:29 PDT)
- RE: AMBER: segmentation fault in SANDER Ross Walker (Tue Apr 29 2008 - 07:15:08 PDT)
AMBER: prmtop spec trivia Lachele Foley (Lists) (Tue Apr 29 2008 - 08:07:29 PDT)
- RE: AMBER: prmtop spec trivia Ross Walker (Tue Apr 29 2008 - 08:34:04 PDT)
  - Re: AMBER: prmtop spec trivia Lachele Foley (Lists) (Tue Apr 29 2008 - 09:13:41 PDT)
    - RE: AMBER: prmtop spec trivia Ross Walker (Tue Apr 29 2008 - 10:55:02 PDT)
    - Re: AMBER: prmtop spec trivia Lachele Foley (Lists) (Tue Apr 29 2008 - 11:25:53 PDT)
    - Re: AMBER: prmtop spec trivia David A. Case (Tue Apr 29 2008 - 11:58:30 PDT)
    - Re: AMBER: prmtop spec trivia Lachele Foley (Lists) (Tue Apr 29 2008 - 12:21:43 PDT)
AMBER: regarding segfault during energy minimization Anamika Awasthi (Tue Apr 29 2008 - 22:13:21 PDT)
- RE: AMBER: regarding segfault during energy minimization Ross Walker (Tue Apr 29 2008 - 22:40:21 PDT)
  - Re: AMBER: regarding segfault during energy minimization Anamika Awasthi (Wed Apr 30 2008 - 22:57:35 PDT)
AMBER: distance matrix command priya priya (Wed Apr 30 2008 - 02:01:24 PDT)
AMBER: Constat area simulation gurpreet singh (Wed Apr 30 2008 - 04:23:35 PDT)
AMBER: Dose AMBER 10 pmemd support openmpi? Hu, Shaowen (JSC-SK)[USRA] (Wed Apr 30 2008 - 06:04:28 PDT)
- Re: AMBER: Dose AMBER 10 pmemd support openmpi? Robert Duke (Wed Apr 30 2008 - 08:16:58 PDT)
- Re: AMBER: Dose AMBER 10 pmemd support openmpi? David A. Case (Wed Apr 30 2008 - 08:22:48 PDT)
- Re: AMBER: Dose AMBER 10 pmemd support openmpi? Robert Duke (Wed Apr 30 2008 - 08:40:44 PDT)
  - RE: AMBER: Dose AMBER 10 pmemd support openmpi? Hu, Shaowen (JSC-SK)[USRA] (Wed Apr 30 2008 - 09:07:39 PDT)
AMBER: amber 9 compilation problem on IBM SP5 Andrew Emerson (Wed Apr 30 2008 - 05:44:38 PDT)
- Re: AMBER: amber 9 compilation problem on IBM SP5 David A. Case (Wed Apr 30 2008 - 11:37:11 PDT)
  - AMBER: Re: amber 9 compilation problem on IBM SP5 Andrew Emerson (Mon May 05 2008 - 00:57:53 PDT)
AMBER: about glycam06 WANG,YING (Wed Apr 30 2008 - 09:00:12 PDT)
- Re: AMBER: about glycam06 Austin B. Yongye (Wed Apr 30 2008 - 10:26:44 PDT)
- Re: AMBER: about glycam06 Austin B. Yongye (Wed Apr 30 2008 - 14:47:32 PDT)
- Re: AMBER: about glycam06 Austin B. Yongye (Sat May 03 2008 - 18:59:47 PDT)
AMBER: calibration of constant pH simulations Lillian Chong (Wed Apr 30 2008 - 10:17:47 PDT)
- Re: AMBER: calibration of constant pH simulations Adrian Roitberg (Wed Apr 30 2008 - 11:05:33 PDT)
- Re: AMBER: calibration of constant pH simulations Pradipta Bandyopadhyay (Wed Apr 30 2008 - 21:02:55 PDT)
AMBER: Cysteine sulphonic acid parameters Rima Chaudhuri (Wed Apr 30 2008 - 15:48:42 PDT)
- Re: AMBER: Cysteine sulphonic acid parameters David A. Case (Wed Apr 30 2008 - 17:06:02 PDT)
- Re: AMBER: Cysteine sulphonic acid parameters FyD (Thu May 01 2008 - 05:03:19 PDT)
  - Re: AMBER: Cysteine sulphonic acid parameters Rima Chaudhuri (Thu May 01 2008 - 08:43:48 PDT)
AMBER: Discontinuous Constant pH Restarts Neil Bruce (Thu May 01 2008 - 06:41:21 PDT)
- Re: AMBER: Discontinuous Constant pH Restarts David A. Case (Fri May 02 2008 - 12:44:31 PDT)
  - Re: AMBER: Discontinuous Constant pH Restarts Neil Bruce (Wed May 07 2008 - 13:21:28 PDT)
    - Re: AMBER: Discontinuous Constant pH Restarts David A. Case (Wed May 07 2008 - 14:34:23 PDT)
    - Re: AMBER: Discontinuous Constant pH Restarts Smriti Sharma (Thu May 08 2008 - 04:05:31 PDT)
    - Re: AMBER: Discontinuous Constant pH Restarts David A. Case (Thu May 08 2008 - 10:21:57 PDT)
AMBER: Water residue tracking Steve Seibold (Thu May 01 2008 - 09:19:42 PDT)
AMBER: Installation problem of AMBER on cluster sudipta sinha (Thu May 01 2008 - 11:16:44 PDT)
- Re: AMBER: Installation problem of AMBER on cluster David A. Case (Thu May 01 2008 - 11:55:17 PDT)
  - Re: AMBER: Installation problem of AMBER on cluster sudipta sinha (Fri May 02 2008 - 00:39:09 PDT)
    - Re: AMBER: Installation problem of AMBER on cluster Bertrand P. S. Russell (Fri May 02 2008 - 03:11:15 PDT)
    - RE: AMBER: Installation problem of AMBER on cluster Ross Walker (Fri May 02 2008 - 08:41:48 PDT)
    - Re: AMBER: Installation problem of AMBER on cluster sudipta sinha (Fri May 02 2008 - 11:29:37 PDT)
    - RE: AMBER: Installation problem of AMBER on cluster Ross Walker (Fri May 02 2008 - 12:07:10 PDT)
    - Re: AMBER: Installation problem of AMBER on cluster sudipta sinha (Fri May 02 2008 - 13:29:38 PDT)
    - Re: AMBER: Installation problem of AMBER on cluster Gustavo Seabra (Fri May 02 2008 - 14:16:22 PDT)
    - RE: AMBER: Installation problem of AMBER on cluster Ross Walker (Fri May 02 2008 - 14:18:48 PDT)
    - RE: AMBER: Installation problem of AMBER on cluster Ross Walker (Fri May 02 2008 - 14:33:48 PDT)
    - Re: AMBER: Installation problem of AMBER on cluster sudipta sinha (Fri May 02 2008 - 22:59:23 PDT)
    - Re: AMBER: Installation problem of AMBER on cluster David A. Case (Sat May 03 2008 - 16:56:32 PDT)
    - Re: AMBER: Installation problem of AMBER on cluster sudipta sinha (Sun May 04 2008 - 05:31:22 PDT)
    - Re: AMBER: Installation problem of AMBER on cluster David A. Case (Sun May 04 2008 - 18:32:02 PDT)
    - Re: AMBER: Installation problem of AMBER on cluster Bertrand P. S. Russell (Sun May 04 2008 - 18:50:13 PDT)
    - Re: AMBER: Installation problem of AMBER on cluster sudipta sinha (Sun May 04 2008 - 23:52:58 PDT)
    - Re: AMBER: Installation problem of AMBER on cluster Bertrand P. S. Russell (Mon May 05 2008 - 00:03:39 PDT)
    - Re: AMBER: Installation problem of AMBER on cluster Bertrand P. S. Russell (Mon May 05 2008 - 00:09:20 PDT)
    - Re: AMBER: Installation problem of AMBER on cluster sudipta sinha (Mon May 05 2008 - 02:47:38 PDT)
    - AMBER: misplacement of TER by leap Jena M (Mon May 05 2008 - 04:00:55 PDT)
    - Re: AMBER: misplacement of TER by leap Tim Meyer (Mon May 05 2008 - 06:03:54 PDT)
    - Re: AMBER: misplacement of TER by leap David A. Case (Mon May 05 2008 - 11:55:29 PDT)
    - Re: AMBER: Installation problem of AMBER on cluster sudipta sinha (Mon May 05 2008 - 04:24:29 PDT)
    - Re: AMBER: Installation problem of AMBER on cluster Bertrand P. S. Russell (Mon May 05 2008 - 05:40:56 PDT)
AMBER: Amber10 installation error juyong Lee (Thu May 01 2008 - 19:28:07 PDT)
- RE: AMBER: Amber10 installation error Ross Walker (Thu May 01 2008 - 21:01:02 PDT)
  - Re: AMBER: Amber10 installation error juyong Lee (Thu May 01 2008 - 21:52:10 PDT)
    - RE: AMBER: Amber10 installation error Ross Walker (Fri May 02 2008 - 08:33:43 PDT)
    - Re: AMBER: Amber10 installation error David A. Case (Fri May 02 2008 - 09:07:50 PDT)
AMBER: test.parallel.QMMM problem Carra, Claudio (JSC-SK)[USRA] (Fri May 02 2008 - 06:37:28 PDT)
- RE: AMBER: test.parallel.QMMM problem Ross Walker (Fri May 02 2008 - 08:50:31 PDT)
AMBER: silhouette width/coefficient after clustering by PTRAJ9.9 sychen (Fri May 02 2008 - 07:22:50 PDT)
- Re: AMBER: silhouette width/coefficient after clustering by PTRAJ9.9 Jianyin Shao (Fri May 09 2008 - 13:05:39 PDT)
  - Re: AMBER: silhouette width/coefficient after clustering by PTRAJ9.9 Dong Xu (Mon May 12 2008 - 21:09:11 PDT)
    - RE: AMBER: silhouette width/coefficient after clustering by PTRAJ9.9 Ross Walker (Tue May 13 2008 - 08:08:08 PDT)
- Re: AMBER: silhouette width/coefficient after clustering by PTRAJ9.9 Jianyin Shao (Tue May 27 2008 - 08:37:57 PDT)
  - Re: AMBER: silhouette width/coefficient after clustering by PTRAJ9.9 Jianyin Shao (Tue May 27 2008 - 09:03:54 PDT)
    - Re: AMBER: silhouette width/coefficient after clustering by PTRAJ9.9 Dong Xu (Tue May 27 2008 - 11:20:09 PDT)
    - Re: AMBER: silhouette width/coefficient after clustering by PTRAJ9.9 Jianyin Shao (Tue May 27 2008 - 12:29:43 PDT)
- Re: AMBER: silhouette width/coefficient after clustering by PTRAJ9.9 Jianyin Shao (Wed May 28 2008 - 08:51:12 PDT)
- Re: AMBER: silhouette width/coefficient after clustering by PTRAJ9.9 Jianyin Shao (Wed May 28 2008 - 21:07:18 PDT)
- Re: AMBER: silhouette width/coefficient after clustering by PTRAJ9.9 Jianyin Shao (Thu May 29 2008 - 11:15:15 PDT)
  - Re: AMBER: silhouette width/coefficient after clustering by PTRAJ9.9 Dong Xu (Thu May 29 2008 - 12:19:53 PDT)
    - Re: AMBER: silhouette width/coefficient after clustering by PTRAJ9.9 Jianyin Shao (Thu May 29 2008 - 14:47:43 PDT)
- Re: AMBER: silhouette width/coefficient after clustering by PTRAJ9.9 Jianyin Shao (Fri May 30 2008 - 10:11:24 PDT)
  - Re: AMBER: silhouette width/coefficient after clustering by PTRAJ9.9 Dong Xu (Thu Jul 03 2008 - 23:28:44 PDT)
    - Re: AMBER: silhouette width/coefficient after clustering by PTRAJ9.9 Dong Xu (Thu Jul 03 2008 - 23:33:03 PDT)
    - Re: AMBER: silhouette width/coefficient after clustering by PTRAJ9.9 Dong Xu (Fri Jul 04 2008 - 12:21:31 PDT)
    - Re: AMBER: silhouette width/coefficient after clustering by PTRAJ9.9 Jianyin Shao (Mon Jul 07 2008 - 15:41:03 PDT)
    - Re: AMBER: silhouette width/coefficient after clustering by PTRAJ9.9 Dong Xu (Mon Jul 07 2008 - 23:37:54 PDT)
    - Re: AMBER: silhouette width/coefficient after clustering by PTRAJ9.9 Jianyin Shao (Tue Jul 08 2008 - 21:45:46 PDT)
    - Re: AMBER: silhouette width/coefficient after clustering by PTRAJ9.9 Dong Xu (Tue Jul 29 2008 - 00:40:04 PDT)
    - Re: AMBER: silhouette width/coefficient after clustering by PTRAJ9.9 Jianyin Shao (Fri Aug 01 2008 - 12:43:14 PDT)
- Re: AMBER: silhouette width/coefficient after clustering by PTRAJ9.9 Jianyin Shao (Sat Aug 02 2008 - 19:23:53 PDT)
AMBER: Help with NMODE Seth Lilavivat (Fri May 02 2008 - 08:24:25 PDT)
- Re: AMBER: Help with NMODE David A. Case (Fri May 02 2008 - 09:23:34 PDT)
  - Re: AMBER: Help with NMODE Seth Lilavivat (Fri May 02 2008 - 09:50:35 PDT)
    - Re: AMBER: Help with NMODE David A. Case (Fri May 02 2008 - 10:06:33 PDT)
    - Re: AMBER: Help with NMODE Seth Lilavivat (Fri May 02 2008 - 11:05:19 PDT)
    - Re: AMBER: Help with NMODE David A. Case (Fri May 02 2008 - 12:28:51 PDT)
    - Re: AMBER: Help with NMODE Seth Lilavivat (Sun May 04 2008 - 15:15:53 PDT)
    - Re: AMBER: Help with NMODE David A. Case (Sun May 04 2008 - 18:26:07 PDT)
    - Re: AMBER: Help with NMODE Seth Lilavivat (Mon May 05 2008 - 12:39:06 PDT)
AMBER: cfortran.h error with xlf90 compiler juyong Lee (Fri May 02 2008 - 09:35:32 PDT)
- RE: AMBER: cfortran.h error with xlf90 compiler Ross Walker (Fri May 02 2008 - 09:58:27 PDT)
- Re: AMBER: cfortran.h error with xlf90 compiler David A. Case (Fri May 02 2008 - 10:10:54 PDT)
AMBER: Compiling amber10 with xlf90 fortran compiler juyong Lee (Fri May 02 2008 - 11:27:10 PDT)
AMBER: Mn2+ parameters in AMBER jitrayut jitonnom (Fri May 02 2008 - 11:46:25 PDT)
- Re: AMBER: Mn2+ parameters in AMBER Guillermo Mulliert Carlín (Thu May 22 2008 - 23:26:51 PDT)
  - Re: AMBER: Mn2+ parameters in AMBER jitrayut jitonnom (Fri May 23 2008 - 01:58:10 PDT)
AMBER: Inquiry on B-factor of NMR James Thomas (Fri May 02 2008 - 12:31:09 PDT)
AMBER: printing dipoles in Amber10 (and earlier) Piotr Cieplak (Fri May 02 2008 - 13:29:49 PDT)
- AMBER: point charges Chih-Ying Lin (Fri May 02 2008 - 13:53:50 PDT)
  - RE: AMBER: point charges Ross Walker (Fri May 02 2008 - 14:32:43 PDT)
    - Re: RE: AMBER: point charges Chih-Ying Lin (Fri May 02 2008 - 15:42:18 PDT)
    - RE: RE: AMBER: point charges Ross Walker (Fri May 02 2008 - 16:03:08 PDT)
    - Re: RE: RE: AMBER: point charges Chih-Ying Lin (Sat May 03 2008 - 14:47:23 PDT)
    - Re: RE: RE: AMBER: point charges David A. Case (Sat May 03 2008 - 17:36:08 PDT)
    - AMBER: NON-BONDED parameters Chih-Ying Lin (Mon May 05 2008 - 10:32:23 PDT)
    - Re: AMBER: NON-BONDED parameters Thomas Steinbrecher (Mon May 05 2008 - 11:14:59 PDT)
    - Re: AMBER: NON-BONDED parameters Chih-Ying Lin (Mon May 05 2008 - 15:10:05 PDT)
    - Re: AMBER: NON-BONDED parameters David A. Case (Mon May 05 2008 - 16:54:32 PDT)
- RE: AMBER: printing dipoles in Amber10 (and earlier) Ross Walker (Fri May 02 2008 - 14:16:08 PDT)
AMBER: Water tracking Steve Seibold (Fri May 02 2008 - 08:09:35 PDT)
- Re: AMBER: Water tracking Thomas Cheatham III (Fri May 02 2008 - 09:14:21 PDT)
AMBER: Example .prepi file for nonstandard amino acids finke.oakland.edu (Fri May 02 2008 - 15:00:45 PDT)
- Re: AMBER: Example .prepi file for nonstandard amino acids David A. Case (Fri May 02 2008 - 15:54:03 PDT)
- Re: AMBER: Example .prepi file for nonstandard amino acids finke.oakland.edu (Fri May 02 2008 - 18:06:30 PDT)
AMBER: about glycam06 WANG,YING (Sat May 03 2008 - 16:22:18 PDT)
- Re: AMBER: about glycam06 WANG,YING (Wed Apr 30 2008 - 12:49:46 PDT)
- Re: AMBER: about glycam06 David A. Case (Sat May 03 2008 - 16:49:27 PDT)
- Re: AMBER: about glycam06 WANG,YING (Sat May 03 2008 - 16:55:11 PDT)
- Re: AMBER: about glycam06 WANG,YING (Sat May 03 2008 - 16:57:35 PDT)
  - Re: AMBER: about glycam06 David A. Case (Sat May 03 2008 - 17:32:10 PDT)
- Re: AMBER: about glycam06 WANG,YING (Sat May 03 2008 - 19:35:05 PDT)
- Re: AMBER: about glycam06 WANG,YING (Sat May 03 2008 - 19:40:14 PDT)
- Re: AMBER: about glycam06 Bill Ross (Sun May 04 2008 - 15:46:05 PDT)
- Re: AMBER: about glycam06 WANG,YING (Mon May 05 2008 - 07:30:19 PDT)
AMBER: Amber10 Installation error - incorrect file suffix juyong Lee (Sun May 04 2008 - 05:46:10 PDT)
- Re: AMBER: Amber10 Installation error - incorrect file suffix David A. Case (Sun May 04 2008 - 18:20:55 PDT)
  - Re: AMBER: Amber10 Installation error - incorrect file suffix juyong Lee (Sun May 04 2008 - 19:01:02 PDT)
AMBER: Deriving Force Field Parameters Shultz, Jack (Sun May 04 2008 - 14:32:03 PDT)
- AMBER: GAFF Schema Shultz, Jack (Sun May 04 2008 - 15:11:37 PDT)
  - Re: AMBER: GAFF Schema David A. Case (Sun May 04 2008 - 18:21:59 PDT)
- Re: AMBER: Deriving Force Field Parameters FyD (Mon May 05 2008 - 07:14:22 PDT)
AMBER: Jarzinsky relationship E.M. (Sun May 04 2008 - 19:39:51 PDT)
- Re: AMBER: Jarzinsky relationship Adrian Roitberg (Mon May 05 2008 - 07:46:53 PDT)
  - Re: AMBER: Jarzinsky relationship E.M. (Mon May 05 2008 - 08:02:49 PDT)
    - Re: AMBER: Jarzinsky relationship Adrian Roitberg (Mon May 05 2008 - 08:13:51 PDT)
    - Re: AMBER: Jarzinsky relationship E.M. (Thu May 08 2008 - 03:58:10 PDT)
    - Re: AMBER: Jarzinsky relationship David Mobley (Thu May 08 2008 - 14:29:29 PDT)
AMBER: Torsion angle restrains and Jarzinsky E.M. (Mon May 05 2008 - 00:06:56 PDT)
AMBER: Installation error on IBM cluster juyong Lee (Mon May 05 2008 - 01:40:59 PDT)
- RE: AMBER: Installation error on IBM cluster Ross Walker (Mon May 05 2008 - 08:06:11 PDT)
AMBER: unable to compile AmberTools 1.0 Rabin (Mon May 05 2008 - 10:07:00 PDT)
- Re: AMBER: unable to compile AmberTools 1.0 David A. Case (Mon May 05 2008 - 11:14:44 PDT)
  - Re: AMBER: unable to compile AmberTools 1.0 Yu Chen (Mon May 05 2008 - 12:06:26 PDT)
AMBER: About reading in heme and CO molecule together with myoglobin Yang, Lee-Wei (Mon May 05 2008 - 11:08:53 PDT)
- Re: AMBER: About reading in heme and CO molecule together with myoglobin David A. Case (Mon May 05 2008 - 16:51:44 PDT)
AMBER: AMBER Parallel test error jitrayut jitonnom (Mon May 05 2008 - 11:37:39 PDT)
- RE: AMBER: AMBER Parallel test error Ross Walker (Mon May 05 2008 - 12:42:09 PDT)
  - Re: AMBER: AMBER Parallel test error jitrayut jitonnom (Tue May 06 2008 - 06:09:10 PDT)
    - Re: AMBER: AMBER Parallel test error jitrayut jitonnom (Tue May 06 2008 - 06:38:53 PDT)
    - RE: AMBER: AMBER Parallel test error Ross Walker (Tue May 06 2008 - 08:25:46 PDT)
    - Re: AMBER: AMBER Parallel test error sudipta sinha (Wed May 07 2008 - 09:09:28 PDT)
    - Re: AMBER: AMBER Parallel test error jitrayut jitonnom (Thu May 08 2008 - 02:10:49 PDT)
AMBER: DCCM correlation analysis Ibrahim Moustafa (Mon May 05 2008 - 13:21:37 PDT)
AMBER: Units, units units E.M. (Mon May 05 2008 - 15:18:37 PDT)
- Re: AMBER: Units, units units David A. Case (Mon May 05 2008 - 16:02:57 PDT)
AMBER: Minimization in Octahedric Box guardiani.fi.infn.it (Tue May 06 2008 - 04:31:50 PDT)
- Re: AMBER: Minimization in Octahedric Box David A. Case (Tue May 06 2008 - 10:28:20 PDT)
- RE: AMBER: Minimization in Octahedric Box Ross Walker (Tue May 06 2008 - 10:22:39 PDT)
AMBER: rmsd per residue Furia Gargano (Tue May 06 2008 - 07:28:59 PDT)
AMBER: steered MD initial state M. L. Dodson (Tue May 06 2008 - 09:04:09 PDT)
- Re: AMBER: steered MD initial state Gustavo Seabra (Tue May 06 2008 - 09:37:54 PDT)
  - Re: AMBER: steered MD initial state Adrian Roitberg (Tue May 06 2008 - 10:16:52 PDT)
    - Re: AMBER: steered MD initial state M. L. Dodson (Tue May 06 2008 - 10:39:04 PDT)
  - Re: AMBER: steered MD initial state M. L. Dodson (Tue May 06 2008 - 10:27:03 PDT)
AMBER: mm_pbsa.pl not reading parameters for nmode Seth Lilavivat (Tue May 06 2008 - 10:50:18 PDT)
- Re: AMBER: mm_pbsa.pl not reading parameters for nmode David A. Case (Tue May 06 2008 - 11:13:54 PDT)
  - AMBER: Improper dihedral parameters Chih-Ying Lin (Tue May 06 2008 - 12:00:36 PDT)
  - AMBER: single stranded DNA Taufik Al-Sarraj (Tue May 06 2008 - 15:37:41 PDT)
    - Re: AMBER: single stranded DNA David A. Case (Tue May 06 2008 - 15:41:29 PDT)
    - Re: AMBER: single stranded DNA Taufik Al-Sarraj (Tue May 06 2008 - 17:11:07 PDT)
Re: AMBER: Improper dihedral parameters Bill Ross (Tue May 06 2008 - 12:23:55 PDT)
- Re: AMBER: Improper dihedral parameters Da-Wei Li (Tue May 06 2008 - 12:30:29 PDT)
AMBER: DFTB parameters for O-P Carra, Claudio (JSC-SK)[USRA] (Tue May 06 2008 - 13:01:55 PDT)
- Re: AMBER: DFTB parameters for O-P Gustavo Seabra (Wed May 07 2008 - 12:19:50 PDT)
AMBER: Amber Parameter Schema Shultz, Jack (Tue May 06 2008 - 17:22:02 PDT)
AMBER: Ewald error estimate 欧阳德方 (Wed May 07 2008 - 01:25:22 PDT)
- Re: AMBER: Ewald error estimate David A. Case (Wed May 07 2008 - 08:57:03 PDT)
  - RE: AMBER: Ewald error estimate 欧阳德方 (Wed May 07 2008 - 20:38:18 PDT)
    - RE: AMBER: Ewald error estimate Thomas Cheatham (Wed May 07 2008 - 20:51:55 PDT)
    - RE: AMBER: Ewald error estimate 欧阳德方 (Wed May 07 2008 - 22:04:05 PDT)
    - RE: AMBER: Ewald error estimate Ross Walker (Thu May 08 2008 - 08:27:15 PDT)
    - Re: AMBER: Ewald error estimate David A. Case (Thu May 08 2008 - 10:16:43 PDT)
    - RE: AMBER: Ewald error estimate Thomas Cheatham III (Thu May 08 2008 - 10:21:38 PDT)
- AMBER: to unsubscribe email Rabin (Mon May 12 2008 - 08:47:43 PDT)
  - Re: AMBER: to unsubscribe email Bill Ross (Mon May 12 2008 - 10:46:24 PDT)
    - Re: AMBER: to unsubscribe email Rabin (Mon May 12 2008 - 14:29:56 PDT)
AMBER: molsurf jacopo.sgrignani.unifi.it (Wed May 07 2008 - 04:11:34 PDT)
AMBER: uninstall of AMBER sudipta sinha (Wed May 07 2008 - 08:50:37 PDT)
- Re: AMBER: uninstall of AMBER David A. Case (Wed May 07 2008 - 09:07:25 PDT)
- RE: AMBER: uninstall of AMBER Ross Walker (Wed May 07 2008 - 10:05:20 PDT)
AMBER: nmode: number of atoms limitation Qi Yan (Wed May 07 2008 - 11:25:58 PDT)
- RE: AMBER: nmode: number of atoms limitation Ross Walker (Wed May 07 2008 - 14:39:44 PDT)
- AMBER: Azobenzene: AMBER+Gromos Force Field parameters Chih-Ying Lin (Wed May 07 2008 - 14:43:17 PDT)
AMBER: GBSA SA calculation Titus, Jamie $bairdje$ (Wed May 07 2008 - 11:32:43 PDT)
- Re: AMBER: GBSA SA calculation Carlos Simmerling (Wed May 07 2008 - 12:05:44 PDT)
- Re: AMBER: GBSA SA calculation David A. Case (Wed May 07 2008 - 14:17:07 PDT)
  - Re: AMBER: GBSA SA calculation Carlos Simmerling (Wed May 07 2008 - 15:05:26 PDT)
- Re: AMBER: GBSA SA calculation Carlos Simmerling (Tue May 13 2008 - 10:46:30 PDT)
AMBER: Hydroxyprolines!!! Titus, Jamie $bairdje$ (Wed May 07 2008 - 11:54:03 PDT)
- Re: AMBER: Hydroxyprolines!!! David A. Case (Wed May 07 2008 - 18:26:16 PDT)
AMBER: Harmonic Force Constant Shultz, Jack (Wed May 07 2008 - 12:32:18 PDT)
- RE: AMBER: Harmonic Force Constant Shultz, Jack (Thu May 08 2008 - 13:21:00 PDT)
AMBER: How to transfer unformatted coordinates into formatted ones Qi Yan (Wed May 07 2008 - 12:44:10 PDT)
- Re: AMBER: How to transfer unformatted coordinates into formatted ones David A. Case (Wed May 07 2008 - 18:14:04 PDT)
- RE: AMBER: How to transfer unformatted coordinates into formatted ones Qi Yan (Wed May 07 2008 - 19:55:18 PDT)
  - Re: AMBER: How to transfer unformatted coordinates into formatted ones David A. Case (Thu May 08 2008 - 10:13:59 PDT)
AMBER: nmode: number of atoms limitation Qi Yan (Wed May 07 2008 - 11:10:48 PDT)
AMBER: Compilation of PMEMD sudipta sinha (Thu May 08 2008 - 04:07:28 PDT)
- Re: AMBER: Compilation of PMEMD Robert Duke (Thu May 08 2008 - 05:17:43 PDT)
AMBER: mm_pbsa problem: bad atom type: IP mori.cerm.unifi.it (Thu May 08 2008 - 04:59:12 PDT)
- Re: AMBER: mm_pbsa problem: bad atom type: IP David A. Case (Thu May 08 2008 - 10:27:22 PDT)
AMBER: nmode "Atom out of bounds" for min of multiple ligands Seth Lilavivat (Thu May 08 2008 - 07:30:24 PDT)
- RE: AMBER: nmode "Atom out of bounds" for min of multiple ligands Ross Walker (Thu May 08 2008 - 10:19:34 PDT)
  - Re: AMBER: nmode "Atom out of bounds" for min of multiple ligands Seth Lilavivat (Thu May 08 2008 - 13:01:45 PDT)
    - Re: AMBER: nmode "Atom out of bounds" for min of multiple ligands David A. Case (Thu May 08 2008 - 13:49:31 PDT)
AMBER: can amber read .xyz files? WANG,YING (Thu May 08 2008 - 08:29:57 PDT)
- RE: AMBER: can amber read .xyz files? Ross Walker (Thu May 08 2008 - 10:23:16 PDT)
AMBER: velocity autocorrelation function for SPC felxible water model Rahaman, Asif (Thu May 08 2008 - 10:07:41 PDT)
- Re: AMBER: velocity autocorrelation function for SPC felxible water model David A. Case (Thu May 08 2008 - 11:00:28 PDT)
- RE: AMBER: velocity autocorrelation function for SPC felxible water model Rahaman, Asif (Thu May 08 2008 - 13:42:22 PDT)
  - Re: AMBER: velocity autocorrelation function for SPC felxible water model David A. Case (Thu May 08 2008 - 15:54:57 PDT)
    - AMBER: drawing repeated units Taufik Al-Sarraj (Fri May 09 2008 - 08:10:19 PDT)
    - RE: AMBER: drawing repeated units Ross Walker (Fri May 09 2008 - 09:03:28 PDT)
    - Re: AMBER: drawing repeated units Taufik Al-Sarraj (Fri May 09 2008 - 11:10:56 PDT)
    - Re: AMBER: drawing repeated units Taufik Al-Sarraj (Tue Jun 03 2008 - 15:25:59 PDT)
    - RE: AMBER: drawing repeated units Ross Walker (Tue Jun 03 2008 - 14:50:23 PDT)
    - Re: AMBER: drawing repeated units Taufik Al-Sarraj (Tue Jun 03 2008 - 16:58:25 PDT)
    - RE: AMBER: drawing repeated units Ross Walker (Tue Jun 03 2008 - 16:49:54 PDT)
    - Re: AMBER: drawing repeated units Taufik Al-Sarraj (Wed Jun 04 2008 - 13:17:57 PDT)
    - Re: AMBER: drawing repeated units Taufik Al-Sarraj (Tue Jun 24 2008 - 15:15:39 PDT)
    - RE: AMBER: drawing repeated units Ross Walker (Tue Jun 24 2008 - 14:40:26 PDT)
AMBER: AmberTools on OS X fails tests Hans Martin Senn (Thu May 08 2008 - 11:59:12 PDT)
- Re: AMBER: AmberTools on OS X fails tests Wei Zhang (Thu May 08 2008 - 12:15:46 PDT)
- Re: AMBER: AmberTools on OS X fails tests David A. Case (Thu May 08 2008 - 12:30:53 PDT)
AMBER: QM/MM Syed Tarique Moin (Fri May 09 2008 - 01:28:06 PDT)
- Re: AMBER: QM/MM Gustavo Seabra (Fri May 09 2008 - 07:18:21 PDT)
AMBER: distance Urszula Uciechowska (Fri May 09 2008 - 07:36:18 PDT)
- Re: AMBER: distance E.M. (Fri May 09 2008 - 07:43:12 PDT)
- Re: AMBER: distance Ibrahim Moustafa (Fri May 09 2008 - 07:49:37 PDT)
AMBER: help to install AMBER9 Jeffrey (Fri May 09 2008 - 07:47:16 PDT)
- Re: AMBER: help to install AMBER9 Ye Mei (Fri May 09 2008 - 07:55:56 PDT)
- Re: AMBER: help to install AMBER9 Gustavo Seabra (Fri May 09 2008 - 08:01:04 PDT)
- RE: AMBER: help to install AMBER9 Ross Walker (Fri May 09 2008 - 09:12:53 PDT)
- Re: AMBER: help to install AMBER9 Jeffrey (Sun May 11 2008 - 02:12:18 PDT)
  - Re: AMBER: help to install AMBER9 Gustavo Seabra (Mon May 12 2008 - 07:56:41 PDT)
    - Re: Re: AMBER: help to install AMBER9 Jeffrey (Mon May 12 2008 - 17:51:46 PDT)
AMBER: MM_PBSA output file Qi Yan (Fri May 09 2008 - 09:03:38 PDT)
- Re: AMBER: MM_PBSA output file Navnit Kumar Mishra (Fri May 09 2008 - 09:21:17 PDT)
- Re: AMBER: MM_PBSA output file Alessandro Nascimento (Fri May 09 2008 - 09:22:35 PDT)
AMBER: neutral C-terminus and N-terminus parameters for amber Lisa Perez (Fri May 09 2008 - 10:32:13 PDT)
- Re: AMBER: neutral C-terminus and N-terminus parameters for amber FyD (Sat May 10 2008 - 00:52:10 PDT)
AMBER: cannot read big .pdb files WANG,YING (Fri May 09 2008 - 19:00:29 PDT)
- Re: AMBER: cannot read big .pdb files David A. Case (Sat May 10 2008 - 08:24:41 PDT)
- Re: AMBER: cannot read big .pdb files Lynn F. Ten Eyck (Sat May 10 2008 - 09:37:02 PDT)
- Re: AMBER: cannot read big .pdb files WANG,YING (Sun May 11 2008 - 06:38:41 PDT)
- Re: AMBER: cannot read big .pdb files WANG,YING (Sun May 11 2008 - 06:36:48 PDT)
  - Re: AMBER: cannot read big .pdb files Wei Zhang (Mon May 12 2008 - 07:34:40 PDT)
- Re: AMBER: cannot read big .pdb files WANG,YING (Mon May 12 2008 - 07:37:24 PDT)
- Re: AMBER: cannot read big .pdb files WANG,YING (Mon May 12 2008 - 12:42:27 PDT)
  - Re: AMBER: cannot read big .pdb files David Watson (Mon May 12 2008 - 16:32:49 PDT)
- Re: AMBER: cannot read big .pdb files WANG,YING (Tue May 13 2008 - 06:40:34 PDT)
AMBER: parmbsc0 parameters for RNA.DNA systems Cenk $Jenk$ Andac (Sat May 10 2008 - 06:47:50 PDT)
- Re: AMBER: parmbsc0 parameters for RNA.DNA systems David A. Case (Sat May 10 2008 - 08:27:36 PDT)
AMBER: Calculate number of ions Dong Xu (Sat May 10 2008 - 11:32:01 PDT)
- Re: AMBER: Calculate number of ions Mathy Froeyen (Tue May 13 2008 - 00:50:29 PDT)
  - Re: AMBER: Calculate number of ions Ruchi Sachdeva (Wed May 14 2008 - 00:24:08 PDT)
    - AMBER: Weighting factors in RESP charge fitting Anselm Horn (Fri May 16 2008 - 05:32:22 PDT)
    - Re: AMBER: Weighting factors in RESP charge fitting Piotr Cieplak (Fri May 16 2008 - 11:46:51 PDT)
AMBER: Solvent mixture box Francesco Pietra (Sun May 11 2008 - 10:04:52 PDT)
AMBER: Ewald PARAMETER RANGE WRONG WANG,YING (Sun May 11 2008 - 11:01:09 PDT)
- Re: AMBER: Ewald PARAMETER RANGE WRONG David A. Case (Mon May 12 2008 - 09:00:44 PDT)
- Re: AMBER: Ewald PARAMETER RANGE WRONG WANG,YING (Mon May 12 2008 - 10:06:03 PDT)
AMBER: rms Urszula Uciechowska (Mon May 12 2008 - 04:19:41 PDT)
- Re: AMBER: rms Vlad Cojocaru (Mon May 12 2008 - 05:40:46 PDT)
  - Re: AMBER: rms Urszula Uciechowska (Mon May 12 2008 - 06:41:06 PDT)
    - Re: AMBER: rms Cenk $Jenk$ Andac (Mon May 12 2008 - 06:51:56 PDT)
    - Re: AMBER: rms Vlad Cojocaru (Wed May 14 2008 - 07:01:17 PDT)
AMBER: About Hydrophobic Interactions. cgji (Mon May 12 2008 - 09:14:00 PDT)
AMBER: Problems installing Amber Tools for Amber 10 Sam Danziger (Mon May 12 2008 - 11:20:23 PDT)
- Re: AMBER: Problems installing Amber Tools for Amber 10 David A. Case (Thu May 15 2008 - 21:47:19 PDT)
  - Re: AMBER: Problems installing Amber Tools for Amber 10 Lynn F. Ten Eyck (Fri May 16 2008 - 08:12:49 PDT)
  - Re: AMBER: Problems installing Amber Tools for Amber 10 Sam Danziger (Fri May 16 2008 - 10:06:05 PDT)
    - Re: AMBER: Problems installing Amber Tools for Amber 10 Sam Danziger (Fri May 16 2008 - 10:41:31 PDT)
    - Re: AMBER: Problems installing Amber Tools for Amber 10 Sam Danziger (Fri May 16 2008 - 11:29:32 PDT)
    - Re: AMBER: Problems installing Amber Tools for Amber 10 David A. Case (Fri May 16 2008 - 13:24:08 PDT)
  - Re: AMBER: Problems installing Amber Tools for Amber 10 Scott Brozell (Tue May 27 2008 - 10:17:19 PDT)
AMBER: Ligand energy minimization Dong Xu (Mon May 12 2008 - 15:07:31 PDT)
- RE: AMBER: Ligand energy minimization Ross Walker (Tue May 13 2008 - 08:14:53 PDT)
  - AMBER: Prepgen Rajendra P. OJHA (Wed May 14 2008 - 02:45:47 PDT)
    - Re: AMBER: Prepgen Junmei Wang (Thu May 15 2008 - 08:46:34 PDT)
    - Re: AMBER: Prepgen Heikki Salo (Wed Jul 30 2008 - 01:58:28 PDT)
    - Re: AMBER: Prepgen Grange Hermitage (Thu Jul 31 2008 - 19:29:45 PDT)
    - Re: AMBER: Prepgen Grange Hermitage (Thu Jul 31 2008 - 20:21:54 PDT)
    - Re: AMBER: Prepgen Junmei Wang (Tue Aug 05 2008 - 08:50:00 PDT)
    - Re: AMBER: Prepgen Grange Hermitage (Mon Aug 11 2008 - 00:10:00 PDT)
    - Re: AMBER: Prepgen Junmei Wang (Tue Aug 12 2008 - 15:30:45 PDT)
    - Re: AMBER: Prepgen Grange Hermitage (Thu Aug 14 2008 - 23:12:50 PDT)
    - Re: AMBER: Prepgen Junmei Wang (Fri Aug 15 2008 - 06:52:27 PDT)
    - Re: AMBER: Prepgen Grange Hermitage (Sun Aug 17 2008 - 20:22:32 PDT)
AMBER: nab Rabin (Mon May 12 2008 - 17:40:54 PDT)
- Re: AMBER: nab Alessandro Nascimento (Mon May 12 2008 - 17:59:27 PDT)
- Re: AMBER: nab Andreas Svrcek-Seiler (Tue May 13 2008 - 02:39:19 PDT)
  - Re: AMBER: nab Rabin (Tue May 13 2008 - 06:17:51 PDT)
AMBER: from Gromax to AMBER Cristina Sisu (Tue May 13 2008 - 03:00:24 PDT)
- RE: AMBER: from Gromax to AMBER jacopo.sgrignani.unifi.it (Tue May 13 2008 - 06:19:19 PDT)
  - AMBER: building quadruplex with nab Rabin (Tue May 13 2008 - 06:38:15 PDT)
    - Re: AMBER: building quadruplex with nab Rabin (Tue May 20 2008 - 15:30:17 PDT)
    - Re: AMBER: building quadruplex with nab David A. Case (Tue May 20 2008 - 22:08:10 PDT)
  - Re: AMBER: from Gromax to AMBER Cristina Sisu (Tue May 13 2008 - 06:49:12 PDT)
AMBER: An enquiry about dynamic simulations of oxygen binding to myoglobin (Ann N Y Acad Sci. 1986;482:222- Catein Catherine (Tue May 13 2008 - 03:17:29 PDT)
- Re: AMBER: An enquiry about dynamic simulations of oxygen binding to myoglobin (Ann N Y Acad Sci. 1986;482:222- David A. Case (Sun May 18 2008 - 13:09:00 PDT)
AMBER: CAVITY_SURFTEN & CAVITY_OFFSET default params Marcin Krol (Tue May 13 2008 - 06:44:48 PDT)
- RE: AMBER: CAVITY_SURFTEN & CAVITY_OFFSET default params Ray Luo (Thu May 22 2008 - 13:37:04 PDT)
  - Re: AMBER: CAVITY_SURFTEN & CAVITY_OFFSET default params ke dong (Sat May 24 2008 - 07:46:19 PDT)
AMBER: periodic boundary condition WANG,YING (Tue May 13 2008 - 06:55:00 PDT)
- Re: AMBER: periodic boundary condition David A. Case (Wed May 14 2008 - 06:50:40 PDT)
- RE: AMBER: periodic boundary condition WANG,YING (Sun May 25 2008 - 06:58:20 PDT)
AMBER: Free Energy Calculations - parameters for MM Seth Lilavivat (Tue May 13 2008 - 09:29:23 PDT)
- AMBER: initial velocities of MD Jena M (Tue May 13 2008 - 09:37:31 PDT)
  - Re: AMBER: initial velocities of MD Carlos Simmerling (Tue May 13 2008 - 09:59:26 PDT)
  - RE: AMBER: initial velocities of MD Ross Walker (Tue May 13 2008 - 10:05:05 PDT)
AMBER: divcon E.M. (Tue May 13 2008 - 09:58:49 PDT)
- Re: AMBER: divcon Gustavo Seabra (Tue May 13 2008 - 10:43:35 PDT)
AMBER: Amber10 testing problem Cenk $Jenk$ Andac (Tue May 13 2008 - 12:46:02 PDT)
- RE: AMBER: Amber10 testing problem Ross Walker (Tue May 13 2008 - 14:20:53 PDT)
  - RE: AMBER: Amber10 testing problem Cenk $Jenk$ Andac (Wed May 14 2008 - 02:13:13 PDT)
    - AMBER: AMBER PBSA Thomas Leonard (Wed May 14 2008 - 02:35:54 PDT)
AMBER: simulating the pull out of Carbon Nanotube from polymer with AMBER yuan li (Tue May 13 2008 - 19:53:10 PDT)
AMBER: MM_PBSA problem in binding_energy mori.cerm.unifi.it (Wed May 14 2008 - 07:17:40 PDT)
- Re: AMBER: MM_PBSA problem in binding_energy jacopo sgrignani (Wed May 14 2008 - 11:43:55 PDT)
AMBER: about addles:“forrtl: severe (71): integer divide by zero”. 成全 (Wed May 14 2008 - 07:57:25 PDT)
- AMBER: RE: AMBER: about addles:“forrtl: severe (71): integer divide by zero”. Ross Walker (Wed May 14 2008 - 09:30:51 PDT)
  - AMBER: RE: AMBER: RE: AMBER: about addles:“forrtl: severe (71): integer divide by zero”. 成全 (Wed May 14 2008 - 17:18:05 PDT)
    - AMBER: RE: AMBER: RE: AMBER: RE: AMBER: about addles:“forrtl: severe (71): integer divide by zero”. Ross Walker (Thu May 15 2008 - 10:37:22 PDT)
    - AMBER: RE: AMBER: RE: AMBER: RE: AMBER: RE: AMBER: about addles:“forrtl: severe (71): integer divide by z 成全 (Thu May 15 2008 - 23:56:34 PDT)
    - AMBER: about addles:“forrtl: severe (71): integer divide by z Ross Walker (Fri May 16 2008 - 11:00:34 PDT)
AMBER: subscribe amber wangluohuaxue (Wed May 14 2008 - 07:40:04 PDT)
AMBER: simulate dipole moment Qiuting Hong (Wed May 14 2008 - 13:52:33 PDT)
- Re: AMBER: simulate dipole moment Neelanjana Sengupta (Wed May 14 2008 - 14:14:54 PDT)
- RE: AMBER: simulate dipole moment Ross Walker (Wed May 14 2008 - 14:25:33 PDT)
AMBER: AMBER entropy calculation Thomas Leonard (Wed May 14 2008 - 16:00:45 PDT)
- Re: AMBER: AMBER entropy calculation Dong Xu (Wed May 14 2008 - 17:37:27 PDT)
- Re: AMBER: AMBER entropy calculation Swarup Gupta (Wed May 14 2008 - 19:20:07 PDT)
  - AMBER: how to calculate delta G from IC50 Thomas Leonard (Mon May 19 2008 - 22:12:04 PDT)
    - Re: AMBER: how to calculate delta G from IC50 Chris Moth (Tue May 20 2008 - 05:30:29 PDT)
AMBER: Amber10:Compiling with gcc 2.4.1 yongleli (Thu May 15 2008 - 08:36:29 PDT)
- Re: AMBER: Amber10:Compiling with gcc 2.4.1 Gustavo Seabra (Thu May 15 2008 - 15:58:05 PDT)
- Re: AMBER: Amber10:Compiling with gcc 2.4.1 David A. Case (Thu May 15 2008 - 20:42:31 PDT)
- Re: Re: AMBER: Amber10:Compiling with gcc 2.4.1 yongleli (Thu May 15 2008 - 21:03:41 PDT)
- Re: Re: AMBER: Amber10:Compiling with gcc 2.4.1 David A. Case (Fri May 16 2008 - 13:16:56 PDT)
AMBER: Points on a Sphere Justine Condo (Thu May 15 2008 - 09:27:06 PDT)
AMBER: MKL libraries/Amber10 Francesco Pietra (Thu May 15 2008 - 11:01:34 PDT)
- Re: AMBER: MKL libraries/Amber10 Gustavo Seabra (Thu May 15 2008 - 16:02:42 PDT)
- Re: AMBER: MKL libraries/Amber10 yongleli (Thu May 15 2008 - 19:03:57 PDT)
  - RE: AMBER: MKL libraries/Amber10 Ross Walker (Thu May 15 2008 - 19:59:16 PDT)
    - RE: AMBER: MKL libraries/Amber10 Francesco Pietra (Fri May 16 2008 - 09:31:17 PDT)
    - RE: AMBER: MKL libraries/Amber10 Ross Walker (Fri May 16 2008 - 11:25:36 PDT)
    - RE: AMBER: MKL libraries/Amber10 Francesco Pietra (Sat May 17 2008 - 10:12:06 PDT)
    - Fw: RE: AMBER: MKL libraries/Amber10 Francesco Pietra (Sat May 17 2008 - 10:33:10 PDT)
    - Fw: RE: AMBER: MKL libraries/Amber10 Francesco Pietra (Sat May 17 2008 - 14:14:18 PDT)
    - Fw: RE: AMBER: MKL libraries/Amber10 Francesco Pietra (Sun May 18 2008 - 10:33:54 PDT)
    - Re: Fw: RE: AMBER: MKL libraries/Amber10 Gustavo Seabra (Mon May 19 2008 - 07:18:07 PDT)
    - Re: Fw: RE: AMBER: MKL libraries/Amber10 Francesco Pietra (Mon May 19 2008 - 08:24:43 PDT)
    - RE: Fw: RE: AMBER: MKL libraries/Amber10 Ross Walker (Mon May 19 2008 - 08:41:59 PDT)
    - RE: Fw: RE: AMBER: MKL libraries/Amber10 Cenk $Jenk$ Andac (Mon May 19 2008 - 09:48:21 PDT)
    - RE: Fw: RE: AMBER: MKL libraries/Amber10 Ross Walker (Mon May 19 2008 - 10:19:37 PDT)
    - RE: Fw: RE: AMBER: MKL libraries/Amber10 Cenk $Jenk$ Andac (Mon May 19 2008 - 13:40:37 PDT)
    - RE: Fw: RE: AMBER: MKL libraries/Amber10 Ross Walker (Mon May 19 2008 - 14:25:45 PDT)
    - RE: Fw: RE: AMBER: MKL libraries/Amber10 Cenk $Jenk$ Andac (Mon May 19 2008 - 14:18:11 PDT)
    - RE: Fw: RE: AMBER: MKL libraries/Amber10 Francesco Pietra (Mon May 19 2008 - 14:17:25 PDT)
    - RE: Fw: RE: AMBER: MKL libraries/Amber10 Cenk $Jenk$ Andac (Thu May 22 2008 - 15:24:33 PDT)
    - RE: Fw: RE: AMBER: MKL libraries/Amber10 Cenk $Jenk$ Andac (Sat May 24 2008 - 05:26:37 PDT)
    - RE: Fw: RE: AMBER: MKL libraries/Amber10 Cenk $Jenk$ Andac (Thu May 29 2008 - 17:24:38 PDT)
    - RE: Fw: RE: AMBER: MKL libraries/Amber10 Ross Walker (Thu May 29 2008 - 21:50:30 PDT)
    - RE: Fw: RE: AMBER: MKL libraries/Amber10 Francesco Pietra (Fri May 30 2008 - 02:40:41 PDT)
    - RE: Fw: RE: AMBER: MKL libraries/Amber10 Ross Walker (Fri May 30 2008 - 15:41:51 PDT)
    - RE: Fw: RE: AMBER: MKL libraries/Amber10 Francesco Pietra (Fri May 30 2008 - 23:44:24 PDT)
    - Fw: RE: Fw: RE: AMBER: MKL libraries/Amber10 Francesco Pietra (Sat May 31 2008 - 07:22:35 PDT)
    - Re: AMBER: MKL libraries/Amber10 David A. Case (Fri May 16 2008 - 13:27:40 PDT)
    - Re: AMBER: MKL libraries/Amber10 Thomas Patko (Fri May 16 2008 - 14:26:33 PDT)
    - AMBER: Versions of mopac David A. Case (Fri May 16 2008 - 19:04:10 PDT)
- RE: Fw: RE: AMBER: MKL libraries/Amber10 Cenk $Jenk$ Andac (Wed May 21 2008 - 06:33:35 PDT)
  - RE: Fw: RE: AMBER: MKL libraries/Amber10 Ross Walker (Wed May 21 2008 - 11:05:20 PDT)
    - RE: Fw: RE: AMBER: MKL libraries/Amber10 Francesco Pietra (Wed May 21 2008 - 12:09:10 PDT)
    - RE: Fw: RE: AMBER: MKL libraries/Amber10 Francesco Pietra (Thu May 22 2008 - 03:06:48 PDT)
    - RE: Fw: RE: AMBER: MKL libraries/Amber10 Cenk $Jenk$ Andac (Thu May 22 2008 - 15:28:34 PDT)
    - RE: Fw: RE: AMBER: MKL libraries/Amber10 Cenk $Jenk$ Andac (Thu May 22 2008 - 15:29:55 PDT)
    - RE: Fw: RE: AMBER: MKL libraries/Amber10 Ross Walker (Thu May 22 2008 - 15:40:54 PDT)
    - RE: Fw: RE: AMBER: MKL libraries/Amber10 Cenk $Jenk$ Andac (Fri May 23 2008 - 07:57:48 PDT)
    - RE: Fw: RE: AMBER: MKL libraries/Amber10 Cenk $Jenk$ Andac (Fri May 23 2008 - 09:35:36 PDT)
    - AMBER: Restart MD Simulation dpandit.brandeis.edu (Fri May 23 2008 - 14:56:23 PDT)
    - RE: AMBER: Restart MD Simulation Ross Walker (Fri May 23 2008 - 15:28:16 PDT)
    - AMBER: ff94 vs. ff03 Swarup Gupta (Fri May 23 2008 - 17:26:46 PDT)
    - RE: AMBER: ff94 vs. ff03 Ross Walker (Fri May 23 2008 - 19:58:45 PDT)
    - RE: AMBER: Restart MD Simulation dpandit.brandeis.edu (Sat May 24 2008 - 06:40:40 PDT)
    - RE: Fw: RE: AMBER: MKL libraries/Amber10 Cenk $Jenk$ Andac (Sat May 24 2008 - 05:02:34 PDT)
AMBER: RESP and Jaguar Seth Lilavivat (Thu May 15 2008 - 13:52:35 PDT)
AMBER: solvatebox error WANG,YING (Thu May 15 2008 - 14:47:06 PDT)
- RE: AMBER: solvatebox error Ross Walker (Thu May 15 2008 - 14:54:08 PDT)
- RE: AMBER: solvatebox error WANG,YING (Thu May 15 2008 - 15:16:17 PDT)
AMBER: reading PDB trajectory Mark Abraham (Thu May 15 2008 - 20:49:55 PDT)
AMBER: PGI amber9 problems Lorenzo Gontrani (Fri May 16 2008 - 02:52:21 PDT)
- Re: AMBER: PGI amber9 problems David A. Case (Fri May 16 2008 - 04:29:06 PDT)
  - Re: AMBER: PGI amber9 problems Lorenzo Gontrani (Fri May 16 2008 - 05:02:53 PDT)
    - RE: AMBER: PGI amber9 problems Ross Walker (Fri May 16 2008 - 11:06:14 PDT)
AMBER: RESP charges of an unusual substrate Jiayun Pang (Fri May 16 2008 - 03:45:54 PDT)
- Re: AMBER: RESP charges of an unusual substrate FyD (Sun May 18 2008 - 23:46:40 PDT)
AMBER: STEERED MD fatima.chami.durham.ac.uk (Fri May 16 2008 - 09:25:55 PDT)
- Re: AMBER: STEERED MD Robert Duke (Fri May 16 2008 - 10:15:40 PDT)
- Re: AMBER: STEERED MD Robert Duke (Fri May 16 2008 - 10:29:29 PDT)
  - Re: AMBER: STEERED MD fatima.chami.durham.ac.uk (Sat May 17 2008 - 03:26:28 PDT)
- Re: AMBER: STEERED MD Robert Duke (Sat May 17 2008 - 06:21:10 PDT)
AMBER: build proline Qiuting Hong (Fri May 16 2008 - 14:32:47 PDT)
AMBER: Amber 10 ambpdb bug? Sam Danziger (Sat May 17 2008 - 19:17:44 PDT)
- Re: AMBER: Amber 10 ambpdb bug? David A. Case (Sat May 17 2008 - 21:37:09 PDT)
  - Re: AMBER: Amber 10 ambpdb bug? Sam Danziger (Sun May 18 2008 - 20:41:43 PDT)
AMBER: ambertools: static linking of user binaries is not supported on Mac OS X Alan (Mon May 19 2008 - 02:39:32 PDT)
- Re: AMBER: ambertools: static linking of user binaries is not supported on Mac OS X Hans Martin Senn (Mon May 19 2008 - 03:35:24 PDT)
AMBER: parameters in ff03 and ff99 Peter Kiss (Mon May 19 2008 - 04:21:21 PDT)
AMBER: Hybrid REMD amber10 Geoff Wood (Mon May 19 2008 - 05:41:54 PDT)
- RE: AMBER: Hybrid REMD amber10 Ross Walker (Mon May 19 2008 - 08:51:13 PDT)
  - Re: AMBER: Hybrid REMD amber10 Carlos Simmerling (Mon May 19 2008 - 23:55:06 PDT)
    - Re: AMBER: Hybrid REMD amber10 Geoff Wood (Tue May 20 2008 - 07:24:11 PDT)
AMBER: anal Marina Grabar (Mon May 19 2008 - 06:30:13 PDT)
- Re: AMBER: anal David A. Case (Tue May 20 2008 - 01:25:13 PDT)
  - Re: AMBER: anal Marina Grabar (Tue May 20 2008 - 02:20:04 PDT)
AMBER: nfft1-3 too large WANG,YING (Mon May 19 2008 - 07:46:51 PDT)
AMBER: gasteiger is not working with ambertools 1.0 Alan (Mon May 19 2008 - 07:51:05 PDT)
- Re: AMBER: gasteiger is not working with ambertools 1.0 David A. Case (Mon Jun 02 2008 - 17:12:55 PDT)
  - Re: AMBER: gasteiger is not working with ambertools 1.0 Alan (Tue Jun 03 2008 - 07:44:07 PDT)
AMBER: atom type in glycam06 tinni sona (Mon May 19 2008 - 10:06:57 PDT)
- Re: AMBER: atom type in glycam06 Lachele Foley (Lists) (Wed May 21 2008 - 06:37:51 PDT)
AMBER: bye frustrated modeller (Mon May 19 2008 - 11:29:40 PDT)
- Re: AMBER: bye Sara Alexandra Moura (Tue May 20 2008 - 07:14:51 PDT)
AMBER: analysis REMD rebeca (Mon May 19 2008 - 11:41:15 PDT)
- Re: AMBER: analysis REMD Carlos Simmerling (Mon May 19 2008 - 23:51:22 PDT)
  - Re: AMBER: analysis REMD rebeca.mmb.pcb.ub.es (Tue May 20 2008 - 03:49:00 PDT)
- Re: AMBER: analysis REMD Carlos Simmerling (Tue May 20 2008 - 05:11:29 PDT)
  - Re: AMBER: analysis REMD rebeca.mmb.pcb.ub.es (Tue May 20 2008 - 11:31:30 PDT)
    - Re: AMBER: analysis REMD Adrian Roitberg (Tue May 20 2008 - 12:17:39 PDT)
    - Re: AMBER: analysis REMD rebeca.mmb.pcb.ub.es (Wed May 21 2008 - 10:03:59 PDT)
    - Re: AMBER: analysis REMD Carlos Simmerling (Wed May 21 2008 - 10:18:06 PDT)
AMBER: 3rd Annual CMM Workshop on QM/MM Simulations Ross Walker (Mon May 19 2008 - 16:33:55 PDT)
- AMBER: parallel test / libmpi_f90.so.0 Arturas Ziemys (Wed May 28 2008 - 08:10:36 PDT)
  - Re: AMBER: parallel test / libmpi_f90.so.0 Arturas Ziemys (Wed May 28 2008 - 08:24:14 PDT)
AMBER: MM-PBSA for carbohydrates Neha Gandhi (Mon May 19 2008 - 19:07:24 PDT)
- Re: AMBER: MM-PBSA for carbohydrates Navnit Kumar Mishra (Tue May 20 2008 - 04:25:20 PDT)
AMBER: massively parallel computation Mingfeng Yang (Tue May 20 2008 - 00:03:51 PDT)
- Re: AMBER: massively parallel computation Adrian Roitberg (Tue May 20 2008 - 07:11:46 PDT)
  - Re: AMBER: massively parallel computation Lars Skjærven (Tue May 20 2008 - 07:28:24 PDT)
    - Re: AMBER: massively parallel computation Atro Tossavainen (Wed May 21 2008 - 00:17:10 PDT)
    - Re: AMBER: massively parallel computation Robert Duke (Wed May 21 2008 - 10:37:34 PDT)
    - Re: AMBER: massively parallel computation Atro Tossavainen (Wed May 21 2008 - 10:49:03 PDT)
- Re: AMBER: massively parallel computation Robert Duke (Tue May 20 2008 - 07:22:56 PDT)
  - Re: AMBER: massively parallel computation Mingfeng Yang (Tue May 20 2008 - 09:58:56 PDT)
- Re: AMBER: massively parallel computation Robert Duke (Tue May 20 2008 - 07:32:22 PDT)
- Re: AMBER: massively parallel computation Robert Duke (Tue May 20 2008 - 07:46:34 PDT)
AMBER: xLeap compilation issues Sasha Buzko (Tue May 20 2008 - 16:41:49 PDT)
- Re: AMBER: xLeap compilation issues David A. Case (Tue May 20 2008 - 22:27:53 PDT)
  - Re: AMBER: xLeap compilation issues Sasha Buzko (Wed May 21 2008 - 08:52:00 PDT)
AMBER: How to set a ZN atom radius for PB calculations Sam Danziger (Tue May 20 2008 - 17:23:30 PDT)
- RE: AMBER: How to set a ZN atom radius for PB calculations Ray Luo (Thu May 22 2008 - 13:41:36 PDT)
AMBER: Regarding binding free energy calculation using MM_PBSA method nag raj (Wed May 21 2008 - 00:01:14 PDT)
- RE: AMBER: Regarding binding free energy calculation using MM_PBSA method nag raj (Thu May 22 2008 - 05:18:59 PDT)
AMBER: $AMBERHOME/dat/slko Francesco Pietra (Wed May 21 2008 - 05:47:59 PDT)
- Re: AMBER: $AMBERHOME/dat/slko Gustavo Seabra (Wed May 21 2008 - 07:29:35 PDT)
  - Re: AMBER: $AMBERHOME/dat/slko Francesco Pietra (Thu May 22 2008 - 02:14:55 PDT)
    - RE: AMBER: $AMBERHOME/dat/slko Ross Walker (Thu May 22 2008 - 08:24:47 PDT)
    - RE: AMBER: $AMBERHOME/dat/slko Francesco Pietra (Thu May 22 2008 - 08:44:10 PDT)
    - Re: AMBER: $AMBERHOME/dat/slko Gustavo Seabra (Thu May 22 2008 - 10:00:36 PDT)
    - Re: AMBER: $AMBERHOME/dat/slko Francesco Pietra (Thu May 22 2008 - 10:48:49 PDT)
    - Re: AMBER: $AMBERHOME/dat/slko Gustavo Seabra (Thu May 22 2008 - 11:41:41 PDT)
AMBER: ptraj analyze matrix Seth Lilavivat (Wed May 21 2008 - 07:53:28 PDT)
AMBER: amber tools installation vijayaraj.clri.info (Wed May 21 2008 - 08:22:37 PDT)
- Re: AMBER: amber tools installation David A. Case (Wed May 21 2008 - 08:30:32 PDT)
  - Re: AMBER: amber tools installation vijayaraj.clri.info (Thu May 22 2008 - 01:55:00 PDT)
AMBER: pressure regulation methods Vlad Cojocaru (Wed May 21 2008 - 09:25:08 PDT)
AMBER: ff99 and ff03 forcefield parameters Peter Kiss (Wed May 21 2008 - 14:01:47 PDT)
- Re: AMBER: ff99 and ff03 forcefield parameters Vlad Cojocaru (Fri May 23 2008 - 02:31:47 PDT)
  - Re: AMBER: ff99 and ff03 forcefield parameters Vlad Cojocaru (Fri May 23 2008 - 02:43:38 PDT)
    - Re: AMBER: ff99 and ff03 forcefield parameters Peter Kiss (Fri May 23 2008 - 07:27:15 PDT)
    - Re: AMBER: ff99 and ff03 forcefield parameters Vlad Cojocaru (Fri May 23 2008 - 08:52:03 PDT)
    - Re: AMBER: ff99 and ff03 forcefield parameters Peter Kiss (Fri May 23 2008 - 11:42:48 PDT)
AMBER: Parallel Self-guided Langevin simulation Dirar Homouz (Wed May 21 2008 - 15:23:27 PDT)
- Re: AMBER: Parallel Self-guided Langevin simulation David A. Case (Thu May 22 2008 - 03:16:23 PDT)
  - RE: AMBER: Parallel Self-guided Langevin simulation Dirar Homouz (Thu May 22 2008 - 08:58:27 PDT)
    - Re: AMBER: Parallel Self-guided Langevin simulation David A. Case (Sun May 25 2008 - 23:06:03 PDT)
    - RE: AMBER: Parallel Self-guided Langevin simulation Dirar Homouz (Tue May 27 2008 - 23:31:03 PDT)
    - Re: AMBER: Parallel Self-guided Langevin simulation David A. Case (Wed May 28 2008 - 09:46:55 PDT)
    - RE: AMBER: Parallel Self-guided Langevin simulation Dirar Homouz (Wed May 28 2008 - 22:18:34 PDT)
AMBER: about hydrogen bond in amber force field WANG,YING (Wed May 21 2008 - 19:24:47 PDT)
- RE: AMBER: about hydrogen bond in amber force field Ross Walker (Wed May 21 2008 - 20:32:06 PDT)
- Re: AMBER: about hydrogen bond in amber force field Carlos Simmerling (Thu May 22 2008 - 00:08:08 PDT)
AMBER: COM RESTRAINT fatima.chami.durham.ac.uk (Thu May 22 2008 - 05:17:09 PDT)
- Re: AMBER: COM RESTRAINT David A. Case (Thu May 22 2008 - 22:19:24 PDT)
AMBER: potassium ion Lars Skjærven (Thu May 22 2008 - 06:09:59 PDT)
- Re: AMBER: potassium ion Bill Ross (Sat Jun 14 2008 - 13:04:31 PDT)
AMBER: amber10 installation vijayaraj.clri.info (Thu May 22 2008 - 07:22:47 PDT)
- Re: AMBER: amber10 installation Ibrahim Moustafa (Thu May 22 2008 - 08:03:15 PDT)
  - AMBER: Force field in water and in vacuum ?? Chih-Ying Lin (Thu May 22 2008 - 08:46:15 PDT)
    - RE: AMBER: Force field in water and in vacuum ?? Ross Walker (Thu May 22 2008 - 09:06:36 PDT)
- RE: AMBER: amber10 installation Ross Walker (Thu May 22 2008 - 08:40:20 PDT)
AMBER: AMBER file preparation for protein-carbohydrate complex Neha Gandhi (Thu May 22 2008 - 07:31:50 PDT)
- Re: AMBER: AMBER file preparation for protein-carbohydrate complex Lachele Foley (Lists) (Thu May 22 2008 - 14:39:44 PDT)
  - Re: AMBER: AMBER file preparation for protein-carbohydrate complex n.gandhiau.gmail.com (Sun May 25 2008 - 00:17:55 PDT)
    - Re: AMBER: AMBER file preparation for protein-carbohydrate complex Karl Kirschner (Sun May 25 2008 - 02:25:35 PDT)
AMBER: Bond-angle-dihedral-improper-vdw energy terms for part of a system Pavan G (Thu May 22 2008 - 08:37:56 PDT)
- RE: AMBER: Bond-angle-dihedral-improper-vdw energy terms for part of a system Ross Walker (Thu May 22 2008 - 08:54:51 PDT)
Re: AMBER: potassium ion Bill Ross (Thu May 22 2008 - 11:27:21 PDT)
- Re: AMBER: potassium ion Lars Skjærven (Thu Jun 12 2008 - 10:46:36 PDT)
AMBER: Calculate the RESP charge Fe3+ of heme (p450) chen bents (Thu May 22 2008 - 19:16:12 PDT)
- Re: AMBER: Calculate the RESP charge Fe3+ of heme (p450) David A. Case (Thu May 22 2008 - 22:35:29 PDT)
AMBER: self-diffusion coefficient and Berendsen Jennifer.Thomas.cbt.uhp-nancy.fr (Fri May 23 2008 - 01:03:49 PDT)
- Re: AMBER: self-diffusion coefficient and Berendsen Andreas Svrcek-Seiler (Fri May 23 2008 - 02:22:57 PDT)
- Re: AMBER: self-diffusion coefficient and Berendsen David A. Case (Sat May 24 2008 - 13:20:27 PDT)
  - Re: AMBER: self-diffusion coefficient and Berendsen Jennifer.Thomas.cbt.uhp-nancy.fr (Sun May 25 2008 - 03:47:22 PDT)
    - Re: AMBER: self-diffusion coefficient and Berendsen David A. Case (Sun May 25 2008 - 21:09:32 PDT)
AMBER: help MD running error Qiuting Hong (Fri May 23 2008 - 01:40:12 PDT)
- RE: AMBER: help MD running error Ross Walker (Fri May 23 2008 - 08:30:03 PDT)
AMBER: PBC in 2D fatima.chami.durham.ac.uk (Fri May 23 2008 - 06:13:39 PDT)
AMBER: how generate the final output file using mmpbsa luzhenw1.msu.edu (Fri May 23 2008 - 13:49:33 PDT)
- Re: AMBER: how generate the final output file using mmpbsa Miguel Ortiz-Lombardía (Fri May 23 2008 - 23:40:40 PDT)
AMBER: how to extract energy WANG,YING (Fri May 23 2008 - 18:08:13 PDT)
- RE: AMBER: how to extract energy Ross Walker (Fri May 23 2008 - 20:07:41 PDT)
  - RE: AMBER: how to extract energy Francesco Pietra (Sat May 24 2008 - 00:24:13 PDT)
  - Re: AMBER: how to extract energy David A. Case (Sat May 24 2008 - 13:21:22 PDT)
- RE: AMBER: how to extract energy WANG,YING (Sun May 25 2008 - 06:57:20 PDT)
AMBER: periodic bondary condition WANG,YING (Fri May 23 2008 - 18:16:34 PDT)
- RE: AMBER: periodic boundary condition Ross Walker (Fri May 23 2008 - 20:09:39 PDT)
AMBER: ptraj mask not working with psf file Dong Xu (Fri May 23 2008 - 19:53:27 PDT)
AMBER: Amber9 vs Amber10+MKL benchmark Francesco Pietra (Sat May 24 2008 - 06:48:12 PDT)
AMBER: Fw: Amber9 vs Amber10+MKL benchmark Francesco Pietra (Sat May 24 2008 - 06:51:53 PDT)
AMBER: calculating the energy from the restart file priya priya (Sat May 24 2008 - 07:03:46 PDT)
AMBER: Fw: Amber9 vs Amber10+MKL benchmark Francesco Pietra (Sat May 24 2008 - 07:50:45 PDT)
AMBER: caculating nonpolar solvation energies ke dong (Sat May 24 2008 - 07:53:17 PDT)
AMBER: trajectories into trajectory Hakkim Boy (Sun May 25 2008 - 04:30:22 PDT)
- Re: AMBER: trajectories into trajectory Florian Haberl (Sun May 25 2008 - 05:10:41 PDT)
AMBER: mass weighted rms fit Dong Xu (Sun May 25 2008 - 09:11:43 PDT)
- Re: AMBER: mass weighted rms fit Adrian Roitberg (Sun May 25 2008 - 09:26:11 PDT)
  - AMBER: using amber ports in Gromacs Cristina Sisu (Sun May 25 2008 - 11:28:26 PDT)
    - Re: AMBER: using amber ports in Gromacs Carlos Simmerling (Sun May 25 2008 - 12:32:05 PDT)
AMBER: using amber ports in gromacs Cristina Sisu (Sun May 25 2008 - 11:22:58 PDT)
AMBER: is in vacuo simulation neccessary? Anamika Awasthi (Sun May 25 2008 - 22:18:58 PDT)
- Re: AMBER: is in vacuo simulation neccessary? Mark Abraham (Sun May 25 2008 - 22:44:20 PDT)
AMBER: Umbrella Sampling for proteins German Erlenkamp (Mon May 26 2008 - 02:23:56 PDT)
AMBER: peptide at the box center during NVT-MD Darek Czapiewski (Mon May 26 2008 - 03:01:45 PDT)
- Re: AMBER: peptide at the box center during NVT-MD David A. Case (Mon May 26 2008 - 09:09:51 PDT)
AMBER: B-factor calculation from data with different write frequencies Sally Pias (Mon May 26 2008 - 21:19:42 PDT)
- Re: AMBER: B-factor calculation from data with different write frequencies Bill Ross (Wed May 28 2008 - 10:47:28 PDT)
  - Re: AMBER: B-factor calculation from data with different write frequencies Adrian Roitberg (Wed May 28 2008 - 10:54:09 PDT)
- Re: AMBER: B-factor calculation from data with different write frequencies Bill Ross (Wed May 28 2008 - 11:11:30 PDT)
  - Re: AMBER: B-factor calculation from data with different write frequencies Adrian Roitberg (Wed May 28 2008 - 11:58:53 PDT)
- Re: AMBER: B-factor calculation from data with different write frequencies Bill Ross (Wed May 28 2008 - 11:18:06 PDT)
AMBER: Which is best temperature controlling method sudipta sinha (Tue May 27 2008 - 03:25:02 PDT)
- Re: AMBER: Which is best temperature controlling method David A. Case (Tue May 27 2008 - 21:59:23 PDT)
  - Re: AMBER: Which is best temperature controlling method Reena ..... (Tue May 27 2008 - 22:34:39 PDT)
    - Re: AMBER: Which is best temperature controlling method sudipta sinha (Tue May 27 2008 - 23:43:32 PDT)
    - Re: AMBER: Which is best temperature controlling method Mark Abraham (Wed May 28 2008 - 00:02:14 PDT)
    - Re: AMBER: Which is best temperature controlling method David A. Case (Wed May 28 2008 - 10:32:33 PDT)
    - Re: AMBER: Which is best temperature controlling method Adrian Roitberg (Wed May 28 2008 - 10:43:09 PDT)
    - Re: AMBER: Which is best temperature controlling method sudipta sinha (Wed May 28 2008 - 11:02:53 PDT)
    - Re: AMBER: Which is best temperature controlling method Germain Vallverdu (Wed May 28 2008 - 13:24:55 PDT)
    - Re: AMBER: Which is best temperature controlling method David A. Case (Thu May 29 2008 - 07:35:36 PDT)
- Re: AMBER: Which is best temperature controlling method Robert Duke (Thu May 29 2008 - 05:19:22 PDT)
Re: AMBER: B-factor calculation from data with different write frequencies Bill Ross (Tue May 27 2008 - 09:44:23 PDT)
- Re: AMBER: B-factor calculation from data with different write frequencies Sally Pias (Tue May 27 2008 - 20:42:13 PDT)
AMBER: error when read inpcrd WANG,YING (Tue May 27 2008 - 13:32:02 PDT)
- RE: AMBER: error when read inpcrd Ross Walker (Tue May 27 2008 - 13:50:23 PDT)
- RE: AMBER: error when read inpcrd WANG,YING (Tue May 27 2008 - 14:14:02 PDT)
AMBER: bugfix (imin=5) in amber9 Xioling Chuang (Tue May 27 2008 - 21:23:09 PDT)
- Re: AMBER: bugfix (imin=5) in amber9 David A. Case (Tue May 27 2008 - 22:16:40 PDT)
AMBER: compilation problem with AMBER10 bhargav patel (Tue May 27 2008 - 22:56:15 PDT)
- Re: AMBER: compilation problem with AMBER10 Atro Tossavainen (Wed May 28 2008 - 01:04:09 PDT)
AMBER: Hydration free energies of charged ions using PME Markus Kaukonen (Tue May 27 2008 - 23:51:26 PDT)
- Re: AMBER: Hydration free energies of charged ions using PME David A. Case (Wed May 28 2008 - 09:51:26 PDT)
AMBER: install amber tools Alejandro Valbuena (Wed May 28 2008 - 03:14:35 PDT)
- AMBER: energy pairwise decomposition in GB/SA simulation wfli.biophy.nju.edu.cn (Wed May 28 2008 - 03:29:42 PDT)
- Re: AMBER: install amber tools David A. Case (Wed May 28 2008 - 09:56:30 PDT)
AMBER: Segmentation faults trying to run sander mpi Idan Gabdank (Wed May 28 2008 - 03:59:09 PDT)
- Re: AMBER: Segmentation faults trying to run sander mpi David A. Case (Wed May 28 2008 - 10:00:34 PDT)
- Re: AMBER: Segmentation faults trying to run sander mpi Idan Gabdank (Thu May 29 2008 - 07:57:07 PDT)
  - Re: AMBER: Segmentation faults trying to run sander mpi David A. Case (Thu May 29 2008 - 08:20:08 PDT)
AMBER: restarting molecular dynamics Germain Vallverdu (Wed May 28 2008 - 06:18:16 PDT)
- Re: AMBER: restarting molecular dynamics Adrian Roitberg (Wed May 28 2008 - 06:34:17 PDT)
  - Re: AMBER: restarting molecular dynamics Germain Vallverdu (Wed May 28 2008 - 07:25:23 PDT)
    - Re: AMBER: restarting molecular dynamics Adrian Roitberg (Wed May 28 2008 - 08:48:45 PDT)
AMBER: mbondi radii for gaff atom types Sara J (Wed May 28 2008 - 08:03:52 PDT)
- Re: AMBER: mbondi radii for gaff atom types David A. Case (Wed May 28 2008 - 10:31:30 PDT)
AMBER: note on the molsurf and "Assertion `sarg1 >= 0.0' failed" error Kateryna Miroshnychenko (Wed May 28 2008 - 08:08:19 PDT)
- Re: AMBER: note on the molsurf and "Assertion `sarg1 >= 0.0' failed" error David A. Case (Wed May 28 2008 - 10:27:31 PDT)
  - Re: AMBER: note on the molsurf and "Assertion `sarg1 >= 0.0' failed" error Kateryna Miroshnychenko (Thu May 29 2008 - 00:22:17 PDT)
    - Re: AMBER: note on the molsurf and "Assertion `sarg1 >= 0.0' failed" error David A. Case (Mon Jun 02 2008 - 16:23:46 PDT)
    - Re: AMBER: note on the molsurf and "Assertion `sarg1 >= 0.0' failed" error Kateryna Miroshnychenko (Tue Jun 03 2008 - 00:05:51 PDT)
AMBER: protonate in Amber10 Benjamin Juhl (Wed May 28 2008 - 07:55:06 PDT)
- Re: AMBER: protonate in Amber10 David A. Case (Thu May 29 2008 - 14:10:34 PDT)
AMBER: rmsd vs frame Francesco Pietra (Wed May 28 2008 - 15:56:24 PDT)
AMBER: Fw: rmsd vs frame Francesco Pietra (Wed May 28 2008 - 16:19:11 PDT)
AMBER: VMD Movie Campbell, Patrick (Wed May 28 2008 - 16:33:39 PDT)
- Re: AMBER: VMD Movie Carlos Simmerling (Wed May 28 2008 - 17:10:03 PDT)
AMBER: silhouette width/coefficient after clustering by PTRAJ9.9 Dong Xu (Wed May 28 2008 - 22:56:48 PDT)
AMBER: ligand unit charge is not zero amor san juan (Thu May 29 2008 - 01:44:58 PDT)
- Re: AMBER: ligand unit charge is not zero mori.cerm.unifi.it (Thu May 29 2008 - 02:17:55 PDT)
  - Re: AMBER: ligand unit charge is not zero amor san juan (Thu May 29 2008 - 05:32:57 PDT)
    - Re: AMBER: ligand unit charge is not zero Swarup Gupta (Thu May 29 2008 - 05:48:13 PDT)
- AMBER: how to overcome theunusual bonds formation Thomas Leonard (Thu May 29 2008 - 04:03:29 PDT)
  - Re: AMBER: how to overcome theunusual bonds formation Florian Haberl (Thu May 29 2008 - 04:54:20 PDT)
    - Re: AMBER: how to overcome theunusual bonds formation Thomas Leonard (Thu May 29 2008 - 05:01:43 PDT)
    - Re: AMBER: how to overcome theunusual bonds formation Adrian Roitberg (Thu May 29 2008 - 05:07:14 PDT)
    - Re: AMBER: how to overcome theunusual bonds formation Swarup Gupta (Thu May 29 2008 - 05:27:36 PDT)
AMBER: solvatebox fatima.chami.durham.ac.uk (Thu May 29 2008 - 04:46:42 PDT)
- RE: AMBER: solvatebox Ross Walker (Thu May 29 2008 - 08:22:53 PDT)
AMBER: Installing PMEMD with Amber10 Justin A. Lemkul (Thu May 29 2008 - 06:23:05 PDT)
- Re: AMBER: Installing PMEMD with Amber10 Robert Duke (Thu May 29 2008 - 07:44:38 PDT)
  - Re: AMBER: Installing PMEMD with Amber10 Justin A. Lemkul (Thu May 29 2008 - 12:12:26 PDT)
- Re: AMBER: Installing PMEMD with Amber10 Robert Duke (Thu May 29 2008 - 13:16:39 PDT)
  - Re: AMBER: Installing PMEMD with Amber10 Justin A. Lemkul (Thu May 29 2008 - 13:41:30 PDT)
- Re: AMBER: Installing PMEMD with Amber10 Atro Tossavainen (Thu May 29 2008 - 23:42:02 PDT)
  - Re: AMBER: Installing PMEMD with Amber10 Justin A. Lemkul (Fri May 30 2008 - 03:42:53 PDT)
    - Re: AMBER: Installing PMEMD with Amber10 Atro Tossavainen (Sat May 31 2008 - 04:23:31 PDT)
    - Re: AMBER: Installing PMEMD with Amber10 Justin A. Lemkul (Sat May 31 2008 - 05:24:30 PDT)
AMBER: VMD Movie 2 Campbell, Patrick (Thu May 29 2008 - 10:39:20 PDT)
- Re: AMBER: VMD Movie 2 Carlos Simmerling (Thu May 29 2008 - 10:48:10 PDT)
AMBER: ptraj rmsd calculation Pavan G (Thu May 29 2008 - 11:08:36 PDT)
AMBER: VMD Movie 3 Campbell, Patrick (Thu May 29 2008 - 11:12:20 PDT)
- RE: AMBER: VMD Movie 3 Ross Walker (Thu May 29 2008 - 11:47:52 PDT)
  - AMBER: NTC and NTF dpandit.brandeis.edu (Thu May 29 2008 - 12:18:14 PDT)
    - RE: AMBER: NTC and NTF Ross Walker (Thu May 29 2008 - 12:30:28 PDT)
    - RE: AMBER: NTC and NTF dpandit.brandeis.edu (Thu May 29 2008 - 12:39:33 PDT)
  - Re: AMBER: VMD Movie 3 Ibrahim Moustafa (Thu May 29 2008 - 14:03:16 PDT)
AMBER: VMD Movie 4 Campbell, Patrick (Thu May 29 2008 - 12:37:43 PDT)
AMBER: ptraj has trouble with x-plor psf file from VMD Dong Xu (Thu May 29 2008 - 13:23:56 PDT)
- Re: AMBER: ptraj has trouble with x-plor psf file from VMD Jufang Shan (Mon Jun 02 2008 - 08:52:28 PDT)
AMBER: Ptraj | Multiple trajout commands? Ian (Fri May 30 2008 - 01:39:23 PDT)
- Re: AMBER: Ptraj | Multiple trajout commands? Jianyin Shao (Sat May 31 2008 - 17:02:17 PDT)
AMBER: Jarzynski fatima.chami.durham.ac.uk (Fri May 30 2008 - 04:44:41 PDT)
- Re: AMBER: Jarzynski David Mobley (Fri May 30 2008 - 09:02:28 PDT)
  - Re: AMBER: Jarzynski fatima.chami.durham.ac.uk (Sat May 31 2008 - 04:50:24 PDT)
    - Re: AMBER: Jarzynski David Mobley (Mon Jun 02 2008 - 10:25:16 PDT)
    - AMBER: Vaccum Simulations in PMEMD !! Sampath Koppole (Thu Jun 05 2008 - 05:53:35 PDT)
    - Re: AMBER: Vaccum Simulations in PMEMD !! Robert Duke (Thu Jun 05 2008 - 07:17:13 PDT)
AMBER: nab Joachim Reichelt (Fri May 30 2008 - 02:48:56 PDT)
- Re: AMBER: nab David A. Case (Fri May 30 2008 - 07:55:10 PDT)
AMBER: Iron-Sulfur Cluster Joachim Reichelt (Fri May 30 2008 - 02:46:30 PDT)
- Re: AMBER: Iron-Sulfur Cluster Justine Condo (Fri May 30 2008 - 10:52:24 PDT)
- Re: AMBER: Iron-Sulfur Cluster FyD (Sat May 31 2008 - 05:35:31 PDT)
AMBER: Sander instead of PMEMD Cristina Sisu (Fri May 30 2008 - 06:47:13 PDT)
- Re: AMBER: Sander instead of PMEMD Robert Duke (Fri May 30 2008 - 07:13:20 PDT)
  - Re: AMBER: Sander instead of PMEMD Cristina Sisu (Fri May 30 2008 - 07:32:27 PDT)
    - Re: AMBER: Sander instead of PMEMD Florian Haberl (Fri May 30 2008 - 08:06:42 PDT)
    - Re: AMBER: Sander instead of PMEMD Francesco Pietra (Fri May 30 2008 - 08:17:15 PDT)
    - Re: AMBER: Sander instead of PMEMD Robert Duke (Fri May 30 2008 - 08:28:24 PDT)
    - Re: AMBER: Sander instead of PMEMD Francesco Pietra (Fri May 30 2008 - 10:59:35 PDT)
    - Re: AMBER: Sander instead of PMEMD Florian Haberl (Fri May 30 2008 - 08:31:18 PDT)
    - RE: AMBER: Sander instead of PMEMD Hu, Shaowen (JSC-SK)[USRA] (Fri May 30 2008 - 09:24:39 PDT)
    - Re: AMBER: Sander instead of PMEMD Francesco Pietra (Fri May 30 2008 - 10:47:57 PDT)
    - Re: AMBER: Sander instead of PMEMD Cristina Sisu (Fri May 30 2008 - 08:22:10 PDT)
- Re: AMBER: Sander instead of PMEMD Robert Duke (Fri May 30 2008 - 07:50:36 PDT)
AMBER: VMD Movie 3 Campbell, Patrick (Fri May 30 2008 - 07:56:41 PDT)
AMBER: tleap error message Wang,Ying (Fri May 30 2008 - 09:08:14 PDT)
AMBER: igb and ibelly Holly Freedman (Fri May 30 2008 - 12:23:21 PDT)
- RE: AMBER: igb and ibelly Ross Walker (Fri May 30 2008 - 13:16:11 PDT)
- Re: AMBER: igb and ibelly David A. Case (Fri May 30 2008 - 13:20:52 PDT)
- RE: AMBER: igb and ibelly Holly Freedman (Fri May 30 2008 - 13:21:06 PDT)
- Re: AMBER: igb and ibelly Holly Freedman (Fri May 30 2008 - 15:36:03 PDT)
AMBER: SANDER and PMEMD with openmpi Ross Walker (Fri May 30 2008 - 15:18:04 PDT)
AMBER: MMPBSA error Cristina Sisu (Sat May 31 2008 - 07:00:08 PDT)
- Re: AMBER: MMPBSA error Peter Gannett (Sat May 31 2008 - 07:15:40 PDT)
  - Re: AMBER: MMPBSA error Cristina Sisu (Sat May 31 2008 - 07:53:32 PDT)
AMBER: ptraj analyze modes from nmode Miguel Ortiz-Lombardía (Sat May 31 2008 - 08:40:50 PDT)
Re: AMBER: SANDER and PMEMD with openmpi. Failure 'make test.pmemd' Francesco Pietra (Sat May 31 2008 - 11:31:04 PDT)
- RE: AMBER: SANDER and PMEMD with openmpi. Failure 'make test.pmemd' Ross Walker (Sat May 31 2008 - 13:57:48 PDT)
  - RE: AMBER: SANDER and PMEMD with openmpi. Failure 'make test.pmemd' Francesco Pietra (Sun Jun 01 2008 - 00:12:12 PDT)
    - RE: AMBER: SANDER and PMEMD with openmpi. Failure 'make test.pmemd' Ross Walker (Mon Jun 02 2008 - 10:52:33 PDT)
AMBER: amber9 , ptraj vector commad issue Vijay Singh (Sat May 31 2008 - 16:34:23 PDT)
AMBER: PCA - analysis Ibrahim Moustafa (Sun Jun 01 2008 - 11:00:35 PDT)
Fw: RE: AMBER: SANDER and PMEMD with openmpi. NO MORE failure 'make test.pmemd' Francesco Pietra (Mon Jun 02 2008 - 03:22:38 PDT)
AMBER: Building ppc64 AMBER10 with xlf fortran 11.1 Jarrod Smith (Mon Jun 02 2008 - 09:43:24 PDT)
- Re: AMBER: Building ppc64 AMBER10 with xlf fortran 11.1 David A. Case (Mon Jun 02 2008 - 10:56:16 PDT)
  - Re: AMBER: Building ppc64 AMBER10 with xlf fortran 11.1 Jarrod Smith (Tue Jun 03 2008 - 12:29:31 PDT)
    - RE: AMBER: Building ppc64 AMBER10 with xlf fortran 11.1 Ross Walker (Tue Jun 03 2008 - 13:43:43 PDT)
AMBER: VMD file generation 4 - mdcrd ptraj analysis Campbell, Patrick (Mon Jun 02 2008 - 11:26:15 PDT)
- Re: AMBER: VMD file generation 4 - mdcrd ptraj analysis Carlos Simmerling (Mon Jun 02 2008 - 12:11:24 PDT)
  - AMBER: MAXAT can not be changed for AMBERTool 1.0 Hu, Shaowen (JSC-SK)[USRA] (Mon Jun 02 2008 - 12:41:54 PDT)
    - Re: AMBER: MAXAT can not be changed for AMBERTool 1.0 David A. Case (Mon Jun 02 2008 - 16:15:38 PDT)
- RE:AMBER: VMD file generation 4 - mdcrd ptraj analysis Campbell, Patrick (Mon Jun 02 2008 - 12:54:06 PDT)
  - Re: AMBER: VMD file generation 4 - mdcrd ptraj analysis Carlos Simmerling (Mon Jun 02 2008 - 13:06:39 PDT)
AMBER: VMD file generation 4 - mdcrd analysis Campbell, Patrick (Mon Jun 02 2008 - 13:21:00 PDT)
AMBER: PCA analysis Ibrahim Moustafa (Mon Jun 02 2008 - 14:09:17 PDT)
AMBER: Missing gaff angle parameters for dimethyl esters Lin, Pohan (Mon Jun 02 2008 - 14:20:24 PDT)
- AMBER: Error message: Install Amber9 on fedora 9 Chih-Ying Lin (Mon Jun 02 2008 - 15:33:42 PDT)
  - Re: AMBER: Error message: Install Amber9 on fedora 9 David A. Case (Mon Jun 02 2008 - 16:04:48 PDT)
    - AMBER: writing a script in amber Taufik Al-Sarraj (Mon Jun 02 2008 - 17:28:39 PDT)
    - Re: AMBER: Error message: Install Amber9 on fedora 9 Chih-Ying Lin (Wed Jun 04 2008 - 20:54:29 PDT)
    - Re: AMBER: Error message: Install Amber9 on fedora 9 David A. Case (Thu Jun 05 2008 - 12:17:50 PDT)
- Re: AMBER: Missing gaff angle parameters for dimethyl esters Junmei Wang (Tue Jun 03 2008 - 06:19:25 PDT)
  - RE: AMBER: Missing gaff angle parameters for dimethyl esters Lin, Pohan (Tue Jun 03 2008 - 12:56:32 PDT)
AMBER: corrupted restart file yavuzturkm.prc.boun.edu.tr (Tue Jun 03 2008 - 02:18:25 PDT)
- Re: AMBER: corrupted restart file Cenk $Jenk$ Andac (Tue Jun 03 2008 - 03:13:29 PDT)
- Re: AMBER: corrupted restart file Carlos Simmerling (Tue Jun 03 2008 - 03:15:21 PDT)
AMBER: Temperature controlling method in AMBER tinni sona (Tue Jun 03 2008 - 02:43:11 PDT)
- Re: AMBER: Temperature controlling method in AMBER David A. Case (Tue Jun 03 2008 - 07:56:51 PDT)
AMBER: Trajectory in "Sietraj" Alfredo Quevedo (Tue Jun 03 2008 - 06:35:20 PDT)
- RE: AMBER: Trajectory in "Sietraj" Purisima, Enrico (Tue Jun 03 2008 - 06:55:20 PDT)
  - Re: AMBER: Trajectory in "Sietraj" Alfredo Quevedo (Tue Jun 03 2008 - 07:08:56 PDT)
    - RE: AMBER: Trajectory in "Sietraj" Purisima, Enrico (Tue Jun 03 2008 - 07:39:49 PDT)
    - Re: AMBER: Trajectory in "Sietraj" Alfredo Quevedo (Tue Jun 03 2008 - 08:29:24 PDT)
- Re: AMBER: Trajectory in "Sietraj" Florian Haberl (Tue Jun 03 2008 - 06:41:31 PDT)
AMBER: solvate box : buffer list fatima.chami.durham.ac.uk (Tue Jun 03 2008 - 10:51:55 PDT)
- Re: AMBER: solvate box : buffer list David A. Case (Tue Jun 03 2008 - 11:22:16 PDT)
  - Re: AMBER: solvate box : buffer list fatima.chami.durham.ac.uk (Wed Jun 04 2008 - 03:07:06 PDT)
AMBER: problems with sleap Alan (Wed Jun 04 2008 - 08:40:04 PDT)
- Re: AMBER: problems with sleap David A. Case (Wed Jun 04 2008 - 16:52:00 PDT)
  - Re: AMBER: problems with sleap Alan (Wed Jun 04 2008 - 23:48:03 PDT)
    - Re: AMBER: problems with sleap David A. Case (Mon Jun 16 2008 - 08:48:42 PDT)
    - Re: AMBER: problems with sleap Alan (Mon Jun 16 2008 - 09:07:24 PDT)
    - Re: AMBER: problems with sleap Qi Zhang (Mon Jun 16 2008 - 04:46:26 PDT)
AMBER: How to calculate RMSIP after PCA analysis by PTRAJ? sychen (Wed Jun 04 2008 - 05:27:45 PDT)
AMBER: NMODE units and hrmax value for Langevine modes Yang, Lee-Wei (Wed Jun 04 2008 - 09:27:00 PDT)
- Re: AMBER: NMODE units and hrmax value for Langevine modes David A. Case (Wed Jun 04 2008 - 10:30:36 PDT)
  - RE: AMBER: NMODE units and hrmax value for Langevine modes Yang, Lee-Wei (Wed Jun 04 2008 - 20:55:45 PDT)
    - Re: AMBER: NMODE units and hrmax value for Langevine modes David A. Case (Thu Jun 05 2008 - 11:12:24 PDT)
AMBER: amber installation on cluster Pankaj R. Daga (Wed Jun 04 2008 - 10:27:57 PDT)
- Re: AMBER: amber installation on cluster David A. Case (Wed Jun 04 2008 - 10:55:39 PDT)
- RE: AMBER: amber installation on cluster Ross Walker (Wed Jun 04 2008 - 10:54:36 PDT)
AMBER: NAB documentation for programmers ramu.vt.edu (Wed Jun 04 2008 - 11:59:27 PDT)
AMBER: ptraj imaging issue Vlad Cojocaru (Wed Jun 04 2008 - 12:07:44 PDT)
- AMBER: syn and anti conformation Rabin (Wed Jun 04 2008 - 12:29:58 PDT)
  - Re: AMBER: syn and anti conformation Carlos Simmerling (Wed Jun 04 2008 - 12:34:31 PDT)
- Re: AMBER: ptraj imaging issue Jianyin Shao (Wed Jun 04 2008 - 14:25:27 PDT)
  - Re: AMBER: ptraj imaging issue Vlad Cojocaru (Thu Jun 05 2008 - 01:48:43 PDT)
    - Re: AMBER: ptraj imaging issue Vlad Cojocaru (Thu Jun 05 2008 - 07:30:42 PDT)
    - Re: AMBER: ptraj imaging issue Jianyin Shao (Thu Jun 05 2008 - 09:23:52 PDT)
AMBER: MM-PBSA in AMBER 10 Daniel Oehme (Wed Jun 04 2008 - 22:27:39 PDT)
- AMBER: MM-PBSA in AMBER 10 Daniel Oehme (Thu Jun 05 2008 - 20:52:12 PDT)
AMBER: problem of install amber9 Xioling Chuang (Thu Jun 05 2008 - 01:37:27 PDT)
- RE: AMBER: problem of install amber9 Xioling Chuang (Thu Jun 05 2008 - 02:09:27 PDT)
AMBER: NAN errors in Etot, EPtot, EKtot and EELEC Praveena Gopal (Thu Jun 05 2008 - 05:04:00 PDT)
- Re: AMBER: NAN errors in Etot, EPtot, EKtot and EELEC Carlos Simmerling (Thu Jun 05 2008 - 05:16:22 PDT)
  - Re: AMBER: NAN errors in Etot, EPtot, EKtot and EELEC Praveena Gopal (Thu Jun 05 2008 - 23:16:40 PDT)
  - AMBER: NAN errors still exist Praveena Gopal (Fri Jun 06 2008 - 02:56:58 PDT)
    - Re: AMBER: NAN errors still exist Carlos Simmerling (Fri Jun 06 2008 - 03:57:49 PDT)
AMBER: Free energy of dissociation fatima.chami.durham.ac.uk (Thu Jun 05 2008 - 05:02:43 PDT)
- Re: AMBER: Free energy of dissociation Gustavo Seabra (Thu Jun 05 2008 - 06:41:03 PDT)
  - Re: AMBER: Free energy of dissociation fatima.chami.durham.ac.uk (Thu Jun 05 2008 - 08:13:03 PDT)
- Re: AMBER: Free energy of dissociation David Mobley (Thu Jun 05 2008 - 09:22:24 PDT)
AMBER: netcdf configure returned 1 Jens Lattig (Thu Jun 05 2008 - 06:46:45 PDT)
AMBER: netcdf configure returned 1 - PROBLEM SOLVED Jens Lattig (Thu Jun 05 2008 - 07:42:03 PDT)
AMBER: A problem of installing Amber10 Yicun Ni (Thu Jun 05 2008 - 08:55:53 PDT)
- Re: AMBER: A problem of installing Amber10 David A. Case (Thu Jun 05 2008 - 10:49:58 PDT)
  - Re: AMBER: A problem of installing Amber10 Harry Ni (Thu Jun 05 2008 - 11:27:23 PDT)
    - Re: AMBER: A problem of installing Amber10 David A. Case (Thu Jun 05 2008 - 12:13:16 PDT)
    - Re: AMBER: A problem of installing Amber10 Harry Ni (Fri Jun 06 2008 - 12:00:19 PDT)
    - Re: AMBER: A problem of installing Amber10 David A. Case (Fri Jun 06 2008 - 13:21:52 PDT)
    - Re: AMBER: A problem of installing Amber10 Harry Ni (Fri Jun 06 2008 - 14:36:48 PDT)
AMBER: Nmode - entropy calculation of receptor - should I apply restraint? Seth Lilavivat (Thu Jun 05 2008 - 10:03:08 PDT)
- Re: AMBER: Nmode - entropy calculation of receptor - should I apply restraint? David A. Case (Thu Jun 05 2008 - 11:50:16 PDT)
AMBER: RE: solvating RNA in 8M urea box Ross Walker (Thu Jun 05 2008 - 17:12:42 PDT)
AMBER: Query on MM-PBSA Neha Gandhi (Thu Jun 05 2008 - 22:46:32 PDT)
AMBER: PROBLEM: AmberTools Installation using Ubuntu Jens Lattig (Fri Jun 06 2008 - 01:13:06 PDT)
- Re: AMBER: PROBLEM: AmberTools Installation using Ubuntu David Case (Fri Jun 06 2008 - 09:25:45 PDT)
  - Re: AMBER: PROBLEM: AmberTools Installation using Ubuntu Jens Lattig (Tue Jun 10 2008 - 01:00:08 PDT)
    - Re: AMBER: PROBLEM: AmberTools Installation using Ubuntu Mark Williamson (Tue Jun 10 2008 - 04:31:48 PDT)
    - Re: AMBER: PROBLEM: AmberTools Installation using Ubuntu Jens Lattig (Wed Jun 11 2008 - 01:59:12 PDT)
    - AMBER: QM/MM Taufik Al-Sarraj (Wed Jun 11 2008 - 09:09:24 PDT)
    - Re: AMBER: QM/MM Gustavo Seabra (Wed Jun 11 2008 - 08:22:16 PDT)
    - Re: AMBER: QM/MM Taufik Al-Sarraj (Wed Jun 11 2008 - 09:28:34 PDT)
    - AMBER: Equilibration/Heating - Protein fixed -Problem dpandit.brandeis.edu (Wed Jun 11 2008 - 08:31:40 PDT)
    - RE: AMBER: Equilibration/Heating - Protein fixed -Problem Vahdati N. (Wed Jun 11 2008 - 10:38:50 PDT)
    - RE: AMBER: Equilibration/Heating - Protein fixed -Problem dpandit.brandeis.edu (Wed Jun 11 2008 - 11:17:56 PDT)
    - AMBER: Trajectory - Average Structure - Equilibration dpandit.brandeis.edu (Wed Jun 11 2008 - 12:37:46 PDT)
    - Re: AMBER: PROBLEM: AmberTools Installation using Ubuntu David A. Case (Wed Jun 11 2008 - 08:15:00 PDT)
    - Re: AMBER: PROBLEM: AmberTools Installation using Ubuntu Mark Williamson (Sat Jun 14 2008 - 08:13:18 PDT)
    - Re: AMBER: PROBLEM: AmberTools Installation using Ubuntu David A. Case (Sat Jun 14 2008 - 12:09:02 PDT)
AMBER: Ptraj / ambmask | Using distance-based masks to strip a trajectory Ian (Fri Jun 06 2008 - 02:19:58 PDT)
- Re: AMBER: Ptraj / ambmask | Using distance-based masks to strip a trajectory Vlad Cojocaru (Fri Jun 06 2008 - 02:59:54 PDT)
- Re: AMBER: Ptraj / ambmask | Using distance-based masks to strip a trajectory David Case (Fri Jun 06 2008 - 09:27:06 PDT)
  - AMBER: Problems simulating a protein-ligand complex Sasha Buzko (Fri Jun 06 2008 - 10:55:05 PDT)
    - Re: AMBER: Problems simulating a protein-ligand complex David A. Case (Fri Jun 06 2008 - 11:59:52 PDT)
    - Re: AMBER: Problems simulating a protein-ligand complex Sasha Buzko (Fri Jun 06 2008 - 15:16:29 PDT)
    - RE: AMBER: Problems simulating a protein-ligand complex Ross Walker (Fri Jun 06 2008 - 15:55:37 PDT)
    - RE: AMBER: Problems simulating a protein-ligand complex Sasha Buzko (Fri Jun 06 2008 - 16:13:19 PDT)
    - RE: AMBER: Problems simulating a protein-ligand complex Ross Walker (Fri Jun 06 2008 - 16:34:39 PDT)
    - RE: AMBER: Problems simulating a protein-ligand complex Sasha Buzko (Fri Jun 06 2008 - 16:40:07 PDT)
    - RE: AMBER: Problems simulating a protein-ligand complex Ross Walker (Fri Jun 06 2008 - 22:15:32 PDT)
    - Re: AMBER: Problems simulating a protein-ligand complex Sasha Buzko (Fri Jun 06 2008 - 22:37:53 PDT)
    - Re: AMBER: Problems simulating a protein-ligand complex Adrian Roitberg (Sat Jun 07 2008 - 05:36:21 PDT)
    - Re: AMBER: Problems simulating a protein-ligand complex M. L. Dodson (Sat Jun 07 2008 - 07:53:57 PDT)
    - Re: AMBER: Problems simulating a protein-ligand complex Sasha Buzko (Mon Jun 09 2008 - 10:57:20 PDT)
  - Re: AMBER: Ptraj / ambmask | Using distance-based masks to strip a trajectory Vlad Cojocaru (Fri Jun 06 2008 - 11:50:55 PDT)
    - Re: AMBER: Ptraj / ambmask | Using distance-based masks to strip a trajectory Ian (Wed Jun 11 2008 - 03:53:42 PDT)
    - Re: AMBER: Ptraj / ambmask | Using distance-based masks to strip a trajectory Jianyin Shao (Wed Jun 11 2008 - 08:55:12 PDT)
AMBER: Problem While Installing Amber Ranga Swamy (Fri Jun 06 2008 - 02:34:17 PDT)
- RE: AMBER: Problem While Installing Amber Ross Walker (Fri Jun 06 2008 - 08:30:26 PDT)
AMBER: VMD Movie .mdcrd file ptraj Campbell, Patrick (Fri Jun 06 2008 - 06:22:50 PDT)
- Re: AMBER: VMD Movie .mdcrd file ptraj David Watson (Fri Jun 06 2008 - 07:57:16 PDT)
AMBER: NAB documentation David Case (Fri Jun 06 2008 - 09:24:44 PDT)
- Re: AMBER: NAB documentation Ramu Anandakrishnan (Fri Jun 06 2008 - 21:08:51 PDT)
  - Re: AMBER: NAB documentation David A. Case (Sun Jun 08 2008 - 18:38:05 PDT)
Re:AMBER:VMD Movie.mdcrd Campbell, Patrick (Fri Jun 06 2008 - 11:56:52 PDT)
AMBER: 100 short MD runs within a single Sander script? Sebastian Stolzenberg (Fri Jun 06 2008 - 21:55:37 PDT)
- RE: AMBER: 100 short MD runs within a single Sander script? Ross Walker (Fri Jun 06 2008 - 22:22:36 PDT)
AMBER: Problem of Ptraj analyze matrix Qi Yan (Sat Jun 07 2008 - 11:24:55 PDT)
- Re: AMBER: Problem of Ptraj analyze matrix David A. Case (Sun Jun 08 2008 - 18:38:13 PDT)
- RE: AMBER: Problem of Ptraj analyze matrix Qi Yan (Mon Jun 09 2008 - 07:47:16 PDT)
AMBER: Combine mdcrd while stripping WAT problem Francesco Pietra (Sun Jun 08 2008 - 08:40:07 PDT)
- Re: AMBER: Combine mdcrd while stripping WAT problem Gustavo Seabra (Sun Jun 08 2008 - 11:58:34 PDT)
  - Re: AMBER: Combine mdcrd while stripping WAT problem Carlos Simmerling (Sun Jun 08 2008 - 12:33:47 PDT)
    - Re: AMBER: Combine mdcrd while stripping WAT problem Francesco Pietra (Tue Jun 10 2008 - 00:37:34 PDT)
    - Re: AMBER: Combine mdcrd while stripping WAT problem Carlos Simmerling (Tue Jun 10 2008 - 01:03:02 PDT)
    - Re: AMBER: Combine mdcrd while stripping WAT problem Francesco Pietra (Wed Jun 11 2008 - 07:57:59 PDT)
    - Re: AMBER: Combine mdcrd while stripping WAT problem Alexander Metz (Wed Jun 11 2008 - 22:59:18 PDT)
    - Re: AMBER: Combine mdcrd while stripping WAT problem Francesco Pietra (Thu Jun 12 2008 - 00:09:28 PDT)
    - Re: AMBER: Combine mdcrd while stripping WAT problem Alexander Metz (Thu Jun 12 2008 - 01:04:08 PDT)
    - Re: AMBER: Combine mdcrd while stripping WAT problem Carlos Simmerling (Thu Jun 12 2008 - 01:05:15 PDT)
AMBER: problem in starting sander Qiuting Hong (Sun Jun 08 2008 - 11:25:43 PDT)
- Re: AMBER: problem in starting sander Carlos Simmerling (Sun Jun 08 2008 - 12:53:33 PDT)
  - Re: AMBER: problem in starting sander Qiuting Hong (Sun Jun 08 2008 - 14:52:34 PDT)
- RE: AMBER: problem in starting sander Ross Walker (Sun Jun 08 2008 - 15:30:17 PDT)
  - Re: AMBER: problem in starting sander Qiuting Hong (Sun Jun 08 2008 - 19:40:52 PDT)
    - Re: AMBER: problem in starting sander Carlos Simmerling (Sun Jun 08 2008 - 21:36:32 PDT)
AMBER: MM-PBSA and delphi Neha Gandhi (Sun Jun 08 2008 - 22:49:54 PDT)
- Re: AMBER: MM-PBSA and delphi Neha Gandhi (Sun Jun 08 2008 - 22:56:00 PDT)
  - Re: AMBER: MM-PBSA and delphi Navnit Kumar Mishra (Mon Jun 09 2008 - 02:05:38 PDT)
    - Re: AMBER: MM-PBSA and delphi Neha Gandhi (Mon Jun 09 2008 - 02:57:21 PDT)
- RE: AMBER: MM-PBSA and delphi Qi Yan (Mon Jun 09 2008 - 12:58:28 PDT)
AMBER: Problem of Ptraj analyze matrix Qi Yan (Mon Jun 09 2008 - 06:37:01 PDT)
- Re: AMBER: Problem of Ptraj analyze matrix Adrian Roitberg (Mon Jun 09 2008 - 06:51:42 PDT)
AMBER: Calcium and Magnesium LJ parameters Daniel Smith (Mon Jun 09 2008 - 16:02:28 PDT)
AMBER: Help--Great distortion of N terminal nitrogen at the very beginning of heating xiaonan zhang (Tue Jun 10 2008 - 05:24:02 PDT)
- Re: AMBER: Help--Great distortion of N terminal nitrogen at the very beginning of heating David A. Case (Tue Jun 10 2008 - 05:50:27 PDT)
  - Re: AMBER: Help--Great distortion of N terminal nitrogen at the very beginning of heating xiaonan zhang (Tue Jun 10 2008 - 07:23:15 PDT)
    - Re: AMBER: Help--Great distortion of N terminal nitrogen at the very beginning of heating David A. Case (Wed Jun 11 2008 - 10:53:20 PDT)
AMBER: SMD pulling velocity fatima.chami.durham.ac.uk (Tue Jun 10 2008 - 07:06:38 PDT)
- Re: AMBER: SMD pulling velocity Gustavo Seabra (Tue Jun 10 2008 - 07:22:48 PDT)
AMBER: how to calculate the interaction energy Wang,Ying (Tue Jun 10 2008 - 07:52:10 PDT)
- Re: AMBER: how to calculate the interaction energy Thomas Steinbrecher (Tue Jun 10 2008 - 09:45:16 PDT)
  - AMBER: amber10 installation problem Ed Pate (Tue Jun 10 2008 - 13:59:47 PDT)
    - AMBER: PTRAJ - Segmentation Fault dpandit.brandeis.edu (Tue Jun 10 2008 - 14:36:08 PDT)
    - Re: AMBER: PTRAJ - Segmentation Fault Jianyin Shao (Wed Jun 11 2008 - 09:01:07 PDT)
    - Re: AMBER: PTRAJ - Segmentation Fault dpandit.brandeis.edu (Wed Jun 11 2008 - 10:48:54 PDT)
    - Re: AMBER: PTRAJ - Segmentation Fault Thomas Cheatham (Wed Jun 11 2008 - 11:15:00 PDT)
    - Re: AMBER: PTRAJ - Segmentation Fault dpandit.brandeis.edu (Wed Jun 11 2008 - 12:40:25 PDT)
    - Re: AMBER: amber10 installation problem Robert Duke (Tue Jun 10 2008 - 15:02:54 PDT)
    - RE: AMBER: amber10 installation problem Ross Walker (Tue Jun 10 2008 - 15:04:51 PDT)
- Re: AMBER: how to calculate the interaction energy Wang,Ying (Tue Jun 10 2008 - 12:12:17 PDT)
AMBER: Simulating complexes with magnesium atoms Sasha Buzko (Tue Jun 10 2008 - 14:32:13 PDT)
AMBER: box shape changed at NVT fatima.chami.durham.ac.uk (Wed Jun 11 2008 - 07:25:09 PDT)
- Re: AMBER: box shape changed at NVT David A. Case (Wed Jun 11 2008 - 08:18:46 PDT)
AMBER: sander.MPI / openmpi on PBS Arturas Ziemys (Wed Jun 11 2008 - 11:59:52 PDT)
AMBER: 2D RMS plot Steve Spronk (Wed Jun 11 2008 - 12:18:32 PDT)
- Re: AMBER: 2D RMS plot Jianyin Shao (Wed Jun 11 2008 - 15:17:43 PDT)
  - RE: AMBER: 2D RMS plot Steve Spronk (Thu Jun 12 2008 - 05:42:41 PDT)
AMBER: Question for how to get all eigenvalues by "analyze matrix" Qi Yan (Wed Jun 11 2008 - 14:34:40 PDT)
AMBER: Antechamber and topology file TAEJIN KIM (Wed Jun 11 2008 - 16:05:14 PDT)
- Re: AMBER: Antechamber and topology file David A. Case (Thu Jun 12 2008 - 09:03:50 PDT)
AMBER: Coordinated Zinc Khaled Barakat (Wed Jun 11 2008 - 12:29:18 PDT)
- Re: AMBER: Coordinated Zinc David A. Case (Thu Jun 12 2008 - 08:59:42 PDT)
  - Re: AMBER: Coordinated Zinc FyD (Fri Jun 13 2008 - 00:56:08 PDT)
  - AMBER: Simulating protein conformational changes? Sasha Buzko (Fri Aug 01 2008 - 15:42:07 PDT)
    - AMBER: MOIL-View: is there a command line version? Sasha Buzko (Wed Aug 20 2008 - 11:35:24 PDT)
    - Re: AMBER: MOIL-View: is there a command line version? Carlos Simmerling (Wed Aug 20 2008 - 11:46:12 PDT)
    - Re: AMBER: MOIL-View: is there a command line version? Sasha Buzko (Wed Aug 20 2008 - 11:50:39 PDT)
    - AMBER: MOIL-View is for SGI. How do we analyze LES trajectories? Sasha Buzko (Wed Aug 20 2008 - 15:42:01 PDT)
    - Re: AMBER: MOIL-View is for SGI. How do we analyze LES trajectories? Carlos Simmerling (Sat Aug 23 2008 - 05:39:16 PDT)
    - Re: AMBER: MOIL-View is for SGI. How do we analyze LES trajectories? Sasha Buzko (Sat Aug 23 2008 - 13:19:07 PDT)
AMBER: updating documentation Alan (Thu Jun 12 2008 - 02:52:40 PDT)
- Re: AMBER: updating documentation David A. Case (Thu Jun 12 2008 - 08:10:36 PDT)
  - Re: AMBER: updating documentation Alan (Thu Jun 12 2008 - 16:09:24 PDT)
    - Re: AMBER: updating documentation David A. Case (Fri Jun 13 2008 - 09:52:14 PDT)
AMBER: using Velocity-Verlet algorithm oguz gurbulak (Thu Jun 12 2008 - 05:07:20 PDT)
- Re: AMBER: using Velocity-Verlet algorithm David A. Case (Thu Jun 12 2008 - 09:09:49 PDT)
AMBER: anisotropic pressure scaling ntp=2 fatima.chami.durham.ac.uk (Thu Jun 12 2008 - 06:18:13 PDT)
- Re: AMBER: anisotropic pressure scaling ntp=2 David A. Case (Thu Jun 12 2008 - 08:13:52 PDT)
AMBER: SMD RESTRAINTS fatima.chami.durham.ac.uk (Thu Jun 12 2008 - 09:23:00 PDT)
- Re: AMBER: SMD RESTRAINTS Adrian Roitberg (Thu Jun 12 2008 - 09:51:56 PDT)
  - Re: AMBER: SMD RESTRAINTS fatima.chami.durham.ac.uk (Thu Jun 12 2008 - 10:07:49 PDT)
    - Re: AMBER: SMD RESTRAINTS Adrian Roitberg (Thu Jun 12 2008 - 12:23:26 PDT)
AMBER: Compile amber10 parallel with suppied LAM James W. Caldwell (Thu Jun 12 2008 - 09:31:03 PDT)
- RE: AMBER: Compile amber10 parallel with suppied LAM James W. Caldwell (Thu Jun 12 2008 - 10:32:13 PDT)
  - Re: AMBER: Compile amber10 parallel with suppied LAM Gustavo Seabra (Thu Jun 12 2008 - 10:39:34 PDT)
    - RE: AMBER: Compile amber10 parallel with suppied LAM James W. Caldwell (Thu Jun 12 2008 - 11:08:54 PDT)
    - Re: AMBER: Compile amber10 parallel with suppied LAM Gustavo Seabra (Thu Jun 12 2008 - 11:20:24 PDT)
    - RE: AMBER: Compile amber10 parallel with suppied LAM James W. Caldwell (Fri Jun 13 2008 - 10:06:19 PDT)
    - RE: AMBER: Compile amber10 parallel with suppied LAM James W. Caldwell (Fri Jun 13 2008 - 10:17:57 PDT)
  - AMBER: How to get all eigenvalues by "analyze matrix" Qi Yan (Thu Jun 12 2008 - 10:39:52 PDT)
AMBER: Sander crashes >99999 atoms plmallip.mail.uh.edu (Thu Jun 12 2008 - 16:26:57 PDT)
- Re: AMBER: Sander crashes >99999 atoms David A. Case (Thu Jun 12 2008 - 18:25:31 PDT)
  - Re: AMBER: Sander crashes >99999 atoms plmallip.mail.uh.edu (Thu Jun 12 2008 - 21:47:47 PDT)
    - Re: AMBER: Sander crashes >99999 atoms David A. Case (Fri Jun 13 2008 - 09:59:32 PDT)
  - AMBER: MM-GBSA with very positive GB value Catein Catherine (Fri Jun 13 2008 - 00:05:02 PDT)
    - Re: AMBER: MM-GBSA with very positive GB value Carlos Simmerling (Fri Jun 13 2008 - 00:46:55 PDT)
    - RE: AMBER: MM-GBSA with very positive GB value Catein Catherine (Fri Jun 13 2008 - 18:49:53 PDT)
AMBER: PCAL and polar contribution in the output file Neha Gandhi (Thu Jun 12 2008 - 22:42:54 PDT)
- Re: AMBER: PCAL and polar contribution in the output file Hannes Kopitz (Sun Jun 15 2008 - 06:30:23 PDT)
  - Re: AMBER: PCAL and polar contribution in the output file Neha Gandhi (Sun Jun 15 2008 - 06:56:20 PDT)
AMBER: amber10 make fails for static/parallel James W. Caldwell (Fri Jun 13 2008 - 15:50:19 PDT)
AMBER: Ewald error estimate Pavan G (Sun Jun 15 2008 - 07:22:48 PDT)
AMBER: Problem with running refinement of NMR structures with RDCs Qi Zhang (Sun Jun 15 2008 - 13:20:21 PDT)
- Re: AMBER: Problem with running refinement of NMR structures with RDCs David A. Case (Sun Jun 15 2008 - 18:50:53 PDT)
AMBER: Eigenmode dynamics in Ptraj fatima.chami.durham.ac.uk (Mon Jun 16 2008 - 05:59:42 PDT)
AMBER: the SPCFW water model Vlad Cojocaru (Mon Jun 16 2008 - 09:19:34 PDT)
AMBER: sander.MPI / parallel Arturas Ziemys (Mon Jun 16 2008 - 10:00:34 PDT)
- Re: AMBER: sander.MPI / parallel Carlos Simmerling (Mon Jun 16 2008 - 10:43:39 PDT)
  - Re: AMBER: sander.MPI / parallel Arturas Ziemys (Mon Jun 16 2008 - 10:56:57 PDT)
    - Re: AMBER: sander.MPI / parallel David LeBard (Mon Jun 16 2008 - 11:07:21 PDT)
    - Re: AMBER: sander.MPI / parallel David LeBard (Mon Jun 16 2008 - 11:08:20 PDT)
    - Re: AMBER: sander.MPI / parallel Arturas Ziemys (Mon Jun 16 2008 - 11:19:36 PDT)
    - Re: AMBER: sander.MPI / parallel David A. Case (Mon Jun 16 2008 - 11:33:35 PDT)
    - Re: AMBER: sander.MPI / parallel Carlos Simmerling (Mon Jun 16 2008 - 11:28:04 PDT)
AMBER: [Fwd: segmentation fault in nmode] Guillaume Renvez (Mon Jun 16 2008 - 07:31:12 PDT)
- Re: AMBER: [Fwd: segmentation fault in nmode] David A. Case (Mon Jun 16 2008 - 16:42:47 PDT)
  - Re: AMBER: [Fwd: segmentation fault in nmode] JAMES W CALDWELL (Mon Jun 16 2008 - 17:53:03 PDT)
  - Re: AMBER: [Fwd: segmentation fault in nmode] Guillaume Renvez (Tue Jun 17 2008 - 00:48:34 PDT)
- Re: AMBER: [Fwd: segmentation fault in nmode] Guillaume Renvez (Tue Jun 17 2008 - 00:50:33 PDT)
  - Re: AMBER: [Fwd: segmentation fault in nmode] David A. Case (Thu Jun 19 2008 - 17:22:34 PDT)
    - Re: AMBER: [Fwd: segmentation fault in nmode] Guillaume Renvez (Mon Jun 23 2008 - 01:27:27 PDT)
AMBER: about resp charges WanJ Ding (Mon Jun 16 2008 - 12:44:55 PDT)
- Re: AMBER: about resp charges FyD (Tue Jun 17 2008 - 05:58:03 PDT)
  - Re: AMBER: about resp charges wanjian ding (Wed Jun 18 2008 - 13:43:35 PDT)
AMBER: IRED to time correlation fatima.chami.durham.ac.uk (Mon Jun 16 2008 - 13:25:22 PDT)
AMBER: program to calculate rmsd rams rams (Mon Jun 16 2008 - 19:28:24 PDT)
- RE: AMBER: program to calculate rmsd Ross Walker (Tue Jun 17 2008 - 01:26:53 PDT)
AMBER: How to solve - Missing BELE for MM in 1 in amber. Thomas Leonard (Mon Jun 16 2008 - 20:05:59 PDT)
AMBER: How to solve - Missing BELE for MM in 1 in amber. Thomas Leonard (Mon Jun 16 2008 - 20:06:01 PDT)
- Re: AMBER: How to solve - Missing BELE for MM in 1 in amber. Hannes Kopitz (Tue Jun 17 2008 - 01:32:31 PDT)
AMBER: improving GAFF sulfonamide parameters Floris Buelens (Tue Jun 17 2008 - 02:57:46 PDT)
- Re: AMBER: improving GAFF sulfonamide parameters Junmei Wang (Tue Jun 24 2008 - 07:34:28 PDT)
  - Re: AMBER: improving GAFF sulfonamide parameters David Mobley (Thu Jun 26 2008 - 13:50:03 PDT)
AMBER: ligand complexed simulation Siddharth Rastogi (Tue Jun 17 2008 - 03:56:15 PDT)
- Re: AMBER: ligand complexed simulation mori.cerm.unifi.it (Tue Jun 17 2008 - 04:15:11 PDT)
AMBER: suggestion for next amberTools 1.1 Alan (Tue Jun 17 2008 - 04:01:06 PDT)
- Re: AMBER: suggestion for next amberTools 1.1 David A. Case (Tue Jun 17 2008 - 08:42:14 PDT)
  - libpdb, ptraj, and nab Was: Re: AMBER: suggestion for next amberTools 1.1 M. L. Dodson (Wed Jun 18 2008 - 08:43:44 PDT)
    - Re: libpdb, ptraj, and nab Was: Re: AMBER: suggestion for next amberTools 1.1 David A. Case (Wed Jun 18 2008 - 17:32:36 PDT)
AMBER: "Dumping RAW 2D RMS data is not yet implemented"? Steve Spronk (Tue Jun 17 2008 - 07:00:08 PDT)
- Re: AMBER: "Dumping RAW 2D RMS data is not yet implemented"? David A. Case (Tue Jun 17 2008 - 08:18:08 PDT)
  - RE: AMBER: "Dumping RAW 2D RMS data is not yet implemented"? Steve Spronk (Tue Jun 17 2008 - 08:54:04 PDT)
- Re: AMBER: "Dumping RAW 2D RMS data is not yet implemented"? Jianyin Shao (Tue Jun 17 2008 - 08:36:01 PDT)
AMBER: to understand GAFF: about A and B coefficients Alan (Tue Jun 17 2008 - 09:42:34 PDT)
- Re: AMBER: to understand GAFF: about A and B coefficients David A. Case (Tue Jun 17 2008 - 09:52:41 PDT)
AMBER: multiple dihedral restraints using group (in Amber 10) mkseo (Tue Jun 17 2008 - 14:00:50 PDT)
- Re: AMBER: multiple dihedral restraints using group (in Amber 10) fatima.chami.durham.ac.uk (Wed Jun 18 2008 - 03:05:40 PDT)
AMBER: MM-PBSA Neha Gandhi (Wed Jun 18 2008 - 00:37:33 PDT)
- AW: AMBER: MM-PBSA Alexander Metz (Wed Jun 18 2008 - 03:43:18 PDT)
  - Re: AMBER: MM-PBSA Miguel Ortiz-Lombardía (Wed Jun 18 2008 - 07:41:12 PDT)
AMBER: Eigenmode dynamics - imaging traj fatima.chami.durham.ac.uk (Wed Jun 18 2008 - 03:09:26 PDT)
- Re: AMBER: Eigenmode dynamics - imaging traj E.M. (Wed Jun 18 2008 - 04:16:49 PDT)
  - Re: AMBER: Eigenmode dynamics - imaging traj Myunggi Yi (Wed Jun 18 2008 - 06:33:07 PDT)
AMBER: about gaff.dat in ambeTools 1.0 Alan (Wed Jun 18 2008 - 07:44:02 PDT)
- Re: AMBER: about gaff.dat in ambeTools 1.0 Junmei Wang (Tue Jun 24 2008 - 06:37:09 PDT)
AMBER: ptraj fatima.chami.durham.ac.uk (Wed Jun 18 2008 - 08:21:50 PDT)
AMBER: cross correlation function using iRED matrix fatima.chami.durham.ac.uk (Wed Jun 18 2008 - 10:07:25 PDT)
- Re: AMBER: cross correlation function using iRED matrix Myunggi Yi (Wed Jun 18 2008 - 11:07:03 PDT)
AMBER: tip3p water and shake Wang,Ying (Wed Jun 18 2008 - 13:07:13 PDT)
- RE: AMBER: tip3p water and shake Ross Walker (Wed Jun 18 2008 - 14:35:30 PDT)
- RE: AMBER: tip3p water and shake Wang,Ying (Wed Jun 18 2008 - 18:03:55 PDT)
- RE: AMBER: tip3p water and shake Wang,Ying (Wed Jun 18 2008 - 20:44:27 PDT)
  - Re: AMBER: tip3p water and shake David A. Case (Wed Jun 18 2008 - 22:15:48 PDT)
AMBER: sp carbon notation? Laura Benton (Wed Jun 18 2008 - 16:16:35 PDT)
- Re: AMBER: sp carbon notation? David A. Case (Wed Jun 18 2008 - 17:22:14 PDT)
AMBER: questions about gaff yzhao (Wed Jun 18 2008 - 19:01:45 PDT)
- Re: AMBER: questions about gaff Mark Williamson (Wed Jun 18 2008 - 19:35:42 PDT)
- Re: Re: AMBER: questions about gaff Steven (Fri Jun 20 2008 - 07:11:08 PDT)
AMBER: [Fwd: failure to load box parameters] Daniel Smith (Wed Jun 18 2008 - 20:58:10 PDT)
- Re: AMBER: [Fwd: failure to load box parameters] David A. Case (Wed Jun 18 2008 - 22:35:53 PDT)
  - Re: AMBER: [Fwd: failure to load box parameters] Daniel Smith (Mon Jun 23 2008 - 14:26:22 PDT)
    - Re: AMBER: [Fwd: failure to load box parameters] David A. Case (Tue Jun 24 2008 - 08:14:51 PDT)
    - Re: AMBER: [Fwd: failure to load box parameters] Daniel Smith (Wed Jun 25 2008 - 11:30:18 PDT)
    - Re: AMBER: [Fwd: failure to load box parameters] David A. Case (Wed Jun 25 2008 - 12:09:28 PDT)
AMBER: How to create average structure? Shen, Lingling (Wed Jun 18 2008 - 21:44:03 PDT)
- Re: AMBER: How to create average structure? Carlos Simmerling (Wed Jun 18 2008 - 21:52:35 PDT)
AMBER: how to extract x,y,z of a set of atoms from an MD trajectories fatima.chami.durham.ac.uk (Thu Jun 19 2008 - 02:16:52 PDT)
AMBER: Correlation functions from iRED analysis Samuel Genheden (a03samge) (Thu Jun 19 2008 - 03:22:53 PDT)
- Re: AMBER: Correlation functions from iRED analysis Myunggi Yi (Thu Jun 19 2008 - 05:52:55 PDT)
- RE: AMBER: Correlation functions from iRED analysis Samuel Genheden (a03samge) (Thu Jun 19 2008 - 06:10:51 PDT)
  - Re: AMBER: Correlation functions from iRED analysis Myunggi Yi (Thu Jun 19 2008 - 06:14:51 PDT)
  - RE: AMBER: Correlation functions from iRED analysis fatima.chami.durham.ac.uk (Thu Jun 19 2008 - 06:43:39 PDT)
- RE: AMBER: Correlation functions from iRED analysis Samuel Genheden (a03samge) (Thu Jun 19 2008 - 06:33:46 PDT)
  - RE: AMBER: Correlation functions from iRED analysis fatima.chami.durham.ac.uk (Thu Jun 19 2008 - 06:46:22 PDT)
    - Re: AMBER: Correlation functions from iRED analysis Myunggi Yi (Thu Jun 19 2008 - 09:06:36 PDT)
AMBER: Installation Problem of AMBER10 bhargav patel (Thu Jun 19 2008 - 03:57:26 PDT)
- Re: AMBER: Installation Problem of AMBER10 Carlos Simmerling (Thu Jun 19 2008 - 04:05:21 PDT)
- Re: AMBER: Installation Problem of AMBER10 David A. Case (Thu Jun 19 2008 - 07:53:03 PDT)
  - Re: AMBER: Installation Problem of AMBER10 bhargav patel (Fri Jun 20 2008 - 02:07:12 PDT)
    - AMBER: trajout input Thomas Leonard (Fri Jun 20 2008 - 02:23:55 PDT)
    - Re: AMBER: trajout input Barbault Florent (Fri Jun 20 2008 - 02:43:28 PDT)
    - Re: AMBER: trajout input Thomas Leonard (Fri Jun 20 2008 - 03:05:55 PDT)
    - Re: AMBER: trajout input Swarup Gupta (Sun Jun 22 2008 - 20:01:31 PDT)
    - Re: AMBER: trajout input Thomas Cheatham III (Fri Jun 20 2008 - 10:57:43 PDT)
    - Re: AMBER: Installation Problem of AMBER10 David A. Case (Fri Jun 20 2008 - 12:34:09 PDT)
    - Re: AMBER: Installation Problem of AMBER10 bhargav patel (Tue Jun 24 2008 - 03:06:45 PDT)
    - Re: AMBER: Installation Problem of AMBER10 Atro Tossavainen (Tue Jun 24 2008 - 07:37:57 PDT)
    - Re: AMBER: Installation Problem of AMBER10 David A. Case (Tue Jun 24 2008 - 07:49:26 PDT)
- Re: AMBER: Installation Problem of AMBER10 Bill Ross (Thu Jun 19 2008 - 10:31:42 PDT)
- Re: AMBER: Installation Problem of AMBER10 Bill Ross (Fri Jun 20 2008 - 13:46:35 PDT)
AMBER: How to extract solvent box information from .rst or .mdcrd files? Panwang Zhou (Thu Jun 19 2008 - 07:13:18 PDT)
- Re: AMBER: How to extract solvent box information from .rst or .mdcrd files? fatima.chami.durham.ac.uk (Thu Jun 19 2008 - 07:47:50 PDT)
- Re: Re: AMBER: How to extract solvent box information from .rst or .mdcrd files? Panwang Zhou (Thu Jun 19 2008 - 08:34:02 PDT)
  - Re: Re: AMBER: How to extract solvent box information from .rst or .mdcrd files? fatima.chami.durham.ac.uk (Thu Jun 19 2008 - 09:00:32 PDT)
- Re: AMBER: How to extract solvent box information from .rst or .mdcrd files? David A. Case (Sat Jun 28 2008 - 09:37:45 PDT)
SV: AMBER: Correlation functions from iRED analysis Samuel Genheden (a03samge) (Thu Jun 19 2008 - 08:53:29 PDT)
- Re: SV: AMBER: Correlation functions from iRED analysis fatima.chami.durham.ac.uk (Thu Jun 19 2008 - 09:05:36 PDT)
SV: SV: AMBER: Correlation functions from iRED analysis Samuel Genheden (a03samge) (Thu Jun 19 2008 - 13:06:17 PDT)
AMBER: simple sander James W. Caldwell (Thu Jun 19 2008 - 16:30:39 PDT)
- Re: AMBER: simple sander David A. Case (Thu Jun 19 2008 - 18:40:46 PDT)
  - Re: AMBER: simple sander JAMES W CALDWELL (Thu Jun 19 2008 - 18:47:32 PDT)
AMBER: ligand complexed simulation Siddharth Rastogi (Fri Jun 20 2008 - 00:14:18 PDT)
AMBER: GAFF for organic crystals Rabone, Jeremy (Fri Jun 20 2008 - 01:05:18 PDT)
- Re: AMBER: GAFF for organic crystals Junmei Wang (Mon Jun 23 2008 - 08:16:50 PDT)
AMBER: rdparm help Alan (Fri Jun 20 2008 - 04:12:17 PDT)
- Re: AMBER: rdparm help Thomas Cheatham (Fri Jun 20 2008 - 07:35:36 PDT)
  - Re: AMBER: rdparm help Alan (Mon Jun 23 2008 - 08:23:50 PDT)
AMBER: AmberTools 1.0 installation error: x86_64 Matthew Danielson (Fri Jun 20 2008 - 08:44:21 PDT)
- Re: AMBER: AmberTools 1.0 installation error: x86_64 David A. Case (Fri Jun 20 2008 - 09:17:35 PDT)
AMBER: Amber 10 timing Ed Pate (Fri Jun 20 2008 - 10:08:37 PDT)
- Re: AMBER: Amber 10 timing Robert Duke (Fri Jun 20 2008 - 14:29:00 PDT)
AMBER: SIZE.h problems 欧阳德方 (Sat Jun 21 2008 - 05:33:49 PDT)
- Re: AMBER: SIZE.h problems Mark Williamson (Sat Jun 21 2008 - 14:22:37 PDT)
AMBER: (no subject) Daniel B. Kaplan (Sun Jun 22 2008 - 16:46:17 PDT)
- Re: AMBER: (no subject) Junmei Wang (Mon Jun 23 2008 - 08:01:39 PDT)
AMBER: MM-PBSA in AMBER 10 Daniel Oehme (Sun Jun 22 2008 - 22:07:34 PDT)
- AMBER: MM-PBSA in AMBER 10 Daniel Oehme (Mon Jun 23 2008 - 18:32:24 PDT)
  - Re: AMBER: MM-PBSA in AMBER 10 David A. Case (Mon Jun 23 2008 - 18:47:44 PDT)
AMBER: How to adjust the problem of "Vlimit exceeded" Biman Jana (Mon Jun 23 2008 - 00:28:27 PDT)
- Re: AMBER: How to adjust the problem of "Vlimit exceeded" David A. Case (Mon Jun 23 2008 - 08:16:05 PDT)
AMBER: How to confirm atom types of small molecule perceived by antechamber xiaonan zhang (Mon Jun 23 2008 - 01:39:30 PDT)
- Re: AMBER: How to confirm atom types of small molecule perceived by antechamber David A. Case (Mon Jun 23 2008 - 07:56:17 PDT)
- Re: AMBER: How to confirm atom types of small molecule perceived by antechamber Junmei Wang (Mon Jun 23 2008 - 07:57:18 PDT)
AMBER: source of AMBER9 Germain Vallverdu (Mon Jun 23 2008 - 07:09:29 PDT)
AMBER: amber10/dat/leap/cmd/README need update Alan (Mon Jun 23 2008 - 07:59:21 PDT)
- Re: AMBER: amber10/dat/leap/cmd/README need update Vlad Cojocaru (Mon Jun 23 2008 - 08:12:29 PDT)
AMBER: Antechamber Question Daniel B. Kaplan (Mon Jun 23 2008 - 09:51:28 PDT)
- Re: AMBER: Antechamber Question Junmei Wang (Tue Jun 24 2008 - 06:33:58 PDT)
AMBER: problems form the pdb to the mol2 Rilei Yu (Mon Jun 23 2008 - 18:01:33 PDT)
- Re: AMBER: problems form the pdb to the mol2 David A. Case (Mon Jun 23 2008 - 18:51:46 PDT)
- Re: AMBER: problems form the pdb to the mol2 Junmei Wang (Tue Jun 24 2008 - 06:47:24 PDT)
  - AMBER: Further request answers from Dr. Junmei Wang Rilei Yu (Tue Jun 24 2008 - 08:59:05 PDT)
    - Re: AMBER: Further request answers from Dr. Junmei Wang Junmei Wang (Tue Jun 24 2008 - 09:58:49 PDT)
- Re: AMBER: problems form the pdb to the mol2 Cyril Bauvais (Tue Jun 24 2008 - 07:05:36 PDT)
  - ： Re: AMBER: problems form the pdb to the mol2 Rilei Yu (Tue Jun 24 2008 - 09:14:15 PDT)
    - AMBER: Re: ： Re: AMBER: problems form the pdb to the mol2 Cyril Bauvais (Wed Jun 25 2008 - 06:00:54 PDT)
    - AMBER: Re: AMBER: Re: ： Re: AMBER: problems form the pdb to the mol2 Junmei Wang (Wed Jun 25 2008 - 09:29:44 PDT)
AMBER: dihedral energy calculation inconsistent with gaussian's result Q733 (Mon Jun 23 2008 - 19:43:36 PDT)
- Re: AMBER: dihedral energy calculation inconsistent with gaussian's result Jerome.GOLEBIOWSKI.unice.fr (Tue Jun 24 2008 - 01:01:35 PDT)
AMBER: unsubscribe amber sanket.deshmukh.ucd.ie (Tue Jun 24 2008 - 04:07:42 PDT)
- AMBER: unsubscribe amber Rabin (Wed Jun 25 2008 - 17:48:51 PDT)
AMBER: A-prime RNA input file 欧阳德方 (Tue Jun 24 2008 - 04:16:27 PDT)
AMBER: qmmm_DFTB problem Dr. Xiaofeng (Frank) Duan (Tue Jun 24 2008 - 06:58:46 PDT)
- Re: AMBER: qmmm_DFTB problem Gustavo Seabra (Tue Jun 24 2008 - 07:31:15 PDT)
AMBER: Compilation of amber8 patched with ramd Francesco Pietra (Tue Jun 24 2008 - 07:32:54 PDT)
- Re: AMBER: Compilation of amber8 patched with ramd David A. Case (Tue Jun 24 2008 - 07:55:10 PDT)
- Re: AMBER: Compilation of amber8 patched with ramd Vlad Cojocaru (Tue Jun 24 2008 - 08:07:03 PDT)
  - Re: AMBER: Compilation of amber8 patched with ramd Francesco Pietra (Tue Jun 24 2008 - 09:28:18 PDT)
    - Re: AMBER: Compilation of amber8 patched with ramd Francesco Pietra (Tue Jun 24 2008 - 14:52:09 PDT)
    - Re: AMBER: Compilation of amber8 patched with ramd David A. Case (Tue Jun 24 2008 - 15:06:15 PDT)
    - Re: AMBER: Compilation of amber8 patched with ramd Francesco Pietra (Wed Jun 25 2008 - 01:17:59 PDT)
    - Re: AMBER: Compilation of amber8 patched with ramd Vlad Cojocaru (Wed Jun 25 2008 - 02:00:10 PDT)
AMBER: dihedral potential with odd periodicity Germain Vallverdu (Tue Jun 24 2008 - 07:43:26 PDT)
AMBER: Using AMBER forces Steven Winfield (Tue Jun 24 2008 - 08:44:41 PDT)
- RE: AMBER: Using AMBER forces Ross Walker (Tue Jun 24 2008 - 09:22:25 PDT)
  - Re: AMBER: Using AMBER forces Steven Winfield (Tue Jun 24 2008 - 09:54:49 PDT)
    - RE: AMBER: Using AMBER forces Ross Walker (Tue Jun 24 2008 - 11:19:13 PDT)
    - Re: AMBER: Using AMBER forces Germain Vallverdu (Tue Sep 09 2008 - 06:48:32 PDT)
AMBER: rdparm Segmentation fault on Ubuntu Alan (Tue Jun 24 2008 - 08:50:12 PDT)
AMBER: how to derive torsional angle parameters in gaff Junmei Wang (Tue Jun 24 2008 - 18:45:42 PDT)
- AMBER: local coordinate system question caoch (Wed Jun 25 2008 - 02:33:15 PDT)
  - Re: AMBER: local coordinate system question David A. Case (Wed Jun 25 2008 - 07:32:16 PDT)
- Re: AMBER: how to derive torsional angle parameters in gaff Balazs JOJART (Thu Jun 26 2008 - 01:53:40 PDT)
AMBER: Debugf AMBER9 John Palmeri (Wed Jun 25 2008 - 00:38:53 PDT)
AMBER: TI calculations in Amber10 Samuel Genheden (a03samge) (Wed Jun 25 2008 - 04:58:28 PDT)
- Re: AMBER: TI calculations in Amber10 Thomas Steinbrecher (Wed Jun 25 2008 - 09:15:47 PDT)
AMBER: A problem of dihedral angle Harry (Yicun) Ni (Wed Jun 25 2008 - 08:31:24 PDT)
- RE: AMBER: A problem of dihedral angle Ross Walker (Wed Jun 25 2008 - 08:48:56 PDT)
  - Re: AMBER: A problem of dihedral angle Harry (Yicun) Ni (Wed Jun 25 2008 - 12:42:09 PDT)
- Re: AMBER: A problem of dihedral angle Carlos Simmerling (Wed Jun 25 2008 - 08:53:16 PDT)
AMBER: amber10 compile gfortran question James W. Caldwell (Wed Jun 25 2008 - 11:10:58 PDT)
- Re: AMBER: amber10 compile gfortran question David A. Case (Wed Jun 25 2008 - 12:03:54 PDT)
  - RE: AMBER: amber10 compile gfortran question James W. Caldwell (Wed Jun 25 2008 - 12:11:58 PDT)
AMBER: sleap - TER-card In Hee Park (Wed Jun 25 2008 - 12:14:39 PDT)
- Re: AMBER: sleap - TER-card David A. Case (Wed Jun 25 2008 - 15:05:59 PDT)
  - Re: AMBER: sleap - TER-card In Hee Park (Thu Jun 26 2008 - 17:31:40 PDT)
    - Re: AMBER: sleap - TER-card David A. Case (Thu Jun 26 2008 - 18:19:01 PDT)
AMBER: rdparm Segmentation fault Alan (Wed Jun 25 2008 - 14:24:34 PDT)
- Re: AMBER: rdparm Segmentation fault David A. Case (Wed Jun 25 2008 - 17:07:20 PDT)
AMBER: Antechamber/mopac am1-bcc charge Dong Xu (Wed Jun 25 2008 - 15:09:39 PDT)
- Re: AMBER: Antechamber/mopac am1-bcc charge Junmei Wang (Wed Jun 25 2008 - 15:44:07 PDT)
  - Re: AMBER: Antechamber/mopac am1-bcc charge Dong Xu (Wed Jun 25 2008 - 23:21:03 PDT)
    - Re: AMBER: Antechamber/mopac am1-bcc charge Junmei Wang (Thu Jun 26 2008 - 07:33:44 PDT)
    - Re: AMBER: Antechamber/mopac am1-bcc charge Francesco Pietra (Thu Jun 26 2008 - 10:29:12 PDT)
    - Re: AMBER: Antechamber/mopac am1-bcc charge Junmei Wang (Thu Jun 26 2008 - 11:27:10 PDT)
    - Re: AMBER: Antechamber/mopac am1-bcc charge FyD (Thu Jun 26 2008 - 13:53:20 PDT)
    - Re: AMBER: Antechamber/mopac am1-bcc charge Junmei Wang (Thu Jun 26 2008 - 15:25:32 PDT)
    - Re: AMBER: Antechamber/mopac am1-bcc charge FyD (Fri Jun 27 2008 - 02:07:45 PDT)
    - Re: AMBER: Antechamber/mopac am1-bcc charge Junmei Wang (Fri Jun 27 2008 - 08:35:23 PDT)
    - Re: AMBER: Antechamber/mopac am1-bcc charge Francesco Pietra (Fri Jun 27 2008 - 15:02:21 PDT)
    - Re: AMBER: Antechamber/mopac am1-bcc charge FyD (Sat Jun 28 2008 - 00:47:54 PDT)
    - Re: AMBER: Antechamber/mopac am1-bcc charge Francesco Pietra (Sat Jun 28 2008 - 10:22:44 PDT)
    - Re: AMBER: Antechamber/mopac am1-bcc charge FyD (Sun Jun 29 2008 - 06:18:15 PDT)
AMBER: (no subject) Daniel B. Kaplan (Wed Jun 25 2008 - 19:23:43 PDT)
AMBER: Amber:unsubscribe amber sanket.deshmukh.ucd.ie (Thu Jun 26 2008 - 04:53:22 PDT)
AMBER: concerning force fields Adrien Delmont (Thu Jun 26 2008 - 08:14:15 PDT)
- Re: AMBER: concerning force fields Carlos Simmerling (Thu Jun 26 2008 - 09:16:48 PDT)
- Re: AMBER: concerning force fields Adrien Delmont (Thu Jun 26 2008 - 11:29:39 PDT)
  - Re: AMBER: concerning force fields Carlos Simmerling (Thu Jun 26 2008 - 12:25:04 PDT)
- Re: AMBER: concerning force fields Adrien Delmont (Fri Jun 27 2008 - 05:22:08 PDT)
  - Re: AMBER: concerning force fields Carlos Simmerling (Fri Jun 27 2008 - 05:34:21 PDT)
  - Re: AMBER: concerning force fields Karl Kirschner (kkirschn) (Fri Jun 27 2008 - 06:02:03 PDT)
- Re: AMBER: concerning force fields Adrien Delmont (Sat Jun 28 2008 - 09:10:05 PDT)
AMBER: Peseckis, Steven M. (Thu Jun 26 2008 - 08:54:05 PDT)
- Re: AMBER: David A. Case (Fri Jun 27 2008 - 11:55:04 PDT)
  - AMBER: RE: AMBER 10 failure to run in UBUNTU Peseckis, Steven M. (Sun Jun 29 2008 - 17:13:38 PDT)
AMBER: ligand partial charge and conformation question Dong Xu (Thu Jun 26 2008 - 11:01:31 PDT)
AMBER: output file AMBER9_MPI Vijay Manickam Achari (Thu Jun 26 2008 - 12:06:19 PDT)
AMBER: Dihedral Angle Parameters Ilyas Yildirim (Thu Jun 26 2008 - 14:07:16 PDT)
- Re: AMBER: Dihedral Angle Parameters Carlos Simmerling (Thu Jun 26 2008 - 14:30:53 PDT)
  - Re: AMBER: Dihedral Angle Parameters Ilyas Yildirim (Thu Jun 26 2008 - 15:07:55 PDT)
    - RE: AMBER: Dihedral Angle Parameters Ross Walker (Thu Jun 26 2008 - 15:18:52 PDT)
    - Re: AMBER: Dihedral Angle Parameters Carlos Simmerling (Thu Jun 26 2008 - 15:20:41 PDT)
AMBER: REMD Amber10 : error in reading namelist cntrl rebeca (Fri Jun 27 2008 - 02:01:26 PDT)
- Re: AMBER: REMD Amber10 : error in reading namelist cntrl Carlos Simmerling (Fri Jun 27 2008 - 07:47:42 PDT)
AMBER: Group specification problem fatima.chami.durham.ac.uk (Fri Jun 27 2008 - 05:59:09 PDT)
AMBER: pmemd 10 output Vlad Cojocaru (Fri Jun 27 2008 - 08:48:35 PDT)
- RE: AMBER: pmemd 10 output Ross Walker (Fri Jun 27 2008 - 09:16:44 PDT)
  - Re: AMBER: pmemd 10 output Vlad Cojocaru (Fri Jun 27 2008 - 09:24:58 PDT)
    - RE: AMBER: pmemd 10 output Ross Walker (Fri Jun 27 2008 - 09:40:48 PDT)
    - Re: AMBER: pmemd 10 output Vlad Cojocaru (Thu Jul 10 2008 - 03:19:08 PDT)
  - Re: AMBER: pmemd 10 output Vlad Cojocaru (Fri Jun 27 2008 - 09:34:37 PDT)
- Re: AMBER: pmemd 10 output Robert Duke (Thu Jul 10 2008 - 06:12:25 PDT)
  - Re: AMBER: pmemd 10 output Vlad Cojocaru (Thu Jul 10 2008 - 06:26:01 PDT)
  - Re: AMBER: pmemd 10 output Vlad Cojocaru (Thu Jul 10 2008 - 06:29:17 PDT)
- Re: AMBER: pmemd 10 output Robert Duke (Thu Jul 10 2008 - 06:44:19 PDT)
  - Re: AMBER: pmemd 10 output Vlad Cojocaru (Thu Jul 10 2008 - 07:18:28 PDT)
AMBER: Test scripts James W. Caldwell (Fri Jun 27 2008 - 09:35:26 PDT)
- Re: AMBER: Test scripts David A. Case (Fri Jun 27 2008 - 09:44:25 PDT)
  - RE: AMBER: Test scripts James W. Caldwell (Fri Jun 27 2008 - 09:54:56 PDT)
AMBER: ptraj - read in part of trajectory Seth Lilavivat (Fri Jun 27 2008 - 09:41:51 PDT)
- Re: AMBER: ptraj - read in part of trajectory Vlad Cojocaru (Fri Jun 27 2008 - 09:59:14 PDT)
- Re: AMBER: ptraj - read in part of trajectory Carlos Simmerling (Fri Jun 27 2008 - 10:00:32 PDT)
- Re: AMBER: ptraj - read in part of trajectory Seth Lilavivat (Fri Jun 27 2008 - 10:01:03 PDT)
AMBER: question about the charge Harry (Yicun) Ni (Fri Jun 27 2008 - 13:37:55 PDT)
- Re: AMBER: question about the charge Carlos Simmerling (Fri Jun 27 2008 - 13:52:22 PDT)
  - Re: AMBER: question about the charge Harry (Yicun) Ni (Fri Jun 27 2008 - 16:57:37 PDT)
AMBER: Seed for random number generator Francesco Pietra (Sun Jun 29 2008 - 01:22:12 PDT)
AMBER: Constrained group fatima.chami.durham.ac.uk (Mon Jun 30 2008 - 02:54:02 PDT)
- Re: AMBER: Constrained group Robert Duke (Mon Jun 30 2008 - 09:03:15 PDT)
AMBER: NMR refinement teresa.ierano.unina.it (Mon Jun 30 2008 - 03:37:48 PDT)
- Re: AMBER: NMR refinement David A. Case (Mon Jun 30 2008 - 07:44:51 PDT)
AMBER: nmode analysis Joachim Reichelt (Mon Jun 30 2008 - 04:53:21 PDT)
- Re: AMBER: nmode analysis Mark Williamson (Mon Jun 30 2008 - 05:12:09 PDT)
  - Re: AMBER: nmode analysis Joachim Reichelt (Mon Jun 30 2008 - 05:36:32 PDT)
    - RE: AMBER: nmode analysis Vahdati N. (Mon Jun 30 2008 - 05:41:40 PDT)
    - AMBER: ptraj problem with centering in the box Hannes Wallnoefer (Wed Jul 02 2008 - 07:00:33 PDT)
    - RE: AMBER: ptraj problem with centering in the box Ross Walker (Wed Jul 02 2008 - 08:31:51 PDT)
AMBER: hold atoms fixed Boutheina Kerkeni (Mon Jun 30 2008 - 05:51:17 PDT)
- Re: AMBER: hold atoms fixed Carlos Simmerling (Mon Jun 30 2008 - 06:02:19 PDT)
  - Re: AMBER: hold atoms fixed Boutheina Kerkeni (Mon Jun 30 2008 - 06:12:33 PDT)
- Re: AMBER: hold atoms fixed fatima.chami.durham.ac.uk (Mon Jun 30 2008 - 06:16:09 PDT)
- Re: AMBER: hold atoms fixed Gustavo Seabra (Mon Jun 30 2008 - 07:10:53 PDT)
AMBER: wrapping a restart file fatima.chami.durham.ac.uk (Mon Jun 30 2008 - 07:40:58 PDT)
- Re: AMBER: wrapping a restart file Gustavo Seabra (Mon Jun 30 2008 - 08:31:53 PDT)
- Re: AMBER: wrapping a restart file Robert Duke (Mon Jun 30 2008 - 09:34:54 PDT)
AMBER: watershell cero? rebeca (Mon Jun 30 2008 - 09:22:11 PDT)
AMBER: (no subject) fatima.chami.durham.ac.uk (Mon Jun 30 2008 - 09:26:23 PDT)
- Re: AMBER: (no subject) Robert Duke (Mon Jun 30 2008 - 09:43:11 PDT)
AMBER: MM-PBSA calculation problem Wei Huang (Mon Jun 30 2008 - 09:41:16 PDT)
AMBER: error in reading namelist cntrl Maria Frushicheva (Mon Jun 30 2008 - 13:02:50 PDT)
- Re: AMBER: error in reading namelist cntrl David A. Case (Mon Jun 30 2008 - 13:28:36 PDT)
- RE: AMBER: error in reading namelist cntrl Ross Walker (Mon Jun 30 2008 - 13:26:38 PDT)
AMBER: Regarding force field ff02 and ion library Abhishek Singh (Mon Jun 30 2008 - 13:54:52 PDT)
- Re: AMBER: Regarding force field ff02 and ion library David A. Case (Mon Jun 30 2008 - 14:14:37 PDT)
  - Re: AMBER: Regarding force field ff02 and ion library Thomas Cheatham III (Mon Jun 30 2008 - 14:30:05 PDT)
    - Re: AMBER: Regarding force field ff02 and ion library Abhishek Singh (Tue Jul 01 2008 - 12:02:28 PDT)
AMBER: missing torsion parameters John Bennett (Mon Jun 30 2008 - 14:06:07 PDT)
- RE: AMBER: missing torsion parameters Ross Walker (Mon Jun 30 2008 - 15:46:45 PDT)
AMBER: concerning force fields ( to Karl Kirschner ) Adrien Delmont (Tue Jul 01 2008 - 01:04:45 PDT)
- Re: AMBER: concerning force fields ( to Karl Kirschner ) Karl Kirschner (kkirschn) (Tue Jul 01 2008 - 08:06:29 PDT)
AMBER: Anna Reymer (Tue Jul 01 2008 - 01:36:12 PDT)
- Re: AMBER: Carlos Simmerling (Tue Jul 01 2008 - 05:15:15 PDT)
  - Re: AMBER: Anna Reymer (Tue Jul 01 2008 - 05:46:24 PDT)
AMBER: AMBER10: ambpdb problems Anna Reymer (Tue Jul 01 2008 - 01:37:38 PDT)
AMBER: RDF in ptraj fatima.chami.durham.ac.uk (Tue Jul 01 2008 - 06:34:35 PDT)
AMBER: "radius = 0.000" Arturas Ziemys (Tue Jul 01 2008 - 09:08:45 PDT)
- Re: AMBER: "radius = 0.000" Carlos Simmerling (Tue Jul 01 2008 - 09:16:38 PDT)
  - Re: AMBER: "radius = 0.000" Arturas Ziemys (Tue Jul 01 2008 - 10:17:54 PDT)
    - Re: AMBER: "radius = 0.000" Thomas Steinbrecher (Tue Jul 01 2008 - 10:36:17 PDT)
  - Re: AMBER: "radius = 0.000" Robert Duke (Tue Jul 01 2008 - 11:00:38 PDT)
    - Re: AMBER: "radius = 0.000" Arturas Ziemys (Tue Jul 01 2008 - 13:19:32 PDT)
    - AMBER: Inconsistent types (INTEGER(4)/REAL(8)) - Is it serious ? Arturas Ziemys (Wed Jul 02 2008 - 15:10:47 PDT)
    - Re: AMBER: Inconsistent types (INTEGER(4)/REAL(8)) - Is it serious ? David A. Case (Wed Jul 02 2008 - 15:25:18 PDT)
    - Re: AMBER: Inconsistent types (INTEGER(4)/REAL(8)) - Is it serious ? David A. Case (Wed Jul 02 2008 - 15:58:36 PDT)
    - AMBER: is amber workshop available this summer?? Chih-Ying Lin (Wed Jul 02 2008 - 16:29:03 PDT)
    - RE: AMBER: is amber workshop available this summer?? Ross Walker (Wed Jul 02 2008 - 21:19:31 PDT)
    - Re: AMBER: Inconsistent types (INTEGER(4)/REAL(8)) - Is it serious ? Robert Duke (Wed Jul 02 2008 - 15:28:10 PDT)
    - Re: AMBER: Inconsistent types (INTEGER(4)/REAL(8)) - Is it serious ? Robert Duke (Wed Jul 02 2008 - 15:29:52 PDT)
    - RE: AMBER: Inconsistent types (INTEGER(4)/REAL(8)) - Is it serious ? Ross Walker (Wed Jul 02 2008 - 15:30:21 PDT)
    - Re: AMBER: Inconsistent types (INTEGER(4)/REAL(8)) - Is it serious ? Arturas Ziemys (Wed Jul 02 2008 - 15:48:47 PDT)
    - Re: AMBER: Inconsistent types (INTEGER(4)/REAL(8)) - Is it serious ? Robert Duke (Wed Jul 02 2008 - 15:36:12 PDT)
    - Re: AMBER: Inconsistent types (INTEGER(4)/REAL(8)) - Is it serious ? Robert Duke (Wed Jul 02 2008 - 17:00:07 PDT)
    - Re: AMBER: Inconsistent types (INTEGER(4)/REAL(8)) - Is it serious ? Robert Duke (Wed Jul 02 2008 - 17:06:22 PDT)
- Re: AMBER: "radius = 0.000" Robert Duke (Tue Jul 01 2008 - 09:24:10 PDT)
- Re: AMBER: "radius = 0.000" Thomas Steinbrecher (Tue Jul 01 2008 - 09:39:30 PDT)
AMBER: Protonated Phosphate Problem Kliman, Michal (Tue Jul 01 2008 - 10:20:14 PDT)
- Re: AMBER: Protonated Phosphate Problem Thomas Steinbrecher (Tue Jul 01 2008 - 10:41:55 PDT)
AMBER: compile amber10 on Mac Junmei Wang (Tue Jul 01 2008 - 14:45:31 PDT)
- Re: AMBER: compile amber10 on Mac Scott Brozell (Thu Jul 03 2008 - 18:38:19 PDT)
AMBER: parameters for Fe coordinated to four CYS ? Jose Borreguero (Tue Jul 01 2008 - 17:12:37 PDT)
AMBER: NMR refinement teresa.ierano.unina.it (Wed Jul 02 2008 - 01:38:57 PDT)
- Re: AMBER: NMR refinement Wenyong Tong (Fri Jan 18 2008 - 20:18:18 PST)
  - Re: AMBER: NMR refinement David A. Case (Sat Jan 19 2008 - 10:39:08 PST)
- Re: AMBER: NMR refinement Ilyas Yildirim (Wed Jul 02 2008 - 02:58:05 PDT)
  - Re: AMBER: NMR refinement teresa.ierano.unina.it (Thu Jul 03 2008 - 02:37:02 PDT)
- Re: AMBER: NMR refinement David A. Case (Wed Jul 02 2008 - 17:21:54 PDT)
AMBER: NONBONDED_PARM_INDEX Max (Wed Jul 02 2008 - 01:54:35 PDT)
- Re: AMBER: NONBONDED_PARM_INDEX David A. Case (Wed Jul 02 2008 - 08:04:26 PDT)
AMBER: ptraj problem with imaging fatima.chami.durham.ac.uk (Wed Jul 02 2008 - 09:52:32 PDT)
- RE: AMBER: ptraj problem with imaging Ross Walker (Wed Jul 02 2008 - 13:06:42 PDT)
  - RE: AMBER: ptraj problem with imaging fatima.chami.durham.ac.uk (Thu Jul 03 2008 - 09:11:19 PDT)
AMBER: For help: Thermodynamic Integration of solvation free energy using soft-core potential yongleli (Wed Jul 02 2008 - 11:19:03 PDT)
- Re: AMBER: For help: Thermodynamic Integration of solvation free energy using soft-core potential Thomas Steinbrecher (Wed Jul 02 2008 - 12:08:40 PDT)
AMBER: RED III execution problem ben rodriguez (Wed Jul 02 2008 - 18:24:19 PDT)
- Re: AMBER: RED III execution problem FyD (Thu Jul 03 2008 - 02:25:24 PDT)
  - RE: AMBER: RED III execution problem ben rodriguez (Mon Jul 07 2008 - 12:21:11 PDT)
    - RE: AMBER: RED III execution problem FyD (Mon Jul 07 2008 - 13:54:30 PDT)
AMBER: How to obtain the oriented trajectories? Panwang Zhou (Thu Jul 03 2008 - 07:06:58 PDT)
- Re: AMBER: How to obtain the oriented trajectories? Carlos Simmerling (Thu Jul 03 2008 - 07:22:03 PDT)
AMBER: PMEMD and polarized force field ff 02 Abhishek Singh (Thu Jul 03 2008 - 07:50:00 PDT)
AMBER: PMEMD and polarized force field ff 02 Abhishek Singh (Thu Jul 03 2008 - 07:53:36 PDT)
- RE: AMBER: PMEMD and polarized force field ff 02 Ross Walker (Thu Jul 03 2008 - 08:02:17 PDT)
- Re: AMBER: PMEMD and polarized force field ff 02 David A. Case (Thu Jul 03 2008 - 08:10:06 PDT)
  - AMBER: Force Field parameters : A new chemical compound Chih-Ying Lin (Thu Jul 03 2008 - 10:52:17 PDT)
AMBER: bellymask for DNA backbone doesn't seem to work Seth Lilavivat (Thu Jul 03 2008 - 13:13:40 PDT)
- Re: AMBER: bellymask for DNA backbone doesn't seem to work Thomas Cheatham III (Thu Jul 03 2008 - 13:40:47 PDT)
AMBER: about QMMM output linfu (Thu Jul 03 2008 - 19:40:33 PDT)
- Re: AMBER: about QMMM output Gustavo Seabra (Fri Jul 04 2008 - 08:33:06 PDT)
  - RE: AMBER: about QMMM output Ross Walker (Fri Jul 04 2008 - 09:30:09 PDT)
    - Re: RE: AMBER: about QMMM output linfu (Fri Jul 04 2008 - 10:09:23 PDT)
    - RE: RE: AMBER: about QMMM output Ross Walker (Fri Jul 04 2008 - 12:55:10 PDT)
    - RE: RE: AMBER: about QMMM output linfu (Sat Jul 05 2008 - 19:25:47 PDT)
AMBER: RESP calculation on Copper containing molecule Vidana.Epa.csiro.au (Fri Jul 04 2008 - 00:16:24 PDT)
- Re: AMBER: RESP calculation on Copper containing molecule FyD (Fri Jul 04 2008 - 03:25:42 PDT)
AMBER: Boutheina Kerkeni (Fri Jul 04 2008 - 03:34:55 PDT)
- Re: AMBER: Carlos Simmerling (Fri Jul 04 2008 - 03:42:27 PDT)
  - Re: AMBER: Boutheina Kerkeni (Fri Jul 04 2008 - 04:02:10 PDT)
    - Re: AMBER: Carlos Simmerling (Fri Jul 04 2008 - 04:09:07 PDT)
    - Re: AMBER: Boutheina Kerkeni (Fri Jul 04 2008 - 04:44:20 PDT)
    - Re: AMBER: Carlos Simmerling (Fri Jul 04 2008 - 04:50:44 PDT)
    - Re: AMBER: Boutheina Kerkeni (Fri Jul 04 2008 - 05:27:59 PDT)
    - Re: AMBER: Carlos Simmerling (Fri Jul 04 2008 - 05:37:29 PDT)
    - Re: Re: AMBER: Chen (Fri Jul 30 2004 - 20:55:14 PDT)
    - Re: Re: AMBER: emilia wu (Mon Apr 04 2005 - 23:43:49 PDT)
    - RE: Re: AMBER: Wells, David H (Tue Apr 05 2005 - 00:13:56 PDT)
    - RE: Re: AMBER: glc0358.vip.sina.com (Sat Jul 09 2005 - 03:37:54 PDT)
    - AMBER: Position Restraints! Karthikeyan Pasupathy (Sat Jul 09 2005 - 10:24:51 PDT)
    - Re: AMBER: Position Restraints! justin litchfield (Sat Jul 09 2005 - 17:08:15 PDT)
    - RE: Re: AMBER: Shan Jufang (Sat Jul 09 2005 - 12:37:54 PDT)
    - Re: RE: Re: AMBER: emilia wu (Tue Apr 05 2005 - 05:25:42 PDT)
    - Re: RE: Re: AMBER: Zhiguo Liu (Sun Jul 10 2005 - 00:37:36 PDT)
    - Re: Re: AMBER: Qingning Shu (Tue Aug 29 2006 - 09:26:34 PDT)
    - AMBER: mm_pbsa_statistical.pl William Wei (Tue Aug 29 2006 - 14:02:32 PDT)
    - Re: AMBER: mm_pbsa_statistical.pl Jianyin Shao (Wed Aug 30 2006 - 10:52:56 PDT)
    - Re: AMBER: mm_pbsa_statistical.pl William Wei (Wed Aug 30 2006 - 14:11:51 PDT)
    - AMBER: Re: FF problem: RG residue minimizes to non-planar structure David A. Case (Thu Sep 07 2006 - 11:53:33 PDT)
AMBER: trouble interpreting <P2> time correlation function data Sally Pias (Sat Jul 05 2008 - 23:59:57 PDT)
- Re: AMBER: trouble interpreting <P2> time correlation function data David A. Case (Sun Jul 06 2008 - 08:04:30 PDT)
 - Re: AMBER: trouble interpreting <P2> time correlation function data Sally Pias (Sun Jul 06 2008 - 10:08:18 PDT)
AMBER: For help: how to perform double decoupling thermodynamic integration calculation in AMBER10 yongleli (Mon Jul 07 2008 - 15:04:53 PDT)
- Re: AMBER: For help: how to perform double decoupling thermodynamic integration calculation in AMBER10 Thomas Steinbrecher (Mon Jul 07 2008 - 15:56:49 PDT)
AMBER: Constant pH with new parameters (amber10) Markus Kaukonen (Tue Jul 08 2008 - 00:39:57 PDT)
- Re: AMBER: Constant pH with new parameters (amber10) David A. Case (Fri Jul 11 2008 - 11:41:09 PDT)
  - Re: AMBER: Constant pH with new parameters (amber10) Markus Kaukonen (Sat Jul 12 2008 - 12:24:05 PDT)
    - Re: AMBER: Constant pH with new parameters (amber10) Adrian Roitberg (Sat Jul 12 2008 - 16:47:41 PDT)
    - Re: AMBER: Constant pH with new parameters (amber10) Markus Kaukonen (Sun Jul 20 2008 - 01:08:35 PDT)
AMBER: [amber/glycam] dealing with fucose... Waqas Nasir (Tue Jul 08 2008 - 07:56:31 PDT)
- Re: AMBER: [amber/glycam] dealing with fucose... Lachele Foley (Lists) (Tue Jul 08 2008 - 09:08:52 PDT)
- Re: AMBER: [amber/glycam] dealing with fucose... Waqas Nasir (Thu Jul 10 2008 - 05:59:34 PDT)
  - Re: AMBER: [amber/glycam] dealing with fucose... Lachele Foley (Lists) (Thu Jul 10 2008 - 10:24:41 PDT)
    - Re: AMBER: [amber/glycam] dealing with fucose... Waqas Nasir (Fri Jul 11 2008 - 02:47:36 PDT)
    - Re: AMBER: [amber/glycam] dealing with fucose... Lachele Foley (Lists) (Fri Jul 11 2008 - 07:19:17 PDT)
- Re: AMBER: [amber/glycam] dealing with fucose... Waqas Nasir (Sat Jul 12 2008 - 12:44:13 PDT)
  - Re: AMBER: [amber/glycam] dealing with fucose... Lachele Foley (Lists) (Tue Jul 15 2008 - 07:45:19 PDT)
AMBER: Force fields for REMD with GB solvent guardiani.fi.infn.it (Tue Jul 08 2008 - 09:24:27 PDT)
- Re: AMBER: Force fields for REMD with GB solvent Carlos Simmerling (Tue Jul 08 2008 - 15:03:31 PDT)
  - Re: AMBER: Force fields for REMD with GB solvent guardiani.fi.infn.it (Wed Jul 09 2008 - 02:37:43 PDT)
    - Re: AMBER: Force fields for REMD with GB solvent Carlos Simmerling (Wed Jul 09 2008 - 06:37:36 PDT)
AMBER: analysing normal modes Vahdati N. (Tue Jul 08 2008 - 11:03:39 PDT)
AMBER: Distance diagnolization matrix plot Siddharth Rastogi (Wed Jul 09 2008 - 00:04:08 PDT)
AMBER: REMD temperature profile guardiani.fi.infn.it (Wed Jul 09 2008 - 06:47:13 PDT)
- Re: AMBER: REMD temperature profile Carlos Simmerling (Wed Jul 09 2008 - 08:28:59 PDT)
AMBER: XLeap Problems Schwehm, Jeffrey M. (Wed Jul 09 2008 - 09:26:14 PDT)
- Re: AMBER: XLeap Problems Mark Williamson (Wed Jul 09 2008 - 09:41:51 PDT)
- RE: AMBER: XLeap Problems Ross Walker (Wed Jul 09 2008 - 11:08:50 PDT)
AMBER: amber9 / difference of igb=0 and igb=6 Arturas Ziemys (Wed Jul 09 2008 - 12:45:32 PDT)
- RE: AMBER: amber9 / difference of igb=0 and igb=6 Ross Walker (Wed Jul 09 2008 - 13:54:54 PDT)
  - Re: AMBER: amber9 / difference of igb=0 and igb=6 Arturas Ziemys (Wed Jul 09 2008 - 14:03:32 PDT)
AMBER: analysing normal modes Chris Moth (Wed Jul 09 2008 - 12:45:57 PDT)
- RE: AMBER: analysing normal modes Vahdati N. (Thu Jul 10 2008 - 05:49:15 PDT)
AMBER: Question about loading frcmod.ionsjc_tip3p in xleap Jeff Schwinefus (Wed Jul 09 2008 - 14:27:46 PDT)
- Re: AMBER: Question about loading frcmod.ionsjc_tip3p in xleap Thomas Cheatham III (Thu Jul 10 2008 - 15:20:04 PDT)
  - Re: AMBER: Question about loading frcmod.ionsjc_tip3p in xleap David A. Case (Thu Jul 10 2008 - 21:42:28 PDT)
    - Re: AMBER: Question about loading frcmod.ionsjc_tip3p in xleap Jeff Schwinefus (Fri Jul 11 2008 - 09:41:21 PDT)
    - Re: AMBER: Question about loading frcmod.ionsjc_tip3p in xleap Scott Brozell (Thu Jul 31 2008 - 15:40:43 PDT)
AMBER: ptraj selection Ilyas Yildirim (Wed Jul 09 2008 - 18:07:39 PDT)
- Re: AMBER: ptraj selection David Watson (Wed Jul 09 2008 - 19:11:16 PDT)
  - Re: AMBER: ptraj selection Ilyas Yildirim (Wed Jul 09 2008 - 20:13:22 PDT)
    - Re: AMBER: ptraj selection David Watson (Wed Jul 09 2008 - 20:59:27 PDT)
    - Re: AMBER: ptraj selection Ilyas Yildirim (Wed Jul 09 2008 - 21:27:35 PDT)
    - Re: AMBER: ptraj selection David Watson (Wed Jul 09 2008 - 23:01:01 PDT)
- Re: AMBER: ptraj selection Jianyin Shao (Thu Jul 10 2008 - 08:56:55 PDT)
  - Re: AMBER: ptraj selection Ilyas Yildirim (Thu Jul 10 2008 - 17:58:08 PDT)
AMBER: mm_pbsa incorrect complex prmtop file xiaonan zhang (Thu Jul 10 2008 - 00:44:58 PDT)
- Re: AMBER: mm_pbsa incorrect complex prmtop file Neha Gandhi (Thu Jul 10 2008 - 01:02:27 PDT)
AMBER: replicas trapped in a few low temperatures Ye Mei (Thu Jul 10 2008 - 02:13:25 PDT)
- Re: AMBER: replicas trapped in a few low temperatures Carlos Simmerling (Thu Jul 10 2008 - 03:59:03 PDT)
- Re: Re: AMBER: replicas trapped in a few low temperatures Ye Mei (Thu Jul 10 2008 - 04:16:59 PDT)
  - Re: Re: AMBER: replicas trapped in a few low temperatures Carlos Simmerling (Thu Jul 10 2008 - 04:23:39 PDT)
  - Re: Re: AMBER: replicas trapped in a few low temperatures Carlos Simmerling (Thu Jul 10 2008 - 05:00:58 PDT)
- Re: Re: Re: AMBER: replicas trapped in a few low temperatures Ye Mei (Thu Jul 10 2008 - 04:49:08 PDT)
  - Re: Re: Re: AMBER: replicas trapped in a few low temperatures Carlos Simmerling (Thu Jul 10 2008 - 05:12:51 PDT)
- Re: Re: Re: AMBER: replicas trapped in a few low temperatures Ye Mei (Thu Jul 10 2008 - 05:11:28 PDT)
- Re: Re: Re: AMBER: replicas trapped in a few low temperatures Ye Mei (Thu Jul 10 2008 - 05:35:41 PDT)
  - Re: Re: Re: AMBER: replicas trapped in a few low temperatures Carlos Simmerling (Thu Jul 10 2008 - 06:11:33 PDT)
AMBER: antechamber and charmm Alan (Thu Jul 10 2008 - 02:43:58 PDT)
- Re: AMBER: antechamber and charmm Junmei Wang (Thu Jul 17 2008 - 07:33:23 PDT)
  - Re: AMBER: antechamber and charmm Alan (Thu Jul 17 2008 - 09:05:40 PDT)
    - Re: AMBER: antechamber and charmm David A. Case (Thu Jul 17 2008 - 09:16:02 PDT)
AMBER: bond command Boutheina Kerkeni (Thu Jul 10 2008 - 10:30:46 PDT)
- Re: AMBER: bond command Wang,Ying (Thu Jul 10 2008 - 10:56:01 PDT)
- Re: AMBER: bond command M. L. Dodson (Thu Jul 10 2008 - 11:34:33 PDT)
- RE: AMBER: bond command Ross Walker (Thu Jul 10 2008 - 12:15:53 PDT)
  - Re: AMBER: bond command Boutheina Kerkeni (Fri Jul 11 2008 - 05:00:48 PDT)
AMBER: problem with restraints Barbault Florent (Thu Jul 10 2008 - 11:59:15 PDT)
AMBER: difference between sander and NAB Hu, Shaowen (JSC-SK)[USRA] (Thu Jul 10 2008 - 12:44:41 PDT)
- Re: AMBER: difference between sander and NAB David A. Case (Thu Jul 10 2008 - 15:22:49 PDT)
  - RE: AMBER: difference between sander and NAB Hu, Shaowen (JSC-SK)[USRA] (Fri Jul 11 2008 - 06:02:51 PDT)
AMBER: problem with rdparm Harry (Yicun) Ni (Thu Jul 10 2008 - 15:05:41 PDT)
- Re: AMBER: problem with rdparm Thomas Cheatham III (Thu Jul 10 2008 - 15:13:35 PDT)
AMBER: timing info output from pmemd Vlad Cojocaru (Fri Jul 11 2008 - 01:49:28 PDT)
- Re: AMBER: timing info output from pmemd Robert Duke (Fri Jul 11 2008 - 05:14:29 PDT)
  - Re: AMBER: timing info output from pmemd Vlad Cojocaru (Fri Jul 11 2008 - 05:33:31 PDT)
- Re: AMBER: timing info output from pmemd Robert Duke (Fri Jul 11 2008 - 06:41:21 PDT)
  - Re: AMBER: timing info output from pmemd Vlad Cojocaru (Fri Jul 11 2008 - 06:54:02 PDT)
AMBER: configure_amber (10) for pg compilers Vlad Cojocaru (Fri Jul 11 2008 - 04:51:47 PDT)
- Re: AMBER: configure_amber (10) for pg compilers Robert Duke (Fri Jul 11 2008 - 05:27:02 PDT)
AMBER: size of pdb Boutheina Kerkeni (Fri Jul 11 2008 - 08:13:57 PDT)
- Re: AMBER: size of pdb David A. Case (Sat Jul 12 2008 - 07:45:51 PDT)
AMBER: question about the improper torsion Harry (Yicun) Ni (Fri Jul 11 2008 - 09:34:17 PDT)
- Re: AMBER: question about the improper torsion David A. Case (Sat Jul 12 2008 - 07:43:46 PDT)
  - Re: AMBER: question about the improper torsion Harry (Yicun) Ni (Mon Jul 14 2008 - 21:12:57 PDT)
- Re: AMBER: question about the improper torsion Bill Ross (Tue Jul 15 2008 - 09:48:24 PDT)
AMBER: NMA Steve Seibold (Fri Jul 11 2008 - 09:34:00 PDT)
- Re: AMBER: NMA David A. Case (Fri Jul 11 2008 - 11:19:06 PDT)
AMBER: Installation on Mac OSX G5 dual processor George Tzotzos (Fri Jul 11 2008 - 13:30:21 PDT)
AMBER: Installation of Amber 10 on Dual-Core Intel Mac George Tzotzos (Fri Jul 11 2008 - 13:33:55 PDT)
AMBER: empty output Boutheina Kerkeni (Sat Jul 12 2008 - 08:29:47 PDT)
- RE: AMBER: empty output Ross Walker (Sat Jul 12 2008 - 09:54:01 PDT)
  - RE: AMBER: empty output Boutheina Kerkeni (Tue Jul 15 2008 - 10:31:50 PDT)
AMBER: Atom type with 10-12 and 6-12 interactions in Amber9 Brad Lambeth (Sat Jul 12 2008 - 17:20:09 PDT)
AMBER: Nmode entropy calcs Sergio Wong (Sat Jul 12 2008 - 18:09:51 PDT)
- Re: AMBER: Nmode entropy calcs David A. Case (Sun Jul 13 2008 - 08:45:56 PDT)
AMBER: Model of deoxyadenosine in Cornell 95 paper Ilyas Yildirim (Sun Jul 13 2008 - 16:14:48 PDT)
- Re: AMBER: Model of deoxyadenosine in Cornell 95 paper Piotr Cieplak (Tue Jul 15 2008 - 23:32:08 PDT)
AMBER: AmberTools1.1 (and 1.0) antechamber endless loop Grange Hermitage (Sun Jul 13 2008 - 18:06:33 PDT)
- RE: AMBER: AmberTools1.1 (and 1.0) antechamber endless loop Ross Walker (Sun Jul 13 2008 - 21:35:42 PDT)
  - Re: AMBER: AmberTools1.1 (and 1.0) antechamber endless loop Grange Hermitage (Mon Jul 14 2008 - 00:41:40 PDT)
    - RE: AMBER: AmberTools1.1 (and 1.0) antechamber endless loop Ross Walker (Tue Jul 15 2008 - 08:50:20 PDT)
  - Re: AMBER: AmberTools1.1 (and 1.0) antechamber endless loop Grange Hermitage (Mon Jul 14 2008 - 17:18:40 PDT)
    - RE: AMBER: AmberTools1.1 (and 1.0) antechamber endless loop Ross Walker (Tue Jul 15 2008 - 09:01:55 PDT)
AMBER: POL3 with gaff and ff02EP Grange Hermitage (Sun Jul 13 2008 - 18:15:43 PDT)
- RE: AMBER: POL3 with gaff and ff02EP Ross Walker (Sun Jul 13 2008 - 21:40:02 PDT)
AMBER: Alanine scanning Khaled Barakat (Sun Jul 13 2008 - 18:50:47 PDT)
AMBER: querry dipti lele (Mon Jul 14 2008 - 01:05:15 PDT)
- Re: AMBER: querry Sandeep Kaushik (Tue Jul 22 2008 - 05:09:08 PDT)
  - Re: AMBER: querry Lachele Foley (Lists) (Tue Jul 22 2008 - 06:55:08 PDT)
AMBER: Tutorial 6 Beale, John (Mon Jul 14 2008 - 09:48:21 PDT)
- RE: AMBER: Tutorial 6 Ross Walker (Mon Jul 14 2008 - 11:48:05 PDT)
AMBER: bad nonbon in nmode (amber9) Enghui Yap (Mon Jul 14 2008 - 09:25:29 PDT)
- AMBER: Res minimization Thomas Leonard (Tue Jul 15 2008 - 00:34:47 PDT)
  - RE: AMBER: Res minimization Ross Walker (Tue Jul 15 2008 - 08:53:46 PDT)
  - Re: AMBER: Res minimization gurpreet singh (Tue Jul 15 2008 - 21:25:54 PDT)
AMBER: Error when performing Alanine scanning Khaled Barakat (Mon Jul 14 2008 - 18:41:26 PDT)
AMBER: files in Amber directory ( to Junmei Wang ) John Bennett (Tue Jul 15 2008 - 04:10:40 PDT)
- Re: AMBER: files in Amber directory ( to Junmei Wang ) David A. Case (Tue Jul 15 2008 - 11:55:41 PDT)
- Re: AMBER: files in Amber directory ( to Junmei Wang ) Junmei Wang (Thu Jul 17 2008 - 07:56:06 PDT)
  - Re: AMBER: files in Amber directory ( to Junmei Wang ) John Bennett (Fri Jul 18 2008 - 04:25:38 PDT)
AMBER: ptraj: projection command missing in dispatch.c (AMBER 10) Vlad Cojocaru (Tue Jul 15 2008 - 06:45:11 PDT)
- Re: AMBER: ptraj: projection command missing in dispatch.c (AMBER 10) David A. Case (Tue Jul 15 2008 - 11:57:52 PDT)
AMBER: sleap test failures Vlad Cojocaru (Tue Jul 15 2008 - 07:14:23 PDT)
- Re: AMBER: sleap test failures David A. Case (Tue Jul 15 2008 - 15:46:00 PDT)
  - Re: AMBER: sleap test failures Vlad Cojocaru (Wed Jul 16 2008 - 01:07:48 PDT)
  - Re: AMBER: sleap test failures Vlad Cojocaru (Wed Jul 16 2008 - 05:40:12 PDT)
AMBER: test of parallel sander 10 fail Vlad Cojocaru (Tue Jul 15 2008 - 10:05:51 PDT)
- Re: AMBER: test of parallel sander 10 fail Thomas Cheatham III (Tue Jul 15 2008 - 10:41:12 PDT)
AMBER: RMSD per residue luzhenw1.msu.edu (Tue Jul 15 2008 - 13:28:08 PDT)
- Re: AMBER: RMSD per residue gurpreet singh (Tue Jul 15 2008 - 21:13:59 PDT)
AMBER: Ligand force field generation, and its consistency with the force field of the protein. SeungPyo Hong (Wed Jul 16 2008 - 05:15:48 PDT)
- Re: AMBER: Ligand force field generation, and its consistency with the force field of the protein. Alan (Wed Jul 16 2008 - 05:46:15 PDT)
- AMBER:Some questions about replica exchan ge huzehan19870731.126.com (Wed Jul 16 2008 - 06:07:46 PDT)
  - RE: AMBER:Some questions about replica exchan ge Ross Walker (Wed Jul 16 2008 - 07:45:38 PDT)
    - Re: AMBER:Some questions about replica exchan ge Carlos Simmerling (Wed Jul 16 2008 - 08:04:25 PDT)
- Re: AMBER: Ligand force field generation, and its consistency with the force field of the protein. Gustavo Seabra (Wed Jul 16 2008 - 07:08:45 PDT)
  - Re: AMBER: Ligand force field generation, and its consistency with the force field of the protein. SeungPyo Hong (Wed Jul 16 2008 - 18:50:31 PDT)
AMBER: about RMSD per residue luzhenw1.msu.edu (Wed Jul 16 2008 - 06:48:05 PDT)
- Re: AMBER: about RMSD per residue Wei Huang (Wed Jul 16 2008 - 07:20:03 PDT)
  - RE: AMBER: about RMSD per residue Ross Walker (Wed Jul 16 2008 - 07:52:38 PDT)
    - RE: AMBER: about RMSD per residue Wei Huang (Wed Jul 16 2008 - 08:08:36 PDT)
    - Re: AMBER: about RMSD per residue Gustavo Seabra (Wed Jul 16 2008 - 08:22:39 PDT)
    - Re: AMBER: about RMSD per residue Wei Huang (Wed Jul 16 2008 - 08:31:24 PDT)
- RE: AMBER: about RMSD per residue Ross Walker (Wed Jul 16 2008 - 09:40:42 PDT)
AMBER: free energy Boutheina Kerkeni (Wed Jul 16 2008 - 08:54:39 PDT)
- Re: AMBER: free energy Christopher Gaughan (Wed Jul 16 2008 - 09:03:26 PDT)
  - Re: AMBER: free energy Adrian Roitberg (Wed Jul 16 2008 - 07:10:41 PDT)
    - Re: AMBER: free energy Boutheina Kerkeni (Wed Jul 16 2008 - 09:30:44 PDT)
- Re: AMBER: free energy Thomas Steinbrecher (Wed Jul 16 2008 - 09:22:45 PDT)
AMBER: amber 10 and mpich2 (got eof on console error message from mpich2) Vlad Cojocaru (Thu Jul 17 2008 - 06:30:24 PDT)
- AMBER: Re: amber 10 and mpich2 (got eof on console error message from mpich2) Vlad Cojocaru (Thu Jul 17 2008 - 06:33:04 PDT)
- AMBER: entropy of released water Swarup Gupta (Thu Aug 07 2008 - 05:36:32 PDT)
AMBER: SCC-DFTB for Zinc atom Jifeng Wang (Thu Jul 17 2008 - 08:33:15 PDT)
- Re: AMBER: SCC-DFTB for Zinc atom Gustavo Seabra (Thu Jul 17 2008 - 08:48:33 PDT)
  - Re: AMBER: SCC-DFTB for Zinc atom Jifeng Wang (Fri Jul 18 2008 - 10:10:17 PDT)
    - Re: AMBER: SCC-DFTB for Zinc atom Gustavo Seabra (Fri Jul 18 2008 - 16:21:45 PDT)
AMBER: paricular atom coordinates? Vijay Singh (Thu Jul 17 2008 - 09:13:30 PDT)
AMBER: The list-directed or NAMELIST READ statement cannot be completed rebeca (Thu Jul 17 2008 - 09:42:25 PDT)
- Re: AMBER: The list-directed or NAMELIST READ statement cannot be completed Carlos Simmerling (Thu Jul 17 2008 - 09:47:24 PDT)
- RE: AMBER: The list-directed or NAMELIST READ statement cannot be completed Ross Walker (Thu Jul 17 2008 - 09:55:22 PDT)
AMBER: AmberTools-1.1 port for FreeBSD M. L. Dodson (Thu Jul 17 2008 - 10:59:05 PDT)
AMBER: the plot of the groove width versus time for RNA 欧阳德方 (Thu Jul 17 2008 - 16:35:31 PDT)
AMBER: how to generate psf file using the AMBER topology file tinni sona (Fri Jul 18 2008 - 03:41:11 PDT)
- Re: AMBER: how to generate psf file using the AMBER topology file Balazs JOJART (Fri Jul 18 2008 - 04:09:21 PDT)
  - Re: AMBER: how to generate psf file using the AMBER topology file tinni sona (Fri Jul 18 2008 - 05:08:48 PDT)
    - RE: AMBER: how to generate psf file using the AMBER topology file Ross Walker (Fri Jul 18 2008 - 09:57:14 PDT)
    - Re: AMBER: how to generate psf file using the AMBER topology file tinni sona (Sat Jul 19 2008 - 22:38:10 PDT)
AMBER: Restarting Problem in MD Simulation khuram sb (Fri Jul 18 2008 - 03:37:07 PDT)
- RE: AMBER: Restarting Problem in MD Simulation Ross Walker (Fri Jul 18 2008 - 10:08:46 PDT)
AMBER: Problems with Frozen atoms julliane Yoneda (Fri Jul 18 2008 - 13:06:54 PDT)
AMBER: a link for Amber ff ported to Charmm Alan (Sat Jul 19 2008 - 02:07:27 PDT)
- Re: AMBER: a link for Amber ff ported to Charmm David A. Case (Sat Jul 19 2008 - 11:29:18 PDT)
  - Re: AMBER: a link for Amber ff ported to Charmm Alan (Sat Jul 19 2008 - 14:50:25 PDT)
    - Re: AMBER: a link for Amber ff ported to Charmm Adrian Roitberg (Sat Jul 19 2008 - 15:10:58 PDT)
    - RE: AMBER: a link for Amber ff ported to Charmm Ross Walker (Sat Jul 19 2008 - 15:28:24 PDT)
    - Re: AMBER: a link for Amber ff ported to Charmm Alan (Sat Jul 19 2008 - 22:50:22 PDT)
AMBER: parmbsc0 Dr. Suzie Byun (Sat Jul 19 2008 - 08:40:05 PDT)
AMBER: antechamber generated input for gaussian error Grange Hermitage (Sat Jul 19 2008 - 17:53:49 PDT)
- Re: AMBER: antechamber generated input for gaussian error Junmei Wang (Wed Jul 23 2008 - 08:29:21 PDT)
AMBER: Trans proline dipti lele (Sat Jul 19 2008 - 22:53:00 PDT)
- Re: AMBER: Trans proline Barbault Florent (Sat Jul 19 2008 - 23:27:37 PDT)
- Re: AMBER: Trans proline Carlos Simmerling (Sun Jul 20 2008 - 04:50:39 PDT)
  - Re: AMBER: Trans proline Adrian Roitberg (Sun Jul 20 2008 - 05:27:45 PDT)
    - Re: AMBER: Trans proline Brent Krueger (Sat Aug 02 2008 - 20:47:16 PDT)
AMBER: Release of version 1.2 of AmberTools David A. Case (Mon Jul 21 2008 - 10:01:29 PDT)
AMBER: Where is ICO read from the ix array? Brad Lambeth (Mon Jul 21 2008 - 12:49:44 PDT)
- Re: AMBER: Where is ICO read from the ix array? David A. Case (Mon Jul 21 2008 - 16:54:18 PDT)
AMBER: Amber tools 1.2 test failure (installation) Myunggi Yi (Mon Jul 21 2008 - 15:17:05 PDT)
- Re: AMBER: Amber tools 1.2 test failure (installation) David A. Case (Mon Jul 21 2008 - 16:36:16 PDT)
  - Re: AMBER: Amber tools 1.2 test failure (installation) Myunggi Yi (Thu Jul 24 2008 - 10:09:11 PDT)
AMBER: Problem with box dimension in AmberTools ptraj Steve Spronk (Mon Jul 21 2008 - 23:35:47 PDT)
- Re: AMBER: Problem with box dimension in AmberTools ptraj Thomas Cheatham (Tue Jul 22 2008 - 09:47:42 PDT)
AMBER: amber ff and how it deals with out-plane chiral C Alan (Tue Jul 22 2008 - 00:59:05 PDT)
- Re: AMBER: amber ff and how it deals with out-plane chiral C Carlos Simmerling (Tue Jul 22 2008 - 04:57:04 PDT)
  - Re: AMBER: amber ff and how it deals with out-plane chiral C Alan (Tue Jul 22 2008 - 07:41:27 PDT)
    - Re: AMBER: amber ff and how it deals with out-plane chiral C Carlos Simmerling (Tue Jul 22 2008 - 08:15:56 PDT)
- Re: AMBER: amber ff and how it deals with out-plane chiral C Bill Ross (Tue Jul 22 2008 - 14:44:36 PDT)
AMBER: targeted MD Germain Vallverdu (Tue Jul 22 2008 - 03:08:04 PDT)
- Re: AMBER: targeted MD Carlos Simmerling (Tue Jul 22 2008 - 04:48:15 PDT)
- AMBER: Indentifying cluster center structures in trajectory Anselm Horn (Wed Jul 23 2008 - 00:14:41 PDT)
  - RE: AMBER: Indentifying cluster center structures in trajectory Ross Walker (Wed Jul 23 2008 - 02:14:27 PDT)
AMBER: Amber9 vs AmberTools 1.0: weird imaging problem with ptraj? Hannes Loeffler (Tue Jul 22 2008 - 07:08:36 PDT)
- Re: AMBER: Amber9 vs AmberTools 1.0: weird imaging problem with ptraj? Thomas Cheatham (Tue Jul 22 2008 - 09:45:12 PDT)
  - Re: AMBER: Amber9 vs AmberTools 1.0: weird imaging problem with ptraj? Hannes Loeffler (Wed Jul 23 2008 - 04:11:57 PDT)
AMBER: FreeBSD "port" for AmberTools-1.2 M. L. Dodson (Tue Jul 22 2008 - 12:15:48 PDT)
- Re: AMBER: FreeBSD "port" for AmberTools-1.2 M. L. Dodson (Tue Jul 22 2008 - 12:30:27 PDT)
- AMBER: Re: FreeBSD "port" for AmberTools-1.2 M. L. Dodson (Wed Jul 23 2008 - 07:17:56 PDT)
AMBER: SHIFTS compile error IN SUK JOUNG (Tue Jul 22 2008 - 13:25:43 PDT)
- Re: AMBER: SHIFTS compile error David A. Case (Wed Jul 23 2008 - 10:22:32 PDT)
AMBER: protonated guanine, cytosine parameters Kliman, Michal (Tue Jul 22 2008 - 15:22:19 PDT)
AMBER: improper dihedral in ff03 united atom forcefield 秦姗姗 (Tue Jul 22 2008 - 18:49:28 PDT)
AMBER: improper dihedrals in 03 united atom force field Q733 (Tue Jul 22 2008 - 19:00:03 PDT)
Re: AMBER: improper dihedral in ff03 united atom forcefield Bill Ross (Tue Jul 22 2008 - 21:28:07 PDT)
- Re: Re: AMBER: improper dihedral in ff03 united atom forcefield 秦姗姗 (Tue Jul 22 2008 - 22:14:11 PDT)
- Re: Re: AMBER: improper dihedral in ff03 united atom forcefield Bill Ross (Wed Jul 23 2008 - 11:19:31 PDT)
AMBER: 1.5ns rst file to PDB file Conversion Error khuram sb (Tue Jul 22 2008 - 22:07:24 PDT)
- RE: AMBER: 1.5ns rst file to PDB file Conversion Error Ross Walker (Wed Jul 23 2008 - 02:08:46 PDT)
AMBER: High force constant for MD ??? Waqas Nasir (Wed Jul 23 2008 - 02:49:46 PDT)
- Re: AMBER: High force constant for MD ??? Carlos Simmerling (Wed Jul 23 2008 - 04:02:13 PDT)
- Re: AMBER: High force constant for MD ??? Waqas Nasir (Thu Jul 24 2008 - 03:42:13 PDT)
AMBER: Polarizable force field for divalent ions? Yi-Ming Cheng (Wed Jul 23 2008 - 03:59:08 PDT)
AMBER: Trans proline dipti lele (Wed Jul 23 2008 - 04:01:28 PDT)
AMBER: Problems in restrained minimization julliane Yoneda (Wed Jul 23 2008 - 06:08:32 PDT)
AMBER: Hydroxyproline in AMBER Michael Entz (Wed Jul 23 2008 - 08:40:05 PDT)
- Re: AMBER: Hydroxyproline in AMBER Carlos Simmerling (Wed Jul 23 2008 - 09:03:01 PDT)
- Re: AMBER: Hydroxyproline in AMBER Adrian Roitberg (Wed Jul 23 2008 - 09:14:06 PDT)
AMBER: Query about the charge of atoms in the parmtop file tinni sona (Wed Jul 23 2008 - 09:48:19 PDT)
- Re: AMBER: Query about the charge of atoms in the parmtop file Carlos Simmerling (Wed Jul 23 2008 - 10:16:09 PDT)
  - Re: AMBER: Query about the charge of atoms in the parmtop file tinni sona (Thu Jul 24 2008 - 00:19:26 PDT)
    - RE: AMBER: Query about the charge of atoms in the parmtop file Ross Walker (Thu Jul 24 2008 - 05:49:03 PDT)
    - Re: AMBER: Query about the charge of atoms in the parmtop file Carlos Simmerling (Thu Jul 24 2008 - 06:09:45 PDT)
    - Re: AMBER: Query about the charge of atoms in the parmtop file Alan (Fri Jul 25 2008 - 12:13:43 PDT)
AMBER: Which CO2 potential? Jones de Andrade (Wed Jul 23 2008 - 17:27:58 PDT)
- Re: AMBER: Which CO2 potential? gustavo.seabra.gmail.com (Wed Jul 23 2008 - 20:32:58 PDT)
  - Re: AMBER: Which CO2 potential? Jones de Andrade (Wed Jul 23 2008 - 20:45:00 PDT)
    - Re: AMBER: Which CO2 potential? Gustavo Seabra (Thu Jul 24 2008 - 06:08:53 PDT)
AMBER: amber9 install problem hklwatergod (Wed Jul 23 2008 - 23:11:33 PDT)
- Re: AMBER: amber9 install problem David A. Case (Thu Jul 24 2008 - 08:08:21 PDT)
  - AMBER: AMBER 10: Fortran Runtime Error George Tzotzos (Fri Jul 25 2008 - 07:38:32 PDT)
AMBER: EVB tests failure Vlad Cojocaru (Thu Jul 24 2008 - 01:34:52 PDT)
AMBER: solvate dna in TIP3PBOX 10.0 Collins Nganou (Thu Jul 24 2008 - 02:28:44 PDT)
- RE: AMBER: solvate dna in TIP3PBOX 10.0 Ross Walker (Thu Jul 24 2008 - 05:29:51 PDT)
AMBER: adding missing residues soumick (Thu Jul 24 2008 - 04:09:16 PDT)
- RE: AMBER: adding missing residues Ross Walker (Thu Jul 24 2008 - 05:35:41 PDT)
- Re: AMBER: adding missing residues David A. Case (Thu Jul 24 2008 - 08:37:36 PDT)
AMBER: calculating the enthalpy of evaporation jessica stolee (Thu Jul 24 2008 - 12:24:40 PDT)
- Re: AMBER: calculating the enthalpy of evaporation David A. Case (Thu Jul 24 2008 - 13:31:01 PDT)
AMBER: Running patch "bugfix.at.all" with AmberTools 1.2 Mike Hanby (Thu Jul 24 2008 - 14:47:34 PDT)
- Re: AMBER: Running patch "bugfix.at.all" with AmberTools 1.2 David A. Case (Thu Jul 24 2008 - 16:37:32 PDT)
  - RE: AMBER: Running patch "bugfix.at.all" with AmberTools 1.2 Mike Hanby (Fri Jul 25 2008 - 09:16:37 PDT)
    - RE: AMBER: Running patch "bugfix.at.all" with AmberTools 1.2 Scott Brozell (Thu Jul 31 2008 - 15:04:55 PDT)
AMBER: big molecule numbers Adrien Delmont (Thu Jul 24 2008 - 15:27:22 PDT)
- Re: AMBER: big molecule numbers David A. Case (Thu Jul 24 2008 - 18:43:26 PDT)
  - AMBER: AMBER10: Fortran Runtime Error George Tzotzos (Fri Jul 25 2008 - 08:19:03 PDT)
    - RE: AMBER: AMBER10: Fortran Runtime Error Ross Walker (Fri Jul 25 2008 - 14:22:16 PDT)
- RE: AMBER: big molecule numbers Ross Walker (Fri Jul 25 2008 - 01:10:05 PDT)
AMBER: solvate dna in TIP3PBOX 10.0 Collins Nganou (Thu Jul 24 2008 - 23:51:54 PDT)
- RE: AMBER: solvate dna in TIP3PBOX 10.0 Ross Walker (Fri Jul 25 2008 - 01:14:26 PDT)
AMBER: Regarding ff03 forcefield Reena ..... (Fri Jul 25 2008 - 00:24:41 PDT)
- RE: AMBER: Regarding ff03 forcefield Ross Walker (Fri Jul 25 2008 - 01:16:57 PDT)
- RE: AMBER: Regarding ff03 forcefield Yong Duan (Fri Jul 25 2008 - 09:24:19 PDT)
- RE: AMBER: Regarding ff03 forcefield Bill Ross (Fri Jul 25 2008 - 13:32:02 PDT)
  - Re: AMBER: Regarding ff03 forcefield David A. Case (Fri Jul 25 2008 - 13:46:26 PDT)
AMBER: Charge neutralization, GlcNac & GalNac improper torsional angles from old PREP Sandeep Kaushik (Fri Jul 25 2008 - 03:04:11 PDT)
- Re: AMBER: Charge neutralization, GlcNac & GalNac improper torsional angles from old PREP Lachele Foley (Lists) (Fri Jul 25 2008 - 07:47:54 PDT)
  - Re: AMBER: Charge neutralization, GlcNac & GalNac improper torsional angles from old PREP Sandeep Kaushik (Mon Jul 28 2008 - 05:30:16 PDT)
- Re: AMBER: Charge neutralization, GlcNac & GalNac improper torsional angles from old PREP Bill Ross (Mon Jul 28 2008 - 17:26:35 PDT)
AMBER: amber 10: sander and pmemd performance Vlad Cojocaru (Fri Jul 25 2008 - 02:57:45 PDT)
- Re: AMBER: amber 10: sander and pmemd performance Robert Duke (Fri Jul 25 2008 - 07:31:30 PDT)
  - Re: AMBER: amber 10: sander and pmemd performance Vlad Cojocaru (Fri Jul 25 2008 - 08:14:08 PDT)
- Re: AMBER: amber 10: sander and pmemd performance Robert Duke (Fri Jul 25 2008 - 09:06:41 PDT)
AMBER: simulation with many formamide molecules Adrien Delmont (Fri Jul 25 2008 - 03:44:23 PDT)
- AMBER: the pmemd problem hklwatergod (Fri Jul 25 2008 - 04:51:32 PDT)
  - Re: AMBER: the pmemd problem Robert Duke (Fri Jul 25 2008 - 06:46:24 PDT)
AMBER: # of ligands and receptors in mmpbsa Christopher Gaughan (Fri Jul 25 2008 - 07:57:03 PDT)
- Re: AMBER: # of ligands and receptors in mmpbsa Scott Brozell (Thu Jul 31 2008 - 19:14:50 PDT)
AMBER: Energy analysis aneesh cna (Fri Jul 25 2008 - 08:12:10 PDT)
AMBER: amber10: pmemd gfortran James W. Caldwell (Fri Jul 25 2008 - 11:23:06 PDT)
- Re: AMBER: amber10: pmemd gfortran Robert Duke (Fri Jul 25 2008 - 12:01:27 PDT)
- Re: AMBER: amber10: pmemd gfortran David A. Case (Fri Jul 25 2008 - 12:05:23 PDT)
  - RE: AMBER: amber10: pmemd gfortran James W. Caldwell (Fri Jul 25 2008 - 15:06:01 PDT)
    - RE: AMBER: amber10: pmemd gfortran Scott Brozell (Thu Jul 31 2008 - 20:16:45 PDT)
AMBER: Does clustering involve fitting? Steve Spronk (Fri Jul 25 2008 - 13:02:09 PDT)
- Re: AMBER: Does clustering involve fitting? Jianyin Shao (Wed Jul 30 2008 - 14:29:57 PDT)
Re: AMBER: solvate dna in TIP3PBOX 10.0 Bill Ross (Fri Jul 25 2008 - 13:28:46 PDT)
- Re: AMBER: solvate dna in TIP3PBOX 10.0 Bill Ross (Sat Jul 26 2008 - 11:11:44 PDT)
Re: AMBER: Charge neutralization, GlcNac & GalNac improper torsional angles from old PREP Bill Ross (Fri Jul 25 2008 - 13:40:27 PDT)
AMBER: fortran runtime error in "make test.serial" with gfortran Jaber Jahanbin Sardroodi (Fri Jul 25 2008 - 15:23:25 PDT)
- Re: AMBER: fortran runtime error in "make test.serial" with gfortran David A. Case (Fri Jul 25 2008 - 16:03:57 PDT)
AMBER: NPRO net charge in amber10/dat/leap/lib/all_aminont03.lib is 0.900026, why? Alan (Sat Jul 26 2008 - 01:33:46 PDT)
- Re: AMBER: NPRO net charge in amber10/dat/leap/lib/all_aminont03.lib is 0.900026, why? Alan (Mon Jul 28 2008 - 03:54:31 PDT)
  - Re: AMBER: NPRO net charge in amber10/dat/leap/lib/all_aminont03.lib is 0.900026, why? FyD (Mon Jul 28 2008 - 05:28:50 PDT)
    - Re: AMBER: NPRO net charge in amber10/dat/leap/lib/all_aminont03.lib is 0.900026, why? Carlos Simmerling (Mon Jul 28 2008 - 05:54:51 PDT)
    - Re: AMBER: NPRO net charge in amber10/dat/leap/lib/all_aminont03.lib is 0.900026, why? Alan (Mon Jul 28 2008 - 06:21:35 PDT)
    - Re: AMBER: NPRO net charge in amber10/dat/leap/lib/all_aminont03.lib is 0.900026, why? Carlos Simmerling (Mon Jul 28 2008 - 06:52:08 PDT)
    - Re: AMBER: NPRO net charge in amber10/dat/leap/lib/all_aminont03.lib is 0.900026, why? Alan (Mon Jul 28 2008 - 07:50:00 PDT)
AMBER: big molecule numbers ( simulation with many formamide molecules ) Adrien Delmont (Sat Jul 26 2008 - 02:04:08 PDT)
- RE: AMBER: big molecule numbers ( simulation with many formamide molecules ) Ross Walker (Sat Jul 26 2008 - 06:58:34 PDT)
- Re: AMBER: big molecule numbers ( simulation with many formamide molecules ) Adrien Delmont (Sat Jul 26 2008 - 08:55:11 PDT)
  - RE: AMBER: big molecule numbers ( simulation with many formamide molecules ) Ross Walker (Sun Jul 27 2008 - 02:19:41 PDT)
AMBER: solvate dna in TIP3PBOX 10.0 Collins Nganou (Sat Jul 26 2008 - 02:08:26 PDT)
AMBER: RE: AMBER Question Ross Walker (Sat Jul 26 2008 - 06:53:25 PDT)
AMBER: interaction energies in Amber and VMD/NAMD Alessandro Nascimento (Sat Jul 26 2008 - 09:09:38 PDT)
- Re: AMBER: interaction energies in Amber and VMD/NAMD Carlos Simmerling (Sat Jul 26 2008 - 10:20:11 PDT)
- Re: AMBER: interaction energies in Amber and VMD/NAMD David A. Case (Sat Jul 26 2008 - 17:36:46 PDT)
  - Re: AMBER: interaction energies in Amber and VMD/NAMD Carlos Simmerling (Sat Jul 26 2008 - 17:46:58 PDT)
    - Re: AMBER: interaction energies in Amber and VMD/NAMD Alan (Sat Jul 26 2008 - 23:26:32 PDT)
    - Re: AMBER: interaction energies in Amber and VMD/NAMD Alessandro Nascimento (Sun Jul 27 2008 - 17:38:56 PDT)
    - Re: AMBER: interaction energies in Amber and VMD/NAMD Alan (Tue Jul 29 2008 - 01:19:16 PDT)
    - Re: AMBER: interaction energies in Amber and VMD/NAMD Alan (Tue Jul 29 2008 - 03:10:48 PDT)
AMBER: the install problem hklwatergod (Sat Jul 26 2008 - 23:34:55 PDT)
- RE: AMBER: the install problem Ross Walker (Sun Jul 27 2008 - 02:00:59 PDT)
- Re: RE: AMBER: the install problem hklwatergod (Mon Jul 28 2008 - 07:22:58 PDT)
- Re: Re: RE: AMBER: the install problem hklwatergod (Tue Oct 14 2008 - 00:19:02 PDT)
AMBER: Query dipti lele (Sat Jul 26 2008 - 23:40:54 PDT)
- RE: AMBER: Query Ross Walker (Sun Jul 27 2008 - 02:04:57 PDT)
AMBER: radius of calcium ion in MM_PBSA Hannes Wallnoefer (Mon Jul 28 2008 - 01:18:22 PDT)
- Re: AMBER: radius of calcium ion in MM_PBSA Neha Gandhi (Mon Jul 28 2008 - 01:46:50 PDT)
  - Re: AMBER: radius of calcium ion in MM_PBSA Hannes Wallnoefer (Mon Jul 28 2008 - 02:28:01 PDT)
    - Re: AMBER: radius of calcium ion in MM_PBSA Navnit Kumar Mishra (Mon Jul 28 2008 - 02:55:33 PDT)
AMBER: Problem in .parmtop file sudipta sinha (Mon Jul 28 2008 - 08:30:09 PDT)
AMBER: Amber 10 on the BlueGene Mike Hanby (Mon Jul 28 2008 - 09:15:58 PDT)
- Re: AMBER: Amber 10 on the BlueGene Robert Duke (Mon Jul 28 2008 - 10:17:18 PDT)
  - Re: AMBER: Amber 10 on the BlueGene Carlos Simmerling (Mon Jul 28 2008 - 11:37:59 PDT)
Re: AMBER: interaction energies in Amber Alessandro Nascimento (Mon Jul 28 2008 - 17:51:01 PDT)
AMBER: Energy minimization of protein-ligand complex Dong Xu (Tue Jul 29 2008 - 00:18:57 PDT)
AMBER: PMEND 9 compilation problems Nick Holway (Tue Jul 29 2008 - 09:04:36 PDT)
- Re: AMBER: PMEND 9 compilation problems Robert Duke (Tue Jul 29 2008 - 10:41:54 PDT)
  - Re: AMBER: PMEND 9 compilation problems Nick Holway (Wed Jul 30 2008 - 06:50:42 PDT)
- Re: AMBER: PMEND 9 compilation problems Robert Duke (Wed Jul 30 2008 - 07:40:00 PDT)
AMBER: Volume of ucell too big baohua zhang (Tue Jul 29 2008 - 20:30:43 PDT)
- Re: AMBER: Volume of ucell too big David A. Case (Tue Jul 29 2008 - 22:19:31 PDT)
AMBER: for mask in rms Wenyong Tong (Tue Jul 29 2008 - 20:35:23 PDT)
AMBER: DMSOBOX jacopo.sgrignani.unifi.it (Wed Jul 30 2008 - 00:05:00 PDT)
- Re: AMBER: DMSOBOX Panwang Zhou (Wed Jul 30 2008 - 00:31:53 PDT)
Re: AMBER: interaction energies in Amber and VMD/NAMD (SOLVED) Alessandro Nascimento (Wed Jul 30 2008 - 08:29:47 PDT)
AMBER: mask for oligosaccharide Wenyong Tong (Wed Jul 30 2008 - 11:23:58 PDT)
- Re: AMBER: mask for oligosaccharide Jianyin Shao (Wed Jul 30 2008 - 15:26:31 PDT)
  - Re: AMBER: mask for oligosaccharide Wenyong Tong (Wed Jul 30 2008 - 21:13:08 PDT)
AMBER: Q: ntc = 3 parallel runnable not compiled in Amber 9? Qicun Shi (Wed Jul 30 2008 - 20:51:17 PDT)
- Re: AMBER: Q: ntc = 3 parallel runnable not compiled in Amber 9? Carlos Simmerling (Thu Jul 31 2008 - 05:07:21 PDT)
AMBER: how to get the potential energy of a protein from the system TaoPaul (Thu Jul 31 2008 - 01:29:08 PDT)
- Re: AMBER: how to get the potential energy of a protein from the system David A. Case (Thu Jul 31 2008 - 07:45:47 PDT)
  - AMBER: addles Urszula Uciechowska (Tue Aug 05 2008 - 01:30:20 PDT)
    - Re: AMBER: addles Carlos Simmerling (Tue Aug 05 2008 - 04:02:47 PDT)
  - AMBER: linear interaction energy Urszula Uciechowska (Thu Aug 07 2008 - 06:55:18 PDT)
AMBER: opls/aa in Amber status Alan (Thu Jul 31 2008 - 01:41:58 PDT)
AMBER: amb2gmx for big systems rebeca.mmb.pcb.ub.es (Thu Jul 31 2008 - 03:40:39 PDT)
AMBER: ACPYPI announcement Alan (Thu Jul 31 2008 - 04:17:02 PDT)
AMBER: imin = 5 and PBC sai kumar ramadugu (Thu Jul 31 2008 - 07:51:21 PDT)
AMBER: prepare an initial structure in Amber oguz gurbulak (Thu Jul 31 2008 - 09:58:24 PDT)
- Fwd: AMBER: prepare an initial structure in Amber Lachele Foley (Lists) (Fri Aug 01 2008 - 07:52:50 PDT)
AMBER: Compailation problum in Amber 10 srinivas sudani (Thu Jul 31 2008 - 23:59:00 PDT)
- Re: AMBER: Compailation problum in Amber 10 David A. Case (Fri Aug 01 2008 - 12:48:55 PDT)
  - Re: AMBER: Compailation problum in Amber 10 srinivas sudani (Sun Aug 03 2008 - 22:41:13 PDT)
    - AMBER: Compailation problum in Amber 10 srinivas sudani (Wed Aug 06 2008 - 02:24:51 PDT)
    - RE: AMBER: Compailation problum in Amber 10 Ross Walker (Wed Aug 06 2008 - 07:50:05 PDT)
    - RE: AMBER: Compailation problum in Amber 10 Ranga Swamy (Fri Aug 08 2008 - 01:12:56 PDT)
    - Re: AMBER: Compailation problum in Amber 10 David A. Case (Fri Aug 08 2008 - 15:50:55 PDT)
AMBER: bacteriochlorophyll ff Anna Karawajczyk (Fri Aug 01 2008 - 03:04:44 PDT)
AMBER: Bonds getting shorter in sander Peter Gannett (Fri Aug 01 2008 - 05:47:02 PDT)
- Re: AMBER: Bonds getting shorter in sander Carlos Simmerling (Fri Aug 01 2008 - 06:18:36 PDT)
AMBER: respgen -a charge groups function ineffective unless Grange Hermitage (Fri Aug 01 2008 - 22:00:29 PDT)
- Re: AMBER: respgen -a charge groups function ineffective unless Junmei Wang (Wed Aug 27 2008 - 13:55:47 PDT)
AMBER: PDB files in Amber10 Francesco Pietra (Sat Aug 02 2008 - 00:21:58 PDT)
- Re: AMBER: PDB files in Amber10 Scott Brozell (Mon Aug 25 2008 - 14:32:16 PDT)
AMBER: error in parallel amber 9 test Jaber Jahanbin Sardroodi (Sat Aug 02 2008 - 14:12:07 PDT)
- Re: AMBER: error in parallel amber 9 test David A. Case (Sat Aug 02 2008 - 18:37:10 PDT)
  - Re: AMBER: error in parallel amber 9 test Jaber Jahanbin Sardroodi (Sun Aug 03 2008 - 01:15:19 PDT)
    - Re: AMBER: error in parallel amber 9 test David A. Case (Sun Aug 03 2008 - 21:28:45 PDT)
AMBER: Problem with setting the NMR restraints Alex Spasic (Mon Aug 04 2008 - 07:15:25 PDT)
- Re: AMBER: Problem with setting the NMR restraints David A. Case (Mon Aug 04 2008 - 08:26:51 PDT)
  - Re: AMBER: Problem with setting the NMR restraints Alex Spasic (Mon Aug 04 2008 - 09:58:17 PDT)
    - Re: AMBER: Problem with setting the NMR restraints Carlos Simmerling (Mon Aug 04 2008 - 11:28:36 PDT)
    - Re: AMBER: Problem with setting the NMR restraints Alex Spasic (Mon Aug 04 2008 - 12:35:20 PDT)
AMBER: Set 251 is corrupted, ptraj error... Waqas Nasir (Mon Aug 04 2008 - 07:54:09 PDT)
- Re: AMBER: Set 251 is corrupted, ptraj error... David A. Case (Mon Aug 04 2008 - 08:31:28 PDT)
- Re: AMBER: Set 251 is corrupted, ptraj error... Waqas Nasir (Tue Aug 05 2008 - 04:23:47 PDT)
AMBER: Biased MD with Amber 10 Francesco Pietra (Mon Aug 04 2008 - 11:35:31 PDT)
AMBER: divcon.rst ?? IN SUK JOUNG (Mon Aug 04 2008 - 17:06:43 PDT)
AMBER: help me for filling a nanotube with water?? Jaber Jahanbin Sardroodi (Mon Aug 04 2008 - 18:39:05 PDT)
- Re: AMBER: help me for filling a nanotube with water?? Markus Kaukonen (Tue Aug 12 2008 - 23:29:48 PDT)
  - Re: AMBER: help me for filling a nanotube with water?? Thomas Steinbrecher (Wed Aug 13 2008 - 09:40:22 PDT)
AMBER: NMR structure as initial structure Siddharth Rastogi (Mon Aug 04 2008 - 23:40:54 PDT)
- Re: AMBER: NMR structure as initial structure David A. Case (Tue Aug 05 2008 - 17:09:25 PDT)
AMBER: Need help with force field parameters for Lipopolysaccharide (LPS) dipti lele (Tue Aug 05 2008 - 03:03:10 PDT)
- Re: AMBER: Need help with force field parameters for Lipopolysaccharide (LPS) Wenyong Tong (Tue Aug 05 2008 - 07:51:31 PDT)
  - RE: AMBER: Need help with force field parameters for Lipopolysaccharide (LPS) Matthew Tessier (Tue Aug 05 2008 - 08:07:22 PDT)
- Re: AMBER: Need help with force field parameters for Lipopolysaccharide (LPS) Wenyong Tong (Tue Aug 05 2008 - 12:32:31 PDT)
AMBER: MM_PBSA snapshot statistic calc problem Hannes Wallnoefer (Tue Aug 05 2008 - 05:45:48 PDT)
- Re: AMBER: MM_PBSA snapshot statistic calc problem haixiao jin (Fri Sep 26 2008 - 23:40:20 PDT)
  - Re: AMBER: MM_PBSA snapshot statistic calc problem Vasu Chandrasekaran (Mon Sep 29 2008 - 12:08:15 PDT)
    - RE: AMBER: MM_PBSA snapshot statistic calc problem Peterson, Matthew W. (Mon Sep 29 2008 - 14:25:57 PDT)
AMBER: NAB: getseq_from_pdb() IN SUK JOUNG (Tue Aug 05 2008 - 17:00:21 PDT)
AMBER: Problems with the charge (membrane simulation) rebeca.mmb.pcb.ub.es (Wed Aug 06 2008 - 11:20:30 PDT)
- AMBER: Not integral charge increasing with number of lipids rebeca.mmb.pcb.ub.es (Thu Aug 07 2008 - 03:18:01 PDT)
  - RE: AMBER: Not integral charge increasing with number of lipids Ross Walker (Thu Aug 07 2008 - 08:24:28 PDT)
- RE: AMBER: Problems with the charge (membrane simulation) Ross Walker (Thu Aug 07 2008 - 08:18:12 PDT)
AMBER: Re: entropy of released water Swarup Gupta (Thu Aug 07 2008 - 05:40:26 PDT)
AMBER: aggregation or cluster detection fatima.chami.durham.ac.uk (Thu Aug 07 2008 - 06:41:24 PDT)
- RE: AMBER: aggregation or cluster detection Ross Walker (Thu Aug 07 2008 - 08:29:28 PDT)
  - Re: AMBER: aggregation or cluster detection Carlos Simmerling (Thu Aug 07 2008 - 08:38:52 PDT)
- Re: AMBER: aggregation or cluster detection Lachele Foley (Lists) (Thu Aug 07 2008 - 08:44:07 PDT)
AMBER: NAB conjgrad returns error? Carra, Claudio (JSC-SK)[USRA] (Thu Aug 07 2008 - 08:04:38 PDT)
- Re: AMBER: NAB conjgrad returns error? Andreas Svrcek-Seiler (Thu Aug 07 2008 - 08:33:28 PDT)
  - RE: AMBER: NAB conjgrad returns error? Carra, Claudio (JSC-SK)[USRA] (Thu Aug 07 2008 - 09:19:52 PDT)
- RE: AMBER: NAB conjgrad returns error? NIEL MICHAEL HENRIKSEN (Fri Aug 08 2008 - 06:50:05 PDT)
  - RE: AMBER: NAB conjgrad returns error? Andreas Svrcek-Seiler (Fri Aug 08 2008 - 08:48:28 PDT)
  - RE: AMBER: NAB conjgrad returns error? Carra, Claudio (JSC-SK)[USRA] (Mon Aug 11 2008 - 14:14:12 PDT)
    - Re: AMBER: NAB conjgrad returns error? David A. Case (Mon Aug 11 2008 - 14:40:49 PDT)
    - RE: AMBER: NAB conjgrad returns error? Carra, Claudio (JSC-SK)[USRA] (Mon Aug 11 2008 - 15:44:09 PDT)
    - [AMBER] projections of trajectories onto the first 2 principal eigenvectors Carra, Claudio (JSC-SK)[USRA] (Thu Feb 12 2009 - 10:22:20 PST)
    - Re: [AMBER] projections of trajectories onto the first 2 principal eigenvectors Hannes Loeffler (Fri Feb 13 2009 - 00:32:20 PST)
    - Re: [AMBER] projections of trajectories onto the first 2 principal eigenvectors Hannes Loeffler (Fri Feb 13 2009 - 01:33:19 PST)
- RE: AMBER: NAB conjgrad returns error? NIEL MICHAEL HENRIKSEN (Fri Aug 08 2008 - 12:31:13 PDT)
- RE: AMBER: NAB conjgrad returns error? NIEL MICHAEL HENRIKSEN (Mon Aug 11 2008 - 16:07:27 PDT)
AMBER: problem with minimization luzhenw1.msu.edu (Thu Aug 07 2008 - 08:13:17 PDT)
- Re: AMBER: problem with minimization Carlos Simmerling (Thu Aug 07 2008 - 08:29:10 PDT)
- RE: AMBER: problem with minimization Ross Walker (Thu Aug 07 2008 - 08:40:46 PDT)
  - AMBER: parameters Thomas Leonard (Thu Aug 07 2008 - 22:45:09 PDT)
AMBER: value of Pi in Amber Alan (Fri Aug 08 2008 - 03:36:06 PDT)
- AMBER: LES Urszula Uciechowska (Fri Aug 08 2008 - 05:31:56 PDT)
- Re: AMBER: value of Pi in Amber Scott Brozell (Tue Aug 26 2008 - 15:07:49 PDT)
  - AMBER: molecular structure Chih-Ying Lin (Tue Aug 26 2008 - 15:24:29 PDT)
    - Re: AMBER: molecular structure Carlos Simmerling (Tue Aug 26 2008 - 15:32:51 PDT)
AMBER: PBCAL in MM_PBSA Hannes Wallnoefer (Fri Aug 08 2008 - 07:19:30 PDT)
- RE: AMBER: PBCAL in MM_PBSA Ray Luo (Fri Aug 08 2008 - 11:27:17 PDT)
  - AMBER: PBCAL in MM_PBSA Thomas Leonard (Mon Aug 11 2008 - 01:12:51 PDT)
    - AMBER: mmpbsa Urszula Uciechowska (Mon Aug 11 2008 - 01:43:17 PDT)
AMBER: Is G_disp calculated in MM_PBSA now? cgji (Sat Aug 09 2008 - 05:51:55 PDT)
- RE: AMBER: Is G_disp calculated in MM_PBSA now? Ray Luo (Mon Aug 11 2008 - 12:33:14 PDT)
AMBER: Minimization methods teresa.ierano.unina.it (Mon Aug 11 2008 - 05:11:23 PDT)
- Re: AMBER: Minimization methods E.M. (Mon Aug 11 2008 - 05:22:25 PDT)
  - Re: AMBER: Minimization methods M. L. Dodson (Mon Aug 11 2008 - 08:34:05 PDT)
    - Re: AMBER: Minimization methods teresa.ierano.unina.it (Mon Aug 11 2008 - 09:39:30 PDT)
- RE: AMBER: Minimization methods Ross Walker (Mon Aug 11 2008 - 07:43:47 PDT)
  - RE: AMBER: Minimization methods teresa.ierano.unina.it (Mon Aug 11 2008 - 09:30:50 PDT)
AMBER: GPCR membrane simulation, setting surface tension Fiona McRobb (Mon Aug 11 2008 - 18:42:47 PDT)
- Re: AMBER: GPCR membrane simulation, setting surface tension Vlad Cojocaru (Tue Aug 12 2008 - 01:45:08 PDT)
  - RE: [!!!] - Re: AMBER: GPCR membrane simulation, setting surface tension - Message is from an unknown sender Fiona McRobb (Tue Aug 12 2008 - 22:09:49 PDT)
AMBER: questions about previous posts Naser Alijabbari (Mon Aug 11 2008 - 21:17:40 PDT)
- RE: AMBER: questions about previous posts Ross Walker (Mon Aug 11 2008 - 23:18:49 PDT)
- Re: AMBER: questions about previous posts David A. Case (Sat Aug 16 2008 - 08:00:38 PDT)
AMBER: Querry about simulating a glycopeptide dipti lele (Tue Aug 12 2008 - 03:23:24 PDT)
- Re: AMBER: Querry about simulating a glycopeptide Lachele Foley (Lists) (Tue Aug 12 2008 - 07:03:14 PDT)
AMBER: Using RDCs for structure refinement David Witte (Tue Aug 12 2008 - 00:52:53 PDT)
- Re: AMBER: Using RDCs for structure refinement David A. Case (Tue Aug 12 2008 - 09:36:24 PDT)
AMBER: MM-PBSA Issue in Amber 10 Peterson, Matthew W. (Tue Aug 12 2008 - 10:44:29 PDT)
AMBER: empty frcmod file but missing parameters moitrayee.mbu.iisc.ernet.in (Tue Aug 12 2008 - 14:20:19 PDT)
- Re: AMBER: empty frcmod file but missing parameters Alessandro Nascimento (Tue Aug 12 2008 - 15:02:01 PDT)
  - Re: AMBER: empty frcmod file but missing parameters moitrayee.mbu.iisc.ernet.in (Tue Aug 12 2008 - 15:10:03 PDT)
AMBER: frcmod:attn needs revision moitrayee.mbu.iisc.ernet.in (Tue Aug 12 2008 - 15:18:02 PDT)
- Re: AMBER: frcmod:attn needs revision Junmei Wang (Wed Aug 13 2008 - 09:45:11 PDT)
  - Re: AMBER: frcmod:attn needs revision moitrayee.mbu.iisc.ernet.in (Wed Aug 13 2008 - 09:55:40 PDT)
    - Re: AMBER: frcmod:attn needs revision Junmei Wang (Wed Aug 13 2008 - 12:34:50 PDT)
    - Re: AMBER: frcmod:attn needs revision moitrayee.mbu.iisc.ernet.in (Wed Aug 13 2008 - 21:51:50 PDT)
AMBER: glycoprotein setup Arturas Ziemys (Tue Aug 12 2008 - 20:35:35 PDT)
AMBER: general question Gigil Toton (Tue Aug 12 2008 - 23:49:12 PDT)
AMBER: amber 9 on Intel Harpertown Geoff Wood (Wed Aug 13 2008 - 02:45:36 PDT)
- RE: AMBER: amber 9 on Intel Harpertown Ross Walker (Wed Aug 13 2008 - 07:24:47 PDT)
AMBER: problem with prep file generation aneesh cna (Wed Aug 13 2008 - 05:05:58 PDT)
- Re: AMBER: problem with prep file generation Junmei Wang (Wed Aug 13 2008 - 09:59:49 PDT)
AMBER: modified parmtop file from ptraj? Hannes Wallnoefer (Wed Aug 13 2008 - 05:14:34 PDT)
- Re: AMBER: modified parmtop file from ptraj? Florian Haberl (Wed Aug 13 2008 - 05:47:21 PDT)
- Re: AMBER: modified parmtop file from ptraj? Daniel Cappel (Wed Aug 13 2008 - 06:37:19 PDT)
- Re: AMBER: modified parmtop file from ptraj? Thomas Cheatham (Wed Aug 13 2008 - 10:43:24 PDT)
AMBER: Querry dipti lele (Wed Aug 13 2008 - 05:15:11 PDT)
- RE: AMBER: Querry Ross Walker (Wed Aug 13 2008 - 07:48:19 PDT)
  - Re: AMBER: Querry Lachele Foley (Lists) (Wed Aug 13 2008 - 08:03:49 PDT)
AMBER: mm-pbsa / sander.MPI ? Arturas Ziemys (Wed Aug 13 2008 - 15:26:56 PDT)
- Re: AMBER: mm-pbsa / sander.MPI ? Miguel Ortiz-Lombardía (Thu Aug 14 2008 - 00:58:54 PDT)
  - Re: AMBER: mm-pbsa / sander.MPI ? Arturas Ziemys (Thu Aug 14 2008 - 07:42:02 PDT)
AMBER: Compile AMBER 9 on TACC Ranger super computer jialei (Wed Aug 13 2008 - 15:26:07 PDT)
- RE: AMBER: Compile AMBER 9 on TACC Ranger super computer Ross Walker (Wed Aug 13 2008 - 20:39:47 PDT)
- Re:AMBER: Compile AMBER 9 on TACC Ranger super computer 张勇 (Thu Aug 14 2008 - 06:32:30 PDT)
  - RE: AMBER: Compile AMBER 9 on TACC Ranger super computer Ross Walker (Thu Aug 14 2008 - 09:00:02 PDT)
    - Re: AMBER: Compile AMBER 9 on TACC Ranger super computer David LeBard (Thu Aug 14 2008 - 12:43:52 PDT)
    - RE: AMBER: Compile AMBER 9 on TACC Ranger super computer jialei (Thu Aug 14 2008 - 17:15:39 PDT)
    - RE: AMBER: Compile AMBER 9 on TACC Ranger super computer Ross Walker (Thu Aug 14 2008 - 17:38:30 PDT)
    - RE: AMBER: Compile AMBER 9 on TACC Ranger super computer jialei (Fri Aug 15 2008 - 09:38:38 PDT)
    - RE: AMBER: Compile AMBER 9 on TACC Ranger super computer Ross Walker (Fri Aug 15 2008 - 10:36:36 PDT)
AMBER: how to choose the appropriate ensemble for a given problem Ruchi Sachdeva (Wed Aug 13 2008 - 21:09:28 PDT)
AMBER: MD with NMR restraints Sally Pias (Wed Aug 13 2008 - 21:25:56 PDT)
- Re: AMBER: MD with NMR restraints David A. Case (Wed Aug 20 2008 - 10:07:15 PDT)
AMBER: amber9 hangas after job submission Vijay Manickam Achari (Wed Aug 13 2008 - 23:40:03 PDT)
- Re: AMBER: amber9 hangas after job submission Carlos Simmerling (Thu Aug 14 2008 - 03:45:14 PDT)
- Re: AMBER: amber9 hangas after job submission Robert Duke (Thu Aug 14 2008 - 05:54:43 PDT)
AMBER: minimization stops or does not write anything rebeca.mmb.pcb.ub.es (Thu Aug 14 2008 - 02:01:17 PDT)
- Re: AMBER: minimization stops or does not write anything Robert Duke (Thu Aug 14 2008 - 05:39:01 PDT)
AMBER: Glycoprotein once again.......... dipti lele (Thu Aug 14 2008 - 05:10:10 PDT)
- Re: AMBER: Glycoprotein once again.......... Lachele Foley (Lists) (Thu Aug 14 2008 - 06:28:30 PDT)
AMBER: constph shubhra srivastava (Thu Aug 14 2008 - 04:54:57 PDT)
AMBER: interaction energies Arturas Ziemys (Thu Aug 14 2008 - 08:21:34 PDT)
- Re: AMBER: interaction energies Alessandro Nascimento (Fri Aug 15 2008 - 09:18:05 PDT)
AMBER: Help compiling Nab programs for AMBER tools Ragnarok sdf (Thu Aug 14 2008 - 12:36:04 PDT)
- Re: AMBER: Help compiling Nab programs for AMBER tools M. L. Dodson (Thu Aug 14 2008 - 12:50:51 PDT)
AMBER: generate topology file for alanine scanning (mmpbsa) luzhenw1.msu.edu (Thu Aug 14 2008 - 12:32:56 PDT)
AMBER: Proton Parameters Shultz, Jack (Thu Aug 14 2008 - 13:34:54 PDT)
- Re: AMBER: Proton Parameters David A. Case (Wed Aug 20 2008 - 10:12:02 PDT)
AMBER: impropers over bonds between sidechains Grange Hermitage (Thu Aug 14 2008 - 18:12:05 PDT)
- Re: AMBER: impropers over bonds between sidechains M. L. Dodson (Thu Aug 14 2008 - 19:29:54 PDT)
  - Re: AMBER: impropers over bonds between sidechains Grange Hermitage (Thu Aug 14 2008 - 20:08:49 PDT)
    - Re: AMBER: impropers over bonds between sidechains David A. Case (Wed Aug 20 2008 - 10:14:03 PDT)
AMBER: solvatebox TIP4PEWBOX amb2gmx gives TIP3P in top TIP4PEW in gro Grange Hermitage (Sun Aug 17 2008 - 19:28:17 PDT)
- Re: AMBER: solvatebox TIP4PEWBOX amb2gmx gives TIP3P in top TIP4PEW in gro Grange Hermitage (Sun Aug 17 2008 - 22:04:18 PDT)
  - Re: AMBER: solvatebox TIP4PEWBOX amb2gmx gives TIP3P in top TIP4PEW in gro Alan (Mon Aug 18 2008 - 00:42:35 PDT)
    - Re: AMBER: solvatebox TIP4PEWBOX amb2gmx gives TIP3P in top TIP4PEW in gro Grange Hermitage (Mon Aug 18 2008 - 02:01:38 PDT)
    - Re: AMBER: solvatebox TIP4PEWBOX amb2gmx gives TIP3P in top TIP4PEW in gro Alan (Mon Aug 18 2008 - 02:34:03 PDT)
    - Re: AMBER: solvatebox TIP4PEWBOX amb2gmx gives TIP3P in top TIP4PEW in gro Grange Hermitage (Mon Aug 18 2008 - 17:30:25 PDT)
AMBER: Negative dihedral coefficients in amber99 - Possible? Ilyas Yildirim (Sun Aug 17 2008 - 19:33:16 PDT)
- RE: AMBER: Negative dihedral coefficients in amber99 - Possible? Ross Walker (Sun Aug 17 2008 - 22:15:45 PDT)
AMBER: trying ff99SP Grange Hermitage (Sun Aug 17 2008 - 23:12:33 PDT)
- Re: AMBER: trying ff99SP David A. Case (Wed Aug 20 2008 - 11:31:22 PDT)
AMBER: unsubscribe khuram sb (Mon Aug 18 2008 - 01:56:36 PDT)
AMBER: RDF output file format aneesh cna (Mon Aug 18 2008 - 02:48:45 PDT)
- Re: AMBER: RDF output file format Bertrand P. S. Russell (Mon Aug 18 2008 - 03:26:08 PDT)
AMBER: Initial structure from NMR structures Siddharth Rastogi (Mon Aug 18 2008 - 23:15:44 PDT)
- RE: AMBER: Initial structure from NMR structures Ross Walker (Tue Aug 19 2008 - 07:05:43 PDT)
AMBER: How to convert a CHARMM trajectory to AMBER format? Jeffrey (Tue Aug 19 2008 - 04:30:35 PDT)
- Re: AMBER: How to convert a CHARMM trajectory to AMBER format? Wei Huang (Tue Aug 19 2008 - 07:02:22 PDT)
  - RE: AMBER: How to convert a CHARMM trajectory to AMBER format? Ross Walker (Tue Aug 19 2008 - 07:26:25 PDT)
    - Re: RE: AMBER: How to convert a CHARMM trajectory to AMBER format? Jeffrey (Tue Aug 19 2008 - 17:43:58 PDT)
    - Re: Re: RE: AMBER: How to convert a CHARMM trajectory to AMBER format? Jeffrey (Thu Aug 21 2008 - 00:11:55 PDT)
AMBER: Compile Error Shultz, Jack (Tue Aug 19 2008 - 08:44:25 PDT)
AMBER: Amber compile Shultz, Jack (Tue Aug 19 2008 - 11:21:18 PDT)
- RE: AMBER: Amber compile Shultz, Jack (Tue Aug 19 2008 - 12:25:56 PDT)
AMBER: IGB=10 in Amber10 In Hee Park (Tue Aug 19 2008 - 11:55:05 PDT)
AMBER: Problem loading the leaprc.amoeba force field file in Amber 10. Zhao, Zhen (zhaozh) (Tue Aug 19 2008 - 13:20:00 PDT)
- Re: AMBER: Problem loading the leaprc.amoeba force field file in Amber 10. David A. Case (Wed Aug 20 2008 - 10:24:17 PDT)
AMBER: Problems with sleap and amoeba Neil J. Henson (Tue Aug 19 2008 - 16:16:17 PDT)
- AMBER: Force field equation Chih-Ying Lin (Wed Aug 20 2008 - 09:05:39 PDT)
  - Re: AMBER: Force field equation Carlos Simmerling (Wed Aug 20 2008 - 10:53:03 PDT)
    - Re: AMBER: Force field equation Chih-Ying Lin (Wed Aug 20 2008 - 22:16:42 PDT)
    - AMBER: pdb file ?? Chih-Ying Lin (Wed Aug 20 2008 - 23:21:47 PDT)
    - Re: AMBER: Force field equation Carlos Simmerling (Thu Aug 21 2008 - 05:21:55 PDT)
Re: AMBER: Problems with sleap and amoeba Bill Ross (Tue Aug 19 2008 - 16:51:18 PDT)
- Re: AMBER: Problems with sleap and amoeba Neil J. Henson (Tue Aug 19 2008 - 17:03:52 PDT)
AMBER: Questions about Locally enhanced sampling (LES) and Replica exchange xiaonan zhang (Wed Aug 20 2008 - 00:25:43 PDT)
- Re: AMBER: Questions about Locally enhanced sampling (LES) and Replica exchange Carlos Simmerling (Wed Aug 20 2008 - 10:47:12 PDT)
AMBER: Trouble installing Amber 9 Sampath Koppole (Wed Aug 20 2008 - 03:28:58 PDT)
AMBER: Silicon parameters Abdul Hameed, MohamedDiwanMo (Wed Aug 20 2008 - 09:15:56 PDT)
- Re: AMBER: Silicon parameters Junmei Wang (Fri Aug 22 2008 - 13:29:05 PDT)
AMBER: Using Na+ ions as input to leap? Pablo Englebienne (Wed Aug 20 2008 - 10:40:11 PDT)
AMBER: NMR average structure Gigil Toton (Wed Aug 20 2008 - 10:42:08 PDT)
- Re: AMBER: NMR average structure Carlos Simmerling (Wed Aug 20 2008 - 10:50:28 PDT)
Re: AMBER: Using Na+ ions as input to leap? - solved Pablo Englebienne (Wed Aug 20 2008 - 12:25:25 PDT)
AMBER: Vlimit Exceeded and inhomogeneous system !!!!!! Piyush Wanjari (Wed Aug 20 2008 - 21:36:20 PDT)
- Re: AMBER: Vlimit Exceeded and inhomogeneous system !!!!!! David A. Case (Fri Aug 22 2008 - 20:11:14 PDT)
  - Re: AMBER: Vlimit Exceeded and inhomogeneous system !!!!!! Piyush Wanjari (Mon Aug 25 2008 - 12:52:37 PDT)
    - Re: AMBER: Vlimit Exceeded and inhomogeneous system !!!!!! Piyush Wanjari (Mon Aug 25 2008 - 15:00:33 PDT)
AMBER: new residues in AMOEBA Grange Hermitage (Thu Aug 21 2008 - 00:14:59 PDT)
AMBER: Fwd: Welcome to amber Maicon Sartin (Thu Aug 21 2008 - 05:33:08 PDT)
AMBER: SANDER Parallel Maicon Sartin (Thu Aug 21 2008 - 05:36:56 PDT)
AMBER: Gohlke in-house iRED Simulated Order Parameter Script Titus, Jamie (bairdje) (Thu Aug 21 2008 - 05:53:09 PDT)
AMBER: DFTB QMMM parameters ambiguity in AMBER10 docs M. L. Dodson (Thu Aug 21 2008 - 10:56:38 PDT)
AMBER: Error when compiling and testing AmberTools Ben Roberts (Thu Aug 21 2008 - 14:46:43 PDT)
- Re: AMBER: Error when compiling and testing AmberTools Andreas Svrcek-Seiler (Fri Aug 22 2008 - 02:11:14 PDT)
AMBER: all & united atoms force field fatima.chami.durham.ac.uk (Thu Aug 21 2008 - 15:05:12 PDT)
- Re: AMBER: all & united atoms force field cgji (Thu Aug 21 2008 - 15:28:49 PDT)
  - Re: AMBER: all & united atoms force field fatima.chami.durham.ac.uk (Fri Aug 22 2008 - 06:31:34 PDT)
    - Re: AMBER: all & united atoms force field Ray Luo (Fri Aug 22 2008 - 10:44:16 PDT)
    - Re: AMBER: all & united atoms force field fatima.chami.durham.ac.uk (Fri Aug 22 2008 - 13:46:11 PDT)
    - RE: AMBER: all & united atoms force field Yong Duan (Fri Aug 22 2008 - 17:39:23 PDT)
AMBER: Error runing Addles Shultz, Jack (Thu Aug 21 2008 - 20:25:17 PDT)
- Re: AMBER: Error runing Addles Carlos Simmerling (Fri Aug 22 2008 - 05:48:07 PDT)
AMBER: united atom force field Adrien Delmont (Fri Aug 22 2008 - 05:35:06 PDT)
- Re: AMBER: united atom force field Ray Luo (Fri Aug 22 2008 - 10:37:38 PDT)
- Re: AMBER: united atom force field Adrien Delmont (Fri Aug 22 2008 - 12:17:10 PDT)
  - RE: AMBER: united atom force field Ray Luo (Tue Aug 26 2008 - 16:11:47 PDT)
AMBER: vdw 6-9 potential fatima.chami.durham.ac.uk (Fri Aug 22 2008 - 13:56:57 PDT)
- Re: AMBER: vdw 6-9 potential Carlos Simmerling (Fri Aug 22 2008 - 14:02:48 PDT)
  - Re: AMBER: vdw 6-9 potential fatima.chami.durham.ac.uk (Sat Aug 23 2008 - 03:34:57 PDT)
    - Re: AMBER: vdw 6-9 potential Carlos Simmerling (Sat Aug 23 2008 - 03:51:24 PDT)
    - Re: AMBER: vdw 6-9 potential fatima.chami.durham.ac.uk (Tue Aug 26 2008 - 09:03:55 PDT)
AMBER: Dell 2 Quad Core System Performance Ilyas Yildirim (Fri Aug 22 2008 - 18:16:49 PDT)
- AMBER: Re: Dell 2 Quad Core System Performance Ilyas Yildirim (Wed Aug 27 2008 - 14:04:14 PDT)
  - Re: AMBER: Re: Dell 2 Quad Core System Performance Carlos Simmerling (Wed Aug 27 2008 - 15:15:42 PDT)
  - RE: AMBER: Re: Dell 2 Quad Core System Performance Ross Walker (Wed Aug 27 2008 - 16:01:59 PDT)
AMBER: LES trajectories Urszula Uciechowska (Mon Aug 25 2008 - 01:12:23 PDT)
- AMBER: Is there a way to cluster frames of a trajectory? Sasha Buzko (Wed Aug 27 2008 - 17:45:01 PDT)
  - Re: AMBER: Is there a way to cluster frames of a trajectory? Adrian Roitberg (Wed Aug 27 2008 - 17:56:08 PDT)
    - Re: AMBER: Is there a way to cluster frames of a trajectory? Sasha Buzko (Wed Aug 27 2008 - 17:57:07 PDT)
  - Re: AMBER: Is there a way to cluster frames of a trajectory? Carlos Simmerling (Wed Aug 27 2008 - 17:58:27 PDT)
    - Re: AMBER: Is there a way to cluster frames of a trajectory? Sasha Buzko (Mon Sep 08 2008 - 13:34:22 PDT)
    - Re: AMBER: Is there a way to cluster frames of a trajectory? Carlos Simmerling (Mon Sep 08 2008 - 13:46:45 PDT)
    - Re: AMBER: Is there a way to cluster frames of a trajectory? Sasha Buzko (Mon Sep 08 2008 - 15:11:04 PDT)
AMBER: pmemd iwrap trouble Lars Skjærven (Mon Aug 25 2008 - 03:25:09 PDT)
- Re: AMBER: pmemd iwrap trouble Robert Duke (Mon Aug 25 2008 - 05:40:03 PDT)
  - Re: AMBER: pmemd iwrap trouble Lars Skjærven (Mon Aug 25 2008 - 06:32:26 PDT)
    - Re: AMBER: pmemd iwrap trouble Lars Skjærven (Mon Aug 25 2008 - 07:58:01 PDT)
- Re: AMBER: pmemd iwrap trouble Robert Duke (Mon Aug 25 2008 - 08:45:03 PDT)
  - Re: AMBER: pmemd iwrap trouble Carlos Simmerling (Mon Aug 25 2008 - 09:35:53 PDT)
  - Re: AMBER: pmemd iwrap trouble Lars Skjærven (Mon Aug 25 2008 - 15:03:14 PDT)
- Re: AMBER: pmemd iwrap trouble Robert Duke (Mon Aug 25 2008 - 20:38:13 PDT)
- Re: AMBER: pmemd iwrap trouble Robert Duke (Mon Aug 25 2008 - 21:22:44 PDT)
- Re: AMBER: pmemd iwrap trouble Robert Duke (Mon Aug 25 2008 - 21:38:40 PDT)
  - Re: AMBER: pmemd iwrap trouble Carlos Simmerling (Tue Aug 26 2008 - 07:26:53 PDT)
    - Re: AMBER: pmemd iwrap trouble Lars Skjærven (Tue Aug 26 2008 - 09:23:31 PDT)
    - Re: AMBER: pmemd iwrap trouble Thomas Cheatham III (Tue Aug 26 2008 - 09:48:04 PDT)
    - Re: AMBER: pmemd iwrap trouble Carlos Simmerling (Tue Aug 26 2008 - 09:57:28 PDT)
- Re: AMBER: pmemd iwrap trouble Robert Duke (Tue Aug 26 2008 - 09:59:34 PDT)
  - Re: AMBER: pmemd iwrap trouble Lars Skjærven (Tue Aug 26 2008 - 11:36:06 PDT)
- Re: AMBER: pmemd iwrap trouble Robert Duke (Tue Aug 26 2008 - 12:49:18 PDT)
- Re: AMBER: pmemd iwrap trouble Robert Duke (Tue Aug 26 2008 - 20:17:29 PDT)
  - Re: AMBER: pmemd iwrap trouble Carlos Simmerling (Wed Aug 27 2008 - 06:26:54 PDT)
    - Re: AMBER: pmemd iwrap trouble Lars Skjærven (Thu Aug 28 2008 - 03:38:02 PDT)
    - Re: AMBER: pmemd iwrap trouble Thomas Cheatham III (Thu Aug 28 2008 - 14:47:51 PDT)
    - AMBER: xleap fails to savemol2 taufik.alsarraj.utoronto.ca (Thu Aug 28 2008 - 15:43:07 PDT)
    - Re: AMBER: xleap fails to savemol2 FyD (Thu Aug 28 2008 - 21:58:08 PDT)
    - Re: AMBER: xleap fails to savemol2 taufik.alsarraj.utoronto.ca (Fri Aug 29 2008 - 10:28:33 PDT)
    - Re: AMBER: xleap fails to savemol2 FyD (Fri Aug 29 2008 - 14:14:42 PDT)
    - Re: AMBER: xleap fails to savemol2 taufik.alsarraj.utoronto.ca (Fri Aug 29 2008 - 14:28:52 PDT)
    - Re: AMBER: xleap fails to savemol2 FyD (Fri Aug 29 2008 - 23:58:21 PDT)
    - Re: AMBER: xleap fails to savemol2 FyD (Thu Sep 04 2008 - 12:45:49 PDT)
    - Re: AMBER: xleap fails to savemol2 alsarraj (Thu Sep 18 2008 - 13:15:20 PDT)
    - Re: AMBER: xleap fails to savemol2 alsarraj (Fri Sep 19 2008 - 13:59:44 PDT)
    - Re: AMBER: xleap fails to savemol2 Mark Williamson (Mon Sep 22 2008 - 11:43:35 PDT)
    - Re: AMBER: xleap fails to savemol2 taufik.alsarraj.utoronto.ca (Wed Oct 08 2008 - 14:57:30 PDT)
    - Re: AMBER: xleap fails to savemol2 FyD (Wed Oct 08 2008 - 23:54:05 PDT)
    - Re: AMBER: xleap fails to savemol2 FyD (Tue Oct 14 2008 - 12:15:48 PDT)
    - AMBER: join two units in amber9 or amber10 taufik.alsarraj.utoronto.ca (Fri Aug 29 2008 - 14:17:58 PDT)
    - [AMBER] Re: join two units in amber9 or amber10 Taufik Al-Sarraj (Mon Mar 16 2009 - 14:11:30 PDT)
- Re: AMBER: pmemd iwrap trouble Robert Duke (Thu Aug 28 2008 - 15:05:05 PDT)
AMBER: mol2, xleap, Segmentation fault Anna Karawajczyk (Mon Aug 25 2008 - 06:01:31 PDT)
- Re: AMBER: mol2, xleap, Segmentation fault Cenk $Jenk$ Andac (Mon Aug 25 2008 - 07:38:28 PDT)
AMBER: Parameters for chloride ion in contact with a protein Francesco Pietra (Mon Aug 25 2008 - 07:25:13 PDT)
AMBER: Problem with the prmtop file generated by sleap and leaprc.amoeba in Amber 10. Zhao, Zhen (zhaozh) (Mon Aug 25 2008 - 08:04:34 PDT)
AMBER: tan luo radii Jacopo Sgrignani (Tue Aug 26 2008 - 02:06:39 PDT)
- RE: AMBER: tan luo radii Ray Luo (Tue Aug 26 2008 - 12:12:57 PDT)
AMBER: installation amber on suse11.0 selami ercan (Tue Aug 26 2008 - 03:57:12 PDT)
- Re: AMBER: installation amber on suse11.0 Cenk $Jenk$ Andac (Tue Aug 26 2008 - 07:40:30 PDT)
- RE: AMBER: installation amber on suse11.0 Ross Walker (Tue Aug 26 2008 - 07:39:31 PDT)
  - Re: AMBER: installation amber on suse11.0 selami ercan (Wed Aug 27 2008 - 11:50:13 PDT)
- Re: AMBER: installation amber on suse11.0 Maicon Sartin (Tue Aug 26 2008 - 07:52:01 PDT)
AMBER: Bennett acceptance ratio with Amber10 Samuel Genheden (a03samge) (Tue Aug 26 2008 - 04:58:13 PDT)
- Re: AMBER: Bennett acceptance ratio with Amber10 steinbrt.scripps.edu (Tue Aug 26 2008 - 06:45:55 PDT)
- RE: AMBER: Bennett acceptance ratio with Amber10 Samuel Genheden (a03samge) (Tue Aug 26 2008 - 23:04:28 PDT)
- RE: AMBER: Bennett acceptance ratio with Amber10 steinbrt.scripps.edu (Wed Aug 27 2008 - 09:28:13 PDT)
AMBER: latest update on residuegen Junmei Wang (Tue Aug 26 2008 - 06:55:09 PDT)
AMBER: Querry dipti lele (Tue Aug 26 2008 - 04:50:32 PDT)
- Re: AMBER: Querry Carlos Simmerling (Tue Aug 26 2008 - 07:09:25 PDT)
  - Re: AMBER: Querry dipti lele (Wed Aug 27 2008 - 02:00:46 PDT)
    - Re: AMBER: Querry Carlos Simmerling (Wed Aug 27 2008 - 06:20:55 PDT)
    - Re: AMBER: Querry dipti lele (Wed Aug 27 2008 - 06:33:45 PDT)
AMBER: Source FIles of SANDER Maicon Sartin (Tue Aug 26 2008 - 12:17:39 PDT)
- Re: AMBER: Source FIles of SANDER Carlos Simmerling (Tue Aug 26 2008 - 12:20:40 PDT)
Re: AMBER: Source FIles of SANDER Bill Ross (Tue Aug 26 2008 - 12:28:34 PDT)
- Re: AMBER: Source FIles of SANDER Maicon Sartin (Tue Aug 26 2008 - 16:18:49 PDT)
  - Re: AMBER: Source FIles of SANDER Carlos Simmerling (Tue Aug 26 2008 - 16:21:31 PDT)
    - RE: AMBER: Source FIles of SANDER Ross Walker (Tue Aug 26 2008 - 16:57:55 PDT)
    - Re: AMBER: Source FIles of SANDER Maicon Sartin (Wed Aug 27 2008 - 05:47:47 PDT)
AMBER: net charge Gigil Toton (Tue Aug 26 2008 - 22:03:19 PDT)
AMBER: coordinate change of pdb structure using xleap Henrik Öberg (Tue Aug 26 2008 - 23:26:42 PDT)
- Re: AMBER: coordinate change of pdb structure using xleap saurabh agrawal (Wed Aug 27 2008 - 00:23:09 PDT)
AMBER: constant ph (cpinutil file) shubhra srivastava (Tue Aug 26 2008 - 23:46:36 PDT)
AMBER: querry dipti lele (Wed Aug 27 2008 - 02:07:52 PDT)
AMBER: MM-PBSA multiple trajectory problem Carra, Claudio (JSC-SK)[USRA] (Wed Aug 27 2008 - 07:16:38 PDT)
AMBER: solvent interaction in active site Hakkim Boy (Wed Aug 27 2008 - 19:41:24 PDT)
- Re: AMBER: solvent interaction in active site Carlos Simmerling (Mon Sep 01 2008 - 06:49:20 PDT)
  - Re: AMBER: solvent interaction in active site S.Sundar Raman (Mon Sep 01 2008 - 07:28:10 PDT)
AMBER: Membrane simulations priya priya (Thu Aug 28 2008 - 01:31:57 PDT)
AMBER: to understand how frcmod.ff99SB works Alan (Thu Aug 28 2008 - 03:29:18 PDT)
- Re: AMBER: to understand how frcmod.ff99SB works Melinda Layten (Thu Aug 28 2008 - 07:55:40 PDT)
- RE: AMBER: to understand how frcmod.ff99SB works Ross Walker (Thu Aug 28 2008 - 09:59:09 PDT)
  - Re: AMBER: to understand how frcmod.ff99SB works Alan (Thu Aug 28 2008 - 11:36:55 PDT)
  - RE: AMBER: to understand how frcmod.ff99SB works Ilyas Yildirim (Thu Aug 28 2008 - 14:58:03 PDT)
    - Re: AMBER: to understand how frcmod.ff99SB works Alan (Fri Aug 29 2008 - 02:00:01 PDT)
    - RE: AMBER: to understand how frcmod.ff99SB works Ross Walker (Fri Aug 29 2008 - 08:17:27 PDT)
AMBER: output file format in SANDER.MPI & PMEMD fatima.chami.durham.ac.uk (Thu Aug 28 2008 - 03:47:17 PDT)
- Re: AMBER: output file format in SANDER.MPI & PMEMD Robert Duke (Thu Aug 28 2008 - 05:34:44 PDT)
  - Re: AMBER: output file format in SANDER.MPI & PMEMD fatima.chami.durham.ac.uk (Thu Aug 28 2008 - 05:53:42 PDT)
- RE: AMBER: output file format in SANDER.MPI & PMEMD Ross Walker (Thu Aug 28 2008 - 10:09:38 PDT)
AMBER: Critical patch for pmemd 10 extra points code Robert Duke (Thu Aug 28 2008 - 08:20:59 PDT)
- Re: AMBER: Critical patch for pmemd 10 extra points code Carlos Simmerling (Sun Aug 31 2008 - 06:54:33 PDT)
- Re: AMBER: Critical patch for pmemd 10 extra points code Robert Duke (Sun Aug 31 2008 - 09:48:56 PDT)
AMBER: RE: Personal favor Ross Walker (Thu Aug 28 2008 - 09:39:59 PDT)
- Re: AMBER: RE: Personal favor fatima.chami.durham.ac.uk (Mon Sep 01 2008 - 04:29:46 PDT)
AMBER: conversion from crd to netcdf returns almost identical file! Jose Borreguero (Thu Aug 28 2008 - 13:38:50 PDT)
AMBER: Problem in calculation of resp charges using RED III moitrayee.mbu.iisc.ernet.in (Thu Aug 28 2008 - 23:56:24 PDT)
- Re: AMBER: Problem in calculation of resp charges using RED III FyD (Fri Aug 29 2008 - 00:50:42 PDT)
  - Re: AMBER: Problem in calculation of resp charges using RED III moitrayee.mbu.iisc.ernet.in (Fri Aug 29 2008 - 04:41:21 PDT)
    - Re: AMBER: Problem in calculation of resp charges using RED III FyD (Fri Aug 29 2008 - 08:19:23 PDT)
AMBER: Solvent Accesible Surface Area (SASA) - Confused Deepangi Pandit (Fri Aug 29 2008 - 11:45:19 PDT)
AMBER: wrapping w/ ptraj Arturas Ziemys (Fri Aug 29 2008 - 14:57:52 PDT)
AMBER: compilation problem john smith (Sat Aug 30 2008 - 04:51:07 PDT)
- RE: AMBER: compilation problem Ross Walker (Sat Aug 30 2008 - 11:33:13 PDT)
  - Re: AMBER: compilation problem john smith (Tue Sep 02 2008 - 03:03:14 PDT)
    - Re: AMBER: compilation problem Vlad Cojocaru (Tue Sep 02 2008 - 03:16:13 PDT)
    - Re: AMBER: compilation problem David A. Case (Tue Sep 02 2008 - 07:32:45 PDT)
    - Re: AMBER: compilation problem john smith (Thu Sep 11 2008 - 22:51:22 PDT)
    - Re: AMBER: compilation problem David A. Case (Fri Sep 12 2008 - 05:04:59 PDT)
    - Re: AMBER: compilation problem john smith (Mon Sep 22 2008 - 04:59:17 PDT)
    - Re: AMBER: compilation problem David A. Case (Mon Sep 22 2008 - 05:19:47 PDT)
    - Re: AMBER: compilation problem Atro Tossavainen (Thu Sep 25 2008 - 12:32:06 PDT)
    - Re: AMBER: compilation problem David A. Case (Fri Sep 26 2008 - 09:06:46 PDT)
    - Re: AMBER: compilation problem Atro Tossavainen (Sat Sep 27 2008 - 12:18:13 PDT)
- Re: AMBER: compilation problem Manikandan Chandrasekaran (Fri Sep 26 2008 - 20:51:50 PDT)
  - Re: AMBER: compilation problem David A. Case (Sat Sep 27 2008 - 05:29:53 PDT)
AMBER: vlimit exceeded Wang,Ying (Sat Aug 30 2008 - 08:49:03 PDT)
- RE: AMBER: vlimit exceeded Ross Walker (Sat Aug 30 2008 - 11:41:02 PDT)
- RE: AMBER: vlimit exceeded Wang,Ying (Sat Aug 30 2008 - 16:14:21 PDT)
AMBER: RESP charges fitting for polarizable force fields Grange Hermitage (Sat Aug 30 2008 - 21:48:37 PDT)
AMBER: AMBER under cygwin on 64 bit Vista Charles Letner, Ph.D. (Sun Aug 31 2008 - 14:30:08 PDT)
AMBER: tleap and Zn parameter Aust, Susanne (Mon Sep 01 2008 - 01:14:53 PDT)
- Re: AMBER: tleap and Zn parameter David A. Case (Mon Sep 01 2008 - 06:53:26 PDT)
AMBER: ptraj and netcdf with AmberTools1.2 ? Lars Skjærven (Mon Sep 01 2008 - 02:11:23 PDT)
- Re: AMBER: ptraj and netcdf with AmberTools1.2 ? Dave Rogers (Wed Nov 05 2008 - 13:34:21 PST)
  - Re: AMBER: ptraj and netcdf with AmberTools1.2 ? David A. Case (Thu Nov 06 2008 - 04:08:00 PST)
AW: AMBER: tleap and Zn parameter Aust, Susanne (Mon Sep 01 2008 - 23:46:23 PDT)
- Re: AMBER: tleap and Zn parameter David A. Case (Tue Sep 02 2008 - 13:41:21 PDT)
AMBER: mmpbsa Henrik Öberg (Tue Sep 02 2008 - 04:36:55 PDT)
- Re: AMBER: mmpbsa Neha Gandhi (Tue Sep 02 2008 - 05:49:33 PDT)
- Re: AMBER: mmpbsa Matthew Peterson (Tue Sep 02 2008 - 06:57:24 PDT)
  - RE: AMBER: mmpbsa Henrik Öberg (Tue Sep 02 2008 - 07:18:56 PDT)
    - Re: AMBER: mmpbsa Hannes Kopitz (Tue Sep 02 2008 - 11:15:47 PDT)
    - RE: AMBER: mmpbsa Henrik Öberg (Wed Sep 03 2008 - 00:30:43 PDT)
    - Re: RE: AMBER: mmpbsa Hannes Kopitz (Wed Sep 03 2008 - 02:15:19 PDT)
AMBER: AMBER9 installation problen with open mpi saurabh agrawal (Tue Sep 02 2008 - 04:41:55 PDT)
- Re: AMBER: AMBER9 installation problen with open mpi Vlad Cojocaru (Tue Sep 02 2008 - 05:00:33 PDT)
  - Re: AMBER: AMBER9 installation problen with open mpi saurabh agrawal (Wed Sep 03 2008 - 07:55:31 PDT)
    - RE: AMBER: AMBER9 installation problen with open mpi Ross Walker (Wed Sep 03 2008 - 08:35:43 PDT)
AMBER: ptraj & imaging of velocities FyD (Tue Sep 02 2008 - 06:06:08 PDT)
- Re: AMBER: ptraj & imaging of velocities Lars Skjærven (Tue Sep 02 2008 - 06:15:49 PDT)
AMBER: a question about matrix command? TaoPaul (Tue Sep 02 2008 - 18:01:04 PDT)
AMBER: MM_PBSA - SASA - Question Deepangi Pandit (Tue Sep 02 2008 - 19:10:13 PDT)
AW: AMBER: tleap and Zn parameter Aust, Susanne (Wed Sep 03 2008 - 00:18:28 PDT)
- RE: AMBER: tleap and Zn parameter Ross Walker (Wed Sep 03 2008 - 08:31:26 PDT)
AMBER: Need help... High energies for complex... Waqas Nasir (Wed Sep 03 2008 - 04:20:01 PDT)
- Re: AMBER: Need help... High energies for complex... Carlos Simmerling (Wed Sep 03 2008 - 04:27:06 PDT)
AMBER: help...ptraj does not output bounding box info Jose Borreguero (Wed Sep 03 2008 - 08:39:41 PDT)
- Re: AMBER: help...ptraj does not output bounding box info Carlos Simmerling (Wed Sep 03 2008 - 08:41:48 PDT)
  - Re: AMBER: help...ptraj does not output bounding box info Jose Borreguero (Wed Sep 03 2008 - 09:12:30 PDT)
    - Re: AMBER: help...ptraj does not output bounding box info Carlos Simmerling (Wed Sep 03 2008 - 09:23:28 PDT)
    - Re: AMBER: help...ptraj does not output bounding box info Jose Borreguero (Wed Sep 03 2008 - 10:26:57 PDT)
    - Re: AMBER: help...ptraj does not output bounding box info Carlos Simmerling (Wed Sep 03 2008 - 10:53:33 PDT)
    - Re: AMBER: help...ptraj does not output bounding box info Jose Borreguero (Wed Sep 03 2008 - 11:28:02 PDT)
- Re: AMBER: help...ptraj does not output bounding box info Bill Ross (Wed Sep 03 2008 - 09:22:18 PDT)
AMBER: Marisa Frechero (Wed Sep 03 2008 - 11:38:06 PDT)
- RE: AMBER: Ross Walker (Wed Sep 03 2008 - 14:14:21 PDT)
  - RE: AMBER: Install problems Marisa Frechero (Mon Sep 08 2008 - 11:35:08 PDT)
    - Re: AMBER: Install problems Gustavo Seabra (Mon Sep 08 2008 - 11:58:02 PDT)
    - Re: AMBER: Install problems Mark Williamson (Mon Sep 08 2008 - 16:56:35 PDT)
    - Re: AMBER: Install problems David A. Case (Tue Sep 09 2008 - 04:37:16 PDT)
    - Re: AMBER: Install problems Mark Williamson (Tue Sep 09 2008 - 11:16:38 PDT)
    - Re: AMBER: Install problems M. L. Dodson (Tue Sep 09 2008 - 11:41:07 PDT)
    - Re: AMBER: Install problems David A. Case (Tue Sep 09 2008 - 12:53:18 PDT)
AMBER: matrix correl Steve Seibold (Wed Sep 03 2008 - 11:40:28 PDT)
AMBER: nmode units Arturas Ziemys (Wed Sep 03 2008 - 15:28:44 PDT)
- Re: AMBER: nmode units Chris Moth (Wed Sep 03 2008 - 16:10:19 PDT)
  - Re: AMBER: nmode units Arturas Ziemys (Thu Sep 04 2008 - 07:26:57 PDT)
    - Re: AMBER: nmode units David A. Case (Thu Sep 04 2008 - 07:58:22 PDT)
    - Re: AMBER: nmode units Arturas Ziemys (Thu Sep 04 2008 - 08:22:41 PDT)
AMBER: mmpbsa molsurf.c error Ilyas Yildirim (Wed Sep 03 2008 - 16:56:59 PDT)
- Re: AMBER: mmpbsa molsurf.c error Ilyas Yildirim (Thu Sep 04 2008 - 17:45:58 PDT)
  - Re: AMBER: mmpbsa molsurf.c error David A. Case (Wed Sep 17 2008 - 05:10:40 PDT)
    - Re: AMBER: mmpbsa molsurf.c error parvesh singh (Mon Sep 22 2008 - 02:26:29 PDT)
AMBER: No bond and angle parameters for - -????? Waqas Nasir (Thu Sep 04 2008 - 03:15:37 PDT)
- Re: AMBER: No bond and angle parameters for - -????? Lachele Foley (Lists) (Thu Sep 04 2008 - 07:03:08 PDT)
AMBER: Need help... High energies for complex... Waqas Nasir (Thu Sep 04 2008 - 03:38:53 PDT)
- Re: AMBER: Need help... High energies for complex... Waqas Nasir (Wed Sep 03 2008 - 04:45:20 PDT)
  - Re: AMBER: Need help... High energies for complex... Carlos Simmerling (Wed Sep 03 2008 - 05:04:07 PDT)
    - Re: AMBER: Need help... High energies for complex... Neha Gandhi (Wed Sep 03 2008 - 05:41:16 PDT)
- Re: AMBER: Need help... High energies for complex... Waqas Nasir (Thu Sep 04 2008 - 03:08:49 PDT)
  - Re: AMBER: Need help... High energies for complex... Carlos Simmerling (Thu Sep 04 2008 - 03:39:48 PDT)
- Re: AMBER: Need help... High energies for complex... Waqas Nasir (Thu Sep 04 2008 - 07:12:21 PDT)
  - Re: AMBER: Need help... High energies for complex... Carlos Simmerling (Thu Sep 04 2008 - 07:33:32 PDT)
    - Re: AMBER: Need help... High energies for complex... Carlos Simmerling (Thu Sep 04 2008 - 07:35:02 PDT)
  - Re: AMBER: Need help... High energies for complex... David A. Case (Thu Sep 04 2008 - 07:36:37 PDT)
- Re: AMBER: Need help... High energies for complex... Waqas Nasir (Thu Sep 04 2008 - 08:22:55 PDT)
  - Re: AMBER: Need help... High energies for complex... Carlos Simmerling (Thu Sep 04 2008 - 08:41:38 PDT)
- Re: AMBER: Need help... High energies for complex... Waqas Nasir (Thu Sep 04 2008 - 09:14:35 PDT)
  - Re: AMBER: Need help... High energies for complex... Carlos Simmerling (Thu Sep 04 2008 - 09:21:42 PDT)
- Re: AMBER: Need help... High energies for complex... Waqas Nasir (Fri Sep 05 2008 - 02:15:59 PDT)
  - Re: AMBER: Need help... High energies for complex... Carlos Simmerling (Fri Sep 05 2008 - 03:07:01 PDT)
- Re: AMBER: Need help... High energies for complex... Waqas Nasir (Mon Sep 08 2008 - 09:06:26 PDT)
  - Re: AMBER: Need help... High energies for complex... Carlos Simmerling (Mon Sep 08 2008 - 09:45:51 PDT)
- Re: AMBER: Need help... High energies for complex... Waqas Nasir (Tue Sep 09 2008 - 06:16:29 PDT)
  - Re: AMBER: Need help... High energies for complex... Carlos Simmerling (Tue Sep 09 2008 - 06:46:19 PDT)
  - Re: AMBER: Need help... High energies for complex... Carlos Simmerling (Tue Sep 09 2008 - 06:56:00 PDT)
  - Re: AMBER: Need help... High energies for complex... Lachele Foley (Lists) (Tue Sep 09 2008 - 07:09:06 PDT)
- Re: AMBER: Need help... High energies for complex... Waqas Nasir (Tue Sep 09 2008 - 07:06:18 PDT)
AMBER: antechamber cannot generate prep files moitrayee.mbu.iisc.ernet.in (Thu Sep 04 2008 - 04:47:17 PDT)
AMBER: help... structure factors from amber trajectories? Jose Borreguero (Thu Sep 04 2008 - 10:35:57 PDT)
AMBER: resp and 99999 Markus Kaukonen (Thu Sep 04 2008 - 23:13:10 PDT)
- RE: AMBER: resp and 99999 Ross Walker (Fri Sep 05 2008 - 07:31:51 PDT)
AMBER: help...sander "segmentation fault" after 2hours of minimization Jose Borreguero (Fri Sep 05 2008 - 08:06:42 PDT)
- Re: AMBER: help...sander "segmentation fault" after 2hours of minimization David A. Case (Fri Sep 05 2008 - 08:20:40 PDT)
  - Re: AMBER: help...sander "segmentation fault" after 2hours of minimization Jose Borreguero (Fri Sep 05 2008 - 08:43:39 PDT)
    - RE: AMBER: help...sander "segmentation fault" after 2hours of minimization Ross Walker (Fri Sep 05 2008 - 09:07:27 PDT)
- RE: AMBER: help...sander "segmentation fault" after 2hours of minimization Ross Walker (Fri Sep 05 2008 - 08:23:42 PDT)
  - Re: AMBER: help...sander "segmentation fault" after 2hours of minimization Jose Borreguero (Fri Sep 05 2008 - 09:26:23 PDT)
    - RE: AMBER: help...sander "segmentation fault" after 2hours of minimization Ross Walker (Fri Sep 05 2008 - 10:02:30 PDT)
AMBER: error when using tleap with leaprc.ff02EP Yongmei Pan (Fri Sep 05 2008 - 08:49:38 PDT)
- RE: AMBER: error when using tleap with leaprc.ff02EP Ross Walker (Fri Sep 05 2008 - 09:06:13 PDT)
AMBER: RE: reference paper - pls help Ross Walker (Fri Sep 05 2008 - 09:37:24 PDT)
- AMBER: Question: GAFF Chih-Ying Lin (Fri Sep 05 2008 - 14:33:14 PDT)
  - AMBER: QM/MM Chih-Ying Lin (Fri Sep 05 2008 - 15:33:23 PDT)
AMBER: mm_pbsa error : Scale paremeter for PBSA CHAMI F. (Fri Sep 05 2008 - 10:26:46 PDT)
- RE: AMBER: mm_pbsa error : Scale paremeter for PBSA Ray Luo (Fri Sep 05 2008 - 10:45:12 PDT)
AMBER: ESURF - SASA - isolate residues Deepangi Pandit (Fri Sep 05 2008 - 07:23:23 PDT)
AMBER: Problem in EVB and Trajectory analysis sai kumar ramadugu (Fri Sep 05 2008 - 14:20:17 PDT)
AMBER: Explanation of the energy unit ? Marek Malý (Sat Sep 06 2008 - 07:29:06 PDT)
- Re: AMBER: Explanation of the energy unit ? David A. Case (Sun Sep 07 2008 - 15:12:22 PDT)
  - Re: AMBER: Explanation of the energy unit ? Marek Malý (Mon Sep 08 2008 - 08:01:10 PDT)
    - Re: AMBER: Explanation of the energy unit ? Carlos Simmerling (Mon Sep 08 2008 - 07:56:48 PDT)
    - Re: AMBER: Explanation of the energy unit ? Marek Malý (Mon Sep 08 2008 - 12:02:37 PDT)
    - Re: AMBER: Explanation of the energy unit ? Carlos Simmerling (Mon Sep 08 2008 - 11:51:49 PDT)
    - Re: AMBER: Explanation of the energy unit ? Marek Malý (Mon Sep 08 2008 - 13:19:47 PDT)
    - Re: AMBER: Explanation of the energy unit ? Gustavo Seabra (Mon Sep 08 2008 - 12:07:28 PDT)
    - Re: AMBER: Explanation of the energy unit ? Marek Malý (Mon Sep 08 2008 - 13:15:43 PDT)
    - Re: AMBER: Explanation of the energy unit ? Carlos Simmerling (Mon Sep 08 2008 - 13:16:16 PDT)
    - Re: AMBER: Explanation of the energy unit ? David A. Case (Mon Sep 08 2008 - 13:51:50 PDT)
    - Re: AMBER: Explanation of the energy unit ? Marek Malý (Wed Sep 10 2008 - 03:24:17 PDT)
AMBER: Test error in installing amber 10 using four threads on a single-cpu machine haixiao jin (Sun Sep 07 2008 - 02:42:10 PDT)
- Re: AMBER: Test error in installing amber 10 using four threads on a single-cpu machine David A. Case (Sun Sep 07 2008 - 05:50:57 PDT)
  - Re: AMBER: Test error in installing amber 10 using four threads on a single-cpu machine haixiao jin (Sun Sep 07 2008 - 06:26:31 PDT)
    - Re: AMBER: Test error in installing amber 10 using four threads on a single-cpu machine David A. Case (Sun Sep 07 2008 - 15:07:14 PDT)
AMBER: PMEMD installation problem. Cenk $Jenk$ Andac (Sun Sep 07 2008 - 23:58:42 PDT)
- RE: AMBER: PMEMD installation problem. Ross Walker (Mon Sep 08 2008 - 01:21:17 PDT)
  - RE: AMBER: PMEMD installation problem. Cenk $Jenk$ Andac (Mon Sep 08 2008 - 02:16:38 PDT)
    - Re: AMBER: PMEMD installation problem. Robert Duke (Mon Sep 08 2008 - 05:20:15 PDT)
    - Re: AMBER: PMEMD installation problem. Cenk $Jenk$ Andac (Mon Sep 08 2008 - 05:46:19 PDT)
AMBER: amber minimisation Majeed Shaik (Mon Sep 08 2008 - 05:32:17 PDT)
- Re: AMBER: amber minimisation Carlos Simmerling (Mon Sep 08 2008 - 05:40:44 PDT)
- Re: AMBER: amber minimisation David A. Case (Mon Sep 08 2008 - 05:59:26 PDT)
AMBER: Changes in the Amber web site David A. Case (Mon Sep 08 2008 - 06:25:41 PDT)
- RE: AMBER: Changes in the Amber web site Majeed Shaik (Mon Sep 08 2008 - 08:07:21 PDT)
  - Re: AMBER: Changes in the Amber web site Carlos Simmerling (Mon Sep 08 2008 - 08:14:33 PDT)
AMBER: problem when running energy minimization with polarizable potential Yongmei Pan (Mon Sep 08 2008 - 08:32:30 PDT)
- Re: AMBER: problem when running energy minimization with polarizable potential David A. Case (Tue Sep 09 2008 - 11:32:27 PDT)
  - Re: AMBER: problem when running energy minimization with polarizable potential Yongmei Pan (Tue Sep 09 2008 - 13:36:33 PDT)
AMBER: Problem compiling Amber with Intel 10 compilers - "undefined reference" errors Ben Roberts (Mon Sep 08 2008 - 08:43:47 PDT)
- Re: AMBER: Problem compiling Amber with Intel 10 compilers - "undefined reference" errors David A. Case (Mon Sep 08 2008 - 14:09:53 PDT)
  - Re: AMBER: Problem compiling Amber with Intel 10 compilers - "undefined reference" errors Ben Roberts (Mon Sep 08 2008 - 14:24:30 PDT)
    - Re: AMBER: Problem compiling Amber with Intel 10 compilers - "undefined reference" errors Ben Roberts (Tue Sep 09 2008 - 10:38:56 PDT)
AMBER: Another problem when trying to compile Sander in debug mode Ben Roberts (Mon Sep 08 2008 - 08:49:52 PDT)
AMBER: who can give a sample input file regarding the energy decomposition with sander? Yongmei Pan (Mon Sep 08 2008 - 13:41:37 PDT)
- Re: AMBER: who can give a sample input file regarding the energy decomposition with sander? David A. Case (Mon Sep 08 2008 - 14:31:50 PDT)
AMBER: NAB parameter: wcons ramu.vt.edu (Mon Sep 08 2008 - 14:06:54 PDT)
- Re: AMBER: NAB parameter: wcons David A. Case (Wed Sep 10 2008 - 05:19:32 PDT)
AMBER: energy decomposition with sander? Yongmei Pan (Mon Sep 08 2008 - 14:32:32 PDT)
AMBER: PMEMD and sander.MPI Germain Vallverdu (Tue Sep 09 2008 - 06:50:40 PDT)
- Re: AMBER: PMEMD and sander.MPI Robert Duke (Tue Sep 09 2008 - 07:14:52 PDT)
AMBER: Amber10 Compilation Anthony Cruz (Tue Sep 09 2008 - 07:26:04 PDT)
- AMBER: D2O Chih-Ying Lin (Tue Sep 09 2008 - 10:00:59 PDT)
  - Re: AMBER: D2O Carlos Simmerling (Tue Sep 09 2008 - 11:08:37 PDT)
    - Re: AMBER: D2O Chih-Ying Lin (Tue Sep 09 2008 - 12:59:13 PDT)
    - Re: AMBER: D2O Carlos Simmerling (Tue Sep 09 2008 - 16:09:41 PDT)
    - Re: AMBER: D2O Chih-Ying Lin (Thu Sep 11 2008 - 07:32:03 PDT)
    - Re: AMBER: D2O Carlos Simmerling (Thu Sep 11 2008 - 07:44:06 PDT)
    - Re: AMBER: D2O Adrian Roitberg (Thu Sep 11 2008 - 08:20:07 PDT)
    - Re: AMBER: D2O Chih-Ying Lin (Thu Sep 11 2008 - 17:51:03 PDT)
    - Re: AMBER: D2O Nicolas Lux Fawzi (Mon Sep 15 2008 - 09:54:17 PDT)
  - Re: AMBER: D2O David A. Case (Tue Sep 09 2008 - 11:21:37 PDT)
- RE: AMBER: Amber10 Compilation Ross Walker (Wed Sep 10 2008 - 05:31:47 PDT)
AMBER: about NMR refinement in explicit solvent Rogelio Hernández (Tue Sep 09 2008 - 12:15:19 PDT)
- Re: AMBER: about NMR refinement in explicit solvent David A. Case (Thu Sep 11 2008 - 10:24:37 PDT)
AMBER: Emperical Valence Bond sai kumar ramadugu (Tue Sep 09 2008 - 14:46:25 PDT)
AMBER: Preparing peptides with D-amino acids David Watson (Tue Sep 09 2008 - 17:06:58 PDT)
- Re: AMBER: Preparing peptides with D-amino acids Carlos Simmerling (Tue Sep 09 2008 - 17:26:20 PDT)
  - Re: AMBER: Preparing peptides with D-amino acids Carlos Simmerling (Tue Sep 09 2008 - 17:28:08 PDT)
    - Re: AMBER: Preparing peptides with D-amino acids David Watson (Tue Sep 09 2008 - 18:04:44 PDT)
    - Re: AMBER: Preparing peptides with D-amino acids Carlos Simmerling (Tue Sep 09 2008 - 18:14:34 PDT)
AMBER: RDF: Segmentation fault Sergey Samsonov (Wed Sep 10 2008 - 01:13:29 PDT)
AMBER: steered MD Germain Vallverdu (Wed Sep 10 2008 - 03:26:31 PDT)
- Re: AMBER: steered MD Carlos Simmerling (Wed Sep 10 2008 - 03:32:02 PDT)
  - Re: AMBER: steered MD Germain Vallverdu (Wed Sep 10 2008 - 04:17:10 PDT)
    - Re: AMBER: steered MD Carlos Simmerling (Wed Sep 10 2008 - 04:23:51 PDT)
    - Re: AMBER: steered MD Adrian Roitberg (Wed Sep 10 2008 - 04:31:19 PDT)
    - Re: AMBER: steered MD Germain Vallverdu (Wed Sep 10 2008 - 05:10:49 PDT)
- Re: AMBER: steered MD David A. Case (Wed Sep 10 2008 - 04:30:27 PDT)
AMBER: Cutoff list exceeds largest sphere in unit cell Majeed Shaik (Wed Sep 10 2008 - 07:54:58 PDT)
- RE: AMBER: Cutoff list exceeds largest sphere in unit cell Ross Walker (Wed Sep 10 2008 - 09:01:18 PDT)
  - RE: AMBER: Cutoff list exceeds largest sphere in unit cell Majeed Shaik (Wed Sep 10 2008 - 10:44:52 PDT)
  - RE: AMBER: Cutoff list exceeds largest sphere in unit cell Majeed Shaik (Wed Sep 10 2008 - 10:42:58 PDT)
    - RE: AMBER: Cutoff list exceeds largest sphere in unit cell Ross Walker (Wed Sep 10 2008 - 13:08:53 PDT)
    - RE: AMBER: Cutoff list exceeds largest sphere in unit cell Majeed Shaik (Thu Sep 11 2008 - 04:49:09 PDT)
AMBER: binding energy: high ELE CHAMI F. (Wed Sep 10 2008 - 08:15:40 PDT)
- Re: AMBER: binding energy: high ELE David A. Case (Thu Sep 11 2008 - 08:42:56 PDT)
- RE: AMBER: binding energy: high ELE CHAMI F. (Thu Sep 11 2008 - 10:24:23 PDT)
AMBER: Nonbonded FE parameter missing in frcmod. moitrayee.mbu.iisc.ernet.in (Thu Sep 11 2008 - 05:22:58 PDT)
- Re: AMBER: Nonbonded FE parameter missing in frcmod. David A. Case (Thu Sep 11 2008 - 10:19:53 PDT)
  - Re: AMBER: Nonbonded FE parameter missing in frcmod. moitrayee.mbu.iisc.ernet.in (Thu Sep 11 2008 - 10:16:34 PDT)
AMBER: Help...which commands in ptraj does clustering by RMSD? Jose Borreguero (Thu Sep 11 2008 - 13:28:49 PDT)
- Re: AMBER: Help...which commands in ptraj does clustering by RMSD? Sasha Buzko (Thu Sep 11 2008 - 13:39:44 PDT)
  - Re: AMBER: Help...which commands in ptraj does clustering by RMSD? Jose Borreguero (Thu Sep 11 2008 - 14:12:00 PDT)
    - Re: AMBER: Help...which commands in ptraj does clustering by RMSD? Sasha Buzko (Thu Sep 11 2008 - 14:48:14 PDT)
    - Re: AMBER: Help...which commands in ptraj does clustering by RMSD? Jose Borreguero (Thu Sep 11 2008 - 15:01:02 PDT)
    - AMBER: xleap and Sirius on ubuntu 8.04 alsarraj (Thu Sep 11 2008 - 19:45:54 PDT)
    - Re: AMBER: xleap and Sirius on ubuntu 8.04 Gustavo Seabra (Thu Sep 11 2008 - 20:13:58 PDT)
    - Re: AMBER: xleap and Sirius on ubuntu 8.04 Sasha Buzko (Thu Sep 11 2008 - 20:22:38 PDT)
AMBER: EVB allocation problem sai kumar ramadugu (Fri Sep 12 2008 - 09:08:41 PDT)
AMBER: Comment: constant pH, non-integer charge -> weird error Markus Kaukonen (Sun Sep 14 2008 - 00:51:58 PDT)
AMBER: mulliken charges in QM/MM calculation Barbault Florent (Sun Sep 14 2008 - 01:26:25 PDT)
- RE: AMBER: mulliken charges in QM/MM calculation Ross Walker (Sun Sep 14 2008 - 01:44:00 PDT)
AMBER: Failure of antechamber in amber10 Francesco Pietra (Sun Sep 14 2008 - 07:18:49 PDT)
AMBER: problem in installing parallel version of amber10 with lam Shibasish Chowdhury (Sun Sep 14 2008 - 21:20:12 PDT)
- RE: AMBER: problem in installing parallel version of amber10 with lam Ross Walker (Mon Sep 15 2008 - 19:02:48 PDT)
- RE: AMBER: problem in installing parallel version of amber10 with lam Shibasish Chowdhury (Tue Sep 16 2008 - 03:37:06 PDT)
AMBER: 3fe-4s cluster parameter file generation moitrayee.mbu.iisc.ernet.in (Sun Sep 14 2008 - 23:35:39 PDT)
- Re: AMBER: 3fe-4s cluster parameter file generation David A. Case (Mon Sep 15 2008 - 04:15:52 PDT)
  - Re: AMBER: 3fe-4s cluster parameter file generation moitrayee.mbu.iisc.ernet.in (Mon Sep 15 2008 - 04:20:19 PDT)
    - Re: AMBER: 3fe-4s cluster parameter file generation David A. Case (Mon Sep 15 2008 - 05:06:08 PDT)
    - Re: AMBER: 3fe-4s cluster parameter file generation moitrayee.mbu.iisc.ernet.in (Mon Sep 15 2008 - 04:46:56 PDT)
    - Re: AMBER: 3fe-4s cluster parameter file generation David A. Case (Mon Sep 15 2008 - 07:15:12 PDT)
    - Re: AMBER: 3fe-4s cluster parameter file generation moitrayee.mbu.iisc.ernet.in (Mon Sep 15 2008 - 08:36:31 PDT)
    - Re: AMBER: 3fe-4s cluster parameter file generation S.Sundar Raman (Mon Sep 15 2008 - 10:21:44 PDT)
    - Re: AMBER: 3fe-4s cluster parameter file generation Hakkim Boy (Mon Sep 15 2008 - 05:30:04 PDT)
    - Re: AMBER: 3fe-4s cluster parameter file generation S.Sundar Raman (Mon Sep 15 2008 - 05:56:36 PDT)
    - Re: AMBER: 3fe-4s cluster parameter file generation moitrayee.mbu.iisc.ernet.in (Tue Sep 16 2008 - 11:12:24 PDT)
- Re: AMBER: 3fe-4s cluster parameter file generation Bill Ross (Mon Sep 15 2008 - 11:51:29 PDT)
  - Re: AMBER: 3fe-4s cluster parameter file generation moitrayee.mbu.iisc.ernet.in (Tue Sep 16 2008 - 04:39:25 PDT)
- Re: AMBER: 3fe-4s cluster parameter file generation Bill Ross (Tue Sep 16 2008 - 10:47:00 PDT)
  - Re: AMBER: 3fe-4s cluster parameter file generation moitrayee.mbu.iisc.ernet.in (Tue Sep 16 2008 - 11:01:59 PDT)
- Re: AMBER: 3fe-4s cluster parameter file generation Bill Ross (Tue Sep 16 2008 - 12:15:52 PDT)
- Re: AMBER: 3fe-4s cluster parameter file generation Bill Ross (Tue Sep 16 2008 - 12:36:24 PDT)
  - Re: AMBER: 3fe-4s cluster parameter file generation moitrayee.mbu.iisc.ernet.in (Tue Sep 16 2008 - 23:43:49 PDT)
    - Re: AMBER: 3fe-4s cluster parameter file generation David A. Case (Wed Sep 17 2008 - 04:26:07 PDT)
- Re: AMBER: 3fe-4s cluster parameter file generation Bill Ross (Wed Sep 17 2008 - 10:41:28 PDT)
- Re: AMBER: 3fe-4s cluster parameter file generation Bill Ross (Wed Sep 17 2008 - 11:04:32 PDT)
AMBER: question about dihedral angles Harry (Yicun) Ni (Mon Sep 15 2008 - 07:41:31 PDT)
- Re: AMBER: question about dihedral angles Ilyas Yildirim (Mon Sep 15 2008 - 08:10:55 PDT)
AMBER: Hydrogen bond energies in explicit solvent. Waqas Nasir (Mon Sep 15 2008 - 07:56:34 PDT)
- Re: AMBER: Hydrogen bond energies in explicit solvent. Carlos Simmerling (Mon Sep 15 2008 - 08:01:41 PDT)
- Re: AMBER: Hydrogen bond energies in explicit solvent. Waqas Nasir (Mon Sep 15 2008 - 08:47:00 PDT)
  - Re: AMBER: Hydrogen bond energies in explicit solvent. Carlos Simmerling (Mon Sep 15 2008 - 08:54:25 PDT)
- Re: AMBER: Hydrogen bond energies in explicit solvent. Waqas Nasir (Mon Sep 15 2008 - 09:17:04 PDT)
  - Re: AMBER: Hydrogen bond energies in explicit solvent. Carlos Simmerling (Mon Sep 15 2008 - 09:24:07 PDT)
AMBER: Minimizaton stops after Ncyc steps only mon_sharma.research.iiit.ac.in (Mon Sep 15 2008 - 09:34:22 PDT)
- Re: AMBER: Minimizaton stops after Ncyc steps only Carlos Simmerling (Mon Sep 15 2008 - 10:23:00 PDT)
AMBER: Announcement of ACS COMP Division CCG and HP award deadlines for Spring 2009 meeting Carlos Simmerling (Mon Sep 15 2008 - 09:39:58 PDT)
AMBER: parallel amber 10 sander.MPI (low cpu utilization) meandme meandme (Mon Sep 15 2008 - 10:27:06 PDT)
AMBER: amber 10 parallel cpu utlization meandme meandme (Mon Sep 15 2008 - 10:30:49 PDT)
- RE: AMBER: amber 10 parallel cpu utlization Ross Walker (Mon Sep 15 2008 - 19:09:37 PDT)
AMBER: AMBER10 Compilation (SGI Altix) Anthony Cruz (Mon Sep 15 2008 - 11:21:49 PDT)
- RE: AMBER: AMBER10 Compilation (SGI Altix) Ross Walker (Mon Sep 15 2008 - 19:15:54 PDT)
  - Re: AMBER: AMBER10 Compilation (SGI Altix) Anthony Cruz (Tue Sep 16 2008 - 09:56:45 PDT)
AMBER: MM-PBSA/NMODE in Amber 10 Peterson, Matthew W. (MPETERSON) (Mon Sep 15 2008 - 13:37:41 PDT)
- Re: AMBER: MM-PBSA/NMODE in Amber 10 Daniel Oehme (Mon Sep 15 2008 - 18:23:26 PDT)
- Re: AMBER: MM-PBSA/NMODE in Amber 10 Daniel Oehme (Mon Sep 22 2008 - 00:13:55 PDT)
AMBER: Temperature regulation julliane Yoneda (Mon Sep 15 2008 - 17:48:50 PDT)
- Re: AMBER: Temperature regulation Carlos Simmerling (Mon Sep 15 2008 - 18:07:57 PDT)
  - Re: AMBER: Temperature regulation julliane Yoneda (Tue Sep 16 2008 - 11:05:27 PDT)
    - Re: AMBER: Temperature regulation Carlos Simmerling (Tue Sep 16 2008 - 11:22:55 PDT)
    - Re: AMBER: Temperature regulation Myunggi Yi (Tue Sep 16 2008 - 14:28:21 PDT)
    - Re: AMBER: Temperature regulation julliane Yoneda (Tue Sep 16 2008 - 16:34:52 PDT)
    - Re: AMBER: Temperature regulation julliane Yoneda (Tue Sep 16 2008 - 16:36:01 PDT)
  - Re: AMBER: Temperature regulation julliane Yoneda (Wed Oct 01 2008 - 10:22:06 PDT)
    - Re: AMBER: Temperature regulation Carlos Simmerling (Wed Oct 01 2008 - 10:49:26 PDT)
    - Re: AMBER: Temperature regulation julliane Yoneda (Wed Oct 01 2008 - 18:10:27 PDT)
    - Re: AMBER: Temperature regulation Carlos Simmerling (Wed Oct 01 2008 - 19:04:36 PDT)
    - Re: AMBER: Temperature regulation julliane Yoneda (Wed Oct 08 2008 - 10:52:52 PDT)
AMBER: top and crd files without hydrogen Waqas Nasir (Tue Sep 16 2008 - 02:18:08 PDT)
- Re: AMBER: top and crd files without hydrogen Carlos Simmerling (Tue Sep 16 2008 - 03:04:36 PDT)
- Re: AMBER: top and crd files without hydrogen Waqas Nasir (Tue Sep 16 2008 - 03:32:42 PDT)
AMBER: nmode/nab entropy calculations memory issues chaitanya koppisetty (Tue Sep 16 2008 - 07:58:01 PDT)
- Re: AMBER: nmode/nab entropy calculations memory issues Andreas Svrcek-Seiler (Tue Sep 16 2008 - 08:50:11 PDT)
  - AMBER: nmode/nab entropy calculations without hydrogens chaitanya koppisetty (Wed Sep 17 2008 - 00:47:58 PDT)
AMBER: problem with editing with xleap moitrayee.mbu.iisc.ernet.in (Tue Sep 16 2008 - 08:50:38 PDT)
- Re: AMBER: problem with editing with xleap David A. Case (Wed Sep 17 2008 - 04:30:55 PDT)
AMBER: AMBER9 Compilation chen bents (Tue Sep 16 2008 - 18:25:59 PDT)
AMBER: amber 9 install chen bents (Tue Sep 16 2008 - 20:14:47 PDT)
- Re: AMBER: amber 9 install Ye Mei (Tue Sep 16 2008 - 20:26:07 PDT)
  - Re: AMBER: amber 9 install chen bents (Wed Sep 17 2008 - 00:44:46 PDT)
AMBER: acetone box parvesh singh (Wed Sep 17 2008 - 04:09:01 PDT)
AMBER: Question Beale, John (Wed Sep 17 2008 - 04:14:15 PDT)
- Re: AMBER: Question Carlos Simmerling (Wed Sep 17 2008 - 04:18:19 PDT)
AMBER: MD simulation crashed Aust, Susanne (Wed Sep 17 2008 - 06:10:17 PDT)
- Re: AMBER: MD simulation crashed Carlos Simmerling (Wed Sep 17 2008 - 06:27:59 PDT)
AMBER: adding new potential function Harianto Tjong (Wed Sep 17 2008 - 12:12:34 PDT)
AMBER: Some Problems With the Installation of Ambertools Manikandan Chandrasekaran (Wed Sep 17 2008 - 16:21:06 PDT)
- Re: AMBER: Some Problems With the Installation of Ambertools Atro Tossavainen (Thu Sep 18 2008 - 01:06:57 PDT)
- Re: AMBER: Some Problems With the Installation of Ambertools David A. Case (Thu Sep 18 2008 - 04:10:12 PDT)
  - Re: AMBER: Some Problems With the Installation of Ambertools Manikandan Chandrasekaran (Thu Sep 18 2008 - 09:43:39 PDT)
    - Re: AMBER: Some Problems With the Installation of Ambertools David A. Case (Thu Sep 18 2008 - 11:35:27 PDT)
    - Re: AMBER: Some Problems With the Installation of Ambertools Manikandan Chandrasekaran (Fri Sep 19 2008 - 12:49:41 PDT)
    - Re: AMBER: Some Problems With the Installation of Ambertools David A. Case (Sat Sep 20 2008 - 05:38:55 PDT)
AMBER: Dihedral: ptraj waqasuddin.khan.iccs.edu (Wed Sep 17 2008 - 23:39:33 PDT)
- Re: AMBER: Dihedral: ptraj Carlos Simmerling (Thu Sep 18 2008 - 02:04:24 PDT)
  - Re: AMBER: Dihedral: ptraj waqasuddin.khan.iccs.edu (Thu Sep 18 2008 - 02:14:50 PDT)
    - Re: AMBER: Dihedral: ptraj Carlos Simmerling (Thu Sep 18 2008 - 02:32:38 PDT)
AMBER: Single point energy calculations with explicit solvent. Waqas Nasir (Thu Sep 18 2008 - 05:48:47 PDT)
- Re: AMBER: Single point energy calculations with explicit solvent. Carlos Simmerling (Thu Sep 18 2008 - 05:55:00 PDT)
AMBER: problem with traj and strip waters Steve Seibold (Thu Sep 18 2008 - 06:08:21 PDT)
- Re: AMBER: problem with traj and strip waters Carlos Simmerling (Thu Sep 18 2008 - 06:19:17 PDT)
- Re: AMBER: problem with traj and strip waters David A. Case (Thu Sep 18 2008 - 06:34:18 PDT)
AMBER: problem with traj and strip waters Steve Seibold (Thu Sep 18 2008 - 07:13:38 PDT)
- Re: AMBER: problem with traj and strip waters Carlos Simmerling (Thu Sep 18 2008 - 07:22:30 PDT)
AMBER: Error: PB bomb in pb_reslist(): maxnbr too small Rajendra P. OJHA (Thu Sep 18 2008 - 07:34:15 PDT)
AMBER: RMSD restraint in umbrella sampling nurith.rice.edu (Thu Sep 18 2008 - 13:36:24 PDT)
- Re: AMBER: RMSD restraint in umbrella sampling Carlos Simmerling (Thu Sep 18 2008 - 14:23:01 PDT)
AMBER: help can amber couple part of the system to different heat bath? Jose Borreguero (Thu Sep 18 2008 - 14:09:23 PDT)
AMBER: help can amber couple part of the system to different heat bath? Jose Borreguero (Thu Sep 18 2008 - 14:09:27 PDT)
AMBER: problems with ptraj and strip waters Steve Seibold (Thu Sep 18 2008 - 14:19:25 PDT)
- Re: AMBER: problems with ptraj and strip waters Carlos Simmerling (Thu Sep 18 2008 - 14:29:56 PDT)
- Re: AMBER: problems with ptraj and strip waters Gustavo Seabra (Thu Sep 18 2008 - 16:18:44 PDT)
AMBER: increasing temperature smoothly Germain Vallverdu (Fri Sep 19 2008 - 08:17:56 PDT)
- Re: AMBER: increasing temperature smoothly David A. Case (Fri Sep 19 2008 - 09:49:46 PDT)
- RE: AMBER: increasing temperature smoothly Ross Walker (Fri Sep 19 2008 - 11:29:31 PDT)
  - Re: AMBER: increasing temperature smoothly Germain Vallverdu (Mon Sep 22 2008 - 02:00:19 PDT)
    - AMBER: The forming of micelle Chih-Ying Lin (Mon Sep 22 2008 - 11:06:24 PDT)
    - Re: AMBER: The forming of micelle Adrian Roitberg (Mon Sep 22 2008 - 11:20:50 PDT)
    - Re: AMBER: The forming of micelle Chih-Ying Lin (Mon Sep 22 2008 - 12:02:30 PDT)
    - Re: AMBER: The forming of micelle Chih-Ying Lin (Tue Sep 23 2008 - 17:07:47 PDT)
    - Re: AMBER: The forming of micelle (CMC) Chih-Ying Lin (Wed Sep 24 2008 - 11:02:22 PDT)
    - Re: AMBER: The forming of micelle (CMC) Gustavo Seabra (Wed Sep 24 2008 - 15:00:45 PDT)
    - AMBER: The size of the simulation box and the # of solute / water molecules? Chih-Ying Lin (Mon Sep 22 2008 - 12:19:06 PDT)
- Re: AMBER: increasing temperature smoothly Germain Vallverdu (Mon Sep 22 2008 - 04:31:56 PDT)
  - Re: AMBER: increasing temperature smoothly David A. Case (Mon Sep 22 2008 - 04:44:02 PDT)
AMBER: molecule drift out of water box? Qiuting Hong (Fri Sep 19 2008 - 16:39:42 PDT)
- Re: AMBER: molecule drift out of water box? Ilyas Yildirim (Fri Sep 19 2008 - 17:00:03 PDT)
  - Re: AMBER: molecule drift out of water box? Qiuting Hong (Sun Sep 21 2008 - 13:22:19 PDT)
    - Re: AMBER: molecule drift out of water box? Ilyas Yildirim (Sun Sep 21 2008 - 13:45:45 PDT)
    - Re: AMBER: molecule drift out of water box? Qiuting Hong (Sun Sep 21 2008 - 18:43:38 PDT)
    - Re: AMBER: molecule drift out of water box? Ilyas Yildirim (Sun Sep 21 2008 - 19:52:17 PDT)
AMBER: Dihedral Drive Hashem Taha (Sat Sep 20 2008 - 00:31:13 PDT)
- Re: AMBER: Dihedral Drive Ilyas Yildirim (Sat Sep 20 2008 - 01:07:07 PDT)
AMBER: Is there any way I can extract the potential energy of the solute with the solvent instead of the total energy in Amber? Zhao, Zhen (zhaozh) (Sat Sep 20 2008 - 13:01:59 PDT)
- Re: AMBER: Is there any way I can extract the potential energy of the solute with the solvent instead of the total energy in Amber? Barbault Florent (Sat Sep 20 2008 - 13:40:34 PDT)
AMBER: bis(trifluoromethylsulfonyl)imide (Tf2N) babak minoofar (Sun Sep 21 2008 - 07:34:39 PDT)
- Re: AMBER: bis(trifluoromethylsulfonyl)imide (Tf2N) David Watson (Sun Sep 21 2008 - 09:01:04 PDT)
AMBER: multiple heat baths in a single simulation? Jose Borreguero (Sun Sep 21 2008 - 16:09:41 PDT)
AMBER: fix for POL3 heating problem? Grange Hermitage (Mon Sep 22 2008 - 02:35:02 PDT)
AMBER: Re: reaction coordinate in umbrella sampling Sudha Mani Karra (Mon Sep 22 2008 - 08:00:42 PDT)
- Re: AMBER: Re: reaction coordinate in umbrella sampling Jerome.GOLEBIOWSKI.unice.fr (Tue Sep 23 2008 - 00:33:43 PDT)
AMBER: Position: Postdoctoral Fellow Willy Valdivia-Granda (Mon Sep 22 2008 - 08:50:48 PDT)
AMBER: Problem of "Too many dipole-dipole interactions allocated" when using amoeba. Zhao, Zhen (zhaozh) (Mon Sep 22 2008 - 12:02:27 PDT)
- Re: AMBER: Problem of "Too many dipole-dipole interactions allocated" when using amoeba. Tom Darden (Mon Sep 22 2008 - 13:51:53 PDT)
  - RE: AMBER: Problem of "Too many dipole-dipole interactions allocated" when using amoeba. Zhao, Zhen (zhaozh) (Tue Sep 23 2008 - 07:11:23 PDT)
AMBER: MMPBSA error Cristina Sisu (Tue Sep 23 2008 - 03:30:38 PDT)
AMBER: replica exchange with amber9 greddy1.umd.edu (Tue Sep 23 2008 - 15:44:24 PDT)
- Re: AMBER: replica exchange with amber9 Carlos Simmerling (Tue Sep 23 2008 - 15:52:04 PDT)
AMBER: MD goes wrong baohua zhang (Tue Sep 23 2008 - 19:17:57 PDT)
- Re: AMBER: MD goes wrong Adrian Roitberg (Tue Sep 23 2008 - 20:19:19 PDT)
- RE: AMBER: MD goes wrong Ross Walker (Tue Sep 23 2008 - 21:33:43 PDT)
AMBER: to prepare pdb file fro unusual amino acid. priya priya (Wed Sep 24 2008 - 01:03:06 PDT)
- Re: AMBER: to prepare pdb file fro unusual amino acid. Hakkim Boy (Wed Sep 24 2008 - 07:41:33 PDT)
- Re: AMBER: to prepare pdb file fro unusual amino acid. FyD (Wed Sep 24 2008 - 11:36:03 PDT)
- Re: AMBER: to prepare pdb file fro unusual amino acid. waqasuddin.khan.iccs.edu (Wed Sep 24 2008 - 22:55:51 PDT)
- RE: AMBER: to prepare pdb file fro unusual amino acid. Ross Walker (Wed Sep 24 2008 - 23:36:08 PDT)
- RE: AMBER: to prepare pdb file fro unusual amino acid. Ross Walker (Thu Sep 25 2008 - 07:55:21 PDT)
- Re: AMBER: to prepare pdb file fro unusual amino acid. priya priya (Thu Sep 25 2008 - 09:40:07 PDT)
AMBER: error while running REMD in amber9 priya priya (Wed Sep 24 2008 - 10:53:09 PDT)
- Re: AMBER: error while running REMD in amber9 Carlos Simmerling (Wed Sep 24 2008 - 11:27:22 PDT)
- Re: AMBER: error while running REMD in amber9 priya priya (Thu Sep 25 2008 - 09:49:28 PDT)
  - Re: AMBER: error while running REMD in amber9 Carlos Simmerling (Thu Sep 25 2008 - 09:55:35 PDT)
- Re: AMBER: error while running REMD in amber9 priya priya (Thu Sep 25 2008 - 10:44:13 PDT)
  - Re: AMBER: error while running REMD in amber9 Carlos Simmerling (Thu Sep 25 2008 - 10:51:58 PDT)
- Re: AMBER: error while running REMD in amber9 priya priya (Thu Sep 25 2008 - 11:04:26 PDT)
  - Re: AMBER: error while running REMD in amber9 Carlos Simmerling (Thu Sep 25 2008 - 11:28:17 PDT)
AMBER: Compiling Amber10 PMEMD with MVAPICH, InfiniBand support Pablo Englebienne (Wed Sep 24 2008 - 12:04:46 PDT)
- Re: AMBER: Compiling Amber10 PMEMD with MVAPICH, InfiniBand support Robert Duke (Wed Sep 24 2008 - 12:39:30 PDT)
  - Re: AMBER: Compiling Amber10 PMEMD with MVAPICH, InfiniBand support Pablo Englebienne (Thu Sep 25 2008 - 12:07:48 PDT)
AMBER: solvate without translating Anuradha Mittal (Wed Sep 24 2008 - 12:38:31 PDT)
- RE: AMBER: solvate without translating Ross Walker (Wed Sep 24 2008 - 23:46:52 PDT)
- RE: AMBER: solvate without translating Ross Walker (Thu Sep 25 2008 - 07:55:53 PDT)
AMBER: how to enlarge the TIP3PBOX size Qiuting Hong (Wed Sep 24 2008 - 15:56:10 PDT)
- Re: AMBER: how to enlarge the TIP3PBOX size Carlos Simmerling (Wed Sep 24 2008 - 16:01:44 PDT)
  - AMBER: Amber on Infiniband clusters: SDR vs DDR cables? Sasha Buzko (Thu Sep 25 2008 - 16:06:44 PDT)
- Re: AMBER: how to enlarge the TIP3PBOX size waqasuddin.khan.iccs.edu (Wed Sep 24 2008 - 23:01:57 PDT)
- RE: AMBER: how to enlarge the TIP3PBOX size Ross Walker (Wed Sep 24 2008 - 23:40:21 PDT)
  - Re: AMBER: how to enlarge the TIP3PBOX size Qiuting Hong (Fri Sep 26 2008 - 00:28:53 PDT)
    - Re: AMBER: how to enlarge the TIP3PBOX size David A. Case (Fri Sep 26 2008 - 09:06:37 PDT)
- RE: AMBER: how to enlarge the TIP3PBOX size Ross Walker (Thu Sep 25 2008 - 07:55:38 PDT)
AMBER: Amber GB problems on PMEMD !! Sampath Koppole (Thu Sep 25 2008 - 02:09:30 PDT)
- Re: AMBER: Amber GB problems on PMEMD !! Robert Duke (Thu Sep 25 2008 - 05:22:06 PDT)
  - Re: AMBER: Amber GB problems on PMEMD !! Sampath Koppole (Thu Sep 25 2008 - 06:02:42 PDT)
    - Re: AMBER: Amber GB problems on PMEMD !! Andreas Svrcek-Seiler (Thu Sep 25 2008 - 08:12:59 PDT)
- RE: AMBER: Amber GB problems on PMEMD !! Ross Walker (Thu Sep 25 2008 - 08:23:44 PDT)
AMBER: Problem In Paralklel Amber Ranga Swamy (Fri Sep 26 2008 - 04:10:13 PDT)
- Re: AMBER: Problem In Paralklel Amber Carlos Simmerling (Fri Sep 26 2008 - 04:52:00 PDT)
  - Re: AMBER: Problem In Paralklel Amber Ranga Swamy (Sun Sep 28 2008 - 22:23:57 PDT)
    - RE: AMBER: Problem In Paralklel Amber Ross Walker (Mon Sep 29 2008 - 07:35:50 PDT)
AMBER: MD at a given pH Beale, John (Fri Sep 26 2008 - 09:44:32 PDT)
- Re: AMBER: MD at a given pH David A. Case (Sat Sep 27 2008 - 04:53:56 PDT)
AMBER: Harmonic restraint between two atoms greddy1.umd.edu (Fri Sep 26 2008 - 11:37:34 PDT)
- Re: AMBER: Harmonic restraint between two atoms Adrian Roitberg (Fri Sep 26 2008 - 11:42:55 PDT)
AMBER: mmpbsa errors in redoing the tutorial A3:MMPBSA haixiao jin (Sat Sep 27 2008 - 00:45:06 PDT)
AMBER: Constant pH simulation force field Soonmin Jang (Sat Sep 27 2008 - 02:13:51 PDT)
- Re: AMBER: Constant pH simulation force field David A. Case (Sat Sep 27 2008 - 05:10:39 PDT)
AMBER: Leap atoms CL and OXT do not have a type Francesco Pietra (Sat Sep 27 2008 - 06:46:10 PDT)
- Re: AMBER: Leap atoms CL and OXT do not have a type Carlos Simmerling (Sat Sep 27 2008 - 06:56:22 PDT)
- Re: AMBER: Leap atoms CL and OXT do not have a type David A. Case (Sat Sep 27 2008 - 07:12:40 PDT)
  - Re: AMBER: Leap atoms CL and OXT do not have a type Francesco Pietra (Sat Sep 27 2008 - 08:36:47 PDT)
    - Re: AMBER: Leap atoms CL and OXT do not have a type David A. Case (Sat Sep 27 2008 - 09:29:23 PDT)
    - Re: AMBER: Leap atoms CL and OXT do not have a type Carlos Simmerling (Sat Sep 27 2008 - 10:07:03 PDT)
    - Re: AMBER: Leap atoms CL and OXT do not have a type Francesco Pietra (Sat Sep 27 2008 - 11:11:49 PDT)
    - Re: AMBER: Leap atoms CL and OXT do not have a type Carlos Simmerling (Sat Sep 27 2008 - 11:21:19 PDT)
    - Re: AMBER: Leap atoms CL and OXT do not have a type Francesco Pietra (Sat Sep 27 2008 - 12:31:51 PDT)
- Re: AMBER: Leap atoms CL and OXT do not have a type Bill Ross (Mon Sep 29 2008 - 11:38:46 PDT)
  - Re: AMBER: Leap atoms CL and OXT do not have a type Francesco Pietra (Mon Sep 29 2008 - 13:13:05 PDT)
- Re: AMBER: Leap atoms CL and OXT do not have a type Bill Ross (Mon Sep 29 2008 - 15:03:28 PDT)
  - Re: AMBER: Leap atoms CL and OXT do not have a type Francesco Pietra (Tue Sep 30 2008 - 03:05:13 PDT)
  - Re: AMBER: Leap atoms CL and OXT do not have a type Francesco Pietra (Thu Oct 02 2008 - 08:47:31 PDT)
- Re: AMBER: Leap atoms CL and OXT do not have a type Bill Ross (Tue Sep 30 2008 - 11:11:12 PDT)
- Re: AMBER: Leap atoms CL and OXT do not have a type Bill Ross (Thu Oct 02 2008 - 10:36:58 PDT)
  - Re: AMBER: Leap atoms CL and OXT do not have a type Francesco Pietra (Thu Oct 02 2008 - 12:15:54 PDT)
- Re: AMBER: Leap atoms CL and OXT do not have a type Bill Ross (Thu Oct 02 2008 - 13:09:53 PDT)
AMBER: a question Adrien Delmont (Sun Sep 28 2008 - 15:08:00 PDT)
- RE: AMBER: a question Ross Walker (Sun Sep 28 2008 - 21:56:00 PDT)
  - RE: AMBER: a question oguz gurbulak (Mon Sep 29 2008 - 02:55:29 PDT)
    - RE: AMBER: a question Ross Walker (Mon Sep 29 2008 - 07:41:54 PDT)
  - RE: AMBER: a question oguz gurbulak (Mon Sep 29 2008 - 03:23:09 PDT)
- Re: AMBER: a question Adrien Delmont (Mon Sep 29 2008 - 05:53:51 PDT)
AMBER: energy terms in hybrid REMD calculation Ye Mei (Mon Sep 29 2008 - 02:28:13 PDT)
AMBER: Location of vdw radii and partial charges for ff99SB Charles Letner, Ph.D. (Mon Sep 29 2008 - 06:08:27 PDT)
- RE: AMBER: Location of vdw radii and partial charges for ff99SB Ross Walker (Mon Sep 29 2008 - 07:51:44 PDT)
- Re: AMBER: Location of vdw radii and partial charges for ff99SB Carlos Simmerling (Mon Sep 29 2008 - 07:58:45 PDT)
AMBER: unsubscribe amber steinbrt.scripps.edu (Mon Sep 29 2008 - 07:57:50 PDT)
AMBER: coordinate file question Robert Hanson (Mon Sep 29 2008 - 20:16:25 PDT)
- RE: AMBER: coordinate file question Ross Walker (Mon Sep 29 2008 - 20:33:10 PDT)
  - Re: AMBER: coordinate file question Robert Hanson (Tue Sep 30 2008 - 06:30:21 PDT)
    - RE: AMBER: coordinate file question Ross Walker (Tue Sep 30 2008 - 06:55:57 PDT)
    - Re: AMBER: coordinate file question Robert Hanson (Tue Sep 30 2008 - 10:24:47 PDT)
AMBER: Ac-Co Parameters for Amber suhaib sh (Tue Sep 30 2008 - 04:49:41 PDT)
- Re: AMBER: Ac-Co Parameters for Amber suhaib sh (Tue Sep 30 2008 - 15:18:48 PDT)
  - Re: AMBER: Ac-Co Parameters for Amber FyD (Tue Sep 30 2008 - 23:14:39 PDT)
    - Re: AMBER: Ac-Co Parameters for Amber suhaib sh (Wed Oct 01 2008 - 02:05:31 PDT)
    - Re: AMBER: Ac-Co Parameters for Amber FyD (Wed Oct 01 2008 - 14:26:54 PDT)
    - Re: AMBER: Ac-Co Parameters for Amber suhaib sh (Thu Oct 02 2008 - 02:34:08 PDT)
AMBER: Ca ions not recognized Cristina Sisu (Tue Sep 30 2008 - 07:00:24 PDT)
- RE: AMBER: Ca ions not recognized Peterson, Matthew W. (Tue Sep 30 2008 - 07:08:16 PDT)
AMBER: Buckingham potential Diddo Diddens (Tue Sep 30 2008 - 07:16:47 PDT)
- Re: AMBER: Buckingham potential Andreas Svrcek-Seiler (Tue Sep 30 2008 - 07:47:27 PDT)
  - Re: AMBER: Buckingham potential Diddo Diddens (Tue Sep 30 2008 - 08:01:57 PDT)
    - Re: AMBER: Buckingham potential Adrian Roitberg (Tue Sep 30 2008 - 08:14:53 PDT)
AMBER: cluster for running amber10 Guillermo Mulliert Carlín (Tue Sep 30 2008 - 08:14:07 PDT)
- RE: AMBER: cluster for running amber10 Ross Walker (Tue Sep 30 2008 - 08:25:09 PDT)
  - AMBER: MM-PBSA problem : Missing PBCAV for PB Carra, Claudio (JSC-SK)[USRA] (Tue Sep 30 2008 - 09:49:26 PDT)
  - AMBER: MM-PBSA problem : Use of uninitialized value in multiplicatiom with Amber10 Carra, Claudio (JSC-SK)[USRA] (Wed Oct 01 2008 - 10:05:55 PDT)
AMBER: problem with parmchck aneesh cna (Tue Sep 30 2008 - 10:10:28 PDT)
AMBER: XLF problem in compiling AMBER8 on IBM PPC64 SUSE liu junjun (Tue Sep 30 2008 - 11:07:09 PDT)
- RE: AMBER: XLF problem in compiling AMBER8 on IBM PPC64 SUSE Ross Walker (Tue Sep 30 2008 - 11:18:44 PDT)
  - Re: AMBER: XLF problem in compiling AMBER8 on IBM PPC64 SUSE liu junjun (Tue Sep 30 2008 - 11:48:11 PDT)
- Re: AMBER: XLF problem in compiling AMBER8 on IBM PPC64 SUSE Jed W Pitera (Tue Sep 30 2008 - 11:56:18 PDT)
  - Re: AMBER: XLF problem in compiling AMBER8 on IBM PPC64 SUSE liu junjun (Tue Sep 30 2008 - 12:17:26 PDT)
AMBER: FW: Amber 9 mhamed.birzeit.edu (Tue Sep 30 2008 - 10:22:07 PDT)
- Re: AMBER: FW: Amber 9 Gustavo Seabra (Tue Sep 30 2008 - 12:12:19 PDT)
AMBER: problem of use MPICHI2 to run RMED on amber10 xwu.purdue.edu (Tue Sep 30 2008 - 13:31:24 PDT)
- Re: AMBER: problem of use MPICHI2 to run RMED on amber10 Carlos Simmerling (Tue Sep 30 2008 - 13:45:58 PDT)
  - Re: AMBER: problem of use MPICHI2 to run RMED on amber10 xwu.purdue.edu (Tue Sep 30 2008 - 14:03:08 PDT)
    - Re: AMBER: problem of use MPICHI2 to run RMED on amber10 Carlos Simmerling (Tue Sep 30 2008 - 14:09:59 PDT)
    - Re: AMBER: problem of use MPICHI2 to run RMED on amber10 xwu.purdue.edu (Tue Sep 30 2008 - 14:29:19 PDT)
    - Re: AMBER: problem of use MPICHI2 to run RMED on amber10 Carlos Simmerling (Tue Sep 30 2008 - 14:33:12 PDT)
AMBER: How to set up a water slab in Amber? Zhao, Zhen (zhaozh) (Tue Sep 30 2008 - 14:23:06 PDT)
- Re: AMBER: How to set up a water slab in Amber? David A. Case (Wed Oct 01 2008 - 04:51:17 PDT)
AMBER: F modified RNA is split in two parts when running sander simulated annealing Peter Podbevšek (Wed Oct 01 2008 - 02:01:52 PDT)
- Re: AMBER: F modified RNA is split in two parts when running sander simulated annealing Andreas Svrcek-Seiler (Wed Oct 01 2008 - 02:56:38 PDT)
- RE: AMBER: F modified RNA is split in two parts when running sander simulated annealing Peter Podbevšek (Thu Oct 02 2008 - 06:08:51 PDT)
AMBER: Sources of disruption during NVE Naser Alijabbari (Wed Oct 01 2008 - 08:59:29 PDT)
- Re: AMBER: Sources of disruption during NVE Gustavo Seabra (Wed Oct 01 2008 - 12:32:06 PDT)
  - Re: AMBER: Sources of disruption during NVE Naser Alijabbari (Wed Oct 01 2008 - 18:10:43 PDT)
    - Re: AMBER: Sources of disruption during NVE Gustavo Seabra (Fri Oct 03 2008 - 06:39:05 PDT)
- Re: AMBER: Sources of disruption during NVE Bill Ross (Fri Oct 03 2008 - 08:27:37 PDT)
AMBER: amber10 installation on sgi_mips Rima Chaudhuri (Wed Oct 01 2008 - 12:05:06 PDT)
- Re: AMBER: amber10 installation on sgi_mips David A. Case (Wed Oct 01 2008 - 12:24:56 PDT)
  - Re: AMBER: amber10 installation on sgi_mips Rima Chaudhuri (Wed Oct 01 2008 - 13:47:14 PDT)
  - Re: AMBER: amber10 installation on sgi_mips Atro Tossavainen (Thu Oct 02 2008 - 02:59:34 PDT)
    - Re: AMBER: amber10 installation on sgi_mips Rima Chaudhuri (Thu Oct 02 2008 - 09:42:25 PDT)
    - Re: AMBER: amber10 installation on sgi_mips Atro Tossavainen (Thu Oct 02 2008 - 12:39:33 PDT)
- Re: AMBER: amber10 installation on sgi_mips Bill Ross (Wed Oct 01 2008 - 15:11:08 PDT)
  - Re: AMBER: amber10 installation on sgi_mips Rima Chaudhuri (Wed Oct 01 2008 - 19:31:06 PDT)
- Re: AMBER: amber10 installation on sgi_mips Bill Ross (Thu Oct 02 2008 - 10:05:17 PDT)
AMBER: thermodynamic integration with Amber9 Sadhna Rana (Thu Oct 02 2008 - 08:12:47 PDT)
- RE: AMBER: thermodynamic integration with Amber9 Ross Walker (Thu Oct 02 2008 - 08:24:01 PDT)
- RE: AMBER: thermodynamic integration with Amber9 Sadhna Rana (Thu Oct 02 2008 - 09:08:27 PDT)
  - RE: AMBER: thermodynamic integration with Amber9 Ross Walker (Thu Oct 02 2008 - 10:10:57 PDT)
AMBER: Oct 6 deadline for ACS computational chemistry awards Carlos Simmerling (Thu Oct 02 2008 - 10:45:35 PDT)
AMBER: Support for intel mpi in pmemd 10; better support for intel MKL Robert Duke (Thu Oct 02 2008 - 13:56:07 PDT)
- Re: AMBER: Support for intel mpi in pmemd 10; better support for intel MKL Francesco Pietra (Thu Oct 02 2008 - 14:35:45 PDT)
- Re: AMBER: Support for intel mpi in pmemd 10; better support for intel MKL Robert Duke (Thu Oct 02 2008 - 15:39:28 PDT)
- Re: AMBER: Support for intel mpi in pmemd 10; better support for intel MKL Robert Duke (Fri Oct 03 2008 - 08:43:22 PDT)
AMBER: shake the molecule amit jain (Thu Oct 02 2008 - 22:26:33 PDT)
- Re: AMBER: shake the molecule David A. Case (Fri Oct 03 2008 - 09:28:32 PDT)
AMBER: amber10 on SiCortex hardware Peter Varnai (Fri Oct 03 2008 - 09:27:21 PDT)
AMBER: ptraj average structure Yunierkis Perez Castillo (Sat Oct 04 2008 - 06:25:42 PDT)
- Re: AMBER: ptraj average structure Carlos Simmerling (Sat Oct 04 2008 - 06:55:31 PDT)
- RE: AMBER: ptraj average structure Ross Walker (Sat Oct 04 2008 - 07:55:51 PDT)
AMBER: Parameters for alkali cations and halogen anions Francesco Pietra (Sun Oct 05 2008 - 00:29:45 PDT)
AMBER: MM_PBSA problems in AMBER9 欧阳德方 (Sun Oct 05 2008 - 14:30:12 PDT)
- Re: AMBER: MM_PBSA problems in AMBER9 Ray Luo (Sun Oct 05 2008 - 20:20:01 PDT)
  - Re: AMBER: MM_PBSA problems in AMBER9 Alessandro Nascimento (Mon Oct 06 2008 - 06:04:37 PDT)
    - RE: AMBER: MM_PBSA problems in AMBER9 欧阳德方 (Mon Oct 06 2008 - 22:19:54 PDT)
AMBER: internal energy INT is not zero from MM_GBSA Fan Yanping (Mon Oct 06 2008 - 23:08:14 PDT)
AMBER: internal energy INT is not zero from MM_GBSA flyanping (Mon Oct 06 2008 - 23:18:49 PDT)
- Re: AMBER: internal energy INT is not zero from MM_GBSA sobereva (Tue Oct 07 2008 - 07:22:57 PDT)
AMBER: Amber heme parameters Shaikh Abdul R S Ramaju (Mon Oct 06 2008 - 23:31:34 PDT)
- Re: AMBER: Amber heme parameters sobereva (Tue Oct 07 2008 - 07:02:12 PDT)
  - RE: AMBER: Amber heme parameters Shaikh Abdul R S Ramaju (Tue Oct 07 2008 - 23:38:59 PDT)
AMBER: Zn2+ Bondi radius value Sergey Samsonov (Tue Oct 07 2008 - 01:50:10 PDT)
- Re: AMBER: Zn2+ Bondi radius value Enguerran Vanquelef (Wed Oct 08 2008 - 04:55:21 PDT)
AMBER: Once again, with feeling --- Support for intel mpi in pmemd 10; better support for intel MKL Robert Duke (Tue Oct 07 2008 - 10:02:51 PDT)
- Re: AMBER: Once again, with feeling --- Support for intel mpi in pmemd 10; better support for intel MKL David A. Case (Tue Oct 07 2008 - 14:05:07 PDT)
AMBER: Question on Urea box Antonios Samiotakis (Tue Oct 07 2008 - 12:31:44 PDT)
AMBER: saveamberparm error Shaikh Abdul R S Ramaju (Wed Oct 08 2008 - 04:33:31 PDT)
- RE: AMBER: saveamberparm error Ross Walker (Wed Oct 08 2008 - 08:23:12 PDT)
  - RE: AMBER: saveamberparm error Shaikh Abdul R S Ramaju (Wed Oct 08 2008 - 19:24:58 PDT)
    - Re: AMBER: saveamberparm error Wei Zhang (Thu Oct 09 2008 - 03:22:45 PDT)
    - RE: AMBER: saveamberparm error Shaikh Abdul R S Ramaju (Thu Oct 09 2008 - 03:53:35 PDT)
AMBER: AMBER force field for glycolipid Stephane Abel (Wed Oct 08 2008 - 05:25:12 PDT)
- RE: AMBER: AMBER force field for glycolipid Matthew Tessier (Thu Oct 09 2008 - 06:57:59 PDT)
  - Re: AMBER: AMBER force field for glycolipid Stephane Abel (Thu Oct 09 2008 - 07:08:49 PDT)
AMBER: ptraj - closest command Ryan Pavlovicz (Wed Oct 08 2008 - 10:36:17 PDT)
- Re: AMBER: ptraj - closest command Jianyin Shao (Wed Oct 08 2008 - 12:50:29 PDT)
  - Re: AMBER: ptraj - closest command Ryan Pavlovicz (Wed Oct 08 2008 - 13:49:08 PDT)
    - Re: AMBER: ptraj - closest command sobereva (Wed Oct 08 2008 - 19:49:46 PDT)
AMBER: Jmol 11.7.1 pre-release version reads AMBER trajectory/coordinate files Robert Hanson (Wed Oct 08 2008 - 11:16:55 PDT)
- Re: AMBER: Jmol 11.7.1 pre-release version reads AMBER trajectory/coordinate files FyD (Wed Oct 08 2008 - 12:00:33 PDT)
  - Re: AMBER: Jmol 11.7.1 pre-release version reads AMBER trajectory/coordinate files Robert Hanson (Wed Oct 08 2008 - 13:55:26 PDT)
    - Re: AMBER: Jmol 11.7.1 pre-release version reads AMBER trajectory/coordinate files Robert Hanson (Thu Oct 09 2008 - 09:30:32 PDT)
- Re: AMBER: Jmol 11.7.1 pre-release version reads AMBER trajectory/coordinate files Robert Hanson (Thu Oct 09 2008 - 06:59:20 PDT)
AMBER: velocity-verlet algorithm and ensembles oguz gurbulak (Wed Oct 08 2008 - 11:59:46 PDT)
- Re: AMBER: velocity-verlet algorithm and ensembles David A. Case (Thu Oct 09 2008 - 05:46:08 PDT)
Fwd: Re: AMBER: Jmol 11.7.1 pre-release version reads AMBER trajectory/coordinate files FyD (Thu Oct 09 2008 - 09:57:07 PDT)
- AMBER: changing pdb structure taufik.alsarraj.utoronto.ca (Thu Oct 09 2008 - 19:35:07 PDT)
  - Re: AMBER: changing pdb structure Robert Hanson (Thu Oct 09 2008 - 20:23:48 PDT)
  - RE: AMBER: changing pdb structure Ross Walker (Thu Oct 09 2008 - 20:29:24 PDT)
    - Re: AMBER: changing pdb structure Ibrahim Moustafa (Fri Oct 10 2008 - 07:24:30 PDT)
    - Re: AMBER: changing pdb structure Taufik Al-Sarraj (Mon Nov 10 2008 - 12:31:39 PST)
    - Re: AMBER: changing pdb structure Carlos Simmerling (Mon Nov 10 2008 - 12:37:32 PST)
    - Re: AMBER: changing pdb structure Taufik Al-Sarraj (Mon Nov 10 2008 - 13:10:23 PST)
    - Re: AMBER: changing pdb structure Carlos Simmerling (Tue Nov 11 2008 - 03:35:42 PST)
    - Re: AMBER: changing pdb structure Taufik Al-Sarraj (Mon Nov 24 2008 - 15:37:24 PST)
  - Re: AMBER: changing pdb structure Sasha Buzko (Thu Oct 09 2008 - 20:48:43 PDT)
  - Re: AMBER: changing pdb structure Sally Pias (Sat Oct 11 2008 - 22:00:38 PDT)
    - Re: AMBER: changing pdb structure Taufik Al-Sarraj (Tue Oct 14 2008 - 13:26:33 PDT)
Re: [Jmol-users] AMBER: Jmol 11.7.1 pre-release version reads AMBER trajectory/coordinate files Robert Hanson (Thu Oct 09 2008 - 16:12:52 PDT)
AMBER: nscm code Naser Alijabbari (Thu Oct 09 2008 - 22:05:59 PDT)
- Re: AMBER: nscm code Carlos Simmerling (Fri Oct 10 2008 - 03:32:25 PDT)
  - Re: AMBER: nscm code Andreas Svrcek-Seiler (Fri Oct 10 2008 - 04:37:09 PDT)
AMBER: Question about resp charges for a charged molecule... Alberto Sergio Garay (Fri Oct 10 2008 - 03:54:22 PDT)
- Re: AMBER: Question about resp charges for a charged molecule... Germain Vallverdu (Fri Oct 10 2008 - 04:20:45 PDT)
- Re: AMBER: Question about resp charges for a charged molecule... FyD (Fri Oct 10 2008 - 06:37:48 PDT)
AMBER: AddIons approach parul sharma (Fri Oct 10 2008 - 04:13:51 PDT)
- Re: AMBER: AddIons approach Carlos Simmerling (Fri Oct 10 2008 - 04:17:08 PDT)
  - Re: AMBER: AddIons approach Germain Vallverdu (Fri Oct 10 2008 - 04:23:00 PDT)
  - Re: AMBER: AddIons approach parul sharma (Fri Oct 10 2008 - 04:44:41 PDT)
    - Re: AMBER: AddIons approach David A. Case (Fri Oct 10 2008 - 04:52:52 PDT)
AMBER: Radius of Gyration Beale, John (Fri Oct 10 2008 - 04:27:22 PDT)
- Re: AMBER: Radius of Gyration Carlos Simmerling (Fri Oct 10 2008 - 04:48:21 PDT)
AMBER: Ring flips Beale, John (Fri Oct 10 2008 - 10:09:52 PDT)
- Re: AMBER: Ring flips David Watson (Fri Oct 10 2008 - 10:30:37 PDT)
- Re: AMBER: Ring flips David Watson (Fri Oct 10 2008 - 10:36:36 PDT)
AMBER: antechamber dipti lele (Sat Oct 11 2008 - 21:43:33 PDT)
- Re: AMBER: antechamber David A. Case (Mon Oct 13 2008 - 15:43:00 PDT)
AMBER: removing COM and rotation in explicit solvation Naser Alijabbari (Sun Oct 12 2008 - 13:02:22 PDT)
- Re: AMBER: removing COM and rotation in explicit solvation David A. Case (Sun Oct 12 2008 - 14:32:54 PDT)
AMBER: pairwise interaction energies Thomas Leonard (Sun Oct 12 2008 - 23:12:11 PDT)
- Re: AMBER: pairwise interaction energies Alessandro Nascimento (Mon Oct 13 2008 - 03:35:39 PDT)
AMBER: PDB standards Francesco Pietra (Mon Oct 13 2008 - 01:18:23 PDT)
AMBER: Ptraj pucker for pyranose Neha Gandhi (Mon Oct 13 2008 - 02:43:33 PDT)
AMBER: question about pression Yunierkis Perez Castillo (Mon Oct 13 2008 - 07:45:38 PDT)
- Re: AMBER: question about pression David A. Case (Mon Oct 13 2008 - 07:55:57 PDT)
  - RE: AMBER: question about pression Yunierkis Perez Castillo (Mon Oct 13 2008 - 08:33:45 PDT)
AMBER: LEU as first residue Francesco Pietra (Mon Oct 13 2008 - 09:20:00 PDT)
AMBER: amber: parameters for 5' nucleotide monophosphates Jeff Schwinefus (Mon Oct 13 2008 - 10:52:55 PDT)
- Re: AMBER: amber: parameters for 5' nucleotide monophosphates FyD (Mon Oct 13 2008 - 12:44:47 PDT)
AMBER: High Bfactor values for the terminal residues/atoms Siddharth Rastogi (Mon Oct 13 2008 - 21:19:52 PDT)
- AMBER: Segmentation fault hklwatergod (Mon Oct 13 2008 - 23:52:36 PDT)
  - RE: AMBER: Segmentation fault Ross Walker (Tue Oct 14 2008 - 07:53:08 PDT)
- Re: AMBER: High Bfactor values for the terminal residues/atoms Carlos Simmerling (Tue Oct 14 2008 - 03:25:25 PDT)
AMBER: large number of solvent molecules were added for protein with 221 AA residues Siddharth Rastogi (Mon Oct 13 2008 - 21:34:58 PDT)
- Re: AMBER: large number of solvent molecules were added for protein with 221 AA residues Carlos Simmerling (Tue Oct 14 2008 - 03:21:46 PDT)
AMBER: antechamber test failure john smith (Mon Oct 13 2008 - 22:47:28 PDT)
- RE: AMBER: antechamber test failure Meg McCarrick (Tue Nov 18 2003 - 09:06:12 PST)
  - Re: AMBER: antechamber test failure David A. Case (Tue Nov 18 2003 - 14:22:16 PST)
- Re: AMBER: antechamber test failure David A. Case (Wed Oct 15 2008 - 06:16:06 PDT)
  - Re: AMBER: antechamber test failure john smith (Wed Oct 15 2008 - 22:53:50 PDT)
    - Re: AMBER: antechamber test failure David A. Case (Thu Oct 16 2008 - 04:04:13 PDT)
AMBER: LEaP problem with LEU first residue? Francesco Pietra (Tue Oct 14 2008 - 03:26:25 PDT)
- Re: AMBER: LEaP problem with LEU first residue? Carlos Simmerling (Tue Oct 14 2008 - 03:41:01 PDT)
  - Re: AMBER: LEaP problem with LEU first residue? Francesco Pietra (Tue Oct 14 2008 - 06:42:55 PDT)
    - Fwd: AMBER: LEaP problem with LEU first residue? Francesco Pietra (Tue Oct 14 2008 - 10:58:33 PDT)
    - Re: Fwd: AMBER: LEaP problem with LEU first residue? Scott Brozell (Tue Oct 14 2008 - 14:46:36 PDT)
    - Re: Fwd: AMBER: LEaP problem with LEU first residue? Francesco Pietra (Tue Oct 14 2008 - 15:58:08 PDT)
- Re: AMBER: LEaP problem with LEU first residue? David A. Case (Wed Oct 15 2008 - 06:18:58 PDT)
- Re: AMBER: LEaP problem with LEU first residue? KazuoOhta (Sun Oct 19 2008 - 20:04:38 PDT)
  - Re: AMBER: LEaP problem with LEU first residue? David A. Case (Mon Oct 20 2008 - 04:00:09 PDT)
AMBER: amber10 installation problem in cygwin vijayaraj.clri.res.in (Tue Oct 14 2008 - 08:21:19 PDT)
- Re: AMBER: amber10 installation problem in cygwin Gustavo Seabra (Tue Oct 14 2008 - 08:56:20 PDT)
- RE: AMBER: amber10 installation problem in cygwin Ross Walker (Tue Oct 14 2008 - 09:32:06 PDT)
AMBER: Amber dipole printout. Zhao, Zhen (zhaozh) (Tue Oct 14 2008 - 10:25:40 PDT)
- Re: AMBER: Amber dipole printout. Dave Rogers (Tue Oct 14 2008 - 11:14:21 PDT)
- RE: AMBER: Amber dipole printout. Ross Walker (Tue Oct 14 2008 - 13:05:38 PDT)
AMBER: Installation Error Jagan Mohan (Wed Oct 15 2008 - 00:50:18 PDT)
- Re: AMBER: Installation Error Scott Brozell (Wed Oct 15 2008 - 01:05:48 PDT)
  - Re: AMBER: Installation Error Jagan Mohan (Wed Oct 15 2008 - 01:51:03 PDT)
    - Re: AMBER: Installation Error Gustavo Seabra (Wed Oct 15 2008 - 06:21:14 PDT)
    - Re: AMBER: Installation Error Jagan Mohan (Wed Oct 15 2008 - 07:03:04 PDT)
    - Re: AMBER: Installation Error David A. Case (Wed Oct 15 2008 - 06:35:19 PDT)
- Re: Re: AMBER: Installation Error Ye Mei (Wed Oct 15 2008 - 01:54:57 PDT)
AMBER: Amber10: Problem with tgtmd and ncsu testing Dmitri Nilov (Wed Oct 15 2008 - 06:00:11 PDT)
AMBER: Origin of periodic box Naser Alijabbari (Wed Oct 15 2008 - 18:34:00 PDT)
- RE: AMBER: Origin of periodic box Ross Walker (Wed Oct 15 2008 - 18:57:47 PDT)
- Re: AMBER: Origin of periodic box Gustavo Seabra (Thu Oct 16 2008 - 06:24:50 PDT)
AMBER: Differentiating the force constant of distance restraints Francesca Poletti (Thu Oct 16 2008 - 01:40:16 PDT)
- Re: AMBER: Differentiating the force constant of distance restraints Germain Vallverdu (Thu Oct 16 2008 - 02:07:07 PDT)
AMBER: regarding rigid molecules aneesh cna (Thu Oct 16 2008 - 02:34:36 PDT)
- Re: AMBER: regarding rigid molecules Germain Vallverdu (Thu Oct 16 2008 - 04:02:49 PDT)
- Re: AMBER: regarding rigid molecules David A. Case (Thu Oct 16 2008 - 04:06:42 PDT)
  - Re: AMBER: regarding rigid molecules Steven Winfield (Thu Oct 16 2008 - 04:30:31 PDT)
- Re: AMBER: regarding rigid molecules Gustavo Seabra (Thu Oct 16 2008 - 06:34:56 PDT)
  - RE: AMBER: regarding rigid molecules Ross Walker (Thu Oct 16 2008 - 07:53:29 PDT)
    - Re: AMBER: regarding rigid molecules Gustavo Seabra (Thu Oct 16 2008 - 08:16:39 PDT)
AMBER: Clarification re qmmask Benjamin Roberts (Thu Oct 16 2008 - 10:24:45 PDT)
- RE: AMBER: Clarification re qmmask Ross Walker (Thu Oct 16 2008 - 11:14:04 PDT)
- Re: AMBER: Clarification re qmmask Gustavo Seabra (Thu Oct 16 2008 - 11:22:41 PDT)
AMBER: antechamber Marcela Madrid (Thu Oct 16 2008 - 13:37:07 PDT)
- Re: AMBER: antechamber Amber admin (Wed May 05 2004 - 13:51:22 PDT)
  - Re: AMBER: antechamber Scott Brozell (Wed May 05 2004 - 14:30:17 PDT)
- Re: AMBER: antechamber Bill Ross (Fri Jul 16 2004 - 10:48:07 PDT)
- Re: AMBER: antechamber David A. Case (Thu Oct 16 2008 - 14:25:17 PDT)
  - Re: AMBER: antechamber Marcela Madrid (Tue Oct 21 2008 - 10:02:54 PDT)
    - AMBER: HOLD fixed vs restraint mask Taufik Al-Sarraj (Tue Oct 21 2008 - 11:02:34 PDT)
    - RE: AMBER: HOLD fixed vs restraint mask Ross Walker (Tue Oct 21 2008 - 11:33:32 PDT)
AMBER: Using charmm force field in amber Harry (Yicun) Ni (Thu Oct 16 2008 - 14:20:45 PDT)
- RE: AMBER: Using charmm force field in amber Ross Walker (Thu Oct 16 2008 - 14:44:30 PDT)
- Re: AMBER: Using charmm force field in amber David A. Case (Thu Oct 16 2008 - 14:51:45 PDT)
AMBER: capping with non charged residues Francesco Pietra (Thu Oct 16 2008 - 15:24:44 PDT)
AMBER: antechamber errors oguz gurbulak (Fri Oct 17 2008 - 06:07:37 PDT)
- Re: AMBER: antechamber errors David A. Case (Fri Oct 17 2008 - 07:20:51 PDT)
AMBER: Restricting the system to simulate Francesco Pietra (Fri Oct 17 2008 - 09:00:50 PDT)
- Fwd: AMBER: Restricting the system to simulate Francesco Pietra (Sat Oct 18 2008 - 00:44:19 PDT)
AMBER: NAD+ parameters problem using tleap Dmitri Nilov (Fri Oct 17 2008 - 09:24:50 PDT)
- RE: AMBER: NAD+ parameters problem using tleap Ross Walker (Fri Oct 17 2008 - 11:16:41 PDT)
AMBER: using ptraj Adrien Delmont (Fri Oct 17 2008 - 14:44:16 PDT)
- AMBER: How to assign /make the ionion bond? Chih-Ying Lin (Fri Oct 17 2008 - 15:30:07 PDT)
  - Re: AMBER: How to assign /make the ionion bond? steinbrt.rci.rutgers.edu (Fri Oct 17 2008 - 16:06:26 PDT)
- Re: AMBER: using ptraj Gustavo Seabra (Fri Oct 17 2008 - 18:35:23 PDT)
AMBER: REDvIII_I_lack_of_charges_in_mol2 Karol Kaszuba (Sat Oct 18 2008 - 04:08:53 PDT)
- Re: AMBER: REDvIII_I_lack_of_charges_in_mol2 FyD (Sat Oct 18 2008 - 04:54:56 PDT)
  - Re: AMBER: REDvIII_I_lack_of_charges_in_mol2 Karol Kaszuba (Sat Oct 18 2008 - 09:32:58 PDT)
    - Re: AMBER: REDvIII_I_lack_of_charges_in_mol2 FyD (Sat Oct 18 2008 - 14:30:33 PDT)
    - Re: AMBER: REDvIII_I_lack_of_charges_in_mol2 Karol Kaszuba (Sat Oct 18 2008 - 23:57:23 PDT)
    - Re: AMBER: REDvIII_I_lack_of_charges_in_mol2 FyD (Sun Oct 19 2008 - 01:12:03 PDT)
    - Re: AMBER: REDvIII_I_lack_of_charges_in_mol2 Karol Kaszuba (Sun Oct 19 2008 - 06:00:35 PDT)
- Re: AMBER: REDvIII_I_lack_of_charges_in_mol2 FyD (Wed Oct 22 2008 - 08:15:15 PDT)
AMBER: Addions in GB Mode? Rogelio Hernández (Sun Oct 19 2008 - 10:04:32 PDT)
- Re: AMBER: Addions in GB Mode? parul sharma (Mon Oct 20 2008 - 02:25:22 PDT)
  - Re: AMBER: Addions in GB Mode? Carlos Simmerling (Mon Oct 20 2008 - 03:12:52 PDT)
    - AMBER: input Urszula Uciechowska (Tue Oct 21 2008 - 02:14:28 PDT)
    - Re: AMBER: input Germain Vallverdu (Tue Oct 21 2008 - 02:36:40 PDT)
    - AMBER: equilibration Urszula Uciechowska (Tue Oct 21 2008 - 03:44:54 PDT)
    - Re: AMBER: equilibration Carlos Simmerling (Tue Oct 21 2008 - 04:01:54 PDT)
    - Re: AMBER: equilibration Urszula Uciechowska (Tue Oct 21 2008 - 04:17:08 PDT)
    - Re: AMBER: equilibration Carlos Simmerling (Tue Oct 21 2008 - 04:20:13 PDT)
    - Re: AMBER: equilibration Urszula Uciechowska (Tue Oct 21 2008 - 04:28:17 PDT)
    - Re: AMBER: equilibration Carlos Simmerling (Tue Oct 21 2008 - 04:30:12 PDT)
AMBER: question about simulation box Adrien Delmont (Sun Oct 19 2008 - 14:04:24 PDT)
- Re: AMBER: question about simulation box Gustavo Seabra (Mon Oct 20 2008 - 06:09:03 PDT)
- Re: AMBER: question about simulation box Adrien Delmont (Tue Oct 21 2008 - 06:43:24 PDT)
AMBER: Error in creating topology file musa özboyacı (Mon Oct 20 2008 - 04:00:48 PDT)
- Re: AMBER: Error in creating topology file Wei Zhang (Mon Oct 20 2008 - 05:34:40 PDT)
AMBER: Contacts Beale, John (Mon Oct 20 2008 - 07:29:06 PDT)
AMBER: about SASA and AMBER Yunierkis Perez Castillo (Mon Oct 20 2008 - 08:58:06 PDT)
- Re: AMBER: about SASA and AMBER Lachele Foley (Lists) (Mon Oct 20 2008 - 10:07:06 PDT)
  - Re: AMBER: about SASA and AMBER Carlos Simmerling (Mon Oct 20 2008 - 10:17:42 PDT)
AMBER: mm_pbsa_statistics / 3 traj Arturas Ziemys (Mon Oct 20 2008 - 09:18:26 PDT)
AMBER: drug/protein interaction modeling setup Sean Johnston (Mon Oct 20 2008 - 13:10:52 PDT)
- Re: AMBER: drug/protein interaction modeling setup Alessandro Nascimento (Mon Oct 20 2008 - 13:21:05 PDT)
- Re: AMBER: drug/protein interaction modeling setup Barbault Florent (Mon Oct 20 2008 - 13:37:24 PDT)
- Re: AMBER: drug/protein interaction modeling setup Bill Ross (Mon Oct 20 2008 - 15:39:04 PDT)
  - Re: AMBER: drug/protein interaction modeling setup Sean Johnston (Fri Oct 31 2008 - 12:31:56 PDT)
AMBER: cnstph test case failure or expected divergence? Melinda Layten (Mon Oct 20 2008 - 13:23:08 PDT)
- RE: AMBER: cnstph test case failure or expected divergence? Ross Walker (Mon Oct 20 2008 - 13:41:27 PDT)
  - Re: AMBER: cnstph test case failure or expected divergence? Melinda Layten (Tue Oct 21 2008 - 08:38:31 PDT)
AMBER: scyld beowulf --amber10--openmpi Rima Chaudhuri (Mon Oct 20 2008 - 17:00:27 PDT)
- RE: AMBER: scyld beowulf --amber10--openmpi Ross Walker (Mon Oct 20 2008 - 18:38:04 PDT)
  - Re: AMBER: scyld beowulf --amber10--openmpi Rima Chaudhuri (Mon Oct 20 2008 - 18:46:13 PDT)
    - Re: AMBER: scyld beowulf --amber10--openmpi Gustavo Seabra (Mon Oct 20 2008 - 19:56:35 PDT)
AMBER: Heme cysteine Shaikh Abdul R S Ramaju (Tue Oct 21 2008 - 00:16:50 PDT)
- RE: AMBER: Heme cysteine Ross Walker (Tue Oct 21 2008 - 08:17:08 PDT)
  - RE: AMBER: Heme cysteine Shaikh Abdul R S Ramaju (Tue Oct 21 2008 - 19:46:09 PDT)
AMBER: ptraj John Bennett (Tue Oct 21 2008 - 07:32:07 PDT)
AMBER: Does LEaP understant capping with ACE/NME? Francesco Pietra (Tue Oct 21 2008 - 08:57:12 PDT)
- Re: AMBER: Does LEaP understant capping with ACE/NME? Carlos Simmerling (Tue Oct 21 2008 - 09:02:41 PDT)
  - Re: AMBER: Does LEaP understant capping with ACE/NME? Francesco Pietra (Tue Oct 21 2008 - 10:31:36 PDT)
Re: AMBER: Heme cysteine Bill Ross (Tue Oct 21 2008 - 09:20:38 PDT)
AMBER: Again: Installation problem of AMBER on cluster Dmitri Nilov (Tue Oct 21 2008 - 09:31:52 PDT)
- RE: AMBER: Again: Installation problem of AMBER on cluster Ross Walker (Tue Oct 21 2008 - 09:49:50 PDT)
  - Re: AMBER: Again: Installation problem of AMBER on cluster Dmitri Nilov (Sat Oct 25 2008 - 05:30:43 PDT)
AMBER: MM_PBSA doesn't terminate Khaled Barakat (Tue Oct 21 2008 - 09:58:12 PDT)
AMBER: DNA structure analysis Bert (Wed Oct 22 2008 - 04:27:38 PDT)
AMBER: MM_PBSA doesn't terminate Khaled Barakat (Wed Oct 22 2008 - 08:27:55 PDT)
AMBER: stripping water from a restart file CHAMI F. (Wed Oct 22 2008 - 09:11:46 PDT)
- Re: AMBER: stripping water from a restart file Carlos Simmerling (Wed Oct 22 2008 - 09:29:32 PDT)
- RE: AMBER: stripping water from a restart file Bill Ross (Wed Oct 22 2008 - 13:38:11 PDT)
  - RE: AMBER: stripping water from a restart file CHAMI F. (Thu Oct 23 2008 - 04:33:29 PDT)
    - Re: AMBER: stripping water from a restart file Carlos Simmerling (Thu Oct 23 2008 - 05:22:00 PDT)
- RE: AMBER: stripping water from a restart file CHAMI F. (Thu Oct 23 2008 - 05:45:19 PDT)
- RE: AMBER: stripping water from a restart file Bill Ross (Thu Oct 23 2008 - 11:13:43 PDT)
  - RE: AMBER: stripping water from a restart file CHAMI F. (Thu Oct 23 2008 - 14:59:03 PDT)
    - Re: AMBER: stripping water from a restart file Carlos Simmerling (Thu Oct 23 2008 - 15:05:07 PDT)
- RE: AMBER: stripping water from a restart file Bill Ross (Thu Oct 23 2008 - 16:48:59 PDT)
  - RE: AMBER: stripping water from a restart file CHAMI F. (Fri Oct 24 2008 - 02:58:58 PDT)
    - Re: AMBER: stripping water from a restart file Gustavo Seabra (Mon Oct 27 2008 - 10:12:04 PDT)
- RE: AMBER: stripping water from a restart file Bill Ross (Fri Oct 24 2008 - 08:21:59 PDT)
Re: AMBER: stripping water from a restart file Bill Ross (Wed Oct 22 2008 - 10:12:29 PDT)
- RE: AMBER: stripping water from a restart file CHAMI F. (Wed Oct 22 2008 - 13:29:45 PDT)
AMBER: installing amber on new linux Jan Goeman (Wed Oct 22 2008 - 14:06:48 PDT)
- Re: AMBER: installing amber on new linux Scott Brozell (Wed Oct 22 2008 - 16:53:50 PDT)
- Re: AMBER: installing amber on new linux Jan Goeman (Sun Oct 26 2008 - 17:25:49 PDT)
AMBER: MM-PBSA -energy decomposition error Cristina Sisu (Wed Oct 22 2008 - 15:07:43 PDT)
AMBER: energy leakage? Sally Pias (Thu Oct 23 2008 - 00:25:59 PDT)
- Re: AMBER: energy leakage? David A. Case (Thu Oct 23 2008 - 04:00:29 PDT)
  - Re: AMBER: energy leakage? Sally Pias (Thu Oct 23 2008 - 07:47:28 PDT)
AMBER: Metal parameter values musa özboyacı (Thu Oct 23 2008 - 04:59:13 PDT)
AMBER: Non bond list error Wang,Ying (Thu Oct 23 2008 - 10:19:49 PDT)
- RE: AMBER: Non bond list error Ross Walker (Thu Oct 23 2008 - 11:38:09 PDT)
- RE: AMBER: Non bond list error Wang,Ying (Thu Oct 23 2008 - 12:26:26 PDT)
  - AMBER: pdb structure is only half the molecule. Taufik Al-Sarraj (Thu Oct 23 2008 - 12:42:24 PDT)
    - RE: AMBER: pdb structure is only half the molecule. Joel Tyndall (Thu Oct 23 2008 - 13:18:36 PDT)
    - Re: AMBER: pdb structure is only half the molecule. Taufik Al-Sarraj (Fri Oct 24 2008 - 16:15:52 PDT)
    - Re: AMBER: pdb structure is only half the molecule. Gustavo Seabra (Thu Oct 23 2008 - 13:19:05 PDT)
    - Re: AMBER: pdb structure is only half the molecule. Ye Mei (Thu Oct 23 2008 - 20:21:59 PDT)
    - Re: AMBER: pdb structure is only half the molecule. Florian Haberl (Fri Oct 24 2008 - 03:18:45 PDT)
  - Re: AMBER: Non bond list error Robert Duke (Thu Oct 23 2008 - 13:14:13 PDT)
- Re: AMBER: Non bond list error Robert Duke (Thu Oct 23 2008 - 13:44:29 PDT)
  - Re: AMBER: Non bond list error neville forlemu (Thu Oct 23 2008 - 21:48:01 PDT)
    - RE: AMBER: Non bond list error Ross Walker (Thu Oct 23 2008 - 21:56:32 PDT)
    - RE: AMBER: Non bond list error neville forlemu (Thu Oct 23 2008 - 22:13:13 PDT)
    - RE: AMBER: Non bond list error Ross Walker (Thu Oct 23 2008 - 23:12:20 PDT)
    - RE: AMBER: Non bond list error neville forlemu (Fri Oct 24 2008 - 09:34:44 PDT)
    - Re: AMBER: Non bond list error Robert Duke (Fri Oct 24 2008 - 09:40:24 PDT)
    - Re: AMBER: Non bond list error neville forlemu (Fri Oct 24 2008 - 11:12:58 PDT)
    - Re: AMBER: Non bond list error Robert Duke (Fri Oct 24 2008 - 11:47:33 PDT)
    - Re: AMBER: Non bond list error Robert Duke (Fri Oct 24 2008 - 12:04:53 PDT)
    - Re: AMBER: Non bond list error neville forlemu (Fri Oct 24 2008 - 12:40:08 PDT)
- Re: AMBER: Non bond list error Wang,Ying (Thu Oct 23 2008 - 14:58:06 PDT)
- Fw: AMBER: Non bond list error Robert Duke (Fri Oct 24 2008 - 06:20:29 PDT)
Re: AMBER: Metal parameter values Bill Ross (Thu Oct 23 2008 - 11:23:08 PDT)
- Re: AMBER: Metal parameter values musa özboyacı (Thu Oct 23 2008 - 12:09:35 PDT)
AMBER: problem with running mm-pbsa moitrayee.mbu.iisc.ernet.in (Fri Oct 24 2008 - 00:14:49 PDT)
- Re: AMBER: problem with running mm-pbsa Ray Luo (Fri Oct 24 2008 - 09:24:59 PDT)
  - Re: AMBER: problem with running mm-pbsa moitrayee.mbu.iisc.ernet.in (Fri Oct 24 2008 - 23:30:11 PDT)
AMBER: something puzzled with mm_pbsa TaoPaul (Fri Oct 24 2008 - 03:50:04 PDT)
- Re: AMBER: something puzzled with mm_pbsa Ray Luo (Fri Oct 24 2008 - 09:21:59 PDT)
  - RE: AMBER: something puzzled with mm_pbsa TaoPaul (Fri Oct 24 2008 - 19:08:50 PDT)
    - RE: AMBER: something puzzled with mm_pbsa Ray Luo (Mon Oct 27 2008 - 09:56:54 PDT)
AMBER: problem with amber8 installation moitrayee.mbu.iisc.ernet.in (Fri Oct 24 2008 - 05:20:17 PDT)
AMBER: problem with amber8 installation moitrayee.mbu.iisc.ernet.in (Fri Oct 24 2008 - 05:22:40 PDT)
- RE: AMBER: problem with amber8 installation Ross Walker (Fri Oct 24 2008 - 07:57:52 PDT)
  - RE: AMBER: problem with amber8 installation moitrayee.mbu.iisc.ernet.in (Fri Oct 24 2008 - 23:36:27 PDT)
    - Re: AMBER: problem with amber8 installation David A. Case (Sat Oct 25 2008 - 06:30:30 PDT)
AMBER: Regarding sleap - documentation and output behavior Keith Van Nostrand (Fri Oct 24 2008 - 08:26:58 PDT)
AMBER: Atom names CL and four characters Francesco Pietra (Fri Oct 24 2008 - 11:55:05 PDT)
- Re: AMBER: Atom names CL and four characters David A. Case (Fri Oct 24 2008 - 12:21:51 PDT)
  - Re: AMBER: Atom names CL and four characters Francesco Pietra (Fri Oct 24 2008 - 15:44:31 PDT)
AMBER: Restraining with PMEMD 10 Francesco Pietra (Sat Oct 25 2008 - 02:32:39 PDT)
- Re: AMBER: Restraining with PMEMD 10 Robert Duke (Sat Oct 25 2008 - 05:57:03 PDT)
  - Re: AMBER: Restraining with PMEMD 10 Francesco Pietra (Sat Oct 25 2008 - 09:33:57 PDT)
    - RE: AMBER: Restraining with PMEMD 10 Ross Walker (Sat Oct 25 2008 - 10:25:08 PDT)
    - Re: AMBER: Restraining with PMEMD 10 Francesco Pietra (Sat Oct 25 2008 - 11:57:40 PDT)
- Re: AMBER: Restraining with PMEMD 10 Robert Duke (Sat Oct 25 2008 - 10:12:20 PDT)
AMBER: the question about "RADIOPT" option in mm_pbsa TaoPaul (Sat Oct 25 2008 - 04:11:04 PDT)
AMBER: Is it possible to recover the umbrella file in ABMD simulation after hard disk failure? Ye Mei (Sat Oct 25 2008 - 05:32:25 PDT)
AMBER: Conversion between truncated octahedron and orthorohombic box #NGUYEN CONG TRI# (Sat Oct 25 2008 - 19:36:30 PDT)
- RE: AMBER: Conversion between truncated octahedron and orthorohombic box Ross Walker (Sun Oct 26 2008 - 09:56:50 PDT)
- Re: AMBER: Conversion between truncated octahedron and orthorohombic box Gustavo Seabra (Mon Oct 27 2008 - 10:19:59 PDT)
AMBER: Duplicate entries with different parameters in gaff.dat from AmberTools 1.2 John Chodera (Sun Oct 26 2008 - 18:16:48 PDT)
AMBER: atom type for carbon and nitrogen atoms Catein Catherine (Mon Oct 27 2008 - 01:56:06 PDT)
- Re: AMBER: atom type for carbon and nitrogen atoms Gustavo Seabra (Mon Oct 27 2008 - 10:28:31 PDT)
AMBER: atom type for carbon and nitrogen atoms Catein Catherine (Mon Oct 27 2008 - 01:58:51 PDT)
AMBER: peptide MD Beale, John (Mon Oct 27 2008 - 08:38:48 PDT)
- Re: AMBER: peptide MD Carlos Simmerling (Mon Oct 27 2008 - 10:05:00 PDT)
  - RE: AMBER: peptide MD Beale, John (Mon Oct 27 2008 - 10:13:47 PDT)
    - Re: AMBER: peptide MD Carlos Simmerling (Mon Oct 27 2008 - 10:35:57 PDT)
    - Re: AMBER: peptide MD Gustavo Seabra (Mon Oct 27 2008 - 10:36:35 PDT)
    - RE: AMBER: peptide MD Beale, John (Mon Oct 27 2008 - 10:47:42 PDT)
    - Re: AMBER: peptide MD Gustavo Seabra (Mon Oct 27 2008 - 10:52:25 PDT)
    - Re: AMBER: peptide MD Carlos Simmerling (Mon Oct 27 2008 - 11:07:11 PDT)
AMBER: 2'-5'-branched RNA Volodymyr Zloy (Mon Oct 27 2008 - 09:10:00 PDT)
AMBER: Identification of improper torsions in small molecules parameterized with GAFF by antechamber John Chodera (Mon Oct 27 2008 - 15:12:31 PDT)
- Re: AMBER: Identification of improper torsions in small molecules parameterized with GAFF by antechamber David A. Case (Tue Oct 28 2008 - 05:57:22 PDT)
  - Re: AMBER: Identification of improper torsions in small molecules parameterized with GAFF by antechamber John Chodera (Tue Oct 28 2008 - 08:57:42 PDT)
    - Re: AMBER: Identification of improper torsions in small molecules parameterized with GAFF by antechamber David A. Case (Tue Oct 28 2008 - 15:15:11 PDT)
AMBER: aromatic bent ligand Arturas Ziemys (Mon Oct 27 2008 - 19:34:49 PDT)
AMBER: SPCFW problems Naser Alijabbari (Mon Oct 27 2008 - 19:37:12 PDT)
- Re: AMBER: SPCFW problems David A. Case (Tue Oct 28 2008 - 03:49:37 PDT)
  - Re: AMBER: SPCFW problems Naser Alijabbari (Tue Oct 28 2008 - 08:50:49 PDT)
    - Re: AMBER: SPCFW problems David A. Case (Tue Oct 28 2008 - 10:25:23 PDT)
    - Re: AMBER: SPCFW problems Naser Alijabbari (Tue Oct 28 2008 - 10:57:59 PDT)
    - Re: AMBER: SPCFW problems David A. Case (Tue Oct 28 2008 - 15:12:02 PDT)
AMBER: antechamber bug? produces incorrect NEWPDB.PDB file Robert Hanson (Tue Oct 28 2008 - 09:46:08 PDT)
- Re: AMBER: antechamber bug? produces incorrect NEWPDB.PDB file David A. Case (Tue Oct 28 2008 - 10:41:45 PDT)
  - Re: AMBER: antechamber bug? produces incorrect NEWPDB.PDB file David A. Case (Tue Oct 28 2008 - 10:57:49 PDT)
    - Re: AMBER: antechamber bug? produces incorrect NEWPDB.PDB file Robert Hanson (Tue Oct 28 2008 - 11:21:59 PDT)
    - Re: AMBER: antechamber bug? produces incorrect NEWPDB.PDB file David A. Case (Tue Oct 28 2008 - 15:09:38 PDT)
    - Re: AMBER: antechamber bug? produces incorrect NEWPDB.PDB file Robert Hanson (Tue Oct 28 2008 - 15:42:19 PDT)
    - Re: AMBER: antechamber bug? produces incorrect NEWPDB.PDB file David A. Case (Wed Oct 29 2008 - 03:49:06 PDT)
    - Re: AMBER: antechamber bug? produces incorrect NEWPDB.PDB file Robert Hanson (Wed Oct 29 2008 - 04:50:35 PDT)
    - Re: AMBER: antechamber bug? produces incorrect NEWPDB.PDB file FyD (Wed Oct 29 2008 - 00:19:41 PDT)
AMBER: Problem installing PMEMD with intel mpi, ifort Rupesh Nanjunda (Tue Oct 28 2008 - 14:07:01 PDT)
- RE: AMBER: Problem installing PMEMD with intel mpi, ifort Ross Walker (Tue Oct 28 2008 - 17:41:39 PDT)
- Re: AMBER: Problem installing PMEMD with intel mpi, ifort Robert Duke (Tue Oct 28 2008 - 18:12:17 PDT)
  - Re: AMBER: Problem installing PMEMD with intel mpi, ifort Rupesh Nanjunda (Wed Oct 29 2008 - 10:57:06 PDT)
  - Re: AMBER: Problem installing PMEMD with intel mpi, ifort Rupesh Nanjunda (Thu Oct 30 2008 - 08:07:56 PDT)
AMBER: ANAL Madhumalar Arumugam (Wed Oct 29 2008 - 01:44:57 PDT)
AMBER: problem with Dihedral angle potentials aneesh cna (Wed Oct 29 2008 - 02:23:57 PDT)
- Re: AMBER: problem with Dihedral angle potentials Carlos Simmerling (Wed Oct 29 2008 - 03:09:15 PDT)
  - Re: AMBER: problem with Dihedral angle potentials aneesh cna (Thu Oct 30 2008 - 02:11:48 PDT)
    - Re: AMBER: problem with Dihedral angle potentials Carlos Simmerling (Thu Oct 30 2008 - 03:20:59 PDT)
    - Re: AMBER: problem with Dihedral angle potentials aneesh cna (Thu Oct 30 2008 - 09:35:00 PDT)
    - Re: AMBER: problem with Dihedral angle potentials Carlos Simmerling (Thu Oct 30 2008 - 15:07:27 PDT)
AMBER: Huge difference between pbtot and gbtot in mm-pbsa calculations moitrayee.mbu.iisc.ernet.in (Wed Oct 29 2008 - 06:07:23 PDT)
- RE: AMBER: Huge difference between pbtot and gbtot in mm-pbsa calculations Ray Luo (Wed Oct 29 2008 - 09:41:38 PDT)
  - RE: AMBER: Huge difference between pbtot and gbtot in mm-pbsa calculations moitrayee.mbu.iisc.ernet.in (Wed Oct 29 2008 - 22:56:51 PDT)
    - Re: AMBER: Huge difference between pbtot and gbtot in mm-pbsa calculations David A. Case (Thu Oct 30 2008 - 04:24:12 PDT)
    - Re: AMBER: Huge difference between pbtot and gbtot in mm-pbsa calculations moitrayee.mbu.iisc.ernet.in (Thu Oct 30 2008 - 05:49:44 PDT)
    - Re: AMBER: Huge difference between pbtot and gbtot in mm-pbsa calculations David A. Case (Thu Oct 30 2008 - 06:17:12 PDT)
AMBER: Folate parameters Michael Lerner (Wed Oct 29 2008 - 10:03:06 PDT)
- Re: AMBER: Folate parameters Barbault Florent (Thu Oct 30 2008 - 07:03:09 PDT)
AMBER: Optimal compiling of amber on XT3 Patrick McCarren (Wed Oct 29 2008 - 21:30:56 PDT)
- Re: AMBER: Optimal compiling of amber on XT3 Robert Duke (Wed Oct 29 2008 - 22:31:49 PDT)
  - Re: AMBER: Optimal compiling of amber on XT3 Patrick McCarren (Sat Nov 01 2008 - 00:13:08 PDT)
- RE: AMBER: Optimal compiling of amber on XT3 Ross Walker (Wed Oct 29 2008 - 22:33:35 PDT)
- Re: AMBER: Optimal compiling of amber on XT3 Robert Duke (Wed Oct 29 2008 - 22:59:21 PDT)
  - Re: AMBER: Optimal compiling of amber on XT3 Carlos Simmerling (Thu Oct 30 2008 - 03:22:35 PDT)
AMBER: Packing density calculation Siddharth Rastogi (Thu Oct 30 2008 - 03:41:58 PDT)
AMBER: Lone pairs in antechamber Diddo Diddens (Thu Oct 30 2008 - 06:25:35 PDT)
- Re: AMBER: Lone pairs in antechamber David A. Case (Thu Oct 30 2008 - 07:27:31 PDT)
amber-developers: FW: AMBER: Duplicate entries with different parameters in gaff.dat from AmberTools 1.2 Ross Walker (Thu Oct 30 2008 - 10:41:27 PDT)
AMBER: minimization Jacopo Sgrignani (Thu Oct 30 2008 - 11:03:29 PDT)
- RE: AMBER: minimization Ross Walker (Thu Oct 30 2008 - 11:48:11 PDT)
AMBER: MM_PBSA binding error Larry Layne (Thu Oct 30 2008 - 11:54:24 PDT)
- RE: AMBER: MM_PBSA binding error Ray Luo (Thu Oct 30 2008 - 12:35:36 PDT)
  - RE: AMBER: MM_PBSA binding error Larry Layne (Fri Oct 31 2008 - 05:56:42 PDT)
    - Re: AMBER: MM_PBSA binding error Ray Luo (Fri Oct 31 2008 - 15:16:41 PDT)
    - Re: AMBER: MM_PBSA binding error Larry Layne (Tue Nov 04 2008 - 05:51:22 PST)
    - RE: AMBER: MM_PBSA binding error Ray Luo (Tue Nov 04 2008 - 11:18:54 PST)
AMBER: Setting GROUP for pmemd Francesco Pietra (Thu Oct 30 2008 - 12:10:39 PDT)
- Re: AMBER: Setting GROUP for pmemd Robert Duke (Thu Oct 30 2008 - 12:29:27 PDT)
  - Re: AMBER: Setting GROUP for pmemd Francesco Pietra (Thu Oct 30 2008 - 14:56:27 PDT)
  - Re: AMBER: Setting GROUP for pmemd Francesco Pietra (Fri Nov 28 2008 - 02:12:07 PST)
- Re: AMBER: Setting GROUP for pmemd Robert Duke (Thu Oct 30 2008 - 15:30:07 PDT)
  - Re: AMBER: Setting GROUP for pmemd Francesco Pietra (Thu Oct 30 2008 - 16:28:37 PDT)
- Re: AMBER: Setting GROUP for pmemd Robert Duke (Thu Oct 30 2008 - 19:02:05 PDT)
  - Re: AMBER: Setting GROUP for pmemd Francesco Pietra (Thu Oct 30 2008 - 23:25:44 PDT)
AMBER: Query on restart file Neha Gandhi (Thu Oct 30 2008 - 18:49:30 PDT)
- Re: AMBER: Query on restart file Carlos Simmerling (Thu Oct 30 2008 - 19:03:53 PDT)
- Re: AMBER: Query on restart file Robert Duke (Thu Oct 30 2008 - 19:14:40 PDT)
  - Re: AMBER: Query on restart file Neha Gandhi (Thu Oct 30 2008 - 19:22:49 PDT)
AMBER: error message of xleap Catein Catherine (Thu Oct 30 2008 - 20:40:49 PDT)
- RE: AMBER: error message of xleap Ross Walker (Thu Oct 30 2008 - 21:09:47 PDT)
  - RE: AMBER: error message of xleap Catein Catherine (Mon Nov 03 2008 - 01:52:24 PST)
    - RE: AMBER: error message of xleap Ross Walker (Mon Nov 03 2008 - 09:05:54 PST)
    - AMBER: temperature error in md calculation Catein Catherine (Wed Nov 05 2008 - 00:11:41 PST)
    - Re: AMBER: temperature error in md calculation David A. Case (Wed Nov 05 2008 - 06:10:41 PST)
AMBER: how to ger resp charge for a residue? WJ Ding (Thu Oct 30 2008 - 21:20:05 PDT)
- RE: AMBER: how to ger resp charge for a residue? Ross Walker (Thu Oct 30 2008 - 21:46:43 PDT)
- Re: AMBER: how to ger resp charge for a residue? FyD (Thu Oct 30 2008 - 23:33:42 PDT)
  - Re: AMBER: how to ger resp charge for a residue? Francesco Pietra (Fri Oct 31 2008 - 00:59:31 PDT)
    - Re: AMBER: how to ger resp charge for a residue? FyD (Fri Oct 31 2008 - 06:21:13 PDT)
    - Re: AMBER: how to ger resp charge for a residue? WJ Ding (Fri Oct 31 2008 - 07:26:48 PDT)
AMBER: problem with zMatrix in tleap WJ Ding (Thu Oct 30 2008 - 21:40:59 PDT)
- Re: AMBER: problem with zMatrix in tleap David A. Case (Fri Oct 31 2008 - 05:33:44 PDT)
  - Re: AMBER: problem with zMatrix in tleap WJ Ding (Fri Oct 31 2008 - 07:23:45 PDT)
    - Re: AMBER: problem with zMatrix in tleap David A. Case (Fri Oct 31 2008 - 07:37:11 PDT)
    - Re: AMBER: problem with zMatrix in tleap WJ Ding (Fri Oct 31 2008 - 08:48:27 PDT)
    - Re: AMBER: problem with zMatrix in tleap David A. Case (Sun Nov 09 2008 - 09:17:02 PST)
AMBER: minimization Jacopo Sgrignani (Fri Oct 31 2008 - 01:52:12 PDT)
- RE: AMBER: minimization Ross Walker (Fri Oct 31 2008 - 08:44:49 PDT)
AMBER: Question on AMBER MD Implications Campbell, Patrick (Fri Oct 31 2008 - 09:27:41 PDT)
- Re: AMBER: Question on AMBER MD Implications Carlos Simmerling (Fri Oct 31 2008 - 09:51:21 PDT)
AMBER: Trouble compiling Amber 9 leap programs on SGI Altix system John Finke (Fri Oct 31 2008 - 11:05:57 PDT)
- RE: AMBER: Trouble compiling Amber 9 leap programs on SGI Altix system Ross Walker (Fri Oct 31 2008 - 11:22:13 PDT)
AMBER: MM-PBSA error in Amber10: possible bug? Pablo Englebienne (Fri Oct 31 2008 - 20:38:15 PDT)
AMBER: Question on AMBER MD Implications Campbell, Patrick (Sat Nov 01 2008 - 03:01:17 PDT)
AMBER: Minimisation and heating under GB conditions Francesco Pietra (Mon Nov 03 2008 - 00:58:58 PST)
- Re: AMBER: Minimisation and heating under GB conditions Carlos Simmerling (Mon Nov 03 2008 - 03:29:25 PST)
  - Re: AMBER: Minimisation and heating under GB conditions David A. Case (Mon Nov 03 2008 - 06:01:59 PST)
    - Re: AMBER: Minimisation and heating under GB conditions Francesco Pietra (Mon Nov 03 2008 - 06:17:34 PST)
    - Re: AMBER: Minimisation and heating under GB conditions Francesco Pietra (Mon Nov 03 2008 - 10:07:14 PST)
    - Re: AMBER: Minimisation and heating under GB conditions Carlos Simmerling (Mon Nov 03 2008 - 10:52:23 PST)
    - Re: AMBER: Minimisation and heating under GB conditions Francesco Pietra (Mon Nov 03 2008 - 23:27:55 PST)
  - Re: AMBER: Minimisation and heating under GB conditions Francesco Pietra (Mon Nov 03 2008 - 06:08:42 PST)
    - Re: AMBER: Minimisation and heating under GB conditions Carlos Simmerling (Mon Nov 03 2008 - 06:45:22 PST)
AMBER: Problems compiling leap on Altix Cluster John Finke (Mon Nov 03 2008 - 12:51:54 PST)
- RE: AMBER: Problems compiling leap on Altix Cluster Ross Walker (Mon Nov 03 2008 - 13:47:06 PST)
  - Re: AMBER: Problems compiling leap on Altix Cluster John Finke (Mon Nov 03 2008 - 15:43:09 PST)
    - RE: AMBER: Problems compiling leap on Altix Cluster Ross Walker (Mon Nov 03 2008 - 16:06:07 PST)
AMBER: Prem Prakash Pathak (Mon Nov 03 2008 - 19:20:09 PST)
AMBER: process_mdout modify Naser Alijabbari (Mon Nov 03 2008 - 22:20:07 PST)
- RE: AMBER: process_mdout modify Ross Walker (Tue Nov 04 2008 - 07:41:33 PST)
AMBER: problem with group input and NMR restaints priya priya (Tue Nov 04 2008 - 07:20:09 PST)
- Re: AMBER: problem with group input and NMR restaints Carlos Simmerling (Tue Nov 04 2008 - 07:35:46 PST)
- RE: AMBER: problem with group input and NMR restaints Ross Walker (Tue Nov 04 2008 - 07:46:17 PST)
  - RE: AMBER: problem with group input and NMR restaints priya priya (Tue Nov 04 2008 - 08:16:34 PST)
    - Re: AMBER: problem with group input and NMR restaints Carlos Simmerling (Tue Nov 04 2008 - 08:41:22 PST)
    - Re: AMBER: problem with group input and NMR restaints priya priya (Tue Nov 04 2008 - 09:38:37 PST)
    - Re: AMBER: problem with group input and NMR restaints Carlos Simmerling (Tue Nov 04 2008 - 09:53:48 PST)
    - Re: AMBER: problem with group input and NMR restaints priya priya (Wed Nov 05 2008 - 08:05:05 PST)
    - Re: AMBER: problem with group input and NMR restaints Carlos Simmerling (Wed Nov 05 2008 - 08:53:09 PST)
    - AMBER: Br - ion defined ? Chih-Ying Lin (Wed Nov 05 2008 - 09:20:36 PST)
    - Re: AMBER: problem with group input and NMR restaints priya priya (Wed Nov 05 2008 - 09:22:33 PST)
    - Re: AMBER: problem with group input and NMR restaints Carlos Simmerling (Wed Nov 05 2008 - 10:13:29 PST)
    - Re: AMBER: problem with group input and NMR restaints priya priya (Wed Nov 05 2008 - 12:00:48 PST)
    - Re: AMBER: problem with group input and NMR restaints Carlos Simmerling (Wed Nov 05 2008 - 12:39:29 PST)
    - AMBER: AMBER10: QMMM parallel test error Yang, Ping (Wed Nov 05 2008 - 15:44:27 PST)
    - RE: AMBER: AMBER10: QMMM parallel test error Yang, Ping (Wed Nov 05 2008 - 19:57:29 PST)
    - RE: AMBER: AMBER10: QMMM parallel test error Ross Walker (Wed Nov 05 2008 - 17:41:27 PST)
AMBER: Steered MD and Jarzynski in pulling simulations Samuel Genheden (Wed Nov 05 2008 - 06:48:33 PST)
- Re: AMBER: Steered MD and Jarzynski in pulling simulations M. L. Dodson (Wed Nov 05 2008 - 07:04:23 PST)
- Re: AMBER: Steered MD and Jarzynski in pulling simulations Gustavo Seabra (Sun Nov 09 2008 - 18:36:38 PST)
AMBER: Glycam Neha Gandhi (Wed Nov 05 2008 - 20:02:01 PST)
- Re: AMBER: Glycam Lachele Foley (Lists) (Thu Nov 06 2008 - 07:01:48 PST)
AMBER: RE: Poly(A)-Poly(T) DNA Tutorial Query Ross Walker (Thu Nov 06 2008 - 00:18:22 PST)
AMBER: Force field for Gd (gadolinium)? Lili Peng (Thu Nov 06 2008 - 01:05:26 PST)
AMBER: gigabit ethernet cards and switches Alessandro Nascimento (Thu Nov 06 2008 - 08:51:43 PST)
- RE: AMBER: gigabit ethernet cards and switches Ross Walker (Thu Nov 06 2008 - 10:37:04 PST)
  - Re: AMBER: gigabit ethernet cards and switches Alessandro Nascimento (Thu Nov 06 2008 - 11:28:46 PST)
    - Re: AMBER: gigabit ethernet cards and switches Mengjuei Hsieh (Thu Nov 06 2008 - 18:39:23 PST)
AMBER: ptraj new mask parser: differences from ambmask and core dumps M. L. Dodson (Thu Nov 06 2008 - 10:31:07 PST)
- Re: AMBER: ptraj new mask parser: differences from ambmask and core dumps Jianyin Shao (Thu Nov 06 2008 - 14:48:47 PST)
  - Re: AMBER: ptraj new mask parser: differences from ambmask and core dumps M. L. Dodson (Thu Nov 06 2008 - 15:49:49 PST)
    - Re: AMBER: ptraj new mask parser: differences from ambmask and core dumps Jianyin Shao (Fri Nov 07 2008 - 08:24:03 PST)
    - Re: AMBER: ptraj new mask parser: differences from ambmask and core dumps M. L. Dodson (Fri Nov 07 2008 - 15:15:06 PST)
    - Re: AMBER: ptraj new mask parser: differences from ambmask and core dumps M. L. Dodson (Mon Nov 10 2008 - 10:23:17 PST)
AMBER: RE: Poly(A)-Poly(T) DNA Tutorial Query Ross Walker (Thu Nov 06 2008 - 10:37:04 PST)
AMBER: RE: QUERRY? Ross Walker (Thu Nov 06 2008 - 10:37:04 PST)
AMBER: RE: Problem with the NEB tutorial Ross Walker (Thu Nov 06 2008 - 11:24:30 PST)
AMBER: RE: problems about TMD in your tutorial Ross Walker (Thu Nov 06 2008 - 11:32:58 PST)
- AMBER: coot mutation Taufik Al-Sarraj (Thu Nov 06 2008 - 12:19:00 PST)
AMBER: Extracting periodic box size deviation CJ Dickson (Thu Nov 06 2008 - 15:29:20 PST)
AMBER: using "EP" for dummy atom Ashish Sangwai (Thu Nov 06 2008 - 17:24:23 PST)
- RE: AMBER: using "EP" for dummy atom Ross Walker (Thu Nov 06 2008 - 18:05:22 PST)
Re: AMBER: Extracting periodic box size deviation Bill Ross (Thu Nov 06 2008 - 17:42:35 PST)
AMBER: AMBER : Inconsistent MD length and no of angles after ptraj parul sharma (Fri Nov 07 2008 - 01:52:07 PST)
- Re: AMBER: AMBER : Inconsistent MD length and no of angles after ptraj David A. Case (Fri Nov 07 2008 - 21:33:48 PST)
AMBER: Building O-Ac modified monosaccharides consistent with Glycam force field parameters Francois Theillet (Fri Nov 07 2008 - 07:24:36 PST)
- Re: AMBER: Building O-Ac modified monosaccharides consistent with Glycam force field parameters Lachele Foley (Lists) (Fri Nov 07 2008 - 13:25:18 PST)
AMBER: AMBER question: perturbed charge twice the unperturbed Edward M (Sat Nov 08 2008 - 21:36:54 PST)
- Re: AMBER: AMBER question: perturbed charge twice the unperturbed David A. Case (Sun Nov 09 2008 - 09:16:52 PST)
  - Re: AMBER: AMBER question: perturbed charge twice the unperturbed E.M. (Sun Nov 09 2008 - 15:08:05 PST)
    - Re: AMBER: AMBER question: perturbed charge twice the unperturbed David A. Case (Thu Nov 13 2008 - 12:39:41 PST)
AMBER: looks like I have problem with "make clean" command drugdesign (Sun Nov 09 2008 - 23:27:22 PST)
- Re: AMBER: looks like I have problem with "make clean" command David A. Case (Mon Nov 10 2008 - 04:39:26 PST)
AMBER: RE: problems about TMD in your tutorial Ross Walker (Mon Nov 10 2008 - 00:20:18 PST)
AMBER: ff02 in nmode gives error "too many dihedrals" ? Jacob Kongsted (Mon Nov 10 2008 - 01:16:36 PST)
- Re: AMBER: ff02 in nmode gives error "too many dihedrals" ? David A. Case (Wed Nov 12 2008 - 07:13:45 PST)
AMBER: test sander error in amber7 Saiful Islam (Mon Nov 10 2008 - 05:43:45 PST)
- Re: AMBER: test sander error in amber7 Saiful Islam (Mon Nov 10 2008 - 23:36:30 PST)
  - Re: AMBER: test sander error in amber7 David A. Case (Tue Nov 11 2008 - 04:15:51 PST)
AMBER: mm_pbsa.pl and Amber10 Stephan.Reiling.sanofi-aventis.com (Mon Nov 10 2008 - 08:05:27 PST)
- Re: AMBER: mm_pbsa.pl and Amber10 Holger Gohlke (Mon Nov 10 2008 - 09:12:16 PST)
AMBER: Amber 9 installation problems drugdesign (Mon Nov 10 2008 - 03:27:39 PST)
- Re: AMBER: Amber 9 installation problems Shozeb Haider (Mon Nov 10 2008 - 08:37:54 PST)
- Re: AMBER: Amber 9 installation problems David A. Case (Mon Nov 10 2008 - 09:32:39 PST)
- Re: AMBER: Amber 9 installation problems drugdesign (Tue Nov 11 2008 - 06:13:32 PST)
  - Re: AMBER: Amber 9 installation problems David A. Case (Tue Nov 11 2008 - 15:22:54 PST)
- Re: AMBER: Amber 9 installation problems drugdesign (Tue Nov 11 2008 - 23:36:51 PST)
  - RE: AMBER: Amber 9 installation problems Ross Walker (Wed Nov 12 2008 - 07:21:59 PST)
    - Re: AMBER: Amber 9 installation problems drugdesign (Wed Nov 12 2008 - 11:09:47 PST)
    - RE: AMBER: Amber 9 installation problems Ross Walker (Wed Nov 12 2008 - 13:16:03 PST)
    - AMBER: Your "bellymask-patch" Jochen Heil (Thu Nov 13 2008 - 05:45:30 PST)
    - RE: AMBER: Your "bellymask-patch" Ross Walker (Thu Nov 13 2008 - 10:17:58 PST)
    - AMBER: Restraints Joseph Nachman (Thu Nov 13 2008 - 10:59:23 PST)
    - Re: AMBER: Restraints Ashish Sangwai (Thu Nov 13 2008 - 11:11:45 PST)
    - RE: AMBER: Restraints Ross Walker (Thu Nov 13 2008 - 11:11:53 PST)
    - Re: AMBER: Amber 9 installation problems drugdesign (Thu Nov 13 2008 - 08:25:34 PST)
AMBER: xLeap error Lili Peng (Mon Nov 10 2008 - 12:45:58 PST)
- Re: AMBER: xLeap error Lili Peng (Mon Nov 10 2008 - 13:49:53 PST)
- Re: AMBER: xLeap error Mark Williamson (Mon Nov 10 2008 - 13:58:27 PST)
AMBER: resp charges in parameterization Mark M Huntress (Wed Nov 12 2008 - 08:24:55 PST)
- Re: AMBER: resp charges in parameterization steinbrt.rci.rutgers.edu (Wed Nov 12 2008 - 08:44:17 PST)
AMBER: Newbie question: partial minimization in implicit solvent Jochen Heil (Wed Nov 12 2008 - 09:48:38 PST)
- Re: AMBER: Newbie question: partial minimization in implicit solvent Carlos Simmerling (Wed Nov 12 2008 - 12:47:56 PST)
- RE: AMBER: Newbie question: partial minimization in implicit solvent Ross Walker (Wed Nov 12 2008 - 13:00:39 PST)
AMBER: Problem with evaporating water over longer simulation times Sasha Buzko (Wed Nov 12 2008 - 11:14:00 PST)
- Re: AMBER: Problem with evaporating water over longer simulation times Gustavo Seabra (Wed Nov 12 2008 - 11:48:01 PST)
  - Re: AMBER: Problem with evaporating water over longer simulation times steinbrt.rci.rutgers.edu (Wed Nov 12 2008 - 11:57:33 PST)
    - Re: AMBER: Problem with evaporating water over longer simulation times Sasha Buzko (Wed Nov 12 2008 - 12:56:16 PST)
    - Re: AMBER: Problem with evaporating water over longer simulation times Sasha Buzko (Wed Nov 12 2008 - 16:53:06 PST)
    - Re: AMBER: Problem with evaporating water over longer simulation times Adrian Roitberg (Wed Nov 12 2008 - 17:06:38 PST)
AMBER: question about ptraj rai001.student.ucr.edu (Wed Nov 12 2008 - 22:30:48 PST)
- Re: AMBER: question about ptraj Jianyin Shao (Thu Nov 13 2008 - 15:38:44 PST)
- Re: AMBER: question about ptraj rai001.student.ucr.edu (Thu Nov 13 2008 - 15:56:49 PST)
AMBER: PB Radii Swarup Gupta (Wed Nov 12 2008 - 23:06:34 PST)
- Re: AMBER: PB Radii David A. Case (Thu Nov 13 2008 - 04:01:57 PST)
  - Re: AMBER: PB Radii Swarup Gupta (Sat Nov 15 2008 - 19:44:25 PST)
- Re: AMBER: PB Radii Swarup Gupta (Mon Nov 17 2008 - 03:24:42 PST)
  - Re: AMBER: PB Radii Carlos Simmerling (Mon Nov 17 2008 - 03:30:41 PST)
AMBER: load opls force field oguz gurbulak (Thu Nov 13 2008 - 02:38:11 PST)
- Re: AMBER: load opls force field David A. Case (Thu Nov 13 2008 - 04:06:40 PST)
- Re: AMBER: load opls force field Bill Ross (Thu Nov 13 2008 - 12:32:19 PST)
AMBER: Chloride anion ligands leave the protein during MD Francesco Pietra (Thu Nov 13 2008 - 07:06:06 PST)
- Re: AMBER: Chloride anion ligands leave the protein during MD Gustavo Seabra (Fri Nov 14 2008 - 05:40:45 PST)
  - Re: AMBER: Chloride anion ligands leave the protein during MD Adrian Roitberg (Fri Nov 14 2008 - 06:00:33 PST)
    - Re: AMBER: Chloride anion ligands leave the protein during MD Jiri Sponer (Fri Nov 14 2008 - 06:19:33 PST)
  - Re: AMBER: Chloride anion ligands leave the protein during MD Francesco Pietra (Sun Nov 16 2008 - 03:17:00 PST)
AMBER: MM-PBSA and trajectory input Arturas Ziemys (Thu Nov 13 2008 - 09:22:36 PST)
AMBER: segmentation fault when restarting periodic structure Diddo Diddens (Fri Nov 14 2008 - 04:47:23 PST)
- AMBER: subroutine for torsional potential CHAMI F. (Fri Nov 14 2008 - 06:16:37 PST)
  - Re: AMBER: subroutine for torsional potential steinbrt.rci.rutgers.edu (Fri Nov 14 2008 - 06:49:25 PST)
- Re: AMBER: segmentation fault when restarting periodic structure David A. Case (Tue Nov 18 2008 - 06:20:41 PST)
AMBER: how to remove counter ions ( K+ / Cl- ions) using rdparm? Siddharth Rastogi (Fri Nov 14 2008 - 06:02:34 PST)
AMBER: NMR optimization with group averages (IGR1 / IGR2) Ryan Pavlovicz (Fri Nov 14 2008 - 07:59:36 PST)
AMBER: Sander *.top and *.crd file from PDB file Chin, Keith B (Fri Nov 14 2008 - 11:43:41 PST)
- Re: AMBER: Sander *.top and *.crd file from PDB file Gustavo Seabra (Fri Nov 14 2008 - 12:30:21 PST)
  - RE: AMBER: Sander *.top and *.crd file from PDB file Chin, Keith B (Fri Nov 14 2008 - 12:55:57 PST)
    - Re: AMBER: Sander *.top and *.crd file from PDB file Carlos Simmerling (Fri Nov 14 2008 - 13:00:30 PST)
AMBER: Ptraj Normal Mode Analysis Jesse Jun (Fri Nov 14 2008 - 13:19:31 PST)
AMBER: organic solvents Marcelo Puiatti (Fri Nov 14 2008 - 15:20:30 PST)
- Re: AMBER: organic solvents Mark Williamson (Fri Nov 14 2008 - 15:28:10 PST)
- Re: AMBER: organic solvents FyD (Fri Nov 14 2008 - 23:56:30 PST)
AMBER: Trajectory file ended and unit 24 error on open inptraj Siddharth Rastogi (Sat Nov 15 2008 - 07:33:10 PST)
- Re: AMBER: Trajectory file ended and unit 24 error on open inptraj Carlos Simmerling (Sat Nov 15 2008 - 07:44:32 PST)
  - Re: AMBER: Trajectory file ended and unit 24 error on open inptraj Siddharth Rastogi (Sat Nov 15 2008 - 22:18:59 PST)
    - Re: AMBER: Trajectory file ended and unit 24 error on open inptraj Carlos Simmerling (Sun Nov 16 2008 - 04:42:22 PST)
- Re: AMBER: Trajectory file ended and unit 24 error on open inptraj Gustavo Seabra (Sun Nov 16 2008 - 08:05:42 PST)
AMBER: How to create *.top & *.crd file with hexagonal lattice Chin, Keith B (Sun Nov 16 2008 - 17:02:05 PST)
- Re: AMBER: How to create *.top & *.crd file with hexagonal lattice David A. Case (Tue Nov 18 2008 - 06:05:12 PST)
AMBER: problem Arturas Ziemys (Sun Nov 16 2008 - 21:07:38 PST)
- Re: AMBER: problem FyD (Sun Nov 16 2008 - 23:40:33 PST)
- RE: AMBER: problem Arturas Ziemys (Mon Nov 17 2008 - 20:36:25 PST)
  - Re: AMBER: problem David A. Case (Tue Nov 18 2008 - 04:15:57 PST)
    - Re: AMBER: problem Arturas Ziemys (Tue Nov 18 2008 - 07:07:19 PST)
AMBER: High ESURF Siddharth Rastogi (Mon Nov 17 2008 - 00:07:57 PST)
- Re: AMBER: High ESURF Andreas Svrcek-Seiler (Mon Nov 17 2008 - 00:24:02 PST)
AMBER: velocity units? Jose Borreguero (Mon Nov 17 2008 - 08:14:35 PST)
- Re: AMBER: velocity units? David A. Case (Mon Nov 17 2008 - 08:53:19 PST)
AMBER: ptraj closest command steinbrt.rci.rutgers.edu (Mon Nov 17 2008 - 08:14:11 PST)
- Re: AMBER: ptraj closest command Gustavo Seabra (Mon Nov 17 2008 - 08:51:42 PST)
AMBER: RESTRAINTS: no valid redirection found Francesco Pietra (Mon Nov 17 2008 - 09:15:17 PST)
- Fwd: AMBER: RESTRAINTS: no valid redirection found Francesco Pietra (Mon Nov 17 2008 - 09:35:04 PST)
- Re: AMBER: RESTRAINTS: no valid redirection found Robert Duke (Mon Nov 17 2008 - 09:34:50 PST)
  - Re: AMBER: RESTRAINTS: no valid redirection found Francesco Pietra (Mon Nov 17 2008 - 10:00:25 PST)
  - Re: AMBER: RESTRAINTS: no valid redirection found Francesco Pietra (Mon Nov 17 2008 - 11:21:01 PST)
- Re: AMBER: RESTRAINTS: no valid redirection found Robert Duke (Mon Nov 17 2008 - 11:58:18 PST)
  - Re: AMBER: RESTRAINTS: no valid redirection found Francesco Pietra (Mon Nov 17 2008 - 13:30:54 PST)
AMBER: AMBER10 installation question Jeffrey (Mon Nov 17 2008 - 19:20:14 PST)
- Re: AMBER: AMBER10 installation question David A. Case (Tue Nov 18 2008 - 04:05:07 PST)
  - Re: Re: AMBER: AMBER10 installation question Jeffrey (Wed Nov 19 2008 - 05:27:13 PST)
AMBER: SPCFW temperature oscillations Naser Alijabbari (Mon Nov 17 2008 - 20:19:12 PST)
- Re: AMBER: SPCFW temperature oscillations David A. Case (Tue Nov 18 2008 - 04:13:16 PST)
- Re: AMBER: SPCFW temperature oscillations Robert Duke (Tue Nov 18 2008 - 05:16:27 PST)
AMBER: Equilibration protocol for large protein Dmitri Nilov (Tue Nov 18 2008 - 08:33:26 PST)
AMBER: Duplicate entries with different parameters in gaff.dat from AmberTools 1.2 (resend) John Chodera (Tue Nov 18 2008 - 11:58:22 PST)
- Re: AMBER: Duplicate entries with different parameters in gaff.dat from AmberTools 1.2 (resend) David A. Case (Wed Nov 19 2008 - 06:35:45 PST)
  - Re: AMBER: Duplicate entries with different parameters in gaff.dat from AmberTools 1.2 (resend) Alan (Thu Nov 20 2008 - 03:48:56 PST)
    - Re: AMBER: Duplicate entries with different parameters in gaff.dat from AmberTools 1.2 (resend) Alan (Thu Nov 20 2008 - 04:13:09 PST)
    - Re: AMBER: Duplicate entries with different parameters in gaff.dat from AmberTools 1.2 (resend) David A. Case (Thu Nov 20 2008 - 05:38:37 PST)
    - Re: AMBER: Duplicate entries with different parameters in gaff.dat from AmberTools 1.2 (resend) David A. Case (Thu Nov 20 2008 - 05:36:48 PST)
AMBER: AMBER10 compiling SANDER parallel problem Hazard, E. Starr (Tue Nov 18 2008 - 12:48:31 PST)
- Re: AMBER: AMBER10 compiling SANDER parallel problem David A. Case (Tue Nov 18 2008 - 13:25:23 PST)
AMBER: Chin, Keith B (Tue Nov 18 2008 - 15:39:26 PST)
AMBER: PMEMD with AMOEBA parms including a lone pair site Margaret Johnson (Tue Nov 18 2008 - 18:29:04 PST)
- Re: AMBER: PMEMD with AMOEBA parms including a lone pair site Robert Duke (Tue Nov 18 2008 - 18:50:14 PST)
AMBER: question - gaff and leaprc.ff03ua oguz gurbulak (Wed Nov 19 2008 - 05:56:17 PST)
- Re: AMBER: question - gaff and leaprc.ff03ua David A. Case (Wed Nov 19 2008 - 07:08:02 PST)
  - Re: AMBER: question - gaff and leaprc.ff03ua oguz gurbulak (Sun Nov 23 2008 - 08:43:48 PST)
    - Re: AMBER: question - gaff and leaprc.ff03ua David A. Case (Sun Nov 23 2008 - 13:49:37 PST)
AMBER: MOLYBDENUM Joachim Reichelt (Wed Nov 19 2008 - 06:14:31 PST)
AMBER: problem with cartesian restraints with NTP simulations Barbault Florent (Wed Nov 19 2008 - 06:50:13 PST)
- Re: AMBER: problem with cartesian restraints with NTP simulations David A. Case (Wed Nov 19 2008 - 07:02:56 PST)
AMBER: Amber on linux Marudachalam S (Wed Nov 19 2008 - 09:58:10 PST)
- Re: AMBER: Amber on linux steinbrt.rci.rutgers.edu (Wed Nov 19 2008 - 11:47:45 PST)
AMBER: How to manually adjust periodic boundary conditions (PBC) Chin, Keith B (Wed Nov 19 2008 - 11:58:41 PST)
- Re: AMBER: How to manually adjust periodic boundary conditions (PBC) David A. Case (Wed Nov 19 2008 - 15:35:33 PST)
  - RE: AMBER: How to manually adjust periodic boundary conditions (PBC) Chin, Keith B (Wed Nov 19 2008 - 17:15:17 PST)
    - Re: AMBER: How to manually adjust periodic boundary conditions (PBC) David A. Case (Thu Nov 20 2008 - 12:52:57 PST)
AMBER: compiling ambertools with intel compilers Alan (Thu Nov 20 2008 - 02:27:26 PST)
- Re: AMBER: compiling ambertools with intel compilers David A. Case (Thu Nov 20 2008 - 04:04:22 PST)
  - Re: AMBER: compiling ambertools with intel compilers Alan (Thu Nov 20 2008 - 04:10:58 PST)
  - Re: AMBER: compiling ambertools with intel compilers Francesco Pietra (Thu Nov 20 2008 - 08:38:29 PST)
    - Re: AMBER: compiling ambertools with intel compilers Francesco Pietra (Thu Nov 20 2008 - 10:44:21 PST)
    - Re: AMBER: compiling ambertools with intel compilers David A. Case (Thu Nov 20 2008 - 12:50:27 PST)
  - Re: AMBER: compiling ambertools with intel compilers Thomas Patko (Thu Nov 20 2008 - 14:15:58 PST)
    - Re: AMBER: compiling ambertools with intel compilers David A. Case (Fri Nov 21 2008 - 09:44:58 PST)
AMBER: AMBER forfield choose Wang,Ying (Thu Nov 20 2008 - 06:32:24 PST)
- Re: AMBER: AMBER forfield choose Barbault Florent (Thu Nov 20 2008 - 06:45:20 PST)
  - Re: AMBER: AMBER forfield choose Carlos Simmerling (Thu Nov 20 2008 - 07:51:18 PST)
    - Re: AMBER: AMBER forfield choose Barbault Florent (Thu Nov 20 2008 - 08:21:17 PST)
    - Re: AMBER: AMBER forfield choose Carlos Simmerling (Thu Nov 20 2008 - 08:21:51 PST)
- Re: AMBER: AMBER forfield choose Wang,Ying (Thu Nov 20 2008 - 07:05:28 PST)
  - Re: AMBER: AMBER forfield choose mori.cerm.unifi.it (Thu Nov 20 2008 - 07:09:28 PST)
- Re: AMBER: AMBER forfield choose Wang,Ying (Thu Nov 20 2008 - 07:17:45 PST)
AMBER: CG and HC atoms partial charges in AMBER Stephane Abel (Thu Nov 20 2008 - 07:40:17 PST)
- Re: AMBER: CG and HC atoms partial charges in AMBER David A. Case (Thu Nov 20 2008 - 07:56:15 PST)
  - Re: AMBER: CG and HC atoms partial charges in AMBER Stephane Abel (Thu Nov 20 2008 - 08:26:10 PST)
    - RE: AMBER: CG and HC atoms partial charges in AMBER Matthew Tessier (Thu Nov 20 2008 - 08:40:43 PST)
    - Re: AMBER: CG and HC atoms partial charges in AMBER Stephane Abel (Thu Nov 20 2008 - 08:51:25 PST)
    - RE: AMBER: CG and HC atoms partial charges in AMBER Matthew Tessier (Thu Nov 20 2008 - 09:09:16 PST)
    - Re: AMBER: CG and HC atoms partial charges in AMBER Stephane Abel (Thu Nov 20 2008 - 09:07:07 PST)
- RE: AMBER: CG and HC atoms partial charges in AMBER Matthew Tessier (Thu Nov 20 2008 - 08:15:56 PST)
AMBER: pmemd Jeremy Harris (Thu Nov 20 2008 - 08:27:14 PST)
- RE: AMBER: pmemd Ross Walker (Thu Nov 20 2008 - 08:36:51 PST)
- Re: AMBER: pmemd Robert Duke (Thu Nov 20 2008 - 08:40:36 PST)
Re: AMBER: Force field for Gd3+ (metal ion)? Lili Peng (Thu Nov 20 2008 - 16:00:29 PST)
- AMBER: Problems for use manganese molecules vallespardojl.chem.leidenuniv.nl (Fri Nov 21 2008 - 01:06:37 PST)
  - Re: AMBER: Problems for use manganese molecules David A. Case (Fri Nov 21 2008 - 04:46:22 PST)
AMBER: ptraj center problem robaldo.dna.uba.ar (Fri Nov 21 2008 - 09:31:27 PST)
- Re: AMBER: ptraj center problem Carlos Simmerling (Fri Nov 21 2008 - 10:42:17 PST)
  - Re: AMBER: ptraj center problem robaldo.dna.uba.ar (Fri Nov 21 2008 - 12:04:56 PST)
AMBER: Electrostatic Energy Components guardiani.fi.infn.it (Fri Nov 21 2008 - 11:29:08 PST)
- RE: AMBER: Electrostatic Energy Components Ross Walker (Fri Nov 21 2008 - 13:36:20 PST)
  - RE: AMBER: Electrostatic Energy Components Ilyas Yildirim (Fri Nov 21 2008 - 14:11:14 PST)
    - RE: AMBER: Electrostatic Energy Components Ross Walker (Fri Nov 21 2008 - 14:33:30 PST)
    - Re: AMBER: Electrostatic Energy Components Carlos Simmerling (Fri Nov 21 2008 - 15:46:10 PST)
    - RE: AMBER: Electrostatic Energy Components Ilyas Yildirim (Fri Nov 21 2008 - 16:12:44 PST)
    - RE: AMBER: Electrostatic Energy Components Ross Walker (Fri Nov 21 2008 - 16:20:56 PST)
    - Re: AMBER: Electrostatic Energy Components Jojart Balazs (Fri Nov 21 2008 - 23:53:46 PST)
    - RE: AMBER: Electrostatic Energy Components Ross Walker (Sat Nov 22 2008 - 09:21:22 PST)
    - Re: AMBER: Electrostatic Energy Components Carlos Simmerling (Sat Nov 22 2008 - 09:42:53 PST)
    - Re: AMBER: Electrostatic Energy Components David A. Case (Sat Nov 22 2008 - 12:37:51 PST)
    - Re: AMBER: Electrostatic Energy Components Jojart Balazs (Sun Nov 23 2008 - 00:34:01 PST)
    - Re: AMBER: Electrostatic Energy Components David A. Case (Mon Nov 24 2008 - 04:14:13 PST)
    - Re: AMBER: Electrostatic Energy Components Balazs JOJART (Mon Nov 24 2008 - 04:19:42 PST)
    - AMBER: nonbonded parameters for titanium saurabh agrawal (Mon Nov 24 2008 - 08:57:56 PST)
    - Re: AMBER: Electrostatic Energy Components Carlos Simmerling (Sat Nov 22 2008 - 09:41:48 PST)
- Re: AMBER: Electrostatic Energy Components Junmei Wang (Sun Nov 23 2008 - 19:36:38 PST)
AMBER: RE: About restart amber Ross Walker (Fri Nov 21 2008 - 13:45:16 PST)
- Re: AMBER: RE: About restart amber Francesco Pietra (Sat Nov 22 2008 - 08:03:02 PST)
  - RE: AMBER: RE: About restart amber Ross Walker (Sat Nov 22 2008 - 09:18:57 PST)
    - Re: AMBER: RE: About restart amber Francesco Pietra (Mon Nov 24 2008 - 13:22:44 PST)
    - Re: AMBER: RE: About restart amber Francesco Pietra (Tue Nov 25 2008 - 00:00:38 PST)
- Re: AMBER: RE: About restart amber Robert Duke (Tue Nov 25 2008 - 06:27:16 PST)
  - Re: AMBER: RE: About restart amber Francesco Pietra (Tue Nov 25 2008 - 12:59:35 PST)
- Re: AMBER: RE: About restart amber Robert Duke (Tue Nov 25 2008 - 13:23:09 PST)
  - Re: AMBER: RE: About restart amber Francesco Pietra (Tue Nov 25 2008 - 13:47:35 PST)
- Re: AMBER: RE: About restart amber Robert Duke (Tue Nov 25 2008 - 13:55:15 PST)
AMBER: compiling amber 10 Andrei Neamtu (Fri Nov 21 2008 - 23:26:58 PST)
- Re: AMBER: compiling amber 10 David A. Case (Sat Nov 22 2008 - 12:33:54 PST)
AMBER: QM/MM simulation Syed Tarique Moin (Sat Nov 22 2008 - 00:00:36 PST)
- Re: AMBER: QM/MM simulation David A. Case (Sat Nov 22 2008 - 06:53:50 PST)
  - Re: AMBER: QM/MM simulation Syed Tarique Moin (Sat Nov 22 2008 - 07:11:12 PST)
    - RE: AMBER: QM/MM simulation Ross Walker (Sat Nov 22 2008 - 08:59:49 PST)
    - Re: AMBER: QM/MM simulation Gustavo Seabra (Sat Nov 22 2008 - 11:19:22 PST)
AMBER: AMBER10 failing to compile PMEMD Hazard, E. Starr (Sat Nov 22 2008 - 14:06:03 PST)
- Re: AMBER: AMBER10 failing to compile PMEMD Robert Duke (Sat Nov 22 2008 - 14:42:50 PST)
AMBER: AdoMet parameterization with antechamber Jeffrey (Sun Nov 23 2008 - 07:55:30 PST)
- Re: AMBER: AdoMet parameterization with antechamber David A. Case (Sun Nov 23 2008 - 13:13:23 PST)
  - Re: AMBER: AdoMet parameterization with antechamber Alan (Mon Nov 24 2008 - 02:46:52 PST)
    - Re: Re: AMBER: AdoMet parameterization with antechamber Jeffrey (Mon Nov 24 2008 - 08:19:41 PST)
    - Re: Re: AMBER: AdoMet parameterization with antechamber Wei Huang (Mon Nov 24 2008 - 08:41:12 PST)
    - Re: Re: AMBER: AdoMet parameterization with antechamber David A. Case (Mon Nov 24 2008 - 09:19:54 PST)
    - Re: Re: Re: AMBER: AdoMet parameterization with antechamber Jeffrey (Tue Nov 25 2008 - 08:14:44 PST)
    - Re: Re: Re: Re: AMBER: AdoMet parameterization with antechamber Jeffrey (Wed Nov 26 2008 - 06:44:27 PST)
    - RE: Re: Re: Re: AMBER: AdoMet parameterization with antechamber Ross Walker (Wed Nov 26 2008 - 09:28:51 PST)
    - Re: RE: Re: Re: Re: AMBER: AdoMet parameterization with antechamber Jeffrey (Thu Nov 27 2008 - 07:30:33 PST)
AMBER: GB versus explicit medium Francesco Pietra (Mon Nov 24 2008 - 01:39:58 PST)
- Re: AMBER: GB versus explicit medium Carlos Simmerling (Mon Nov 24 2008 - 03:08:40 PST)
  - Re: AMBER: GB versus explicit medium Francesco Pietra (Mon Nov 24 2008 - 07:33:43 PST)
    - Re: AMBER: GB versus explicit medium M. L. Dodson (Mon Nov 24 2008 - 07:43:52 PST)
AMBER: Ewald troubles when running very big boxes steinbrt.rci.rutgers.edu (Mon Nov 24 2008 - 12:50:50 PST)
- Re: AMBER: Ewald troubles when running very big boxes Robert Duke (Mon Nov 24 2008 - 18:09:23 PST)
AMBER: unsubscribe amber Su Nwe (Mon Nov 24 2008 - 23:12:02 PST)
AMBER: Gradual releasing of position restraints Dmitri Nilov (Tue Nov 25 2008 - 06:23:02 PST)
- RE: AMBER: Gradual releasing of position restraints Ross Walker (Tue Nov 25 2008 - 08:48:13 PST)
- Re: AMBER: Gradual releasing of position restraints David A. Case (Wed Nov 26 2008 - 09:00:41 PST)
AMBER: molsurf fails Arturas Ziemys (Tue Nov 25 2008 - 07:27:27 PST)
- Re: AMBER: molsurf fails David A. Case (Tue Nov 25 2008 - 11:26:14 PST)
AMBER: using packmol file in Amber oguz gurbulak (Tue Nov 25 2008 - 07:49:19 PST)
- Re: AMBER: using packmol file in Amber David A. Case (Tue Nov 25 2008 - 11:45:29 PST)
- Re: AMBER: using packmol file in Amber oguz gurbulak (Tue Dec 02 2008 - 03:06:10 PST)
  - Re: AMBER: using packmol file in Amber David A. Case (Tue Dec 02 2008 - 04:14:47 PST)
    - Re: AMBER: using packmol file in Amber oguz gurbulak (Tue Dec 02 2008 - 06:02:59 PST)
    - Re: AMBER: using packmol file in Amber David A. Case (Tue Dec 02 2008 - 06:19:20 PST)
    - Re: AMBER: using packmol file in Amber oguz gurbulak (Thu Dec 04 2008 - 07:36:03 PST)
    - Re: AMBER: using packmol file in Amber David A. Case (Thu Dec 04 2008 - 08:32:49 PST)
    - Re: AMBER: using packmol file in Amber oguz gurbulak (Fri Dec 05 2008 - 07:49:39 PST)
    - Re: AMBER: using packmol file in Amber David A. Case (Fri Dec 05 2008 - 07:58:51 PST)
    - Re: AMBER: using packmol file in Amber oguz gurbulak (Mon Dec 15 2008 - 07:57:08 PST)
    - Re: AMBER: using packmol file in Amber Gustavo Seabra (Mon Dec 15 2008 - 08:39:53 PST)
AMBER: Test failure with Amber 10 Kevin Parkes (Wed Nov 26 2008 - 02:33:35 PST)
- Re: AMBER: Test failure with Amber 10 David A. Case (Wed Nov 26 2008 - 04:46:41 PST)
  - RE: AMBER: Test failure with Amber 10 Kevin Parkes (Wed Nov 26 2008 - 06:36:36 PST)
    - RE: AMBER: Test failure with Amber 10 Ross Walker (Wed Nov 26 2008 - 08:30:42 PST)
- Re: AMBER: Test failure with Amber 10 Robert Duke (Wed Nov 26 2008 - 09:28:14 PST)
AMBER: About antechamber and GAFF Stephane Abel (Wed Nov 26 2008 - 03:02:00 PST)
AMBER: About antechamber and GAFF [UPDATED] Stephane Abel (Wed Nov 26 2008 - 03:21:52 PST)
- AMBER: subroutine Work : Jarynski work theorem CHAMI F. (Wed Nov 26 2008 - 04:21:07 PST)
  - Re: AMBER: subroutine Work : Jarynski work theorem Gustavo Seabra (Wed Dec 03 2008 - 05:59:06 PST)
- Re: AMBER: About antechamber and GAFF [UPDATED] Navnit Kumar Mishra (Wed Nov 26 2008 - 05:04:20 PST)
- RE: AMBER: About antechamber and GAFF [UPDATED] Ross Walker (Wed Nov 26 2008 - 08:39:30 PST)
  - Re: AMBER: About antechamber and GAFF [UPDATED] Stephane Abel (Thu Nov 27 2008 - 03:33:56 PST)
- Re: AMBER: About antechamber and GAFF [UPDATED] Wenyong Tong (Wed Nov 26 2008 - 09:13:34 PST)
AMBER: Choline chloride salt CHAMI F. (Wed Nov 26 2008 - 06:49:45 PST)
- AMBER: Referencing AMBER Joseph Nachman (Wed Nov 26 2008 - 08:01:57 PST)
  - Re: AMBER: Referencing AMBER David A. Case (Wed Nov 26 2008 - 08:25:20 PST)
AMBER: Problem running NEB in AMBER10 Chris C. (Wed Nov 26 2008 - 10:38:17 PST)
- RE: AMBER: Problem running NEB in AMBER10 Ross Walker (Wed Nov 26 2008 - 11:04:55 PST)
  - Re: AMBER: Problem running NEB in AMBER10 Chris C. (Wed Dec 03 2008 - 10:29:48 PST)
AMBER: problem with AMOEBA j00323240.students.jsums.edu (Wed Nov 26 2008 - 11:07:13 PST)
AMBER: Question fot Amber 10 Benchmarks sychen (Wed Nov 26 2008 - 23:50:11 PST)
- Re: AMBER: Question fot Amber 10 Benchmarks Robert Duke (Thu Nov 27 2008 - 06:37:20 PST)
- RE: AMBER: Question fot Amber 10 Benchmarks Ross Walker (Thu Nov 27 2008 - 08:57:06 PST)
  - Re[2]: AMBER: Question fot Amber 10 Benchmarks sychen (Thu Nov 27 2008 - 18:18:00 PST)
AMBER: Problems of MM/MM-GBSA calculations Sergey Samsonov (Thu Nov 27 2008 - 02:53:53 PST)
AMBER: antechamber and gaff for a homodimer rebeca (Thu Nov 27 2008 - 03:12:23 PST)
- Re: AMBER: antechamber and gaff for a homodimer Alan (Thu Nov 27 2008 - 04:27:31 PST)
  - Re: AMBER: antechamber and gaff for a homodimer rebeca (Thu Nov 27 2008 - 05:33:19 PST)
    - Re: AMBER: antechamber and gaff for a homodimer FyD (Thu Nov 27 2008 - 08:02:55 PST)
AMBER: seeking help regrading Zinc protein GBSA minimization S.Sundar Raman (Thu Nov 27 2008 - 04:32:08 PST)
- Re: AMBER: seeking help regrading Zinc protein GBSA minimization Carlos Simmerling (Fri Nov 28 2008 - 04:33:16 PST)
  - Re: AMBER: seeking help regrading Zinc protein GBSA minimization Sergey Samsonov (Mon Dec 01 2008 - 00:14:36 PST)
    - Re: AMBER: seeking help regrading Zinc protein GBSA minimization Carlos Simmerling (Mon Dec 01 2008 - 03:16:02 PST)
AMBER: Is there an easy way to calculate the electric field at the center of a group of atoms Ye Mei (Thu Nov 27 2008 - 07:12:51 PST)
- Re: AMBER: Is there an easy way to calculate the electric field at the center of a group of atoms David A. Case (Mon Dec 01 2008 - 07:34:47 PST)
AMBER: cis - trans isomerization Nina Fischer (Thu Nov 27 2008 - 06:39:21 PST)
AMBER: Heating up Francesco Pietra (Thu Nov 27 2008 - 10:29:30 PST)
- Re: AMBER: Heating up Carlos Simmerling (Fri Nov 28 2008 - 04:30:29 PST)
  - Re: AMBER: Heating up Francesco Pietra (Fri Nov 28 2008 - 07:57:49 PST)
AMBER: normal-vector of a plane with 'corrplane' Gert Kiss (Thu Nov 27 2008 - 12:28:46 PST)
AMBER: Who success in setting up a covalent bond between ligand and enzyme with tLeap ? jitrayut jitonnom (Thu Nov 27 2008 - 17:26:54 PST)
- Re: AMBER: Who success in setting up a covalent bond between ligand and enzyme with tLeap ? Guillermo Mulliert Carlín (Thu Nov 27 2008 - 23:20:30 PST)
  - Re: AMBER: Who success in setting up a covalent bond between ligand and enzyme with tLeap ? jitrayut jitonnom (Fri Nov 28 2008 - 15:34:43 PST)
    - Re: AMBER: Who success in setting up a covalent bond between ligand and enzyme with tLeap ? FyD (Fri Nov 28 2008 - 23:30:19 PST)
- RE: AMBER: Who success in setting up a covalent bond between ligand and enzyme with tLeap ? Ross Walker (Fri Nov 28 2008 - 18:11:49 PST)
AMBER: N(CN2)- ion babak minoofar (Fri Nov 28 2008 - 05:12:26 PST)
- Re: AMBER: N(CN2)- ion David A. Case (Mon Dec 01 2008 - 06:47:14 PST)
- Re: AMBER: N(CN2)- ion babak minoofar (Thu Dec 04 2008 - 08:00:58 PST)
  - Re: AMBER: N(CN2)- ion David A. Case (Fri Dec 05 2008 - 04:23:05 PST)
- Re: AMBER: N(CN2)- ion babak minoofar (Fri Dec 12 2008 - 01:29:54 PST)
AMBER: Questions on TIP4P model? Chin, Keith B (Fri Nov 28 2008 - 11:20:38 PST)
- Re: AMBER: Questions on TIP4P model? Carlos Simmerling (Fri Nov 28 2008 - 12:03:14 PST)
- Re: AMBER: Questions on TIP4P model? David A. Case (Sat Nov 29 2008 - 11:21:01 PST)
  - RE: AMBER: Questions on TIP4P model? Chin, Keith B (Sat Nov 29 2008 - 15:43:21 PST)
AMBER: RED vIII-lack of charges in mol2 Neha Gandhi (Sat Nov 29 2008 - 06:24:30 PST)
- Re: AMBER: RED vIII-lack of charges in mol2 FyD (Sat Nov 29 2008 - 08:23:34 PST)
AMBER: QM/MM and unpaired spin Markus Kaukonen (Sun Nov 30 2008 - 23:30:02 PST)
- RE: AMBER: QM/MM and unpaired spin Ross Walker (Mon Dec 01 2008 - 08:40:20 PST)
- Re: AMBER: QM/MM and unpaired spin Gustavo Seabra (Tue Dec 02 2008 - 19:11:25 PST)
  - RE: AMBER: QM/MM and unpaired spin Ross Walker (Tue Dec 02 2008 - 19:42:37 PST)
    - AMBER: DNA-Gold parameters Xioling Chuang (Wed Dec 03 2008 - 03:37:55 PST)
    - Re: AMBER: QM/MM and unpaired spin Gustavo Seabra (Wed Dec 03 2008 - 05:53:00 PST)
AMBER: reg.dnasaveparm&tcrd balaji nagarajan (Mon Dec 01 2008 - 06:05:52 PST)
- Re: AMBER: reg.dnasaveparm&tcrd David A. Case (Mon Dec 01 2008 - 06:29:41 PST)
  - RE: AMBER: reg.dnasaveparm&tcrd balaji nagarajan (Mon Dec 01 2008 - 08:51:00 PST)
- RE: AMBER: reg.dnasaveparm&tcrd Ross Walker (Mon Dec 01 2008 - 08:44:57 PST)
  - RE: AMBER: reg.dnasaveparm&tcrd balaji nagarajan (Mon Dec 01 2008 - 08:56:44 PST)
AMBER: How do you evaluate forces on a fixed atom? Bill K (Mon Dec 01 2008 - 10:45:42 PST)
- Re: AMBER: How do you evaluate forces on a fixed atom? David A. Case (Tue Dec 02 2008 - 06:39:37 PST)
  - Re: AMBER: How do you evaluate forces on a fixed atom? Bill K (Tue Dec 02 2008 - 17:54:35 PST)
    - [AMBER] Re: AMBER: How do you evaluate forces on a fixed atom? Bill Kowallis (Wed Feb 18 2009 - 17:55:47 PST)
AMBER: makeDIST_RST error -- no map function for HH TYR Ryan Pavlovicz (Mon Dec 01 2008 - 11:30:01 PST)
- Re: AMBER: makeDIST_RST error -- no map function for HH TYR David A. Case (Mon Dec 01 2008 - 13:22:46 PST)
AMBER: Variable PBCAL values in MM-PBSA calculations Daniel Oehme (Mon Dec 01 2008 - 15:45:23 PST)
- RE: AMBER: Variable PBCAL values in MM-PBSA calculations Ray Luo (Mon Dec 01 2008 - 17:55:37 PST)
  - Re: AMBER: Variable PBCAL values in MM-PBSA calculations Daniel Oehme (Wed Dec 03 2008 - 22:34:42 PST)
    - RE: AMBER: Variable PBCAL values in MM-PBSA calculations Ray Luo (Thu Dec 04 2008 - 11:06:45 PST)
    - Re: AMBER: Variable PBCAL values in MM-PBSA calculations Daniel Oehme (Sun Dec 07 2008 - 21:56:58 PST)
AMBER: Simulating peptide linkers with AMBER Sasha Buzko (Tue Dec 02 2008 - 12:03:42 PST)
AMBER: MM/GBSA Error during deccomposition N.R. Jena (Wed Dec 03 2008 - 04:01:04 PST)
- Re: AMBER: MM/GBSA Error during deccomposition Barbault Florent (Wed Dec 03 2008 - 12:32:14 PST)
  - Re: AMBER: MM/GBSA Error during deccomposition N.R. Jena (Thu Dec 04 2008 - 03:01:36 PST)
    - Re: AMBER: MM/GBSA Error during deccomposition Cristina Sisu (Thu Dec 04 2008 - 03:27:48 PST)
    - Re: AMBER: MM/GBSA Error during deccomposition N.R. Jena (Thu Dec 04 2008 - 05:08:45 PST)
    - Re: AMBER: MM/GBSA Error during deccomposition N.R. Jena (Thu Dec 04 2008 - 20:13:44 PST)
AMBER: ptraj: how to select all non-hydrogen atoms Mingfeng Yang (Wed Dec 03 2008 - 11:37:00 PST)
- Re: AMBER: ptraj: how to select all non-hydrogen atoms Hannes Kopitz (Wed Dec 03 2008 - 12:27:33 PST)
  - AMBER: unable to open pdb file Taufik Al-Sarraj (Wed Dec 03 2008 - 18:44:09 PST)
    - Re: AMBER: unable to open pdb file David A. Case (Thu Dec 04 2008 - 03:41:32 PST)
AMBER: reg unstability of structure in md balaji nagarajan (Wed Dec 03 2008 - 20:17:51 PST)
- Re: AMBER: reg unstability of structure in md Carlos Simmerling (Thu Dec 04 2008 - 03:28:12 PST)
  - RE: AMBER: reg unstability of structure in md balaji nagarajan (Thu Dec 04 2008 - 20:32:21 PST)
    - Re: AMBER: reg unstability of structure in md N.R. Jena (Thu Dec 04 2008 - 22:48:50 PST)
    - Re: AMBER: reg unstability of structure in md Carlos Simmerling (Fri Dec 05 2008 - 03:41:40 PST)
AMBER: makeDIST_RST computation of r3 value with IAT < 0 Ryan Pavlovicz (Wed Dec 03 2008 - 15:13:32 PST)
- Re: AMBER: makeDIST_RST computation of r3 value with IAT < 0 David A. Case (Fri Dec 05 2008 - 08:45:20 PST)
AMBER: side chain expression Yunierkis Perez Castillo (Thu Dec 04 2008 - 08:43:14 PST)
AMBER: LINMIN error in geometrically constrained minimization . MM-PB/SA conditions Alexander Metz (Thu Dec 04 2008 - 09:04:03 PST)
AMBER: compiling PMEMD spits out lots of -tp not supported and hangs . pmemd.f90 Hazard, E. Starr (Fri Dec 05 2008 - 12:12:54 PST)
- Re: AMBER: compiling PMEMD spits out lots of -tp not supported and hangs . pmemd.f90 David Watson (Fri Dec 05 2008 - 12:32:45 PST)
  - Re: AMBER: compiling PMEMD spits out lots of -tp not supported and hangs @ pmemd.f90 Starr Hazard (Fri Dec 05 2008 - 13:10:11 PST)
- Re: AMBER: compiling PMEMD spits out lots of -tp not supported and hangs . pmemd.f90 Robert Duke (Fri Dec 05 2008 - 12:32:04 PST)
- Re: AMBER: compiling PMEMD spits out lots of -tp not supported and hangs . pmemd.f90 Robert Duke (Fri Dec 05 2008 - 13:15:55 PST)
  - Re: AMBER: compiling PMEMD spits out lots of -tp not supported and hangs . pmemd.f90 David Watson (Fri Dec 05 2008 - 13:53:15 PST)
    - Re: AMBER: compiling PMEMD spits out lots of -tp not supported and hangs @ pmemd.f90 Starr Hazard (Fri Dec 05 2008 - 14:11:58 PST)
    - Re: AMBER: compiling PMEMD spits out lots of -tp not supported and hangs . pmemd.f90 David Watson (Fri Dec 05 2008 - 14:30:32 PST)
- Re: AMBER: compiling PMEMD spits out lots of -tp not supported and hangs . pmemd.f90 Robert Duke (Fri Dec 05 2008 - 14:46:57 PST)
- Re: AMBER: compiling PMEMD spits out lots of -tp not supported and hangs . pmemd.f90 sychen (Fri Dec 05 2008 - 19:46:20 PST)
Re: AMBER: compiling PMEMD spits out lots of -tp not supported and hangs @ pmemd.f90 Starr Hazard (Fri Dec 05 2008 - 12:53:14 PST)
AMBER: regad-tutorial-dna-polyAT balaji nagarajan (Sun Dec 07 2008 - 20:45:10 PST)
- Re: AMBER: regad-tutorial-dna-polyAT jani sahil (Sun Dec 07 2008 - 21:13:30 PST)
  - RE: AMBER: regad-tutorial-dna-polyAT balaji nagarajan (Sun Dec 07 2008 - 22:40:39 PST)
AMBER: GB offset for proteins Sally Pias (Sun Dec 07 2008 - 21:14:58 PST)
- Re: AMBER: GB offset for proteins David A. Case (Wed Dec 24 2008 - 11:11:21 PST)
AMBER: reg-adding ions balaji nagarajan (Mon Dec 08 2008 - 00:20:05 PST)
- RE: AMBER: reg-adding ions Ross Walker (Mon Dec 08 2008 - 08:33:18 PST)
  - RE: AMBER: reg-adding ions balaji nagarajan (Mon Dec 08 2008 - 20:32:14 PST)
    - RE: AMBER: reg-adding ions Ross Walker (Tue Dec 09 2008 - 07:05:04 PST)
AMBER: interaction energies Marina Grabar (Mon Dec 08 2008 - 03:29:36 PST)
- Re: AMBER: interaction energies David A. Case (Mon Dec 08 2008 - 08:59:28 PST)
  - AMBER: prep files ATP-MG++ and for phosphorylated threonine mirzo.jinr.ru (Tue Dec 09 2008 - 00:01:42 PST)
    - Re: AMBER: prep files ATP-MG++ and for phosphorylated threonine Anselm Horn (Tue Dec 09 2008 - 02:06:17 PST)
    - Re: AMBER: prep files ATP-MG++ and for phosphorylated threonine mirzo.jinr.ru (Tue Dec 09 2008 - 02:23:08 PST)
AMBER: Problem with MMPBSA Daniel Emery (Mon Dec 08 2008 - 08:28:22 PST)
- RE: AMBER: Problem with MMPBSA Ray Luo (Mon Dec 08 2008 - 11:47:15 PST)
AMBER: MM-PBSA : bad atom type: ZN jitrayut jitonnom (Mon Dec 08 2008 - 08:51:12 PST)
AMBER: RESP GAUSSIAN AMBER SilasConnor.gmx.at (Mon Dec 08 2008 - 10:31:24 PST)
- Re: AMBER: RESP GAUSSIAN AMBER FyD (Thu Dec 11 2008 - 03:42:20 PST)
  - RE: AMBER: RESP GAUSSIAN AMBER Ross Walker (Thu Dec 11 2008 - 20:00:27 PST)
    - AMBER: DNA: GB solvent with salt Catein Catherine (Fri Dec 12 2008 - 01:31:13 PST)
    - Re: AMBER: DNA: GB solvent with salt Carlos Simmerling (Fri Dec 12 2008 - 03:33:14 PST)
    - Re: AMBER: RESP GAUSSIAN AMBER Francesco Pietra (Fri Dec 12 2008 - 03:13:13 PST)
    - Re: AMBER: RESP GAUSSIAN AMBER FyD (Fri Dec 12 2008 - 07:16:01 PST)
    - RE: AMBER: RESP GAUSSIAN AMBER FyD (Fri Dec 12 2008 - 06:25:06 PST)
    - RE: AMBER: RESP GAUSSIAN AMBER Ross Walker (Fri Dec 12 2008 - 11:04:49 PST)
    - RE: AMBER: RESP GAUSSIAN AMBER Piotr Cieplak (Fri Dec 12 2008 - 12:12:20 PST)
    - RE: AMBER: RESP GAUSSIAN AMBER FyD (Fri Dec 12 2008 - 23:23:10 PST)
    - Re: AMBER: RESP GAUSSIAN AMBER Brent Krueger (Sun Dec 14 2008 - 18:52:14 PST)
    - RE: AMBER: RESP GAUSSIAN AMBER Ross Walker (Mon Dec 15 2008 - 09:36:27 PST)
    - Re: AMBER: RESP GAUSSIAN AMBER M. L. Dodson (Mon Dec 15 2008 - 09:52:48 PST)
    - Re: AMBER: RESP GAUSSIAN AMBER FyD (Mon Dec 15 2008 - 12:41:24 PST)
    - Re: AMBER: RESP GAUSSIAN AMBER M. L. Dodson (Mon Dec 15 2008 - 13:36:08 PST)
    - Re: AMBER: RESP GAUSSIAN AMBER FyD (Mon Dec 15 2008 - 14:05:46 PST)
    - RE: AMBER: RESP GAUSSIAN AMBER FyD (Wed Dec 17 2008 - 01:12:38 PST)
    - RE: AMBER: RESP GAUSSIAN AMBER FyD (Sat Dec 13 2008 - 00:02:23 PST)
AMBER: RE: bugfix 11 & 12 Ross Walker (Mon Dec 08 2008 - 13:12:42 PST)
AMBER: how to add new solvent type in Amber iccy liu (Mon Dec 08 2008 - 16:23:11 PST)
- Re: AMBER: how to add new solvent type in Amber David A. Case (Wed Dec 10 2008 - 15:18:56 PST)
  - AMBER: solvent box again iccy liu (Tue Dec 16 2008 - 10:32:32 PST)
    - RE: AMBER: solvent box again Ross Walker (Tue Dec 16 2008 - 10:57:01 PST)
    - RE: AMBER: solvent box again iccy liu (Thu Dec 18 2008 - 11:41:41 PST)
    - Re: AMBER: solvent box again David A. Case (Tue Dec 16 2008 - 12:02:05 PST)
AMBER: Radial Distribution Function prabhakar g (Mon Dec 08 2008 - 18:37:52 PST)
- Re: AMBER: Radial Distribution Function Gustavo Seabra (Tue Dec 09 2008 - 07:38:54 PST)
  - Re: AMBER: Radial Distribution Function prabhakar g (Tue Dec 09 2008 - 19:33:27 PST)
    - Re: AMBER: Radial Distribution Function Gustavo Seabra (Wed Dec 10 2008 - 05:49:42 PST)
    - Re: AMBER: Radial Distribution Function prabhakar g (Fri Dec 12 2008 - 18:31:48 PST)
    - Re: AMBER: Radial Distribution Function Gustavo Seabra (Sun Dec 14 2008 - 23:41:02 PST)
AMBER: (no subject) waleed zalloum (Tue Dec 09 2008 - 04:22:39 PST)
- RE: AMBER: (no subject) Ross Walker (Tue Dec 09 2008 - 07:07:18 PST)
  - RE: AMBER: (no subject) Scott Brozell (Tue Dec 09 2008 - 07:17:06 PST)
AMBER: Constant pH dynamics Beale, John (Tue Dec 09 2008 - 04:51:39 PST)
- Re: AMBER: Constant pH dynamics Adrian Roitberg (Tue Dec 09 2008 - 08:24:17 PST)
- Re: AMBER: Constant pH dynamics David A. Case (Tue Dec 09 2008 - 07:27:51 PST)
AMBER: parallel installation balaji nagarajan (Tue Dec 09 2008 - 19:56:20 PST)
- Re: AMBER: parallel installation David A. Case (Wed Dec 10 2008 - 05:09:00 PST)
AMBER: forrtl severe(174) error with minimization and md john smith (Tue Dec 09 2008 - 22:20:57 PST)
- RE: AMBER: forrtl severe(174) error with minimization and md Ross Walker (Wed Dec 10 2008 - 07:57:42 PST)
  - Re: AMBER: forrtl severe(174) error with minimization and md john smith (Mon Dec 15 2008 - 00:46:56 PST)
AMBER: reg-antichamber run balaji nagarajan (Wed Dec 10 2008 - 09:08:17 PST)
- Re: AMBER: reg-antichamber run David A. Case (Wed Dec 10 2008 - 15:14:31 PST)
  - Re: AMBER: reg-antichamber run FyD (Thu Dec 11 2008 - 01:57:26 PST)
AMBER: Building Amber 10 with Intel MKL and compiler mini howto Ben Eisenbraun (Wed Dec 10 2008 - 09:45:04 PST)
AMBER: Running md using glycam in AMBER Neha Gandhi (Wed Dec 10 2008 - 23:15:54 PST)
- RE: AMBER: Running md using glycam in AMBER Matthew Tessier (Thu Dec 11 2008 - 12:52:28 PST)
AMBER: Distorted ring... Waqas Nasir (Thu Dec 11 2008 - 03:48:45 PST)
- Re: AMBER: Distorted ring... Carlos Simmerling (Thu Dec 11 2008 - 04:15:57 PST)
AMBER: tutorial A1, file missing readit.f ABEL Stephane 175950 (Thu Dec 11 2008 - 04:22:41 PST)
- Re: AMBER: tutorial A1, file missing readit.f David A. Case (Thu Dec 11 2008 - 05:19:38 PST)
AMBER: Pulling using restraintmask Dirar Homouz (Thu Dec 11 2008 - 12:30:00 PST)
- Re: AMBER: Pulling using restraintmask Alessandro Nascimento (Thu Dec 11 2008 - 12:58:51 PST)
AMBER: reg.building ions balaji nagarajan (Fri Dec 12 2008 - 02:40:07 PST)
- Re: AMBER: reg.building ions David A. Case (Fri Dec 12 2008 - 04:04:58 PST)
  - RE: AMBER: reg.building ions balaji nagarajan (Fri Dec 12 2008 - 04:14:57 PST)
    - Re: AMBER: reg.building ions David A. Case (Fri Dec 12 2008 - 04:42:28 PST)
AMBER: building new ions CHAMI F. (Fri Dec 12 2008 - 04:23:20 PST)
AMBER: ff99 (PK/IDIVF) saurabh agrawal (Fri Dec 12 2008 - 05:26:58 PST)
- Re: AMBER: ff99 (PK/IDIVF) Carlos Simmerling (Fri Dec 12 2008 - 06:05:11 PST)
  - RE: AMBER: ff99 (PK/IDIVF) Ross Walker (Fri Dec 12 2008 - 09:06:22 PST)
    - RE: AMBER: ff99 (PK/IDIVF) saurabh agrawal (Sun Dec 14 2008 - 10:29:39 PST)
    - Re: AMBER: ff99 (PK/IDIVF) Carlos Simmerling (Sun Dec 14 2008 - 10:38:23 PST)
    - Re: AMBER: ff99 (PK/IDIVF) saurabh agrawal (Tue Dec 16 2008 - 03:47:09 PST)
    - Re: AMBER: ff99 (PK/IDIVF) Carlos Simmerling (Tue Dec 16 2008 - 04:01:32 PST)
AMBER: ld: cannot find -lgcc_s moitrayee.mbu.iisc.ernet.in (Fri Dec 12 2008 - 05:52:08 PST)
- Re: AMBER: ld: cannot find -lgcc_s David A. Case (Fri Dec 12 2008 - 06:26:00 PST)
AMBER: reg.concentration of ions balaji nagarajan (Fri Dec 12 2008 - 08:34:49 PST)
AMBER: RESP charge derivation using the Ante_R.E.D. and R.E.D. III programs... problems ABEL Stephane 175950 (Fri Dec 12 2008 - 08:41:19 PST)
- Re: AMBER: RESP charge derivation using the Ante_R.E.D. and R.E.D. III programs... problems Jifeng Wang (Fri Dec 12 2008 - 08:50:56 PST)
  - Re: AMBER: RESP charge derivation using the Ante_R.E.D. and R.E.D. III programs... problems FyD (Fri Dec 12 2008 - 09:14:05 PST)
AMBER: RESP charge derivation using the Ante_R.E.D. and R.E.D. III programs... problems ABEL Stephane 175950 (Fri Dec 12 2008 - 09:33:44 PST)
- Re: AMBER: RESP charge derivation using the Ante_R.E.D. and R.E.D. III programs... problems FyD (Fri Dec 12 2008 - 10:24:25 PST)
AMBER: sgi4700 the time of MD simulation is 30 minute for 1ps about 2500 atom using 1cpu llduan.itcc.nju.edu.cn (Sat Dec 13 2008 - 06:36:45 PST)
- Re: AMBER: sgi4700 the time of MD simulation is 30 minute for 1ps about 2500 atom using 1cpu steinbrt.rci.rutgers.edu (Sat Dec 13 2008 - 10:58:18 PST)
AMBER: problem with toturial A3 (MM-PBSA) Maryam Hamzehee (Sat Dec 13 2008 - 07:22:58 PST)
- Re: AMBER: problem with toturial A3 (MM-PBSA) Carlos Simmerling (Sat Dec 13 2008 - 07:35:13 PST)
  - Re: AMBER: problem with toturial A3 (MM-PBSA) Maryam Hamzehee (Sun Dec 14 2008 - 03:25:00 PST)
    - Re: AMBER: problem with toturial A3 (MM-PBSA) Carlos Simmerling (Tue Dec 16 2008 - 05:57:42 PST)
AMBER: Compiling AMBER 10 on SGI MIPS and Sun SPARC Atro Tossavainen (Sat Dec 13 2008 - 13:18:45 PST)
- Re: AMBER: Compiling AMBER 10 on SGI MIPS and Sun SPARC Atro Tossavainen (Sat Dec 13 2008 - 14:12:30 PST)
- Re: AMBER: Compiling AMBER 10 on SGI MIPS and Sun SPARC David A. Case (Sun Dec 14 2008 - 06:20:36 PST)
  - Re: AMBER: Compiling AMBER 10 on SGI MIPS and Sun SPARC Atro Tossavainen (Sun Dec 14 2008 - 12:11:53 PST)
    - Re: AMBER: Compiling AMBER 10 on SGI MIPS and Sun SPARC Atro Tossavainen (Mon Dec 15 2008 - 01:36:09 PST)
    - Re: AMBER: Compiling AMBER 10 on SGI MIPS and Sun SPARC Atro Tossavainen (Mon Dec 15 2008 - 02:06:51 PST)
    - Re: AMBER: Compiling AMBER 10 on SGI MIPS and Sun SPARC Atro Tossavainen (Mon Dec 15 2008 - 03:12:53 PST)
    - Re: AMBER: Compiling AMBER 10 on SGI MIPS and Sun SPARC David A. Case (Mon Dec 15 2008 - 04:54:33 PST)
    - Re: AMBER: Compiling AMBER 10 on SGI MIPS and Sun SPARC Atro Tossavainen (Mon Dec 15 2008 - 06:27:05 PST)
AMBER: Calculating the dielectrostatic constant from simulation? Jeffrey (Sun Dec 14 2008 - 23:07:25 PST)
- Re: AMBER: Calculating the dielectrostatic constant from simulation? Adrian Roitberg (Mon Dec 15 2008 - 05:44:09 PST)
  - Re: Re: AMBER: Calculating the dielectrostatic constant from simulation? Jeffrey (Mon Dec 15 2008 - 17:34:54 PST)
AMBER: pressure component chengtao.sjtu.edu.cn (Mon Dec 15 2008 - 00:17:21 PST)
- Re: AMBER: pressure component David A. Case (Mon Dec 15 2008 - 04:43:44 PST)
  - Re: AMBER: pressure component chengtao.sjtu.edu.cn (Tue Dec 16 2008 - 00:42:00 PST)
AMBER: AMBER 10 PMEMD / SGI_MIPS Atro Tossavainen (Mon Dec 15 2008 - 04:51:16 PST)
- Re: AMBER: AMBER 10 PMEMD / SGI_MIPS Robert Duke (Mon Dec 15 2008 - 05:45:34 PST)
  - Re: AMBER: AMBER 10 PMEMD / SGI_MIPS Atro Tossavainen (Mon Dec 15 2008 - 06:40:41 PST)
    - Re: AMBER: AMBER 10 PMEMD / SGI_MIPS Robert Duke (Mon Dec 15 2008 - 07:26:12 PST)
    - Re: AMBER: AMBER 10 PMEMD / SGI_MIPS Atro Tossavainen (Tue Dec 16 2008 - 04:17:48 PST)
    - RE: AMBER: AMBER 10 PMEMD / SGI_MIPS Ross Walker (Tue Dec 16 2008 - 08:16:11 PST)
AMBER: Initial velocities based on date and time are NOT changing ? Markus Kaukonen (Mon Dec 15 2008 - 05:14:38 PST)
- Re: AMBER: Initial velocities based on date and time are NOT changing ? David A. Case (Mon Dec 15 2008 - 05:38:03 PST)
  - Re: AMBER: Initial velocities based on date and time are NOT changing ? Markus Kaukonen (Tue Dec 16 2008 - 01:41:40 PST)
AMBER: building new ions CHAMI F. (Mon Dec 15 2008 - 05:50:50 PST)
- Re: AMBER: building new ions FyD (Mon Dec 15 2008 - 06:09:04 PST)
AMBER: launching a job works with sander.MPI and fail with pmemd.MPI unknown charset (Mon Dec 15 2008 - 06:41:55 PST)
- RE: AMBER: launching a job works with sander.MPI and fail with pmemd.MPI Ross Walker (Mon Dec 15 2008 - 07:18:04 PST)
  - RE: AMBER: launching a job works with sander.MPI and fail with pmemd.MPI unknown charset (Tue Dec 16 2008 - 04:57:05 PST)
- Fw: AMBER: launching a job works with sander.MPI and fail with pmemd.MPI Robert Duke (Tue Dec 16 2008 - 06:56:13 PST)
  - AMBER: install amber 10 on linux with openSUSE 10.2 (x86-64) wl2290.columbia.edu (Fri Dec 19 2008 - 10:16:39 PST)
    - Re: AMBER: install amber 10 on linux with openSUSE 10.2 (x86-64) David A. Case (Sat Dec 20 2008 - 15:48:23 PST)
    - Re: AMBER: install amber 10 on linux with openSUSE 10.2 (x86-64) wl2290.columbia.edu (Mon Dec 22 2008 - 15:26:10 PST)
    - Re: AMBER: install amber 10 on linux with openSUSE 10.2 (x86-64) David A. Case (Tue Dec 23 2008 - 05:26:15 PST)
    - Re: AMBER: install amber 10 on linux with openSUSE 10.2 (x86-64) wl2290.columbia.edu (Tue Dec 23 2008 - 07:52:39 PST)
    - Re: AMBER: install amber 10 on linux with openSUSE 10.2 (x86-64) wl2290.columbia.edu (Tue Dec 30 2008 - 09:54:58 PST)
    - Re: AMBER: install amber 10 on linux with openSUSE 10.2 (x86-64) David A. Case (Tue Dec 30 2008 - 13:31:56 PST)
    - Re: AMBER: install amber 10 on linux with openSUSE 10.2 (x86-64) wl2290.columbia.edu (Tue Dec 30 2008 - 14:15:59 PST)
    - Re: AMBER: install amber 10 on linux with openSUSE 10.2 (x86-64) Scott Brozell (Tue Jan 06 2009 - 11:23:29 PST)
- Re: AMBER: launching a job works with sander.MPI and fail with pmemd.MPI Robert Duke (Tue Dec 16 2008 - 05:55:47 PST)
  - AMBER: comparison of MD trajectories recorded with pmemd and sander unknown charset (Wed Dec 17 2008 - 06:04:26 PST)
    - Re: AMBER: comparison of MD trajectories recorded with pmemd and sander Carlos Simmerling (Wed Dec 17 2008 - 07:12:32 PST)
    - Re: AMBER: comparison of MD trajectories recorded with pmemd and sander Adrian Roitberg (Wed Dec 17 2008 - 08:40:23 PST)
    - Re: AMBER: comparison of MD trajectories recorded with pmemd and sander Thomas Cheatham III (Wed Dec 17 2008 - 09:16:47 PST)
    - Re: AMBER: comparison of MD trajectories recorded with pmemd and sander Robert Duke (Wed Dec 17 2008 - 08:42:07 PST)
    - RE: AMBER: comparison of MD trajectories recorded with pmemd and sander Ross Walker (Wed Dec 17 2008 - 09:01:37 PST)
    - Re: AMBER: comparison of MD trajectories recorded with pmemd and sander Robert Duke (Wed Dec 17 2008 - 09:18:46 PST)
    - Fw: AMBER: comparison of MD trajectories recorded with pmemd and sander Robert Duke (Wed Dec 17 2008 - 09:20:40 PST)
    - Re: AMBER: comparison of MD trajectories recorded with pmemd and sander Robert Duke (Wed Dec 17 2008 - 09:02:25 PST)
    - Re: AMBER: comparison of MD trajectories recorded with pmemd and sander Gustavo Seabra (Thu Dec 18 2008 - 06:58:13 PST)
AMBER: relative weight of RDC constraints David Witte (Mon Dec 15 2008 - 08:21:34 PST)
- Re: AMBER: relative weight of RDC constraints David A. Case (Mon Dec 15 2008 - 08:44:19 PST)
  - AMBER: distance restraint in minimization Taufik Al-Sarraj (Tue Dec 16 2008 - 10:46:22 PST)
    - Re: AMBER: distance restraint in minimization David A. Case (Tue Dec 16 2008 - 11:57:44 PST)
    - Re: AMBER: distance restraint in minimization Taufik Al-Sarraj (Tue Dec 16 2008 - 13:16:43 PST)
    - AMBER: distance restraint in minimization Taufik Al-Sarraj (Tue Dec 16 2008 - 14:44:35 PST)
    - Re: AMBER: distance restraint in minimization luzhenw1.msu.edu (Wed Dec 17 2008 - 07:10:49 PST)
    - Re: AMBER: distance restraint in minimization Taufik Al-Sarraj (Wed Dec 17 2008 - 09:44:55 PST)
    - Re: AMBER: distance restraint in minimization luzhenw1.msu.edu (Wed Dec 17 2008 - 10:17:28 PST)
    - Re: AMBER: distance restraint in minimization David A. Case (Wed Dec 17 2008 - 10:49:56 PST)
    - Re: AMBER: distance restraint in minimization Taufik Al-Sarraj (Wed Dec 17 2008 - 11:34:22 PST)
    - Re: AMBER: distance restraint in minimization Taufik Al-Sarraj (Wed Dec 17 2008 - 12:16:18 PST)
    - AMBER: distance restraint between non-bonded molecules Taufik Al-Sarraj (Wed Dec 17 2008 - 16:13:36 PST)
    - Re: AMBER: distance restraint between non-bonded molecules Carlos Simmerling (Thu Dec 18 2008 - 03:45:13 PST)
    - Re: AMBER: distance restraint between non-bonded molecules Taufik Al-Sarraj (Thu Dec 18 2008 - 08:49:51 PST)
    - Re: AMBER: distance restraint between non-bonded molecules Ilyas Yildirim (Thu Dec 18 2008 - 11:29:30 PST)
    - Re: AMBER: distance restraint between non-bonded molecules Taufik Al-Sarraj (Thu Dec 18 2008 - 12:41:05 PST)
    - Re: AMBER: distance restraint between non-bonded molecules Ilyas Yildirim (Thu Dec 18 2008 - 13:29:26 PST)
    - Re: AMBER: distance restraint between non-bonded molecules Taufik Al-Sarraj (Fri Dec 19 2008 - 07:14:51 PST)
    - Re: AMBER: distance restraint between non-bonded molecules Ilyas Yildirim (Fri Dec 19 2008 - 07:22:32 PST)
    - Re: AMBER: distance restraint between non-bonded molecules Carlos Simmerling (Fri Dec 19 2008 - 07:24:09 PST)
    - Re: AMBER: distance restraint in minimization Taufik Al-Sarraj (Wed Dec 17 2008 - 10:52:01 PST)
    - Re: AMBER: distance restraint in minimization Jifeng Wang (Wed Dec 17 2008 - 10:16:08 PST)
    - Re: AMBER: distance restraint in minimization Taufik Al-Sarraj (Wed Dec 17 2008 - 10:15:24 PST)
AMBER: RESP charge derivation using the Ante_R.E.D. and R.E.D. III ABEL Stephane 175950 (Tue Dec 16 2008 - 03:28:56 PST)
- Re: AMBER: RESP charge derivation using the Ante_R.E.D. and R.E.D. III FyD (Tue Dec 16 2008 - 04:17:15 PST)
AMBER: alascan MUTANT_KEEP error Larry Layne (Tue Dec 16 2008 - 11:07:51 PST)
AMBER: restraintmask - reference file is not working Dirar Homouz (Tue Dec 16 2008 - 16:05:24 PST)
- Re: AMBER: restraintmask - reference file is not working Carlos Simmerling (Tue Dec 16 2008 - 16:38:14 PST)
  - RE: AMBER: restraintmask - reference file is not working Dirar Homouz (Tue Dec 16 2008 - 16:45:44 PST)
  - RE: AMBER: restraintmask - reference file is not working Dirar Homouz (Tue Dec 16 2008 - 16:51:08 PST)
    - Re: AMBER: restraintmask - reference file is not working Carlos Simmerling (Tue Dec 16 2008 - 17:05:03 PST)
    - RE: AMBER: restraintmask - reference file is not working Dirar Homouz (Wed Dec 17 2008 - 01:41:00 PST)
    - Re: AMBER: restraintmask - reference file is not working Carlos Simmerling (Wed Dec 17 2008 - 05:19:25 PST)
    - RE: AMBER: restraintmask - reference file is not working Dirar Homouz (Wed Dec 17 2008 - 11:40:48 PST)
    - Re: AMBER: restraintmask - reference file is not working Carlos Simmerling (Wed Dec 17 2008 - 11:51:35 PST)
    - Re: AMBER: restraintmask - reference file is not working Carlos Simmerling (Thu Dec 18 2008 - 04:14:27 PST)
    - RE: AMBER: restraintmask - reference file is not working Dirar Homouz (Thu Dec 18 2008 - 15:46:23 PST)
AMBER: unsubscribe amber Prem Prakash Pathak (Tue Dec 16 2008 - 19:09:54 PST)
AMBER: AMBER minimization problems Lili Peng (Tue Dec 16 2008 - 23:14:00 PST)
- RE: AMBER: AMBER minimization problems Ross Walker (Wed Dec 17 2008 - 08:18:06 PST)
  - Re: AMBER: AMBER minimization problems Lili Peng (Wed Dec 17 2008 - 08:35:58 PST)
    - RE: AMBER: AMBER minimization problems Ross Walker (Thu Dec 18 2008 - 09:46:45 PST)
    - Re: AMBER: AMBER minimization problems Lili Peng (Sat Dec 20 2008 - 15:53:54 PST)
- Re: AMBER: AMBER minimization problems Robert Duke (Sat Dec 20 2008 - 16:10:03 PST)
AMBER: from dihe parameters to torsional energy Jeffrey (Wed Dec 17 2008 - 01:15:17 PST)
- RE: AMBER: from dihe parameters to torsional energy Ross Walker (Wed Dec 17 2008 - 08:36:14 PST)
  - RE: AMBER: from dihe parameters to torsional energy Ilyas Yildirim (Wed Dec 17 2008 - 09:10:13 PST)
    - RE: AMBER: from dihe parameters to torsional energy Ross Walker (Wed Dec 17 2008 - 09:28:21 PST)
    - Re: RE: AMBER: from dihe parameters to torsional energy Jeffrey (Wed Dec 17 2008 - 18:18:29 PST)
AMBER: alascan error Larry Layne (Wed Dec 17 2008 - 12:19:22 PST)
AMBER: Hydroxide ion in POL3 water D.J. Cole (Thu Dec 18 2008 - 04:13:58 PST)
AMBER: Solvatebox problem musa özboyacı (Fri Dec 19 2008 - 02:24:56 PST)
- Re: AMBER: Solvatebox problem David A. Case (Fri Dec 19 2008 - 05:19:18 PST)
Re: AMBER: distance restraint between non-bonded molecules] Ilyas Yildirim (Fri Dec 19 2008 - 15:06:35 PST)
- Re: AMBER: distance restraint between non-bonded molecules] Taufik Al-Sarraj (Sat Dec 20 2008 - 10:44:43 PST)
  - AMBER: xleap (measureGeom) Taufik Al-Sarraj (Sat Dec 20 2008 - 13:02:56 PST)
    - Re: AMBER: xleap (measureGeom) Scott Brozell (Mon Dec 22 2008 - 14:10:46 PST)
  - Re: AMBER: distance restraint between non-bonded molecules] Ilyas Yildirim (Sun Dec 21 2008 - 19:08:38 PST)
    - AMBER: Re: Taufik Al-Sarraj (Mon Dec 22 2008 - 10:08:17 PST)
AMBER: idecomp=2 & RRES/LRES group specification In Hee Park (Fri Dec 19 2008 - 17:19:43 PST)
AMBER: amber 9 compilation error with mvapich and intel compilers Amit Bajaj (Sat Dec 20 2008 - 06:17:03 PST)
- Re: AMBER: amber 9 compilation error with mvapich and intel compilers David A. Case (Sat Dec 20 2008 - 14:42:28 PST)
  - Re: AMBER: amber 9 compilation error with mvapich and intel compilers Amit Bajaj (Sun Dec 21 2008 - 21:41:35 PST)
    - Re: AMBER: amber 9 compilation error with mvapich and intel compilers David A. Case (Mon Dec 22 2008 - 05:35:28 PST)
    - Re: AMBER: amber 9 compilation error with mvapich and intel compilers amit (Mon Dec 22 2008 - 09:12:41 PST)
    - RE: AMBER: amber 9 compilation error with mvapich and intel compilers Ross Walker (Mon Dec 22 2008 - 09:46:58 PST)
    - AMBER: Materials and methods Taufik Al-Sarraj (Mon Dec 22 2008 - 10:05:22 PST)
    - RE: AMBER: amber 9 compilation error with mvapich and intel compilers amit (Mon Dec 22 2008 - 10:15:34 PST)
AMBER: Error: tutorial one for md simulation of DNA Catein Catherine (Sun Dec 21 2008 - 19:33:41 PST)
- RE: AMBER: Error: tutorial one for md simulation of DNA balaji nagarajan (Sun Dec 21 2008 - 20:06:55 PST)
  - RE: AMBER: Error: tutorial one for md simulation of DNA Catein Catherine (Sun Dec 21 2008 - 21:12:32 PST)
AMBER: balaji nagarajan (Mon Dec 22 2008 - 05:36:38 PST)
- RE: AMBER: Ross Walker (Mon Dec 22 2008 - 08:41:23 PST)
Re: AMBER: amber 9 compilation error with mvapich and intelcompilers Robert Duke (Mon Dec 22 2008 - 06:36:33 PST)
AMBER: Playstation 3 Benchmarks Andrew Ring (Mon Dec 22 2008 - 16:40:44 PST)
- Re: AMBER: Playstation 3 Benchmarks David Watson (Mon Dec 22 2008 - 17:17:57 PST)
- RE: AMBER: Playstation 3 Benchmarks Ross Walker (Mon Dec 22 2008 - 17:20:38 PST)
AMBER: installation amber9 in fedora9 Vijay Manickam Achari (Mon Dec 22 2008 - 20:44:12 PST)
- Re: AMBER: installation amber9 in fedora9 Scott Brozell (Mon Dec 22 2008 - 21:41:22 PST)
- Re: AMBER: installation amber9 in fedora9 sobereva (Tue Dec 23 2008 - 01:52:00 PST)
AMBER: AMBER10 AMBERTools antechamber Starr Hazard (Tue Dec 23 2008 - 08:36:05 PST)
- Re: AMBER: AMBER10 AMBERTools antechamber M. L. Dodson (Tue Dec 23 2008 - 08:45:46 PST)
- RE: AMBER: AMBER10 AMBERTools antechamber Ross Walker (Tue Dec 23 2008 - 09:09:54 PST)
  - Re: AMBER: AMBER10 AMBERTools antechamber David A. Case (Tue Dec 23 2008 - 11:45:06 PST)
    - Re: AMBER: AMBER10 AMBERTools antechamber M. L. Dodson (Tue Dec 23 2008 - 12:00:13 PST)
AMBER: Switching function in NAMD musa özboyacı (Tue Dec 23 2008 - 11:52:37 PST)
- Re: AMBER: Switching function in NAMD Adrian Roitberg (Tue Dec 23 2008 - 11:56:58 PST)
AMBER: about mmpbsa out data ecustipp (Tue Dec 23 2008 - 18:21:22 PST)
- Re: AMBER: about mmpbsa out data steinbrt.rci.rutgers.edu (Tue Dec 23 2008 - 20:53:02 PST)
  - Re:Re: AMBER: about mmpbsa out data ecustipp (Wed Dec 24 2008 - 01:11:50 PST)
AMBER: installation amber9 in fedora9 using bash shell Vijay Manickam Achari (Tue Dec 23 2008 - 20:05:28 PST)
- Re: AMBER: installation amber9 in fedora9 using bash shell David A. Case (Wed Dec 24 2008 - 11:07:35 PST)
AMBER: How to build a cubic box of a newly synthesized compound? Jeffrey (Tue Dec 23 2008 - 22:34:13 PST)
- Re: AMBER: How to build a cubic box of a newly synthesized compound? M. L. Dodson (Wed Dec 24 2008 - 09:45:23 PST)
AMBER: xleap error Vijay Manickam Achari (Wed Dec 24 2008 - 01:58:17 PST)
- Re: AMBER: xleap error David A. Case (Wed Dec 24 2008 - 11:02:11 PST)
AMBER: Beale, John (Wed Dec 24 2008 - 05:19:48 PST)
- Re: AMBER: Zhiguo Liu (Sat Jul 09 2005 - 01:39:43 PDT)
AMBER: mpirun Permission denied. drugdesign (Wed Dec 24 2008 - 22:49:31 PST)
- Re: AMBER: mpirun Permission denied. Jackie. J. Shen (Tue Dec 30 2008 - 18:32:17 PST)
  - Re: AMBER: mpirun Permission denied. David Watson (Tue Dec 30 2008 - 21:04:40 PST)
AMBER: a question about ff03ua oguz gurbulak (Thu Dec 25 2008 - 06:06:33 PST)
- Re: AMBER: a question about ff03ua David A. Case (Thu Dec 25 2008 - 13:01:56 PST)
  - Re: AMBER: a question about ff03ua oguz gurbulak (Fri Jan 02 2009 - 07:30:46 PST)
    - Re: AMBER: a question about ff03ua David A. Case (Fri Jan 02 2009 - 08:35:15 PST)
    - Re: AMBER: a question about ff03ua FyD (Fri Jan 02 2009 - 12:20:37 PST)
AMBER: definition of dihedral in amber Jeffrey (Thu Dec 25 2008 - 07:38:38 PST)
AMBER: vertex atom mismatch ecustipp (Fri Dec 26 2008 - 02:09:45 PST)
AMBER: (no subject) Rajendra P. OJHA (Fri Dec 26 2008 - 04:35:12 PST)
- Re: AMBER: (no subject) ecustipp.163.com (Sun Dec 28 2008 - 23:58:20 PST)
AMBER: SMD-related questions Alessandro Nascimento (Mon Dec 29 2008 - 05:07:05 PST)
- Re: AMBER: SMD-related questions M. L. Dodson (Mon Dec 29 2008 - 10:25:19 PST)
- Re: AMBER: SMD-related questions Jackie. J. Shen (Tue Dec 30 2008 - 18:27:16 PST)
- Re: AMBER: SMD-related questions Gustavo Seabra (Fri Jan 02 2009 - 05:21:53 PST)
AMBER: mwcovar limit? Carra, Claudio (JSC-SK)[USRA] (Mon Dec 29 2008 - 14:31:27 PST)
- RE: AMBER: mwcovar limit? Ross Walker (Wed Dec 31 2008 - 20:44:33 PST)
AMBER: FAD RESP charges and parameters Cenk $Jenk$ Andac (Mon Dec 29 2008 - 14:51:49 PST)
- Re: AMBER: FAD RESP charges and parameters FyD (Tue Dec 30 2008 - 00:45:01 PST)
  - Re: AMBER: FAD RESP charges and parameters Cenk $Jenk$ Andac (Tue Dec 30 2008 - 04:28:41 PST)
    - Re: AMBER: FAD RESP charges and parameters FyD (Tue Dec 30 2008 - 06:19:15 PST)
    - Re: AMBER: FAD RESP charges and parameters Cenk $Jenk$ Andac (Tue Dec 30 2008 - 08:03:17 PST)
AMBER: mdout file details aneesh cna (Mon Dec 29 2008 - 22:20:40 PST)
- Re: AMBER: mdout file details David A. Case (Wed Dec 31 2008 - 08:50:05 PST)
AMBER: periodic boundary Sally Pias (Wed Dec 31 2008 - 00:37:25 PST)
AMBER: RMS plot Beale, John (Wed Dec 31 2008 - 11:11:39 PST)
- Re: AMBER: RMS plot Carlos Simmerling (Fri Jan 02 2009 - 06:08:44 PST)
  - RE: AMBER: RMS plot Duggan, Brendan M. (Tue Jan 06 2009 - 11:54:04 PST)
    - Re: AMBER: RMS plot Carlos Simmerling (Tue Jan 06 2009 - 11:57:50 PST)
AMBER: energy jumps during molecule minimization Paul Ledbetter (Thu Jan 01 2009 - 19:33:30 PST)
- Re: AMBER: energy jumps during molecule minimization David A. Case (Fri Jan 02 2009 - 04:48:23 PST)
AMBER: apparent error in closest function in ptraj 10 Roman Osman (Fri Jan 02 2009 - 07:54:48 PST)
- Re: AMBER: apparent error in closest function in ptraj 10 D.J. Cole (Fri Jan 02 2009 - 08:06:01 PST)
  - Re: AMBER: apparent error in closest function in ptraj 10 Roman Osman (Fri Jan 02 2009 - 09:37:09 PST)
AMBER: Dielectric constant musa özboyacı (Sat Jan 03 2009 - 10:54:06 PST)
AMBER: IMPORTANT INFORMATION: Notice regarding transition of AMBER mailing list to new address. Ross Walker (Sat Jan 03 2009 - 14:12:19 PST)
AMBER: CHCl3 solvent box WJ Ding (Sun Jan 04 2009 - 14:24:48 PST)
- Re: AMBER: CHCl3 solvent box David A. Case (Mon Jan 05 2009 - 05:48:44 PST)
  - Re: AMBER: CHCl3 solvent box WJ Ding (Mon Jan 05 2009 - 13:21:32 PST)
AMBER: reg sander crashing on more than 32 cores over IB Amit Bajaj (Sun Jan 04 2009 - 22:33:15 PST)
- Re: AMBER: reg sander crashing on more than 32 cores over IB David A. Case (Mon Jan 05 2009 - 04:47:01 PST)
AMBER: bug of the mm_pbsa module in ambertools 1.2 Ye Mei (Mon Jan 05 2009 - 07:28:02 PST)
- Re: AMBER: bug of the mm_pbsa module in ambertools 1.2 Scott Brozell (Tue Jan 06 2009 - 10:59:15 PST)
AMBER: ligand parameter Bo Baker (Mon Jan 05 2009 - 14:05:18 PST)
- RE: AMBER: ligand parameter Ross Walker (Mon Jan 05 2009 - 21:48:13 PST)
  - [AMBER] Re: AMBER: ligand parameter Bo Baker (Tue Jan 06 2009 - 19:59:19 PST)
    - RE: [AMBER] Re: AMBER: ligand parameter Ross Walker (Tue Jan 06 2009 - 20:25:20 PST)
    - Re: [AMBER] Re: AMBER: ligand parameter Bo Baker (Tue Jan 06 2009 - 21:05:00 PST)
    - Re: [AMBER] Re: AMBER: ligand parameter David A. Case (Wed Jan 07 2009 - 05:08:27 PST)
    - Re: [AMBER] Re: AMBER: ligand parameter Bo Baker (Wed Jan 07 2009 - 18:18:02 PST)
    - RE: [AMBER] Re: AMBER: ligand parameter Ross Walker (Wed Jan 07 2009 - 20:10:20 PST)
    - Re: [AMBER] Re: AMBER: ligand parameter Bo Baker (Sun Jan 11 2009 - 16:20:08 PST)
    - Re: [AMBER] Re: AMBER: ligand parameter David Watson (Sun Jan 11 2009 - 16:39:02 PST)
    - Re: [AMBER] Re: AMBER: ligand parameter Bo Baker (Sun Jan 11 2009 - 16:52:19 PST)
    - Re: [AMBER] Re: AMBER: ligand parameter Yu Chen (Sun Jan 11 2009 - 17:25:41 PST)
AMBER: error in amber 10 archana sonawani (Mon Jan 05 2009 - 23:19:03 PST)
- Re: AMBER: error in amber 10 David A. Case (Tue Jan 06 2009 - 04:18:23 PST)
  - Re: AMBER: error in amber 10 David A. Case (Tue Jan 06 2009 - 04:28:54 PST)
AMBER: questions about equilibram wei zhang (Tue Jan 06 2009 - 03:18:47 PST)
- [AMBER] Re: AMBER: questions about equilibram David A. Case (Wed Jan 07 2009 - 04:54:10 PST)
  - RE: [AMBER] Re: AMBER: questions about equilibram wei zhang (Tue Jan 13 2009 - 04:58:51 PST)
AMBER: Re: nmode error: bad nonbon (amber 10) Jeremy Harris (Tue Jan 06 2009 - 05:37:21 PST)
- Re: AMBER: Re: nmode error: bad nonbon (amber 10) David A. Case (Tue Jan 06 2009 - 06:32:48 PST)
  - [AMBER] Re: AMBER: Re: nmode error: bad nonbon (amber 10) Jeremy Harris (Tue Jan 13 2009 - 13:58:36 PST)
    - Re: [AMBER] Re: AMBER: Re: nmode error: bad nonbon (amber 10) David A. Case (Wed Jan 14 2009 - 05:13:18 PST)
AMBER: install amber10 wl2290.columbia.edu (Tue Jan 06 2009 - 09:23:01 PST)
- Re: AMBER: install amber10 Scott Brozell (Tue Jan 06 2009 - 11:33:21 PST)
AMBER: problem with ptraj image command in Amber 10? Ryan Pavlovicz (Tue Jan 06 2009 - 09:28:27 PST)
- Re: AMBER: problem with ptraj image command in Amber 10? Carlos Simmerling (Tue Jan 06 2009 - 09:37:51 PST)
AMBER: xleap problem Bala subramanian (Tue Jan 06 2009 - 10:57:53 PST)
- Re: AMBER: xleap problem hj zou (Tue May 04 2004 - 19:44:43 PDT)
- Re: AMBER: xleap problem Carlos Simmerling (Tue Jan 06 2009 - 11:05:31 PST)
  - Re: AMBER: xleap problem Bala subramanian (Tue Jan 06 2009 - 11:43:00 PST)
    - Re: Re: AMBER: xleap problem hj zou (Mon May 03 2004 - 01:02:34 PDT)
    - Re: AMBER: xleap problem scopio (Mon May 03 2004 - 01:51:03 PDT)
    - Re: Re: AMBER: xleap problem David A. Case (Mon May 03 2004 - 08:45:34 PDT)
    - Re: Re: AMBER: xleap problem hj zou (Sat Jul 10 2004 - 23:16:19 PDT)
    - Re: AMBER: xleap problem scopio (Mon Jul 12 2004 - 07:09:47 PDT)
    - Re: Re: AMBER: xleap problem hj zou (Mon Jul 12 2004 - 07:56:55 PDT)
    - AMBER: How to apply OPLS force field? Wu Lei (Tue Jul 13 2004 - 20:23:04 PDT)
    - Re: AMBER: How to apply OPLS force field? mcpreto.fc.up.pt (Wed Jul 14 2004 - 06:26:04 PDT)
    - Re: AMBER: How to apply OPLS force field? Sichun Yang (Wed Jul 14 2004 - 09:21:41 PDT)
    - Re: AMBER: How to apply OPLS force field? David A. Case (Wed Jul 14 2004 - 09:29:59 PDT)
    - Re: AMBER: How to apply OPLS force field? Wu Lei (Wed Jul 14 2004 - 21:12:50 PDT)
    - RE: AMBER: How to apply OPLS force field? Ross Walker (Wed Jul 14 2004 - 21:20:58 PDT)
    - Re: AMBER: How to apply OPLS force field? Wu Lei (Thu Jul 15 2004 - 00:45:31 PDT)
    - Re: AMBER: How to apply OPLS force field? David A. Case (Thu Jul 15 2004 - 10:04:22 PDT)
    - RE: AMBER: How to apply OPLS force field? Bill Ross (Thu Jul 15 2004 - 09:08:22 PDT)
    - [AMBER] RE: AMBER: xleap problem Ross Walker (Tue Jan 06 2009 - 19:58:26 PST)
    - Re: [AMBER] RE: AMBER: xleap problem Bala subramanian (Wed Jan 07 2009 - 02:53:24 PST)
    - Re: [AMBER] RE: AMBER: xleap problem David A. Case (Wed Jan 07 2009 - 05:06:19 PST)
    - Re: [AMBER] RE: AMBER: xleap problem Bala subramanian (Wed Jan 07 2009 - 05:34:43 PST)
    - Re: [AMBER] RE: AMBER: xleap problem David A. Case (Wed Jan 07 2009 - 05:43:16 PST)
    - Re: [AMBER] RE: AMBER: xleap problem Bala subramanian (Wed Jan 07 2009 - 06:54:44 PST)
AMBER: IMPORTANT Information regarding AMBER Mailing List - please read. Ross Walker (Tue Jan 06 2009 - 12:40:00 PST)
AMBER: mail list Mark M Huntress (Tue Jan 06 2009 - 15:06:57 PST)
- [AMBER] RE: AMBER: mail list Ross Walker (Tue Jan 06 2009 - 15:47:08 PST)
  - Re: [AMBER] RE: AMBER: mail list James W. Caldwell (Tue Jan 06 2009 - 17:24:12 PST)
  - Re: [AMBER] RE: AMBER: mail list M. L. Dodson (Wed Jan 07 2009 - 08:04:02 PST)
[AMBER] amber.ambermd.org open for business Ross Walker (Tue Jan 06 2009 - 15:34:31 PST)
[AMBER] TEST Message - please ignore. Ross Walker (Tue Jan 06 2009 - 17:00:39 PST)
[AMBER] AMBER: Problems in solvation with xleap vallespardojl.chem.leidenuniv.nl (Wed Jan 07 2009 - 05:39:56 PST)
[AMBER] MD Beale, John (Wed Jan 07 2009 - 06:40:07 PST)
- RE: [AMBER] MD Ross Walker (Wed Jan 07 2009 - 16:33:46 PST)
[AMBER] four prepin/frcmod files be read simultaneously by leap Yi Mao (Wed Jan 07 2009 - 06:46:05 PST)
- Re: [AMBER] four prepin/frcmod files be read simultaneously by leap rpaduri.chem.wayne.edu (Wed Jan 07 2009 - 08:05:09 PST)
  - Re: [AMBER] four prepin/frcmod files be read simultaneously by leap Yi Mao (Wed Jan 07 2009 - 08:38:52 PST)
    - Re: [AMBER] four prepin/frcmod files be read simultaneously by leap David A. Case (Wed Jan 07 2009 - 10:39:56 PST)
[AMBER] PBSA: PB bomb in pb_setgrd() Larry Layne (Wed Jan 07 2009 - 07:33:57 PST)
- RE: [AMBER] PBSA: PB bomb in pb_setgrd() Ray Luo (Wed Jan 07 2009 - 10:24:15 PST)
[AMBER] RE: RE: amber force filed for RNA Ross Walker (Wed Jan 07 2009 - 08:49:41 PST)
[AMBER] RE: same result Ross Walker (Wed Jan 07 2009 - 08:59:39 PST)
- Re: [AMBER] RE: same result zgong.hust (Thu Jan 08 2009 - 00:49:29 PST)
[AMBER] Amber Parameters for Iron Heme covalently boud to carbon monoxide Osmar Norberto de Souza (Wed Jan 07 2009 - 10:23:06 PST)
[AMBER] PHOSPHOTHREONINE Khaled Barakat (Wed Jan 07 2009 - 11:11:43 PST)
- Re: [AMBER] PHOSPHOTHREONINE David A. Case (Wed Jan 07 2009 - 11:29:35 PST)
[AMBER] Using GAFF with a covalently bound ligand or label Sale, Kenneth L (Wed Jan 07 2009 - 17:30:10 PST)
- Re: [AMBER] Using GAFF with a covalently bound ligand or label David A. Case (Wed Jan 07 2009 - 18:42:27 PST)
- Re: [AMBER] Using GAFF with a covalently bound ligand or label Markus Kaukonen (Thu Jan 15 2009 - 22:31:53 PST)
  - Re: [AMBER] Using GAFF with a covalently bound ligand or label FyD (Fri Jan 16 2009 - 01:13:43 PST)
[AMBER] Non-planarity of amide atoms after optimization Sanghwa Han (Wed Jan 07 2009 - 19:17:18 PST)
[AMBER] how many processors for parallel test michael (Thu Jan 08 2009 - 03:01:41 PST)
- Re: [AMBER] how many processors for parallel test David A. Case (Thu Jan 08 2009 - 04:08:06 PST)
  - Re: [AMBER] how many processors for parallel test michael bane (Thu Jan 08 2009 - 05:31:31 PST)
    - Re: [AMBER] how many processors for parallel test David A. Case (Thu Jan 08 2009 - 05:44:52 PST)
    - Re: [AMBER] how many processors for parallel test michael bane (Thu Jan 08 2009 - 05:56:59 PST)
[AMBER] Can we use Amber? Casey,Richard (Thu Jan 08 2009 - 09:16:50 PST)
[AMBER] Can we use AMBER? Casey,Richard (Thu Jan 08 2009 - 09:25:57 PST)
- RE: [AMBER] Can we use AMBER? Ross Walker (Thu Jan 08 2009 - 10:47:18 PST)
[AMBER] mairun wl2290.columbia.edu (Thu Jan 08 2009 - 09:30:05 PST)
- RE: [AMBER] mairun Ross Walker (Thu Jan 08 2009 - 10:25:26 PST)
  - RE: [AMBER] mairun wl2290.columbia.edu (Thu Jan 08 2009 - 14:33:52 PST)
    - RE: [AMBER] mairun Ross Walker (Thu Jan 08 2009 - 14:51:49 PST)
    - RE: [AMBER] mairun wl2290.columbia.edu (Thu Jan 08 2009 - 15:11:56 PST)
[AMBER] lone pairs on CYX and MET Beale, John (Thu Jan 08 2009 - 10:08:42 PST)
- RE: [AMBER] lone pairs on CYX and MET Ross Walker (Thu Jan 08 2009 - 10:17:52 PST)
[AMBER] Need help with point to plane distance calculation in nab M. L. Dodson (Thu Jan 08 2009 - 10:39:16 PST)
- Re: [AMBER] Need help with point to plane distance calculation in nab IN SUK JOUNG (Thu Jan 08 2009 - 11:00:20 PST)
  - Re: [AMBER] Need help with point to plane distance calculation in nab M. L. Dodson (Thu Jan 08 2009 - 11:16:51 PST)
    - Re: [AMBER] Need help with point to plane distance calculation in nab IN SUK JOUNG (Thu Jan 08 2009 - 11:41:09 PST)
    - Re: [AMBER] Need help with point to plane distance calculation in nab M. L. Dodson (Thu Jan 08 2009 - 11:54:15 PST)
RE: [AMBER] mpirun Ross Walker (Thu Jan 08 2009 - 15:28:12 PST)
[AMBER] force-field for cyclic oligosaccharide using leap Madhurima Jana (Thu Jan 08 2009 - 20:50:18 PST)
- [AMBER] force-field for cyclic oligosaccharide using leap Madhurima Jana (Sun Jan 11 2009 - 20:21:23 PST)
[AMBER] NAB entropy calcualtion chaitanya koppisetty (Fri Jan 09 2009 - 01:01:13 PST)
- Re: [AMBER] NAB entropy calcualtion Andreas Svrcek-Seiler (Fri Jan 09 2009 - 01:28:48 PST)
- Re: [AMBER] NAB entropy calcualtion David A. Case (Fri Jan 09 2009 - 05:13:32 PST)
[AMBER] ambpdb is changing atom names, a feature or bug? Markus Kaukonen (Fri Jan 09 2009 - 04:55:41 PST)
- Re: [AMBER] ambpdb is changing atom names, a feature or bug? David A. Case (Fri Jan 09 2009 - 05:01:54 PST)
[AMBER] problem building AmberTools/sleap on AIX Shan-ho Tsai (Fri Jan 09 2009 - 08:27:56 PST)
- Re: [AMBER] problem building AmberTools/sleap on AIX Wei Zhang (Fri Jan 09 2009 - 08:37:43 PST)
  - Re: [AMBER] problem building AmberTools/sleap on AIX Shan-ho Tsai (Fri Jan 09 2009 - 08:46:59 PST)
- Re: [AMBER] problem building AmberTools/sleap on AIX Bill Ross (Fri Jan 09 2009 - 09:45:55 PST)
  - Re: [AMBER] problem building AmberTools/sleap on AIX Shan-ho Tsai (Fri Jan 09 2009 - 13:49:17 PST)
    - Re: [AMBER] problem building AmberTools/sleap on AIX Wei Zhang (Fri Jan 09 2009 - 14:28:08 PST)
    - Re: [AMBER] problem building AmberTools/sleap on AIX Shan-ho Tsai (Mon Jan 12 2009 - 07:31:51 PST)
    - Re: [AMBER] problem building AmberTools/sleap on AIX Shan-ho Tsai (Fri Jan 16 2009 - 12:58:53 PST)
    - Re: [AMBER] problem building AmberTools/sleap on AIX Wei Zhang (Fri Jan 16 2009 - 13:19:42 PST)
    - Re: [AMBER] problem building AmberTools/sleap on AIX Shan-ho Tsai (Wed Jan 21 2009 - 13:53:00 PST)
[AMBER] "bad atom type" Akansha Saxena (Fri Jan 09 2009 - 09:15:11 PST)
Re: [AMBER] ambpdb is changing atom names, a feature or bug? Bill Ross (Fri Jan 09 2009 - 09:53:23 PST)
- Re: [AMBER] ambpdb is changing atom names, a feature or bug? David A. Case (Fri Jan 09 2009 - 10:58:20 PST)
- Re: Re: [AMBER] ambpdb is changing atom names, a feature or bug? Ye Mei (Sat Jan 10 2009 - 00:03:10 PST)
  - Re: Re: [AMBER] ambpdb is changing atom names, a feature or bug? David A. Case (Sat Jan 10 2009 - 08:02:53 PST)
[AMBER] number-of-EPS-exceeds-MAXESP Karol Kaszuba (Fri Jan 09 2009 - 13:07:13 PST)
- Re: [AMBER] number-of-EPS-exceeds-MAXESP FyD (Sat Jan 10 2009 - 00:26:13 PST)
  - Re: [AMBER] number-of-EPS-exceeds-MAXESP Karol Kaszuba (Sat Jan 10 2009 - 07:27:08 PST)
    - Re: [AMBER] number-of-EPS-exceeds-MAXESP FyD (Sat Jan 10 2009 - 23:00:40 PST)
    - Re: [AMBER] number-of-EPS-exceeds-MAXESP Karol Kaszuba (Sun Jan 11 2009 - 00:01:07 PST)
- Re: [AMBER] number-of-EPS-exceeds-MAXESP FyD (Sun Jan 11 2009 - 23:43:48 PST)
  - Re: [AMBER] number-of-EPS-exceeds-MAXESP Karol Kaszuba (Sun Jan 11 2009 - 23:57:50 PST)
    - Re: [AMBER] number-of-EPS-exceeds-MAXESP Karol Kaszuba (Sat Jan 17 2009 - 02:41:22 PST)
[AMBER] implicit and explicit simulation: salt effect Catein Catherine (Fri Jan 09 2009 - 19:03:35 PST)
- Re: [AMBER] implicit and explicit simulation: salt effect David Watson (Fri Jan 09 2009 - 19:49:48 PST)
  - Re: [AMBER] implicit and explicit simulation: salt effect David LeBard (Fri Jan 09 2009 - 20:23:24 PST)
    - Re: [AMBER] implicit and explicit simulation: salt effect David A. Case (Sat Jan 10 2009 - 08:26:45 PST)
- Re: [AMBER] implicit and explicit simulation: salt effect David A. Case (Sat Jan 10 2009 - 08:23:08 PST)
[AMBER] mm-GBSA from implicit Catein Catherine (Fri Jan 09 2009 - 19:13:28 PST)
- Re: [AMBER] mm-GBSA from implicit Carlos Simmerling (Sat Jan 10 2009 - 05:25:10 PST)
[AMBER] Off topic. Hardware problem Francesco Pietra (Sat Jan 10 2009 - 00:26:55 PST)
[AMBER] Can't reproduce RESP charges Sanghwa Han (Sun Jan 11 2009 - 21:57:15 PST)
- Re: [AMBER] Can't reproduce RESP charges FyD (Tue Jan 13 2009 - 03:52:13 PST)
[AMBER] Amber 9 installation problem on Ubuntu drugdesign (Sun Jan 11 2009 - 22:26:34 PST)
- Re: [AMBER] Amber 9 installation problem on Ubuntu David A. Case (Mon Jan 12 2009 - 04:01:31 PST)
[AMBER] Release of the R.E.D.-III.1 tools FyD (Mon Jan 12 2009 - 03:59:14 PST)
[AMBER] Parallelepiped periodic box Ian Streeter (Mon Jan 12 2009 - 07:57:55 PST)
- Re: [AMBER] Parallelepiped periodic box David A. Case (Fri Jan 16 2009 - 11:50:32 PST)
[AMBER] Writing out trajectory in NAB xxxzzzyyy xxxzzzyyy (Mon Jan 12 2009 - 08:43:33 PST)
- Re: [AMBER] Writing out trajectory in NAB David A. Case (Mon Jan 12 2009 - 09:22:58 PST)
[AMBER] crystal waters Carmen Domene (Mon Jan 12 2009 - 12:04:24 PST)
- Re: [AMBER] crystal waters steinbrt.rci.rutgers.edu (Mon Jan 12 2009 - 12:16:25 PST)
  - Re: [AMBER] crystal waters Carmen Domene (Mon Jan 12 2009 - 12:32:28 PST)
    - Re: [AMBER] crystal waters steinbrt.rci.rutgers.edu (Mon Jan 12 2009 - 12:37:34 PST)
[AMBER] multisander error Justine Condo (Mon Jan 12 2009 - 14:03:37 PST)
- Re: [AMBER] multisander error David Watson (Mon Jan 12 2009 - 14:15:26 PST)
- RE: [AMBER] multisander error Ross Walker (Mon Jan 12 2009 - 14:20:06 PST)
  - Re: [AMBER] multisander error Justine Condo (Mon Jan 12 2009 - 14:32:31 PST)
  - Re: [AMBER] multisander error Justine Condo (Mon Jan 12 2009 - 14:39:44 PST)
    - RE: [AMBER] multisander error Ross Walker (Mon Jan 12 2009 - 14:51:48 PST)
    - Re: [AMBER] multisander error Justine Condo (Mon Jan 12 2009 - 15:01:41 PST)
[AMBER] error in sander (Amber10) archana sonawani (Tue Jan 13 2009 - 00:21:09 PST)
[AMBER] errorin sander---Amber10 archana sonawani (Tue Jan 13 2009 - 01:27:43 PST)
- Re: [AMBER] errorin sander---Amber10 David A. Case (Tue Jan 13 2009 - 05:22:36 PST)
[AMBER] amber9 in fedora10 Bala subramanian (Tue Jan 13 2009 - 09:51:49 PST)
- Re: [AMBER] amber9 in fedora10 Mark Williamson (Tue Jan 13 2009 - 09:56:31 PST)
- RE: [AMBER] amber9 in fedora10 Ross Walker (Tue Jan 13 2009 - 10:00:33 PST)
  - Re: [AMBER] amber9 in fedora10 Bala subramanian (Tue Jan 13 2009 - 10:16:19 PST)
    - Re: [AMBER] amber9 in fedora10 Eric (Tue Jan 13 2009 - 10:28:33 PST)
  - [AMBER] PTRAJ: solvent accessible surface area Catein Catherine (Tue Jan 13 2009 - 23:32:15 PST)
    - Re: [AMBER] PTRAJ: solvent accessible surface area steinbrt.rci.rutgers.edu (Wed Jan 14 2009 - 06:59:19 PST)
    - Re: [AMBER] PTRAJ: solvent accessible surface area Carlos Simmerling (Wed Jan 14 2009 - 07:00:59 PST)
[AMBER] principal component vector onto C-alpha Carra, Claudio (JSC-SK)[USRA] (Tue Jan 13 2009 - 12:52:31 PST)
- Re: [AMBER] principal component vector onto C-alpha S.Sundar Raman (Tue Jan 13 2009 - 14:46:20 PST)
[AMBER] Divcon or Mopac Cen Gao (Tue Jan 13 2009 - 15:54:33 PST)
- Re: [AMBER] Divcon or Mopac Martin Peters (Wed Jan 14 2009 - 01:01:12 PST)
[AMBER] ptraj, CHARMM PSF and CMAP Hannes Loeffler (Wed Jan 14 2009 - 01:45:07 PST)
- RE: [AMBER] ptraj, CHARMM PSF and CMAP Ross Walker (Wed Jan 14 2009 - 08:46:17 PST)
[AMBER] charges in topology file vallespardojl.chem.leidenuniv.nl (Wed Jan 14 2009 - 02:33:35 PST)
- Re: [AMBER] charges in topology file Carlos Simmerling (Wed Jan 14 2009 - 03:24:52 PST)
- Re: [AMBER] charges in topology file Jeffrey (Fri Jul 10 2009 - 09:20:01 PDT)
[AMBER] reaction coordinates Rausch, Felix (Wed Jan 14 2009 - 03:54:57 PST)
- Re: [AMBER] reaction coordinates David A. Case (Wed Jan 14 2009 - 05:00:59 PST)
  - RE: [AMBER] reaction coordinates Catein Catherine (Wed Jan 14 2009 - 21:25:31 PST)
[AMBER] antechamber cation failure Rausch, Felix (Wed Jan 14 2009 - 05:32:04 PST)
- RE: [AMBER] antechamber cation failure Ross Walker (Wed Jan 14 2009 - 09:45:43 PST)
[AMBER] NPT md with PME method for a water box Jeffrey (Wed Jan 14 2009 - 06:41:24 PST)
- RE: [AMBER] NPT md with PME method for a water box Ross Walker (Wed Jan 14 2009 - 10:07:13 PST)
[AMBER] molecular mechanic minimisation with amber momo momo (Wed Jan 14 2009 - 06:58:47 PST)
- RE: [AMBER] molecular mechanic minimisation with amber Ross Walker (Wed Jan 14 2009 - 09:56:23 PST)
[AMBER] Dipole command in ptraj musa özboyacı (Wed Jan 14 2009 - 07:41:07 PST)
[AMBER] pmemd | Compilation problem with ifort and mvapich environment fohm fohm (Wed Jan 14 2009 - 09:23:50 PST)
- RE: [AMBER] pmemd | Compilation problem with ifort and mvapich environment Ross Walker (Wed Jan 14 2009 - 09:53:20 PST)
[AMBER] bad energy??!! momo momo (Wed Jan 14 2009 - 11:19:20 PST)
- RE: [AMBER] bad energy??!! Ross Walker (Wed Jan 14 2009 - 11:40:24 PST)
[AMBER] Postdoc Position Available at SDSC/UCSD Ross Walker (Wed Jan 14 2009 - 12:35:52 PST)
[AMBER] Dipole command in ptraj musa özboyacı (Wed Jan 14 2009 - 15:15:26 PST)
[AMBER] xmgrace and plotting time evolution of a defined variable Naser Alijabbari (Wed Jan 14 2009 - 16:20:31 PST)
- Re: [AMBER] xmgrace and plotting time evolution of a defined variable Mark Williamson (Wed Jan 14 2009 - 16:38:17 PST)
[AMBER] Error in xleap archana sonawani (Wed Jan 14 2009 - 23:39:16 PST)
- RE: [AMBER] Error in xleap Ross Walker (Thu Jan 15 2009 - 08:01:20 PST)
[AMBER] Using a restart file Simone Swift (Thu Jan 15 2009 - 08:40:38 PST)
- Re: [AMBER] Using a restart file Carlos Simmerling (Thu Jan 15 2009 - 08:45:27 PST)
- RE: [AMBER] Using a restart file Ross Walker (Thu Jan 15 2009 - 08:52:44 PST)
[AMBER] Ligand Diffusion Studies? Jason A. Ford-Green (Thu Jan 15 2009 - 09:42:03 PST)
[AMBER] restraint of REMD z g (Thu Jan 15 2009 - 18:51:46 PST)
- Re: [AMBER] restraint of REMD Carlos Simmerling (Fri Jan 16 2009 - 03:57:29 PST)
[AMBER] sander not working archana sonawani (Thu Jan 15 2009 - 21:52:48 PST)
- Re: [AMBER] sander not working David A. Case (Fri Jan 16 2009 - 06:58:50 PST)
- Re: [AMBER] sander not working Carlos Simmerling (Fri Jan 16 2009 - 07:01:34 PST)
[AMBER] nab conjgrad min problem Jeremy Harris (Fri Jan 16 2009 - 07:11:12 PST)
- Re: [AMBER] nab conjgrad min problem David A. Case (Fri Jan 16 2009 - 07:33:01 PST)
  - Re: [AMBER] nab conjgrad min problem Jeremy Harris (Mon Jan 19 2009 - 07:00:30 PST)
[AMBER] RE: Tutorial 5 Ross Walker (Fri Jan 16 2009 - 09:10:51 PST)
- Re: [AMBER] RE: Tutorial 5 George Tzotzos (Fri Jan 16 2009 - 12:31:11 PST)
[AMBER] (no subject) Lake, Thomas (Fri Jan 16 2009 - 09:38:09 PST)
- Re: [AMBER] (no subject) Carlos Simmerling (Fri Jan 16 2009 - 09:43:26 PST)
  - Re: [AMBER] (no subject) Jenny Iskrenova (Fri Jan 16 2009 - 10:42:08 PST)
    - Re: [AMBER] (no subject) Carlos Simmerling (Fri Jan 16 2009 - 10:46:11 PST)
    - Re: [AMBER] (no subject) David A. Case (Fri Jan 16 2009 - 11:10:33 PST)
    - Re: [AMBER] (no subject) Jenny Iskrenova (Fri Jan 16 2009 - 15:20:46 PST)
    - Re: [AMBER] (no subject) David A. Case (Sat Jan 17 2009 - 18:48:25 PST)
    - Re: [AMBER] (no subject) Carlos Simmerling (Sun Jan 18 2009 - 05:08:41 PST)
    - RE: [AMBER] (no subject) Ross Walker (Sun Jan 18 2009 - 10:07:24 PST)
    - RE: [AMBER] Duplicate residues George Tzotzos (Mon Jan 19 2009 - 04:54:37 PST)
    - Re: [AMBER] Duplicate residues David A. Case (Mon Jan 19 2009 - 05:16:28 PST)
    - Re: [AMBER] Duplicate residues Bill Ross (Mon Jan 19 2009 - 11:20:01 PST)
    - Re: [AMBER] (no subject) Jenny Iskrenova (Mon Jan 19 2009 - 10:54:39 PST)
- RE: [AMBER] (no subject) david.lisgarten.canterbury.ac.uk (Tue Jun 09 2009 - 06:56:32 PDT)
- RE: [AMBER] (no subject) david.lisgarten.canterbury.ac.uk (Thu Jun 11 2009 - 01:28:56 PDT)
  - Re: [AMBER] (no subject) David A. Case (Thu Jun 11 2009 - 04:54:38 PDT)
- Re: [AMBER] (no subject) DEBOSTUTI GHOSHDASTIDAR (Wed May 16 2012 - 10:31:44 PDT)
  - Re: [AMBER] (no subject) case (Wed May 16 2012 - 18:23:59 PDT)
    - Re: [AMBER] (no subject) DEBOSTUTI GHOSHDASTIDAR (Sat May 19 2012 - 02:16:36 PDT)
    - Re: [AMBER] (no subject) case (Sat May 19 2012 - 06:12:40 PDT)
    - Re: [AMBER] (no subject) case (Sat May 19 2012 - 06:18:51 PDT)
    - Re: [AMBER] (no subject) DEBOSTUTI GHOSHDASTIDAR (Sat May 19 2012 - 11:13:26 PDT)
    - Re: [AMBER] (no subject) DEBOSTUTI GHOSHDASTIDAR (Sat May 19 2012 - 11:14:34 PDT)
    - Re: [AMBER] (no subject) DEBOSTUTI GHOSHDASTIDAR (Mon Jun 18 2012 - 06:51:01 PDT)
    - Re: [AMBER] (no subject) David A. Case (Mon Jun 18 2012 - 10:42:18 PDT)
    - Re: [AMBER] (no subject) DEBOSTUTI GHOSHDASTIDAR (Wed Jun 20 2012 - 09:56:38 PDT)
    - Re: [AMBER] (no subject) David A. Case (Fri Jun 22 2012 - 15:41:21 PDT)
    - Re: [AMBER] (no subject) DEBOSTUTI GHOSHDASTIDAR (Mon Jun 25 2012 - 11:00:31 PDT)
    - Re: [AMBER] (no subject) Jason Swails (Mon Jun 25 2012 - 12:22:24 PDT)
    - Re: [AMBER] (no subject) DEBOSTUTI GHOSHDASTIDAR (Mon Jun 25 2012 - 23:09:17 PDT)
- Re: [AMBER] (no subject) BERGY (Tue Feb 05 2013 - 07:05:31 PST)
  - Re: [AMBER] (no subject) Jason Swails (Tue Feb 05 2013 - 07:16:45 PST)
- Re: [AMBER] (no subject) Rajiv Gandhi (Sun Mar 16 2014 - 23:43:40 PDT)
  - Re: [AMBER] (no subject) Jason Swails (Mon Mar 17 2014 - 05:10:14 PDT)
- Re: [AMBER] (no subject) Hossein Geraili (Thu Oct 05 2017 - 02:20:22 PDT)
[AMBER] Heat and Equilibrate Hybrid GB solvent? Jason A. Ford-Green (Fri Jan 16 2009 - 13:14:41 PST)
- Re: [AMBER] Heat and Equilibrate Hybrid GB solvent? Carlos Simmerling (Fri Jan 16 2009 - 13:21:27 PST)
[AMBER] Use of Amber in distributed calculations drugdesign (Fri Jan 16 2009 - 23:33:55 PST)
- Re: [AMBER] Use of Amber in distributed calculations M. L. Dodson (Sat Jan 17 2009 - 05:48:42 PST)
  - Re: [AMBER] Use of Amber in distributed calculations M. L. Dodson (Sat Jan 17 2009 - 06:01:36 PST)
[AMBER] To stop the AMBER's list Furia Gargano (Sat Jan 17 2009 - 09:59:48 PST)
[AMBER] to remove AMBER list Furia Gargano (Sat Jan 17 2009 - 10:02:26 PST)
- RE: [AMBER] to remove AMBER list Ross Walker (Sat Jan 17 2009 - 13:32:19 PST)
[AMBER] AMBER efficiency: Intel vs. AMD Swarup Gupta (Sun Jan 18 2009 - 17:43:32 PST)
- Re: [AMBER] AMBER efficiency: Intel vs. AMD Ye MEI (Sun Jan 18 2009 - 18:20:47 PST)
- RE: [AMBER] AMBER efficiency: Intel vs. AMD Ross Walker (Mon Jan 19 2009 - 07:39:33 PST)
[AMBER] how to set up "Two molecules tied with an Elastic band of 20A in implicit solvent" Jagadeesh, M.N., Ph.D. (Mon Jan 19 2009 - 01:03:39 PST)
- Re: [AMBER] how to set up "Two molecules tied with an Elastic band of 20A in implicit solvent" Carlos Simmerling (Tue Jan 20 2009 - 06:33:55 PST)
[AMBER] RESP charges for Fe in heme Carina Backtorp (Mon Jan 19 2009 - 05:48:11 PST)
[AMBER] Atom types George Tzotzos (Mon Jan 19 2009 - 06:04:09 PST)
- RE: [AMBER] Atom types Ross Walker (Mon Jan 19 2009 - 07:46:10 PST)
- RE: [AMBER] Atom types George Tzotzos (Mon Jan 19 2009 - 10:02:42 PST)
[AMBER] errors on REMD z g (Mon Jan 19 2009 - 18:41:35 PST)
- Re: [AMBER] errors on REMD Carlos Simmerling (Tue Jan 20 2009 - 03:02:06 PST)
  - Re: [AMBER] errors on REMD z g (Tue Jan 20 2009 - 05:39:12 PST)
    - Re: [AMBER] errors on REMD Carlos Simmerling (Tue Jan 20 2009 - 06:29:07 PST)
    - Re: [AMBER] errors on REMD z g (Thu Jan 22 2009 - 17:02:08 PST)
    - Re: [AMBER] errors on REMD Carlos Simmerling (Mon Jan 26 2009 - 09:38:39 PST)
[AMBER] analysis Adrien Delmont (Tue Jan 20 2009 - 09:03:16 PST)
[AMBER] Problem with entropy calculation of bigger system using NMODE and NAB. Marek Malý (Tue Jan 20 2009 - 10:24:55 PST)
- RE: [AMBER] Problem with entropy calculation of bigger system using NMODE and NAB. Niel Henriksen (Tue Jan 20 2009 - 12:49:38 PST)
- Re: [AMBER] Problem with entropy calculation of bigger system using NMODE and NAB. David A. Case (Tue Jan 20 2009 - 12:53:48 PST)
  - [AMBER] MD vs scattering Chih-Ying Lin (Tue Jan 20 2009 - 13:10:47 PST)
    - RE: [AMBER] MD vs scattering Ross Walker (Tue Jan 20 2009 - 13:18:26 PST)
    - Re: RE: [AMBER] MD vs scattering Chih-Ying Lin (Tue Jan 20 2009 - 13:26:49 PST)
  - Re: [AMBER] Problem with entropy calculation of bigger system using NMODE and NAB. Marek Malý (Tue Jan 20 2009 - 18:48:03 PST)
    - Re: [AMBER] Problem with entropy calculation of bigger system using NMODE and NAB. David A. Case (Wed Jan 21 2009 - 06:52:33 PST)
    - Re: [AMBER] Problem with entropy calculation of bigger system using NMODE and NAB. Marek Malý (Wed Jan 21 2009 - 14:48:58 PST)
    - Re: [AMBER] Problem with entropy calculation of bigger system using NMODE and NAB. David A. Case (Sat Jan 24 2009 - 06:37:31 PST)
[AMBER] solvent mixture iccy liu (Tue Jan 20 2009 - 14:08:34 PST)
- Re: [AMBER] solvent mixture Gustavo Seabra (Sat Jan 24 2009 - 18:44:31 PST)
[AMBER] How to calculate cavity volume from MD structures? ben rodriguez (Tue Jan 20 2009 - 14:21:43 PST)
- Re: [AMBER] How to calculate cavity volume from MD structures? Jason A. Ford-Green (Wed Jan 21 2009 - 07:39:57 PST)
[AMBER] prot-DNA simulation deepti nayar (Wed Jan 21 2009 - 03:16:09 PST)
- Re: [AMBER] prot-DNA simulation Thomas Cheatham III (Wed Jan 21 2009 - 13:55:52 PST)
[AMBER] AMBER External keyword Mahmoud A. A. Ibrahim (Wed Jan 21 2009 - 07:59:33 PST)
- Re: [AMBER] AMBER External keyword Gustavo Seabra (Sat Jan 24 2009 - 18:32:10 PST)
[AMBER] how to use those water models off the list in amber? GZ Zhang (Wed Jan 21 2009 - 13:39:50 PST)
- Re: [AMBER] how to use those water models off the list in amber? Lauren Wickstrom (Wed Jan 21 2009 - 15:58:22 PST)
- Re: [AMBER] how to use those water models off the list in amber? David A. Case (Thu Jan 22 2009 - 05:29:41 PST)
  - Re: [AMBER] how to use those water models off the list in amber? GZ Zhang (Thu Jan 22 2009 - 12:47:02 PST)
[AMBER] reg . parallel run balaji nagarajan (Wed Jan 21 2009 - 21:34:03 PST)
- RE: [AMBER] reg . parallel run Ross Walker (Thu Jan 22 2009 - 07:52:55 PST)
[AMBER] (no subject) Lake, Thomas (Thu Jan 22 2009 - 05:43:59 PST)
- [AMBER] restraining atoms neville forlemu (Thu Jan 22 2009 - 06:53:48 PST)
  - Re: [AMBER] restraining atoms Carlos Simmerling (Thu Jan 22 2009 - 06:55:35 PST)
- RE: [AMBER] (no subject) Ross Walker (Thu Jan 22 2009 - 07:46:56 PST)
[AMBER] MM - PBSA problem musa özboyacı (Thu Jan 22 2009 - 09:06:54 PST)
- RE: [AMBER] MM - PBSA problem Ray Luo (Thu Jan 22 2009 - 09:31:53 PST)
  - Re: [AMBER] MM - PBSA problem musa özboyacı (Thu Jan 22 2009 - 11:52:10 PST)
    - Re: [AMBER] MM - PBSA problem Cenk $Jenk$ Andac (Thu Jan 22 2009 - 14:00:13 PST)
- RE: [AMBER] MM - PBSA problem Niel Henriksen (Thu Jan 22 2009 - 16:52:09 PST)
  - Re: [AMBER] MM - PBSA problem musa özboyacı (Fri Jan 23 2009 - 05:14:05 PST)
    - Re: [AMBER] MM - PBSA problem Cenk $Jenk$ Andac (Fri Jan 23 2009 - 06:34:46 PST)
    - Re: [AMBER] MM - PBSA problem musa özboyacı (Sun Jan 25 2009 - 05:12:05 PST)
    - Re: [AMBER] MM - PBSA problem David A. Case (Sun Jan 25 2009 - 06:21:33 PST)
    - Re: [AMBER] MM - PBSA problem David A. Case (Sun Jan 25 2009 - 06:26:07 PST)
    - Re: [AMBER] MM - PBSA problem Cenk $Jenk$ Andac (Sun Jan 25 2009 - 12:38:16 PST)
    - Re: [AMBER] MM - PBSA problem musa özboyacı (Mon Jan 26 2009 - 03:15:13 PST)
    - Re: [AMBER] MM - PBSA problem Cenk $Jenk$ Andac (Mon Jan 26 2009 - 04:14:52 PST)
    - Re: [AMBER] MM - PBSA problem musa özboyacı (Mon Jan 26 2009 - 04:43:33 PST)
    - Re: [AMBER] MM - PBSA problem Cenk $Jenk$ Andac (Mon Jan 26 2009 - 08:20:25 PST)
    - Re: [AMBER] MM - PBSA problem musa özboyacı (Mon Jan 26 2009 - 08:32:40 PST)
[AMBER] non-natural amino acids Arturas Ziemys (Thu Jan 22 2009 - 09:32:11 PST)
- Re: [AMBER] non-natural amino acids FyD (Thu Jan 22 2009 - 15:25:31 PST)
[AMBER] reg.parallel run error balaji nagarajan (Thu Jan 22 2009 - 10:41:25 PST)
- RE: [AMBER] reg.parallel run error Ross Walker (Thu Jan 22 2009 - 12:06:33 PST)
[AMBER] REM_hybrid test fails on AIX Shan-ho Tsai (Thu Jan 22 2009 - 12:28:04 PST)
- Re: [AMBER] REM_hybrid test fails on AIX Shan-ho Tsai (Thu Feb 05 2009 - 08:44:43 PST)
[AMBER] reg.error in parallel run balaji nagarajan (Fri Jan 23 2009 - 02:05:21 PST)
- RE: [AMBER] reg.error in parallel run Ross Walker (Fri Jan 23 2009 - 07:52:20 PST)
[AMBER] charge derivation for ATP molecule using antechamber prachi munjal (Fri Jan 23 2009 - 05:19:27 PST)
- Re: [AMBER] charge derivation for ATP molecule using antechamber David A. Case (Fri Jan 23 2009 - 08:51:49 PST)
[AMBER] RE: errors on remd Ross Walker (Fri Jan 23 2009 - 08:38:06 PST)
Re: [AMBER] "Could not find bond parameter" George Tzotzos (Fri Jan 23 2009 - 10:16:34 PST)
- RE: [AMBER] "Could not find bond parameter" Ross Walker (Fri Jan 23 2009 - 10:29:46 PST)
[AMBER] reg.parallel.run error balaji nagarajan (Fri Jan 23 2009 - 17:59:21 PST)
- RE: [AMBER] reg.parallel.run error Ross Walker (Fri Jan 23 2009 - 22:05:50 PST)
[AMBER] error on open distatance restraint gmail (Fri Jan 23 2009 - 18:58:27 PST)
- Re: [AMBER] error on open distatance restraint David A. Case (Fri Jan 23 2009 - 19:18:17 PST)
  - Re: [AMBER] error on open distatance restraint xiaonan zhang (Sat Jan 24 2009 - 19:56:02 PST)
[AMBER] reg.parallel.run.error balaji nagarajan (Sat Jan 24 2009 - 07:09:49 PST)
[AMBER] Very weird topology problem ranqi zhu (Sat Jan 24 2009 - 13:14:24 PST)
- Re: [AMBER] Very weird topology problem Peter Gannett (Sat Jan 24 2009 - 15:17:26 PST)
[AMBER] AmberTools and ptraj clustering on Mac OS X David Watson (Sat Jan 24 2009 - 13:41:04 PST)
[AMBER] xleap problem oguz gurbulak (Sun Jan 25 2009 - 03:56:12 PST)
- Re: [AMBER] xleap problem David A. Case (Sun Jan 25 2009 - 05:57:41 PST)
  - Re: [AMBER] xleap problem oguz gurbulak (Sun Jan 25 2009 - 08:02:50 PST)
[AMBER] RE:xleap problem oguz gurbulak (Sun Jan 25 2009 - 08:08:26 PST)
[AMBER] xleap problem oguz gurbulak (Sun Jan 25 2009 - 08:27:48 PST)
[AMBER] xleap problem oguz gurbulak (Sun Jan 25 2009 - 08:34:39 PST)
- Re: [AMBER] xleap problem David A. Case (Sun Jan 25 2009 - 15:30:47 PST)
[AMBER] xleap problem oguz gurbulak (Sun Jan 25 2009 - 03:49:28 PST)
[AMBER] deduce correlation from covariance matrix Yi Mao (Sun Jan 25 2009 - 13:01:05 PST)
[AMBER] using binary trajectories from NAMD in PTRAJ karthik s (Sun Jan 25 2009 - 23:11:29 PST)
- RE: [AMBER] using binary trajectories from NAMD in PTRAJ Wei Huang (Mon Jan 26 2009 - 06:41:22 PST)
  - Re: [AMBER] using binary trajectories from NAMD in PTRAJ karthik s (Mon Jan 26 2009 - 22:49:13 PST)
[AMBER] thioglycoside Alexander Schierholt (Mon Jan 26 2009 - 06:46:28 PST)
- Re: [AMBER] thioglycoside FyD (Mon Jan 26 2009 - 07:07:37 PST)
- Re: [AMBER] thioglycoside Lachele Foley (Lists) (Mon Jan 26 2009 - 07:36:26 PST)
Re: [AMBER] Antechamber Connectivity George Tzotzos (Mon Jan 26 2009 - 10:23:58 PST)
- Re: [AMBER] Antechamber Connectivity David Watson (Mon Jan 26 2009 - 11:59:58 PST)
[AMBER] antechamber : missed atoms Khaled Barakat (Mon Jan 26 2009 - 10:54:07 PST)
- Re: [AMBER] antechamber : missed atoms Khaled Barakat (Mon Jan 26 2009 - 11:15:33 PST)
  - Re: [AMBER] antechamber : missed atoms David A. Case (Tue Jan 27 2009 - 07:23:27 PST)
- Re: [AMBER] antechamber : missed atoms Khaled Barakat (Mon Jan 26 2009 - 11:20:52 PST)
  - Re: [AMBER] antechamber : missed atoms Sean Johnston (Mon Jan 26 2009 - 11:40:59 PST)
- Re: [AMBER] antechamber : missed atoms Khaled Barakat (Mon Jan 26 2009 - 12:22:14 PST)
[AMBER] RE:xleap problem oguz gurbulak (Mon Jan 26 2009 - 11:48:11 PST)
- Re: [AMBER] RE:xleap problem M. L. Dodson (Mon Jan 26 2009 - 12:47:26 PST)
  - Re: [AMBER] RE:xleap problem oguz gurbulak (Mon Jan 26 2009 - 13:40:22 PST)
    - Re: [AMBER] RE:xleap problem David A. Case (Tue Jan 27 2009 - 07:18:53 PST)
    - Re: [AMBER] RE:xleap problem oguz gurbulak (Thu Jan 29 2009 - 07:53:30 PST)
    - Re: [AMBER] RE:xleap problem M. L. Dodson (Thu Jan 29 2009 - 08:22:22 PST)
[AMBER] atom types deepti nayar (Tue Jan 27 2009 - 01:47:12 PST)
- Re: [AMBER] atom types David A. Case (Tue Jan 27 2009 - 07:13:30 PST)
[AMBER] reg: targeted molecular dynamics balaji nagarajan (Tue Jan 27 2009 - 05:02:03 PST)
- Re: [AMBER] reg: targeted molecular dynamics Carlos Simmerling (Tue Jan 27 2009 - 05:04:57 PST)
[AMBER] Rosetta Academic Training Workshop Nir London (Tue Jan 27 2009 - 05:07:24 PST)
[AMBER] reg.Targeted molecular dynamics balaji nagarajan (Tue Jan 27 2009 - 05:56:54 PST)
[AMBER] reg.Targeted molecular dynamics balaji nagarajan (Tue Jan 27 2009 - 05:57:01 PST)
- Re: [AMBER] reg.Targeted molecular dynamics Carlos Simmerling (Wed Jan 28 2009 - 10:01:43 PST)
Re: [AMBER] Antechamber ligand prep George Tzotzos (Tue Jan 27 2009 - 06:48:11 PST)
- Re: [AMBER] Antechamber ligand prep David A. Case (Tue Jan 27 2009 - 06:59:47 PST)
  - Re: [AMBER] Antechamber ligand prep George Tzotzos (Tue Jan 27 2009 - 07:24:30 PST)
    - Re: [AMBER] Antechamber ligand prep David A. Case (Tue Jan 27 2009 - 07:33:57 PST)
    - Re: [AMBER] Antechamber ligand prep George Tzotzos (Tue Jan 27 2009 - 07:43:19 PST)
    - Re: [AMBER] Antechamber ligand prep George Tzotzos (Tue Jan 27 2009 - 08:44:06 PST)
    - Re: [AMBER] Antechamber ligand prep David Watson (Tue Jan 27 2009 - 07:34:25 PST)
[AMBER] NOTICE: File size limits on AMBER reflector Ross Walker (Tue Jan 27 2009 - 08:35:50 PST)
[AMBER] distance restraint and SHAKE Michael J Yonkunas (Tue Jan 27 2009 - 09:39:56 PST)
- Re: [AMBER] distance restraint and SHAKE Thomas Cheatham III (Tue Jan 27 2009 - 10:16:30 PST)
Re: [AMBER] Building atom and angle parameters George Tzotzos (Tue Jan 27 2009 - 10:24:52 PST)
[AMBER] topology file for GLY with amino and carboxyl group? Jose Borreguero (Tue Jan 27 2009 - 10:57:45 PST)
- Re: [AMBER] topology file for GLY with amino and carboxyl group? FyD (Tue Jan 27 2009 - 12:02:14 PST)
[AMBER] large resp charges for non-natural amino acid Arturas Ziemys (Tue Jan 27 2009 - 14:40:49 PST)
- Re: [AMBER] large resp charges for non-natural amino acid FyD (Wed Jan 28 2009 - 20:04:11 PST)
  - Re: [AMBER] large resp charges for non-natural amino acid Arturas Ziemys (Thu Jan 29 2009 - 07:10:50 PST)
    - Re: [AMBER] large resp charges for non-natural amino acid FyD (Thu Jan 29 2009 - 12:57:51 PST)
    - Re: [AMBER] large resp charges for non-natural amino acid Arturas Ziemys (Thu Jan 29 2009 - 13:38:12 PST)
    - Re: [AMBER] large resp charges for non-natural amino acid FyD (Thu Jan 29 2009 - 13:58:34 PST)
- Re: [AMBER] large resp charges for non-natural amino acid Arturas Ziemys (Sat Jan 31 2009 - 09:03:09 PST)
- Re: [AMBER] large resp charges for non-natural amino acid Arturas Ziemys (Sat Jan 31 2009 - 09:03:44 PST)
[AMBER] PhD position in Computational Structural Biology at Cambridge, UK Swanand Gore (Wed Jan 28 2009 - 02:31:16 PST)
[AMBER] GAFF conjugated ring system dihedrals Floris Buelens (Wed Jan 28 2009 - 04:04:55 PST)
- Re: [AMBER] GAFF conjugated ring system dihedrals David A. Case (Thu Jan 29 2009 - 10:37:24 PST)
[AMBER] Watercap... some querries Waqas Nasir (Wed Jan 28 2009 - 06:54:00 PST)
- Re: [AMBER] Watercap... some querries David A. Case (Wed Jan 28 2009 - 07:01:46 PST)
- Re: [AMBER] Watercap... some querries Waqas Nasir (Wed Jan 28 2009 - 07:10:48 PST)
- Re: [AMBER] Watercap... some querries Robert Duke (Wed Jan 28 2009 - 10:46:02 PST)
[AMBER] generating top file using antechmaber sarvin moghaddam (Wed Jan 28 2009 - 11:49:20 PST)
- Re: [AMBER] generating top file using antechmaber Wei Zhang (Wed Jan 28 2009 - 12:12:20 PST)
  - Re: [AMBER] generating top file using antechmaber sarvin moghaddam (Thu Jan 29 2009 - 07:24:50 PST)
    - Re: [AMBER] generating top file using antechmaber Wei Zhang (Thu Jan 29 2009 - 08:26:22 PST)
- Re: [AMBER] generating top file using antechmaber Wei Zhang (Wed Jan 28 2009 - 12:23:21 PST)
  - Re: [AMBER] generating top file using antechmaber sarvin moghaddam (Wed Jan 28 2009 - 12:33:00 PST)
    - Re: [AMBER] generating top file using antechmaber David A. Case (Thu Jan 29 2009 - 04:51:56 PST)
[AMBER] Compilation and usage of NAB in parallel ? Marek Malý (Wed Jan 28 2009 - 14:25:24 PST)
- Re: [AMBER] Compilation and usage of NAB in parallel ? David A. Case (Thu Jan 29 2009 - 05:22:08 PST)
  - Re: [AMBER] Compilation and usage of NAB in parallel ? Marek Malý (Fri Jan 30 2009 - 06:59:07 PST)
    - Re: [AMBER] Compilation and usage of NAB in parallel ? David A. Case (Fri Jan 30 2009 - 07:51:31 PST)
    - Re: [AMBER] Compilation and usage of NAB in parallel ? Marek Malý (Fri Jan 30 2009 - 08:01:06 PST)
[AMBER] atomic charge m m (Thu Jan 29 2009 - 00:08:47 PST)
- Re: [AMBER] atomic charge Barbault Florent (Thu Jan 29 2009 - 00:24:48 PST)
[AMBER] Problem in pb simulation, PB_Bomb Waqas Nasir (Thu Jan 29 2009 - 01:08:22 PST)
[AMBER] Dr. Ramesh here kureeckal ramesh (Thu Jan 29 2009 - 02:41:10 PST)
- Re: [AMBER] Dr. Ramesh here rpaduri.chem.wayne.edu (Thu Jan 29 2009 - 09:22:20 PST)
  - Re: [AMBER] Dr. Ramesh here kureeckal ramesh (Thu Jan 29 2009 - 17:41:17 PST)
  - Re: [AMBER] Dr. Ramesh here kureeckal ramesh (Thu Jan 29 2009 - 19:18:33 PST)
    - Re: [AMBER] Dr. Ramesh here David A. Case (Fri Jan 30 2009 - 08:08:43 PST)
    - Re: [AMBER] Dr. Ramesh here kureeckal ramesh (Mon Feb 02 2009 - 06:22:51 PST)
[AMBER] Atome Type Mahmoud A. A. Ibrahim (Thu Jan 29 2009 - 02:59:42 PST)
- Re: [AMBER] Atome Type David A. Case (Thu Jan 29 2009 - 05:08:09 PST)
[AMBER] Installation error - Amber10 Ananda Rama Krishnan Selvaraj (Thu Jan 29 2009 - 03:47:44 PST)
- Re: [AMBER] Installation error - Amber10 Andreas Svrcek-Seiler (Thu Jan 29 2009 - 03:52:44 PST)
  - Re: [AMBER] Installation error - Amber10 David A. Case (Thu Jan 29 2009 - 10:33:33 PST)
[AMBER] Problem in watercap simulation, PB_Bomb Waqas Nasir (Thu Jan 29 2009 - 06:21:20 PST)
- RE: [AMBER] Problem in watercap simulation, PB_Bomb Ray Luo (Thu Jan 29 2009 - 09:45:33 PST)
[AMBER] Alpha helix plot Beale, John (Thu Jan 29 2009 - 12:10:11 PST)
- Re: [AMBER] Alpha helix plot Carlos Simmerling (Fri Jan 30 2009 - 14:11:10 PST)
[AMBER] failure to run antechamber with amber 10 Francesco Pietra (Thu Jan 29 2009 - 14:29:18 PST)
- Re: [AMBER] failure to run antechamber with amber 10 David A. Case (Thu Jan 29 2009 - 14:45:53 PST)
  - Re: [AMBER] failure to run antechamber with amber 10 Francesco Pietra (Fri Jan 30 2009 - 00:04:33 PST)
- Re: [AMBER] failure to run antechamber with amber 10 George Tzotzos (Thu Jan 29 2009 - 14:48:50 PST)
[AMBER] AmberTools 1.2 James W. Caldwell (Thu Jan 29 2009 - 16:04:36 PST)
- Re: [AMBER] AmberTools 1.2 David A. Case (Fri Jan 30 2009 - 04:04:41 PST)
[AMBER] adding MG2 problem balaji nagarajan (Fri Jan 30 2009 - 01:45:58 PST)
- Re: [AMBER] adding MG2 problem Scott Brozell (Tue Feb 03 2009 - 11:09:32 PST)
- RE: [AMBER] adding MG2 problem Rausch, Felix (Wed Feb 04 2009 - 05:04:51 PST)
[AMBER] Xleap - solvatebox - counterions Arnaud (Fri Jan 30 2009 - 02:44:58 PST)
- Re: [AMBER] Xleap - solvatebox - counterions David A. Case (Fri Jan 30 2009 - 08:04:23 PST)
  - RE: [AMBER] Xleap - solvatebox - counterions amirhossein taghavi (Sat Jan 31 2009 - 09:34:10 PST)
[AMBER] help momo momo (Fri Jan 30 2009 - 04:35:22 PST)
- RE: [AMBER] help Ross Walker (Fri Jan 30 2009 - 05:42:33 PST)
[AMBER] Amber top file to Charmm top file sarvin moghaddam (Fri Jan 30 2009 - 06:48:44 PST)
[AMBER] REMD fixed atoms Maxime Louet (Fri Jan 30 2009 - 09:26:08 PST)
- Re: [AMBER] REMD fixed atoms Carlos Simmerling (Sun Feb 01 2009 - 10:00:33 PST)
Re: [AMBER] Xleap - solvatebox - counterions Bill Ross (Fri Jan 30 2009 - 10:40:07 PST)
[AMBER] thermo, entropy by quasiharmonic method Carra, Claudio (JSC-SK)[USRA] (Fri Jan 30 2009 - 13:35:37 PST)
- Re: [AMBER] thermo, entropy by quasiharmonic method David A. Case (Fri Jan 30 2009 - 15:40:38 PST)
[AMBER] RE: Tutorial 5 Ross Walker (Fri Jan 30 2009 - 17:32:03 PST)
- Re: [AMBER] RE: Tutorial 5 George Tzotzos (Sun Feb 01 2009 - 13:04:36 PST)
[AMBER] Test run on Solaris 10 X 86 Manikandan Chandrasekaran (Sat Jan 31 2009 - 10:39:14 PST)
- Re: [AMBER] Test run on Solaris 10 X 86 David A. Case (Sat Jan 31 2009 - 18:49:22 PST)
  - [AMBER] Citing AMBER Tools... Aydin, Cihan (Sat Jan 31 2009 - 21:08:36 PST)
    - Re: [AMBER] Citing AMBER Tools... David A. Case (Thu Feb 05 2009 - 07:44:37 PST)
- Re: [AMBER] Test run on Solaris 10 X 86 Atro Tossavainen (Sat Jan 31 2009 - 23:10:30 PST)
  - Re: [AMBER] Test run on Solaris 10 X 86 Manikandan Chandrasekaran (Mon Feb 02 2009 - 11:16:32 PST)
    - Re: [AMBER] Test run on Solaris 10 X 86 Atro Tossavainen (Mon Feb 02 2009 - 15:06:49 PST)
    - Re: [AMBER] Test run on Solaris 10 X 86 Manikandan Chandrasekaran (Tue Feb 03 2009 - 12:28:37 PST)
    - Re: [AMBER] Test run on Solaris 10 X 86 Atro Tossavainen (Wed Feb 04 2009 - 04:33:25 PST)
    - Re: [AMBER] Test run on Solaris 10 X 86 Manikandan Chandrasekaran (Wed Feb 04 2009 - 10:37:21 PST)
    - Re: [AMBER] Test run on Solaris 10 X 86 Atro Tossavainen (Wed Feb 04 2009 - 23:50:12 PST)
    - Re: [AMBER] Test run on Solaris 10 X 86 Manikandan Chandrasekaran (Fri Feb 06 2009 - 09:39:54 PST)
[AMBER] Question on heating for homology based model. drugdesign (Sat Jan 31 2009 - 10:43:06 PST)
- Re: [AMBER] Question on heating for homology based model. Carlos Simmerling (Sun Feb 01 2009 - 09:47:02 PST)
[AMBER] Can bonded pair of atoms be restrainted by NMR distance restraint? liu junjun (Sat Jan 31 2009 - 23:51:39 PST)
- Re: [AMBER] Can bonded pair of atoms be restrainted by NMR distance restraint? Carlos Simmerling (Sun Feb 01 2009 - 09:55:54 PST)
- Re: [AMBER] Can bonded pair of atoms be restrainted by NMR distance restraint? David A. Case (Sun Feb 01 2009 - 10:35:03 PST)
  - Re: [AMBER] Can bonded pair of atoms be restrainted by NMR distance restraint? liu junjun (Mon Feb 02 2009 - 08:25:41 PST)
[AMBER] the output files oguz gurbulak (Sun Feb 01 2009 - 03:13:02 PST)
- Re: [AMBER] the output files Carlos Simmerling (Sun Feb 01 2009 - 10:11:51 PST)
  - Re: [AMBER] the output files oguz gurbulak (Mon Feb 09 2009 - 05:03:47 PST)
    - Re: [AMBER] the output files Carlos Simmerling (Mon Feb 09 2009 - 05:06:41 PST)
    - Re: [AMBER] the output files oguz gurbulak (Tue Feb 10 2009 - 03:14:58 PST)
    - Re: [AMBER] the output files Carlos Simmerling (Tue Feb 10 2009 - 03:22:04 PST)
    - Re: [AMBER] the output files oguz gurbulak (Tue Feb 10 2009 - 06:11:44 PST)
    - Re: [AMBER] the output files Carlos Simmerling (Tue Feb 10 2009 - 06:18:34 PST)
    - RE: [AMBER] the output files Ross Walker (Tue Feb 10 2009 - 09:45:37 PST)
[AMBER] strip frames from crd file aneesh cna (Mon Feb 02 2009 - 01:33:16 PST)
- Re: [AMBER] strip frames from crd file Carlos Simmerling (Mon Feb 02 2009 - 04:12:27 PST)
[AMBER] strip frames from crd file aneesh cna (Mon Feb 02 2009 - 01:35:11 PST)
[AMBER] md simulation on parallel PMEMD oguz gurbulak (Mon Feb 02 2009 - 05:32:31 PST)
- Re: [AMBER] md simulation on parallel PMEMD David A. Case (Mon Feb 02 2009 - 05:54:58 PST)
- Re: [AMBER] md simulation on parallel PMEMD Carlos Simmerling (Mon Feb 02 2009 - 05:55:44 PST)
- Re: [AMBER] md simulation on parallel PMEMD Robert Duke (Mon Feb 02 2009 - 06:03:59 PST)
[AMBER] precision in the trajectory files Jenny Iskrenova (Mon Feb 02 2009 - 06:43:38 PST)
- Re: [AMBER] precision in the trajectory files Adrian Roitberg (Mon Feb 02 2009 - 06:46:49 PST)
- Re: [AMBER] precision in the trajectory files David A. Case (Mon Feb 02 2009 - 06:55:40 PST)
  - Re: [AMBER] precision in the trajectory files Jenny Iskrenova (Tue Feb 03 2009 - 09:07:58 PST)
[AMBER] Radius of Gyration Beale, John (Mon Feb 02 2009 - 09:34:35 PST)
- Re: [AMBER] Radius of Gyration priya priya (Tue Feb 03 2009 - 21:30:07 PST)
[AMBER] Langevin dynamics Antonios Samiotakis (Mon Feb 02 2009 - 09:54:31 PST)
- Re: [AMBER] Langevin dynamics David A. Case (Mon Feb 02 2009 - 11:24:59 PST)
[AMBER] DFT SK parameter for P atom Qizhi Cui (Mon Feb 02 2009 - 11:59:19 PST)
- Re: [AMBER] DFT SK parameter for P atom Adrian Roitberg (Mon Feb 02 2009 - 12:24:00 PST)
  - Re: [AMBER] DFT SK parameter for P atom Qizhi Cui (Mon Feb 02 2009 - 13:37:41 PST)
[AMBER] Micelles set-up?? Alexander Schierholt (Tue Feb 03 2009 - 02:09:52 PST)
[AMBER] creating a restart file from md.out oguz gurbulak (Tue Feb 03 2009 - 02:44:10 PST)
- Re: [AMBER] creating a restart file from md.out Carlos Simmerling (Tue Feb 03 2009 - 03:30:44 PST)
  - Re: [AMBER] creating a restart file from md.out oguz gurbulak (Tue Feb 03 2009 - 05:22:45 PST)
    - Re: [AMBER] creating a restart file from md.out Carlos Simmerling (Tue Feb 03 2009 - 05:36:44 PST)
    - Re: [AMBER] creating a restart file from md.out oguz gurbulak (Tue Feb 03 2009 - 07:29:47 PST)
    - Re: [AMBER] creating a restart file from md.out Carlos Simmerling (Tue Feb 03 2009 - 07:34:44 PST)
[AMBER] nab compile error with -scalapack chaitanya koppisetty (Tue Feb 03 2009 - 05:23:46 PST)
- Re: [AMBER] nab compile error with -scalapack David A. Case (Tue Feb 03 2009 - 06:27:24 PST)
  - Re: [AMBER] nab compile error with -scalapack chaitanya koppisetty (Tue Feb 03 2009 - 10:52:54 PST)
[AMBER] -MMTSB instalation flag ? Marek Malý (Tue Feb 03 2009 - 07:31:38 PST)
- Re: [AMBER] -MMTSB instalation flag ? Scott Brozell (Tue Feb 03 2009 - 09:06:47 PST)
  - Re: [AMBER] -MMTSB instalation flag ? Marek Malý (Tue Feb 03 2009 - 09:15:04 PST)
    - Re: [AMBER] -MMTSB instalation flag ? Scott Brozell (Tue Feb 03 2009 - 09:38:11 PST)
[AMBER] Unit 5 Error on OPEN:mdin on clustuer with mpirun drugdesign (Tue Feb 03 2009 - 09:03:20 PST)
- Re: [AMBER] Unit 5 Error on OPEN:mdin on clustuer with mpirun Ye MEI (Tue Feb 03 2009 - 09:12:54 PST)
  - RE: [AMBER] Unit 5 Error on OPEN:mdin on clustuer with mpirun Ross Walker (Tue Feb 03 2009 - 09:21:07 PST)
    - Re: [AMBER] Unit 5 Error on OPEN:mdin on clustuer with mpirun Carlos Simmerling (Tue Feb 03 2009 - 09:39:58 PST)
- Re: [AMBER] Unit 5 Error on OPEN:mdin on clustuer with mpirun Carlos Simmerling (Tue Feb 03 2009 - 09:17:53 PST)
- Re: [AMBER] Unit 5 Error on OPEN:mdin on clustuer with mpirun drugdesign (Tue Feb 03 2009 - 21:46:19 PST)
  - Re: [AMBER] Unit 5 Error on OPEN:mdin on clustuer with mpirun Carlos Simmerling (Wed Feb 04 2009 - 03:16:34 PST)
[AMBER] out error . .. (Tue Feb 03 2009 - 10:58:46 PST)
- Re: [AMBER] out error Carlos Simmerling (Tue Feb 03 2009 - 11:18:39 PST)
[AMBER] MKL error ? Marek Malý (Tue Feb 03 2009 - 15:00:03 PST)
- RE: [AMBER] MKL error ? Ross Walker (Tue Feb 03 2009 - 21:22:48 PST)
  - Re: [AMBER] MKL error ? Marek Malý (Thu Feb 05 2009 - 04:26:05 PST)
    - RE: [AMBER] MKL error ? Ross Walker (Thu Feb 05 2009 - 10:29:45 PST)
    - Re: [AMBER] MKL error ? Marek Malý (Thu Feb 05 2009 - 12:00:10 PST)
[AMBER] a question about umbrella sampling (US) xiaoqin huang (Wed Feb 04 2009 - 09:12:02 PST)
- Re: [AMBER] a question about umbrella sampling (US) Carlos Simmerling (Wed Feb 04 2009 - 09:20:46 PST)
  - RE: [AMBER] a question about umbrella sampling (US) xiaoqin huang (Wed Feb 04 2009 - 14:23:12 PST)
[AMBER] PDB of a specific frame Jason A. Ford-Green (Wed Feb 04 2009 - 11:46:52 PST)
- Re: [AMBER] PDB of a specific frame Carlos Simmerling (Wed Feb 04 2009 - 11:52:49 PST)
[AMBER] compiling errors Gard Nelson (Wed Feb 04 2009 - 16:30:22 PST)
- Re: [AMBER] compiling errors Carlos Simmerling (Wed Feb 04 2009 - 16:35:28 PST)
- RE: [AMBER] compiling errors Ross Walker (Wed Feb 04 2009 - 16:48:14 PST)
[AMBER] Restarting an MD Simulation Hopkins, Robert (Wed Feb 04 2009 - 16:34:16 PST)
- RE: [AMBER] Restarting an MD Simulation Ross Walker (Wed Feb 04 2009 - 19:03:36 PST)
  - RE: [AMBER] Restarting an MD Simulation Ross Walker (Wed Feb 04 2009 - 19:24:56 PST)
[AMBER] pmemd installation in intelmpi Vijay Manickam Achari (Wed Feb 04 2009 - 19:16:06 PST)
- Re: [AMBER] pmemd installation in intelmpi Robert Duke (Wed Feb 04 2009 - 20:34:37 PST)
  - Re: [AMBER] pmemd installation in intelmpi Vijay Manickam Achari (Thu Feb 05 2009 - 00:38:38 PST)
[AMBER] Compiling Carnal Amber7 in Amber9 Vijay Manickam Achari (Wed Feb 04 2009 - 19:21:14 PST)
- RE: [AMBER] Compiling Carnal Amber7 in Amber9 Bill Ross (Wed Feb 11 2009 - 11:04:53 PST)
  - RE: [AMBER] Compiling Carnal Amber7 in Amber9 Vijay Manickam Achari (Thu Feb 12 2009 - 01:12:29 PST)
    - Re: [AMBER] Compiling Carnal Amber7 in Amber9 David A. Case (Thu Feb 12 2009 - 04:58:03 PST)
    - RE: [AMBER] Compiling Carnal Amber7 in Amber9 Ross Walker (Thu Feb 12 2009 - 06:55:54 PST)
- RE: [AMBER] Compiling Carnal Amber7 in Amber9 Bill Ross (Thu Feb 12 2009 - 12:32:29 PST)
[AMBER] production run terminates due to (*) symbols in xxx.rst Vijay Manickam Achari (Wed Feb 04 2009 - 20:17:38 PST)
- Re: [AMBER] production run terminates due to (*) symbols in xxx.rst vallespardojl.chem.leidenuniv.nl (Thu Feb 05 2009 - 02:28:33 PST)
  - Re: [AMBER] production run terminates due to (*) symbols in xxx.rst Vijay Manickam Achari (Thu Feb 05 2009 - 02:58:26 PST)
- Re: [AMBER] production run terminates due to (*) symbols in xxx.rst Bill Ross (Thu Feb 05 2009 - 09:42:55 PST)
  - Re: [AMBER] production run terminates due to (*) symbols in xxx.rst Vijay Manickam Achari (Thu Feb 05 2009 - 18:50:20 PST)
- RE: [AMBER] production run terminates due to (*) symbols in xxx.rst Ross Walker (Thu Feb 05 2009 - 10:58:41 PST)
[AMBER] how can i deal with large number atoms Wang,Ying (Wed Feb 04 2009 - 21:04:23 PST)
[AMBER] How to build reference coordinate file for targeted MD gmail (Wed Feb 04 2009 - 22:44:22 PST)
- Re: [AMBER] How to build reference coordinate file for targeted MD Carlos Simmerling (Thu Feb 05 2009 - 03:19:12 PST)
  - Re: [AMBER] How to build reference coordinate file for targeted MD xiaonan zhang (Thu Feb 05 2009 - 04:00:38 PST)
- Re: [AMBER] How to build reference coordinate file for targeted MD gmail (Thu Feb 05 2009 - 21:20:59 PST)
  - RE: [AMBER] How to build reference coordinate file for targeted MD Ross Walker (Fri Feb 06 2009 - 00:14:14 PST)
[AMBER] error in executing sander.MPI in amber9 Vijay Manickam Achari (Thu Feb 05 2009 - 00:37:09 PST)
- Re: [AMBER] error in executing sander.MPI in amber9 Atro Tossavainen (Thu Feb 05 2009 - 03:08:59 PST)
[AMBER] Solvation potential and free energies guardiani.fi.infn.it (Thu Feb 05 2009 - 04:27:21 PST)
- Re: [AMBER] Solvation potential and free energies Carlos Simmerling (Thu Feb 05 2009 - 04:33:08 PST)
- Re: [AMBER] Solvation potential and free energies Lorenzo Gontrani (Thu Feb 05 2009 - 04:34:47 PST)
- Re: [AMBER] Solvation potential and free energies David A. Case (Fri Feb 06 2009 - 05:34:25 PST)
[AMBER] parameter files for D-amino acid Vsatheesh Patil (Thu Feb 05 2009 - 05:04:12 PST)
- Re: [AMBER] parameter files for D-amino acid Carlos Simmerling (Thu Feb 05 2009 - 05:37:32 PST)
  - Re: [AMBER] parameter files for D-amino acid vijayaraj.clri.res.in (Thu Feb 05 2009 - 06:49:56 PST)
    - Re: [AMBER] parameter files for D-amino acid FyD (Thu Feb 05 2009 - 07:00:55 PST)
    - Re: [AMBER] parameter files for D-amino acid Carlos Simmerling (Thu Feb 05 2009 - 07:06:09 PST)
    - Re: [AMBER] parameter files for D-amino acid Andrew Purkiss-Trew (Thu Feb 05 2009 - 07:02:25 PST)
    - Re: [AMBER] parameter files for D-amino acid Carlos Simmerling (Thu Feb 05 2009 - 07:10:18 PST)
[AMBER] pmemd on BlueGene/P? Hannes Loeffler (Thu Feb 05 2009 - 05:09:45 PST)
- Re: [AMBER] pmemd on BlueGene/P? Robert Duke (Thu Feb 05 2009 - 05:42:32 PST)
- Re: [AMBER] pmemd on BlueGene/P? Carlos P Sosa (Thu Feb 05 2009 - 12:48:57 PST)
  - Re: [AMBER] pmemd on BlueGene/P? Hannes Loeffler (Fri Feb 06 2009 - 01:01:37 PST)
Re: [AMBER] Compiling Carnal Amber7 in Amber9 Bill Ross (Thu Feb 05 2009 - 09:36:00 PST)
- Re: [AMBER] Compiling Carnal Amber7 in Amber9 Vijay Manickam Achari (Tue Feb 10 2009 - 23:58:08 PST)
  - RE: [AMBER] Compiling Carnal Amber7 in Amber9 Ross Walker (Wed Feb 11 2009 - 08:53:10 PST)
[AMBER] amber9 installation problem in SMP IA64 Vijay Manickam Achari (Thu Feb 05 2009 - 23:00:16 PST)
- Re: [AMBER] amber9 installation problem in SMP IA64 David A. Case (Fri Feb 06 2009 - 05:25:55 PST)
  - Re: [AMBER] amber9 installation problem in SMP IA64 Vijay Manickam Achari (Tue Feb 10 2009 - 00:30:55 PST)
    - Re: [AMBER] amber9 installation problem in SMP IA64 David A. Case (Tue Feb 10 2009 - 04:41:29 PST)
    - RE: [AMBER] amber9 installation problem in SMP IA64 Ross Walker (Tue Feb 10 2009 - 09:56:22 PST)
    - RE: [AMBER] amber9 installation problem in SMP IA64 Vijay Manickam Achari (Wed Feb 11 2009 - 01:36:31 PST)
    - Re: [AMBER] amber9 installation problem in SMP IA64 David A. Case (Wed Feb 11 2009 - 05:07:48 PST)
    - Re: [AMBER] amber9 installation problem in SMP IA64 Vijay Manickam Achari (Thu Feb 12 2009 - 01:13:55 PST)
    - RE: [AMBER] amber9 installation problem in SMP IA64 Ross Walker (Thu Feb 12 2009 - 06:54:49 PST)
    - RE: [AMBER] amber9 installation problem in SMP IA64 Vijay Manickam Achari (Thu Feb 12 2009 - 01:21:01 PST)
[AMBER] mpirun problem in HPC Vijay Manickam Achari (Thu Feb 05 2009 - 23:01:29 PST)
- RE: [AMBER] mpirun problem in HPC Ross Walker (Fri Feb 06 2009 - 00:05:37 PST)
[AMBER] second derivative matrix calculation Marie Brut (Fri Feb 06 2009 - 02:47:18 PST)
- Re: [AMBER] second derivative matrix calculation David A. Case (Fri Feb 06 2009 - 05:19:52 PST)
[AMBER] extract frames from a .mdcrd vallespardojl.chem.leidenuniv.nl (Fri Feb 06 2009 - 02:48:23 PST)
- Re: [AMBER] extract frames from a .mdcrd Carlos Simmerling (Fri Feb 06 2009 - 03:12:00 PST)
  - Re: [AMBER] extract frames from a .mdcrd vallespardojl.chem.leidenuniv.nl (Tue Feb 10 2009 - 00:52:19 PST)
    - Re: [AMBER] extract frames from a .mdcrd Carlos Simmerling (Tue Feb 10 2009 - 02:58:12 PST)
- Re: [AMBER] extract frames from a .mdcrd Bill Ross (Fri Feb 06 2009 - 11:13:27 PST)
[AMBER] MSD and stress tensors oguz gurbulak (Fri Feb 06 2009 - 03:09:12 PST)
[AMBER] script to convert GLYCAM ff in CHARMM format ABEL Stephane 175950 (Fri Feb 06 2009 - 06:39:04 PST)
- Re: [AMBER] script to convert GLYCAM ff in CHARMM format Lachele Foley (Lists) (Fri Feb 06 2009 - 06:57:17 PST)
RE : [AMBER] script to convert GLYCAM ff in CHARMM format ABEL Stephane 175950 (Fri Feb 06 2009 - 07:03:19 PST)
[AMBER] Resp charge . .. (Fri Feb 06 2009 - 09:34:12 PST)
[AMBER] ptraj fails to recognize binary REMD output Kevin Wiehe (Fri Feb 06 2009 - 09:44:21 PST)
[AMBER] distance calculation by reading in the restraint file xiaoqin huang (Fri Feb 06 2009 - 09:52:56 PST)
- RE: [AMBER] distance calculation by reading in the restraint file xiaoqin huang (Fri Feb 06 2009 - 10:34:34 PST)
  - Re: [AMBER] distance calculation by reading in the restraint file David A. Case (Fri Feb 06 2009 - 14:35:55 PST)
    - RE: [AMBER] distance calculation by reading in the restraint file xiaoqin huang (Fri Feb 06 2009 - 15:28:59 PST)
- Re: [AMBER] distance calculation by reading in the restraint file David A. Case (Fri Feb 06 2009 - 14:03:08 PST)
[AMBER] MD analysis oguz gurbulak (Sat Feb 07 2009 - 06:56:10 PST)
[AMBER] Stability of a long NPT md trajectory? Bill K (Sun Feb 08 2009 - 23:07:24 PST)
- Re: [AMBER] Stability of a long NPT md trajectory? Carlos Simmerling (Mon Feb 09 2009 - 04:08:29 PST)
- Re: [AMBER] Stability of a long NPT md trajectory? Robert Duke (Mon Feb 09 2009 - 05:25:10 PST)
  - Re: [AMBER] Stability of a long NPT md trajectory? Bill K (Mon Feb 09 2009 - 12:56:53 PST)
    - Re: [AMBER] Stability of a long NPT md trajectory? Carlos Simmerling (Mon Feb 09 2009 - 16:56:50 PST)
    - Re: [AMBER] Stability of a long NPT md trajectory? Adrian Roitberg (Mon Feb 09 2009 - 17:03:45 PST)
- Re: [AMBER] Stability of a long NPT md trajectory? Robert Duke (Mon Feb 09 2009 - 18:21:31 PST)
  - Re: [AMBER] Stability of a long NPT md trajectory? Carlos Simmerling (Mon Feb 09 2009 - 19:10:55 PST)
- Re: [AMBER] Stability of a long NPT md trajectory? Robert Duke (Mon Feb 09 2009 - 20:20:57 PST)
  - Re: [AMBER] Stability of a long NPT md trajectory? Bill K (Mon Feb 09 2009 - 23:37:31 PST)
- Re: [AMBER] Stability of a long NPT md trajectory? Robert Duke (Tue Feb 10 2009 - 05:40:55 PST)
  - Re: [AMBER] Stability of a long NPT md trajectory? Bill K (Tue Feb 10 2009 - 11:39:22 PST)
- Re: [AMBER] Stability of a long NPT md trajectory? Robert Duke (Tue Feb 10 2009 - 12:29:15 PST)
[AMBER] second derivative matrix Marie Brut (Mon Feb 09 2009 - 00:53:01 PST)
- Re: [AMBER] second derivative matrix Adrian Roitberg (Mon Feb 09 2009 - 06:29:51 PST)
- Re: [AMBER] second derivative matrix David A. Case (Mon Feb 09 2009 - 07:05:18 PST)
[AMBER] NAB md function prints strange output Jochen Heil (Mon Feb 09 2009 - 03:30:21 PST)
- Re: [AMBER] NAB md function prints strange output David A. Case (Mon Feb 09 2009 - 04:58:43 PST)
  - Re: [AMBER] NAB md function prints strange output Jochen Heil (Tue Feb 10 2009 - 04:19:56 PST)
    - Re: [AMBER] NAB md function prints strange output David A. Case (Tue Feb 10 2009 - 04:46:40 PST)
    - Re: [AMBER] NAB md function prints strange output Scott Brozell (Thu Mar 12 2009 - 14:04:15 PDT)
[AMBER] APS & ff03 Mahmoud A. A. Ibrahim (Mon Feb 09 2009 - 06:49:56 PST)
[AMBER] parmchk s. Bill (Mon Feb 09 2009 - 07:55:20 PST)
- RE: [AMBER] parmchk Ross Walker (Mon Feb 09 2009 - 08:28:20 PST)
[AMBER] hbond analysis aneesh cna (Mon Feb 09 2009 - 09:55:25 PST)
- Re: [AMBER] hbond analysis Bala subramanian (Mon Feb 09 2009 - 10:33:39 PST)
- Re: [AMBER] hbond analysis Carlos Simmerling (Mon Feb 09 2009 - 10:52:14 PST)
[AMBER] Solvating inside of a channel Daniel Smith (Mon Feb 09 2009 - 13:03:16 PST)
[AMBER] Confusion regarding box size parul sharma (Mon Feb 09 2009 - 23:20:01 PST)
- Re: [AMBER] Confusion regarding box size vallespardojl.chem.leidenuniv.nl (Tue Feb 10 2009 - 00:35:24 PST)
- Re: [AMBER] Confusion regarding box size Wei Zhang (Tue Feb 10 2009 - 05:07:38 PST)
  - Re: [AMBER] Confusion regarding box size parul sharma (Tue Feb 10 2009 - 05:29:38 PST)
[AMBER] Irregularity in box during md parul sharma (Tue Feb 10 2009 - 02:35:18 PST)
- Re: [AMBER] Irregularity in box during md Carlos Simmerling (Tue Feb 10 2009 - 02:57:02 PST)
- Re: [AMBER] Irregularity in box during md Bill Ross (Tue Feb 10 2009 - 09:24:12 PST)
[AMBER] RED-vIII: Scratch directory for Gaussian [NOT FOUND] Patrick Schopf (Tue Feb 10 2009 - 06:15:42 PST)
- RE : [AMBER] RED-vIII: Scratch directory for Gaussian [NOT FOUND] ABEL Stephane 175950 (Tue Feb 10 2009 - 06:39:17 PST)
- Re: [AMBER] RED-vIII: Scratch directory for Gaussian [NOT FOUND] FyD (Tue Feb 10 2009 - 07:05:56 PST)
[AMBER] Scaling of dipole interactions Diddo Diddens (Tue Feb 10 2009 - 06:33:18 PST)
[AMBER] formate parameters Dmitri Nilov (Tue Feb 10 2009 - 06:47:31 PST)
[AMBER] array out of bound in Amber10 tests Shan-ho Tsai (Tue Feb 10 2009 - 08:19:42 PST)
- Re: [AMBER] array out of bound in Amber10 tests David A. Case (Tue Feb 10 2009 - 08:39:43 PST)
  - Re: [AMBER] array out of bound in Amber10 tests Shan-ho Tsai (Tue Feb 10 2009 - 13:04:43 PST)
    - Re: [AMBER] array out of bound in Amber10 tests David A. Case (Tue Feb 10 2009 - 13:30:36 PST)
    - Re: [AMBER] array out of bound in Amber10 tests Shan-ho Tsai (Wed Feb 11 2009 - 07:38:23 PST)
    - Re: [AMBER] array out of bound in Amber10 tests Carlos Simmerling (Wed Feb 11 2009 - 08:14:49 PST)
    - Re: [AMBER] array out of bound in Amber10 tests Shan-ho Tsai (Wed Feb 11 2009 - 14:24:10 PST)
    - Re: [AMBER] array out of bound in Amber10 tests Carlos Simmerling (Fri Feb 13 2009 - 08:38:04 PST)
    - Re: [AMBER] array out of bound in Amber10 tests Shan-ho Tsai (Mon Feb 16 2009 - 08:53:05 PST)
[AMBER] reg . run TMD balaji nagarajan (Tue Feb 10 2009 - 09:36:28 PST)
- Re: [AMBER] reg . run TMD Carlos Simmerling (Tue Feb 10 2009 - 09:48:22 PST)
[AMBER] Solvating the interior of a channel Daniel Smith (Tue Feb 10 2009 - 12:42:09 PST)
- Re: [AMBER] Solvating the interior of a channel Shozeb Haider (Wed Feb 11 2009 - 05:15:07 PST)
- Re: [AMBER] Solvating the interior of a channel Jason A. Ford-Green (Wed Feb 11 2009 - 08:04:24 PST)
  - Re: [AMBER] Solvating the interior of a channel Daniel Smith (Fri Feb 13 2009 - 13:02:24 PST)
    - Re: [AMBER] Solvating the interior of a channel Daniel Smith (Sun Feb 15 2009 - 14:40:23 PST)
[AMBER] AMBER: chiral restraint on protein amit jain (Tue Feb 10 2009 - 16:48:12 PST)
- Re: [AMBER] AMBER: chiral restraint on protein David A. Case (Wed Feb 11 2009 - 04:56:05 PST)
[AMBER] how to get amber 10 Prem Prakash Pathak (Tue Feb 10 2009 - 18:42:37 PST)
- RE: [AMBER] how to get amber 10 Ross Walker (Tue Feb 10 2009 - 19:20:33 PST)
[AMBER] nmr refinement of dimer Sally Pias (Wed Feb 11 2009 - 01:05:56 PST)
- Re: [AMBER] nmr refinement of dimer Therese Malliavin (Wed Feb 11 2009 - 02:57:06 PST)
- Re: [AMBER] nmr refinement of dimer David A. Case (Wed Feb 11 2009 - 05:02:37 PST)
  - Re: [AMBER] nmr refinement of dimer Sally Pias (Thu Feb 12 2009 - 01:17:44 PST)
    - Re: [AMBER] nmr refinement of dimer David A. Case (Thu Feb 12 2009 - 05:08:08 PST)
[AMBER] Chlorine containing molecule CHAMI F. (Wed Feb 11 2009 - 05:39:19 PST)
- Re: [AMBER] Chlorine containing molecule Carlos Simmerling (Wed Feb 11 2009 - 05:48:27 PST)
[AMBER] Optimization problem Daniel Emery (Thu Feb 12 2009 - 02:01:49 PST)
- Re: [AMBER] Optimization problem David A. Case (Thu Feb 12 2009 - 04:58:17 PST)
  - Re: [AMBER] Optimization problem Daniel Emery (Thu Feb 12 2009 - 06:11:14 PST)
    - Re: [AMBER] Optimization problem Carlos Simmerling (Thu Feb 12 2009 - 06:21:28 PST)
    - Re: [AMBER] Optimization problem David A. Case (Thu Feb 12 2009 - 06:35:52 PST)
    - [AMBER] non bonded parameteters index Swarup Gupta (Thu Feb 12 2009 - 16:07:46 PST)
    - Re: [AMBER] non bonded parameteters index Alessandro Nascimento (Thu Feb 12 2009 - 16:14:44 PST)
    - Re: [AMBER] non bonded parameteters index Adrian Roitberg (Thu Feb 12 2009 - 16:15:33 PST)
- Re: [AMBER] Optimization problem Gustavo Seabra (Thu Feb 12 2009 - 06:48:23 PST)
[AMBER] error in xleap: ligand binding using MMand QMMM tech kureeckal ramesh (Thu Feb 12 2009 - 02:27:41 PST)
- Re: [AMBER] error in xleap: ligand binding using MMand QMMM tech Gustavo Seabra (Thu Feb 12 2009 - 06:32:17 PST)
[AMBER] H-bond information Beale, John (Thu Feb 12 2009 - 07:32:30 PST)
[AMBER] atoms fly out of the box in NVT calculations iccy liu (Thu Feb 12 2009 - 13:48:24 PST)
- Re: [AMBER] atoms fly out of the box in NVT calculations Carlos Simmerling (Thu Feb 12 2009 - 14:05:10 PST)
- Re: [AMBER] atoms fly out of the box in NVT calculations Ross Walker (Thu Feb 12 2009 - 18:22:57 PST)
  - RE: [AMBER] atoms fly out of the box in NVT calculations iccy liu (Sun Feb 15 2009 - 15:34:37 PST)
[AMBER] How to jude whether the trajectory is stable or not Jeffrey (Thu Feb 12 2009 - 18:33:53 PST)
[AMBER] Beginner question Heath Watts (Fri Feb 13 2009 - 13:18:42 PST)
- Re: [AMBER] Beginner question Carlos Simmerling (Fri Feb 13 2009 - 13:24:37 PST)
  - Re: [AMBER] Beginner question Heath Watts (Fri Feb 13 2009 - 17:19:44 PST)
- Re: [AMBER] Beginner question Barbault Florent (Fri Feb 13 2009 - 13:25:13 PST)
  - Re: [AMBER] Beginner question Heath Watts (Fri Feb 13 2009 - 17:20:46 PST)
[AMBER] Question about improper torsions... Antonios Samiotakis (Fri Feb 13 2009 - 14:57:03 PST)
- Re: [AMBER] Question about improper torsions... David A. Case (Sat Feb 14 2009 - 05:32:21 PST)
[AMBER] New atom type with 7 bonds Akansha Saxena (Fri Feb 13 2009 - 15:56:47 PST)
- Re: [AMBER] New atom type with 7 bonds David A. Case (Mon Feb 16 2009 - 06:28:25 PST)
[AMBER] install Amber 10 to Macbook Adrien Delmont (Sat Feb 14 2009 - 03:06:50 PST)
- Re: [AMBER] install Amber 10 to Macbook David A. Case (Sat Feb 14 2009 - 15:17:53 PST)
  - Re: [AMBER] install Amber 10 to Macbook Tyler Luchko (Sun Feb 15 2009 - 11:27:53 PST)
    - Re: [AMBER] install Amber 10 to Macbook David Watson (Sun Feb 15 2009 - 11:52:36 PST)
[AMBER] Any link to a major QM code? Francesco Pietra (Sun Feb 15 2009 - 09:58:30 PST)
- Re: [AMBER] Any link to a major QM code? Gustavo Seabra (Sun Feb 15 2009 - 16:17:32 PST)
  - Re: [AMBER] Any link to a major QM code? Adrian Roitberg (Sun Feb 15 2009 - 18:59:01 PST)
    - Re: [AMBER] Any link to a major QM code? Francesco Pietra (Mon Feb 16 2009 - 06:47:04 PST)
    - Re: [AMBER] Any link to a major QM code? Gustavo Seabra (Mon Feb 16 2009 - 08:51:03 PST)
[AMBER] Error running sander.MPI Vijay Manickam Achari (Mon Feb 16 2009 - 00:23:05 PST)
- Re: [AMBER] Error running sander.MPI Carlos Simmerling (Mon Feb 16 2009 - 03:51:08 PST)
- RE: [AMBER] Error running sander.MPI Rausch, Felix (Tue Feb 17 2009 - 00:15:19 PST)
  - Re: [AMBER] Error running sander.MPI Anselm Horn (Tue Feb 17 2009 - 02:28:47 PST)
[AMBER] Error installing Amber David Patiño (Mon Feb 16 2009 - 04:02:31 PST)
- Re: [AMBER] Error installing Amber David A. Case (Mon Feb 16 2009 - 06:21:41 PST)
  - Re: [AMBER] Error installing Amber David Patiño (Tue Feb 17 2009 - 06:58:05 PST)
[AMBER] Iron 2+ parameters Hrvoje Brkić (Mon Feb 16 2009 - 05:53:57 PST)
- Re: [AMBER] Iron 2+ parameters Syed Tarique Moin (Mon Feb 16 2009 - 08:25:34 PST)
- Re: [AMBER] Iron 2+ parameters FyD (Mon Feb 16 2009 - 10:25:45 PST)
[AMBER] density and volume in NVT ensamble oguz gurbulak (Mon Feb 16 2009 - 05:58:13 PST)
- Re: [AMBER] density and volume in NVT ensamble Carlos Simmerling (Mon Feb 16 2009 - 06:04:22 PST)
  - Re: [AMBER] density and volume in NVT ensamble oguz gurbulak (Mon Feb 16 2009 - 06:25:52 PST)
    - Re: [AMBER] density and volume in NVT ensamble oguz gurbulak (Mon Feb 16 2009 - 06:27:01 PST)
    - Re: [AMBER] density and volume in NVT ensamble Carlos Simmerling (Mon Feb 16 2009 - 06:30:02 PST)
    - Re: [AMBER] density and volume in NVT ensamble Adrian Roitberg (Fri Feb 06 2009 - 06:31:24 PST)
- Re: [AMBER] density and volume in NVT ensamble Andrew Purkiss-Trew (Mon Feb 16 2009 - 06:14:40 PST)
  - Re: [AMBER] density and volume in NVT ensamble oguz gurbulak (Mon Feb 16 2009 - 06:32:07 PST)
    - Re: [AMBER] density and volume in NVT ensamble Andrew Purkiss-Trew (Mon Feb 16 2009 - 06:45:25 PST)
[AMBER] contant force pulling simulation with amber 10 li hui (Mon Feb 16 2009 - 09:01:36 PST)
- Re: [AMBER] contant force pulling simulation with amber 10 Gustavo Seabra (Mon Feb 16 2009 - 10:11:40 PST)
[AMBER] can ptraj output the trajectory of the residue CM? Jose Borreguero (Mon Feb 16 2009 - 11:47:34 PST)
[AMBER] using ptraj Molecular Dynamics (Mon Feb 16 2009 - 12:31:42 PST)
- Re: [AMBER] using ptraj Carlos Simmerling (Mon Feb 16 2009 - 12:41:54 PST)
- Re: [AMBER] using ptraj Molecular Dynamics (Tue Feb 17 2009 - 03:44:09 PST)
  - Re: [AMBER] using ptraj Carlos Simmerling (Tue Feb 17 2009 - 04:37:15 PST)
- Re: [AMBER] using ptraj Molecular Dynamics (Tue Feb 17 2009 - 05:31:02 PST)
  - Re: [AMBER] using ptraj Carlos Simmerling (Tue Feb 17 2009 - 05:34:33 PST)
- Re: [AMBER] using ptraj Molecular Dynamics (Tue Feb 17 2009 - 06:11:16 PST)
  - Re: [AMBER] using ptraj Carlos Simmerling (Tue Feb 17 2009 - 06:29:07 PST)
[AMBER] Normal errors on job kill? ben rodriguez (Mon Feb 16 2009 - 18:35:43 PST)
- Re: [AMBER] Normal errors on job kill? David A. Case (Mon Feb 16 2009 - 20:25:54 PST)
[AMBER] Amber 9 Install - AMBERBUILDFLAGS error ben rodriguez (Mon Feb 16 2009 - 19:39:14 PST)
- Re: [AMBER] Amber 9 Install - AMBERBUILDFLAGS error David A. Case (Mon Feb 16 2009 - 20:29:41 PST)
[AMBER] parallel run error balaji nagarajan (Tue Feb 17 2009 - 00:19:23 PST)
- Re: [AMBER] parallel run error Carlos Simmerling (Tue Feb 17 2009 - 04:40:03 PST)
[AMBER] constph tutorial help Prem Prakash Pathak (Tue Feb 17 2009 - 04:53:37 PST)
[AMBER] (no subject) Beale, John (Tue Feb 17 2009 - 05:02:25 PST)
- Re: [AMBER] (no subject) Carlos Simmerling (Tue Feb 17 2009 - 05:10:49 PST)
[AMBER] MD simulation with a partially flexible system Jeffrey (Tue Feb 17 2009 - 06:38:10 PST)
- Re: [AMBER] MD simulation with a partially flexible system Carlos Simmerling (Tue Feb 17 2009 - 06:45:33 PST)
  - Re: Re: [AMBER] MD simulation with a partially flexible system Jeffrey (Tue Feb 17 2009 - 18:19:47 PST)
    - Re: Re: [AMBER] MD simulation with a partially flexible system Carlos Simmerling (Wed Feb 18 2009 - 04:35:40 PST)
[AMBER] DM complexation . .. (Tue Feb 17 2009 - 07:10:49 PST)
- Re: [AMBER] DM complexation Carlos Simmerling (Tue Feb 17 2009 - 07:28:34 PST)
  - RE: [AMBER] DM complexation . .. (Tue Feb 17 2009 - 07:36:01 PST)
    - Re: [AMBER] DM complexation Carlos Simmerling (Tue Feb 17 2009 - 07:59:15 PST)
[AMBER] How to get the energy of a molecule in a whole system Wang,Ying (Tue Feb 17 2009 - 08:28:39 PST)
[AMBER] restraint angle m m (Tue Feb 17 2009 - 09:17:00 PST)
- Re: [AMBER] restraint angle David A. Case (Tue Feb 17 2009 - 09:52:49 PST)
[AMBER] PMF calculation Arnaud (Tue Feb 17 2009 - 10:10:18 PST)
- Re: [AMBER] PMF calculation David A. Case (Tue Feb 17 2009 - 18:23:20 PST)
[AMBER] Need suggestion on payment for Ph.D student majored in molecular simulation Xu Dong (Tue Feb 17 2009 - 10:54:58 PST)
- Re: [AMBER] Need suggestion on payment for Ph.D student majored in molecular simulation Adrian Roitberg (Tue Feb 17 2009 - 10:57:56 PST)
[AMBER] glycam and solvateoct command Heath Watts (Tue Feb 17 2009 - 11:51:13 PST)
- Re: [AMBER] glycam and solvateoct command Barbault Florent (Tue Feb 17 2009 - 12:13:58 PST)
  - Re: [AMBER] glycam and solvateoct command Heath Watts (Tue Feb 17 2009 - 14:31:35 PST)
    - Re: [AMBER] glycam and solvateoct command Lachele Foley (Lists) (Wed Feb 18 2009 - 07:00:34 PST)
[AMBER] problem compiling nmode.c Shan-ho Tsai (Tue Feb 17 2009 - 12:38:00 PST)
- Re: [AMBER] problem compiling nmode.c David A. Case (Tue Feb 17 2009 - 18:45:03 PST)
  - [AMBER] NVT vs NPT Chih-Ying Lin (Tue Feb 17 2009 - 19:23:05 PST)
    - [AMBER] Scientific Linux 5.2 Catein Catherine (Tue Feb 17 2009 - 23:13:23 PST)
    - Re: [AMBER] NVT vs NPT Carlos Simmerling (Wed Feb 18 2009 - 04:18:49 PST)
    - [AMBER] g(r) extrapolation Lorenzo Gontrani (Wed Feb 18 2009 - 07:16:26 PST)
    - Re: [AMBER] g(r) extrapolation Thomas Cheatham III (Wed Feb 18 2009 - 09:15:36 PST)
    - Re: [AMBER] g(r) extrapolation Lorenzo Gontrani (Thu Feb 19 2009 - 01:23:19 PST)
  - Re: [AMBER] problem compiling nmode.c Shan-ho Tsai (Thu Feb 19 2009 - 06:49:39 PST)
[AMBER] reg.Targeted molecular dynamics balaji nagarajan (Tue Feb 17 2009 - 21:26:49 PST)
- Re: [AMBER] reg.Targeted molecular dynamics Simon Becker (Wed Feb 18 2009 - 03:38:54 PST)
  - RE: [AMBER] reg.Targeted molecular dynamics balaji nagarajan (Wed Feb 18 2009 - 06:07:09 PST)
[AMBER] protein monomerizartion times and simulation with implicit solvent drugdesign (Wed Feb 18 2009 - 02:27:17 PST)
- Re: [AMBER] protein monomerizartion times and simulation with implicit solvent Carlos Simmerling (Wed Feb 18 2009 - 04:16:00 PST)
[AMBER] Re: AMBER: GBSA EGB = NaN Markus Kaukonen (Wed Feb 18 2009 - 04:26:28 PST)
- [AMBER] Re: AMBER: GBSA EGB = NaN Markus Kaukonen (Thu Feb 19 2009 - 05:34:38 PST)
[AMBER] IG not change at each restart of NPT simulation Jeffrey (Wed Feb 18 2009 - 04:49:47 PST)
- Re: [AMBER] IG not change at each restart of NPT simulation Robert Duke (Wed Feb 18 2009 - 05:57:35 PST)
  - Re: [AMBER] IG not change at each restart of NPT simulation Carlos Simmerling (Wed Feb 18 2009 - 06:04:47 PST)
    - Re: [AMBER] IG not change at each restart of NPT simulation Adrian Roitberg (Wed Feb 18 2009 - 06:46:36 PST)
- Re: [AMBER] IG not change at each restart of NPT simulation Robert Duke (Wed Feb 18 2009 - 06:15:00 PST)
- Re: [AMBER] IG not change at each restart of NPT simulation Hopkins, Robert (Wed Mar 18 2009 - 15:55:33 PDT)
- RE: [AMBER] IG not change at each restart of NPT simulation Ross Walker (Wed Mar 18 2009 - 16:07:07 PDT)
  - RE: [AMBER] IG not change at each restart of NPT simulation Hopkins, Robert (Wed Mar 18 2009 - 16:15:54 PDT)
- RE: [AMBER] IG not change at each restart of NPT simulation Rajesh Raju (Thu Mar 19 2009 - 05:54:26 PDT)
- Re: [AMBER] IG not change at each restart of NPT simulation Robert Duke (Thu Mar 19 2009 - 06:24:02 PDT)
  - Re: [AMBER] IG not change at each restart of NPT simulation Adrian Roitberg (Thu Mar 19 2009 - 06:30:10 PDT)
- Re: [AMBER] IG not change at each restart of NPT simulation Robert Duke (Thu Mar 19 2009 - 07:05:35 PDT)
  - Re: [AMBER] IG not change at each restart of NPT simulation Rajesh Raju (Fri Mar 20 2009 - 06:20:09 PDT)
- Re: [AMBER] IG not change at each restart of NPT simulation Robert Duke (Fri Mar 20 2009 - 06:58:18 PDT)
[AMBER] How to constrain the hydrogen bonding distances... Majeed Shaik (Wed Feb 18 2009 - 06:11:37 PST)
- Re: [AMBER] How to constrain the hydrogen bonding distances... Carlos Simmerling (Wed Feb 18 2009 - 06:25:47 PST)
- Re: [AMBER] How to constrain the hydrogen bonding distances... David A. Case (Wed Feb 18 2009 - 06:28:56 PST)
[AMBER] ./configure_amber: line 1211: cd: netcdf/src: No such file or directory Andrew Olson (Wed Feb 18 2009 - 09:08:57 PST)
- Re: [AMBER] ./configure_amber: line 1211: cd: netcdf/src: No such file or directory David A. Case (Wed Feb 18 2009 - 10:11:56 PST)
[AMBER] question about ptraj hydrogen bond analysis monica bhattacharee (Wed Feb 18 2009 - 11:45:17 PST)
- Re: [AMBER] question about ptraj hydrogen bond analysis Thomas Cheatham III (Wed Feb 18 2009 - 12:21:27 PST)
[AMBER] (NTB /= 0 && NTP /= 0) but IFBOX == 0 error Majeed Shaik (Wed Feb 18 2009 - 12:09:17 PST)
- Re: [AMBER] (NTB /= 0 && NTP /= 0) but IFBOX == 0 error David A. Case (Wed Feb 18 2009 - 12:35:12 PST)
[AMBER] test charge Dan Kaps (Wed Feb 18 2009 - 18:27:32 PST)
- Re: [AMBER] test charge David A. Case (Wed Feb 18 2009 - 20:24:04 PST)
- Re: [AMBER] test charge Dan Kaps (Thu Feb 19 2009 - 18:22:31 PST)
  - Re: [AMBER] test charge David A. Case (Thu Feb 19 2009 - 20:48:29 PST)
- Re: [AMBER] test charge Dan Kaps (Fri Feb 20 2009 - 08:58:17 PST)
  - Re: [AMBER] test charge Jenny Iskrenova (Fri Feb 20 2009 - 12:32:14 PST)
[AMBER] distance matrix plot and secondary structure analysis Siddharth Rastogi (Wed Feb 18 2009 - 22:17:47 PST)
- Re: [AMBER] distance matrix plot and secondary structure analysis Carlos Simmerling (Thu Feb 19 2009 - 04:48:57 PST)
[AMBER] Protein motions comparison Dmitry Osolodkin (Thu Feb 19 2009 - 03:58:24 PST)
- Re: [AMBER] Protein motions comparison Hannes Loeffler (Thu Feb 19 2009 - 04:07:47 PST)
[AMBER] secstruct Beale, John (Thu Feb 19 2009 - 05:22:20 PST)
- Re: [AMBER] secstruct Carlos Simmerling (Thu Feb 19 2009 - 05:30:16 PST)
[AMBER] dipole correlation function Jeffrey (Thu Feb 19 2009 - 06:18:20 PST)
- Re: [AMBER] dipole correlation function Carlos Simmerling (Thu Feb 19 2009 - 06:39:16 PST)
  - Re: Re: [AMBER] dipole correlation function Jeffrey (Thu Feb 19 2009 - 08:39:15 PST)
    - Re: Re: [AMBER] dipole correlation function Carlos Simmerling (Thu Feb 19 2009 - 09:23:03 PST)
    - [AMBER] linux install problem Andrew Olson (Thu Feb 19 2009 - 10:44:14 PST)
    - Re: [AMBER] linux install problem Gustavo Seabra (Thu Feb 19 2009 - 12:47:18 PST)
    - Re: Re: Re: [AMBER] dipole correlation function Jeffrey (Thu Feb 19 2009 - 17:31:08 PST)
[AMBER] paper of interest for FF development/solvent models David Mobley (Thu Feb 19 2009 - 07:15:04 PST)
[AMBER] (no subject) Andrew Olson (Thu Feb 19 2009 - 11:46:24 PST)
[AMBER] Antechamber kureeckal ramesh (Thu Feb 19 2009 - 17:36:03 PST)
[AMBER] Problem with NVT and NPT parul sharma (Fri Feb 20 2009 - 05:07:36 PST)
- Re: [AMBER] Problem with NVT and NPT Adrian Roitberg (Fri Feb 20 2009 - 05:14:23 PST)
  - Re: [AMBER] Problem with NVT and NPT parul sharma (Fri Feb 20 2009 - 05:27:51 PST)
    - Re: [AMBER] Problem with NVT and NPT Carlos Simmerling (Fri Feb 20 2009 - 05:30:26 PST)
[AMBER] Parmchk wrongly calculates missing parameters (fwd) Gijs Schaftenaar (Fri Feb 20 2009 - 05:16:17 PST)
[AMBER] ACS computational chemistry awards - March 9th deadline Carlos Simmerling (Fri Feb 20 2009 - 08:27:18 PST)
[AMBER] order of "upper" and "lower" bounds in the makeDIS_RST inputs Piotr Cieplak (Fri Feb 20 2009 - 13:40:14 PST)
- Re: [AMBER] order of "upper" and "lower" bounds in the makeDIS_RST inputs David A. Case (Sat Feb 21 2009 - 15:51:38 PST)
[AMBER] reg.targeted molecular dynamics balaji nagarajan (Fri Feb 20 2009 - 21:10:50 PST)
- Re: [AMBER] reg.targeted molecular dynamics Carlos Simmerling (Sat Feb 21 2009 - 04:35:05 PST)
  - RE: [AMBER] reg.targeted molecular dynamics balaji nagarajan (Sun Feb 22 2009 - 06:45:29 PST)
    - Re: [AMBER] reg.targeted molecular dynamics Carlos Simmerling (Sun Feb 22 2009 - 07:06:32 PST)
    - RE: [AMBER] reg.targeted molecular dynamics balaji nagarajan (Sun Feb 22 2009 - 22:45:18 PST)
    - Re: [AMBER] reg.targeted molecular dynamics Carlos Simmerling (Mon Feb 23 2009 - 03:16:00 PST)
    - RE: [AMBER] reg.targeted molecular dynamics balaji nagarajan (Wed Feb 25 2009 - 01:18:10 PST)
    - RE: [AMBER] reg.targeted molecular dynamics balaji nagarajan (Wed Feb 25 2009 - 01:34:57 PST)
    - Re: [AMBER] reg.targeted molecular dynamics Carlos Simmerling (Wed Feb 25 2009 - 03:21:39 PST)
    - RE: [AMBER] reg.targeted molecular dynamics Ross Walker (Wed Feb 25 2009 - 07:12:29 PST)
    - RE: [AMBER] reg.targeted molecular dynamics balaji nagarajan (Fri Feb 27 2009 - 02:28:02 PST)
    - RE: [AMBER] reg.targeted molecular dynamics Ross Walker (Fri Feb 27 2009 - 07:11:44 PST)
[AMBER] A beginner's question for using AMBER to do cell membrane simulation and molecular transportation Xu Dong (Sat Feb 21 2009 - 12:27:29 PST)
- Re: [AMBER] A beginner's question for using AMBER to do cell membrane simulation and molecular transportation Carlos Simmerling (Sat Feb 21 2009 - 13:33:31 PST)
  - Re: [AMBER] A beginner's question for using AMBER to do cell membrane simulation and molecular transportation Xu Dong (Sat Feb 21 2009 - 13:40:03 PST)
[AMBER] PME doesn't work parul sharma (Mon Feb 23 2009 - 01:43:40 PST)
- Re: [AMBER] PME doesn't work Carlos Simmerling (Mon Feb 23 2009 - 03:19:27 PST)
  - Re: [AMBER] PME doesn't work parul sharma (Mon Feb 23 2009 - 04:03:54 PST)
    - Re: [AMBER] PME doesn't work Carlos Simmerling (Mon Feb 23 2009 - 04:08:07 PST)
- Re: [AMBER] PME doesn't work Robert Duke (Mon Feb 23 2009 - 05:48:04 PST)
[AMBER] PMEMD vs GROMACS? Sasha Buzko (Mon Feb 23 2009 - 11:55:27 PST)
- Re: [AMBER] PMEMD vs GROMACS? Vlad Cojocaru (Tue Feb 24 2009 - 00:24:16 PST)
  - Re: [AMBER] PMEMD vs GROMACS? Hannes Loeffler (Tue Feb 24 2009 - 00:39:29 PST)
    - Re: [AMBER] PMEMD vs GROMACS? Vlad Cojocaru (Tue Feb 24 2009 - 00:46:36 PST)
  - Re: [AMBER] PMEMD vs GROMACS? Sasha Buzko (Tue Feb 24 2009 - 09:15:59 PST)
[AMBER] problem with amber installation nicholus bhattacharjee (Mon Feb 23 2009 - 22:50:12 PST)
- Re: [AMBER] problem with amber installation Carlos Simmerling (Tue Feb 24 2009 - 03:47:20 PST)
  - Re: [AMBER] problem with amber installation nicholus bhattacharjee (Tue Feb 24 2009 - 20:29:11 PST)
    - Re: [AMBER] problem with amber installation Carlos Simmerling (Wed Feb 25 2009 - 03:25:34 PST)
    - [AMBER] PMEMD error message neville forlemu (Sun Mar 08 2009 - 13:37:09 PDT)
    - Re: [AMBER] PMEMD error message Robert Duke (Sun Mar 08 2009 - 13:47:16 PDT)
    - RE: [AMBER] PMEMD error message Ross Walker (Sun Mar 08 2009 - 14:52:01 PDT)
    - [AMBER] PMEMD error message neville forlemu (Tue Mar 10 2009 - 07:55:31 PDT)
    - Re: [AMBER] PMEMD error message Robert Duke (Tue Mar 10 2009 - 08:39:38 PDT)
    - Re: [AMBER] problem with amber installation David A. Case (Wed Feb 25 2009 - 04:45:01 PST)
    - RE: [AMBER] problem with amber installation Ross Walker (Wed Feb 25 2009 - 07:05:26 PST)
    - Re: [AMBER] problem with amber installation nicholus bhattacharjee (Tue Mar 24 2009 - 10:14:10 PDT)
[AMBER] follow-up to previous discussion: nmr refinement of dimer Sally Pias (Mon Feb 23 2009 - 23:50:41 PST)
- Re: [AMBER] follow-up to previous discussion: nmr refinement of dimer David A. Case (Tue Feb 24 2009 - 05:15:27 PST)
[AMBER] About the croase grainded FF James W (Mon Feb 23 2009 - 23:58:12 PST)
- Re: [AMBER] About the croase grainded FF Vlad Cojocaru (Tue Feb 24 2009 - 00:40:53 PST)
[AMBER] (no subject) Beale, John (Tue Feb 24 2009 - 03:59:51 PST)
[AMBER] amber tools reading netcdf files Jeremy Harris (Tue Feb 24 2009 - 07:54:09 PST)
- Re: [AMBER] amber tools reading netcdf files Chris Moth (Tue Feb 24 2009 - 09:35:22 PST)
- RE: [AMBER] amber tools reading netcdf files Cojocaru,Vlad (Tue Feb 24 2009 - 10:46:27 PST)
[AMBER] perform an analysis using ptraj oguz gurbulak (Tue Feb 24 2009 - 08:19:11 PST)
[AMBER] Equilibration Scaling to System Size Hopkins, Robert (Tue Feb 24 2009 - 14:31:37 PST)
- Re: [AMBER] Equilibration Scaling to System Size Carlos Simmerling (Tue Feb 24 2009 - 14:49:10 PST)
[AMBER] problem about trajectory analysis Adrien Delmont (Wed Feb 25 2009 - 06:24:41 PST)
- Re: [AMBER] problem about trajectory analysis Thomas Cheatham III (Wed Feb 25 2009 - 16:57:49 PST)
[AMBER] (no subject) waleed zalloum (Wed Feb 25 2009 - 08:41:14 PST)
- Re: [AMBER] (no subject) Thomas Cheatham III (Wed Feb 25 2009 - 16:48:56 PST)
[AMBER] ptraj analyze Beale, John (Wed Feb 25 2009 - 08:56:59 PST)
- Re: [AMBER] ptraj analyze Thomas Cheatham III (Wed Feb 25 2009 - 16:45:17 PST)
[AMBER] Simulated annealing Ibrahim Moustafa (Wed Feb 25 2009 - 16:26:37 PST)
- Re: [AMBER] Simulated annealing Carlos Simmerling (Wed Feb 25 2009 - 17:31:30 PST)
  - Re: [AMBER] Simulated annealing Ibrahim Moustafa (Thu Feb 26 2009 - 07:28:44 PST)
    - Re: [AMBER] Simulated annealing David A. Case (Thu Feb 26 2009 - 07:52:18 PST)
    - Re: [AMBER] Simulated annealing Ibrahim Moustafa (Thu Feb 26 2009 - 08:32:32 PST)
    - Re: [AMBER] Simulated annealing Carlos Simmerling (Thu Feb 26 2009 - 07:55:41 PST)
    - RE: [AMBER] Simulated annealing Hu, Shaowen (JSC-SK)[Universities Space Research Association (USRA)] (Thu Feb 26 2009 - 08:22:59 PST)
    - Re: [AMBER] Simulated annealing Carlos Simmerling (Thu Feb 26 2009 - 08:27:04 PST)
    - RE: [AMBER] Simulated annealing Hu, Shaowen (JSC-SK)[Universities Space Research Association (USRA)] (Thu Feb 26 2009 - 08:30:47 PST)
[AMBER] Error in using Amber sri noraima othman (Wed Feb 25 2009 - 19:27:29 PST)
- RE: [AMBER] Error in using Amber Ross Walker (Wed Feb 25 2009 - 22:03:12 PST)
  - Re: [AMBER] Error in using Amber sri noraima othman (Wed Feb 25 2009 - 22:27:14 PST)
[AMBER] tleap errors !! Sampath Koppole (Thu Feb 26 2009 - 01:47:48 PST)
- Re: [AMBER] tleap errors !! David A. Case (Thu Feb 26 2009 - 05:45:49 PST)
[AMBER] MD simulation at constant pH Francesco Pietra (Thu Feb 26 2009 - 02:52:47 PST)
[AMBER] Current Amber10 bugfix.all doesn't apply cleanly Mark Dixon (Thu Feb 26 2009 - 03:54:03 PST)
- Re: [AMBER] Current Amber10 bugfix.all doesn't apply cleanly Mark Dixon (Fri Feb 27 2009 - 08:44:28 PST)
[AMBER] PLUMED release 1.0.0 available Massimiliano Bonomi (Thu Feb 26 2009 - 05:11:54 PST)
[AMBER] extra torsion terms in tleap.top-file Astrid Maaß (Thu Feb 26 2009 - 06:32:30 PST)
[AMBER] H-Bonds Beale, John (Thu Feb 26 2009 - 06:38:04 PST)
- Re: [AMBER] H-Bonds Thomas Cheatham III (Wed Mar 04 2009 - 13:00:30 PST)
  - [AMBER] What is the default position of the partial charges? Chih-Ying Lin (Wed Mar 04 2009 - 13:06:16 PST)
    - Re: [AMBER] What is the default position of the partial charges? Thomas Cheatham III (Wed Mar 04 2009 - 13:44:20 PST)
  - [AMBER] solvent and counter ions Taufik Al-Sarraj (Wed Mar 04 2009 - 13:36:36 PST)
    - Re: [AMBER] solvent and counter ions Thomas Cheatham III (Wed Mar 04 2009 - 13:49:35 PST)
    - Re: [AMBER] solvent and counter ions Taufik Al-Sarraj (Thu Mar 05 2009 - 15:16:24 PST)
    - Re: [AMBER] solvent and counter ions Bill Ross (Thu Mar 05 2009 - 15:29:50 PST)
[AMBER] (no subject) Lake, Thomas (Thu Feb 26 2009 - 08:19:53 PST)
- Re: [AMBER] (no subject) Carlos Simmerling (Thu Feb 26 2009 - 08:24:40 PST)
- [AMBER] MD simulations on a protein with FAD and NADH Mannan (Thu Feb 26 2009 - 17:11:54 PST)
  - RE: [AMBER] MD simulations on a protein with FAD and NADH Ross Walker (Thu Feb 26 2009 - 20:32:05 PST)
  - Re: [AMBER] MD simulations on a protein with FAD and NADH FyD (Fri Feb 27 2009 - 00:24:37 PST)
[AMBER] A problem with xleap and pdb file nancy4619 (Fri Feb 27 2009 - 04:28:01 PST)
- Re: [AMBER] A problem with xleap and pdb file David A. Case (Fri Feb 27 2009 - 05:56:26 PST)
  - Re:Re: [AMBER] A problem with xleap and pdb file nancy4619 (Fri Feb 27 2009 - 06:20:17 PST)
    - Re:Re: [AMBER] A problem with xleap and pdb file Peter Gannett (Fri Feb 27 2009 - 06:32:20 PST)
    - RE: Re: [AMBER] A problem with xleap and pdb file Ross Walker (Fri Feb 27 2009 - 07:55:23 PST)
[AMBER] Re: Antechamber kureeckal ramesh (Fri Feb 27 2009 - 04:56:58 PST)
- Re: [AMBER] Re: Antechamber FyD (Fri Feb 27 2009 - 05:12:16 PST)
[AMBER] I need a professional help about xleap and pdb file nancy4619 (Fri Feb 27 2009 - 05:56:14 PST)
- Re: [AMBER] I need a professional help about xleap and pdb file Peter Gannett (Fri Feb 27 2009 - 06:17:31 PST)
[AMBER] using Gromacs for analysis oguz gurbulak (Fri Feb 27 2009 - 09:03:54 PST)
- Re: [AMBER] using Gromacs for analysis Bala subramanian (Fri Feb 27 2009 - 10:16:46 PST)
- [AMBER] Re: using Gromacs for analysis oguz gurbulak (Mon Mar 02 2009 - 08:17:45 PST)
[AMBER] Partial entropy calculations ? Marek Malý (Fri Feb 27 2009 - 10:21:29 PST)
- Re: [AMBER] Partial entropy calculations ? Piotr Cieplak (Fri Feb 27 2009 - 10:44:21 PST)
[AMBER] PCL waleed zalloum (Sat Feb 28 2009 - 09:17:51 PST)
- RE: [AMBER] PCL Ross Walker (Sat Feb 28 2009 - 09:23:30 PST)
[AMBER] a query Molecular Dynamics (Sat Feb 28 2009 - 11:45:46 PST)
[AMBER] IMPORTANT INFO: Regarding Anonymous postings to the AMBER mailing list. Ross Walker (Sat Feb 28 2009 - 14:19:16 PST)
[AMBER] Question about NAB module Wei Huang (Sat Feb 28 2009 - 16:23:49 PST)
- Re: [AMBER] Question about NAB module David A. Case (Sun Mar 01 2009 - 05:52:19 PST)
  - RE: [AMBER] Question about NAB module Wei Huang (Sun Mar 01 2009 - 06:57:50 PST)
    - RE: [AMBER] Question about NAB module Andreas Svrcek-Seiler (Mon Mar 02 2009 - 01:23:52 PST)
Re: [AMBER] binding free energy Barbault Florent (Sun Mar 01 2009 - 04:20:39 PST)
- Re: [AMBER] binding free energy Don.Bashford.stjude.org (Sun Mar 01 2009 - 09:18:39 PST)
  - RE: [AMBER] binding free energy Ross Walker (Sun Mar 01 2009 - 09:29:35 PST)
    - RE: [AMBER] binding free energy Ross Walker (Mon Mar 02 2009 - 12:16:55 PST)
- Re: [AMBER] binding free energy Robert Duke (Mon Mar 02 2009 - 05:22:22 PST)
[AMBER] Pseudoatoms waleed zalloum (Mon Mar 02 2009 - 04:12:33 PST)
- Re: [AMBER] Pseudoatoms David A. Case (Mon Mar 02 2009 - 15:25:29 PST)
  - [AMBER] How to restart the umbrella sampling jobs? Catein Catherine (Mon Mar 02 2009 - 21:52:16 PST)
    - RE: [AMBER] How to restart the umbrella sampling jobs? Ross Walker (Tue Mar 03 2009 - 08:00:04 PST)
    - Re: [AMBER] How to restart the umbrella sampling jobs? Gustavo Seabra (Tue Mar 03 2009 - 12:41:25 PST)
[AMBER] calculate shear viscosity oguz gurbulak (Mon Mar 02 2009 - 05:35:06 PST)
Re: [AMBER] How can I use the charge I calculated (using mol2 file) ? David A. Case (Mon Mar 02 2009 - 06:56:54 PST)
- Re: Re: [AMBER] How can I use the charge I calculated (using mol2 file) ? David A. Case (Tue Mar 03 2009 - 05:39:26 PST)
  - Re: [AMBER] How can I use the charge I calculated (using mol2 file) ? FyD (Tue Mar 03 2009 - 06:12:18 PST)
[AMBER] assigning velocities to each atom without heating the system Parimal Kar (Mon Mar 02 2009 - 08:44:26 PST)
- Re: [AMBER] assigning velocities to each atom without heating the system Gustavo Seabra (Mon Mar 02 2009 - 09:31:09 PST)
  - Re: [AMBER] assigning velocities to each atom without heating the system Parimal Kar (Mon Mar 02 2009 - 09:46:25 PST)
- RE: [AMBER] assigning velocities to each atom without heating the system Ross Walker (Mon Mar 02 2009 - 12:23:22 PST)
[AMBER] specification of antechamber AC file format? Nicholas Musolino (Mon Mar 02 2009 - 23:53:23 PST)
- Re: [AMBER] specification of antechamber AC file format? David A. Case (Wed Mar 04 2009 - 14:39:44 PST)
  - [AMBER] AMBER installation : compilation error Catein Catherine (Wed Mar 04 2009 - 18:53:54 PST)
  - Re: [AMBER] specification of antechamber AC file format? Nicholas Musolino (Tue Apr 07 2009 - 12:43:57 PDT)
  - Re: [AMBER] specification of antechamber AC file format? Nicholas Musolino (Wed Apr 15 2009 - 15:07:32 PDT)
    - Re: [AMBER] specification of antechamber AC file format? David A. Case (Thu Apr 16 2009 - 05:29:46 PDT)
    - Re: [AMBER] specification of antechamber AC file format? Nicholas Musolino (Thu Apr 16 2009 - 06:18:32 PDT)
[AMBER] inpcrd and prmtop m m (Tue Mar 03 2009 - 01:27:06 PST)
- Re: [AMBER] inpcrd and prmtop Hannes Loeffler (Tue Mar 03 2009 - 01:37:16 PST)
  - RE: [AMBER] inpcrd and prmtop m m (Tue Mar 03 2009 - 02:08:51 PST)
  - Re: [AMBER] inpcrd and prmtop FyD (Tue Mar 03 2009 - 02:19:43 PST)
- Re: [AMBER] inpcrd and prmtop Gustavo Seabra (Tue Mar 03 2009 - 12:20:38 PST)
[AMBER] Fail to allocate ff Madhurima Jana (Tue Mar 03 2009 - 03:17:57 PST)
- Re: [AMBER] Fail to allocate ff Nicholas Musolino (Tue Mar 03 2009 - 05:10:21 PST)
  - Re: [AMBER] Fail to allocate ff Madhurima Jana (Tue Mar 03 2009 - 06:27:41 PST)
- Re: [AMBER] Fail to allocate ff Gustavo Seabra (Tue Mar 03 2009 - 12:36:53 PST)
[AMBER] A good way to use an Amber force field with NAMD? Sasha Buzko (Tue Mar 03 2009 - 13:37:29 PST)
- Re: [AMBER] A good way to use an Amber force field with NAMD? Gustavo Seabra (Tue Mar 03 2009 - 16:08:33 PST)
  - Re: [AMBER] A good way to use an Amber force field with NAMD? Adrian Roitberg (Tue Mar 03 2009 - 16:11:49 PST)
    - Re: [AMBER] A good way to use an Amber force field with NAMD? Sasha Buzko (Tue Mar 03 2009 - 16:26:44 PST)
    - RE: [AMBER] A good way to use an Amber force field with NAMD? Ross Walker (Tue Mar 03 2009 - 17:33:58 PST)
    - Re: [AMBER] A good way to use an Amber force field with NAMD? Sasha Buzko (Tue Mar 03 2009 - 18:55:56 PST)
- Re: [AMBER] A good way to use an Amber force field with NAMD? Robert Duke (Tue Mar 03 2009 - 20:26:59 PST)
  - Re: [AMBER] A good way to use an Amber force field with NAMD? Sasha Buzko (Wed Mar 04 2009 - 09:58:09 PST)
[AMBER] Amber: water-water hydrogen bonding analysis on a subset of waters in a trajectory Jeff Schwinefus (Tue Mar 03 2009 - 14:18:25 PST)
- Re: [AMBER] Amber: water-water hydrogen bonding analysis on a subset of waters in a trajectory Thomas Cheatham III (Wed Mar 04 2009 - 11:59:30 PST)
  - Re: [AMBER] Amber: water-water hydrogen bonding analysis on a subset of waters in a trajectory Jeff Schwinefus (Wed Mar 04 2009 - 21:22:34 PST)
[AMBER] angle between ligand ring plane and axis Jia Xu (Wed Mar 04 2009 - 03:00:08 PST)
[AMBER] hydrogen bond . .. (Wed Mar 04 2009 - 03:12:33 PST)
- Re: [AMBER] hydrogen bond Carlos Simmerling (Wed Mar 04 2009 - 03:20:53 PST)
- RE: [AMBER] hydrogen bond Ross Walker (Wed Mar 04 2009 - 08:39:49 PST)
[AMBER] Regarding leap aneesh cna (Wed Mar 04 2009 - 03:43:52 PST)
- Re: [AMBER] Regarding leap Carlos Simmerling (Wed Mar 04 2009 - 03:48:30 PST)
- Re: [AMBER] Regarding leap Gustavo Seabra (Wed Mar 04 2009 - 14:05:25 PST)
  - Re: [AMBER] Regarding leap aneesh cna (Wed Mar 04 2009 - 20:29:17 PST)
    - Re: [AMBER] Regarding leap Gustavo Seabra (Thu Mar 05 2009 - 07:32:56 PST)
[AMBER] unning MMPBSA in CHCl3 environment SAFAK OZHAN (Wed Mar 04 2009 - 03:55:52 PST)
- Re: [AMBER] unning MMPBSA in CHCl3 environment Ray Luo (Wed Mar 04 2009 - 09:15:55 PST)
[AMBER] Thermodynamic Intergration problem Xiaohui Jiang [Contractor] (Wed Mar 04 2009 - 07:36:14 PST)
- RE: [AMBER] Thermodynamic Intergration problem Ross Walker (Wed Mar 04 2009 - 08:45:24 PST)
  - RE: [AMBER] Thermodynamic Intergration problem Xiaohui Jiang [Contractor] (Wed Mar 04 2009 - 09:00:06 PST)
[AMBER] Compilation and qmmm_div Benjamin Roberts (Wed Mar 04 2009 - 07:48:16 PST)
- RE: [AMBER] Compilation and qmmm_div Ross Walker (Wed Mar 04 2009 - 08:36:07 PST)
  - Re: [AMBER] Compilation and qmmm_div Benjamin Roberts (Wed Mar 04 2009 - 16:15:37 PST)
[AMBER] radial distribution function mask iccy liu (Wed Mar 04 2009 - 10:57:08 PST)
[AMBER] Segmentation faults Benjamin Roberts (Wed Mar 04 2009 - 16:17:50 PST)
Re: [AMBER] solvent and counter ions Bill Ross (Wed Mar 04 2009 - 16:20:45 PST)
[AMBER] DNA simulation: Problem with RMSD BERGY (Wed Mar 04 2009 - 19:44:26 PST)
- Re: [AMBER] DNA simulation: Problem with RMSD Thomas Cheatham (Wed Mar 04 2009 - 20:04:53 PST)
  - Re: [AMBER] DNA simulation: Problem with RMSD BERGY (Thu Mar 05 2009 - 22:20:00 PST)
[AMBER] Fwd: please help me out bharat lakhani (Wed Mar 04 2009 - 20:42:06 PST)
[AMBER] Re: Fw:How to creat .frcmod file FyD (Wed Mar 04 2009 - 22:22:56 PST)
[AMBER] please help me out bharat lakhani (Thu Mar 05 2009 - 00:35:44 PST)
- Re: [AMBER] please help me out FyD (Thu Mar 05 2009 - 01:22:20 PST)
  - Re: [AMBER] please help me out bharat lakhani (Thu Mar 05 2009 - 03:16:45 PST)
  - Re: [AMBER] please help me out bharat lakhani (Sun Mar 08 2009 - 22:04:45 PDT)
    - Re: [AMBER] please help me out FyD (Mon Mar 09 2009 - 01:10:08 PDT)
    - Re: [AMBER] please help me out bharat lakhani (Mon Mar 09 2009 - 01:43:08 PDT)
[AMBER] chemical shift penalty Jacopo Sgrignani (Thu Mar 05 2009 - 01:47:03 PST)
- Re: [AMBER] chemical shift penalty David A. Case (Thu Mar 05 2009 - 15:59:33 PST)
[AMBER] divcon error during antechamber run, convergence problem drugdesign (Thu Mar 05 2009 - 05:53:59 PST)
- Re: [AMBER] divcon error during antechamber run, convergence problem Martin Peters (Thu Mar 05 2009 - 06:21:19 PST)
- Re: [AMBER] divcon error during antechamber run, convergence problem Andrew Voronkov (Fri Mar 06 2009 - 10:04:55 PST)
  - Re: [AMBER] divcon error during antechamber run, convergence problem David A. Case (Fri Mar 06 2009 - 10:33:24 PST)
    - Re: [AMBER] divcon error during antechamber run, convergence problem Andrew Voronkov (Sat Mar 07 2009 - 07:58:19 PST)
[AMBER] secstruct Beale, John (Thu Mar 05 2009 - 05:54:20 PST)
- RE: [AMBER] secstruct Maxime Louet (Thu Feb 19 2009 - 06:17:17 PST)
  - Re: [AMBER] secstruct Carlos Simmerling (Thu Feb 19 2009 - 06:45:47 PST)
- Re: [AMBER] secstruct Carlos Simmerling (Thu Mar 05 2009 - 06:27:18 PST)
[AMBER] MM-PBSA decomp by residue and snapshot? Bradshaw, Richard (Thu Mar 05 2009 - 09:55:05 PST)
[AMBER] Warning: name change in pdb file residue Donald Keidel (Thu Mar 05 2009 - 11:25:38 PST)
- RE: [AMBER] Warning: name change in pdb file residue Duggan, Brendan M. (Thu Mar 05 2009 - 12:42:21 PST)
[AMBER] GBSA: dielectric symmetry Giacomo Bastianelli (Thu Mar 05 2009 - 15:29:50 PST)
- Re: [AMBER] GBSA: dielectric symmetry David A. Case (Thu Mar 05 2009 - 16:05:51 PST)
[AMBER] High RMSD for DNA: A to B transition study BERGY (Thu Mar 05 2009 - 23:26:57 PST)
- Re: [AMBER] High RMSD for DNA: A to B transition study David A. Case (Fri Mar 06 2009 - 06:57:02 PST)
  - Re: [AMBER] High RMSD for DNA: A to B transition study SENTHIL KUMAR (Thu Mar 12 2009 - 23:36:43 PDT)
    - Re: [AMBER] High RMSD for DNA: A to B transition study David A. Case (Fri Mar 13 2009 - 05:00:40 PDT)
[AMBER] Quality/size of HDD for Amber Francesco Pietra (Fri Mar 06 2009 - 01:26:03 PST)
- Re: [AMBER] Quality/size of HDD for Amber M. L. Dodson (Fri Mar 06 2009 - 07:44:45 PST)
  - Re: [AMBER] Quality/size of HDD for Amber Gustavo Seabra (Mon Mar 09 2009 - 10:44:54 PDT)
[AMBER] Solvate Box od amoeba water Hemant Gangwar (Fri Mar 06 2009 - 01:50:01 PST)
- Re: [AMBER] Solvate Box od amoeba water Wei Zhang (Fri Mar 06 2009 - 06:20:09 PST)
  - Re: [AMBER] Solvate Box od amoeba water Hemant Kumar (Sun Mar 22 2009 - 09:06:01 PDT)
[AMBER] catenan simulation problems Cristina Sisu (Fri Mar 06 2009 - 05:16:08 PST)
- Re: [AMBER] catenan simulation problems David A. Case (Fri Mar 06 2009 - 06:59:24 PST)
  - Re: [AMBER] catenan simulation problems Cristina Sisu (Fri Mar 06 2009 - 07:28:00 PST)
    - Re: [AMBER] catenan simulation problems David A. Case (Sat Mar 07 2009 - 15:25:07 PST)
    - Re: [AMBER] catenan simulation problems David A. Case (Wed Mar 18 2009 - 04:47:32 PDT)
  - Re: [AMBER] catenan simulation problems Cristina S.D. Sisu (Fri Mar 06 2009 - 07:35:46 PST)
[AMBER] Help with torsions in parm99.dat file Gregersen, Brent (Fri Mar 06 2009 - 14:44:17 PST)
- RE: [AMBER] Help with torsions in parm99.dat file Ross Walker (Fri Mar 06 2009 - 16:52:05 PST)
  - RE: [AMBER] Help with torsions in parm99.dat file Gregersen, Brent (Fri Mar 06 2009 - 18:15:11 PST)
    - RE: [AMBER] Help with torsions in parm99.dat file Ross Walker (Fri Mar 06 2009 - 22:32:23 PST)
  - Re: [AMBER] Help with torsions in parm99.dat file Astrid Maaß (Mon Mar 09 2009 - 06:27:30 PDT)
    - Re: [AMBER] Help with torsions in parm99.dat file Wei Zhang (Mon Mar 09 2009 - 07:38:56 PDT)
[AMBER] Problem with particle-mesh Ewald method Yunjie Zhao (Fri Mar 06 2009 - 19:29:02 PST)
- Re: [AMBER] Problem with particle-mesh Ewald method steinbrt.rci.rutgers.edu (Fri Mar 06 2009 - 19:42:26 PST)
- RE: [AMBER] Problem with particle-mesh Ewald method Ross Walker (Fri Mar 06 2009 - 22:10:34 PST)
[AMBER] analysis on Amber oguz gurbulak (Sat Mar 07 2009 - 10:04:19 PST)
- Re: [AMBER] analysis on Amber Thomas Cheatham (Sat Mar 07 2009 - 10:18:58 PST)
[AMBER] Fw:how to select force field Nancy (Sun Mar 08 2009 - 07:07:48 PDT)
- RE: [AMBER] Fw:how to select force field Ross Walker (Sun Mar 08 2009 - 10:52:56 PDT)
[AMBER] nmoldyn2 with Amber Adrien Delmont (Sun Mar 08 2009 - 07:37:40 PDT)
- Re: [AMBER] nmoldyn2 with Amber David Watson (Sun Mar 08 2009 - 07:54:57 PDT)
  - Re: [AMBER] nmoldyn2 with Amber M. L. Dodson (Sun Mar 08 2009 - 11:32:22 PDT)
    - Re: [AMBER] nmoldyn2 with Amber David Watson (Sun Mar 08 2009 - 13:00:39 PDT)
    - Re: [AMBER] nmoldyn2 with Amber Thomas Cheatham (Sun Mar 08 2009 - 13:10:17 PDT)
- Re: [AMBER] nmoldyn2 with Amber David Watson (Sun Mar 08 2009 - 08:02:55 PDT)
  - Re: [AMBER] nmoldyn2 with Amber M. L. Dodson (Sun Mar 08 2009 - 11:34:03 PDT)
[AMBER] addles segmentation fault gmail (Mon Mar 09 2009 - 01:28:56 PDT)
- Re: [AMBER] addles segmentation fault Carlos Simmerling (Mon Mar 09 2009 - 04:45:24 PDT)
  - Re: [AMBER] addles segmentation fault xiaonan zhang (Mon Mar 09 2009 - 06:08:47 PDT)
[AMBER] Particle-mesh Ewald method Yunjie Zhao (Mon Mar 09 2009 - 02:46:15 PDT)
- RE: [AMBER] Particle-mesh Ewald method Ross Walker (Mon Mar 09 2009 - 12:53:52 PDT)
[AMBER] 8Mureabox anna berteotti (Mon Mar 09 2009 - 03:07:52 PDT)
- Re: [AMBER] 8Mureabox David A. Case (Tue Mar 10 2009 - 05:51:08 PDT)
  - RE: [AMBER] 8Mureabox anna berteotti (Wed Mar 11 2009 - 01:45:03 PDT)
[AMBER] Restraint Mask length restriction !! Sampath Koppole (Mon Mar 09 2009 - 06:32:35 PDT)
- Re: [AMBER] Restraint Mask length restriction !! David A. Case (Mon Mar 09 2009 - 06:43:34 PDT)
- Re: [AMBER] Restraint Mask length restriction !! Sampath Koppole (Mon Mar 09 2009 - 07:06:23 PDT)
  - Re: [AMBER] Restraint Mask length restriction !! David A. Case (Mon Mar 09 2009 - 07:30:16 PDT)
- Re: [AMBER] Restraint Mask length restriction !! Sampath Koppole (Mon Mar 09 2009 - 07:39:38 PDT)
  - RE: [AMBER] Restraint Mask length restriction !! Ross Walker (Mon Mar 09 2009 - 12:50:08 PDT)
[AMBER] generalized distance restraint Rausch, Felix (Mon Mar 09 2009 - 06:48:01 PDT)
- Re: [AMBER] generalized distance restraint Carlos Simmerling (Mon Mar 09 2009 - 08:13:50 PDT)
- RE: [AMBER] generalized distance restraint Rausch, Felix (Mon Mar 09 2009 - 09:15:11 PDT)
  - Re: [AMBER] generalized distance restraint Carlos Simmerling (Mon Mar 09 2009 - 09:39:43 PDT)
    - Re: [AMBER] generalized distance restraint M. L. Dodson (Mon Mar 09 2009 - 09:51:19 PDT)
- RE: [AMBER] generalized distance restraint Rausch, Felix (Wed Mar 11 2009 - 00:39:05 PDT)
[AMBER] Free Energy Decomposition Problem ozlem ulucan (Mon Mar 09 2009 - 06:55:45 PDT)
[AMBER] Changing Force Fields in "Midstream" Hopkins, Robert (Mon Mar 09 2009 - 17:12:27 PDT)
- RE: [AMBER] Changing Force Fields in "Midstream" Ross Walker (Mon Mar 09 2009 - 17:21:15 PDT)
  - RE: [AMBER] Changing Force Fields in "Midstream" Hopkins, Robert (Tue Mar 10 2009 - 16:29:44 PDT)
  - RE: [AMBER] Changing Force Fields in "Midstream" Hopkins, Robert (Wed Mar 11 2009 - 14:36:12 PDT)
    - Re: [AMBER] Changing Force Fields in "Midstream" Wei Zhang (Wed Mar 11 2009 - 14:42:52 PDT)
    - Re: [AMBER] Changing Force Fields in "Midstream" David A. Case (Wed Mar 11 2009 - 15:36:56 PDT)
    - RE: [AMBER] Changing Force Fields in "Midstream" Hopkins, Robert (Thu Mar 12 2009 - 13:45:46 PDT)
    - RE: [AMBER] Changing Force Fields in "Midstream" Kristina Furse (Wed Mar 11 2009 - 14:58:06 PDT)
[AMBER] problem in rmsd Parimal Kar (Mon Mar 09 2009 - 20:18:48 PDT)
- Re: [AMBER] problem in rmsd Thomas Cheatham (Mon Mar 09 2009 - 20:25:18 PDT)
  - Re: [AMBER] problem in rmsd Parimal Kar (Mon Mar 09 2009 - 20:36:13 PDT)
    - Re: [AMBER] problem in rmsd Thomas Cheatham (Mon Mar 09 2009 - 20:48:53 PDT)
    - Re: [AMBER] problem in rmsd Hannes Loeffler (Tue Mar 10 2009 - 01:30:16 PDT)
    - Re: [AMBER] problem in rmsd Carlos Simmerling (Tue Mar 10 2009 - 03:29:20 PDT)
    - [AMBER] mol2 - pdb conversion Taufik Al-Sarraj (Mon Mar 16 2009 - 14:38:09 PDT)
    - Re: [AMBER] mol2 - pdb conversion David A. Case (Tue Mar 17 2009 - 08:47:53 PDT)
    - Re: [AMBER] mol2 - pdb conversion Taufik Al-Sarraj (Wed Mar 18 2009 - 12:20:54 PDT)
    - Re: [AMBER] mol2 - pdb conversion David A. Case (Wed Mar 18 2009 - 14:53:06 PDT)
[AMBER] PB Bomb from MM-PBSA of Amber 10 Zhu, Yong-Liang (Mon Mar 09 2009 - 21:30:33 PDT)
- RE: [AMBER] PB Bomb from MM-PBSA of Amber 10 Wei Huang (Tue Mar 10 2009 - 03:30:50 PDT)
  - RE: [AMBER] PB Bomb from MM-PBSA of Amber 10 Zhu, Yong-Liang (Tue Mar 10 2009 - 09:06:43 PDT)
    - RE: [AMBER] PB Bomb from MM-PBSA of Amber 10 Wei Huang (Tue Mar 10 2009 - 09:20:29 PDT)
- RE: [AMBER] PB Bomb from MM-PBSA of Amber 10 Ray Luo (Tue Mar 10 2009 - 09:28:15 PDT)
[AMBER] sulfotyrosine parameters Ryan Pavlovicz (Tue Mar 10 2009 - 08:05:59 PDT)
[AMBER] wrong estimation of hydrogen velocities when using SHAKE? Jose Borreguero (Tue Mar 10 2009 - 09:09:48 PDT)
- Re: [AMBER] wrong estimation of hydrogen velocities when using SHAKE? David A. Case (Wed Mar 11 2009 - 04:08:17 PDT)
  - Re: [AMBER] wrong estimation of hydrogen velocities when using SHAKE? Jose Borreguero (Wed Mar 11 2009 - 10:28:21 PDT)
    - Re: [AMBER] wrong estimation of hydrogen velocities when using SHAKE? steinbrt.rci.rutgers.edu (Wed Mar 11 2009 - 10:45:56 PDT)
    - Re: [AMBER] wrong estimation of hydrogen velocities when using SHAKE? Jose Borreguero (Wed Mar 11 2009 - 11:46:29 PDT)
    - Re: [AMBER] wrong estimation of hydrogen velocities when using SHAKE? steinbrt.rci.rutgers.edu (Wed Mar 11 2009 - 11:56:15 PDT)
    - Re: [AMBER] wrong estimation of hydrogen velocities when using SHAKE? Jose Borreguero (Wed Mar 11 2009 - 14:56:03 PDT)
[AMBER] about MD simulation 廖青华 (Wed Mar 11 2009 - 02:19:28 PDT)
- Re: [AMBER] about MD simulation Carlos Simmerling (Wed Mar 11 2009 - 03:56:43 PDT)
[AMBER] Seeking for suggestion related to plot the cluster out file S.Sundar Raman (Wed Mar 11 2009 - 05:44:17 PDT)
- RE: [AMBER] Seeking for suggestion related to plot the cluster out file Ross Walker (Wed Mar 11 2009 - 07:33:38 PDT)
  - Re: [AMBER] Seeking for suggestion related to plot the cluster out file S.Sundar Raman (Wed Mar 11 2009 - 07:57:40 PDT)
    - RE: [AMBER] Seeking for suggestion related to plot the cluster out file Ross Walker (Wed Mar 11 2009 - 08:55:38 PDT)
    - Re: [AMBER] Seeking for suggestion related to plot the cluster out file S.Sundar Raman (Wed Mar 11 2009 - 09:07:25 PDT)
回复： [AMBER] about MD simulation 廖青华 (Wed Mar 11 2009 - 09:25:05 PDT)
[AMBER] installing AmberTools on Windows machines David A. Case (Wed Mar 11 2009 - 13:27:07 PDT)
[AMBER] polarizable force field and solvent zeinab bagheri (Wed Mar 11 2009 - 15:02:06 PDT)
[AMBER] Understanding the all.out file in the MM-PBSA output gmail (Wed Mar 11 2009 - 18:39:10 PDT)
- Re: [AMBER] Understanding the all.out file in the MM-PBSA output Hannes Kopitz (Thu Mar 12 2009 - 03:54:27 PDT)
  - RE: [AMBER] Understanding the all.out file in the MM-PBSA output Ray Luo (Thu Mar 12 2009 - 09:29:22 PDT)
[AMBER] polarizable force field and solvent zeinab bagheri (Wed Mar 11 2009 - 22:40:33 PDT)
[AMBER] Problem with REMD parul sharma (Thu Mar 12 2009 - 00:45:09 PDT)
- Re: [AMBER] Problem with REMD Carlos Simmerling (Thu Mar 12 2009 - 04:00:07 PDT)
[AMBER] Problems with MM-PBSA Calculation after MD German Erlenkamp (Thu Mar 12 2009 - 02:28:23 PDT)
- Re: [AMBER] Problems with MM-PBSA Calculation after MD Hannes Kopitz (Thu Mar 12 2009 - 04:06:54 PDT)
[AMBER] SMD in Amber10 Dmitri Nilov (Thu Mar 12 2009 - 11:12:13 PDT)
- Re: [AMBER] SMD in Amber10 Adrian Roitberg (Thu Mar 12 2009 - 11:46:14 PDT)
  - Re: [AMBER] SMD in Amber10 Dmitri Nilov (Fri Mar 13 2009 - 01:52:26 PDT)
    - Re: [AMBER] SMD in Amber10 Adrian Roitberg (Fri Mar 13 2009 - 06:45:39 PDT)
    - Re: [AMBER] SMD in Amber10 Dmitri Nilov (Fri Mar 13 2009 - 07:54:07 PDT)
    - Re: [AMBER] SMD in Amber10 Adrian Roitberg (Fri Mar 13 2009 - 08:01:31 PDT)
    - Re: [AMBER] SMD in Amber10 Dmitri Nilov (Fri Mar 13 2009 - 08:17:44 PDT)
[AMBER] Thermodynamic Integration at higher values of clambda using AMBER 9 PRADEEP VENKATARAMAN (Thu Mar 12 2009 - 14:56:59 PDT)
- Re: [AMBER] Thermodynamic Integration at higher values of clambda using AMBER 9 steinbrt.rci.rutgers.edu (Thu Mar 12 2009 - 17:37:08 PDT)
[AMBER] Problem running test.pmemd.AMOEBA mloureiro.cesga.es (Fri Mar 13 2009 - 04:45:30 PDT)
- [AMBER] Problem build pmemd Yiannis Georgiadis (Fri Mar 13 2009 - 17:14:49 PDT)
  - Re: [AMBER] Problem build pmemd Robert Duke (Fri Mar 13 2009 - 05:40:09 PDT)
  - Re: [AMBER] Problem build pmemd Atro Tossavainen (Sat Mar 14 2009 - 12:10:53 PDT)
  - Re: [AMBER] Problem build pmemd Giorgos Lamprinidis (Wed Mar 18 2009 - 06:28:06 PDT)
  - Re: [AMBER] Problem build pmemd Robert Duke (Wed Mar 18 2009 - 06:53:17 PDT)
- Re: [AMBER] Problem running test.pmemd.AMOEBA Robert Duke (Fri Mar 13 2009 - 07:33:55 PDT)
[AMBER] to understand multiplicity in antechamber Alan (Fri Mar 13 2009 - 05:06:45 PDT)
[AMBER] to understand multiplicity in antechamber Alan (Fri Mar 13 2009 - 07:43:45 PDT)
- Re: [AMBER] to understand multiplicity in antechamber Scott Brozell (Fri Mar 13 2009 - 12:05:06 PDT)
  - Re: [AMBER] to understand multiplicity in antechamber Alan (Fri Mar 13 2009 - 15:43:28 PDT)
[AMBER] doubt-reg_ Targeted molecular dynamics balaji nagarajan (Fri Mar 13 2009 - 09:20:41 PDT)
[AMBER] problems compiling ambertool Per Jr. Greisen (Fri Mar 13 2009 - 12:08:36 PDT)
- Re: [AMBER] problems compiling ambertool David A. Case (Fri Mar 13 2009 - 12:54:56 PDT)
  - Re: [AMBER] problems compiling ambertool Per Jr. Greisen (Fri Mar 13 2009 - 15:01:35 PDT)
  - Re: [AMBER] problems compiling ambertool Atro Tossavainen (Sat Mar 14 2009 - 12:09:36 PDT)
  - Re: [AMBER] problems compiling ambertool Atro Tossavainen (Mon Mar 16 2009 - 03:18:58 PDT)
    - Re: [AMBER] problems compiling ambertool David A. Case (Mon Mar 16 2009 - 05:13:23 PDT)
    - Re: [AMBER] problems compiling ambertool Per Jr. Greisen (Mon Mar 16 2009 - 06:29:37 PDT)
    - Re: [AMBER] problems compiling ambertool David A. Case (Mon Mar 16 2009 - 06:50:24 PDT)
    - Re: [AMBER] problems compiling ambertool Per Jr. Greisen (Mon Mar 16 2009 - 07:00:14 PDT)
    - Re: [AMBER] problems compiling ambertool David A. Case (Mon Mar 16 2009 - 07:27:26 PDT)
    - Re: [AMBER] problems compiling ambertool Per Jr. Greisen (Mon Mar 16 2009 - 07:41:26 PDT)
    - Re: [AMBER] problems compiling ambertool David A. Case (Mon Mar 16 2009 - 08:12:40 PDT)
    - Re: [AMBER] problems compiling ambertool Per Jr. Greisen (Mon Mar 16 2009 - 15:35:38 PDT)
- Re: [AMBER] problems compiling ambertool Bill Ross (Mon Mar 16 2009 - 15:50:44 PDT)
  - Re: [AMBER] problems compiling ambertool Per Jr. Greisen (Tue Mar 17 2009 - 01:10:20 PDT)
    - Re: [AMBER] problems compiling ambertool David A. Case (Tue Mar 17 2009 - 05:49:20 PDT)
    - Re: [AMBER] problems compiling ambertool Per Jr. Greisen (Tue Mar 17 2009 - 09:06:00 PDT)
    - Re: [AMBER] problems compiling ambertool David A. Case (Tue Mar 17 2009 - 09:13:30 PDT)
- Re: [AMBER] problems compiling ambertool Bill Ross (Tue Mar 17 2009 - 10:10:01 PDT)
- Re: [AMBER] problems compiling ambertool Bill Ross (Tue Mar 17 2009 - 10:24:48 PDT)
  - Re: [AMBER] problems compiling ambertool Per Jr. Greisen (Wed Mar 18 2009 - 04:49:57 PDT)
    - Re: [AMBER] problems compiling ambertool David A. Case (Wed Mar 18 2009 - 05:39:38 PDT)
    - Re: [AMBER] problems compiling ambertool Per Jr. Greisen (Wed Mar 18 2009 - 05:45:53 PDT)
    - [AMBER] lipid bliayers Urszula Uciechowska (Wed Mar 18 2009 - 06:00:32 PDT)
    - Re: [AMBER] lipid bliayers Hannes Loeffler (Wed Mar 18 2009 - 06:17:04 PDT)
[AMBER] suggestions for PB simulation Bala subramanian (Sat Mar 14 2009 - 09:41:19 PDT)
[AMBER] sander.MPI and pmemd.MPI in Fedora 8 John Bennett (Sun Mar 15 2009 - 14:23:16 PDT)
[AMBER] Unit 5 Error on OPEN: nan.in Nancy (Mon Mar 16 2009 - 05:49:31 PDT)
[AMBER] about mm-pbsa 廖青华 (Mon Mar 16 2009 - 07:59:40 PDT)
[AMBER] about mm-pbsa 廖青华 (Mon Mar 16 2009 - 08:02:49 PDT)
- RE: [AMBER] about mm-pbsa Wei Huang (Mon Mar 16 2009 - 08:17:30 PDT)
[AMBER] minimisation with igb=10 Bala subramanian (Mon Mar 16 2009 - 08:43:10 PDT)
- Re: [AMBER] minimisation with igb=10 Carlos Simmerling (Mon Mar 16 2009 - 08:45:47 PDT)
  - Re: [AMBER] minimisation with igb=10 Bala subramanian (Mon Mar 16 2009 - 08:56:48 PDT)
    - Re: [AMBER] minimisation with igb=10 Carlos Simmerling (Mon Mar 16 2009 - 09:04:37 PDT)
    - RE: [AMBER] minimisation with igb=10 Ray Luo (Mon Mar 16 2009 - 09:34:21 PDT)
[AMBER] Actual force constant in SMD Dmitri Nilov (Mon Mar 16 2009 - 11:07:09 PDT)
Re: [AMBER] Re: join two units in amber9 or amber10 Bill Ross (Mon Mar 16 2009 - 15:56:01 PDT)
[AMBER] Unit 5 Error on OPEN: nan.in Nancy (Mon Mar 16 2009 - 18:02:09 PDT)
[AMBER] Input file of the second stage RESP fitting Cen Gao (Mon Mar 16 2009 - 21:29:17 PDT)
- Re: [AMBER] Input file of the second stage RESP fitting FyD (Tue Mar 17 2009 - 06:32:58 PDT)
  - Re: [AMBER] Input file of the second stage RESP fitting Cen Gao (Tue Mar 17 2009 - 14:24:24 PDT)
[AMBER] regarding tutorial on united atom force field jani sahil (Mon Mar 16 2009 - 21:51:16 PDT)
- Re: [AMBER] regarding tutorial on united atom force field Ray Luo (Tue Mar 17 2009 - 09:22:01 PDT)
[AMBER] Unit 5 Error on OPEN: nan.in Nancy (Tue Mar 17 2009 - 02:11:10 PDT)
- Re: [AMBER] Unit 5 Error on OPEN: nan.in mathew k varghese (Mon Mar 16 2009 - 06:36:57 PDT)
  - Re:Re: [AMBER] Unit 5 Error on OPEN: nan.in Nancy (Mon Mar 16 2009 - 07:01:14 PDT)
    - Re: Re: [AMBER] Unit 5 Error on OPEN: nan.in Carlos Simmerling (Mon Mar 16 2009 - 07:32:02 PDT)
- Re: [AMBER] Unit 5 Error on OPEN: nan.in mathew k varghese (Tue Mar 17 2009 - 04:22:08 PDT)
  - Re: [AMBER] Unit 5 Error on OPEN: nan.in Jenny Iskrenova (Tue Mar 17 2009 - 05:34:00 PDT)
  - Re:Re: [AMBER] Unit 5 Error on OPEN: nan.in Nancy (Tue Mar 17 2009 - 06:37:44 PDT)
[AMBER] removing center of mass Bala subramanian (Tue Mar 17 2009 - 08:21:28 PDT)
[AMBER] convert .mol2 file to .pdb with atomtype definitions Pansy Patel (Tue Mar 17 2009 - 08:50:57 PDT)
- Re: [AMBER] convert .mol2 file to .pdb with atomtype definitions David A. Case (Tue Mar 17 2009 - 09:00:19 PDT)
  - Re: [AMBER] convert .mol2 file to .pdb with atomtype definitions Pansy Patel (Tue Mar 17 2009 - 09:09:10 PDT)
    - Re: [AMBER] convert .mol2 file to .pdb with atomtype definitions Wei Zhang (Tue Mar 17 2009 - 09:33:27 PDT)
    - RE: [AMBER] convert .mol2 file to .pdb with atomtype definitions Pankaj R. Daga (Tue Mar 17 2009 - 09:41:20 PDT)
[AMBER] temperature rises with igb=1 Bala subramanian (Tue Mar 17 2009 - 09:35:41 PDT)
- Re: [AMBER] temperature rises with igb=1 Carlos Simmerling (Tue Mar 17 2009 - 09:44:32 PDT)
- RE: [AMBER] temperature rises with igb=1 Ross Walker (Tue Mar 17 2009 - 09:53:04 PDT)
  - Re: [AMBER] temperature rises with igb=1 Carlos Simmerling (Tue Mar 17 2009 - 09:58:05 PDT)
    - Re: [AMBER] temperature rises with igb=1 Bala subramanian (Thu Mar 19 2009 - 04:24:45 PDT)
    - Re: [AMBER] temperature rises with igb=1 David A. Case (Thu Mar 19 2009 - 05:04:54 PDT)
Re: [AMBER] Unit 5 Error on OPEN: nan.in Bill Ross (Tue Mar 17 2009 - 10:12:07 PDT)
[AMBER] CCL4 simulation sudipta (Tue Mar 17 2009 - 11:18:07 PDT)
- Re: [AMBER] CCL4 simulation David A. Case (Tue Mar 17 2009 - 19:14:51 PDT)
  - Re: [AMBER] CCL4 simulation sudipta (Wed Mar 18 2009 - 00:47:48 PDT)
    - Re: [AMBER] CCL4 simulation David A. Case (Wed Mar 18 2009 - 04:06:30 PDT)
[AMBER] error in constructing DNA from nucgen Pansy Patel (Tue Mar 17 2009 - 11:43:49 PDT)
- Re: [AMBER] error in constructing DNA from nucgen Carlos Simmerling (Tue Mar 17 2009 - 11:53:05 PDT)
  - Re: [AMBER] error in constructing DNA from nucgen Pansy Patel (Tue Mar 17 2009 - 12:24:58 PDT)
    - RE: [AMBER] error in constructing DNA from nucgen Ross Walker (Tue Mar 17 2009 - 12:31:16 PDT)
- Re: [AMBER] error in constructing DNA from nucgen Bill Ross (Tue Mar 17 2009 - 15:47:07 PDT)
[AMBER] About error of "vertex atom mismatch" 廖青华 (Wed Mar 18 2009 - 01:30:29 PDT)
[AMBER] errors about install amber9 on MAC OS zgong.hust (Wed Mar 18 2009 - 01:41:19 PDT)
- Re: [AMBER] errors about install amber9 on MAC OS David A. Case (Wed Mar 18 2009 - 04:08:44 PDT)
[AMBER] protein protrudes from unit cell Jeffrey (Wed Mar 18 2009 - 01:59:06 PDT)
- Re: [AMBER] protein protrudes from unit cell Hannes Loeffler (Wed Mar 18 2009 - 02:08:41 PDT)
- RE: [AMBER] protein protrudes from unit cell Ross Walker (Wed Mar 18 2009 - 08:39:23 PDT)
  - Re: [AMBER] protein protrudes from unit cell Carlos Simmerling (Wed Mar 18 2009 - 08:49:43 PDT)
Re: [AMBER] TMD Carlos Simmerling (Wed Mar 18 2009 - 03:32:14 PDT)
[AMBER] sleap and check Alan (Wed Mar 18 2009 - 04:18:27 PDT)
- Re: [AMBER] sleap and check Wei Zhang (Wed Mar 18 2009 - 07:40:57 PDT)
  - Re: [AMBER] sleap and check Alan (Wed Mar 18 2009 - 14:23:51 PDT)
Re: [AMBER] problem in running sander Carlos Simmerling (Wed Mar 18 2009 - 07:58:04 PDT)
- Re: [AMBER] problem in running sander Carlos Simmerling (Wed Mar 18 2009 - 08:51:07 PDT)
  - Re: [AMBER] problem in running sander Kshatresh Dutta Dubey (Thu Mar 19 2009 - 00:17:21 PDT)
    - Re: [AMBER] problem in running sander David A. Case (Thu Mar 19 2009 - 05:13:11 PDT)
[AMBER] Mass of LP PRADEEP VENKATARAMAN (Wed Mar 18 2009 - 20:27:24 PDT)
- Re: [AMBER] Mass of LP David A. Case (Thu Mar 19 2009 - 04:27:48 PDT)
[AMBER] simulation in water-oil (or water/hydrophobic-solvent) box ranga nath (Wed Mar 18 2009 - 21:27:54 PDT)
- Re: [AMBER] simulation in water-oil (or water/hydrophobic-solvent) box David A. Case (Thu Mar 19 2009 - 10:38:52 PDT)
  - [AMBER] protein PDB Chih-Ying Lin (Thu Mar 19 2009 - 13:43:15 PDT)
  - Re: [AMBER] simulation in water-oil (or water/hydrophobic-solvent) box ranga nath (Sat Mar 21 2009 - 19:04:13 PDT)
[AMBER] Metal in MD simulation priya priya (Wed Mar 18 2009 - 23:25:09 PDT)
- Re: [AMBER] Metal in MD simulation Jagadeesh, M.N., Ph.D. (Thu Mar 19 2009 - 07:48:28 PDT)
- RE: [AMBER] Metal in MD simulation Ross Walker (Thu Mar 19 2009 - 08:12:24 PDT)
- Re: [AMBER] Metal in MD simulation Bill Ross (Thu Mar 19 2009 - 14:22:12 PDT)
- Re: [AMBER] Metal in MD simulation priya priya (Thu Mar 19 2009 - 23:15:06 PDT)
[AMBER] About mm-pbsa 廖青华 (Wed Mar 18 2009 - 23:48:21 PDT)
[AMBER] [about advanced tutorial 1] How could I get conformations for gaussian that have minimum energy? Youn Kyeung Lee (Thu Mar 19 2009 - 00:31:16 PDT)
- Re: [AMBER] [about advanced tutorial 1] How could I get conformations for gaussian that have minimum energy? FyD (Sun Mar 22 2009 - 13:12:17 PDT)
[AMBER] error for nmode Dechang Li (Thu Mar 19 2009 - 04:00:09 PDT)
- Re: [AMBER] error for nmode David A. Case (Thu Mar 19 2009 - 04:31:24 PDT)
[AMBER] pmemd compile error.... Giorgos Lamprinidis (Thu Mar 19 2009 - 08:06:04 PDT)
- Re: [AMBER] pmemd compile error.... Robert Duke (Thu Mar 19 2009 - 08:24:29 PDT)
- Re: [AMBER] pmemd compile error.... Robert Duke (Thu Mar 19 2009 - 08:25:04 PDT)
- Re: [AMBER] pmemd compile error.... case (Tue Mar 24 2009 - 05:12:46 PDT)
- Re: [AMBER] pmemd compile error.... Robert Duke (Tue Mar 24 2009 - 05:19:45 PDT)
[AMBER] Parametrisation of Silicon based molecules for Amber simulations ? Marek Malý (Thu Mar 19 2009 - 16:49:21 PDT)
- [AMBER] FF Parameters Transformations ...? Marek Malý (Wed Apr 01 2009 - 10:29:26 PDT)
  - Re: [AMBER] FF Parameters Transformations ...? Karl Kirschner (Mon Apr 06 2009 - 00:39:31 PDT)
    - Re: [AMBER] FF Parameters Transformations ...? Marek Malý (Mon Apr 06 2009 - 13:03:58 PDT)
[AMBER] Help needed in amber parallel installation sushobhan.iiar.res.in (Thu Mar 19 2009 - 23:39:36 PDT)
- Re: [AMBER] Help needed in amber parallel installation Carlos Simmerling (Fri Mar 20 2009 - 04:34:31 PDT)
- RE: [AMBER] Help needed in amber parallel installation Ross Walker (Fri Mar 20 2009 - 08:40:30 PDT)
Re: [AMBER] analysing DNA trajectory Bala subramanian (Fri Mar 20 2009 - 01:06:08 PDT)
[AMBER] QM/MM charges Jacopo Sgrignani (Fri Mar 20 2009 - 02:38:30 PDT)
- RE: [AMBER] QM/MM charges Ross Walker (Fri Mar 20 2009 - 08:37:34 PDT)
[AMBER] Announcement of Model(l)ing'09 - The annual 2009 MGMS Meeting in Erlangen, Germany Harald Lanig (Fri Mar 20 2009 - 04:25:09 PDT)
[AMBER] MMGBSA IG Value Rajesh Raju (Fri Mar 20 2009 - 10:20:52 PDT)
- Re: [AMBER] MMGBSA IG Value Carlos Simmerling (Fri Mar 20 2009 - 10:25:38 PDT)
  - Re: [AMBER] MMGBSA IG Value Rajesh Raju (Fri Mar 20 2009 - 10:36:37 PDT)
    - Re: [AMBER] MMGBSA IG Value Carlos Simmerling (Fri Mar 20 2009 - 10:42:14 PDT)
[AMBER] xmgrace Nancy (Fri Mar 20 2009 - 21:41:33 PDT)
[AMBER] adding chain id to ptraj pdb output Paul Brandt (Sat Mar 21 2009 - 19:09:59 PDT)
- Re: [AMBER] adding chain id to ptraj pdb output Bala subramanian (Mon Mar 23 2009 - 04:37:43 PDT)
- Re: [AMBER] adding chain id to ptraj pdb output Joe Krahn (Mon Mar 23 2009 - 16:20:30 PDT)
[AMBER] about mm-pbsa 廖青华 (Mon Mar 23 2009 - 02:10:29 PDT)
[AMBER] leap and chirality Karl Kirschner (Mon Mar 23 2009 - 02:54:29 PDT)
- Re: [AMBER] leap and chirality David A. Case (Mon Mar 23 2009 - 06:16:14 PDT)
  - Re: [AMBER] leap and chirality Karl Kirschner (Mon Mar 23 2009 - 07:05:56 PDT)
    - Re: [AMBER] leap and chirality Wei Zhang (Mon Mar 23 2009 - 11:36:54 PDT)
    - Re: [AMBER] leap and chirality Karl Kirschner (Tue Mar 24 2009 - 01:11:38 PDT)
    - Re: [AMBER] leap and chirality Wei Zhang (Tue Mar 24 2009 - 05:55:47 PDT)
[AMBER] problem in installing AMBER10 Dr. Debaprasad Giri (Mon Mar 23 2009 - 03:31:26 PDT)
- Re: [AMBER] problem in installing AMBER10 David A. Case (Mon Mar 23 2009 - 04:07:17 PDT)
  - Re: [AMBER] problem in installing AMBER10 Dr. Debaprasad Giri (Fri Mar 27 2009 - 03:16:47 PDT)
    - Re: [AMBER] problem in installing AMBER10 David A. Case (Fri Mar 27 2009 - 05:05:31 PDT)
    - Re: [AMBER] problem in installing AMBER10 Dr. Debaprasad Giri (Sat Apr 04 2009 - 05:13:46 PDT)
[AMBER] Regarding use of PME along with Implict solvation jani sahil (Mon Mar 23 2009 - 03:38:39 PDT)
- Re: [AMBER] Regarding use of PME along with Implict solvation parul sharma (Mon Mar 23 2009 - 03:55:24 PDT)
  - Re: [AMBER] Regarding use of PME along with Implict solvation jani sahil (Mon Mar 23 2009 - 06:04:15 PDT)
Re: [AMBER] helical parameters Bala subramanian (Mon Mar 23 2009 - 11:14:29 PDT)
[AMBER] pmemd compile error Giorgos Lamprinidis (Mon Mar 23 2009 - 13:54:37 PDT)
- Re: [AMBER] pmemd compile error Robert Duke (Mon Mar 23 2009 - 14:03:45 PDT)
[AMBER] errors on reading time series file in WHAM calculation gmail (Mon Mar 23 2009 - 17:35:02 PDT)
- Re: [AMBER] errors on reading time series file in WHAM calculation Jenny Iskrenova (Tue Mar 24 2009 - 07:35:51 PDT)
[AMBER] validation of parameters and request of suggestions Jeffrey (Mon Mar 23 2009 - 19:16:35 PDT)
[AMBER] continuam water Mannan (Mon Mar 23 2009 - 21:11:50 PDT)
- Re: [AMBER] continuam water Carlos Simmerling (Tue Mar 24 2009 - 06:36:15 PDT)
[AMBER] change in protein ligand order Hannes Wallnoefer (Tue Mar 24 2009 - 04:05:36 PDT)
- Re: [AMBER] change in protein ligand order Hannes Loeffler (Tue Mar 24 2009 - 04:27:24 PDT)
  - Re: [AMBER] change in protein ligand order Hannes Wallnoefer (Tue Mar 24 2009 - 05:38:18 PDT)
- Re: [AMBER] change in protein ligand order Bill Ross (Tue Mar 24 2009 - 11:07:42 PDT)
  - Re: [AMBER] change in protein ligand order Hannes Wallnoefer (Tue Mar 24 2009 - 13:45:16 PDT)
[AMBER] validation of parameters and request suggestions Jeffrey (Tue Mar 24 2009 - 04:52:19 PDT)
[AMBER] POLARIZABLE WATER MODEL CHAMI F. (Tue Mar 24 2009 - 11:03:25 PDT)
[AMBER] create new crd files from transformed coordinates Donald Keidel (Tue Mar 24 2009 - 18:49:03 PDT)
- Re: [AMBER] create new crd files from transformed coordinates case (Wed Mar 25 2009 - 05:26:29 PDT)
[AMBER] question about pair wise per-residue energy decomposition; idecomp=3 wfli.biophy.nju.edu.cn (Wed Mar 25 2009 - 02:48:29 PDT)
- Re: [AMBER] question about pair wise per-residue energy decomposition; idecomp=3 case (Wed Mar 25 2009 - 11:58:02 PDT)
[AMBER] About Free energy decomposition Rajesh Raju (Wed Mar 25 2009 - 07:08:00 PDT)
[AMBER] Rosetta Academic Training Webinar Nir London (Wed Mar 25 2009 - 09:14:21 PDT)
[AMBER] How to reproduce a parallel PMEMD run? Siang Yip (Wed Mar 25 2009 - 15:33:56 PDT)
- Re: [AMBER] How to reproduce a parallel PMEMD run? Robert Duke (Wed Mar 25 2009 - 16:45:49 PDT)
[AMBER] Amber 10 and core i7 Supat Jiranusornkul (Thu Mar 26 2009 - 02:13:10 PDT)
[AMBER] To find radial distribution curve nicholus bhattacharjee (Thu Mar 26 2009 - 10:16:07 PDT)
[AMBER] installing resp on linux 64bit aditya chhikara (Thu Mar 26 2009 - 10:24:27 PDT)
- Re: [AMBER] installing resp on linux 64bit FyD (Thu Mar 26 2009 - 12:37:22 PDT)
  - Re: [AMBER] installing resp on linux 64bit aditya chhikara (Thu Mar 26 2009 - 14:36:50 PDT)
[AMBER] Problem with "Atom does not have a type" Richard Tseng (Thu Mar 26 2009 - 16:17:19 PDT)
- Re: [AMBER] Problem with "Atom does not have a type" David A. Case (Fri Mar 27 2009 - 04:44:22 PDT)
  - Re: [AMBER] Problem with "Atom does not have a type" Richard Tseng (Fri Mar 27 2009 - 14:51:32 PDT)
    - Re: [AMBER] Problem with "Atom does not have a type" Richard Tseng (Fri Mar 27 2009 - 15:08:34 PDT)
    - Re: [AMBER] Problem with "Atom does not have a type" David A. Case (Sat Mar 28 2009 - 06:25:33 PDT)
    - Re: [AMBER] Problem with "Atom does not have a type" Richard Tseng (Sun Mar 29 2009 - 12:20:37 PDT)
    - Re: [AMBER] Problem with "Atom does not have a type" case (Mon Mar 30 2009 - 05:46:59 PDT)
[AMBER] Fwd: AMBER: MM-PBSA in AMBER 10 Daniel Oehme (Thu Mar 26 2009 - 16:44:59 PDT)
- Re: [AMBER] Fwd: AMBER: MM-PBSA in AMBER 10 Ray Luo (Thu Mar 26 2009 - 16:54:17 PDT)
[AMBER] Problem reading PDB file into XLEAP Hopkins, Robert (Thu Mar 26 2009 - 17:01:26 PDT)
- Re: [AMBER] Problem reading PDB file into XLEAP David A. Case (Fri Mar 27 2009 - 05:39:26 PDT)
  - RE: [AMBER] Problem reading PDB file into XLEAP Hopkins, Robert (Fri Mar 27 2009 - 15:09:11 PDT)
- Re: [AMBER] Problem reading PDB file into XLEAP David A. Case (Sat Mar 28 2009 - 06:28:53 PDT)
[AMBER] Antechamber problem 欧阳德方 (Thu Mar 26 2009 - 21:44:24 PDT)
- Re: [AMBER] Antechamber problem David A. Case (Fri Mar 27 2009 - 05:29:48 PDT)
- Re: [AMBER] Antechamber problem Junmei Wang (Fri Mar 27 2009 - 14:21:33 PDT)
  - RE: [AMBER] Antechamber problem 欧阳德方 (Fri Mar 27 2009 - 17:55:03 PDT)
[AMBER] problem using amoeba Hemant Gangwar (Fri Mar 27 2009 - 03:41:26 PDT)
- Re: [AMBER] problem using amoeba Robert Duke (Fri Mar 27 2009 - 05:22:31 PDT)
[AMBER] Question Kshatresh Dutta Dubey (Fri Mar 27 2009 - 06:06:09 PDT)
- RE: [AMBER] Question Rausch, Felix (Fri Mar 27 2009 - 06:37:29 PDT)
  - Re: [AMBER] Question Kshatresh Dutta Dubey (Sat Mar 28 2009 - 02:16:03 PDT)
    - Re: [AMBER] Question David A. Case (Sat Mar 28 2009 - 06:38:49 PDT)
- [AMBER] BINDER/xaLeap Taufik Al-Sarraj (Mon Mar 30 2009 - 18:00:10 PDT)
  - RE: [AMBER] BINDER/xaLeap Ross Walker (Mon Mar 30 2009 - 18:29:46 PDT)
    - RE: [AMBER] BINDER/xaLeap taufik.alsarraj.utoronto.ca (Mon Mar 30 2009 - 19:16:32 PDT)
    - [AMBER] ambmol2? Taufik Al-Sarraj (Tue Mar 31 2009 - 15:28:51 PDT)
    - Re: [AMBER] ambmol2? Junmei Wang (Tue Mar 31 2009 - 16:08:25 PDT)
    - Re: [AMBER] ambmol2? Taufik Al-Sarraj (Tue Mar 31 2009 - 19:15:00 PDT)
    - Re: [AMBER] ambmol2? Junmei Wang (Tue Mar 31 2009 - 19:41:35 PDT)
    - Re: [AMBER] ambmol2? David A. Case (Wed Apr 01 2009 - 06:19:00 PDT)
[AMBER] PMEMD 9 on MVAPICH / Infiniband problem Nick Holway (Fri Mar 27 2009 - 08:55:38 PDT)
- RE: [AMBER] PMEMD 9 on MVAPICH / Infiniband problem Ross Walker (Fri Mar 27 2009 - 18:04:04 PDT)
  - Re: [AMBER] PMEMD 9 on MVAPICH / Infiniband problem fohm fohm (Tue Mar 31 2009 - 04:04:10 PDT)
- Re: [AMBER] PMEMD 9 on MVAPICH / Infiniband problem Robert Duke (Tue Mar 31 2009 - 05:21:22 PDT)
[AMBER] Load protein complex to Xleap (Combine) Rilei Yu (Fri Mar 27 2009 - 19:30:04 PDT)
- Re: [AMBER] Load protein complex to Xleap (Combine) David A. Case (Sat Mar 28 2009 - 14:39:35 PDT)
- Re: [AMBER] Load protein complex to Xleap (Combine) Rilei Yu (Sat Mar 28 2009 - 18:17:21 PDT)
  - Re: [AMBER] Load protein complex to Xleap (Combine) David A. Case (Sat Mar 28 2009 - 19:26:58 PDT)
- Re: [AMBER] Load protein complex to Xleap (Combine) Rilei Yu (Sat Mar 28 2009 - 20:07:47 PDT)
- Re: [AMBER] Load protein complex to Xleap (Combine) Rilei Yu (Sat Mar 28 2009 - 21:00:00 PDT)
  - Re: [AMBER] Load protein complex to Xleap (Combine) David A. Case (Sun Mar 29 2009 - 11:41:13 PDT)
RE: [AMBER] Problem reading PDB file into XLEAP - SLEAP Hopkins, Robert (Sat Mar 28 2009 - 16:12:06 PDT)
- Re: [AMBER] Problem reading PDB file into XLEAP - SLEAP Wei Zhang (Sat Mar 28 2009 - 16:29:20 PDT)
  - RE: [AMBER] Problem reading PDB file into XLEAP - SLEAP Hopkins, Robert (Sun Mar 29 2009 - 11:27:09 PDT)
  - Re: [AMBER] Problem reading PDB file into XLEAP - SLEAP David A. Case (Sun Mar 29 2009 - 11:37:35 PDT)
    - RE: [AMBER] Problem reading PDB file into XLEAP - SLEAP Hopkins, Robert (Wed Apr 01 2009 - 16:10:44 PDT)
[AMBER] .rst file generation problem. Aravind S (Sun Mar 29 2009 - 22:48:55 PDT)
- Re: [AMBER] .rst file generation problem. Aravind S (Sun Mar 29 2009 - 23:32:12 PDT)
- Re: [AMBER] .rst file generation problem. Carlos Simmerling (Mon Mar 30 2009 - 04:30:58 PDT)
- Re: [AMBER] .rst file generation problem. Aravind S (Tue Mar 31 2009 - 01:49:17 PDT)
  - Re: [AMBER] .rst file generation problem. Carlos Simmerling (Tue Mar 31 2009 - 04:28:35 PDT)
[AMBER] "rfree: End of file on unit 5" Remya S R (Sun Mar 29 2009 - 23:21:53 PDT)
- Re: [AMBER] "rfree: End of file on unit 5" mathew k varghese (Mon Mar 30 2009 - 02:57:44 PDT)
[AMBER] mm_pbsa problem Giorgos Lamprinidis (Mon Mar 30 2009 - 03:02:07 PDT)
- Re: [AMBER] mm_pbsa problem case (Mon Mar 30 2009 - 05:48:05 PDT)
  - Re: [AMBER] mm_pbsa problem Giorgos Lamprinidis (Mon Mar 30 2009 - 06:59:55 PDT)
    - RE: [AMBER] mm_pbsa problem Ray Luo (Mon Mar 30 2009 - 10:27:59 PDT)
    - Re: [AMBER] mm_pbsa problem Giorgos Lamprinidis (Wed Apr 01 2009 - 00:36:53 PDT)
[AMBER] Creating conditions for biased MD Francesco Pietra (Mon Mar 30 2009 - 03:16:54 PDT)
- Re: [AMBER] Creating conditions for biased MD Carlos Simmerling (Mon Mar 30 2009 - 04:56:36 PDT)
  - Re: [AMBER] Creating conditions for biased MD Francesco Pietra (Mon Apr 20 2009 - 10:31:52 PDT)
    - Re: [AMBER] Creating conditions for biased MD Carlos Simmerling (Mon Apr 20 2009 - 11:46:41 PDT)
    - Re: [AMBER] Creating conditions for biased MD Francesco Pietra (Tue Apr 21 2009 - 11:40:35 PDT)
    - Re: [AMBER] Creating conditions for biased MD Carlos Simmerling (Tue Apr 21 2009 - 12:44:03 PDT)
    - Re: [AMBER] Creating conditions for biased MD Francesco Pietra (Tue Apr 21 2009 - 14:29:36 PDT)
    - Re: [AMBER] Creating conditions for biased MD Carlos Simmerling (Tue Apr 21 2009 - 14:32:09 PDT)
    - Re: [AMBER] Creating conditions for biased MD Francesco Pietra (Tue Apr 21 2009 - 14:49:14 PDT)
    - Re: [AMBER] Creating conditions for biased MD Francesco Pietra (Wed Apr 22 2009 - 03:16:11 PDT)
- Re: [AMBER] Creating conditions for biased MD Bill Ross (Wed Apr 22 2009 - 09:19:20 PDT)
  - Re: [AMBER] Creating conditions for biased MD Francesco Pietra (Wed Apr 22 2009 - 11:01:39 PDT)
[AMBER] amber tools installation Jayalakshmi Sridhar (Mon Mar 30 2009 - 08:44:57 PDT)
- Re: [AMBER] amber tools installation case (Mon Mar 30 2009 - 09:28:38 PDT)
[AMBER] Announcing NMR validation web interface iCing Alan (Mon Mar 30 2009 - 09:55:00 PDT)
[AMBER] problem with the results in the .out file! Aravind S (Mon Mar 30 2009 - 22:30:57 PDT)
- Re: [AMBER] problem with the results in the .out file! Gustavo Seabra (Tue Mar 31 2009 - 06:01:41 PDT)
  - Re: [AMBER] problem with the results in the .out file! Aravind S (Wed Apr 01 2009 - 22:49:19 PDT)
[AMBER] how to convert secstruct output file into plot or pictorial representation Siddharth Rastogi (Tue Mar 31 2009 - 03:56:37 PDT)
[AMBER] modifying LYN Marius Retegan (Tue Mar 31 2009 - 06:36:21 PDT)
- Re: [AMBER] modifying LYN FyD (Tue Mar 31 2009 - 08:41:56 PDT)
  - Re: [AMBER] modifying LYN Marius Retegan (Tue Mar 31 2009 - 09:58:06 PDT)
[AMBER] combine many coord files into trajectory file Peter Gannett (Tue Mar 31 2009 - 06:51:16 PDT)
- Re: [AMBER] combine many coord files into trajectory file Carlos Simmerling (Tue Mar 31 2009 - 06:55:58 PDT)
  - Re: [AMBER] combine many coord files into trajectory file Peter Gannett (Tue Mar 31 2009 - 07:25:00 PDT)
[AMBER] Maxwell-Boltzmann distribution and ig=-1 Naser Alijabbari (Tue Mar 31 2009 - 18:35:43 PDT)
- Re: [AMBER] Maxwell-Boltzmann distribution and ig=-1 Carlos Simmerling (Tue Mar 31 2009 - 18:41:49 PDT)
  - Re: [AMBER] Maxwell-Boltzmann distribution and ig=-1 Naser Alijabbari (Tue Mar 31 2009 - 19:15:13 PDT)
    - Re: [AMBER] Maxwell-Boltzmann distribution and ig=-1 Carlos Simmerling (Tue Mar 31 2009 - 19:24:34 PDT)
    - Re: [AMBER] Maxwell-Boltzmann distribution and ig=-1 Naser Alijabbari (Tue Mar 31 2009 - 19:43:28 PDT)
    - RE: [AMBER] Maxwell-Boltzmann distribution and ig=-1 Ross Walker (Tue Mar 31 2009 - 20:52:42 PDT)
    - Re: [AMBER] Maxwell-Boltzmann distribution and ig=-1 Carlos Simmerling (Wed Apr 01 2009 - 04:01:51 PDT)
[AMBER] a layer of water Nancy (Tue Mar 31 2009 - 18:37:51 PDT)
- Re: [AMBER] a layer of water oguz gurbulak (Wed Apr 01 2009 - 00:26:46 PDT)
[AMBER] constant-pH: appearance of not titrated residues during the Monte Carlo simulation Therese Malliavin (Wed Apr 01 2009 - 02:06:19 PDT)
- Re: [AMBER] constant-pH: appearance of not titrated residues during the Monte Carlo simulation David A. Case (Sat Apr 04 2009 - 06:20:28 PDT)
[AMBER] run protein with structural Ca+ sarah genare (Wed Apr 01 2009 - 04:01:24 PDT)
[AMBER] Failure to compile amber9 serial ifort gcc Francesco Pietra (Wed Apr 01 2009 - 04:04:18 PDT)
- Re: [AMBER] Failure to compile amber9 serial ifort gcc Alessandro Nascimento (Wed Apr 01 2009 - 04:09:42 PDT)
- Re: [AMBER] Failure to compile amber9 serial ifort gcc Francesco Pietra (Thu Apr 02 2009 - 04:16:36 PDT)
  - RE: [AMBER] Failure to compile amber9 serial ifort gcc Ross Walker (Thu Apr 02 2009 - 08:45:19 PDT)
    - Re: [AMBER] Failure to compile amber9 serial ifort gcc Francesco Pietra (Thu Apr 02 2009 - 09:00:46 PDT)
[AMBER] fillratio error in mmpbsa m m (Wed Apr 01 2009 - 04:42:45 PDT)
- Re: [AMBER] fillratio error in mmpbsa Han Ming (Wed Apr 01 2009 - 08:06:08 PDT)
- RE: [AMBER] fillratio error in mmpbsa Ray Luo (Wed Apr 01 2009 - 12:24:20 PDT)
[AMBER] calculation of Pi-Pi interaction energy aneesh cna (Wed Apr 01 2009 - 05:01:51 PDT)
[AMBER] calculation of Pi-Pi interaction energy Jacopo Sgrignani (Wed Apr 01 2009 - 05:24:28 PDT)
- Re: [AMBER] calculation of Pi-Pi interaction energy Jiri Sponer (Wed Apr 01 2009 - 05:38:49 PDT)
[AMBER] yacc parser Francesco Pietra (Wed Apr 01 2009 - 07:58:01 PDT)
- Re: [AMBER] yacc parser Mark Williamson (Wed Apr 01 2009 - 10:15:56 PDT)
- [AMBER] Fwd: yacc parser Francesco Pietra (Wed Apr 01 2009 - 13:53:01 PDT)
- Re: [AMBER] yacc parser David A. Case (Thu Apr 02 2009 - 05:03:06 PDT)
  - Re: [AMBER] yacc parser Francesco Pietra (Thu Apr 02 2009 - 08:37:53 PDT)
[AMBER] make test.serial.QMMM michael bane (Wed Apr 01 2009 - 08:44:51 PDT)
- Re: [AMBER] make test.serial.QMMM Seth Hayik (Wed Apr 01 2009 - 10:26:21 PDT)
[AMBER] ptraj and namd charmm dcd Sandro L. Fornili (Wed Apr 01 2009 - 08:59:37 PDT)
- Re: [AMBER] ptraj and namd charmm dcd Thomas Cheatham III (Wed Apr 01 2009 - 09:08:51 PDT)
Re: [AMBER] AmberTools compilation error Marius Retegan (Wed Apr 01 2009 - 13:03:59 PDT)
[AMBER] Help: An error happened when I calculate mm/pbsa thirsty (Thu Apr 02 2009 - 01:12:25 PDT)
- Re: [AMBER] Help: An error happened when I calculate mm/pbsa Carlos Simmerling (Thu Apr 02 2009 - 04:19:04 PDT)
  - Re: [AMBER] Help: An error happened when I calculate mm/pbsa thirsty (Fri Apr 03 2009 - 00:11:19 PDT)
[AMBER] please help me out bharat lakhani (Thu Apr 02 2009 - 03:13:48 PDT)
- Re: [AMBER] please help me out David A. Case (Thu Apr 02 2009 - 10:48:10 PDT)
[AMBER] Counter-ions waleed zalloum (Thu Apr 02 2009 - 03:15:12 PDT)
RE: [AMBER] problem in input Rausch, Felix (Thu Apr 02 2009 - 04:08:27 PDT)
- RE: [AMBER] problem in input balaji nagarajan (Thu Apr 02 2009 - 13:23:18 PDT)
- RE: [AMBER] problem in input Rausch, Felix (Fri Apr 03 2009 - 01:04:36 PDT)
[AMBER] number of waters in first and second solvation shell Siddharth Rastogi (Thu Apr 02 2009 - 04:40:21 PDT)
[AMBER] explicit ion with igb=1 Bala subramanian (Thu Apr 02 2009 - 06:39:10 PDT)
- Re: [AMBER] explicit ion with igb=1 Carlos Simmerling (Thu Apr 02 2009 - 06:53:54 PDT)
[AMBER] Averaging simulations Naser Alijabbari (Thu Apr 02 2009 - 08:21:41 PDT)
- Re: [AMBER] Averaging simulations Carlos Simmerling (Thu Apr 02 2009 - 08:24:28 PDT)
[AMBER] Error in trajin and rms Pansy Patel (Thu Apr 02 2009 - 11:58:47 PDT)
- RE: [AMBER] Error in trajin and rms iccy liu (Thu Apr 02 2009 - 12:19:16 PDT)
  - RE: [AMBER] Error in trajin and rms Pansy Patel (Thu Apr 02 2009 - 12:25:58 PDT)
- Re: [AMBER] Error in trajin and rms Carlos Simmerling (Thu Apr 02 2009 - 12:19:39 PDT)
[AMBER] parallel installation of amber on sun Per Jr. Greisen (Thu Apr 02 2009 - 12:02:47 PDT)
- Re: [AMBER] parallel installation of amber on sun Atro Tossavainen (Thu Apr 02 2009 - 13:23:05 PDT)
  - Re: [AMBER] parallel installation of amber on sun Per Jr. Greisen (Thu Apr 02 2009 - 13:38:54 PDT)
- Re: [AMBER] parallel installation of amber on sun Atro Tossavainen (Fri Apr 03 2009 - 02:39:25 PDT)
  - Re: [AMBER] parallel installation of amber on sun Per Jr. Greisen (Fri Apr 03 2009 - 03:22:45 PDT)
    - Re: [AMBER] parallel installation of amber on sun Atro Tossavainen (Fri Apr 03 2009 - 14:40:42 PDT)
    - Re: [AMBER] parallel installation of amber on sun Atro Tossavainen (Fri Apr 03 2009 - 15:33:52 PDT)
[AMBER] long polymer chain and image command in ptraj iccy liu (Thu Apr 02 2009 - 12:11:26 PDT)
- Re: [AMBER] long polymer chain and image command in ptraj Karl Kirschner (Mon Apr 06 2009 - 01:15:00 PDT)
[AMBER] Contour plot Beale, John (Thu Apr 02 2009 - 12:31:22 PDT)
- Re: [AMBER] Contour plot Gustavo Seabra (Thu Apr 02 2009 - 12:47:14 PDT)
[AMBER] How to delete the frames at specific intervals Mannan (Thu Apr 02 2009 - 18:16:49 PDT)
- Re: [AMBER] How to delete the frames at specific intervals Bala subramanian (Fri Apr 03 2009 - 02:55:35 PDT)
[AMBER] How to find out residence time of water molecules Mannan (Thu Apr 02 2009 - 18:52:36 PDT)
- Re: [AMBER] How to find out residence time of water molecules Bala subramanian (Thu Apr 02 2009 - 23:12:18 PDT)
- Re: [AMBER] How to find out residence time of water molecules Hannes Loeffler (Fri Apr 03 2009 - 00:31:32 PDT)
[AMBER] (no subject) chenquan (Fri Apr 03 2009 - 03:12:14 PDT)
- Re: [AMBER] (no subject) David A. Case (Fri Apr 03 2009 - 05:17:36 PDT)
[AMBER] How to create parameter file for unknown residue nicholus bhattacharjee (Fri Apr 03 2009 - 03:33:03 PDT)
- Re: [AMBER] How to create parameter file for unknown residue Marius Retegan (Fri Apr 03 2009 - 03:50:30 PDT)
[AMBER] Could not find angle parameter chenquan (Fri Apr 03 2009 - 03:46:47 PDT)
- Re: [AMBER] Could not find angle parameter Marius Retegan (Fri Apr 03 2009 - 03:58:47 PDT)
[AMBER] antechamber & multiple low-energy conformations Alessandro Nascimento (Fri Apr 03 2009 - 05:01:39 PDT)
[AMBER] amber9 serial compilation issues Francesco Pietra (Fri Apr 03 2009 - 11:38:12 PDT)
- Re: [AMBER] amber9 serial compilation issues David A. Case (Fri Apr 03 2009 - 13:01:02 PDT)
  - Re: [AMBER] amber9 serial compilation issues Francesco Pietra (Fri Apr 03 2009 - 15:04:17 PDT)
[AMBER] NALA-ALA-CALA peptide with antechamber Alan (Fri Apr 03 2009 - 09:33:17 PDT)
- Re: [AMBER] NALA-ALA-CALA peptide with antechamber David A. Case (Sat Apr 04 2009 - 06:04:32 PDT)
[AMBER] ptraj problem Ed Pate (Fri Apr 03 2009 - 13:13:37 PDT)
- Re: [AMBER] ptraj problem Thomas Cheatham III (Fri Apr 03 2009 - 13:23:21 PDT)
[AMBER] Generate AM1-CM2 charges using antechamber Sishi Tang (Fri Apr 03 2009 - 15:36:46 PDT)
[AMBER] parameter for amoeba Hemant Kumar (Sat Apr 04 2009 - 04:46:01 PDT)
[AMBER] LYN again Marius Retegan (Sat Apr 04 2009 - 06:12:09 PDT)
- Re: [AMBER] LYN again FyD (Sun Apr 05 2009 - 12:24:27 PDT)
  - Re: [AMBER] LYN again Marius Retegan (Mon Apr 06 2009 - 06:55:24 PDT)
    - Re: [AMBER] LYN again FyD (Mon Apr 06 2009 - 07:26:14 PDT)
Re: [AMBER] Umbrella test David A. Case (Sat Apr 04 2009 - 06:12:13 PDT)
[AMBER] deffision Nancy (Sat Apr 04 2009 - 07:30:50 PDT)
[AMBER] error in MM PBSA Vikas Sharma (Sat Apr 04 2009 - 10:06:57 PDT)
- Re: [AMBER] error in MM PBSA Hemant Gangwar (Sat Apr 04 2009 - 10:08:08 PDT)
- Re: [AMBER] error in MM PBSA David A. Case (Sat Apr 04 2009 - 14:16:42 PDT)
[AMBER] error in MM PBSA Vikas Sharma (Sat Apr 04 2009 - 23:09:35 PDT)
[AMBER] error in MM PBSA Vikas Sharma (Sun Apr 05 2009 - 21:27:21 PDT)
[AMBER] pmemd compilation/make failed - mkl_vml_service_threader_z_1i_c_1o Vijay Manickam Achari (Mon Apr 06 2009 - 00:27:24 PDT)
- Re: [AMBER] pmemd compilation/make failed -mkl_vml_service_threader_z_1i_c_1o Robert Duke (Mon Apr 06 2009 - 07:25:14 PDT)
  - Re: [AMBER] pmemd compilation/make failed -mkl_vml_service_threader_z_1i_c_1o Vijay Manickam Achari (Mon Apr 06 2009 - 21:25:36 PDT)
    - Re: [AMBER] pmemd compilation/make failed-mkl_vml_service_threader_z_1i_c_1o Robert Duke (Tue Apr 07 2009 - 05:43:36 PDT)
[AMBER] sander.MPI parallel run problem Dechang Li (Mon Apr 06 2009 - 00:44:12 PDT)
- Re: [AMBER] sander.MPI parallel run problem Carlos Simmerling (Mon Apr 06 2009 - 03:09:11 PDT)
  - Re: Re: [AMBER] sander.MPI parallel run problem Dechang Li (Mon Apr 06 2009 - 03:56:53 PDT)
    - Re: Re: [AMBER] sander.MPI parallel run problem Carlos Simmerling (Mon Apr 06 2009 - 04:02:13 PDT)
    - Re: Re: Re: [AMBER] sander.MPI parallel run problem Dechang Li (Mon Apr 06 2009 - 04:09:04 PDT)
[AMBER] faulty .rst file with "************" signs for the coordinates of a certain molecule. Soni Mufaddal Saifee (Mon Apr 06 2009 - 02:07:51 PDT)
- Re: [AMBER] faulty .rst file with "************" signs for the coordinates of a certain molecule. Carlos Simmerling (Mon Apr 06 2009 - 03:07:09 PDT)
  - Re: [AMBER] faulty .rst file with "************" signs for the coordinates of a certain molecule. Soni Mufaddal Saifee (Tue Apr 07 2009 - 21:19:25 PDT)
[AMBER] MM-PBSA error while running heat.in Vikas Sharma (Mon Apr 06 2009 - 02:32:55 PDT)
[AMBER] ssh and make test.parallel Francesco Pietra (Mon Apr 06 2009 - 02:58:39 PDT)
- Re: [AMBER] ssh and make test.parallel Atro Tossavainen (Mon Apr 06 2009 - 03:33:21 PDT)
  - Re: [AMBER] ssh and make test.parallel Francesco Pietra (Mon Apr 06 2009 - 07:29:19 PDT)
    - Re: [AMBER] ssh and make test.parallel Atro Tossavainen (Mon Apr 06 2009 - 13:21:07 PDT)
    - [AMBER] number_rec_numbers in mm_pbsa Zhu, Yong-Liang (Mon Apr 06 2009 - 16:52:06 PDT)
    - 回复： [AMBER] number_rec_numbers in mm_pbsa 廖青华 (Mon Apr 06 2009 - 17:18:54 PDT)
    - Re: [AMBER] ssh and make test.parallel Francesco Pietra (Wed Apr 08 2009 - 00:19:36 PDT)
[AMBER] problem with secstruct action command in ptraj nicholus bhattacharjee (Mon Apr 06 2009 - 04:49:44 PDT)
[AMBER] testing RRR with antechamber Alan (Mon Apr 06 2009 - 05:10:27 PDT)
[AMBER] zwitterionic form of ARG and antechamber Alan (Mon Apr 06 2009 - 05:33:31 PDT)
[AMBER] Amber with AMOEBA force-field Tomasio, Susana (Mon Apr 06 2009 - 05:41:18 PDT)
- Re: [AMBER] Amber with AMOEBA force-field David A. Case (Mon Apr 06 2009 - 05:47:11 PDT)
- Re: [AMBER] Amber with AMOEBA force-field Wei Zhang (Mon Apr 06 2009 - 05:48:28 PDT)
- RE: [AMBER] Amber with AMOEBA force-field Tomasio, Susana (Mon Apr 06 2009 - 05:49:28 PDT)
  - Re: [AMBER] Amber with AMOEBA force-field Wei Zhang (Mon Apr 06 2009 - 05:55:59 PDT)
- RE: [AMBER] Amber with AMOEBA force-field Tomasio, Susana (Mon Apr 06 2009 - 05:52:01 PDT)
  - Re: [AMBER] Amber with AMOEBA force-field Wei Zhang (Mon Apr 06 2009 - 05:57:21 PDT)
  - Re: [AMBER] Amber with AMOEBA force-field David A. Case (Mon Apr 06 2009 - 06:00:47 PDT)
- RE: [AMBER] Amber with AMOEBA force-field Tomasio, Susana (Mon Apr 06 2009 - 06:14:22 PDT)
- RE: [AMBER] Amber with AMOEBA force-field Tomasio, Susana (Mon Apr 06 2009 - 06:40:49 PDT)
[AMBER] Sander waleed_zalloum.yahoo.com (Mon Apr 06 2009 - 06:17:34 PDT)
[AMBER] MM-PBSA: decompose energy error Lucilla Angeli (Mon Apr 06 2009 - 07:35:58 PDT)
- Re: [AMBER] MM-PBSA: decompose energy error Maria Mirza (Sun Aug 16 2009 - 12:49:06 PDT)
  - Re: [AMBER] MM-PBSA: decompose energy error Ryan Pavlovicz (Fri Feb 19 2010 - 11:30:54 PST)
[AMBER] Sander Stalling Steve Seibold (Mon Apr 06 2009 - 09:21:51 PDT)
- RE: [AMBER] Sander Stalling Ross Walker (Mon Apr 06 2009 - 09:58:58 PDT)
- [AMBER] sequence function taufik.alsarraj.utoronto.ca (Mon Apr 06 2009 - 10:03:20 PDT)
  - Re: [AMBER] sequence function taufik.alsarraj.utoronto.ca (Mon Apr 06 2009 - 10:06:50 PDT)
- Re: [AMBER] Sander Stalling Robert Duke (Mon Apr 06 2009 - 09:57:18 PDT)
[AMBER] Do I need to modify the cap residues nicholus bhattacharjee (Mon Apr 06 2009 - 09:45:20 PDT)
- RE: [AMBER] Do I need to modify the cap residues Ross Walker (Mon Apr 06 2009 - 10:00:05 PDT)
  - Re: [AMBER] Do I need to modify the cap residues nicholus bhattacharjee (Mon Apr 06 2009 - 10:19:41 PDT)
    - Re: [AMBER] Do I need to modify the cap residues David A. Case (Mon Apr 06 2009 - 11:57:02 PDT)
    - Re: [AMBER] Do I need to modify the cap residues nicholus bhattacharjee (Mon Apr 06 2009 - 21:51:22 PDT)
    - RE: [AMBER] Do I need to modify the cap residues Ross Walker (Mon Apr 06 2009 - 21:59:37 PDT)
[AMBER] Negative "number of measurements" in PTRAJ Jenny Iskrenova (Mon Apr 06 2009 - 10:28:59 PDT)
- Re: [AMBER] Negative "number of measurements" in PTRAJ Thomas Cheatham (Tue Apr 07 2009 - 09:57:28 PDT)
[AMBER] Amber on GPU Sasha Buzko (Mon Apr 06 2009 - 17:56:31 PDT)
- RE: [AMBER] Amber on GPU Ross Walker (Mon Apr 06 2009 - 18:14:07 PDT)
  - Re: [AMBER] Amber on GPU Sasha Buzko (Mon Apr 06 2009 - 23:11:24 PDT)
  - Re: [AMBER] Amber on GPU Sasha Buzko (Thu Apr 09 2009 - 17:54:29 PDT)
  - [AMBER] MD on GPU: an existing commercial implementation Sasha Buzko (Sat Apr 11 2009 - 17:47:46 PDT)
[AMBER] deffision coefficient Nancy (Mon Apr 06 2009 - 18:18:32 PDT)
- Re: [AMBER] deffision coefficient David A. Case (Mon Apr 06 2009 - 19:16:39 PDT)
[AMBER] A question about SMD force constant Jackie. J. Shen (Mon Apr 06 2009 - 18:40:13 PDT)
- Re: [AMBER] A question about SMD force constant Carlos Simmerling (Tue Apr 07 2009 - 03:32:09 PDT)
[AMBER] ambmask question Ed Pate (Mon Apr 06 2009 - 21:36:40 PDT)
[AMBER] Problems with running two separate jobs in the same time Antonija Tomić (Tue Apr 07 2009 - 01:08:53 PDT)
- RE: [AMBER] Problems with running two separate jobs in the same time Ross Walker (Tue Apr 07 2009 - 08:01:14 PDT)
  - RE: [AMBER] Problems with running two separate jobs in the same time Antonija Tomić (Thu Apr 09 2009 - 03:33:03 PDT)
[AMBER] how to add charge in metal ion bharat lakhani (Tue Apr 07 2009 - 02:11:23 PDT)
- RE: [AMBER] how to add charge in metal ion Ross Walker (Tue Apr 07 2009 - 08:01:14 PDT)
  - Re: [AMBER] how to add charge in metal ion bharat lakhani (Tue Apr 14 2009 - 05:49:44 PDT)
[AMBER] missing violations of the covalent geometry Helena P M Tossavainen (Tue Apr 07 2009 - 02:36:44 PDT)
- Re: [AMBER] missing violations of the covalent geometry David A. Case (Tue Apr 07 2009 - 04:10:42 PDT)
  - Re: [AMBER] missing violations of the covalent geometry Helena P M Tossavainen (Tue Apr 07 2009 - 05:10:16 PDT)
[AMBER] errors while testing Per Jr. Greisen (Tue Apr 07 2009 - 03:00:19 PDT)
- Re: [AMBER] errors while testing Atro Tossavainen (Tue Apr 07 2009 - 03:18:08 PDT)
  - Re: [AMBER] errors while testing Per Jr. Greisen (Wed Apr 08 2009 - 04:06:40 PDT)
[AMBER] Problem with CAP residues Tomasio, Susana (Tue Apr 07 2009 - 03:17:27 PDT)
- Re: [AMBER] Problem with CAP residues FyD (Tue Apr 07 2009 - 04:01:35 PDT)
[AMBER] TI production runs stop after a certain Step number Hannes Wallnoefer (Tue Apr 07 2009 - 04:48:45 PDT)
- Re: [AMBER] TI production runs stop after a certain Step number steinbrt.rci.rutgers.edu (Tue Apr 07 2009 - 07:49:57 PDT)
  - Re: [AMBER] TI production runs stop after a certain Step number Hannes Wallnoefer (Wed Apr 08 2009 - 04:48:31 PDT)
    - Re: [AMBER] TI production runs stop after a certain Step number steinbrt.rci.rutgers.edu (Wed Apr 08 2009 - 07:35:11 PDT)
    - Re: [AMBER] TI production runs stop after a certain Step number Hannes Wallnoefer (Wed Apr 08 2009 - 08:14:32 PDT)
- Re: [AMBER] TI production runs stop after a certain Step number Ilyas Yildirim (Tue Apr 07 2009 - 12:08:31 PDT)
Re: [AMBER] pmemd compilation/makefailed-mkl_vml_service_threader_z_1i_c_1o Robert Duke (Tue Apr 07 2009 - 05:55:00 PDT)
- Re: [AMBER] pmemd compilation/makefailed-mkl_vml_service_threader_z_1i_c_1o Vijay Manickam Achari (Tue Apr 07 2009 - 23:27:46 PDT)
  - Re: [AMBER] pmemdcompilation/makefailed-mkl_vml_service_threader_z_1i_c_1o Robert Duke (Wed Apr 08 2009 - 05:13:23 PDT)
  - Re: [AMBER] pmemdcompilation/makefailed-mkl_vml_service_threader_z_1i_c_1o Robert Duke (Wed Apr 08 2009 - 06:35:49 PDT)
    - RE: [AMBER] pmemdcompilation/makefailed-mkl_vml_service_threade_z_1i_c_1o Ross Walker (Wed Apr 08 2009 - 07:53:31 PDT)
    - RE: [AMBER] pmemdcompilation/makefailed-mkl_vml_service_threade_z_1i_c_1o Vijay Manickam Achari (Thu Apr 09 2009 - 02:55:53 PDT)
[AMBER] test/amoeba - forrtl: severe (64): input conversion error Tomasio, Susana (Tue Apr 07 2009 - 08:16:08 PDT)
- Re: [AMBER] test/amoeba - forrtl: severe (64): input conversion error David A. Case (Tue Apr 07 2009 - 09:29:18 PDT)
RE: [AMBER] test/amoeba - forrtl: severe (64): input conversion error Tomasio, Susana (Tue Apr 07 2009 - 09:34:57 PDT)
- Re: [AMBER] test/amoeba - forrtl: severe (64): input conversion error Wei Zhang (Tue Apr 07 2009 - 11:34:11 PDT)
- RE: [AMBER] test/amoeba - forrtl: severe (64): input conversion error Tomasio, Susana (Tue Apr 07 2009 - 12:34:26 PDT)
- RE: [AMBER] test/amoeba - forrtl: severe (64): input conversion error Tomasio, Susana (Tue Apr 07 2009 - 13:12:19 PDT)
  - Re: [AMBER] test/amoeba - forrtl: severe (64): input conversion error David A. Case (Tue Apr 07 2009 - 13:41:21 PDT)
- RE: [AMBER] test/amoeba - forrtl: severe (64): input conversion error Tomasio, Susana (Tue Apr 07 2009 - 15:45:57 PDT)
  - Re: [AMBER] test/amoeba - forrtl: severe (64): input conversion error Wei Zhang (Wed Apr 08 2009 - 08:38:50 PDT)
- RE: [AMBER] test/amoeba - forrtl: severe (64): input conversion error Tomasio, Susana (Wed Apr 08 2009 - 09:02:48 PDT)
  - [AMBER] test/amoeba: forrtl: error (78): process killed (SIGTERM) Tomasio, Susana (Wed Apr 29 2009 - 10:45:36 PDT)
    - Re: [AMBER] test/amoeba: forrtl: error (78): process killed (SIGTERM) Wei Zhang (Wed Apr 29 2009 - 11:00:28 PDT)
    - RE: [AMBER] test/amoeba: forrtl: error (78): process killed (SIGTERM) Tomasio, Susana (Wed Apr 29 2009 - 13:15:02 PDT)
    - [AMBER] ongoing issues using sander with AMOEBA Tomasio, Susana (Wed May 13 2009 - 03:00:00 PDT)
[AMBER] Testing parallel amber10: no libmkl_lapack.so Francesco Pietra (Tue Apr 07 2009 - 11:56:25 PDT)
- [AMBER] prmtop residue format taufik.alsarraj.utoronto.ca (Tue Apr 07 2009 - 13:04:25 PDT)
  - Re: [AMBER] prmtop residue format David A. Case (Tue Apr 07 2009 - 13:35:40 PDT)
    - Re: [AMBER] top2mol2 taufik.alsarraj.utoronto.ca (Tue Apr 07 2009 - 15:39:34 PDT)
    - [AMBER] ptraj randomizeions taufik.alsarraj.utoronto.ca (Tue Apr 07 2009 - 16:32:23 PDT)
- Re: [AMBER] Testing parallel amber10: no libmkl_lapack.so Atro Tossavainen (Wed Apr 08 2009 - 02:35:17 PDT)
  - Re: [AMBER] Testing parallel amber10: no libmkl_lapack.so Francesco Pietra (Wed Apr 08 2009 - 03:03:09 PDT)
    - Re: [AMBER] Testing parallel amber10: no libmkl_lapack.so Atro Tossavainen (Wed Apr 08 2009 - 04:20:27 PDT)
    - Re: [AMBER] Testing parallel amber10: no libmkl_lapack.so Francesco Pietra (Wed Apr 08 2009 - 08:14:43 PDT)
    - Fwd: [AMBER] Testing parallel amber10: no libmkl_lapack.so Francesco Pietra (Wed Apr 08 2009 - 08:23:58 PDT)
    - Re: Fwd: [AMBER] Testing parallel amber10: no libmkl_lapack.so Atro Tossavainen (Wed Apr 08 2009 - 15:25:54 PDT)
    - Re: Fwd: [AMBER] Testing parallel amber10: no libmkl_lapack.so Francesco Pietra (Wed Apr 08 2009 - 16:20:02 PDT)
    - Re: Fwd: [AMBER] Testing parallel amber10: no libmkl_lapack.so Atro Tossavainen (Wed Apr 08 2009 - 16:36:53 PDT)
    - Re: [AMBER] Testing parallel amber10: no libmkl_lapack.so M. L. Dodson (Wed Apr 08 2009 - 09:06:09 PDT)
    - Re: [AMBER] Testing parallel amber10: no libmkl_lapack.so Atro Tossavainen (Wed Apr 08 2009 - 15:24:52 PDT)
    - Re: [AMBER] Testing parallel amber10: no libmkl_lapack.so Francesco Pietra (Wed Apr 08 2009 - 16:17:38 PDT)
    - Re: [AMBER] Testing parallel amber10: no libmkl_lapack.so Atro Tossavainen (Wed Apr 08 2009 - 16:39:30 PDT)
    - Re: [AMBER] Testing parallel amber10: no libmkl_lapack.so Francesco Pietra (Sun Apr 19 2009 - 07:36:02 PDT)
[AMBER] PBSA Radii option quantum_mania.yahoo.com (Tue Apr 07 2009 - 12:31:18 PDT)
- [AMBER] Source of new CYX residue parameters in ff03ua Chris Moth (Tue Apr 07 2009 - 12:48:46 PDT)
  - [AMBER] Source of new CYX residue parameters in ff03ua Chris Moth (Tue Apr 14 2009 - 17:42:33 PDT)
  - RE: [AMBER] Source of new CYX residue parameters in ff03ua Ross Walker (Tue Apr 14 2009 - 21:08:14 PDT)
[AMBER] MMPB(GB)SA on trimer quantum_mania.yahoo.com (Tue Apr 07 2009 - 18:01:39 PDT)
[AMBER] compare MMPBSA result m m (Tue Apr 07 2009 - 23:28:06 PDT)
- RE: [AMBER] compare MMPBSA result Ray Luo (Wed Apr 08 2009 - 10:02:41 PDT)
[AMBER] problem with antechamber aneesh cna (Tue Apr 07 2009 - 23:32:32 PDT)
- Re:Re: [AMBER] problem with antechamber sculiujl (Fri Dec 04 2009 - 04:18:24 PST)
[AMBER] please help me out bharat lakhani (Wed Apr 08 2009 - 02:18:41 PDT)
- RE: [AMBER] please help me out Ross Walker (Wed Apr 08 2009 - 08:34:51 PDT)
  - Re: [AMBER] please help me out Hugh Heldenbrand (Wed Apr 08 2009 - 08:44:54 PDT)
    - Re: [AMBER] please help me out David A. Case (Wed Apr 08 2009 - 11:10:04 PDT)
  - [AMBER] ntwr taufik.alsarraj.utoronto.ca (Wed Apr 08 2009 - 14:45:01 PDT)
    - Re: [AMBER] ntwr Carlos Simmerling (Wed Apr 08 2009 - 14:47:04 PDT)
    - Re: [AMBER] ntwr taufik.alsarraj.utoronto.ca (Wed Apr 08 2009 - 15:35:57 PDT)
    - Re: [AMBER] ntwr Carlos Simmerling (Wed Apr 08 2009 - 15:45:57 PDT)
[AMBER] Failures of tests Per Jr. Greisen (Wed Apr 08 2009 - 08:41:34 PDT)
- RE: [AMBER] Failures of tests Seetin, Matthew (Wed Apr 08 2009 - 08:57:27 PDT)
  - Re: [AMBER] Failures of tests Per Jr. Greisen (Wed Apr 08 2009 - 09:17:16 PDT)
- Re: [AMBER] Failures of tests Atro Tossavainen (Wed Apr 08 2009 - 15:43:08 PDT)
  - Re: [AMBER] Failures of tests Per Jr. Greisen (Thu Apr 09 2009 - 05:52:32 PDT)
[AMBER] Thermodynamic Integration and belly Ignacio J. General (Wed Apr 08 2009 - 12:52:51 PDT)
[AMBER] force fields Mark M Huntress (Wed Apr 08 2009 - 17:23:38 PDT)
- RE: [AMBER] force fields Ross Walker (Wed Apr 08 2009 - 17:36:05 PDT)
- Re: [AMBER] force fields Gustavo Seabra (Wed Apr 15 2009 - 05:43:49 PDT)
[AMBER] please help me out bharat lakhani (Wed Apr 08 2009 - 22:10:22 PDT)
- Re: [AMBER] please help me out David A. Case (Thu Apr 09 2009 - 04:46:12 PDT)
[AMBER] how to plot this kind of map? lnin_1431.sina.com (Thu Apr 09 2009 - 01:36:45 PDT)
- Re: [AMBER] how to plot this kind of map? Dechang Li (Thu Apr 09 2009 - 01:46:16 PDT)
Re: [AMBER] hpux sander.serial failure info David A. Case (Thu Apr 09 2009 - 04:56:51 PDT)
- Re: [AMBER] hpux sander.serial failure info David A. Case (Wed Apr 15 2009 - 05:07:45 PDT)
[AMBER] RST file waleed zalloum (Thu Apr 09 2009 - 07:06:37 PDT)
- Re: [AMBER] RST file David A. Case (Fri Apr 10 2009 - 05:21:19 PDT)
[AMBER] Release of R.E.D. Server FyD (Thu Apr 09 2009 - 01:31:30 PDT)
[AMBER] antechamber problems Jia Xu (Thu Apr 09 2009 - 10:12:44 PDT)
- Re: [AMBER] antechamber problems David A. Case (Thu Apr 09 2009 - 11:04:51 PDT)
- Re: [AMBER] antechamber problems Nicholas Musolino (Thu Apr 09 2009 - 11:03:45 PDT)
  - Re: [AMBER] antechamber problems Jia Xu (Fri Apr 10 2009 - 07:41:53 PDT)
[AMBER] Sander and multiple residues Dan Kaps (Thu Apr 09 2009 - 11:48:55 PDT)
- Re: [AMBER] Sander and multiple residues Carlos Simmerling (Thu Apr 09 2009 - 12:21:56 PDT)
  - Re: [AMBER] Sander and multiple residues Dan Kaps (Thu Apr 09 2009 - 13:02:46 PDT)
    - Re: [AMBER] Sander and multiple residues Carlos Simmerling (Thu Apr 09 2009 - 13:05:23 PDT)
    - Re: [AMBER] Sander and multiple residues Dan Kaps (Fri Apr 10 2009 - 05:56:53 PDT)
- Re: [AMBER] Sander and multiple residues Bill Ross (Thu Apr 09 2009 - 13:12:10 PDT)
  - Re: [AMBER] Sander and multiple residues Dan Kaps (Fri Apr 10 2009 - 05:57:54 PDT)
    - Re: [AMBER] Sander and multiple residues David A. Case (Fri Apr 10 2009 - 07:03:57 PDT)
    - Re: [AMBER] Sander and multiple residues Dan Kaps (Fri Apr 10 2009 - 08:01:08 PDT)
- Re: [AMBER] Sander and multiple residues Bill Ross (Fri Apr 10 2009 - 09:42:36 PDT)
  - Re: [AMBER] Sander and multiple residues Dan Kaps (Fri Apr 10 2009 - 10:46:49 PDT)
  - [AMBER] ptraj (vector and corrplane) taufik.alsarraj.utoronto.ca (Fri Apr 10 2009 - 17:45:46 PDT)
- Re: [AMBER] Sander and multiple residues Bill Ross (Fri Apr 10 2009 - 13:42:14 PDT)
[AMBER] igb=0 vs. igb=6 give different answers Hugh Heldenbrand (Thu Apr 09 2009 - 13:51:02 PDT)
- Re: [AMBER] igb=0 vs. igb=6 give different answers David A. Case (Thu Apr 09 2009 - 19:48:31 PDT)
[AMBER] basepair balaji nagarajan (Thu Apr 09 2009 - 22:30:57 PDT)
- Re: [AMBER] basepair Bala subramanian (Tue Apr 14 2009 - 04:09:21 PDT)
[AMBER] Amber 1.2 tools test suite failure? Jim Parker (Sat Apr 11 2009 - 10:41:54 PDT)
- RE: [AMBER] Amber 1.2 tools test suite failure? Ross Walker (Sat Apr 11 2009 - 11:00:45 PDT)
  - Re: [AMBER] Solved-Amber 1.2 tools test suite failure Jim Parker (Sat Apr 11 2009 - 12:29:55 PDT)
    - RE: [AMBER] Solved-Amber 1.2 tools test suite failure Ross Walker (Sat Apr 11 2009 - 12:51:13 PDT)
[AMBER] install and test Amber 10 parallel on Ubuntu 8.10 Jim Parker (Sat Apr 11 2009 - 17:20:25 PDT)
- [AMBER] Re: install and test Amber 10 parallel on Ubuntu 8.10 Jim Parker (Sat Apr 11 2009 - 21:47:19 PDT)
[AMBER] why amber10/dat/leap/gleap/ and amber10/dat/leap/parm Alan (Sun Apr 12 2009 - 02:30:15 PDT)
- Re: [AMBER] why amber10/dat/leap/gleap/ and amber10/dat/leap/parm Wei Zhang (Sun Apr 12 2009 - 06:24:47 PDT)
  - Re: [AMBER] why amber10/dat/leap/gleap/ and amber10/dat/leap/parm Alan (Sun Apr 12 2009 - 08:58:18 PDT)
[AMBER] problem with explicit solvent in TMD balaji nagarajan (Mon Apr 13 2009 - 04:37:21 PDT)
- Re: [AMBER] problem with explicit solvent in TMD Carlos Simmerling (Mon Apr 13 2009 - 04:41:41 PDT)
- RE: [AMBER] problem with explicit solvent in TMD Ross Walker (Mon Apr 13 2009 - 08:29:11 PDT)
[AMBER] Energy minimisation and NaN vivek.viv.sharma.gmail.com (Mon Apr 13 2009 - 04:55:55 PDT)
- Re: [AMBER] Energy minimisation and NaN David A. Case (Mon Apr 13 2009 - 12:28:10 PDT)
[AMBER] atom types in pdb files Dan Kaps (Mon Apr 13 2009 - 07:23:58 PDT)
- RE: [AMBER] atom types in pdb files Kristina Furse (Mon Apr 13 2009 - 09:30:05 PDT)
- Re: [AMBER] atom types in pdb files Dan Kaps (Mon Apr 13 2009 - 12:29:43 PDT)
  - Re: [AMBER] atom types in pdb files David A. Case (Mon Apr 13 2009 - 13:25:04 PDT)
[AMBER] Thermodynamic Integration and belly Ignacio J. General (Mon Apr 13 2009 - 08:24:15 PDT)
- Re: [AMBER] Thermodynamic Integration and belly steinbrt.rci.rutgers.edu (Mon Apr 13 2009 - 09:46:19 PDT)
  - Re: [AMBER] Thermodynamic Integration and belly Ignacio J. General (Mon Apr 13 2009 - 10:26:16 PDT)
[AMBER] error saving prmtop and inpcrd files of complex in MM-PBSA Vikas Sharma (Mon Apr 13 2009 - 13:11:07 PDT)
[AMBER] restrained minimization quantum_mania.yahoo.com (Mon Apr 13 2009 - 17:12:35 PDT)
- Re: [AMBER] restrained minimization David A. Case (Mon Apr 13 2009 - 19:03:11 PDT)
  - Re: [AMBER] Restrained minimization pancham lal gupta (Sat Jul 21 2012 - 23:10:47 PDT)
    - Re: [AMBER] Restrained minimization Hirdesh Kumar (Sun Jul 22 2012 - 01:30:43 PDT)
    - Re: [AMBER] Restrained minimization Jason Swails (Sun Jul 22 2012 - 11:17:31 PDT)
[AMBER] Possibility to use ff99 + GAFF + GLYCAM_06 in one time for complex system ? Marek Malý (Mon Apr 13 2009 - 20:29:17 PDT)
- RE: [AMBER] Possibility to use ff99 + GAFF + GLYCAM_06 in one time for complex system ? Ross Walker (Mon Apr 13 2009 - 21:10:38 PDT)
  - Re: [AMBER] Possibility to use ff99 + GAFF + GLYCAM_06 in one time for complex system ? Marek Malý (Tue Apr 14 2009 - 16:18:18 PDT)
    - RE: [AMBER] Possibility to use ff99 + GAFF + GLYCAM_06 in one time for complex system ? Ross Walker (Tue Apr 14 2009 - 16:27:37 PDT)
    - Re: [AMBER] Possibility to use ff99 + GAFF + GLYCAM_06 in one time for complex system ? Marek Malý (Tue Apr 14 2009 - 17:40:22 PDT)
    - Re: [AMBER] Possibility to use ff99 + GAFF + GLYCAM_06 in one time for complex system ? Karl Kirschner (Wed Apr 15 2009 - 00:07:00 PDT)
    - Re: [AMBER] Possibility to use ff99 + GAFF + GLYCAM_06 in one time for complex system ? Carlos Simmerling (Wed Apr 15 2009 - 06:33:00 PDT)
    - Re: [AMBER] Possibility to use ff99 + GAFF + GLYCAM_06 in one time for complex system ? Marek Malý (Thu Apr 16 2009 - 14:25:12 PDT)
[AMBER] chosing complex in amber Vikas Sharma (Mon Apr 13 2009 - 22:18:43 PDT)
[AMBER] Questions on targeted MD with explicit solvent Hu, Shaowen (JSC-SK)[Universities Space Research Association USRA]. (Tue Apr 14 2009 - 06:51:40 PDT)
[AMBER] [qm/mm] qmcharge for acidic a.a. in proteins sychen (Tue Apr 14 2009 - 09:33:03 PDT)
- RE: [AMBER] [qm/mm] qmcharge for acidic a.a. in proteins Ross Walker (Tue Apr 14 2009 - 12:45:06 PDT)
[AMBER] antechamber and wrong net charge with gasteiger method Alan (Tue Apr 14 2009 - 10:41:30 PDT)
- Re: [AMBER] antechamber and wrong net charge with gasteiger method David A. Case (Tue Apr 14 2009 - 11:42:14 PDT)
[AMBER] my FF m m (Tue Apr 14 2009 - 15:21:38 PDT)
- Re: [AMBER] my FF David A. Case (Wed Apr 15 2009 - 05:28:16 PDT)
[AMBER] water bonding with protein Mark M Huntress (Tue Apr 14 2009 - 19:55:39 PDT)
- Re: [AMBER] water bonding with protein David A. Case (Wed Apr 15 2009 - 04:58:17 PDT)
[AMBER] hbond_ptraj_eror balaji nagarajan (Tue Apr 14 2009 - 23:53:29 PDT)
[AMBER] mean of character in frcmod.ff03 chenquan (Wed Apr 15 2009 - 05:26:38 PDT)
- RE: [AMBER] mean of character in frcmod.ff03 Ross Walker (Wed Apr 15 2009 - 07:58:31 PDT)
  - RE: [AMBER] mean of character in frcmod.ff03 chenquan (Wed Apr 15 2009 - 16:36:32 PDT)
[AMBER] help- regarding - TMD balaji nagarajan (Wed Apr 15 2009 - 09:19:59 PDT)
- RE: [AMBER] help- regarding - TMD Hu, Shaowen (JSC-SK)[Universities Space Research Association USRA]. (Wed Apr 15 2009 - 10:56:07 PDT)
  - RE: [AMBER] help- regarding - TMD balaji nagarajan (Wed Apr 15 2009 - 22:21:26 PDT)
    - RE: [AMBER] help- regarding - TMD Hu, Shaowen (JSC-SK)[Universities Space Research Association USRA]. (Thu Apr 16 2009 - 06:30:22 PDT)
    - RE: [AMBER] help- regarding - TMD balaji nagarajan (Thu Apr 16 2009 - 10:01:39 PDT)
- RE: [AMBER] help- regarding - TMD Hu, Shaowen (JSC-SK)[Universities Space Research Association USRA]. (Mon Apr 20 2009 - 08:05:38 PDT)
  - Re: [AMBER] help- regarding - TMD Carlos Simmerling (Mon Apr 20 2009 - 08:12:40 PDT)
    - RE: [AMBER] help- regarding - TMD Hu, Shaowen (JSC-SK)[Universities Space Research Association USRA]. (Mon Apr 20 2009 - 08:28:30 PDT)
    - Re: [AMBER] help- regarding - TMD Carlos Simmerling (Mon Apr 20 2009 - 08:30:52 PDT)
    - RE: [AMBER] help- regarding - TMD Hu, Shaowen (JSC-SK)[Universities Space Research Association USRA]. (Mon Apr 20 2009 - 09:21:06 PDT)
    - Re: [AMBER] help- regarding - TMD Carlos Simmerling (Tue Apr 21 2009 - 12:46:41 PDT)
    - RE: [AMBER] help- regarding - TMD Hu, Shaowen (JSC-SK)[Universities Space Research Association USRA]. (Tue Apr 21 2009 - 13:25:15 PDT)
    - Re: [AMBER] help- regarding - TMD Carlos Simmerling (Tue Apr 21 2009 - 14:23:23 PDT)
    - RE: [AMBER] help- regarding - TMD Hu, Shaowen (JSC-SK)[Universities Space Research Association USRA]. (Tue Apr 21 2009 - 15:40:36 PDT)
    - Re: [AMBER] help- regarding - TMD Carlos Simmerling (Tue Apr 21 2009 - 16:35:42 PDT)
[AMBER] please help me out bharat lakhani (Wed Apr 15 2009 - 23:41:08 PDT)
[AMBER] missing amber force field parameters Neha Gandhi (Thu Apr 16 2009 - 02:19:57 PDT)
- Re: [AMBER] missing amber force field parameters FyD (Thu Apr 16 2009 - 02:41:44 PDT)
[AMBER] pmemd in amber10 - compile failed in HPC Vijay Manickam Achari (Thu Apr 16 2009 - 03:13:49 PDT)
- Re: [AMBER] pmemd in amber10 - compile failed in HPC Robert Duke (Thu Apr 16 2009 - 05:24:45 PDT)
[AMBER] 1-4 vdW, GB MM difference Jimmy Heimdal (Thu Apr 16 2009 - 04:57:01 PDT)
- Re: [AMBER] 1-4 vdW, GB MM difference David A. Case (Thu Apr 16 2009 - 07:47:55 PDT)
[AMBER] ambertools failed - SMP IA64 Vijay Manickam Achari (Thu Apr 16 2009 - 06:17:34 PDT)
- Re: [AMBER] ambertools failed - SMP IA64 David A. Case (Thu Apr 16 2009 - 07:10:20 PDT)
[AMBER] Van der Waals atom types Antonio Morreale (Thu Apr 16 2009 - 07:39:14 PDT)
[AMBER] Amber and CHARMM summer school David A. Case (Thu Apr 16 2009 - 08:04:18 PDT)
[AMBER] Bad value during integer read by sander Collins Nganou (Thu Apr 16 2009 - 08:09:45 PDT)
[AMBER] sulfonamide parameters valeria.lapietra.unina.it (Thu Apr 16 2009 - 08:16:49 PDT)
[AMBER] polarizable force field for 18-crown-6 Gert von Helden (Thu Apr 16 2009 - 10:33:15 PDT)
- Re: [AMBER] polarizable force field for 18-crown-6 Piotr Cieplak (Fri Apr 17 2009 - 00:48:03 PDT)
[AMBER] help regarding force fields Vikas Sharma (Thu Apr 16 2009 - 23:06:32 PDT)
[AMBER] Right force fields Vikas Sharma (Thu Apr 16 2009 - 23:22:16 PDT)
- Re: [AMBER] Right force fields Patrick Schopf (Fri Apr 17 2009 - 05:48:14 PDT)
  - Re: [AMBER] Right force fields Vikas Sharma (Fri Apr 17 2009 - 06:14:04 PDT)
    - Re: [AMBER] Right force fields Patrick Schopf (Fri Apr 17 2009 - 06:34:04 PDT)
[AMBER] radius of gyration Beale, John (Fri Apr 17 2009 - 04:39:31 PDT)
[AMBER] Density in MD simulation Ibrahim Moustafa (Fri Apr 17 2009 - 09:09:16 PDT)
- Re: [AMBER] Density in MD simulation Carlos Simmerling (Fri Apr 17 2009 - 09:10:51 PDT)
  - Re: [AMBER] Density in MD simulation Ibrahim Moustafa (Fri Apr 17 2009 - 16:26:46 PDT)
[AMBER] Possibility to use ff99 + GAFF + GLYCAM_06 in one time for complex system ? quantum_mania.yahoo.com (Fri Apr 17 2009 - 10:52:28 PDT)
- Re: [AMBER] Possibility to use ff99 + GAFF + GLYCAM_06 in one time for complex system ? Lachele Foley (Lists) (Fri Apr 17 2009 - 11:13:49 PDT)
[AMBER] Backbone restraint Rilei Yu (Fri Apr 17 2009 - 19:30:38 PDT)
- Re: [AMBER] Backbone restraint Carlos Simmerling (Fri Apr 17 2009 - 19:35:26 PDT)
- Re: [AMBER] Backbone restraint Rilei Yu (Fri Apr 17 2009 - 20:29:12 PDT)
  - Re: [AMBER] Backbone restraint Carlos Simmerling (Sat Apr 18 2009 - 04:08:39 PDT)
    - Re: Re: [AMBER] Backbone restraint Rilei Yu (Mon Apr 20 2009 - 18:21:09 PDT)
  - Re: Re: [AMBER] Backbone restraint Jackie. J. Shen (Mon Apr 20 2009 - 18:12:13 PDT)
[AMBER] help_me to know the reason balaji nagarajan (Fri Apr 17 2009 - 21:30:07 PDT)
- Re: [AMBER] help_me to know the reason Carlos Simmerling (Sat Apr 18 2009 - 03:53:50 PDT)
[AMBER] please read this mail bharat lakhani (Sat Apr 18 2009 - 00:38:12 PDT)
- Re: [AMBER] please read this mail David A. Case (Sat Apr 18 2009 - 06:01:08 PDT)
[AMBER] about saltcon zgong.hust (Sat Apr 18 2009 - 19:45:53 PDT)
- Re: [AMBER] about saltcon Carlos Simmerling (Sun Apr 19 2009 - 03:49:57 PDT)
[AMBER] Atom type error Vikas Sharma (Sun Apr 19 2009 - 02:48:01 PDT)
- Re: [AMBER] Atom type error nicholus bhattacharjee (Sun Apr 19 2009 - 03:55:37 PDT)
  - Re: [AMBER] Atom type error Carlos Simmerling (Sun Apr 19 2009 - 04:06:07 PDT)
    - Re: [AMBER] Atom type error Vikas Sharma (Sun Apr 19 2009 - 09:49:53 PDT)
  - Re: [AMBER] Atom type error Vikas Sharma (Sun Apr 19 2009 - 09:50:28 PDT)
    - Re: [AMBER] Atom type error David A. Case (Sun Apr 19 2009 - 10:41:11 PDT)
    - Re: [AMBER] Atom type error Vikas Sharma (Sun Apr 19 2009 - 11:33:36 PDT)
    - RE: [AMBER] Atom type error Ross Walker (Sun Apr 19 2009 - 14:23:38 PDT)
    - Re: [AMBER] Atom type error Vikas Sharma (Mon Apr 20 2009 - 03:46:34 PDT)
    - Re: [AMBER] Atom type error Vikas Sharma (Mon Apr 20 2009 - 23:55:24 PDT)
[AMBER] Possibility to use ff99 + GAFF + GLYCAM_06 in one time for complex system ? - Last detail Marek Malý (Mon Apr 20 2009 - 04:52:36 PDT)
- Re: [AMBER] Possibility to use ff99 + GAFF + GLYCAM_06 in one time for complex system ? - Last detail Karl Kirschner (Mon Apr 20 2009 - 05:27:45 PDT)
  - Re: [AMBER] Possibility to use ff99 + GAFF + GLYCAM_06 in one time for complex system ? - Last detail Marek Malý (Mon Apr 20 2009 - 20:52:46 PDT)
    - Re: [AMBER] Possibility to use ff99 + GAFF + GLYCAM_06 in one time for complex system ? - Last detail Karl Kirschner (Tue Apr 21 2009 - 00:24:18 PDT)
    - Re: [AMBER] Possibility to use ff99 + GAFF + GLYCAM_06 in one time for complex system ? - Last detail Marek Malý (Tue Apr 21 2009 - 19:31:34 PDT)
    - Re: [AMBER] Possibility to use ff99 + GAFF + GLYCAM_06 in one time for complex system ? - Last detail Karl Kirschner (Thu Apr 23 2009 - 04:43:31 PDT)
    - Re: [AMBER] Possibility to use ff99 + GAFF + GLYCAM_06 in one time for complex system ? - Last detail Marek Malý (Thu Apr 23 2009 - 06:41:03 PDT)
    - Re: [AMBER] Possibility to use ff99 + GAFF + GLYCAM_06 in one time for complex system ? - Last detail Karl Kirschner (Thu Apr 23 2009 - 06:54:14 PDT)
    - Re: [AMBER] Possibility to use ff99 + GAFF + GLYCAM_06 in one time for complex system ? - Last detail Marek Malý (Thu Apr 23 2009 - 07:30:07 PDT)
- Re: [AMBER] Possibility to use ff99 + GAFF + GLYCAM_06 in one time for complex system ? - Last detail FyD (Mon Apr 20 2009 - 07:50:12 PDT)
[AMBER] Partial interactions Ignacio J. General (Mon Apr 20 2009 - 14:07:24 PDT)
- Re: [AMBER] Partial interactions steinbrt.rci.rutgers.edu (Mon Apr 20 2009 - 14:47:35 PDT)
  - Re: [AMBER] Partial interactions Ignacio J. General (Tue Apr 21 2009 - 07:31:26 PDT)
    - Re: [AMBER] Partial interactions steinbrt.rci.rutgers.edu (Tue Apr 21 2009 - 08:17:55 PDT)
    - Re: [AMBER] Partial interactions Ignacio J. General (Wed Apr 22 2009 - 12:02:00 PDT)
    - Re: [AMBER] Partial interactions steinbrt.rci.rutgers.edu (Wed Apr 22 2009 - 19:55:52 PDT)
    - Re: [AMBER] Partial interactions Ignacio J. General (Fri Apr 24 2009 - 07:49:07 PDT)
    - Re: [AMBER] Partial interactions steinbrt.rci.rutgers.edu (Fri Apr 24 2009 - 09:20:21 PDT)
    - Re: [AMBER] Partial interactions Ignacio J. General (Fri Apr 24 2009 - 10:11:31 PDT)
    - Re: [AMBER] Partial interactions steinbrt.rci.rutgers.edu (Fri Apr 24 2009 - 10:48:58 PDT)
[AMBER] My step size Vikas Sharma (Mon Apr 20 2009 - 23:50:16 PDT)
- RE: [AMBER] My step size Ross Walker (Tue Apr 21 2009 - 04:27:07 PDT)
  - Re: [AMBER] My step size Vikas Sharma (Tue Apr 21 2009 - 08:01:25 PDT)
  - Re: [AMBER] My step size Vikas Sharma (Tue Apr 21 2009 - 21:49:47 PDT)
[AMBER] atom numbers Vikas Sharma (Tue Apr 21 2009 - 04:12:27 PDT)
- Re: [AMBER] atom numbers David A. Case (Tue Apr 21 2009 - 04:54:37 PDT)
  - Re: [AMBER] atom numbers Vikas Sharma (Tue Apr 21 2009 - 08:33:12 PDT)
    - Re: [AMBER] atom numbers David A. Case (Tue Apr 21 2009 - 08:52:22 PDT)
    - Re: [AMBER] atom numbers Vikas Sharma (Tue Apr 21 2009 - 09:58:41 PDT)
    - Re: [AMBER] atom numbers David A. Case (Tue Apr 21 2009 - 10:26:32 PDT)
- Re: [AMBER] atom numbers Vikas Sharma (Tue Apr 21 2009 - 10:15:07 PDT)
- Re: [AMBER] atom numbers Vikas Sharma (Tue Apr 21 2009 - 11:36:35 PDT)
[AMBER] Number of LES copies in ptraj Thomas Exner (Tue Apr 21 2009 - 08:28:41 PDT)
[AMBER] Set start timestep for mdcrd traj output quantum_mania.yahoo.com (Tue Apr 21 2009 - 09:38:53 PDT)
- Re: [AMBER] Set start timestep for mdcrd traj output Carlos Simmerling (Tue Apr 21 2009 - 16:26:02 PDT)
  - Re: [AMBER] Set start timestep for mdcrd traj output Dong Xu (Tue Apr 21 2009 - 16:44:50 PDT)
[AMBER] Set start timestep for mdcrd traj output quantum_mania.yahoo.com (Tue Apr 21 2009 - 09:31:45 PDT)
[AMBER] Flexible ring simulation Dong Xu (Tue Apr 21 2009 - 16:04:55 PDT)
[AMBER] per atom energies in sander/pmemd Tamara Rogers (Tue Apr 21 2009 - 16:41:27 PDT)
[AMBER] Disulfide bond Dong Xu (Tue Apr 21 2009 - 18:37:46 PDT)
- Re: [AMBER] Disulfide bond Wei Zhang (Tue Apr 21 2009 - 18:46:19 PDT)
  - Re: [AMBER] Disulfide bond Dong Xu (Tue Apr 21 2009 - 19:41:02 PDT)
    - Re: [AMBER] Disulfide bond Wei Zhang (Tue Apr 21 2009 - 20:30:36 PDT)
    - Re: [AMBER] Disulfide bond quantum_mania.yahoo.com (Tue Apr 21 2009 - 22:25:45 PDT)
    - Re: [AMBER] Disulfide bond Wei Zhang (Wed Apr 22 2009 - 08:00:02 PDT)
[AMBER] bintraj and amber 10 Naser Alijabbari (Tue Apr 21 2009 - 23:31:51 PDT)
- RE: [AMBER] bintraj and amber 10 Ross Walker (Wed Apr 22 2009 - 03:59:47 PDT)
  - Re: [AMBER] bintraj and amber 10 Naser Alijabbari (Wed Apr 22 2009 - 18:05:21 PDT)
    - RE: [AMBER] bintraj and amber 10 Ross Walker (Thu Apr 23 2009 - 06:31:08 PDT)
    - Re: [AMBER] bintraj and amber 10 Chris Moth (Thu Apr 23 2009 - 10:46:44 PDT)
    - Re: [AMBER] bintraj and amber 10 Naser Alijabbari (Thu Apr 23 2009 - 17:37:06 PDT)
    - Re: [AMBER] bintraj and amber 10 Naser Alijabbari (Sat Apr 25 2009 - 11:47:34 PDT)
[AMBER] help regarding step size Vikas Sharma (Wed Apr 22 2009 - 01:57:31 PDT)
- Re: [AMBER] help regarding step size Carlos Simmerling (Wed Apr 22 2009 - 03:13:54 PDT)
  - Re: [AMBER] help regarding step size Vikas Sharma (Wed Apr 22 2009 - 03:50:27 PDT)
    - Re: [AMBER] help regarding step size Carlos Simmerling (Wed Apr 22 2009 - 04:03:28 PDT)
    - Re: [AMBER] help regarding step size Vikas Sharma (Wed Apr 22 2009 - 21:40:33 PDT)
[AMBER] uncharged c and n terminal amino acids Christopher Materese (Wed Apr 22 2009 - 11:05:38 PDT)
- Re: [AMBER] uncharged c and n terminal amino acids David A. Case (Wed Apr 22 2009 - 11:16:19 PDT)
[AMBER] Problem with RNA hairpin unwinding in explicit water Sasha Buzko (Wed Apr 22 2009 - 14:55:58 PDT)
- RE: [AMBER] Problem with RNA hairpin unwinding in explicit water Seetin, Matthew (Wed Apr 22 2009 - 15:22:29 PDT)
- Re: [AMBER] Problem with RNA hairpin unwinding in explicit water Carlos Simmerling (Wed Apr 22 2009 - 15:25:47 PDT)
  - Re: [AMBER] Problem with RNA hairpin unwinding in explicit water Sasha Buzko (Wed Apr 22 2009 - 15:34:35 PDT)
    - Re: [AMBER] Problem with RNA hairpin unwinding in explicit water Carlos Simmerling (Wed Apr 22 2009 - 15:53:33 PDT)
    - RE: [AMBER] Problem with RNA hairpin unwinding in explicit water matthew_seetin.urmc.rochester.edu (Wed Apr 22 2009 - 16:59:02 PDT)
    - Re: [AMBER] Problem with RNA hairpin unwinding in explicit water Sasha Buzko (Wed Apr 22 2009 - 16:59:14 PDT)
    - Re: [AMBER] Problem with RNA hairpin unwinding in explicit water Sasha Buzko (Fri Apr 24 2009 - 10:20:13 PDT)
- Re: [AMBER] Problem with RNA hairpin unwinding in explicit water Thomas Cheatham III (Wed Apr 22 2009 - 15:56:25 PDT)
  - Re: [AMBER] Problem with RNA hairpin unwinding in explicit water Sasha Buzko (Wed Apr 22 2009 - 16:10:55 PDT)
[AMBER] Amber Sulfate Ion Parameters Gary Clark (Wed Apr 22 2009 - 15:31:00 PDT)
- Re: [AMBER] Amber Sulfate Ion Parameters FyD (Wed Apr 22 2009 - 22:18:28 PDT)
- Re: [AMBER] Amber Sulfate Ion Parameters FyD (Wed Apr 22 2009 - 23:07:40 PDT)
  - Re: [AMBER] Amber Sulfate Ion Parameters Gary Clark (Thu Apr 23 2009 - 12:55:24 PDT)
[AMBER] error in output file Vikas Sharma (Thu Apr 23 2009 - 04:39:42 PDT)
- Re: [AMBER] error in output file Carlos Simmerling (Thu Apr 23 2009 - 04:42:02 PDT)
  - Re: [AMBER] error in output file Vikas Sharma (Thu Apr 23 2009 - 04:58:24 PDT)
    - Re: [AMBER] error in output file Hemant Kumar (Thu Apr 23 2009 - 05:20:25 PDT)
    - Re: [AMBER] error in output file Vikas Sharma (Thu Apr 23 2009 - 06:33:49 PDT)
    - RE: [AMBER] error in output file Ross Walker (Thu Apr 23 2009 - 06:28:18 PDT)
    - Re: [AMBER] error in output file Vikas Sharma (Thu Apr 23 2009 - 06:55:20 PDT)
[AMBER] nmod no run proprely in mmbsa mohamed mohamed (Thu Apr 23 2009 - 05:20:36 PDT)
- Re: [AMBER] nmod no run proprely in mmbsa David A. Case (Thu Apr 23 2009 - 05:47:44 PDT)
[AMBER] Regarding syntax for freezing different atoms Jorgen Simonsen (Thu Apr 23 2009 - 05:50:43 PDT)
- RE: [AMBER] Regarding syntax for freezing different atoms Ross Walker (Thu Apr 23 2009 - 06:24:55 PDT)
[AMBER] Amber Installation problem 주태성 (Thu Apr 23 2009 - 06:10:42 PDT)
- RE: [AMBER] Amber Installation problem Ross Walker (Thu Apr 23 2009 - 06:16:18 PDT)
[AMBER] NAB bug with parmbsc0 David A. Case (Thu Apr 23 2009 - 09:25:27 PDT)
Re: [AMBER] Problem with RNA hairpin unwinding in explicit water Bill Ross (Thu Apr 23 2009 - 10:53:40 PDT)
- Re: [AMBER] Problem with RNA hairpin unwinding in explicit water Sasha Buzko (Thu Apr 23 2009 - 10:55:58 PDT)
[AMBER] Unit name with loadMol2 command Nicholas Musolino (Thu Apr 23 2009 - 12:30:30 PDT)
- Re: [AMBER] Unit name with loadMol2 command David A. Case (Thu Apr 23 2009 - 15:54:02 PDT)
[AMBER] CY3 dye parameters jcmoore.student.umass.edu (Thu Apr 23 2009 - 14:42:59 PDT)
- Re: [AMBER] CY3 dye parameters FyD (Fri Apr 24 2009 - 23:04:22 PDT)
- Re: [AMBER] CY3 dye parameters Brent Krueger (Sat Apr 25 2009 - 12:33:40 PDT)
[AMBER] Amber Installation problem 주태성 (Thu Apr 23 2009 - 18:35:46 PDT)
[AMBER] Equilibrium bond lengths and angle values Dmitri Nilov (Fri Apr 24 2009 - 06:19:56 PDT)
- Re: [AMBER] Equilibrium bond lengths and angle values FyD (Fri Apr 24 2009 - 14:05:42 PDT)
  - Re: [AMBER] Equilibrium bond lengths and angle values Dmitri Nilov (Tue Apr 28 2009 - 03:56:38 PDT)
[AMBER] Simulated annealing waleed zalloum (Fri Apr 24 2009 - 07:31:36 PDT)
- Re: [AMBER] Simulated annealing Carlos Simmerling (Fri Apr 24 2009 - 07:49:40 PDT)
[AMBER] restraint constant Dong Xu (Sat Apr 25 2009 - 15:15:22 PDT)
[AMBER] Papers on Amber package usage Andrew Voronkov (Sat Apr 25 2009 - 22:07:42 PDT)
- Re: [AMBER] Papers on Amber package usage David A. Case (Sun Apr 26 2009 - 05:48:31 PDT)
[AMBER] amber question Vikas Sharma (Sat Apr 25 2009 - 23:00:06 PDT)
- Re: [AMBER] amber question Barbault Florent (Sun Apr 26 2009 - 01:48:31 PDT)
  - Re: [AMBER] amber question Vikas Sharma (Sun Apr 26 2009 - 02:51:38 PDT)
  - Re: [AMBER] amber question Vikas Sharma (Sun Apr 26 2009 - 02:56:26 PDT)
[AMBER] Water-molecules sikander azam (Sun Apr 26 2009 - 06:11:33 PDT)
- Re: [AMBER] Water-molecules case (Sun Apr 26 2009 - 15:35:36 PDT)
  - [AMBER] MM-GBSA Free enegy decomposition Rajesh Raju (Mon Apr 27 2009 - 05:27:23 PDT)
[AMBER] Install 주태성 (Sun Apr 26 2009 - 06:45:45 PDT)
[AMBER] Using smd with fixed atom nandy.physics.iisc.ernet.in (Sun Apr 26 2009 - 07:57:45 PDT)
RE: [AMBER] AmberTools compiling error Ross Walker (Sun Apr 26 2009 - 18:55:06 PDT)
- Re: [AMBER] AmberTools compiling error Farly Walsh (Wed Apr 29 2009 - 12:49:27 PDT)
[AMBER] Error with calculation of the potential energy Per Jr. Greisen (Mon Apr 27 2009 - 04:03:44 PDT)
- Re: [AMBER] Error with calculation of the potential energy Carlos Simmerling (Mon Apr 27 2009 - 04:08:47 PDT)
  - Re: [AMBER] Error with calculation of the potential energy Per Jr. Greisen (Mon Apr 27 2009 - 10:11:32 PDT)
- Re: [AMBER] Error with calculation of the potential energy Robert Duke (Mon Apr 27 2009 - 11:25:14 PDT)
  - Re: [AMBER] Error with calculation of the potential energy Per Jr. Greisen (Mon Apr 27 2009 - 11:57:58 PDT)
- Re: [AMBER] Error with calculation of the potential energy Robert Duke (Mon Apr 27 2009 - 11:46:43 PDT)
- Re: [AMBER] Error with calculation of the potential energy Robert Duke (Mon Apr 27 2009 - 12:26:06 PDT)
[AMBER] Mixing of forcefields in case of covaletly bonded systems Marek Malý (Mon Apr 27 2009 - 05:06:38 PDT)
[AMBER] Polarizable force field problem: non constant total Energy, EPOLZ is increasing Tommaso Cupido (Mon Apr 27 2009 - 07:10:12 PDT)
- Re: [AMBER] Polarizable force field problem: non constant total Energy, EPOLZ is increasing David A. Case (Mon Apr 27 2009 - 10:30:55 PDT)
  - Re: [AMBER] Polarizable force field problem: non constant total Energy, EPOLZ is increasing Piotr Cieplak (Mon Apr 27 2009 - 12:07:38 PDT)
  - [AMBER] ERROR In Restraint file. Catein Catherine (Tue Apr 28 2009 - 08:12:34 PDT)
    - [AMBER] ERROR In Restraint file. Catein Catherine (Tue Apr 28 2009 - 08:27:18 PDT)
    - Re: [AMBER] ERROR In Restraint file. David A. Case (Tue Apr 28 2009 - 09:17:36 PDT)
    - RE: [AMBER] ERROR In Restraint file. Catein Catherine (Tue Apr 28 2009 - 16:32:26 PDT)
    - Re: [AMBER] ERROR In Restraint file. David A. Case (Tue Apr 28 2009 - 17:05:23 PDT)
[AMBER] pmemd compilation error john smith (Mon Apr 27 2009 - 20:30:21 PDT)
- Re: [AMBER] pmemd compilation error Robert Duke (Mon Apr 27 2009 - 21:09:15 PDT)
  - Re: [AMBER] pmemd compilation error john smith (Tue May 05 2009 - 04:20:08 PDT)
[AMBER] Best rms fit for correlation and covariance analysis Cihan Aydin (Mon Apr 27 2009 - 22:02:14 PDT)
[AMBER] dipole autocorrelation functions aneesh cna (Mon Apr 27 2009 - 23:23:05 PDT)
Fwd: [AMBER] MM-GBSA Free enegy decomposition Rajesh Raju (Tue Apr 28 2009 - 04:28:17 PDT)
[AMBER] transport properties oguz gurbulak (Tue Apr 28 2009 - 07:11:05 PDT)
Re: [AMBER] Best rms fit for correlation and covariance analysis Bill Ross (Tue Apr 28 2009 - 09:57:10 PDT)
[AMBER] Restraining counterions? Francesco Pietra (Tue Apr 28 2009 - 10:32:18 PDT)
Re: [AMBER] reg-TMD Carlos Simmerling (Tue Apr 28 2009 - 10:48:18 PDT)
- Re: [AMBER] reg-TMD Carlos Simmerling (Wed Apr 29 2009 - 03:28:35 PDT)
- Re: [AMBER] reg-TMD Carlos Simmerling (Wed Apr 29 2009 - 04:33:40 PDT)
Re: [AMBER] Restraining counterions? Bill Ross (Tue Apr 28 2009 - 11:59:52 PDT)
[AMBER] ANAL problems E.M. (Tue Apr 28 2009 - 13:12:04 PDT)
Re: [AMBER] ANAL problems Bill Ross (Tue Apr 28 2009 - 13:40:59 PDT)
- Re: [AMBER] ANAL problems Edward M (Tue Apr 28 2009 - 16:01:34 PDT)
[AMBER] Using AMBER force fields in NAMD Michael Zimmermann (Tue Apr 28 2009 - 14:25:56 PDT)
- RE: [AMBER] Using AMBER force fields in NAMD Ross Walker (Tue Apr 28 2009 - 15:17:06 PDT)
  - RE: [AMBER] Using AMBER force fields in NAMD Piotr Cieplak (Tue Apr 28 2009 - 15:23:15 PDT)
  - RE: [AMBER] Using AMBER force fields in NAMD Thomas Cheatham III (Tue Apr 28 2009 - 15:45:15 PDT)
[AMBER] parallel problem of QM/MM calculation for AMBER 9 liu junjun (Tue Apr 28 2009 - 14:53:06 PDT)
- RE: [AMBER] parallel problem of QM/MM calculation for AMBER 9 Ross Walker (Tue Apr 28 2009 - 15:24:12 PDT)
  - Re: [AMBER] parallel problem of QM/MM calculation for AMBER 9 liu junjun (Tue Apr 28 2009 - 19:18:31 PDT)
[AMBER] The PDB file was not recognized by Amber, what can i do? Houyang Chen (Tue Apr 28 2009 - 15:00:05 PDT)
- Re: [AMBER] The PDB file was not recognized by Amber, what can i do? Carlos Simmerling (Tue Apr 28 2009 - 15:03:57 PDT)
- Re: [AMBER] The PDB file was not recognized by Amber, what can i do? Barbault Florent (Tue Apr 28 2009 - 16:00:55 PDT)
  - RE: [AMBER] The PDB file was not recognized by Amber, what can i do? Houyang Chen (Tue Apr 28 2009 - 20:42:39 PDT)
    - RE: [AMBER] The PDB file was not recognized by Amber, what can i do? Ross Walker (Tue Apr 28 2009 - 20:56:27 PDT)
    - Re: [AMBER] The PDB file was not recognized by Amber, what can i do? Barbault Florent (Tue Apr 28 2009 - 23:56:09 PDT)
- Re: [AMBER] The PDB file was not recognized by Amber, what can i do? Markus Kaukonen (Wed Apr 29 2009 - 00:16:30 PDT)
  - RE: [AMBER] The PDB file was not recognized by Amber, what can i do? Houyang Chen (Wed Apr 29 2009 - 15:17:51 PDT)
[AMBER] Nonterminal, was not found in name map Sunita Patel (Tue Apr 28 2009 - 17:50:08 PDT)
- RE: [AMBER] Nonterminal, was not found in name map Ross Walker (Tue Apr 28 2009 - 19:49:50 PDT)
- RE: [AMBER] Nonterminal, was not found in name map Bill Ross (Tue Apr 28 2009 - 22:05:12 PDT)
[AMBER] REd program! R. A. (Tue Apr 28 2009 - 21:37:38 PDT)
- Re: [AMBER] REd program! FyD (Wed Apr 29 2009 - 06:53:12 PDT)
[AMBER] (no subject) waleed zalloum (Wed Apr 29 2009 - 05:15:12 PDT)
- Re: [AMBER] (no subject) David A. Case (Wed Apr 29 2009 - 10:56:28 PDT)
[AMBER] input error in TI calculation Hannes Wallnoefer (Wed Apr 29 2009 - 08:40:58 PDT)
- Re: [AMBER] input error in TI calculation David A. Case (Wed Apr 29 2009 - 11:48:04 PDT)
RE: [AMBER] reg-TMD Hu, Shaowen (JSC-SK)[Universities Space Research Association USRA]. (Wed Apr 29 2009 - 13:56:07 PDT)
- RE: [AMBER] reg-TMD balaji nagarajan (Wed Apr 29 2009 - 18:44:32 PDT)
[AMBER] chain restrain x TI Josmar R. da Rocha (Wed Apr 29 2009 - 15:04:52 PDT)
- Re: [AMBER] chain restrain x TI David A. Case (Thu Apr 30 2009 - 11:01:13 PDT)
  - Re: [AMBER] chain restrain x TI Josmar R. da Rocha (Sat May 02 2009 - 10:09:53 PDT)
[AMBER] Amber FF and Glycam Dong Xu (Wed Apr 29 2009 - 18:42:55 PDT)
- Re: [AMBER] Amber FF and Glycam Lachele Foley (Lists) (Thu Apr 30 2009 - 10:16:17 PDT)
- Re: [AMBER] Amber FF and Glycam Carlos Simmerling (Thu Apr 30 2009 - 11:36:21 PDT)
  - Re: [AMBER] Amber FF and Glycam Hannes Loeffler (Fri May 01 2009 - 01:33:34 PDT)
    - Re: [AMBER] Amber FF and Glycam Carlos Simmerling (Fri May 01 2009 - 05:41:35 PDT)
    - [AMBER] Cyclodextrin forcefield Rajesh Raju (Fri May 01 2009 - 07:51:17 PDT)
    - Re: [AMBER] Cyclodextrin forcefield Lachele Foley (Lists) (Fri May 01 2009 - 08:23:37 PDT)
    - Re: [AMBER] Cyclodextrin forcefield Rajesh Raju (Fri May 01 2009 - 10:21:21 PDT)
[AMBER] MM-PBSA energy decomposition Dong Xu (Wed Apr 29 2009 - 19:03:34 PDT)
- Re: [AMBER] MM-PBSA energy decomposition Hannes Kopitz (Thu Apr 30 2009 - 03:37:35 PDT)
[AMBER] hbond-error in amber9 balaji nagarajan (Wed Apr 29 2009 - 19:09:17 PDT)
- Re: [AMBER] hbond-error in amber9 Alessandro S. Nascimento (Thu Apr 30 2009 - 03:46:02 PDT)
[AMBER] Influence about HIS-HIE-HIS-HIP Rilei Yu (Wed Apr 29 2009 - 20:25:48 PDT)
- Re: [AMBER] Influence about HIS-HIE-HIS-HIP David A. Case (Thu Apr 30 2009 - 07:27:02 PDT)
- Re: [AMBER] Influence about HIS-HIE-HIS-HIP Rilei Yu (Thu Apr 30 2009 - 17:37:17 PDT)
[AMBER] how to add charge on metal ions bharat lakhani (Wed Apr 29 2009 - 23:44:46 PDT)
[AMBER] Request an error Collins Nganou (Thu Apr 30 2009 - 10:41:48 PDT)
[AMBER] (no subject) Collins Nganou (Thu Apr 30 2009 - 12:34:36 PDT)
- Re: [AMBER] (no subject) David A. Case (Thu Apr 30 2009 - 13:16:35 PDT)
[AMBER] Make parallel test faillure Collins Nganou (Thu Apr 30 2009 - 12:36:55 PDT)
- RE: [AMBER] Make parallel test faillure Ross Walker (Thu Apr 30 2009 - 12:48:06 PDT)
RE: [Subject Filtered] [AMBER] hbond-error in amber9 8% Hopkins, Robert (Thu Apr 30 2009 - 17:02:34 PDT)
- RE: [Subject Filtered] [AMBER] hbond-error in amber9 8% Thomas Cheatham III (Fri May 01 2009 - 11:07:40 PDT)
[AMBER] unable to start xleap Jayalakshmi Sridhar (Fri May 01 2009 - 11:32:27 PDT)
- Re: [AMBER] unable to start xleap Wei Zhang (Fri May 01 2009 - 11:39:03 PDT)
[AMBER] charge of Fe-heme 董昊 (Fri May 01 2009 - 12:08:12 PDT)
- Re: [AMBER] charge of Fe-heme David A. Case (Fri May 01 2009 - 15:52:45 PDT)
- Re: [AMBER] charge of Fe-heme FyD (Sat May 02 2009 - 09:02:48 PDT)
[AMBER] how to assign radii parameters to certain atoms when fitting RESP charge using antechamber Ye MEI (Sat May 02 2009 - 05:00:06 PDT)
[AMBER] how to assign radii parameters to certain atoms when fitting RESP charge using antechamber Ye MEI (Sat May 02 2009 - 05:01:20 PDT)
- Re: [AMBER] how to assign radii parameters to certain atoms when fitting RESP charge using antechamber FyD (Sat May 02 2009 - 09:06:28 PDT)
[AMBER] equilibration stops for dimer simulation with REMD Sunita Patel (Sat May 02 2009 - 13:11:48 PDT)
- Re: [AMBER] equilibration stops for dimer simulation with REMD Carlos Simmerling (Sun May 03 2009 - 04:11:07 PDT)
- Re: [AMBER] equilibration stops for dimer simulation with REMD Sunita Patel (Sun May 03 2009 - 18:30:05 PDT)
- Re: [AMBER] equilibration stops for dimer simulation with REMD Sunita Patel (Tue May 05 2009 - 09:33:40 PDT)
  - Re: [AMBER] equilibration stops for dimer simulation with REMD Carlos Simmerling (Tue May 05 2009 - 09:39:52 PDT)
- Re: [AMBER] equilibration stops for dimer simulation with REMD Sunita Patel (Tue May 05 2009 - 10:26:09 PDT)
  - Re: [AMBER] equilibration stops for dimer simulation with REMD Carlos Simmerling (Tue May 05 2009 - 10:32:42 PDT)
- Re: [AMBER] equilibration stops for dimer simulation with REMD Sunita Patel (Thu May 07 2009 - 11:35:59 PDT)
[AMBER] QM/MM assigns Cd to C, Se to S C Liu (Sat May 02 2009 - 19:09:27 PDT)
- RE: [AMBER] QM/MM assigns Cd to C, Se to S Ross Walker (Sat May 02 2009 - 21:45:41 PDT)
- RE: [AMBER] QM/MM assigns Cd to C, Se to S Ross Walker (Fri May 08 2009 - 00:16:09 PDT)
[AMBER] LCPO or Molsurf? Dong Xu (Sat May 02 2009 - 20:14:55 PDT)
[AMBER] High energy during minimization aneesh cna (Sat May 02 2009 - 21:26:16 PDT)
- Re: [AMBER] High energy during minimization David A. Case (Sun May 03 2009 - 06:40:22 PDT)
- Re: [AMBER] High energy during minimization Bill Ross (Sun May 03 2009 - 11:00:32 PDT)
  - Re: [AMBER] High energy during minimization aneesh cna (Tue May 05 2009 - 22:58:00 PDT)
    - RE: [AMBER] High energy during minimization Ross Walker (Tue May 05 2009 - 23:24:30 PDT)
[AMBER] help with RESP tutorial using antechamber and gaussian Josmar R. da Rocha (Sun May 03 2009 - 10:59:23 PDT)
[AMBER] make test.parallel.MM error Collins Nganou (Sun May 03 2009 - 14:20:51 PDT)
[AMBER] prmtop Mark M Huntress (Sun May 03 2009 - 16:20:39 PDT)
- RE: [AMBER] prmtop Ross Walker (Sun May 03 2009 - 19:18:04 PDT)
[AMBER] problem with cutoff Yunjie Zhao (Sun May 03 2009 - 20:53:00 PDT)
- RE: [AMBER] problem with cutoff Ross Walker (Sun May 03 2009 - 22:02:04 PDT)
  - Re: [AMBER] problem with cutoff Yunjie Zhao (Mon May 04 2009 - 05:58:00 PDT)
    - RE: [AMBER] problem with cutoff Ross Walker (Mon May 04 2009 - 08:35:40 PDT)
[AMBER] "Parameter file not generated" Remya S R (Sun May 03 2009 - 23:17:23 PDT)
[AMBER] Parameter file not saved Remya S R (Sun May 03 2009 - 23:30:19 PDT)
[AMBER] creating new residue adds none wanted ter Jorgen Simonsen (Mon May 04 2009 - 00:49:47 PDT)
- [AMBER] Error message for tutorial 1 (run in parallel) Catein Catherine (Mon May 04 2009 - 02:05:17 PDT)
  - Re: [AMBER] Error message for tutorial 1 (run in parallel) David A. Case (Mon May 04 2009 - 05:40:36 PDT)
    - RE: [AMBER] Error message for tutorial 1 (run in parallel) Catein Catherine (Mon May 04 2009 - 06:31:05 PDT)
- Re: [AMBER] creating new residue adds none wanted ter David A. Case (Mon May 04 2009 - 06:35:41 PDT)
  - Re: [AMBER] creating new residue adds none wanted ter Jorgen Simonsen (Mon May 04 2009 - 07:09:08 PDT)
    - Re: [AMBER] creating new residue adds none wanted ter David A. Case (Mon May 04 2009 - 11:27:58 PDT)
    - Re: [AMBER] creating new residue adds none wanted ter Jorgen Simonsen (Tue May 05 2009 - 02:57:29 PDT)
    - Re: [AMBER] creating new residue adds none wanted ter David A. Case (Tue May 05 2009 - 05:07:53 PDT)
[AMBER] MM_PBSA problem in Amber 9 Sean Zhao (Mon May 04 2009 - 02:09:14 PDT)
[AMBER] Script for parallel runs Catein Catherine (Mon May 04 2009 - 02:17:42 PDT)
- [AMBER] Script for parallel runs 2 Catein Catherine (Mon May 04 2009 - 02:41:58 PDT)
  - RE: [AMBER] Script for parallel runs 2 Ross Walker (Mon May 04 2009 - 08:39:27 PDT)
- Re: [AMBER] Script for parallel runs Gustavo Seabra (Tue May 05 2009 - 09:31:38 PDT)
[AMBER] Non-zero internal energy in single trajectory MM-PBSA calculations Dmitry Osolodkin (Mon May 04 2009 - 02:24:59 PDT)
[AMBER] normal mode analysis Hannes Wallnoefer (Mon May 04 2009 - 02:39:16 PDT)
- Re: [AMBER] normal mode analysis David A. Case (Mon May 04 2009 - 06:37:02 PDT)
  - [AMBER] Why the job idle before the sentence "| Running AMBER/MPI version on 2 nodes"? Catein Catherine (Mon May 04 2009 - 08:16:08 PDT)
  - Re: [AMBER] normal mode analysis Hannes Wallnoefer (Mon May 04 2009 - 08:56:11 PDT)
    - [AMBER] Number of processor in pmemd Hemant Kumar (Mon May 04 2009 - 10:17:13 PDT)
    - Re: [AMBER] Number of processor in pmemd Carlos Simmerling (Mon May 04 2009 - 10:27:06 PDT)
    - Re: [AMBER] Number of processor in pmemd Robert Duke (Mon May 04 2009 - 10:28:11 PDT)
    - Re: [AMBER] normal mode analysis David A. Case (Mon May 04 2009 - 11:06:32 PDT)
[AMBER] Parameter file not saved Remya S R (Mon May 04 2009 - 05:03:08 PDT)
- Re: [AMBER] Parameter file not saved Carlos Simmerling (Mon May 04 2009 - 05:19:14 PDT)
[AMBER] MMPBSA- interaction energy for every frame Jack Colis (Mon May 04 2009 - 07:38:38 PDT)
- RE: [AMBER] MMPBSA- interaction energy for every frame Wei Huang (Mon May 04 2009 - 07:58:26 PDT)
  - Re: [AMBER] MMPBSA- interaction energy for every frame Jack Colis (Tue May 05 2009 - 01:22:35 PDT)
[AMBER] QM/MM Syed Tarique Moin (Mon May 04 2009 - 08:32:29 PDT)
- RE: [AMBER] QM/MM Ross Walker (Mon May 04 2009 - 10:47:21 PDT)
[AMBER] xleap segmentation fault Jayalakshmi Sridhar (Mon May 04 2009 - 08:50:06 PDT)
[AMBER] Error in PMEMD run Marek Malý (Mon May 04 2009 - 18:23:33 PDT)
- Re: [AMBER] Error in PMEMD run Robert Duke (Mon May 04 2009 - 18:35:54 PDT)
  - Re: [AMBER] Error in PMEMD run Marek Malý (Mon May 04 2009 - 19:19:20 PDT)
- Re: [AMBER] Error in PMEMD run Robert Duke (Mon May 04 2009 - 21:08:37 PDT)
  - Re: [AMBER] Error in PMEMD run Marek Malý (Wed May 06 2009 - 08:58:33 PDT)
    - RE: [AMBER] Error in PMEMD run Ross Walker (Wed May 06 2009 - 10:07:01 PDT)
    - Re: [AMBER] Error in PMEMD run Marek Malý (Wed May 06 2009 - 11:51:03 PDT)
- Re: [AMBER] Error in PMEMD run Robert Duke (Wed May 06 2009 - 10:30:43 PDT)
  - Re: [AMBER] Error in PMEMD run Marek Malý (Wed May 06 2009 - 11:30:43 PDT)
    - Re: [AMBER] Error in PMEMD run Marek Malý (Wed May 06 2009 - 11:42:36 PDT)
- Re: [AMBER] Error in PMEMD run Robert Duke (Wed May 06 2009 - 12:20:37 PDT)
  - Re: [AMBER] Error in PMEMD run Marek Malý (Wed May 06 2009 - 12:48:26 PDT)
- Re: [AMBER] Error in PMEMD run Robert Duke (Wed May 06 2009 - 12:29:41 PDT)
  - RE: [AMBER] Error in PMEMD run Ross Walker (Wed May 06 2009 - 12:41:10 PDT)
    - Re: [AMBER] Error in PMEMD run Marek Malý (Wed May 06 2009 - 13:02:11 PDT)
- Re: [AMBER] Error in PMEMD run Robert Duke (Wed May 06 2009 - 12:55:49 PDT)
- Re: [AMBER] Error in PMEMD run Robert Duke (Wed May 06 2009 - 12:58:29 PDT)
- Re: [AMBER] Error in PMEMD run Robert Duke (Wed May 06 2009 - 13:08:56 PDT)
  - Re: [AMBER] Error in PMEMD run Marek Malý (Wed May 06 2009 - 13:26:58 PDT)
    - RE: [AMBER] Error in PMEMD run Ross Walker (Wed May 06 2009 - 13:36:36 PDT)
    - Re: [AMBER] Error in PMEMD run Marek Malý (Wed May 06 2009 - 14:27:17 PDT)
- Re: [AMBER] Error in PMEMD run Robert Duke (Wed May 06 2009 - 13:40:29 PDT)
  - Re: [AMBER] Error in PMEMD run Marek Malý (Wed May 06 2009 - 14:25:02 PDT)
    - RE: [AMBER] Error in PMEMD run Ross Walker (Wed May 06 2009 - 14:53:07 PDT)
- Re: [AMBER] Error in PMEMD run Robert Duke (Wed May 06 2009 - 16:04:10 PDT)
  - Re: [AMBER] Error in PMEMD run Marek Malý (Thu May 07 2009 - 16:59:23 PDT)
- Re: [AMBER] Error in PMEMD run Robert Duke (Thu May 07 2009 - 17:11:25 PDT)
  - Re: [AMBER] Error in PMEMD run Marek Malý (Fri May 08 2009 - 05:54:57 PDT)
  - Re: [AMBER] Error in PMEMD run Marek Malý (Fri May 08 2009 - 09:38:27 PDT)
    - Re: [AMBER] Error in PMEMD run Gustavo Seabra (Fri May 08 2009 - 10:28:35 PDT)
    - Re: [AMBER] Error in PMEMD run Marek Malý (Fri May 08 2009 - 10:57:36 PDT)
    - RE: [AMBER] Error in PMEMD run Ross Walker (Fri May 08 2009 - 11:11:19 PDT)
    - Re: [AMBER] Error in PMEMD run Robert Duke (Fri May 08 2009 - 11:24:35 PDT)
    - Re: [AMBER] Error in PMEMD run Marek Malý (Fri May 08 2009 - 12:10:41 PDT)
    - Re: [AMBER] Error in PMEMD run Robert Duke (Fri May 08 2009 - 12:44:08 PDT)
    - Re: [AMBER] Error in PMEMD run Marek Malý (Fri May 08 2009 - 16:37:28 PDT)
    - Re: [AMBER] Error in PMEMD run Robert Duke (Fri May 08 2009 - 17:01:23 PDT)
    - Re: [AMBER] Error in PMEMD run Marek Malý (Fri May 08 2009 - 18:05:40 PDT)
    - Re: [AMBER] Error in PMEMD run Robert Duke (Fri May 08 2009 - 18:26:37 PDT)
    - Re: [AMBER] Error in PMEMD run Marek Malý (Fri May 08 2009 - 18:36:49 PDT)
- Re: [AMBER] Error in PMEMD run Robert Duke (Fri May 08 2009 - 06:29:48 PDT)
  - Re: [AMBER] Error in PMEMD run Marek Malý (Fri May 08 2009 - 11:02:53 PDT)
- Re: [AMBER] Error in PMEMD run Robert Duke (Fri May 08 2009 - 11:06:17 PDT)
- Re: [AMBER] Error in PMEMD run Robert Duke (Fri May 08 2009 - 11:14:12 PDT)
  - Re: [AMBER] Error in PMEMD run Marek Malý (Fri May 08 2009 - 11:27:20 PDT)
[AMBER] A confusion about tutorial B1 Houyang Chen (Mon May 04 2009 - 22:01:31 PDT)
- RE: [AMBER] A confusion about tutorial B1 Ross Walker (Mon May 04 2009 - 22:18:43 PDT)
  - RE: [AMBER] A confusion about tutorial B1 Houyang Chen (Mon May 04 2009 - 22:24:39 PDT)
    - RE: [AMBER] A confusion about tutorial B1 Ross Walker (Tue May 05 2009 - 08:29:23 PDT)
    - Re: [AMBER] A confusion about tutorial B1 David A. Case (Tue May 05 2009 - 08:41:54 PDT)
    - RE: [AMBER] A confusion about tutorial B1 Houyang Chen (Tue May 05 2009 - 10:39:18 PDT)
- Re: [AMBER] A confusion about tutorial B1 Carlos Simmerling (Tue May 05 2009 - 03:11:43 PDT)
[AMBER] Problem in production run nicholus bhattacharjee (Mon May 04 2009 - 22:50:07 PDT)
- Re: [AMBER] Problem in production run Carlos Simmerling (Tue May 05 2009 - 03:07:11 PDT)
[AMBER] Suggestion for restraining chain of a protein nicholus bhattacharjee (Mon May 04 2009 - 23:29:54 PDT)
- Re: [AMBER] Suggestion for restraining chain of a protein Carlos Simmerling (Tue May 05 2009 - 03:05:16 PDT)
  - Re: [AMBER] Suggestion for restraining chain of a protein nicholus bhattacharjee (Tue May 05 2009 - 05:20:44 PDT)
    - Re: [AMBER] Suggestion for restraining chain of a protein Carlos Simmerling (Tue May 05 2009 - 05:27:05 PDT)
[AMBER] Charge problem Remya S R (Tue May 05 2009 - 04:43:47 PDT)
- Re: [AMBER] Charge problem Carlos Simmerling (Tue May 05 2009 - 05:16:32 PDT)
  - Re: [AMBER] Charge problem Remya S R (Tue May 05 2009 - 05:19:51 PDT)
    - Re: [AMBER] Charge problem Carlos Simmerling (Tue May 05 2009 - 05:58:31 PDT)
[AMBER] Problems with PMEMD installation for AMBER10 German Erlenkamp (Tue May 05 2009 - 05:40:56 PDT)
- Re: [AMBER] Problems with PMEMD installation for AMBER10 Robert Duke (Tue May 05 2009 - 06:00:54 PDT)
  - Re: [AMBER] Problems with PMEMD installation for AMBER10 German Erlenkamp (Tue May 05 2009 - 06:07:13 PDT)
- Re: [AMBER] Problems with PMEMD installation for AMBER10 Robert Duke (Tue May 05 2009 - 06:48:06 PDT)
  - Re: [AMBER] Problems with PMEMD installation for AMBER10 German Erlenkamp (Thu May 07 2009 - 00:18:36 PDT)
[AMBER] skip parallel test Collins Nganou (Tue May 05 2009 - 06:09:00 PDT)
- Re: [AMBER] skip parallel test David A. Case (Tue May 05 2009 - 08:34:14 PDT)
- RE: [AMBER] skip parallel test Ross Walker (Tue May 05 2009 - 08:43:34 PDT)
[AMBER] Can bond clevage & formation conducted by qm/mm via sander? sychen (Tue May 05 2009 - 06:12:32 PDT)
- Re: [AMBER] Can bond clevage & formation conducted by qm/mm via sander? Gustavo Seabra (Tue May 05 2009 - 10:04:37 PDT)
- Re: [AMBER] Can bond clevage & formation conducted by qm/mm via sander? Mahmoud A. A. Ibrahim (Tue May 05 2009 - 10:15:18 PDT)
  - Re: [AMBER] Can bond clevage & formation conducted by qm/mm via sander? Gustavo Seabra (Tue May 05 2009 - 10:28:10 PDT)
[AMBER] Error: cannot run prepgen Rose Tamil (Tue May 05 2009 - 08:20:52 PDT)
[AMBER] difference in temperature Naser Alijabbari (Tue May 05 2009 - 17:02:28 PDT)
- Re: [AMBER] difference in temperature David A. Case (Wed May 06 2009 - 05:08:01 PDT)
  - Re: [AMBER] difference in temperature Naser Alijabbari (Wed May 06 2009 - 05:29:48 PDT)
[AMBER] ntf, ntc with softcore potentials and TI in amber10 Matthew Wilce (Tue May 05 2009 - 18:33:28 PDT)
- Re: [AMBER] ntf, ntc with softcore potentials and TI in amber10 steinbrt.rci.rutgers.edu (Tue May 05 2009 - 20:39:02 PDT)
[AMBER] Error in MM PBSA Vikas Sharma (Wed May 06 2009 - 01:35:57 PDT)
[AMBER] Conformation of sulfated Glucosamine Neha Gandhi (Wed May 06 2009 - 02:54:31 PDT)
- RE: [AMBER] Conformation of sulfated Glucosamine Matthew Tessier (Wed May 06 2009 - 08:19:22 PDT)
[AMBER] positive value of binding enrgy after MM PBSA Vikas Sharma (Wed May 06 2009 - 08:07:03 PDT)
[AMBER] xleap input pdb problem Majeed Shaik (Wed May 06 2009 - 11:47:45 PDT)
- Re: [AMBER] xleap input pdb problem David A. Case (Wed May 06 2009 - 19:16:10 PDT)
  - [AMBER] Error in parallel run Catein Catherine (Wed May 06 2009 - 19:46:02 PDT)
  - [AMBER] AMBER for dual core processor? Catein Catherine (Thu May 07 2009 - 01:05:17 PDT)
    - RE: [AMBER] AMBER for dual core processor? Ross Walker (Thu May 07 2009 - 08:26:09 PDT)
[AMBER] multiple chain specification in Sander Siddharth Rastogi (Wed May 06 2009 - 20:17:57 PDT)
- Re: [AMBER] multiple chain specification in Sander Carlos Simmerling (Thu May 07 2009 - 03:19:09 PDT)
  - Re: [AMBER] multiple chain specification in Sander Siddharth Rastogi (Thu May 07 2009 - 13:29:28 PDT)
[AMBER] ptraj PCA - Highest Eigenvalues or First 2 Calculated? Patrick Gedeon (Wed May 06 2009 - 21:12:39 PDT)
- Re: [AMBER] ptraj PCA - Highest Eigenvalues or First 2 Calculated? Hannes Loeffler (Thu May 07 2009 - 00:47:23 PDT)
[AMBER] Error in binding energy (MM PBSA) Vikas Sharma (Wed May 06 2009 - 22:47:33 PDT)
- Re: [AMBER] Error in binding energy (MM PBSA) David A. Case (Thu May 07 2009 - 04:33:20 PDT)
  - Re: [AMBER] Error in binding energy (MM PBSA) Vikas Sharma (Thu May 07 2009 - 06:29:22 PDT)
- RE: [AMBER] Error in binding energy (MM PBSA) Ray Luo (Thu May 07 2009 - 11:12:18 PDT)
  - Re: [AMBER] Error in binding energy (MM PBSA) Vikas Sharma (Thu May 07 2009 - 23:42:32 PDT)
    - RE: [AMBER] Error in binding energy (MM PBSA) Ray Luo (Fri May 08 2009 - 09:42:58 PDT)
  - Re: [AMBER] Error in binding energy (MM PBSA) Vikas Sharma (Thu May 07 2009 - 23:50:40 PDT)
[AMBER] free enrgy error in MM PBSA Vikas Sharma (Thu May 07 2009 - 03:11:44 PDT)
[AMBER] ambertools for NAMD Jorgen Simonsen (Thu May 07 2009 - 05:35:24 PDT)
- Re: [AMBER] ambertools for NAMD Carlos Simmerling (Thu May 07 2009 - 06:36:27 PDT)
  - Re: [AMBER] ambertools for NAMD David A. Case (Thu May 07 2009 - 07:09:55 PDT)
    - Re: [AMBER] ambertools for NAMD Carlos Simmerling (Thu May 07 2009 - 07:23:25 PDT)
    - Re: [AMBER] ambertools for NAMD Andrew Purkiss-Trew (Thu May 07 2009 - 07:30:14 PDT)
    - RE: [AMBER] ambertools for NAMD Wei Huang (Thu May 07 2009 - 07:51:06 PDT)
    - RE: [AMBER] ambertools for NAMD Andrew Purkiss-Trew (Thu May 07 2009 - 08:16:40 PDT)
    - Re: [AMBER] ambertools for NAMD Jorgen Simonsen (Thu May 07 2009 - 11:29:41 PDT)
[AMBER] dftb_disper problem Fernando Martín García (Thu May 07 2009 - 05:30:25 PDT)
- Re: [AMBER] dftb_disper problem Gustavo Seabra (Thu May 07 2009 - 06:01:42 PDT)
  - Re: [Barracuda SPAM] Re: [AMBER] dftb_disper problem Fernando Martín García (Thu May 07 2009 - 06:32:06 PDT)
  - Re: [AMBER] dftb_disper problem Fernando Martín García (Fri May 08 2009 - 05:43:19 PDT)
    - RE: [AMBER] dftb_disper problem Ross Walker (Fri May 08 2009 - 08:47:39 PDT)
    - RE: [AMBER] dftb_disper problem fmgarcia.cbm.uam.es (Fri May 08 2009 - 09:27:30 PDT)
    - RE: [AMBER] dftb_disper problem Fernando Martín García (Mon May 11 2009 - 05:34:01 PDT)
    - Re: [AMBER] dftb_disper problem Gustavo Seabra (Fri May 08 2009 - 09:34:39 PDT)
[AMBER] Problems in the result of MM_PBSA Sean Zhao (Thu May 07 2009 - 18:30:24 PDT)
- RE: [AMBER] Problems in the result of MM_PBSA Ray Luo (Thu May 07 2009 - 19:02:58 PDT)
- Re: [AMBER] Problems in the result of MM_PBSA David A. Case (Fri May 08 2009 - 05:45:19 PDT)
  - Re: [AMBER] Problems in the result of MM_PBSA Sean Zhao (Fri May 08 2009 - 20:44:29 PDT)
    - RE: [AMBER] Problems in the result of MM_PBSA Ray Luo (Sat May 09 2009 - 18:36:04 PDT)
    - Re: [AMBER] Problems in the result of MM_PBSA Sean Zhao (Sun May 10 2009 - 01:23:19 PDT)
    - RE: [AMBER] Problems in the result of MM_PBSA Ray Luo (Mon May 11 2009 - 10:55:12 PDT)
[AMBER] RE: Listing gaff parameters in frcmod Bokun Cho (Thu May 07 2009 - 21:20:46 PDT)
- RE: [AMBER] RE: Listing gaff parameters in frcmod Ross Walker (Thu May 07 2009 - 21:34:08 PDT)
  - Re: [AMBER] RE: Listing gaff parameters in frcmod Bokun Cho (Thu May 07 2009 - 22:00:47 PDT)
    - Re: [AMBER] RE: Listing gaff parameters in frcmod steinbrt.rci.rutgers.edu (Fri May 08 2009 - 07:23:45 PDT)
[AMBER] Error in binding energy (MM PBSA) Vikas Sharma (Thu May 07 2009 - 23:44:33 PDT)
- Re: [AMBER] Error in binding energy (MM PBSA) Vikas Sharma (Sat May 09 2009 - 00:19:20 PDT)
  - RE: [AMBER] Error in binding energy (MM PBSA) Ray Luo (Sat May 09 2009 - 18:39:05 PDT)
    - Re: [AMBER] Error in binding energy (MM PBSA) Vikas Sharma (Sun May 10 2009 - 02:03:07 PDT)
- Re: [AMBER] Error in binding energy (MM PBSA) Vikas Sharma (Sat May 09 2009 - 00:20:09 PDT)
- Re: [AMBER] Error in binding energy (MM PBSA) Vikas Sharma (Mon May 11 2009 - 01:08:28 PDT)
  - RE: [AMBER] Error in binding energy (MM PBSA) Ray Luo (Mon May 11 2009 - 11:14:20 PDT)
    - [AMBER] Protein Docking Chih-Ying Lin (Mon May 11 2009 - 13:21:45 PDT)
    - Re: [AMBER] Protein Docking steinbrt.rci.rutgers.edu (Mon May 11 2009 - 13:33:15 PDT)
    - Re: [AMBER] Protein Docking Simon Becker (Tue May 12 2009 - 08:23:02 PDT)
    - Re: [AMBER] Protein Docking Chih-Ying Lin (Thu May 14 2009 - 21:28:43 PDT)
    - Re: [AMBER] Error in binding energy (MM PBSA) Vikas Sharma (Mon May 11 2009 - 22:05:08 PDT)
[AMBER] Re: Marek Malý (Fri May 08 2009 - 12:12:39 PDT)
[AMBER] Can I use only a single point calculation to derive RESP charges? Josmar R. da Rocha (Fri May 08 2009 - 17:08:54 PDT)
- Re: [AMBER] Can I use only a single point calculation to derive RESP charges? FyD (Fri May 08 2009 - 23:00:36 PDT)
  - Re: [AMBER] Can I use only a single point calculation to derive RESP charges? Josmar R. da Rocha (Sat May 09 2009 - 08:19:07 PDT)
    - Re: [AMBER] Can I use only a single point calculation to derive RESP charges? FyD (Sat May 09 2009 - 23:52:12 PDT)
[AMBER] Modifying a water molecule Jorgen Simonsen (Sat May 09 2009 - 06:16:54 PDT)
[AMBER] AMBER 94 Charges for terminal LYN, GLH, ASH and CYM residues and some other unusual cases. todd.semichem.com (Sat May 09 2009 - 09:27:52 PDT)
- Re: [AMBER] AMBER 94 Charges for terminal LYN, GLH, ASH and CYM residues and some other unusual cases. Adrian Roitberg (Sat May 09 2009 - 11:07:08 PDT)
  - Re: [AMBER] AMBER 94 Charges for terminal LYN, GLH, ASH and CYM residues and some other unusual cases. todd.semichem.com (Sat May 09 2009 - 11:36:17 PDT)
    - Re: [AMBER] AMBER 94 Charges for terminal LYN, GLH, ASH and CYM residues and some other unusual cases. FyD (Sat May 09 2009 - 22:49:55 PDT)
    - Re: [AMBER] AMBER 94 Charges for terminal LYN, GLH, ASH and CYM residues and some other unusual cases. todd.semichem.com (Sun May 10 2009 - 14:56:24 PDT)
[AMBER] molsurf and probe radius David Watson (Sat May 09 2009 - 10:32:43 PDT)
- Re: [AMBER] molsurf and probe radius David A. Case (Mon May 11 2009 - 08:03:10 PDT)
[AMBER] xleap, mac number problem Mark M Huntress (Sat May 09 2009 - 12:46:46 PDT)
- [AMBER] RE: xleap, mac number problem Mark M Huntress (Sat May 09 2009 - 15:29:50 PDT)
[AMBER] please help me out Nancy (Sun May 10 2009 - 00:56:33 PDT)
- Re: [AMBER] please help me out FyD (Mon Mar 09 2009 - 03:05:06 PDT)
  - Re: [AMBER] please help me out bharat lakhani (Wed Mar 11 2009 - 23:04:00 PDT)
    - Re: [AMBER] please help me out rpaduri.chem.wayne.edu (Thu Mar 12 2009 - 09:37:09 PDT)
    - Re: [AMBER] please help me out bharat lakhani (Sat Mar 14 2009 - 04:04:37 PDT)
    - Re: [AMBER] please help me out David A. Case (Sat Mar 14 2009 - 06:06:34 PDT)
    - RE: [AMBER] please help me out Ross Walker (Sat Mar 14 2009 - 09:54:22 PDT)
    - Re: [AMBER] please help me out bharat lakhani (Mon Mar 23 2009 - 00:58:52 PDT)
    - Re: [AMBER] please help me out bharat lakhani (Tue Mar 24 2009 - 06:57:18 PDT)
- Re: [AMBER] please help me out Wei Zhang (Sun May 10 2009 - 06:21:06 PDT)
[AMBER] MM-PBSA statistics Musa Ozboyaci (Sun May 10 2009 - 03:00:19 PDT)
[AMBER] The resonable way to create single strand DNA with NAB ? Marek Malý (Sun May 10 2009 - 10:12:09 PDT)
- Re: [AMBER] The resonable way to create single strand DNA with NAB ? David A. Case (Mon May 11 2009 - 04:34:16 PDT)
  - Re: [AMBER] The resonable way to create single strand DNA with NAB ? Marek Malý (Mon May 11 2009 - 05:18:06 PDT)
[AMBER] building quadruplex with NAB Peter Varnai (Sun May 10 2009 - 16:27:38 PDT)
- Re: [AMBER] building quadruplex with NAB David A. Case (Wed May 13 2009 - 04:48:38 PDT)
  - Re: [AMBER] building quadruplex with NAB Peter Varnai (Tue Oct 27 2009 - 13:00:09 PDT)
    - Re: [AMBER] building quadruplex with NAB case (Tue Oct 27 2009 - 19:23:29 PDT)
[AMBER] Adding non standard residues Jorgen Simonsen (Mon May 11 2009 - 01:54:25 PDT)
- Re: [AMBER] Adding non standard residues David A. Case (Mon May 11 2009 - 10:30:56 PDT)
  - Re: [AMBER] Adding non standard residues Jorgen Simonsen (Mon May 11 2009 - 14:11:49 PDT)
[AMBER] molecular crystal simulation Simona Irrera (Tue May 12 2009 - 04:04:26 PDT)
- Re: [AMBER] molecular crystal simulation David A. Case (Wed May 13 2009 - 15:28:37 PDT)
[AMBER] ptraj netcdf Bala subramanian (Tue May 12 2009 - 05:04:00 PDT)
- Re: [AMBER] ptraj netcdf Chris Moth (Tue May 12 2009 - 08:46:31 PDT)
  - [AMBER] anal output: Entalphy or Free Energy? E.M. (Tue May 12 2009 - 15:25:41 PDT)
[AMBER] anal output: Entalphy or Free Energy? Edward M (Tue May 12 2009 - 17:14:37 PDT)
[AMBER] Question about Thermal Integration with Softcore Elodie Laine (Wed May 13 2009 - 02:13:22 PDT)
- Re: [AMBER] Question about Thermal Integration with Softcore steinbrt.rci.rutgers.edu (Wed May 13 2009 - 08:11:16 PDT)
[AMBER] amber9 in fedora10 Bala subramanian (Wed May 13 2009 - 02:50:25 PDT)
- RE: [AMBER] amber9 in fedora10 Ross Walker (Wed May 13 2009 - 16:22:20 PDT)
[AMBER] essential dynamics Chunliyan (Wed May 13 2009 - 09:23:23 PDT)
- Re: [AMBER] essential dynamics David A. Case (Wed May 13 2009 - 10:15:50 PDT)
[AMBER] re: essential dynamics Chunliyan (Wed May 13 2009 - 10:25:57 PDT)
- Re: [AMBER] re: essential dynamics David A. Case (Wed May 13 2009 - 10:48:42 PDT)
  - RE: [AMBER] re: essential dynamics Niel Henriksen (Wed May 13 2009 - 11:28:22 PDT)
[AMBER] normal modes calculation Neha Gandhi (Wed May 13 2009 - 20:12:13 PDT)
- Re: [AMBER] normal modes calculation chaitanya koppisetty (Thu May 14 2009 - 01:51:28 PDT)
[AMBER] Amber - Leap- SolvateBox help Shubhra Gupta (Wed May 13 2009 - 22:04:16 PDT)
- RE: [AMBER] Amber - Leap- SolvateBox help Ross Walker (Thu May 14 2009 - 05:28:36 PDT)
- Re: [AMBER] Amber - Leap- SolvateBox help David A. Case (Fri May 15 2009 - 16:57:00 PDT)
- Re: [AMBER] Amber - Leap- SolvateBox help Shubhra Gupta (Mon May 18 2009 - 20:54:23 PDT)
  - Re: [AMBER] Amber - Leap- SolvateBox help David A. Case (Tue May 19 2009 - 04:48:39 PDT)
- Re: [AMBER] Amber - Leap- SolvateBox help Remya S R (Mon May 18 2009 - 23:22:12 PDT)
- RE: [AMBER] Amber - Leap- SolvateBox help Ross Walker (Tue May 19 2009 - 22:20:50 PDT)
[AMBER] pmemd running very slow in amber10 Vijay Manickam Achari (Wed May 13 2009 - 22:41:40 PDT)
- Re: [AMBER] pmemd running very slow in amber10 Carlos Simmerling (Thu May 14 2009 - 03:09:11 PDT)
  - RE: [AMBER] pmemd running very slow in amber10 Ross Walker (Thu May 14 2009 - 05:57:43 PDT)
- Re: [AMBER] pmemd running very slow in amber10 Robert Duke (Thu May 14 2009 - 06:38:29 PDT)
Re: [OFFLIST] Re: [AMBER] amber9 in fedora10 Bala subramanian (Thu May 14 2009 - 01:18:07 PDT)
[AMBER] MM-PBSA tutorial Workalemhu Berhanu (Thu May 14 2009 - 10:16:55 PDT)
- Re: [AMBER] MM-PBSA tutorial steinbrt.rci.rutgers.edu (Thu May 14 2009 - 10:26:50 PDT)
  - Re: [AMBER] MM-PBSA tutorial Cihan Aydin (Thu May 14 2009 - 18:19:04 PDT)
- Re: [AMBER] MM-PBSA tutorial Workalemhu Berhanu (Thu May 14 2009 - 11:53:25 PDT)
[AMBER] xmin Peter Varnai (Thu May 14 2009 - 14:29:09 PDT)
- Re: [AMBER] xmin Scott Brozell (Sun May 17 2009 - 13:45:27 PDT)
  - [AMBER] What is the purpose to do the bond constraints? Chih-Ying Lin (Sun May 17 2009 - 15:09:04 PDT)
    - [AMBER] The protein swell? Chih-Ying Lin (Sun May 17 2009 - 15:17:51 PDT)
    - RE: [AMBER] What is the purpose to do the bond constraints? Ross Walker (Sun May 17 2009 - 20:38:52 PDT)
    - RE: [AMBER] What is the purpose to do the bond constraints? Bill Ross (Mon May 18 2009 - 12:39:42 PDT)
  - Re: [AMBER] xmin Peter Varnai (Sun May 17 2009 - 17:58:00 PDT)
    - Re: [AMBER] xmin Scott Brozell (Mon May 18 2009 - 13:30:17 PDT)
[AMBER] MM-PBSA with explicit water mathew k varghese (Thu May 14 2009 - 23:45:23 PDT)
[AMBER] xleap reading hydrogens giving error Jorgen Simonsen (Fri May 15 2009 - 00:47:10 PDT)
- Re: [AMBER] xleap reading hydrogens giving error David A. Case (Fri May 15 2009 - 07:17:04 PDT)
  - Re: [AMBER] xleap reading hydrogens giving error Jorgen Simonsen (Fri May 15 2009 - 08:54:17 PDT)
    - Re: [AMBER] xleap reading hydrogens giving error David A. Case (Fri May 15 2009 - 09:25:11 PDT)
    - [AMBER] how to make the different/specific displacement of ligand around protein? Chih-Ying Lin (Fri May 15 2009 - 16:55:49 PDT)
[AMBER] Fw: MM-PBSA with explicit water mathew k varghese (Thu May 14 2009 - 23:43:46 PDT)
[AMBER] scee term Neha Gandhi (Fri May 15 2009 - 02:03:48 PDT)
- RE: [AMBER] scee term Ross Walker (Fri May 15 2009 - 08:02:09 PDT)
[AMBER] adding a standard amino acid as ligand sheerychen (Fri May 15 2009 - 02:37:51 PDT)
- Re: [AMBER] adding a standard amino acid as ligand FyD (Fri May 15 2009 - 06:39:18 PDT)
[AMBER] secstruct with ptraj Bala subramanian (Fri May 15 2009 - 03:19:54 PDT)
[AMBER] Issue related to vector saving S.Sundar Raman (Fri May 15 2009 - 06:35:01 PDT)
[AMBER] MM-GBSA energy decomposition and pairwise decomposition question Dong Xu (Fri May 15 2009 - 15:05:52 PDT)
[AMBER] FE: unexpected coordination 4 - using nonstandard tree type '4' ben rodriguez (Fri May 15 2009 - 15:09:44 PDT)
- Re: [AMBER] FE: unexpected coordination 4 - using nonstandard tree type '4' David A. Case (Fri May 15 2009 - 16:56:34 PDT)
[AMBER] Alignment of small molecule on peptide fragment Workalemhu Berhanu (Sat May 16 2009 - 02:31:08 PDT)
[AMBER] Alignment of small molecule on peptide fragment Workalemhu Berhanu (Sat May 16 2009 - 02:32:38 PDT)
[AMBER] Issue related to saving the vector in ptraj S.Sundar Raman (Sat May 16 2009 - 05:41:10 PDT)
- [AMBER] How to setup the pH value? Chih-Ying Lin (Sat May 16 2009 - 10:29:21 PDT)
  - Re: [AMBER] How to setup the pH value? David A. Case (Tue May 19 2009 - 12:08:53 PDT)
    - [AMBER] What are the elements to speed up the simulation? Chih-Ying Lin (Tue May 19 2009 - 15:17:07 PDT)
[AMBER] Amber 10 install parallel problem Hopkins, Robert (Sat May 16 2009 - 17:38:16 PDT)
[AMBER] Running PTRAJ command line scripts in background Hopkins, Robert (Sat May 16 2009 - 17:47:38 PDT)
- Re: [AMBER] Running PTRAJ command line scripts in background Jia Xu (Sun May 17 2009 - 00:16:49 PDT)
  - RE: [AMBER] Running PTRAJ command line scripts in background Hopkins, Robert (Sun May 17 2009 - 09:55:48 PDT)
- RE: [AMBER] Running PTRAJ command line scripts in background Ross Walker (Sun May 17 2009 - 20:35:09 PDT)
  - RE: [AMBER] Running PTRAJ command line scripts in background Hopkins, Robert (Mon May 18 2009 - 15:50:06 PDT)
[AMBER] makeDIST_RST: no map function for ambiguous restraint Peter Varnai (Sun May 17 2009 - 11:41:24 PDT)
- Re: [AMBER] makeDIST_RST: no map function for ambiguous restraint David A. Case (Tue May 19 2009 - 05:35:31 PDT)
  - Re: [AMBER] makeDIST_RST: no map function for ambiguous restraint Peter Varnai (Mon Jun 01 2009 - 12:49:36 PDT)
[AMBER] parallel amber on cluster Siavoush Dastmalchi (Sun May 17 2009 - 23:04:58 PDT)
- Re: [AMBER] parallel amber on cluster David A. Case (Mon May 18 2009 - 04:54:18 PDT)
[AMBER] Problem in Nmode Kshatresh Dutta Dubey (Sun May 17 2009 - 23:07:52 PDT)
[AMBER] Modification of His Jorgen Simonsen (Mon May 18 2009 - 03:51:50 PDT)
- Re: [AMBER] Modification of His David A. Case (Mon May 18 2009 - 04:58:34 PDT)
  - Re: [AMBER] Modification of His Jorgen Simonsen (Mon May 18 2009 - 05:16:10 PDT)
    - Re: [AMBER] Modification of His David A. Case (Mon May 18 2009 - 05:31:33 PDT)
- Re: [AMBER] Modification of His Bill Ross (Mon May 18 2009 - 13:06:16 PDT)
[AMBER] Error running MM _PBSA.pl script Vikas Sharma (Mon May 18 2009 - 05:00:13 PDT)
- 回复： [AMBER] Error running MM _PBSA.pl script 廖青华 (Mon May 18 2009 - 05:08:47 PDT)
  - Re: 回复： [AMBER] Error running MM _PBSA.pl script Vikas Sharma (Mon May 18 2009 - 07:06:49 PDT)
    - 回复：回复： [AMBER] Error running MM _PBSA.pl script 廖青华 (Mon May 18 2009 - 07:41:14 PDT)
- RE: [AMBER] Error running MM _PBSA.pl script Ray Luo (Mon May 18 2009 - 10:43:30 PDT)
  - Re: [AMBER] Error running MM _PBSA.pl script Vikas Sharma (Mon May 18 2009 - 21:34:18 PDT)
    - Re: [AMBER] Error running MM _PBSA.pl script liuhui (Tue May 19 2009 - 07:29:23 PDT)
- Re: [AMBER] Error running MM _PBSA.pl script Vikas Sharma (Tue May 19 2009 - 08:02:21 PDT)
  - Re: [AMBER] Error running MM _PBSA.pl script liuhui (Tue May 19 2009 - 09:15:24 PDT)
    - Re: [AMBER] Error running MM _PBSA.pl script Vikas Sharma (Tue May 19 2009 - 11:21:47 PDT)
    - Re: [AMBER] Error running MM _PBSA.pl script liuhui (Tue May 19 2009 - 19:20:26 PDT)
    - Re: [AMBER] Error running MM _PBSA.pl script Vikas Sharma (Wed May 20 2009 - 01:29:42 PDT)
[AMBER] problem with parmchk rebeca (Mon May 18 2009 - 06:59:51 PDT)
- Re: [AMBER] problem with parmchk David A. Case (Mon May 18 2009 - 07:19:54 PDT)
  - Re: [AMBER] problem with parmchk rebeca (Mon May 18 2009 - 07:34:31 PDT)
    - Re: [AMBER] problem with parmchk David A. Case (Mon May 18 2009 - 13:00:07 PDT)
[AMBER] no equilibrium Nancy (Mon May 18 2009 - 19:32:01 PDT)
[AMBER] no equilibrium Nancy (Mon May 18 2009 - 19:44:03 PDT)
- Re: [AMBER] no equilibrium steinbrt.rci.rutgers.edu (Mon May 18 2009 - 20:00:40 PDT)
[AMBER] The largest AMBER calculation(s)? Vlad (Mon May 18 2009 - 19:58:27 PDT)
[AMBER] Problem with Nmode Kshatresh Dutta Dubey (Mon May 18 2009 - 21:25:05 PDT)
- Re: [AMBER] Problem with Nmode David A. Case (Wed May 20 2009 - 11:02:44 PDT)
  - Re: [AMBER] Problem with Nmode Kshatresh Dutta Dubey (Wed May 20 2009 - 22:14:50 PDT)
    - Re: [AMBER] Problem with Nmode David A. Case (Thu May 21 2009 - 05:29:06 PDT)
[AMBER] AMBER 10 output Sergey Samsonov (Tue May 19 2009 - 00:33:21 PDT)
- Re: [AMBER] AMBER 10 output steinbrt.rci.rutgers.edu (Tue May 19 2009 - 06:53:03 PDT)
  - Re: [AMBER] AMBER 10 output Sergey Samsonov (Tue May 19 2009 - 07:53:41 PDT)
[AMBER] Problem with nonstandard residues moitrayee.mbu.iisc.ernet.in (Tue May 19 2009 - 04:48:33 PDT)
- Re: [AMBER] Problem with nonstandard residues David A. Case (Tue May 19 2009 - 05:54:14 PDT)
  - Re: [AMBER] Problem with nonstandard residues moitrayee.mbu.iisc.ernet.in (Tue May 19 2009 - 06:10:00 PDT)
    - Re: [AMBER] Problem with nonstandard residues David A. Case (Tue May 19 2009 - 08:22:15 PDT)
    - Re: [AMBER] Problem with nonstandard residues moitrayee.mbu.iisc.ernet.in (Tue May 19 2009 - 09:47:38 PDT)
[AMBER] gaff and aromatic compounds rebeca (Tue May 19 2009 - 08:50:02 PDT)
- Re: [AMBER] gaff and aromatic compounds David A. Case (Tue May 19 2009 - 09:07:29 PDT)
- Re: [AMBER] gaff and aromatic compounds Junmei Wang (Thu May 21 2009 - 18:24:52 PDT)
  - Re: [AMBER] gaff and aromatic compounds rebeca (Fri May 22 2009 - 02:04:45 PDT)
    - Re: [AMBER] gaff and aromatic compounds Junmei Wang (Tue May 26 2009 - 09:03:53 PDT)
[AMBER] loadpdb atom type Mark M Huntress (Tue May 19 2009 - 09:20:20 PDT)
- Re: [AMBER] loadpdb atom type Carlos Simmerling (Tue May 19 2009 - 10:09:29 PDT)
  - RE: [AMBER] loadpdb atom type Mark M Huntress (Tue May 19 2009 - 11:15:02 PDT)
- Re: [AMBER] loadpdb atom type David A. Case (Tue May 19 2009 - 11:19:44 PDT)
[AMBER] Tutorial A1 Workalemhu Berhanu (Tue May 19 2009 - 16:05:15 PDT)
[AMBER] resp charge R. A. (Tue May 19 2009 - 19:35:25 PDT)
- [AMBER] resp charge FyD (Wed May 20 2009 - 00:42:07 PDT)
- RE: [AMBER] resp charge Ross Walker (Wed May 20 2009 - 08:05:20 PDT)
[AMBER] gaff and aromatic compounds rebeca (Wed May 20 2009 - 01:54:43 PDT)
- Re: [AMBER] gaff and aromatic compounds David A. Case (Wed May 20 2009 - 05:04:05 PDT)
[AMBER] MM PBSA output Vikas Sharma (Wed May 20 2009 - 04:53:57 PDT)
- 回复： [AMBER] MM PBSA output 廖青华 (Wed May 20 2009 - 05:15:04 PDT)
  - Re: 回复： [AMBER] MM PBSA output Vikas Sharma (Wed May 20 2009 - 10:54:32 PDT)
[AMBER] Amber/CHARMM summer school David A. Case (Wed May 20 2009 - 05:40:39 PDT)
- RE: [AMBER] Amber/CHARMM summer school CHAMI F. (Thu May 21 2009 - 04:56:23 PDT)
[AMBER] ptraj questions Jia Xu (Wed May 20 2009 - 07:39:13 PDT)
- Re: [AMBER] ptraj questions Myunggi Yi (Fri May 22 2009 - 06:57:08 PDT)
  - Re: [AMBER] ptraj questions Jia Xu (Sat May 23 2009 - 22:06:10 PDT)
[AMBER] RE: add magnesium Ross Walker (Wed May 20 2009 - 14:30:09 PDT)
[AMBER] how to use two dimensions periodic boundary ? Nancy (Wed May 20 2009 - 18:32:50 PDT)
[AMBER] errors when add ions zgong.hust (Wed May 20 2009 - 19:51:48 PDT)
- Re: [AMBER] errors when add ions David A. Case (Thu May 21 2009 - 05:23:08 PDT)
- [AMBER] Why does protein carry charges? Chih-Ying Lin (Fri May 22 2009 - 21:09:21 PDT)
  - [AMBER] How to choose the counter ions for proteins? Chih-Ying Lin (Fri May 22 2009 - 22:42:40 PDT)
    - RE: [AMBER] How to choose the counter ions for proteins? Ross Walker (Sat May 23 2009 - 11:09:27 PDT)
    - Re: RE: [AMBER] How to choose the counter ions for proteins? Chih-Ying Lin (Sat May 23 2009 - 11:16:49 PDT)
  - RE: [AMBER] Why does protein carry charges? Ross Walker (Sat May 23 2009 - 11:06:57 PDT)
[AMBER] Protein with HETATM, am I doing the nicholus bhattacharjee (Wed May 20 2009 - 21:48:42 PDT)
- Re: [AMBER] Protein with HETATM, am I doing the Amit Bajaj (Wed May 20 2009 - 22:26:49 PDT)
  - Re: [AMBER] Protein with HETATM, am I doing the nicholus bhattacharjee (Wed May 20 2009 - 23:43:37 PDT)
    - Re: [AMBER] Protein with HETATM, am I doing the amit (Mon May 25 2009 - 08:26:15 PDT)
[AMBER] Radius for Bromine in MMPBSA calculation john smith (Wed May 20 2009 - 22:24:05 PDT)
- RE: [AMBER] Radius for Bromine in MMPBSA calculation Ray Luo (Thu May 21 2009 - 09:32:41 PDT)
  - Re: [AMBER] Radius for Bromine in MMPBSA calculation john smith (Sun May 24 2009 - 21:52:48 PDT)
    - RE: [AMBER] Radius for Bromine in MMPBSA calculation Ray Luo (Mon May 25 2009 - 14:10:41 PDT)
    - Re: [AMBER] Radius for Bromine in MMPBSA calculation john smith (Mon May 25 2009 - 22:00:52 PDT)
    - RE: [AMBER] Radius for Bromine in MMPBSA calculation Ray Luo (Tue May 26 2009 - 12:02:27 PDT)
[AMBER] Protein with HETATM, am I doing the right thing nicholus bhattacharjee (Thu May 21 2009 - 04:21:15 PDT)
- Re: [AMBER] Protein with HETATM, am I doing the right thing David A. Case (Thu May 21 2009 - 05:39:14 PDT)
  - Re: [AMBER] Protein with HETATM, am I doing the right thing nicholus bhattacharjee (Thu May 21 2009 - 09:28:52 PDT)
    - Re: [AMBER] Protein with HETATM, am I doing the right thing David A. Case (Sat May 23 2009 - 05:13:01 PDT)
    - [AMBER] Why NaCl or KCl solution? Chih-Ying Lin (Sat May 23 2009 - 09:41:33 PDT)
    - Re: [AMBER] Why NaCl or KCl solution? Thomas Cheatham (Wed May 27 2009 - 17:50:56 PDT)
    - Re: [AMBER] Why NaCl or KCl solution? Chih-Ying Lin (Wed May 27 2009 - 19:11:21 PDT)
[AMBER] Loading PDB of complex Vikas Sharma (Thu May 21 2009 - 06:13:36 PDT)
- Re: [AMBER] Loading PDB of complex Carlos Simmerling (Thu May 21 2009 - 06:48:06 PDT)
  - Re: [AMBER] Loading PDB of complex Vikas Sharma (Thu May 21 2009 - 22:56:36 PDT)
[AMBER] Installation directory Thomas Spraggins (Thu May 21 2009 - 11:02:59 PDT)
- Re: [AMBER] Installation directory David A. Case (Thu May 21 2009 - 11:19:28 PDT)
  - Re: [AMBER] Installation directory Thomas Spraggins (Thu May 21 2009 - 12:18:13 PDT)
    - Re: [AMBER] Installation directory Atro Tossavainen (Mon May 25 2009 - 01:10:34 PDT)
[AMBER] Segmentation error in Ptraj Kshatresh Dutta Dubey (Fri May 22 2009 - 00:17:27 PDT)
[AMBER] lipid membrane(dppc) in amber xueqin pang (Fri May 22 2009 - 01:42:54 PDT)
- Re: [AMBER] lipid membrane(dppc) in amber Myunggi Yi (Fri May 22 2009 - 06:45:20 PDT)
[AMBER] lipid membrane(dppc) in amber xueqin pang (Fri May 22 2009 - 02:01:26 PDT)
[AMBER] decomposition and alanine scanning 廖青华 (Fri May 22 2009 - 07:13:49 PDT)
[AMBER] MMPBSA extract coordinate vijayaraj.clri.res.in (Fri May 22 2009 - 11:00:57 PDT)
[AMBER] Nab units ? Marek Maly (Fri May 22 2009 - 17:20:14 PDT)
- Re: [AMBER] Nab units ? David A. Case (Fri May 22 2009 - 18:33:34 PDT)
  - Re: [AMBER] Nab units ? Marek Maly (Fri May 22 2009 - 18:43:41 PDT)
[AMBER] 2 atoms not in residue template Workalemhu Berhanu (Sat May 23 2009 - 17:11:12 PDT)
[AMBER] file contains 2 atoms not in residue templates Workalemhu Berhanu (Sat May 23 2009 - 17:17:09 PDT)
- Re: [AMBER] file contains 2 atoms not in residue templates David A. Case (Sun May 24 2009 - 06:12:14 PDT)
[AMBER] problem with MM-PBSA Maryam Hamzehee (Sat May 23 2009 - 21:48:05 PDT)
[AMBER] nanoseconds of simulation with nscm=0 Naser Alijabbari (Sun May 24 2009 - 10:20:18 PDT)
- Re: [AMBER] nanoseconds of simulation with nscm=0 Thomas Cheatham (Sun May 24 2009 - 11:27:33 PDT)
  - Re: [AMBER] nanoseconds of simulation with nscm=0 Naser Alijabbari (Sun May 24 2009 - 12:56:28 PDT)
    - Re: [AMBER] nanoseconds of simulation with nscm=0 Thomas Cheatham (Sun May 24 2009 - 13:37:23 PDT)
[AMBER] Unit 8 Error on OPEN: prmtop Workalemhu Berhanu (Sun May 24 2009 - 10:27:38 PDT)
- Re: [AMBER] Unit 8 Error on OPEN: prmtop Peter Gannett (Sun May 24 2009 - 10:46:47 PDT)
- Re: [AMBER] Unit 8 Error on OPEN: prmtop Alessandro Nascimento (Sun May 24 2009 - 11:28:26 PDT)
  - Re: [AMBER] Unit 8 Error on OPEN: prmtop Peter Gannett (Sun May 24 2009 - 12:29:58 PDT)
  - Re: [AMBER] Unit 8 Error on OPEN: prmtop Workalemhu Berhanu (Sun May 24 2009 - 15:12:00 PDT)
[AMBER] Strange high temperature in softcore TI Tom Joseph (Sun May 24 2009 - 18:54:43 PDT)
- Re: [AMBER] Strange high temperature in softcore TI steinbrt.rci.rutgers.edu (Sun May 24 2009 - 19:26:28 PDT)
  - Re: [AMBER] Strange high temperature in softcore TI Tom Joseph (Sun May 24 2009 - 20:20:20 PDT)
    - Re: [AMBER] Strange high temperature in softcore TI steinbrt.rci.rutgers.edu (Sun May 24 2009 - 21:13:38 PDT)
[AMBER] How to know that the md is stable in equilibration run nicholus bhattacharjee (Mon May 25 2009 - 04:54:25 PDT)
- [AMBER] Re: How to know that the md is stable in equilibration run nicholus bhattacharjee (Mon May 25 2009 - 09:11:39 PDT)
[AMBER] Problem with MM-PBSA energy calculation Rubben Torella (Mon May 25 2009 - 08:58:41 PDT)
- Re: [AMBER] Problem with MM-PBSA energy calculation Barbault Florent (Mon May 25 2009 - 11:57:19 PDT)
  - Re: [AMBER] Problem with MM-PBSA energy calculation Rubben Torella (Tue May 26 2009 - 04:24:56 PDT)
[AMBER] Question about &dipoles printing in AMBER 8 Karen Callahan (Mon May 25 2009 - 16:46:00 PDT)
[AMBER] partial charge and topology of intrastrand cross-link DNA Shuang Ding (Mon May 25 2009 - 19:27:43 PDT)
- Re: [AMBER] partial charge and topology of intrastrand cross-link DNA FyD (Tue May 26 2009 - 22:27:40 PDT)
[AMBER] problem with MM-PBSA Maryam Hamzehee (Mon May 25 2009 - 21:52:29 PDT)
- Re: [AMBER] problem with MM-PBSA David A. Case (Tue May 26 2009 - 04:37:31 PDT)
- RE: [AMBER] problem with MM-PBSA Ray Luo (Tue May 26 2009 - 09:44:14 PDT)
- Re: [AMBER] problem with MM-PBSA Thomas Cheatham (Wed May 27 2009 - 17:35:30 PDT)
[AMBER] Molecular simulation of a protein using special H2O cluster Rilei Yu (Tue May 26 2009 - 01:20:56 PDT)
- Re: [AMBER] Molecular simulation of a protein using special H2O cluster Carlos Simmerling (Tue May 26 2009 - 04:45:50 PDT)
- Re: [AMBER] Molecular simulation of a protein using special H2O cluster Rilei Yu (Tue May 26 2009 - 17:21:15 PDT)
  - Re: [AMBER] Molecular simulation of a protein using special H2O cluster Carlos Simmerling (Tue May 26 2009 - 17:25:03 PDT)
[AMBER] Re: About Amber installations Alan (Tue May 26 2009 - 02:53:37 PDT)
- Re: [AMBER] Re: About Amber installations jacky zhao (Tue May 26 2009 - 04:18:25 PDT)
[AMBER] ligand QM/semi-empirical coords optmisation Alan (Tue May 26 2009 - 03:55:09 PDT)
- Re: [AMBER] ligand QM/semi-empirical coords optmisation David A. Case (Tue May 26 2009 - 04:41:25 PDT)
  - Re: [AMBER] ligand QM/semi-empirical coords optmisation Alan (Thu Jun 04 2009 - 07:19:28 PDT)
    - Re: [AMBER] ligand QM/semi-empirical coords optmisation David A. Case (Thu Jun 04 2009 - 08:06:28 PDT)
    - Re: [AMBER] ligand QM/semi-empirical coords optmisation Alan (Thu Jun 04 2009 - 11:05:27 PDT)
  - Re: [AMBER] ligand QM/semi-empirical coords optmisation Junmei Wang (Fri Jun 05 2009 - 08:01:32 PDT)
    - Re: [AMBER] ligand QM/semi-empirical coords optmisation Francesco Pietra (Fri Jun 05 2009 - 11:17:45 PDT)
[AMBER] problem with program anal within Amber10 Marina Grabar (Tue May 26 2009 - 04:48:38 PDT)
- Re: [AMBER] problem with program anal within Amber10 David A. Case (Tue May 26 2009 - 05:03:01 PDT)
[AMBER] partial charges of lipid membrane for GPCR system xueqin pang (Tue May 26 2009 - 06:34:34 PDT)
[AMBER] mdfil: Error unknown flag during sander minimization Workalemhu Berhanu (Tue May 26 2009 - 06:57:29 PDT)
- Re: [AMBER] mdfil: Error unknown flag during sander minimization David A. Case (Tue May 26 2009 - 07:05:37 PDT)
- Re: [AMBER] mdfil: Error unknown flag during sander minimization Shubhra Gupta (Tue May 26 2009 - 21:07:25 PDT)
[AMBER] RE: About Amber10 installation "Possible Failure" Ross Walker (Tue May 26 2009 - 08:38:19 PDT)
[AMBER] get typeid of -1, sleap - AMBER with amoeba ff Tomasio, Susana (Tue May 26 2009 - 08:51:18 PDT)
[AMBER] Tutorial 4 Please check the total charge and your -nc flag Workalemhu Berhanu (Tue May 26 2009 - 12:47:07 PDT)
- Re: [AMBER] Tutorial 4 Please check the total charge and your -nc flag David A. Case (Wed May 27 2009 - 04:42:29 PDT)
[AMBER] FATAL error in creating topology and coordinate files for organic molecules with Antechamber Workalemhu Berhanu (Tue May 26 2009 - 14:45:55 PDT)
- Re: [AMBER] FATAL error in creating topology and coordinate files for organic molecules with Antechamber Rubben Torella (Tue May 26 2009 - 15:33:18 PDT)
[AMBER] Re: Help with xleap Taufik Al-Sarraj (Tue May 26 2009 - 16:58:00 PDT)
[AMBER] ACE residue - amoeba_amino.off and amoeba_aminont.off - different labels Tomasio, Susana (Wed May 27 2009 - 04:25:35 PDT)
- Re: [AMBER] ACE residue - amoeba_amino.off and amoeba_aminont.off - different labels David A. Case (Wed May 27 2009 - 04:57:07 PDT)
RE: [AMBER] ACE residue - amoeba_amino.off and amoeba_aminont.off- different labels Tomasio, Susana (Wed May 27 2009 - 05:13:58 PDT)
[AMBER] PARMCAL calculation ? Marek Maly (Wed May 27 2009 - 07:19:48 PDT)
[AMBER] MM-PBSA and NetCDF Bradshaw, Richard (Wed May 27 2009 - 08:38:13 PDT)
[AMBER] Tutorial 4 Parameter file was not saved Workalemhu Berhanu (Wed May 27 2009 - 09:00:30 PDT)
- RE: [AMBER] Tutorial 4 Parameter file was not saved Ross Walker (Wed May 27 2009 - 10:31:30 PDT)
[AMBER] heating advice Mark M Huntress (Wed May 27 2009 - 13:44:26 PDT)
Re: [AMBER] hbond_ptraj Thomas Cheatham (Wed May 27 2009 - 17:39:15 PDT)
[AMBER] SANDER BOMB PRADEEP VENKATARAMAN (Wed May 27 2009 - 19:39:56 PDT)
- Re: [AMBER] SANDER BOMB David A. Case (Thu May 28 2009 - 07:29:50 PDT)
[AMBER] Changing bond length manoj singh (Wed May 27 2009 - 20:47:52 PDT)
- RE: [AMBER] Changing bond length Ross Walker (Wed May 27 2009 - 21:38:59 PDT)
  - Re: [AMBER] Changing bond length manoj singh (Thu May 28 2009 - 10:00:14 PDT)
[AMBER] AMOEBA and carbon nanotubes + include parameters Tomasio, Susana (Thu May 28 2009 - 03:23:00 PDT)
[AMBER] MM-PBSA nmode statistics Dmitry Osolodkin (Thu May 28 2009 - 04:54:18 PDT)
- Re: [AMBER] MM-PBSA nmode statistics Kshatresh Dutta Dubey (Thu May 28 2009 - 22:13:34 PDT)
  - Re: [AMBER] MM-PBSA nmode statistics Dmitry Osolodkin (Fri May 29 2009 - 03:53:27 PDT)
    - RE: [AMBER] MM-PBSA nmode statistics Ray Luo (Fri May 29 2009 - 11:01:36 PDT)
    - Re: [AMBER] MM-PBSA nmode statistics Dmitry Osolodkin (Sat May 30 2009 - 10:25:46 PDT)
    - RE: [AMBER] MM-PBSA nmode statistics Ray Luo (Sun May 31 2009 - 10:32:49 PDT)
    - Re: [AMBER] MM-PBSA nmode statistics Dmitry Osolodkin (Mon Jun 01 2009 - 06:12:15 PDT)
    - RE: [AMBER] MM-PBSA nmode statistics Ray Luo (Mon Jun 01 2009 - 12:05:48 PDT)
[AMBER] contacts in ptraj 欧阳德方 (Thu May 28 2009 - 04:55:28 PDT)
[AMBER] how to know that adequate equilibration from rmsd curve of equilibration nicholus bhattacharjee (Thu May 28 2009 - 06:37:29 PDT)
- Re: [AMBER] how to know that adequate equilibration from rmsd curve of equilibration Bill Ross (Thu May 28 2009 - 08:42:13 PDT)
  - Re: [AMBER] how to know that adequate equilibration from rmsd curve of equilibration nicholus bhattacharjee (Thu May 28 2009 - 11:08:52 PDT)
    - Re: [AMBER] how to know that adequate equilibration from rmsd curve of equilibration Carlos Simmerling (Thu May 28 2009 - 11:15:09 PDT)
    - Re: [AMBER] how to know that adequate equilibration from rmsd curve of equilibration Cihan Aydin (Sat Jun 27 2009 - 07:29:21 PDT)
    - Re: [AMBER] how to know that adequate equilibration from rmsd curve of equilibration Naser Alijabbari (Sat Jun 27 2009 - 11:19:23 PDT)
    - Re: [AMBER] how to know that adequate equilibration from rmsd curve of equilibration Cihan Aydin (Sun Jun 28 2009 - 09:19:07 PDT)
[AMBER] FW: About Amber10 installation "Possible Failure" Ross Walker (Thu May 28 2009 - 07:06:31 PDT)
Re: [AMBER] Minimization error on protonated system? Please help. Thanks! David A. Case (Thu May 28 2009 - 08:17:59 PDT)
[AMBER] Minimization on MM-PBSA Rubben Torella (Thu May 28 2009 - 08:23:07 PDT)
[AMBER] xleap segmentation fault Jayalakshmi Sridhar (Thu May 28 2009 - 09:29:47 PDT)
- Re: [AMBER] xleap segmentation fault David A. Case (Thu May 28 2009 - 13:05:12 PDT)
- Re: [AMBER] xleap segmentation fault Jayalakshmi Sridhar (Fri May 29 2009 - 08:45:25 PDT)
[AMBER] ask for parm99MOD xiaoqin huang (Thu May 28 2009 - 11:16:35 PDT)
- RE: [AMBER] ask for parm99MOD xiaoqin huang (Thu May 28 2009 - 12:31:14 PDT)
  - Re: [AMBER] ask for parm99MOD Adrian Roitberg (Thu May 28 2009 - 12:38:23 PDT)
    - Re: [AMBER] ask for parm99MOD Carlos Simmerling (Thu May 28 2009 - 12:41:20 PDT)
    - RE: [AMBER] ask for parm99MOD xiaoqin huang (Thu May 28 2009 - 12:41:54 PDT)
    - Re: [AMBER] ask for parm99MOD Adrian Roitberg (Thu May 28 2009 - 12:44:08 PDT)
    - RE: [AMBER] ask for parm99MOD xiaoqin huang (Thu May 28 2009 - 12:46:23 PDT)
    - Re: [AMBER] ask for parm99MOD Carlos Simmerling (Thu May 28 2009 - 12:56:26 PDT)
    - Re: [AMBER] ask for parm99MOD Carlos Simmerling (Thu May 28 2009 - 12:44:41 PDT)
    - RE: [AMBER] ask for parm99MOD xiaoqin huang (Thu May 28 2009 - 12:51:59 PDT)
    - Re: [AMBER] ask for parm99MOD Carlos Simmerling (Thu May 28 2009 - 12:57:24 PDT)
    - RE: [AMBER] ask for parm99MOD xiaoqin huang (Thu May 28 2009 - 13:09:28 PDT)
    - Re: [AMBER] ask for parm99MOD Carlos Simmerling (Thu May 28 2009 - 13:22:31 PDT)
    - RE: [AMBER] ask for parm99MOD xiaoqin huang (Thu May 28 2009 - 13:32:02 PDT)
    - Re: [AMBER] ask for parm99MOD Carlos Simmerling (Thu May 28 2009 - 13:52:56 PDT)
    - Re: [AMBER] ask for parm99MOD Adrian Roitberg (Thu May 28 2009 - 13:56:14 PDT)
    - RE: [AMBER] ask for parm99MOD xiaoqin huang (Thu May 28 2009 - 14:09:26 PDT)
    - Re: [AMBER] ask for parm99MOD Carlos Simmerling (Thu May 28 2009 - 14:17:05 PDT)
    - RE: [AMBER] ask for parm99MOD xiaoqin huang (Thu May 28 2009 - 14:43:15 PDT)
    - Re: [AMBER] ask for parm99MOD David A. Case (Thu May 28 2009 - 14:52:29 PDT)
    - Re: [AMBER] ask for parm99MOD Carlos Simmerling (Mon Jun 01 2009 - 13:12:47 PDT)
    - RE: [AMBER] ask for parm99MOD xiaoqin huang (Mon Jun 01 2009 - 13:25:02 PDT)
    - [AMBER] question of ibelly used in pmemd xiaoqin huang (Wed Jul 15 2009 - 10:34:20 PDT)
    - Re: [AMBER] question of ibelly used in pmemd Robert Duke (Wed Jul 15 2009 - 11:22:23 PDT)
    - RE: [AMBER] question of ibelly used in pmemd xiaoqin huang (Wed Jul 15 2009 - 14:28:52 PDT)
    - RE: [AMBER] question of ibelly used in pmemd Ross Walker (Wed Jul 15 2009 - 18:32:07 PDT)
    - RE: [AMBER] question of ibelly used in pmemd xiaoqin huang (Fri Jul 17 2009 - 07:36:06 PDT)
    - Re: [AMBER] question of ibelly used in pmemd Robert Duke (Wed Jul 15 2009 - 14:56:00 PDT)
    - RE: [AMBER] question of ibelly used in pmemd xiaoqin huang (Fri Jul 17 2009 - 07:54:55 PDT)
    - Re: [AMBER] question of ibelly used in pmemd Robert Duke (Fri Jul 17 2009 - 08:48:41 PDT)
    - RE: [AMBER] question of ibelly used in pmemd xiaoqin huang (Mon Jul 20 2009 - 07:21:20 PDT)
    - Re: [AMBER] question of ibelly used in pmemd Robert Duke (Mon Jul 20 2009 - 07:42:15 PDT)
    - RE: [AMBER] question of ibelly used in pmemd xiaoqin huang (Mon Jul 20 2009 - 08:20:32 PDT)
    - Re: [AMBER] question of ibelly used in pmemd Robert Duke (Mon Jul 20 2009 - 08:53:50 PDT)
    - RE: [AMBER] question of ibelly used in pmemd xiaoqin huang (Mon Jul 20 2009 - 09:28:42 PDT)
    - RE: [AMBER] question of ibelly used in pmemd Kristina Furse (Mon Jul 20 2009 - 09:56:26 PDT)
    - Re: [AMBER] question of ibelly used in pmemd Robert Duke (Mon Jul 20 2009 - 10:10:03 PDT)
    - Re: [AMBER] question of ibelly used in pmemd Robert Duke (Mon Jul 20 2009 - 09:42:08 PDT)
    - RE: [AMBER] question of ibelly used in pmemd xiaoqin huang (Mon Jul 20 2009 - 10:20:36 PDT)
    - RE: [AMBER] question of ibelly used in pmemd Ross Walker (Mon Jul 20 2009 - 10:32:08 PDT)
    - RE: [AMBER] question of ibelly used in pmemd xiaoqin huang (Mon Jul 20 2009 - 10:39:16 PDT)
    - Re: [AMBER] question of ibelly used in pmemd Robert Duke (Mon Jul 20 2009 - 10:55:23 PDT)
    - Re: [AMBER] question of ibelly used in pmemd Robert Duke (Tue Jul 21 2009 - 06:15:20 PDT)
    - RE: [AMBER] question of ibelly used in pmemd Kristina Furse (Tue Jul 21 2009 - 06:53:21 PDT)
    - Re: [AMBER] question of ibelly used in pmemd Robert Duke (Tue Jul 21 2009 - 07:16:21 PDT)
    - RE: [AMBER] question of ibelly used in pmemd Kristina Furse (Tue Jul 21 2009 - 09:27:29 PDT)
Re: [AMBER] unnatural amino acid FyD (Thu May 28 2009 - 11:46:27 PDT)
[AMBER] How to take into account the charge in GAFF parameterization Workalemhu Berhanu (Thu May 28 2009 - 16:22:07 PDT)
- Re: [AMBER] How to take into account the charge in GAFF parameterization cgji (Thu May 28 2009 - 23:49:44 PDT)
[AMBER] J coupling constant calculation Neha Gandhi (Thu May 28 2009 - 22:24:37 PDT)
- Re: [AMBER] J coupling constant calculation Dechang Li (Thu May 28 2009 - 22:31:06 PDT)
- Re: [AMBER] J coupling constant calculation Gustavo Seabra (Tue Jun 02 2009 - 07:18:08 PDT)
[AMBER] broken Ligand Shubhra Gupta (Fri May 29 2009 - 06:28:22 PDT)
- Re: [AMBER] broken Ligand David A. Case (Fri May 29 2009 - 07:45:20 PDT)
  - Re: [AMBER] broken Ligand Shubhra Gupta (Fri May 29 2009 - 23:35:46 PDT)
    - Re: [AMBER] broken Ligand David A. Case (Sun May 31 2009 - 05:50:57 PDT)
[AMBER] QQD psuedoatom restraints Titus, Jamie (bairdje) (Fri May 29 2009 - 07:02:31 PDT)
- Re: [AMBER] QQD psuedoatom restraints David A. Case (Fri May 29 2009 - 08:18:29 PDT)
  - RE: [AMBER] QQD psuedoatom restraints Titus, Jamie (bairdje) (Fri May 29 2009 - 12:01:34 PDT)
    - Re: [AMBER] QQD psuedoatom restraints David A. Case (Fri May 29 2009 - 12:26:27 PDT)
    - RE: [AMBER] QQD psuedoatom restraints Titus, Jamie (bairdje) (Mon Jun 01 2009 - 04:21:19 PDT)
  - RE: [AMBER] QQD psuedoatom restraints Titus, Jamie (bairdje) (Fri Jun 12 2009 - 11:51:25 PDT)
    - Re: [AMBER] QQD psuedoatom restraints David A. Case (Mon Jun 15 2009 - 05:00:23 PDT)
[AMBER] Targeted MD and QM/MM Gabriel Urquiza (Fri May 29 2009 - 13:09:31 PDT)
- [AMBER] protein molecular weight? Chih-Ying Lin (Fri May 29 2009 - 15:44:24 PDT)
  - Re: [AMBER] protein molecular weight? Tom Joseph (Fri May 29 2009 - 16:40:58 PDT)
- Re: [AMBER] Targeted MD and QM/MM Gustavo Seabra (Tue Jun 02 2009 - 07:43:35 PDT)
  - Re: [AMBER] Targeted MD and QM/MM Gabriel Urquiza (Tue Jun 02 2009 - 15:08:11 PDT)
[AMBER] the atom number exceeds the MAXATOM, reallocate memory automatically Workalemhu Berhanu (Sat May 30 2009 - 04:20:03 PDT)
- Re: [AMBER] the atom number exceeds the MAXATOM, reallocate memory automatically David A. Case (Sat May 30 2009 - 06:11:59 PDT)
[AMBER] ERROR in ptrajInitializeState(): Attempting .... Siavoush Dastmalchi (Sat May 30 2009 - 09:06:51 PDT)
[AMBER] RE: ERROR in ptrajInitializeState(): Attempting .... Siavoush Dastmalchi (Sat May 30 2009 - 10:11:55 PDT)
[AMBER] Parameter file content manoj singh (Sat May 30 2009 - 18:53:37 PDT)
- Re: [AMBER] Parameter file content Tom Joseph (Sat May 30 2009 - 19:23:48 PDT)
[AMBER] create a simulation box Workalemhu Berhanu (Sat May 30 2009 - 20:06:24 PDT)
- Re: [AMBER] create a simulation box Gustavo Seabra (Tue Jun 02 2009 - 08:08:46 PDT)
[AMBER] can I get partial charge for lipid membrane with Antechamber and RESP xueqin pang (Sun May 31 2009 - 05:43:09 PDT)
- Re: [AMBER] can I get partial charge for lipid membrane with Antechamber and RESP FyD (Sun May 31 2009 - 05:51:50 PDT)
[AMBER] Can we use GROMACS or NAMD for MD, and then use MM-PBSA to culculate binding energy xueqin pang (Sun May 31 2009 - 05:47:57 PDT)
- Re: [AMBER] Can we use GROMACS or NAMD for MD, and then use MM-PBSA to culculate binding energy Gustavo Seabra (Tue Jun 02 2009 - 07:53:19 PDT)
- Re: [AMBER] Can we use GROMACS or NAMD for MD, and then use MM-PBSA to culculate binding energy Marc Baaden (Tue Jun 02 2009 - 13:56:29 PDT)
  - Re: [AMBER] Can we use GROMACS or NAMD for MD, and then use MM-PBSA to culculate binding energy jacky zhao (Wed Jun 03 2009 - 06:44:12 PDT)
[AMBER] solutes in a simulation box Workalemhu Berhanu (Sun May 31 2009 - 09:59:39 PDT)
[AMBER] Choice of force feild manoj singh (Sun May 31 2009 - 10:12:23 PDT)
- Re: [AMBER] Choice of force feild Gustavo Seabra (Tue Jun 02 2009 - 07:58:11 PDT)
[AMBER] Choice of force field manoj singh (Sun May 31 2009 - 13:39:13 PDT)
- Re: [AMBER] Choice of force field Carlos Simmerling (Mon Jun 01 2009 - 04:14:09 PDT)
[AMBER] sleap and delete FyD (Mon Jun 01 2009 - 00:35:32 PDT)
[AMBER] converting vibrational frequency aneesh cna (Mon Jun 01 2009 - 04:22:01 PDT)
- Re: [AMBER] converting vibrational frequency David A. Case (Mon Jun 01 2009 - 04:39:32 PDT)
  - Re: [AMBER] converting vibrational frequency aneesh cna (Mon Jun 01 2009 - 09:53:22 PDT)
[AMBER] atom number exceeds the MAXATOM when running antechamber xueqin pang (Mon Jun 01 2009 - 05:53:23 PDT)
- Re: [AMBER] atom number exceeds the MAXATOM when running antechamber Gustavo Seabra (Tue Jun 02 2009 - 08:04:33 PDT)
[AMBER] different comformations to choose for RESP xueqin pang (Mon Jun 01 2009 - 06:47:30 PDT)
- Re: [AMBER] different comformations to choose for RESP FyD (Mon Jun 01 2009 - 07:32:21 PDT)
[AMBER] minimization to reduce covalent deviation Peter Varnai (Mon Jun 01 2009 - 13:25:07 PDT)
- Re: [AMBER] minimization to reduce covalent deviation David A. Case (Tue Jun 02 2009 - 06:38:58 PDT)
[AMBER] how to choose different comformations for RESP xueqin pang (Mon Jun 01 2009 - 17:32:51 PDT)
- Re: [AMBER] how to choose different comformations for RESP cgji (Mon Jun 01 2009 - 22:14:02 PDT)
[AMBER] MMPBSA and mm_pbsa_statistics.pl error john smith (Mon Jun 01 2009 - 22:38:54 PDT)
- Re: [AMBER] MMPBSA and mm_pbsa_statistics.pl error Ray Luo (Tue Jun 02 2009 - 21:49:34 PDT)
[AMBER] how to add ions bharat lakhani (Tue Jun 02 2009 - 00:25:46 PDT)
[AMBER] Atom names Rose Tamil (Tue Jun 02 2009 - 03:53:50 PDT)
- Re: [AMBER] Atom names Carlos Simmerling (Tue Jun 02 2009 - 04:39:25 PDT)
- Re: [AMBER] Atom names David A. Case (Tue Jun 02 2009 - 04:44:39 PDT)
  - Re: [AMBER] Atom names Rose Tamil (Tue Jun 02 2009 - 04:50:47 PDT)
    - Re: [AMBER] Atom names Rose Tamil (Wed Jun 03 2009 - 07:53:51 PDT)
    - Re: [AMBER] Atom names David A. Case (Wed Jun 03 2009 - 09:00:15 PDT)
    - Re: [AMBER] Atom names Rose Tamil (Wed Jun 03 2009 - 13:43:56 PDT)
    - [AMBER] atom type Taufik Al-Sarraj (Thu Jun 04 2009 - 18:03:14 PDT)
    - Re: [AMBER] atom type David A. Case (Fri Jun 05 2009 - 05:32:45 PDT)
    - Re: [AMBER] atom type Taufik Al-Sarraj (Fri Jun 05 2009 - 06:58:50 PDT)
    - Re: [AMBER] atom type Taufik Al-Sarraj (Fri Jun 05 2009 - 09:07:14 PDT)
[AMBER] help with parameters for ions rebeca (Tue Jun 02 2009 - 05:46:14 PDT)
- Re: [AMBER] help with parameters for ions David A. Case (Tue Jun 02 2009 - 06:46:40 PDT)
  - Re: [AMBER] help with parameters for ions rebeca (Tue Jun 02 2009 - 08:10:17 PDT)
    - Re: [AMBER] help with parameters for ions InSuk Joung (Tue Jun 02 2009 - 08:28:55 PDT)
  - Re: [AMBER] help with parameters for ions rebeca (Tue Jun 02 2009 - 10:38:00 PDT)
    - Re: [AMBER] help with parameters for ions InSuk Joung (Tue Jun 02 2009 - 11:14:46 PDT)
[AMBER] Error in MM PBSA Vikas Sharma (Tue Jun 02 2009 - 06:42:16 PDT)
- Re: [AMBER] Error in MM PBSA David A. Case (Tue Jun 02 2009 - 07:05:09 PDT)
  - 回复： [AMBER] Error in MM PBSA 廖青华 (Tue Jun 02 2009 - 07:30:47 PDT)
    - Re: 回复： [AMBER] Error in MM PBSA David A. Case (Tue Jun 02 2009 - 07:36:39 PDT)
  - Re: [AMBER] Error in MM PBSA Vikas Sharma (Tue Jun 02 2009 - 23:45:35 PDT)
  - Re: [AMBER] Error in MM PBSA Vikas Sharma (Tue Jun 02 2009 - 23:46:03 PDT)
  - Re: [AMBER] Error in MM PBSA Vikas Sharma (Tue Jun 02 2009 - 23:46:06 PDT)
    - Re: [AMBER] Error in MM PBSA David A. Case (Wed Jun 03 2009 - 04:43:54 PDT)
    - Re: [AMBER] Error in MM PBSA Vikas Sharma (Wed Jun 03 2009 - 07:24:14 PDT)
Fwd: Re: [AMBER] help with parameters for ions rebeca (Tue Jun 02 2009 - 11:33:41 PDT)
[AMBER] PARMSCAN alegil.fq.uh.cu (Tue Jun 02 2009 - 15:26:42 PDT)
[AMBER] PARMSCAN alegil.fq.uh.cu (Tue Jun 02 2009 - 15:41:54 PDT)
[AMBER] preparation of two solutes of organic molecules in a simulation box Workalemhu Berhanu (Tue Jun 02 2009 - 16:09:04 PDT)
[AMBER] addions Shubhra Gupta (Tue Jun 02 2009 - 22:47:11 PDT)
- [AMBER] Re: addions Shubhra Gupta (Wed Jun 03 2009 - 04:12:32 PDT)
  - Re: [AMBER] Re: addions nicholus bhattacharjee (Wed Jun 03 2009 - 06:44:51 PDT)
  - [AMBER] Re: addions Peter Gannett (Wed Jun 03 2009 - 07:17:57 PDT)
    - Re: [AMBER] Re: addions Shubhra Gupta (Thu Jun 04 2009 - 21:38:20 PDT)
[AMBER] Distance restraints between groups of atoms Germain Vallverdu (Tue Jun 02 2009 - 23:58:57 PDT)
- Re: [AMBER] Distance restraints between groups of atoms David A. Case (Wed Jun 03 2009 - 05:27:04 PDT)
  - [AMBER] AMBER10: error message mdfil flag..... Catein Catherine (Wed Jun 03 2009 - 07:14:50 PDT)
    - Re: [AMBER] AMBER10: error message mdfil flag..... David A. Case (Wed Jun 03 2009 - 07:30:08 PDT)
  - Re: [AMBER] Distance restraints between groups of atoms Germain Vallverdu (Wed Jun 03 2009 - 07:43:37 PDT)
    - Re: [AMBER] Distance restraints between groups of atoms David A. Case (Wed Jun 03 2009 - 09:32:33 PDT)
    - Re: [AMBER] Distance restraints between groups of atoms Germain Vallverdu (Tue Jun 09 2009 - 01:39:45 PDT)
    - Re: [AMBER] Distance restraints between groups of atoms David A. Case (Tue Jun 09 2009 - 04:45:14 PDT)
[AMBER] use of random seed in multiple runs Andrew Voronkov (Wed Jun 03 2009 - 02:28:52 PDT)
- Re: [AMBER] use of random seed in multiple runs Carlos Simmerling (Wed Jun 03 2009 - 03:13:23 PDT)
  - Re: [AMBER] use of random seed in multiple runs Andrew Voronkov (Wed Jun 03 2009 - 10:00:32 PDT)
- Re: [AMBER] use of random seed in multiple runs Gustavo Seabra (Wed Jun 03 2009 - 06:55:24 PDT)
- Re: [AMBER] use of random seed in multiple runs Andrew Voronkov (Wed Jun 03 2009 - 12:26:48 PDT)
  - Re: [AMBER] use of random seed in multiple runs Gustavo Seabra (Wed Jun 03 2009 - 19:00:51 PDT)
- Re: [AMBER] use of random seed in multiple runs Robert Duke (Wed Jun 03 2009 - 20:59:48 PDT)
  - Re: [AMBER] use of random seed in multiple runs Jifeng Wang (Thu Jun 04 2009 - 07:10:50 PDT)
- Re: [AMBER] use of random seed in multiple runs Robert Duke (Thu Jun 04 2009 - 07:31:32 PDT)
  - Re: [AMBER] use of random seed in multiple runs Jifeng Wang (Thu Jun 04 2009 - 07:43:25 PDT)
  - Re: [AMBER] use of random seed in multiple runs Marek Maly (Thu Jun 04 2009 - 09:35:57 PDT)
  - Re: [AMBER] use of random seed in multiple runs Gustavo Seabra (Fri Jun 05 2009 - 06:28:03 PDT)
- Re: [AMBER] use of random seed in multiple runs Robert Duke (Thu Jun 04 2009 - 10:02:58 PDT)
  - Re: [AMBER] use of random seed in multiple runs Marek Maly (Thu Jun 04 2009 - 12:16:50 PDT)
    - Re: [AMBER] use of random seed in multiple runs Carlos Simmerling (Thu Jun 04 2009 - 12:20:59 PDT)
    - Re: [AMBER] use of random seed in multiple runs Marek Maly (Thu Jun 04 2009 - 13:01:54 PDT)
    - Re: [AMBER] use of random seed in multiple runs Gustavo Seabra (Fri Jun 05 2009 - 06:37:42 PDT)
    - Re: [AMBER] use of random seed in multiple runs Marek Maly (Fri Jun 05 2009 - 06:49:14 PDT)
    - Re: [AMBER] use of random seed in multiple runs Gustavo Seabra (Fri Jun 05 2009 - 12:18:35 PDT)
    - Re: [AMBER] use of random seed in multiple runs Marek Maly (Fri Jun 05 2009 - 12:40:13 PDT)
- Re: [AMBER] use of random seed in multiple runs Robert Duke (Fri Jun 05 2009 - 07:37:14 PDT)
  - Re: [AMBER] use of random seed in multiple runs Gustavo Seabra (Fri Jun 05 2009 - 08:16:00 PDT)
- Re: [AMBER] use of random seed in multiple runs Robert Duke (Fri Jun 05 2009 - 07:45:32 PDT)
  - Re: [AMBER] use of random seed in multiple runs Naser Alijabbari (Fri Jun 05 2009 - 08:30:55 PDT)
- Re: [AMBER] use of random seed in multiple runs Robert Duke (Fri Jun 05 2009 - 08:45:09 PDT)
[AMBER] only ff94 and ff99 for GBSA? Andrew Voronkov (Wed Jun 03 2009 - 03:28:15 PDT)
- Re: [AMBER] only ff94 and ff99 for GBSA? Carlos Simmerling (Wed Jun 03 2009 - 03:51:09 PDT)
- Re: [AMBER] only ff94 and ff99 for GBSA? Andrew Voronkov (Wed Jun 03 2009 - 04:52:13 PDT)
  - Re: [AMBER] only ff94 and ff99 for GBSA? David A. Case (Wed Jun 03 2009 - 05:24:56 PDT)
    - Re: [AMBER] only ff94 and ff99 for GBSA? Andrew Voronkov (Mon Jul 27 2009 - 09:41:27 PDT)
    - Re: [AMBER] only ff94 and ff99 for GBSA? case (Mon Jul 27 2009 - 10:05:48 PDT)
    - Re: [AMBER] only ff94 and ff99 for GBSA? Andrew Voronkov (Mon Jul 27 2009 - 23:12:15 PDT)
    - Re: [AMBER] only ff94 and ff99 for GBSA? FyD (Tue Jul 28 2009 - 00:32:52 PDT)
[AMBER] NO output when running espgen? xueqin pang (Wed Jun 03 2009 - 06:13:06 PDT)
[AMBER] Pentavalent Phosphorous and Antechamber Peterson, Matthew W. (Wed Jun 03 2009 - 07:12:44 PDT)
- Re: [AMBER] Pentavalent Phosphorous and Antechamber David A. Case (Wed Jun 03 2009 - 09:35:26 PDT)
- Re: [AMBER] Pentavalent Phosphorous and Antechamber Shubhra Gupta (Wed Jun 03 2009 - 21:37:08 PDT)
- Re: [AMBER] Pentavalent Phosphorous and Antechamber FyD (Wed Jun 03 2009 - 23:29:59 PDT)
[AMBER] spc.itp for the Amber force field rebeca (Wed Jun 03 2009 - 07:46:46 PDT)
- Re: [AMBER] spc.itp for the Amber force field Alan (Wed Jun 03 2009 - 08:38:56 PDT)
[AMBER] problems with EP of TIP4PEW rebeca (Wed Jun 03 2009 - 08:43:58 PDT)
- Re: [AMBER] problems with EP of TIP4PEW David A. Case (Wed Jun 03 2009 - 09:29:43 PDT)
  - Re: [AMBER] problems with EP of TIP4PEW rebeca (Wed Jun 03 2009 - 11:40:12 PDT)
Re: [AMBER] hbond_DNAtraj Jianyin Shao (Wed Jun 03 2009 - 09:52:41 PDT)
[AMBER] creating bond Jorgen Simonsen (Wed Jun 03 2009 - 10:04:11 PDT)
- Re: [AMBER] creating bond David A. Case (Wed Jun 03 2009 - 11:32:57 PDT)
- Re: [AMBER] creating bond Bill Ross (Wed Jun 03 2009 - 11:40:52 PDT)
  - Re: [AMBER] creating bond Jorgen Simonsen (Wed Jun 03 2009 - 12:56:29 PDT)
- Re: [AMBER] creating bond Bill Ross (Wed Jun 03 2009 - 14:40:09 PDT)
  - [AMBER] AMBER 10: sleap diff errors? Catein Catherine (Wed Jun 03 2009 - 22:37:35 PDT)
    - Re: [AMBER] AMBER 10: sleap diff errors? David A. Case (Thu Jun 04 2009 - 12:19:44 PDT)
[AMBER] ptraj image in non-orthorhombic cell Joanna Panecka (Wed Jun 03 2009 - 13:19:52 PDT)
[AMBER] no output when running Antechamber(espgen) xueqin pang (Wed Jun 03 2009 - 23:02:32 PDT)
[AMBER] how to add water for membrane, in Z direction only or xyz xueqin pang (Thu Jun 04 2009 - 01:13:07 PDT)
[AMBER] Binding Energy Vikas Sharma (Thu Jun 04 2009 - 04:25:01 PDT)
[AMBER] Error in MM PBSA Vikas Sharma (Thu Jun 04 2009 - 07:58:43 PDT)
- Re: [AMBER] Error in MM PBSA Ray Luo (Thu Jun 04 2009 - 14:00:51 PDT)
- Re: [AMBER] Error in MM PBSA Vikas Sharma (Sat Jun 06 2009 - 02:03:22 PDT)
  - Re: [AMBER] Error in MM PBSA Ray Luo (Sat Jun 06 2009 - 07:37:43 PDT)
    - Re: [AMBER] Error in MM PBSA Vikas Sharma (Sun Jun 07 2009 - 10:02:03 PDT)
    - Re: [AMBER] Error in MM PBSA Ray Luo (Sun Jun 07 2009 - 12:17:30 PDT)
    - Re: [AMBER] Error in MM PBSA Vikas Sharma (Mon Jun 08 2009 - 10:44:06 PDT)
    - Re: [AMBER] Error in MM PBSA Ray Luo (Mon Jun 08 2009 - 11:12:22 PDT)
[AMBER] mol2 file to amber pdb file format balaji nagarajan (Thu Jun 04 2009 - 09:32:06 PDT)
- Re: [AMBER] mol2 file to amber pdb file format David A. Case (Thu Jun 04 2009 - 09:55:39 PDT)
[AMBER] rescaling velocities abi ghanem (Thu Jun 04 2009 - 09:39:02 PDT)
- Re: [AMBER] rescaling velocities Carlos Simmerling (Thu Jun 04 2009 - 09:43:20 PDT)
[AMBER] ptraj_hbond_problem balaji nagarajan (Thu Jun 04 2009 - 15:08:24 PDT)
- Re: [AMBER] ptraj_hbond_problem Thomas Cheatham (Thu Jun 04 2009 - 22:28:11 PDT)
[AMBER] Warning: No sp2 improper torsion term for Alan (Fri Jun 05 2009 - 05:26:55 PDT)
- RE: [AMBER] Warning: No sp2 improper torsion term for Ross Walker (Fri Jun 05 2009 - 07:13:53 PDT)
  - Re: [AMBER] Warning: No sp2 improper torsion term for Alan (Mon Jun 08 2009 - 07:54:50 PDT)
[AMBER] parameter for dihedral angle Jorgen Simonsen (Fri Jun 05 2009 - 08:16:56 PDT)
- Re: [AMBER] parameter for dihedral angle David A. Case (Fri Jun 05 2009 - 12:50:03 PDT)
- Re: [AMBER] parameter for dihedral angle raja pandian (Fri Jun 05 2009 - 22:13:52 PDT)
  - Re: [AMBER] parameter for dihedral angle David A. Case (Sat Jun 06 2009 - 05:47:35 PDT)
    - RE: [AMBER] parameter for dihedral angle Catein Catherine (Sun Jun 07 2009 - 20:08:17 PDT)
    - [AMBER] Error message? INFO: Old style inpcrd file read Catein Catherine (Sun Jun 07 2009 - 20:11:27 PDT)
    - Re: [AMBER] Error message? INFO: Old style inpcrd file read Robert Duke (Sun Jun 07 2009 - 20:19:38 PDT)
    - RE: [AMBER] Error message? INFO: Old style inpcrd file read Catein Catherine (Sun Jun 07 2009 - 20:55:28 PDT)
    - [AMBER] What is the parallel efficiency of amber10 Catein Catherine (Sun Jun 07 2009 - 20:19:37 PDT)
    - Re: [AMBER] What is the parallel efficiency of amber10 Tom Joseph (Sun Jun 07 2009 - 23:07:29 PDT)
    - Re: [AMBER] What is the parallel efficiency of amber10 David A. Case (Mon Jun 08 2009 - 05:23:11 PDT)
    - [AMBER] Can we define +1 or -1 charge for an organic drug using GAFF? Catein Catherine (Mon Jun 08 2009 - 08:16:23 PDT)
    - Re: [AMBER] Can we define +1 or -1 charge for an organic drug using GAFF? David A. Case (Mon Jun 08 2009 - 09:47:54 PDT)
    - [AMBER] PDMED Catein Catherine (Mon Jun 08 2009 - 21:28:58 PDT)
    - RE: [AMBER] PDMED Ross Walker (Mon Jun 08 2009 - 22:19:36 PDT)
    - RE: [AMBER] PDMED Catein Catherine (Mon Jun 08 2009 - 23:18:59 PDT)
    - RE: [AMBER] PDMED Ross Walker (Mon Jun 08 2009 - 23:35:25 PDT)
    - Re: [AMBER] What is the parallel efficiency of amber10 Gustavo Seabra (Mon Jun 08 2009 - 06:44:26 PDT)
[AMBER] Proper ISTRNG value ? Marek Maly (Fri Jun 05 2009 - 09:24:58 PDT)
[AMBER] Computational Alanine Scanning using mm_pbsa, any tutorial for amber9 or amber 10 version? Haizhen Zhong (Fri Jun 05 2009 - 16:17:01 PDT)
[AMBER] average torsional energy Francesco Pietra (Sat Jun 06 2009 - 09:57:49 PDT)
- Re: [AMBER] average torsional energy Adrian Roitberg (Sun Jun 07 2009 - 09:09:14 PDT)
  - Re: [AMBER] average torsional energy Carlos Simmerling (Sun Jun 07 2009 - 09:14:17 PDT)
    - Re: [AMBER] average torsional energy Karl Kirschner (Mon Jun 08 2009 - 01:29:05 PDT)
    - Re: [AMBER] average torsional energy Francesco Pietra (Mon Jun 08 2009 - 02:11:52 PDT)
- [AMBER] Fwd: average torsional energy Francesco Pietra (Sun Jun 07 2009 - 09:09:37 PDT)
- [AMBER] How to calculate the distance of CA of all residues in the trajectory Thomas Leonard (Sun Jun 07 2009 - 18:45:54 PDT)
[AMBER] MaxRad ? Marek Maly (Sat Jun 06 2009 - 13:56:44 PDT)
[AMBER] POL3 Hemant Kumar (Sun Jun 07 2009 - 11:27:29 PDT)
[AMBER] vs_vikassharma.yahoo.co.in has sent you a private message Vikas S (Sun Jun 07 2009 - 12:28:03 PDT)
[AMBER] Max filename length in Sander? Paul Mortenson (Mon Jun 08 2009 - 03:59:52 PDT)
- Re: [AMBER] Max filename length in Sander? David A. Case (Mon Jun 08 2009 - 05:28:41 PDT)
- Re: [AMBER] Max filename length in Sander? David A. Case (Mon Jun 08 2009 - 05:36:32 PDT)
- Re: [AMBER] Max filename length in Sander? Robert Duke (Mon Jun 08 2009 - 10:30:47 PDT)
  - RE: [AMBER] Max filename length in Sander? Paul Mortenson (Tue Jun 09 2009 - 07:47:57 PDT)
    - Re: [AMBER] Max filename length in Sander? Robert Duke (Tue Jun 09 2009 - 08:01:39 PDT)
[AMBER] (no subject) Vishal Maingi (Mon Jun 08 2009 - 04:14:22 PDT)
- Re: [AMBER] (no subject) Karl Kirschner (Mon Jun 08 2009 - 04:38:42 PDT)
- Re: [AMBER] (no subject) FyD (Mon Jun 08 2009 - 10:14:05 PDT)
[AMBER] Lost mail Robert Duke (Mon Jun 08 2009 - 04:58:02 PDT)
[AMBER] problem with creation of prmtop and prmcrd files moitrayee.mbu.iisc.ernet.in (Mon Jun 08 2009 - 06:00:18 PDT)
- Re: [AMBER] problem with creation of prmtop and prmcrd files Tom Joseph (Wed Jun 10 2009 - 18:30:19 PDT)
[AMBER] Problem with modified trna[Fwd: problem with creation of prmtop and prmcrd files] moitrayee.mbu.iisc.ernet.in (Mon Jun 08 2009 - 07:28:14 PDT)
[AMBER] sander error Beale, John (Mon Jun 08 2009 - 07:43:24 PDT)
- RE: [AMBER] sander error Ross Walker (Mon Jun 08 2009 - 18:41:06 PDT)
- Re: [AMBER] sander error Robert Duke (Mon Jun 08 2009 - 20:27:52 PDT)
[AMBER] Problem with modified trna[Fwd: problem with creation of prmtop and prmcrd files]] moitrayee.mbu.iisc.ernet.in (Mon Jun 08 2009 - 07:30:21 PDT)
[AMBER] Unknown residue: MOL number: 30 type: Terminal/last Workalemhu Berhanu (Mon Jun 08 2009 - 11:30:43 PDT)
- Re: [AMBER] Unknown residue: MOL number: 30 type: Terminal/last David A. Case (Tue Jun 09 2009 - 04:51:42 PDT)
[AMBER] mm_pbsa_statistics-CALC DELTA parameter ? Marek Maly (Mon Jun 08 2009 - 12:16:19 PDT)
[AMBER] Strange contacts with water molecules Jordan MONNET (Mon Jun 08 2009 - 14:39:26 PDT)
- RE: [AMBER] Strange contacts with water molecules Ross Walker (Mon Jun 08 2009 - 20:16:41 PDT)
  - Re: [AMBER] Strange contacts with water molecules Jordan MONNET (Tue Jun 09 2009 - 09:01:53 PDT)
    - Re: [AMBER] Strange contacts with water molecules Jordan MONNET (Wed Jun 17 2009 - 10:00:46 PDT)
[AMBER] Error in MM PBSA (vertex atom mismatch) Vikas Sharma (Mon Jun 08 2009 - 23:33:38 PDT)
[AMBER] ptraj quasiharmonic analysis Neha Gandhi (Mon Jun 08 2009 - 23:38:01 PDT)
- Re: [AMBER] ptraj quasiharmonic analysis Hannes Loeffler (Tue Jun 09 2009 - 00:19:23 PDT)
[AMBER] (no subject) david.lisgarten.canterbury.ac.uk (Tue Jun 09 2009 - 03:23:57 PDT)
- Re: [AMBER] (no subject) David A. Case (Tue Jun 09 2009 - 04:47:59 PDT)
[AMBER] SOS - too high binding energy Marek Maly (Tue Jun 09 2009 - 03:49:43 PDT)
- Re: [AMBER] SOS - too high binding energy Marek Maly (Wed Jun 10 2009 - 12:47:58 PDT)
[AMBER] unit of charge in prep files moitrayee.mbu.iisc.ernet.in (Tue Jun 09 2009 - 04:35:51 PDT)
- Re: [AMBER] unit of charge in prep files David A. Case (Tue Jun 09 2009 - 06:07:08 PDT)
  - Re: [AMBER] unit of charge in prep files moitrayee.mbu.iisc.ernet.in (Tue Jun 09 2009 - 18:18:58 PDT)
[AMBER] Question of about MM-PBSA and mm_pbsa_createinput.pm script Samuel Genheden (Tue Jun 09 2009 - 05:43:19 PDT)
- Re: [AMBER] Question of about MM-PBSA and mm_pbsa_createinput.pm script David A. Case (Tue Jun 09 2009 - 06:20:22 PDT)
[AMBER] Vertex atom mismatch in Amber Vikas Sharma (Tue Jun 09 2009 - 06:41:33 PDT)
[AMBER] DNA as well as protein distorted during MD run in sander Jayalakshmi Sridhar (Tue Jun 09 2009 - 07:30:39 PDT)
- Re: [AMBER] DNA as well as protein distorted during MD run in sander Carlos Simmerling (Tue Jun 09 2009 - 07:38:14 PDT)
- Re: [AMBER] DNA as well as protein distorted during MD run in sander Jayalakshmi Sridhar (Tue Jun 09 2009 - 08:33:51 PDT)
  - Re: [AMBER] DNA as well as protein distorted during MD run in sander Carlos Simmerling (Tue Jun 09 2009 - 08:36:50 PDT)
- RE: [AMBER] DNA as well as protein distorted during MD run in sander Jesse Dylan Ziebarth (jziebrth) (Tue Jun 09 2009 - 08:47:34 PDT)
- Re: [AMBER] DNA as well as protein distorted during MD run in sander Carlos Simmerling (Tue Jun 09 2009 - 08:48:30 PDT)
- Re: [AMBER] DNA as well as protein distorted during MD run in sander Jayalakshmi Sridhar (Tue Jun 09 2009 - 09:02:56 PDT)
[AMBER] Improper dihedrals between residues? Ben Roberts (Tue Jun 09 2009 - 09:11:15 PDT)
- Re: [AMBER] Improper dihedrals between residues? Carlos Simmerling (Tue Jun 09 2009 - 09:28:04 PDT)
  - Re: [AMBER] Improper dihedrals between residues? David A. Case (Tue Jun 09 2009 - 10:14:57 PDT)
    - Re: [AMBER] Improper dihedrals between residues? Carlos Simmerling (Tue Jun 09 2009 - 10:51:40 PDT)
- Re: [AMBER] Improper dihedrals between residues? Bill Ross (Tue Jun 09 2009 - 14:17:03 PDT)
  - [AMBER] radial distribution without normalization CHAMI F. (Wed Jun 10 2009 - 08:48:12 PDT)
    - Re: [AMBER] radial distribution without normalization Thomas Cheatham (Wed Jun 10 2009 - 15:11:40 PDT)
Re: [AMBER] Improper dihedrals between residues? Bill Ross (Tue Jun 09 2009 - 12:04:02 PDT)
- Re: [AMBER] Improper dihedrals between residues? Ben Roberts (Tue Jun 09 2009 - 12:12:07 PDT)
[AMBER] POL3 & SHAKE Hemant Gangwar (Tue Jun 09 2009 - 13:53:27 PDT)
- Re: [AMBER] POL3 & SHAKE David A. Case (Wed Jun 10 2009 - 12:11:40 PDT)
[AMBER] MM PBSA ( Vertex atom mismatch in Amber) Vikas Sharma (Tue Jun 09 2009 - 20:28:22 PDT)
[AMBER] unit of force constant aneesh cna (Tue Jun 09 2009 - 22:06:50 PDT)
[AMBER] GAFF and solvents.lib error Vishal Maingi (Wed Jun 10 2009 - 03:25:38 PDT)
- Re: [AMBER] GAFF and solvents.lib error David A. Case (Wed Jun 10 2009 - 08:54:05 PDT)
[AMBER] Thermodynamic parameters in mm_PBSA - NAB ? Marek Maly (Wed Jun 10 2009 - 03:33:59 PDT)
- Re: [AMBER] Thermodynamic parameters in mm_PBSA - NAB ? David A. Case (Wed Jun 10 2009 - 09:01:26 PDT)
  - Re: [AMBER] Thermodynamic parameters in mm_PBSA - NAB ? Marek Maly (Wed Jun 10 2009 - 12:47:41 PDT)
[AMBER] partial charges from AM1-BCC and RESP differ a lot xueqin pang (Wed Jun 10 2009 - 05:39:31 PDT)
- Re: [AMBER] partial charges from AM1-BCC and RESP differ a lot FyD (Thu Jun 11 2009 - 11:59:27 PDT)
  - RE:Re: [AMBER] partial charges from AM1-BCC and RESP differ a lot xueqin pang (Tue Jun 16 2009 - 00:57:25 PDT)
    - RE:Re: [AMBER] partial charges from AM1-BCC and RESP differ a lot FyD (Tue Jun 16 2009 - 23:32:11 PDT)
[AMBER] force.f routine Brad Dickson (Wed Jun 10 2009 - 05:56:39 PDT)
- Re: [AMBER] force.f routine David A. Case (Wed Jun 10 2009 - 07:09:47 PDT)
[AMBER] Completed installation of AmberTools, version 1.1 Alan (Wed Jun 10 2009 - 06:13:37 PDT)
- Re: [AMBER] Completed installation of AmberTools, version 1.1 David A. Case (Wed Jun 10 2009 - 07:10:22 PDT)
  - [AMBER] ptraj amber 10 file. Catein Catherine (Wed Jun 10 2009 - 09:02:32 PDT)
[AMBER] Error in AMBER ( Vertex atom mismatch in Amber) Vikas Sharma (Wed Jun 10 2009 - 06:14:28 PDT)
[AMBER] question lev kantorovich (Wed Jun 10 2009 - 07:20:08 PDT)
- RE: [AMBER] question Ross Walker (Wed Jun 10 2009 - 20:19:01 PDT)
[AMBER] compiling amber10 with mac intel, ifort/icc and mpi Alan (Wed Jun 10 2009 - 07:47:00 PDT)
- Re: [AMBER] compiling amber10 with mac intel, ifort/icc and mpi David A. Case (Wed Jun 10 2009 - 08:34:59 PDT)
  - Re: [AMBER] compiling amber10 with mac intel, ifort/icc and mpi Alan (Wed Jun 10 2009 - 09:26:13 PDT)
    - Re: [AMBER] compiling amber10 with mac intel, ifort/icc and mpi David A. Case (Wed Jun 10 2009 - 09:54:38 PDT)
    - Re: [AMBER] compiling amber10 with mac intel, ifort/icc and mpi Alan (Thu Jun 11 2009 - 04:14:42 PDT)
    - Re: [AMBER] compiling amber10 with mac intel, ifort/icc and mpi David Watson (Thu Jun 11 2009 - 05:43:28 PDT)
    - Re: [AMBER] compiling amber10 with mac intel, ifort/icc and mpi Alan (Sat Jun 13 2009 - 11:37:54 PDT)
[AMBER] RNA and polarizable force field Abhishek Singh (Wed Jun 10 2009 - 08:30:29 PDT)
[AMBER] glycopeptide Parametrization guardiani.fi.infn.it (Wed Jun 10 2009 - 08:41:14 PDT)
- Re: [AMBER] glycopeptide Parametrization Ahammadunny Pathiaseril (Wed Jun 10 2009 - 13:25:21 PDT)
- Re: [AMBER] glycopeptide Parametrization FyD (Fri Jun 12 2009 - 00:05:51 PDT)
  - Re: [AMBER] glycopeptide Parametrization guardiani.fi.infn.it (Fri Jun 12 2009 - 07:06:24 PDT)
    - Re: [AMBER] glycopeptide Parametrization Karl Kirschner (Fri Jun 12 2009 - 08:06:17 PDT)
    - RE: [AMBER] glycopeptide Parametrization Ross Walker (Fri Jun 12 2009 - 09:09:37 PDT)
    - RE: [AMBER] glycopeptide Parametrization FyD (Sat Jun 13 2009 - 00:40:00 PDT)
    - [AMBER] IGB=7 vs IGB=5 guardiani.fi.infn.it (Thu Jun 25 2009 - 04:20:15 PDT)
    - [AMBER] H-bond vs. VdW Taufik Al-Sarraj (Fri Jul 03 2009 - 11:48:12 PDT)
    - Re: [AMBER] H-bond vs. VdW FyD (Fri Jul 03 2009 - 22:01:58 PDT)
    - Re: [AMBER] H-bond vs. VdW Cihan Aydin (Mon Jul 06 2009 - 08:13:39 PDT)
    - Re: [AMBER] H-bond vs. VdW case (Mon Jul 06 2009 - 10:29:49 PDT)
    - Re: [AMBER] IGB=7 vs IGB=5 Carlos Simmerling (Tue Jul 21 2009 - 06:51:22 PDT)
[AMBER] GAFF atom type question Cen Gao (Wed Jun 10 2009 - 08:49:00 PDT)
[AMBER] entangle-less building Vishal Maingi (Wed Jun 10 2009 - 10:52:51 PDT)
[AMBER] Generating LeAP file for helix containing non-standard amino acid Brothers, Michael Charles (Wed Jun 10 2009 - 11:26:32 PDT)
- Re: [AMBER] Generating LeAP file for helix containing non-standard amino acid David A. Case (Wed Jun 10 2009 - 12:14:49 PDT)
  - Re: [AMBER] Generating LeAP file for helix containing non-standard amino acid David A. Case (Wed Jun 10 2009 - 12:23:36 PDT)
    - RE: [AMBER] Generating LeAP file for helix containing non-standard amino acid Brothers, Michael Charles (Wed Jun 10 2009 - 12:40:21 PDT)
- Re: [AMBER] Generating LeAP file for helix containing non-standard amino acid FyD (Wed Jun 10 2009 - 23:48:27 PDT)
  - RE: [AMBER] Generating LeAP file for helix containing non-standard amino acid Brothers, Michael Charles (Thu Jun 18 2009 - 10:38:53 PDT)
    - RE: [AMBER] Generating LeAP file for helix containing non-standard amino acid FyD (Thu Jun 18 2009 - 12:55:34 PDT)
    - RE: [AMBER] Generating LeAP file for helix containing non-standard amino acid Brothers, Michael Charles (Thu Jun 18 2009 - 14:01:52 PDT)
    - RE: [AMBER] Generating LeAP file for helix containing non-standard amino acid FyD (Thu Jun 18 2009 - 22:41:54 PDT)
    - RE: [AMBER] Generating LeAP file for helix containing non-standard amino acid Brothers, Michael Charles (Fri Jun 19 2009 - 10:46:25 PDT)
[AMBER] input coordinates for vdW transition step in Amber 10 TI Jodi Hadden (Wed Jun 10 2009 - 13:27:16 PDT)
- Re: [AMBER] input coordinates for vdW transition step in Amber 10 TI Tom Joseph (Wed Jun 10 2009 - 18:02:51 PDT)
- Re: [AMBER] input coordinates for vdW transition step in Amber 10 TI Ye MEI (Thu Jun 11 2009 - 01:22:34 PDT)
- Re: [AMBER] input coordinates for vdW transition step in Amber 10 TI steinbrt.rci.rutgers.edu (Thu Jun 11 2009 - 03:42:51 PDT)
Re: [AMBER] entangle-less building Bill Ross (Wed Jun 10 2009 - 15:38:31 PDT)
- [AMBER] Constant pH simulation Rukman Hertadi (Wed Jun 10 2009 - 17:56:59 PDT)
  - Re: [AMBER] Constant pH simulation Tom Joseph (Wed Jun 10 2009 - 18:08:36 PDT)
[AMBER] Vertex atom mismatch in Amber Vikas Sharma (Wed Jun 10 2009 - 20:29:57 PDT)
[AMBER] zinc coordination of benzimidazole Aust, Susanne (Thu Jun 11 2009 - 00:09:59 PDT)
- Re: [AMBER] zinc coordination of benzimidazole Urszula Uciechowska (Thu Jun 11 2009 - 01:49:45 PDT)
  - [AMBER] ptraj "image" "center" commands Catein Catherine (Thu Jun 11 2009 - 02:13:38 PDT)
    - RE: [AMBER] ptraj "image" "center" commands Ross Walker (Thu Jun 11 2009 - 08:30:08 PDT)
[AMBER] NOE Beale, John (Thu Jun 11 2009 - 05:30:36 PDT)
- Re: [AMBER] NOE David A. Case (Thu Jun 11 2009 - 10:29:06 PDT)
[AMBER] GAFF atom type question Cen Gao (Thu Jun 11 2009 - 06:36:52 PDT)
- RE: [AMBER] GAFF atom type question Ross Walker (Thu Jun 11 2009 - 08:43:50 PDT)
  - Re: [AMBER] GAFF atom type question Cen Gao (Thu Jun 11 2009 - 17:31:25 PDT)
    - [AMBER] Is the result of sander same as that of pmemd? Catein Catherine (Fri Jun 12 2009 - 07:04:38 PDT)
    - Re: [AMBER] Is the result of sander same as that of pmemd? Robert Duke (Fri Jun 12 2009 - 07:09:45 PDT)
    - RE: [AMBER] Is the result of sander same as that of pmemd? Catein Catherine (Fri Jun 12 2009 - 19:55:10 PDT)
    - RE: [AMBER] Is the result of sander same as that of pmemd? Ross Walker (Sat Jun 13 2009 - 09:12:51 PDT)
    - [AMBER] Are ntrp=1000, ntwx=1000, ntwr=500 reasonable for long MD simulations? Catein Catherine (Mon Jun 15 2009 - 03:04:53 PDT)
    - RE: [AMBER] Are ntrp=1000, ntwx=1000, ntwr=500 reasonable for long MD simulations? Ross Walker (Mon Jun 15 2009 - 07:49:43 PDT)
  - Re: [AMBER] GAFF atom type question Cen Gao (Sun Jun 14 2009 - 21:12:19 PDT)
- [AMBER] cpin error Rukman Hertadi (Fri Jul 24 2009 - 00:18:52 PDT)
  - Re: [AMBER] cpin error case (Fri Jul 24 2009 - 12:41:00 PDT)
    - RE: [AMBER] cpin error Rukman Hertadi (Mon Jul 27 2009 - 22:22:18 PDT)
    - Re: [AMBER] cpin error case (Tue Sep 01 2009 - 05:23:04 PDT)
  - Re: [AMBER] cpin error Arjun Sharma (Fri Aug 28 2015 - 07:00:23 PDT)
    - Re: [AMBER] cpin error Jason Swails (Fri Aug 28 2015 - 07:22:29 PDT)
[AMBER] Copper semiempirical parameters Jacopo Sgrignani (Thu Jun 11 2009 - 06:49:50 PDT)
- RE: [AMBER] Copper semiempirical parameters Ross Walker (Thu Jun 11 2009 - 09:09:14 PDT)
[AMBER] PRINCIPAL QUESTION Marek Maly (Thu Jun 11 2009 - 08:41:42 PDT)
[AMBER] setBox truncated octahedron Myunggi Yi (Thu Jun 11 2009 - 10:27:26 PDT)
AW: [AMBER] zinc coordination of benzimidazole Aust, Susanne (Thu Jun 11 2009 - 23:13:19 PDT)
[AMBER] MM PBSA ERROR Vikas Sharma (Fri Jun 12 2009 - 07:04:25 PDT)
[AMBER] Residues KIRTANA S (Fri Jun 12 2009 - 07:10:39 PDT)
- Re: [AMBER] Residues FyD (Fri Jun 12 2009 - 07:24:35 PDT)
  - Re: [AMBER] Residues KIRTANA S (Fri Jun 12 2009 - 08:07:50 PDT)
    - Re: [AMBER] Residues FyD (Fri Jun 12 2009 - 08:36:10 PDT)
    - Re: [AMBER] Residues KIRTANA S (Fri Jun 12 2009 - 12:41:02 PDT)
    - Re: [AMBER] Residues KIRTANA S (Sat Jun 13 2009 - 17:14:31 PDT)
    - Re: [AMBER] Residues FyD (Sun Jun 14 2009 - 00:02:02 PDT)
- Re: [AMBER] Residues Bill Ross (Fri Jun 12 2009 - 12:49:09 PDT)
- [AMBER] Re: Residues KIRTANA S (Fri Jun 12 2009 - 18:15:20 PDT)
- Re: [AMBER] Residues FyD (Sun Jun 14 2009 - 23:51:56 PDT)
- Re: [AMBER] Residues KIRTANA S (Thu Jun 18 2009 - 12:57:11 PDT)
  - Re: [AMBER] Residues FyD (Thu Jun 18 2009 - 13:24:16 PDT)
- Re: [AMBER] Residues Bill Ross (Thu Jun 18 2009 - 14:13:53 PDT)
  - Re: [AMBER] Residues Roman Osman (Thu Jun 18 2009 - 14:58:53 PDT)
[AMBER] help KIRTANA S (Fri Jun 12 2009 - 06:42:04 PDT)
- RE: [AMBER] help Ross Walker (Fri Jun 12 2009 - 09:02:06 PDT)
[AMBER] dipole printing Hemant Kumar (Fri Jun 12 2009 - 08:58:29 PDT)
- RE: [AMBER] dipole printing Ross Walker (Fri Jun 12 2009 - 09:13:30 PDT)
  - RE: [AMBER] dipole printing Hemant Kumar (Fri Jun 12 2009 - 12:03:17 PDT)
[AMBER] AMBER ERROR Vikas Sharma (Sat Jun 13 2009 - 00:16:52 PDT)
[AMBER] Re: [Contact q4md] qurey reagarding RED Server FyD (Sat Jun 13 2009 - 01:08:26 PDT)
[AMBER] too high in binding energy (MM-PBSA) Maryam Hamzehee (Sat Jun 13 2009 - 02:53:43 PDT)
- 回复： [AMBER] too high in binding energy (MM-PBSA) 廖青华 (Sat Jun 13 2009 - 05:44:31 PDT)
  - Re: 回复： [AMBER] too high in binding energy (MM-PBSA) Maryam Hamzehee (Sat Jun 13 2009 - 06:56:16 PDT)
    - 回复：回复： [AMBER] too high in binding energy (MM-PBSA) 廖青华 (Sat Jun 13 2009 - 08:23:38 PDT)
    - Re: 回复：回复： [AMBER] too high in binding energy (MM-PBSA) Maryam Hamzehee (Sat Jun 13 2009 - 11:02:16 PDT)
    - Re: 回复：回复： [AMBER] too high in binding energy (MM-PBSA) Maryam Hamzehee (Sat Jun 13 2009 - 11:02:06 PDT)
    - Re: 回复：回复： [AMBER] too high in binding energy (MM-PBSA) Maryam Hamzehee (Sat Jun 13 2009 - 11:02:57 PDT)
    - Re: 回复：回复： [AMBER] too high in binding energy (MM-PBSA) Ilyas Yildirim (Sat Jun 13 2009 - 11:19:09 PDT)
    - 回复：回复：回复： [AMBER] too high in binding energy (MM-PBSA) 廖青华 (Sat Jun 13 2009 - 17:48:59 PDT)
    - Re: 回复：回复：回复： [AMBER] too high in binding energy (MM-PBSA) Maryam Hamzehee (Mon Jun 15 2009 - 03:00:50 PDT)
    - 回复：回复：回复：回复： [AMBER] too high in binding energy (MM-PBSA) 廖青华 (Mon Jun 15 2009 - 03:45:09 PDT)
[AMBER] PLEASE HELP - PDB Modification s_bill36.yahoo.co.uk (Sun Jun 14 2009 - 10:29:31 PDT)
- Re: [AMBER] PLEASE HELP - PDB Modification Tom Joseph (Sun Jun 14 2009 - 16:36:16 PDT)
[AMBER] parallel error 廖青华 (Mon Jun 15 2009 - 00:31:27 PDT)
- Re: [AMBER] parallel error Tom Joseph (Mon Jun 15 2009 - 04:54:19 PDT)
  - 回复： [AMBER] parallel error 廖青华 (Mon Jun 15 2009 - 05:08:27 PDT)
    - Re: 回复： [AMBER] parallel error Tom Joseph (Mon Jun 15 2009 - 05:51:49 PDT)
    - 回复：回复： [AMBER] parallel error 廖青华 (Mon Jun 15 2009 - 06:13:56 PDT)
    - Re: 回复：回复： [AMBER] parallel error Tom Joseph (Mon Jun 15 2009 - 06:25:30 PDT)
    - 回复：回复：回复： [AMBER] parallel error 廖青华 (Mon Jun 15 2009 - 06:35:58 PDT)
    - Re: 回复：回复：回复： [AMBER] parallel error Tom Joseph (Mon Jun 15 2009 - 07:06:05 PDT)
    - 回复：回复：回复：回复： [AMBER] parallel error 廖青华 (Mon Jun 15 2009 - 07:20:59 PDT)
[AMBER] covalent interaction 廖青华 (Mon Jun 15 2009 - 01:06:52 PDT)
[AMBER] total charge for NPRO in ff03ua Edyta Malolepsza (Mon Jun 15 2009 - 03:09:35 PDT)
- RE: [AMBER] total charge for NPRO in ff03ua Jun Wang (Mon Jun 15 2009 - 16:35:39 PDT)
  - Re: [AMBER] total charge for NPRO in ff03ua Edyta Malolepsza (Tue Jun 16 2009 - 02:42:55 PDT)
[AMBER] to unsubscribe email Urszula Uciechowska (Mon Jun 15 2009 - 05:59:46 PDT)
- RE: [AMBER] to unsubscribe email Ross Walker (Mon Jun 15 2009 - 09:59:06 PDT)
- [AMBER] to unsubscribe email backy (Wed Jun 17 2009 - 00:13:02 PDT)
  - RE: [AMBER] to unsubscribe email Ross Walker (Wed Jun 17 2009 - 01:09:39 PDT)
- Re: [AMBER] to unsubscribe email backy (Wed Jun 17 2009 - 01:22:19 PDT)
[AMBER] Antechamber am1bcc questions gilbert.bluemarble.net (Mon Jun 15 2009 - 06:04:19 PDT)
[AMBER] to check basepair in ptraj balaji nagarajan (Mon Jun 15 2009 - 07:23:28 PDT)
[AMBER] Histidine, which form? s_bill36.yahoo.co.uk (Mon Jun 15 2009 - 07:54:05 PDT)
- Re: [AMBER] Histidine, which form? Carlos Simmerling (Mon Jun 15 2009 - 07:57:40 PDT)
- RE: [AMBER] Histidine, which form? Ross Walker (Mon Jun 15 2009 - 08:06:49 PDT)
- Re: [AMBER] Histidine, which form? s. Bill (Mon Jun 15 2009 - 09:28:27 PDT)
  - RE: [AMBER] Histidine, which form? Ross Walker (Mon Jun 15 2009 - 09:39:04 PDT)
    - Re: [AMBER] Histidine, which form? M. L. Dodson (Mon Jun 15 2009 - 09:45:25 PDT)
[AMBER] pKa data base.... s. Bill (Mon Jun 15 2009 - 09:01:14 PDT)
[AMBER] Need help with nab code to access the m_prm struct in a molecule M. L. Dodson (Mon Jun 15 2009 - 12:49:02 PDT)
[AMBER] Re: connect KIRTANA S (Mon Jun 15 2009 - 13:18:54 PDT)
- RE: [AMBER] Re: connect Ross Walker (Mon Jun 15 2009 - 18:43:46 PDT)
- [AMBER] Distance-covariance and PCA questions... Cihan Aydin (Mon Jun 15 2009 - 21:18:58 PDT)
  - Re: [AMBER] Distance-covariance and PCA questions... Hannes Loeffler (Wed Jun 17 2009 - 00:41:42 PDT)
Re: [AMBER] Re: connect Bill Ross (Mon Jun 15 2009 - 13:39:32 PDT)
[AMBER] problem in pressure equillibration wong105.llnl.gov (Mon Jun 15 2009 - 23:18:22 PDT)
- Re: [AMBER] problem in pressure equillibration David A. Case (Tue Jun 16 2009 - 04:56:34 PDT)
[AMBER] Fix the local structure as a rigid body Yunjie Zhao (Tue Jun 16 2009 - 06:11:43 PDT)
- Re: [AMBER] Fix the local structure as a rigid body Carlos Simmerling (Tue Jun 16 2009 - 06:15:12 PDT)
  - Re: [AMBER] Fix the local structure as a rigid body Yunjie Zhao (Tue Jun 16 2009 - 06:57:10 PDT)
    - Re: [AMBER] Fix the local structure as a rigid body Carlos Simmerling (Tue Jun 16 2009 - 07:13:45 PDT)
    - Re: [AMBER] Fix the local structure as a rigid body David A. Case (Tue Jun 16 2009 - 08:41:04 PDT)
[AMBER] Sander imin=5 option Paul Mortenson (Tue Jun 16 2009 - 07:46:37 PDT)
- Re: [AMBER] Sander imin=5 option Carlos Simmerling (Tue Jun 16 2009 - 07:50:43 PDT)
  - RE: [AMBER] Sander imin=5 option Paul Mortenson (Tue Jun 16 2009 - 08:09:54 PDT)
[AMBER] MM decomp energy - zero values for Eele, Evdw Thomas Lake (Tue Jun 16 2009 - 08:36:50 PDT)
[AMBER] connecting residues KIRTANA S (Tue Jun 16 2009 - 08:59:37 PDT)
Re: [AMBER] Distance-covariance and PCA questions... Bill Ross (Tue Jun 16 2009 - 09:18:40 PDT)
Re: [AMBER] connecting residues Bill Ross (Tue Jun 16 2009 - 09:37:33 PDT)
- Re: [AMBER] connecting residues Bill Ross (Tue Jun 16 2009 - 09:39:02 PDT)
[AMBER] Seg-fault when creating residue Valla Fatemi (Tue Jun 16 2009 - 18:28:43 PDT)
- [AMBER] Re: Seg-fault when creating residue Valla Fatemi (Wed Jun 17 2009 - 10:41:47 PDT)
[AMBER] improper torsion problem Youn Kyeung Lee (Tue Jun 16 2009 - 19:36:14 PDT)
[AMBER] GLYCAM: warnings by writing topology Sergey Samsonov (Tue Jun 16 2009 - 23:38:56 PDT)
- Re: [AMBER] GLYCAM: warnings by writing topology FyD (Wed Jun 17 2009 - 00:30:26 PDT)
  - Re: [AMBER] GLYCAM: warnings by writing topology Sergey Samsonov (Wed Jun 17 2009 - 00:50:46 PDT)
    - Re: [AMBER] GLYCAM: warnings by writing topology Karl Kirschner (Wed Jun 17 2009 - 01:33:55 PDT)
    - Re: [AMBER] GLYCAM: warnings by writing topology Sergey Samsonov (Wed Jun 17 2009 - 02:09:23 PDT)
    - Re: [AMBER] GLYCAM: warnings by writing topology Shubhra Gupta (Wed Jun 17 2009 - 03:33:50 PDT)
    - Re: [AMBER] GLYCAM: warnings by writing topology FyD (Wed Jun 17 2009 - 08:40:06 PDT)
  - Re: [AMBER] GLYCAM: warnings by writing topology Sergey Samsonov (Wed Jun 17 2009 - 01:18:33 PDT)
- Re: [AMBER] GLYCAM: warnings by writing topology Bill Ross (Wed Jun 17 2009 - 01:01:28 PDT)
  - Re: [AMBER] GLYCAM: warnings by writing topology Sergey Samsonov (Wed Jun 17 2009 - 01:10:33 PDT)
- Re: [AMBER] GLYCAM: warnings by writing topology Bill Ross (Wed Jun 17 2009 - 10:32:43 PDT)
  - Re: [AMBER] GLYCAM: warnings by writing topology Sergey Samsonov (Thu Jun 18 2009 - 05:49:31 PDT)
[AMBER] How to calculate SASA in vmd Mannan (Tue Jun 16 2009 - 23:40:05 PDT)
Re: [AMBER] improper torsion problem Bill Ross (Wed Jun 17 2009 - 00:47:12 PDT)
Re: [AMBER] Seg-fault when creating residue Bill Ross (Wed Jun 17 2009 - 00:51:02 PDT)
[AMBER] vlimit in TI with soft core potential Ye MEI (Wed Jun 17 2009 - 01:20:31 PDT)
- Re: [AMBER] vlimit in TI with soft core potential steinbrt.rci.rutgers.edu (Wed Jun 17 2009 - 01:47:38 PDT)
  - Re: [AMBER] vlimit in TI with soft core potential Ye MEI (Wed Jun 17 2009 - 02:13:40 PDT)
[AMBER] Antechamber: stuck at bondtype Jack Shultz (Wed Jun 17 2009 - 05:50:11 PDT)
- Re: [AMBER] Antechamber: stuck at bondtype David A. Case (Wed Jun 17 2009 - 06:28:15 PDT)
- Re: [AMBER] Antechamber: stuck at bondtype Ye MEI (Wed Jun 17 2009 - 06:48:18 PDT)
[AMBER] bond length energy Thomas Lake (Wed Jun 17 2009 - 07:04:55 PDT)
- Re: [AMBER] bond length energy Mark Williamson (Wed Jun 17 2009 - 10:29:09 PDT)
- Re: [AMBER] bond length energy Karl Kirschner (Fri Jun 19 2009 - 02:57:04 PDT)
[AMBER] Specifying improper dihedrals Ben Roberts (Wed Jun 17 2009 - 08:24:14 PDT)
- Re: [AMBER] Specifying improper dihedrals Mark Williamson (Wed Jun 17 2009 - 10:12:08 PDT)
  - Re: [AMBER] Specifying improper dihedrals David A. Case (Wed Jun 17 2009 - 10:56:20 PDT)
    - Re: [AMBER] Specifying improper dihedrals Ben Roberts (Wed Jun 17 2009 - 12:17:12 PDT)
- Re: [AMBER] Specifying improper dihedrals Bill Ross (Wed Jun 17 2009 - 10:56:26 PDT)
  - Re: [AMBER] Specifying improper dihedrals Ben Roberts (Wed Jun 17 2009 - 12:18:41 PDT)
- Re: [AMBER] Specifying improper dihedrals Bill Ross (Wed Jun 17 2009 - 12:25:55 PDT)
[AMBER] Coarse grained MD in AMBER ? Siddharth Rastogi (Wed Jun 17 2009 - 11:50:13 PDT)
- Re: [AMBER] Coarse grained MD in AMBER ? Lili Peng (Wed Jun 17 2009 - 11:57:58 PDT)
[AMBER] where to I get the parameters for Mg divalent ion Mannan (Wed Jun 17 2009 - 21:11:19 PDT)
- Re: [AMBER] where to I get the parameters for Mg divalent ion Tom Joseph (Thu Jun 18 2009 - 20:53:01 PDT)
[AMBER] force units Brad Dickson (Thu Jun 18 2009 - 00:14:31 PDT)
- [AMBER] Re: force units Brad Dickson (Thu Jun 18 2009 - 02:31:16 PDT)
  - Re: [AMBER] Re: force units David A. Case (Thu Jun 18 2009 - 04:32:18 PDT)
    - [AMBER] ptraj correlation Catein Catherine (Thu Jun 18 2009 - 06:47:01 PDT)
    - RE: [AMBER] Re: force units Catein Catherine (Thu Jun 18 2009 - 07:01:40 PDT)
  - [AMBER] Re: force units Brad Dickson (Fri Jun 19 2009 - 06:22:40 PDT)
[AMBER] Improper dihedrals from .off and .lib files Johan Sund (Thu Jun 18 2009 - 03:15:37 PDT)
- Re: [AMBER] Improper dihedrals from .off and .lib files David A. Case (Thu Jun 18 2009 - 04:28:40 PDT)
[AMBER] guntheyp.aston.ac.uk (Thu Jun 18 2009 - 04:48:21 PDT)
- Re: [AMBER] Raja Pandian (Thu Jun 18 2009 - 05:35:10 PDT)
[AMBER] how to create prmtop and inpcrd files for covalent neutral phenylalanine Madhurima Jana (Thu Jun 18 2009 - 05:39:03 PDT)
[AMBER] Sulfates parameterization for GAGs in GLYCAM_06 Sergey Samsonov (Thu Jun 18 2009 - 06:07:17 PDT)
[AMBER] Dyndom Chunliyan (Thu Jun 18 2009 - 08:12:44 PDT)
[AMBER] Fix Residue continued... Vishal Maingi (Thu Jun 18 2009 - 11:48:03 PDT)
- Re: [AMBER] Fix Residue continued... Carlos Simmerling (Thu Jun 18 2009 - 11:56:54 PDT)
[AMBER] residue KIRTANA S (Thu Jun 18 2009 - 12:59:50 PDT)
[AMBER] Re: R.E.D. error message FyD (Thu Jun 18 2009 - 13:13:41 PDT)
[AMBER] Postdoc position in biomolecular simulation Ivaylo, Ivanov (Thu Jun 18 2009 - 16:26:05 PDT)
[AMBER] From DLG to Antechamber Jack Shultz (Thu Jun 18 2009 - 17:04:15 PDT)
- Re: [AMBER] From DLG to Antechamber FyD (Fri Jun 19 2009 - 02:26:46 PDT)
  - Re: [AMBER] From DLG to Antechamber Jack Shultz (Fri Jun 19 2009 - 05:27:20 PDT)
- Re: [AMBER] From DLG to Antechamber gilbert.bluemarble.net (Fri Jun 19 2009 - 05:57:04 PDT)
  - Re: [AMBER] From DLG to Antechamber Jack Shultz (Fri Jun 19 2009 - 06:09:06 PDT)
    - Re: [AMBER] From DLG to Antechamber gilbert.bluemarble.net (Fri Jun 19 2009 - 07:17:09 PDT)
    - Re: [AMBER] From DLG to Antechamber Jack Shultz (Fri Jun 19 2009 - 07:21:37 PDT)
    - Re: [AMBER] From DLG to Antechamber Jack Shultz (Fri Jun 19 2009 - 07:34:33 PDT)
- Re: [AMBER] From DLG to Antechamber FyD (Fri Jun 19 2009 - 08:54:05 PDT)
[AMBER] Force field parameter for Unionized Phenylalanine HOOC-CH(NH2)-CH2-C6H5 Madhurima Jana (Thu Jun 18 2009 - 23:40:43 PDT)
- Re: [AMBER] Force field parameter for Unionized Phenylalanine HOOC-CH(NH2)-CH2-C6H5 FyD (Fri Jun 19 2009 - 01:47:39 PDT)
[AMBER] 2 restraints with different force constants Aust, Susanne (Fri Jun 19 2009 - 00:14:50 PDT)
- Re: [AMBER] 2 restraints with different force constants David A. Case (Fri Jun 19 2009 - 04:41:01 PDT)
AW: [AMBER] 2 restraints with different force constants Aust, Susanne (Fri Jun 19 2009 - 04:51:21 PDT)
- Re: [AMBER] 2 restraints with different force constants David A. Case (Fri Jun 19 2009 - 05:06:18 PDT)
[AMBER] methyl group at the N-terminal Francesca Poletti (Fri Jun 19 2009 - 05:03:56 PDT)
- Re: [AMBER] methyl group at the N-terminal FyD (Fri Jun 19 2009 - 05:12:36 PDT)
AW: [AMBER] 2 restraints with different force constants Aust, Susanne (Fri Jun 19 2009 - 05:39:34 PDT)
[AMBER] Re: residue KIRTANA S (Fri Jun 19 2009 - 08:03:31 PDT)
[AMBER] RED Geometry Calculation Error Brothers, Michael Charles (Fri Jun 19 2009 - 11:52:37 PDT)
- Re: [AMBER] RED Geometry Calculation Error FyD (Fri Jun 19 2009 - 12:19:00 PDT)
  - RE: [AMBER] RED Geometry Calculation Error Brothers, Michael Charles (Fri Jun 19 2009 - 14:10:12 PDT)
    - RE: [AMBER] RED Geometry Calculation Error FyD (Fri Jun 19 2009 - 23:41:46 PDT)
    - [AMBER] PTRAJ, rms for separated residues. Catein Catherine (Mon Jun 22 2009 - 02:20:36 PDT)
    - Re: [AMBER] PTRAJ, rms for separated residues. Germain Vallverdu (Mon Jun 22 2009 - 02:27:43 PDT)
[AMBER] atom type no recognize - xleap version 10 but fine in v 9 Peter Gannett (Fri Jun 19 2009 - 12:40:47 PDT)
- Re: [AMBER] atom type no recognize - xleap version 10 but fine in v 9 case (Sat Jun 20 2009 - 11:31:40 PDT)
[AMBER] PMEMD compilation manoj singh (Fri Jun 19 2009 - 15:49:31 PDT)
- RE: [AMBER] PMEMD compilation Ross Walker (Sat Jun 20 2009 - 10:36:14 PDT)
  - Re: [AMBER] PMEMD compilation manoj singh (Sat Jun 20 2009 - 21:05:44 PDT)
    - RE: [AMBER] PMEMD compilation Ross Walker (Sat Jun 20 2009 - 21:15:23 PDT)
    - Re: [AMBER] PMEMD compilation manoj singh (Sat Jun 20 2009 - 21:22:01 PDT)
    - RE: [AMBER] PMEMD compilation Ross Walker (Sat Jun 20 2009 - 21:32:18 PDT)
    - Re: [AMBER] PMEMD compilation manoj singh (Sat Jun 20 2009 - 21:30:17 PDT)
[AMBER] Hard limit in Amber10? Yang, Ping (Fri Jun 19 2009 - 17:21:14 PDT)
- RE: [AMBER] Hard limit in Amber10? Ross Walker (Sat Jun 20 2009 - 10:40:46 PDT)
- RE: [AMBER] Hard limit in Amber10? Yang, Ping (Sat Jun 20 2009 - 16:44:11 PDT)
  - RE: [AMBER] Hard limit in Amber10? Yang, Ping (Mon Jun 22 2009 - 18:52:39 PDT)
    - RE: [AMBER] Hard limit in Amber10? Ross Walker (Wed Jun 24 2009 - 09:02:17 PDT)
R: [AMBER] Amber10 Parallel Installation sgrignani.cerm.unifi.it (Sat Jun 20 2009 - 13:14:38 PDT)
Re: [AMBER] Amber10 Parallel Installation case (Sat Jun 20 2009 - 15:04:14 PDT)
[AMBER] Your private message from Vikas is about to expire Vikas S (Sat Jun 20 2009 - 23:41:57 PDT)
[AMBER] Reference Correction Mahmoud A. A. Ibrahim (Sun Jun 21 2009 - 13:11:34 PDT)
[AMBER] reclaiming space from amber10 installation Alan (Sun Jun 21 2009 - 15:04:53 PDT)
- [AMBER] correlation motion at production simulation period still changing. Is it normal? Catein Catherine (Mon Jun 22 2009 - 02:26:40 PDT)
- RE: [AMBER] reclaiming space from amber10 installation Ross Walker (Mon Jun 22 2009 - 18:26:36 PDT)
[AMBER] parameters Fe4S4 cluster KIRTANA S (Sun Jun 21 2009 - 19:30:08 PDT)
[AMBER] Atom Type List Javier Klett (Mon Jun 22 2009 - 02:54:43 PDT)
- Re: [AMBER] Atom Type List case (Mon Jun 22 2009 - 04:38:24 PDT)
  - Re: [Barracuda SPAM] Re: [AMBER] Atom Type List Javier Klett (Mon Jun 22 2009 - 09:34:43 PDT)
    - Re: [Barracuda SPAM] Re: [AMBER] Atom Type List Bill Ross (Mon Jun 22 2009 - 09:43:39 PDT)
[AMBER] About the Amber tutorial Aurum Bai (Mon Jun 22 2009 - 03:03:49 PDT)
[AMBER] About the "FATAL: Atom err!" Aurum Bai (Mon Jun 22 2009 - 03:12:23 PDT)
[AMBER] About the "FATAL: Atom err"! Aurum Bai (Mon Jun 22 2009 - 03:14:20 PDT)
- Re: [AMBER] About the "FATAL: Atom err"! case (Mon Jun 22 2009 - 04:47:59 PDT)
[AMBER] Error on equilibriation of Amber10 Masakazu SEKIJIMA (Mon Jun 22 2009 - 03:59:55 PDT)
- Re: [AMBER] Problems using nmode in NAB Andreas Svrcek-Seiler (Wed Jun 24 2009 - 01:52:30 PDT)
  - Re: [AMBER] Problems using nmode in NAB E.M. (Wed Jun 24 2009 - 02:09:44 PDT)
  - Re: [AMBER] Problems using nmode in NAB E.M. (Wed Jun 24 2009 - 21:15:38 PDT)
    - Re: [AMBER] Problems using nmode in NAB Andreas Svrcek-Seiler (Thu Jun 25 2009 - 06:03:15 PDT)
- [AMBER] Re: Error on equilibriation of Amber10 Masakazu SEKIJIMA (Thu Jun 25 2009 - 03:45:31 PDT)
  - Re: [AMBER] Re: Error on equilibriation of Amber10 case (Thu Jun 25 2009 - 05:07:20 PDT)
    - Re: [AMBER] Re: Error on equilibriation of Amber10 Masakazu SEKIJIMA (Thu Jun 25 2009 - 10:41:39 PDT)
    - Re: [AMBER] Re: Error on equilibriation of Amber10 case (Fri Jun 26 2009 - 05:17:42 PDT)
[AMBER] max atoms for antechamber Alan (Mon Jun 22 2009 - 05:37:39 PDT)
- Re: [AMBER] max atoms for antechamber case (Mon Jun 22 2009 - 05:48:43 PDT)
  - Re: [AMBER] max atoms for antechamber Alan (Mon Jun 22 2009 - 06:00:48 PDT)
[AMBER] making leap to recognize 5' phosphate Bala subramanian (Mon Jun 22 2009 - 06:45:43 PDT)
- Re: [AMBER] making leap to recognize 5' phosphate FyD (Tue Jun 23 2009 - 00:45:31 PDT)
  - Re: [AMBER] making leap to recognize 5' phosphate Bala subramanian (Tue Jun 23 2009 - 01:49:05 PDT)
    - Re: [AMBER] making leap to recognize 5' phosphate FyD (Tue Jun 23 2009 - 02:48:34 PDT)
- Re: [AMBER] making leap to recognize 5' phosphate FyD (Tue Jun 23 2009 - 23:02:42 PDT)
[AMBER] Re: Regd: Fe4S4 case (Mon Jun 22 2009 - 11:39:57 PDT)
RE: [Subject Filtered] Re: [AMBER] Amber10 Parallel Installation 8% Hopkins, Robert (Mon Jun 22 2009 - 12:54:17 PDT)
[AMBER] bad atom type: MN Edward M (Mon Jun 22 2009 - 16:10:54 PDT)
[AMBER] bad atom type: MN Edward M (Mon Jun 22 2009 - 16:12:09 PDT)
[AMBER] AMBER question: bad atom type: MN Edward M (Mon Jun 22 2009 - 20:05:51 PDT)
[AMBER] REMD Shaikh Abdul R S Ramaju (Mon Jun 22 2009 - 22:32:34 PDT)
- Re: [AMBER] REMD Carlos Simmerling (Tue Jun 23 2009 - 03:07:39 PDT)
[AMBER] guessing the charge of a small molecule Alan (Tue Jun 23 2009 - 01:06:51 PDT)
[AMBER] Compiling amber 9 with openMPI Myunggi Yi (Tue Jun 23 2009 - 06:31:58 PDT)
- Re: [AMBER] Compiling amber 9 with openMPI case (Tue Jun 23 2009 - 07:13:18 PDT)
  - Re: [AMBER] Compiling amber 9 with openMPI Myunggi Yi (Tue Jun 23 2009 - 11:11:46 PDT)
[AMBER] net charge Vishal Maingi (Tue Jun 23 2009 - 07:19:51 PDT)
- Re: [AMBER] net charge case (Tue Jun 23 2009 - 07:34:07 PDT)
[AMBER] SANDER BOMB in subroutine nonbond_list Siddharth Rastogi (Tue Jun 23 2009 - 09:39:58 PDT)
Re: [AMBER] SANDER BOMB in subroutine nonbond_list Bill Ross (Tue Jun 23 2009 - 09:54:30 PDT)
[AMBER] re: net charge Vishal Maingi (Tue Jun 23 2009 - 11:56:52 PDT)
- Re: [AMBER] re: net charge case (Tue Jun 23 2009 - 12:22:28 PDT)
  - Re: [AMBER] re: net charge Junmei Wang (Tue Jun 23 2009 - 13:41:24 PDT)
[AMBER] "loadoff tRNA.lib" in Leap Ju Zhang (Tue Jun 23 2009 - 13:55:25 PDT)
[AMBER] 2-step vs 3-step TI, and softcores question Jodi Hadden (Tue Jun 23 2009 - 15:00:02 PDT)
- Re: [AMBER] 2-step vs 3-step TI, and softcores question steinbrt.rci.rutgers.edu (Tue Jun 23 2009 - 15:27:46 PDT)
[AMBER] How to build amide bond etween two protein chains journal.update (Tue Jun 23 2009 - 21:36:07 PDT)
- Re: [AMBER] How to build amide bond etween two protein chains FyD (Tue Jun 23 2009 - 23:18:25 PDT)
[AMBER] error in tleap of AMBER 10 kureeckal ramesh (Tue Jun 23 2009 - 22:03:55 PDT)
- Re: [AMBER] error in tleap of AMBER 10 case (Thu Jun 25 2009 - 04:54:47 PDT)
[AMBER] Problems using nmode in NAB E.M. (Tue Jun 23 2009 - 23:05:50 PDT)
[AMBER] calculating the hydrogen bonding energy between the two molecule bharat lakhani (Wed Jun 24 2009 - 02:19:01 PDT)
[AMBER] Trying to patch amber 9 Jack Shultz (Wed Jun 24 2009 - 06:24:40 PDT)
- Re: [AMBER] Trying to patch amber 9 case (Wed Jun 24 2009 - 07:58:48 PDT)
  - Re: [AMBER] Trying to patch amber 9 Jack Shultz (Wed Jun 24 2009 - 08:18:23 PDT)
    - Re: [AMBER] Trying to patch amber 9 Jack Shultz (Wed Jun 24 2009 - 08:25:41 PDT)
[AMBER] Half charge reported during NN ? Marek Maly (Wed Jun 24 2009 - 09:33:54 PDT)
- Re: [AMBER] Half charge reported during NN ? case (Wed Jun 24 2009 - 10:31:45 PDT)
  - Re: [AMBER] Half charge reported during NN ? Marek Maly (Wed Jun 24 2009 - 10:43:26 PDT)
[AMBER] problem with parametrization janzso.brc.hu (Wed Jun 24 2009 - 11:24:45 PDT)
- RE: [AMBER] problem with parametrization Brothers, Michael Charles (Wed Jun 24 2009 - 11:34:16 PDT)
- Re: [AMBER] problem with parametrization FyD (Wed Jun 24 2009 - 22:15:23 PDT)
  - Re: [AMBER] problem with parametrization janzso.brc.hu (Thu Jun 25 2009 - 02:49:50 PDT)
- Re: [AMBER] problem with parametrization FyD (Thu Jun 25 2009 - 03:04:27 PDT)
  - Re: [AMBER] problem with parametrization janzso.brc.hu (Thu Jun 25 2009 - 04:40:35 PDT)
    - Re: [AMBER] problem with parametrization FyD (Thu Jun 25 2009 - 04:52:45 PDT)
    - Re: [AMBER] problem with parametrization janzso.brc.hu (Thu Jun 25 2009 - 05:04:27 PDT)
    - Re: [AMBER] problem with parametrization FyD (Thu Jun 25 2009 - 06:47:31 PDT)
    - Re: [AMBER] problem with parametrization janzso.brc.hu (Mon Jun 29 2009 - 02:30:50 PDT)
[AMBER] Amber tools 1.2 , Bug report (PTRAJ: dumpq with strip) Myunggi Yi (Wed Jun 24 2009 - 11:57:25 PDT)
[AMBER] NAB memory increase E.M. (Wed Jun 24 2009 - 13:12:09 PDT)
- Re: [AMBER] NAB memory increase case (Thu Jun 25 2009 - 04:33:03 PDT)
- Re: [AMBER] NAB memory increase Bill Ross (Thu Jun 25 2009 - 09:34:58 PDT)
[AMBER] setting atomic radii for GB version 7 Workalemhu Berhanu (Wed Jun 24 2009 - 20:12:55 PDT)
- Re: [AMBER] setting atomic radii for GB version 7 case (Thu Jun 25 2009 - 05:20:36 PDT)
Re: [AMBER] atomtypes in gaff FyD (Thu Jun 25 2009 - 01:55:03 PDT)
[AMBER] Re: question about ff FyD (Thu Jun 25 2009 - 02:12:40 PDT)
[AMBER] ADD SALT Rilei Yu (Thu Jun 25 2009 - 02:22:20 PDT)
- Re: [AMBER] ADD SALT Simon Becker (Thu Jun 25 2009 - 02:57:37 PDT)
AW: [AMBER] atomtypes in gaff Aust, Susanne (Thu Jun 25 2009 - 02:24:07 PDT)
- Re: AW: [AMBER] atomtypes in gaff FyD (Thu Jun 25 2009 - 03:32:33 PDT)
AW: AW: [AMBER] atomtypes in gaff Aust, Susanne (Thu Jun 25 2009 - 04:27:19 PDT)
- Re: AW: AW: [AMBER] atomtypes in gaff FyD (Thu Jun 25 2009 - 04:36:20 PDT)
- Re: [AMBER] atomtypes in gaff FyD (Thu Jun 25 2009 - 04:45:16 PDT)
[AMBER] PCA for CA of specific resiudes Patrick Gedeon (Thu Jun 25 2009 - 04:43:20 PDT)
- Re: [AMBER] PCA for CA of specific resiudes case (Thu Jun 25 2009 - 05:27:01 PDT)
AW: AW: AW: [AMBER] atomtypes in gaff Aust, Susanne (Thu Jun 25 2009 - 04:44:58 PDT)
AW: [AMBER] atomtypes in gaff Aust, Susanne (Thu Jun 25 2009 - 05:05:10 PDT)
- Re: AW: [AMBER] atomtypes in gaff FyD (Thu Jun 25 2009 - 23:56:35 PDT)
[AMBER] Error when installing amber11 on OpenSuse steinbrt.rci.rutgers.edu (Thu Jun 25 2009 - 05:19:59 PDT)
[AMBER] ADD SALT additional question Simon Becker (Thu Jun 25 2009 - 05:34:36 PDT)
- Re: [AMBER] ADD SALT additional question Vlad Cojocaru (Thu Jun 25 2009 - 07:51:54 PDT)
- Re: [AMBER] ADD SALT additional question Vlad Cojocaru (Thu Jun 25 2009 - 07:55:15 PDT)
[AMBER] ptraj clustering with sieve- unexpected Bus Error Rachel Rice (Thu Jun 25 2009 - 08:24:25 PDT)
- Re: [AMBER] ptraj clustering with sieve- unexpected Bus Error David Watson (Thu Jun 25 2009 - 11:53:16 PDT)
  - Re: [AMBER] ptraj clustering with sieve- unexpected Bus Error Rachel Rice (Thu Jun 25 2009 - 17:54:31 PDT)
    - Re: [AMBER] ptraj clustering with sieve- unexpected Bus Error David Watson (Thu Jun 25 2009 - 19:28:22 PDT)
    - Re: [AMBER] ptraj clustering with sieve- unexpected Bus Error Rachel Rice (Thu Jun 25 2009 - 19:36:06 PDT)
    - Re: [AMBER] ptraj clustering with sieve- unexpected Bus Error David Watson (Thu Jun 25 2009 - 19:51:11 PDT)
    - Re: [AMBER] ptraj clustering with sieve- unexpected Bus Error Rachel Rice (Thu Jun 25 2009 - 20:24:18 PDT)
    - Re: [AMBER] ptraj clustering with sieve- unexpected Bus Error David Watson (Fri Jun 26 2009 - 04:31:26 PDT)
    - Re: [AMBER] ptraj clustering with sieve- unexpected Bus Error Rachel Rice (Tue Jun 30 2009 - 08:06:03 PDT)
Re: AW: [AMBER] atomtypes in gaff Bill Ross (Thu Jun 25 2009 - 09:42:01 PDT)
[AMBER] Compiling and running NAB programs in parallel using MPI Kaushik Raha (Thu Jun 25 2009 - 14:36:35 PDT)
- Re: [AMBER] Compiling and running NAB programs in parallel using MPI case (Fri Jun 26 2009 - 06:19:04 PDT)
  - Re: [AMBER] Compiling and running NAB programs in parallel using MPI Kaushik Raha (Fri Jun 26 2009 - 08:12:11 PDT)
    - Re: [AMBER] Compiling and running NAB programs in parallel using MPI case (Mon Jun 29 2009 - 05:19:10 PDT)
    - Re: [AMBER] Compiling and running NAB programs in parallel using MPI Kaushik Raha (Tue Jun 30 2009 - 07:48:11 PDT)
    - Re: [AMBER] Compiling and running NAB programs in parallel using MPI case (Tue Jun 30 2009 - 09:02:57 PDT)
[AMBER] Thanks Simon and Vlad! Rilei Yu (Thu Jun 25 2009 - 16:32:35 PDT)
[AMBER] error in tleap of AMBER 10 kureeckal ramesh (Fri Jun 26 2009 - 00:10:56 PDT)
- Re: [AMBER] error in tleap of AMBER 10 case (Fri Jun 26 2009 - 05:09:58 PDT)
[AMBER] Box Center Jagan Mohan (Fri Jun 26 2009 - 01:02:05 PDT)
[AMBER] installation of RESP programm subarna thakur (Fri Jun 26 2009 - 01:52:57 PDT)
- Re: [AMBER] installation of RESP programm FyD (Fri Jun 26 2009 - 02:15:39 PDT)
[AMBER] Problem with radial distribution function aneesh cna (Fri Jun 26 2009 - 01:56:09 PDT)
[AMBER] query about the charge fitting procedure about C- and N-terminal residues Ye MEI (Fri Jun 26 2009 - 02:19:47 PDT)
- Re: [AMBER] query about the charge fitting procedure about C- and N-terminal residues FyD (Fri Jun 26 2009 - 02:41:52 PDT)
[AMBER] a method or program to try to guess the net charge of a small molecule Alan (Fri Jun 26 2009 - 03:00:48 PDT)
[AMBER] force field choice ahmed said (Fri Jun 26 2009 - 01:21:16 PDT)
[AMBER] NAB memory E.M. (Fri Jun 26 2009 - 11:06:41 PDT)
- Re: [AMBER] NAB memory case (Fri Jun 26 2009 - 11:42:03 PDT)
[AMBER] explicit solvent NMR refinement Sally Pias (Sun Jun 28 2009 - 01:46:56 PDT)
- Re: [AMBER] explicit solvent NMR refinement Carlos Simmerling (Sun Jun 28 2009 - 05:36:42 PDT)
- Re: [AMBER] explicit solvent NMR refinement case (Sun Jun 28 2009 - 06:19:11 PDT)
[AMBER] Velocity rescaling and ig... Cihan Aydin (Sun Jun 28 2009 - 07:52:30 PDT)
- Re: [AMBER] Velocity rescaling and ig... Carlos Simmerling (Sun Jun 28 2009 - 08:35:37 PDT)
  - Re: [AMBER] Velocity rescaling and ig... Cihan Aydin (Sun Jun 28 2009 - 09:08:32 PDT)
    - RE: [AMBER] Velocity rescaling and ig... Ross Walker (Sun Jun 28 2009 - 09:18:08 PDT)
    - RE: [AMBER] Velocity rescaling and ig... Cihan Aydin (Sun Jun 28 2009 - 09:22:29 PDT)
[AMBER] how to creat an mixture sovlent of hexane and water TaoPaul (Sun Jun 28 2009 - 08:58:19 PDT)
[AMBER] Analysis of the solt-bridge Rilei Yu (Sun Jun 28 2009 - 15:24:28 PDT)
- Re: [AMBER] Analysis of the solt-bridge Alessandro Nascimento (Mon Jun 29 2009 - 05:58:49 PDT)
  - Re: [AMBER] Analysis of the solt-bridge Rilei Yu (Mon Jun 29 2009 - 15:42:23 PDT)
[AMBER] Simulations including RNA-protein complexes... Cihan Aydin (Sun Jun 28 2009 - 15:29:10 PDT)
[AMBER] RESP Syed Tarique Moin (Mon Jun 29 2009 - 00:42:51 PDT)
- Re: [AMBER] RESP case (Mon Jun 29 2009 - 04:52:19 PDT)
[AMBER] Steps for NMR structure minimization Prem Prakash Pathak (Mon Jun 29 2009 - 07:09:34 PDT)
- Re: [AMBER] Steps for NMR structure minimization case (Wed Jul 01 2009 - 05:48:13 PDT)
[AMBER] steps for NMR structure minimization of protein Prem Prakash Pathak (Mon Jun 29 2009 - 07:12:40 PDT)
[AMBER] steps for NMR structure minimization of protein Prem Prakash Pathak (Mon Jun 29 2009 - 07:13:33 PDT)
[AMBER] problems with ptraj option IMAGE Antonija Tomić (Mon Jun 29 2009 - 07:48:54 PDT)
- Re: [AMBER] problems with ptraj option IMAGE Carlos Simmerling (Mon Jun 29 2009 - 08:00:59 PDT)
  - Re: [AMBER] problems with ptraj option IMAGE Antonija Tomić (Mon Jun 29 2009 - 08:27:54 PDT)
[AMBER] Regd: parameter Fe4S4 KIRTANA S (Mon Jun 29 2009 - 09:11:49 PDT)
- Re: [AMBER] Regd: parameter Fe4S4 FyD (Mon Jun 29 2009 - 12:03:22 PDT)
[AMBER] Nonstandard molecules simulated with parm99EP ? Marek Maly (Mon Jun 29 2009 - 10:06:27 PDT)
- Re: [AMBER] Nonstandard molecules simulated with parm99EP ? FyD (Mon Jun 29 2009 - 11:28:19 PDT)
  - Re: [AMBER] Nonstandard molecules simulated with parm99EP ? Marek Maly (Mon Jun 29 2009 - 13:48:52 PDT)
    - Re: [AMBER] Nonstandard molecules simulated with parm99EP ? FyD (Tue Jun 30 2009 - 00:31:53 PDT)
    - Re: [AMBER] Nonstandard molecules simulated with parm99EP ? case (Tue Jun 30 2009 - 09:19:00 PDT)
    - Re: [AMBER] Nonstandard molecules simulated with parm99EP ? Marek Maly (Wed Jul 01 2009 - 09:02:29 PDT)
    - Re: [AMBER] Nonstandard molecules simulated with parm99EP ? Marek Maly (Wed Jul 01 2009 - 08:47:04 PDT)
[AMBER] Fe-S topology subarna thakur (Mon Jun 29 2009 - 23:29:16 PDT)
- Re: [AMBER] Fe-S topology Markus Kaukonen (Tue Jun 30 2009 - 00:28:51 PDT)
  - Re: [AMBER] Fe-S topology case (Tue Jun 30 2009 - 10:45:27 PDT)
[AMBER] Saccharides chains termini Sergey Samsonov (Tue Jun 30 2009 - 07:32:53 PDT)
- Re: [AMBER] Saccharides chains termini Lachele Foley (Lists) (Tue Jun 30 2009 - 07:46:09 PDT)
- Re: [AMBER] Saccharides chains termini Karl Kirschner (Tue Jun 30 2009 - 07:57:46 PDT)
- Re: [AMBER] Saccharides chains termini FyD (Tue Jun 30 2009 - 08:47:04 PDT)
[AMBER] Partial charges of heme Justine Shaw Condo (Tue Jun 30 2009 - 11:28:11 PDT)
[AMBER] Fe and Mn simulations Alessandro Nascimento (Tue Jun 30 2009 - 13:22:14 PDT)
[AMBER] antechamber R. A. (Wed Jul 01 2009 - 02:17:51 PDT)
- Re: [AMBER] antechamber Alan (Wed Jul 01 2009 - 04:37:40 PDT)
  - Re: [AMBER] antechamber case (Wed Jul 01 2009 - 05:04:02 PDT)
  - Re: [AMBER] antechamber gilbert.bluemarble.net (Wed Jul 01 2009 - 05:11:17 PDT)
    - Re: [AMBER] antechamber FyD (Wed Jul 01 2009 - 05:26:39 PDT)
[AMBER] antechamber R. A. (Wed Jul 01 2009 - 02:19:54 PDT)
[AMBER] The problem of restart file Jeffrey (Wed Jul 01 2009 - 05:15:34 PDT)
- Re: [AMBER] The problem of restart file Carlos Simmerling (Wed Jul 01 2009 - 05:49:32 PDT)
- Re: [AMBER] The problem of restart file Jeffrey (Wed Jul 01 2009 - 07:07:08 PDT)
[AMBER] amber9 in fedora10 Bala subramanian (Wed Jul 01 2009 - 07:09:15 PDT)
- RE: [AMBER] amber9 in fedora10 Ross Walker (Wed Jul 01 2009 - 09:36:33 PDT)
  - Re: [AMBER] amber9 in fedora10 Bala subramanian (Thu Jul 02 2009 - 00:02:54 PDT)
    - Re: [AMBER] amber9 in fedora10 Bala subramanian (Thu Jul 02 2009 - 01:05:55 PDT)
[AMBER] pmemd/bintraj and ifort 10.1.0.21 Peter Varnai (Wed Jul 01 2009 - 11:28:30 PDT)
- Re: [AMBER] pmemd/bintraj and ifort 10.1.0.21 Robert Duke (Wed Jul 01 2009 - 11:54:52 PDT)
[AMBER] default integration scheme in 7 vs. 10 Paul Brandt (Wed Jul 01 2009 - 13:48:46 PDT)
- RE: [AMBER] default integration scheme in 7 vs. 10 Ross Walker (Wed Jul 01 2009 - 14:29:12 PDT)
- Re: [AMBER] default integration scheme in 7 vs. 10 case (Thu Jul 02 2009 - 04:37:17 PDT)
[AMBER] missing Halogen parameters (radii) for PBSA/GBSA calculations - PB Bomb in pb_aaradi(): No radius assigned for atom suhaib sh (Thu Jul 02 2009 - 06:18:05 PDT)
- 回复： [AMBER] missing Halogen parameters (radii) for PBSA/GBSA calculations - PB Bomb in pb_aaradi(): No radius assigned for atom 廖青华 (Thu Jul 02 2009 - 21:53:09 PDT)
[AMBER] MM-PBSA problem Giorgos Lamprinidis (Fri Jul 03 2009 - 06:50:36 PDT)
- Re: [AMBER] MM-PBSA problem Rubben Torella (Fri Jul 03 2009 - 06:57:09 PDT)
  - Re: [AMBER] MM-PBSA problem Giorgos Lamprinidis (Mon Jul 06 2009 - 01:07:14 PDT)
[AMBER] Re: Error in REDIII FyD (Fri Jul 03 2009 - 07:59:30 PDT)
[AMBER] calculation of the solvent accessibility Rilei Yu (Sat Jul 04 2009 - 01:54:23 PDT)
[AMBER] Boundary Condition Problem Pepe` Falahat (Sat Jul 04 2009 - 05:10:59 PDT)
- Re: [AMBER] Boundary Condition Problem case (Sat Jul 04 2009 - 06:45:45 PDT)
[AMBER] Leap Questions... Cihan Aydin (Sat Jul 04 2009 - 18:41:39 PDT)
- RE: [AMBER] Leap Questions... Ross Walker (Sun Jul 05 2009 - 21:01:34 PDT)
[AMBER] RED: Charge derivation of transtion state analogue manoj singh (Sat Jul 04 2009 - 23:10:57 PDT)
- Re: [AMBER] RED: Charge derivation of transtion state analogue FyD (Sun Jul 05 2009 - 02:39:13 PDT)
  - Re: [AMBER] RED: Charge derivation of transtion state analogue manoj singh (Sun Jul 05 2009 - 22:03:27 PDT)
    - Re: [AMBER] RED: Charge derivation of transtion state analogue FyD (Sun Jul 05 2009 - 23:29:11 PDT)
    - Re: [AMBER] RED: Charge derivation of transtion state analogue FyD (Sun Jul 05 2009 - 23:45:13 PDT)
[AMBER] Re: [q4md-fft] Charge calculation or non standard residue FyD (Sun Jul 05 2009 - 01:30:50 PDT)
[AMBER] RE: question about TUTORIAL A1 Ross Walker (Sun Jul 05 2009 - 19:29:38 PDT)
[AMBER] RE: ask for help (zn parameters) Ross Walker (Sun Jul 05 2009 - 19:56:50 PDT)
[AMBER] non standard residue Neha Gandhi (Mon Jul 06 2009 - 01:07:35 PDT)
- Re: [AMBER] non standard residue FyD (Tue Jul 07 2009 - 00:50:09 PDT)
- Re: [AMBER] non standard residue FyD (Mon Jul 13 2009 - 23:47:00 PDT)
- Re: [AMBER] non standard residue FyD (Tue Jul 14 2009 - 13:01:32 PDT)
[AMBER] Re: non aminoacid Residue Neha Gandhi (Mon Jul 06 2009 - 01:43:56 PDT)
- RE: [AMBER] Re: non aminoacid Residue Ross Walker (Mon Jul 06 2009 - 09:21:44 PDT)
[AMBER] unable to read MM charges Vishal Maingi (Mon Jul 06 2009 - 02:32:29 PDT)
[AMBER] need charges of FE-S cluster subarna thakur (Mon Jul 06 2009 - 03:44:05 PDT)
- Re: [AMBER] need charges of FE-S cluster case (Mon Jul 06 2009 - 05:35:19 PDT)
- Re: [AMBER] need charges of FE-S cluster Markus Kaukonen (Tue Jul 21 2009 - 11:50:39 PDT)
[AMBER] RE: question about TUTORIAL A1 Ross Walker (Mon Jul 06 2009 - 09:58:47 PDT)
[AMBER] unsolved verbosity when running minimization albert albert (Mon Jul 06 2009 - 12:09:02 PDT)
- Re: [AMBER] unsolved verbosity when running minimization Carlos Simmerling (Mon Jul 06 2009 - 12:28:08 PDT)
  - Re: [AMBER] unsolved verbosity when running minimization albert albert (Wed Jul 08 2009 - 04:10:43 PDT)
    - Re: [AMBER] unsolved verbosity when running minimization Carlos Simmerling (Wed Jul 08 2009 - 04:34:20 PDT)
[AMBER] Directory - GAFF Parameter File? Patrick Gedeon (Mon Jul 06 2009 - 16:31:49 PDT)
- [AMBER] Re: Directory - GAFF Parameter File? Patrick Gedeon (Mon Jul 06 2009 - 16:38:57 PDT)
[AMBER] RE: suggestions Ross Walker (Mon Jul 06 2009 - 18:01:51 PDT)
- Re: [AMBER] RE: suggestions Cihan Aydin (Mon Jul 06 2009 - 18:29:22 PDT)
[AMBER] Tleap input error, atom not found in residue template Brothers, Michael Charles (Mon Jul 06 2009 - 18:25:00 PDT)
- RE: [AMBER] Tleap input error, atom not found in residue template Ross Walker (Mon Jul 06 2009 - 21:28:46 PDT)
  - RE: [AMBER] Tleap input error, atom not found in residue template Brothers, Michael Charles (Tue Jul 07 2009 - 09:08:00 PDT)
  - [AMBER] Is rmsd ~ 3 A reasonable for a 4ns simulation? Catein Catherine (Wed Jul 08 2009 - 02:45:41 PDT)
[AMBER] unable to read MM charges (no reply yet) Vishal Maingi (Mon Jul 06 2009 - 20:32:07 PDT)
[AMBER] Principle Questions s_bill36.yahoo.co.uk (Tue Jul 07 2009 - 00:50:53 PDT)
- RE: [AMBER] Principle Questions Ross Walker (Tue Jul 07 2009 - 16:42:42 PDT)
[AMBER] DCCM Raja Pandian (Tue Jul 07 2009 - 04:05:20 PDT)
- RE: [AMBER] DCCM Duggan, Brendan M. (Wed Jul 15 2009 - 09:06:57 PDT)
[AMBER] Steered MD---more than one pair of atoms Hlengisizwe Ndlovu (Tue Jul 07 2009 - 06:27:59 PDT)
[AMBER] Zinc ion, help Mahmoud A. A. Ibrahim (Tue Jul 07 2009 - 07:26:48 PDT)
- Re: [AMBER] Zinc ion, help FyD (Wed Jul 08 2009 - 02:43:26 PDT)
[AMBER] rdparm bug? Paul Mortenson (Tue Jul 07 2009 - 09:29:44 PDT)
[AMBER] QMMM outupts Myeong Lee (Tue Jul 07 2009 - 10:13:27 PDT)
- Re: [AMBER] QMMM outupts Gustavo Seabra (Thu Jul 09 2009 - 09:58:30 PDT)
AW: [AMBER] Steered MD---more than one pair of atoms Aust, Susanne (Tue Jul 07 2009 - 23:47:56 PDT)
[AMBER] amber10 installation problem Lan JIN (Tue Jul 07 2009 - 23:49:05 PDT)
- Re: [AMBER] amber10 installation problem case (Wed Jul 08 2009 - 04:56:19 PDT)
[AMBER] Installing of amber10 Rilei Yu (Wed Jul 08 2009 - 01:34:24 PDT)
- Re: [AMBER] Installing of amber10 case (Wed Jul 08 2009 - 04:42:02 PDT)
[AMBER] installing of amber10 problem Rilei Yu (Wed Jul 08 2009 - 01:47:13 PDT)
[AMBER] MPI process terminated unexpectedly forrtl: error (69): process interrupted (SIGINT) Andrew Voronkov (Wed Jul 08 2009 - 02:39:03 PDT)
- Re: [AMBER] MPI process terminated unexpectedly forrtl: error (69): process interrupted (SIGINT) Andrew Voronkov (Wed Jul 08 2009 - 03:05:52 PDT)
- RE: [AMBER] MPI process terminated unexpectedly forrtl: error (69): process interrupted (SIGINT) Ross Walker (Wed Jul 08 2009 - 08:01:24 PDT)
[AMBER] suitable force field Jio M (Wed Jul 08 2009 - 03:06:35 PDT)
[AMBER] ouput trajectory of only CA atom Bala subramanian (Wed Jul 08 2009 - 06:24:56 PDT)
- Re: [AMBER] ouput trajectory of only CA atom Carlos Simmerling (Wed Jul 08 2009 - 07:41:25 PDT)
  - Re: [AMBER] ouput trajectory of only CA atom Bala subramanian (Wed Jul 08 2009 - 08:01:27 PDT)
    - Re: [AMBER] ouput trajectory of only CA atom Vlad Cojocaru (Wed Jul 08 2009 - 08:07:30 PDT)
    - Re: [AMBER] ouput trajectory of only CA atom Jordan Monnet (Wed Jul 08 2009 - 09:03:32 PDT)
[AMBER] ff parameters oguz gurbulak (Wed Jul 08 2009 - 07:35:40 PDT)
- Re: [AMBER] ff parameters case (Thu Jul 09 2009 - 06:23:31 PDT)
[AMBER] rmsd_dna balaji nagarajan (Wed Jul 08 2009 - 09:15:02 PDT)
- Re: [AMBER] rmsd_dna Carlos Simmerling (Wed Jul 08 2009 - 11:21:29 PDT)
  - RE: [AMBER] rmsd_dna balaji nagarajan (Wed Jul 08 2009 - 18:55:53 PDT)
[AMBER] bug in antechamber David Mobley (Wed Jul 08 2009 - 09:19:12 PDT)
- [AMBER] Re: bug in antechamber David Mobley (Mon Jul 13 2009 - 10:41:01 PDT)
[AMBER] suitable force field Jio M (Wed Jul 08 2009 - 00:14:12 PDT)
[AMBER] MM-PBSA delphi.crg and delphi.siz Manish Kumar (Wed Jul 08 2009 - 14:29:40 PDT)
- [AMBER] Re: MM-PBSA delphi.crg and delphi.siz Manish Kumar (Thu Jul 09 2009 - 20:33:01 PDT)
  - Re: [AMBER] Re: MM-PBSA delphi.crg and delphi.siz suhaib sh (Fri Jul 10 2009 - 07:17:52 PDT)
  - Re: [AMBER] Re: MM-PBSA delphi.crg and delphi.siz Ray Luo (Fri Jul 10 2009 - 09:32:18 PDT)
    - Re: [AMBER] Re: MM-PBSA delphi.crg and delphi.siz Manish Kumar (Sun Jul 19 2009 - 12:36:35 PDT)
    - Re: [AMBER] Re: MM-PBSA delphi.crg and delphi.siz Ray Luo (Sun Jul 19 2009 - 15:45:29 PDT)
    - Re: [AMBER] Re: MM-PBSA delphi.crg and delphi.siz Manish Kumar (Mon Jul 20 2009 - 14:11:20 PDT)
    - Re: [AMBER] Re: MM-PBSA delphi.crg and delphi.siz Ray Luo (Tue Jul 21 2009 - 07:24:40 PDT)
    - Re: [AMBER] Re: MM-PBSA delphi.crg and delphi.siz Manish Kumar (Thu Jul 23 2009 - 00:10:51 PDT)
    - [AMBER] MM-PBSA cannot finish without error message. Catein Catherine (Thu Jul 23 2009 - 02:57:00 PDT)
[AMBER] Acetylate and Amidate Alison Saunders (Wed Jul 08 2009 - 15:19:44 PDT)
- Re: [AMBER] Acetylate and Amidate Carlos Simmerling (Wed Jul 08 2009 - 15:22:58 PDT)
  - Re: [AMBER] Acetylate and Amidate Alison Saunders (Wed Jul 08 2009 - 15:47:59 PDT)
    - Re: [AMBER] Acetylate and Amidate Carlos Simmerling (Thu Jul 09 2009 - 04:52:28 PDT)
- Re: [AMBER] Acetylate and Amidate Bill Ross (Wed Jul 08 2009 - 16:13:09 PDT)
[AMBER] rmsd_ptraj balaji nagarajan (Wed Jul 08 2009 - 21:19:56 PDT)
- RE: [AMBER] rmsd_ptraj Ross Walker (Wed Jul 08 2009 - 21:35:59 PDT)
  - RE: [AMBER] rmsd_ptraj balaji nagarajan (Wed Jul 08 2009 - 22:50:10 PDT)
    - RE: [AMBER] rmsd_ptraj Thomas Cheatham (Thu Jul 09 2009 - 00:08:53 PDT)
[AMBER] charged or not s. Bill (Thu Jul 09 2009 - 05:33:05 PDT)
- Re: [AMBER] charged or not case (Thu Jul 09 2009 - 08:10:14 PDT)
[AMBER] Antechamber prep question Andrew Olson (Thu Jul 09 2009 - 07:39:25 PDT)
- Re: [AMBER] Antechamber prep question case (Thu Jul 09 2009 - 08:16:17 PDT)
- Re: [AMBER] Antechamber prep question Andrew Olson (Thu Jul 09 2009 - 08:22:18 PDT)
  - Re: [AMBER] Antechamber prep question case (Thu Jul 09 2009 - 09:48:44 PDT)
- Re: [AMBER] Antechamber prep question Andrew Olson (Thu Jul 09 2009 - 10:00:19 PDT)
  - Re: [AMBER] Antechamber prep question case (Thu Jul 09 2009 - 11:54:44 PDT)
    - Re: [AMBER] Antechamber prep question FyD (Thu Jul 09 2009 - 22:52:12 PDT)
    - Re: [AMBER] Antechamber prep question gilbert.bluemarble.net (Fri Jul 10 2009 - 06:10:32 PDT)
- Re: [AMBER] Antechamber prep question Andrew Olson (Fri Jul 10 2009 - 06:33:09 PDT)
  - Re: [AMBER] Antechamber prep question FyD (Fri Jul 10 2009 - 08:24:08 PDT)
[AMBER] Re: pls help and suggest Gustavo Seabra (Thu Jul 09 2009 - 09:14:42 PDT)
- Fw: [AMBER] Re: pls help and suggest Vishal Maingi (Thu Jul 09 2009 - 11:45:21 PDT)
  - Re: Fw: [AMBER] Re: pls help and suggest Gustavo Seabra (Fri Jul 17 2009 - 09:50:59 PDT)
[AMBER] reference re. determining size of timestep Paul Brandt (Thu Jul 09 2009 - 11:07:50 PDT)
- Re: [AMBER] reference re. determining size of timestep Gustavo Seabra (Fri Jul 17 2009 - 09:53:46 PDT)
[AMBER] AMBER windows version ? Siddharth Rastogi (Thu Jul 09 2009 - 14:14:05 PDT)
- RE: [AMBER] AMBER windows version ? Ross Walker (Thu Jul 09 2009 - 15:45:49 PDT)
  - Re: [AMBER] AMBER windows version ? Siddharth Rastogi (Thu Jul 09 2009 - 16:17:33 PDT)
[AMBER] question of mm_pbsa 廖青华 (Thu Jul 09 2009 - 18:49:40 PDT)
- Re: [AMBER] question of mm_pbsa Hannes Kopitz (Fri Jul 10 2009 - 02:36:44 PDT)
  - 回复： [AMBER] question of mm_pbsa 廖青华 (Fri Jul 10 2009 - 17:50:55 PDT)
  - 回复： [AMBER] question of mm_pbsa 廖青华 (Fri Jul 10 2009 - 18:22:25 PDT)
- Re: [AMBER] question of mm_pbsa Ray Luo (Fri Jul 10 2009 - 09:47:12 PDT)
  - 回复： [AMBER] question of mm_pbsa 廖青华 (Sat Jul 11 2009 - 17:03:33 PDT)
[AMBER] unexplained blow-up at restart Sally Pias (Fri Jul 10 2009 - 01:02:42 PDT)
- Re: [AMBER] unexplained blow-up at restart Carlos Simmerling (Fri Jul 10 2009 - 03:55:51 PDT)
  - Re: [AMBER] unexplained blow-up at restart Sally Pias (Fri Jul 10 2009 - 08:29:01 PDT)
    - Re: [AMBER] unexplained blow-up at restart Sally Pias (Fri Jul 10 2009 - 09:31:59 PDT)
    - Re: [AMBER] unexplained blow-up at restart Carlos Simmerling (Fri Jul 10 2009 - 10:02:39 PDT)
    - Re: [AMBER] unexplained blow-up at restart Sally Pias (Fri Jul 10 2009 - 10:20:27 PDT)
    - Re: [AMBER] unexplained blow-up at restart Carlos Simmerling (Fri Jul 10 2009 - 10:25:10 PDT)
    - Re: [AMBER] unexplained blow-up at restart Carlos Simmerling (Fri Jul 10 2009 - 10:58:15 PDT)
    - Re: [AMBER] unexplained blow-up at restart Sally Pias (Fri Jul 10 2009 - 11:59:24 PDT)
    - Re: [AMBER] unexplained blow-up at restart Sally Pias (Mon Jul 13 2009 - 00:01:29 PDT)
    - Re: [AMBER] unexplained blow-up at restart Carlos Simmerling (Mon Jul 13 2009 - 03:24:23 PDT)
    - Re: [AMBER] unexplained blow-up at restart Sally Pias (Mon Jul 13 2009 - 09:11:08 PDT)
    - Re: [AMBER] unexplained blow-up at restart case (Mon Jul 13 2009 - 09:51:46 PDT)
- Re: [AMBER] unexplained blow-up at restart Simon Becker (Fri Jul 10 2009 - 06:24:13 PDT)
[AMBER] Restrained backbone conformation MD simulation" Prem Prakash Pathak (Fri Jul 10 2009 - 04:27:38 PDT)
- Re: [AMBER] Restrained backbone conformation MD simulation" Carlos Simmerling (Fri Jul 10 2009 - 04:47:20 PDT)
[AMBER] Manganese bondi radii Chunliyan (Fri Jul 10 2009 - 06:39:51 PDT)
[AMBER] Manganese Chunliyan (Fri Jul 10 2009 - 06:39:51 PDT)
[AMBER] manganese bondi radii for mm_pbsa calculation Chunliyan (Fri Jul 10 2009 - 06:39:51 PDT)
[AMBER] radius for Manganese ion Chunliyan (Fri Jul 10 2009 - 06:39:51 PDT)
[AMBER] Manganese bondi radii for mm/pbsa calculation Chunliyan (Fri Jul 10 2009 - 06:39:51 PDT)
[AMBER] EPtot for Alpha-L- methyl fucose Sushil Mishra (Fri Jul 10 2009 - 06:47:26 PDT)
- Re: [AMBER] EPtot for Alpha-L- methyl fucose Carlos Simmerling (Fri Jul 10 2009 - 06:57:34 PDT)
  - Re: [AMBER] EPtot for Alpha-L- methyl fucose Sushil Mishra (Fri Jul 10 2009 - 07:12:28 PDT)
[AMBER] Regarding Running QM/MM NEB with PM3-PDDG using Amber10 Keith Van Nostrand (Fri Jul 10 2009 - 08:27:12 PDT)
- RE: [AMBER] Regarding Running QM/MM NEB with PM3-PDDG using Amber10 Ross Walker (Fri Jul 10 2009 - 09:21:11 PDT)
  - Re: [AMBER] Regarding Running QM/MM NEB with PM3-PDDG using Amber10 Keith Van Nostrand (Thu Jul 16 2009 - 14:08:04 PDT)
    - RE: [AMBER] Regarding Running QM/MM NEB with PM3-PDDG using Amber10 Ross Walker (Thu Jul 16 2009 - 20:34:13 PDT)
    - Re: [AMBER] Regarding Running QM/MM NEB with PM3-PDDG using Amber10 Keith Van Nostrand (Wed Jul 22 2009 - 08:58:08 PDT)
[AMBER] implicit solvent (GB version2) MD simulation workalemahu berhanu (Fri Jul 10 2009 - 08:53:47 PDT)
- Re: [AMBER] implicit solvent (GB version2) MD simulation Carlos Simmerling (Fri Jul 10 2009 - 08:57:57 PDT)
[AMBER] Need help for PMEMD 10 installation Jun Dong (Fri Jul 10 2009 - 09:05:49 PDT)
- RE: [AMBER] Need help for PMEMD 10 installation Ross Walker (Fri Jul 10 2009 - 09:26:29 PDT)
  - RE: [AMBER] Need help for PMEMD 10 installation Jun Dong (Fri Jul 10 2009 - 10:25:03 PDT)
    - RE: [AMBER] Need help for PMEMD 10 installation Ross Walker (Fri Jul 10 2009 - 11:52:13 PDT)
    - RE: [AMBER] Need help for PMEMD 10 installation Jun Dong (Mon Jul 13 2009 - 11:10:34 PDT)
    - RE: [AMBER] Need help for PMEMD 10 installation Ross Walker (Mon Jul 13 2009 - 12:18:26 PDT)
    - Re: [AMBER] Need help for PMEMD 10 installation Giorgos Lamprinidis (Tue Jul 14 2009 - 00:29:09 PDT)
- Re: [AMBER] Need help for PMEMD 10 installation Robert Duke (Tue Jul 14 2009 - 04:50:26 PDT)
[AMBER] problem with energy calculations Thomas Lake (Fri Jul 10 2009 - 09:13:55 PDT)
- Re: [AMBER] problem with energy calculations Carlos Simmerling (Fri Jul 10 2009 - 10:25:56 PDT)
  - RE: [AMBER] problem with energy calculations Lake, Thomas (Sun Jul 12 2009 - 06:35:33 PDT)
    - Re: [AMBER] problem with energy calculations Carlos Simmerling (Sun Jul 12 2009 - 06:42:35 PDT)
    - Re: [AMBER] problem with energy calculations Thomas Lake (Sun Jul 12 2009 - 07:10:58 PDT)
    - Re: [AMBER] problem with energy calculations Carlos Simmerling (Sun Jul 12 2009 - 07:15:39 PDT)
TMD: was: Re: [AMBER] charges in topology file Carlos Simmerling (Fri Jul 10 2009 - 09:36:30 PDT)
[AMBER] Peptide bond broken Syed Tarique Moin (Fri Jul 10 2009 - 11:19:02 PDT)
- Re: [AMBER] Peptide bond broken FyD (Fri Jul 10 2009 - 23:58:06 PDT)
- Re: [AMBER] Peptide bond broken case (Sun Jul 12 2009 - 19:35:35 PDT)
  - Re: [AMBER] Peptide bond broken Shubhra Gupta (Sun Jul 12 2009 - 21:17:31 PDT)
- Re: [AMBER] Peptide bond broken Syed Tarique Moin (Mon Jul 13 2009 - 06:20:02 PDT)
[AMBER] calculation of binding energy for lectin and fucuse.. Sushil Mishra (Fri Jul 10 2009 - 11:26:20 PDT)
[AMBER] ligand/protein minimization Andrew Olson (Fri Jul 10 2009 - 14:00:26 PDT)
- Re: [AMBER] ligand/protein minimization case (Sun Jul 12 2009 - 19:32:29 PDT)
- Re: [AMBER] ligand/protein minimization Andrew Olson (Mon Jul 13 2009 - 08:53:11 PDT)
  - Re: [AMBER] ligand/protein minimization case (Mon Jul 13 2009 - 09:29:06 PDT)
- Re: [AMBER] ligand/protein minimization Andrew Olson (Mon Jul 13 2009 - 10:10:18 PDT)
[AMBER] R.E.D intra-mcc and reorientation Ganesh Krishnan (Fri Jul 10 2009 - 15:00:35 PDT)
- Re: [AMBER] R.E.D intra-mcc and reorientation FyD (Sat Jul 11 2009 - 01:05:56 PDT)
  - Re: [AMBER] R.E.D intra-mcc and reorientation Ganesh Krishnan (Sat Jul 11 2009 - 15:56:18 PDT)
[AMBER] Syntax Bellymask Brothers, Michael Charles (Fri Jul 10 2009 - 16:59:01 PDT)
[AMBER] TMD: solvation and equilibration questions Jeffrey (Fri Jul 10 2009 - 18:07:55 PDT)
[AMBER] How to fix specific atoms? (not residue) Myeong Lee (Sat Jul 11 2009 - 04:46:06 PDT)
- Re: [AMBER] How to fix specific atoms? (not residue) Tom Joseph (Sat Jul 11 2009 - 15:01:04 PDT)
[AMBER] problem with the energetics of the system Mahmoud A. A. Ibrahim (Sat Jul 11 2009 - 16:23:13 PDT)
- Re: [AMBER] problem with the energetics of the system Ross Walker (Sat Jul 11 2009 - 16:52:42 PDT)
  - Re: [AMBER] problem with the energetics of the system Mahmoud A. A. Ibrahim (Sun Jul 12 2009 - 03:37:37 PDT)
[AMBER] amber dihedral format s. Bill (Sun Jul 12 2009 - 07:05:23 PDT)
- Re: [AMBER] amber dihedral format case (Sun Jul 12 2009 - 14:49:12 PDT)
[AMBER] help needed for HID s. Bill (Sun Jul 12 2009 - 11:16:08 PDT)
- Re: [AMBER] help needed for HID Marius Retegan (Sun Jul 12 2009 - 11:24:40 PDT)
- Re: [AMBER] help needed for HID FyD (Mon Jul 13 2009 - 13:27:13 PDT)
[AMBER] Amber10, Serial compilation with ifort Aldo Humberto Romero (Sun Jul 12 2009 - 13:57:40 PDT)
- RE: [AMBER] Amber10, Serial compilation with ifort Ross Walker (Sun Jul 12 2009 - 14:41:07 PDT)
[AMBER] ptraj mask selection Patrick Gedeon (Sun Jul 12 2009 - 20:45:56 PDT)
- Re: [AMBER] ptraj mask selection Jianyin Shao (Mon Jul 13 2009 - 10:57:23 PDT)
  - Re: [AMBER] ptraj mask selection case (Mon Jul 13 2009 - 11:10:46 PDT)
    - Re: [AMBER] ptraj mask selection Jianyin Shao (Mon Jul 13 2009 - 12:02:03 PDT)
    - Re: [AMBER] ptraj mask selection Patrick Gedeon (Mon Jul 13 2009 - 12:58:18 PDT)
[AMBER] Exclamation marks in trajectory Hugh Heldenbrand (Mon Jul 13 2009 - 08:16:26 PDT)
- RE: [AMBER] Exclamation marks in trajectory Ross Walker (Mon Jul 13 2009 - 11:13:17 PDT)
  - Re: [AMBER] Exclamation marks in trajectory Hugh Heldenbrand (Mon Jul 13 2009 - 11:52:37 PDT)
    - RE: [AMBER] Exclamation marks in trajectory Ross Walker (Mon Jul 13 2009 - 12:20:37 PDT)
[AMBER] Re: reference re. size of dt case (Mon Jul 13 2009 - 09:56:46 PDT)
[AMBER] Trouble saving amberparm files Alison Saunders (Mon Jul 13 2009 - 10:07:28 PDT)
- Re: [AMBER] Trouble saving amberparm files Tom Joseph (Mon Jul 13 2009 - 13:16:27 PDT)
  - Re: [AMBER] Trouble saving amberparm files Alison Saunders (Mon Jul 13 2009 - 14:06:12 PDT)
    - Re: [AMBER] Trouble saving amberparm files Tom Joseph (Mon Jul 13 2009 - 14:13:14 PDT)
    - Re: [AMBER] Trouble saving amberparm files Tom Joseph (Mon Jul 13 2009 - 14:14:39 PDT)
    - Re: [AMBER] Trouble saving amberparm files Alison Saunders (Mon Jul 13 2009 - 14:43:40 PDT)
[AMBER] (no subject) Beale, John (Mon Jul 13 2009 - 10:35:46 PDT)
[AMBER] GAFF and NME, ACE terminal res Jio M (Mon Jul 13 2009 - 13:51:06 PDT)
- Re: [AMBER] GAFF and NME, ACE terminal res FyD (Tue Jul 14 2009 - 00:40:00 PDT)
  - Re: [AMBER] GAFF and NME, ACE terminal res Jio M (Wed Jul 15 2009 - 21:29:08 PDT)
    - Re: [AMBER] GAFF and NME, ACE terminal res FyD (Wed Jul 15 2009 - 23:25:03 PDT)
[AMBER] Problem with amber9 installation moitrayee.mbu.iisc.ernet.in (Mon Jul 13 2009 - 13:31:18 PDT)
- RE: [AMBER] Problem with amber9 installation Ross Walker (Mon Jul 13 2009 - 20:34:54 PDT)
  - RE: [AMBER] Problem with amber9 installation moitrayee.mbu.iisc.ernet.in (Tue Jul 14 2009 - 00:02:39 PDT)
[AMBER] Re: Request to mailing list AMBER rejected E.M. (Mon Jul 13 2009 - 20:37:46 PDT)
[AMBER] mpirun noticed that process rank 1 ... on signal 1 (Hangup). Naser Alijabbari (Tue Jul 14 2009 - 03:41:39 PDT)
- [AMBER] Re: mpirun noticed that process rank 1 ... on signal 1 (Hangup). Naser Alijabbari (Tue Jul 14 2009 - 03:49:14 PDT)
  - RE: [AMBER] Re: mpirun noticed that process rank 1 ... on signal 1 (Hangup). Ross Walker (Tue Jul 14 2009 - 05:33:49 PDT)
    - Re: [AMBER] Re: mpirun noticed that process rank 1 ... on signal 1 (Hangup). Naser Alijabbari (Tue Jul 14 2009 - 09:30:55 PDT)
[AMBER] RE: pmemd parallel Ross Walker (Tue Jul 14 2009 - 05:24:06 PDT)
- Re: [AMBER] RE: pmemd parallel Jun Dong (Wed Jul 15 2009 - 08:00:49 PDT)
[AMBER] Could not find bond parameter for O2 - ca Yogesh Aher (Tue Jul 14 2009 - 05:53:35 PDT)
- Re: [AMBER] Could not find bond parameter for O2 - ca case (Tue Jul 14 2009 - 20:28:02 PDT)
  - Re: [AMBER] Could not find bond parameter for O2 - ca Yogesh Aher (Thu Jul 16 2009 - 23:37:52 PDT)
[AMBER] Molecular Modeling Workshop and Model(l)ing'09 in Erlangen, Germany Harald Lanig (Tue Jul 14 2009 - 07:02:16 PDT)
[AMBER] Holding ligand rigid for minimization Andrew Olson (Tue Jul 14 2009 - 08:14:38 PDT)
[AMBER] Holding ligand rigid for minimization Andrew Olson (Tue Jul 14 2009 - 08:23:01 PDT)
- Re: [AMBER] Holding ligand rigid for minimization Andrew Olson (Tue Jul 14 2009 - 11:23:31 PDT)
[AMBER] PMEMD in a Cygwin Environment Hopkins, Robert (Tue Jul 14 2009 - 12:48:41 PDT)
- Re: [AMBER] PMEMD in a Cygwin Environment Robert Duke (Tue Jul 14 2009 - 13:16:46 PDT)
[AMBER] Counterion release and Free energy of binding ? Marek Maly (Tue Jul 14 2009 - 15:27:18 PDT)
- Re: [AMBER] Counterion release and Free energy of binding ? case (Tue Jul 14 2009 - 20:10:18 PDT)
  - Re: [AMBER] Counterion release and Free energy of binding ? Marek Maly (Fri Jul 17 2009 - 04:10:40 PDT)
[AMBER] Equilibrium water density Myeong Lee (Wed Jul 15 2009 - 01:58:52 PDT)
- Re: [AMBER] Equilibrium water density case (Wed Jul 15 2009 - 12:53:54 PDT)
[AMBER] Alpha-L-Methys Fucose structure problem bond 0fA.d.C1 OME.d.O "S" Sushil Mishra (Wed Jul 15 2009 - 03:36:26 PDT)
- Re: [AMBER] Alpha-L-Methys Fucose structure problem bond 0fA.d.C1 OME.d.O "S" Shubhra Gupta (Wed Jul 15 2009 - 05:38:34 PDT)
  - Re: [AMBER] Alpha-L-Methys Fucose structure problem bond 0fA.d.C1 OME.d.O "S" Sushil Mishra (Wed Jul 15 2009 - 06:58:13 PDT)
- Re: [AMBER] Alpha-L-Methys Fucose structure problem bond 0fA.d.C1 OME.d.O "S" Bill Ross (Wed Jul 15 2009 - 09:53:41 PDT)
[AMBER] Please help me out bharat lakhani (Wed Jul 15 2009 - 03:43:21 PDT)
- Re: [AMBER] Please help me out case (Wed Jul 15 2009 - 12:55:21 PDT)
[AMBER] R.E.D. help please s. Bill (Wed Jul 15 2009 - 07:11:46 PDT)
- Re: [AMBER] R.E.D. help please FyD (Wed Jul 15 2009 - 09:35:57 PDT)
[AMBER] position v time graph Shozeb Haider (Wed Jul 15 2009 - 11:21:35 PDT)
[AMBER] Can I get the torsion angle between base-pairs using ptraj ? Myeong Lee (Wed Jul 15 2009 - 14:51:02 PDT)
- Re: [AMBER] Can I get the torsion angle between base-pairs using ptraj ? Jordan Monnet (Wed Jul 15 2009 - 15:56:12 PDT)
[AMBER] different results for antechamber/mopac for the same input Alan (Wed Jul 15 2009 - 15:05:07 PDT)
- Re: [AMBER] different results for antechamber/mopac for the same input case (Thu Jul 16 2009 - 04:30:08 PDT)
[AMBER] ptraj - cluster Cihan Aydin (Wed Jul 15 2009 - 22:55:07 PDT)
- RE: [AMBER] ptraj - cluster Wei Huang (Fri Jul 17 2009 - 05:34:00 PDT)
  - RE: [AMBER] ptraj - cluster Cihan Aydin (Fri Jul 17 2009 - 07:22:37 PDT)
[AMBER] ptraj-radial distribution function Nancy (Wed Jul 15 2009 - 23:34:12 PDT)
- Re: [AMBER] ptraj-radial distribution function Christof Jaeger (Thu Jul 16 2009 - 01:22:02 PDT)
[AMBER] questions about RESP Jeffrey (Wed Jul 15 2009 - 23:57:28 PDT)
- Re: [AMBER] questions about RESP FyD (Thu Jul 16 2009 - 07:27:44 PDT)
- Re: [AMBER] questions about RESP Jeffrey (Mon Jul 20 2009 - 00:42:29 PDT)
  - Re: [AMBER] questions about RESP FyD (Mon Jul 20 2009 - 13:46:04 PDT)
- Re: [AMBER] questions about RESP Jeffrey (Thu Jul 23 2009 - 05:51:34 PDT)
  - Re: [AMBER] questions about RESP FyD (Thu Jul 23 2009 - 10:49:23 PDT)
    - Re: [AMBER] xleap installation error Bokun Cho (Sun Aug 02 2009 - 22:18:00 PDT)
    - Re: [AMBER] xleap installation error Scott Brozell (Mon Aug 03 2009 - 09:57:18 PDT)
[AMBER] carbonic anhydrase (CA) simulation vhakkim boy (Thu Jul 16 2009 - 00:03:23 PDT)
- Re: [AMBER] carbonic anhydrase (CA) simulation case (Thu Jul 16 2009 - 04:36:17 PDT)
[AMBER] command for RESP fitting bharat lakhani (Thu Jul 16 2009 - 00:10:33 PDT)
- Re: [AMBER] command for RESP fitting FyD (Thu Jul 16 2009 - 07:34:28 PDT)
  - Re: [AMBER] command for RESP fitting bharat lakhani (Mon Jul 20 2009 - 00:01:23 PDT)
[AMBER] query regarding FE4S4 subarna thakur (Thu Jul 16 2009 - 00:14:27 PDT)
- Re: [AMBER] query regarding FE4S4 case (Thu Jul 16 2009 - 04:45:06 PDT)
[AMBER] Coordinate resetting (SHAKE) cannot be accomplished, Zhongjie Liang (Thu Jul 16 2009 - 01:37:29 PDT)
- Re: [AMBER] Coordinate resetting (SHAKE) cannot be accomplished, steinbrt.rci.rutgers.edu (Thu Jul 16 2009 - 02:01:15 PDT)
  - 答复: [AMBER] Coordinate resetting (SHAKE) cannot be accomplished, Zhongjie Liang (Thu Jul 16 2009 - 02:16:02 PDT)
[AMBER] IDIVF and PN s. Bill (Thu Jul 16 2009 - 05:11:27 PDT)
- RE: [AMBER] IDIVF and PN Ross Walker (Thu Jul 16 2009 - 20:40:11 PDT)
[AMBER] production phase s. Bill (Thu Jul 16 2009 - 05:18:25 PDT)
- RE: [AMBER] production phase Ross Walker (Thu Jul 16 2009 - 20:56:13 PDT)
[AMBER] vlimit exceeded....nscu_SMD!! Hlengisizwe Ndlovu (Thu Jul 16 2009 - 05:53:50 PDT)
[AMBER] Disappearing common atoms in Amber 10 with TI Khavrutskii, Ilja (Thu Jul 16 2009 - 06:38:43 PDT)
- Re: [AMBER] Disappearing common atoms in Amber 10 with TI steinbrt.rci.rutgers.edu (Thu Jul 16 2009 - 07:09:39 PDT)
  - Re: [AMBER] Disappearing common atoms in Amber 10 with TI Khavrutskii, Ilja (Thu Jul 16 2009 - 14:02:10 PDT)
    - Re: [AMBER] Disappearing common atoms in Amber 10 with TI steinbrt.rci.rutgers.edu (Fri Jul 17 2009 - 01:53:19 PDT)
    - Re: [AMBER] Disappearing common atoms in Amber 10 with TI case (Fri Jul 17 2009 - 04:41:39 PDT)
    - Re: [AMBER] Disappearing common atoms in Amber 10 with TI Khavrutskii, Ilja (Mon Jul 20 2009 - 04:46:38 PDT)
    - Re: [AMBER] Disappearing common atoms in Amber 10 with TI steinbrt.rci.rutgers.edu (Mon Jul 20 2009 - 05:05:24 PDT)
[AMBER] ntt=3 and ibelly=1 Kristina Furse (Thu Jul 16 2009 - 09:07:23 PDT)
- RE: [AMBER] ntt=3 and ibelly=1 Ross Walker (Thu Jul 16 2009 - 20:44:47 PDT)
  - RE: [AMBER] ntt=3 and ibelly=1 Kristina Furse (Fri Jul 17 2009 - 09:41:29 PDT)
[AMBER] amino acids caps for truncated proteins Andrew Voronkov (Thu Jul 16 2009 - 09:31:18 PDT)
- Re: [AMBER] amino acids caps for truncated proteins FyD (Thu Jul 16 2009 - 09:58:32 PDT)
[AMBER] Umbrella Sampling Hemant Kumar (Thu Jul 16 2009 - 11:01:40 PDT)
- Re: [AMBER] Umbrella Sampling case (Thu Jul 16 2009 - 13:03:29 PDT)
- RE: [AMBER] Umbrella Sampling Seetin, Matthew (Thu Jul 16 2009 - 13:13:59 PDT)
  - RE: [AMBER] Umbrella Sampling Hemant Kumar (Sat Jul 18 2009 - 12:28:19 PDT)
[AMBER] amber10 parallel compiling error Nam Kim (Thu Jul 16 2009 - 17:50:57 PDT)
- RE: [AMBER] amber10 parallel compiling error Ross Walker (Thu Jul 16 2009 - 20:43:15 PDT)
- Re: [AMBER] amber10 parallel compiling error nam kim (Mon Jul 20 2009 - 10:24:14 PDT)
  - RE: [AMBER] amber10 parallel compiling error Ross Walker (Mon Jul 20 2009 - 10:33:08 PDT)
    - Re: [AMBER] amber10 parallel compiling error nam kim (Mon Jul 20 2009 - 11:15:16 PDT)
    - Re: [AMBER] amber10 parallel compiling error nam kim (Mon Jul 20 2009 - 11:34:41 PDT)
    - Re: [AMBER] amber10 parallel compiling error nam kim (Mon Jul 20 2009 - 15:53:24 PDT)
    - Re: [AMBER] amber10 parallel compiling error nam kim (Tue Jul 21 2009 - 10:06:32 PDT)
- Re: [AMBER] amber10 parallel compiling error Toshifumi Yui (Mon Jul 20 2009 - 22:46:11 PDT)
  - Re: [AMBER] amber10 parallel compiling error case (Wed Jul 22 2009 - 19:15:50 PDT)
    - Re: [AMBER] amber10 parallel compiling error nam kim (Thu Jul 23 2009 - 21:32:14 PDT)
  - [AMBER] Re: Ambertools 1.2 installation error Bokun Cho (Sun Jul 26 2009 - 23:51:49 PDT)
    - Re: [AMBER] Re: Ambertools 1.2 installation error case (Mon Jul 27 2009 - 07:38:28 PDT)
回复： [AMBER] amber10 parallel compiling error 廖青华 (Thu Jul 16 2009 - 18:27:05 PDT)
[AMBER] File conversion for from Amber to Charmm Yogesh Aher (Thu Jul 16 2009 - 23:45:11 PDT)
- Re: [AMBER] File conversion for from Amber to Charmm case (Fri Jul 17 2009 - 04:53:06 PDT)
[AMBER] diffusion coeficients felix (Fri Jul 17 2009 - 01:15:35 PDT)
- Re: [AMBER] diffusion coeficients case (Fri Jul 17 2009 - 04:59:41 PDT)
  - Re: [AMBER] diffusion coeficients felix (Fri Jul 17 2009 - 06:41:43 PDT)
[AMBER] Steered MD.....SHAKE error!! Hlengisizwe Ndlovu (Fri Jul 17 2009 - 01:50:11 PDT)
- Re: [AMBER] Steered MD.....SHAKE error!! case (Fri Jul 17 2009 - 05:01:03 PDT)
[AMBER] vlimit error after heating restart AL Olson (Fri Jul 17 2009 - 07:26:05 PDT)
[AMBER] The Right Neutralization Procedure and Ionic Strength Calculation ? Marek Maly (Fri Jul 17 2009 - 09:34:44 PDT)
- Re: [AMBER] The Right Neutralization Procedure and Ionic Strength Calculation ? Thomas Cheatham III (Fri Jul 17 2009 - 09:50:15 PDT)
  - Re: [AMBER] The Right Neutralization Procedure and Ionic Strength Calculation ? Marek Maly (Fri Jul 17 2009 - 11:37:02 PDT)
- Re: [AMBER] The Right Neutralization Procedure and Ionic Strength Calculation ? Andrew Voronkov (Tue Jul 28 2009 - 21:19:41 PDT)
[AMBER] RESP fit E.M. (Fri Jul 17 2009 - 16:00:08 PDT)
- Re: [AMBER] RESP fit FyD (Fri Jul 17 2009 - 23:29:56 PDT)
[AMBER] charge not zero on group: RESP Jio M (Fri Jul 17 2009 - 22:14:58 PDT)
- Re: [AMBER] charge not zero on group: RESP Ben Roberts (Sat Jul 18 2009 - 05:45:10 PDT)
[AMBER] RE: charge not zero on group:''''.respin1 attached Jio M (Sat Jul 18 2009 - 07:40:18 PDT)
- Re: [AMBER] RE: charge not zero on group:''''.respin1 attached FyD (Sun Jul 19 2009 - 00:41:17 PDT)
[AMBER] amber10 parallel compiling error nam kim (Sat Jul 18 2009 - 10:19:39 PDT)
[AMBER] Box shape change Hemant Kumar (Sat Jul 18 2009 - 12:38:46 PDT)
- Re: [AMBER] Box shape change Carlos Simmerling (Sat Jul 18 2009 - 18:35:41 PDT)
  - Re: [AMBER] Box shape change Hemant Kumar (Sun Jul 19 2009 - 04:00:18 PDT)
    - Re: [AMBER] Box shape change Carlos Simmerling (Sun Jul 19 2009 - 04:40:03 PDT)
    - Re: [AMBER] Box shape change Hemant Kumar (Sun Jul 19 2009 - 05:05:04 PDT)
    - Re: [AMBER] Box shape change Carlos Simmerling (Sun Jul 19 2009 - 06:51:44 PDT)
    - Re: [AMBER] Box shape change Hemant Kumar (Sun Jul 19 2009 - 10:38:43 PDT)
[AMBER] Different machines s. Bill (Sun Jul 19 2009 - 02:55:48 PDT)
- RE: [AMBER] Different machines Ross Walker (Sun Jul 19 2009 - 09:28:52 PDT)
[AMBER] -a flag :RESP Jio M (Sun Jul 19 2009 - 03:48:20 PDT)
[AMBER] which keyword s. Bill (Sun Jul 19 2009 - 05:21:23 PDT)
[AMBER] (no subject) gunajyoti das (Sun Jul 19 2009 - 08:14:20 PDT)
- Re: [AMBER] setting AMBERHOME case (Wed Jul 22 2009 - 19:15:34 PDT)
[AMBER] (no subject) gunajyoti das (Sun Jul 19 2009 - 08:13:01 PDT)
[AMBER] Tutorial A3 s. Bill (Sun Jul 19 2009 - 12:33:58 PDT)
- RE: [AMBER] Tutorial A3 Ross Walker (Mon Jul 20 2009 - 12:03:44 PDT)
[AMBER] bugfix 10 failing for ambertools1.2 Alan (Mon Jul 20 2009 - 01:14:16 PDT)
- [AMBER] Re: bugfix 10 failing for ambertools1.2 Alan (Mon Jul 20 2009 - 01:25:55 PDT)
  - Re: [AMBER] Re: bugfix 10 failing for ambertools1.2 case (Mon Jul 27 2009 - 08:03:24 PDT)
[AMBER] nasty memory bug in calculatePrincipalAxis Hannes Loeffler (Mon Jul 20 2009 - 01:30:38 PDT)
- Re: [AMBER] nasty memory bug in calculatePrincipalAxis Scott Brozell (Mon Oct 12 2009 - 14:38:06 PDT)
[AMBER] MM-PBSA tail: equil.out: file truncated during equilibration of salivated complex Sushil Mishra (Mon Jul 20 2009 - 01:32:32 PDT)
[AMBER] Output file truncated during equilibration of salivated complex in MM-PBSA Sushil Mishra (Mon Jul 20 2009 - 03:40:51 PDT)
[AMBER] file truncated : Output file truncated during equilibration of salivated complex in MM-PBSA Sushil Mishra (Mon Jul 20 2009 - 05:26:27 PDT)
[AMBER] RE: DCCM Duggan, Brendan M. (Mon Jul 20 2009 - 07:29:46 PDT)
[AMBER] nonbon.f question Rizwan Tai (Mon Jul 20 2009 - 12:31:17 PDT)
[AMBER] RE: the copper paramter Ross Walker (Mon Jul 20 2009 - 14:38:14 PDT)
[AMBER] equivalent atoms Ye MEI (Mon Jul 20 2009 - 21:56:52 PDT)
[AMBER] ptraj grid option Youn Kyeung Lee (Tue Jul 21 2009 - 00:15:11 PDT)
[AMBER] Output forces in Sander Frank X. Vázquez (Tue Jul 21 2009 - 14:58:36 PDT)
- Re: [AMBER] Output forces in Sander case (Mon Jul 27 2009 - 08:11:30 PDT)
[AMBER] Compiling Amber 10 (serial) on Mac OS X 10.5.7 w/ gcc, Intel Fortan 11.0 and MKL 10.0 David Watson (Tue Jul 21 2009 - 14:20:36 PDT)
- Re: [AMBER] Compiling Amber 10 (serial) on Mac OS X 10.5.7 w/ gcc, Intel Fortan 11.0 and MKL 10.0 vitor.felix (Tue Jul 21 2009 - 20:15:06 PDT)
- Re: [AMBER] Compiling Amber 10 (serial) on Mac OS X 10.5.7 w/ gcc, Intel Fortan 11.0 and MKL 10.0 Scott Brozell (Wed Jul 22 2009 - 12:52:59 PDT)
[AMBER] RE: Questions about QMMM Ross Walker (Tue Jul 21 2009 - 15:47:49 PDT)
[AMBER] Patching terminal Manish Kumar (Tue Jul 21 2009 - 16:53:54 PDT)
[AMBER] ESP charges of Fe4S4 subarna thakur (Tue Jul 21 2009 - 22:19:48 PDT)
[AMBER] Regarding Hbond interactions aneesh cna (Tue Jul 21 2009 - 23:30:10 PDT)
- Re: [AMBER] Regarding Hbond interactions Thomas Cheatham (Thu Jul 23 2009 - 15:57:57 PDT)
[AMBER] Equilibration step Olotu Odunayo (Wed Jul 22 2009 - 02:47:37 PDT)
- Re: [AMBER] Equilibration step Tom Joseph (Wed Jul 22 2009 - 05:35:15 PDT)
- RE: [AMBER] Equilibration step Olotu Odunayo (Wed Jul 22 2009 - 09:41:13 PDT)
  - Re: [AMBER] Equilibration step Tom Joseph (Wed Jul 22 2009 - 12:05:58 PDT)
- RE: [AMBER] Equilibration step Olotu Odunayo (Wed Jul 22 2009 - 09:46:12 PDT)
- RE: [AMBER] Equilibration step Olotu Odunayo (Wed Jul 22 2009 - 23:52:50 PDT)
[AMBER] errors of PMEMD installation 廖青华 (Wed Jul 22 2009 - 07:28:45 PDT)
- Re: [AMBER] errors of PMEMD installation Mengjuei Hsieh (Thu Jul 23 2009 - 12:25:27 PDT)
  - 回复： [AMBER] errors of PMEMD installation 廖青华 (Thu Jul 23 2009 - 18:27:51 PDT)
    - Re: 回复： [AMBER] errors of PMEMD installation Mengjuei Hsieh (Fri Jul 24 2009 - 01:41:05 PDT)
    - Re: 回复： [AMBER] errors of PMEMD installation Qinghua Liao (Fri Jul 24 2009 - 02:18:44 PDT)
    - Re: 回复： [AMBER] errors of PMEMD installation Qinghua Liao (Fri Jul 24 2009 - 02:59:03 PDT)
    - Re: 回复： [AMBER] errors of PMEMD installation Mengjuei Hsieh (Fri Jul 24 2009 - 11:12:00 PDT)
    - Re: 回复： [AMBER] errors of PMEMD installation Qinghua Liao (Fri Jul 24 2009 - 18:24:10 PDT)
    - Re: [AMBER] errors of PMEMD installation Mengjuei Hsieh (Sat Jul 25 2009 - 20:10:11 PDT)
[AMBER] saquinavir parameterization with antechamber Oliver Kuhn (Wed Jul 22 2009 - 08:42:49 PDT)
- Re: [AMBER] saquinavir parameterization with antechamber FyD (Wed Jul 22 2009 - 11:41:21 PDT)
  - Re: [AMBER] saquinavir parameterization with antechamber Oliver Kuhn (Thu Jul 23 2009 - 00:02:49 PDT)
    - Re: [AMBER] saquinavir parameterization with antechamber FyD (Thu Jul 23 2009 - 00:29:57 PDT)
    - Re: [AMBER] saquinavir parameterization with antechamber Oliver Kuhn (Thu Jul 23 2009 - 01:06:00 PDT)
[AMBER] [ALERT]: It's the time to come out on streets and stop the complete nation on it's place - Take immediate actions at once with full force. Organization (Wed Jul 22 2009 - 12:13:37 PDT)
[AMBER] how to launch XLEaP from SSH Secure Shell? Yana Berezovskaya (Wed Jul 22 2009 - 15:44:45 PDT)
- Re: [AMBER] how to launch XLEaP from SSH Secure Shell? Robert Duke (Wed Jul 22 2009 - 16:07:24 PDT)
  - Re: [AMBER] how to launch XLEaP from SSH Secure Shell? Tom Joseph (Wed Jul 22 2009 - 16:24:56 PDT)
    - Re: [AMBER] how to launch XLEaP from SSH Secure Shell? David Watson (Wed Jul 22 2009 - 17:30:12 PDT)
    - Re: [AMBER] how to launch XLEaP from SSH Secure Shell? Thomas Patko (Wed Jul 22 2009 - 17:47:51 PDT)
[AMBER] Replacing DNA base with analog amoreno.wesleyan.edu (Thu Jul 23 2009 - 07:20:08 PDT)
- RE: [AMBER] Replacing DNA base with analog Kristina Furse (Thu Jul 23 2009 - 07:36:26 PDT)
[AMBER] Compiling AMBER 10 (parallel, MPICH2) on Mac OS X Intel w/gcc, ifort, icc David Watson (Thu Jul 23 2009 - 13:03:59 PDT)
RE: [Subject Filtered] Re: [AMBER] PMEMD in a Cygwin Environment 8% Hopkins, Robert (Thu Jul 23 2009 - 13:37:12 PDT)
[AMBER] Langevin Dynamics in AMBER10 Biswaranjan Meher (Thu Jul 23 2009 - 14:54:58 PDT)
- Re: [AMBER] Langevin Dynamics in AMBER10 Carlos Simmerling (Thu Jul 23 2009 - 14:57:44 PDT)
  - Re: [AMBER] Langevin Dynamics in AMBER10 Biswaranjan Meher (Thu Jul 23 2009 - 16:12:59 PDT)
    - Re: [AMBER] Langevin Dynamics in AMBER10 Carlos Simmerling (Fri Jul 24 2009 - 05:01:28 PDT)
[AMBER] mailing list Qinghua Liao (Thu Jul 23 2009 - 18:45:50 PDT)
[AMBER] radical simulation Jeffrey (Fri Jul 24 2009 - 00:34:53 PDT)
- Re: [AMBER] radical simulation Manish Kumar (Fri Jul 24 2009 - 00:48:01 PDT)
- Re: [AMBER] radical simulation FyD (Fri Jul 24 2009 - 03:27:34 PDT)
- Re: [AMBER] radical simulation Jeffrey (Sun Jul 26 2009 - 05:28:39 PDT)
[AMBER] xleap facility to insert a residue Sergey Samsonov (Fri Jul 24 2009 - 06:07:27 PDT)
[AMBER] thymidine monophosphate parametrization Yvonne.Westermaier.unige.ch (Fri Jul 24 2009 - 08:18:18 PDT)
- Re: [AMBER] thymidine monophosphate parametrization case (Mon Jul 27 2009 - 07:47:38 PDT)
  - Re: [AMBER] thymidine monophosphate parametrization Yvonne.Westermaier.unige.ch (Tue Jul 28 2009 - 05:10:43 PDT)
[AMBER] loading a mol2 file in xleap vallespardojl.chem.leidenuniv.nl (Fri Jul 24 2009 - 10:40:13 PDT)
- Re: [AMBER] loading a mol2 file in xleap FyD (Fri Jul 24 2009 - 13:00:41 PDT)
  - Re: [AMBER] loading a mol2 file in xleap vallespardojl.chem.leidenuniv.nl (Mon Jul 27 2009 - 05:40:13 PDT)
    - Re: [AMBER] loading a mol2 file in xleap FyD (Mon Jul 27 2009 - 06:44:50 PDT)
- [AMBER] Could not find type: MG Parameter file was not saved. Mannan (Sat Jul 25 2009 - 20:41:24 PDT)
  - [AMBER] Could not find type: MG Parameter file was not saved. though it was loaded Mannan (Sun Jul 26 2009 - 20:49:54 PDT)
    - Re: [AMBER] Could not find type: MG Parameter file was not saved. though it was loaded FyD (Sun Jul 26 2009 - 22:03:00 PDT)
[AMBER] DNA + intercalator Rodrigo Galindo (Fri Jul 24 2009 - 15:22:35 PDT)
Re: [AMBER] DNA + intercalator Bill Ross (Fri Jul 24 2009 - 16:03:06 PDT)
- Re: [AMBER] DNA + intercalator Ashish Runthala (Fri Jul 24 2009 - 20:12:27 PDT)
[AMBER] Simulation with United atom force field in Implicit solvent. Manish Kumar (Sat Jul 25 2009 - 20:55:42 PDT)
- Re: [AMBER] Simulation with United atom force field in Implicit solvent. Ray Luo (Sun Jul 26 2009 - 00:09:07 PDT)
  - Re: [AMBER] Simulation with United atom force field in Implicit solvent. Manish Kumar (Sun Jul 26 2009 - 11:22:40 PDT)
[AMBER] Removed proton in protein (Advanced Tutorials A1 old) albert albert (Sun Jul 26 2009 - 23:57:20 PDT)
- Re: [AMBER] Removed proton in protein (Advanced Tutorials A1 old) Ashish Runthala (Mon Jul 27 2009 - 02:09:23 PDT)
- Re: [AMBER] Removed proton in protein (Advanced Tutorials A1 old) Bill Ross (Mon Jul 27 2009 - 09:17:29 PDT)
  - Re: [AMBER] Removed proton in protein (Advanced Tutorials A1 old) Ashish Runthala (Tue Jul 28 2009 - 03:28:40 PDT)
    - Re: [AMBER] Removed proton in protein (Advanced Tutorials A1 old) FyD (Tue Jul 28 2009 - 04:59:51 PDT)
    - Re: [AMBER] Removed proton in protein (Advanced Tutorials A1 old) Ashish Runthala (Tue Jul 28 2009 - 06:08:48 PDT)
    - Re: [AMBER] Removed proton in protein (Advanced Tutorials A1 old) albert albert (Fri Jul 31 2009 - 12:27:02 PDT)
[AMBER] How to read md trajectory for each time slice as an input coordinate Myeong Lee (Mon Jul 27 2009 - 01:16:47 PDT)
[AMBER] error in antechamber Qinghua Liao (Mon Jul 27 2009 - 04:57:50 PDT)
- Re: [AMBER] error in antechamber Mengjuei Hsieh (Mon Jul 27 2009 - 15:29:06 PDT)
  - Re: [AMBER] error in antechamber Qinghua Liao (Mon Jul 27 2009 - 18:02:26 PDT)
    - Re: [AMBER] error in antechamber case (Mon Jul 27 2009 - 21:23:54 PDT)
    - Re: [AMBER] error in antechamber Qinghua Liao (Mon Jul 27 2009 - 22:13:49 PDT)
[AMBER] Average structure over simulation Olotu Odunayo (Mon Jul 27 2009 - 06:38:59 PDT)
- [AMBER] RE: Average structure over simulation Niel Henriksen (Mon Jul 27 2009 - 07:56:40 PDT)
  - RE: [AMBER] RE: Average structure over simulation Olotu Odunayo (Mon Jul 27 2009 - 08:47:20 PDT)
[AMBER] residues lacking connect0/connect1 Jio M (Mon Jul 27 2009 - 09:10:06 PDT)
Re: [AMBER] residues lacking connect0/connect1 Bill Ross (Mon Jul 27 2009 - 09:40:31 PDT)
[AMBER] nonbon.f question Rizwan Tai (Mon Jul 27 2009 - 12:30:12 PDT)
- Re: [AMBER] nonbon.f question Carlos Simmerling (Mon Jul 27 2009 - 12:34:20 PDT)
  - Re: [AMBER] nonbon.f question Rizwan Tai (Mon Aug 03 2009 - 09:13:21 PDT)
    - RE: [AMBER] nonbon.f question Ross Walker (Mon Aug 03 2009 - 11:32:18 PDT)
[AMBER] Using idecomp=3 with igb=10 (PB) Chris Whittleston (Mon Jul 27 2009 - 13:04:14 PDT)
- Re: [AMBER] Using idecomp=3 with igb=10 (PB) Hannes Kopitz (Tue Jul 28 2009 - 03:09:01 PDT)
  - Re: [AMBER] Using idecomp=3 with igb=10 (PB) Chris Whittleston (Tue Jul 28 2009 - 03:54:09 PDT)
    - Re: [AMBER] Using idecomp=3 with igb=10 (PB) Hannes Kopitz (Tue Jul 28 2009 - 05:47:15 PDT)
    - Re: [AMBER] Using idecomp=3 with igb=10 (PB) Ashish Runthala (Tue Jul 28 2009 - 07:33:02 PDT)
    - Re: [AMBER] Using idecomp=3 with igb=10 (PB) Chris Whittleston (Wed Oct 07 2009 - 09:57:25 PDT)
    - Re: [AMBER] Using idecomp=3 with igb=10 (PB) Chris Whittleston (Thu Oct 08 2009 - 03:47:22 PDT)
    - Re: [AMBER] Using idecomp=3 with igb=10 (PB) Hannes Kopitz (Thu Oct 08 2009 - 13:30:19 PDT)
    - Re: [AMBER] Using idecomp=3 with igb=10 (PB) Chris Whittleston (Fri Oct 09 2009 - 08:16:53 PDT)
    - Re: [AMBER] Using idecomp=3 with igb=10 (PB) Hannes Kopitz (Sun Oct 11 2009 - 14:13:45 PDT)
    - Re: [AMBER] Using idecomp=3 with igb=10 (PB) Chris Whittleston (Mon Oct 12 2009 - 08:56:06 PDT)
    - Re: [AMBER] Using idecomp=3 with igb=10 (PB) Hannes Kopitz (Mon Oct 12 2009 - 12:51:23 PDT)
    - Re: [AMBER] Using idecomp=3 with igb=10 (PB) Chris Whittleston (Tue Oct 13 2009 - 03:02:17 PDT)
[AMBER] QM/MM s. Bill (Mon Jul 27 2009 - 23:44:15 PDT)
- Re: [AMBER] QM/MM steinbrt.rci.rutgers.edu (Tue Jul 28 2009 - 00:19:32 PDT)
[AMBER] PLUMED release 1.1.0 available Massimiliano Bonomi (Tue Jul 28 2009 - 01:10:39 PDT)
- [AMBER] How to visualize PCA results without IED? Catein Catherine (Tue Jul 28 2009 - 02:30:22 PDT)
  - Re: [AMBER] How to visualize PCA results without IED? Vlad Cojocaru (Tue Jul 28 2009 - 02:58:50 PDT)
  - Re: [AMBER] How to visualize PCA results without IED? Hannes Loeffler (Tue Jul 28 2009 - 03:12:04 PDT)
    - Re: [AMBER] How to visualize PCA results without IED? Vlad Cojocaru (Tue Jul 28 2009 - 03:42:05 PDT)
  - Re: [AMBER] How to visualize PCA results without IED? Shozeb Haider (Tue Jul 28 2009 - 04:02:22 PDT)
[AMBER] RE: MM-PBSA test jobs error messages Catein Catherine (Tue Jul 28 2009 - 02:24:31 PDT)
[AMBER] pulling two atoms in SMD Santosh Mogurampelly (Tue Jul 28 2009 - 05:10:12 PDT)
[AMBER] Error in Sander Output File Alison Saunders (Tue Jul 28 2009 - 10:00:12 PDT)
[AMBER] Am I doing the right thing nicholus bhattacharjee (Tue Jul 28 2009 - 10:20:57 PDT)
- Re: [AMBER] Am I doing the right thing Ashish Runthala (Tue Jul 28 2009 - 18:35:09 PDT)
- Re: [AMBER] Am I doing the right thing Bill Ross (Tue Jul 28 2009 - 19:39:48 PDT)
  - Re: [AMBER] Am I doing the right thing Ashish Runthala (Tue Jul 28 2009 - 20:44:59 PDT)
    - Re: [AMBER] Am I doing the right thing nicholus bhattacharjee (Tue Jul 28 2009 - 21:36:31 PDT)
[AMBER] Question on REST and VALUE1 keywords hwu.clarku.edu (Tue Jul 28 2009 - 14:06:34 PDT)
- Re: [AMBER] Question on REST and VALUE1 keywords Carlos Simmerling (Tue Jul 28 2009 - 14:14:20 PDT)
  - Re: [AMBER] Question on REST and VALUE1 keywords Ashish Runthala (Tue Jul 28 2009 - 18:26:19 PDT)
[AMBER] how to choose exclusion policy for GPCR xueqin pang (Tue Jul 28 2009 - 19:12:33 PDT)
[AMBER] RE: MM-PBSA test jobs error messages (with bugfix.all) Catein Catherine (Tue Jul 28 2009 - 22:50:50 PDT)
[AMBER] pdb file no bond and charges Jio M (Tue Jul 28 2009 - 23:28:48 PDT)
[AMBER] RED.III: Invalid Optimization OUTPUT s. Bill (Wed Jul 29 2009 - 01:37:27 PDT)
- Re: Solved it thanks [AMBER] RED.III: Invalid Optimization OUTPUT s. Bill (Wed Jul 29 2009 - 05:14:02 PDT)
[AMBER] Re: MM-PBSA test jobs error messages (Can i fix the problem without recompile the amber?) Catein Catherine (Wed Jul 29 2009 - 02:39:02 PDT)
[AMBER] MPI error vhakkim boy (Wed Jul 29 2009 - 02:44:35 PDT)
- Re: [AMBER] MPI error Robert Duke (Wed Jul 29 2009 - 05:05:57 PDT)
[AMBER] MM/PBSA, MM/GBSA and NMODE Analysis Matthias Negri (Wed Jul 29 2009 - 03:55:46 PDT)
- Re: [AMBER] MM/PBSA, MM/GBSA and NMODE Analysis Ray Luo (Wed Jul 29 2009 - 17:25:14 PDT)
[AMBER] Compiling AmberTools 1.2 with intel compilers for Mac Osx in 64 bits Alan (Wed Jul 29 2009 - 09:00:42 PDT)
- Re: [AMBER] Compiling AmberTools 1.2 with intel compilers for Mac Osx in 64 bits David Watson (Wed Jul 29 2009 - 09:21:50 PDT)
  - Re: [AMBER] Compiling AmberTools 1.2 with intel compilers for Mac Osx in 64 bits Alan (Thu Jul 30 2009 - 06:39:03 PDT)
    - Re: [AMBER] Compiling AmberTools 1.2 with intel compilers for Mac Osx in 64 bits David Watson (Thu Jul 30 2009 - 12:10:39 PDT)
[AMBER] Installing Amber10 on Ubuntu David Dubins (Wed Jul 29 2009 - 11:50:12 PDT)
- Re: [AMBER] Installing Amber10 on Ubuntu Rodrigo Galindo (Wed Jul 29 2009 - 12:49:33 PDT)
[AMBER] Re: problem of installation of amber10 Mengjuei Hsieh (Wed Jul 29 2009 - 12:41:52 PDT)
[AMBER] Normal mode analysis of water bharat lakhani (Thu Jul 30 2009 - 02:27:19 PDT)
- Re: [AMBER] Normal mode analysis of water case (Thu Jul 30 2009 - 07:11:23 PDT)
[AMBER] PCA analysis: the first vector is the movement of whole molecule. Catein Catherine (Thu Jul 30 2009 - 03:37:49 PDT)
- Re: [AMBER] PCA analysis: the first vector is the movement of whole molecule. Hannes Loeffler (Thu Jul 30 2009 - 03:52:48 PDT)
  - RE: [AMBER] PCA analysis: the first vector is the movement of whole molecule. Catein Catherine (Thu Jul 30 2009 - 20:46:49 PDT)
    - RE: [AMBER] PCA analysis: the first vector is the movement of whole molecule. Hannes Loeffler (Fri Jul 31 2009 - 00:27:54 PDT)
    - RE: [AMBER] PCA analysis: the first vector is the movement of whole molecule. Catein Catherine (Sun Aug 02 2009 - 20:47:07 PDT)
[AMBER] ambpdb problem Jio M (Thu Jul 30 2009 - 12:12:10 PDT)
- Re: [AMBER] ambpdb problem Jordan Monnet (Thu Jul 30 2009 - 12:32:57 PDT)
  - Re: [AMBER] ambpdb problem Ashish Runthala (Thu Jul 30 2009 - 20:44:10 PDT)
- Re: [AMBER] ambpdb problem Jio M (Fri Jul 31 2009 - 00:11:32 PDT)
  - Re: [AMBER] ambpdb problem Jordan Monnet (Fri Jul 31 2009 - 07:30:54 PDT)
    - Re: [AMBER] ambpdb problem Ashish Runthala (Fri Jul 31 2009 - 18:28:42 PDT)
[AMBER] Non-Standard Amino Acid Residue LEAP ERROR Brothers, Michael Charles (Thu Jul 30 2009 - 15:28:43 PDT)
- Re: [AMBER] Non-Standard Amino Acid Residue LEAP ERROR Ashish Runthala (Thu Jul 30 2009 - 20:40:45 PDT)
  - RE: [AMBER] Non-Standard Amino Acid Residue LEAP ERROR Brothers, Michael Charles (Fri Jul 31 2009 - 10:36:10 PDT)
    - Re: [AMBER] Non-Standard Amino Acid Residue LEAP ERROR Ashish Runthala (Fri Jul 31 2009 - 18:39:54 PDT)
[AMBER] What is the meaning of "rms first *" Catein Catherine (Thu Jul 30 2009 - 20:49:17 PDT)
[AMBER] query bharat lakhani (Fri Jul 31 2009 - 00:42:04 PDT)
- [AMBER] Re: query bharat lakhani (Sat Aug 01 2009 - 05:07:24 PDT)
  - Re: [AMBER] Re: query Ashish Runthala (Sat Aug 01 2009 - 05:21:47 PDT)
[AMBER] Compilation error with pmemd (amber10) on fedora9 64 bits Nicolas SAPAY (Fri Jul 31 2009 - 02:41:21 PDT)
- Re: [AMBER] Compilation error with pmemd (amber10) on fedora9 64 bits Robert Duke (Fri Jul 31 2009 - 05:33:52 PDT)
  - Re: [AMBER] Compilation error with pmemd (amber10) on fedora9 64 bits Nicolas SAPAY (Fri Jul 31 2009 - 05:55:18 PDT)
[AMBER] vertex atom mismatch Clark, Tiffany D (Fri Jul 31 2009 - 06:14:15 PDT)
- Re: [AMBER] vertex atom mismatch Guillermo Mulliert Carlín (Fri Jul 31 2009 - 07:33:46 PDT)
[AMBER] problem from xleap Qinghua Liao (Fri Jul 31 2009 - 07:38:18 PDT)
- Re: [AMBER] problem from xleap Tom Joseph (Fri Jul 31 2009 - 09:41:49 PDT)
  - Re: [AMBER] problem from xleap Qinghua Liao (Fri Jul 31 2009 - 18:38:19 PDT)
    - Re: [AMBER] problem from xleap Ashish Runthala (Fri Jul 31 2009 - 20:33:10 PDT)
    - Re: [AMBER] problem from xleap Tom Joseph (Sat Aug 01 2009 - 04:19:22 PDT)
[AMBER] Protonated or not s. Bill (Fri Jul 31 2009 - 10:15:32 PDT)
- Re: [AMBER] Protonated or not Adrian Roitberg (Fri Jul 31 2009 - 10:32:50 PDT)
  - [AMBER] Protein Activity Chih-Ying Lin (Tue Aug 04 2009 - 10:57:54 PDT)
  - [AMBER] Protein Domain Motion Chih-Ying Lin (Thu Aug 13 2009 - 12:20:09 PDT)
    - Re: [AMBER] Protein Domain Motion Carlos Simmerling (Thu Aug 13 2009 - 12:39:39 PDT)
    - Re: [AMBER] Protein Domain Motion Chih-Ying Lin (Thu Aug 13 2009 - 18:51:14 PDT)
    - Re: [AMBER] Protein Domain Motion Carlos Simmerling (Fri Aug 14 2009 - 05:17:28 PDT)
[AMBER] Metalloproteins - Ligand Protonation s. Bill (Fri Jul 31 2009 - 11:01:42 PDT)
[AMBER] radial distribution function Dharmik Meghana shankar (Fri Jul 31 2009 - 22:33:58 PDT)
[AMBER] Timescales and restraints for protein-small ligands movement simulations Andrew Voronkov (Fri Jul 31 2009 - 23:23:19 PDT)
- Re: [AMBER] Timescales and restraints for protein-small ligands movement simulations Andrew Voronkov (Sat Aug 01 2009 - 07:14:49 PDT)
  - Re: [AMBER] Timescales and restraints for protein-small ligands movement simulations Vivek Sharma (Sat Aug 01 2009 - 23:29:13 PDT)
[AMBER] Showing error bharat lakhani (Sat Aug 01 2009 - 06:12:00 PDT)
[AMBER] Showing error in energy minimization bharat lakhani (Sat Aug 01 2009 - 23:22:30 PDT)
- Re: [AMBER] Showing error in energy minimization case (Sun Aug 02 2009 - 07:25:04 PDT)
  - [AMBER] Do we need to need to rms fit all atoms before calculating correlation motion between residues? Catein Catherine (Sun Aug 02 2009 - 20:45:19 PDT)
- Re: [AMBER] Showing error in energy minimization Ashish Runthala (Sun Aug 02 2009 - 20:05:06 PDT)
[AMBER] showing error when creating topology and coordinate file bharat lakhani (Mon Aug 03 2009 - 00:19:59 PDT)
- [AMBER] Re: showing error when creating topology and coordinate file bharat lakhani (Mon Aug 03 2009 - 21:54:36 PDT)
  - RE: [AMBER] Re: showing error when creating topology and coordinate file Olotu Odunayo (Tue Aug 04 2009 - 06:08:32 PDT)
[AMBER] optimization step length ondrej.prenosil.marge.uochb.cas.cz (Mon Aug 03 2009 - 03:40:15 PDT)
- Re: [AMBER] optimization step length Ashish Runthala (Mon Aug 03 2009 - 07:26:28 PDT)
[AMBER] Problem with Amber8 Sebastian Petruczynik (Mon Aug 03 2009 - 06:28:56 PDT)
- Re: [AMBER] Problem with Amber8 ondrej.prenosil.marge.uochb.cas.cz (Mon Aug 03 2009 - 06:37:01 PDT)
- RE: [AMBER] Problem with Amber8 Ross Walker (Mon Aug 03 2009 - 12:41:28 PDT)
  - Re: [AMBER] Problem with Amber8 Sebastian Petruczynik (Wed Aug 05 2009 - 04:33:05 PDT)
[AMBER] What is the meaning of IED values for PCA analysis? Catein Catherine (Mon Aug 03 2009 - 07:30:15 PDT)
- Re: [AMBER] What is the meaning of IED values for PCA analysis? case (Wed Aug 05 2009 - 09:39:30 PDT)
[AMBER] How to solve the problem "RESTARTED DUE to LINMIN FAILURE" Jianping Lin (Mon Aug 03 2009 - 07:57:28 PDT)
- RE: [AMBER] How to solve the problem "RESTARTED DUE to LINMIN FAILURE" Ross Walker (Mon Aug 03 2009 - 12:38:23 PDT)
  - Re: [AMBER] How to solve the problem "RESTARTED DUE to LINMIN FAILURE" Jianping Lin (Fri Aug 07 2009 - 13:32:47 PDT)
- [AMBER] Re: How to solve the problem "RESTARTED DUE to LINMIN FAILURE" Jianping Lin (Mon Aug 10 2009 - 16:18:44 PDT)
  - Re: [AMBER] Re: How to solve the problem "RESTARTED DUE to LINMIN FAILURE" Bill Ross (Mon Aug 10 2009 - 18:17:05 PDT)
    - Re: [AMBER] Re: How to solve the problem "RESTARTED DUE to LINMIN FAILURE" Jianping Lin (Mon Aug 10 2009 - 18:23:44 PDT)
  - Re: [AMBER] Re: How to solve the problem "RESTARTED DUE to LINMIN FAILURE" Bill Ross (Mon Aug 10 2009 - 18:30:07 PDT)
[AMBER] Lennard Jones potential Rizwan Tai (Mon Aug 03 2009 - 10:13:16 PDT)
- RE: [AMBER] Lennard Jones potential Ross Walker (Mon Aug 03 2009 - 12:28:06 PDT)
  - Re: [AMBER] Lennard Jones potential Antonios Samiotakis (Thu Mar 18 2010 - 16:50:51 PDT)
[AMBER] parmchk problem isaac sugden (Tue Aug 04 2009 - 07:12:29 PDT)
- Re: [AMBER] parmchk problem case (Wed Aug 05 2009 - 09:36:27 PDT)
  - Re: [AMBER] parmchk problem isaac sugden (Wed Aug 05 2009 - 10:21:53 PDT)
    - Re: [AMBER] parmchk problem case (Tue Aug 11 2009 - 06:51:57 PDT)
Re: [AMBER] Protein Activity Bill Ross (Tue Aug 04 2009 - 12:19:32 PDT)
- Re: [AMBER] Protein Activity Chih-Ying Lin (Tue Aug 04 2009 - 12:42:42 PDT)
- Re: [AMBER] Protein Activity Bill Ross (Tue Aug 04 2009 - 12:59:40 PDT)
  - Re: [AMBER] Protein Activity Ashish Runthala (Tue Aug 04 2009 - 20:42:11 PDT)
[AMBER] problem of mm_pbsa Qinghua Liao (Tue Aug 04 2009 - 22:46:51 PDT)
- Re: [AMBER] problem of mm_pbsa case (Wed Aug 05 2009 - 08:42:56 PDT)
  - Re: [AMBER] problem of mm_pbsa Qinghua Liao (Wed Aug 05 2009 - 17:22:13 PDT)
  - Re: [AMBER] problem of mm_pbsa Rubben Torella (Thu Aug 06 2009 - 08:53:47 PDT)
    - Re: [AMBER] problem of mm_pbsa Qinghua Liao (Thu Aug 06 2009 - 16:58:55 PDT)
    - Re: [AMBER] problem of mm_pbsa Jordan Monnet (Fri Aug 07 2009 - 16:13:57 PDT)
    - Re: [AMBER] problem of mm_pbsa Qinghua Liao (Fri Aug 07 2009 - 18:11:43 PDT)
    - Re: [AMBER] problem of mm_pbsa Jordan Monnet (Mon Aug 10 2009 - 12:37:55 PDT)
    - Re: [AMBER] problem of mm_pbsa Qinghua Liao (Thu Aug 13 2009 - 06:58:24 PDT)
    - Re: [AMBER] problem of mm_pbsa Jordan Monnet (Thu Aug 13 2009 - 13:04:37 PDT)
[AMBER] USE A VERSION COMPILED WITHOUT -DLES s. Bill (Wed Aug 05 2009 - 03:50:01 PDT)
- Solved THNAKS Re: [AMBER] USE A VERSION COMPILED WITHOUT -DLES s. Bill (Wed Aug 05 2009 - 04:55:55 PDT)
[AMBER] TWO restraints with different force constants s. Bill (Wed Aug 05 2009 - 04:54:18 PDT)
- Re: [AMBER] TWO restraints with different force constants A. Gomez-Sicilia (Wed Aug 05 2009 - 05:20:54 PDT)
AW: [AMBER] TWO restraints with different force constants Aust, Susanne (Wed Aug 05 2009 - 05:31:38 PDT)
[AMBER] Computational Resources s. Bill (Wed Aug 05 2009 - 08:17:34 PDT)
- RE: [AMBER] Computational Resources Ross Walker (Wed Aug 05 2009 - 09:08:21 PDT)
[AMBER] ptraj failure to parse psf input Sasha Buzko (Wed Aug 05 2009 - 09:39:57 PDT)
- Re: [AMBER] ptraj failure to parse psf input case (Wed Aug 05 2009 - 10:32:00 PDT)
  - Re: [AMBER] ptraj failure to parse psf input Sasha Buzko (Wed Aug 05 2009 - 12:33:54 PDT)
- Re: [AMBER] ptraj failure to parse psf input Sasha Buzko (Wed Aug 12 2009 - 14:16:07 PDT)
- Re: [AMBER] ptraj failure to parse psf input Thomas Cheatham (Wed Aug 12 2009 - 21:27:34 PDT)
  - Re: [AMBER] ptraj failure to parse psf input Sasha Buzko (Thu Aug 13 2009 - 09:25:32 PDT)
- Re: [AMBER] ptraj failure to parse psf input Sasha Buzko (Thu Aug 13 2009 - 16:34:07 PDT)
[AMBER] nmode output Vahdati N. (Wed Aug 05 2009 - 15:26:11 PDT)
[AMBER] implicit solvent simulation Manish Kumar (Wed Aug 05 2009 - 21:49:30 PDT)
- Re: [AMBER] implicit solvent simulation Ashish Runthala (Wed Aug 05 2009 - 22:00:50 PDT)
  - Re: [AMBER] implicit solvent simulation Manish Kumar (Wed Aug 05 2009 - 22:19:11 PDT)
- RE: [AMBER] implicit solvent simulation Ross Walker (Wed Aug 05 2009 - 23:32:24 PDT)
  - Re: [AMBER] implicit solvent simulation Manish Kumar (Wed Aug 05 2009 - 23:53:54 PDT)
[AMBER] Model(l)ing'09 in Erlangen, Germany: Registration Open Until August 31st Harald Lanig (Thu Aug 06 2009 - 01:39:07 PDT)
[AMBER] Extreme optimization problems ondrej.prenosil.marge.uochb.cas.cz (Thu Aug 06 2009 - 05:04:09 PDT)
- Re: [AMBER] Extreme optimization problems case (Thu Aug 06 2009 - 08:51:23 PDT)
Re: [AMBER] parameters for HIV protease inhibitors Carlos Simmerling (Thu Aug 06 2009 - 08:29:39 PDT)
- Re: [AMBER] parameters for HIV protease inhibitors Oliver Kuhn (Tue Aug 11 2009 - 07:57:24 PDT)
- Re: [AMBER] parameters for HIV protease inhibitors FyD (Wed Aug 12 2009 - 05:56:18 PDT)
[AMBER] Regd : gaff force field KIRTANA S (Thu Aug 06 2009 - 13:09:14 PDT)
- Re: [AMBER] Regd : gaff force field Nicholas Musolino (Thu Aug 06 2009 - 13:22:37 PDT)
- RE: [AMBER] Regd : gaff force field Ross Walker (Thu Aug 06 2009 - 13:42:14 PDT)
  - Re: [AMBER] Regd : gaff force field KIRTANA S (Thu Aug 06 2009 - 15:12:15 PDT)
    - Re: [AMBER] Regd : gaff force field Ashish Runthala (Fri Aug 07 2009 - 02:08:43 PDT)
    - RE: [AMBER] Regd : gaff force field Ross Walker (Fri Aug 07 2009 - 08:52:07 PDT)
    - Re: [AMBER] Regd : gaff force field Ashish Runthala (Sat Aug 08 2009 - 05:17:37 PDT)
[AMBER] How to keep the closest solvent mols to each atoms by PTRAJ? u8613020.msg.ndhu.edu.tw (Thu Aug 06 2009 - 18:40:17 PDT)
[AMBER] implicit solvent simulation with new ligand Manish Kumar (Thu Aug 06 2009 - 20:29:37 PDT)
- [AMBER] Re: implicit solvent simulation with new ligand Manish Kumar (Fri Aug 07 2009 - 11:22:57 PDT)
  - Re: [AMBER] Re: implicit solvent simulation with new ligand Carlos Simmerling (Fri Aug 07 2009 - 11:29:46 PDT)
    - [AMBER] Parameters for haloacetates Joseph Nachman (Fri Aug 07 2009 - 11:22:34 PDT)
    - Re: [AMBER] Parameters for haloacetates Lili Peng (Fri Aug 07 2009 - 21:43:50 PDT)
    - Re: [AMBER] Parameters for haloacetates Joseph Nachman (Mon Aug 10 2009 - 07:54:13 PDT)
    - Re: [AMBER] Re: implicit solvent simulation with new ligand Manish Kumar (Fri Aug 07 2009 - 12:08:59 PDT)
    - Re: [AMBER] Re: implicit solvent simulation with new ligand Carlos Simmerling (Mon Aug 10 2009 - 07:42:33 PDT)
[AMBER] query bharat lakhani (Fri Aug 07 2009 - 02:11:42 PDT)
[AMBER] pmemd michael (Fri Aug 07 2009 - 02:50:29 PDT)
- Re: [AMBER] pmemd case (Fri Aug 07 2009 - 08:18:52 PDT)
  - Re: [AMBER] pmemd michael (Mon Aug 10 2009 - 12:51:59 PDT)
    - RE: [AMBER] pmemd Ross Walker (Mon Aug 10 2009 - 17:00:12 PDT)
    - Re: [AMBER] pmemd michael (Sat Aug 15 2009 - 04:30:28 PDT)
- Re: [AMBER] pmemd Robert Duke (Mon Aug 24 2009 - 06:42:05 PDT)
[AMBER] query regarding resp subarna thakur (Fri Aug 07 2009 - 05:14:35 PDT)
- Re: [AMBER] query regarding resp Oliver Kuhn (Tue Aug 11 2009 - 07:24:19 PDT)
[AMBER] (no subject) Beale, John (Fri Aug 07 2009 - 05:16:58 PDT)
- Re: [AMBER] (no subject) Ashish Runthala (Fri Aug 07 2009 - 06:27:04 PDT)
- RE: [AMBER] (no subject) Ross Walker (Fri Aug 07 2009 - 08:35:32 PDT)
  - Re: [AMBER] (no subject) case (Fri Aug 07 2009 - 16:54:18 PDT)
[AMBER] MM-PBSA results Dmitry Osolodkin (Fri Aug 07 2009 - 07:31:48 PDT)
[AMBER] Appropriate nmode input file for gas and vacuum phase simulation Scott Pendley (Fri Aug 07 2009 - 10:48:52 PDT)
- Re: [AMBER] Appropriate nmode input file for gas and vacuum phase simulation case (Sat Aug 08 2009 - 12:20:37 PDT)
[AMBER] antechamber am1-bcc issues David Mobley (Fri Aug 07 2009 - 11:19:53 PDT)
- [AMBER] Re: antechamber am1-bcc issues case (Fri Aug 07 2009 - 16:54:38 PDT)
  - Re: [AMBER] Re: antechamber am1-bcc issues gilbert.bluemarble.net (Sat Aug 08 2009 - 06:55:40 PDT)
    - Re: [AMBER] Re: antechamber am1-bcc issues case (Sat Aug 08 2009 - 12:20:44 PDT)
    - Re: [AMBER] Re: antechamber am1-bcc issues David Mobley (Thu Aug 13 2009 - 06:25:52 PDT)
  - Re: [AMBER] Re: antechamber am1-bcc issues Khavrutskii, Ilja (Fri Aug 21 2009 - 09:27:28 PDT)
    - Re: [AMBER] Re: antechamber am1-bcc issues Khavrutskii, Ilja (Fri Aug 21 2009 - 12:32:34 PDT)
- Re: [AMBER] antechamber am1-bcc issues Khavrutskii, Ilja (Tue Aug 18 2009 - 14:00:03 PDT)
  - Re: [AMBER] antechamber am1-bcc issues Alan (Thu Aug 20 2009 - 01:28:09 PDT)
    - Re: [AMBER] antechamber am1-bcc issues Khavrutskii, Ilja (Thu Aug 20 2009 - 04:37:47 PDT)
    - RE: [AMBER] antechamber am1-bcc issues Ross Walker (Thu Aug 20 2009 - 07:29:14 PDT)
    - Re: [AMBER] antechamber am1-bcc issues Khavrutskii, Ilja (Thu Aug 20 2009 - 05:03:43 PDT)
    - Re: [AMBER] antechamber am1-bcc issues gilbert.bluemarble.net (Thu Aug 20 2009 - 05:37:53 PDT)
    - Re: [AMBER] antechamber am1-bcc issues Khavrutskii, Ilja (Thu Aug 20 2009 - 06:04:44 PDT)
- Re: [AMBER] antechamber am1-bcc issues case (Thu Aug 20 2009 - 04:18:52 PDT)
[AMBER] Error in equilibration: file _ew_box.f Biswaranjan Meher (Fri Aug 07 2009 - 13:39:00 PDT)
- Re: [AMBER] Error in equilibration: file _ew_box.f case (Fri Aug 07 2009 - 15:34:29 PDT)
[AMBER] Why..QM/MM s. Bill (Sat Aug 08 2009 - 04:26:46 PDT)
- RE: [AMBER] Why..QM/MM Ross Walker (Sat Aug 08 2009 - 10:00:27 PDT)
[AMBER] hydrogen bond? Jio M (Sun Aug 09 2009 - 04:29:23 PDT)
[AMBER] Regarding Minimization maxcyc Ashish Runthala (Sun Aug 09 2009 - 07:09:58 PDT)
- Re: [AMBER] Regarding Minimization maxcyc case (Mon Aug 10 2009 - 07:43:00 PDT)
[AMBER] DivCon - QM/MM s. Bill (Mon Aug 10 2009 - 07:11:39 PDT)
- Solved thanks Re: [AMBER] DivCon - QM/MM s. Bill (Tue Aug 11 2009 - 00:54:38 PDT)
[AMBER] Any Comment, please s. Bill (Tue Aug 11 2009 - 00:56:20 PDT)
AW: [AMBER] Any Comment, please Aust, Susanne (Tue Aug 11 2009 - 01:17:18 PDT)
- Re: AW: [AMBER] Any Comment, please s. Bill (Tue Aug 11 2009 - 01:22:16 PDT)
AW: AW: [AMBER] Any Comment, please Aust, Susanne (Tue Aug 11 2009 - 01:36:34 PDT)
- [AMBER] MM-GBSA nmode error for explicit solvent system only but not for implicit solvent system. Why? Catein Catherine (Tue Aug 11 2009 - 04:10:09 PDT)
  - Re: [AMBER] MM-GBSA nmode error for explicit solvent system only but not for implicit solvent system. Why? case (Tue Aug 11 2009 - 04:54:43 PDT)
    - RE: [AMBER] MM-GBSA nmode error for explicit solvent system only but not for implicit solvent system. Why? Catein Catherine (Wed Aug 12 2009 - 19:23:40 PDT)
    - Re: [AMBER] MM-GBSA nmode error for explicit solvent system only but not for implicit solvent system. Why? case (Thu Aug 13 2009 - 04:46:02 PDT)
    - RE: [AMBER] MM-GBSA nmode error for explicit solvent system only but not for implicit solvent system. Why? Catein Catherine (Thu Aug 13 2009 - 20:38:02 PDT)
    - Re: [AMBER] MM-GBSA nmode error for explicit solvent system only but not for implicit solvent system. Why? Ashish Runthala (Fri Aug 14 2009 - 23:05:53 PDT)
    - RE: [AMBER] MM-GBSA nmode error for explicit solvent system only but not for implicit solvent system. Why? Catein Catherine (Sat Aug 15 2009 - 19:45:34 PDT)
    - Re: [AMBER] MM-GBSA nmode error for explicit solvent system only but not for implicit solvent system. Why? Ashish Runthala (Sat Aug 15 2009 - 20:59:11 PDT)
    - RE: [AMBER] MM-GBSA nmode error for explicit solvent system only but not for implicit solvent system. Why? Catein Catherine (Sat Aug 15 2009 - 21:12:42 PDT)
    - [AMBER] Should I neutralize the models with Na+ or Mg2+ containing DNA and protein residues Catein Catherine (Sat Aug 15 2009 - 21:18:28 PDT)
    - Re: [AMBER] Should I neutralize the models with Na+ or Mg2+ containing DNA and protein residues case (Sun Aug 16 2009 - 06:14:14 PDT)
    - RE: [AMBER] MM-GBSA nmode error for explicit solvent system only but not for implicit solvent system. Why? Ross Walker (Sat Aug 15 2009 - 21:40:26 PDT)
    - RE: [AMBER] MM-GBSA nmode error for explicit solvent system only but not for implicit solvent system. Why? Catein Catherine (Sun Aug 16 2009 - 22:58:49 PDT)
    - Re: [AMBER] MM-GBSA nmode error for explicit solvent system only but not for implicit solvent system. Why? Ashish Runthala (Sun Aug 16 2009 - 23:21:45 PDT)
    - [AMBER] MM_PBSA decomp problem B. Nandy (Tue Sep 22 2009 - 05:29:23 PDT)
    - Re: [AMBER] MM-GBSA nmode error for explicit solvent system only but not for implicit solvent system. Why? case (Mon Aug 17 2009 - 19:56:17 PDT)
    - Re: [AMBER] MM-GBSA nmode error for explicit solvent system only but not for implicit solvent system. Why? Ashish Runthala (Mon Aug 17 2009 - 20:02:43 PDT)
    - [AMBER] Is it the correct procedures to strip water for MM/GBSA calculations? Catein Catherine (Mon Aug 17 2009 - 22:06:18 PDT)
    - [AMBER] How to strip water for MM/GBSA calculations? Catein Catherine (Fri Aug 21 2009 - 03:38:27 PDT)
    - Re: [AMBER] How to strip water for MM/GBSA calculations? Carlos Simmerling (Fri Aug 21 2009 - 03:53:59 PDT)
    - [AMBER] Can I do DNA bending with AMBER? Catein Catherine (Sat Aug 15 2009 - 21:15:26 PDT)
    - [AMBER] What is the parameters for Mg2+? Catein Catherine (Sat Aug 15 2009 - 21:21:46 PDT)
    - Re: [AMBER] What is the parameters for Mg2+? Tom Joseph (Sun Aug 16 2009 - 09:00:35 PDT)
    - RE: [AMBER] What is the parameters for Mg2+? Catein Catherine (Sun Aug 16 2009 - 22:59:23 PDT)
    - Re: [AMBER] What is the parameters for Mg2+? Jesper Sørensen (Mon Jan 16 2012 - 18:30:58 PST)
    - Re: [AMBER] What is the parameters for Mg2+? Brian Radak (Mon Jan 16 2012 - 20:08:30 PST)
    - Re: [AMBER] What is the parameters for Mg2+? Jesper Sørensen (Mon Jan 16 2012 - 21:29:35 PST)
    - Re: [AMBER] Can I do DNA bending with AMBER? case (Sun Aug 16 2009 - 06:13:05 PDT)
    - RE: [AMBER] Can I do DNA bending with AMBER? Catein Catherine (Sun Aug 16 2009 - 23:00:08 PDT)
[AMBER] Amber99SB eric johnson (Tue Aug 11 2009 - 07:33:34 PDT)
- Re: [AMBER] Amber99SB Carlos Simmerling (Tue Aug 11 2009 - 07:42:44 PDT)
[AMBER] suggestions pls Jio M (Tue Aug 11 2009 - 10:44:19 PDT)
- [AMBER] measuring volume of the binding pocket Mannan (Tue Aug 11 2009 - 19:03:49 PDT)
  - [AMBER] Measuring volume of the binding pocket Mannan (Tue Aug 11 2009 - 19:31:18 PDT)
- Re: [AMBER] suggestions pls Ashish Runthala (Tue Aug 11 2009 - 19:40:40 PDT)
  - Re: [AMBER] suggestions pls Jio M (Wed Aug 12 2009 - 06:04:16 PDT)
[AMBER] query regarding fes cluster subarna thakur (Tue Aug 11 2009 - 22:39:55 PDT)
- Re: [AMBER] query regarding fes cluster FyD (Wed Aug 12 2009 - 06:00:37 PDT)
[AMBER] gaussian 98 input/output for antechamber/resp wong105.llnl.gov (Wed Aug 12 2009 - 11:41:45 PDT)
- Re: [AMBER] gaussian 98 input/output for antechamber/resp Karl Kirschner (Wed Aug 12 2009 - 23:57:41 PDT)
- Re: [AMBER] gaussian 98 input/output for antechamber/resp Karl Kirschner (Thu Aug 13 2009 - 00:26:12 PDT)
[AMBER] REMD using hybrid solvent model Morad Mustafa (Wed Aug 12 2009 - 12:05:40 PDT)
[AMBER] CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS FULL PDB Manish Kumar (Wed Aug 12 2009 - 12:44:37 PDT)
- Re: [AMBER] CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS FULL PDB case (Wed Aug 12 2009 - 12:57:33 PDT)
  - Re: [AMBER] CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS FULL PDB Hector A. Baldoni (Wed Aug 12 2009 - 13:43:28 PDT)
[Amber]: REMD using hybrid solvent model Morad Mustafa (Wed Aug 12 2009 - 14:30:01 PDT)
- Re: [Amber]: REMD using hybrid solvent model Carlos Simmerling (Wed Aug 12 2009 - 16:52:56 PDT)
  - Re: [Amber]: REMD using hybrid solvent model Morad Mustafa (Fri Aug 14 2009 - 05:44:44 PDT)
    - [AMBER] Gaussian network model (GNM) Chih-Ying Lin (Fri Aug 21 2009 - 17:39:07 PDT)
    - Re: [AMBER] Gaussian network model (GNM) Adrian Roitberg (Fri Aug 21 2009 - 17:49:04 PDT)
- Re: [Amber]: REMD using hybrid solvent model Carlos Simmerling (Wed Aug 12 2009 - 16:54:20 PDT)
[AMBER] sourcing leap commands in log file Donald Keidel (Wed Aug 12 2009 - 17:32:31 PDT)
Re: [AMBER] sourcing leap commands in log file Bill Ross (Wed Aug 12 2009 - 17:47:57 PDT)
- Re: [AMBER] sourcing leap commands in log file Ashish Runthala (Fri Aug 14 2009 - 23:50:31 PDT)
[AMBER] reset velocity Parimal Kar (Wed Aug 12 2009 - 18:01:33 PDT)
- Re: [AMBER] reset velocity Tom Joseph (Wed Aug 12 2009 - 23:26:48 PDT)
[AMBER] ptraj imaging of namd generated trajectories Vlad Cojocaru (Thu Aug 13 2009 - 02:35:49 PDT)
- [AMBER] Re: ptraj imaging of namd generated trajectories Vlad Cojocaru (Thu Aug 13 2009 - 03:10:54 PDT)
[AMBER] ptraj-image Nancy (Thu Aug 13 2009 - 03:35:01 PDT)
[AMBER] box problem Nancy (Thu Aug 13 2009 - 04:20:20 PDT)
- Re: [AMBER] box problem case (Thu Aug 13 2009 - 04:50:54 PDT)
  - Re:Re: [AMBER] box problem Nancy (Thu Aug 13 2009 - 19:43:02 PDT)
    - Re: Re: [AMBER] box problem Ashish Runthala (Fri Aug 14 2009 - 23:12:10 PDT)
    - Re:Re: Re: [AMBER] box problem Nancy (Sun Aug 16 2009 - 00:31:02 PDT)
    - Re: Re: Re: [AMBER] box problem Ashish Runthala (Sun Aug 16 2009 - 07:00:50 PDT)
    - [AMBER] Conference or workshop on AMBER? Catein Catherine (Sun Aug 16 2009 - 22:56:41 PDT)
    - RE: [AMBER] Conference or workshop on AMBER? Ross Walker (Mon Aug 17 2009 - 07:22:14 PDT)
    - RE: [AMBER] Conference or workshop on AMBER? Catein Catherine (Mon Aug 17 2009 - 19:30:04 PDT)
    - RE: [AMBER] Conference or workshop on AMBER? Ross Walker (Mon Aug 17 2009 - 20:00:14 PDT)
    - Re: [AMBER] Conference or workshop on AMBER? Ashish Runthala (Mon Aug 17 2009 - 20:04:12 PDT)
    - RE: [AMBER] Conference or workshop on AMBER? Ross Walker (Mon Aug 17 2009 - 21:15:52 PDT)
    - RE: [AMBER] Conference or workshop on AMBER? Thank you. Catein Catherine (Mon Aug 17 2009 - 23:44:45 PDT)
    - RE: [AMBER] Conference or workshop on AMBER? Dharmik Meghana shankar (Mon Aug 17 2009 - 22:25:25 PDT)
    - Re: [AMBER] box problem Nancy (Mon Aug 17 2009 - 20:02:21 PDT)
    - Re: [AMBER] box problem Ashish Runthala (Mon Aug 17 2009 - 20:08:28 PDT)
    - Re:Re: [AMBER] box problem Nancy (Mon Aug 17 2009 - 20:18:02 PDT)
    - Re:Re: [AMBER] box problem Nancy (Mon Aug 17 2009 - 20:27:59 PDT)
    - RE: Re: [AMBER] box problem Ross Walker (Sun Aug 16 2009 - 09:59:59 PDT)
  - Re:Re: [AMBER] box problem Nancy (Mon Aug 17 2009 - 19:49:20 PDT)
[AMBER] NAB optimization ondrej.prenosil.marge.uochb.cas.cz (Thu Aug 13 2009 - 06:45:26 PDT)
- Re: [AMBER] NAB optimization case (Thu Aug 13 2009 - 06:56:28 PDT)
[AMBER] drying of solvent possible ? Jio M (Thu Aug 13 2009 - 06:49:00 PDT)
[AMBER] Strange QM/MM Divcon - help me out s. Bill (Thu Aug 13 2009 - 08:37:54 PDT)
- Re: [AMBER] Strange QM/MM Divcon - help me out case (Thu Aug 13 2009 - 08:52:34 PDT)
  - Re: [AMBER] Strange QM/MM Divcon - help me out Ashish Runthala (Fri Aug 14 2009 - 23:42:38 PDT)
    - RE: [AMBER] Strange QM/MM Divcon - help me out Ross Walker (Sun Aug 16 2009 - 09:55:01 PDT)
[AMBER] QM/MM types. ros.servidor.unam.mx (Thu Aug 13 2009 - 08:49:02 PDT)
- RE: [AMBER] QM/MM types. Ross Walker (Thu Aug 13 2009 - 09:11:57 PDT)
Re: [AMBER] drying of solvent possible ? Bill Ross (Thu Aug 13 2009 - 09:21:35 PDT)
- Re: [AMBER] drying of solvent possible ? Jio M (Fri Aug 14 2009 - 22:59:08 PDT)
[AMBER] Charge Problem s. Bill (Fri Aug 14 2009 - 01:25:05 PDT)
- Re: [AMBER] Charge Problem Karl Kirschner (Fri Aug 14 2009 - 01:55:07 PDT)
- Re: [AMBER] Charge Problem FyD (Sat Aug 15 2009 - 05:06:45 PDT)
[AMBER] MM_PBSA not successful workalemahu berhanu (Fri Aug 14 2009 - 14:45:41 PDT)
- Re: [AMBER] MM_PBSA not successful Jordan Monnet (Fri Aug 14 2009 - 17:05:00 PDT)
  - Re: [AMBER] MM_PBSA not successful workalemahu berhanu (Fri Aug 14 2009 - 19:21:32 PDT)
- Re: [AMBER] MM_PBSA not successful Qinghua Liao (Fri Aug 14 2009 - 18:20:55 PDT)
  - Re: [AMBER] MM_PBSA not successful workalemahu berhanu (Fri Aug 14 2009 - 19:36:39 PDT)
    - Re: [AMBER] MM_PBSA not successful Qinghua Liao (Fri Aug 14 2009 - 19:43:23 PDT)
    - Re: [AMBER] MM_PBSA not successful workalemahu berhanu (Fri Aug 14 2009 - 21:22:57 PDT)
    - Re: [AMBER] MM_PBSA not successful Qinghua Liao (Fri Aug 14 2009 - 23:55:40 PDT)
- Re: [AMBER] MM_PBSA not successful monnet.jordan.free.fr (Sat Aug 15 2009 - 15:10:08 PDT)
  - Re: [AMBER] MM_PBSA not successful workalemahu berhanu (Sun Aug 16 2009 - 10:22:01 PDT)
    - RE: [AMBER] MM_PBSA not successful Ross Walker (Sun Aug 16 2009 - 11:15:42 PDT)
[AMBER] AMBER job restart problem Kefa Lu (Sat Aug 15 2009 - 01:22:08 PDT)
- Re: [AMBER] AMBER job restart problem Ashish Runthala (Sat Aug 15 2009 - 02:57:48 PDT)
  - Re: [AMBER] AMBER job restart problem Kefa Lu (Sat Aug 15 2009 - 03:12:21 PDT)
- Re: [AMBER] AMBER job restart problem case (Sat Aug 15 2009 - 06:49:44 PDT)
  - Re: [AMBER] AMBER job restart problem Ashish Runthala (Sat Aug 15 2009 - 07:39:56 PDT)
    - Re: [AMBER] AMBER job restart problem case (Sat Aug 15 2009 - 08:40:51 PDT)
- Re: [AMBER] AMBER job restart problem Thomas Cheatham (Sat Aug 15 2009 - 08:49:10 PDT)
  - Re: [AMBER] AMBER job restart problem Kefa Lu (Sat Aug 15 2009 - 21:36:59 PDT)
    - Re: [AMBER] AMBER job restart problem Thomas Cheatham (Sat Aug 15 2009 - 21:44:27 PDT)
    - Re: [AMBER] AMBER job restart problem Kefa Lu (Sat Aug 15 2009 - 22:09:22 PDT)
[AMBER] AMBER on a Mac Mini cluster PoC Abdul Rehman Gani (Sun Aug 16 2009 - 08:51:44 PDT)
- RE: [AMBER] AMBER on a Mac Mini cluster PoC Ross Walker (Sun Aug 16 2009 - 10:08:47 PDT)
  - Re: [AMBER] AMBER on a Mac Mini cluster PoC Alan (Sun Aug 16 2009 - 15:30:19 PDT)
  - Re: [AMBER] AMBER on a Mac Mini cluster PoC Abdul Rehman Gani (Mon Aug 17 2009 - 01:13:38 PDT)
    - Re: [AMBER] AMBER on a Mac Mini cluster PoC Alan (Mon Aug 17 2009 - 03:50:30 PDT)
    - Re: [AMBER] AMBER on a Mac Mini cluster PoC Abdul Rehman Gani (Mon Aug 17 2009 - 05:31:37 PDT)
    - Re: [AMBER] AMBER on a Mac Mini cluster PoC - solved Abdul Rehman Gani (Mon Aug 17 2009 - 07:44:07 PDT)
[AMBER] Variations of the number of total hydrogen bond in MD simulations using ptraj workalemahu berhanu (Sun Aug 16 2009 - 13:13:21 PDT)
- RE: [AMBER] Variations of the number of total hydrogen bond in MD simulations using ptraj Ross Walker (Sun Aug 16 2009 - 17:30:47 PDT)
  - Re: [AMBER] Variations of the number of total hydrogen bond in MD simulations using ptraj workalemahu berhanu (Mon Aug 17 2009 - 06:26:35 PDT)
    - Re: [AMBER] Variations of the number of total hydrogen bond in MD simulations using ptraj Paul Frybarger (Mon Aug 17 2009 - 10:57:28 PDT)
[AMBER] gaussain output subarna thakur (Mon Aug 17 2009 - 00:11:00 PDT)
- Re: [AMBER] gaussain output FyD (Mon Aug 17 2009 - 02:50:53 PDT)
  - Re: [AMBER] gaussain output FyD (Mon Aug 17 2009 - 15:59:39 PDT)
[AMBER] [AmberTool] xleap problem 주태성 (Mon Aug 17 2009 - 01:57:37 PDT)
[AMBER] amber 10 test fails with pathscale 3.2 Raj (Mon Aug 17 2009 - 05:54:45 PDT)
- RE: [AMBER] amber 10 test fails with pathscale 3.2 Ross Walker (Mon Aug 17 2009 - 09:34:28 PDT)
[AMBER] amber test fails with ICC 11.0.081 Raj (Mon Aug 17 2009 - 07:57:57 PDT)
- Re: [AMBER] amber test fails with ICC 11.0.081 Carlos Simmerling (Mon Aug 17 2009 - 08:16:26 PDT)
[AMBER] Can i link and refine two domains of a single protein Ashish Runthala (Mon Aug 17 2009 - 08:32:33 PDT)
[AMBER] Re: [q4md-fft] charge calculation FyD (Mon Aug 17 2009 - 16:40:49 PDT)
[AMBER] AMBER is running silently Kefa Lu (Mon Aug 17 2009 - 15:47:34 PDT)
Re: [AMBER] AMBER is running silently Bill Ross (Mon Aug 17 2009 - 16:04:02 PDT)
- Re: [AMBER] AMBER is running silently Kefa Lu (Mon Aug 17 2009 - 16:10:17 PDT)
  - RE: [AMBER] AMBER is running silently Ross Walker (Mon Aug 17 2009 - 16:33:09 PDT)
    - Re: [AMBER] AMBER is running silently Kefa Lu (Mon Aug 17 2009 - 18:25:14 PDT)
[AMBER] antechamber execution subarna thakur (Mon Aug 17 2009 - 23:06:52 PDT)
- Re: [AMBER] antechamber execution FyD (Tue Aug 18 2009 - 16:59:40 PDT)
[AMBER] Can i link and refine the modeled domains with different proteins bound on it Ashish Runthala (Tue Aug 18 2009 - 04:13:23 PDT)
[AMBER] RDC import from PALES Thomas Pochapsky (Tue Aug 18 2009 - 07:33:42 PDT)
- Re: [AMBER] RDC import from PALES case (Fri Aug 28 2009 - 05:01:30 PDT)
[AMBER] Dimethyl Sulfoxide (DMSO) cartesian coordinates? Jose Borreguero (Tue Aug 18 2009 - 07:37:39 PDT)
- Re: [AMBER] Dimethyl Sulfoxide (DMSO) cartesian coordinates? FyD (Tue Aug 18 2009 - 17:05:19 PDT)
  - Re: [AMBER] Dimethyl Sulfoxide (DMSO) cartesian coordinates? Jose Borreguero (Tue Aug 18 2009 - 15:33:32 PDT)
- Re: [AMBER] Dimethyl Sulfoxide (DMSO) cartesian coordinates? Bill Ross (Tue Aug 18 2009 - 15:59:12 PDT)
[AMBER] ***PROBLEMS WITH GROUPLRES Maria Mirza (Tue Aug 18 2009 - 17:34:41 PDT)
[AMBER] Distance restraint and periodic boundary conditions Cyril Falvo (Tue Aug 18 2009 - 17:58:29 PDT)
- Re: [AMBER] Distance restraint and periodic boundary conditions Thomas Cheatham (Tue Aug 18 2009 - 18:23:56 PDT)
- Re: [AMBER] Distance restraint and periodic boundary conditions case (Tue Aug 18 2009 - 19:02:45 PDT)
  - Re: [AMBER] Distance restraint and periodic boundary conditions Peter Varnai (Wed Aug 19 2009 - 08:13:04 PDT)
    - Re: [AMBER] Distance restraint and periodic boundary conditions Peter Varnai (Wed Aug 19 2009 - 09:16:01 PDT)
    - Re: [AMBER] Distance restraint and periodic boundary conditions Keith Van Nostrand (Wed Aug 19 2009 - 09:44:49 PDT)
    - Re: [AMBER] Distance restraint and periodic boundary conditions case (Wed Aug 19 2009 - 17:53:15 PDT)
    - Re: [AMBER] Distance restraint and periodic boundary conditions Peter Varnai (Thu Aug 20 2009 - 08:23:48 PDT)
- Re: [AMBER] Distance restraint and periodic boundary conditions Robert Duke (Sun Aug 23 2009 - 07:50:56 PDT)
[AMBER] RESP charges of Fe4S4 cluster subarna thakur (Wed Aug 19 2009 - 00:53:20 PDT)
- Re: [AMBER] RESP charges of Fe4S4 cluster vhakkim boy (Wed Aug 19 2009 - 01:40:59 PDT)
- Re: [AMBER] RESP charges of Fe4S4 cluster case (Fri Aug 21 2009 - 07:13:23 PDT)
AW: [AMBER] Conference or workshop on AMBER? Aust, Susanne (Wed Aug 19 2009 - 01:16:21 PDT)
[AMBER] resp calculation for rubredoxin vhakkim boy (Wed Aug 19 2009 - 03:11:22 PDT)
[AMBER] Problem with loading PDB into tleap Kamali Sripathi (Wed Aug 19 2009 - 06:21:30 PDT)
- Re: [AMBER] Problem with loading PDB into tleap Ashish Runthala (Wed Aug 19 2009 - 06:56:59 PDT)
  - Re: [AMBER] Problem with loading PDB into tleap Kamali Sripathi (Wed Aug 19 2009 - 07:06:15 PDT)
    - Re: [AMBER] Problem with loading PDB into tleap Ashish Runthala (Wed Aug 19 2009 - 08:03:19 PDT)
    - Re: [AMBER] Problem with loading PDB into tleap ksripath.umich.edu (Wed Aug 19 2009 - 12:00:22 PDT)
    - [AMBER] angle with ptraj E.M. (Wed Aug 19 2009 - 12:27:29 PDT)
    - RE: [AMBER] angle with ptraj Seetin, Matthew (Wed Aug 19 2009 - 12:42:07 PDT)
    - [AMBER] Re: angle with ptraj E.M. (Wed Aug 19 2009 - 12:44:56 PDT)
- Re: [AMBER] Problem with loading PDB into tleap case (Wed Aug 19 2009 - 16:55:52 PDT)
  - Re: [AMBER] Problem with loading PDB into tleap Ashish Runthala (Wed Aug 19 2009 - 19:53:04 PDT)
    - Re: [AMBER] Problem with loading PDB into tleap Kamali Sripathi (Tue Sep 08 2009 - 06:49:20 PDT)
    - Re: [AMBER] Problem with loading PDB into tleap Ashish Runthala (Tue Sep 08 2009 - 08:14:46 PDT)
[AMBER] why is nonpolar solvation energy not implemented for dynamic in amber TaoPaul (Wed Aug 19 2009 - 08:29:38 PDT)
[AMBER] ptraj cluster - snapshot number of a representative structure Marcin Krol (Thu Aug 20 2009 - 01:26:09 PDT)
- Re: [AMBER] ptraj cluster - snapshot number of a representative structure Jianyin Shao (Thu Aug 20 2009 - 08:50:22 PDT)
[AMBER] box volume not understood? Jio M (Thu Aug 20 2009 - 06:54:52 PDT)
- RE: [AMBER] box volume not understood? Ross Walker (Thu Aug 20 2009 - 08:43:42 PDT)
  - RE: [AMBER] box volume not understood? Jio M (Thu Aug 20 2009 - 11:26:41 PDT)
    - RE: [AMBER] box volume not understood? Ross Walker (Thu Aug 20 2009 - 16:21:00 PDT)
    - RE: [AMBER] box volume not understood? Jio M (Thu Aug 20 2009 - 21:43:31 PDT)
- RE: [AMBER] box volume not understood? Bill Ross (Thu Aug 20 2009 - 19:53:52 PDT)
- RE: [AMBER] box volume not understood? Bill Ross (Fri Aug 21 2009 - 09:15:51 PDT)
[AMBER] center of mass dhacademic (Thu Aug 20 2009 - 13:50:47 PDT)
[AMBER] mm_pbsa-Binding and Stability tests? Antonija Tomić (Fri Aug 21 2009 - 03:04:35 PDT)
- RE: [AMBER] mm_pbsa-Binding and Stability tests? Niel Henriksen (Fri Aug 21 2009 - 07:52:49 PDT)
  - RE: [AMBER] mm_pbsa-Binding and Stability tests? Antonija Tomić (Mon Aug 24 2009 - 02:51:28 PDT)
    - RE: [AMBER] mm_pbsa-Binding and Stability tests? Niel Henriksen (Mon Aug 24 2009 - 10:24:09 PDT)
    - RE: [AMBER] mm_pbsa-Binding and Stability tests? Antonija Tomić (Wed Aug 26 2009 - 02:15:54 PDT)
- Re: [AMBER] mm_pbsa-Binding and Stability tests? Ray Luo (Fri Aug 21 2009 - 14:29:58 PDT)
[AMBER] update on am1-bcc charge problem in antechamber case (Fri Aug 21 2009 - 09:32:30 PDT)
RE: [AMBER] PMEMD 10 overflow issues Ross Walker (Fri Aug 21 2009 - 13:57:12 PDT)
- RE: [AMBER] PMEMD 10 overflow issues ben rodriguez (Fri Aug 21 2009 - 14:17:36 PDT)
  - Re: [AMBER] PMEMD 10 overflow issues Ashish Runthala (Fri Aug 21 2009 - 19:52:55 PDT)
    - RE: [AMBER] PMEMD 10 overflow issues Ross Walker (Sat Aug 22 2009 - 10:21:30 PDT)
  - RE: [AMBER] PMEMD 10 overflow issues Ross Walker (Sat Aug 22 2009 - 10:25:31 PDT)
[AMBER] protein-ligand binding simulation times Andrew Voronkov (Fri Aug 21 2009 - 22:09:54 PDT)
- Re: [AMBER] protein-ligand binding simulation times steinbrt.rci.rutgers.edu (Sat Aug 22 2009 - 02:50:35 PDT)
  - Re: [AMBER] protein-ligand binding simulation times Andrew Voronkov (Sat Aug 22 2009 - 03:32:42 PDT)
[AMBER] ambpdb water removal for rst files Andrew Voronkov (Fri Aug 21 2009 - 23:53:14 PDT)
- Re: [AMBER] ambpdb water removal for rst files Andrew Voronkov (Sun Dec 06 2009 - 11:44:28 PST)
- Re: [AMBER] ambpdb water removal for rst files Bill Ross (Sun Dec 06 2009 - 12:03:00 PST)
- Re: [AMBER] ambpdb water removal for rst files Bill Ross (Sun Dec 06 2009 - 12:09:26 PST)
  - Re: [AMBER] ambpdb water removal for rst files Andrew Voronkov (Sun May 29 2011 - 10:35:32 PDT)
    - Re: [AMBER] ambpdb water removal for rst files Anselm Horn (Sun May 29 2011 - 13:00:12 PDT)
    - Re: [AMBER] ambpdb water removal for rst files Jason Swails (Sun May 29 2011 - 19:40:42 PDT)
- Re: [AMBER] ambpdb water removal for rst files Bill Ross (Sun May 29 2011 - 17:27:36 PDT)
Re: [AMBER] ambpdb water removal for rst files Bill Ross (Sat Aug 22 2009 - 07:45:30 PDT)
[AMBER] ptraj-rms vs carnal; questions on RMSD of ligand drift Andrew Voronkov (Sun Aug 23 2009 - 04:55:01 PDT)
[AMBER] Re: AMBER: WARNING in readAmberTrajectory(): Set #7918 is corrupted (-) Andrew Voronkov (Sun Aug 23 2009 - 06:48:07 PDT)
[AMBER] acetone lib and frcmod files? Jose Borreguero (Sun Aug 23 2009 - 14:36:43 PDT)
- RE: [AMBER] acetone lib and frcmod files? Ross Walker (Sun Aug 23 2009 - 22:08:16 PDT)
  - RE: [AMBER] acetone lib and frcmod files? FyD (Mon Aug 24 2009 - 00:31:40 PDT)
    - Re: [AMBER] acetone lib and frcmod files? Jose Borreguero (Mon Aug 24 2009 - 05:56:51 PDT)
    - Re: [AMBER] acetone lib and frcmod files? FyD (Mon Aug 24 2009 - 13:13:33 PDT)
    - Re: [AMBER] acetone lib and frcmod files? Jose Borreguero (Mon Aug 24 2009 - 14:34:07 PDT)
    - Re: [AMBER] acetone lib and frcmod files? FyD (Tue Aug 25 2009 - 00:47:50 PDT)
    - Re: [AMBER] acetone lib and frcmod files? FyD (Tue Aug 25 2009 - 00:50:57 PDT)
[AMBER] ABMD Reaction Coordinates stephane acoca (Sun Aug 23 2009 - 20:11:09 PDT)
[AMBER] ABMD Reaction Coordinates stephane acoca (Sun Aug 23 2009 - 20:24:32 PDT)
[AMBER] ABMD Reaction Coordinates stephane acoca (Sun Aug 23 2009 - 20:25:43 PDT)
[AMBER] ABMD Reaction Coordinates stephane acoca (Sun Aug 23 2009 - 22:04:58 PDT)
[AMBER] Note regarding posting of the same message multiple times Ross Walker (Sun Aug 23 2009 - 22:19:36 PDT)
[AMBER] Meaning of GMAX E.M. (Mon Aug 24 2009 - 02:05:10 PDT)
- Re: [AMBER] Meaning of GMAX case (Mon Aug 24 2009 - 04:44:34 PDT)
  - Re: [AMBER] Meaning of GMAX Ashish Runthala (Mon Aug 24 2009 - 07:59:53 PDT)
    - Re: [AMBER] Meaning of GMAX Adrian Roitberg (Mon Aug 24 2009 - 08:05:36 PDT)
    - Re: [AMBER] Meaning of GMAX Ashish Runthala (Mon Aug 24 2009 - 08:38:46 PDT)
[AMBER] how to add a new atomtype for MM/GB/SA decomposition analysis TaoPaul (Mon Aug 24 2009 - 07:03:51 PDT)
[AMBER] ptraj limit on trajectory size Sasha Buzko (Mon Aug 24 2009 - 09:59:30 PDT)
- RE: [AMBER] ptraj limit on trajectory size Ross Walker (Mon Aug 24 2009 - 15:07:00 PDT)
  - Re: [AMBER] ptraj limit on trajectory size Sasha Buzko (Mon Aug 24 2009 - 15:31:14 PDT)
[AMBER] problem compiling amber tools with gcc-4.4.1 gilbert.bluemarble.net (Mon Aug 24 2009 - 20:07:44 PDT)
- Re: [AMBER] problem compiling amber tools with gcc-4.4.1 case (Tue Aug 25 2009 - 05:52:35 PDT)
[AMBER] sander does not print out all residues in range. Maria Mirza (Mon Aug 24 2009 - 21:32:31 PDT)
- RE: [AMBER] sander does not print out all residues in range. Ross Walker (Mon Aug 24 2009 - 22:00:03 PDT)
  - Re: [AMBER] sander does not print out all residues in range. Maria Mirza (Mon Aug 24 2009 - 22:17:59 PDT)
[AMBER] NATOM in prmtop and inpcrd files does not agree with the input Maria Mirza (Mon Aug 24 2009 - 21:41:39 PDT)
- RE: [AMBER] NATOM in prmtop and inpcrd files does not agree with the input Ross Walker (Mon Aug 24 2009 - 21:55:52 PDT)
  - Re: [AMBER] NATOM in prmtop and inpcrd files does not agree with the input Ashish Runthala (Mon Aug 24 2009 - 22:45:33 PDT)
    - RE: [AMBER] NATOM in prmtop and inpcrd files does not agree with the input Ross Walker (Tue Aug 25 2009 - 10:55:39 PDT)
[AMBER] ambertools test faied subarna thakur (Tue Aug 25 2009 - 04:01:12 PDT)
- Re: [AMBER] ambertools test faied case (Tue Aug 25 2009 - 04:39:16 PDT)
[AMBER] Epsilon value for Iron bharat lakhani (Tue Aug 25 2009 - 05:24:10 PDT)
- [AMBER] how much % of the total protein motion are described by the first eigenvector? Catein Catherine (Wed Aug 26 2009 - 02:05:17 PDT)
  - Re: [AMBER] how much % of the total protein motion are described by the first eigenvector? Hannes Loeffler (Wed Aug 26 2009 - 02:41:31 PDT)
    - RE: [AMBER] how much % of the total protein motion are described by the first eigenvector? Catein Catherine (Wed Aug 26 2009 - 22:58:27 PDT)
    - RE: [AMBER] how much % of the total protein motion are described by the first eigenvector? Hannes Loeffler (Thu Aug 27 2009 - 00:21:28 PDT)
    - RE: [AMBER] how much % of the total protein motion are described by the first eigenvector? Catein Catherine (Thu Aug 27 2009 - 03:02:37 PDT)
    - Re: [AMBER] how much % of the total protein motion are described by the first eigenvector? jackie (Thu Aug 27 2009 - 08:52:19 PDT)
    - [AMBER] How to use AMBER 10 for PCA analysis. Catein Catherine (Tue Sep 01 2009 - 08:30:56 PDT)
[AMBER] Single Adenine ros (Tue Aug 25 2009 - 23:09:23 PDT)
- Re: [AMBER] Single Adenine case (Wed Aug 26 2009 - 04:36:09 PDT)
  - Re: [AMBER] Single Adenine case (Wed Aug 26 2009 - 04:48:36 PDT)
    - Re: [AMBER] Single Adenine ros (Wed Aug 26 2009 - 10:50:54 PDT)
    - Re: [AMBER] Single Adenine FyD (Thu Aug 27 2009 - 00:05:54 PDT)
    - Re: [AMBER] Single Adenine ros (Thu Aug 27 2009 - 09:27:06 PDT)
    - Re: [AMBER] Single Adenine FyD (Thu Aug 27 2009 - 14:20:48 PDT)
- Re: [AMBER] Single Adenine Bill Ross (Wed Aug 26 2009 - 12:28:31 PDT)
[AMBER] Chirality error in pdb xiawei (Wed Aug 26 2009 - 00:02:43 PDT)
- Re: [AMBER] Chirality error in pdb case (Wed Aug 26 2009 - 04:52:18 PDT)
  - RE: [AMBER] Chirality error in pdb xiawei (Thu Aug 27 2009 - 23:41:45 PDT)
    - Re: [AMBER] Chirality error in pdb case (Fri Aug 28 2009 - 04:33:41 PDT)
[AMBER] ZPVE simple question ondrej.prenosil.marge.uochb.cas.cz (Wed Aug 26 2009 - 02:42:04 PDT)
- Re: [AMBER] ZPVE simple question Jerome.GOLEBIOWSKI.unice.fr (Wed Aug 26 2009 - 04:15:00 PDT)
- Re: [AMBER] ZPVE simple question case (Wed Aug 26 2009 - 04:41:27 PDT)
[AMBER] Need you help bharat lakhani (Wed Aug 26 2009 - 06:41:17 PDT)
- Re: [AMBER] Need you help Carlos Simmerling (Wed Aug 26 2009 - 06:48:20 PDT)
[AMBER] Re: question_on_MMPBSA jackie (Wed Aug 26 2009 - 08:08:01 PDT)
- RE: [AMBER] Re: question_on_MMPBSA Catein Catherine (Wed Aug 26 2009 - 22:55:59 PDT)
  - Re: [AMBER] Re: question_on_MMPBSA jackie (Thu Aug 27 2009 - 08:41:28 PDT)
[AMBER] Inquiries about antechamber Yikan Chen (Wed Aug 26 2009 - 10:07:20 PDT)
- Re: [AMBER] Inquiries about antechamber Nicholas Musolino (Wed Aug 26 2009 - 14:02:21 PDT)
  - Re: [AMBER] Inquiries about antechamber Yikan Chen (Wed Aug 26 2009 - 19:05:40 PDT)
    - Re: [AMBER] Inquiries about antechamber FyD (Wed Aug 26 2009 - 23:15:55 PDT)
  - Re: [AMBER] Inquiries about antechamber jackie (Thu Aug 27 2009 - 08:48:24 PDT)
[AMBER] SCC-DFTB MD for mercury ions in proteins Vaida Arcišauskaitė (Thu Aug 27 2009 - 09:41:17 PDT)
- Re: [AMBER] SCC-DFTB MD for mercury ions in proteins Adrian Roitberg (Thu Aug 27 2009 - 09:51:21 PDT)
[AMBER] Setting a constrain in one direction Darren Yang (Thu Aug 27 2009 - 20:15:30 PDT)
- Re: [AMBER] Setting a constrain in one direction Nicholas Musolino (Thu Aug 27 2009 - 20:40:54 PDT)
- RE: [AMBER] Setting a constrain in one direction matthew_seetin.urmc.rochester.edu (Fri Aug 28 2009 - 07:35:57 PDT)
  - [AMBER] nmr restraint for angle between vectors Peter Varnai (Fri Aug 28 2009 - 18:10:20 PDT)
[AMBER] Regarding principal component analysis using ptraj Arvind Marathe (Thu Aug 27 2009 - 23:54:40 PDT)
- Re: [AMBER] Regarding principal component analysis using ptraj Hannes Loeffler (Fri Aug 28 2009 - 00:28:29 PDT)
  - Re: [AMBER] Regarding principal component analysis using ptraj Arvind Marathe (Fri Aug 28 2009 - 04:04:22 PDT)
    - Re: [AMBER] Regarding principal component analysis using ptraj Hannes Loeffler (Fri Aug 28 2009 - 04:45:05 PDT)
    - Re: [AMBER] Regarding principal component analysis using ptraj Arvind Marathe (Fri Aug 28 2009 - 04:56:53 PDT)
[AMBER] (no subject) workalemahu berhanu (Fri Aug 28 2009 - 07:06:56 PDT)
- Re: [AMBER] (no subject) workalemahu berhanu (Fri Aug 28 2009 - 09:22:31 PDT)
[AMBER] about file format Jia Xu (Sat Aug 29 2009 - 00:55:49 PDT)
- Re: [AMBER] about file format Tom Joseph (Sat Aug 29 2009 - 07:50:37 PDT)
  - Re: [AMBER] about file format Jia Xu (Sat Aug 29 2009 - 22:32:30 PDT)
[AMBER] radius for Manganese ion Chunliyan (Sat Aug 29 2009 - 07:43:00 PDT)
- Re: [AMBER] radius for Manganese ion E.M. (Sun Aug 30 2009 - 16:38:38 PDT)
[AMBER] Dyndom Chunliyan (Sat Aug 29 2009 - 07:43:00 PDT)
- Re: [AMBER] Dyndom Carlos Simmerling (Sat Aug 29 2009 - 07:59:23 PDT)
- RE: [AMBER] Dyndom Loeffler, Hannes (STFC,DL,CSE) (Sat Aug 29 2009 - 08:18:18 PDT)
[AMBER] (no subject) workalemahu berhanu (Sat Aug 29 2009 - 08:29:34 PDT)
- Re: [AMBER] (no subject) workalemahu berhanu (Sun Aug 30 2009 - 22:19:27 PDT)
[AMBER] problem with 4-Hydroxyl-Proline tutorial Jia Xu (Sun Aug 30 2009 - 00:46:18 PDT)
- Re: [AMBER] problem with 4-Hydroxyl-Proline tutorial FyD (Mon Aug 31 2009 - 13:10:52 PDT)
  - Re: [AMBER] problem with 4-Hydroxyl-Proline tutorial Jia Xu (Mon Aug 31 2009 - 22:10:50 PDT)
[AMBER] Changing pH of the system nicholus bhattacharjee (Sun Aug 30 2009 - 04:13:17 PDT)
- Re: [AMBER] Changing pH of the system Adrian Roitberg (Sun Aug 30 2009 - 08:26:01 PDT)
  - Re: [AMBER] Changing pH of the system nicholus bhattacharjee (Sun Aug 30 2009 - 08:40:42 PDT)
    - Re: [AMBER] Changing pH of the system Adrian Roitberg (Sun Aug 30 2009 - 09:18:32 PDT)
    - [AMBER] WATERSHELL Mannan (Sun Aug 30 2009 - 22:02:51 PDT)
    - Re: [AMBER] Changing pH of the system nicholus bhattacharjee (Tue Sep 01 2009 - 06:43:01 PDT)
[AMBER] How to derive charges from the output bharat lakhani (Sun Aug 30 2009 - 22:33:21 PDT)
- Re: [AMBER] How to derive charges from the output Barbault Florent (Mon Aug 31 2009 - 00:38:09 PDT)
  - Re: [AMBER] How to derive charges from the output bharat lakhani (Mon Aug 31 2009 - 06:43:15 PDT)
    - Re: [AMBER] How to derive charges from the output FyD (Mon Aug 31 2009 - 13:35:46 PDT)
    - Re: [AMBER] How to derive charges from the output bharat lakhani (Tue Sep 01 2009 - 01:46:12 PDT)
[AMBER] Query regarding watershell command Mannan (Mon Aug 31 2009 - 03:38:08 PDT)
- [AMBER] How to remove Hydrogen using ptraj Mannan (Tue Sep 01 2009 - 03:50:44 PDT)
  - Re: [AMBER] How to remove Hydrogen using ptraj Thomas Cheatham III (Tue Sep 01 2009 - 08:55:43 PDT)
    - Re: [AMBER] How to remove Hydrogen using ptraj case (Tue Sep 01 2009 - 10:19:51 PDT)
    - Re: [AMBER] How to remove Hydrogen using ptraj Thomas Cheatham III (Tue Sep 01 2009 - 10:25:10 PDT)
[AMBER] divcon question Andrei Neamtu (Mon Aug 31 2009 - 04:31:35 PDT)
- Re: [AMBER] divcon question case (Mon Aug 31 2009 - 05:34:14 PDT)
Re: [AMBER] ATP/GTP parameters case (Mon Aug 31 2009 - 05:41:22 PDT)
- Re: [AMBER] ATP/GTP parameters FyD (Mon Aug 31 2009 - 13:20:50 PDT)
  - Re: [AMBER] ATP/GTP parameters E.M. (Mon Aug 31 2009 - 13:50:09 PDT)
    - Re: [AMBER] ATP/GTP parameters FyD (Mon Aug 31 2009 - 23:10:41 PDT)
  - Re: [AMBER] ATP/GTP parameters E.M. (Mon Aug 31 2009 - 21:48:39 PDT)
    - Re: [AMBER] ATP/GTP parameters wang (Mon Aug 31 2009 - 22:02:08 PDT)
  - RE: [AMBER] ATP/GTP parameters Steve Seibold (Tue Sep 01 2009 - 04:42:09 PDT)
    - RE: [AMBER] ATP/GTP parameters FyD (Tue Sep 01 2009 - 09:25:45 PDT)
    - RE: [AMBER] ATP/GTP parameters Steve Seibold (Tue Sep 01 2009 - 09:29:59 PDT)
    - Re: [AMBER] ATP/GTP parameters E.M. (Wed Jan 13 2010 - 17:31:22 PST)
    - Re: [AMBER] ATP/GTP parameters FyD (Thu Jan 14 2010 - 07:23:27 PST)
  - Re: [AMBER] ATP/GTP parameters E.M. (Tue Dec 08 2009 - 20:36:19 PST)
[AMBER] momentum in MD simulation dhacademic (Mon Aug 31 2009 - 07:37:42 PDT)
- Re: [AMBER] momentum in MD simulation case (Tue Sep 01 2009 - 04:48:52 PDT)
[AMBER] antechamber bug report Matthew Walsh (Mon Aug 31 2009 - 09:43:08 PDT)
- Re: [AMBER] antechamber bug report case (Mon Aug 31 2009 - 10:36:33 PDT)
[AMBER] ACE and NME patch: VMD ??? Siddharth Rastogi (Mon Aug 31 2009 - 17:25:47 PDT)
- RE: [AMBER] ACE and NME patch: VMD ??? Ross Walker (Tue Sep 01 2009 - 10:54:38 PDT)
Re: [AMBER] Docking with Amber case (Mon Aug 31 2009 - 17:58:49 PDT)
[AMBER] how to pull a dna balaji nagarajan (Mon Aug 31 2009 - 19:39:10 PDT)
- Re: [AMBER] how to pull a dna Sam Danziger (Tue Sep 01 2009 - 04:17:09 PDT)
[AMBER] symbol lookup error Bala subramanian (Tue Sep 01 2009 - 01:43:51 PDT)
- RE: [AMBER] symbol lookup error Ross Walker (Tue Sep 01 2009 - 12:42:49 PDT)
[AMBER] how to pull a dna balaji nagarajan (Tue Sep 01 2009 - 07:24:29 PDT)
[AMBER] Reg. snapshot_statistics.out.snap Rose Tamil (Tue Sep 01 2009 - 10:04:08 PDT)
Re: [AMBER] Creating new counterions Bill Ross (Tue Sep 01 2009 - 12:58:55 PDT)
Re: [AMBER] Creating new counterions case (Tue Sep 01 2009 - 13:03:48 PDT)
- [AMBER] Question regarding PCA analysis. Catein Catherine (Tue Sep 01 2009 - 20:53:10 PDT)
  - Re: [AMBER] Question regarding PCA analysis. Chris Moth (Thu Sep 03 2009 - 07:17:42 PDT)
    - RE: [AMBER] Question regarding PCA analysis. Catein Catherine (Thu Sep 03 2009 - 19:55:42 PDT)
    - [AMBER] MM-GBAS decomp error Catein Catherine (Fri Sep 04 2009 - 03:29:35 PDT)
[AMBER] Simulation short peptide and protein interaction Rilei Yu (Tue Sep 01 2009 - 17:50:29 PDT)
- Re: [AMBER] Simulation short peptide and protein interaction case (Wed Sep 02 2009 - 05:15:06 PDT)
  - [AMBER] How to find water-mediated hydrogen bond? Catein Catherine (Wed Sep 02 2009 - 07:10:37 PDT)
    - Re: [AMBER] How to find water-mediated hydrogen bond? Hannes Loeffler (Thu Sep 03 2009 - 00:53:51 PDT)
  - Re: [AMBER] Simulation short peptide and protein interaction Rilei Yu (Thu Sep 03 2009 - 05:22:10 PDT)
    - Re: [AMBER] Simulation short peptide and protein interaction Carlos Simmerling (Thu Sep 03 2009 - 06:34:27 PDT)
[AMBER] question about ptraj Jeffrey (Wed Sep 02 2009 - 01:20:12 PDT)
- RE: [AMBER] question about ptraj Niel Henriksen (Wed Sep 02 2009 - 07:37:39 PDT)
[AMBER] how to give force values in TMD balaji nagarajan (Wed Sep 02 2009 - 03:03:41 PDT)
[AMBER] Active site - Ion - Search engine s. Bill (Wed Sep 02 2009 - 07:53:39 PDT)
[AMBER] What is dual topology Ashish Runthala (Wed Sep 02 2009 - 08:25:19 PDT)
- Re: [AMBER] What is dual topology case (Wed Sep 02 2009 - 08:48:51 PDT)
[AMBER] How to consider the off centre charges Ashish Runthala (Wed Sep 02 2009 - 08:28:40 PDT)
- Re: [AMBER] How to consider the off centre charges case (Wed Sep 02 2009 - 08:50:12 PDT)
[AMBER] unit of force constant balaji nagarajan (Wed Sep 02 2009 - 09:57:25 PDT)
[AMBER] antechamber bug: output of incorrect bond character Matthew Walsh (Wed Sep 02 2009 - 11:37:44 PDT)
- Re: [AMBER] antechamber bug: output of incorrect bond character case (Wed Sep 02 2009 - 18:53:37 PDT)
  - Re: [AMBER] antechamber bug: output of incorrect bond character Matthew Walsh (Wed Sep 02 2009 - 21:30:04 PDT)
    - Re: [AMBER] antechamber bug: output of incorrect bond character case (Thu Sep 03 2009 - 04:26:19 PDT)
    - Re: [AMBER] antechamber bug: output of incorrect bond character Matthew Walsh (Thu Sep 03 2009 - 08:15:00 PDT)
    - Re: [AMBER] antechamber bug: output of incorrect bond character case (Thu Sep 03 2009 - 09:29:03 PDT)
[AMBER] Question about the debug forces Faezeh Salehi (Wed Sep 02 2009 - 14:30:47 PDT)
[AMBER] how to deal with aromatic nitro group with antechamber Lin Xu (Wed Sep 02 2009 - 15:04:13 PDT)
- Re: [AMBER] how to deal with aromatic nitro group with antechamber case (Wed Sep 02 2009 - 19:15:14 PDT)
[AMBER] Heme + Fe(II) + O2 + histidine parameter Haining Liu (Wed Sep 02 2009 - 20:36:31 PDT)
- Re: [AMBER] Heme + Fe(II) + O2 + histidine parameter FyD (Thu Sep 03 2009 - 00:03:45 PDT)
  - Re: [AMBER] Heme + Fe(II) + O2 + histidine parameter Haining Liu (Thu Sep 03 2009 - 14:13:09 PDT)
    - Re: [AMBER] Heme + Fe(II) + O2 + histidine parameter FyD (Fri Sep 04 2009 - 00:43:00 PDT)
[AMBER] ATP and GTP parameters E.M. (Wed Sep 02 2009 - 22:29:47 PDT)
- Re: [AMBER] ATP and GTP parameters FyD (Wed Sep 02 2009 - 23:15:54 PDT)
  - Re: [AMBER] ATP and GTP parameters E.M. (Wed Sep 02 2009 - 23:30:31 PDT)
    - Re: [AMBER] ATP and GTP parameters Sergey Samsonov (Wed Sep 02 2009 - 23:35:33 PDT)
    - Re: [AMBER] ATP and GTP parameters FyD (Thu Sep 03 2009 - 02:36:45 PDT)
    - Re: [AMBER] ATP and GTP parameters Carlos Simmerling (Thu Sep 03 2009 - 04:54:13 PDT)
    - Re: [AMBER] ATP and GTP parameters E.M. (Thu Sep 03 2009 - 19:08:02 PDT)
    - Re: [AMBER] ATP and GTP parameters FyD (Thu Sep 03 2009 - 01:35:11 PDT)
[AMBER] What should be the standard input file when imin=5 Ashish Runthala (Thu Sep 03 2009 - 00:25:49 PDT)
- Re: [AMBER] What should be the standard input file when imin=5 Carlos Simmerling (Thu Sep 03 2009 - 04:55:48 PDT)
[AMBER] QM/MM simulation gaurav panwar (Thu Sep 03 2009 - 13:11:42 PDT)
- RE: [AMBER] QM/MM simulation Ross Walker (Thu Sep 03 2009 - 13:43:45 PDT)
[AMBER] Problem about adding a small residue to DNA Yikan Chen (Thu Sep 03 2009 - 21:33:52 PDT)
- 回复： [AMBER] Problem about adding a small residue to DNA Rilei Yu (Thu Sep 03 2009 - 23:33:50 PDT)
  - Re: 回复： [AMBER] Problem about adding a small residue to DNA Yikan Chen (Fri Sep 04 2009 - 12:51:38 PDT)
    - Re: 回复： [AMBER] Problem about adding a small residue to DNA Yikan Chen (Fri Sep 04 2009 - 13:03:54 PDT)
    - Re: 回复： [AMBER] Problem about adding a small residue to DNA case (Fri Sep 04 2009 - 13:37:23 PDT)
    - Re: 回复： [AMBER] Problem about adding a small residue to DNA Yikan Chen (Fri Sep 04 2009 - 14:38:27 PDT)
    - Re: 回复： [AMBER] Problem about adding a small residue to DNA case (Sun Sep 06 2009 - 05:30:23 PDT)
    - Re: 回复： [AMBER] Problem about adding a small residue to DNA Yikan Chen (Sun Sep 06 2009 - 08:47:04 PDT)
    - Re: [AMBER] Problem about adding a small residue to DNA FyD (Mon Sep 07 2009 - 02:53:14 PDT)
- Re: [AMBER] Problem about adding a small residue to DNA case (Fri Sep 04 2009 - 12:32:53 PDT)
[AMBER] Kinetics Soumya Lipsa Rath (Thu Sep 03 2009 - 23:39:54 PDT)
- Re: [AMBER] Kinetics case (Fri Sep 04 2009 - 12:29:24 PDT)
  - Re: [AMBER] Kinetics Soumya Lipsa Rath (Mon Sep 07 2009 - 23:36:18 PDT)
    - [AMBER] Enquiry about MM/GBSA output file. Catein Catherine (Tue Sep 08 2009 - 00:14:19 PDT)
[AMBER] prep file Jio M (Fri Sep 04 2009 - 02:24:04 PDT)
- Re: [AMBER] prep file case (Fri Sep 04 2009 - 07:09:06 PDT)
[AMBER] Dummy atoms and MM-PBSA Alireza Shaneh (Fri Sep 04 2009 - 09:48:16 PDT)
- Re: [AMBER] Dummy atoms and MM-PBSA Ray Luo (Fri Sep 04 2009 - 11:25:33 PDT)
[AMBER] nmropt option Jio M (Fri Sep 04 2009 - 11:05:25 PDT)
- Re: [AMBER] nmropt option Carlos Simmerling (Fri Sep 04 2009 - 11:15:13 PDT)
  - Re: [AMBER] nmropt option Jio M (Fri Sep 04 2009 - 22:23:09 PDT)
    - Re: [AMBER] nmropt option Carlos Simmerling (Sat Sep 05 2009 - 03:59:04 PDT)
[AMBER] Provisional Support for AMBER 10 PMEMD on NVIDIA GPUs Ross Walker (Fri Sep 04 2009 - 11:51:44 PDT)
[AMBER] Antechamber generate a prep file in a wrong order... Yikan Chen (Sat Sep 05 2009 - 12:37:53 PDT)
- Re: [AMBER] Antechamber generate a prep file in a wrong order... case (Sun Sep 06 2009 - 05:26:02 PDT)
[AMBER] How to find a protein's energy Ashish Runthala (Sat Sep 05 2009 - 20:48:01 PDT)
- Re: [AMBER] How to find a protein's energy Carlos Simmerling (Sun Sep 06 2009 - 04:49:53 PDT)
  - Re: [AMBER] How to find a protein's energy Ashish Runthala (Sun Sep 06 2009 - 05:30:26 PDT)
[AMBER] R.E.D. : Gaussian Error manoj singh (Sun Sep 06 2009 - 11:40:48 PDT)
- Re: [AMBER] R.E.D. : Gaussian Error FyD (Sun Sep 06 2009 - 12:41:41 PDT)
  - Re: [AMBER] R.E.D. : Gaussian Error manoj singh (Sun Sep 06 2009 - 21:22:44 PDT)
    - Re: [AMBER] R.E.D. : Gaussian Error FyD (Sun Sep 06 2009 - 22:07:34 PDT)
    - Re: [AMBER] R.E.D. : Gaussian Error manoj singh (Sun Sep 06 2009 - 22:46:54 PDT)
[AMBER] (no subject) gunajyoti das (Mon Sep 07 2009 - 02:21:45 PDT)
[AMBER] problem in QM/MM input file gaurav panwar (Mon Sep 07 2009 - 10:33:20 PDT)
- Re: [AMBER] problem in QM/MM input file Tom Joseph (Tue Sep 08 2009 - 05:37:56 PDT)
[AMBER] loadpdb Jagdeesh C (Mon Sep 07 2009 - 10:36:58 PDT)
- Re: [AMBER] loadpdb Carlos Simmerling (Mon Sep 07 2009 - 11:01:10 PDT)
  - Re: [AMBER] loadpdb Jagdeesh C (Mon Sep 07 2009 - 11:31:42 PDT)
    - Re: [AMBER] loadpdb Ashish Runthala (Mon Sep 07 2009 - 20:00:47 PDT)
    - [AMBER] problem of PBCAL/GB Qinghua Liao (Mon Sep 07 2009 - 22:05:37 PDT)
    - Re: [AMBER] problem of PBCAL/GB Ray Luo (Mon Sep 07 2009 - 22:58:44 PDT)
    - Re: [AMBER] problem of PBCAL/GB Qinghua Liao (Tue Sep 08 2009 - 02:40:42 PDT)
    - Re: [AMBER] loadpdb Tom Joseph (Tue Sep 08 2009 - 05:31:56 PDT)
    - Re: [AMBER] loadpdb Carlos Simmerling (Tue Sep 08 2009 - 06:39:12 PDT)
- Re: [AMBER] loadpdb Bill Ross (Tue Sep 08 2009 - 09:58:12 PDT)
  - Re: [AMBER] loadpdb Jagdeesh C (Tue Sep 08 2009 - 18:55:36 PDT)
    - Re: [AMBER] loadpdb Carlos Simmerling (Wed Sep 09 2009 - 04:35:04 PDT)
    - [AMBER] Any tutorial on the proper way to merge a ligand and protein? Dean Cuebas (Wed Sep 09 2009 - 11:26:02 PDT)
    - Re: [AMBER] Any tutorial on the proper way to merge a ligand and protein? case (Wed Sep 09 2009 - 11:50:13 PDT)
    - Re: [AMBER] Any tutorial on the proper way to merge a ligand and protein? Dean Cuebas (Wed Sep 09 2009 - 12:12:00 PDT)
    - Re: [AMBER] Any tutorial on the proper way to merge a ligand and protein? Scott Brozell (Fri Oct 16 2009 - 12:40:56 PDT)
    - RE: [AMBER] Any tutorial on the proper way to merge a ligand and protein? cc cc (Fri Sep 11 2009 - 11:16:55 PDT)
    - Re: [AMBER] Any tutorial on the proper way to merge a ligand and protein? case (Fri Sep 11 2009 - 12:54:39 PDT)
    - [AMBER] What is the unit of RMSF? Catein Catherine (Sat Sep 12 2009 - 01:13:02 PDT)
    - Re: [AMBER] What is the unit of RMSF? case (Sat Sep 12 2009 - 06:37:42 PDT)
    - [AMBER] how to calculate correct RMSF? Catein Catherine (Mon Sep 14 2009 - 04:21:52 PDT)
    - Re: [AMBER] how to calculate correct RMSF? case (Mon Sep 14 2009 - 05:33:29 PDT)
    - RE: [AMBER] how to calculate correct RMSF? Catein Catherine (Mon Sep 14 2009 - 17:57:20 PDT)
- Re: [AMBER] loadpdb Bill Ross (Tue Sep 08 2009 - 19:53:32 PDT)
[AMBER] general query: implicit solvation Jio M (Tue Sep 08 2009 - 02:28:49 PDT)
- Re: [AMBER] general query: implicit solvation Carlos Simmerling (Tue Sep 08 2009 - 03:11:24 PDT)
[AMBER] loading PDB of a RNA sequence gunajyoti das (Tue Sep 08 2009 - 03:31:47 PDT)
- Re: [AMBER] loading PDB of a RNA sequence Carlos Simmerling (Tue Sep 08 2009 - 03:33:57 PDT)
- Re: [AMBER] loading PDB of a RNA sequence case (Tue Sep 08 2009 - 04:38:34 PDT)
[AMBER] No sp2 improper torsion term for NB-CA-CB-CB qiaoyan (Tue Sep 08 2009 - 05:29:17 PDT)
- Re: [AMBER] No sp2 improper torsion term for NB-CA-CB-CB case (Tue Sep 08 2009 - 05:58:33 PDT)
[AMBER] unit of force constant balaji nagarajan (Tue Sep 08 2009 - 06:16:08 PDT)
- Re: [AMBER] unit of force constant Carlos Simmerling (Tue Sep 08 2009 - 06:21:40 PDT)
  - RE: [AMBER] unit of force constant balaji nagarajan (Tue Sep 08 2009 - 06:41:37 PDT)
[AMBER] How to denature DNA balaji nagarajan (Tue Sep 08 2009 - 07:00:43 PDT)
- Re: [AMBER] How to denature DNA Adrian Roitberg (Tue Sep 08 2009 - 07:04:30 PDT)
  - RE: [AMBER] How to denature DNA balaji nagarajan (Tue Sep 08 2009 - 09:29:57 PDT)
    - Re: [AMBER] How to denature DNA Adrian Roitberg (Tue Sep 08 2009 - 09:46:51 PDT)
    - RE: [AMBER] How to denature DNA balaji nagarajan (Tue Sep 08 2009 - 09:58:36 PDT)
    - Re: [AMBER] How to denature DNA Adrian Roitberg (Tue Sep 08 2009 - 10:12:00 PDT)
- RE: [AMBER] How to denature DNA Bill Ross (Tue Sep 08 2009 - 10:33:09 PDT)
  - RE: [AMBER] How to denature DNA balaji nagarajan (Tue Sep 08 2009 - 21:01:55 PDT)
- RE: [AMBER] How to denature DNA Bill Ross (Wed Sep 09 2009 - 09:38:04 PDT)
  - RE: [AMBER] How to denature DNA balaji nagarajan (Wed Sep 09 2009 - 10:14:37 PDT)
[AMBER] AmberTools 1.3 / CHAMBER Mag. Thomas Taylor (Tue Sep 08 2009 - 07:29:23 PDT)
[AMBER] amoeba.prm problem? Ivan Gladich (Tue Sep 08 2009 - 07:31:43 PDT)
- Re: [AMBER] amoeba.prm problem? case (Wed Sep 09 2009 - 12:17:39 PDT)
  - Re: [AMBER] amoeba.prm problem? Ivan Gladich (Fri Sep 11 2009 - 13:34:07 PDT)
    - Re: [AMBER] amoeba.prm problem? case (Sat Sep 12 2009 - 06:46:52 PDT)
    - Re: [AMBER] amoeba.prm problem? Ivan Gladich (Fri Sep 18 2009 - 12:57:39 PDT)
[AMBER] TI in Amber9/10 Alessandro S. Nascimento (Tue Sep 08 2009 - 08:47:26 PDT)
- Re: [AMBER] TI in Amber9/10 steinbrt.rci.rutgers.edu (Tue Sep 08 2009 - 10:41:32 PDT)
- Re: [AMBER] TI in Amber9/10 Ilyas Yildirim (Tue Sep 08 2009 - 11:07:40 PDT)
Re: [AMBER] loadpdb Bill Ross (Tue Sep 08 2009 - 09:53:03 PDT)
[AMBER] logdvdl does not work helde010.umn.edu (Tue Sep 08 2009 - 09:53:14 PDT)
- Re: [AMBER] logdvdl does not work steinbrt.rci.rutgers.edu (Tue Sep 08 2009 - 10:37:31 PDT)
[AMBER] loading a following attached protein in amber 10 albert albert (Tue Sep 08 2009 - 10:09:09 PDT)
- Re: [AMBER] loading a following attached protein in amber 10 David Watson (Tue Sep 08 2009 - 10:26:19 PDT)
- Re: [AMBER] loading a following attached protein in amber 10 case (Tue Sep 08 2009 - 10:27:47 PDT)
  - Re: [AMBER] loading a following attached protein in amber 10 albert albert (Tue Sep 08 2009 - 10:43:55 PDT)
[AMBER] QMMM NEB with PM3-PDDG fails with ASSERTion 'ierr.eq.0' pimd_init.f line 320 Keith Van Nostrand (Tue Sep 08 2009 - 12:26:14 PDT)
- Re: [AMBER] QMMM NEB with PM3-PDDG fails with ASSERTion 'ierr.eq.0' pimd_init.f line 320 case (Sat Sep 12 2009 - 07:17:16 PDT)
[AMBER] Hbond analysis: Direction of the hydrogen Age.Skjevik.biomed.uib.no (Tue Sep 08 2009 - 12:45:19 PDT)
- Re: [AMBER] Hbond analysis: Direction of the hydrogen Shulin Zhuang (Tue Sep 08 2009 - 12:54:22 PDT)
  - Re: [AMBER] Hbond analysis: Direction of the hydrogen Age.Skjevik.biomed.uib.no (Tue Sep 08 2009 - 14:56:50 PDT)
[AMBER] Leap warning manoj singh (Tue Sep 08 2009 - 22:38:33 PDT)
- Re: [AMBER] Leap warning Ashish Runthala (Wed Sep 09 2009 - 00:21:03 PDT)
- Re: [AMBER] Leap warning case (Wed Sep 09 2009 - 04:31:36 PDT)
[AMBER] about the number of residues after MD Qinghua Liao (Wed Sep 09 2009 - 00:23:03 PDT)
Re: [AMBER] PK zero for specific dihedral and parmchk Carlos Simmerling (Wed Sep 09 2009 - 03:23:31 PDT)
- Re: [AMBER] PK zero for specific dihedral and parmchk case (Wed Sep 09 2009 - 04:32:51 PDT)
[AMBER] gaff.dat questions gilbert.bluemarble.net (Wed Sep 09 2009 - 07:02:28 PDT)
- Re: [AMBER] gaff.dat questions case (Wed Sep 09 2009 - 07:16:23 PDT)
[AMBER] parameterization of protein-ligand complex cc cc (Wed Sep 09 2009 - 09:29:07 PDT)
- Re: [AMBER] parameterization of protein-ligand complex case (Wed Sep 09 2009 - 09:39:05 PDT)
  - RE: [AMBER] parameterization of protein-ligand complex cc cc (Wed Sep 09 2009 - 10:44:17 PDT)
- RE: [AMBER] parameterization of protein-ligand complex Jeff Yeo (Mon Sep 14 2009 - 08:03:25 PDT)
Re: [AMBER] parameterization of protein-ligand complex Bill Ross (Wed Sep 09 2009 - 10:12:28 PDT)
- RE: [AMBER] parameterization of protein-ligand complex cc cc (Wed Sep 09 2009 - 10:41:52 PDT)
[AMBER] Solvate in an alkaline solution vallespardojl.chem.leidenuniv.nl (Thu Sep 10 2009 - 01:07:07 PDT)
- Re: [AMBER] Solvate in an alkaline solution case (Thu Sep 10 2009 - 05:05:44 PDT)
[AMBER] input file Mag. Thomas Taylor (Thu Sep 10 2009 - 03:48:06 PDT)
- Re: [AMBER] input file Carlos Simmerling (Thu Sep 10 2009 - 04:03:17 PDT)
  - Re: [AMBER] input file / skinnb Mag. Thomas Taylor (Wed Sep 16 2009 - 00:49:32 PDT)
    - Re: [AMBER] input file / skinnb case (Wed Sep 16 2009 - 04:56:01 PDT)
    - Re: [AMBER] input file / skinnb Mag. Thomas Taylor (Wed Sep 16 2009 - 22:50:16 PDT)
    - Re: [AMBER] input file / skinnb Robert Duke (Wed Sep 16 2009 - 07:23:06 PDT)
- Re: [AMBER] input file Jenny Iskrenova (Thu Sep 10 2009 - 06:05:03 PDT)
  - Re: [AMBER] input file Ashish Runthala (Thu Sep 10 2009 - 07:05:32 PDT)
[AMBER] QM/MM minimization gaurav panwar (Thu Sep 10 2009 - 07:05:37 PDT)
Re: [AMBER] input file Bill Ross (Thu Sep 10 2009 - 09:51:10 PDT)
[AMBER] question with radial distribution function Ganesh Kamath (Thu Sep 10 2009 - 15:08:34 PDT)
[AMBER] periodic boundary condition for implicit solvent simulation and SHORT command Workalemahu Berhanu (Thu Sep 10 2009 - 15:37:32 PDT)
- Re: [AMBER] periodic boundary condition for implicit solvent simulation and SHORT command case (Thu Sep 10 2009 - 19:04:53 PDT)
[AMBER] DMF solvent box Abhishek Banerjee (Thu Sep 10 2009 - 19:40:21 PDT)
- Re: [AMBER] DMF solvent box Jio M (Fri Sep 11 2009 - 08:00:40 PDT)
- Re: [AMBER] DMF solvent box FyD (Sat Sep 12 2009 - 07:07:30 PDT)
  - Re: [AMBER] DMF solvent box Abhishek Banerjee (Sat Sep 12 2009 - 22:33:39 PDT)
  - Re: [AMBER] DMF solvent box Abhishek Banerjee (Sun Sep 13 2009 - 01:56:18 PDT)
    - Re: [AMBER] DMF solvent box FyD (Sun Sep 13 2009 - 02:25:33 PDT)
- Re: [AMBER] DMF solvent box Abhishek Banerjee (Sun Sep 13 2009 - 07:24:04 PDT)
  - Re: [AMBER] DMF solvent box FyD (Sun Sep 13 2009 - 10:01:13 PDT)
- Re: [AMBER] DMF solvent box Abhishek Banerjee (Mon Sep 14 2009 - 06:18:30 PDT)
  - Re: [AMBER] DMF solvent box FyD (Mon Sep 14 2009 - 08:04:58 PDT)
    - Re: [AMBER] DMF solvent box Abhishek Banerjee (Tue Sep 15 2009 - 21:33:23 PDT)
    - Re: [AMBER] DMF solvent box FyD (Tue Sep 15 2009 - 22:09:42 PDT)
- Re: [AMBER] DMF solvent box Abhishek Banerjee (Wed Sep 16 2009 - 23:15:53 PDT)
  - Re: [AMBER] DMF solvent box FyD (Thu Sep 17 2009 - 00:00:06 PDT)
    - Re: [AMBER] DMF solvent box Abhishek Banerjee (Fri Sep 18 2009 - 22:24:08 PDT)
    - Re: [AMBER] DMF solvent box FyD (Fri Sep 18 2009 - 23:36:20 PDT)
- Re: [AMBER] DMF solvent box Abhishek Banerjee (Tue Oct 06 2009 - 21:10:22 PDT)
  - Re: [AMBER] DMF solvent box FyD (Wed Oct 07 2009 - 13:34:35 PDT)
- Re: [AMBER] DMF solvent box Abhishek Banerjee (Thu Oct 08 2009 - 20:41:02 PDT)
  - Re: [AMBER] DMF solvent box FyD (Thu Oct 08 2009 - 21:08:59 PDT)
[AMBER] PBSA for gp41 binding free energy shuqing wang (Thu Sep 10 2009 - 23:42:59 PDT)
- Re: [AMBER] PBSA for gp41 binding free energy Ray Luo (Fri Sep 11 2009 - 18:59:07 PDT)
[AMBER] dihedral force calculation Germain Vallverdu (Fri Sep 11 2009 - 07:35:08 PDT)
- Re: [AMBER] dihedral force calculation case (Sat Sep 12 2009 - 07:04:34 PDT)
[AMBER] RESP RED s. Bill (Fri Sep 11 2009 - 11:40:24 PDT)
- Re: [AMBER] RESP RED FyD (Sat Sep 12 2009 - 07:35:16 PDT)
[AMBER] charge consideration Jio M (Fri Sep 11 2009 - 13:17:34 PDT)
- Re: [AMBER] charge consideration case (Sat Sep 12 2009 - 06:59:56 PDT)
[AMBER] "nan" in gaussian input files generated by antechamber Yikan Chen (Fri Sep 11 2009 - 13:19:04 PDT)
- Re: [AMBER] "nan" in gaussian input files generated by antechamber case (Sat Sep 12 2009 - 06:55:14 PDT)
- Re: [AMBER] "nan" in gaussian input files generated by antechamber FyD (Sat Sep 12 2009 - 07:58:52 PDT)
[AMBER] What is the Optimum Ph for solvating a protein Ashish Runthala (Sun Sep 13 2009 - 06:08:40 PDT)
- Re: [AMBER] What is the Optimum Ph for solvating a protein case (Sun Sep 13 2009 - 14:19:24 PDT)
[AMBER] load .crd & .top in xleap vallespardojl.chem.leidenuniv.nl (Sun Sep 13 2009 - 07:21:15 PDT)
- Re: [AMBER] load .crd & .top in xleap oguz gurbulak (Sun Sep 13 2009 - 12:20:26 PDT)
[AMBER] re: charge interaction Jio M (Sun Sep 13 2009 - 07:38:43 PDT)
- Re: [AMBER] re: charge interaction case (Sun Sep 13 2009 - 14:13:19 PDT)
  - Re: [AMBER] re: charge interaction case (Sun Sep 13 2009 - 14:37:55 PDT)
[AMBER] variable header for ABMD stephane acoca (Sun Sep 13 2009 - 20:03:00 PDT)
[AMBER] re: charge consideration Jio M (Mon Sep 14 2009 - 01:38:27 PDT)
[AMBER] How to prepare the coordinate and toplogy files in leap ? xuemeiwang1103 (Mon Sep 14 2009 - 02:03:59 PDT)
- Re: [AMBER] How to prepare the coordinate and toplogy files in leap ? case (Mon Sep 14 2009 - 04:56:08 PDT)
[AMBER] error xleap: XaLeap_wcl is empty Mari Carmen Pérez (Mon Sep 14 2009 - 02:59:09 PDT)
- Re: [AMBER] error xleap: XaLeap_wcl is empty case (Mon Sep 14 2009 - 05:02:12 PDT)
[AMBER] Ki and G s. Bill (Mon Sep 14 2009 - 04:39:20 PDT)
- Re: [AMBER] Ki and G steinbrt.rci.rutgers.edu (Mon Sep 14 2009 - 04:59:40 PDT)
  - Re: [AMBER] Ki and G Adrian Roitberg (Mon Sep 14 2009 - 07:28:57 PDT)
  - Re: [AMBER] Ki and G Marek Maly (Mon Sep 14 2009 - 10:02:36 PDT)
    - Re: [AMBER] Ki and G case (Mon Sep 14 2009 - 10:23:49 PDT)
    - Re: [AMBER] Ki and G Marek Maly (Mon Sep 14 2009 - 11:41:33 PDT)
    - Re: [AMBER] Ki and G steinbrt.rci.rutgers.edu (Mon Sep 14 2009 - 13:09:55 PDT)
    - Re: [AMBER] Ki and G case (Mon Sep 14 2009 - 13:24:05 PDT)
    - Re: [AMBER] Ki and G Marek Maly (Tue Sep 15 2009 - 04:58:07 PDT)
[AMBER] Carbon Nanotube Library file (CNT) Christopher Stiles (Mon Sep 14 2009 - 06:59:57 PDT)
[AMBER] radial distribution function in amber Ganesh Kamath (Mon Sep 14 2009 - 07:58:56 PDT)
[AMBER] Question on ECAVITY term of MM_PBSA Gianluca Degliesposti (Mon Sep 14 2009 - 08:28:12 PDT)
[AMBER] makeDIST_RST: no map function Workalemahu Berhanu (Mon Sep 14 2009 - 12:30:15 PDT)
- RE: [AMBER] makeDIST_RST: no map function Duggan, Brendan M. (Tue Sep 15 2009 - 06:40:00 PDT)
- Re: [AMBER] makeDIST_RST: no map function case (Tue Sep 15 2009 - 07:38:23 PDT)
  - Re: [AMBER] makeDIST_RST: no map function Workalemahu Berhanu (Tue Sep 15 2009 - 08:11:27 PDT)
  - Re: [AMBER] makeDIST_RST: no map function Workalemahu Berhanu (Tue Sep 15 2009 - 08:24:56 PDT)
[AMBER] Problem on PMEMD zyxism (Mon Sep 14 2009 - 18:11:57 PDT)
- Re: [AMBER] Problem on PMEMD Tom Joseph (Mon Sep 14 2009 - 18:34:11 PDT)
  - Re: [AMBER] Problem on PMEMD Adrian Roitberg (Mon Sep 14 2009 - 18:40:35 PDT)
- Re: Re: [AMBER] Problem on PMEMD zyxism (Mon Sep 14 2009 - 18:41:50 PDT)
- Re: [AMBER] Problem on PMEMD Robert Duke (Mon Sep 14 2009 - 18:46:16 PDT)
[AMBER] Error in minimal xuemeiwang1103 (Tue Sep 15 2009 - 00:27:18 PDT)
- Re: [AMBER] Error in minimal case (Tue Sep 15 2009 - 04:56:02 PDT)
  - Re:Re: [AMBER] Error in minimal xuemeiwang1103 (Tue Sep 15 2009 - 06:54:58 PDT)
    - Re: Re: [AMBER] Error in minimal case (Tue Sep 15 2009 - 15:15:06 PDT)
[AMBER] problem running pmemd gbrna tests wong105.llnl.gov (Tue Sep 15 2009 - 11:07:14 PDT)
[AMBER] can antechamber convert a prep file from cartesian to internal coordinates? Paul Ledbetter (Tue Sep 15 2009 - 13:25:56 PDT)
- Re: [AMBER] can antechamber convert a prep file from cartesian to internal coordinates? case (Tue Sep 15 2009 - 15:12:25 PDT)
  - Re: [AMBER] can antechamber convert a prep file from cartesian to internal coordinates? Paul Ledbetter (Tue Sep 15 2009 - 16:34:54 PDT)
- Re: [AMBER] can antechamber convert a prep file from cartesian to internal coordinates? Bill Ross (Tue Sep 15 2009 - 15:15:38 PDT)
  - Re: [AMBER] can antechamber convert a prep file from cartesian to internal coordinates? Paul Ledbetter (Tue Sep 15 2009 - 16:40:09 PDT)
[AMBER] About the PMEMD compiling for CUDA wang (Tue Sep 15 2009 - 22:17:52 PDT)
- RE: [AMBER] About the PMEMD compiling for CUDA Ross Walker (Tue Sep 15 2009 - 23:55:11 PDT)
[AMBER] About the PMEMD compiling for CUDA Ross Walker (Tue Sep 15 2009 - 22:26:19 PDT)
[AMBER] database Steve Seibold (Wed Sep 16 2009 - 07:59:14 PDT)
- Re: [AMBER] database case (Wed Sep 16 2009 - 08:26:24 PDT)
  - RE: [AMBER] database Steve Seibold (Wed Sep 16 2009 - 09:11:47 PDT)
    - Re: [AMBER] database case (Wed Sep 16 2009 - 09:53:56 PDT)
    - RE: [AMBER] database FyD (Wed Sep 16 2009 - 09:59:30 PDT)
    - RE: [AMBER] database Steve Seibold (Wed Sep 16 2009 - 10:14:46 PDT)
    - RE: [AMBER] database FyD (Wed Sep 16 2009 - 11:56:16 PDT)
    - RE: [AMBER] database Steve Seibold (Thu Sep 17 2009 - 06:43:25 PDT)
    - RE: [AMBER] database FyD (Thu Sep 17 2009 - 09:00:22 PDT)
    - RE: [AMBER] database Steve Seibold (Thu Sep 17 2009 - 12:46:20 PDT)
    - RE: [AMBER] database Jeff Yeo (Thu Sep 17 2009 - 14:01:48 PDT)
    - RE: [AMBER] database FyD (Thu Sep 17 2009 - 14:54:29 PDT)
    - Re: [AMBER] database case (Thu Sep 17 2009 - 15:23:30 PDT)
    - Re: [AMBER] database FyD (Fri Sep 18 2009 - 00:28:53 PDT)
    - RE: [AMBER] database Steve Seibold (Fri Sep 18 2009 - 08:03:44 PDT)
    - Re: [AMBER] database case (Fri Sep 18 2009 - 10:23:08 PDT)
    - RE: [AMBER] database Steve Seibold (Fri Sep 18 2009 - 12:10:19 PDT)
    - RE: [AMBER] database FyD (Fri Sep 18 2009 - 17:49:17 PDT)
    - Re: [AMBER] database case (Fri Sep 18 2009 - 19:46:39 PDT)
- RE: [AMBER] database Bill Ross (Wed Sep 16 2009 - 10:54:47 PDT)
  - [AMBER] antechamber error Taufik Al-Sarraj (Wed Sep 16 2009 - 11:18:32 PDT)
    - Re: [AMBER] antechamber error case (Wed Sep 16 2009 - 11:43:56 PDT)
    - Re: [AMBER] antechamber error Taufik Al-Sarraj (Wed Sep 16 2009 - 11:52:26 PDT)
    - Re: [AMBER] antechamber error Taufik Al-Sarraj (Wed Sep 16 2009 - 12:11:26 PDT)
    - RE: [AMBER] antechamber error Mike Hanby (Thu Dec 10 2009 - 14:34:30 PST)
    - Re: [AMBER] antechamber error David Watson (Thu Dec 10 2009 - 15:26:00 PST)
    - Re: [AMBER] antechamber error case (Fri Dec 11 2009 - 04:51:44 PST)
    - RE: [AMBER] antechamber error Mike Hanby (Wed Jan 27 2010 - 13:51:42 PST)
    - Re: [AMBER] antechamber error case (Wed Jan 05 2011 - 05:20:35 PST)
    - Re: [AMBER] antechamber error Andre Serobian (Wed Jan 05 2011 - 13:59:08 PST)
    - Re: [AMBER] antechamber error Andre Serobian (Wed Jan 05 2011 - 16:22:42 PST)
    - Re: [AMBER] antechamber error Jason Swails (Wed Jan 05 2011 - 21:25:56 PST)
  - RE: [AMBER] database FyD (Wed Sep 16 2009 - 11:58:38 PDT)
[AMBER] RDC analysis: "No restraint defined" Michael Durney (Wed Sep 16 2009 - 09:10:34 PDT)
- Re: [AMBER] RDC analysis: "No restraint defined" case (Wed Sep 16 2009 - 09:47:41 PDT)
[AMBER] question with hbond Ganesh Kamath (Wed Sep 16 2009 - 14:36:18 PDT)
[AMBER] loading RNA sequence in xleap gunajyoti das (Thu Sep 17 2009 - 01:27:49 PDT)
- Re: [AMBER] loading RNA sequence in xleap FyD (Thu Sep 17 2009 - 02:39:09 PDT)
- Re: [AMBER] loading RNA sequence in xleap case (Thu Sep 17 2009 - 05:13:38 PDT)
[AMBER] PES QM and MM s. Bill (Thu Sep 17 2009 - 03:53:46 PDT)
[AMBER] Force Field Fitting s. Bill (Thu Sep 17 2009 - 04:36:33 PDT)
- Re: [AMBER] Force Field Fitting manoj singh (Thu Sep 17 2009 - 10:20:50 PDT)
  - [AMBER] Discrepancy between AMBER and VMD calculation Sunita Patel (Thu Sep 17 2009 - 12:11:07 PDT)
  - Re: [AMBER] Force Field Fitting s. Bill (Thu Sep 17 2009 - 12:27:46 PDT)
    - Re: [AMBER] Force Field Fitting manoj singh (Thu Sep 17 2009 - 12:32:33 PDT)
[AMBER] install ambertools Karl Kirschner (Thu Sep 17 2009 - 05:55:22 PDT)
- Re: [AMBER] install ambertools case (Thu Sep 17 2009 - 06:40:28 PDT)
[AMBER] NAB syntax Michael Durney (Thu Sep 17 2009 - 07:58:58 PDT)
- Re: [AMBER] NAB syntax Andreas Svrcek-Seiler (Thu Sep 17 2009 - 08:21:51 PDT)
- Re: [AMBER] NAB syntax case (Thu Sep 17 2009 - 08:22:29 PDT)
[AMBER] pH calculations Michael Durney (Thu Sep 17 2009 - 08:01:08 PDT)
Re: [AMBER] PES QM and MM Bill Ross (Thu Sep 17 2009 - 09:08:35 PDT)
[AMBER] how to ouput the electrostatic potential at a single atomic position? Jose Borreguero (Thu Sep 17 2009 - 12:06:54 PDT)
[AMBER] LINMIN failure notice Jio M (Fri Sep 18 2009 - 03:20:18 PDT)
- Re: [AMBER] LINMIN failure notice Ashish Runthala (Fri Sep 18 2009 - 03:46:09 PDT)
  - RE: [AMBER] LINMIN failure notice Ross Walker (Fri Sep 18 2009 - 16:41:33 PDT)
- Re: [AMBER] LINMIN failure notice case (Fri Sep 18 2009 - 04:38:33 PDT)
- Re: [AMBER] LINMIN failure notice Bill Ross (Fri Sep 18 2009 - 09:18:41 PDT)
[AMBER] PROBLEM WITH CHCL3BOX pdb Silvia Carlotto (Fri Sep 18 2009 - 05:49:12 PDT)
- Re: [AMBER] PROBLEM WITH CHCL3BOX pdb case (Fri Sep 18 2009 - 06:26:40 PDT)
  - Re: [AMBER] PROBLEM WITH CHCL3BOX pdb Hannes Loeffler (Fri Sep 18 2009 - 08:16:06 PDT)
    - Re: [AMBER] PROBLEM WITH CHCL3BOX pdb case (Fri Sep 18 2009 - 15:01:23 PDT)
[AMBER] how to make 50% aqueous TFE box? parul sharma (Fri Sep 18 2009 - 06:47:01 PDT)
- Re: [AMBER] how to make 50% aqueous TFE box? FyD (Fri Sep 18 2009 - 17:22:35 PDT)
[AMBER] Cygwin Home Directory Wallace Kunin (Fri Sep 18 2009 - 10:51:17 PDT)
- Re: [AMBER] Cygwin Home Directory Bill Ross (Fri Sep 18 2009 - 13:56:17 PDT)
  - Re: [AMBER] Cygwin Home Directory Wallace Kunin (Sat Sep 19 2009 - 09:13:20 PDT)
    - Re: [AMBER] Cygwin Home Directory case (Sat Sep 19 2009 - 15:11:57 PDT)
    - Re: [AMBER] Cygwin Home Directory Ashish Runthala (Sat Sep 19 2009 - 19:51:11 PDT)
    - Re: [AMBER] Cygwin Home Directory Wallace Kunin (Mon Sep 21 2009 - 09:29:11 PDT)
    - Re: [AMBER] Cygwin Home Directory case (Mon Sep 21 2009 - 10:14:59 PDT)
- Re: [AMBER] Cygwin Home Directory Bill Ross (Sat Sep 19 2009 - 10:29:59 PDT)
- Re: [AMBER] Cygwin Home Directory Bill Ross (Mon Sep 21 2009 - 10:45:02 PDT)
Re: [AMBER] Cygwin Home Directory Bill Ross (Fri Sep 18 2009 - 11:19:44 PDT)
- Re: [AMBER] Cygwin Home Directory Wallace Kunin (Fri Sep 18 2009 - 12:12:22 PDT)
  - Re: [AMBER] Cygwin Home Directory manoj singh (Fri Sep 18 2009 - 12:30:28 PDT)
[AMBER] warning in dispatchToken Jeff Yeo (Sun Sep 20 2009 - 03:30:57 PDT)
- Re: [AMBER] warning in dispatchToken case (Sun Sep 20 2009 - 06:14:49 PDT)
[AMBER] combining MD runs for post-MD analysis Jeff Yeo (Sun Sep 20 2009 - 17:02:12 PDT)
- Re: [AMBER] combining MD runs for post-MD analysis Qinghua Liao (Sun Sep 20 2009 - 18:01:22 PDT)
- Re: [AMBER] combining MD runs for post-MD analysis case (Sun Sep 20 2009 - 18:35:08 PDT)
[AMBER] Regarding united atom force field aneesh cna (Mon Sep 21 2009 - 03:17:20 PDT)
- Re: [AMBER] Regarding united atom force field Ray Luo (Mon Sep 21 2009 - 10:32:34 PDT)
- Re: [AMBER] Regarding united atom force field FyD (Mon Sep 21 2009 - 23:13:03 PDT)
[AMBER] problem building sander.apbs Oliver Kuhn (Mon Sep 21 2009 - 03:49:48 PDT)
- Re: [AMBER] problem building sander.apbs case (Mon Sep 21 2009 - 04:39:41 PDT)
- Re: [AMBER] problem building sander.apbs Oliver Kuhn (Mon Sep 21 2009 - 07:03:34 PDT)
  - Re: [AMBER] problem building sander.apbs case (Mon Sep 21 2009 - 07:38:20 PDT)
- Re: [AMBER] problem building sander.apbs Oliver Kuhn (Tue Sep 22 2009 - 01:10:10 PDT)
  - Re: [AMBER] problem building sander.apbs case (Tue Sep 22 2009 - 12:12:50 PDT)
  - Re: [AMBER] problem building sander.apbs Robert Konecny (Tue Sep 22 2009 - 12:55:40 PDT)
[AMBER] Question on ECAVITY term of MM_PBSA Gianluca Degliesposti (Mon Sep 21 2009 - 04:18:27 PDT)
- Re: [AMBER] Question on ECAVITY term of MM_PBSA Ray Luo (Mon Sep 21 2009 - 10:30:57 PDT)
- Re: [AMBER] Question on ECAVITY term of MM_PBSA Ray Luo (Mon Sep 21 2009 - 18:28:32 PDT)
[AMBER] generate prmtop file from CHARMM psf file Jeffrey (Mon Sep 21 2009 - 07:34:59 PDT)
Re: [AMBER] combining MD runs for post-MD analysis Bill Ross (Mon Sep 21 2009 - 10:32:53 PDT)
[AMBER] ACS COMP division awards- Oct 19th deadline Carlos Simmerling (Mon Sep 21 2009 - 10:49:28 PDT)
[AMBER] Installing AmberTools and Amber10 in Ubuntu - Instructions. David Dubins (Mon Sep 21 2009 - 16:02:47 PDT)
- Re: [AMBER] Installing AmberTools and Amber10 in Ubuntu - Instructions. oguz gurbulak (Mon Sep 21 2009 - 23:46:27 PDT)
[AMBER] Pentane UA model aneesh cna (Mon Sep 21 2009 - 23:23:35 PDT)
- Re: [AMBER] Pentane UA model FyD (Tue Sep 22 2009 - 00:02:50 PDT)
[AMBER] RMSDf of heavy atoms Syed Tarique Moin (Tue Sep 22 2009 - 04:45:26 PDT)
[AMBER] Compiling Amber10 Williams, John (Tue Sep 22 2009 - 05:56:43 PDT)
[AMBER] ambertools and Snow Leopard 64 bits kernel Alan (Tue Sep 22 2009 - 06:55:25 PDT)
- Re: [AMBER] ambertools and Snow Leopard 64 bits kernel Tom Joseph (Tue Sep 22 2009 - 11:12:55 PDT)
  - Re: [AMBER] ambertools and Snow Leopard 64 bits kernel Alan (Tue Sep 22 2009 - 14:41:18 PDT)
    - Re: [AMBER] ambertools and Snow Leopard 64 bits kernel Tom Joseph (Tue Sep 22 2009 - 17:18:17 PDT)
    - Re: [AMBER] ambertools and Snow Leopard 64 bits kernel gilbert.bluemarble.net (Tue Sep 22 2009 - 19:18:12 PDT)
    - Re: [AMBER] ambertools and Snow Leopard 64 bits kernel Alan (Wed Sep 23 2009 - 07:21:30 PDT)
    - Re: [AMBER] ambertools and Snow Leopard 64 bits kernel Scott Brozell (Wed Dec 09 2009 - 13:48:30 PST)
  - Re: [AMBER] ambertools and Snow Leopard 64 bits kernel case (Wed Sep 23 2009 - 13:26:16 PDT)
[AMBER] Installation issue Ashveen Seenauth (Tue Sep 22 2009 - 09:17:49 PDT)
Re: [AMBER] Installation issue Bill Ross (Tue Sep 22 2009 - 09:31:47 PDT)
- Re: [AMBER] Installation issue Ashveen Seenauth (Tue Sep 22 2009 - 09:45:13 PDT)
  - Re: [AMBER] Installation issue Tom Joseph (Tue Sep 22 2009 - 09:55:20 PDT)
    - Re: [AMBER] Installation issue Ashveen Seenauth (Tue Sep 22 2009 - 10:25:12 PDT)
    - Re: [AMBER] Installation issue Tom Joseph (Tue Sep 22 2009 - 10:41:51 PDT)
[AMBER] Parameter Problem manoj singh (Tue Sep 22 2009 - 12:35:53 PDT)
[AMBER] group distance restraint XIAOHUICANG (Tue Sep 22 2009 - 12:36:03 PDT)
[AMBER] Problem regarding Hbond analysis Abhishek Singh (Tue Sep 22 2009 - 12:43:50 PDT)
[AMBER] Parameter Problem manoj singh (Tue Sep 22 2009 - 12:46:59 PDT)
- Re: [AMBER] Parameter Problem FyD (Wed Sep 23 2009 - 01:28:49 PDT)
  - Re: [AMBER] Parameter Problem Manish Kumar (Wed Sep 23 2009 - 06:28:11 PDT)
Re: [AMBER] Problem regarding Hbond analysis Bill Ross (Tue Sep 22 2009 - 13:00:55 PDT)
[AMBER] parameter for manganese Yuqin Cai (Tue Sep 22 2009 - 15:48:41 PDT)
- Re: [AMBER] parameter for manganese Mahmoud A. A. Ibrahim (Thu Sep 24 2009 - 05:17:29 PDT)
[AMBER] apbs-amber Rilei Yu (Tue Sep 22 2009 - 15:58:40 PDT)
- Re: [AMBER] apbs-amber Robert Konecny (Tue Sep 22 2009 - 16:18:28 PDT)
  - Re: [AMBER] apbs-amber Rilei Yu (Tue Sep 22 2009 - 18:41:08 PDT)
[AMBER] solvent accessible surface area Ganesh Kamath (Wed Sep 23 2009 - 12:07:23 PDT)
- Re: [AMBER] solvent accessible surface area Carlos Simmerling (Wed Sep 23 2009 - 12:20:24 PDT)
  - Re: [AMBER] solvent accessible surface area Ganesh Kamath (Wed Sep 23 2009 - 12:26:33 PDT)
    - Re: [AMBER] solvent accessible surface area Carlos Simmerling (Wed Sep 23 2009 - 12:29:57 PDT)
    - Re: [AMBER] solvent accessible surface area Siddharth Rastogi (Thu Oct 08 2009 - 02:54:01 PDT)
    - Re: [AMBER] solvent accessible surface area Ray Luo (Thu Oct 08 2009 - 11:17:09 PDT)
    - [AMBER] solvent accessible surface area Siddharth Rastogi (Thu Oct 08 2009 - 03:02:20 PDT)
[AMBER] fatal "does not have a type" error in tleap for a protein-ligand complex Jeff Yeo (Wed Sep 23 2009 - 16:24:51 PDT)
- Re: [AMBER] fatal "does not have a type" error in tleap for a protein-ligand complex case (Thu Sep 24 2009 - 15:13:39 PDT)
[AMBER] Teragrid Beale, John (Thu Sep 24 2009 - 05:08:56 PDT)
- Re: [AMBER] Teragrid Carlos Simmerling (Thu Sep 24 2009 - 05:11:41 PDT)
[AMBER] CH3Hg+ parameters babak minoofar (Thu Sep 24 2009 - 05:08:12 PDT)
[AMBER] Ewald error estimated xuemeiwang1103 (Thu Sep 24 2009 - 20:01:02 PDT)
- Re: [AMBER] Ewald error estimated Qinghua Liao (Fri Sep 25 2009 - 00:48:14 PDT)
- Re: [AMBER] Ewald error estimated case (Fri Sep 25 2009 - 08:15:31 PDT)
- Re: [AMBER] Ewald error estimated Robert Duke (Fri Sep 25 2009 - 08:50:18 PDT)
[AMBER] Ewald error estimated xuemeiwang1103 (Thu Sep 24 2009 - 20:01:05 PDT)
[AMBER] pmemd and internal dielectric Serguei Vassiliev (Fri Sep 25 2009 - 08:47:50 PDT)
- Re: [AMBER] pmemd and internal dielectric Robert Duke (Fri Sep 25 2009 - 09:07:06 PDT)
  - Re: [AMBER] pmemd and internal dielectric Adrian Roitberg (Fri Sep 25 2009 - 09:44:56 PDT)
  - Re: [AMBER] pmemd and internal dielectric Serguei Vassiliev (Fri Sep 25 2009 - 12:47:46 PDT)
- Re: [AMBER] pmemd and internal dielectric Robert Duke (Fri Sep 25 2009 - 13:10:57 PDT)
  - Re: [AMBER] pmemd and internal dielectric case (Fri Sep 25 2009 - 14:59:56 PDT)
- Re: [AMBER] pmemd and internal dielectric Robert Duke (Fri Sep 25 2009 - 15:19:10 PDT)
[AMBER] Attaching a ligand to a protein residue. Kipras Redeckas (Fri Sep 25 2009 - 14:33:58 PDT)
- Re: [AMBER] Attaching a ligand to a protein residue. case (Sat Sep 26 2009 - 07:23:18 PDT)
  - Re: [AMBER] Attaching a ligand to a protein residue. Kipras Redeckas (Sun Sep 27 2009 - 03:23:42 PDT)
[AMBER] problem when doing mm/pbsa: bad atom type Br Baifan Wang (Sun Sep 27 2009 - 19:50:46 PDT)
- Re: [AMBER] problem when doing mm/pbsa: bad atom type Br Ray Luo (Sun Sep 27 2009 - 20:10:25 PDT)
  - Re: [AMBER] problem when doing mm/pbsa: bad atom type Br Baifan Wang (Mon Sep 28 2009 - 00:26:06 PDT)
[AMBER] How to obtain amber top and crd from pdb file with POPE lipids? decastro.physics.usyd.edu.au (Sun Sep 27 2009 - 21:52:20 PDT)
- Re: [AMBER] How to obtain amber top and crd from pdb file with POPE lipids? Hannes Loeffler (Mon Sep 28 2009 - 00:34:12 PDT)
[AMBER] Your help about ptraj in AmberTools!]] Rosina Noto (Mon Sep 28 2009 - 02:59:09 PDT)
[AMBER] trouble using iAPBS Oliver Kuhn (Mon Sep 28 2009 - 05:08:27 PDT)
- Re: [AMBER] trouble using iAPBS Robert Konecny (Mon Sep 28 2009 - 07:20:31 PDT)
- Re: [AMBER] trouble using iAPBS Oliver Kuhn (Thu Oct 01 2009 - 04:31:51 PDT)
  - Re: [AMBER] trouble using iAPBS Robert Konecny (Thu Oct 01 2009 - 10:27:42 PDT)
[AMBER] Gap in rst file Katrina Lexa (Mon Sep 28 2009 - 07:47:43 PDT)
[AMBER] LJ-partial charges and force field parameters for ethylene glycol and glycerol Ganesh Kamath (Mon Sep 28 2009 - 10:03:13 PDT)
- Re: [AMBER] LJ-partial charges and force field parameters for ethylene glycol and glycerol FyD (Mon Sep 28 2009 - 11:23:20 PDT)
[AMBER] partial charges in Amber force field Jihang Wang (Mon Sep 28 2009 - 10:52:28 PDT)
- Re: [AMBER] partial charges in Amber force field FyD (Mon Sep 28 2009 - 11:32:42 PDT)
[AMBER] why should one restrain the position of the counterions? Jose Borreguero (Mon Sep 28 2009 - 11:28:20 PDT)
[AMBER] Problem in compiling AMBER9 in parallel ! Pradipta Bandyopadhyay (Tue Sep 29 2009 - 06:04:47 PDT)
- Re: [AMBER] Problem in compiling AMBER9 in parallel ! Abhishek Banerjee (Tue Sep 29 2009 - 10:25:36 PDT)
- Re: [AMBER] Problem in compiling AMBER9 in parallel ! case (Tue Sep 29 2009 - 11:08:41 PDT)
[AMBER] Problem in test run Kshatresh Dutta Dubey (Tue Sep 29 2009 - 07:21:56 PDT)
- Re: [AMBER] Problem in test run Carlos Simmerling (Tue Sep 29 2009 - 07:26:38 PDT)
  - Re: [AMBER] Problem in test run Kshatresh Dutta Dubey (Tue Sep 29 2009 - 08:05:13 PDT)
    - Re: [AMBER] Problem in test run Carlos Simmerling (Tue Sep 29 2009 - 08:06:55 PDT)
    - Re: [AMBER] Problem in test run Kshatresh Dutta Dubey (Tue Sep 29 2009 - 08:14:35 PDT)
    - Re: [AMBER] Problem in test run Kshatresh Dutta Dubey (Tue Sep 29 2009 - 08:23:29 PDT)
- Re: [AMBER] Problem in test run case (Tue Sep 29 2009 - 09:50:19 PDT)
[AMBER] Zinc Sel Ercan (Tue Sep 29 2009 - 14:26:53 PDT)
- Re: [AMBER] Zinc Rubben Torella (Tue Sep 29 2009 - 14:31:31 PDT)
  - Re: [AMBER] Zinc Roman Osman (Tue Sep 29 2009 - 17:08:28 PDT)
[AMBER] Compiling Amber with gfortran-4.5.0 on a mac Ben Roberts (Tue Sep 29 2009 - 14:37:31 PDT)
- Re: [AMBER] Compiling Amber with gfortran-4.5.0 on a mac case (Fri Oct 02 2009 - 06:19:11 PDT)
  - Re: [AMBER] Compiling Amber with gfortran-4.5.0 on a mac Ben Roberts (Fri Oct 02 2009 - 07:20:47 PDT)
    - Re: [AMBER] Compiling Amber with gfortran-4.5.0 on a mac Mengjuei Hsieh (Tue Oct 06 2009 - 19:05:54 PDT)
[AMBER] MM_PBSA Zhongjie Liang (Tue Sep 29 2009 - 18:30:40 PDT)
[AMBER] too many missing parameters in frcmod for the prep of my ligand xueqin pang (Wed Sep 30 2009 - 02:21:31 PDT)
- Re: [AMBER] too many missing parameters in frcmod for the prep of my ligand FyD (Wed Sep 30 2009 - 03:30:32 PDT)
[AMBER] No restrt file xuemeiwang1103 (Wed Sep 30 2009 - 02:32:38 PDT)
- Re: [AMBER] No restrt file case (Wed Sep 30 2009 - 03:29:32 PDT)
  - Re:Re: [AMBER] No restrt file null (Wed Sep 30 2009 - 04:39:24 PDT)
    - Re: Re: [AMBER] No restrt file case (Wed Sep 30 2009 - 05:06:47 PDT)
[AMBER] xleap problem ! balaji nagarajan (Wed Sep 30 2009 - 11:40:58 PDT)
[AMBER] decomposing energies Beroza, Paul (Thu Oct 01 2009 - 09:15:07 PDT)
[AMBER] Environment Variables in Cygwin Don't Remain Wallace Kunin (Thu Oct 01 2009 - 09:54:29 PDT)
- Re: [AMBER] Environment Variables in Cygwin Don't Remain Jack Shultz (Thu Oct 01 2009 - 10:12:19 PDT)
Re: [AMBER] Environment Variables in Cygwin Don't Remain Bill Ross (Thu Oct 01 2009 - 11:57:43 PDT)
[AMBER] method used to determine partial charges? Paul Brandt (Thu Oct 01 2009 - 13:25:54 PDT)
- Re: [AMBER] method used to determine partial charges? Jihang Wang (Thu Oct 01 2009 - 13:36:31 PDT)
- Re: [AMBER] method used to determine partial charges? Bill Ross (Thu Oct 01 2009 - 14:19:29 PDT)
  - Re: [AMBER] method used to determine partial charges? Jihang Wang (Thu Oct 01 2009 - 14:28:45 PDT)
- Re: [AMBER] method used to determine partial charges? Bill Ross (Thu Oct 01 2009 - 15:18:01 PDT)
  - Re: [AMBER] method used to determine partial charges? Jihang Wang (Thu Oct 01 2009 - 15:26:24 PDT)
    - Re: [AMBER] method used to determine partial charges? Carlos Simmerling (Thu Oct 01 2009 - 15:30:21 PDT)
    - Re: [AMBER] method used to determine partial charges? Jihang Wang (Thu Oct 01 2009 - 15:42:38 PDT)
    - Re: [AMBER] method used to determine partial charges? FyD (Thu Oct 01 2009 - 21:27:13 PDT)
[AMBER] Dipole moment visualization. K.R. (Thu Oct 01 2009 - 14:37:29 PDT)
[AMBER] red problem James Moore (Thu Oct 01 2009 - 18:52:46 PDT)
- Re: [AMBER] red problem FyD (Thu Oct 01 2009 - 21:48:57 PDT)
[AMBER] Protein and charged surface rrd (Thu Oct 01 2009 - 20:49:18 PDT)
[AMBER] Different optimized structures with HF and B3LYP Sanghwa Han (Fri Oct 02 2009 - 00:50:10 PDT)
- Re: [AMBER] Different optimized structures with HF and B3LYP Karl Kirschner (Fri Oct 02 2009 - 01:07:08 PDT)
[AMBER] MM_PBSA decomposition pair question Rubben Torella (Fri Oct 02 2009 - 04:09:38 PDT)
[AMBER] minimization error balaji nagarajan (Fri Oct 02 2009 - 04:42:54 PDT)
- Re: [AMBER] minimization error case (Fri Oct 02 2009 - 05:00:52 PDT)
[AMBER] Missing X11 Libraries Wallace Kunin (Fri Oct 02 2009 - 09:43:59 PDT)
- [AMBER] Re: Missing X11 Libraries Wallace Kunin (Fri Oct 02 2009 - 09:55:34 PDT)
- Re: [AMBER] Missing X11 Libraries case (Fri Oct 02 2009 - 11:56:34 PDT)
  - Re: [AMBER] Missing X11 Libraries Wallace Kunin (Fri Oct 02 2009 - 12:57:49 PDT)
    - Re: [AMBER] Missing X11 Libraries Wallace Kunin (Sat Oct 03 2009 - 10:02:05 PDT)
    - [AMBER] File format for reading in charges in antechamber Dean Cuebas (Sun Oct 04 2009 - 13:20:42 PDT)
    - Re: [AMBER] Missing X11 Libraries Wallace Kunin (Wed Oct 07 2009 - 11:04:39 PDT)
    - Re: [AMBER] Missing X11 Libraries Mengjuei Hsieh (Wed Oct 07 2009 - 13:19:20 PDT)
    - Re: [AMBER] Missing X11 Libraries FyD (Wed Oct 07 2009 - 13:45:34 PDT)
    - Re: [AMBER] Missing X11 Libraries Wallace Kunin (Wed Oct 07 2009 - 14:10:34 PDT)
    - Re: [AMBER] Missing X11 Libraries Thomas Patko (Wed Oct 07 2009 - 14:14:15 PDT)
- Re: [AMBER] Missing X11 Libraries Bill Ross (Wed Oct 07 2009 - 15:28:34 PDT)
  - Re: [AMBER] Missing X11 Libraries Wallace Kunin (Thu Oct 08 2009 - 10:09:55 PDT)
    - Re: [AMBER] Missing X11 Libraries Thomas Patko (Thu Oct 08 2009 - 10:26:26 PDT)
    - Re: [AMBER] Missing X11 Libraries Wallace Kunin (Fri Oct 09 2009 - 09:59:06 PDT)
    - Re: [AMBER] Missing X11 Libraries Wallace Kunin (Fri Oct 09 2009 - 10:03:51 PDT)
    - Re: [AMBER] Missing X11 Libraries Thomas Patko (Fri Oct 09 2009 - 10:13:22 PDT)
- Re: [AMBER] Missing X11 Libraries Bill Ross (Thu Oct 08 2009 - 10:25:32 PDT)
- Re: [AMBER] Missing X11 Libraries Bill Ross (Fri Oct 09 2009 - 10:52:01 PDT)
  - Re: [AMBER] Missing X11 Libraries Wallace Kunin (Fri Oct 09 2009 - 12:20:00 PDT)
    - Re: [AMBER] Missing X11 Libraries case (Fri Oct 09 2009 - 13:02:06 PDT)
    - Re: [AMBER] Missing X11 Libraries FyD (Fri Oct 09 2009 - 13:35:59 PDT)
    - Re: [AMBER] Missing X11 Libraries Thomas Patko (Fri Oct 09 2009 - 13:53:14 PDT)
    - Re: [AMBER] Missing X11 Libraries FyD (Fri Oct 09 2009 - 14:06:20 PDT)
- Re: [AMBER] Missing X11 Libraries Bill Ross (Fri Oct 09 2009 - 17:24:47 PDT)
[AMBER] RMSD vs time and RMSD vs residues Olotu Odunayo (Fri Oct 02 2009 - 10:40:40 PDT)
- Re: [AMBER] RMSD vs time and RMSD vs residues Luis Gracia (Fri Oct 02 2009 - 11:07:10 PDT)
- Re: [AMBER] RMSD vs time and RMSD vs residues case (Fri Oct 02 2009 - 12:12:23 PDT)
- Re: [AMBER] RMSD vs time and RMSD vs residues Sally Pias (Fri Oct 02 2009 - 12:16:33 PDT)
[AMBER] probelm-APBS Rilei Yu (Fri Oct 02 2009 - 22:41:07 PDT)
- Re: [AMBER] probelm-APBS Robert Konecny (Sun Oct 04 2009 - 17:20:18 PDT)
  - Re: [AMBER] probelm-APBS Rilei Yu (Sun Oct 04 2009 - 17:51:10 PDT)
[AMBER] MMPBSA: No radius found for F Jeff Yeo (Sun Oct 04 2009 - 17:10:12 PDT)
[AMBER] TiO2 modeling stefano_elli.libero.it (Mon Oct 05 2009 - 09:00:59 PDT)
- [AMBER] new process_mdout.pl script???? Dean Cuebas (Mon Oct 05 2009 - 11:11:49 PDT)
  - RE: [AMBER] new process_mdout.pl script???? Ross Walker (Mon Oct 05 2009 - 11:38:17 PDT)
[AMBER] R.E.D.-III.3 tools release - q4md-forcefieldtools.org FyD (Sun Oct 04 2009 - 07:37:06 PDT)
[AMBER] pucker calculation for six member rings Ganesh Kamath (Mon Oct 05 2009 - 11:03:15 PDT)
[AMBER] MM/PBSA: NaN, Infinity and ************* in snapshot_com.all.out Jeff Yeo (Mon Oct 05 2009 - 16:22:53 PDT)
- Re: [AMBER] MM/PBSA: NaN, Infinity and ************* in snapshot_com.all.out Rubben Torella (Tue Oct 06 2009 - 00:56:18 PDT)
[AMBER] MM_PBSA: abnormal VDW interaction energy LIU Huanxiang (Mon Oct 05 2009 - 19:43:21 PDT)
- Re: [AMBER] MM_PBSA: abnormal VDW interaction energy steinbrt.rci.rutgers.edu (Tue Oct 06 2009 - 01:09:27 PDT)
  - Re: [AMBER] MM_PBSA: abnormal VDW interaction energy LIU Huanxiang (Tue Oct 06 2009 - 19:54:49 PDT)
[AMBER] mm_pbsa- Decomposition: bad atom type Antonija Tomić (Tue Oct 06 2009 - 06:53:25 PDT)
[AMBER] Problem with memory in nmode analysis Alireza Shaneh (Tue Oct 06 2009 - 08:23:55 PDT)
[AMBER] using RESP program gunajyoti das (Wed Oct 07 2009 - 03:30:27 PDT)
- Re: [AMBER] using RESP program Ganesh Kamath (Wed Oct 07 2009 - 03:36:13 PDT)
  - Re: [AMBER] using RESP program FyD (Wed Oct 07 2009 - 13:04:38 PDT)
[AMBER] Re: Fw: Help required in Amber10 Installation Sudeep Narayan Banerjee (Wed Oct 07 2009 - 08:48:02 PDT)
- Re: [AMBER] Re: Fw: Help required in Amber10 Installation David Watson (Wed Oct 07 2009 - 08:53:26 PDT)
- Re: [AMBER] Re: Fw: Help required in Amber10 Installation Sudeep Narayan Banerjee (Thu Oct 15 2009 - 06:30:25 PDT)
  - Re: [AMBER] Re: Fw: Help required in Amber10 Installation case (Thu Oct 15 2009 - 06:45:42 PDT)
- Re: [AMBER] Re: Fw: Help required in Amber10 Installation Bill Ross (Thu Oct 15 2009 - 09:28:26 PDT)
Re: [AMBER] Re: Fw: Help required in Amber10 Installation Bill Ross (Wed Oct 07 2009 - 09:59:21 PDT)
- Re: [AMBER] Re: Fw: Help required in Amber10 Installation Chris Whittleston (Wed Oct 07 2009 - 10:48:18 PDT)
  - Re: [AMBER] Re: Fw: Help required in Amber10 Installation Sudeep Narayan Banerjee (Thu Oct 15 2009 - 05:11:01 PDT)
    - Re: [AMBER] Re: Fw: Help required in Amber10 Installation Nicolas Sapay (Thu Oct 15 2009 - 05:34:28 PDT)
    - Re: [AMBER] Re: Fw: Help required in Amber10 Installation Sudeep Narayan Banerjee (Thu Oct 15 2009 - 05:53:42 PDT)
    - Re: [AMBER] Re: Fw: Help required in Amber10 Installation Jason Swails (Thu Oct 15 2009 - 05:55:31 PDT)
    - Re: [AMBER] Re: Fw: Help required in Amber10 Installation Jason Swails (Thu Oct 15 2009 - 06:01:38 PDT)
    - Re: [AMBER] Re: Fw: Help required in Amber10 Installation Sudeep Narayan Banerjee (Thu Oct 15 2009 - 06:13:27 PDT)
    - Re: [AMBER] Re: Fw: Help required in Amber10 Installation Abhishek Banerjee (Thu Oct 15 2009 - 08:51:56 PDT)
[AMBER] Combine and rename group of residues in xleap Lili Peng (Wed Oct 07 2009 - 14:49:23 PDT)
- Re: [AMBER] Combine and rename group of residues in xleap case (Fri Oct 09 2009 - 06:32:57 PDT)
[AMBER] The hydrophobic contribution Rilei Yu (Wed Oct 07 2009 - 22:48:32 PDT)
- Re: [AMBER] The hydrophobic contribution case (Thu Oct 08 2009 - 05:41:28 PDT)
[AMBER] Fwd: Group specification Pavan G (Thu Oct 08 2009 - 11:30:09 PDT)
- Re: [AMBER] Fwd: Group specification Carlos Simmerling (Thu Oct 08 2009 - 11:35:43 PDT)
Re: [AMBER] Fwd: Group specification Bill Ross (Thu Oct 08 2009 - 13:15:44 PDT)
- Re: [AMBER] Fwd: Group specification Bill Ross (Thu Oct 08 2009 - 13:22:54 PDT)
[AMBER] RE: VDW and TI for free energy Ross Walker (Thu Oct 08 2009 - 17:43:48 PDT)
[AMBER] ff03 parameter for GDP and GTP mmg8.ualberta.ca (Thu Oct 08 2009 - 18:05:18 PDT)
- Re: [AMBER] ff03 parameter for GDP and GTP FyD (Fri Oct 09 2009 - 03:37:40 PDT)
  - Re: [AMBER] ff03 parameter for GDP and GTP Carlos Simmerling (Fri Oct 09 2009 - 05:45:04 PDT)
    - Re: [AMBER] ff03 parameter for GDP and GTP case (Fri Oct 09 2009 - 06:03:02 PDT)
    - Re: [AMBER] ff03 parameter for GDP and GTP Carlos Simmerling (Fri Oct 09 2009 - 06:09:32 PDT)
    - Re: [AMBER] ff03 parameter for GDP and GTP FyD (Fri Oct 09 2009 - 22:52:27 PDT)
    - Re: [AMBER] ff03 parameter for GDP and GTP Carlos Simmerling (Sat Oct 10 2009 - 04:36:35 PDT)
    - Re: [AMBER] ff03 parameter for GDP and GTP FyD (Sun Oct 11 2009 - 04:42:25 PDT)
  - Re: [AMBER] ff03 parameter for GDP and GTP mmg8.ualberta.ca (Fri Oct 09 2009 - 07:30:46 PDT)
    - Re: [AMBER] ff03 parameter for GDP and GTP FyD (Fri Oct 09 2009 - 13:38:08 PDT)
[AMBER] Some queries about pH simulation nicholus bhattacharjee (Thu Oct 08 2009 - 21:36:56 PDT)
- Re: [AMBER] Some queries about pH simulation Jason Swails (Fri Oct 09 2009 - 11:48:44 PDT)
  - Re: [AMBER] Some queries about pH simulation Carlos Simmerling (Fri Oct 09 2009 - 11:59:17 PDT)
    - Re: [AMBER] Some queries about pH simulation nicholus bhattacharjee (Fri Oct 09 2009 - 22:07:21 PDT)
    - Re: [AMBER] Some queries about pH simulation nicholus bhattacharjee (Mon Nov 02 2009 - 23:34:02 PST)
    - Re: [AMBER] Some queries about pH simulation case (Tue Nov 03 2009 - 03:30:07 PST)
[AMBER] DG improper torsion problem, two missing parameters Youn Kyeung Lee (Fri Oct 09 2009 - 00:02:03 PDT)
- Re: [AMBER] DG improper torsion problem, two missing parameters case (Fri Oct 09 2009 - 04:46:34 PDT)
[AMBER] Distance Replica Exchange Steve Seibold (Fri Oct 09 2009 - 06:18:44 PDT)
- Re: [AMBER] Distance Replica Exchange Carlos Simmerling (Fri Oct 09 2009 - 06:40:17 PDT)
  - RE: [AMBER] Distance Replica Exchange Steve Seibold (Fri Oct 09 2009 - 07:21:13 PDT)
Re: [AMBER] DG improper torsion problem, two missing parameters Bill Ross (Fri Oct 09 2009 - 10:25:30 PDT)
[AMBER] The -c option in Sander phani ghanakota (Fri Oct 09 2009 - 17:47:18 PDT)
- Re: [AMBER] The -c option in Sander case (Fri Oct 09 2009 - 18:54:05 PDT)
[AMBER] RE: VDW and TI for free energy Qicun Shi (Fri Oct 09 2009 - 19:00:08 PDT)
- Re: [AMBER] RE: VDW and TI for free energy steinbrt.rci.rutgers.edu (Sat Oct 10 2009 - 01:44:31 PDT)
  - Re: [AMBER] RE: VDW and TI for free energy Qicun Shi (Sat Oct 10 2009 - 21:05:20 PDT)
[AMBER] decomposition and calculation of entropy Qinghua Liao (Fri Oct 09 2009 - 23:13:49 PDT)
[AMBER] xleap-does not work Rilei Yu (Sat Oct 10 2009 - 01:30:06 PDT)
- Re: [AMBER] xleap-does not work case (Sat Oct 10 2009 - 05:27:01 PDT)
  - Re: [AMBER] xleap-does not work Rilei Yu (Sat Oct 10 2009 - 06:35:53 PDT)
    - Re: [AMBER] xleap-does not work case (Sat Oct 10 2009 - 06:53:57 PDT)
    - Re: [AMBER] xleap-does not work(Being solved!) Rilei Yu (Sat Oct 10 2009 - 07:13:28 PDT)
    - Re: [AMBER] xleap-does not work Jason Swails (Sat Oct 10 2009 - 10:08:08 PDT)
    - Re: [AMBER] xleap-does not work Rilei Yu (Sun Oct 11 2009 - 04:01:07 PDT)
[AMBER] A bug in LEaP ? FyD (Sun Oct 11 2009 - 05:08:37 PDT)
[AMBER] Energy-from-MM/PBSA-VS-experiment Rilei Yu (Sun Oct 11 2009 - 05:53:00 PDT)
- Re: [AMBER] Energy-from-MM/PBSA-VS-experiment Jason Swails (Sun Oct 11 2009 - 07:54:08 PDT)
  - Re: [AMBER] Energy-from-MM/PBSA-VS-experiment Rilei Yu (Sun Oct 11 2009 - 15:51:26 PDT)
[AMBER] S-S problem-in protein Rilei Yu (Sun Oct 11 2009 - 18:53:24 PDT)
- Re: [AMBER] S-S problem-in protein Jason Swails (Sun Oct 11 2009 - 19:15:10 PDT)
  - Re: [AMBER] S-S problem-in protein Jason Swails (Sun Oct 11 2009 - 21:24:51 PDT)
    - Re: [AMBER] S-S problem-in protein Rilei Yu (Sun Oct 11 2009 - 23:28:14 PDT)
    - Re: [AMBER] S-S problem-in protein Rilei Yu (Mon Oct 12 2009 - 02:16:15 PDT)
    - Re: [AMBER] S-S problem-in protein Jason Swails (Mon Oct 12 2009 - 04:23:25 PDT)
    - Re: [AMBER] S-S problem-in protein Rilei Yu (Mon Oct 12 2009 - 15:14:02 PDT)
[AMBER] unit converter for force constants GÜL ALTINBAŞ (Mon Oct 12 2009 - 05:22:00 PDT)
[AMBER] unit convertion for force constants GÜL ALTINBAŞ (Mon Oct 12 2009 - 05:47:42 PDT)
- Re: [AMBER] unit convertion for force constants vhakkim boy (Mon Oct 12 2009 - 06:26:05 PDT)
[AMBER] OpenMP Ben Roberts (Mon Oct 12 2009 - 10:35:35 PDT)
- RE: [AMBER] OpenMP Ross Walker (Mon Oct 12 2009 - 11:29:45 PDT)
- Re: [AMBER] OpenMP michael (Tue Oct 13 2009 - 07:43:09 PDT)
[AMBER] Simulating transmembrane protein. Jayalakshmi Sridhar (Mon Oct 12 2009 - 11:42:11 PDT)
- Re: [AMBER] Simulating transmembrane protein. case (Mon Oct 12 2009 - 14:55:42 PDT)
[AMBER] Is iwrap mapping water molecules to my protein cavity? ben rodriguez (Mon Oct 12 2009 - 11:55:23 PDT)
- Re: [AMBER] Is iwrap mapping water molecules to my protein cavity? Carlos Simmerling (Mon Oct 12 2009 - 12:28:12 PDT)
Re: [AMBER] Simulating transmembrane protein. Bill Ross (Mon Oct 12 2009 - 12:04:36 PDT)
- Re: [AMBER] Simulating transmembrane protein. Jayalakshmi Sridhar (Mon Oct 12 2009 - 12:57:02 PDT)
- Re: [AMBER] Simulating transmembrane protein. Bill Ross (Mon Oct 12 2009 - 15:37:50 PDT)
Re: [AMBER] Is iwrap mapping water molecules to my protein cavity? Bill Ross (Mon Oct 12 2009 - 12:12:19 PDT)
[AMBER] Computing an Hessian matrix using NAB Brut Marie (Mon Oct 12 2009 - 15:12:44 PDT)
- Re: [AMBER] Computing an Hessian matrix using NAB case (Tue Oct 13 2009 - 05:13:42 PDT)
  - Re: [AMBER] Computing an Hessian matrix using NAB Brut Marie (Tue Oct 13 2009 - 11:56:19 PDT)
  - Re: [AMBER] Computing an Hessian matrix using NAB Brut Marie (Tue Oct 13 2009 - 12:00:53 PDT)
[AMBER] How to prepare the acetate ion file in leap? xuemeiwang1103 (Tue Oct 13 2009 - 00:05:57 PDT)
- Re: [AMBER] How to prepare the acetate ion file in leap? Balazs Jojart (Tue Oct 13 2009 - 00:36:03 PDT)
[AMBER] "Cannot open file ATOMTYPE.INF, exit" when using antechamber haifeng yuan (Tue Oct 13 2009 - 00:44:55 PDT)
- Re: [AMBER] "Cannot open file ATOMTYPE.INF, exit" when using antechamber case (Wed Oct 14 2009 - 04:37:35 PDT)
[AMBER] iAPBS - how to set the right grid dimensions Oliver Kuhn (Tue Oct 13 2009 - 01:36:27 PDT)
- Re: [AMBER] iAPBS - how to set the right grid dimensions Robert Konecny (Tue Oct 13 2009 - 07:42:12 PDT)
- Re: [AMBER] iAPBS - how to set the right grid dimensions Oliver Kuhn (Tue Oct 13 2009 - 08:17:06 PDT)
  - Re: [AMBER] iAPBS - how to set the right grid dimensions Robert Konecny (Tue Oct 13 2009 - 10:12:04 PDT)
- Re: [AMBER] iAPBS - how to set the right grid dimensions Oliver Kuhn (Wed Oct 14 2009 - 06:16:28 PDT)
  - Re: [AMBER] iAPBS - how to set the right grid dimensions Robert Konecny (Wed Oct 14 2009 - 06:21:07 PDT)
[AMBER] LES and NEB problem Rima Chaudhuri (Tue Oct 13 2009 - 12:35:37 PDT)
- Re: [AMBER] LES and NEB problem Carlos Simmerling (Wed Oct 14 2009 - 07:14:04 PDT)
  - Re: [AMBER] LES and NEB problem Rima Chaudhuri (Thu Oct 15 2009 - 09:50:08 PDT)
    - Re: [AMBER] LES and NEB problem Carlos Simmerling (Thu Oct 15 2009 - 09:54:18 PDT)
    - Re: [AMBER] LES and NEB problem Rima Chaudhuri (Thu Oct 15 2009 - 10:53:41 PDT)
    - Re: [AMBER] LES and NEB problem Jason Swails (Thu Oct 15 2009 - 11:09:14 PDT)
    - Re: [AMBER] LES and NEB problem Carlos Simmerling (Thu Oct 15 2009 - 11:09:34 PDT)
[AMBER] mean square displacment Nancy (Tue Oct 13 2009 - 16:59:15 PDT)
Re: [AMBER] mean square displacment Bill Ross (Tue Oct 13 2009 - 17:09:49 PDT)
[Amber]AMBER: MM_PBSA problems in AMBER10 He Hongqing (Tue Oct 13 2009 - 20:43:57 PDT)
- 回复： [Amber]AMBER: MM_PBSA problems in AMBER10 Rilei Yu (Tue Oct 13 2009 - 22:47:02 PDT)
  - Re: 回复： [Amber]AMBER: MM_PBSA problems in AMBER10 He Hongqing (Wed Oct 14 2009 - 00:32:25 PDT)
    - Re: 回复： [Amber]AMBER: MM_PBSA problems in AMBER10 Rilei Yu (Wed Oct 14 2009 - 01:18:34 PDT)
- Re: [Amber]AMBER: MM_PBSA problems in AMBER10 Ray Luo (Wed Oct 14 2009 - 09:48:48 PDT)
[AMBER] How to add a hydrogen to the residue? xuemeiwang1103 (Tue Oct 13 2009 - 20:57:53 PDT)
- Re: [AMBER] How to add a hydrogen to the residue? case (Wed Oct 14 2009 - 04:51:08 PDT)
Re: Re: 回复： [Amber]AMBER: MM_PBSA problemsin AMBER10 He Hongqing (Wed Oct 14 2009 - 01:39:33 PDT)
- Re: Re: 回复： [Amber]AMBER: MM_PBSA problemsin AMBER10 Qinghua Liao (Wed Oct 14 2009 - 02:22:41 PDT)
  - Re: Re: Re: 回复： [Amber]AMBER: MM_PBSA problemsin AMBER10 Bill Ross (Wed Oct 14 2009 - 09:56:41 PDT)
[AMBER] Add the hydrogen to the carboxyl of the GLU residue? xuemeiwang1103 (Wed Oct 14 2009 - 05:05:48 PDT)
- Re: [AMBER] Add the hydrogen to the carboxyl of the GLU residue? Andrew Purkiss-Trew (Wed Oct 14 2009 - 05:19:43 PDT)
- Re: [AMBER] Add the hydrogen to the carboxyl of the GLU residue? FyD (Wed Oct 14 2009 - 06:40:09 PDT)
  - Re: [AMBER] Add the hydrogen to the carboxyl of the GLU residue? Carlos Simmerling (Wed Oct 14 2009 - 06:49:00 PDT)
[AMBER] ptraj and prmtop Beale, John (Wed Oct 14 2009 - 05:46:11 PDT)
- Re: [AMBER] ptraj and prmtop Carlos Simmerling (Wed Oct 14 2009 - 06:41:04 PDT)
[AMBER] six member pucker calculation Ganesh Kamath (Wed Oct 14 2009 - 07:27:24 PDT)
[AMBER] nab normal mode analysis has imaginary frequencies Junmei Wang (Wed Oct 14 2009 - 09:05:06 PDT)
- Re: [AMBER] nab normal mode analysis has imaginary frequencies case (Wed Oct 14 2009 - 11:34:05 PDT)
- [AMBER] Re: nab normal mode analysis has imaginary frequencies Junmei Wang (Wed Dec 09 2009 - 15:34:28 PST)
  - Re: [AMBER] Re: nab normal mode analysis has imaginary frequencies case (Thu Dec 10 2009 - 06:46:20 PST)
[AMBER] installation of Amber on OSX Ramgopal Mettu (Wed Oct 14 2009 - 14:46:59 PDT)
- Re: [AMBER] installation of Amber on OSX David Watson (Wed Oct 14 2009 - 15:03:51 PDT)
- Re: [AMBER] installation of Amber on OSX case (Wed Oct 14 2009 - 15:10:04 PDT)
  - Re: [AMBER] installation of Amber on OSX Jason Swails (Wed Oct 14 2009 - 15:41:31 PDT)
[AMBER] Simulated annealing waleed zalloum (Thu Oct 15 2009 - 03:59:29 PDT)
- Re: [AMBER] Simulated annealing Carlos Simmerling (Thu Oct 15 2009 - 04:43:56 PDT)
[AMBER] part of the protein escaped from the water box qiaoyan (Thu Oct 15 2009 - 04:33:00 PDT)
- Re: [AMBER] part of the protein escaped from the water box Carlos Simmerling (Thu Oct 15 2009 - 04:39:40 PDT)
- Re: [AMBER] part of the protein escaped from the water box case (Thu Oct 15 2009 - 04:40:53 PDT)
- Re: [AMBER] part of the protein escaped from the water box Jason Swails (Thu Oct 15 2009 - 04:43:00 PDT)
[AMBER] Large File Support Beale, John (Thu Oct 15 2009 - 05:40:27 PDT)
- RE: [AMBER] Large File Support Ross Walker (Thu Oct 15 2009 - 11:14:01 PDT)
[AMBER] AMBER 11. Peter Winn (Thu Oct 15 2009 - 09:27:39 PDT)
- Re: [AMBER] AMBER 11. case (Thu Oct 15 2009 - 09:52:51 PDT)
[AMBER] B-factor Cristina Sisu (Thu Oct 15 2009 - 10:04:25 PDT)
- Re: [AMBER] B-factor Thomas Cheatham III (Fri Oct 16 2009 - 15:16:35 PDT)
  - Re: [AMBER] B-factor Cristina Sisu (Sat Oct 17 2009 - 03:58:34 PDT)
    - [AMBER] Time scale of the Protein domain motion ? Chih-Ying Lin (Sat Oct 17 2009 - 12:18:34 PDT)
    - Re: [AMBER] Time scale of the Protein domain motion ? Carlos Simmerling (Sat Oct 17 2009 - 12:23:34 PDT)
    - Re: [AMBER] Time scale of the Protein domain motion ? Chih-Ying Lin (Sat Oct 17 2009 - 12:36:18 PDT)
    - Re: [AMBER] Time scale of the Protein domain motion ? Carlos Simmerling (Sat Oct 17 2009 - 12:42:01 PDT)
    - Re: [AMBER] Time scale of the Protein domain motion ? Chih-Ying Lin (Sat Oct 17 2009 - 12:46:37 PDT)
[AMBER] cross correlation analysis with ptraj Junmei Wang (Thu Oct 15 2009 - 09:49:29 PDT)
[AMBER] question with pucker in six member ring Ganesh Kamath (Thu Oct 15 2009 - 12:55:45 PDT)
- Re: [AMBER] question with pucker in six member ring Nicolas Sapay (Fri Oct 16 2009 - 08:04:24 PDT)
- Re: [AMBER] question with pucker in six member ring Thomas Cheatham III (Fri Oct 16 2009 - 11:23:05 PDT)
  - Re: [AMBER] question with pucker in six member ring Ganesh Kamath (Fri Oct 16 2009 - 11:36:41 PDT)
- Re: [AMBER] question with pucker in six member ring Bill Ross (Fri Oct 16 2009 - 11:43:56 PDT)
  - Re: [AMBER] question with pucker in six member ring Ganesh Kamath (Fri Oct 16 2009 - 12:31:31 PDT)
- Re: [AMBER] question with pucker in six member ring Bill Ross (Fri Oct 16 2009 - 12:48:04 PDT)
  - Re: [AMBER] question with pucker in six member ring Ganesh Kamath (Mon Oct 19 2009 - 10:42:17 PDT)
- Re: [AMBER] question with pucker in six member ring Bill Ross (Mon Oct 19 2009 - 10:54:03 PDT)
[AMBER] why is TAUTP scaled by "e" ? Jose Borreguero (Thu Oct 15 2009 - 13:49:18 PDT)
- RE: [AMBER] why is TAUTP scaled by "e" ? Ross Walker (Thu Oct 15 2009 - 15:08:52 PDT)
- Re: [AMBER] why is TAUTP scaled by "e" ? case (Fri Oct 16 2009 - 06:30:53 PDT)
  - Re: [AMBER] why is TAUTP scaled by "e" ? Jose Borreguero (Fri Oct 16 2009 - 12:13:42 PDT)
[AMBER] eigenvalues add up to more than trace of matrix Yaw Sing TAN (Thu Oct 15 2009 - 20:14:59 PDT)
- Re: [AMBER] eigenvalues add up to more than trace of matrix Jason Swails (Fri Oct 16 2009 - 06:29:13 PDT)
- Re: [AMBER] eigenvalues add up to more than trace of matrix Hannes Loeffler (Fri Oct 16 2009 - 06:50:50 PDT)
[AMBER] How to introduce the second protein molecule into simulation box? Siddharth Rastogi (Fri Oct 16 2009 - 00:00:03 PDT)
- Re: [AMBER] How to introduce the second protein molecule into simulation box? Jason Swails (Fri Oct 16 2009 - 06:15:57 PDT)
[AMBER] Re: AMBER: periodic bondary condition Markus Kaukonen (Fri Oct 16 2009 - 00:38:03 PDT)
- Re: [AMBER] Re: AMBER: periodic bondary condition case (Fri Oct 16 2009 - 06:13:49 PDT)
  - Re: [AMBER] Re: AMBER: periodic bondary condition Markus Kaukonen (Mon Oct 26 2009 - 01:14:48 PDT)
[AMBER] binding energy Simon Becker (Fri Oct 16 2009 - 02:28:39 PDT)
- Re: [AMBER] binding energy steinbrt.rci.rutgers.edu (Fri Oct 16 2009 - 04:27:24 PDT)
[AMBER] MMTSB cluster analysis versus ptraj cluster analysis Cenk $Jenk$ Andac (Fri Oct 16 2009 - 05:19:24 PDT)
- Re: [AMBER] MMTSB cluster analysis versus ptraj cluster analysis Thomas Cheatham III (Fri Oct 16 2009 - 08:33:22 PDT)
  - Re: [AMBER] MMTSB cluster analysis versus ptraj cluster analysis Cenk $Jenk$ Andac (Sat Oct 17 2009 - 00:02:20 PDT)
    - Re: [AMBER] MMTSB cluster analysis versus ptraj cluster analysis Jianyin Shao (Mon Oct 19 2009 - 11:16:47 PDT)
    - Re: [AMBER] MMTSB cluster analysis versus ptraj cluster analysis Cenk $Jenk$ Andac (Mon Oct 19 2009 - 14:44:42 PDT)
[AMBER] AMBER FF and NAMD stefano_elli\.libero\.it (Fri Oct 16 2009 - 07:26:14 PDT)
- Re: [AMBER] AMBER FF and NAMD Hannes Loeffler (Fri Oct 16 2009 - 07:45:25 PDT)
- Re: [AMBER] AMBER FF and NAMD Nicolas Sapay (Fri Oct 16 2009 - 07:59:53 PDT)
- Re: [AMBER] AMBER FF and NAMD FyD (Fri Oct 16 2009 - 12:19:13 PDT)
[AMBER] Dihedral energy profile in a single molecule Frank X. Vázquez (Fri Oct 16 2009 - 07:55:53 PDT)
- Re: [AMBER] Dihedral energy profile in a single molecule Jason Swails (Fri Oct 16 2009 - 08:02:35 PDT)
[AMBER] RDC and alignment tensor Eliana Asciutto (Fri Oct 16 2009 - 13:21:34 PDT)
- Re: [AMBER] RDC and alignment tensor Thomas Cheatham III (Fri Oct 16 2009 - 13:45:25 PDT)
  - Re: [AMBER] RDC and alignment tensor Eliana Asciutto (Mon Oct 19 2009 - 09:50:31 PDT)
    - Re: [AMBER] RDC and alignment tensor case (Mon Oct 19 2009 - 10:36:16 PDT)
    - Re: [AMBER] RDC and alignment tensor Eliana Asciutto (Mon Oct 19 2009 - 12:03:43 PDT)
    - Re: [AMBER] RDC and alignment tensor case (Tue Oct 20 2009 - 05:24:45 PDT)
  - Re: [AMBER] RDC and alignment tensor Eliana Asciutto (Fri Oct 23 2009 - 12:19:00 PDT)
[AMBER] (no subject) Prakash Patodia (Sat Oct 17 2009 - 00:12:39 PDT)
[AMBER] How create PRMTOP and INCPRD for surface? rrd (Sat Oct 17 2009 - 19:40:02 PDT)
[AMBER] how to get hold of older versions of MKL ? Nahoum Anthony (Mon Oct 19 2009 - 01:59:57 PDT)
- Re: [AMBER] how to get hold of older versions of MKL ? Jason Swails (Mon Oct 19 2009 - 03:54:45 PDT)
- RE: [AMBER] how to get hold of older versions of MKL ? Ross Walker (Mon Oct 19 2009 - 09:58:54 PDT)
AW: [AMBER] Add the hydrogen to the carboxyl of the GLU residue? Aust, Susanne (Mon Oct 19 2009 - 02:01:27 PDT)
[AMBER] error message from iAPBS Oliver Kuhn (Mon Oct 19 2009 - 04:47:32 PDT)
[AMBER] Re: RDC and alignment tensor Eliana Asciutto (Mon Oct 19 2009 - 10:51:50 PDT)
- Re: [AMBER] Re: RDC and alignment tensor case (Mon Oct 19 2009 - 11:22:47 PDT)
[AMBER] Centering and reimaging with ptraj- stop rotating. ben rodriguez (Mon Oct 19 2009 - 20:00:26 PDT)
- Re: [AMBER] Centering and reimaging with ptraj- stop rotating. Thomas Cheatham (Mon Oct 19 2009 - 20:47:07 PDT)
- Re: [AMBER] Centering and reimaging with ptraj- stop rotating. Bill Ross (Mon Oct 19 2009 - 22:14:10 PDT)
[AMBER] Error: unable to find mopac charges in mopac.out Rilei Yu (Mon Oct 19 2009 - 22:34:34 PDT)
- RE: [AMBER] Error: unable to find mopac charges in mopac.out Ross Walker (Mon Oct 19 2009 - 22:50:17 PDT)
- RE: [AMBER] Error: unable to find mopac charges in mopac.out Rilei Yu (Tue Oct 20 2009 - 00:12:19 PDT)
  - Re: [AMBER] Error: unable to find mopac charges in mopac.out case (Tue Oct 20 2009 - 04:45:59 PDT)
[AMBER] How to create FF for diamond. rrd (Mon Oct 19 2009 - 23:16:07 PDT)
[AMBER] GAFF parameter stefano_elli\.libero\.it (Tue Oct 20 2009 - 06:26:26 PDT)
- Re: [AMBER] GAFF parameter Jason Swails (Tue Oct 20 2009 - 07:57:09 PDT)
- RE: [AMBER] GAFF parameter Ross Walker (Tue Oct 20 2009 - 11:50:18 PDT)
[AMBER] question with hbond in carnal Ganesh Kamath (Tue Oct 20 2009 - 06:58:36 PDT)
[AMBER] HBOND analysis Marcin Krol (Tue Oct 20 2009 - 08:42:35 PDT)
Re: [AMBER] question with hbond in carnal Bill Ross (Tue Oct 20 2009 - 09:32:56 PDT)
[AMBER] can I run EVB in other ensemble than NVE? Jose Borreguero (Tue Oct 20 2009 - 09:57:04 PDT)
- Re: [AMBER] can I run EVB in other ensemble than NVE? case (Tue Oct 20 2009 - 10:08:58 PDT)
[AMBER] man pages? Louis-Frédéric Feuillette (Tue Oct 20 2009 - 10:09:09 PDT)
- Re: [AMBER] man pages? Ben Roberts (Tue Oct 20 2009 - 10:33:16 PDT)
  - Re: [AMBER] man pages? Louis-Frédéric Feuillette (Tue Oct 20 2009 - 13:17:52 PDT)
    - Re: [AMBER] man pages? Jason Swails (Tue Oct 20 2009 - 14:28:56 PDT)
[AMBER] amber8 pmemd trajectory coordinates problem wong105.llnl.gov (Tue Oct 20 2009 - 17:32:24 PDT)
- Re: [AMBER] amber8 pmemd trajectory coordinates problem Thomas Cheatham (Tue Oct 20 2009 - 17:39:22 PDT)
  - Re: [AMBER] amber8 pmemd trajectory coordinates problem Sergio Wong (Tue Oct 20 2009 - 17:49:11 PDT)
- Re: [AMBER] amber8 pmemd trajectory coordinates problem Robert Duke (Tue Oct 20 2009 - 18:03:37 PDT)
- Re: [AMBER] amber8 pmemd trajectory coordinates problem Robert Duke (Tue Oct 20 2009 - 18:15:56 PDT)
[AMBER] simulation blown up moitrayee.mbu.iisc.ernet.in (Tue Oct 20 2009 - 10:41:29 PDT)
- Re: [AMBER] simulation blown up Jason Swails (Tue Oct 20 2009 - 19:58:47 PDT)
- Re: [AMBER] simulation blown up Robert Duke (Tue Oct 20 2009 - 20:55:39 PDT)
[AMBER] Problem with running anal module in amber moitrayee.mbu.iisc.ernet.in (Tue Oct 20 2009 - 23:47:17 PDT)
[AMBER] "extra points" incompatibility with pmemd mousumi (Wed Oct 21 2009 - 00:57:51 PDT)
- Re: [AMBER] "extra points" incompatibility with pmemd Robert Duke (Wed Oct 21 2009 - 05:02:54 PDT)
  - Re: [AMBER] "extra points" incompatibility with pmemd Brent Krueger (Wed Oct 21 2009 - 05:28:58 PDT)
    - Re: [AMBER] "extra points" incompatibility with pmemd mousumi (Wed Oct 21 2009 - 22:20:48 PDT)
- Re: [AMBER] "extra points" incompatibility with pmemd case (Wed Oct 21 2009 - 05:22:28 PDT)
[AMBER] Can I use other ntb options in constant pH simulation nicholus bhattacharjee (Wed Oct 21 2009 - 02:26:43 PDT)
- Re: [AMBER] Can I use other ntb options in constant pH simulation Jason Swails (Wed Oct 21 2009 - 04:42:42 PDT)
[AMBER] Why the calculation ofen stop with the calculation process not end? xuemeiwang1103 (Wed Oct 21 2009 - 07:04:57 PDT)
[AMBER] xleap editing window icons inactive Jayalakshmi Sridhar (Wed Oct 21 2009 - 11:20:01 PDT)
- RE: [AMBER] xleap editing window icons inactive Niel Henriksen (Wed Oct 21 2009 - 11:21:54 PDT)
  - RE: [AMBER] xleap editing window icons inactive Jayalakshmi Sridhar (Wed Oct 21 2009 - 11:32:46 PDT)
[AMBER] Circular RNA topology file Kasprzak, Wojciech (NIH/NCI) [C] (Wed Oct 21 2009 - 11:26:04 PDT)
- Re: [AMBER] Circular RNA topology file case (Wed Oct 21 2009 - 12:06:17 PDT)
  - [AMBER] translate multiple residues Taufik Al-Sarraj (Wed Oct 21 2009 - 13:33:12 PDT)
    - Re: [AMBER] translate multiple residues Bill Ross (Wed Oct 21 2009 - 15:40:51 PDT)
  - Re: [AMBER] Circular RNA topology file Filip Lankas (Mon Oct 26 2009 - 03:13:46 PDT)
Re: [AMBER] translate multiple residues Bill Ross (Wed Oct 21 2009 - 13:53:20 PDT)
- Re: [AMBER] translate multiple residues Taufik Al-Sarraj (Wed Oct 21 2009 - 14:32:30 PDT)
[AMBER] Ptraj Segmentation Fault Katrina Hill (Wed Oct 21 2009 - 19:15:31 PDT)
[AMBER] too many undefined parameters in frcmod xueqin pang (Thu Oct 22 2009 - 01:52:57 PDT)
- Re: [AMBER] too many undefined parameters in frcmod FyD (Thu Oct 22 2009 - 02:37:46 PDT)
  - Re: [AMBER] too many undefined parameters in frcmod Jason Swails (Thu Oct 22 2009 - 04:59:55 PDT)
    - Re: [AMBER] too many undefined parameters in frcmod Junmei Wang (Mon Oct 26 2009 - 07:45:04 PDT)
    - Re: [AMBER] too many undefined parameters in frcmod xueqin pang (Thu Oct 29 2009 - 06:06:24 PDT)
  - [AMBER] Salt bridge time scale Mannan (Sun Oct 25 2009 - 18:57:20 PDT)
[AMBER] units of measures lorenzo (Thu Oct 22 2009 - 04:20:26 PDT)
- Re: [AMBER] units of measures case (Thu Oct 22 2009 - 05:42:11 PDT)
[AMBER] problem with minimization moitrayee.mbu.iisc.ernet.in (Thu Oct 22 2009 - 04:01:14 PDT)
[AMBER] [Fwd: problem with minimization] moitrayee.mbu.iisc.ernet.in (Thu Oct 22 2009 - 05:46:32 PDT)
[AMBER] parameters for O2 molecule Jeffrey (Thu Oct 22 2009 - 06:32:07 PDT)
- Re: [AMBER] parameters for O2 molecule Jason Swails (Thu Oct 22 2009 - 07:19:51 PDT)
  - Re: [AMBER] parameters for O2 molecule Jeffrey (Thu Oct 29 2009 - 06:01:44 PDT)
[AMBER] charges for heme-cys in p450 Jayalakshmi Sridhar (Thu Oct 22 2009 - 09:03:08 PDT)
- Re: [AMBER] charges for heme-cys in p450 FyD (Fri Oct 23 2009 - 03:57:43 PDT)
[AMBER] Unable to correctly identify element when running QM/MM in amber10 Jifeng Wang (Thu Oct 22 2009 - 09:20:30 PDT)
- RE: [AMBER] Unable to correctly identify element when running QM/MM in amber10 Ross Walker (Thu Oct 22 2009 - 12:03:40 PDT)
Re: [AMBER] [Fwd: problem with minimization] Bill Ross (Thu Oct 22 2009 - 09:49:45 PDT)
- Re: [AMBER] [Fwd: problem with minimization] moitrayee.mbu.iisc.ernet.in (Thu Oct 22 2009 - 11:53:11 PDT)
- Re: [AMBER] [Fwd: problem with minimization] Bill Ross (Fri Oct 23 2009 - 10:40:57 PDT)
[AMBER] XServe cluster Abdul Rehman Gani (Thu Oct 22 2009 - 12:14:36 PDT)
- Re: [AMBER] XServe cluster Jim Paugh (Thu Oct 22 2009 - 12:24:37 PDT)
  - Re: [AMBER] XServe cluster Abdul Rehman Gani (Thu Oct 22 2009 - 12:40:11 PDT)
    - Re: [AMBER] XServe cluster Jim Paugh (Thu Oct 22 2009 - 14:10:49 PDT)
- RE: [AMBER] XServe cluster Richard Owczarzy (Thu Oct 22 2009 - 13:02:24 PDT)
[AMBER] Question about distance restraint ? xuemeiwang1103 (Fri Oct 23 2009 - 03:07:47 PDT)
- Re: [AMBER] Question about distance restraint ? Carlos Simmerling (Fri Oct 23 2009 - 03:56:24 PDT)
[AMBER] amber parallel test fail Nahoum Anthony (Fri Oct 23 2009 - 03:20:45 PDT)
- Re: [AMBER] amber parallel test fail Jason Swails (Fri Oct 23 2009 - 04:58:19 PDT)
  - RE: [AMBER] amber parallel test fail Nahoum Anthony (Fri Oct 23 2009 - 08:12:40 PDT)
[AMBER] software to hydrate protein pockets Vlad Cojocaru (Fri Oct 23 2009 - 05:23:54 PDT)
- Re: [AMBER] software to hydrate protein pockets Alessandro Nascimento (Fri Oct 23 2009 - 05:50:05 PDT)
- Re: [AMBER] software to hydrate protein pockets Hannes Kopitz (Fri Oct 23 2009 - 06:11:26 PDT)
[AMBER] pmemd ifort problem Sel Ercan (Fri Oct 23 2009 - 07:57:59 PDT)
- Re: [AMBER] pmemd ifort problem Robert Duke (Fri Oct 23 2009 - 08:33:27 PDT)
[AMBER] inhibitor prepin not recognized in xleap Jayalakshmi Sridhar (Fri Oct 23 2009 - 08:56:40 PDT)
[AMBER] inhibitor prepin not recognized in xleap Jayalakshmi Sridhar (Fri Oct 23 2009 - 09:05:46 PDT)
[AMBER] xleap not reconizing inhibitor prepin Jayalakshmi Sridhar (Fri Oct 23 2009 - 09:21:07 PDT)
- Re: [AMBER] xleap not reconizing inhibitor prepin Junmei Wang (Mon Oct 26 2009 - 07:51:41 PDT)
Re: [AMBER] inhibitor prepin not recognized in xleap Bill Ross (Fri Oct 23 2009 - 11:32:03 PDT)
Re: [AMBER] xleap not reconizing inhibitor prepin Bill Ross (Fri Oct 23 2009 - 11:33:44 PDT)
[AMBER] the criterion of equilibrium qiaoyan (Fri Oct 23 2009 - 19:19:58 PDT)
[AMBER] resp_problem vhakkim boy (Sat Oct 24 2009 - 03:16:22 PDT)
- RE: [AMBER] resp_problem Ross Walker (Sat Oct 24 2009 - 15:39:01 PDT)
- Re: [AMBER] resp_problem FyD (Sat Oct 24 2009 - 23:12:31 PDT)
Re: [AMBER] the criterion of equilibrium Bill Ross (Sat Oct 24 2009 - 10:19:09 PDT)
- Re: [AMBER] the criterion of equilibrium Adrian Roitberg (Sat Oct 24 2009 - 11:22:25 PDT)
[AMBER] A bug in LEaP II ? FyD (Sun Oct 25 2009 - 05:58:36 PDT)
[AMBER] error in AMBer distance constraint xuemeiwang1103 (Sun Oct 25 2009 - 19:24:09 PDT)
- Re: [AMBER] error in AMBer distance constraint Carlos Simmerling (Sun Oct 25 2009 - 19:38:23 PDT)
  - Re:Re: [AMBER] error in AMBer distance constraint xuemeiwang1103 (Mon Oct 26 2009 - 00:35:08 PDT)
    - Re: Re: [AMBER] error in AMBer distance constraint Carlos Simmerling (Tue Oct 27 2009 - 04:28:22 PDT)
Re: [AMBER] error in AMBer distance constraint Bill Ross (Sun Oct 25 2009 - 20:03:19 PDT)
[AMBER] Preparing distance restraints Yunjie Zhao (Mon Oct 26 2009 - 01:44:58 PDT)
- Re: [AMBER] Preparing distance restraints case (Mon Oct 26 2009 - 14:26:26 PDT)
[AMBER] contradictive hydrogen bonds using ptraj Binbin Liu (Mon Oct 26 2009 - 09:42:20 PDT)
[AMBER] [amber10] atom groups used in torsion constrain Han Zheng (Mon Oct 26 2009 - 11:09:07 PDT)
[AMBER] PEMD Cristina Sisu (Mon Oct 26 2009 - 14:44:42 PDT)
- Re: [AMBER] PEMD Tom Joseph (Mon Oct 26 2009 - 16:03:26 PDT)
[AMBER] Possible bug in "com" group torsion angle constrain? Thanks! Han Zheng (Tue Oct 27 2009 - 10:28:16 PDT)
- RE: [AMBER] Possible bug in "com" group torsion angle constrain? Thanks! Seetin, Matthew (Tue Oct 27 2009 - 14:17:41 PDT)
  - Re: [AMBER] Possible bug in "com" group torsion angle constrain? Thanks! Han Zheng (Tue Oct 27 2009 - 15:47:20 PDT)
    - Re: [AMBER] Possible bug in "com" group torsion angle constrain? Thanks! Carlos Simmerling (Tue Oct 27 2009 - 16:22:43 PDT)
[AMBER] NMR restraint xuemeiwang1103 (Tue Oct 27 2009 - 19:31:39 PDT)
- Re: [AMBER] NMR restraint Sally Pias (Tue Oct 27 2009 - 21:32:33 PDT)
[AMBER] Simulated annealing Shaikh Abdul R S Ramaju (Tue Oct 27 2009 - 22:44:33 PDT)
- Re: [AMBER] Simulated annealing Carlos Simmerling (Wed Oct 28 2009 - 03:51:41 PDT)
[AMBER] Conversion of Gaussian output file to mol2 megha bajaj (Wed Oct 28 2009 - 00:49:51 PDT)
[AMBER] Conversion of Gaussian output file into mol2 megha bajaj (Wed Oct 28 2009 - 01:00:35 PDT)
- Re: [AMBER] Conversion of Gaussian output file into mol2 Junmei Wang (Thu Oct 29 2009 - 08:45:27 PDT)
[AMBER] error in distance restraint xuemeiwang1103 (Wed Oct 28 2009 - 06:56:48 PDT)
- Re: [AMBER] error in distance restraint Adrian Roitberg (Wed Oct 28 2009 - 07:01:07 PDT)
  - [AMBER] vlimit Taufik Al-Sarraj (Wed Oct 28 2009 - 14:16:32 PDT)
    - RE: [AMBER] vlimit Ross Walker (Wed Oct 28 2009 - 14:29:21 PDT)
    - Re: [AMBER] vlimit Taufik Al-Sarraj (Wed Oct 28 2009 - 15:02:43 PDT)
    - RE: [AMBER] vlimit Ross Walker (Wed Oct 28 2009 - 15:35:15 PDT)
    - [AMBER] pmemd vs sander.MPI Taufik Al-Sarraj (Wed Nov 04 2009 - 09:32:05 PST)
    - RE: [AMBER] pmemd vs sander.MPI Ross Walker (Wed Nov 04 2009 - 10:33:23 PST)
    - Re: [AMBER] pmemd vs sander.MPI Marek Maly (Thu Nov 05 2009 - 05:36:39 PST)
    - Re: [AMBER] pmemd vs sander.MPI Robert Duke (Thu Nov 05 2009 - 05:35:41 PST)
    - Re: [AMBER] pmemd vs sander.MPI Marek Maly (Thu Nov 05 2009 - 10:03:08 PST)
    - RE: [AMBER] pmemd vs sander.MPI Ross Walker (Thu Nov 05 2009 - 10:27:19 PST)
    - Re: [AMBER] pmemd vs sander.MPI Marek Maly (Thu Nov 05 2009 - 10:47:06 PST)
    - RE: [AMBER] pmemd vs sander.MPI Ross Walker (Thu Nov 05 2009 - 14:58:37 PST)
    - Re: [AMBER] pmemd vs sander.MPI Marek Maly (Thu Nov 05 2009 - 15:58:50 PST)
    - Re: [AMBER] pmemd vs sander.MPI Robert Duke (Thu Nov 05 2009 - 10:06:24 PST)
    - Re: [AMBER] pmemd vs sander.MPI Marek Maly (Thu Nov 05 2009 - 10:34:31 PST)
    - RE: [AMBER] vlimit Bill Ross (Wed Oct 28 2009 - 14:55:55 PDT)
- Re: [AMBER] error in distance restraint Carlos Simmerling (Wed Oct 28 2009 - 13:48:13 PDT)
  - Re:Re: [AMBER] error in distance restraint xuemeiwang1103 (Wed Oct 28 2009 - 20:43:55 PDT)
    - Re: Re: [AMBER] error in distance restraint Carlos Simmerling (Thu Oct 29 2009 - 03:20:13 PDT)
[AMBER] pairwise per-residue decomposition manoj singh (Wed Oct 28 2009 - 21:34:32 PDT)
- Re: [AMBER] pairwise per-residue decomposition Carlos Simmerling (Thu Oct 29 2009 - 03:20:55 PDT)
  - Re: [AMBER] pairwise per-residue decomposition manoj singh (Thu Oct 29 2009 - 10:32:38 PDT)
- Re: [AMBER] pairwise per-residue decomposition Tom Joseph (Thu Oct 29 2009 - 17:30:51 PDT)
- Re: [AMBER] pairwise per-residue decomposition Tom Joseph (Thu Oct 29 2009 - 22:15:40 PDT)
  - Re: [AMBER] pairwise per-residue decomposition manoj singh (Thu Oct 29 2009 - 22:46:22 PDT)
    - Re: [AMBER] pairwise per-residue decomposition Tom Joseph (Fri Oct 30 2009 - 11:18:52 PDT)
    - Re: [AMBER] pairwise per-residue decomposition manoj singh (Fri Oct 30 2009 - 11:26:14 PDT)
    - Re: [AMBER] pairwise per-residue decomposition manoj singh (Sat Oct 31 2009 - 21:59:38 PDT)
[AMBER] Thermodynamic Integration calculation on an artificial anion receptor Huifang (Wed Oct 28 2009 - 21:38:05 PDT)
- Re: [AMBER] Thermodynamic Integration calculation on an artificial anion receptor steinbrt.rci.rutgers.edu (Thu Oct 29 2009 - 03:35:24 PDT)
[AMBER] ligand exiting a protein cavity moitrayee.mbu.iisc.ernet.in (Thu Oct 29 2009 - 05:27:58 PDT)
[AMBER] [Fwd: ligand exiting a protein cavity] moitrayee.mbu.iisc.ernet.in (Thu Oct 29 2009 - 05:36:13 PDT)
- Re: [AMBER] [Fwd: ligand exiting a protein cavity] Kshatresh Dutta Dubey (Thu Oct 29 2009 - 07:44:28 PDT)
  - Re: [AMBER] [Fwd: ligand exiting a protein cavity] Jason Swails (Thu Oct 29 2009 - 08:17:40 PDT)
    - Re: [AMBER] [Fwd: ligand exiting a protein cavity] moitrayee.mbu.iisc.ernet.in (Thu Oct 29 2009 - 22:43:22 PDT)
    - Re: [AMBER] [Fwd: ligand exiting a protein cavity] Jason Swails (Fri Oct 30 2009 - 06:07:17 PDT)
    - Re: [AMBER] [Fwd: ligand exiting a protein cavity] moitrayee.mbu.iisc.ernet.in (Fri Oct 30 2009 - 06:42:57 PDT)
    - Re: [AMBER] [Fwd: ligand exiting a protein cavity] Jason Swails (Fri Oct 30 2009 - 09:23:29 PDT)
[AMBER] rms fit of mutant with respect to wild type structure Siddharth Rastogi (Thu Oct 29 2009 - 06:55:12 PDT)
- Re: [AMBER] rms fit of mutant with respect to wild type structure Carlos Simmerling (Thu Oct 29 2009 - 07:03:35 PDT)
[AMBER] Parallel sander & polarisability Thomas Taylor (Thu Oct 29 2009 - 09:19:14 PDT)
- RE: [AMBER] Parallel sander & polarisability Ross Walker (Thu Oct 29 2009 - 10:00:13 PDT)
- Re: [AMBER] Parallel sander & polarisability case (Thu Oct 29 2009 - 10:02:28 PDT)
[AMBER] Analyzing per-residue decomposition data manoj singh (Thu Oct 29 2009 - 13:18:45 PDT)
[AMBER] stacking clusters Shaikh Abdul R S Ramaju (Thu Oct 29 2009 - 19:44:59 PDT)
[AMBER] some queries on -states flag in constant pH simulation nicholus bhattacharjee (Thu Oct 29 2009 - 21:21:27 PDT)
- Re: [AMBER] some queries on -states flag in constant pH simulation Jason Swails (Fri Oct 30 2009 - 06:00:37 PDT)
  - Re: [AMBER] some queries on -states flag in constant pH simulation nicholus bhattacharjee (Fri Oct 30 2009 - 23:31:31 PDT)
    - Re: [AMBER] some queries on -states flag in constant pH simulation Jason Swails (Sat Oct 31 2009 - 05:28:22 PDT)
[AMBER] Ligand covalent bonds appear to be broken moitrayee.mbu.iisc.ernet.in (Thu Oct 29 2009 - 23:32:39 PDT)
- Re: [AMBER] Ligand covalent bonds appear to be broken Tom Joseph (Fri Oct 30 2009 - 04:53:44 PDT)
  - Re: [AMBER] Ligand covalent bonds appear to be broken Jason Swails (Fri Oct 30 2009 - 06:11:03 PDT)
    - Re: [AMBER] Ligand covalent bonds appear to be broken moitrayee.mbu.iisc.ernet.in (Fri Oct 30 2009 - 06:43:25 PDT)
- Re: [AMBER] Ligand covalent bonds appear to be broken Thomas Cheatham (Fri Oct 30 2009 - 08:48:07 PDT)
[AMBER] Is it the way to do simulation in vacuum nicholus bhattacharjee (Fri Oct 30 2009 - 03:18:45 PDT)
- Re: [AMBER] Is it the way to do simulation in vacuum Carlos Simmerling (Fri Oct 30 2009 - 03:21:49 PDT)
  - Re: [AMBER] Is it the way to do simulation in vacuum nicholus bhattacharjee (Fri Oct 30 2009 - 04:11:03 PDT)
    - Re: [AMBER] Is it the way to do simulation in vacuum case (Fri Oct 30 2009 - 05:49:46 PDT)
    - Re: [AMBER] Is it the way to do simulation in vacuum Carlos Simmerling (Fri Oct 30 2009 - 06:26:20 PDT)
    - Re: [AMBER] Is it the way to do simulation in vacuum Jason Swails (Fri Oct 30 2009 - 09:06:14 PDT)
    - Re: [AMBER] Is it the way to do simulation in vacuum Carlos Simmerling (Fri Oct 30 2009 - 09:10:22 PDT)
    - RE: [AMBER] Is it the way to do simulation in vacuum Ross Walker (Fri Oct 30 2009 - 12:15:01 PDT)
[AMBER] SPC/E HOH angle Hemant Kumar (Fri Oct 30 2009 - 03:36:55 PDT)
- Re: [AMBER] SPC/E HOH angle case (Fri Oct 30 2009 - 05:51:41 PDT)
- Re: [AMBER] SPC/E HOH angle Carlos Simmerling (Fri Oct 30 2009 - 06:47:18 PDT)
[AMBER] RESP charges with -a and without -a flag Jio M (Fri Oct 30 2009 - 06:36:43 PDT)
- Re: [AMBER] RESP charges with -a and without -a flag Junmei Wang (Fri Oct 30 2009 - 09:49:00 PDT)
  - Re: [AMBER] RESP charges with -a and without -a flag Jio M (Fri Oct 30 2009 - 22:13:03 PDT)
[AMBER] Lennard Jones Potential A and B coefficients in Topology file Peter Schmidtke (Fri Oct 30 2009 - 11:32:32 PDT)
- Re: [AMBER] Lennard Jones Potential A and B coefficients in Topology file Tom Joseph (Fri Oct 30 2009 - 15:04:43 PDT)
  - Re: [AMBER] Lennard Jones Potential A and B coefficients in Topology file Peter Schmidtke (Fri Oct 30 2009 - 17:09:46 PDT)
    - Re: [AMBER] Lennard Jones Potential A and B coefficients in Topology file Tom Joseph (Fri Oct 30 2009 - 22:23:03 PDT)
    - Re: [AMBER] Lennard Jones Potential A and B coefficients in Topology file Tom Joseph (Sat Oct 31 2009 - 07:59:14 PDT)
    - Re: [AMBER] Lennard Jones Potential A and B coefficients in Topology file Peter Schmidtke (Sat Oct 31 2009 - 08:10:12 PDT)
- Re: [AMBER] Lennard Jones Potential A and B coefficients in Topology file Crowley, Michael (Sat Oct 31 2009 - 10:32:12 PDT)
[AMBER] Re: (files attached) RESP with -a and witout -a flag Jio M (Fri Oct 30 2009 - 22:17:55 PDT)
- [AMBER] Re: RESP with -a and witout -a flag Jio M (Sun Nov 01 2009 - 21:58:58 PST)
  - Re: [AMBER] Re: RESP with -a and witout -a flag Junmei Wang (Mon Nov 02 2009 - 08:48:48 PST)
    - [AMBER] Re: RESP with -a and witout -a flag Jio M (Tue Nov 03 2009 - 22:47:55 PST)
[AMBER] surface binding protein sadaf iqbal (Fri Oct 30 2009 - 22:28:22 PDT)
- Re: [AMBER] surface binding protein Jason Swails (Sat Oct 31 2009 - 05:35:44 PDT)
[AMBER] Gaussian log file error megha bajaj (Sat Oct 31 2009 - 06:10:22 PDT)
- Re: [AMBER] Gaussian log file error Ben Roberts (Mon Nov 02 2009 - 07:16:23 PST)
- Re: [AMBER] Gaussian log file error Junmei Wang (Mon Nov 02 2009 - 07:58:10 PST)
[AMBER] Different results for different computers cyk5056 (Sat Oct 31 2009 - 12:39:59 PDT)
- Re: [AMBER] Different results for different computers manoj singh (Sat Oct 31 2009 - 12:47:36 PDT)
  - Re: [AMBER] Different results for different computers Jason Swails (Sat Oct 31 2009 - 12:57:34 PDT)
- Re: [AMBER] Different results for different computers Robert Duke (Sat Oct 31 2009 - 15:56:28 PDT)
[AMBER] retinal lib file, params? Mark M Huntress (Sun Nov 01 2009 - 09:59:34 PST)
- Re: [AMBER] retinal lib file, params? Simon Becker (Mon Nov 02 2009 - 00:34:14 PST)
[AMBER] Is it taking too much time nicholus bhattacharjee (Sun Nov 01 2009 - 22:08:46 PST)
- Re: [AMBER] Is it taking too much time manoj singh (Sun Nov 01 2009 - 23:31:07 PST)
  - Re: [AMBER] Is it taking too much time nicholus bhattacharjee (Mon Nov 02 2009 - 00:37:28 PST)
    - Re: [AMBER] Is it taking too much time manoj singh (Mon Nov 02 2009 - 05:50:21 PST)
    - Re: [AMBER] Is it taking too much time Nicolas SAPAY (Mon Nov 02 2009 - 06:19:17 PST)
    - Re: [AMBER] Is it taking too much time nicholus bhattacharjee (Mon Nov 02 2009 - 06:40:25 PST)
    - Re: [AMBER] Is it taking too much time Nicolas SAPAY (Mon Nov 02 2009 - 07:00:58 PST)
    - Re: [AMBER] Is it taking too much time nicholus bhattacharjee (Mon Nov 02 2009 - 21:14:26 PST)
    - Re: [AMBER] Is it taking too much time nicholus bhattacharjee (Mon Nov 02 2009 - 21:35:04 PST)
    - Re: [AMBER] Is it taking too much time Nicolas Sapay (Tue Nov 03 2009 - 00:57:55 PST)
    - RE: [AMBER] Is it taking too much time Ross Walker (Mon Nov 02 2009 - 15:36:48 PST)
[AMBER] MPI process terminated unexpectedly after cluster upgrade Dmitri Nilov (Mon Nov 02 2009 - 01:17:19 PST)
- Re: [AMBER] MPI process terminated unexpectedly after cluster upgrade Jason Swails (Mon Nov 02 2009 - 04:15:19 PST)
  - Re: [AMBER] MPI process terminated unexpectedly after cluster upgrade Dmitri Nilov (Mon Nov 02 2009 - 05:11:15 PST)
    - Re: [AMBER] MPI process terminated unexpectedly after cluster upgrade Jason Swails (Mon Nov 02 2009 - 09:04:14 PST)
    - RE: [AMBER] MPI process terminated unexpectedly after cluster upgrade Ross Walker (Mon Nov 02 2009 - 15:36:48 PST)
    - Re: [AMBER] MPI process terminated unexpectedly after cluster upgrade Dmitri Nilov (Tue Nov 03 2009 - 05:20:17 PST)
    - Re: [AMBER] MPI process terminated unexpectedly after cluster upgrade Dmitri Nilov (Tue Nov 03 2009 - 06:06:11 PST)
    - RE: [AMBER] MPI process terminated unexpectedly after cluster upgrade Ross Walker (Tue Nov 03 2009 - 15:13:45 PST)
    - Re: [AMBER] MPI process terminated unexpectedly after cluster upgrade Dmitri Nilov (Thu Nov 05 2009 - 05:39:59 PST)
    - Re: [AMBER] MPI process terminated unexpectedly after cluster upgrade Jason Swails (Thu Nov 05 2009 - 06:12:39 PST)
    - Re: [AMBER] MPI process terminated unexpectedly after cluster upgrade Dmitri Nilov (Thu Nov 05 2009 - 06:38:32 PST)
    - Re: [AMBER] MPI process terminated unexpectedly after cluster upgrade Dmitri Nilov (Thu Nov 05 2009 - 06:55:16 PST)
    - RE: [AMBER] MPI process terminated unexpectedly after cluster upgrade Ross Walker (Thu Nov 05 2009 - 08:22:19 PST)
    - Re: [AMBER] MPI process terminated unexpectedly after cluster upgrade Jason Swails (Tue Nov 03 2009 - 06:11:48 PST)
[AMBER] amber 10 test failures... peker milas (Mon Nov 02 2009 - 06:18:29 PST)
- RE: [AMBER] amber 10 test failures... Ross Walker (Mon Nov 02 2009 - 15:36:48 PST)
  - Re: [AMBER] amber 10 test failures... Mark Williamson (Mon Nov 02 2009 - 16:11:40 PST)
    - Re: [AMBER] amber 10 test failures... Jason Swails (Mon Nov 02 2009 - 16:19:43 PST)
    - Re: [AMBER] amber 10 test failures... peker milas (Tue Nov 03 2009 - 06:11:01 PST)
[AMBER] 60 giga output file .mdcrd file Silvia Carlotto (Mon Nov 02 2009 - 09:41:32 PST)
- Re: [AMBER] 60 giga output file .mdcrd file Peter Schmidtke (Mon Nov 02 2009 - 10:40:48 PST)
- RE: [AMBER] 60 giga output file .mdcrd file Ross Walker (Mon Nov 02 2009 - 15:36:48 PST)
  - Re: [AMBER] 60 giga output file .mdcrd file Silvia Carlotto (Tue Nov 03 2009 - 02:24:03 PST)
    - Re: [AMBER] 60 giga output file .mdcrd file Fernando Martín García (Tue Nov 03 2009 - 02:35:41 PST)
    - Re: [AMBER] 60 giga output file .mdcrd file Jason Swails (Tue Nov 03 2009 - 05:49:01 PST)
    - Re: [AMBER] 60 giga output file .mdcrd file case (Wed Nov 04 2009 - 04:17:47 PST)
    - RE: [AMBER] 60 giga output file .mdcrd file Richard Owczarzy (Tue Nov 03 2009 - 07:14:44 PST)
    - Re: [AMBER] 60 giga output file .mdcrd file Silvia Carlotto (Tue Nov 03 2009 - 08:42:43 PST)
    - RE: [AMBER] 60 giga output file .mdcrd file Ross Walker (Tue Nov 03 2009 - 15:10:17 PST)
[AMBER] Is it possible to simulate transmembrane protein with GB model ? cgji (Mon Nov 02 2009 - 12:52:44 PST)
[AMBER] RE: question Ross Walker (Mon Nov 02 2009 - 15:36:48 PST)
- [AMBER] Re: question Marek Maly (Tue Nov 03 2009 - 12:22:16 PST)
- Re: [AMBER] RE: question rrd (Wed Nov 04 2009 - 18:52:04 PST)
  - Re: [AMBER] RE: question steinbrt.rci.rutgers.edu (Thu Nov 05 2009 - 00:12:47 PST)
    - Re: [AMBER] RE: question Marek Maly (Thu Nov 05 2009 - 05:28:03 PST)
    - Re: [AMBER] RE: question rrd (Thu Nov 05 2009 - 16:09:11 PST)
[AMBER] sander.APBS install problem Rilei Yu (Mon Nov 02 2009 - 17:58:30 PST)
- Re: [AMBER] sander.APBS install problem Robert Konecny (Mon Nov 02 2009 - 20:52:09 PST)
[AMBER] Phosphorylated Threonine Beale, John (Tue Nov 03 2009 - 08:31:09 PST)
- Re: [AMBER] Phosphorylated Threonine FyD (Tue Nov 03 2009 - 11:41:49 PST)
[AMBER] AMBER: segmentation fault when running parmchk Alexander Boncheff (Tue Nov 03 2009 - 11:41:55 PST)
- Re: [AMBER] AMBER: segmentation fault when running parmchk Jason Swails (Tue Nov 03 2009 - 12:22:10 PST)
  - Re: [AMBER] AMBER: segmentation fault when running parmchk Alexander Boncheff (Tue Nov 03 2009 - 14:29:00 PST)
    - Re: [AMBER] AMBER: segmentation fault when running parmchk Alexander Boncheff (Wed Nov 04 2009 - 08:02:50 PST)
    - Re: [AMBER] AMBER: segmentation fault when running parmchk Mark Williamson (Wed Nov 04 2009 - 09:06:53 PST)
    - Re: [AMBER] AMBER: segmentation fault when running parmchk Scott Brozell (Mon Dec 14 2009 - 10:14:15 PST)
- Re: [AMBER] AMBER: segmentation fault when running parmchk Bill Ross (Tue Nov 03 2009 - 15:15:00 PST)
- Re: [AMBER] AMBER: segmentation fault when running parmchk Bill Ross (Wed Nov 04 2009 - 10:39:32 PST)
- Re: [AMBER] AMBER: segmentation fault when running parmchk Junmei Wang (Wed Nov 04 2009 - 11:22:54 PST)
[AMBER] error in reading namelist cntrl Giuseppe De Marco (Tue Nov 03 2009 - 11:44:01 PST)
- RE: [AMBER] error in reading namelist cntrl Ross Walker (Tue Nov 03 2009 - 14:57:58 PST)
[AMBER] Antechamber and Parmchk problems cyk5056 (Tue Nov 03 2009 - 18:22:38 PST)
- Re: [AMBER] Antechamber and Parmchk problems case (Wed Nov 04 2009 - 07:26:03 PST)
  - Re: [AMBER] Antechamber and Parmchk problems Junmei Wang (Wed Nov 04 2009 - 11:21:25 PST)
- Re: Re: [AMBER] Antechamber and Parmchk problems cyk5056 (Wed Nov 04 2009 - 11:56:32 PST)
- Re: Re: [AMBER] Antechamber and Parmchk problems cyk5056 (Wed Nov 04 2009 - 12:37:55 PST)
  - Re: Re: [AMBER] Antechamber and Parmchk problems Junmei Wang (Wed Nov 04 2009 - 13:07:35 PST)
- Re: Re: Re: [AMBER] Antechamber and Parmchk problems cyk5056 (Thu Nov 05 2009 - 10:59:28 PST)
  - Re: Re: Re: [AMBER] Antechamber and Parmchk problems Junmei Wang (Thu Nov 05 2009 - 13:16:51 PST)
[AMBER] amber parameter file creation and usage Donald Keidel (Tue Nov 03 2009 - 20:47:36 PST)
- Re: [AMBER] amber parameter file creation and usage Jason Swails (Tue Nov 03 2009 - 21:29:30 PST)
  - Re: [AMBER] amber parameter file creation and usage Donald Keidel (Wed Nov 04 2009 - 09:53:23 PST)
[AMBER] errors on leap for a RNA+Adenine pdb structure zgong.hust (Tue Nov 03 2009 - 22:18:41 PST)
- Re: [AMBER] errors on leap for a RNA+Adenine pdb structure case (Wed Nov 04 2009 - 04:17:53 PST)
- Re: Re: [AMBER] errors on leap for a RNA+Adenine pdb structure zgong.hust (Wed Nov 04 2009 - 04:59:20 PST)
  - Re: [AMBER] errors on leap for a RNA+Adenine pdb structure FyD (Wed Nov 04 2009 - 05:39:02 PST)
[AMBER] total number of hydrogen bonds of the system as a function of time Markus Kaukonen (Wed Nov 04 2009 - 05:59:17 PST)
- Re: [AMBER] total number of hydrogen bonds of the system as a function of time Jason Swails (Wed Nov 04 2009 - 06:08:21 PST)
[AMBER] errors on leap for a RNA+Adenine pdb structure with antechamber zgong.hust (Wed Nov 04 2009 - 07:07:23 PST)
- Re: [AMBER] errors on leap for a RNA+Adenine pdb structure with antechamber FyD (Wed Nov 04 2009 - 07:28:04 PST)
[AMBER] HB for each snapshot Marcin Krol (Wed Nov 04 2009 - 11:14:41 PST)
- Re: [AMBER] HB for each snapshot Jason Swails (Wed Nov 04 2009 - 11:35:07 PST)
- Re: [AMBER] HB for each snapshot Nicolas Sapay (Thu Nov 05 2009 - 00:30:51 PST)
Re: Re: [AMBER] errors on leap for a RNA+Adenine pdb structure withantechamber zgong.hust (Wed Nov 04 2009 - 18:18:52 PST)
- Re: [AMBER] errors on leap for a RNA+Adenine pdb structure withantechamber FyD (Wed Nov 04 2009 - 21:42:43 PST)
[AMBER] Phosphothreonine Beale, John (Thu Nov 05 2009 - 05:03:58 PST)
- Re: [AMBER] Phosphothreonine Anselm Horn (Thu Nov 05 2009 - 05:17:59 PST)
[AMBER] Calculaiton stop ? xuemeiwang1103 (Thu Nov 05 2009 - 05:11:31 PST)
[AMBER] zeros in excluded atom list in topology file Peter Schmidtke (Thu Nov 05 2009 - 09:06:41 PST)
- Re: [AMBER] zeros in excluded atom list in topology file Carlos Simmerling (Thu Nov 05 2009 - 16:39:56 PST)
  - Re: [AMBER] zeros in excluded atom list in topology file Peter Schmidtke (Fri Nov 06 2009 - 00:54:57 PST)
- Re: [AMBER] zeros in excluded atom list in topology file case (Fri Nov 06 2009 - 14:44:04 PST)
  - Re: [AMBER] zeros in excluded atom list in topology file Peter Schmidtke (Fri Nov 06 2009 - 16:07:44 PST)
- Re: [AMBER] zeros in excluded atom list in topology file Bill Ross (Fri Nov 06 2009 - 16:09:39 PST)
[AMBER] Segmentation Fault Beale, John (Thu Nov 05 2009 - 10:04:52 PST)
- RE: [AMBER] Segmentation Fault Ross Walker (Thu Nov 05 2009 - 10:29:20 PST)
[AMBER] RESP using antechamber with Se atom Donald Keidel (Thu Nov 05 2009 - 11:21:37 PST)
- Re: [AMBER] RESP using antechamber with Se atom Junmei Wang (Thu Nov 05 2009 - 13:39:46 PST)
- Re: [AMBER] RESP using antechamber with Se atom subarna thakur (Thu Nov 05 2009 - 21:21:46 PST)
- Re: [AMBER] RESP using antechamber with Se atom Eric Pettersen (Fri Nov 06 2009 - 08:49:16 PST)
[AMBER] ff fitting ? Marek Maly (Thu Nov 05 2009 - 13:38:38 PST)
- Re: [AMBER] ff fitting ? case (Sun Nov 08 2009 - 09:42:42 PST)
  - Re: [AMBER] ff fitting ? Marek Maly (Mon Nov 09 2009 - 04:38:35 PST)
[AMBER] varying positional restraints with PMEMD Julian Garrec (Thu Nov 05 2009 - 16:43:35 PST)
- Re: [AMBER] varying positional restraints with PMEMD case (Sun Nov 08 2009 - 09:37:53 PST)
[AMBER] error in kclust of MMTB_tool set kureeckal ramesh (Thu Nov 05 2009 - 23:33:01 PST)
- [AMBER] -np not 2^x a problem w/ sander??? Dean Cuebas (Fri Nov 06 2009 - 11:27:48 PST)
  - RE: [AMBER] -np not 2^x a problem w/ sander??? Ross Walker (Fri Nov 06 2009 - 17:43:04 PST)
- [AMBER] -np not 2^x a problem w/ sander??? update Dean Cuebas (Fri Nov 06 2009 - 11:46:39 PST)
  - RE: [AMBER] -np not 2^x a problem w/ sander??? update Ross Walker (Sat Nov 07 2009 - 08:31:36 PST)
- [AMBER] ptraj script for H bond for protein (explicit ) kureeckal ramesh (Fri Nov 06 2009 - 23:38:29 PST)
[AMBER] amber9 compilation Myunggi Yi (Fri Nov 06 2009 - 07:10:03 PST)
- Re: [AMBER] amber9 compilation David Watson (Fri Nov 06 2009 - 07:19:31 PST)
  - Re: [AMBER] amber9 compilation Myunggi Yi (Fri Nov 06 2009 - 07:50:25 PST)
    - Re: [AMBER] amber9 compilation David Watson (Fri Nov 06 2009 - 08:16:58 PST)
[AMBER] amber 9 compilation Myunggi Yi (Fri Nov 06 2009 - 07:13:00 PST)
[AMBER] unable to find mopac charges in mopac.out Richard Tseng (Fri Nov 06 2009 - 17:14:20 PST)
- Re: [AMBER] unable to find mopac charges in mopac.out case (Sat Nov 07 2009 - 05:59:43 PST)
  - Re: [AMBER] unable to find mopac charges in mopac.out Richard Tseng (Mon Nov 09 2009 - 08:39:51 PST)
    - Re: [AMBER] unable to find mopac charges in mopac.out case (Mon Nov 09 2009 - 08:47:01 PST)
    - Re: [AMBER] unable to find mopac charges in mopac.out Richard Tseng (Mon Nov 09 2009 - 11:25:11 PST)
Re: [AMBER] unable to find mopac charges in mopac.out Bill Ross (Fri Nov 06 2009 - 17:22:22 PST)
[AMBER] Low frequency Raman spectra babak minoofar (Sat Nov 07 2009 - 04:53:37 PST)
- Re: [AMBER] Low frequency Raman spectra case (Sat Nov 07 2009 - 07:02:02 PST)
[AMBER] the problem of nucgen.dat liangchen88.ucla.edu (Sat Nov 07 2009 - 06:41:49 PST)
- Re: [AMBER] the problem of nucgen.dat case (Sat Nov 07 2009 - 06:51:57 PST)
  - Re: [AMBER] the problem of nucgen.dat liangchen88.ucla.edu (Sat Nov 07 2009 - 19:48:54 PST)
    - Re: [AMBER] the problem of nucgen.dat case (Sun Nov 08 2009 - 08:19:03 PST)
[AMBER] linux version for Amber10 liangchen88.ucla.edu (Sat Nov 07 2009 - 07:28:05 PST)
- Re: [AMBER] linux version for Amber10 Peter Schmidtke (Sat Nov 07 2009 - 07:58:18 PST)
  - Re: [AMBER]Amber10 + g95 Sudeep Narayan Banerjee (Sat Nov 07 2009 - 18:56:39 PST)
    - Re: [AMBER]Amber10 + g95 Abhishek Banerjee (Sat Nov 07 2009 - 19:41:54 PST)
    - Re: [AMBER]Amber10 + g95 jacky zhao (Tue Nov 17 2009 - 00:26:56 PST)
  - Re: [AMBER] linux version for Amber10 Sudeep Narayan Banerjee (Sat Nov 07 2009 - 18:56:19 PST)
    - Re: [AMBER] linux version for Amber10 Jason Swails (Sat Nov 07 2009 - 19:38:41 PST)
  - Re: [AMBER] linux version for Amber10 liangchen88.ucla.edu (Sat Nov 07 2009 - 19:59:53 PST)
[AMBER] build up solvate box Huikuan Chao (Sat Nov 07 2009 - 12:29:50 PST)
[AMBER] sleap fastbld error Oliver Kuhn (Sat Nov 07 2009 - 12:39:29 PST)
[AMBER] sleap fastbld error is not an error Oliver Kuhn (Sat Nov 07 2009 - 13:07:35 PST)
[AMBER] LJ parameters for HO and HW manoj singh (Sat Nov 07 2009 - 21:21:22 PST)
- Re: [AMBER] LJ parameters for HO and HW Jason Swails (Sat Nov 07 2009 - 21:50:03 PST)
  - Re: [AMBER] LJ parameters for HO and HW manoj singh (Sat Nov 07 2009 - 22:09:13 PST)
    - Re: [AMBER] LJ parameters for HO and HW Jason Swails (Sun Nov 08 2009 - 07:14:45 PST)
    - Re: [AMBER] LJ parameters for HO and HW steinbrt.rci.rutgers.edu (Mon Nov 09 2009 - 00:23:20 PST)
- Re: [AMBER] LJ parameters for HO and HW Bill Ross (Mon Nov 09 2009 - 09:29:40 PST)
[AMBER] solvent Jio M (Sun Nov 08 2009 - 06:12:34 PST)
[AMBER] MM_PBSA enquiries s. Bill (Sun Nov 08 2009 - 06:53:04 PST)
- Re: [AMBER] MM_PBSA enquiries manoj singh (Sun Nov 08 2009 - 07:21:12 PST)
[AMBER] pmemd failure Francesco Pietra (Sun Nov 08 2009 - 08:52:28 PST)
- Re: [AMBER] pmemd failure Robert Duke (Sun Nov 08 2009 - 09:00:52 PST)
  - Re: [AMBER] pmemd failure Francesco Pietra (Sun Nov 08 2009 - 11:08:53 PST)
[AMBER] Gly -> Ala mutation manoj singh (Sun Nov 08 2009 - 09:25:46 PST)
- Re: [AMBER] Gly -> Ala mutation Jason Swails (Sun Nov 08 2009 - 09:53:29 PST)
  - Re: [AMBER] Gly -> Ala mutation manoj singh (Sun Nov 08 2009 - 11:14:23 PST)
    - Re: [AMBER] Gly -> Ala mutation Jason Swails (Sun Nov 08 2009 - 12:16:42 PST)
    - Re: [AMBER] Gly -> Ala mutation manoj singh (Sun Nov 08 2009 - 13:18:37 PST)
    - Re: [AMBER] Gly -> Ala mutation Carlos Simmerling (Mon Nov 09 2009 - 07:13:08 PST)
    - Re: [AMBER] Gly -> Ala mutation manoj singh (Mon Nov 09 2009 - 08:10:40 PST)
    - Re: [AMBER] Gly -> Ala mutation Adrian Roitberg (Mon Nov 09 2009 - 08:13:11 PST)
    - Re: [AMBER] Gly -> Ala mutation manoj singh (Mon Nov 09 2009 - 08:26:00 PST)
[AMBER] error in kclust of MMTB_tool set kureeckal ramesh (Sun Nov 08 2009 - 16:10:58 PST)
[AMBER] analyzeMatrix: cannot find a match in the matrixInfoStack Naser Alijabbari (Sun Nov 08 2009 - 17:43:56 PST)
[AMBER] conversion of kelvin to kcal/mol aneesh cna (Sun Nov 08 2009 - 21:08:33 PST)
- Re: [AMBER] conversion of kelvin to kcal/mol manoj singh (Sun Nov 08 2009 - 21:17:03 PST)
  - Re: [AMBER] conversion of kelvin to kcal/mol aneesh cna (Sun Nov 08 2009 - 22:56:36 PST)
[AMBER] sander.mpi. mdfil: Error unknown flag: sander Andrew Voronkov (Mon Nov 09 2009 - 04:24:17 PST)
- Re: [AMBER] sander.mpi. mdfil: Error unknown flag: sander case (Mon Nov 09 2009 - 05:17:23 PST)
[AMBER] Task is running on supercomputer without any output Andrew Voronkov (Mon Nov 09 2009 - 04:39:36 PST)
- Re: [AMBER] Task is running on supercomputer without any output michael bane (Mon Nov 09 2009 - 04:51:17 PST)
  - Re: [AMBER] Task is running on supercomputer without any output Andrew Voronkov (Thu Nov 12 2009 - 05:24:56 PST)
[AMBER] PCA analysis with ptraj Alessandro Contini (Mon Nov 09 2009 - 09:00:19 PST)
- RE: [AMBER] PCA analysis with ptraj hannes.loeffler.stfc.ac.uk (Tue Nov 10 2009 - 00:13:29 PST)
  - RE: [AMBER] PCA analysis with ptraj Alessandro Contini (Tue Nov 10 2009 - 04:03:48 PST)
[AMBER] AmberTools 1.2 Installation on Ubuntu 9.10 Karmic Koala Wallace Kunin (Mon Nov 09 2009 - 11:14:25 PST)
- Re: [AMBER] AmberTools 1.2 Installation on Ubuntu 9.10 Karmic Koala David Watson (Mon Nov 09 2009 - 11:28:31 PST)
- Re: [AMBER] AmberTools 1.2 Installation on Ubuntu 9.10 Karmic Koala case (Mon Nov 09 2009 - 12:02:42 PST)
  - Re: [AMBER] AmberTools 1.2 Installation on Ubuntu 9.10 Karmic Koala Mark Williamson (Mon Nov 09 2009 - 12:14:03 PST)
    - Re: [AMBER] AmberTools 1.2 Installation on Ubuntu 9.10 Karmic Koala case (Mon Nov 09 2009 - 12:41:59 PST)
  - Re: [AMBER] AmberTools 1.2 Installation on Ubuntu 9.10 Karmic Koala Wallace Kunin (Mon Nov 09 2009 - 14:05:32 PST)
    - Re: [AMBER] AmberTools 1.2 Installation on Ubuntu 9.10 Karmic Koala David Watson (Mon Nov 09 2009 - 14:35:32 PST)
    - Re: [AMBER] AmberTools 1.2 Installation on Ubuntu 9.10 Karmic Koala David Watson (Mon Nov 09 2009 - 16:25:12 PST)
    - Re: [AMBER] AmberTools 1.2 Installation on Ubuntu 9.10 Karmic Koala Wallace Kunin (Tue Nov 10 2009 - 07:41:18 PST)
    - Re: [AMBER] AmberTools 1.2 Installation on Ubuntu 9.10 Karmic Koala case (Tue Nov 10 2009 - 08:28:17 PST)
    - Re: [AMBER] AmberTools 1.2 Installation on Ubuntu 9.10 Karmic Koala Wallace Kunin (Wed Nov 11 2009 - 06:17:42 PST)
    - Re: [AMBER] AmberTools 1.2 Installation on Ubuntu 9.10 Karmic Koala Giorgio Maccari (Wed Nov 11 2009 - 08:53:04 PST)
    - Re: [AMBER] AmberTools 1.2 Installation on Ubuntu 9.10 Karmic Koala David Watson (Wed Nov 11 2009 - 08:56:01 PST)
- Re: [AMBER] AmberTools 1.2 Installation on Ubuntu 9.10 Karmic Koala Bill Ross (Wed Nov 11 2009 - 09:54:01 PST)
  - Re: [AMBER] AmberTools 1.2 Installation on Ubuntu 9.10 Karmic Koala Wallace Kunin (Wed Nov 11 2009 - 14:04:28 PST)
    - Re: [AMBER] AmberTools 1.2 Installation on Ubuntu 9.10 Karmic Koala Jason Swails (Wed Nov 11 2009 - 14:30:35 PST)
    - Re: [AMBER] AmberTools 1.2 Installation on Ubuntu 9.10 Karmic Koala case (Wed Nov 11 2009 - 14:36:59 PST)
    - Re: [AMBER] AmberTools 1.2 Installation on Ubuntu 9.10 Karmic Koala Wallace Kunin (Thu Nov 12 2009 - 00:15:40 PST)
    - RE: [AMBER] AmberTools 1.2 Installation on Ubuntu 9.10 Karmic Koala Ross Walker (Thu Nov 12 2009 - 02:52:44 PST)
    - Re: [AMBER] AmberTools 1.2 Installation on Ubuntu 9.10 Karmic Koala Wallace Kunin (Thu Nov 12 2009 - 08:05:03 PST)
[AMBER] Getting minimized .pdb file without non-polar hydrogens Francesco Pietra (Mon Nov 09 2009 - 11:31:40 PST)
[AMBER] rectangular box with PME problem Ivan Gladich (Mon Nov 09 2009 - 14:18:16 PST)
[AMBER] three trials to create topologies with sleap and tleap Oliver Kuhn (Tue Nov 10 2009 - 01:34:36 PST)
[AMBER] error in kclust of MMTB_tool set kureeckal ramesh (Tue Nov 10 2009 - 04:41:31 PST)
[AMBER] MMTSB tool set PDF kureeckal ramesh (Tue Nov 10 2009 - 06:02:39 PST)
[AMBER] matrixinfoStack Naser Alijabbari (Tue Nov 10 2009 - 06:45:12 PST)
[AMBER] error reading namelist cntrl Shaikh Abdul R S Ramaju (Tue Nov 10 2009 - 22:51:45 PST)
- Re: [AMBER] error reading namelist cntrl Jason Swails (Wed Nov 11 2009 - 06:01:42 PST)
[AMBER] coarse-grained MD Francesco Pietra (Wed Nov 11 2009 - 00:27:27 PST)
- [AMBER] Increase Temperature to 550 K Chih-Ying Lin (Wed Nov 11 2009 - 07:27:41 PST)
  - [AMBER] High-temperature simulation ? Chih-Ying Lin (Wed Nov 11 2009 - 07:36:16 PST)
    - Re: [AMBER] High-temperature simulation ? Carlos Simmerling (Wed Nov 11 2009 - 09:26:15 PST)
  - Re: [AMBER] Increase Temperature to 550 K Carlos Simmerling (Wed Nov 11 2009 - 09:52:55 PST)
    - Re: [AMBER] Increase Temperature to 550 K Chih-Ying Lin (Wed Nov 11 2009 - 13:08:12 PST)
    - Re: [AMBER] Increase Temperature to 550 K Carlos Simmerling (Wed Nov 11 2009 - 13:14:24 PST)
    - Re: [AMBER] Increase Temperature to 550 K FyD (Wed Nov 11 2009 - 23:51:24 PST)
    - Re: [AMBER] Increase Temperature to 550 K case (Thu Nov 12 2009 - 04:55:18 PST)
    - Re: [AMBER] Increase Temperature to 550 K Carlos Simmerling (Thu Nov 12 2009 - 06:22:08 PST)
    - Re: [AMBER] Increase Temperature to 550 K Chih-Ying Lin (Thu Nov 12 2009 - 13:59:11 PST)
    - Re: [AMBER] Increase Temperature to 550 K Carlos Simmerling (Thu Nov 12 2009 - 14:29:13 PST)
    - Re: [AMBER] Increase Temperature to 550 K Chih-Ying Lin (Thu Nov 12 2009 - 20:36:07 PST)
    - Re: [AMBER] Increase Temperature to 550 K Carlos Simmerling (Fri Nov 13 2009 - 05:35:28 PST)
    - [AMBER] MSD of ligand?? Chih-Ying Lin (Tue Nov 17 2009 - 11:07:12 PST)
    - [AMBER] The decreasing MSD of ligand?? Chih-Ying Lin (Wed Nov 18 2009 - 13:19:35 PST)
    - [AMBER] The MSD and periodic boundary condition Chih-Ying Lin (Thu Nov 19 2009 - 15:30:46 PST)
    - Re: [AMBER] The MSD and periodic boundary condition Jason Swails (Thu Nov 19 2009 - 16:00:30 PST)
  - Re: [AMBER] Increase Temperature to 550 K FyD (Fri Nov 13 2009 - 03:43:48 PST)
[AMBER] Creating new residue with tleap. rrd (Wed Nov 11 2009 - 03:02:23 PST)
- Re: [AMBER] Creating new residue with tleap. case (Wed Nov 11 2009 - 04:37:47 PST)
[AMBER] Lisp library for amber analysis? Eric Shamay (Wed Nov 11 2009 - 13:54:12 PST)
[AMBER] reg. GBA balaji nagarajan (Thu Nov 12 2009 - 04:06:30 PST)
- Re: [AMBER] reg. GBA case (Thu Nov 12 2009 - 05:02:43 PST)
[AMBER] MD snapshots of most probable protein conformations in Amber Andrew Voronkov (Thu Nov 12 2009 - 05:23:22 PST)
- Re: [AMBER] MD snapshots of most probable protein conformations in Amber Adrian Roitberg (Thu Nov 12 2009 - 05:30:53 PST)
  - Re: [AMBER] MD snapshots of most probable protein conformations in Amber Andrew Voronkov (Wed Nov 18 2009 - 05:09:52 PST)
    - Re: [AMBER] MD snapshots of most probable protein conformations in Amber Renata KWIECIEN (Wed Nov 18 2009 - 05:39:52 PST)
    - Re: [AMBER] MD snapshots of most probable protein conformations in Amber Carlos Simmerling (Wed Nov 18 2009 - 05:53:14 PST)
    - Re: [AMBER] MD snapshots of most probable protein conformations in Amber Andrew Voronkov (Wed Nov 18 2009 - 07:32:11 PST)
    - Re: [AMBER] MD snapshots of most probable protein conformations in Amber Carlos Simmerling (Wed Nov 18 2009 - 09:14:50 PST)
    - Re: [AMBER] MD snapshots of most probable protein conformations in Amber Andrew Voronkov (Mon Nov 30 2009 - 04:56:42 PST)
    - Re: [AMBER] MD snapshots of most probable protein conformations in Amber Andrew Voronkov (Wed Nov 18 2009 - 07:33:54 PST)
[AMBER] MM_PBSA energy per residue Hemant Kumar (Thu Nov 12 2009 - 06:27:22 PST)
[AMBER] slope Jio M (Thu Nov 12 2009 - 11:28:02 PST)
[AMBER] R.E.D. resp error s. Bill (Thu Nov 12 2009 - 12:23:31 PST)
- Re: [AMBER] R.E.D. resp error FyD (Thu Nov 12 2009 - 21:36:44 PST)
[AMBER] R.E.D. too small charges Andrei Neamtu (Fri Nov 13 2009 - 00:57:04 PST)
- Re: [AMBER] R.E.D. too small charges FyD (Fri Nov 13 2009 - 05:06:51 PST)
[AMBER] enquiry regarding parameter file to be used bharat lakhani (Fri Nov 13 2009 - 05:35:30 PST)
- Re: [AMBER] enquiry regarding parameter file to be used Carlos Simmerling (Fri Nov 13 2009 - 05:41:50 PST)
  - Re: [AMBER] enquiry regarding parameter file to be used bharat lakhani (Fri Nov 13 2009 - 21:52:58 PST)
    - Re: [AMBER] enquiry regarding parameter file to be used Carlos Simmerling (Mon Nov 16 2009 - 03:40:49 PST)
    - Re: [AMBER] enquiry regarding parameter file to be used bharat lakhani (Thu Nov 19 2009 - 21:35:14 PST)
    - Re: [AMBER] enquiry regarding parameter file to be used Carlos Simmerling (Fri Nov 20 2009 - 03:20:05 PST)
[AMBER] matrixInfoStack Naser Alijabbari (Fri Nov 13 2009 - 06:52:52 PST)
[AMBER] request sculiujl (Fri Nov 13 2009 - 18:59:22 PST)
[AMBER] the different RMSD? qiaoyan (Fri Nov 13 2009 - 19:37:36 PST)
- Re: [AMBER] the different RMSD? Thomas Cheatham (Fri Nov 13 2009 - 19:40:56 PST)
- Re: Re: [AMBER] the different RMSD? qiaoyan (Fri Nov 13 2009 - 20:16:27 PST)
  - Re: Re: [AMBER] the different RMSD? Thomas Cheatham (Sat Nov 14 2009 - 08:25:43 PST)
- Re: Re: Re: [AMBER] the different RMSD? qiaoyan (Sat Nov 14 2009 - 18:02:53 PST)
[AMBER] is rst file the last structure? qiaoyan (Fri Nov 13 2009 - 20:52:40 PST)
- Re: [AMBER] is rst file the last structure? Jason Swails (Sat Nov 14 2009 - 09:18:22 PST)
  - Re: [AMBER] is rst file the last structure? case (Sun Nov 15 2009 - 06:33:16 PST)
[AMBER] Hydrogen bond analysis for protein dna complex using ptraj shamoon siddiqui (Sat Nov 14 2009 - 07:56:04 PST)
- Re: [AMBER] Hydrogen bond analysis for protein dna complex using ptraj Carlos Simmerling (Sat Nov 14 2009 - 08:00:39 PST)
  - Re: [AMBER] Hydrogen bond analysis for protein dna complex using ptraj shamoon siddiqui (Sat Nov 14 2009 - 08:19:04 PST)
    - Re: [AMBER] Hydrogen bond analysis for protein dna complex using ptraj Thomas Cheatham (Sat Nov 14 2009 - 09:06:15 PST)
[AMBER] How to split mdcrd files shamoon siddiqui (Sun Nov 15 2009 - 09:22:52 PST)
- Re: [AMBER] How to split mdcrd files Carlos Simmerling (Sun Nov 15 2009 - 09:28:06 PST)
  - Re: [AMBER] How to split mdcrd files Carlos Simmerling (Sun Nov 15 2009 - 09:56:48 PST)
- Re: [AMBER] How to split mdcrd files Jason Swails (Sun Nov 15 2009 - 09:35:24 PST)
- Re: [AMBER] How to split mdcrd files Thomas Cheatham (Sun Nov 15 2009 - 13:06:34 PST)
[AMBER] slope {no reply} Jio M (Sun Nov 15 2009 - 11:03:17 PST)
- Re: [AMBER] slope {no reply} Carlos Simmerling (Sun Nov 15 2009 - 11:07:02 PST)
  - Re: [AMBER] slope Jio M (Sun Nov 15 2009 - 20:42:52 PST)
    - Re: [AMBER] slope Carlos Simmerling (Mon Nov 16 2009 - 03:11:46 PST)
    - Re: [AMBER] slope Jio M (Mon Nov 16 2009 - 20:07:07 PST)
    - Re: [AMBER] slope Carlos Simmerling (Tue Nov 17 2009 - 03:10:35 PST)
- Re: [AMBER] slope {no reply} Bill Ross (Mon Nov 16 2009 - 09:48:22 PST)
  - Re: [AMBER] slope {no reply} Jio M (Mon Nov 16 2009 - 21:13:44 PST)
    - Re: [AMBER] slope {no reply} Carlos Simmerling (Tue Nov 17 2009 - 03:11:23 PST)
    - Re: [AMBER] slope {no reply} Jio M (Tue Nov 17 2009 - 11:13:06 PST)
    - Re: [AMBER] slope {no reply} Carlos Simmerling (Tue Nov 17 2009 - 15:49:39 PST)
    - Re: [AMBER] slope {no reply} Jio M (Tue Nov 17 2009 - 21:09:34 PST)
    - Re: [AMBER] slope {no reply} Sally Pias (Wed Nov 18 2009 - 21:39:53 PST)
    - Re: [AMBER] slope {no reply} Jio M (Thu Nov 19 2009 - 09:15:25 PST)
    - Re: [AMBER] slope {no reply} Sally Pias (Sat Nov 21 2009 - 22:53:39 PST)
- Re: [AMBER] slope {no reply} Bill Ross (Tue Nov 17 2009 - 09:51:08 PST)
- Re: [AMBER] slope {no reply} Bill Ross (Tue Nov 17 2009 - 17:04:48 PST)
[AMBER] Etot positive Jio M (Sun Nov 15 2009 - 21:06:22 PST)
- Re: [AMBER] Etot positive Carlos Simmerling (Mon Nov 16 2009 - 03:13:55 PST)
- RE: [AMBER] Etot positive Ross Walker (Mon Nov 16 2009 - 18:50:02 PST)
[AMBER] Segmentation fault in antechamber albert albert (Mon Nov 16 2009 - 07:28:20 PST)
- Re: [AMBER] Segmentation fault in antechamber case (Mon Nov 16 2009 - 07:53:30 PST)
  - Re: [AMBER] Segmentation fault in antechamber albert albert (Mon Nov 16 2009 - 08:23:02 PST)
    - Re: [AMBER] Segmentation fault in antechamber Mark Williamson (Mon Nov 16 2009 - 09:48:32 PST)
    - Re: [AMBER] Segmentation fault in antechamber albert albert (Tue Nov 17 2009 - 09:04:46 PST)
    - Re: [AMBER] Segmentation fault in antechamber case (Tue Nov 17 2009 - 20:28:14 PST)
    - Re: [AMBER] Segmentation fault in antechamber albert albert (Mon Nov 23 2009 - 07:23:00 PST)
- Re: [AMBER] Segmentation fault in antechamber Scott Brozell (Mon Dec 14 2009 - 21:34:39 PST)
[AMBER] Installing AMBER 10 on Ubuntu 9.10 Karmic Koala Wallace Kunin (Mon Nov 16 2009 - 08:43:18 PST)
- Re: [AMBER] Installing AMBER 10 on Ubuntu 9.10 Karmic Koala Mark Williamson (Mon Nov 16 2009 - 09:37:18 PST)
  - Re: [AMBER] Installing AMBER 10 on Ubuntu 9.10 Karmic Koala Wallace Kunin (Mon Nov 16 2009 - 11:07:20 PST)
    - Re: [AMBER] Installing AMBER 10 on Ubuntu 9.10 Karmic Koala Mark Williamson (Mon Nov 16 2009 - 11:49:58 PST)
    - Re: [AMBER] Installing AMBER 10 on Ubuntu 9.10 Karmic Koala Wallace Kunin (Tue Nov 17 2009 - 07:20:13 PST)
    - Re: [AMBER] Installing AMBER 10 on Ubuntu 9.10 Karmic Koala case (Tue Nov 17 2009 - 09:29:42 PST)
    - Re: [AMBER] Installing AMBER 10 on Ubuntu 9.10 Karmic Koala Wallace Kunin (Wed Nov 18 2009 - 06:21:57 PST)
    - Re: [AMBER] Installing AMBER 10 on Ubuntu 9.10 Karmic Koala Jason Swails (Wed Nov 18 2009 - 11:00:09 PST)
[AMBER] Re:Etot positive Jio M (Mon Nov 16 2009 - 20:59:26 PST)
[AMBER] compilation problem of amber9 sculiujl (Mon Nov 16 2009 - 23:03:22 PST)
- Re: [AMBER] compilation problem of amber9 Jason Swails (Tue Nov 17 2009 - 06:55:46 PST)
[AMBER] compilation problem of amber sculiujl (Mon Nov 16 2009 - 23:33:52 PST)
- Re: [AMBER] compilation problem of amber Jason Swails (Tue Nov 17 2009 - 06:51:42 PST)
[AMBER] which is the best intel complier for amber 10? jacky zhao (Tue Nov 17 2009 - 00:24:30 PST)
[AMBER] About zinc parameters ? xuemeiwang1103 (Tue Nov 17 2009 - 00:52:56 PST)
- Re: [AMBER] About zinc parameters ? steinbrt.rci.rutgers.edu (Tue Nov 17 2009 - 02:35:24 PST)
  - Re: [AMBER] About zinc parameters ? Sally Pias (Tue Nov 17 2009 - 09:38:29 PST)
- Re: [AMBER] About zinc parameters ? Jason Swails (Tue Nov 17 2009 - 07:17:23 PST)
[AMBER] non standart residue library creation with tleap (Zn atom) Andrew Voronkov (Tue Nov 17 2009 - 07:47:12 PST)
- Re: [AMBER] non standart residue library creation with tleap (Zn atom) Jason Swails (Tue Nov 17 2009 - 07:57:41 PST)
  - Re: [AMBER] non standart residue library creation with tleap (Zn atom) Andrew Voronkov (Tue Nov 17 2009 - 08:34:33 PST)
    - Re: [AMBER] non standart residue library creation with tleap (Zn atom) Jason Swails (Tue Nov 17 2009 - 10:05:05 PST)
    - Re: [AMBER] non standart residue library creation with tleap (Zn atom) FyD (Tue Nov 17 2009 - 12:10:03 PST)
- RE: [AMBER] non standart residue library creation with tleap (Zn atom) intra\\sa175950 (Tue Nov 17 2009 - 08:18:38 PST)
- Re: [AMBER] non standart residue library creation with tleap (Zn atom) Andrew Voronkov (Wed Nov 18 2009 - 05:19:58 PST)
  - Re: [AMBER] non standart residue library creation with tleap (Zn atom) FyD (Wed Nov 18 2009 - 06:29:14 PST)
    - Re: [AMBER] non standart residue library creation with tleap (Zn atom) Andrew Voronkov (Fri Nov 20 2009 - 03:35:31 PST)
    - Re: [AMBER] non standart residue library creation with tleap (Zn atom) case (Fri Nov 20 2009 - 05:30:54 PST)
    - Re: [AMBER] non standart residue library creation with tleap (Zn atom) FyD (Fri Nov 20 2009 - 05:42:58 PST)
    - Re: [AMBER] non standart residue library creation with tleap (Zn atom) Andrew Voronkov (Fri Nov 20 2009 - 07:25:30 PST)
    - Re: [AMBER] non standart residue library creation with tleap (Zn atom) FyD (Fri Nov 20 2009 - 07:40:50 PST)
    - Re: [AMBER] non standart residue library creation with tleap (Zn atom) Andrew Voronkov (Fri Nov 20 2009 - 08:02:57 PST)
    - Re: [AMBER] non standart residue library creation with tleap (Zn atom) FyD (Fri Nov 20 2009 - 09:47:00 PST)
    - Re: [AMBER] non standart residue library creation with tleap (Zn atom) Andrew Voronkov (Mon Nov 23 2009 - 04:35:55 PST)
    - Re: [AMBER] non standart residue library creation with tleap (Zn atom) FyD (Mon Nov 23 2009 - 05:25:15 PST)
    - Re: [AMBER] non standart residue library creation with tleap (Zn atom) Andrew Voronkov (Mon Nov 23 2009 - 07:44:45 PST)
    - Re: [AMBER] non standart residue library creation with tleap (Zn atom) FyD (Mon Nov 23 2009 - 08:06:01 PST)
    - Re: [AMBER] non standart residue library creation with tleap (Zn atom) Andrew Voronkov (Mon Nov 23 2009 - 08:35:51 PST)
    - Re: [AMBER] non standart residue library creation with tleap (Zn atom) FyD (Mon Nov 23 2009 - 09:22:23 PST)
    - Re: [AMBER] non standart residue library creation with tleap (Zn atom) FyD (Mon Nov 23 2009 - 09:31:31 PST)
    - Re: [AMBER] non standart residue library creation with tleap (Zn atom) Andrew Voronkov (Mon Nov 23 2009 - 09:38:28 PST)
    - Re: [AMBER] non standart residue library creation with tleap (Zn atom) FyD (Mon Nov 23 2009 - 09:49:05 PST)
    - Re: [AMBER] non standart residue library creation with tleap (Zn atom) FyD (Mon Nov 23 2009 - 11:50:42 PST)
    - RE: [AMBER] non standart residue library creation with tleap (Zn atom) Ross Walker (Tue Nov 24 2009 - 08:29:42 PST)
    - RE: [AMBER] non standart residue library creation with tleap (Zn atom) Ross Walker (Tue Nov 24 2009 - 08:28:21 PST)
- Re: [AMBER] non standart residue library creation with tleap (Zn atom) Andrew Voronkov (Tue Nov 24 2009 - 00:40:42 PST)
  - Re: [AMBER] non standart residue library creation with tleap (Zn atom) FyD (Tue Nov 24 2009 - 01:26:37 PST)
    - Re: [AMBER] non standart residue library creation with tleap (Zn atom) Andrew Voronkov (Tue Nov 24 2009 - 02:12:53 PST)
    - Re: [AMBER] non standart residue library creation with tleap (Zn atom) FyD (Tue Nov 24 2009 - 06:16:54 PST)
    - Re: [AMBER] non standart residue library creation with tleap (Zn atom) Andrew Voronkov (Tue Nov 24 2009 - 06:57:30 PST)
    - Re: [AMBER] non standart residue library creation with tleap (Zn atom) Andrew Voronkov (Wed Oct 26 2011 - 05:19:32 PDT)
    - Re: [AMBER] non standart residue library creation with tleap (Zn atom) FyD (Thu Oct 27 2011 - 00:33:55 PDT)
- Re: [AMBER] non standart residue library creation with tleap (Zn atom) Bill Ross (Tue Nov 24 2009 - 10:09:45 PST)
  - Re: Re: [AMBER] non standart residue library creation with tleap (Zn atom) Andrew Voronkov (Fri Jan 08 2010 - 01:09:39 PST)
[AMBER] tleap maximum coordination exceeded Jack Shultz (Tue Nov 17 2009 - 08:52:20 PST)
- Re: [AMBER] tleap maximum coordination exceeded FyD (Tue Nov 17 2009 - 12:18:20 PST)
- Re: [AMBER] tleap maximum coordination exceeded case (Tue Nov 17 2009 - 12:24:09 PST)
  - Re: [AMBER] tleap maximum coordination exceeded Jack Shultz (Tue Nov 17 2009 - 17:51:38 PST)
    - Re: [AMBER] tleap maximum coordination exceeded Jack Shultz (Tue Nov 17 2009 - 19:05:41 PST)
    - Re: [AMBER] tleap maximum coordination exceeded case (Tue Nov 17 2009 - 20:45:55 PST)
[AMBER] combining parameter files of ligand and enzyme Amire-Brahimi Benjamin (Tue Nov 17 2009 - 14:31:32 PST)
- Re: [AMBER] combining parameter files of ligand and enzyme FyD (Tue Nov 17 2009 - 23:49:23 PST)
[AMBER] have a question jacky zhao (Tue Nov 17 2009 - 17:54:36 PST)
Re: [AMBER] have a question Bill Ross (Tue Nov 17 2009 - 18:02:45 PST)
[AMBER] the different RMSD? qiaoyan (Tue Nov 17 2009 - 18:47:42 PST)
- 回复： [AMBER] the different RMSD? Rilei Yu (Tue Nov 17 2009 - 21:25:17 PST)
[AMBER] How to change the input matrix for "analyze matrix" instruction? cyk5056 (Tue Nov 17 2009 - 20:37:43 PST)
- Re:[AMBER] How to change the input matrix for "analyze matrix" instruction? 陈一侃 (Wed Nov 18 2009 - 08:18:51 PST)
[AMBER] Can I get an average trajectory? cyk5056 (Tue Nov 17 2009 - 20:46:25 PST)
- Re: [AMBER] Can I get an average trajectory? Carlos Simmerling (Wed Nov 18 2009 - 04:08:59 PST)
- Re: Re: [AMBER] Can I get an average trajectory? cyk5056 (Wed Nov 18 2009 - 08:02:38 PST)
[AMBER] GB and Atom Type Alexander Seifert (Wed Nov 18 2009 - 00:58:32 PST)
- Re: [AMBER] GB and Atom Type Sally Pias (Wed Nov 18 2009 - 21:11:27 PST)
[AMBER] Asking help for parallel installation of Amber9 nicholus bhattacharjee (Wed Nov 18 2009 - 04:27:03 PST)
- Re: [AMBER] Asking help for parallel installation of Amber9 David Watson (Wed Nov 18 2009 - 04:36:03 PST)
  - Re: [AMBER] Asking help for parallel installation of Amber9 nicholus bhattacharjee (Wed Nov 18 2009 - 05:00:36 PST)
    - Re: [AMBER] Asking help for parallel installation of Amber9 David Watson (Wed Nov 18 2009 - 05:23:17 PST)
[AMBER] read substrate into leap sculiujl (Wed Nov 18 2009 - 05:37:19 PST)
- Re: [AMBER] read substrate into leap Jason Swails (Wed Nov 18 2009 - 10:53:30 PST)
  - Re:Re: [AMBER] read substrate into leap sculiujl (Wed Nov 18 2009 - 17:12:13 PST)
    - Re: Re: [AMBER] read substrate into leap Jason Swails (Wed Nov 18 2009 - 17:35:37 PST)
  - Re:Re: [AMBER] read substrate into leap Bill Ross (Wed Nov 18 2009 - 17:59:33 PST)
[AMBER] about divcon Alan (Wed Nov 18 2009 - 08:24:51 PST)
- Re: [AMBER] about divcon case (Wed Nov 18 2009 - 08:53:16 PST)
  - Re: [AMBER] about divcon Alan (Wed Nov 18 2009 - 09:07:44 PST)
    - Re: [AMBER] about divcon Jason Swails (Wed Nov 18 2009 - 11:09:43 PST)
Re: [AMBER] Asking help for parallel installation of Amber9 Bill Ross (Wed Nov 18 2009 - 09:48:51 PST)
- Re: [AMBER] Asking help for parallel installation of Amber9 David Watson (Wed Nov 18 2009 - 10:04:38 PST)
[AMBER] Is the integral value from RDF the same as average number of atoms? Gustaf Olsson (go22bi.student.hik.se) (Wed Nov 18 2009 - 13:56:31 PST)
- Re: [AMBER] Is the integral value from RDF the same as average number of atoms? fatima chami (Sat Jan 16 2010 - 03:38:36 PST)
[AMBER] AmberTools 1.3 has a likely release date? Alan (Thu Nov 19 2009 - 10:15:30 PST)
- Re: [AMBER] AmberTools 1.3 has a likely release date? case (Fri Nov 20 2009 - 06:50:23 PST)
[AMBER] implicit_run_error balaji nagarajan (Thu Nov 19 2009 - 10:37:21 PST)
- Re: [AMBER] implicit_run_error case (Fri Nov 20 2009 - 06:53:31 PST)
[AMBER] errors on leap for a RNA + Non-Standard molecule pdb structure Yunjie Zhao (Thu Nov 19 2009 - 20:37:34 PST)
[AMBER] rmsd Taufik Al-Sarraj (Fri Nov 20 2009 - 08:32:24 PST)
- Re: [AMBER] rmsd Thomas Cheatham (Sat Nov 21 2009 - 13:44:41 PST)
  - Re: [AMBER] rmsd Taufik Al-Sarraj (Mon Nov 23 2009 - 11:24:49 PST)
- Re: [AMBER] rmsd 김준기 (Mon Sep 16 2013 - 23:43:10 PDT)
  - Re: [AMBER] rmsd Sajeewa Pemasinghe (Tue Sep 17 2013 - 04:34:30 PDT)
    - Re: [AMBER] rmsd 김준기 (Tue Sep 17 2013 - 08:41:54 PDT)
    - Re: [AMBER] rmsd Daniel Roe (Tue Sep 17 2013 - 08:51:06 PDT)
    - Re: [AMBER] rmsd Sajeewa Pemasinghe (Tue Sep 17 2013 - 08:52:10 PDT)
[AMBER] standard way to upload a lipid bilayer Syed Kashif Zafar (Sat Nov 21 2009 - 03:40:08 PST)
- Re: [AMBER] standard way to upload a lipid bilayer David Watson (Sat Nov 21 2009 - 05:06:29 PST)
[AMBER] looking for parameters for DHFR substrates and inhibitors... Sidney Elmer (Sat Nov 21 2009 - 20:47:50 PST)
[AMBER] NAD - mmpbsa Urszula Uciechowska (Sun Nov 22 2009 - 03:02:22 PST)
[AMBER] Polarizable simulation of the slab Jan Heyda (Sun Nov 22 2009 - 05:13:16 PST)
- Re: [AMBER] Polarizable simulation of the slab Robert Duke (Fri Nov 27 2009 - 08:48:07 PST)
[AMBER] Fortran error in standard simulation Oliver Kuhn (Mon Nov 23 2009 - 01:26:30 PST)
- RE: [AMBER] Fortran error in standard simulation Ross Walker (Tue Nov 24 2009 - 08:21:33 PST)
[AMBER] Fortran error in standard simulation 2 Oliver Kuhn (Mon Nov 23 2009 - 01:34:21 PST)
[AMBER] Fortran error in standard simulation 3 Oliver Kuhn (Mon Nov 23 2009 - 01:47:44 PST)
[AMBER] matrixInfoStack Naser Alijabbari (Mon Nov 23 2009 - 06:42:43 PST)
[AMBER] hbond analysis by ptraj- segmentation fault Jayalakshmi Sridhar (Mon Nov 23 2009 - 07:51:00 PST)
- Re: [AMBER] hbond analysis by ptraj- segmentation fault Daniel Roe (Mon Nov 23 2009 - 09:42:49 PST)
- Re: [AMBER] hbond analysis by ptraj- segmentation fault Daniel Roe (Mon Nov 23 2009 - 09:49:23 PST)
  - Re: [AMBER] hbond analysis by ptraj- segmentation fault Jayalakshmi Sridhar (Mon Nov 23 2009 - 10:36:25 PST)
[AMBER] Regarding Urey-Bradley term in amber calculation aneesh cna (Mon Nov 23 2009 - 22:48:04 PST)
- Re: [AMBER] Regarding Urey-Bradley term in amber calculation Jason Swails (Tue Nov 24 2009 - 04:48:31 PST)
- RE: [AMBER] Regarding Urey-Bradley term in amber calculation Ross Walker (Tue Nov 24 2009 - 08:36:49 PST)
[AMBER] How to get total energy of asystem gunajyoti das (Tue Nov 24 2009 - 01:14:06 PST)
- Re: [AMBER] How to get total energy of asystem steinbrt.rci.rutgers.edu (Tue Nov 24 2009 - 01:43:06 PST)
- Re: [AMBER] How to get total energy of asystem case (Tue Nov 24 2009 - 04:36:30 PST)
[AMBER] Hbond analysis output giving no hbonds Jayalakshmi Sridhar (Tue Nov 24 2009 - 08:32:41 PST)
- RE: [AMBER] Hbond analysis output giving no hbonds Thomas Cheatham (Tue Nov 24 2009 - 08:58:27 PST)
  - RE: [AMBER] Hbond analysis output giving no hbonds Jayalakshmi Sridhar (Tue Nov 24 2009 - 09:52:47 PST)
[AMBER] trouble with antechamber Jennifer L. Muzyka (Tue Nov 24 2009 - 12:13:46 PST)
- Re: [AMBER] trouble with antechamber case (Tue Nov 24 2009 - 12:41:24 PST)
  - RE: [AMBER] trouble with antechamber Jennifer L. Muzyka (Mon Nov 30 2009 - 06:39:15 PST)
    - Re: [AMBER] trouble with antechamber case (Mon Nov 30 2009 - 06:57:26 PST)
    - RE: [AMBER] trouble with antechamber Jennifer L. Muzyka (Tue Dec 01 2009 - 07:10:40 PST)
[AMBER] how to use amber to verify the reason for difference in affinity Josmar R. da Rocha (Tue Nov 24 2009 - 14:01:34 PST)
- Re: [AMBER] how to use amber to verify the reason for difference in affinity case (Sun Nov 29 2009 - 18:55:38 PST)
[AMBER] check MAXPR in locmem.f error on minimization Jodi Hadden (Tue Nov 24 2009 - 15:46:03 PST)
- Re: [AMBER] check MAXPR in locmem.f error on minimization case (Wed Nov 25 2009 - 05:29:41 PST)
  - Re: [AMBER] check MAXPR in locmem.f error on minimization Jodi Hadden (Wed Nov 25 2009 - 10:29:51 PST)
    - Re: [AMBER] check MAXPR in locmem.f error on minimization Jason Swails (Wed Nov 25 2009 - 10:50:43 PST)
- Re: [AMBER] check MAXPR in locmem.f error on minimization Robert Duke (Fri Nov 27 2009 - 06:44:36 PST)
[AMBER] MM-PBSA NMODE Zhongjie Liang (Tue Nov 24 2009 - 19:12:38 PST)
- Re: [AMBER] MM-PBSA NMODE case (Wed Nov 25 2009 - 05:31:28 PST)
[AMBER] i-APBS and apbs Rilei Yu (Tue Nov 24 2009 - 21:14:18 PST)
- Re: [AMBER] i-APBS and apbs Robert Konecny (Tue Nov 24 2009 - 21:33:37 PST)
- Re: [AMBER] i-APBS and apbs Jason Swails (Tue Nov 24 2009 - 21:33:31 PST)
- Re: [AMBER] i-APBS and apbs Rilei Yu (Wed Nov 25 2009 - 03:14:15 PST)
[AMBER] Not able to compile pmemd with openmpi in Amber9 Kito (Tue Nov 24 2009 - 22:39:42 PST)
- Re: [AMBER] Not able to compile pmemd with openmpi in Amber9 Jason Swails (Tue Nov 24 2009 - 23:06:14 PST)
- Re: [AMBER] Not able to compile pmemd with openmpi in Amber9 Kito (Tue Nov 24 2009 - 23:11:00 PST)
  - Re: Re: [AMBER] Not able to compile pmemd with openmpi in Amber9 Kito (Tue Nov 24 2009 - 23:50:25 PST)
    - Re: Re: Re: [AMBER] Not able to compile pmemd with openmpi in Amber9 Kito (Wed Nov 25 2009 - 00:12:51 PST)
    - Re: Re: Re: [AMBER] Not able to compile pmemd with openmpi in Amber9 Jason Swails (Wed Nov 25 2009 - 08:50:41 PST)
    - RE: Re: Re: [AMBER] Not able to compile pmemd with openmpi in Amber9 Ross Walker (Wed Nov 25 2009 - 12:24:23 PST)
    - Re: Re: Re: [AMBER] Not able to compile pmemd with openmpi in Amber9 case (Wed Nov 25 2009 - 13:06:53 PST)
- Re: Re: Re: [AMBER] Not able to compile pmemd with openmpi in Amber9 Robert Duke (Wed Nov 25 2009 - 14:48:21 PST)
[AMBER] MM-PB/GBSA NMODE Zhongjie Liang (Tue Nov 24 2009 - 22:50:50 PST)
[AMBER] heme (united-atom) Simon Becker (Wed Nov 25 2009 - 08:30:51 PST)
- Re: [AMBER] heme (united-atom) case (Wed Nov 25 2009 - 08:39:10 PST)
  - Re: [AMBER] heme (united-atom) Simon Becker (Thu Nov 26 2009 - 06:34:59 PST)
    - Re: [AMBER] heme (united-atom) case (Mon Nov 30 2009 - 05:28:05 PST)
[AMBER] Verlet update time in explicit water Replica Exchange MD Da-Wei Li (Wed Nov 25 2009 - 09:05:55 PST)
- Re: [AMBER] Verlet update time in explicit water Replica Exchange MD Carlos Simmerling (Wed Nov 25 2009 - 09:10:56 PST)
  - Re: [AMBER] Verlet update time in explicit water Replica Exchange MD Da-Wei Li (Wed Nov 25 2009 - 09:14:17 PST)
    - Re: [AMBER] Verlet update time in explicit water Replica Exchange MD Da-Wei Li (Wed Nov 25 2009 - 09:28:27 PST)
    - RE: [AMBER] Verlet update time in explicit water Replica Exchange MD Ross Walker (Wed Nov 25 2009 - 12:29:03 PST)
- [AMBER] Re: Verlet update time in explicit water Replica Exchange MD Da-Wei Li (Wed Nov 25 2009 - 09:12:23 PST)
- Re: [AMBER] Verlet update time in explicit water Replica Exchange MD Robert Duke (Wed Nov 25 2009 - 09:38:24 PST)
  - Re: [AMBER] Verlet update time in explicit water Replica Exchange MD Da-Wei Li (Wed Nov 25 2009 - 11:43:58 PST)
[AMBER] difference between two inputs Jio M (Wed Nov 25 2009 - 22:32:12 PST)
- Re: [AMBER] difference between two inputs case (Fri Nov 27 2009 - 06:59:01 PST)
[AMBER] rings getting planar Jio M (Thu Nov 26 2009 - 01:33:09 PST)
- Re: [AMBER] rings getting planar Jio M (Thu Nov 26 2009 - 06:40:34 PST)
- Re: [AMBER] rings getting planar case (Thu Nov 26 2009 - 07:07:43 PST)
[AMBER] ligand parameterization Nahoum Anthony (Thu Nov 26 2009 - 02:49:51 PST)
- Re: [AMBER] ligand parameterization case (Thu Nov 26 2009 - 07:09:05 PST)
  - Re: [AMBER] ligand parameterization Jason Swails (Thu Nov 26 2009 - 07:47:58 PST)
    - RE: [AMBER] ligand parameterization Nahoum Anthony (Thu Nov 26 2009 - 09:19:47 PST)
    - Re: [AMBER] ligand parameterization Jason Swails (Thu Nov 26 2009 - 14:12:34 PST)
    - Re: [AMBER] ligand parameterization Ilyas Yildirim (Thu Nov 26 2009 - 16:13:09 PST)
[AMBER] Atomic radii assignment for WAT molecules DIMAS SUAREZ RODRIGUEZ (Thu Nov 26 2009 - 08:43:33 PST)
- Re: [AMBER] Atomic radii assignment for WAT molecules Ray Luo (Sat Nov 28 2009 - 10:13:42 PST)
[AMBER] Polarizable simulation of the slab Jan Heyda (Thu Nov 26 2009 - 10:20:52 PST)
- Re: [AMBER] Polarizable simulation of the slab case (Fri Nov 27 2009 - 06:24:41 PST)
  - Re: [AMBER] Polarizable simulation of the slab Jan Heyda (Fri Nov 27 2009 - 06:53:57 PST)
    - Re: [AMBER] Polarizable simulation of the slab case (Fri Nov 27 2009 - 08:10:38 PST)
    - Re: [AMBER] Polarizable simulation of the slab Jan Heyda (Fri Nov 27 2009 - 08:27:13 PST)
    - [AMBER] GAFF polarizability - source Jan.Heyda.seznam.cz (Fri Dec 24 2010 - 08:53:40 PST)
    - Re: [AMBER] GAFF polarizability - source case (Fri Dec 24 2010 - 12:46:18 PST)
[AMBER] MM_PBSA error Jagdeesh C (Thu Nov 26 2009 - 20:28:44 PST)
- [AMBER] Re: MM_PBSA error Jagdeesh C (Fri Nov 27 2009 - 01:20:27 PST)
  - Re: [AMBER] Re: MM_PBSA error Mengjuei Hsieh (Fri Nov 27 2009 - 01:39:54 PST)
    - Re: [AMBER] Re: MM_PBSA error Jagdeesh C (Fri Nov 27 2009 - 02:13:36 PST)
    - Re: [AMBER] Re: MM_PBSA error Ray Luo (Sat Nov 28 2009 - 10:07:26 PST)
[AMBER] Regarding rigid bond aneesh cna (Fri Nov 27 2009 - 09:29:15 PST)
- Re: [AMBER] Regarding rigid bond Carlos Simmerling (Fri Nov 27 2009 - 10:24:35 PST)
  - Re: [AMBER] Regarding rigid bond aneesh cna (Mon Nov 30 2009 - 21:35:03 PST)
    - Re: [AMBER] Regarding rigid bond Carlos Simmerling (Tue Dec 01 2009 - 03:28:58 PST)
    - Re: [AMBER] Regarding rigid bond case (Tue Dec 01 2009 - 04:50:15 PST)
    - Re: [AMBER] Regarding rigid bond Carlos Simmerling (Tue Dec 01 2009 - 04:55:17 PST)
- Re: [AMBER] Regarding rigid bond Bill Ross (Tue Dec 01 2009 - 09:37:27 PST)
  - Re: [AMBER] Regarding rigid bond Adrian Roitberg (Tue Dec 01 2009 - 09:40:30 PST)
- Re: [AMBER] Regarding rigid bond Bill Ross (Tue Dec 01 2009 - 09:41:44 PST)
  - Re: [AMBER] Regarding rigid bond aneesh cna (Tue Dec 01 2009 - 21:17:46 PST)
- Re: [AMBER] Regarding rigid bond Bill Ross (Wed Dec 02 2009 - 09:20:52 PST)
[AMBER] LYS-ASP s. Bill (Fri Nov 27 2009 - 13:47:28 PST)
- Re: [AMBER] LYS-ASP Jason Swails (Fri Nov 27 2009 - 17:25:33 PST)
- Re: [AMBER] LYS-ASP case (Fri Nov 27 2009 - 19:08:58 PST)
[AMBER] where to get leaprc.ff99sb? Jack Shultz (Sat Nov 28 2009 - 16:20:03 PST)
- Re: [AMBER] where to get leaprc.ff99sb? Jason Swails (Sat Nov 28 2009 - 17:39:20 PST)
  - Re: [AMBER] where to get leaprc.ff99sb? Jack Shultz (Sat Nov 28 2009 - 19:19:33 PST)
    - Re: [AMBER] where to get leaprc.ff99sb? Jason Swails (Sat Nov 28 2009 - 19:51:39 PST)
[AMBER] Scripting tleap Jack Shultz (Sat Nov 28 2009 - 19:42:00 PST)
- Re: [AMBER] Scripting tleap Tom Joseph (Sat Nov 28 2009 - 19:45:40 PST)
  - Re: [AMBER] Scripting tleap Jack Shultz (Sat Nov 28 2009 - 19:54:25 PST)
    - Re: [AMBER] Scripting tleap Jio M (Thu Dec 03 2009 - 22:04:01 PST)
    - Re: [AMBER] Scripting tleap case (Sun Dec 06 2009 - 12:11:02 PST)
    - Re: [AMBER] Scripting tleap Jio M (Sun Dec 06 2009 - 22:56:59 PST)
[AMBER] How to compile and recompile ptraj? cyk5056 (Sun Nov 29 2009 - 14:06:55 PST)
- [AMBER] Re: How to compile and recompile ptraj? cyk5056 (Sun Nov 29 2009 - 14:53:37 PST)
  - Re: [AMBER] Re: How to compile and recompile ptraj? case (Sun Nov 29 2009 - 17:41:24 PST)
[AMBER] how to use GLYCAM04 for carbonhydrate in amber9? sculiujl (Sun Nov 29 2009 - 19:39:08 PST)
- Re: [AMBER] how to use GLYCAM04 for carbonhydrate in amber9? Karl Kirschner (Mon Nov 30 2009 - 00:53:27 PST)
[AMBER] reagarding Dihedral PCA jani sahil (Sun Nov 29 2009 - 22:24:28 PST)
[AMBER] regarding Dihedral PCA jani sahil (Sun Nov 29 2009 - 22:25:08 PST)
[AMBER] distance-dependent dielectric constant minimization Rilei Yu (Sun Nov 29 2009 - 23:02:32 PST)
- Re: [AMBER] distance-dependent dielectric constant minimization case (Mon Nov 30 2009 - 05:02:11 PST)
  - Re: [AMBER] distance-dependent dielectric constant minimization Rilei Yu (Mon Nov 30 2009 - 21:31:58 PST)
    - Re: [AMBER] distance-dependent dielectric constant minimization case (Tue Dec 01 2009 - 04:48:32 PST)
- Re: [AMBER] distance-dependent dielectric constant minimization Robert Duke (Tue Dec 01 2009 - 05:06:40 PST)
  - Re: [AMBER] SGLD in pmemd?? Dean Cuebas (Tue Dec 01 2009 - 11:31:21 PST)
    - Re: [AMBER] SGLD in pmemd?? Robert Duke (Tue Dec 01 2009 - 12:04:14 PST)
  - Re: [AMBER] distance-dependent dielectric constant minimization Rilei Yu (Sat Dec 05 2009 - 00:21:58 PST)
    - Re: [AMBER] distance-dependent dielectric constant minimization case (Sat Dec 05 2009 - 19:03:47 PST)
    - Re: [AMBER] distance-dependent dielectric constant minimization Rilei Yu (Sat Dec 05 2009 - 23:37:13 PST)
- Re: [AMBER] distance-dependent dielectric constant minimization Bill Ross (Sat Dec 05 2009 - 09:30:09 PST)
[AMBER] trajout problem Anna Reymer (Mon Nov 30 2009 - 04:03:38 PST)
- Re: [AMBER] trajout problem Carlos Simmerling (Mon Nov 30 2009 - 04:09:05 PST)
  - RE: [AMBER] trajout problem Anna Reymer (Mon Nov 30 2009 - 04:58:39 PST)
    - Re: [AMBER] trajout problem Carlos Simmerling (Mon Nov 30 2009 - 05:56:43 PST)
    - Re: [AMBER] trajout problem Daniel Roe (Tue Dec 01 2009 - 04:34:34 PST)
    - RE: [AMBER] trajout problem Anna Reymer (Tue Dec 01 2009 - 05:23:22 PST)
- Re: [AMBER] trajout problem Sally Pias (Mon Nov 30 2009 - 11:01:52 PST)
[AMBER] problem with FAD in tleap M. Shahid (Mon Nov 30 2009 - 04:17:09 PST)
- Re: [AMBER] problem with FAD in tleap FyD (Mon Nov 30 2009 - 05:02:59 PST)
  - Re: [AMBER] problem with FAD in tleap M. Shahid (Mon Nov 30 2009 - 07:54:26 PST)
    - Re: [AMBER] problem with FAD in tleap case (Mon Nov 30 2009 - 09:15:19 PST)
    - Re: [AMBER] problem with FAD in tleap M. Shahid (Mon Nov 30 2009 - 10:33:35 PST)
    - Re: [AMBER] problem with FAD in tleap FyD (Mon Nov 30 2009 - 11:25:15 PST)
    - Re: [AMBER] problem with FAD in tleap FyD (Mon Nov 30 2009 - 11:15:56 PST)
    - Re: [AMBER] problem with FAD in tleap M. Shahid (Tue Dec 01 2009 - 03:54:04 PST)
- Re: [AMBER] problem with FAD in tleap case (Mon Nov 30 2009 - 05:26:37 PST)
[AMBER] Output Does Not Match in Tutorial B1 Wallace Kunin (Mon Nov 30 2009 - 10:38:07 PST)
- Re: [AMBER] Output Does Not Match in Tutorial B1 case (Mon Nov 30 2009 - 11:01:20 PST)
  - Re: [AMBER] Output Does Not Match in Tutorial B1 Wallace Kunin (Mon Nov 30 2009 - 11:11:02 PST)
    - Re: [AMBER] Output Does Not Match in Tutorial B1 case (Mon Nov 30 2009 - 11:50:34 PST)
    - Re: [AMBER] Output Does Not Match in Tutorial B1 Wallace Kunin (Tue Dec 01 2009 - 10:00:48 PST)
    - Re: [AMBER] Output Does Not Match in Tutorial B1 Wallace Kunin (Tue Dec 01 2009 - 10:41:08 PST)
Re: [AMBER] Output Does Not Match in Tutorial B1 Bill Ross (Mon Nov 30 2009 - 11:03:19 PST)
[AMBER] fillratio Qinghua Liao (Mon Nov 30 2009 - 18:38:34 PST)
- Re: [AMBER] fillratio Ray Luo (Mon Nov 30 2009 - 19:30:50 PST)
  - Re: [AMBER] fillratio Qinghua Liao (Mon Nov 30 2009 - 21:59:05 PST)
[AMBER] ptraj utility Neha Bharat Gajaria (Tue Dec 01 2009 - 00:30:07 PST)
- Re: [AMBER] ptraj utility Daniel Roe (Tue Dec 01 2009 - 04:45:19 PST)
  - Re: [AMBER] ptraj utility Carlos Simmerling (Tue Dec 01 2009 - 04:48:27 PST)
- Re: [AMBER] ptraj utility case (Tue Dec 01 2009 - 04:56:52 PST)
  - Re: [AMBER] ptraj utility Neha Bharat Gajaria (Tue Dec 01 2009 - 18:13:41 PST)
[AMBER] XLEaP Error on Closing Edit Wallace Kunin (Tue Dec 01 2009 - 10:43:27 PST)
- RE: [AMBER] XLEaP Error on Closing Edit Ross Walker (Tue Dec 01 2009 - 11:02:58 PST)
[AMBER] Re: looking for parameters for DHFR substrates and inhibitors... [one more try] Sidney Elmer (Tue Dec 01 2009 - 15:34:36 PST)
- Re: [AMBER] looking for parameters for DHFR substrates and inhibitors... [one more try] FyD (Wed Dec 02 2009 - 00:19:00 PST)
[AMBER] How to get total energy of a system from QM/MM gunajyoti das (Wed Dec 02 2009 - 00:56:06 PST)
- Re: [AMBER] How to get total energy of a system from QM/MM steinbrt.rci.rutgers.edu (Wed Dec 02 2009 - 01:53:03 PST)
[AMBER] MMGBSA Zhongjie Liang (Wed Dec 02 2009 - 17:17:44 PST)
[AMBER] look at Amber's slides, email Sally Pias (Wed Dec 02 2009 - 21:08:47 PST)
[AMBER] Segmentation fault gurunath katagi (Wed Dec 02 2009 - 22:45:20 PST)
- Re: [AMBER] Segmentation fault Seibold, Stephen (Sat Oct 02 2010 - 15:53:54 PDT)
  - Re: [AMBER] Segmentation fault Jason Swails (Sat Oct 02 2010 - 18:56:53 PDT)
- Re: [AMBER] Segmentation fault Seibold, Stephen (Mon Oct 04 2010 - 16:18:25 PDT)
  - Re: [AMBER] Segmentation fault Jason Swails (Mon Oct 04 2010 - 18:47:12 PDT)
  - Re: [AMBER] Segmentation fault Daniel Roe (Mon Oct 04 2010 - 20:31:49 PDT)
- Re: [AMBER] Segmentation fault Ben Roberts (Thu Mar 29 2012 - 02:37:53 PDT)
[AMBER] NAB example scripts in AmberTools (Amber 10) Christopher Wassman (Thu Dec 03 2009 - 01:08:37 PST)
- Re: [AMBER] NAB example scripts in AmberTools (Amber 10) case (Thu Dec 03 2009 - 05:12:27 PST)
[AMBER] binding energy of multiple ligand-receptor complex 欧阳德方 (Thu Dec 03 2009 - 02:51:17 PST)
- Re: [AMBER] binding energy of multiple ligand-receptor complex Oliver Kuhn (Fri Dec 04 2009 - 01:10:39 PST)
  - Re: [AMBER] binding energy of multiple ligand-receptor complex steinbrt.rci.rutgers.edu (Fri Dec 04 2009 - 01:47:26 PST)
    - Re: [AMBER] binding energy of multiple ligand-receptor complex Jason Swails (Fri Dec 04 2009 - 12:20:58 PST)
    - RE: [AMBER] binding energy of multiple ligand-receptor complex 欧阳德方 (Fri Dec 04 2009 - 13:59:21 PST)
[AMBER] QM/MM input file error mahesh kumar (Thu Dec 03 2009 - 06:05:25 PST)
- RE: [AMBER] QM/MM input file error Ross Walker (Thu Dec 03 2009 - 09:36:47 PST)
[AMBER] semiempirical copper Jacopo Sgrignani (Thu Dec 03 2009 - 06:09:57 PST)
- RE: [AMBER] semiempirical copper Ross Walker (Thu Dec 03 2009 - 09:28:45 PST)
[AMBER] Comparison of the CHARMM and AMBER parameters for alkane intra\\sa175950 (Thu Dec 03 2009 - 08:49:28 PST)
- RE: [AMBER] Comparison of the CHARMM and AMBER parameters for alkane Ross Walker (Thu Dec 03 2009 - 09:52:58 PST)
  - RE: [AMBER] Comparison of the CHARMM and AMBER parameters for alkane intra\\sa175950 (Fri Dec 04 2009 - 01:54:55 PST)
    - RE: [AMBER] Comparison of the CHARMM and AMBER parameters for alkane FyD (Fri Dec 04 2009 - 09:44:57 PST)
    - RE: [AMBER] Comparison of the CHARMM and AMBER parameters for alkane Ross Walker (Fri Dec 04 2009 - 11:16:50 PST)
    - RE: [AMBER] Comparison of the CHARMM and AMBER parameters for alkane FyD (Fri Dec 04 2009 - 12:02:17 PST)
- Re: [AMBER] Comparison of the CHARMM and AMBER parameters for alkane FyD (Thu Dec 03 2009 - 11:43:10 PST)
[AMBER] AmberTools modifications for Ubuntu 9.10 peker milas (Thu Dec 03 2009 - 13:58:31 PST)
- Re: [AMBER] AmberTools modifications for Ubuntu 9.10 case (Fri Dec 04 2009 - 07:31:16 PST)
[AMBER] help with TIP4P and mpi pmemd Hashem Taha (Thu Dec 03 2009 - 14:16:22 PST)
- Re: [AMBER] help with TIP4P and mpi pmemd Robert Duke (Thu Dec 03 2009 - 14:37:14 PST)
  - [AMBER] parameter file for the sulphate ion Fenghui Fan (Thu Dec 03 2009 - 16:02:30 PST)
  - Re: [AMBER] help with TIP4P and mpi pmemd Hashem Taha (Thu Dec 03 2009 - 18:26:57 PST)
    - Re: [AMBER] help with TIP4P and mpi pmemd Hashem Taha (Thu Dec 03 2009 - 21:29:38 PST)
- Re: [AMBER] help with TIP4P and mpi pmemd Robert Duke (Thu Dec 03 2009 - 21:58:58 PST)
  - Re: [AMBER] help with TIP4P and mpi pmemd Hashem Taha (Fri Dec 04 2009 - 13:01:50 PST)
    - Re: [AMBER] help with TIP4P and mpi pmemd case (Fri Dec 04 2009 - 13:16:22 PST)
- Re: [AMBER] help with TIP4P and mpi pmemd Robert Duke (Fri Dec 04 2009 - 13:26:41 PST)
  - Re: [AMBER] help with TIP4P and mpi pmemd Hashem Taha (Fri Dec 04 2009 - 13:44:44 PST)
- Re: [AMBER] help with TIP4P and mpi pmemd Lizzard Man (Fri Dec 04 2009 - 14:47:08 PST)
[AMBER] Amber 10 installation: /bin/sh: ./Makelist: not found Diego Javier Alonso de Armiño (Thu Dec 03 2009 - 17:47:08 PST)
- Re: [AMBER] Amber 10 installation: /bin/sh: ./Makelist: not found Mengjuei Hsieh (Thu Dec 03 2009 - 18:52:48 PST)
- Re: [AMBER] Amber 10 installation: /bin/sh: ./Makelist: not found Jason Swails (Thu Dec 03 2009 - 18:55:09 PST)
  - [AMBER] clarification DNA forcefield Taufik Al-Sarraj (Thu Dec 03 2009 - 20:01:02 PST)
    - Re: [AMBER] clarification DNA forcefield Jiri Sponer (Fri Dec 04 2009 - 01:19:05 PST)
    - Re: [AMBER] clarification DNA forcefield Taufik Al-Sarraj (Mon Dec 07 2009 - 16:22:33 PST)
  - Re: [AMBER] Amber 10 installation: /bin/sh: ./Makelist: not found Diego Javier Alonso de Armiño (Fri Dec 04 2009 - 04:09:04 PST)
  - Re: [AMBER] Amber 10 installation: /bin/sh: ./Makelist: not found case (Fri Dec 04 2009 - 06:18:09 PST)
    - Re: [AMBER] Amber 10 installation: /bin/sh: ./Makelist: not found Jason Swails (Fri Dec 04 2009 - 09:42:19 PST)
[AMBER] sodium ions before or after solvation makes a difference Naser Alijabbari (Thu Dec 03 2009 - 21:01:13 PST)
- Re: [AMBER] sodium ions before or after solvation makes a difference Thomas Cheatham III (Fri Dec 04 2009 - 09:09:17 PST)
- Re: [AMBER] sodium ions before or after solvation makes a difference Bill Ross (Fri Dec 04 2009 - 10:23:44 PST)
[AMBER] mm_pbsa- Decomposition: bad atom type Antonija Tomić (Fri Dec 04 2009 - 01:27:31 PST)
- Re: [AMBER] mm_pbsa- Decomposition: bad atom type Hannes Kopitz (Fri Dec 04 2009 - 02:45:10 PST)
  - Re: [AMBER] mm_pbsa- Decomposition: bad atom type Antonija Tomić (Fri Dec 04 2009 - 02:57:59 PST)
[AMBER] ptraj usage for clustering of protein ensembles manual or tutorial Andrew Voronkov (Fri Dec 04 2009 - 01:55:05 PST)
- Re: [AMBER] ptraj usage for clustering of protein ensembles manual or tutorial Thomas Cheatham III (Fri Dec 04 2009 - 09:01:35 PST)
  - Re: [AMBER] ptraj usage for clustering of protein ensembles manual or tutorial Andrew Voronkov (Fri Dec 04 2009 - 11:09:58 PST)
    - Re: [AMBER] ptraj usage for clustering of protein ensembles manual or tutorial Thomas Cheatham III (Fri Dec 04 2009 - 11:20:21 PST)
    - Re: [AMBER] ptraj usage for clustering of protein ensembles manual or tutorial Andrew Voronkov (Sun Dec 06 2009 - 03:58:41 PST)
    - Re: [AMBER] ptraj usage for clustering of protein ensembles manual or tutorial Thomas Cheatham (Sun Dec 06 2009 - 09:23:48 PST)
    - Re: Re: [AMBER] ptraj usage for clustering of protein ensembles manual or tutorial Andrew Voronkov (Tue Dec 08 2009 - 06:48:56 PST)
    - Re: Re: [AMBER] ptraj usage for clustering of protein ensembles manual or tutorial Carlos Simmerling (Tue Dec 08 2009 - 06:59:48 PST)
    - [AMBER] preparation of small molecule libraries with most probable conformations using Amber Andrew Voronkov (Sat Dec 26 2009 - 03:38:09 PST)
    - Re: Re: [AMBER] ptraj usage for clustering of protein ensembles manual or tutorial Andrew Voronkov (Mon Jan 04 2010 - 13:33:23 PST)
- Re: [AMBER] ptraj usage for clustering of protein ensembles manual or tutorial Andrew Voronkov (Sun Dec 06 2009 - 05:39:39 PST)
[AMBER] aromatic ring getting distorted Jio M (Fri Dec 04 2009 - 02:03:49 PST)
- Re: [AMBER] aromatic ring getting distorted case (Sun Dec 06 2009 - 12:14:45 PST)
  - Re: [AMBER] aromatic ring getting distorted Jio M (Sun Dec 06 2009 - 23:04:55 PST)
[AMBER] problem with antechamber sculiujl (Fri Dec 04 2009 - 03:38:04 PST)
- Re: [AMBER] problem with antechamber Junmei Wang (Wed Dec 09 2009 - 15:24:11 PST)
[AMBER] COOH group troubling Jio M (Sun Dec 06 2009 - 05:57:06 PST)
- Re: [AMBER] COOH group troubling Jason Swails (Sun Dec 06 2009 - 07:05:07 PST)
Re: [AMBER] COOH group troubling Bill Ross (Sun Dec 06 2009 - 08:46:58 PST)
- Re: [AMBER] COOH group troubling Jio M (Sun Dec 06 2009 - 10:53:22 PST)
- Re: [AMBER] COOH group troubling Bill Ross (Sun Dec 06 2009 - 11:07:44 PST)
[AMBER] how to restart the stopped MM-GBSA job Zhongjie Liang (Sun Dec 06 2009 - 17:36:56 PST)
[AMBER] Problem of MM-PBSA 欧阳德方 (Sun Dec 06 2009 - 21:09:47 PST)
- Re: [AMBER] Problem of MM-PBSA Ray Luo (Mon Dec 07 2009 - 10:19:02 PST)
  - RE: [AMBER] Problem of MM-PBSA 欧阳德方 (Mon Dec 07 2009 - 14:30:41 PST)
    - Re: [AMBER] Problem of MM-PBSA Ray Luo (Mon Dec 07 2009 - 14:44:53 PST)
[AMBER] force field parameters Piotr Cieplak (Sun Dec 06 2009 - 23:25:03 PST)
[AMBER] phosphorus to carbon on minimization Alexander Boncheff (Mon Dec 07 2009 - 07:48:45 PST)
- Re: [AMBER] phosphorus to carbon on minimization Jason Swails (Mon Dec 07 2009 - 10:43:05 PST)
- Re: [AMBER] phosphorus to carbon on minimization FyD (Mon Dec 07 2009 - 10:56:28 PST)
[AMBER] Topology Reorder for EVB Andrea Coletta (Mon Dec 07 2009 - 07:58:50 PST)
- Re: [AMBER] Topology Reorder for EVB Jason Swails (Mon Dec 07 2009 - 10:59:23 PST)
  - Re: [AMBER] Topology Reorder for EVB Andrea Coletta (Tue Dec 08 2009 - 01:40:23 PST)
- Re: [AMBER] Topology Reorder for EVB E.M. (Mon Dec 07 2009 - 11:17:44 PST)
[AMBER] Parametrizing charges for modified DNA bases Bob Johnson (Mon Dec 07 2009 - 10:05:09 PST)
- Re: [AMBER] Parametrizing charges for modified DNA bases FyD (Mon Dec 07 2009 - 11:31:02 PST)
  - [AMBER] Re: EEL = ************* Taufik Al-Sarraj (Tue Dec 08 2009 - 10:34:35 PST)
    - [AMBER] ptraj image Taufik Al-Sarraj (Tue Dec 08 2009 - 13:37:55 PST)
    - Re: [AMBER] ptraj image Thomas Cheatham (Tue Dec 08 2009 - 13:50:09 PST)
    - Re: [AMBER] Re: EEL = ************* case (Thu Dec 10 2009 - 12:13:15 PST)
[AMBER] question about failures peker milas (Mon Dec 07 2009 - 19:37:40 PST)
- Re: [AMBER] question about failures Jason Swails (Mon Dec 07 2009 - 20:51:28 PST)
  - Re: [AMBER] question about failures peker milas (Mon Dec 07 2009 - 21:31:06 PST)
    - Re: [AMBER] question about failures Jason Swails (Mon Dec 07 2009 - 22:00:00 PST)
    - Re: [AMBER] question about failures peker milas (Mon Dec 07 2009 - 22:25:10 PST)
[AMBER] myristate to palmitate transformation Anthony Pemberton (Tue Dec 08 2009 - 08:24:59 PST)
[AMBER] Custom RNA modeling Wallace Kunin (Tue Dec 08 2009 - 12:27:55 PST)
- Re: [AMBER] Custom RNA modeling Ilyas Yildirim (Tue Dec 08 2009 - 14:01:42 PST)
  - Re: [AMBER] Custom RNA modeling Wallace Kunin (Wed Dec 09 2009 - 08:10:44 PST)
    - Re: [AMBER] Custom RNA modeling Wallace Kunin (Mon Dec 14 2009 - 09:50:25 PST)
    - Re: [AMBER] Custom RNA modeling case (Mon Dec 14 2009 - 10:32:11 PST)
    - Re: [AMBER] Custom RNA modeling Thomas Cheatham (Mon Dec 14 2009 - 10:35:44 PST)
    - Re: [AMBER] Custom RNA modeling Wallace Kunin (Mon Dec 14 2009 - 13:49:29 PST)
    - Re: [AMBER] Custom RNA modeling Carlos Simmerling (Mon Dec 14 2009 - 13:55:20 PST)
    - Re: [AMBER] Custom RNA modeling Jiri Sponer (Mon Dec 14 2009 - 14:08:07 PST)
Re: [AMBER] ptraj image Bill Ross (Tue Dec 08 2009 - 14:08:42 PST)
- Re: [AMBER] ptraj image Taufik Al-Sarraj (Tue Dec 08 2009 - 15:54:46 PST)
  - Re: [AMBER] ptraj image Daniel Roe (Wed Dec 09 2009 - 08:21:18 PST)
[AMBER] Nmode "not running properly" problem in MM_PBSA Du Yun (Tue Dec 08 2009 - 17:56:48 PST)
- Re: [AMBER] Nmode "not running properly" problem in MM_PBSA case (Sun Dec 13 2009 - 07:06:36 PST)
[AMBER] PIMD test stalling peker milas (Tue Dec 08 2009 - 18:23:45 PST)
- [AMBER] Re: PIMD test stalling peker milas (Tue Dec 08 2009 - 19:11:44 PST)
[AMBER] how to add desired number of water balaji nagarajan (Tue Dec 08 2009 - 19:18:49 PST)
- Re: [AMBER] how to add desired number of water Simon Becker (Wed Dec 09 2009 - 08:09:51 PST)
[AMBER] ptraj image Neha Bharat Gajaria (Tue Dec 08 2009 - 22:13:36 PST)
- Re: [AMBER] ptraj image Bill Ross (Tue Dec 08 2009 - 16:29:03 PST)
- Re: [AMBER] ptraj image Thomas Cheatham (Wed Dec 09 2009 - 05:41:54 PST)
[AMBER] Re: ATP/GTP parameters FyD (Tue Dec 08 2009 - 22:51:03 PST)
[AMBER] Re: COOH troubling Jio M (Wed Dec 09 2009 - 04:16:17 PST)
- Re: [AMBER] Re: COOH troubling case (Wed Dec 09 2009 - 05:40:10 PST)
  - Re: [AMBER] Re: COOH troubling Jio M (Wed Dec 09 2009 - 07:01:30 PST)
- Re: [AMBER] Re: COOH troubling Junmei Wang (Wed Dec 09 2009 - 15:17:12 PST)
  - Re: [AMBER] Re: COOH troubling Dean Cuebas (Wed Dec 09 2009 - 16:00:40 PST)
    - Re: [AMBER] Re: COOH troubling Jio M (Wed Dec 09 2009 - 22:21:24 PST)
    - Re: [AMBER] Re: COOH troubling Jio M (Thu Dec 10 2009 - 03:03:59 PST)
    - Re: [AMBER] Re: COOH troubling Junmei Wang (Thu Dec 10 2009 - 13:45:43 PST)
    - Re: [AMBER] Re: COOH troubling Dean Cuebas (Sat Dec 12 2009 - 08:47:42 PST)
    - Re: [AMBER] Re: COOH troubling Dean Cuebas (Thu Dec 10 2009 - 22:41:27 PST)
    - Re: [AMBER] Re: COOH troubling case (Fri Dec 11 2009 - 05:27:09 PST)
    - Re: [AMBER] Re: COOH troubling Jio M (Fri Dec 11 2009 - 11:37:39 PST)
- Re: [AMBER] Re: COOH troubling Jio M (Fri Dec 11 2009 - 22:27:25 PST)
[AMBER] Re: COOH group trouble Jio M (Wed Dec 09 2009 - 08:38:09 PST)
Re: [AMBER] how to add desired number of water Bill Ross (Wed Dec 09 2009 - 09:46:59 PST)
[AMBER] pressure tensor components Silvia Carlotto (Thu Dec 10 2009 - 05:12:51 PST)
- Re: [AMBER] pressure tensor components case (Sun Dec 13 2009 - 07:10:02 PST)
[AMBER] MMPBSA on a selected region ERIK.LAURINI.phd.units.it (Thu Dec 10 2009 - 10:20:19 PST)
- Re: [AMBER] MMPBSA on a selected region Jason Swails (Thu Dec 10 2009 - 11:15:58 PST)
[AMBER] why is the ff03 force field in Amber8 and Amber10 different for Ala2 dipeptide Dongshan Wei (Thu Dec 10 2009 - 15:40:19 PST)
- Re: [AMBER] why is the ff03 force field in Amber8 and Amber10 different for Ala2 dipeptide Carlos Simmerling (Thu Dec 10 2009 - 15:52:40 PST)
- RE: [AMBER] why is the ff03 force field in Amber8 and Amber10 different for Ala2 dipeptide Ross Walker (Thu Dec 10 2009 - 16:02:16 PST)
  - Re: [AMBER] why is the ff03 force field in Amber8 and Amber10 different for Ala2 dipeptide Dongshan Wei (Thu Dec 10 2009 - 16:14:12 PST)
[AMBER] QM/MM minimization Hashem Taha (Fri Dec 11 2009 - 10:24:25 PST)
- RE: [AMBER] QM/MM minimization Ross Walker (Fri Dec 11 2009 - 19:39:55 PST)
[AMBER] amber10 pmemd fail Aragorn Steiger (Fri Dec 11 2009 - 12:35:49 PST)
- Re: [AMBER] amber10 pmemd fail Robert Duke (Fri Dec 11 2009 - 13:40:31 PST)
- RE: [AMBER] amber10 pmemd fail Ross Walker (Fri Dec 11 2009 - 19:43:53 PST)
FW: Solvent/solute ratio? Re: [AMBER] how to add desired number of water Hopkins, Robert (Fri Dec 11 2009 - 14:05:51 PST)
- Re: FW: Solvent/solute ratio? Re: [AMBER] how to add desired number of water Bill Ross (Fri Dec 11 2009 - 14:19:57 PST)
  - RE: FW: Solvent/solute ratio? Re: [AMBER] how to add desired numberof water Richard Owczarzy (Fri Dec 11 2009 - 16:19:31 PST)
    - RE: FW: Solvent/solute ratio? Re: [AMBER] how to add desired numberof water Bill Ross (Fri Dec 11 2009 - 16:57:41 PST)
  - RE: FW: Solvent/solute ratio? Re: [AMBER] how to add desired number of water Ross Walker (Fri Dec 11 2009 - 19:47:19 PST)
Re: FW: Solvent/solute ratio? Re: [AMBER] how to add desired numberof water Hopkins, Robert (Fri Dec 11 2009 - 14:24:02 PST)
- Re: Solvent/solute ratio? Re: [AMBER] how to add desired numberof water Dean Cuebas (Mon Dec 14 2009 - 18:40:25 PST)
RE: [Possible Spam: 10%] RE: FW: Solvent/solute ratio? Re: [AMBER] how to add desirednumberof water Hopkins, Robert (Sat Dec 12 2009 - 16:29:04 PST)
[AMBER] amber.ambermd.org shumao.cqut.edu.cn (Sun Dec 13 2009 - 19:01:18 PST)
[AMBER] How to run LEaP in a shell file? SongLin (Sun Dec 13 2009 - 23:10:00 PST)
- Re: [AMBER] How to run LEaP in a shell file? case (Mon Dec 14 2009 - 04:44:29 PST)
  - Re: [AMBER] How to run LEaP in a shell file? SongLin (Mon Dec 14 2009 - 05:45:03 PST)
[AMBER] Different simulation times for similar systems Oliver Kuhn (Mon Dec 14 2009 - 04:31:50 PST)
- Re: [AMBER] Different simulation times for similar systems Carlos Simmerling (Mon Dec 14 2009 - 10:11:56 PST)
[AMBER] how can i include ANP residue Bradley Dickson (Mon Dec 14 2009 - 07:07:50 PST)
- Re: [AMBER] how can i include ANP residue FyD (Mon Dec 14 2009 - 12:29:42 PST)
  - Re: [AMBER] how can i include ANP residue Bradley Dickson (Mon Dec 14 2009 - 14:00:32 PST)
    - Re: [AMBER] how can i include ANP residue David Watson (Mon Dec 14 2009 - 14:44:30 PST)
[AMBER] Installation on MacOSX Freedman, Tanya (Mon Dec 14 2009 - 10:59:06 PST)
- Re: [AMBER] Installation on MacOSX David Watson (Mon Dec 14 2009 - 12:01:52 PST)
  - Re: [AMBER] Installation on MacOSX Alan (Tue Dec 15 2009 - 02:26:48 PST)
    - Re: [AMBER] Installation on MacOSX Jason Swails (Tue Dec 15 2009 - 03:43:47 PST)
    - Re: [AMBER] Installation on MacOSX David Watson (Tue Dec 15 2009 - 04:54:06 PST)
    - Re: [AMBER] Installation on MacOSX Alan (Tue Dec 15 2009 - 08:11:20 PST)
[AMBER] comparing coordinates from restart file and ptraj outputs Sidney Elmer (Mon Dec 14 2009 - 17:23:50 PST)
- Re: [AMBER] comparing coordinates from restart file and ptraj outputs Jason Swails (Mon Dec 14 2009 - 17:53:39 PST)
- Re: [AMBER] comparing coordinates from restart file and ptraj outputs case (Mon Dec 14 2009 - 19:28:32 PST)
  - Re: [AMBER] comparing coordinates from restart file and ptraj outputs Sidney Elmer (Tue Dec 15 2009 - 00:21:35 PST)
    - Re: [AMBER] comparing coordinates from restart file and ptraj outputs Jason Swails (Tue Dec 15 2009 - 04:00:41 PST)
    - Re: [AMBER] comparing coordinates from restart file and ptraj outputs Daniel Roe (Tue Dec 15 2009 - 07:45:20 PST)
    - Re: [AMBER] comparing coordinates from restart file and ptraj outputs Sidney Elmer (Tue Dec 15 2009 - 12:15:06 PST)
[AMBER] Number of Cycles s. Bill (Tue Dec 15 2009 - 00:31:21 PST)
- Re: [AMBER] Number of Cycles Jason Swails (Tue Dec 15 2009 - 04:10:02 PST)
- Re: [AMBER] Number of Cycles Robert Duke (Tue Dec 15 2009 - 05:16:51 PST)
- Re: [AMBER] Number of Cycles Robert Duke (Tue Dec 15 2009 - 05:23:04 PST)
  - Re: [AMBER] Number of Cycles Carlos Simmerling (Tue Dec 15 2009 - 05:31:09 PST)
- Re: [AMBER] Number of Cycles Jason Swails (Tue Dec 15 2009 - 05:32:31 PST)
  - Re: [AMBER] Number of Cycles Jason Swails (Tue Dec 15 2009 - 05:34:29 PST)
- Re: [AMBER] Number of Cycles Robert Duke (Tue Dec 15 2009 - 06:55:31 PST)
  - Re: [AMBER] Number of Cycles Carlos Simmerling (Tue Dec 15 2009 - 08:53:06 PST)
    - Re: [AMBER] Number of Cycles Jason Swails (Tue Dec 15 2009 - 09:10:31 PST)
    - Re: [AMBER] Number of Cycles Carlos Simmerling (Tue Dec 15 2009 - 09:13:17 PST)
    - Re: [AMBER] Number of Cycles Jason Swails (Tue Dec 15 2009 - 09:18:37 PST)
- Re: [AMBER] Number of Cycles Robert Duke (Tue Dec 15 2009 - 09:09:42 PST)
- Re: [AMBER] Number of Cycles Robert Duke (Tue Dec 15 2009 - 09:29:22 PST)
  - RE: [AMBER] Number of Cycles Niel Henriksen (Tue Dec 15 2009 - 09:41:55 PST)
- Re: [AMBER] Number of Cycles Bill Ross (Tue Dec 15 2009 - 09:53:24 PST)
- Re: [AMBER] Number of Cycles Robert Duke (Tue Dec 15 2009 - 09:54:28 PST)
  - RE: [AMBER] Number of Cycles Niel Henriksen (Tue Dec 15 2009 - 10:11:08 PST)
    - Re: [AMBER] Number of Cycles Jason Swails (Tue Dec 15 2009 - 10:32:40 PST)
    - RE: [AMBER] Number of Cycles Ross Walker (Tue Dec 15 2009 - 11:01:40 PST)
- Re: [AMBER] Number of Cycles Robert Duke (Tue Dec 15 2009 - 11:00:19 PST)
[AMBER] addles - neb error balaji nagarajan (Tue Dec 15 2009 - 06:38:53 PST)
- RE: [AMBER] addles - neb error Ross Walker (Tue Dec 15 2009 - 08:45:19 PST)
  - RE: [AMBER] addles - neb error balaji nagarajan (Tue Dec 15 2009 - 19:26:51 PST)
    - Re: [AMBER] addles - neb error case (Wed Dec 16 2009 - 13:01:20 PST)
    - RE: [AMBER] addles - neb error balaji nagarajan (Wed Dec 16 2009 - 19:20:22 PST)
[AMBER] non standard residue and bond command Neha Bharat Gajaria (Wed Dec 16 2009 - 01:50:02 PST)
- Re: [AMBER] non standard residue and bond command case (Wed Dec 16 2009 - 13:06:34 PST)
- Re: [AMBER] non standard residue and bond command Bill Ross (Wed Dec 16 2009 - 13:20:08 PST)
[AMBER] chemical shifts: nter and cter Eliana Asciutto (Wed Dec 16 2009 - 11:55:14 PST)
- Re: [AMBER] chemical shifts: nter and cter case (Wed Dec 16 2009 - 12:52:11 PST)
[AMBER] NAMD dcd files in ptraj Ganesh Kamath (Wed Dec 16 2009 - 13:04:25 PST)
[AMBER] Parameters for HYP and CGU Rilei Yu (Wed Dec 16 2009 - 19:17:40 PST)
- Re: [AMBER] Parameters for HYP and CGU Adrian Roitberg (Wed Dec 16 2009 - 19:27:25 PST)
  - Re: [AMBER] Parameters for HYP and CGU Rilei Yu (Wed Dec 16 2009 - 21:58:26 PST)
- Re: [AMBER] Parameters for HYP and CGU Jason Swails (Wed Dec 16 2009 - 19:58:02 PST)
  - Re: [AMBER] Parameters for HYP and CGU Rilei Yu (Wed Dec 16 2009 - 21:57:13 PST)
- Re: [AMBER] Parameters for HYP and CGU FyD (Thu Dec 17 2009 - 00:46:55 PST)
  - Re: [AMBER] Parameters for HYP and CGU Alessandro Contini (Thu Dec 17 2009 - 01:11:44 PST)
  - [AMBER] branched aminoacids Alessandro Contini (Thu Dec 17 2009 - 01:14:34 PST)
    - Re: [AMBER] branched aminoacids FyD (Thu Dec 17 2009 - 01:49:16 PST)
    - Re: [AMBER] branched aminoacids Alessandro Contini (Thu Dec 17 2009 - 03:22:56 PST)
[AMBER] C1, C2 & C3 carbon types in generalized Born implementation igb=5 Nils Jan Daniel Drechsel (Thu Dec 17 2009 - 01:52:59 PST)
- Re: [AMBER] C1, C2 & C3 carbon types in generalized Born implementation igb=5 case (Thu Dec 17 2009 - 05:03:27 PST)
  - Re: [AMBER] C1, C2 & C3 carbon types in generalized Born implementation igb=5 Nils Jan Daniel Drechsel (Fri Dec 18 2009 - 02:37:53 PST)
[AMBER] what the value of "Br" bondi radii, and how to modify "fillratio" error message. 木野　亮平 (Thu Dec 17 2009 - 01:59:29 PST)
[AMBER] MM_PBSA Problem (no radius for ion) s. Bill (Thu Dec 17 2009 - 11:39:49 PST)
- Re: [AMBER] MM_PBSA Problem (no radius for ion) Scott Brozell (Thu Dec 17 2009 - 19:07:21 PST)
  - Re: [AMBER] MM_PBSA Problem (no radius for ion) s. Bill (Fri Dec 18 2009 - 07:33:57 PST)
[AMBER] Compatibility of ONIOM and Amber vaibhav dixit (Thu Dec 17 2009 - 22:30:32 PST)
[AMBER] Inorganic Phosphate Parameters Cihan Aydin (Fri Dec 18 2009 - 12:19:21 PST)
- Re: [AMBER] Inorganic Phosphate Parameters. . Don.Bashford.stjude.org (Fri Dec 18 2009 - 14:12:58 PST)
  - Re: [AMBER] Inorganic Phosphate Parameters. . Jason Swails (Fri Dec 18 2009 - 14:54:39 PST)
  - Re: [AMBER] Inorganic Phosphate Parameters. . case (Sat Dec 19 2009 - 09:39:28 PST)
[AMBER] antechamber bond type error Mark M Huntress (Fri Dec 18 2009 - 14:26:57 PST)
- Re: [AMBER] antechamber bond type error case (Sat Dec 19 2009 - 09:33:40 PST)
  - RE: [AMBER] antechamber bond type error Mark M Huntress (Tue Jan 05 2010 - 16:18:51 PST)
    - Re: [AMBER] antechamber bond type error case (Tue Jan 05 2010 - 20:36:15 PST)
    - Re: [AMBER] antechamber bond type error Dean Cuebas (Tue Jan 05 2010 - 21:48:41 PST)
    - RE: [AMBER] antechamber bond type error Mark M Huntress (Wed Jan 06 2010 - 13:10:25 PST)
[AMBER] note on Antechamber error Mark M Huntress (Fri Dec 18 2009 - 14:27:50 PST)
[AMBER] SQM and AMBER Jio M (Fri Dec 18 2009 - 22:36:05 PST)
[AMBER] Non-Standard Atoms Jack Shultz (Sat Dec 19 2009 - 17:56:28 PST)
- Re: [AMBER] Non-Standard Atoms Jason Swails (Sat Dec 19 2009 - 18:54:20 PST)
- Re: [AMBER] Non-Standard Atoms case (Sun Dec 20 2009 - 11:02:46 PST)
  - Re: [AMBER] Non-Standard Atoms Jack Shultz (Sun Dec 20 2009 - 16:40:26 PST)
[AMBER] hi ashish pandey (Sun Dec 20 2009 - 22:45:40 PST)
- Re: [AMBER] hi David Watson (Mon Dec 21 2009 - 01:09:53 PST)
[AMBER] Sander crash, corrupt rst file... Waqas Nasir (Mon Dec 21 2009 - 03:44:42 PST)
[AMBER] (No reply) Compatibility of ONIOM and Amber vaibhav dixit (Mon Dec 21 2009 - 05:58:03 PST)
[AMBER] Release of AmberTools, version 1.3 David A. Case (Mon Dec 21 2009 - 06:33:20 PST)
[AMBER] Gaff compatible with ff899.SB Pol Boudard (Mon Dec 21 2009 - 07:03:25 PST)
- Re: [AMBER] Gaff compatible with ff899.SB Carlos Simmerling (Mon Dec 21 2009 - 07:32:40 PST)
[AMBER] MM PBSA stats Peter Jones (Mon Dec 21 2009 - 21:57:51 PST)
[AMBER] PQR file - HELP PLEASE s. Bill (Tue Dec 22 2009 - 04:57:48 PST)
- Re: [AMBER] PQR file - HELP PLEASE Jason Swails (Tue Dec 22 2009 - 09:21:41 PST)
  - Re: [AMBER] PQR file - HELP PLEASE s. Bill (Tue Dec 22 2009 - 13:27:48 PST)
[AMBER] MMGBSA error Zhongjie Liang (Tue Dec 22 2009 - 05:04:09 PST)
- Re: [AMBER] MMGBSA error Carlos Simmerling (Tue Dec 22 2009 - 05:05:41 PST)
  - 答复: [AMBER] MMGBSA error Zhongjie Liang (Wed Dec 23 2009 - 05:12:07 PST)
[AMBER] sqm x mopac in AmberTools 1.3 Alan (Tue Dec 22 2009 - 07:02:22 PST)
- Re: [AMBER] sqm x mopac in AmberTools 1.3 David Watson (Tue Dec 22 2009 - 07:20:37 PST)
  - Re: [AMBER] sqm x mopac in AmberTools 1.3 David Watson (Tue Dec 22 2009 - 07:58:56 PST)
  - Re: [AMBER] sqm x mopac in AmberTools 1.3 David A. Case (Tue Dec 22 2009 - 19:53:20 PST)
- Re: [AMBER] sqm x mopac in AmberTools 1.3 David A. Case (Tue Dec 22 2009 - 19:50:35 PST)
  - Re: [AMBER] sqm x mopac in AmberTools 1.3 Alan (Tue Dec 29 2009 - 10:49:26 PST)
    - Re: [AMBER] sqm x mopac in AmberTools 1.3 case (Tue Dec 29 2009 - 11:49:26 PST)
    - Re: [AMBER] sqm x mopac in AmberTools 1.3 Alan (Tue Dec 29 2009 - 11:52:44 PST)
[AMBER] Van der Waals and electrostatic Forces Frank X. Vázquez (Tue Dec 22 2009 - 09:42:33 PST)
- Re: [AMBER] Van der Waals and electrostatic Forces David A. Case (Wed Dec 23 2009 - 18:56:50 PST)
[AMBER] HOW TO OPTIMISE INDI-DIELC_MM VALUE for MM_PBSA calculation ? Marek Maly (Tue Dec 22 2009 - 10:49:42 PST)
[AMBER] pupil and amber davide branduardi (Tue Dec 22 2009 - 12:29:37 PST)
- Re: [AMBER] pupil and amber Ben Roberts (Tue Dec 22 2009 - 18:59:04 PST)
  - Re: [AMBER] pupil and amber Ben Roberts (Thu Jan 14 2010 - 07:19:06 PST)
[AMBER] atom type shamoon siddiqui (Tue Dec 22 2009 - 21:31:42 PST)
- Re: [AMBER] atom type FyD (Wed Dec 23 2009 - 05:00:39 PST)
[AMBER] AmberTools-1.3 not compiling on MacOsX Cesar Millan (Tue Dec 22 2009 - 22:37:37 PST)
- Re: [AMBER] AmberTools-1.3 not compiling on MacOsX David Watson (Tue Dec 22 2009 - 22:59:09 PST)
  - Re: [AMBER] AmberTools-1.3 not compiling on MacOsX Mengjuei Hsieh (Wed Dec 23 2009 - 01:12:19 PST)
    - Re: [AMBER] AmberTools-1.3 not compiling on MacOsX Mengjuei Hsieh (Wed Dec 23 2009 - 02:05:48 PST)
    - Re: [AMBER] AmberTools-1.3 not compiling on MacOsX Jason Swails (Wed Dec 23 2009 - 03:38:08 PST)
[AMBER] typo in AmberTools.pdf (release 1.3) Alan (Wed Dec 23 2009 - 01:51:01 PST)
- Re: [AMBER] typo in AmberTools.pdf (release 1.3) David A. Case (Wed Dec 23 2009 - 06:26:51 PST)
[AMBER] using sqm from AmberTools 1.3 Alan (Wed Dec 23 2009 - 02:35:33 PST)
- Re: [AMBER] using sqm from AmberTools 1.3 David A. Case (Wed Dec 23 2009 - 06:16:04 PST)
  - Re: [AMBER] using sqm from AmberTools 1.3 David A. Case (Wed Dec 23 2009 - 06:26:36 PST)
- RE: [AMBER] using sqm from AmberTools 1.3 Ross Walker (Thu Dec 24 2009 - 15:17:47 PST)
  - Re: [AMBER] using sqm from AmberTools 1.3 Alan (Tue Dec 29 2009 - 09:35:06 PST)
    - Re: [AMBER] using sqm from AmberTools 1.3 David Watson (Tue Dec 29 2009 - 11:34:28 PST)
    - Re: [AMBER] using sqm from AmberTools 1.3 case (Tue Dec 29 2009 - 11:36:21 PST)
    - Re: [AMBER] using sqm from AmberTools 1.3 Alan (Tue Dec 29 2009 - 12:10:56 PST)
    - Re: [AMBER] using sqm from AmberTools 1.3 case (Tue Dec 29 2009 - 13:01:18 PST)
[AMBER] NEB-error balaji nagarajan (Wed Dec 23 2009 - 08:04:46 PST)
- Re: [AMBER] NEB-error Carlos Simmerling (Wed Dec 23 2009 - 08:12:01 PST)
  - [AMBER] How to put another 10 ligands into the simulation system? Chih-Ying Lin (Wed Dec 23 2009 - 08:18:47 PST)
    - Re: [AMBER] How to put another 10 ligands into the simulation system? David A. Case (Thu Dec 24 2009 - 09:17:11 PST)
- Re: Re: [AMBER] NEB-error xmzpzengs (Wed Dec 23 2009 - 08:44:36 PST)
  - Re: Re: [AMBER] NEB-error Carlos Simmerling (Wed Dec 23 2009 - 08:46:59 PST)
    - [AMBER] How to put another 10 ligands into the simulation system? Chih-Ying Lin (Wed Dec 23 2009 - 08:51:23 PST)
    - [AMBER] How to put another 10 ligands into the simulation system? Chih-Ying Lin (Wed Dec 23 2009 - 20:00:02 PST)
[AMBER] CHARMM psf file to Amber prmtop file Sarvin Moghaddam (Wed Dec 23 2009 - 08:20:30 PST)
- Re: [AMBER] CHARMM psf file to Amber prmtop file xmzpzengs (Wed Dec 23 2009 - 08:40:28 PST)
- Re: [AMBER] CHARMM psf file to Amber prmtop file Jason Swails (Wed Dec 23 2009 - 12:32:11 PST)
- Re: [AMBER] CHARMM psf file to Amber prmtop file David A. Case (Wed Dec 23 2009 - 18:39:24 PST)
- RE: [AMBER] CHARMM psf file to Amber prmtop file Ross Walker (Thu Dec 24 2009 - 15:11:36 PST)
[AMBER] iron in prepi file generation for heme Donald Keidel (Wed Dec 23 2009 - 14:27:10 PST)
- Re: [AMBER] iron in prepi file generation for heme David A. Case (Thu Dec 24 2009 - 09:27:07 PST)
[AMBER] Adding single distance restraint Adler, Marc (Wed Dec 23 2009 - 18:00:35 PST)
- Re: [AMBER] Adding single distance restraint Jason Swails (Wed Dec 23 2009 - 19:11:48 PST)
[AMBER] SQM and AMBER :again Jio M (Wed Dec 23 2009 - 21:18:37 PST)
[AMBER] OE and CG types Jio M (Thu Dec 24 2009 - 01:26:43 PST)
- Re: [AMBER] OE and CG types Jason Swails (Thu Dec 24 2009 - 04:46:35 PST)
  - Re: [AMBER] OE and CG types Jio M (Thu Dec 24 2009 - 07:18:31 PST)
    - Re: [AMBER] OE and CG types Carlos Simmerling (Thu Dec 24 2009 - 07:38:24 PST)
    - Re: [AMBER] OE and CG types Jio M (Thu Dec 24 2009 - 23:29:19 PST)
    - Re: [AMBER] OE and CG types Jason Swails (Fri Dec 25 2009 - 04:32:03 PST)
    - Re: [AMBER] OE and CG types Carlos Simmerling (Mon Dec 28 2009 - 09:42:41 PST)
    - Re: [AMBER] OE and CG types Jio M (Tue Dec 29 2009 - 20:18:51 PST)
    - Re: [AMBER] OE and CG types Dean Cuebas (Sat Dec 26 2009 - 17:10:06 PST)
[AMBER] implicit solvent MD with fixed residues Hakan Gunaydin (Thu Dec 24 2009 - 15:43:13 PST)
- Re: [AMBER] implicit solvent MD with fixed residues David A. Case (Fri Dec 25 2009 - 12:22:31 PST)
[AMBER] RE: Amber question Ross Walker (Thu Dec 24 2009 - 15:44:54 PST)
[AMBER] a problem in building oligosaccharides using LEaP Song Lin (Thu Dec 24 2009 - 18:12:10 PST)
[AMBER] MMGBSA error Zhongjie Liang (Thu Dec 24 2009 - 22:59:16 PST)
- Re: [AMBER] MMGBSA error Jason Swails (Fri Dec 25 2009 - 05:28:15 PST)
  - Re: [AMBER] MMGBSA error David A. Case (Fri Dec 25 2009 - 14:17:26 PST)
    - 答复: [AMBER] MMGBSA error Zhongjie Liang (Fri Dec 25 2009 - 20:30:00 PST)
[AMBER] FW: how to change velocities balaji nagarajan (Fri Dec 25 2009 - 02:23:57 PST)
- Re: [AMBER] FW: how to change velocities Carlos Simmerling (Fri Dec 25 2009 - 04:13:44 PST)
  - RE: [AMBER] FW: how to change velocities balaji nagarajan (Fri Dec 25 2009 - 22:02:58 PST)
    - Re: [AMBER] FW: how to change velocities Carlos Simmerling (Sat Dec 26 2009 - 05:26:17 PST)
[AMBER] a question about ptraj qiaoyan (Fri Dec 25 2009 - 05:58:44 PST)
[AMBER] PQR files s. Bill (Fri Dec 25 2009 - 06:38:36 PST)
- Re: [AMBER] PQR files Jason Swails (Fri Dec 25 2009 - 08:57:51 PST)
  - Re: [AMBER] PQR files s. Bill (Fri Dec 25 2009 - 10:27:22 PST)
[AMBER] heating system in NEB balaji nagarajan (Sat Dec 26 2009 - 03:29:35 PST)
[AMBER] reg.changing velocity balaji nagarajan (Sat Dec 26 2009 - 10:47:10 PST)
- Re: [AMBER] reg.changing velocity David A. Case (Sat Dec 26 2009 - 19:01:18 PST)
[AMBER] neb error while heating balaji nagarajan (Sat Dec 26 2009 - 19:09:00 PST)
- Re: [AMBER] neb error while heating Carlos Simmerling (Mon Dec 28 2009 - 09:34:56 PST)
[AMBER] .rst file error ZhaoLei (Sun Dec 27 2009 - 06:46:37 PST)
- RE: [AMBER] .rst file error ZhaoLei (Sun Dec 27 2009 - 18:37:57 PST)
  - RE: [AMBER] .rst file error ZhaoLei (Sun Dec 27 2009 - 19:09:24 PST)
- Re: [AMBER] .rst file error Jia Xu (Mon Dec 28 2009 - 00:00:57 PST)
  - RE: [AMBER] .rst file error ZhaoLei (Mon Dec 28 2009 - 02:36:17 PST)
    - Re: [AMBER] .rst file error Jason Swails (Mon Dec 28 2009 - 07:44:38 PST)
    - RE: [AMBER] .rst file error ZhaoLei (Mon Dec 28 2009 - 17:37:40 PST)
    - Re: [AMBER] .rst file error Jason Swails (Mon Dec 28 2009 - 18:09:04 PST)
    - RE: [AMBER] .rst file error ZhaoLei (Mon Dec 28 2009 - 18:57:34 PST)
[AMBER] coarse grained Francesco Pietra (Sun Dec 27 2009 - 12:36:02 PST)
[AMBER] ERROR: Could not read coords from {filename} Paul Brandt (Sun Dec 27 2009 - 20:14:50 PST)
- Re: [AMBER] ERROR: Could not read coords from {filename} case (Mon Dec 28 2009 - 05:00:34 PST)
  - RE: [AMBER] ERROR: Could not read coords from {filename} ZhaoLei (Mon Dec 28 2009 - 06:12:54 PST)
    - Re: [AMBER] ERROR: Could not read coords from {filename} case (Mon Dec 28 2009 - 06:57:11 PST)
    - RE: [AMBER] ERROR: Could not read coords from {filename} ZhaoLei (Mon Dec 28 2009 - 17:34:29 PST)
    - Re: [AMBER] ERROR: Could not read coords from {filename} Carlos Simmerling (Mon Dec 28 2009 - 18:04:27 PST)
    - RE: [AMBER] ERROR: Could not read coords from {filename} ZhaoLei (Mon Dec 28 2009 - 18:58:53 PST)
  - RE: [AMBER] ERROR: Could not read coords from {filename} Paul Brandt (Tue Dec 29 2009 - 01:46:55 PST)
[AMBER] problem in installing amber tools on Mac OSX 10.6 Chun-Wei Pao (Sun Dec 27 2009 - 23:54:26 PST)
- Re: [AMBER] problem in installing amber tools on Mac OSX 10.6 David Watson (Mon Dec 28 2009 - 05:06:30 PST)
- Re: [AMBER] problem in installing amber tools on Mac OSX 10.6 case (Mon Dec 28 2009 - 05:07:48 PST)
[AMBER] About APBS radiopt Youn Kyeung Lee (Mon Dec 28 2009 - 02:12:07 PST)
- Re: [AMBER] About APBS radiopt Robert Konecny (Mon Dec 28 2009 - 07:43:18 PST)
[AMBER] NEB-NAN error balaji nagarajan (Mon Dec 28 2009 - 07:16:43 PST)
[AMBER] mpirun error Vijay Manickam Achari (Mon Dec 28 2009 - 19:00:11 PST)
[AMBER] nab installation Lixia Jin Day (Tue Dec 29 2009 - 09:32:37 PST)
- Re: [AMBER] nab installation case (Tue Dec 29 2009 - 11:26:35 PST)
[AMBER] can I install amber11 on a windowsPC under cygwin? Lixia Jin Day (Tue Dec 29 2009 - 10:06:30 PST)
- Re: [AMBER] can I install amber11 on a windowsPC under cygwin? Jason Swails (Tue Dec 29 2009 - 11:42:34 PST)
- Re: [AMBER] can I install amber11 on a windowsPC under cygwin? Mengjuei Hsieh (Tue Dec 29 2009 - 11:44:06 PST)
- Re: [AMBER] can I install amber11 on a windowsPC under cygwin? case (Tue Dec 29 2009 - 11:44:18 PST)
- Re: [AMBER] can I install amber11 on a windowsPC under cygwin? Bill Ross (Tue Dec 29 2009 - 13:05:07 PST)
  - Re: [AMBER] can I install amber11 on a windowsPC under cygwin? Jason Swails (Tue Dec 29 2009 - 15:08:38 PST)
    - Re: [AMBER] can I install amber11 on a windowsPC under cygwin? case (Tue Dec 29 2009 - 15:36:46 PST)
[AMBER] sleap in AmberTools 1.3 is not working anymore for me Alan (Tue Dec 29 2009 - 12:27:57 PST)
- Re: [AMBER] sleap in AmberTools 1.3 is not working anymore for me David Watson (Tue Dec 29 2009 - 13:02:05 PST)
  - Re: [AMBER] sleap in AmberTools 1.3 is not working anymore for me Alan (Tue Dec 29 2009 - 13:47:52 PST)
- Re: [AMBER] sleap in AmberTools 1.3 is not working anymore for me case (Tue Dec 29 2009 - 19:40:26 PST)
[AMBER] Tests to check for proper MMPBSA.py installation RANAJIT SHINDE (Wed Dec 30 2009 - 04:15:48 PST)
- Re: [AMBER] Tests to check for proper MMPBSA.py installation case (Wed Dec 30 2009 - 06:23:57 PST)
[AMBER] exchange attempt in REMD zgong.hust (Wed Dec 30 2009 - 18:34:21 PST)
- Re: [AMBER] exchange attempt in REMD Carlos Simmerling (Wed Dec 30 2009 - 19:09:02 PST)
- Re: Re: [AMBER] exchange attempt in REMD zgong.hust (Wed Dec 30 2009 - 20:22:54 PST)
  - Re: Re: [AMBER] exchange attempt in REMD Carlos Simmerling (Thu Dec 31 2009 - 07:50:24 PST)
[AMBER] Zinc parameters? xuemeiwang1103 (Wed Dec 30 2009 - 19:37:21 PST)
- Re: [AMBER] Zinc parameters? Ray Luo, Ph.D. (Thu Dec 31 2009 - 18:11:45 PST)
- Re: [AMBER] Zinc parameters? vhakkim boy (Thu Dec 31 2009 - 20:56:50 PST)
[AMBER] hbond analysis qiaoyan (Thu Dec 31 2009 - 00:40:22 PST)
- Re: [AMBER] hbond analysis Thomas Cheatham III (Mon Jan 04 2010 - 09:07:18 PST)
[AMBER] problem with MM-PBSA Maryam Hamzehee (Sat Jan 02 2010 - 00:48:16 PST)
- Re: [AMBER] problem with MM-PBSA case (Sat Jan 02 2010 - 06:02:13 PST)
  - Re: [AMBER] problem with MM-PBSA Maryam Hamzehee (Sat Jan 02 2010 - 11:43:35 PST)
    - Re: [AMBER] problem with MM-PBSA Ray Luo, Ph.D. (Sat Jan 02 2010 - 16:39:00 PST)
- Re: [AMBER] problem with MM-PBSA Jason Swails (Sat Jan 02 2010 - 06:03:24 PST)
[AMBER] Enquiry regarding MD run bharat lakhani (Sat Jan 02 2010 - 05:26:46 PST)
- Re: [AMBER] Enquiry regarding MD run case (Sat Jan 02 2010 - 06:08:05 PST)
  - Re: [AMBER] Enquiry regarding MD run bharat lakhani (Mon Jan 04 2010 - 00:10:45 PST)
    - Re: [AMBER] Enquiry regarding MD run Jason Swails (Mon Jan 04 2010 - 04:37:51 PST)
[AMBER] vlimit exceeded John S (Sat Jan 02 2010 - 07:15:12 PST)
- Re: [AMBER] vlimit exceeded xmzpzengs (Sat Jan 02 2010 - 07:32:50 PST)
  - Re: [AMBER] vlimit exceeded John S (Sat Jan 02 2010 - 08:03:31 PST)
    - Re: [AMBER] vlimit exceeded Jason Swails (Sat Jan 02 2010 - 10:26:07 PST)
- Re: [AMBER] vlimit exceeded Jackie. J. Shen (Mon Jan 04 2010 - 16:55:25 PST)
  - [AMBER] low concentration simulation ? Chih-Ying Lin (Mon Jan 04 2010 - 22:57:41 PST)
    - [AMBER] low concentration simulation ? Chih-Ying Lin (Mon Jan 04 2010 - 23:20:40 PST)
    - Re: [AMBER] low concentration simulation ? case (Tue Jan 05 2010 - 05:11:20 PST)
    - 回覆：Re: [AMBER] low concentration simulation ? Chih-Ying Lin (Tue Jan 05 2010 - 13:39:21 PST)
    - Re: ¦^ÂÐ¡GRe: [AMBER] low concentration simulation ? steinbrt.rci.rutgers.edu (Wed Jan 06 2010 - 05:44:45 PST)
  - Re: [AMBER] vlimit exceeded mani grover (Fri Jan 08 2010 - 04:30:48 PST)
    - Re: [AMBER] vlimit exceeded case (Fri Jan 08 2010 - 06:06:06 PST)
[AMBER] C60 molecules interaction using GAFF? Chun-Wei Pao (Sun Jan 03 2010 - 06:48:08 PST)
- [AMBER] How to calculate torsional energy between two chiral carbons? Dean Cuebas (Sun Jan 03 2010 - 17:02:42 PST)
[AMBER] error with mm-pbsa.py: no output value of VDWAALS from Sander xueqin pang (Mon Jan 04 2010 - 00:56:18 PST)
- Re: [AMBER] error with mm-pbsa.py: no output value of VDWAALS from Sander Jason Swails (Mon Jan 04 2010 - 04:32:52 PST)
[AMBER] Installation of Amber11 under Cygwin on WindowXP Lixia Jin Day (Mon Jan 04 2010 - 12:20:38 PST)
- [AMBER] Re: Installation of Amber11 under Cygwin on WindowXP Lixia Jin Day (Mon Jan 04 2010 - 12:39:14 PST)
  - Re: [AMBER] Re: Installation of Amber11 under Cygwin on WindowXP case (Mon Jan 04 2010 - 12:49:00 PST)
    - Re: [AMBER] Re: Installation of Amber11 under Cygwin on WindowXP Lixia Jin Day (Mon Jan 04 2010 - 14:14:13 PST)
    - Re: [AMBER] Re: Installation of Amber11 under Cygwin on WindowXP Lixia Jin Day (Mon Jan 04 2010 - 14:22:16 PST)
    - Re: [AMBER] Re: Installation of Amber11 under Cygwin on WindowXP Mengjuei Hsieh (Mon Jan 04 2010 - 23:41:44 PST)
    - Re: [AMBER] Re: Installation of Amber11 under Cygwin on WindowXP Lixia Jin Day (Wed Jan 06 2010 - 09:00:26 PST)
    - Re: [AMBER] Re: Installation of Amber11 under Cygwin on WindowXP case (Wed Jan 06 2010 - 09:17:52 PST)
    - Re: [AMBER] Re: Installation of Amber11 under Cygwin on WindowXP Marek Maly (Wed Jan 06 2010 - 12:51:15 PST)
    - Re: [AMBER] Re: Installation of Amber11 under Cygwin on WindowXP Jason Swails (Wed Jan 06 2010 - 13:00:08 PST)
    - Re: [AMBER] Re: Installation of Amber11 under Cygwin on WindowXP Mengjuei Hsieh (Wed Jan 06 2010 - 13:01:17 PST)
    - Re: [AMBER] Re: Installation of Amber11 under Cygwin on WindowXP Marek Maly (Wed Jan 06 2010 - 13:08:21 PST)
    - Re: [AMBER] Re: Installation of Amber11 under Cygwin on WindowXP Lixia Jin Day (Thu Jan 07 2010 - 12:36:58 PST)
    - Re: [AMBER] Re: Installation of Amber11 under Cygwin on WindowXP case (Thu Jan 07 2010 - 14:52:34 PST)
[AMBER] energy per residue Hemant Kumar (Mon Jan 04 2010 - 22:52:29 PST)
- Re: [AMBER] energy per residue case (Tue Jan 05 2010 - 05:43:03 PST)
  - Re: [AMBER] energy per residue Hemant Kumar (Wed Jan 06 2010 - 01:29:28 PST)
    - Re: [AMBER] energy per residue case (Wed Jan 06 2010 - 05:36:26 PST)
[lachele.gmail.com: Re: [songlin@moon.ibp.ac.cn: [AMBER] a problem in building oligosaccharides using LEaP]] case (Tue Jan 05 2010 - 04:50:28 PST)
[AMBER] TI - SHAKE lists are not compatible in the two groups! Oliver Kuhn (Tue Jan 05 2010 - 05:43:20 PST)
[AMBER] TI - SHAKE lists are not compatible in the two groups! Oliver Kuhn (Tue Jan 05 2010 - 06:33:35 PST)
- Re: [AMBER] TI - SHAKE lists are not compatible in the two groups! steinbrt.rci.rutgers.edu (Tue Jan 05 2010 - 07:11:38 PST)
[AMBER] mm-pbsa error Anuradha Mittal (Tue Jan 05 2010 - 19:39:57 PST)
- Re: [AMBER] mm-pbsa error Ray Luo (Wed Jan 06 2010 - 10:52:03 PST)
[AMBER] ff99SB in DNA tutorial Donald Thomas (Tue Jan 05 2010 - 20:31:02 PST)
- RE: [AMBER] ff99SB in DNA tutorial Ross Walker (Tue Jan 05 2010 - 20:43:27 PST)
- Re: [AMBER] ff99SB in DNA tutorial case (Tue Jan 05 2010 - 20:52:40 PST)
[AMBER] QM/MM in reaction pathway 欧阳德方 (Tue Jan 05 2010 - 21:46:13 PST)
[AMBER] Error: PB bomb in pb_reslist(): maxnbr too small xueqin pang (Wed Jan 06 2010 - 05:23:31 PST)
- Re: [AMBER] Error: PB bomb in pb_reslist(): maxnbr too small Ray Luo (Wed Jan 06 2010 - 11:04:18 PST)
[AMBER] PDB file Ganesh Kamath (Wed Jan 06 2010 - 05:56:26 PST)
[AMBER] low concentration simulation ? Chih-Ying Lin (Wed Jan 06 2010 - 13:30:32 PST)
- Re: [AMBER] low concentration simulation ? Dean Cuebas (Wed Jan 06 2010 - 14:49:22 PST)
  - 回覆：Re: [AMBER] low concentration simulation ? Chih-Ying Lin (Wed Jan 06 2010 - 15:50:52 PST)
    - Re: ¦^ÂÐ¡GRe: [AMBER] low concentration simulation ? steinbrt.rci.rutgers.edu (Thu Jan 07 2010 - 02:32:09 PST)
    - Re: ¦^ÂÐ¡GRe: [AMBER] low concentration simulation ? mani grover (Thu Jan 07 2010 - 05:39:10 PST)
    - Re: ¦^ÂÐ¡GRe: [AMBER] low concentration simulation ? Jason Swails (Thu Jan 07 2010 - 05:43:25 PST)
    - Re: ¦^ÂÐ¡GRe: [AMBER] low concentration simulation ? mani grover (Thu Jan 07 2010 - 05:57:03 PST)
    - Re: ¦^ÂÐ¡GRe: [AMBER] low concentration simulation ? mani grover (Thu Jan 07 2010 - 06:05:15 PST)
    - Re: ¦^ÂÐ¡GRe: [AMBER] low concentration simulation ? Jason Swails (Thu Jan 07 2010 - 06:09:52 PST)
    - Re: ¦^ÂÐ¡GRe: [AMBER] low concentration simulation ? mani grover (Thu Jan 07 2010 - 06:11:02 PST)
    - Re: ¦^ÂÐ¡GRe: [AMBER] low concentration simulation ? steinbrt.rci.rutgers.edu (Thu Jan 07 2010 - 06:11:22 PST)
[AMBER] MM-PBSA exist when "Calc delta from raw data" xueqin pang (Thu Jan 07 2010 - 01:44:33 PST)
[AMBER] Atom number **** Fernando Martín García (Thu Jan 07 2010 - 06:09:39 PST)
- Re: [AMBER] Atom number **** Jason Swails (Thu Jan 07 2010 - 06:35:53 PST)
  - Re: [AMBER] Atom number **** Fernando Martín García (Thu Jan 07 2010 - 07:09:18 PST)
    - Re: [AMBER] Atom number **** case (Thu Jan 07 2010 - 07:29:15 PST)
    - Re: [AMBER] Atom number **** Fernando Martín García (Thu Jan 07 2010 - 07:47:42 PST)
    - Re: [AMBER] Atom number **** case (Thu Jan 07 2010 - 08:19:17 PST)
    - Re: [AMBER] Atom number **** Fernando Martín García (Fri Jan 08 2010 - 05:45:33 PST)
[AMBER] A note on computing bcc charges in AmberTools1.3 case (Thu Jan 07 2010 - 07:15:19 PST)
[AMBER] Amber parameters and resp charge for Fe (or Zn) Hari Lamichhane (Thu Jan 07 2010 - 07:44:45 PST)
- Re: [AMBER] Amber parameters and resp charge for Fe (or Zn) FyD (Thu Jan 07 2010 - 13:31:31 PST)
- RE: [AMBER] Amber parameters and resp charge for Fe (or Zn) Ross Walker (Thu Jan 07 2010 - 15:08:44 PST)
[AMBER] how to compute the hyphobic surface area qiaoyan (Thu Jan 07 2010 - 18:46:59 PST)
- Re: [AMBER] how to compute the hyphobic surface area Ray Luo (Thu Jan 07 2010 - 19:02:39 PST)
[AMBER] AMBER9 - mm_pbsa error: bad atom type Stephan Jakobi (Fri Jan 08 2010 - 00:12:40 PST)
[AMBER] Error with mm-pbsa amber10 xueqin pang (Fri Jan 08 2010 - 07:24:25 PST)
- Re: [AMBER] Error with mm-pbsa amber10 Mengjuei Hsieh (Fri Jan 08 2010 - 11:38:14 PST)
: [AMBER] Error mani grover (Fri Jan 08 2010 - 22:33:51 PST)
- Re: : [AMBER] Error mani grover (Sat Jan 09 2010 - 01:00:48 PST)
- Re: : [AMBER] Error Carlos Simmerling (Sat Jan 09 2010 - 04:39:37 PST)
[AMBER] Add residue from PDB file Xihui Yin (Sat Jan 09 2010 - 00:08:45 PST)
- Re: [AMBER] Add residue from PDB file case (Sat Jan 09 2010 - 06:01:37 PST)
- Re: [AMBER] Add residue from PDB file Dean Cuebas (Sat Jan 09 2010 - 16:39:44 PST)
[AMBER] -bash: kclust: command not found qiaoyan (Sat Jan 09 2010 - 03:57:56 PST)
- Re: [AMBER] -bash: kclust: command not found case (Sat Jan 09 2010 - 06:07:45 PST)
[AMBER] Re: error when doing mm-pbsa xueqin pang (Sat Jan 09 2010 - 05:27:10 PST)
- Re: [AMBER] Re: error when doing mm-pbsa Ray Luo (Mon Jan 11 2010 - 11:22:25 PST)
[AMBER] pucker: Error in specification of the first mask qiaoyan (Sat Jan 09 2010 - 17:44:36 PST)
- Re: [AMBER] pucker: Error in specification of the first mask Thomas Cheatham III (Tue Jan 12 2010 - 10:14:47 PST)
[AMBER] rmsd problem luzhenw1.msu.edu (Sun Jan 10 2010 - 12:34:24 PST)
- Re: [AMBER] rmsd problem Carlos Simmerling (Sun Jan 10 2010 - 12:49:52 PST)
  - Re: [AMBER] rmsd problem luzhenw1.msu.edu (Sun Jan 10 2010 - 19:22:27 PST)
- Re: [AMBER] rmsd problem Bill Ross (Mon Jan 11 2010 - 10:15:10 PST)
  - Re: [AMBER] rmsd problem luzhenw1.msu.edu (Mon Jan 11 2010 - 14:12:26 PST)
- Re: [AMBER] rmsd problem Bill Ross (Mon Jan 11 2010 - 17:31:02 PST)
  - Re: [AMBER] rmsd problem luzhenw1.msu.edu (Tue Jan 12 2010 - 07:45:21 PST)
[AMBER] hbond analysis output qiaoyan (Sun Jan 10 2010 - 18:51:57 PST)
- Re: [AMBER] hbond analysis output Thomas Cheatham III (Mon Jan 11 2010 - 11:49:43 PST)
  - Re: [AMBER] hbond analysis output Marcin Krol (Mon Jan 11 2010 - 13:10:26 PST)
[AMBER] in minimization bharat lakhani (Mon Jan 11 2010 - 01:19:57 PST)
- Re: [AMBER] in minimization case (Mon Jan 11 2010 - 05:28:21 PST)
[AMBER] error in minimization mani grover (Mon Jan 11 2010 - 01:41:39 PST)
- Re: [AMBER] error in minimization steinbrt.rci.rutgers.edu (Mon Jan 11 2010 - 04:44:34 PST)
- Re: [AMBER] error in minimization case (Mon Jan 11 2010 - 05:30:43 PST)
[AMBER] Making Ambiguous Distance Restraints Titus, Jamie (bairdje) (Mon Jan 11 2010 - 06:53:20 PST)
- Re: [AMBER] Making Ambiguous Distance Restraints case (Mon Jan 11 2010 - 07:51:30 PST)
  - RE: [AMBER] Making Ambiguous Distance Restraints Titus, Jamie (bairdje) (Mon Jan 11 2010 - 08:31:35 PST)
Re: : [AMBER] Error Bill Ross (Mon Jan 11 2010 - 09:12:19 PST)
[AMBER] CHAMBER (AmberTools 1.3) and AMBER 10 Mag. Thomas Taylor (Tue Jan 12 2010 - 02:05:28 PST)
- Re: [AMBER] CHAMBER (AmberTools 1.3) and AMBER 10 Mark Williamson (Tue Jan 12 2010 - 17:35:54 PST)
  - Re: [AMBER] CHAMBER (AmberTools 1.3) and AMBER 10 Mag. Thomas Taylor (Thu Jan 21 2010 - 00:30:25 PST)
[AMBER] The unperturbed charge of the unit: 0.010000 is not integral. Alan (Tue Jan 12 2010 - 05:56:23 PST)
- Re: [AMBER] The unperturbed charge of the unit: 0.010000 is not integral. case (Tue Jan 12 2010 - 06:29:59 PST)
  - Re: [AMBER] The unperturbed charge of the unit: 0.010000 is not integral. Alan (Tue Jan 12 2010 - 10:02:17 PST)
    - Re: [AMBER] The unperturbed charge of the unit: 0.010000 is not integral. case (Wed Jan 13 2010 - 05:36:11 PST)
[AMBER] Install problem Stefan weber (Tue Jan 12 2010 - 06:13:59 PST)
- Re: [AMBER] Install problem Daniel Roe (Tue Jan 12 2010 - 06:32:32 PST)
  - Re: [AMBER] Install problem Stefan weber (Tue Jan 12 2010 - 06:47:37 PST)
    - Re: [AMBER] Install problem Jason Swails (Tue Jan 12 2010 - 07:06:08 PST)
    - Re: [AMBER] Install problem case (Tue Jan 12 2010 - 07:08:24 PST)
    - Re: [AMBER] Install problem John E. Kerrigan (Thu Jan 14 2010 - 11:06:27 PST)
    - Re: [AMBER] Install problem case (Thu Jan 14 2010 - 16:50:15 PST)
    - Re: [AMBER] Install problem Daniel Roe (Tue Jan 12 2010 - 07:17:55 PST)
    - Re: [AMBER] Install problem -- solved Stefan weber (Tue Jan 12 2010 - 22:53:17 PST)
[AMBER] TSvib terms Giovanni Grazioso (Tue Jan 12 2010 - 07:05:19 PST)
[AMBER] PTRAJ clustering atom /hetatm problem Andrew Voronkov (Tue Jan 12 2010 - 08:50:40 PST)
- Re: [AMBER] PTRAJ clustering atom /hetatm problem Dmitry Mukha (Tue Jan 12 2010 - 09:44:19 PST)
  - Re: Re: [AMBER] PTRAJ clustering atom /hetatm problem Andrew Voronkov (Thu Jan 14 2010 - 01:13:20 PST)
Re: [AMBER] Install problem Bill Ross (Tue Jan 12 2010 - 09:58:16 PST)
- Re: [AMBER] Install problem Bill Ross (Tue Jan 12 2010 - 10:21:13 PST)
[AMBER] AT 1.3 Parallel Install Problem (pNetCDF) Cihan Aydin (Tue Jan 12 2010 - 10:01:03 PST)
- Re: [AMBER] AT 1.3 Parallel Install Problem (pNetCDF) Jason Swails (Tue Jan 12 2010 - 10:08:10 PST)
  - Re: [AMBER] AT 1.3 Parallel Install Problem (pNetCDF) Cihan Aydin (Tue Jan 12 2010 - 10:13:36 PST)
    - Re: [AMBER] AT 1.3 Parallel Install Problem (pNetCDF) Jason Swails (Tue Jan 12 2010 - 10:16:28 PST)
    - Re: [AMBER] AT 1.3 Parallel Install Problem (pNetCDF) Cihan Aydin (Tue Jan 12 2010 - 10:30:12 PST)
    - Re: [AMBER] AT 1.3 Parallel Install Problem (pNetCDF) Cihan Aydin (Tue Jan 12 2010 - 10:36:08 PST)
    - Re: [AMBER] AT 1.3 Parallel Install Problem (pNetCDF) case (Tue Jan 12 2010 - 15:02:47 PST)
[AMBER] TI in Amber 10 with ifsc=2, energy decomposition and restraints Samuel Genheden (Wed Jan 13 2010 - 02:02:28 PST)
- Re: [AMBER] TI in Amber 10 with ifsc=2, energy decomposition and restraints steinbrt.rci.rutgers.edu (Wed Jan 13 2010 - 02:36:07 PST)
  - Re: [AMBER] TI in Amber 10 with ifsc=2, energy decomposition and restraints Samuel Genheden (Wed Jan 13 2010 - 02:46:05 PST)
    - Re: [AMBER] TI in Amber 10 with ifsc=2, energy decomposition and restraints steinbrt.rci.rutgers.edu (Wed Jan 13 2010 - 03:21:11 PST)
    - Re: [AMBER] TI in Amber 10 with ifsc=2, energy decomposition and restraints Samuel Genheden (Wed Jan 13 2010 - 04:06:59 PST)
    - Re: [AMBER] TI in Amber 10 with ifsc=2, energy decomposition and restraints steinbrt.rci.rutgers.edu (Wed Jan 13 2010 - 04:37:38 PST)
    - Re: [AMBER] TI in Amber 10 with ifsc=2, energy decomposition and restraints Samuel Genheden (Wed Jan 13 2010 - 04:58:40 PST)
    - Re: [AMBER] TI in Amber 10 with ifsc=2, energy decomposition and restraints steinbrt.rci.rutgers.edu (Wed Jan 13 2010 - 05:05:35 PST)
- Re: [AMBER] TI in Amber 10 with ifsc=2, energy decomposition and restraints Hannes Kopitz (Wed Jan 13 2010 - 03:48:36 PST)
  - Re: [AMBER] TI in Amber 10 with ifsc=2, energy decomposition and restraints Samuel Genheden (Wed Jan 13 2010 - 04:03:41 PST)
  - Re: [AMBER] TI in Amber 10 with ifsc=2, energy decomposition and restraints case (Wed Jan 13 2010 - 04:56:10 PST)
[AMBER] How to avoid Zn parametrization? Andrew Voronkov (Wed Jan 13 2010 - 02:10:36 PST)
- RE: [AMBER] How to avoid Zn parametrization? Ross Walker (Wed Jan 13 2010 - 09:47:02 PST)
  - Re: RE: [AMBER] How to avoid Zn parametrization? Andrew Voronkov (Thu Jan 14 2010 - 05:17:40 PST)
    - RE: RE: [AMBER] How to avoid Zn parametrization? Ross Walker (Thu Jan 14 2010 - 11:54:50 PST)
    - Re: [AMBER] How to avoid Zn parametrization? Andrew Voronkov (Wed Oct 26 2011 - 05:36:28 PDT)
  - Re: RE: [AMBER] How to avoid Zn parametrization? Andrew Voronkov (Mon Jan 18 2010 - 01:32:05 PST)
    - RE: [AMBER] How to avoid Zn parametrization? FyD (Mon Jan 18 2010 - 03:41:20 PST)
    - Re: RE: [AMBER] How to avoid Zn parametrization? Bill Ross (Thu Jan 14 2010 - 09:32:57 PST)
    - Re: Re: RE: [AMBER] How to avoid Zn parametrization? Andrew Voronkov (Thu Jan 14 2010 - 12:59:53 PST)
    - Re: RE: [AMBER] How to avoid Zn parametrization? Andrew Voronkov (Mon Jan 18 2010 - 04:25:49 PST)
  - Re: [AMBER] How to avoid Zn parametrization? Andrew Voronkov (Wed Sep 14 2011 - 03:18:08 PDT)
    - Re: [AMBER] How to avoid Zn parametrization? FyD (Thu Sep 15 2011 - 00:10:18 PDT)
  - Re: [AMBER] How to avoid Zn parametrization? Andrew Voronkov (Wed Oct 26 2011 - 05:32:56 PDT)
    - Re: [AMBER] How to avoid Zn parametrization? FyD (Thu Oct 27 2011 - 01:16:07 PDT)
- RE: [AMBER] How to avoid Zn parametrization? Bill Ross (Wed Jan 13 2010 - 10:20:19 PST)
  - Re: RE: [AMBER] How to avoid Zn parametrization? Andrew Voronkov (Thu Jan 14 2010 - 01:08:48 PST)
    - RE: RE: [AMBER] How to avoid Zn parametrization? Ross Walker (Thu Jan 14 2010 - 11:57:20 PST)
[AMBER] TEST_FAILURES.diff zoran matovic (Wed Jan 13 2010 - 07:56:48 PST)
- RE: [AMBER] TEST_FAILURES.diff Ross Walker (Wed Jan 13 2010 - 09:38:20 PST)
- Re: [AMBER] TEST_FAILURES.diff zoran matovic (Thu Jan 14 2010 - 05:42:10 PST)
[AMBER] how to work with backbone atoms only ? Brut Marie (Wed Jan 13 2010 - 12:28:58 PST)
[AMBER] making pdb file sare Sorur (Wed Jan 13 2010 - 12:40:46 PST)
- Re: [AMBER] making pdb file Carlos Simmerling (Wed Jan 13 2010 - 12:46:49 PST)
- Re: [AMBER] making pdb file Kevin Hauser (Wed Jan 13 2010 - 18:49:28 PST)
  - [AMBER] error in extract_centroids.awk Mannan (Wed Jan 13 2010 - 19:07:07 PST)
    - RE: [AMBER] error in extract_centroids.awk Ross Walker (Thu Jan 14 2010 - 12:03:31 PST)
[AMBER] No restart file written every ntwr steps? Cihan Aydin (Wed Jan 13 2010 - 12:50:25 PST)
- RE: [AMBER] No restart file written every ntwr steps? Ross Walker (Wed Jan 13 2010 - 13:34:02 PST)
  - RE: [AMBER] No restart file written every ntwr steps? Cihan Aydin (Wed Jan 13 2010 - 13:48:46 PST)
    - Re: [AMBER] No restart file written every ntwr steps? case (Wed Jan 13 2010 - 18:38:26 PST)
[AMBER] PTRAJ problem luzhenw1.msu.edu (Wed Jan 13 2010 - 14:15:26 PST)
[AMBER] Distance analysis Shaikh Abdul R S Ramaju (Wed Jan 13 2010 - 20:33:05 PST)
- Re: [AMBER] Distance analysis E.M. (Wed Jan 13 2010 - 20:41:13 PST)
- FW: [AMBER] Distance analysis Shaikh Abdul R S Ramaju (Wed Jan 13 2010 - 23:08:01 PST)
  - Re: FW: [AMBER] Distance analysis Jason Swails (Thu Jan 14 2010 - 05:34:47 PST)
[AMBER] sqm failed to fail Alan (Thu Jan 14 2010 - 04:12:54 PST)
- Re: [AMBER] sqm failed to fail case (Thu Jan 14 2010 - 06:11:39 PST)
  - Re: [AMBER] sqm failed to fail Alan (Thu Jan 14 2010 - 07:30:42 PST)
    - Re: [AMBER] sqm failed to fail case (Thu Jan 14 2010 - 08:43:42 PST)
[AMBER] rms fit to a incomplete file qiaoyan (Thu Jan 14 2010 - 04:29:50 PST)
- Re: [AMBER] rms fit to a incomplete file Carlos Simmerling (Thu Jan 14 2010 - 04:33:22 PST)
- Re: Re: [AMBER] rms fit to a incomplete file qiaoyan (Thu Jan 14 2010 - 04:57:44 PST)
  - Re: Re: [AMBER] rms fit to a incomplete file Carlos Simmerling (Thu Jan 14 2010 - 05:00:47 PST)
[AMBER] no Bond Vdwaals and 1-4VDW values when doing mm-pbsa xueqin pang (Thu Jan 14 2010 - 07:58:44 PST)
- Re: [AMBER] no Bond Vdwaals and 1-4VDW values when doing mm-pbsa Jason Swails (Thu Jan 14 2010 - 08:13:29 PST)
  - Re: [AMBER] no Bond Vdwaals and 1-4VDW values when doing mm-pbsa case (Thu Jan 14 2010 - 08:47:38 PST)
[AMBER] Thermodynamic Integration to calculate binding energy of Benzene in t4_lysozyme Sushil Mishra (Thu Jan 14 2010 - 08:42:32 PST)
- Re: [AMBER] Thermodynamic Integration to calculate binding energy of Benzene in t4_lysozyme steinbrt.rci.rutgers.edu (Thu Jan 14 2010 - 09:40:17 PST)
- Re: [AMBER] Thermodynamic Integration to calculate binding energy of Benzene in t4_lysozyme Sushil Mishra (Fri Jan 15 2010 - 01:19:31 PST)
[AMBER] Add external E-field in Amber Keith Chin (Thu Jan 14 2010 - 09:55:18 PST)
[AMBER] how to combine MD trajectories with two different time steps Jayalakshmi Sridhar (Thu Jan 14 2010 - 09:59:15 PST)
- Re: [AMBER] how to combine MD trajectories with two different time steps Carlos Simmerling (Thu Jan 14 2010 - 10:16:14 PST)
  - Re: [AMBER] how to combine MD trajectories with two different time steps Jayalakshmi Sridhar (Thu Jan 14 2010 - 10:19:44 PST)
[AMBER] add external electric field sim in Amber Keith Chin (Thu Jan 14 2010 - 10:54:27 PST)
[AMBER] atom expression in NAB -superimpose Lixia Jin Day (Thu Jan 14 2010 - 13:15:00 PST)
- Re: [AMBER] atom expression in NAB -superimpose case (Thu Jan 14 2010 - 20:15:00 PST)
[AMBER] problem with MMPBSA.py xueqin pang (Thu Jan 14 2010 - 19:50:21 PST)
- RE: [AMBER] problem with MMPBSA.py xueqin pang (Thu Jan 14 2010 - 23:32:18 PST)
  - Re: [AMBER] problem with MMPBSA.py Jason Swails (Thu Jan 14 2010 - 23:50:21 PST)
    - Re: [AMBER] problem with MMPBSA.py xueqin pang (Fri Jan 15 2010 - 00:19:13 PST)
    - Re: [AMBER] problem with MMPBSA.py Jason Swails (Fri Jan 15 2010 - 00:42:16 PST)
    - Re: [AMBER] problem with MMPBSA.py xueqin pang (Fri Jan 15 2010 - 00:58:59 PST)
    - Re: [AMBER] problem with MMPBSA.py xueqin pang (Fri Jan 15 2010 - 22:44:59 PST)
    - Re: [AMBER] problem with MMPBSA.py Mengjuei Hsieh (Fri Jan 15 2010 - 23:15:40 PST)
    - Re: [AMBER] problem with MMPBSA.py xueqin pang (Mon Jan 18 2010 - 05:13:43 PST)
[AMBER] error while installation of amber9 at fedora 12 saurabh agrawal (Fri Jan 15 2010 - 06:50:27 PST)
- Re: [AMBER] error while installation of amber9 at fedora 12 case (Fri Jan 15 2010 - 07:07:13 PST)
  - Re: [AMBER] error while installation of amber9 at fedora 12 saurabh agrawal (Fri Jan 15 2010 - 10:08:51 PST)
[AMBER] DECOMP in mm_pbsa.in file ERIK.LAURINI.phd.units.it (Fri Jan 15 2010 - 07:10:08 PST)
[AMBER] question on exact ionic strength format and some questions on other GB calculations parameters Andrew Voronkov (Fri Jan 15 2010 - 07:21:05 PST)
- Re: [AMBER] question on exact ionic strength format and some questions on other GB calculations parameters case (Fri Jan 15 2010 - 09:00:01 PST)
[AMBER] Thermodynamic Integration (transformation of --H in to ---CH3) atom naming doubt Sushil Mishra (Fri Jan 15 2010 - 09:01:19 PST)
- Re: [AMBER] Thermodynamic Integration (transformation of --H in to ---CH3) atom naming doubt steinbrt.rci.rutgers.edu (Fri Jan 15 2010 - 09:27:08 PST)
  - Re: [AMBER] Thermodynamic Integration (transformation of --H in to ---CH3) atom naming doubt Sushil Mishra (Fri Jan 15 2010 - 10:01:13 PST)
    - Re: [AMBER] Thermodynamic Integration (transformation of --H in to ---CH3) atom naming doubt Sushil Mishra (Fri Jan 15 2010 - 10:08:26 PST)
    - Re: [AMBER] Thermodynamic Integration (transformation of --H in to ---CH3) atom naming doubt steinbrt.rci.rutgers.edu (Fri Jan 15 2010 - 10:17:22 PST)
    - Re: [AMBER] Thermodynamic Integration (transformation of --H in to ---CH3) atom naming doubt Sushil Mishra (Fri Jan 15 2010 - 10:58:31 PST)
[AMBER] error regarding NMR restrains mani grover (Sat Jan 16 2010 - 10:55:46 PST)
- Re: [AMBER] error regarding NMR restrains case (Sat Jan 16 2010 - 12:28:15 PST)
  - Re: [AMBER] error regarding NMR restrains mani grover (Sat Jan 16 2010 - 13:17:42 PST)
    - Re: [AMBER] error regarding NMR restrains case (Sat Jan 16 2010 - 14:24:26 PST)
[AMBER] Lennard-Jones Parameters in prmtop Jianhui Tian (Sun Jan 17 2010 - 09:07:42 PST)
- Re: [AMBER] Lennard-Jones Parameters in prmtop Jason Swails (Sun Jan 17 2010 - 11:14:23 PST)
  - Re: [AMBER] Lennard-Jones Parameters in prmtop Jianhui Tian (Sun Jan 17 2010 - 12:08:18 PST)
- Re: [AMBER] Lennard-Jones Parameters in prmtop Dean Cuebas (Sun Jan 17 2010 - 15:27:41 PST)
  - Re: [AMBER] Lennard-Jones Parameters in prmtop Jianhui Tian (Sun Jan 17 2010 - 17:53:14 PST)
    - Re: [AMBER] Lennard-Jones Parameters in prmtop case (Sun Jan 17 2010 - 19:18:25 PST)
    - Re: [AMBER] Lennard-Jones Parameters in prmtop fatima chami (Sat Jan 23 2010 - 16:27:41 PST)
    - Re: [AMBER] Lennard-Jones Parameters in prmtop Dean Cuebas (Sun Jan 24 2010 - 11:04:52 PST)
    - Re: [AMBER] Lennard-Jones Parameters in prmtop InSuk Joung (Sun Jan 24 2010 - 12:17:44 PST)
    - Re: [AMBER] Lennard-Jones Parameters in prmtop Jianhui Tian (Tue Jan 26 2010 - 12:02:47 PST)
- Re: [AMBER] Lennard-Jones Parameters in prmtop Bill Ross (Mon Jan 18 2010 - 11:18:46 PST)
  - Re: [AMBER] Lennard-Jones Parameters in prmtop Jianhui Tian (Mon Jan 18 2010 - 11:41:46 PST)
- Re: [AMBER] Lennard-Jones Parameters in prmtop Bill Ross (Mon Jan 18 2010 - 11:57:50 PST)
[AMBER] problem with DC of mmgbsa xueqin pang (Sun Jan 17 2010 - 18:23:45 PST)
- Re: [AMBER] problem with DC of mmgbsa Hannes Kopitz (Mon Jan 18 2010 - 12:24:21 PST)
  - Re: [AMBER] problem with DC of mmgbsa xueqin pang (Tue Jan 19 2010 - 06:07:39 PST)
    - Re: [AMBER] problem with DC of mmgbsa xueqin pang (Tue Jan 19 2010 - 23:13:49 PST)
    - Re: [AMBER] problem with DC of mmgbsa Hannes Kopitz (Fri Jan 22 2010 - 07:58:08 PST)
- [AMBER] Parameters for sulfate in amber Mannan (Tue Jan 19 2010 - 18:50:17 PST)
  - Re: [AMBER] Parameters for sulfate in amber FyD (Thu Jan 21 2010 - 05:22:17 PST)
[AMBER] plz help YOGESH NARKHEDE (Sun Jan 17 2010 - 20:20:15 PST)
[AMBER] Energy function NAB chaitanya koppisetty (Mon Jan 18 2010 - 02:19:01 PST)
- Re: [AMBER] Energy function NAB case (Mon Jan 18 2010 - 06:44:33 PST)
[AMBER] The RESP program FyD (Mon Jan 18 2010 - 03:13:51 PST)
- Re: [AMBER] The RESP program Alan (Mon Jan 18 2010 - 06:17:18 PST)
  - Re: [AMBER] The RESP program FyD (Mon Jan 18 2010 - 07:10:51 PST)
[AMBER] Installation problem gunajyoti das (Mon Jan 18 2010 - 05:38:29 PST)
- Re: [AMBER] Installation problem David Watson (Mon Jan 18 2010 - 06:10:33 PST)
  - Re: [AMBER] Installation problem Sudeep Narayan Banerjee (Mon Jan 18 2010 - 19:51:49 PST)
- Re: [AMBER] Installation problem case (Mon Jan 18 2010 - 06:46:25 PST)
[AMBER] amber11 Steve Seibold (Mon Jan 18 2010 - 05:43:52 PST)
[AMBER] Query About QMMM Energy Minimization gunajyoti das (Mon Jan 18 2010 - 06:13:08 PST)
- Re: [AMBER] Query About QMMM Energy Minimization Jason Swails (Mon Jan 18 2010 - 08:27:25 PST)
- RE: [AMBER] Query About QMMM Energy Minimization Ross Walker (Mon Jan 18 2010 - 21:47:19 PST)
[AMBER] Parameters for a new ligand Christine Baranski (Mon Jan 18 2010 - 09:47:14 PST)
- Re: [AMBER] Parameters for a new ligand Jason Swails (Mon Jan 18 2010 - 09:52:12 PST)
- Re: [AMBER] Parameters for a new ligand FyD (Tue Jan 19 2010 - 00:07:29 PST)
[AMBER] Center of Mass Harmonic Potentials Keith Battle (Mon Jan 18 2010 - 16:56:34 PST)
- Re: [AMBER] Center of Mass Harmonic Potentials Carlos Simmerling (Mon Jan 18 2010 - 17:35:29 PST)
[AMBER] AmberTools-1.3 Install Problem Hopkins, Robert (Mon Jan 18 2010 - 17:10:07 PST)
- Re: [AMBER] AmberTools-1.3 Install Problem case (Mon Jan 18 2010 - 17:51:34 PST)
- Re: Re: [AMBER] AmberTools-1.3 Install Problem Hopkins, Robert (Mon Jan 25 2010 - 12:37:32 PST)
[AMBER] Slab babak minoofar (Tue Jan 19 2010 - 04:08:58 PST)
- Re: [AMBER] Slab case (Tue Jan 19 2010 - 05:57:13 PST)
[AMBER] Error in parallel compiling of Amber nicee.srivastava.imtech.res.in (Tue Jan 19 2010 - 04:17:04 PST)
- Re: [AMBER] Error in parallel compiling of Amber Mark Williamson (Tue Jan 19 2010 - 11:40:05 PST)
  - Re: [AMBER] Error in parallel compiling of Amber nicee.srivastava.imtech.res.in (Wed Jan 20 2010 - 03:48:19 PST)
- RE: [AMBER] Error in parallel compiling of Amber Ross Walker (Tue Jan 19 2010 - 11:39:35 PST)
  - RE: [AMBER] Error in parallel compiling of Amber nicee.srivastava.imtech.res.in (Tue Jan 19 2010 - 20:31:58 PST)
    - Re: [AMBER] Error in parallel compiling of Amber case (Tue Jan 19 2010 - 21:06:18 PST)
[AMBER] MD integrator in AMBER Neha Bharat Gajaria (Tue Jan 19 2010 - 06:36:35 PST)
- RE: [AMBER] MD integrator in AMBER Ross Walker (Tue Jan 19 2010 - 11:42:18 PST)
[AMBER] phosphorylated amino acids Christine Baranski (Tue Jan 19 2010 - 07:31:41 PST)
- Re: [AMBER] phosphorylated amino acids Carlos Simmerling (Tue Jan 19 2010 - 07:33:24 PST)
- Re: [AMBER] phosphorylated amino acids Jason Swails (Tue Jan 19 2010 - 07:35:40 PST)
[AMBER] Computing Hessian in Internal Coordinates? Kevin Wiehe (Tue Jan 19 2010 - 09:49:14 PST)
- Re: [AMBER] Computing Hessian in Internal Coordinates? case (Tue Jan 19 2010 - 11:30:59 PST)
[AMBER] (no subject) sangita.imtech.res.in (Wed Jan 20 2010 - 01:07:50 PST)
- Re: [AMBER] (no subject) case (Wed Jan 20 2010 - 05:11:39 PST)
  - Re: [AMBER] (no subject) Sangita Kachhap (Wed Jan 20 2010 - 23:41:43 PST)
[AMBER] error of cutoff list exceeds largest sphere in unit cell sangita.imtech.res.in (Wed Jan 20 2010 - 01:11:39 PST)
[AMBER] segmentation fault mani grover (Wed Jan 20 2010 - 06:23:49 PST)
- Re: [AMBER] segmentation fault case (Wed Jan 20 2010 - 09:04:29 PST)
[AMBER] Error reading namelist cntrl MASLYK, MACIEJ MARCIN (Wed Jan 20 2010 - 08:34:59 PST)
- Re: [AMBER] Error reading namelist cntrl Carlos Simmerling (Wed Jan 20 2010 - 08:38:34 PST)
- Re: [AMBER] Error reading namelist cntrl case (Wed Jan 20 2010 - 09:01:42 PST)
[AMBER] Cannot read parm file tprmtop Lixia Jin Day (Wed Jan 20 2010 - 09:09:01 PST)
- Re: [AMBER] Cannot read parm file tprmtop case (Wed Jan 20 2010 - 09:27:45 PST)
  - Re: [AMBER] Cannot read parm file tprmtop Lixia Jin Day (Wed Jan 20 2010 - 09:42:07 PST)
    - Re: [AMBER] Cannot read parm file tprmtop case (Wed Jan 20 2010 - 10:00:06 PST)
    - Re: [AMBER] Cannot read parm file tprmtop Lixia Jin Day (Wed Jan 20 2010 - 10:30:46 PST)
Re: [AMBER] segmentation fault Bill Ross (Wed Jan 20 2010 - 09:54:59 PST)
[AMBER] Residue DA not in library dna.amber94.rlb. Lixia Jin Day (Wed Jan 20 2010 - 14:39:26 PST)
- Re: [AMBER] Residue DA not in library dna.amber94.rlb. case (Sat Jan 23 2010 - 14:15:13 PST)
[AMBER] Re: Can't post in Amber reflector forum-help Keith Chin (Wed Jan 20 2010 - 15:01:16 PST)
[AMBER] Fwd: Can't post in Amber reflector forum-help Keith Chin (Wed Jan 20 2010 - 15:04:55 PST)
[AMBER] ligands mutagenesis approach in MM_PBSA Qinghua Liao (Wed Jan 20 2010 - 16:36:57 PST)
[AMBER] need help in MM_PBSA calculation geyan (Thu Jan 21 2010 - 01:20:06 PST)
- 回复： [AMBER] need help in MM_PBSA calculation xueqin pang (Thu Jan 21 2010 - 04:32:34 PST)
- Re: [AMBER] need help in MM_PBSA calculation Ray Luo (Thu Jan 21 2010 - 10:35:59 PST)
- Re: Re: [AMBER] need help in MM_PBSA calculation geyan (Tue Jan 26 2010 - 18:55:25 PST)
  - Re: [AMBER] need help in MM_PBSA calculation Ray Luo (Wed Jan 27 2010 - 11:05:38 PST)
[AMBER] PMEMD10 - energy summation bug? Mag. Thomas Taylor (Thu Jan 21 2010 - 04:32:19 PST)
[AMBER] Re: PMEMD10 - energy summation bug? NO Mag. Thomas Taylor (Thu Jan 21 2010 - 04:47:23 PST)
RE: [Subject Filtered] Re: [AMBER] AmberTools-1.3 Install Problem 10% Hopkins, Robert (Thu Jan 21 2010 - 13:34:13 PST)
- RE: [Subject Filtered] Re: [AMBER] AmberTools-1.3 Install Problem 10% Bill Ross (Thu Jan 21 2010 - 17:38:00 PST)
[AMBER] (no subject) gunajyoti das (Fri Jan 22 2010 - 01:22:13 PST)
[AMBER] test.MMPBSA_Nmode Antonija Tomić (Fri Jan 22 2010 - 03:01:21 PST)
- Re: [AMBER] test.MMPBSA_Nmode Ray Luo, Ph.D. (Fri Jan 22 2010 - 06:51:41 PST)
  - Re: [AMBER] test.MMPBSA_Nmode Antonija Tomić (Mon Jan 25 2010 - 01:58:17 PST)
    - Re: [AMBER] test.MMPBSA_Nmode Ray Luo (Mon Jan 25 2010 - 10:50:44 PST)
    - Re: [AMBER] test.MMPBSA_Nmode Antonija Tomić (Tue Jan 26 2010 - 01:17:41 PST)
[AMBER] Amber10 Installation sikander azam (Fri Jan 22 2010 - 03:51:46 PST)
- Re: [AMBER] Amber10 Installation David Watson (Fri Jan 22 2010 - 06:43:39 PST)
  - Re: [AMBER] Amber10 Installation sikander azam (Sat Jan 23 2010 - 04:23:05 PST)
    - Re: [AMBER] Amber10 Installation David Watson (Sat Jan 23 2010 - 06:48:07 PST)
    - Re: [AMBER] Amber10 Installation sikander azam (Mon Jan 25 2010 - 06:08:54 PST)
    - Re: [AMBER] Amber10 Installation case (Mon Jan 25 2010 - 07:04:41 PST)
[AMBER] how to calculate the different compoents of their interaction energies qiaoyan (Fri Jan 22 2010 - 04:54:24 PST)
- Re: [AMBER] how to calculate the different compoents of their interaction energies Jason Swails (Fri Jan 22 2010 - 07:13:41 PST)
[AMBER] AMBER on AMD Istanbul versus intel Nehalem with infiniband Vlad Cojocaru (Fri Jan 22 2010 - 06:45:28 PST)
[AMBER] heat further an equilibrated system Jayalakshmi Sridhar (Fri Jan 22 2010 - 08:55:47 PST)
- Re: [AMBER] heat further an equilibrated system Jason Swails (Fri Jan 22 2010 - 08:58:47 PST)
  - Re: [AMBER] heat further an equilibrated system Jayalakshmi Sridhar (Fri Jan 22 2010 - 09:40:28 PST)
    - Re: [AMBER] heat further an equilibrated system Jason Swails (Fri Jan 22 2010 - 09:52:02 PST)
    - Re: [AMBER] heat further an equilibrated system Jayalakshmi Sridhar (Fri Jan 22 2010 - 09:57:30 PST)
    - Re: [AMBER] heat further an equilibrated system Jason Swails (Fri Jan 22 2010 - 10:11:39 PST)
    - Re: [AMBER] heat further an equilibrated system Jayalakshmi Sridhar (Fri Jan 22 2010 - 10:17:14 PST)
    - Re: [AMBER] heat further an equilibrated system Jason Swails (Fri Jan 22 2010 - 10:28:25 PST)
    - Re: [AMBER] heat further an equilibrated system Jayalakshmi Sridhar (Fri Jan 22 2010 - 10:38:48 PST)
  - Re: [AMBER] heat further an equilibrated system Jayalakshmi Sridhar (Fri Jan 22 2010 - 09:53:01 PST)
[AMBER] heat further an equilibrated system Jayalakshmi Sridhar (Fri Jan 22 2010 - 09:04:19 PST)
[AMBER] how to get partial charges and parameters for Acetyl-CoA which could be used in Amber simulations Lan Hua (Fri Jan 22 2010 - 09:22:33 PST)
- Re: [AMBER] how to get partial charges and parameters for Acetyl-CoA which could be used in Amber simulations FyD (Fri Jan 22 2010 - 12:10:31 PST)
  - Re: [AMBER] how to get partial charges and parameters for Acetyl-CoA which could be used in Amber simulations Lan Hua (Fri Jan 22 2010 - 12:38:51 PST)
[AMBER] AMBER10 installation failure: NETCDF configure failed Siddharth Rastogi (Fri Jan 22 2010 - 15:27:30 PST)
- Re: [AMBER] AMBER10 installation failure: NETCDF configure failed David Watson (Fri Jan 22 2010 - 16:00:52 PST)
- Re: [AMBER] AMBER10 installation failure: NETCDF configure failed case (Sat Jan 23 2010 - 12:06:47 PST)
  - Re: [AMBER] AMBER10 installation failure: NETCDF configure failed Siddharth Rastogi (Sun Jan 31 2010 - 15:05:21 PST)
[AMBER] Trouble visualizing with VMD Jagdeesh C (Fri Jan 22 2010 - 18:10:50 PST)
- Re: [AMBER] Trouble visualizing with VMD Nicholas Musolino (Fri Jan 22 2010 - 18:36:07 PST)
  - Re: [AMBER] Trouble visualizing with VMD Jagdeesh C (Fri Jan 22 2010 - 18:57:44 PST)
    - Re: [AMBER] Trouble visualizing with VMD Jason Swails (Fri Jan 22 2010 - 22:18:14 PST)
[AMBER] problem with vmd mahesh kumar (Sat Jan 23 2010 - 01:18:32 PST)
- Re: [AMBER] problem with vmd Jason Swails (Sat Jan 23 2010 - 05:42:57 PST)
  - RE: [AMBER] problem with vmd Ross Walker (Sun Jan 24 2010 - 22:26:57 PST)
[AMBER] trouble with cooling down the system song_jianing_hi (Sat Jan 23 2010 - 02:04:01 PST)
- RE: [AMBER] trouble with cooling down the system Ross Walker (Sun Jan 24 2010 - 22:26:57 PST)
  - [AMBER] Thanks , Ross! song_jianing_hi (Mon Jan 25 2010 - 22:16:16 PST)
[AMBER] trouble with MD simulation song_jianing_hi (Sat Jan 23 2010 - 02:15:06 PST)
[AMBER] query regarding neutralisation of protein before minimisation nicee.srivastava.imtech.res.in (Sat Jan 23 2010 - 03:01:22 PST)
- RE: [AMBER] query regarding neutralisation of protein before minimisation Ross Walker (Sun Jan 24 2010 - 22:26:57 PST)
[AMBER] can nmode run in parallel from xueqin pang (Sat Jan 23 2010 - 04:21:15 PST)
- Re: [AMBER] can nmode run in parallel from case (Sat Jan 23 2010 - 11:46:25 PST)
[AMBER] can nmode restart xueqin pang (Sat Jan 23 2010 - 05:02:51 PST)
[AMBER] explanation of the pucker output qiaoyan (Sat Jan 23 2010 - 05:31:58 PST)
[AMBER] error in installing amber tools nicee.srivastava.imtech.res.in (Sun Jan 24 2010 - 22:15:52 PST)
- Re: [AMBER] error in installing amber tools liangchen88.ucla.edu (Mon Jan 25 2010 - 01:48:57 PST)
- Re: [AMBER] error in installing amber tools Nicee (Mon Jan 25 2010 - 02:09:24 PST)
[AMBER] error in installing amber10 even after installing amber tools Nicee (Mon Jan 25 2010 - 02:45:29 PST)
- Re: [AMBER] error in installing amber10 even after installing amber tools case (Mon Jan 25 2010 - 07:02:34 PST)
[AMBER] Is this Amber10 install error important? Hopkins, Robert (Mon Jan 25 2010 - 07:22:48 PST)
- Re: [AMBER] Is this Amber10 install error important? Jason Swails (Mon Jan 25 2010 - 08:22:31 PST)
[AMBER] URE residue not recognized in xleap Antonios Samiotakis (Mon Jan 25 2010 - 09:06:08 PST)
- Re: [AMBER] URE residue not recognized in xleap Jason Swails (Mon Jan 25 2010 - 09:16:23 PST)
  - Re: [AMBER] URE residue not recognized in xleap Antonios Samiotakis (Mon Jan 25 2010 - 09:41:51 PST)
    - Re: [AMBER] URE residue not recognized in xleap Jason Swails (Mon Jan 25 2010 - 11:16:41 PST)
    - Re: [AMBER] URE residue not recognized in xleap Antonios Samiotakis (Mon Jan 25 2010 - 12:11:33 PST)
    - Re: [AMBER] URE residue not recognized in xleap Jason Swails (Mon Jan 25 2010 - 13:40:28 PST)
    - Re: [AMBER] URE residue not recognized in xleap Antonios Samiotakis (Mon Jan 25 2010 - 15:14:31 PST)
[AMBER-Developers] Mailing list TEST MESSAGE - Please ignore. Ross Walker (Mon Jan 25 2010 - 15:09:37 PST)
[AMBER] Aborted tests for AmberTools-1.3 Hopkins, Robert (Mon Jan 25 2010 - 16:03:26 PST)
[AMBER] TEST_FAILURES sikander azam (Mon Jan 25 2010 - 20:49:24 PST)
- Re: [AMBER] TEST_FAILURES David Watson (Mon Jan 25 2010 - 21:02:02 PST)
- Re: [AMBER] TEST_FAILURES David Watson (Mon Jan 25 2010 - 21:11:25 PST)
  - Re: [AMBER] TEST_FAILURES sikander azam (Wed Jan 27 2010 - 06:47:38 PST)
    - Re: [AMBER] TEST_FAILURES case (Wed Jan 27 2010 - 07:04:59 PST)
    - Re: [AMBER] TEST_FAILURES sikander azam (Thu Jan 28 2010 - 05:18:27 PST)
    - Re: [AMBER] TEST_FAILURES case (Thu Jan 28 2010 - 05:34:36 PST)
    - Re: [AMBER] TEST_FAILURES sikander azam (Thu Feb 04 2010 - 05:37:44 PST)
    - Re: [AMBER] TEST_FAILURES Jason Swails (Thu Feb 04 2010 - 07:41:54 PST)
    - RE: [AMBER] TEST_FAILURES Ross Walker (Thu Feb 04 2010 - 12:48:05 PST)
    - Re: [AMBER] TEST_FAILURES sikander azam (Tue Feb 16 2010 - 04:55:09 PST)
[AMBER] problem with nmode xueqin pang (Mon Jan 25 2010 - 23:20:45 PST)
- Re: [AMBER] problem with nmode Hannes Kopitz (Mon Jan 25 2010 - 23:48:02 PST)
[AMBER] problem with MMPBSA.py nmode calculation xueqin pang (Tue Jan 26 2010 - 00:29:33 PST)
[AMBER] PLUMED tutorial announcement Massimiliano Bonomi (Tue Jan 26 2010 - 00:39:54 PST)
[AMBER] need help in MM_PBSA calculation geyan (Tue Jan 26 2010 - 00:42:59 PST)
- Re: [AMBER] need help in MM_PBSA calculation Ray Luo (Tue Jan 26 2010 - 11:00:23 PST)
[AMBER] Installing AMBER 10 on OSX Snow Leopard George Tzotzos (Tue Jan 26 2010 - 02:01:07 PST)
- Re: [AMBER] Installing AMBER 10 on OSX Snow Leopard case (Tue Jan 26 2010 - 04:43:45 PST)
[AMBER] changing intrinsic GB radii Peter Winn (Tue Jan 26 2010 - 07:13:19 PST)
- Re: [AMBER] changing intrinsic GB radii Carlos Simmerling (Tue Jan 26 2010 - 07:17:06 PST)
[AMBER] Bridged HBONDS Marcin Krol (Tue Jan 26 2010 - 07:42:51 PST)
Re: [AMBER] problem with nmode Bill Ross (Tue Jan 26 2010 - 10:15:31 PST)
[AMBER] Ammonia solvation box Giovanni Bellesia (Tue Jan 26 2010 - 11:25:42 PST)
[AMBER] stdinput - getline Lixia Jin Day (Tue Jan 26 2010 - 12:25:56 PST)
[AMBER] fscanf Lixia Jin Day (Tue Jan 26 2010 - 13:34:37 PST)
- Re: [AMBER] fscanf Daniel Roe (Tue Jan 26 2010 - 14:12:13 PST)
  - Re: [AMBER] fscanf Lixia Jin Day (Tue Jan 26 2010 - 16:05:27 PST)
    - [AMBER] fscanf Chris Moth (Tue Jan 26 2010 - 19:48:38 PST)
    - Re: [AMBER] fscanf Bill Ross (Tue Jan 26 2010 - 16:10:08 PST)
    - Re: [AMBER] fscanf case (Wed Jan 27 2010 - 07:10:22 PST)
[AMBER] TI with soft core potentials Wood Geoffrey (Tue Jan 26 2010 - 20:18:22 PST)
- Re: [AMBER] TI with soft core potentials steinbrt.rci.rutgers.edu (Wed Jan 27 2010 - 00:49:33 PST)
  - [AMBER] workshop Nicolas.Baurin.sanofi-aventis.com (Wed Jan 27 2010 - 01:32:25 PST)
    - Re: [AMBER] workshop steinbrt.rci.rutgers.edu (Wed Jan 27 2010 - 02:04:30 PST)
    - Re: [AMBER] workshop Deepangi Pandit (Wed Jan 27 2010 - 06:21:09 PST)
    - RE: [AMBER] workshop Ross Walker (Wed Jan 27 2010 - 13:40:13 PST)
    - Re: [AMBER] workshop Christine Baranski (Wed Jan 27 2010 - 16:01:06 PST)
    - RE: [AMBER] workshop Ross Walker (Wed Jan 27 2010 - 16:05:17 PST)
    - RE: [AMBER] workshop Anna Reymer (Wed Jan 27 2010 - 23:44:25 PST)
    - RE: [AMBER] workshop steinbrt.rci.rutgers.edu (Thu Jan 28 2010 - 07:50:25 PST)
    - RE: [AMBER] workshop #ZHAO LINA# (Wed Jan 27 2010 - 06:28:38 PST)
- Re: [AMBER] TI with soft core potentials Samuel Genheden (Wed Jan 27 2010 - 06:03:35 PST)
  - Re: [AMBER] TI with soft core potentials steinbrt.rci.rutgers.edu (Wed Jan 27 2010 - 06:55:00 PST)
    - Re: [AMBER] TI with soft core potentials Samuel Genheden (Thu Jan 28 2010 - 03:09:17 PST)
    - Re: [AMBER] TI with soft core potentials case (Thu Jan 28 2010 - 05:10:06 PST)
    - Re: [AMBER] TI with soft core potentials Samuel Genheden (Thu Jan 28 2010 - 05:30:07 PST)
    - Re: [AMBER] TI with soft core potentials steinbrt.rci.rutgers.edu (Thu Jan 28 2010 - 07:55:40 PST)
[AMBER] ambmask - distance-dependend selection Oliver Kuhn (Wed Jan 27 2010 - 01:36:59 PST)
- Re: [AMBER] ambmask - distance-dependend selection Jason Swails (Wed Jan 27 2010 - 05:43:27 PST)
[AMBER] Problems while working with Phosphothreonine MUHAMMAD IMTIA SHAFIQ (Wed Jan 27 2010 - 02:18:04 PST)
- Re: [AMBER] Problems while working with Phosphothreonine Soumya Lipsa Rath (Wed Jan 27 2010 - 04:44:20 PST)
- Re: [AMBER] Problems while working with Phosphothreonine Anselm Horn (Wed Jan 27 2010 - 05:01:57 PST)
  - Re: [AMBER] Problems while working with Phosphothreonine imtiaz shafiq (Wed Jan 27 2010 - 05:13:28 PST)
[AMBER] tleap N and C terminal Antonija Tomić (Wed Jan 27 2010 - 03:46:29 PST)
- Re: [AMBER] tleap N and C terminal Carlos Simmerling (Wed Jan 27 2010 - 03:58:44 PST)
  - Re: [AMBER] tleap N and C terminal Antonija Tomić (Wed Jan 27 2010 - 04:52:13 PST)
[AMBER] Re: about xmin Jason Swails (Wed Jan 27 2010 - 05:36:35 PST)
[AMBER] AmberTools 1.3 and amber10 Mike Hanby (Wed Jan 27 2010 - 09:45:38 PST)
- Re: [AMBER] AmberTools 1.3 and amber10 case (Wed Jan 27 2010 - 09:48:51 PST)
[AMBER] sscanf again Lixia Jin Day (Wed Jan 27 2010 - 10:22:10 PST)
- Re: [AMBER] sscanf again Chris Moth (Wed Jan 27 2010 - 11:25:19 PST)
[AMBER] Question of Tutorials-A1 about charges compuation from Guassian for Amber Tom Williams (Wed Jan 27 2010 - 13:45:31 PST)
- RE: [AMBER] Question of Tutorials-A1 about charges compuation from Guassian for Amber Ross Walker (Wed Jan 27 2010 - 14:27:24 PST)
  - Re: [AMBER] Question of Tutorials-A1 about charges compuation from Guassian for Amber Tom Williams (Wed Jan 27 2010 - 15:11:02 PST)
    - Re: [AMBER] Question of Tutorials-A1 about charges compuation from Guassian for Amber Jason Swails (Wed Jan 27 2010 - 15:31:42 PST)
    - Re: [AMBER] Question of Tutorials-A1 about charges compuation from Guassian for Amber Tom Williams (Thu Jan 28 2010 - 16:41:40 PST)
    - Re: [AMBER] Question of Tutorials-A1 about charges compuation from Guassian for Amber case (Fri Jan 29 2010 - 05:29:03 PST)
[AMBER] still sscanf Lixia Jin Day (Wed Jan 27 2010 - 14:53:38 PST)
[AMBER] Amber10 on Snow Leopard Christine Baranski (Wed Jan 27 2010 - 16:00:02 PST)
- Re: [AMBER] Amber10 on Snow Leopard Jason Swails (Wed Jan 27 2010 - 16:57:01 PST)
  - Re: [AMBER] Amber10 on Snow Leopard Mengjuei Hsieh (Wed Jan 27 2010 - 17:11:20 PST)
    - Re: [AMBER] Amber10 on Snow Leopard Christine Baranski (Thu Jan 28 2010 - 01:13:55 PST)
    - Re: [AMBER] Amber10 on Snow Leopard case (Thu Jan 28 2010 - 05:14:48 PST)
- Re: [AMBER] Amber10 on Snow Leopard Scott Brozell (Thu Jan 28 2010 - 14:48:37 PST)
[AMBER] Problem in running MMPBSA installation Christine Baranski (Wed Jan 27 2010 - 16:08:18 PST)
- Re: [AMBER] Problem in running MMPBSA installation Billy Miller III (Wed Jan 27 2010 - 16:34:39 PST)
  - Re: [AMBER] Problem in running MMPBSA installation Christine Baranski (Wed Jan 27 2010 - 16:53:53 PST)
    - Re: [AMBER] Problem in running MMPBSA installation Billy Miller III (Wed Jan 27 2010 - 17:08:17 PST)
[AMBER] minimization question Ed Pate (Wed Jan 27 2010 - 21:14:54 PST)
- Re: [AMBER] minimization question Jason Swails (Wed Jan 27 2010 - 21:57:20 PST)
[AMBER] compilation error of PMEMD Sangita Kachhap (Wed Jan 27 2010 - 09:11:09 PST)
- Re: [AMBER] compilation error of PMEMD Jason Swails (Wed Jan 27 2010 - 23:52:06 PST)
[AMBER] PMEMD compilation error Sangita Kachhap (Wed Jan 27 2010 - 07:35:28 PST)
- Re: [AMBER] PMEMD compilation error case (Thu Jan 28 2010 - 04:39:32 PST)
[AMBER] questions with nmode xueqin pang (Thu Jan 28 2010 - 02:19:06 PST)
- Re: [AMBER] questions with nmode case (Thu Jan 28 2010 - 05:21:33 PST)
  - Re: [AMBER] questions with nmode xueqin pang (Thu Jan 28 2010 - 19:43:34 PST)
    - Re: [AMBER] questions with nmode case (Fri Jan 29 2010 - 09:07:50 PST)
    - [AMBER] Force Fields Parameters Files Jana Sefcikova (Fri Jan 29 2010 - 09:49:06 PST)
    - Re: [AMBER] Force Fields Parameters Files Carlos Simmerling (Fri Jan 29 2010 - 10:00:32 PST)
    - Re: [AMBER] Force Fields Parameters Files FyD (Sat Jan 30 2010 - 02:43:26 PST)
[AMBER] questions when doing nmode xueqin pang (Thu Jan 28 2010 - 03:22:29 PST)
[AMBER] Potential bug in TI softcore code of AMBER 11 Hugh Heldenbrand (Thu Jan 28 2010 - 10:03:49 PST)
- RE: [AMBER] Potential bug in TI softcore code of AMBER 11 Ross Walker (Thu Jan 28 2010 - 11:51:36 PST)
- Re: [AMBER] Potential bug in TI softcore code of AMBER 11 steinbrt.rci.rutgers.edu (Fri Jan 29 2010 - 01:13:50 PST)
- Re: [AMBER] Potential bug in TI softcore code of AMBER 11 case (Fri Jan 29 2010 - 05:16:10 PST)
- Re: [AMBER] Potential bug in TI softcore code of AMBER 11 Hugh Heldenbrand (Sat Jan 30 2010 - 07:21:42 PST)
[AMBER] mol file format of Gaussian and Amber Jim Miller (Thu Jan 28 2010 - 16:12:48 PST)
- Re: [AMBER] mol file format of Gaussian and Amber FyD (Thu Jan 28 2010 - 19:43:56 PST)
  - Re: [AMBER] mol file format of Gaussian and Amber Jim Miller (Thu Jan 28 2010 - 22:18:50 PST)
[AMBER] Merz-Kollmann Radius for Iodine Matthias Wildauer (Fri Jan 29 2010 - 02:40:21 PST)
[AMBER] Serial Installation John Wil (Fri Jan 29 2010 - 04:53:11 PST)
- Re: [AMBER] Serial Installation case (Fri Jan 29 2010 - 09:35:42 PST)
- Re: [AMBER] Serial Installation Sudeep Narayan Banerjee (Fri Jan 29 2010 - 23:29:00 PST)
- Re: [AMBER] Serial Installation Sudeep Narayan Banerjee (Fri Jan 29 2010 - 23:29:47 PST)
[AMBER] Parameters for unusual residues Rilei Yu (Fri Jan 29 2010 - 07:26:09 PST)
- Re: [AMBER] Parameters for unusual residues Lachele Foley (Lists) (Fri Jan 29 2010 - 07:41:16 PST)
- Re: [AMBER] Parameters for unusual residues Carlos Simmerling (Fri Jan 29 2010 - 07:48:44 PST)
[AMBER] problem while running amber in parallel (wall time ?) imtiaz shafiq (Fri Jan 29 2010 - 11:05:16 PST)
- Re: [AMBER] problem while running amber in parallel (wall time ?) Jason Swails (Fri Jan 29 2010 - 12:06:28 PST)
  - Re: [AMBER] problem while running amber in parallel (wall time ?) MUHAMMAD IMTIA SHAFIQ (Fri Jan 29 2010 - 12:17:07 PST)
    - Re: [AMBER] problem while running amber in parallel (wall time ?) Jason Swails (Fri Jan 29 2010 - 12:25:54 PST)
  - Re: [AMBER] problem while running amber in parallel (wall time ?) MUHAMMAD IMTIA SHAFIQ (Fri Jan 29 2010 - 15:15:50 PST)
[AMBER] qm2_parameters.h s. Bill (Fri Jan 29 2010 - 17:25:13 PST)
- Re: [AMBER] qm2_parameters.h case (Fri Jan 29 2010 - 19:03:29 PST)
[AMBER] AmberTools 1.3, Intel 11.0, on Ubuntu fails? ben rodriguez (Fri Jan 29 2010 - 20:19:11 PST)
- Re: [AMBER] AmberTools 1.3, Intel 11.0, on Ubuntu fails? Jason Swails (Fri Jan 29 2010 - 20:24:30 PST)
[AMBER] disulfide bond error in the xleap jacky zhao (Fri Jan 29 2010 - 22:39:02 PST)
- Re: [AMBER] disulfide bond error in the xleap Jason Swails (Fri Jan 29 2010 - 22:55:37 PST)
  - Re: [AMBER] disulfide bond error in the xleap jacky zhao (Fri Jan 29 2010 - 23:46:47 PST)
    - Re: [AMBER] disulfide bond error in the xleap Jason Swails (Fri Jan 29 2010 - 23:51:06 PST)
    - Re: [AMBER] disulfide bond error in the xleap jacky zhao (Sat Jan 30 2010 - 02:02:20 PST)
[AMBER] sander.MPI running only on one node in parallel mode ? MUHAMMAD IMTIA SHAFIQ (Sat Jan 30 2010 - 07:20:43 PST)
- Re: [AMBER] sander.MPI running only on one node in parallel mode ? Jason Swails (Sat Jan 30 2010 - 08:55:02 PST)
- Re: [AMBER] sander.MPI running only on one node in parallel mode ? Ross Walker (Sat Jan 30 2010 - 09:54:14 PST)
- Re: [AMBER] sander.MPI running only on one node in parallel mode ? Mengjuei Hsieh (Sat Jan 30 2010 - 12:10:38 PST)
  - Re: [AMBER] sander.MPI running only on one node in parallel mode ? MUHAMMAD IMTIA SHAFIQ (Sat Jan 30 2010 - 15:07:04 PST)
[AMBER] mmpbsa error: No data for 0+2 MM BOND 200 xueqin pang (Sun Jan 31 2010 - 03:56:48 PST)
[AMBER] Tutorial for Glycoprotein simulation Siddharth Rastogi (Sun Jan 31 2010 - 15:08:40 PST)
- Re: [AMBER] Tutorial for Glycoprotein simulation Lachele Foley (Lists) (Mon Feb 01 2010 - 06:34:15 PST)
  - Re: [AMBER] Tutorial for Glycoprotein simulation Siddharth Rastogi (Tue Feb 02 2010 - 16:56:28 PST)
[AMBER] Problem in setting parameters for non standard DG residue:O6-Methylguanine N.R. Jena (Mon Feb 01 2010 - 03:47:47 PST)
- Re: [AMBER] Problem in setting parameters for non standard DG residue:O6-Methylguanine Carlos Simmerling (Mon Feb 01 2010 - 03:53:36 PST)
  - Re: [AMBER] Problem in setting parameters for non standard DG residue:O6-Methylguanine Jason Swails (Mon Feb 01 2010 - 04:52:39 PST)
    - Re: [AMBER] Problem in setting parameters for non standard DG residue:O6-Methylguanine case (Mon Feb 01 2010 - 08:04:51 PST)
    - Re: [AMBER] Problem in setting parameters for non standard DG residue:O6-Methylguanine N.R. Jena (Thu Mar 25 2010 - 22:43:38 PDT)
    - Re: [AMBER] Problem in setting parameters for non standard DG residue:O6-Methylguanine N.R. Jena (Thu Mar 25 2010 - 22:58:00 PDT)
    - Re: [AMBER] Problem in setting parameters for non standard DG residue:O6-Methylguanine Jason Swails (Thu Mar 25 2010 - 23:32:03 PDT)
    - Re: [AMBER] Problem in setting parameters for non standard DG residue:O6-Methylguanine N.R. Jena (Fri Mar 26 2010 - 05:59:06 PDT)
- Re: [AMBER] Problem in setting parameters for non standard DG residue:O6-Methylguanine Bill Ross (Fri Mar 26 2010 - 09:42:06 PDT)
- Re: [AMBER] Problem in setting parameters for non standard DG residue:O6-Methylguanine Xiaoting Mao (Sat Apr 13 2019 - 02:48:14 PDT)
[AMBER] MMPBSA s. Bill (Mon Feb 01 2010 - 03:43:11 PST)
- Re: [AMBER] MMPBSA Billy Miller III (Mon Feb 01 2010 - 04:24:03 PST)
- Re: [AMBER] MMPBSA Jason Swails (Mon Feb 01 2010 - 04:38:57 PST)
- Re: [AMBER] MMPBSA Ray Luo, Ph.D. (Thu May 29 2014 - 09:44:56 PDT)
  - Re: [AMBER] MMPBSA Hallel Freedman (Thu May 29 2014 - 11:34:28 PDT)
    - Re: [AMBER] MMPBSA Jason Swails (Thu May 29 2014 - 12:07:09 PDT)
    - Re: [AMBER] MMPBSA Hallel Freedman (Thu May 29 2014 - 12:28:07 PDT)
    - Re: [AMBER] MMPBSA Jason Swails (Thu May 29 2014 - 12:40:20 PDT)
    - Re: [AMBER] MMPBSA Hallel Freedman (Thu May 29 2014 - 15:22:03 PDT)
    - Re: [AMBER] MMPBSA Ray Luo, Ph.D. (Thu May 29 2014 - 15:53:02 PDT)
    - Re: [AMBER] MMPBSA Hallel Freedman (Thu May 29 2014 - 16:59:53 PDT)
- Re: [AMBER] MMPBSA Sourav Purohit (Thu Sep 18 2014 - 07:24:31 PDT)
  - Re: [AMBER] MMPBSA Jason Swails (Thu Sep 18 2014 - 07:38:27 PDT)
- Re: [AMBER] MMPBSA Sourav Purohit (Thu Sep 18 2014 - 08:47:18 PDT)
  - Re: [AMBER] MMPBSA Jason Swails (Thu Sep 18 2014 - 08:58:02 PDT)
  - Re: [AMBER] MMPBSA Daniel Roe (Thu Sep 18 2014 - 08:54:13 PDT)
    - Re: [AMBER] MMPBSA Sourav Purohit (Thu Sep 18 2014 - 09:08:02 PDT)
    - Re: [AMBER] MMPBSA Jason Swails (Thu Sep 18 2014 - 09:27:17 PDT)
[AMBER] VDW parameter for Cobalt and Nickel Raja Pandian (Mon Feb 01 2010 - 06:17:21 PST)
[AMBER] Solvating a protein - tleap works where sleap does not? Ben Roberts (Mon Feb 01 2010 - 07:10:56 PST)
[AMBER] errors in leap Beale, John (Mon Feb 01 2010 - 07:09:06 PST)
- Re: [AMBER] errors in leap Jason Swails (Mon Feb 01 2010 - 07:32:13 PST)
- Re: [AMBER] errors in leap case (Mon Feb 01 2010 - 08:19:13 PST)
[AMBER] Converting Gaussian output format to the RESP input format imtiaz shafiq (Mon Feb 01 2010 - 07:44:45 PST)
- Re: [AMBER] Converting Gaussian output format to the RESP input format Jason Swails (Mon Feb 01 2010 - 07:54:59 PST)
  - Re: [AMBER] Converting Gaussian output format to the RESP input format imtiaz shafiq (Mon Feb 01 2010 - 23:53:06 PST)
    - Re: [AMBER] Converting Gaussian output format to the RESP input format imtiaz shafiq (Tue Feb 02 2010 - 00:31:36 PST)
- Re: [AMBER] Converting Gaussian output format to the RESP input format FyD (Mon Feb 01 2010 - 11:25:38 PST)
Re: [AMBER] errors in leap Bill Ross (Mon Feb 01 2010 - 09:24:50 PST)
[AMBER] Test log s. Bill (Mon Feb 01 2010 - 09:48:10 PST)
- Re: [AMBER] Test log case (Mon Feb 01 2010 - 10:49:22 PST)
- Re: [AMBER] Test log s. Bill (Mon Feb 01 2010 - 12:41:28 PST)
  - Re: [AMBER] Test log Jason Swails (Mon Feb 01 2010 - 13:24:43 PST)
[AMBER] interaction energy of single residue to its environment luzhenw1.msu.edu (Mon Feb 01 2010 - 10:49:56 PST)
- Re: [AMBER] interaction energy of single residue to its environment Carlos Simmerling (Mon Feb 01 2010 - 11:04:16 PST)
[AMBER] plotting RMS vs. residue number Beale, John (Mon Feb 01 2010 - 11:15:39 PST)
[AMBER] mmpbsa error: No data for 0+2 MM BOND 200 xueqin pang (Mon Feb 01 2010 - 17:25:55 PST)
- Re: [AMBER] mmpbsa error: No data for 0+2 MM BOND 200 Jason Swails (Mon Feb 01 2010 - 20:16:20 PST)
  - Re: [AMBER] mmpbsa error: No data for 0+2 MM BOND 200 xueqin pang (Mon Feb 01 2010 - 22:46:08 PST)
[AMBER] How to construct the methyl-animo acid? Aurum Bai (Tue Feb 02 2010 - 01:17:02 PST)
- Re: [AMBER] How to construct the methyl-animo acid? FyD (Tue Feb 02 2010 - 03:24:24 PST)
[AMBER] Announcement: Amber MD Workshop 2010 in Duesseldorf, Germany April 26-30th steinbrt.rci.rutgers.edu (Tue Feb 02 2010 - 02:45:53 PST)
- Re: [AMBER] Announcement: Amber MD Workshop 2010 in Duesseldorf, Germany April 26-30th xueping chin (Wed Feb 03 2010 - 15:47:53 PST)
  - Re: [AMBER] Announcement: Amber MD Workshop 2010 in Duesseldorf, Germany April 26-30th steinbrt.rci.rutgers.edu (Thu Feb 04 2010 - 00:37:17 PST)
    - Re: [AMBER] Announcement: Amber MD Workshop 2010 in Duesseldorf, Germany April 26-30th xueping chin (Thu Feb 04 2010 - 01:35:07 PST)
[AMBER] parameters for heme-CO Francesco Pietra (Tue Feb 02 2010 - 10:51:12 PST)
- Re: [AMBER] parameters for heme-CO FyD (Wed Feb 03 2010 - 06:38:07 PST)
[AMBER] MOL2 Output through LEAP Matthew Tessier (Tue Feb 02 2010 - 11:20:54 PST)
- Re: [AMBER] MOL2 Output through LEAP Jason Swails (Tue Feb 02 2010 - 11:41:19 PST)
  - RE: [AMBER] MOL2 Output through LEAP Matthew Tessier (Tue Feb 02 2010 - 12:01:15 PST)
    - Re: [AMBER] MOL2 Output through LEAP Jason Swails (Tue Feb 02 2010 - 12:30:21 PST)
- Re: [AMBER] MOL2 Output through LEAP FyD (Tue Feb 02 2010 - 13:19:20 PST)
- Re: [AMBER] MOL2 Output through LEAP case (Tue Feb 02 2010 - 13:28:59 PST)
[AMBER] If this is normal for 3 or 4 sander.MPI jobs appearing on one node MUHAMMAD IMTIA SHAFIQ (Tue Feb 02 2010 - 11:46:31 PST)
- Re: [AMBER] If this is normal for 3 or 4 sander.MPI jobs appearing on one node Carlos Simmerling (Tue Feb 02 2010 - 11:51:57 PST)
[AMBER] deuterate protein atoms by editing the topology file Jose Borreguero (Tue Feb 02 2010 - 12:16:43 PST)
- Re: [AMBER] deuterate protein atoms by editing the topology file case (Tue Feb 02 2010 - 13:31:41 PST)
  - Re: [AMBER] deuterate protein atoms by editing the topology file Jose Borreguero (Tue Feb 02 2010 - 13:35:24 PST)
[AMBER] tleap command for disulfide bonds: for chain A and Chain B ??? Siddharth Rastogi (Tue Feb 02 2010 - 17:19:28 PST)
- Re: [AMBER] tleap command for disulfide bonds: for chain A and Chain B ??? case (Tue Feb 02 2010 - 20:32:11 PST)
  - Re: [AMBER] tleap command for disulfide bonds: for chain A and Chain B ??? Jason Swails (Tue Feb 02 2010 - 23:50:16 PST)
  - Re: [AMBER] tleap command for disulfide bonds: for chain A and Chain B ??? Anselm Horn (Wed Feb 03 2010 - 01:17:40 PST)
[AMBER] failure when doing bugfix patch for amber10 and tools V1.2 xueqin pang (Tue Feb 02 2010 - 22:52:56 PST)
- Re: [AMBER] failure when doing bugfix patch for amber10 and tools V1.2 Ray Luo (Wed Feb 03 2010 - 10:03:45 PST)
  - Re: [AMBER] failure when doing bugfix patch for amber10 and tools V1.2 xueqin pang (Thu Feb 04 2010 - 17:45:05 PST)
[AMBER] Information regarding how to group atoms for ionic liquid dhilip kumar ramalingam (Wed Feb 03 2010 - 01:10:31 PST)
- Re: [AMBER] Information regarding how to group atoms for ionic liquid case (Wed Feb 03 2010 - 10:40:30 PST)
[AMBER] AMBER 9 parallel compilation problem on Mac OS X 10.6 pelaez.usal.es (Wed Feb 03 2010 - 04:15:43 PST)
- Re: [AMBER] AMBER 9 parallel compilation problem on Mac OS X 10.6 case (Wed Feb 03 2010 - 04:48:43 PST)
- Re: [AMBER] AMBER 9 parallel compilation problem on Mac OS X 10.6 David Watson (Wed Feb 03 2010 - 06:21:11 PST)
[AMBER] parmchk lists multiple values of the same parameter Sidney Elmer (Wed Feb 03 2010 - 09:12:39 PST)
- Re: [AMBER] parmchk lists multiple values of the same parameter Jason Swails (Wed Feb 03 2010 - 10:05:05 PST)
[AMBER] adding atom types to leapfrc Francesco Pietra (Wed Feb 03 2010 - 10:53:00 PST)
Re: [AMBER] adding atom types to leapfrc Bill Ross (Wed Feb 03 2010 - 11:11:56 PST)
- Re: [AMBER] adding atom types to leapfrc Francesco Pietra (Thu Feb 04 2010 - 02:50:41 PST)
- Re: [AMBER] adding atom types to leapfrc Francesco Pietra (Thu Feb 04 2010 - 02:50:15 PST)
  - Re: [AMBER] adding atom types to leapfrc Jason Swails (Thu Feb 04 2010 - 07:34:05 PST)
[AMBER] Addles and makeDIST_RST Titus, Jamie (bairdje) (Wed Feb 03 2010 - 12:08:20 PST)
- Re: [AMBER] Addles and makeDIST_RST case (Wed Feb 03 2010 - 14:45:12 PST)
- [AMBER] Addles and makeDIST_RST Titus, Jamie (bairdje) (Thu Feb 04 2010 - 04:58:13 PST)
[AMBER] dielectric constant in NMODE Jeffrey (Wed Feb 03 2010 - 18:45:26 PST)
[AMBER] Amber11 vs Amber10 Steve Seibold (Thu Feb 04 2010 - 10:58:59 PST)
- Re: [AMBER] Amber11 vs Amber10 case (Thu Feb 04 2010 - 11:20:16 PST)
[AMBER] multiple intercalating waters wong105.llnl.gov (Thu Feb 04 2010 - 11:05:32 PST)
[AMBER] loading parm7 and coords with tLeap? Nicholas Musolino (Thu Feb 04 2010 - 12:41:10 PST)
- Re: [AMBER] loading parm7 and coords with tLeap? case (Thu Feb 04 2010 - 19:35:03 PST)
  - Re: [AMBER] loading parm7 and coords with tLeap? Nicholas Musolino (Fri Feb 05 2010 - 08:48:52 PST)
[AMBER] Problem reading PDB residues in AmberTools-1.3 Hopkins, Robert (Thu Feb 04 2010 - 18:10:04 PST)
- Re: [AMBER] Problem reading PDB residues in AmberTools-1.3 case (Thu Feb 04 2010 - 19:28:36 PST)
- [AMBER] FW: Problem reading PDB residues in AmberTools-1.3 Hopkins, Robert (Fri Feb 05 2010 - 07:37:09 PST)
  - Re: [AMBER] FW: Problem reading PDB residues in AmberTools-1.3 case (Fri Feb 05 2010 - 10:44:41 PST)
[AMBER] What is the ".ac" files as input of respgen and how to generate it? Aurum Bai (Thu Feb 04 2010 - 21:42:37 PST)
[AMBER] load pdb into xleap Jim Miller (Fri Feb 05 2010 - 01:12:12 PST)
- Re: [AMBER] load pdb into xleap case (Fri Feb 05 2010 - 04:27:14 PST)
[AMBER] reimaging the trajectory Shaikh Abdul R S Ramaju (Fri Feb 05 2010 - 02:25:53 PST)
- Re: [AMBER] reimaging the trajectory Carlos Simmerling (Fri Feb 05 2010 - 03:15:00 PST)
[AMBER] Add charge on quaternary nitrogen Pol Boudard (Fri Feb 05 2010 - 05:40:34 PST)
[AMBER] AMBER10 build - failing "jar" and "jar_multi" tests Mark Dixon (Fri Feb 05 2010 - 06:55:29 PST)
- Re: [AMBER] AMBER10 build - failing "jar" and "jar_multi" tests Jason Swails (Fri Feb 05 2010 - 07:02:57 PST)
  - Re: [AMBER] AMBER10 build - failing "jar" and "jar_multi" tests Mark Dixon (Fri Feb 05 2010 - 07:15:02 PST)
[AMBER] About the err of antechamber's tutorial! Aurum Bai (Fri Feb 05 2010 - 07:07:49 PST)
- Re: [AMBER] About the err of antechamber's tutorial! David Watson (Fri Feb 05 2010 - 07:25:06 PST)
- Re: [AMBER] About the err of antechamber's tutorial! David Watson (Fri Feb 05 2010 - 08:00:03 PST)
- Re: [AMBER] About the err of antechamber's tutorial! FyD (Fri Feb 05 2010 - 09:27:27 PST)
RE: [Possible Spam: 10%] Re: [AMBER] FW: Problem reading PDB residues in AmberTools-1.3 Hopkins, Robert (Fri Feb 05 2010 - 10:51:25 PST)
[AMBER] softcore TI lambda values of 0 and 1 Hugh Heldenbrand (Fri Feb 05 2010 - 12:49:05 PST)
- Re: [AMBER] softcore TI lambda values of 0 and 1 steinbrt.rci.rutgers.edu (Sun Feb 07 2010 - 02:01:55 PST)
[AMBER] positional restraints of different strengths Jose Borreguero (Fri Feb 05 2010 - 15:55:28 PST)
- Re: [AMBER] positional restraints of different strengths case (Sat Feb 06 2010 - 08:53:38 PST)
  - Re: [AMBER] positional restraints of different strengths Jose Borreguero (Tue Feb 09 2010 - 05:00:06 PST)
Re: [AMBER] positional restraints of different strengths Bill Ross (Fri Feb 05 2010 - 16:51:16 PST)
- Re: [AMBER] positional restraints of different strengths Jose Borreguero (Sat Feb 06 2010 - 03:33:10 PST)
[AMBER] Problem in Ptraj Kshatresh Dutta Dubey (Fri Feb 05 2010 - 22:41:12 PST)
- Re: [AMBER] Problem in Ptraj Jason Swails (Fri Feb 05 2010 - 23:22:19 PST)
[AMBER] antechamber with carbon monoxide Francesco Pietra (Sat Feb 06 2010 - 02:52:54 PST)
[AMBER] Question of Tutorials-A: the total charge is not integer Tom Williams (Sun Feb 07 2010 - 00:00:39 PST)
- [AMBER] RE: Question of Tutorials-A: the total charge is not integer Ross Walker (Sun Feb 07 2010 - 02:02:40 PST)
[AMBER] Energy Minimization of a Complex MUHAMMAD IMTIA SHAFIQ (Sun Feb 07 2010 - 16:22:57 PST)
- Re: [AMBER] Energy Minimization of a Complex Dean Cuebas (Sun Feb 07 2010 - 17:53:49 PST)
[AMBER] Regarding restraints during minimisation stage 1 in explicit solvent Asfa Ali (Sun Feb 07 2010 - 21:23:12 PST)
- Re: [AMBER] Regarding restraints during minimisation stage 1 in explicit solvent Carlos Simmerling (Mon Feb 08 2010 - 03:39:15 PST)
[AMBER] 10_12 potential aapeters.ncsu.edu (Mon Feb 08 2010 - 00:14:39 PST)
- Re: [AMBER] 10_12 potential case (Mon Feb 08 2010 - 05:19:34 PST)
  - Re: [AMBER] 10_12 potential aapeters.ncsu.edu (Mon Feb 08 2010 - 08:54:09 PST)
    - Re: [AMBER] 10_12 potential case (Mon Feb 08 2010 - 18:40:39 PST)
    - Re: [AMBER] 10_12 potential aapeters.ncsu.edu (Tue Feb 09 2010 - 06:38:42 PST)
- Re: [AMBER] 10_12 potential aapeters.ncsu.edu (Mon Feb 08 2010 - 12:40:11 PST)
[AMBER] [Fwd: 10_12 potential] aapeters.ncsu.edu (Mon Feb 08 2010 - 03:01:35 PST)
[AMBER] Charges of ASN in all_aminoct03 CR Gregor (Mon Feb 08 2010 - 05:27:20 PST)
- Re: [AMBER] Charges of ASN in all_aminoct03 FyD (Mon Feb 08 2010 - 08:55:04 PST)
[AMBER] limit of joining residues Jio M (Mon Feb 08 2010 - 05:38:54 PST)
- Re: [AMBER] limit of joining residues FyD (Thu Feb 11 2010 - 02:47:34 PST)
  - Re: [AMBER] limit of joining residues Jio M (Sat Feb 13 2010 - 00:20:58 PST)
    - Re: [AMBER] limit of joining residues FyD (Sat Feb 13 2010 - 00:37:50 PST)
- Re: [AMBER] limit of joining residues Bill Ross (Sat Feb 13 2010 - 11:22:33 PST)
  - Re: [AMBER] limit of joining residues Jio M (Sun Feb 14 2010 - 03:42:34 PST)
- Re: [AMBER] limit of joining residues Bill Ross (Sun Feb 14 2010 - 12:10:17 PST)
  - Re: [AMBER] limit of joining residues Jio M (Sun Feb 14 2010 - 21:03:49 PST)
- Re: [AMBER] limit of joining residues Bill Ross (Mon Feb 15 2010 - 14:10:00 PST)
  - Re: [AMBER] limit of joining residues Jio M (Wed Feb 17 2010 - 06:56:32 PST)
[AMBER] sleap crash with single water molecule and amoeba Neil Henson (Mon Feb 08 2010 - 06:14:45 PST)
- Re: [AMBER] sleap crash with single water molecule and amoeba case (Mon Feb 15 2010 - 13:14:15 PST)
  - Re: [AMBER] sleap crash with single water molecule and amoeba Alan (Tue Feb 16 2010 - 04:17:47 PST)
    - Re: [AMBER] sleap crash with single water molecule and amoeba Neil Henson (Tue Feb 16 2010 - 08:20:22 PST)
    - Re: [AMBER] sleap crash with single water molecule and amoeba case (Tue Feb 16 2010 - 09:19:04 PST)
Re: [AMBER] limit of joining residues Bill Ross (Mon Feb 08 2010 - 09:32:57 PST)
- Re: [AMBER] limit of joining residues Jio M (Wed Feb 10 2010 - 08:12:58 PST)
- Re: [AMBER] limit of joining residues Bill Ross (Wed Feb 10 2010 - 10:00:43 PST)
  - Re: [AMBER] limit of joining residues Jio M (Thu Feb 11 2010 - 00:34:52 PST)
- Re: [AMBER] limit of joining residues Bill Ross (Thu Feb 11 2010 - 09:46:04 PST)
[AMBER] Problem in creating cubic water box Sangita Kachhap (Mon Feb 08 2010 - 09:51:28 PST)
- Re: [AMBER] Problem in creating cubic water box case (Tue Feb 09 2010 - 09:46:12 PST)
  - Re: [AMBER] Problem in creating cubic water box Sangita Kachhap (Sat Feb 13 2010 - 00:43:54 PST)
Re: [AMBER] Problem in creating cubic water box Bill Ross (Mon Feb 08 2010 - 10:21:47 PST)
[AMBER] Imaging difficulty Hopkins, Robert (Mon Feb 08 2010 - 12:39:59 PST)
[AMBER] QM/MM new parameters s. Bill (Mon Feb 08 2010 - 15:32:59 PST)
- Re: [AMBER] QM/MM new parameters Adrian Roitberg (Mon Feb 08 2010 - 15:40:10 PST)
  - Re: [AMBER] QM/MM new parameters s. Bill (Mon Feb 08 2010 - 15:53:52 PST)
    - RE: [AMBER] QM/MM new parameters Ross Walker (Tue Feb 09 2010 - 04:14:38 PST)
- RE: [AMBER] QM/MM new parameters s. Bill (Tue Feb 09 2010 - 14:40:08 PST)
[AMBER] (no subject) mani grover (Mon Feb 08 2010 - 22:19:15 PST)
[AMBER] Antechamber: imidazole=aromatic, imidazolium=not aromatic? Gabriel Rocklin (Mon Feb 08 2010 - 23:33:17 PST)
- Re: [AMBER] Antechamber: imidazole=aromatic, imidazolium=not aromatic? FyD (Tue Feb 09 2010 - 22:41:34 PST)
- Re: [AMBER] Antechamber: imidazole=aromatic, imidazolium=not aromatic? Dmitry Mukha (Wed Feb 10 2010 - 00:17:43 PST)
[AMBER] how to fix or restraint atoms in molecules Jim Miller (Tue Feb 09 2010 - 00:30:20 PST)
[AMBER] Reducing RMS errors in TI calculation ET (Tue Feb 09 2010 - 13:02:48 PST)
- Re: [AMBER] Reducing RMS errors in TI calculation steinbrt.rci.rutgers.edu (Tue Feb 09 2010 - 23:19:56 PST)
[AMBER] mailing list manikanthan bhavaraju (Tue Feb 09 2010 - 13:22:45 PST)
[AMBER] problem of chenge of the water box during equilibration Sangita Kachhap (Wed Feb 10 2010 - 08:48:34 PST)
- Re: [AMBER] problem of chenge of the water box during equilibration Jason Swails (Wed Feb 10 2010 - 08:54:07 PST)
  - [AMBER] plumed and sander.MPI Giuseppe De Marco (Fri Feb 12 2010 - 10:07:08 PST)
    - Re: [AMBER] plumed and sander.MPI Jason Swails (Fri Feb 12 2010 - 15:26:37 PST)
  - Re: [AMBER] problem of chenge of the water box during equilibration Sangita Kachhap (Sat Feb 13 2010 - 00:42:32 PST)
[AMBER] Re: Antechamber: imidazole=aromatic, imidazolium=not aromatic? Gabriel Rocklin (Wed Feb 10 2010 - 11:23:24 PST)
[AMBER] Problem compiling Amber 10 after applying latest bugfix file Sanders, Larry R. (Wed Feb 10 2010 - 12:17:40 PST)
[AMBER] MMPBSA.py error s. Bill (Wed Feb 10 2010 - 15:46:34 PST)
- Re: [AMBER] MMPBSA.py error s. Bill (Wed Feb 10 2010 - 16:40:13 PST)
  - Re: [AMBER] MMPBSA.py error Jason Swails (Wed Feb 10 2010 - 16:57:52 PST)
    - Re: [AMBER] MMPBSA.py error s. Bill (Thu Feb 11 2010 - 04:14:18 PST)
- Re: [AMBER] MMPBSA.py error Jason Swails (Wed Apr 20 2011 - 10:37:07 PDT)
- Re: [AMBER] MMPBSA.py error Jason Swails (Tue Apr 26 2011 - 19:46:48 PDT)
- Re: [AMBER] MMPBSA.py error Pratul Agarwal (Fri Jan 04 2019 - 06:28:09 PST)
[AMBER] About RAMD gokul algates (Thu Feb 11 2010 - 06:27:32 PST)
- Re: [AMBER] About RAMD Vlad Cojocaru (Thu Feb 11 2010 - 06:57:20 PST)
  - Re: [AMBER] About RAMD Francesco Pietra (Thu Feb 11 2010 - 08:57:32 PST)
- RE: [AMBER] About RAMD Cojocaru,Vlad (Thu Feb 11 2010 - 13:18:28 PST)
[AMBER] RE: Problem compiling Amber 10 after applying latest bugfix file Sanders, Larry R. (Thu Feb 11 2010 - 06:35:06 PST)
[AMBER] mm_pbsa statistics problem Marina Grabar (Thu Feb 11 2010 - 06:51:01 PST)
- Re: [AMBER] mm_pbsa statistics problem Dwight McGee (Thu Feb 11 2010 - 07:09:14 PST)
  - Re: [AMBER] mm_pbsa statistics problem Marina Grabar (Thu Feb 11 2010 - 07:22:05 PST)
    - Re: [AMBER] mm_pbsa statistics problem Ray Luo (Thu Feb 11 2010 - 09:20:54 PST)
    - Re: [AMBER] mm_pbsa statistics problem Marina Grabar (Fri Feb 12 2010 - 03:57:24 PST)
    - Re: [AMBER] mm_pbsa statistics problem Dwight McGee (Fri Feb 12 2010 - 07:28:55 PST)
    - Re: [AMBER] mm_pbsa statistics problem Ray Luo (Fri Feb 12 2010 - 09:51:27 PST)
    - Re: [AMBER] mm_pbsa statistics problem Marina Grabar (Mon Feb 15 2010 - 04:48:17 PST)
[AMBER] Small Molecule Parameters imtiaz shafiq (Thu Feb 11 2010 - 10:44:18 PST)
Re: [AMBER] Small Molecule Parameters Bill Ross (Thu Feb 11 2010 - 11:05:32 PST)
- Re: [AMBER] Small Molecule Parameters MUHAMMAD IMTIA SHAFIQ (Thu Feb 11 2010 - 13:51:59 PST)
- [AMBER] Glycerol Models Mannan (Fri Feb 12 2010 - 00:39:45 PST)
  - Re: [AMBER] Glycerol Models FyD (Sat Feb 13 2010 - 00:45:16 PST)
    - Re: [AMBER] Glycerol Models Mannan (Wed Feb 17 2010 - 06:50:27 PST)
    - Re: [AMBER] Glycerol Models FyD (Wed Feb 17 2010 - 15:02:07 PST)
[AMBER] strange behavior in QMMM simulation M. L. Dodson (Thu Feb 11 2010 - 12:35:25 PST)
- Re: [AMBER] strange behavior in QMMM simulation M. L. Dodson (Sat Feb 13 2010 - 12:21:06 PST)
  - Re: [AMBER] strange behavior in QMMM simulation case (Sat Feb 13 2010 - 19:28:38 PST)
    - Re: [AMBER] strange behavior in QMMM simulation M. L. Dodson (Sun Feb 14 2010 - 06:19:00 PST)
[AMBER] PMEMD compiling errors Dian Jiao (Thu Feb 11 2010 - 15:56:31 PST)
- Re: [AMBER] PMEMD compiling errors Jason Swails (Thu Feb 11 2010 - 18:10:34 PST)
  - Re: [AMBER] PMEMD compiling errors Dian Jiao (Thu Feb 11 2010 - 19:10:46 PST)
[AMBER] Problems with PMEMD compilation Alex Rodriguez (Fri Feb 12 2010 - 02:45:09 PST)
[AMBER] Problem with specifying mask for MMPBSA.py script Arvind Marathe (Fri Feb 12 2010 - 07:09:03 PST)
- Re: [AMBER] Problem with specifying mask for MMPBSA.py script Billy Miller III (Fri Feb 12 2010 - 07:50:44 PST)
  - Re: [AMBER] Problem with specifying mask for MMPBSA.py script Arvind Marathe (Fri Feb 12 2010 - 09:54:45 PST)
[AMBER] compiling amber on intel xeon 5500 series cpu Max Wang (Fri Feb 12 2010 - 12:16:29 PST)
- Re: [AMBER] compiling amber on intel xeon 5500 series cpu Bill Ross (Fri Feb 12 2010 - 14:22:56 PST)
Re: [AMBER] compiling amber on intel xeon 5500 series cpu Bill Ross (Fri Feb 12 2010 - 12:26:17 PST)
- Re: [AMBER] compiling amber on intel xeon 5500 series cpu Max Wang (Fri Feb 12 2010 - 14:10:19 PST)
[AMBER] MM PBSA problem Jagdeesh C (Sat Feb 13 2010 - 08:49:19 PST)
- Re: [AMBER] MM PBSA problem Ray Luo (Sat Feb 13 2010 - 09:31:59 PST)
  - Re: [AMBER] MM PBSA problem Jagdeesh C (Sat Feb 13 2010 - 09:53:32 PST)
[AMBER] mmpbsa.py ion radius s. Bill (Sat Feb 13 2010 - 18:02:43 PST)
- Re: [AMBER] mmpbsa.py ion radius Billy Miller III (Sat Feb 13 2010 - 18:25:08 PST)
  - Re: [AMBER] mmpbsa.py ion radius s. Bill (Mon Feb 15 2010 - 10:16:29 PST)
    - Re: [AMBER] mmpbsa.py ion radius Jason Swails (Mon Feb 15 2010 - 10:29:27 PST)
    - Re: [AMBER] mmpbsa.py ion radius Dian Jiao (Mon Feb 15 2010 - 10:38:16 PST)
    - Re: [AMBER] mmpbsa.py ion radius Jason Swails (Mon Feb 15 2010 - 10:58:08 PST)
[AMBER] question about how to fix the number of water molecule mirage . (Sun Feb 14 2010 - 23:39:29 PST)
- Re: [AMBER] question about how to fix the number of water molecule Ilyas Yildirim (Mon Feb 15 2010 - 05:40:14 PST)
[AMBER] how is better to measure ligand drift against protein in Amber Andrew Voronkov (Mon Feb 15 2010 - 06:21:02 PST)
[AMBER] Binding energy calculation using MMPBSA.py: Sander from amber9 complains "mdfil: Error unknown flag: -y" Arvind Marathe (Mon Feb 15 2010 - 06:30:04 PST)
- Re: [AMBER] Binding energy calculation using MMPBSA.py: Sander from amber9 complains "mdfil: Error unknown flag: -y" Jason Swails (Mon Feb 15 2010 - 06:40:22 PST)
  - Re: [AMBER] Binding energy calculation using MMPBSA.py: Sander from amber9 complains "mdfil: Error unknown flag: -y" Arvind Marathe (Tue Feb 16 2010 - 01:26:14 PST)
[AMBER] Fitting Torsional parameters stephane acoca (Mon Feb 15 2010 - 07:48:07 PST)
- Re: [AMBER] Fitting Torsional parameters Ilyas Yildirim (Mon Feb 15 2010 - 08:07:05 PST)
  - Re: [AMBER] Fitting Torsional parameters Jason Swails (Mon Feb 15 2010 - 09:42:31 PST)
    - Re: [AMBER] Fitting Torsional parameters stephane acoca (Mon Feb 15 2010 - 13:49:24 PST)
    - Re: [AMBER] Fitting Torsional parameters stephane acoca (Wed Feb 17 2010 - 08:07:09 PST)
    - Re: [AMBER] Fitting Torsional parameters Ilyas Yildirim (Wed Feb 17 2010 - 17:36:07 PST)
[AMBER] RDF with ptraj Dian Jiao (Mon Feb 15 2010 - 12:45:00 PST)
[AMBER] Re: Antechamber: imidazole=aromatic, imidazolium=not aromatic? Gabriel Rocklin (Mon Feb 15 2010 - 15:21:45 PST)
[AMBER] PARMSCAN E.M. (Mon Feb 15 2010 - 19:58:15 PST)
[AMBER] enquiry regarding distance-dependent dielectric constant minimization bharat lakhani (Mon Feb 15 2010 - 23:35:44 PST)
- Re: [AMBER] enquiry regarding distance-dependent dielectric constant minimization David A. Case (Thu Feb 18 2010 - 04:59:22 PST)
[AMBER] (no subject) Yubo Fan (Tue Feb 16 2010 - 00:31:46 PST)
- Re: [AMBER] (no subject) case (Tue Feb 16 2010 - 04:34:33 PST)
  - Re: [AMBER] (no subject) Yubo Fan (Tue Feb 16 2010 - 10:23:15 PST)
[AMBER] (no subject) Rebeca García Fandiño (Tue Feb 16 2010 - 10:14:45 PST)
[AMBER] VMD and Amber coordinates Rebeca García Fandiño (Tue Feb 16 2010 - 10:25:25 PST)
- Re: [AMBER] VMD and Amber coordinates InSuk Joung (Tue Feb 16 2010 - 10:52:12 PST)
- Re: [AMBER] VMD and Amber coordinates Bill Ross (Tue Feb 16 2010 - 13:19:35 PST)
[AMBER] sander compilation s. Bill (Tue Feb 16 2010 - 17:23:47 PST)
- Re: [AMBER] sander compilation Jason Swails (Tue Feb 16 2010 - 17:59:45 PST)
[AMBER] PARMSCAN E.M. (Tue Feb 16 2010 - 20:08:45 PST)
[AMBER] Calcium and Phosphate sikander azam (Tue Feb 16 2010 - 22:12:22 PST)
- Re: [AMBER] Calcium and Phosphate Syed Tarique Moin (Wed Feb 17 2010 - 02:29:02 PST)
[AMBER] Virtual waters Fernando Martín García (Wed Feb 17 2010 - 02:59:05 PST)
- Re: [AMBER] Virtual waters case (Wed Feb 17 2010 - 09:45:45 PST)
  - Re: [AMBER] Virtual waters Fernando Martín García (Wed Feb 17 2010 - 23:39:09 PST)
    - Re: [AMBER] Virtual waters David A. Case (Thu Feb 18 2010 - 04:37:35 PST)
    - Re: [AMBER] Virtual waters Fernando Martín García (Thu Feb 18 2010 - 05:35:45 PST)
[AMBER] how to generate acetone box parvesh singh (Wed Feb 17 2010 - 03:10:09 PST)
- Re: [AMBER] how to generate acetone box FyD (Wed Feb 17 2010 - 14:47:03 PST)
[AMBER] makeCHIR_RST and LES Titus, Jamie (bairdje) (Wed Feb 17 2010 - 08:34:13 PST)
- Re: [AMBER] makeCHIR_RST and LES Carlos Simmerling (Fri Feb 19 2010 - 06:51:37 PST)
  - RE: [AMBER] makeCHIR_RST and LES Titus, Jamie (bairdje) (Fri Feb 19 2010 - 07:40:55 PST)
[AMBER] relaxed PES eric henon (Wed Feb 17 2010 - 11:58:50 PST)
- Re: [AMBER] relaxed PES Jason Swails (Wed Feb 17 2010 - 12:05:06 PST)
  - Re: [AMBER] relaxed PES eric henon (Wed Feb 17 2010 - 13:19:47 PST)
Re: [AMBER] ccl4 simulation FyD (Wed Feb 17 2010 - 15:10:30 PST)
- Re: [AMBER] ccl4 simulation Sandro L. Fornili (Thu Feb 18 2010 - 01:02:52 PST)
[AMBER] New Bursaries and Plenary Speaker - Molecular Modeling Workshop 2010 in Erlangen, Germany Harald Lanig (Thu Feb 18 2010 - 02:39:24 PST)
[AMBER] Script Beale, John (Thu Feb 18 2010 - 04:35:26 PST)
- Re: [AMBER] Script Carlos Simmerling (Thu Feb 18 2010 - 04:40:57 PST)
  - RE: [AMBER] Script Beale, John (Thu Feb 18 2010 - 04:42:50 PST)
  - RE: [AMBER] Script Beale, John (Thu Feb 18 2010 - 04:47:21 PST)
    - Re: [AMBER] Script Carlos Simmerling (Thu Feb 18 2010 - 04:59:03 PST)
    - RE: [AMBER] Script Beale, John (Thu Feb 18 2010 - 05:15:59 PST)
    - Re: [AMBER] Script Lachele Foley (Lists) (Thu Feb 18 2010 - 07:43:23 PST)
    - Re: [AMBER] Script Carlos Simmerling (Sun Feb 21 2010 - 06:15:51 PST)
    - Re: [AMBER] Script Josmar R. da Rocha (Mon Feb 22 2010 - 09:50:03 PST)
[AMBER] Segmentation fault with xleap while loading a leaprc Nicolas Sapay (Thu Feb 18 2010 - 05:48:00 PST)
- Re: [AMBER] Segmentation fault with xleap while loading a leaprc case (Thu Feb 18 2010 - 06:07:47 PST)
  - Re: [AMBER] Segmentation fault with xleap while loading a leaprc Nicolas Sapay (Thu Feb 18 2010 - 06:29:54 PST)
    - Re: [AMBER] Segmentation fault with xleap while loading a leaprc case (Thu Feb 18 2010 - 08:27:55 PST)
    - Re: [AMBER] Segmentation fault with xleap while loading a leaprc Nicolas Sapay (Thu Feb 18 2010 - 08:42:59 PST)
- Re: [AMBER] Segmentation fault with xleap while loading a leaprc Bill Ross (Thu Feb 18 2010 - 10:43:31 PST)
- Re: [AMBER] Segmentation fault with xleap while loading a leaprc Nicolas Sapay (Thu Feb 18 2010 - 11:48:18 PST)
- Re: [AMBER] Segmentation fault with xleap while loading a leaprc Bill Ross (Thu Feb 18 2010 - 11:56:53 PST)
  - Re: [AMBER] Segmentation fault with xleap while loading a leaprc Nicolas Sapay (Fri Feb 19 2010 - 06:42:00 PST)
[AMBER] help vaibhav jain (Thu Feb 18 2010 - 05:54:02 PST)
- Re: [AMBER] help Billy Miller III (Thu Feb 18 2010 - 05:58:04 PST)
- ODP: [AMBER] help MASLYK, MACIEJ MARCIN (Thu Feb 18 2010 - 05:58:58 PST)
  - Re: ODP: [AMBER] help lina (Thu Feb 18 2010 - 06:06:22 PST)
[AMBER] References of all force fields for citations Sushil Mishra (Thu Feb 18 2010 - 06:18:26 PST)
- Re: [AMBER] References of all force fields for citations case (Thu Feb 18 2010 - 06:21:33 PST)
[AMBER] amoeba--Too many dipole_dipole interactions for allocated Dian Jiao (Thu Feb 18 2010 - 08:25:45 PST)
- Re: [AMBER] amoeba--Too many dipole_dipole interactions for allocated case (Thu Feb 18 2010 - 08:43:51 PST)
  - Re: [AMBER] amoeba--Too many dipole_dipole interactions for allocated Dian Jiao (Thu Feb 18 2010 - 12:03:27 PST)
    - Re: [AMBER] amoeba--Too many dipole_dipole interactions for allocated case (Thu Feb 18 2010 - 14:49:03 PST)
[AMBER] mm-pbsa receptor and ligand masking Workalemhu Berhanu (Thu Feb 18 2010 - 13:26:03 PST)
- Re: [AMBER] mm-pbsa receptor and ligand masking Billy Miller III (Thu Feb 18 2010 - 13:32:58 PST)
- Re: [AMBER] mm-pbsa receptor and ligand masking Jason Swails (Thu Feb 18 2010 - 13:35:31 PST)
  - Re: [AMBER] mm-pbsa receptor and ligand masking Jio M (Fri Feb 19 2010 - 06:07:49 PST)
    - Re: [AMBER] mm-pbsa receptor and ligand masking Billy Miller III (Fri Feb 19 2010 - 06:32:24 PST)
    - Re: [AMBER] mm-pbsa receptor and ligand masking Jio M (Fri Feb 19 2010 - 07:52:54 PST)
- [AMBER] chamber - psf/pdb from VMD Balazs Jojart (Thu Feb 18 2010 - 13:45:18 PST)
  - Re: [AMBER] chamber - psf/pdb from VMD Mark Williamson (Thu Feb 18 2010 - 15:08:48 PST)
    - Re: [AMBER] chamber - psf/pdb from VMD Mark Williamson (Thu Feb 18 2010 - 18:12:14 PST)
    - Re: [AMBER] chamber - psf/pdb from VMD Balazs Jojart (Thu Feb 18 2010 - 23:27:48 PST)
    - Re: [AMBER] chamber - psf/pdb from VMD Alan (Fri Feb 19 2010 - 00:48:31 PST)
    - Re: [AMBER] chamber - psf/pdb from VMD Mark Williamson (Fri Feb 19 2010 - 10:41:08 PST)
- Re: [AMBER] mm-pbsa receptor and ligand masking Workalemhu Berhanu (Thu Feb 18 2010 - 15:38:41 PST)
  - Re: [AMBER] mm-pbsa receptor and ligand masking Jason Swails (Thu Feb 18 2010 - 16:17:42 PST)
[AMBER] Re: Antechamber: imidazole=aromatic, imidazolium=not aromatic? Gabriel Rocklin (Thu Feb 18 2010 - 15:21:27 PST)
- Re: [AMBER] Re: Antechamber: imidazole=aromatic, imidazolium=not aromatic? Alan (Fri Feb 19 2010 - 00:42:08 PST)
- Re: [AMBER] Re: Antechamber: imidazole=aromatic, imidazolium=not aromatic? Gabriel Rocklin (Fri Feb 19 2010 - 15:51:24 PST)
  - RE: [AMBER] Re: Antechamber: imidazole=aromatic, imidazolium=not aromatic? Niel Henriksen (Wed Feb 24 2010 - 17:42:36 PST)
[AMBER] pmemd.cuda progress Trevor Gokey (Thu Feb 18 2010 - 16:44:15 PST)
- RE: [AMBER] pmemd.cuda progress Ross Walker (Thu Feb 18 2010 - 18:51:51 PST)
[AMBER] TI calculation of absolute dG with restraint and energy decomposition Samuel Genheden (Fri Feb 19 2010 - 01:10:45 PST)
- Re: [AMBER] TI calculation of absolute dG with restraint and energy decomposition Hannes Kopitz (Fri Feb 19 2010 - 07:33:47 PST)
  - Re: [AMBER] TI calculation of absolute dG with restraint and energy decomposition Samuel Genheden (Sat Feb 20 2010 - 03:11:01 PST)
[AMBER] Question about transition from AMBER6 to AMBER9 坂庭　大輔 (Fri Feb 19 2010 - 02:19:27 PST)
- Re: [AMBER] Question about transition from AMBER6 to AMBER9 case (Sat Feb 20 2010 - 19:35:00 PST)
  - Re: [AMBER] Question about transition from AMBER6 to AMBER9 坂庭　大輔 (Sat Feb 27 2010 - 02:07:53 PST)
    - Re: [AMBER] Question about transition from AMBER6 to AMBER9 case (Sat Feb 27 2010 - 06:08:14 PST)
    - Re: [AMBER] Question about transition from AMBER6 to AMBER9 坂庭　大輔 (Sat Feb 27 2010 - 07:30:33 PST)
    - Re: [AMBER] Question about transition from AMBER6 to AMBER9 case (Sat Feb 27 2010 - 08:06:58 PST)
[AMBER] help on minimization bharat lakhani (Fri Feb 19 2010 - 05:44:18 PST)
[AMBER] help on minimization bharat lakhani (Fri Feb 19 2010 - 05:51:29 PST)
[AMBER] deriving charges for use with gaff Sidney Elmer (Fri Feb 19 2010 - 12:00:06 PST)
- Re: [AMBER] deriving charges for use with gaff FyD (Sat Feb 20 2010 - 05:39:30 PST)
[AMBER] are translations applied in the 'average' command of ptraj? Jose Borreguero (Fri Feb 19 2010 - 16:02:22 PST)
- Re: [AMBER] are translations applied in the 'average' command of ptraj? Thomas Cheatham (Sat Feb 20 2010 - 01:20:01 PST)
[AMBER] parmscan Peter Charles Kahuna (Fri Feb 19 2010 - 19:13:56 PST)
[AMBER] Amber 8 sander.f file, force.f file gokul algates (Fri Feb 19 2010 - 21:14:34 PST)
[AMBER] how to identify closest waters to protein surface? Jose Borreguero (Sat Feb 20 2010 - 15:47:54 PST)
- Re: [AMBER] how to identify closest waters to protein surface? Tom Joseph (Sat Feb 20 2010 - 16:01:24 PST)
  - Re: [AMBER] how to identify closest waters to protein surface? Jose Borreguero (Sat Feb 20 2010 - 16:24:40 PST)
[AMBER] enquire of NAB tutorial or any detailed introduction xueqin pang (Sun Feb 21 2010 - 06:41:08 PST)
- Re: [AMBER] enquire of NAB tutorial or any detailed introduction case (Sun Feb 21 2010 - 18:28:03 PST)
[AMBER] Perturbed charges and types s. Bill (Sun Feb 21 2010 - 08:01:14 PST)
- Re: [AMBER] Perturbed charges and types case (Mon Feb 22 2010 - 07:44:22 PST)
[AMBER] PARMSCAN Peter Charles Kahuna (Sun Feb 21 2010 - 18:38:14 PST)
- RE: [AMBER] PARMSCAN Ross Walker (Sun Feb 21 2010 - 19:50:25 PST)
[AMBER] MPICH2 and AMBER9 dxli75 (Mon Feb 22 2010 - 12:37:25 PST)
- Re: [AMBER] MPICH2 and AMBER9 Jason Swails (Mon Feb 22 2010 - 12:43:31 PST)
[AMBER] Protein Stability in amber mmpbsa tutorial MUHAMMAD IMTIA SHAFIQ (Mon Feb 22 2010 - 12:54:54 PST)
[AMBER] ptraj.MPI issue with "uninterruptible sleep" Trevor Gokey (Mon Feb 22 2010 - 16:04:28 PST)
- Re: [AMBER] ptraj.MPI issue with "uninterruptible sleep" Jason Swails (Mon Feb 22 2010 - 16:38:29 PST)
  - Re: [AMBER] ptraj.MPI issue with Trevor Gokey (Mon Feb 22 2010 - 17:11:25 PST)
- RE: [AMBER] ptraj.MPI issue with "uninterruptible sleep" Ross Walker (Mon Feb 22 2010 - 17:37:23 PST)
[AMBER] RDF analysis Shaikh Abdul R S Ramaju (Tue Feb 23 2010 - 00:05:58 PST)
- [AMBER] helicity of a peptide Mannan (Wed Feb 24 2010 - 00:56:41 PST)
  - Re: [AMBER] helicity of a peptide Carlos Simmerling (Wed Feb 24 2010 - 04:45:21 PST)
[AMBER] installation problem gunajyoti das (Tue Feb 23 2010 - 00:51:52 PST)
- Re: [AMBER] installation problem case (Tue Feb 23 2010 - 04:50:10 PST)
[AMBER] parallel test error Nicee (Tue Feb 23 2010 - 01:34:00 PST)
- Re: [AMBER] parallel test error Jason Swails (Tue Feb 23 2010 - 07:23:49 PST)
[AMBER] trouble with cooling down the system song_jianing_hi (Tue Feb 23 2010 - 02:43:39 PST)
- Re: [AMBER] trouble with cooling down the system Carlos Simmerling (Tue Feb 23 2010 - 03:10:16 PST)
[AMBER] AMBER MD simulation Nancy (Tue Feb 23 2010 - 02:56:50 PST)
[AMBER] trouble with cooling down a system Nancy (Tue Feb 23 2010 - 02:56:49 PST)
- Re: [AMBER] trouble with cooling down a system Carlos Simmerling (Tue Feb 23 2010 - 03:08:18 PST)
[AMBER] AmberTools1.3 installation error Anna Dejardin (Tue Feb 23 2010 - 03:23:54 PST)
- Re: [AMBER] AmberTools1.3 installation error case (Tue Feb 23 2010 - 05:01:37 PST)
  - Re: [AMBER] AmberTools1.3 installation error Atro Tossavainen (Tue Feb 23 2010 - 05:36:51 PST)
  - Re: [AMBER] AmberTools1.3 installation error Anna Dejardin (Tue Feb 23 2010 - 05:45:35 PST)
- Re: [AMBER] AmberTools1.3 installation error Bill Ross (Tue Feb 23 2010 - 10:06:01 PST)
  - Re: [AMBER] AmberTools1.3 installation error Anna Dejardin (Wed Feb 24 2010 - 02:38:26 PST)
    - Re: [AMBER] AmberTools1.3 installation error Jason Swails (Wed Feb 24 2010 - 09:30:40 PST)
- Re: [AMBER] AmberTools1.3 installation error Bill Ross (Wed Feb 24 2010 - 09:58:16 PST)
- Re: [AMBER] AmberTools1.3 installation error Bill Ross (Wed Feb 24 2010 - 10:18:52 PST)
  - Re: [AMBER] AmberTools1.3 installation error case (Wed Feb 24 2010 - 11:35:43 PST)
    - Re: [AMBER] AmberTools1.3 installation error Anna Dejardin (Wed Mar 03 2010 - 03:47:28 PST)
    - Re: [AMBER] AmberTools1.3 installation error case (Wed Mar 03 2010 - 05:21:05 PST)
    - Re: [AMBER] AmberTools1.3 installation error Anna Dejardin (Wed Mar 03 2010 - 06:20:09 PST)
    - Re: [AMBER] AmberTools1.3 installation error case (Wed Mar 03 2010 - 06:57:08 PST)
- Re: [AMBER] AmberTools1.3 installation error Bill Ross (Wed Mar 03 2010 - 10:02:21 PST)
  - Re: [AMBER] AmberTools1.3 installation error Anna Dejardin (Thu Mar 04 2010 - 02:43:54 PST)
[AMBER] use tleap through stdin Peter Schmidtke (Tue Feb 23 2010 - 09:41:04 PST)
- Re: [AMBER] use tleap through stdin case (Thu Feb 25 2010 - 06:31:16 PST)
  - Re: [AMBER] use tleap through stdin Peter Schmidtke (Thu Feb 25 2010 - 06:47:29 PST)
[AMBER] Charge protocol for OLP, HYP Emmanuel Baribefe Naziga (Tue Feb 23 2010 - 17:52:43 PST)
- Re: [AMBER] Charge protocol for OLP, HYP FyD (Wed Feb 24 2010 - 06:20:29 PST)
  - Re: [AMBER] Charge protocol for OLP, HYP Carlos Simmerling (Wed Feb 24 2010 - 06:28:17 PST)
    - Re: [AMBER] Charge protocol for OLP, HYP Lachele Foley (Lists) (Wed Feb 24 2010 - 06:59:36 PST)
    - Re: [AMBER] Charge protocol for OLP, HYP Emmanuel Baribefe Naziga (Wed Feb 24 2010 - 07:36:14 PST)
    - Re: [AMBER] Charge protocol for OLP, HYP Lachele Foley (Lists) (Thu Feb 25 2010 - 09:27:15 PST)
    - Re: [AMBER] Charge protocol for OLP, HYP Emmanuel Baribefe Naziga (Thu Feb 25 2010 - 09:33:32 PST)
    - Re: [AMBER] Charge protocol for OLP, HYP Lachele Foley (Lists) (Fri Feb 26 2010 - 07:56:44 PST)
    - Re: [AMBER] Charge protocol for OLP, HYP Emmanuel Baribefe Naziga (Fri Feb 26 2010 - 08:28:22 PST)
    - Re: [AMBER] Charge protocol for OLP, HYP Lachele Foley (Lists) (Fri Feb 26 2010 - 10:12:18 PST)
    - Re: [AMBER] Charge protocol for OLP, HYP FyD (Sat Feb 27 2010 - 09:10:22 PST)
    - Re: [AMBER] Charge protocol for OLP, HYP Emmanuel Baribefe Naziga (Sat Feb 27 2010 - 16:29:55 PST)
    - Re: [AMBER] Charge protocol for OLP, HYP FyD (Sat Feb 27 2010 - 23:24:44 PST)
    - Re: [AMBER] Charge protocol for OLP, HYP Lachele Foley (Lists) (Mon Mar 15 2010 - 08:39:31 PDT)
    - Re: [AMBER] Charge protocol for OLP, HYP Emmanuel Baribefe Naziga (Mon Mar 15 2010 - 08:53:20 PDT)
- Re: [AMBER] Charge protocol for OLP, HYP FyD (Sat Feb 27 2010 - 23:27:48 PST)
[AMBER] Final PDB after Energy minimization Shaandar Nyamtulga (Tue Feb 23 2010 - 19:03:15 PST)
- Re: [AMBER] Final PDB after Energy minimization Carlos Simmerling (Tue Feb 23 2010 - 19:39:15 PST)
  - [AMBER] How to unsolvate solvated protein? Shaandar Nyamtulga (Tue Feb 23 2010 - 21:17:21 PST)
Re: [AMBER] How to unsolvate solvated protein? Bill Ross (Tue Feb 23 2010 - 21:34:52 PST)
- Re: [AMBER] How to unsolvate solvated protein? Jason Swails (Tue Feb 23 2010 - 21:51:47 PST)
  - [AMBER] Simple question on EM Shaandar Nyamtulga (Wed Feb 24 2010 - 19:42:03 PST)
    - Re: [AMBER] Simple question on EM Jason Swails (Wed Feb 24 2010 - 20:06:40 PST)
    - [AMBER] Simple question on EM again Shaandar Nyamtulga (Wed Feb 24 2010 - 21:24:41 PST)
    - Re: [AMBER] Simple question on EM again Jason Swails (Wed Feb 24 2010 - 22:56:32 PST)
    - Re: [AMBER] Simple question on EM again MQO.Carlos Javier Nunez Aguero (Wed Feb 24 2010 - 23:12:01 PST)
    - Re: [AMBER] Simple question on EM again Carlos Simmerling (Thu Feb 25 2010 - 05:12:00 PST)
    - [AMBER] Simple question on EM again Shaandar Nyamtulga (Thu Feb 25 2010 - 19:00:39 PST)
    - Re: [AMBER] Simple question on EM again Jason Swails (Thu Feb 25 2010 - 19:54:45 PST)
    - Re: [AMBER] Simple question on EM again Bill Ross (Thu Feb 25 2010 - 20:21:46 PST)
    - Re: [AMBER] Simple question on EM again Jason Swails (Thu Feb 25 2010 - 20:31:30 PST)
    - Re: [AMBER] Simple question on EM again MQO.Carlos Javier Nunez Aguero (Thu Feb 25 2010 - 22:17:00 PST)
    - [AMBER] Amber, CASP Shaandar Nyamtulga (Wed Mar 03 2010 - 18:48:55 PST)
    - Re: [AMBER] Amber, CASP Carlos Simmerling (Wed Mar 03 2010 - 18:52:31 PST)
    - Re: [AMBER] Amber, CASP case (Wed Mar 03 2010 - 19:23:26 PST)
    - [AMBER] Amber, CASP again Shaandar Nyamtulga (Thu Mar 04 2010 - 00:52:20 PST)
    - Re: [AMBER] Amber, CASP again Carlos Simmerling (Thu Mar 04 2010 - 04:25:19 PST)
    - Re: [AMBER] Amber, CASP again Imtiaz Shafiq (Thu Mar 04 2010 - 04:36:29 PST)
[AMBER] Question on applying restraints in absolute dG calculations with TI in Amber 10 Samuel Genheden (Wed Feb 24 2010 - 01:03:21 PST)
- Re: [AMBER] Question on applying restraints in absolute dG calculations with TI in Amber 10 steinbrt.rci.rutgers.edu (Wed Feb 24 2010 - 03:52:30 PST)
  - Re: [AMBER] Question on applying restraints in absolute dG calculations with TI in Amber 10 Samuel Genheden (Wed Feb 24 2010 - 04:19:08 PST)
    - Re: [AMBER] Question on applying restraints in absolute dG calculations with TI in Amber 10 steinbrt.rci.rutgers.edu (Wed Feb 24 2010 - 07:52:36 PST)
    - Re: [AMBER] Question on applying restraints in absolute dG calculations with TI in Amber 10 Samuel Genheden (Wed Feb 24 2010 - 10:55:19 PST)
    - Re: [AMBER] Question on applying restraints in absolute dG calculations with TI in Amber 10 steinbrt.rci.rutgers.edu (Thu Feb 25 2010 - 02:15:13 PST)
[AMBER] GUI Competition Matthew Tessier (Wed Feb 24 2010 - 06:18:20 PST)
- Re: [AMBER] GUI Competition case (Wed Feb 24 2010 - 07:53:15 PST)
- Re: [AMBER] GUI Competition Vlad (Wed Feb 24 2010 - 15:21:52 PST)
[AMBER] design of peptides to stabilize proteins Simon Becker (Wed Feb 24 2010 - 06:55:24 PST)
- Re: [AMBER] design of peptides to stabilize proteins Jason Swails (Wed Feb 24 2010 - 09:27:47 PST)
[AMBER] trajectory alignment to a reference frame Oliver Kuhn (Wed Feb 24 2010 - 07:17:39 PST)
- Re: [AMBER] trajectory alignment to a reference frame Thomas Cheatham III (Thu Feb 25 2010 - 12:39:13 PST)
  - [AMBER] trajectory momentum for a substructure Taufik Al-Sarraj (Mon Mar 08 2010 - 10:20:01 PST)
[AMBER] Sander jac benchmark segfaults with non-power of two processors Manjunath Sripadarao (Wed Feb 24 2010 - 23:05:52 PST)
- RE: [AMBER] Sander jac benchmark segfaults with non-power of two processors Ross Walker (Thu Feb 25 2010 - 09:55:37 PST)
[AMBER] Query about xmin gunajyoti das (Wed Feb 24 2010 - 23:58:14 PST)
- Re: [AMBER] Query about xmin case (Thu Feb 25 2010 - 05:33:33 PST)
[AMBER] Problem in MM-PBSA Hyma vathi (Thu Feb 25 2010 - 01:54:48 PST)
- Re: [AMBER] Problem in MM-PBSA Jason Swails (Thu Feb 25 2010 - 08:08:34 PST)
[AMBER] Query about LMOD gunajyoti das (Thu Feb 25 2010 - 03:53:31 PST)
[AMBER] ptraj, imaging for NAMD generated dcd files, Error in tokenize Monika Sharma (Thu Feb 25 2010 - 04:20:16 PST)
- [AMBER] ptraj, imaging for NAMD generated dcd files, Error in tokenize Monika Sharma (Thu Feb 25 2010 - 04:24:20 PST)
  - Re: [AMBER] ptraj, imaging for NAMD generated dcd files, Error in tokenize Hannes Loeffler (Thu Feb 25 2010 - 04:55:08 PST)
    - Re: [AMBER] ptraj, imaging for NAMD generated dcd files, Error in tokenize Monika Sharma (Thu Feb 25 2010 - 05:02:53 PST)
[AMBER] Not runing the Nmode! Aurum Bai (Thu Feb 25 2010 - 07:02:18 PST)
- Re: [AMBER] Not runing the Nmode! Billy Miller III (Thu Feb 25 2010 - 07:52:25 PST)
[AMBER] serial compilation of pmemd bbalta.itu.edu.tr (Thu Feb 25 2010 - 07:45:00 PST)
- Re: [AMBER] serial compilation of pmemd case (Thu Feb 25 2010 - 08:16:59 PST)
  - Re: [AMBER] serial compilation of pmemd bbalta.itu.edu.tr (Mon Mar 22 2010 - 06:51:02 PDT)
  - [AMBER] replica exchange with GPU bbalta.itu.edu.tr (Fri Feb 28 2020 - 04:14:59 PST)
    - Re: [AMBER] replica exchange with GPU Carlos Simmerling (Fri Feb 28 2020 - 04:22:05 PST)
    - Re: [AMBER] replica exchange with GPU bbalta.itu.edu.tr (Mon Mar 02 2020 - 01:21:20 PST)
    - Re: [AMBER] replica exchange with GPU Alessandro Contini (Mon Mar 02 2020 - 02:43:16 PST)
    - Re: [AMBER] replica exchange with GPU Cruzeiro,Vinicius Wilian D (Mon Mar 02 2020 - 08:45:44 PST)
[AMBER] NMR complex and vlimit exceeded Michael Durney (Thu Feb 25 2010 - 08:00:50 PST)
- Re: [AMBER] NMR complex and vlimit exceeded Carlos Simmerling (Thu Feb 25 2010 - 13:46:29 PST)
[AMBER] Re: SOS: make CYX bond using xleap Jason Swails (Thu Feb 25 2010 - 18:34:53 PST)
[AMBER] Periodic Boundary in AMBER(PMEMD) GPU Acceleration support ? Hiromasa WATANABE (Thu Feb 25 2010 - 19:05:41 PST)
- RE: [AMBER] Periodic Boundary in AMBER(PMEMD) GPU Acceleration support ? Ross Walker (Thu Feb 25 2010 - 22:22:09 PST)
  - Re: [AMBER] Periodic Boundary in AMBER(PMEMD) GPU Acceleration support ? Hiromasa WATANABE (Thu Feb 25 2010 - 22:40:26 PST)
    - RE: [AMBER] Periodic Boundary in AMBER(PMEMD) GPU Acceleration support ? ZhaoLei (Fri Feb 26 2010 - 19:57:59 PST)
    - RE: [AMBER] Periodic Boundary in AMBER(PMEMD) GPU Acceleration support ? Ross Walker (Fri Feb 26 2010 - 21:40:56 PST)
    - Re: [AMBER] Periodic Boundary in AMBER(PMEMD) GPU Acceleration support ? jacky zhao (Sat Feb 27 2010 - 00:42:45 PST)
[AMBER] swiss cheese water shell Mark M Huntress (Fri Feb 26 2010 - 21:40:25 PST)
- Re: [AMBER] swiss cheese water shell Barbault Florent (Sat Feb 27 2010 - 03:48:29 PST)
  - RE: [AMBER] swiss cheese water shell Mark M Huntress (Sat Feb 27 2010 - 13:46:07 PST)
    - RE: [AMBER] swiss cheese water shell Ross Walker (Sat Feb 27 2010 - 14:03:20 PST)
- Re: [AMBER] swiss cheese water shell Nicholas Musolino (Sat Feb 27 2010 - 06:08:54 PST)
  - Re: [AMBER] swiss cheese water shell Peter Schmidtke (Sat Feb 27 2010 - 12:34:11 PST)
[AMBER] msd calculation using ptraj diffusion Monika Sharma (Fri Feb 26 2010 - 22:05:39 PST)
- RE: [AMBER] msd calculation using ptraj diffusion hannes.loeffler.stfc.ac.uk (Sat Feb 27 2010 - 01:22:20 PST)
  - Re: [AMBER] msd calculation using ptraj diffusion Monika Sharma (Sat Feb 27 2010 - 01:30:09 PST)
- RE: [AMBER] msd calculation using ptraj diffusion hannes.loeffler.stfc.ac.uk (Sat Feb 27 2010 - 05:18:59 PST)
[AMBER] xmin_verbosity gunajyoti das (Sat Feb 27 2010 - 05:40:59 PST)
- Re: [AMBER] xmin_verbosity case (Sat Feb 27 2010 - 06:16:25 PST)
[AMBER] Installation error of amber10 after compile Ambertools1.3 albert albert (Sat Feb 27 2010 - 12:37:51 PST)
- Re: [AMBER] Installation error of amber10 after compile Ambertools1.3 Jason Swails (Sat Feb 27 2010 - 12:46:48 PST)
  - Re: [AMBER] Installation error of amber10 after compile Ambertools1.3 Trevor Gokey (Sun Feb 28 2010 - 00:35:08 PST)
    - Re: [AMBER] Installation error of amber10 after compile Ambertools1.3 Jason Swails (Sun Feb 28 2010 - 09:07:11 PST)
  - Re: [AMBER] Installation error of amber10 after compile Ambertools1.3 albert albert (Mon Mar 01 2010 - 03:43:31 PST)
[AMBER] Instaltion parallel amber on macbook pro Christine Baranski (Sun Feb 28 2010 - 04:15:00 PST)
- Re: [AMBER] Instaltion parallel amber on macbook pro Jason Swails (Sun Feb 28 2010 - 09:01:51 PST)
  - [AMBER] Problem with translate restrt file Ivan Gladich (Sun Feb 28 2010 - 11:00:06 PST)
    - Re: [AMBER] Problem with translate restrt file Jason Swails (Sun Feb 28 2010 - 11:07:53 PST)
    - Re: [AMBER] Problem with translate restrt file Ivan Gladich (Sun Feb 28 2010 - 14:17:45 PST)
    - Re: [AMBER] Problem with translate restrt file Jason Swails (Sun Feb 28 2010 - 16:32:12 PST)
    - Re: [AMBER] Problem with translate restrt file Ivan Gladich (Mon Mar 01 2010 - 10:00:06 PST)
    - Re: [AMBER] Problem with translate restrt file Jason Swails (Mon Mar 01 2010 - 10:24:28 PST)
    - Re: [AMBER] Problem with translate restrt file Ivan Gladich (Mon Mar 01 2010 - 11:47:18 PST)
[AMBER] Protein + Bilayer Simulations: Role of salt Lalit Dubey (Sun Feb 28 2010 - 13:32:05 PST)
- Re: [AMBER] Protein + Bilayer Simulations: Role of salt Barbault Florent (Sun Feb 28 2010 - 14:16:07 PST)
  - Re: [AMBER] Protein + Bilayer Simulations: Role of salt Lalit Dubey (Sun Feb 28 2010 - 15:35:05 PST)
    - Re: [AMBER] Protein + Bilayer Simulations: Role of salt Jason Swails (Sun Feb 28 2010 - 16:40:37 PST)
    - Re: [AMBER] Protein + Bilayer Simulations: Role of salt Lalit Dubey (Mon Mar 01 2010 - 06:43:48 PST)
[AMBER] MMPBSA problems with Fe and Zn Cristina Sisu (Mon Mar 01 2010 - 03:53:11 PST)
- Re: [AMBER] MMPBSA problems with Fe and Zn mattia (Mon Mar 01 2010 - 04:00:56 PST)
  - Re: [AMBER] MMPBSA problems with Fe and Zn Jason Swails (Mon Mar 01 2010 - 06:07:53 PST)
    - Re: [AMBER] MMPBSA problems with Fe and Zn Cristina Sisu (Mon Mar 01 2010 - 08:04:05 PST)
    - Re: [AMBER] MMPBSA problems with Fe and Zn Dwight McGee (Mon Mar 01 2010 - 08:14:43 PST)
    - Re: [AMBER] MMPBSA problems with Fe and Zn Billy Miller III (Mon Mar 01 2010 - 08:21:30 PST)
    - Re: [AMBER] MMPBSA problems with Fe and Zn Cristina Sisu (Mon Mar 01 2010 - 09:05:23 PST)
    - Re: [AMBER] MMPBSA problems with Fe and Zn Billy Miller III (Mon Mar 01 2010 - 09:11:01 PST)
    - Re: [AMBER] MMPBSA problems with Fe and Zn Billy Miller III (Mon Mar 01 2010 - 09:18:32 PST)
    - Re: [AMBER] MMPBSA problems with Fe and Zn Cristina Sisu (Mon Mar 01 2010 - 09:20:28 PST)
Re: [AMBER] swiss cheese water shell Bill Ross (Mon Mar 01 2010 - 09:26:30 PST)
Re: [OFFLIST] Re: [AMBER] Protein + Bilayer Simulations: Role of salt Lalit Dubey (Mon Mar 01 2010 - 12:28:57 PST)
- Re: [OFFLIST] Re: [AMBER] Protein + Bilayer Simulations: Role of salt Balazs Jojart (Tue Mar 02 2010 - 23:32:50 PST)
[AMBER] PBC interactions Ganesh Krishnan (Mon Mar 01 2010 - 13:51:14 PST)
- Re: [AMBER] PBC interactions Jason Swails (Mon Mar 01 2010 - 17:37:15 PST)
  - Re: [AMBER] PBC interactions Markus Kaukonen (Mon Mar 01 2010 - 23:35:19 PST)
[AMBER] OMe fragment Lekpa Duukori (Mon Mar 01 2010 - 14:37:55 PST)
- Re: [AMBER] OMe fragment Jason Swails (Mon Mar 01 2010 - 17:55:45 PST)
  - Re: [AMBER] OMe fragment Jason Swails (Mon Mar 01 2010 - 18:02:44 PST)
    - Re: [AMBER] OMe fragment Lekpa Duukori (Mon Mar 01 2010 - 18:08:55 PST)
    - Re: [AMBER] OMe fragment Lachele Foley (Lists) (Mon Mar 01 2010 - 18:27:53 PST)
    - Re: [AMBER] OMe fragment Jason Swails (Mon Mar 01 2010 - 19:07:10 PST)
- Re: [AMBER] OMe fragment FyD (Tue Mar 02 2010 - 02:29:06 PST)
  - Re: [AMBER] OMe fragment Lekpa Duukori (Tue Mar 02 2010 - 07:03:43 PST)
    - Re: [AMBER] OMe fragment Lekpa Duukori (Tue Mar 02 2010 - 18:40:01 PST)
    - Re: [AMBER] OMe fragment FyD (Tue Mar 02 2010 - 20:44:00 PST)
    - Re: [AMBER] OMe fragment Lekpa Duukori (Tue Mar 02 2010 - 21:02:47 PST)
    - Re: [AMBER] OMe fragment FyD (Tue Mar 02 2010 - 21:58:23 PST)
    - [AMBER] Parameters for trimethylated Lysine? Mannan (Wed Mar 03 2010 - 02:14:03 PST)
    - Re: [AMBER] Parameters for trimethylated Lysine? Carlos Simmerling (Wed Mar 03 2010 - 03:35:23 PST)
    - Re: [AMBER] OMe fragment Lekpa Duukori (Wed Mar 03 2010 - 10:26:09 PST)
    - Re: [AMBER] OMe fragment FyD (Wed Mar 03 2010 - 12:51:02 PST)
    - Re: [AMBER] OMe fragment Lekpa Duukori (Wed Mar 03 2010 - 13:48:09 PST)
[AMBER] Cyclic compounds John S (Mon Mar 01 2010 - 20:50:35 PST)
- Re: [AMBER] Cyclic compounds Jason Swails (Mon Mar 01 2010 - 21:24:08 PST)
  - Re: [AMBER] Cyclic compounds John S (Tue Mar 02 2010 - 10:39:50 PST)
    - Re: [AMBER] Cyclic compounds Jason Swails (Tue Mar 02 2010 - 10:50:53 PST)
- Re: [AMBER] Cyclic compounds Bill Ross (Tue Mar 02 2010 - 10:46:32 PST)
[AMBER] CITATION PROBLEM ABOUT i-APBS Rilei Yu (Tue Mar 02 2010 - 04:12:55 PST)
- Re: [AMBER] CITATION PROBLEM ABOUT i-APBS Robert Konecny (Tue Mar 02 2010 - 11:08:29 PST)
[AMBER] parameter file for modified nucleosides (O6-methyl guanine) N.R. Jena (Tue Mar 02 2010 - 04:24:59 PST)
- [AMBER] parameter file for modified nucleosides (O6-methyl guanine) N.R. Jena (Tue Mar 02 2010 - 04:53:39 PST)
  - Re: [AMBER] parameter file for modified nucleosides (O6-methyl guanine) Bill Ross (Tue Mar 02 2010 - 10:20:12 PST)
    - Re: [AMBER] parameter file for modified nucleosides (O6-methyl guanine) N.R. Jena (Tue Mar 02 2010 - 20:20:21 PST)
  - Re: [AMBER] parameter file for modified nucleosides (O6-methyl guanine) Bill Ross (Wed Mar 03 2010 - 09:41:36 PST)
    - Re: [AMBER] parameter file for modified nucleosides (O6-methyl guanine) N.R. Jena (Mon Mar 08 2010 - 23:04:22 PST)
  - Re: [AMBER] parameter file for modified nucleosides (O6-methyl guanine) Bill Ross (Tue Mar 09 2010 - 10:07:41 PST)
- Re: [AMBER] parameter file for modified nucleosides (O6-methyl guanine) case (Tue Mar 02 2010 - 05:11:16 PST)
  - Re: [AMBER] parameter file for modified nucleosides (O6-methyl guanine) N.R. Jena (Tue Mar 02 2010 - 08:59:38 PST)
    - Re: [AMBER] parameter file for modified nucleosides (O6-methyl guanine) Jason Swails (Tue Mar 02 2010 - 09:37:19 PST)
    - Re: [AMBER] parameter file for modified nucleosides (O6-methyl guanine) N.R. Jena (Thu Mar 04 2010 - 02:40:13 PST)
- [AMBER] AMBER10 installation: make test error 1 Anna Dejardin (Fri Mar 05 2010 - 06:30:37 PST)
  - Re: [AMBER] AMBER10 installation: make test error 1 Jason Swails (Fri Mar 05 2010 - 16:11:40 PST)
    - Re: [AMBER] AMBER10 installation: make test error 1 Anna Dejardin (Wed Mar 31 2010 - 08:09:00 PDT)
    - Re: [AMBER] AMBER10 installation: make test error 1 case (Wed Mar 31 2010 - 10:56:33 PDT)
    - Re: [AMBER] AMBER10 installation: make test error 1 Anna Dejardin (Wed Apr 07 2010 - 02:47:39 PDT)
  - Re: [AMBER] AMBER10 installation: make test error 1 Bill Ross (Fri Mar 05 2010 - 16:17:11 PST)
[AMBER] RMSF calculation is correct ? Sarra Geranil (Tue Mar 02 2010 - 09:35:07 PST)
[AMBER] Vdw radii params in antechamber Denny Bromley (Tue Mar 02 2010 - 21:08:11 PST)
- Re: [AMBER] Vdw radii params in antechamber Jason Swails (Tue Mar 02 2010 - 21:40:17 PST)
  - RE: [AMBER] Vdw radii params in antechamber Denny Bromley (Wed Mar 03 2010 - 10:00:55 PST)
    - Re: [AMBER] Vdw radii params in antechamber Jason Swails (Wed Mar 03 2010 - 11:53:26 PST)
    - RE: [AMBER] Vdw radii params in antechamber Denny Bromley (Wed Mar 03 2010 - 12:58:00 PST)
  - Re: [AMBER] Vdw radii params in antechamber Dian Jiao (Wed Mar 03 2010 - 10:17:42 PST)
    - Re: [AMBER] Vdw radii params in antechamber Thomas Cheatham (Wed Mar 03 2010 - 11:55:39 PST)
- Re: [AMBER] Vdw radii params in antechamber Bill Ross (Wed Mar 03 2010 - 11:32:20 PST)
[AMBER] Enquiry regarding MD run bharat lakhani (Tue Mar 02 2010 - 21:42:10 PST)
- Re: [AMBER] Enquiry regarding MD run Jason Swails (Tue Mar 02 2010 - 22:04:23 PST)
[AMBER] Regarding energy in mdout file in SANDER aneesh cna (Wed Mar 03 2010 - 02:19:33 PST)
- Re: [AMBER] Regarding energy in mdout file in SANDER Carlos Simmerling (Wed Mar 03 2010 - 03:34:54 PST)
[AMBER] atom-type cz ??? Barbault Florent (Wed Mar 03 2010 - 05:30:59 PST)
- Re: [AMBER] atom-type cz ??? case (Wed Mar 03 2010 - 07:26:18 PST)
  - Re: [AMBER] atom-type cz ??? Barbault Florent (Wed Mar 03 2010 - 07:59:58 PST)
    - Re: [AMBER] atom-type cz ??? case (Wed Mar 03 2010 - 18:56:47 PST)
    - Re: [AMBER] atom-type cz ??? M. Shahid (Thu Jul 08 2010 - 06:43:39 PDT)
    - Re: [AMBER] atom-type cz ??? David A. Case (Thu Jul 08 2010 - 13:06:23 PDT)
    - Re: [AMBER] atom-type cz ??? Jason Swails (Thu Jul 08 2010 - 13:13:32 PDT)
    - Re: [AMBER] atom-type cz ??? M. Shahid (Thu Jul 08 2010 - 15:02:31 PDT)
    - Re: [AMBER] atom-type cz ??? Jason Swails (Thu Jul 08 2010 - 15:25:56 PDT)
    - Re: [AMBER] atom-type cz ??? case (Fri Jul 09 2010 - 05:20:46 PDT)
[AMBER] Segmentation fault Asfa Ali (Wed Mar 03 2010 - 07:20:28 PST)
[AMBER] force field parameters for isopropanol Ganesh Kamath (Wed Mar 03 2010 - 07:27:13 PST)
- Re: [AMBER] force field parameters for isopropanol Karl Kirschner (Thu Mar 04 2010 - 00:36:16 PST)
Re: [AMBER] Enquiry regarding MD run Bill Ross (Wed Mar 03 2010 - 09:47:21 PST)
Re: [AMBER] Segmentation fault Bill Ross (Wed Mar 03 2010 - 10:11:02 PST)
[AMBER] neb/amber 10 Guillermina Estiu (Wed Mar 03 2010 - 11:12:05 PST)
- Re: [AMBER] neb/amber 10 Carlos Simmerling (Wed Mar 03 2010 - 12:57:13 PST)
- Re: [AMBER] neb/amber 10 Carlos Simmerling (Sat Mar 13 2010 - 05:21:55 PST)
  - Re: [AMBER] neb/amber 10 Carlos Simmerling (Fri Mar 26 2010 - 08:13:14 PDT)
[AMBER] Generating cpin file for constant pH in Amber9 Jamie Romnes (Wed Mar 03 2010 - 11:11:41 PST)
- Re: [AMBER] Generating cpin file for constant pH in Amber9 Jason Swails (Wed Mar 03 2010 - 11:30:36 PST)
  - Re: [AMBER] Generating cpin file for constant pH in Amber9 Jamie Romnes (Wed Mar 03 2010 - 11:41:09 PST)
- Re: [AMBER] Generating cpin file for constant pH in Amber9 Bill Ross (Wed Mar 03 2010 - 11:47:12 PST)
  - Re: [AMBER] Generating cpin file for constant pH in Amber9 Jason Swails (Wed Mar 03 2010 - 11:52:18 PST)
    - Re: [AMBER] Generating cpin file for constant pH in Amber9 Jamie Romnes (Wed Mar 03 2010 - 12:39:05 PST)
[AMBER] The error information zhihong ke (Wed Mar 03 2010 - 17:38:08 PST)
Re: [AMBER] The error information Bill Ross (Wed Mar 03 2010 - 17:47:04 PST)
[AMBER] AMBER Asfa Ali (Thu Mar 04 2010 - 01:16:31 PST)
- Re: [AMBER] AMBER Imtiaz Shafiq (Thu Mar 04 2010 - 02:09:56 PST)
  - Re: [AMBER] AMBER Asfa Ali (Thu Mar 04 2010 - 21:24:15 PST)
    - Re: [AMBER] AMBER case (Fri Mar 05 2010 - 04:50:47 PST)
- Re: [AMBER] Amber 姜笑楠 (Mon Apr 25 2011 - 04:57:19 PDT)
[AMBER] _getcor.f Fortran runtime error: End of file sikander azam (Thu Mar 04 2010 - 02:26:49 PST)
[AMBER] Errors while running Amber Nkwe Monama (Thu Mar 04 2010 - 03:05:10 PST)
- Re: [AMBER] Errors while running Amber Carlos Simmerling (Thu Mar 04 2010 - 04:22:59 PST)
- Re: [AMBER] Errors while running Amber Nkwe Monama (Thu Mar 04 2010 - 04:56:52 PST)
  - Re: [AMBER] Errors while running Amber Carlos Simmerling (Thu Mar 04 2010 - 05:00:50 PST)
- Re: [AMBER] Errors while running Amber Nkwe Monama (Thu Mar 04 2010 - 05:17:50 PST)
  - Re: [AMBER] Errors while running Amber Carlos Simmerling (Thu Mar 04 2010 - 05:24:59 PST)
- Re: [AMBER] Errors while running Amber Nkwe Monama (Fri Mar 05 2010 - 01:17:03 PST)
  - Re: [AMBER] Errors while running Amber Robert Duke (Fri Mar 05 2010 - 05:37:00 PST)
    - [AMBER] savePdb in leap Peter Schmidtke (Fri Mar 05 2010 - 05:47:34 PST)
    - Re: [AMBER] savePdb in leap Jason Swails (Fri Mar 05 2010 - 15:58:50 PST)
    - Re: [AMBER] savePdb in leap case (Sat Mar 06 2010 - 07:15:41 PST)
- Re: [AMBER] Errors while running Amber Nkwe Monama (Fri Mar 05 2010 - 06:46:59 PST)
  - RE: [AMBER] Errors while running Amber Ross Walker (Fri Mar 05 2010 - 08:51:32 PST)
[AMBER] Please help me out bharat lakhani (Thu Mar 04 2010 - 03:23:35 PST)
[AMBER] PARMSCAN Peter Charles Kahuna (Thu Mar 04 2010 - 05:39:13 PST)
[AMBER] sleap help InSuk Joung (Thu Mar 04 2010 - 13:55:15 PST)
[AMBER] electric fields Ganesh Kamath (Thu Mar 04 2010 - 14:44:04 PST)
[AMBER] Protein Crystal Buried Waters and Amber Simulation ? Christine Baranski (Thu Mar 04 2010 - 16:04:16 PST)
Re: [AMBER] Protein Crystal Buried Waters and Amber Simulation ? Bill Ross (Thu Mar 04 2010 - 16:14:07 PST)
[AMBER] _getcor.f Fortran runtime error: End of file sikander azam (Fri Mar 05 2010 - 00:25:58 PST)
- Re: [AMBER] _getcor.f Fortran runtime error: End of file Syed Tarique Moin (Fri Mar 05 2010 - 02:44:42 PST)
- Re: [AMBER] _getcor.f Fortran runtime error: End of file Bill Ross (Fri Mar 05 2010 - 09:30:18 PST)
  - Re: [AMBER] _getcor.f Fortran runtime error: End of file Jason Swails (Fri Mar 05 2010 - 16:19:26 PST)
[AMBER] Query on Minimization bharat lakhani (Fri Mar 05 2010 - 00:41:36 PST)
Re: [AMBER] Query on Minimization Bill Ross (Fri Mar 05 2010 - 09:26:28 PST)
[AMBER] Quantifying Errors in PBSA D.J. Cole (Fri Mar 05 2010 - 11:47:45 PST)
[AMBER] residual dipolar couplings (RDC) Danny Xu (Fri Mar 05 2010 - 14:51:00 PST)
- Re: [AMBER] residual dipolar couplings (RDC) Carlos Simmerling (Fri Mar 05 2010 - 15:21:18 PST)
- Re: [AMBER] residual dipolar couplings (RDC) case (Sat Mar 06 2010 - 06:41:09 PST)
[AMBER] CPU Load for Amber Running In Parallel Imtiaz Shafiq (Fri Mar 05 2010 - 19:37:27 PST)
- RE: [AMBER] CPU Load for Amber Running In Parallel Ross Walker (Fri Mar 05 2010 - 20:47:27 PST)
[AMBER] error - during minimization in AMBER10 kureeckal ramesh (Fri Mar 05 2010 - 19:54:13 PST)
- Re: [AMBER] error - during minimization in AMBER10 Imtiaz Shafiq (Fri Mar 05 2010 - 20:06:13 PST)
  - Re: [AMBER] error - during minimization in AMBER10 Jason Swails (Fri Mar 05 2010 - 20:39:21 PST)
- Re: [AMBER] error - during minimization in AMBER10 Jason Swails (Fri Mar 05 2010 - 20:45:12 PST)
[AMBER] sander bomb: volume of ucell too big Nancy (Fri Mar 05 2010 - 23:25:35 PST)
- Re: [AMBER] sander bomb: volume of ucell too big case (Sat Mar 06 2010 - 06:50:56 PST)
  - Re:Re: [AMBER] sander bomb: volume of ucell too big Nancy (Sat Mar 06 2010 - 23:13:43 PST)
  - Re:Re: [AMBER] sander bomb: volume of ucell too big Bill Ross (Mon Mar 08 2010 - 09:26:02 PST)
[AMBER] combining coordinate and velocity files into one Amire-Brahimi Benjamin (Sun Mar 07 2010 - 13:42:57 PST)
- Re: [AMBER] combining coordinate and velocity files into one Jason Swails (Sun Mar 07 2010 - 14:48:23 PST)
- Re: [AMBER] combining coordinate and velocity files into one Amire-Brahimi Benjamin (Tue Mar 09 2010 - 15:02:06 PST)
  - Re: [AMBER] combining coordinate and velocity files into one Jason Swails (Tue Mar 09 2010 - 15:15:31 PST)
- Re: [AMBER] combining coordinate and velocity files into one Bill Ross (Tue Mar 09 2010 - 15:39:37 PST)
[AMBER] Protein, Water and Amber Imtiaz Shafiq (Sun Mar 07 2010 - 15:15:40 PST)
- Re: [AMBER] Protein, Water and Amber steinbrt.rci.rutgers.edu (Mon Mar 08 2010 - 00:54:59 PST)
[AMBER] Distortions Asfa Ali (Mon Mar 08 2010 - 01:22:26 PST)
- [AMBER] Distortions Asfa Ali (Tue Mar 09 2010 - 05:03:08 PST)
  - Re: [AMBER] Distortions Carlos Simmerling (Tue Mar 09 2010 - 06:01:14 PST)
[AMBER] Error decoding variable Fernando Martín García (Mon Mar 08 2010 - 03:34:55 PST)
- Re: [AMBER] Error decoding variable case (Thu Mar 11 2010 - 07:56:53 PST)
[AMBER] problem with bugfix.all for amber10 Philipp Marquetand (Mon Mar 08 2010 - 04:43:47 PST)
- Re: [AMBER] problem with bugfix.all for amber10 case (Mon Mar 08 2010 - 07:11:49 PST)
[AMBER] Amber 10 and bugfix.all Dr. Lars Packschies (Mon Mar 08 2010 - 04:52:50 PST)
- Re: [AMBER] Amber 10 and bugfix.all Philipp Marquetand (Mon Mar 08 2010 - 05:23:36 PST)
  - Re: [AMBER] Amber 10 and bugfix.all Lars Packschies (Mon Mar 08 2010 - 08:04:11 PST)
[AMBER] Removed proton in proteins Francesca Cantini (Mon Mar 08 2010 - 06:32:04 PST)
- Re: [AMBER] Removed proton in proteins case (Mon Mar 08 2010 - 07:25:20 PST)
[AMBER] MMPBSA err! Aurum Bai (Mon Mar 08 2010 - 06:30:06 PST)
- Re: [AMBER] MMPBSA err! Dwight McGee (Mon Mar 08 2010 - 10:29:19 PST)
[AMBER] Xleap : Improper torsions applied Sushil Mishra (Mon Mar 08 2010 - 06:55:26 PST)
- [AMBER] Fwd: Xleap : Improper torsions applied Sushil Mishra (Mon Mar 08 2010 - 08:32:44 PST)
[AMBER] minimization residues around the ligand Rilei Yu (Mon Mar 08 2010 - 17:56:21 PST)
[AMBER] Enquiry regarding MD run Pallavi Mohanty (Mon Mar 08 2010 - 20:42:32 PST)
- Re: [AMBER] Enquiry regarding MD run Carlos Simmerling (Tue Mar 09 2010 - 03:31:00 PST)
  - Re: [AMBER] Enquiry regarding MD run Pallavi Mohanty (Wed Mar 10 2010 - 02:11:51 PST)
    - Re: [AMBER] Enquiry regarding MD run Carlos Simmerling (Wed Mar 10 2010 - 03:36:07 PST)
    - Re: [AMBER] Enquiry regarding MD run Pallavi Mohanty (Wed Mar 10 2010 - 06:02:21 PST)
    - Re: [AMBER] Enquiry regarding MD run Carlos Simmerling (Wed Mar 10 2010 - 06:06:30 PST)
[AMBER] ATP force field deepti nayar (Mon Mar 08 2010 - 23:14:53 PST)
- Re: [AMBER] ATP force field aneesh cna (Tue Mar 09 2010 - 01:11:36 PST)
[AMBER] question about AMBER 9 Chinh Su Tran To (Tue Mar 09 2010 - 02:06:18 PST)
- Re: [AMBER] question about AMBER 9 Carlos Simmerling (Tue Mar 09 2010 - 03:30:06 PST)
[AMBER] Various Errors in Tests Philipp Marquetand (Tue Mar 09 2010 - 02:45:28 PST)
- Re: [AMBER] Various Errors in Tests Philipp Marquetand (Tue Mar 09 2010 - 02:52:24 PST)
- Re: [AMBER] Various Errors in Tests case (Tue Mar 09 2010 - 05:42:28 PST)
  - Re: [AMBER] Various Errors in Tests Philipp Marquetand (Fri Mar 12 2010 - 03:19:08 PST)
    - Re: [AMBER] Various Errors in Tests case (Fri Mar 12 2010 - 04:56:39 PST)
[AMBER] regarding compiling amber10 jani vinod (Tue Mar 09 2010 - 03:54:50 PST)
- Re: [AMBER] regarding compiling amber10 Jason Swails (Tue Mar 09 2010 - 07:07:15 PST)
[AMBER] CIS proline Francesca Cantini (Tue Mar 09 2010 - 04:31:08 PST)
- Re: [AMBER] CIS proline Carlos Simmerling (Tue Mar 09 2010 - 04:46:35 PST)
[AMBER] chamber error message Hannes Loeffler (Tue Mar 09 2010 - 05:46:00 PST)
- Re: [AMBER] chamber error message Mark Williamson (Tue Mar 09 2010 - 13:10:09 PST)
[AMBER] Fortran run time error Asfa Ali (Tue Mar 09 2010 - 06:30:54 PST)
- Re: [AMBER] Fortran run time error Tom Joseph (Tue Mar 09 2010 - 06:49:22 PST)
- Re: [AMBER] Fortran run time error Jason Swails (Tue Mar 09 2010 - 06:50:01 PST)
  - Re: [AMBER] Fortran run time error Asfa Ali (Tue Mar 09 2010 - 20:25:29 PST)
[AMBER] 10Gb Interconnect profile Alessandro Nascimento (Tue Mar 09 2010 - 06:42:17 PST)
- RE: [AMBER] 10Gb Interconnect profile Ross Walker (Wed Mar 10 2010 - 07:07:27 PST)
[AMBER] energy calculation rui (Tue Mar 09 2010 - 10:37:22 PST)
- Re: [AMBER] energy calculation Jason Swails (Tue Mar 09 2010 - 11:01:55 PST)
- Re: [AMBER] energy calculation Jason Swails (Fri Mar 12 2010 - 09:25:21 PST)
  - Re: [AMBER] energy calculation Dwight McGee (Fri Mar 12 2010 - 13:33:04 PST)
[AMBER] ERROR: PGFIO-F-239/namelist read/unit=5/entity name is not member of group. lee lior (Tue Mar 09 2010 - 13:41:51 PST)
- Re: [AMBER] ERROR: PGFIO-F-239/namelist read/unit=5/entity name is not member of group. case (Wed Mar 10 2010 - 07:35:01 PST)
[AMBER] MMPBSA in case of highly water accessible molecules ? Marek Maly (Tue Mar 09 2010 - 13:43:11 PST)
[AMBER] Extract potential energy from ptraj? Lili Peng (Tue Mar 09 2010 - 20:05:56 PST)
- Re: [AMBER] Extract potential energy from ptraj? Adrian Roitberg (Tue Mar 09 2010 - 20:18:04 PST)
[AMBER] Simulating a protein with nmr structure nicholus bhattacharjee (Wed Mar 10 2010 - 01:50:23 PST)
- Re: [AMBER] Simulating a protein with nmr structure Carlos Simmerling (Wed Mar 10 2010 - 03:37:25 PST)
  - Re: [AMBER] Simulating a protein with nmr structure Deepangi Pandit (Wed Mar 10 2010 - 10:45:12 PST)
    - Re: [AMBER] Simulating a protein with nmr structure nicholus bhattacharjee (Thu Mar 11 2010 - 03:10:42 PST)
[AMBER] problem to generate parameters files of DNA Ananya Paul (Wed Mar 10 2010 - 02:18:28 PST)
- Re: [AMBER] problem to generate parameters files of DNA case (Wed Mar 10 2010 - 05:09:47 PST)
  - Re: [AMBER] problem to generate parameters files of DNA Ananya Paul (Wed Mar 10 2010 - 06:37:40 PST)
    - Re: [AMBER] problem to generate parameters files of DNA case (Wed Mar 10 2010 - 07:12:27 PST)
[AMBER] Extract coordinate residues form mdcrd Silvia Carlotto (Wed Mar 10 2010 - 06:38:47 PST)
- Re: [AMBER] Extract coordinate residues form mdcrd Carlos Simmerling (Wed Mar 10 2010 - 06:40:17 PST)
[AMBER] Re: Fw:SOS for mmpbsa Ray Luo (Wed Mar 10 2010 - 10:17:07 PST)
[AMBER] how to do analysis of the local structure Nancy (Wed Mar 10 2010 - 21:17:29 PST)
- Re: [AMBER] how to do analysis of the local structure Dwight McGee (Wed Mar 10 2010 - 22:45:37 PST)
[AMBER] how to do analysis of the local structure Nancy (Wed Mar 10 2010 - 23:13:30 PST)
- Re: [AMBER] how to do analysis of the local structure Carlos Simmerling (Thu Mar 11 2010 - 03:31:38 PST)
[AMBER] problem to generate parameters files from NMR solved DNA structure Ananya Paul (Wed Mar 10 2010 - 23:30:08 PST)
- Re: [AMBER] problem to generate parameters files from NMR solved DNA structure case (Thu Mar 11 2010 - 04:46:58 PST)
  - Re: [AMBER] problem to generate parameters files from NMR solved DNA structure Ananya Paul (Thu Mar 11 2010 - 05:40:54 PST)
    - Re: [AMBER] problem to generate parameters files from NMR solved DNA structure case (Thu Mar 11 2010 - 06:04:44 PST)
[AMBER] mdinfor error Chinh Su Tran To (Thu Mar 11 2010 - 02:34:23 PST)
- Re: [AMBER] mdinfor error Carlos Simmerling (Thu Mar 11 2010 - 03:27:51 PST)
  - Re: [AMBER] mdinfor error Chinh Su Tran To (Thu Mar 11 2010 - 03:31:23 PST)
    - Re: [AMBER] mdinfor error Carlos Simmerling (Thu Mar 11 2010 - 03:37:35 PST)
    - Re: [AMBER] mdinfor error Chinh Su Tran To (Thu Mar 11 2010 - 03:43:08 PST)
- Re: [AMBER] mdinfor error Bill Ross (Thu Mar 11 2010 - 10:03:22 PST)
- Re: [AMBER] mdinfor error Bill Ross (Thu Mar 11 2010 - 10:04:20 PST)
[AMBER] ligand-protein complex parametrization problems Andrew Voronkov (Thu Mar 11 2010 - 07:39:52 PST)
- Re: [AMBER] ligand-protein complex parametrization problems Billy Miller III (Thu Mar 11 2010 - 07:50:26 PST)
  - Re: Re: [AMBER] ligand-protein complex parametrization problems Andrew Voronkov (Fri Mar 12 2010 - 04:17:16 PST)
    - Re: Re: [AMBER] ligand-protein complex parametrization problems case (Fri Mar 12 2010 - 05:08:57 PST)
[AMBER] Re: Fw:Re:Re: Fw:SOS for mmpbsa Jason Swails (Thu Mar 11 2010 - 08:25:18 PST)
[AMBER] Ptraj problems Ganesh Krishnan (Thu Mar 11 2010 - 09:43:05 PST)
Re: [AMBER] Ptraj problems Bill Ross (Thu Mar 11 2010 - 10:27:56 PST)
- Re: [AMBER] Ptraj problems Ganesh Krishnan (Thu Mar 11 2010 - 10:55:07 PST)
  - Re: [AMBER] Ptraj problems Carlos Simmerling (Thu Mar 11 2010 - 10:56:31 PST)
[AMBER] Difference of ff99 and ff03 in building DNA duplex Qinqin Ji (Thu Mar 11 2010 - 19:08:14 PST)
- Re: [AMBER] Difference of ff99 and ff03 in building DNA duplex case (Thu Mar 11 2010 - 19:21:12 PST)
  - Re: [AMBER] Difference of ff99 and ff03 in building DNA duplex Asfa Ali (Thu Mar 11 2010 - 20:40:37 PST)
    - Re: [AMBER] Difference of ff99 and ff03 in building DNA duplex Jason Swails (Thu Mar 11 2010 - 20:49:16 PST)
    - RE: [AMBER] Difference of ff99 and ff03 in building DNA duplex Ross Walker (Thu Mar 11 2010 - 20:49:40 PST)
    - Re: [AMBER] Difference of ff99 and ff03 in building DNA duplex Ilyas Yildirim (Thu Mar 11 2010 - 21:03:32 PST)
    - Re: [AMBER] Difference of ff99 and ff03 in building DNA duplex Kevin Hauser (Thu Mar 11 2010 - 21:05:42 PST)
- Re: [AMBER] Difference of ff99 and ff03 in building DNA duplex Thomas Cheatham (Thu Mar 11 2010 - 19:21:51 PST)
[AMBER] Antechamber question: all my residue carbons are the same 'c3' atom type. Denny Bromley (Thu Mar 11 2010 - 20:33:05 PST)
- Re: [AMBER] Antechamber question: all my residue carbons are the same 'c3' atom type. case (Fri Mar 12 2010 - 04:47:28 PST)
  - Re: [AMBER] Antechamber question: all my residue carbons are the same 'c3' atom type. Dean Cuebas (Fri Mar 12 2010 - 09:39:54 PST)
  - RE: [AMBER] Antechamber question: all my residue carbons are the same 'c3' atom type. Denny Bromley (Fri Mar 12 2010 - 09:50:27 PST)
    - Re: [AMBER] Antechamber question: all my residue carbons are the same 'c3' atom type. Dean Cuebas (Fri Mar 12 2010 - 10:07:21 PST)
    - RE: [AMBER] Antechamber question: all my residue carbons are the same 'c3' atom type. Denny Bromley (Fri Mar 12 2010 - 12:40:12 PST)
    - Re: [AMBER] Antechamber question: all my residue carbons are the same 'c3' atom type. Jason Swails (Fri Mar 12 2010 - 13:16:56 PST)
    - Re: [AMBER] Antechamber question: all my residue carbons are the same 'c3' atom type. Dean Cuebas (Fri Mar 12 2010 - 14:44:17 PST)
- RE: [AMBER] Antechamber question: all my residue carbons are the same 'c3' atom type. Bill Ross (Fri Mar 12 2010 - 12:57:40 PST)
[AMBER] tleap and xleap problem in loading mol2 files d96543015.ntu.edu.tw (Thu Mar 11 2010 - 20:51:41 PST)
- Re: [AMBER] tleap and xleap problem in loading mol2 files Jason Swails (Thu Mar 11 2010 - 21:10:02 PST)
[AMBER] G03: ONIOM Arash Farahmand (Fri Mar 12 2010 - 06:59:33 PST)
- Re: [AMBER] G03: ONIOM Jason Swails (Fri Mar 12 2010 - 07:33:22 PST)
[AMBER] box of spc water Ganesh Kamath (Fri Mar 12 2010 - 09:19:08 PST)
[AMBER] Mask selection John S (Fri Mar 12 2010 - 14:21:12 PST)
- Re: [AMBER] Mask selection Thomas Cheatham III (Fri Mar 12 2010 - 14:23:30 PST)
  - Re: [AMBER] Mask selection John S (Fri Mar 12 2010 - 14:44:10 PST)
[AMBER] Binding Energy Calculation by QM/MM method Kshatresh Dutta Dubey (Fri Mar 12 2010 - 21:31:27 PST)
- [AMBER] Binding Energy Calculation by QM/MM method Kshatresh Dutta Dubey (Sat Mar 13 2010 - 21:45:17 PST)
  - Re: [AMBER] Binding Energy Calculation by QM/MM method Billy Miller III (Sun Mar 14 2010 - 07:40:19 PDT)
    - RE: [AMBER] Binding Energy Calculation by QM/MM method Ross Walker (Sun Mar 14 2010 - 11:13:40 PDT)
    - Re: [AMBER] Binding Energy Calculation by QM/MM method Kshatresh Dutta Dubey (Sun Mar 14 2010 - 11:52:49 PDT)
[AMBER] Enquiry regarding Minimisation Pallavi Mohanty (Sat Mar 13 2010 - 02:50:22 PST)
- Re: [AMBER] Enquiry regarding Minimisation Carlos Simmerling (Sat Mar 13 2010 - 03:48:10 PST)
[AMBER] addions or solvate-which one first Nicee (Sat Mar 13 2010 - 02:51:06 PST)
- Re: [AMBER] addions or solvate-which one first InSuk Joung (Sat Mar 13 2010 - 08:46:03 PST)
- Re: [AMBER] addions or solvate-which one first Bill Ross (Sat Mar 13 2010 - 12:25:58 PST)
  - Re: [AMBER] addions or solvate-which one first Nicee (Sun Mar 14 2010 - 21:00:22 PDT)
[AMBER] Spline order too small when using AMOEBA force field Workalemhu Berhanu (Sat Mar 13 2010 - 04:42:55 PST)
- Re: [AMBER] Spline order too small when using AMOEBA force field case (Sat Mar 13 2010 - 09:34:34 PST)
[AMBER] ptraj rms s. Bill (Sat Mar 13 2010 - 07:36:51 PST)
- Re: [AMBER] ptraj rms s. Bill (Sat Mar 13 2010 - 08:08:41 PST)
[AMBER] Fwd: understanding AMBER FORCES parm files? whimsica.aol.com (Sat Mar 13 2010 - 10:18:37 PST)
- Re: [AMBER] Fwd: understanding AMBER FORCES parm files? case (Sat Mar 13 2010 - 10:59:50 PST)
[AMBER] RE: About amber10 installation Ross Walker (Sat Mar 13 2010 - 10:22:44 PST)
Re: [AMBER] addions or solvate-which one first Bill Ross (Sat Mar 13 2010 - 12:18:46 PST)
[AMBER] can't get the final "snapshot_statistics.out" file geyan (Sat Mar 13 2010 - 19:25:52 PST)
- Re: [AMBER] can't get the final "snapshot_statistics.out" file Billy Miller III (Sun Mar 14 2010 - 07:21:40 PDT)
- Re: Re: [AMBER] can't get the final "snapshot_statistics.out" file geyan (Mon Mar 15 2010 - 01:35:50 PDT)
  - AW: Re: [AMBER] can't get the final "snapshot_statistics.out" file Alexander Metz (Mon Mar 15 2010 - 04:52:50 PDT)
  - Re: Re: [AMBER] can't get the final "snapshot_statistics.out" file Rama krishnan (Mon Mar 15 2010 - 05:23:54 PDT)
    - Re: Re: [AMBER] can't get the final "snapshot_statistics.out" file Billy Miller III (Mon Mar 15 2010 - 05:42:11 PDT)
[AMBER] MMPBSA.py problem s. Bill (Sun Mar 14 2010 - 03:56:25 PDT)
- Re: [AMBER] MMPBSA.py problem Billy Miller III (Sun Mar 14 2010 - 07:18:20 PDT)
- Re: [AMBER] MMPBSA.py problem Jason Swails (Sun Mar 14 2010 - 09:47:40 PDT)
[AMBER] Particle insertion and deletion Dian Jiao (Sun Mar 14 2010 - 13:14:20 PDT)
- Re: [AMBER] Particle insertion and deletion Carlos Simmerling (Sun Mar 14 2010 - 14:06:51 PDT)
- Re: [AMBER] Particle insertion and deletion Roman Osman (Sun Mar 14 2010 - 14:12:25 PDT)
[AMBER] Enquiry regarding MD run Pallavi Mohanty (Mon Mar 15 2010 - 00:29:58 PDT)
- [AMBER] unsubscribe whimsica.aol.com (Mon Mar 15 2010 - 00:40:54 PDT)
- Re: [AMBER] Enquiry regarding MD run Sushil Mishra (Mon Mar 15 2010 - 00:44:22 PDT)
  - Re: [AMBER] Enquiry regarding MD run Pallavi Mohanty (Mon Mar 15 2010 - 01:07:16 PDT)
    - Re: [AMBER] Enquiry regarding MD run Sushil Mishra (Mon Mar 15 2010 - 02:00:19 PDT)
- Re: [AMBER] Enquiry regarding MD run Bill Ross (Mon Mar 15 2010 - 10:51:49 PDT)
  - Re: [AMBER] Enquiry regarding MD run Pallavi Mohanty (Mon Mar 15 2010 - 10:59:17 PDT)
- Re: [AMBER] Enquiry regarding MD run Bill Ross (Mon Mar 15 2010 - 11:45:51 PDT)
[AMBER] wrong? geyan (Mon Mar 15 2010 - 01:27:58 PDT)
- Re: [AMBER] wrong? Hannes Loeffler (Mon Mar 15 2010 - 01:34:45 PDT)
  - Re: [AMBER] wrong? steinbrt.rci.rutgers.edu (Mon Mar 15 2010 - 01:49:54 PDT)
[AMBER] Calculating Amber Force fields from Wikipedia whimsica.aol.com (Mon Mar 15 2010 - 06:46:22 PDT)
- Re: [AMBER] Calculating Amber Force fields from Wikipedia Carlos Simmerling (Mon Mar 15 2010 - 07:47:36 PDT)
  - Re: [AMBER] Calculating Amber Force fields from Wikipedia Whimsica.aol.com (Mon Mar 15 2010 - 08:32:57 PDT)
    - Re: [AMBER] Calculating Amber Force fields from Wikipedia Carlos Simmerling (Mon Mar 15 2010 - 08:38:05 PDT)
    - RE: [AMBER] Calculating Amber Force fields from Wikipedia Ross Walker (Mon Mar 15 2010 - 19:16:29 PDT)
    - Re: [AMBER] Calculating Amber Force fields from Wikipedia whimsica.aol.com (Mon Mar 15 2010 - 19:42:50 PDT)
    - Re: [AMBER] Calculating Amber Force fields from Wikipedia M. L. Dodson (Mon Mar 15 2010 - 20:45:26 PDT)
    - Re: [AMBER] Calculating Amber Force fields from Wikipedia Whimsica.aol.com (Tue Mar 16 2010 - 14:30:34 PDT)
    - Re: [AMBER] Calculating Amber Force fields from Wikipedia M. L. Dodson (Tue Mar 16 2010 - 14:58:00 PDT)
    - Re: [AMBER] Calculating Amber Force fields from Wikipedia whimsica.aol.com (Tue Mar 16 2010 - 17:32:02 PDT)
    - Re: [AMBER] Calculating Amber Force fields from Wikipedia Carlos Simmerling (Tue Mar 16 2010 - 18:12:07 PDT)
    - Re: [AMBER] Calculating Amber Force fields from Wikipedia Carlos Simmerling (Tue Mar 16 2010 - 16:09:24 PDT)
    - Re: [AMBER] Calculating Amber Force fields from Wikipedia Kevin Hauser (Tue Mar 16 2010 - 17:41:08 PDT)
    - Re: [AMBER] Calculating Amber Force fields from Wikipedia whimsica.aol.com (Tue Mar 16 2010 - 17:43:41 PDT)
[AMBER] Can anyone tell me what the parm99.dat values correspond to? whimsica.aol.com (Mon Mar 15 2010 - 13:58:28 PDT)
- Re: [AMBER] Can anyone tell me what the parm99.dat values correspond to? Bill Ross (Mon Mar 15 2010 - 14:11:34 PDT)
  - Re: [AMBER] Can anyone tell me what the parm99.dat values correspond to? whimsica.aol.com (Mon Mar 15 2010 - 17:00:34 PDT)
    - Re: [AMBER] Can anyone tell me what the parm99.dat values correspond to? Carlos Simmerling (Mon Mar 15 2010 - 17:21:38 PDT)
- Re: [AMBER] Can anyone tell me what the parm99.dat values correspond to? M. L. Dodson (Mon Mar 15 2010 - 14:24:38 PDT)
  - Re: [AMBER] Can anyone tell me what the parm99.dat values correspond to? whimsica.aol.com (Mon Mar 15 2010 - 17:10:26 PDT)
    - Re: [AMBER] Can anyone tell me what the parm99.dat values correspond to? M. L. Dodson (Mon Mar 15 2010 - 18:31:31 PDT)
    - Re: [AMBER] Can anyone tell me what the parm99.dat values correspond to? whimsica.aol.com (Mon Mar 15 2010 - 18:52:39 PDT)
  - [AMBER] Minimization Failure Taufik Al-Sarraj (Tue Mar 16 2010 - 11:04:53 PDT)
    - Re: [AMBER] Minimization Failure case (Tue Mar 16 2010 - 11:24:44 PDT)
    - Re: [AMBER] Minimization Failure Bill Ross (Tue Mar 16 2010 - 11:36:17 PDT)
    - Re: [AMBER] Minimization Failure Taufik Al-Sarraj (Tue Mar 16 2010 - 11:37:28 PDT)
    - Re: [AMBER] Minimization Failure Taufik Al-Sarraj (Wed Mar 24 2010 - 12:39:21 PDT)
- Re: [AMBER] Can anyone tell me what the parm99.dat values correspond to? Bill Ross (Mon Mar 15 2010 - 17:05:50 PDT)
  - Re: [AMBER] Can anyone tell me what the parm99.dat values correspond to? whimsica.aol.com (Mon Mar 15 2010 - 17:32:03 PDT)
    - Re: [AMBER] Can anyone tell me what the parm99.dat values correspond to? Carlos Simmerling (Mon Mar 15 2010 - 18:04:59 PDT)
- Re: [AMBER] Can anyone tell me what the parm99.dat values correspond to? Bill Ross (Mon Mar 15 2010 - 17:13:35 PDT)
- Re: [AMBER] Can anyone tell me what the parm99.dat values correspond to? Bill Ross (Mon Mar 15 2010 - 18:37:43 PDT)
- Re: [AMBER] Can anyone tell me what the parm99.dat values correspond to? Bill Ross (Mon Mar 15 2010 - 18:45:12 PDT)
  - Re: [AMBER] Can anyone tell me what the parm99.dat values correspond to? M. L. Dodson (Mon Mar 15 2010 - 20:20:31 PDT)
[AMBER] sleap not built Robert Wohlhueter (Mon Mar 15 2010 - 15:51:24 PDT)
- Re: [AMBER] sleap not built Wei Zhang (Mon Mar 15 2010 - 16:27:49 PDT)
[AMBER] start from scratch geyan (Tue Mar 16 2010 - 00:30:49 PDT)
[AMBER] force field with neutral terminal Ramya Narasimhan (Tue Mar 16 2010 - 00:56:21 PDT)
- Re: [AMBER] force field with neutral terminal Carlos Simmerling (Tue Mar 16 2010 - 03:36:36 PDT)
  - Re: Re: [AMBER] force field with neutral terminal Ramya Narasimhan (Tue Mar 16 2010 - 23:59:04 PDT)
    - Re: Re: [AMBER] force field with neutral terminal Jason Swails (Wed Mar 17 2010 - 08:16:40 PDT)
    - Re: Re: [AMBER] force field with neutral terminal Carlos Simmerling (Wed Mar 17 2010 - 08:20:56 PDT)
    - Re: Re: Re: [AMBER] force field with neutral terminal Ramya Narasimhan (Thu Mar 18 2010 - 22:07:34 PDT)
    - Re: Re: Re: Re: [AMBER] force field with neutral terminal Ramya Narasimhan (Thu Mar 18 2010 - 23:24:34 PDT)
[AMBER] regarding NMR structures Asfa Ali (Tue Mar 16 2010 - 06:08:20 PDT)
- Re: [AMBER] regarding NMR structures Carlos Simmerling (Tue Mar 16 2010 - 06:25:30 PDT)
- Re: [AMBER] regarding NMR structures case (Tue Mar 16 2010 - 09:41:28 PDT)
  - Re: [AMBER] regarding NMR structures case (Tue Mar 16 2010 - 10:05:50 PDT)
    - Re: [AMBER] regarding NMR structures Asfa Ali (Tue Mar 16 2010 - 23:51:41 PDT)
[AMBER] RESP, AM1BCC & geometries Aiko Matsumoto (Tue Mar 16 2010 - 06:34:55 PDT)
[AMBER] Regarding SGLD aneesh cna (Tue Mar 16 2010 - 06:40:02 PDT)
[AMBER] How to apply extra dihedrals Lekpa Duukori (Tue Mar 16 2010 - 08:19:18 PDT)
- Re: [AMBER] How to apply extra dihedrals InSuk Joung (Tue Mar 16 2010 - 18:03:06 PDT)
- Re: [AMBER] How to apply extra dihedrals Jason Swails (Tue Mar 16 2010 - 20:29:20 PDT)
- Re: [AMBER] How to apply extra dihedrals Bill Ross (Tue Mar 16 2010 - 20:57:03 PDT)
  - Re: [AMBER] How to apply extra dihedrals Lekpa Duukori (Tue Mar 16 2010 - 21:19:52 PDT)
  - Re: [AMBER] How to apply extra dihedrals Jason Swails (Tue Mar 16 2010 - 21:22:06 PDT)
Re: [AMBER] Minimization Failure Bill Ross (Tue Mar 16 2010 - 11:18:29 PDT)
- Re: [AMBER] Minimization Failure Taufik Al-Sarraj (Tue Mar 16 2010 - 11:26:42 PDT)
[AMBER] Can you give me some suggestion on how to use NetCDF to obtain a binary formate trajectory with AMBER Nancy (Tue Mar 16 2010 - 18:51:25 PDT)
- Re: [AMBER] Can you give me some suggestion on how to use NetCDF to obtain a binary formate trajectory with AMBER Jason Swails (Tue Mar 16 2010 - 19:05:21 PDT)
[AMBER] Confirm compiling Amber10/Tools1.3 breaks with intel v 11.1? Trevor Gokey (Tue Mar 16 2010 - 21:34:26 PDT)
- RE: [AMBER] Confirm compiling Amber10/Tools1.3 breaks with intel v 11.1? Ross Walker (Tue Mar 16 2010 - 22:48:30 PDT)
  - RE: [AMBER] Confirm compiling Amber10/Tools1.3 breaks with intel v 11.1? Trevor Gokey (Tue Mar 16 2010 - 23:04:58 PDT)
- Re: [AMBER] Confirm compiling Amber10/Tools1.3 breaks with intel v 11.1? case (Wed Mar 17 2010 - 09:01:13 PDT)
[AMBER] Nucgen Jagdeesh C (Tue Mar 16 2010 - 22:11:05 PDT)
- RE: [AMBER] Nucgen Ross Walker (Tue Mar 16 2010 - 22:52:11 PDT)
[AMBER] IMPROPER TERM CONTRIBUTION Peter Charles Kahuna (Wed Mar 17 2010 - 02:43:30 PDT)
- Re: [AMBER] IMPROPER TERM CONTRIBUTION case (Wed Mar 17 2010 - 04:49:19 PDT)
  - Re: [AMBER] IMPROPER TERM CONTRIBUTION Alan (Wed Mar 17 2010 - 05:17:16 PDT)
    - Re: [AMBER] IMPROPER TERM CONTRIBUTION Carlos Simmerling (Wed Mar 17 2010 - 05:26:43 PDT)
    - Re: [AMBER] IMPROPER TERM CONTRIBUTION Alan (Thu Mar 18 2010 - 08:04:15 PDT)
    - Re: [AMBER] IMPROPER TERM CONTRIBUTION case (Thu Mar 18 2010 - 08:12:07 PDT)
    - Re: [AMBER] IMPROPER TERM CONTRIBUTION Alan (Thu Mar 18 2010 - 08:47:57 PDT)
- Re: [AMBER] IMPROPER TERM CONTRIBUTION Bill Ross (Wed Mar 17 2010 - 09:45:48 PDT)
[AMBER] problem in minimisation Hyma vathi (Wed Mar 17 2010 - 08:04:12 PDT)
- Re: [AMBER] problem in minimisation Carlos Simmerling (Wed Mar 17 2010 - 08:22:16 PDT)
[AMBER] Large FIle Beale, John (Wed Mar 17 2010 - 08:54:14 PDT)
- Re: [AMBER] Large FIle Jason Swails (Wed Mar 17 2010 - 09:08:19 PDT)
- Re: [AMBER] Large FIle Jason Swails (Wed Mar 17 2010 - 09:12:38 PDT)
  - RE: [AMBER] Large FIle Gannett, Peter (Wed Mar 17 2010 - 09:27:40 PDT)
- Re: [AMBER] Large FIle Bill Ross (Wed Mar 17 2010 - 10:09:24 PDT)
  - Re: [AMBER] Large FIle Jason Swails (Wed Mar 17 2010 - 12:49:53 PDT)
Re: [AMBER] problem in minimisation Bill Ross (Wed Mar 17 2010 - 09:58:37 PDT)
[AMBER] sander bomb and maxpr question Andrew Olson (Wed Mar 17 2010 - 11:51:36 PDT)
- Re: [AMBER] sander bomb and maxpr question case (Wed Mar 17 2010 - 12:56:21 PDT)
  - Re: [AMBER] sander bomb and maxpr question Andrew Olson (Wed Mar 17 2010 - 15:30:05 PDT)
    - Re: [AMBER] sander bomb and maxpr question case (Wed Mar 17 2010 - 17:36:14 PDT)
    - Re: [AMBER] sander bomb and maxpr question Andrew Olson (Wed Mar 24 2010 - 07:08:15 PDT)
    - Re: [AMBER] sander bomb and maxpr question case (Fri Mar 26 2010 - 07:53:56 PDT)
[AMBER] ptraj hydrogen bond analysis error Jamie Romnes (Wed Mar 17 2010 - 14:47:53 PDT)
- Re: [AMBER] ptraj hydrogen bond analysis error Daniel Roe (Wed Mar 17 2010 - 15:42:13 PDT)
[AMBER] ACS Division of Computers in Chemistry: award applications due March 30 Carlos Simmerling (Wed Mar 17 2010 - 16:16:20 PDT)
- RE: [AMBER] ACS Division of Computers in Chemistry: award applications due March 30 Ross Walker (Wed Mar 17 2010 - 17:03:29 PDT)
  - RE: [AMBER] ACS Division of Computers in Chemistry: award applications due March 30 Ross Walker (Wed Mar 17 2010 - 17:09:46 PDT)
    - Re: [AMBER] ACS Division of Computers in Chemistry: award applications due March 30 Carlos Simmerling (Wed Mar 17 2010 - 17:20:57 PDT)
[AMBER] AMBER prmtop and mdcrd files to CHARMM psf and dcd files Nancy (Wed Mar 17 2010 - 19:42:52 PDT)
[AMBER] Re :checkoverlap John S (Wed Mar 17 2010 - 20:45:37 PDT)
- [AMBER] Re: Re :checkoverlap John S (Thu Mar 18 2010 - 12:55:55 PDT)
[AMBER] PBSOL not equal to PBSUR + PBCAL? Jeffrey (Thu Mar 18 2010 - 01:01:34 PDT)
- Re: [AMBER] PBSOL not equal to PBSUR + PBCAL? Ray Luo (Thu Mar 18 2010 - 09:59:40 PDT)
[AMBER] MMPBSA calculation Jeffrey (Thu Mar 18 2010 - 05:23:36 PDT)
- Re: [AMBER] MMPBSA calculation Billy Miller III (Thu Mar 18 2010 - 07:45:45 PDT)
- Re: [AMBER] MMPBSA calculation Ray Luo (Thu Mar 18 2010 - 10:09:06 PDT)
[AMBER] Polarization Scaling Down Ivan Gladich (Thu Mar 18 2010 - 07:02:52 PDT)
[AMBER] vlimit exceeded for step Hyma vathi (Thu Mar 18 2010 - 07:28:29 PDT)
- Re: [AMBER] vlimit exceeded for step Carlos Simmerling (Thu Mar 18 2010 - 07:29:49 PDT)
  - Re: [AMBER] vlimit exceeded for step Hyma vathi (Thu Mar 18 2010 - 07:35:10 PDT)
    - Re: [AMBER] vlimit exceeded for step Carlos Simmerling (Thu Mar 18 2010 - 07:42:08 PDT)
- Re: [AMBER] vlimit exceeded for step Jason Swails (Thu Mar 18 2010 - 09:07:34 PDT)
- Re: [AMBER] vlimit exceeded for step case (Thu Mar 18 2010 - 12:27:40 PDT)
[AMBER] antechamber changing atom name case, is it right? Alan (Thu Mar 18 2010 - 10:03:36 PDT)
[AMBER] How to obtain an ideal helix structure of Alanine 5 peptide (ACE-Ala5-NME) ? Dongshan Wei (Thu Mar 18 2010 - 14:28:54 PDT)
- Re: [AMBER] How to obtain an ideal helix structure of Alanine 5 peptide (ACE-Ala5-NME) ? Adrian Roitberg (Thu Mar 18 2010 - 14:36:06 PDT)
  - Re: [AMBER] How to obtain an ideal helix structure of Alanine 5 peptide (ACE-Ala5-NME) ? M. L. Dodson (Thu Mar 18 2010 - 17:49:14 PDT)
    - Re: [AMBER] How to obtain an ideal helix structure of Alanine 5 peptide (ACE-Ala5-NME) ? Dongshan Wei (Fri Mar 19 2010 - 09:39:33 PDT)
    - Re: [AMBER] How to obtain an ideal helix structure of Alanine 5 peptide (ACE-Ala5-NME) ? Carlos Simmerling (Fri Mar 19 2010 - 10:24:14 PDT)
[AMBER] ATP charge convergence Eric Pettersen (Thu Mar 18 2010 - 17:07:10 PDT)
- Re: [AMBER] ATP charge convergence Eric Pettersen (Thu Mar 18 2010 - 17:11:18 PDT)
  - Re: [AMBER] ATP charge convergence Eric Pettersen (Thu Mar 18 2010 - 17:17:58 PDT)
    - Re: [AMBER] ATP charge convergence Alan (Fri Mar 19 2010 - 09:34:22 PDT)
    - Re: [AMBER] ATP charge convergence Eric Pettersen (Fri Mar 19 2010 - 09:50:20 PDT)
[AMBER] Check overlap John S (Thu Mar 18 2010 - 18:41:09 PDT)
[AMBER] RMSD between two different proteins nicholus bhattacharjee (Fri Mar 19 2010 - 00:10:04 PDT)
- Re: [AMBER] RMSD between two different proteins Jagan Mohan (Fri Mar 19 2010 - 00:26:37 PDT)
  - Re: [AMBER] RMSD between two different proteins nicholus bhattacharjee (Fri Mar 19 2010 - 01:17:42 PDT)
    - Re: [AMBER] RMSD between two different proteins Jagan Mohan (Fri Mar 19 2010 - 02:16:36 PDT)
[AMBER] Energy and Density Unites Christine Baranski (Fri Mar 19 2010 - 06:17:57 PDT)
[AMBER] Adenine in water ros (Fri Mar 19 2010 - 06:42:23 PDT)
- Re: [AMBER] Adenine in water Jason Swails (Sat Mar 20 2010 - 23:41:35 PDT)
[AMBER] Error during MMPBSA calc. Jagan Mohan (Fri Mar 19 2010 - 07:02:13 PDT)
- Re: [AMBER] Error during MMPBSA calc. Billy Miller III (Fri Mar 19 2010 - 07:15:39 PDT)
  - Re: [AMBER] Error during MMPBSA calc. Jagan Mohan (Fri Mar 19 2010 - 08:55:27 PDT)
    - Re: [AMBER] Error during MMPBSA calc. David Watson (Fri Mar 19 2010 - 09:16:42 PDT)
    - Re: [AMBER] Error during MMPBSA calc. Jagan Mohan (Sat Mar 20 2010 - 01:59:12 PDT)
[AMBER] regarding ambertools Asfa Ali (Fri Mar 19 2010 - 10:52:40 PDT)
- Re: [AMBER] regarding ambertools Jason Swails (Sat Mar 20 2010 - 07:51:54 PDT)
  - Re: [AMBER] regarding ambertools Asfa Ali (Sat Mar 20 2010 - 09:53:42 PDT)
[AMBER] general query:RMSD Jio M (Fri Mar 19 2010 - 13:21:57 PDT)
- Re: [AMBER] general query:RMSD Carlos Simmerling (Sat Mar 20 2010 - 09:41:57 PDT)
  - Re: [AMBER] general query:RMSD Jio M (Sun Mar 21 2010 - 02:01:04 PDT)
- Re: [AMBER] general query:RMSD Jio M (Sat Mar 27 2010 - 03:38:03 PDT)
[AMBER] error when doing MMPBSA pxq (Sun Mar 21 2010 - 00:27:59 PDT)
- Re: [AMBER] error when doing MMPBSA Jason Swails (Sun Mar 21 2010 - 07:43:45 PDT)
- Re: [AMBER] error when doing MMPBSA Ray Luo (Sun Mar 21 2010 - 12:06:29 PDT)
[AMBER] PDB Database s. Bill (Sun Mar 21 2010 - 03:08:07 PDT)
- Re: [AMBER] PDB Database Sushil Mishra (Sun Mar 21 2010 - 03:29:02 PDT)
[AMBER] mbonbi and mbondi2 s. Bill (Sun Mar 21 2010 - 12:55:58 PDT)
- Re: [AMBER] mbonbi and mbondi2 Kevin Hauser (Sun Mar 21 2010 - 13:29:44 PDT)
  - Re: [AMBER] mbonbi and mbondi2 Carlos Simmerling (Sun Mar 21 2010 - 14:01:54 PDT)
[AMBER] Regd:vlimit John S (Sun Mar 21 2010 - 21:03:18 PDT)
- Re: [AMBER] Regd:vlimit case (Sun Mar 21 2010 - 23:10:13 PDT)
[AMBER] about amber force field geyan (Mon Mar 22 2010 - 01:12:44 PDT)
- Re: [AMBER] about amber force field mattia (Mon Mar 22 2010 - 06:08:48 PDT)
  - Re: [AMBER] about amber force field Alan (Mon Mar 22 2010 - 06:59:35 PDT)
  - Re: [AMBER] about amber force field Carlos Simmerling (Mon Mar 22 2010 - 07:24:39 PDT)
    - Re: [AMBER] about amber force field case (Mon Mar 22 2010 - 07:41:43 PDT)
    - Re: [AMBER] about amber force field Alan (Mon Mar 22 2010 - 07:47:26 PDT)
    - Re: [AMBER] about amber force field Alan (Mon Mar 22 2010 - 07:43:47 PDT)
    - Re: [AMBER] about amber force field mattia (Mon Mar 22 2010 - 08:04:01 PDT)
    - Re: [AMBER] about amber force field Alan (Mon Mar 22 2010 - 08:20:11 PDT)
    - Re: [AMBER] about amber force field Carlos Simmerling (Mon Mar 22 2010 - 08:34:29 PDT)
    - Re: [AMBER] about amber force field Carlos Simmerling (Mon Mar 22 2010 - 08:37:47 PDT)
- Re: Re: [AMBER] about amber force field geyan (Mon Mar 22 2010 - 19:36:44 PDT)
[AMBER] Distance between two atoms vs time imtiaz shafiq (Mon Mar 22 2010 - 05:24:26 PDT)
- Re: [AMBER] Distance between two atoms vs time Billy Miller III (Mon Mar 22 2010 - 05:57:13 PDT)
- Re: [AMBER] Distance between two atoms vs time Bill Ross (Mon Mar 22 2010 - 10:03:15 PDT)
[AMBER] Amber: heme atom identification SimonKao (Mon Mar 22 2010 - 09:05:40 PDT)
- Re: [AMBER] Amber: heme atom identification Jason Swails (Mon Mar 22 2010 - 15:16:01 PDT)
- Re: [AMBER] Amber: heme atom identification Bill Ross (Mon Mar 22 2010 - 15:19:14 PDT)
[AMBER] NOT IN RESIDUE TEMPLATES sikander azam (Mon Mar 22 2010 - 09:11:17 PDT)
- Re: [AMBER] NOT IN RESIDUE TEMPLATES Carlos Simmerling (Mon Mar 22 2010 - 09:15:41 PDT)
Re: [AMBER] NOT IN RESIDUE TEMPLATES Bill Ross (Mon Mar 22 2010 - 10:16:47 PDT)
- Re: [AMBER] NOT IN RESIDUE TEMPLATES sikander azam (Thu Mar 25 2010 - 23:34:40 PDT)
  - Re: [AMBER] NOT IN RESIDUE TEMPLATES Jason Swails (Thu Mar 25 2010 - 23:56:14 PDT)
[AMBER] simulation under pressure Yang Li (Mon Mar 22 2010 - 20:05:45 PDT)
- Re: [AMBER] simulation under pressure case (Fri Mar 26 2010 - 07:54:10 PDT)
  - RE: [AMBER] simulation under pressure Yang Li (Mon Mar 29 2010 - 12:53:01 PDT)
    - Re: [AMBER] simulation under pressure Carlos Simmerling (Mon Mar 29 2010 - 12:58:40 PDT)
    - RE: [AMBER] simulation under pressure Yang Li (Mon Mar 29 2010 - 18:40:41 PDT)
    - Re: [AMBER] simulation under pressure Daniel Roe (Mon Mar 29 2010 - 19:23:07 PDT)
    - Re: [AMBER] simulation under pressure Jason Swails (Mon Mar 29 2010 - 20:30:26 PDT)
    - Re: [AMBER] simulation under pressure Marek Maly (Tue Mar 30 2010 - 02:53:25 PDT)
[AMBER] mmpbsa doesn't work qiaoyan (Mon Mar 22 2010 - 20:38:48 PDT)
- Re: [AMBER] mmpbsa doesn't work Billy Miller III (Tue Mar 23 2010 - 06:22:55 PDT)
[AMBER] problem with antechamber for C60 Chun-Wei Pao (Mon Mar 22 2010 - 20:47:00 PDT)
- [AMBER] problem with antechamber for C60 Chun-Wei Pao (Mon Mar 22 2010 - 23:10:59 PDT)
  - Re: [AMBER] problem with antechamber for C60 Dean Cuebas (Tue Mar 23 2010 - 13:13:37 PDT)
- Re: [AMBER] problem with antechamber for C60 Chun-Wei Pao (Tue Mar 23 2010 - 07:44:19 PDT)
[AMBER] Regarding problem with self guided molecular dynamics aneesh cna (Mon Mar 22 2010 - 23:02:18 PDT)
- Re: [AMBER] Regarding problem with self guided molecular dynamics Jason Swails (Tue Mar 23 2010 - 10:21:11 PDT)
[AMBER] MMPBSA error Soumya Lipsa Rath (Tue Mar 23 2010 - 01:21:41 PDT)
- Re: [AMBER] MMPBSA error Dwight McGee (Tue Mar 23 2010 - 07:32:47 PDT)
  - Re: [AMBER] MMPBSA error Soumya Lipsa Rath (Tue Mar 23 2010 - 21:51:30 PDT)
    - Re: [AMBER] MMPBSA error Jason Swails (Tue Mar 23 2010 - 23:21:40 PDT)
    - Re: [AMBER] MMPBSA error Soumya Lipsa Rath (Wed Mar 24 2010 - 19:52:46 PDT)
    - Re: [AMBER] MMPBSA error Jason Swails (Wed Mar 24 2010 - 21:47:48 PDT)
    - Re: [AMBER] MMPBSA error Shulin Zhuang (Wed Mar 24 2010 - 21:57:32 PDT)
    - Re: [AMBER] MMPBSA error Jason Swails (Wed Mar 24 2010 - 22:41:06 PDT)
    - Re: [AMBER] MMPBSA error Dwight McGee (Thu Mar 25 2010 - 07:08:13 PDT)
    - Re: [AMBER] MMPBSA error Soumya Lipsa Rath (Thu Mar 25 2010 - 20:43:08 PDT)
    - Re: [AMBER] MMPBSA error Shulin Zhuang (Thu Mar 25 2010 - 23:22:02 PDT)
    - Re: [AMBER] MMPBSA error Soumya Lipsa Rath (Fri Mar 26 2010 - 01:48:35 PDT)
    - Re: [AMBER] MMPBSA error Soumya Lipsa Rath (Fri Mar 26 2010 - 01:50:35 PDT)
    - Re: [AMBER] MMPBSA error Dwight McGee (Fri Mar 26 2010 - 06:45:57 PDT)
    - Re: [AMBER] MMPBSA error Shulin Zhuang (Fri Mar 26 2010 - 14:32:08 PDT)
- Re: [AMBER] MMPBSA error Vaibhav Jain (Mon Apr 25 2011 - 10:35:39 PDT)
  - Re: [AMBER] MMPBSA error Jason Swails (Mon Apr 25 2011 - 10:53:40 PDT)
    - Re: [AMBER] MMPBSA error Vaibhav Jain (Mon Apr 25 2011 - 11:04:40 PDT)
    - Re: [AMBER] MMPBSA error Jason Swails (Mon Apr 25 2011 - 11:56:18 PDT)
- Re: [AMBER] MMPBSA error Abhishek Tyagi (Fri Mar 27 2015 - 09:39:50 PDT)
  - Re: [AMBER] MMPBSA error Jason Swails (Fri Mar 27 2015 - 10:56:03 PDT)
    - Re: [AMBER] MMPBSA error Kenneth Huang (Fri Mar 27 2015 - 15:49:25 PDT)
  - Re: [AMBER] MMPBSA error Abhishek TYAGI (Wed Apr 01 2015 - 06:35:10 PDT)
    - Re: [AMBER] MMPBSA error Daniel Roe (Wed Apr 01 2015 - 07:13:29 PDT)
    - Re: [AMBER] MMPBSA error Abhishek TYAGI (Mon Apr 06 2015 - 20:05:55 PDT)
    - Re: [AMBER] MMPBSA error Abhishek TYAGI (Mon Apr 06 2015 - 20:28:08 PDT)
    - Re: [AMBER] MMPBSA error Jason Swails (Mon Apr 06 2015 - 20:30:39 PDT)
    - Re: [AMBER] MMPBSA error Daniel Roe (Mon Apr 06 2015 - 20:51:00 PDT)
- Re: [AMBER] MMPBSA error Abhishek TYAGI (Thu Apr 09 2015 - 21:12:06 PDT)
  - Re: [AMBER] MMPBSA error Jason Swails (Fri Apr 10 2015 - 03:14:26 PDT)
[AMBER] Solvatebox on Amber8 pellegrini (Tue Mar 23 2010 - 03:29:32 PDT)
[AMBER] radgyr Beale, John (Tue Mar 23 2010 - 03:44:05 PDT)
- Re: [AMBER] radgyr Carlos Simmerling (Tue Mar 23 2010 - 06:56:01 PDT)
[AMBER] problem with steered MD nicholus bhattacharjee (Tue Mar 23 2010 - 05:41:26 PDT)
- Re: [AMBER] problem with steered MD Adrian Roitberg (Tue Mar 23 2010 - 07:16:35 PDT)
  - Re: [AMBER] problem with steered MD nicholus bhattacharjee (Tue Mar 23 2010 - 08:34:52 PDT)
    - Re: [AMBER] problem with steered MD Adrian Roitberg (Tue Mar 23 2010 - 15:50:19 PDT)
    - Re: [AMBER] problem with steered MD nicholus bhattacharjee (Wed Mar 24 2010 - 21:37:37 PDT)
    - Re: [AMBER] problem with steered MD John Chuang莊曜遠 (Mon Mar 29 2010 - 20:25:21 PDT)
    - Re: [AMBER] problem with steered MD Dmitri Nilov (Mon Mar 29 2010 - 23:37:51 PDT)
[AMBER] Problem with solvationbox command pellegrini (Tue Mar 23 2010 - 06:11:17 PDT)
- RE: [AMBER] Problem with solvationbox command Ross Walker (Tue Mar 23 2010 - 15:22:46 PDT)
  - Re: [AMBER] Problem with solvationbox command pellegrini (Wed Mar 24 2010 - 03:26:43 PDT)
- Re: [AMBER] Problem with solvationbox command monica.imtech.res.in (Thu Apr 01 2010 - 02:08:32 PDT)
[AMBER] Energy units in mm-pbsa calculations moitrayee.mbu.iisc.ernet.in (Tue Mar 23 2010 - 05:57:30 PDT)
- Re: [AMBER] Energy units in mm-pbsa calculations Billy Miller III (Tue Mar 23 2010 - 06:40:07 PDT)
  - Re: [AMBER] Energy units in mm-pbsa calculations moitrayee.mbu.iisc.ernet.in (Thu Mar 25 2010 - 03:44:59 PDT)
    - Re: [AMBER] Energy units in mm-pbsa calculations Billy Miller III (Thu Mar 25 2010 - 06:51:13 PDT)
    - Re: [AMBER] Energy units in mm-pbsa calculations moitrayee.mbu.iisc.ernet.in (Thu Mar 25 2010 - 09:42:10 PDT)
    - Re: [AMBER] Energy units in mm-pbsa calculations Billy Miller III (Thu Mar 25 2010 - 19:31:34 PDT)
    - Re: [AMBER] Energy units in mm-pbsa calculations moitrayee.mbu.iisc.ernet.in (Fri Mar 26 2010 - 05:34:41 PDT)
    - Re: [AMBER] Energy units in mm-pbsa calculations Billy Miller III (Fri Mar 26 2010 - 06:32:22 PDT)
    - Re: [AMBER] Energy units in mm-pbsa calculations moitrayee.mbu.iisc.ernet.in (Fri Mar 26 2010 - 07:41:37 PDT)
    - Re: [AMBER] Energy units in mm-pbsa calculations moitrayee.mbu.iisc.ernet.in (Fri Mar 26 2010 - 23:59:40 PDT)
    - Re: [AMBER] Energy units in mm-pbsa calculations Billy Miller III (Sat Mar 27 2010 - 07:00:03 PDT)
    - Re: [AMBER] Energy units in mm-pbsa calculations moitrayee.mbu.iisc.ernet.in (Sat Mar 27 2010 - 10:21:39 PDT)
    - Re: [AMBER] Energy units in mm-pbsa calculations moitrayee.mbu.iisc.ernet.in (Tue Mar 30 2010 - 03:34:05 PDT)
    - Re: [AMBER] Energy units in mm-pbsa calculations moitrayee.mbu.iisc.ernet.in (Wed Apr 07 2010 - 05:42:24 PDT)
    - Re: [AMBER] Energy units in mm-pbsa calculations Jason Swails (Wed Apr 07 2010 - 06:36:13 PDT)
    - Re: [AMBER] Energy units in mm-pbsa calculations moitrayee.mbu.iisc.ernet.in (Wed Apr 07 2010 - 21:45:44 PDT)
    - Re: [AMBER] Energy units in mm-pbsa calculations Jason Swails (Thu Apr 08 2010 - 05:45:43 PDT)
- Re: [AMBER] Energy units in mm-pbsa calculations Ray Luo (Wed Mar 24 2010 - 10:48:28 PDT)
[AMBER] error in save prmtop geyan (Tue Mar 23 2010 - 07:04:34 PDT)
- Re: [AMBER] error in save prmtop Carlos Simmerling (Tue Mar 23 2010 - 07:08:10 PDT)
- Re: Re: [AMBER] error in save prmtop geyan (Tue Mar 23 2010 - 07:30:07 PDT)
  - Re: Re: [AMBER] error in save prmtop Carlos Simmerling (Tue Mar 23 2010 - 07:32:51 PDT)
- Re: Re: Re: [AMBER] error in save prmtop geyan (Tue Mar 23 2010 - 07:44:12 PDT)
[AMBER] Using 6-12 / 10-12 potential in AMBER Alessandro Nascimento (Tue Mar 23 2010 - 08:44:01 PDT)
- Re: [AMBER] Using 6-12 / 10-12 potential in AMBER Jason Swails (Tue Mar 23 2010 - 10:12:09 PDT)
Re: [AMBER] error in save prmtop Bill Ross (Tue Mar 23 2010 - 10:37:37 PDT)
[AMBER] Regarding amber molecular dynamics PalaniMuthu M (Tue Mar 23 2010 - 10:34:53 PDT)
- [AMBER] Regarding amber molecular dynamics PalaniMuthu M (Tue Mar 23 2010 - 10:41:49 PDT)
- Re: [AMBER] Regarding amber molecular dynamics Bill Ross (Tue Mar 23 2010 - 21:38:20 PDT)
Re: [AMBER] Regarding amber molecular dynamics Bill Ross (Tue Mar 23 2010 - 11:31:22 PDT)
- Re: [AMBER] Regarding amber molecular dynamics PalaniMuthu M (Tue Mar 23 2010 - 21:01:55 PDT)
[AMBER] Specification of solventCap causing atoms to collapse into each other Ben Roberts (Tue Mar 23 2010 - 11:42:44 PDT)
[AMBER] how to achieve the 2D periodic boundary kecy_w.sina.com (Tue Mar 23 2010 - 18:45:24 PDT)
[AMBER] ligand parameterization gurunath katagi (Tue Mar 23 2010 - 23:05:24 PDT)
- Re: [AMBER] ligand parameterization Dean Cuebas (Wed Mar 24 2010 - 10:46:41 PDT)
  - Re: [AMBER] ligand parameterization Dean Cuebas (Wed Mar 24 2010 - 11:33:45 PDT)
[AMBER] Problems on Tutorial A8 tianyuan meng (Wed Mar 24 2010 - 00:15:58 PDT)
- RE: [AMBER] Problems on Tutorial A8 Ross Walker (Wed Mar 24 2010 - 11:22:10 PDT)
[AMBER] help for restraint minimization jacky zhao (Wed Mar 24 2010 - 02:23:38 PDT)
- Re: [AMBER] help for restraint minimization Carlos Simmerling (Wed Mar 24 2010 - 06:18:52 PDT)
[AMBER] crdgrow Steve Seibold (Wed Mar 24 2010 - 09:15:58 PDT)
- Re: [AMBER] crdgrow case (Thu Mar 25 2010 - 10:48:08 PDT)
[AMBER] difference in output from bnda and fd_helix functions Igor Sizov (Wed Mar 24 2010 - 11:19:08 PDT)
- Re: [AMBER] difference in output from bnda and fd_helix functions case (Thu Mar 25 2010 - 10:26:18 PDT)
  - Re: [AMBER] difference in output from bnda and fd_helix functions Igor Sizov (Thu Mar 25 2010 - 12:07:07 PDT)
[AMBER] Missing values for MM BGAS:error in mm-pbsa moitrayee.mbu.iisc.ernet.in (Wed Mar 24 2010 - 11:53:26 PDT)
- Re: [AMBER] Missing values for MM BGAS:error in mm-pbsa lidansa.mail.ustc.edu.cn (Wed Mar 24 2010 - 18:07:29 PDT)
  - Re: [AMBER] Missing values for MM BGAS:error in mm-pbsa moitrayee.mbu.iisc.ernet.in (Thu Mar 25 2010 - 00:05:34 PDT)
[AMBER] crdgrow AMBER 8 Steve Seibold (Wed Mar 24 2010 - 12:45:57 PDT)
Re: [AMBER] crdgrow AMBER 8 Bill Ross (Wed Mar 24 2010 - 13:01:45 PDT)
[AMBER] DUMPAVE lee lior (Wed Mar 24 2010 - 13:58:32 PDT)
[AMBER] AMBER plus GLYCAM Lekpa Duukori (Wed Mar 24 2010 - 15:43:32 PDT)
- RE: [AMBER] AMBER plus GLYCAM Ross Walker (Wed Mar 24 2010 - 16:00:55 PDT)
  - Re: [AMBER] AMBER plus GLYCAM Lekpa Duukori (Wed Mar 24 2010 - 16:28:35 PDT)
[AMBER] how to get the hydrophobic area for a particlar region qiaoyan (Wed Mar 24 2010 - 19:59:14 PDT)
- Re: [AMBER] how to get the hydrophobic area for a particlar region Ray Luo (Thu Mar 25 2010 - 09:49:27 PDT)
  - Re: [AMBER] how to get the hydrophobic area for a particlar region Balazs Jojart (Thu Mar 25 2010 - 11:14:33 PDT)
    - Re: [AMBER] how to get the hydrophobic area for a particlar region Ray Luo (Thu Mar 25 2010 - 11:36:39 PDT)
- Re: Re: [AMBER] how to get the hydrophobic area for a particlar region qiaoyan (Fri Mar 26 2010 - 19:26:02 PDT)
  - Re: Re: [AMBER] how to get the hydrophobic area for a particlar region Jason Swails (Fri Mar 26 2010 - 19:42:04 PDT)
  - Re: Re: [AMBER] how to get the hydrophobic area for a particlar region Billy Miller III (Fri Mar 26 2010 - 19:44:40 PDT)
  - Re: [AMBER] how to get the hydrophobic area for a particlar region Balazs Jojart (Sat Mar 27 2010 - 05:28:13 PDT)
[AMBER] Running several jobs under one script Nkwe Monama (Thu Mar 25 2010 - 02:47:57 PDT)
- Re: [AMBER] Running several jobs under one script Jason Swails (Thu Mar 25 2010 - 09:27:45 PDT)
[AMBER] Bad atom type Br pandb09.lzu.cn (Thu Mar 25 2010 - 02:05:04 PDT)
[AMBER] Lone Pair s. Bill (Thu Mar 25 2010 - 06:29:39 PDT)
- Re: [AMBER] Lone Pair Carlos Simmerling (Thu Mar 25 2010 - 10:29:21 PDT)
[AMBER] Script for creating topology files , running minimization and MD simulation using amoeba force field Workalemhu Berhanu (Thu Mar 25 2010 - 07:31:22 PDT)
- Re: [AMBER] Script for creating topology files , running minimization and MD simulation using amoeba force field case (Thu Mar 25 2010 - 10:39:36 PDT)
[AMBER] MD simulation in gas phase-AMBER 10 Dian Jiao (Thu Mar 25 2010 - 10:30:45 PDT)
- Re: [AMBER] MD simulation in gas phase-AMBER 10 Carlos Simmerling (Thu Mar 25 2010 - 10:34:55 PDT)
- Re: [AMBER] MD simulation in gas phase-AMBER 10 case (Thu Mar 25 2010 - 10:41:14 PDT)
  - Re: [AMBER] MD simulation in gas phase-AMBER 10 Dian Jiao (Thu Mar 25 2010 - 10:45:59 PDT)
    - Re: [AMBER] MD simulation in gas phase-AMBER 10 case (Thu Mar 25 2010 - 10:50:10 PDT)
    - Re: [AMBER] MD simulation in gas phase-AMBER 10 Dian Jiao (Thu Mar 25 2010 - 11:02:15 PDT)
    - Re: [AMBER] MD simulation in gas phase-AMBER 10 Carlos Simmerling (Fri Mar 26 2010 - 08:40:01 PDT)
[AMBER] Antechamber problems. Steve Seibold (Thu Mar 25 2010 - 10:44:18 PDT)
- Re: [AMBER] Antechamber problems. case (Thu Mar 25 2010 - 10:52:31 PDT)
[AMBER] Binding cooprativety and binding order of ligands Sushil Mishra (Thu Mar 25 2010 - 10:53:41 PDT)
Re: [AMBER] Antechamber problems. Bill Ross (Thu Mar 25 2010 - 11:05:36 PDT)
[AMBER] antechamber problems Steve Seibold (Thu Mar 25 2010 - 11:15:34 PDT)
[AMBER] Script for creating topology files , running minimization and MD simulation in amber Palanimuthu M (Thu Mar 25 2010 - 22:23:07 PDT)
- Re: [AMBER] Script for creating topology files , running minimization and MD simulation in amber manoj singh (Thu Mar 25 2010 - 22:24:47 PDT)
  - Re: [AMBER] Script for creating topology files , running minimization and MD simulation in amber Palanimuthu M (Thu Mar 25 2010 - 22:55:53 PDT)
    - Re: [AMBER] Script for creating topology files , running minimization and MD simulation in amber Jason Swails (Thu Mar 25 2010 - 23:22:33 PDT)
[AMBER] error in parallel md run Nicee (Thu Mar 25 2010 - 22:43:22 PDT)
- Re: [AMBER] error in parallel md run Jason Swails (Thu Mar 25 2010 - 22:54:26 PDT)
  - Re: [AMBER] error in parallel md run Nicee (Fri Mar 26 2010 - 01:17:13 PDT)
[AMBER] NAMD-parameter set up Rilei Yu (Fri Mar 26 2010 - 04:22:37 PDT)
[AMBER] Average structure waleed zalloum (Fri Mar 26 2010 - 04:55:17 PDT)
- Re: [AMBER] Average structure Billy Miller III (Fri Mar 26 2010 - 05:44:29 PDT)
- Re: [AMBER] Average structure Bill Ross (Fri Mar 26 2010 - 09:58:02 PDT)
[AMBER] Amber:antechamber & heme(metal?) problems SimonKao (Fri Mar 26 2010 - 13:40:36 PDT)
- Re: [AMBER] Amber:antechamber & heme(metal?) problems case (Sat Mar 27 2010 - 11:49:47 PDT)
- RE: [AMBER] Amber:antechamber & heme(metal?) problems Shaikh Abdul R S Ramaju (Sun Mar 28 2010 - 23:00:11 PDT)
[AMBER] Run.dip: Program Error during test run after Amber 10 installation Senthil Natesan (Fri Mar 26 2010 - 13:44:43 PDT)
- Re: [AMBER] Run.dip: Program Error during test run after Amber 10 installation case (Sun Mar 28 2010 - 06:48:03 PDT)
[AMBER] Post-processing with AMBER 10 Dian Jiao (Fri Mar 26 2010 - 14:05:14 PDT)
- Re: [AMBER] Post-processing with AMBER 10 Daniel Roe (Fri Mar 26 2010 - 14:31:51 PDT)
  - Re: [AMBER] Post-processing with AMBER 10 Dian Jiao (Fri Mar 26 2010 - 15:02:21 PDT)
[AMBER] transforming Antechamber GAFF parameters into another force field Denny Bromley (Fri Mar 26 2010 - 15:00:26 PDT)
- Re: [AMBER] transforming Antechamber GAFF parameters into another force field Nicholas Musolino (Fri Mar 26 2010 - 15:16:04 PDT)
  - RE: [AMBER] transforming Antechamber GAFF parameters into another force field Denny Bromley (Fri Mar 26 2010 - 16:26:06 PDT)
- RE: [AMBER] transforming Antechamber GAFF parameters into another force field Bill Ross (Fri Mar 26 2010 - 16:41:12 PDT)
- Re: [AMBER] transforming Antechamber GAFF parameters into another force field Gustavo Seabra (Sat Mar 27 2010 - 21:30:54 PDT)
  - Re: [AMBER] transforming Antechamber GAFF parameters into another force field Alan (Sun Mar 28 2010 - 04:51:11 PDT)
    - RE: [AMBER] transforming Antechamber GAFF parameters into another force field Denny Bromley (Mon Mar 29 2010 - 09:40:31 PDT)
[AMBER] amber job hangs Ed Pate (Fri Mar 26 2010 - 17:29:33 PDT)
- Re: [AMBER] amber job hangs Robert Duke (Fri Mar 26 2010 - 17:53:43 PDT)
[AMBER] RMSD of Specific Atoms Jagdeesh C (Sat Mar 27 2010 - 00:29:45 PDT)
- Re: [AMBER] RMSD of Specific Atoms Jason Swails (Sat Mar 27 2010 - 07:44:04 PDT)
[AMBER] SMD of QM part in QMMM MD simulation Dmitri Nilov (Sat Mar 27 2010 - 05:39:47 PDT)
- Re: [AMBER] SMD of QM part in QMMM MD simulation M. L. Dodson (Sat Mar 27 2010 - 06:27:16 PDT)
[AMBER] MM-PBSA not generating snapshot_lig.all.out and snapshot_statistics.out files mish (Sat Mar 27 2010 - 11:25:49 PDT)
- Re: [AMBER] MM-PBSA not generating snapshot_lig.all.out and snapshot_statistics.out files Billy Miller III (Sat Mar 27 2010 - 12:05:19 PDT)
[AMBER] Which shake option to be used nicholus bhattacharjee (Sun Mar 28 2010 - 03:21:51 PDT)
- Re: [AMBER] Which shake option to be used case (Sun Mar 28 2010 - 06:35:24 PDT)
[AMBER] Installing AmberTools Thomas Stockner (Sun Mar 28 2010 - 06:39:38 PDT)
- Re: [AMBER] Installing AmberTools Jason Swails (Sun Mar 28 2010 - 08:43:01 PDT)
  - Re: [AMBER] Installing AmberTools Thomas Stockner (Sun Mar 28 2010 - 11:00:57 PDT)
[AMBER] Error in MMPBSA pandb09.lzu.cn (Sun Mar 28 2010 - 17:14:44 PDT)
[AMBER] minimization really make protein better? geyan (Sun Mar 28 2010 - 21:48:21 PDT)
- Re: [AMBER] minimization really make protein better? Carlos Simmerling (Mon Mar 29 2010 - 04:35:28 PDT)
- Re: Re: [AMBER] minimization really make protein better? geyan (Mon Mar 29 2010 - 20:15:55 PDT)
  - Re: Re: [AMBER] minimization really make protein better? Dmitri Nilov (Tue Mar 30 2010 - 00:03:10 PDT)
  - Re: Re: [AMBER] minimization really make protein better? Carlos Simmerling (Tue Mar 30 2010 - 04:22:48 PDT)
[AMBER] CASP Shaandar Nyamtulga (Sun Mar 28 2010 - 23:47:50 PDT)
- [AMBER] AMBER ff99sb Mannan (Mon Mar 29 2010 - 02:04:59 PDT)
  - Re: [AMBER] AMBER ff99sb gloglo_at_work (Mon Mar 29 2010 - 03:03:33 PDT)
  - Re: [AMBER] AMBER ff99sb Carlos Simmerling (Mon Mar 29 2010 - 04:32:27 PDT)
    - Re: [AMBER] AMBER ff99sb Mannan (Tue Mar 30 2010 - 03:26:44 PDT)
    - Re: [AMBER] AMBER ff99sb Carlos Simmerling (Tue Mar 30 2010 - 04:19:40 PDT)
[AMBER] reg REMD maya maya (Mon Mar 29 2010 - 04:49:08 PDT)
- Re: [AMBER] reg REMD Carlos Simmerling (Mon Mar 29 2010 - 05:02:16 PDT)
  - Re: [AMBER] reg REMD Dongshan Wei (Mon May 31 2010 - 12:04:48 PDT)
    - Re: [AMBER] reg REMD Jason Swails (Mon May 31 2010 - 18:06:21 PDT)
    - Re: [AMBER] reg REMD Dongshan Wei (Tue Jun 01 2010 - 09:21:13 PDT)
    - Re: [AMBER] reg REMD Daniel Roe (Tue Jun 01 2010 - 10:30:05 PDT)
[AMBER] is iwrap=1 a key parameter? Nancy (Mon Mar 29 2010 - 05:49:24 PDT)
- Re: [AMBER] is iwrap=1 a key parameter? Ben Roberts (Mon Mar 29 2010 - 06:40:06 PDT)
- Re: [AMBER] is iwrap=1 a key parameter? case (Mon Mar 29 2010 - 07:19:26 PDT)
  - Re:Re: [AMBER] is iwrap=1 a key parameter? Nancy (Mon Mar 29 2010 - 22:11:17 PDT)
[AMBER] How to find conserved coordinated waters? Sasha Buzko (Mon Mar 29 2010 - 14:51:30 PDT)
- Re: [AMBER] How to find conserved coordinated waters? Thomas Cheatham III (Mon Mar 29 2010 - 14:57:48 PDT)
[AMBER] how to convert to standard Amber PDB input geyan (Mon Mar 29 2010 - 20:26:17 PDT)
- Re: [AMBER] how to convert to standard Amber PDB input case (Tue Mar 30 2010 - 05:24:14 PDT)
[AMBER] (no subject) Nicee (Mon Mar 29 2010 - 21:31:51 PDT)
[AMBER] vlimit error during equilibration step Nicee (Mon Mar 29 2010 - 21:37:28 PDT)
- Re: [AMBER] vlimit error during equilibration step Carlos Simmerling (Tue Mar 30 2010 - 04:29:12 PDT)
  - Re: [AMBER] vlimit error during equilibration step Nicee (Tue Mar 30 2010 - 04:48:17 PDT)
- Re: [AMBER] vlimit error during equilibration step Nicee (Tue Mar 30 2010 - 21:04:21 PDT)
  - Re: [AMBER] vlimit error during equilibration step jani vinod (Wed Mar 31 2010 - 00:00:12 PDT)
    - Re: [AMBER] vlimit error during equilibration step Nicee (Wed Mar 31 2010 - 00:26:02 PDT)
    - Re: [AMBER] vlimit error during equilibration step Carlos Simmerling (Wed Mar 31 2010 - 04:12:38 PDT)
[AMBER] angular velocity trajectory Madhurima Jana (Mon Mar 29 2010 - 21:48:37 PDT)
[AMBER] how to deal with the system with negative charge ? sculiujl (Tue Mar 30 2010 - 01:20:18 PDT)
- Re: [AMBER] how to deal with the system with negative charge ? Dmitry Mukha (Tue Mar 30 2010 - 01:47:57 PDT)
- Re: [AMBER] how to deal with the system with negative charge ? case (Tue Mar 30 2010 - 05:33:20 PDT)
[AMBER] schlegel diagram meandme meandme (Tue Mar 30 2010 - 03:22:45 PDT)
[AMBER] FW: MENZIES G. (569332) (Tue Mar 30 2010 - 03:45:34 PDT)
- Re: [AMBER] FW: case (Tue Mar 30 2010 - 05:36:09 PDT)
  - Re: [AMBER] FW: Jason Swails (Tue Mar 30 2010 - 10:58:22 PDT)
    - [AMBER] Running without flex case (Tue Mar 30 2010 - 11:32:17 PDT)
[AMBER] how to deal with the system with negative charge ? sculiujl (Tue Mar 30 2010 - 04:10:13 PDT)
- Re: [AMBER] how to deal with the system with negative charge ? Bill Ross (Tue Mar 30 2010 - 10:19:37 PDT)
[AMBER] QMMM of protein-ligand complex: Unable to achieve self consistency Dmitri Nilov (Tue Mar 30 2010 - 07:41:00 PDT)
- Re: [AMBER] QMMM of protein-ligand complex: Unable to achieve self consistency M. L. Dodson (Tue Mar 30 2010 - 08:09:27 PDT)
- RE: [AMBER] QMMM of protein-ligand complex: Unable to achieve self consistency Ross Walker (Tue Mar 30 2010 - 14:10:45 PDT)
  - Re: [AMBER] QMMM of protein-ligand complex: Unable to achieve self consistency Dmitri Nilov (Wed Mar 31 2010 - 01:10:21 PDT)
    - Re: [AMBER] QMMM of protein-ligand complex: Unable to achieve self consistency M. L. Dodson (Wed Mar 31 2010 - 06:36:05 PDT)
- Re: [AMBER] QMMM of protein-ligand complex: Unable to achieve self consistency Markus Kaukonen (Wed Mar 31 2010 - 11:34:32 PDT)
  - Re: [AMBER] QMMM of protein-ligand complex: Unable to achieve self consistency Adrian Roitberg (Wed Mar 31 2010 - 11:50:23 PDT)
[AMBER] tleap savepdb command and organic lignads in proteins imtiaz shafiq (Tue Mar 30 2010 - 10:43:50 PDT)
- Re: [AMBER] tleap savepdb command and organic lignads in proteins Jason Swails (Tue Mar 30 2010 - 10:45:32 PDT)
  - Re: [AMBER] tleap savepdb command and organic lignads in proteins imtiaz shafiq (Tue Mar 30 2010 - 10:50:11 PDT)
    - Re: [AMBER] tleap savepdb command and organic lignads in proteins Jason Swails (Tue Mar 30 2010 - 10:51:11 PDT)
    - Re: [AMBER] tleap savepdb command and organic lignads in proteins imtiaz shafiq (Tue Mar 30 2010 - 14:45:00 PDT)
- Re: [AMBER] tleap savepdb command and organic lignads in proteins Bill Ross (Tue Mar 30 2010 - 14:48:16 PDT)
  - Re: [AMBER] tleap savepdb command and organic lignads in proteins imtiaz shafiq (Wed Mar 31 2010 - 06:43:46 PDT)
[AMBER] issues with pmemd Ganesh Kamath (Tue Mar 30 2010 - 10:57:48 PDT)
- Re: [AMBER] issues with pmemd Robert Duke (Tue Mar 30 2010 - 11:18:43 PDT)
- Re: [AMBER] issues with pmemd case (Tue Mar 30 2010 - 11:23:19 PDT)
  - Re: [AMBER] issues with pmemd Ganesh Kamath (Tue Mar 30 2010 - 12:14:54 PDT)
    - RE: [AMBER] issues with pmemd Ross Walker (Tue Mar 30 2010 - 14:05:04 PDT)
- RE: [AMBER] issues with pmemd Bill Ross (Tue Mar 30 2010 - 14:10:16 PDT)
[AMBER] Neutral aminogroup of N-terminal residue: N3 atom type choice Dmitri Nilov (Wed Mar 31 2010 - 03:31:44 PDT)
- Re: [AMBER] Neutral aminogroup of N-terminal residue: N3 atom type choice M. L. Dodson (Wed Mar 31 2010 - 06:41:30 PDT)
  - Re: [AMBER] Neutral aminogroup of N-terminal residue: N3 atom type choice Dmitri Nilov (Wed Mar 31 2010 - 07:12:14 PDT)
    - Re: [AMBER] Neutral aminogroup of N-terminal residue: N3 atom type choice Dean Cuebas (Wed Mar 31 2010 - 13:57:42 PDT)
[AMBER] free energy contribution of water Hyma vathi (Wed Mar 31 2010 - 04:30:57 PDT)
[AMBER] disulfide bonds? xuemeiwang1103 (Wed Mar 31 2010 - 06:32:02 PDT)
- Re: [AMBER] disulfide bonds? Carlos Simmerling (Wed Mar 31 2010 - 06:44:01 PDT)
- Re: [AMBER] disulfide bonds? case (Wed Mar 31 2010 - 06:46:07 PDT)
[AMBER] membranes Adrian Roitberg (Wed Mar 31 2010 - 07:29:17 PDT)
- Re: [AMBER] membranes Balazs Jojart (Wed Mar 31 2010 - 07:56:24 PDT)
  - Re: [AMBER] membranes Adrian Roitberg (Wed Mar 31 2010 - 08:24:37 PDT)
    - Re: [AMBER] membranes Gould, Ian R (Wed Mar 31 2010 - 08:32:49 PDT)
    - Re: [AMBER] membranes Vlad Cojocaru (Wed Mar 31 2010 - 08:44:26 PDT)
    - Re: [AMBER] membranes Hannes Loeffler (Wed Mar 31 2010 - 09:00:11 PDT)
    - Re: [AMBER] membranes Balazs Jojart (Wed Mar 31 2010 - 09:00:26 PDT)
- RE: [AMBER] membranes Matthew Tessier (Wed Mar 31 2010 - 08:22:58 PDT)
[AMBER] pKa Calculations Using Thermodynamic Integration imtiaz shafiq (Wed Mar 31 2010 - 08:02:49 PDT)
- Re: [AMBER] pKa Calculations Using Thermodynamic Integration Jason Swails (Wed Mar 31 2010 - 08:08:06 PDT)
[AMBER] reg-Generalized Born Approach maya maya (Wed Mar 31 2010 - 08:51:33 PDT)
- Re: [AMBER] reg-Generalized Born Approach case (Wed Mar 31 2010 - 11:42:39 PDT)
  - Re: [AMBER] reg-Generalized Born Approach maya maya (Wed Mar 31 2010 - 21:49:20 PDT)
    - Re: [AMBER] reg-Generalized Born Approach case (Thu Apr 01 2010 - 05:12:03 PDT)
    - Re: [AMBER] reg-Generalized Born Approach Carlos Simmerling (Thu Apr 01 2010 - 05:12:13 PDT)
[AMBER] COOH group:extra undesired bond Jio M (Wed Mar 31 2010 - 09:41:06 PDT)
Re: [AMBER] reg-Generalized Born Approach Bill Ross (Wed Mar 31 2010 - 10:13:29 PDT)
- Re: [AMBER] reg-Generalized Born Approach maya maya (Wed Mar 31 2010 - 11:19:01 PDT)
  - Re: [AMBER] reg-Generalized Born Approach Carlos Simmerling (Wed Mar 31 2010 - 11:21:35 PDT)
[AMBER] DEBIAN: cannot get rid of xleap Amedeo Capobianco (Wed Mar 31 2010 - 10:31:54 PDT)
- Re: [AMBER] DEBIAN: cannot get rid of xleap case (Wed Mar 31 2010 - 11:09:00 PDT)
Re: [AMBER] DEBIAN: cannot get rid of xleap SOLVED Amedeo Capobianco (Wed Mar 31 2010 - 12:01:35 PDT)
[AMBER] antechamber monica.imtech.res.in (Wed Mar 31 2010 - 23:57:43 PDT)
- Re: [AMBER] antechamber Dmitri Nilov (Thu Apr 01 2010 - 00:37:13 PDT)
  - Re: [AMBER] antechamber monica.imtech.res.in (Thu Apr 01 2010 - 02:53:44 PDT)
    - Re: [AMBER] antechamber Dmitry Nilov (Thu Apr 01 2010 - 03:05:48 PDT)
- Re: [AMBER] antechamber case (Thu Apr 01 2010 - 05:14:19 PDT)
  - Re: [AMBER] antechamber monica.imtech.res.in (Sun Apr 04 2010 - 21:41:48 PDT)
    - Re: [AMBER] antechamber case (Mon Apr 05 2010 - 04:41:14 PDT)
[AMBER] QMMM Iron Dmitry Mukha (Thu Apr 01 2010 - 02:15:23 PDT)
- Re: [AMBER] QMMM Iron Gustavo Seabra (Thu Apr 01 2010 - 11:20:37 PDT)
[AMBER] QMMM Iron Dmitry Mukha (Thu Apr 01 2010 - 03:07:08 PDT)
- RE: [AMBER] QMMM Iron Ross Walker (Thu Apr 01 2010 - 09:00:32 PDT)
- RE: [AMBER] QMMM Iron Ross Walker (Thu Apr 01 2010 - 11:09:45 PDT)
[AMBER] SASA Beale, John (Thu Apr 01 2010 - 03:39:26 PDT)
- Re: [AMBER] SASA case (Thu Apr 01 2010 - 05:17:36 PDT)
[AMBER] Problems during AMBER 10 compilation. Zuzanna K. Scigacz (Thu Apr 01 2010 - 05:10:16 PDT)
- Re: [AMBER] Problems during AMBER 10 compilation. case (Thu Apr 01 2010 - 05:53:05 PDT)
  - Re: [AMBER] Problems during AMBER 10 compilation. Zuzanna K. Ścigacz (Tue Apr 06 2010 - 02:17:18 PDT)
    - Re: [AMBER] Problems during AMBER 10 compilation. case (Tue Apr 06 2010 - 04:58:02 PDT)
    - Re: [AMBER] Problems during AMBER 10 compilation. Zuzanna K. Ścigacz (Tue Apr 06 2010 - 05:09:28 PDT)
    - Re: [AMBER] Problems during AMBER 10 compilation. case (Tue Apr 06 2010 - 05:23:01 PDT)
- Re: [AMBER] Problems during AMBER 10 compilation. Zuzanna K. Ścigacz (Tue Apr 06 2010 - 05:40:49 PDT)
  - Re: [AMBER] Problems during AMBER 10 compilation. case (Tue Apr 06 2010 - 05:55:40 PDT)
    - Re: [AMBER] Problems during AMBER 10 compilation. Zuzanna K. Ścigacz (Tue Apr 06 2010 - 06:13:54 PDT)
    - Re: [AMBER] Problems during AMBER 10 compilation. case (Tue Apr 06 2010 - 06:55:01 PDT)
- Re: [AMBER] Problems during AMBER 10 compilation. Bill Ross (Tue Apr 06 2010 - 10:04:52 PDT)
  - Re: [AMBER] Problems during AMBER 10 compilation. Zuzanna K. Ścigacz (Tue Apr 06 2010 - 10:37:36 PDT)
- Re: [AMBER] Problems during AMBER 10 compilation. Bill Ross (Tue Apr 06 2010 - 10:14:44 PDT)
[AMBER] Water models ? xuemeiwang1103 (Thu Apr 01 2010 - 06:01:05 PDT)
- Re: [AMBER] Water models ? Carlos Simmerling (Thu Apr 01 2010 - 06:07:49 PDT)
[AMBER] SANDER BOMB in subroutine sc_check_and_adjust Atom coordinate disagreement imtiaz shafiq (Thu Apr 01 2010 - 06:15:20 PDT)
[AMBER] correct syntax for assinging scmask to two atoms of different molecules imtiaz shafiq (Thu Apr 01 2010 - 07:00:47 PDT)
- Re: [AMBER] correct syntax for assinging scmask to two atoms of different molecules steinbrt.rci.rutgers.edu (Thu Apr 01 2010 - 07:14:04 PDT)
[AMBER] Segmentation Fault Beale, John (Thu Apr 01 2010 - 11:52:34 PDT)
- RE: [AMBER] Segmentation Fault Ross Walker (Thu Apr 01 2010 - 12:14:42 PDT)
[AMBER] How to perform backbone and residues restraint at the same time Rilei Yu (Thu Apr 01 2010 - 19:20:55 PDT)
- Re: [AMBER] How to perform backbone and residues restraint at the same time case (Fri Apr 02 2010 - 06:57:34 PDT)
  - Re: [AMBER] How to perform backbone and residues restraint at the same time Rilei Yu (Sat Apr 03 2010 - 02:40:27 PDT)
[AMBER] Problem with an output file lee lior (Thu Apr 01 2010 - 21:00:49 PDT)
- Re: [AMBER] Problem with an output file Jason Swails (Thu Apr 01 2010 - 21:21:52 PDT)
[AMBER] how to achieve the 2D periodic boundary kecy_w.sina.com (Fri Apr 02 2010 - 06:59:53 PDT)
[AMBER] problem with frcmod parameter pxq (Fri Apr 02 2010 - 07:50:59 PDT)
- Re: [AMBER] problem with frcmod parameter case (Fri Apr 02 2010 - 08:16:53 PDT)
- Re: [AMBER] problem with frcmod parameter Bill Ross (Fri Apr 02 2010 - 10:03:37 PDT)
  - Re: Re: [AMBER] problem with frcmod parameter pxq (Fri Apr 02 2010 - 19:10:02 PDT)
[AMBER] Regarding RDF calculation in Ptraj aneesh cna (Fri Apr 02 2010 - 21:49:06 PDT)
- Re: [AMBER] Regarding RDF calculation in Ptraj Daniel Roe (Mon Apr 05 2010 - 05:04:31 PDT)
[AMBER] thermodynamic integration Hyma vathi (Fri Apr 02 2010 - 23:00:12 PDT)
- Re: [AMBER] thermodynamic integration steinbrt.rci.rutgers.edu (Sat Apr 03 2010 - 08:02:45 PDT)
[AMBER] COOH group:extra undesired bond::NO reply :-( Jio M (Fri Apr 02 2010 - 23:34:45 PDT)
- Re: [AMBER] COOH group:extra undesired bond::NO reply :-( case (Sat Apr 03 2010 - 07:31:59 PDT)
- Re: [AMBER] COOH group:extra undesired bond::NO reply :-( Jio M (Sun Apr 04 2010 - 00:25:12 PDT)
[AMBER] problem when doing bond in tleap pxq (Sat Apr 03 2010 - 00:32:59 PDT)
- Re: [AMBER] problem when doing bond in tleap case (Sat Apr 03 2010 - 07:34:05 PDT)
  - Re: Re: [AMBER] problem when doing bond in tleap pxq (Sun Apr 04 2010 - 08:09:38 PDT)
[AMBER] MMPBSA-on-cluster Rilei Yu (Sat Apr 03 2010 - 02:47:31 PDT)
[AMBER] 转发: MMPBSA-on-cluster Rilei Yu (Sat Apr 03 2010 - 03:15:25 PDT)
[AMBER] MMPBSA-ON-CLUSTER Rilei Yu (Sat Apr 03 2010 - 03:17:47 PDT)
- Re: [AMBER] MMPBSA-ON-CLUSTER Bill Miller III (Sat Apr 03 2010 - 05:15:31 PDT)
  - Re: [AMBER] MMPBSA-ON-CLUSTER Jason Swails (Sat Apr 03 2010 - 06:43:38 PDT)
    - Re: [AMBER] MMPBSA-ON-CLUSTER Rilei Yu (Sat Apr 03 2010 - 18:56:49 PDT)
    - Re: [AMBER] MMPBSA-ON-CLUSTER Bill Miller III (Sat Apr 03 2010 - 19:09:15 PDT)
    - Re: [AMBER] MMPBSA-ON-CLUSTER Rilei Yu (Sat Apr 03 2010 - 20:42:57 PDT)
    - Re: [AMBER] MMPBSA-ON-CLUSTER Jason Swails (Sat Apr 03 2010 - 21:18:23 PDT)
    - Re: [AMBER] MMPBSA-ON-CLUSTER Rilei Yu (Sun Apr 04 2010 - 03:13:12 PDT)
    - Re: [AMBER] MMPBSA-ON-CLUSTER Bill Miller III (Sun Apr 04 2010 - 05:37:06 PDT)
    - [AMBER] SASA Chih-Ying Lin (Sun Apr 04 2010 - 17:39:45 PDT)
[AMBER] Sorry for my multiple-email (making mistake!) Rilei Yu (Sat Apr 03 2010 - 05:12:51 PDT)
[AMBER] makeANG_rst values Andrew Olson (Sat Apr 03 2010 - 14:52:42 PDT)
- Re: [AMBER] makeANG_rst values case (Sat Apr 03 2010 - 15:18:00 PDT)
  - Re: [AMBER] makeANG_rst values Andrew Olson (Tue Apr 06 2010 - 14:21:19 PDT)
    - Re: [AMBER] makeANG_rst values case (Tue Apr 06 2010 - 15:00:14 PDT)
[AMBER] rna simulation Asfa Ali (Sun Apr 04 2010 - 22:42:33 PDT)
- Re: [AMBER] rna simulation shamoon siddiqui (Sun Apr 04 2010 - 22:50:47 PDT)
  - Re: [AMBER] rna simulation Asfa Ali (Sun Apr 04 2010 - 23:12:59 PDT)
    - Re: [AMBER] rna simulation shamoon siddiqui (Sun Apr 04 2010 - 23:23:34 PDT)
    - Re: [AMBER] rna simulation Asfa Ali (Sun Apr 04 2010 - 23:47:38 PDT)
    - Re: [AMBER] rna simulation shamoon siddiqui (Sun Apr 04 2010 - 23:59:47 PDT)
    - Re: [AMBER] rna simulation Jason Swails (Mon Apr 05 2010 - 02:34:48 PDT)
- Re: [AMBER] rna simulation Bill Ross (Mon Apr 05 2010 - 10:32:50 PDT)
- Re: [AMBER] rna simulation Bill Ross (Mon Apr 05 2010 - 10:50:27 PDT)
[AMBER] antechamber monica.imtech.res.in (Sun Apr 04 2010 - 22:52:36 PDT)
[AMBER] undo iwrap wrapping Paul Brandt (Mon Apr 05 2010 - 00:21:22 PDT)
- Re: [AMBER] undo iwrap wrapping Carlos Simmerling (Mon Apr 05 2010 - 03:30:53 PDT)
[AMBER] error in reading namelist cntrl Hyma vathi (Mon Apr 05 2010 - 05:17:26 PDT)
- Re: [AMBER] error in reading namelist cntrl Carlos Simmerling (Mon Apr 05 2010 - 05:22:16 PDT)
- Re: [AMBER] error in reading namelist cntrl case (Mon Apr 05 2010 - 05:53:16 PDT)
  - Re: [AMBER] error in reading namelist cntrl Hyma vathi (Mon Apr 05 2010 - 07:03:09 PDT)
    - Re: [AMBER] error in reading namelist cntrl case (Mon Apr 05 2010 - 07:17:28 PDT)
[AMBER] not sure of the atomtype in .prep pxq (Mon Apr 05 2010 - 06:02:35 PDT)
[AMBER] amber10 installation on SGI IRIX 6.5 Eruysal, Ferdi (Mon Apr 05 2010 - 13:37:49 PDT)
- Re: [AMBER] amber10 installation on SGI IRIX 6.5 Atro Tossavainen (Mon Apr 05 2010 - 22:58:18 PDT)
Re: [AMBER] amber10 installation on SGI IRIX 6.5 Bill Ross (Mon Apr 05 2010 - 13:44:33 PDT)
[AMBER] ligand exchange John S (Mon Apr 05 2010 - 15:05:34 PDT)
- [AMBER] Re: ligand exchange John S (Tue Apr 06 2010 - 01:35:39 PDT)
  - Re: [AMBER] Re: ligand exchange case (Tue Apr 06 2010 - 04:42:13 PDT)
[AMBER] Unit of atomic fluctuation unit nicholus bhattacharjee (Mon Apr 05 2010 - 22:39:26 PDT)
- Re: [AMBER] Unit of atomic fluctuation unit Kshatresh Dutta Dubey (Mon Apr 05 2010 - 23:22:51 PDT)
[AMBER] antechamber Asfa Ali (Tue Apr 06 2010 - 00:30:13 PDT)
- Re: [AMBER] antechamber case (Tue Apr 06 2010 - 04:46:21 PDT)
[AMBER] USING PTRAJ TO PROCESS PMEMD TRAJECTORY COORDINTES DATA Juan Carlos (Tue Apr 06 2010 - 00:35:40 PDT)
- Re: [AMBER] USING PTRAJ TO PROCESS PMEMD TRAJECTORY COORDINTES DATA Robert Duke (Tue Apr 06 2010 - 06:20:50 PDT)
  - Re: [AMBER] USING PTRAJ TO PROCESS PMEMD TRAJECTORY COORDINTES DATA Daniel Roe (Tue Apr 06 2010 - 09:25:53 PDT)
- Re: [AMBER] USING PTRAJ TO PROCESS PMEMD TRAJECTORY COORDINTES DATA Juan Carlos (Thu Apr 08 2010 - 03:49:08 PDT)
[AMBER] Unit of analyze modes with ptraj Samuel Genheden (Tue Apr 06 2010 - 02:54:28 PDT)
[AMBER] Files for Charged serine in proteins? Dean Cuebas (Tue Apr 06 2010 - 09:39:04 PDT)
[AMBER] radius of gyration Ganesh Kamath (Tue Apr 06 2010 - 11:43:22 PDT)
[AMBER] question about EVB Ganesh Kamath (Tue Apr 06 2010 - 11:45:28 PDT)
[AMBER] COOH group:extra undesired bond Jio M (Tue Apr 06 2010 - 21:09:31 PDT)
[AMBER] Traceback: not available, complile with -ftrace = frame Yunfen Wang (Wed Apr 07 2010 - 06:56:33 PDT)
- Re: [AMBER] Traceback: not available, complile with -ftrace = frame Jason Swails (Wed Apr 07 2010 - 07:00:05 PDT)
  - Re:Re: [AMBER] Traceback: not available, complile with -ftrace = frame Yunfen Wang (Wed Apr 07 2010 - 20:51:39 PDT)
    - Re: Re: [AMBER] Traceback: not available, complile with -ftrace = frame Jason Swails (Wed Apr 07 2010 - 21:03:31 PDT)
    - Re:Re: Re: [AMBER] Traceback: not available, complile with -ftrace = frame Yunfen Wang (Wed Apr 07 2010 - 23:33:58 PDT)
    - Re: Re: Re: [AMBER] Traceback: not available, complile with -ftrace = frame Jason Swails (Thu Apr 08 2010 - 05:51:34 PDT)
    - Re: Re: Re: [AMBER] Traceback: not available, complile with -ftrace = frame Bill Ross (Thu Apr 08 2010 - 09:44:24 PDT)
    - Re:Re: Re: Re: [AMBER] Traceback: not available, complile with -ftrace = frame Yunfen Wang (Thu Apr 08 2010 - 18:35:20 PDT)
    - Re: Re: Re: Re: [AMBER] Traceback: not available, complile with -ftrace = frame Jason Swails (Thu Apr 08 2010 - 18:52:24 PDT)
    - Re:Re: Re: Re: [AMBER] Traceback: not available, complile with -ftrace = frame Bill Ross (Fri Apr 09 2010 - 08:57:00 PDT)
[AMBER] Amber99FFSB parameter files for Gaussian Senthil Natesan (Wed Apr 07 2010 - 07:43:15 PDT)
[AMBER] amber 5 manual William Flak (Wed Apr 07 2010 - 08:10:26 PDT)
- Re: [AMBER] amber 5 manual case (Thu Apr 08 2010 - 11:36:03 PDT)
  - Re: [AMBER] amber 5 manual William Flak (Thu Apr 08 2010 - 12:48:33 PDT)
    - Re: [AMBER] amber 5 manual case (Thu Apr 08 2010 - 13:01:45 PDT)
[AMBER] dummy atom William Flak (Wed Apr 07 2010 - 08:21:31 PDT)
[AMBER] Chirality Restraint Ilyas Yildirim (Wed Apr 07 2010 - 10:46:25 PDT)
- RE: [AMBER] Chirality Restraint Seetin, Matthew (Wed Apr 07 2010 - 10:58:47 PDT)
[AMBER] Umbrella Sampling with distances; setting of r1 and r4 in the restraint Matthias Wildauer (Wed Apr 07 2010 - 11:04:45 PDT)
- RE: [AMBER] Umbrella Sampling with distances; setting of r1 and r4 in the restraint Seetin, Matthew (Wed Apr 07 2010 - 11:50:33 PDT)
- Re: [AMBER] Umbrella Sampling with distances; setting of r1 and r4 in the restraint case (Wed Apr 07 2010 - 11:51:06 PDT)
- Re: [AMBER] Umbrella Sampling with distances; setting of r1 and r4 in the restraint Matthias Wildauer (Wed Apr 07 2010 - 11:53:53 PDT)
[AMBER] non bonded interactions (vanderwaal and electrostatic) Ganesh Kamath (Wed Apr 07 2010 - 11:44:04 PDT)
- Re: [AMBER] non bonded interactions (vanderwaal and electrostatic) Barbault Florent (Wed Apr 07 2010 - 12:14:08 PDT)
[AMBER] energy decomposition Ganesh Kamath (Wed Apr 07 2010 - 14:29:08 PDT)
- Re: [AMBER] energy decomposition Bill Miller III (Wed Apr 07 2010 - 14:45:18 PDT)
[AMBER] contiguous trajectory without iwrap=1 Emmanuel Baribefe Naziga (Wed Apr 07 2010 - 16:03:34 PDT)
- Re: [AMBER] contiguous trajectory without iwrap=1 Bill Ross (Wed Apr 07 2010 - 17:02:50 PDT)
- Re: [AMBER] contiguous trajectory without iwrap=1 Jacky Zhao (Wed Apr 07 2010 - 18:01:09 PDT)
  - Re: [AMBER] contiguous trajectory without iwrap=1 Carlos Simmerling (Wed Apr 07 2010 - 18:13:24 PDT)
Re: [AMBER] contiguous trajectory without iwrap=1 Bill Ross (Wed Apr 07 2010 - 16:11:15 PDT)
- Re: [AMBER] contiguous trajectory without iwrap=1 Emmanuel Baribefe Naziga (Wed Apr 07 2010 - 16:56:42 PDT)
[AMBER] Ptraj Problem Jagdeesh C (Wed Apr 07 2010 - 21:35:57 PDT)
- Re: [AMBER] Ptraj Problem Jason Swails (Wed Apr 07 2010 - 21:47:59 PDT)
[AMBER] question on section 2 of MM-PBSA tutorial Andrew Voronkov (Thu Apr 08 2010 - 00:14:17 PDT)
[AMBER] Fortran runtime error :bad value duiring floating point read Yunfen Wang (Thu Apr 08 2010 - 03:05:50 PDT)
- Re: [AMBER] Fortran runtime error :bad value duiring floating point read Trevor Gokey (Thu Apr 08 2010 - 03:36:24 PDT)
  - Re:Re: [AMBER] Fortran runtime error :bad value duiring floating point read Yunfen Wang (Thu Apr 08 2010 - 05:02:43 PDT)
[AMBER] regGB maya maya (Thu Apr 08 2010 - 03:51:23 PDT)
- Re: [AMBER] regGB case (Thu Apr 08 2010 - 07:59:47 PDT)
  - Re: [AMBER] regGB maya maya (Thu Apr 08 2010 - 23:37:53 PDT)
[AMBER] mmpbsa-job-killed Rilei Yu (Thu Apr 08 2010 - 04:07:25 PDT)
- Re: [AMBER] mmpbsa-job-killed mish (Thu Apr 08 2010 - 04:17:11 PDT)
- RE: [AMBER] mmpbsa-job-killed Ross Walker (Thu Apr 08 2010 - 22:30:43 PDT)
  - RE: [AMBER] mmpbsa-job-killed Rilei Yu (Fri Apr 09 2010 - 16:57:49 PDT)
[AMBER] angle force constants in GAFF João Sardinha (Thu Apr 08 2010 - 04:11:00 PDT)
- Re: [AMBER] angle force constants in GAFF case (Thu Apr 08 2010 - 05:27:43 PDT)
  - Re: [AMBER] angle force constants in GAFF João Sardinha (Thu Apr 08 2010 - 05:59:35 PDT)
[AMBER] I do need your help, please William Flak (Thu Apr 08 2010 - 12:04:50 PDT)
- RE: [AMBER] I do need your help, please Ross Walker (Thu Apr 08 2010 - 22:52:19 PDT)
[AMBER] multiconformational RESP fitting with antechamber Yi Shang (Thu Apr 08 2010 - 12:28:12 PDT)
- RE: [AMBER] multiconformational RESP fitting with antechamber Ross Walker (Thu Apr 08 2010 - 22:54:41 PDT)
  - [AMBER] mmpbsa-problem Dima A Sabbah (Fri Apr 09 2010 - 09:30:59 PDT)
[AMBER] developing amber force field Necmettin Pirinccioglu (Thu Apr 08 2010 - 12:46:10 PDT)
- Re: [AMBER] developing amber force field InSuk Joung (Thu Apr 08 2010 - 18:44:14 PDT)
- Re[2]: [AMBER] developing amber force field Necmettin Pirinccioglu (Fri Apr 09 2010 - 02:03:51 PDT)
- Re: Re[2]: [AMBER] developing amber force field Karl N. Kirschner (Fri Apr 09 2010 - 03:12:14 PDT)
- Re[4]: [AMBER] developing amber force field Necmettin Pirinccioglu (Fri Apr 09 2010 - 03:57:14 PDT)
  - Re: Re[4]: [AMBER] developing amber force field Diego Javier Alonso de Armiño (Fri Apr 09 2010 - 09:52:20 PDT)
[AMBER] vlimit exceeded for step Rilei Yu (Thu Apr 08 2010 - 23:52:31 PDT)
- Re: [AMBER] vlimit exceeded for step Jason Swails (Fri Apr 09 2010 - 05:36:33 PDT)
  - Re: [AMBER] vlimit exceeded for step Rilei Yu (Fri Apr 09 2010 - 16:50:56 PDT)
    - Re: [AMBER] vlimit exceeded for step Jason Swails (Fri Apr 09 2010 - 16:59:01 PDT)
    - Re: [AMBER] vlimit exceeded for step Rilei Yu (Sat Apr 10 2010 - 00:47:33 PDT)
- Re: [AMBER] vlimit exceeded for step Thomas Cheatham III (Fri Apr 09 2010 - 08:02:34 PDT)
- RE: [AMBER] vlimit exceeded for step Ross Walker (Fri Apr 09 2010 - 11:59:53 PDT)
[AMBER] Solvent Beale, John (Fri Apr 09 2010 - 08:41:51 PDT)
- Re: [AMBER] Solvent Ganesh Kamath (Fri Apr 09 2010 - 08:53:36 PDT)
[AMBER] Fwd: .rst file corrupted manikanthan bhavaraju (Fri Apr 09 2010 - 08:48:52 PDT)
[AMBER] AmberTool1.3 - problem with reading .gz trajectory file & failure with lmod optimization test Ibrahim Moustafa (Fri Apr 09 2010 - 15:40:47 PDT)
- Re: [AMBER] AmberTool1.3 - problem with reading .gz trajectory file & failure with lmod optimization test Jason Swails (Fri Apr 09 2010 - 16:02:25 PDT)
  - Re: [AMBER] AmberTool1.3 - problem with reading .gz trajectory file & failure with lmod optimization test Ibrahim Moustafa (Fri Apr 09 2010 - 16:14:25 PDT)
    - Re: [AMBER] AmberTool1.3 - problem with reading .gz trajectory file & failure with lmod optimization test Daniel Roe (Mon Apr 12 2010 - 05:12:44 PDT)
    - Re: [AMBER] AmberTool1.3 - problem with reading .gz trajectory file & failure with lmod optimization test Ibrahim Moustafa (Mon Apr 12 2010 - 06:39:07 PDT)
    - Re: [AMBER] AmberTool1.3 - problem with reading .gz trajectory file & failure with lmod optimization test Daniel Roe (Mon Apr 12 2010 - 08:12:29 PDT)
[AMBER] Install AMBER problem. Trojan 007 (Fri Apr 09 2010 - 16:07:53 PDT)
- Re: [AMBER] Install AMBER problem. Jason Swails (Fri Apr 09 2010 - 16:38:54 PDT)
  - RE: [AMBER] Install AMBER problem. Trojan 007 (Sat Apr 10 2010 - 17:55:43 PDT)
[AMBER] slightly off topic: suggestions for DNA single strand simulations Amedeo Capobianco (Sun Apr 11 2010 - 14:11:02 PDT)
- Re: [AMBER] slightly off topic: suggestions for DNA single strand simulations Thomas Cheatham (Tue Apr 13 2010 - 20:13:55 PDT)
  - Re: [AMBER] slightly off topic: suggestions for DNA single strand simulations Asfa Ali (Tue Apr 13 2010 - 21:21:44 PDT)
- Re: [AMBER] slightly off topic: suggestions for DNA single strand simulations Bill Ross (Wed Apr 14 2010 - 09:43:10 PDT)
  - Re: [AMBER] slightly off topic: suggestions for DNA single strand simulations Asfa Ali (Wed Apr 14 2010 - 10:02:25 PDT)
- Re: [AMBER] slightly off topic: suggestions for DNA single strand simulations Bill Ross (Wed Apr 14 2010 - 10:25:47 PDT)
[AMBER] problem with XLEAP on X-client run on windows machine... Babu Kannappan (Mon Apr 12 2010 - 06:22:37 PDT)
- Re: [AMBER] problem with XLEAP on X-client run on windows machine... Lachele Foley (Lists) (Sun Apr 11 2010 - 18:23:09 PDT)
[AMBER] distrbuting an excess charge Homa Azizian (Sun Apr 11 2010 - 22:50:30 PDT)
- Re: [AMBER] distrbuting an excess charge Jason Swails (Mon Apr 12 2010 - 03:16:30 PDT)
[AMBER] RAMD gokul algates (Sun Apr 11 2010 - 22:51:39 PDT)
- Re: [AMBER] RAMD Vlad Cojocaru (Mon Apr 12 2010 - 01:48:36 PDT)
[AMBER] regarding antechamber Asfa Ali (Sun Apr 11 2010 - 23:17:11 PDT)
- Re: [AMBER] regarding antechamber case (Mon Apr 12 2010 - 04:43:24 PDT)
[AMBER] Installation on sles11 on ibm-power6-cpus German Erlenkamp (Mon Apr 12 2010 - 00:50:15 PDT)
- Re: [AMBER] Installation on sles11 on ibm-power6-cpus German Erlenkamp (Fri Apr 23 2010 - 00:35:04 PDT)
[AMBER] Warning in readAmber trajectory():Set #7659 is corrupted (3.)... Silvia Carlotto (Mon Apr 12 2010 - 02:08:50 PDT)
- Re: [AMBER] Warning in readAmber trajectory():Set #7659 is corrupted (3.)... Jason Swails (Mon Apr 12 2010 - 03:03:35 PDT)
  - Re: [AMBER] Warning in readAmber trajectory():Set #7659 is corrupted (3.)... Silvia Carlotto (Mon Apr 12 2010 - 04:30:36 PDT)
    - Re: [AMBER] Warning in readAmber trajectory():Set #7659 is corrupted (3.)... Carlos Simmerling (Mon Apr 12 2010 - 04:35:12 PDT)
    - Re: [AMBER] Warning in readAmber trajectory():Set #7659 is corrupted (3.)... Daniel Roe (Mon Apr 12 2010 - 05:29:53 PDT)
    - Re: [AMBER] Warning in readAmber trajectory():Set #7659 is corrupted (3.)... Lachele Foley (Lists) (Mon Apr 12 2010 - 05:51:07 PDT)
[AMBER] vacuum bubbles generated after heating Nicee (Mon Apr 12 2010 - 02:59:32 PDT)
- Re: [AMBER] vacuum bubbles generated after heating Jason Swails (Mon Apr 12 2010 - 03:11:45 PDT)
  - Re: [AMBER] vacuum bubbles generated after heating Nicee (Tue Apr 13 2010 - 05:53:40 PDT)
- Re: [AMBER] vacuum bubbles generated after heating jani vinod (Tue Apr 13 2010 - 02:26:34 PDT)
[AMBER] PROBLEM WITH PMEMD PERFORMANCE Juan Carlos (Mon Apr 12 2010 - 03:24:12 PDT)
- Re: [AMBER] PROBLEM WITH PMEMD PERFORMANCE Tom Joseph (Mon Apr 12 2010 - 08:16:03 PDT)
- RE: [AMBER] PROBLEM WITH PMEMD PERFORMANCE Ross Walker (Tue Apr 13 2010 - 09:00:13 PDT)
  - [AMBER] Automatic assignment of HID, HIP, HIE?? Dean Cuebas (Tue Apr 13 2010 - 09:36:09 PDT)
    - Re: [AMBER] Automatic assignment of HID, HIP, HIE?? case (Tue Apr 13 2010 - 09:42:51 PDT)
- RE: [AMBER] PROBLEM WITH PMEMD PERFORMANCE Juan Carlos (Thu Apr 15 2010 - 02:03:46 PDT)
  - RE: [AMBER] PROBLEM WITH PMEMD PERFORMANCE Ross Walker (Thu Apr 15 2010 - 23:38:11 PDT)
[AMBER] Does the frequency of output affect MD simulation in AMBER10? Nancy (Mon Apr 12 2010 - 04:06:05 PDT)
- Re: [AMBER] Does the frequency of output affect MD simulation in AMBER10? Carlos Simmerling (Mon Apr 12 2010 - 04:09:45 PDT)
  - Re:Re: [AMBER] Does the frequency of output affect MD simulation in AMBER10? Jianing (Mon Apr 12 2010 - 05:12:08 PDT)
    - Re: Re: [AMBER] Does the frequency of output affect MD simulation in AMBER10? Carlos Simmerling (Mon Apr 12 2010 - 05:13:31 PDT)
    - Re: Re: [AMBER] Does the frequency of output affect MD simulation in AMBER10? Jianing (Mon Apr 12 2010 - 05:37:30 PDT)
    - Re: Re: [AMBER] Does the frequency of output affect MD simulation in AMBER10? Carlos Simmerling (Mon Apr 12 2010 - 07:02:01 PDT)
    - Re: Re: [AMBER] Does the frequency of output affect MD simulation in AMBER10? Jianing (Mon Apr 12 2010 - 21:57:38 PDT)
    - Re: Re: [AMBER] Does the frequency of output affect MD simulation in AMBER10? Carlos Simmerling (Tue Apr 13 2010 - 04:57:06 PDT)
    - Re: Re: [AMBER] Does the frequency of output affect MD simulation in AMBER10? Jianing (Tue Apr 13 2010 - 06:15:14 PDT)
    - Re: Re: [AMBER] Does the frequency of output affect MD simulation in AMBER10? case (Tue Apr 13 2010 - 04:59:04 PDT)
    - Re: Re: [AMBER] Does the frequency of output affect MD simulation in AMBER10? Jianing (Tue Apr 13 2010 - 06:25:29 PDT)
- Re: [AMBER] Does the frequency of output affect MD simulation in AMBER10? Bill Ross (Mon Apr 12 2010 - 11:13:25 PDT)
  - Re:Re: [AMBER] Does the frequency of output affect MD simulation in AMBER10? Jianing (Mon Apr 12 2010 - 22:17:46 PDT)
  - Re:Re: [AMBER] Does the frequency of output affect MD simulation in AMBER10? Bill Ross (Tue Apr 13 2010 - 09:57:28 PDT)
    - Re:Re: [AMBER] Does the frequency of output affect MD simulation in AMBER10? Jianing (Tue Apr 13 2010 - 19:44:33 PDT)
    - Re: Re: [AMBER] Does the frequency of output affect MD simulation in AMBER10? Carlos Simmerling (Tue Apr 13 2010 - 19:46:52 PDT)
    - Re: Re: [AMBER] Does the frequency of output affect MD simulation in AMBER10? Jianing (Wed Apr 14 2010 - 05:25:28 PDT)
    - Re: Re: [AMBER] Does the frequency of output affect MD simulation in AMBER10? Carlos Simmerling (Wed Apr 14 2010 - 05:37:48 PDT)
    - Re: Re: [AMBER] Does the frequency of output affect MD simulation in AMBER10? Jianing (Wed Apr 14 2010 - 06:13:22 PDT)
  - Re:Re: [AMBER] Does the frequency of output affect MD simulation in AMBER10? Bill Ross (Wed Apr 14 2010 - 09:38:23 PDT)
    - Re:Re: [AMBER] Does the frequency of output affect MD simulation in AMBER10? Jianing (Wed Apr 14 2010 - 18:33:07 PDT)
[AMBER] Second Request Dima A Sabbah (Mon Apr 12 2010 - 06:59:56 PDT)
[AMBER] trying to use antechamber with -nc 0 for a molecule Alan (Mon Apr 12 2010 - 07:03:13 PDT)
- Re: [AMBER] trying to use antechamber with -nc 0 for a molecule case (Mon Apr 12 2010 - 07:23:50 PDT)
  - Re: [AMBER] trying to use antechamber with -nc 0 for a molecule Alan (Mon Apr 12 2010 - 08:29:57 PDT)
- Re: [AMBER] trying to use antechamber with -nc 0 for a molecule zoran matovic (Mon Apr 12 2010 - 08:50:03 PDT)
  - Re: [AMBER] trying to use antechamber with -nc 0 for a molecule Alan (Mon Apr 12 2010 - 09:14:35 PDT)
[AMBER] how to pick certain water molecular from a .mdcrd pxq (Mon Apr 12 2010 - 07:08:38 PDT)
[AMBER] Vlimit error in ABMD Emmanuel Baribefe Naziga (Mon Apr 12 2010 - 09:06:44 PDT)
[AMBER] Amber11, pure QM PBC aapeters.ncsu.edu (Mon Apr 12 2010 - 09:07:26 PDT)
- Re: [AMBER] Amber11, pure QM PBC case (Mon Apr 12 2010 - 09:18:05 PDT)
- RE: [AMBER] Amber11, pure QM PBC Ross Walker (Tue Apr 13 2010 - 08:57:12 PDT)
Re: [AMBER] vacuum bubbles generated after heating Bill Ross (Mon Apr 12 2010 - 10:41:30 PDT)
- [AMBER] How do you know when to include improper dihedrals???? Dean Cuebas (Mon Apr 12 2010 - 12:30:07 PDT)
  - Re: [AMBER] How do you know when to include improper dihedrals???? Dmitry Nilov (Thu Apr 15 2010 - 03:05:13 PDT)
    - Re: [AMBER] How do you know when to include improper dihedrals???? Dean Cuebas (Thu Apr 15 2010 - 08:23:12 PDT)
  - Re: [AMBER] How do you know when to include improper dihedrals???? Dmitry Nilov (Thu Apr 15 2010 - 05:42:21 PDT)
    - Re: [AMBER] How do you know when to include improper dihedrals???? Dean Cuebas (Thu Apr 15 2010 - 08:33:31 PDT)
    - [AMBER] angle between DNA (vector) and a plane Taufik Al-Sarraj (Thu Apr 15 2010 - 10:04:14 PDT)
  - Re: [AMBER] How do you know when to include improper dihedrals???? Karl N. Kirschner (Thu Apr 15 2010 - 06:18:02 PDT)
- Re: [AMBER] vacuum bubbles generated after heating Bill Ross (Mon Apr 12 2010 - 13:49:47 PDT)
[AMBER] Amber10 Cuda compile failure aapeters.ncsu.edu (Mon Apr 12 2010 - 14:35:49 PDT)
- Re: [AMBER] Amber10 Cuda compile failure Robert Duke (Mon Apr 12 2010 - 14:53:07 PDT)
- RE: [AMBER] Amber10 Cuda compile failure Ross Walker (Mon Apr 12 2010 - 14:57:36 PDT)
  - RE: [AMBER] Amber10 Cuda compile failure Ross Walker (Tue Apr 13 2010 - 08:54:59 PDT)
    - RE: [AMBER] Amber10 Cuda compile failure aapeters.ncsu.edu (Wed Apr 14 2010 - 14:16:28 PDT)
    - RE: [AMBER] Amber10 Cuda compile failure Ross Walker (Wed Apr 14 2010 - 20:04:09 PDT)
[AMBER] Is the variation of C-Cl bond length normal? Shulin Zhuang (Mon Apr 12 2010 - 15:26:12 PDT)
- [AMBER] Re: Is the variation of C-Cl bond length normal? Shulin Zhuang (Tue Apr 13 2010 - 11:25:58 PDT)
- RE: [AMBER] Is the variation of C-Cl bond length normal? Ross Walker (Tue Apr 13 2010 - 12:57:03 PDT)
[AMBER] Regarding parameter files of dna-lig complex Asfa Ali (Mon Apr 12 2010 - 23:08:18 PDT)
- Re: [AMBER] Regarding parameter files of dna-lig complex Jason Swails (Tue Apr 13 2010 - 06:46:49 PDT)
[AMBER] how to pick certain water molecular from a .mdcrd pxq (Mon Apr 12 2010 - 23:35:08 PDT)
- Re: [AMBER] how to pick certain water molecular from a .mdcrd Jason Swails (Tue Apr 13 2010 - 05:13:36 PDT)
- Re: [AMBER] how to pick certain water molecular from a .mdcrd Thomas Cheatham (Tue Apr 13 2010 - 20:00:27 PDT)
[AMBER] loadmol2 Segmentation fault Rui Li (Tue Apr 13 2010 - 02:55:34 PDT)
- Re: [AMBER] loadmol2 Segmentation fault FyD (Tue Apr 13 2010 - 03:30:40 PDT)
  - Re: [AMBER] loadmol2 Segmentation fault FyD (Tue Apr 13 2010 - 03:51:11 PDT)
    - Re: [AMBER] loadmol2 Segmentation fault case (Tue Apr 13 2010 - 05:18:51 PDT)
    - Re: [AMBER] loadmol2 Segmentation fault FyD (Tue Apr 13 2010 - 11:25:51 PDT)
  - Re: [AMBER] loadmol2 Segmentation fault Rui Li (Tue Apr 13 2010 - 23:30:20 PDT)
    - Re: [AMBER] loadmol2 Segmentation fault Scott Brozell (Wed Apr 14 2010 - 12:07:02 PDT)
    - Re: [AMBER] loadmol2 Segmentation fault FyD (Wed Apr 14 2010 - 12:56:26 PDT)
    - Re: [AMBER] loadmol2 Segmentation fault Scott Brozell (Wed Apr 14 2010 - 13:02:41 PDT)
    - Re: [AMBER] loadmol2 Segmentation fault FyD (Thu Apr 15 2010 - 00:44:45 PDT)
    - Re: [AMBER] loadmol2 Segmentation fault David A. Case (Thu Apr 15 2010 - 08:02:38 PDT)
    - Re: [AMBER] loadmol2 Segmentation fault FyD (Thu Apr 15 2010 - 10:23:09 PDT)
    - Re: [AMBER] loadmol2 Segmentation fault Rui Li (Wed Apr 14 2010 - 23:39:52 PDT)
- Re: [AMBER] loadmol2 Segmentation fault case (Tue Apr 13 2010 - 05:16:28 PDT)
- Re: [AMBER] loadmol2 Segmentation fault FyD (Thu Apr 15 2010 - 01:23:24 PDT)
[AMBER] How to prepare the two tolopogy files when doing TI calculation? fancy2012 (Tue Apr 13 2010 - 05:29:17 PDT)
- Re: [AMBER] How to prepare the two tolopogy files when doing TI calculation? steinbrt.rci.rutgers.edu (Tue Apr 13 2010 - 05:35:46 PDT)
  - Re:Re: [AMBER] How to prepare the two tolopogy files when doing TI calculation? fancy2012 (Tue Apr 13 2010 - 05:58:53 PDT)
- Re: [AMBER] How to prepare the two tolopogy files when doing TIcalculation? Ramu Anandakrishnan (Tue Apr 13 2010 - 05:40:46 PDT)
[AMBER] Asking help for some analysis section nicholus bhattacharjee (Tue Apr 13 2010 - 07:04:03 PDT)
- Re: [AMBER] Asking help for some analysis section case (Tue Apr 13 2010 - 07:39:29 PDT)
Re: [AMBER] Regarding parameter files of dna-lig complex Bill Ross (Tue Apr 13 2010 - 10:01:14 PDT)
[AMBER] amber <-> desmond conversion tools Parish, Carol (Tue Apr 13 2010 - 11:13:22 PDT)
- Re: [AMBER] amber <-> desmond conversion tools Cen Gao (Tue Apr 13 2010 - 22:25:43 PDT)
[AMBER] regarding parameter file creation of dna-lig complex Asfa Ali (Tue Apr 13 2010 - 12:37:15 PDT)
Re: [AMBER] regarding parameter file creation of dna-lig complex Bill Ross (Tue Apr 13 2010 - 13:29:25 PDT)
- Re: [AMBER] regarding parameter file creation of dna-lig complex Asfa Ali (Tue Apr 13 2010 - 21:40:45 PDT)
[AMBER] About restart-job Rilei Yu (Tue Apr 13 2010 - 15:48:14 PDT)
- Re: [AMBER] About restart-job Matthias Wildauer (Wed Apr 14 2010 - 05:53:50 PDT)
[AMBER] Chirality of amines in GAFF Dmitry Nilov (Wed Apr 14 2010 - 00:43:47 PDT)
- Re: [AMBER] Chirality of amines in GAFF Jason Swails (Wed Apr 14 2010 - 05:44:39 PDT)
  - Re: [AMBER] Chirality of amines in GAFF Alan (Wed Apr 14 2010 - 06:23:28 PDT)
- Re: [AMBER] Chirality of amines in GAFF FyD (Wed Apr 14 2010 - 12:51:52 PDT)
  - Re: [AMBER] Chirality of amines in GAFF Dean Cuebas (Wed Apr 14 2010 - 15:12:51 PDT)
    - Re: [AMBER] Chirality of amines in GAFF David A. Case (Wed Apr 14 2010 - 15:34:01 PDT)
[AMBER] the volume is always getting bigger and bigger until crash Yunfen Wang (Wed Apr 14 2010 - 00:56:11 PDT)
- Re: [AMBER] the volume is always getting bigger and bigger until crash Carlos Simmerling (Wed Apr 14 2010 - 03:05:14 PDT)
  - Re:Re: [AMBER] the volume is always getting bigger and bigger until crash Yunfen Wang (Wed Apr 14 2010 - 17:47:38 PDT)
    - Re: Re: [AMBER] the volume is always getting bigger and bigger until crash Carlos Simmerling (Wed Apr 14 2010 - 17:50:04 PDT)
[AMBER] periodic boundary condition juan zeng (Wed Apr 14 2010 - 02:34:40 PDT)
- [AMBER] periodic boundary condition juan zeng (Wed Apr 14 2010 - 22:11:52 PDT)
  - Re: [AMBER] periodic boundary condition Jason Swails (Thu Apr 15 2010 - 04:02:39 PDT)
  - Re: [AMBER] periodic boundary condition Bill Ross (Thu Apr 15 2010 - 08:01:16 PDT)
    - Re: [AMBER] periodic boundary condition Jason Swails (Thu Apr 15 2010 - 09:39:25 PDT)
  - Re: [AMBER] periodic boundary condition Bill Ross (Thu Apr 15 2010 - 11:12:03 PDT)
    - Re: [AMBER] periodic boundary condition juan zeng (Fri Apr 16 2010 - 00:34:53 PDT)
[AMBER] 1-4 EEL Jio M (Wed Apr 14 2010 - 04:44:08 PDT)
[AMBER] (no subject) Waad RHAIEM (Wed Apr 14 2010 - 07:12:15 PDT)
[AMBER] RAMD random number generator Waad RHAIEM (Wed Apr 14 2010 - 07:20:59 PDT)
- Re: [AMBER] RAMD random number generator Vlad Cojocaru (Thu Apr 15 2010 - 01:20:09 PDT)
[AMBER] Thole screening in sander Diddo Diddens (Wed Apr 14 2010 - 07:31:23 PDT)
- Re: [AMBER] Thole screening in sander case (Wed Apr 14 2010 - 08:09:49 PDT)
[AMBER] NMR refinment issues rolandmarques.aol.com (Wed Apr 14 2010 - 09:17:44 PDT)
- Re: [AMBER] NMR refinment issues rolandmarques.aol.com (Thu Apr 15 2010 - 12:54:32 PDT)
- Re: [AMBER] NMR refinment issues David A. Case (Sat Apr 17 2010 - 01:53:44 PDT)
[AMBER] Entropy-problem Rilei Yu (Wed Apr 14 2010 - 15:11:36 PDT)
- Re: [AMBER] Entropy-problem Jason Swails (Wed Apr 14 2010 - 15:31:37 PDT)
  - Re: [AMBER] Entropy-problem Rilei Yu (Wed Apr 14 2010 - 18:47:02 PDT)
[AMBER] Trajectory Smoothing Ganesh Krishnan (Wed Apr 14 2010 - 19:23:15 PDT)
- Re: [AMBER] Trajectory Smoothing Bill Miller III (Thu Apr 15 2010 - 04:09:28 PDT)
- Re: [AMBER] Trajectory Smoothing Bill Ross (Sun Apr 18 2010 - 12:12:56 PDT)
[AMBER] PMEMD.CUDA on GTX275 Levi Pierce (Wed Apr 14 2010 - 21:36:40 PDT)
- RE: [AMBER] PMEMD.CUDA on GTX275 Ross Walker (Wed Apr 14 2010 - 22:56:56 PDT)
  - RE: [AMBER] PMEMD.CUDA on GTX275 Peter Schmidtke (Wed Apr 14 2010 - 23:14:38 PDT)
    - RE: [AMBER] PMEMD.CUDA on GTX275 Ross Walker (Wed Apr 14 2010 - 23:31:54 PDT)
[AMBER] 1-4 EEL Jio M (Thu Apr 15 2010 - 00:47:40 PDT)
Re: [AMBER] Trajectory Smoothing Bill Ross (Thu Apr 15 2010 - 07:47:22 PDT)
- Re: [AMBER] Trajectory Smoothing Ganesh Krishnan (Sat Apr 17 2010 - 09:43:41 PDT)
  - Re: [AMBER] Trajectory Smoothing Daniel Roe (Sat Apr 17 2010 - 13:52:13 PDT)
    - Re: [AMBER] Trajectory Smoothing Jason Swails (Sat Apr 17 2010 - 14:45:22 PDT)
    - Re: [AMBER] Trajectory Smoothing Ganesh Krishnan (Sat Apr 17 2010 - 23:50:58 PDT)
    - Re: [AMBER] Trajectory Smoothing David A. Case (Sun Apr 18 2010 - 00:37:24 PDT)
    - Re: [AMBER] Trajectory Smoothing Ganesh Krishnan (Sun Apr 18 2010 - 10:25:47 PDT)
    - Re: [AMBER] Trajectory Smoothing David A. Case (Sun Apr 18 2010 - 11:19:56 PDT)
    - Re: [AMBER] Trajectory Smoothing Ganesh Krishnan (Sun Apr 18 2010 - 12:02:34 PDT)
    - Re: [AMBER] Trajectory Smoothing Carlos Simmerling (Sun Apr 18 2010 - 12:34:17 PDT)
    - Re: [AMBER] Trajectory Smoothing Ganesh Krishnan (Sun Apr 18 2010 - 13:22:43 PDT)
    - Re: [AMBER] Trajectory Smoothing Ganesh Krishnan (Sun Apr 18 2010 - 12:53:12 PDT)
Re: [AMBER] 1-4 EEL Bill Ross (Thu Apr 15 2010 - 07:56:47 PDT)
- Re: [AMBER] 1-4 EEL Jio M (Thu Apr 15 2010 - 23:32:36 PDT)
- Re: [AMBER] 1-4 EEL Bill Ross (Fri Apr 16 2010 - 09:47:04 PDT)
[AMBER] Steered/Targeted MD Ahmad, Rafi (Thu Apr 15 2010 - 09:08:46 PDT)
[AMBER] Unit of analyze modes with ptraj Samuel Genheden (Thu Apr 15 2010 - 11:22:21 PDT)
- Re: [AMBER] Unit of analyze modes with ptraj David A. Case (Thu Apr 15 2010 - 14:40:51 PDT)
[AMBER] radius of gyration Ganesh Kamath (Thu Apr 15 2010 - 12:42:29 PDT)
- Re: [AMBER] radius of gyration Taufik Al-Sarraj (Fri Apr 16 2010 - 07:28:36 PDT)
[AMBER] BOND TYPE Homa Azizian (Thu Apr 15 2010 - 18:46:49 PDT)
- Re: [AMBER] BOND TYPE Dean Cuebas (Thu Apr 15 2010 - 19:08:43 PDT)
  - Re: [AMBER] BOND TYPE corrections Dean Cuebas (Fri Apr 16 2010 - 09:02:20 PDT)
[AMBER] Nucleic acid aperture Fernando Martín García (Fri Apr 16 2010 - 01:52:34 PDT)
[AMBER] chirality restraints for non-standard residue Jio M (Fri Apr 16 2010 - 04:15:08 PDT)
- Re: [AMBER] chirality restraints for non-standard residue Jason Swails (Fri Apr 16 2010 - 11:37:43 PDT)
  - Re: [AMBER] chirality restraints for non-standard residue Jio M (Fri Apr 16 2010 - 11:54:12 PDT)
- Re: [AMBER] chirality restraints for non-standard residue Jio M (Fri Apr 16 2010 - 12:18:42 PDT)
  - Re: [AMBER] chirality restraints for non-standard residue Jio M (Sun Apr 18 2010 - 01:57:05 PDT)
[AMBER] problem in MMPBSA zgong.hust (Fri Apr 16 2010 - 06:23:57 PDT)
- [AMBER] problem in MMPBSA zgong.hust (Sat Apr 17 2010 - 08:06:47 PDT)
  - Re: [AMBER] problem in MMPBSA Dima A Sabbah (Sat Apr 17 2010 - 10:09:05 PDT)
    - Re: [AMBER] problem in MMPBSA Jason Swails (Sat Apr 17 2010 - 13:53:06 PDT)
    - Re: [AMBER] problem in MMPBSA Dima A Sabbah (Sun Apr 18 2010 - 12:02:11 PDT)
    - Re: [AMBER] problem in MMPBSA Jason Swails (Mon Apr 19 2010 - 04:28:06 PDT)
- Re: Re: [AMBER] problem in MMPBSA zgong.hust (Sat Apr 17 2010 - 18:49:01 PDT)
  - Re: Re: [AMBER] problem in MMPBSA Dima A Sabbah (Sun Apr 18 2010 - 11:52:55 PDT)
[AMBER] PMEMD missing type? - bugfix Josh Berryman (Fri Apr 16 2010 - 06:25:01 PDT)
- Re: [AMBER] PMEMD missing type? - bugfix Robert Duke (Fri Apr 16 2010 - 07:02:05 PDT)
- RE: [AMBER] PMEMD missing type? - bugfix Ross Walker (Fri Apr 16 2010 - 08:48:03 PDT)
- Re: [AMBER] PMEMD missing type? - bugfix Robert Duke (Fri Apr 16 2010 - 08:54:36 PDT)
  - RE: [AMBER] PMEMD missing type? - bugfix Ross Walker (Fri Apr 16 2010 - 09:11:50 PDT)
[AMBER] how is pH treated in Amber - other than constant pH simulations Andrew Voronkov (Fri Apr 16 2010 - 08:44:36 PDT)
- Re: [AMBER] how is pH treated in Amber - other than constant pH simulations Carlos Simmerling (Fri Apr 16 2010 - 09:10:42 PDT)
  - Re: [AMBER] how is pH treated in Amber - other than constant pH simulations Dean Cuebas (Fri Apr 16 2010 - 09:53:34 PDT)
    - Re: Re: [AMBER] how is pH treated in Amber - other than constant pH simulations Andrew Voronkov (Fri Apr 16 2010 - 11:17:32 PDT)
    - Re: [AMBER] how is pH treated in Amber - other than constant pH simulations Dean Cuebas (Fri Apr 16 2010 - 13:05:43 PDT)
    - Re: [AMBER] how is pH treated in Amber - other than constant pH simulations Jason Swails (Fri Apr 16 2010 - 11:25:49 PDT)
    - Re: Re: [AMBER] how is pH treated in Amber - other than constant pH simulations Andrew Voronkov (Tue Apr 20 2010 - 00:32:35 PDT)
    - Re: Re: [AMBER] how is pH treated in Amber - other than constant pH simulations Andrew Voronkov (Tue Apr 20 2010 - 06:24:15 PDT)
    - Re: [AMBER] how is pH treated in Amber - other than constant pH simulations Dean Cuebas (Tue Apr 20 2010 - 08:08:24 PDT)
    - [AMBER] Printing the reaction field in pbsa steinbrt.rci.rutgers.edu (Tue Apr 20 2010 - 08:30:36 PDT)
Re: [AMBER] BOND TYPE Bill Ross (Fri Apr 16 2010 - 09:26:47 PDT)
[AMBER] QM/MM + PIMD aapeters.ncsu.edu (Fri Apr 16 2010 - 10:36:19 PDT)
- Re: [AMBER] QM/MM + PIMD Gustavo Seabra (Fri Apr 16 2010 - 12:20:12 PDT)
[AMBER] Fwd: Re: RE: question on section 2 of MM-PBSA tutorial Andrew Voronkov (Fri Apr 16 2010 - 13:57:54 PDT)
[AMBER] RE: RE: question on section 2 of MM-PBSA tutorial Ross Walker (Fri Apr 16 2010 - 18:29:31 PDT)
[AMBER] analysis for solvation effect for protein Yunfen Wang (Sat Apr 17 2010 - 01:21:14 PDT)
[AMBER] error when running mmpbsa pxq (Sat Apr 17 2010 - 07:25:35 PDT)
- Re: [AMBER] error when running mmpbsa Jason Swails (Sat Apr 17 2010 - 07:58:41 PDT)
  - Re: Re: [AMBER] error when running mmpbsa pxq (Sun Apr 18 2010 - 04:34:44 PDT)
    - Re: Re: [AMBER] error when running mmpbsa Bill Miller III (Sun Apr 18 2010 - 06:50:22 PDT)
    - Re: Re: Re: [AMBER] error when running mmpbsa pxq (Sun Apr 18 2010 - 19:49:37 PDT)
[AMBER] how do MM_PBSA without water geyan (Sun Apr 18 2010 - 00:48:06 PDT)
- Re: [AMBER] how do MM_PBSA without water Bill Miller III (Sun Apr 18 2010 - 06:18:53 PDT)
- Re: Re: [AMBER] how do MM_PBSA without water geyan (Sun Apr 18 2010 - 08:20:57 PDT)
  - Re: Re: [AMBER] how do MM_PBSA without water Bill Miller III (Sun Apr 18 2010 - 08:36:56 PDT)
- Re: Re: Re: [AMBER] how do MM_PBSA without water geyan (Mon Apr 19 2010 - 00:33:23 PDT)
  - Re: Re: Re: [AMBER] how do MM_PBSA without water Bill Miller III (Mon Apr 19 2010 - 06:25:40 PDT)
- Re: Re: Re: [AMBER] how do MM_PBSA without water geyan (Wed Apr 21 2010 - 01:44:53 PDT)
  - Re: Re: Re: [AMBER] how do MM_PBSA without water Jason Swails (Wed Apr 21 2010 - 04:55:36 PDT)
- Re: Re: Re: [AMBER] how do MM_PBSA without water geyan (Thu Apr 22 2010 - 01:21:05 PDT)
  - Re: Re: Re: [AMBER] how do MM_PBSA without water Bill Miller III (Thu Apr 22 2010 - 04:04:48 PDT)
    - Re: Re: Re: Re: [AMBER] how do MM_PBSA without water Bill Ross (Thu Apr 22 2010 - 09:55:00 PDT)
[AMBER] Force constant William Flak (Sun Apr 18 2010 - 08:54:55 PDT)
- Re: [AMBER] Force constant Nicholas Musolino (Sun Apr 18 2010 - 09:08:14 PDT)
  - Re: [AMBER] Force constant William Flak (Sun Apr 18 2010 - 09:56:53 PDT)
    - Re: [AMBER] Force constant Nicholas Musolino (Sun Apr 18 2010 - 11:38:33 PDT)
[AMBER] make a new residue FAD-CYS 030081094 (Mon Apr 19 2010 - 00:29:26 PDT)
[AMBER] how to add a gradually reduced restraint Jianing (Mon Apr 19 2010 - 02:07:00 PDT)
- Re: [AMBER] how to add a gradually reduced restraint Dmitry Nilov (Mon Apr 19 2010 - 07:45:22 PDT)
  - Re:Re: [AMBER] how to add a gradually reduced restraint Jianing (Tue Apr 20 2010 - 00:49:14 PDT)
[AMBER] regarding running Nudged Elastic Band Approach with amber10 jani vinod (Mon Apr 19 2010 - 02:18:29 PDT)
- RE: [AMBER] regarding running Nudged Elastic Band Approach with amber10 Ross Walker (Mon Apr 19 2010 - 13:30:56 PDT)
  - Re: [AMBER] regarding running Nudged Elastic Band Approach with amber10 jani vinod (Mon Apr 19 2010 - 21:11:52 PDT)
    - Re: [AMBER] regarding running Nudged Elastic Band Approach with amber10 Carlos Simmerling (Tue Apr 20 2010 - 03:20:28 PDT)
    - Re: [AMBER] regarding running Nudged Elastic Band Approach with amber10 jani vinod (Tue Apr 20 2010 - 20:12:28 PDT)
    - Re: [AMBER] regarding running Nudged Elastic Band Approach with amber10 Jason Swails (Wed Apr 21 2010 - 05:10:58 PDT)
[AMBER] Simulation of complex Asfa Ali (Mon Apr 19 2010 - 08:22:17 PDT)
- Re: [AMBER] Simulation of complex Shozeb Haider (Mon Apr 19 2010 - 08:26:21 PDT)
  - Re: [AMBER] Simulation of complex steinbrt.rci.rutgers.edu (Mon Apr 19 2010 - 08:42:43 PDT)
    - Re: [AMBER] Simulation of complex Dean Cuebas (Mon Apr 19 2010 - 09:52:00 PDT)
Re: [AMBER] Simulation of complex Bill Ross (Mon Apr 19 2010 - 09:48:56 PDT)
[AMBER] elevated temperature MD Steve Seibold (Mon Apr 19 2010 - 10:10:08 PDT)
- Re: [AMBER] elevated temperature MD Carlos Simmerling (Mon Apr 19 2010 - 10:21:57 PDT)
- Re: [AMBER] elevated temperature MD Nicholas Musolino (Mon Apr 19 2010 - 10:31:05 PDT)
[AMBER] remove water from system Yunfen Wang (Tue Apr 20 2010 - 01:09:01 PDT)
- Re: [AMBER] remove water from system Carlos Simmerling (Tue Apr 20 2010 - 03:06:21 PDT)
- Re: [AMBER] remove water from system Jason Swails (Tue Apr 20 2010 - 05:16:42 PDT)
  - Re:Re: [AMBER] remove water from system Yunfen Wang (Tue Apr 20 2010 - 17:53:36 PDT)
  - Re:Re: [AMBER] remove water from system Yunfen Wang (Wed Apr 21 2010 - 02:42:38 PDT)
    - Re: Re: [AMBER] remove water from system Carlos Simmerling (Wed Apr 21 2010 - 03:29:56 PDT)
    - Re: Re: [AMBER] remove water from system Jason Swails (Wed Apr 21 2010 - 04:37:47 PDT)
- [AMBER] Setup of defined salt concentrations Anselm Horn (Tue Apr 20 2010 - 06:16:33 PDT)
  - Re: [AMBER] Setup of defined salt concentrations InSuk Joung (Tue Apr 20 2010 - 07:44:24 PDT)
    - Re: [AMBER] Setup of defined salt concentrations Dean Cuebas (Tue Apr 20 2010 - 09:14:17 PDT)
  - Re: [AMBER] Setup of defined salt concentrations Bill Ross (Tue Apr 20 2010 - 10:29:24 PDT)
- Re: [AMBER] remove water from system Bill Ross (Tue Apr 20 2010 - 10:02:32 PDT)
[AMBER] How is possible in amber to discriminate by names between protonated\deprotonated C- and N- terminal amido and carboxylic groups? Andrew Voronkov (Tue Apr 20 2010 - 03:23:15 PDT)
- Re: [AMBER] How is possible in amber to discriminate by names between protonated\deprotonated C- and N- terminal amido and carboxylic groups? Dmitry Nilov (Tue Apr 20 2010 - 03:43:52 PDT)
  - Re: Re: [AMBER] How is possible in amber to discriminate by names between protonated\deprotonated C- and N- terminal amido and carboxylic groups? Andrew Voronkov (Tue Apr 20 2010 - 04:27:50 PDT)
    - Re: Re: [AMBER] How is possible in amber to discriminate by names between protonated\deprotonated C- and N- terminal amido and carboxylic groups? Carlos Simmerling (Tue Apr 20 2010 - 04:36:50 PDT)
    - Re: Re: [AMBER] How is possible in amber to discriminate by names between protonated\deprotonated C- and N- terminal amido and carboxylic groups? Dmitry Nilov (Tue Apr 20 2010 - 04:46:20 PDT)
    - Re: Re: Re: [AMBER] How is possible in amber to discriminate by names between protonated\deprotonated C- and N- terminal amido and carboxylic groups? Andrew Voronkov (Tue Apr 20 2010 - 05:28:37 PDT)
    - Re: Re: [AMBER] How is possible in amber to discriminate by names between protonated\deprotonated C- and N- terminal amido and carboxylic groups? Carlos Simmerling (Tue Apr 20 2010 - 06:01:58 PDT)
    - Re: Re: [AMBER] How is possible in amber to discriminate by names between protonated\deprotonated C- and N- terminal amido and carboxylic groups? Dmitry Nilov (Tue Apr 20 2010 - 04:41:26 PDT)
[AMBER] Error: Sander output is missing values Hyma vathi (Tue Apr 20 2010 - 03:31:32 PDT)
- Re: [AMBER] Error: Sander output is missing values Bill Miller III (Tue Apr 20 2010 - 04:36:52 PDT)
  - Re: [AMBER] Error: Sander output is missing values Hyma vathi (Tue Apr 20 2010 - 08:08:31 PDT)
    - Re: [AMBER] Error: Sander output is missing values Jason Swails (Tue Apr 20 2010 - 08:41:03 PDT)
    - Re: [AMBER] Error: Sander output is missing values Hyma vathi (Wed Apr 21 2010 - 08:50:33 PDT)
    - Re: [AMBER] Error: Sander output is missing values Bill Miller III (Wed Apr 21 2010 - 09:25:28 PDT)
- Re: [AMBER] Error: Sander output is missing values Bill Ross (Tue Apr 20 2010 - 10:06:22 PDT)
[AMBER] mm-pbsa: self assembly vijayaraj.clri.res.in (Tue Apr 20 2010 - 04:45:42 PDT)
- Re: [AMBER] mm-pbsa: self assembly Nicholas Musolino (Tue Apr 20 2010 - 04:59:17 PDT)
[AMBER] Strange atom charge in topology file pellegrini (Tue Apr 20 2010 - 06:20:33 PDT)
- Re: [AMBER] Strange atom charge in topology file Yi Shang (Tue Apr 20 2010 - 07:02:23 PDT)
  - Re: [AMBER] Strange atom charge in topology file Yi Shang (Tue Apr 20 2010 - 07:21:07 PDT)
    - Re: [AMBER] Strange atom charge in topology file pellegrini (Tue Apr 20 2010 - 08:12:01 PDT)
[AMBER] Request for MD protocol George Tzotzos (Tue Apr 20 2010 - 07:07:11 PDT)
- Re: [AMBER] Request for MD protocol steinbrt.rci.rutgers.edu (Tue Apr 20 2010 - 07:14:31 PDT)
[AMBER] elevated Temperature MD Steve Seibold (Tue Apr 20 2010 - 09:30:40 PDT)
[AMBER] QM/MM cut problem aapeters.ncsu.edu (Tue Apr 20 2010 - 09:36:18 PDT)
- Re: [AMBER] QM/MM cut problem M. L. Dodson (Tue Apr 20 2010 - 10:04:35 PDT)
- RE: [AMBER] QM/MM cut problem Ross Walker (Tue Apr 20 2010 - 10:20:07 PDT)
  - RE: [AMBER] QM/MM cut problem aapeters.ncsu.edu (Tue Apr 20 2010 - 11:27:46 PDT)
    - RE: [AMBER] QM/MM cut problem Ross Walker (Tue Apr 20 2010 - 15:43:51 PDT)
    - RE: [AMBER] QM/MM cut problem Ross Walker (Thu Apr 29 2010 - 02:09:11 PDT)
    - RE: [AMBER] QM/MM cut problem aapeters.ncsu.edu (Thu Apr 29 2010 - 04:58:49 PDT)
    - RE: [AMBER] QM/MM cut problem Ross Walker (Thu Apr 29 2010 - 05:59:52 PDT)
Re: [AMBER] Setup of defined salt concentrations Bill Ross (Tue Apr 20 2010 - 10:13:06 PDT)
[AMBER] mutate function in NAB Alessandro Nascimento (Tue Apr 20 2010 - 11:11:41 PDT)
[AMBER] The resonable way how to protonate protein for Amber simulation in explicit water ? Marek Maly (Tue Apr 20 2010 - 12:54:04 PDT)
- Re: [AMBER] The resonable way how to protonate protein for Amber simulation in explicit water ? Jason Swails (Wed Apr 21 2010 - 06:35:38 PDT)
  - Re: [AMBER] The resonable way how to protonate protein for Amber simulation in explicit water ? Marek Maly (Wed Apr 21 2010 - 10:29:39 PDT)
    - Re: [AMBER] The resonable way how to protonate protein for Amber simulation in explicit water ? Jason Swails (Wed Apr 21 2010 - 13:02:10 PDT)
    - Re: [AMBER] The resonable way how to protonate protein for Amber simulation in explicit water ? Marek Maly (Wed Apr 21 2010 - 16:07:39 PDT)
[AMBER] mm-pbsa *_com.all.out files moitrayee.mbu.iisc.ernet.in (Tue Apr 20 2010 - 23:07:55 PDT)
- Re: [AMBER] mm-pbsa *_com.all.out files Jason Swails (Wed Apr 21 2010 - 05:00:19 PDT)
[AMBER] Simulation of complex Asfa Ali (Wed Apr 21 2010 - 00:19:23 PDT)
- Re: [AMBER] Simulation of complex steinbrt.rci.rutgers.edu (Wed Apr 21 2010 - 02:24:12 PDT)
  - Re: [AMBER] Simulation of complex Asfa Ali (Wed Apr 21 2010 - 03:51:04 PDT)
    - Re: [AMBER] Simulation of complex steinbrt.rci.rutgers.edu (Wed Apr 21 2010 - 04:03:40 PDT)
    - Re: [AMBER] Simulation of complex N.R. Jena (Wed Apr 21 2010 - 04:05:31 PDT)
    - Re: [AMBER] Simulation of complex N.R. Jena (Wed Apr 21 2010 - 04:10:20 PDT)
    - Re: [AMBER] Simulation of complex Asfa Ali (Wed Apr 21 2010 - 04:39:34 PDT)
- Re: [AMBER] Simulation of complex Bill Ross (Wed Apr 21 2010 - 09:34:02 PDT)
[AMBER] about parmjoin Alan (Wed Apr 21 2010 - 01:40:04 PDT)
[AMBER] Do molecular dynamics in the limited space Yunjie Zhao (Wed Apr 21 2010 - 06:40:31 PDT)
- Re: [AMBER] Do molecular dynamics in the limited space Bill Ross (Fri Apr 23 2010 - 10:00:11 PDT)
[AMBER] MOPAC2009 output results into antechamber Alex Boncheff (Wed Apr 21 2010 - 08:14:58 PDT)
- Re: [AMBER] MOPAC2009 output results into antechamber David A. Case (Wed Apr 21 2010 - 10:03:26 PDT)
Re: [AMBER] Do molecular dynamics in the limited space Bill Ross (Wed Apr 21 2010 - 09:59:39 PDT)
- Re: [AMBER] Do molecular dynamics in the limited space Yunjie Zhao (Thu Apr 22 2010 - 19:35:10 PDT)
  - Re: [AMBER] Do molecular dynamics in the limited space case (Fri Apr 23 2010 - 05:50:32 PDT)
[AMBER] effect of pre-processor flags on pmemd? Thomas Zeiser (Wed Apr 21 2010 - 13:12:17 PDT)
- Re: [AMBER] effect of pre-processor flags on pmemd? Robert Duke (Wed Apr 21 2010 - 13:31:20 PDT)
[AMBER] vdW question. ros (Wed Apr 21 2010 - 18:41:38 PDT)
- Re: [AMBER] vdW question. Jason Swails (Wed Apr 21 2010 - 19:29:39 PDT)
  - Re: [AMBER] vdW question. Kevin Hauser (Wed Apr 21 2010 - 20:26:50 PDT)
- Re: [AMBER] vdW question. steinbrt.rci.rutgers.edu (Thu Apr 22 2010 - 00:22:14 PDT)
  - Re: [AMBER] vdW question. ros (Thu Apr 22 2010 - 08:43:25 PDT)
- Re: [AMBER] vdW question. Bill Ross (Thu Apr 22 2010 - 09:40:33 PDT)
- Re: [AMBER] vdW question. Bill Ross (Thu Apr 22 2010 - 10:14:15 PDT)
[AMBER] solvent accessible surface Yunfen Wang (Wed Apr 21 2010 - 20:27:11 PDT)
- Re: [AMBER] solvent accessible surface Bill Miller III (Wed Apr 21 2010 - 20:41:02 PDT)
[AMBER] regarding sqm Asfa Ali (Wed Apr 21 2010 - 23:51:32 PDT)
- Re: [AMBER] regarding sqm Jason Swails (Thu Apr 22 2010 - 05:15:26 PDT)
  - Re: [AMBER] regarding sqm Asfa Ali (Thu Apr 22 2010 - 06:17:13 PDT)
[AMBER] A possible pmemd bug Lijiang Yang (Thu Apr 22 2010 - 04:59:42 PDT)
- Re: [AMBER] A possible pmemd bug Robert Duke (Thu Apr 22 2010 - 07:01:24 PDT)
  - Re: [AMBER] A possible pmemd bug Scott Brozell (Thu Apr 22 2010 - 14:19:58 PDT)
  - RE: [AMBER] A possible pmemd bug Ross Walker (Thu Apr 22 2010 - 16:47:49 PDT)
[AMBER] Compiling pmemd (Amber 10) with OpenMPI, pathscale, etc. Paul S. Nerenberg (Thu Apr 22 2010 - 15:58:07 PDT)
- RE: [AMBER] Compiling pmemd (Amber 10) with OpenMPI, pathscale, etc. Ross Walker (Thu Apr 22 2010 - 16:23:37 PDT)
  - Re: [AMBER] Compiling pmemd (Amber 10) with OpenMPI, pathscale, etc. Paul S. Nerenberg (Thu Apr 22 2010 - 16:50:57 PDT)
[AMBER] bond command Siddharth Rastogi (Thu Apr 22 2010 - 17:31:02 PDT)
- Re: [AMBER] bond command Jason Swails (Thu Apr 22 2010 - 17:52:11 PDT)
[AMBER] problem on running saveAmberParm tianyuan meng (Thu Apr 22 2010 - 18:54:39 PDT)
- Re: [AMBER] problem on running saveAmberParm Bill Ross (Fri Apr 23 2010 - 11:00:29 PDT)
  - Re: [AMBER] problem on running saveAmberParm tianyuan meng (Tue May 04 2010 - 02:20:26 PDT)
    - Re: [AMBER] problem on running saveAmberParm case (Tue May 04 2010 - 04:54:23 PDT)
- Re: [AMBER] problem on running saveAmberParm Bill Ross (Tue May 04 2010 - 10:26:56 PDT)
  - Re: [AMBER] problem on running saveAmberParm tianyuan meng (Sun May 09 2010 - 19:11:47 PDT)
[AMBER] H-bond analysis in ptraj Yunfen Wang (Thu Apr 22 2010 - 20:30:27 PDT)
- Re: [AMBER] H-bond analysis in ptraj geyan (Thu Apr 22 2010 - 22:54:22 PDT)
  - Re: [AMBER] H-bond analysis in ptraj Shulin Zhuang (Thu Apr 22 2010 - 23:57:31 PDT)
[AMBER] molecular surface area geyan (Thu Apr 22 2010 - 22:49:01 PDT)
- Re: [AMBER] molecular surface area Balazs Jojart (Thu Apr 22 2010 - 23:26:58 PDT)
- [AMBER] about VMD's molecular surface area calculation geyan (Wed May 05 2010 - 01:45:49 PDT)
  - Re: [AMBER] about VMD's molecular surface area calculation Balazs Jojart (Wed May 05 2010 - 01:56:24 PDT)
    - Re: [AMBER] about VMD's molecular surface area calculation Balazs Jojart (Wed May 05 2010 - 04:53:09 PDT)
    - Re: [AMBER] about VMD's molecular surface area calculation Jason Swails (Wed May 05 2010 - 06:51:09 PDT)
[AMBER] Hydrogen Bond Analysis - explanation needed Srivatsan (Fri Apr 23 2010 - 02:42:33 PDT)
[AMBER] question about Amber Tutorial-A1 Rui Li (Fri Apr 23 2010 - 03:55:26 PDT)
- RE: [AMBER] question about Amber Tutorial-A1 Ross Walker (Fri Apr 23 2010 - 08:04:24 PDT)
  - RE: [AMBER] question about Amber Tutorial-A1 Rui Li (Fri Apr 23 2010 - 21:57:54 PDT)
Re: [AMBER] H-bond analysis in ptraj Bill Ross (Fri Apr 23 2010 - 10:03:58 PDT)
- Re:Re: [AMBER] H-bond analysis in ptraj Yunfen Wang (Fri Apr 23 2010 - 17:56:38 PDT)
  - Re: Re: [AMBER] H-bond analysis in ptraj Jason Swails (Sat Apr 24 2010 - 05:19:26 PDT)
Re: [AMBER] problem on running saveAmberParm Bill Ross (Fri Apr 23 2010 - 10:27:27 PDT)
- Re: [AMBER] problem on running saveAmberParm case (Fri Apr 23 2010 - 10:52:11 PDT)
[AMBER] PMEMD compiling errors Dian Jiao (Fri Apr 23 2010 - 11:25:47 PDT)
- RE: [AMBER] PMEMD compiling errors Ross Walker (Fri Apr 23 2010 - 12:09:19 PDT)
  - Re: [AMBER] PMEMD compiling errors Dian Jiao (Fri Apr 23 2010 - 13:26:47 PDT)
[AMBER] problem with paiwise energy decomposition using mm-pbsa moitrayee.mbu.iisc.ernet.in (Fri Apr 23 2010 - 11:50:14 PDT)
[AMBER] Antechamber, GAFF and methylimidazole typing Ben Roberts (Fri Apr 23 2010 - 14:32:57 PDT)
[AMBER] about IGB geyan (Fri Apr 23 2010 - 18:08:51 PDT)
- RE: [AMBER] about IGB Ross Walker (Fri Apr 23 2010 - 22:55:43 PDT)
- Re: RE: [AMBER] about IGB geyan (Sun Apr 25 2010 - 01:50:17 PDT)
  - Re: RE: [AMBER] about IGB Carlos Simmerling (Sun Apr 25 2010 - 03:54:28 PDT)
- Re: Re: RE: [AMBER] about IGB geyan (Sun Apr 25 2010 - 22:42:32 PDT)
  - Re: Re: RE: [AMBER] about IGB Carlos Simmerling (Mon Apr 26 2010 - 04:11:29 PDT)
[AMBER] pmemd.cuda problem Levi Pierce (Sat Apr 24 2010 - 16:18:57 PDT)
- RE: [AMBER] pmemd.cuda problem Ross Walker (Sat Apr 24 2010 - 18:43:24 PDT)
  - Re: [AMBER] pmemd.cuda problem Levi Pierce (Sat Apr 24 2010 - 19:04:47 PDT)
    - RE: [AMBER] pmemd.cuda problem Ross Walker (Mon Apr 26 2010 - 00:36:16 PDT)
    - Re: [AMBER] pmemd.cuda problem Levi Pierce (Mon Apr 26 2010 - 09:19:46 PDT)
- Re: [AMBER] pmemd.cuda problem case (Sun Apr 25 2010 - 09:23:42 PDT)
[AMBER] RESP Iodine William Flak (Sun Apr 25 2010 - 04:52:21 PDT)
[AMBER] The system has extended beyond the extent of the virtual box kamlesh sahu (Mon Apr 26 2010 - 01:31:23 PDT)
- Re: [AMBER] The system has extended beyond the extent of the virtual box Carlos Simmerling (Mon Apr 26 2010 - 03:50:00 PDT)
  - Re: [AMBER] The system has extended beyond the extent of the virtual box kamlesh sahu (Mon Apr 26 2010 - 17:23:17 PDT)
[AMBER] WARNING: There is a bond of 8.894214 angstroms between Hyma vathi (Mon Apr 26 2010 - 02:19:30 PDT)
- Re: [AMBER] WARNING: There is a bond of 8.894214 angstroms between Dmitry Nilov (Mon Apr 26 2010 - 02:33:01 PDT)
  - Re: [AMBER] WARNING: There is a bond of 8.894214 angstroms between Hyma vathi (Mon Apr 26 2010 - 02:55:59 PDT)
    - Re: [AMBER] WARNING: There is a bond of 8.894214 angstroms between Dmitry Nilov (Mon Apr 26 2010 - 03:53:15 PDT)
- Re: [AMBER] WARNING: There is a bond of 8.894214 angstroms between case (Mon Apr 26 2010 - 05:50:39 PDT)
  - Re: [AMBER] WARNING: There is a bond of 8.894214 angstroms between Hyma vathi (Mon Apr 26 2010 - 09:58:35 PDT)
- Re: [AMBER] WARNING: There is a bond of 8.894214 angstroms between Bill Ross (Mon Apr 26 2010 - 10:19:28 PDT)
- Re: [AMBER] WARNING: There is a bond of 8.894214 angstroms between Bill Ross (Mon Apr 26 2010 - 10:23:21 PDT)
[AMBER] Announcement: release of Amber11 and AmberTools 1.4 case (Mon Apr 26 2010 - 05:41:28 PDT)
[AMBER] Comparing dihedral energy curves Lekpa Duukori (Mon Apr 26 2010 - 09:34:24 PDT)
- Re: [AMBER] Comparing dihedral energy curves Ilyas Yildirim (Mon Apr 26 2010 - 10:15:53 PDT)
  - Re: [AMBER] Comparing dihedral energy curves Lekpa Duukori (Mon Apr 26 2010 - 11:56:50 PDT)
[AMBER] new ambertools folder distribution and Makefile_at Alan (Mon Apr 26 2010 - 09:58:12 PDT)
- Re: [AMBER] new ambertools folder distribution and Makefile_at case (Mon Apr 26 2010 - 13:11:10 PDT)
[AMBER]Fortran runtime error: Bad value during integer read Ying Yang (Mon Apr 26 2010 - 23:59:54 PDT)
- Re: [AMBER]Fortran runtime error: Bad value during integer read Jason Swails (Tue Apr 27 2010 - 05:15:37 PDT)
  - Re: [AMBER]Fortran runtime error: Bad value during integer read Ying Yang (Tue Apr 27 2010 - 19:53:44 PDT)
    - Re: [AMBER]Fortran runtime error: Bad value during integer read Jason Swails (Tue Apr 27 2010 - 21:15:45 PDT)
- Re: [AMBER]Fortran runtime error: Bad value during integer read Jason Swails (Tue Apr 27 2010 - 21:38:13 PDT)
[AMBER] ambertools 1.4, tests Alan (Tue Apr 27 2010 - 03:49:18 PDT)
- Re: [AMBER] ambertools 1.4, tests David Watson (Tue Apr 27 2010 - 06:31:36 PDT)
  - Re: [AMBER] ambertools 1.4, tests Alan (Tue Apr 27 2010 - 08:12:49 PDT)
    - Re: [AMBER] ambertools 1.4, tests Jason Swails (Tue Apr 27 2010 - 09:05:33 PDT)
    - [AMBER] Compiling AmberTools 1.4 on MacOS10.5 Dean Cuebas (Tue Apr 27 2010 - 10:26:37 PDT)
    - Re: [AMBER] Compiling AmberTools 1.4 on MacOS10.5 Jason Swails (Tue Apr 27 2010 - 10:34:33 PDT)
    - Re: [AMBER] Compiling AmberTools 1.4 on MacOS10.5 Alan (Tue Apr 27 2010 - 10:43:06 PDT)
    - Re: [AMBER] Compiling AmberTools 1.4 on MacOS10.5 Dean Cuebas (Tue Apr 27 2010 - 12:42:16 PDT)
- Re: [AMBER] ambertools 1.4, tests Mengjuei Hsieh (Tue Apr 27 2010 - 11:37:29 PDT)
- Re: [AMBER] ambertools 1.4, tests Mengjuei Hsieh (Sun May 02 2010 - 02:47:53 PDT)
  - Re: [AMBER] ambertools 1.4, tests Alan (Sun May 02 2010 - 10:38:58 PDT)
  - Re: [AMBER] ambertools 1.4, tests Mengjuei Hsieh (Mon May 03 2010 - 03:02:52 PDT)
    - Re: [AMBER] ambertools 1.4, tests Alan (Mon May 03 2010 - 03:56:29 PDT)
    - Re: [AMBER] ambertools 1.4, tests Ben Roberts (Mon May 03 2010 - 06:53:38 PDT)
    - Re: [AMBER] ambertools 1.4, tests David Watson (Mon May 03 2010 - 07:19:53 PDT)
    - Re: [AMBER] ambertools 1.4, tests Ben Roberts (Mon May 03 2010 - 07:53:26 PDT)
    - Re: [AMBER] ambertools 1.4, tests case (Mon May 03 2010 - 08:02:58 PDT)
    - Re: [AMBER] ambertools 1.4, tests Alan (Mon May 03 2010 - 08:58:22 PDT)
    - Re: [AMBER] ambertools 1.4, tests Ben Roberts (Tue May 04 2010 - 14:45:23 PDT)
    - Re: [AMBER] ambertools 1.4, tests Ben Roberts (Tue May 04 2010 - 16:35:57 PDT)
    - Re: [AMBER] ambertools 1.4, tests Alan (Wed May 05 2010 - 01:19:38 PDT)
    - Re: [AMBER] ambertools 1.4, tests Ben Roberts (Wed May 05 2010 - 08:04:50 PDT)
    - Re: [AMBER] ambertools 1.4, tests Alan (Wed May 05 2010 - 08:12:43 PDT)
    - Re: [AMBER] ambertools 1.4, tests Ben Roberts (Wed May 05 2010 - 14:34:31 PDT)
    - Re: [AMBER] ambertools 1.4, tests Alan (Thu May 06 2010 - 07:18:53 PDT)
    - Re: [AMBER] ambertools 1.4, tests Ben Roberts (Thu May 06 2010 - 09:26:01 PDT)
    - Re: [AMBER] ambertools 1.4, tests Alan (Thu May 06 2010 - 09:58:57 PDT)
    - Re: [AMBER] ambertools 1.4, tests David Watson (Thu May 06 2010 - 10:23:58 PDT)
    - Re: [AMBER] ambertools 1.4, tests Mengjuei Hsieh (Mon May 03 2010 - 15:39:05 PDT)
    - Re: [AMBER] ambertools 1.4, tests Mengjuei Hsieh (Mon May 03 2010 - 10:13:14 PDT)
Fw: Fwd: Fw: Fw: [AMBER] The resonable way how to protonate protein for Amber simulation in explicit water ? Ramu Anandakrishnan (Tue Apr 27 2010 - 05:43:17 PDT)
- Re: Fw: Fwd: Fw: Fw: [AMBER] The resonable way how to protonate protein for Amber simulation in explicit water ? Marek Maly (Tue Apr 27 2010 - 07:32:04 PDT)
- [AMBER] Addions grid ? Marek Maly (Tue Apr 27 2010 - 07:59:16 PDT)
[AMBER] explicit water MMPBSA Cristina Sisu (Tue Apr 27 2010 - 06:54:56 PDT)
Re: [AMBER] Addions grid ? Bill Ross (Tue Apr 27 2010 - 10:01:36 PDT)
- Re: [AMBER] Addions grid ? Marek Maly (Tue Apr 27 2010 - 10:58:04 PDT)
- Re: [AMBER] Addions grid ? Bill Ross (Tue Apr 27 2010 - 11:09:49 PDT)
  - Re: [AMBER] Addions grid ? Marek Maly (Tue Apr 27 2010 - 11:22:41 PDT)
- Re: [AMBER] Addions grid ? Bill Ross (Tue Apr 27 2010 - 11:32:29 PDT)
  - Re: [AMBER] Addions grid ? Marek Maly (Tue Apr 27 2010 - 14:05:10 PDT)
[AMBER] about skinnb liu junjun (Tue Apr 27 2010 - 10:08:48 PDT)
- Re: [AMBER] about skinnb Robert Duke (Tue Apr 27 2010 - 10:32:34 PDT)
  - Re: [AMBER] about skinnb liu junjun (Wed Apr 28 2010 - 12:05:21 PDT)
- Re: [AMBER] about skinnb Robert Duke (Wed Apr 28 2010 - 12:16:53 PDT)
  - Re: [AMBER] about skinnb liu junjun (Wed Apr 28 2010 - 13:02:42 PDT)
    - Re: [AMBER] about skinnb liu junjun (Wed Apr 28 2010 - 13:27:35 PDT)
- Re: [AMBER] about skinnb Robert Duke (Wed Apr 28 2010 - 14:04:36 PDT)
  - Re: [AMBER] about skinnb liu junjun (Wed Apr 28 2010 - 14:25:58 PDT)
[AMBER] ff99SB-ILDN Titus, Jamie (bairdje) (Tue Apr 27 2010 - 11:38:32 PDT)
[AMBER] Constraint minimisation before MD simulation Amire-Brahimi Benjamin (Tue Apr 27 2010 - 14:48:31 PDT)
- Re: [AMBER] Constraint minimisation before MD simulation Carlos Simmerling (Tue Apr 27 2010 - 14:58:32 PDT)
- Re: [AMBER] Constraint minimisation before MD simulation Bill Ross (Tue Apr 27 2010 - 15:05:46 PDT)
[AMBER] how to load topology file Siddharth Rastogi (Tue Apr 27 2010 - 15:21:33 PDT)
Re: [AMBER] how to load topology file Bill Ross (Tue Apr 27 2010 - 15:27:00 PDT)
- Re: [AMBER] how to load topology file Lachele Foley (Lists) (Tue Apr 27 2010 - 15:32:44 PDT)
[AMBER] Question about RMSD in AMBER Yingjie Lin (Tue Apr 27 2010 - 17:42:55 PDT)
- Re: [AMBER] Question about RMSD in AMBER Carlos Simmerling (Tue Apr 27 2010 - 18:14:46 PDT)
  - Re: [AMBER] Question about RMSD in AMBER Yingjie Lin (Wed Apr 28 2010 - 07:57:04 PDT)
    - Re: [AMBER] Question about RMSD in AMBER Yi Shang (Wed Apr 28 2010 - 08:44:51 PDT)
[AMBER] question about cluster analysis Jianing (Tue Apr 27 2010 - 20:01:11 PDT)
[AMBER] A bugfix for thiazole-imidazole rings Hasan Alniss (Wed Apr 28 2010 - 04:55:08 PDT)
[AMBER] AMBER VS QM energy calculations for dihedrals Palermo Giulia (Wed Apr 28 2010 - 07:09:50 PDT)
- Re: [AMBER] AMBER VS QM energy calculations for dihedrals Ilyas Yildirim (Wed Apr 28 2010 - 07:32:42 PDT)
[AMBER] problem rejoining segmented out files in long simulation g t (Wed Apr 28 2010 - 08:04:59 PDT)
- Re: [AMBER] problem rejoining segmented out files in long simulation Carlos Simmerling (Wed Apr 28 2010 - 08:10:58 PDT)
- Re: [AMBER] problem rejoining segmented out files in long simulation Jason Swails (Wed Apr 28 2010 - 08:31:03 PDT)
  - Re: [AMBER] problem rejoining segmented out files in long simulation g t (Wed Apr 28 2010 - 09:10:20 PDT)
[AMBER] Fortran runtime error: Bad value during integer read João Henriques (Wed Apr 28 2010 - 09:09:35 PDT)
- Re: [AMBER] Fortran runtime error: Bad value during integer read Mengjuei Hsieh (Wed Apr 28 2010 - 18:33:42 PDT)
  - [AMBER] joining out files Homa Azizian (Wed Apr 28 2010 - 20:37:39 PDT)
    - Re: [AMBER] joining out files Homa Azizian (Thu Apr 29 2010 - 04:03:55 PDT)
    - Re: [AMBER] joining out files Bill Miller III (Thu Apr 29 2010 - 04:06:08 PDT)
    - Re: [AMBER] joining out files Homa Azizian (Thu Apr 29 2010 - 14:29:47 PDT)
    - Re: [AMBER] joining out files Jason Swails (Thu Apr 29 2010 - 14:40:21 PDT)
    - Re: [AMBER] joining out files Bill Ross (Thu Apr 29 2010 - 12:49:25 PDT)
  - Re: [AMBER] Fortran runtime error: Bad value during integer read João Henriques (Thu Apr 29 2010 - 04:20:00 PDT)
    - Re: [AMBER] Fortran runtime error: Bad value during integer read Jason Swails (Thu Apr 29 2010 - 05:10:25 PDT)
    - Re: [AMBER] Fortran runtime error: Bad value during integer read João Henriques (Thu Apr 29 2010 - 05:32:58 PDT)
    - Re: [AMBER] Fortran runtime error: Bad value during integer read João Henriques (Thu Apr 29 2010 - 06:19:13 PDT)
    - Re: [AMBER] Fortran runtime error: Bad value during integer read Piotr Cieplak (Thu Apr 29 2010 - 10:56:59 PDT)
    - Re: [AMBER] Fortran runtime error: Bad value during integer read João Henriques (Thu Apr 29 2010 - 11:39:39 PDT)
    - Re: [AMBER] Fortran runtime error: Bad value during integer read FyD (Thu Apr 29 2010 - 12:55:05 PDT)
    - Re: [AMBER] Fortran runtime error: Bad value during integer read João Henriques (Fri Apr 30 2010 - 05:28:51 PDT)
    - Re: [AMBER] Fortran runtime error: Bad value during integer read Piotr Cieplak (Thu Apr 29 2010 - 13:50:51 PDT)
    - Re: [AMBER] Fortran runtime error: Bad value during integer read Jason Swails (Thu Apr 29 2010 - 06:30:45 PDT)
    - Re: [AMBER] Fortran runtime error: Bad value during integer read Piotr Cieplak (Thu Apr 29 2010 - 13:56:54 PDT)
[AMBER] sleap from AT 1.4 doesn't seem ok Alan (Wed Apr 28 2010 - 11:35:12 PDT)
- Re: [AMBER] sleap from AT 1.4 doesn't seem ok case (Thu Apr 29 2010 - 06:43:59 PDT)
[AMBER] forcefield parameters for TiO2/peptides? Tom Williams (Wed Apr 28 2010 - 13:31:01 PDT)
- Re: [AMBER] forcefield parameters for TiO2/peptides? Ben Roberts (Thu Apr 29 2010 - 08:11:40 PDT)
  - Re: [AMBER] forcefield parameters for TiO2/peptides? Tom Williams (Thu Apr 29 2010 - 14:03:48 PDT)
    - Re: [AMBER] forcefield parameters for TiO2/peptides? FyD (Thu Apr 29 2010 - 15:56:39 PDT)
[AMBER] Question: ptraj masks Yingjie Lin (Wed Apr 28 2010 - 14:22:19 PDT)
- Re: [AMBER] Question: ptraj masks Carlos Simmerling (Wed Apr 28 2010 - 14:28:37 PDT)
[AMBER] OT: GLYLIB C libraries for molecular data Lachele Foley (Lists) (Wed Apr 28 2010 - 16:02:42 PDT)
[AMBER] Tesla C2050 atom limit? ben rodriguez (Wed Apr 28 2010 - 17:44:43 PDT)
- RE: [AMBER] Tesla C2050 atom limit? Scott Le Grand (Thu Apr 29 2010 - 00:02:17 PDT)
- RE: [AMBER] Tesla C2050 atom limit? Ross Walker (Thu Apr 29 2010 - 01:12:22 PDT)
[AMBER] to test nab with openmp Alan (Thu Apr 29 2010 - 00:42:59 PDT)
- [AMBER] Re: to test nab with openmp Alan (Thu Apr 29 2010 - 02:13:18 PDT)
  - [AMBER] Re: to test nab with openmp Alan (Thu Apr 29 2010 - 03:09:22 PDT)
[AMBER] AmberTools.pdf (AT 1.4) Alan (Thu Apr 29 2010 - 06:48:41 PDT)
- Re: [AMBER] AmberTools.pdf (AT 1.4) Mengjuei Hsieh (Sun May 02 2010 - 02:52:22 PDT)
[AMBER] failed to compile Amber11 with mpi on Mac Alan (Thu Apr 29 2010 - 07:41:20 PDT)
- Re: [AMBER] failed to compile Amber11 with mpi on Mac Jason Swails (Thu Apr 29 2010 - 07:51:26 PDT)
  - Re: [AMBER] failed to compile Amber11 with mpi on Mac Alan (Thu Apr 29 2010 - 07:59:22 PDT)
- [AMBER] Re: failed to compile Amber11 with mpi on Mac Alan (Thu Apr 29 2010 - 07:51:56 PDT)
- Re: [AMBER] failed to compile Amber11 with mpi on Mac David Watson (Thu Apr 29 2010 - 07:54:08 PDT)
  - Re: [AMBER] failed to compile Amber11 with mpi on Mac case (Thu Apr 29 2010 - 08:08:31 PDT)
    - [AMBER] AmberTool 1.4 with Intel 10.1.014 on snow leopard Yu Chen (Thu Apr 29 2010 - 11:54:16 PDT)
    - Re: [AMBER] AmberTool 1.4 with Intel 10.1.014 on snow leopard Mengjuei Hsieh (Sat May 01 2010 - 18:33:53 PDT)
[AMBER] a possible typo bug while building pmemd with mpi Alan (Thu Apr 29 2010 - 08:18:29 PDT)
- [AMBER] Re: a possible typo bug while building pmemd with mpi Alan (Thu Apr 29 2010 - 08:45:56 PDT)
- Re: [AMBER] a possible typo bug while building pmemd with mpi Jason Swails (Thu Apr 29 2010 - 08:50:28 PDT)
  - Re: [AMBER] a possible typo bug while building pmemd with mpi Alan (Thu Apr 29 2010 - 09:13:03 PDT)
    - Re: [AMBER] a possible typo bug while building pmemd with mpi David Watson (Thu Apr 29 2010 - 09:22:33 PDT)
    - Re: [AMBER] a possible typo bug while building pmemd with mpi Alan (Thu Apr 29 2010 - 09:46:22 PDT)
    - Re: [AMBER] a possible typo bug while building pmemd with mpi Jason Swails (Thu Apr 29 2010 - 09:57:46 PDT)
    - Re: [AMBER] a possible typo bug while building pmemd with mpi Ben Roberts (Thu Apr 29 2010 - 10:13:56 PDT)
    - Re: [AMBER] a possible typo bug while building pmemd with mpi Alan (Thu Apr 29 2010 - 11:08:24 PDT)
    - Re: [AMBER] a possible typo bug while building pmemd with mpi Dean Cuebas (Fri Apr 30 2010 - 10:52:10 PDT)
    - Re: [AMBER] a possible typo bug while building pmemd with mpi Jason Swails (Fri Apr 30 2010 - 20:12:30 PDT)
    - Re: [AMBER] a possible typo bug while building pmemd with mpi Alan (Sat May 01 2010 - 00:04:42 PDT)
    - Re: [AMBER] a possible typo bug while building pmemd with mpi Dean Cuebas (Mon May 03 2010 - 10:43:33 PDT)
[AMBER] Stability Calculation Using MMPBSA.py? Hopkins, Robert (Thu Apr 29 2010 - 12:36:45 PDT)
- Re: [AMBER] Stability Calculation Using MMPBSA.py? Jason Swails (Thu Apr 29 2010 - 12:49:12 PDT)
- RE: [AMBER] Stability Calculation Using MMPBSA.py? Hopkins, Robert (Thu Apr 29 2010 - 13:24:31 PDT)
[AMBER] question about mass card of frcmod file Jim Miller (Thu Apr 29 2010 - 14:50:52 PDT)
Re: [AMBER] question about mass card of frcmod file Bill Ross (Thu Apr 29 2010 - 16:07:25 PDT)
[AMBER] how to write one ptraj file into several smaller files Yunfen Wang (Fri Apr 30 2010 - 05:00:02 PDT)
- Re: [AMBER] how to write one ptraj file into several smaller files Jason Swails (Fri Apr 30 2010 - 05:08:37 PDT)
- Re: [AMBER] how to write one ptraj file into several smaller files monica.imtech.res.in (Fri Apr 30 2010 - 06:19:45 PDT)
[AMBER] "go" keyword in ptraj Ben Roberts (Fri Apr 30 2010 - 06:34:28 PDT)
- RE: [AMBER] "go" keyword in ptraj Ross Walker (Fri Apr 30 2010 - 06:43:10 PDT)
  - RE: [AMBER] "go" keyword in ptraj Thomas Cheatham III (Fri Apr 30 2010 - 08:39:21 PDT)
    - Re: [AMBER] "go" keyword in ptraj Ben Roberts (Fri Apr 30 2010 - 11:36:14 PDT)
[AMBER] Undefined symbols: "___builtin___strcpy_chk" and more Yu Chen (Fri Apr 30 2010 - 07:10:44 PDT)
- Re: [AMBER] Undefined symbols: "___builtin___strcpy_chk" and more David Watson (Fri Apr 30 2010 - 07:29:35 PDT)
  - Re: [AMBER] Undefined symbols: "___builtin___strcpy_chk" and more Yu Chen (Fri Apr 30 2010 - 08:46:55 PDT)
- Re: [AMBER] Undefined symbols: "___builtin___strcpy_chk" and more case (Fri Apr 30 2010 - 07:41:11 PDT)
  - Re: [AMBER] Undefined symbols: "___builtin___strcpy_chk" and more Yu Chen (Fri Apr 30 2010 - 08:25:35 PDT)
    - Re: [AMBER] Undefined symbols: "___builtin___strcpy_chk" and more Mengjuei Hsieh (Sat May 01 2010 - 18:23:06 PDT)
    - Re: [AMBER] Undefined symbols: "___builtin___strcpy_chk" and more case (Sat May 01 2010 - 19:36:13 PDT)
- Re: [AMBER] Undefined symbols: "___builtin___strcpy_chk" and more Bill Ross (Fri Apr 30 2010 - 10:07:57 PDT)
  - Re: [AMBER] Undefined symbols: "___builtin___strcpy_chk" and more Yu Chen (Fri Apr 30 2010 - 11:20:30 PDT)
[AMBER] Problem from ala scanning Rilei Yu (Fri Apr 30 2010 - 07:31:25 PDT)
- Re: [AMBER] Problem from ala scanning Bill Miller III (Fri Apr 30 2010 - 07:52:37 PDT)
  - Re: [AMBER] Problem from ala scanning Rilei Yu (Fri Apr 30 2010 - 15:58:37 PDT)
    - Re: [AMBER] Problem from ala scanning Bill Miller III (Fri Apr 30 2010 - 16:08:57 PDT)
    - Re: [AMBER] Problem from ala scanning Rilei Yu (Fri Apr 30 2010 - 16:42:16 PDT)
    - [AMBER] TER dfinition at the middile of pdb file Homa Azizian (Fri Apr 30 2010 - 17:41:38 PDT)
    - Re: [AMBER] TER dfinition at the middile of pdb file Jason Swails (Fri Apr 30 2010 - 20:29:23 PDT)
[AMBER] distance mapping monica.imtech.res.in (Fri Apr 30 2010 - 07:51:48 PDT)
[AMBER] xgrid in opempi 1.4.1 still broken Alan (Fri Apr 30 2010 - 08:04:24 PDT)
- Re: [AMBER] xgrid in opempi 1.4.1 still broken case (Fri Apr 30 2010 - 09:35:02 PDT)
- Re: [AMBER] xgrid in opempi 1.4.1 still broken Mengjuei Hsieh (Sat May 01 2010 - 18:49:50 PDT)
  - Re: [AMBER] xgrid in opempi 1.4.1 still broken David Watson (Sat May 01 2010 - 19:28:00 PDT)
    - Re: [AMBER] xgrid in opempi 1.4.1 still broken Alan (Sun May 02 2010 - 10:28:04 PDT)
[AMBER] freezing selected residues Senthil Natesan (Fri Apr 30 2010 - 10:11:20 PDT)
- Re: [AMBER] freezing selected residues Jason Swails (Sat May 01 2010 - 15:52:44 PDT)
[AMBER] nmr order parameter and autocorrelation luzhenw1.msu.edu (Fri Apr 30 2010 - 13:43:00 PDT)
- Re: [AMBER] nmr order parameter and autocorrelation Carlos Simmerling (Fri Apr 30 2010 - 13:47:00 PDT)
  - Re: [AMBER] nmr order parameter and autocorrelation luzhenw1.msu.edu (Fri Apr 30 2010 - 14:39:01 PDT)
    - Re: [AMBER] nmr order parameter and autocorrelation Paul S. Nerenberg (Fri Apr 30 2010 - 15:19:51 PDT)
    - Re: [AMBER] nmr order parameter and autocorrelation Samuel Genheden (Fri Apr 30 2010 - 22:55:59 PDT)
    - Re: [AMBER] nmr order parameter and autocorrelation luzhenw1.msu.edu (Mon May 03 2010 - 12:29:52 PDT)
    - Re: [AMBER] nmr order parameter and autocorrelation case (Mon May 03 2010 - 13:33:20 PDT)
    - Re: [AMBER] nmr order parameter and autocorrelation luzhenw1.msu.edu (Mon May 03 2010 - 18:56:36 PDT)
    - [AMBER] Error in umbrella run in AMBER 10 Catein Catherine (Tue May 04 2010 - 03:41:30 PDT)
    - Re: [AMBER] Error in umbrella run in AMBER 10 case (Tue May 04 2010 - 04:41:09 PDT)
    - Re: [AMBER] nmr order parameter and autocorrelation Samuel Genheden (Mon May 03 2010 - 21:59:53 PDT)
  - [AMBER] Shaking up a XRC structure with a slightly different substrate Dean Cuebas (Tue May 04 2010 - 13:09:51 PDT)
[AMBER] MM parameters for TiO2 Piotr Cieplak (Fri Apr 30 2010 - 14:57:28 PDT)
[AMBER] Size of real sop dadoun (Sat May 01 2010 - 06:02:34 PDT)
- Re: [AMBER] size of real Robert Duke (Sat May 01 2010 - 07:39:59 PDT)
  - Re: [AMBER] size of real sop dadoun (Sat May 01 2010 - 15:14:57 PDT)
- Re: [AMBER] size of real Robert Duke (Sat May 01 2010 - 15:33:44 PDT)
  - Re: [AMBER] size of real Tom Joseph (Sat May 01 2010 - 16:11:27 PDT)
- Re: [AMBER] size of real Robert Duke (Sat May 01 2010 - 20:16:55 PDT)
  - Re: [AMBER] size of real Tom Joseph (Sat May 01 2010 - 23:17:42 PDT)
  - RE: [AMBER] size of real Scott Le Grand (Sun May 02 2010 - 11:17:07 PDT)
- Re: [AMBER] size of real Robert Duke (Sun May 02 2010 - 05:31:47 PDT)
- Re: [AMBER] size of real Robert Duke (Sun May 02 2010 - 12:05:11 PDT)
  - RE: [AMBER] size of real Scott Le Grand (Sun May 02 2010 - 12:11:58 PDT)
[AMBER] size of real sop dadoun (Sat May 01 2010 - 06:03:59 PDT)
- Re: [AMBER] size of real Jason Swails (Sat May 01 2010 - 07:25:29 PDT)
[AMBER] Installation of Amber10 jaya c.jose (Sat May 01 2010 - 07:02:12 PDT)
- Re: [AMBER] Installation of Amber10 Jason Swails (Sat May 01 2010 - 07:16:03 PDT)
- [AMBER] Is AMBER 10 compatible with notebook? Catein Catherine (Sat May 01 2010 - 08:18:58 PDT)
  - Re: [AMBER] Is AMBER 10 compatible with notebook? Jason Swails (Sat May 01 2010 - 08:29:15 PDT)
    - RE: [AMBER] Is AMBER 10 compatible with notebook? Catein Catherine (Sat May 01 2010 - 10:20:43 PDT)
  - RE: [AMBER] Is AMBER 10 compatible with notebook? Ross Walker (Sat May 01 2010 - 08:32:09 PDT)
    - RE: [AMBER] Is AMBER 10 compatible with notebook? Catein Catherine (Sat May 01 2010 - 10:19:50 PDT)
[AMBER] ifbox=2 in prmtop but angles are not correct ashutosh shandilya (Sun May 02 2010 - 03:35:01 PDT)
- Re: [AMBER] ifbox=2 in prmtop but angles are not correct case (Mon May 03 2010 - 07:08:03 PDT)
  - Re: [AMBER] ifbox=2 in prmtop but angles are not correct ashutosh shandilya (Tue May 04 2010 - 03:41:04 PDT)
    - Re: [AMBER] ifbox=2 in prmtop but angles are not correct case (Tue May 04 2010 - 04:57:26 PDT)
    - Re: [AMBER] ifbox=2 in prmtop but angles are not correct case (Tue May 04 2010 - 04:58:31 PDT)
[AMBER] md simulation-cap Rilei Yu (Sun May 02 2010 - 05:40:16 PDT)
[AMBER] molecular dynamics set up Rilei Yu (Sun May 02 2010 - 16:58:40 PDT)
- Re: [AMBER] molecular dynamics set up case (Mon May 03 2010 - 06:57:33 PDT)
[AMBER] Re: Fortran runtime error: Bad value during integer read FyD (Mon May 03 2010 - 00:06:22 PDT)
[AMBER] adding salt for MM_PBSA Xioling Chuang (Mon May 03 2010 - 01:53:35 PDT)
- Re: [AMBER] adding salt for MM_PBSA Bill Miller III (Mon May 03 2010 - 03:53:43 PDT)
[AMBER] serial TI with ifsc = 2 and icfe = 0 Josh Berryman (Mon May 03 2010 - 04:08:59 PDT)
- [AMBER] Re: serial TI with ifsc = 2 and icfe = 0 Josh Berryman (Mon May 03 2010 - 10:31:13 PDT)
[AMBER] use of "ambmask" ? Senthil Natesan (Mon May 03 2010 - 08:52:51 PDT)
- Re: [AMBER] use of "ambmask" ? Ben Roberts (Tue May 04 2010 - 06:49:58 PDT)
  - Re: [AMBER] use of "ambmask" ? & freezing selected residues Senthil Natesan (Tue May 04 2010 - 14:23:32 PDT)
[AMBER] Amber with MPI (GNU and Intel) on Mac SL Alan (Mon May 03 2010 - 09:56:13 PDT)
- Re: [AMBER] Amber with MPI (GNU and Intel) on Mac SL Jason Swails (Mon May 03 2010 - 16:09:29 PDT)
  - Re: [AMBER] Amber with MPI (GNU and Intel) on Mac SL Alan (Tue May 04 2010 - 02:26:38 PDT)
    - Re: [AMBER] Amber with MPI (GNU and Intel) on Mac SL Jason Swails (Tue May 04 2010 - 06:12:39 PDT)
[AMBER] davies bouldin index and DME Geoffrey Wood (Mon May 03 2010 - 10:50:17 PDT)
[AMBER] How to make ionic liquid solvent box? 김호신 (Mon May 03 2010 - 12:24:34 PDT)
- RE: [AMBER] How to make ionic liquid solvent box? 킹아기돼지 (Tue May 04 2010 - 13:42:20 PDT)
- RE: [AMBER] How to make ionic liquid solvent box? Hoshin Kim (Tue May 04 2010 - 14:06:39 PDT)
  - Re: [AMBER] How to make ionic liquid solvent box? Jason Swails (Tue May 04 2010 - 15:10:00 PDT)
- Re: [AMBER] How to make ionic liquid solvent box? Hoshin Kim (Tue May 04 2010 - 15:41:56 PDT)
- RE: [AMBER] How to make ionic liquid solvent box? Bill Ross (Tue May 04 2010 - 15:44:14 PDT)
- Re: [AMBER] How to make ionic liquid solvent box? Bill Ross (Tue May 04 2010 - 15:47:41 PDT)
- RE: [AMBER] How to make ionic liquid solvent box? Hoshin Amber (Wed May 05 2010 - 00:35:34 PDT)
- RE: [AMBER] How to make ionic liquid solvent box? Bill Ross (Wed May 05 2010 - 13:54:04 PDT)
Re: [AMBER] How to make ionic liquid solvent box? Bill Ross (Mon May 03 2010 - 13:05:42 PDT)
[AMBER] How to analyze without printing out mdcrd Dian Jiao (Mon May 03 2010 - 13:47:22 PDT)
- Re: [AMBER] How to analyze without printing out mdcrd Bill Miller III (Mon May 03 2010 - 13:57:06 PDT)
- Re: [AMBER] How to analyze without printing out mdcrd Daniel Roe (Tue May 04 2010 - 05:52:31 PDT)
  - Re: [AMBER] How to analyze without printing out mdcrd Dian Jiao (Tue May 04 2010 - 07:03:05 PDT)
[AMBER] Davies Bouldin Index with DME in ptraj Geoffrey Wood (Mon May 03 2010 - 13:48:36 PDT)
- Re: [AMBER] Davies Bouldin Index with DME in ptraj Jianyin Shao (Mon May 10 2010 - 16:10:05 PDT)
  - Re: [AMBER] Davies Bouldin Index with DME in ptraj Geoffrey Wood (Mon Jul 05 2010 - 10:15:26 PDT)
Re: [AMBER] How to analyze without printing out mdcrd Bill Ross (Mon May 03 2010 - 13:55:28 PDT)
[AMBER] molecular dynamics set up Rilei Yu (Mon May 03 2010 - 16:36:06 PDT)
- Re: [AMBER] molecular dynamics set up Carlos Simmerling (Mon May 03 2010 - 16:57:05 PDT)
  - Re: [AMBER] molecular dynamics set up Rilei Yu (Mon May 03 2010 - 17:49:31 PDT)
    - Re: [AMBER] molecular dynamics set up Carlos Simmerling (Tue May 04 2010 - 06:07:37 PDT)
    - Re: [AMBER] molecular dynamics set up Rilei Yu (Tue May 04 2010 - 17:06:44 PDT)
    - Re: [AMBER] crash in minimization step Homa Azizian (Tue May 04 2010 - 21:35:39 PDT)
    - Re: [AMBER] crash in minimization step case (Wed May 05 2010 - 04:56:02 PDT)
- Re: [AMBER] molecular dynamics set up Bill Ross (Tue May 04 2010 - 17:17:11 PDT)
[AMBER] MBAR on TI data Oliver Kuhn (Tue May 04 2010 - 01:32:29 PDT)
- Re: [AMBER] MBAR on TI data steinbrt.rci.rutgers.edu (Tue May 04 2010 - 02:16:33 PDT)
  - Re: [AMBER] MBAR on TI data Oliver Kuhn (Tue May 04 2010 - 22:55:41 PDT)
    - Re: [AMBER] MBAR on TI data steinbrt.rci.rutgers.edu (Tue May 04 2010 - 23:42:21 PDT)
[AMBER] Question about running AMBER on a mac Emily Curtis (Tue May 04 2010 - 06:18:52 PDT)
- Re: [AMBER] Question about running AMBER on a mac Jason Swails (Tue May 04 2010 - 06:29:06 PDT)
- Re: [AMBER] Question about running AMBER on a mac Ben Roberts (Tue May 04 2010 - 06:31:40 PDT)
- Re: [AMBER] Question about running AMBER on a mac David Watson (Tue May 04 2010 - 06:46:15 PDT)
  - Re: [AMBER] Question about running AMBER on a mac Emily Curtis (Tue May 04 2010 - 10:54:01 PDT)
- Re: [AMBER] Question about running AMBER on a mac Mengjuei Hsieh (Tue May 04 2010 - 11:32:57 PDT)
[AMBER] RE: about xleap parameter files Ross Walker (Tue May 04 2010 - 06:31:12 PDT)
[AMBER] nothing is written to .mdcrd file Andrew Voronkov (Tue May 04 2010 - 07:15:51 PDT)
- Re: [AMBER] nothing is written to .mdcrd file Carlos Simmerling (Tue May 04 2010 - 07:32:38 PDT)
[AMBER] MAC version of the GTX 285 and PMEMD.CUDA Axel (Tue May 04 2010 - 07:17:50 PDT)
- RE: [AMBER] MAC version of the GTX 285 and PMEMD.CUDA Ross Walker (Tue May 04 2010 - 08:02:42 PDT)
- Re: [AMBER] MAC version of the GTX 285 and PMEMD.CUDA Jason Swails (Tue May 04 2010 - 08:12:12 PDT)
  - Re: [AMBER] MAC version of the GTX 285 and PMEMD.CUDA Axel (Tue May 04 2010 - 08:33:00 PDT)
  - Re: [AMBER] MAC version of the GTX 285 and PMEMD.CUDA Alan (Wed May 05 2010 - 07:02:50 PDT)
    - Re: [AMBER] MAC version of the GTX 285 and PMEMD.CUDA Jason Swails (Wed May 05 2010 - 07:27:01 PDT)
    - RE: [AMBER] MAC version of the GTX 285 and PMEMD.CUDA Ross Walker (Wed May 05 2010 - 07:27:25 PDT)
    - Re: [AMBER] MAC version of the GTX 285 and PMEMD.CUDA Alan (Wed May 05 2010 - 08:03:26 PDT)
    - RE: [AMBER] MAC version of the GTX 285 and PMEMD.CUDA Scott Le Grand (Wed May 05 2010 - 09:23:13 PDT)
[AMBER] Davies Bouldin Index with DME Geoffrey Wood (Tue May 04 2010 - 07:31:25 PDT)
[AMBER] Davies Bouldin Index with DME Geoffrey Wood (Tue May 04 2010 - 07:41:29 PDT)
[AMBER] Kirkwood g factor Ganesh Kamath (Tue May 04 2010 - 08:46:21 PDT)
- Re: [AMBER] Kirkwood g factor Lachele Foley (Lists) (Tue May 04 2010 - 10:58:21 PDT)
[AMBER] question about errors during make install Emily Curtis (Tue May 04 2010 - 10:53:10 PDT)
- Re: [AMBER] question about errors during make install Bill Ross (Tue May 04 2010 - 11:10:46 PDT)
  - Re: [AMBER] question about errors during make install Emily Curtis (Tue May 04 2010 - 11:12:10 PDT)
    - Re: [AMBER] question about errors during make install David Watson (Tue May 04 2010 - 11:25:39 PDT)
- Re: [AMBER] question about errors during make install Bill Ross (Tue May 04 2010 - 11:23:37 PDT)
- Re: [AMBER] question about errors during make install case (Tue May 04 2010 - 11:29:15 PDT)
  - Re: [AMBER] question about errors during make install Emily Curtis (Tue May 04 2010 - 11:40:17 PDT)
    - Re: [AMBER] question about errors during make install case (Tue May 04 2010 - 12:00:18 PDT)
    - Re: [AMBER] question about errors during make install Jason Swails (Tue May 04 2010 - 12:11:02 PDT)
[AMBER] Announcement: Release of DOCK 6.4 Scott Brozell (Tue May 04 2010 - 18:44:53 PDT)
[AMBER] NMR restraint ? xuemeiwang1103 (Wed May 05 2010 - 00:28:44 PDT)
- Re: [AMBER] NMR restraint ? Carlos Simmerling (Wed May 05 2010 - 03:59:51 PDT)
[AMBER] MM-PBSA problem.. large delta (PBTOT, GAS, VdW, INT) Matthias Negri (Wed May 05 2010 - 03:17:45 PDT)
- Re: [AMBER] MM-PBSA problem.. large delta (PBTOT, GAS, VdW, INT) Dwight McGee (Wed May 05 2010 - 08:04:51 PDT)
  - Re: [AMBER] MM-PBSA problem.. large delta (PBTOT, GAS, VdW, INT) Matthias Negri (Wed May 05 2010 - 16:45:29 PDT)
    - Re: [AMBER] MM-PBSA problem.. large delta (PBTOT, GAS, VdW, INT) Ray Luo, Ph.D. (Wed May 05 2010 - 17:39:27 PDT)
    - Re: [AMBER] MM-PBSA problem.. large delta (PBTOT, GAS, VdW, INT) Matthias Negri (Thu May 06 2010 - 13:11:55 PDT)
    - Re: [AMBER] MM-PBSA problem.. large delta (PBTOT, GAS, VdW, INT) Bill Miller III (Thu May 06 2010 - 13:42:36 PDT)
    - Re: [AMBER] MM-PBSA problem.. large delta (PBTOT, GAS, VdW, INT) Matthias Negri (Thu May 06 2010 - 15:29:12 PDT)
    - Re: [AMBER] MM-PBSA problem.. large delta (PBTOT, GAS, VdW, INT) Ray Luo (Thu May 06 2010 - 14:45:06 PDT)
[AMBER] [Fwd: MM-PBSA problem.. large delta (PBTOT, GAS, VdW, INT)] Matthias Negri (Wed May 05 2010 - 03:47:24 PDT)
[AMBER] Amber 11- updated scripts for constant pH simulations and for MMPB/SA mish (Wed May 05 2010 - 05:20:33 PDT)
- Re: [AMBER] Amber 11- updated scripts for constant pH simulations and for MMPB/SA case (Wed May 05 2010 - 06:14:48 PDT)
[AMBER] to post amber list Navanath Kumbhar (Wed May 05 2010 - 05:22:25 PDT)
- Re: [AMBER] to post amber list Jason Swails (Wed May 05 2010 - 06:54:09 PDT)
[AMBER] AMBER Wiki Steve Seibold (Wed May 05 2010 - 05:38:46 PDT)
- [AMBER] RE: AMBER Wiki Gannett, Peter (Wed May 05 2010 - 05:48:11 PDT)
  - Re: [AMBER] RE: AMBER Wiki Carlos Simmerling (Wed May 05 2010 - 06:23:29 PDT)
    - RE: [AMBER] RE: AMBER Wiki Steve Seibold (Wed May 05 2010 - 06:32:50 PDT)
- Re: [AMBER] AMBER Wiki Jason Swails (Wed May 05 2010 - 06:32:17 PDT)
  - RE: [AMBER] AMBER Wiki Steve Seibold (Wed May 05 2010 - 06:53:59 PDT)
    - Re: [AMBER] AMBER Wiki Jason Swails (Wed May 05 2010 - 07:03:05 PDT)
[AMBER] ntpr ntwx too small Yunfen Wang (Wed May 05 2010 - 07:20:14 PDT)
- Re: [AMBER] ntpr ntwx too small Jason Swails (Wed May 05 2010 - 07:29:45 PDT)
- RE: [AMBER] ntpr ntwx too small Ross Walker (Wed May 05 2010 - 07:29:55 PDT)
[AMBER] NaNs in wham analysis Lekpa Duukori (Wed May 05 2010 - 11:37:15 PDT)
- Re: [AMBER] NaNs in wham analysis Ben Roberts (Wed May 05 2010 - 11:45:00 PDT)
  - Re: [AMBER] NaNs in wham analysis Lekpa Duukori (Wed May 05 2010 - 12:32:33 PDT)
    - Re: [AMBER] NaNs in wham analysis Ben Roberts (Wed May 05 2010 - 14:04:58 PDT)
    - Re: [AMBER] NaNs in wham analysis Lekpa Duukori (Wed May 05 2010 - 14:25:58 PDT)
[AMBER] unsubscribe Cojocaru,Vlad (Thu May 06 2010 - 01:12:19 PDT)
- Re: [AMBER] unsubscribe Robert Elder (Thu May 06 2010 - 05:34:45 PDT)
[AMBER] can't make proper use of IGB flag, it cause "input conversion error" geyan (Thu May 06 2010 - 01:30:43 PDT)
- Re: [AMBER] can't make proper use of IGB flag, it cause "input conversion error" Carlos Simmerling (Thu May 06 2010 - 04:16:48 PDT)
- Re: Re: [AMBER] can't make proper use of IGB flag, it cause "inputconversion error" geyan (Thu May 06 2010 - 06:39:45 PDT)
  - Re: Re: [AMBER] can't make proper use of IGB flag, it cause "inputconversion error" Carlos Simmerling (Thu May 06 2010 - 06:46:37 PDT)
  - Re: [AMBER] can't make proper use of IGB flag, it cause "inputconversion error" Dean Cuebas (Sat May 08 2010 - 17:27:48 PDT)
[AMBER] after equil surface of octahedral water-box have small well shaped arrangement of water mish (Thu May 06 2010 - 05:00:49 PDT)
- Re: [AMBER] after equil surface of octahedral water-box have small well shaped arrangement of water Carlos Simmerling (Thu May 06 2010 - 05:28:11 PDT)
  - Re: [AMBER] after equil surface of octahedral water-box have small well shaped arrangement of water mish (Thu May 06 2010 - 05:56:50 PDT)
    - Re: [AMBER] after equil surface of octahedral water-box have small well shaped arrangement of water Carlos Simmerling (Thu May 06 2010 - 06:01:11 PDT)
- Re: [AMBER] after equil surface of octahedral water-box have small well shaped arrangement of water mish (Sat May 08 2010 - 03:55:05 PDT)
  - Re: [AMBER] after equil surface of octahedral water-box have small well shaped arrangement of water Carlos Simmerling (Sat May 08 2010 - 04:07:26 PDT)
- Re: [AMBER] after equil surface of octahedral water-box have small well shaped arrangement of water Bill Ross (Sat May 08 2010 - 08:16:42 PDT)
[AMBER] Installation of Amber10 jaya c.jose (Thu May 06 2010 - 05:22:10 PDT)
- Re: [AMBER] Installation of Amber10 David Watson (Thu May 06 2010 - 05:32:40 PDT)
- Re: [AMBER] Installation of Amber10 case (Thu May 06 2010 - 05:47:34 PDT)
- Re: [AMBER] Installation of Amber10 Jason Swails (Thu May 06 2010 - 05:52:57 PDT)
  - Re: [AMBER] Installation of Amber10 jaya c.jose (Fri May 07 2010 - 03:25:36 PDT)
[AMBER] conversion to netcdf format Ganesh Kamath (Thu May 06 2010 - 06:31:44 PDT)
- Re: [AMBER] conversion to netcdf format Jason Swails (Thu May 06 2010 - 06:37:18 PDT)
  - Re: [AMBER] conversion to netcdf format Ganesh Kamath (Thu May 06 2010 - 06:59:43 PDT)
    - Re: [AMBER] conversion to netcdf format Jason Swails (Thu May 06 2010 - 07:06:08 PDT)
- Re: [AMBER] conversion to netcdf format Thomas Cheatham III (Thu May 06 2010 - 13:08:23 PDT)
[AMBER] how to get decomposed energies of every snapshot pxq (Thu May 06 2010 - 06:56:39 PDT)
- Re: [AMBER] how to get decomposed energies of every snapshot Bill Miller III (Thu May 06 2010 - 07:06:19 PDT)
- Re: [AMBER] how to get decomposed energies of every snapshot Carlos Simmerling (Thu May 06 2010 - 07:07:35 PDT)
  - Re: Re: [AMBER] how to get decomposed energies of every snapshot pxq (Thu May 06 2010 - 17:30:26 PDT)
Re: Re: Re: [AMBER] can't make proper use of IGB flag, it cause"inputconversion error" geyan (Thu May 06 2010 - 06:56:40 PDT)
- Re: Re: Re: [AMBER] can't make proper use of IGB flag, it cause"inputconversion error" Carlos Simmerling (Thu May 06 2010 - 07:06:51 PDT)
[AMBER] regarding ambertools Asfa Ali (Thu May 06 2010 - 10:38:02 PDT)
- Re: [AMBER] regarding ambertools Jason Swails (Thu May 06 2010 - 10:42:49 PDT)
[AMBER] Iodine ESP William Flak (Thu May 06 2010 - 13:07:55 PDT)
- Re: [AMBER] Iodine ESP FyD (Fri May 07 2010 - 09:45:47 PDT)
  - Re: [AMBER] Iodine ESP William Flak (Sun May 16 2010 - 07:56:38 PDT)
    - Re: [AMBER] Iodine ESP FyD (Mon May 17 2010 - 03:46:58 PDT)
[AMBER] checkgrid command rdparm Katrina Lexa (Thu May 06 2010 - 14:53:18 PDT)
[AMBER] fsetpos failed on when looking for box coordinates Yunfen Wang (Thu May 06 2010 - 17:57:50 PDT)
- Re: [AMBER] fsetpos failed on when looking for box coordinates Daniel Roe (Thu May 06 2010 - 21:46:46 PDT)
  - Re:Re: [AMBER] fsetpos failed on when looking for box coordinates Yunfen Wang (Thu May 06 2010 - 23:48:47 PDT)
    - [AMBER] How to run xleap with PC, when amber10 was installed remoted in supercomputer? Catein Catherine (Fri May 07 2010 - 03:07:55 PDT)
    - Re: [AMBER] How to run xleap with PC, when amber10 was installed remoted in supercomputer? Sushil Mishra (Fri May 07 2010 - 03:13:06 PDT)
    - Re: [AMBER] How to run xleap with PC, when amber10 was installed remoted in supercomputer? Jason Swails (Fri May 07 2010 - 05:49:29 PDT)
    - Re: [AMBER] How to run xleap with PC, when amber10 was installed remoted in supercomputer? Sushil Mishra (Fri May 07 2010 - 03:19:17 PDT)
    - Re: [AMBER] How to run xleap with PC, when amber10 was installed remoted in supercomputer? Daniel Roe (Fri May 07 2010 - 05:53:48 PDT)
    - [AMBER] Sander vs Sander.MPI vs Pmemd Catein Catherine (Fri May 07 2010 - 03:10:23 PDT)
    - Re: [AMBER] Sander vs Sander.MPI vs Pmemd Carlos Simmerling (Fri May 07 2010 - 03:40:33 PDT)
    - Re: Re: [AMBER] fsetpos failed on when looking for box coordinates Jason Swails (Fri May 07 2010 - 05:43:06 PDT)
[AMBER] parsing expressions in the radial function of ptraj Jose Borreguero (Thu May 06 2010 - 18:41:27 PDT)
- Re: [AMBER] parsing expressions in the radial function of ptraj Daniel Roe (Fri May 07 2010 - 05:43:13 PDT)
  - Re: [AMBER] parsing expressions in the radial function of ptraj Ganesh Kamath (Fri May 07 2010 - 05:52:02 PDT)
  - Re: [AMBER] parsing expressions in the radial function of ptraj Jose Borreguero (Fri May 07 2010 - 08:59:23 PDT)
[AMBER] esp and resp with pcgamess peker milas (Fri May 07 2010 - 05:58:03 PDT)
- Re: [AMBER] esp and resp with pcgamess FyD (Fri May 07 2010 - 09:30:55 PDT)
- Re: [AMBER] esp and resp with pcgamess FyD (Fri May 07 2010 - 09:38:19 PDT)
  - Re: [q4md-fft] Re: [AMBER] esp and resp with pcgamess peker milas (Fri May 07 2010 - 09:59:03 PDT)
[AMBER] ptraj clustering output: coordinates transformed? Beroza, Paul (Fri May 07 2010 - 08:45:20 PDT)
[AMBER] Installation of Amber10 jaya c.jose (Fri May 07 2010 - 23:09:24 PDT)
- Re: [AMBER] Installation of Amber10 case (Sat May 08 2010 - 05:42:46 PDT)
  - Re: [AMBER] Installation of Amber10 jaya c.jose (Mon May 10 2010 - 06:07:56 PDT)
    - Re: [AMBER] Installation of Amber10 Jason Swails (Mon May 10 2010 - 06:30:34 PDT)
    - RE: [AMBER] Installation of Amber10 Ross Walker (Mon May 10 2010 - 07:19:28 PDT)
    - Re: [AMBER] Installation of Amber10 jaya c.jose (Fri May 14 2010 - 05:59:06 PDT)
    - RE: [AMBER] Installation of Amber10 Ross Walker (Fri May 14 2010 - 09:21:39 PDT)
    - Re: [AMBER] Installation of Amber10 jaya c.jose (Tue May 18 2010 - 08:20:56 PDT)
    - RE: [AMBER] Installation of Amber10 Ross Walker (Tue May 18 2010 - 08:34:27 PDT)
    - Re: [AMBER] Installation of Amber10 Senthil Natesan (Tue May 18 2010 - 08:38:40 PDT)
[AMBER] How to disable the VDW interaction? Jeffrey (Fri May 07 2010 - 23:51:02 PDT)
- Re: [AMBER] How to disable the VDW interaction? Carlos Simmerling (Sat May 08 2010 - 03:01:02 PDT)
  - Re: [AMBER] How to disable the VDW interaction? Jeffrey (Sat May 08 2010 - 05:44:54 PDT)
    - Re: [AMBER] How to disable the VDW interaction? Jason Swails (Sat May 08 2010 - 06:17:10 PDT)
    - Re: [AMBER] How to disable the VDW interaction? Jeffrey (Sat May 08 2010 - 08:45:37 PDT)
    - Re: [AMBER] How to disable the VDW interaction? Jason Swails (Sat May 08 2010 - 16:06:50 PDT)
    - Re: [AMBER] How to disable the VDW interaction? case (Sun May 09 2010 - 07:10:38 PDT)
    - Re: [AMBER] How to disable the VDW interaction? Jason Swails (Sun May 09 2010 - 21:33:43 PDT)
- Re: [AMBER] How to disable the VDW interaction? Marek Maly (Sat May 08 2010 - 14:58:19 PDT)
  - [AMBER] How to disable the 1-4 interaction Hector A. Baldoni (Mon May 10 2010 - 08:25:21 PDT)
    - Re: [AMBER] How to disable the 1-4 interaction Jason Swails (Mon May 10 2010 - 09:34:46 PDT)
    - Re: [AMBER] How to disable the 1-4 interaction case (Tue May 11 2010 - 05:49:58 PDT)
[AMBER] About MM-PBSA's extracting coordinate scirpt geyan (Sat May 08 2010 - 09:15:50 PDT)
- Re: [AMBER] About MM-PBSA's extracting coordinate scirpt Bill Miller III (Sat May 08 2010 - 20:12:38 PDT)
- Re: Re: [AMBER] About MM-PBSA's extracting coordinate scirpt geyan (Sat May 08 2010 - 23:50:08 PDT)
  - Re: Re: [AMBER] About MM-PBSA's extracting coordinate scirpt Dwight McGee (Sun May 09 2010 - 00:00:13 PDT)
[AMBER] You're invited with Honour to the ..... http://www.billiardprofile.com http://www.cuesportz.com/CueWeb/index.faces?afl=R00004E4 (Sat May 08 2010 - 22:09:34 PDT)
[AMBER] You're invited with Honour to the ..... http://www.billiardprofile.com http://www.cuesportz.com/CueWeb/index.faces?afl=R00004E4 (Sat May 08 2010 - 22:11:03 PDT)
[AMBER] (no subject) Waad RHAIEM (Sun May 09 2010 - 17:13:58 PDT)
[AMBER] simulations RAMD on serial and parallel version of amber8 Waad RHAIEM (Sun May 09 2010 - 17:17:59 PDT)
[AMBER] about mpirun in AMBER kamlesh sahu (Sun May 09 2010 - 17:22:39 PDT)
- [AMBER] NTT=3 or NTT=1 Homa Azizian (Sun May 09 2010 - 18:11:28 PDT)
  - RE: [AMBER] NTT=3 or NTT=1 Ross Walker (Sun May 09 2010 - 19:28:42 PDT)
    - Re: [AMBER] NTT=3 or NTT=1 Tom Joseph (Mon May 10 2010 - 10:59:17 PDT)
    - RE: [AMBER] NTT=3 or NTT=1 Ross Walker (Tue May 11 2010 - 20:19:55 PDT)
    - Re: [AMBER] NTT=3 or NTT=1 Jason Swails (Tue May 11 2010 - 20:28:39 PDT)
    - RE: [AMBER] NTT=3 or NTT=1 Ross Walker (Tue May 11 2010 - 21:09:49 PDT)
    - Re: [AMBER] NTT=3 or NTT=1 Jason Swails (Tue May 11 2010 - 21:21:40 PDT)
    - Re: [AMBER] NTT=3 or NTT=1 Tom Joseph (Tue May 11 2010 - 20:40:39 PDT)
    - Re: [AMBER] NTT=3 or NTT=1 Jason Swails (Tue May 11 2010 - 21:09:55 PDT)
    - RE: [AMBER] NTT=3 or NTT=1 Ross Walker (Tue May 11 2010 - 21:19:32 PDT)
- RE: [AMBER] about mpirun in AMBER Ross Walker (Sun May 09 2010 - 19:38:01 PDT)
  - Re: [AMBER] about mpirun in AMBER kamlesh sahu (Sun May 09 2010 - 21:37:47 PDT)
[AMBER] installation of amber qiaoyan (Sun May 09 2010 - 18:44:11 PDT)
- RE: [AMBER] installation of amber Ross Walker (Sun May 09 2010 - 19:30:50 PDT)
[AMBER] Measure distances and angles with ptraj Fernando Martín García (Mon May 10 2010 - 03:55:29 PDT)
- Re: [AMBER] Measure distances and angles with ptraj Daniel Roe (Mon May 10 2010 - 04:46:55 PDT)
  - Re: [AMBER] Measure distances and angles with ptraj Fernando Martín García (Mon May 10 2010 - 23:23:27 PDT)
[AMBER] Is it necessary to use Gaussian03? Hoshin Amber (Mon May 10 2010 - 00:55:10 PDT)
[AMBER] Anton supercomputer Bill Ross (Mon May 10 2010 - 14:02:57 PDT)
[AMBER] tleap segmentation fault Omair A. Khan (Mon May 10 2010 - 15:23:53 PDT)
- [AMBER] tleap segmentation fault Omair A. Khan (Tue May 11 2010 - 06:19:43 PDT)
[AMBER] viewing resp esout files Sidney Elmer (Mon May 10 2010 - 20:30:04 PDT)
- Re: [AMBER] viewing resp esout files FyD (Thu May 13 2010 - 23:44:17 PDT)
  - Re: [q4md-fft] Re: [AMBER] viewing resp esout files Sidney Elmer (Fri May 14 2010 - 23:29:50 PDT)
[AMBER] [Fwd: problem in bond connection] RINU KHATTRI (Tue May 11 2010 - 05:43:42 PDT)
- Re: [AMBER] [Fwd: problem in bond connection] case (Tue May 11 2010 - 07:03:30 PDT)
- Re: [AMBER] [Fwd: problem in bond connection] Bill Ross (Tue May 11 2010 - 10:44:09 PDT)
[AMBER] SPC/E and TIP3P water models piotrek.vega.umcs.lublin.pl (Tue May 11 2010 - 10:19:12 PDT)
- Re: [AMBER] SPC/E and TIP3P water models case (Tue May 11 2010 - 11:18:31 PDT)
[AMBER] Energy of Water Molecules Hemant Kumar (Tue May 11 2010 - 10:56:10 PDT)
- Re: [AMBER] Energy of Water Molecules Bill Ross (Tue May 11 2010 - 11:16:17 PDT)
  - Re: [AMBER] Energy of Water Molecules Hemant Kumar (Tue May 11 2010 - 11:30:17 PDT)
- Re: [AMBER] Energy of Water Molecules Bill Ross (Tue May 11 2010 - 12:29:38 PDT)
  - Re: [AMBER] Energy of Water Molecules Hemant Kumar (Tue May 11 2010 - 12:27:16 PDT)
    - Re: [AMBER] Energy of Water Molecules Barbault Florent (Tue May 11 2010 - 13:35:39 PDT)
    - Re: [AMBER] Energy of Water Molecules Balazs Jojart (Tue May 11 2010 - 23:47:29 PDT)
- Re: [AMBER] Energy of Water Molecules Bill Ross (Tue May 11 2010 - 12:49:20 PDT)
[AMBER] ESP VS AM1BCC Hoshin Amber (Wed May 12 2010 - 00:12:12 PDT)
- Re: [AMBER] ESP VS AM1BCC Jason Swails (Tue May 11 2010 - 13:43:09 PDT)
  - Re: [AMBER] ESP VS AM1BCC Alan (Wed May 12 2010 - 02:58:39 PDT)
    - Re: [AMBER] ESP VS AM1BCC Jason Swails (Wed May 12 2010 - 05:48:49 PDT)
    - RE: [AMBER] ESP VS AM1BCC Hoshin Amber (Thu May 13 2010 - 00:51:17 PDT)
    - Re: [AMBER] ESP VS AM1BCC Jason Swails (Wed May 12 2010 - 14:11:29 PDT)
    - RE: [AMBER] ESP VS AM1BCC Matthew Tessier (Wed May 12 2010 - 15:37:38 PDT)
    - Re: [AMBER] ESP VS AM1BCC Alan (Thu May 13 2010 - 02:19:42 PDT)
    - [AMBER] AMBER SUPPORT FOR ATI GPUs ? Marek Maly (Thu May 13 2010 - 06:31:48 PDT)
    - Re: [AMBER] AMBER SUPPORT FOR ATI GPUs ? Jason Swails (Thu May 13 2010 - 07:10:54 PDT)
    - Re: [AMBER] AMBER SUPPORT FOR ATI GPUs ? Alan (Thu May 13 2010 - 07:51:38 PDT)
    - RE: [AMBER] AMBER SUPPORT FOR ATI GPUs ? Scott Le Grand (Thu May 13 2010 - 11:41:06 PDT)
    - RE: [AMBER] AMBER SUPPORT FOR ATI GPUs ? Scott Le Grand (Thu May 13 2010 - 11:40:21 PDT)
    - RE: [AMBER] AMBER SUPPORT FOR ATI GPUs ? Ross Walker (Thu May 13 2010 - 09:45:37 PDT)
    - RE: [AMBER] AMBER SUPPORT FOR ATI GPUs ? Scott Le Grand (Thu May 13 2010 - 11:46:38 PDT)
    - Re: [AMBER] AMBER SUPPORT FOR ATI GPUs ? Marek Maly (Sat May 15 2010 - 04:45:48 PDT)
    - Re: [AMBER] ESP VS AM1BCC FyD (Fri May 14 2010 - 00:18:23 PDT)
    - Re: [AMBER] ESP VS AM1BCC Alan (Fri May 14 2010 - 02:09:44 PDT)
    - Re: [AMBER] ESP VS AM1BCC FyD (Fri May 14 2010 - 02:39:02 PDT)
[AMBER] PIMD average trajectory aapeters.ncsu.edu (Tue May 11 2010 - 13:46:45 PDT)
- Re: [AMBER] PIMD average trajectory case (Wed May 12 2010 - 07:32:06 PDT)
- Re: [AMBER] PIMD average trajectory aapeters.ncsu.edu (Tue Oct 05 2010 - 12:58:08 PDT)
[AMBER] PMEMD installation with gfortran Senthil Natesan (Tue May 11 2010 - 15:13:46 PDT)
- Re: [AMBER] PMEMD installation with gfortran Jason Swails (Tue May 11 2010 - 16:10:35 PDT)
  - Re: [AMBER] PMEMD installation with gfortran Senthil Natesan (Tue May 11 2010 - 18:38:05 PDT)
    - [AMBER] How to obtain dialsplot Homa Azizian (Tue May 11 2010 - 19:10:59 PDT)
    - RE: [AMBER] How to obtain dialsplot Niel Henriksen (Wed May 12 2010 - 09:11:44 PDT)
    - Re: [AMBER] PMEMD installation with gfortran Jason Swails (Tue May 11 2010 - 20:14:05 PDT)
    - Re: [AMBER] PMEMD installation with gfortran Jason Swails (Tue May 11 2010 - 20:15:55 PDT)
    - Re: [AMBER] PMEMD installation with gfortran Jason Swails (Tue May 11 2010 - 20:20:05 PDT)
    - Re: [AMBER] PMEMD installation with gfortran case (Wed May 12 2010 - 05:19:31 PDT)
    - Re: [AMBER] PMEMD installation with gfortran Jason Swails (Wed May 12 2010 - 05:41:17 PDT)
    - Re: [AMBER] PMEMD installation with gfortran Senthil Natesan (Wed May 12 2010 - 06:58:11 PDT)
    - Re: [AMBER] PMEMD installation with gfortran Jason Swails (Wed May 12 2010 - 07:19:15 PDT)
    - RE: [AMBER] PMEMD installation with gfortran Ross Walker (Wed May 12 2010 - 07:22:46 PDT)
    - Re: [AMBER] PMEMD installation with gfortran - solved ! Senthil Natesan (Wed May 12 2010 - 08:12:01 PDT)
    - Re: [AMBER] PMEMD installation with gfortran Sidney Elmer (Fri May 14 2010 - 22:57:11 PDT)
[AMBER] protein moves out of the box when using ptraj center image Sun, Yufang (Tue May 11 2010 - 16:52:23 PDT)
- Re: [AMBER] protein moves out of the box when using ptraj center image Carlos Simmerling (Tue May 11 2010 - 16:59:28 PDT)
  - RE: [AMBER] protein moves out of the box when using ptraj center image Sun, Yufang (Wed May 12 2010 - 08:26:56 PDT)
    - Re: [AMBER] protein moves out of the box when using ptraj center image Carlos Simmerling (Wed May 12 2010 - 08:45:10 PDT)
    - RE: [AMBER] protein moves out of the box when using ptraj center image Sun, Yufang (Wed May 12 2010 - 09:32:55 PDT)
    - Re: [AMBER] protein moves out of the box when using ptraj center image Carlos Simmerling (Wed May 12 2010 - 09:48:54 PDT)
- Re: [AMBER] protein moves out of the box when using ptraj center image Thomas Cheatham (Wed May 12 2010 - 09:40:28 PDT)
  - RE: [AMBER] protein moves out of the box when using ptraj center image Sun, Yufang (Wed May 12 2010 - 10:02:21 PDT)
[AMBER] pressure not constant ashutosh shandilya (Tue May 11 2010 - 22:59:13 PDT)
- Re: [AMBER] pressure not constant Jason Swails (Tue May 11 2010 - 23:04:28 PDT)
  - Re: [AMBER] pressure not constant ashutosh shandilya (Tue May 11 2010 - 23:25:07 PDT)
- Re: [AMBER] pressure not constant case (Wed May 12 2010 - 05:26:26 PDT)
- RE: [AMBER] pressure not constant Ross Walker (Wed May 12 2010 - 07:25:31 PDT)
  - Re: [AMBER] pressure not constant ashutosh shandilya (Thu May 13 2010 - 00:08:03 PDT)
    - Re: [AMBER] pressure not constant case (Thu May 13 2010 - 04:40:46 PDT)
[AMBER] a recent review about force fields Alan (Wed May 12 2010 - 08:46:19 PDT)
- Re: [AMBER] a recent review about force fields Kevin Hauser (Wed May 12 2010 - 09:45:25 PDT)
  - Re: [AMBER] a recent review about force fields Alan (Wed May 12 2010 - 10:04:27 PDT)
    - Re: [AMBER] a recent review about force fields Alan (Thu May 13 2010 - 09:09:09 PDT)
[AMBER] skinnb and energy conservation liu junjun (Wed May 12 2010 - 09:39:18 PDT)
- Re: [AMBER] skinnb and energy conservation Robert Duke (Wed May 12 2010 - 09:50:38 PDT)
  - Re: [AMBER] skinnb and energy conservation Crowley, Michael (Wed May 12 2010 - 10:03:14 PDT)
  - [AMBER] non-standard residue parameters Jeffrey (Thu May 13 2010 - 07:09:01 PDT)
    - Re: [AMBER] non-standard residue parameters FyD (Fri May 14 2010 - 00:24:04 PDT)
    - Re: [AMBER] non-standard residue parameters Bill Ross (Fri May 14 2010 - 09:53:53 PDT)
- Re: [AMBER] skinnb and energy conservation case (Wed May 12 2010 - 09:57:21 PDT)
- Re: [AMBER] skinnb and energy conservation Bill Ross (Wed May 12 2010 - 10:00:40 PDT)
- Re: [AMBER] skinnb and energy conservation Robert Duke (Wed May 12 2010 - 10:11:51 PDT)
  - Re: [AMBER] skinnb and energy conservation liu junjun (Wed May 12 2010 - 13:11:52 PDT)
    - Re: [AMBER] skinnb and energy conservation Jason Swails (Wed May 12 2010 - 13:24:26 PDT)
    - RE: [AMBER] skinnb and energy conservation Scott Le Grand (Wed May 12 2010 - 17:27:47 PDT)
    - RE: [AMBER] skinnb and energy conservation Ross Walker (Wed May 12 2010 - 20:07:07 PDT)
[AMBER] Ptraj image problems Jayalakshmi Sridhar (Wed May 12 2010 - 11:26:26 PDT)
- Re: [AMBER] Ptraj image problems Carlos Simmerling (Wed May 12 2010 - 12:02:35 PDT)
- Re: [AMBER] Ptraj image problems Jayalakshmi Sridhar (Wed May 12 2010 - 12:18:35 PDT)
  - Re: [AMBER] Ptraj image problems Jason Swails (Wed May 12 2010 - 12:20:13 PDT)
- Re: [AMBER] Ptraj image problems Carlos Simmerling (Wed May 12 2010 - 12:22:37 PDT)
  - Re: [AMBER] Ptraj image problems Jason Swails (Wed May 12 2010 - 12:30:06 PDT)
- Re: [AMBER] Ptraj image problems Bill Ross (Wed May 12 2010 - 12:25:30 PDT)
- Re: [AMBER] Ptraj image problems Jayalakshmi Sridhar (Wed May 12 2010 - 12:56:42 PDT)
  - Re: [AMBER] Ptraj image problems Jason Swails (Wed May 12 2010 - 13:01:31 PDT)
    - Re: [AMBER] Ptraj image problems Jayalakshmi Sridhar (Wed May 12 2010 - 13:07:28 PDT)
  - Re: [AMBER] Ptraj image problems Thomas Cheatham III (Wed May 12 2010 - 13:06:06 PDT)
    - Re: [AMBER] Ptraj image problems Jayalakshmi Sridhar (Wed May 12 2010 - 13:19:22 PDT)
    - Re: [AMBER] Ptraj image problems Jayalakshmi Sridhar (Wed May 12 2010 - 13:23:10 PDT)
    - Re: [AMBER] Ptraj image problems Jason Swails (Wed May 12 2010 - 14:19:05 PDT)
    - Re: [AMBER] Ptraj image problems Jayalakshmi Sridhar (Thu May 13 2010 - 08:40:50 PDT)
- Re: [AMBER] Ptraj image problems Jayalakshmi Sridhar (Thu May 13 2010 - 08:40:00 PDT)
[AMBER] Error while compiling GPU version of PMEMD in Amber 11 Samuel, Tabitha Kripa (Wed May 12 2010 - 11:42:42 PDT)
- Re: [AMBER] Error while compiling GPU version of PMEMD in Amber 11 case (Wed May 12 2010 - 12:13:31 PDT)
- Re: [AMBER] Error while compiling GPU version of PMEMD in Amber 11 Jason Swails (Wed May 12 2010 - 12:14:36 PDT)
- RE: [AMBER] Error while compiling GPU version of PMEMD in Amber 11 Ross Walker (Wed May 12 2010 - 12:23:25 PDT)
[AMBER] sander and ptraj problem manikanthan bhavaraju (Wed May 12 2010 - 14:49:32 PDT)
- Re: [AMBER] sander and ptraj problem Bill Ross (Wed May 12 2010 - 14:56:31 PDT)
  - Re: [AMBER] sander and ptraj problem manikanthan bhavaraju (Wed May 12 2010 - 15:04:58 PDT)
- Re: [AMBER] sander and ptraj problem Bill Ross (Wed May 12 2010 - 15:16:56 PDT)
  - Re: [AMBER] sander and ptraj problem manikanthan bhavaraju (Wed May 12 2010 - 16:00:20 PDT)
- Re: [AMBER] sander and ptraj problem Bill Ross (Wed May 12 2010 - 16:15:59 PDT)
  - Re: [AMBER] sander and ptraj problem manikanthan bhavaraju (Thu May 13 2010 - 08:42:01 PDT)
- Re: [AMBER] sander and ptraj problem Bill Ross (Thu May 13 2010 - 10:15:57 PDT)
  - Re: [AMBER] sander and ptraj problem manikanthan bhavaraju (Thu May 13 2010 - 10:26:45 PDT)
[AMBER] subscribe sjn_sk.hotmail.com (Wed May 12 2010 - 21:33:28 PDT)
[AMBER] Query regarding Distance Restraints sunita gupta (Thu May 13 2010 - 01:17:35 PDT)
- Re: [AMBER] Query regarding Distance Restraints case (Thu May 13 2010 - 04:45:18 PDT)
[AMBER] color images from 2drms Rebeca García Fandiño (Thu May 13 2010 - 02:33:54 PDT)
- Re: [AMBER] color images from 2drms Jason Swails (Thu May 13 2010 - 07:16:14 PDT)
  - RE: [AMBER] color images from 2drms Rebeca García Fandiño (Thu May 20 2010 - 08:18:00 PDT)
    - Re: [AMBER] color images from 2drms Jason Swails (Thu May 20 2010 - 08:22:53 PDT)
    - Re: [AMBER] color images from 2drms InSuk Joung (Thu May 20 2010 - 08:24:47 PDT)
    - Re: [AMBER] color images from 2drms Ilyas Yildirim (Thu May 20 2010 - 08:44:15 PDT)
    - Re: [AMBER] color images from 2drms M. L. Dodson (Thu May 20 2010 - 09:03:24 PDT)
    - Re: [AMBER] color images from 2drms Roman Osman (Thu May 20 2010 - 09:23:18 PDT)
    - [AMBER] problem about cyclic peptide Rebeca García Fandiño (Tue Jul 20 2010 - 08:33:15 PDT)
    - Re: [AMBER] problem about cyclic peptide Levi Pierce (Tue Jul 20 2010 - 09:37:32 PDT)
    - Re: [AMBER] problem about cyclic peptide Rebeca García Fandiño (Tue Jul 20 2010 - 09:43:59 PDT)
    - [AMBER] SDS parameters in AMBER Rebeca García Fandiño (Tue Apr 15 2014 - 05:28:58 PDT)
    - Re: [AMBER] SDS parameters in AMBER ABEL Stephane 175950 (Tue Apr 15 2014 - 05:36:32 PDT)
- Re: [AMBER] color images from 2drms Thomas Cheatham III (Fri May 14 2010 - 09:03:19 PDT)
  - Re: [AMBER] color images from 2drms InSuk Joung (Fri May 14 2010 - 09:49:07 PDT)
- Re: [AMBER] color images from 2drms Bill Ross (Thu May 20 2010 - 08:28:06 PDT)
[AMBER] segmentation fault while loading mol2 file and recompilation issue in antechamber and tleap vaibhav dixit (Thu May 13 2010 - 03:03:14 PDT)
[AMBER] Query on the trajectory output in PDB format nicholus bhattacharjee (Thu May 13 2010 - 06:15:17 PDT)
- Re: [AMBER] Query on the trajectory output in PDB format Jason Swails (Thu May 13 2010 - 07:24:37 PDT)
[AMBER] DIPOLE MOMENT OUTPUT FILE Juan Carlos (Thu May 13 2010 - 07:34:47 PDT)
[AMBER] about SHAKE and double x single precision Alan (Thu May 13 2010 - 08:04:38 PDT)
- [AMBER] Re: about SHAKE and double x single precision Alan (Thu May 13 2010 - 08:13:36 PDT)
- Re: [AMBER] about SHAKE and double x single precision case (Thu May 13 2010 - 08:59:17 PDT)
  - Re: [AMBER] about SHAKE and double x single precision Alan (Thu May 13 2010 - 09:04:08 PDT)
[AMBER] problem with targeted md simulation map110.pitt.edu (Thu May 13 2010 - 12:19:36 PDT)
- Re: [AMBER] problem with targeted md simulation InSuk Joung (Thu May 13 2010 - 12:36:07 PDT)
  - Re: [AMBER] problem with targeted md simulation map110.pitt.edu (Thu May 13 2010 - 13:30:24 PDT)
    - Re: [AMBER] problem with targeted md simulation InSuk Joung (Thu May 13 2010 - 14:14:57 PDT)
    - Re: [AMBER] problem with targeted md simulation map110.pitt.edu (Fri May 14 2010 - 08:05:45 PDT)
    - Re: [AMBER] problem with targeted md simulation InSuk Joung (Fri May 14 2010 - 09:11:54 PDT)
    - Re: [AMBER] problem with targeted md simulation map110.pitt.edu (Fri May 14 2010 - 10:59:09 PDT)
[AMBER] installation on MacOS10.6 erik zuiderweg (Thu May 13 2010 - 13:52:09 PDT)
- Re: [AMBER] installation on MacOS10.6 David Watson (Thu May 13 2010 - 14:12:08 PDT)
  - Re: [AMBER] installation on MacOS10.6 erik zuiderweg (Thu May 13 2010 - 14:20:19 PDT)
    - Re: [AMBER] installation on MacOS10.6 Jason Swails (Thu May 13 2010 - 14:56:34 PDT)
    - Re: [AMBER] installation on MacOS10.6 Alan (Thu May 13 2010 - 15:04:00 PDT)
    - Re: [AMBER] installation on MacOS10.6 erik zuiderweg (Fri May 14 2010 - 05:43:54 PDT)
    - Re: [AMBER] installation on MacOS10.6 Alan (Fri May 14 2010 - 06:03:59 PDT)
    - Re: [AMBER] installation on MacOS10.6 erik zuiderweg (Fri May 14 2010 - 08:16:22 PDT)
    - Re: [AMBER] installation on MacOS10.6 Mengjuei Hsieh (Fri May 14 2010 - 11:25:18 PDT)
    - Re: [AMBER] installation on MacOS10.6 Jason Swails (Fri May 14 2010 - 11:40:23 PDT)
    - Re: [AMBER] installation on MacOS10.6 Alan (Fri May 14 2010 - 12:51:32 PDT)
    - Re: [AMBER] installation on MacOS10.6 Jason Swails (Fri May 14 2010 - 15:00:41 PDT)
    - Re: [AMBER] installation on MacOS10.6 case (Fri May 14 2010 - 18:00:36 PDT)
    - Re: [AMBER] installation on MacOS10.6 Sidney Elmer (Fri May 14 2010 - 23:22:35 PDT)
    - Re: [AMBER] installation on MacOS10.6 erik zuiderweg (Sat May 15 2010 - 08:11:29 PDT)
    - Re: [AMBER] installation on MacOS10.6 Jason Swails (Sat May 15 2010 - 08:49:42 PDT)
    - Re: [AMBER] installation on MacOS10.6 Paul S. Nerenberg (Sat May 15 2010 - 08:54:43 PDT)
    - Re: [AMBER] installation on MacOS10.6 erik zuiderweg (Sat May 15 2010 - 09:55:23 PDT)
    - Re: [AMBER] installation on MacOS10.6 erik zuiderweg (Sat May 15 2010 - 14:19:33 PDT)
    - Re: [AMBER] installation on MacOS10.6 Jason Swails (Sat May 15 2010 - 14:42:50 PDT)
    - Re: [AMBER] installation on MacOS10.6 Jason Swails (Sat May 15 2010 - 14:45:27 PDT)
    - Re: [AMBER] installation on MacOS10.6 Mengjuei Hsieh (Sat May 15 2010 - 21:25:29 PDT)
    - Re: [AMBER] installation on MacOS10.6 Mengjuei Hsieh (Sun May 16 2010 - 04:04:35 PDT)
    - PROGRESS! [AMBER] installation on MacOS10.6 erik zuiderweg (Sun May 16 2010 - 12:27:10 PDT)
    - Re: PROGRESS! [AMBER] installation on MacOS10.6 Mengjuei Hsieh (Sun May 16 2010 - 13:13:37 PDT)
    - Re: PROGRESS! [AMBER] installation on MacOS10.6 erik zuiderweg (Mon May 17 2010 - 08:57:26 PDT)
    - Re: PROGRESS! [AMBER] installation on MacOS10.6 Paul S. Nerenberg (Mon May 17 2010 - 09:34:09 PDT)
    - Re: PROGRESS! [AMBER] installation on MacOS10.6 erik zuiderweg (Mon May 17 2010 - 10:46:57 PDT)
    - Re: PROGRESS! [AMBER] installation on MacOS10.6 Mengjuei Hsieh (Mon May 17 2010 - 09:44:47 PDT)
    - Re: PROGRESS! [AMBER] installation on MacOS10.6 erik zuiderweg (Mon May 17 2010 - 10:46:38 PDT)
    - Re: PROGRESS! [AMBER] installation on MacOS10.6 Mengjuei Hsieh (Mon May 17 2010 - 11:02:54 PDT)
    - Re: PROGRESS! [AMBER] installation on MacOS10.6 erik zuiderweg (Mon May 17 2010 - 11:30:16 PDT)
    - Re: PROGRESS! [AMBER] installation on MacOS10.6 Jason Swails (Mon May 17 2010 - 11:33:00 PDT)
    - Re: PROGRESS! [AMBER] installation on MacOS10.6 erik zuiderweg (Mon May 17 2010 - 12:44:21 PDT)
    - Re: PROGRESS! [AMBER] installation on MacOS10.6 Mengjuei Hsieh (Mon May 17 2010 - 12:56:20 PDT)
    - Re: PROGRESS! [AMBER] installation on MacOS10.6 erik zuiderweg (Mon May 17 2010 - 15:35:11 PDT)
    - Re: PROGRESS! [AMBER] installation on MacOS10.6 Mengjuei Hsieh (Mon May 17 2010 - 15:45:33 PDT)
    - Re: PROGRESS! [AMBER] installation on MacOS10.6 Jason Swails (Mon May 17 2010 - 13:01:00 PDT)
    - [AMBER] Re: Amber11 installation on MacOS10.6 COMPLETE erik zuiderweg (Tue May 18 2010 - 09:14:53 PDT)
    - Re: [AMBER] Re: Amber11 installation on MacOS10.6 COMPLETE David Watson (Tue May 18 2010 - 09:25:28 PDT)
    - Re: PROGRESS! [AMBER] installation on MacOS10.6 Bill Ross (Mon May 17 2010 - 09:59:11 PDT)
    - Re: [AMBER] installation on MacOS10.6 erik zuiderweg (Sun May 16 2010 - 11:33:33 PDT)
- Re: [AMBER] installation on MacOS10.6 Mengjuei Hsieh (Thu May 13 2010 - 15:58:30 PDT)
  - Re: [AMBER] installation on MacOS10.6 Alan (Thu May 13 2010 - 23:24:51 PDT)
  - Re: [AMBER] installation on MacOS10.6 erik zuiderweg (Fri May 14 2010 - 08:23:08 PDT)
    - Re: [AMBER] installation on MacOS10.6 Jason Swails (Fri May 14 2010 - 08:41:23 PDT)
    - Re: [AMBER] installation on MacOS10.6 erik zuiderweg (Fri May 14 2010 - 09:22:17 PDT)
    - Re: [AMBER] installation on MacOS10.6 David Watson (Fri May 14 2010 - 09:43:21 PDT)
[AMBER] make test.parallel never finishes Jan Schulze (Fri May 14 2010 - 07:19:38 PDT)
- Re: [AMBER] make test.parallel never finishes case (Fri May 14 2010 - 17:45:27 PDT)
  - Re: [AMBER] make test.parallel never finishes Jan Schulze (Mon May 17 2010 - 04:43:10 PDT)
    - RE: [AMBER] make test.parallel never finishes Ross Walker (Mon May 17 2010 - 09:18:53 PDT)
- Re: [AMBER] make test.parallel never finishes Dmitry Mukha (Fri May 14 2010 - 20:57:28 PDT)
[AMBER] solvent MD - poor equilibration Senthil Natesan (Fri May 14 2010 - 12:31:48 PDT)
- Re: [AMBER] solvent MD - poor equilibration Bill Ross (Fri May 14 2010 - 13:08:32 PDT)
  - Re: [AMBER] solvent MD - poor equilibration Senthil Natesan (Mon May 17 2010 - 06:46:25 PDT)
- Re: [AMBER] solvent MD - poor equilibration Bill Ross (Mon May 17 2010 - 09:48:19 PDT)
  - Re: [AMBER] solvent MD - poor equilibration Senthil Natesan (Mon May 17 2010 - 10:34:56 PDT)
    - Re: [AMBER] solvent MD - poor equilibration Carlos Simmerling (Mon May 17 2010 - 10:40:51 PDT)
    - Re: [AMBER] solvent MD - poor equilibration Paul S. Nerenberg (Mon May 17 2010 - 10:47:38 PDT)
    - Re: [AMBER] solvent MD - poor equilibration Senthil Natesan (Mon May 17 2010 - 12:12:07 PDT)
    - RE: [AMBER] solvent MD - poor equilibration Ross Walker (Mon May 17 2010 - 13:26:10 PDT)
    - Re: [AMBER] solvent MD - poor equilibration Paul S. Nerenberg (Mon May 17 2010 - 13:53:44 PDT)
    - Re: [AMBER] solvent MD - poor equilibration Senthil Natesan (Mon May 17 2010 - 15:57:01 PDT)
    - Re: [AMBER] solvent MD - poor equilibration Carlos Simmerling (Mon May 17 2010 - 19:41:59 PDT)
    - Re: [AMBER] solvent MD - poor equilibration Senthil Natesan (Tue May 18 2010 - 07:17:03 PDT)
    - Re: [AMBER] solvent MD - poor equilibration Carlos Simmerling (Tue May 18 2010 - 08:04:52 PDT)
    - RE: [AMBER] solvent MD - poor equilibration Ross Walker (Tue May 18 2010 - 08:30:45 PDT)
- Re: [AMBER] solvent MD - poor equilibration Bill Ross (Mon May 17 2010 - 10:46:14 PDT)
- Re: [AMBER] solvent MD - poor equilibration Bill Ross (Mon May 17 2010 - 12:31:12 PDT)
  - Re: [AMBER] solvent MD - poor equilibration Senthil Natesan (Mon May 17 2010 - 13:14:59 PDT)
- Re: [AMBER] solvent MD - poor equilibration Bill Ross (Mon May 17 2010 - 13:54:51 PDT)
- Re: [AMBER] solvent MD - poor equilibration Bill Ross (Mon May 17 2010 - 13:58:16 PDT)
- Re: [AMBER] solvent MD - poor equilibration Bill Ross (Mon May 17 2010 - 16:14:48 PDT)
  - Re: [AMBER] solvent MD - poor equilibration Senthil Natesan (Mon May 17 2010 - 18:33:10 PDT)
[AMBER] tleap problems in Fedora Core 12 case (Fri May 14 2010 - 12:58:27 PDT)
- Re: [AMBER] tleap problems in Fedora Core 12 Jason Swails (Fri May 14 2010 - 14:35:11 PDT)
  - Re: [AMBER] tleap problems in Fedora Core 12 case (Fri May 14 2010 - 18:17:30 PDT)
    - Re: [AMBER] tleap problems in Fedora Core 12 Omair A. Khan (Mon May 17 2010 - 11:49:24 PDT)
    - Re: [AMBER] tleap problems in Fedora Core 12 Jason Swails (Mon May 17 2010 - 11:54:54 PDT)
[AMBER] problems enabling CUDA for Amber 11 on Mac OS X 10.6 Steve Constable (Fri May 14 2010 - 13:16:58 PDT)
- Re: [AMBER] problems enabling CUDA for Amber 11 on Mac OS X 10.6 Jason Swails (Fri May 14 2010 - 14:58:43 PDT)
  - Re: [AMBER] problems enabling CUDA for Amber 11 on Mac OS X 10.6 Thomas Patko (Fri May 14 2010 - 15:03:48 PDT)
    - Re: [AMBER] problems enabling CUDA for Amber 11 on Mac OS X 10.6 Jason Swails (Fri May 14 2010 - 15:12:05 PDT)
[AMBER] regarding H-bond & torsion angles Asfa Ali (Fri May 14 2010 - 22:30:44 PDT)
- Re: [AMBER] regarding H-bond & torsion angles shamoon siddiqui (Fri May 14 2010 - 22:37:46 PDT)
  - Re: [AMBER] regarding H-bond & torsion angles Asfa Ali (Sat May 15 2010 - 00:25:20 PDT)
    - Re: [AMBER] regarding H-bond & torsion angles shamoon siddiqui (Sat May 15 2010 - 00:31:35 PDT)
[AMBER] entropy problem Rilei Yu (Sat May 15 2010 - 18:13:55 PDT)
- Re: [AMBER] entropy problem Jason Swails (Sat May 15 2010 - 18:46:27 PDT)
  - Re: [AMBER] entropy problem Rilei Yu (Sat May 15 2010 - 19:16:44 PDT)
[AMBER] error - binding_energy.mmpbsa run Andrew Voronkov (Sun May 16 2010 - 03:53:52 PDT)
- Re: [AMBER] error - binding_energy.mmpbsa run Jason Swails (Sun May 16 2010 - 04:40:22 PDT)
  - Re: Re: [AMBER] error - binding_energy.mmpbsa run Andrew Voronkov (Mon May 17 2010 - 22:49:27 PDT)
    - Re: Re: [AMBER] error - binding_energy.mmpbsa run Bill Miller III (Tue May 18 2010 - 03:57:19 PDT)
[AMBER] Hybridization state effects William Flak (Sun May 16 2010 - 08:01:05 PDT)
- Re: [AMBER] Hybridization state effects Bill Ross (Sun May 16 2010 - 12:25:43 PDT)
[AMBER] Missing BELE for MM in 1 (residue 1) Hyma vathi (Sun May 16 2010 - 22:56:28 PDT)
[AMBER] analysis of results Asfa Ali (Mon May 17 2010 - 03:08:43 PDT)
- Re: [AMBER] analysis of results Jason Swails (Mon May 17 2010 - 06:38:06 PDT)
[AMBER] amber compilation error Sangita Kachhap (Mon May 17 2010 - 08:58:00 PDT)
- Re: [AMBER] amber compilation error Jason Swails (Mon May 17 2010 - 11:08:06 PDT)
[AMBER] QMMM and Thermodynamic integration InSuk Joung (Mon May 17 2010 - 09:27:00 PDT)
- RE: [AMBER] QMMM and Thermodynamic integration Ross Walker (Mon May 17 2010 - 09:45:34 PDT)
  - Re: [AMBER] QMMM and Thermodynamic integration InSuk Joung (Mon May 17 2010 - 09:49:10 PDT)
- Re: [AMBER] QMMM and Thermodynamic integration Bill Ross (Mon May 17 2010 - 10:05:19 PDT)
  - Re: [AMBER] QMMM and Thermodynamic integration InSuk Joung (Mon May 17 2010 - 10:58:05 PDT)
- Re: [AMBER] QMMM and Thermodynamic integration Bill Ross (Mon May 17 2010 - 11:01:17 PDT)
  - Re: [AMBER] QMMM and Thermodynamic integration InSuk Joung (Mon May 17 2010 - 11:28:11 PDT)
- Re: [AMBER] QMMM and Thermodynamic integration Bill Ross (Mon May 17 2010 - 11:39:41 PDT)
  - Re: [AMBER] QMMM and Thermodynamic integration InSuk Joung (Mon May 17 2010 - 11:50:20 PDT)
    - Re: [AMBER] QMMM and Thermodynamic integration InSuk Joung (Mon May 17 2010 - 11:51:19 PDT)
- Re: [AMBER] QMMM and Thermodynamic integration Bill Ross (Mon May 17 2010 - 11:59:25 PDT)
- Re: [AMBER] QMMM and Thermodynamic integration Bill Ross (Mon May 17 2010 - 12:09:28 PDT)
[AMBER] hbond and acceptor definition Ganesh Kamath (Mon May 17 2010 - 14:25:33 PDT)
- Re: [AMBER] hbond and acceptor definition Daniel Roe (Tue May 18 2010 - 08:32:59 PDT)
  - Re: [AMBER] hbond and acceptor definition Ganesh Kamath (Tue May 18 2010 - 09:43:12 PDT)
    - Re: [AMBER] hbond and acceptor definition Daniel Roe (Tue May 18 2010 - 11:46:03 PDT)
[AMBER] entropy-problem Rilei Yu (Mon May 17 2010 - 18:29:51 PDT)
- Re: [AMBER] entropy-problem Jason Swails (Mon May 17 2010 - 18:43:01 PDT)
- Re: [AMBER] entropy-problem Bill Miller III (Mon May 17 2010 - 18:55:28 PDT)
  - [AMBER] reducing number of fram in out data file Homa Azizian (Mon May 17 2010 - 19:34:36 PDT)
    - Re: [AMBER] reducing number of fram in out data file Mengjuei Hsieh (Fri May 21 2010 - 14:59:06 PDT)
  - Re: [AMBER] entropy-problem Rilei Yu (Tue May 18 2010 - 06:10:31 PDT)
    - Re: [AMBER] entropy-problem Jason Swails (Tue May 18 2010 - 13:59:28 PDT)
    - Re: [AMBER] entropy-problem Rilei Yu (Tue May 18 2010 - 18:50:20 PDT)
[AMBER] meaning of time correlation function Homa Azizian (Mon May 17 2010 - 20:13:19 PDT)
- Re: [AMBER] meaning of time correlation function Mengjuei Hsieh (Fri May 21 2010 - 14:48:38 PDT)
[AMBER] amber10 installation error in linux Sangita Kachhap (Mon May 17 2010 - 21:03:33 PDT)
- Re: [AMBER] amber10 installation error in linux David Watson (Mon May 17 2010 - 21:17:30 PDT)
- Re: [AMBER] amber10 installation error in linux David Watson (Mon May 17 2010 - 21:46:47 PDT)
  - Re: [AMBER] amber10 installation error in linux (openmpi error) Sangita Kachhap (Mon May 17 2010 - 23:10:33 PDT)
    - Re: [AMBER] amber10 installation error in linux (openmpi error) Jason Swails (Tue May 18 2010 - 05:05:45 PDT)
[AMBER] remd convergence jani vinod (Mon May 17 2010 - 23:20:21 PDT)
- Re: [AMBER] remd convergence Carlos Simmerling (Tue May 18 2010 - 03:54:14 PDT)
[AMBER] How to obtain interdomain angles Tan Yaw Sing (Mon May 17 2010 - 23:30:38 PDT)
- Re: [AMBER] How to obtain interdomain angles Lachele Foley (Lists) (Tue May 18 2010 - 13:08:38 PDT)
[AMBER] B-factor ashutosh shandilya (Tue May 18 2010 - 00:14:44 PDT)
- Re: [AMBER] B-factor Jason Swails (Tue May 18 2010 - 05:06:41 PDT)
[AMBER] Chloroform solvent model ashutosh shandilya (Tue May 18 2010 - 00:19:21 PDT)
- Re: [AMBER] Chloroform solvent model steinbrt.rci.rutgers.edu (Tue May 18 2010 - 00:55:56 PDT)
- Re: [AMBER] Chloroform solvent model Necmettin Pirinccioglu (Tue May 18 2010 - 01:34:51 PDT)
[AMBER] PLUMED release 1.2.0 available Massimiliano Bonomi (Tue May 18 2010 - 04:45:02 PDT)
[AMBER] Contour plots of 2D WHAM Lekpa Duukori (Tue May 18 2010 - 07:43:10 PDT)
- Re: [AMBER] Contour plots of 2D WHAM Jason Swails (Tue May 18 2010 - 09:42:17 PDT)
  - Re: [AMBER] Contour plots of 2D WHAM Lekpa Duukori (Tue May 18 2010 - 14:17:47 PDT)
[AMBER] AT1.4 installation errors (logs are attached) Dmitry Mukha (Tue May 18 2010 - 08:19:13 PDT)
- Re: [AMBER] AT1.4 installation errors (logs are attached) David A. Case (Tue May 18 2010 - 20:09:02 PDT)
  - Re: [AMBER] AT1.4 installation errors (logs are attached) Dmitry Mukha (Tue May 18 2010 - 21:13:15 PDT)
    - Re: [AMBER] AT1.4 installation errors (logs are attached) David A. Case (Wed May 19 2010 - 05:09:19 PDT)
  - Re: [AMBER] AT1.4 installation errors (logs are attached) Mengjuei Hsieh (Wed May 19 2010 - 10:17:02 PDT)
    - Re: [AMBER] AT1.4 installation errors (logs are attached) David A. Case (Wed May 19 2010 - 10:44:50 PDT)
    - Re: [AMBER] AT1.4 installation errors (logs are attached) Mengjuei Hsieh (Thu May 20 2010 - 01:31:12 PDT)
    - Re: [AMBER] AT1.4 installation errors (logs are attached) Dmitry Mukha (Fri May 21 2010 - 06:00:46 PDT)
    - Re: [AMBER] AT1.4 installation errors (logs are attached) case (Fri May 21 2010 - 07:00:58 PDT)
    - Re: [AMBER] AT1.4 installation errors (logs are attached) Mengjuei Hsieh (Fri May 21 2010 - 22:49:18 PDT)
    - Re: [AMBER] AT1.4 installation errors (logs are attached) Mengjuei Hsieh (Sat May 22 2010 - 02:02:14 PDT)
    - Re: [AMBER] AT1.4 installation errors (logs are attached) Dmitry Mukha (Sat May 22 2010 - 04:08:15 PDT)
    - Re: [AMBER] AT1.4 installation errors (logs are attached) Mengjuei Hsieh (Sat May 22 2010 - 12:38:30 PDT)
    - [AMBER] Can I define target MD or steered MD with mean square internal deviation (MSID) using AMBER 10? Catein Catherine (Sat May 22 2010 - 04:55:34 PDT)
- Re: [AMBER] AT1.4 installation errors (logs are attached) Bill Ross (Sat May 22 2010 - 10:45:56 PDT)
  - Re: [AMBER] AT1.4 installation errors (logs are attached) Mengjuei Hsieh (Sat May 22 2010 - 13:17:32 PDT)
    - Re: [AMBER] AT1.4 installation errors (logs are attached) Mengjuei Hsieh (Thu May 27 2010 - 02:02:41 PDT)
[AMBER] Compiling MPI and CUDA on Amber 11 Samuel, Tabitha Kripa (Tue May 18 2010 - 08:36:43 PDT)
- RE: [AMBER] Compiling MPI and CUDA on Amber 11 Ross Walker (Tue May 18 2010 - 08:47:37 PDT)
[AMBER] Can I get interaction energy between two motifs in diffrent domains in the same protein through MD simulations? Zhihong Yu (Tue May 18 2010 - 09:00:33 PDT)
[AMBER] Can I get interaction energy between two motifs in diffrent domains in the same protein through MD simulations? Zhihong Yu (Tue May 18 2010 - 09:26:15 PDT)
[AMBER] ntx value for MMPBSA normal mode analysis Seungyeul Yoo (Tue May 18 2010 - 15:11:45 PDT)
- Re: [AMBER] ntx value for MMPBSA normal mode analysis Dwight McGee (Tue May 18 2010 - 15:18:08 PDT)
  - Re: [AMBER] ntx value for MMPBSA normal mode analysis Seungyeul Yoo (Tue May 18 2010 - 15:31:03 PDT)
    - Re: [AMBER] ntx value for MMPBSA normal mode analysis Bill Miller III (Tue May 18 2010 - 15:44:18 PDT)
    - Re: [AMBER] ntx value for MMPBSA normal mode analysis Seungyeul Yoo (Tue May 18 2010 - 15:53:40 PDT)
[AMBER] Can I get interaction energy between two motifs in diffrent domains in the same protein through MD simulations? YuZhihong (Tue May 18 2010 - 16:15:38 PDT)
- Re: [AMBER] Can I get interaction energy between two motifs in diffrent domains in the same protein through MD simulations? Bill Miller III (Tue May 18 2010 - 17:05:59 PDT)
  - RE: [AMBER] Can I get interaction energy between two motifs in diffrent domains in the same protein through MD simulations? YuZhihong (Wed May 19 2010 - 09:12:58 PDT)
    - Re: [AMBER] Can I get interaction energy between two motifs in diffrent domains in the same protein through MD simulations? Bill Miller III (Wed May 19 2010 - 20:37:59 PDT)
[AMBER] Odd softcore potential TI problem Paul S. Nerenberg (Tue May 18 2010 - 18:24:11 PDT)
- Re: [AMBER] Odd softcore potential TI problem InSuk Joung (Tue May 18 2010 - 18:48:00 PDT)
  - Re: [AMBER] Odd softcore potential TI problem Paul S. Nerenberg (Tue May 18 2010 - 19:14:49 PDT)
[AMBER] External Electric Field peikun (Tue May 18 2010 - 20:32:04 PDT)
[AMBER] nmr restraints eduardo.troche.uvigo.es (Wed May 19 2010 - 01:25:48 PDT)
- Re: [AMBER] nmr restraints case (Fri May 21 2010 - 12:15:52 PDT)
[AMBER] Production run for MM/PBSA mish (Wed May 19 2010 - 07:27:54 PDT)
- Re: [AMBER] Production run for MM/PBSA Bill Ross (Wed May 19 2010 - 10:24:04 PDT)
[AMBER] Positive Etot value Hoshin Amber (Tue May 18 2010 - 19:55:54 PDT)
- Re: [AMBER] Positive Etot value Bill Ross (Wed May 19 2010 - 10:18:08 PDT)
[AMBER] equilibration John S (Wed May 19 2010 - 11:05:03 PDT)
- Re: [AMBER] equilibration Bill Ross (Wed May 19 2010 - 11:55:19 PDT)
- Re: [AMBER] equilibration Carlos Simmerling (Wed May 19 2010 - 13:11:39 PDT)
  - Re: [AMBER] equilibration John S (Thu May 20 2010 - 20:16:17 PDT)
[AMBER] Coordinate arrays in sander Antonios Samiotakis (Wed May 19 2010 - 15:59:39 PDT)
- Re: [AMBER] Coordinate arrays in sander Jason Swails (Wed May 19 2010 - 16:42:29 PDT)
  - Re: [AMBER] Coordinate arrays in sander Antonios Samiotakis (Tue May 25 2010 - 13:24:06 PDT)
    - Re: [AMBER] Coordinate arrays in sander case (Wed May 26 2010 - 05:00:22 PDT)
[AMBER] explanation for three rdf files Yunfen Wang (Wed May 19 2010 - 20:19:30 PDT)
- Re: [AMBER] explanation for three rdf files Mengjuei Hsieh (Thu May 20 2010 - 01:10:01 PDT)
[AMBER] Ambertools 1.4 installation cygwin Steve Henderson (Wed May 19 2010 - 20:34:38 PDT)
- Re: [AMBER] Ambertools 1.4 installation cygwin Jason Swails (Wed May 19 2010 - 21:19:31 PDT)
- Re: [AMBER] Ambertools 1.4 installation cygwin Bill Ross (Wed May 19 2010 - 23:10:50 PDT)
  - [AMBER] umbrella sampling method or steered MD should be used? Catein Catherine (Wed May 19 2010 - 23:27:29 PDT)
    - Re: [AMBER] umbrella sampling method or steered MD should be used? steinbrt.rci.rutgers.edu (Thu May 20 2010 - 00:41:56 PDT)
    - Re: [AMBER] umbrella sampling method or steered MD should be used? Jerome Golebiowski (Thu May 20 2010 - 01:24:54 PDT)
    - RE: [AMBER] umbrella sampling method or steered MD should be used? Catein Catherine (Thu May 20 2010 - 02:29:44 PDT)
    - RE: [AMBER] umbrella sampling method or steered MD should be used? Jerome Golebiowski (Thu May 20 2010 - 02:58:48 PDT)
    - Re: [AMBER] umbrella sampling method or steered MD should be used? Adrian Roitberg (Thu May 20 2010 - 12:41:36 PDT)
    - RE: [AMBER] umbrella sampling method or steered MD should be used? Catein Catherine (Thu May 20 2010 - 16:22:07 PDT)
    - [AMBER] How to design starting geometries for steered MD? How to check convergence of the results? Catein Catherine (Thu May 20 2010 - 02:42:46 PDT)
    - [AMBER] RDF of centers of masses ? Marek Maly (Fri May 21 2010 - 07:33:07 PDT)
[AMBER] 1,2 -dichloroethane solvent model Lalit Dubey (Wed May 19 2010 - 21:35:53 PDT)
- Re: [AMBER] 1,2 -dichloroethane solvent model FyD (Fri May 21 2010 - 23:00:47 PDT)
  - Re: [AMBER] 1,2 -dichloroethane solvent model Lalit Dubey (Sun May 23 2010 - 21:23:20 PDT)
[AMBER] AMBER10 installation on OSX Kensuke Nakamura (Wed May 19 2010 - 22:07:49 PDT)
- Re: [AMBER] AMBER10 installation on OSX Mengjuei Hsieh (Thu May 20 2010 - 01:26:36 PDT)
  - Re: [AMBER] AMBER10 installation on OSX Kensuke Nakamura (Thu May 20 2010 - 17:44:28 PDT)
    - Re: [AMBER] AMBER10 installation on OSX Jason Swails (Thu May 20 2010 - 17:50:31 PDT)
    - Re: [AMBER] AMBER10 installation on OSX Kensuke Nakamura (Thu May 20 2010 - 18:55:51 PDT)
    - Re: [AMBER] AMBER10 installation on OSX case (Thu May 20 2010 - 19:03:53 PDT)
    - Re: [AMBER] AMBER10 installation on OSX Jason Swails (Thu May 20 2010 - 19:39:34 PDT)
    - Re: [AMBER] AMBER10 installation on OSX Kensuke Nakamura (Thu May 20 2010 - 20:24:30 PDT)
    - Re: [AMBER] AMBER10 installation on OSX Jason Swails (Thu May 20 2010 - 20:45:17 PDT)
    - Re: [AMBER] AMBER10 installation on OSX Mengjuei Hsieh (Thu May 20 2010 - 22:53:04 PDT)
    - Re: [AMBER] AMBER10 installation on OSX Jason Swails (Fri May 21 2010 - 05:51:43 PDT)
    - Re: [AMBER] AMBER10 installation on OSX Mengjuei Hsieh (Fri May 21 2010 - 10:55:19 PDT)
    - Re: [AMBER] AMBER10 installation on OSX David Watson (Fri May 21 2010 - 06:05:56 PDT)
    - Re: [AMBER] AMBER10 installation on OSX Kensuke Nakamura (Fri May 21 2010 - 17:17:57 PDT)
- Re: [AMBER] AMBER10 installation on OSX case (Thu May 20 2010 - 06:17:39 PDT)
- Re: [AMBER] AMBER10 installation on OSX erik zuiderweg (Thu May 20 2010 - 07:53:12 PDT)
[AMBER] parameters for MSE (selenomethionine) kamlesh sahu (Thu May 20 2010 - 01:26:59 PDT)
[AMBER] PMEMD.CUDA on GTS250 Josmar R. da Rocha (Thu May 20 2010 - 10:29:35 PDT)
- RE: [AMBER] PMEMD.CUDA on GTS250 Scott Le Grand (Thu May 20 2010 - 10:37:34 PDT)
  - Re: [AMBER] PMEMD.CUDA on GTS250 Jason Swails (Thu May 20 2010 - 10:40:36 PDT)
    - Re: [AMBER] PMEMD.CUDA on GTS250 Josmar R. da Rocha (Thu May 20 2010 - 11:19:36 PDT)
- RE: [AMBER] PMEMD.CUDA on GTS250 Ross Walker (Thu May 20 2010 - 14:31:27 PDT)
[AMBER] sander.MPI problem peker milas (Thu May 20 2010 - 12:19:07 PDT)
- Re: [AMBER] sander.MPI problem Jason Swails (Thu May 20 2010 - 12:56:41 PDT)
  - Re: [AMBER] sander.MPI problem peker milas (Thu May 20 2010 - 13:22:26 PDT)
    - Re: [AMBER] sander.MPI problem Gustavo Seabra (Thu May 20 2010 - 13:35:23 PDT)
    - Re: [AMBER] sander.MPI problem peker milas (Fri May 21 2010 - 05:47:45 PDT)
    - Re: [AMBER] sander.MPI problem Gustavo Seabra (Fri May 21 2010 - 08:28:27 PDT)
    - Re: [AMBER] sander.MPI problem peker milas (Fri May 21 2010 - 12:30:29 PDT)
    - Re: [AMBER] sander.MPI problem peker milas (Fri May 21 2010 - 12:33:53 PDT)
    - Re: [AMBER] sander.MPI problem Dmitry Mukha (Sat May 22 2010 - 07:49:13 PDT)
[AMBER] sleap bugs or compilation problem?! Dino Rogerio Coinete Franklin (Thu May 20 2010 - 14:09:40 PDT)
- Re: [AMBER] sleap bugs or compilation problem?! Bill Ross (Thu May 20 2010 - 14:22:19 PDT)
- Re: [AMBER] sleap bugs or compilation problem?! case (Fri May 21 2010 - 07:48:09 PDT)
[AMBER] minimization with pmemd and gbsa=1 Paul Brandt (Fri May 21 2010 - 00:19:11 PDT)
- RE: [AMBER] minimization with pmemd and gbsa=1 Paul Brandt (Fri May 21 2010 - 02:27:30 PDT)
- RE: [AMBER] minimization with pmemd and gbsa=1 Ross Walker (Fri May 21 2010 - 07:20:48 PDT)
[AMBER] The force field xuemeiwang1103 (Fri May 21 2010 - 02:13:14 PDT)
- Re: [AMBER] The force field FyD (Fri May 21 2010 - 22:36:25 PDT)
[AMBER] Mutations and minimizations Cristina Sisu (Fri May 21 2010 - 03:35:21 PDT)
- Re: [AMBER] Mutations and minimizations Bill Ross (Fri May 21 2010 - 09:20:12 PDT)
[AMBER] compiling problem, Syed Tarique Moin (Fri May 21 2010 - 05:52:16 PDT)
- Re: [AMBER] compiling problem, case (Fri May 21 2010 - 06:55:57 PDT)
  - Re: [AMBER] compiling problem, Syed Tarique Moin (Fri May 21 2010 - 12:09:39 PDT)
    - Re: [AMBER] compiling problem, Daniel Roe (Fri May 21 2010 - 12:17:26 PDT)
    - Re: [AMBER] compiling problem, Syed Tarique Moin (Fri May 21 2010 - 18:49:21 PDT)
[AMBER] leap issues Alex Boncheff (Fri May 21 2010 - 10:09:39 PDT)
- Re: [AMBER] leap issues Jason Swails (Fri May 21 2010 - 10:14:42 PDT)
  - Re: [AMBER] leap issues Lachele Foley (Lists) (Fri May 21 2010 - 10:26:56 PDT)
- Re: [AMBER] leap issues Bill Ross (Fri May 21 2010 - 10:20:48 PDT)
- Re: [AMBER] leap issues case (Fri May 21 2010 - 10:28:35 PDT)
- Re: [AMBER] leap issues Alex Boncheff (Fri May 21 2010 - 10:43:09 PDT)
  - Re: [AMBER] leap issues case (Fri May 21 2010 - 11:43:45 PDT)
- Re: [AMBER] leap issues Bill Ross (Fri May 21 2010 - 10:52:55 PDT)
[AMBER] NMR distance restraints read but not used Douglas Kojetin (Fri May 21 2010 - 10:40:15 PDT)
- Re: [AMBER] NMR distance restraints read but not used case (Fri May 21 2010 - 11:19:38 PDT)
  - Re: [AMBER] NMR distance restraints read but not used Douglas Kojetin (Fri May 21 2010 - 11:30:33 PDT)
    - Re: [AMBER] NMR distance restraints read but not used Douglas Kojetin (Fri May 21 2010 - 12:03:43 PDT)
  - Re: [AMBER] NMR distance restraints read but not used Douglas Kojetin (Fri May 21 2010 - 11:40:19 PDT)
    - Re: [AMBER] NMR distance restraints read but not used case (Fri May 21 2010 - 12:01:38 PDT)
    - Re: [AMBER] NMR distance restraints read but not used Douglas Kojetin (Sat May 22 2010 - 10:00:11 PDT)
    - Re: [AMBER] NMR distance restraints read but not used Douglas Kojetin (Sat May 22 2010 - 10:23:56 PDT)
    - Re: [AMBER] NMR distance restraints read but not used Douglas Kojetin (Thu May 27 2010 - 08:36:58 PDT)
[AMBER] Calculating Self-Diffusion Coefficients Matthew Tessier (Fri May 21 2010 - 11:13:34 PDT)
[AMBER] help about test failures peker milas (Fri May 21 2010 - 13:32:34 PDT)
- Re: [AMBER] help about test failures Daniel Roe (Fri May 21 2010 - 14:15:03 PDT)
  - Re: [AMBER] help about test failures peker milas (Fri May 21 2010 - 15:50:51 PDT)
    - Re: [AMBER] help about test failures case (Sat May 22 2010 - 17:24:15 PDT)
    - Re: [AMBER] help about test failures peker milas (Sat May 22 2010 - 17:28:51 PDT)
    - Re: [AMBER] help about test failures Jason Swails (Sat May 22 2010 - 18:16:42 PDT)
[AMBER] AT 1.4 DFTB Guanglei Cui (Fri May 21 2010 - 15:01:35 PDT)
[AMBER] TI Job crashes at some lambda values during heating sunita gupta (Sat May 22 2010 - 05:20:52 PDT)
- Re: [AMBER] TI Job crashes at some lambda values during heating case (Sat May 22 2010 - 17:18:44 PDT)
  - Re: [AMBER] TI Job crashes at some lambda values during heating manikanthan bhavaraju (Sat May 22 2010 - 20:47:19 PDT)
    - Re: [AMBER] TI Job crashes at some lambda values during heating sunita gupta (Mon May 24 2010 - 03:14:43 PDT)
    - Re: [AMBER] TI Job crashes at some lambda values during heating manikanthan bhavaraju (Mon May 24 2010 - 17:50:47 PDT)
    - Re: [AMBER] TI Job crashes at some lambda values during heating sunita gupta (Mon May 24 2010 - 23:43:57 PDT)
    - Re: [AMBER] TI Job crashes at some lambda values during heating manikanthan bhavaraju (Tue May 25 2010 - 08:35:45 PDT)
[AMBER] EP with ff99SB William Flak (Sun May 23 2010 - 14:46:42 PDT)
- Re: [AMBER] EP with ff99SB case (Sun May 23 2010 - 15:32:26 PDT)
  - Re: [AMBER] EP with ff99SB William Flak (Sun May 23 2010 - 15:53:02 PDT)
    - Re: [AMBER] EP with ff99SB Carlos Simmerling (Sun May 23 2010 - 19:26:24 PDT)
    - [AMBER] Dynamic Cross Correlation Map Homa Azizian (Sun May 23 2010 - 19:53:46 PDT)
[AMBER] RESP check William Flak (Sun May 23 2010 - 15:03:21 PDT)
- Re: [AMBER] RESP check FyD (Mon May 24 2010 - 00:10:58 PDT)
[AMBER] Problem on Running Shell Script tianyuan meng (Mon May 24 2010 - 02:38:54 PDT)
[AMBER] Percholate ions Hemant Kumar (Mon May 24 2010 - 02:34:25 PDT)
[AMBER] (no subject) Nicee (Mon May 24 2010 - 02:54:01 PDT)
[AMBER] Atom out of bounds/prepin file problem Nicee (Mon May 24 2010 - 02:55:48 PDT)
- Re: [AMBER] Atom out of bounds/prepin file problem case (Mon May 24 2010 - 05:58:24 PDT)
  - [AMBER] How to do clustering with ptraj? Catein Catherine (Mon May 24 2010 - 09:11:30 PDT)
    - Re: [AMBER] How to do clustering with ptraj? Bill Miller III (Mon May 24 2010 - 09:31:04 PDT)
    - Re: [AMBER] How to do clustering with ptraj? case (Mon May 24 2010 - 09:33:04 PDT)
  - Re: [AMBER] Atom out of bounds/prepin file problem Nicee (Mon May 24 2010 - 23:06:46 PDT)
    - Re: [AMBER] Atom out of bounds/prepin file problem Nicee (Tue May 25 2010 - 00:01:49 PDT)
[AMBER] Thank you all William Flak (Mon May 24 2010 - 08:12:39 PDT)
- [AMBER] Is the results of NAMD equals to AMBER's sander? Catein Catherine (Mon May 24 2010 - 09:06:30 PDT)
  - [AMBER] How to calculate ensemble-averaged electrostatic calculations with VMD? Catein Catherine (Mon May 24 2010 - 09:17:52 PDT)
  - Re: [AMBER] Is the results of NAMD equals to AMBER's sander? Robert Elder (Mon May 24 2010 - 12:49:31 PDT)
    - Re: [AMBER] Is the results of NAMD equals to AMBER's sander? Tom Joseph (Mon May 24 2010 - 13:49:38 PDT)
[AMBER] Compiling Amber10 on Mac Snow Leopard with gcc/gfortran Aurora Clark (Mon May 24 2010 - 10:22:34 PDT)
- Re: [AMBER] Compiling Amber10 on Mac Snow Leopard with gcc/gfortran case (Mon May 24 2010 - 10:39:16 PDT)
  - Re: [AMBER] Compiling Amber10 on Mac Snow Leopard with gcc/gfortran erik zuiderweg (Mon May 24 2010 - 11:04:42 PDT)
[AMBER] radius of gyration in ptraj Jayalakshmi Sridhar (Mon May 24 2010 - 11:30:06 PDT)
- Re: [AMBER] radius of gyration in ptraj Daniel Roe (Mon May 24 2010 - 18:36:28 PDT)
[AMBER] MMPBSA.py update Jason Swails (Mon May 24 2010 - 15:53:24 PDT)
- FW: [AMBER] MMPBSA.py update Beroza, Paul (Mon May 24 2010 - 17:39:51 PDT)
  - Re: FW: [AMBER] MMPBSA.py update Jason Swails (Mon May 24 2010 - 18:07:34 PDT)
    - [AMBER] MMPBSA.py update install problem Rilei Yu (Mon May 24 2010 - 22:56:24 PDT)
    - Re: [AMBER] MMPBSA.py update install problem Bill Miller III (Tue May 25 2010 - 04:18:38 PDT)
    - Re: [AMBER] MMPBSA.py update install problem case (Tue May 25 2010 - 05:06:37 PDT)
    - Re: [AMBER] MMPBSA.py update install problem Jason Swails (Tue May 25 2010 - 05:21:25 PDT)
    - Re: [AMBER] MMPBSA.py update install problem Rilei Yu (Thu May 27 2010 - 23:21:49 PDT)
    - Re: [AMBER] MMPBSA.py update install problem Bill Miller III (Fri May 28 2010 - 04:05:31 PDT)
    - Re: [AMBER] MMPBSA.py update install problem Bill Ross (Fri May 28 2010 - 10:20:24 PDT)
    - Re: [AMBER] MMPBSA.py update install problem Jason Swails (Fri May 28 2010 - 13:38:25 PDT)
    - Re: [AMBER] MMPBSA.py update install problem Rilei Yu (Sat May 29 2010 - 04:21:31 PDT)
    - Re: [AMBER] MMPBSA.py update install problem Jason Swails (Sat May 29 2010 - 06:55:22 PDT)
    - Re: [AMBER] MMPBSA.py update install problem Rilei Yu (Sat May 29 2010 - 20:09:13 PDT)
    - Re: [AMBER] MMPBSA.py update install problem Jason Swails (Sat May 29 2010 - 21:00:39 PDT)
    - Re: [AMBER] MMPBSA.py update install problem Rilei Yu (Sat May 29 2010 - 22:28:22 PDT)
    - Re: [AMBER] MMPBSA.py update install problem Jason Swails (Sun May 30 2010 - 06:32:14 PDT)
    - Re: [AMBER] MMPBSA.py update install problem Rilei Yu (Sun May 30 2010 - 17:26:28 PDT)
    - Re: [AMBER] MMPBSA.py update install problem Bill Miller III (Sun May 30 2010 - 17:44:09 PDT)
    - Re: [AMBER] MMPBSA.py update install problem Jason Swails (Sun May 30 2010 - 17:50:38 PDT)
    - [AMBER] 'process_mdout.perl' script Homa Azizian (Sun May 30 2010 - 18:21:50 PDT)
    - RE: [AMBER] 'process_mdout.perl' script Ross Walker (Mon May 31 2010 - 16:15:20 PDT)
    - Re: [AMBER] MMPBSA.py update install problem Rilei Yu (Sun May 30 2010 - 18:59:28 PDT)
    - Re: [AMBER] MMPBSA.py update install problem Jason Swails (Sun May 30 2010 - 20:33:44 PDT)
    - Re: [AMBER] MMPBSA.py update install problem Rilei Yu (Sun May 30 2010 - 22:25:30 PDT)
    - Re: [AMBER] MMPBSA.py update install problem Bill Miller III (Mon May 31 2010 - 05:10:59 PDT)
    - Re: [AMBER] MMPBSA.py update install problem Jason Swails (Mon May 31 2010 - 06:07:49 PDT)
    - Re: [AMBER] MMPBSA.py update install problem Rilei Yu (Mon May 31 2010 - 16:59:09 PDT)
    - Re: [AMBER] MMPBSA.py update install problem Jason Swails (Mon May 31 2010 - 17:29:18 PDT)
    - Re: [AMBER] MMPBSA.py update install problem Rilei Yu (Tue Jun 01 2010 - 23:18:26 PDT)
    - Re: [AMBER] MMPBSA.py update install problem Dwight McGee (Wed Jun 02 2010 - 01:14:54 PDT)
    - Re: [AMBER] MMPBSA.py update install problem Rilei Yu (Wed Jun 02 2010 - 01:53:16 PDT)
    - Re: [AMBER] MMPBSA.py update install problem Bill Miller III (Wed Jun 02 2010 - 04:30:04 PDT)
    - Re: [AMBER] MMPBSA.py update install problem Jason Swails (Wed Jun 02 2010 - 06:14:24 PDT)
    - Re: [AMBER] MMPBSA.py update install problem Rilei Yu (Wed Jun 02 2010 - 17:37:44 PDT)
    - [AMBER] time-correlation fluctuation Homa Azizian (Thu Jun 03 2010 - 02:06:06 PDT)
    - Re: [AMBER] MMPBSA.py update install problem Bill Miller III (Mon May 31 2010 - 17:29:43 PDT)
    - [AMBER] Entropy for my system works now Rilei Yu (Sat Jun 05 2010 - 19:15:58 PDT)
    - [AMBER] entropy calculation failed again! Rilei Yu (Fri Jun 04 2010 - 18:28:10 PDT)
    - Re: [AMBER] entropy calculation failed again! Dwight McGee (Fri Jun 04 2010 - 18:32:34 PDT)
    - Re: [AMBER] entropy calculation failed again! Bill Miller III (Fri Jun 04 2010 - 18:35:20 PDT)
    - Re: [AMBER] entropy calculation failed again! Dwight McGee (Fri Jun 04 2010 - 19:04:18 PDT)
    - Re: [AMBER] entropy calculation failed again! Rilei Yu (Fri Jun 04 2010 - 19:44:09 PDT)
    - Re: [AMBER] entropy calculation failed again! Bill Miller III (Fri Jun 04 2010 - 20:02:37 PDT)
    - Re: [AMBER] entropy calculation failed again! Dwight McGee (Fri Jun 04 2010 - 20:02:59 PDT)
    - Re: [AMBER] entropy calculation failed again! Rilei Yu (Fri Jun 04 2010 - 21:30:06 PDT)
    - Re: [AMBER] entropy calculation failed again! case (Sat Jun 05 2010 - 05:03:43 PDT)
    - Re: [AMBER] MMPBSA.py update install problem Bill Miller III (Sun May 30 2010 - 06:33:09 PDT)
  - Re: FW: [AMBER] MMPBSA.py update Bill Miller III (Mon May 24 2010 - 18:07:42 PDT)
- Re: [AMBER] MMPBSA.py update Alan (Mon May 24 2010 - 23:37:21 PDT)
[AMBER] Square planar complex and improper torsions Robert Elder (Mon May 24 2010 - 16:36:47 PDT)
- Re: [AMBER] Square planar complex and improper torsions Bill Ross (Mon May 24 2010 - 17:06:49 PDT)
  - Re: [AMBER] Square planar complex and improper torsions Robert Elder (Tue May 25 2010 - 09:01:54 PDT)
- Re: [AMBER] Square planar complex and improper torsions Bill Ross (Tue May 25 2010 - 10:58:34 PDT)
  - Re: [AMBER] Square planar complex and improper torsions Robert Elder (Wed May 26 2010 - 16:40:19 PDT)
[AMBER] writing in ptraj a new action requiring prior knowledge of the average coordinates Jose Borreguero (Mon May 24 2010 - 17:41:33 PDT)
- RE: [AMBER] writing in ptraj a new action requiring prior knowledge of the average coordinates Ross Walker (Mon May 24 2010 - 18:25:25 PDT)
  - Re: [AMBER] writing in ptraj a new action requiring prior knowledge of the average coordinates Jose Borreguero (Mon May 24 2010 - 18:39:54 PDT)
  - Re: [AMBER] writing in ptraj a new action requiring prior knowledge of the average coordinates Daniel Roe (Mon May 24 2010 - 18:45:40 PDT)
    - Re: [AMBER] writing in ptraj a new action requiring prior knowledge of the average coordinates Jose Borreguero (Mon May 24 2010 - 20:22:06 PDT)
[AMBER] The lib file xuemeiwang1103 (Mon May 24 2010 - 19:23:54 PDT)
[AMBER] Problem about Sander with large system Tom Williams (Mon May 24 2010 - 19:58:53 PDT)
- Re: [AMBER] Problem about Sander with large system Adrian Roitberg (Mon May 24 2010 - 20:03:24 PDT)
  - Re: [AMBER] Problem about Sander with large system Tom Williams (Mon May 24 2010 - 20:45:18 PDT)
- Re: [AMBER] Problem about Sander with large system Bill Ross (Mon May 24 2010 - 22:50:03 PDT)
  - Re: [AMBER] Problem about Sander with large system Tom Williams (Tue May 25 2010 - 07:55:09 PDT)
    - Re: [AMBER] Problem about Sander with large system Jason Swails (Tue May 25 2010 - 08:00:28 PDT)
[AMBER] AMBER Asfa Ali (Mon May 24 2010 - 22:40:35 PDT)
[AMBER] regarding MMPBSA Asfa Ali (Tue May 25 2010 - 03:15:05 PDT)
- Re: [AMBER] regarding MMPBSA Bill Miller III (Tue May 25 2010 - 03:57:03 PDT)
[AMBER] MMPBSA.py.MPI Alan (Tue May 25 2010 - 03:17:23 PDT)
- Re: [AMBER] MMPBSA.py.MPI Bill Miller III (Tue May 25 2010 - 04:03:08 PDT)
  - Re: [AMBER] MMPBSA.py.MPI Jason Swails (Tue May 25 2010 - 05:32:37 PDT)
    - Re: [AMBER] MMPBSA.py.MPI Alan (Tue May 25 2010 - 05:39:16 PDT)
[AMBER] problem with MMPBSA Chanchal (Tue May 25 2010 - 06:54:18 PDT)
- Re: [AMBER] problem with MMPBSA Bill Miller III (Tue May 25 2010 - 07:20:14 PDT)
[AMBER] Dipoles calculation Sergey Samsonov (Tue May 25 2010 - 07:17:03 PDT)
- Re: [AMBER] Dipoles calculation Gustavo Seabra (Tue May 25 2010 - 13:42:41 PDT)
[AMBER] unable to view grid file of ptraj Hyma vathi (Tue May 25 2010 - 07:42:41 PDT)
- Re: [AMBER] unable to view grid file of ptraj Thomas Cheatham III (Tue May 25 2010 - 08:29:24 PDT)
  - Re: [AMBER] unable to view grid file of ptraj Hyma vathi (Tue May 25 2010 - 10:35:17 PDT)
    - [AMBER] Reply on closest waters problem Thomas Cheatham III (Wed May 26 2010 - 10:21:51 PDT)
    - Re: [AMBER] Reply on closest waters problem Bill Ross (Wed May 26 2010 - 10:36:17 PDT)
[AMBER] Setting Atom Types Alex Boncheff (Tue May 25 2010 - 08:32:27 PDT)
[AMBER] ptraj rms error Beale, John (Tue May 25 2010 - 08:33:01 PDT)
- Re: [AMBER] ptraj rms error Daniel Roe (Tue May 25 2010 - 12:59:24 PDT)
[AMBER] Setting Atom Types Alex Boncheff (Tue May 25 2010 - 08:44:17 PDT)
- Re: [AMBER] Setting Atom Types Bill Ross (Tue May 25 2010 - 10:45:03 PDT)
  - Re: [AMBER] Setting Atom Types Alex Boncheff (Tue May 25 2010 - 11:20:44 PDT)
    - Re: [AMBER] Setting Atom Types case (Tue May 25 2010 - 12:48:14 PDT)
    - Re: [AMBER] Setting Atom Types Alex Boncheff (Tue May 25 2010 - 22:00:28 PDT)
    - Re: [AMBER] Setting Atom Types case (Wed May 26 2010 - 05:30:06 PDT)
    - Re: [AMBER] Setting Atom Types Mengjuei Hsieh (Thu May 27 2010 - 01:45:05 PDT)
    - Re: [AMBER] Setting Atom Types Dmitry Mukha (Thu May 27 2010 - 08:10:27 PDT)
    - Re: [AMBER] Setting Atom Types case (Thu May 27 2010 - 09:03:23 PDT)
    - Re: [AMBER] Setting Atom Types Dmitry Mukha (Fri May 28 2010 - 00:33:56 PDT)
    - [AMBER] CPU core requirements for GPU Amber? Sasha Buzko (Wed May 26 2010 - 14:09:18 PDT)
    - Re: [AMBER] CPU core requirements for GPU Amber? Jason Swails (Wed May 26 2010 - 15:09:28 PDT)
    - Re: [AMBER] CPU core requirements for GPU Amber? Levi Pierce (Wed May 26 2010 - 15:22:04 PDT)
    - Re: [AMBER] CPU core requirements for GPU Amber? Sasha Buzko (Wed May 26 2010 - 15:35:26 PDT)
    - RE: [AMBER] CPU core requirements for GPU Amber? Ross Walker (Wed May 26 2010 - 15:40:25 PDT)
    - RE: [AMBER] CPU core requirements for GPU Amber? Richard Owczarzy (Wed May 26 2010 - 15:52:57 PDT)
    - RE: [AMBER] CPU core requirements for GPU Amber? Ross Walker (Wed May 26 2010 - 16:03:32 PDT)
    - RE: [AMBER] CPU core requirements for GPU Amber? Scott Le Grand (Wed May 26 2010 - 16:16:32 PDT)
    - RE: [AMBER] CPU core requirements for GPU Amber? Scott Le Grand (Wed May 26 2010 - 16:18:09 PDT)
    - [AMBER] what is the meaning of GBSA decompostion results for drug-drug interaction? Catein Catherine (Thu May 27 2010 - 00:37:58 PDT)
    - Re: [AMBER] what is the meaning of GBSA decompostion results for drug-drug interaction? Jason Swails (Thu May 27 2010 - 06:36:25 PDT)
    - [AMBER] Why different binding energy is obtained from GBSA calculations? Catein Catherine (Mon May 31 2010 - 20:43:15 PDT)
    - [AMBER] pmemd.cuda segmentation fault with iwrap=1 on NVT/NVE Sasha Buzko (Fri May 28 2010 - 09:39:46 PDT)
    - RE: [AMBER] pmemd.cuda segmentation fault with iwrap=1 on NVT/NVE Scott Le Grand (Fri May 28 2010 - 13:00:42 PDT)
    - Re: [AMBER] pmemd.cuda segmentation fault with iwrap=1 on NVT/NVE Levi Pierce (Thu Jun 10 2010 - 14:01:29 PDT)
    - Re: [AMBER] pmemd.cuda segmentation fault with iwrap=1 on NVT/NVE Sasha Buzko (Thu Jun 10 2010 - 14:01:06 PDT)
    - Re: [AMBER] pmemd.cuda segmentation fault with iwrap=1 on NVT/NVE Levi Pierce (Thu Jun 10 2010 - 14:24:21 PDT)
    - Re: [AMBER] pmemd.cuda segmentation fault with iwrap=1 on NVT/NVE Scott Le Grand (Fri Jun 25 2010 - 16:53:49 PDT)
    - Re: [AMBER] pmemd.cuda segmentation fault with iwrap=1 on NVT/NVE Levi Pierce (Fri Jun 25 2010 - 19:22:12 PDT)
    - Re: [AMBER] pmemd.cuda segmentation fault with iwrap=1 on NVT/NVE case (Sun Jun 27 2010 - 18:53:59 PDT)
    - Re: [AMBER] CPU core requirements for GPU Amber? Jason Swails (Wed May 26 2010 - 15:55:12 PDT)
    - RE: [AMBER] CPU core requirements for GPU Amber? Ross Walker (Wed May 26 2010 - 16:01:05 PDT)
    - RE: [AMBER] CPU core requirements for GPU Amber? Scott Le Grand (Wed May 26 2010 - 16:15:01 PDT)
    - RE: [AMBER] CPU core requirements for GPU Amber? Scott Le Grand (Wed May 26 2010 - 16:17:19 PDT)
    - RE: [AMBER] CPU core requirements for GPU Amber? Ross Walker (Wed May 26 2010 - 15:36:43 PDT)
- Re: [AMBER] Setting Atom Types Bill Ross (Tue May 25 2010 - 11:29:45 PDT)
[AMBER] Re: parallel problem for systems only including bond, angle and dihedral interactions Dongshan Wei (Tue May 25 2010 - 10:16:36 PDT)
[AMBER] writing mode Qian Wang (Tue May 25 2010 - 12:59:34 PDT)
Fwd: [AMBER] Problem about Sander with large system Jason Swails (Tue May 25 2010 - 13:46:13 PDT)
- Re: [AMBER] Problem about Sander with large system Tom Williams (Wed May 26 2010 - 09:33:06 PDT)
  - Re: [AMBER] Problem about Sander with large system Jason Swails (Wed May 26 2010 - 15:02:26 PDT)
[AMBER] personalized addition of H atoms in proteins with tleap rivalta.unical.it (Tue May 25 2010 - 16:14:08 PDT)
- Re: [AMBER] personalized addition of H atoms in proteins with tleap Jason Swails (Tue May 25 2010 - 16:35:41 PDT)
  - Re: [AMBER] personalized addition of H atoms in proteins with tleap rivalta.unical.it (Tue May 25 2010 - 17:34:36 PDT)
    - Re: [AMBER] personalized addition of H atoms in proteins with tleap Gustavo Seabra (Tue May 25 2010 - 21:13:10 PDT)
    - Re: [AMBER] personalized addition of H atoms in proteins with tleap rivalta.unical.it (Wed May 26 2010 - 07:28:07 PDT)
- Re: [AMBER] personalized addition of H atoms in proteins with tleap Bill Ross (Tue May 25 2010 - 16:39:17 PDT)
- Re: [AMBER] personalized addition of H atoms in proteins with tleap Bill Ross (Tue May 25 2010 - 16:41:01 PDT)
- Re: [AMBER] personalized addition of H atoms in proteins with tleap Bill Ross (Tue May 25 2010 - 17:56:39 PDT)
[AMBER] Dynamic Cross Correlation Map Homa Azizian (Tue May 25 2010 - 19:56:57 PDT)
- Re: [AMBER] Dynamic Cross Correlation Map Bill Ross (Wed May 26 2010 - 09:22:50 PDT)
[AMBER] distance restraint qiaoyan (Tue May 25 2010 - 19:58:07 PDT)
- RE: [AMBER] distance restraint matthew_seetin.urmc.rochester.edu (Tue May 25 2010 - 21:57:17 PDT)
[AMBER] antechamber missing_grace.sina.com (Tue May 25 2010 - 21:57:27 PDT)
- Re: [AMBER] antechamber Gustavo Seabra (Wed May 26 2010 - 07:12:55 PDT)
[AMBER] amber missing_grace.sina.com (Tue May 25 2010 - 21:59:02 PDT)
- Re: [AMBER] amber Jason Swails (Tue May 25 2010 - 22:21:58 PDT)
  - Re: [AMBER] amber Jason Swails (Tue May 25 2010 - 22:25:35 PDT)
    - [AMBER] How to interpret ptraj clustering results Catein Catherine (Wed May 26 2010 - 01:02:10 PDT)
    - Re: [AMBER] How to interpret ptraj clustering results Thomas Cheatham III (Wed May 26 2010 - 10:54:57 PDT)
    - RE: [AMBER] How to interpret ptraj clustering results Catein Catherine (Thu May 27 2010 - 00:40:24 PDT)
    - [AMBER] How to interpret the results of ptraj/contacts Catein Catherine (Wed May 26 2010 - 01:12:04 PDT)
    - RE: [AMBER] How to interpret the results of ptraj/contacts Catein Catherine (Wed May 26 2010 - 01:21:30 PDT)
- Re: [AMBER] amber Levi Pierce (Tue May 25 2010 - 22:24:37 PDT)
[AMBER] antechamber missing_grace.sina.com (Tue May 25 2010 - 22:08:53 PDT)
- Re: [AMBER] antechamber JoRDi (Wed May 26 2010 - 02:00:44 PDT)
  - Re: [AMBER] antechamber Jason Swails (Wed May 26 2010 - 07:00:28 PDT)
[AMBER] DIPOLE MOMENT OF HEPARAN SULPHATE MODELS Juan Carlos (Wed May 26 2010 - 01:16:53 PDT)
[AMBER] TI using soft-core potential Sushil Mishra (Wed May 26 2010 - 02:54:07 PDT)
- Re: [AMBER] TI using soft-core potential steinbrt.rci.rutgers.edu (Wed May 26 2010 - 04:49:19 PDT)
  - Re: [AMBER] TI using soft-core potential Sushil Mishra (Wed May 26 2010 - 04:55:00 PDT)
    - Re: [AMBER] TI using soft-core potential steinbrt.rci.rutgers.edu (Wed May 26 2010 - 06:03:32 PDT)
    - Re: [AMBER] TI using soft-core potential case (Wed May 26 2010 - 06:06:51 PDT)
    - Re: [AMBER] TI using soft-core potential Sushil Mishra (Wed May 26 2010 - 06:26:08 PDT)
- Re: [AMBER] TI using soft-core potential case (Wed May 26 2010 - 05:35:46 PDT)
[AMBER] NUCGEN monica.imtech.res.in (Wed May 26 2010 - 04:10:02 PDT)
- Re: [AMBER] NUCGEN Jason Swails (Wed May 26 2010 - 07:27:38 PDT)
  - Re: [AMBER] NUCGEN Levi Pierce (Wed May 26 2010 - 10:18:54 PDT)
[AMBER] B-DNA monica.imtech.res.in (Wed May 26 2010 - 04:18:02 PDT)
- Re: [AMBER] B-DNA steinbrt.rci.rutgers.edu (Wed May 26 2010 - 04:45:20 PDT)
- Re: [AMBER] B-DNA case (Wed May 26 2010 - 05:38:14 PDT)
- Re: [AMBER] B-DNA Ilyas Yildirim (Wed May 26 2010 - 08:08:50 PDT)
[AMBER] Solvate box JoRDi (Wed May 26 2010 - 05:07:26 PDT)
- Re: [AMBER] Solvate box Gustavo Seabra (Wed May 26 2010 - 06:44:15 PDT)
[AMBER] Energy minimization OR black art M. Reza Ganjalikhany (Wed May 26 2010 - 05:41:45 PDT)
- Re: [AMBER] Energy minimization OR black art steinbrt.rci.rutgers.edu (Wed May 26 2010 - 05:57:10 PDT)
  - Re: [AMBER] Energy minimization OR black art M. Reza Ganjalikhany (Wed May 26 2010 - 06:29:01 PDT)
    - RE: [AMBER] Energy minimization OR black art Ross Walker (Wed May 26 2010 - 08:44:57 PDT)
- Re: [AMBER] Energy minimization OR black art Gustavo Seabra (Wed May 26 2010 - 07:11:22 PDT)
  - Re: [AMBER] Energy minimization OR black art Jason Swails (Wed May 26 2010 - 07:22:05 PDT)
[AMBER] installing AmberTools 1.4 on AIX Mirko Cestari (Wed May 26 2010 - 06:16:38 PDT)
- Re: [AMBER] installing AmberTools 1.4 on AIX case (Sat May 29 2010 - 19:32:42 PDT)
  - Re: [AMBER] installing AmberTools 1.4 on AIX Mirko Cestari (Mon May 31 2010 - 06:57:52 PDT)
    - Re: [AMBER] installing AmberTools 1.4 on AIX Mirko Cestari (Thu Jul 01 2010 - 00:44:23 PDT)
    - Re: [AMBER] installing AmberTools 1.4 on AIX case (Thu Jul 01 2010 - 05:26:01 PDT)
    - Re: [AMBER] installing AmberTools 1.4 on AIX Mirko Cestari (Wed Jul 07 2010 - 05:52:27 PDT)
[AMBER] Can mm_pbsa.pl read NETCDF format trajectory file ? Sushil Mishra (Wed May 26 2010 - 06:36:17 PDT)
- Re: [AMBER] Can mm_pbsa.pl read NETCDF format trajectory file ? Jason Swails (Wed May 26 2010 - 07:14:40 PDT)
[AMBER] how to add Mg2+ Sangita Kachhap (Thu May 27 2010 - 10:21:53 PDT)
- Re: [AMBER] how to add Mg2+ Bill Miller III (Thu May 27 2010 - 10:34:20 PDT)
  - Re: [AMBER] how to add Mg2+ Bill Ross (Thu May 27 2010 - 10:44:01 PDT)
    - Re: [AMBER] how to add Mg2+ Jason Swails (Thu May 27 2010 - 11:09:24 PDT)
    - Re: [AMBER] how to add Mg2+ Sangita Kachhap (Fri May 28 2010 - 06:56:39 PDT)
    - Re: [AMBER] how to add Mg2+ Sangita Kachhap (Fri May 28 2010 - 06:58:38 PDT)
  - Re: [AMBER] how to add Mg2+ Sangita Kachhap (Fri May 28 2010 - 06:59:48 PDT)
[AMBER] Installing AmberTools 1.4 in Ubuntu 10.04 David Dubins (Thu May 27 2010 - 11:36:23 PDT)
- Re: [AMBER] Installing AmberTools 1.4 in Ubuntu 10.04 Jason Swails (Thu May 27 2010 - 12:20:41 PDT)
  - Re: [AMBER] Installing AmberTools 1.4 in Ubuntu 10.04 Levi Pierce (Thu May 27 2010 - 14:08:25 PDT)
[AMBER] Amber 11 SRPM? Marc Moreau (Thu May 27 2010 - 14:05:39 PDT)
- Re: [AMBER] Amber 11 SRPM? Mengjuei Hsieh (Thu May 27 2010 - 17:18:43 PDT)
[AMBER] Does AMBER10 support REMD with AMOEBA? Yue Shi (Thu May 27 2010 - 15:52:29 PDT)
[AMBER] question proximal radial distribution function Tom Williams (Thu May 27 2010 - 19:32:12 PDT)
[AMBER] amber11 PMEMD cuda problem. (sometimes stopped...) Wookyung Yu (Thu May 27 2010 - 19:50:47 PDT)
- RE: [AMBER] amber11 PMEMD cuda problem. (sometimes stopped...) Ross Walker (Thu May 27 2010 - 20:32:57 PDT)
  - Re: [AMBER] amber11 PMEMD cuda problem. (sometimes stopped...) Wookyung Yu (Thu May 27 2010 - 21:57:51 PDT)
- RE: [AMBER] amber11 PMEMD cuda problem. (sometimes stopped...) Ross Walker (Thu Jun 03 2010 - 07:44:12 PDT)
[AMBER] regarding K+ ions Asfa Ali (Thu May 27 2010 - 22:32:45 PDT)
- Re: [AMBER] regarding K+ ions Jiri Sponer (Thu May 27 2010 - 23:28:31 PDT)
- Re: [AMBER] regarding K+ ions Bill Ross (Fri May 28 2010 - 10:11:09 PDT)
- Re: [AMBER] regarding K+ ions Bill Ross (Fri May 28 2010 - 10:15:35 PDT)
[AMBER] test run error during compilation of amber10 in linux Sangita Kachhap (Fri May 28 2010 - 07:11:55 PDT)
- Re: [AMBER] test run error during compilation of amber10 in linux Jason Swails (Fri May 28 2010 - 07:36:21 PDT)
[AMBER] interaction free energy between a polycyclic aromatic hydrocarbon covalently linked to DNA and the DNA Yuqin Cai (Fri May 28 2010 - 11:44:02 PDT)
[AMBER] test run error in amber10 installation Sangita Kachhap (Sat May 29 2010 - 04:12:22 PDT)
- Re: [AMBER] test run error in amber10 installation case (Sat May 29 2010 - 08:20:04 PDT)
[AMBER] FF02EP force field William Flak (Sat May 29 2010 - 13:59:14 PDT)
- Re: [AMBER] FF02EP force field case (Sat May 29 2010 - 14:43:40 PDT)
[AMBER] Defunction of ibelly in Sander Jim Miller (Sun May 30 2010 - 10:25:26 PDT)
- Re: [AMBER] Defunction of ibelly in Sander Bill Ross (Sun May 30 2010 - 11:22:26 PDT)
- RE: [AMBER] Defunction of ibelly in Sander Ross Walker (Sun May 30 2010 - 11:55:03 PDT)
  - Re: [AMBER] Defunction of ibelly in Sander Jim Miller (Sun May 30 2010 - 20:55:45 PDT)
[AMBER] MM-PB/SA (ERROR IN SETPAR() upon atom distribution) Sushil Mishra (Sun May 30 2010 - 11:21:28 PDT)
[AMBER] How to output partial part of the result in output file Jim Miller (Sun May 30 2010 - 21:07:41 PDT)
- Re: [AMBER] How to output partial part of the result in output file Jason Swails (Sun May 30 2010 - 21:35:14 PDT)
[AMBER] amber 10 parallel test run error Nicee (Sun May 30 2010 - 21:33:11 PDT)
[AMBER] Parallel installation of AMBER 11 on MacOSX George Tzotzos (Mon May 31 2010 - 02:09:41 PDT)
- Re: [AMBER] Parallel installation of AMBER 11 on MacOSX Jason Swails (Mon May 31 2010 - 06:18:59 PDT)
  - Re: [AMBER] Parallel installation of AMBER 11 on MacOSX George Tzotzos (Mon May 31 2010 - 06:47:27 PDT)
    - Re: [AMBER] Parallel installation of AMBER 11 on MacOSX Jason Swails (Mon May 31 2010 - 07:01:03 PDT)
    - Re: [AMBER] Parallel installation of AMBER 11 on MacOSX George Tzotzos (Mon May 31 2010 - 07:52:07 PDT)
    - Re: [AMBER] Parallel installation of AMBER 11 on MacOSX case (Mon May 31 2010 - 09:35:38 PDT)
    - Re: [AMBER] Parallel installation of AMBER 11 on MacOSX George Tzotzos (Mon May 31 2010 - 09:58:36 PDT)
    - Re: [AMBER] Parallel installation of AMBER 11 on MacOSX case (Mon May 31 2010 - 11:02:25 PDT)
    - Re: [AMBER] Parallel installation of AMBER 11 on MacOSX David Watson (Mon May 31 2010 - 11:16:47 PDT)
    - Re: [AMBER] Parallel installation of AMBER 11 on MacOSX Jason Swails (Mon May 31 2010 - 11:19:42 PDT)
    - Re: [AMBER] Parallel installation of AMBER 11 on MacOSX George Tzotzos (Wed Jun 02 2010 - 10:14:14 PDT)
    - Re: [AMBER] Parallel installation of AMBER 11 on MacOSX Jason Swails (Wed Jun 02 2010 - 10:28:55 PDT)
    - Re: [AMBER] Parallel installation of AMBER 11 on MacOSX George Tzotzos (Wed Jun 02 2010 - 10:32:25 PDT)
    - Re: [AMBER] Parallel installation of AMBER 11 on MacOSX George Tzotzos (Wed Jun 02 2010 - 10:48:26 PDT)
    - [AMBER] AMBER 11 with OpenMPI and Intel Compiler on MacOSX Kazuo Ohta (Thu Sep 09 2010 - 23:01:21 PDT)
- Re: [AMBER] Parallel installation of AMBER 11 on MacOSX Bill Ross (Wed Jun 02 2010 - 10:35:27 PDT)
  - Re: [AMBER] Parallel installation of AMBER 11 on MacOSX George Tzotzos (Wed Jun 02 2010 - 10:37:56 PDT)
    - Re: [AMBER] Parallel installation of AMBER 11 on MacOSX Jason Swails (Wed Jun 02 2010 - 10:42:34 PDT)
- Re: [AMBER] Parallel installation of AMBER 11 on MacOSX Bill Ross (Wed Jun 02 2010 - 10:43:52 PDT)
[AMBER] Is it possible to plot RMSd VS residue number for a protein? M. Reza Ganjalikhany (Mon May 31 2010 - 06:49:48 PDT)
- Re: [AMBER] Is it possible to plot RMSd VS residue number for a protein? Homa Azizian (Mon May 31 2010 - 16:58:53 PDT)
  - Re: [AMBER] Is it possible to plot RMSd VS residue number for a protein? M. Reza Ganjalikhany (Tue Jun 01 2010 - 09:27:20 PDT)
[AMBER] AmberTools-1.4 Test Problem Hopkins, Robert (Mon May 31 2010 - 07:31:53 PDT)
- Re: [AMBER] AmberTools-1.4 Test Problem case (Mon May 31 2010 - 07:57:34 PDT)
- Re: [AMBER] AmberTools-1.4 Test Problem Gustavo Seabra (Wed Jun 02 2010 - 05:45:35 PDT)
[AMBER] amber10 installtion error in parallel Sangita Kachhap (Mon May 31 2010 - 10:35:35 PDT)
- Re: [AMBER] amber10 installtion error in parallel Jason Swails (Mon May 31 2010 - 17:43:52 PDT)
- Re: [AMBER] amber10 installtion error in parallel Jignesh Patel (Mon May 31 2010 - 21:25:25 PDT)
  - Re: [AMBER] amber10 installtion error in parallel Jason Swails (Tue Jun 01 2010 - 06:32:29 PDT)
[AMBER] CUDA Segfault GTX470 Levi Pierce (Mon May 31 2010 - 15:24:18 PDT)
- RE: [AMBER] CUDA Segfault GTX470 Ross Walker (Mon May 31 2010 - 16:35:15 PDT)
  - Re: [AMBER] CUDA Segfault GTX470 Jason Swails (Mon May 31 2010 - 17:41:16 PDT)
    - Re: [AMBER] CUDA Segfault GTX470 Levi Pierce (Tue Jun 01 2010 - 12:23:04 PDT)
    - RE: [AMBER] CUDA Segfault GTX470 Ross Walker (Tue Jun 01 2010 - 12:28:14 PDT)
    - Re: [AMBER] CUDA Segfault GTX470 Levi Pierce (Tue Jun 01 2010 - 13:16:30 PDT)
[AMBER] Prepare the mutants file for ala scanning Rilei Yu (Mon May 31 2010 - 17:11:07 PDT)
- Re: [AMBER] Prepare the mutants file for ala scanning Jason Swails (Mon May 31 2010 - 17:32:01 PDT)
- Re: [AMBER] Prepare the mutants file for ala scanning Gustavo Seabra (Tue Jun 01 2010 - 02:59:43 PDT)
[AMBER] Problem on B-factor Calculation tianyuan meng (Mon May 31 2010 - 19:06:52 PDT)
- Re: [AMBER] Problem on B-factor Calculation Jason Swails (Mon May 31 2010 - 19:32:41 PDT)
[AMBER] discontinous residues Jio M (Mon May 31 2010 - 23:58:27 PDT)
[AMBER] discontinuous residues Jio M (Tue Jun 01 2010 - 00:05:02 PDT)
- Re: [AMBER] discontinuous residues Jason Swails (Tue Jun 01 2010 - 07:07:48 PDT)
  - Re: [AMBER] discontinuous residues Jio M (Tue Jun 01 2010 - 12:10:35 PDT)
[AMBER] Polak Ribiere Jagdeesh C (Tue Jun 01 2010 - 01:21:27 PDT)
- Re: [AMBER] Polak Ribiere Mengjuei Hsieh (Tue Jun 01 2010 - 02:31:37 PDT)
- Re: [AMBER] Polak Ribiere Bill Ross (Tue Jun 01 2010 - 10:44:33 PDT)
[AMBER] Error in estrogen-raloxifene tutorial vaibhav dixit (Tue Jun 01 2010 - 02:34:21 PDT)
- Re: [AMBER] Error in estrogen-raloxifene tutorial Jason Swails (Tue Jun 01 2010 - 06:41:22 PDT)
[AMBER] MMPBSA problem binding energy calculation kamlesh sahu (Tue Jun 01 2010 - 02:42:35 PDT)
- Re: [AMBER] MMPBSA problem binding energy calculation Bill Miller III (Tue Jun 01 2010 - 04:02:09 PDT)
  - Re: [AMBER] MMPBSA problem binding energy calculation kamlesh sahu (Tue Jun 01 2010 - 18:05:10 PDT)
    - Re: [AMBER] MMPBSA problem binding energy calculation Bill Miller III (Tue Jun 01 2010 - 18:18:39 PDT)
    - Re: [AMBER] MMPBSA problem binding energy calculation kamlesh sahu (Tue Jun 01 2010 - 18:21:41 PDT)
- Re: [AMBER] MMPBSA problem binding energy calculation Dwight McGee (Tue Jun 01 2010 - 06:55:15 PDT)
  - Re: [AMBER] MMPBSA problem binding energy calculation kamlesh sahu (Tue Jun 01 2010 - 17:35:25 PDT)
    - Re: [AMBER] MMPBSA problem binding energy calculation Jason Swails (Tue Jun 01 2010 - 17:43:14 PDT)
    - Re: [AMBER] MMPBSA problem binding energy calculation kamlesh sahu (Tue Jun 01 2010 - 18:24:12 PDT)
    - Re: [AMBER] MMPBSA problem binding energy calculation Bill Miller III (Tue Jun 01 2010 - 18:35:03 PDT)
- [AMBER] Fwd: MMPBSA problem binding energy calculation kamlesh sahu (Mon Jun 07 2010 - 18:08:07 PDT)
  - Re: [AMBER] Fwd: MMPBSA problem binding energy calculation Bill Ross (Mon Jun 07 2010 - 18:26:14 PDT)
    - Re: [AMBER] Fwd: MMPBSA problem binding energy calculation Sushil Mishra (Mon Jun 07 2010 - 23:02:30 PDT)
    - [AMBER] pmemd.cuda error: launch timeout.. Sasha Buzko (Tue Jun 08 2010 - 09:54:23 PDT)
    - RE: [AMBER] pmemd.cuda error: launch timeout.. Scott Le Grand (Tue Jun 08 2010 - 10:15:37 PDT)
    - Re: [AMBER] pmemd.cuda error: launch timeout.. Sasha Buzko (Tue Jun 08 2010 - 10:17:47 PDT)
    - RE: [AMBER] pmemd.cuda error: launch timeout.. Scott Le Grand (Tue Jun 08 2010 - 10:25:44 PDT)
    - Re: [AMBER] pmemd.cuda error: launch timeout.. Sasha Buzko (Tue Jun 08 2010 - 10:55:18 PDT)
    - RE: [AMBER] pmemd.cuda error: launch timeout.. Scott Le Grand (Tue Jun 08 2010 - 11:23:32 PDT)
    - RE: [AMBER] pmemd.cuda error: launch timeout.. Scott Le Grand (Tue Jun 08 2010 - 13:24:01 PDT)
    - Re: [AMBER] pmemd.cuda error: launch timeout.. Sasha Buzko (Tue Jun 08 2010 - 13:51:42 PDT)
    - RE: [AMBER] pmemd.cuda error: launch timeout.. Ross Walker (Tue Jun 08 2010 - 14:04:42 PDT)
    - Re: [AMBER] pmemd.cuda error: launch timeout.. Sasha Buzko (Tue Jun 08 2010 - 17:55:23 PDT)
    - [AMBER] How to modify config.h if I cannot get g77 running? Pls kindly help. Catein Catherine (Tue Jun 08 2010 - 00:35:20 PDT)
    - Re: [AMBER] How to modify config.h if I cannot get g77 running? Pls kindly help. Jason Swails (Tue Jun 08 2010 - 04:23:56 PDT)
    - RE: [AMBER] How to modify config.h if I cannot get g77 running? Pls kindly help. Catein Catherine (Tue Jun 08 2010 - 07:27:43 PDT)
    - [AMBER] Installing amber10 on ubunta, some hints please. Catein Catherine (Wed Jun 09 2010 - 08:24:39 PDT)
    - Re: [AMBER] Installing amber10 on ubunta, some hints please. Jason Swails (Wed Jun 09 2010 - 08:49:43 PDT)
    - Re: [AMBER] Installing amber10 on ubunta, some hints please. Paul S. Nerenberg (Wed Jun 09 2010 - 08:55:22 PDT)
    - Re: [AMBER] Installing amber10 on ubunta, some hints please. Ye MEI (Wed Jun 09 2010 - 09:15:27 PDT)
    - RE: [AMBER] Installing amber10 on ubunta, some hints please. David Dubins (Wed Jun 09 2010 - 12:58:17 PDT)
[AMBER] error: mask from topology files! vaibhav dixit (Tue Jun 01 2010 - 07:46:52 PDT)
- Re: [AMBER] error: mask from topology files! Bill Miller III (Tue Jun 01 2010 - 07:53:09 PDT)
[AMBER] sleap log Omair A. Khan (Tue Jun 01 2010 - 09:10:10 PDT)
- Re: [AMBER] sleap log case (Tue Jun 01 2010 - 15:28:15 PDT)
  - Re: [AMBER] sleap log Omair A. Khan (Thu Jun 03 2010 - 12:14:29 PDT)
    - Re: [AMBER] sleap log case (Thu Jun 03 2010 - 13:06:33 PDT)
[AMBER] amber10 compilation Sangita Kachhap (Tue Jun 01 2010 - 09:18:03 PDT)
- Re: [AMBER] amber10 compilation Jason Swails (Tue Jun 01 2010 - 10:30:59 PDT)
  - Re: [AMBER] amber10 compilation Daniel Roe (Tue Jun 01 2010 - 10:34:58 PDT)
[AMBER] AMBER10 TI calculations manikanthan bhavaraju (Tue Jun 01 2010 - 12:20:48 PDT)
- Re: [AMBER] AMBER10 TI calculations case (Tue Jun 01 2010 - 13:22:30 PDT)
[AMBER] MM_PBSA: multiple processes, single point output along the trajecotry and cropped structures Yuqin Cai (Tue Jun 01 2010 - 12:55:42 PDT)
- Re: [AMBER] MM_PBSA: multiple processes, single point output along the trajecotry and cropped structures Dwight McGee (Tue Jun 01 2010 - 13:21:19 PDT)
  - Re: [AMBER] MM_PBSA: multiple processes, single point output along the trajecotry and cropped structures Dwight McGee (Tue Jun 01 2010 - 13:25:31 PDT)
- Re: [AMBER] MM_PBSA: multiple processes, single point output along the trajecotry and cropped structures Jason Swails (Tue Jun 01 2010 - 14:33:16 PDT)
[AMBER] pmemd.cuda - ewald error estimate? Paul Brandt (Tue Jun 01 2010 - 15:43:01 PDT)
- RE: [AMBER] pmemd.cuda - ewald error estimate? Ross Walker (Tue Jun 01 2010 - 16:23:25 PDT)
[AMBER] The charge xuemeiwang1103 (Tue Jun 01 2010 - 23:27:58 PDT)
- Re: [AMBER] The charge Ray Luo (Wed Jun 02 2010 - 13:32:47 PDT)
[AMBER] Error: No potential terms in sander output! vaibhav dixit (Wed Jun 02 2010 - 03:37:15 PDT)
- [AMBER] Re: Error: No potential terms in sander output! Bill Miller III (Wed Jun 02 2010 - 04:47:51 PDT)
  - Re: [AMBER] Re: Error: No potential terms in sander output! Jim Paugh (Wed Jun 02 2010 - 05:30:53 PDT)
[AMBER] distance restraints qiaoyan (Wed Jun 02 2010 - 06:14:00 PDT)
- Re: [AMBER] distance restraints Jason Swails (Wed Jun 02 2010 - 06:20:13 PDT)
Fwd: Re: Re: [AMBER] error - binding_energy.mmpbsa run Andrew Voronkov (Wed Jun 02 2010 - 06:15:56 PDT)
- Re: Re: Re: [AMBER] error - binding_energy.mmpbsa run Jason Swails (Wed Jun 02 2010 - 06:20:52 PDT)
  - Re: Re: Re: Re: [AMBER] error - binding_energy.mmpbsa runRe: Re: Re: Re: [AMBER] error - binding_energy.mmpbsa run Andrew Voronkov (Thu Jun 03 2010 - 03:33:21 PDT)
    - Re: Re: Re: Re: [AMBER] error - binding_energy.mmpbsa runRe: Re: Re: Re: [AMBER] error - binding_energy.mmpbsa run Bill Miller III (Thu Jun 03 2010 - 04:34:13 PDT)
[AMBER] restraint in umbrella sampling dhacademic (Wed Jun 02 2010 - 11:17:57 PDT)
- Re: [AMBER] restraint in umbrella sampling Jason Swails (Wed Jun 02 2010 - 11:25:55 PDT)
[AMBER] Is it possible to revome water molecules during simulation? Hoshin Kim (Wed Jun 02 2010 - 23:40:11 PDT)
- Re: [AMBER] Is it possible to revome water molecules during simulation? Bill Ross (Wed Jun 02 2010 - 12:53:48 PDT)
  - RE: [AMBER] Is it possible to revome water molecules during simulation? Hoshin Kim (Thu Jun 03 2010 - 00:59:27 PDT)
- Re: [AMBER] Is it possible to revome water molecules during simulation? Jason Swails (Wed Jun 02 2010 - 12:57:59 PDT)
- RE: [AMBER] Is it possible to revome water molecules during simulation? Bill Ross (Wed Jun 02 2010 - 14:26:43 PDT)
[AMBER] mm_pbsa error on ambertools 1.4 amber11 ANDREA.MEZGEZ.dicamp.units.it (Thu Jun 03 2010 - 08:39:30 PDT)
- Re: [AMBER] mm_pbsa error on ambertools 1.4 amber11 Jason Swails (Thu Jun 03 2010 - 09:03:52 PDT)
- [AMBER] cutoff fancy2012 (Fri Jun 04 2010 - 02:03:38 PDT)
  - Re: [AMBER] cutoff Bill Ross (Fri Jun 04 2010 - 10:12:50 PDT)
    - Re:Re: [AMBER] cutoff fancy2012 (Sat Jun 05 2010 - 06:20:38 PDT)
    - RE: Re: [AMBER] cutoff Ross Walker (Sat Jun 05 2010 - 12:28:45 PDT)
    - Re:RE: Re: [AMBER] cutoff fancy2012 (Sun Jun 06 2010 - 00:50:34 PDT)
    - Re: [AMBER] cutoff Dean Cuebas (Sat Jun 05 2010 - 15:39:27 PDT)
    - RE: [AMBER] cutoff Ross Walker (Sun Jun 06 2010 - 14:14:13 PDT)
    - Re: [AMBER] cutoff Dean Cuebas (Sun Jun 06 2010 - 18:23:44 PDT)
    - Re:Re: [AMBER] cutoff Bill Ross (Sat Jun 05 2010 - 15:21:31 PDT)
    - RE: Re: [AMBER] cutoff Bill Ross (Sat Jun 05 2010 - 15:38:45 PDT)
    - [AMBER] amber.cuda performance on Nvidia S2050? Sasha Buzko (Mon Jun 07 2010 - 09:23:57 PDT)
    - RE: [AMBER] amber.cuda performance on Nvidia S2050? Scott Le Grand (Mon Jun 07 2010 - 10:52:59 PDT)
    - Re: [AMBER] amber.cuda performance on Nvidia S2050? Sasha Buzko (Mon Jun 07 2010 - 11:10:32 PDT)
  - Re: [AMBER] cutoff Bill Ross (Sat Jun 05 2010 - 16:03:31 PDT)
- RE: [AMBER] mm_pbsa error on ambertools 1.4 amber11 ANDREA.MEZGEZ.dicamp.units.it (Fri Jun 04 2010 - 03:59:55 PDT)
  - Re: [AMBER] mm_pbsa error on ambertools 1.4 amber11 Jason Swails (Fri Jun 04 2010 - 06:01:22 PDT)
[AMBER] Lmod, NAB error Cristina Sisu (Thu Jun 03 2010 - 09:04:50 PDT)
- Re: [AMBER] Lmod, NAB error Jason Swails (Thu Jun 03 2010 - 09:17:50 PDT)
  - Re: [AMBER] Lmod, NAB error Cristina Sisu (Thu Jun 03 2010 - 09:23:16 PDT)
- Re: [AMBER] Lmod, NAB error Bill Ross (Thu Jun 03 2010 - 09:49:01 PDT)
  - Re: [AMBER] Lmod, NAB error Cristina Sisu (Thu Jun 03 2010 - 09:51:12 PDT)
[AMBER] ALASCAN (Alanine scanning mutagens ) Sushil Mishra (Thu Jun 03 2010 - 10:09:36 PDT)
- Re: [AMBER] ALASCAN (Alanine scanning mutagens ) Dwight McGee (Fri Jun 04 2010 - 07:52:10 PDT)
  - Re: [AMBER] ALASCAN (Alanine scanning mutagens ) Sushil Mishra (Fri Jun 04 2010 - 08:03:35 PDT)
    - Re: [AMBER] ALASCAN (Alanine scanning mutagens ) Dwight McGee (Fri Jun 04 2010 - 08:31:01 PDT)
[AMBER] How to restart the remd simulation following the remd tutorial? Dongshan Wei (Thu Jun 03 2010 - 13:29:43 PDT)
- Re: [AMBER] How to restart the remd simulation following the remd tutorial? Daniel Roe (Fri Jun 04 2010 - 05:01:59 PDT)
  - Re: [AMBER] How to restart the remd simulation following the remd tutorial? Dongshan Wei (Wed Jun 09 2010 - 23:02:11 PDT)
[AMBER] About water molecule analysis gokul algates (Fri Jun 04 2010 - 04:19:38 PDT)
[AMBER] tleap: C-N triple bond and sp1 hybridization vedat durmaz (Fri Jun 04 2010 - 05:26:46 PDT)
- Re: [AMBER] tleap: C-N triple bond and sp1 hybridization case (Fri Jun 04 2010 - 05:43:38 PDT)
  - Re: [AMBER] tleap: C-N triple bond and sp1 hybridization vedat durmaz (Fri Jun 04 2010 - 07:14:40 PDT)
    - Re: [AMBER] tleap: C-N triple bond and sp1 hybridization case (Fri Jun 04 2010 - 09:49:34 PDT)
- Re: [AMBER] tleap: C-N triple bond and sp1 hybridization Bill Ross (Fri Jun 04 2010 - 10:01:19 PDT)
[AMBER] simulation of protein ashutosh shandilya (Fri Jun 04 2010 - 09:32:48 PDT)
[AMBER] simulation of protein ashutosh shandilya (Fri Jun 04 2010 - 09:45:44 PDT)
- Re: [AMBER] simulation of protein Bill Ross (Fri Jun 04 2010 - 10:22:59 PDT)
  - Re: [AMBER] simulation of protein ashutosh shandilya (Fri Jun 04 2010 - 10:40:06 PDT)
- Re: [AMBER] simulation of protein Gustavo Seabra (Fri Jun 04 2010 - 10:34:54 PDT)
  - Re: [AMBER] simulation of protein ashutosh shandilya (Fri Jun 04 2010 - 10:58:29 PDT)
- Re: [AMBER] simulation of protein Bill Ross (Fri Jun 04 2010 - 10:56:06 PDT)
  - Re: [AMBER] simulation of protein ashutosh shandilya (Fri Jun 04 2010 - 11:05:50 PDT)
    - Re: [AMBER] simulation of protein Jason Swails (Fri Jun 04 2010 - 11:13:41 PDT)
- Re: [AMBER] simulation of protein Bill Ross (Fri Jun 04 2010 - 11:43:09 PDT)
[AMBER] Amber on BlueGene/P T. Andrew Binkowski (Fri Jun 04 2010 - 10:49:11 PDT)
- Re: [AMBER] Amber on BlueGene/P case (Fri Jun 04 2010 - 11:35:22 PDT)
[AMBER] gb working but not pb & gives No potential terms in sander output! error vaibhav dixit (Fri Jun 04 2010 - 22:25:43 PDT)
- [AMBER] Re: gb working but not pb & gives No potential terms in sander output! error Bill Miller III (Sat Jun 05 2010 - 03:53:17 PDT)
  - [AMBER] Re: gb working but not pb & gives No potential terms in sander output! error vaibhav dixit (Sun Jun 06 2010 - 02:37:55 PDT)
    - [AMBER] Re: gb working but not pb & gives No potential terms in sander output! error Bill Miller III (Sun Jun 06 2010 - 04:15:30 PDT)
    - [AMBER] Re: gb working but not pb & gives No potential terms in sander output! error vaibhav dixit (Sun Jun 06 2010 - 22:15:02 PDT)
[AMBER] MMPBSA.py calculations...bad atom type RANAJIT SHINDE (Fri Jun 04 2010 - 22:44:23 PDT)
[AMBER] MMPBSA.py calculations...bad atom type RANAJIT SHINDE (Fri Jun 04 2010 - 22:45:16 PDT)
- Re: [AMBER] MMPBSA.py calculations...bad atom type Bill Miller III (Sat Jun 05 2010 - 04:04:53 PDT)
  - Re: [AMBER] MMPBSA.py calculations...bad atom type Jason Swails (Sat Jun 05 2010 - 06:40:27 PDT)
    - Re: [AMBER] MMPBSA.py calculations...bad atom type RANAJIT SHINDE (Sun Jun 06 2010 - 21:49:37 PDT)
[AMBER] Thr -> Met in TI calculation fancy2012 (Sat Jun 05 2010 - 06:33:12 PDT)
- Re: [AMBER] Thr -> Met in TI calculation Jason Swails (Sat Jun 05 2010 - 06:45:34 PDT)
[AMBER] Fourier terms Hector A. Baldoni (Sat Jun 05 2010 - 15:04:32 PDT)
[AMBER] Entropy calculation using nmode in mm_pbsa.pl Sushil Mishra (Sun Jun 06 2010 - 05:22:26 PDT)
[AMBER] The err of sander.PUPIL Aurum Bai (Sun Jun 06 2010 - 22:13:32 PDT)
- Re: [AMBER] The err of sander.PUPIL Jason Swails (Sun Jun 06 2010 - 23:19:36 PDT)
  - Re: [AMBER] The err of sander.PUPIL Aurum Bai (Mon Jun 07 2010 - 02:04:18 PDT)
    - Re: [AMBER] The err of sander.PUPIL Joan Torras (Mon Jun 07 2010 - 11:37:09 PDT)
[AMBER] #RECMAP + #LIGMAP != #COMPRI in .DECOMP of mm_pbsa.pl Sushil Mishra (Sun Jun 06 2010 - 23:41:42 PDT)
- [AMBER] Error installing AMBER 10 on ubuntu Catein Catherine (Mon Jun 07 2010 - 01:43:31 PDT)
  - RE: [AMBER] Error installing AMBER 10 on ubuntu Catein Catherine (Mon Jun 07 2010 - 01:58:13 PDT)
  - Re: [AMBER] Error installing AMBER 10 on ubuntu case (Mon Jun 07 2010 - 05:22:16 PDT)
    - RE: [AMBER] Error installing AMBER 10 on ubuntu Catein Catherine (Mon Jun 07 2010 - 07:04:45 PDT)
    - Re: [AMBER] Error installing AMBER 10 on ubuntu case (Mon Jun 07 2010 - 07:20:00 PDT)
- [AMBER] Re: #RECMAP + #LIGMAP != #COMPRI in .DECOMP of mm_pbsa.pl Sushil Mishra (Mon Jun 07 2010 - 03:13:17 PDT)
[AMBER] about ewald error estimate Navanath Kumbhar (Mon Jun 07 2010 - 02:32:43 PDT)
- Re: [AMBER] about ewald error estimate case (Mon Jun 07 2010 - 05:12:29 PDT)
  - Re: [AMBER] about ewald error estimate Navanath Kumbhar (Tue Jun 08 2010 - 09:56:53 PDT)
    - Re: [AMBER] about ewald error estimate case (Tue Jun 08 2010 - 11:36:35 PDT)
    - Re: [AMBER] about ewald error estimate Navanath Kumbhar (Wed Jun 09 2010 - 02:45:53 PDT)
[AMBER] Amber11: running ptraj George Tzotzos (Mon Jun 07 2010 - 03:10:05 PDT)
- Re: [AMBER] Amber11: running ptraj case (Mon Jun 07 2010 - 04:53:43 PDT)
[AMBER] AMBER11 compilation Steve Seibold (Mon Jun 07 2010 - 05:23:32 PDT)
- Re: [AMBER] AMBER11 compilation case (Mon Jun 07 2010 - 05:51:53 PDT)
  - RE: [AMBER] AMBER11 compilation Steve Seibold (Mon Jun 07 2010 - 06:46:03 PDT)
    - Re: [AMBER] AMBER11 compilation case (Mon Jun 07 2010 - 07:15:51 PDT)
[AMBER] Fwd: FW: Requesting your help in amber Jenny Iskrenova (Mon Jun 07 2010 - 07:26:49 PDT)
[AMBER] random number generators visible from nab: choice necessary? M. L. Dodson (Mon Jun 07 2010 - 13:22:43 PDT)
- Re: [AMBER] random number generators visible from nab: choice necessary? case (Mon Jun 07 2010 - 15:10:47 PDT)
  - Re: [AMBER] random number generators visible from nab: choice necessary? M. L. Dodson (Mon Jun 07 2010 - 15:47:17 PDT)
  - Re: [AMBER] random number generators visible from nab: choice necessary? M. L. Dodson (Tue Jun 08 2010 - 09:16:46 PDT)
    - Re: [AMBER] random number generators visible from nab: choice necessary? case (Fri Jun 11 2010 - 18:39:25 PDT)
[AMBER] GAFF 1.4 Masahiro HIGASHI (Tue Jun 08 2010 - 00:20:53 PDT)
[AMBER] Error on running ptraj tianyuan meng (Tue Jun 08 2010 - 00:45:07 PDT)
- Re: [AMBER] Error on running ptraj case (Tue Jun 08 2010 - 05:02:42 PDT)
- Re: [AMBER] Error on running ptraj Daniel Roe (Tue Jun 08 2010 - 07:46:10 PDT)
  - [AMBER] P450 ff from Rydberg et al. Renata KWIECIEN (Tue Jun 08 2010 - 07:50:16 PDT)
    - Re: [AMBER] P450 ff from Rydberg et al. case (Tue Jun 08 2010 - 11:25:47 PDT)
    - Re: [AMBER] P450 ff from Rydberg et al. Adrian Roitberg (Tue Jun 08 2010 - 11:29:39 PDT)
[AMBER] Regarding temperature accelerated MD Ramya Narasimhan (Tue Jun 08 2010 - 02:50:50 PDT)
[AMBER] comparing DeltaG, docking and IC50 vaibhav dixit (Tue Jun 08 2010 - 03:21:36 PDT)
[AMBER] gcc44 compiler Steve Seibold (Tue Jun 08 2010 - 05:08:01 PDT)
- Re: [AMBER] gcc44 compiler case (Tue Jun 08 2010 - 05:16:44 PDT)
  - RE: [AMBER] gcc44 compiler Steve Seibold (Tue Jun 08 2010 - 05:41:18 PDT)
    - Re: [AMBER] gcc44 compiler Lachele Foley (Lists) (Tue Jun 08 2010 - 07:04:27 PDT)
    - RE: [AMBER] gcc44 compiler Steve Seibold (Tue Jun 08 2010 - 07:29:04 PDT)
[AMBER] is it possible to improve amino acids dihedral angles using Amber? Andrew Voronkov (Tue Jun 08 2010 - 05:21:58 PDT)
[AMBER] Re: FW: Requesting your help in amber Jenny Iskrenova (Tue Jun 08 2010 - 06:04:22 PDT)
- Re: [AMBER] Re: FW: Requesting your help in amber Jason Swails (Tue Jun 08 2010 - 06:32:19 PDT)
[AMBER] nfft1-3 too large! check on MAXNFFT in ew_bspline.f Ehsan Habibi (Tue Jun 08 2010 - 06:49:06 PDT)
- Re: [AMBER] nfft1-3 too large! check on MAXNFFT in ew_bspline.f case (Tue Jun 08 2010 - 07:38:26 PDT)
- Re: [AMBER] nfft1-3 too large! check on MAXNFFT in ew_bspline.f Bill Ross (Tue Jun 08 2010 - 11:07:19 PDT)
[AMBER] how to cut phosphodiester bond Sangita Kachhap (Tue Jun 08 2010 - 09:30:04 PDT)
- Re: [AMBER] how to cut phosphodiester bond case (Tue Jun 08 2010 - 11:33:12 PDT)
  - Re: [AMBER] how to cut phosphodiester bond Sangita Kachhap (Wed Jun 09 2010 - 02:13:49 PDT)
[AMBER] SURFTEN / SURFOFF values are not consistent across *.all.out files Sushil Mishra (Tue Jun 08 2010 - 11:44:34 PDT)
- Re: [AMBER] SURFTEN / SURFOFF values are not consistent across *.all.out files Dwight McGee (Tue Jun 08 2010 - 12:11:36 PDT)
  - Re: [AMBER] SURFTEN / SURFOFF values are not consistent across *.all.out files Sushil Mishra (Tue Jun 08 2010 - 13:04:40 PDT)
[AMBER] free energy profile Lars Skjærven (Tue Jun 08 2010 - 12:47:49 PDT)
- Re: [AMBER] free energy profile steinbrt.rci.rutgers.edu (Wed Jun 09 2010 - 00:16:26 PDT)
  - Re: [AMBER] free energy profile Lars Skjærven (Wed Jun 09 2010 - 15:42:25 PDT)
    - Re: [AMBER] free energy profile steinbrt.rci.rutgers.edu (Thu Jun 10 2010 - 00:23:29 PDT)
[AMBER] solvent-solute interaction energy Hoshin Kim (Tue Jun 08 2010 - 02:26:24 PDT)
- Re: [AMBER] solvent-solute interaction energy Bill Ross (Tue Jun 08 2010 - 15:42:28 PDT)
- Re: [AMBER] solvent-solute interaction energy durmaz.zib.de (Tue Jun 08 2010 - 16:11:56 PDT)
- Re: [AMBER] solvent-solute interaction energy Bill Ross (Tue Jun 08 2010 - 16:50:09 PDT)
  - Re: [AMBER] solvent-solute interaction energy Adrian Roitberg (Tue Jun 08 2010 - 16:51:41 PDT)
    - Re: [AMBER] solvent-solute interaction energy vedat durmaz (Wed Jun 09 2010 - 01:19:41 PDT)
[AMBER] regarding forcefield for rna Asfa Ali (Wed Jun 09 2010 - 04:10:19 PDT)
- Re: [AMBER] regarding forcefield for rna Gustavo Seabra (Wed Jun 09 2010 - 04:18:35 PDT)
  - Re: [AMBER] regarding forcefield for rna Asfa Ali (Wed Jun 09 2010 - 04:35:21 PDT)
    - Re: [AMBER] regarding forcefield for rna Jiri Sponer (Wed Jun 09 2010 - 04:45:25 PDT)
    - Re: [AMBER] regarding forcefield for rna Asfa Ali (Thu Jun 10 2010 - 06:47:52 PDT)
    - Re: [AMBER] regarding forcefield for rna Jiri Sponer (Thu Jun 10 2010 - 06:55:14 PDT)
    - Re: [AMBER] regarding forcefield for rna Jiri Sponer (Thu Jun 10 2010 - 06:59:26 PDT)
  - Re: [AMBER] regarding forcefield for rna Jiri Sponer (Wed Jun 09 2010 - 04:25:08 PDT)
- Re: [AMBER] regarding forcefield for rna InSuk Joung (Wed Jun 09 2010 - 04:39:57 PDT)
  - Re: [AMBER] regarding forcefield for rna Asfa Ali (Wed Jun 09 2010 - 06:04:42 PDT)
    - Re: [AMBER] regarding forcefield for rna Monika Sharma (Wed Jun 09 2010 - 06:15:11 PDT)
    - Re: [AMBER] regarding forcefield for rna InSuk Joung (Wed Jun 09 2010 - 06:21:13 PDT)
    - Re: [AMBER] regarding forcefield for rna Jason Swails (Wed Jun 09 2010 - 06:43:26 PDT)
    - Re: [AMBER] regarding forcefield for rna Asfa Ali (Wed Jun 09 2010 - 06:51:15 PDT)
    - Re: [AMBER] regarding forcefield for rna Asfa Ali (Wed Jun 09 2010 - 06:55:39 PDT)
    - Re: [AMBER] regarding forcefield for rna case (Wed Jun 09 2010 - 17:23:30 PDT)
- Re: [AMBER] regarding forcefield for rna Ilyas Yildirim (Wed Jun 09 2010 - 07:40:02 PDT)
- Re: [AMBER] regarding forcefield for rna Bill Ross (Wed Jun 09 2010 - 10:12:18 PDT)
- Re: [AMBER] regarding forcefield for rna Bill Ross (Thu Jun 10 2010 - 10:14:43 PDT)
  - Re: [AMBER] regarding forcefield for rna Jiri Sponer (Thu Jun 10 2010 - 11:30:52 PDT)
- Re: [AMBER] regarding forcefield for rna Bill Ross (Thu Jun 10 2010 - 19:36:48 PDT)
  - Re: [AMBER] regarding forcefield for rna Jiri Sponer (Fri Jun 11 2010 - 03:42:13 PDT)
    - Re: [AMBER] regarding forcefield for rna Asfa Ali (Fri Jun 11 2010 - 04:09:24 PDT)
    - Re: [AMBER] regarding forcefield for rna Jiri Sponer (Fri Jun 11 2010 - 04:17:03 PDT)
- Re: [AMBER] regarding forcefield for rna Bill Ross (Fri Jun 11 2010 - 08:14:08 PDT)
  - Re: [AMBER] regarding forcefield for rna Asfa Ali (Fri Jun 11 2010 - 23:03:38 PDT)
- Re: [AMBER] regarding forcefield for rna Bill Ross (Sat Jun 12 2010 - 12:57:04 PDT)
  - Re: [AMBER] regarding forcefield for rna Asfa Ali (Sun Jun 13 2010 - 21:57:40 PDT)
[AMBER] antechamber failing with -mul option and sqm Alan (Wed Jun 09 2010 - 04:15:11 PDT)
- Re: [AMBER] antechamber failing with -mul option and sqm case (Wed Jun 09 2010 - 18:18:41 PDT)
[AMBER] Strange results for vaibhav dixit (Wed Jun 09 2010 - 04:24:31 PDT)
- Re: [AMBER] Strange results for Bill Miller III (Fri Jun 11 2010 - 08:01:46 PDT)
[AMBER] PTRAJ: setting up donor and acceptor masks for ligands for hbond analysis George Tzotzos (Wed Jun 09 2010 - 06:40:31 PDT)
- [AMBER] reduce George Tzotzos (Fri Jun 11 2010 - 02:03:02 PDT)
  - Re: [AMBER] reduce case (Fri Jun 11 2010 - 06:15:51 PDT)
[AMBER] simple question, FATAL: Atom .R<NGLU 1>.A<H 18> does not have a type. Andrew Voronkov (Wed Jun 09 2010 - 07:17:31 PDT)
- Re: [AMBER] simple question, FATAL: Atom .R<NGLU 1>.A<H 18> does not have a type. Jason Swails (Wed Jun 09 2010 - 08:53:35 PDT)
 - Re: [AMBER] simple question, FATAL: Atom .R<NGLU 1>.A<H 18> does not have a type. Bill Ross (Wed Jun 09 2010 - 10:27:10 PDT)
 - Re: [AMBER] simple question, FATAL: Atom .R<NGLU 1>.A<H 18> does not have a type. Andrew Voronkov (Thu Jun 10 2010 - 05:42:56 PDT)
 - Re: [AMBER] simple question, FATAL: Atom .R<NGLU 1>.A<H 18> does not have a type. Andrew Voronkov (Thu Jun 10 2010 - 06:19:02 PDT)
 - Re: [AMBER] simple question, FATAL: Atom .R<NGLU 1>.A<H 18> does not have a type. case (Thu Jun 10 2010 - 18:08:51 PDT)
 - Re: [AMBER] simple question, FATAL: Atom .R<NGLU 1>.A<H 18> does not have a type. Bill Ross (Thu Jun 10 2010 - 09:49:50 PDT)
 - Re: [AMBER] simple question, FATAL: Atom .R<NGLU 1>.A<H 18> does not have a type. Bill Ross (Thu Jun 10 2010 - 10:03:37 PDT)
[AMBER] question about radial distribution function Ganesh Kamath (Wed Jun 09 2010 - 07:51:24 PDT)
[AMBER] how to get frcmod.mod_phipsi.1 for constant pH MD simulation Sangita Kachhap (Wed Jun 09 2010 - 08:13:29 PDT)
- Re: [AMBER] how to get frcmod.mod_phipsi.1 for constant pH MD simulation Jason Swails (Wed Jun 09 2010 - 08:46:54 PDT)
  - Re: [AMBER] how to get frcmod.mod_phipsi.1 for constant pH MD simulation Sangita Kachhap (Wed Jun 09 2010 - 10:06:38 PDT)
    - Re: [AMBER] how to get frcmod.mod_phipsi.1 for constant pH MD simulation Jason Swails (Wed Jun 09 2010 - 10:31:41 PDT)
    - Re: [AMBER] how to get frcmod.mod_phipsi.1 for constant pH MD simulation Sangita Kachhap (Thu Jun 10 2010 - 08:09:28 PDT)
[AMBER] MMPBSA binding calculations shenna shearin (Wed Jun 09 2010 - 13:44:34 PDT)
- Re: [AMBER] MMPBSA binding calculations Jason Swails (Wed Jun 09 2010 - 13:52:26 PDT)
  - Re: [AMBER] MMPBSA binding calculations shenna shearin (Sat Jun 12 2010 - 13:10:40 PDT)
    - Re: [AMBER] MMPBSA binding calculations shenna shearin (Sat Jun 12 2010 - 13:13:13 PDT)
    - Re: [AMBER] MMPBSA binding calculations Jason Swails (Sat Jun 12 2010 - 13:38:50 PDT)
    - Re: [AMBER] MMPBSA binding calculations shenna shearin (Sat Jun 12 2010 - 14:13:08 PDT)
    - Re: [AMBER] MMPBSA binding calculations shenna shearin (Sat Jun 12 2010 - 14:49:52 PDT)
    - Re: [AMBER] MMPBSA binding calculations Bill Miller III (Sat Jun 12 2010 - 15:06:20 PDT)
    - Re: [AMBER] MMPBSA binding calculations shenna shearin (Sat Jun 12 2010 - 16:02:02 PDT)
    - [AMBER] (no subject) Catein Catherine (Sun Jun 13 2010 - 08:20:45 PDT)
    - [AMBER] Why different results were obtained for two runs using the same prmtop files? Catein Catherine (Sun Jun 13 2010 - 09:03:21 PDT)
    - Re: [AMBER] (no subject) Jason Swails (Sun Jun 13 2010 - 09:44:11 PDT)
    - Re: [AMBER] (no subject) shenna shearin (Fri Jun 25 2010 - 08:46:53 PDT)
    - [AMBER] Can I did MM/GBSA analysis for a partial equilibrated system? Catein Catherine (Sun Jun 13 2010 - 09:00:44 PDT)
    - Re: [AMBER] Can I did MM/GBSA analysis for a partial equilibrated system? Jason Swails (Sun Jun 13 2010 - 09:57:44 PDT)
[AMBER] Error while compiling AT1.4 on OS X Gustaf Olsson (Wed Jun 09 2010 - 23:54:39 PDT)
- Re: [AMBER] Error while compiling AT1.4 on OS X case (Thu Jun 10 2010 - 04:58:34 PDT)
  - Re: [AMBER] Error while compiling AT1.4 on OS X Gustaf Olsson (Thu Jun 10 2010 - 05:07:29 PDT)
  - Re: [AMBER] Error while compiling AT1.4 on OS X Gustaf Olsson (Thu Jun 10 2010 - 05:16:47 PDT)
  - [AMBER] Can I neglect the error message of sleap in amber tool? Catein Catherine (Thu Jun 10 2010 - 08:10:22 PDT)
    - Re: [AMBER] Can I neglect the error message of sleap in amber tool? Gustaf Olsson (Thu Jun 10 2010 - 13:24:30 PDT)
    - Re: [AMBER] Can I neglect the error message of sleap in amber tool? case (Thu Jun 10 2010 - 18:09:10 PDT)
    - Re: [AMBER] Can I neglect the error message of sleap in amber tool? Here is my OS and compiler information. please kindly help. Catein Catherine (Thu Jun 10 2010 - 20:12:49 PDT)
    - Re: [AMBER] Can I neglect the error message of sleap in amber tool? Here is my OS and compiler information. please kindly help. Jason Swails (Thu Jun 10 2010 - 20:25:42 PDT)
    - Re: [AMBER] Can I neglect the error message of sleap in amber tool? Here is my OS and compiler information. please kindly help. case (Fri Jun 11 2010 - 06:01:08 PDT)
- Re: [AMBER] Error while compiling AT1.4 on OS X Bill Ross (Thu Jun 10 2010 - 09:44:11 PDT)
  - Re: [AMBER] Error while compiling AT1.4 on OS X Gustaf Olsson (Thu Jun 10 2010 - 13:18:48 PDT)
[AMBER] ambertools1.2 compilation error colvin (Thu Jun 10 2010 - 00:43:54 PDT)
- Re: [AMBER] ambertools1.2 compilation error Gustaf Olsson (Thu Jun 10 2010 - 01:18:21 PDT)
  - Re: [AMBER] ambertools1.2 compilation error colvin (Thu Jun 10 2010 - 01:28:57 PDT)
    - Re: [AMBER] ambertools1.2 compilation error Gustaf Olsson (Thu Jun 10 2010 - 01:44:28 PDT)
    - Re: [AMBER] ambertools1.2 compilation error colvin (Thu Jun 10 2010 - 01:54:19 PDT)
    - Re: [AMBER] ambertools1.2 compilation error Gustaf Olsson (Thu Jun 10 2010 - 02:26:42 PDT)
- Re: [AMBER] ambertools1.2 compilation error case (Thu Jun 10 2010 - 19:06:52 PDT)
  - Re: [AMBER] ambertools1.2 compilation error colvin (Thu Jun 10 2010 - 22:58:06 PDT)
    - Re: [AMBER] ambertools1.2 compilation error case (Fri Jun 11 2010 - 05:58:56 PDT)
    - Re: [AMBER] ambertools1.2 compilation error xueping chin (Fri Jun 11 2010 - 06:05:51 PDT)
[AMBER] Building a slab between two vacuums? Gustaf Olsson (Thu Jun 10 2010 - 06:13:15 PDT)
- Re: [AMBER] Building a slab between two vacuums? Bill Ross (Thu Jun 10 2010 - 09:57:14 PDT)
[AMBER] DNA analysis ros (Thu Jun 10 2010 - 06:25:01 PDT)
- Re: [AMBER] DNA analysis Robert Elder (Thu Jun 10 2010 - 08:13:48 PDT)
  - Re: [AMBER] DNA analysis case (Thu Jun 10 2010 - 18:08:57 PDT)
[AMBER] about sybylmol2 file Navanath Kumbhar (Thu Jun 10 2010 - 07:33:59 PDT)
- Re: [AMBER] about sybylmol2 file Jason Swails (Thu Jun 10 2010 - 17:14:46 PDT)
- Re: [AMBER] about sybylmol2 file case (Thu Jun 10 2010 - 18:09:04 PDT)
  - Re: [AMBER] about sybylmol2 file Navanath Kumbhar (Fri Jun 11 2010 - 03:27:20 PDT)
    - Re: [AMBER] about sybylmol2 file FyD (Fri Jun 11 2010 - 06:08:30 PDT)
    - Re: [AMBER] about sybylmol2 file case (Fri Jun 11 2010 - 06:19:52 PDT)
    - Re: [AMBER] about sybylmol2 file Navanath Kumbhar (Sat Jun 12 2010 - 03:29:08 PDT)
    - Re: [AMBER] about sybylmol2 file case (Sat Jun 12 2010 - 05:31:15 PDT)
- Re: [AMBER] about sybylmol2 file Bill Ross (Sat Jun 12 2010 - 12:39:28 PDT)
[AMBER] 2drms Beale, John (Thu Jun 10 2010 - 07:40:24 PDT)
- Re: [AMBER] 2drms Niel Henriksen (Thu Jun 10 2010 - 07:57:27 PDT)
  - Re: [AMBER] 2drms case (Thu Jun 10 2010 - 18:27:15 PDT)
[AMBER] MMPBSA.py nmode maxcyc problem Niel Henriksen (Thu Jun 10 2010 - 07:51:08 PDT)
- Re: [AMBER] MMPBSA.py nmode maxcyc problem Jason Swails (Thu Jun 10 2010 - 16:24:16 PDT)
  - Re: [AMBER] MMPBSA.py nmode maxcyc problem Jason Swails (Thu Jun 10 2010 - 17:01:55 PDT)
    - Re: [AMBER] MMPBSA.py nmode maxcyc problem Jason Swails (Thu Jun 10 2010 - 21:19:47 PDT)
[AMBER] pmemd.cuda DPDP performance on GTX480 vs C2050? Sasha Buzko (Thu Jun 10 2010 - 09:21:18 PDT)
- Re: [AMBER] pmemd.cuda DPDP performance on GTX480 vs C2050? Ross Walker (Fri Jun 11 2010 - 07:50:26 PDT)
  - Re: [AMBER] pmemd.cuda DPDP performance on GTX480 vs C2050? Scott Le Grand (Fri Jun 11 2010 - 09:41:35 PDT)
    - Re: [AMBER] pmemd.cuda DPDP performance on GTX480 vs C2050? Sasha Buzko (Fri Jun 11 2010 - 10:21:33 PDT)
  - Re: [AMBER] pmemd.cuda DPDP performance on GTX480 vs C2050? Sasha Buzko (Mon Jun 14 2010 - 12:09:38 PDT)
    - Re: [AMBER] pmemd.cuda DPDP performance on GTX480 vs C2050? michael bane (Mon Jun 14 2010 - 12:35:36 PDT)
    - Re: [AMBER] pmemd.cuda DPDP performance on GTX480 vs C2050? Ross Walker (Mon Jun 14 2010 - 13:34:47 PDT)
    - Re: [AMBER] pmemd.cuda DPDP performance on GTX480 vs C2050? Ross Walker (Mon Jun 14 2010 - 13:30:39 PDT)
    - Re: [AMBER] pmemd.cuda DPDP performance on GTX480 vs C2050? Scott Le Grand (Mon Jun 14 2010 - 14:02:23 PDT)
    - Re: [AMBER] pmemd.cuda DPDP performance on GTX480 vs C2050? Ross Walker (Mon Jun 14 2010 - 15:08:20 PDT)
    - [AMBER] forrtl: severe (64): input conversion error, unit 9, file Homa Azizian (Mon Jun 14 2010 - 22:03:19 PDT)
    - Re: [AMBER] forrtl: severe (64): input conversion error, unit 9, file Jason Swails (Mon Jun 14 2010 - 22:29:11 PDT)
    - Re: [AMBER] forrtl: severe (64): input conversion error, unit 9, file Bill Ross (Tue Jun 15 2010 - 09:39:50 PDT)
[AMBER] info on ff10? Sidney Elmer (Thu Jun 10 2010 - 09:53:20 PDT)
- Re: [AMBER] info on ff10? case (Thu Jun 10 2010 - 18:09:19 PDT)
[AMBER] Stuck on pmemd.f90 Paul Go (Thu Jun 10 2010 - 10:22:44 PDT)
- Re: [AMBER] Stuck on pmemd.f90 Jason Swails (Thu Jun 10 2010 - 17:29:26 PDT)
- Re: [AMBER] Stuck on pmemd.f90 case (Thu Jun 10 2010 - 18:09:26 PDT)
[AMBER] RESP fit calculation Valerie Fako (Thu Jun 10 2010 - 11:07:58 PDT)
- Re: [AMBER] RESP fit calculation FyD (Thu Jun 10 2010 - 21:06:32 PDT)
[AMBER] Solute and solvent temperatures in mden Mickey Richards (Thu Jun 10 2010 - 15:45:35 PDT)
- Re: [AMBER] Solute and solvent temperatures in mden Adrian Roitberg (Thu Jun 10 2010 - 15:57:19 PDT)
  - Re: [AMBER] Solute and solvent temperatures in mden Mickey Richards (Thu Jun 10 2010 - 16:10:02 PDT)
- Re: [AMBER] Solute and solvent temperatures in mden Bill Ross (Thu Jun 10 2010 - 16:02:34 PDT)
- Re: [AMBER] Solute and solvent temperatures in mden case (Thu Jun 10 2010 - 18:32:03 PDT)
[AMBER] correlation luzhenw1.msu.edu (Thu Jun 10 2010 - 22:16:47 PDT)
[AMBER] simulation of DNA-protein interaction Ehsan Habibi (Fri Jun 11 2010 - 02:31:55 PDT)
[AMBER] Conserving water bridges? Waqas Nasir (Fri Jun 11 2010 - 02:56:46 PDT)
- Re: [AMBER] Conserving water bridges? steinbrt.rci.rutgers.edu (Fri Jun 11 2010 - 03:18:25 PDT)
  - Re: [AMBER] Conserving water bridges? need help... Waqas Nasir (Mon Jun 14 2010 - 03:20:36 PDT)
    - Re: [AMBER] Conserving water bridges? need help... steinbrt.rci.rutgers.edu (Mon Jun 14 2010 - 04:39:59 PDT)
    - Re: [AMBER] Conserving water bridges? need help... Bill Ross (Mon Jun 14 2010 - 09:35:51 PDT)
- Re: [AMBER] Conserving water bridges? Jason Swails (Fri Jun 11 2010 - 10:00:21 PDT)
[AMBER] correlation matrix in PTRAJ luzhenw1.msu.edu (Fri Jun 11 2010 - 06:54:18 PDT)
[AMBER] Invitation to connect on LinkedIn hyma srinivas (Fri Jun 11 2010 - 08:58:51 PDT)
[AMBER] protonation states of histidines - is there any way to treat it accurately. Andrew Voronkov (Fri Jun 11 2010 - 09:01:23 PDT)
- Re: [AMBER] protonation states of histidines - is there any way to treat it accurately. Jason Swails (Fri Jun 11 2010 - 10:18:33 PDT)
[AMBER] Amber10 installation problem in linux Sangita Kachhap (Fri Jun 11 2010 - 09:28:11 PDT)
- Re: [AMBER] Amber10 installation problem in linux Mark Williamson (Fri Jun 11 2010 - 10:09:54 PDT)
[AMBER] Can mm-pbsa be limited to simulating a fragment of a large protein? Sasha Buzko (Fri Jun 11 2010 - 10:50:35 PDT)
[AMBER] Lennard Jones calculation Antonios Samiotakis (Fri Jun 11 2010 - 16:01:24 PDT)
- Re: [AMBER] Lennard Jones calculation case (Fri Jun 11 2010 - 17:48:59 PDT)
  - Re: [AMBER] Lennard Jones calculation Antonios Samiotakis (Fri Jun 11 2010 - 18:52:50 PDT)
  - Re: [AMBER] Lennard Jones calculation Antonios Samiotakis (Sat Jun 12 2010 - 08:15:13 PDT)
    - Re: [AMBER] Lennard Jones calculation case (Sat Jun 19 2010 - 07:23:55 PDT)
[AMBER] Modifying the bond energy calculation - adding a cubic bond term (hacking the sander code) Eric Shamay (Fri Jun 11 2010 - 17:13:56 PDT)
[AMBER] torsion angle define Navanath Kumbhar (Sat Jun 12 2010 - 04:04:56 PDT)
- Re: [AMBER] torsion angle define Ilyas Yildirim (Sat Jun 12 2010 - 04:16:23 PDT)
  - Re: [AMBER] torsion angle define Navanath Kumbhar (Sat Jun 12 2010 - 05:40:11 PDT)
    - Re: [AMBER] torsion angle define Ilyas Yildirim (Sat Jun 12 2010 - 05:54:03 PDT)
- Re: [AMBER] torsion angle define Bill Ross (Sat Jun 12 2010 - 12:34:49 PDT)
- Re: [AMBER] torsion angle define Bill Ross (Sat Jun 12 2010 - 12:37:41 PDT)
- Re: [AMBER] torsion angle define Bill Ross (Sat Jun 12 2010 - 12:40:35 PDT)
[AMBER] Postdoc position available at SDSC. Ross Walker (Sat Jun 12 2010 - 07:37:17 PDT)
[AMBER] CUDA (GPU): Implementation does not support extra points. ashutosh shandilya (Sat Jun 12 2010 - 11:18:06 PDT)
- Re: [AMBER] CUDA (GPU): Implementation does not support extra points. Ross Walker (Sat Jun 12 2010 - 11:42:30 PDT)
  - Re: [AMBER] CUDA (GPU): Implementation does not support extra points. ashutosh shandilya (Sun Jun 13 2010 - 23:08:10 PDT)
    - Re: [AMBER] CUDA (GPU): Implementation does not support extra points. case (Mon Jun 14 2010 - 07:09:25 PDT)
[AMBER] constant pH simulation (protonation state specification) Sangita Kachhap (Sun Jun 13 2010 - 09:16:34 PDT)
- Re: [AMBER] constant pH simulation (protonation state specification) Jason Swails (Sun Jun 13 2010 - 09:40:57 PDT)
  - Re: [AMBER] constant pH simulation (protonation state specification) Sangita Kachhap (Sun Jun 13 2010 - 21:46:54 PDT)
    - Re: [AMBER] constant pH simulation (protonation state specification) Jason Swails (Sun Jun 13 2010 - 23:33:23 PDT)
[AMBER] antechamber monica.imtech.res.in (Mon Jun 14 2010 - 00:43:00 PDT)
[AMBER] Ptraj problems Samuel Genheden (Mon Jun 14 2010 - 01:47:25 PDT)
- Re: [AMBER] Ptraj problems Thomas Cheatham (Mon Jun 14 2010 - 02:46:47 PDT)
  - Re: [AMBER] Ptraj problems Samuel Genheden (Mon Jun 14 2010 - 03:56:46 PDT)
[AMBER] Free Energy profile Anna Reymer (Mon Jun 14 2010 - 02:47:57 PDT)
[AMBER] parallel compiling failure of Amber 11 Yubo Fan (Mon Jun 14 2010 - 08:58:52 PDT)
- Re: [AMBER] parallel compiling failure of Amber 11 Ross Walker (Mon Jun 14 2010 - 09:25:51 PDT)
- Re: [AMBER] parallel compiling failure of Amber 11 case (Mon Jun 14 2010 - 09:34:13 PDT)
  - Re: [AMBER] parallel compiling failure of Amber 11 Yubo Fan (Mon Jun 21 2010 - 13:25:10 PDT)
    - Re: [AMBER] parallel compiling failure of Amber 11 Jason Swails (Mon Jun 21 2010 - 13:29:43 PDT)
    - Re: [AMBER] parallel compiling failure of Amber 11 Yubo Fan (Mon Jun 21 2010 - 17:15:43 PDT)
    - Re: [AMBER] parallel compiling failure of Amber 11 Gustavo Seabra (Tue Jun 22 2010 - 01:54:42 PDT)
    - [AMBER] Compiling failure of Amber 9 Yubo Fan (Tue Jun 29 2010 - 06:39:37 PDT)
    - Re: [AMBER] Compiling failure of Amber 9 Jason Swails (Tue Jun 29 2010 - 06:46:24 PDT)
    - Re: [AMBER] Compiling failure of Amber 9 Yubo Fan (Tue Jun 29 2010 - 11:41:44 PDT)
    - Re: [AMBER] Compiling failure of Amber 9 Jason Swails (Tue Jun 29 2010 - 12:27:29 PDT)
    - Re: [AMBER] Compiling failure of Amber 9 Yubo Fan (Thu Jul 22 2010 - 08:43:18 PDT)
    - Re: [AMBER] Compiling failure of Amber 9 David Watson (Thu Jul 22 2010 - 09:22:56 PDT)
    - Re: [AMBER] Compiling failure of Amber 9 Yubo Fan (Fri Jul 23 2010 - 07:17:08 PDT)
    - Re: [AMBER] Compiling failure of Amber 9 case (Fri Jul 23 2010 - 11:52:16 PDT)
    - Re: [AMBER] parallel compiling failure of Amber 11 Yubo Fan (Tue Jun 22 2010 - 07:56:54 PDT)
    - Re: [AMBER] parallel compiling failure of Amber 11 Jason Swails (Tue Jun 22 2010 - 08:12:26 PDT)
    - Re: [AMBER] parallel compiling failure of Amber 11 Yubo Fan (Tue Jun 22 2010 - 09:13:46 PDT)
    - Re: [AMBER] parallel compiling failure of Amber 11 Jason Swails (Tue Jun 22 2010 - 09:58:16 PDT)
    - Re: [AMBER] parallel compiling failure of Amber 11 Yubo Fan (Tue Jun 22 2010 - 10:49:25 PDT)
    - Re: [AMBER] parallel compiling failure of Amber 11 Yubo Fan (Tue Jun 22 2010 - 18:05:40 PDT)
    - Re: [AMBER] parallel compiling failure of Amber 11 Jason Swails (Tue Jun 22 2010 - 18:24:26 PDT)
    - Re: [AMBER] parallel compiling failure of Amber 11 case (Tue Jun 22 2010 - 21:33:52 PDT)
- Re: [AMBER] parallel compiling failure of Amber 11 Bill Ross (Tue Jun 22 2010 - 22:10:40 PDT)
[AMBER] visualising frame of minimisation Alan (Mon Jun 14 2010 - 09:02:42 PDT)
- Re: [AMBER] visualising frame of minimisation Jason Swails (Thu Jun 17 2010 - 06:39:17 PDT)
[AMBER] MMPBSA.py error George Tzotzos (Mon Jun 14 2010 - 09:10:06 PDT)
- Re: [AMBER] MMPBSA.py error Dwight McGee (Mon Jun 14 2010 - 09:42:44 PDT)
  - Re: [AMBER] MMPBSA.py error Jason Swails (Mon Jun 14 2010 - 10:32:12 PDT)
    - Re: [AMBER] MMPBSA.py error George Tzotzos (Mon Jun 14 2010 - 23:42:56 PDT)
    - Re: [AMBER] MMPBSA.py error Jason Swails (Mon Jun 14 2010 - 23:52:06 PDT)
[AMBER] peptide leaving box, image command not working Omair A. Khan (Mon Jun 14 2010 - 10:51:08 PDT)
- Re: [AMBER] peptide leaving box, image command not working Niel Henriksen (Tue Jun 15 2010 - 06:58:21 PDT)
[AMBER] About md parameters for unuaual amino acid residues Rilei Yu (Mon Jun 14 2010 - 22:12:57 PDT)
- Re: [AMBER] About md parameters for unuaual amino acid residues Jason Swails (Mon Jun 14 2010 - 22:44:27 PDT)
  - Re: [AMBER] About md parameters for unuaual amino acid residues Rilei Yu (Tue Jun 15 2010 - 00:23:44 PDT)
[AMBER] about atom type Navanath Kumbhar (Mon Jun 14 2010 - 22:25:29 PDT)
- Re: [AMBER] about atom type case (Tue Jun 15 2010 - 09:03:25 PDT)
[AMBER] want to keep water from the pdb vaibhav dixit (Mon Jun 14 2010 - 23:50:03 PDT)
- Re: [AMBER] want to keep water from the pdb Jason Swails (Tue Jun 15 2010 - 00:00:44 PDT)
  - Re: [AMBER] want to keep water from the pdb vaibhav dixit (Tue Jun 15 2010 - 02:42:50 PDT)
- Re: [AMBER] want to keep water from the pdb Bill Ross (Tue Jun 15 2010 - 09:46:04 PDT)
[AMBER] Polarizability and induced dipoles Mag. Thomas Taylor (Tue Jun 15 2010 - 01:53:33 PDT)
- Re: [AMBER] Polarizability and induced dipoles Ross Walker (Tue Jun 15 2010 - 02:31:16 PDT)
  - Re: [AMBER] Polarizability and induced dipoles Mag. Thomas Taylor (Tue Jun 15 2010 - 03:47:47 PDT)
    - Re: [AMBER] Polarizability and induced dipoles Ross Walker (Tue Jun 15 2010 - 05:00:48 PDT)
[AMBER] how can i run min.in heat.in density.in equil.in as one sander job? vaibhav dixit (Tue Jun 15 2010 - 03:15:58 PDT)
- Re: [AMBER] how can i run min.in heat.in density.in equil.in as one sander job? Gustavo Seabra (Tue Jun 15 2010 - 04:00:16 PDT)
  - [AMBER] problems with NAB and SHIFTS Jakob Toudahl Nielsen (Tue Jun 15 2010 - 04:19:23 PDT)
    - Re: [AMBER] problems with NAB and SHIFTS Jason Swails (Tue Jun 15 2010 - 05:41:12 PDT)
    - Re: [AMBER] problems with NAB and SHIFTS Jakob Toudahl Nielsen (Tue Jun 15 2010 - 06:15:22 PDT)
    - Re: [AMBER] problems with NAB and SHIFTS case (Tue Jun 15 2010 - 06:17:28 PDT)
    - Re: [AMBER] problems with NAB and SHIFTS Jakob Toudahl Nielsen (Tue Jun 15 2010 - 06:43:59 PDT)
    - Re: [AMBER] problems with NAB and SHIFTS case (Tue Jun 15 2010 - 07:09:46 PDT)
    - Re: [AMBER] problems with NAB and SHIFTS Jakob Toudahl Nielsen (Tue Jun 15 2010 - 11:16:20 PDT)
    - Re: [AMBER] problems with NAB and SHIFTS Jason Swails (Tue Jun 15 2010 - 12:12:58 PDT)
    - Re: [AMBER] problems with NAB and SHIFTS case (Tue Jun 15 2010 - 12:19:24 PDT)
    - Re: [AMBER] problems with NAB and SHIFTS Jakob Toudahl Nielsen (Wed Jun 16 2010 - 00:56:43 PDT)
    - Re: [AMBER] problems with NAB and SHIFTS Jason Swails (Wed Jun 16 2010 - 06:15:51 PDT)
    - Re: [AMBER] problems with NAB and SHIFTS case (Wed Jun 16 2010 - 06:37:43 PDT)
    - Re: [AMBER] problems with NAB and SHIFTS Bill Ross (Tue Jun 15 2010 - 11:23:18 PDT)
    - Re: [AMBER] problems with NAB and SHIFTS Eric Shamay (Tue Jun 15 2010 - 11:41:35 PDT)
    - Re: [AMBER] problems with NAB and SHIFTS Xinfu Xia (Thu Jul 15 2010 - 08:30:41 PDT)
    - Re: [AMBER] problems with NAB and SHIFTS Jason Swails (Thu Jul 15 2010 - 08:54:49 PDT)
    - Re: [AMBER] problems with NAB and SHIFTS Xinfu Xia (Thu Jul 15 2010 - 10:31:08 PDT)
    - Re: [AMBER] problems with NAB and SHIFTS case (Thu Jul 15 2010 - 11:28:47 PDT)
    - Re: [AMBER] problems with NAB and SHIFTS case (Thu Jul 15 2010 - 10:32:06 PDT)
  - Re: [AMBER] how can i run min.in heat.in density.in equil.in as one sander job? vaibhav dixit (Wed Jun 16 2010 - 01:57:00 PDT)
    - Re: [AMBER] how can i run min.in heat.in density.in equil.in as one sander job? Gustavo Seabra (Wed Jun 16 2010 - 02:26:20 PDT)
    - Re: [AMBER] how can i run min.in heat.in density.in equil.in as one sander job? Ross Walker (Wed Jun 16 2010 - 02:49:41 PDT)
[AMBER] nmr refinment problem shirishkumar pawar (Tue Jun 15 2010 - 03:16:12 PDT)
- Re: [AMBER] nmr refinment problem case (Tue Jun 15 2010 - 06:21:12 PDT)
  - Re: [AMBER] nmr refinment problem shirishkumar pawar (Tue Jun 15 2010 - 22:05:33 PDT)
[AMBER] plz help!!! monica.imtech.res.in (Tue Jun 15 2010 - 03:20:52 PDT)
- Re: [AMBER] plz help!!! Nicee (Tue Jun 15 2010 - 04:16:09 PDT)
[AMBER] to understand 1-4 interactions in Amber FF Alan (Tue Jun 15 2010 - 04:16:31 PDT)
- Re: [AMBER] to understand 1-4 interactions in Amber FF Ross Walker (Tue Jun 15 2010 - 05:24:15 PDT)
  - Re: [AMBER] to understand 1-4 interactions in Amber FF Alan (Tue Jun 15 2010 - 06:13:28 PDT)
- Re: [AMBER] to understand 1-4 interactions in Amber FF Bill Ross (Tue Jun 15 2010 - 09:56:12 PDT)
Re: [AMBER] constant pH simulation (syn and anti position) Sangita Kachhap (Tue Jun 15 2010 - 06:50:36 PDT)
[AMBER] MD simulation of methylated DNA: addition of methyl groups to .pdb file Ehsan Habibi (Tue Jun 15 2010 - 10:23:45 PDT)
- Re: [AMBER] MD simulation of methylated DNA: addition of methyl groups to .pdb file Bill Ross (Tue Jun 15 2010 - 10:36:18 PDT)
- Re: [AMBER] MD simulation of methylated DNA: addition of methyl groups to .pdb file case (Tue Jun 15 2010 - 11:19:27 PDT)
[AMBER] picky nab compiler: is this really necessary? M. L. Dodson (Tue Jun 15 2010 - 12:32:26 PDT)
- Re: [AMBER] picky nab compiler: is this really necessary? case (Wed Jun 16 2010 - 09:57:52 PDT)
  - Re: [AMBER] picky nab compiler: is this really necessary? M. L. Dodson (Wed Jun 16 2010 - 10:54:37 PDT)
    - Re: [AMBER] picky nab compiler: is this really necessary? case (Wed Jun 16 2010 - 17:01:54 PDT)
Re: [AMBER] density John S (Tue Jun 15 2010 - 12:57:51 PDT)
[AMBER] Rdf and density John S (Tue Jun 15 2010 - 22:55:37 PDT)
[AMBER] pH based conformational study Sangita Kachhap (Tue Jun 15 2010 - 23:55:18 PDT)
- Re: [AMBER] pH based conformational study Jason Swails (Wed Jun 16 2010 - 06:19:32 PDT)
  - Re: [AMBER] pH based conformational study Sangita Kachhap (Wed Jun 16 2010 - 06:34:01 PDT)
[AMBER] sietraj Yossa Dwi Hartono (Wed Jun 16 2010 - 00:10:14 PDT)
- Re: [AMBER] sietraj Purisima, Enrico (Wed Jun 16 2010 - 07:11:10 PDT)
  - Re: [AMBER] sietraj Yossa Dwi Hartono (Wed Jun 16 2010 - 22:52:47 PDT)
[AMBER] frcdump for CHARMM Mag. Thomas Taylor (Wed Jun 16 2010 - 02:08:00 PDT)
- Re: [AMBER] frcdump for CHARMM Ross Walker (Wed Jun 16 2010 - 02:44:26 PDT)
[AMBER] amber10 installation problem Devlina Chakravarty (Wed Jun 16 2010 - 05:01:16 PDT)
- Re: [AMBER] amber10 installation problem Lan JIN (Wed Jul 08 2009 - 19:46:22 PDT)
  - Re: [AMBER] amber10 installation problem case (Thu Jul 09 2009 - 05:38:01 PDT)
- Re: [AMBER] amber10 installation problem Lan JIN (Fri Jul 10 2009 - 00:41:34 PDT)
- Re: [AMBER] amber10 installation problem case (Wed Jun 16 2010 - 09:58:16 PDT)
  - Re: [AMBER] amber10 installation problem Indrajit Deb (Thu Jun 17 2010 - 00:22:06 PDT)
    - Re: [AMBER] amber10 installation problem Sudeep Narayan Banerjee (Thu Jun 17 2010 - 01:05:40 PDT)
[AMBER] MMPBSA : SA Bomb in sa_arc : Allocation aborted error Cristina Sisu (Wed Jun 16 2010 - 07:58:52 PDT)
- Re: [AMBER] MMPBSA : SA Bomb in sa_arc : Allocation aborted error Ray Luo (Wed Jun 16 2010 - 11:08:35 PDT)
[AMBER] FW: frcdump for CHARMM Ross Walker (Wed Jun 16 2010 - 08:10:35 PDT)
[AMBER] ptraj rms error Beale, John (Wed Jun 16 2010 - 08:30:48 PDT)
- Re: [AMBER] ptraj rms error Daniel Roe (Wed Jun 16 2010 - 12:53:32 PDT)
  - Re: [AMBER] ptraj rms error Beale, John (Thu Jun 17 2010 - 03:38:00 PDT)
    - Re: [AMBER] ptraj rms error case (Thu Jun 17 2010 - 06:52:11 PDT)
    - [AMBER] What's the mean of this ptraj error message? thanks in advance. Catein Catherine (Thu Jun 17 2010 - 09:01:23 PDT)
    - Re: [AMBER] What's the mean of this ptraj error message? thanks in advance. Jason Swails (Thu Jun 17 2010 - 09:06:52 PDT)
    - Re: [AMBER] What's the mean of this ptraj error message? thanks in advance. Paul S. Nerenberg (Thu Jun 17 2010 - 09:06:48 PDT)
  - Re: [AMBER] ptraj rms error Beale, John (Thu Jun 17 2010 - 04:30:58 PDT)
[AMBER] high bidning energy MMPBSA kamlesh sahu (Wed Jun 16 2010 - 18:45:55 PDT)
- Re: [AMBER] high bidning energy MMPBSA Bill Miller III (Wed Jun 16 2010 - 18:49:05 PDT)
  - Re: [AMBER] high bidning energy MMPBSA kamlesh sahu (Wed Jun 16 2010 - 18:56:25 PDT)
    - Re: [AMBER] high bidning energy MMPBSA Bill Miller III (Wed Jun 16 2010 - 19:22:06 PDT)
  - Re: [AMBER] high bidning energy MMPBSA kamlesh sahu (Wed Jun 16 2010 - 19:13:22 PDT)
    - Re: [AMBER] high bidning energy MMPBSA Jason Swails (Wed Jun 16 2010 - 19:21:42 PDT)
    - Re: [AMBER] high bidning energy MMPBSA kamlesh sahu (Wed Jun 16 2010 - 19:38:58 PDT)
    - [AMBER] problem with the energetics of the system Homa Azizian (Wed Jun 16 2010 - 20:05:48 PDT)
    - Re: [AMBER] problem with the energetics of the system Gustavo Seabra (Wed Jun 16 2010 - 20:09:48 PDT)
    - Re: [AMBER] problem with the energetics of the system Homa Azizian (Wed Jun 16 2010 - 21:37:56 PDT)
    - Re: [AMBER] problem with the energetics of the system Bill Ross (Wed Jun 16 2010 - 22:33:59 PDT)
    - Re: [AMBER] problem with the energetics of the system Bill Ross (Wed Jun 16 2010 - 22:38:15 PDT)
    - Re: [AMBER] problem with the energetics of the system Homa Azizian (Thu Jun 17 2010 - 18:02:09 PDT)
    - Re: [AMBER] problem with the energetics of the system Jason Swails (Thu Jun 17 2010 - 18:26:55 PDT)
    - Re: [AMBER] problem with the energetics of the system Bill Ross (Fri Jun 18 2010 - 09:47:00 PDT)
    - Re: [AMBER] problem with the energetics of the system Homa Azizian (Fri Jun 18 2010 - 23:04:51 PDT)
    - Re: [AMBER] problem with the energetics of the system Jason Swails (Sat Jun 19 2010 - 08:53:57 PDT)
    - Re: [AMBER] problem with the energetics of the system case (Sat Jun 19 2010 - 13:47:55 PDT)
    - Re: [AMBER] problem with the energetics of the system Bill Ross (Sat Jun 19 2010 - 09:35:26 PDT)
- [AMBER] Fwd: high bidning energy MMPBSA kamlesh sahu (Wed Jun 16 2010 - 18:51:11 PDT)
Re: [AMBER] Creating topology files for protein-ligand complex case (Wed Jun 16 2010 - 19:51:26 PDT)
- Re: [AMBER] Creating topology files for protein-ligand complex Heather Condurso (Wed Jun 16 2010 - 20:26:28 PDT)
[AMBER] rhombicity Peter Podbevšek (Thu Jun 17 2010 - 02:18:57 PDT)
- Re: [AMBER] rhombicity case (Thu Jun 17 2010 - 19:29:06 PDT)
[AMBER] Parameters for Nickel Dian Jiao (Thu Jun 17 2010 - 08:14:41 PDT)
- Re: [AMBER] Parameters for Nickel Jason Swails (Thu Jun 17 2010 - 08:27:08 PDT)
[AMBER] bond angle and distance calculation Hoshin Kim (Thu Jun 17 2010 - 01:48:18 PDT)
[AMBER] Solvation free energy of a capped 9mer peptide Lekpa Duukori (Thu Jun 17 2010 - 15:52:14 PDT)
- Re: [AMBER] Solvation free energy of a capped 9mer peptide Ray Luo (Thu Jun 17 2010 - 16:32:03 PDT)
[AMBER] MMPBSA warning George Tzotzos (Fri Jun 18 2010 - 03:54:54 PDT)
- Re: [AMBER] MMPBSA warning Jason Swails (Fri Jun 18 2010 - 06:09:18 PDT)
[AMBER] mmpbsa RANAJIT SHINDE (Fri Jun 18 2010 - 04:30:25 PDT)
- Re: [AMBER] mmpbsa Jason Swails (Fri Jun 18 2010 - 05:59:51 PDT)
  - Re: [AMBER] mmpbsa RANAJIT SHINDE (Fri Jun 18 2010 - 22:28:19 PDT)
[AMBER] a query about analysis oguz gurbulak (Fri Jun 18 2010 - 04:37:51 PDT)
- Re: [AMBER] a query about analysis Jason Swails (Fri Jun 18 2010 - 06:14:10 PDT)
- Re: [AMBER] a query about analysis Cenk $Jenk$ Andac (Mon Jun 21 2010 - 00:59:15 PDT)
[AMBER] PBC in umbrella sampling dhacademic (Fri Jun 18 2010 - 07:45:14 PDT)
- Re: [AMBER] PBC in umbrella sampling case (Fri Jun 18 2010 - 15:15:41 PDT)
[AMBER] bond angle and distance problem Hoshin Kim (Thu Jun 17 2010 - 21:54:01 PDT)
[AMBER] radial distribution function Ganesh Kamath (Fri Jun 18 2010 - 13:39:33 PDT)
[AMBER] how to use a distant-dependent dielectric constant of "epsilon = 4r" DeChang Li (Fri Jun 18 2010 - 20:54:48 PDT)
- [AMBER] graphical analysis of H-bond Homa Azizian (Fri Jun 18 2010 - 23:12:13 PDT)
- Re: [AMBER] how to use a distant-dependent dielectric constant of "epsilon = 4r" case (Sat Jun 19 2010 - 06:36:56 PDT)
[AMBER] antechamber issue and parameters for heme of cyp3a4 vaibhav dixit (Fri Jun 18 2010 - 22:00:47 PDT)
- Re: [AMBER] antechamber issue and parameters for heme of cyp3a4 Jio M (Sat Jun 19 2010 - 11:03:27 PDT)
  - Re: [AMBER] antechamber issue and parameters for heme of cyp3a4 vaibhav dixit (Sat Jun 19 2010 - 21:25:35 PDT)
[AMBER] constant pH equilibration confusion Sangita Kachhap (Sat Jun 19 2010 - 00:55:52 PDT)
- Re: [AMBER] constant pH equilibration confusion manikanthan bhavaraju (Sat Jun 19 2010 - 02:32:30 PDT)
- Re: [AMBER] constant pH equilibration confusion Jason Swails (Sat Jun 19 2010 - 08:49:15 PDT)
  - Re: [AMBER] constant pH equilibration confusion Sangita Kachhap (Sat Jun 19 2010 - 13:09:27 PDT)
    - Re: [AMBER] constant pH equilibration confusion Jason Swails (Sat Jun 19 2010 - 14:10:20 PDT)
- Re: [AMBER] constant pH equilibration confusion Bill Ross (Sat Jun 19 2010 - 09:38:16 PDT)
  - Re: [AMBER] constant pH equilibration confusion Sangita Kachhap (Sat Jun 19 2010 - 12:59:26 PDT)
    - Re: [AMBER] constant pH equilibration confusion Jason Swails (Sat Jun 19 2010 - 13:07:37 PDT)
    - Re: [AMBER] constant pH equilibration confusion Sangita Kachhap (Sat Jun 19 2010 - 13:30:53 PDT)
    - Re: [AMBER] constant pH equilibration confusion Jason Swails (Sat Jun 19 2010 - 14:11:23 PDT)
- Re: [AMBER] constant pH equilibration confusion Bill Ross (Sat Jun 19 2010 - 18:13:34 PDT)
[AMBER] two questions about Amber annealing Yiyu Li (Sat Jun 19 2010 - 20:17:08 PDT)
- Re: [AMBER] two questions about Amber annealing Bill Ross (Sat Jun 19 2010 - 21:19:50 PDT)
- Re: [AMBER] two questions about Amber annealing Ross Walker (Sat Jun 19 2010 - 21:55:47 PDT)
- Re: [AMBER] two questions about Amber annealing Bill Ross (Sun Jun 20 2010 - 00:18:48 PDT)
[AMBER] Query- Heating after Equilibration Jagdeesh C (Sat Jun 19 2010 - 23:16:19 PDT)
- Re: [AMBER] Query- Heating after Equilibration case (Sun Jun 20 2010 - 08:32:40 PDT)
  - Re: [AMBER] Query- Heating after Equilibration Jason Swails (Sun Jun 20 2010 - 08:47:04 PDT)
    - Re: [AMBER] Query- Heating after Equilibration Jagdeesh C (Tue Jun 22 2010 - 19:59:54 PDT)
    - Re: [AMBER] Query- Heating after Equilibration case (Tue Jun 22 2010 - 21:43:19 PDT)
    - Re: [AMBER] Query- Heating after Equilibration Jagdeesh C (Wed Jun 23 2010 - 04:28:15 PDT)
  - [AMBER] xleap problem for terminal DNA base pairs. Catein Catherine (Sun Jun 20 2010 - 08:56:59 PDT)
    - Re: [AMBER] xleap problem for terminal DNA base pairs. Jason Swails (Sun Jun 20 2010 - 09:06:17 PDT)
    - [AMBER] Is AmberTools 1.4 compatible with AMBER10? Catein Catherine (Sun Jun 20 2010 - 09:14:04 PDT)
    - Re: [AMBER] Is AmberTools 1.4 compatible with AMBER10? Jason Swails (Sun Jun 20 2010 - 09:51:53 PDT)
    - [AMBER] Is it a bug in the xleap of AmberTools 1.2 and 1.4. Catein Catherine (Sun Jun 20 2010 - 23:32:52 PDT)
    - Re: [AMBER] Is it a bug in the xleap of AmberTools 1.2 and 1.4. case (Mon Jun 21 2010 - 06:51:50 PDT)
    - [AMBER] How to read the motion of PCA? Catein Catherine (Tue Jun 22 2010 - 08:16:36 PDT)
    - Re: [AMBER] How to read the motion of PCA? Hannes Loeffler (Wed Jun 23 2010 - 02:19:34 PDT)
    - Re: [AMBER] Is it a bug in the xleap of AmberTools 1.2 and 1.4. Catein Catherine (Tue Jun 22 2010 - 09:40:47 PDT)
    - Re: [AMBER] Is it a bug in the xleap of AmberTools 1.2 and 1.4. case (Tue Jun 22 2010 - 15:30:00 PDT)
    - [AMBER] Error encounter when running tutorial 4b when running xleap with AMBER 10 and AmberTools 1.2 Catein Catherine (Thu Jun 24 2010 - 06:57:43 PDT)
    - Re: [AMBER] Error encounter when running tutorial 4b when running xleap with AMBER 10 and AmberTools 1.2 Jason Swails (Thu Jun 24 2010 - 07:02:01 PDT)
    - Re: [AMBER] Error encounter when running tutorial 4b when running xleap with AMBER 10 and AmberTools 1.2 Catein Catherine (Thu Jun 24 2010 - 09:44:31 PDT)
    - Re: [AMBER] Error encounter when running tutorial 4b when running xleap with AMBER 10 and AmberTools 1.2 Jason Swails (Thu Jun 24 2010 - 09:50:38 PDT)
    - [AMBER] Can i use DA instead of DA3/DA5 for teminal residues? Catein Catherine (Thu Jun 24 2010 - 07:02:03 PDT)
    - Re: [AMBER] Can i use DA instead of DA3/DA5 for teminal residues? case (Thu Jun 24 2010 - 07:30:01 PDT)
    - [AMBER] Is xleap part of Ambertool or Amber10? Catein Catherine (Sun Jun 20 2010 - 09:08:45 PDT)
    - Re: [AMBER] Is xleap part of Ambertool or Amber10? Jason Swails (Sun Jun 20 2010 - 09:45:49 PDT)
    - Re: [AMBER] xleap problem for terminal DNA base pairs. Bill Ross (Sun Jun 20 2010 - 10:18:37 PDT)
- Re: [AMBER] Query- Heating after Equilibration Bill Ross (Tue Jun 22 2010 - 22:12:48 PDT)
[AMBER] "prepin", ".frcmod" and "pdb" files of 5-methylcytidine (for DNA (dC) no RNA) Ehsan Habibi (Sun Jun 20 2010 - 03:25:47 PDT)
[AMBER] Problem with pmed installation: Amber 10 Devlina Chakravarty (Mon Jun 21 2010 - 03:53:15 PDT)
- Re: [AMBER] Problem with pmed installation: Amber 10 Jason Swails (Mon Jun 21 2010 - 07:18:19 PDT)
- Re: [AMBER] Problem with pmed installation: Amber 10 Ross Walker (Mon Jun 21 2010 - 07:40:37 PDT)
[AMBER] constant pH simulation ERROR "vlimit exceeded for step" Sangita Kachhap (Mon Jun 21 2010 - 04:10:28 PDT)
- Re: [AMBER] constant pH simulation ERROR "vlimit exceeded for step" Jason Swails (Mon Jun 21 2010 - 07:25:26 PDT)
  - Re: [AMBER] constant pH simulation ERROR "vlimit exceeded for step" Sangita Kachhap (Mon Jun 21 2010 - 08:10:59 PDT)
    - Re: [AMBER] constant pH simulation ERROR "vlimit exceeded for step" Jason Swails (Mon Jun 21 2010 - 09:04:21 PDT)
    - Re: [AMBER] constant pH simulation ERROR "vlimit exceeded for step" Sangita Kachhap (Mon Jun 21 2010 - 09:20:35 PDT)
  - Re: [AMBER] constant pH simulation ERROR "vlimit exceeded for step" Bill Ross (Tue Jun 22 2010 - 12:53:33 PDT)
    - Re: [AMBER] constant pH simulation ERROR "vlimit exceeded for step" Sangita Kachhap (Tue Jun 22 2010 - 13:10:37 PDT)
    - Re: [AMBER] constant pH simulation ERROR "vlimit exceeded for step" Sangita Kachhap (Tue Jun 22 2010 - 13:20:10 PDT)
  - Re: [AMBER] constant pH simulation ERROR "vlimit exceeded for step" Bill Ross (Tue Jun 22 2010 - 13:22:51 PDT)
    - Re: [AMBER] constant pH simulation ERROR "vlimit exceeded for step" Sangita Kachhap (Tue Jun 22 2010 - 13:30:05 PDT)
    - Re: [AMBER] constant pH simulation ERROR "vlimit exceeded for step" Sangita Kachhap (Tue Jun 22 2010 - 23:33:36 PDT)
  - Re: [AMBER] constant pH simulation ERROR "vlimit exceeded for step" Bill Ross (Tue Jun 22 2010 - 13:44:34 PDT)
  - Re: [AMBER] constant pH simulation ERROR "vlimit exceeded for step" Bill Ross (Wed Jun 23 2010 - 09:55:40 PDT)
[AMBER] unexpected "vlimit exceeded for step" error Cristina Sisu (Mon Jun 21 2010 - 10:25:49 PDT)
- Re: [AMBER] unexpected "vlimit exceeded for step" error case (Mon Jun 21 2010 - 10:48:29 PDT)
- Re: [AMBER] unexpected "vlimit exceeded for step" error Ross Walker (Mon Jun 21 2010 - 10:51:17 PDT)
  - Re: [AMBER] unexpected "vlimit exceeded for step" error Cristina Sisu (Tue Jun 22 2010 - 06:20:15 PDT)
    - Re: [AMBER] unexpected "vlimit exceeded for step" error Ross Walker (Tue Jun 22 2010 - 08:34:17 PDT)
- Re: [AMBER] unexpected "vlimit exceeded for step" error Bill Ross (Tue Jun 22 2010 - 10:10:26 PDT)
  - Re: [AMBER] unexpected "vlimit exceeded for step" error Cristina Sisu (Tue Jun 22 2010 - 12:13:16 PDT)
- Re: [AMBER] unexpected "vlimit exceeded for step" error Bill Ross (Tue Jun 22 2010 - 12:19:50 PDT)
  - Re: [AMBER] unexpected "vlimit exceeded for step" error Cristina Sisu (Wed Jun 23 2010 - 03:49:07 PDT)
- Re: [AMBER] unexpected "vlimit exceeded for step" error Ross Walker (Wed Jun 23 2010 - 09:46:31 PDT)
  - Re: [AMBER] unexpected "vlimit exceeded for step" error Cristina Sisu (Thu Jun 24 2010 - 03:23:15 PDT)
- Re: [AMBER] unexpected "vlimit exceeded for step" error Bill Ross (Wed Jun 23 2010 - 10:02:36 PDT)
[AMBER] periodic images of truc. octahedron in vmd Paul Brandt (Mon Jun 21 2010 - 13:52:06 PDT)
- Re: [AMBER] periodic images of truc. octahedron in vmd Bill Ross (Mon Jun 21 2010 - 14:10:37 PDT)
  - Re: [AMBER] periodic images of truc. octahedron in vmd Paul Brandt (Mon Jun 21 2010 - 14:54:09 PDT)
    - Re: [AMBER] periodic images of truc. octahedron in vmd Paul Brandt (Mon Jun 21 2010 - 16:06:33 PDT)
[AMBER] (no subject) moitrayee.mbu.iisc.ernet.in (Mon Jun 21 2010 - 22:16:45 PDT)
- [AMBER] center and image Homa Azizian (Mon Jun 21 2010 - 22:55:49 PDT)
  - Re: [AMBER] center and image Jason Swails (Tue Jun 22 2010 - 06:39:49 PDT)
    - [AMBER] stripping water Homa Azizian (Tue Jun 22 2010 - 17:58:20 PDT)
    - Re: [AMBER] stripping water Ross Walker (Tue Jun 22 2010 - 22:14:28 PDT)
[AMBER] improper for NH2 group in guanosine Dmitry Nilov (Tue Jun 22 2010 - 03:11:51 PDT)
- Re: [AMBER] improper for NH2 group in guanosine case (Tue Jun 22 2010 - 16:05:01 PDT)
  - Re: [AMBER] improper for NH2 group in guanosine Dmitry Nilov (Wed Jun 23 2010 - 02:12:10 PDT)
[AMBER] Unknown clustering algorithm_ptraj_ambertools1.4 moitrayee.mbu.iisc.ernet.in (Tue Jun 22 2010 - 06:56:23 PDT)
- Re: [AMBER] Unknown clustering algorithm_ptraj_ambertools1.4 Dwight McGee (Tue Jun 22 2010 - 07:18:42 PDT)
- Re: [AMBER] Unknown clustering algorithm_ptraj_ambertools1.4 Fredrick Devadoss (Tue Jun 22 2010 - 07:59:42 PDT)
[AMBER] about alanine scanning lidansa.mail.ustc.edu.cn (Tue Jun 22 2010 - 08:47:53 PDT)
- Re: [AMBER] about alanine scanning Sushil Mishra (Tue Jun 22 2010 - 09:42:24 PDT)
  - Re: [AMBER] about alanine scanning lidansa.mail.ustc.edu.cn (Tue Jun 22 2010 - 17:55:48 PDT)
    - Re: [AMBER] about alanine scanning Sushil Mishra (Tue Jun 22 2010 - 23:48:44 PDT)
    - Re: [AMBER] about alanine scanning lidansa.mail.ustc.edu.cn (Wed Jun 23 2010 - 01:57:22 PDT)
- Re: [AMBER] about alanine scanning Dwight McGee (Tue Jun 22 2010 - 10:05:28 PDT)
[AMBER] how to modify the code to save the trajectory of ONLY one part of atoms in .mdcrd file ? Dongshan Wei (Tue Jun 22 2010 - 09:16:16 PDT)
- Re: [AMBER] how to modify the code to save the trajectory of ONLY one part of atoms in .mdcrd file ? Jason Swails (Tue Jun 22 2010 - 10:08:11 PDT)
  - Re: [AMBER] how to modify the code to save the trajectory of ONLY one part of atoms in .mdcrd file ? Jason Swails (Tue Jun 22 2010 - 10:09:24 PDT)
    - Re: [AMBER] how to modify the code to save the trajectory of ONLY one part of atoms in .mdcrd file ? Gustavo Seabra (Tue Jun 22 2010 - 13:16:02 PDT)
    - Re: [AMBER] how to modify the code to save the trajectory of ONLY one part of atoms in .mdcrd file ? Dongshan Wei (Tue Jun 22 2010 - 17:32:24 PDT)
[AMBER] radial distribution function in amber Ganesh Kamath (Tue Jun 22 2010 - 10:10:24 PDT)
[AMBER] constant pH simulation ERROR "vlimit exceeded for step" Sangita Kachhap (Tue Jun 22 2010 - 12:42:18 PDT)
[AMBER] antechamber/gasteiger problem with FMN Eric Pettersen (Tue Jun 22 2010 - 13:08:46 PDT)
- Re: [AMBER] antechamber/gasteiger problem with FMN Eric Pettersen (Tue Jun 22 2010 - 13:11:28 PDT)
[AMBER] stripping water and cross-correlation analysis Homa Azizian (Tue Jun 22 2010 - 18:23:08 PDT)
- Re: [AMBER] stripping water and cross-correlation analysis case (Tue Jun 22 2010 - 21:29:07 PDT)
[AMBER] speed of analysis Homa Azizian (Tue Jun 22 2010 - 22:04:13 PDT)
- Re: [AMBER] speed of analysis Ross Walker (Tue Jun 22 2010 - 22:12:06 PDT)
[AMBER] simulating in urea monica.imtech.res.in (Tue Jun 22 2010 - 23:30:11 PDT)
- Re: [AMBER] simulating in urea case (Wed Jun 23 2010 - 06:53:26 PDT)
  - Re: [AMBER] simulating in urea monica.imtech.res.in (Wed Jun 23 2010 - 08:24:15 PDT)
    - Re: [AMBER] simulating in urea case (Wed Jun 23 2010 - 09:11:21 PDT)
    - Re: [AMBER] simulating in urea monica.imtech.res.in (Wed Jun 23 2010 - 22:36:46 PDT)
    - Re: [AMBER] simulating in urea monica.imtech.res.in (Wed Jun 23 2010 - 22:42:12 PDT)
- Re: [AMBER] simulating in urea Bill Ross (Wed Jun 23 2010 - 09:53:09 PDT)
[AMBER] dna monica.imtech.res.in (Wed Jun 23 2010 - 02:16:48 PDT)
- Re: [AMBER] dna case (Wed Jun 23 2010 - 07:02:42 PDT)
  - Re: [AMBER] dna monica.imtech.res.in (Wed Jun 23 2010 - 08:40:18 PDT)
    - Re: [AMBER] dna case (Wed Jun 23 2010 - 09:20:37 PDT)
    - Re: [AMBER] dna monica.imtech.res.in (Fri Jun 25 2010 - 00:54:33 PDT)
    - Re: [AMBER] dna case (Fri Jun 25 2010 - 06:54:08 PDT)
    - Re: [AMBER] dna monica.imtech.res.in (Sat Jun 26 2010 - 21:50:02 PDT)
    - Re: [AMBER] dna Kevin Hauser (Sun Jun 27 2010 - 09:56:03 PDT)
    - Re: [AMBER] dna case (Mon Jun 28 2010 - 19:07:46 PDT)
    - Re: [AMBER] dna Kevin Hauser (Wed Jun 23 2010 - 09:34:05 PDT)
[AMBER] dna Kevin Hauser (Wed Jun 23 2010 - 05:45:29 PDT)
[AMBER] pre-processing of trajectories moitrayee.mbu.iisc.ernet.in (Wed Jun 23 2010 - 07:02:08 PDT)
- Re: [AMBER] pre-processing of trajectories Hannes Loeffler (Wed Jun 23 2010 - 07:33:25 PDT)
  - Re: [AMBER] pre-processing of trajectories moitrayee.mbu.iisc.ernet.in (Wed Jun 23 2010 - 11:21:20 PDT)
- Re: [AMBER] pre-processing of trajectories hannes.loeffler.stfc.ac.uk (Wed Jun 23 2010 - 12:41:24 PDT)
  - Re: [AMBER] pre-processing of trajectories moitrayee.mbu.iisc.ernet.in (Thu Jun 24 2010 - 00:20:46 PDT)
    - Re: [AMBER] pre-processing of trajectories Hannes Loeffler (Thu Jun 24 2010 - 03:04:25 PDT)
    - Re: [AMBER] pre-processing of trajectories monica.imtech.res.in (Fri Jun 25 2010 - 00:37:30 PDT)
    - Re: [AMBER] pre-processing of trajectories Hannes Loeffler (Fri Jun 25 2010 - 06:52:51 PDT)
    - Re: [AMBER] pre-processing of trajectories monica.imtech.res.in (Sat Jun 26 2010 - 21:20:06 PDT)
    - Re: [AMBER] pre-processing of trajectories case (Sun Jun 27 2010 - 18:39:07 PDT)
[AMBER] restraint during constant pH Sangita Kachhap (Wed Jun 23 2010 - 07:39:35 PDT)
- Re: [AMBER] restraint during constant pH Jason Swails (Wed Jun 23 2010 - 07:42:06 PDT)
  - Re: [AMBER] restraint during constant pH Sangita Kachhap (Wed Jun 23 2010 - 09:49:03 PDT)
    - Re: [AMBER] restraint during constant pH Jason Swails (Wed Jun 23 2010 - 10:48:52 PDT)
    - Re: [AMBER] restraint during constant pH Sangita Kachhap (Wed Jun 23 2010 - 21:52:28 PDT)
    - Re: [AMBER] restraint during constant pH Jason Swails (Wed Jun 23 2010 - 22:05:50 PDT)
[AMBER] Ptraj error - ERROR in safe_malloc Siddharth Rastogi (Wed Jun 23 2010 - 09:45:19 PDT)
- Re: [AMBER] Ptraj error - ERROR in safe_malloc case (Wed Jun 23 2010 - 11:01:07 PDT)
  - Re: [AMBER] Ptraj error - ERROR in safe_malloc Siddharth Rastogi (Wed Jun 23 2010 - 13:24:31 PDT)
[AMBER] MMPBSA.py install problem Oliver Grant (Wed Jun 23 2010 - 09:48:39 PDT)
- Re: [AMBER] MMPBSA.py install problem Bill Miller III (Wed Jun 23 2010 - 09:55:51 PDT)
[AMBER] amberhome not set Ping (Wed Jun 23 2010 - 13:42:06 PDT)
- Re: [AMBER] amberhome not set Heather Condurso (Wed Jun 23 2010 - 13:45:26 PDT)
- Re: [AMBER] amberhome not set Bill Ross (Wed Jun 23 2010 - 13:57:48 PDT)
- Re: [AMBER] amberhome not set Ping (Wed Jun 23 2010 - 14:07:09 PDT)
  - Re: [AMBER] amberhome not set Jason Swails (Wed Jun 23 2010 - 14:26:50 PDT)
[AMBER] How to build a TT dimer Shi Choong (Wed Jun 23 2010 - 19:40:55 PDT)
- Re: [AMBER] How to build a TT dimer M. L. Dodson (Thu Jun 24 2010 - 07:11:06 PDT)
[AMBER] Restraint John S (Wed Jun 23 2010 - 21:10:07 PDT)
- Re: [AMBER] Restraint case (Thu Jun 24 2010 - 07:34:30 PDT)
[AMBER] [Fwd: Re: pre-processing of trajectories] moitrayee.mbu.iisc.ernet.in (Thu Jun 24 2010 - 00:21:16 PDT)
[AMBER] Kinetic energy after heating is zero Ashutosh Shandilya (Thu Jun 24 2010 - 03:28:14 PDT)
- Re: [AMBER] Kinetic energy after heating is zero Jason Swails (Thu Jun 24 2010 - 05:30:00 PDT)
- Re: [AMBER] Kinetic energy after heating is zero case (Thu Jun 24 2010 - 07:22:57 PDT)
  - Re: [AMBER] Kinetic energy after heating is zero Jason Swails (Thu Jun 24 2010 - 07:28:30 PDT)
[AMBER] inter_intra - energy balaji nagarajan (Thu Jun 24 2010 - 05:35:55 PDT)
[AMBER] RESP charge of heavy metal contained complex Jia Xu (Thu Jun 24 2010 - 08:37:00 PDT)
- Re: [AMBER] RESP charge of heavy metal contained complex FyD (Thu Jun 24 2010 - 22:25:19 PDT)
  - Re: [AMBER] [q4md-fft] Re: RESP charge of heavy metal contained complex Jia Xu (Sun Jun 27 2010 - 20:29:37 PDT)
    - [AMBER] reducing the fram for analysing Homa Azizian (Sun Jun 27 2010 - 23:40:27 PDT)
    - Re: [AMBER] reducing the fram for analysing Jason Swails (Mon Jun 28 2010 - 04:47:00 PDT)
    - Re: [AMBER] [q4md-fft] Re: RESP charge of heavy metal contained complex FyD (Tue Jun 29 2010 - 23:07:22 PDT)
    - Re: [AMBER] [q4md-fft] Re: RESP charge of heavy metal contained complex Jia Xu (Wed Jun 30 2010 - 08:48:32 PDT)
[AMBER] AmberTool 1.4 ptraj error Steve Seibold (Thu Jun 24 2010 - 08:58:44 PDT)
[AMBER] intra-inter energy balaji nagarajan (Thu Jun 24 2010 - 09:05:38 PDT)
[AMBER] AMBER11 and AmberTools1.4 errors Steve Seibold (Thu Jun 24 2010 - 10:18:46 PDT)
- Re: [AMBER] AMBER11 and AmberTools1.4 errors Jason Swails (Thu Jun 24 2010 - 10:30:00 PDT)
[AMBER] (no subject) Steve Seibold (Thu Jun 24 2010 - 11:14:19 PDT)
- Re: [AMBER] (no subject) Paul S. Nerenberg (Thu Jun 24 2010 - 11:33:37 PDT)
  - Re: [AMBER] (no subject) Paul S. Nerenberg (Thu Jun 24 2010 - 11:37:28 PDT)
[AMBER] (no subject) Steve Seibold (Thu Jun 24 2010 - 12:50:24 PDT)
[AMBER] MMPBSA.py NameError: global name 'diffstdev' is not defined Oliver Grant (Fri Jun 25 2010 - 01:58:14 PDT)
- Re: [AMBER] MMPBSA.py NameError: global name 'diffstdev' is not defined Oliver Grant (Fri Jun 25 2010 - 04:12:12 PDT)
  - Re: [AMBER] MMPBSA.py NameError: global name 'diffstdev' is not defined Jason Swails (Fri Jun 25 2010 - 06:45:12 PDT)
    - Re: [AMBER] MMPBSA.py NameError: global name 'diffstdev' is not defined Jason Swails (Fri Jun 25 2010 - 07:02:07 PDT)
[AMBER] Can't locate mm_pbsa_global.pm in .INC fancy2012 (Fri Jun 25 2010 - 02:05:37 PDT)
- Re: [AMBER] Can't locate mm_pbsa_global.pm in .INC Jason Swails (Fri Jun 25 2010 - 06:47:04 PDT)
  - Re: [AMBER] Can't locate mm_pbsa_global.pm in .INC fancy2012 (Fri Jun 25 2010 - 18:04:49 PDT)
[AMBER] Combine trajectory files error Steve Seibold (Fri Jun 25 2010 - 07:54:26 PDT)
- Re: [AMBER] Combine trajectory files error Daniel Roe (Thu Jul 08 2010 - 07:35:09 PDT)
  - Re: [AMBER] Combine trajectory files error Steve Seibold (Fri Jul 09 2010 - 05:32:45 PDT)
[AMBER] AMBER, shenna shearin has invited you to open a Google mail account shenna shearin (Fri Jun 25 2010 - 08:47:42 PDT)
[AMBER] cluster analysis shenna shearin (Fri Jun 25 2010 - 11:11:27 PDT)
[AMBER] mme and mme2 produce different energies Kevin Wiehe (Fri Jun 25 2010 - 11:36:50 PDT)
- Re: [AMBER] mme and mme2 produce different energies case (Tue Jun 29 2010 - 07:59:52 PDT)
[AMBER] Checksums? Marc Moreau (Fri Jun 25 2010 - 12:58:26 PDT)
- Re: [AMBER] Checksums? Ross Walker (Fri Jun 25 2010 - 15:34:46 PDT)
[AMBER] ptraj (AT 1.4) hiccups with gzipped trajectory files Paul S. Nerenberg (Fri Jun 25 2010 - 16:55:26 PDT)
- Re: [AMBER] ptraj (AT 1.4) hiccups with gzipped trajectory files Paul S. Nerenberg (Mon Jun 28 2010 - 14:35:01 PDT)
- Re: [AMBER] ptraj (AT 1.4) hiccups with gzipped trajectory files Daniel Roe (Wed Jun 30 2010 - 06:46:56 PDT)
- Re: [AMBER] ptraj (AT 1.4) hiccups with gzipped trajectory files Daniel Roe (Thu Jul 08 2010 - 12:42:13 PDT)
  - Re: [AMBER] ptraj (AT 1.4) hiccups with gzipped trajectory files Daniel Roe (Sun Jul 18 2010 - 06:37:47 PDT)
- Re: [AMBER] ptraj (AT 1.4) hiccups with gzipped trajectory files Kamali Sripathi (Sun Feb 06 2011 - 09:51:22 PST)
  - Re: [AMBER] ptraj (AT 1.4) hiccups with gzipped trajectory files Daniel Roe (Sun Feb 06 2011 - 11:37:46 PST)
    - Re: [AMBER] ptraj (AT 1.4) hiccups with gzipped trajectory files Kamali Sripathi (Fri Feb 11 2011 - 07:40:46 PST)
- Re: [AMBER] ptraj (AT 1.4) hiccups with gzipped trajectory files Kamali Sripathi (Sun May 08 2011 - 05:44:08 PDT)
  - Re: [AMBER] ptraj (AT 1.4) hiccups with gzipped trajectory files Jason Swails (Sun May 08 2011 - 05:56:47 PDT)
[AMBER] Segmentation fault Jagdeesh C (Sat Jun 26 2010 - 03:06:23 PDT)
- Re: [AMBER] Segmentation fault case (Sat Jun 26 2010 - 15:53:18 PDT)
  - Re: [AMBER] Segmentation fault Jagdeesh C (Sat Jun 26 2010 - 23:01:18 PDT)
    - Re: [AMBER] Segmentation fault case (Wed Jun 30 2010 - 09:31:54 PDT)
    - Re: [AMBER] Segmentation fault Jagdeesh C (Mon Jul 05 2010 - 20:10:11 PDT)
[AMBER] Constant protonation vs. constant pH simulation nicholus bhattacharjee (Sat Jun 26 2010 - 05:19:18 PDT)
- Re: [AMBER] Constant protonation vs. constant pH simulation Adrian Roitberg (Sat Jun 26 2010 - 05:24:17 PDT)
  - Re: [AMBER] Constant protonation vs. constant pH simulation nicholus bhattacharjee (Sat Jun 26 2010 - 05:50:51 PDT)
    - Re: [AMBER] Constant protonation vs. constant pH simulation Jason Swails (Sat Jun 26 2010 - 06:41:48 PDT)
[AMBER] ptraj.MPI in Ambertools1.4 : Compression is not currently supported for parallel ptraj M. Reza Ganjalikhany (Sun Jun 27 2010 - 02:52:28 PDT)
- Re: [AMBER] ptraj.MPI in Ambertools1.4 : Compression is not currently supported for parallel ptraj M. Reza Ganjalikhany (Sun Jun 27 2010 - 04:36:21 PDT)
- Re: [AMBER] ptraj.MPI in Ambertools1.4 : Compression is not currently supported for parallel ptraj Jason Swails (Sun Jun 27 2010 - 08:44:21 PDT)
  - Re: [AMBER] ptraj.MPI in Ambertools1.4 : Compression is not currently supported for parallel ptraj M. Reza Ganjalikhany (Sun Jun 27 2010 - 14:10:13 PDT)
    - Re: [AMBER] ptraj.MPI in Ambertools1.4 : Compression is not currently supported for parallel ptraj Daniel Roe (Wed Jun 30 2010 - 07:16:14 PDT)
[AMBER] mmpbsa installation rameshwar prajapati (Sun Jun 27 2010 - 04:53:48 PDT)
- Re: [AMBER] mmpbsa installation Jason Swails (Sun Jun 27 2010 - 07:55:59 PDT)
  - [AMBER] mmpbsa error of missing SVIB, when nm=0 Catein Catherine (Sun Jun 27 2010 - 08:56:07 PDT)
[AMBER] RMSD calculation per reside wise not rmse/time by ptraj REENU KHATTRI (Sun Jun 27 2010 - 06:55:50 PDT)
- Re: [AMBER] RMSD calculation per reside wise not rmse/time by ptraj Jason Swails (Sun Jun 27 2010 - 07:52:57 PDT)
[AMBER] is there any command to superimpose/align a protein in amber8 to get less RMSD residue wise REENU KHATTRI (Sun Jun 27 2010 - 18:40:24 PDT)
[AMBER] how to allign the protein with average pdb REENU KHATTRI (Sun Jun 27 2010 - 23:50:46 PDT)
- Re: [AMBER] how to allign the protein with average pdb Jason Swails (Mon Jun 28 2010 - 04:35:50 PDT)
[AMBER] inter- intra energy balaji nagarajan (Mon Jun 28 2010 - 01:01:02 PDT)
[AMBER] (no subject) Beale, John (Mon Jun 28 2010 - 04:54:02 PDT)
- Re: [AMBER] (no subject) Emmanuel Baribefe Naziga (Mon Jun 28 2010 - 08:26:32 PDT)
- Re: [AMBER] (no subject) Thomas Cheatham III (Tue Jun 29 2010 - 10:53:33 PDT)
[AMBER] Fwd: how to allign the protein with average pdb REENU KHATTRI (Mon Jun 28 2010 - 09:09:33 PDT)
- Re: [AMBER] Fwd: how to allign the protein with average pdb Jason Swails (Mon Jun 28 2010 - 17:04:53 PDT)
  - [AMBER] Fwd: Fwd: how to allign the protein with average pdb REENU KHATTRI (Tue Jun 29 2010 - 05:32:26 PDT)
Re: [AMBER] TUTORIAL A7 Replica Exchange Simulations with AMBER 10 Ross Walker (Mon Jun 28 2010 - 11:36:43 PDT)
[AMBER] solute ans solvation box Emmanuel Baribefe Naziga (Mon Jun 28 2010 - 13:40:49 PDT)
[AMBER] Errors in installing amber10 in cygwin (winxp) Yan Gao (Mon Jun 28 2010 - 15:53:56 PDT)
- Re: [AMBER] Errors in installing amber10 in cygwin (winxp) case (Mon Jun 28 2010 - 18:32:22 PDT)
[AMBER] How to insert a dimer into the pdb file Shi Choong (Mon Jun 28 2010 - 16:43:29 PDT)
[AMBER] regarding ptraj Asfa Ali (Mon Jun 28 2010 - 22:09:02 PDT)
- Re: [AMBER] regarding ptraj Gustavo Seabra (Tue Jun 29 2010 - 03:27:47 PDT)
- Re: [AMBER] regarding ptraj Bill Ross (Tue Jun 29 2010 - 09:41:52 PDT)
[AMBER] force field parameter and resp charge calculation colvin (Tue Jun 29 2010 - 04:03:30 PDT)
- Re: [AMBER] force field parameter and resp charge calculation FyD (Tue Jun 29 2010 - 09:27:08 PDT)
- Re: [AMBER] force field parameter and resp charge calculation FyD (Tue Jun 29 2010 - 23:21:14 PDT)
  - Re: [AMBER] force field parameter and resp charge calculation xueping chin (Tue Jun 29 2010 - 23:36:46 PDT)
    - Re: [AMBER] force field parameter and resp charge calculation FyD (Tue Jun 29 2010 - 23:57:41 PDT)
  - Re: [AMBER] force field parameter and resp charge calculation colvin (Tue Jun 29 2010 - 23:51:58 PDT)
    - Re: [AMBER] force field parameter and resp charge calculation FyD (Wed Jun 30 2010 - 00:15:50 PDT)
    - Re: [AMBER] force field parameter and resp charge calculation colvin (Wed Jun 30 2010 - 01:45:14 PDT)
    - Re: [AMBER] force field parameter and resp charge calculation FyD (Wed Jun 30 2010 - 02:27:02 PDT)
    - Re: [AMBER] force field parameter and resp charge calculation colvin (Wed Jun 30 2010 - 07:13:43 PDT)
    - Re: [AMBER] force field parameter and resp charge calculation FyD (Wed Jun 30 2010 - 07:58:33 PDT)
    - Re: [AMBER] force field parameter and resp charge calculation colvin (Thu Jul 01 2010 - 04:00:34 PDT)
[AMBER] make test.parallel Steve Seibold (Tue Jun 29 2010 - 07:14:34 PDT)
- Re: [AMBER] make test.parallel case (Tue Jun 29 2010 - 07:23:50 PDT)
  - Re: [AMBER] make test.parallel Steve Seibold (Wed Jun 30 2010 - 05:00:43 PDT)
    - Re: [AMBER] make test.parallel case (Thu Jul 01 2010 - 07:39:15 PDT)
[AMBER] similarity of quasi-harmonic modes dependent on reference conformation Jose Borreguero (Tue Jun 29 2010 - 19:34:52 PDT)
- Re: [AMBER] similarity of quasi-harmonic modes dependent on reference conformation Jason Swails (Tue Jun 29 2010 - 20:37:57 PDT)
  - Re: [AMBER] similarity of quasi-harmonic modes dependent on reference conformation Jose Borreguero (Wed Jun 30 2010 - 05:35:24 PDT)
[AMBER] Questions with input file in constant pH MD nicholus bhattacharjee (Tue Jun 29 2010 - 22:37:32 PDT)
- Re: [AMBER] Questions with input file in constant pH MD Bill Miller III (Wed Jun 30 2010 - 06:50:44 PDT)
  - Re: [AMBER] Questions with input file in constant pH MD nicholus bhattacharjee (Wed Jun 30 2010 - 23:53:26 PDT)
    - Re: [AMBER] Questions with input file in constant pH MD Bill Miller III (Thu Jul 01 2010 - 06:28:50 PDT)
[AMBER] mmgbsa tricky output Amor San Juan (Wed Jun 30 2010 - 02:19:53 PDT)
- Re: [AMBER] mmgbsa tricky output Amor San Juan (Thu Jul 01 2010 - 00:39:51 PDT)
  - Re: [AMBER] mmgbsa tricky output Ray Luo (Thu Jul 01 2010 - 15:46:37 PDT)
    - Re: [AMBER] mmgbsa tricky output Amor San Juan (Sun Jul 04 2010 - 20:49:01 PDT)
    - Re: [AMBER] mmgbsa tricky output Amor San Juan (Sun Jul 04 2010 - 23:22:13 PDT)
    - Re: [AMBER] mmgbsa tricky output: PART 2 Amor San Juan (Mon Jul 05 2010 - 23:48:35 PDT)
    - Re: [AMBER] mmgbsa tricky output: PART 2 Jason Swails (Tue Jul 06 2010 - 06:00:59 PDT)
    - Re: [AMBER] mmgbsa tricky output: PART 2 Amor San Juan (Wed Jul 07 2010 - 03:03:10 PDT)
    - [AMBER] mmgbsa for ternary system Amor San Juan (Wed Jul 07 2010 - 03:42:50 PDT)
    - Re: [AMBER] mmgbsa for ternary system Jason Swails (Wed Jul 07 2010 - 07:15:08 PDT)
    - Re: [AMBER] mmgbsa for ternary system Amor San Juan (Thu Jul 08 2010 - 03:23:16 PDT)
    - [AMBER] MMPBSA.PY with two parts receptor Amor San Juan (Tue Jul 13 2010 - 22:48:57 PDT)
    - Re: [AMBER] MMPBSA.PY with two parts receptor Bill Miller III (Wed Jul 14 2010 - 03:21:48 PDT)
    - Re: [AMBER] MMPBSA.PY with two parts receptor Amor San Juan (Mon Jul 19 2010 - 01:05:43 PDT)
    - Re: [AMBER] MMPBSA.PY with two parts receptor Jason Swails (Mon Jul 19 2010 - 07:57:29 PDT)
    - [AMBER] Segmentation fault in MMPBSA.PY with two parts receptor Amor San Juan (Tue Jul 20 2010 - 03:16:57 PDT)
    - Re: [AMBER] Segmentation fault in MMPBSA.PY with two parts receptor Oliver Grant (Tue Jul 20 2010 - 03:30:45 PDT)
    - [AMBER] Thank you Jason, Bill and Oliver Amor San Juan (Wed Jul 21 2010 - 00:12:51 PDT)
    - Re: [AMBER] mmgbsa tricky output: PART 2 Jason Swails (Wed Jul 07 2010 - 07:04:56 PDT)
    - [AMBER] MMPBSA.py source files Amor San Juan (Fri Jul 09 2010 - 01:36:35 PDT)
    - [AMBER] What is the way to change from MMPBSA+GBSA to MMGBSA only input file. Catein Catherine (Fri Jul 09 2010 - 03:50:40 PDT)
    - Re: [AMBER] What is the way to change from MMPBSA+GBSA to MMGBSA only input file. Oliver Grant (Fri Jul 09 2010 - 03:57:02 PDT)
    - [AMBER] How to find the angle bond etc parameters used for practicular atom type used in AMBER? Catein Catherine (Fri Jul 09 2010 - 04:23:22 PDT)
    - Re: [AMBER] How to find the angle bond etc parameters used for practicular atom type used in AMBER? James Maier (Fri Jul 09 2010 - 07:21:55 PDT)
    - Re: [AMBER] How to find the angle bond etc parameters used for practicular atom type used in AMBER? Catein Catherine (Fri Jul 09 2010 - 08:11:58 PDT)
    - [AMBER] Do I have to keep the Na+ counterions in prmtop and snapshot generation when I do mmGBSA/PBSA calculation? Catein Catherine (Fri Jul 09 2010 - 04:14:24 PDT)
    - Re: [AMBER] Do I have to keep the Na+ counterions in prmtop and snapshot generation when I do mmGBSA/PBSA calculation? Oliver Grant (Fri Jul 09 2010 - 04:24:38 PDT)
    - Re: [AMBER] Do I have to keep the Na+ counterions in prmtop and snapshot generation when I do mmGBSA/PBSA calculation? Mahmoud A. A. Ibrahim (Fri Jul 09 2010 - 04:29:37 PDT)
    - Re: [AMBER] Do I have to keep the Na+ counterions in prmtop and snapshot generation when I do mmGBSA/PBSA calculation? Oliver Grant (Fri Jul 09 2010 - 04:42:32 PDT)
    - Re: [AMBER] MMPBSA.py source files case (Fri Jul 09 2010 - 05:26:43 PDT)
    - Re: [AMBER] mmgbsa tricky output Mannan (Wed Jul 07 2010 - 20:08:01 PDT)
- Re: [AMBER] mmgbsa tricky output Bill Ross (Thu Jul 01 2010 - 10:09:39 PDT)
[AMBER] regarding mmpbsa Asfa Ali (Wed Jun 30 2010 - 03:47:49 PDT)
- Re: [AMBER] regarding mmpbsa Bill Miller III (Wed Jun 30 2010 - 06:10:00 PDT)
  - Re: [AMBER] regarding mmpbsa Jason Swails (Wed Jun 30 2010 - 07:28:06 PDT)
    - Re: [AMBER] regarding mmpbsa Asfa Ali (Wed Jun 30 2010 - 07:40:44 PDT)
    - Re: [AMBER] regarding mmpbsa Jason Swails (Wed Jun 30 2010 - 08:07:12 PDT)
    - Re: [AMBER] regarding mmpbsa Asfa Ali (Wed Jun 30 2010 - 22:01:45 PDT)
    - Re: [AMBER] regarding mmpbsa Dwight McGee (Thu Jul 01 2010 - 07:09:20 PDT)
[AMBER] Adding Ions. Ajay Ummat (Wed Jun 30 2010 - 11:05:25 PDT)
- Re: [AMBER] Adding Ions. case (Wed Jun 30 2010 - 11:15:56 PDT)
  - Re: [AMBER] Adding Ions. Ajay Ummat (Fri Jul 02 2010 - 07:45:03 PDT)
    - Re: [AMBER] Adding Ions. Jason Swails (Fri Jul 02 2010 - 09:00:47 PDT)
    - [AMBER] MMPBSA.py install error Catein Catherine (Sat Jul 03 2010 - 04:38:33 PDT)
    - Re: [AMBER] MMPBSA.py install error Jason Swails (Sat Jul 03 2010 - 07:44:41 PDT)
    - [AMBER] How do define phospho-tyrosine-DA linkage? Catein Catherine (Sat Jul 03 2010 - 10:38:41 PDT)
    - [AMBER] Amber web page is slow David A. Case (Sat Jul 03 2010 - 11:00:13 PDT)
    - [AMBER] Question about xleap: How to define a linkage between DNA and phosphotyrosine. Catein Catherine (Sun Jul 04 2010 - 01:06:27 PDT)
    - Re: [AMBER] Question about xleap: How to define a linkage between DNA and phosphotyrosine. FyD (Sun Jul 04 2010 - 23:44:44 PDT)
    - Re: [AMBER] Question about xleap: How to define a linkage between DNA and phosphotyrosine. Catein Catherine (Mon Jul 05 2010 - 02:39:58 PDT)
    - [AMBER] Should I define drug intercalation site of a DNA as internal (DT/DA) or terminal (DT3/DA5) unit ? Catein Catherine (Mon Jul 05 2010 - 02:59:23 PDT)
    - Re: [AMBER] Should I define drug intercalation site of a DNA as internal (DT/DA) or terminal (DT3/DA5) unit ? ros (Mon Jul 05 2010 - 06:27:01 PDT)
    - Re: [AMBER] Should I define drug intercalation site of a DNA as internal (DT/DA) or terminal (DT3/DA5) unit ? Jason Swails (Mon Jul 05 2010 - 07:15:51 PDT)
    - Re: [AMBER] Question about xleap: How to define a linkage between DNA and phosphotyrosine. FyD (Mon Jul 05 2010 - 23:32:17 PDT)
    - [AMBER] What is the command to add two tails for a new residue in xleap? Catein Catherine (Mon Jul 05 2010 - 02:42:36 PDT)
    - Re: [AMBER] What is the command to add two tails for a new residue in xleap? Bill Ross (Mon Jul 05 2010 - 13:38:53 PDT)
    - Re: [AMBER] How do define phospho-tyrosine-DA linkage? Bill Ross (Sat Jul 03 2010 - 11:02:46 PDT)
- Re: [AMBER] Adding Ions. Bill Ross (Wed Jun 30 2010 - 11:19:37 PDT)
- Re: [AMBER] Adding Ions. Hugh Heldenbrand (Wed Jun 30 2010 - 11:27:04 PDT)
- Re: [AMBER] Adding Ions. Dean Cuebas (Wed Jun 30 2010 - 21:29:39 PDT)
[AMBER] vlimit exceeded for step Le, Shu-Yun (NIH/NCI) [E] (Wed Jun 30 2010 - 13:58:57 PDT)
- Re: [AMBER] vlimit exceeded for step Jason Swails (Wed Jun 30 2010 - 16:29:39 PDT)
- Re: [AMBER] vlimit exceeded for step case (Thu Jul 01 2010 - 05:03:09 PDT)
[AMBER] Any way to apply different dt(time/step) to different steps Yiyu Li (Wed Jun 30 2010 - 19:25:08 PDT)
- Re: [AMBER] Any way to apply different dt(time/step) to different steps Daniel Roe (Wed Jun 30 2010 - 20:33:16 PDT)
[AMBER] adding counterions Ping (Wed Jun 30 2010 - 19:58:34 PDT)
- Re: [AMBER] adding counterions Jason Swails (Wed Jun 30 2010 - 22:49:33 PDT)
- Re: [AMBER] adding counterions Bill Ross (Thu Jul 01 2010 - 10:40:27 PDT)
- Re: [AMBER] adding counterions Ping (Thu Jul 01 2010 - 11:12:24 PDT)
- Re: [AMBER] adding counterions Bill Ross (Thu Jul 01 2010 - 11:19:58 PDT)
  - Re: [AMBER] adding counterions Ping (Thu Jul 01 2010 - 11:37:47 PDT)
    - Re: [AMBER] adding counterions Paul S. Nerenberg (Thu Jul 01 2010 - 11:39:44 PDT)
- Re: [AMBER] adding counterions Bill Ross (Thu Jul 01 2010 - 11:41:40 PDT)
[AMBER] AmberTools installation in Cygwin Yan Gao (Wed Jun 30 2010 - 20:12:03 PDT)
- Re: [AMBER] AmberTools installation in Cygwin Jason Swails (Wed Jun 30 2010 - 22:59:45 PDT)
  - Re: [AMBER] AmberTools installation in Cygwin Yan Gao (Thu Jul 01 2010 - 10:22:02 PDT)
  - Re: [AMBER] AmberTools installation in Cygwin Yan Gao (Thu Jul 01 2010 - 11:52:51 PDT)
    - Re: [AMBER] AmberTools installation in Cygwin case (Thu Jul 01 2010 - 13:21:21 PDT)
    - Re: [AMBER] AmberTools installation in Cygwin Yan Gao (Thu Jul 01 2010 - 14:11:33 PDT)
[AMBER] ld: duplicate symbol _gauss in ../lib/sys.a(random.o) and rand2.o Yu Chen (Wed Jun 30 2010 - 20:19:27 PDT)
- Re: [AMBER] ld: duplicate symbol _gauss in ../lib/sys.a(random.o) and rand2.o case (Thu Jul 01 2010 - 05:58:33 PDT)
  - Re: [AMBER] ld: duplicate symbol _gauss in ../lib/sys.a(random.o) and rand2.o Yu Chen (Thu Jul 01 2010 - 06:58:33 PDT)
    - Re: [AMBER] ld: duplicate symbol _gauss in ../lib/sys.a(random.o) and rand2.o case (Thu Jul 01 2010 - 07:52:30 PDT)
    - Re: [AMBER] ld: duplicate symbol _gauss in ../lib/sys.a(random.o) and rand2.o Jason Swails (Thu Jul 01 2010 - 08:00:16 PDT)
    - Re: [AMBER] ld: duplicate symbol _gauss in ../lib/sys.a(random.o) and rand2.o Yu Chen (Thu Jul 01 2010 - 08:24:09 PDT)
    - Re: [AMBER] ld: duplicate symbol _gauss in ../lib/sys.a(random.o) and rand2.o Yu Chen (Thu Jul 01 2010 - 08:37:46 PDT)
    - Re: [AMBER] ld: duplicate symbol _gauss in ../lib/sys.a(random.o) and rand2.o case (Thu Jul 01 2010 - 09:52:11 PDT)
    - Re: [AMBER] ld: duplicate symbol _gauss in ../lib/sys.a(random.o) and rand2.o Yu Chen (Thu Jul 01 2010 - 14:16:04 PDT)
    - Re: [AMBER] ld: duplicate symbol _gauss in ../lib/sys.a(random.o) and rand2.o case (Thu Jul 01 2010 - 14:58:56 PDT)
    - Re: [AMBER] ld: duplicate symbol _gauss in ../lib/sys.a(random.o) and rand2.o Jason Swails (Thu Jul 01 2010 - 20:55:20 PDT)
    - Re: [AMBER] ld: duplicate symbol _gauss in ../lib/sys.a(random.o) and rand2.o Yu Chen (Fri Jul 02 2010 - 06:50:24 PDT)
    - Re: [AMBER] ld: duplicate symbol _gauss in ../lib/sys.a(random.o) and rand2.o Jason Swails (Fri Jul 02 2010 - 07:19:51 PDT)
    - Re: [AMBER] ld: duplicate symbol _gauss in ../lib/sys.a(random.o) and rand2.o Yu Chen (Fri Jul 02 2010 - 06:31:44 PDT)
[AMBER] maintaining temperature scheme missing_grace.sina.com (Wed Jun 30 2010 - 21:05:21 PDT)
- Re: [AMBER] maintaining temperature scheme Jason Swails (Wed Jun 30 2010 - 23:11:16 PDT)
[AMBER] File MAKE_CRD is not found fancy2012 (Wed Jun 30 2010 - 23:59:21 PDT)
- Re: [AMBER] File MAKE_CRD is not found Jason Swails (Thu Jul 01 2010 - 06:41:31 PDT)
[AMBER] Regarding Antechamber Tutorial sonali dhindwal (Thu Jul 01 2010 - 00:23:09 PDT)
- Re: [AMBER] Regarding Antechamber Tutorial vaibhav dixit (Thu Jul 01 2010 - 00:49:30 PDT)
  - Re: [AMBER] Regarding Antechamber Tutorial sonali dhindwal (Thu Jul 01 2010 - 01:43:05 PDT)
- Re: [AMBER] Regarding Antechamber Tutorial case (Thu Jul 01 2010 - 05:17:09 PDT)
[AMBER] hydrogen bond printout Beale, John (Thu Jul 01 2010 - 04:29:14 PDT)
[AMBER] results calculated by mmpbsa.pl and mmpbsa.py lidansa.mail.ustc.edu.cn (Thu Jul 01 2010 - 07:18:09 PDT)
- Re: [AMBER] results calculated by mmpbsa.pl and mmpbsa.py Jason Swails (Thu Jul 01 2010 - 07:55:50 PDT)
[AMBER] 3D-RISM in NAB AmberTools: what is tolerance and initial guess Andrey Frolov (Thu Jul 01 2010 - 09:09:51 PDT)
- Re: [AMBER] 3D-RISM in NAB AmberTools: what is tolerance and initial guess Tyler Luchko (Fri Jul 02 2010 - 06:39:18 PDT)
[AMBER] 3D-RISM in NAB AmberTools: 2) what is tolerance Andrey Frolov (Thu Jul 01 2010 - 09:16:38 PDT)
- Re: [AMBER] 3D-RISM in NAB AmberTools: 2) what is tolerance Tyler Luchko (Fri Jul 02 2010 - 07:08:41 PDT)
Re: [AMBER] AmberTools installation in Cygwin --- thanks and new errors Yan Gao (Thu Jul 01 2010 - 11:53:34 PDT)
[AMBER] Conformation capture in molecular dynamics Yuqin Cai (Thu Jul 01 2010 - 18:46:01 PDT)
- [AMBER] create a prmtop file without water & ions, Homa Azizian (Thu Jul 01 2010 - 20:13:52 PDT)
  - Re: [AMBER] create a prmtop file without water & ions, Jason Swails (Thu Jul 01 2010 - 22:46:17 PDT)
[AMBER] About the ptraj problem c00jsw00 (Thu Jul 01 2010 - 22:12:40 PDT)
- Re: [AMBER] About the ptraj problem Jason Swails (Thu Jul 01 2010 - 22:48:06 PDT)
  - Re: [AMBER] About the ptraj problem c00jsw00 (Fri Jul 02 2010 - 00:13:34 PDT)
    - Re: [AMBER] About the ptraj problem Jason Swails (Fri Jul 02 2010 - 07:24:59 PDT)
- Re: [AMBER] About the ptraj problem Bill Ross (Fri Jul 02 2010 - 10:18:41 PDT)
[AMBER] WARNING: Local coordinate 1 differs from partner coordinate 1 ! sunita gupta (Fri Jul 02 2010 - 00:43:25 PDT)
- Re: [AMBER] WARNING: Local coordinate 1 differs from partner coordinate 1 ! steinbrt.rci.rutgers.edu (Fri Jul 02 2010 - 01:33:19 PDT)
  - Re: [AMBER] WARNING: Local coordinate 1 differs from partner coordinate 1 ! sunita gupta (Fri Jul 02 2010 - 02:01:51 PDT)
    - [AMBER] Any parameters for Mg2+? Catein Catherine (Fri Jul 02 2010 - 02:30:24 PDT)
    - [AMBER] What ab initio methods can be choose for QM/MM package in AMBER10? Catein Catherine (Fri Jul 02 2010 - 02:34:31 PDT)
    - Re: [AMBER] What ab initio methods can be choose for QM/MM package in AMBER10? Gustavo Seabra (Fri Jul 02 2010 - 03:40:03 PDT)
    - Re: [AMBER] Any parameters for Mg2+? Jason Swails (Fri Jul 02 2010 - 07:28:41 PDT)
    - Re: [AMBER] WARNING: Local coordinate 1 differs from partner coordinate 1 ! steinbrt.rci.rutgers.edu (Fri Jul 02 2010 - 03:43:09 PDT)
    - Re: [AMBER] WARNING: Local coordinate 1 differs from partner coordinate 1 ! sunita gupta (Thu Jul 08 2010 - 01:10:27 PDT)
    - Re: [AMBER] WARNING: Local coordinate 1 differs from partner coordinate 1 ! steinbrt.rci.rutgers.edu (Thu Jul 08 2010 - 01:49:49 PDT)
    - Re: [AMBER] WARNING: Local coordinate 1 differs from partner coordinate 1 ! sunita gupta (Fri Jul 09 2010 - 05:11:40 PDT)
    - Re: [AMBER] WARNING: Local coordinate 1 differs from partner coordinate 1 ! case (Fri Jul 09 2010 - 05:36:01 PDT)
    - Re: [AMBER] WARNING: Local coordinate 1 differs from partner coordinate 1 ! steinbrt.rci.rutgers.edu (Fri Jul 09 2010 - 05:43:47 PDT)
[AMBER] Solvation in water Hoshin Kim (Thu Jul 01 2010 - 19:39:42 PDT)
- Re: [AMBER] Solvation in water Jason Swails (Fri Jul 02 2010 - 08:57:37 PDT)
[AMBER] nmode problem with mm_pbsa.pl RANAJIT SHINDE (Fri Jul 02 2010 - 11:51:12 PDT)
[AMBER] Checking multiple production run nicholus bhattacharjee (Sat Jul 03 2010 - 01:41:11 PDT)
- Re: [AMBER] Checking multiple production run Jason Swails (Sat Jul 03 2010 - 04:22:04 PDT)
- Re: [AMBER] Checking multiple production run Gustavo Seabra (Sat Jul 03 2010 - 06:18:11 PDT)
[AMBER] PMEMD installation error M. Reza Ganjalikhany (Sat Jul 03 2010 - 01:51:14 PDT)
- Re: [AMBER] PMEMD installation error M. Reza Ganjalikhany (Sun Jul 04 2010 - 01:26:14 PDT)
[AMBER] simulations in urea monica.imtech.res.in (Sat Jul 03 2010 - 05:14:38 PDT)
- Re: [AMBER] simulations in urea Bill Ross (Sat Jul 03 2010 - 10:58:38 PDT)
[AMBER] h bond analysis REENU KHATTRI (Sat Jul 03 2010 - 20:45:25 PDT)
[AMBER] WARNING: Local coordinate 382 differs from partner coordinate 382 ! kirsten (Sun Jul 04 2010 - 05:07:08 PDT)
- Re: [AMBER] WARNING: Local coordinate 382 differs from partner coordinate 382 ! steinbrt.rci.rutgers.edu (Sun Jul 04 2010 - 07:53:00 PDT)
[AMBER] RESP charges outside Gaussian Francesco Pietra (Sun Jul 04 2010 - 08:13:20 PDT)
- Re: [AMBER] RESP charges outside Gaussian Jason Swails (Sun Jul 04 2010 - 09:01:22 PDT)
  - Re: [AMBER] RESP charges outside Gaussian FyD (Sun Jul 04 2010 - 09:11:41 PDT)
[AMBER] Steered MD calc eduardo.troche.uvigo.es (Sun Jul 04 2010 - 09:24:55 PDT)
- Re: [AMBER] Steered MD calc Jason Swails (Sun Jul 04 2010 - 16:16:27 PDT)
- Re: [AMBER] Steered MD calc Adrian Roitberg (Sun Jul 04 2010 - 20:12:49 PDT)
[AMBER] No potential terms in sander output! Check out put files - MMPBSA.py.MPI kamlesh sahu (Sun Jul 04 2010 - 18:56:21 PDT)
- Re: [AMBER] No potential terms in sander output! Check out put files - MMPBSA.py.MPI Jason Swails (Sun Jul 04 2010 - 20:04:45 PDT)
  - Re: [AMBER] No potential terms in sander output! Check out put files - MMPBSA.py.MPI kamlesh sahu (Sun Jul 04 2010 - 23:08:08 PDT)
[AMBER] Problems using library file containing multiple residues to make a complex Chris Whittleston (Mon Jul 05 2010 - 08:57:13 PDT)
- Re: [AMBER] Problems using library file containing multiple residues to make a complex Daniel Roe (Mon Jul 05 2010 - 10:53:57 PDT)
  - Re: [AMBER] Problems using library file containing multiple residues to make a complex Chris Whittleston (Tue Jul 06 2010 - 02:05:30 PDT)
    - Re: [AMBER] Problems using library file containing multiple residues to make a complex Daniel Roe (Tue Jul 06 2010 - 05:54:28 PDT)
[AMBER] AMBER purchase ros (Mon Jul 05 2010 - 10:40:07 PDT)
[AMBER] step 0 of minimization ? balaji nagarajan (Mon Jul 05 2010 - 12:28:06 PDT)
- Re: [AMBER] step 0 of minimization ? James Maier (Mon Jul 05 2010 - 17:55:37 PDT)
[AMBER] H3O+ force field file 강지영 (Mon Jul 05 2010 - 17:52:17 PDT)
[AMBER] error massage in constant pH simulation nicholus bhattacharjee (Tue Jul 06 2010 - 02:16:35 PDT)
- Re: [AMBER] error massage in constant pH simulation Jason Swails (Tue Jul 06 2010 - 05:53:07 PDT)
[AMBER] License sonali dhindwal (Tue Jul 06 2010 - 07:01:38 PDT)
- Re: [AMBER] License Ross Walker (Tue Jul 06 2010 - 08:06:26 PDT)
  - Re: [AMBER] License sonali dhindwal (Tue Jul 06 2010 - 09:37:24 PDT)
[AMBER] Restrain with PMEMD Giovanni Doni (Tue Jul 06 2010 - 09:08:18 PDT)
- Re: [AMBER] Restrain with PMEMD Ross Walker (Tue Jul 06 2010 - 09:19:30 PDT)
[AMBER] segmentation fault David A. Case (Tue Jul 06 2010 - 10:37:32 PDT)
- Re: [AMBER] segmentation fault Jagdeesh C (Thu Jul 22 2010 - 02:51:15 PDT)
  - Re: [AMBER] segmentation fault case (Thu Jul 22 2010 - 06:53:22 PDT)
[AMBER] dyld: lazy symbol binding failed: Symbol not found: _iconv_open Yu Chen (Tue Jul 06 2010 - 11:17:51 PDT)
- Re: [AMBER] dyld: lazy symbol binding failed: Symbol not found: _iconv_open Yu Chen (Tue Jul 06 2010 - 13:26:42 PDT)
[AMBER] Release of the R.E.D.-III.4 tools FyD (Wed Jul 07 2010 - 00:04:36 PDT)
[AMBER] TI calculation using softcore potentials. simultaneous density and temperature equilibration g t (Wed Jul 07 2010 - 11:07:33 PDT)
- Re: [AMBER] TI calculation using softcore potentials. simultaneous density and temperature equilibration steinbrt.rci.rutgers.edu (Thu Jul 08 2010 - 01:53:53 PDT)
  - Re: [AMBER] TI calculation using softcore potentials. simultaneous density and temperature equilibration g t (Thu Jul 08 2010 - 03:07:58 PDT)
- Re: [AMBER] TI calculation using softcore potentials. simultaneous density and temperature equilibration 冉挺 (Fri Jul 09 2010 - 19:52:33 PDT)
- Re: [AMBER] TI calculation using softcore potentials. simultaneous density and temperature equilibration Bill Ross (Fri Jul 09 2010 - 22:22:01 PDT)
- Re: [AMBER] TI calculation using softcore potentials. simultaneous density and temperature equilibration Bill Ross (Fri Jul 09 2010 - 22:58:16 PDT)
[AMBER] rfree: Error decoding variable 2 2 Vaibhav Jain (Wed Jul 07 2010 - 11:43:28 PDT)
- Re: [AMBER] rfree: Error decoding variable 2 2 David A. Case (Wed Jul 07 2010 - 14:06:13 PDT)
  - [AMBER] rms command Homa Azizian (Wed Jul 07 2010 - 21:57:40 PDT)
    - Re: [AMBER] rms command Jason Swails (Thu Jul 08 2010 - 04:18:46 PDT)
    - Re: [AMBER] rms command Daniel Roe (Thu Jul 08 2010 - 04:48:03 PDT)
[AMBER] problem with 2d-rmsd based clustering moitrayee.mbu.iisc.ernet.in (Wed Jul 07 2010 - 12:37:06 PDT)
[AMBER] compile ambertools on mac Jorgen Simonsen (Wed Jul 07 2010 - 16:21:28 PDT)
- Re: [AMBER] compile ambertools on mac Jason Swails (Wed Jul 07 2010 - 17:58:22 PDT)
  - [AMBER] analysising trajectory Homa Azizian (Wed Jul 07 2010 - 19:05:30 PDT)
  - Re: [AMBER] compile ambertools on mac Jorgen Simonsen (Thu Jul 08 2010 - 03:42:16 PDT)
    - Re: [AMBER] compile ambertools on mac Jason Swails (Thu Jul 08 2010 - 04:14:26 PDT)
    - Re: [AMBER] compile ambertools on mac Jorgen Simonsen (Thu Jul 08 2010 - 05:41:04 PDT)
    - Re: [AMBER] compile ambertools on mac Jason Swails (Thu Jul 08 2010 - 05:52:07 PDT)
    - Re: [AMBER] compile ambertools on mac Jorgen Simonsen (Sun Jul 11 2010 - 13:56:46 PDT)
    - Re: [AMBER] compile ambertools on mac case (Mon Jul 12 2010 - 05:31:18 PDT)
    - Re: [AMBER] compile ambertools on mac Jorgen Simonsen (Mon Jul 12 2010 - 05:57:58 PDT)
    - Re: [AMBER] compile ambertools on mac case (Mon Jul 12 2010 - 06:08:02 PDT)
    - Re: [AMBER] compile ambertools on mac Jorgen Simonsen (Mon Jul 12 2010 - 13:50:13 PDT)
    - Re: [AMBER] compile ambertools on mac Jason Swails (Mon Jul 12 2010 - 14:03:17 PDT)
    - Re: [AMBER] compile ambertools on mac Jorgen Simonsen (Mon Jul 12 2010 - 14:34:39 PDT)
    - Re: [AMBER] compile ambertools on mac case (Tue Jul 13 2010 - 05:05:04 PDT)
    - Re: [AMBER] compile ambertools on mac Jorgen Simonsen (Tue Jul 13 2010 - 05:22:49 PDT)
    - Re: [AMBER] compile ambertools on mac case (Tue Jul 13 2010 - 05:47:51 PDT)
    - Re: [AMBER] compile ambertools on mac Mengjuei Hsieh (Tue Jul 13 2010 - 11:55:05 PDT)
    - Re: [AMBER] compile ambertools on mac Mengjuei Hsieh (Thu Jul 15 2010 - 11:22:33 PDT)
    - Re: [AMBER] compile ambertools on mac Mengjuei Hsieh (Thu Jul 15 2010 - 16:11:19 PDT)
    - Re: [AMBER] compile ambertools on mac Mengjuei Hsieh (Sun Jul 25 2010 - 04:54:38 PDT)
    - Re: [AMBER] compile ambertools on mac case (Mon Jul 26 2010 - 07:06:27 PDT)
    - Re: [AMBER] compile ambertools on mac Adelene Sim (Mon Jul 26 2010 - 09:37:11 PDT)
    - Re: [AMBER] compile ambertools on mac Paul S. Nerenberg (Mon Jul 26 2010 - 09:57:57 PDT)
    - Re: [AMBER] compile ambertools on mac Mengjuei Hsieh (Mon Jul 26 2010 - 14:32:53 PDT)
    - Re: [AMBER] compile ambertools on mac Mengjuei Hsieh (Mon Jul 26 2010 - 14:17:09 PDT)
[AMBER] Is It Possible to Prevent Center-of-Mass Rotation During MD? Logan Ahlstrom (Wed Jul 07 2010 - 19:41:47 PDT)
- Re: [AMBER] Is It Possible to Prevent Center-of-Mass Rotation During MD? Jason Swails (Wed Jul 07 2010 - 21:15:03 PDT)
  - Re: [AMBER] Is It Possible to Prevent Center-of-Mass Rotation During MD? Gustavo Seabra (Thu Jul 08 2010 - 05:30:31 PDT)
[AMBER] 1D-RISM in AmberTools: atom order in output, a bug? Andrey Frolov (Thu Jul 08 2010 - 08:04:06 PDT)
- Re: [AMBER] 1D-RISM in AmberTools: atom order in output, a bug? Tyler Luchko (Fri Jul 09 2010 - 08:06:30 PDT)
[AMBER] 1D-RISM in AmberTools: the reference for ion parameters and LJ parameters Andrey Frolov (Thu Jul 08 2010 - 08:23:55 PDT)
- Re: [AMBER] 1D-RISM in AmberTools: the reference for ion parameters and LJ parameters Tyler Luchko (Fri Jul 09 2010 - 08:21:27 PDT)
  - [AMBER] Missing BELE for MM in 1 ( residue 1) Catein Catherine (Fri Jul 09 2010 - 08:48:47 PDT)
[AMBER] Converting topology information from Gromacs to Amber for carbon nanotubes Yan Gao (Thu Jul 08 2010 - 10:20:35 PDT)
- [AMBER] Converting topology information from Gromacs to Amber for carbon nanotubes Yan Gao (Thu Jul 08 2010 - 10:21:21 PDT)
- [AMBER] Converting topology information from Gromacs to Amber for carbon nanotubes Yan Gao (Thu Jul 08 2010 - 13:57:34 PDT)
  - Re: [AMBER] Converting topology information from Gromacs to Amber for carbon nanotubes Bill Ross (Thu Jul 08 2010 - 14:28:25 PDT)
[AMBER] OpenMP programs Marc Moreau (Thu Jul 08 2010 - 10:46:21 PDT)
- Re: [AMBER] OpenMP programs Ross Walker (Thu Jul 08 2010 - 12:23:04 PDT)
- Re: [AMBER] OpenMP programs David A. Case (Thu Jul 08 2010 - 13:14:21 PDT)
  - Re: [AMBER] OpenMP programs Marc Moreau (Thu Jul 08 2010 - 14:10:49 PDT)
Re: [AMBER] Converting topology information from Gromacs to Amber for carbon nanotubes -- thanks and more questions Yan Gao (Thu Jul 08 2010 - 16:26:55 PDT)
- Re: [AMBER] Converting topology information from Gromacs to Amber for carbon nanotubes -- thanks and more questions Bill Ross (Thu Jul 08 2010 - 16:46:29 PDT)
  - Re: [AMBER] Converting topology information from Gromacs to Amber for carbon nanotubes -- thanks and more questions Yan Gao (Thu Jul 08 2010 - 21:41:23 PDT)
- Re: [AMBER] Converting topology information from Gromacs to Amber for carbon nanotubes -- thanks and more questions Jason Swails (Thu Jul 08 2010 - 20:26:08 PDT)
  - Re: [AMBER] Converting topology information from Gromacs to Amber for carbon nanotubes -- thanks and more questions Yan Gao (Thu Jul 08 2010 - 21:51:24 PDT)
    - Re: [AMBER] Converting topology information from Gromacs to Amber for carbon nanotubes -- thanks and more questions Gustavo Seabra (Fri Jul 09 2010 - 03:50:06 PDT)
    - Re: [AMBER] Converting topology information from Gromacs to Amber for carbon nanotubes -- thanks and more questions Yan Gao (Fri Jul 09 2010 - 06:45:41 PDT)
    - Re: [AMBER] Converting topology information from Gromacs to Amber for carbon nanotubes -- thanks and more questions Jason Swails (Fri Jul 09 2010 - 08:09:00 PDT)
    - Re: [AMBER] Converting topology information from Gromacs to Amber for carbon nanotubes -- thanks and more questions Yan Gao (Fri Jul 09 2010 - 08:57:00 PDT)
[AMBER] counterions placings Jio M (Thu Jul 08 2010 - 23:46:48 PDT)
- [AMBER] MMPBSA using counterions Giorgos Lamprinidis (Fri Jul 09 2010 - 00:08:33 PDT)
  - Re: [AMBER] MMPBSA using counterions Jason Swails (Fri Jul 09 2010 - 07:44:04 PDT)
    - [AMBER] Are there any GPU clusters that offer compute time? Sasha Buzko (Fri Jul 09 2010 - 17:09:52 PDT)
    - Re: [AMBER] Are there any GPU clusters that offer compute time? Carlos Simmerling (Fri Jul 09 2010 - 17:30:41 PDT)
    - Re: [AMBER] Are there any GPU clusters that offer compute time? Sasha Buzko (Fri Jul 09 2010 - 17:33:49 PDT)
    - Re: [AMBER] Are there any GPU clusters that offer compute time? Ross Walker (Fri Jul 09 2010 - 19:08:40 PDT)
    - [AMBER] The system size limitations for Tesla C2050 ? Marek Maly (Mon Jul 12 2010 - 01:37:43 PDT)
    - Re: [AMBER] The system size limitations for Tesla C2050 ? Dairsie Latimer (Mon Jul 12 2010 - 02:04:12 PDT)
    - Re: [AMBER] The system size limitations for Tesla C2050 ? Marek Maly (Mon Jul 12 2010 - 06:59:10 PDT)
    - Re: [AMBER] The system size limitations for Tesla C2050 ? Scott Le Grand (Mon Jul 12 2010 - 09:13:05 PDT)
    - Re: [AMBER] The system size limitations for Tesla C2050 ? Marek Maly (Mon Jul 12 2010 - 09:49:55 PDT)
    - Re: [AMBER] The system size limitations for Tesla C2050 ? Scott Le Grand (Mon Jul 12 2010 - 10:23:53 PDT)
    - Re: [AMBER] The system size limitations for Tesla C2050 ? Ross Walker (Mon Jul 12 2010 - 11:02:19 PDT)
    - Re: [AMBER] The system size limitations for Tesla C2050 ? Scott Le Grand (Mon Jul 12 2010 - 11:27:35 PDT)
    - Re: [AMBER] The system size limitations for Tesla C2050 ? Marek Maly (Tue Jul 13 2010 - 09:45:37 PDT)
    - Re: [AMBER] The system size limitations for Tesla C2050 ? Scott Le Grand (Tue Jul 13 2010 - 14:37:19 PDT)
    - Re: [AMBER] The system size limitations for Tesla C2050 ? Marek Maly (Tue Jul 13 2010 - 14:47:17 PDT)
    - Re: [AMBER] The system size limitations for Tesla C2050 ? Scott Le Grand (Tue Jul 13 2010 - 15:13:14 PDT)
    - Re: [AMBER] The system size limitations for Tesla C2050 ? Marek Maly (Tue Jul 13 2010 - 16:04:01 PDT)
    - Re: [AMBER] The system size limitations for Tesla C2050 ? Scott Le Grand (Mon Jul 12 2010 - 09:11:27 PDT)
- Re: [AMBER] counterions placings Jason Swails (Fri Jul 09 2010 - 07:48:22 PDT)
- Re: [AMBER] counterions placings Bill Ross (Fri Jul 09 2010 - 10:11:02 PDT)
  - Re: [AMBER] counterions placings Jio M (Fri Jul 09 2010 - 21:45:52 PDT)
- Re: [AMBER] counterions placings Bill Ross (Fri Jul 09 2010 - 22:45:52 PDT)
  - Re: [AMBER] counterions placings Jio M (Sat Jul 10 2010 - 03:23:00 PDT)
- Re: [AMBER] counterions placings Bill Ross (Sat Jul 10 2010 - 10:32:06 PDT)
[AMBER] distance between two residues from their center of mass Siddharth Rastogi (Fri Jul 09 2010 - 02:28:10 PDT)
- Re: [AMBER] distance between two residues from their center of mass v.satish.iitg.ernet.in (Fri Jul 09 2010 - 05:13:19 PDT)
- Re: [AMBER] distance between two residues from their center of mass Bill Ross (Fri Jul 09 2010 - 09:39:36 PDT)
[AMBER] ptraj clustering:*** glibc detected *** /soft/amber11/exe/ptraj: double free or corruption moitrayee.mbu.iisc.ernet.in (Fri Jul 09 2010 - 05:12:18 PDT)
- Re: [AMBER] ptraj clustering:*** glibc detected *** /soft/amber11/exe/ptraj: double free or corruption Daniel Roe (Fri Jul 09 2010 - 05:41:00 PDT)
- Re: [AMBER] ptraj clustering:*** glibc detected *** /soft/amber11/exe/ptraj: double free or corruption Daniel Roe (Fri Jul 09 2010 - 09:07:01 PDT)
  - Re: [AMBER] ptraj clustering:*** glibc detected *** /soft/amber11/exe/ptraj: double free or corruption moitrayee.mbu.iisc.ernet.in (Fri Jul 09 2010 - 11:14:31 PDT)
[AMBER] No solvent overlap Thomas Exner (Fri Jul 09 2010 - 07:13:31 PDT)
- Re: [AMBER] No solvent overlap Jason Swails (Fri Jul 09 2010 - 07:58:36 PDT)
  - Re: [AMBER] No solvent overlap Thomas Exner (Tue Aug 03 2010 - 04:12:31 PDT)
    - Re: [AMBER] No solvent overlap case (Wed Aug 04 2010 - 04:23:44 PDT)
- Re: [AMBER] No solvent overlap Bill Ross (Fri Jul 09 2010 - 09:56:12 PDT)
  - Re: [AMBER] No solvent overlap Thomas Exner (Sat Jul 10 2010 - 00:23:01 PDT)
- Re: [AMBER] No solvent overlap case (Sat Jul 10 2010 - 07:37:51 PDT)
- Re: [AMBER] No solvent overlap Bill Ross (Sat Jul 10 2010 - 10:29:24 PDT)
[AMBER] xleap error Steve Seibold (Fri Jul 09 2010 - 08:38:31 PDT)
- Re: [AMBER] xleap error Daniel Roe (Fri Jul 09 2010 - 08:48:15 PDT)
  - Re: [AMBER] xleap error Steve Seibold (Fri Jul 09 2010 - 09:21:33 PDT)
  - Re: [AMBER] xleap error Steve Seibold (Fri Jul 09 2010 - 10:05:23 PDT)
    - Re: [AMBER] xleap error case (Fri Jul 09 2010 - 11:28:21 PDT)
- Re: [AMBER] xleap error Bill Ross (Fri Jul 09 2010 - 10:16:28 PDT)
  - Re: [AMBER] xleap error Steve Seibold (Fri Jul 09 2010 - 10:26:13 PDT)
- Re: [AMBER] xleap error Bill Ross (Fri Jul 09 2010 - 10:41:29 PDT)
[AMBER] compiling amber 10 with mpi Jorgen Simonsen (Fri Jul 09 2010 - 10:13:37 PDT)
- Re: [AMBER] compiling amber 10 with mpi ros (Fri Jul 09 2010 - 11:54:33 PDT)
  - Re: [AMBER] compiling amber 10 with mpi Jorgen Simonsen (Fri Jul 09 2010 - 12:53:57 PDT)
    - Re: [AMBER] compiling amber 10 with mpi Jason Swails (Fri Jul 09 2010 - 13:13:12 PDT)
[AMBER] Align two ligands Yubo Fan (Fri Jul 09 2010 - 10:43:10 PDT)
[AMBER] Question about increasing the max number of atoms in mopac in antechamber Guoxiong Su (Fri Jul 09 2010 - 12:47:16 PDT)
- Re: [AMBER] Question about increasing the max number of atoms in mopac in antechamber case (Fri Jul 09 2010 - 13:39:13 PDT)
[AMBER] (no subject) llduan.itcs.ecnu.edu.cn (Sat Jul 10 2010 - 00:04:33 PDT)
- Re: [AMBER] (no subject) case (Sat Jul 10 2010 - 05:55:54 PDT)
- [AMBER] amber02pol: sequence: Illegal UNIT named: NHE llduan.itcs.ecnu.edu.cn (Tue Jul 13 2010 - 07:49:05 PDT)
  - Re: [AMBER] amber02pol: sequence: Illegal UNIT named: NHE Paul S. Nerenberg (Tue Jul 13 2010 - 07:52:40 PDT)
    - Re: [AMBER] amber02pol: sequence: Illegal UNIT named: NHE llduan.itcs.ecnu.edu.cn (Wed Jul 14 2010 - 00:19:09 PDT)
    - Re: [AMBER] amber02pol: sequence: Illegal UNIT named: NHE Paul S. Nerenberg (Wed Jul 14 2010 - 07:53:54 PDT)
    - Re: [AMBER] amber02pol: sequence: Illegal UNIT named: NHE cieplak.cgl.ucsf.edu (Thu Jul 15 2010 - 14:39:24 PDT)
[AMBER] same dihedral with different parameter in FRCMOD file Xioling Chuang (Sat Jul 10 2010 - 05:39:14 PDT)
- Re: [AMBER] same dihedral with different parameter in FRCMOD file case (Sat Jul 10 2010 - 06:52:48 PDT)
  - Re: [AMBER] same dihedral with different parameter in FRCMOD file Xioling Chuang (Sun Jul 11 2010 - 06:57:59 PDT)
- Re: [AMBER] same dihedral with different parameter in FRCMOD file Dmitry Mukha (Sat Jul 10 2010 - 07:21:22 PDT)
  - Re: [AMBER] same dihedral with different parameter in FRCMOD file case (Sat Jul 10 2010 - 07:43:22 PDT)
[AMBER] [Fwd: Re: ptraj clustering:*** glibc detected *** /soft/amber11/exe/ptraj: double free or corruption] moitrayee.mbu.iisc.ernet.in (Sat Jul 10 2010 - 05:45:54 PDT)
[AMBER] problem in converting cprestrt to cpin2 file in constant pH md nicholus bhattacharjee (Sun Jul 11 2010 - 21:23:25 PDT)
- Re: [AMBER] problem in converting cprestrt to cpin2 file in constant pH md Jason Swails (Mon Jul 12 2010 - 07:04:30 PDT)
  - Re: [AMBER] problem in converting cprestrt to cpin2 file in constant pH md nicholus bhattacharjee (Wed Jul 21 2010 - 06:37:26 PDT)
    - Re: [AMBER] problem in converting cprestrt to cpin2 file in constant pH md Jason Swails (Wed Jul 21 2010 - 09:33:03 PDT)
    - Re: [AMBER] problem in converting cprestrt to cpin2 file in constant pH md nicholus bhattacharjee (Thu Jul 22 2010 - 02:37:35 PDT)
    - Re: [AMBER] problem in converting cprestrt to cpin2 file in constant pH md nicholus bhattacharjee (Thu Jul 22 2010 - 04:41:31 PDT)
    - Re: [AMBER] problem in converting cprestrt to cpin2 file in constant pH md Jason Swails (Thu Jul 22 2010 - 05:06:00 PDT)
    - Re: [AMBER] problem in converting cprestrt to cpin2 file in constant pH md nicholus bhattacharjee (Thu Jul 22 2010 - 06:42:39 PDT)
    - Re: [AMBER] problem in converting cprestrt to cpin2 file in constant pH md Jason Swails (Thu Jul 22 2010 - 07:26:56 PDT)
[AMBER] residue wise rmsd, not getting expected results vaibhav dixit (Mon Jul 12 2010 - 01:30:55 PDT)
- Re: [AMBER] residue wise rmsd, not getting expected results Daniel Roe (Mon Jul 12 2010 - 06:47:14 PDT)
  - Re: [AMBER] residue wise rmsd, not getting expected results Daniel Roe (Mon Jul 12 2010 - 06:48:01 PDT)
    - Re: [AMBER] residue wise rmsd, not getting expected results vaibhav dixit (Mon Jul 12 2010 - 06:57:16 PDT)
    - Re: [AMBER] residue wise rmsd, not getting expected results Jason Swails (Mon Jul 12 2010 - 06:59:39 PDT)
    - Re: [AMBER] residue wise rmsd, not getting expected results vaibhav dixit (Mon Jul 12 2010 - 09:19:45 PDT)
    - [AMBER] mm_pbsa.pl in PARALLEL does not finish Anselm Horn (Mon Jul 12 2010 - 09:55:32 PDT)
    - Re: [AMBER] mm_pbsa.pl in PARALLEL does not finish Jason Swails (Mon Jul 12 2010 - 10:32:57 PDT)
    - Re: [AMBER] mm_pbsa.pl in PARALLEL does not finish Anselm Horn (Mon Jul 12 2010 - 12:23:37 PDT)
    - Re: [AMBER] mm_pbsa.pl in PARALLEL does not finish Thomas Zeiser (Thu Jul 22 2010 - 07:22:38 PDT)
- Re: [AMBER] residue wise rmsd, not getting expected results Bill Ross (Mon Jul 12 2010 - 09:41:29 PDT)
[AMBER] simulation runs very slow.. Vijay Manickam Achari (Mon Jul 12 2010 - 01:54:24 PDT)
- Re: [AMBER] simulation runs very slow.. James Maier (Mon Jul 12 2010 - 08:11:47 PDT)
  - Re: [AMBER] simulation runs very slow.. Catein Catherine (Mon Jul 12 2010 - 08:18:02 PDT)
    - Re: [AMBER] simulation runs very slow.. Jason Swails (Mon Jul 12 2010 - 08:22:09 PDT)
- Re: [AMBER] simulation runs very slow.. Bill Ross (Mon Jul 12 2010 - 08:16:28 PDT)
- Re: [AMBER] simulation runs very slow.. Bill Ross (Mon Jul 12 2010 - 08:41:43 PDT)
[AMBER] ptraj Steve Seibold (Mon Jul 12 2010 - 09:52:07 PDT)
[AMBER] AmberTools citation Jason Swails (Mon Jul 12 2010 - 13:00:05 PDT)
[AMBER] source code to calculate electrostatic interaction in amber6 Qian Wang (Mon Jul 12 2010 - 13:37:51 PDT)
- Re: [AMBER] source code to calculate electrostatic interaction in amber6 Bill Ross (Mon Jul 12 2010 - 13:41:58 PDT)
  - Re: [AMBER] source code to calculate electrostatic interaction in amber6 Qian Wang (Mon Jul 12 2010 - 13:48:32 PDT)
[AMBER] Units for mass weighted covariance matrix in ptraj Lekpa Duukori (Mon Jul 12 2010 - 18:34:38 PDT)
- Re: [AMBER] Units for mass weighted covariance matrix in ptraj Jason Swails (Mon Jul 12 2010 - 19:56:23 PDT)
  - Re: [AMBER] Units for mass weighted covariance matrix in ptraj Lekpa Duukori (Tue Jul 13 2010 - 08:27:36 PDT)
    - Re: [AMBER] Units for mass weighted covariance matrix in ptraj Lekpa Duukori (Tue Jul 13 2010 - 11:16:54 PDT)
[AMBER] error 126 when install AmberTool1.4 Yan Gao (Mon Jul 12 2010 - 22:42:31 PDT)
- [AMBER] reference structure Homa Azizian (Mon Jul 12 2010 - 23:42:15 PDT)
  - Re: [AMBER] reference structure Ross Walker (Mon Jul 12 2010 - 23:54:39 PDT)
    - Re: [AMBER] reference structure Homa Azizian (Tue Jul 13 2010 - 00:09:47 PDT)
- Re: [AMBER] error 126 when install AmberTool1.4 case (Tue Jul 13 2010 - 05:18:34 PDT)
  - Re: [AMBER] error 126 when install AmberTool1.4 Yan Gao (Tue Jul 13 2010 - 09:07:01 PDT)
    - Re: [AMBER] error 126 when install AmberTool1.4 case (Tue Jul 13 2010 - 09:34:09 PDT)
- Re: [AMBER] error 126 when install AmberTool1.4 Daniel Roe (Tue Jul 13 2010 - 05:44:37 PDT)
  - Re: [AMBER] error 126 when install AmberTool1.4 Yan Gao (Tue Jul 13 2010 - 09:09:23 PDT)
[AMBER] 3D-RISM disabled? Daniel Sindhikara (Tue Jul 13 2010 - 01:26:29 PDT)
- Re: [AMBER] 3D-RISM disabled? case (Tue Jul 13 2010 - 05:24:20 PDT)
  - Re: [AMBER] 3D-RISM disabled? Daniel Sindhikara (Tue Jul 13 2010 - 19:05:52 PDT)
[AMBER] Periodic Neighbor Distance Logan Ahlstrom (Tue Jul 13 2010 - 16:23:58 PDT)
- Re: [AMBER] Periodic Neighbor Distance Paul S. Nerenberg (Tue Jul 13 2010 - 16:49:00 PDT)
[AMBER] please, units of LENNARD_JONES_ACOEF in prmptop? Jose Borreguero (Tue Jul 13 2010 - 16:45:07 PDT)
- Re: [AMBER] please, units of LENNARD_JONES_ACOEF in prmptop? Paul S. Nerenberg (Tue Jul 13 2010 - 17:31:13 PDT)
  - Re: [AMBER] please, units of LENNARD_JONES_ACOEF in prmptop? Jose Borreguero (Wed Jul 14 2010 - 07:56:08 PDT)
[AMBER] general enquiry monica.imtech.res.in (Wed Jul 14 2010 - 00:40:40 PDT)
- Re: [AMBER] general enquiry Jason Swails (Wed Jul 14 2010 - 03:56:34 PDT)
[AMBER] Error Compiling NAB o AMBER Tools 1.2 Giorgos Lamprinidis (Wed Jul 14 2010 - 03:02:16 PDT)
- Re: [AMBER] Error Compiling NAB o AMBER Tools 1.2 Jason Swails (Wed Jul 14 2010 - 03:47:36 PDT)
  - Re: [AMBER] Error Compiling NAB o AMBER Tools 1.2 Giorgos Lamprinidis (Wed Jul 14 2010 - 07:30:25 PDT)
    - Re: [AMBER] Error Compiling NAB o AMBER Tools 1.2 Jason Swails (Wed Jul 14 2010 - 08:24:27 PDT)
    - Re: [AMBER] Error Compiling NAB o AMBER Tools 1.2 Giorgos Lamprinidis (Wed Jul 14 2010 - 08:44:59 PDT)
    - Re: [AMBER] Error Compiling NAB o AMBER Tools 1.2 Jason Swails (Wed Jul 14 2010 - 12:18:53 PDT)
- Re: [AMBER] Error Compiling NAB o AMBER Tools 1.2 case (Wed Jul 14 2010 - 13:26:49 PDT)
  - Re: [AMBER] Error Compiling NAB o AMBER Tools 1.2 Giorgos Lamprinidis (Thu Jul 15 2010 - 07:34:59 PDT)
    - Re: [AMBER] Error Compiling NAB o AMBER Tools 1.2 Jason Swails (Thu Jul 15 2010 - 08:56:31 PDT)
- Re: [AMBER] Error Compiling NAB o AMBER Tools 1.2 Janusz Mordarski (Wed Nov 24 2010 - 04:49:01 PST)
  - Re: [AMBER] Error Compiling NAB o AMBER Tools 1.2 case (Wed Nov 24 2010 - 09:36:48 PST)
[AMBER] NAB rdparm seg fault Josh Berryman (Wed Jul 14 2010 - 05:03:41 PDT)
- Re: [AMBER] NAB rdparm seg fault case (Wed Jul 14 2010 - 09:36:36 PDT)
  - Re: [AMBER] NAB rdparm seg fault Josh Berryman (Thu Jul 15 2010 - 04:49:13 PDT)
    - Re: [AMBER] NAB rdparm seg fault case (Thu Jul 15 2010 - 05:37:20 PDT)
    - Re: [AMBER] NAB rdparm seg fault case (Thu Jul 15 2010 - 06:02:31 PDT)
    - Re: [AMBER] NAB rdparm seg fault Josh Berryman (Mon Jul 26 2010 - 04:54:47 PDT)
[AMBER] Query regarding Abscissa and their corresponding weights in Thermodynamic Integration sunita gupta (Wed Jul 14 2010 - 05:16:05 PDT)
- Re: [AMBER] Query regarding Abscissa and their corresponding weights in Thermodynamic Integration Jason Swails (Wed Jul 14 2010 - 08:18:23 PDT)
[AMBER] mm_pbsa.pl in PARALLEL - part 2 Anselm Horn (Wed Jul 14 2010 - 05:26:53 PDT)
[AMBER] problem with tleap and xleap moacyr comar (Wed Jul 14 2010 - 07:05:38 PDT)
- Re: [AMBER] problem with tleap and xleap Jason Swails (Wed Jul 14 2010 - 08:22:32 PDT)
[AMBER] RDF analysis of glucose made by GLYCAM problem Hoshin Kim (Tue Jul 13 2010 - 18:10:30 PDT)
- Re: [AMBER] RDF analysis of glucose made by GLYCAM problem Lachele Foley (Lists) (Wed Jul 14 2010 - 07:53:54 PDT)
[AMBER] sign me off please~ Qiuting Hong (Wed Jul 14 2010 - 09:35:00 PDT)
- Re: [AMBER] sign me off please~ Paul S. Nerenberg (Wed Jul 14 2010 - 09:47:48 PDT)
[AMBER] entropy from mass weighted covariance matrix Lekpa Duukori (Wed Jul 14 2010 - 09:50:41 PDT)
- Re: [AMBER] entropy from mass weighted covariance matrix Jason Swails (Wed Jul 14 2010 - 12:30:32 PDT)
  - Re: [AMBER] entropy from mass weighted covariance matrix Lekpa Duukori (Wed Jul 14 2010 - 14:29:18 PDT)
[AMBER] TIP4P question hong-bin Xie (Wed Jul 14 2010 - 10:16:33 PDT)
- Re: [AMBER] TIP4P question case (Wed Jul 14 2010 - 10:46:24 PDT)
  - Re: [AMBER] TIP4P question hong-bin Xie (Wed Jul 14 2010 - 10:53:17 PDT)
[AMBER] The atom number exceeds the MAXATOM, reallocate memory Segmentation fault (core dumped) Yan Gao (Wed Jul 14 2010 - 11:02:12 PDT)
- Re: [AMBER] The atom number exceeds the MAXATOM, reallocate memory Segmentation fault (core dumped) Bill Ross (Wed Jul 14 2010 - 11:27:04 PDT)
Re: [AMBER] The atom number exceeds the MAXATOM, reallocate memory Segmentation fault (core dumped) --- thank you and more questions! Yan Gao (Wed Jul 14 2010 - 12:12:42 PDT)
- Re: [AMBER] The atom number exceeds the MAXATOM, reallocate memory Segmentation fault (core dumped) --- thank you and more questions! Bill Ross (Wed Jul 14 2010 - 13:12:53 PDT)
[AMBER] how to create a mixture solvent of hexane and water setyanto tri wahyudi (Wed Jul 14 2010 - 20:43:24 PDT)
- [AMBER] amber tool installing problem Homa Azizian (Wed Jul 14 2010 - 22:11:39 PDT)
  - [AMBER] About RAMD gokul algates (Wed Jul 14 2010 - 23:03:15 PDT)
    - Re: [AMBER] About RAMD Jason Swails (Thu Jul 15 2010 - 04:41:12 PDT)
    - Re: [AMBER] About RAMD gokul algates (Thu Jul 15 2010 - 07:34:44 PDT)
  - Re: [AMBER] amber tool installing problem Jason Swails (Thu Jul 15 2010 - 04:37:35 PDT)
  - Re: [AMBER] amber tool installing problem case (Thu Jul 15 2010 - 04:54:14 PDT)
- Re: [AMBER] how to create a mixture solvent of hexane and water case (Thu Jul 15 2010 - 05:16:10 PDT)
  - Re: [AMBER] how to create a mixture solvent of hexane and water setyanto tri wahyudi (Fri Jul 23 2010 - 03:21:41 PDT)
[AMBER] vlimit exceeding situtaion with ntt option Vijay Manickam Achari (Thu Jul 15 2010 - 01:30:20 PDT)
[AMBER] Simulation cell reduction Lorenzo Gontrani (Thu Jul 15 2010 - 03:15:47 PDT)
[AMBER] About RAMD gokul algates (Thu Jul 15 2010 - 07:46:06 PDT)
[AMBER] website down Sidney Elmer (Thu Jul 15 2010 - 18:17:57 PDT)
- Re: [AMBER] website down Yan Gao (Thu Jul 15 2010 - 19:17:11 PDT)
- [AMBER] Can I calculate the interaction energy between two connected domains of a protein? Catein Catherine (Mon Jul 19 2010 - 00:40:54 PDT)
  - Re: [AMBER] Can I calculate the interaction energy between two connected domains of a protein? Rubben Torella (Mon Jul 19 2010 - 00:45:08 PDT)
    - Re: [AMBER] Can I calculate the interaction energy between two connected domains of a protein? Catein Catherine (Mon Jul 19 2010 - 01:04:23 PDT)
    - Re: [AMBER] Can I calculate the interaction energy between two connected domains of a protein? Jason Swails (Mon Jul 19 2010 - 08:12:43 PDT)
    - [AMBER] Can I calculate the interaction energy between two connected domains of a protein using mmpbsa.py? Catein Catherine (Mon Jul 19 2010 - 08:12:55 PDT)
    - Re: [AMBER] Can I calculate the interaction energy between two connected domains of a protein using mmpbsa.py? Jason Swails (Mon Jul 19 2010 - 10:54:32 PDT)
    - Re: [AMBER] Can I calculate the interaction energy between two connected domains of a protein? Purisima, Enrico (Mon Jul 19 2010 - 08:56:39 PDT)
[AMBER] residues lacking connect Jorgen Simonsen (Sat Jul 17 2010 - 11:54:06 PDT)
- Re: [AMBER] residues lacking connect case (Sun Jul 18 2010 - 15:24:28 PDT)
- Re: [AMBER] residues lacking connect Bill Ross (Sun Jul 18 2010 - 20:26:20 PDT)
[AMBER] Problem with sander.MPI moacyr comar (Sat Jul 17 2010 - 12:15:42 PDT)
- Re: [AMBER] Problem with sander.MPI Ross Walker (Sun Jul 18 2010 - 02:21:16 PDT)
[AMBER] questions of decomposition using mm/gbsa fancy2012 (Sun Jul 18 2010 - 00:01:45 PDT)
- Re: [AMBER] questions of decomposition using mm/gbsa fancy2012 (Sun Jul 18 2010 - 00:11:39 PDT)
[AMBER] How to remove PBC effects? Oliver Kuhn (Mon Jul 19 2010 - 05:04:23 PDT)
- Re: [AMBER] How to remove PBC effects? Daniel Sindhikara (Mon Jul 19 2010 - 06:06:11 PDT)
  - Re: [AMBER] How to remove PBC effects? Oliver Kuhn (Mon Jul 19 2010 - 06:55:31 PDT)
    - Re: [AMBER] How to remove PBC effects? Jason Swails (Mon Jul 19 2010 - 08:08:07 PDT)
    - Re: [AMBER] How to remove PBC effects? Oliver Kuhn (Tue Jul 20 2010 - 01:36:10 PDT)
[AMBER] protein distance constraints Beale, John (Mon Jul 19 2010 - 08:18:11 PDT)
- Re: [AMBER] protein distance constraints case (Mon Jul 19 2010 - 10:40:50 PDT)
[AMBER] Problem with pmemd.cuda ros (Mon Jul 19 2010 - 09:11:12 PDT)
- Re: [AMBER] Problem with pmemd.cuda case (Mon Jul 19 2010 - 10:34:57 PDT)
  - Re: [AMBER] Problem with pmemd.cuda ros (Mon Jul 19 2010 - 11:34:02 PDT)
    - Re: [AMBER] Problem with pmemd.cuda case (Mon Jul 19 2010 - 12:30:54 PDT)
    - Re: [AMBER] Problem with pmemd.cuda Levi Pierce (Mon Jul 19 2010 - 12:49:19 PDT)
    - Re: [AMBER] Problem with pmemd.cuda ros (Mon Jul 19 2010 - 13:14:18 PDT)
- Re: [AMBER] Problem with pmemd.cuda Bill Ross (Mon Jul 19 2010 - 13:18:32 PDT)
  - Re: [AMBER] Problem with pmemd.cuda ros (Mon Jul 19 2010 - 13:55:26 PDT)
- Re: [AMBER] Problem with pmemd.cuda Bill Ross (Mon Jul 19 2010 - 14:15:52 PDT)
  - Re: [AMBER] Problem with pmemd.cuda ros (Mon Jul 19 2010 - 14:42:58 PDT)
    - Re: [AMBER] Problem with pmemd.cuda case (Mon Jul 19 2010 - 17:41:37 PDT)
    - Re: [AMBER] Problem with pmemd.cuda ros (Mon Jul 19 2010 - 22:16:45 PDT)
    - Re: [AMBER] Problem with pmemd.cuda ros (Mon Jul 19 2010 - 22:53:36 PDT)
    - Re: [AMBER] Problem with pmemd.cuda ros (Mon Jul 19 2010 - 23:30:02 PDT)
[AMBER] Head-Tail covalently bound substrate and arikcohen (Mon Jul 19 2010 - 11:04:24 PDT)
- Re: [AMBER] Head-Tail covalently bound substrate and Jason Swails (Mon Jul 19 2010 - 11:20:34 PDT)
  - Re: [AMBER] Head-Tail covalently bound substrate and arikcohen (Mon Jul 19 2010 - 11:47:29 PDT)
    - [AMBER] Parameters missing after changing topology arikcohen (Mon Jul 19 2010 - 14:45:36 PDT)
    - Re: [AMBER] Parameters missing after changing topology Jason Swails (Mon Jul 19 2010 - 18:36:05 PDT)
[AMBER] problem with the total charge Yan Gao (Mon Jul 19 2010 - 20:25:37 PDT)
- Re: [AMBER] problem with the total charge Jason Swails (Mon Jul 19 2010 - 21:27:08 PDT)
- Re: [AMBER] problem with the total charge case (Tue Jul 20 2010 - 04:44:48 PDT)
  - Re: [AMBER] problem with the total charge Yan Gao (Tue Jul 20 2010 - 09:48:44 PDT)
[AMBER] adding ion concentration Neha Gandhi (Tue Jul 20 2010 - 02:08:05 PDT)
- Re: [AMBER] adding ion concentration Jason Swails (Tue Jul 20 2010 - 05:36:04 PDT)
[AMBER] Performance from pmemd.cuda Gould, Ian R (Tue Jul 20 2010 - 02:36:46 PDT)
- Re: [AMBER] Performance from pmemd.cuda Ross Walker (Tue Jul 20 2010 - 11:01:33 PDT)
[AMBER] How to calculate the radial distribution function of one of the atom(say P) of one residue ( say R1) to the center of the another residue (R2) Siddharth Rastogi (Tue Jul 20 2010 - 04:48:14 PDT)
[AMBER] ANALYSES LIGAND EXIT TRAJECTORIES sophie fourtanier (Tue Jul 20 2010 - 05:49:16 PDT)
[AMBER] radial distribution function Siddharth Rastogi (Tue Jul 20 2010 - 06:06:20 PDT)
[AMBER] Warning: Input error! "nmode_igb=1" is an invalid option. Sushil Mishra (Tue Jul 20 2010 - 08:24:08 PDT)
- Re: [AMBER] Warning: Input error! "nmode_igb=1" is an invalid option. Bill Miller III (Tue Jul 20 2010 - 08:32:19 PDT)
[AMBER] L and D peptides Jorgen Simonsen (Tue Jul 20 2010 - 09:52:30 PDT)
- Re: [AMBER] L and D peptides Jason Swails (Tue Jul 20 2010 - 12:51:41 PDT)
- Re: [AMBER] L and D peptides Bill Ross (Tue Jul 20 2010 - 13:12:08 PDT)
  - Re: [AMBER] L and D peptides Jorgen Simonsen (Tue Jul 20 2010 - 14:20:05 PDT)
- Re: [AMBER] L and D peptides Bill Ross (Tue Jul 20 2010 - 14:34:16 PDT)
- Re: [AMBER] L and D peptides case (Tue Jul 20 2010 - 18:18:32 PDT)
  - Re: [AMBER] L and D peptides FyD (Wed Jul 21 2010 - 00:39:32 PDT)
    - Re: [AMBER] L and D peptides Jason Swails (Wed Jul 21 2010 - 07:51:15 PDT)
    - Re: [AMBER] L and D peptides Roman Osman (Wed Jul 21 2010 - 08:13:00 PDT)
    - [AMBER] installation of Ambertools Rebeca García Fandiño (Thu Sep 02 2010 - 05:14:17 PDT)
    - Re: [AMBER] installation of Ambertools Jason Swails (Thu Sep 02 2010 - 05:49:57 PDT)
    - [AMBER] charged molecule with antechamber Rebeca García Fandiño (Wed Feb 13 2013 - 10:45:47 PST)
    - Re: [AMBER] charged molecule with antechamber Ismail, Mohd F. (Wed Feb 13 2013 - 10:56:48 PST)
    - Re: [AMBER] charged molecule with antechamber Rebeca García Fandiño (Wed Feb 13 2013 - 11:19:56 PST)
    - [AMBER] problem with parmchk and a big organic molecule Rebeca García Fandiño (Tue May 21 2013 - 05:29:04 PDT)
    - Re: [AMBER] problem with parmchk and a big organic molecule Jason Swails (Fri Jun 14 2013 - 08:24:29 PDT)
- Re: [AMBER] L and D peptides Karl N. Kirschner (Wed Jul 21 2010 - 03:26:21 PDT)
[AMBER] Workaround for gfortran-4.1.2? Marc Moreau (Tue Jul 20 2010 - 16:19:53 PDT)
- Re: [AMBER] Workaround for gfortran-4.1.2? Mark Williamson (Tue Jul 20 2010 - 16:51:43 PDT)
- Re: [AMBER] Workaround for gfortran-4.1.2? case (Tue Jul 20 2010 - 18:31:06 PDT)
  - Re: [AMBER] Workaround for gfortran-4.1.2? Marc Moreau (Tue Jul 20 2010 - 18:39:11 PDT)
    - Re: [AMBER] Workaround for gfortran-4.1.2? Marc Moreau (Wed Jul 21 2010 - 18:38:38 PDT)
  - [AMBER] Enquiry about NED calculation in AMBER10 Catein Catherine (Tue Jul 20 2010 - 19:53:08 PDT)
    - Re: [AMBER] Enquiry about NED calculation in AMBER10 case (Wed Jul 21 2010 - 05:04:31 PDT)
- Re: [AMBER] Workaround for gfortran-4.1.2? Richard Owczarzy (Wed Aug 25 2010 - 12:51:15 PDT)
  - Re: [AMBER] Workaround for gfortran-4.1.2? Jason Swails (Wed Aug 25 2010 - 13:10:50 PDT)
    - Re: [AMBER] Workaround for gfortran-4.1.2? Lachele Foley (Lists) (Wed Aug 25 2010 - 15:18:11 PDT)
  - Re: [AMBER] Workaround for gfortran-4.1.2? Marc Moreau (Wed Aug 25 2010 - 21:23:49 PDT)
[AMBER] errors of energy decomposition fancy2012 (Tue Jul 20 2010 - 23:20:30 PDT)
- Re: [AMBER] errors of energy decomposition Amor San Juan (Tue Jul 20 2010 - 23:58:36 PDT)
  - Re: [AMBER] errors of energy decomposition fancy2012 (Wed Jul 21 2010 - 00:23:38 PDT)
[AMBER] Getting missing force constants for Amber from Gaussian? Markus Knauth (Wed Jul 21 2010 - 01:00:02 PDT)
[AMBER] mm_pbsa.pl in PARALLEL - part 3 Anselm Horn (Wed Jul 21 2010 - 03:33:00 PDT)
- Re: [AMBER] mm_pbsa.pl in PARALLEL - part 3 Asfa Ali (Wed Jul 21 2010 - 04:05:57 PDT)
- Re: [AMBER] mm_pbsa.pl in PARALLEL - part 3 Anselm Horn (Wed Jul 21 2010 - 04:21:20 PDT)
  - Re: [AMBER] mm_pbsa.pl in PARALLEL - part 3 Asfa Ali (Wed Jul 21 2010 - 04:32:05 PDT)
    - Re: [AMBER] mm_pbsa.pl in PARALLEL - part 3 Bill Miller III (Wed Jul 21 2010 - 04:48:18 PDT)
    - Re: [AMBER] mm_pbsa.pl in PARALLEL - part 3 Jason Swails (Wed Jul 21 2010 - 07:59:52 PDT)
- Re: [AMBER] mm_pbsa.pl in PARALLEL - part 3 Thomas Zeiser (Thu Jul 22 2010 - 05:13:08 PDT)
[AMBER] FATAL: Atom .R<LIG 1184>.A<CAA 1> does not have a type. kamlesh sahu (Wed Jul 21 2010 - 05:11:34 PDT)
- Re: [AMBER] FATAL: Atom .R<LIG 1184>.A<CAA 1> does not have a type. case (Wed Jul 21 2010 - 06:09:11 PDT)
 - Re: [AMBER] FATAL: Atom .R<LIG 1184>.A<CAA 1> does not have a type. Jason Swails (Wed Jul 21 2010 - 08:10:56 PDT)
 - Re: [AMBER] FATAL: Atom .R<LIG 1184>.A<CAA 1> does not have a type. kamlesh sahu (Wed Jul 21 2010 - 20:06:36 PDT)
[AMBER] external electric field? Wong, Sergio E. (Wed Jul 21 2010 - 11:42:08 PDT)
[AMBER] Issue with preparing pdb, top and crd files via leap for a non-standard residue Valerie Fako (Wed Jul 21 2010 - 14:29:54 PDT)
- Re: [AMBER] Issue with preparing pdb, top and crd files via leap for a non-standard residue Levi Pierce (Wed Jul 21 2010 - 14:40:11 PDT)
[AMBER] How to make oligo-peptides using AMBER ? Siddharth Rastogi (Wed Jul 21 2010 - 15:51:02 PDT)
- Re: [AMBER] How to make oligo-peptides using AMBER ? Gustavo Seabra (Wed Jul 21 2010 - 16:07:09 PDT)
[AMBER] POPC parameters Vasillis Myrianthopoulos (Thu Jul 22 2010 - 04:57:27 PDT)
- Re: [AMBER] POPC parameters Hannes Loeffler (Thu Jul 22 2010 - 05:33:40 PDT)
[AMBER] scee EEL and scnb VDW 1-4 CHAMI F. (Thu Jul 22 2010 - 05:34:36 PDT)
[AMBER] minimization segmentation fault Jorgen Simonsen (Thu Jul 22 2010 - 06:16:02 PDT)
- Re: [AMBER] minimization segmentation fault Daniel Roe (Thu Jul 22 2010 - 06:33:30 PDT)
- Re: [AMBER] minimization segmentation fault Jason Swails (Thu Jul 22 2010 - 07:42:00 PDT)
- Re: [AMBER] minimization segmentation fault Bill Ross (Thu Jul 22 2010 - 10:03:27 PDT)
  - Re: [AMBER] minimization segmentation fault Jorgen Simonsen (Tue Jul 27 2010 - 11:37:24 PDT)
- Re: [AMBER] minimization segmentation fault Bill Ross (Tue Jul 27 2010 - 11:53:25 PDT)
  - Re: [AMBER] minimization segmentation fault Jorgen Simonsen (Fri Jul 30 2010 - 04:11:31 PDT)
- Re: [AMBER] minimization segmentation fault Bill Ross (Fri Jul 30 2010 - 09:52:50 PDT)
  - Re: [AMBER] minimization segmentation fault Jorgen Simonsen (Mon Aug 02 2010 - 00:59:46 PDT)
- Re: [AMBER] minimization segmentation fault Bill Ross (Mon Aug 02 2010 - 09:50:34 PDT)
[AMBER] pmemd amber10 compilation error Marcela Madrid (Thu Jul 22 2010 - 07:49:00 PDT)
- Re: [AMBER] pmemd amber10 compilation error Jason Swails (Thu Jul 22 2010 - 07:54:21 PDT)
  - Re: [AMBER] pmemd amber10 compilation error Jason Swails (Thu Jul 22 2010 - 07:55:40 PDT)
- Re: [AMBER] pmemd amber10 compilation error Ross Walker (Thu Jul 22 2010 - 07:57:51 PDT)
[AMBER] file format monica.imtech.res.in (Thu Jul 22 2010 - 08:12:37 PDT)
- Re: [AMBER] file format James Maier (Thu Jul 22 2010 - 12:31:06 PDT)
- Re: [AMBER] file format Jason Swails (Thu Jul 22 2010 - 16:00:46 PDT)
[AMBER] question about bond command Philippe Pinard (Thu Jul 22 2010 - 10:36:38 PDT)
- Re: [AMBER] question about bond command Bill Ross (Thu Jul 22 2010 - 10:43:58 PDT)
- Re: [AMBER] question about bond command ros (Thu Jul 22 2010 - 11:06:19 PDT)
  - Re: [AMBER] question about bond command Philippe Pinard (Thu Jul 22 2010 - 11:34:11 PDT)
- Re: [AMBER] question about bond command Bill Ross (Thu Jul 22 2010 - 11:50:28 PDT)
  - Re: [AMBER] question about bond command Philippe Pinard (Thu Jul 22 2010 - 12:16:38 PDT)
- Re: [AMBER] question about bond command Bill Ross (Thu Jul 22 2010 - 11:54:31 PDT)
- Re: [AMBER] question about bond command Bill Ross (Thu Jul 22 2010 - 12:38:28 PDT)
  - Re: [AMBER] question about bond command Philippe Pinard (Thu Jul 22 2010 - 14:41:26 PDT)
    - Re: [AMBER] question about bond command case (Thu Jul 22 2010 - 18:58:12 PDT)
    - Re: [AMBER] question about bond command Philippe Pinard (Thu Jul 22 2010 - 19:38:33 PDT)
    - [AMBER] mandatory command lines in MMPBSA.PY Amor San Juan (Thu Jul 22 2010 - 21:16:25 PDT)
    - Re: [AMBER] mandatory command lines in MMPBSA.PY Oliver Grant (Fri Jul 23 2010 - 03:55:56 PDT)
    - Re: [AMBER] mandatory command lines in MMPBSA.PY Jason Swails (Fri Jul 23 2010 - 05:06:24 PDT)
    - [AMBER] How to identify water molecules at the interface ? Amor San Juan (Sun Aug 15 2010 - 20:51:47 PDT)
    - Re: [AMBER] How to identify water molecules at the interface ? Jason Swails (Mon Aug 16 2010 - 05:59:25 PDT)
    - Re: [AMBER] question about bond command case (Fri Jul 23 2010 - 04:36:00 PDT)
- Re: [AMBER] question about bond command Bill Ross (Thu Jul 22 2010 - 14:55:48 PDT)
- Re: [AMBER] question about bond command Bill Ross (Fri Jul 23 2010 - 09:36:47 PDT)
  - Re: [AMBER] question about bond command Philippe Pinard (Sat Jul 24 2010 - 09:34:19 PDT)
    - Re: [AMBER] question about bond command Jason Swails (Sat Jul 24 2010 - 22:04:18 PDT)
    - Re: [AMBER] question about bond command Philippe Pinard (Sun Jul 25 2010 - 20:52:21 PDT)
    - Re: [AMBER] question about bond command Jason Swails (Sat Jul 24 2010 - 22:13:51 PDT)
- Re: [AMBER] question about bond command Bill Ross (Fri Jul 23 2010 - 09:44:08 PDT)
- Re: [AMBER] question about bond command Bill Ross (Fri Jul 23 2010 - 10:00:49 PDT)
- Re: [AMBER] question about bond command Bill Ross (Sat Jul 24 2010 - 13:57:32 PDT)
  - Re: [AMBER] question about bond command Philippe Pinard (Sat Jul 24 2010 - 17:13:45 PDT)
- Re: [AMBER] question about bond command Bill Ross (Sat Jul 24 2010 - 17:22:44 PDT)
  - Re: [AMBER] question about bond command Philippe Pinard (Sat Jul 24 2010 - 19:38:39 PDT)
    - Re: [AMBER] question about bond command case (Sat Jul 24 2010 - 20:44:40 PDT)
- Re: [AMBER] question about bond command Bill Ross (Sat Jul 24 2010 - 20:05:24 PDT)
[AMBER] Coulson vs. Mulliken, CM1, etc. in antechamber + mopac Don.Bashford.stjude.org (Thu Jul 22 2010 - 13:59:42 PDT)
- Re: [AMBER] Coulson vs. Mulliken, CM1, etc. in antechamber + mopac case (Thu Jul 22 2010 - 19:32:55 PDT)
- Re: [AMBER] Coulson vs. Mulliken, CM1, etc. in antechamber + mopac Timothy J Giese (Mon Jul 26 2010 - 08:22:50 PDT)
[AMBER] clustering analysis changes my coordinates Geoffrey Wood (Thu Jul 22 2010 - 18:55:46 PDT)
- Re: [AMBER] clustering analysis changes my coordinates Daniel Roe (Fri Jul 23 2010 - 07:46:04 PDT)
  - Re: [AMBER] clustering analysis changes my coordinates Geoffrey Wood (Fri Jul 23 2010 - 08:14:28 PDT)
    - Re: [AMBER] clustering analysis changes my coordinates Thomas Cheatham III (Fri Jul 23 2010 - 08:51:43 PDT)
    - Re: [AMBER] clustering analysis changes my coordinates Geoffrey Wood (Sat Jul 24 2010 - 18:06:52 PDT)
    - [AMBER] Where can I find a tutorial/manual on the IED in VMD for visualizing PCA data from ABMER? Catein Catherine (Fri Jul 23 2010 - 08:54:49 PDT)
    - Re: [AMBER] Where can I find a tutorial/manual on the IED in VMD for visualizing PCA data from ABMER? hannes.loeffler.stfc.ac.uk (Fri Jul 23 2010 - 10:43:57 PDT)
    - Re: [AMBER] Where can I find a tutorial/manual on the IED in VMD for visualizing PCA data from ABMER? Catein Catherine (Fri Jul 23 2010 - 20:47:43 PDT)
    - Re: [AMBER] Where can I find a tutorial/manual on the IED in VMD for visualizing PCA data from ABMER? hannes.loeffler.stfc.ac.uk (Sat Jul 24 2010 - 00:26:27 PDT)
    - Re: [AMBER] Where can I find a tutorial/manual on the IED in VMD for visualizing PCA data from ABMER? Catein Catherine (Sun Jul 25 2010 - 01:09:17 PDT)
    - Re: [AMBER] Where can I find a tutorial/manual on the IED in VMD for visualizing PCA data from ABMER? hannes.loeffler.stfc.ac.uk (Sun Jul 25 2010 - 03:10:18 PDT)
[AMBER] ptraj-clustering Necmettin Pirinccioglu (Fri Jul 23 2010 - 00:28:30 PDT)
- Re: [AMBER] ptraj-clustering Daniel Roe (Fri Jul 23 2010 - 07:36:22 PDT)
- Re: [AMBER] ptraj-clustering Necmettin Pirinccioglu (Sun Jul 25 2010 - 23:46:12 PDT)
- Re: [AMBER] ptraj-clustering Daniel Roe (Mon Jul 26 2010 - 20:14:20 PDT)
  - Re: [AMBER] ptraj-clustering Jianyin Shao (Tue Jul 27 2010 - 12:37:22 PDT)
[AMBER] atomic radii of ions Xioling Chuang (Fri Jul 23 2010 - 01:04:41 PDT)
- Re: [AMBER] atomic radii of ions case (Fri Jul 23 2010 - 04:44:28 PDT)
  - Re: [AMBER] atomic radii of ions Xioling Chuang (Sun Jul 25 2010 - 08:27:52 PDT)
    - Re: [AMBER] atomic radii of ions Paul S. Nerenberg (Sun Jul 25 2010 - 08:46:30 PDT)
    - Re: [AMBER] atomic radii of ions case (Sun Jul 25 2010 - 13:28:06 PDT)
[AMBER] test of parallel NAB and PTRAJ Vlad Cojocaru (Fri Jul 23 2010 - 02:52:25 PDT)
- Re: [AMBER] test of parallel NAB and PTRAJ Vlad Cojocaru (Fri Jul 23 2010 - 03:09:08 PDT)
[AMBER] How to make hexane parameter using antechamber ? setyanto tri wahyudi (Fri Jul 23 2010 - 03:42:05 PDT)
- Re: [AMBER] How to make hexane parameter using antechamber ? case (Fri Jul 23 2010 - 04:47:15 PDT)
- Re: [AMBER] How to make hexane parameter using antechamber ? FyD (Fri Jul 23 2010 - 05:28:32 PDT)
  - Re: [AMBER] How to make hexane parameter using antechamber ? setyanto tri wahyudi (Sun Jul 25 2010 - 18:21:24 PDT)
[AMBER] PM6 in Amber 11 Zora Strelcova (Fri Jul 23 2010 - 06:13:34 PDT)
- Re: [AMBER] PM6 in Amber 11 Jason Swails (Fri Jul 23 2010 - 06:39:45 PDT)
  - Re: [AMBER] PM6 in Amber 11 Zora Strelcova (Fri Jul 23 2010 - 06:54:58 PDT)
    - Re: [AMBER] PM6 in Amber 11 Jason Swails (Fri Jul 23 2010 - 07:05:54 PDT)
- Re: [AMBER] PM6 in Amber 11 case (Fri Jul 23 2010 - 12:25:46 PDT)
  - Re: [AMBER] PM6 in Amber 11 Zora Strelcova (Mon Jul 26 2010 - 00:32:27 PDT)
[AMBER] b-factor Syed Tarique Moin (Fri Jul 23 2010 - 06:42:41 PDT)
[AMBER] Relax command for tleap Valerie Fako (Fri Jul 23 2010 - 09:11:43 PDT)
- Re: [AMBER] Relax command for tleap Paul S. Nerenberg (Fri Jul 23 2010 - 09:33:04 PDT)
- Re: [AMBER] Relax command for tleap Bill Ross (Fri Jul 23 2010 - 09:56:27 PDT)
  - Re: [AMBER] Relax command for tleap Paul S. Nerenberg (Fri Jul 23 2010 - 10:32:42 PDT)
[AMBER] antechamber vs. REDDB ros (Fri Jul 23 2010 - 11:19:16 PDT)
- Re: [AMBER] antechamber vs. RED FyD (Sun Jul 25 2010 - 01:46:42 PDT)
[AMBER] random number seed - range g t (Sat Jul 24 2010 - 05:21:51 PDT)
- Re: [AMBER] random number seed - range case (Sat Jul 24 2010 - 06:22:14 PDT)
  - Re: [AMBER] random number seed - range g t (Sat Jul 24 2010 - 12:45:57 PDT)
    - Re: [AMBER] random number seed - range Tom Joseph (Sat Jul 24 2010 - 15:27:14 PDT)
    - Re: [AMBER] random number seed - range Ross Walker (Sat Jul 24 2010 - 16:12:15 PDT)
    - Re: [AMBER] random number seed - range Paul S. Nerenberg (Sat Jul 24 2010 - 18:11:00 PDT)
    - Re: [AMBER] random number seed - range g t (Sun Jul 25 2010 - 06:30:30 PDT)
    - Re: [AMBER] random number seed - range Keith Van Nostrand (Tue Jul 27 2010 - 07:25:19 PDT)
    - Re: [AMBER] random number seed - range Paul S. Nerenberg (Tue Jul 27 2010 - 07:44:38 PDT)
    - Re: [AMBER] random number seed - range case (Tue Jul 27 2010 - 12:02:54 PDT)
- Re: [AMBER] random number seed - range Bill Ross (Sat Jul 24 2010 - 13:54:59 PDT)
- Re: [AMBER] random number seed - range Robert Duke (Tue Jul 27 2010 - 12:13:00 PDT)
- Re: [AMBER] random number seed - range Hopkins, Robert (Fri Aug 13 2010 - 14:03:53 PDT)
  - Re: [AMBER] random number seed - range Ross Walker (Fri Aug 13 2010 - 14:55:20 PDT)
- Re: [AMBER] random number seed - range Robert Duke (Fri Aug 13 2010 - 14:40:35 PDT)
  - Re: [AMBER] random number seed - range Paul S. Nerenberg (Fri Aug 13 2010 - 14:58:55 PDT)
- Re: [AMBER] random number seed - range Robert Duke (Fri Aug 13 2010 - 14:59:42 PDT)
  - Re: [AMBER] random number seed - range Ross Walker (Fri Aug 13 2010 - 15:08:39 PDT)
- Re: [AMBER] random number seed - range Robert Duke (Fri Aug 13 2010 - 15:05:34 PDT)
  - Re: [AMBER] random number seed - range Dean Cuebas (Fri Aug 13 2010 - 15:16:27 PDT)
    - Re: [AMBER] random number seed - range Ross Walker (Fri Aug 13 2010 - 15:22:11 PDT)
  - Re: [AMBER] random number seed - range Ross Walker (Fri Aug 13 2010 - 15:16:43 PDT)
[AMBER] about grid & radial distribution function M. Reza Ganjalikhany (Sun Jul 25 2010 - 03:59:36 PDT)
- Re: [AMBER] about grid & radial distribution function Thomas Cheatham (Thu Jul 29 2010 - 19:03:07 PDT)
[AMBER] Mutation of DNA sudipta (Sun Jul 25 2010 - 05:15:03 PDT)
- Re: [AMBER] Mutation of DNA kurisaki ikuo (Sun Jul 25 2010 - 17:57:42 PDT)
[AMBER] Check out my photos on Facebook Ashish Pandey (Sun Jul 25 2010 - 06:43:22 PDT)
[AMBER] Check out my photos on Facebook Ashish Pandey (Sun Jul 25 2010 - 06:50:09 PDT)
[AMBER] MM-PBSA/MM-GBSA: mono valent salt Xioling Chuang (Sun Jul 25 2010 - 08:45:38 PDT)
- Re: [AMBER] MM-PBSA/MM-GBSA: mono valent salt case (Sun Jul 25 2010 - 13:32:21 PDT)
[AMBER] gbsa for 1 or 2 fancy2012 (Sun Jul 25 2010 - 09:19:41 PDT)
[AMBER] For atom: .R<Na+ 1525>.A<Na+ 1> Could not find type: Na+ Jorgen Simonsen (Sun Jul 25 2010 - 10:45:27 PDT)
- Re: [AMBER] For atom: .R<Na+ 1525>.A<Na+ 1> Could not find type: Na+ Bill Ross (Sun Jul 25 2010 - 11:01:10 PDT)
 - Re: [AMBER] For atom: .R<Na+ 1525>.A<Na+ 1> Could not find type: Na+ Jorgen Simonsen (Sun Jul 25 2010 - 11:27:38 PDT)
- Re: [AMBER] For atom: .R<Na+ 1525>.A<Na+ 1> Could not find type: Na+ Bill Ross (Sun Jul 25 2010 - 11:34:38 PDT)
 - Re: [AMBER] For atom: .R<Na+ 1525>.A<Na+ 1> Could not find type: Na+ case (Sun Jul 25 2010 - 13:52:30 PDT)
[AMBER] AmberTools1.3 with amber9 Xioling Chuang (Sun Jul 25 2010 - 20:47:31 PDT)
- Re: [AMBER] AmberTools1.3 with amber9 case (Mon Jul 26 2010 - 04:44:32 PDT)
[AMBER] Error report please fix it Shubhra Gupta (Mon Jul 26 2010 - 00:25:42 PDT)
- Re: [AMBER] Error report please fix it case (Mon Jul 26 2010 - 04:47:51 PDT)
  - Re: [AMBER] Error report please fix it Shubhra Gupta (Mon Jul 26 2010 - 22:42:13 PDT)
    - Re: [AMBER] Error report please fix it Shubhra Gupta (Mon Jul 26 2010 - 22:45:54 PDT)
    - [AMBER] Fwd: Error report please fix it Shubhra Gupta (Tue Jul 27 2010 - 21:25:24 PDT)
    - Re: [AMBER] Fwd: Error report please fix it Daniel Roe (Tue Jul 27 2010 - 22:22:51 PDT)
    - Re: [AMBER] Fwd: Error report please fix it Shubhra Gupta (Wed Jul 28 2010 - 00:28:34 PDT)
[AMBER] radius of K+ ions Asfa Ali (Mon Jul 26 2010 - 03:06:16 PDT)
- Re: [AMBER] radius of K+ ions Jorgen Simonsen (Mon Jul 26 2010 - 03:19:36 PDT)
  - Re: [AMBER] radius of K+ ions Asfa Ali (Mon Jul 26 2010 - 03:42:36 PDT)
- Re: [AMBER] radius of K+ ions case (Mon Jul 26 2010 - 04:54:23 PDT)
[AMBER] NAB: pbc calculations available after all? Josh Berryman (Mon Jul 26 2010 - 05:06:20 PDT)
- Re: [AMBER] NAB: pbc calculations available after all? case (Mon Jul 26 2010 - 07:03:46 PDT)
  - Re: [AMBER] NAB: pbc calculations available after all? Josh Berryman (Mon Jul 26 2010 - 07:24:57 PDT)
[AMBER] regarding remd Jorgen Simonsen (Mon Jul 26 2010 - 06:29:31 PDT)
- Re: [AMBER] regarding remd Daniel Sindhikara (Mon Jul 26 2010 - 07:24:14 PDT)
- Re: [AMBER] regarding remd Carlos Simmerling (Mon Jul 26 2010 - 07:44:47 PDT)
  - Re: [AMBER] regarding remd Jorgen Simonsen (Mon Jul 26 2010 - 12:44:46 PDT)
[AMBER] energies in amber, namd and gromacs Alan (Mon Jul 26 2010 - 07:50:18 PDT)
[AMBER] Question about sqm in antechamber Guoxiong Su (Mon Jul 26 2010 - 09:45:20 PDT)
- Re: [AMBER] Question about sqm in antechamber case (Mon Jul 26 2010 - 11:01:37 PDT)
  - Re: [AMBER] Question about sqm in antechamber Guoxiong Su (Mon Jul 26 2010 - 11:25:49 PDT)
- [AMBER] RDF 3 files and 3 columns Philippe Pinard (Mon Jul 26 2010 - 15:19:33 PDT)
  - Re: [AMBER] RDF 3 files and 3 columns Bill Ross (Tue Jul 27 2010 - 10:48:59 PDT)
  - Re: [AMBER] RDF 3 files and 3 columns Bill Ross (Thu Jul 29 2010 - 13:28:42 PDT)
[AMBER] simulate large molecules with implicit water model (GB) Yan Gao (Mon Jul 26 2010 - 10:42:59 PDT)
- Re: [AMBER] simulate large molecules with implicit water model (GB) Carlos Simmerling (Mon Jul 26 2010 - 10:46:50 PDT)
  - Re: [AMBER] simulate large molecules with implicit water model (GB) Yan Gao (Mon Jul 26 2010 - 11:28:23 PDT)
[AMBER] Segmentation fault with translate command Yan Gao (Mon Jul 26 2010 - 11:28:30 PDT)
- Re: [AMBER] Segmentation fault with translate command case (Tue Jul 27 2010 - 04:53:44 PDT)
  - Re: [AMBER] Segmentation fault with translate command Yan Gao (Tue Jul 27 2010 - 08:43:05 PDT)
[AMBER] Permission to post Admin processes? Marc Moreau (Mon Jul 26 2010 - 12:31:05 PDT)
- Re: [AMBER] Permission to post Admin processes? case (Mon Jul 26 2010 - 13:19:32 PDT)
  - Re: [AMBER] Permission to post Admin processes? Marc Moreau (Mon Jul 26 2010 - 13:33:32 PDT)
    - Re: [AMBER] Permission to post Admin processes? case (Tue Jul 27 2010 - 04:55:20 PDT)
    - Re: [AMBER] Permission to post Admin processes? Marc Moreau (Wed Aug 04 2010 - 10:49:42 PDT)
[AMBER] vlimit exceeded after 10ns MD Siddharth Rastogi (Mon Jul 26 2010 - 14:37:36 PDT)
- Re: [AMBER] vlimit exceeded after 10ns MD Bill Ross (Mon Jul 26 2010 - 17:21:02 PDT)
- Re: [AMBER] vlimit exceeded after 10ns MD case (Mon Jul 26 2010 - 18:05:33 PDT)
- Re: [AMBER] vlimit exceeded after 10ns MD Bill Ross (Mon Jul 26 2010 - 18:13:30 PDT)
[AMBER] RDF 3 files and 3 columns Philippe Pinard (Mon Jul 26 2010 - 14:43:12 PDT)
- Re: [AMBER] RDF 3 files and 3 columns Thomas Cheatham III (Mon Jul 26 2010 - 15:49:24 PDT)
  - Re: [AMBER] RDF 3 files and 3 columns Philippe Pinard (Tue Jul 27 2010 - 06:37:37 PDT)
    - Re: [AMBER] RDF 3 files and 3 columns Daniel Roe (Tue Jul 27 2010 - 06:47:29 PDT)
    - Re: [AMBER] RDF 3 files and 3 columns Thomas Cheatham III (Tue Jul 27 2010 - 08:39:29 PDT)
    - Re: [AMBER] RDF 3 files and 3 columns Philippe Pinard (Tue Jul 27 2010 - 09:48:19 PDT)
    - Re: [AMBER] RDF 3 files and 3 columns Thomas Cheatham III (Tue Jul 27 2010 - 10:11:15 PDT)
    - Re: [AMBER] RDF 3 files and 3 columns Philippe Pinard (Thu Jul 29 2010 - 12:50:55 PDT)
    - Re: [AMBER] RDF 3 files and 3 columns Thomas Cheatham (Thu Jul 29 2010 - 18:44:56 PDT)
    - Re: [AMBER] RDF 3 files and 3 columns Philippe Pinard (Sat Jul 31 2010 - 17:03:39 PDT)
    - Re: [AMBER] RDF 3 files and 3 columns Thomas Cheatham III (Tue Jul 27 2010 - 08:41:30 PDT)
[AMBER] A clear procedure to do WHAM based on the REMD simulations outputs Dongshan Wei (Mon Jul 26 2010 - 15:43:58 PDT)
- Re: [AMBER] A clear procedure to do WHAM based on the REMD simulations outputs Daniel Sindhikara (Tue Jul 27 2010 - 04:15:10 PDT)
  - Re: [AMBER] A clear procedure to do WHAM based on the REMD simulations outputs Carlos Simmerling (Tue Jul 27 2010 - 04:18:41 PDT)
    - Re: [AMBER] A clear procedure to do WHAM based on the REMD simulations outputs Daniel Sindhikara (Tue Jul 27 2010 - 04:34:29 PDT)
    - Re: [AMBER] A clear procedure to do WHAM based on the REMD simulations outputs Dongshan Wei (Sat Jul 31 2010 - 12:19:00 PDT)
    - Re: [AMBER] A clear procedure to do WHAM based on the REMD simulations outputs Daniel Sindhikara (Sun Aug 01 2010 - 21:12:52 PDT)
[AMBER] mpi with openmpi Yan Gao (Mon Jul 26 2010 - 18:26:55 PDT)
- Re: [AMBER] mpi with openmpi Bill Ross (Mon Jul 26 2010 - 18:39:11 PDT)
- Re: [AMBER] mpi with openmpi David Watson (Mon Jul 26 2010 - 18:47:59 PDT)
  - Re: [AMBER] mpi with openmpi Yan Gao (Mon Jul 26 2010 - 19:38:35 PDT)
    - Re: [AMBER] mpi with openmpi David Watson (Mon Jul 26 2010 - 20:04:50 PDT)
Re: [AMBER] mpi with openmpi - with input files Yan Gao (Mon Jul 26 2010 - 18:45:25 PDT)
- Re: [AMBER] mpi with openmpi - with input files Jason Swails (Tue Jul 27 2010 - 10:57:32 PDT)
  - Re: [AMBER] mpi with openmpi - with input files Yan Gao (Tue Jul 27 2010 - 12:15:00 PDT)
[AMBER] very high and unstable RMSD Sangita Kachhap (Tue Jul 27 2010 - 03:15:20 PDT)
- Re: [AMBER] very high and unstable RMSD Jason Swails (Tue Jul 27 2010 - 09:07:41 PDT)
  - Re: [AMBER] very high and unstable RMSD Sangita Kachhap (Wed Jul 28 2010 - 12:06:12 PDT)
    - Re: [AMBER] very high and unstable RMSD Jason Swails (Wed Jul 28 2010 - 13:56:51 PDT)
    - Re: [AMBER] very high and unstable RMSD Sangita Kachhap (Wed Jul 28 2010 - 21:17:24 PDT)
    - Re: [AMBER] very high and unstable RMSD Kevin Hauser (Wed Jul 28 2010 - 21:32:21 PDT)
    - Re: [AMBER] very high and unstable RMSD Kevin Hauser (Wed Jul 28 2010 - 21:34:36 PDT)
    - Re: [AMBER] very high and unstable RMSD Sangita Kachhap (Wed Jul 28 2010 - 21:44:49 PDT)
[AMBER] make test trouble with Amber11 池田輝彦 (Tue Jul 27 2010 - 05:46:46 PDT)
- Re: [AMBER] make test trouble with Amber11 case (Tue Jul 27 2010 - 06:16:01 PDT)
[AMBER] Calculation of Intramolecular hydrogen bonding using ptraj Sudha Mani Karra (Tue Jul 27 2010 - 07:20:05 PDT)
- Re: [AMBER] Calculation of Intramolecular hydrogen bonding using ptraj Thomas Cheatham III (Tue Jul 27 2010 - 08:46:12 PDT)
  - Re: [AMBER] Calculation of Intramolecular hydrogen bonding using ptraj Sudha Mani Karra (Tue Jul 27 2010 - 09:51:55 PDT)
    - Re: [AMBER] Calculation of Intramolecular hydrogen bonding using ptraj Thomas Cheatham III (Tue Jul 27 2010 - 10:15:43 PDT)
[AMBER] MM-PBSA per residue decompostion manoj singh (Tue Jul 27 2010 - 08:39:08 PDT)
- Re: [AMBER] MM-PBSA per residue decompostion Catein Catherine (Tue Jul 27 2010 - 21:19:55 PDT)
  - [AMBER] How to prepare the same prmtop from two PDBs for NED analysis? Catein Catherine (Tue Jul 27 2010 - 21:27:55 PDT)
    - Re: [AMBER] How to prepare the same prmtop from two PDBs for NED analysis? case (Wed Jul 28 2010 - 05:08:32 PDT)
[AMBER] cumulative patch with two bugfixes for threaded mm_pbsa.pl Thomas Zeiser (Tue Jul 27 2010 - 09:13:57 PDT)
Re: [AMBER] mpi with openmpi - SGE error Yan Gao (Tue Jul 27 2010 - 19:47:05 PDT)
[AMBER] about dielectric constant.. Wookyung Yu (Tue Jul 27 2010 - 20:18:19 PDT)
- Re: [AMBER] about dielectric constant.. Jason Swails (Wed Jul 28 2010 - 04:59:16 PDT)
- Re: [AMBER] about dielectric constant.. case (Wed Jul 28 2010 - 05:32:24 PDT)
  - [AMBER] Solid surface simulation in Amber - the recommended approach ? Marek Maly (Tue Aug 03 2010 - 11:35:28 PDT)
    - Re: [AMBER] Solid surface simulation in Amber - the recommended approach ? Marek Maly (Fri Aug 06 2010 - 18:26:22 PDT)
    - Re: [AMBER] Solid surface simulation in Amber - the recommended approach ? peker milas (Mon Jun 20 2011 - 10:17:17 PDT)
    - Re: [AMBER] Solid surface simulation in Amber - the recommended approach ? Marek Maly (Mon Jun 20 2011 - 11:53:55 PDT)
    - Re: [AMBER] Solid surface simulation in Amber - the recommended approach ? peker milas (Tue Jun 21 2011 - 05:03:09 PDT)
- Re: [AMBER] about dielectric constant.. Robert Duke (Wed Jul 28 2010 - 06:09:59 PDT)
[AMBER] Reference of ion parameters employed in parm99 kurisaki ikuo (Tue Jul 27 2010 - 20:21:09 PDT)
- Re: [AMBER] Reference of ion parameters employed in parm99 Paul S. Nerenberg (Tue Jul 27 2010 - 21:04:12 PDT)
  - Re: [AMBER] Reference of ion parameters employed in parm99 kurisaki ikuo (Tue Jul 27 2010 - 21:33:54 PDT)
    - Re: [AMBER] Reference of ion parameters employed in parm99 Paul S. Nerenberg (Tue Jul 27 2010 - 21:45:38 PDT)
    - Re: [AMBER] Reference of ion parameters employed in parm99 kurisaki ikuo (Tue Jul 27 2010 - 22:13:44 PDT)
- Re: [AMBER] Reference of ion parameters employed in parm99 kurisaki ikuo (Tue Jul 27 2010 - 22:22:00 PDT)
[AMBER] how to develop parameter for organotin Shulin Zhuang (Wed Jul 28 2010 - 00:04:31 PDT)
- Re: [AMBER] how to develop parameter for organotin FyD (Wed Jul 28 2010 - 01:51:35 PDT)
[AMBER] calculation of sasa Asfa Ali (Wed Jul 28 2010 - 07:06:56 PDT)
- Re: [AMBER] calculation of sasa case (Wed Jul 28 2010 - 18:43:31 PDT)
  - [AMBER] What is the max atom can be run by addles in amber10? Catein Catherine (Wed Jul 28 2010 - 20:42:25 PDT)
  - Re: [AMBER] calculation of sasa Asfa Ali (Wed Jul 28 2010 - 23:47:59 PDT)
    - Re: [AMBER] calculation of sasa case (Thu Jul 29 2010 - 04:45:01 PDT)
[AMBER] Invitation to connect on LinkedIn rameshwar prajapati (Wed Jul 28 2010 - 09:39:52 PDT)
[AMBER] Parallel test times Marc Moreau (Wed Jul 28 2010 - 10:03:42 PDT)
- Re: [AMBER] Parallel test times Marc Moreau (Wed Jul 28 2010 - 10:08:17 PDT)
  - Re: [AMBER] Parallel test times Daniel Roe (Wed Jul 28 2010 - 10:14:08 PDT)
[AMBER] RESP "too many charge-group constraints" error Justine Shaw (Wed Jul 28 2010 - 13:24:05 PDT)
- Re: [AMBER] RESP "too many charge-group constraints" error FyD (Wed Jul 28 2010 - 13:32:49 PDT)
  - Re: [AMBER] RESP "too many charge-group constraints" error Justine Shaw (Wed Jul 28 2010 - 13:51:57 PDT)
    - Re: [AMBER] RESP "too many charge-group constraints" error FyD (Wed Jul 28 2010 - 14:04:11 PDT)
    - Re: [AMBER] RESP "too many charge-group constraints" error Justine Shaw (Wed Jul 28 2010 - 14:18:19 PDT)
    - Re: [AMBER] RESP "too many charge-group constraints" error Justine Shaw (Thu Jul 29 2010 - 09:37:38 PDT)
[AMBER] NAB problem with a metallic atom InSuk Joung (Wed Jul 28 2010 - 14:34:19 PDT)
- Re: [AMBER] NAB problem with a metallic atom Bill Ross (Wed Jul 28 2010 - 14:49:13 PDT)
  - Re: [AMBER] NAB problem with a metallic atom InSuk Joung (Wed Jul 28 2010 - 14:59:15 PDT)
- Re: [AMBER] NAB problem with a metallic atom Bill Ross (Wed Jul 28 2010 - 15:19:25 PDT)
  - Re: [AMBER] NAB problem with a metallic atom InSuk Joung (Wed Jul 28 2010 - 16:16:46 PDT)
[AMBER] PMF from EVB calculations Ewa Chudyk (Wed Jul 28 2010 - 15:13:31 PDT)
[AMBER] PMF from EVB calculations Ewa Chudyk (Thu Jul 29 2010 - 04:57:13 PDT)
[AMBER] 1D PMF D.J. Cole (Thu Jul 29 2010 - 07:03:52 PDT)
[AMBER] how to generate porcupine plot Jia Xu (Thu Jul 29 2010 - 09:31:36 PDT)
- Re: [AMBER] how to generate porcupine plot Hector A. Baldoni (Thu Jul 29 2010 - 15:43:24 PDT)
  - [AMBER] Parallel pmemd.cuda: any preliminary cross-node tests? Sasha Buzko (Thu Jul 29 2010 - 16:52:01 PDT)
    - Re: [AMBER] Parallel pmemd.cuda: any preliminary cross-node tests? Ross Walker (Thu Jul 29 2010 - 19:09:20 PDT)
    - Re: [AMBER] Parallel pmemd.cuda: any preliminary cross-node tests? Scott Le Grand (Sat Jul 31 2010 - 10:12:29 PDT)
    - Re: [AMBER] Parallel pmemd.cuda: any preliminary cross-node tests? Thomas Zeiser (Sun Aug 01 2010 - 00:32:04 PDT)
    - Re: [AMBER] Parallel pmemd.cuda: any preliminary cross-node tests? Scott Le Grand (Mon Aug 02 2010 - 10:08:25 PDT)
    - [AMBER] Parallel pmemd.cuda: local bandwidth question. Are dual host PCI-E cards make any sense? Sasha Buzko (Wed Aug 04 2010 - 20:57:37 PDT)
    - Re: [AMBER] Parallel pmemd.cuda: local bandwidth question. Are dual host PCI-E cards make any sense? Ross Walker (Thu Aug 05 2010 - 07:02:57 PDT)
    - Re: [AMBER] Parallel pmemd.cuda: local bandwidth question. Are dual host PCI-E cards make any sense? Scott Le Grand (Thu Aug 05 2010 - 08:03:42 PDT)
    - Re: [AMBER] Parallel pmemd.cuda: local bandwidth question. Are dual host PCI-E cards make any sense? Sasha Buzko (Thu Aug 05 2010 - 10:10:10 PDT)
    - Re: [AMBER] Parallel pmemd.cuda: local bandwidth question. Are dual host PCI-E cards make any sense? Scott Le Grand (Thu Aug 05 2010 - 10:17:58 PDT)
    - Re: [AMBER] Parallel pmemd.cuda: local bandwidth question. Are dual host PCI-E cards make any sense? Ross Walker (Thu Aug 05 2010 - 18:26:26 PDT)
    - [AMBER] Horrific pmemd.cuda performance on an 8-GPU system Sasha Buzko (Wed Aug 11 2010 - 12:15:59 PDT)
    - Re: [AMBER] Horrific pmemd.cuda performance on an 8-GPU system Ross Walker (Wed Aug 11 2010 - 13:04:25 PDT)
    - Re: [AMBER] Horrific pmemd.cuda performance on an 8-GPU system Sasha Buzko (Thu Aug 12 2010 - 09:23:50 PDT)
    - Re: [AMBER] Horrific pmemd.cuda performance on an 8-GPU system michael (Wed Aug 11 2010 - 14:48:36 PDT)
  - Re: [AMBER] how to generate porcupine plot Jia Xu (Sun Aug 01 2010 - 01:27:12 PDT)
[AMBER] Minor Typo bug. Marc Moreau (Thu Jul 29 2010 - 10:20:22 PDT)
- Re: [AMBER] Minor Typo bug. Mengjuei Hsieh (Thu Jul 29 2010 - 11:59:04 PDT)
[AMBER] tleap and sander minimization Hegazy,Lamees (Thu Jul 29 2010 - 11:35:45 PDT)
- Re: [AMBER] tleap and sander minimization Ben Roberts (Thu Jul 29 2010 - 11:52:06 PDT)
- Re: [AMBER] tleap and sander minimization Bill Ross (Thu Jul 29 2010 - 11:53:49 PDT)
- Re: [AMBER] tleap and sander minimization Hegazy,Lamees (Thu Jul 29 2010 - 12:02:06 PDT)
[AMBER] Which one, ESP calculation? William Flak (Thu Jul 29 2010 - 20:41:50 PDT)
[AMBER] how to prepare a system with solvent of ethanol + water ? vasu mathi (Fri Jul 30 2010 - 03:06:37 PDT)
- Re: [AMBER] how to prepare a system with solvent of ethanol + water ? setyanto tri wahyudi (Fri Jul 30 2010 - 04:00:30 PDT)
- Re: [AMBER] how to prepare a system with solvent of ethanol + water ? vasu mathi (Sat Jul 31 2010 - 09:57:31 PDT)
[AMBER] dipole moment of binary mixture box Ganesh Kamath (Fri Jul 30 2010 - 05:33:03 PDT)
[AMBER] addles Hegazy,Lamees (Fri Jul 30 2010 - 10:23:42 PDT)
- Re: [AMBER] addles Carlos Simmerling (Fri Jul 30 2010 - 10:28:11 PDT)
[AMBER] fix CM riya david (Fri Jul 30 2010 - 12:43:16 PDT)
- Re: [AMBER] fix CM Jason Swails (Fri Jul 30 2010 - 13:14:28 PDT)
[AMBER] regarding IWRAP in Sander aneesh cna (Fri Jul 30 2010 - 22:50:23 PDT)
- Re: [AMBER] regarding IWRAP in Sander case (Sat Jul 31 2010 - 06:03:17 PDT)
[AMBER] Constant pH simulation at pH 7 nicholus bhattacharjee (Sat Jul 31 2010 - 07:19:00 PDT)
- Re: [AMBER] Constant pH simulation at pH 7 Jason Swails (Sat Jul 31 2010 - 07:39:55 PDT)
[AMBER] obtain a .pdb file from a .prepin/.frcmod file Ehsan Habibi (Sat Jul 31 2010 - 12:42:29 PDT)
- Re: [AMBER] obtain a .pdb file from a .prepin/.frcmod file Alessandro Nascimento (Sat Jul 31 2010 - 12:56:27 PDT)
  - Re: [AMBER] obtain a .pdb file from a .prepin/.frcmod file Jason Swails (Sat Jul 31 2010 - 13:45:57 PDT)
[AMBER] how to extract temperatur and other data from mdout setyanto tri wahyudi (Sun Aug 01 2010 - 20:45:20 PDT)
- Re: [AMBER] how to extract temperatur and other data from mdout Bill Ross (Sun Aug 01 2010 - 22:24:04 PDT)
  - Re: [AMBER] how to extract temperatur and other data from mdout setyanto tri wahyudi (Sun Aug 01 2010 - 23:06:10 PDT)
    - Re: [AMBER] how to extract temperatur and other data from mdout Jason Swails (Mon Aug 02 2010 - 05:27:55 PDT)
- Re: [AMBER] how to extract temperatur and other data from mdout Bill Ross (Mon Aug 02 2010 - 09:52:08 PDT)
  - Re: [AMBER] how to extract temperatur and other data from mdout setyanto tri wahyudi (Mon Aug 02 2010 - 20:25:55 PDT)
[AMBER] error in heating rameshwar prajapati (Sun Aug 01 2010 - 22:31:55 PDT)
- Re: [AMBER] error in heating Bill Ross (Sun Aug 01 2010 - 22:48:40 PDT)
- Re: [AMBER] error in heating Bill Ross (Sun Aug 01 2010 - 22:52:25 PDT)
[AMBER] errror in heating rameshwar prajapati (Sun Aug 01 2010 - 22:47:51 PDT)
- Re: [AMBER] errror in heating Bill Ross (Sun Aug 01 2010 - 22:56:46 PDT)
  - Re: [AMBER] errror in heating rameshwar prajapati (Sun Aug 01 2010 - 23:22:37 PDT)
    - Re: [AMBER] errror in heating Jason Swails (Mon Aug 02 2010 - 04:37:25 PDT)
- Re: [AMBER] errror in heating Bill Ross (Mon Aug 02 2010 - 08:28:21 PDT)
[AMBER] NVE Philippe Pinard (Sun Aug 01 2010 - 22:53:53 PDT)
- Re: [AMBER] NVE steinbrt.rci.rutgers.edu (Mon Aug 02 2010 - 00:59:02 PDT)
- Re: [AMBER] NVE Jason Swails (Mon Aug 02 2010 - 04:23:08 PDT)
  - [AMBER] antechamber Philippe Pinard (Mon Aug 02 2010 - 11:56:26 PDT)
    - [AMBER] RDPARM Philippe Pinard (Mon Aug 02 2010 - 16:12:20 PDT)
    - Re: [AMBER] RDPARM Thomas Cheatham III (Mon Aug 02 2010 - 16:24:40 PDT)
    - Re: [AMBER] RDPARM Philippe Pinard (Tue Aug 03 2010 - 08:41:54 PDT)
    - Re: [AMBER] RDPARM Thomas Cheatham III (Tue Aug 03 2010 - 14:11:58 PDT)
    - Re: [AMBER] RDPARM Philippe Pinard (Tue Aug 03 2010 - 14:32:10 PDT)
    - Re: [AMBER] RDPARM Thomas Cheatham III (Tue Aug 03 2010 - 15:00:07 PDT)
    - Re: [AMBER] RDPARM case (Tue Aug 03 2010 - 15:26:49 PDT)
    - Re: [AMBER] RDPARM Philippe Pinard (Wed Aug 04 2010 - 09:35:49 PDT)
    - Re: [AMBER] RDPARM case (Wed Aug 04 2010 - 14:48:36 PDT)
    - Re: [AMBER] RDPARM Philippe Pinard (Wed Aug 04 2010 - 17:24:56 PDT)
    - Re: [AMBER] RDPARM case (Wed Aug 04 2010 - 17:37:18 PDT)
    - Re: [AMBER] RDPARM Philippe Pinard (Tue Aug 03 2010 - 14:40:03 PDT)
    - Re: [AMBER] antechamber case (Mon Aug 02 2010 - 18:30:33 PDT)
[AMBER] Problem with running PMEMD on a cluster ali naserian nik (Mon Aug 02 2010 - 00:37:12 PDT)
[AMBER] Gradually Compress Volume to Increase Density Shubhra Gupta (Mon Aug 02 2010 - 01:59:45 PDT)
- Re: [AMBER] Gradually Compress Volume to Increase Density Jason Swails (Mon Aug 02 2010 - 04:17:55 PDT)
  - Re: [AMBER] Gradually Compress Volume to Increase Density Shubhra Gupta (Mon Aug 02 2010 - 05:19:34 PDT)
    - Re: [AMBER] Gradually Compress Volume to Increase Density Jason Swails (Mon Aug 02 2010 - 05:33:46 PDT)
- Re: [AMBER] Gradually Compress Volume to Increase Density Bill Ross (Mon Aug 02 2010 - 08:21:10 PDT)
[AMBER] Writing trajectory for C-alpha atoms Ibrahim Moustafa (Mon Aug 02 2010 - 08:31:33 PDT)
- Re: [AMBER] Writing trajectory for C-alpha atoms Daniel Roe (Mon Aug 02 2010 - 08:43:59 PDT)
  - Re: [AMBER] Writing trajectory for C-alpha atoms Ibrahim Moustafa (Mon Aug 02 2010 - 10:38:25 PDT)
    - Re: [AMBER] Writing trajectory for C-alpha atoms Jason Swails (Mon Aug 02 2010 - 11:35:47 PDT)
    - Re: [AMBER] Writing trajectory for C-alpha atoms Ibrahim Moustafa (Mon Aug 02 2010 - 11:56:57 PDT)
- Re: [AMBER] Writing trajectory for C-alpha atoms Bill Ross (Mon Aug 02 2010 - 11:54:57 PDT)
  - Re: [AMBER] Writing trajectory for C-alpha atoms Ibrahim Moustafa (Mon Aug 02 2010 - 12:16:48 PDT)
[AMBER] conversion of the CYANA upl into amber format: QE, QD of Tyr and Phe Francesca Cantini (Mon Aug 02 2010 - 09:35:31 PDT)
- Re: [AMBER] conversion of the CYANA upl into amber format: QE, QD of Tyr and Phe case (Mon Aug 02 2010 - 16:52:43 PDT)
[AMBER] restraining only heavy atoms in PMEMD Senthil Natesan (Mon Aug 02 2010 - 11:37:33 PDT)
[AMBER] Mistake in using amber Rilei Yu (Mon Aug 02 2010 - 17:55:47 PDT)
- Re: [AMBER] Mistake in using amber Gustavo Seabra (Mon Aug 02 2010 - 18:01:41 PDT)
- Re: [AMBER] Mistake in using amber Bill Ross (Mon Aug 02 2010 - 18:02:42 PDT)
  - Re: [AMBER] Mistake in using amber Rilei Yu (Mon Aug 02 2010 - 18:10:40 PDT)
- Re: [AMBER] Mistake in using amber steinbrt.rci.rutgers.edu (Tue Aug 03 2010 - 00:32:53 PDT)
[AMBER] questions about installing pmend.cuda 宋德寿 (Mon Aug 02 2010 - 21:45:49 PDT)
- Re: [AMBER] questions about installing pmend.cuda maluyao (Mon Aug 02 2010 - 21:55:06 PDT)
  - Re: [AMBER] questions about installing pmend.cuda 宋德寿 (Mon Aug 02 2010 - 22:26:25 PDT)
  - Re: [AMBER] questions about installing pmend.cuda 宋德寿 (Mon Aug 02 2010 - 23:39:45 PDT)
    - Re: [AMBER] questions about installing pmend.cuda Jason Swails (Tue Aug 03 2010 - 04:26:21 PDT)
    - Re: [AMBER] questions about installing pmend.cuda 宋德寿 (Tue Aug 03 2010 - 05:07:32 PDT)
    - Re: [AMBER] questions about installing pmend.cuda 宋德寿 (Tue Aug 03 2010 - 20:03:24 PDT)
- Re: [AMBER] questions about installing pmend.cuda case (Tue Aug 03 2010 - 06:20:09 PDT)
- Re: [AMBER] questions about installing pmend.cuda Ross Walker (Tue Aug 03 2010 - 11:04:15 PDT)
  - Re: [AMBER] questions about installing pmend.cuda 宋德寿 (Tue Aug 03 2010 - 19:59:02 PDT)
[AMBER] how to run entropy calculation using pmemd fancy2012 (Tue Aug 03 2010 - 02:50:13 PDT)
- Re: [AMBER] how to run entropy calculation using pmemd Jason Swails (Tue Aug 03 2010 - 04:29:47 PDT)
  - Re: [AMBER] how to run entropy calculation using pmemd fancy2012 (Tue Aug 03 2010 - 04:36:05 PDT)
[AMBER] ptraj and image Thomas Exner (Tue Aug 03 2010 - 04:08:11 PDT)
- Re: [AMBER] ptraj and image steinbrt.rci.rutgers.edu (Tue Aug 03 2010 - 04:13:13 PDT)
[AMBER] How to parametrize ligand using AMOEBA polarizable potential sunita gupta (Tue Aug 03 2010 - 04:43:25 PDT)
[AMBER] PTRAJ: problem with image command Xioling Chuang (Tue Aug 03 2010 - 07:30:46 PDT)
- Re: [AMBER] PTRAJ: problem with image command InSuk Joung (Tue Aug 03 2010 - 08:20:13 PDT)
  - Re: [AMBER] PTRAJ: problem with image command Xioling Chuang (Tue Aug 03 2010 - 09:17:02 PDT)
    - Re: [AMBER] PTRAJ: problem with image command InSuk Joung (Tue Aug 03 2010 - 11:04:32 PDT)
    - Re: [AMBER] PTRAJ: problem with image command InSuk Joung (Tue Aug 03 2010 - 11:05:56 PDT)
    - Re: [AMBER] PTRAJ: problem with image command Xioling Chuang (Tue Aug 03 2010 - 20:43:39 PDT)
Re: [AMBER] Solid surface simulation in Amber Bill Ross (Tue Aug 03 2010 - 12:14:57 PDT)
- Re: [AMBER] Solid surface simulation in Amber Marek Maly (Tue Aug 03 2010 - 15:23:34 PDT)
- Re: [AMBER] Solid surface simulation in Amber Bill Ross (Tue Aug 03 2010 - 16:03:49 PDT)
- Re: [AMBER] Solid surface simulation in Amber Bill Ross (Tue Aug 03 2010 - 16:08:20 PDT)
  - Re: [AMBER] Solid surface simulation in Amber Marek Maly (Tue Aug 03 2010 - 16:00:24 PDT)
    - Re: [AMBER] Solid surface simulation in Amber Tom Williams (Tue Aug 03 2010 - 23:06:47 PDT)
    - Re: [AMBER] Solid surface simulation in Amber case (Wed Aug 04 2010 - 04:23:11 PDT)
    - Re: [AMBER] Solid surface simulation in Amber Marek Maly (Wed Aug 04 2010 - 08:03:54 PDT)
    - Re: [AMBER] Solid surface simulation in Amber Tom Williams (Wed Aug 04 2010 - 09:35:57 PDT)
[AMBER] ptraj question Jia Xu (Tue Aug 03 2010 - 15:29:36 PDT)
- Re: [AMBER] ptraj question Jason Swails (Tue Aug 03 2010 - 17:27:16 PDT)
  - [AMBER] How to define putative reaction coordinates in AMBER? Catein Catherine (Tue Aug 03 2010 - 23:09:01 PDT)
    - [AMBER] Error message in runing Steered MD in AMBER 10 (tutorial A10) Catein Catherine (Wed Aug 04 2010 - 02:59:40 PDT)
    - Re: [AMBER] Error message in runing Steered MD in AMBER 10 (tutorial A10) Jason Swails (Wed Aug 04 2010 - 06:17:34 PDT)
    - Re: [AMBER] How to define putative reaction coordinates in AMBER? Jason Swails (Wed Aug 04 2010 - 05:29:45 PDT)
[AMBER] analysis of mm_pbsa Asfa Ali (Tue Aug 03 2010 - 23:50:33 PDT)
- Re: [AMBER] analysis of mm_pbsa Jason Swails (Wed Aug 04 2010 - 05:36:32 PDT)
  - Re: [AMBER] analysis of mm_pbsa Asfa Ali (Wed Aug 04 2010 - 06:19:02 PDT)
    - Re: [AMBER] analysis of mm_pbsa Jason Swails (Wed Aug 04 2010 - 06:27:18 PDT)
    - Re: [AMBER] analysis of mm_pbsa Asfa Ali (Wed Aug 04 2010 - 06:36:46 PDT)
[AMBER] entropy calculation using nmode Asfa Ali (Wed Aug 04 2010 - 03:46:59 PDT)
[AMBER] simulation with multiple docked ligand Ashutosh Shandilya (Wed Aug 04 2010 - 05:47:07 PDT)
- Re: [AMBER] simulation with multiple docked ligand steinbrt.rci.rutgers.edu (Wed Aug 04 2010 - 05:55:10 PDT)
[AMBER] Energy abrupt rise in Energy minimization Jiang Yusheng (Wed Aug 04 2010 - 10:37:32 PDT)
- Re: [AMBER] Energy abrupt rise in Energy minimization Bill Ross (Wed Aug 04 2010 - 11:33:21 PDT)
  - Re: [AMBER] Energy abrupt rise in Energy minimization Jiang Yusheng (Wed Aug 04 2010 - 11:49:16 PDT)
- Re: [AMBER] Energy abrupt rise in Energy minimization Bill Ross (Wed Aug 04 2010 - 12:10:48 PDT)
  - Re: [AMBER] Energy abrupt rise in Energy minimization Jiang Yusheng (Wed Aug 04 2010 - 12:31:15 PDT)
- Re: [AMBER] Energy abrupt rise in Energy minimization Bill Ross (Wed Aug 04 2010 - 13:25:40 PDT)
  - Re: [AMBER] Energy abrupt rise in Energy minimization Jiang Yusheng (Thu Aug 05 2010 - 07:00:04 PDT)
[AMBER] How to make parameter files of GTP from PDB file. kurisaki ikuo (Wed Aug 04 2010 - 20:12:59 PDT)
- Re: [AMBER] How to make parameter files of GTP from PDB file. kurisaki ikuo (Wed Aug 04 2010 - 20:43:37 PDT)
- Re: [AMBER] How to make parameter files of GTP from PDB file. Bill Ross (Thu Aug 05 2010 - 10:28:45 PDT)
[AMBER] Parametrization of Ligand using AMOEBA potential sunita gupta (Thu Aug 05 2010 - 00:32:55 PDT)
- Re: [AMBER] Parametrization of Ligand using AMOEBA potential Dian Jiao (Thu Aug 05 2010 - 07:15:05 PDT)
[AMBER] Tutorial3 George Tzotzos (Thu Aug 05 2010 - 09:52:37 PDT)
- [AMBER] Tutorial3 George Tzotzos (Thu Aug 05 2010 - 10:22:02 PDT)
[AMBER] error message about memory in antechamber Guoxiong Su (Thu Aug 05 2010 - 11:16:27 PDT)
- Re: [AMBER] error message about memory in antechamber case (Thu Aug 05 2010 - 12:48:26 PDT)
  - [AMBER] Can I use LCOD command for umbrella sampling PMF calculation? Catein Catherine (Fri Aug 06 2010 - 00:46:58 PDT)
    - Re: [AMBER] Can I use LCOD command for umbrella sampling PMF calculation? Jason Swails (Fri Aug 06 2010 - 05:52:43 PDT)
  - Re: [AMBER] error message about memory in antechamber Guoxiong Su (Mon Aug 09 2010 - 08:47:52 PDT)
    - Re: [AMBER] error message about memory in antechamber case (Mon Aug 09 2010 - 11:47:52 PDT)
    - Re: [AMBER] error message about memory in antechamber Guoxiong Su (Tue Aug 10 2010 - 12:26:20 PDT)
    - Re: [AMBER] error message about memory in antechamber case (Wed Aug 11 2010 - 09:03:54 PDT)
[AMBER] Post-processing error arikcohen (Thu Aug 05 2010 - 17:15:54 PDT)
- Re: [AMBER] Post-processing error - NO NEED TO ANSWER, PROBLEM SOLVED arikcohen (Fri Aug 06 2010 - 16:41:45 PDT)
  - Re: [AMBER] Post-processing error - NO NEED TO ANSWER, PROBLEM SOLVED Bill Ross (Fri Aug 06 2010 - 16:50:17 PDT)
    - Re: [AMBER] Post-processing error - NO NEED TO ANSWER, PROBLEM SOLVED arikcohen (Fri Aug 06 2010 - 18:02:09 PDT)
[AMBER] H-bonding analysis Asfa Ali (Thu Aug 05 2010 - 23:19:19 PDT)
- [AMBER] Can I convert the umberlla sampling results to LCOD for 1D-PMF analysis? Catein Catherine (Fri Aug 06 2010 - 00:57:17 PDT)
  - [AMBER] Error message when doing A10 tutorial (SMD with LCOD) with AMBER 10. Catein Catherine (Fri Aug 06 2010 - 01:11:15 PDT)
    - [AMBER] How to run LCOD in AMBER 10? Catein Catherine (Sun Aug 08 2010 - 21:26:17 PDT)
    - [AMBER] Where to apply find computer resources to run AMBER? Catein Catherine (Sun Aug 08 2010 - 21:55:33 PDT)
    - [AMBER] How can I run Random Acceleration Molecular Dynamics with AMBER10? Catein Catherine (Sun Aug 08 2010 - 22:58:09 PDT)
    - Re: [AMBER] How can I run Random Acceleration Molecular Dynamics with AMBER10? Jason Swails (Mon Aug 09 2010 - 05:51:42 PDT)
    - Re: [AMBER] How can I run Random Acceleration Molecular Dynamics with AMBER10? Vlad Cojocaru (Mon Aug 09 2010 - 06:51:15 PDT)
    - Re: [AMBER] Where to apply find computer resources to run AMBER? Ross Walker (Mon Aug 09 2010 - 06:20:15 PDT)
    - Re: [AMBER] Where to apply find computer resources to run AMBER? Catein Catherine (Mon Aug 09 2010 - 07:21:04 PDT)
    - Re: [AMBER] How to run LCOD in AMBER 10? Jason Swails (Mon Aug 09 2010 - 06:10:37 PDT)
    - Re: [AMBER] How to run LCOD in AMBER 10? Catein Catherine (Mon Aug 09 2010 - 07:14:37 PDT)
    - Re: [AMBER] How to run LCOD in AMBER 10? M. L. Dodson (Mon Aug 09 2010 - 08:30:40 PDT)
  - Re: [AMBER] Can I convert the umberlla sampling results to LCOD for 1D-PMF analysis? Jason Swails (Fri Aug 06 2010 - 06:02:21 PDT)
- Re: [AMBER] H-bonding analysis Bill Ross (Fri Aug 06 2010 - 09:52:37 PDT)
[AMBER] peptides not folding in remd with changing sequence of D and L isomer Jorgen Simonsen (Sun Aug 08 2010 - 09:44:35 PDT)
- Re: [AMBER] peptides not folding in remd with changing sequence of D and L isomer Jason Swails (Sun Aug 08 2010 - 10:47:53 PDT)
  - Re: [AMBER] peptides not folding in remd with changing sequence of D and L isomer Daniel Sindhikara (Sun Aug 08 2010 - 23:54:52 PDT)
    - Re: [AMBER] peptides not folding in remd with changing sequence of D and L isomer Jorgen Simonsen (Mon Aug 09 2010 - 00:02:03 PDT)
    - Re: [AMBER] peptides not folding in remd with changing sequence of D and L isomer Carlos Simmerling (Mon Aug 09 2010 - 04:21:22 PDT)
    - Re: [AMBER] peptides not folding in remd with changing sequence of D and L isomer Jorgen Simonsen (Mon Aug 09 2010 - 04:52:25 PDT)
    - Re: [AMBER] peptides not folding in remd with changing sequence of D and L isomer Carlos Simmerling (Mon Aug 09 2010 - 04:54:07 PDT)
    - Re: [AMBER] peptides not folding in remd with changing sequence of D and L isomer Jorgen Simonsen (Mon Aug 09 2010 - 05:02:05 PDT)
    - Re: [AMBER] peptides not folding in remd with changing sequence of D and L isomer Carlos Simmerling (Mon Aug 09 2010 - 07:20:43 PDT)
    - Re: [AMBER] peptides not folding in remd with changing sequence of D and L isomer Jorgen Simonsen (Mon Aug 09 2010 - 08:12:50 PDT)
    - Re: [AMBER] peptides not folding in remd with changing sequence of D and L isomer Carlos Simmerling (Mon Aug 09 2010 - 08:18:16 PDT)
[AMBER] dear sir selva raj (Sun Aug 08 2010 - 10:42:59 PDT)
- Re: [AMBER] dear sir Sushil Mishra (Sun Aug 08 2010 - 10:50:50 PDT)
  - Re: [AMBER] dear sir Sushil Mishra (Sun Aug 08 2010 - 10:52:11 PDT)
[AMBER] The Result of PARMCHK setyanto tri wahyudi (Sun Aug 08 2010 - 23:32:47 PDT)
- Re: [AMBER] The Result of PARMCHK case (Mon Aug 09 2010 - 04:57:37 PDT)
  - Re: [AMBER] The Result of PARMCHK setyanto tri wahyudi (Mon Aug 09 2010 - 20:09:34 PDT)
    - Re: [AMBER] The Result of PARMCHK case (Tue Aug 10 2010 - 04:33:20 PDT)
    - Re: [AMBER] The Result of PARMCHK setyanto tri wahyudi (Wed Aug 11 2010 - 19:41:19 PDT)
[AMBER] Soft-core Coulomb potential Samuel Genheden (Mon Aug 09 2010 - 00:52:31 PDT)
- Re: [AMBER] Soft-core Coulomb potential case (Mon Aug 09 2010 - 04:58:59 PDT)
[AMBER] error when compiling pmemd Jorgen Simonsen (Mon Aug 09 2010 - 03:56:13 PDT)
- Re: [AMBER] error when compiling pmemd case (Mon Aug 09 2010 - 05:05:36 PDT)
  - Re: [AMBER] error when compiling pmemd Jorgen Simonsen (Mon Aug 09 2010 - 05:15:08 PDT)
    - Re: [AMBER] error when compiling pmemd Ross Walker (Mon Aug 09 2010 - 06:06:44 PDT)
    - Re: [AMBER] error when compiling pmemd Jorgen Simonsen (Mon Aug 09 2010 - 09:20:42 PDT)
    - Re: [AMBER] error when compiling pmemd Jason Swails (Mon Aug 09 2010 - 12:57:40 PDT)
    - Re: [AMBER] error when compiling pmemd Jorgen Simonsen (Mon Aug 09 2010 - 23:55:56 PDT)
    - Re: [AMBER] error when compiling pmemd Jason Swails (Tue Aug 10 2010 - 06:05:14 PDT)
    - Re: [AMBER] error when compiling pmemd Jorgen Simonsen (Tue Aug 10 2010 - 09:37:08 PDT)
    - Re: [AMBER] error when compiling pmemd Ross Walker (Tue Aug 10 2010 - 10:35:28 PDT)
    - Re: [AMBER] error when compiling pmemd Jorgen Simonsen (Tue Aug 10 2010 - 11:14:43 PDT)
    - Re: [AMBER] error when compiling pmemd Daniel Roe (Tue Aug 10 2010 - 11:21:32 PDT)
    - Re: [AMBER] error when compiling pmemd Ross Walker (Tue Aug 10 2010 - 11:32:07 PDT)
    - Re: [AMBER] error when compiling pmemd Jorgen Simonsen (Tue Aug 10 2010 - 11:37:19 PDT)
[AMBER] question about empirical valence bond theory Ganesh Kamath (Mon Aug 09 2010 - 07:06:38 PDT)
[AMBER] using nab to create peptides and minimise Alan (Mon Aug 09 2010 - 07:32:33 PDT)
- Re: [AMBER] using nab to create peptides and minimise case (Mon Aug 09 2010 - 07:54:15 PDT)
[AMBER] SASA over trajectory Beale, John (Mon Aug 09 2010 - 07:58:22 PDT)
- Re: [AMBER] SASA over trajectory Carlos Simmerling (Mon Aug 09 2010 - 08:01:06 PDT)
[AMBER] Amber: saveamberparm error Karan Mehra (Mon Aug 09 2010 - 11:49:16 PDT)
- Re: [AMBER] Amber: saveamberparm error Bill Ross (Mon Aug 09 2010 - 12:04:43 PDT)
- Re: [AMBER] Amber: saveamberparm error case (Tue Aug 10 2010 - 04:48:24 PDT)
  - Re: [AMBER] Amber: saveamberparm error Karan Mehra (Wed Aug 11 2010 - 12:38:11 PDT)
    - Re: [AMBER] Amber: saveamberparm error case (Wed Aug 11 2010 - 12:47:49 PDT)
[AMBER] Name for Glucosamine Shubhra Gupta (Mon Aug 09 2010 - 22:39:17 PDT)
- Re: [AMBER] Name for Glucosamine Shubhra Gupta (Tue Aug 10 2010 - 05:21:52 PDT)
  - Re: [AMBER] Name for Glucosamine Lachele Foley (Lists) (Tue Aug 10 2010 - 08:16:42 PDT)
[AMBER] AMBER ff02 r1 Neha Gandhi (Tue Aug 10 2010 - 02:14:08 PDT)
[AMBER] Resource for trying out various GPU setups with AMBER Ross Walker (Tue Aug 10 2010 - 08:26:20 PDT)
[AMBER] restrain group specification for GPU Qizhi Cui (Tue Aug 10 2010 - 08:40:11 PDT)
- Re: [AMBER] restrain group specification for GPU Scott Le Grand (Tue Aug 10 2010 - 09:33:08 PDT)
- Re: [AMBER] restrain group specification for GPU Bill Ross (Tue Aug 10 2010 - 09:59:08 PDT)
  - Re: [AMBER] restrain group specification for GPU Qizhi Cui (Tue Aug 10 2010 - 12:59:37 PDT)
- Re: [AMBER] restrain group specification for GPU Ross Walker (Tue Aug 10 2010 - 10:30:02 PDT)
  - Re: [AMBER] restrain group specification for GPU Qizhi Cui (Tue Aug 10 2010 - 15:26:39 PDT)
    - Re: [AMBER] restrain group specification for GPU Scott Le Grand (Tue Aug 10 2010 - 17:15:20 PDT)
    - Re: [AMBER] restrain group specification for GPU Scott Le Grand (Wed Aug 11 2010 - 08:32:30 PDT)
[AMBER] determining closest water molecules Beale, John (Tue Aug 10 2010 - 08:51:53 PDT)
- Re: [AMBER] determining closest water molecules Thomas Cheatham III (Tue Aug 10 2010 - 09:26:05 PDT)
[AMBER] simulation output for explicit and implicit model Yan Gao (Tue Aug 10 2010 - 15:32:27 PDT)
- Re: [AMBER] simulation output for explicit and implicit model Jason Swails (Tue Aug 10 2010 - 15:45:17 PDT)
[AMBER] simulation output for explicit and implicit model--please disregard the previous message Yan Gao (Tue Aug 10 2010 - 15:43:57 PDT)
- Re: [AMBER] simulation output for explicit and implicit model--please disregard the previous message Bill Ross (Tue Aug 10 2010 - 16:11:48 PDT)
[AMBER] nonbond interactions Philippe Pinard (Tue Aug 10 2010 - 15:46:17 PDT)
- Re: [AMBER] nonbond interactions Jason Swails (Tue Aug 10 2010 - 17:34:52 PDT)
[AMBER] BUG and FIX: pmemd crashes when vlimit exceeded Don.Bashford.stjude.org (Tue Aug 10 2010 - 17:46:58 PDT)
- Re: [AMBER] BUG and FIX: pmemd crashes when vlimit exceeded Robert Duke (Tue Aug 10 2010 - 18:15:32 PDT)
  - Re: [AMBER] BUG and FIX: pmemd crashes when vlimit exceeded. . Don.Bashford.stjude.org (Wed Aug 11 2010 - 14:29:48 PDT)
    - Re: [AMBER] BUG and FIX: pmemd crashes when vlimit exceeded. . Jason Swails (Wed Aug 11 2010 - 14:45:41 PDT)
    - Re: [AMBER] BUG and FIX: pmemd crashes when vlimit exceeded. .. . Don.Bashford.stjude.org (Thu Aug 12 2010 - 12:19:11 PDT)
    - Re: [AMBER] BUG and FIX: pmemd crashes when vlimit exceeded. .. . Jason Swails (Thu Aug 12 2010 - 12:27:51 PDT)
    - Re: [AMBER] BUG and FIX: pmemd crashes when vlimit exceeded. . Robert Duke (Thu Aug 12 2010 - 07:03:53 PDT)
[AMBER] How to change temperature in mm_pbsa.pl script pxq (Tue Aug 10 2010 - 18:28:29 PDT)
- Re: [AMBER] How to change temperature in mm_pbsa.pl script Jason Swails (Wed Aug 11 2010 - 08:03:06 PDT)
- Re: [AMBER] How to change temperature in mm_pbsa.pl script pxq (Thu Aug 12 2010 - 07:52:49 PDT)
  - Re: [AMBER] How to change temperature in mm_pbsa.pl script Bill Miller III (Thu Aug 12 2010 - 08:04:01 PDT)
[AMBER] constant volume Jorgen Simonsen (Wed Aug 11 2010 - 01:06:26 PDT)
- [AMBER] How to define "generalized distance coordinate restraint" in AMBER10? Catein Catherine (Wed Aug 11 2010 - 02:55:02 PDT)
  - Re: [AMBER] How to define "generalized distance coordinate restraint" in AMBER10? Jason Swails (Wed Aug 11 2010 - 05:46:42 PDT)
    - Re: [AMBER] How to define "generalized distance coordinate restraint" in AMBER10? Catein Catherine (Thu Aug 12 2010 - 02:57:55 PDT)
    - Re: [AMBER] How to define "generalized distance coordinate restraint" in AMBER10? Jason Swails (Thu Aug 12 2010 - 04:40:00 PDT)
- Re: [AMBER] constant volume case (Wed Aug 11 2010 - 04:41:39 PDT)
  - Re: [AMBER] constant volume Andrew Purkiss-Trew (Wed Aug 11 2010 - 05:30:56 PDT)
    - Re: [AMBER] constant volume Jorgen Simonsen (Wed Aug 11 2010 - 05:34:02 PDT)
    - Re: [AMBER] constant volume Jorgen Simonsen (Wed Aug 11 2010 - 05:45:27 PDT)
[AMBER] test $AMBERHOME/AmberTools/test/sqm/nma/Run: check_slko_files.x should be executable Alan (Wed Aug 11 2010 - 02:52:49 PDT)
- Re: [AMBER] test $AMBERHOME/AmberTools/test/sqm/nma/Run: check_slko_files.x should be executable Andreas Goetz (Wed Aug 11 2010 - 03:03:28 PDT)
[AMBER] query on invoking ff99SB and ff99 Bala subramanian (Wed Aug 11 2010 - 08:35:00 PDT)
- Re: [AMBER] query on invoking ff99SB and ff99 Jason Swails (Wed Aug 11 2010 - 09:00:05 PDT)
  - Re: [AMBER] query on invoking ff99SB and ff99 case (Wed Aug 11 2010 - 09:12:30 PDT)
    - Re: [AMBER] query on invoking ff99SB and ff99 Alan (Thu Aug 12 2010 - 03:11:52 PDT)
    - Re: [AMBER] query on invoking ff99SB and ff99 case (Thu Aug 12 2010 - 04:51:44 PDT)
    - Re: [AMBER] query on invoking ff99SB and ff99 Alan (Thu Aug 12 2010 - 05:23:44 PDT)
    - Re: [AMBER] query on invoking ff99SB and ff99 case (Thu Aug 12 2010 - 06:49:25 PDT)
- Re: [AMBER] query on invoking ff99SB and ff99 Bill Ross (Wed Aug 11 2010 - 10:26:50 PDT)
[AMBER] NMR refinement = increase in RMSD Andrew Olson (Wed Aug 11 2010 - 08:59:55 PDT)
- Re: [AMBER] NMR refinement = increase in RMSD case (Fri Aug 13 2010 - 04:39:28 PDT)
[AMBER] drawing sphere in each frame and update Sun, Yufang (Wed Aug 11 2010 - 13:31:20 PDT)
- Re: [AMBER] drawing sphere in each frame and update steinbrt.rci.rutgers.edu (Thu Aug 12 2010 - 00:10:15 PDT)
[AMBER] snapshots Philippe Pinard (Wed Aug 11 2010 - 15:30:48 PDT)
- Re: [AMBER] snapshots arikcohen (Wed Aug 11 2010 - 15:33:47 PDT)
  - Re: [AMBER] snapshots Jason Swails (Wed Aug 11 2010 - 16:27:41 PDT)
    - [AMBER] Bug in MMPBSA.py.MPI Matthias Negri (Wed Aug 11 2010 - 17:05:36 PDT)
    - Re: [AMBER] Bug in MMPBSA.py.MPI Jason Swails (Wed Aug 11 2010 - 18:53:01 PDT)
[AMBER] Ionic Strength Limits for MMPBSA Hopkins, Robert (Wed Aug 11 2010 - 15:33:28 PDT)
[AMBER] How to change fillratio in mm_pbsa.pl pxq (Thu Aug 12 2010 - 07:59:13 PDT)
- Re: [AMBER] How to change fillratio in mm_pbsa.pl Jason Swails (Thu Aug 12 2010 - 08:04:04 PDT)
Re: [AMBER] Installation_problem_Ambertools1.4_in Mac OSX Raman Parkesh (Thu Aug 12 2010 - 11:18:39 PDT)
- Re: [AMBER] Installation_problem_Ambertools1.4_in Mac OSX Jason Swails (Thu Aug 12 2010 - 11:32:26 PDT)
  - Re: [AMBER] Installation_problem_Ambertools1.4_in Mac OSX Raman Parkesh (Thu Aug 12 2010 - 11:39:49 PDT)
[AMBER] gbsa in pmemd Yi Xue (Thu Aug 12 2010 - 14:00:57 PDT)
- Re: [AMBER] gbsa in pmemd Ross Walker (Thu Aug 12 2010 - 16:48:12 PDT)
  - [AMBER] How to define center of mass for two separate residues in the restraint file? Catein Catherine (Thu Aug 12 2010 - 20:04:09 PDT)
    - Re: [AMBER] How to define center of mass for two separate residues in the restraint file? Jason Swails (Thu Aug 12 2010 - 20:18:19 PDT)
    - [AMBER] Double bonds ? Marek Maly (Tue Aug 17 2010 - 10:15:14 PDT)
    - Re: [AMBER] Double bonds ? case (Tue Aug 17 2010 - 15:18:00 PDT)
    - Re: [AMBER] Double bonds ? Marek Maly (Wed Aug 18 2010 - 04:55:29 PDT)
    - [AMBER] Trivial syntax problem ? Marek Maly (Wed Aug 18 2010 - 13:29:43 PDT)
    - Re: [AMBER] Trivial syntax problem ? case (Wed Aug 18 2010 - 18:33:27 PDT)
    - [AMBER] How to define twist angle with DOC? Catein Catherine (Wed Aug 18 2010 - 21:26:44 PDT)
    - [AMBER] Extremely high activation energy was found for a PMF. Any potential source of errors? Catein Catherine (Wed Aug 18 2010 - 21:32:46 PDT)
    - Re: [AMBER] Extremely high activation energy was found for a PMF. Any potential source of errors? Jason Swails (Wed Aug 18 2010 - 23:13:05 PDT)
    - Re: [AMBER] Trivial syntax problem ? Marek Maly (Thu Aug 19 2010 - 09:50:05 PDT)
[AMBER] mm_pbsa analysis failure Sangita Kachhap (Fri Aug 13 2010 - 04:36:49 PDT)
- Re: [AMBER] mm_pbsa analysis failure Anselm Horn (Fri Aug 13 2010 - 05:17:26 PDT)
[AMBER] Query regarding radius of H atoms of TIP3 water model sunita gupta (Fri Aug 13 2010 - 05:52:02 PDT)
- Re: [AMBER] Query regarding radius of H atoms of TIP3 water model case (Fri Aug 13 2010 - 06:53:41 PDT)
[AMBER] problem of NM calculations fancy2012 (Fri Aug 13 2010 - 06:01:27 PDT)
- Re: [AMBER] problem of NM calculations Jason Swails (Fri Aug 13 2010 - 12:50:29 PDT)
  - Re: [AMBER] problem of NM calculations fancy2012 (Sat Aug 14 2010 - 01:31:01 PDT)
- Re: [AMBER] problem of NM calculations fancy2012 (Sun Aug 15 2010 - 02:37:52 PDT)
[AMBER] makeCHIR_RST and proline Jorgen Simonsen (Fri Aug 13 2010 - 06:53:37 PDT)
[AMBER] Deleting bonds in sleap Ben Roberts (Fri Aug 13 2010 - 12:29:33 PDT)
- Re: [AMBER] Deleting bonds in sleap case (Fri Aug 13 2010 - 12:51:47 PDT)
  - Re: [AMBER] Deleting bonds in sleap Ben Roberts (Fri Aug 13 2010 - 13:08:54 PDT)
    - Re: [AMBER] Deleting bonds in sleap Andreas Goetz (Fri Aug 13 2010 - 13:13:49 PDT)
    - Re: [AMBER] Deleting bonds in sleap Ben Roberts (Fri Aug 13 2010 - 13:40:02 PDT)
    - Re: [AMBER] Deleting bonds in sleap case (Sat Aug 14 2010 - 06:20:09 PDT)
    - [AMBER] How to include parmbsc0 force field in preparing prmtop/inpcrd files? Catein Catherine (Sat Aug 14 2010 - 20:52:09 PDT)
    - Re: [AMBER] How to include parmbsc0 force field in preparing prmtop/inpcrd files? Paul S. Nerenberg (Sat Aug 14 2010 - 23:39:45 PDT)
    - Re: [AMBER] How to include parmbsc0 force field in preparing prmtop/inpcrd files? Catein Catherine (Sun Aug 15 2010 - 22:44:22 PDT)
    - [AMBER] how to overcome the memory issues in mm-gbsa calculation for DS analysis? Catein Catherine (Mon Aug 16 2010 - 02:36:11 PDT)
    - Re: [AMBER] Deleting bonds in sleap Ben Roberts (Mon Aug 16 2010 - 15:13:43 PDT)
- Re: [AMBER] Deleting bonds in sleap Bill Ross (Fri Aug 13 2010 - 13:19:03 PDT)
  - Re: [AMBER] Deleting bonds in sleap Ben Roberts (Fri Aug 13 2010 - 15:45:41 PDT)
[AMBER] regarding random number generator Sangita Kachhap (Sat Aug 14 2010 - 09:07:41 PDT)
- Re: [AMBER] regarding random number generator Ross Walker (Sat Aug 14 2010 - 11:28:22 PDT)
  - Re: [AMBER] regarding random number generator Sangita Kachhap (Sat Aug 14 2010 - 12:22:34 PDT)
[AMBER] AmberTools and OS X John McGuigan (Sat Aug 14 2010 - 22:04:53 PDT)
- Re: [AMBER] AmberTools and OS X Paul S. Nerenberg (Sat Aug 14 2010 - 23:45:46 PDT)
  - Re: [AMBER] AmberTools and OS X John McGuigan (Sun Aug 15 2010 - 13:44:40 PDT)
Re: [AMBER] How to identify water molecules at the interface ? follow up .... Amor San Juan (Sun Aug 15 2010 - 23:19:59 PDT)
- Re: [AMBER] How to identify water molecules at the interface ? follow up .... Jason Swails (Mon Aug 16 2010 - 06:03:42 PDT)
  - [AMBER] Creating new topology file from close.mdcrd file Amor San Juan (Tue Aug 17 2010 - 02:42:40 PDT)
    - [AMBER] How to find the most important drug dissociation pathway theoretically? PMF? Catein Catherine (Tue Aug 17 2010 - 04:00:31 PDT)
    - Re: [AMBER] How to find the most important drug dissociation pathway theoretically? PMF? Jason Swails (Tue Aug 17 2010 - 05:56:29 PDT)
    - Re: [AMBER] How to find the most important drug dissociation pathway theoretically? PMF? Catein Catherine (Tue Aug 17 2010 - 08:36:35 PDT)
    - Re: [AMBER] How to find the most important drug dissociation pathway theoretically? PMF? Jason Swails (Tue Aug 17 2010 - 09:04:01 PDT)
    - Re: [AMBER] How to find the most important drug dissociation pathway theoretically? PMF? Daniel Sindhikara (Tue Aug 17 2010 - 09:04:53 PDT)
    - Re: [AMBER] How to find the most important drug dissociation pathway theoretically? PMF? Jason Swails (Tue Aug 17 2010 - 10:49:53 PDT)
    - Re: [AMBER] How to find the most important drug dissociation pathway theoretically? PMF? Balazs Jojart (Tue Aug 17 2010 - 12:49:42 PDT)
    - Re: [AMBER] How to find the most important drug dissociation pathway theoretically? PMF? danglena1411.gmail.com (Wed Aug 18 2010 - 00:40:55 PDT)
    - Re: [AMBER] Creating new topology file from close.mdcrd file Jason Swails (Tue Aug 17 2010 - 05:52:18 PDT)
    - [AMBER] Cut-off distance "in Closest" command of ptraj Amor San Juan (Tue Aug 17 2010 - 22:35:36 PDT)
    - Re: [AMBER] Cut-off distance "in Closest" command of ptraj Jason Swails (Wed Aug 18 2010 - 06:43:32 PDT)
    - Re: [AMBER] Cut-off distance "in Closest" command of ptraj Amor San Juan (Thu Aug 19 2010 - 00:14:28 PDT)
    - Re: [AMBER] Cut-off distance "in Closest" command of ptraj Jason Swails (Thu Aug 19 2010 - 07:04:56 PDT)
    - [AMBER] PTRAJ: closest & strip in one script or separate Amor San Juan (Fri Aug 20 2010 - 02:33:50 PDT)
    - Re: [AMBER] PTRAJ: closest & strip in one script or separate Jason Swails (Fri Aug 20 2010 - 05:03:24 PDT)
    - Re: [AMBER] Cut-off distance "in Closest" command of ptraj Amor San Juan (Wed Sep 01 2010 - 19:41:07 PDT)
    - Re: [AMBER] Cut-off distance "in Closest" command of ptraj Carlos Simmerling (Thu Sep 02 2010 - 04:20:46 PDT)
[AMBER] protonate kamlesh sahu (Mon Aug 16 2010 - 00:43:21 PDT)
- Re: [AMBER] protonate case (Mon Aug 16 2010 - 04:41:15 PDT)
  - Re: [AMBER] protonate kamlesh sahu (Mon Aug 16 2010 - 08:21:02 PDT)
[AMBER] segmentation fault - ptrajin image familiar Jorgen Simonsen (Mon Aug 16 2010 - 01:01:25 PDT)
- Re: [AMBER] segmentation fault - ptrajin image familiar manikanthan bhavaraju (Mon Aug 16 2010 - 01:56:33 PDT)
- Re: [AMBER] segmentation fault - ptrajin image familiar case (Mon Aug 16 2010 - 04:45:06 PDT)
- Re: [AMBER] segmentation fault - ptrajin image familiar Daniel Roe (Mon Aug 16 2010 - 05:18:12 PDT)
  - Re: [AMBER] segmentation fault - ptrajin image familiar Jorgen Simonsen (Mon Aug 16 2010 - 06:00:10 PDT)
    - Re: [AMBER] segmentation fault - ptrajin image familiar Jason Swails (Mon Aug 16 2010 - 06:06:18 PDT)
[AMBER] Configure gnu P Bhattacharya (Mon Aug 16 2010 - 07:03:01 PDT)
- Re: [AMBER] Configure gnu Daniel Roe (Mon Aug 16 2010 - 07:18:16 PDT)
  - Re: [AMBER] Configure gnu P Bhattacharya (Mon Aug 16 2010 - 07:55:59 PDT)
[AMBER] Unit for Van der Waals and Electrostatic Eq. Hector Chang (Mon Aug 16 2010 - 08:26:55 PDT)
- Re: [AMBER] Unit for Van der Waals and Electrostatic Eq. Paul S. Nerenberg (Mon Aug 16 2010 - 08:32:56 PDT)
- Re: [AMBER] Unit for Van der Waals and Electrostatic Eq. case (Mon Aug 16 2010 - 08:37:15 PDT)
  - Re: [AMBER] Unit for Van der Waals and Electrostatic Eq. Jason Swails (Mon Aug 16 2010 - 11:48:32 PDT)
[AMBER] Adding lambda points less than 0.1 and greater than 0.9 in TI calculations g t (Mon Aug 16 2010 - 11:56:23 PDT)
- Re: [AMBER] Adding lambda points less than 0.1 and greater than 0.9 in TI calculations steinbrt.rci.rutgers.edu (Mon Aug 16 2010 - 12:13:52 PDT)
  - Re: [AMBER] Adding lambda points less than 0.1 and greater than 0.9 in TI calculations g t (Thu Aug 19 2010 - 08:58:23 PDT)
[AMBER] single-point energy calculation on selected atoms Yi Xue (Mon Aug 16 2010 - 17:43:36 PDT)
Re: [AMBER] Creating new topology file from close.mdcrd file : SOLUTION found Amor San Juan (Tue Aug 17 2010 - 03:58:40 PDT)
[AMBER] Created a new atom named: H within residue: .R<NASP 1> Jorgen Simonsen (Tue Aug 17 2010 - 05:47:32 PDT)
- Re: [AMBER] Created a new atom named: H within residue: .R<NASP 1> case (Tue Aug 17 2010 - 07:34:43 PDT)
[AMBER] Question about mdinfo file. Mayank Daga (Tue Aug 17 2010 - 08:10:26 PDT)
- Re: [AMBER] Question about mdinfo file. Jason Swails (Tue Aug 17 2010 - 08:31:11 PDT)
  - Re: [AMBER] Question about mdinfo file. Mayank Daga (Tue Aug 17 2010 - 08:55:11 PDT)
    - Re: [AMBER] Question about mdinfo file. Jason Swails (Tue Aug 17 2010 - 09:00:16 PDT)
    - Re: [AMBER] Question about mdinfo file. Mayank Daga (Tue Aug 17 2010 - 09:42:21 PDT)
    - Re: [AMBER] Question about mdinfo file. Ross Walker (Tue Aug 17 2010 - 10:04:23 PDT)
    - Re: [AMBER] Question about mdinfo file. Mayank Daga (Tue Aug 17 2010 - 10:19:11 PDT)
    - Re: [AMBER] Question about mdinfo file. Ross Walker (Tue Aug 17 2010 - 10:39:18 PDT)
    - Re: [AMBER] Question about mdinfo file. Mayank Daga (Tue Aug 17 2010 - 11:41:02 PDT)
    - Re: [AMBER] Question about mdinfo file. Ross Walker (Tue Aug 17 2010 - 11:56:31 PDT)
    - Re: [AMBER] Question about mdinfo file. Mayank Daga (Tue Aug 17 2010 - 12:51:46 PDT)
    - Re: [AMBER] Question about mdinfo file. Jason Swails (Tue Aug 17 2010 - 13:02:52 PDT)
    - Re: [AMBER] Question about mdinfo file. Ross Walker (Tue Aug 17 2010 - 09:52:19 PDT)
- Re: [AMBER] Question about mdinfo file. Robert Duke (Tue Aug 17 2010 - 08:49:38 PDT)
- Re: [AMBER] Question about mdinfo file. Robert Duke (Tue Aug 17 2010 - 08:58:42 PDT)
- Re: [AMBER] Question about mdinfo file. Robert Duke (Tue Aug 17 2010 - 10:08:06 PDT)
- Re: [AMBER] Question about mdinfo file. Robert Duke (Tue Aug 17 2010 - 10:25:17 PDT)
[AMBER] amber ：FAD parameters and RESP charge xqkong (Tue Aug 17 2010 - 08:14:57 PDT)
[AMBER] parmbsc0 Jason Swails (Tue Aug 17 2010 - 12:25:23 PDT)
- Re: [AMBER] parmbsc0 case (Tue Aug 17 2010 - 15:21:31 PDT)
[AMBER] Diffusion coefficient in PTRAJ. Hoshin Kim (Tue Aug 17 2010 - 00:52:41 PDT)
Re: [AMBER] entropy calculations MMPBSA.py.MPI Matthias Negri (Tue Aug 17 2010 - 15:45:34 PDT)
[AMBER] combination of CPU + GPU for Amber 11 CHAMI F. (Tue Aug 17 2010 - 16:39:10 PDT)
- Re: [AMBER] combination of CPU + GPU for Amber 11 Ross Walker (Tue Aug 17 2010 - 17:36:51 PDT)
- Re: [AMBER] combination of CPU + GPU for Amber 11 CHAMI F. (Wed Aug 18 2010 - 02:53:42 PDT)
- Re: [AMBER] combination of CPU + GPU for Amber 11 CHAMI F. (Wed Aug 18 2010 - 02:58:01 PDT)
[AMBER] (no subject) xqkong (Tue Aug 17 2010 - 17:47:28 PDT)
[AMBER] Error in snader execution arikcohen (Tue Aug 17 2010 - 18:53:00 PDT)
- Re: [AMBER] Error in snader execution Jason Swails (Tue Aug 17 2010 - 19:11:40 PDT)
  - Re: [AMBER] Error in snader execution arikcohen (Wed Aug 18 2010 - 11:03:11 PDT)
[AMBER] MMPBSA Warnings George Tzotzos (Wed Aug 18 2010 - 00:56:45 PDT)
- Re: [AMBER] MMPBSA Warnings Bill Miller III (Wed Aug 18 2010 - 04:28:08 PDT)
  - Re: [AMBER] MMPBSA Warnings Jason Swails (Wed Aug 18 2010 - 07:15:48 PDT)
[AMBER] Defining restraint by distance Olotu Odunayo (Wed Aug 18 2010 - 01:19:26 PDT)
[AMBER] antechamber issue with gasteiger Alan (Wed Aug 18 2010 - 01:41:20 PDT)
- Re: [AMBER] antechamber issue with gasteiger Jason Swails (Wed Aug 18 2010 - 07:12:37 PDT)
  - Re: [AMBER] antechamber issue with gasteiger Alan (Wed Aug 18 2010 - 08:55:16 PDT)
  - Re: [AMBER] antechamber issue with gasteiger Alan (Tue Aug 24 2010 - 08:33:23 PDT)
    - Re: [AMBER] antechamber issue with gasteiger Jason Swails (Tue Aug 24 2010 - 08:39:54 PDT)
[AMBER] Calculating diffusion coefficient in PTRAJ Hoshin Kim (Tue Aug 17 2010 - 22:10:13 PDT)
[AMBER] FAD parameters and RESP charge xqkong (Wed Aug 18 2010 - 17:36:45 PDT)
- Re: [AMBER] FAD parameters and RESP charge Jason Swails (Wed Aug 18 2010 - 17:54:28 PDT)
- Re: [AMBER] FAD parameters and RESP charge xqkong (Wed Aug 18 2010 - 18:40:20 PDT)
[AMBER] MMPBSA.py error message. Wookyung Yu (Wed Aug 18 2010 - 21:55:25 PDT)
- Re: [AMBER] MMPBSA.py error message. Jason Swails (Wed Aug 18 2010 - 23:07:35 PDT)
[AMBER] restart reimage manikanthan bhavaraju (Wed Aug 18 2010 - 23:24:01 PDT)
- Re: [AMBER] restart reimage Jason Swails (Thu Aug 19 2010 - 07:07:32 PDT)
[AMBER] O2'methyl RNA waleed zalloum (Thu Aug 19 2010 - 05:37:25 PDT)
- Re: [AMBER] O2'methyl RNA Jason Swails (Thu Aug 19 2010 - 07:23:41 PDT)
  - Re: [AMBER] O2'methyl RNA waleed zalloum (Thu Aug 19 2010 - 07:34:26 PDT)
    - Re: [AMBER] O2'methyl RNA Jason Swails (Thu Aug 19 2010 - 08:04:14 PDT)
    - Re: [AMBER] O2'methyl RNA waleed zalloum (Fri Aug 20 2010 - 07:05:08 PDT)
[AMBER] Unit for Van der Waals and Electrostatic Eq. Hector Chang (Thu Aug 19 2010 - 09:34:20 PDT)
- Re: [AMBER] Unit for Van der Waals and Electrostatic Eq. Bill Ross (Thu Aug 19 2010 - 09:42:04 PDT)
[AMBER] Basic question: is protonation of receptor amino acid recidues needed for MD calculations? George Tzotzos (Thu Aug 19 2010 - 09:45:33 PDT)
- Re: [AMBER] Basic question: is protonation of receptor amino acid recidues needed for MD calculations? Jason Swails (Thu Aug 19 2010 - 09:51:21 PDT)
- Re: [AMBER] Basic question: is protonation of receptor amino acid recidues needed for MD calculations? Hegazy,Lamees (Thu Aug 19 2010 - 09:59:22 PDT)
[AMBER] MM-PBSA fails with a division by zero error Sasha Buzko (Thu Aug 19 2010 - 11:32:54 PDT)
- Re: [AMBER] MM-PBSA fails with a division by zero error Jason Swails (Thu Aug 19 2010 - 12:19:52 PDT)
[AMBER] Syntax for using RRES and LRES to turn on per residue decomposition (idecomp = 2) in a TI calculation g t (Thu Aug 19 2010 - 12:05:59 PDT)
- Re: [AMBER] Syntax for using RRES and LRES to turn on per residue decomposition (idecomp = 2) in a TI calculation Jason Swails (Thu Aug 19 2010 - 12:29:09 PDT)
  - Re: [AMBER] Syntax for using RRES and LRES to turn on per residue decomposition (idecomp = 2) in a TI calculation g t (Thu Aug 19 2010 - 12:45:24 PDT)
  - [AMBER] How to run NED in amber10? PIMD or MPI or LES.MPI? Catein Catherine (Fri Aug 20 2010 - 02:39:44 PDT)
    - Re: [AMBER] How to run NED in amber10? PIMD or MPI or LES.MPI? Jason Swails (Fri Aug 20 2010 - 05:06:35 PDT)
    - Re: [AMBER] How to run NED in amber10? PIMD or MPI or LES.MPI? Carlos Simmerling (Fri Aug 20 2010 - 09:25:05 PDT)
[AMBER] PBC arikcohen (Thu Aug 19 2010 - 17:35:21 PDT)
- Re: [AMBER] PBC Jason Swails (Fri Aug 20 2010 - 04:31:52 PDT)
  - Re: [AMBER] PBC arikcohen (Fri Aug 20 2010 - 12:43:24 PDT)
    - Re: [AMBER] PBC Jason Swails (Fri Aug 20 2010 - 12:49:21 PDT)
    - Re: [AMBER] PBC arikcohen (Fri Aug 20 2010 - 14:36:50 PDT)
    - Re: [AMBER] PBC case (Fri Aug 20 2010 - 13:38:01 PDT)
    - Re: [AMBER] PBC arikcohen (Fri Aug 20 2010 - 14:38:18 PDT)
[AMBER] bond energy spikes in conjugent gradient minimization Vickie Roberts (Fri Aug 20 2010 - 00:55:21 PDT)
- Re: [AMBER] bond energy spikes in conjugent gradient minimization case (Fri Aug 20 2010 - 04:48:47 PDT)
- Re: [AMBER] bond energy spikes in conjugent gradient minimization Jason Swails (Fri Aug 20 2010 - 04:56:37 PDT)
[AMBER] mm_pbsa failure Sangita Kachhap (Fri Aug 20 2010 - 03:58:34 PDT)
[AMBER] sander.MPI error George Tzotzos (Fri Aug 20 2010 - 06:43:41 PDT)
- Re: [AMBER] sander.MPI error case (Fri Aug 20 2010 - 07:03:19 PDT)
  - Re: [AMBER] sander.MPI error George Tzotzos (Fri Aug 20 2010 - 07:31:40 PDT)
    - Re: [AMBER] sander.MPI error Jason Swails (Fri Aug 20 2010 - 08:37:20 PDT)
[AMBER] exchange probability in remd Lekpa Duukori (Fri Aug 20 2010 - 10:14:40 PDT)
- Re: [AMBER] exchange probability in remd Carlos Simmerling (Fri Aug 20 2010 - 10:18:19 PDT)
  - Re: [AMBER] exchange probability in remd Lekpa Duukori (Fri Aug 20 2010 - 10:25:58 PDT)
[AMBER] too many titratable groups piotrek.vega.umcs.lublin.pl (Fri Aug 20 2010 - 11:26:42 PDT)
- Re: [AMBER] too many titratable groups Jason Swails (Fri Aug 20 2010 - 11:43:20 PDT)
[AMBER] Implicit Solvent Equation Hector Chang (Fri Aug 20 2010 - 13:17:44 PDT)
- Re: [AMBER] Implicit Solvent Equation case (Sun Aug 22 2010 - 05:58:17 PDT)
[AMBER] About dipoles hong-bin Xie (Fri Aug 20 2010 - 14:32:59 PDT)
- Re: [AMBER] About dipoles Ross Walker (Mon Aug 23 2010 - 08:46:31 PDT)
  - Re: [AMBER] About dipoles hong-bin Xie (Mon Aug 23 2010 - 09:08:47 PDT)
    - Re: [AMBER] About dipoles Ross Walker (Mon Aug 23 2010 - 09:19:37 PDT)
    - Re: [AMBER] About dipoles hong-bin Xie (Mon Aug 23 2010 - 09:25:44 PDT)
    - Re: [AMBER] About dipoles Ross Walker (Mon Aug 23 2010 - 12:16:19 PDT)
    - Re: [AMBER] About dipoles hong-bin Xie (Tue Sep 07 2010 - 10:22:46 PDT)
    - Re: [AMBER] About dipoles Ross Walker (Mon Aug 23 2010 - 11:32:55 PDT)
    - Re: [AMBER] About dipoles Adrian Roitberg (Mon Aug 23 2010 - 11:38:12 PDT)
[AMBER] FEP help William Flak (Fri Aug 20 2010 - 21:50:14 PDT)
- Re: [AMBER] FEP help case (Sat Aug 21 2010 - 06:19:02 PDT)
[AMBER] protein protein interaction manikanthan bhavaraju (Fri Aug 20 2010 - 22:28:58 PDT)
- Re: [AMBER] protein protein interaction case (Sat Aug 21 2010 - 06:20:29 PDT)
  - Re: [AMBER] protein protein interaction manikanthan bhavaraju (Sun Aug 22 2010 - 12:46:43 PDT)
    - Re: [AMBER] protein protein interaction Carlos Simmerling (Sun Aug 22 2010 - 13:08:41 PDT)
    - Re: [AMBER] protein protein interaction manikanthan bhavaraju (Sun Aug 22 2010 - 15:13:34 PDT)
    - Re: [AMBER] protein protein interaction Carlos Simmerling (Sun Aug 22 2010 - 15:33:02 PDT)
[AMBER] hydration status monica.imtech.res.in (Sat Aug 21 2010 - 07:14:33 PDT)
[AMBER] volume in a cavity Ganesh Kamath (Sat Aug 21 2010 - 07:21:19 PDT)
[AMBER] questions for the different atom style and resp charge xqkong (Sun Aug 22 2010 - 01:59:48 PDT)
- Re: [AMBER] questions for the different atom style and resp charge xqkong (Sun Aug 22 2010 - 03:11:50 PDT)
  - Re: [AMBER] questions for the different atom style and resp charge FyD (Mon Aug 23 2010 - 00:28:37 PDT)
    - Re: [AMBER] questions for the different atom style and resp charge xqkong (Mon Aug 23 2010 - 08:00:11 PDT)
    - Re: [AMBER] questions for the different atom style and resp charge FyD (Mon Aug 23 2010 - 12:22:06 PDT)
    - Re: [AMBER] questions for the different atom style and resp charge xqkong (Mon Aug 23 2010 - 18:31:21 PDT)
    - Re: [AMBER] questions for the different atom style and resp charge FyD (Mon Aug 23 2010 - 23:08:36 PDT)
    - Re: [AMBER] questions for the different atom style and resp charge xqkong (Mon Aug 23 2010 - 18:46:38 PDT)
    - Re: [AMBER] questions for the different atom style and resp charge xqkong (Mon Aug 23 2010 - 23:44:10 PDT)
    - Re: [AMBER] questions for the different atom style and resp charge FyD (Tue Aug 24 2010 - 12:01:05 PDT)
    - Re: [AMBER] questions for the different atom style and resp charge xqkong (Wed Aug 25 2010 - 02:53:30 PDT)
[AMBER] mm_pbsa ERROR Sangita Kachhap (Sun Aug 22 2010 - 03:52:49 PDT)
Re: [AMBER] AMBER question Ross Walker (Sun Aug 22 2010 - 07:52:32 PDT)
[AMBER] Dipole moment in QM/MM hong-bin Xie (Sun Aug 22 2010 - 10:14:48 PDT)
[AMBER] entropies from nmode in MMPBSA Cristina Sisu (Sun Aug 22 2010 - 17:28:24 PDT)
- Re: [AMBER] entropies from nmode in MMPBSA Bill Miller III (Mon Aug 23 2010 - 03:48:22 PDT)
  - Re: [AMBER] entropies from nmode in MMPBSA Cristina Sisu (Mon Aug 23 2010 - 04:14:03 PDT)
[AMBER] Equilibration M. Reza Ganjalikhany (Mon Aug 23 2010 - 02:01:39 PDT)
- Re: [AMBER] Equilibration Gustavo Seabra (Mon Aug 23 2010 - 07:26:59 PDT)
  - Re: [AMBER] Equilibration M. Reza Ganjalikhany (Mon Aug 23 2010 - 13:03:15 PDT)
    - Re: [AMBER] Equilibration manikanthan bhavaraju (Mon Aug 23 2010 - 15:18:36 PDT)
    - Re: [AMBER] Equilibration Gustavo Seabra (Mon Aug 23 2010 - 18:28:29 PDT)
    - Re: [AMBER] Equilibration M. Reza Ganjalikhany (Tue Aug 24 2010 - 00:48:38 PDT)
    - Re: [AMBER] Equilibration Gustavo Seabra (Tue Aug 24 2010 - 06:40:35 PDT)
[AMBER] how we increase the number of sugar molecule in a system subrata paul (Mon Aug 23 2010 - 02:02:50 PDT)
- Re: [AMBER] how we increase the number of sugar molecule in a system Sushil Mishra (Mon Aug 23 2010 - 02:10:39 PDT)
  - Re: [AMBER] how we increase the number of sugar molecule in a system subrata paul (Mon Aug 23 2010 - 02:46:11 PDT)
[AMBER] Dipole moment calculation from ptraj Siddharth Rastogi (Mon Aug 23 2010 - 02:33:46 PDT)
- Re: [AMBER] Dipole moment calculation from ptraj case (Mon Aug 23 2010 - 05:17:16 PDT)
[AMBER] Interaction energy_mm_pbsa moitrayee.mbu.iisc.ernet.in (Mon Aug 23 2010 - 03:17:52 PDT)
- Re: [AMBER] Interaction energy_mm_pbsa Bill Miller III (Mon Aug 23 2010 - 03:58:44 PDT)
  - Re: [AMBER] Interaction energy_mm_pbsa moitrayee.mbu.iisc.ernet.in (Mon Aug 23 2010 - 04:15:07 PDT)
    - Re: [AMBER] Interaction energy_mm_pbsa Bill Miller III (Mon Aug 23 2010 - 04:20:51 PDT)
    - Re: [AMBER] Interaction energy_mm_pbsa moitrayee.mbu.iisc.ernet.in (Mon Aug 23 2010 - 04:33:13 PDT)
[AMBER] amber11: Applying restraint weights George Tzotzos (Mon Aug 23 2010 - 03:57:50 PDT)
- Re: [AMBER] amber11: Applying restraint weights Carlos Simmerling (Mon Aug 23 2010 - 04:30:26 PDT)
- Re: [AMBER] amber11: Applying restraint weights case (Mon Aug 23 2010 - 05:24:55 PDT)
[AMBER] ptraj "closest" Amor San Juan (Mon Aug 23 2010 - 04:10:11 PDT)
- Re: [AMBER] ptraj "closest" Daniel Roe (Mon Aug 23 2010 - 07:07:17 PDT)
  - Re: [AMBER] ptraj "closest" Amor San Juan (Tue Aug 24 2010 - 04:32:30 PDT)
  - [AMBER] MMPBSA.py indexError Amor San Juan (Tue Aug 24 2010 - 04:53:30 PDT)
    - Re: [AMBER] MMPBSA.py indexError Bill Miller III (Tue Aug 24 2010 - 04:59:55 PDT)
    - Re: [AMBER] MMPBSA.py indexError Jason Swails (Tue Aug 24 2010 - 05:30:57 PDT)
    - Re: [AMBER] MMPBSA.py indexError Amor San Juan (Wed Aug 25 2010 - 02:09:53 PDT)
    - [AMBER] Water deeply buried for MMPBSA calculations Amor San Juan (Wed Aug 25 2010 - 03:54:54 PDT)
    - Re: [AMBER] Water deeply buried for MMPBSA calculations Jason Swails (Wed Aug 25 2010 - 04:19:55 PDT)
    - Re: [AMBER] Water deeply buried for MMPBSA calculations Amor San Juan (Thu Aug 26 2010 - 04:05:43 PDT)
[AMBER] [Fwd: Re: Interaction energy_mm_pbsa] moitrayee.mbu.iisc.ernet.in (Mon Aug 23 2010 - 04:35:40 PDT)
- Re: [AMBER] [Fwd: Re: Interaction energy_mm_pbsa] Bill Miller III (Mon Aug 23 2010 - 04:37:31 PDT)
  - Re: [AMBER] [Fwd: Re: Interaction energy_mm_pbsa] moitrayee.mbu.iisc.ernet.in (Mon Aug 23 2010 - 04:47:21 PDT)
    - Re: [AMBER] [Fwd: Re: Interaction energy_mm_pbsa] Jason Swails (Mon Aug 23 2010 - 06:27:50 PDT)
    - Re: [AMBER] [Fwd: Re: Interaction energy_mm_pbsa] moitrayee.mbu.iisc.ernet.in (Tue Aug 24 2010 - 02:11:05 PDT)
[AMBER] slowly releasing restraint_wt force Sangita Kachhap (Mon Aug 23 2010 - 08:29:13 PDT)
[AMBER] calculation of volume of active site Ganesh Kamath (Mon Aug 23 2010 - 09:30:38 PDT)
- Re: [AMBER] calculation of volume of active site Jia Xu (Mon Aug 23 2010 - 10:08:48 PDT)
- Re: [AMBER] calculation of volume of active site Peter Schmidtke (Mon Aug 23 2010 - 10:15:41 PDT)
  - Re: [AMBER] calculation of volume of active site Ganesh Kamath (Mon Aug 23 2010 - 10:20:58 PDT)
    - Re: [AMBER] calculation of volume of active site Peter Schmidtke (Tue Aug 24 2010 - 03:03:14 PDT)
[AMBER] ACS Division of Computers in Chemistry: award applications due October 15 Carlos Simmerling (Mon Aug 23 2010 - 10:06:16 PDT)
- Re: [AMBER] ACS Division of Computers in Chemistry: award applications due October 15 Carlos Simmerling (Mon Aug 23 2010 - 10:10:32 PDT)
  - Re: [AMBER] ACS Division of Computers in Chemistry: award applications due October 15 Carlos Simmerling (Mon Aug 23 2010 - 10:33:01 PDT)
- Re: [AMBER] ACS Division of Computers in Chemistry: award applications due October 15 Dima A Sabbah (Mon Aug 23 2010 - 11:01:24 PDT)
[AMBER] Installing Amber9 on Ubuntu platform Arun Gupta (Mon Aug 23 2010 - 11:57:30 PDT)
- Re: [AMBER] Installing Amber9 on Ubuntu platform Jason Swails (Mon Aug 23 2010 - 12:22:55 PDT)
- Re: [AMBER] Installing Amber9 on Ubuntu platform Bill Ross (Mon Aug 23 2010 - 12:25:41 PDT)
- Re: [AMBER] Installing Amber9 on Ubuntu platform case (Mon Aug 23 2010 - 12:27:59 PDT)
- Re: [AMBER] Installing Amber9 on Ubuntu platform Arun Gupta (Wed Sep 01 2010 - 05:19:54 PDT)
  - Re: [AMBER] Installing Amber9 on Ubuntu platform Jason Swails (Wed Sep 01 2010 - 05:34:23 PDT)
[AMBER] Problem: ambertool1.2 mopac is ok for my molecules, but ambertool1.4 sqm fails Shulin Zhuang (Mon Aug 23 2010 - 18:06:43 PDT)
- Re: [AMBER] Problem: ambertool1.2 mopac is ok for my molecules, but ambertool1.4 sqm fails Gustavo Seabra (Mon Aug 23 2010 - 18:17:24 PDT)
  - Re: [AMBER] Problem: ambertool1.2 mopac is ok for my molecules, but ambertool1.4 sqm fails Shulin Zhuang (Mon Aug 23 2010 - 18:20:43 PDT)
- Re: [AMBER] Problem: ambertool1.2 mopac is ok for my molecules, but ambertool1.4 sqm fails case (Tue Aug 24 2010 - 04:21:56 PDT)
  - Re: [AMBER] Problem: ambertool1.2 mopac is ok for my molecules, but ambertool1.4 sqm fails Shulin Zhuang (Tue Aug 24 2010 - 05:32:19 PDT)
[AMBER] solvateBox - what is the suitable value for distance? colvin (Mon Aug 23 2010 - 18:23:43 PDT)
- Re: [AMBER] solvateBox - what is the suitable value for distance? case (Tue Aug 24 2010 - 09:40:23 PDT)
  - Re: [AMBER] solvateBox - what is the suitable value for distance? Brent Krueger (Tue Aug 24 2010 - 10:07:10 PDT)
[AMBER] Running AMBER on a GPU Cluster. Mayank Daga (Mon Aug 23 2010 - 18:35:30 PDT)
- Re: [AMBER] Running AMBER on a GPU Cluster. Sasha Buzko (Tue Aug 24 2010 - 10:13:40 PDT)
- Re: [AMBER] Running AMBER on a GPU Cluster. Ross Walker (Tue Aug 24 2010 - 10:34:15 PDT)
  - Re: [AMBER] Running AMBER on a GPU Cluster. Mayank Daga (Tue Aug 24 2010 - 10:56:39 PDT)
[AMBER] flying out William Flak (Mon Aug 23 2010 - 21:02:38 PDT)
- Re: [AMBER] flying out manikanthan bhavaraju (Mon Aug 23 2010 - 21:14:43 PDT)
- Re: [AMBER] flying out case (Tue Aug 24 2010 - 04:28:20 PDT)
[AMBER] acceptance ration in rem.log Toshifumi Yui (Mon Aug 23 2010 - 22:12:35 PDT)
- Re: [AMBER] acceptance ration in rem.log Carlos Simmerling (Tue Aug 24 2010 - 05:47:18 PDT)
[AMBER] Quantifying Hydrophobic interaction aneesh cna (Mon Aug 23 2010 - 22:16:28 PDT)
- Re: [AMBER] Quantifying Hydrophobic interaction case (Tue Aug 24 2010 - 04:32:17 PDT)
  - Re: [AMBER] Quantifying Hydrophobic interaction aneesh cna (Tue Aug 24 2010 - 06:23:53 PDT)
    - Re: [AMBER] Quantifying Hydrophobic interaction case (Tue Aug 24 2010 - 09:35:52 PDT)
[AMBER] loading MG.off (./MG.off is not a valid database) Ehsan Habibi (Tue Aug 24 2010 - 01:16:48 PDT)
- Re: [AMBER] loading MG.off (./MG.off is not a valid database) case (Tue Aug 24 2010 - 04:37:54 PDT)
[AMBER] Packmol file cannot minimized setyanto tri wahyudi (Tue Aug 24 2010 - 03:34:10 PDT)
- Re: [AMBER] Packmol file cannot minimized Jason Swails (Tue Aug 24 2010 - 04:39:50 PDT)
- Re: [AMBER] Packmol file cannot minimized case (Tue Aug 24 2010 - 04:42:25 PDT)
  - Re: [AMBER] Packmol file cannot minimized setyanto tri wahyudi (Thu Aug 26 2010 - 00:02:17 PDT)
    - Re: [AMBER] Packmol file cannot minimized case (Thu Aug 26 2010 - 04:34:35 PDT)
    - Re: [AMBER] Packmol file cannot minimized Jason Swails (Thu Aug 26 2010 - 05:24:49 PDT)
[AMBER] Dipole moment calculation from ptraj v.satish.iitg.ernet.in (Tue Aug 24 2010 - 05:50:52 PDT)
- Re: [AMBER] Dipole moment calculation from ptraj Thomas Cheatham III (Wed Aug 25 2010 - 09:09:12 PDT)
[AMBER] question on improper dihedrals Jason Swails (Tue Aug 24 2010 - 12:19:07 PDT)
- Re: [AMBER] question on improper dihedrals case (Tue Aug 24 2010 - 12:55:57 PDT)
  - Re: [AMBER] question on improper dihedrals Jason Swails (Tue Aug 24 2010 - 13:04:10 PDT)
[AMBER] simulation of a restrained protein fragment + pmemd.cuda issues Sasha Buzko (Tue Aug 24 2010 - 17:09:06 PDT)
- Re: [AMBER] simulation of a restrained protein fragment + pmemd.cuda issues Ross Walker (Wed Aug 25 2010 - 11:29:26 PDT)
  - Re: [AMBER] simulation of a restrained protein fragment +pmemd.cuda issues Paul Mortenson (Thu Aug 26 2010 - 02:33:09 PDT)
    - Re: [AMBER] simulation of a restrained protein fragment +pmemd.cuda issues Ross Walker (Thu Aug 26 2010 - 04:40:26 PDT)
[AMBER] average structre William Flak (Tue Aug 24 2010 - 18:58:48 PDT)
[AMBER] Tutorial 3: MM-PBSA George Tzotzos (Tue Aug 24 2010 - 23:46:29 PDT)
- [AMBER] MMPBSA.py nmode Amor San Juan (Wed Aug 25 2010 - 02:40:02 PDT)
  - Re: [AMBER] MMPBSA.py nmode Bill Miller III (Wed Aug 25 2010 - 04:05:13 PDT)
    - Re: [AMBER] MMPBSA.py nmode Amor San Juan (Thu Aug 26 2010 - 03:36:39 PDT)
    - Re: [AMBER] MMPBSA.py nmode Bill Miller III (Thu Aug 26 2010 - 03:51:51 PDT)
    - Re: [AMBER] MMPBSA.py nmode Amor San Juan (Thu Aug 26 2010 - 04:18:57 PDT)
    - Re: [AMBER] MMPBSA.py nmode Bill Miller III (Thu Aug 26 2010 - 04:22:24 PDT)
    - [AMBER] Hbond Analysis Mannan (Fri Sep 03 2010 - 02:03:02 PDT)
    - Re: [AMBER] Hbond Analysis Daniel Roe (Fri Sep 03 2010 - 04:55:27 PDT)
    - Re: [AMBER] Hbond Analysis Mannan (Fri Sep 03 2010 - 05:20:52 PDT)
    - [AMBER] AMBER 11: Line minimizer aborted: step at lower bound Amor San Juan (Thu Sep 23 2010 - 23:40:23 PDT)
    - Re: [AMBER] AMBER 11: Line minimizer aborted: step at lower bound hirdesh kumar (Thu Sep 23 2010 - 23:51:28 PDT)
    - Re: [AMBER] AMBER 11: Line minimizer aborted: step at lower bound Amor San Juan (Fri Sep 24 2010 - 02:03:43 PDT)
    - Re: [AMBER] AMBER 11: Line minimizer aborted: step at lower bound case (Fri Sep 24 2010 - 05:15:09 PDT)
    - Re: [AMBER] AMBER 11: Line minimizer aborted: step at lower bound Amor San Juan (Sun Sep 26 2010 - 19:25:59 PDT)
- Re: [AMBER] Tutorial 3: MM-PBSA Jason Swails (Wed Aug 25 2010 - 04:27:22 PDT)
[AMBER] To obtain academic license of AMBER 11 program package sonali dhindwal (Tue Aug 24 2010 - 23:57:25 PDT)
[AMBER] how we increase the number of sugar molecule in a system subrata paul (Wed Aug 25 2010 - 00:22:19 PDT)
- Re: [AMBER] how we increase the number of sugar molecule in a system Lachele Foley (Lists) (Wed Aug 25 2010 - 06:42:37 PDT)
  - Re: [AMBER] how we increase the number of sugar molecule in a system subrata paul (Thu Aug 26 2010 - 01:50:59 PDT)
    - Re: [AMBER] how we increase the number of sugar molecule in a system case (Thu Aug 26 2010 - 04:38:04 PDT)
    - Re: [AMBER] how we increase the number of sugar molecule in a system ros (Thu Aug 26 2010 - 08:21:44 PDT)
    - Re: [AMBER] how we increase the number of sugar molecule in a system Lachele Foley (Lists) (Thu Aug 26 2010 - 09:16:53 PDT)
    - [AMBER] dipole moment of molecule of trans and cis azobenzene ? Chih-Ying Lin (Thu Aug 26 2010 - 10:01:58 PDT)
[AMBER] Enthalpy estimate Lekpa Duukori (Wed Aug 25 2010 - 12:39:35 PDT)
- Re: [AMBER] Enthalpy estimate Jason Swails (Wed Aug 25 2010 - 13:40:08 PDT)
  - Re: [AMBER] Enthalpy estimate Lekpa Duukori (Wed Aug 25 2010 - 13:50:57 PDT)
- Re: [AMBER] Enthalpy estimate case (Thu Aug 26 2010 - 04:48:37 PDT)
[AMBER] Parameter extraction arikcohen (Wed Aug 25 2010 - 13:01:14 PDT)
- Re: [AMBER] Parameter extraction Jason Swails (Wed Aug 25 2010 - 13:16:07 PDT)
  - Re: [AMBER] Parameter extraction arikcohen (Wed Aug 25 2010 - 14:25:17 PDT)
[AMBER] To obtain academic license of AMBER 11 program package sonali dhindwal (Thu Aug 26 2010 - 03:47:59 PDT)
- Re: [AMBER] To obtain academic license of AMBER 11 program package case (Thu Aug 26 2010 - 04:40:59 PDT)
  - Re: [AMBER] To obtain academic license of AMBER 11 program package sonali dhindwal (Thu Aug 26 2010 - 06:45:28 PDT)
[AMBER] Antechamber issue P Bhattacharya (Thu Aug 26 2010 - 09:07:59 PDT)
- Re: [AMBER] Antechamber issue case (Thu Aug 26 2010 - 10:00:39 PDT)
  - Re: [AMBER] Antechamber issue P Bhattacharya (Thu Aug 26 2010 - 14:51:40 PDT)
    - Re: [AMBER] Antechamber issue Jason Swails (Thu Aug 26 2010 - 16:38:51 PDT)
    - Re: [AMBER] Antechamber issue P Bhattacharya (Fri Aug 27 2010 - 14:57:53 PDT)
    - Re: [AMBER] Antechamber issue case (Fri Aug 27 2010 - 18:34:31 PDT)
    - Re: [AMBER] Antechamber issue P Bhattacharya (Mon Aug 30 2010 - 08:58:38 PDT)
    - Re: [AMBER] Antechamber issue Jason Swails (Mon Aug 30 2010 - 09:21:16 PDT)
    - Re: [AMBER] Antechamber issue P Bhattacharya (Mon Aug 30 2010 - 10:12:12 PDT)
    - Re: [AMBER] Antechamber issue P Bhattacharya (Mon Aug 30 2010 - 14:22:29 PDT)
    - Re: [AMBER] Antechamber issue David A. Case (Mon Aug 30 2010 - 14:28:37 PDT)
    - Re: [AMBER] Antechamber issue P Bhattacharya (Wed Sep 01 2010 - 13:10:09 PDT)
    - Re: [AMBER] Antechamber issue David A. Case (Wed Sep 01 2010 - 14:24:28 PDT)
Re: [AMBER] how we increase the number of sugar molecule in a system FyD (Thu Aug 26 2010 - 10:18:38 PDT)
- Re: [AMBER] how we increase the number of sugar molecule in a system subrata paul (Thu Sep 02 2010 - 05:19:01 PDT)
  - Re: [AMBER] how we increase the number of sugar molecule in a system Lachele Foley (Lists) (Thu Sep 02 2010 - 09:27:22 PDT)
[AMBER] vlimit and shake manikanthan bhavaraju (Thu Aug 26 2010 - 13:25:30 PDT)
- Re: [AMBER] vlimit and shake manikanthan bhavaraju (Thu Aug 26 2010 - 13:45:50 PDT)
- Re: [AMBER] vlimit and shake Jason Swails (Thu Aug 26 2010 - 18:31:00 PDT)
  - Re: [AMBER] vlimit and shake manikanthan bhavaraju (Thu Aug 26 2010 - 19:32:25 PDT)
    - Re: [AMBER] vlimit and shake Daniel Roe (Thu Aug 26 2010 - 22:31:56 PDT)
[AMBER] ptraj help William Flak (Thu Aug 26 2010 - 16:58:48 PDT)
- Re: [AMBER] ptraj help Jason Swails (Thu Aug 26 2010 - 17:39:26 PDT)
  - Re: [AMBER] ptraj help William Flak (Thu Aug 26 2010 - 19:45:40 PDT)
[AMBER] cuda lauch time out error in Amber 11 Sergio R Aragon (Thu Aug 26 2010 - 17:01:43 PDT)
- Re: [AMBER] cuda lauch time out error in Amber 11 Sasha Buzko (Thu Aug 26 2010 - 17:26:15 PDT)
  - Re: [AMBER] cuda lauch time out error in Amber 11 Sergio R Aragon (Thu Aug 26 2010 - 17:45:05 PDT)
    - Re: [AMBER] cuda lauch time out error in Amber 11 Sasha Buzko (Thu Aug 26 2010 - 18:07:36 PDT)
    - Re: [AMBER] cuda lauch time out error in Amber 11 Scott Le Grand (Thu Aug 26 2010 - 18:20:50 PDT)
    - Re: [AMBER] cuda launch time out error in Amber 11 Sergio R Aragon (Thu Aug 26 2010 - 23:23:19 PDT)
    - Re: [AMBER] cuda launch time out error in Amber 11 Ross Walker (Fri Aug 27 2010 - 06:12:54 PDT)
    - Re: [AMBER] cuda launch time out error in Amber 11 Sasha Buzko (Fri Aug 27 2010 - 10:26:25 PDT)
    - Re: [AMBER] cuda lauch time out error in Amber 11 Scott Le Grand (Thu Aug 26 2010 - 18:21:29 PDT)
  - Re: [AMBER] cuda lauch time out error in Amber 11 Ross Walker (Fri Aug 27 2010 - 06:01:31 PDT)
- Re: [AMBER] cuda lauch time out error in Amber 11 Ross Walker (Fri Aug 27 2010 - 05:57:45 PDT)
  - Re: [AMBER] cuda launch time out error in Amber 11 Sergio R Aragon (Fri Aug 27 2010 - 11:06:42 PDT)
    - Re: [AMBER] cuda launch time out error in Amber 11 Scott Le Grand (Fri Aug 27 2010 - 21:29:24 PDT)
    - Re: [AMBER] cuda launch time out error in Amber 11 Sergio R Aragon (Fri Aug 27 2010 - 22:46:59 PDT)
[AMBER] error in mmpbsa Asfa Ali (Fri Aug 27 2010 - 02:20:40 PDT)
- Re: [AMBER] error in mmpbsa Amor San Juan (Fri Aug 27 2010 - 03:02:14 PDT)
  - Re: [AMBER] error in mmpbsa Asfa Ali (Fri Aug 27 2010 - 04:16:00 PDT)
- Re: [AMBER] error in mmpbsa Ray Luo (Fri Aug 27 2010 - 10:04:56 PDT)
[AMBER] very slow work of ptraj on cluster Andrew Voronkov (Fri Aug 27 2010 - 09:33:09 PDT)
- Re: [AMBER] very slow work of ptraj on cluster Daniel Roe (Fri Aug 27 2010 - 13:08:26 PDT)
  - Re: [AMBER] very slow work of ptraj on cluster Andrew Voronkov (Sat Aug 28 2010 - 04:33:06 PDT)
    - Re: [AMBER] very slow work of ptraj on cluster Daniel Roe (Sat Aug 28 2010 - 05:54:54 PDT)
    - Re: [AMBER] very slow work of ptraj on cluster Andrew Voronkov (Sat Aug 28 2010 - 09:36:31 PDT)
    - Re: [AMBER] very slow work of ptraj on cluster Daniel Roe (Sat Aug 28 2010 - 15:47:30 PDT)
    - Re: [AMBER] very slow work of ptraj on cluster Andrew Voronkov (Mon Aug 30 2010 - 02:10:24 PDT)
[AMBER] Latest Na+ and Cl- ion parameters Ilyas Yildirim (Fri Aug 27 2010 - 13:08:41 PDT)
- Re: [AMBER] Latest Na+ and Cl- ion parameters Dean Cuebas (Fri Aug 27 2010 - 14:12:23 PDT)
  - [AMBER] Binary trajectory format in Amber8 Anselm Horn (Sat Aug 28 2010 - 01:32:23 PDT)
    - Re: [AMBER] Binary trajectory format in Amber8 case (Sat Aug 28 2010 - 06:32:05 PDT)
    - Re: [AMBER] Binary trajectory format in Amber8 Anselm Horn (Sat Aug 28 2010 - 08:40:06 PDT)
[AMBER] force field parameters for ionic liquids Ganesh Kamath (Sat Aug 28 2010 - 06:27:55 PDT)
[AMBER] FEP with EP William Flak (Sat Aug 28 2010 - 18:53:51 PDT)
[AMBER] ERROR: Bond: Maximum coordination exceededon .R<Ca2 193>.A<Ca1> Majid Taghdir (Sun Aug 29 2010 - 02:17:48 PDT)
- Re: [AMBER] ERROR: Bond: Maximum coordination exceededon .R<Ca2 193>.A<Ca1> Jason Swails (Sun Aug 29 2010 - 07:52:23 PDT)
 - [AMBER] How to define an unbiased reaction coordinate for potential of mean force calculations? Catein Catherine (Sun Aug 29 2010 - 23:09:31 PDT)
 - Re: [AMBER] ERROR: Bond: Maximum coordination exceededon .R<Ca2 193>.A<Ca1> Majid Taghdir (Mon Aug 30 2010 - 03:43:05 PDT)
 - Re: [AMBER] ERROR: Bond: Maximum coordination exceededon .R<Ca2 193>.A<Ca1> Jason Swails (Mon Aug 30 2010 - 05:15:59 PDT)
 - Re: [AMBER] ERROR: Bond: Maximum coordination exceededon .R<Ca2 193>.A<Ca1> Majid Taghdir (Mon Aug 30 2010 - 06:26:29 PDT)
 - Re: [AMBER] ERROR: Bond: Maximum coordination exceededon .R<Ca2 193>.A<Ca1> Jason Swails (Mon Aug 30 2010 - 07:12:09 PDT)
 - [AMBER] How to calculate the equilbrium constant for a protein-drug binding reaction Catein Catherine (Mon Aug 30 2010 - 07:44:27 PDT)
 - Re: [AMBER] How to calculate the equilbrium constant for a protein-drug binding reaction Jason Swails (Mon Aug 30 2010 - 08:50:03 PDT)
[AMBER] Is there any training program in Europe in the future? albert (Mon Aug 30 2010 - 00:22:33 PDT)
[AMBER] Regarding protein diffusion aneesh cna (Mon Aug 30 2010 - 01:24:12 PDT)
- [AMBER] RE : Regarding protein diffusion ABEL Stephane 175950 (Mon Aug 30 2010 - 07:04:33 PDT)
[AMBER] Free energy using MMPBSA shenna shearin (Mon Aug 30 2010 - 07:12:35 PDT)
- Re: [AMBER] Free energy using MMPBSA Bill Miller III (Mon Aug 30 2010 - 08:29:04 PDT)
  - Re: [AMBER] Free energy using MMPBSA Jason Swails (Mon Aug 30 2010 - 08:39:40 PDT)
[AMBER] parameters for ionic liquids Ganesh Kamath (Mon Aug 30 2010 - 07:14:07 PDT)
[AMBER] amber11: segmentation fault error George Tzotzos (Mon Aug 30 2010 - 08:50:19 PDT)
- Re: [AMBER] amber11: segmentation fault error Jason Swails (Mon Aug 30 2010 - 09:07:30 PDT)
[AMBER] the modified Bondi radii zhihong ke (Mon Aug 30 2010 - 10:15:24 PDT)
- Re: [AMBER] the modified Bondi radii Jason Swails (Mon Aug 30 2010 - 10:20:16 PDT)
  - Re: [AMBER] the modified Bondi radii zhihong ke (Mon Aug 30 2010 - 10:30:29 PDT)
    - Re: [AMBER] the modified Bondi radii Jason Swails (Mon Aug 30 2010 - 15:55:34 PDT)
    - Re: [AMBER] the modified Bondi radii Asfa Ali (Tue Aug 31 2010 - 05:36:31 PDT)
[AMBER] How to solvate a molecule in a water spherocylinder in leap? Guoxiong Su (Mon Aug 30 2010 - 14:07:29 PDT)
- Re: [AMBER] How to solvate a molecule in a water spherocylinder in leap? David A. Case (Mon Aug 30 2010 - 14:31:11 PDT)
  - Re: [AMBER] How to solvate a molecule in a water spherocylinder in leap? Guoxiong Su (Tue Aug 31 2010 - 07:12:30 PDT)
[AMBER] pmemd installation problem Carra, Claudio (JSC-SK)[Universities Space Research Association] (Mon Aug 30 2010 - 16:09:50 PDT)
- Re: [AMBER] pmemd installation problem Jason Swails (Mon Aug 30 2010 - 21:30:42 PDT)
- Re: [AMBER] pmemd installation problem Ross Walker (Tue Aug 31 2010 - 01:33:38 PDT)
  - Re: [AMBER] pmemd installation problem Carra, Claudio (JSC-SK)[Universities Space Research Association] (Tue Aug 31 2010 - 16:21:21 PDT)
[AMBER] addions2 function missing from sleap Ben Roberts (Mon Aug 30 2010 - 17:15:14 PDT)
[AMBER] Another missing sleap command: check Ben Roberts (Mon Aug 30 2010 - 17:28:36 PDT)
- Re: [AMBER] Another missing sleap command: check Ben Roberts (Tue Aug 31 2010 - 07:49:36 PDT)
[AMBER] addions causes "assertion failed" in sleap Ben Roberts (Mon Aug 30 2010 - 18:26:41 PDT)
- Re: [AMBER] addions causes "assertion failed" in sleap Jason Swails (Tue Aug 31 2010 - 06:39:55 PDT)
[AMBER] Amber9 compilation/Westmere platform eric henon (Tue Aug 31 2010 - 01:11:29 PDT)
- Re: [AMBER] Amber9 compilation/Westmere platform Jason Swails (Tue Aug 31 2010 - 06:12:06 PDT)
- [AMBER] Amber9 compilation/Westmere platform eric henon (Tue Aug 31 2010 - 06:41:43 PDT)
[AMBER] MMPBSA.py: minimization issue with nmode Nicolas SAPAY (Tue Aug 31 2010 - 05:14:47 PDT)
- Re: [AMBER] MMPBSA.py: minimization issue with nmode Bill Miller III (Tue Aug 31 2010 - 05:31:05 PDT)
  - Re: [AMBER] MMPBSA.py: minimization issue with nmode Jason Swails (Tue Aug 31 2010 - 05:55:43 PDT)
    - Re: [AMBER] MMPBSA.py: minimization issue with nmode Jason Swails (Tue Aug 31 2010 - 06:04:33 PDT)
    - Re: [AMBER] MMPBSA.py: minimization issue with nmode Nicolas SAPAY (Tue Aug 31 2010 - 06:24:56 PDT)
    - Re: [AMBER] MMPBSA.py: minimization issue with nmode Nicolas SAPAY (Thu Sep 02 2010 - 03:07:30 PDT)
    - Re: [AMBER] MMPBSA.py: minimization issue with nmode Nicolas SAPAY (Tue Aug 31 2010 - 06:21:13 PDT)
[AMBER] regarding trap simulation Jorgen Simonsen (Tue Aug 31 2010 - 06:27:26 PDT)
- Re: [AMBER] regarding trap simulation Jason Swails (Tue Aug 31 2010 - 06:30:45 PDT)
  - Re: [AMBER] regarding trap simulation Jorgen Simonsen (Tue Aug 31 2010 - 06:44:43 PDT)
    - Re: [AMBER] regarding trap simulation Jason Swails (Tue Aug 31 2010 - 06:49:51 PDT)
[AMBER] phenylalanine amide Francesco Pietra (Tue Aug 31 2010 - 09:31:49 PDT)
- Re: [AMBER] phenylalanine amide Paul S. Nerenberg (Tue Aug 31 2010 - 09:40:14 PDT)
  - Re: [AMBER] phenylalanine amide Francesco Pietra (Tue Aug 31 2010 - 09:59:05 PDT)
    - Re: [AMBER] phenylalanine amide Paul S. Nerenberg (Tue Aug 31 2010 - 10:34:05 PDT)
    - Re: [AMBER] phenylalanine amide Francesco Pietra (Tue Aug 31 2010 - 14:12:24 PDT)
- Re: [AMBER] phenylalanine amide FyD (Thu Sep 02 2010 - 11:43:07 PDT)
  - Re: [AMBER] phenylalanine amide Francesco Pietra (Fri Sep 03 2010 - 03:01:34 PDT)
    - Re: [AMBER] phenylalanine amide FyD (Fri Sep 03 2010 - 11:12:31 PDT)
[AMBER] PB warning in pb_miccg 宋德寿 (Tue Aug 31 2010 - 22:30:38 PDT)
[AMBER] PB warning in pb_miccg 宋德寿 (Tue Aug 31 2010 - 22:32:21 PDT)
- Re: [AMBER] PB warning in pb_miccg Bill Miller III (Wed Sep 01 2010 - 05:20:10 PDT)
- Re: [AMBER] PB warning in pb_miccg Ray Luo (Wed Sep 01 2010 - 09:30:43 PDT)
- [AMBER] PB warning in pb_miccg 宋德寿 (Wed Sep 01 2010 - 18:34:17 PDT)
[AMBER] Residue name problem in PTRAJ Hoshin Kim (Tue Aug 31 2010 - 15:32:19 PDT)
- Re: [AMBER] Residue name problem in PTRAJ Fredrick Devadoss (Tue Aug 31 2010 - 23:47:25 PDT)
[AMBER] MD and LES Computational Chemist (Tue Aug 31 2010 - 23:13:45 PDT)
- Re: [AMBER] MD and LES Carlos Simmerling (Wed Sep 01 2010 - 07:04:37 PDT)
[AMBER] hydrogen bond analysis Ehsan Habibi (Wed Sep 01 2010 - 02:05:53 PDT)
- Re: [AMBER] hydrogen bond analysis Daniel Roe (Wed Sep 01 2010 - 05:18:03 PDT)
[AMBER] ERROR in MM-PBSA Siddharth Rastogi (Wed Sep 01 2010 - 08:10:33 PDT)
- Re: [AMBER] ERROR in MM-PBSA Dwight McGee (Wed Sep 01 2010 - 08:31:49 PDT)
  - Re: [AMBER] ERROR in MM-PBSA Jason Swails (Wed Sep 01 2010 - 16:29:41 PDT)
  - Re: [AMBER] ERROR in MM-PBSA Siddharth Rastogi (Wed Sep 01 2010 - 17:18:44 PDT)
    - Re: [AMBER] ERROR in MM-PBSA Jason Swails (Wed Sep 01 2010 - 18:30:42 PDT)
    - Re: [AMBER] ERROR in MM-PBSA Siddharth Rastogi (Thu Sep 02 2010 - 11:48:21 PDT)
    - Re: [AMBER] ERROR in MM-PBSA Siddharth Rastogi (Fri Sep 03 2010 - 17:07:38 PDT)
- Re: [AMBER] ERROR in MM-PBSA Bill Ross (Fri Sep 03 2010 - 17:14:26 PDT)
  - Re: [AMBER] ERROR in MM-PBSA Siddharth Rastogi (Wed Sep 08 2010 - 17:49:44 PDT)
    - Re: [AMBER] ERROR in MM-PBSA Jason Swails (Wed Sep 08 2010 - 20:11:05 PDT)
    - Re: [AMBER] ERROR in MM-PBSA Siddharth Rastogi (Tue Sep 14 2010 - 09:29:58 PDT)
    - Re: [AMBER] ERROR in MM-PBSA Jason Swails (Tue Sep 14 2010 - 09:49:07 PDT)
    - Re: [AMBER] ERROR in MM-PBSA Siddharth Rastogi (Thu Sep 16 2010 - 16:01:19 PDT)
    - Re: [AMBER] ERROR in MM-PBSA Jason Swails (Thu Sep 16 2010 - 16:49:42 PDT)
    - Re: [AMBER] ERROR in MM-PBSA Siddharth Rastogi (Thu Sep 23 2010 - 15:05:25 PDT)
    - Re: [AMBER] ERROR in MM-PBSA Jason Swails (Thu Sep 23 2010 - 16:47:56 PDT)
[AMBER] Trivial VMD question Computational Chemist (Wed Sep 01 2010 - 09:30:34 PDT)
- Re: [AMBER] Trivial VMD question steinbrt.rci.rutgers.edu (Wed Sep 01 2010 - 09:46:14 PDT)
  - Re: [AMBER] Trivial VMD question Jason Swails (Wed Sep 01 2010 - 16:33:22 PDT)
[AMBER] mm_pbsa fails xue wang (Wed Sep 01 2010 - 13:14:11 PDT)
- Re: [AMBER] mm_pbsa fails Ray Luo (Wed Sep 01 2010 - 14:49:16 PDT)
  - Re: [AMBER] mm_pbsa fails xue wang (Fri Sep 17 2010 - 13:08:43 PDT)
    - Re: [AMBER] mm_pbsa fails Bill Miller III (Fri Sep 17 2010 - 13:19:13 PDT)
    - Re: [AMBER] mm_pbsa fails xue wang (Fri Sep 17 2010 - 13:57:49 PDT)
[AMBER] visualizing the output from PTRAJ -Cluster Senthil Natesan (Wed Sep 01 2010 - 14:14:45 PDT)
- Re: [AMBER] visualizing the output from PTRAJ -Cluster Jianyin Shao (Wed Sep 01 2010 - 15:21:24 PDT)
  - Re: [AMBER] visualizing the output from PTRAJ -Cluster Senthil Natesan (Wed Sep 01 2010 - 16:01:53 PDT)
    - Re: [AMBER] visualizing the output from PTRAJ -Cluster Jianyin Shao (Thu Sep 02 2010 - 16:28:37 PDT)
[AMBER] PB warning in pb_miccg 宋德寿 (Wed Sep 01 2010 - 18:35:52 PDT)
[AMBER] Amber10 tests and benchmark verification failures across compilers Rasale, Anupama (Thu Sep 02 2010 - 04:08:41 PDT)
- Re: [AMBER] Amber10 tests and benchmark verification failures across compilers Jason Swails (Thu Sep 02 2010 - 05:57:55 PDT)
[AMBER] how to add Zn into a protein structure. Chinh Su Tran To (Thu Sep 02 2010 - 05:35:04 PDT)
- Re: [AMBER] how to add Zn into a protein structure. case (Sat Sep 04 2010 - 07:54:26 PDT)
[AMBER] 'cluster' option of ptraj: Is it possible to directly feed a file with rmsd values as input? Arvind (Thu Sep 02 2010 - 07:52:14 PDT)
- Re: [AMBER] 'cluster' option of ptraj: Is it possible to directly feed a file with rmsd values as input? Jianyin Shao (Fri Sep 03 2010 - 10:39:27 PDT)
  - Re: [AMBER] 'cluster' option of ptraj: Is it possible to directly feed a file with rmsd values as input? Arvind (Sun Sep 12 2010 - 22:59:36 PDT)
- Re: [AMBER] 'cluster' option of ptraj: Is it possible to directly feed a file with rmsd values as input? Bill Ross (Fri Sep 03 2010 - 10:58:31 PDT)
  - Re: [AMBER] 'cluster' option of ptraj: Is it possible to directly feed a file with rmsd values as input? Jianyin Shao (Fri Sep 03 2010 - 12:14:22 PDT)
[AMBER] Is there any Amber training programm in Europe? albert (Thu Sep 02 2010 - 09:39:45 PDT)
- Re: [AMBER] Is there any Amber training programm in Europe? Ross Walker (Fri Sep 03 2010 - 01:24:44 PDT)
  - Re: [AMBER] Is there any Amber training programm in Europe? Renata KWIECIEN (Wed Jan 05 2011 - 02:46:44 PST)
    - Re: [AMBER] Is there any Amber training programm in Europe? Ross Walker (Wed Jan 05 2011 - 08:09:58 PST)
[AMBER] eV to kcal/mol conversion factor Ben Roberts (Thu Sep 02 2010 - 10:33:32 PDT)
- Re: [AMBER] eV to kcal/mol conversion factor Adrian Roitberg (Thu Sep 02 2010 - 10:50:54 PDT)
  - Re: [AMBER] eV to kcal/mol conversion factor Ben Roberts (Fri Sep 03 2010 - 06:34:08 PDT)
    - Re: [AMBER] eV to kcal/mol conversion factor Gustavo Seabra (Fri Sep 03 2010 - 06:51:41 PDT)
- Re: [AMBER] eV to kcal/mol conversion factor case (Sat Sep 04 2010 - 06:18:02 PDT)
[AMBER] Symposium on Accelerating Biology jani vinod (Thu Sep 02 2010 - 22:10:37 PDT)
- Re: [AMBER] Symposium on Accelerating Biology Indrajit Deb (Thu Sep 02 2010 - 23:44:55 PDT)
  - Re: [AMBER] Symposium on Accelerating Biology vhakkim boy (Thu Sep 02 2010 - 23:48:38 PDT)
  - Re: [AMBER] Symposium on Accelerating Biology Kshatresh Dutta Dubey (Thu Sep 02 2010 - 23:50:48 PDT)
[AMBER] QUESTION ON AMBER WORKSHOP or SYMPOSIUM Indrajit Deb (Thu Sep 02 2010 - 23:47:37 PDT)
[AMBER] explicitly set the ig variable for ntt=3 colvin (Fri Sep 03 2010 - 00:49:40 PDT)
- Re: [AMBER] explicitly set the ig variable for ntt=3 hirdesh kumar (Fri Sep 03 2010 - 01:16:25 PDT)
  - Re: [AMBER] explicitly set the ig variable for ntt=3 Jason Swails (Fri Sep 03 2010 - 05:01:53 PDT)
  - [AMBER] Nvidia driver bug for GTX400 series gpu's Sergio R Aragon (Fri Sep 03 2010 - 19:35:19 PDT)
    - Re: [AMBER] Nvidia driver bug for GTX400 series gpu's Scott Le Grand (Sat Sep 04 2010 - 09:48:30 PDT)
    - Re: [AMBER] Nvidia driver bug for GTX400 series gpu's Scott Le Grand (Sat Sep 04 2010 - 09:57:11 PDT)
    - Re: [AMBER] Nvidia driver bug for GTX400 series gpu's Sergio R Aragon (Sun Sep 05 2010 - 13:55:01 PDT)
    - Re: [AMBER] Nvidia driver bug for GTX400 series gpu's Ross Walker (Sat Sep 04 2010 - 10:35:51 PDT)
    - Re: [AMBER] Nvidia driver bug for GTX400 series gpu's Scott Le Grand (Sat Sep 04 2010 - 10:49:26 PDT)
    - Re: [AMBER] Nvidia driver bug for GTX400 series gpu's/update 1 Sergio R Aragon (Sun Sep 05 2010 - 21:34:43 PDT)
[AMBER] Heating up the sytem hirdesh kumar (Fri Sep 03 2010 - 01:51:49 PDT)
- Re: [AMBER] Heating up the sytem Sangita Kachhap (Fri Sep 03 2010 - 03:36:45 PDT)
- Re: [AMBER] Heating up the sytem Senthil Natesan (Sat Sep 04 2010 - 07:57:10 PDT)
Re: [AMBER] about the tutorials Carlos Simmerling (Fri Sep 03 2010 - 05:08:44 PDT)
[AMBER] extended conjugated systems - possible? Hannes Loeffler (Fri Sep 03 2010 - 06:32:59 PDT)
[AMBER] cis/trans transition Jorgen Simonsen (Fri Sep 03 2010 - 08:25:50 PDT)
- Re: [AMBER] cis/trans transition Carlos Simmerling (Fri Sep 03 2010 - 08:58:51 PDT)
[AMBER] printing rdc violations Eliana Asciutto (Fri Sep 03 2010 - 09:40:54 PDT)
- Re: [AMBER] printing rdc violations case (Sat Sep 04 2010 - 08:01:26 PDT)
[AMBER] how to set charge and radius of my own custom ion Anbang Li (Fri Sep 03 2010 - 16:14:27 PDT)
- Re: [AMBER] how to set charge and radius of my own custom ion Bill Ross (Fri Sep 03 2010 - 16:38:27 PDT)
- Re: [AMBER] how to set charge and radius of my own custom ion Bill Ross (Fri Sep 03 2010 - 16:49:02 PDT)
  - Re: [AMBER] how to set charge and radius of my own custom ion Anbang Li (Fri Sep 03 2010 - 19:24:23 PDT)
    - Re: [AMBER] how to set charge and radius of my own custom ion Jason Swails (Fri Sep 03 2010 - 20:47:32 PDT)
- Re: [AMBER] how to set charge and radius of my own custom ion Bill Ross (Fri Sep 03 2010 - 20:06:16 PDT)
[AMBER] ptraj-problem Rilei Yu (Fri Sep 03 2010 - 18:04:38 PDT)
- Re: [AMBER] ptraj-problem Jason Swails (Sat Sep 04 2010 - 05:44:28 PDT)
[AMBER] mm_pbsa nmode error Sangita Kachhap (Sat Sep 04 2010 - 04:41:33 PDT)
- Re: [AMBER] mm_pbsa nmode error Bill Miller III (Sat Sep 04 2010 - 04:47:35 PDT)
  - Re: [AMBER] mm_pbsa nmode error Sangita Kachhap (Sat Sep 04 2010 - 05:07:42 PDT)
[AMBER] ERROR in safe_malloc: Error in alloc of -2030981184 bytes Ehsan Habibi (Sat Sep 04 2010 - 09:23:15 PDT)
- Re: [AMBER] ERROR in safe_malloc: Error in alloc of -2030981184 bytes Jason Swails (Sat Sep 04 2010 - 13:03:00 PDT)
- Re: [AMBER] ERROR in safe_malloc: Error in alloc of -2030981184 bytes Thomas Cheatham (Sat Sep 04 2010 - 13:51:34 PDT)
[AMBER] read the traj file to analyzing hbonds Ehsan Habibi (Sun Sep 05 2010 - 10:47:47 PDT)
- Re: [AMBER] read the traj file to analyzing hbonds Daniel Roe (Mon Sep 06 2010 - 06:06:33 PDT)
  - Re: [AMBER] read the traj file to analyzing hbonds Ehsan Habibi (Mon Sep 06 2010 - 07:15:35 PDT)
    - Re: [AMBER] read the traj file to analyzing hbonds Daniel Roe (Tue Sep 07 2010 - 05:52:50 PDT)
[AMBER] significance of time-average or representative structures from MD Senthil Natesan (Sun Sep 05 2010 - 11:01:55 PDT)
- Re: [AMBER] significance of time-average or representative structures from MD Jason Swails (Sun Sep 05 2010 - 19:28:49 PDT)
  - Re: [AMBER] significance of time-average or representative structures from MD Senthil Natesan (Mon Sep 06 2010 - 14:13:18 PDT)
[AMBER] builiding an oxide substrate tomba.uni-bremen.de (Sun Sep 05 2010 - 15:22:27 PDT)
[AMBER] pmemd.cuda errors on GTX400 series cards - USER POLL Sasha Buzko (Sun Sep 05 2010 - 15:47:41 PDT)
- Re: [AMBER] pmemd.cuda errors on GTX400 series cards - USER POLL Christophe Deprez (Thu Sep 09 2010 - 09:11:45 PDT)
[AMBER] Water Box Shape hirdesh kumar (Sun Sep 05 2010 - 23:17:06 PDT)
- Re: [AMBER] Water Box Shape Sushil Mishra (Mon Sep 06 2010 - 00:07:36 PDT)
  - Re: [AMBER] Water Box Shape hirdesh kumar (Mon Sep 06 2010 - 02:35:24 PDT)
[AMBER] which conformation to choose asaki asaki (Mon Sep 06 2010 - 03:18:34 PDT)
- Re: [AMBER] which conformation to choose FyD (Wed Sep 08 2010 - 04:49:43 PDT)
[AMBER] problem of GTX480 running pmemd.cuda Yi Xue (Mon Sep 06 2010 - 08:23:18 PDT)
- Re: [AMBER] problem of GTX480 running pmemd.cuda Sasha Buzko (Mon Sep 06 2010 - 14:20:37 PDT)
  - Re: [AMBER] problem of GTX480 running pmemd.cuda Yi Xue (Mon Sep 06 2010 - 14:44:24 PDT)
  - Re: [AMBER] problem of GTX480 running pmemd.cuda Ross Walker (Mon Sep 06 2010 - 17:54:10 PDT)
    - Re: [AMBER] problem of GTX480 running pmemd.cuda Yi Xue (Mon Sep 06 2010 - 18:28:03 PDT)
    - Re: [AMBER] problem of GTX480 running pmemd.cuda Sasha Buzko (Mon Sep 06 2010 - 18:46:06 PDT)
    - [AMBER] problem of GTX470 running pmemd.cuda_DPDP/input file access provided Sergio R Aragon (Wed Sep 08 2010 - 11:34:51 PDT)
    - Re: [AMBER] problem of GTX470 running pmemd.cuda_DPDP/input file access provided Scott Le Grand (Wed Sep 08 2010 - 12:52:13 PDT)
    - Re: [AMBER] problem of GTX470 running pmemd.cuda_DPDP/input file access provided Sasha Buzko (Wed Sep 08 2010 - 13:43:10 PDT)
    - Re: [AMBER] problem of GTX470 running pmemd.cuda_DPDP/input file access provided Scott Le Grand (Wed Sep 08 2010 - 13:55:06 PDT)
    - Re: [AMBER] problem of GTX470 running pmemd.cuda_DPDP/input file access provided Ross Walker (Wed Sep 08 2010 - 14:02:03 PDT)
    - Re: [AMBER] problem of GTX470 running pmemd.cuda_DPDP/input file access provided Sasha Buzko (Wed Sep 08 2010 - 14:17:52 PDT)
    - [AMBER] JAC test on GTX 470 started Sergio R Aragon (Wed Sep 08 2010 - 15:22:42 PDT)
    - Re: [AMBER] JAC test on GTX 470 started Scott Le Grand (Wed Sep 08 2010 - 15:41:59 PDT)
    - [AMBER] JAC test on GTX 470 error produced Sergio R Aragon (Wed Sep 08 2010 - 18:17:13 PDT)
    - Re: [AMBER] JAC test on GTX 470 error produced Jason Swails (Wed Sep 08 2010 - 19:26:20 PDT)
    - Re: [AMBER] JAC test on GTX 470 error produced/run again w/o changes/need help Sergio R Aragon (Wed Sep 08 2010 - 20:07:25 PDT)
    - Re: [AMBER] JAC test on GTX 470 error produced/run again w/o changes/need help Ross Walker (Wed Sep 08 2010 - 20:42:12 PDT)
    - [AMBER] JAC error reproduced 3 times on GTX 470 Sergio R Aragon (Thu Sep 09 2010 - 09:20:06 PDT)
    - Re: [AMBER] JAC error reproduced 3 times on GTX 470 Mark Williamson (Fri Sep 10 2010 - 08:15:11 PDT)
    - Re: [AMBER] JAC error reproduced 3 times on GTX 470 Scott Le Grand (Fri Sep 10 2010 - 08:33:15 PDT)
    - [AMBER] GPU memory test program Sergio R Aragon (Fri Sep 10 2010 - 10:17:42 PDT)
    - Re: [AMBER] GPU memory test program Scott Le Grand (Fri Sep 10 2010 - 11:32:54 PDT)
    - [AMBER] debug run Sergio R Aragon (Fri Sep 10 2010 - 12:03:20 PDT)
    - Re: [AMBER] debug run Jason Swails (Fri Sep 10 2010 - 12:26:29 PDT)
    - Re: [AMBER] debug run Scott Le Grand (Fri Sep 10 2010 - 13:34:42 PDT)
    - Re: [AMBER] debug run Sergio R Aragon (Fri Sep 10 2010 - 15:36:35 PDT)
    - Re: [AMBER] Memory test con GTX 470 Sergio R Aragon (Sun Sep 12 2010 - 08:00:54 PDT)
    - Re: [AMBER] Memory test con GTX 470 Scott Le Grand (Sun Sep 12 2010 - 20:15:11 PDT)
    - Re: [AMBER] Debug pmemd.cuda Sergio R Aragon (Mon Sep 13 2010 - 12:29:14 PDT)
    - Re: [AMBER] Debug pmemd.cuda Scott Le Grand (Mon Sep 13 2010 - 13:10:32 PDT)
    - Re: [AMBER] how to set clock rate? temperature in a C2050 card? hardware replacement? Sergio R Aragon (Mon Sep 13 2010 - 13:34:11 PDT)
    - Re: [AMBER] how to set clock rate? temperature in a C2050 card? hardware replacement? Scott Le Grand (Mon Sep 13 2010 - 13:58:36 PDT)
    - Re: [AMBER] problem of GTX470 running pmemd.cuda_DPDP/input file access provided Ross Walker (Thu Sep 09 2010 - 09:16:22 PDT)
[AMBER] GLYCAM residue naming manoj singh (Mon Sep 06 2010 - 09:05:28 PDT)
- Re: [AMBER] GLYCAM residue naming Lachele Foley (Lists) (Mon Sep 06 2010 - 09:24:39 PDT)
  - Re: [AMBER] GLYCAM residue naming manoj singh (Mon Sep 06 2010 - 18:56:00 PDT)
    - Re: [AMBER] GLYCAM residue naming Lachele Foley (Lists) (Tue Sep 07 2010 - 07:05:59 PDT)
    - Re: [AMBER] GLYCAM residue naming manoj singh (Tue Sep 07 2010 - 13:51:39 PDT)
    - Re: [AMBER] GLYCAM residue naming Lachele Foley (Lists) (Wed Sep 08 2010 - 06:35:36 PDT)
    - Re: [AMBER] GLYCAM residue naming manoj singh (Wed Sep 08 2010 - 13:30:50 PDT)
    - Re: [AMBER] GLYCAM residue naming Lachele Foley (Lists) (Wed Sep 08 2010 - 13:46:49 PDT)
    - Re: [AMBER] GLYCAM residue naming manoj singh (Wed Sep 08 2010 - 13:51:06 PDT)
    - Re: [AMBER] GLYCAM residue naming Lachele Foley (Lists) (Wed Sep 08 2010 - 14:12:48 PDT)
    - Re: [AMBER] GLYCAM residue naming Lekpa Duukori (Wed Sep 08 2010 - 14:14:32 PDT)
    - Re: [AMBER] GLYCAM residue naming manoj singh (Wed Sep 08 2010 - 14:16:56 PDT)
    - Re: [AMBER] GLYCAM residue naming Lachele Foley (Lists) (Wed Sep 08 2010 - 14:22:31 PDT)
    - Re: [AMBER] GLYCAM residue naming manoj singh (Wed Sep 08 2010 - 14:28:41 PDT)
    - Re: [AMBER] GLYCAM residue naming Lekpa Duukori (Wed Sep 08 2010 - 14:22:52 PDT)
    - Re: [AMBER] GLYCAM residue naming manoj singh (Wed Sep 08 2010 - 15:31:37 PDT)
    - Re: [AMBER] GLYCAM residue naming Lachele Foley (Lists) (Wed Sep 08 2010 - 16:14:11 PDT)
    - Re: [AMBER] GLYCAM residue naming manoj singh (Wed Sep 08 2010 - 22:19:50 PDT)
- Re: [AMBER] GLYCAM residue naming Bill Ross (Tue Sep 07 2010 - 14:01:03 PDT)
  - Re: [AMBER] GLYCAM residue naming manoj singh (Tue Sep 07 2010 - 15:02:54 PDT)
- Re: [AMBER] GLYCAM residue naming Bill Ross (Wed Sep 08 2010 - 15:02:23 PDT)
[AMBER] Gamma_ln in REMD Lekpa Duukori (Mon Sep 06 2010 - 16:37:19 PDT)
- Re: [AMBER] Gamma_ln in REMD Carlos Simmerling (Tue Sep 07 2010 - 03:36:56 PDT)
  - Re: [AMBER] Gamma_ln in REMD Lekpa Duukori (Tue Sep 07 2010 - 07:03:54 PDT)
[AMBER] Quasiharmonic Analysis Tyler Glembo (Mon Sep 06 2010 - 22:55:40 PDT)
- Re: [AMBER] Quasiharmonic Analysis case (Tue Sep 07 2010 - 05:01:52 PDT)
[AMBER] NMR multiple structures Baptiste Legrand (Tue Sep 07 2010 - 02:30:05 PDT)
- Re: [AMBER] NMR multiple structures Jason Swails (Tue Sep 07 2010 - 04:38:37 PDT)
- Re: [AMBER] NMR multiple structures case (Tue Sep 07 2010 - 05:03:14 PDT)
  - Re: [AMBER] NMR multiple structures Baptiste Legrand (Tue Sep 07 2010 - 07:09:48 PDT)
    - Re: [AMBER] NMR multiple structures Jason Swails (Tue Sep 07 2010 - 08:31:41 PDT)
    - Re: [AMBER] NMR multiple structures Baptiste Legrand (Tue Sep 07 2010 - 09:45:36 PDT)
    - Re: [AMBER] NMR multiple structures case (Tue Sep 07 2010 - 09:54:33 PDT)
- Re: [AMBER] NMR multiple structures Bill Ross (Tue Sep 07 2010 - 10:49:35 PDT)
  - Re: [AMBER] NMR multiple structures Baptiste Legrand (Wed Sep 08 2010 - 09:55:37 PDT)
- Re: [AMBER] NMR multiple structures Bill Ross (Wed Sep 08 2010 - 10:06:27 PDT)
  - Re: [AMBER] NMR multiple structures Baptiste Legrand (Wed Sep 15 2010 - 05:33:45 PDT)
    - Re: [AMBER] NMR multiple structures Jason Swails (Wed Sep 15 2010 - 05:55:19 PDT)
    - Re: [AMBER] NMR multiple structures Baptiste Legrand (Wed Sep 15 2010 - 06:36:48 PDT)
    - Re: [AMBER] NMR multiple structures Baptiste Legrand (Thu Sep 16 2010 - 07:27:46 PDT)
    - Re: [AMBER] NMR multiple structures case (Thu Sep 16 2010 - 09:19:06 PDT)
    - Re: [AMBER] NMR multiple structures Baptiste Legrand (Thu Sep 16 2010 - 10:23:04 PDT)
[AMBER] NAMD -trajectory and amber10 mm_pbsa Sangita Kachhap (Tue Sep 07 2010 - 06:44:52 PDT)
[AMBER] Query regarding the Hydrogen Bond duration analysis hirdesh kumar (Tue Sep 07 2010 - 07:17:02 PDT)
- Re: [AMBER] Query regarding the Hydrogen Bond duration analysis monica.imtech.res.in (Wed Sep 08 2010 - 03:16:35 PDT)
  - Re: [AMBER] Query regarding the Hydrogen Bond duration analysis hirdesh kumar (Wed Sep 08 2010 - 03:37:14 PDT)
[AMBER] $AMBERHOME/test/LES_noPME/Run.LESmd Alan (Tue Sep 07 2010 - 10:33:15 PDT)
- Re: [AMBER] $AMBERHOME/test/LES_noPME/Run.LESmd Jason Swails (Tue Sep 07 2010 - 10:54:40 PDT)
  - Re: [AMBER] $AMBERHOME/test/LES_noPME/Run.LESmd Alan (Tue Sep 07 2010 - 11:09:09 PDT)
[AMBER] Confirmation of System equilibration ? hirdesh kumar (Tue Sep 07 2010 - 20:38:41 PDT)
- Re: [AMBER] Confirmation of System equilibration ? manikanthan bhavaraju (Tue Sep 07 2010 - 21:11:53 PDT)
  - Re: [AMBER] Confirmation of System equilibration ? hirdesh kumar (Tue Sep 07 2010 - 21:15:18 PDT)
    - Re: [AMBER] Confirmation of System equilibration ? Jason Swails (Wed Sep 08 2010 - 04:53:50 PDT)
[AMBER] amber7 vs xleap on 64bit machine Rossella Noschese (Wed Sep 08 2010 - 02:48:44 PDT)
- Re: [AMBER] amber7 vs xleap on 64bit machine Jason Swails (Wed Sep 08 2010 - 04:51:59 PDT)
  - Re: [AMBER] amber7 vs xleap on 64bit machine Rossella Noschese (Wed Sep 08 2010 - 06:06:00 PDT)
    - Re: [AMBER] amber7 vs xleap on 64bit machine Jason Swails (Wed Sep 08 2010 - 06:24:47 PDT)
    - Re: [AMBER] amber7 vs xleap on 64bit machine Frank Thommen (Wed Sep 08 2010 - 06:45:58 PDT)
    - Re: [AMBER] amber7 vs xleap on 64bit machine Jason Swails (Wed Sep 08 2010 - 07:00:23 PDT)
    - Re: [AMBER] amber7 vs xleap on 64bit machine Rossella Noschese (Wed Sep 08 2010 - 07:50:04 PDT)
    - Re: [AMBER] amber7 vs xleap on 64bit machine case (Wed Sep 08 2010 - 08:04:04 PDT)
    - Re: [AMBER] amber7 vs xleap on 64bit machine Rossella Noschese (Wed Sep 08 2010 - 08:37:29 PDT)
    - Re: [AMBER] amber7 vs xleap on 64bit machine Jason Swails (Wed Sep 08 2010 - 09:53:33 PDT)
    - Re: [AMBER] amber7 vs xleap on 64bit machine case (Wed Sep 08 2010 - 13:31:57 PDT)
    - Re: [AMBER] amber7 vs xleap on 64bit machine Scott Brozell (Wed Sep 08 2010 - 16:49:23 PDT)
- Re: [AMBER] amber7 vs xleap on 64bit machine case (Wed Sep 08 2010 - 05:07:54 PDT)
[AMBER] Compilation problems for amber9/parallel (aka: How to use g77?) Frank Thommen (Wed Sep 08 2010 - 05:37:37 PDT)
- Re: [AMBER] Compilation problems for amber9/parallel (aka: How to use g77?) Jason Swails (Wed Sep 08 2010 - 05:49:46 PDT)
  - Re: [AMBER] Compilation problems for amber9/parallel (aka: How to use g77?) Frank Thommen (Wed Sep 08 2010 - 06:32:14 PDT)
    - Re: [AMBER] Compilation problems for amber9/parallel (aka: How to use g77?) peter.stauffert.boehringer-ingelheim.com (Wed Sep 08 2010 - 06:52:45 PDT)
    - Re: [AMBER] Compilation problems for amber9/parallel (aka: How to use g77?) Frank Thommen (Wed Sep 08 2010 - 07:00:25 PDT)
    - Re: [AMBER] Compilation problems for amber9/parallel (aka: How to use g77?) Jason Swails (Wed Sep 08 2010 - 07:04:10 PDT)
    - Re: [AMBER] Compilation problems for amber9/parallel (aka: How to use g77?) Frank Thommen (Wed Sep 08 2010 - 07:12:15 PDT)
[AMBER] mixing GAFF with CHARMM Alan (Wed Sep 08 2010 - 10:35:32 PDT)
- Re: [AMBER] mixing GAFF with CHARMM Ross Walker (Wed Sep 08 2010 - 11:03:23 PDT)
  - Re: [AMBER] mixing GAFF with CHARMM Alan (Wed Sep 08 2010 - 14:19:59 PDT)
[AMBER] Create a carbon nanotube. moacyr comar (Wed Sep 08 2010 - 11:28:18 PDT)
[AMBER] Atom selection Rahul Banerjee (Wed Sep 08 2010 - 19:27:42 PDT)
- Re: [AMBER] Atom selection Senthil Natesan (Fri Sep 10 2010 - 06:54:07 PDT)
[AMBER] pmemd installation colvin (Thu Sep 09 2010 - 02:04:17 PDT)
- Re: [AMBER] pmemd installation Per Jr. Greisen (Thu Sep 09 2010 - 02:19:13 PDT)
  - Re: [AMBER] pmemd installation colvin (Thu Sep 09 2010 - 02:36:10 PDT)
    - Re: [AMBER] pmemd installation Jason Swails (Thu Sep 09 2010 - 06:10:55 PDT)
    - Re: [AMBER] pmemd installation colvin (Sun Sep 12 2010 - 18:36:02 PDT)
    - Re: [AMBER] pmemd installation Jason Swails (Sun Sep 12 2010 - 18:50:51 PDT)
    - Re: [AMBER] pmemd installation colvin (Sun Sep 12 2010 - 18:56:36 PDT)
    - Re: [AMBER] pmemd installation Jason Swails (Sun Sep 12 2010 - 19:18:26 PDT)
    - Re: [AMBER] pmemd installation colvin (Mon Sep 13 2010 - 05:01:33 PDT)
[AMBER] Varying restraint values on subsets of a restraint mask in sander/pmemd Matthew Tessier (Thu Sep 09 2010 - 07:02:48 PDT)
[AMBER] Restraints for Glycan in REMD Lekpa Duukori (Thu Sep 09 2010 - 08:24:06 PDT)
- Re: [AMBER] Restraints for Glycan in REMD Lachele Foley (Lists) (Thu Sep 09 2010 - 09:09:19 PDT)
  - Re: [AMBER] Restraints for Glycan in REMD Lekpa Duukori (Thu Sep 09 2010 - 09:43:10 PDT)
[AMBER] installation of python script for mm_pbsa Sangita Kachhap (Thu Sep 09 2010 - 09:17:03 PDT)
- Re: [AMBER] installation of python script for mm_pbsa Bill Miller III (Thu Sep 09 2010 - 09:22:11 PDT)
[AMBER] mmpbsa problem Lidong Wang (Thu Sep 09 2010 - 09:43:24 PDT)
[AMBER] Building a sequence using a new molecular fragment Millen, Andrea (Thu Sep 09 2010 - 17:04:06 PDT)
- Re: [AMBER] Building a sequence using a new molecular fragment FyD (Thu Sep 09 2010 - 23:45:58 PDT)
  - Re: [AMBER] Building a sequence using a new molecular fragment Millen, Andrea (Mon Sep 20 2010 - 10:59:17 PDT)
[AMBER] compilation fails ALL make.parallel tests Daniel Sindhikara (Fri Sep 10 2010 - 02:56:09 PDT)
- Re: [AMBER] compilation fails ALL make.parallel tests case (Fri Sep 10 2010 - 04:42:12 PDT)
  - Re: [AMBER] compilation fails ALL make.parallel tests Daniel Sindhikara (Sun Sep 12 2010 - 03:07:54 PDT)
    - Re: [AMBER] compilation fails ALL make.parallel tests case (Sun Sep 12 2010 - 06:44:43 PDT)
    - Re: [AMBER] compilation fails ALL make.parallel tests Daniel Sindhikara (Sun Sep 12 2010 - 23:52:03 PDT)
    - Re: [AMBER] compilation fails ALL make.parallel tests case (Mon Sep 13 2010 - 04:40:33 PDT)
    - Re: [AMBER] compilation fails ALL make.parallel tests Daniel Sindhikara (Mon Sep 13 2010 - 22:58:02 PDT)
[AMBER] Complex distorts during pressure adjustment in equilibration Alexander Metz (Fri Sep 10 2010 - 03:40:47 PDT)
- Re: [AMBER] Complex distorts during pressure adjustment in equilibration Sergio R Aragon (Fri Sep 10 2010 - 10:26:41 PDT)
  - Re: [AMBER] Complex distorts during pressure adjustment in equilibration Alexander Metz (Fri Sep 10 2010 - 11:28:46 PDT)
  - Re: [AMBER] Complex distorts during pressure adjustment in equilibr ation. . Don.Bashford.stjude.org (Fri Sep 10 2010 - 16:44:31 PDT)
- Re: [AMBER] Complex distorts during pressure adjustment in equilibration Thomas Cheatham III (Fri Sep 10 2010 - 17:21:17 PDT)
[AMBER] PTRAJ residue naming problem. Hoshin Kim (Fri Sep 10 2010 - 11:26:31 PDT)
- Re: [AMBER] PTRAJ residue naming problem. Jason Swails (Fri Sep 10 2010 - 11:32:03 PDT)
  - Re: [AMBER] PTRAJ residue naming problem. Kevin Hauser (Fri Sep 10 2010 - 11:42:16 PDT)
- Re: [AMBER] PTRAJ residue naming problem. Bill Ross (Fri Sep 10 2010 - 11:46:07 PDT)
[AMBER] Questions on Minimization Jiang Yusheng (Fri Sep 10 2010 - 12:21:20 PDT)
- Re: [AMBER] Questions on Minimization Jason Swails (Fri Sep 10 2010 - 12:32:04 PDT)
  - [AMBER] curves question Temiz, Nuri (NIH/NCI) [C] (Fri Sep 10 2010 - 12:41:24 PDT)
  - Re: [AMBER] Questions on Minimization Jiang Yusheng (Fri Sep 10 2010 - 14:10:27 PDT)
    - Re: [AMBER] Questions on Minimization Kevin Hauser (Fri Sep 10 2010 - 14:13:03 PDT)
    - Re: [AMBER] Questions on Minimization Jason Swails (Fri Sep 10 2010 - 14:14:23 PDT)
    - Re: [AMBER] Questions on Minimization Jiang Yusheng (Fri Sep 10 2010 - 14:19:20 PDT)
    - Re: [AMBER] Questions on Minimization Jason Swails (Fri Sep 10 2010 - 14:50:51 PDT)
[AMBER] sleap error manoj singh (Fri Sep 10 2010 - 12:47:57 PDT)
- Re: [AMBER] sleap error Jason Swails (Fri Sep 10 2010 - 12:51:12 PDT)
  - Re: [AMBER] sleap error manoj singh (Fri Sep 10 2010 - 12:55:27 PDT)
    - Re: [AMBER] sleap error Jason Swails (Fri Sep 10 2010 - 12:56:38 PDT)
    - Re: [AMBER] sleap error manoj singh (Fri Sep 10 2010 - 13:07:43 PDT)
[AMBER] pmemd 11 (parallel) compilation error Paul S. Nerenberg (Fri Sep 10 2010 - 16:27:25 PDT)
- Re: [AMBER] pmemd 11 (parallel) compilation error Ross Walker (Fri Sep 10 2010 - 16:46:35 PDT)
  - Re: [AMBER] pmemd 11 (parallel) compilation error Jason Swails (Fri Sep 10 2010 - 17:03:41 PDT)
    - Re: [AMBER] pmemd 11 (parallel) compilation error Paul S. Nerenberg (Fri Sep 10 2010 - 17:21:54 PDT)
  - Re: [AMBER] pmemd 11 (parallel) compilation error Paul S. Nerenberg (Fri Sep 10 2010 - 17:03:45 PDT)
- Re: [AMBER] pmemd 11 (parallel) compilation error Ross Walker (Sat Sep 11 2010 - 10:09:11 PDT)
  - Re: [AMBER] pmemd 11 (parallel) compilation error Paul S. Nerenberg (Sat Sep 11 2010 - 16:04:48 PDT)
[AMBER] RESP calculation using non-Gaussian software? Ilyas Yildirim (Fri Sep 10 2010 - 17:51:11 PDT)
- Re: [AMBER] RESP calculation using non-Gaussian software? Jason Swails (Fri Sep 10 2010 - 18:12:40 PDT)
  - Re: [AMBER] RESP calculation using non-Gaussian software? FyD (Fri Sep 10 2010 - 23:14:05 PDT)
[AMBER] How to control the speed of heating? xqkong (Sat Sep 11 2010 - 01:59:36 PDT)
- Re: [AMBER] How to control the speed of heating? Daniel Sindhikara (Sat Sep 11 2010 - 02:12:21 PDT)
- Re: [AMBER] How to control the speed of heating? xqkong (Sat Sep 11 2010 - 03:39:06 PDT)
  - Re: [AMBER] How to control the speed of heating? Carlos Simmerling (Sat Sep 11 2010 - 03:40:30 PDT)
- Re: [AMBER] How to control the speed of heating? xqkong (Sat Sep 11 2010 - 03:59:49 PDT)
  - Re: [AMBER] How to control the speed of heating? Carlos Simmerling (Sat Sep 11 2010 - 04:01:51 PDT)
  - Re: [AMBER] How to control the speed of heating? cieplak.cgl.ucsf.edu (Sat Sep 11 2010 - 22:53:56 PDT)
- Re: [AMBER] How to control the speed of heating? xqkong (Sat Sep 11 2010 - 23:15:10 PDT)
[AMBER] ig value M. Reza Ganjalikhany (Sat Sep 11 2010 - 14:44:32 PDT)
- Re: [AMBER] ig value Daniel Sindhikara (Sat Sep 11 2010 - 15:00:40 PDT)
  - [AMBER] list of atoms with associated total forces ? Marek Maly (Tue Sep 14 2010 - 08:32:43 PDT)
    - Re: [AMBER] list of atoms with associated total forces ? Ben Roberts (Tue Sep 14 2010 - 13:45:39 PDT)
    - Re: [AMBER] list of atoms with associated total forces ? Marek Maly (Tue Sep 14 2010 - 14:09:54 PDT)
    - Re: [AMBER] list of atomsG4 with amber with associated total forces ? Philippe Pinard (Thu Sep 16 2010 - 08:53:06 PDT)
    - Re: [AMBER] list of atomsG4 with amber with associated total forces ? Marek Maly (Thu Sep 16 2010 - 09:51:34 PDT)
[AMBER] MMPBSA.py installation error Sangita Kachhap (Sun Sep 12 2010 - 03:59:22 PDT)
- Re: [AMBER] MMPBSA.py installation error Jason Swails (Sun Sep 12 2010 - 05:21:45 PDT)
  - Re: [AMBER] MMPBSA.py installation error Sangita Kachhap (Sun Sep 12 2010 - 06:39:12 PDT)
    - Re: [AMBER] MMPBSA.py installation error Jason Swails (Sun Sep 12 2010 - 07:02:39 PDT)
[AMBER] PMEMD with CUDA support for Windows? Thomas Patko (Sun Sep 12 2010 - 06:35:59 PDT)
- Re: [AMBER] PMEMD with CUDA support for Windows? Ross Walker (Sun Sep 12 2010 - 12:37:38 PDT)
[AMBER] memory allocation problem? Seibold, Stephen (Sun Sep 12 2010 - 09:21:43 PDT)
- Re: [AMBER] memory allocation problem? Daniel Roe (Sun Sep 12 2010 - 12:31:02 PDT)
- Re: [AMBER] memory allocation problem? Seibold, Stephen (Sun Sep 12 2010 - 13:23:29 PDT)
[AMBER] contacts command Andrew Voronkov (Sun Sep 12 2010 - 13:41:01 PDT)
[AMBER] question on diffusion comand in ptraj Andrew Voronkov (Sun Sep 12 2010 - 13:54:10 PDT)
[AMBER] remd coordinate output Jorgen Simonsen (Mon Sep 13 2010 - 03:19:43 PDT)
- Re: [AMBER] remd coordinate output Carlos Simmerling (Mon Sep 13 2010 - 03:41:30 PDT)
  - Re: [AMBER] remd coordinate output Jorgen Simonsen (Mon Sep 13 2010 - 04:04:23 PDT)
    - Re: [AMBER] remd coordinate output Carlos Simmerling (Mon Sep 13 2010 - 04:09:42 PDT)
    - Re: [AMBER] remd coordinate output Adrian Roitberg (Mon Sep 13 2010 - 04:13:24 PDT)
    - Re: [AMBER] remd coordinate output Jorgen Simonsen (Mon Sep 13 2010 - 04:35:26 PDT)
    - Re: [AMBER] remd coordinate output Carlos Simmerling (Mon Sep 13 2010 - 05:45:50 PDT)
    - Re: [AMBER] remd coordinate output Jorgen Simonsen (Mon Sep 13 2010 - 07:06:09 PDT)
[AMBER] Average distance between two hydrogens over a 1 ns simulation Edward M. (Mon Sep 13 2010 - 04:39:17 PDT)
- Re: [AMBER] Average distance between two hydrogens over a 1 ns simulation Peter Schmidtke (Mon Sep 13 2010 - 04:50:06 PDT)
[AMBER] MD based on 3D-RISM can be really used in AMBER11? kyousuke_tsumura.fujifilm.co.jp (Mon Sep 13 2010 - 04:44:46 PDT)
- Re: [AMBER] MD based on 3D-RISM can be really used in AMBER11? case (Mon Sep 13 2010 - 06:12:33 PDT)
[AMBER] regarding wham analysis jani vinod (Mon Sep 13 2010 - 04:45:13 PDT)
- Re: [AMBER] regarding wham analysis Carlos Simmerling (Mon Sep 13 2010 - 04:46:58 PDT)
  - Re: [AMBER] regarding wham analysis jani vinod (Mon Sep 13 2010 - 05:37:25 PDT)
    - Re: [AMBER] regarding wham analysis Carlos Simmerling (Mon Sep 13 2010 - 05:40:57 PDT)
    - Re: [AMBER] regarding wham analysis jani vinod (Mon Sep 13 2010 - 20:11:11 PDT)
    - Re: [AMBER] regarding wham analysis Daniel Sindhikara (Mon Sep 13 2010 - 21:24:53 PDT)
[AMBER] ptraj hbond analysis George Tzotzos (Mon Sep 13 2010 - 06:55:13 PDT)
- Re: [AMBER] ptraj hbond analysis Alexander Metz (Mon Sep 13 2010 - 07:38:12 PDT)
- Re: [AMBER] ptraj hbond analysis rameshwar prajapati (Sun Sep 19 2010 - 00:20:54 PDT)
[AMBER] ptraj image, overlap of molecules Nadine Utz (Mon Sep 13 2010 - 07:22:57 PDT)
[AMBER] chamber At line 2692 of file _psfprm.f Jorgen Simonsen (Mon Sep 13 2010 - 08:00:30 PDT)
- Re: [AMBER] chamber At line 2692 of file _psfprm.f Mark Williamson (Mon Sep 13 2010 - 08:10:30 PDT)
  - Re: [AMBER] chamber At line 2692 of file _psfprm.f Ross Walker (Mon Sep 13 2010 - 09:01:23 PDT)
    - Re: [AMBER] chamber At line 2692 of file _psfprm.f Jorgen Simonsen (Wed Sep 22 2010 - 04:30:40 PDT)
[AMBER] Question about Heating and equilibration protocol? M. Reza Ganjalikhany (Mon Sep 13 2010 - 10:25:36 PDT)
- Re: [AMBER] Question about Heating and equilibration protocol? case (Mon Sep 13 2010 - 11:04:09 PDT)
  - [AMBER] AMBER 10 on OPENMPI CHAMI F. (Tue Sep 14 2010 - 03:19:55 PDT)
    - Re: [AMBER] AMBER 10 on OPENMPI Ye MEI (Tue Sep 14 2010 - 03:42:47 PDT)
- Re: [AMBER] Question about Heating and equilibration protocol? manikanthan bhavaraju (Mon Sep 13 2010 - 11:05:48 PDT)
- Re: [AMBER] Question about Heating and equilibration protocol? Bill Ross (Mon Sep 13 2010 - 11:23:02 PDT)
[AMBER] Pressure in bar or atm? Ben Roberts (Mon Sep 13 2010 - 13:01:46 PDT)
- Re: [AMBER] Pressure in bar or atm? case (Wed Sep 15 2010 - 05:19:50 PDT)
  - Re: [AMBER] Pressure in bar or atm? Ben Roberts (Fri Sep 17 2010 - 14:19:27 PDT)
    - Re: [AMBER] Pressure in bar or atm? case (Sun Sep 19 2010 - 14:52:14 PDT)
    - Re: [AMBER] Pressure in bar or atm? Ben Roberts (Fri Oct 08 2010 - 08:34:36 PDT)
    - Re: [AMBER] Pressure in bar or atm? case (Fri Oct 08 2010 - 11:18:04 PDT)
    - Re: [AMBER] Pressure in bar or atm? Ben Roberts (Mon Oct 11 2010 - 10:05:11 PDT)
[AMBER] Exactly the same energy output over multiple runs of cuda_SPDP Trevor Gokey (Mon Sep 13 2010 - 16:33:29 PDT)
- Re: [AMBER] Exactly the same energy output over multiple runs of cuda_SPDP Ross Walker (Mon Sep 13 2010 - 16:55:28 PDT)
  - Re: [AMBER] Exactly the same energy output over multiple runs of cuda_SPDP Trevor Gokey (Mon Sep 13 2010 - 18:26:13 PDT)
    - Re: [AMBER] Exactly the same energy output over multiple runs of cuda_SPDP Scott Le Grand (Mon Sep 13 2010 - 18:37:03 PDT)
    - [AMBER] restraints in pmemd.cuda Sasha Buzko (Fri Sep 17 2010 - 15:55:15 PDT)
    - Re: [AMBER] restraints in pmemd.cuda Scott Le Grand (Fri Sep 17 2010 - 17:11:11 PDT)
    - Re: [AMBER] restraints in pmemd.cuda Ross Walker (Sat Sep 18 2010 - 07:52:35 PDT)
[AMBER] LD and SGLD runs (Simulations) shaktis.gbu.ac.in (Mon Sep 13 2010 - 18:53:40 PDT)
- Re: [AMBER] LD and SGLD runs (Simulations) Daniel Sindhikara (Mon Sep 13 2010 - 19:46:37 PDT)
  - Re: [AMBER] LD and SGLD runs (Simulations) Carlos Simmerling (Tue Sep 14 2010 - 03:36:38 PDT)
[AMBER] unit of Bfactor Ashutosh Shandilya (Mon Sep 13 2010 - 22:52:30 PDT)
- Re: [AMBER] unit of Bfactor hirdesh kumar (Mon Sep 13 2010 - 23:02:44 PDT)
- Re: [AMBER] unit of Bfactor Kshatresh Dutta Dubey (Mon Sep 13 2010 - 23:11:04 PDT)
  - Re: [AMBER] unit of Bfactor hirdesh kumar (Mon Sep 13 2010 - 23:13:01 PDT)
[AMBER] Residues with multiple conformations George Tzotzos (Tue Sep 14 2010 - 06:54:15 PDT)
- Re: [AMBER] Residues with multiple conformations Alexander Metz (Tue Sep 14 2010 - 07:55:40 PDT)
- Re: [AMBER] Residues with multiple conformations Sergio R Aragon (Tue Sep 14 2010 - 08:09:09 PDT)
[AMBER] set coordinate axis eduardo.troche.uvigo.es (Tue Sep 14 2010 - 07:09:27 PDT)
- Re: [AMBER] set coordinate axis Jason Swails (Tue Sep 14 2010 - 10:43:24 PDT)
[AMBER] units of eigenvalues from pca moitrayee.mbu.iisc.ernet.in (Tue Sep 14 2010 - 11:43:50 PDT)
- Re: [AMBER] units of eigenvalues from pca case (Wed Sep 15 2010 - 05:07:14 PDT)
[AMBER] mm_pbsa.pl error for per residue decomposition. manoj singh (Tue Sep 14 2010 - 18:59:28 PDT)
- Re: [AMBER] mm_pbsa.pl error for per residue decomposition. Jason Swails (Tue Sep 14 2010 - 19:52:05 PDT)
  - Re: [AMBER] mm_pbsa.pl error for per residue decomposition. manoj singh (Tue Sep 14 2010 - 19:55:57 PDT)
    - Re: [AMBER] mm_pbsa.pl error for per residue decomposition. Jason Swails (Tue Sep 14 2010 - 20:06:28 PDT)
    - Re: [AMBER] mm_pbsa.pl error for per residue decomposition. manoj singh (Tue Sep 14 2010 - 20:12:19 PDT)
    - Re: [AMBER] mm_pbsa.pl error for per residue decomposition. manoj singh (Mon Sep 20 2010 - 11:32:53 PDT)
[AMBER] comparison of PDBs from clustering - representative, average and from rst file Andrew Voronkov (Wed Sep 15 2010 - 11:57:19 PDT)
- Re: [AMBER] comparison of PDBs from clustering - representative, average and from rst file Thomas Cheatham III (Wed Sep 15 2010 - 15:18:22 PDT)
  - Re: [AMBER] comparison of PDBs from clustering - representative, average and from rst file Andrew Voronkov (Wed Sep 15 2010 - 23:10:55 PDT)
    - Re: [AMBER] comparison of PDBs from clustering - representative, average and from rst file Thomas Cheatham III (Thu Sep 16 2010 - 08:39:41 PDT)
    - Re: [AMBER] comparison of PDBs from clustering - representative, average and from rst file Andrew Voronkov (Sat Sep 18 2010 - 04:24:03 PDT)
  - Re: [AMBER] comparison of PDBs from clustering - representative, average and from rst file Andrew Voronkov (Thu Sep 16 2010 - 03:25:57 PDT)
[AMBER] Domainwise rmsd using ptraj rms moitrayee.mbu.iisc.ernet.in (Wed Sep 15 2010 - 13:25:54 PDT)
- Re: [AMBER] Domainwise rmsd using ptraj rms Daniel Roe (Wed Sep 15 2010 - 14:40:56 PDT)
  - Re: [AMBER] Domainwise rmsd using ptraj rms moitrayee.mbu.iisc.ernet.in (Wed Sep 15 2010 - 23:20:52 PDT)
  - Re: [AMBER] Domainwise rmsd using ptraj rms moitrayee.mbu.iisc.ernet.in (Sun Sep 26 2010 - 04:35:35 PDT)
[AMBER] Fwd: comparison of PDBs from clustering - representative, average and from rst file Andrew Voronkov (Wed Sep 15 2010 - 13:37:44 PDT)
[AMBER] Compaliation of sander.APBS Hemant Kumar (Wed Sep 15 2010 - 17:11:33 PDT)
- Re: [AMBER] Compaliation of sander.APBS Robert Konecny (Thu Sep 16 2010 - 14:12:39 PDT)
[AMBER] Nudge elastic band, DNA Replica temperature does not go to zero. Abhishek Singh (Thu Sep 16 2010 - 09:21:17 PDT)
[AMBER] Nudge elastic band, DNA Replica temperature does not go to zero. Abhishek Singh (Thu Sep 16 2010 - 09:28:53 PDT)
- Re: [AMBER] Nudge elastic band, DNA Replica temperature does not go to zero. Carlos Simmerling (Thu Sep 16 2010 - 09:42:22 PDT)
[AMBER] pmemd.MPI problem George Tzotzos (Thu Sep 16 2010 - 10:35:10 PDT)
- [AMBER] pmemd.MPI problem George Tzotzos (Thu Sep 16 2010 - 10:46:23 PDT)
  - Re: [AMBER] pmemd.MPI problem Jason Swails (Thu Sep 16 2010 - 10:50:28 PDT)
    - Re: [AMBER] pmemd.MPI problem George Tzotzos (Thu Sep 16 2010 - 11:27:40 PDT)
    - Re: [AMBER] pmemd.MPI problem Jason Swails (Thu Sep 16 2010 - 11:45:52 PDT)
    - Re: [AMBER] pmemd.MPI problem George Tzotzos (Fri Sep 17 2010 - 04:45:06 PDT)
    - Re: [AMBER] pmemd.MPI problem Ben Roberts (Fri Sep 17 2010 - 05:23:43 PDT)
- Re: [AMBER] pmemd.MPI problem Jason Swails (Thu Sep 16 2010 - 10:47:15 PDT)
[AMBER] netCDF support for mmpbsa.py + general question Trevor Gokey (Thu Sep 16 2010 - 11:12:22 PDT)
- Re: [AMBER] netCDF support for mmpbsa.py + general question Jason Swails (Thu Sep 16 2010 - 11:39:14 PDT)
  - Re: [AMBER] netCDF support for mmpbsa.py + general question Trevor Gokey (Thu Sep 16 2010 - 13:36:58 PDT)
    - Re: [AMBER] netCDF support for mmpbsa.py + general question Jason Swails (Thu Sep 16 2010 - 13:53:48 PDT)
Re: [AMBER] Using AMBER force field for ionic compounds Preshit Dandekar (Thu Sep 16 2010 - 12:07:36 PDT)
- Re: [AMBER] Using AMBER force field for ionic compounds Preshit Dandekar (Fri Sep 17 2010 - 06:45:41 PDT)
[AMBER] Sander/pmemd usage: refc question mdkvia.yahoo.com (Thu Sep 16 2010 - 12:10:39 PDT)
- Re: [AMBER] Sander/pmemd usage: refc question Jason Swails (Thu Sep 16 2010 - 12:23:34 PDT)
- Re: [AMBER] Sander/pmemd usage: refc question mdkvia.yahoo.com (Thu Sep 16 2010 - 13:05:35 PDT)
  - Re: [AMBER] Sander/pmemd usage: refc question Scott Le Grand (Thu Sep 16 2010 - 13:23:59 PDT)
  - Re: [AMBER] Sander/pmemd usage: refc question Jason Swails (Thu Sep 16 2010 - 13:36:27 PDT)
    - Re: [AMBER] Sander/pmemd usage: refc question mdkvia.yahoo.com (Thu Sep 16 2010 - 14:01:36 PDT)
[AMBER] ambertools1.4 install problem Anuradha Mittal (Thu Sep 16 2010 - 15:36:52 PDT)
- Re: [AMBER] ambertools1.4 install problem Jason Swails (Thu Sep 16 2010 - 16:42:26 PDT)
  - Re: [AMBER] ambertools1.4 install problem Anuradha Mittal (Thu Sep 16 2010 - 19:15:47 PDT)
    - Re: [AMBER] ambertools1.4 install problem Jason Swails (Thu Sep 16 2010 - 20:09:23 PDT)
    - Re: [AMBER] ambertools1.4 install problem Anuradha Mittal (Thu Sep 16 2010 - 20:20:54 PDT)
    - Re: [AMBER] ambertools1.4 install problem case (Fri Sep 17 2010 - 05:09:45 PDT)
    - Re: [AMBER] ambertools1.4 install problem Anuradha Mittal (Fri Sep 17 2010 - 08:17:08 PDT)
    - Re: [AMBER] ambertools1.4 install problem manoj singh (Fri Sep 17 2010 - 08:35:49 PDT)
    - Re: [AMBER] ambertools1.4 install problem case (Fri Sep 17 2010 - 09:06:36 PDT)
    - Re: [AMBER] ambertools1.4 install problem case (Fri Sep 17 2010 - 09:01:35 PDT)
- Re: [AMBER] ambertools1.4 install problem Bill Ross (Fri Sep 17 2010 - 10:16:18 PDT)
[AMBER] Restraint of atom distance during minimization tong Zhu (Thu Sep 16 2010 - 23:32:06 PDT)
- Re: [AMBER] Restraint of atom distance during minimization Jason Swails (Fri Sep 17 2010 - 04:17:17 PDT)
[AMBER] ptraj clustering for long trajetories Senthil Natesan (Fri Sep 17 2010 - 07:51:18 PDT)
[AMBER] Water pdb parameterization Anthony Costa (Fri Sep 17 2010 - 13:29:01 PDT)
- Re: [AMBER] Water pdb parameterization case (Sat Sep 18 2010 - 05:49:48 PDT)
  - Re: [AMBER] Water pdb parameterization Anthony Costa (Sat Sep 18 2010 - 09:58:15 PDT)
    - Re: [AMBER] Water pdb parameterization case (Sun Sep 19 2010 - 11:26:11 PDT)
    - Re: [AMBER] Water pdb parameterization Anthony Costa (Tue Sep 21 2010 - 08:46:10 PDT)
    - Re: [AMBER] Water pdb parameterization case (Tue Sep 21 2010 - 12:36:31 PDT)
    - Re: [AMBER] Water pdb parameterization Anthony Costa (Wed Sep 22 2010 - 11:58:15 PDT)
    - Re: [AMBER] Water pdb parameterization case (Wed Sep 22 2010 - 13:11:47 PDT)
    - Re: [AMBER] Water pdb parameterization Anthony Costa (Wed Sep 22 2010 - 13:18:43 PDT)
[AMBER] Nudge elastic band, DNA Replica temperature does not go to zero. Abhishek Singh (Fri Sep 17 2010 - 14:54:20 PDT)
- Re: [AMBER] Nudge elastic band, DNA Replica temperature does not go to zero. Carlos Simmerling (Sat Sep 18 2010 - 15:18:39 PDT)
  - Re: [AMBER] Nudge elastic band, DNA Replica temperature does not go to zero. Abhishek Singh (Sat Sep 18 2010 - 17:08:47 PDT)
    - Re: [AMBER] Nudge elastic band, DNA Replica temperature does not go to zero. Carlos Simmerling (Sat Sep 18 2010 - 17:24:47 PDT)
    - Re: [AMBER] Nudge elastic band, DNA Replica temperature does not go to zero. Abhishek Singh (Sat Sep 18 2010 - 17:28:53 PDT)
    - Re: [AMBER] Nudge elastic band, DNA Replica temperature does not go to zero. Abhishek Singh (Sat Sep 18 2010 - 17:34:56 PDT)
    - Re: [AMBER] Nudge elastic band, DNA Replica temperature does not go to zero. Carlos Simmerling (Sat Sep 18 2010 - 17:37:40 PDT)
    - Re: [AMBER] Nudge elastic band, DNA Replica temperature does not go to zero. Abhishek Singh (Sat Sep 18 2010 - 17:52:52 PDT)
    - Re: [AMBER] Nudge elastic band, DNA Replica temperature does not go to zero. Carlos Simmerling (Sat Sep 18 2010 - 18:16:24 PDT)
    - Re: [AMBER] Nudge elastic band, DNA Replica temperature does not go to zero. Abhishek Singh (Sun Sep 19 2010 - 11:50:01 PDT)
[AMBER] A question regarding mm_pbsa_statistics.pl bin wang (Fri Sep 17 2010 - 15:39:25 PDT)
- Re: [AMBER] A question regarding mm_pbsa_statistics.pl Jason Swails (Fri Sep 17 2010 - 15:49:38 PDT)
  - Re: [AMBER] A question regarding mm_pbsa_statistics.pl bin wang (Mon Sep 20 2010 - 12:37:09 PDT)
    - Re: [AMBER] A question regarding mm_pbsa_statistics.pl manoj singh (Mon Sep 20 2010 - 17:42:23 PDT)
    - Re: [AMBER] A question regarding mm_pbsa_statistics.pl bin wang (Wed Sep 22 2010 - 06:42:16 PDT)
    - Re: [AMBER] A question regarding mm_pbsa_statistics.pl Alexander Metz (Wed Sep 22 2010 - 08:23:07 PDT)
    - Re: [AMBER] A question regarding mm_pbsa_statistics.pl bin wang (Mon Sep 27 2010 - 10:25:14 PDT)
[AMBER] problem of nmode calculation fancy2012 (Fri Sep 17 2010 - 19:01:21 PDT)
- Re: [AMBER] problem of nmode calculation Jason Swails (Fri Sep 17 2010 - 19:09:32 PDT)
[AMBER] Restrainmask problem xue wang (Fri Sep 17 2010 - 20:08:54 PDT)
- Re: [AMBER] Restrainmask problem Jason Swails (Fri Sep 17 2010 - 20:49:14 PDT)
  - Re: [AMBER] Restrainmask problem xue wang (Sat Sep 18 2010 - 19:14:31 PDT)
    - Re: [AMBER] Restrainmask problem xue wang (Sat Sep 18 2010 - 19:19:46 PDT)
[AMBER] Regarding atomic charges in parmtop file aneesh cna (Sat Sep 18 2010 - 03:26:37 PDT)
- Re: [AMBER] Regarding atomic charges in parmtop file Alessandro Nascimento (Sat Sep 18 2010 - 05:35:18 PDT)
  - Re: [AMBER] Regarding atomic charges in parmtop file Jason Swails (Sat Sep 18 2010 - 07:32:55 PDT)
    - Re: [AMBER] Regarding atomic charges in parmtop file aneesh cna (Sun Sep 19 2010 - 21:11:59 PDT)
[AMBER] Clarification: nscm and iwrap mdkvia.yahoo.com (Sat Sep 18 2010 - 04:36:11 PDT)
[AMBER] inconsistency between steered Md and GBSA MEHMET ALI OZTURK (Sat Sep 18 2010 - 12:57:37 PDT)
- Re: [AMBER] inconsistency between steered Md and GBSA Jason Swails (Sat Sep 18 2010 - 14:42:39 PDT)
[AMBER] Blowing array Seibold, Stephen (Sat Sep 18 2010 - 14:19:20 PDT)
- Re: [AMBER] Blowing array Daniel Roe (Sat Sep 18 2010 - 15:25:32 PDT)
- Re: [AMBER] Blowing array case (Sun Sep 19 2010 - 11:28:41 PDT)
[AMBER] Amber11 compile issue Anuradha Mittal (Sat Sep 18 2010 - 19:00:48 PDT)
- Re: [AMBER] Amber11 compile issue Jason Swails (Sat Sep 18 2010 - 19:05:57 PDT)
  - Re: [AMBER] Amber11 compile issue Anuradha Mittal (Sat Sep 18 2010 - 19:10:51 PDT)
    - Re: [AMBER] Amber11 compile issue Jason Swails (Sat Sep 18 2010 - 20:14:15 PDT)
    - Re: [AMBER] Amber11 compile issue Anuradha Mittal (Sat Sep 18 2010 - 20:15:58 PDT)
    - Re: [AMBER] Amber11 compile issue Ross Walker (Sat Sep 18 2010 - 22:03:14 PDT)
    - Re: [AMBER] Amber11 compile issue Anuradha Mittal (Sat Sep 18 2010 - 22:11:54 PDT)
    - Re: [AMBER] Amber11 compile issue Ross Walker (Sat Sep 18 2010 - 23:28:40 PDT)
    - Re: [AMBER] Amber11 compile issue Anuradha Mittal (Sun Sep 19 2010 - 08:27:27 PDT)
[AMBER] a pdb-trajout problems bingbing zhang (Sun Sep 19 2010 - 07:57:39 PDT)
- Re: [AMBER] a pdb-trajout problems bingbing zhang (Sun Sep 19 2010 - 18:40:24 PDT)
- Re: [AMBER] a pdb-trajout problems Daniel Roe (Tue Sep 21 2010 - 07:42:53 PDT)
  - Re: [AMBER] a pdb-trajout problems bingbing zhang (Tue Sep 21 2010 - 19:44:32 PDT)
    - Re: [AMBER] a pdb-trajout problems Trevor Gokey (Tue Sep 21 2010 - 22:08:19 PDT)
    - Re: [AMBER] a pdb-trajout problems bingbing zhang (Sat Sep 25 2010 - 03:54:14 PDT)
[AMBER] Minimization terminated without any output xue wang (Sun Sep 19 2010 - 08:07:48 PDT)
- Re: [AMBER] Minimization terminated without any output case (Sun Sep 19 2010 - 14:07:26 PDT)
  - Re: [AMBER] Minimization terminated without any output xue wang (Mon Sep 20 2010 - 13:31:43 PDT)
    - Re: [AMBER] Minimization terminated without any output case (Mon Sep 20 2010 - 18:17:05 PDT)
[AMBER] making bond to water molecule Jorgen Simonsen (Sun Sep 19 2010 - 12:20:03 PDT)
- Re: [AMBER] making bond to water molecule Bill Ross (Sun Sep 19 2010 - 13:45:16 PDT)
[AMBER] Error due to ***s in restart file Arvind (Sun Sep 19 2010 - 14:07:22 PDT)
- Re: [AMBER] Error due to ***s in restart file case (Sun Sep 19 2010 - 14:14:46 PDT)
  - Re: [AMBER] Error due to ***s in restart file Arvind (Mon Sep 20 2010 - 03:51:10 PDT)
    - Re: [AMBER] Error due to ***s in restart file Trevor Gokey (Tue Sep 21 2010 - 22:16:31 PDT)
    - Re: [AMBER] Error due to ***s in restart file Arvind (Wed Sep 22 2010 - 11:32:44 PDT)
[AMBER] Blowing array Seibold, Stephen (Sun Sep 19 2010 - 16:00:42 PDT)
- Re: [AMBER] Blowing array Yi Shang (Sun Sep 19 2010 - 18:19:46 PDT)
- Re: [AMBER] Blowing array case (Sun Sep 19 2010 - 18:23:24 PDT)
- Re: [AMBER] Blowing array Daniel Roe (Tue Sep 21 2010 - 07:31:23 PDT)
  - Re: [AMBER] Blowing array Seibold, Stephen (Tue Sep 21 2010 - 07:41:55 PDT)
  - Re: [AMBER] Blowing array Seibold, Stephen (Wed Sep 22 2010 - 06:31:24 PDT)
[AMBER] molecular dynamics simulation-water-box-diffution problem Rilei Yu (Sun Sep 19 2010 - 19:51:29 PDT)
- Re: [AMBER] molecular dynamics simulation-water-box-diffution problem Ye MEI (Sun Sep 19 2010 - 20:02:11 PDT)
  - Re: [AMBER] molecular dynamics simulation-water-box-diffution problem Trevor Gokey (Tue Sep 21 2010 - 22:22:40 PDT)
    - Re: [AMBER] molecular dynamics simulation-water-box-diffution problem hirdesh kumar (Tue Sep 21 2010 - 22:33:49 PDT)
    - Re: [AMBER] molecular dynamics simulation-water-box-diffution problem Ross Walker (Tue Sep 21 2010 - 22:46:59 PDT)
    - Re: [AMBER] molecular dynamics simulation-water-box-diffution problem Trevor Gokey (Wed Sep 22 2010 - 00:31:52 PDT)
    - Re: [AMBER] molecular dynamics simulation-water-box-diffution problem hirdesh kumar (Wed Sep 22 2010 - 02:59:39 PDT)
[AMBER] problems with xleap Rossella Noschese (Mon Sep 20 2010 - 02:55:42 PDT)
- Re: [AMBER] problems with xleap Rossella Noschese (Mon Sep 20 2010 - 03:13:12 PDT)
  - Re: [AMBER] problems with xleap Jason Swails (Mon Sep 20 2010 - 03:39:54 PDT)
    - Re: [AMBER] problems with xleap Rossella Noschese (Tue Sep 21 2010 - 00:59:34 PDT)
    - Re: [AMBER] problems with xleap case (Tue Sep 21 2010 - 04:28:23 PDT)
[AMBER] PTRAJ Hbond analysis George Tzotzos (Mon Sep 20 2010 - 02:56:18 PDT)
[AMBER] GRID-enabled web portal for the use of the AMBER Lucio Ferella (Mon Sep 20 2010 - 05:11:27 PDT)
- Re: [AMBER] GRID-enabled web portal for the use of the AMBER Sergio R Aragon (Mon Sep 20 2010 - 10:42:30 PDT)
  - Re: [AMBER] GRID-enabled web portal for the use of the AMBER Lucio Ferella (Thu Dec 16 2010 - 05:05:25 PST)
[AMBER] on gas phase energies calculation pxq (Mon Sep 20 2010 - 07:55:38 PDT)
[AMBER] changing mdcrd file to XYZ hong-bin Xie (Mon Sep 20 2010 - 10:01:44 PDT)
- Re: [AMBER] changing mdcrd file to XYZ Jason Swails (Mon Sep 20 2010 - 10:43:53 PDT)
- Re: [AMBER] changing mdcrd file to XYZ Lekpa Duukori (Mon Sep 20 2010 - 10:44:03 PDT)
  - Re: [AMBER] changing mdcrd file to XYZ hong-bin Xie (Mon Sep 20 2010 - 10:48:27 PDT)
[AMBER] Aromatic C and N atom type problems in Antechamber Gabriel Rocklin (Mon Sep 20 2010 - 13:20:45 PDT)
- Re: [AMBER] Aromatic C and N atom type problems in Antechamber Sasha Buzko (Mon Sep 20 2010 - 13:30:16 PDT)
- Re: [AMBER] Aromatic C and N atom type problems in Antechamber Gabriel Rocklin (Mon Sep 27 2010 - 21:29:38 PDT)
- Re: [AMBER] Aromatic C and N atom type problems in Antechamber Gabriel Rocklin (Mon Oct 25 2010 - 15:21:00 PDT)
[AMBER] constraint of bond Jorgen Simonsen (Mon Sep 20 2010 - 13:28:28 PDT)
- Re: [AMBER] constraint of bond case (Mon Sep 20 2010 - 18:09:12 PDT)
[AMBER] Running MM-PBSA at different temperatures Khaled Barakat (Mon Sep 20 2010 - 17:39:53 PDT)
- Re: [AMBER] Running MM-PBSA at different temperatures manoj singh (Mon Sep 20 2010 - 18:29:25 PDT)
  - Re: [AMBER] Running MM-PBSA at different temperatures Khaled Barakat (Mon Sep 20 2010 - 18:44:08 PDT)
    - Re: [AMBER] Running MM-PBSA at different temperatures manoj singh (Mon Sep 20 2010 - 18:52:59 PDT)
- Re: [AMBER] Running MM-PBSA at different temperatures Thomas Cheatham (Mon Sep 20 2010 - 19:04:14 PDT)
  - Re: [AMBER] Running MM-PBSA at different temperatures manoj singh (Mon Sep 20 2010 - 19:22:58 PDT)
    - Re: [AMBER] Running MM-PBSA at different temperatures Khaled Barakat (Mon Sep 20 2010 - 20:19:11 PDT)
    - Re: [AMBER] Running MM-PBSA at different temperatures manoj singh (Mon Sep 20 2010 - 21:32:31 PDT)
    - Re: [AMBER] Running MM-PBSA at different temperatures manoj singh (Mon Sep 20 2010 - 21:37:01 PDT)
    - Re: [AMBER] Running MM-PBSA at different temperatures Khaled Barakat (Mon Sep 20 2010 - 21:41:48 PDT)
    - Re: [AMBER] Running MM-PBSA at different temperatures Jason Swails (Tue Sep 21 2010 - 07:59:35 PDT)
[AMBER] how to calculate the interaction energies pxq (Mon Sep 20 2010 - 19:30:07 PDT)
[AMBER] Problems with Amber 8 PMEMD Su Qiu (Tue Sep 21 2010 - 00:06:08 PDT)
- Re: [AMBER] Problems with Amber 8 PMEMD case (Tue Sep 21 2010 - 04:23:18 PDT)
  - Re: [AMBER] Problems with Amber 8 PMEMD Su Qiu (Sat Sep 25 2010 - 01:39:22 PDT)
    - Re: [AMBER] Problems with Amber 8 PMEMD case (Sat Sep 25 2010 - 06:10:27 PDT)
    - Re: [AMBER] Problems with Amber 8 PMEMD Su Qiu (Sat Sep 25 2010 - 18:59:10 PDT)
- Re: [AMBER] Problems with Amber 8 PMEMD Bill Ross (Sat Sep 25 2010 - 11:48:34 PDT)
  - Re: [AMBER] Problems with Amber 8 PMEMD Su Qiu (Sun Sep 26 2010 - 18:11:48 PDT)
[AMBER] 2D radial distribution function Lekpa Duukori (Tue Sep 21 2010 - 02:36:45 PDT)
- Re: [AMBER] 2D radial distribution function Daniel Sindhikara (Tue Sep 21 2010 - 03:40:14 PDT)
  - Re: [AMBER] 2D radial distribution function Lekpa Duukori (Tue Sep 21 2010 - 04:08:38 PDT)
    - Re: [AMBER] 2D radial distribution function Daniel Sindhikara (Tue Sep 21 2010 - 04:40:24 PDT)
    - Re: [AMBER] 2D radial distribution function Lekpa Duukori (Tue Sep 21 2010 - 07:39:00 PDT)
[AMBER] Creation of a mol2/pdb initial structure file of a pharmaceutical compound. Baptiste Legrand (Tue Sep 21 2010 - 02:45:08 PDT)
- Re: [AMBER] Creation of a mol2/pdb initial structure file of a pharmaceutical compound. case (Tue Sep 21 2010 - 04:37:14 PDT)
  - Re: [AMBER] Creation of a mol2/pdb initial structure file of a pharmaceutical compound. Baptiste Legrand (Tue Sep 21 2010 - 06:12:06 PDT)
    - Re: [AMBER] Creation of a mol2/pdb initial structure file of a pharmaceutical compound. case (Tue Sep 21 2010 - 08:58:12 PDT)
    - Re: [AMBER] Creation of a mol2/pdb initial structure file of a pharmaceutical compound. Trevor Gokey (Wed Sep 22 2010 - 00:52:58 PDT)
    - Re: [AMBER] Creation of a mol2/pdb initial structure file of a pharmaceutical compound. Baptiste Legrand (Wed Sep 22 2010 - 07:55:54 PDT)
    - Re: [AMBER] Creation of a mol2/pdb initial structure file of a pharmaceutical compound. Andreas Goetz (Wed Sep 22 2010 - 09:47:15 PDT)
    - [AMBER] NMR refinement in explicite water Baptiste Legrand (Wed Sep 29 2010 - 06:15:03 PDT)
    - Re: [AMBER] NMR refinement in explicite water Daniel Roe (Wed Sep 29 2010 - 07:54:09 PDT)
    - Re: [AMBER] NMR refinement in explicite water Baptiste Legrand (Thu Sep 30 2010 - 04:55:33 PDT)
    - Re: [AMBER] NMR refinement in explicite water Daniel Roe (Thu Sep 30 2010 - 10:57:03 PDT)
    - Re: [AMBER] NMR refinement in explicite water Baptiste Legrand (Mon Oct 04 2010 - 07:13:50 PDT)
    - Re: [AMBER] NMR refinement in explicite water Dima A Sabbah (Mon Oct 04 2010 - 07:25:24 PDT)
    - Re: [AMBER] NMR refinement in explicite water Jason Swails (Mon Oct 04 2010 - 07:49:08 PDT)
    - [AMBER] Error in running NM=1 with mmpbsa.pl Catein Catherine (Mon Oct 04 2010 - 07:59:43 PDT)
    - Re: [AMBER] NMR refinement in explicite water Baptiste Legrand (Thu Oct 07 2010 - 02:53:39 PDT)
    - Re: [AMBER] NMR refinement in explicite water David A. Case (Thu Oct 07 2010 - 04:45:01 PDT)
    - Re: [AMBER] NMR refinement in explicite water Baptiste Legrand (Thu Oct 07 2010 - 05:26:14 PDT)
    - Re: [AMBER] NMR refinement in explicite water Dima A Sabbah (Thu Oct 07 2010 - 06:53:23 PDT)
    - [AMBER] Remove solvent molecules from the rst files Baptiste Legrand (Tue Nov 02 2010 - 08:21:33 PDT)
    - Re: [AMBER] Remove solvent molecules from the rst files Lekpa Duukori (Tue Nov 02 2010 - 08:28:39 PDT)
    - Re: [AMBER] Remove solvent molecules from the rst files Jason Swails (Tue Nov 02 2010 - 08:59:33 PDT)
    - Re: [AMBER] NMR refinement in explicite water Sabbah, Dima (Thu Oct 07 2010 - 06:55:22 PDT)
    - Re: [AMBER] NMR refinement in explicite water Baptiste Legrand (Thu Oct 07 2010 - 07:15:00 PDT)
    - Re: [AMBER] NMR refinement in explicite water Sabbah, Dima (Thu Oct 07 2010 - 07:51:15 PDT)
    - Re: [AMBER] NMR refinement in explicite water Sabbah, Dima (Tue Oct 05 2010 - 09:31:57 PDT)
[AMBER] MM_PBSA fillratio error/ compiling mm_pbsa.pl Oliver Grant (Tue Sep 21 2010 - 03:07:28 PDT)
- Re: [AMBER] MM_PBSA fillratio error/ compiling mm_pbsa.pl Bill Miller III (Tue Sep 21 2010 - 03:53:56 PDT)
  - Re: [AMBER] MM_PBSA fillratio error/ compiling mm_pbsa.pl Oliver Grant (Tue Sep 21 2010 - 04:39:35 PDT)
[AMBER] How to calculate total potential energy for protein chain only? Liu, Jingyuan (Tue Sep 21 2010 - 06:42:40 PDT)
[AMBER] error in MMPBSA calculation Chanchal (Tue Sep 21 2010 - 07:57:10 PDT)
- Re: [AMBER] error in MMPBSA calculation Bill Miller III (Tue Sep 21 2010 - 09:44:24 PDT)
  - Re: [AMBER] error in MMPBSA calculation Chanchal (Tue Sep 21 2010 - 13:13:01 PDT)
  - Re: [AMBER] error in MMPBSA calculation Chanchal (Wed Sep 22 2010 - 10:41:41 PDT)
    - Re: [AMBER] error in MMPBSA calculation Jason Swails (Wed Sep 22 2010 - 10:51:44 PDT)
    - Re: [AMBER] error in MMPBSA calculation Chanchal (Wed Sep 22 2010 - 13:21:54 PDT)
    - Re: [AMBER] error in MMPBSA calculation Chanchal (Thu Sep 23 2010 - 08:10:43 PDT)
    - Re: [AMBER] error in MMPBSA calculation Jason Swails (Thu Sep 23 2010 - 08:15:57 PDT)
    - Re: [AMBER] error in MMPBSA calculation Chanchal (Thu Sep 23 2010 - 14:51:37 PDT)
    - Re: [AMBER] error in MMPBSA calculation Bill Miller III (Thu Sep 23 2010 - 15:00:56 PDT)
    - Re: [AMBER] error in MMPBSA calculation Chanchal (Fri Sep 24 2010 - 00:49:29 PDT)
[AMBER] How to calculate total potential energy for protein chain only? Liu, Jingyuan (Tue Sep 21 2010 - 08:34:34 PDT)
[AMBER] MM-PBSA analysis on a protein ligand complex with 32000 atoms marta.gomes.fc.up.pt (Tue Sep 21 2010 - 08:38:20 PDT)
- Re: [AMBER] MM-PBSA analysis on a protein ligand complex with 32000 atoms Dwight McGee (Tue Sep 21 2010 - 09:24:07 PDT)
[AMBER] How to calculate total potential energy for protein chain only? Liu, Jingyuan (Tue Sep 21 2010 - 08:39:25 PDT)
- Re: [AMBER] How to calculate total potential energy for protein chain only? Bill Ross (Tue Sep 21 2010 - 10:42:43 PDT)
  - Re: [AMBER] How to calculate total potential energy for protein chain only? steinbrt.rci.rutgers.edu (Tue Sep 21 2010 - 21:18:03 PDT)
    - Re: [AMBER] How to calculate total potential energy for protein chain only? hirdesh kumar (Tue Sep 21 2010 - 21:30:43 PDT)
    - Re: [AMBER] How to calculate total potential energy for protein chain only? Jason Swails (Tue Sep 21 2010 - 21:45:14 PDT)
    - Re: [AMBER] How to calculate total potential energy for protein chain only? steinbrt.rci.rutgers.edu (Tue Sep 21 2010 - 21:47:26 PDT)
    - Re: [AMBER] How to calculate total potential energy for protein chain only? Liu, Jingyuan (Wed Sep 22 2010 - 06:56:30 PDT)
    - Re: [AMBER] How to calculate total potential energy for protein chain only? steinbrt.rci.rutgers.edu (Wed Sep 22 2010 - 23:55:33 PDT)
[AMBER] problems compiling amber10 Jeffrey Sanders (Tue Sep 21 2010 - 09:28:29 PDT)
- Re: [AMBER] problems compiling amber10 case (Tue Sep 21 2010 - 09:55:43 PDT)
  - Re: [AMBER] problems compiling amber10 Jeffrey Sanders (Tue Sep 21 2010 - 11:57:58 PDT)
[AMBER] hydrogen-deuterium exchange: iso program or papers that outline methods Sidney Elmer (Tue Sep 21 2010 - 09:28:17 PDT)
- Re: [AMBER] hydrogen-deuterium exchange: iso program or papers that outline methods case (Tue Sep 21 2010 - 12:39:26 PDT)
[AMBER] pmemd performance colvin (Wed Sep 22 2010 - 01:02:13 PDT)
- Re: [AMBER] pmemd performance case (Wed Sep 22 2010 - 05:09:01 PDT)
- Re: [AMBER] pmemd performance Gustavo Seabra (Wed Sep 22 2010 - 06:03:25 PDT)
  - Re: [AMBER] pmemd performance michael bane (Wed Sep 22 2010 - 06:28:30 PDT)
[AMBER] Confirmation of stabilisation of protein at equilibrium step shweta (Wed Sep 22 2010 - 01:35:28 PDT)
- Re: [AMBER] Confirmation of stabilisation of protein at equilibrium step steinbrt.rci.rutgers.edu (Wed Sep 22 2010 - 02:36:26 PDT)
[AMBER] Query regarding Hydrogen Bond Duration map hirdesh kumar (Wed Sep 22 2010 - 02:53:04 PDT)
[AMBER] MM_PBSA stopped at the last step zhihong ke (Wed Sep 22 2010 - 08:40:34 PDT)
- Re: [AMBER] MM_PBSA stopped at the last step Oliver Grant (Thu Sep 23 2010 - 03:30:15 PDT)
- Re: [AMBER] MM_PBSA stopped at the last step rameshwar prajapati (Sun Sep 26 2010 - 02:24:07 PDT)
[AMBER] MD on an array of small molecules Joe Bozell (Wed Sep 22 2010 - 11:20:36 PDT)
- Re: [AMBER] MD on an array of small molecules case (Wed Sep 22 2010 - 13:07:43 PDT)
- [AMBER] FW: MD on an array of small molecules Bozell, Joseph John (Thu Sep 23 2010 - 06:46:02 PDT)
  - Re: [AMBER] FW: MD on an array of small molecules M. L. Dodson (Thu Sep 23 2010 - 07:13:06 PDT)
    - Re: [AMBER] FW: MD on an array of small molecules Bozell, Joseph John (Fri Sep 24 2010 - 06:02:08 PDT)
    - Re: [AMBER] FW: MD on an array of small molecules Jason Swails (Fri Sep 24 2010 - 06:13:35 PDT)
    - Re: [AMBER] FW: MD on an array of small molecules Bozell, Joseph John (Fri Sep 24 2010 - 13:55:54 PDT)
    - Re: [AMBER] FW: MD on an array of small molecules Jason Swails (Fri Sep 24 2010 - 14:22:47 PDT)
[AMBER] Minimum Energy Conformational Structures of Saccharides in Solution Sushil Mishra (Thu Sep 23 2010 - 03:21:21 PDT)
- Re: [AMBER] Minimum Energy Conformational Structures of Saccharides in Solution Lachele Foley (Lists) (Thu Sep 23 2010 - 15:10:00 PDT)
  - Re: [AMBER] Minimum Energy Conformational Structures of Saccharides in Solution Sushil Mishra (Thu Sep 23 2010 - 21:36:10 PDT)
[AMBER] AmberTools 1.4 installation problem Shradha Chopra Phd2009,BIC (Thu Sep 23 2010 - 04:50:02 PDT)
- Re: [AMBER] AmberTools 1.4 installation problem Jason Swails (Thu Sep 23 2010 - 05:12:46 PDT)
- Re: [AMBER] AmberTools 1.4 installation problem case (Thu Sep 23 2010 - 06:33:22 PDT)
  - Re: [AMBER] AmberTools 1.4 installation problem Jason Swails (Thu Sep 23 2010 - 06:53:07 PDT)
[AMBER] PMEMD 10 on OpenMPI with Intel compiler issues CHAMI F. (Thu Sep 23 2010 - 07:28:01 PDT)
- Re: [AMBER] PMEMD 10 on OpenMPI with Intel compiler issues Jason Swails (Thu Sep 23 2010 - 08:07:57 PDT)
- Re: [AMBER] PMEMD 10 on OpenMPI with Intel compiler issues case (Thu Sep 23 2010 - 08:26:00 PDT)
[AMBER] MD for large proteins Laura Perissinotti (Thu Sep 23 2010 - 08:46:58 PDT)
- Re: [AMBER] MD for large proteins Jason Swails (Thu Sep 23 2010 - 09:24:03 PDT)
- Re: [AMBER] MD for large proteins case (Thu Sep 23 2010 - 13:04:01 PDT)
[AMBER] Shake errors Justine Shaw (Thu Sep 23 2010 - 09:01:47 PDT)
- Re: [AMBER] Shake errors Bill Ross (Thu Sep 23 2010 - 12:14:16 PDT)
- Re: [AMBER] Shake errors case (Thu Sep 23 2010 - 13:02:20 PDT)
  - Re: [AMBER] Shake errors Justine Shaw (Mon Oct 11 2010 - 12:43:01 PDT)
- Re: [AMBER] Shake errors Bill Ross (Mon Oct 11 2010 - 13:07:48 PDT)
  - Re: [AMBER] Shake errors Justine Shaw (Tue Oct 12 2010 - 11:25:03 PDT)
    - Re: [AMBER] Shake errors case (Tue Oct 12 2010 - 12:15:03 PDT)
    - Re: [AMBER] Shake errors Justine Shaw (Tue Oct 12 2010 - 14:53:06 PDT)
- Re: [AMBER] Shake errors Bill Ross (Tue Oct 12 2010 - 11:48:07 PDT)
  - Re: [AMBER] Shake errors Justine Shaw (Wed Oct 13 2010 - 11:09:23 PDT)
- Re: [AMBER] Shake errors Bill Ross (Wed Oct 13 2010 - 11:17:07 PDT)
[AMBER] amber11 installation error Sangita Kachhap (Thu Sep 23 2010 - 09:07:02 PDT)
- Re: [AMBER] amber11 installation error case (Thu Sep 23 2010 - 09:21:55 PDT)
  - Re: [AMBER] amber11 installation error Sangita Kachhap (Thu Sep 23 2010 - 09:50:44 PDT)
    - Re: [AMBER] amber11 installation error Paul S. Nerenberg (Thu Sep 23 2010 - 09:56:53 PDT)
    - Re: [AMBER] amber11 installation error Sangita Kachhap (Thu Sep 23 2010 - 10:11:42 PDT)
    - Re: [AMBER] amber11 installation error Paul S. Nerenberg (Thu Sep 23 2010 - 10:54:58 PDT)
    - Re: [AMBER] amber11 installation error Sangita Kachhap (Thu Sep 23 2010 - 21:03:44 PDT)
    - Re: [AMBER] amber11 installation error Paul S. Nerenberg (Thu Sep 23 2010 - 21:46:02 PDT)
    - Re: [AMBER] amber11 installation error Jason Swails (Thu Sep 23 2010 - 22:52:36 PDT)
    - Re: [AMBER] amber11 installation error Sangita Kachhap (Fri Sep 24 2010 - 02:38:17 PDT)
    - Re: [AMBER] amber11 installation error case (Fri Sep 24 2010 - 05:08:26 PDT)
[AMBER] mm_pbsa.pl frozen, hanging, stopped at end. Oliver Grant (Thu Sep 23 2010 - 12:12:05 PDT)
- Re: [AMBER] mm_pbsa.pl frozen, hanging, stopped at end. Ray Luo (Fri Sep 24 2010 - 16:16:52 PDT)
  - Re: [AMBER] mm_pbsa.pl frozen, hanging, stopped at end. Oliver Grant (Sat Sep 25 2010 - 05:15:51 PDT)
[AMBER] problem with AMOEBA force field Igor Sizov (Thu Sep 23 2010 - 12:16:05 PDT)
- Re: [AMBER] problem with AMOEBA force field case (Thu Sep 23 2010 - 12:59:42 PDT)
[AMBER] 10-12 hbond terms Philippe Pinard (Thu Sep 23 2010 - 14:36:35 PDT)
- Re: [AMBER] 10-12 hbond terms case (Fri Sep 24 2010 - 06:04:56 PDT)
[AMBER] Disulphide Bond Cleavage hirdesh kumar (Thu Sep 23 2010 - 21:01:31 PDT)
- Re: [AMBER] Disulphide Bond Cleavage Jason Swails (Thu Sep 23 2010 - 22:55:58 PDT)
  - Re: [AMBER] Disulphide Bond Cleavage hirdesh kumar (Thu Sep 23 2010 - 23:31:17 PDT)
    - Re: [AMBER] Disulphide Bond Cleavage Aditya Padhi (Fri Sep 24 2010 - 03:55:47 PDT)
    - Re: [AMBER] Disulphide Bond Cleavage case (Fri Sep 24 2010 - 04:56:25 PDT)
[AMBER] ERROR: The unperturbed charge of the unit: 0.010000 is not integral Bongkeun Kim (Thu Sep 23 2010 - 23:30:06 PDT)
- Re: [AMBER] ERROR: The unperturbed charge of the unit: 0.010000 is not integral James Maier (Fri Sep 24 2010 - 05:31:18 PDT)
  - Re: [AMBER] ERROR: The unperturbed charge of the unit: 0.010000 is not integral Bongkeun Kim (Fri Sep 24 2010 - 08:50:04 PDT)
    - Re: [AMBER] ERROR: The unperturbed charge of the unit: 0.010000 is not integral James Maier (Fri Sep 24 2010 - 10:46:37 PDT)
    - Re: [AMBER] ERROR: The unperturbed charge of the unit: 0.010000 is not integral Bongkeun Kim (Fri Sep 24 2010 - 11:43:31 PDT)
    - Re: [AMBER] ERROR: The unperturbed charge of the unit: 0.010000 is not integral FyD (Sat Sep 25 2010 - 03:27:44 PDT)
    - Re: [AMBER] ERROR: The unperturbed charge of the unit: 0.010000 is not integral Bongkeun Kim (Sat Sep 25 2010 - 10:01:18 PDT)
- Re: [AMBER] ERROR: The unperturbed charge of the unit: 0.010000 is not integral FyD (Fri Sep 24 2010 - 07:30:04 PDT)
[AMBER] Analysis of MD simulation Ashutosh Shandilya (Thu Sep 23 2010 - 23:48:00 PDT)
- [AMBER] Analysis of MD simulation Ashutosh Shandilya (Fri Sep 24 2010 - 21:15:27 PDT)
  - Re: [AMBER] Analysis of MD simulation steinbrt.rci.rutgers.edu (Fri Sep 24 2010 - 21:38:38 PDT)
    - Re: [AMBER] Analysis of MD simulation Ashutosh Shandilya (Fri Sep 24 2010 - 21:50:49 PDT)
  - Re: [AMBER] Analysis of MD simulation Peter Charles Kahuna (Sat Sep 25 2010 - 11:20:37 PDT)
    - Re: [AMBER] Analysis of MD simulation steinbrt.rci.rutgers.edu (Sat Sep 25 2010 - 21:39:12 PDT)
[AMBER] Extracting backbone dihedral angles Harald Lanig (Fri Sep 24 2010 - 04:07:58 PDT)
- Re: [AMBER] Extracting backbone dihedral angles Jason Swails (Fri Sep 24 2010 - 06:01:46 PDT)
[AMBER] Neutralization of the system by Na+ or Cl- ions are needed or not for constant pH MD simulation nicholus bhattacharjee (Fri Sep 24 2010 - 05:33:54 PDT)
- Re: [AMBER] Neutralization of the system by Na+ or Cl- ions are needed or not for constant pH MD simulation Carlos Simmerling (Fri Sep 24 2010 - 05:38:04 PDT)
- Re: [AMBER] Neutralization of the system by Na+ or Cl- ions are needed or not for constant pH MD simulation case (Fri Sep 24 2010 - 05:41:14 PDT)
[AMBER] chamber At line 2692 of file _psfprm.f Jorgen Simonsen (Fri Sep 24 2010 - 07:05:57 PDT)
- Re: [AMBER] chamber At line 2692 of file _psfprm.f Mark Williamson (Fri Sep 24 2010 - 07:33:02 PDT)
- Re: [AMBER] chamber At line 2692 of file _psfprm.f Ross Walker (Fri Sep 24 2010 - 07:33:53 PDT)
[AMBER] missing parameters (dihe) in parm10.dat? Alan (Fri Sep 24 2010 - 07:42:29 PDT)
- Re: [AMBER] missing parameters (dihe) in parm10.dat? Jason Swails (Fri Sep 24 2010 - 07:58:30 PDT)
  - Re: [AMBER] missing parameters (dihe) in parm10.dat? Alan (Fri Sep 24 2010 - 08:45:28 PDT)
- Re: [AMBER] missing parameters (dihe) in parm10.dat? case (Fri Sep 24 2010 - 09:05:50 PDT)
  - Re: [AMBER] missing parameters (dihe) in parm10.dat? Alan (Sat Sep 25 2010 - 05:30:35 PDT)
    - Re: [AMBER] missing parameters (dihe) in parm10.dat? Jason Swails (Sat Sep 25 2010 - 10:21:21 PDT)
    - Re: [AMBER] missing parameters (dihe) in parm10.dat? case (Sun Sep 26 2010 - 06:56:21 PDT)
    - Re: [AMBER] missing parameters (dihe) in parm10.dat? Alan (Wed Sep 29 2010 - 04:50:15 PDT)
    - Re: [AMBER] missing parameters (dihe) in parm10.dat? Jason Swails (Wed Sep 29 2010 - 05:52:06 PDT)
    - Re: [AMBER] missing parameters (dihe) in parm10.dat? Alan (Thu Sep 30 2010 - 03:11:26 PDT)
    - Re: [AMBER] missing parameters (dihe) in parm10.dat? Alan (Thu Sep 30 2010 - 05:34:38 PDT)
Re: [AMBER] Xplor_to_Amber Raman Parkesh (Fri Sep 24 2010 - 14:56:15 PDT)
- Re: [AMBER] Xplor_to_Amber case (Wed Sep 29 2010 - 05:01:56 PDT)
  - Re: [AMBER] Xplor_to_Amber Raman Parkesh (Wed Sep 29 2010 - 06:18:07 PDT)
    - Re: [AMBER] Xplor_to_Amber case (Wed Sep 29 2010 - 07:43:11 PDT)
    - Re: [AMBER] Xplor_to_Amber Raman Parkesh (Wed Sep 29 2010 - 11:38:14 PDT)
    - Re: [AMBER] Xplor_to_Amber case (Wed Sep 29 2010 - 12:18:00 PDT)
    - Re: [AMBER] Xplor_to_Amber Raman Parkesh (Wed Sep 29 2010 - 13:57:55 PDT)
[AMBER] Histamine Hydrogen hirdesh kumar (Fri Sep 24 2010 - 23:42:02 PDT)
- Re: [AMBER] Histamine Hydrogen Jason Swails (Sat Sep 25 2010 - 09:56:33 PDT)
  - Re: [AMBER] Histamine Hydrogen hirdesh kumar (Sat Sep 25 2010 - 10:38:07 PDT)
[AMBER] Query about restraint minimization hirdesh kumar (Sat Sep 25 2010 - 00:53:57 PDT)
- Re: [AMBER] Query about restraint minimization case (Sat Sep 25 2010 - 06:02:02 PDT)
[AMBER] integer divide by zero Pete Kekenes-Huskey (Sat Sep 25 2010 - 10:24:11 PDT)
- Re: [AMBER] integer divide by zero case (Mon Sep 27 2010 - 06:43:25 PDT)
  - Re: [AMBER] integer divide by zero Pete Kekenes-Huskey (Mon Sep 27 2010 - 07:26:06 PDT)
    - Re: [AMBER] integer divide by zero case (Mon Sep 27 2010 - 08:27:30 PDT)
[AMBER] Cieplak work on RESP charges derivation Josmar R. da Rocha (Sat Sep 25 2010 - 14:25:56 PDT)
- Re: [AMBER] Cieplak work on RESP charges derivation Kevin Hauser (Sat Sep 25 2010 - 15:35:26 PDT)
[AMBER] can't save the PDB file to produce topology and coordinates file geyan (Sat Sep 25 2010 - 21:43:53 PDT)
- Re: [AMBER] can't save the PDB file to produce topology and coordinates file dhacademic (Sun Sep 26 2010 - 06:25:10 PDT)
- Re: [AMBER] can't save the PDB file to produce topology andcoordinates file geyan (Mon Sep 27 2010 - 03:14:14 PDT)
[AMBER] can't save the PDB file to produce topology and coordinates file geyan (Sun Sep 26 2010 - 00:20:57 PDT)
- Re: [AMBER] can't save the PDB file to produce topology and coordinates file Bill Ross (Sun Sep 26 2010 - 14:39:02 PDT)
  - Re: [AMBER] can't save the PDB file to produce topology andcoordinates file geyan (Mon Sep 27 2010 - 03:21:50 PDT)
    - Re: [AMBER] can't save the PDB file to produce topology andcoordinates file Jason Swails (Mon Sep 27 2010 - 04:14:06 PDT)
[AMBER] Phosphate group treatment shweta (Sun Sep 26 2010 - 01:32:45 PDT)
- Re: [AMBER] Phosphate group treatment case (Sun Sep 26 2010 - 06:49:43 PDT)
  - Re: [AMBER] Phosphate group treatment shweta (Sun Sep 26 2010 - 21:39:57 PDT)
[AMBER] disulfide bonds in amoeba case (Sun Sep 26 2010 - 06:55:34 PDT)
[AMBER] loop relaxation with les Simon Becker (Sun Sep 26 2010 - 07:34:06 PDT)
- Re: [AMBER] loop relaxation with les Carlos Simmerling (Wed Sep 29 2010 - 12:38:07 PDT)
[AMBER] problem with MMPBSA juzer stationwala (Sun Sep 26 2010 - 07:45:55 PDT)
- Re: [AMBER] problem with MMPBSA Oliver Grant (Sun Sep 26 2010 - 08:29:01 PDT)
  - Re: [AMBER] problem with MMPBSA juzer stationwala (Mon Sep 27 2010 - 03:42:31 PDT)
    - Re: [AMBER] problem with MMPBSA Bill Miller III (Mon Sep 27 2010 - 03:48:00 PDT)
    - Re: [AMBER] problem with MMPBSA juzer stationwala (Mon Sep 27 2010 - 03:55:54 PDT)
    - Re: [AMBER] problem with MMPBSA Jason Swails (Mon Sep 27 2010 - 04:11:42 PDT)
    - Re: [AMBER] problem with MMPBSA juzer stationwala (Mon Sep 27 2010 - 04:25:31 PDT)
    - Re: [AMBER] problem with MMPBSA Jason Swails (Mon Sep 27 2010 - 04:36:27 PDT)
    - Re: [AMBER] problem with MMPBSA juzer stationwala (Mon Sep 27 2010 - 04:48:54 PDT)
    - Re: [AMBER] problem with MMPBSA Bill Miller III (Mon Sep 27 2010 - 04:53:08 PDT)
    - Re: [AMBER] problem with MMPBSA Sushil Mishra (Mon Sep 27 2010 - 04:54:40 PDT)
    - Re: [AMBER] problem with MMPBSA juzer stationwala (Tue Sep 28 2010 - 05:13:53 PDT)
    - Re: [AMBER] problem with MMPBSA Sushil Mishra (Tue Sep 28 2010 - 05:23:54 PDT)
    - Re: [AMBER] problem with MMPBSA Jason Swails (Tue Sep 28 2010 - 07:07:43 PDT)
    - Re: [AMBER] problem with MMPBSA juzer stationwala (Wed Sep 29 2010 - 03:54:00 PDT)
[AMBER] How to disable the function to look for N terminal in leap? Hugh Cheng (Sun Sep 26 2010 - 21:51:19 PDT)
- Re: [AMBER] How to disable the function to look for N terminal in leap? Jason Swails (Mon Sep 27 2010 - 04:22:11 PDT)
[AMBER] cubic box subrata paul (Sun Sep 26 2010 - 22:19:35 PDT)
- Re: [AMBER] cubic box case (Mon Sep 27 2010 - 04:43:17 PDT)
  - Re: [AMBER] cubic box subrata paul (Tue Sep 28 2010 - 00:17:59 PDT)
    - Re: [AMBER] cubic box case (Tue Sep 28 2010 - 04:52:13 PDT)
    - Re: [AMBER] cubic box subrata paul (Tue Sep 28 2010 - 06:04:21 PDT)
    - Re: [AMBER] cubic box case (Tue Sep 28 2010 - 08:40:48 PDT)
    - Re: [AMBER] cubic box Daniel Roe (Tue Sep 28 2010 - 08:54:47 PDT)
    - Re: [AMBER] cubic box Andrew Jewett (Wed Sep 29 2010 - 17:06:00 PDT)
- Re: [AMBER] cubic box Bill Ross (Wed Sep 29 2010 - 17:22:33 PDT)
[AMBER] Addition of extra-interaction term to LJ-potential: modification of souce code kurisaki ikuo (Mon Sep 27 2010 - 00:12:51 PDT)
[AMBER] rmsd of a subunit I w.r.t subunit II moitrayee.mbu.iisc.ernet.in (Mon Sep 27 2010 - 03:04:54 PDT)
- Re: [AMBER] rmsd of a subunit I w.r.t subunit II Thomas Cheatham III (Wed Sep 29 2010 - 14:33:47 PDT)
[AMBER] mmpbsa.py.mpi error Anuradha Mittal (Mon Sep 27 2010 - 10:05:08 PDT)
- Re: [AMBER] mmpbsa.py.mpi error Bill Miller III (Mon Sep 27 2010 - 10:42:46 PDT)
  - Re: [AMBER] mmpbsa.py.mpi error Anuradha Mittal (Mon Sep 27 2010 - 11:00:52 PDT)
    - Re: [AMBER] mmpbsa.py.mpi error Jason Swails (Mon Sep 27 2010 - 12:05:11 PDT)
[AMBER] AMBER RESTART QUESTIONS Yu, Bingwu (Mon Sep 27 2010 - 10:41:39 PDT)
- Re: [AMBER] AMBER RESTART QUESTIONS Paul S. Nerenberg (Mon Sep 27 2010 - 11:03:53 PDT)
- Re: [AMBER] AMBER RESTART QUESTIONS case (Mon Sep 27 2010 - 11:14:00 PDT)
[AMBER] Missing atom types between leaprc.ff99SB and parm99.dat Christopher Roberts (Mon Sep 27 2010 - 12:29:01 PDT)
- Re: [AMBER] Missing atom types between leaprc.ff99SB and parm99.dat case (Wed Sep 29 2010 - 12:24:03 PDT)
[AMBER] AMBER RESTART QUESTIONS Yu, Bingwu (Mon Sep 27 2010 - 13:54:44 PDT)
[AMBER] sander gb post-processing fail Trevor Gokey (Mon Sep 27 2010 - 14:25:16 PDT)
- Re: [AMBER] sander gb post-processing fail Trevor Gokey (Fri Oct 01 2010 - 12:11:23 PDT)
  - Re: [AMBER] sander gb post-processing fail Daniel Roe (Fri Oct 01 2010 - 18:15:55 PDT)
    - Re: [AMBER] sander gb post-processing fail Trevor Gokey (Fri Oct 01 2010 - 21:14:36 PDT)
    - Re: [AMBER] sander gb post-processing fail Trevor Gokey (Fri Oct 01 2010 - 21:22:41 PDT)
[AMBER] ibelly doesn't work qiaoyan (Mon Sep 27 2010 - 19:01:55 PDT)
- Re: [AMBER] ibelly doesn't work steinbrt.rci.rutgers.edu (Mon Sep 27 2010 - 21:13:47 PDT)
- Re: [AMBER] ibelly doesn't work David Watson (Mon Sep 27 2010 - 23:04:34 PDT)
[AMBER] parameters of SEP and TPO can't match SEP TPO fancy2012 (Mon Sep 27 2010 - 20:14:23 PDT)
- Re: [AMBER] parameters of SEP and TPO can't match SEP TPO Anselm Horn (Tue Sep 28 2010 - 00:41:53 PDT)
  - Re: [AMBER] parameters of SEP and TPO can't match SEP TPO fancy2012 (Tue Sep 28 2010 - 01:46:00 PDT)
  - Re: [AMBER] parameters of SEP and TPO can't match SEP TPO fancy2012 (Tue Sep 28 2010 - 06:36:10 PDT)
    - Re: [AMBER] parameters of SEP and TPO can't match SEP TPO Daniel Roe (Tue Sep 28 2010 - 08:42:37 PDT)
    - Re: [AMBER] parameters of SEP and TPO can't match SEP TPO Anselm Horn (Wed Sep 29 2010 - 01:08:01 PDT)
[AMBER] Disulphide bond breakage during minimization hirdesh kumar (Mon Sep 27 2010 - 22:48:25 PDT)
- Re: [AMBER] Disulphide bond breakage during minimization steinbrt.rci.rutgers.edu (Mon Sep 27 2010 - 23:01:38 PDT)
  - Re: [AMBER] Disulphide bond breakage during minimization hirdesh kumar (Mon Sep 27 2010 - 23:08:56 PDT)
    - Re: [AMBER] Disulphide bond breakage during minimization steinbrt.rci.rutgers.edu (Mon Sep 27 2010 - 23:53:34 PDT)
    - Re: [AMBER] Disulphide bond breakage during minimization hirdesh kumar (Tue Sep 28 2010 - 00:51:45 PDT)
    - Re: [AMBER] Disulphide bond breakage during minimization Hannes Loeffler (Tue Sep 28 2010 - 01:05:44 PDT)
    - Re: [AMBER] Disulphide bond breakage during minimization hirdesh kumar (Tue Sep 28 2010 - 02:36:44 PDT)
    - Re: [AMBER] Disulphide bond breakage during minimization Hannes Loeffler (Tue Sep 28 2010 - 02:51:10 PDT)
    - Re: [AMBER] Disulphide bond breakage during minimization steinbrt.rci.rutgers.edu (Tue Sep 28 2010 - 03:55:45 PDT)
    - Re: [AMBER] Disulphide bond breakage during minimization Carlos Simmerling (Tue Sep 28 2010 - 03:59:06 PDT)
    - Re: [AMBER] Disulphide bond breakage during minimization hirdesh kumar (Tue Sep 28 2010 - 04:37:24 PDT)
    - Re: [AMBER] Disulphide bond breakage during minimization hirdesh kumar (Tue Sep 28 2010 - 04:00:08 PDT)
    - Re: [AMBER] Disulphide bond breakage during minimization case (Tue Sep 28 2010 - 04:49:10 PDT)
[AMBER] calculation of inter atomic distances Ashutosh Shandilya (Tue Sep 28 2010 - 00:16:55 PDT)
- Re: [AMBER] calculation of inter atomic distances Daniel Roe (Tue Sep 28 2010 - 08:37:25 PDT)
[AMBER] running pmemd fails Vijay Manickam Achari (Tue Sep 28 2010 - 02:08:26 PDT)
- Re: [AMBER] running pmemd fails case (Tue Sep 28 2010 - 04:55:47 PDT)
  - Re: [AMBER] running pmemd fails Kevin Hauser (Tue Sep 28 2010 - 09:38:14 PDT)
    - Re: [AMBER] running pmemd fails Paul S. Nerenberg (Tue Sep 28 2010 - 10:39:32 PDT)
    - Re: [AMBER] running pmemd fails Vijay Manickam Achari (Tue Sep 28 2010 - 19:37:08 PDT)
  - Re: [AMBER] running pmemd fails Vijay Manickam Achari (Tue Sep 28 2010 - 20:36:03 PDT)
    - Re: [AMBER] running pmemd fails case (Wed Sep 29 2010 - 04:39:55 PDT)
    - Re: [AMBER] running pmemd fails Vijay Manickam Achari (Wed Sep 29 2010 - 23:25:55 PDT)
    - Re: [AMBER] running pmemd fails Daniel Roe (Thu Sep 30 2010 - 06:04:33 PDT)
[AMBER] Solvent accessible surface of certain residues hirdesh kumar (Tue Sep 28 2010 - 02:52:58 PDT)
- Re: [AMBER] Solvent accessible surface of certain residues Daniel Roe (Tue Sep 28 2010 - 09:03:45 PDT)
  - Re: [AMBER] Solvent accessible surface of certain residues hirdesh kumar (Tue Sep 28 2010 - 21:46:35 PDT)
[AMBER] H-bonb calculation Sangita Kachhap (Tue Sep 28 2010 - 05:58:54 PDT)
- Re: [AMBER] H-bonb calculation Jason Swails (Tue Sep 28 2010 - 07:17:26 PDT)
[AMBER] ptraj, unit cell wrapping and velocities Ben Roberts (Tue Sep 28 2010 - 13:23:36 PDT)
- Re: [AMBER] ptraj, unit cell wrapping and velocities case (Wed Sep 29 2010 - 04:32:22 PDT)
  - Re: [AMBER] ptraj, unit cell wrapping and velocities Ben Roberts (Wed Sep 29 2010 - 10:59:42 PDT)
[AMBER] Question on simulation Jiang Yusheng (Tue Sep 28 2010 - 15:14:16 PDT)
- Re: [AMBER] Question on simulation Jason Swails (Tue Sep 28 2010 - 17:53:59 PDT)
- Re: [AMBER] Question on simulation Bill Ross (Tue Sep 28 2010 - 20:01:56 PDT)
  - Re: [AMBER] Question on simulation Jiang Yusheng (Wed Sep 29 2010 - 07:07:58 PDT)
    - Re: [AMBER] Question on simulation Guoxiong Su (Wed Sep 29 2010 - 07:16:42 PDT)
    - Re: [AMBER] Question on simulation case (Wed Sep 29 2010 - 07:53:18 PDT)
    - Re: [AMBER] Question on simulation Jiang Yusheng (Wed Sep 29 2010 - 09:43:43 PDT)
- Re: [AMBER] Question on simulation Bill Ross (Wed Sep 29 2010 - 09:32:40 PDT)
[AMBER] implicit solvent model and charged chain Jorgen Simonsen (Tue Sep 28 2010 - 22:07:12 PDT)
- Re: [AMBER] implicit solvent model and charged chain manoj singh (Tue Sep 28 2010 - 22:23:22 PDT)
- Re: [AMBER] implicit solvent model and charged chain case (Wed Sep 29 2010 - 05:15:02 PDT)
[AMBER] prep file Andrei Neamtu (Tue Sep 28 2010 - 23:33:35 PDT)
- Re: [AMBER] prep file case (Wed Sep 29 2010 - 05:16:15 PDT)
- Re: [AMBER] prep file Bill Ross (Wed Sep 29 2010 - 09:14:37 PDT)
  - Re: [AMBER] prep file Andrei Neamtu (Thu Sep 30 2010 - 04:26:29 PDT)
[AMBER] FW: Atom type assignment for formyl group Carter M.K. (Wed Sep 29 2010 - 04:59:48 PDT)
[AMBER] tLeap memory leak Martin Brieg (Wed Sep 29 2010 - 06:34:07 PDT)
- Re: [AMBER] tLeap memory leak Jason Swails (Wed Sep 29 2010 - 06:44:18 PDT)
  - Re: [AMBER] tLeap memory leak Jason Swails (Wed Sep 29 2010 - 06:46:30 PDT)
    - Re: [AMBER] tLeap memory leak Martin Brieg (Thu Sep 30 2010 - 04:48:00 PDT)
    - Re: [AMBER] tLeap memory leak Jason Swails (Thu Sep 30 2010 - 06:00:42 PDT)
- Re: [AMBER] tLeap memory leak Bill Ross (Wed Sep 29 2010 - 09:26:46 PDT)
- Re: [AMBER] tLeap memory leak Bill Ross (Thu Sep 30 2010 - 09:49:41 PDT)
[AMBER] MMPBSA.py.MPI with MVAPICH2 Senthil Natesan (Wed Sep 29 2010 - 08:45:59 PDT)
- Re: [AMBER] MMPBSA.py.MPI with MVAPICH2 Jason Swails (Wed Sep 29 2010 - 09:13:48 PDT)
  - Re: [AMBER] MMPBSA.py.MPI with MVAPICH2 Senthil Natesan (Wed Sep 29 2010 - 09:31:39 PDT)
    - Re: [AMBER] MMPBSA.py.MPI with MVAPICH2 Jason Swails (Wed Sep 29 2010 - 09:37:42 PDT)
    - Re: [AMBER] MMPBSA.py.MPI with MVAPICH2 Senthil Natesan (Thu Sep 30 2010 - 06:01:37 PDT)
    - Re: [AMBER] MMPBSA.py.MPI with MVAPICH2 Jason Swails (Thu Sep 30 2010 - 08:04:48 PDT)
[AMBER] leap for peptide with new residue Francesco Pietra (Wed Sep 29 2010 - 09:48:14 PDT)
[AMBER] vlimit exceeds nicholus bhattacharjee (Wed Sep 29 2010 - 09:48:32 PDT)
- Re: [AMBER] vlimit exceeds Jason Swails (Wed Sep 29 2010 - 09:57:47 PDT)
- Re: [AMBER] vlimit exceeds case (Wed Sep 29 2010 - 11:55:34 PDT)
[AMBER] Cluster analysis ros (Wed Sep 29 2010 - 17:48:10 PDT)
- Re: [AMBER] Cluster analysis Niel Henriksen (Wed Sep 29 2010 - 18:07:44 PDT)
  - Re: [AMBER] Cluster analysis ros (Thu Sep 30 2010 - 07:24:07 PDT)
[AMBER] TI-Problems Kirsten Heitmann (Thu Sep 30 2010 - 00:14:20 PDT)
- Re: [AMBER] TI-Problems case (Thu Sep 30 2010 - 06:35:46 PDT)
  - Re: [AMBER] TI-Problems Kirsten Heitmann (Thu Sep 30 2010 - 09:52:47 PDT)
    - Re: [AMBER] TI-Problems case (Fri Oct 01 2010 - 04:55:45 PDT)
    - Re: [AMBER] TI-Problems Kirsten Heitmann (Fri Oct 01 2010 - 13:30:08 PDT)
    - Re: [AMBER] TI-Problems Jason Swails (Fri Oct 01 2010 - 13:40:22 PDT)
    - Re: [AMBER] TI-Problems Kirsten Heitmann (Sat Oct 02 2010 - 02:30:21 PDT)
    - Re: [AMBER] TI-Problems case (Sat Oct 02 2010 - 04:58:46 PDT)
    - Re: [AMBER] TI-Problems steinbrt.rci.rutgers.edu (Sat Oct 02 2010 - 05:44:02 PDT)
    - Re: [AMBER] TI-Problems Kirsten Heitmann (Mon Oct 04 2010 - 03:01:10 PDT)
    - [AMBER] nmode problem Dima A Sabbah (Fri Oct 01 2010 - 13:55:48 PDT)
    - Re: [AMBER] TI-Problems steinbrt.rci.rutgers.edu (Fri Oct 01 2010 - 21:28:50 PDT)
    - Re: [AMBER] TI-Problems Kirsten Heitmann (Sat Oct 02 2010 - 01:05:20 PDT)
[AMBER] spc/e water subrata paul (Thu Sep 30 2010 - 01:29:16 PDT)
- Re: [AMBER] spc/e water case (Fri Oct 01 2010 - 05:05:44 PDT)
[AMBER] bonded model xuemeiwang1103 (Thu Sep 30 2010 - 01:51:58 PDT)
[AMBER] Incorrect handling of phenylalanine amide by antechamber Francesco Pietra (Thu Sep 30 2010 - 02:25:58 PDT)
- Re: [AMBER] Incorrect handling of phenylalanine amide by antechamber case (Thu Sep 30 2010 - 04:28:53 PDT)
  - Re: [AMBER] Incorrect handling of phenylalanine amide by antechamber Francesco Pietra (Thu Sep 30 2010 - 06:41:25 PDT)
    - Re: [AMBER] Incorrect handling of phenylalanine amide by antechamber case (Thu Sep 30 2010 - 07:24:36 PDT)
    - Re: [AMBER] Incorrect handling of phenylalanine amide by antechamber Francesco Pietra (Thu Sep 30 2010 - 09:35:35 PDT)
    - [AMBER] Fwd: Incorrect handling of phenylalanine amide by antechamber Francesco Pietra (Fri Oct 01 2010 - 03:04:57 PDT)
    - Re: [AMBER] Fwd: Incorrect handling of phenylalanine amide by antechamber case (Fri Oct 01 2010 - 04:35:28 PDT)
    - Re: [AMBER] Fwd: Incorrect handling of phenylalanine amide by antechamber Francesco Pietra (Sun Oct 03 2010 - 14:44:16 PDT)
    - Re: [AMBER] Fwd: Incorrect handling of phenylalanine amide by antechamber Francesco Pietra (Mon Oct 04 2010 - 01:56:32 PDT)
    - [AMBER] Fwd: Fwd: Incorrect handling of phenylalanine amide by antechamber Francesco Pietra (Mon Oct 04 2010 - 02:02:40 PDT)
    - [AMBER] Fwd: Fwd: Incorrect handling of phenylalanine amide by antechamber Francesco Pietra (Tue Oct 05 2010 - 13:10:55 PDT)
    - Re: [AMBER] Incorrect handling of phenylalanine amide by antechamber FyD (Tue Oct 05 2010 - 23:19:20 PDT)
    - Re: [AMBER] Incorrect handling of phenylalanine amide by antechamber Francesco Pietra (Wed Oct 06 2010 - 01:21:35 PDT)
    - [AMBER] Fwd: Incorrect handling of phenylalanine amide by antechamber Francesco Pietra (Wed Oct 06 2010 - 02:03:03 PDT)
    - Re: [AMBER] Fwd: Incorrect handling of phenylalanine amide by antechamber FyD (Wed Oct 06 2010 - 02:29:05 PDT)
    - Re: [AMBER] Fwd: Incorrect handling of phenylalanine amide by antechamber Francesco Pietra (Wed Oct 06 2010 - 03:07:28 PDT)
    - [AMBER] Fwd: Fwd: Incorrect handling of phenylalanine amide by antechamber Francesco Pietra (Wed Oct 06 2010 - 04:17:03 PDT)
    - Re: [AMBER] Fwd: Fwd: Incorrect handling of phenylalanine amide by antechamber FyD (Wed Oct 06 2010 - 04:51:48 PDT)
    - Re: [AMBER] Fwd: Fwd: Incorrect handling of phenylalanine amide by antechamber Francesco Pietra (Wed Oct 06 2010 - 06:54:07 PDT)
    - Re: [AMBER] Fwd: Fwd: Incorrect handling of phenylalanine amide by antechamber FyD (Wed Oct 06 2010 - 08:16:32 PDT)
    - Re: [AMBER] Fwd: Fwd: Incorrect handling of phenylalanine amide by antechamber Francesco Pietra (Wed Oct 06 2010 - 08:40:55 PDT)
    - Re: [AMBER] Incorrect handling of phenylalanine amide by antechamber FyD (Thu Oct 07 2010 - 02:56:35 PDT)
    - Re: [AMBER] Incorrect handling of phenylalanine amide by antechamber Francesco Pietra (Thu Oct 07 2010 - 07:57:30 PDT)
    - [AMBER] Fwd: Incorrect handling of phenylalanine amide by antechamber Francesco Pietra (Thu Oct 07 2010 - 08:08:25 PDT)
    - Re: [AMBER] Fwd: Incorrect handling of phenylalanine amide by antechamber Jason Swails (Thu Oct 07 2010 - 08:36:07 PDT)
    - Re: [AMBER] Fwd: Incorrect handling of phenylalanine amide by antechamber Paul S. Nerenberg (Thu Oct 07 2010 - 09:14:09 PDT)
    - Re: [AMBER] Fwd: Incorrect handling of phenylalanine amide by antechamber Paul S. Nerenberg (Thu Oct 07 2010 - 10:17:11 PDT)
    - Re: [AMBER] Fwd: Incorrect handling of phenylalanine amide by antechamber Francesco Pietra (Thu Oct 07 2010 - 13:26:19 PDT)
    - Re: [AMBER] Fwd: Incorrect handling of phenylalanine amide by antechamber FyD (Wed Oct 06 2010 - 04:44:50 PDT)
[AMBER] Cu2+ parameters babak minoofar (Thu Sep 30 2010 - 02:36:34 PDT)
- Re: [AMBER] Cu2+ parameters ros (Thu Sep 30 2010 - 05:36:49 PDT)
[AMBER] GBOBC cutoff distances David Tanner (Thu Sep 30 2010 - 09:42:36 PDT)
- Re: [AMBER] GBOBC cutoff distances Carlos Simmerling (Thu Sep 30 2010 - 11:05:23 PDT)
Re: [AMBER] pmemd.cuda error with group restraint Ross Walker (Thu Sep 30 2010 - 17:35:12 PDT)
- Re: [AMBER] pmemd.cuda error with group restraint Ross Walker (Fri Oct 01 2010 - 16:59:30 PDT)
[AMBER] runing mmpbsa.pl on cluster Giorgos Lamprinidis (Fri Oct 01 2010 - 01:58:54 PDT)
- Re: [AMBER] running mmpbsa.py Mannan (Fri Oct 01 2010 - 02:51:32 PDT)
  - Re: [AMBER] running mmpbsa.py Jason Swails (Fri Oct 01 2010 - 03:48:32 PDT)
  - Re: [AMBER] running mmpbsa.py Bill Miller III (Fri Oct 01 2010 - 03:49:10 PDT)
- Re: [AMBER] runing mmpbsa.pl on cluster Jason Swails (Fri Oct 01 2010 - 03:37:08 PDT)
  - Re: [AMBER] runing mmpbsa.pl on cluster Giorgos Lamprinidis (Fri Oct 01 2010 - 04:46:39 PDT)
    - Re: [AMBER] runing mmpbsa.pl on cluster Oliver Grant (Fri Oct 01 2010 - 04:50:39 PDT)
    - Re: [AMBER] runing mmpbsa.pl on cluster Oliver Grant (Fri Oct 01 2010 - 04:53:44 PDT)
    - Re: [AMBER] runing mmpbsa.pl on cluster Jason Swails (Fri Oct 01 2010 - 05:11:54 PDT)
    - Re: [AMBER] runing mmpbsa.pl on cluster Jason Swails (Fri Oct 01 2010 - 05:13:08 PDT)
[AMBER] MMPBSA.py - very high energy terms Senthil Natesan (Fri Oct 01 2010 - 06:27:18 PDT)
- Re: [AMBER] MMPBSA.py - very high energy terms Jason Swails (Fri Oct 01 2010 - 06:47:36 PDT)
  - Re: [AMBER] MMPBSA.py - very high energy terms Senthil Natesan (Fri Oct 01 2010 - 07:20:51 PDT)
    - Re: [AMBER] MMPBSA.py - very high energy terms Jason Swails (Fri Oct 01 2010 - 07:33:06 PDT)
[AMBER] undefined reference in compiling amber10/gfortran Francesco Pietra (Fri Oct 01 2010 - 09:15:44 PDT)
- Re: [AMBER] undefined reference in compiling amber10/gfortran case (Fri Oct 01 2010 - 09:45:37 PDT)
  - [AMBER] Error message (link) in running mmpbsa in amber11. Catein Catherine (Fri Oct 01 2010 - 11:47:04 PDT)
[AMBER] sander is running... nicholus bhattacharjee (Fri Oct 01 2010 - 09:41:43 PDT)
- Re: [AMBER] sander is running... Ross Walker (Fri Oct 01 2010 - 11:55:09 PDT)
[AMBER] sander.MPI error Sangita Kachhap (Sat Oct 02 2010 - 07:52:42 PDT)
- Re: [AMBER] sander.MPI error Jason Swails (Sat Oct 02 2010 - 08:04:28 PDT)
[AMBER] Segmentation fault Seibold, Stephen (Sat Oct 02 2010 - 14:33:41 PDT)
- Re: [AMBER] Segmentation fault Jason Swails (Sat Oct 02 2010 - 15:40:52 PDT)
[AMBER] mmpbsa.py error Anuradha Mittal (Sat Oct 02 2010 - 23:17:22 PDT)
- Re: [AMBER] mmpbsa.py error Jason Swails (Sun Oct 03 2010 - 14:51:17 PDT)
  - [AMBER] How to define trivalent Sulphur ligand atom Mannan (Mon Nov 08 2010 - 00:00:39 PST)
    - Re: [AMBER] How to define trivalent Sulphur ligand atom Jason Swails (Mon Nov 08 2010 - 08:18:42 PST)
[AMBER] ptraj- cluster analysis - Error Senthil Natesan (Sun Oct 03 2010 - 10:15:01 PDT)
- Re: [AMBER] ptraj- cluster analysis - Error Daniel Roe (Mon Oct 04 2010 - 04:50:42 PDT)
  - Re: [AMBER] ptraj- cluster analysis - Error Senthil Natesan (Mon Oct 04 2010 - 06:11:57 PDT)
    - Re: [AMBER] ptraj- cluster analysis - Error Daniel Roe (Thu Oct 07 2010 - 14:13:07 PDT)
    - Re: [AMBER] ptraj- cluster analysis - Error - fixed ! Senthil Natesan (Fri Oct 08 2010 - 06:42:47 PDT)
[AMBER] MMPBSA Warning William Flak (Sun Oct 03 2010 - 11:12:47 PDT)
- Re: [AMBER] MMPBSA Warning Bill Miller III (Sun Oct 03 2010 - 11:18:09 PDT)
[AMBER] Citations William Flak (Sun Oct 03 2010 - 16:16:12 PDT)
- Re: [AMBER] Citations Jason Swails (Sun Oct 03 2010 - 16:41:33 PDT)
- Re: [AMBER] Citations Ross Walker (Sun Oct 03 2010 - 16:47:01 PDT)
  - Re: [AMBER] Citations Jiri Sponer (Mon Oct 04 2010 - 02:13:24 PDT)
[AMBER] Fwd: Amber installation Hadrian Djohari (Sun Oct 03 2010 - 22:30:39 PDT)
- Re: [AMBER] Fwd: Amber installation Paul S. Nerenberg (Sun Oct 03 2010 - 22:40:05 PDT)
  - Re: [AMBER] Fwd: Amber installation Hadrian Djohari (Mon Oct 04 2010 - 21:52:08 PDT)
    - Re: [AMBER] Fwd: Amber installation Paul S. Nerenberg (Mon Oct 04 2010 - 23:01:44 PDT)
    - Re: [AMBER] Fwd: Amber installation Hadrian Djohari (Tue Oct 05 2010 - 22:57:57 PDT)
- Re: [AMBER] Fwd: Amber installation Paul S. Nerenberg (Sun Oct 03 2010 - 22:59:23 PDT)
- Re: [AMBER] Fwd: Amber installation case (Mon Oct 04 2010 - 04:58:42 PDT)
[AMBER] Hydrogen Minimization and gradually relieving restraint on the DNA. abc def (Mon Oct 04 2010 - 00:11:38 PDT)
- Re: [AMBER] Hydrogen Minimization and gradually relieving restraint on the DNA. Daniel Roe (Mon Oct 04 2010 - 05:01:33 PDT)
[AMBER] mdcrd file subrata paul (Mon Oct 04 2010 - 04:04:22 PDT)
- Re: [AMBER] mdcrd file hirdesh kumar (Mon Oct 04 2010 - 04:07:47 PDT)
- Re: [AMBER] mdcrd file Carlos Simmerling (Mon Oct 04 2010 - 04:07:35 PDT)
[AMBER] make.parallel test got stuck !! any updates? Senthil Natesan (Mon Oct 04 2010 - 06:25:40 PDT)
- Re: [AMBER] make.parallel test got stuck !! any updates? case (Mon Oct 04 2010 - 06:41:23 PDT)
  - Re: [AMBER] make.parallel test got stuck !! any updates? Senthil Natesan (Mon Oct 04 2010 - 06:52:43 PDT)
    - Re: [AMBER] make.parallel test got stuck !! any updates? case (Mon Oct 04 2010 - 06:59:10 PDT)
[AMBER] nmode Problem Dima A Sabbah (Mon Oct 04 2010 - 06:51:35 PDT)
[AMBER] Potential Energy calculation in AMBER force field Ilyas Yildirim (Mon Oct 04 2010 - 12:34:37 PDT)
- Re: [AMBER] Potential Energy calculation in AMBER force field Bill Ross (Mon Oct 04 2010 - 13:58:55 PDT)
  - [AMBER] Enquiry about tutorial A5 - section 7 on nudged elastic band calculation Catein Catherine (Mon Oct 04 2010 - 14:12:25 PDT)
    - Re: [AMBER] Enquiry about tutorial A5 - section 7 on nudged elastic band calculation Christina Bergonzo (Tue Oct 05 2010 - 06:59:14 PDT)
  - Re: [AMBER] Potential Energy calculation in AMBER force field Ilyas Yildirim (Mon Oct 04 2010 - 16:59:41 PDT)
- Re: [AMBER] Potential Energy calculation in AMBER force field Jason Swails (Mon Oct 04 2010 - 14:40:44 PDT)
- Re: [AMBER] Potential Energy calculation in AMBER force field Bill Ross (Mon Oct 04 2010 - 17:38:15 PDT)
  - Re: [AMBER] Potential Energy calculation in AMBER force field Ilyas Yildirim (Mon Oct 04 2010 - 19:00:06 PDT)
[AMBER] Water bridge - MMPBSA William Flak (Mon Oct 04 2010 - 15:25:09 PDT)
- Re: [AMBER] Water bridge - MMPBSA Bill Miller III (Mon Oct 04 2010 - 15:52:01 PDT)
- Re: [AMBER] Water bridge - MMPBSA Jason Swails (Mon Oct 04 2010 - 18:45:19 PDT)
  - Re: [AMBER] Water bridge - MMPBSA William Flak (Tue Oct 05 2010 - 02:31:56 PDT)
    - Re: [AMBER] Water bridge - MMPBSA Bill Miller III (Tue Oct 05 2010 - 03:39:18 PDT)
    - Re: [AMBER] Water bridge - MMPBSA William Flak (Wed Oct 06 2010 - 12:46:13 PDT)
    - Re: [AMBER] Water bridge - MMPBSA Bill Miller III (Wed Oct 06 2010 - 13:09:24 PDT)
    - Re: [AMBER] Water bridge - MMPBSA Jason Swails (Wed Oct 06 2010 - 13:16:47 PDT)
[AMBER] Water bridges Lekpa Duukori (Mon Oct 04 2010 - 15:34:18 PDT)
- Re: [AMBER] Water bridges Jason Swails (Mon Oct 04 2010 - 18:48:49 PDT)
[AMBER] Query regarding RMSD calculcation hirdesh kumar (Mon Oct 04 2010 - 22:51:22 PDT)
- Re: [AMBER] Query regarding RMSD calculcation Kshatresh Dutta Dubey (Mon Oct 04 2010 - 22:59:15 PDT)
  - Re: [AMBER] Query regarding RMSD calculcation hirdesh kumar (Mon Oct 04 2010 - 23:25:36 PDT)
    - Re: [AMBER] Query regarding RMSD calculcation Daniel Roe (Tue Oct 05 2010 - 07:14:13 PDT)
    - Re: [AMBER] Query regarding RMSD calculcation hirdesh kumar (Tue Oct 05 2010 - 22:22:18 PDT)
    - Re: [AMBER] Query regarding RMSD calculcation Daniel Roe (Wed Oct 06 2010 - 15:44:55 PDT)
    - Re: [AMBER] Query regarding RMSD calculcation hirdesh kumar (Wed Oct 06 2010 - 21:42:06 PDT)
    - Re: [AMBER] Query regarding RMSD calculcation Jason Swails (Thu Oct 07 2010 - 06:08:29 PDT)
    - Re: [AMBER] Query regarding RMSD calculcation hirdesh kumar (Thu Oct 07 2010 - 06:36:21 PDT)
[AMBER] TI +- variance is coming out to be very high sunita gupta (Tue Oct 05 2010 - 00:17:20 PDT)
- Re: [AMBER] TI +- variance is coming out to be very high steinbrt.rci.rutgers.edu (Tue Oct 05 2010 - 00:34:16 PDT)
  - Re: [AMBER] TI +- variance is coming out to be very high sunita gupta (Tue Oct 05 2010 - 02:09:28 PDT)
- Re: [AMBER] TI +- variance is coming out to be very high steinbrt.rci.rutgers.edu (Tue Oct 05 2010 - 03:31:27 PDT)
  - Re: [AMBER] TI +- variance is coming out to be very high sunita gupta (Wed Oct 06 2010 - 00:07:13 PDT)
    - Re: [AMBER] TI +- variance is coming out to be very high steinbrt.rci.rutgers.edu (Wed Oct 06 2010 - 05:48:26 PDT)
    - Re: [AMBER] TI +- variance is coming out to be very high sunita gupta (Thu Oct 07 2010 - 05:16:15 PDT)
    - Re: [AMBER] TI +- variance is coming out to be very high sunita gupta (Mon Nov 08 2010 - 22:20:30 PST)
[AMBER] Query regarding solvent accessible surface area of individual residue hirdesh kumar (Tue Oct 05 2010 - 01:49:57 PDT)
- Re: [AMBER] Query regarding solvent accessible surface area of individual residue Jason Swails (Tue Oct 05 2010 - 05:10:24 PDT)
[AMBER] Sugars flexibility vs ionic strength Sergey Samsonov (Tue Oct 05 2010 - 03:00:13 PDT)
- Re: [AMBER] Sugars flexibility vs ionic strength Lachele Foley (Lists) (Tue Oct 05 2010 - 06:36:38 PDT)
  - Re: [AMBER] Sugars flexibility vs ionic strength Sergey Samsonov (Tue Oct 05 2010 - 08:07:32 PDT)
    - Re: [AMBER] Sugars flexibility vs ionic strength Lachele Foley (Lists) (Tue Oct 05 2010 - 11:36:24 PDT)
    - Re: [AMBER] Sugars flexibility vs ionic strength Sergey Samsonov (Wed Oct 06 2010 - 00:32:21 PDT)
[AMBER] unexpected numnghbr array William Flak (Tue Oct 05 2010 - 07:17:33 PDT)
- Re: [AMBER] unexpected numnghbr array case (Tue Oct 05 2010 - 11:50:09 PDT)
[AMBER] MMBPSA residue selection Federica Chiappori (Tue Oct 05 2010 - 08:01:05 PDT)
- Re: [AMBER] MMBPSA residue selection Jason Swails (Tue Oct 05 2010 - 08:14:35 PDT)
[AMBER] nmode problem Sabbah, Dima (Tue Oct 05 2010 - 09:02:12 PDT)
[AMBER] no nuclear spin in PIMD? aapeters.ncsu.edu (Tue Oct 05 2010 - 09:19:00 PDT)
- Re: [AMBER] no nuclear spin in PIMD? case (Tue Oct 05 2010 - 11:50:49 PDT)
[AMBER] how to stop printing restrt file in AMBER 11 Dian Jiao (Tue Oct 05 2010 - 16:31:45 PDT)
- Re: [AMBER] how to stop printing restrt file in AMBER 11 Jason Swails (Tue Oct 05 2010 - 16:50:14 PDT)
- Re: [AMBER] how to stop printing restrt file in AMBER 11 Bill Ross (Tue Oct 05 2010 - 17:07:08 PDT)
[AMBER] mmpbsa error Anuradha Mittal (Tue Oct 05 2010 - 17:06:49 PDT)
- Re: [AMBER] mmpbsa error Jason Swails (Tue Oct 05 2010 - 17:24:15 PDT)
[AMBER] charges in prmtop file amit dong (Tue Oct 05 2010 - 18:34:01 PDT)
- Re: [AMBER] charges in prmtop file Bill Ross (Tue Oct 05 2010 - 19:43:31 PDT)
- Re: [AMBER] charges in prmtop file Bill Ross (Tue Oct 05 2010 - 19:46:43 PDT)
[AMBER] intra-molecular energies of a water molecule Dian Jiao (Wed Oct 06 2010 - 00:11:53 PDT)
- Re: [AMBER] intra-molecular energies of a water molecule Carlos Simmerling (Wed Oct 06 2010 - 03:39:23 PDT)
  - Re: [AMBER] intra-molecular energies of a water molecule Dian Jiao (Wed Oct 06 2010 - 08:26:44 PDT)
[AMBER] TI problem - Antechamber changes the atom order FCUP (Wed Oct 06 2010 - 03:34:10 PDT)
- [AMBER] TI problem - Antechamber changes the atom order FCUP (Tue Feb 15 2011 - 03:27:31 PST)
[AMBER] TI - vacuum problems FCUP (Wed Oct 06 2010 - 03:45:55 PDT)
[AMBER] DNA and igb=2, igb=5 Ali M. Naserian-Nik (Wed Oct 06 2010 - 04:22:35 PDT)
- Re: [AMBER] DNA and igb=2, igb=5 David A. Case (Wed Oct 06 2010 - 04:46:15 PDT)
[AMBER] Protocol for structure determination of DNA duplex by NMR Olivier Julien (Wed Oct 06 2010 - 10:53:23 PDT)
- Re: [AMBER] Protocol for structure determination of DNA duplex by NMR David A. Case (Thu Oct 07 2010 - 04:36:22 PDT)
[AMBER] generating restraints Jorgen Simonsen (Wed Oct 06 2010 - 11:10:36 PDT)
- Re: [AMBER] generating restraints David A. Case (Thu Oct 07 2010 - 04:38:56 PDT)
[AMBER] Ptraj Error- Analysis on Trajectory files Ajay Ummat (Wed Oct 06 2010 - 11:45:44 PDT)
- Re: [AMBER] Ptraj Error- Analysis on Trajectory files Bill Ross (Wed Oct 06 2010 - 11:54:51 PDT)
- Re: [AMBER] Ptraj Error- Analysis on Trajectory files Daniel Roe (Wed Oct 06 2010 - 15:20:58 PDT)
- Re: [AMBER] Ptraj Error- Analysis on Trajectory files Bill Ross (Wed Oct 06 2010 - 15:43:23 PDT)
  - Re: [AMBER] Ptraj Error- Analysis on Trajectory files Ajay Ummat (Wed Oct 06 2010 - 16:06:54 PDT)
[AMBER] nab function transformmol() returned value docs are inconsistent M. L. Dodson (Wed Oct 06 2010 - 11:58:12 PDT)
- Re: [AMBER] nab function transformmol() returned value docs are inconsistent David A. Case (Thu Oct 07 2010 - 06:27:47 PDT)
[AMBER] Stability problem shweta (Wed Oct 06 2010 - 18:56:18 PDT)
- Re: [AMBER] Stability problem Carlos Simmerling (Thu Oct 07 2010 - 03:54:56 PDT)
  - Re: [AMBER] Stability problem shweta (Thu Oct 07 2010 - 07:30:47 PDT)
[AMBER] RMSD doubt Soumya Lipsa Rath (Thu Oct 07 2010 - 00:49:22 PDT)
- [AMBER] RMSD doubt Soumya Lipsa Rath (Thu Oct 07 2010 - 09:55:37 PDT)
  - Re: [AMBER] RMSD doubt Carlos Simmerling (Thu Oct 07 2010 - 10:48:59 PDT)
    - Re: [AMBER] RMSD doubt Soumya Lipsa Rath (Thu Oct 07 2010 - 20:41:07 PDT)
[AMBER] maximum coordination exceeded $ set pert true William Flak (Thu Oct 07 2010 - 06:58:38 PDT)
- Re: [AMBER] maximum coordination exceeded $ set pert true Jason Swails (Thu Oct 07 2010 - 07:07:35 PDT)
  - Re: [AMBER] maximum coordination exceeded $ set pert true William Flak (Thu Oct 07 2010 - 07:25:50 PDT)
  - [AMBER] adding ions to structures Stefano Pieraccini (Thu Oct 07 2010 - 07:26:07 PDT)
    - Re: [AMBER] adding ions to structures Bill Ross (Thu Oct 07 2010 - 09:44:53 PDT)
    - Re: [AMBER] adding ions to structures Bill Ross (Thu Oct 07 2010 - 09:51:02 PDT)
    - Re: [AMBER] adding ions to structures Andrew Jewett (Thu Oct 07 2010 - 19:06:38 PDT)
[AMBER] phosphorylated residues priyanka (Thu Oct 07 2010 - 09:43:20 PDT)
- Re: [AMBER] phosphorylated residues Jason Swails (Thu Oct 07 2010 - 10:54:39 PDT)
  - Re: [AMBER] phosphorylated residues priyanka (Thu Oct 07 2010 - 20:36:07 PDT)
[AMBER] Question about limitations of the nudged elastic band method patrick wintrode (Thu Oct 07 2010 - 17:43:22 PDT)
- Re: [AMBER] Question about limitations of the nudged elastic band method Carlos Simmerling (Thu Oct 07 2010 - 17:49:26 PDT)
  - Re: [AMBER] Question about limitations of the nudged elastic band method patrick wintrode (Thu Oct 07 2010 - 18:39:39 PDT)
    - Re: [AMBER] Question about limitations of the nudged elastic band method Carlos Simmerling (Thu Oct 07 2010 - 18:47:38 PDT)
[AMBER] ptraj mask Tyler Glembo (Thu Oct 07 2010 - 22:50:00 PDT)
- Re: [AMBER] ptraj mask Jason Swails (Fri Oct 08 2010 - 05:15:51 PDT)
  - Re: [AMBER] ptraj mask Tyler Glembo (Fri Oct 08 2010 - 10:41:32 PDT)
    - Re: [AMBER] ptraj mask Jason Swails (Fri Oct 08 2010 - 11:00:00 PDT)
    - Re: [AMBER] ptraj mask Tyler Glembo (Fri Oct 08 2010 - 12:04:50 PDT)
    - Re: [AMBER] ptraj mask Jianyin Shao (Fri Oct 08 2010 - 20:35:45 PDT)
[AMBER] installation of pmemd fancy2012 (Fri Oct 08 2010 - 01:25:08 PDT)
- Re: [AMBER] installation of pmemd Jason Swails (Fri Oct 08 2010 - 06:03:01 PDT)
  - [AMBER] How to convert mdcrd to pdb for display? Catein Catherine (Fri Oct 08 2010 - 07:46:12 PDT)
    - Re: [AMBER] How to convert mdcrd to pdb for display? Jason Swails (Fri Oct 08 2010 - 07:50:48 PDT)
    - Re: [AMBER] How to convert mdcrd to pdb for display? Catein Catherine (Fri Oct 08 2010 - 09:55:07 PDT)
    - Re: [AMBER] How to convert mdcrd to pdb for display? Jason Swails (Fri Oct 08 2010 - 11:05:45 PDT)
  - Re: [AMBER] installation of pmemd fancy2012 (Fri Oct 08 2010 - 18:15:14 PDT)
[AMBER] fix the positions of EP William Flak (Fri Oct 08 2010 - 07:56:50 PDT)
- Re: [AMBER] fix the positions of EP case (Fri Oct 08 2010 - 08:24:47 PDT)
[AMBER] Searching for a keyword William Flak (Fri Oct 08 2010 - 14:27:17 PDT)
- Re: [AMBER] Searching for a keyword case (Sat Oct 09 2010 - 05:48:02 PDT)
[AMBER] tutorials of TMD and REMD fancy2012 (Fri Oct 08 2010 - 20:15:31 PDT)
- Re: [AMBER] tutorials of TMD and REMD Jason Swails (Fri Oct 08 2010 - 20:22:51 PDT)
- [AMBER] Newton-Raphson minimization fancy2012 (Mon Oct 11 2010 - 02:22:40 PDT)
  - Re: [AMBER] Newton-Raphson minimization case (Mon Oct 11 2010 - 04:48:01 PDT)
[AMBER] V-limit exceeded in replica-exchang MD Cheng-I Lee (Fri Oct 08 2010 - 21:50:56 PDT)
- Re: [AMBER] V-limit exceeded in replica-exchang MD Paul S. Nerenberg (Fri Oct 08 2010 - 22:15:39 PDT)
[AMBER] prepare the heme parameters juan zeng (Sat Oct 09 2010 - 00:18:08 PDT)
- Re: [AMBER] prepare the heme parameters case (Sat Oct 09 2010 - 05:52:03 PDT)
  - Re: [AMBER] prepare the heme parameters juan zeng (Sat Oct 09 2010 - 06:54:45 PDT)
    - Re: [AMBER] prepare the heme parameters ros (Sat Oct 09 2010 - 10:35:36 PDT)
    - Re: [AMBER] prepare the heme parameters juan zeng (Sun Oct 10 2010 - 18:49:45 PDT)
  - Re: [AMBER] prepare the heme parameters FyD (Mon Oct 11 2010 - 00:16:18 PDT)
    - Re: [AMBER] prepare the heme parameters juan zeng (Mon Oct 11 2010 - 03:54:59 PDT)
[AMBER] Phosphorylated aspartate residue Rahul Banerjee (Sat Oct 09 2010 - 07:13:10 PDT)
- Re: [AMBER] Phosphorylated aspartate residue FyD (Mon Oct 11 2010 - 00:19:09 PDT)
- Re: [AMBER] Phosphorylated aspartate residue case (Mon Oct 11 2010 - 04:59:50 PDT)
[AMBER] ptraj closest command William Flak (Sat Oct 09 2010 - 08:44:17 PDT)
[AMBER] ligand geometry after simulation Computational Chemist (Sat Oct 09 2010 - 12:59:59 PDT)
- Re: [AMBER] ligand geometry after simulation Bill Ross (Sat Oct 09 2010 - 13:03:29 PDT)
- Re: [AMBER] ligand geometry after simulation Jason Swails (Sat Oct 09 2010 - 18:04:27 PDT)
  - [AMBER] multi input for parmchk Xioling Chuang (Sun Oct 10 2010 - 20:31:50 PDT)
    - Re: [AMBER] multi input for parmchk case (Mon Oct 11 2010 - 04:41:14 PDT)
[AMBER] trajectory and topology file format Sangita Kachhap (Sun Oct 10 2010 - 06:49:08 PDT)
[AMBER] restraint between two centers of mass? Jose Borreguero (Sun Oct 10 2010 - 07:35:44 PDT)
[AMBER] partition error in shake xuemeiwang1103 (Sun Oct 10 2010 - 20:20:17 PDT)
- Re: [AMBER] partition error in shake case (Mon Oct 11 2010 - 04:40:30 PDT)
  - Re: [AMBER] partition error in shake xuemeiwang1103 (Mon Oct 11 2010 - 18:36:11 PDT)
    - Re: [AMBER] partition error in shake case (Mon Oct 11 2010 - 20:36:27 PDT)
    - Re: [AMBER] partition error in shake xuemeiwang1103 (Tue Oct 12 2010 - 01:25:13 PDT)
    - Re: [AMBER] partition error in shake case (Wed Oct 13 2010 - 07:05:44 PDT)
[AMBER] Ptraj LES split problem Bradshaw, Richard (Mon Oct 11 2010 - 05:08:35 PDT)
- Re: [AMBER] Ptraj LES split problem (followup) Bradshaw, Richard (Wed Oct 13 2010 - 06:39:45 PDT)
  - Re: [AMBER] Ptraj LES split problem (followup) Carlos Simmerling (Wed Oct 13 2010 - 06:42:55 PDT)
[AMBER] remap umbrella sampling free-energy Giuseppe De Marco (Mon Oct 11 2010 - 10:57:22 PDT)
[AMBER] xleap Siavoush Dastmalchi (Mon Oct 11 2010 - 21:54:48 PDT)
- Re: [AMBER] xleap Scott Brozell (Mon Oct 11 2010 - 22:14:21 PDT)
- Re: [AMBER] xleap Siavoush Dastmalchi (Mon Oct 11 2010 - 22:36:38 PDT)
  - Re: [AMBER] xleap Scott Brozell (Mon Oct 11 2010 - 23:22:02 PDT)
- Re: [AMBER] xleap Siavoush Dastmalchi (Tue Oct 12 2010 - 01:21:48 PDT)
- Re: [AMBER] xleap Siavoush Dastmalchi (Tue Oct 12 2010 - 01:24:28 PDT)
  - [AMBER] xleap menu bar problem Siavoush Dastmalchi (Tue Oct 12 2010 - 06:11:46 PDT)
    - Re: [AMBER] xleap menu bar problem Jose Borreguero (Tue Oct 12 2010 - 06:20:48 PDT)
    - Re: [AMBER] xleap menu bar problem Siavoush Dastmalchi (Tue Oct 12 2010 - 06:30:24 PDT)
- Re: [AMBER] xleap David A Case (Thu May 27 2021 - 05:08:45 PDT)
  - Re: [AMBER] xleap Wu Xu (Tue Jun 01 2021 - 12:04:20 PDT)
[AMBER] error in atomic charge calculation in RED server Chinh Su Tran To (Mon Oct 11 2010 - 22:19:34 PDT)
- Re: [AMBER] error in atomic charge calculation in RED server FyD (Mon Oct 11 2010 - 23:17:56 PDT)
  - Re: [AMBER] error in atomic charge calculation in RED server Chinh Su Tran To (Mon Oct 11 2010 - 23:37:37 PDT)
    - Re: [AMBER] error in atomic charge calculation in RED server FyD (Mon Oct 11 2010 - 23:55:21 PDT)
- Re: [AMBER] error in atomic charge calculation in RED server FyD (Mon Oct 11 2010 - 23:37:36 PDT)
  - Re: [AMBER] error in atomic charge calculation in RED server Chinh Su Tran To (Tue Oct 12 2010 - 00:06:10 PDT)
    - Re: [AMBER] error in atomic charge calculation in RED server FyD (Tue Oct 12 2010 - 00:30:37 PDT)
    - Re: [AMBER] error in atomic charge calculation in RED server Chinh Su Tran To (Tue Oct 12 2010 - 00:36:40 PDT)
    - Re: [AMBER] error in atomic charge calculation in RED server Chinh Su Tran To (Wed Oct 20 2010 - 04:21:57 PDT)
    - Re: [AMBER] error in atomic charge calculation in RED server FyD (Wed Oct 20 2010 - 05:47:20 PDT)
[AMBER] proton spin effects with Semi-empirical or DFTB qm/mm? aapeters.ncsu.edu (Tue Oct 12 2010 - 12:59:56 PDT)
- Re: [AMBER] proton spin effects with Semi-empirical or DFTB qm/mm? Andreas Goetz (Tue Oct 12 2010 - 13:21:29 PDT)
[AMBER] cz atom type Balazs Jojart (Tue Oct 12 2010 - 13:10:38 PDT)
- Re: [AMBER] cz atom type case (Wed Oct 13 2010 - 06:59:26 PDT)
[AMBER] Solvate water moleculer in a TIP3PBOX oscarjiao.gmail.com (Tue Oct 12 2010 - 13:59:32 PDT)
- Re: [AMBER] Solvate water moleculer in a TIP3PBOX case (Wed Oct 13 2010 - 07:01:52 PDT)
  - Re: [AMBER] Solvate water moleculer in a TIP3PBOX Dian Jiao (Wed Oct 13 2010 - 09:37:33 PDT)
- [AMBER] RNA simulation problems: bad input, force field issue or incorrect reference structure? Sasha Buzko (Fri Oct 15 2010 - 15:08:17 PDT)
  - Re: [AMBER] RNA simulation problems: bad input, force field issue or incorrect reference structure? Carlos Simmerling (Fri Oct 15 2010 - 15:58:53 PDT)
    - Re: [AMBER] RNA simulation problems: bad input, force field issue or incorrect reference structure? Sasha Buzko (Fri Oct 15 2010 - 16:03:37 PDT)
    - Re: [AMBER] RNA simulation problems: bad input, force field issue or incorrect reference structure? Jiri Sponer (Fri Oct 15 2010 - 16:29:22 PDT)
    - Re: [AMBER] RNA simulation problems: bad input, force field issue or incorrect reference structure? Sasha Buzko (Fri Oct 15 2010 - 16:42:38 PDT)
    - Re: [AMBER] RNA simulation problems: bad input, force field issue or incorrect reference structure? Jiri Sponer (Sat Oct 16 2010 - 00:11:52 PDT)
  - Re: [AMBER] RNA simulation problems: bad input, force field issue or incorrect reference structure? Jiri Sponer (Fri Oct 15 2010 - 16:26:04 PDT)
[AMBER] limitation of the protein size Cheng-I Lee (Tue Oct 12 2010 - 20:44:42 PDT)
- Re: [AMBER] limitation of the protein size Bill Ross (Tue Oct 12 2010 - 21:04:42 PDT)
  - [AMBER] advenced tutorial 13 (crystal simulations) Stefano Pieraccini (Wed Oct 13 2010 - 03:34:51 PDT)
    - Re: [AMBER] advenced tutorial 13 (crystal simulations) Matthias Negri (Wed Oct 13 2010 - 04:32:34 PDT)
[AMBER] Normal mode analysis with QM potential 전종구 (Tue Oct 12 2010 - 22:52:22 PDT)
- Re: [AMBER] Normal mode analysis with QM potential case (Wed Oct 13 2010 - 05:34:55 PDT)
[AMBER] ptraj box information Dickson, Callum (Wed Oct 13 2010 - 03:15:50 PDT)
- Re: [AMBER] ptraj box information Daniel Roe (Thu Oct 14 2010 - 06:46:27 PDT)
[AMBER] Water box deformed after heating step xue wang (Wed Oct 13 2010 - 07:09:41 PDT)
- Re: [AMBER] Water box deformed after heating step Carlos Simmerling (Wed Oct 13 2010 - 07:18:48 PDT)
  - Re: [AMBER] Water box deformed after heating step xue wang (Wed Oct 13 2010 - 08:50:33 PDT)
    - Re: [AMBER] Water box deformed after heating step Carlos Simmerling (Wed Oct 13 2010 - 09:37:29 PDT)
[AMBER] new_type_solvent lara lara (Wed Oct 13 2010 - 09:00:15 PDT)
[AMBER] new_solvent_type lara lara (Wed Oct 13 2010 - 09:23:53 PDT)
[AMBER] Amber heme parameters Nitu Bansal (Wed Oct 13 2010 - 10:16:02 PDT)
- Re: [AMBER] Amber heme parameters Bill Ross (Wed Oct 13 2010 - 10:22:10 PDT)
  - Re: [AMBER] Amber heme parameters Nitu Bansal (Wed Oct 13 2010 - 22:36:25 PDT)
    - Re: [AMBER] Amber heme parameters case (Thu Oct 14 2010 - 04:37:52 PDT)
    - Re: [AMBER] Amber heme parameters Nitu Bansal (Thu Oct 14 2010 - 11:07:08 PDT)
    - Re: [AMBER] Amber heme parameters Paul S. Nerenberg (Thu Oct 14 2010 - 11:37:36 PDT)
- Re: [AMBER] Amber heme parameters Bill Ross (Thu Oct 14 2010 - 11:12:55 PDT)
  - Re: [AMBER] Amber heme parameters case (Thu Oct 14 2010 - 12:18:32 PDT)
    - Re: [AMBER] Amber heme parameters Nitu Bansal (Fri Oct 15 2010 - 09:01:11 PDT)
[AMBER] output pairwise energies Dian Jiao (Wed Oct 13 2010 - 10:25:04 PDT)
- Re: [AMBER] output pairwise energies Jason Swails (Wed Oct 13 2010 - 10:34:01 PDT)
[AMBER] xleap: SegFault on loadpdb Maura Catherine Mooney (Wed Oct 13 2010 - 10:41:40 PDT)
- Re: [AMBER] xleap: SegFault on loadpdb Jason Swails (Wed Oct 13 2010 - 10:52:08 PDT)
  - Re: [AMBER] xleap: SegFault on loadpdb Maura Catherine Mooney (Wed Oct 13 2010 - 10:56:19 PDT)
[AMBER] restart file error shweta (Wed Oct 13 2010 - 10:57:43 PDT)
- Re: [AMBER] restart file error Daniel Roe (Thu Oct 14 2010 - 05:18:57 PDT)
  - Re: [AMBER] restart file error case (Thu Oct 14 2010 - 05:55:56 PDT)
[AMBER] MMPBSA protein-protein interaction Lars Skjærven (Thu Oct 14 2010 - 02:59:23 PDT)
- Re: [AMBER] MMPBSA protein-protein interaction Oliver Grant (Thu Oct 14 2010 - 04:17:06 PDT)
- Re: [AMBER] MMPBSA protein-protein interaction case (Thu Oct 14 2010 - 06:06:16 PDT)
  - Re: [AMBER] MMPBSA protein-protein interaction Lars Skjærven (Fri Oct 15 2010 - 10:15:20 PDT)
    - Re: [AMBER] MMPBSA protein-protein interaction Jason Swails (Fri Oct 15 2010 - 11:49:05 PDT)
    - Re: [AMBER] MMPBSA protein-protein interaction case (Sat Oct 16 2010 - 07:45:53 PDT)
    - Re: [AMBER] MMPBSA protein-protein interaction Lars Skjærven (Wed Oct 20 2010 - 08:24:33 PDT)
    - Re: [AMBER] MMPBSA protein-protein interaction David A. Case (Fri Oct 22 2010 - 07:33:43 PDT)
[AMBER] Issue regarding buckling of planar ligand during simulations abc def (Thu Oct 14 2010 - 04:43:31 PDT)
- Re: [AMBER] Issue regarding buckling of planar ligand during simulations Andreas Goetz (Thu Oct 14 2010 - 07:12:38 PDT)
[AMBER] antechamber error when processing the graphite structure Bongkeun Kim (Thu Oct 14 2010 - 13:02:13 PDT)
- [AMBER] antechamber error when processing the graphite structure Gustavo Seabra (Thu Oct 14 2010 - 14:14:25 PDT)
- Re: [AMBER] antechamber error when processing the graphite structure Bill Ross (Thu Oct 14 2010 - 14:36:52 PDT)
  - Re: [AMBER] antechamber error when processing the graphite structure Bongkeun Kim (Thu Oct 14 2010 - 14:48:58 PDT)
[AMBER] About RMSD calculations hong-bin Xie (Thu Oct 14 2010 - 16:47:43 PDT)
- Re: [AMBER] About RMSD calculations Bill Ross (Thu Oct 14 2010 - 17:01:58 PDT)
  - Re: [AMBER] About RMSD calculations hong-bin Xie (Thu Oct 14 2010 - 17:11:15 PDT)
[AMBER] memory issue- CPHF- gamess calculation kamlesh sahu (Thu Oct 14 2010 - 18:24:35 PDT)
- Re: [AMBER] memory issue- CPHF- gamess calculation Paul S. Nerenberg (Thu Oct 14 2010 - 18:57:43 PDT)
  - Re: [AMBER] memory issue- CPHF- gamess calculation kamlesh sahu (Thu Oct 14 2010 - 19:38:42 PDT)
  - [AMBER] How to genrate a movie from a trajectory? Catein Catherine (Thu Oct 14 2010 - 20:54:16 PDT)
    - Re: [AMBER] How to genrate a movie from a trajectory? hirdesh kumar (Thu Oct 14 2010 - 21:30:59 PDT)
    - Re: [AMBER] How to genrate a movie from a trajectory? Jason Swails (Fri Oct 15 2010 - 04:47:54 PDT)
    - Re: [AMBER] How to genrate a movie from a trajectory? Catein Catherine (Fri Oct 15 2010 - 07:47:06 PDT)
    - Re: [AMBER] How to genrate a movie from a trajectory? Eric Pettersen (Sat Oct 16 2010 - 08:29:21 PDT)
[AMBER] Is it a typo in TUTORIAL A13: Simulation of a protein crystal? Ye MEI (Thu Oct 14 2010 - 21:05:25 PDT)
- Re: [AMBER] Is it a typo in TUTORIAL A13: Simulation of a protein crystal? dcerutti.rci.rutgers.edu (Fri Oct 15 2010 - 08:56:27 PDT)
[AMBER] build starting structure with >250 residues Cheng-I Lee (Thu Oct 14 2010 - 22:13:13 PDT)
- Re: [AMBER] build starting structure with >250 residues Ross Walker (Thu Oct 14 2010 - 22:36:17 PDT)
[AMBER] solvent_box_type lara lara (Thu Oct 14 2010 - 23:24:35 PDT)
[AMBER] a question about replica-exchange MD Cheng-I Lee (Thu Oct 14 2010 - 23:24:32 PDT)
- Re: [AMBER] a question about replica-exchange MD Carlos Simmerling (Fri Oct 15 2010 - 03:55:34 PDT)
  - Re: [AMBER] a question about replica-exchange MD Cheng-I Lee (Fri Oct 15 2010 - 22:02:46 PDT)
    - Re: [AMBER] a question about replica-exchange MD case (Sat Oct 16 2010 - 07:18:54 PDT)
    - Re: [AMBER] a question about replica-exchange MD Carlos Simmerling (Sun Oct 17 2010 - 05:02:44 PDT)
[AMBER] mm_pbsa dependence on GB 0 or GB 1 Antonija Tomić (Fri Oct 15 2010 - 08:14:11 PDT)
- Re: [AMBER] mm_pbsa dependence on GB 0 or GB 1 case (Fri Oct 15 2010 - 11:10:41 PDT)
  - Re: [AMBER] mm_pbsa dependence on GB 0 or GB 1 Antonija Tomić (Mon Oct 18 2010 - 01:32:15 PDT)
    - Re: [AMBER] mm_pbsa dependence on GB 0 or GB 1 Jason Swails (Mon Oct 18 2010 - 04:45:06 PDT)
[AMBER] AMBER parallel version ying yu (Fri Oct 15 2010 - 21:40:31 PDT)
- Re: [AMBER] AMBER parallel version Bill Miller III (Sat Oct 16 2010 - 05:00:30 PDT)
- Re: [AMBER] AMBER parallel version Jason Swails (Sat Oct 16 2010 - 06:41:12 PDT)
  - Re: [AMBER] AMBER parallel version ying yu (Sat Oct 16 2010 - 13:23:14 PDT)
[AMBER] binding free energy difference between PBTOT and GBTOT xue wang (Sun Oct 17 2010 - 07:07:39 PDT)
[AMBER] mm-pbsa yan zhang (Sun Oct 17 2010 - 07:19:21 PDT)
- Re: [AMBER] mm-pbsa Bill Miller III (Sun Oct 17 2010 - 07:35:38 PDT)
[AMBER] question on antechamber parametrization / unable to find mopac charges error Andrew Voronkov (Sun Oct 17 2010 - 10:35:07 PDT)
- Re: [AMBER] question on antechamber parametrization / unable to find mopac charges error Andrew Voronkov (Tue Oct 19 2010 - 05:23:01 PDT)
- Re: [AMBER] question on antechamber parametrization / unable to find mopac charges error David A. Case (Wed Oct 20 2010 - 05:53:59 PDT)
[AMBER] PMEMD terminated abnormally! Ashutosh Shandilya (Mon Oct 18 2010 - 00:12:11 PDT)
- Re: [AMBER] PMEMD terminated abnormally! Jason Swails (Mon Oct 18 2010 - 04:33:35 PDT)
  - Re: [AMBER] PMEMD terminated abnormally! Ashutosh Shandilya (Mon Oct 18 2010 - 23:21:59 PDT)
    - Re: [AMBER] PMEMD terminated abnormally! Ross Walker (Mon Oct 18 2010 - 23:41:15 PDT)
- Re: [AMBER] PMEMD terminated abnormally! Ashutosh Shandilya (Tue Oct 19 2010 - 01:37:30 PDT)
  - Re: [AMBER] PMEMD terminated abnormally! Adrian Roitberg (Tue Oct 19 2010 - 01:40:40 PDT)
    - Re: [AMBER] PMEMD terminated abnormally! Ashutosh Shandilya (Tue Oct 19 2010 - 02:45:37 PDT)
    - Re: [AMBER] PMEMD terminated abnormally! Ashutosh Shandilya (Tue Oct 19 2010 - 04:26:34 PDT)
[AMBER] amber84 ASH parameters Francesco Pietra (Mon Oct 18 2010 - 00:59:15 PDT)
[AMBER] solvent_shell_minimization_error balaji nagarajan (Mon Oct 18 2010 - 01:28:40 PDT)
- Re: [AMBER] solvent_shell_minimization_error Jason Swails (Mon Oct 18 2010 - 04:39:57 PDT)
[AMBER] Output problem on Amber 9 Seren Soner (Mon Oct 18 2010 - 02:16:44 PDT)
- Re: [AMBER] Output problem on Amber 9 Adrian Roitberg (Mon Oct 18 2010 - 03:40:34 PDT)
  - Re: [AMBER] Output problem on Amber 9 Seren Soner (Fri Oct 29 2010 - 09:09:38 PDT)
    - Re: [AMBER] Output problem on Amber 9 Ross Walker (Fri Oct 29 2010 - 09:21:26 PDT)
    - Re: [AMBER] Output problem on Amber 9 Jason Swails (Fri Oct 29 2010 - 09:28:31 PDT)
    - Re: [AMBER] Output problem on Amber 9 Seren Soner (Fri Oct 29 2010 - 09:33:16 PDT)
    - Re: [AMBER] Output problem on Amber 9 Jason Swails (Fri Oct 29 2010 - 10:25:08 PDT)
    - Re: [AMBER] Output problem on Amber 9 Seren Soner (Sat Oct 30 2010 - 13:23:41 PDT)
    - Re: [AMBER] Output problem on Amber 9 Jason Swails (Sat Oct 30 2010 - 13:28:23 PDT)
    - Re: [AMBER] Output problem on Amber 9 Seren Soner (Sat Oct 30 2010 - 13:33:17 PDT)
    - Re: [AMBER] Output problem on Amber 9 Jason Swails (Sat Oct 30 2010 - 13:46:12 PDT)
    - Re: [AMBER] Output problem on Amber 9 Seren Soner (Sat Oct 30 2010 - 13:48:05 PDT)
    - Re: [AMBER] Output problem on Amber 9 Jason Swails (Sat Oct 30 2010 - 13:51:00 PDT)
    - Re: [AMBER] Output problem on Amber 9 Seren Soner (Sat Oct 30 2010 - 14:15:37 PDT)
- Re: [AMBER] Output problem on Amber 9 tanya singh (Fri Oct 29 2010 - 09:42:58 PDT)
  - Re: [AMBER] Output problem on Amber 9 Jason Swails (Fri Oct 29 2010 - 10:33:41 PDT)
[AMBER] Problem with formyl group parameters Carter M.K. (Mon Oct 18 2010 - 03:36:44 PDT)
- Re: [AMBER] Problem with formyl group parameters Jason Swails (Mon Oct 18 2010 - 04:43:07 PDT)
[AMBER] residence time of water molecule and life time of hydrogen bonds atila petrosian (Mon Oct 18 2010 - 03:45:20 PDT)
[AMBER] Parameters for succinimide Stephan Jakobi (Mon Oct 18 2010 - 05:17:57 PDT)
- Re: [AMBER] Parameters for succinimide FyD (Mon Oct 18 2010 - 06:46:05 PDT)
[AMBER] QMMM: Unable to achieve self consistency to the tolerances specified sunita gupta (Mon Oct 18 2010 - 05:20:19 PDT)
- Re: [AMBER] QMMM: Unable to achieve self consistency to the tolerances specified Gustavo Seabra (Mon Oct 18 2010 - 05:29:32 PDT)
[AMBER] binding affinity calculation Sangita Kachhap (Mon Oct 18 2010 - 05:34:45 PDT)
- Re: [AMBER] binding affinity calculation David A. Case (Tue Oct 19 2010 - 02:36:01 PDT)
[AMBER] The result of entropy calculation DeChang Li (Mon Oct 18 2010 - 07:44:58 PDT)
- Re: [AMBER] The result of entropy calculation Dima A Sabbah (Mon Oct 18 2010 - 07:59:41 PDT)
[AMBER] sphere_problem balaji nagarajan (Mon Oct 18 2010 - 09:19:12 PDT)
- Re: [AMBER] sphere_problem Jason Swails (Mon Oct 18 2010 - 09:54:56 PDT)
  - [AMBER] AMBER support Red Hat Enterprise Linux (RHEL) Version 5.5? ethan.chen (Mon Oct 18 2010 - 18:18:19 PDT)
    - Re: [AMBER] AMBER support Red Hat Enterprise Linux (RHEL) Version 5.5? Ross Walker (Mon Oct 18 2010 - 21:21:15 PDT)
    - Re: [AMBER] AMBER support Red Hat Enterprise Linux (RHEL) Version5.5? ethan.chen (Mon Oct 18 2010 - 23:09:49 PDT)
- Re: [AMBER] sphere_problem M. L. Dodson (Mon Oct 18 2010 - 10:07:51 PDT)
  - Re: [AMBER] sphere_problem M. L. Dodson (Mon Oct 18 2010 - 10:13:24 PDT)
Re: [AMBER] NMR_ensemble Raman Parkesh (Mon Oct 18 2010 - 15:20:41 PDT)
- Re: [AMBER] NMR_ensemble David A. Case (Tue Oct 19 2010 - 02:59:49 PDT)
  - Re: [AMBER] NMR_ensemble Raman Parkesh (Tue Oct 19 2010 - 06:18:03 PDT)
[AMBER] interaction_energy balaji nagarajan (Mon Oct 18 2010 - 20:13:49 PDT)
- Re: [AMBER] interaction_energy Sushil Mishra (Mon Oct 18 2010 - 21:03:10 PDT)
  - Re: [AMBER] interaction_energy Daniel Sindhikara (Mon Oct 18 2010 - 22:02:03 PDT)
    - Re: [AMBER] interaction_energy Sushil Mishra (Tue Oct 19 2010 - 00:22:05 PDT)
    - Re: [AMBER] interaction_energy lara lara (Tue Oct 19 2010 - 01:11:24 PDT)
    - Re: [AMBER] interaction_energy Jason Swails (Tue Oct 19 2010 - 07:38:14 PDT)
[AMBER] nmode calculation rameshwar prajapati (Tue Oct 19 2010 - 00:22:11 PDT)
- Re: [AMBER] nmode calculation Jason Swails (Tue Oct 19 2010 - 07:40:33 PDT)
[AMBER] Mimiciking infinite DNA abc def (Tue Oct 19 2010 - 02:15:03 PDT)
- Re: [AMBER] Mimiciking infinite DNA David A. Case (Tue Oct 19 2010 - 02:53:28 PDT)
[AMBER] amb2gmx.pl script ignores negative values of PK? Andrei Neamtu (Tue Oct 19 2010 - 05:27:02 PDT)
[AMBER] Umbrella sampling with temperature and pressure coupling method problem DeChang Li (Tue Oct 19 2010 - 05:57:33 PDT)
- Re: [AMBER] Umbrella sampling with temperature and pressure coupling method problem Daniel Sindhikara (Tue Oct 19 2010 - 08:02:15 PDT)
  - Re: [AMBER] Umbrella sampling with temperature and pressure coupling method problem DeChang Li (Tue Oct 19 2010 - 08:29:29 PDT)
    - Re: [AMBER] Umbrella sampling with temperature and pressure coupling method problem Daniel Sindhikara (Tue Oct 19 2010 - 17:08:01 PDT)
    - Re: [AMBER] Umbrella sampling with temperature and pressure coupling method problem Andrew Jewett (Tue Oct 19 2010 - 20:19:50 PDT)
[AMBER] magnesium ion parametrization question Andrew Voronkov (Tue Oct 19 2010 - 07:12:33 PDT)
- Re: [AMBER] magnesium ion parametrization question Dmitry Nilov (Wed Oct 20 2010 - 06:36:15 PDT)
  - Re: [AMBER] magnesium ion parametrization question Andrew Voronkov (Wed Oct 20 2010 - 09:02:56 PDT)
  - Re: [AMBER] magnesium ion parametrization question Andrew Voronkov (Wed Oct 20 2010 - 09:18:52 PDT)
    - Re: [AMBER] magnesium ion parametrization question InSuk Joung (Wed Oct 20 2010 - 10:10:52 PDT)
    - Re: [AMBER] magnesium ion parametrization question Dmitry Nilov (Wed Oct 20 2010 - 10:11:27 PDT)
    - Re: [AMBER] magnesium ion parametrization question Andrew Voronkov (Thu Oct 21 2010 - 00:15:04 PDT)
[AMBER] H-Bonding Beale, John (Tue Oct 19 2010 - 09:15:20 PDT)
- Re: [AMBER] H-Bonding case (Tue Oct 19 2010 - 11:51:39 PDT)
[AMBER] xmin fails with error in load_lbfgs() Don.Bashford.stjude.org (Tue Oct 19 2010 - 12:53:04 PDT)
[AMBER] Amber10 build/installation problems Yazlovitsky, Boris (Tue Oct 19 2010 - 16:04:16 PDT)
- Re: [AMBER] Amber10 build/installation problems Bill Ross (Tue Oct 19 2010 - 17:22:20 PDT)
- Re: [AMBER] Amber10 build/installation problems Ross Walker (Tue Oct 19 2010 - 17:29:09 PDT)
  - Re: [AMBER] Amber10 build/installation problems Yazlovitsky, Boris (Thu Oct 21 2010 - 11:21:29 PDT)
[AMBER] Problem using graphite strucute in equil MD Bongkeun Kim (Tue Oct 19 2010 - 22:24:19 PDT)
- Re: [AMBER] Problem using graphite strucute in equil MD InSuk Joung (Wed Oct 20 2010 - 09:46:54 PDT)
- Re: [AMBER] Problem using graphite strucute in equil MD Bill Ross (Wed Oct 20 2010 - 10:02:35 PDT)
  - Re: [AMBER] Problem using graphite strucute in equil MD Bongkeun Kim (Wed Oct 20 2010 - 10:31:18 PDT)
- Re: [AMBER] Problem using graphite strucute in equil MD Bill Ross (Wed Oct 20 2010 - 11:03:56 PDT)
  - Re: [AMBER] Problem using graphite strucute in equil MD Bongkeun Kim (Wed Oct 20 2010 - 11:19:35 PDT)
- Re: [AMBER] Problem using graphite strucute in equil MD Bill Ross (Wed Oct 20 2010 - 11:44:38 PDT)
  - Re: [AMBER] Problem using graphite strucute in equil MD Bongkeun Kim (Wed Oct 20 2010 - 13:54:28 PDT)
- Re: [AMBER] Problem using graphite strucute in equil MD Bill Ross (Wed Oct 20 2010 - 14:26:33 PDT)
  - Re: [AMBER] Problem using graphite strucute in equil MD Bongkeun Kim (Wed Oct 20 2010 - 15:48:09 PDT)
- Re: [AMBER] Problem using graphite strucute in equil MD Bill Ross (Wed Oct 20 2010 - 16:34:21 PDT)
  - Re: [AMBER] Problem using graphite strucute in equil MD Bongkeun Kim (Wed Oct 20 2010 - 16:38:24 PDT)
  - Re: [AMBER] Problem using graphite strucute in equil MD Bongkeun Kim (Wed Oct 20 2010 - 23:13:43 PDT)
- Re: [AMBER] Problem using graphite strucute in equil MD Bill Ross (Thu Oct 21 2010 - 10:00:05 PDT)
  - Re: [AMBER] Problem using graphite strucute in equil MD Bongkeun Kim (Thu Oct 21 2010 - 11:13:45 PDT)
- Re: [AMBER] Problem using graphite strucute in equil MD Bill Ross (Thu Oct 21 2010 - 11:39:25 PDT)
  - Re: [AMBER] Problem using graphite structure in equil MD Bongkeun Kim (Thu Oct 21 2010 - 16:09:14 PDT)
    - Re: [AMBER] Problem using graphite structure in equil MD Bill Ross (Thu Oct 21 2010 - 16:31:02 PDT)
[AMBER] Problem in mm_pbsa Kshatresh Dutta Dubey (Wed Oct 20 2010 - 00:00:54 PDT)
- Re: [AMBER] Problem in mm_pbsa Rubben Torella (Wed Oct 20 2010 - 00:41:40 PDT)
  - Re: [AMBER] Problem in mm_pbsa Kshatresh Dutta Dubey (Wed Oct 20 2010 - 01:14:49 PDT)
    - Re: [AMBER] Problem in mm_pbsa juzer stationwala (Wed Oct 20 2010 - 22:04:19 PDT)
    - Re: [AMBER] Problem in mm_pbsa Kshatresh Dutta Dubey (Thu Oct 21 2010 - 00:51:36 PDT)
[AMBER] calculate free energies using TI João Sardinha (Wed Oct 20 2010 - 04:01:55 PDT)
Re: [AMBER] Residue not recognized case (Wed Oct 20 2010 - 06:45:11 PDT)
- Re: [AMBER] Residue not recognized FyD (Wed Oct 20 2010 - 08:17:51 PDT)
- Re: [AMBER] Residue not recognized Millen, Andrea (Wed Oct 20 2010 - 09:50:23 PDT)
- Re: [AMBER] Residue not recognized Bill Ross (Wed Oct 20 2010 - 09:52:19 PDT)
[AMBER] residence time of water molecule and life time of hydrogen bonds atila petrosian (Wed Oct 20 2010 - 07:19:19 PDT)
[AMBER] Can not addions with AMOEBA ff Igor Sizov (Wed Oct 20 2010 - 10:14:39 PDT)
- Re: [AMBER] Can not addions with AMOEBA ff case (Wed Oct 20 2010 - 13:42:05 PDT)
  - Re: [AMBER] Can not addions with AMOEBA ff case (Wed Oct 20 2010 - 13:48:08 PDT)
[AMBER] NMR-restrained RNA structure refinement with amber Michael F. Summers (Wed Oct 20 2010 - 11:03:09 PDT)
[AMBER] pmemd 11 (parallel) compilation error - revisiting Alok Juneja (Wed Oct 20 2010 - 12:41:55 PDT)
- Re: [AMBER] pmemd 11 (parallel) compilation error - revisiting Ross Walker (Wed Oct 20 2010 - 13:12:00 PDT)
  - Re: [AMBER] pmemd 11 (parallel) compilation error - revisiting Alok Juneja (Wed Oct 20 2010 - 13:26:06 PDT)
    - Re: [AMBER] pmemd 11 (parallel) compilation error - revisiting Alok Juneja (Wed Oct 20 2010 - 18:31:01 PDT)
    - Re: [AMBER] pmemd 11 (parallel) compilation error - revisiting Ross Walker (Wed Oct 20 2010 - 18:48:50 PDT)
    - Re: [AMBER] pmemd 11 (parallel) compilation error - revisiting Alok Juneja (Thu Oct 21 2010 - 08:35:53 PDT)
[AMBER] J-coupling restraints Mickey Richards (Wed Oct 20 2010 - 19:12:03 PDT)
- Re: [AMBER] J-coupling restraints David A. Case (Thu Oct 21 2010 - 08:42:20 PDT)
  - Re: [AMBER] J-coupling restraints Mickey Richards (Thu Oct 21 2010 - 09:45:27 PDT)
    - Re: [AMBER] J-coupling restraints Mickey Richards (Thu Oct 21 2010 - 10:44:04 PDT)
- Re: [AMBER] J-coupling restraints Bill Ross (Thu Oct 21 2010 - 10:01:49 PDT)
[AMBER] ncsu input eduardo.troche.uvigo.es (Thu Oct 21 2010 - 08:22:05 PDT)
- Re: [AMBER] ncsu input Daniel Sindhikara (Thu Oct 21 2010 - 21:40:40 PDT)
  - Re: [AMBER] ncsu input eduardo.troche.uvigo.es (Fri Oct 22 2010 - 03:55:53 PDT)
    - Re: [AMBER] ncsu input Daniel Sindhikara (Fri Oct 22 2010 - 05:25:06 PDT)
    - Re: [AMBER] ncsu input eduardo.troche.uvigo.es (Fri Oct 22 2010 - 08:41:32 PDT)
    - Re: [AMBER] ncsu input Daniel Sindhikara (Sat Oct 23 2010 - 18:44:12 PDT)
[AMBER] Infinite covalently bonded crystals Andrew Jewett (Thu Oct 21 2010 - 17:31:58 PDT)
- Re: [AMBER] Infinite covalently bonded crystals Bill Ross (Thu Oct 21 2010 - 20:17:42 PDT)
- Re: [AMBER] Infinite covalently bonded crystals David A. Case (Fri Oct 22 2010 - 05:28:40 PDT)
[AMBER] E(QM), E(MM), and E(QM/MM) components of the potential energy in sander output Dmitry Nilov (Fri Oct 22 2010 - 05:27:48 PDT)
- Re: [AMBER] E(QM), E(MM), and E(QM/MM) components of the potential energy in sander output Andreas Goetz (Fri Oct 22 2010 - 11:37:56 PDT)
  - Re: [AMBER] E(QM), E(MM), and E(QM/MM) components of the potential energy in sander output Kshatresh Dutta Dubey (Fri Oct 22 2010 - 22:32:50 PDT)
    - Re: [AMBER] E(QM), E(MM), and E(QM/MM) components of the potential energy in sander output Dmitry Nilov (Sat Oct 23 2010 - 06:53:06 PDT)
[AMBER] Triclinic box condition for PBC Bongkeun Kim (Fri Oct 22 2010 - 10:39:04 PDT)
- Re: [AMBER] Triclinic box condition for PBC Bill Ross (Fri Oct 22 2010 - 10:56:32 PDT)
- Re: [AMBER] Triclinic box condition for PBC dcerutti.rci.rutgers.edu (Fri Oct 22 2010 - 11:14:56 PDT)
  - Re: [AMBER] Triclinic box condition for PBC Bongkeun Kim (Fri Oct 22 2010 - 12:04:24 PDT)
- Re: [AMBER] Triclinic box condition for PBC Bill Ross (Fri Oct 22 2010 - 11:35:54 PDT)
[AMBER] MMPBSA in AMBER11 zhihong ke (Fri Oct 22 2010 - 12:42:39 PDT)
- Re: [AMBER] MMPBSA in AMBER11 Bill Miller III (Fri Oct 22 2010 - 12:54:25 PDT)
- Re: [AMBER] MMPBSA in AMBER11 Jason Swails (Fri Oct 22 2010 - 18:03:19 PDT)
  - Re: [AMBER] MMPBSA in AMBER11 zhihong ke (Thu Oct 28 2010 - 13:48:10 PDT)
    - Re: [AMBER] MMPBSA in AMBER11 Bill Miller III (Thu Oct 28 2010 - 13:56:26 PDT)
    - Re: [AMBER] MMPBSA in AMBER11 Jason Swails (Thu Oct 28 2010 - 14:01:38 PDT)
[AMBER] Measure relative orientations in amber 9 Neha Gandhi (Sat Oct 23 2010 - 01:38:22 PDT)
- Re: [AMBER] Measure relative orientations in amber 9 Bill Ross (Sat Oct 23 2010 - 10:10:10 PDT)
[AMBER] Switching from NAMD to Amber for membrane Simulations Joshua Adelman (Sat Oct 23 2010 - 07:53:32 PDT)
- Re: [AMBER] Switching from NAMD to Amber for membrane Simulations Ross Walker (Sat Oct 23 2010 - 10:30:10 PDT)
  - Re: [AMBER] Switching from NAMD to Amber for membrane Simulations Francesco Pietra (Sat Oct 23 2010 - 10:55:35 PDT)
[AMBER] Nose Hoover thermostat Sangita Kachhap (Sat Oct 23 2010 - 11:43:21 PDT)
- Re: [AMBER] Nose Hoover thermostat case (Mon Oct 25 2010 - 05:32:14 PDT)
  - Re: [AMBER] Nose Hoover thermostat Francesco Paesani (Tue Oct 26 2010 - 07:19:45 PDT)
  - Re: [AMBER] Nose Hoover thermostat Sangita Kachhap (Thu Oct 28 2010 - 22:08:52 PDT)
    - [AMBER] leap reading of pdb files Stefano Pieraccini (Fri Oct 29 2010 - 02:51:05 PDT)
    - Re: [AMBER] leap reading of pdb files case (Fri Oct 29 2010 - 05:51:43 PDT)
[AMBER] about replica exchange Cheng-I Lee (Sun Oct 24 2010 - 17:01:08 PDT)
- Re: [AMBER] about replica exchange Daniel Roe (Mon Oct 25 2010 - 04:46:01 PDT)
  - Re: [AMBER] about replica exchange Cheng-I Lee (Mon Oct 25 2010 - 05:10:38 PDT)
[AMBER] pmemd installation error M. Reza Ganjalikhany (Mon Oct 25 2010 - 02:29:10 PDT)
- Re: [AMBER] pmemd installation error Jason Swails (Mon Oct 25 2010 - 04:23:19 PDT)
  - [AMBER] xleap, xaLeap is missing after Amber10 installation Shaandar Nyamtulga (Mon Oct 25 2010 - 22:54:49 PDT)
    - Re: [AMBER] xleap, xaLeap is missing after Amber10 installation Ross Walker (Mon Oct 25 2010 - 23:07:15 PDT)
    - Re: [AMBER] xleap, xaLeap is missing after Amber10 installation Shaandar Nyamtulga (Tue Oct 26 2010 - 05:55:08 PDT)
    - [AMBER] xleap, xaLeap and X11 Shaandar Nyamtulga (Tue Oct 26 2010 - 22:49:32 PDT)
    - Re: [AMBER] xleap, xaLeap and X11 Jason Swails (Wed Oct 27 2010 - 10:25:09 PDT)
  - Re: [AMBER] pmemd installation error M. Reza Ganjalikhany (Thu Oct 28 2010 - 04:01:00 PDT)
    - Re: [AMBER] pmemd installation error Per Jr. Greisen (Thu Oct 28 2010 - 04:09:02 PDT)
[AMBER] water molecule positions Beale, John (Mon Oct 25 2010 - 06:03:47 PDT)
[AMBER] UREABOX tleap Michela Candotti (Mon Oct 25 2010 - 08:01:56 PDT)
- Re: [AMBER] UREABOX tleap M. L. Dodson (Mon Oct 25 2010 - 08:09:08 PDT)
- Re: [AMBER] UREABOX tleap Bill Ross (Mon Oct 25 2010 - 10:02:04 PDT)
[AMBER] Can we run sanders on GPU ? setyanto md (Mon Oct 25 2010 - 22:24:32 PDT)
- Re: [AMBER] Can we run sanders on GPU ? Ross Walker (Mon Oct 25 2010 - 22:38:37 PDT)
  - Re: [AMBER] Can we run sanders on GPU ? c00jsw00 (Mon Oct 25 2010 - 22:59:58 PDT)
    - Re: [AMBER] Can we run sanders on GPU ? Ross Walker (Mon Oct 25 2010 - 23:00:10 PDT)
    - Re: [AMBER] Can we run sanders on GPU ? setyanto md (Mon Nov 22 2010 - 19:25:44 PST)
    - Re: [AMBER] Can we run sanders on GPU ? Jason Swails (Tue Nov 23 2010 - 05:52:11 PST)
    - Re: [AMBER] Can we run sanders on GPU ? setyanto md (Thu Nov 25 2010 - 07:06:22 PST)
  - Re: [AMBER] Can we run sanders on GPU ? setyanto md (Mon Oct 25 2010 - 23:58:29 PDT)
    - Re: [AMBER] Can we run sanders on GPU ? Ross Walker (Tue Oct 26 2010 - 09:02:28 PDT)
[AMBER] about Error while mapping in energy decomposition (Amber 10) Liane Saiz Urra (Tue Oct 26 2010 - 02:42:44 PDT)
[AMBER] HOW TO PREPARE MODIFIED NUCLEOSIDE Indrajit Deb (Tue Oct 26 2010 - 05:11:07 PDT)
- Re: [AMBER] HOW TO PREPARE MODIFIED NUCLEOSIDE Dmitry Nilov (Tue Oct 26 2010 - 05:59:13 PDT)
[AMBER] Trajectory Minimization John S (Tue Oct 26 2010 - 06:57:23 PDT)
- Re: [AMBER] Trajectory Minimization Thomas Cheatham (Tue Oct 26 2010 - 07:26:00 PDT)
  - Re: [AMBER] Trajectory Minimization John S (Tue Oct 26 2010 - 07:43:53 PDT)
    - Re: [AMBER] Trajectory Minimization John S (Tue Oct 26 2010 - 09:24:08 PDT)
    - Re: [AMBER] Trajectory Minimization Thomas Cheatham (Tue Oct 26 2010 - 09:33:49 PDT)
[AMBER] Removing rotational motion John S (Tue Oct 26 2010 - 07:08:00 PDT)
- Re: [AMBER] Removing rotational motion Jason Swails (Wed Oct 27 2010 - 10:28:11 PDT)
[AMBER] How to get the PDB file? xuemeiwang1103 (Tue Oct 26 2010 - 18:24:24 PDT)
- Re: [AMBER] How to get the PDB file? Bill Miller III (Tue Oct 26 2010 - 18:31:15 PDT)
- Re: [AMBER] How to get the PDB file? Dima A Sabbah (Wed Oct 27 2010 - 08:02:23 PDT)
[AMBER] sidechain side chain interaction within one protein Rilei Yu (Tue Oct 26 2010 - 21:30:19 PDT)
[AMBER] radial distibution function subrata paul (Tue Oct 26 2010 - 21:41:05 PDT)
- Re: [AMBER] radial distibution function M. L. Dodson (Wed Oct 27 2010 - 07:36:54 PDT)
[AMBER] cannot generate snapshot_statistics.in file bin wang (Wed Oct 27 2010 - 08:52:49 PDT)
- Re: [AMBER] cannot generate snapshot_statistics.in file Bill Miller III (Wed Oct 27 2010 - 08:57:58 PDT)
  - Re: [AMBER] cannot generate snapshot_statistics.in file bin wang (Wed Oct 27 2010 - 15:58:03 PDT)
    - Re: [AMBER] cannot generate snapshot_statistics.in file Dwight McGee (Wed Oct 27 2010 - 16:11:27 PDT)
    - Re: [AMBER] cannot generate snapshot_statistics.in file bin wang (Fri Oct 29 2010 - 07:10:42 PDT)
    - Re: [AMBER] cannot generate snapshot_statistics.in file Bill Miller III (Fri Oct 29 2010 - 07:41:31 PDT)
    - Re: [AMBER] cannot generate snapshot_statistics.in file Dwight McGee (Wed Oct 27 2010 - 16:14:22 PDT)
[AMBER] Trajectory John S (Wed Oct 27 2010 - 10:15:23 PDT)
- Re: [AMBER] Trajectory Carlos Simmerling (Wed Oct 27 2010 - 11:17:17 PDT)
  - Re: [AMBER] Trajectory John S (Mon Nov 22 2010 - 22:27:12 PST)
    - Re: [AMBER] Trajectory Carlos Simmerling (Tue Nov 23 2010 - 05:43:26 PST)
    - Re: [AMBER] Trajectory John S (Tue Nov 23 2010 - 11:18:40 PST)
    - Re: [AMBER] Trajectory Thomas Cheatham III (Tue Nov 23 2010 - 13:40:21 PST)
    - Re: [AMBER] Trajectory John S (Tue Nov 23 2010 - 15:04:31 PST)
    - Re: [AMBER] Trajectory Carlos Simmerling (Tue Nov 23 2010 - 15:42:49 PST)
    - Re: [AMBER] Trajectory John S (Tue Nov 23 2010 - 18:13:15 PST)
    - Re: [AMBER] Trajectory Carlos Simmerling (Wed Nov 24 2010 - 03:22:18 PST)
    - Re: [AMBER] Trajectory John S (Thu Dec 09 2010 - 14:52:19 PST)
[AMBER] Time-average restraint question Mickey Richards (Wed Oct 27 2010 - 11:03:37 PDT)
[AMBER] 1D-RISM in NAB: compressibility units Andrej Frolov (Thu Oct 28 2010 - 00:52:26 PDT)
- Re: [AMBER] 1D-RISM in NAB: compressibility units Tyler Luchko (Thu Oct 28 2010 - 07:50:07 PDT)
[AMBER] free energy landscape fancy2012 (Thu Oct 28 2010 - 01:11:42 PDT)
- Re: [AMBER] free energy landscape Jason Swails (Thu Oct 28 2010 - 06:17:16 PDT)
- Re: [AMBER] free energy landscape Gustavo Seabra (Thu Oct 28 2010 - 09:41:06 PDT)
[AMBER] 3D-RISM in NAB: solvent susceptibility function support Andrej Frolov (Thu Oct 28 2010 - 01:11:52 PDT)
- Re: [AMBER] 3D-RISM in NAB: solvent susceptibility function support Tyler Luchko (Thu Oct 28 2010 - 07:35:38 PDT)
  - Re: [AMBER] 3D-RISM in NAB: solvent susceptibility function support Andrej Frolov (Thu Oct 28 2010 - 07:53:43 PDT)
    - Re: [AMBER] 3D-RISM in NAB: solvent susceptibility function support Tyler Luchko (Thu Oct 28 2010 - 08:54:41 PDT)
[AMBER] regarding 'ambpdb' command in amber tools 1.4 aneesh cna (Thu Oct 28 2010 - 03:33:51 PDT)
- Re: [AMBER] regarding 'ambpdb' command in amber tools 1.4 Dmitry Nilov (Thu Oct 28 2010 - 03:38:04 PDT)
- Re: [AMBER] regarding 'ambpdb' command in amber tools 1.4 case (Thu Oct 28 2010 - 04:41:08 PDT)
[AMBER] sander termination for large [NaCl] concentration Santosh Mogurampelly (Thu Oct 28 2010 - 05:17:50 PDT)
- Re: [AMBER] sander termination for large [NaCl] concentration Ben Roberts (Thu Oct 28 2010 - 06:12:56 PDT)
[AMBER] 2drms in ptraj Beale, John (Thu Oct 28 2010 - 06:03:37 PDT)
- Re: [AMBER] 2drms in ptraj Carlos Simmerling (Thu Oct 28 2010 - 08:48:38 PDT)
- Re: [AMBER] 2drms in ptraj Daniel Sindhikara (Thu Oct 28 2010 - 23:24:10 PDT)
[AMBER] Update of renamed "initial_traj" to"strip_mdcrd" for MMPBSA.py in AMBER 11 Manual. Rafi Ahmad (Thu Oct 28 2010 - 06:58:26 PDT)
- Re: [AMBER] Update of renamed "initial_traj" to"strip_mdcrd" for MMPBSA.py in AMBER 11 Manual. Jason Swails (Thu Oct 28 2010 - 07:15:03 PDT)
[AMBER] cyclic_peptide lara lara (Thu Oct 28 2010 - 08:50:24 PDT)
- Re: [AMBER] cyclic_peptide Carlos Simmerling (Thu Oct 28 2010 - 08:51:42 PDT)
- Re: [AMBER] cyclic_peptide Jason Swails (Thu Oct 28 2010 - 08:58:14 PDT)
[AMBER] Protein Folding Jordan, Brad (Thu Oct 28 2010 - 11:25:40 PDT)
- Re: [AMBER] Protein Folding Carlos Simmerling (Thu Oct 28 2010 - 11:34:02 PDT)
[AMBER] Targeted MD Jordan, Brad (Thu Oct 28 2010 - 13:57:26 PDT)
[AMBER] MMGBSA issue with covalently bound parameterized ligand Christopher Roberts (Thu Oct 28 2010 - 14:29:31 PDT)
- [AMBER] OpenMPI or MPICH2 for paralel installation? Shaandar Nyamtulga (Thu Oct 28 2010 - 19:31:41 PDT)
  - Re: [AMBER] OpenMPI or MPICH2 for paralel installation? Ye MEI (Thu Oct 28 2010 - 20:49:48 PDT)
  - Re: [AMBER] OpenMPI or MPICH2 for paralel installation? Vitaly Chaban (Thu Oct 28 2010 - 21:31:24 PDT)
    - Re: [AMBER] OpenMPI or MPICH2 for paralel installation? Jason Swails (Fri Oct 29 2010 - 06:01:05 PDT)
[AMBER] PARMSCAN Sarath Chandra Dantu (Fri Oct 29 2010 - 07:34:40 PDT)
[AMBER] Error message from binding_energy.mmpbsa bin wang (Fri Oct 29 2010 - 07:50:19 PDT)
- Re: [AMBER] Error message from binding_energy.mmpbsa Bill Miller III (Fri Oct 29 2010 - 08:09:03 PDT)
  - Re: [AMBER] Error message from binding_energy.mmpbsa bin wang (Fri Oct 29 2010 - 08:46:13 PDT)
    - Re: [AMBER] Error message from binding_energy.mmpbsa Jason Swails (Fri Oct 29 2010 - 08:50:13 PDT)
    - Re: [AMBER] Error message from binding_energy.mmpbsa bin wang (Fri Oct 29 2010 - 12:13:58 PDT)
    - Re: [AMBER] Error message from binding_energy.mmpbsa Jason Swails (Fri Oct 29 2010 - 12:17:18 PDT)
    - Re: [AMBER] Error message from binding_energy.mmpbsa bin wang (Fri Oct 29 2010 - 13:10:44 PDT)
    - Re: [AMBER] Error message from binding_energy.mmpbsa Jason Swails (Fri Oct 29 2010 - 13:16:44 PDT)
    - Re: [AMBER] Error message from binding_energy.mmpbsa bin wang (Fri Oct 29 2010 - 13:35:28 PDT)
- Re: [AMBER] Error message from binding_energy.mmpbsa Jason Swails (Thu Nov 04 2010 - 04:49:21 PDT)
  - Re: [AMBER] Error message from binding_energy.mmpbsa bin wang (Thu Nov 04 2010 - 06:49:36 PDT)
    - Re: [AMBER] Error message from binding_energy.mmpbsa Jason Swails (Thu Nov 04 2010 - 06:52:30 PDT)
    - Re: [AMBER] Error message from binding_energy.mmpbsa bin wang (Thu Nov 04 2010 - 11:53:52 PDT)
[AMBER] extract distribution from PairwiseDistances Yannick SPILL (Fri Oct 29 2010 - 07:57:18 PDT)
- Re: [AMBER] extract distribution from PairwiseDistances Jianyin Shao (Fri Oct 29 2010 - 09:02:28 PDT)
  - Re: [AMBER] extract distribution from PairwiseDistances Yannick Spill (Fri Oct 29 2010 - 10:03:09 PDT)
    - Re: [AMBER] extract distribution from PairwiseDistances Jianyin Shao (Fri Oct 29 2010 - 11:47:39 PDT)
    - Re: [AMBER] extract distribution from PairwiseDistances Yannick SPILL (Tue Nov 02 2010 - 06:12:14 PDT)
- Re: [AMBER] extract distribution from PairwiseDistances Bill Ross (Tue Nov 02 2010 - 10:14:48 PDT)
[AMBER] Targeted MD - minimization problem Jordan, Brad (Fri Oct 29 2010 - 09:33:51 PDT)
- Re: [AMBER] Targeted MD - minimization problem Carlos Simmerling (Fri Oct 29 2010 - 09:36:26 PDT)
  - Re: [AMBER] Targeted MD - minimization problem Jason Swails (Fri Oct 29 2010 - 10:39:14 PDT)
    - Re: [AMBER] Targeted MD - minimization problem Jordan, Brad (Wed Nov 03 2010 - 11:05:31 PDT)
[AMBER] Running NAB Arun Gupta (Fri Oct 29 2010 - 12:56:47 PDT)
- Re: [AMBER] Running NAB case (Fri Oct 29 2010 - 13:04:52 PDT)
  - Re: [AMBER] Running NAB Arun Gupta (Fri Oct 29 2010 - 13:09:17 PDT)
    - Re: [AMBER] Running NAB Jason Swails (Fri Oct 29 2010 - 13:13:45 PDT)
    - Re: [AMBER] Running NAB Arun Gupta (Fri Oct 29 2010 - 13:22:09 PDT)
[AMBER] Stitching amino acid templates- sequence command tanya singh (Sat Oct 30 2010 - 08:51:42 PDT)
[AMBER] GPU high temperature unfolding simulation andy ng (Sat Oct 30 2010 - 20:30:36 PDT)
- Re: [AMBER] GPU high temperature unfolding simulation Ross Walker (Sat Oct 30 2010 - 22:47:36 PDT)
  - Re: [AMBER] GPU high temperature unfolding simulation Carlos Simmerling (Sun Oct 31 2010 - 04:49:52 PDT)
    - Re: [AMBER] GPU high temperature unfolding simulation andy ng (Tue Nov 02 2010 - 17:29:27 PDT)
- Re: [AMBER] GPU high temperature unfolding simulation Ye MEI (Sun Oct 31 2010 - 09:29:04 PDT)
  - Re: [AMBER] GPU high temperature unfolding simulation Ross Walker (Sun Oct 31 2010 - 11:25:59 PDT)
  - Re: [AMBER] GPU high temperature unfolding simulation Ross Walker (Tue Nov 02 2010 - 09:07:13 PDT)
[AMBER] MMPBSA ligand/receptor selections Logan Ahlstrom (Sun Oct 31 2010 - 15:14:20 PDT)
- Re: [AMBER] MMPBSA ligand/receptor selections Jason Swails (Sun Oct 31 2010 - 15:30:57 PDT)
- Re: [AMBER] MMPBSA ligand/receptor selections mirage . (Fri Nov 05 2010 - 04:52:35 PDT)
[AMBER] Interaction energy calculation aneesh cna (Sun Oct 31 2010 - 22:04:46 PDT)
- Re: [AMBER] Interaction energy calculation Alessandro Nascimento (Mon Nov 01 2010 - 09:39:19 PDT)
[AMBER] SCC-DFT orbitals arikcohen (Sun Oct 31 2010 - 22:24:38 PDT)
- Re: [AMBER] SCC-DFT orbitals Gustavo Seabra (Mon Nov 01 2010 - 04:30:06 PDT)
  - Re: [AMBER] SCC-DFT orbitals arikcohen (Mon Nov 01 2010 - 11:20:39 PDT)
    - Re: [AMBER] SCC-DFT orbitals Gustavo Seabra (Mon Nov 01 2010 - 11:28:58 PDT)
[AMBER] Forward: Sander file name length bug Don.Bashford.stjude.org (Mon Nov 01 2010 - 09:10:58 PDT)
- Re: [AMBER] Forward: Sander file name length bug case (Mon Nov 01 2010 - 09:49:33 PDT)
[AMBER] possible bug: problem with defining per-residue energies using RRES & LRES g t (Mon Nov 01 2010 - 12:54:26 PDT)
- Re: [AMBER] possible bug: problem with defining per-residue energies using RRES & LRES Jason Swails (Mon Nov 01 2010 - 13:06:12 PDT)
  - Re: [AMBER] possible bug: problem with defining per-residue energies using RRES & LRES g t (Fri Nov 05 2010 - 10:43:25 PDT)
    - Re: [AMBER] possible bug: problem with defining per-residue energies using RRES & LRES Jason Swails (Fri Nov 05 2010 - 11:03:45 PDT)
    - Re: [AMBER] possible bug: problem with defining per-residue energies using RRES & LRES g t (Fri Nov 05 2010 - 11:05:42 PDT)
    - Re: [AMBER] possible bug: problem with defining per-residue energies using RRES & LRES case (Fri Nov 05 2010 - 12:53:23 PDT)
    - Re: [AMBER] possible bug: problem with defining per-residue energies using RRES & LRES Jason Swails (Fri Nov 05 2010 - 14:20:33 PDT)
[AMBER] RESP at antechamber juan roman (Mon Nov 01 2010 - 21:16:55 PDT)
- Re: [AMBER] RESP at antechamber Jason Swails (Tue Nov 02 2010 - 06:13:53 PDT)
  - Re: [AMBER] RESP at antechamber juan roman (Sat Nov 06 2010 - 15:49:08 PDT)
    - Re: [AMBER] RESP at antechamber juan roman (Sat Nov 06 2010 - 15:50:46 PDT)
[AMBER] AMBER: molsurf.c error 王亚茹 (Tue Nov 02 2010 - 03:10:05 PDT)
- Re: [AMBER] AMBER: molsurf.c error Jason Swails (Tue Nov 02 2010 - 06:18:33 PDT)
[AMBER] Amber10 segmentation fault with AIX Andrew Emerson (Tue Nov 02 2010 - 04:22:00 PDT)
- Re: [AMBER] Amber10 segmentation fault with AIX Ross Walker (Tue Nov 02 2010 - 09:07:13 PDT)
  - Re: [AMBER] Amber10 segmentation fault with AIX Andrew Emerson (Thu Nov 04 2010 - 02:45:50 PDT)
[AMBER] Cluster PairwiseDistances Beale, John (Tue Nov 02 2010 - 06:29:58 PDT)
[AMBER] Plumed David Beveridge (Tue Nov 02 2010 - 07:13:06 PDT)
[AMBER] Proj into RMSD Space David Beveridge (Tue Nov 02 2010 - 07:15:50 PDT)
[AMBER] Plumed David Beveridge (Tue Nov 02 2010 - 07:42:03 PDT)
[AMBER] Problem of RMSd plotting using merged tarjectories Hoshin Kim (Tue Nov 02 2010 - 22:48:32 PDT)
- Re: [AMBER] Problem of RMSd plotting using merged tarjectories Bill Ross (Tue Nov 02 2010 - 12:21:43 PDT)
[AMBER] R.E.D.III.x tutorial1 question Computational Chemist (Tue Nov 02 2010 - 13:12:42 PDT)
- Re: [AMBER] R.E.D.III.x tutorial1 question Jason Swails (Tue Nov 02 2010 - 14:47:52 PDT)
- Re: [AMBER] R.E.D.III.x tutorial1 question FyD (Tue Nov 02 2010 - 23:53:31 PDT)
[AMBER] j-restrained peptide Rossella Noschese (Wed Nov 03 2010 - 06:07:23 PDT)
- Re: [AMBER] j-restrained peptide case (Wed Nov 03 2010 - 07:36:23 PDT)
  - Re: [AMBER] j-restrained peptide Rossella Noschese (Wed Nov 03 2010 - 09:01:55 PDT)
    - Re: [AMBER] j-restrained peptide case (Wed Nov 03 2010 - 18:01:17 PDT)
    - Re: [AMBER] j-restrained peptide Rossella Noschese (Mon Nov 22 2010 - 03:23:54 PST)
    - Re: [AMBER] j-restrained peptide Rossella Noschese (Thu Dec 02 2010 - 01:30:13 PST)
    - Re: [AMBER] j-restrained peptide case (Thu Dec 02 2010 - 05:54:35 PST)
    - Re: [AMBER] j-restrained peptide Rossella Noschese (Thu Dec 02 2010 - 06:08:33 PST)
    - Re: [AMBER] j-restrained peptide case (Wed Dec 15 2010 - 06:00:04 PST)
    - Re: [AMBER] j-restrained peptide Rossella Noschese (Wed Dec 15 2010 - 08:15:07 PST)
    - Re: [AMBER] j-restrained peptide case (Wed Dec 15 2010 - 08:37:26 PST)
    - Re: [AMBER] j-restrained peptide Rossella Noschese (Wed Dec 15 2010 - 08:49:24 PST)
    - Re: [AMBER] j-restrained peptide case (Wed Dec 15 2010 - 08:56:12 PST)
    - Re: [AMBER] j-restrained peptide Rossella Noschese (Wed Dec 15 2010 - 09:33:53 PST)
    - Re: [AMBER] j-restrained peptide case (Fri Dec 17 2010 - 11:40:14 PST)
    - Re: [AMBER] j-restrained peptide Rossella Noschese (Mon Dec 20 2010 - 02:44:34 PST)
[AMBER] using MM-PBSA with Zn ions. Roman Osman (Wed Nov 03 2010 - 09:17:13 PDT)
- Re: [AMBER] using MM-PBSA with Zn ions. Bill Miller III (Wed Nov 03 2010 - 10:02:37 PDT)
  - Re: [AMBER] using MM-PBSA with Zn ions. Roman Osman (Wed Nov 03 2010 - 11:09:44 PDT)
  - Re: [AMBER] using MM-PBSA with Zn ions. Roman Osman (Mon Nov 08 2010 - 20:05:29 PST)
[AMBER] Targeted MD Jordan, Brad (Wed Nov 03 2010 - 09:55:46 PDT)
- Re: [AMBER] Targeted MD Carlos Simmerling (Wed Nov 03 2010 - 10:03:13 PDT)
  - Re: [AMBER] Targeted MD Jordan, Brad (Wed Nov 03 2010 - 10:09:31 PDT)
[AMBER] how to change the charge in all_amino94.lib zhihong ke (Wed Nov 03 2010 - 12:53:54 PDT)
- Re: [AMBER] how to change the charge in all_amino94.lib FyD (Wed Nov 03 2010 - 13:18:32 PDT)
- Re: [AMBER] how to change the charge in all_amino94.lib Bill Ross (Wed Nov 03 2010 - 13:29:25 PDT)
- Re: [AMBER] how to change the charge in all_amino94.lib Bill Ross (Wed Nov 03 2010 - 13:32:10 PDT)
  - Re: [AMBER] how to change the charge in all_amino94.lib zhihong ke (Wed Nov 03 2010 - 13:42:56 PDT)
- Re: [AMBER] how to change the charge in all_amino94.lib Bill Ross (Wed Nov 03 2010 - 13:58:14 PDT)
[AMBER] How the box info is used Ilyas Yildirim (Wed Nov 03 2010 - 14:54:24 PDT)
- Re: [AMBER] How the box info is used Bill Ross (Wed Nov 03 2010 - 15:01:28 PDT)
  - Re: [AMBER] How the box info is used Ilyas Yildirim (Wed Nov 03 2010 - 15:22:24 PDT)
    - Re: [AMBER] How the box info is used Thomas Cheatham III (Wed Nov 03 2010 - 15:30:48 PDT)
    - Re: [AMBER] How the box info is used Ilyas Yildirim (Wed Nov 03 2010 - 18:00:56 PDT)
- Re: [AMBER] How the box info is used Bill Ross (Wed Nov 03 2010 - 15:34:27 PDT)
  - Re: [AMBER] How the box info is used Ilyas Yildirim (Wed Nov 03 2010 - 17:39:38 PDT)
- Re: [AMBER] How the box info is used Bill Ross (Wed Nov 03 2010 - 19:44:53 PDT)
  - Re: [AMBER] How the box info is used Ilyas Yildirim (Wed Nov 03 2010 - 21:48:21 PDT)
[AMBER] MMPBSA parameters Michael Petersen (Wed Nov 03 2010 - 14:58:30 PDT)
- Re: [AMBER] MMPBSA parameters Jason Swails (Wed Nov 03 2010 - 16:09:19 PDT)
[AMBER] SASA Beale, John (Thu Nov 04 2010 - 04:33:43 PDT)
- Re: [AMBER] SASA Jason Swails (Thu Nov 04 2010 - 06:13:02 PDT)
[AMBER] ptraj-area per lipid and order parameter colvin (Thu Nov 04 2010 - 05:34:33 PDT)
[AMBER] mm_pbsa.pl doesn't work after the bugfixes bin wang (Thu Nov 04 2010 - 06:58:25 PDT)
[AMBER] Binding energy and conformation John S (Thu Nov 04 2010 - 08:54:13 PDT)
- Re: [AMBER] Binding energy and conformation Jason Swails (Thu Nov 04 2010 - 09:22:35 PDT)
[AMBER] AMBER QMMM MPI scaling Xiaohu Li (Thu Nov 04 2010 - 09:10:11 PDT)
- Re: [AMBER] AMBER QMMM MPI scaling Ross Walker (Thu Nov 04 2010 - 10:38:23 PDT)
[AMBER] Release of R.E.D. Server 2.0 FyD (Thu Nov 04 2010 - 02:50:36 PDT)
[AMBER] amber tool 1.4 Install error Alice Wang (Thu Nov 04 2010 - 20:58:38 PDT)
- Re: [AMBER] amber tool 1.4 Install error David Watson (Thu Nov 04 2010 - 21:04:57 PDT)
  - Re: [AMBER] amber tool 1.4 Install error Alice Wang (Thu Nov 04 2010 - 21:08:51 PDT)
    - Re: [AMBER] amber tool 1.4 Install error Alice Wang (Thu Nov 04 2010 - 21:15:03 PDT)
    - Re: [AMBER] amber tool 1.4 Install error David Watson (Thu Nov 04 2010 - 21:21:26 PDT)
    - Re: [AMBER] amber tool 1.4 Install error case (Fri Nov 05 2010 - 06:43:27 PDT)
    - Re: [AMBER] amber tool 1.4 Install error Tru Huynh (Sun Nov 07 2010 - 16:33:44 PST)
[AMBER] Question about FEP and GPU TJ Mustard (Fri Nov 05 2010 - 15:26:54 PDT)
- Re: [AMBER] Question about FEP and GPU Jason Swails (Fri Nov 05 2010 - 20:20:09 PDT)
[AMBER] (no subject) kanon gemini (Sat Nov 06 2010 - 03:09:27 PDT)
[AMBER] solvatebox John S (Sat Nov 06 2010 - 15:17:44 PDT)
- Re: [AMBER] solvatebox case (Sat Nov 06 2010 - 19:14:33 PDT)
[AMBER] QM/MM energy terms Davide Branduardi (Sun Nov 07 2010 - 16:04:44 PST)
- Re: [AMBER] QM/MM energy terms Andreas Goetz (Sun Nov 07 2010 - 16:56:59 PST)
[AMBER] Extra points Jason S Grosch (Sun Nov 07 2010 - 19:05:15 PST)
- Re: [AMBER] Extra points case (Mon Nov 08 2010 - 05:58:55 PST)
[AMBER] How to prepare the MMPBSA file? xuemeiwang1103 (Mon Nov 08 2010 - 00:03:46 PST)
[AMBER] mmpbsa error Alice Wang (Mon Nov 08 2010 - 00:46:29 PST)
- Re: [AMBER] mmpbsa error Alice Wang (Mon Nov 08 2010 - 06:26:43 PST)
  - Re: [AMBER] mmpbsa error Ray Luo, Ph.D. (Mon Nov 08 2010 - 10:05:22 PST)
    - Re: [AMBER] mmpbsa error Alice Wang (Mon Nov 08 2010 - 15:39:47 PST)
    - Re: [AMBER] mmpbsa error Alice Wang (Mon Nov 08 2010 - 16:15:19 PST)
[AMBER] How to prepare the MMPBSA file? xuemeiwang1103 (Mon Nov 08 2010 - 01:24:23 PST)
- Re: [AMBER] How to prepare the MMPBSA file? Bill Miller III (Mon Nov 08 2010 - 03:45:12 PST)
  - Re: [AMBER] How to prepare the MMPBSA file? Jason Swails (Mon Nov 08 2010 - 08:07:21 PST)
[AMBER] About NEB calculation form amber 11 Buddhadev Maiti (Mon Nov 08 2010 - 11:26:46 PST)
- Re: [AMBER] About NEB calculation form amber 11 Carlos Simmerling (Mon Nov 08 2010 - 11:42:01 PST)
[AMBER] About NEB calculation from amber 11 Buddhadev Maiti (Mon Nov 08 2010 - 12:12:12 PST)
Re: [AMBER] Amber force-field compatibility Ross Walker (Mon Nov 08 2010 - 13:32:50 PST)
- Re: [AMBER] Amber force-field compatibility Carlos Simmerling (Mon Nov 08 2010 - 14:06:43 PST)
[AMBER] About NEB calculation from amber 11 Buddhadev Maiti (Mon Nov 08 2010 - 14:41:14 PST)
- Re: [AMBER] About NEB calculation from amber 11 Carlos Simmerling (Mon Nov 08 2010 - 16:52:44 PST)
[AMBER] Amber 11 single and multiple GPU question Frank X. Vázquez (Mon Nov 08 2010 - 15:17:15 PST)
- Re: [AMBER] Amber 11 single and multiple GPU question Scott Le Grand (Mon Nov 08 2010 - 15:52:44 PST)
- Re: [AMBER] Amber 11 single and multiple GPU question Ross Walker (Mon Nov 08 2010 - 16:50:51 PST)
[AMBER] (no subject) Yokota_Akihiro.takeda.co.jp (Tue Nov 09 2010 - 01:19:08 PST)
- Re: [AMBER] (no subject) Jason Swails (Tue Nov 09 2010 - 08:26:41 PST)
[AMBER] "excluded atoms" declaration Yokota_Akihiro.takeda.co.jp (Tue Nov 09 2010 - 01:24:23 PST)
- Re: [AMBER] "excluded atoms" declaration Carlos Simmerling (Tue Nov 09 2010 - 04:03:37 PST)
  - Re: [AMBER] "excluded atoms" declaration Jason Swails (Tue Nov 09 2010 - 09:11:10 PST)
    - Re: [AMBER] "excluded atoms" declaration Yokota_Akihiro.takeda.co.jp (Tue Nov 09 2010 - 16:55:58 PST)
  - Re: [AMBER] "excluded atoms" declaration Yokota_Akihiro.takeda.co.jp (Tue Nov 09 2010 - 16:37:44 PST)
[AMBER] RMSD vs reference substructure Kasprzak, Wojciech (NIH/NCI) [C] (Tue Nov 09 2010 - 06:29:19 PST)
- Re: [AMBER] RMSD vs reference substructure Thomas Cheatham (Tue Nov 09 2010 - 06:45:14 PST)
[AMBER] Problem in MD simulations of DNA using ABC protocol abc def (Tue Nov 09 2010 - 09:54:25 PST)
- Re: [AMBER] Problem in MD simulations of DNA using ABC protocol Thomas Cheatham III (Tue Nov 09 2010 - 10:35:29 PST)
[AMBER] Inquire about AMBER10 ? Xingqing Xiao (Tue Nov 09 2010 - 14:15:24 PST)
- Re: [AMBER] Inquire about AMBER10 ? Jason Swails (Tue Nov 09 2010 - 15:06:15 PST)
  - Re: [AMBER] Inquire about AMBER10 ? Jason Swails (Tue Nov 09 2010 - 15:10:01 PST)
[AMBER] mmpbsa.py - weird nmode results Khaled Barakat (Tue Nov 09 2010 - 16:08:45 PST)
- Re: [AMBER] mmpbsa.py - weird nmode results Bill Miller III (Tue Nov 09 2010 - 18:03:16 PST)
  - Re: [AMBER] mmpbsa.py - weird nmode results Jason Swails (Wed Nov 10 2010 - 07:01:35 PST)
[AMBER] Counting water molecules aneesh cna (Tue Nov 09 2010 - 21:36:39 PST)
- [AMBER] about dihedralcluster Balazs Jojart (Wed Nov 10 2010 - 04:56:49 PST)
  - Re: [AMBER] about dihedralcluster Daniel Roe (Wed Nov 10 2010 - 09:04:36 PST)
    - Re: [AMBER] about dihedralcluster Balazs Jojart (Wed Nov 10 2010 - 11:36:52 PST)
[AMBER] About NEB calculation in NPT ensemble Buddhadev Maiti (Wed Nov 10 2010 - 08:06:28 PST)
- Re: [AMBER] About NEB calculation in NPT ensemble Carlos Simmerling (Wed Nov 10 2010 - 08:08:00 PST)
[AMBER] MMPBSA.py Error: Unknown block, '&decomp'. Check input! kbarakat.ualberta.ca (Wed Nov 10 2010 - 12:09:19 PST)
- Re: [AMBER] MMPBSA.py Error: Unknown block, '&decomp'. Check input! Bill Miller III (Wed Nov 10 2010 - 12:18:09 PST)
  - Re: [AMBER] MMPBSA.py Error: Unknown block, '&decomp'. Check input! Jason Swails (Wed Nov 10 2010 - 13:44:40 PST)
[AMBER] relaxation of the density correlation functions of a molecule Philippe Pinard (Wed Nov 10 2010 - 14:06:57 PST)
- Re: [AMBER] relaxation of the density correlation functions of a molecule Philippe Pinard (Fri Nov 12 2010 - 08:20:30 PST)
[AMBER] Serious problem at specific time point Hoshin Kim (Wed Nov 10 2010 - 00:39:34 PST)
- Re: [AMBER] Serious problem at specific time point Bill Ross (Wed Nov 10 2010 - 15:48:47 PST)
- Re: [AMBER] Serious problem at specific time point Jason Swails (Wed Nov 10 2010 - 15:53:24 PST)
- Re: [AMBER] Serious problem at specific time point Thomas Cheatham III (Wed Nov 10 2010 - 16:09:37 PST)
  - Re: [AMBER] Serious problem at specific time point Jason Swails (Thu Nov 11 2010 - 05:46:40 PST)
    - Re: [AMBER] Serious problem at specific time point Hoshin Kim (Wed Nov 10 2010 - 23:31:01 PST)
- Re: [AMBER] Serious problem at specific time point Bill Ross (Thu Nov 11 2010 - 13:35:27 PST)
- Re: [AMBER] Serious problem at specific time point Hoshin Kim (Wed Dec 01 2010 - 20:34:44 PST)
[AMBER] To All - Consider Switching to NetCDF Daniel Roe (Thu Nov 11 2010 - 05:58:30 PST)
[AMBER] Compiling Ambertools 1.4 on MacBook SnowLeopard10.6.4 Dean Cuebas (Thu Nov 11 2010 - 08:19:03 PST)
- Re: [AMBER] Compiling Ambertools 1.4 on MacBook SnowLeopard10.6.4 Jason Swails (Thu Nov 11 2010 - 08:36:37 PST)
  - Re: [AMBER] Compiling Ambertools 1.4 on MacBook SnowLeopard10.6.4 Dean Cuebas (Fri Nov 12 2010 - 12:16:06 PST)
    - Re: [AMBER] Compiling Ambertools 1.4 on MacBook SnowLeopard10.6.4 Jason Swails (Fri Nov 12 2010 - 12:42:22 PST)
    - Re: [AMBER] Compiling Ambertools 1.4 on MacBook SnowLeopard10.6.4 Dean Cuebas (Fri Nov 12 2010 - 14:28:52 PST)
- Re: [AMBER] Compiling Ambertools 1.4 on MacBook SnowLeopard10.6.4 David Watson (Thu Nov 11 2010 - 08:37:20 PST)
  - Re: [AMBER] Compiling Ambertools 1.4 on MacBook SnowLeopard10.6.4 Jason Swails (Thu Nov 11 2010 - 09:18:54 PST)
- Re: [AMBER] Compiling Ambertools 1.4 on MacBook SnowLeopard10.6.4 Daniel Roe (Thu Nov 11 2010 - 08:42:11 PST)
  - Re: [AMBER] Compiling Ambertools 1.4 on MacBook SnowLeopard10.6.4 Jason Swails (Thu Nov 11 2010 - 09:23:50 PST)
- Re: [AMBER] Compiling Ambertools 1.4 on MacBook SnowLeopard10.6.4 Bill Ross (Thu Nov 11 2010 - 09:42:00 PST)
[AMBER] mm_pbsa.pl and MMPBSA.py issues in Amber-11 Jemmy Hu (Thu Nov 11 2010 - 10:52:18 PST)
- Re: [AMBER] mm_pbsa.pl and MMPBSA.py issues in Amber-11 Jason Swails (Thu Nov 11 2010 - 10:59:06 PST)
  - Re: [AMBER] mm_pbsa.pl and MMPBSA.py issues in Amber-11 Jemmy Hu (Thu Nov 11 2010 - 11:46:35 PST)
    - Re: [AMBER] mm_pbsa.pl and MMPBSA.py issues in Amber-11 Jason Swails (Thu Nov 11 2010 - 12:50:12 PST)
[AMBER] Atom type assignment using GAFF abc def (Thu Nov 11 2010 - 18:02:43 PST)
- [AMBER] Fwd: Atom type assignment using GAFF abc def (Fri Nov 12 2010 - 06:55:37 PST)
[AMBER] decomposition problems fancy2012 (Thu Nov 11 2010 - 18:13:42 PST)
- Re: [AMBER] decomposition problems Bill Miller III (Thu Nov 11 2010 - 18:18:53 PST)
- Re: [AMBER] decomposition problems fancy2012 (Sat Nov 13 2010 - 01:34:44 PST)
- Re: [AMBER] decomposition problems fancy2012 (Sat Nov 13 2010 - 17:46:31 PST)
[AMBER] about MMPBSA xuemeiwang1103 (Fri Nov 12 2010 - 00:07:21 PST)
[AMBER] Regarding Hydrogen Bonds Ashish Runthala (Fri Nov 12 2010 - 01:11:42 PST)
[AMBER] nonpolar term in MM-PBSA Chanchal (Fri Nov 12 2010 - 07:50:17 PST)
- Re: [AMBER] nonpolar term in MM-PBSA Jason Swails (Fri Nov 12 2010 - 08:02:11 PST)
  - Re: [AMBER] nonpolar term in MM-PBSA Chanchal (Fri Nov 12 2010 - 08:14:52 PST)
[AMBER] protonate a non standard residu Philippe Pinard (Fri Nov 12 2010 - 08:19:22 PST)
- Re: [AMBER] protonate a non standard residu Jason Swails (Fri Nov 12 2010 - 08:34:55 PST)
- Re: [AMBER] protonate a non standard residu Philippe Pinard (Fri Nov 12 2010 - 08:41:46 PST)
[AMBER] how to configure/compile to get sander.RISM? Magdalena Gruziel (Fri Nov 12 2010 - 10:40:11 PST)
- Re: [AMBER] how to configure/compile to get sander.RISM? Jason Swails (Fri Nov 12 2010 - 11:12:13 PST)
  - Re: [AMBER] how to configure/compile to get sander.RISM? Tyler Luchko (Fri Nov 12 2010 - 11:29:24 PST)
[AMBER] can mmpbsa calculation be restarted by the file "restrt"? Alice Wang (Sat Nov 13 2010 - 19:17:13 PST)
- Re: [AMBER] can mmpbsa calculation be restarted by the file "restrt"? Jason Swails (Sat Nov 13 2010 - 22:02:56 PST)
  - [AMBER] Amber10 installation problem on MPICH1 Shaandar Nyamtulga (Mon Nov 15 2010 - 20:02:14 PST)
    - Re: [AMBER] Amber10 installation problem on MPICH1 Ye MEI (Mon Nov 15 2010 - 20:24:19 PST)
    - Re: [AMBER] Amber10 installation problem on MPICH1 Shaandar Nyamtulga (Mon Nov 15 2010 - 20:45:34 PST)
    - Re: [AMBER] Amber10 installation problem on MPICH1 Ye MEI (Mon Nov 15 2010 - 20:59:29 PST)
    - Re: [AMBER] Amber10 installation problem on MPICH1 Shaandar Nyamtulga (Mon Nov 15 2010 - 21:33:13 PST)
    - Re: [AMBER] Amber10 installation problem on MPICH1 case (Tue Nov 16 2010 - 04:29:34 PST)
    - Re: [AMBER] Amber10 installation problem on MPICH1 Shaandar Nyamtulga (Tue Nov 16 2010 - 18:21:24 PST)
    - Re: [AMBER] Amber10 installation problem on MPICH1 Shaandar Nyamtulga (Tue Nov 16 2010 - 18:38:52 PST)
    - Re: [AMBER] Amber10 installation problem on MPICH1 Jason Swails (Tue Nov 16 2010 - 20:04:12 PST)
    - Re: [AMBER] Amber10 installation problem on MPICH1 Shaandar Nyamtulga (Thu Nov 18 2010 - 00:32:37 PST)
    - Re: [AMBER] Amber10 installation problem on MPICH1 case (Thu Nov 18 2010 - 04:51:17 PST)
    - [AMBER] Amber10 installation problem Shaandar Nyamtulga (Tue Nov 23 2010 - 19:43:57 PST)
    - Re: [AMBER] Amber10 installation problem case (Wed Nov 24 2010 - 07:29:03 PST)
[AMBER] about MMPBSA xuemeiwang1103 (Sat Nov 13 2010 - 19:59:42 PST)
- Re: [AMBER] about MMPBSA Dwight McGee (Sun Nov 14 2010 - 15:19:07 PST)
[AMBER] GPU related issues Ye MEI (Sun Nov 14 2010 - 19:45:11 PST)
- Re: [AMBER] GPU related issues case (Mon Nov 15 2010 - 04:48:03 PST)
- Re: [AMBER] GPU related issues Ross Walker (Fri Nov 19 2010 - 09:23:48 PST)
  - Re: [AMBER] GPU related issues Scott Le Grand (Fri Nov 19 2010 - 09:38:12 PST)
    - Re: [AMBER] GPU related issues/GTX400 series Sergio R Aragon (Fri Nov 19 2010 - 10:16:56 PST)
    - Re: [AMBER] GPU related issues/GTX400 series Scott Le Grand (Fri Nov 19 2010 - 20:23:13 PST)
    - Re: [AMBER] GPU related issues/GTX400 series Gould, Ian R (Sat Nov 20 2010 - 02:44:08 PST)
    - Re: [AMBER] GPU related issues/GTX400 series and GTX580 Gould, Ian R (Wed Nov 24 2010 - 03:23:55 PST)
    - Re: [AMBER] GPU related issues/GTX400 series tanya singh (Sat Nov 20 2010 - 04:32:04 PST)
[AMBER] ptraj distance mirage . (Mon Nov 15 2010 - 00:19:51 PST)
[AMBER] Watershell fernando (Mon Nov 15 2010 - 01:18:23 PST)
[AMBER] metadynamics fancy2012 (Mon Nov 15 2010 - 05:31:16 PST)
- Re: [AMBER] metadynamics Jason Swails (Mon Nov 15 2010 - 06:25:18 PST)
  - Re: [AMBER] metadynamics fancy2012 (Tue Nov 16 2010 - 03:10:00 PST)
- Re: [AMBER] metadynamics Marek Maly (Mon Nov 15 2010 - 06:46:58 PST)
  - [AMBER] Citation of Amber Giorgos Lamprinidis (Mon Nov 15 2010 - 06:59:16 PST)
    - Re: [AMBER] Citation of Amber Marek Maly (Mon Nov 15 2010 - 07:08:08 PST)
- Re: [AMBER] metadynamics Davide Branduardi (Mon Nov 15 2010 - 07:21:51 PST)
[AMBER] mmpbsa with rigid bonds ? Jose Borreguero (Mon Nov 15 2010 - 06:01:25 PST)
- Re: [AMBER] mmpbsa with rigid bonds ? Bill Miller III (Mon Nov 15 2010 - 06:14:41 PST)
  - Re: [AMBER] mmpbsa with rigid bonds ? Jose Borreguero (Mon Nov 15 2010 - 07:40:41 PST)
    - Re: [AMBER] mmpbsa with rigid bonds ? Jason Swails (Mon Nov 15 2010 - 07:47:54 PST)
    - Re: [AMBER] mmpbsa with rigid bonds ? Jose Borreguero (Mon Nov 15 2010 - 08:20:40 PST)
- Re: [AMBER] mmpbsa with rigid bonds ? Adrian Roitberg (Mon Nov 15 2010 - 06:37:45 PST)
[AMBER] Sander with restrained atoms Dian Jiao (Mon Nov 15 2010 - 14:04:31 PST)
- Re: [AMBER] Sander with restrained atoms case (Mon Nov 15 2010 - 18:52:16 PST)
  - Re: [AMBER] Sander with restrained atoms Dian Jiao (Mon Nov 15 2010 - 20:37:48 PST)
    - Re: [AMBER] Sander with restrained atoms case (Tue Nov 16 2010 - 04:13:48 PST)
[AMBER] Restraints questions Mickey Richards (Mon Nov 15 2010 - 15:17:41 PST)
- Re: [AMBER] Restraints questions case (Mon Nov 22 2010 - 08:39:27 PST)
  - Re: [AMBER] Restraints questions Mickey Richards (Mon Nov 22 2010 - 10:41:48 PST)
[AMBER] STOP no longer optional in mm_pbsa.pl Don.Bashford.stjude.org (Tue Nov 16 2010 - 04:01:28 PST)
[AMBER] gaff-parametrisation - how many conformation for a flexible molecule Schlesier, Thomas (Tue Nov 16 2010 - 14:14:40 PST)
- Re: [AMBER] gaff-parametrisation - how many conformation for a flexible molecule FyD (Wed Nov 17 2010 - 00:18:27 PST)
[AMBER] nmode error xuemeiwang1103 (Wed Nov 17 2010 - 04:37:20 PST)
- Re: [AMBER] nmode error xuemeiwang1103 (Thu Nov 18 2010 - 03:43:23 PST)
  - Re: [AMBER] nmode error Jason Swails (Thu Nov 18 2010 - 07:21:45 PST)
[AMBER] D2O Philippe Pinard (Wed Nov 17 2010 - 05:56:37 PST)
- Re: [AMBER] D2O Adrian Roitberg (Wed Nov 17 2010 - 06:00:19 PST)
  - Re: [AMBER] D2O setyanto md (Sun Nov 21 2010 - 15:04:40 PST)
    - Re: [AMBER] D2O Jason Swails (Sun Nov 21 2010 - 15:20:18 PST)
    - Re: [AMBER] D2O case (Sun Nov 21 2010 - 18:27:30 PST)
- Re: [AMBER] D2O Bill Ross (Mon Nov 22 2010 - 09:36:05 PST)
[AMBER] Amber 11 installation problems Linus Johannissen (Wed Nov 17 2010 - 08:39:47 PST)
- Re: [AMBER] Amber 11 installation problems Jason Swails (Wed Nov 17 2010 - 08:47:27 PST)
  - Re: [AMBER] Amber 11 installation problems Linus Johannissen (Wed Nov 17 2010 - 09:44:21 PST)
    - Re: [AMBER] Amber 11 installation problems case (Wed Nov 17 2010 - 10:36:00 PST)
    - Re: [AMBER] Amber 11 installation problems Tru Huynh (Wed Nov 17 2010 - 10:40:54 PST)
    - Re: [AMBER] Amber 11 installation problems Linus Johannissen (Wed Nov 17 2010 - 14:34:53 PST)
    - Re: [AMBER] Amber 11 installation problems Jason Swails (Wed Nov 17 2010 - 15:17:28 PST)
    - Re: [AMBER] Amber 11 installation problems Scott Brozell (Wed Nov 17 2010 - 19:37:08 PST)
    - [AMBER] Clarification in HBond analysis kureeckal ramesh (Wed Nov 17 2010 - 22:35:00 PST)
    - [AMBER] Clarification in HBond analysis kureeckal ramesh (Mon Nov 22 2010 - 19:13:29 PST)
    - [AMBER] Error message in AMBER when running protein-protein complexes. Catein Catherine (Wed Nov 17 2010 - 20:34:08 PST)
    - Re: [AMBER] Error message in AMBER when running protein-protein complexes. Jason Swails (Thu Nov 18 2010 - 07:02:06 PST)
    - [AMBER] How to study the dissociation pathway for two proteins with AMBER10? Catein Catherine (Thu Nov 18 2010 - 18:59:54 PST)
    - Re: [AMBER] How to study the dissociation pathway for two proteins with AMBER10? Jason Swails (Fri Nov 19 2010 - 07:47:42 PST)
[AMBER] about velocity output hong-bin Xie (Wed Nov 17 2010 - 14:59:39 PST)
- Re: [AMBER] about velocity output Jason Swails (Wed Nov 17 2010 - 15:21:22 PST)
  - Re: [AMBER] about velocity output hong-bin Xie (Wed Nov 17 2010 - 16:06:34 PST)
    - Re: [AMBER] about velocity output Jason Swails (Wed Nov 17 2010 - 16:28:05 PST)
    - Re: [AMBER] about velocity output hong-bin Xie (Wed Nov 17 2010 - 16:43:46 PST)
    - Re: [AMBER] about velocity output M. L. Dodson (Wed Nov 17 2010 - 19:17:01 PST)
    - Re: [AMBER] about velocity output George Madalin Giambasu (Thu Nov 18 2010 - 05:33:12 PST)
    - Re: [AMBER] about velocity output hong-bin Xie (Thu Nov 18 2010 - 10:32:09 PST)
[AMBER] LJ interactions and cutoff manoj singh (Wed Nov 17 2010 - 22:45:49 PST)
- Re: [AMBER] LJ interactions and cutoff case (Thu Nov 18 2010 - 04:45:54 PST)
[AMBER] Truncated Octahedron Box in Amber9 Bertrand Russell (Wed Nov 17 2010 - 23:44:07 PST)
- Re: [AMBER] Truncated Octahedron Box in Amber9 Alexander Metz (Thu Nov 18 2010 - 00:53:50 PST)
[AMBER] distance restraint, recenter Nadine Utz (Thu Nov 18 2010 - 05:35:29 PST)
- Re: [AMBER] distance restraint, recenter case (Thu Nov 18 2010 - 06:04:30 PST)
  - Re: [AMBER] distance restraint, recenter Niel Henriksen (Thu Nov 18 2010 - 06:51:47 PST)
[AMBER] xray_interface.f verified to work with PGI7.1-1 Rathbone, Dan L (Thu Nov 18 2010 - 06:52:51 PST)
- Re: [AMBER] xray_interface.f verified to work with PGI7.1-1 case (Thu Nov 18 2010 - 07:36:16 PST)
  - [AMBER] Thanks - xray_interface.f verified to work with PGI7.1-1 Rathbone, Dan L (Thu Nov 18 2010 - 09:04:39 PST)
[AMBER] MMPBSA.py patch failed bin wang (Thu Nov 18 2010 - 07:38:19 PST)
- Re: [AMBER] MMPBSA.py patch failed Jason Swails (Thu Nov 18 2010 - 08:33:16 PST)
  - Re: [AMBER] MMPBSA.py patch failed bin wang (Thu Nov 18 2010 - 13:08:32 PST)
[AMBER] non-bonding parameters Eliac Brown (Thu Nov 18 2010 - 12:32:15 PST)
- Re: [AMBER] non-bonding parameters Jason Swails (Thu Nov 18 2010 - 14:09:41 PST)
  - Re: [AMBER] non-bonding parameters Eliac Brown (Fri Nov 19 2010 - 05:59:32 PST)
    - [AMBER] freezing bonds in parallel version Stefano Pieraccini (Fri Nov 19 2010 - 06:57:23 PST)
    - Re: [AMBER] freezing bonds in parallel version case (Mon Nov 22 2010 - 08:30:20 PST)
    - Re: [AMBER] non-bonding parameters Jason Swails (Fri Nov 19 2010 - 07:02:21 PST)
- Re: [AMBER] non-bonding parameters Bill Ross (Fri Nov 19 2010 - 09:49:15 PST)
  - Re: [AMBER] non-bonding parameters Eliac Brown (Fri Nov 19 2010 - 16:09:03 PST)
    - Re: [AMBER] non-bonding parameters Eliac Brown (Fri Nov 19 2010 - 16:24:44 PST)
- Re: [AMBER] non-bonding parameters Bill Ross (Fri Nov 19 2010 - 16:32:33 PST)
  - Re: [AMBER] non-bonding parameters Jason Swails (Fri Nov 19 2010 - 17:03:38 PST)
[AMBER] The problems with constant pH cwt (Thu Nov 18 2010 - 23:36:47 PST)
- Re: [AMBER] The problems with constant pH Jason Swails (Fri Nov 19 2010 - 07:13:50 PST)
[AMBER] nmode problem with mm-pbsa.pl Khaled Barakat (Fri Nov 19 2010 - 18:05:04 PST)
- Re: [AMBER] nmode problem with mm-pbsa.pl case (Sun Nov 21 2010 - 05:20:39 PST)
[AMBER] AMBER, tanya singh has invited you to open a Gmail account tanya singh (Sat Nov 20 2010 - 04:32:23 PST)
[AMBER] regarding hierarchical clustering jani vinod (Mon Nov 22 2010 - 00:22:02 PST)
- Re: [AMBER] regarding hierarchical clustering Jianyin Shao (Mon Nov 22 2010 - 11:56:34 PST)
  - Re: [AMBER] regarding hierarchical clustering jani vinod (Tue Nov 23 2010 - 21:05:05 PST)
[AMBER] Difference of internal energy Kshatresh Dutta Dubey (Mon Nov 22 2010 - 06:06:30 PST)
- Re: [AMBER] Difference of internal energy Jason Swails (Mon Nov 22 2010 - 06:33:41 PST)
[AMBER] average structure aneesh cna (Mon Nov 22 2010 - 08:31:11 PST)
- Re: [AMBER] average structure Carlos Simmerling (Mon Nov 22 2010 - 08:41:00 PST)
[AMBER] nmode: dihedral angle error Michael Petersen (Mon Nov 22 2010 - 10:53:08 PST)
- Re: [AMBER] nmode: dihedral angle error case (Fri Nov 26 2010 - 06:46:12 PST)
[AMBER] ptraj and ambpdb problem in Amber Tools 1.4 Michael F. Bruist (Mon Nov 22 2010 - 11:16:09 PST)
- Re: [AMBER] ptraj and ambpdb problem in Amber Tools 1.4 Thomas Cheatham III (Mon Nov 22 2010 - 11:34:20 PST)
[AMBER] binding free energy by MM_PBSA Shuang Ding (Mon Nov 22 2010 - 13:02:33 PST)
- Re: [AMBER] binding free energy by MM_PBSA Carlos Simmerling (Mon Nov 22 2010 - 13:16:22 PST)
[AMBER] SASA and Molecular Volume Hopkins, Robert (Mon Nov 22 2010 - 14:35:47 PST)
[AMBER] To continue the job-Reg....... parasu raman (Mon Nov 22 2010 - 22:18:09 PST)
- Re: [AMBER] To continue the job-Reg....... Mark Williamson (Tue Nov 23 2010 - 05:17:28 PST)
[AMBER] does the "set UNIT box { X Y Z }" command create a periodic box? Jose Borreguero (Tue Nov 23 2010 - 07:09:09 PST)
- Re: [AMBER] does the "set UNIT box { X Y Z }" command create a periodic box? case (Tue Nov 23 2010 - 07:25:31 PST)
  - Re: [AMBER] does the "set UNIT box { X Y Z }" command create a periodic box? Jose Borreguero (Tue Nov 23 2010 - 07:27:40 PST)
  - [AMBER] Any Force field parameters for Zn, Mg and Mn in AMBER? Catein Catherine (Tue Nov 23 2010 - 07:56:31 PST)
[AMBER] REMD replicas blowing up Janzsó Gábor (Tue Nov 23 2010 - 07:21:08 PST)
- Re: [AMBER] REMD replicas blowing up Carlos Simmerling (Tue Nov 23 2010 - 09:10:58 PST)
  - Re: [AMBER] REMD replicas blowing up Janzsó Gábor (Tue Nov 23 2010 - 10:07:30 PST)
    - Re: [AMBER] REMD replicas blowing up Carlos Simmerling (Tue Nov 23 2010 - 16:09:49 PST)
    - Re: [AMBER] REMD replicas blowing up Janzsó Gábor (Mon Nov 29 2010 - 11:19:16 PST)
    - Re: [AMBER] REMD replicas blowing up Carlos Simmerling (Tue Nov 30 2010 - 05:59:03 PST)
    - Re: [AMBER] REMD replicas blowing up Adrian Roitberg (Tue Nov 30 2010 - 06:04:31 PST)
    - Re: [AMBER] REMD replicas blowing up Janzsó Gábor (Wed Dec 08 2010 - 08:44:27 PST)
    - Re: [AMBER] REMD replicas blowing up Carlos Simmerling (Wed Dec 08 2010 - 08:47:00 PST)
    - Re: [AMBER] REMD replicas blowing up Janzsó Gábor (Wed Dec 08 2010 - 08:57:37 PST)
    - Re: [AMBER] REMD replicas blowing up Carlos Simmerling (Thu Dec 09 2010 - 05:37:19 PST)
    - Re: [AMBER] REMD replicas blowing up Janzsó Gábor (Thu Dec 09 2010 - 09:18:19 PST)
[AMBER] small organic molecule Rossella Noschese (Tue Nov 23 2010 - 07:36:36 PST)
- Re: [AMBER] small organic molecule case (Tue Nov 23 2010 - 10:34:41 PST)
  - Re: [AMBER] small organic molecule Rossella Noschese (Thu Dec 02 2010 - 01:31:54 PST)
[AMBER] Parameterization of ffamber99sb for octane box YUVRAJ UBOVEJA (Tue Nov 23 2010 - 11:09:06 PST)
- Re: [AMBER] Parameterization of ffamber99sb for octane box YUVRAJ UBOVEJA (Wed Dec 08 2010 - 20:21:21 PST)
  - Re: [AMBER] Parameterization of ffamber99sb for octane box FyD (Wed Dec 08 2010 - 23:47:01 PST)
[AMBER] lib and frcmod files for sucrose? Jose Borreguero (Tue Nov 23 2010 - 14:56:53 PST)
- Re: [AMBER] lib and frcmod files for sucrose? Lachele Foley (Lists) (Tue Nov 23 2010 - 17:07:37 PST)
  - Re: [AMBER] lib and frcmod files for sucrose? Jose Borreguero (Tue Nov 23 2010 - 17:27:41 PST)
    - Re: [AMBER] lib and frcmod files for sucrose? Lachele Foley (Lists) (Tue Nov 23 2010 - 17:48:18 PST)
    - Re: [AMBER] lib and frcmod files for sucrose? Jose Borreguero (Tue Nov 23 2010 - 18:20:40 PST)
[AMBER] MMPBSA John S (Tue Nov 23 2010 - 20:26:22 PST)
- Re: [AMBER] MMPBSA Jason Swails (Tue Nov 23 2010 - 21:02:20 PST)
  - Re: [AMBER] MMPBSA Roman Osman (Tue Nov 23 2010 - 21:09:09 PST)
    - Re: [AMBER] MMPBSA John S (Wed Nov 24 2010 - 07:57:10 PST)
    - Re: [AMBER] MMPBSA Jason Swails (Wed Nov 24 2010 - 11:15:19 PST)
[AMBER] Error when running MMPBSA.py bin wang (Wed Nov 24 2010 - 09:20:51 PST)
- Re: [AMBER] Error when running MMPBSA.py Bill Miller III (Wed Nov 24 2010 - 11:09:12 PST)
[AMBER] Excluded atoms list Jason S Grosch (Wed Nov 24 2010 - 14:41:57 PST)
- Re: [AMBER] Excluded atoms list Bill Ross (Wed Nov 24 2010 - 14:56:12 PST)
- Re: [AMBER] Excluded atoms list Ross Walker (Wed Nov 24 2010 - 16:24:57 PST)
[AMBER] I can unzip Amber 9 in Linux Ubuntu. But when i follow the install instruction g95 i have some problems Tiefeng Peng (Wed Nov 24 2010 - 16:16:58 PST)
- Re: [AMBER] I can unzip Amber 9 in Linux Ubuntu. But when i follow the install instruction g95 i have some problems Tiefeng Peng (Wed Nov 24 2010 - 16:56:22 PST)
  - Re: [AMBER] I can unzip Amber 9 in Linux Ubuntu. But when i follow the install instruction g95 i have some problems case (Thu Nov 25 2010 - 05:15:29 PST)
    - Re: [AMBER] I can unzip Amber 9 in Linux Ubuntu. But when i follow the install instruction g95 i have some problems Tiefeng Peng (Thu Nov 25 2010 - 16:16:05 PST)
    - Re: [AMBER] I can unzip Amber 9 in Linux Ubuntu. But when i follow the install instruction g95 i have some problems case (Thu Nov 25 2010 - 19:43:21 PST)
[AMBER] solute in TIP4P box Aiko Matsumoto (Wed Nov 24 2010 - 16:20:19 PST)
[AMBER] vlimit exceeded for step Coordinate resetting (SHAKE) cannot be accomplished, deviation is too large sunita gupta (Wed Nov 24 2010 - 22:06:38 PST)
- Re: [AMBER] vlimit exceeded for step Coordinate resetting (SHAKE) cannot be accomplished, deviation is too large case (Fri Nov 26 2010 - 06:31:47 PST)
[AMBER] Leap adding an extra incorrect hydrogen Almus (Thu Nov 25 2010 - 06:49:03 PST)
- Re: [AMBER] Leap adding an extra incorrect hydrogen Jason Swails (Thu Nov 25 2010 - 08:12:05 PST)
  - Re: [AMBER] Leap adding an extra incorrect hydrogen Almus (Fri Nov 26 2010 - 03:07:12 PST)
    - Re: [AMBER] Leap adding an extra incorrect hydrogen case (Fri Nov 26 2010 - 05:29:21 PST)
[AMBER] where to check output restraint-wt (ntr=1) decleared with restraintmask xueqin pang (Thu Nov 25 2010 - 06:52:18 PST)
- Re: [AMBER] where to check output restraint-wt (ntr=1) decleared with restraintmask Jason Swails (Thu Nov 25 2010 - 07:54:57 PST)
- Re: [AMBER] where to check output restraint-wt (ntr=1) decleared with restraintmask xueqin pang (Fri Nov 26 2010 - 00:41:42 PST)
  - Re: [AMBER] where to check output restraint-wt (ntr=1) decleared with restraintmask case (Fri Nov 26 2010 - 05:38:55 PST)
[AMBER] sander: Cannot match namelist object name scee Andre Serobian (Thu Nov 25 2010 - 18:34:00 PST)
- Re: [AMBER] sander: Cannot match namelist object name scee Scott Brozell (Thu Nov 25 2010 - 19:11:26 PST)
[AMBER] solute in TIP4P box Aiko Matsumoto (Fri Nov 26 2010 - 03:26:28 PST)
- Re: [AMBER] solute in TIP4P box case (Fri Nov 26 2010 - 05:32:53 PST)
[AMBER] Could not read velocities from amin.crd Ashutosh Shandilya (Fri Nov 26 2010 - 22:50:13 PST)
- Re: [AMBER] Could not read velocities from amin.crd case (Sat Nov 27 2010 - 05:16:16 PST)
  - Re: [AMBER] Could not read velocities from amin.crd case (Sat Nov 27 2010 - 06:48:52 PST)
- Re: [AMBER] Could not read velocities from amin.crd Bill Ross (Sat Nov 27 2010 - 13:34:12 PST)
[AMBER] force field searching Eliac Brown (Sat Nov 27 2010 - 17:02:12 PST)
- Re: [AMBER] force field searching case (Sat Nov 27 2010 - 19:03:56 PST)
[AMBER] Monte Carlo Alok Juneja (Mon Nov 29 2010 - 12:52:51 PST)
- Re: [AMBER] Monte Carlo case (Mon Nov 29 2010 - 19:21:23 PST)
[AMBER] problem with TMD Su Qiu (Tue Nov 30 2010 - 01:22:59 PST)
[AMBER] Benzene Stacking in AMBER Eliac Brown (Tue Nov 30 2010 - 09:04:33 PST)
- Re: [AMBER] Benzene Stacking in AMBER Adrian Roitberg (Tue Nov 30 2010 - 09:12:53 PST)
  - Re: [AMBER] Benzene Stacking in AMBER Eliac Brown (Tue Nov 30 2010 - 09:17:41 PST)
    - Re: [AMBER] Benzene Stacking in AMBER Adrian Roitberg (Tue Nov 30 2010 - 09:21:35 PST)
    - Re: [AMBER] Benzene Stacking in AMBER Ross Walker (Tue Nov 30 2010 - 17:55:47 PST)
    - Re: [AMBER] Benzene Stacking in AMBER Thomas Cheatham (Tue Nov 30 2010 - 18:00:54 PST)
    - Re: [AMBER] Benzene Stacking in AMBER Jiri Sponer (Wed Dec 01 2010 - 02:40:31 PST)
[AMBER] (no subject) Nilmeier, Jerome P. (Tue Nov 30 2010 - 14:35:29 PST)
- Re: [AMBER] (no subject) case (Wed Dec 01 2010 - 08:05:30 PST)
  - Re: [AMBER] (no subject) Adrian Roitberg (Wed Dec 01 2010 - 08:09:38 PST)
    - Re: [AMBER] (no subject) Nilmeier, Jerome P. (Wed Dec 01 2010 - 13:20:22 PST)
    - Re: [AMBER] (no subject) Ross Walker (Wed Dec 01 2010 - 13:38:45 PST)
    - Re: [AMBER] (no subject) Nilmeier, Jerome P. (Wed Dec 01 2010 - 13:41:28 PST)
    - Re: [AMBER] (no subject) Jason Swails (Wed Dec 01 2010 - 13:44:58 PST)
    - Re: [AMBER] (no subject) Carlos Simmerling (Wed Dec 01 2010 - 13:48:28 PST)
    - Re: [AMBER] (no subject) Nilmeier, Jerome P. (Wed Dec 01 2010 - 14:03:52 PST)
    - Re: [AMBER] (no subject) case (Thu Dec 02 2010 - 05:31:20 PST)
    - Re: [AMBER] (no subject) Nilmeier, Jerome P. (Thu Dec 02 2010 - 16:05:26 PST)
[AMBER] GLYCAM with FF99SB Lishan Yao (Tue Nov 30 2010 - 17:55:16 PST)
- Re: [AMBER] GLYCAM with FF99SB Emmanuel Baribefe Naziga (Tue Nov 30 2010 - 18:06:21 PST)
  - Re: [AMBER] GLYCAM with FF99SB Lachele Foley (Lists) (Tue Nov 30 2010 - 19:31:41 PST)
- Re: [AMBER] GLYCAM with FF99SB Lishan Yao (Tue Nov 30 2010 - 19:41:47 PST)
[AMBER] top and crd-reg.............. parasu raman (Tue Nov 30 2010 - 20:05:14 PST)
- Re: [AMBER] top and crd-reg.............. Ross Walker (Tue Nov 30 2010 - 20:20:35 PST)
[AMBER] solvent overlap when "iwrap=1" chicago.ecnu (Tue Nov 30 2010 - 20:58:25 PST)
- Re: [AMBER] solvent overlap when "iwrap=1" Jason Swails (Wed Dec 01 2010 - 06:40:00 PST)
- Re: [AMBER] solvent overlap when "iwrap=1" Daniel Roe (Wed Dec 01 2010 - 06:58:10 PST)
[AMBER] What is the Value of C° (standard concentration) sunita gupta (Tue Nov 30 2010 - 21:43:03 PST)
[AMBER] AmberTools serial compilation with intel compiler 12.0.0: final link failed Vlad Cojocaru (Wed Dec 01 2010 - 03:34:24 PST)
- Re: [AMBER] AmberTools serial compilation with intel compiler 12.0.0: final link failed Daniel Roe (Wed Dec 01 2010 - 05:49:29 PST)
  - Re: [AMBER] AmberTools serial compilation with intel compiler 12.0.0: final link failed Jason Swails (Wed Dec 01 2010 - 06:29:59 PST)
    - Re: [AMBER] AmberTools serial compilation with intel compiler 12.0.0: final link failed Vlad Cojocaru (Wed Dec 01 2010 - 07:33:58 PST)
    - Re: [AMBER] AmberTools serial compilation with intel compiler 12.0.0: final link failed Ross Walker (Wed Dec 01 2010 - 09:03:53 PST)
[AMBER] Distances between amino acid residues Beale, John (Wed Dec 01 2010 - 07:39:54 PST)
- Re: [AMBER] Distances between amino acid residues Jason Swails (Wed Dec 01 2010 - 08:55:32 PST)
- Re: [AMBER] Distances between amino acid residues Su Qiu (Wed Dec 01 2010 - 18:46:36 PST)
[AMBER] AMBER 11 on multiple GPUs Ross Walker (Wed Dec 01 2010 - 09:51:31 PST)
- Re: [AMBER] AMBER 11 on multiple GPUs Gould, Ian R (Wed Dec 01 2010 - 10:04:34 PST)
  - Re: [AMBER] AMBER 11 on multiple GPUs Ross Walker (Wed Dec 01 2010 - 10:14:51 PST)
    - [AMBER] The good choice of the linux system for Amber 11 calculations on Tesla C2050 GPUs ? Marek Maly (Wed Dec 01 2010 - 10:50:14 PST)
    - Re: [AMBER] The good choice of the linux system for Amber 11 calculations on Tesla C2050 GPUs ? Gould, Ian R (Wed Dec 01 2010 - 11:03:56 PST)
    - Re: [AMBER] The good choice of the linux system for Amber 11 calculations on Tesla C2050 GPUs ? Marek Maly (Thu Dec 02 2010 - 02:26:18 PST)
    - Re: [AMBER] The good choice of the linux system for Amber 11 calculations on Tesla C2050 GPUs ? Igor Marques (Thu Dec 02 2010 - 06:10:01 PST)
    - Re: [AMBER] The good choice of the linux system for Amber 11 calculations on Tesla C2050 GPUs ? Marek Maly (Thu Dec 02 2010 - 06:59:17 PST)
    - Re: [AMBER] The good choice of the linux system for Amber 11 calculations on Tesla C2050 GPUs ? Ross Walker (Wed Dec 01 2010 - 11:12:01 PST)
    - Re: [AMBER] The good choice of the linux system for Amber 11 calculations on Tesla C2050 GPUs ? ros (Wed Dec 01 2010 - 11:23:50 PST)
    - Re: [AMBER] The good choice of the linux system for Amber 11 calculations on Tesla C2050 GPUs ? Igor Marques (Wed Dec 01 2010 - 11:57:25 PST)
    - Re: [AMBER] The good choice of the linux system for Amber 11 calculations on Tesla C2050 GPUs ? Marek Maly (Thu Dec 02 2010 - 02:34:01 PST)
[AMBER] energy calculation error after extracting peptide from the explicit water simulation Bongkeun Kim (Wed Dec 01 2010 - 11:49:04 PST)
- Re: [AMBER] energy calculation error after extracting peptide from the explicit water simulation Jason Swails (Wed Dec 01 2010 - 12:31:16 PST)
  - Re: [AMBER] energy calculation error after extracting peptide from the explicit water simulation Bongkeun Kim (Wed Dec 01 2010 - 12:47:49 PST)
    - Re: [AMBER] energy calculation error after extracting peptide from the explicit water simulation Jason Swails (Wed Dec 01 2010 - 12:55:26 PST)
    - Re: [AMBER] energy calculation error after extracting peptide from the explicit water simulation Bongkeun Kim (Wed Dec 01 2010 - 13:18:25 PST)
    - Re: [AMBER] energy calculation error after extracting peptide from the explicit water simulation Daniel Roe (Thu Dec 02 2010 - 11:29:42 PST)
[AMBER] some problems of restart MD cwt (Wed Dec 01 2010 - 18:21:41 PST)
- Re: [AMBER] some problems of restart MD Jason Swails (Wed Dec 01 2010 - 20:43:59 PST)
  - Re: [AMBER] some problems of restart MD cwt (Wed Dec 01 2010 - 22:25:30 PST)
    - Re: [AMBER] some problems of restart MD Jason Swails (Thu Dec 02 2010 - 06:57:38 PST)
[AMBER] MM-PBSA energy-decomposition yan zhang (Wed Dec 01 2010 - 22:15:59 PST)
[AMBER] editing parm in LEAP Alex Rodriguez (Thu Dec 02 2010 - 08:15:36 PST)
- Re: [AMBER] editing parm in LEAP Jason Swails (Thu Dec 02 2010 - 08:21:10 PST)
  - Re: [AMBER] editing parm in LEAP Catein Catherine (Thu Dec 02 2010 - 08:38:13 PST)
    - Re: [AMBER] editing parm in LEAP Jason Swails (Thu Dec 02 2010 - 09:26:44 PST)
  - [AMBER] Please help! MM-GBSA per-residue energy calculation. Catein Catherine (Thu Dec 02 2010 - 08:43:39 PST)
    - Re: [AMBER] Please help! MM-GBSA per-residue energy calculation. Jason Swails (Thu Dec 02 2010 - 09:27:32 PST)
    - Re: [AMBER] Please help! MM-GBSA per-residue energy calculation. Catein Catherine (Fri Dec 03 2010 - 00:01:03 PST)
    - Re: [AMBER] Please help! MM-GBSA per-residue energy calculation. Bill Miller III (Fri Dec 03 2010 - 03:47:35 PST)
[AMBER] MMPBSA calculation of a zinc-enzyme zhihong ke (Thu Dec 02 2010 - 09:53:06 PST)
- Re: [AMBER] MMPBSA calculation of a zinc-enzyme Bill Ross (Thu Dec 02 2010 - 11:47:19 PST)
  - Re: [AMBER] MMPBSA calculation of a zinc-enzyme zhihong ke (Thu Dec 02 2010 - 12:14:42 PST)
- Re: [AMBER] MMPBSA calculation of a zinc-enzyme Bill Ross (Thu Dec 02 2010 - 12:20:20 PST)
  - Re: [AMBER] MMPBSA calculation of a zinc-enzyme zhihong ke (Thu Dec 02 2010 - 12:33:31 PST)
- Re: [AMBER] MMPBSA calculation of a zinc-enzyme Bill Ross (Thu Dec 02 2010 - 13:56:22 PST)
[AMBER] I've got an error msg, ptraj: double free or corruption Hoshin Kim (Wed Dec 01 2010 - 20:46:54 PST)
- Re: [AMBER] I've got an error msg, ptraj: double free or corruption Daniel Roe (Thu Dec 02 2010 - 10:54:26 PST)
[AMBER] what is correct atom type descriptor to add binding-site water molecules in tleap g t (Thu Dec 02 2010 - 10:51:43 PST)
- Re: [AMBER] what is correct atom type descriptor to add binding-site water molecules in tleap case (Thu Dec 02 2010 - 19:41:50 PST)
  - Re: [AMBER] what is correct atom type descriptor to add binding-site water molecules in tleap g t (Fri Dec 03 2010 - 09:10:07 PST)
[AMBER] installing Amber 11 & tools 1.4 on Fedora 14 Andre Serobian (Thu Dec 02 2010 - 19:51:14 PST)
- Re: [AMBER] installing Amber 11 & tools 1.4 on Fedora 14 Vlad Cojocaru (Fri Dec 03 2010 - 00:38:02 PST)
[AMBER] AmberTools 1.4 serial tests failures Vlad Cojocaru (Fri Dec 03 2010 - 06:27:07 PST)
- Re: [AMBER] AmberTools 1.4 serial tests failures Daniel Roe (Fri Dec 03 2010 - 06:48:36 PST)
  - Re: [AMBER] AmberTools 1.4 serial tests failures Timothy J Giese (Fri Dec 03 2010 - 06:53:14 PST)
  - Re: [AMBER] AmberTools 1.4 serial tests failures Vlad Cojocaru (Fri Dec 03 2010 - 07:01:23 PST)
    - Re: [AMBER] AmberTools 1.4 serial tests failures David Watson (Fri Dec 03 2010 - 07:08:49 PST)
    - Re: [AMBER] AmberTools 1.4 serial tests failures Vlad Cojocaru (Fri Dec 03 2010 - 07:32:49 PST)
    - Re: [AMBER] AmberTools 1.4 serial tests failures Vlad Cojocaru (Sat Dec 04 2010 - 05:32:44 PST)
[AMBER] amoeba waters Geoffrey Wood (Fri Dec 03 2010 - 13:12:48 PST)
- Re: [AMBER] amoeba waters Jason Swails (Fri Dec 03 2010 - 13:17:59 PST)
  - Re: [AMBER] amoeba waters Geoffrey Wood (Fri Dec 03 2010 - 13:39:11 PST)
    - Re: [AMBER] amoeba waters Jason Swails (Fri Dec 03 2010 - 13:49:47 PST)
[AMBER] 'final link failed' error independent of intel compiler version Vlad Cojocaru (Sat Dec 04 2010 - 03:11:32 PST)
[AMBER] Box volume calculated by sander Hopkins, Robert (Sat Dec 04 2010 - 09:48:58 PST)
[AMBER] MM-PBSA with DELPHI Khaled Barakat (Sat Dec 04 2010 - 17:00:25 PST)
[AMBER] hydrogen bond analysis of gromacs simulation by amber (direct and water mediated HB) leila karami (Sun Dec 05 2010 - 00:56:07 PST)
- Re: [AMBER] hydrogen bond analysis of gromacs simulation by amber (direct and water mediated HB) Jason Swails (Sun Dec 05 2010 - 11:26:40 PST)
[AMBER] problem with entropy computations by mm_pbsa_nabnmode Cenk $Jenk$ Andac (Sun Dec 05 2010 - 01:17:07 PST)
- Re: [AMBER] problem with entropy computations by mm_pbsa_nabnmode Cenk $Jenk$ Andac (Sun Dec 05 2010 - 03:22:50 PST)
[AMBER] Query: ABMD Kshatresh Dutta Dubey (Sun Dec 05 2010 - 01:29:38 PST)
- Re: [AMBER] Query: ABMD case (Sun Dec 05 2010 - 07:01:19 PST)
  - Re: [AMBER] Query: ABMD Kshatresh Dutta Dubey (Sun Dec 05 2010 - 20:43:58 PST)
    - Re: [AMBER] Query: ABMD case (Mon Dec 06 2010 - 04:39:42 PST)
[AMBER] High STD Value in pbsa Alice Wang (Sun Dec 05 2010 - 18:26:24 PST)
- Re: [AMBER] High STD Value in pbsa Jason Swails (Sun Dec 05 2010 - 18:51:37 PST)
  - Re: [AMBER] High STD Value in pbsa Alice Wang (Sun Dec 05 2010 - 19:12:02 PST)
    - Re: [AMBER] High STD Value in pbsa Ray Luo, Ph.D. (Sun Dec 05 2010 - 22:06:35 PST)
    - Re: [AMBER] High STD Value in pbsa Alice Wang (Sun Dec 05 2010 - 23:24:17 PST)
    - Re: [AMBER] High STD Value in pbsa Alice Wang (Sun Dec 05 2010 - 23:48:05 PST)
    - Re: [AMBER] High STD Value in pbsa Ray Luo (Mon Dec 06 2010 - 10:05:18 PST)
[AMBER] building error of multi-GPU pmemd.cuda Masakazu SEKIJIMA (Sun Dec 05 2010 - 23:30:19 PST)
- Re: [AMBER] building error of multi-GPU pmemd.cuda case (Mon Dec 06 2010 - 04:47:08 PST)
  - Re: [AMBER] building error of multi-GPU pmemd.cuda Jason Swails (Mon Dec 06 2010 - 08:55:03 PST)
[AMBER] hydrogen bond analysis of gromacs simulation by amber (direct and water mediated HB) leila karami (Mon Dec 06 2010 - 00:13:35 PST)
- Re: [AMBER] hydrogen bond analysis of gromacs simulation by amber (direct and water mediated HB) Jason Swails (Mon Dec 06 2010 - 08:49:48 PST)
[AMBER] Analytical and empirical parametrization of dihedrals in Amber Dmitry Nilov (Mon Dec 06 2010 - 00:43:56 PST)
[AMBER] Installation problem on Mac George Tzotzos (Mon Dec 06 2010 - 05:28:29 PST)
- Re: [AMBER] Installation problem on Mac Timothy J Giese (Mon Dec 06 2010 - 06:00:59 PST)
  - Re: [AMBER] Installation problem on Mac case (Mon Dec 06 2010 - 07:06:26 PST)
    - Re: [AMBER] Installation problem on Mac George Tzotzos (Mon Dec 06 2010 - 07:17:04 PST)
    - Re: [AMBER] Installation problem on Mac M. Shahid (Mon Dec 06 2010 - 07:44:27 PST)
    - Re: [AMBER] Installation problem on Mac Jason Swails (Mon Dec 06 2010 - 13:08:13 PST)
    - Re: [AMBER] Installation problem on Mac Jason Swails (Mon Dec 06 2010 - 09:03:40 PST)
[AMBER] force constant parameters in amberports Jarmila Husby (Mon Dec 06 2010 - 06:11:52 PST)
[AMBER] questions on molsurf program Senthil Natesan (Mon Dec 06 2010 - 07:36:33 PST)
- Re: [AMBER] questions on molsurf program Jason Swails (Mon Dec 06 2010 - 09:29:07 PST)
  - Re: [AMBER] questions on molsurf program Senthil Natesan (Mon Dec 06 2010 - 09:42:04 PST)
- Re: [AMBER] questions on molsurf program Ray Luo (Mon Dec 06 2010 - 10:29:36 PST)
[AMBER] How to set up NMR distance restraint between surface and peptide? Bongkeun Kim (Mon Dec 06 2010 - 13:40:13 PST)
- Re: [AMBER] How to set up NMR distance restraint between surface and peptide? Jason Swails (Mon Dec 06 2010 - 14:16:58 PST)
  - Re: [AMBER] How to set up NMR distance restraint between surface and peptide? Bongkeun Kim (Mon Dec 06 2010 - 14:31:21 PST)
    - Re: [AMBER] How to set up NMR distance restraint between surface and peptide? Bongkeun Kim (Mon Dec 06 2010 - 15:41:02 PST)
    - Re: [AMBER] How to set up NMR distance restraint between surface and peptide? Jason Swails (Mon Dec 06 2010 - 16:30:43 PST)
[AMBER] Map function for custom residue to generate distace restraints? Bongkeun Kim (Mon Dec 06 2010 - 16:21:02 PST)
- Re: [AMBER] Map function for custom residue to generate distace restraints? case (Mon Dec 06 2010 - 18:48:30 PST)
[AMBER] What can we do with velocities file ? setyanto md (Mon Dec 06 2010 - 18:03:28 PST)
- Re: [AMBER] What can we do with velocities file ? Jason Swails (Mon Dec 06 2010 - 18:31:46 PST)
[AMBER] Error: Sander output is missing values! VDWAALS = ************* kamlesh sahu (Mon Dec 06 2010 - 20:21:46 PST)
- Re: [AMBER] Error: Sander output is missing values! VDWAALS = ************* Bill Miller III (Mon Dec 06 2010 - 20:29:56 PST)
- Re: [AMBER] Error: Sander output is missing values! VDWAALS = ************* Jason Swails (Tue Dec 07 2010 - 11:15:40 PST)
  - Re: [AMBER] Error: Sander output is missing values! VDWAALS = ************* kamlesh sahu (Tue Dec 07 2010 - 21:06:37 PST)
[AMBER] hydrogen bond analysis of gromacs simulation by amber (direct and water mediated HB) leila karami (Mon Dec 06 2010 - 22:26:01 PST)
[AMBER] vdW parameters steinbrt.rci.rutgers.edu (Mon Dec 06 2010 - 23:49:26 PST)
[AMBER] solvatebox leila karami (Tue Dec 07 2010 - 04:00:09 PST)
- Re: [AMBER] solvatebox Oliver Grant (Tue Dec 07 2010 - 07:21:47 PST)
  - Re: [AMBER] solvatebox Igor Marques (Tue Dec 07 2010 - 07:39:30 PST)
    - Re: [AMBER] solvatebox dcerutti.rci.rutgers.edu (Tue Dec 07 2010 - 10:25:41 PST)
Re: [AMBER] pmemd.cuda on Snow Leopard 10.6.5 M. Shahid (Tue Dec 07 2010 - 04:33:57 PST)
- Re: [AMBER] pmemd.cuda on Snow Leopard 10.6.5 Jason Swails (Tue Dec 07 2010 - 07:43:20 PST)
  - Re: [AMBER] pmemd.cuda on Snow Leopard 10.6.5 M. Shahid (Tue Dec 07 2010 - 13:05:20 PST)
[AMBER] Illegal CONECT record in pdb file / The file contained 1 atoms not in residue templates leila karami (Tue Dec 07 2010 - 06:40:47 PST)
- Re: [AMBER] Illegal CONECT record in pdb file / The file contained 1 atoms not in residue templates Oliver Grant (Tue Dec 07 2010 - 07:20:16 PST)
- Re: [AMBER] Illegal CONECT record in pdb file / The file contained 1 atoms not in residue templates Jason Swails (Wed Dec 08 2010 - 06:21:47 PST)
[AMBER] Work Smarter, Not Harder - I will earn for you - You sit and relax. Kalpesh Sharma (Tue Dec 07 2010 - 20:43:59 PST)
[AMBER] Regarding energy decomposition aneesh cna (Wed Dec 08 2010 - 04:40:17 PST)
- Re: [AMBER] Regarding energy decomposition Bill Ross (Wed Dec 08 2010 - 10:46:52 PST)
  - Re: [AMBER] Regarding energy decomposition aneesh cna (Sat Dec 11 2010 - 02:24:47 PST)
[AMBER] Closest waters Beale, John (Wed Dec 08 2010 - 04:44:42 PST)
- Re: [AMBER] Closest waters ros (Wed Dec 08 2010 - 05:41:50 PST)
- Re: [AMBER] Closest waters Jason Swails (Wed Dec 08 2010 - 06:27:36 PST)
- Re: [AMBER] Closest waters Igor Sizov (Mon Dec 13 2010 - 07:44:44 PST)
[AMBER] error for antecamber to establish small molecule Zhou Gong (Wed Dec 08 2010 - 06:58:49 PST)
- Re: [AMBER] error for antecamber to establish small molecule case (Wed Dec 08 2010 - 07:31:54 PST)
  - [AMBER] How to define two receptors in MM/GBSA calculation? Catein Catherine (Wed Dec 08 2010 - 08:38:36 PST)
    - Re: [AMBER] How to define two receptors in MM/GBSA calculation? Jason Swails (Wed Dec 08 2010 - 08:43:36 PST)
    - Re: [AMBER] How to define two receptors in MM/GBSA calculation? Jason Swails (Wed Dec 08 2010 - 08:45:30 PST)
  - [AMBER] 答复: error for antecamber to establish small molecule Zhou Gong (Wed Dec 08 2010 - 18:33:02 PST)
    - Re: [AMBER] : error for antecamber to establish small molecule FyD (Thu Dec 09 2010 - 02:22:58 PST)
    - Re: [AMBER] 答复: error for antecamber to establish small molecule case (Thu Dec 09 2010 - 04:49:22 PST)
[AMBER] Umbrella Sampling lnedialkova.gmail.com (Wed Dec 08 2010 - 10:18:02 PST)
[AMBER] MMPBSA calculation for chlorine anion zhihong ke (Wed Dec 08 2010 - 11:25:19 PST)
[AMBER] Some errors in the Amber test cwt (Wed Dec 08 2010 - 18:14:53 PST)
- Re: [AMBER] Some errors in the Amber test case (Thu Dec 09 2010 - 04:47:32 PST)
[AMBER] Tin-foil boundary condition kurisaki ikuo (Wed Dec 08 2010 - 20:51:14 PST)
- Re: [AMBER] Tin-foil boundary condition case (Thu Dec 09 2010 - 04:51:09 PST)
[AMBER] Does MMPBSA.py mutant only one residue? zjxu (Wed Dec 08 2010 - 23:31:39 PST)
- Re: [AMBER] Does MMPBSA.py mutant only one residue? Bill Miller III (Thu Dec 09 2010 - 03:40:59 PST)
  - Re: [AMBER] Does MMPBSA.py mutant only one residue? zjxu (Thu Dec 09 2010 - 04:45:09 PST)
    - Re: [AMBER] Does MMPBSA.py mutant only one residue? Jason Swails (Thu Dec 09 2010 - 07:35:47 PST)
    - Re: [AMBER] Does MMPBSA.py mutant only one residue? zjxu (Thu Dec 09 2010 - 18:05:11 PST)
[AMBER] using mol2 files with tleap Jan Wahl (Thu Dec 09 2010 - 00:53:14 PST)
- Re: [AMBER] using mol2 files with tleap M. Shahid (Thu Dec 09 2010 - 01:37:11 PST)
- Re: [AMBER] using mol2 files with tleap FyD (Thu Dec 09 2010 - 02:29:41 PST)
[AMBER] cyclic peptide Rossella Noschese (Thu Dec 09 2010 - 02:50:41 PST)
- Re: [AMBER] cyclic peptide FyD (Thu Dec 09 2010 - 04:37:43 PST)
- Re: [AMBER] cyclic peptide case (Thu Dec 09 2010 - 05:03:07 PST)
  - Re: [AMBER] cyclic peptide FyD (Thu Dec 09 2010 - 06:42:34 PST)
    - Re: [AMBER] cyclic peptide Rossella Noschese (Thu Dec 09 2010 - 07:31:22 PST)
    - Re: [AMBER] cyclic peptide case (Thu Dec 09 2010 - 09:45:58 PST)
    - Re: [AMBER] cyclic peptide Rossella Noschese (Tue Dec 14 2010 - 05:29:46 PST)
    - Re: [AMBER] cyclic peptide Jason Swails (Tue Dec 14 2010 - 06:38:31 PST)
    - Re: [AMBER] cyclic peptide FyD (Tue Dec 14 2010 - 10:52:39 PST)
[AMBER] sleap loadmol2 bug Floris Buelens (Thu Dec 09 2010 - 04:39:40 PST)
- Re: [AMBER] sleap loadmol2 bug Wei Zhang (Wed Dec 15 2010 - 23:27:41 PST)
[AMBER] problem with resp charge generation with multiple orientations Thomas Schlesier (Thu Dec 09 2010 - 13:10:21 PST)
- Re: [AMBER] problem with resp charge generation with multiple orientations FyD (Fri Dec 10 2010 - 00:08:04 PST)
  - Re: [AMBER] problem with resp charge generation with multiple orientations Thomas Schlesier (Fri Dec 10 2010 - 04:26:10 PST)
    - Re: [AMBER] problem with resp charge generation with multiple orientations FyD (Fri Dec 10 2010 - 08:13:40 PST)
    - Re: [AMBER] problem with resp charge generation with multiple orientations Thomas Schlesier (Mon Dec 13 2010 - 02:01:19 PST)
[AMBER] Could the energy decomposition be carried out in the AmberTools? Yao-Chi Chen (Thu Dec 09 2010 - 17:23:19 PST)
- Re: [AMBER] Could the energy decomposition be carried out in the AmberTools? Jason Swails (Thu Dec 09 2010 - 17:45:24 PST)
  - Re: [AMBER] Could the energy decomposition be carried out in the AmberTools? Yao-Chi Chen (Thu Dec 09 2010 - 22:48:28 PST)
    - Re: [AMBER] Could the energy decomposition be carried out in the AmberTools? case (Fri Dec 10 2010 - 06:32:10 PST)
[AMBER] HEME parameters Karan Mehra (Thu Dec 09 2010 - 17:38:21 PST)
- Re: [AMBER] HEME parameters Nitu Bansal (Fri Dec 10 2010 - 04:33:28 PST)
  - Re: [AMBER] HEME parameters Karan Mehra (Fri Dec 10 2010 - 13:37:33 PST)
    - Re: [AMBER] HEME parameters Nitu Bansal (Fri Dec 10 2010 - 21:16:30 PST)
    - Re: [AMBER] HEME parameters Karan Mehra (Sat Dec 11 2010 - 11:24:31 PST)
- Re: [AMBER] HEME parameters Bill Ross (Sat Dec 11 2010 - 11:29:30 PST)
- Re: [AMBER] HEME parameters Bill Ross (Sat Dec 11 2010 - 11:46:21 PST)
- Re: [AMBER] HEME parameters CHAMI F. (Wed Mar 02 2011 - 03:53:54 PST)
  - Re: [AMBER] HEME parameters Scott Brozell (Thu Mar 03 2011 - 19:10:11 PST)
[AMBER] Polyglycine simulation YUVRAJ UBOVEJA (Fri Dec 10 2010 - 02:28:53 PST)
- Re: [AMBER] Polyglycine simulation Bill Miller III (Fri Dec 10 2010 - 03:38:51 PST)
[AMBER] phosphorylated residues baljinder (Fri Dec 10 2010 - 02:54:05 PST)
- Re: [AMBER] phosphorylated residues Anselm Horn (Fri Dec 10 2010 - 07:04:56 PST)
  - Re: [AMBER] phosphorylated residues Jason Swails (Fri Dec 10 2010 - 07:36:21 PST)
[AMBER] Fwd: simulation terminates for no apparent reason Gabriel Urquiza (Fri Dec 10 2010 - 05:14:22 PST)
- Re: [AMBER] Fwd: simulation terminates for no apparent reason Jason Swails (Fri Dec 10 2010 - 07:55:29 PST)
- Re: [AMBER] Fwd: simulation terminates for no apparent reason Sergio R Aragon (Fri Dec 10 2010 - 10:15:33 PST)
  - Re: [AMBER] Fwd: simulation terminates for no apparent reason Ross Walker (Fri Dec 10 2010 - 11:07:12 PST)
[AMBER] ambpdb error when usind mdcrd file lnedialkova.gmail.com (Fri Dec 10 2010 - 09:50:23 PST)
- Re: [AMBER] ambpdb error when usind mdcrd file case (Fri Dec 10 2010 - 11:14:34 PST)
[AMBER] compile pmemd using gcc Jorgen Simonsen (Fri Dec 10 2010 - 09:53:26 PST)
- Re: [AMBER] compile pmemd using gcc Jason Swails (Fri Dec 10 2010 - 09:55:54 PST)
  - Re: [AMBER] compile pmemd using gcc Jorgen Simonsen (Fri Dec 10 2010 - 11:05:08 PST)
    - Re: [AMBER] compile pmemd using gcc Jason Swails (Fri Dec 10 2010 - 11:27:32 PST)
[AMBER] Translate command with ptraj Logan Ahlstrom (Fri Dec 10 2010 - 17:21:24 PST)
- Re: [AMBER] Translate command with ptraj Logan Ahlstrom (Sat Dec 11 2010 - 15:22:36 PST)
  - Re: [AMBER] Translate command with ptraj Thomas Cheatham III (Sat Dec 11 2010 - 16:19:14 PST)
    - Re: [AMBER] Translate command with ptraj Logan Ahlstrom (Sat Dec 11 2010 - 19:06:51 PST)
    - Re: [AMBER] Translate command with ptraj Logan Ahlstrom (Sun Dec 12 2010 - 06:27:41 PST)
[AMBER] Residues lacking connect0/connect1 - these don't have chain types marked: leila karami (Sat Dec 11 2010 - 03:33:37 PST)
- Re: [AMBER] Residues lacking connect0/connect1 - these don't have chain types marked: Jason Swails (Sat Dec 11 2010 - 10:34:36 PST)
[AMBER] comparision of gromacs and amber atila petrosian (Sat Dec 11 2010 - 04:55:49 PST)
- Re: [AMBER] comparision of gromacs and amber zjxu (Sat Dec 11 2010 - 05:49:49 PST)
- Re: [AMBER] comparision of gromacs and amber Vitaly Chaban (Sat Dec 11 2010 - 07:19:53 PST)
- Re: [AMBER] comparision of gromacs and amber Karl N. Kirschner (Mon Dec 13 2010 - 02:05:26 PST)
[AMBER] Atomic fluctuation John S (Sat Dec 11 2010 - 22:36:06 PST)
- Re: [AMBER] Atomic fluctuation Logan Ahlstrom (Sun Dec 12 2010 - 06:24:11 PST)
[AMBER] error on running sander.MPI George Tzotzos (Sun Dec 12 2010 - 05:59:53 PST)
- Re: [AMBER] error on running sander.MPI George Tzotzos (Sun Dec 12 2010 - 06:10:10 PST)
  - Re: [AMBER] error on running sander.MPI case (Sun Dec 12 2010 - 06:32:29 PST)
    - Re: [AMBER] error on running sander.MPI George Tzotzos (Sun Dec 12 2010 - 06:46:39 PST)
    - Re: [AMBER] error on running sander.MPI George Tzotzos (Sun Dec 12 2010 - 08:10:19 PST)
    - Re: [AMBER] error on running sander.MPI Jason Swails (Sun Dec 12 2010 - 09:33:33 PST)
    - Re: [AMBER] error on running sander.MPI Ross Walker (Sun Dec 12 2010 - 10:09:04 PST)
    - Re: [AMBER] error on running sander.MPI George Tzotzos (Sun Dec 12 2010 - 10:14:34 PST)
    - Re: [AMBER] error on running sander.MPI Ross Walker (Sun Dec 12 2010 - 10:22:19 PST)
[AMBER] Residues lacking connect0/connect1 - these don't have chain types marked: leila karami (Sun Dec 12 2010 - 01:05:47 PST)
- Re: [AMBER] Residues lacking connect0/connect1 - these don't have chain types marked: Bill Ross (Sat Dec 11 2010 - 11:23:10 PST)
- Re: [AMBER] Residues lacking connect0/connect1 - these don't have chain types marked: Bill Ross (Mon Dec 13 2010 - 11:05:52 PST)
[AMBER] problem during MD process 蒋峻峰 (Sun Dec 12 2010 - 18:09:16 PST)
- Re: [AMBER] problem during MD process case (Sun Dec 12 2010 - 19:53:05 PST)
- Re: [AMBER] problem during MD process 蒋峻峰 (Mon Dec 13 2010 - 00:06:41 PST)
- Re: [AMBER] problem during MD process Dean Cuebas (Wed Dec 15 2010 - 10:13:53 PST)
- Re: [AMBER] problem during MD process 蒋峻峰 (Wed Dec 15 2010 - 17:38:26 PST)
[AMBER] error regarding periodic prmtop Jio M (Sun Dec 12 2010 - 20:55:13 PST)
- Re: [AMBER] error regarding periodic prmtop Jason Swails (Sun Dec 12 2010 - 22:19:30 PST)
  - Re: [AMBER] error regarding periodic prmtop Jio M (Sun Dec 12 2010 - 23:24:26 PST)
    - Re: [AMBER] error regarding periodic prmtop Jason Swails (Mon Dec 13 2010 - 09:13:06 PST)
[AMBER] problem during TMD simulation Dachuan Guo (Mon Dec 13 2010 - 00:45:10 PST)
- Re: [AMBER] problem during TMD simulation Simon Becker (Mon Dec 13 2010 - 01:23:48 PST)
[AMBER] use of packmol in amber subrata paul (Mon Dec 13 2010 - 02:43:03 PST)
- Re: [AMBER] use of packmol in amber case (Mon Dec 13 2010 - 04:43:29 PST)
  - Re: [AMBER] use of packmol in amber subrata paul (Mon Dec 13 2010 - 19:57:29 PST)
    - Re: [AMBER] use of packmol in amber Gopalakrishnan.R (Mon Dec 13 2010 - 20:36:07 PST)
- Re: [AMBER] use of packmol in amber Bill Ross (Mon Dec 13 2010 - 20:16:39 PST)
  - Re: [AMBER] use of packmol in amber subrata paul (Mon Dec 13 2010 - 20:29:39 PST)
- Re: [AMBER] use of packmol in amber Bill Ross (Mon Dec 13 2010 - 20:41:20 PST)
  - Re: [AMBER] use of packmol in amber subrata paul (Tue Dec 14 2010 - 03:23:58 PST)
    - Re: [AMBER] use of packmol in amber case (Tue Dec 14 2010 - 04:44:02 PST)
    - Re: [AMBER] use of packmol in amber M. L. Dodson (Tue Dec 14 2010 - 06:09:19 PST)
    - Re: [AMBER] use of packmol in amber M. L. Dodson (Tue Dec 14 2010 - 11:06:18 PST)
    - Re: [AMBER] use of packmol in amber subrata paul (Tue Dec 14 2010 - 23:13:58 PST)
    - Re: [AMBER] use of packmol in amber M. L. Dodson (Wed Dec 15 2010 - 06:46:29 PST)
- Re: [AMBER] use of packmol in amber Bill Ross (Tue Dec 14 2010 - 10:14:35 PST)
- Re: [AMBER] use of packmol in amber Bill Ross (Tue Dec 14 2010 - 10:24:23 PST)
[AMBER] maxocc and life time atila petrosian (Mon Dec 13 2010 - 02:57:40 PST)
[AMBER] reference for gbsa = 2 Jio M (Mon Dec 13 2010 - 06:25:03 PST)
[AMBER] Using offsets to image with ptraj Logan Ahlstrom (Mon Dec 13 2010 - 12:17:36 PST)
[AMBER] .mdin file content Bozell, Joseph John (Mon Dec 13 2010 - 13:36:15 PST)
- Re: [AMBER] .mdin file content Jason Swails (Mon Dec 13 2010 - 14:54:15 PST)
- Re: [AMBER] .mdin file content Richard Owczarzy (Mon Dec 13 2010 - 15:28:25 PST)
- Re: [AMBER] .mdin file content Bill Ross (Mon Dec 13 2010 - 15:34:30 PST)
[AMBER] Are there polarized ion models in Amber? kurisaki ikuo (Mon Dec 13 2010 - 17:55:22 PST)
[AMBER] running amber in amazon ec2 cloud environment Tomáš Kučera (Tue Dec 14 2010 - 01:58:46 PST)
- Re: [AMBER] running amber in amazon ec2 cloud environment Jarmila Husby (Tue Dec 14 2010 - 02:38:38 PST)
  - Re: [AMBER] running amber in amazon ec2 cloud environment Richard Owczarzy (Tue Dec 14 2010 - 06:17:14 PST)
- Re: [AMBER] running amber in amazon ec2 cloud environment Jarmila Husby (Tue Dec 14 2010 - 03:00:55 PST)
- Re: [AMBER] running amber in amazon ec2 cloud environment Ross Walker (Tue Dec 14 2010 - 08:31:27 PST)
[AMBER] allocation failure in vector: problem in MMPBSA.py.MPI mish (Tue Dec 14 2010 - 04:11:48 PST)
- Re: [AMBER] allocation failure in vector: problem in MMPBSA.py.MPI Bill Miller III (Tue Dec 14 2010 - 04:22:52 PST)
  - Re: [AMBER] allocation failure in vector: problem in MMPBSA.py.MPI mish (Tue Dec 14 2010 - 04:35:23 PST)
    - Re: [AMBER] allocation failure in vector: problem in MMPBSA.py.MPI mish (Wed Dec 15 2010 - 03:11:14 PST)
    - [AMBER] pmemd with mpi number of cpus Stefano Pieraccini (Wed Dec 15 2010 - 03:26:38 PST)
    - Re: [AMBER] pmemd with mpi number of cpus case (Wed Dec 15 2010 - 06:22:11 PST)
    - Re: [AMBER] pmemd with mpi number of cpus Ross Walker (Wed Dec 15 2010 - 11:59:54 PST)
    - Re: [AMBER] allocation failure in vector: problem in MMPBSA.py.MPI Jason Swails (Wed Dec 15 2010 - 07:40:22 PST)
    - Re: [AMBER] allocation failure in vector: problem in MMPBSA.py.MPI Sushil Mishra (Wed Dec 15 2010 - 07:49:55 PST)
    - Re: [AMBER] allocation failure in vector: problem in MMPBSA.py.MPI Jason Swails (Wed Dec 15 2010 - 09:47:38 PST)
    - Re: [AMBER] allocation failure in vector: problem in MMPBSA.py.MPI Sushil Mishra (Wed Dec 15 2010 - 12:26:05 PST)
    - Re: [AMBER] allocation failure in vector: problem in MMPBSA.py.MPI Jason Swails (Wed Dec 15 2010 - 12:39:07 PST)
    - Re: [AMBER] allocation failure in vector: problem in MMPBSA.py.MPI Sushil Mishra (Wed Dec 15 2010 - 23:01:33 PST)
    - Re: [AMBER] allocation failure in vector: problem in MMPBSA.py.MPI Jason Swails (Thu Dec 16 2010 - 06:58:07 PST)
[AMBER] Problem on nmropt option in amber 11 Giachetti Andrea - CERM (Tue Dec 14 2010 - 06:24:36 PST)
- Re: [AMBER] Problem on nmropt option in amber 11 Carlos Simmerling (Tue Dec 14 2010 - 06:27:32 PST)
  - Re: [AMBER] Problem on nmropt option in amber 11 Giachetti Andrea - CERM (Tue Dec 14 2010 - 06:57:31 PST)
    - Re: [AMBER] Problem on nmropt option in amber 11 case (Tue Dec 14 2010 - 07:22:03 PST)
    - [AMBER] How to study protein-protein complex are stabilized/destabilized upon complexation? Catein Catherine (Tue Dec 14 2010 - 09:26:25 PST)
    - Re: [AMBER] How to study protein-protein complex are stabilized/destabilized upon complexation? Carlos Simmerling (Tue Dec 14 2010 - 09:29:15 PST)
    - Re: [AMBER] Problem on nmropt option in amber 11 Giachetti Andrea - CERM (Wed Dec 15 2010 - 03:07:42 PST)
[AMBER] Building polymer John S (Tue Dec 14 2010 - 08:48:19 PST)
- Re: [AMBER] Building polymer Jason Swails (Tue Dec 14 2010 - 10:47:11 PST)
- Re: [AMBER] Building polymer Bill Ross (Tue Dec 14 2010 - 11:03:26 PST)
- Re: [AMBER] Building polymer Marek Maly (Tue Dec 14 2010 - 11:47:26 PST)
[AMBER] Problems compiling pmemd.cuda.MPI for InfiniBand Sasha Buzko (Tue Dec 14 2010 - 15:02:02 PST)
- Re: [AMBER] Problems compiling pmemd.cuda.MPI for InfiniBand Ross Walker (Tue Dec 14 2010 - 15:49:29 PST)
  - Re: [AMBER] Problems compiling pmemd.cuda.MPI for InfiniBand Sasha Buzko (Tue Dec 14 2010 - 15:57:08 PST)
[AMBER] torsion parameters in parm99.dat xqkong (Tue Dec 14 2010 - 22:42:19 PST)
- Re: [AMBER] torsion parameters in parm99.dat Dmitry Nilov (Tue Dec 14 2010 - 23:21:24 PST)
  - Re: [AMBER] torsion parameters in parm99.dat xqkong (Fri Dec 17 2010 - 17:57:27 PST)
    - Re: [AMBER] torsion parameters in parm99.dat Dmitry Nilov (Fri Dec 17 2010 - 23:50:01 PST)
    - Re: [AMBER] torsion parameters in parm99.dat Dmitry Nilov (Fri Dec 17 2010 - 23:55:44 PST)
  - Re: [AMBER] torsion parameters in parm99.dat xqkong (Fri Dec 17 2010 - 18:01:11 PST)
  - Re: [AMBER] torsion parameters in parm99.dat xqkong (Sat Dec 18 2010 - 04:02:30 PST)
- Re: [AMBER] torsion parameters in parm99.dat Jason Swails (Wed Dec 15 2010 - 06:55:56 PST)
[AMBER] Entropy calculation of a molecule in water Markus Kaukonen (Wed Dec 15 2010 - 02:07:31 PST)
- Re: [AMBER] Entropy calculation of a molecule in water case (Wed Dec 15 2010 - 05:21:24 PST)
  - Re: [AMBER] Entropy calculation of a molecule in water Markus Kaukonen (Thu Dec 16 2010 - 00:02:21 PST)
    - Re: [AMBER] Entropy calculation of a molecule in water Daniel Roe (Thu Dec 16 2010 - 04:53:07 PST)
[AMBER] MMPBSA.py Internal energies Eliac Brown (Wed Dec 15 2010 - 05:58:41 PST)
- Re: [AMBER] MMPBSA.py Internal energies Bill Miller III (Wed Dec 15 2010 - 06:06:17 PST)
[AMBER] count number of solvent molecules inside the protein iccy liu (Wed Dec 15 2010 - 15:11:24 PST)
[AMBER] QM/MM energy terms with DFTB Markus Kaukonen (Thu Dec 16 2010 - 07:49:50 PST)
- Re: [AMBER] QM/MM energy terms with DFTB Ross Walker (Thu Dec 16 2010 - 14:17:35 PST)
  - Re: [AMBER] QM/MM energy terms with DFTB Markus Kaukonen (Sat Dec 18 2010 - 07:29:51 PST)
- Re: [AMBER] QM/MM energy terms with DFTB Andreas Goetz (Thu Dec 16 2010 - 14:18:37 PST)
  - Re: [AMBER] QM/MM energy terms with DFTB Dmitry Nilov (Fri Dec 17 2010 - 04:31:33 PST)
    - Re: [AMBER] QM/MM energy terms with DFTB Andreas Goetz (Fri Dec 17 2010 - 12:01:32 PST)
    - Re: [AMBER] QM/MM energy terms with DFTB Jason Swails (Fri Dec 17 2010 - 18:02:49 PST)
    - Re: [AMBER] QM/MM energy terms with DFTB Dmitry Nilov (Sat Dec 18 2010 - 00:39:52 PST)
[AMBER] restart md simulation from different points Jorgen Simonsen (Thu Dec 16 2010 - 08:45:29 PST)
- Re: [AMBER] restart md simulation from different points Jason Swails (Thu Dec 16 2010 - 11:38:41 PST)
[AMBER] cnts topology federica de leo (Thu Dec 16 2010 - 09:28:22 PST)
- Re: [AMBER] cnts topology Bill Ross (Thu Dec 16 2010 - 13:36:10 PST)
- Re: [AMBER] cnts topology Vitaly Chaban (Thu Dec 16 2010 - 15:18:19 PST)
[AMBER] NAMD cal with AMBER forces: Polarizable parameters in AMBER Xiao Ju Zhang (Thu Dec 16 2010 - 11:22:16 PST)
- Re: [AMBER] NAMD cal with AMBER forces: Polarizable parameters in AMBER Jason Swails (Thu Dec 16 2010 - 11:44:53 PST)
[AMBER] Issues with Calculating P^2 values with RMS fits Daniel Scott (Thu Dec 16 2010 - 12:05:56 PST)
- Re: [AMBER] Issues with Calculating P^2 values with RMS fits Jason Swails (Thu Dec 16 2010 - 21:32:02 PST)
[AMBER] force field John S (Thu Dec 16 2010 - 15:30:46 PST)
- Re: [AMBER] force field XiaoJu Zhang (Thu Dec 16 2010 - 18:51:19 PST)
[AMBER] Residue building and controlling the substitutes John S (Thu Dec 16 2010 - 15:39:48 PST)
- Re: [AMBER] Residue building and controlling the substitutes Bill Ross (Thu Dec 16 2010 - 15:53:57 PST)
[AMBER] error in MD of modeled & docked protein - DAN complex Sangita Kachhap (Thu Dec 16 2010 - 01:22:38 PST)
- Re: [AMBER] error in MD of modeled & docked protein - DAN complex case (Fri Dec 17 2010 - 06:07:59 PST)
  - Re: [AMBER] error in MD of modeled & docked protein - DAN complex Sangita Kachhap (Fri Dec 17 2010 - 08:27:34 PST)
    - Re: [AMBER] error in MD of modeled & docked protein - DAN complex case (Fri Dec 17 2010 - 08:44:49 PST)
    - Re: [AMBER] error in MD of modeled & docked protein - DAN complex Sangita Kachhap (Fri Dec 17 2010 - 10:04:33 PST)
[AMBER] Is this output OK from the hybrid remd? Bongkeun Kim (Fri Dec 17 2010 - 00:13:31 PST)
- Re: [AMBER] Is this output OK from the hybrid remd? Jason Swails (Fri Dec 17 2010 - 04:32:56 PST)
  - Re: [AMBER] Is this output OK from the hybrid remd? Bongkeun Kim (Fri Dec 17 2010 - 08:13:47 PST)
- Re: [AMBER] Is this output OK from the hybrid remd? case (Fri Dec 17 2010 - 06:19:07 PST)
  - Re: [AMBER] Is this output OK from the hybrid remd? Bongkeun Kim (Fri Dec 17 2010 - 08:43:59 PST)
    - Re: [AMBER] Is this output OK from the hybrid remd? Jason Swails (Fri Dec 17 2010 - 19:37:41 PST)
    - Re: [AMBER] Is this output OK from the hybrid remd? Bongkeun Kim (Fri Dec 17 2010 - 20:33:39 PST)
    - Re: [AMBER] Is this output OK from the hybrid remd? Bongkeun Kim (Fri Dec 17 2010 - 21:00:14 PST)
    - Re: [AMBER] Is this output OK from the hybrid remd? Jason Swails (Sat Dec 18 2010 - 04:16:13 PST)
    - Re: [AMBER] Is this output OK from the hybrid remd? Bongkeun Kim (Sat Dec 18 2010 - 08:52:39 PST)
    - Re: [AMBER] Is this output OK from the hybrid remd? Carlos Simmerling (Sat Dec 18 2010 - 10:45:44 PST)
    - Re: [AMBER] Is this output OK from the hybrid remd? Bongkeun Kim (Sat Dec 18 2010 - 11:23:36 PST)
    - Re: [AMBER] Is this output OK from the hybrid remd? Carlos Simmerling (Sun Dec 19 2010 - 09:16:10 PST)
    - [AMBER] Any one reported a drug dissociation barrier could be as high as 100 kcal/mol ? Catein Catherine (Sun Dec 19 2010 - 10:32:36 PST)
    - Re: [AMBER] Any one reported a drug dissociation barrier could be as high as 100 kcal/mol ? case (Sun Dec 19 2010 - 10:44:38 PST)
    - [AMBER] A drug dissociation barrier/energy was found to be as high as 100 kcal/mol. Catein Catherine (Sun Dec 19 2010 - 21:17:31 PST)
    - Re: [AMBER] Any one reported a drug dissociation barrier could be as high as 100 kcal/mol ? Dmitry Mukha (Sun Dec 19 2010 - 10:53:38 PST)
    - Re: [AMBER] Any one reported a drug dissociation barrier could be as high as 100 kcal/mol ? Jason Swails (Sun Dec 19 2010 - 21:36:03 PST)
    - Re: [AMBER] Is this output OK from the hybrid remd? Bongkeun Kim (Sun Dec 19 2010 - 10:44:03 PST)
    - Re: [AMBER] Is this output OK from the hybrid remd? Bongkeun Kim (Sun Dec 19 2010 - 11:02:17 PST)
    - Re: [AMBER] Is this output OK from the hybrid remd? Jason Swails (Mon Dec 20 2010 - 08:53:51 PST)
    - Re: [AMBER] Is this output OK from the hybrid remd? Bongkeun Kim (Mon Dec 20 2010 - 09:30:43 PST)
    - Re: [AMBER] Is this output OK from the hybrid remd? Carlos Simmerling (Mon Dec 20 2010 - 09:36:41 PST)
    - Re: [AMBER] Is this output OK from the hybrid remd? Jason Swails (Mon Dec 20 2010 - 09:37:34 PST)
    - Re: [AMBER] Is this output OK from the hybrid remd? Bongkeun Kim (Mon Dec 20 2010 - 11:35:10 PST)
    - Re: [AMBER] Is this output OK from the hybrid remd? Daniel Roe (Tue Dec 21 2010 - 14:33:21 PST)
    - Re: [AMBER] Is this output OK from the hybrid remd? Bongkeun Kim (Wed Dec 22 2010 - 11:21:03 PST)
    - Re: [AMBER] Is this output OK from the hybrid remd? Daniel Roe (Wed Dec 22 2010 - 12:35:47 PST)
    - Re: [AMBER] Is this output OK from the hybrid remd? Bongkeun Kim (Wed Dec 22 2010 - 13:12:37 PST)
[AMBER] SCC-DFTB failure Dmitry Nilov (Fri Dec 17 2010 - 03:24:47 PST)
- Re: [AMBER] SCC-DFTB failure Gustavo Seabra (Fri Dec 17 2010 - 04:43:46 PST)
  - Re: [AMBER] SCC-DFTB failure Dmitry Nilov (Fri Dec 17 2010 - 05:20:14 PST)
[AMBER] MMPBAS.py.MPI George Tzotzos (Fri Dec 17 2010 - 07:37:24 PST)
- Re: [AMBER] MMPBAS.py.MPI Bill Miller III (Fri Dec 17 2010 - 07:59:42 PST)
  - Re: [AMBER] MMPBAS.py.MPI George Tzotzos (Fri Dec 17 2010 - 08:02:56 PST)
    - Re: [AMBER] MMPBAS.py.MPI Bill Miller III (Fri Dec 17 2010 - 08:12:12 PST)
    - Re: [AMBER] MMPBAS.py.MPI George Tzotzos (Fri Dec 17 2010 - 08:36:36 PST)
    - Re: [AMBER] MMPBAS.py.MPI Bill Miller III (Fri Dec 17 2010 - 08:50:27 PST)
    - Re: [AMBER] MMPBAS.py.MPI George Tzotzos (Fri Dec 17 2010 - 08:55:13 PST)
    - Re: [AMBER] MMPBAS.py.MPI Bill Miller III (Fri Dec 17 2010 - 09:04:09 PST)
[AMBER] Generation of separate crd files Anindya Sarkar (Fri Dec 17 2010 - 09:21:37 PST)
- Re: [AMBER] Generation of separate crd files case (Fri Dec 17 2010 - 11:35:41 PST)
- Re: [AMBER] Generation of separate crd files Bill Ross (Fri Dec 17 2010 - 11:55:39 PST)
  - Re: [AMBER] Generation of separate crd files Jason Swails (Fri Dec 17 2010 - 17:52:18 PST)
    - Re: [AMBER] Generation of separate crd files Anindya Sarkar (Tue Dec 21 2010 - 09:14:19 PST)
[AMBER] Error on applying MMPBSA.py Bug Fixes George Tzotzos (Fri Dec 17 2010 - 09:58:28 PST)
- Re: [AMBER] Error on applying MMPBSA.py Bug Fixes Bill Miller III (Fri Dec 17 2010 - 10:03:20 PST)
  - Re: [AMBER] Error on applying MMPBSA.py Bug Fixes George Tzotzos (Fri Dec 17 2010 - 10:05:45 PST)
[AMBER] MMPBSA test fail George Tzotzos (Fri Dec 17 2010 - 11:07:17 PST)
- Re: [AMBER] MMPBSA test fail Bill Miller III (Fri Dec 17 2010 - 11:16:22 PST)
  - Re: [AMBER] MMPBSA test fail George Tzotzos (Fri Dec 17 2010 - 11:31:26 PST)
    - Re: [AMBER] MMPBSA test fail Bill Miller III (Fri Dec 17 2010 - 11:36:24 PST)
- Re: [AMBER] MMPBSA test fail Jason Swails (Fri Dec 17 2010 - 16:39:05 PST)
  - Re: [AMBER] MMPBSA test fail George Tzotzos (Sat Dec 18 2010 - 05:06:41 PST)
    - Re: [AMBER] MMPBSA test fail George Tzotzos (Sat Dec 18 2010 - 05:10:58 PST)
    - Re: [AMBER] MMPBSA test fail Bill Miller III (Sat Dec 18 2010 - 05:24:06 PST)
    - Re: [AMBER] MMPBSA test fail George Tzotzos (Sat Dec 18 2010 - 05:40:33 PST)
    - Re: [AMBER] MMPBSA test fail Bill Miller III (Sat Dec 18 2010 - 05:49:26 PST)
    - Re: [AMBER] MMPBSA test fail George Tzotzos (Sat Dec 18 2010 - 06:11:27 PST)
    - Re: [AMBER] MMPBSA test fail Bill Miller III (Sat Dec 18 2010 - 06:15:24 PST)
    - Re: [AMBER] MMPBSA test fail George Tzotzos (Sat Dec 18 2010 - 06:22:17 PST)
    - Re: [AMBER] MMPBSA test fail Jason Swails (Sat Dec 18 2010 - 11:45:05 PST)
[AMBER] problem with MM-PBSA Maryam Hamzehee (Sun Dec 19 2010 - 03:06:33 PST)
- Re: [AMBER] problem with MM-PBSA Bill Miller III (Sun Dec 19 2010 - 04:46:08 PST)
  - Re: [AMBER] problem with MM-PBSA Maryam Hamzehee (Mon Dec 20 2010 - 05:30:41 PST)
  - [AMBER] MMPBSA.py.MPI tests George Tzotzos (Tue Dec 21 2010 - 07:39:18 PST)
    - Re: [AMBER] MMPBSA.py.MPI tests Bill Miller III (Tue Dec 21 2010 - 07:43:38 PST)
    - Re: [AMBER] MMPBSA.py.MPI tests George Tzotzos (Tue Dec 21 2010 - 08:20:45 PST)
    - Re: [AMBER] MMPBSA.py.MPI tests Bill Miller III (Tue Dec 21 2010 - 08:42:19 PST)
    - Re: [AMBER] MMPBSA.py.MPI tests George Tzotzos (Tue Dec 21 2010 - 08:45:19 PST)
[AMBER] Error with multiple GPU run: kCalculateMolecularVirial Andre Serobian (Sun Dec 19 2010 - 03:05:45 PST)
- Re: [AMBER] Error with multiple GPU run: kCalculateMolecularVirial Gould, Ian R (Sun Dec 19 2010 - 05:20:08 PST)
- Re: [AMBER] Error with multiple GPU run: kCalculateMolecularVirial Ross Walker (Sun Dec 19 2010 - 08:22:59 PST)
[AMBER] reordering of atoms in mdcrd file leila karami (Sun Dec 19 2010 - 10:28:29 PST)
[AMBER] problem of ptraj fancy2012 (Sun Dec 19 2010 - 18:54:16 PST)
- Re: [AMBER] problem of ptraj Jason Swails (Sun Dec 19 2010 - 21:25:02 PST)
  - Re: [AMBER] problem of ptraj fancy2012 (Mon Dec 20 2010 - 02:32:55 PST)
    - Re: [AMBER] problem of ptraj Daniel Roe (Mon Dec 20 2010 - 08:40:42 PST)
    - Re: [AMBER] problem of ptraj fancy2012 (Sun Dec 26 2010 - 19:28:30 PST)
[AMBER] watershell / number of waters and which waters? leila karami (Mon Dec 20 2010 - 03:05:19 PST)
[AMBER] AmberTools NAB corrections Markus Kaukonen (Mon Dec 20 2010 - 05:32:00 PST)
- Re: [AMBER] AmberTools NAB corrections case (Mon Dec 20 2010 - 05:55:12 PST)
[AMBER] compiling error for amber10 in parallel version with g++4.3.2, gfortan 4.3, mpich or lam or openmpi michelle.dupont.ulg.ac.be (Mon Dec 20 2010 - 07:52:49 PST)
- Re: [AMBER] compiling error for amber10 in parallel version with g++4.3.2, gfortan 4.3, mpich or lam or openmpi case (Mon Dec 20 2010 - 20:21:23 PST)
[AMBER] Flip chirality John S (Mon Dec 20 2010 - 10:21:50 PST)
- Re: [AMBER] Flip chirality Per Jr. Greisen (Mon Dec 20 2010 - 10:26:35 PST)
- Re: [AMBER] Flip chirality FyD (Tue Dec 21 2010 - 05:46:12 PST)
  - [AMBER] Possibly wrong dihedrals assignment in the frcmod.parmbsc0 file Alex Spasic (Tue Dec 21 2010 - 09:01:18 PST)
    - Re: [AMBER] Possibly wrong dihedrals assignment in the frcmod.parmbsc0 file Thomas Cheatham III (Tue Apr 05 2011 - 09:31:08 PDT)
    - Re: [AMBER] Possibly wrong dihedrals assignment in the frcmod.parmbsc0 file Alex Spasic (Tue Apr 05 2011 - 12:03:02 PDT)
    - Re: [AMBER] Possibly wrong dihedrals assignment in the frcmod.parmbsc0 file Thomas Cheatham III (Tue Apr 05 2011 - 12:42:56 PDT)
    - Re: [AMBER] Possibly wrong dihedrals assignment in the frcmod.parmbsc0 file Alex Spasic (Tue Apr 05 2011 - 13:44:05 PDT)
[AMBER] suppose.nab Mark Foster (Mon Dec 20 2010 - 11:53:08 PST)
- Re: [AMBER] suppose.nab Richard Owczarzy (Mon Dec 20 2010 - 12:58:11 PST)
- Re: [AMBER] suppose.nab case (Mon Dec 20 2010 - 13:16:36 PST)
  - Re: [AMBER] suppose.nab Mark Foster (Mon Dec 20 2010 - 13:54:27 PST)
    - Re: [AMBER] suppose.nab case (Mon Dec 20 2010 - 19:48:33 PST)
[AMBER] evaluating physical meaning of Amber results Bozell, Joseph John (Mon Dec 20 2010 - 13:54:19 PST)
- Re: [AMBER] evaluating physical meaning of Amber results Richard Owczarzy (Mon Dec 20 2010 - 15:13:54 PST)
  - Re: [AMBER] evaluating physical meaning of Amber results Bozell, Joseph John (Wed Dec 22 2010 - 04:55:46 PST)
[AMBER] What is the Value of C° (standard concentration) in calculating Free Energy sunita gupta (Mon Dec 20 2010 - 22:56:52 PST)
- Re: [AMBER] What is the Value of C° (standard concentration) in calculating Free Energy Adrian Roitberg (Mon Dec 20 2010 - 23:57:20 PST)
[AMBER] Regarding Anal energy decomposition aneesh cna (Tue Dec 21 2010 - 00:51:10 PST)
[AMBER] RESP Dipole moment Eliac Brown (Tue Dec 21 2010 - 09:31:53 PST)
- Re: [AMBER] RESP Dipole moment Andreas Goetz (Wed Dec 22 2010 - 13:07:04 PST)
- Re: [AMBER] RESP Dipole moment FyD (Thu Dec 23 2010 - 02:00:44 PST)
[AMBER] Test Message - Do not reply. Ross Walker (Tue Dec 21 2010 - 23:35:20 PST)
[AMBER] RMSD for two trajectories Maryam Hamzehee (Wed Dec 22 2010 - 04:31:26 PST)
- Re: [AMBER] RMSD for two trajectories Bill Ross (Wed Dec 22 2010 - 15:45:05 PST)
- Re: [AMBER] RMSD for two trajectories Niel Henriksen (Wed Dec 22 2010 - 17:20:30 PST)
- Re: [AMBER] RMSD for two trajectories setyanto md (Wed Dec 22 2010 - 18:04:46 PST)
- Re: [AMBER] RMSD for two trajectories Bill Ross (Wed Dec 22 2010 - 18:39:45 PST)
[AMBER] water molecules Beale, John (Wed Dec 22 2010 - 04:48:38 PST)
- Re: [AMBER] water molecules M. L. Dodson (Wed Dec 22 2010 - 06:04:20 PST)
[AMBER] Possibly wrong dihedrals assignment in the frcmod.parmbsc0 file Alex Spasic (Wed Dec 22 2010 - 10:26:10 PST)
- Re: [AMBER] Possibly wrong dihedrals assignment in the frcmod.parmbsc0 file case (Wed Dec 22 2010 - 10:47:25 PST)
- Re: [AMBER] Possibly wrong dihedrals assignment in the frcmod.parmbsc0 file Hopkins, Robert (Mon Mar 28 2011 - 12:16:33 PDT)
[AMBER] Using REDUCE George Tzotzos (Wed Dec 22 2010 - 10:44:38 PST)
- Re: [AMBER] Using REDUCE case (Wed Dec 22 2010 - 10:51:38 PST)
[AMBER] Could not find angle parameter: FE - o - c3 Ashutosh Shandilya (Wed Dec 22 2010 - 21:15:30 PST)
[AMBER] Join my network on LinkedIn Maryam Hamzehee via LinkedIn (Thu Dec 23 2010 - 05:34:44 PST)
[AMBER] 25th Molecular Modelling Workshop 2011 Announcement Tatyana Shubina (Thu Dec 23 2010 - 07:20:44 PST)
[AMBER] native number of contacts Rilei Yu (Fri Dec 24 2010 - 07:17:49 PST)
[AMBER] GTX470 and Amber 11 Cuda tests filip fratev (Fri Dec 24 2010 - 23:14:04 PST)
- Re: [AMBER] GTX470 and Amber 11 Cuda tests filip fratev (Sat Dec 25 2010 - 03:09:11 PST)
  - Re: [AMBER] GTX470 and Amber 11 Cuda tests Sergio R Aragon (Sat Dec 25 2010 - 10:41:14 PST)
[AMBER] REMD number of replica Sangita Kachhap (Sat Dec 25 2010 - 04:53:28 PST)
- Re: [AMBER] REMD number of replica Carlos Simmerling (Sat Dec 25 2010 - 08:33:37 PST)
  - Re: [AMBER] REMD number of replica Sangita Kachhap (Sat Dec 25 2010 - 11:07:49 PST)
    - Re: [AMBER] REMD number of replica Carlos Simmerling (Sun Dec 26 2010 - 09:27:11 PST)
    - Re: [AMBER] REMD number of replica Sangita Kachhap (Mon Dec 27 2010 - 08:25:30 PST)
[AMBER] conversion of gromacs trajrctory file (xtc) to amber trajectory file (mdcrd) / problem in water moecules. leila karami (Sun Dec 26 2010 - 03:24:02 PST)
- Re: [AMBER] conversion of gromacs trajrctory file (xtc) to amber trajectory file (mdcrd) / problem in water moecules. Oliver Grant (Sun Dec 26 2010 - 07:33:36 PST)
- Re: [AMBER] conversion of gromacs trajrctory file (xtc) to amber trajectory file (mdcrd) / problem in water moecules. case (Sun Dec 26 2010 - 15:34:13 PST)
  - Re: [AMBER] conversion of gromacs trajrctory file (xtc) to amber trajectory file (mdcrd) / problem in water moecules. Jason Swails (Sun Dec 26 2010 - 15:38:06 PST)
[AMBER] watershell / number of waters and which waters? leila karami (Sun Dec 26 2010 - 06:01:07 PST)
[AMBER] conversion of gromacs trajrctory file (xtc) to amber trajectory file (mdcrd) / problem in water moecules. leila karami (Sun Dec 26 2010 - 07:47:01 PST)
- Re: [AMBER] conversion of gromacs trajrctory file (xtc) to amber trajectory file (mdcrd) / problem in water moecules. Bill Ross (Sun Dec 26 2010 - 10:59:22 PST)
- Re: [AMBER] conversion of gromacs trajrctory file (xtc) to amber trajectory file (mdcrd) / problem in water moecules. Bill Ross (Sun Dec 26 2010 - 20:36:28 PST)
  - Re: [AMBER] conversion of gromacs trajrctory file (xtc) to amber trajectory file (mdcrd) / problem in water moecules. case (Mon Dec 27 2010 - 06:02:52 PST)
[AMBER] QM/MM-MD binding energy Eliac Brown (Sun Dec 26 2010 - 08:49:51 PST)
- Re: [AMBER] QM/MM-MD binding energy Markus Kaukonen (Sun Dec 26 2010 - 09:23:12 PST)
  - Re: [AMBER] QM/MM-MD binding energy Eliac Brown (Sun Dec 26 2010 - 09:28:17 PST)
    - Re: [AMBER] QM/MM-MD binding energy Markus Kaukonen (Sun Dec 26 2010 - 09:46:58 PST)
    - Re: [AMBER] QM/MM-MD binding energy Jason Swails (Sun Dec 26 2010 - 15:06:20 PST)
    - Re: [AMBER] QM/MM-MD binding energy Eliac Brown (Sun Dec 26 2010 - 18:42:44 PST)
    - Re: [AMBER] QM/MM-MD binding energy Jason Swails (Sun Dec 26 2010 - 20:26:18 PST)
    - Re: [AMBER] QM/MM-MD binding energy Eliac Brown (Sun Dec 26 2010 - 20:51:28 PST)
    - Re: [AMBER] QM/MM-MD binding energy Jason Swails (Sun Dec 26 2010 - 21:23:18 PST)
    - Re: [AMBER] QM/MM-MD binding energy case (Mon Dec 27 2010 - 07:54:14 PST)
[AMBER] about the Sietraj xuemeiwang1103 (Sun Dec 26 2010 - 22:22:44 PST)
[AMBER] conversion of gromacs trajectory file (xtc) to amber trajectory file (mdcrd) / problem in water molecules leila karami (Mon Dec 27 2010 - 01:28:03 PST)
- Re: [AMBER] conversion of gromacs trajectory file (xtc) to amber trajectory file (mdcrd) / problem in water molecules case (Mon Dec 27 2010 - 06:12:43 PST)
[AMBER] time in ptraj atila petrosian (Mon Dec 27 2010 - 01:43:51 PST)
- Re: [AMBER] time in ptraj case (Mon Dec 27 2010 - 06:13:25 PST)
[AMBER] conversion of gromacs trajectory file (xtc) to amber trajectory file (mdcrd) / problem in water molecules leila karami (Mon Dec 27 2010 - 06:40:14 PST)
[AMBER] conversion of gromacs trajectory file (xtc) to amber trajectory file (mdcrd) / problem in water molecules leila karami (Mon Dec 27 2010 - 10:27:54 PST)
- Re: [AMBER] conversion of gromacs trajectory file (xtc) to amber trajectory file (mdcrd) / problem in water molecules case (Tue Dec 28 2010 - 05:59:42 PST)
[AMBER] problem with MM-PBSA Maryam Hamzehee (Tue Dec 28 2010 - 03:17:03 PST)
- Re: [AMBER] problem with MM-PBSA case (Tue Dec 28 2010 - 06:19:22 PST)
  - Re: [AMBER] problem with MM-PBSA Maryam Hamzehee (Tue Dec 28 2010 - 09:37:53 PST)
    - Re: [AMBER] problem with MM-PBSA case (Wed Dec 29 2010 - 06:01:05 PST)
    - [AMBER] Is MM-PBSA energy for protein-DNA (~ 40 base pairs) as large as -400 kcal/mol reasonable? Catein Catherine (Wed Dec 29 2010 - 07:26:58 PST)
    - Re: [AMBER] Is MM-PBSA energy for protein-DNA (~ 40 base pairs) as large as -400 kcal/mol reasonable? Kevin Hauser (Wed Dec 29 2010 - 08:02:42 PST)
    - Re: [AMBER] Is MM-PBSA energy for protein-DNA (~ 40 base pairs) as large as -400 kcal/mol reasonable? Jason Swails (Wed Dec 29 2010 - 10:42:01 PST)
    - [AMBER] Are MM-PBSA/GBSA analysis based on MD in implicit or explicit solvent are both aceptable? Catein Catherine (Wed Dec 29 2010 - 07:31:37 PST)
    - Re: [AMBER] Are MM-PBSA/GBSA analysis based on MD in implicit or explicit solvent are both aceptable? Jason Swails (Wed Dec 29 2010 - 10:46:50 PST)
[AMBER] flag dihedrals in the .prmtop Z.Xiao (Tue Dec 28 2010 - 23:43:24 PST)
- Re: [AMBER] flag dihedrals in the .prmtop Jason Swails (Wed Dec 29 2010 - 00:24:04 PST)
  - Re: [AMBER] flag dihedrals in the .prmtop Z.Xiao (Wed Dec 29 2010 - 01:38:23 PST)
[AMBER] conversion of gromacs trajectory file (xtc) to amber trajectory file (mdcrd) / problem in water molecules leila karami (Wed Dec 29 2010 - 02:47:59 PST)
- Re: [AMBER] conversion of gromacs trajectory file (xtc) to amber trajectory file (mdcrd) / problem in water molecules case (Wed Dec 29 2010 - 05:57:42 PST)
[AMBER] can I use ambmask for trajectory file (mdcrd)? atila petrosian (Wed Dec 29 2010 - 06:13:59 PST)
[AMBER] MMPBSA binding energy Eliac Brown (Wed Dec 29 2010 - 17:11:44 PST)
- Re: [AMBER] MMPBSA binding energy Jason Swails (Wed Dec 29 2010 - 21:01:16 PST)
[AMBER] how to add phosphate group in protein Sangita Kachhap (Thu Dec 30 2010 - 01:45:02 PST)
- Re: [AMBER] how to add phosphate group in protein Jason Swails (Thu Dec 30 2010 - 08:42:28 PST)
  - Re: [AMBER] how to add phosphate group in protein Sangita Kachhap (Thu Dec 30 2010 - 08:48:54 PST)
  - Re: [AMBER] how to add phosphate group in protein Sangita Kachhap (Sat Jan 08 2011 - 01:32:25 PST)
  - Re: [AMBER] how to add phosphate group in protein Sangita Kachhap (Sat Jan 08 2011 - 01:45:22 PST)
    - Re: [AMBER] how to add phosphate group in protein case (Sat Jan 08 2011 - 05:16:37 PST)
    - Re: [AMBER] how to add phosphate group in protein Sangita Kachhap (Sat Jan 08 2011 - 07:03:38 PST)
    - Re: [AMBER] how to add phosphate group in protein case (Sat Jan 08 2011 - 07:54:31 PST)
    - Re: [AMBER] how to add phosphate group in protein Sangita Kachhap (Sat Jan 08 2011 - 08:59:20 PST)
    - Re: [AMBER] how to add phosphate group in protein Jason Swails (Sat Jan 08 2011 - 09:42:21 PST)
    - Re: [AMBER] how to add phosphate group in protein Sangita Kachhap (Sat Jan 08 2011 - 11:59:32 PST)
    - Re: [AMBER] how to add phosphate group in protein Jason Swails (Sat Jan 08 2011 - 12:25:22 PST)
[AMBER] Fw: configuring options for Amber tools amit banerjee (Thu Dec 30 2010 - 02:16:47 PST)
- Re: [AMBER] Fw: configuring options for Amber tools case (Thu Dec 30 2010 - 05:26:09 PST)
  - Re: [AMBER] Fw: configuring options for Amber tools Catein Catherine (Thu Dec 30 2010 - 06:47:16 PST)
    - [AMBER] How to define self-rotation of the molecule in VMD when preparing movie of a MD simulation? Catein Catherine (Thu Dec 30 2010 - 06:49:59 PST)
    - Re: [AMBER] Fw: configuring options for Amber tools Jason Swails (Thu Dec 30 2010 - 08:35:13 PST)
  - Re: [AMBER] Fw: configuring options for Amber tools amit banerjee (Thu Dec 30 2010 - 22:29:46 PST)
[AMBER] conversion of gromacs trajectory file (xtc) to amber trajectory file (mdcrd) / problem in water molecules leila karami (Thu Dec 30 2010 - 02:34:03 PST)
- Re: [AMBER] conversion of gromacs trajectory file (xtc) to amber trajectory file (mdcrd) / problem in water molecules Bill Ross (Mon Dec 27 2010 - 09:56:00 PST)
- Re: [AMBER] conversion of gromacs trajectory file (xtc) to amber trajectory file (mdcrd) / problem in water molecules Bill Ross (Wed Dec 29 2010 - 09:46:27 PST)
  - Re: [AMBER] conversion of gromacs trajectory file (xtc) to amber trajectory file (mdcrd) / problem in water molecules leila karami (Wed Dec 29 2010 - 22:43:25 PST)
[AMBER] dissacharide subrata paul (Thu Dec 30 2010 - 04:49:42 PST)
- Re: [AMBER] dissacharide Daniel Roe (Thu Dec 30 2010 - 06:58:56 PST)
[AMBER] can I use ambmask for trajectory file (mdcrd)? atila petrosian (Thu Dec 30 2010 - 05:39:36 PST)
[AMBER] rdf subrata paul (Thu Dec 30 2010 - 07:26:53 PST)
[AMBER] about the Sietraj xuemeiwang1103 (Thu Dec 30 2010 - 17:11:47 PST)
- Re: [AMBER] about the Sietraj case (Thu Dec 30 2010 - 18:57:19 PST)
- Re: [AMBER] about the Sietraj Qizhi Cui (Fri Dec 31 2010 - 16:48:38 PST)
  - Re: [AMBER] about the Sietraj xuemeiwang1103 (Wed Jan 05 2011 - 05:03:17 PST)
- Re: [AMBER] about the Sietraj Purisima, Enrico (Fri Jan 07 2011 - 13:23:21 PST)
[AMBER] Luck or Black Box Eliac Brown (Thu Dec 30 2010 - 20:55:59 PST)
- Re: [AMBER] Luck or Black Box manoj singh (Thu Dec 30 2010 - 21:40:11 PST)
[AMBER] where are the parameters controlling the cis/trans configuration of Proline ? Jose Borreguero (Fri Dec 31 2010 - 09:32:06 PST)
- Re: [AMBER] where are the parameters controlling the cis/trans configuration of Proline ? steinbrt.rci.rutgers.edu (Fri Dec 31 2010 - 21:12:13 PST)
  - Re: [AMBER] where are the parameters controlling the cis/trans configuration of Proline ? Jose Borreguero (Sat Jan 01 2011 - 06:56:02 PST)
    - Re: [AMBER] where are the parameters controlling the cis/trans configuration of Proline ? Carlos Simmerling (Sat Jan 01 2011 - 07:02:05 PST)
    - Re: [AMBER] where are the parameters controlling the cis/trans configuration of Proline ? Jose Borreguero (Sat Jan 01 2011 - 08:30:44 PST)
[AMBER] GTP parameters Jacopo Sgrignani (Fri Dec 31 2010 - 09:36:06 PST)
- Re: [AMBER] GTP parameters Jason Swails (Fri Dec 31 2010 - 16:09:39 PST)
[AMBER] Determining rings in a molecule Pooja Khurana (Sat Jan 01 2011 - 01:51:14 PST)
- Re: [AMBER] Determining rings in a molecule manoj singh (Sat Jan 01 2011 - 13:49:35 PST)
- Re: [AMBER] Determining rings in a molecule Bill Ross (Tue Jan 04 2011 - 12:57:59 PST)
  - Re: [AMBER] Determining rings in a molecule gilbert (Tue Jan 04 2011 - 19:07:30 PST)
[AMBER] H-bond analysis Sangita Kachhap (Sat Jan 01 2011 - 11:04:47 PST)
[AMBER] QM/MM energy Eliac Brown (Sat Jan 01 2011 - 20:03:41 PST)
- Re: [AMBER] QM/MM energy Jason Swails (Sat Jan 01 2011 - 21:52:03 PST)
[AMBER] MM-PBSA AND mm_pbsa_statistics.pl Maryam Hamzehee (Sun Jan 02 2011 - 04:42:04 PST)
[AMBER] calculations failed on GPU with ntr=1 (with bugfix 11 applied) Dmitry Mukha (Sun Jan 02 2011 - 06:12:13 PST)
- Re: [AMBER] calculations failed on GPU with ntr=1 (with bugfix 11 applied) Ross Walker (Sun Jan 02 2011 - 09:17:32 PST)
  - [AMBER] Can we doing potential of mean force for two protein complex? Catein Catherine (Mon Jan 03 2011 - 03:32:04 PST)
    - [AMBER] Problem in using MMPBSA.py with Amber10 Wei Huang (Mon Jan 03 2011 - 08:52:38 PST)
    - Re: [AMBER] Problem in using MMPBSA.py with Amber10 Jason Swails (Mon Jan 03 2011 - 11:27:18 PST)
    - Re: [AMBER] Problem in using MMPBSA.py with Amber10 Wei Huang (Mon Jan 03 2011 - 11:58:15 PST)
    - Re: [AMBER] Problem in using MMPBSA.py with Amber10 Jason Swails (Mon Jan 03 2011 - 15:29:38 PST)
  - Re: [AMBER] calculations failed on GPU with ntr=1 (with bugfix 11 applied) peker milas (Mon Jan 03 2011 - 07:39:46 PST)
    - Re: [AMBER] calculations failed on GPU with ntr=1 (with bugfix 11 applied) Ross Walker (Mon Jan 03 2011 - 10:17:21 PST)
[AMBER] water mediated hydrogen bonds - ptraj leila karami (Sun Jan 02 2011 - 07:25:51 PST)
[AMBER] Progress of calculation in MMPBSA.py.MPI mish (Mon Jan 03 2011 - 04:21:42 PST)
- Re: [AMBER] Progress of calculation in MMPBSA.py.MPI Jason Swails (Mon Jan 03 2011 - 15:19:37 PST)
[AMBER] How to setup QM/MM-GBSA calculation ? mish (Mon Jan 03 2011 - 09:35:21 PST)
[AMBER] H-bond analysis interpratation Sangita Kachhap (Mon Jan 03 2011 - 19:57:44 PST)
- Re: [AMBER] H-bond analysis interpratation aneesh cna (Tue Jan 04 2011 - 04:20:41 PST)
  - [AMBER] Any beta-alanine parameter in amber? Catein Catherine (Tue Jan 04 2011 - 06:04:13 PST)
    - [AMBER] Any way to restraint the helicity of an alpha-helix chains Catein Catherine (Tue Jan 04 2011 - 06:10:49 PST)
    - Re: [AMBER] Any way to restraint the helicity of an alpha-helix chains Ilyas Yildirim (Tue Jan 04 2011 - 07:50:31 PST)
    - [AMBER] Can I use bfactor (rmsf) to conclude if the protein is stabilized upon drug binding? Catein Catherine (Tue Jan 04 2011 - 08:26:21 PST)
  - Re: [AMBER] H-bond analysis interpratation Sangita Kachhap (Tue Jan 04 2011 - 10:09:38 PST)
    - Re: [AMBER] H-bond analysis interpratation aneesh cna (Wed Jan 05 2011 - 02:16:52 PST)
    - Re: [AMBER] H-bond analysis interpratation Sangita Kachhap (Wed Jan 05 2011 - 03:40:56 PST)
    - Re: [AMBER] H-bond analysis interpratation Thomas Cheatham III (Wed Jan 05 2011 - 12:10:57 PST)
    - Re: [AMBER] H-bond analysis interpratation Sangita Kachhap (Wed Jan 05 2011 - 20:47:14 PST)
[AMBER] MMPBSA.py.MPI - Output discrepancies George Tzotzos (Tue Jan 04 2011 - 02:41:00 PST)
- Re: [AMBER] MMPBSA.py.MPI - Output discrepancies mish (Tue Jan 04 2011 - 02:52:47 PST)
  - Re: [AMBER] MMPBSA.py.MPI - Output discrepancies George Tzotzos (Tue Jan 04 2011 - 03:02:03 PST)
    - Re: [AMBER] MMPBSA.py.MPI - Output discrepancies mish (Tue Jan 04 2011 - 09:22:30 PST)
    - Re: [AMBER] MMPBSA.py.MPI - Output discrepancies George Tzotzos (Tue Jan 04 2011 - 10:03:56 PST)
    - Re: [AMBER] MMPBSA.py.MPI - Output discrepancies Jason Swails (Tue Jan 04 2011 - 11:02:57 PST)
- Re: [AMBER] MMPBSA.py.MPI - Output discrepancies Jason Swails (Tue Jan 04 2011 - 10:59:45 PST)
  - Re: [AMBER] MMPBSA.py.MPI - Output discrepancies George Tzotzos (Tue Jan 04 2011 - 11:35:01 PST)
    - Re: [AMBER] MMPBSA.py.MPI - Output discrepancies Jason Swails (Tue Jan 04 2011 - 13:32:42 PST)
    - Re: [AMBER] MMPBSA.py.MPI - Output discrepancies George Tzotzos (Wed Jan 05 2011 - 04:28:12 PST)
    - Re: [AMBER] MMPBSA.py.MPI - Output discrepancies Jason Swails (Wed Jan 05 2011 - 08:18:29 PST)
[AMBER] AMBER Shesh Nath (Tue Jan 04 2011 - 20:21:53 PST)
- Re: [AMBER] AMBER Raman Parkesh (Tue Jan 04 2011 - 20:29:36 PST)
  - Re: [AMBER] AMBER peker milas (Tue Jan 04 2011 - 20:48:55 PST)
  - Re: [AMBER] AMBER Shesh Nath (Tue Jan 04 2011 - 22:04:57 PST)
    - Re: [AMBER] AMBER peker milas (Tue Jan 04 2011 - 22:15:08 PST)
    - Re: [AMBER] AMBER Shesh Nath (Tue Jan 04 2011 - 22:25:48 PST)
[AMBER] antechamber error Andre Serobian (Tue Jan 04 2011 - 22:55:07 PST)
[AMBER] heavy atom rms Beale, John (Wed Jan 05 2011 - 05:06:26 PST)
- Re: [AMBER] heavy atom rms Bill Ross (Wed Jan 05 2011 - 12:16:29 PST)
- Re: [AMBER] heavy atom rms Thomas Cheatham III (Wed Jan 05 2011 - 12:19:52 PST)
[AMBER] rdf subrata paul (Wed Jan 05 2011 - 05:18:31 PST)
- Re: [AMBER] rdf Thomas Cheatham III (Wed Jan 05 2011 - 13:57:45 PST)
[AMBER] compile Amber 11 on IBM Power 7 Yubo Fan (Wed Jan 05 2011 - 06:07:56 PST)
- Re: [AMBER] compile Amber 11 on IBM Power 7 Jason Swails (Wed Jan 05 2011 - 08:13:52 PST)
[AMBER] Troubleshooting script <measure_equil_rmsd.ptraj> George Tzotzos (Wed Jan 05 2011 - 08:12:31 PST)
- Re: [AMBER] Troubleshooting script <measure_equil_rmsd.ptraj> Daniel Roe (Thu Jan 06 2011 - 06:47:28 PST)
 - Re: [AMBER] Troubleshooting script <measure_equil_rmsd.ptraj> George Tzotzos (Thu Jan 06 2011 - 07:06:21 PST)
[AMBER] sander.MPI compiled with mvapich2 fails to exit upon completion Vlad Cojocaru (Wed Jan 05 2011 - 09:44:44 PST)
[AMBER] EGB AM1 Eliac Brown (Wed Jan 05 2011 - 16:31:50 PST)
- Re: [AMBER] EGB AM1 Andreas Goetz (Wed Jan 05 2011 - 21:59:28 PST)
[AMBER] TI calculation: viewing lambda trajectories that are not 0 or 1 - (writing parm files) g t (Wed Jan 05 2011 - 23:02:15 PST)
- Re: [AMBER] TI calculation: viewing lambda trajectories that are not 0 or 1 - (writing parm files) steinbrt.rci.rutgers.edu (Thu Jan 06 2011 - 02:36:49 PST)
  - Re: [AMBER] TI calculation: viewing lambda trajectories that are not 0 or 1 - (writing parm files) g t (Thu Jan 06 2011 - 04:04:01 PST)
    - Re: [AMBER] TI calculation: viewing lambda trajectories that are not 0 or 1 - (writing parm files) Jason Swails (Thu Jan 06 2011 - 05:04:29 PST)
    - Re: [AMBER] TI calculation: viewing lambda trajectories that are not 0 or 1 - (writing parm files) g t (Fri Jan 07 2011 - 02:53:14 PST)
[AMBER] distance and angle cutoff values for hydrogen bond analysis atila petrosian (Wed Jan 05 2011 - 23:30:14 PST)
[AMBER] waters in interface between protein and dna / water mediated hydrogen bonds leila karami (Wed Jan 05 2011 - 23:46:55 PST)
[AMBER] SQM error case (Thu Jan 06 2011 - 04:53:48 PST)
[AMBER] Amber 11 - Bugfix 9 Bill Snapko (Thu Jan 06 2011 - 13:12:24 PST)
- Re: [AMBER] Amber 11 - Bugfix 9 Ross Walker (Thu Jan 06 2011 - 13:26:35 PST)
[AMBER] EEL energy term Eliac Brown (Thu Jan 06 2011 - 16:06:32 PST)
- Re: [AMBER] EEL energy term Eliac Brown (Thu Jan 06 2011 - 16:34:48 PST)
[AMBER] Heating the system from 100K to 300K nicholus bhattacharjee (Fri Jan 07 2011 - 00:44:38 PST)
- Re: [AMBER] Heating the system from 100K to 300K Carlos Simmerling (Fri Jan 07 2011 - 05:50:10 PST)
- Re: [AMBER] Heating the system from 100K to 300K Bill Ross (Fri Jan 07 2011 - 11:00:39 PST)
  - Re: [AMBER] Heating the system from 100K to 300K nicholus bhattacharjee (Fri Jan 07 2011 - 21:02:31 PST)
- Re: [AMBER] Heating the system from 100K to 300K Bill Ross (Sun Jan 09 2011 - 09:47:56 PST)
[AMBER] How to clean dihedral angles plot? Baptiste Legrand (Fri Jan 07 2011 - 06:23:37 PST)
- Re: [AMBER] How to clean dihedral angles plot? Baptiste Legrand (Mon Jan 10 2011 - 01:25:22 PST)
- Re: [AMBER] How to clean dihedral angles plot? Carlos Simmerling (Mon Jan 10 2011 - 03:21:26 PST)
  - Re: [AMBER] How to clean dihedral angles plot? Baptiste Legrand (Mon Jan 10 2011 - 05:51:12 PST)
[AMBER] NMR refinement in water: which water box? Baptiste Legrand (Fri Jan 07 2011 - 08:40:21 PST)
- Re: [AMBER] NMR refinement in water: which water box? case (Sat Jan 08 2011 - 05:00:35 PST)
- [AMBER] How to clean dihedral angles plot? Baptiste Legrand (Mon Jan 10 2011 - 00:41:49 PST)
[AMBER] Drifting RMSD George Tzotzos (Fri Jan 07 2011 - 10:32:58 PST)
- Re: [AMBER] Drifting RMSD Jason Swails (Fri Jan 07 2011 - 10:38:01 PST)
- Re: [AMBER] Drifting RMSD Sergio R Aragon (Fri Jan 07 2011 - 10:57:56 PST)
- Re: [AMBER] Drifting RMSD Thomas Cheatham III (Fri Jan 07 2011 - 11:00:48 PST)
[AMBER] local REMD Baldoni Hector Armando (Fri Jan 07 2011 - 11:06:35 PST)
[AMBER] Amber Shesh Nath (Sat Jan 08 2011 - 01:08:25 PST)
- Re: [AMBER] Amber case (Sat Jan 08 2011 - 05:12:19 PST)
  - Re: [AMBER] Amber Shesh Nath (Sun Jan 09 2011 - 21:19:22 PST)
    - [AMBER] problem with amber11 dcd file when runing a 20ns MD at a time xueqin pang (Mon Jan 10 2011 - 05:04:12 PST)
    - Re: [AMBER] problem with amber11 dcd file when runing a 20ns MD at a time case (Mon Jan 10 2011 - 06:05:50 PST)
    - Re: [AMBER] problem with amber11 dcd file when runing a 20ns MD at a time xueqin pang (Mon Jan 10 2011 - 07:08:31 PST)
[AMBER] waters in interface between protein and dna / water mediated hydrogen bonds leila karami (Sat Jan 08 2011 - 03:50:17 PST)
- Re: [AMBER] waters in interface between protein and dna / water mediated hydrogen bonds Bill Ross (Sun Jan 09 2011 - 09:53:33 PST)
[AMBER] GPU Code Update Ross Walker (Sat Jan 08 2011 - 08:57:28 PST)
- Re: [AMBER] GPU Code Update filip fratev (Sat Jan 08 2011 - 13:27:11 PST)
- Re: [AMBER] GPU Code Update filip fratev (Sun Jan 09 2011 - 16:26:56 PST)
[AMBER] Mutational energy on the protein Rilei Yu (Sat Jan 08 2011 - 23:21:07 PST)
- Re: [AMBER] Mutational energy on the protein Jason Swails (Sun Jan 09 2011 - 04:29:25 PST)
  - Re: [AMBER] Mutational energy on the protein Roman Osman (Sun Jan 09 2011 - 08:22:07 PST)
[AMBER] How to build Amber topology and other files for inorganic crystalline material? malay rana (Sun Jan 09 2011 - 02:06:52 PST)
- Re: [AMBER] How to build Amber topology and other files for inorganic crystalline material? case (Mon Jan 10 2011 - 06:22:28 PST)
[AMBER] water simulation subrata paul (Mon Jan 10 2011 - 06:21:38 PST)
- Re: [AMBER] water simulation case (Mon Jan 10 2011 - 06:56:13 PST)
  - Re: [AMBER] water simulation subrata paul (Mon Jan 10 2011 - 20:39:56 PST)
[AMBER] MMPBSA.py.MPI query amit dong (Mon Jan 10 2011 - 14:30:55 PST)
- Re: [AMBER] MMPBSA.py.MPI query Jason Swails (Mon Jan 10 2011 - 15:34:56 PST)
  - Re: [AMBER] MMPBSA.py.MPI query amit dong (Tue Jan 11 2011 - 09:25:17 PST)
    - Re: [AMBER] MMPBSA.py.MPI query Jason Swails (Wed Jan 12 2011 - 07:08:14 PST)
[AMBER] stripWAT command and saving a new trajectory Daniel Scott (Mon Jan 10 2011 - 14:52:56 PST)
- Re: [AMBER] stripWAT command and saving a new trajectory Jason Swails (Mon Jan 10 2011 - 15:41:31 PST)
[AMBER] problem with antechamber Ed Pate (Mon Jan 10 2011 - 19:54:36 PST)
- Re: [AMBER] problem with antechamber David A. Case (Tue Jan 11 2011 - 12:00:30 PST)
[AMBER] Amber Shesh Nath (Mon Jan 10 2011 - 20:19:19 PST)
- Re: [AMBER] Amber Jason Swails (Tue Jan 11 2011 - 07:15:32 PST)
  - [AMBER] Is it an artifact for potential-of-mean force calculation? Catein Catherine (Tue Jan 11 2011 - 07:59:40 PST)
    - Re: [AMBER] Is it an artifact for potential-of-mean force calculation? Carlos Simmerling (Tue Jan 11 2011 - 08:02:48 PST)
    - Re: [AMBER] Is it an artifact for potential-of-mean force calculation? Dmitry Nilov (Tue Jan 11 2011 - 08:31:31 PST)
- Re: [AMBER] Amber Daniel Roe (Tue Jan 11 2011 - 07:18:18 PST)
- Re: [AMBER] Amber David A. Case (Tue Jan 11 2011 - 12:00:45 PST)
  - Re: [AMBER] Amber Shesh Nath (Tue Jan 11 2011 - 20:06:57 PST)
[AMBER] QMMM-IGB=2 Eliac Brown (Mon Jan 10 2011 - 22:14:11 PST)
- Re: [AMBER] QMMM-IGB=2 Ross Walker (Tue Jan 11 2011 - 09:58:17 PST)
[AMBER] LINMIN FAILURE using amber 11 Jan Wahl (Tue Jan 11 2011 - 05:11:02 PST)
- Re: [AMBER] LINMIN FAILURE using amber 11 Jason Swails (Tue Jan 11 2011 - 07:05:07 PST)
  - Re: [AMBER] LINMIN FAILURE using amber 11 Jan Wahl (Tue Jan 11 2011 - 07:22:31 PST)
    - Re: [AMBER] LINMIN FAILURE using amber 11 Ben Roberts (Tue Jan 11 2011 - 08:38:32 PST)
    - Re: [AMBER] LINMIN FAILURE using amber 11 Jan Wahl (Tue Jan 11 2011 - 11:05:13 PST)
    - Re: [AMBER] LINMIN FAILURE using amber 11 Jason Swails (Tue Jan 11 2011 - 11:15:49 PST)
    - Re: [AMBER] LINMIN FAILURE using amber 11 Jan Wahl (Wed Jan 12 2011 - 01:03:12 PST)
  - [AMBER] ATOM TYPES for MODIFIED dCTP Jana Sefcikova 1 (Wed Nov 30 2011 - 12:32:39 PST)
- Re: [AMBER] LINMIN FAILURE using amber 11 Bill Ross (Wed Jan 12 2011 - 09:44:50 PST)
[AMBER] rmsf byres for crystal structure Ye MEI (Tue Jan 11 2011 - 06:22:36 PST)
[AMBER] Multiple-step Structural Overlay Edward M. (Tue Jan 11 2011 - 07:47:53 PST)
- Re: [AMBER] Multiple-step Structural Overlay Carlos Simmerling (Tue Jan 11 2011 - 07:57:04 PST)
- Re: [AMBER] Multiple-step Structural Overlay Federica Chiappori (Tue Jan 11 2011 - 09:40:32 PST)
[AMBER] problem with amber11 dcd file when runing a 20ns MD at a time xueqin pang (Tue Jan 11 2011 - 08:22:26 PST)
- Re: [AMBER] problem with amber11 dcd file when runing a 20ns MD at a time Jason Swails (Tue Jan 11 2011 - 08:44:06 PST)
[AMBER] the INP was not defined in MMPBSA.pl zhihong ke (Tue Jan 11 2011 - 09:53:59 PST)
[AMBER] Running 606580 atoms system on Kraken Hector Chang (Tue Jan 11 2011 - 11:52:39 PST)
- Re: [AMBER] Running 606580 atoms system on Kraken Adrian Roitberg (Tue Jan 11 2011 - 11:56:34 PST)
[AMBER] Different Versions of Amber: Comparable results? david condon (Tue Jan 11 2011 - 12:05:26 PST)
- Re: [AMBER] Different Versions of Amber: Comparable results? Jason Swails (Tue Jan 11 2011 - 12:20:38 PST)
- Re: [AMBER] Different Versions of Amber: Comparable results? Ross Walker (Tue Jan 11 2011 - 12:45:17 PST)
  - Re: [AMBER] Different Versions of Amber: Comparable results? david condon (Wed Jan 12 2011 - 13:32:03 PST)
[AMBER] using ptraj contacts command: double printing of last residue Liz Wheatley (Tue Jan 11 2011 - 12:17:54 PST)
[AMBER] strip :WAT command in ptraj Daniel Scott (Tue Jan 11 2011 - 12:39:52 PST)
- Re: [AMBER] strip :WAT command in ptraj Daniel Roe (Tue Jan 11 2011 - 13:48:21 PST)
[AMBER] Benchmarking sander.MPI and pmemd on a linux cluster with infiniband switch Ilyas Yildirim (Tue Jan 11 2011 - 12:58:54 PST)
- Re: [AMBER] Benchmarking sander.MPI and pmemd on a linux cluster with infiniband switch Jason Swails (Tue Jan 11 2011 - 14:32:24 PST)
  - Re: [AMBER] Benchmarking sander.MPI and pmemd on a linux cluster with infiniband switch Ilyas Yildirim (Wed Jan 12 2011 - 10:49:55 PST)
    - Re: [AMBER] Benchmarking sander.MPI and pmemd on a linux cluster with infiniband switch Jason Swails (Wed Jan 12 2011 - 11:45:14 PST)
    - Re: [AMBER] Benchmarking sander.MPI and pmemd on a linux cluster with infiniband switch Ilyas Yildirim (Wed Jan 12 2011 - 13:06:06 PST)
[AMBER] Disactivation torsional potential term in amber-NAMD stefano_elli.libero.it (Tue Jan 11 2011 - 15:49:58 PST)
[AMBER] Monte Carlo Steps in Constant pH simulation nicholus bhattacharjee (Wed Jan 12 2011 - 02:27:42 PST)
- Re: [AMBER] Monte Carlo Steps in Constant pH simulation Adrian Roitberg (Wed Jan 12 2011 - 02:52:23 PST)
[AMBER] MMPBSA.py.MPI fails to run on multiple nodes Jesper Sørensen (Wed Jan 12 2011 - 08:50:23 PST)
- Re: [AMBER] MMPBSA.py.MPI fails to run on multiple nodes Jason Swails (Wed Jan 12 2011 - 10:23:19 PST)
  - Re: [AMBER] MMPBSA.py.MPI fails to run on multiple nodes Jesper Sørensen (Sun Jan 16 2011 - 10:44:41 PST)
[AMBER] SGLD Sangita Kachhap (Wed Jan 12 2011 - 09:05:11 PST)
- Re: [AMBER] SGLD David A. Case (Wed Jan 12 2011 - 10:03:04 PST)
  - Re: [AMBER] SGLD Sangita Kachhap (Wed Jan 12 2011 - 10:21:03 PST)
[AMBER] parmchk tsurma.umich.edu (Wed Jan 12 2011 - 09:55:14 PST)
- Re: [AMBER] parmchk Jason Swails (Wed Jan 12 2011 - 10:26:15 PST)
  - Re: [AMBER] parmchk tsurma.umich.edu (Wed Jan 12 2011 - 10:40:13 PST)
- Re: [AMBER] parmchk David A. Case (Wed Jan 12 2011 - 10:25:46 PST)
  - Re: [AMBER] parmchk tsurma.umich.edu (Wed Jan 12 2011 - 10:41:03 PST)
[AMBER] Can we load rst files in leap? Baptiste Legrand (Wed Jan 12 2011 - 10:36:04 PST)
- Re: [AMBER] Can we load rst files in leap? Jason Swails (Wed Jan 12 2011 - 10:38:32 PST)
- Re: [AMBER] Can we load rst files in leap? Bill Ross (Wed Jan 12 2011 - 11:22:43 PST)
  - Re: [AMBER] Can we load rst files in leap? Baptiste Legrand (Thu Jan 13 2011 - 01:15:25 PST)
    - Re: [AMBER] Can we load rst files in leap? Jason Swails (Thu Jan 13 2011 - 05:31:40 PST)
    - Re: [AMBER] Can we load rst files in leap? Baptiste Legrand (Thu Jan 13 2011 - 05:53:25 PST)
    - Re: [AMBER] Can we load rst files in leap? Jason Swails (Thu Jan 13 2011 - 06:09:33 PST)
    - Re: [AMBER] Can we load rst files in leap? Baptiste Legrand (Thu Jan 13 2011 - 06:19:57 PST)
    - Re: [AMBER] Can we load rst files in leap? Jason Swails (Thu Jan 13 2011 - 06:39:48 PST)
    - Re: [AMBER] Can we load rst files in leap? Baptiste Legrand (Thu Jan 13 2011 - 09:07:37 PST)
[AMBER] Analyzing module for the glycosylations in glyco-protein using AMBER Anindya Sarkar (Wed Jan 12 2011 - 21:27:14 PST)
- Re: [AMBER] Analyzing module for the glycosylations in glyco-protein using AMBER Lachele Foley (Lists) (Thu Jan 13 2011 - 06:36:35 PST)
  - Re: [AMBER] Analyzing module for the glycosylations in glyco-protein using AMBER Anindya Sarkar (Thu Jan 13 2011 - 07:29:43 PST)
    - Re: [AMBER] Analyzing module for the glycosylations in glyco-protein using AMBER Oliver Grant (Thu Jan 13 2011 - 08:37:36 PST)
    - Re: [AMBER] Analyzing module for the glycosylations in glyco-protein using AMBER Anindya Sarkar (Thu Jan 13 2011 - 08:57:14 PST)
[AMBER] amber Shesh Nath (Wed Jan 12 2011 - 22:27:14 PST)
[AMBER] PowerEdge M710 with Intel Xeon Siavoush Dastmalchi (Thu Jan 13 2011 - 03:11:17 PST)
[AMBER] REMD maximum temperature Sangita Kachhap (Thu Jan 13 2011 - 10:30:32 PST)
- Re: [AMBER] REMD maximum temperature Carlos Simmerling (Thu Jan 13 2011 - 10:34:09 PST)
  - Re: [AMBER] REMD maximum temperature Sangita Kachhap (Thu Jan 13 2011 - 20:23:42 PST)
    - Re: [AMBER] REMD maximum temperature Carlos Simmerling (Mon Jan 17 2011 - 09:39:07 PST)
    - Re: [AMBER] REMD maximum temperature Sangita Kachhap (Mon Jan 17 2011 - 10:09:00 PST)
    - Re: [AMBER] REMD maximum temperature Carlos Simmerling (Mon Jan 17 2011 - 10:17:05 PST)
[AMBER] Local REMD Hector A. Baldoni (Thu Jan 13 2011 - 14:31:17 PST)
- Re: [AMBER] Local REMD Daniel Sindhikara (Thu Jan 13 2011 - 19:53:14 PST)
[AMBER] compilation failure of amber 10 Yubo Fan (Thu Jan 13 2011 - 15:01:25 PST)
- Re: [AMBER] compilation failure of amber 10 Jason Swails (Thu Jan 13 2011 - 15:11:11 PST)
  - Re: [AMBER] compilation failure of amber 10 Yubo Fan (Thu Jan 13 2011 - 18:42:13 PST)
    - Re: [AMBER] compilation failure of amber 10 Jason Swails (Thu Jan 13 2011 - 20:01:48 PST)
[AMBER] MMPBSA John S (Thu Jan 13 2011 - 19:22:24 PST)
- Re: [AMBER] MMPBSA Jason Swails (Thu Jan 13 2011 - 20:14:35 PST)
  - Re: [AMBER] MMPBSA John S (Fri Jan 14 2011 - 11:06:53 PST)
[AMBER] bad atom type: IP MMPBSA.py sodium Na+ ion [SOLVED] Oliver Grant (Fri Jan 14 2011 - 03:03:30 PST)
[AMBER] md Ashutosh Shandilya (Fri Jan 14 2011 - 04:11:49 PST)
- Re: [AMBER] md Jason Swails (Fri Jan 14 2011 - 05:55:12 PST)
- Re: [AMBER] md Ilyas Yildirim (Fri Jan 14 2011 - 07:16:25 PST)
[AMBER] Protein-Water Interaction Energy Beale, John (Fri Jan 14 2011 - 05:00:18 PST)
- Re: [AMBER] Protein-Water Interaction Energy Jason Swails (Fri Jan 14 2011 - 05:49:51 PST)
[AMBER] Use leaprc.ff99SB force field Jan Wahl (Fri Jan 14 2011 - 06:21:34 PST)
- Re: [AMBER] Use leaprc.ff99SB force field David A. Case (Fri Jan 14 2011 - 07:12:45 PST)
  - Re: [AMBER] Use leaprc.ff99SB force field Jan Wahl (Fri Jan 14 2011 - 07:40:57 PST)
    - Re: [AMBER] Use leaprc.ff99SB force field case (Sat Jan 15 2011 - 06:48:24 PST)
- Re: [AMBER] Use leaprc.ff99SB force field Bill Ross (Fri Jan 14 2011 - 09:47:08 PST)
  - Re: [AMBER] Use leaprc.ff99SB force field Jan Wahl (Fri Jan 14 2011 - 17:08:11 PST)
[AMBER] VMD Movie Daniel Scott (Fri Jan 14 2011 - 09:04:31 PST)
- Re: [AMBER] VMD Movie Jason Swails (Fri Jan 14 2011 - 09:22:16 PST)
[AMBER] MMPBSA increasing the number of receptor groups John S (Fri Jan 14 2011 - 17:27:50 PST)
[AMBER] phosphorylated cysteine Zhongjie Liang (Sat Jan 15 2011 - 01:38:37 PST)
- Re: [AMBER] phosphorylated cysteine FyD (Mon Jan 17 2011 - 03:02:11 PST)
[AMBER] Parameter missing in Glycan Jianhui Tian (Sat Jan 15 2011 - 19:20:34 PST)
- Re: [AMBER] Parameter missing in Glycan Lachele Foley (Lists) (Sat Jan 15 2011 - 20:44:15 PST)
  - Re: [AMBER] Parameter missing in Glycan Jianhui Tian (Sun Jan 16 2011 - 09:22:58 PST)
    - Re: [AMBER] Parameter missing in Glycan Lachele Foley (Lists) (Sun Jan 16 2011 - 09:38:31 PST)
    - Re: [AMBER] Parameter missing in Glycan Jianhui Tian (Sun Jan 16 2011 - 09:55:53 PST)
    - Re: [AMBER] Parameter missing in Glycan Lachele Foley (Lists) (Sun Jan 16 2011 - 10:10:02 PST)
[AMBER] AMBER Shesh Nath (Sun Jan 16 2011 - 20:38:45 PST)
- Re: [AMBER] AMBER david condon (Mon Jan 17 2011 - 05:49:11 PST)
  - Re: [AMBER] AMBER peker milas (Mon Jan 17 2011 - 06:58:28 PST)
[AMBER] Torsional parameters for S-C-C-N bond Millen, Andrea (Mon Jan 17 2011 - 15:45:39 PST)
- Re: [AMBER] Torsional parameters for S-C-C-N bond Jason Swails (Mon Jan 17 2011 - 21:00:06 PST)
  - Re: [AMBER] Torsional parameters for S-C-C-N bond Millen, Andrea (Tue Jan 18 2011 - 10:20:12 PST)
    - Re: [AMBER] Torsional parameters for S-C-C-N bond Jason Swails (Tue Jan 18 2011 - 10:26:52 PST)
[AMBER] AMBER Shesh Nath (Mon Jan 17 2011 - 20:29:49 PST)
- Re: [AMBER] AMBER juzer stationwala (Mon Jan 17 2011 - 20:36:39 PST)
  - Re: [AMBER] AMBER Jason Swails (Mon Jan 17 2011 - 21:00:58 PST)
    - Re: [AMBER] AMBER Shesh Nath (Mon Jan 17 2011 - 22:36:10 PST)
    - [AMBER] Any review or article commands on the use of amber to study protein-DNA complexes? Catein Catherine (Tue Jan 18 2011 - 02:24:09 PST)
[AMBER] RMSD and reference structure Siti Mohamad (Mon Jan 17 2011 - 20:45:28 PST)
- Re: [AMBER] RMSD and reference structure Jason Swails (Mon Jan 17 2011 - 21:13:52 PST)
- Re: [AMBER] RMSD and reference structure Daniel Roe (Mon Jan 17 2011 - 21:18:10 PST)
[AMBER] rdf subrata paul (Tue Jan 18 2011 - 02:44:59 PST)
- Re: [AMBER] rdf Thomas Cheatham III (Tue Jan 18 2011 - 11:06:57 PST)
[AMBER] Amber11 using CUDA-enabled GPUs Massimiliano Porrini (Tue Jan 18 2011 - 11:31:42 PST)
- Re: [AMBER] Amber11 using CUDA-enabled GPUs Dairsie Latimer (Tue Jan 18 2011 - 11:35:22 PST)
- Re: [AMBER] Amber11 using CUDA-enabled GPUs Ross Walker (Tue Jan 18 2011 - 15:35:54 PST)
[AMBER] docking in AMBER for protein complex Chinh Su Tran To (Tue Jan 18 2011 - 19:22:15 PST)
- Re: [AMBER] docking in AMBER for protein complex case (Thu Jan 20 2011 - 08:38:05 PST)
  - Re: [AMBER] docking in AMBER for protein complex filip fratev (Thu Jan 20 2011 - 10:37:06 PST)
  - Re: [AMBER] docking in AMBER for protein complex Guillermo Mulliert Carlín (Fri Jan 21 2011 - 00:24:47 PST)
[AMBER] antechamber is failing for a molecule Alan Wilter Sousa da Silva (Wed Jan 19 2011 - 03:30:04 PST)
- Re: [AMBER] antechamber is failing for a molecule case (Thu Jan 20 2011 - 08:59:52 PST)
[AMBER] Density of a solution water/propylene glycol tommaso.casalini.mail.polimi.it (Wed Jan 19 2011 - 03:34:23 PST)
[AMBER] missing parameter not present in antechamber generated frcmod Sangita Kachhap (Wed Jan 19 2011 - 09:42:20 PST)
- Re: [AMBER] missing parameter not present in antechamber generated frcmod Jason Swails (Wed Jan 19 2011 - 10:07:24 PST)
- Re: [AMBER] missing parameter not present in antechamber generated frcmod case (Thu Jan 20 2011 - 11:29:41 PST)
[AMBER] MMPBSA.py.MPI Nmode problem filip fratev (Wed Jan 19 2011 - 14:26:53 PST)
- Re: [AMBER] MMPBSA.py.MPI Nmode problem Jason Swails (Wed Jan 19 2011 - 15:20:52 PST)
  - Re: [AMBER] MMPBSA.py.MPI Nmode problem filip fratev (Wed Jan 19 2011 - 17:14:18 PST)
    - Re: [AMBER] MMPBSA.py.MPI Nmode problem Jason Swails (Wed Jan 19 2011 - 19:21:11 PST)
    - Re: [AMBER] MMPBSA.py.MPI Nmode problem case (Thu Jan 20 2011 - 05:19:37 PST)
    - Re: [AMBER] MMPBSA.py.MPI Nmode problem Jason Swails (Thu Jan 20 2011 - 09:13:24 PST)
  - Re: [AMBER] MMPBSA.py.MPI Nmode problem Jesper Sørensen (Wed Jan 26 2011 - 05:14:42 PST)
    - Re: [AMBER] MMPBSA.py.MPI Nmode problem Jason Swails (Wed Jan 26 2011 - 06:10:02 PST)
    - Re: [AMBER] MMPBSA.py.MPI Nmode problem Jesper Sørensen (Wed Jan 26 2011 - 10:39:17 PST)
[AMBER] Story of bugfix 18-Amber10 Eliac Brown (Wed Jan 19 2011 - 15:46:36 PST)
- Re: [AMBER] Story of bugfix 18-Amber10 case (Wed Jan 19 2011 - 19:43:52 PST)
  - Re: [AMBER] Story of bugfix 18-Amber10 Eliac Brown (Wed Jan 19 2011 - 23:26:12 PST)
    - Re: [AMBER] Story of bugfix 18-Amber10 case (Thu Jan 20 2011 - 05:21:43 PST)
[AMBER] Query regarding Linmin error Hirdesh Kumar (Wed Jan 19 2011 - 21:58:07 PST)
- Re: [AMBER] Query regarding Linmin error Jason Swails (Thu Jan 20 2011 - 05:50:15 PST)
  - Re: [AMBER] Query regarding Linmin error Hirdesh Kumar (Thu Jan 20 2011 - 20:18:43 PST)
    - Re: [AMBER] Query regarding Linmin error Hirdesh Kumar (Fri Jan 21 2011 - 01:05:13 PST)
[AMBER] image for lipid/water system dhacademic (Thu Jan 20 2011 - 07:21:46 PST)
- Re: [AMBER] image for lipid/water system Jason Swails (Thu Jan 20 2011 - 08:05:01 PST)
  - Re: [AMBER] image for lipid/water system dhacademic (Thu Jan 20 2011 - 08:47:02 PST)
    - Re: [AMBER] image for lipid/water system Jason Swails (Thu Jan 20 2011 - 08:56:23 PST)
    - Re: [AMBER] image for lipid/water system dhacademic (Thu Jan 20 2011 - 09:02:30 PST)
[AMBER] concentration subrata paul (Thu Jan 20 2011 - 07:29:45 PST)
- Re: [AMBER] concentration Bill Ross (Thu Jan 20 2011 - 11:01:19 PST)
  - Re: [AMBER] concentration Ilyas Yildirim (Thu Jan 20 2011 - 11:26:24 PST)
- Re: [AMBER] concentration Bill Ross (Thu Jan 20 2011 - 11:09:39 PST)
  - Re: [AMBER] concentration Jason Swails (Thu Jan 20 2011 - 11:59:54 PST)
[AMBER] NaN error on traj and output with AMBER CUDA Bongkeun Kim (Thu Jan 20 2011 - 13:14:14 PST)
- Re: [AMBER] NaN error on traj and output with AMBER CUDA Ross Walker (Thu Jan 20 2011 - 16:54:42 PST)
- Re: [AMBER] NaN error on traj and output with AMBER CUDA Jason Swails (Thu Jan 20 2011 - 17:44:24 PST)
  - Re: [AMBER] NaN error on traj and output with AMBER CUDA Jason Swails (Thu Jan 20 2011 - 17:46:06 PST)
  - Re: [AMBER] NaN error on traj and output with AMBER CUDA Ross Walker (Thu Jan 20 2011 - 18:02:14 PST)
  - Re: [AMBER] NaN error on traj and output with AMBER CUDA David Case (Thu Jan 20 2011 - 19:02:47 PST)
  - Re: [AMBER] NaN error on traj and output with AMBER CUDA Bongkeun Kim (Thu Jan 20 2011 - 19:08:29 PST)
    - Re: [AMBER] NaN error on traj and output with AMBER CUDA peker milas (Thu Jan 20 2011 - 20:04:48 PST)
    - Re: [AMBER] NaN error on traj and output with AMBER CUDA - strange reproducable error Marek Maly (Fri Jan 21 2011 - 19:05:40 PST)
    - Re: [AMBER] NaN error on traj and output with AMBER CUDA - strange reproducable error Jason Swails (Fri Jan 21 2011 - 23:11:57 PST)
    - Re: [AMBER] NaN error on traj and output with AMBER CUDA - strange reproducable error Marek Maly (Sat Jan 22 2011 - 05:23:50 PST)
    - Re: [AMBER] NaN error on traj and output with AMBER CUDA - strange reproducable error Jason Swails (Sat Jan 22 2011 - 07:54:04 PST)
    - Re: [AMBER] NaN error on traj and output with AMBER CUDA - strange reproducable error Marek Maly (Sat Jan 22 2011 - 16:44:06 PST)
    - Re: [AMBER] NaN error on traj and output with AMBER CUDA - strange reproducable error Ross Walker (Sat Jan 22 2011 - 12:24:33 PST)
    - Re: [AMBER] NaN error on traj and output with AMBER CUDA - strange reproducable error Marek Maly (Sat Jan 22 2011 - 16:47:06 PST)
[AMBER] maximum number of atoms Marc-André Dubois (Thu Jan 20 2011 - 14:47:46 PST)
- Re: [AMBER] maximum number of atoms Jason Swails (Thu Jan 20 2011 - 15:26:27 PST)
  - Re: [AMBER] maximum number of atoms Marc-André Dubois (Thu Jan 20 2011 - 15:36:42 PST)
    - Re: [AMBER] maximum number of atoms Jason Swails (Thu Jan 20 2011 - 15:44:41 PST)
- Re: [AMBER] maximum number of atoms David Case (Thu Jan 20 2011 - 18:54:20 PST)
  - Re: [AMBER] maximum number of atoms Marc-André Dubois (Thu Jan 20 2011 - 18:58:32 PST)
    - Re: [AMBER] maximum number of atoms case (Mon Jan 24 2011 - 05:24:08 PST)
[AMBER] problem with GB REMD trajectories and ptraj Mark Abraham (Thu Jan 20 2011 - 18:05:08 PST)
- Re: [AMBER] problem with GB REMD trajectories and ptraj Daniel Roe (Thu Jan 20 2011 - 18:47:18 PST)
  - Re: [AMBER] problem with GB REMD trajectories and ptraj Mark Abraham (Thu Jan 20 2011 - 19:08:57 PST)
[AMBER] Current opinions on compilers Brent Krueger (Fri Jan 21 2011 - 06:26:37 PST)
- Re: [AMBER] Current opinions on compilers case (Fri Jan 21 2011 - 06:50:37 PST)
[AMBER] Dihedral parameters for TFE with GAFF Stephane Abel (Fri Jan 21 2011 - 06:51:04 PST)
- Re: [AMBER] Dihedral parameters for TFE with GAFF Jason Swails (Fri Jan 21 2011 - 07:15:29 PST)
  - Re: [AMBER] Dihedral parameters for TFE with GAFF Stephane Abel (Fri Jan 21 2011 - 07:32:42 PST)
- Re: [AMBER] Dihedral parameters for TFE with GAFF Ilyas Yildirim (Fri Jan 21 2011 - 07:28:43 PST)
- Re: [AMBER] Dihedral parameters for TFE with GAFF case (Fri Jan 21 2011 - 09:15:05 PST)
- Re: [AMBER] Dihedral parameters for TFE with GAFF FyD (Fri Jan 21 2011 - 22:51:30 PST)
[AMBER] contacts Beale, John (Fri Jan 21 2011 - 07:01:01 PST)
[AMBER] question on diffusion coefficient calculation using ptraj Ganesh Kamath (Fri Jan 21 2011 - 07:19:16 PST)
[AMBER] PATH/evironment problem on Mac OS X Gustaf Olsson (Fri Jan 21 2011 - 07:33:14 PST)
- Re: [AMBER] PATH/evironment problem on Mac OS X Jason Swails (Fri Jan 21 2011 - 08:48:35 PST)
  - Re: [AMBER] PATH/evironment problem on Mac OS X Gustaf Olsson (Fri Jan 21 2011 - 09:46:44 PST)
    - Re: [AMBER] PATH/evironment problem on Mac OS X Ben Roberts (Fri Jan 21 2011 - 10:00:50 PST)
    - Re: [AMBER] PATH/evironment problem on Mac OS X Gustaf Olsson (Fri Jan 21 2011 - 10:08:39 PST)
    - Re: [AMBER] PATH/evironment problem on Mac OS X Ben Roberts (Fri Jan 21 2011 - 10:18:07 PST)
    - Re: [AMBER] PATH/evironment problem on Mac OS X Gustaf Olsson (Fri Jan 21 2011 - 10:40:16 PST)
    - Re: [AMBER] PATH/evironment problem on Mac OS X Jason Swails (Fri Jan 21 2011 - 10:56:15 PST)
    - Re: [AMBER] PATH/evironment problem on Mac OS X David Watson (Fri Jan 21 2011 - 11:07:15 PST)
    - Re: [AMBER] PATH/evironment problem on Mac OS X Gustaf Olsson (Fri Jan 21 2011 - 11:19:27 PST)
    - Re: [AMBER] PATH/evironment problem on Mac OS X Jason Swails (Fri Jan 21 2011 - 11:50:14 PST)
    - Re: [AMBER] PATH/evironment problem on Mac OS X Gustaf Olsson (Fri Jan 21 2011 - 11:57:19 PST)
    - Re: [AMBER] PATH/evironment problem on Mac OS X Jason Swails (Fri Jan 21 2011 - 10:45:14 PST)
    - Re: [AMBER] PATH/evironment problem on Mac OS X David Watson (Fri Jan 21 2011 - 10:01:47 PST)
    - Re: [AMBER] PATH/evironment problem on Mac OS X Gustaf Olsson (Fri Jan 21 2011 - 10:20:00 PST)
[AMBER] parametrize perchlorate Enrico Caldarulo (Fri Jan 21 2011 - 07:46:35 PST)
- Re: [AMBER] parametrize perchlorate tommaso.casalini.mail.polimi.it (Fri Jan 21 2011 - 08:26:05 PST)
[AMBER] RE : Dihedral parameters for TFE with GAFF ABEL Stephane 175950 (Fri Jan 21 2011 - 09:21:52 PST)
[AMBER] Imidazolium parameters Lorenzo Gontrani (Fri Jan 21 2011 - 09:49:32 PST)
[AMBER] Using Chamber to convert psf to prmtop Frank X. Vázquez (Fri Jan 21 2011 - 12:33:04 PST)
[AMBER] Ptraj for diffusion coefficient of water Ganesh Kamath (Fri Jan 21 2011 - 12:52:54 PST)
- Re: [AMBER] Ptraj for diffusion coefficient of water Sergio R Aragon (Fri Jan 21 2011 - 15:10:19 PST)
- Re: [AMBER] Ptraj for diffusion coefficient of water case (Sat Jan 22 2011 - 07:03:22 PST)
  - Re: [AMBER] Ptraj for diffusion coefficient of water Ganesh Kamath (Sat Jan 22 2011 - 12:32:33 PST)
    - Re: [AMBER] Ptraj for diffusion coefficient of water case (Sat Jan 22 2011 - 14:39:25 PST)
    - Re: [AMBER] Ptraj for diffusion coefficient of water Ganesh Kamath (Sun Jan 23 2011 - 10:01:36 PST)
[AMBER] Problem regarding Same coordinate for two atoms Hirdesh Kumar (Fri Jan 21 2011 - 22:34:37 PST)
- Re: [AMBER] Problem regarding Same coordinate for two atoms Jason Swails (Fri Jan 21 2011 - 23:14:35 PST)
  - Re: [AMBER] Problem regarding Same coordinate for two atoms Hirdesh Kumar (Sat Jan 22 2011 - 00:05:46 PST)
    - Re: [AMBER] Problem regarding Same coordinate for two atoms Jason Swails (Sat Jan 22 2011 - 00:13:45 PST)
    - Re: [AMBER] Problem regarding Same coordinate for two atoms Hirdesh Kumar (Sat Jan 22 2011 - 01:24:12 PST)
    - Re: [AMBER] Problem regarding Same coordinate for two atoms Sangita Kachhap (Sat Jan 22 2011 - 02:49:37 PST)
- Re: [AMBER] Problem regarding Same coordinate for two atoms Bill Ross (Sun Jan 23 2011 - 19:29:27 PST)
[AMBER] error in prmtop,inpcrd subrata paul (Sat Jan 22 2011 - 06:14:21 PST)
- Re: [AMBER] error in prmtop,inpcrd case (Sat Jan 22 2011 - 06:54:11 PST)
  - Re: [AMBER] error in prmtop,inpcrd subrata paul (Sun Jan 23 2011 - 20:35:56 PST)
    - Re: [AMBER] error in prmtop,inpcrd Jason Swails (Sun Jan 23 2011 - 20:46:02 PST)
    - Re: [AMBER] error in prmtop,inpcrd subrata paul (Sun Jan 23 2011 - 21:47:57 PST)
[AMBER] Ptraj: Hbond and Bfactor analyses Kamali Sripathi (Sat Jan 22 2011 - 08:33:28 PST)
- [AMBER] Ptraj: Hbond and Bfactor analyses Kamali Sripathi (Mon Jan 24 2011 - 14:26:18 PST)
  - Re: [AMBER] Ptraj: Hbond and Bfactor analyses Thomas Cheatham (Mon Jan 24 2011 - 15:04:14 PST)
    - Re: [AMBER] Ptraj: Hbond and Bfactor analyses Kamali Sripathi (Wed Jan 26 2011 - 08:44:48 PST)
    - Re: [AMBER] Ptraj: Hbond and Bfactor analyses Thomas Cheatham III (Wed Jan 26 2011 - 09:21:54 PST)
    - Re: [AMBER] Ptraj: Hbond and Bfactor analyses Kamali Sripathi (Wed Jan 26 2011 - 16:27:55 PST)
    - Re: [AMBER] Ptraj: Hbond and Bfactor analyses Kamali Sripathi (Wed Jan 26 2011 - 16:55:11 PST)
    - Re: [AMBER] Ptraj: Hbond and Bfactor analyses Kamali Sripathi (Thu Mar 17 2011 - 18:49:21 PDT)
[AMBER] trehalose concentation subrata paul (Sun Jan 23 2011 - 21:58:36 PST)
- Re: [AMBER] trehalose concentation Jason Swails (Mon Jan 24 2011 - 04:17:54 PST)
  - Re: [AMBER] trehalose concentation Lachele Foley (Lists) (Mon Jan 24 2011 - 06:19:34 PST)
    - Re: [AMBER] trehalose concentation subrata paul (Mon Jan 24 2011 - 06:47:45 PST)
    - Re: [AMBER] trehalose concentation subrata paul (Mon Jan 24 2011 - 06:49:08 PST)
    - Re: [AMBER] trehalose concentation Jason Swails (Mon Jan 24 2011 - 07:17:43 PST)
    - Re: [AMBER] trehalose concentation subrata paul (Mon Jan 24 2011 - 23:18:57 PST)
    - Re: [AMBER] trehalose concentation Jason Swails (Mon Jan 24 2011 - 23:29:43 PST)
    - Re: [AMBER] trehalose concentation subrata paul (Tue Jan 25 2011 - 01:40:24 PST)
[AMBER] Query regarding restrain during minimization Hirdesh Kumar (Sun Jan 23 2011 - 23:15:18 PST)
- Re: [AMBER] Query regarding restrain during minimization sunita gupta (Mon Jan 24 2011 - 01:26:53 PST)
  - Re: [AMBER] Query regarding restrain during minimization Hirdesh Kumar (Mon Jan 24 2011 - 03:39:27 PST)
    - Re: [AMBER] Query regarding restrain during minimization Dmitry Nilov (Mon Jan 24 2011 - 03:54:57 PST)
[AMBER] calculate entropy ptraj Jorgen Simonsen (Mon Jan 24 2011 - 08:15:10 PST)
- Re: [AMBER] calculate entropy ptraj Jason Swails (Mon Jan 24 2011 - 08:41:41 PST)
  - Re: [AMBER] calculate entropy ptraj Jorgen Simonsen (Tue Jan 25 2011 - 01:03:50 PST)
    - Re: [AMBER] calculate entropy ptraj case (Tue Jan 25 2011 - 05:33:29 PST)
[AMBER] NaN error in .rst files peker milas (Mon Jan 24 2011 - 14:42:22 PST)
- Re: [AMBER] NaN error in .rst files Ross Walker (Mon Jan 24 2011 - 19:54:03 PST)
  - Re: [AMBER] NaN error in .rst files peker milas (Mon Jan 24 2011 - 21:30:03 PST)
    - Re: [AMBER] NaN error in .rst files Ross Walker (Mon Jan 24 2011 - 21:45:04 PST)
    - Re: [AMBER] NaN error in .rst files Jason Swails (Mon Jan 24 2011 - 21:57:01 PST)
    - Re: [AMBER] NaN error in .rst files Jason Swails (Mon Jan 24 2011 - 21:45:50 PST)
- Re: [AMBER] NaN error in .rst files filip fratev (Tue Jan 25 2011 - 00:25:08 PST)
  - Re: [AMBER] NaN error in .rst files peker milas (Tue Jan 25 2011 - 05:28:06 PST)
  - Re: [AMBER] NaN error in .rst files Ross Walker (Tue Jan 25 2011 - 07:10:44 PST)
    - Re: [AMBER] NaN error in .rst files peker milas (Tue Jan 25 2011 - 07:28:26 PST)
    - Re: [AMBER] NaN error in .rst files Ross Walker (Tue Jan 25 2011 - 08:36:44 PST)
    - Re: [AMBER] NaN error in .rst files Gould, Ian R (Tue Jan 25 2011 - 09:10:31 PST)
    - Re: [AMBER] NaN error in .rst files filip fratev (Tue Jan 25 2011 - 10:09:17 PST)
    - Re: [AMBER] NaN error in .rst files peker milas (Tue Jan 25 2011 - 14:30:53 PST)
    - Re: [AMBER] NaN error in .rst files Marek Maly (Wed Jan 26 2011 - 04:19:45 PST)
    - Re: [AMBER] NaN error in .rst files case (Wed Jan 26 2011 - 06:04:16 PST)
    - Re: [AMBER] NaN error in .rst files Jason Swails (Wed Jan 26 2011 - 06:14:25 PST)
    - Re: [AMBER] NaN error in .rst files Marek Maly (Wed Jan 26 2011 - 06:28:09 PST)
    - Re: [AMBER] NaN error in .rst files Marek Maly (Wed Jan 26 2011 - 06:21:26 PST)
    - Re: [AMBER] NaN error in .rst files Marek Maly (Wed Jan 26 2011 - 08:23:01 PST)
    - Re: [AMBER] NaN error in .rst files Jason Swails (Wed Jan 26 2011 - 08:36:48 PST)
    - Re: [AMBER] NaN error in .rst files Jason Swails (Wed Jan 26 2011 - 08:37:49 PST)
    - Re: [AMBER] NaN error in .rst files Marek Maly (Wed Jan 26 2011 - 08:37:52 PST)
    - Re: [AMBER] NaN error in .rst files Jason Swails (Wed Jan 26 2011 - 10:04:32 PST)
    - Re: [AMBER] NaN error in .rst files peker milas (Wed Jan 26 2011 - 15:32:38 PST)
    - Re: [AMBER] NaN error in .rst files Marek Maly (Wed Jan 26 2011 - 15:49:34 PST)
    - Re: [AMBER] NaN error in .rst files peker milas (Wed Jan 26 2011 - 16:06:08 PST)
    - Re: [AMBER] NaN error in .rst files Marek Maly (Wed Jan 26 2011 - 16:16:52 PST)
    - Re: [AMBER] NaN error in .rst files Ross Walker (Wed Jan 26 2011 - 22:51:11 PST)
    - Re: [AMBER] NaN error in .rst files Ross Walker (Wed Jan 26 2011 - 22:59:31 PST)
    - Re: [AMBER] NaN error in .rst files Marek Maly (Thu Jan 27 2011 - 02:21:48 PST)
    - Re: [AMBER] NaN error in .rst files Ross Walker (Wed Jan 26 2011 - 19:05:00 PST)
    - Re: [AMBER] NaN error in .rst files peker milas (Wed Jan 26 2011 - 21:41:36 PST)
    - Re: [AMBER] NaN error in .rst files peker milas (Wed Jan 26 2011 - 22:07:34 PST)
    - Re: [AMBER] NaN error in .rst files Ross Walker (Wed Jan 26 2011 - 22:46:15 PST)
    - Re: [AMBER] NaN error in .rst files Marek Maly (Wed Jan 26 2011 - 09:34:52 PST)
    - Re: [AMBER] NaN error in .rst files Ross Walker (Wed Jan 26 2011 - 08:45:07 PST)
    - Re: [AMBER] NaN error in .rst files Marek Maly (Wed Jan 26 2011 - 09:49:53 PST)
    - Re: [AMBER] NaN error in .rst files - UPDATE Marek Maly (Wed Jan 26 2011 - 14:58:43 PST)
    - Re: [AMBER] NaN error in .rst files - UPDATE peker milas (Thu Jan 27 2011 - 07:07:31 PST)
    - Re: [AMBER] NaN error in .rst files - UPDATE Marek Maly (Thu Jan 27 2011 - 07:04:24 PST)
    - Re: [AMBER] NaN error in .rst files - UPDATE filip fratev (Thu Jan 27 2011 - 07:42:56 PST)
    - Re: [AMBER] NaN error in .rst files - UPDATE peker milas (Thu Jan 27 2011 - 08:09:42 PST)
    - Re: [AMBER] NaN error in .rst files - UPDATE Marek Maly (Thu Jan 27 2011 - 08:32:21 PST)
    - Re: [AMBER] NaN error in .rst files - UPDATE Jason Swails (Thu Jan 27 2011 - 08:58:06 PST)
    - Re: [AMBER] NaN error in .rst files - UPDATE Marek Maly (Thu Jan 27 2011 - 09:29:06 PST)
    - Re: [AMBER] NaN error in .rst files - UPDATE peker milas (Thu Jan 27 2011 - 10:28:55 PST)
    - Re: [AMBER] NaN error in .rst files - UPDATE Marek Maly (Thu Jan 27 2011 - 10:46:17 PST)
    - Re: [AMBER] NaN error in .rst files - UPDATE Ross Walker (Thu Jan 27 2011 - 18:20:42 PST)
    - Re: [AMBER] NaN error in .rst files - UPDATE Marek Maly (Thu Jan 27 2011 - 08:18:35 PST)
    - Re: [AMBER] NaN error in .rst files - UPDATE filip fratev (Thu Jan 27 2011 - 10:53:50 PST)
    - Re: [AMBER] NaN error in .rst files - UPDATE Marek Maly (Thu Jan 27 2011 - 14:10:55 PST)
- Re: [AMBER] NaN error in .rst files filip fratev (Thu Jan 27 2011 - 07:33:30 PST)
[AMBER] Compiling Ambertools 1.4 on MacBook SnowLeopard10.6.3 Siti Mohamad (Mon Jan 24 2011 - 19:52:44 PST)
- Re: [AMBER] Compiling Ambertools 1.4 on MacBook SnowLeopard10.6.3 Jason Swails (Mon Jan 24 2011 - 20:45:17 PST)
  - Re: [AMBER] Compiling Ambertools 1.4 on MacBook SnowLeopard10.6.3 Siti Mohamad (Tue Jan 25 2011 - 01:09:34 PST)
[AMBER] Query regarding unusual water box in vmd Hirdesh Kumar (Mon Jan 24 2011 - 22:05:38 PST)
- [AMBER] Fwd: Query regarding unusual water box in vmd Hirdesh Kumar (Mon Jan 24 2011 - 22:12:39 PST)
  - Re: [AMBER] Fwd: Query regarding unusual water box in vmd Jason Swails (Mon Jan 24 2011 - 22:20:49 PST)
    - Re: [AMBER] Fwd: Query regarding unusual water box in vmd Hirdesh Kumar (Tue Jan 25 2011 - 02:22:32 PST)
    - Re: [AMBER] Fwd: Query regarding unusual water box in vmd Adrian Roitberg (Tue Jan 25 2011 - 02:29:21 PST)
    - Re: [AMBER] Fwd: Query regarding unusual water box in vmd Hirdesh Kumar (Tue Jan 25 2011 - 03:12:29 PST)
    - Re: [AMBER] Fwd: Query regarding unusual water box in vmd Oliver Grant (Tue Jan 25 2011 - 04:10:48 PST)
    - Re: [AMBER] Fwd: Query regarding unusual water box in vmd Hirdesh Kumar (Tue Jan 25 2011 - 04:14:52 PST)
Re: [AMBER] AMBER: SPCFW problems Josh Berryman (Tue Jan 25 2011 - 06:36:42 PST)
- Re: [AMBER] AMBER: SPCFW problems case (Tue Jan 25 2011 - 06:51:16 PST)
  - Re: [AMBER] AMBER: SPCFW problems Josh Berryman (Mon Jan 31 2011 - 02:44:01 PST)
[AMBER] Problems with TIP5P water tommaso.casalini.mail.polimi.it (Tue Jan 25 2011 - 08:09:09 PST)
- Re: [AMBER] Problems with TIP5P water Ross Walker (Tue Jan 25 2011 - 08:31:53 PST)
  - Re: [AMBER] Problems with TIP5P water tommaso.casalini.mail.polimi.it (Tue Jan 25 2011 - 08:55:32 PST)
    - Re: [AMBER] Problems with TIP5P water Ross Walker (Tue Jan 25 2011 - 09:18:21 PST)
- Re: [AMBER] Problems with TIP5P water Bill Ross (Tue Jan 25 2011 - 10:11:11 PST)
- Re: [AMBER] Problems with TIP5P water Bill Ross (Tue Jan 25 2011 - 11:29:06 PST)
  - Re: [AMBER] Problems with TIP5P water tommaso.casalini.mail.polimi.it (Wed Jan 26 2011 - 02:21:40 PST)
    - Re: [AMBER] Problems with TIP5P water case (Wed Jan 26 2011 - 06:01:54 PST)
[AMBER] PCA analysis for side chain atoms and backbone atoms Jorgen Simonsen (Tue Jan 25 2011 - 11:31:03 PST)
- Re: [AMBER] PCA analysis for side chain atoms and backbone atoms Dwight McGee (Tue Jan 25 2011 - 12:06:38 PST)
- Re: [AMBER] PCA analysis for side chain atoms and backbone atoms Jason Swails (Tue Jan 25 2011 - 12:31:10 PST)
- Re: [AMBER] PCA analysis for side chain atoms and backbone atoms Hannes Loeffler (Wed Jan 26 2011 - 00:48:07 PST)
  - Re: [AMBER] PCA analysis for side chain atoms and backbone atoms Jorgen Simonsen (Wed Jan 26 2011 - 01:52:42 PST)
    - Re: [AMBER] PCA analysis for side chain atoms and backbone atoms Hannes Loeffler (Wed Jan 26 2011 - 02:27:02 PST)
    - Re: [AMBER] PCA analysis for side chain atoms and backbone atoms Jorgen Simonsen (Wed Jan 26 2011 - 03:12:10 PST)
    - Re: [AMBER] PCA analysis for side chain atoms and backbone atoms Hannes Loeffler (Wed Jan 26 2011 - 05:47:52 PST)
    - Re: [AMBER] PCA analysis for side chain atoms and backbone atoms case (Wed Jan 26 2011 - 06:43:49 PST)
    - Re: [AMBER] PCA analysis for side chain atoms and backbone atoms Hannes Loeffler (Wed Jan 26 2011 - 07:02:49 PST)
[AMBER] Error with MM-PBSA Jagur Lambix (Tue Jan 25 2011 - 13:05:31 PST)
[AMBER] Query regarding parmchk poll.chemie.uni-hamburg.de (Wed Jan 26 2011 - 01:49:57 PST)
- Re: [AMBER] Query regarding parmchk Dmitry Nilov (Wed Jan 26 2011 - 02:22:57 PST)
  - Re: [AMBER] Query regarding parmchk poll.chemie.uni-hamburg.de (Wed Jan 26 2011 - 08:11:05 PST)
    - Re: [AMBER] Query regarding parmchk case (Wed Jan 26 2011 - 08:53:24 PST)
[AMBER] MM-PBSA error about protein + Mg2+ 肖正涛 (Wed Jan 26 2011 - 03:36:29 PST)
- Re: [AMBER] MM-PBSA error about protein + Mg2+ Jason Swails (Wed Jan 26 2011 - 06:17:50 PST)
[AMBER] residue topology files Baptiste Legrand (Wed Jan 26 2011 - 06:32:19 PST)
- Re: [AMBER] residue topology files case (Wed Jan 26 2011 - 06:46:09 PST)
  - Re: [AMBER] residue topology files Baptiste Legrand (Wed Jan 26 2011 - 07:31:31 PST)
    - Re: [AMBER] residue topology files Jason Swails (Wed Jan 26 2011 - 07:35:29 PST)
    - Re: [AMBER] residue topology files case (Wed Jan 26 2011 - 08:41:34 PST)
[AMBER] Solvate box John S (Wed Jan 26 2011 - 11:31:27 PST)
- Re: [AMBER] Solvate box Carlos Simmerling (Wed Jan 26 2011 - 11:46:06 PST)
[AMBER] free radicals in amber Ashutosh Shandilya (Thu Jan 27 2011 - 00:15:08 PST)
- Re: [AMBER] free radicals in amber case (Thu Jan 27 2011 - 05:54:29 PST)
  - Re: [AMBER] free radicals in amber Ashutosh Shandilya (Fri Feb 04 2011 - 06:09:03 PST)
[AMBER] amber11 installation bugfix problem Julia Romanowska (Thu Jan 27 2011 - 02:31:58 PST)
- Re: [AMBER] amber11 installation bugfix problem Jason Swails (Thu Jan 27 2011 - 04:12:59 PST)
[AMBER] urea force field subrata paul (Thu Jan 27 2011 - 04:01:05 PST)
- Re: [AMBER] urea force field case (Thu Jan 27 2011 - 05:32:06 PST)
  - Re: [AMBER] urea force field subrata paul (Fri Jan 28 2011 - 04:14:49 PST)
[AMBER] conformation search Sangita Kachhap (Thu Jan 27 2011 - 06:26:23 PST)
- Re: [AMBER] conformation search Carlos Simmerling (Thu Jan 27 2011 - 07:25:55 PST)
  - Re: [AMBER] conformation search Sangita Kachhap (Thu Jan 27 2011 - 08:10:09 PST)
    - Re: [AMBER] conformation search Carlos Simmerling (Thu Jan 27 2011 - 08:13:02 PST)
    - Re: [AMBER] conformation search Sangita Kachhap (Thu Jan 27 2011 - 08:29:52 PST)
[AMBER] GPU vs CPU test Massimiliano Porrini (Thu Jan 27 2011 - 07:06:29 PST)
- Re: [AMBER] GPU vs CPU test Jason Swails (Thu Jan 27 2011 - 08:13:50 PST)
  - Re: [AMBER] GPU vs CPU test Ross Walker (Thu Jan 27 2011 - 08:46:17 PST)
    - Re: [AMBER] GPU vs CPU test Scott Le Grand (Thu Jan 27 2011 - 13:19:38 PST)
    - Re: [AMBER] GPU vs CPU test Massimiliano Porrini (Fri Jan 28 2011 - 03:44:46 PST)
- Re: [AMBER] GPU vs CPU test Scott Le Grand (Thu Jan 27 2011 - 13:12:48 PST)
Re: [AMBER] NaN error in .rst files - A request for some 'Clarity' Ross Walker (Thu Jan 27 2011 - 18:26:48 PST)
- Re: [AMBER] NaN error in .rst files - A request for some 'Clarity' peker milas (Thu Jan 27 2011 - 20:38:57 PST)
- Re: [AMBER] NaN error in .rst files - A request for some 'Clarity' Marek Maly (Fri Jan 28 2011 - 01:49:02 PST)
  - Re: [AMBER] NaN error in .rst files - A request for some 'Clarity' peker milas (Sat Jan 29 2011 - 14:59:51 PST)
    - Re: [AMBER] NaN error in .rst files - A request for some 'Clarity' peker milas (Sat Jan 29 2011 - 15:08:41 PST)
    - Re: [AMBER] NaN error in .rst files - A request for some 'Clarity' Marek Maly (Sat Jan 29 2011 - 18:43:51 PST)
    - Re: [AMBER] NaN error in .rst files - A request for some 'Clarity' peker milas (Mon Jan 31 2011 - 05:44:08 PST)
[AMBER] Amber usage and enquiry - 280111 Ken Choy (Thu Jan 27 2011 - 21:12:17 PST)
- Re: [AMBER] Amber usage and enquiry - 280111 Jason Swails (Thu Jan 27 2011 - 21:29:03 PST)
[AMBER] MM-PBSA error about protein + Mg2+ 肖正涛 (Thu Jan 27 2011 - 23:47:44 PST)
- Re: [AMBER] MM-PBSA error about protein + Mg2+ Jason Swails (Fri Jan 28 2011 - 05:55:59 PST)
[AMBER] installing ambertools1.4 Vijay Manickam Achari (Fri Jan 28 2011 - 01:40:45 PST)
- Re: [AMBER] installing ambertools1.4 case (Fri Jan 28 2011 - 05:09:53 PST)
  - Re: [AMBER] installing ambertools1.4 Vijay Manickam Achari (Tue Feb 01 2011 - 23:57:43 PST)
[AMBER] sander on amber12 setyanto md (Fri Jan 28 2011 - 02:36:59 PST)
- Re: [AMBER] sander on amber12 Jason Swails (Fri Jan 28 2011 - 05:57:16 PST)
- Re: [AMBER] sander on amber12 Ross Walker (Fri Jan 28 2011 - 07:30:59 PST)
  - Re: [AMBER] sander on amber12 setyanto md (Sun Jan 30 2011 - 21:09:59 PST)
    - Re: [AMBER] sander on amber12 Ross Walker (Sun Jan 30 2011 - 21:41:22 PST)
    - Re: [AMBER] sander on amber12 setyanto md (Mon Jan 31 2011 - 18:58:42 PST)
[AMBER] QM/MM-GBSA calculation : No convergence in SCF after 1000 steps. mish (Fri Jan 28 2011 - 03:31:53 PST)
- Re: [AMBER] QM/MM-GBSA calculation : No convergence in SCF after 1000 steps. case (Fri Jan 28 2011 - 05:14:17 PST)
  - Re: [AMBER] QM/MM-GBSA calculation : No convergence in SCF after 1000 steps. mish (Fri Jan 28 2011 - 23:32:19 PST)
[AMBER] Only Hydrogen Minimization Hirdesh Kumar (Fri Jan 28 2011 - 04:20:02 PST)
- Re: [AMBER] Only Hydrogen Minimization Dmitry Nilov (Fri Jan 28 2011 - 05:05:48 PST)
  - Re: [AMBER] Only Hydrogen Minimization Hirdesh Kumar (Fri Jan 28 2011 - 05:49:14 PST)
[AMBER] Display CPU time in mdout file Hirdesh Kumar (Fri Jan 28 2011 - 04:37:12 PST)
- Re: [AMBER] Display CPU time in mdout file Ross Walker (Fri Jan 28 2011 - 07:27:30 PST)
  - Re: [AMBER] Display CPU time in mdout file Hirdesh Kumar (Fri Jan 28 2011 - 08:09:14 PST)
    - Re: [AMBER] Display CPU time in mdout file Ross Walker (Fri Jan 28 2011 - 10:42:56 PST)
    - Re: [AMBER] Display CPU time in mdout file Hirdesh Kumar (Fri Jan 28 2011 - 23:23:48 PST)
[AMBER] Problem During Gradual Heating Hirdesh Kumar (Fri Jan 28 2011 - 05:58:20 PST)
- Re: [AMBER] Problem During Gradual Heating Carlos Simmerling (Fri Jan 28 2011 - 06:15:16 PST)
  - Re: [AMBER] Problem During Gradual Heating Hirdesh Kumar (Fri Jan 28 2011 - 06:18:51 PST)
    - Re: [AMBER] Problem During Gradual Heating Carlos Simmerling (Fri Jan 28 2011 - 06:23:25 PST)
    - Re: [AMBER] Problem During Gradual Heating Jason Swails (Fri Jan 28 2011 - 06:42:28 PST)
    - Re: [AMBER] Problem During Gradual Heating Hirdesh Kumar (Fri Jan 28 2011 - 08:33:37 PST)
    - Re: [AMBER] Problem During Gradual Heating Jason Swails (Fri Jan 28 2011 - 08:48:10 PST)
[AMBER] Solvate box John S (Fri Jan 28 2011 - 08:13:27 PST)
- Re: [AMBER] Solvate box Bill Ross (Wed May 26 2010 - 09:46:22 PDT)
- Re: [AMBER] Solvate box Bill Ross (Wed Jan 26 2011 - 11:44:42 PST)
- Re: [AMBER] Solvate box Bill Ross (Wed Jan 26 2011 - 12:04:19 PST)
  - Re: [AMBER] Solvate box John S (Wed Jan 26 2011 - 14:39:51 PST)
    - Re: [AMBER] Solvate box M. L. Dodson (Wed Jan 26 2011 - 15:25:45 PST)
- Re: [AMBER] Solvate box Bill Ross (Wed Jan 26 2011 - 15:52:00 PST)
  - Re: [AMBER] Solvate box M. L. Dodson (Wed Jan 26 2011 - 16:04:51 PST)
- Re: [AMBER] Solvate box Jason Swails (Fri Jan 28 2011 - 08:14:59 PST)
  - Re: [AMBER] Solvate box John S (Fri Jan 28 2011 - 10:50:11 PST)
    - Re: [AMBER] Solvate box Jason Swails (Fri Jan 28 2011 - 10:54:57 PST)
    - Re: [AMBER] Solvate box John S (Fri Jan 28 2011 - 12:35:42 PST)
- Re: [AMBER] Solvate box Bill Ross (Fri Jan 28 2011 - 11:02:30 PST)
  - Re: [AMBER] Solvate box John S (Fri Jan 28 2011 - 12:40:29 PST)
- Re: [AMBER] Solvate box Bill Ross (Fri Jan 28 2011 - 12:53:20 PST)
[AMBER] AMBER11 parallel compiling problem Zhu, James (Fri Jan 28 2011 - 08:16:20 PST)
- Re: [AMBER] AMBER11 parallel compiling problem Jason Swails (Fri Jan 28 2011 - 08:41:10 PST)
  - Re: [AMBER] AMBER11 parallel compiling problem Zhu, James (Fri Jan 28 2011 - 09:08:36 PST)
[AMBER] Using packmol to produce multiple instances of the same molecule Maria Pikoula (Fri Jan 28 2011 - 09:34:27 PST)
- Re: [AMBER] Using packmol to produce multiple instances of the same molecule Bill Ross (Fri Jan 28 2011 - 10:17:34 PST)
- Re: [AMBER] Using packmol to produce multiple instances of the same molecule case (Sat Jan 29 2011 - 06:55:34 PST)
[AMBER] problem in minimization with POL3 piotrek.vega.umcs.lublin.pl (Fri Jan 28 2011 - 11:01:38 PST)
- Re: [AMBER] problem in minimization with POL3 Hirdesh Kumar (Sat Jan 29 2011 - 00:40:02 PST)
  - Re: [AMBER] problem in minimization with POL3 piotrek.vega.umcs.lublin.pl (Mon Jan 31 2011 - 08:09:47 PST)
[AMBER] Query regarding NVT ensemble with less restraint on solute Hirdesh Kumar (Sat Jan 29 2011 - 00:45:50 PST)
- Re: [AMBER] Query regarding NVT ensemble with less restraint on solute Sangita Kachhap (Sat Jan 29 2011 - 01:08:49 PST)
- Re: [AMBER] Query regarding NVT ensemble with less restraint on solute case (Sat Jan 29 2011 - 06:21:27 PST)
  - Re: [AMBER] Query regarding NVT ensemble with less restraint on solute Hirdesh Kumar (Sat Jan 29 2011 - 09:55:43 PST)
    - Re: [AMBER] Query regarding NVT ensemble with less restraint on solute Jason Swails (Sat Jan 29 2011 - 12:05:27 PST)
[AMBER] REMD equilibration restart Sangita Kachhap (Sat Jan 29 2011 - 23:45:45 PST)
- Re: [AMBER] REMD equilibration restart Carlos Simmerling (Mon Jan 31 2011 - 05:51:47 PST)
  - Re: [AMBER] REMD equilibration restart Sangita Kachhap (Mon Jan 31 2011 - 08:39:29 PST)
    - Re: [AMBER] REMD equilibration restart Nadine Utz (Mon Jan 31 2011 - 09:28:43 PST)
    - Re: [AMBER] REMD equilibration restart Sangita Kachhap (Mon Jan 31 2011 - 19:28:21 PST)
    - Re: [AMBER] REMD equilibration restart Carlos Simmerling (Mon Jan 31 2011 - 09:28:32 PST)
    - Re: [AMBER] REMD equilibration restart Sangita Kachhap (Mon Jan 31 2011 - 19:35:22 PST)
    - [AMBER] MM_PBSA questions Marek Maly (Mon Jan 31 2011 - 09:23:30 PST)
[AMBER] 回复： MM-PBSA error about protein + Mg2+ 475649770 (Sun Jan 30 2011 - 01:18:00 PST)
- Re: [AMBER] 回复： MM-PBSA error about protein + Mg2+ Bill Miller III (Sun Jan 30 2011 - 05:52:20 PST)
[AMBER] NPT and restraints Dmitry Mukha (Sun Jan 30 2011 - 07:13:22 PST)
- Re: [AMBER] NPT and restraints Dmitry Mukha (Mon Jan 31 2011 - 07:35:22 PST)
[AMBER] Any recommendations regarding IGB parameter in Normal Mode section of mm_pbsa analyses ? Marek Maly (Sun Jan 30 2011 - 12:51:30 PST)
- Re: [AMBER] Any recommendations regarding IGB parameter in Normal Mode section of mm_pbsa analyses ? case (Sun Jan 30 2011 - 18:11:57 PST)
  - Re: [AMBER] Any recommendations regarding IGB parameter in Normal Mode section of mm_pbsa analyses ? Marek Maly (Mon Jan 31 2011 - 01:59:59 PST)
[AMBER] 回复：回复： MM-PBSA error about protein + Mg2+ 475649770 (Mon Jan 31 2011 - 03:34:43 PST)
- Re: [AMBER] 回复：回复： MM-PBSA error about protein + Mg2+ Bill Miller III (Mon Jan 31 2011 - 03:46:27 PST)
[AMBER] 回复：回复：回复： MM-PBSA error about protein + Mg2+ 475649770 (Mon Jan 31 2011 - 06:04:18 PST)
- Re: [AMBER] 回复：回复：回复： MM-PBSA error about protein + Mg2+ Jason Swails (Mon Jan 31 2011 - 06:39:01 PST)
[AMBER] AmberTool parallel compiling error Zhu, James (Mon Jan 31 2011 - 10:32:35 PST)
- Re: [AMBER] AmberTool parallel compiling error Jason Swails (Mon Jan 31 2011 - 10:47:40 PST)
Re: [AMBER] Doubts in the installation of Amber11 vani panguluri (Mon Jan 31 2011 - 10:48:03 PST)
- Re: [AMBER] Doubts in the installation of Amber11 Jason Swails (Mon Jan 31 2011 - 10:54:40 PST)
- Re: [AMBER] Doubts in the installation of Amber11 Ben Roberts (Mon Jan 31 2011 - 10:57:02 PST)
- Re: [AMBER] Doubts in the installation of Amber11 peker milas (Mon Jan 31 2011 - 10:56:55 PST)
  - Re: [AMBER] Doubts in the installation of Amber11 vani panguluri (Mon Jan 31 2011 - 11:15:29 PST)
    - Re: [AMBER] Doubts in the installation of Amber11 Ben Roberts (Mon Jan 31 2011 - 11:21:55 PST)
    - Re: [AMBER] Doubts in the installation of Amber11 peker milas (Mon Jan 31 2011 - 12:29:28 PST)
[AMBER] MM-PBSA and handling of ions Jagur Lambix (Mon Jan 31 2011 - 14:12:06 PST)
- Re: [AMBER] MM-PBSA and handling of ions Bill Miller III (Mon Jan 31 2011 - 14:51:57 PST)
[AMBER] 回复：回复：回复：回复： MM-PBSA error about protein + Mg2+ 475649770 (Mon Jan 31 2011 - 22:29:30 PST)
- Re: [AMBER] 回复：回复：回复：回复： MM-PBSA error about protein + Mg2+ Jason Swails (Tue Feb 01 2011 - 06:44:35 PST)
[AMBER] MMPBSA printres syntax Jesper Sørensen (Tue Feb 01 2011 - 01:30:29 PST)
- Re: [AMBER] MMPBSA printres syntax Jason Swails (Tue Feb 01 2011 - 06:46:33 PST)
[AMBER] TI in vacuum FCUP (Tue Feb 01 2011 - 06:36:55 PST)
- Re: [AMBER] TI in vacuum steinbrt.rci.rutgers.edu (Tue Feb 01 2011 - 06:46:03 PST)
  - Re: [AMBER] TI in vacuum FCUP (Tue Feb 01 2011 - 08:28:14 PST)
    - Re: [AMBER] TI in vacuum steinbrt.rci.rutgers.edu (Tue Feb 01 2011 - 08:31:54 PST)
    - Re: [AMBER] TI in vacuum FCUP (Tue Feb 01 2011 - 09:02:40 PST)
    - Re: [AMBER] TI in vacuum FCUP (Tue Feb 01 2011 - 09:08:22 PST)
    - Re: [AMBER] TI in vacuum steinbrt.rci.rutgers.edu (Wed Feb 02 2011 - 01:17:29 PST)
    - Re: [AMBER] TI in vacuum FCUP (Tue Feb 08 2011 - 01:43:24 PST)
    - Re: [AMBER] TI in vacuum steinbrt.rci.rutgers.edu (Tue Feb 08 2011 - 01:57:30 PST)
    - Re: [AMBER] TI in vacuum FCUP (Tue Feb 08 2011 - 08:34:25 PST)
    - Re: [AMBER] TI in vacuum steinbrt.rci.rutgers.edu (Tue Feb 08 2011 - 09:43:29 PST)
    - Re: [AMBER] TI in vacuum FCUP (Wed Feb 09 2011 - 03:11:30 PST)
[AMBER] frcmod.urea subrata paul (Tue Feb 01 2011 - 07:07:49 PST)
- Re: [AMBER] frcmod.urea Adrian Roitberg (Tue Feb 01 2011 - 07:11:34 PST)
  - Re: [AMBER] frcmod.urea case (Tue Feb 01 2011 - 09:25:06 PST)
  - Re: [AMBER] frcmod.urea subrata paul (Wed Feb 02 2011 - 07:02:48 PST)
    - Re: [AMBER] frcmod.urea Jason Swails (Wed Feb 02 2011 - 07:12:00 PST)
[AMBER] Amber11 parallel testing error Zhu, James (Tue Feb 01 2011 - 08:36:18 PST)
- Re: [AMBER] Amber11 parallel testing error Daniel Roe (Wed Feb 02 2011 - 10:03:57 PST)
  - Re: [AMBER] Amber11 parallel testing error Zhu, James (Wed Feb 02 2011 - 12:53:46 PST)
    - Re: [AMBER] Amber11 parallel testing error Daniel Roe (Wed Feb 02 2011 - 14:02:17 PST)
    - Re: [AMBER] Amber11 parallel testing error Zhu, James (Thu Feb 03 2011 - 10:37:24 PST)
    - Re: [AMBER] Amber11 parallel testing error Zhu, James (Thu Feb 03 2011 - 11:19:14 PST)
    - Re: [AMBER] Amber11 parallel testing error case (Thu Feb 03 2011 - 11:31:43 PST)
    - Re: [AMBER] Amber11 parallel testing error Jason Swails (Thu Feb 03 2011 - 11:33:27 PST)
[AMBER] Regarding NVIDIA Graphics Card Hirdesh Kumar (Tue Feb 01 2011 - 09:05:19 PST)
- Re: [AMBER] Regarding NVIDIA Graphics Card Ross Walker (Tue Feb 01 2011 - 17:05:40 PST)
  - Re: [AMBER] Regarding NVIDIA Graphics Card Hirdesh Kumar (Wed Feb 02 2011 - 00:32:51 PST)
[AMBER] PMF problem dhacademic (Tue Feb 01 2011 - 12:55:30 PST)
- Re: [AMBER] PMF problem Daniel Sindhikara (Tue Feb 01 2011 - 18:49:33 PST)
  - Re: [AMBER] PMF problem dhacademic (Wed Feb 02 2011 - 07:40:26 PST)
    - Re: [AMBER] PMF problem Carlos Simmerling (Wed Feb 02 2011 - 07:45:21 PST)
[AMBER] Create EtOHbox Mattei, Alessandra (Tue Feb 01 2011 - 14:43:45 PST)
- Re: [AMBER] Create EtOHbox FyD (Wed Feb 02 2011 - 00:26:05 PST)
  - Re: [AMBER] Create EtOHbox Mattei, Alessandra (Fri Feb 04 2011 - 11:12:59 PST)
    - Re: [AMBER] Create EtOHbox FyD (Sat Feb 05 2011 - 01:03:14 PST)
    - Re: [AMBER] Create EtOHbox setyanto md (Mon Feb 14 2011 - 00:03:04 PST)
    - Re: [AMBER] Create EtOHbox FyD (Mon Feb 14 2011 - 01:41:37 PST)
    - Re: [AMBER] Create EtOHbox setyanto md (Mon Feb 14 2011 - 02:51:03 PST)
- Re: [AMBER] Create EtOHbox tommaso.casalini.mail.polimi.it (Thu Feb 03 2011 - 09:27:22 PST)
[AMBER] Energy calculation with namdenergy and amber Jakob Luchner (Wed Feb 02 2011 - 09:15:46 PST)
- Re: [AMBER] Energy calculation with namdenergy and amber case (Wed Feb 02 2011 - 10:35:06 PST)
[AMBER] Amber11 parallel configure error Zhu, James (Wed Feb 02 2011 - 09:53:10 PST)
- Re: [AMBER] Amber11 parallel configure error Daniel Roe (Wed Feb 02 2011 - 10:08:32 PST)
[AMBER] Can anyone suggest me solution vani panguluri (Wed Feb 02 2011 - 11:33:16 PST)
- Re: [AMBER] Can anyone suggest me solution peker milas (Wed Feb 02 2011 - 11:38:29 PST)
  - Re: [AMBER] Can anyone suggest me solution vani panguluri (Wed Feb 02 2011 - 11:44:44 PST)
    - Re: [AMBER] Can anyone suggest me solution Jason Swails (Wed Feb 02 2011 - 11:50:10 PST)
    - Re: [AMBER] Can anyone suggest me solution peker milas (Wed Feb 02 2011 - 11:58:01 PST)
- Re: [AMBER] Can anyone suggest me solution Dmitry Nilov (Wed Feb 02 2011 - 11:59:39 PST)
  - Re: [AMBER] Can anyone suggest me solution Dmitry Nilov (Wed Feb 02 2011 - 12:15:22 PST)
- Re: [AMBER] Can anyone suggest me solution Bill Ross (Wed Feb 02 2011 - 12:07:26 PST)
- Re: [AMBER] Can anyone suggest me solution Bill Ross (Wed Feb 02 2011 - 12:24:56 PST)
  - Re: [AMBER] Can anyone suggest me solution Jason Swails (Wed Feb 02 2011 - 14:07:04 PST)
    - Re: [AMBER] Can anyone suggest me solution Hirdesh Kumar (Wed Feb 02 2011 - 19:47:35 PST)
    - Re: [AMBER] Can anyone suggest me solution case (Wed Feb 02 2011 - 20:14:33 PST)
    - Re: [AMBER] Can anyone suggest me solution Dmitry Nilov (Wed Feb 02 2011 - 22:09:26 PST)
    - Re: [AMBER] Can anyone suggest me solution Hirdesh Kumar (Thu Feb 03 2011 - 00:38:53 PST)
[AMBER] pol3 water droplet Yubo Fan (Wed Feb 02 2011 - 12:33:22 PST)
[AMBER] clustering by attribute Massimiliano Porrini (Wed Feb 02 2011 - 15:20:22 PST)
- [AMBER] Fwd: clustering by attribute Massimiliano Porrini (Mon Feb 07 2011 - 07:58:26 PST)
- Re: [AMBER] clustering by attribute Daniel Roe (Mon Feb 07 2011 - 09:19:42 PST)
  - Re: [AMBER] clustering by attribute Massimiliano Porrini (Mon Feb 07 2011 - 10:06:08 PST)
[AMBER] Dielectric constant for solute mish (Thu Feb 03 2011 - 06:31:22 PST)
- Re: [AMBER] Dielectric constant for solute Jason Swails (Thu Feb 03 2011 - 06:59:46 PST)
[AMBER] pol3 water droplet Yubo Fan (Thu Feb 03 2011 - 13:11:30 PST)
- Re: [AMBER] pol3 water droplet Bill Ross (Thu Feb 03 2011 - 13:29:51 PST)
[AMBER] Membrane Protein Simulation Hirdesh Kumar (Thu Feb 03 2011 - 20:44:25 PST)
[AMBER] REMD production run restart Sangita Kachhap (Fri Feb 04 2011 - 07:21:28 PST)
- Re: [AMBER] REMD production run restart Carlos Simmerling (Fri Feb 04 2011 - 07:23:13 PST)
  - Re: [AMBER] REMD production run restart Sangita Kachhap (Fri Feb 04 2011 - 08:21:18 PST)
    - Re: [AMBER] REMD production run restart Carlos Simmerling (Fri Feb 04 2011 - 08:23:55 PST)
    - Re: [AMBER] REMD production run restart Sangita Kachhap (Fri Feb 04 2011 - 08:43:24 PST)
    - Re: [AMBER] REMD production run restart Carlos Simmerling (Fri Feb 04 2011 - 08:45:07 PST)
    - Re: [AMBER] REMD production run restart Sangita Kachhap (Fri Feb 04 2011 - 09:02:28 PST)
    - Re: [AMBER] REMD production run restart Carlos Simmerling (Fri Feb 04 2011 - 09:17:26 PST)
    - Re: [AMBER] REMD production run restart Sangita Kachhap (Fri Feb 04 2011 - 09:41:13 PST)
    - Re: [AMBER] REMD production run restart Sangita Kachhap (Fri Feb 04 2011 - 21:06:53 PST)
    - [AMBER] PMEMD and restraint problem Emanuele Galletta (Mon Feb 21 2011 - 00:46:55 PST)
    - Re: [AMBER] PMEMD and restraint problem Daniel Roe (Mon Feb 21 2011 - 07:57:28 PST)
- Re: [AMBER] REMD production run restart Daniel Roe (Fri Feb 04 2011 - 07:51:57 PST)
[AMBER] MOIL-view alternatives Emanuele G (Fri Feb 04 2011 - 08:29:07 PST)
- Re: [AMBER] MOIL-view alternatives Carlos Simmerling (Fri Feb 04 2011 - 08:45:57 PST)
  - Re: [AMBER] MOIL-view alternatives Emanuele G (Fri Feb 04 2011 - 08:49:47 PST)
    - Re: [AMBER] MOIL-view alternatives Carlos Simmerling (Fri Feb 04 2011 - 08:51:19 PST)
[AMBER] 3 GB GTX580s Scott Le Grand (Fri Feb 04 2011 - 14:29:33 PST)
[AMBER] MM-PBSA error Jagur Lambix (Fri Feb 04 2011 - 15:39:09 PST)
[AMBER] measruement of effect of perticular water molecule on affinity and specificity Sangita Kachhap (Fri Feb 04 2011 - 23:13:31 PST)
- Re: [AMBER] measruement of effect of perticular water molecule on affinity and specificity Jason Swails (Sat Feb 05 2011 - 11:47:11 PST)
  - Re: [AMBER] measruement of effect of perticular water molecule on affinity and specificity Sangita Kachhap (Sun Feb 06 2011 - 07:28:31 PST)
  - Re: [AMBER] measruement of effect of perticular water molecule on affinity and specificity Sangita Kachhap (Mon Feb 07 2011 - 07:50:40 PST)
    - Re: [AMBER] measruement of effect of perticular water molecule on affinity and specificity Jason Swails (Mon Feb 07 2011 - 08:27:52 PST)
    - Re: [AMBER] measruement of effect of perticular water molecule on affinity and specificity Sangita Kachhap (Mon Feb 07 2011 - 10:20:09 PST)
    - Re: [AMBER] measruement of effect of perticular water molecule on affinity and specificity Jason Swails (Mon Feb 07 2011 - 10:27:12 PST)
    - Re: [AMBER] measruement of effect of perticular water molecule on affinity and specificity Sangita Kachhap (Mon Feb 07 2011 - 10:53:17 PST)
[AMBER] pdb error subrata paul (Sat Feb 05 2011 - 21:27:09 PST)
- Re: [AMBER] pdb error Barbault Florent (Sun Feb 06 2011 - 01:31:05 PST)
- Re: [AMBER] pdb error Jason Swails (Sun Feb 06 2011 - 06:44:26 PST)
[AMBER] Kindly help me out for the following errors during installation of AmberTools amit banerjee (Sun Feb 06 2011 - 22:11:56 PST)
- Re: [AMBER] Kindly help me out for the following errors during installation of AmberTools Ross Walker (Sun Feb 06 2011 - 22:26:15 PST)
- Re: [AMBER] Kindly help me out for the following errors during installation of AmberTools Jason Swails (Mon Feb 07 2011 - 06:38:09 PST)
[AMBER] AMBER11 MMPBSA.py tutorial section 3.6 Yokota_Akihiro.takeda.co.jp (Sun Feb 06 2011 - 23:54:11 PST)
- Re: [AMBER] AMBER11 MMPBSA.py tutorial section 3.6 Jason Swails (Wed Feb 09 2011 - 18:46:25 PST)
  - Re: [AMBER] AMBER11 MMPBSA.py tutorial section 3.6 Yokota_Akihiro.takeda.co.jp (Wed Feb 09 2011 - 22:04:56 PST)
  - Re: [AMBER] AMBER11 MMPBSA.py tutorial section 3.6 case (Thu Feb 10 2011 - 04:55:24 PST)
[AMBER] ncsu-umbrella-slice utility in AMBER11 Mark Santer (Mon Feb 07 2011 - 04:07:15 PST)
[AMBER] Distance restraints Beale, John (Mon Feb 07 2011 - 09:59:35 PST)
- Re: [AMBER] Distance restraints case (Mon Feb 07 2011 - 11:06:54 PST)
[AMBER] softcore TI with more than 2 procs? Niel Henriksen (Mon Feb 07 2011 - 10:40:26 PST)
- Re: [AMBER] softcore TI with more than 2 procs? steinbrt.rci.rutgers.edu (Tue Feb 08 2011 - 00:31:59 PST)
  - Re: [AMBER] softcore TI with more than 2 procs? Niel Henriksen (Tue Feb 08 2011 - 15:34:31 PST)
[AMBER] Structural alignment & RMSD calculation Rahul Banerjee (Mon Feb 07 2011 - 10:50:14 PST)
- Re: [AMBER] Structural alignment & RMSD calculation Daniel Roe (Tue Feb 08 2011 - 08:10:41 PST)
[AMBER] Ionic strength in MM-PBSA Robert Elder (Mon Feb 07 2011 - 13:14:28 PST)
- Re: [AMBER] Ionic strength in MM-PBSA Ray Luo, Ph.D. (Mon Feb 07 2011 - 14:33:53 PST)
  - Re: [AMBER] Ionic strength in MM-PBSA Jason Swails (Mon Feb 07 2011 - 14:40:27 PST)
    - Re: [AMBER] Ionic strength in MM-PBSA Ray Luo, Ph.D. (Mon Feb 07 2011 - 14:56:02 PST)
- Re: [AMBER] Ionic strength in MM-PBSA Jason Swails (Mon Feb 07 2011 - 14:37:51 PST)
[AMBER] AmberTools 1.4 parallel programs Martin M. Ossowski (Mon Feb 07 2011 - 13:44:13 PST)
- Re: [AMBER] AmberTools 1.4 parallel programs Jason Swails (Mon Feb 07 2011 - 14:45:39 PST)
  - Re: [AMBER] AmberTools 1.4 parallel programs Martin M. Ossowski (Tue Feb 08 2011 - 08:23:52 PST)
    - Re: [AMBER] AmberTools 1.4 parallel programs David Case (Tue Feb 08 2011 - 09:39:57 PST)
    - Re: [AMBER] AmberTools 1.4 parallel programs Martin M. Ossowski (Tue Feb 08 2011 - 13:21:58 PST)
    - Re: [AMBER] AmberTools 1.4 parallel programs David Case (Tue Feb 08 2011 - 16:48:54 PST)
[AMBER] XMIN ERROR in LMOD calculation Wong, Sergio E. (Mon Feb 07 2011 - 16:34:18 PST)
- Re: [AMBER] XMIN ERROR in LMOD calculation Daniel Roe (Mon Feb 07 2011 - 18:12:30 PST)
  - Re: [AMBER] XMIN ERROR in LMOD calculation Wong, Sergio E. (Tue Feb 08 2011 - 17:46:21 PST)
[AMBER] Ptraj Translate Error Hirdesh Kumar (Mon Feb 07 2011 - 21:02:58 PST)
- Re: [AMBER] Ptraj Translate Error Daniel Roe (Mon Feb 07 2011 - 21:09:51 PST)
  - Re: [AMBER] Ptraj Translate Error Hirdesh Kumar (Mon Feb 07 2011 - 21:23:40 PST)
    - Re: [AMBER] Ptraj Translate Error Daniel Roe (Tue Feb 08 2011 - 06:00:07 PST)
[AMBER] New to Amber Ashok Das Mahapatra (Tue Feb 08 2011 - 04:00:42 PST)
- Re: [AMBER] New to Amber Carlos Simmerling (Tue Feb 08 2011 - 04:11:52 PST)
  - Re: [AMBER] New to Amber Igor Marques (Tue Feb 08 2011 - 04:15:25 PST)
- Re: [AMBER] New to Amber steinbrt.rci.rutgers.edu (Tue Feb 08 2011 - 04:14:43 PST)
[AMBER] compilation failure of amber 11 on Itanium2 Yubo Fan (Tue Feb 08 2011 - 12:18:48 PST)
- Re: [AMBER] compilation failure of amber 11 on Itanium2 Martin M. Ossowski (Tue Feb 08 2011 - 12:37:09 PST)
- Re: [AMBER] compilation failure of amber 11 on Itanium2 Daniel Roe (Tue Feb 08 2011 - 14:01:10 PST)
  - Re: [AMBER] compilation failure of amber 11 on Itanium2 Lachele Foley (Lists) (Tue Feb 08 2011 - 14:12:30 PST)
[AMBER] pmemd.cuda issues on Tesla S2050 Sasha Buzko (Tue Feb 08 2011 - 16:57:37 PST)
- Re: [AMBER] pmemd.cuda issues on Tesla S2050 Scott Le Grand (Tue Feb 08 2011 - 17:22:37 PST)
- Re: [AMBER] pmemd.cuda issues on Tesla S2050 Peter Schmidtke (Tue Feb 08 2011 - 17:21:30 PST)
  - Re: [AMBER] pmemd.cuda issues on Tesla S2050 Ross Walker (Tue Feb 08 2011 - 19:29:08 PST)
    - Re: [AMBER] pmemd.cuda issues on Tesla S2050 Sasha Buzko (Wed Feb 09 2011 - 09:24:08 PST)
    - Re: [AMBER] pmemd.cuda issues on Tesla S2050 Ross Walker (Wed Feb 09 2011 - 22:37:09 PST)
    - Re: [AMBER] pmemd.cuda issues on Tesla S2050 Scott Le Grand (Thu Feb 10 2011 - 06:51:21 PST)
    - Re: [AMBER] pmemd.cuda issues on Tesla S2050 Scott Le Grand (Thu Feb 10 2011 - 07:01:25 PST)
    - Re: [AMBER] pmemd.cuda issues on Tesla S2050 Sasha Buzko (Thu Feb 10 2011 - 10:13:11 PST)
    - Re: [AMBER] pmemd.cuda issues on Tesla S2050 Sasha Buzko (Wed Mar 02 2011 - 09:54:08 PST)
- Re: [AMBER] pmemd.cuda issues on Tesla S2050 Ross Walker (Tue Feb 08 2011 - 17:27:14 PST)
- Re: [AMBER] pmemd.cuda issues on Tesla S2050 Ross Walker (Tue Feb 08 2011 - 19:26:43 PST)
[AMBER] How to rename GLYCAM residue names of a sugar to the same name for one complete sugar (in tleap or xleap) mish (Wed Feb 09 2011 - 07:30:02 PST)
- Re: [AMBER] How to rename GLYCAM residue names of a sugar to the same name for one complete sugar (in tleap or xleap) Lachele Foley (Lists) (Wed Feb 09 2011 - 08:08:57 PST)
  - Re: [AMBER] How to rename GLYCAM residue names of a sugar to the same name for one complete sugar (in tleap or xleap) mish (Wed Feb 09 2011 - 09:18:39 PST)
    - Re: [AMBER] How to rename GLYCAM residue names of a sugar to the same name for one complete sugar (in tleap or xleap) Lachele Foley (Lists) (Wed Feb 09 2011 - 09:39:14 PST)
    - Re: [AMBER] How to rename GLYCAM residue names of a sugar to the same name for one complete sugar (in tleap or xleap) mish (Tue Apr 05 2011 - 09:20:38 PDT)
    - Re: [AMBER] How to rename GLYCAM residue names of a sugar to the same name for one complete sugar (in tleap or xleap) Lachele Foley (Lists) (Tue Apr 05 2011 - 09:46:06 PDT)
    - Re: [AMBER] How to rename GLYCAM residue names of a sugar to the same name for one complete sugar (in tleap or xleap) mish (Tue Apr 05 2011 - 10:05:12 PDT)
    - Re: [AMBER] How to rename GLYCAM residue names of a sugar to the same name for one complete sugar (in tleap or xleap) Lachele Foley (Lists) (Tue Apr 05 2011 - 10:32:45 PDT)
[AMBER] break down of simulation after approximately 60 ns Jakob Luchner (Wed Feb 09 2011 - 11:36:25 PST)
- Re: [AMBER] break down of simulation after approximately 60 ns case (Wed Feb 09 2011 - 11:52:36 PST)
- Re: [AMBER] break down of simulation after approximately 60 ns Bill Ross (Wed Feb 09 2011 - 11:54:58 PST)
[AMBER] problems with mm_pbsa on amber8 Waqas Nasir (Thu Feb 10 2011 - 04:22:59 PST)
- Re: [AMBER] problems with mm_pbsa on amber8 case (Thu Feb 10 2011 - 05:03:51 PST)
[AMBER] parametrization of sugar modified nucleic acids Aparna P (Fri Feb 11 2011 - 01:46:13 PST)
- Re: [AMBER] parametrization of sugar modified nucleic acids Stephane Abel (Fri Feb 11 2011 - 05:43:05 PST)
- Re: [AMBER] parametrization of sugar modified nucleic acids cieplak.cgl.ucsf.edu (Fri Feb 11 2011 - 11:25:19 PST)
  - Re: [AMBER] parametrization of sugar modified nucleic acids Aparna P (Sun Feb 13 2011 - 22:31:37 PST)
    - [AMBER] AMBER 9 install gfortran gromacs (Sun Feb 13 2011 - 23:15:07 PST)
    - Re: [AMBER] AMBER 9 install gfortran Jason Swails (Mon Feb 14 2011 - 04:41:27 PST)
    - [AMBER] AMBER 9 install gfortran, not need AmberTool gromacs (Mon Feb 14 2011 - 16:20:24 PST)
    - Re: [AMBER] AMBER 9 install gfortran, not need AmberTool Jason Swails (Mon Feb 14 2011 - 16:42:54 PST)
    - Re: [AMBER] AMBER 9 install gfortran, not need AmberTool gromacs (Mon Feb 14 2011 - 17:04:24 PST)
    - Re: [AMBER] AMBER 9 install gfortran, not need AmberTool Jason Swails (Mon Feb 14 2011 - 17:47:39 PST)
    - Re: [AMBER] AMBER 9 install gfortran, not need AmberTool gromacs (Mon Feb 14 2011 - 17:20:11 PST)
    - Re: [AMBER] AMBER 9 install gfortran, not need AmberTool Jason Swails (Mon Feb 14 2011 - 17:48:59 PST)
    - Re: [AMBER] AMBER 9 install gfortran, not need AmberTool gromacs (Mon Feb 14 2011 - 17:41:16 PST)
    - Re: [AMBER] AMBER 9 install gfortran, not need AmberTool Jason Swails (Mon Feb 14 2011 - 17:53:13 PST)
    - Re: [AMBER] AMBER 9 install gfortran, not need AmberTool gromacs (Mon Feb 14 2011 - 18:47:17 PST)
    - Re: [AMBER] AMBER 9 install gfortran, not need AmberTool David Case (Mon Feb 14 2011 - 19:17:46 PST)
    - Re: [AMBER] AMBER 9 install gfortran, not need AmberTool gromacs (Mon Feb 14 2011 - 19:27:00 PST)
    - Re: [AMBER] AMBER 9 install gfortran, not need AmberTool case (Tue Feb 15 2011 - 04:45:15 PST)
    - [AMBER] AMBER 9 install gfortran, If i install xorg-dev package, there will be error; However if i did not install xorg-dev, i cannot pass the test of tleap. gromacs (Mon Feb 14 2011 - 19:17:39 PST)
    - Re: [AMBER] AMBER 9 install gfortran, If i install xorg-dev package, there will be error; However if i did not install xorg-dev, i cannot pass the test of tleap. Jason Swails (Mon Feb 14 2011 - 19:40:05 PST)
    - Re: [AMBER] AMBER 9 install gfortran case (Mon Feb 14 2011 - 05:04:40 PST)
[AMBER] Consistency between temperatures in mdout and mdcrd in REMD Daniel Sindhikara (Fri Feb 11 2011 - 02:08:05 PST)
- Re: [AMBER] Consistency between temperatures in mdout and mdcrd in REMD Daniel Roe (Fri Feb 11 2011 - 10:57:49 PST)
  - Re: [AMBER] Consistency between temperatures in mdout and mdcrd in REMD Daniel Sindhikara (Sat Feb 12 2011 - 00:20:12 PST)
[AMBER] MMPBSA.py - dimer energy calculations Julia Romanowska (Fri Feb 11 2011 - 03:34:02 PST)
- Re: [AMBER] MMPBSA.py - dimer energy calculations cieplak.cgl.ucsf.edu (Fri Feb 11 2011 - 11:15:34 PST)
[AMBER] Polymeric lattice building tommaso.casalini.mail.polimi.it (Fri Feb 11 2011 - 03:45:18 PST)
[AMBER] ERROR IN SETPAR() when REMD running Bongkeun Kim (Fri Feb 11 2011 - 09:25:40 PST)
[AMBER] Cluster considerations peker milas (Fri Feb 11 2011 - 16:33:39 PST)
- Re: [AMBER] Cluster considerations Brent Krueger (Fri Feb 11 2011 - 18:08:00 PST)
- Re: [AMBER] Cluster considerations Ross Walker (Fri Feb 11 2011 - 20:12:15 PST)
  - Re: [AMBER] Cluster considerations peker milas (Fri Feb 18 2011 - 19:29:18 PST)
    - Re: [AMBER] Cluster considerations Marek Maly (Fri Feb 18 2011 - 20:42:59 PST)
[AMBER] create urea molecule. subrata paul (Fri Feb 11 2011 - 23:22:54 PST)
- Re: [AMBER] create urea molecule. FyD (Fri Feb 11 2011 - 23:38:15 PST)
  - Re: [AMBER] create urea molecule. subrata paul (Sat Feb 12 2011 - 03:53:22 PST)
    - Re: [AMBER] create urea molecule. FyD (Sat Feb 12 2011 - 08:28:53 PST)
    - [AMBER] nab problems: compile and use on different machines Anselm Horn (Sat Feb 12 2011 - 09:55:40 PST)
    - Re: [AMBER] nab problems: compile and use on different machines David Case (Sat Feb 12 2011 - 14:15:43 PST)
    - Re: [AMBER] nab problems: compile and use on different machines Anselm Horn (Sat Feb 12 2011 - 14:47:54 PST)
    - Re: [AMBER] nab problems: compile and use on different machines Jason Swails (Sat Feb 12 2011 - 21:29:38 PST)
    - Re: [AMBER] nab problems: compile and use on different machines Anselm Horn (Sun Feb 13 2011 - 13:51:37 PST)
    - Re: [AMBER] nab problems: compile and use on different machines Jason Swails (Sun Feb 13 2011 - 16:05:26 PST)
    - Re: [AMBER] nab problems: compile and use on different machines Anselm Horn (Mon Feb 14 2011 - 04:52:00 PST)
    - [AMBER] AmberTools manual: AA residue names Anselm Horn (Wed Feb 16 2011 - 00:21:50 PST)
    - Re: [AMBER] AmberTools manual: AA residue names case (Wed Feb 16 2011 - 07:08:41 PST)
    - Re: [AMBER] create urea molecule. subrata paul (Tue Feb 15 2011 - 04:24:33 PST)
    - Re: [AMBER] create urea molecule. case (Tue Feb 15 2011 - 04:52:30 PST)
[AMBER] problem with analyzing trajectaries bharat lakhani (Sat Feb 12 2011 - 00:41:32 PST)
- Re: [AMBER] problem with analyzing trajectaries Daniel Roe (Sat Feb 12 2011 - 06:45:40 PST)
[AMBER] parametrization of acetyl-coa using antechamber Knut Jørgen Bjuland (Sat Feb 12 2011 - 10:29:24 PST)
- Re: [AMBER] parametrization of acetyl-coa using antechamber David Case (Sat Feb 12 2011 - 14:19:49 PST)
  - Re: [AMBER] parametrization of acetyl-coa using antechamber snoze pa (Sat Feb 12 2011 - 22:55:53 PST)
  - Re: [AMBER] parametrization of acetyl-coa using antechamber Knut Jørgen Bjuland (Sun Feb 13 2011 - 01:00:02 PST)
    - Re: [AMBER] parametrization of acetyl-coa using antechamber case (Mon Feb 14 2011 - 09:30:44 PST)
  - Re: [AMBER] parametrization of acetyl-coa using antechamber Dean Cuebas (Sun Feb 13 2011 - 12:09:20 PST)
[AMBER] EVB with time-dependent coupling parameter? Jose Borreguero (Sat Feb 12 2011 - 11:15:59 PST)
- Re: [AMBER] EVB with time-dependent coupling parameter? case (Tue Feb 15 2011 - 05:27:32 PST)
  - Re: [AMBER] EVB with time-dependent coupling parameter? Jose Borreguero (Tue Feb 15 2011 - 06:09:37 PST)
    - Re: [AMBER] EVB with time-dependent coupling parameter? case (Tue Feb 15 2011 - 07:40:54 PST)
[AMBER] slowly relaxing individual residues Andre Serobian (Sun Feb 13 2011 - 12:07:21 PST)
[AMBER] Two fragments minimization Eliac Brown (Sun Feb 13 2011 - 13:23:00 PST)
[AMBER] ISTRNG in PBSA script does not work properly Xioling Chuang (Sun Feb 13 2011 - 23:24:05 PST)
- [AMBER] parameter "ISTRNG" in PBSA script does not work properly (2nd post) Xioling Chuang (Wed Feb 16 2011 - 22:13:53 PST)
[AMBER] Problem with QMMM umbrella sampling Wook Lee (Mon Feb 14 2011 - 02:06:19 PST)
- Re: [AMBER] Problem with QMMM umbrella sampling Adrian Roitberg (Mon Feb 14 2011 - 10:34:21 PST)
[AMBER] new force field ff99SBildn not supported for normal mode analysis in amber11 Tan Yaw Sing (Mon Feb 14 2011 - 10:23:29 PST)
- Re: [AMBER] new force field ff99SBildn not supported for normal mode analysis in amber11 Daniel Roe (Mon Feb 14 2011 - 11:23:34 PST)
- Re: [AMBER] new force field ff99SBildn not supported for normal mode analysis in amber11 case (Mon Feb 14 2011 - 11:54:52 PST)
  - Re: [AMBER] new force field ff99SBildn not supported for normal mode analysis in amber11 Jason Swails (Mon Feb 14 2011 - 12:20:22 PST)
[AMBER] Regarding AMBER help command and Ewald Namelist Variables Specifications Naveen Samala (Mon Feb 14 2011 - 11:06:34 PST)
- Re: [AMBER] Regarding AMBER help command and Ewald Namelist Variables Specifications case (Tue Feb 15 2011 - 05:24:28 PST)
[AMBER] max pairlist cutoff error on octahedral box Bongkeun Kim (Mon Feb 14 2011 - 11:11:50 PST)
- Re: [AMBER] max pairlist cutoff error on octahedral box Ross Walker (Mon Feb 14 2011 - 13:36:45 PST)
  - Re: [AMBER] max pairlist cutoff error on octahedral box Bongkeun Kim (Mon Feb 14 2011 - 13:57:13 PST)
    - Re: [AMBER] max pairlist cutoff error on octahedral box Bill Miller III (Tue Feb 15 2011 - 04:12:32 PST)
    - Re: [AMBER] max pairlist cutoff error on octahedral box Scott Le Grand (Tue Feb 15 2011 - 08:24:36 PST)
    - [AMBER] cuda_DPDP problems; large cutoff radius problems case (Tue Feb 15 2011 - 09:17:17 PST)
    - Re: [AMBER] cuda_DPDP problems; large cutoff radius problems Scott Le Grand (Tue Feb 15 2011 - 09:39:56 PST)
    - Re: [AMBER] cuda_DPDP problems; large cutoff radius problems Scott Le Grand (Thu Feb 17 2011 - 08:28:13 PST)
    - Re: [AMBER] max pairlist cutoff error on octahedral box Scott Le Grand (Wed Feb 16 2011 - 08:47:49 PST)
    - Re: [AMBER] max pairlist cutoff error on octahedral box Ross Walker (Tue Feb 15 2011 - 12:50:58 PST)
    - Re: [AMBER] max pairlist cutoff error on octahedral box Bill Miller III (Tue Feb 15 2011 - 13:34:01 PST)
[AMBER] ESURF term error in a one-step sander calculation Yao-Chi Chen (Mon Feb 14 2011 - 18:00:44 PST)
- [AMBER] ESURF term error in a one-step sander calculation Yao-Chi Chen (Mon Feb 14 2011 - 18:01:45 PST)
  - Re: [AMBER] ESURF term error in a one-step sander calculation case (Tue Feb 15 2011 - 06:08:48 PST)
[AMBER] parameters for CO2+ moitrayee.mbu.iisc.ernet.in (Mon Feb 14 2011 - 22:05:31 PST)
[AMBER] Simulation of DNA using generalized Born model Ali M. Naserian-Nik (Tue Feb 15 2011 - 00:15:46 PST)
- Re: [AMBER] Simulation of DNA using generalized Born model Adrian Roitberg (Tue Feb 15 2011 - 00:23:05 PST)
  - Re: [AMBER] Simulation of DNA using generalized Born model Ali M. Naserian-Nik (Tue Feb 15 2011 - 03:19:30 PST)
  - Re: [AMBER] Simulation of DNA using generalized Born model Ali M. Naserian-Nik (Tue Feb 15 2011 - 02:45:39 PST)
- Re: [AMBER] Simulation of DNA using generalized Born model Jiri Sponer (Tue Feb 15 2011 - 03:01:41 PST)
[AMBER] increasing rmsd value Siti Mohamad (Tue Feb 15 2011 - 05:07:04 PST)
- Re: [AMBER] increasing rmsd value Fredrick Devadoss (Tue Feb 15 2011 - 05:17:52 PST)
- Re: [AMBER] increasing rmsd value Bill Ross (Tue Feb 15 2011 - 10:49:03 PST)
  - Re: [AMBER] increasing rmsd value Siti Mohamad (Tue Feb 15 2011 - 17:13:57 PST)
    - Re: [AMBER] increasing rmsd value Sangita Kachhap (Tue Feb 15 2011 - 21:56:15 PST)
- Re: [AMBER] increasing rmsd value Bill Ross (Tue Feb 15 2011 - 17:42:35 PST)
[AMBER] 回复：回复：回复：回复：回复： MM-PBSA error about protein + Mg2+ 475649770 (Tue Feb 15 2011 - 05:05:31 PST)
- Re: [AMBER] 回复：回复：回复：回复：回复： MM-PBSA error about protein + Mg2+ Bill Miller III (Tue Feb 15 2011 - 05:47:22 PST)
  - Re: [AMBER] 回复：回复：回复：回复：回复： MM-PBSA error about protein + Mg2+ Jason Swails (Tue Feb 15 2011 - 06:46:42 PST)
  - [AMBER] MMPBSA.py: Factoring in the contribution of individual HOH molecules to delta G George Tzotzos (Tue Feb 15 2011 - 08:40:00 PST)
    - Re: [AMBER] MMPBSA.py: Factoring in the contribution of individual HOH molecules to delta G Bill Miller III (Tue Feb 15 2011 - 08:57:32 PST)
    - Re: [AMBER] MMPBSA.py: Factoring in the contribution of individual HOH molecules to delta G Jason Swails (Tue Feb 15 2011 - 09:03:03 PST)
    - Re: [AMBER] MMPBSA.py: Factoring in the contribution of individual HOH molecules to delta G George Tzotzos (Tue Feb 15 2011 - 09:45:47 PST)
    - Re: [AMBER] MMPBSA.py: Factoring in the contribution of individual HOH molecules to delta G Jason Swails (Tue Feb 15 2011 - 11:18:07 PST)
    - [AMBER] MMPBSA: Trajectory pre-processing George Tzotzos (Fri May 06 2011 - 03:30:05 PDT)
    - Re: [AMBER] MMPBSA: Trajectory pre-processing Bill Miller III (Fri May 06 2011 - 04:38:06 PDT)
    - Re: [AMBER] MMPBSA: Trajectory pre-processing George Tzotzos (Fri May 06 2011 - 07:21:25 PDT)
    - Re: [AMBER] MMPBSA: Trajectory pre-processing Bill Miller III (Fri May 06 2011 - 07:28:31 PDT)
    - Re: [AMBER] MMPBSA: Trajectory pre-processing George Tzotzos (Fri May 06 2011 - 07:33:13 PDT)
[AMBER] REMD at constant pH Cheng-I Lee (Tue Feb 15 2011 - 05:30:26 PST)
- Re: [AMBER] REMD at constant pH Adrian Roitberg (Tue Feb 15 2011 - 05:34:29 PST)
  - Re: [AMBER] REMD at constant pH Cheng-I Lee (Wed Feb 16 2011 - 03:55:45 PST)
    - Re: [AMBER] REMD at constant pH Adrian Roitberg (Wed Feb 16 2011 - 06:27:11 PST)
    - Re: [AMBER] REMD at constant pH Cheng-I Lee (Tue Feb 22 2011 - 20:50:39 PST)
    - Re: [AMBER] REMD at constant pH Jason Swails (Wed Feb 23 2011 - 05:36:54 PST)
- Re: [AMBER] REMD at constant pH Jason Swails (Tue Feb 15 2011 - 05:41:29 PST)
  - Re: [AMBER] REMD at constant pH Cheng-I Lee (Wed Feb 23 2011 - 12:26:48 PST)
    - Re: [AMBER] REMD at constant pH Jason Swails (Wed Feb 23 2011 - 16:59:49 PST)
    - Re: [AMBER] REMD at constant pH Cheng-I Lee (Wed Feb 23 2011 - 18:48:57 PST)
[AMBER] Fwd: ESURF term error in a one-step sander calculation Yao-Chi Chen (Tue Feb 15 2011 - 10:10:31 PST)
- Re: [AMBER] Fwd: ESURF term error in a one-step sander calculation case (Tue Feb 15 2011 - 12:49:54 PST)
[AMBER] 回复：回复：回复：回复：回复： MM-PBSA error about protein + Mg2+ 475649770 (Tue Feb 15 2011 - 05:07:49 PST)
[AMBER] xleap does not want to impose my dihedrals steinbrt.rci.rutgers.edu (Tue Feb 15 2011 - 10:27:27 PST)
- Re: [AMBER] xleap does not want to impose my dihedrals FyD (Tue Feb 15 2011 - 13:20:42 PST)
[AMBER] xleap or rather ff10 bug? update steinbrt.rci.rutgers.edu (Tue Feb 15 2011 - 10:47:25 PST)
- Re: [AMBER] xleap or rather ff10 bug? update case (Tue Feb 15 2011 - 14:56:04 PST)
[AMBER] FATAL ERROR vani panguluri (Tue Feb 15 2011 - 16:02:09 PST)
- Re: [AMBER] FATAL ERROR peker milas (Tue Feb 15 2011 - 16:20:38 PST)
  - Re: [AMBER] FATAL ERROR vani panguluri (Tue Feb 15 2011 - 16:36:51 PST)
- Re: [AMBER] FATAL ERROR case (Tue Feb 15 2011 - 16:29:06 PST)
  - Re: [AMBER] FATAL ERROR vani panguluri (Tue Feb 15 2011 - 16:40:06 PST)
    - Re: [AMBER] FATAL ERROR peker milas (Tue Feb 15 2011 - 16:44:13 PST)
- Re: [AMBER] FATAL ERROR Bill Ross (Tue Feb 15 2011 - 17:30:08 PST)
- Re: [AMBER] FATAL ERROR Bill Ross (Tue Feb 15 2011 - 17:36:30 PST)
  - Re: [AMBER] FATAL ERROR Jason Swails (Tue Feb 15 2011 - 17:52:00 PST)
    - Re: [AMBER] FATAL ERROR vani panguluri (Tue Feb 15 2011 - 18:04:16 PST)
- Re: [AMBER] FATAL ERROR Bill Ross (Tue Feb 15 2011 - 19:02:30 PST)
  - Re: [AMBER] FATAL ERROR vani panguluri (Tue Feb 15 2011 - 20:44:09 PST)
    - Re: [AMBER] FATAL ERROR Sangita Kachhap (Tue Feb 15 2011 - 22:50:08 PST)
    - Re: [AMBER] FATAL ERROR vani panguluri (Wed Feb 16 2011 - 08:38:53 PST)
    - Re: [AMBER] FATAL ERROR case (Wed Feb 16 2011 - 09:28:53 PST)
    - Re: [AMBER] FATAL ERROR Sangita Kachhap (Wed Feb 16 2011 - 09:32:23 PST)
    - Re: [AMBER] FATAL ERROR Sangita Kachhap (Wed Feb 16 2011 - 09:39:02 PST)
    - Re: [AMBER] FATAL ERROR case (Wed Feb 16 2011 - 07:06:59 PST)
[AMBER] 回复：回复：回复：回复：回复：回复： MM-PBSA error about protein + Mg2+ 475649770 (Tue Feb 15 2011 - 16:56:59 PST)
- Re: [AMBER] 回复：回复：回复：回复：回复：回复： MM-PBSA error about protein + Mg2+ Jason Swails (Tue Feb 15 2011 - 17:47:19 PST)
[AMBER] ERROR IN SETPAR() upon atom distribution with FF03, 03.r1 Bongkeun Kim (Tue Feb 15 2011 - 17:19:56 PST)
- Re: [AMBER] ERROR IN SETPAR() upon atom distribution with FF03, 03.r1 case (Wed Feb 16 2011 - 06:51:39 PST)
  - Re: [AMBER] ERROR IN SETPAR() upon atom distribution with FF03, 03.r1 Bongkeun Kim (Wed Feb 16 2011 - 09:03:37 PST)
    - Re: [AMBER] ERROR IN SETPAR() upon atom distribution with FF03, 03.r1 Bongkeun Kim (Wed Feb 16 2011 - 20:48:20 PST)
    - Re: [AMBER] ERROR IN SETPAR() upon atom distribution with FF03, 03.r1 case (Thu Feb 17 2011 - 05:00:17 PST)
    - Re: [AMBER] ERROR IN SETPAR() upon atom distribution with FF03, 03.r1 Bongkeun Kim (Thu Feb 17 2011 - 10:26:19 PST)
    - Re: [AMBER] ERROR IN SETPAR() upon atom distribution with FF03, 03.r1 case (Thu Feb 17 2011 - 13:15:33 PST)
    - Re: [AMBER] ERROR IN SETPAR() upon atom distribution with FF03, 03.r1 Bongkeun Kim (Fri Feb 18 2011 - 10:05:00 PST)
    - Re: [AMBER] ERROR IN SETPAR() upon atom distribution with FF03, 03.r1 Daniel Roe (Thu Feb 17 2011 - 05:19:17 PST)
[AMBER] 回复：回复：回复：回复：回复：回复：回复： MM-PBSA error about protein + Mg2+ 475649770 (Wed Feb 16 2011 - 00:45:15 PST)
- Re: [AMBER] 回复：回复：回复：回复：回复：回复：回复： MM-PBSA error about protein + Mg2+ Bill Miller III (Wed Feb 16 2011 - 03:46:24 PST)
[AMBER] cluster using ptraj 475649770 (Wed Feb 16 2011 - 01:29:20 PST)
- Re: [AMBER] cluster using ptraj Massimiliano Porrini (Wed Feb 16 2011 - 04:42:59 PST)
  - Re: [AMBER] cluster using ptraj João Henriques (Wed Feb 16 2011 - 20:29:26 PST)
[AMBER] MD of protein with NADPH Aditya Padhi (Wed Feb 16 2011 - 01:50:48 PST)
- Re: [AMBER] MD of protein with NADPH Dmitry Nilov (Wed Feb 16 2011 - 02:24:07 PST)
  - Re: [AMBER] MD of protein with NADPH Aditya Padhi (Wed Feb 16 2011 - 03:22:02 PST)
[AMBER] 回复：回复：回复：回复：回复：回复：回复：回复： MM-PBSA error about protein + Mg2+ 475649770 (Wed Feb 16 2011 - 04:42:27 PST)
- Re: [AMBER] 回复：回复：回复：回复：回复：回复：回复：回复： MM-PBSA error about protein + Mg2+ Jason Swails (Wed Feb 16 2011 - 05:25:20 PST)
[AMBER] Fwd: About long simulation haris p (Wed Feb 16 2011 - 07:47:19 PST)
- Re: [AMBER] Fwd: About long simulation Daniel Roe (Wed Feb 16 2011 - 11:34:35 PST)
  - Re: [AMBER] Fwd: About long simulation haris p (Wed Feb 16 2011 - 12:08:23 PST)
    - Re: [AMBER] Fwd: About long simulation Daniel Roe (Wed Feb 16 2011 - 12:57:30 PST)
    - Re: [AMBER] Fwd: About long simulation haris p (Wed Feb 16 2011 - 13:13:34 PST)
    - Re: [AMBER] Fwd: About long simulation Jason Swails (Wed Feb 16 2011 - 16:18:44 PST)
    - Re: [AMBER] Fwd: About long simulation Daniel Roe (Thu Feb 17 2011 - 05:25:28 PST)
- Re: [AMBER] Fwd: About long simulation Bill Ross (Wed Feb 16 2011 - 12:59:40 PST)
  - Re: [AMBER] Fwd: About long simulation haris p (Wed Feb 16 2011 - 13:08:30 PST)
[AMBER] V5 dihedrals serena_leone.libero.it (Wed Feb 16 2011 - 08:21:50 PST)
- Re: [AMBER] V5 dihedrals case (Wed Feb 16 2011 - 09:14:47 PST)
  - Re: [AMBER] V5 dihedrals Jason Swails (Wed Feb 16 2011 - 10:10:46 PST)
[AMBER] restraining protons with pmemd Francesco Pietra (Wed Feb 16 2011 - 10:11:50 PST)
[AMBER] R: Re: V5 dihedrals serena_leone.libero.it (Wed Feb 16 2011 - 10:29:00 PST)
- Re: [AMBER] R: Re: V5 dihedrals Jason Swails (Wed Feb 16 2011 - 11:04:24 PST)
- [AMBER] Positive value of DELTA INT using one trajectory approach Marek Maly (Wed Feb 16 2011 - 11:31:34 PST)
[AMBER] AMBER Workshop in Barcelona, Spain, May 3rd to 6th 2011. Ross Walker (Wed Feb 16 2011 - 12:16:01 PST)
[AMBER] Simple NAB script from manual segfaults at call to md() Chris King (Wed Feb 16 2011 - 14:35:26 PST)
- Re: [AMBER] Simple NAB script from manual segfaults at call to md() case (Thu Feb 17 2011 - 04:52:20 PST)
[AMBER] Query regarding atom type using xleap Hirdesh Kumar (Wed Feb 16 2011 - 22:37:28 PST)
- Re: [AMBER] Query regarding atom type using xleap Bill Ross (Thu Feb 17 2011 - 00:11:29 PST)
[AMBER] setBox command in sleap AMBER11 Antje Wolf (Thu Feb 17 2011 - 04:02:52 PST)
[AMBER] center of mass motion siddesh southekal (Thu Feb 17 2011 - 05:09:28 PST)
- Re: [AMBER] center of mass motion Daniel Sindhikara (Thu Feb 17 2011 - 18:57:33 PST)
  - Re: [AMBER] center of mass motion siddesh southekal (Fri Feb 25 2011 - 03:31:56 PST)
    - Re: [AMBER] center of mass motion Daniel Roe (Fri Feb 25 2011 - 04:05:55 PST)
[AMBER] binding energy calculation problem poll.chemie.uni-hamburg.de (Thu Feb 17 2011 - 07:13:25 PST)
- Re: [AMBER] binding energy calculation problem steinbrt.rci.rutgers.edu (Thu Feb 17 2011 - 07:21:43 PST)
  - Re: [AMBER] binding energy calculation problem poll.chemie.uni-hamburg.de (Thu Feb 17 2011 - 08:38:07 PST)
    - Re: [AMBER] binding energy calculation problem Jason Swails (Thu Feb 17 2011 - 09:27:12 PST)
    - Re: [AMBER] binding energy calculation problem poll.chemie.uni-hamburg.de (Tue Feb 22 2011 - 06:26:07 PST)
    - Re: [AMBER] binding energy calculation problem Jason Swails (Tue Feb 22 2011 - 06:54:27 PST)
    - Re: [AMBER] binding energy calculation problem poll.chemie.uni-hamburg.de (Tue Feb 22 2011 - 08:16:57 PST)
    - Re: [AMBER] binding energy calculation problem Jason Swails (Tue Feb 22 2011 - 08:47:25 PST)
    - Re: [AMBER] binding energy calculation problem poll.chemie.uni-hamburg.de (Thu Feb 24 2011 - 02:27:28 PST)
    - Re: [AMBER] binding energy calculation problem Bill Miller III (Thu Feb 24 2011 - 03:56:40 PST)
    - Re: [AMBER] binding energy calculation problem poll.chemie.uni-hamburg.de (Thu Feb 24 2011 - 05:09:00 PST)
    - Re: [AMBER] binding energy calculation problem Bill Miller III (Thu Feb 24 2011 - 18:18:35 PST)
[AMBER] problem with parametrization of an organo-metallic cluster using RED server moitrayee.mbu.iisc.ernet.in (Thu Feb 17 2011 - 00:18:13 PST)
- Re: [AMBER] problem with parametrization of an organo-metallic cluster using RED server FyD (Thu Feb 17 2011 - 12:37:43 PST)
[AMBER] Scale sander.MPI to 64 ncpus - Amber11 Leong Wye Kit Damien (Thu Feb 17 2011 - 09:05:09 PST)
- Re: [AMBER] Scale sander.MPI to 64 ncpus - Amber11 case (Thu Feb 17 2011 - 12:47:20 PST)
  - Re: [AMBER] Scale sander.MPI to 64 ncpus - Amber11 Leong Wye Kit Damien (Thu Feb 17 2011 - 18:22:51 PST)
[AMBER] MD simulation of protein with Calcium ion Aditya Padhi (Thu Feb 17 2011 - 21:31:28 PST)
- Re: [AMBER] MD simulation of protein with Calcium ion Sangita Kachhap (Thu Feb 17 2011 - 21:55:14 PST)
  - Re: [AMBER] MD simulation of protein with Calcium ion Aditya Padhi (Thu Feb 17 2011 - 22:01:25 PST)
    - Re: [AMBER] MD simulation of protein with Calcium ion Sangita Kachhap (Fri Feb 18 2011 - 00:47:38 PST)
    - [AMBER] Memory problem with NPT simulation of 124K atoms on GeForce GTX 470 ... Marek Maly (Fri Feb 18 2011 - 18:46:50 PST)
    - Re: [AMBER] Memory problem with NPT simulation of 124K atoms on GeForce GTX 470 ... Ross Walker (Fri Feb 18 2011 - 21:03:48 PST)
    - Re: [AMBER] Memory problem with NPT simulation of 124K atoms on GeForce GTX 470 ... Marek Maly (Fri Feb 18 2011 - 21:40:00 PST)
- Re: [AMBER] MD simulation of protein with Calcium ion Jason Swails (Fri Feb 18 2011 - 05:27:19 PST)
  - Re: [AMBER] MD simulation of protein with Calcium ion Aditya Padhi (Fri Feb 18 2011 - 21:13:46 PST)
    - [AMBER] MD simulation of protein with Calcium ion Aditya Padhi (Fri Feb 18 2011 - 21:14:18 PST)
    - Re: [AMBER] MD simulation of protein with Calcium ion Catein Catherine (Mon Feb 21 2011 - 02:36:14 PST)
- Re: [AMBER] MD simulation of protein with Calcium ion Dmitry Nilov (Wed Mar 02 2011 - 03:02:46 PST)
[AMBER] How to simulate hydration free energy with thermodynamic integration? Junjian Miao (Fri Feb 18 2011 - 05:32:18 PST)
- Re: [AMBER] How to simulate hydration free energy with thermodynamic integration? steinbrt.rci.rutgers.edu (Fri Feb 18 2011 - 07:11:31 PST)
[AMBER] How to simulate hydration free energy with thermodynamic integration? Junjian Miao (Fri Feb 18 2011 - 05:45:49 PST)
[AMBER] Probelm with antechamber for resp charge derivation Rajesh Raju (Fri Feb 18 2011 - 09:52:50 PST)
- Re: [AMBER] Probelm with antechamber for resp charge derivation FyD (Sat Feb 19 2011 - 02:42:23 PST)
  - Re: [AMBER] Probelm with antechamber for resp charge derivation Rajesh Raju (Sat Feb 19 2011 - 11:15:33 PST)
    - Re: [AMBER] Probelm with antechamber for resp charge derivation federica de leo (Sat Feb 19 2011 - 21:02:32 PST)
    - Re: [AMBER] Probelm with antechamber for resp charge derivation FyD (Sun Feb 20 2011 - 08:52:57 PST)
    - Re: [AMBER] Probelm with antechamber for resp charge derivation Rajesh Raju (Tue Feb 22 2011 - 14:27:30 PST)
    - Re: [AMBER] Probelm with antechamber for resp charge derivation FyD (Tue Feb 22 2011 - 23:59:13 PST)
[AMBER] Extracting replica trajectories Cheng-I Lee (Sun Feb 20 2011 - 01:11:04 PST)
- Re: [AMBER] Extracting replica trajectories Daniel Sindhikara (Sun Feb 20 2011 - 05:48:35 PST)
[AMBER] Angle setting tommaso.casalini.mail.polimi.it (Sun Feb 20 2011 - 06:37:30 PST)
- Re: [AMBER] Angle setting Bill Ross (Tue Feb 22 2011 - 11:02:40 PST)
[AMBER] reimaging failure Francesco Pietra (Sun Feb 20 2011 - 09:29:53 PST)
- [AMBER] Fwd: reimaging failure Francesco Pietra (Sun Feb 20 2011 - 13:30:46 PST)
  - [AMBER] Large different between experimental and MM-GBSA absolute energy, any potential source of error? Catein Catherine (Mon Feb 21 2011 - 02:38:12 PST)
    - Re: [AMBER] Large different between experimental and MM-GBSA absolute energy, any potential source of error? Jason Swails (Mon Feb 21 2011 - 09:58:23 PST)
[AMBER] How to generate MM/PBSA statistics from recovered Job mish (Mon Feb 21 2011 - 07:38:24 PST)
- Re: [AMBER] How to generate MM/PBSA statistics from recovered Job Jason Swails (Mon Feb 21 2011 - 09:08:22 PST)
  - Re: [AMBER] How to generate MM/PBSA statistics from recovered Job mish (Mon Feb 21 2011 - 10:18:46 PST)
    - Re: [AMBER] How to generate MM/PBSA statistics from recovered Job Jason Swails (Mon Feb 21 2011 - 11:05:45 PST)
    - Re: [AMBER] How to generate MM/PBSA statistics from recovered Job mish (Tue Feb 22 2011 - 01:51:43 PST)
    - Re: [AMBER] How to generate MM/PBSA statistics from recovered Job Sushil Mishra (Tue Feb 22 2011 - 02:54:17 PST)
    - Re: [AMBER] How to generate MM/PBSA statistics from recovered Job Jason Swails (Tue Feb 22 2011 - 06:59:57 PST)
    - [AMBER] What is the unit for RMSF result? Catein Catherine (Mon Feb 21 2011 - 22:37:00 PST)
[AMBER] PTRAJ and segmentation faults Seibold, Stephen (Mon Feb 21 2011 - 12:56:03 PST)
- Re: [AMBER] PTRAJ and segmentation faults Daniel Roe (Mon Feb 21 2011 - 13:00:25 PST)
  - Re: [AMBER] PTRAJ and segmentation faults Seibold, Stephen (Mon Feb 21 2011 - 13:18:25 PST)
    - Re: [AMBER] PTRAJ and segmentation faults Daniel Roe (Mon Feb 21 2011 - 14:07:47 PST)
    - Re: [AMBER] PTRAJ and segmentation faults david condon (Mon Feb 21 2011 - 15:10:05 PST)
    - Re: [AMBER] PTRAJ and segmentation faults Daniel Roe (Mon Feb 21 2011 - 20:25:23 PST)
    - Re: [AMBER] PTRAJ and segmentation faults Seibold, Stephen (Sun Feb 27 2011 - 10:53:29 PST)
    - Re: [AMBER] PTRAJ and segmentation faults Daniel Roe (Sun Feb 27 2011 - 12:12:30 PST)
[AMBER] MM-PBSA: PB bomb in pb_reslist(): maxnbr too small manikanthan bhavaraju (Mon Feb 21 2011 - 18:02:22 PST)
- Re: [AMBER] MM-PBSA: PB bomb in pb_reslist(): maxnbr too small Ray Luo, Ph.D. (Mon Feb 21 2011 - 19:17:38 PST)
  - Re: [AMBER] MM-PBSA: PB bomb in pb_reslist(): maxnbr too small manikanthan bhavaraju (Tue Feb 22 2011 - 11:02:49 PST)
    - Re: [AMBER] MM-PBSA: PB bomb in pb_reslist(): maxnbr too small Ray Luo, Ph.D. (Tue Feb 22 2011 - 17:40:30 PST)
[AMBER] restraints in Targeted Molecular dynamics siddesh southekal (Tue Feb 22 2011 - 02:20:52 PST)
- Re: [AMBER] restraints in Targeted Molecular dynamics Carlos Simmerling (Sat Feb 26 2011 - 12:00:37 PST)
[AMBER] Problems with mmpbsa moacyr comar (Tue Feb 22 2011 - 05:15:23 PST)
- Re: [AMBER] Problems with mmpbsa Jason Swails (Wed Feb 19 2014 - 04:53:05 PST)
[AMBER] Use of semiempirical QM/MM method in Amber to obtain free energy profile of a reaction Dmitry Nilov (Tue Feb 22 2011 - 08:11:29 PST)
- Re: [AMBER] Use of semiempirical QM/MM method in Amber to obtain free energy profile of a reaction Gustavo Seabra (Tue Feb 22 2011 - 09:53:31 PST)
[AMBER] Energy Calculation Problem Nitu Bansal (Tue Feb 22 2011 - 08:33:07 PST)
- Re: [AMBER] Energy Calculation Problem Sushil Mishra (Tue Feb 22 2011 - 11:06:53 PST)
  - Re: [AMBER] Energy Calculation Problem Nitu Bansal (Tue Feb 22 2011 - 20:54:03 PST)
    - Re: [AMBER] Energy Calculation Problem Sushil Mishra (Tue Feb 22 2011 - 21:38:05 PST)
    - Re: [AMBER] Energy Calculation Problem Nitu Bansal (Tue Feb 22 2011 - 22:12:01 PST)
    - Re: [AMBER] Energy Calculation Problem Sushil Mishra (Tue Feb 22 2011 - 22:39:55 PST)
    - Re: [AMBER] Energy Calculation Problem Nitu Bansal (Tue Feb 22 2011 - 22:47:36 PST)
    - Re: [AMBER] Energy Calculation Problem Sushil Mishra (Tue Feb 22 2011 - 23:01:49 PST)
    - Re: [AMBER] Energy Calculation Problem Nitu Bansal (Thu Feb 24 2011 - 04:08:43 PST)
[AMBER] Fwd: [ics.uci.edu #33898] Fwd: Amber11 download instructions Lane Votapka (Tue Feb 22 2011 - 09:30:40 PST)
[AMBER] developing parameters for Zn-binding site Jorgen Simonsen (Tue Feb 22 2011 - 09:44:10 PST)
- Re: [AMBER] developing parameters for Zn-binding site FyD (Tue Feb 22 2011 - 14:28:47 PST)
  - Re: [AMBER] developing parameters for Zn-binding site Jorgen Simonsen (Tue Feb 22 2011 - 23:41:58 PST)
    - Re: [AMBER] developing parameters for Zn-binding site FyD (Wed Feb 23 2011 - 00:16:58 PST)
[AMBER] Gasteiger parameter Eliac Brown (Tue Feb 22 2011 - 16:45:57 PST)
- [AMBER] A bit off-topic? Comments Dean Cuebas (Tue Feb 22 2011 - 17:28:53 PST)
- Re: [AMBER] Gasteiger parameter David A. Case (Tue Feb 22 2011 - 19:18:00 PST)
  - Re: [AMBER] Gasteiger parameter Eliac Brown (Wed Feb 23 2011 - 11:15:51 PST)
[AMBER] how to simulate solute in vacuum with TI Junjian Miao (Tue Feb 22 2011 - 17:34:19 PST)
- [AMBER] Simultaneous calculations on one GPU ? Marek Maly (Tue Feb 22 2011 - 18:22:42 PST)
  - Re: [AMBER] Simultaneous calculations on one GPU ? Ross Walker (Tue Feb 22 2011 - 18:59:41 PST)
    - Re: [AMBER] Simultaneous calculations on one GPU ? Marek Maly (Tue Feb 22 2011 - 18:57:36 PST)
- Re: [AMBER] how to simulate solute in vacuum with TI steinbrt.rci.rutgers.edu (Wed Feb 23 2011 - 00:39:59 PST)
[AMBER] pdb error subrata paul (Tue Feb 22 2011 - 22:46:02 PST)
- Re: [AMBER] pdb error Hirdesh Kumar (Tue Feb 22 2011 - 23:03:54 PST)
[AMBER] nonbonding parameters Jorgen Simonsen (Tue Feb 22 2011 - 23:14:51 PST)
- Re: [AMBER] nonbonding parameters Jorgen Simonsen (Wed Feb 23 2011 - 03:37:26 PST)
  - Re: [AMBER] nonbonding parameters Jason Swails (Wed Feb 23 2011 - 05:35:19 PST)
    - Re: [AMBER] nonbonding parameters Jorgen Simonsen (Wed Feb 23 2011 - 06:28:37 PST)
    - Re: [AMBER] nonbonding parameters David A. Case (Wed Feb 23 2011 - 06:55:13 PST)
[AMBER] REDserver {urea molecule} subrata paul (Wed Feb 23 2011 - 03:20:47 PST)
- Re: [AMBER] REDserver {urea molecule} FyD (Wed Feb 23 2011 - 06:56:37 PST)
[AMBER] Calculation of molecular surface for calcium JORGE IULEK (Wed Feb 23 2011 - 03:55:30 PST)
[AMBER] Principal COORDINATES analysis Massimiliano Porrini (Wed Feb 23 2011 - 04:33:00 PST)
- Re: [AMBER] Principal COORDINATES analysis Antje Wolf (Thu Feb 24 2011 - 04:19:49 PST)
[AMBER] how to understand disappearing atoms no contribution to DVdl Junjian Miao (Wed Feb 23 2011 - 06:13:45 PST)
- Re: [AMBER] how to understand disappearing atoms no contribution to DVdl David A. Case (Wed Feb 23 2011 - 06:52:53 PST)
[AMBER] Problem with dihedral angles tommaso.casalini.mail.polimi.it (Wed Feb 23 2011 - 10:09:03 PST)
[AMBER] Calculation of molecular surface for calcium Jorge Iulek (Wed Feb 23 2011 - 11:14:27 PST)
[AMBER] sleap bugfixes Scott Brozell (Wed Feb 23 2011 - 13:34:03 PST)
[AMBER] AMBER specific GPU test drive. Ross Walker (Wed Feb 23 2011 - 18:13:15 PST)
[AMBER] temperature setting in REMD Cheng-I Lee (Wed Feb 23 2011 - 18:55:32 PST)
- Re: [AMBER] temperature setting in REMD Carlos Simmerling (Wed Feb 23 2011 - 18:57:27 PST)
[AMBER] Antechamber - bug Mahmoud A. A. Ibrahim (Wed Feb 23 2011 - 19:25:30 PST)
[AMBER] High temperature at the beginning A. Gomez-Sicilia (Thu Feb 24 2011 - 01:17:27 PST)
- Re: [AMBER] High temperature at the beginning case (Thu Feb 24 2011 - 04:51:31 PST)
[AMBER] Protonation of C terminal residue Elisa Frezza (Thu Feb 24 2011 - 02:55:46 PST)
- Re: [AMBER] Protonation of C terminal residue FyD (Thu Feb 24 2011 - 04:12:06 PST)
[AMBER] MMPBSA.py keep_files Jesper Sørensen (Thu Feb 24 2011 - 03:03:04 PST)
- Re: [AMBER] MMPBSA.py keep_files Bill Miller III (Thu Feb 24 2011 - 03:59:45 PST)
[AMBER] No energy conservation in NVE ensemble amber 11 Ivan Gladich (Thu Feb 24 2011 - 03:49:18 PST)
- Re: [AMBER] No energy conservation in NVE ensemble amber 11 Mark Williamson (Thu Feb 24 2011 - 03:37:02 PST)
  - Re: [AMBER] No energy conservation in NVE ensemble amber 11 Ivan Gladich (Fri Feb 25 2011 - 02:50:23 PST)
[AMBER] Question Beale, John (Thu Feb 24 2011 - 03:39:59 PST)
[AMBER] chamber colvin (Thu Feb 24 2011 - 04:15:39 PST)
- Re: [AMBER] chamber Mark Williamson (Thu Feb 24 2011 - 11:10:44 PST)
  - Re: [AMBER] chamber colvin (Thu Feb 24 2011 - 22:48:18 PST)
    - Re: [AMBER] chamber Mark Williamson (Wed Mar 02 2011 - 08:18:27 PST)
    - Re: [AMBER] chamber colvin (Thu Mar 03 2011 - 01:24:53 PST)
    - Re: [AMBER] chamber Mark Williamson (Thu Mar 03 2011 - 01:53:24 PST)
[AMBER] Open MPI invalid message type 10 Katharina Lang (Thu Feb 24 2011 - 08:21:47 PST)
[AMBER] (UNKNOWN ATOM TYPE: UA) Jorgen Simonsen (Thu Feb 24 2011 - 13:00:11 PST)
- Re: [AMBER] (UNKNOWN ATOM TYPE: UA) Bill Ross (Thu Feb 24 2011 - 13:14:33 PST)
- Re: [AMBER] (UNKNOWN ATOM TYPE: UA) David Case (Thu Feb 24 2011 - 14:43:34 PST)
  - Re: [AMBER] (UNKNOWN ATOM TYPE: UA) Jorgen Simonsen (Thu Feb 24 2011 - 15:18:11 PST)
    - Re: [AMBER] (UNKNOWN ATOM TYPE: UA) David Case (Thu Feb 24 2011 - 19:20:18 PST)
    - Re: [AMBER] (UNKNOWN ATOM TYPE: UA) Jorgen Simonsen (Sat Feb 26 2011 - 00:19:37 PST)
    - Re: [AMBER] (UNKNOWN ATOM TYPE: UA) FyD (Sat Feb 26 2011 - 00:51:09 PST)
    - Re: [AMBER] (UNKNOWN ATOM TYPE: UA) Jorgen Simonsen (Sat Feb 26 2011 - 04:37:58 PST)
    - Re: [AMBER] (UNKNOWN ATOM TYPE: UA) FyD (Sat Feb 26 2011 - 06:14:52 PST)
    - Re: [AMBER] (UNKNOWN ATOM TYPE: UA) case (Sat Feb 26 2011 - 06:25:25 PST)
- Re: [AMBER] (UNKNOWN ATOM TYPE: UA) Bill Ross (Sat Feb 26 2011 - 12:17:51 PST)
[AMBER] Explanation of energy "genBorn" column in 3D-RISM calculation? Is solvation free energy computed? Chris King (Thu Feb 24 2011 - 15:15:31 PST)
- Re: [AMBER] Explanation of energy "genBorn" column in 3D-RISM calculation? Is solvation free energy computed? Tyler Luchko (Thu Feb 24 2011 - 18:48:19 PST)
[AMBER] MM-PBSA error: Missing BELE for MM in residue 1 Jagur Lambix (Thu Feb 24 2011 - 16:03:38 PST)
- Re: [AMBER] MM-PBSA error: Missing BELE for MM in residue 1 Yao-Chi Chen (Thu Feb 24 2011 - 17:54:57 PST)
[AMBER] What is the unit for RMSF result? Ashutosh Shandilya (Thu Feb 24 2011 - 20:39:30 PST)
[AMBER] TI with softcores: size of scmask and crgmask thomas.fox.boehringer-ingelheim.com (Thu Feb 24 2011 - 23:06:10 PST)
- Re: [AMBER] TI with softcores: size of scmask and crgmask steinbrt.rci.rutgers.edu (Fri Feb 25 2011 - 00:35:27 PST)
[AMBER] water mediated H-Bond analysis Sangita Kachhap (Fri Feb 25 2011 - 00:32:10 PST)
- Re: [AMBER] water mediated H-Bond analysis Daniel Roe (Fri Feb 25 2011 - 04:25:56 PST)
  - Re: [AMBER] water mediated H-Bond analysis Sangita Kachhap (Sat Feb 26 2011 - 02:19:14 PST)
    - Re: [AMBER] water mediated H-Bond analysis case (Sat Feb 26 2011 - 06:28:53 PST)
    - Re: [AMBER] water mediated H-Bond analysis Sangita Kachhap (Sat Feb 26 2011 - 09:55:56 PST)
    - Re: [AMBER] water mediated H-Bond analysis case (Sat Feb 26 2011 - 10:54:44 PST)
    - Re: [AMBER] water mediated H-Bond analysis case (Sat Feb 26 2011 - 12:42:30 PST)
    - Re: [AMBER] water mediated H-Bond analysis Sangita Kachhap (Sat Feb 26 2011 - 23:24:47 PST)
    - Re: [AMBER] water mediated H-Bond analysis Sangita Kachhap (Sat Feb 26 2011 - 23:37:38 PST)
    - Re: [AMBER] water mediated H-Bond analysis Sangita Kachhap (Sat Feb 26 2011 - 09:59:14 PST)
[AMBER] sqm out error kala (Fri Feb 25 2011 - 07:42:02 PST)
- Re: [AMBER] sqm out error case (Fri Feb 25 2011 - 09:25:03 PST)
  - [AMBER] To fix dihedral angles during a simulation. Baptiste Legrand (Fri Feb 25 2011 - 09:54:53 PST)
    - Re: [AMBER] To fix dihedral angles during a simulation. case (Sat Feb 26 2011 - 13:47:44 PST)
    - Re: [AMBER] To fix dihedral angles during a simulation. Baptiste Legrand (Wed Mar 02 2011 - 02:08:37 PST)
    - Re: [AMBER] To fix dihedral angles during a simulation. case (Wed Mar 02 2011 - 06:39:37 PST)
    - [AMBER] Generating an average structure from a rst/pdb list? Baptiste Legrand (Thu Mar 03 2011 - 09:21:14 PST)
    - Re: [AMBER] Generating an average structure from a rst/pdb list? Daniel Roe (Thu Mar 03 2011 - 10:54:31 PST)
    - Re: [AMBER] Generating an average structure from a rst/pdb list? Baptiste Legrand (Thu Mar 03 2011 - 13:02:04 PST)
    - Re: [AMBER] Generating an average structure from a rst/pdb list? Baptiste Legrand (Fri Mar 04 2011 - 02:06:25 PST)
  - Re: [AMBER] sqm out error kala (Sat Feb 26 2011 - 08:52:34 PST)
[AMBER] improper dihedral torsion parameters for fused rings on tryptophan Sidney Elmer (Fri Feb 25 2011 - 10:37:23 PST)
- Re: [AMBER] improper dihedral torsion parameters for fused rings on tryptophan FyD (Fri Feb 25 2011 - 12:18:06 PST)
- Re: [AMBER] improper dihedral torsion parameters for fused rings on tryptophan case (Fri Feb 25 2011 - 12:46:42 PST)
  - Re: [AMBER] improper dihedral torsion parameters for fused rings on tryptophan Sidney Elmer (Mon Feb 28 2011 - 10:22:10 PST)
[AMBER] Temperature generator of REMD in AMBER? Cheng-I Lee (Fri Feb 25 2011 - 18:22:28 PST)
- Re: [AMBER] Temperature generator of REMD in AMBER? Jason Swails (Fri Feb 25 2011 - 19:40:08 PST)
  - Re: [AMBER] Temperature generator of REMD in AMBER? Cheng-I Lee (Fri Feb 25 2011 - 20:48:03 PST)
  - Re: [AMBER] Temperature generator of REMD in AMBER? Cheng-I Lee (Fri Feb 25 2011 - 21:31:41 PST)
    - Re: [AMBER] Temperature generator of REMD in AMBER? Jason Swails (Sat Feb 26 2011 - 07:35:59 PST)
[AMBER] how to decide water mediated interaction betwen Sangita Kachhap (Sun Feb 27 2011 - 20:44:31 PST)
[AMBER] How to defining a bond between the Cβ of the substrate and the Cα of the catalytic serine py (Sun Feb 27 2011 - 21:34:48 PST)
- Re: [AMBER] How to defining a bond between the Cβ of the substrate and the Cα of the catalytic serine Jason Swails (Tue Mar 01 2011 - 05:41:15 PST)
- Re: [AMBER] How to defining a bond between the Cβ of the substrate and the Cα of the catalytic serine py (Tue Mar 01 2011 - 06:28:17 PST)
Re: [AMBER] chamber - resend colvin (Mon Feb 28 2011 - 00:49:09 PST)
[AMBER] NPT simulation crash using a GPU CARD for a simulation carried out in a organic explicit solvent vitor.felix.ua.pt (Mon Feb 28 2011 - 01:05:25 PST)
- Re: [AMBER] NPT simulation crash using a GPU CARD for a simulation carried out in a organic explicit solvent Ross Walker (Mon Feb 28 2011 - 16:37:35 PST)
  - Re: [AMBER] NPT simulation crash using a GPU CARD for a simulation carried out in a organic explicit solvent Antje Wolf (Tue Mar 01 2011 - 23:44:39 PST)
- Re: [AMBER] NPT simulation crash using a GPU CARD for a simulation carried out in a organic explicit solvent Ross Walker (Wed May 04 2011 - 09:16:28 PDT)
[AMBER] Restart Problem: The results of an integrated simulation and restarted simulations are not equal! Ali M. Naserian-Nik (Mon Feb 28 2011 - 09:56:40 PST)
- Re: [AMBER] Restart Problem: The results of an integrated simulation and restarted simulations are not equal! case (Mon Feb 28 2011 - 10:56:26 PST)
  - Re: [AMBER] Restart Problem: The results of an integrated simulation and restarted simulations are not equal! Ali M. Naserian-Nik (Tue Mar 01 2011 - 00:42:52 PST)
    - Re: [AMBER] Restart Problem: The results of an integrated simulation and restarted simulations are not equal! case (Tue Mar 01 2011 - 04:47:41 PST)
[AMBER] checking interaction between periodic images Bala subramanian (Tue Mar 01 2011 - 02:37:04 PST)
- Re: [AMBER] checking interaction between periodic images Jason Swails (Tue Mar 01 2011 - 05:29:33 PST)
- Re: [AMBER] checking interaction between periodic images Daniel Roe (Tue Mar 01 2011 - 06:54:42 PST)
- Re: [AMBER] checking interaction between periodic images Hannes Loeffler (Tue Mar 01 2011 - 08:29:18 PST)
[AMBER] xleap not installed sonali dhindwal (Tue Mar 01 2011 - 05:56:24 PST)
- Re: [AMBER] xleap not installed Bill Miller III (Tue Mar 01 2011 - 06:12:09 PST)
  - Re: [AMBER] xleap not installed sonali dhindwal (Tue Mar 01 2011 - 06:24:57 PST)
    - Re: [AMBER] xleap not installed Jason Swails (Tue Mar 01 2011 - 06:36:42 PST)
    - Re: [AMBER] xleap not installed sonali dhindwal (Tue Mar 01 2011 - 20:54:11 PST)
- Re: [AMBER] xleap not installed sonali dhindwal (Wed Mar 02 2011 - 20:26:17 PST)
  - Re: [AMBER] xleap not installed Jason Swails (Wed Mar 02 2011 - 22:49:13 PST)
    - Re: [AMBER] xleap not installed sonali dhindwal (Thu Mar 03 2011 - 02:19:48 PST)
    - Re: [AMBER] xleap not installed case (Thu Mar 03 2011 - 04:20:26 PST)
    - Re: [AMBER] xleap not installed sonali dhindwal (Sat Mar 05 2011 - 04:54:59 PST)
    - Re: [AMBER] xleap not installed Jason Swails (Sat Mar 05 2011 - 07:02:28 PST)
    - Re: [AMBER] xleap not installed Mengjuei Hsieh (Sat Mar 05 2011 - 07:29:29 PST)
    - Re: [AMBER] xleap not installed sonali dhindwal (Sun Mar 06 2011 - 22:15:04 PST)
    - Re: [AMBER] xleap not installed Ben Roberts (Tue Mar 08 2011 - 09:13:47 PST)
- Re: [AMBER] xleap not installed sonali dhindwal (Tue Mar 08 2011 - 04:00:31 PST)
[AMBER] water mediated H-Bond Sangita Kachhap (Tue Mar 01 2011 - 09:37:31 PST)
- Re: [AMBER] water mediated H-Bond Bill Ross (Tue Mar 01 2011 - 10:09:20 PST)
  - Re: [AMBER] water mediated H-Bond Sangita Kachhap (Tue Mar 01 2011 - 10:17:14 PST)
- Re: [AMBER] water mediated H-Bond Bill Ross (Tue Mar 01 2011 - 12:02:28 PST)
  - Re: [AMBER] water mediated H-Bond Sangita Kachhap (Wed Mar 02 2011 - 00:41:36 PST)
    - Re: [AMBER] water mediated H-Bond Hirdesh Kumar (Wed Mar 02 2011 - 01:25:31 PST)
    - Re: [AMBER] water mediated H-Bond Sangita Kachhap (Wed Mar 02 2011 - 01:52:31 PST)
- Re: [AMBER] water mediated H-Bond Bill Ross (Wed Mar 02 2011 - 11:45:34 PST)
  - Re: [AMBER] water mediated H-Bond Sangita Kachhap (Wed Mar 02 2011 - 19:56:52 PST)
[AMBER] generalized Born question Francesco Oteri (Tue Mar 01 2011 - 10:21:00 PST)
[AMBER] CHAMBER prmtop colvin (Tue Mar 01 2011 - 19:46:50 PST)
[AMBER] Will no implementation of feupdateenv cause serious problems? kurisaki.ncube.human.nagoya-u.ac.jp (Tue Mar 01 2011 - 21:55:51 PST)
- Re: [AMBER] Will no implementation of feupdateenv cause serious problems? Ross Walker (Tue Mar 01 2011 - 22:18:00 PST)
  - Re: [AMBER] Will no implementation of feupdateenv cause serious problems? kurisaki.ncube.human.nagoya-u.ac.jp (Tue Mar 01 2011 - 22:29:52 PST)
[AMBER] randomly place counterions thomas.fox.boehringer-ingelheim.com (Wed Mar 02 2011 - 02:55:55 PST)
- Re: [AMBER] randomly place counterions steinbrt.rci.rutgers.edu (Wed Mar 02 2011 - 04:42:17 PST)
  - Re: [AMBER] randomly place counterions Hugh Heldenbrand (Wed Mar 02 2011 - 04:56:01 PST)
    - Re: [AMBER] randomly place counterions Kevin Hauser (Wed Mar 02 2011 - 06:59:18 PST)
    - Re: [AMBER] randomly place counterions Hugh Heldenbrand (Wed Mar 02 2011 - 07:16:29 PST)
    - Re: [AMBER] randomly place counterions thomas.fox.boehringer-ingelheim.com (Wed Mar 02 2011 - 08:25:48 PST)
    - Re: [AMBER] randomly place counterions Kevin Hauser (Wed Mar 02 2011 - 08:52:10 PST)
  - Re: [AMBER] randomly place counterions thomas.fox.boehringer-ingelheim.com (Wed Mar 02 2011 - 08:07:02 PST)
- Re: [AMBER] randomly place counterions Bill Ross (Wed Mar 02 2011 - 12:02:27 PST)
[AMBER] error reading NMR restraints Wong, Sergio E. (Wed Mar 02 2011 - 15:59:56 PST)
- Re: [AMBER] error reading NMR restraints Jason Swails (Wed Mar 02 2011 - 16:25:59 PST)
[AMBER] total charge of NPRO in amber03 force field Ye MEI (Thu Mar 03 2011 - 02:52:23 PST)
- Re: [AMBER] total charge of NPRO in amber03 force field Ye MEI (Thu Mar 03 2011 - 03:00:21 PST)
  - Re: [AMBER] total charge of NPRO in amber03 force field Ray Luo, Ph.D. (Thu Mar 03 2011 - 08:20:59 PST)
[AMBER] MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. hari krishna (Thu Mar 03 2011 - 03:07:36 PST)
- Re: [AMBER] MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. Jason Swails (Thu Mar 03 2011 - 04:26:35 PST)
  - Re: [AMBER] MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. hari krishna (Thu Mar 03 2011 - 08:47:54 PST)
    - Re: [AMBER] MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. Bill Miller III (Mon Mar 07 2011 - 04:57:26 PST)
    - Re: [AMBER] MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. hari krishna (Mon Mar 07 2011 - 05:33:14 PST)
    - Re: [AMBER] MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. Bill Miller III (Mon Mar 07 2011 - 05:41:02 PST)
    - Re: [AMBER] MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. Jason Swails (Mon Mar 07 2011 - 09:07:43 PST)
    - Re: [AMBER] MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. hari krishna (Mon Mar 07 2011 - 20:14:43 PST)
[AMBER] ptraj / water-medited hydrogen bonds leila karami (Thu Mar 03 2011 - 04:26:41 PST)
[AMBER] Blowing array; too many frames!! Sangita Kachhap (Thu Mar 03 2011 - 04:33:30 PST)
- Re: [AMBER] Blowing array; too many frames!! Daniel Roe (Thu Mar 03 2011 - 06:38:50 PST)
  - Re: [AMBER] Blowing array; too many frames!! Sangita Kachhap (Thu Mar 03 2011 - 07:59:50 PST)
    - Re: [AMBER] Blowing array; too many frames!! Daniel Roe (Thu Mar 03 2011 - 08:06:05 PST)
    - Re: [AMBER] Blowing array; too many frames!! Sangita Kachhap (Thu Mar 03 2011 - 08:25:01 PST)
    - Re: [AMBER] Blowing array; too many frames!! Daniel Roe (Thu Mar 03 2011 - 08:31:29 PST)
    - Re: [AMBER] Blowing array; too many frames!! Sangita Kachhap (Thu Mar 03 2011 - 09:00:18 PST)
    - Re: [AMBER] Blowing array; too many frames!! Daniel Roe (Thu Mar 03 2011 - 10:48:15 PST)
    - Re: [AMBER] Blowing array; too many frames!! Sangita Kachhap (Thu Mar 03 2011 - 19:56:52 PST)
    - Re: [AMBER] Blowing array; too many frames!! Sangita Kachhap (Fri Mar 04 2011 - 11:24:04 PST)
    - Re: [AMBER] Blowing array; too many frames!! Sangita Kachhap (Thu Mar 03 2011 - 20:37:48 PST)
- Re: [AMBER] Blowing array; too many frames!! Bill Ross (Fri Mar 04 2011 - 15:30:14 PST)
[AMBER] implicit solvent with cuda Francesco Oteri (Thu Mar 03 2011 - 04:44:07 PST)
- Re: [AMBER] implicit solvent with cuda Ross Walker (Thu Mar 03 2011 - 06:21:56 PST)
[AMBER] ptraj / water-mediated hydrogen bonds leila karami (Thu Mar 03 2011 - 05:11:39 PST)
[AMBER] Unresolved problem about MM/PBSA 祥谦孔 (Thu Mar 03 2011 - 08:01:07 PST)
- Re: [AMBER] Unresolved problem about MM/PBSA Ray Luo, Ph.D. (Thu Mar 03 2011 - 08:09:06 PST)
  - Re: [AMBER] Unresolved problem about MM/PBSA ÏéÇ« ¿× (Thu Mar 03 2011 - 17:25:17 PST)
    - Re: [AMBER] Unresolved problem about MM/PBSA Ray Luo, Ph.D. (Thu Mar 03 2011 - 19:04:02 PST)
- [AMBER] CUDA 4.0 RC filip fratev (Mon Mar 07 2011 - 18:35:28 PST)
  - Re: [AMBER] CUDA 4.0 RC Ross Walker (Mon Mar 07 2011 - 20:53:14 PST)
    - Re: [AMBER] CUDA 4.0 RC Bill Snapko (Thu Jun 23 2011 - 09:12:55 PDT)
    - Re: [AMBER] CUDA 4.0 RC Scott Le Grand (Thu Jun 23 2011 - 09:49:18 PDT)
  - Re: [AMBER] CUDA 4.0 RC Scott Le Grand (Tue Mar 08 2011 - 20:04:31 PST)
[AMBER] how to create periodic box similar to TIP3PBOX? Junjian Miao (Thu Mar 03 2011 - 17:32:35 PST)
[AMBER] Zn Bond Length solvatebox Lowe, Ben (Ext) (Fri Mar 04 2011 - 02:25:53 PST)
- Re: [AMBER] Zn Bond Length solvatebox case (Fri Mar 04 2011 - 04:40:29 PST)
  - Re: [AMBER] Zn Bond Length solvatebox Lowe, Ben (Ext) (Fri Mar 04 2011 - 04:58:37 PST)
[AMBER] hydrogen bonding facility in ptraj Beale, John (Fri Mar 04 2011 - 05:38:11 PST)
[AMBER] non standard Alanine Massimiliano Porrini (Fri Mar 04 2011 - 06:41:59 PST)
- Re: [AMBER] non standard Alanine FyD (Fri Mar 04 2011 - 07:50:50 PST)
- Re: [AMBER] non standard Alanine Anselm Horn (Fri Mar 04 2011 - 07:55:01 PST)
  - [AMBER] Diffusion coefficient Chih-Ying Lin (Fri Mar 04 2011 - 09:41:42 PST)
    - Re: [AMBER] Diffusion coefficient case (Mon Mar 07 2011 - 04:58:38 PST)
    - Re: [AMBER] Diffusion coefficient setyanto md (Tue Mar 08 2011 - 20:33:40 PST)
[AMBER] AMBER parameters for lead Ganesh Kamath (Fri Mar 04 2011 - 12:24:48 PST)
[AMBER] is it possible to identify each mode in Nmode calculation? zhihong ke (Fri Mar 04 2011 - 12:44:28 PST)
- Re: [AMBER] is it possible to identify each mode in Nmode calculation? Bill Miller III (Mon Mar 07 2011 - 04:54:57 PST)
[AMBER] using NMR restraints within LMOD Wong, Sergio E. (Fri Mar 04 2011 - 13:45:12 PST)
- Re: [AMBER] using NMR restraints within LMOD case (Mon Mar 07 2011 - 05:06:45 PST)
  - Re: [AMBER] using NMR restraints within LMOD Wong, Sergio E. (Wed Mar 09 2011 - 10:52:59 PST)
[AMBER] building HA8 (hyaluronic acid 8-mer) using amber leap Madhurima Jana (Fri Mar 04 2011 - 21:36:04 PST)
[AMBER] ACS COMP division awards for Fall 2011 meeting Carlos Simmerling (Sat Mar 05 2011 - 07:44:30 PST)
[AMBER] Zn active site parameterization kala (Sun Mar 06 2011 - 11:59:04 PST)
- Re: [AMBER] Zn active site parameterization Per Jr. Greisen (Mon Mar 07 2011 - 05:12:30 PST)
[AMBER] Showing torsion energy as a function of angle david condon (Sun Mar 06 2011 - 14:46:50 PST)
- Re: [AMBER] Showing torsion energy as a function of angle Carlos Simmerling (Sun Mar 06 2011 - 15:23:11 PST)
[AMBER] missing AMBER features for simulating surfaces and linear assemblies Andrew Jewett (Mon Mar 07 2011 - 02:18:31 PST)
- Re: [AMBER] missing AMBER features for simulating surfaces and linear assemblies David A Case (Wed Mar 09 2011 - 08:54:27 PST)
  - Re: [AMBER] missing AMBER features for simulating surfaces and linear assemblies Andrew Jewett (Wed Mar 09 2011 - 13:00:22 PST)
    - Re: [AMBER] missing AMBER features for simulating surfaces and linear assemblies Andrew Jewett (Wed Mar 09 2011 - 13:08:31 PST)
[AMBER] Pressure regulation and position restraints Andrew Jewett (Mon Mar 07 2011 - 04:33:36 PST)
- Re: [AMBER] Pressure regulation and position restraints David A Case (Wed Mar 09 2011 - 08:57:49 PST)
  - Re: [AMBER] Pressure regulation and position restraints Andrew Jewett (Thu Mar 10 2011 - 18:51:55 PST)
[AMBER] how to deal with flexibility of peptide during prod. process asakiayumikio.gmail.com (Mon Mar 07 2011 - 05:57:37 PST)
- Re: [AMBER] how to deal with flexibility of peptide during prod. process Carlos Simmerling (Mon Mar 07 2011 - 06:18:39 PST)
[AMBER] h-bond donor acceptor definition confusion Jio M (Mon Mar 07 2011 - 06:06:51 PST)
- Re: [AMBER] h-bond donor acceptor definition confusion case (Mon Mar 07 2011 - 06:13:48 PST)
[AMBER] forefile of acetyl coenzyme A asakiayumikio.gmail.com (Mon Mar 07 2011 - 06:07:27 PST)
- Re: [AMBER] forefile of acetyl coenzyme A Ganesh Kamath (Mon Mar 07 2011 - 06:11:37 PST)
- Re: [AMBER] forefile of acetyl coenzyme A asakiayumikio.gmail.com (Mon Mar 07 2011 - 06:16:54 PST)
  - Re: [AMBER] forefile of acetyl coenzyme A Ganesh Kamath (Mon Mar 07 2011 - 06:19:03 PST)
- Re: [AMBER] forefile of acetyl coenzyme A asakiayumikio.gmail.com (Mon Mar 07 2011 - 06:30:06 PST)
Re: [AMBER] how to deal with flexibility of peptide during prod. process asakiayumikio.gmail.com (Mon Mar 07 2011 - 06:28:24 PST)
[AMBER] Fwd: Implicit solvent GB calculation Rubben Torella (Mon Mar 07 2011 - 07:04:35 PST)
- Re: [AMBER] Fwd: Implicit solvent GB calculation Carlos Simmerling (Mon Mar 07 2011 - 07:10:41 PST)
  - Re: [AMBER] Fwd: Implicit solvent GB calculation Rubben Torella (Mon Mar 07 2011 - 07:17:59 PST)
- Re: [AMBER] Fwd: Implicit solvent GB calculation Daniel Roe (Mon Mar 07 2011 - 07:40:34 PST)
  - Re: [AMBER] Fwd: Implicit solvent GB calculation Daniel Roe (Mon Mar 07 2011 - 07:42:19 PST)
    - Re: [AMBER] Fwd: Implicit solvent GB calculation Rubben Torella (Mon Mar 07 2011 - 08:03:16 PST)
[AMBER] Problems with tleap Pegado Luis (Mon Mar 07 2011 - 10:42:55 PST)
- Re: [AMBER] Problems with tleap case (Mon Mar 07 2011 - 10:56:58 PST)
- Re: [AMBER] Problems with tleap Pegado Luis (Tue Mar 08 2011 - 02:04:34 PST)
[AMBER] Is the neutralization necessary for the GB model? zhihong ke (Mon Mar 07 2011 - 13:24:19 PST)
- Re: [AMBER] Is the neutralization necessary for the GB model? Jason Swails (Mon Mar 07 2011 - 13:42:07 PST)
  - Re: [AMBER] Is the neutralization necessary for the GB model? zhihong ke (Mon Mar 07 2011 - 13:51:00 PST)
[AMBER] igb=1 and gbsa=0 Francesco Oteri (Mon Mar 07 2011 - 15:38:43 PST)
- Re: [AMBER] igb=1 and gbsa=0 David A Case (Tue Mar 08 2011 - 05:00:11 PST)
[AMBER] a question about using oplsaa ff in amber Junjian Miao (Mon Mar 07 2011 - 20:12:35 PST)
- Re: [AMBER] a question about using oplsaa ff in amber Ben Roberts (Tue Mar 08 2011 - 08:44:05 PST)
- Re: [AMBER] a question about using oplsaa ff in amber Junjian Miao (Tue Mar 08 2011 - 17:13:58 PST)
[AMBER] Request for a quotation of AMBER aseal.klyuniv.ac.in (Mon Mar 07 2011 - 23:38:14 PST)
- Re: [AMBER] Request for a quotation of AMBER David A Case (Tue Mar 08 2011 - 05:06:22 PST)
[AMBER] sander.MPI running on 8 nodes or 1?? colvin (Tue Mar 08 2011 - 01:11:03 PST)
- Re: [AMBER] sander.MPI running on 8 nodes or 1?? Jason Swails (Tue Mar 08 2011 - 11:27:13 PST)
  - Re: [AMBER] sander.MPI running on 8 nodes or 1?? colvin (Tue Mar 08 2011 - 22:13:57 PST)
[AMBER] acceptance probabilities remd Jorgen Simonsen (Tue Mar 08 2011 - 02:02:59 PST)
- Re: [AMBER] acceptance probabilities remd Adrian Roitberg (Tue Mar 08 2011 - 03:17:58 PST)
- Re: [AMBER] acceptance probabilities remd Carlos Simmerling (Tue Mar 08 2011 - 03:49:14 PST)
  - Re: [AMBER] acceptance probabilities remd Jorgen Simonsen (Tue Mar 08 2011 - 03:58:18 PST)
    - Re: [AMBER] acceptance probabilities remd Carlos Simmerling (Tue Mar 08 2011 - 04:00:14 PST)
[AMBER] Problem installing Amber11/Ambertools1.4 on Ubuntu10.10 John Khan (Tue Mar 08 2011 - 10:01:59 PST)
- Re: [AMBER] Problem installing Amber11/Ambertools1.4 on Ubuntu10.10 Ben Roberts (Tue Mar 08 2011 - 10:09:15 PST)
[AMBER] continuum solvation with low viscosity Mahmoud Soliman (Tue Mar 08 2011 - 12:28:05 PST)
- Re: [AMBER] continuum solvation with low viscosity Carlos Simmerling (Wed Mar 09 2011 - 04:19:58 PST)
  - Re: [AMBER] continuum solvation with low viscosity Mahmoud Soliman (Wed Mar 09 2011 - 06:17:36 PST)
[AMBER] Umbrella sampling coordinate question Rajesh Raju (Tue Mar 08 2011 - 15:21:36 PST)
- Re: [AMBER] Umbrella sampling coordinate question Carlos Simmerling (Wed Mar 09 2011 - 04:04:24 PST)
  - Re: [AMBER] Umbrella sampling coordinate question Rajesh Raju (Wed Mar 09 2011 - 10:55:38 PST)
    - Re: [AMBER] Umbrella sampling coordinate question Carlos Simmerling (Thu Mar 10 2011 - 06:45:41 PST)
    - Re: [AMBER] Umbrella sampling coordinate question Rajesh Raju (Thu Mar 10 2011 - 09:45:22 PST)
    - Re: [AMBER] Umbrella sampling coordinate question Carlos Simmerling (Thu Mar 10 2011 - 09:47:45 PST)
    - Re: [AMBER] Umbrella sampling coordinate question Rajesh Raju (Thu Mar 10 2011 - 09:59:19 PST)
[AMBER] question about the distance of pronton transfer and acetylation asakiayumikio.gmail.com (Tue Mar 08 2011 - 18:19:42 PST)
- Re: [AMBER] question about the distance of pronton transfer and acetylation Dmitry Nilov (Wed Mar 09 2011 - 02:06:46 PST)
[AMBER] about Nmod in amber11 juan zeng (Tue Mar 08 2011 - 23:25:11 PST)
[AMBER] grid action command in ptraj mish (Wed Mar 09 2011 - 04:41:06 PST)
[AMBER] Splitting the interaction energy Eliac Brown (Wed Mar 09 2011 - 06:26:58 PST)
- Re: [AMBER] Splitting the interaction energy Bill Miller III (Wed Mar 09 2011 - 06:44:06 PST)
[AMBER] peek_ewald_inpcrd: SHOULD NOT BE HERE hari krishna (Wed Mar 09 2011 - 06:28:55 PST)
- Re: [AMBER] peek_ewald_inpcrd: SHOULD NOT BE HERE David A Case (Wed Mar 09 2011 - 07:35:32 PST)
  - Re: [AMBER] peek_ewald_inpcrd: SHOULD NOT BE HERE hari krishna (Wed Mar 09 2011 - 20:20:11 PST)
    - Re: [AMBER] peek_ewald_inpcrd: SHOULD NOT BE HERE steinbrt.rci.rutgers.edu (Thu Mar 10 2011 - 00:03:05 PST)
[AMBER] irest Burcu Aykac Fas (Wed Mar 09 2011 - 06:38:38 PST)
- Re: [AMBER] irest Cenk $Jenk$ Andac (Wed Mar 09 2011 - 07:07:05 PST)
[AMBER] Partial Charges for Atom Types Naveen Samala (Wed Mar 09 2011 - 08:17:37 PST)
- Re: [AMBER] Partial Charges for Atom Types Per Jr. Greisen (Wed Mar 09 2011 - 08:42:07 PST)
  - Re: [AMBER] Partial Charges for Atom Types Bill Ross (Wed Mar 09 2011 - 09:51:45 PST)
- Re: [AMBER] Partial Charges for Atom Types David A Case (Wed Mar 09 2011 - 08:44:52 PST)
[AMBER] Nab PB focusing error Bill Miller III (Wed Mar 09 2011 - 12:07:22 PST)
- Re: [AMBER] Nab PB focusing error Ray Luo, Ph.D. (Wed Mar 09 2011 - 12:23:12 PST)
[AMBER] Atom Types involved in Carbon monoxide and Cyanide bonds Naveen Samala (Wed Mar 09 2011 - 12:45:39 PST)
[AMBER] the charge of NPRO in FF03 is equal to 0.9. zhihong ke (Wed Mar 09 2011 - 12:46:40 PST)
- Re: [AMBER] the charge of NPRO in FF03 is equal to 0.9. cieplak.cgl.ucsf.edu (Wed Mar 09 2011 - 23:32:56 PST)
  - Re: [AMBER] the charge of NPRO in FF03 is equal to 0.9. zhihong ke (Thu Mar 10 2011 - 09:13:02 PST)
    - Re: [AMBER] the charge of NPRO in FF03 is equal to 0.9. Ray Luo, Ph.D. (Thu Mar 10 2011 - 09:16:05 PST)
    - Re: [AMBER] the charge of NPRO in FF03 is equal to 0.9. David A Case (Thu Mar 10 2011 - 09:43:47 PST)
    - Re: [AMBER] the charge of NPRO in FF03 is equal to 0.9. Ray Luo, Ph.D. (Thu Mar 10 2011 - 09:48:43 PST)
    - Re: [AMBER] the charge of NPRO in FF03 is equal to 0.9. zhihong ke (Thu Mar 10 2011 - 10:06:29 PST)
    - Re: [AMBER] the charge of NPRO in FF03 is equal to 0.9. Ray Luo, Ph.D. (Thu Mar 10 2011 - 10:26:02 PST)
    - Re: [AMBER] the charge of NPRO in FF03 is equal to 0.9. Mengjuei Hsieh (Thu Mar 10 2011 - 11:47:15 PST)
    - Re: [AMBER] the charge of NPRO in FF03 is equal to 0.9. zhihong ke (Thu Mar 10 2011 - 09:48:11 PST)
[AMBER] Can we relax protein and ligand separately? kurisaki.ncube.human.nagoya-u.ac.jp (Wed Mar 09 2011 - 17:34:38 PST)
[AMBER] Creating distaint restaint in Amber Vivien Landre (Wed Mar 09 2011 - 19:40:37 PST)
- Re: [AMBER] Creating distaint restaint in Amber David A Case (Thu Mar 10 2011 - 05:56:18 PST)
  - Re: [AMBER] Creating distaint restaint in Amber Vivien Landre (Wed Mar 23 2011 - 00:26:30 PDT)
    - Re: [AMBER] Creating distaint restaint in Amber David A Case (Thu Mar 24 2011 - 06:18:14 PDT)
[AMBER] interaction energy Aust, Susanne (Thu Mar 10 2011 - 00:34:28 PST)
- Re: [AMBER] interaction energy steinbrt.rci.rutgers.edu (Thu Mar 10 2011 - 01:39:43 PST)
  - Re: [AMBER] interaction energy Aust, Susanne (Thu Mar 10 2011 - 03:24:16 PST)
    - Re: [AMBER] interaction energy Bill Miller III (Thu Mar 10 2011 - 03:38:51 PST)
    - Re: [AMBER] interaction energy steinbrt.rci.rutgers.edu (Thu Mar 10 2011 - 03:42:48 PST)
    - [AMBER] MM-GBSA with QM/MM Aust, Susanne (Tue Jun 28 2011 - 02:27:34 PDT)
    - Re: [AMBER] MM-GBSA with QM/MM Bill Miller III (Tue Jun 28 2011 - 03:47:06 PDT)
    - Re: [AMBER] MM-GBSA with QM/MM Aust, Susanne (Tue Jun 28 2011 - 04:18:38 PDT)
    - Re: [AMBER] interaction energy Jason Swails (Thu Mar 10 2011 - 07:24:40 PST)
    - Re: [AMBER] interaction energy Aust, Susanne (Mon Mar 14 2011 - 06:32:01 PDT)
[AMBER] Specially For You ros (Thu Mar 10 2011 - 05:55:29 PST)
[AMBER] Ptraj analyze crankshaft Mariano Rech (Thu Mar 10 2011 - 08:12:25 PST)
[AMBER] angle in h-bond analysis mirage . (Fri Mar 11 2011 - 06:10:20 PST)
- Re: [AMBER] angle in h-bond analysis mirage . (Mon Mar 14 2011 - 00:40:47 PDT)
- Re: [AMBER] angle in h-bond analysis Daniel Roe (Mon Mar 14 2011 - 05:58:22 PDT)
[AMBER] Query regarding mmpbsa output file Hirdesh Kumar (Fri Mar 11 2011 - 06:24:33 PST)
- Re: [AMBER] Query regarding mmpbsa output file Bill Miller III (Fri Mar 11 2011 - 06:44:32 PST)
  - Re: [AMBER] Query regarding mmpbsa output file Hirdesh Kumar (Fri Mar 11 2011 - 21:58:04 PST)
    - Re: [AMBER] Query regarding mmpbsa output file Bill Miller III (Sat Mar 12 2011 - 04:26:48 PST)
[AMBER] How to save a restart file Rahul Banerjee (Fri Mar 11 2011 - 08:51:50 PST)
- Re: [AMBER] How to save a restart file david condon (Fri Mar 11 2011 - 08:56:14 PST)
  - Re: [AMBER] How to save a restart file Rahul Banerjee (Fri Mar 11 2011 - 09:04:58 PST)
    - Re: [AMBER] How to save a restart file david condon (Fri Mar 11 2011 - 09:14:43 PST)
    - Re: [AMBER] How to save a restart file Jason Swails (Fri Mar 11 2011 - 09:52:29 PST)
- Re: [AMBER] How to save a restart file Bill Ross (Fri Mar 11 2011 - 10:52:24 PST)
  - Re: [AMBER] How to save a restart file Jason Swails (Fri Mar 11 2011 - 12:13:04 PST)
- [AMBER] PB Bomb in pb_aaradi ? Marek Maly (Tue Mar 15 2011 - 18:45:06 PDT)
  - Re: [AMBER] PB Bomb in pb_aaradi ? Ray Luo, Ph.D. (Tue Mar 15 2011 - 21:43:46 PDT)
    - Re: [AMBER] PB Bomb in pb_aaradi ? Marek Maly (Thu Mar 17 2011 - 03:43:28 PDT)
    - [AMBER] discrepancy after sieve in ptraj Jojart_Balazs (Thu Mar 17 2011 - 05:24:46 PDT)
    - Re: [AMBER] PB Bomb in pb_aaradi ? Ray Luo, Ph.D. (Thu Mar 17 2011 - 10:33:54 PDT)
[AMBER] Nitu Bansal wants to chat Nitu Bansal (Fri Mar 11 2011 - 09:17:44 PST)
[AMBER] how to run PIMD Sangita Kachhap (Fri Mar 11 2011 - 09:29:20 PST)
- Re: [AMBER] how to run PIMD David A Case (Fri Mar 11 2011 - 10:31:03 PST)
  - Re: [AMBER] how to run PIMD Sangita Kachhap (Fri Mar 11 2011 - 11:15:35 PST)
[AMBER] the output of REMD simulations zhihong ke (Fri Mar 11 2011 - 09:35:00 PST)
- Re: [AMBER] the output of REMD simulations Carlos Simmerling (Fri Mar 11 2011 - 09:36:09 PST)
  - Re: [AMBER] the output of REMD simulations zhihong ke (Fri Mar 11 2011 - 09:39:59 PST)
    - Re: [AMBER] the output of REMD simulations Carlos Simmerling (Fri Mar 11 2011 - 09:42:42 PST)
[AMBER] free energy profile for water slab Martina Roeselova (Fri Mar 11 2011 - 10:24:04 PST)
[AMBER] Amber Training Workshop Announcement - Barcelona, Spain. 3-6 May 2011 Ross Walker (Fri Mar 11 2011 - 10:24:53 PST)
[AMBER] AmberTools 1.4 possible bug for secstruct (test case attached) Tru Huynh (Fri Mar 11 2011 - 16:30:57 PST)
- Re: [AMBER] AmberTools 1.4 possible bug for secstruct (test case attached) case (Sat Mar 12 2011 - 05:54:02 PST)
  - Re: [AMBER] AmberTools 1.4 possible bug for secstruct (test case attached) Tru Huynh (Mon Mar 14 2011 - 10:46:34 PDT)
- Re: [AMBER] AmberTools 1.4 possible bug for secstruct (test case attached) Crowley, Michael (Sun Mar 13 2011 - 12:55:31 PDT)
[AMBER] docking evaluation using amber erik zuiderweg (Fri Mar 11 2011 - 17:33:00 PST)
- Re: [AMBER] docking evaluation using amber David Case (Fri Mar 11 2011 - 18:18:26 PST)
  - Re: [AMBER] docking evaluation using amber erik zuiderweg (Sat Mar 12 2011 - 08:17:07 PST)
- Re: [AMBER] docking evaluation using amber filip fratev (Fri Mar 11 2011 - 21:15:23 PST)
- Re: [AMBER] docking evaluation using amber Dmitry Nilov (Mon Mar 14 2011 - 06:32:02 PDT)
  - Re: [AMBER] docking evaluation using amber George Tzotzos (Mon Mar 14 2011 - 11:57:20 PDT)
[AMBER] rdf plot subrata paul (Fri Mar 11 2011 - 19:54:29 PST)
[AMBER] Amber archive mailing list is not working Hirdesh Kumar (Fri Mar 11 2011 - 22:50:55 PST)
- Re: [AMBER] Amber archive mailing list is not working Jason Swails (Fri Mar 11 2011 - 22:55:01 PST)
  - Re: [AMBER] Amber archive mailing list is not working Hirdesh Kumar (Fri Mar 11 2011 - 23:07:13 PST)
    - Re: [AMBER] Amber archive mailing list is not working Jason Swails (Fri Mar 11 2011 - 23:18:58 PST)
    - Re: [AMBER] Amber archive mailing list is not working Ilyas Yildirim (Fri Mar 11 2011 - 23:29:31 PST)
    - Re: [AMBER] Amber archive mailing list is not working Gustavo Seabra (Sat Mar 12 2011 - 03:53:53 PST)
    - Re: [AMBER] Amber archive mailing list is not working Gustavo Seabra (Sat Mar 12 2011 - 03:56:02 PST)
    - Re: [AMBER] Amber archive mailing list is not working Ross Walker (Sat Mar 12 2011 - 10:50:07 PST)
    - Re: [AMBER] Amber archive mailing list is not working Hirdesh Kumar (Sun Mar 13 2011 - 22:04:51 PDT)
    - Re: [AMBER] Amber archive mailing list is not working Ross Walker (Mon Mar 14 2011 - 09:57:23 PDT)
    - Re: [AMBER] Amber archive mailing list is not working David Watson (Mon Mar 14 2011 - 10:37:50 PDT)
- Re: [AMBER] Amber archive mailing list is not working Bill Ross (Sat Mar 12 2011 - 23:50:21 PST)
[AMBER] Energy Decomposition using mmpbsa script Eliac Brown (Sat Mar 12 2011 - 05:05:20 PST)
- Re: [AMBER] Energy Decomposition using mmpbsa script Bill Miller III (Sat Mar 12 2011 - 05:31:16 PST)
- Re: [AMBER] Energy Decomposition using mmpbsa script Eliac Brown (Sat Mar 12 2011 - 07:32:36 PST)
  - Re: [AMBER] Energy Decomposition using mmpbsa script Bill Miller III (Sat Mar 12 2011 - 07:47:56 PST)
- Re: [AMBER] Energy Decomposition using mmpbsa script Eliac Brown (Sat Mar 12 2011 - 10:05:47 PST)
[AMBER] Bad magic number ? Hector A. Baldoni (Sat Mar 12 2011 - 06:41:19 PST)
- Re: [AMBER] Bad magic number ? Bill Miller III (Sat Mar 12 2011 - 07:02:56 PST)
  - Re: [AMBER] Bad magic number ? Jason Swails (Sat Mar 12 2011 - 08:20:59 PST)
[AMBER] GB parameters for Octane Eliac Brown (Sat Mar 12 2011 - 10:10:49 PST)
[AMBER] questions about the input file of MD process asakiayumikio.gmail.com (Sun Mar 13 2011 - 00:45:44 PST)
- Re: [AMBER] questions about the input file of MD process Francesco Oteri (Sun Mar 13 2011 - 07:27:39 PDT)
- Re: [AMBER] questions about the input file of MD process asakiayumikio.gmail.com (Sun Mar 13 2011 - 07:34:15 PDT)
  - Re: [AMBER] questions about the input file of MD process Carlos Simmerling (Sun Mar 13 2011 - 07:38:53 PDT)
  - Re: [AMBER] questions about the input file of MD process Francesco Oteri (Sun Mar 13 2011 - 07:41:04 PDT)
- Re: [AMBER] questions about the input file of MD process asakiayumikio.gmail.com (Sun Mar 13 2011 - 08:04:28 PDT)
- Re: [AMBER] questions about the input file of MD process asakiayumikio.gmail.com (Sun Mar 13 2011 - 08:07:19 PDT)
  - Re: [AMBER] questions about the input file of MD process Francesco Oteri (Sun Mar 13 2011 - 08:09:23 PDT)
[AMBER] strip command usage in ptraj asakiayumikio.gmail.com (Sun Mar 13 2011 - 08:14:46 PDT)
- Re: [AMBER] strip command usage in ptraj Adrian Roitberg (Sun Mar 13 2011 - 08:23:26 PDT)
- Re: [AMBER] strip command usage in ptraj asakiayumikio.gmail.com (Sun Mar 13 2011 - 08:30:26 PDT)
  - Re: [AMBER] strip command usage in ptraj Adrian Roitberg (Sun Mar 13 2011 - 08:41:44 PDT)
- Re: [AMBER] strip command usage in ptraj asakiayumikio.gmail.com (Sun Mar 13 2011 - 08:47:13 PDT)
  - Re: [AMBER] strip command usage in ptraj Adrian Roitberg (Sun Mar 13 2011 - 08:57:31 PDT)
- Re: [AMBER] strip command usage in ptraj asakiayumikio.gmail.com (Sun Mar 13 2011 - 09:05:00 PDT)
- Re: [AMBER] strip command usage in ptraj asakiayumikio.gmail.com (Sun Mar 13 2011 - 18:48:41 PDT)
[AMBER] error in creating prmtop and inpcrd files Chris Bryant (Sun Mar 13 2011 - 10:48:56 PDT)
- Re: [AMBER] error in creating prmtop and inpcrd files Ben Roberts (Sun Mar 13 2011 - 11:42:29 PDT)
  - Re: [AMBER] error in creating prmtop and inpcrd files Chris Bryant (Sun Mar 13 2011 - 13:55:51 PDT)
    - Re: [AMBER] error in creating prmtop and inpcrd files Ben Roberts (Sun Mar 13 2011 - 14:34:48 PDT)
    - Re: [AMBER] error in creating prmtop and inpcrd files Jason Swails (Sun Mar 13 2011 - 14:55:13 PDT)
    - Re: [AMBER] error in creating prmtop and inpcrd files Chris Bryant (Sun Mar 13 2011 - 15:47:45 PDT)
[AMBER] amber11 Installation Test Failures David Cantu (Sun Mar 13 2011 - 18:11:59 PDT)
- Re: [AMBER] amber11 Installation Test Failures Daniel Roe (Sun Mar 13 2011 - 19:21:21 PDT)
  - Re: [AMBER] Would liek to plot GBTOT vs Time Mannan (Sun Mar 13 2011 - 22:59:39 PDT)
    - Re: [AMBER] Would liek to plot GBTOT vs Time Daniel Sindhikara (Sun Mar 13 2011 - 23:40:13 PDT)
    - Re: [AMBER] Would liek to plot GBTOT vs Time Jason Swails (Mon Mar 14 2011 - 00:02:28 PDT)
  - Re: [AMBER] amber11 Installation Test Failures David Cantu (Mon Mar 14 2011 - 00:16:41 PDT)
    - Re: [AMBER] amber11 Installation Test Failures Jason Swails (Mon Mar 14 2011 - 07:08:52 PDT)
    - Re: [AMBER] amber11 Installation Test Failures David Cantu (Tue Mar 15 2011 - 14:31:24 PDT)
    - Re: [AMBER] amber11 Installation Test Failures David Cantu (Tue Mar 15 2011 - 16:16:02 PDT)
    - Re: [AMBER] amber11 Installation Test Failures Daniel Roe (Tue Mar 15 2011 - 16:55:28 PDT)
    - Re: [AMBER] amber11 Installation Test Failures David Cantu (Tue Mar 15 2011 - 16:58:06 PDT)
    - Re: [AMBER] amber11 Installation Test Failures Jason Swails (Tue Mar 15 2011 - 17:14:05 PDT)
    - Re: [AMBER] amber11 Installation Test Failures David Cantu (Tue Mar 15 2011 - 18:40:15 PDT)
    - Re: [AMBER] amber11 Installation Test Failures David Cantu (Tue Mar 15 2011 - 19:08:04 PDT)
    - Re: [AMBER] amber11 Installation Test Failures Tru Huynh (Sat Mar 19 2011 - 17:30:40 PDT)
    - Re: [AMBER] amber11 Installation Test Failures David Cantu (Sat Mar 19 2011 - 23:16:27 PDT)
    - Re: [AMBER] amber11 Installation Test Failures David Cantu (Sat Mar 19 2011 - 23:39:08 PDT)
    - Re: [AMBER] amber11 Installation Test Failures Jason Swails (Sun Mar 20 2011 - 07:36:09 PDT)
    - Re: [AMBER] amber11 Installation Test Failures David Cantu (Sun Mar 20 2011 - 01:34:55 PDT)
    - Re: [AMBER] amber11 Installation Test Failures case (Tue Mar 15 2011 - 18:58:06 PDT)
[AMBER] how to calculate the B-factor of crystal pdb asakiayumikio.gmail.com (Sun Mar 13 2011 - 23:58:43 PDT)
- Re: [AMBER] how to calculate the B-factor of crystal pdb Carlos Simmerling (Mon Mar 14 2011 - 04:23:49 PDT)
- Re: [AMBER] how to calculate the B-factor of crystal pdb asakiayumikio.gmail.com (Mon Mar 14 2011 - 07:59:10 PDT)
[AMBER] Query regarding mmpbsa run Hirdesh Kumar (Mon Mar 14 2011 - 03:59:38 PDT)
[AMBER] how to obtain 4x4x1.1nm water; how to add polarizable models gromacs (Mon Mar 14 2011 - 05:44:42 PDT)
- Re: [AMBER] how to obtain 4x4x1.1nm water; how to add polarizable models David A Case (Mon Mar 14 2011 - 08:16:30 PDT)
- [AMBER] how to obtain 4x4x1.1nm water MD (Wed Apr 06 2011 - 21:16:20 PDT)
  - Re: [AMBER] how to obtain 4x4x1.1nm water Jason Swails (Wed Apr 06 2011 - 23:30:14 PDT)
    - Re: [AMBER] how to obtain 4x4x1.1nm water MD (Thu Apr 07 2011 - 00:08:03 PDT)
    - Re: [AMBER] how to obtain 4x4x1.1nm water David A Case (Thu Apr 07 2011 - 06:20:54 PDT)
[AMBER] Important Notice Re Sleap (especially with Glycam) Lachele Foley (Lists) (Mon Mar 14 2011 - 07:27:12 PDT)
[AMBER] Regarding: Adding New Multi-atom Residue (Ligand) including partial charges Naveen Samala (Mon Mar 14 2011 - 11:30:32 PDT)
- Re: [AMBER] Regarding: Adding New Multi-atom Residue (Ligand) including partial charges FyD (Mon Mar 14 2011 - 23:55:22 PDT)
[AMBER] MD- the enzyme bouncing Mahmoud Soliman (Mon Mar 14 2011 - 13:44:11 PDT)
[AMBER] MD- the enzyme bouncing Mahmoud Soliman (Mon Mar 14 2011 - 13:44:41 PDT)
- Re: [AMBER] MD- the enzyme bouncing Jason Swails (Mon Mar 14 2011 - 15:07:40 PDT)
- Re: [AMBER] MD- the enzyme bouncing Gustavo Seabra (Mon Mar 14 2011 - 17:19:47 PDT)
[AMBER] mm_pbsa input for energy decomposition Lihua Wang (Mon Mar 14 2011 - 16:23:06 PDT)
[AMBER] Compatibility Question Azat Mukhametov (Mon Mar 14 2011 - 17:57:09 PDT)
- Re: [AMBER] Compatibility Question Ross Walker (Mon Mar 14 2011 - 18:44:29 PDT)
[AMBER] Calculation with CUTCAP Roman Osman (Mon Mar 14 2011 - 20:20:43 PDT)
- Re: [AMBER] Calculation with CUTCAP Dwight McGee (Mon Mar 14 2011 - 20:28:35 PDT)
  - Re: [AMBER] Calculation with CUTCAP Osman, Roman (Tue Mar 15 2011 - 06:34:22 PDT)
    - Re: [AMBER] Calculation with CUTCAP Jason Swails (Tue Mar 15 2011 - 07:43:50 PDT)
    - Re: [AMBER] Calculation with CUTCAP Roman Osman (Tue Mar 15 2011 - 07:51:16 PDT)
[AMBER] how to choose the biasing potential based on the coarse free energy curve Ye MEI (Mon Mar 14 2011 - 21:21:12 PDT)
- Re: [AMBER] how to choose the biasing potential based on the coarse free energy curve Daniel Sindhikara (Mon Mar 14 2011 - 23:03:15 PDT)
[AMBER] amber11 intel mpi compile on altix 450 problem Lisa Perez (Mon Mar 14 2011 - 22:09:01 PDT)
- Re: [AMBER] amber11 intel mpi compile on altix 450 problem Jason Swails (Tue Mar 15 2011 - 07:38:03 PDT)
  - Re: [AMBER] amber11 intel mpi compile on altix 450 problem Lisa Perez (Wed Mar 16 2011 - 09:45:03 PDT)
[AMBER] no answer so far - free energy profile for water slab Martina Roeselova (Tue Mar 15 2011 - 02:20:09 PDT)
- Re: [AMBER] no answer so far - free energy profile for water slab Carlos Simmerling (Tue Mar 15 2011 - 04:02:44 PDT)
  - Re: [AMBER] no answer so far - free energy profile for water slab Martina Roeselova (Tue Mar 15 2011 - 07:57:16 PDT)
    - Re: [AMBER] no answer so far - free energy profile for water slab Jojart_Balazs (Wed Mar 16 2011 - 07:38:35 PDT)
Re: [AMBER] how to choose the biasing potential based on the coarsefree energy curve Ye MEI (Tue Mar 15 2011 - 06:41:53 PDT)
- Re: [AMBER] how to choose the biasing potential based on the coarsefree energy curve Carlos Simmerling (Tue Mar 15 2011 - 07:24:17 PDT)
  - Re: [AMBER] how to choose the biasing potential based on the coarsefree energy curve Daniel Sindhikara (Tue Mar 15 2011 - 07:48:55 PDT)
[AMBER] Explicit and implicit n-octanol solvent Eliac Brown (Tue Mar 15 2011 - 07:03:47 PDT)
[AMBER] How to calculate water density around the certain residue or ligand mish (Tue Mar 15 2011 - 07:47:54 PDT)
[AMBER] Add residue copied from other unit Vlastimil Zíma (Tue Mar 15 2011 - 08:24:14 PDT)
[AMBER] AMBER 10 serial compile problem Dmitry Osolodkin (Tue Mar 15 2011 - 09:35:37 PDT)
- Re: [AMBER] AMBER 10 serial compile problem David Watson (Tue Mar 15 2011 - 09:53:41 PDT)
  - Re: [AMBER] AMBER 10 serial compile problem Dmitry Osolodkin (Tue Mar 15 2011 - 09:52:50 PDT)
    - Re: [AMBER] AMBER 10 serial compile problem Jason Swails (Tue Mar 15 2011 - 10:06:17 PDT)
- Re: [AMBER] AMBER 10 serial compile problem Jason Swails (Tue Mar 15 2011 - 09:57:54 PDT)
  - Re: [AMBER] AMBER 10 serial compile problem David A Case (Tue Mar 15 2011 - 10:24:19 PDT)
    - Re: [AMBER] AMBER 10 serial compile problem Dmitry Osolodkin (Tue Mar 15 2011 - 10:29:59 PDT)
    - Re: [AMBER] AMBER 10 serial compile problem Jason Swails (Tue Mar 15 2011 - 10:41:28 PDT)
    - Re: [AMBER] AMBER 10 serial compile problem Dmitry Osolodkin (Tue Mar 15 2011 - 10:45:07 PDT)
    - Re: [AMBER] AMBER 10 serial compile problem Jason Swails (Tue Mar 15 2011 - 11:09:46 PDT)
- Re: [AMBER] AMBER 10 serial compile problem Dmitry Osolodkin (Tue Mar 15 2011 - 13:22:01 PDT)
[AMBER] Missing Parameters Melanie (Tue Mar 15 2011 - 10:29:32 PDT)
- Re: [AMBER] Missing Parameters Ilyas Yildirim (Tue Mar 15 2011 - 11:18:49 PDT)
  - Re: [AMBER] Missing Parameters Melanie (Thu Mar 17 2011 - 12:27:35 PDT)
    - Re: [AMBER] Missing Parameters Ilyas Yildirim (Thu Mar 17 2011 - 12:59:00 PDT)
    - Re: [AMBER] Missing Parameters Marek Maly (Thu Mar 17 2011 - 13:05:02 PDT)
    - Re: [AMBER] Missing Parameters Melanie (Fri Mar 18 2011 - 21:05:47 PDT)
    - Re: [AMBER] Missing Parameters Ilyas Yildirim (Fri Mar 18 2011 - 21:31:00 PDT)
    - Re: [AMBER] Missing Parameters Ilyas Yildirim (Fri Mar 18 2011 - 22:39:11 PDT)
    - Re: [AMBER] Missing Parameters Melanie (Sun Apr 03 2011 - 16:24:32 PDT)
    - Re: [AMBER] Missing Parameters Ilyas Yildirim (Mon Apr 04 2011 - 07:23:58 PDT)
    - Re: [AMBER] Missing Parameters Melanie (Mon Apr 04 2011 - 19:41:47 PDT)
    - Re: [AMBER] Missing Parameters Ilyas Yildirim (Mon Apr 04 2011 - 22:42:10 PDT)
    - Re: [AMBER] Missing Parameters case (Sat Mar 19 2011 - 07:14:43 PDT)
- Re: [AMBER] Missing Parameters Bill Ross (Mon Apr 04 2011 - 20:41:16 PDT)
[AMBER] Assertion failed: nat < 5000, file makeDIST_RST Andre Serobian (Tue Mar 15 2011 - 13:20:47 PDT)
- Re: [AMBER] Assertion failed: nat < 5000, file makeDIST_RST case (Tue Mar 15 2011 - 17:51:21 PDT)
- Re: [AMBER] Assertion failed: nat < 5000, file makeDIST_RST Andre Serobian (Tue Mar 15 2011 - 18:44:02 PDT)
 - Re: [AMBER] Assertion failed: nat < 5000, file makeDIST_RST case (Wed Mar 16 2011 - 04:47:37 PDT)
- Re: [AMBER] Assertion failed: nat < 5000, file makeDIST_RST Andre Serobian (Wed Mar 16 2011 - 17:51:37 PDT)
 - Re: [AMBER] Assertion failed: nat < 5000, file makeDIST_RST case (Thu Mar 17 2011 - 05:34:51 PDT)
[AMBER] AMBER Workshop in Shanghai, China, August 22-26 2011 Andreas Goetz (Tue Mar 15 2011 - 13:29:25 PDT)
[AMBER] free energy calculation with TI Dian Jiao (Tue Mar 15 2011 - 13:55:04 PDT)
- Re: [AMBER] free energy calculation with TI steinbrt.rci.rutgers.edu (Tue Mar 15 2011 - 14:31:38 PDT)
  - Re: [AMBER] free energy calculation with TI Dian Jiao (Tue Mar 15 2011 - 15:12:19 PDT)
    - Re: [AMBER] free energy calculation with TI Dian Jiao (Tue Mar 15 2011 - 20:17:44 PDT)
    - Re: [AMBER] free energy calculation with TI steinbrt.rci.rutgers.edu (Wed Mar 16 2011 - 02:25:15 PDT)
    - Re: [AMBER] free energy calculation with TI steinbrt.rci.rutgers.edu (Wed Mar 16 2011 - 02:21:52 PDT)
[AMBER] how to run amber on mutli-gpu/muti-nodes Haipeng Wei (Tue Mar 15 2011 - 15:08:40 PDT)
- Re: [AMBER] how to run amber on mutli-gpu/muti-nodes Ross Walker (Tue Mar 15 2011 - 15:13:44 PDT)
  - Re: [AMBER] how to run amber on mutli-gpu/muti-nodes Haipeng Wei (Tue Mar 15 2011 - 17:04:52 PDT)
    - Re: [AMBER] how to run amber on mutli-gpu/muti-nodes Jason Swails (Tue Mar 15 2011 - 17:23:29 PDT)
Re: [AMBER] how to choose the biasing potential based on thecoarsefree energy curve Ye MEI (Tue Mar 15 2011 - 20:28:05 PDT)
[AMBER] NCSU David Cantu (Tue Mar 15 2011 - 20:44:00 PDT)
[AMBER] PB Bomb in pb_aaradi ? Marek Maly (Tue Mar 15 2011 - 20:49:14 PDT)
[AMBER] NVT Vs NPT Mahmoud Soliman (Wed Mar 16 2011 - 00:31:07 PDT)
- Re: [AMBER] NVT Vs NPT MD simulations Mahmoud Soliman (Wed Mar 16 2011 - 08:00:46 PDT)
- Re: [AMBER] NVT Vs NPT Jason Swails (Wed Mar 16 2011 - 09:49:39 PDT)
  - Re: [AMBER] NVT Vs NPT Mahmoud Soliman (Wed Mar 16 2011 - 12:36:43 PDT)
  - Re: [AMBER] NVT Vs NPT Marek Maly (Thu Mar 17 2011 - 06:25:27 PDT)
    - Re: [AMBER] NVT Vs NPT Jason Swails (Thu Mar 17 2011 - 08:49:57 PDT)
    - Re: [AMBER] NVT Vs NPT Marek Maly (Thu Mar 17 2011 - 09:10:17 PDT)
    - Re: [AMBER] NVT Vs NPT Ross Walker (Thu Mar 17 2011 - 09:31:23 PDT)
    - Re: [AMBER] NVT Vs NPT Marek Maly (Thu Mar 17 2011 - 10:03:08 PDT)
[AMBER] stacking energy calculation hari krishna (Wed Mar 16 2011 - 03:06:36 PDT)
- Re: [AMBER] stacking energy calculation Jiri Sponer (Wed Mar 16 2011 - 04:02:39 PDT)
[AMBER] distance cutoff of closest command Sangita Kachhap (Wed Mar 16 2011 - 03:07:36 PDT)
- Re: [AMBER] distance cutoff of closest command Daniel Roe (Wed Mar 16 2011 - 05:59:43 PDT)
  - Re: [AMBER] distance cutoff of closest command Daniel Roe (Wed Mar 16 2011 - 06:02:12 PDT)
    - Re: [AMBER] distance cutoff of closest command Sangita Kachhap (Wed Mar 16 2011 - 10:24:38 PDT)
    - Re: [AMBER] distance cutoff of closest command Sangita Kachhap (Wed Mar 16 2011 - 11:05:50 PDT)
[AMBER] Reimaging Problem chandan patel (Wed Mar 16 2011 - 03:43:39 PDT)
- Re: [AMBER] Reimaging Problem manikanthan bhavaraju (Wed Mar 16 2011 - 09:34:05 PDT)
  - Re: [AMBER] Reimaging Problem chandan patel (Thu Mar 17 2011 - 02:40:02 PDT)
[AMBER] using thermodynamic integration, how to deal with absolute pka and conformation change Junjian Miao (Wed Mar 16 2011 - 05:58:58 PDT)
- Re: [AMBER] using thermodynamic integration, how to deal with absolute pka and conformation change David Case (Wed Mar 16 2011 - 06:25:26 PDT)
- Re: [AMBER] using thermodynamic integration, how to deal with absolute pka and conformation change Junjian Miao (Thu Mar 17 2011 - 20:32:55 PDT)
[AMBER] Restraints on equilibration of solvated complexes George Tzotzos (Wed Mar 16 2011 - 07:37:17 PDT)
- Re: [AMBER] Restraints on equilibration of solvated complexes Dmitry Nilov (Wed Mar 16 2011 - 08:10:32 PDT)
  - Re: [AMBER] Restraints on equilibration of solvated complexes George Tzotzos (Wed Mar 16 2011 - 08:25:28 PDT)
    - Re: [AMBER] Restraints on equilibration of solvated complexes Dmitry Nilov (Wed Mar 16 2011 - 08:47:28 PDT)
    - Re: [AMBER] Restraints on equilibration of solvated complexes George Tzotzos (Wed Mar 16 2011 - 10:52:00 PDT)
    - Re: [AMBER] Restraints on equilibration of solvated complexes Dmitry Nilov (Wed Mar 16 2011 - 12:05:22 PDT)
[AMBER] Problem with link atom in QM/MM Wook Lee (Wed Mar 16 2011 - 08:01:31 PDT)
- Re: [AMBER] Problem with link atom in QM/MM Ross Walker (Wed Mar 16 2011 - 09:39:41 PDT)
  - Re: [AMBER] Problem with link atom in QM/MM Wook Lee (Thu Mar 17 2011 - 01:39:47 PDT)
  - Re: [AMBER] Problem with link atom in QM/MM Wook Lee (Thu Mar 17 2011 - 06:29:45 PDT)
[AMBER] Thermodynamic Integration Ignacio J. General (Wed Mar 16 2011 - 14:22:07 PDT)
- Re: [AMBER] Thermodynamic Integration steinbrt.rci.rutgers.edu (Thu Mar 17 2011 - 02:10:20 PDT)
  - Re: [AMBER] Thermodynamic Integration Ignacio J. General (Thu Mar 17 2011 - 07:09:19 PDT)
    - Re: [AMBER] Thermodynamic Integration steinbrt.rci.rutgers.edu (Thu Mar 17 2011 - 08:06:03 PDT)
    - Re: [AMBER] Thermodynamic Integration Ignacio J. General (Thu Mar 17 2011 - 08:22:56 PDT)
    - Re: [AMBER] Thermodynamic Integration steinbrt.rci.rutgers.edu (Fri Mar 18 2011 - 02:11:50 PDT)
[AMBER] Thermostat Diego Javier Alonso de Armiño (Wed Mar 16 2011 - 19:50:05 PDT)
- Re: [AMBER] Thermostat Jason Swails (Thu Mar 17 2011 - 00:05:01 PDT)
  - Re: [AMBER] Thermostat Daniel Sindhikara (Thu Mar 17 2011 - 00:27:17 PDT)
[AMBER] parameters for metal site Jorgen Simonsen (Thu Mar 17 2011 - 02:24:16 PDT)
- Re: [AMBER] parameters for metal site FyD (Thu Mar 17 2011 - 07:03:21 PDT)
  - Re: [AMBER] parameters for metal site Jorgen Simonsen (Thu Mar 17 2011 - 07:39:14 PDT)
    - Re: [AMBER] parameters for metal site FyD (Thu Mar 17 2011 - 11:30:37 PDT)
[AMBER] MMPBSA energy contribution John S (Thu Mar 17 2011 - 08:05:12 PDT)
- Re: [AMBER] MMPBSA energy contribution Jason Swails (Thu Mar 17 2011 - 08:40:34 PDT)
[AMBER] Segmentation fault MASLYK, MACIEJ MARCIN (Wed Mar 16 2011 - 08:50:36 PDT)
- Re: [AMBER] Segmentation fault Jason Swails (Thu Mar 17 2011 - 09:53:44 PDT)
- Re: [AMBER] Segmentation fault Jason Swails (Thu Mar 17 2011 - 09:55:19 PDT)
  - [AMBER] ODP: Segmentation fault MASLYK, MACIEJ MARCIN (Tue Mar 22 2011 - 04:10:55 PDT)
[AMBER] error installing AmberTools-1.2 in ubuntu 10.10 Vijay Manickam Achari (Thu Mar 17 2011 - 12:24:46 PDT)
- Re: [AMBER] error installing AmberTools-1.2 in ubuntu 10.10 Ben Roberts (Thu Mar 17 2011 - 12:52:26 PDT)
  - Re: [AMBER] error installing AmberTools-1.2 in ubuntu 10.10 Jason Swails (Thu Mar 17 2011 - 14:21:25 PDT)
  - Re: [AMBER] error installing AmberTools-1.2 in ubuntu 10.10 Vijay Manickam Achari (Thu Mar 17 2011 - 19:57:11 PDT)
    - Re: [AMBER] error installing AmberTools-1.2 in ubuntu 10.10 Jason Swails (Fri Mar 18 2011 - 01:58:34 PDT)
    - Re: [AMBER] error installing AmberTools-1.2 in ubuntu 10.10 juzer stationwala (Fri Mar 18 2011 - 02:02:50 PDT)
[AMBER] Using Intel compilers on AMD CPU Bongkeun Kim (Thu Mar 17 2011 - 20:10:48 PDT)
- Re: [AMBER] Using Intel compilers on AMD CPU Ross Walker (Fri Mar 18 2011 - 09:09:43 PDT)
[AMBER] changing X Y Z orientation Vijay Manickam Achari (Fri Mar 18 2011 - 03:47:21 PDT)
[AMBER] problem with gas-phase MD simulation in Amber8. marta wiśniewska. (Fri Mar 18 2011 - 04:37:09 PDT)
- Re: [AMBER] problem with gas-phase MD simulation in Amber8. Mengjuei Hsieh (Fri Mar 18 2011 - 05:19:49 PDT)
  - Re: [AMBER] problem with gas-phase MD simulation in Amber8. steinbrt.rci.rutgers.edu (Fri Mar 18 2011 - 05:22:50 PDT)
    - Re: [AMBER] problem with gas-phase MD simulation in Amber8. marta wiśniewska. (Fri Mar 18 2011 - 10:13:03 PDT)
    - Re: [AMBER] problem with gas-phase MD simulation in Amber8. Ross Walker (Fri Mar 18 2011 - 10:54:00 PDT)
    - Re: [AMBER] problem with gas-phase MD simulation in Amber8. marta wiśniewska. (Fri Mar 18 2011 - 12:08:36 PDT)
    - Re: [AMBER] problem with gas-phase MD simulation in Amber8. Jason Swails (Fri Mar 18 2011 - 12:12:54 PDT)
    - Re: [AMBER] problem with gas-phase MD simulation in Amber8. marta wiśniewska. (Fri Mar 18 2011 - 12:20:17 PDT)
[AMBER] Amber11 on osx using port and gcc4.5 Joachim Reichelt (Fri Mar 18 2011 - 05:42:58 PDT)
- Re: [AMBER] Amber11 on osx using port and gcc4.5 case (Fri Mar 18 2011 - 14:31:17 PDT)
[AMBER] trouble with mmpbsa.py Chris Chris (Fri Mar 18 2011 - 09:44:08 PDT)
- Re: [AMBER] trouble with mmpbsa.py Bill Miller III (Fri Mar 18 2011 - 09:50:17 PDT)
  - Re: [AMBER] trouble with mmpbsa.py Chris Chris (Fri Mar 18 2011 - 10:30:59 PDT)
    - Re: [AMBER] trouble with mmpbsa.py Jason Swails (Fri Mar 18 2011 - 10:47:20 PDT)
[AMBER] RMSD Calculation abc def (Fri Mar 18 2011 - 09:47:41 PDT)
[AMBER] Is rst file the last frame of output crd file? Bingwu Yu (Fri Mar 18 2011 - 10:07:04 PDT)
- Re: [AMBER] Is rst file the last frame of output crd file? Mark Williamson (Fri Mar 18 2011 - 10:21:15 PDT)
- Re: [AMBER] Is rst file the last frame of output crd file? Jason Swails (Fri Mar 18 2011 - 10:36:07 PDT)
  - Re: [AMBER] Is rst file the last frame of output crd file? Bingwu Yu (Fri Mar 18 2011 - 11:10:14 PDT)
    - Re: [AMBER] Is rst file the last frame of output crd file? Gustavo Seabra (Fri Mar 18 2011 - 11:20:01 PDT)
    - Re: [AMBER] Is rst file the last frame of output crd file? Bingwu Yu (Fri Mar 18 2011 - 11:24:40 PDT)
[AMBER] Dihedral angles does not match VMD vs ptraj Bingwu Yu (Fri Mar 18 2011 - 13:30:42 PDT)
- Re: [AMBER] Dihedral angles does not match VMD vs ptraj Lachele Foley (Lists) (Fri Mar 18 2011 - 14:08:33 PDT)
  - Re: [AMBER] Dihedral angles does not match VMD vs ptraj Bingwu Yu (Fri Mar 18 2011 - 14:24:12 PDT)
    - Re: [AMBER] Dihedral angles does not match VMD vs ptraj Lachele Foley (Lists) (Fri Mar 18 2011 - 14:40:48 PDT)
    - Re: [AMBER] Dihedral angles does not match VMD vs ptraj Lachele Foley (Lists) (Fri Mar 18 2011 - 14:42:04 PDT)
    - Re: [AMBER] Dihedral angles does not match VMD vs ptraj Bingwu Yu (Fri Mar 18 2011 - 21:08:04 PDT)
[AMBER] convert the atomic b factor to residual b factor zhihong ke (Fri Mar 18 2011 - 14:27:45 PDT)
[AMBER] TI minimizations cannot be performed with > 2 CPUs Dian Jiao (Fri Mar 18 2011 - 22:43:29 PDT)
- Re: [AMBER] TI minimizations cannot be performed with > 2 CPUs g t (Sat Mar 19 2011 - 11:56:38 PDT)
- Re: [AMBER] TI minimizations cannot be performed with > 2 CPUs case (Sun Mar 20 2011 - 06:26:04 PDT)
[AMBER] changing maximum number of frames for mmpbsa.py Chris Chris (Sat Mar 19 2011 - 09:27:03 PDT)
- Re: [AMBER] changing maximum number of frames for mmpbsa.py Bill Miller III (Sat Mar 19 2011 - 09:40:39 PDT)
[AMBER] AmberTools and GROMACS Francesco Oteri (Sat Mar 19 2011 - 11:31:04 PDT)
[AMBER] reference for per-residue decomposition using TI Calculation g t (Sat Mar 19 2011 - 11:49:00 PDT)
- Re: [AMBER] reference for per-residue decomposition using TI Calculation g t (Thu Mar 24 2011 - 09:54:12 PDT)
[AMBER] Differences in the periodic box dimensions Vijay Manickam Achari (Sat Mar 19 2011 - 14:38:25 PDT)
- Re: [AMBER] Differences in the periodic box dimensions Jason Swails (Sat Mar 19 2011 - 16:39:15 PDT)
- Re: [AMBER] Differences in the periodic box dimensions Bill Ross (Tue Mar 22 2011 - 10:07:37 PDT)
  - [AMBER] Force Field question - DLPOLY to AMBER Lorenzo Gontrani (Tue Mar 22 2011 - 10:09:51 PDT)
[AMBER] MMPBSA question Eliac Brown (Sat Mar 19 2011 - 16:35:42 PDT)
- Re: [AMBER] MMPBSA question Jason Swails (Sat Mar 19 2011 - 17:31:02 PDT)
  - Re: [AMBER] MMPBSA question Eliac Brown (Sat Mar 19 2011 - 17:57:52 PDT)
    - Re: [AMBER] MMPBSA question Jason Swails (Sat Mar 19 2011 - 19:11:16 PDT)
[AMBER] symmetry corrected RMSD calculation Pooja Khurana (Sat Mar 19 2011 - 19:38:21 PDT)
[AMBER] AmberTools 1.4 make test Error David Cantu (Sun Mar 20 2011 - 01:39:50 PDT)
[AMBER] Amber11 make test FAILURE and ERROR David Cantu (Sun Mar 20 2011 - 01:45:34 PDT)
- Re: [AMBER] Amber11 make test FAILURE and ERROR Jason Swails (Sun Mar 20 2011 - 07:33:14 PDT)
  - Re: [AMBER] Amber11 make test FAILURE and ERROR David Cantu (Mon Mar 21 2011 - 18:57:02 PDT)
[AMBER] how to calculate scattering trajectory Wen Xu (Sun Mar 20 2011 - 12:51:01 PDT)
- Re: [AMBER] how to calculate scattering trajectory Bill Ross (Sun Mar 20 2011 - 14:06:52 PDT)
  - Re: [AMBER] how to calculate scattering trajectory Adrian Roitberg (Sun Mar 20 2011 - 14:09:47 PDT)
    - Re: [AMBER] how to calculate scattering trajectory Wen Xu (Mon Mar 21 2011 - 08:11:41 PDT)
    - Re: [AMBER] how to calculate scattering trajectory Adrian Roitberg (Mon Mar 21 2011 - 08:16:50 PDT)
[AMBER] charmmgen issues Francesco Pietra (Mon Mar 21 2011 - 04:04:03 PDT)
[AMBER] MM-PBSA Error N.R. Jena (Mon Mar 21 2011 - 04:25:31 PDT)
- Re: [AMBER] MM-PBSA Error Bill Miller III (Mon Mar 21 2011 - 04:30:33 PDT)
  - Re: [AMBER] MM-PBSA Error N.R. Jena (Mon Mar 21 2011 - 04:38:59 PDT)
[AMBER] protein charge Ouaray Z. (Mon Mar 21 2011 - 06:52:23 PDT)
- Re: [AMBER] protein charge Astrid Maaß (Mon Mar 21 2011 - 07:23:04 PDT)
[AMBER] probleme with "reference" using ptraj Muriel Jourdan (Mon Mar 21 2011 - 07:28:09 PDT)
- Re: [AMBER] probleme with "reference" using ptraj Rahul Banerjee (Mon Mar 21 2011 - 07:30:27 PDT)
  - Re: [AMBER] probleme with "reference" using ptraj Muriel Jourdan (Mon Mar 21 2011 - 08:48:59 PDT)
[AMBER] can I calculate binding energy with some restraints Mahmoud Soliman (Mon Mar 21 2011 - 08:06:17 PDT)
- Re: [AMBER] can I calculate binding energy with some restraints case (Mon Mar 21 2011 - 10:23:35 PDT)
  - Re: [AMBER] can I calculate binding energy with some restraints Mahmoud Soliman (Mon Mar 21 2011 - 10:40:24 PDT)
[AMBER] MM/PBSA (Problem in snapshot generation) mish (Mon Mar 21 2011 - 10:00:37 PDT)
- Re: [AMBER] MM/PBSA (Problem in snapshot generation) Dwight McGee (Mon Mar 21 2011 - 10:43:56 PDT)
  - Re: [AMBER] MM/PBSA (Problem in snapshot generation) mish (Mon Mar 21 2011 - 11:06:34 PDT)
    - Re: [AMBER] MM/PBSA (Problem in snapshot generation) Dwight McGee (Mon Mar 21 2011 - 12:14:00 PDT)
[AMBER] nmode memory issue amit dong (Mon Mar 21 2011 - 10:01:05 PDT)
- Re: [AMBER] nmode memory issue Sushil Mishra (Mon Mar 21 2011 - 10:14:52 PDT)
  - Re: [AMBER] nmode memory issue Dima A Sabbah (Mon Mar 21 2011 - 10:50:34 PDT)
[AMBER] calculation of population of each conformers Bingwu Yu (Mon Mar 21 2011 - 14:45:22 PDT)
[AMBER] mmpbsa.pl energy decompistion stopped Eliac Brown (Mon Mar 21 2011 - 16:41:36 PDT)
- Re: [AMBER] mmpbsa.pl energy decompistion stopped Jason Swails (Mon Mar 21 2011 - 18:24:01 PDT)
  - Re: [AMBER] mmpbsa.pl energy decompistion stopped Eliac Brown (Mon Mar 21 2011 - 19:37:26 PDT)
[AMBER] Parallel amber11 Installation FAIL David Cantu (Mon Mar 21 2011 - 16:49:23 PDT)
- Re: [AMBER] Parallel amber11 Installation FAIL Jason Swails (Mon Mar 21 2011 - 18:13:12 PDT)
  - Re: [AMBER] Parallel amber11 Installation FAIL David Cantu (Mon Mar 21 2011 - 19:07:21 PDT)
[AMBER] Flags of secstruct Alessio Atzori (Tue Mar 22 2011 - 08:14:11 PDT)
- Re: [AMBER] Flags of secstruct Daniel Roe (Tue Mar 22 2011 - 10:46:46 PDT)
  - [AMBER] R: Flags of secstruct Alessio Atzori (Thu Mar 24 2011 - 17:21:59 PDT)
[AMBER] Ptraj crashes and Hbond analysis Kamali Sripathi (Tue Mar 22 2011 - 09:43:37 PDT)
- Re: [AMBER] Ptraj crashes and Hbond analysis Thomas Cheatham III (Tue Mar 22 2011 - 16:33:37 PDT)
  - Re: [AMBER] Ptraj crashes and Hbond analysis Kamali Sripathi (Wed Mar 23 2011 - 06:01:05 PDT)
    - Re: [AMBER] Ptraj crashes and Hbond analysis Daniel Roe (Wed Mar 23 2011 - 06:45:14 PDT)
    - Re: [AMBER] Ptraj crashes and Hbond analysis Kamali Sripathi (Wed Mar 23 2011 - 11:44:45 PDT)
    - Re: [AMBER] Ptraj crashes and Hbond analysis Kamali Sripathi (Thu Mar 24 2011 - 06:36:28 PDT)
  - Re: [AMBER] Ptraj crashes and Hbond analysis Kamali Sripathi (Wed Mar 23 2011 - 11:16:15 PDT)
[AMBER] solvation free energy Jorgen Simonsen (Tue Mar 22 2011 - 11:08:57 PDT)
- Re: [AMBER] solvation free energy David A Case (Tue Mar 22 2011 - 11:42:32 PDT)
[AMBER] average structure pdb file looks wrong Bingwu Yu (Tue Mar 22 2011 - 13:39:03 PDT)
- Re: [AMBER] average structure pdb file looks wrong Thomas Cheatham III (Tue Mar 22 2011 - 16:19:03 PDT)
[AMBER] Doubts in MM-PBSA vani panguluri (Tue Mar 22 2011 - 14:52:00 PDT)
- Re: [AMBER] Doubts in MM-PBSA Jason Swails (Tue Mar 22 2011 - 16:05:02 PDT)
- Re: [AMBER] Doubts in MM-PBSA vani panguluri (Tue Mar 22 2011 - 18:01:30 PDT)
  - Re: [AMBER] Doubts in MM-PBSA Jason Swails (Tue Mar 22 2011 - 18:23:29 PDT)
    - Re: [AMBER] Doubts in MM-PBSA vani panguluri (Tue Mar 22 2011 - 21:44:52 PDT)
    - Re: [AMBER] Doubts in MM-PBSA Bill Miller III (Wed Mar 23 2011 - 06:57:05 PDT)
[AMBER] Residuegen Usage Seungyeul Yoo (Tue Mar 22 2011 - 15:26:03 PDT)
[AMBER] compiling AmberTools1.4 with -cuda flag Robert Wohlhueter (Tue Mar 22 2011 - 15:46:56 PDT)
- Re: [AMBER] compiling AmberTools1.4 with -cuda flag Jason Swails (Tue Mar 22 2011 - 16:06:36 PDT)
- Re: [AMBER] compiling AmberTools1.4 with -cuda flag Ross Walker (Tue Mar 22 2011 - 16:09:24 PDT)
[AMBER] how to print out frames from conflib and lmod_traj arrays in NAB Sidney Elmer (Tue Mar 22 2011 - 18:10:43 PDT)
[AMBER] Nmode error of MMPBSA.py 陳昭同 (Wed Mar 23 2011 - 02:30:36 PDT)
- Re: [AMBER] Nmode error of MMPBSA.py Dwight McGee (Wed Mar 23 2011 - 06:17:03 PDT)
[AMBER] Atom name convention/conversion in antechamber thomas.fox.boehringer-ingelheim.com (Wed Mar 23 2011 - 03:47:26 PDT)
- Re: [AMBER] Atom name convention/conversion in antechamber David A Case (Thu Mar 24 2011 - 06:24:11 PDT)
  - [AMBER] How to analysis radius of gyration? Catein Catherine (Thu Mar 24 2011 - 07:50:34 PDT)
    - Re: [AMBER] How to analysis radius of gyration? Carlos Simmerling (Thu Mar 24 2011 - 07:56:14 PDT)
  - Re: [AMBER] Atom name convention/conversion in antechamber thomas.fox.boehringer-ingelheim.com (Thu Mar 24 2011 - 08:42:50 PDT)
    - Re: [AMBER] Atom name convention/conversion in antechamber Mahmoud Soliman (Thu Mar 24 2011 - 09:12:47 PDT)
    - Re: [AMBER] Atom name convention/conversion in antechamber case (Sat Mar 26 2011 - 17:32:53 PDT)
    - Re: [AMBER] Atom name convention/conversion in antechamber Francesco Pietra (Sun Mar 27 2011 - 02:11:56 PDT)
    - Re: [AMBER] Atom name convention/conversion in antechamber thomas.fox.boehringer-ingelheim.com (Mon Mar 28 2011 - 23:45:09 PDT)
    - Re: [AMBER] Atom name convention/conversion in antechamber David A Case (Tue Mar 29 2011 - 04:54:04 PDT)
    - Re: [AMBER] Atom name convention/conversion in antechamber Jason Swails (Tue Mar 29 2011 - 08:46:23 PDT)
[AMBER] Perl Vs Python in MMPBSA calculations in Amber 10 Mahmoud Soliman (Wed Mar 23 2011 - 06:52:04 PDT)
- Re: [AMBER] Perl Vs Python in MMPBSA calculations in Amber 10 Bill Miller III (Wed Mar 23 2011 - 06:53:43 PDT)
  - Re: [AMBER] Perl Vs Python in MMPBSA calculations in Amber 10 Mahmoud Soliman (Wed Mar 23 2011 - 07:23:49 PDT)
[AMBER] scientific question on decomposition analysis in pbsa calculation Mahmoud Soliman (Wed Mar 23 2011 - 07:20:37 PDT)
- Re: [AMBER] scientific question on decomposition analysis in pbsa calculation Ray Luo, Ph.D. (Wed Mar 23 2011 - 07:24:52 PDT)
  - Re: [AMBER] scientific question on decomposition analysis in pbsa calculation Mahmoud Soliman (Wed Mar 23 2011 - 07:38:56 PDT)
    - Re: [AMBER] scientific question on decomposition analysis in pbsa calculation Bill Miller III (Wed Mar 23 2011 - 07:37:59 PDT)
    - Re: [AMBER] scientific question on decomposition analysis in pbsa calculation Mahmoud Soliman (Wed Mar 23 2011 - 08:11:47 PDT)
[AMBER] tleap strange behavior Ignacio J. General (Wed Mar 23 2011 - 08:45:29 PDT)
[AMBER] number of frames read in mmpbsa.py Chris Chris (Wed Mar 23 2011 - 09:44:41 PDT)
- Re: [AMBER] number of frames read in mmpbsa.py Bill Miller III (Wed Mar 23 2011 - 09:52:44 PDT)
  - Re: [AMBER] number of frames read in mmpbsa.py Bill Miller III (Wed Mar 23 2011 - 09:59:00 PDT)
- Re: [AMBER] number of frames read in mmpbsa.py Dwight McGee (Wed Mar 23 2011 - 10:29:09 PDT)
- Re: [AMBER] number of frames read in mmpbsa.py Jason Swails (Wed Mar 23 2011 - 11:55:04 PDT)
[AMBER] error on atom parameters John S (Wed Mar 23 2011 - 11:07:47 PDT)
- Re: [AMBER] error on atom parameters Jason Swails (Wed Mar 23 2011 - 12:03:56 PDT)
[AMBER] how to minimize a protein-ligand system with the protein constrained I.Haldoupis (Wed Mar 23 2011 - 13:09:13 PDT)
- Re: [AMBER] how to minimize a protein-ligand system with the protein constrained Per Jr. Greisen (Wed Mar 23 2011 - 13:14:44 PDT)
  - Re: [AMBER] how to minimize a protein-ligand system with the protein constrained Haldoupis I. (Wed Mar 23 2011 - 14:28:41 PDT)
    - Re: [AMBER] how to minimize a protein-ligand system with the protein constrained Jason Swails (Wed Mar 23 2011 - 17:40:46 PDT)
[AMBER] odd output from rms measurement Chris Chris (Wed Mar 23 2011 - 14:55:44 PDT)
- Re: [AMBER] odd output from rms measurement Carlos Simmerling (Wed Mar 23 2011 - 15:15:58 PDT)
  - Re: [AMBER] odd output from rms measurement Chris Chris (Wed Mar 23 2011 - 16:50:11 PDT)
    - Re: [AMBER] odd output from rms measurement Carlos Simmerling (Wed Mar 23 2011 - 17:24:58 PDT)
    - Re: [AMBER] odd output from rms measurement Chris Chris (Wed Mar 23 2011 - 18:33:52 PDT)
    - Re: [AMBER] odd output from rms measurement Jason Swails (Wed Mar 23 2011 - 18:43:12 PDT)
    - Re: [AMBER] odd output from rms measurement Jason Swails (Wed Mar 23 2011 - 17:35:00 PDT)
    - Re: [AMBER] odd output from rms measurement Daniel Roe (Thu Mar 24 2011 - 00:02:13 PDT)
- Re: [AMBER] odd output from rms measurement 姜笑楠 (Thu Mar 24 2011 - 00:31:34 PDT)
  - Re: [AMBER] odd output from rms measurement Sangita Kachhap (Thu Mar 24 2011 - 02:54:29 PDT)
  - Re: [AMBER] odd output from rms measurement Jason Swails (Thu Mar 24 2011 - 08:41:54 PDT)
[AMBER] PMF calculations in Amber 10 Mahmoud Soliman (Wed Mar 23 2011 - 16:17:28 PDT)
- Re: [AMBER] PMF calculations in Amber 10 Jason Swails (Wed Mar 23 2011 - 16:32:03 PDT)
  - Re: [AMBER] PMF calculations in Amber 10 Dmitry Nilov (Wed Mar 23 2011 - 22:11:02 PDT)
[AMBER] pmemd and generalized NMR torsional restraints in AMBER10 Ilyas Yildirim (Wed Mar 23 2011 - 16:48:27 PDT)
- Re: [AMBER] pmemd and generalized NMR torsional restraints in AMBER10 Jason Swails (Wed Mar 23 2011 - 17:08:15 PDT)
  - Re: [AMBER] pmemd and generalized NMR torsional restraints in AMBER10 Jason Swails (Wed Mar 23 2011 - 17:10:28 PDT)
    - Re: [AMBER] pmemd and generalized NMR torsional restraints in AMBER10 Ilyas Yildirim (Wed Mar 23 2011 - 17:16:04 PDT)
  - Re: [AMBER] pmemd and generalized NMR torsional restraints in AMBER10 Ilyas Yildirim (Wed Mar 23 2011 - 17:14:03 PDT)
    - Re: [AMBER] pmemd and generalized NMR torsional restraints in AMBER10 Jason Swails (Wed Mar 23 2011 - 17:18:52 PDT)
    - Re: [AMBER] pmemd and generalized NMR torsional restraints in AMBER10 Ilyas Yildirim (Wed Mar 23 2011 - 17:24:11 PDT)
[AMBER] extract vdw energy Yuan Ding (Wed Mar 23 2011 - 17:41:33 PDT)
- Re: [AMBER] extract vdw energy Jason Swails (Wed Mar 23 2011 - 18:35:31 PDT)
  - Re: [AMBER] extract vdw energy Yuan Ding (Wed Mar 23 2011 - 18:41:07 PDT)
[AMBER] unsubscribe Jack Lei (Wed Mar 23 2011 - 22:29:20 PDT)
[AMBER] Amber 姜笑楠 (Wed Mar 23 2011 - 23:50:08 PDT)
- Re: [AMBER] Amber Jason Swails (Thu Mar 24 2011 - 08:21:56 PDT)
- Re: [AMBER] Amber David A Case (Thu Mar 24 2011 - 08:34:47 PDT)
[AMBER] How do I plot the angle population distribution Bingwu Yu (Thu Mar 24 2011 - 06:42:36 PDT)
- Re: [AMBER] How do I plot the angle population distribution Jason Swails (Thu Mar 24 2011 - 08:31:21 PDT)
  - [AMBER] Any manual for python or perl to transform a matrix for data analysis? Catein Catherine (Fri Mar 25 2011 - 00:46:53 PDT)
    - Re: [AMBER] Any manual for python or perl to transform a matrix for data analysis? Per Jr. Greisen (Fri Mar 25 2011 - 00:55:13 PDT)
    - Re: [AMBER] Any manual for python or perl to transform a matrix for data analysis? Catein Catherine (Fri Mar 25 2011 - 01:06:14 PDT)
    - [AMBER] Tools to calculate free energies landscape from the MD simulation without doing PMF? Catein Catherine (Fri Mar 25 2011 - 01:13:33 PDT)
    - Re: [AMBER] Tools to calculate free energies landscape from the MD simulation without doing PMF? steinbrt.rci.rutgers.edu (Fri Mar 25 2011 - 01:25:37 PDT)
    - Re: [AMBER] Tools to calculate free energies landscape from the MD simulation without doing PMF? Gustavo Seabra (Fri Mar 25 2011 - 05:33:18 PDT)
    - Re: [AMBER] Any manual for python or perl to transform a matrix for data analysis? steinbrt.rci.rutgers.edu (Fri Mar 25 2011 - 01:31:02 PDT)
    - Re: [AMBER] Any manual for python or perl to transform a matrix for data analysis? Jason Swails (Fri Mar 25 2011 - 08:23:50 PDT)
    - Re: [AMBER] Any manual for python or perl to transform a matrix for data analysis? M. Shahid (Fri Mar 25 2011 - 13:57:33 PDT)
[AMBER] ptraj problems Christoph Malisi (Thu Mar 24 2011 - 07:05:42 PDT)
- [AMBER] How to get the free energy landscape from a MD simulation? Catein Catherine (Thu Mar 24 2011 - 07:55:19 PDT)
  - Re: [AMBER] How to get the free energy landscape from a MD simulation? steinbrt.rci.rutgers.edu (Thu Mar 24 2011 - 08:04:03 PDT)
    - Re: [AMBER] How to get the free energy landscape from a MD simulation? Mahmoud Soliman (Thu Mar 24 2011 - 08:23:10 PDT)
    - Re: [AMBER] How to get the free energy landscape from a MD simulation? Adrian Roitberg (Thu Mar 24 2011 - 08:23:24 PDT)
    - Re: [AMBER] How to get the free energy landscape from a MD simulation? David A Case (Thu Mar 24 2011 - 08:44:16 PDT)
    - Re: [AMBER] How to get the free energy landscape from a MD simulation? Mahmoud Soliman (Thu Mar 24 2011 - 09:06:25 PDT)
    - Re: [AMBER] How to get the free energy landscape from a MD simulation? steinbrt.rci.rutgers.edu (Thu Mar 24 2011 - 08:27:48 PDT)
    - Re: [AMBER] How to get the free energy landscape from a MD simulation? Ilyas Yildirim (Thu Mar 24 2011 - 09:25:00 PDT)
    - Re: [AMBER] How to get the free energy landscape from a MD simulation? Mahmoud Soliman (Thu Mar 24 2011 - 10:50:19 PDT)
    - Re: [AMBER] How to get the free energy landscape from a MD simulation? Ilyas Yildirim (Thu Mar 24 2011 - 11:33:28 PDT)
    - Re: [AMBER] How to get the free energy landscape from a MD simulation? Mahmoud Soliman (Thu Mar 24 2011 - 12:08:30 PDT)
    - [AMBER] Amber CUDA calcualtion on GeForce GTX 590 ? Marek Maly (Wed Mar 30 2011 - 02:39:41 PDT)
    - Re: [AMBER] Amber CUDA calcualtion on GeForce GTX 590 ? filip fratev (Wed Mar 30 2011 - 05:08:35 PDT)
    - Re: [AMBER] Amber CUDA calcualtion on GeForce GTX 590 ? Marek Maly (Wed Mar 30 2011 - 05:34:30 PDT)
    - Re: [AMBER] Amber CUDA calcualtion on GeForce GTX 590 ? Gould, Ian R (Wed Mar 30 2011 - 06:09:19 PDT)
    - Re: [AMBER] Amber CUDA calcualtion on GeForce GTX 590 ? Marek Maly (Wed Mar 30 2011 - 06:48:35 PDT)
    - Re: [AMBER] Amber CUDA calcualtion on GeForce GTX 590 ? filip fratev (Wed Mar 30 2011 - 08:29:13 PDT)
    - Re: [AMBER] Amber CUDA calcualtion on GeForce GTX 590 ? Marek Maly (Wed Mar 30 2011 - 08:24:07 PDT)
    - Re: [AMBER] Amber CUDA calcualtion on GeForce GTX 590 ? filip fratev (Wed Mar 30 2011 - 08:26:29 PDT)
    - Re: [AMBER] Amber CUDA calcualtion on GeForce GTX 590 ? Ross Walker (Wed Mar 30 2011 - 11:29:58 PDT)
    - Re: [AMBER] Amber CUDA calcualtion on GeForce GTX 590 ? Scott Le Grand (Wed Mar 30 2011 - 11:37:21 PDT)
    - Re: [AMBER] Amber CUDA calcualtion on GeForce GTX 590 ? Marek Maly (Wed Mar 30 2011 - 11:59:20 PDT)
    - Re: [AMBER] Amber CUDA calcualtion on GeForce GTX 590 ? Ross Walker (Wed Mar 30 2011 - 12:21:54 PDT)
    - Re: [AMBER] Amber CUDA calcualtion on GeForce GTX 590 ? Marek Maly (Wed Mar 30 2011 - 12:26:50 PDT)
    - Re: [AMBER] Amber CUDA calcualtion on GeForce GTX 590 ? filip fratev (Wed Mar 30 2011 - 15:16:54 PDT)
    - Re: [AMBER] Amber CUDA calcualtion on GeForce GTX 590 ? Ross Walker (Wed Mar 30 2011 - 15:48:37 PDT)
    - Re: [AMBER] Amber CUDA calcualtion on GeForce GTX 590 ? filip fratev (Wed Mar 30 2011 - 16:17:34 PDT)
    - Re: [AMBER] Amber CUDA calcualtion on GeForce GTX 590 ? Marek Maly (Thu Mar 31 2011 - 02:34:38 PDT)
    - Re: [AMBER] Amber CUDA calcualtion on GeForce GTX 590 ? Ross Walker (Thu Mar 31 2011 - 11:23:31 PDT)
    - Re: [AMBER] Amber CUDA calcualtion on GeForce GTX 590 ? Marek Maly (Fri Apr 01 2011 - 03:32:12 PDT)
    - Re: [AMBER] Amber CUDA calcualtion on GeForce GTX 590 ? filip fratev (Thu Apr 07 2011 - 16:52:35 PDT)
    - Re: [AMBER] Amber CUDA calcualtion on GeForce GTX 590 ? Ross Walker (Thu Apr 07 2011 - 17:22:12 PDT)
    - Re: [AMBER] Amber CUDA calcualtion on GeForce GTX 590 ? Marek Maly (Thu Apr 07 2011 - 17:53:04 PDT)
    - Re: [AMBER] Amber CUDA calcualtion on GeForce GTX 590 ? -Test results filip fratev (Fri Apr 08 2011 - 02:04:22 PDT)
    - Re: [AMBER] Amber CUDA calcualtion on GeForce GTX 590 ? filip fratev (Sat Apr 09 2011 - 09:21:32 PDT)
    - Re: [AMBER] Amber CUDA calcualtion on GeForce GTX 590 ? Jason Swails (Sat Apr 09 2011 - 10:31:16 PDT)
    - Re: [AMBER] Amber CUDA calcualtion on GeForce GTX 590 ? Ross Walker (Sat Apr 09 2011 - 21:29:39 PDT)
    - Re: [AMBER] Amber CUDA calcualtion on GeForce GTX 590 ? GTX580 tests? filip fratev (Mon Apr 11 2011 - 22:07:07 PDT)
    - Re: [AMBER] Amber CUDA calcualtion on GeForce GTX 590 ? Scott Le Grand (Thu Mar 31 2011 - 12:33:49 PDT)
    - [AMBER] Can I use PMF to study protein-protein complex formation? Catein Catherine (Mon Apr 04 2011 - 08:51:30 PDT)
    - Re: [AMBER] Amber CUDA calcualtion on GeForce GTX 590 ? Dmitry Mukha (Wed Mar 30 2011 - 12:24:15 PDT)
- Re: [AMBER] ptraj problems Jason Swails (Thu Mar 24 2011 - 08:35:14 PDT)
[AMBER] ptraj: box information for truncated octahedron thomas.fox.boehringer-ingelheim.com (Thu Mar 24 2011 - 10:10:35 PDT)
- Re: [AMBER] ptraj: box information for truncated octahedron Ignacio J. General (Thu Mar 24 2011 - 10:24:08 PDT)
- Re: [AMBER] ptraj: box information for truncated octahedron thomas.fox.boehringer-ingelheim.com (Thu Mar 24 2011 - 11:25:24 PDT)
[AMBER] usage of 2drms John S (Thu Mar 24 2011 - 10:12:36 PDT)
[AMBER] Sander was terminating in the midddle vani panguluri (Thu Mar 24 2011 - 10:47:10 PDT)
- Re: [AMBER] Sander was terminating in the midddle Ben Roberts (Thu Mar 24 2011 - 10:54:56 PDT)
  - Re: [AMBER] Sander was terminating in the midddle vani panguluri (Thu Mar 24 2011 - 11:02:06 PDT)
- Re: [AMBER] Sander was terminating in the midddle Jason Swails (Thu Mar 24 2011 - 10:56:05 PDT)
  - Re: [AMBER] Sander was terminating in the midddle vani panguluri (Thu Mar 24 2011 - 11:09:13 PDT)
- Re: [AMBER] Sander was terminating in the midddle Sangita Kachhap (Thu Mar 24 2011 - 11:28:15 PDT)
  - Re: [AMBER] Sander was terminating in the midddle vani panguluri (Thu Mar 24 2011 - 23:08:39 PDT)
    - Re: [AMBER] Sander was terminating in the midddle Sangita Kachhap (Fri Mar 25 2011 - 07:05:56 PDT)
    - [AMBER] Extract binding free energy for each snapshot Wei Huang (Fri Mar 25 2011 - 07:18:07 PDT)
    - Re: [AMBER] Extract binding free energy for each snapshot Dwight McGee (Fri Mar 25 2011 - 07:39:05 PDT)
    - Re: [AMBER] Extract binding free energy for each snapshot Jason Swails (Fri Mar 25 2011 - 07:54:57 PDT)
    - Re: [AMBER] Extract binding free energy for each snapshot Jason Swails (Fri Mar 25 2011 - 07:56:36 PDT)
    - Re: [AMBER] Extract binding free energy for each snapshot Wei Huang (Fri Mar 25 2011 - 08:17:07 PDT)
[AMBER] deleting protein atoms from prmtop topology files using rdparm g t (Thu Mar 24 2011 - 12:01:36 PDT)
- Re: [AMBER] deleting protein atoms from prmtop topology files using rdparm Jason Swails (Thu Mar 24 2011 - 13:05:58 PDT)
- Re: [AMBER] deleting protein atoms from prmtop topology files using rdparm Chris Chris (Thu Mar 24 2011 - 14:29:25 PDT)
  - Re: [AMBER] deleting protein atoms from prmtop topology files using rdparm g t (Fri Mar 25 2011 - 03:41:55 PDT)
- Re: [AMBER] deleting protein atoms from prmtop topology files using rdparm Bill Ross (Fri Mar 25 2011 - 10:38:19 PDT)
  - Re: [AMBER] deleting protein atoms from prmtop topology files using rdparm g t (Wed Mar 30 2011 - 08:14:59 PDT)
[AMBER] positive GBtot value Hoshin Kim (Thu Mar 24 2011 - 18:02:30 PDT)
- Re: [AMBER] positive GBtot value Jason Swails (Thu Mar 24 2011 - 18:33:23 PDT)
[AMBER] Error with MM-PBSA perl file for pairwise residue decomposition Monika Sharma (Thu Mar 24 2011 - 20:09:16 PDT)
- Re: [AMBER] Error with MM-PBSA perl file for pairwise residue decomposition Jason Swails (Thu Mar 24 2011 - 20:31:44 PDT)
  - Re: [AMBER] Error with MM-PBSA perl file for pairwise residue decomposition Monika Sharma (Fri Mar 25 2011 - 03:18:59 PDT)
    - Re: [AMBER] Error with MM-PBSA perl file for pairwise residue decomposition Bill Miller III (Fri Mar 25 2011 - 04:07:45 PDT)
[AMBER] regrding the anal working dhilip kumar ramalingam (Thu Mar 24 2011 - 22:28:32 PDT)
[AMBER] Help: Clustering trajectories based on dihedral angle? Rajeswari A. (Fri Mar 25 2011 - 01:38:00 PDT)
- Re: [AMBER] Help: Clustering trajectories based on dihedral angle? Thomas Cheatham III (Fri Mar 25 2011 - 15:35:25 PDT)
  - Re: [AMBER] Help: Clustering trajectories based on dihedral angle? Daniel Roe (Fri Mar 25 2011 - 18:43:59 PDT)
    - Re: [AMBER] Help: Clustering trajectories based on dihedral angle? Rajeswari A. (Mon Mar 28 2011 - 05:40:37 PDT)
[AMBER] compiling with cuda Jacopo Sgrignani (Fri Mar 25 2011 - 01:47:49 PDT)
- Re: [AMBER] compiling with cuda Jason Swails (Fri Mar 25 2011 - 08:16:04 PDT)
- Re: [AMBER] compiling with cuda Jacopo Sgrignani (Fri Mar 25 2011 - 08:21:44 PDT)
- Re: [AMBER] compiling with cuda Scott Le Grand (Fri Mar 25 2011 - 08:53:55 PDT)
[AMBER] regarding anal function dhilip kumar ramalingam (Fri Mar 25 2011 - 04:08:02 PDT)
[AMBER] Error: vlimit exceeded for step pankhuri arora (Fri Mar 25 2011 - 04:38:11 PDT)
- Re: [AMBER] Error: vlimit exceeded for step Jason Swails (Fri Mar 25 2011 - 08:09:43 PDT)
[AMBER] Amber Installation error Hirdesh Kumar (Fri Mar 25 2011 - 05:22:25 PDT)
- Re: [AMBER] Amber Installation error Jason Swails (Fri Mar 25 2011 - 08:12:38 PDT)
[AMBER] CUDA Installation URL ros (Fri Mar 25 2011 - 09:40:22 PDT)
[AMBER] Neutral Lysine (LYN) not calculated in MM_PBSA Rubben Torella (Fri Mar 25 2011 - 10:34:17 PDT)
- Re: [AMBER] Neutral Lysine (LYN) not calculated in MM_PBSA Jason Swails (Fri Mar 25 2011 - 14:01:19 PDT)
  - Re: [AMBER] Neutral Lysine (LYN) not calculated in MM_PBSA Rubben Torella (Tue Mar 29 2011 - 03:50:57 PDT)
    - Re: [AMBER] Neutral Lysine (LYN) not calculated in MM_PBSA Jason Swails (Tue Mar 29 2011 - 08:16:53 PDT)
[AMBER] pmemd and nmr restraint marc gueroult (Fri Mar 25 2011 - 10:53:21 PDT)
- Re: [AMBER] pmemd and nmr restraint David A Case (Fri Mar 25 2011 - 12:18:16 PDT)
  - Re: [AMBER] pmemd and nmr restraint marc gueroult (Thu Mar 31 2011 - 08:56:16 PDT)
[AMBER] solvatecap Lucio Ferella (Fri Mar 25 2011 - 11:07:51 PDT)
[AMBER] nmode calculations amit dong (Fri Mar 25 2011 - 11:12:24 PDT)
- Re: [AMBER] nmode calculations Bill Miller III (Fri Mar 25 2011 - 11:23:33 PDT)
  - Re: [AMBER] nmode calculations amit dong (Fri Mar 25 2011 - 11:39:40 PDT)
    - Re: [AMBER] nmode calculations Bill Miller III (Fri Mar 25 2011 - 12:00:42 PDT)
[AMBER] Spatial distribution function Ganesh Kamath (Fri Mar 25 2011 - 11:19:24 PDT)
[AMBER] how critical charge neutralization of a system Mahmoud Soliman (Fri Mar 25 2011 - 14:02:35 PDT)
- Re: [AMBER] how critical charge neutralization of a system Jason Swails (Fri Mar 25 2011 - 15:39:52 PDT)
[AMBER] AMD Opteron system - compiling pmemd with intel or gfortran? Ilyas Yildirim (Fri Mar 25 2011 - 13:54:22 PDT)
- Re: [AMBER] AMD Opteron system - compiling pmemd with intel or gfortran? Sergio R Aragon (Fri Mar 25 2011 - 16:42:19 PDT)
  - Re: [AMBER] AMD Opteron system - compiling pmemd with intel or gfortran? Jason Swails (Fri Mar 25 2011 - 19:21:07 PDT)
    - Re: [AMBER] AMD Opteron system - compiling pmemd with intel or gfortran? Sergio R Aragon (Fri Mar 25 2011 - 22:21:39 PDT)
    - Re: [AMBER] AMD Opteron system - compiling pmemd with intel or gfortran? Jason Swails (Fri Mar 25 2011 - 22:44:48 PDT)
[AMBER] QM/MM error in amber 10 Mahmoud Soliman (Fri Mar 25 2011 - 15:21:16 PDT)
- Re: [AMBER] QM/MM error in amber 10 Yuan Yao (Fri Mar 25 2011 - 15:16:29 PDT)
  - Re: [AMBER] QM/MM error in amber 10 Yuan Yao (Fri Mar 25 2011 - 15:20:04 PDT)
- Re: [AMBER] QM/MM error in amber 10 Jason Swails (Fri Mar 25 2011 - 15:32:25 PDT)
  - Re: [AMBER] QM/MM error in amber 10 Mahmoud Soliman (Sun Mar 27 2011 - 22:46:47 PDT)
[AMBER] AmberTools1.4 question markus metz (Sat Mar 26 2011 - 10:40:56 PDT)
- Re: [AMBER] AmberTools1.4 question Carlos Simmerling (Sat Mar 26 2011 - 10:46:24 PDT)
[AMBER] ff10 Jorgen Simonsen (Sat Mar 26 2011 - 11:39:44 PDT)
- Re: [AMBER] ff10 case (Sat Mar 26 2011 - 14:26:17 PDT)
  - Re: [AMBER] ff10 Jorgen Simonsen (Sun Mar 27 2011 - 00:30:28 PDT)
    - Re: [AMBER] ff10 Jason Swails (Sun Mar 27 2011 - 01:32:19 PDT)
    - Re: [AMBER] ff10 Jorgen Simonsen (Sun Mar 27 2011 - 01:40:55 PDT)
    - Re: [AMBER] ff10 Jason Swails (Sun Mar 27 2011 - 01:45:06 PDT)
    - Re: [AMBER] ff10 Jorgen Simonsen (Sun Mar 27 2011 - 01:47:53 PDT)
[AMBER] GBSA calculations using mm_pbsa.pl manikanthan bhavaraju (Sat Mar 26 2011 - 17:59:38 PDT)
[AMBER] Keep getting LINMIN error. Not sure how to progress. I.Haldoupis (Mon Mar 28 2011 - 05:27:00 PDT)
- Re: [AMBER] Keep getting LINMIN error. Not sure how to progress. Carlos Simmerling (Mon Mar 28 2011 - 05:39:07 PDT)
- Re: [AMBER] Keep getting LINMIN error. Not sure how to progress. Hugh Heldenbrand (Mon Mar 28 2011 - 05:40:50 PDT)
  - Re: [AMBER] Keep getting LINMIN error. Not sure how to progress. Jason Swails (Mon Mar 28 2011 - 08:32:14 PDT)
    - Re: [AMBER] Keep getting LINMIN error. Not sure how to progress. I.Haldoupis (Tue Mar 29 2011 - 03:15:15 PDT)
- Re: [AMBER] Keep getting LINMIN error. Not sure how to progress. Bill Ross (Mon Mar 28 2011 - 11:39:39 PDT)
[AMBER] enzyme MD trajectory looks funny Mahmoud Soliman (Mon Mar 28 2011 - 06:10:38 PDT)
- Re: [AMBER] enzyme MD trajectory looks funny Per Jr. Greisen (Mon Mar 28 2011 - 06:07:55 PDT)
  - Re: [AMBER] enzyme MD trajectory looks funny Rajeswari A. (Mon Mar 28 2011 - 06:19:02 PDT)
  - Re: [AMBER] enzyme MD trajectory looks funny Mahmoud Soliman (Mon Mar 28 2011 - 06:37:21 PDT)
    - Re: [AMBER] enzyme MD trajectory looks funny Jason Swails (Mon Mar 28 2011 - 08:34:23 PDT)
- Re: [AMBER] enzyme MD trajectory looks funny Dmitry Nilov (Mon Mar 28 2011 - 06:20:53 PDT)
  - Re: [AMBER] enzyme MD trajectory looks funny Mahmoud Soliman (Mon Mar 28 2011 - 06:34:35 PDT)
[AMBER] water box deforms during MD Mahmoud Soliman (Mon Mar 28 2011 - 07:02:20 PDT)
- Re: [AMBER] water box deforms during MD steinbrt.rci.rutgers.edu (Mon Mar 28 2011 - 07:05:23 PDT)
  - Re: [AMBER] water box deforms during MD Mahmoud Soliman (Mon Mar 28 2011 - 08:49:06 PDT)
- Re: [AMBER] water box deforms during MD Dmitry Nilov (Mon Mar 28 2011 - 07:17:22 PDT)
[AMBER] RESP: optimized charges not reasonable Ignacio Faustino Plo (Mon Mar 28 2011 - 09:59:52 PDT)
- Re: [AMBER] RESP: optimized charges not reasonable FyD (Tue Mar 29 2011 - 01:36:54 PDT)
  - Re: [AMBER] RESP: optimized charges not reasonable Ignacio Faustino Plo (Tue Mar 29 2011 - 03:46:12 PDT)
- Re: [AMBER] RESP: optimized charges not reasonable FyD (Tue Mar 29 2011 - 04:54:03 PDT)
[AMBER] problem with peptide simulations Hashem Taha (Mon Mar 28 2011 - 12:05:55 PDT)
- Re: [AMBER] problem with peptide simulations Jason Swails (Mon Mar 28 2011 - 12:29:07 PDT)
  - Re: [AMBER] problem with peptide simulations Hashem Taha (Mon Mar 28 2011 - 13:00:58 PDT)
    - Re: [AMBER] problem with peptide simulations Jason Swails (Mon Mar 28 2011 - 13:27:15 PDT)
- Re: [AMBER] problem with peptide simulations David A Case (Mon Mar 28 2011 - 13:04:33 PDT)
[AMBER] ptraj minimum rmsd in presence of homotopic atoms Alexander Metz (Tue Mar 29 2011 - 02:21:21 PDT)
[AMBER] script problem Mahmoud Soliman (Tue Mar 29 2011 - 14:16:15 PDT)
- Re: [AMBER] script problem Jason Swails (Tue Mar 29 2011 - 14:15:22 PDT)
  - Re: [AMBER] script problem Mahmoud Soliman (Tue Mar 29 2011 - 14:44:46 PDT)
[AMBER] nmropt modes for GPU accelerated pmemd 11 Andre Serobian (Wed Mar 30 2011 - 00:24:04 PDT)
- Re: [AMBER] nmropt modes for GPU accelerated pmemd 11 Ross Walker (Wed Mar 30 2011 - 11:27:10 PDT)
- Re: [AMBER] nmropt modes for GPU accelerated pmemd 11 Andre Serobian (Wed Mar 30 2011 - 12:43:10 PDT)
  - Re: [AMBER] nmropt modes for GPU accelerated pmemd 11 Jason Swails (Wed Mar 30 2011 - 12:59:03 PDT)
    - Re: [AMBER] nmropt modes for GPU accelerated pmemd 11 Andre Serobian (Thu Nov 10 2011 - 01:58:37 PST)
    - Re: [AMBER] nmropt modes for GPU accelerated pmemd 11 Ross Walker (Thu Nov 10 2011 - 07:15:53 PST)
- Re: [AMBER] nmropt modes for GPU accelerated pmemd 11 Andre Serobian (Wed Mar 30 2011 - 13:09:43 PDT)
- Re: [AMBER] nmropt modes for GPU accelerated pmemd 11 serobian.a.student.unsw.edu.au (Thu Nov 10 2011 - 15:21:40 PST)
[AMBER] positional restraint on crystal water Sangita Kachhap (Wed Mar 30 2011 - 00:30:16 PDT)
- Re: [AMBER] positional restraint on crystal water Dmitry Nilov (Wed Mar 30 2011 - 01:26:37 PDT)
  - Re: [AMBER] positional restraint on crystal water Sangita Kachhap (Wed Mar 30 2011 - 01:45:42 PDT)
    - Re: [AMBER] positional restraint on crystal water Dmitry Nilov (Wed Mar 30 2011 - 02:03:18 PDT)
    - Re: [AMBER] positional restraint on crystal water Dmitry Nilov (Wed Mar 30 2011 - 02:18:17 PDT)
    - Re: [AMBER] positional restraint on crystal water Sangita Kachhap (Wed Mar 30 2011 - 02:31:53 PDT)
    - Re: [AMBER] positional restraint on crystal water Sangita Kachhap (Wed Mar 30 2011 - 02:40:00 PDT)
    - Re: [AMBER] positional restraint on crystal water Dmitry Nilov (Wed Mar 30 2011 - 02:56:27 PDT)
    - Re: [AMBER] positional restraint on crystal water Sangita Kachhap (Wed Mar 30 2011 - 03:14:44 PDT)
    - Re: [AMBER] positional restraint on crystal water g t (Wed Mar 30 2011 - 09:35:18 PDT)
[AMBER] clustering MD results Jack Lee (Wed Mar 30 2011 - 01:34:06 PDT)
- Re: [AMBER] clustering MD results Thomas Cheatham III (Wed Mar 30 2011 - 14:28:39 PDT)
[AMBER] Exchange Acceptance Ratio Alessio Atzori (Wed Mar 30 2011 - 03:57:36 PDT)
- Re: [AMBER] Exchange Acceptance Ratio Daniel Sindhikara (Wed Mar 30 2011 - 05:00:02 PDT)
  - [AMBER] R: Exchange Acceptance Ratio Alessio Atzori (Wed Mar 30 2011 - 06:21:48 PDT)
    - Re: [AMBER] R: Exchange Acceptance Ratio Carlos Simmerling (Wed Mar 30 2011 - 06:44:25 PDT)
[AMBER] Loading .mol2 file in sleap r smith (Wed Mar 30 2011 - 06:12:15 PDT)
- Re: [AMBER] Loading .mol2 file in sleap Ben Roberts (Wed Mar 30 2011 - 07:43:00 PDT)
  - Re: [AMBER] Loading .mol2 file in sleap r smith (Wed Mar 30 2011 - 09:08:07 PDT)
  - Re: [AMBER] Loading .mol2 file in sleap r smith (Wed Mar 30 2011 - 09:19:21 PDT)
    - Re: [AMBER] Loading .mol2 file in sleap Ben Roberts (Wed Mar 30 2011 - 12:16:20 PDT)
    - Re: [AMBER] Loading .mol2 file in sleap r smith (Wed Mar 30 2011 - 12:30:46 PDT)
    - Re: [AMBER] Loading .mol2 file in sleap Ben Roberts (Wed Mar 30 2011 - 13:19:21 PDT)
    - Re: [AMBER] Loading .mol2 file in sleap case (Wed Mar 30 2011 - 18:52:36 PDT)
    - Re: [AMBER] Loading .mol2 file in sleap Ben Roberts (Wed Mar 30 2011 - 20:16:59 PDT)
    - Re: [AMBER] Loading .mol2 file in sleap r smith (Wed May 04 2011 - 06:04:52 PDT)
    - Re: [AMBER] Loading .mol2 file in sleap Ben Roberts (Wed May 04 2011 - 11:26:37 PDT)
    - Re: [AMBER] Loading .mol2 file in sleap r smith (Wed May 04 2011 - 13:01:24 PDT)
    - Re: [AMBER] Loading .mol2 file in sleap Jason Swails (Wed May 04 2011 - 19:05:21 PDT)
    - [AMBER] How to use perl to replace number to txt? Catein Catherine (Thu Mar 31 2011 - 02:48:48 PDT)
    - Re: [AMBER] How to use perl to replace number to txt? Hannes Loeffler (Thu Mar 31 2011 - 03:19:11 PDT)
    - Re: [AMBER] How to use perl to replace number to txt? M. L. Dodson (Thu Mar 31 2011 - 07:31:36 PDT)
    - Re: [AMBER] How to use perl to replace number to txt? Chris Chris (Thu Mar 31 2011 - 05:17:14 PDT)
[AMBER] The validity of a per-residue decomposition in amber g t (Wed Mar 30 2011 - 06:36:33 PDT)
- Re: [AMBER] The validity of a per-residue decomposition in amber Carlos Simmerling (Wed Mar 30 2011 - 06:47:34 PDT)
  - Re: [AMBER] The validity of a per-residue decomposition in amber g t (Wed Mar 30 2011 - 08:13:26 PDT)
    - Re: [AMBER] The validity of a per-residue decomposition in amber David A Case (Thu Mar 31 2011 - 05:53:02 PDT)
[AMBER] Atom distribution in PMEMD.cuda Francesco Oteri (Wed Mar 30 2011 - 07:02:31 PDT)
[AMBER] Implicit simulation Elisa Frezza (Wed Mar 30 2011 - 10:03:30 PDT)
- Re: [AMBER] Implicit simulation Jason Swails (Wed Mar 30 2011 - 10:13:40 PDT)
  - Re: [AMBER] Implicit simulation Elisa Frezza (Wed Mar 30 2011 - 10:17:12 PDT)
[AMBER] new residue with amoeba Daniel Chipman (Wed Mar 30 2011 - 12:54:11 PDT)
[AMBER] segmentation fault when using mmpbsa.py Chris Chris (Wed Mar 30 2011 - 15:03:46 PDT)
- Re: [AMBER] segmentation fault when using mmpbsa.py Jason Swails (Wed Mar 30 2011 - 16:23:43 PDT)
[AMBER] Add Residue at N-terminal setyanto md (Thu Mar 31 2011 - 06:57:17 PDT)
- Re: [AMBER] Add Residue at N-terminal Dmitry Nilov (Thu Mar 31 2011 - 07:09:54 PDT)
  - Re: [AMBER] Add Residue at N-terminal setyanto md (Thu Mar 31 2011 - 07:17:59 PDT)
[AMBER] PMEMD on the Open Science Grid Steven Cox (Thu Mar 31 2011 - 07:19:42 PDT)
[AMBER] Inconsistencies between reported lines and executed lines in source code Albert Lee (Thu Mar 31 2011 - 11:12:23 PDT)
- Re: [AMBER] Inconsistencies between reported lines and executed lines in source code Adrian Roitberg (Thu Mar 31 2011 - 11:33:19 PDT)
  - Re: [AMBER] Inconsistencies between reported lines and executed lines in source code Albert Lee (Thu Mar 31 2011 - 11:56:06 PDT)
    - Re: [AMBER] Inconsistencies between reported lines and executed lines in source code Jason Swails (Thu Mar 31 2011 - 12:22:01 PDT)
    - Re: [AMBER] Inconsistencies between reported lines and executed lines in source code Albert Lee (Thu Mar 31 2011 - 12:39:13 PDT)
[AMBER] parameter for CNTs Jagur Lambix (Thu Mar 31 2011 - 16:02:14 PDT)
- Re: [AMBER] parameter for CNTs Jason Swails (Thu Mar 31 2011 - 16:54:03 PDT)
  - Re: [AMBER] parameter for CNTs Jagur Lambix (Tue Apr 05 2011 - 15:21:25 PDT)
[AMBER] Ptraj Mask option Rajeswari A. (Fri Apr 01 2011 - 00:03:42 PDT)
- Re: [AMBER] Ptraj Mask option Jason Swails (Fri Apr 01 2011 - 00:44:56 PDT)
  - Re: [AMBER] Ptraj Mask option Rajeswari A. (Fri Apr 01 2011 - 03:00:55 PDT)
[AMBER] bond command in tlaep mish (Fri Apr 01 2011 - 06:20:11 PDT)
- Re: [AMBER] bond command in tlaep Jason Swails (Fri Apr 01 2011 - 08:23:14 PDT)
  - Re: [AMBER] bond command in tlaep mish (Fri Apr 01 2011 - 11:07:36 PDT)
    - Re: [AMBER] bond command in tlaep mish (Wed Apr 20 2011 - 09:31:25 PDT)
    - Re: [AMBER] bond command in tlaep David A Case (Wed Apr 20 2011 - 10:07:06 PDT)
    - Re: [AMBER] bond command in tlaep Catein Catherine (Wed Apr 20 2011 - 23:11:04 PDT)
    - Re: [AMBER] bond command in tlaep juzer stationwala (Wed Apr 20 2011 - 23:17:36 PDT)
    - Re: [AMBER] bond command in tlaep Jason Swails (Thu Apr 21 2011 - 00:11:49 PDT)
- Re: [AMBER] bond command in tlaep Bill Ross (Wed Apr 20 2011 - 10:16:29 PDT)
[AMBER] restart from stopped MMPBSA.py.MPI job Christoph Malisi (Fri Apr 01 2011 - 07:06:04 PDT)
- Re: [AMBER] restart from stopped MMPBSA.py.MPI job Jason Swails (Fri Apr 01 2011 - 08:35:05 PDT)
[AMBER] positive TdS Hector A. Baldoni (Fri Apr 01 2011 - 09:26:01 PDT)
[AMBER] making lib file Mark M Huntress (Fri Apr 01 2011 - 10:57:46 PDT)
- Re: [AMBER] making lib file Jason Swails (Fri Apr 01 2011 - 11:08:55 PDT)
  - Re: [AMBER] making lib file Mark M Huntress (Sat Apr 02 2011 - 07:39:06 PDT)
[AMBER] PBSA calculations for wild type and a mutant Mahmoud Soliman (Fri Apr 01 2011 - 13:15:09 PDT)
- Re: [AMBER] PBSA calculations for wild type and a mutant Bill Miller III (Sat Apr 02 2011 - 07:48:53 PDT)
  - Re: [AMBER] PBSA calculations for wild type and a mutant Mahmoud Soliman (Sat Apr 02 2011 - 10:03:48 PDT)
[AMBER] mm_pbsa.pl error Mahmoud Soliman (Sat Apr 02 2011 - 12:08:18 PDT)
- Re: [AMBER] mm_pbsa.pl error Jason Swails (Sat Apr 02 2011 - 12:01:12 PDT)
  - Re: [AMBER] mm_pbsa.pl error Mahmoud Soliman (Sat Apr 02 2011 - 12:52:46 PDT)
  - Re: [AMBER] mm_pbsa.pl error Mahmoud Soliman (Sat Apr 02 2011 - 15:44:39 PDT)
    - Re: [AMBER] mm_pbsa.pl error Jason Swails (Sat Apr 02 2011 - 16:01:19 PDT)
    - Re: [AMBER] mm_pbsa.pl error Jason Swails (Sat Apr 02 2011 - 16:02:44 PDT)
[AMBER] water mediated interaction Sangita Kachhap (Sun Apr 03 2011 - 08:47:59 PDT)
- [AMBER] opls-aa; ions gromacs (Mon Apr 04 2011 - 03:05:29 PDT)
  - Re: [AMBER] opls-aa; ions David A Case (Mon Apr 04 2011 - 05:20:39 PDT)
[AMBER] ptraj rmsd Sarah Eliabeth Rowe (Mon Apr 04 2011 - 07:00:19 PDT)
- Re: [AMBER] ptraj rmsd Carlos Simmerling (Mon Apr 04 2011 - 07:04:20 PDT)
[AMBER] MMPBSA.py pairwise decomp Christoph Malisi (Mon Apr 04 2011 - 07:11:29 PDT)
- Re: [AMBER] MMPBSA.py pairwise decomp Jason Swails (Mon Apr 04 2011 - 07:24:51 PDT)
  - Re: [AMBER] MMPBSA.py pairwise decomp Christoph Malisi (Mon Apr 04 2011 - 07:35:36 PDT)
    - Re: [AMBER] MMPBSA.py pairwise decomp Jason Swails (Mon Apr 04 2011 - 09:00:21 PDT)
[AMBER] MMPBSA.py ala-scanning output results Jesper Sørensen (Mon Apr 04 2011 - 07:13:17 PDT)
- Re: [AMBER] MMPBSA.py ala-scanning output results Jason Swails (Mon Apr 04 2011 - 09:04:31 PDT)
  - Re: [AMBER] MMPBSA.py ala-scanning output results Jesper Sørensen (Tue Apr 05 2011 - 00:25:47 PDT)
    - Re: [AMBER] MMPBSA.py ala-scanning output results Jason Swails (Tue Apr 05 2011 - 08:40:51 PDT)
    - Re: [AMBER] MMPBSA.py ala-scanning output results Jesper Sørensen (Tue Apr 05 2011 - 10:06:58 PDT)
[AMBER] Question about Amber output file format TAEJIN KIM (Mon Apr 04 2011 - 07:45:51 PDT)
- Re: [AMBER] Question about Amber output file format Jason Swails (Mon Apr 04 2011 - 09:12:53 PDT)
[AMBER] sleap with ff02pol.r1 r smith (Mon Apr 04 2011 - 07:54:19 PDT)
- Re: [AMBER] sleap with ff02pol.r1 Jason Swails (Mon Apr 04 2011 - 10:15:36 PDT)
  - Re: [AMBER] sleap with ff02pol.r1 r smith (Mon Apr 04 2011 - 11:34:59 PDT)
- Re: [AMBER] sleap with ff02pol.r1 Wei Zhang (Mon Apr 04 2011 - 11:33:08 PDT)
  - Re: [AMBER] sleap with ff02pol.r1 r smith (Mon Apr 04 2011 - 11:35:38 PDT)
[AMBER] Umbrella sampling procedure siddesh southekal (Mon Apr 04 2011 - 08:50:15 PDT)
- Re: [AMBER] Umbrella sampling procedure Emmanuel Baribefe Naziga (Mon Apr 04 2011 - 09:07:02 PDT)
[AMBER] No mdcrd file with PMEMD Indrek Morell (Mon Apr 04 2011 - 10:22:14 PDT)
- Re: [AMBER] No mdcrd file with PMEMD Jason Swails (Mon Apr 04 2011 - 11:27:16 PDT)
[AMBER] PMEMD and NEB? patrick wintrode (Mon Apr 04 2011 - 11:53:10 PDT)
- Re: [AMBER] PMEMD and NEB? Carlos Simmerling (Mon Apr 04 2011 - 12:09:35 PDT)
- Re: [AMBER] PMEMD and NEB? Jason Swails (Mon Apr 04 2011 - 12:10:38 PDT)
Re: [AMBER] No mdcrd file with PMEMD reply Jason Swails (Mon Apr 04 2011 - 12:24:56 PDT)
[AMBER] Error im mm_pbsa.pl vani panguluri (Mon Apr 04 2011 - 16:11:40 PDT)
- Re: [AMBER] Error im mm_pbsa.pl Dwight McGee (Tue Apr 05 2011 - 08:37:49 PDT)
  - Re: [AMBER] Error im mm_pbsa.pl vani panguluri (Tue Apr 05 2011 - 11:06:58 PDT)
    - Re: [AMBER] Error im mm_pbsa.pl Jason Swails (Tue Apr 05 2011 - 11:29:23 PDT)
    - Re: [AMBER] Error im mm_pbsa.pl vani panguluri (Tue Apr 05 2011 - 13:44:46 PDT)
    - Re: [AMBER] Error im mm_pbsa.pl Bill Miller III (Tue Apr 05 2011 - 13:56:18 PDT)
    - Re: [AMBER] Error im mm_pbsa.pl vani panguluri (Tue Apr 05 2011 - 15:22:26 PDT)
[AMBER] Sugar ring conformation (QM/MM Vs MM) Mahmoud Soliman (Mon Apr 04 2011 - 21:05:17 PDT)
- Re: [AMBER] Sugar ring conformation (QM/MM Vs MM) Jason Swails (Mon Apr 04 2011 - 21:24:23 PDT)
  - Re: [AMBER] Sugar ring conformation (QM/MM Vs MM) Mahmoud Soliman (Tue Apr 05 2011 - 08:09:40 PDT)
[AMBER] SDSC Dmitry Mukha (Tue Apr 05 2011 - 02:00:53 PDT)
- Re: [AMBER] SDSC Ross Walker (Tue Apr 05 2011 - 10:45:00 PDT)
[AMBER] Modified REMD Almudena Pino (Tue Apr 05 2011 - 04:10:36 PDT)
- Re: [AMBER] Modified REMD Jason Swails (Wed Apr 06 2011 - 14:43:13 PDT)
  - Re: [AMBER] Modified REMD Almudena Pino (Wed Apr 06 2011 - 23:46:12 PDT)
[AMBER] bad atom type Bernhard Poll (Tue Apr 05 2011 - 07:56:34 PDT)
- Re: [AMBER] bad atom type Jason Swails (Wed Apr 06 2011 - 14:31:19 PDT)
  - Re: [AMBER] bad atom type Bernhard Poll (Thu Apr 07 2011 - 01:30:12 PDT)
    - Re: [AMBER] bad atom type Jason Swails (Thu Apr 07 2011 - 08:09:01 PDT)
    - [AMBER] Protein-Drug dissociation PMF: Is large conformational change in protein real or artifacts? Catein Catherine (Thu Apr 07 2011 - 09:10:29 PDT)
    - Re: [AMBER] Protein-Drug dissociation PMF: Is large conformational change in protein real or artifacts? Carlos Simmerling (Thu Apr 07 2011 - 09:21:15 PDT)
    - [AMBER] How to apply restraint based on a reference structure? Catein Catherine (Thu Apr 07 2011 - 10:12:13 PDT)
    - Re: [AMBER] How to apply restraint based on a reference structure? Carlos Simmerling (Thu Apr 07 2011 - 10:16:06 PDT)
    - Re: [AMBER] How to apply restraint based on a reference structure? Catein Catherine (Thu Apr 07 2011 - 10:33:35 PDT)
    - Re: [AMBER] How to apply restraint based on a reference structure? Barbault Florent (Thu Apr 07 2011 - 10:17:08 PDT)
    - Re: [AMBER] How to apply restraint based on a reference structure? Catein Catherine (Thu Apr 07 2011 - 10:30:39 PDT)
    - Re: [AMBER] How to apply restraint based on a reference structure? Ilyas Yildirim (Thu Apr 07 2011 - 10:40:29 PDT)
    - [AMBER] How to apply restraint on the root-mean-square deviation along the z-axis of two proteins Catein Catherine (Thu Apr 07 2011 - 10:18:51 PDT)
    - Re: [AMBER] Protein-Drug dissociation PMF: Is large conformational change in protein real or artifacts? Jérôme Golebiowski (Thu Apr 07 2011 - 09:48:33 PDT)
[AMBER] Solute concentration in MD Lekpa Duukori (Tue Apr 05 2011 - 08:26:09 PDT)
- Re: [AMBER] Solute concentration in MD Francesco Oteri (Mon Apr 11 2011 - 15:50:56 PDT)
  - Re: [AMBER] Solute concentration in MD Lekpa Duukori (Mon Apr 11 2011 - 16:03:14 PDT)
    - [AMBER] packmol and amber11: the solvent box issue Sasha Buzko (Wed Apr 13 2011 - 15:47:16 PDT)
    - Re: [AMBER] packmol and amber11: the solvent box issue Jason Swails (Wed Apr 13 2011 - 15:59:32 PDT)
    - Re: [AMBER] packmol and amber11: the solvent box issue Sasha Buzko (Wed Apr 13 2011 - 16:33:02 PDT)
    - Re: [AMBER] packmol and amber11: the solvent box issue Jason Swails (Wed Apr 13 2011 - 16:53:25 PDT)
    - Re: [AMBER] packmol and amber11: the solvent box issue Sasha Buzko (Wed Apr 13 2011 - 17:07:08 PDT)
    - Re: [AMBER] packmol and amber11: the solvent box issue M. L. Dodson (Wed Apr 13 2011 - 18:30:07 PDT)
    - [AMBER] pmemd.cuda: max pairlist problem with a large system Sasha Buzko (Fri Apr 15 2011 - 13:52:29 PDT)
    - Re: [AMBER] pmemd.cuda: max pairlist problem with a large system Ross Walker (Fri Apr 15 2011 - 14:12:00 PDT)
    - Re: [AMBER] pmemd.cuda: max pairlist problem with a large system Sasha Buzko (Fri Apr 15 2011 - 14:47:23 PDT)
    - Re: [AMBER] packmol and amber11: the solvent box issue M. L. Dodson (Wed Apr 13 2011 - 16:39:25 PDT)
[AMBER] Umbrella sampling Sangita Kachhap (Tue Apr 05 2011 - 10:55:42 PDT)
- Re: [AMBER] Umbrella sampling Carlos Simmerling (Tue Apr 05 2011 - 11:07:18 PDT)
  - Re: [AMBER] Umbrella sampling Sangita Kachhap (Tue Apr 05 2011 - 11:21:17 PDT)
    - Re: [AMBER] Umbrella sampling Carlos Simmerling (Tue Apr 05 2011 - 11:28:22 PDT)
[AMBER] how to estimate the free energy of folding for the C-terminal of a protein? Jose Borreguero (Tue Apr 05 2011 - 17:46:05 PDT)
[AMBER] is GBSA applicable to organic solvent? Junjian Miao (Tue Apr 05 2011 - 20:47:53 PDT)
- Re: [AMBER] is GBSA applicable to organic solvent? David A Case (Wed Apr 06 2011 - 05:38:40 PDT)
[AMBER] amber8-package Rilei Yu (Wed Apr 06 2011 - 01:54:23 PDT)
[AMBER] Se atom type in GAFF Jon Mikel Azpiroz (Wed Apr 06 2011 - 02:33:57 PDT)
[AMBER] The following error i got at the end of MM_PBSA.pl vani panguluri (Wed Apr 06 2011 - 04:18:21 PDT)
- Re: [AMBER] The following error i got at the end of MM_PBSA.pl Bill Miller III (Wed Apr 06 2011 - 04:26:51 PDT)
[AMBER] Problem on SMD Rilei Yu (Wed Apr 06 2011 - 07:15:02 PDT)
- Re: [AMBER] Problem on SMD Dmitry Nilov (Wed Apr 06 2011 - 07:28:52 PDT)
[AMBER] Query regarding considering water molecules sonam bhatia (Wed Apr 06 2011 - 08:46:02 PDT)
- Re: [AMBER] Query regarding considering water molecules Jason Swails (Wed Apr 06 2011 - 10:21:53 PDT)
  - Re: [AMBER] Query regarding considering water molecules Jason Swails (Wed Apr 06 2011 - 10:22:59 PDT)
[AMBER] Vector analysis John S (Wed Apr 06 2011 - 09:01:02 PDT)
Re: [AMBER] problem about addions Ross Walker (Wed Apr 06 2011 - 13:42:46 PDT)
- Re: [AMBER] problem about addions Ross Walker (Sat Apr 09 2011 - 22:20:16 PDT)
  - Re: [AMBER] problem about addions Jason Swails (Sat Apr 09 2011 - 22:56:07 PDT)
[AMBER] Thermodynamic Integration--Input doubt Rajesh Raju (Wed Apr 06 2011 - 14:32:19 PDT)
- Re: [AMBER] Thermodynamic Integration--Input doubt sunita gupta (Wed Apr 06 2011 - 22:24:22 PDT)
[AMBER] output file for contacts John S (Wed Apr 06 2011 - 22:20:44 PDT)
[AMBER] MMPBSA error Kshatresh Dutta Dubey (Thu Apr 07 2011 - 00:52:41 PDT)
- Re: [AMBER] MMPBSA error Bill Miller III (Thu Apr 07 2011 - 04:03:09 PDT)
  - Re: [AMBER] MMPBSA error Kshatresh Dutta Dubey (Thu Apr 07 2011 - 04:53:47 PDT)
    - Re: [AMBER] MMPBSA error Jason Swails (Thu Apr 07 2011 - 12:04:10 PDT)
    - Re: [AMBER] MMPBSA error Kshatresh Dutta Dubey (Sat Apr 09 2011 - 03:37:51 PDT)
    - Re: [AMBER] MMPBSA error Jason Swails (Sat Apr 09 2011 - 10:07:47 PDT)
[AMBER] CHAMBER conversion: problem with IFBOX == 0 Marc van der Kamp (Thu Apr 07 2011 - 00:53:18 PDT)
- Re: [AMBER] CHAMBER conversion: problem with IFBOX == 0 Marc van der Kamp (Thu Apr 07 2011 - 01:38:02 PDT)
[AMBER] parameter about pbsa for sander juan zeng (Thu Apr 07 2011 - 02:07:49 PDT)
- [AMBER] parameter about pbsa for sander juan zeng (Thu Apr 07 2011 - 07:45:14 PDT)
[AMBER] questions about packmol Junjian Miao (Thu Apr 07 2011 - 07:19:26 PDT)
[AMBER] potential energy from remd Jorgen Simonsen (Thu Apr 07 2011 - 09:50:47 PDT)
- Re: [AMBER] potential energy from remd Carlos Simmerling (Thu Apr 07 2011 - 09:55:20 PDT)
[AMBER] MMPBSA.py Tests Aldo Segura (Thu Apr 07 2011 - 13:23:11 PDT)
[AMBER] problems when using mm_pbsa.pl in Amber10 cwt (Thu Apr 07 2011 - 22:58:40 PDT)
- Re: [AMBER] problems when using mm_pbsa.pl in Amber10 Bill Miller III (Fri Apr 08 2011 - 04:03:13 PDT)
[AMBER] new AmberTools Aust, Susanne (Thu Apr 07 2011 - 23:28:13 PDT)
- Re: [AMBER] new AmberTools David A Case (Fri Apr 08 2011 - 05:40:59 PDT)
- Re: [AMBER] new AmberTools Jason Swails (Fri Apr 08 2011 - 08:35:12 PDT)
[AMBER] recalculating atom charges Dachuan Guo (Thu Apr 07 2011 - 23:51:42 PDT)
[AMBER] Default values nicholus bhattacharjee (Fri Apr 08 2011 - 01:33:12 PDT)
- Re: [AMBER] Default values David A Case (Fri Apr 08 2011 - 05:43:16 PDT)
[AMBER] problem of installation of MMPBSA.py fancy2012 (Fri Apr 08 2011 - 01:38:52 PDT)
- Re: [AMBER] problem of installation of MMPBSA.py Bill Miller III (Fri Apr 08 2011 - 04:17:34 PDT)
  - Re: [AMBER] problem of installation of MMPBSA.py fancy2012 (Sun Apr 10 2011 - 03:24:24 PDT)
[AMBER] Maximum number of atoms tommaso.casalini.mail.polimi.it (Fri Apr 08 2011 - 01:40:32 PDT)
- Re: [AMBER] Maximum number of atoms David A Case (Fri Apr 08 2011 - 05:46:11 PDT)
  - Re: [AMBER] Maximum number of atoms Ross Walker (Fri Apr 08 2011 - 12:01:36 PDT)
    - Re: [AMBER] Maximum number of atoms Jason Swails (Fri Apr 08 2011 - 12:24:05 PDT)
    - Re: [AMBER] Maximum number of atoms David A Case (Fri Apr 08 2011 - 13:32:09 PDT)
    - Re: [AMBER] Maximum number of atoms Ross Walker (Fri Apr 08 2011 - 16:37:11 PDT)
[AMBER] Compare simulations done with AMBER9 to ones done with AMBER11 Cuda? Antje Wolf (Fri Apr 08 2011 - 02:45:34 PDT)
- Re: [AMBER] Compare simulations done with AMBER9 to ones done with AMBER11 Cuda? Jason Swails (Fri Apr 08 2011 - 11:37:36 PDT)
  - Re: [AMBER] Compare simulations done with AMBER9 to ones done with AMBER11 Cuda? Ross Walker (Fri Apr 08 2011 - 11:56:26 PDT)
    - Re: [AMBER] Compare simulations done with AMBER9 to ones done with AMBER11 Cuda? Ross Walker (Fri Apr 08 2011 - 13:11:09 PDT)
[AMBER] About of MMPBSA.py results Aldo Segura (Fri Apr 08 2011 - 06:46:00 PDT)
[AMBER] Problem compiling sander.PUPIL: No rule to build target 'mdread.PUPIL.o' ivanquirino1928.gmail.com (Fri Apr 08 2011 - 07:17:08 PDT)
- Re: [AMBER] Problem compiling sander.PUPIL: No rule to build target 'mdread.PUPIL.o' Daniel Roe (Fri Apr 08 2011 - 08:30:40 PDT)
  - Re: [AMBER] Problem compiling sander.PUPIL: No rule to build target 'mdread.PUPIL.o' ivanquirino1928.gmail.com (Fri Apr 08 2011 - 11:41:46 PDT)
[AMBER] pmemd.cuda crashes due to "Inconsistent hydrogen network" Marc van der Kamp (Fri Apr 08 2011 - 08:06:45 PDT)
- Re: [AMBER] pmemd.cuda crashes due to "Inconsistent hydrogen network" Ross Walker (Fri Apr 08 2011 - 11:59:52 PDT)
  - Re: [AMBER] pmemd.cuda crashes due to "Inconsistent hydrogen network" Carlos Simmerling (Fri Apr 08 2011 - 12:01:23 PDT)
- Re: [AMBER] pmemd.cuda crashes due to "Inconsistent hydrogen network" Scott Le Grand (Fri Apr 08 2011 - 16:09:21 PDT)
  - Re: [AMBER] pmemd.cuda crashes due to "Inconsistent hydrogen network" Marc van der Kamp (Sat Apr 09 2011 - 02:41:21 PDT)
    - Re: [AMBER] pmemd.cuda crashes due to "Inconsistent hydrogen network" Ross Walker (Sat Apr 09 2011 - 21:29:39 PDT)
    - Re: [AMBER] pmemd.cuda crashes due to "Inconsistent hydrogen network" Marc van der Kamp (Fri Apr 15 2011 - 02:43:46 PDT)
    - Re: [AMBER] pmemd.cuda crashes due to "Inconsistent hydrogen network" Ross Walker (Fri Apr 15 2011 - 09:20:14 PDT)
[AMBER] Problem with trajin Lui (Fri Apr 08 2011 - 08:48:50 PDT)
- Re: [AMBER] Problem with trajin Daniel Roe (Fri Apr 08 2011 - 08:59:57 PDT)
  - Re: [AMBER] Problem with trajin Lui (Fri Apr 08 2011 - 09:32:53 PDT)
[AMBER] Heme .lib file for heme - problem Indrek Morell (Fri Apr 08 2011 - 09:48:55 PDT)
- Re: [AMBER] Heme .lib file for heme - problem Jacopo Sgrignani (Fri Apr 08 2011 - 10:51:18 PDT)
[AMBER] QUESTION ON MMPBSA vani panguluri (Fri Apr 08 2011 - 10:01:09 PDT)
- Re: [AMBER] QUESTION ON MMPBSA Bill Miller III (Fri Apr 08 2011 - 10:15:25 PDT)
  - Re: [AMBER] QUESTION ON MMPBSA vani panguluri (Fri Apr 08 2011 - 10:48:38 PDT)
    - Re: [AMBER] QUESTION ON MMPBSA Bill Miller III (Fri Apr 08 2011 - 11:01:02 PDT)
    - Re: [AMBER] QUESTION ON MMPBSA vani panguluri (Sun Apr 10 2011 - 09:55:13 PDT)
    - Re: [AMBER] QUESTION ON MMPBSA Jason Swails (Sun Apr 10 2011 - 10:53:02 PDT)
    - Re: [AMBER] QUESTION ON MMPBSA vani panguluri (Sun Apr 10 2011 - 11:01:05 PDT)
    - Re: [AMBER] QUESTION ON MMPBSA Jason Swails (Sun Apr 10 2011 - 11:28:12 PDT)
    - Re: [AMBER] QUESTION ON MMPBSA vani panguluri (Sun Apr 10 2011 - 18:16:40 PDT)
    - Re: [AMBER] QUESTION ON MMPBSA Dwight McGee (Mon Apr 11 2011 - 06:26:50 PDT)
- Re: [AMBER] QUESTION ON MMPBSA vani panguluri (Tue Apr 19 2011 - 19:59:43 PDT)
  - Re: [AMBER] QUESTION ON MMPBSA Jason Swails (Tue Apr 19 2011 - 20:18:51 PDT)
    - [AMBER] Can AMBER10 be installed on 64-bit linux computer? Catein Catherine (Wed Apr 20 2011 - 07:29:54 PDT)
    - [AMBER] Why Gyr and rmsd read mdcrd differently? Catein Catherine (Wed Apr 20 2011 - 07:54:13 PDT)
[AMBER] Restraint potential in Targeted MD Rahul Banerjee (Fri Apr 08 2011 - 10:56:52 PDT)
- Re: [AMBER] Restraint potential in Targeted MD Carlos Simmerling (Fri Apr 08 2011 - 11:06:32 PDT)
  - Re: [AMBER] Restraint potential in Targeted MD Rahul Banerjee (Fri Apr 08 2011 - 11:31:38 PDT)
    - Re: [AMBER] Restraint potential in Targeted MD Carlos Simmerling (Fri Apr 08 2011 - 11:37:37 PDT)
- Re: [AMBER] Restraint potential in Targeted MD Carlos Simmerling (Fri Apr 08 2011 - 13:42:31 PDT)
[AMBER] rfree: Error decoding variable 1 3 from: pmemd.MPI and pmemd error miriam sgobba (Fri Apr 08 2011 - 11:03:21 PDT)
- Re: [AMBER] rfree: Error decoding variable 1 3 from: pmemd.MPI and pmemd error Jason Swails (Fri Apr 08 2011 - 11:33:56 PDT)
[AMBER] tleap problem George Tzotzos (Fri Apr 08 2011 - 14:07:49 PDT)
- Re: [AMBER] tleap problem siddesh southekal (Fri Apr 08 2011 - 14:18:30 PDT)
- Re: [AMBER] tleap problem Daniel Roe (Fri Apr 08 2011 - 14:19:27 PDT)
  - Re: [AMBER] tleap problem George Tzotzos (Sat Apr 09 2011 - 01:32:54 PDT)
    - Re: [AMBER] tleap problem Jason Swails (Sat Apr 09 2011 - 10:05:05 PDT)
    - Re: [AMBER] tleap problem George Tzotzos (Sat Apr 09 2011 - 11:30:57 PDT)
[AMBER] tleap problem George Tzotzos (Fri Apr 08 2011 - 14:11:43 PDT)
[AMBER] distance criteria of TIP3P added to protein-DNA complex Sangita Kachhap (Sat Apr 09 2011 - 09:20:35 PDT)
- Re: [AMBER] distance criteria of TIP3P added to protein-DNA complex Carlos Simmerling (Sat Apr 09 2011 - 09:48:20 PDT)
[AMBER] Editing Protein - Change Bond Melanie (Sun Apr 10 2011 - 02:37:28 PDT)
- Re: [AMBER] Editing Protein - Change Bond case (Sun Apr 10 2011 - 08:55:48 PDT)
[AMBER] Uninstalling Amber Tools majid hasan (Sun Apr 10 2011 - 11:30:05 PDT)
- Re: [AMBER] Uninstalling Amber Tools Jason Swails (Sun Apr 10 2011 - 11:35:26 PDT)
  - Re: [AMBER] Uninstalling Amber Tools majid hasan (Sun Apr 10 2011 - 12:22:53 PDT)
[AMBER] Error in installing Amber Tools majid hasan (Sun Apr 10 2011 - 12:40:40 PDT)
- Re: [AMBER] Error in installing Amber Tools Jason Swails (Sun Apr 10 2011 - 12:55:53 PDT)
  - Re: [AMBER] Error in installing Amber Tools majid hasan (Sun Apr 10 2011 - 13:41:53 PDT)
    - Re: [AMBER] Error in installing Amber Tools Jason Swails (Sun Apr 10 2011 - 13:49:23 PDT)
    - Re: [AMBER] Error in installing Amber Tools majid hasan (Sun Apr 10 2011 - 13:50:19 PDT)
    - Re: [AMBER] Error in installing Amber Tools Jason Swails (Sun Apr 10 2011 - 13:59:35 PDT)
    - Re: [AMBER] Error in installing Amber Tools majid hasan (Sun Apr 10 2011 - 14:18:15 PDT)
    - Re: [AMBER] Error in installing Amber Tools Jason Swails (Sun Apr 10 2011 - 14:43:06 PDT)
    - Re: [AMBER] Error in installing Amber Tools majid hasan (Sun Apr 10 2011 - 15:20:14 PDT)
[AMBER] Error in running MMPBSA.py.MPI with sander.APBS Wei Huang (Sun Apr 10 2011 - 15:52:55 PDT)
- Re: [AMBER] Error in running MMPBSA.py.MPI with sander.APBS Bill Miller III (Sun Apr 10 2011 - 17:25:53 PDT)
  - Re: [AMBER] Error in running MMPBSA.py.MPI with sander.APBS Wei Huang (Sun Apr 10 2011 - 18:34:44 PDT)
    - Re: [AMBER] Error in running MMPBSA.py.MPI with sander.APBS Jason Swails (Sun Apr 10 2011 - 21:01:54 PDT)
    - Re: [AMBER] Error in running MMPBSA.py.MPI with sander.APBS Wei Huang (Sun Apr 10 2011 - 21:25:28 PDT)
[AMBER] creating ssdna from dsdna majid hasan (Sun Apr 10 2011 - 17:23:31 PDT)
[AMBER] AMBER Shesh Nath (Sun Apr 10 2011 - 21:24:04 PDT)
- Re: [AMBER] AMBER Jason Swails (Sun Apr 10 2011 - 22:11:28 PDT)
[AMBER] Multiple links QM-MM Shruti Koulgi (Mon Apr 11 2011 - 02:21:37 PDT)
- Re: [AMBER] Multiple links QM-MM Gustavo Seabra (Mon Apr 11 2011 - 04:21:58 PDT)
[AMBER] peptide-protein complex construction J.F.Jiang (Mon Apr 11 2011 - 04:29:53 PDT)
- [AMBER] Add charges to a prmtop files before simulations Baptiste Legrand (Mon Apr 11 2011 - 07:29:45 PDT)
  - Re: [AMBER] Add charges to a prmtop files before simulations Baldoni Hector Armando (Mon Apr 11 2011 - 07:38:11 PDT)
  - Re: [AMBER] Add charges to a prmtop files before simulations Jason Swails (Mon Apr 11 2011 - 09:32:24 PDT)
    - Re: [AMBER] Add charges to a prmtop files before simulations Baptiste Legrand (Thu Apr 14 2011 - 10:48:37 PDT)
    - Re: [AMBER] Add charges to a prmtop files before simulations David A Case (Thu Apr 14 2011 - 11:03:05 PDT)
[AMBER] problem with ptraj trajout in ambertools moitrayee.mbu.iisc.ernet.in (Mon Apr 11 2011 - 09:20:17 PDT)
- Re: [AMBER] problem with ptraj trajout in ambertools Jason Swails (Mon Apr 11 2011 - 09:34:39 PDT)
  - Re: [AMBER] problem with ptraj trajout in ambertools moitrayee.mbu.iisc.ernet.in (Mon Apr 11 2011 - 10:03:02 PDT)
    - Re: [AMBER] problem with ptraj trajout in ambertools Jason Swails (Mon Apr 11 2011 - 10:24:35 PDT)
    - Re: [AMBER] problem with ptraj trajout in ambertools moitrayee.mbu.iisc.ernet.in (Mon Apr 11 2011 - 11:01:24 PDT)
    - Re: [AMBER] problem with ptraj trajout in ambertools Adrian Roitberg (Mon Apr 11 2011 - 11:03:43 PDT)
    - Re: [AMBER] problem with ptraj trajout in ambertools moitrayee.mbu.iisc.ernet.in (Mon Apr 11 2011 - 11:13:43 PDT)
[AMBER] ambertools 1.5 Francesco Oteri (Mon Apr 11 2011 - 10:34:51 PDT)
- Re: [AMBER] ambertools 1.5 David A Case (Tue Apr 12 2011 - 08:16:15 PDT)
[AMBER] segmentation fault on antechamber when using carbon nano tube Bongkeun Kim (Mon Apr 11 2011 - 13:01:48 PDT)
- Re: [AMBER] segmentation fault on antechamber when using carbon nano tube Jason Swails (Mon Apr 11 2011 - 13:13:01 PDT)
  - Re: [AMBER] segmentation fault on antechamber when using carbon nano tube Bongkeun Kim (Mon Apr 11 2011 - 14:06:00 PDT)
    - Re: [AMBER] segmentation fault on antechamber when using carbon nano tube Jason Swails (Mon Apr 11 2011 - 14:32:56 PDT)
[AMBER] solvate with crystal water Hashem Taha (Mon Apr 11 2011 - 13:09:58 PDT)
- Re: [AMBER] solvate with crystal water Daniel Roe (Tue Apr 12 2011 - 06:20:48 PDT)
  - Re: [AMBER] solvate with crystal water Hashem Taha (Tue Apr 12 2011 - 17:56:39 PDT)
    - Re: [AMBER] solvate with crystal water Hashem Taha (Thu Apr 14 2011 - 08:11:18 PDT)
    - Re: [AMBER] solvate with crystal water Jason Swails (Thu Apr 14 2011 - 08:20:40 PDT)
    - Re: [AMBER] solvate with crystal water Hashem Taha (Thu Apr 14 2011 - 08:37:42 PDT)
    - Re: [AMBER] solvate with crystal water Hashem Taha (Thu Apr 14 2011 - 08:39:02 PDT)
    - Re: [AMBER] solvate with crystal water Hashem Taha (Thu Apr 14 2011 - 09:04:44 PDT)
    - Re: [AMBER] solvate with crystal water Jason Swails (Thu Apr 14 2011 - 09:18:54 PDT)
    - Re: [AMBER] solvate with crystal water David A Case (Thu Apr 14 2011 - 09:30:59 PDT)
    - Re: [AMBER] solvate with crystal water Jason Swails (Thu Apr 14 2011 - 10:04:54 PDT)
    - [AMBER] weird hydrogen names? David A Case (Thu Apr 14 2011 - 10:39:30 PDT)
    - Re: [AMBER] weird hydrogen names? Jason Swails (Thu Apr 14 2011 - 11:23:32 PDT)
- Re: [AMBER] solvate with crystal water Bill Ross (Thu Apr 14 2011 - 10:17:27 PDT)
- Re: [AMBER] solvate with crystal water Bill Ross (Thu Apr 14 2011 - 10:30:14 PDT)
  - Re: [AMBER] solvate with crystal water Hashem Taha (Thu Apr 14 2011 - 12:12:13 PDT)
[AMBER] steered MD versus umbrella sampling? Jose Borreguero (Mon Apr 11 2011 - 14:12:02 PDT)
- Re: [AMBER] steered MD versus umbrella sampling? Carlos Simmerling (Mon Apr 11 2011 - 14:16:23 PDT)
[AMBER] AmberTools install Michael Forrester (Mon Apr 11 2011 - 21:50:35 PDT)
- Re: [AMBER] AmberTools install Jason Swails (Mon Apr 11 2011 - 22:25:07 PDT)
- Re: [AMBER] AmberTools install David Case (Tue Apr 12 2011 - 05:25:31 PDT)
[AMBER] Error on running parameter 'sander' Sanjay kundu (Mon Apr 11 2011 - 22:52:53 PDT)
- Re: [AMBER] Error on running parameter 'sander' Ross Walker (Tue Apr 12 2011 - 15:31:19 PDT)
  - Re: [AMBER] Error on running parameter 'sander' Sanjay kundu (Wed Apr 13 2011 - 02:23:27 PDT)
    - Re: [AMBER] Error on running parameter 'sander' Jason Swails (Wed Apr 13 2011 - 09:21:41 PDT)
[AMBER] How to modify .pdb file for Amber input MD (Tue Apr 12 2011 - 00:09:05 PDT)
- Re: [AMBER] How to modify .pdb file for Amber input Francesco Oteri (Tue Apr 12 2011 - 01:03:00 PDT)
[AMBER] MD with preset start/end structures Bernhard Poll (Tue Apr 12 2011 - 04:43:17 PDT)
- Re: [AMBER] MD with preset start/end structures Carlos Simmerling (Tue Apr 12 2011 - 04:53:03 PDT)
  - Re: [AMBER] MD with preset start/end structures Matthias Negri (Tue Apr 12 2011 - 06:31:31 PDT)
    - Re: [AMBER] MD with preset start/end structures Carlos Simmerling (Thu Apr 14 2011 - 11:41:34 PDT)
    - Re: [AMBER] MD with preset start/end structures and addless "problem in line read" Matthias Negri (Thu Apr 21 2011 - 06:53:40 PDT)
[AMBER] QMMM Jurica Novak (Tue Apr 12 2011 - 05:13:14 PDT)
- Re: [AMBER] QMMM Barbault Florent (Tue Apr 12 2011 - 05:33:02 PDT)
  - Re: [AMBER] QMMM Jurica Novak (Tue Apr 12 2011 - 06:22:21 PDT)
- Re: [AMBER] QMMM Gustavo Seabra (Tue Apr 12 2011 - 06:45:28 PDT)
  - Re: [AMBER] QMMM Jurica Novak (Tue Apr 12 2011 - 07:13:22 PDT)
    - Re: [AMBER] QMMM Jason Swails (Tue Apr 12 2011 - 08:00:19 PDT)
    - Re: [AMBER] QMMM Gustavo Seabra (Tue Apr 12 2011 - 11:05:55 PDT)
    - Re: [AMBER] QMMM Jason Swails (Tue Apr 12 2011 - 11:17:47 PDT)
    - Re: [AMBER] QMMM Andreas Goetz (Tue Apr 12 2011 - 11:26:32 PDT)
    - Re: [AMBER] QMMM Jurica Novak (Mon Apr 18 2011 - 02:38:54 PDT)
    - Re: [AMBER] QMMM David A Case (Mon Apr 18 2011 - 04:53:32 PDT)
    - Re: [AMBER] QMMM Jurica Novak (Mon Apr 18 2011 - 05:19:17 PDT)
    - Re: [AMBER] QMMM Ross Walker (Mon Apr 18 2011 - 07:58:44 PDT)
[AMBER] Processors, cores and threads Hopkins, Robert (Tue Apr 12 2011 - 09:14:32 PDT)
- Re: [AMBER] Processors, cores and threads Jason Swails (Tue Apr 12 2011 - 10:00:13 PDT)
- Re: [AMBER] Processors, cores and threads Hopkins, Robert (Tue Apr 12 2011 - 10:36:19 PDT)
  - Re: [AMBER] Processors, cores and threads Dmitry Mukha (Wed Apr 13 2011 - 01:29:25 PDT)
    - Re: [AMBER] Processors, cores and threads M. Shahid (Wed Apr 13 2011 - 02:04:32 PDT)
[AMBER] errors compiling amber11 for cuda Robert Wohlhueter (Tue Apr 12 2011 - 09:19:04 PDT)
- Re: [AMBER] errors compiling amber11 for cuda Ross Walker (Tue Apr 12 2011 - 15:27:34 PDT)
  - Re: [AMBER] errors compiling amber11 for cuda Robert Wohlhueter (Tue Apr 12 2011 - 16:45:10 PDT)
    - Re: [AMBER] errors compiling amber11 for cuda Jason Swails (Tue Apr 12 2011 - 17:31:13 PDT)
    - Re: [AMBER] errors compiling amber11 for cuda Ross Walker (Tue Apr 12 2011 - 19:25:32 PDT)
    - Re: [AMBER] errors compiling amber11 for cuda Robert Wohlhueter (Tue Apr 12 2011 - 20:07:12 PDT)
[AMBER] python and perl versions of mmpbsa anyiphysics.gmail.com (Tue Apr 12 2011 - 09:22:15 PDT)
- Re: [AMBER] python and perl versions of mmpbsa Bill Miller III (Tue Apr 12 2011 - 09:27:18 PDT)
  - Re: [AMBER] python and perl versions of mmpbsa anyiphysics.gmail.com (Tue Apr 12 2011 - 11:05:57 PDT)
    - Re: [AMBER] python and perl versions of mmpbsa Jason Swails (Tue Apr 12 2011 - 11:13:42 PDT)
[AMBER] Beggining with AMBER Fernando Blanco (Tue Apr 12 2011 - 10:00:21 PDT)
- Re: [AMBER] Beggining with AMBER Ankita Kumari (Tue Apr 12 2011 - 23:01:42 PDT)
- Re: [AMBER] Beggining with AMBER Dmitry Nilov (Wed Apr 13 2011 - 01:31:46 PDT)
  - Re: [AMBER] Beggining with AMBER Fernando Blanco (Wed Apr 13 2011 - 12:32:19 PDT)
    - Re: [AMBER] Beggining with AMBER Dmitry Nilov (Wed Apr 13 2011 - 22:36:49 PDT)
    - Re: [AMBER] Beggining with AMBER Fernando Blanco (Thu Apr 14 2011 - 05:29:10 PDT)
    - Re: [AMBER] Beggining with AMBER Fernando Blanco (Thu Apr 14 2011 - 06:50:08 PDT)
[AMBER] Calculation of forces using steered MD Ali M. Naserian-Nik (Tue Apr 12 2011 - 10:17:05 PDT)
- Re: [AMBER] Calculation of forces using steered MD Dmitry Nilov (Tue Apr 12 2011 - 21:31:59 PDT)
  - Re: [AMBER] Calculation of forces using steered MD Ali M. Naserian-Nik (Tue Apr 12 2011 - 23:20:48 PDT)
    - Re: [AMBER] Calculation of forces using steered MD Dmitry Nilov (Wed Apr 13 2011 - 00:42:25 PDT)
    - Re: [AMBER] Calculation of forces using steered MD Ali M. Naserian-Nik (Wed Apr 13 2011 - 01:04:26 PDT)
    - Re: [AMBER] Calculation of forces using steered MD Barbault Florent (Wed Apr 13 2011 - 01:55:10 PDT)
    - Re: [AMBER] Calculation of forces using steered MD Dmitry Nilov (Wed Apr 13 2011 - 01:59:52 PDT)
[AMBER] fe4s4 cubane force field parameters Hugh Cheng (Tue Apr 12 2011 - 11:54:10 PDT)
- Re: [AMBER] fe4s4 cubane force field parameters David A Case (Fri Apr 15 2011 - 08:39:04 PDT)
[AMBER] how did the SALTCON parameter work in MMPBSA? Yao-Chi Chen (Tue Apr 12 2011 - 12:12:01 PDT)
- Re: [AMBER] how did the SALTCON parameter work in MMPBSA? Jason Swails (Tue Apr 12 2011 - 12:22:51 PDT)
[AMBER] another AmberTools problem Michael Forrester (Tue Apr 12 2011 - 12:36:31 PDT)
- Re: [AMBER] another AmberTools problem David A Case (Tue Apr 12 2011 - 13:06:11 PDT)
[AMBER] Fwd: docked complex file preparation siddesh southekal (Mon Apr 11 2011 - 10:44:17 PDT)
[AMBER] Spatial Distribution Functions Agostino Bruno (Fri Apr 08 2011 - 07:10:10 PDT)
[AMBER] problem of using leap fancy2012 (Tue Apr 12 2011 - 19:46:47 PDT)
- Re: [AMBER] problem of using leap case (Tue Apr 12 2011 - 20:16:38 PDT)
  - Re: [AMBER] problem of using leap fancy2012 (Tue Apr 12 2011 - 22:24:11 PDT)
    - Re: [AMBER] problem of using leap David A Case (Wed Apr 13 2011 - 04:53:42 PDT)
    - Re: [AMBER] problem of using leap fancy2012 (Mon Apr 18 2011 - 22:59:51 PDT)
Re: [AMBER] Coupled torsions from Amber Ross Walker (Tue Apr 12 2011 - 22:41:26 PDT)
[AMBER] mmpbsa - nmode calculation Sangita Kachhap (Wed Apr 13 2011 - 00:40:39 PDT)
- Re: [AMBER] mmpbsa - nmode calculation Jason Swails (Wed Apr 13 2011 - 01:09:18 PDT)
  - Re: [AMBER] mmpbsa - nmode calculation Sangita Kachhap (Wed Apr 13 2011 - 01:58:01 PDT)
[AMBER] velocity units Dmitry Mukha (Wed Apr 13 2011 - 07:04:49 PDT)
- Re: [AMBER] velocity units Daniel Roe (Wed Apr 13 2011 - 08:31:53 PDT)
  - Re: [AMBER] velocity units Dmitry Mukha (Wed Apr 13 2011 - 08:38:23 PDT)
[AMBER] comparing order parameters from MD and NMR Brendan Duggan (Wed Apr 13 2011 - 07:11:44 PDT)
- Re: [AMBER] comparing order parameters from MD and NMR David A Case (Fri Apr 15 2011 - 08:32:35 PDT)
[AMBER] Problem with VMD juzer stationwala (Wed Apr 13 2011 - 07:34:34 PDT)
- Re: [AMBER] Problem with VMD Jason Swails (Wed Apr 13 2011 - 09:22:42 PDT)
  - Re: [AMBER] Problem with VMD juzer.niper.gmail.com (Wed Apr 13 2011 - 10:03:12 PDT)
[AMBER] Error while installing amber11 sonali dhindwal (Wed Apr 13 2011 - 07:42:15 PDT)
- Re: [AMBER] Error while installing amber11 Daniel Roe (Wed Apr 13 2011 - 07:48:10 PDT)
- Re: [AMBER] Error while installing amber11 sonali dhindwal (Wed Apr 13 2011 - 08:52:36 PDT)
  - Re: [AMBER] Error while installing amber11 David A Case (Wed Apr 13 2011 - 09:50:59 PDT)
- Re: [AMBER] Error while installing amber11 sonali dhindwal (Wed Apr 13 2011 - 21:26:21 PDT)
  - Re: [AMBER] Error while installing amber11 Daniel Roe (Thu Apr 14 2011 - 04:41:19 PDT)
    - Re: [AMBER] Error while installing amber11 sonali dhindwal (Thu Apr 14 2011 - 06:52:19 PDT)
[AMBER] Implicit solvent and box Elisa Frezza (Wed Apr 13 2011 - 08:49:50 PDT)
- Re: [AMBER] Implicit solvent and box david condon (Wed Apr 13 2011 - 08:59:15 PDT)
  - Re: [AMBER] Implicit solvent and box Elisa Frezza (Wed Apr 13 2011 - 09:02:26 PDT)
- Re: [AMBER] Implicit solvent and box David A Case (Wed Apr 13 2011 - 09:47:50 PDT)
  - Re: [AMBER] Implicit solvent and box Carlos Simmerling (Wed Apr 13 2011 - 10:46:12 PDT)
    - Re: [AMBER] Implicit solvent and box Adrian Roitberg (Wed Apr 13 2011 - 10:49:16 PDT)
    - Re: [AMBER] Implicit solvent and box Carlos Simmerling (Wed Apr 13 2011 - 10:53:23 PDT)
    - Re: [AMBER] Implicit solvent and box Adrian Roitberg (Wed Apr 13 2011 - 10:55:57 PDT)
    - Re: [AMBER] Implicit solvent and box Carlos Simmerling (Wed Apr 13 2011 - 11:01:16 PDT)
    - Re: [AMBER] Implicit solvent and box Jason Swails (Wed Apr 13 2011 - 11:19:16 PDT)
    - Re: [AMBER] Implicit solvent and box Carlos Simmerling (Wed Apr 13 2011 - 11:38:16 PDT)
    - Re: [AMBER] Implicit solvent and box Jason Swails (Wed Apr 13 2011 - 12:19:08 PDT)
    - Re: [AMBER] Implicit solvent and box Jason Swails (Wed Apr 13 2011 - 12:20:08 PDT)
[AMBER] mmpbsa.py input - radii to use Jesper Sørensen (Wed Apr 13 2011 - 08:54:50 PDT)
[AMBER] Non bonded interactions Lekpa Duukori (Wed Apr 13 2011 - 09:31:51 PDT)
[AMBER] nucleosides Steven M. Graham (Wed Apr 13 2011 - 14:33:10 PDT)
- Re: [AMBER] nucleosides David A Case (Thu Apr 14 2011 - 04:58:00 PDT)
  - Re: [AMBER] nucleosides Steven M. Graham (Thu Apr 14 2011 - 05:26:12 PDT)
[AMBER] Does AMBER 9 has parameters for ions F- Br- I- etc MD (Wed Apr 13 2011 - 20:00:55 PDT)
- Re: [AMBER] Does AMBER 9 has parameters for ions F- Br- I- etc Aldo Segura (Wed Apr 13 2011 - 20:22:52 PDT)
  - Re: [AMBER] Does AMBER 9 has parameters for ions F- Br- I- etc MD (Wed Apr 13 2011 - 20:43:42 PDT)
- Re: [AMBER] Does AMBER 9 has parameters for ions F- Br- I- etc David A Case (Thu Apr 14 2011 - 05:11:50 PDT)
[AMBER] missing coordinates from pdb Sangita Kachhap (Wed Apr 13 2011 - 23:28:30 PDT)
- Re: [AMBER] missing coordinates from pdb juzer stationwala (Wed Apr 13 2011 - 23:33:07 PDT)
[AMBER] Usage of diffuse command kurisaki (Wed Apr 13 2011 - 23:46:46 PDT)
[AMBER] No data for 0+0 MM BOND 0 mirage . (Thu Apr 14 2011 - 00:30:46 PDT)
- Re: [AMBER] No data for 0+0 MM BOND 0 mirage . (Sun Apr 17 2011 - 05:34:25 PDT)
  - Re: [AMBER] No data for 0+0 MM BOND 0 Bill Miller III (Sun Apr 17 2011 - 06:16:38 PDT)
Re: [AMBER] MMPBSA.py.MPI error! mmpbsa amber (Thu Apr 14 2011 - 01:27:35 PDT)
[AMBER] MMPBSA.py.MPI error 陳昭同 (Thu Apr 14 2011 - 02:34:04 PDT)
- Re: [AMBER] MMPBSA.py.MPI error Bill Miller III (Thu Apr 14 2011 - 05:25:12 PDT)
  - Re: [AMBER] MMPBSA.py.MPI error 陳昭同 (Thu Apr 14 2011 - 08:53:11 PDT)
    - Re: [AMBER] MMPBSA.py.MPI error Jason Swails (Thu Apr 14 2011 - 09:10:29 PDT)
    - Re: [AMBER] MMPBSA.py.MPI error 陳昭同 (Thu Apr 14 2011 - 19:02:04 PDT)
    - Re: [AMBER] MMPBSA.py.MPI error Jason Swails (Thu Apr 14 2011 - 19:37:17 PDT)
    - Re: [AMBER] MMPBSA.py.MPI error 陳昭同 (Thu Apr 14 2011 - 19:58:38 PDT)
- Re: [AMBER] MMPBSA.py.MPI error Jason Swails (Thu Apr 14 2011 - 07:34:52 PDT)
[AMBER] Leap error with Zinc ions Manish Datt (Thu Apr 14 2011 - 07:22:29 PDT)
- [AMBER] FW: Leap error with Zinc ions Manish Datt (Mon Apr 18 2011 - 07:42:32 PDT)
  - Re: [AMBER] FW: Leap error with Zinc ions Ross Walker (Mon Apr 18 2011 - 09:10:06 PDT)
    - Re: [AMBER] FW: Leap error with Zinc ions Ben Roberts (Mon Apr 18 2011 - 09:42:50 PDT)
    - Re: [AMBER] FW: Leap error with Zinc ions setyanto md (Tue Apr 19 2011 - 06:21:17 PDT)
[AMBER] How to find Acetyl-coa parameters in R.E.D.DB? Yuan Yao (Thu Apr 14 2011 - 09:26:39 PDT)
- Re: [AMBER] How to find Acetyl-coa parameters in R.E.D.DB? David A Case (Thu Apr 14 2011 - 09:35:01 PDT)
  - Re: [AMBER] How to find Acetyl-coa parameters in R.E.D.DB? Yuan Yao (Thu Apr 14 2011 - 09:46:29 PDT)
    - Re: [AMBER] How to find Acetyl-coa parameters in R.E.D.DB? Adrian Roitberg (Thu Apr 14 2011 - 09:51:49 PDT)
    - Re: [AMBER] How to find Acetyl-coa parameters in R.E.D.DB? Yuan Yao (Thu Apr 14 2011 - 10:05:12 PDT)
- Re: [AMBER] How to find Acetyl-coa parameters in R.E.D.DB? FyD (Thu Apr 14 2011 - 12:02:20 PDT)
  - Re: [AMBER] How to find Acetyl-coa parameters in R.E.D.DB? Yuan Yao (Thu Apr 14 2011 - 14:17:22 PDT)
    - Re: [AMBER] How to find Acetyl-coa parameters in R.E.D.DB? FyD (Thu Apr 14 2011 - 22:05:34 PDT)
[AMBER] Error in Installing MTK++ software Naveen Samala (Thu Apr 14 2011 - 12:58:29 PDT)
- Re: [AMBER] Error in Installing MTK++ software Jason Swails (Thu Apr 14 2011 - 14:18:47 PDT)
[AMBER] Error on compiling cuda_parallel; MPI_Win is undefined Bongkeun Kim (Thu Apr 14 2011 - 13:02:32 PDT)
[AMBER] a problem about tutorial A12 Junjian Miao (Thu Apr 14 2011 - 07:09:03 PDT)
- Re: [AMBER] a problem about tutorial A12 Daniel Roe (Thu Apr 14 2011 - 15:53:34 PDT)
- Re: [AMBER] a problem about tutorial A12 Junjian Miao (Thu Apr 14 2011 - 20:40:16 PDT)
[AMBER] momentum from trajectory peker milas (Thu Apr 14 2011 - 17:24:49 PDT)
- Re: [AMBER] momentum from trajectory Bill Ross (Thu Apr 14 2011 - 17:29:19 PDT)
  - Re: [AMBER] momentum from trajectory peker milas (Thu Apr 14 2011 - 17:33:14 PDT)
    - Re: [AMBER] momentum from trajectory Daniel Sindhikara (Thu Apr 14 2011 - 20:03:28 PDT)
    - Re: [AMBER] momentum from trajectory Jason Swails (Thu Apr 14 2011 - 21:36:44 PDT)
    - Re: [AMBER] momentum from trajectory peker milas (Fri Apr 15 2011 - 06:34:11 PDT)
[AMBER] masking in the QMMM input setyanto md (Thu Apr 14 2011 - 21:25:43 PDT)
- Re: [AMBER] masking in the QMMM input Jason Swails (Thu Apr 14 2011 - 21:32:32 PDT)
  - Re: [AMBER] masking in the QMMM input setyanto md (Thu Apr 14 2011 - 23:23:01 PDT)
    - Re: [AMBER] masking in the QMMM input Jason Swails (Thu Apr 14 2011 - 23:41:43 PDT)
    - Re: [AMBER] masking in the QMMM input setyanto md (Fri Apr 15 2011 - 01:32:03 PDT)
  - Re: [AMBER] masking in the QMMM input Gustavo Seabra (Fri Apr 15 2011 - 05:45:26 PDT)
    - Re: [AMBER] masking in the QMMM input setyanto md (Sun Apr 17 2011 - 20:57:27 PDT)
    - Re: [AMBER] masking in the QMMM input Ross Walker (Mon Apr 18 2011 - 07:51:40 PDT)
    - Re: [AMBER] masking in the QMMM input setyanto md (Tue Apr 19 2011 - 06:14:57 PDT)
[AMBER] Release of AmberTools 1.5 David A Case (Fri Apr 15 2011 - 05:48:14 PDT)
[AMBER] Restraining non-bonded atoms nicholus bhattacharjee (Fri Apr 15 2011 - 06:01:54 PDT)
- Re: [AMBER] Restraining non-bonded atoms Carlos Simmerling (Fri Apr 15 2011 - 06:05:29 PDT)
[AMBER] Query about charge on magnesium Vaibhav Jain (Fri Apr 15 2011 - 07:07:16 PDT)
- Re: [AMBER] Query about charge on magnesium Jacopo Sgrignani (Fri Apr 15 2011 - 08:07:56 PDT)
- Re: [AMBER] Query about charge on magnesium Ye MEI (Fri Apr 15 2011 - 08:51:50 PDT)
[AMBER] PMF calculations Mahmoud Soliman (Fri Apr 15 2011 - 11:06:11 PDT)
[AMBER] puzzle ahout constructing .prepin hanlu0366 (Fri Apr 15 2011 - 18:54:40 PDT)
- Re: [AMBER] puzzle ahout constructing .prepin case (Sat Apr 16 2011 - 06:04:36 PDT)
[AMBER] coordinate updates nicholus bhattacharjee (Fri Apr 15 2011 - 22:01:37 PDT)
- Re: [AMBER] coordinate updates Jason Swails (Fri Apr 15 2011 - 23:12:10 PDT)
[AMBER] NEB calculations in enzyme? Mahmoud Soliman (Sun Apr 17 2011 - 08:49:58 PDT)
- Re: [AMBER] NEB calculations in enzyme? Ross Walker (Mon Apr 18 2011 - 08:51:29 PDT)
  - Re: [AMBER] NEB calculations in enzyme? Carlos Simmerling (Mon Apr 18 2011 - 08:53:52 PDT)
    - Re: [AMBER] NEB calculations in enzyme? Mahmoud Soliman (Mon Apr 18 2011 - 09:18:18 PDT)
  - Re: [AMBER] NEB calculations in enzyme? Mahmoud Soliman (Mon Apr 18 2011 - 09:16:14 PDT)
[AMBER] Can i addIons F- Br- I- using AMBER 9 MD (Sun Apr 17 2011 - 18:35:18 PDT)
- Re: [AMBER] Can i addIons F- Br- I- using AMBER 9 David A Case (Mon Apr 18 2011 - 05:04:04 PDT)
  - [AMBER] How can i save this .pdb file to .top and .crd?? using AMBER 9 MD (Tue Apr 19 2011 - 00:25:30 PDT)
    - Re: [AMBER] How can i save this .pdb file to .top and .crd?? using AMBER 9 David A Case (Tue Apr 19 2011 - 04:40:15 PDT)
    - [AMBER] add polarized ions to pol3 water? Are there polarized ions models in Amber? MD (Tue Apr 19 2011 - 22:26:46 PDT)
[AMBER] Number of MMPBSA_Nmode run Sangita Kachhap (Mon Apr 18 2011 - 01:31:35 PDT)
- Re: [AMBER] Number of MMPBSA_Nmode run Jason Swails (Mon Apr 18 2011 - 08:38:17 PDT)
  - Re: [AMBER] Number of MMPBSA_Nmode run Sangita Kachhap (Mon Apr 18 2011 - 10:19:48 PDT)
    - Re: [AMBER] Number of MMPBSA_Nmode run Jason Swails (Mon Apr 18 2011 - 10:49:49 PDT)
    - Re: [AMBER] Number of MMPBSA_Nmode run Sangita Kachhap (Mon Apr 18 2011 - 10:56:51 PDT)
[AMBER] Restraining distance between a protein atom and a water of crystalization nicholus bhattacharjee (Mon Apr 18 2011 - 02:46:17 PDT)
- Re: [AMBER] Restraining distance between a protein atom and a water of crystalization Carlos Simmerling (Mon Apr 18 2011 - 04:12:17 PDT)
  - Re: [AMBER] Restraining distance between a protein atom and a water of crystalization nicholus bhattacharjee (Mon Apr 18 2011 - 06:29:46 PDT)
    - Re: [AMBER] Restraining distance between a protein atom and a water of crystalization Carlos Simmerling (Mon Apr 18 2011 - 06:33:37 PDT)
    - Re: [AMBER] Restraining distance between a protein atom and a water of crystalization nicholus bhattacharjee (Thu Apr 21 2011 - 22:13:20 PDT)
    - Re: [AMBER] Restraining distance between a protein atom and a water of crystalization Carlos Simmerling (Fri Apr 22 2011 - 04:20:39 PDT)
    - Re: [AMBER] Restraining distance between a protein atom and a water of crystalization nicholus bhattacharjee (Fri Apr 22 2011 - 05:24:51 PDT)
    - Re: [AMBER] Restraining distance between a protein atom and a water of crystalization Carlos Simmerling (Fri Apr 22 2011 - 05:27:47 PDT)
    - Re: [AMBER] Restraining distance between a protein atom and a water of crystalization nicholus bhattacharjee (Fri Apr 22 2011 - 05:46:48 PDT)
    - Re: [AMBER] Restraining distance between a protein atom and a water of crystalization David A Case (Fri Apr 22 2011 - 05:46:52 PDT)
    - Re: [AMBER] Restraining distance between a protein atom and a water of crystalization nicholus bhattacharjee (Tue Apr 26 2011 - 06:01:39 PDT)
    - Re: [AMBER] Restraining distance between a protein atom and a water of crystalization David A Case (Tue Apr 26 2011 - 06:34:14 PDT)
[AMBER] Error installing amber9 for mpi(sander.MPI) Sanjay kundu (Mon Apr 18 2011 - 03:01:24 PDT)
- Re: [AMBER] Error installing amber9 for mpi(sander.MPI) David A Case (Mon Apr 18 2011 - 04:57:43 PDT)
[AMBER] leap solvateoct question Bala subramanian (Mon Apr 18 2011 - 03:23:59 PDT)
- Re: [AMBER] leap solvateoct question Kshatresh Dutta Dubey (Mon Apr 18 2011 - 03:34:41 PDT)
  - Re: [AMBER] leap solvateoct question Bala subramanian (Mon Apr 18 2011 - 03:46:36 PDT)
    - Re: [AMBER] leap solvateoct question Kshatresh Dutta Dubey (Mon Apr 18 2011 - 03:49:12 PDT)
[AMBER] SQM Dachuan Guo (Mon Apr 18 2011 - 06:57:16 PDT)
- Re: [AMBER] SQM Ross Walker (Mon Apr 18 2011 - 08:55:28 PDT)
  - Re: [AMBER] SQM Dachuan Guo (Mon Apr 18 2011 - 22:37:00 PDT)
    - Re: [AMBER] SQM David A Case (Tue Apr 19 2011 - 04:36:50 PDT)
Re: [AMBER] amber parameters for Ni Ben Roberts (Mon Apr 18 2011 - 08:34:18 PDT)
[AMBER] strange background job crash Bala subramanian (Mon Apr 18 2011 - 08:44:02 PDT)
- Re: [AMBER] strange background job crash Ross Walker (Mon Apr 18 2011 - 09:11:50 PDT)
  - Re: [AMBER] strange background job crash Bala subramanian (Mon Apr 18 2011 - 09:24:41 PDT)
    - Re: [AMBER] strange background job crash Ross Walker (Mon Apr 18 2011 - 09:35:20 PDT)
[AMBER] MCPB instructions (was: Re: MCPB program - how to download) Ben Roberts (Mon Apr 18 2011 - 08:45:00 PDT)
[AMBER] 'shake problem' and soft core potential anyiphysics.gmail.com (Mon Apr 18 2011 - 12:05:55 PDT)
- Re: [AMBER] 'shake problem' and soft core potential Niel Henriksen (Mon Apr 18 2011 - 14:19:43 PDT)
  - Re: [AMBER] 'shake problem' and soft core potential David Case (Mon Apr 18 2011 - 14:48:42 PDT)
    - Re: [AMBER] 'shake problem' and soft core potential steinbrt.rci.rutgers.edu (Tue Apr 19 2011 - 02:02:59 PDT)
  - Re: [AMBER] 'shake problem' and soft core potential anyiphysics.gmail.com (Fri Apr 22 2011 - 13:36:08 PDT)
[AMBER] Fwd: QUESTION ON MMPBSA Jason Swails (Mon Apr 18 2011 - 12:28:11 PDT)
[AMBER] Regarding antechamber Naveen Samala (Mon Apr 18 2011 - 13:09:30 PDT)
- Re: [AMBER] Regarding antechamber David A Case (Tue Apr 19 2011 - 04:25:36 PDT)
[AMBER] parallel QM/MM/MD lasts forever Mahmoud Soliman (Tue Apr 19 2011 - 00:17:37 PDT)
- Re: [AMBER] parallel QM/MM/MD lasts forever Ross Walker (Tue Apr 19 2011 - 00:34:24 PDT)
  - Re: [AMBER] parallel QM/MM/MD lasts forever Mahmoud Soliman (Tue Apr 19 2011 - 00:50:37 PDT)
[AMBER] dealing with xleap Sajad Ahrari (Tue Apr 19 2011 - 02:22:07 PDT)
- Re: [AMBER] dealing with xleap David A Case (Tue Apr 19 2011 - 04:42:34 PDT)
[AMBER] Electrostatic term Eliac Brown (Tue Apr 19 2011 - 02:30:13 PDT)
[AMBER] ambertools 1.5, python and Mac Alan Wilter Sousa da Silva (Tue Apr 19 2011 - 03:19:49 PDT)
- Re: [AMBER] ambertools 1.5, python and Mac Jason Swails (Tue Apr 19 2011 - 08:03:45 PDT)
[AMBER] GPU Technology Conference, Singapore Oxana Plis (Tue Apr 19 2011 - 03:30:25 PDT)
[AMBER] AMBER 11 pbsa errors Dmitry Osolodkin (Tue Apr 19 2011 - 05:42:05 PDT)
- Re: [AMBER] AMBER 11 pbsa errors Jason Swails (Tue Apr 19 2011 - 08:12:53 PDT)
  - Re: [AMBER] AMBER 11 pbsa errors Dmitry Osolodkin (Tue Apr 19 2011 - 08:12:14 PDT)
    - Re: [AMBER] AMBER 11 pbsa errors Jason Swails (Tue Apr 19 2011 - 08:18:35 PDT)
    - Re: [AMBER] AMBER 11 pbsa errors Dmitry Osolodkin (Tue Apr 19 2011 - 08:26:13 PDT)
[AMBER] MMPBSA default input anyiphysics.gmail.com (Tue Apr 19 2011 - 08:02:29 PDT)
- Re: [AMBER] MMPBSA default input Jason Swails (Tue Apr 19 2011 - 08:09:19 PDT)
  - Re: [AMBER] MMPBSA default input anyiphysics.gmail.com (Tue Apr 19 2011 - 09:22:44 PDT)
[AMBER] PMF Elisa Frezza (Tue Apr 19 2011 - 08:40:29 PDT)
- Re: [AMBER] PMF jani vinod (Tue Apr 19 2011 - 21:31:45 PDT)
- Re: [AMBER] PMF steinbrt.rci.rutgers.edu (Wed Apr 20 2011 - 01:08:04 PDT)
  - Re: [AMBER] PMF Elisa Frezza (Thu Apr 21 2011 - 06:23:16 PDT)
[AMBER] Regarding understanding MTK++ Document Naveen Samala (Tue Apr 19 2011 - 09:41:49 PDT)
- Re: [AMBER] Regarding understanding MTK++ Document Ben Roberts (Tue Apr 19 2011 - 10:31:59 PDT)
  - Re: [AMBER] Regarding understanding MTK++ Document Ben Roberts (Tue Apr 19 2011 - 10:40:49 PDT)
    - Re: [AMBER] Regarding understanding MTK++ Document Naveen Samala (Tue Apr 19 2011 - 11:28:24 PDT)
[AMBER] Ambertools SDK Francesco Oteri (Tue Apr 19 2011 - 09:54:13 PDT)
- Re: [AMBER] Ambertools SDK Jason Swails (Tue Apr 19 2011 - 10:43:54 PDT)
[AMBER] what do rdparm dihedral numbers mean? david condon (Tue Apr 19 2011 - 09:57:50 PDT)
- Re: [AMBER] what do rdparm dihedral numbers mean? Jason Swails (Tue Apr 19 2011 - 10:36:12 PDT)
  - Re: [AMBER] what do rdparm dihedral numbers mean? david condon (Tue Apr 19 2011 - 11:31:29 PDT)
[AMBER] Best Force Field for Beta Peptides Zachary Davis (Tue Apr 19 2011 - 11:54:49 PDT)
[AMBER] MMPBSA.py error Gabriel Urquiza (Tue Apr 19 2011 - 19:34:37 PDT)
- Re: [AMBER] MMPBSA.py error Bill Miller III (Tue Apr 19 2011 - 19:44:25 PDT)
- Re: [AMBER] MMPBSA.py error Jason Swails (Tue Apr 19 2011 - 20:09:48 PDT)
[AMBER] Side Chain Model building by MCPB Vo Cam Quy (Wed Apr 20 2011 - 09:11:12 PDT)
- Re: [AMBER] Side Chain Model building by MCPB Martin Peters (Wed Apr 20 2011 - 14:24:04 PDT)
[AMBER] Installation Amber Tools 1.5 juzer stationwala (Wed Apr 20 2011 - 10:31:51 PDT)
- Re: [AMBER] Installation Amber Tools 1.5 Jason Swails (Wed Apr 20 2011 - 10:44:33 PDT)
  - Re: [AMBER] Installation Amber Tools 1.5 juzer stationwala (Wed Apr 20 2011 - 21:39:06 PDT)
[AMBER] Regarding MTK++ MCPB tutorials on Small and Large Models of ZN Metalloprotein Naveen Samala (Wed Apr 20 2011 - 12:55:46 PDT)
- Re: [AMBER] Regarding MTK++ MCPB tutorials on Small and Large Models of ZN Metalloprotein Martin Peters (Wed Apr 20 2011 - 14:40:28 PDT)
[AMBER] Question about ptraj artifacts Kamali Sripathi (Wed Apr 20 2011 - 13:06:30 PDT)
- [AMBER] Question about ptraj artifacts Kamali Sripathi (Sun Apr 24 2011 - 06:58:53 PDT)
- Re: [AMBER] Question about ptraj artifacts Jason Swails (Sun Apr 24 2011 - 10:11:10 PDT)
  - [AMBER] Installing Ambertools1.5 on Snow Leopard Dean Cuebas (Sun Apr 24 2011 - 21:13:30 PDT)
    - Re: [AMBER] Installing Ambertools1.5 on Snow Leopard Jason Swails (Sun Apr 24 2011 - 23:39:47 PDT)
    - Re: [AMBER] Installing Ambertools1.5 on Snow Leopard Mengjuei Hsieh (Sun Apr 24 2011 - 23:55:33 PDT)
    - Re: [AMBER] Installing Ambertools1.5 on Snow Leopard Dean Cuebas (Mon Apr 25 2011 - 18:44:01 PDT)
    - Re: [AMBER] Installing Ambertools1.5 on Snow Leopard Jason Swails (Mon Apr 25 2011 - 22:23:51 PDT)
  - Re: [AMBER] Question about ptraj artifacts Kamali Sripathi (Wed Apr 27 2011 - 08:52:26 PDT)
    - Re: [AMBER] Question about ptraj artifacts Thomas Cheatham III (Wed Apr 27 2011 - 09:14:00 PDT)
    - Re: [AMBER] Question about ptraj artifacts Thomas Cheatham III (Wed Apr 27 2011 - 09:31:32 PDT)
    - Re: [AMBER] Question about ptraj artifacts Kamali Sripathi (Fri May 06 2011 - 09:04:46 PDT)
[AMBER] failures in tests of amber tools 1.5 juzer stationwala (Wed Apr 20 2011 - 22:31:26 PDT)
- Re: [AMBER] failures in tests of amber tools 1.5 Jason Swails (Thu Apr 21 2011 - 00:00:57 PDT)
[AMBER] PMEMD does not support intermolecular PRFs! vhakkim boy (Thu Apr 21 2011 - 05:14:56 PDT)
- Re: [AMBER] PMEMD does not support intermolecular PRFs! David A Case (Thu Apr 21 2011 - 05:27:17 PDT)
  - Re: [AMBER] PMEMD does not support intermolecular PRFs! Jason Swails (Thu Apr 21 2011 - 08:17:24 PDT)
Re: [AMBER] gaussian Ben Roberts (Thu Apr 21 2011 - 07:04:05 PDT)
[AMBER] Defining ligand and receptor within MMPBSA.py Oliver Kuhn (Thu Apr 21 2011 - 07:24:34 PDT)
- Re: [AMBER] Defining ligand and receptor within MMPBSA.py Jason Swails (Thu Apr 21 2011 - 08:13:32 PDT)
[AMBER] setting gbsa=0 does not switch off GB calculation Oliver Kuhn (Thu Apr 21 2011 - 09:26:30 PDT)
- Re: [AMBER] setting gbsa=0 does not switch off GB calculation Jason Swails (Thu Apr 21 2011 - 10:03:30 PDT)
[AMBER] MCPB help Hashem Taha (Thu Apr 21 2011 - 15:58:22 PDT)
- Re: [AMBER] MCPB help Hashem Taha (Mon Apr 25 2011 - 10:49:45 PDT)
  - Re: [AMBER] MCPB help Ben Roberts (Tue Apr 26 2011 - 11:30:24 PDT)
    - Re: [AMBER] MCPB help Hashem Taha (Tue May 03 2011 - 08:51:19 PDT)
    - Re: [AMBER] MCPB help Ben Roberts (Tue May 03 2011 - 14:21:07 PDT)
    - Re: [AMBER] MCPB help Martin Peters (Wed May 04 2011 - 01:02:40 PDT)
- Re: [AMBER] MCPB help Hashem Taha (Wed May 25 2011 - 09:19:08 PDT)
  - Re: [AMBER] MCPB help Hashem Taha (Thu May 26 2011 - 08:41:12 PDT)
    - Re: [AMBER] MCPB help Hashem Taha (Thu May 26 2011 - 12:14:52 PDT)
    - Re: [AMBER] MCPB help Hashem Taha (Thu May 26 2011 - 12:15:18 PDT)
    - Re: [AMBER] MCPB help Martin Peters (Fri May 27 2011 - 06:26:05 PDT)
[AMBER] how to get initial inpcrd files in smd directory of tutorial A12? Junjian Miao (Thu Apr 21 2011 - 21:01:07 PDT)
[AMBER] output velocities with ptraj Junjian Miao (Thu Apr 21 2011 - 23:49:36 PDT)
- Re: [AMBER] output velocities with ptraj Jason Swails (Fri Apr 22 2011 - 07:17:47 PDT)
[AMBER] RED conformation weights Junjian Miao (Sat Apr 23 2011 - 05:51:17 PDT)
- Re: [AMBER] RED conformation weights Jason Swails (Sat Apr 23 2011 - 09:50:54 PDT)
- Re: [AMBER] RED conformation weights Junjian Miao (Sun Apr 24 2011 - 02:53:42 PDT)
- Re: [AMBER] RED conformation weights FyD (Tue May 03 2011 - 02:13:13 PDT)
[AMBER] Problems with constant pH calc Amber 11 John Khan (Sat Apr 23 2011 - 15:22:21 PDT)
- Re: [AMBER] Problems with constant pH calc Amber 11 Jason Swails (Sat Apr 23 2011 - 16:12:24 PDT)
  - Re: [AMBER] Problems with constant pH calc Amber 11 John Khan (Sat Apr 23 2011 - 16:55:54 PDT)
    - Re: [AMBER] Problems with constant pH calc Amber 11 Jason Swails (Sat Apr 23 2011 - 17:14:19 PDT)
    - Re: [AMBER] Problems with constant pH calc Amber 11 John Khan (Sat Apr 23 2011 - 17:37:30 PDT)
    - Re: [AMBER] Problems with constant pH calc Amber 11 Jason Swails (Sat Apr 23 2011 - 18:51:59 PDT)
    - Re: [AMBER] Problems with constant pH calc Amber 11 John Khan (Mon Apr 25 2011 - 11:10:24 PDT)
    - Re: [AMBER] Problems with constant pH calc Amber 11 Jason Swails (Mon Apr 25 2011 - 11:55:29 PDT)
    - Re: [AMBER] Problems with constant pH calc Amber 11 John Khan (Mon Apr 25 2011 - 12:23:39 PDT)
[AMBER] mmpbsa, mdfil: Error unknown flag: not Andrew Voronkov (Sun Apr 24 2011 - 07:07:01 PDT)
- Re: [AMBER] mmpbsa, mdfil: Error unknown flag: not Bill Miller III (Sun Apr 24 2011 - 07:54:10 PDT)
  - Re: [AMBER] mmpbsa, mdfil: Error unknown flag: not Andrew Voronkov (Sat May 07 2011 - 11:08:41 PDT)
    - Re: [AMBER] mmpbsa, mdfil: Error unknown flag: not Jason Swails (Sat May 07 2011 - 11:54:01 PDT)
    - Re: [AMBER] mmpbsa, mdfil: Error unknown flag: not Andrew Voronkov (Sun May 08 2011 - 06:57:54 PDT)
    - Re: [AMBER] mmpbsa, mdfil: Error unknown flag: not Andrew Voronkov (Sun May 08 2011 - 08:28:11 PDT)
    - Re: [AMBER] mmpbsa, mdfil: Error unknown flag: not Jason Swails (Sun May 08 2011 - 09:19:27 PDT)
  - Re: [AMBER] mmpbsa, mdfil: Error unknown flag: not Bill Ross (Sun May 08 2011 - 11:10:10 PDT)
    - Re: [AMBER] mmpbsa, mdfil: Error unknown flag: not Andrew Voronkov (Tue May 10 2011 - 09:26:01 PDT)
    - Re: [AMBER] mmpbsa, mdfil: Error unknown flag: not Jason Swails (Tue May 10 2011 - 13:14:30 PDT)
    - Re: [AMBER] mmpbsa, mdfil: Error unknown flag: not Andrew Voronkov (Sun May 15 2011 - 09:18:04 PDT)
    - Re: [AMBER] mmpbsa, mdfil: Error unknown flag: not Bill Miller III (Sun May 15 2011 - 09:21:30 PDT)
    - Re: [AMBER] mmpbsa, mdfil: Error unknown flag: not Andrew Voronkov (Sun May 15 2011 - 14:40:47 PDT)
    - Re: [AMBER] mmpbsa, mdfil: Error unknown flag: not Jason Swails (Sun May 15 2011 - 15:03:50 PDT)
[AMBER] Equilibration: Using restraintmask George Tzotzos (Mon Apr 25 2011 - 04:53:53 PDT)
- Re: [AMBER] Equilibration: Using restraintmask Jason Swails (Mon Apr 25 2011 - 09:02:35 PDT)
  - Re: [AMBER] Equilibration: Using restraintmask George Tzotzos (Mon Apr 25 2011 - 09:05:37 PDT)
[AMBER] Xleap problem souvik sur (Mon Apr 25 2011 - 06:55:54 PDT)
- Re: [AMBER] Xleap problem David A Case (Mon Apr 25 2011 - 07:03:46 PDT)
  - Re: [AMBER] Xleap problem souvik sur (Mon Apr 25 2011 - 22:40:01 PDT)
- Re: [AMBER] Xleap problem Bill Ross (Mon Apr 25 2011 - 22:46:50 PDT)
  - Re: [AMBER] Xleap problem souvik sur (Tue Apr 26 2011 - 00:46:04 PDT)
    - Re: [AMBER] Xleap problem David A Case (Tue Apr 26 2011 - 05:07:06 PDT)
- Re: [AMBER] Xleap problem William Wei (Mon Aug 22 2011 - 14:19:24 PDT)
  - Re: [AMBER] Xleap problem Ross Walker (Mon Aug 22 2011 - 14:43:40 PDT)
[AMBER] MMPBSA error Vaibhav Jain (Mon Apr 25 2011 - 08:16:46 PDT)
- Re: [AMBER] MMPBSA error Jason Swails (Mon Apr 25 2011 - 08:56:08 PDT)
[AMBER] changing restart file format from 6f12.7 to 6f12.6 Santosh Mogurampelly (Mon Apr 25 2011 - 23:30:26 PDT)
- Re: [AMBER] changing restart file format from 6f12.7 to 6f12.6 David A Case (Tue Apr 26 2011 - 05:35:11 PDT)
  - Re: [AMBER] changing restart file format from 6f12.7 to 6f12.6 Santosh Mogurampelly (Tue Apr 26 2011 - 07:45:32 PDT)
[AMBER] MMPBSA.py (AmberTools 1.5) bug in Alanine Scanning (alamdcrd.py) Joseph André (Tue Apr 26 2011 - 02:48:27 PDT)
- Re: [AMBER] MMPBSA.py (AmberTools 1.5) bug in Alanine Scanning (alamdcrd.py) Dwight McGee (Tue Apr 26 2011 - 06:02:55 PDT)
[AMBER] End of protonate method with amber11? Guenegou, Guillaume [ORDFR] (Tue Apr 26 2011 - 04:54:38 PDT)
- Re: [AMBER] End of protonate method with amber11? David A Case (Tue Apr 26 2011 - 06:44:29 PDT)
  - Re: [AMBER] End of protonate method with amber11? Guenegou, Guillaume [ORDFR] (Tue Apr 26 2011 - 07:12:08 PDT)
    - Re: [AMBER] End of protonate method with amber11? Ben Roberts (Tue Apr 26 2011 - 07:21:44 PDT)
    - Re: [AMBER] End of protonate method with amber11? Guenegou, Guillaume [ORDFR] (Tue Apr 26 2011 - 07:33:22 PDT)
[AMBER] Alanine scanning George Tzotzos (Tue Apr 26 2011 - 05:50:00 PDT)
- Re: [AMBER] Alanine scanning Bill Miller III (Tue Apr 26 2011 - 05:59:04 PDT)
  - Re: [AMBER] Alanine scanning George Tzotzos (Tue Apr 26 2011 - 06:26:34 PDT)
    - Re: [AMBER] Alanine scanning Bill Miller III (Tue Apr 26 2011 - 06:32:21 PDT)
[AMBER] xleap problem souvik sur (Tue Apr 26 2011 - 06:21:17 PDT)
[AMBER] usage of secstruct and atomicfluct py (Tue Apr 26 2011 - 06:24:26 PDT)
[AMBER] Problem with cluster? Roman Osman (Tue Apr 26 2011 - 08:39:36 PDT)
- Re: [AMBER] Problem with cluster? Jianyin Shao (Tue Apr 26 2011 - 09:58:58 PDT)
  - Re: [AMBER] Problem with cluster? Roman Osman (Tue Apr 26 2011 - 10:06:04 PDT)
[AMBER] softcore potential and temperature anyiphysics.gmail.com (Tue Apr 26 2011 - 11:19:40 PDT)
- Re: [AMBER] softcore potential and temperature steinbrt.rci.rutgers.edu (Tue Apr 26 2011 - 12:25:44 PDT)
  - Re: [AMBER] softcore potential and temperature anyiphysics.gmail.com (Tue Apr 26 2011 - 14:39:02 PDT)
[AMBER] MTK++ : genMetalFF.sh is not generating gaussian input files Naveen Samala (Tue Apr 26 2011 - 15:22:45 PDT)
- Re: [AMBER] MTK++ : genMetalFF.sh is not generating gaussian input files Ben Roberts (Tue Apr 26 2011 - 15:45:58 PDT)
[AMBER] xleap problem souvik sur (Tue Apr 26 2011 - 20:58:55 PDT)
- Re: [AMBER] xleap problem vhakkim boy (Tue Apr 26 2011 - 21:14:14 PDT)
[AMBER] MCPB install problem setyanto md (Tue Apr 26 2011 - 23:28:09 PDT)
- Re: [AMBER] MCPB install problem Martin Peters (Wed Apr 27 2011 - 00:13:47 PDT)
  - Re: [AMBER] MCPB install problem setyanto md (Thu Apr 28 2011 - 04:47:56 PDT)
    - Re: [AMBER] MCPB install problem Jason Swails (Thu Apr 28 2011 - 05:36:17 PDT)
    - Re: [AMBER] MCPB install problem setyanto md (Wed May 04 2011 - 00:48:35 PDT)
[AMBER] Diffusion coefficient in implicit water tommaso.casalini.mail.polimi.it (Wed Apr 27 2011 - 02:07:53 PDT)
- Re: [AMBER] Diffusion coefficient in implicit water David A. Case (Wed Apr 27 2011 - 05:01:04 PDT)
[AMBER] error while editing charge table in Tutorial A1 by Dr. Walker Chinh Su Tran To (Wed Apr 27 2011 - 02:17:45 PDT)
[AMBER] MMPBSA.py won't understand my trajectories Gabriel Urquiza (Wed Apr 27 2011 - 04:52:51 PDT)
- Re: [AMBER] MMPBSA.py won't understand my trajectories Bill Miller III (Wed Apr 27 2011 - 05:00:52 PDT)
  - Re: [AMBER] MMPBSA.py won't understand my trajectories Gabriel Urquiza (Wed Apr 27 2011 - 06:19:39 PDT)
[AMBER] igb=8 available for MMPBSA.py ? Oliver Kuhn (Wed Apr 27 2011 - 07:48:20 PDT)
- Re: [AMBER] igb=8 available for MMPBSA.py ? Bill Miller III (Wed Apr 27 2011 - 09:11:14 PDT)
- Re: [AMBER] igb=8 available for MMPBSA.py ? Jason Swails (Wed Apr 27 2011 - 09:57:24 PDT)
  - Re: [AMBER] igb=8 available for MMPBSA.py ? Carlos Simmerling (Wed Apr 27 2011 - 10:48:06 PDT)
    - Re: [AMBER] igb=8 available for MMPBSA.py ? Hai Nguyen (Thu Mar 07 2013 - 11:00:15 PST)
[AMBER] Atom types in LYN side chain Paul S. Nerenberg (Wed Apr 27 2011 - 18:08:19 PDT)
- Re: [AMBER] Atom types in LYN side chain cieplak.cgl.ucsf.edu (Wed Apr 27 2011 - 18:52:07 PDT)
[AMBER] MMPBSA.py error - VDW **** Jesper Sørensen (Thu Apr 28 2011 - 00:29:08 PDT)
- Re: [AMBER] MMPBSA.py error - VDW **** Jason Swails (Thu Apr 28 2011 - 00:47:31 PDT)
  - Re: [AMBER] MMPBSA.py error - VDW **** Jesper Sørensen (Fri Apr 29 2011 - 01:38:05 PDT)
[AMBER] Steered MD at constant force Ali M. Naserian-Nik (Thu Apr 28 2011 - 05:55:23 PDT)
- Re: [AMBER] Steered MD at constant force Daniel Roe (Thu Apr 28 2011 - 06:41:56 PDT)
  - Re: [AMBER] Steered MD at constant force Ali M. Naserian-Nik (Thu Apr 28 2011 - 07:26:33 PDT)
[AMBER] Usage of ambermask within MMPBSA.py Oliver Kuhn (Thu Apr 28 2011 - 06:04:33 PDT)
- Re: [AMBER] Usage of ambermask within MMPBSA.py Bill Miller III (Thu Apr 28 2011 - 06:07:10 PDT)
- Re: [AMBER] Usage of ambermask within MMPBSA.py Jason Swails (Thu Apr 28 2011 - 08:36:51 PDT)
[AMBER] Usage of Kongsted Ryde entropy method within MMPBSA.py Oliver Kuhn (Thu Apr 28 2011 - 06:18:12 PDT)
- Re: [AMBER] Usage of Kongsted Ryde entropy method within MMPBSA.py Markus Kaukonen (Thu Apr 28 2011 - 06:38:43 PDT)
- Re: [AMBER] Usage of Kongsted Ryde entropy method within MMPBSA.py Jason Swails (Thu Apr 28 2011 - 08:59:40 PDT)
  - Re: [AMBER] Usage of Kongsted Ryde entropy method within MMPBSA.py Oliver Kuhn (Thu Apr 28 2011 - 09:10:29 PDT)
    - Re: [AMBER] Usage of Kongsted Ryde entropy method within MMPBSA.py Jason Swails (Thu Apr 28 2011 - 17:32:29 PDT)
    - Re: [AMBER] Usage of Kongsted Ryde entropy method within MMPBSA.py Samuel Genheden (Fri Apr 29 2011 - 06:45:06 PDT)
    - Re: [AMBER] Usage of Kongsted Ryde entropy method within MMPBSA.py Jason Swails (Fri Apr 29 2011 - 07:11:44 PDT)
    - Re: [AMBER] Usage of Kongsted Ryde entropy method within MMPBSA.py Samuel Genheden (Fri Apr 29 2011 - 07:34:08 PDT)
    - Re: [AMBER] Usage of Kongsted Ryde entropy method within MMPBSA.py Jason Swails (Fri Apr 29 2011 - 07:39:26 PDT)
    - Re: [AMBER] Usage of Kongsted Ryde entropy method within MMPBSA.py Samuel Genheden (Fri Apr 29 2011 - 07:47:07 PDT)
    - Re: [AMBER] Usage of Kongsted Ryde entropy method within MMPBSA.py Jason Swails (Fri Apr 29 2011 - 07:51:18 PDT)
    - Re: [AMBER] Usage of Kongsted Ryde entropy method within MMPBSA.py Samuel Genheden (Fri Apr 29 2011 - 08:05:59 PDT)
    - Re: [AMBER] Usage of Kongsted Ryde entropy method within MMPBSA.py Oliver Kuhn (Fri Apr 29 2011 - 07:48:18 PDT)
[AMBER] building amber - meaning of file comparison problems? Vernon Bailey (Thu Apr 28 2011 - 09:07:27 PDT)
- Re: [AMBER] building amber - meaning of file comparison problems? Jason Swails (Thu Apr 28 2011 - 09:09:15 PDT)
[AMBER] Regarding Gaussian Calculations for MTK++ example- sidechain model Naveen Samala (Thu Apr 28 2011 - 09:23:07 PDT)
- Re: [AMBER] Regarding Gaussian Calculations for MTK++ example- sidechain model Ben Roberts (Thu Apr 28 2011 - 09:28:12 PDT)
[AMBER] compile errors with AmberTools1.5 + Amber11 Robert Wohlhueter (Thu Apr 28 2011 - 12:52:22 PDT)
- Re: [AMBER] compile errors with AmberTools1.5 + Amber11 Jason Swails (Thu Apr 28 2011 - 17:35:17 PDT)
  - Re: [AMBER] compile errors with AmberTools1.5 + Amber11 Robert Wohlhueter (Fri Apr 29 2011 - 07:06:41 PDT)
    - Re: [AMBER] compile errors with AmberTools1.5 + Amber11 Jason Swails (Fri Apr 29 2011 - 12:52:55 PDT)
    - Re: [AMBER] compile errors with AmberTools1.5 + Amber11 dacase.rci.rutgers.edu (Fri Apr 29 2011 - 13:05:49 PDT)
    - Re: [AMBER] compile errors with AmberTools1.5 + Amber11 Robert Wohlhueter (Sat Apr 30 2011 - 17:04:04 PDT)
    - Re: [AMBER] compile errors with AmberTools1.5 + Amber11 Jason Swails (Sun May 01 2011 - 03:45:05 PDT)
    - Re: [AMBER] compile errors with AmberTools1.5 + Amber11 Robert Wohlhueter (Sun May 01 2011 - 18:46:14 PDT)
[AMBER] ptraj trajectory file size limits? Nicole A. Horenstein (Thu Apr 28 2011 - 20:14:27 PDT)
- Re: [AMBER] ptraj trajectory file size limits? Bill Miller III (Thu Apr 28 2011 - 20:20:15 PDT)
  - Re: [AMBER] ptraj trajectory file size limits? juzer stationwala (Thu Apr 28 2011 - 21:21:59 PDT)
    - Re: [AMBER] ptraj trajectory file size limits? Jason Swails (Fri Apr 29 2011 - 05:10:59 PDT)
    - Re: [AMBER] ptraj trajectory file size limits? Nicole A. Horenstein (Sun May 01 2011 - 08:42:01 PDT)
[AMBER] Free Energy Perturbation in AMBER 10 Chirag Vora (Thu Apr 28 2011 - 21:41:57 PDT)
- Re: [AMBER] Free Energy Perturbation in AMBER 10 steinbrt.rci.rutgers.edu (Fri Apr 29 2011 - 01:53:31 PDT)
  - Re: [AMBER] Free Energy Perturbation in AMBER 10 David A. Case (Fri Apr 29 2011 - 15:06:06 PDT)
[AMBER] Post-Processing MD trajectory sunita gupta (Fri Apr 29 2011 - 04:36:27 PDT)
- Re: [AMBER] Post-Processing MD trajectory Adrian Roitberg (Fri Apr 29 2011 - 04:39:10 PDT)
  - Re: [AMBER] Post-Processing MD trajectory sunita gupta (Fri Apr 29 2011 - 04:42:37 PDT)
    - Re: [AMBER] Post-Processing MD trajectory Jason Swails (Fri Apr 29 2011 - 05:26:53 PDT)
    - Re: [AMBER] Post-Processing MD trajectory sunita gupta (Fri Apr 29 2011 - 05:40:25 PDT)
    - Re: [AMBER] Post-Processing MD trajectory Jason Swails (Fri Apr 29 2011 - 05:44:10 PDT)
    - Re: [AMBER] Post-Processing MD trajectory Carlos Simmerling (Fri Apr 29 2011 - 05:56:01 PDT)
    - Re: [AMBER] Post-Processing MD trajectory sunita gupta (Sat Apr 30 2011 - 01:00:46 PDT)
    - Re: [AMBER] Post-Processing MD trajectory Jason Swails (Sat Apr 30 2011 - 01:51:56 PDT)
[AMBER] New equilibrated solvent box, how to use it? Samuel Genheden (Fri Apr 29 2011 - 05:28:15 PDT)
[AMBER] parameters sodium phosfate Domenica Dibenedetto (Fri Apr 29 2011 - 07:10:09 PDT)
- [AMBER] Fwd: parameters sodium phosfate Domenica Dibenedetto (Mon May 02 2011 - 03:40:33 PDT)
[AMBER] forrtl: severe (64): input conversion error, unit -5, file Internal Formatted Read Katharina Lang (Fri Apr 29 2011 - 07:33:02 PDT)
- Re: [AMBER] forrtl: severe (64): input conversion error, unit -5, file Internal Formatted Read Katharina Lang (Fri May 06 2011 - 07:54:07 PDT)
  - Re: [AMBER] forrtl: severe (64): input conversion error, unit -5, file Internal Formatted Read Jason Swails (Fri May 06 2011 - 09:12:16 PDT)
[AMBER] AmberTools 1.4 PGI failed antechamber/sustiva test Shan-ho Tsai (Fri Apr 29 2011 - 09:25:02 PDT)
- Re: [AMBER] AmberTools 1.4 PGI failed antechamber/sustiva test dacase.rci.rutgers.edu (Fri Apr 29 2011 - 12:35:21 PDT)
  - Re: [AMBER] AmberTools 1.4 PGI failed antechamber/sustiva test Shan-ho Tsai (Fri Apr 29 2011 - 13:41:25 PDT)
    - Re: [AMBER] AmberTools 1.4 PGI failed antechamber/sustiva test Shan-ho Tsai (Tue May 03 2011 - 13:10:38 PDT)
[AMBER] SURFTEN / SURFOFF values are not consistent across *.all.out files zhihong ke (Fri Apr 29 2011 - 09:29:18 PDT)
- Re: [AMBER] SURFTEN / SURFOFF values are not consistent across *.all.out files Jason Swails (Fri Apr 29 2011 - 12:56:44 PDT)
[AMBER] umbrella sampling on a difference of distances RC. iccy liu (Fri Apr 29 2011 - 11:06:17 PDT)
- Re: [AMBER] umbrella sampling on a difference of distances RC. Jason Swails (Fri Apr 29 2011 - 13:03:50 PDT)
- Re: [AMBER] umbrella sampling on a difference of distances RC. David A. Case (Wed May 04 2011 - 06:33:48 PDT)
  - Re: [AMBER] umbrella sampling on a difference of distances RC. Adrian Roitberg (Wed May 04 2011 - 06:57:34 PDT)
    - Re: [AMBER] umbrella sampling on a difference of distances RC. M. L. Dodson (Wed May 04 2011 - 07:11:00 PDT)
    - Re: [AMBER] umbrella sampling on a difference of distances RC. dacase.rci.rutgers.edu (Wed May 04 2011 - 07:51:37 PDT)
[AMBER] help with antechamber tsurma.umich.edu (Fri Apr 29 2011 - 12:12:35 PDT)
- Re: [AMBER] help with antechamber jun kit (Wed Nov 23 2011 - 08:03:06 PST)
- Re: [AMBER] help with antechamber jun kit (Thu Nov 24 2011 - 08:17:52 PST)
- Re: [AMBER] help with antechamber jun kit (Sun Nov 27 2011 - 07:47:26 PST)
  - Re: [AMBER] help with antechamber David A Case (Mon Nov 28 2011 - 09:57:31 PST)
[AMBER] help with antechamber tsurma.umich.edu (Fri Apr 29 2011 - 12:42:57 PDT)
- Re: [AMBER] help with antechamber dacase.rci.rutgers.edu (Fri Apr 29 2011 - 12:52:29 PDT)
  - Re: [AMBER] help with antechamber tsurma.umich.edu (Sun May 01 2011 - 18:37:55 PDT)
[AMBER] mmpbsa nmode problem Yi An (Fri Apr 29 2011 - 13:29:26 PDT)
- Re: [AMBER] mmpbsa nmode problem Bill Miller III (Fri Apr 29 2011 - 19:54:30 PDT)
- Re: [AMBER] mmpbsa nmode problem anyiphysics.gmail.com (Sat Apr 30 2011 - 15:17:36 PDT)
  - Re: [AMBER] mmpbsa nmode problem Bill Miller III (Sat Apr 30 2011 - 15:31:02 PDT)
- Re: [AMBER] mmpbsa nmode problem anyiphysics.gmail.com (Sat Apr 30 2011 - 15:36:18 PDT)
  - Re: [AMBER] mmpbsa nmode problem Jason Swails (Sun May 01 2011 - 03:53:40 PDT)
[AMBER] question on scmask Yi An (Fri Apr 29 2011 - 13:36:15 PDT)
[AMBER] How to add a new force field to Amber 11 hanlu0366 (Fri Apr 29 2011 - 20:12:49 PDT)
[AMBER] MMPBSA for trimerization process Lekpa Duukori (Sun May 01 2011 - 03:19:32 PDT)
- Re: [AMBER] MMPBSA for trimerization process Jason Swails (Sun May 01 2011 - 03:48:52 PDT)
  - Re: [AMBER] MMPBSA for trimerization process Lekpa Duukori (Sun May 01 2011 - 04:04:16 PDT)
[AMBER] question regarding H-bond calculation juzer stationwala (Sun May 01 2011 - 08:15:48 PDT)
- Re: [AMBER] question regarding H-bond calculation Adrian Roitberg (Sun May 01 2011 - 08:18:27 PDT)
[AMBER] Antechamber Problem souvik sur (Sun May 01 2011 - 10:46:40 PDT)
- Re: [AMBER] Antechamber Problem Ross Walker (Mon May 02 2011 - 01:42:51 PDT)
  - Re: [AMBER] Antechamber Problem souvik sur (Mon May 02 2011 - 01:59:52 PDT)
    - Re: [AMBER] Antechamber Problem Jason Swails (Mon May 02 2011 - 03:02:57 PDT)
    - Re: [AMBER] Antechamber Problem souvik sur (Mon May 02 2011 - 03:56:03 PDT)
    - Re: [AMBER] Antechamber Problem Jason Swails (Mon May 02 2011 - 04:10:35 PDT)
[AMBER] help with ewald parameter tsurma.umich.edu (Sun May 01 2011 - 18:37:18 PDT)
- Re: [AMBER] help with ewald parameter Ross Walker (Mon May 02 2011 - 01:41:57 PDT)
  - Re: [AMBER] help with ewald parameter tsurma.umich.edu (Mon May 02 2011 - 08:47:52 PDT)
    - Re: [AMBER] help with ewald parameter Ankita Kumari (Mon May 02 2011 - 22:25:12 PDT)
- Re: [AMBER] help with ewald parameter Bill Ross (Tue May 03 2011 - 10:40:47 PDT)
[AMBER] Hardwares requirement souvik sur (Mon May 02 2011 - 00:38:51 PDT)
- Re: [AMBER] Hardwares requirement Jason Swails (Mon May 02 2011 - 04:11:29 PDT)
  - Re: [AMBER] Hardwares requirement souvik sur (Mon May 02 2011 - 22:31:16 PDT)
    - Re: [AMBER] Hardwares requirement Paul S. Nerenberg (Mon May 02 2011 - 22:38:02 PDT)
    - Re: [AMBER] Hardwares requirement souvik sur (Wed May 04 2011 - 06:42:39 PDT)
    - Re: [AMBER] Hardwares requirement Jason Swails (Wed May 04 2011 - 07:36:47 PDT)
[AMBER] mmpbsa problems with amber 11 Guenegou, Guillaume [ORDFR] (Mon May 02 2011 - 00:48:32 PDT)
- Re: [AMBER] mmpbsa problems with amber 11 Jason Swails (Mon May 02 2011 - 01:45:29 PDT)
  - Re: [AMBER] mmpbsa problems with amber 11 David A. Case (Mon May 02 2011 - 08:27:17 PDT)
    - Re: [AMBER] mmpbsa problems with amber 11 Jason Swails (Tue May 03 2011 - 10:46:30 PDT)
[AMBER] Forcefield for Modified RNA hari krishna (Mon May 02 2011 - 21:49:44 PDT)
- Re: [AMBER] Forcefield for Modified RNA FyD (Tue May 03 2011 - 02:20:10 PDT)
- Re: [AMBER] Forcefield for Modified RNA David A. Case (Tue May 03 2011 - 08:41:12 PDT)
  - Re: [AMBER] Forcefield for Modified RNA hari krishna (Thu May 05 2011 - 03:48:05 PDT)
    - Re: [AMBER] Forcefield for Modified RNA Jason Swails (Thu May 05 2011 - 05:02:54 PDT)
[AMBER] defining the mixed 1-4 scaling in amber 11 and sleap Toshifumi Yui (Thu May 03 2007 - 05:18:52 PDT)
- Re: [AMBER] defining the mixed 1-4 scaling in amber 11 and sleap Jason Swails (Tue May 03 2011 - 11:05:14 PDT)
- Re: [AMBER] defining the mixed 1-4 scaling in amber 11 and sleap Toshifumi Yui (Thu May 03 2007 - 18:25:51 PDT)
  - Re: [AMBER] defining the mixed 1-4 scaling in amber 11 and sleap Jason Swails (Tue May 03 2011 - 22:47:07 PDT)
[AMBER] Usage non-zero IVCAP in MM-PBSA ? Marek Maly (Tue May 03 2011 - 05:48:57 PDT)
[AMBER] MCPB problem Manish (Tue May 03 2011 - 09:31:36 PDT)
- Re: [AMBER] MCPB problem Hashem Taha (Tue May 03 2011 - 12:05:05 PDT)
  - Re: [AMBER] MCPB problem Manish (Tue May 03 2011 - 14:13:04 PDT)
    - Re: [AMBER] MCPB problem Ben Roberts (Tue May 03 2011 - 14:20:18 PDT)
    - Re: [AMBER] MCPB problem Manish (Wed May 04 2011 - 08:22:00 PDT)
    - Re: [AMBER] MCPB problem Martin Peters (Wed May 04 2011 - 08:39:55 PDT)
[AMBER] H-Bond %occupancy Sangita Kachhap (Tue May 03 2011 - 11:11:03 PDT)
- Re: [AMBER] H-Bond %occupancy Thomas Cheatham (Tue May 03 2011 - 11:14:49 PDT)
[AMBER] forrtl: severe (64): input conversion error Jagur Lambix (Tue May 03 2011 - 14:17:03 PDT)
- Re: [AMBER] forrtl: severe (64): input conversion error manikanthan bhavaraju (Tue May 03 2011 - 18:15:23 PDT)
- [AMBER] SANDER ERROR: forrtl: severe (64): input conversion error Jagur Lambix (Thu May 05 2011 - 15:35:21 PDT)
  - Re: [AMBER] SANDER ERROR: forrtl: severe (64): input conversion error Jason Swails (Thu May 05 2011 - 15:42:22 PDT)
  - Re: [AMBER] SANDER ERROR: forrtl: severe (64): input conversion error Carlos Simmerling (Thu May 05 2011 - 15:42:42 PDT)
  - Re: [AMBER] SANDER ERROR: forrtl: severe (64): input conversion error Bill Ross (Thu May 05 2011 - 15:52:19 PDT)
[AMBER] MTK++ MCPB Example: Creating Force Field Modification Files Naveen Samala (Wed May 04 2011 - 10:48:39 PDT)
- Re: [AMBER] MTK++ MCPB Example: Creating Force Field Modification Files Ben Roberts (Wed May 04 2011 - 11:29:49 PDT)
[AMBER] Possibility to define residues pairs for inter-residual hbond analysis ? Marek Maly (Wed May 04 2011 - 11:57:04 PDT)
[AMBER] MTK++/MCPB Error Loading AMBER prep file 1AMP_OH_chg2.prep in xleap Naveen Samala (Wed May 04 2011 - 13:47:17 PDT)
- Re: [AMBER] MTK++/MCPB Error Loading AMBER prep file 1AMP_OH_chg2.prep in xleap Martin Peters (Thu May 05 2011 - 01:27:45 PDT)
  - Re: [AMBER] MTK++/MCPB Error Loading AMBER prep file 1AMP_OH_chg2.prep in xleap Naveen Samala (Thu May 05 2011 - 07:52:55 PDT)
    - Re: [AMBER] MTK++/MCPB Error Loading AMBER prep file 1AMP_OH_chg2.prep in xleap Martin Peters (Thu May 05 2011 - 08:22:41 PDT)
    - Re: [AMBER] MTK++/MCPB Error Loading AMBER prep file 1AMP_OH_chg2.prep in xleap Naveen Samala (Thu May 05 2011 - 08:53:56 PDT)
    - Re: [AMBER] MTK++/MCPB Error Loading AMBER prep file 1AMP_OH_chg2.prep in xleap Martin Peters (Thu May 05 2011 - 13:01:38 PDT)
    - Re: [AMBER] MTK++/MCPB Error Loading AMBER prep file 1AMP_OH_chg2.prep in xleap Naveen Samala (Thu May 05 2011 - 13:26:26 PDT)
- Re: [AMBER] MTK++/MCPB Error Loading AMBER prep file 1AMP_OH_chg2.prep in xleap Bill Ross (Thu May 05 2011 - 11:42:33 PDT)
[AMBER] System configuration requirement for installing Amber9 in cluster souvik sur (Wed May 04 2011 - 20:57:38 PDT)
[AMBER] Error in creating a cpin file pankhuri arora (Wed May 04 2011 - 22:34:38 PDT)
- Re: [AMBER] Error in creating a cpin file Jason Swails (Fri May 06 2011 - 17:33:29 PDT)
  - Re: [AMBER] Error in creating a cpin file pankhuri arora (Mon May 09 2011 - 02:55:25 PDT)
    - Re: [AMBER] Error in creating a cpin file Jason Swails (Mon May 09 2011 - 07:48:29 PDT)
[AMBER] Xleap trouble souvik sur (Wed May 04 2011 - 23:53:11 PDT)
Re: [AMBER] question about scmask Lishan Yao (Thu May 05 2011 - 02:29:43 PDT)
- Re: [AMBER] question about scmask steinbrt.rci.rutgers.edu (Thu May 05 2011 - 03:33:56 PDT)
- Re: [AMBER] question about scmask Lishan Yao (Thu May 05 2011 - 17:53:29 PDT)
  - Re: [AMBER] question about scmask steinbrt.rci.rutgers.edu (Fri May 06 2011 - 00:28:57 PDT)
- Re: [AMBER] question about scmask Lishan Yao (Fri May 06 2011 - 01:05:37 PDT)
  - Re: [AMBER] question about scmask steinbrt.rci.rutgers.edu (Fri May 06 2011 - 01:23:28 PDT)
[AMBER] forrtl: error (78): process killed (SIGTERM), MD simulation ligand molecule docked into protein siddesh southekal (Thu May 05 2011 - 03:07:19 PDT)
- Re: [AMBER] forrtl: error (78): process killed (SIGTERM), MD simulation ligand molecule docked into protein David A Case (Thu May 05 2011 - 06:06:17 PDT)
- Re: [AMBER] forrtl: error (78): process killed (SIGTERM), MD simulation ligand molecule docked into protein Jason Swails (Thu May 05 2011 - 06:36:01 PDT)
  - Re: [AMBER] forrtl: error (78): process killed (SIGTERM), MD simulation ligand molecule docked into protein siddesh southekal (Tue May 17 2011 - 05:37:09 PDT)
    - Re: [AMBER] forrtl: error (78): process killed (SIGTERM), MD simulation ligand molecule docked into protein Jason Swails (Tue May 17 2011 - 07:41:27 PDT)
[AMBER] problem with nmode poll.chemie.uni-hamburg.de (Thu May 05 2011 - 06:59:13 PDT)
- Re: [AMBER] problem with nmode Jason Swails (Thu May 05 2011 - 07:12:44 PDT)
[AMBER] Solvent box John S (Thu May 05 2011 - 11:22:15 PDT)
- [AMBER] Protein drifting out of the solvent box Sasha Buzko (Thu May 05 2011 - 12:03:27 PDT)
  - Re: [AMBER] Protein drifting out of the solvent box Carlos Simmerling (Thu May 05 2011 - 12:12:46 PDT)
    - Re: [AMBER] Protein drifting out of the solvent box Sasha Buzko (Thu May 05 2011 - 13:59:37 PDT)
  - Re: [AMBER] Protein drifting out of the solvent box Jason Swails (Thu May 05 2011 - 14:10:17 PDT)
    - Re: [AMBER] Protein drifting out of the solvent box Sasha Buzko (Thu May 05 2011 - 14:39:46 PDT)
    - Re: [AMBER] Protein drifting out of the solvent box InSuk Joung (Sat May 07 2011 - 21:01:04 PDT)
    - Re: [AMBER] Protein drifting out of the solvent box Sasha Buzko (Mon May 09 2011 - 13:51:56 PDT)
[AMBER] internal energy INT is not zero in mm_pbsa mirage . (Thu May 05 2011 - 12:15:56 PDT)
- Re: [AMBER] internal energy INT is not zero in mm_pbsa Bill Miller III (Thu May 05 2011 - 12:26:59 PDT)
  - Re: [AMBER] internal energy INT is not zero in mm_pbsa Dwight McGee (Thu May 05 2011 - 12:31:04 PDT)
    - Re: [AMBER] internal energy INT is not zero in mm_pbsa mirage . (Fri May 06 2011 - 01:24:11 PDT)
    - Re: [AMBER] internal energy INT is not zero in mm_pbsa mirage . (Sat May 07 2011 - 10:15:07 PDT)
    - Re: [AMBER] internal energy INT is not zero in mm_pbsa Bill Miller III (Sat May 07 2011 - 10:21:27 PDT)
- Re: [AMBER] internal energy INT is not zero in mm_pbsa mirage . (Sun May 08 2011 - 01:43:03 PDT)
  - Re: [AMBER] internal energy INT is not zero in mm_pbsa mirage . (Sun May 08 2011 - 01:56:16 PDT)
    - Re: [AMBER] internal energy INT is not zero in mm_pbsa mirage . (Sun May 08 2011 - 02:43:45 PDT)
    - Re: [AMBER] internal energy INT is not zero in mm_pbsa Jason Swails (Sun May 08 2011 - 03:28:42 PDT)
  - Re: [AMBER] internal energy INT is not zero in mm_pbsa Jason Swails (Sun May 08 2011 - 01:56:07 PDT)
[AMBER] Question about ptraj hbond schematic Kamali Sripathi (Thu May 05 2011 - 13:58:52 PDT)
- Re: [AMBER] Question about ptraj hbond schematic Thomas Cheatham III (Fri May 06 2011 - 14:12:27 PDT)
  - Re: [AMBER] Question about ptraj hbond schematic Kamali Sripathi (Mon Aug 01 2011 - 04:32:41 PDT)
[AMBER] Entropy calculation using MM_PBSA.py mish (Thu May 05 2011 - 14:25:23 PDT)
- Re: [AMBER] Entropy calculation using MM_PBSA.py Bill Miller III (Thu May 05 2011 - 14:31:26 PDT)
  - Re: [AMBER] Entropy calculation using MM_PBSA.py mish (Thu May 05 2011 - 14:35:08 PDT)
[AMBER] TS calculation Mahmoud Soliman (Thu May 05 2011 - 13:40:07 PDT)
[AMBER] TS calculation Mahmoud Soliman (Fri May 06 2011 - 00:39:52 PDT)
- Re: [AMBER] TS calculation Jason Swails (Fri May 06 2011 - 03:11:10 PDT)
- Re: [AMBER] TS calculation Ross Walker (Fri May 06 2011 - 03:15:51 PDT)
  - Re: [AMBER] TS calculation Mahmoud Soliman (Fri May 06 2011 - 03:05:36 PDT)
[AMBER] Antechamber loading Problem souvik sur (Fri May 06 2011 - 05:25:22 PDT)
- Re: [AMBER] Antechamber loading Problem David A Case (Fri May 06 2011 - 07:02:01 PDT)
  - Re: [AMBER] Antechamber loading Problem souvik sur (Fri May 06 2011 - 21:01:27 PDT)
    - Re: [AMBER] Antechamber loading Problem Adrian Roitberg (Sat May 07 2011 - 00:48:04 PDT)
    - Re: [AMBER] Antechamber loading Problem Jason Swails (Sat May 07 2011 - 03:04:08 PDT)
    - Re: [AMBER] Antechamber loading Problem Jason Swails (Sat May 07 2011 - 03:36:35 PDT)
[AMBER] parameter-for-peptide-blocking-group vhakkim boy (Fri May 06 2011 - 05:51:42 PDT)
- Re: [AMBER] parameter-for-peptide-blocking-group FyD (Fri May 06 2011 - 07:35:54 PDT)
[AMBER] hbond solvent output problem ... Marek Maly (Fri May 06 2011 - 13:04:26 PDT)
[AMBER] MTK++/MCPB Side Chain Model Naveen Samala (Fri May 06 2011 - 15:39:46 PDT)
- Re: [AMBER] MTK++/MCPB Side Chain Model Yang, Yue (Fri May 06 2011 - 18:38:19 PDT)
[AMBER] Problem in preparation of log file Sindrila Dutta banik (Sat May 07 2011 - 00:50:08 PDT)
- Re: [AMBER] Problem in preparation of log file case (Sat May 07 2011 - 06:37:25 PDT)
[AMBER] Positive Energy Kshatresh Dutta Dubey (Sat May 07 2011 - 03:22:04 PDT)
- Re: [AMBER] Positive Energy case (Sat May 07 2011 - 06:14:55 PDT)
  - Re: [AMBER] Positive Energy Kshatresh Dutta Dubey (Sat May 07 2011 - 07:26:23 PDT)
[AMBER] Residue Template Sindrila Dutta banik (Sat May 07 2011 - 05:51:57 PDT)
- Re: [AMBER] Residue Template case (Sat May 07 2011 - 06:50:53 PDT)
[AMBER] Clustering baljinder (Sat May 07 2011 - 08:57:42 PDT)
- Re: [AMBER] Clustering Anselm Horn (Sat May 07 2011 - 11:03:21 PDT)
[AMBER] PRCSM baljinder (Sat May 07 2011 - 09:00:11 PDT)
[AMBER] installing ambertools Michael Forrester (Sat May 07 2011 - 11:24:00 PDT)
- Re: [AMBER] installing ambertools Jason Swails (Sat May 07 2011 - 11:55:20 PDT)
- Re: [AMBER] installing ambertools case (Sat May 07 2011 - 11:56:07 PDT)
  - Re: [AMBER] installing ambertools Lachele Foley (Lists) (Fri Jun 24 2011 - 13:54:09 PDT)
    - Re: [AMBER] installing ambertools David A. Case (Fri Jun 24 2011 - 14:15:04 PDT)
[AMBER] selecting hydrogens in -NH groups for the hydrogen bonding facility in PTRAJ Jose Borreguero (Sat May 07 2011 - 12:05:48 PDT)
[AMBER] How to restart the MM-PBSA? geyan (Sun May 08 2011 - 06:16:50 PDT)
- Re: [AMBER] How to restart the MM-PBSA? Bill Miller III (Sun May 08 2011 - 06:20:34 PDT)
- Re: [AMBER] How to restart the MM-PBSA? geyan (Mon May 09 2011 - 08:00:12 PDT)
  - Re: [AMBER] How to restart the MM-PBSA? Jason Swails (Mon May 09 2011 - 08:29:53 PDT)
[AMBER] Questions about compiling AmberToolsv1.4 Kamali Sripathi (Sun May 08 2011 - 06:53:01 PDT)
- Re: [AMBER] Questions about compiling AmberToolsv1.4 Jason Swails (Sun May 08 2011 - 09:24:55 PDT)
  - Re: [AMBER] Questions about compiling AmberToolsv1.4 Kamali Sripathi (Mon May 09 2011 - 11:07:20 PDT)
    - Re: [AMBER] Questions about compiling AmberToolsv1.4 David A Case (Mon May 09 2011 - 11:18:13 PDT)
    - Re: [AMBER] Questions about compiling AmberToolsv1.4 David A Case (Mon May 09 2011 - 12:38:32 PDT)
    - Re: [AMBER] Questions about compiling AmberToolsv1.4 Kamali Sripathi (Tue May 10 2011 - 05:09:58 PDT)
[AMBER] help with antechamber tsurma.umich.edu (Sun May 08 2011 - 13:22:29 PDT)
- Re: [AMBER] help with antechamber case (Sun May 08 2011 - 18:44:12 PDT)
  - Re: [AMBER] help with antechamber tsurma.umich.edu (Mon May 09 2011 - 07:45:46 PDT)
Re: [AMBER] Problem related to the Amber Ross Walker (Sun May 08 2011 - 21:34:58 PDT)
[AMBER] NMODE calculations results doubtful vaibhav dixit (Sun May 08 2011 - 21:46:43 PDT)
- Re: [AMBER] NMODE calculations results doubtful Dwight McGee (Sun May 08 2011 - 22:20:24 PDT)
  - Re: [AMBER] NMODE calculations results doubtful vaibhav dixit (Sun May 08 2011 - 23:34:49 PDT)
    - Re: [AMBER] NMODE calculations results doubtful Dwight McGee (Mon May 09 2011 - 00:10:54 PDT)
[AMBER] new lib loaded, but atom types are not recognized Chinh Su Tran To (Mon May 09 2011 - 01:05:37 PDT)
- Re: [AMBER] new lib loaded, but atom types are not recognized Thomas Cheatham III (Mon May 09 2011 - 10:27:11 PDT)
  - Re: [AMBER] new lib loaded, but atom types are not recognized Chinh Su Tran To (Mon May 09 2011 - 20:31:26 PDT)
    - Re: [AMBER] new lib loaded, but atom types are not recognized Thomas Cheatham (Mon May 09 2011 - 20:49:34 PDT)
    - Re: [AMBER] new lib loaded, but atom types are not recognized Chinh Su Tran To (Tue May 10 2011 - 01:05:53 PDT)
[AMBER] How to add a new force field hanlu0366 (Mon May 09 2011 - 06:13:10 PDT)
- Re: [AMBER] How to add a new force field steinbrt.rci.rutgers.edu (Mon May 09 2011 - 06:23:02 PDT)
[AMBER] Simulated annealing Guenegou, Guillaume [ORDFR] (Mon May 09 2011 - 07:41:12 PDT)
- Re: [AMBER] Simulated annealing waleed zalloum (Fri Apr 24 2009 - 08:04:47 PDT)
  - Re: [AMBER] Simulated annealing Carlos Simmerling (Fri Apr 24 2009 - 08:44:02 PDT)
- Re: [AMBER] Simulated annealing david condon (Mon May 09 2011 - 07:45:49 PDT)
- Re: [AMBER] Simulated annealing Bill Ross (Mon May 09 2011 - 13:46:50 PDT)
[AMBER] Amber 11 compilation Guenegou, Guillaume [ORDFR] (Mon May 09 2011 - 07:52:31 PDT)
- Re: [AMBER] Amber 11 compilation Jason Swails (Mon May 09 2011 - 08:19:52 PDT)
[AMBER] Problem with AMBER 11 and distance restraints Pablo Dans Puiggròs (Mon May 09 2011 - 08:23:31 PDT)
- Re: [AMBER] Problem with AMBER 11 and distance restraints Jason Swails (Mon May 09 2011 - 08:42:53 PDT)
  - Re: [AMBER] Problem with AMBER 11 and distance restraints Pablo Dans Puiggròs (Mon May 09 2011 - 09:39:03 PDT)
Re: [AMBER] lennard Jones water parameters Wong, Sergio E. (Mon May 09 2011 - 10:04:16 PDT)
- Re: [AMBER] lennard Jones water parameters Paul S. Nerenberg (Mon May 09 2011 - 10:32:20 PDT)
- Re: [AMBER] lennard Jones water parameters David A Case (Mon May 09 2011 - 10:47:03 PDT)
[AMBER] nmode calculation Sangita Kachhap (Mon May 09 2011 - 10:42:16 PDT)
- Re: [AMBER] nmode calculation Jason Swails (Mon May 09 2011 - 11:08:12 PDT)
  - Re: [AMBER] nmode calculation Sangita Kachhap (Mon May 09 2011 - 20:40:50 PDT)
  - Re: [AMBER] nmode calculation Sangita Kachhap (Mon May 09 2011 - 21:08:31 PDT)
[AMBER] Amoeba Potential File Modifications r smith (Mon May 09 2011 - 10:44:35 PDT)
- Re: [AMBER] Amoeba Potential File Modifications David A Case (Thu May 12 2011 - 08:24:47 PDT)
[AMBER] set UNIT box George Tzotzos (Mon May 09 2011 - 11:00:13 PDT)
- Re: [AMBER] set UNIT box Jason Swails (Mon May 09 2011 - 11:04:42 PDT)
  - Re: [AMBER] set UNIT box George Tzotzos (Mon May 09 2011 - 11:48:36 PDT)
    - Re: [AMBER] set UNIT box Jason Swails (Mon May 09 2011 - 12:17:56 PDT)
    - Re: [AMBER] set UNIT box George Tzotzos (Mon May 09 2011 - 12:30:43 PDT)
- Re: [AMBER] set UNIT box Bill Ross (Mon May 09 2011 - 12:45:51 PDT)
[AMBER] visualization of large .mdcrd files Bozell, Joseph John (Mon May 09 2011 - 12:46:26 PDT)
- Re: [AMBER] visualization of large .mdcrd files Jason Swails (Mon May 09 2011 - 14:38:03 PDT)
[AMBER] Please help with - closestwater - problem Marek Maly (Mon May 09 2011 - 13:02:34 PDT)
- Re: [AMBER] Please help with - closestwater - problem Thomas Cheatham III (Mon May 09 2011 - 14:31:14 PDT)
  - Re: [AMBER] Please help with - closestwater - problem Marek Maly (Mon May 09 2011 - 16:13:33 PDT)
    - Re: [AMBER] Please help with - closestwater - problem - problem is connected with NETCDF format Marek Maly (Mon May 09 2011 - 17:49:51 PDT)
[AMBER] SASA parameters Amber99 Osvaldo Martin (Tue May 10 2011 - 07:10:28 PDT)
- Re: [AMBER] SASA parameters Amber99 Jason Swails (Tue May 10 2011 - 07:52:46 PDT)
  - Re: [AMBER] SASA parameters Amber99 Osvaldo Martin (Tue May 10 2011 - 08:22:32 PDT)
    - Re: [AMBER] SASA parameters Amber99 Jason Swails (Tue May 10 2011 - 08:34:44 PDT)
- Re: [AMBER] SASA parameters Amber99 David A Case (Tue May 10 2011 - 09:41:17 PDT)
  - Re: [AMBER] SASA parameters Amber99 Osvaldo Martin (Tue May 10 2011 - 09:45:44 PDT)
  - [AMBER] problem with dielectric constant Bernhard Poll (Mon May 30 2011 - 00:40:57 PDT)
    - Re: [AMBER] problem with dielectric constant case (Mon May 30 2011 - 06:08:22 PDT)
    - Re: [AMBER] problem with dielectric constant Bernhard Poll (Mon May 30 2011 - 07:18:59 PDT)
    - Re: [AMBER] problem with dielectric constant case (Mon May 30 2011 - 08:25:42 PDT)
[AMBER] system imaging Alex Rodriguez (Tue May 10 2011 - 09:09:36 PDT)
- Re: [AMBER] system imaging Thomas Cheatham III (Tue May 10 2011 - 09:24:42 PDT)
- Re: [AMBER] system imaging InSuk Joung (Tue May 10 2011 - 09:49:38 PDT)
  - Re: [AMBER] system imaging Alex Rodriguez (Tue May 10 2011 - 10:31:38 PDT)
[AMBER] Ptraj Hbond query. Maura Catherine Mooney (Tue May 10 2011 - 19:23:59 PDT)
- Re: [AMBER] Ptraj Hbond query. Thomas Cheatham (Tue May 10 2011 - 19:49:05 PDT)
  - Re: [AMBER] Ptraj Hbond query. Maura Catherine Mooney (Tue May 10 2011 - 19:58:52 PDT)
[AMBER] question about REMD Massimiliano Porrini (Wed May 11 2011 - 04:19:50 PDT)
- Re: [AMBER] question about REMD Daniel Sindhikara (Wed May 11 2011 - 05:01:57 PDT)
  - Re: [AMBER] question about REMD Massimiliano Porrini (Wed May 11 2011 - 05:32:54 PDT)
    - Re: [AMBER] question about REMD Jason Swails (Wed May 11 2011 - 05:55:33 PDT)
    - Re: [AMBER] question about REMD Carlos Simmerling (Wed May 11 2011 - 05:58:16 PDT)
[AMBER] implicit solvent positional restraint Sangita Kachhap (Wed May 11 2011 - 04:24:45 PDT)
- Re: [AMBER] implicit solvent positional restraint Carlos Simmerling (Wed May 11 2011 - 06:01:26 PDT)
[AMBER] contacts command in ptraj - amber 10 g t (Wed May 11 2011 - 09:18:45 PDT)
- Re: [AMBER] contacts command in ptraj - amber 10 Thomas Cheatham III (Wed May 11 2011 - 11:38:23 PDT)
  - Re: [AMBER] contacts command in ptraj - amber 10 g t (Fri May 13 2011 - 04:11:17 PDT)
[AMBER] ptraj clustering output Lekpa Duukori (Wed May 11 2011 - 10:12:14 PDT)
- Re: [AMBER] ptraj clustering output Thomas Cheatham III (Wed May 11 2011 - 11:35:18 PDT)
  - Re: [AMBER] ptraj clustering output Lekpa Duukori (Wed May 11 2011 - 11:40:05 PDT)
[AMBER] closest command Sangita Kachhap (Wed May 11 2011 - 10:29:30 PDT)
- Re: [AMBER] closest command Marek Maly (Wed May 11 2011 - 11:02:25 PDT)
  - Re: [AMBER] closest command Sangita Kachhap (Wed May 11 2011 - 23:00:57 PDT)
[AMBER] Compiling AMBER on Windows 7 with CUDA Starr Hazard (Wed May 11 2011 - 11:14:16 PDT)
- Re: [AMBER] Compiling AMBER on Windows 7 with CUDA Ross Walker (Wed May 11 2011 - 15:21:54 PDT)
[AMBER] how to use Bennett acceptance ratio in Amber11? xiaodong huang (Wed May 11 2011 - 21:45:51 PDT)
- Re: [AMBER] how to use Bennett acceptance ratio in Amber11? steinbrt.rci.rutgers.edu (Thu May 12 2011 - 00:52:22 PDT)
  - Re: [AMBER] how to use Bennett acceptance ratio in Amber11? David A Case (Fri May 13 2011 - 04:59:45 PDT)
    - Re: [AMBER] how to use Bennett acceptance ratio in Amber11? steinbrt.rci.rutgers.edu (Fri May 13 2011 - 05:51:00 PDT)
[AMBER] MMPBSA.py - entropy only? Jesper Sørensen (Thu May 12 2011 - 02:27:21 PDT)
- Re: [AMBER] MMPBSA.py - entropy only? Bill Miller III (Thu May 12 2011 - 03:54:39 PDT)
  - Re: [AMBER] MMPBSA.py - entropy only? Jesper Sørensen (Thu May 12 2011 - 04:15:24 PDT)
    - Re: [AMBER] MMPBSA.py - entropy only? Bill Miller III (Thu May 12 2011 - 04:27:22 PDT)
    - Re: [AMBER] MMPBSA.py - entropy only? Jesper Sørensen (Thu May 12 2011 - 07:26:36 PDT)
    - Re: [AMBER] MMPBSA.py - entropy only? Bill Miller III (Thu May 12 2011 - 07:40:19 PDT)
    - Re: [AMBER] MMPBSA.py - entropy only? Catein Catherine (Thu May 12 2011 - 07:50:14 PDT)
    - Re: [AMBER] MMPBSA.py - entropy only? Jason Swails (Thu May 12 2011 - 16:07:22 PDT)
    - Re: [AMBER] MMPBSA.py - entropy only? Jesper Sørensen (Fri May 13 2011 - 03:56:27 PDT)
[AMBER] Problem with Equilibration Devlina Chakravarty (Thu May 12 2011 - 05:13:58 PDT)
- Re: [AMBER] Problem with Equilibration Jason Swails (Thu May 12 2011 - 16:13:11 PDT)
  - Re: [AMBER] Problem with Equilibration Sangita Kachhap (Fri May 13 2011 - 04:48:13 PDT)
    - Re: [AMBER] Problem with Equilibration Jason Swails (Fri May 13 2011 - 09:12:34 PDT)
[AMBER] configuring AmberTools 1.5 for Intel MKL Brendan Duggan (Thu May 12 2011 - 09:13:02 PDT)
- Re: [AMBER] configuring AmberTools 1.5 for Intel MKL Jason Swails (Thu May 12 2011 - 16:02:30 PDT)
  - Re: [AMBER] configuring AmberTools 1.5 for Intel MKL Brendan Duggan (Thu May 12 2011 - 18:24:01 PDT)
    - Re: [AMBER] configuring AmberTools 1.5 for Intel MKL case (Thu May 12 2011 - 18:54:08 PDT)
    - Re: [AMBER] configuring AmberTools 1.5 for Intel MKL Jason Swails (Thu May 12 2011 - 23:17:44 PDT)
[AMBER] Regarding MTK++/MCPB program to derive parameters using side chain model Naveen Samala (Thu May 12 2011 - 11:26:53 PDT)
[AMBER] Energy is increasing during minimization Wook Lee (Fri May 13 2011 - 01:20:38 PDT)
[AMBER] error in protein miniminisation dhilip kumar ramalingam (Fri May 13 2011 - 02:17:58 PDT)
- Re: [AMBER] error in protein miniminisation Ben Roberts (Fri May 13 2011 - 06:06:48 PDT)
[AMBER] PhD position in Computational Structural Biology at MPI Muenster Vlad Cojocaru (Fri May 13 2011 - 02:45:23 PDT)
[AMBER] MMPBSA entropy calculation yields different Delta S values sunita gupta (Fri May 13 2011 - 04:42:35 PDT)
[AMBER] strange volume contraction Massimiliano Porrini (Fri May 13 2011 - 05:51:34 PDT)
- Re: [AMBER] strange volume contraction case (Sat May 14 2011 - 06:55:25 PDT)
  - Re: [AMBER] strange volume contraction Massimiliano Porrini (Sat May 14 2011 - 08:37:39 PDT)
    - Re: [AMBER] strange volume contraction case (Sat May 14 2011 - 10:19:27 PDT)
[AMBER] GLYCAM Users Please Read Lachele Foley (Lists) (Fri May 13 2011 - 11:53:20 PDT)
[AMBER] AmberTools 1.4 from Amber11 on MACOSX Bruno Rodrigues (Sat May 14 2011 - 11:48:32 PDT)
- Re: [AMBER] AmberTools 1.4 from Amber11 on MACOSX Jason Swails (Sat May 14 2011 - 12:56:22 PDT)
  - Re: [AMBER] AmberTools 1.4 from Amber11 on MACOSX Bruno Rodrigues (Sat May 14 2011 - 13:34:05 PDT)
    - Re: [AMBER] AmberTools 1.4 from Amber11 on MACOSX Jason Swails (Sat May 14 2011 - 15:02:57 PDT)
[AMBER] ptraj command Sangita Kachhap (Sun May 15 2011 - 05:28:23 PDT)
- Re: [AMBER] ptraj command Thomas Cheatham III (Wed May 18 2011 - 13:34:11 PDT)
  - Re: [AMBER] ptraj command Sangita Kachhap (Wed May 18 2011 - 23:08:09 PDT)
[AMBER] need suggestion about NVIDIA GTX 590 setyanto md (Sun May 15 2011 - 19:34:36 PDT)
- Re: [AMBER] need suggestion about NVIDIA GTX 590 Jason Swails (Mon May 16 2011 - 04:29:02 PDT)
- Re: [AMBER] need suggestion about NVIDIA GTX 590 filip fratev (Mon May 16 2011 - 06:47:37 PDT)
  - Re: [AMBER] need suggestion about NVIDIA GTX 590 setyanto md (Wed May 18 2011 - 03:34:38 PDT)
[AMBER] segmentation fault when running sander Chinh Su Tran To (Sun May 15 2011 - 21:42:40 PDT)
- Re: [AMBER] segmentation fault when running sander Santosh Mogurampelly (Mon May 16 2011 - 00:26:56 PDT)
  - Re: [AMBER] segmentation fault when running sander Chinh Su Tran To (Mon May 16 2011 - 04:12:36 PDT)
- Re: [AMBER] segmentation fault when running sander Jason Swails (Mon May 16 2011 - 04:27:20 PDT)
  - Re: [AMBER] segmentation fault when running sander Chinh Su Tran To (Mon May 16 2011 - 04:46:47 PDT)
    - Re: [AMBER] segmentation fault when running sander Chinh Su Tran To (Tue May 17 2011 - 22:00:29 PDT)
    - Re: [AMBER] segmentation fault when running sander Jason Swails (Wed May 18 2011 - 11:14:31 PDT)
    - Re: [AMBER] segmentation fault when running sander Chinh Su Tran To (Wed May 18 2011 - 18:49:22 PDT)
    - Re: [AMBER] segmentation fault when running sander Chinh Su Tran To (Wed May 18 2011 - 19:31:49 PDT)
    - Re: [AMBER] segmentation fault when running sander Jason Swails (Wed May 18 2011 - 20:30:27 PDT)
    - Re: [AMBER] segmentation fault when running sander Chinh Su Tran To (Wed May 18 2011 - 21:04:51 PDT)
    - Re: [AMBER] segmentation fault when running sander Thomas Cheatham (Wed May 18 2011 - 21:16:15 PDT)
    - Re: [AMBER] segmentation fault when running sander Chinh Su Tran To (Wed May 18 2011 - 21:48:39 PDT)
    - Re: [AMBER] segmentation fault when running sander Jason Swails (Thu May 19 2011 - 04:18:54 PDT)
    - Re: [AMBER] segmentation fault when running sander Chinh Su Tran To (Fri May 20 2011 - 02:02:49 PDT)
[AMBER] Using Gaussian 09 (g09), how can I obtain RESP charges of a new residue? Chiba Suntaro (Sun May 15 2011 - 22:00:19 PDT)
- Re: [AMBER] Using Gaussian 09 (g09), how can I obtain RESP charges of a new residue? FyD (Sun May 15 2011 - 23:07:23 PDT)
  - Re: [AMBER] Using Gaussian 09 (g09), how can I obtain RESP charges of a new residue? Chiba Suntaro (Tue May 17 2011 - 19:51:07 PDT)
    - Re: [AMBER] Using Gaussian 09 (g09), how can I obtain RESP charges of a new residue? FyD (Wed May 18 2011 - 02:03:33 PDT)
    - Re: [AMBER] Using Gaussian 09 (g09), how can I obtain RESP charges of a new residue? Chiba Shuntaro (Wed May 18 2011 - 03:16:22 PDT)
    - Re: [AMBER] Using Gaussian 09 (g09), how can I obtain RESP charges of a new residue? FyD (Wed May 18 2011 - 04:17:02 PDT)
    - Re: [AMBER] Using Gaussian 09 (g09), how can I obtain RESP charges of a new residue? Chiba Shuntaro (Thu May 19 2011 - 01:12:25 PDT)
    - Re: [AMBER] Using Gaussian 09 (g09), how can I obtain RESP charges of a new residue? FyD (Fri May 20 2011 - 00:43:23 PDT)
    - Re: [AMBER] Using Gaussian 09 (g09), how can I obtain RESP charges of a new residue? Chiba Shuntaro (Fri May 20 2011 - 02:18:55 PDT)
    - Re: [AMBER] Using Gaussian 09 (g09), how can I obtain RESP charges of a new residue? FyD (Wed May 18 2011 - 04:24:17 PDT)
[AMBER] MMPBSA.py, systematic error in ptraj entropy results? Jesper Sørensen (Mon May 16 2011 - 06:06:31 PDT)
- Re: [AMBER] MMPBSA.py, systematic error in ptraj entropy results? Jason Swails (Mon May 16 2011 - 13:48:44 PDT)
  - Re: [AMBER] MMPBSA.py, systematic error in ptraj entropy results? Thomas Cheatham III (Mon May 16 2011 - 13:55:33 PDT)
    - Re: [AMBER] MMPBSA.py, systematic error in ptraj entropy results? Jesper Sørensen (Tue May 17 2011 - 03:41:34 PDT)
[AMBER] MMPBSA.py - problem processing trajs with ptraj Oliver Kuhn (Mon May 16 2011 - 07:12:20 PDT)
[AMBER] CUDA Francesco Pietra (Mon May 16 2011 - 09:28:57 PDT)
[AMBER] Hvdw: Non polar contribution to solvation in MMPBSA with solvent layer Lekpa Duukori (Mon May 16 2011 - 10:43:02 PDT)
[AMBER] kclust_SegFault Maura Catherine Mooney (Mon May 16 2011 - 12:25:39 PDT)
[AMBER] Regarding MTK++/MCPB program to derive parameters using side chain model Naveen Samala (Mon May 16 2011 - 13:00:22 PDT)
[AMBER] MMPBSA.py - problem processing trajs with ptraj (in more detail) Oliver Kuhn (Mon May 16 2011 - 13:06:41 PDT)
[AMBER] MMPBSA.py - problem processing trajs with ptraj (in more detail) - add Oliver Kuhn (Mon May 16 2011 - 13:22:23 PDT)
- Re: [AMBER] MMPBSA.py - problem processing trajs with ptraj (in more detail) - add Jason Swails (Mon May 16 2011 - 13:46:46 PDT)
[AMBER] error preparing a ligand using antechamber Paul Rigor (Mon May 16 2011 - 14:18:17 PDT)
- Re: [AMBER] error preparing a ligand using antechamber Paul Rigor (Mon May 16 2011 - 16:45:40 PDT)
- Re: [AMBER] error preparing a ligand using antechamber case (Mon May 16 2011 - 17:13:57 PDT)
  - Re: [AMBER] error preparing a ligand using antechamber Paul Rigor (Mon May 16 2011 - 17:31:11 PDT)
    - Re: [AMBER] error preparing a ligand using antechamber case (Mon May 16 2011 - 18:31:19 PDT)
    - Re: [AMBER] error preparing a ligand using antechamber Paul Rigor (Mon May 16 2011 - 18:50:35 PDT)
[AMBER] rst problem Sel Ercan (Tue May 17 2011 - 00:31:23 PDT)
[AMBER] rst problem selami ercan (Tue May 17 2011 - 01:23:47 PDT)
[AMBER] rst problem Sel Ercan (Tue May 17 2011 - 01:44:52 PDT)
[AMBER] xleap as a molecular viewer Guenegou, Guillaume [ORDFR] (Tue May 17 2011 - 06:12:05 PDT)
- Re: [AMBER] xleap as a molecular viewer Jason Swails (Tue May 17 2011 - 07:01:55 PDT)
- Re: [AMBER] xleap as a molecular viewer Daniel Roe (Tue May 17 2011 - 07:03:24 PDT)
- Re: [AMBER] xleap as a molecular viewer David A Case (Tue May 17 2011 - 07:05:31 PDT)
  - Re: [AMBER] xleap as a molecular viewer Guenegou, Guillaume [ORDFR] (Tue May 17 2011 - 07:09:06 PDT)
    - Re: [AMBER] xleap as a molecular viewer Guenegou, Guillaume [ORDFR] (Tue May 17 2011 - 07:24:31 PDT)
    - Re: [AMBER] xleap as a molecular viewer Jason Swails (Tue May 17 2011 - 07:26:20 PDT)
    - Re: [AMBER] xleap as a molecular viewer Guenegou, Guillaume [ORDFR] (Tue May 17 2011 - 07:46:54 PDT)
    - Re: [AMBER] xleap as a molecular viewer Daniel Roe (Tue May 17 2011 - 07:26:01 PDT)
- Re: [AMBER] xleap as a molecular viewer Gustavo Seabra (Tue May 17 2011 - 10:12:08 PDT)
- [AMBER] xleap as a molecular viewer 2 Guenegou, Guillaume [ORDFR] (Wed May 18 2011 - 01:06:49 PDT)
  - Re: [AMBER] xleap as a molecular viewer 2 steinbrt.rci.rutgers.edu (Wed May 18 2011 - 02:18:52 PDT)
    - Re: [AMBER] xleap as a molecular viewer 2 Guenegou, Guillaume [ORDFR] (Wed May 18 2011 - 02:54:18 PDT)
  - Re: [AMBER] xleap as a molecular viewer 2 Bill Ross (Wed May 18 2011 - 11:37:28 PDT)
  - Re: [AMBER] xleap as a molecular viewer 2 Paul Rigor (Wed May 18 2011 - 11:43:03 PDT)
[AMBER] Amber 10 Eric Kaufmann (Tue May 17 2011 - 11:52:44 PDT)
[AMBER] Large protein hydrogen bonding analysis Dmitry Osolodkin (Tue May 17 2011 - 13:14:13 PDT)
- [AMBER] phosphate group Wu Xu (Tue May 17 2011 - 15:21:46 PDT)
  - Re: [AMBER] phosphate group case (Tue May 17 2011 - 18:16:29 PDT)
    - Re: [AMBER] phosphate group FyD (Wed May 18 2011 - 01:52:49 PDT)
[AMBER] A maximum of two parameters are acceptable kurisaki (Wed May 18 2011 - 02:41:40 PDT)
- Re: [AMBER] A maximum of two parameters are acceptable case (Wed May 18 2011 - 05:47:31 PDT)
  - Re: [AMBER] A maximum of two parameters are acceptable kurisaki (Wed May 18 2011 - 05:57:53 PDT)
[AMBER] Amber 11 Benchmark for GPUs - Binaries and an Evaluation Licenses Qamar Nazir (Wed May 18 2011 - 03:38:21 PDT)
- Re: [AMBER] Amber 11 Benchmark for GPUs - Binaries and an Evaluation Licenses Ross Walker (Wed May 18 2011 - 10:36:01 PDT)
  - Re: [AMBER] Amber 11 Benchmark for GPUs - Binaries and an Evaluation Licenses filip fratev (Thu May 19 2011 - 07:23:13 PDT)
    - Re: [AMBER] Amber 11 Benchmark for GPUs - Binaries and an Evaluation Licenses Scott Le Grand (Thu May 19 2011 - 07:52:27 PDT)
    - Re: [AMBER] Amber 11 Benchmark for GPUs - Binaries and an Evaluation Licenses Ross Walker (Thu May 19 2011 - 09:54:37 PDT)
    - Re: [AMBER] Amber 11 Benchmark for GPUs - Binaries and an Evaluation Licenses filip fratev (Thu May 19 2011 - 13:19:46 PDT)
    - Re: [AMBER] Amber 11 Benchmark for GPUs - Binaries and an Evaluation Licenses Ross Walker (Thu May 19 2011 - 14:16:16 PDT)
    - Re: [AMBER] Amber 11 Benchmark for GPUs - Binaries and an Evaluation Licenses Scott Le Grand (Thu May 19 2011 - 15:51:15 PDT)
    - Re: [AMBER] Amber 11 Benchmark for GPUs - Binaries and an Evaluation Licenses case (Thu May 19 2011 - 19:35:36 PDT)
- Re: [AMBER] Amber 11 Benchmark for GPUs - Binaries and an Evaluation Licenses Bill Ross (Fri May 20 2011 - 00:25:03 PDT)
  - Re: [AMBER] Amber 11 Benchmark for GPUs - Binaries and an Evaluation Licenses Dean Cuebas (Fri May 20 2011 - 07:23:46 PDT)
[AMBER] Hydrogens Langevin dynamics Massimiliano Porrini (Wed May 18 2011 - 05:01:00 PDT)
- Re: [AMBER] Hydrogens Langevin dynamics case (Wed May 18 2011 - 05:53:46 PDT)
[AMBER] regarding LINMIN failure dhilip kumar ramalingam (Wed May 18 2011 - 06:25:46 PDT)
- Re: [AMBER] regarding LINMIN failure Ben Roberts (Wed May 18 2011 - 08:06:19 PDT)
[AMBER] How to minimize buried bad contacts Scott Pendley (Wed May 18 2011 - 09:57:08 PDT)
[AMBER] secundary structure analysis Jorgen Simonsen (Wed May 18 2011 - 10:22:07 PDT)
[AMBER] antechamber ERROR George Tzotzos (Wed May 18 2011 - 11:24:35 PDT)
- Re: [AMBER] antechamber ERROR Jason Swails (Wed May 18 2011 - 12:18:28 PDT)
  - Re: [AMBER] antechamber ERROR George Tzotzos (Wed May 18 2011 - 12:27:37 PDT)
    - Re: [AMBER] antechamber ERROR Jason Swails (Wed May 18 2011 - 12:49:07 PDT)
    - Re: [AMBER] antechamber ERROR George Tzotzos (Wed May 18 2011 - 13:38:09 PDT)
    - Re: [AMBER] antechamber ERROR Jason Swails (Wed May 18 2011 - 16:23:03 PDT)
[AMBER] Estiblish hanlu0366 (Thu May 19 2011 - 02:43:25 PDT)
- Re: [AMBER] Estiblish steinbrt.rci.rutgers.edu (Thu May 19 2011 - 03:35:21 PDT)
[AMBER] Solvation Sindrila Dutta banik (Thu May 19 2011 - 05:01:56 PDT)
- Re: [AMBER] Solvation Carlos Simmerling (Thu May 19 2011 - 05:06:46 PDT)
  - [AMBER] Solvation Sindrila Dutta banik (Thu May 19 2011 - 05:20:56 PDT)
    - Re: [AMBER] Solvation Jason Swails (Thu May 19 2011 - 05:23:01 PDT)
    - Re: [AMBER] Solvation Carlos Simmerling (Thu May 19 2011 - 05:34:29 PDT)
[AMBER] Amber order Rupa Madyal (Thu May 19 2011 - 06:36:31 PDT)
- Re: [AMBER] Amber order Jason Swails (Thu May 19 2011 - 11:29:33 PDT)
[AMBER] Solvation Sindrila Dutta banik (Thu May 19 2011 - 04:11:05 PDT)
[AMBER] Ptraj NAMD dcd imaging Manish (Thu May 19 2011 - 10:01:34 PDT)
- Re: [AMBER] Ptraj NAMD dcd imaging Marek Maly (Thu May 19 2011 - 10:30:13 PDT)
  - Re: [AMBER] Ptraj NAMD dcd imaging George Madalin Giambasu (Thu May 19 2011 - 10:47:13 PDT)
[AMBER] Use of uninitialized value $ENV{"AMBERHOME"} Jagur Lambix (Thu May 19 2011 - 11:46:02 PDT)
- Re: [AMBER] Use of uninitialized value $ENV{"AMBERHOME"} Jason Swails (Thu May 19 2011 - 20:24:13 PDT)
[AMBER] Parametrizing a peptide ligand Gustavo Seabra (Thu May 19 2011 - 13:14:33 PDT)
- Re: [AMBER] Parametrizing a peptide ligand FyD (Fri May 20 2011 - 00:55:28 PDT)
  - Re: [AMBER] Parametrizing a peptide ligand Gustavo Seabra (Fri May 20 2011 - 02:53:18 PDT)
    - Re: [AMBER] Parametrizing a peptide ligand FyD (Fri May 20 2011 - 04:18:26 PDT)
    - Re: [AMBER] Parametrizing a peptide ligand Gustavo Seabra (Fri May 20 2011 - 12:27:47 PDT)
[AMBER] strange dihedral assignment by leap Thomas Gaillard (Thu May 19 2011 - 17:16:53 PDT)
- Re: [AMBER] strange dihedral assignment by leap Jason Swails (Thu May 19 2011 - 20:21:19 PDT)
  - Re: [AMBER] strange dihedral assignment by leap Thomas Gaillard (Fri May 20 2011 - 03:47:17 PDT)
    - Re: [AMBER] strange dihedral assignment by leap Jason Swails (Fri May 20 2011 - 04:16:53 PDT)
    - Re: [AMBER] strange dihedral assignment by leap Thomas Gaillard (Fri May 20 2011 - 05:04:29 PDT)
    - Re: [AMBER] strange dihedral assignment by leap Jason Swails (Fri May 20 2011 - 05:27:11 PDT)
    - Re: [AMBER] strange dihedral assignment by leap Thomas Gaillard (Fri May 20 2011 - 06:27:43 PDT)
[AMBER] ptraj closest command supriyah.imtech.res.in (Fri May 20 2011 - 04:30:08 PDT)
[AMBER] compilation of amber tools 1.5 with intel 11.1.059 Vlad Cojocaru (Fri May 20 2011 - 06:35:49 PDT)
- Re: [AMBER] compilation of amber tools 1.5 with intel 11.1.059 Vlad Cojocaru (Fri May 20 2011 - 07:56:22 PDT)
  - Re: [AMBER] compilation of amber tools 1.5 with intel 11.1.059 Daniel Roe (Fri May 20 2011 - 12:32:58 PDT)
    - Re: [AMBER] compilation of amber tools 1.5 with intel 11.1.059 Vlad Cojocaru (Sat May 21 2011 - 02:59:11 PDT)
[AMBER] How to use mmpbsa.py for three-trajectory protocol? bin wang (Fri May 20 2011 - 07:00:55 PDT)
- Re: [AMBER] How to use mmpbsa.py for three-trajectory protocol? Bill Miller III (Fri May 20 2011 - 07:07:02 PDT)
  - Re: [AMBER] How to use mmpbsa.py for three-trajectory protocol? bin wang (Fri May 20 2011 - 07:44:30 PDT)
    - Re: [AMBER] How to use mmpbsa.py for three-trajectory protocol? Bill Miller III (Fri May 20 2011 - 07:46:37 PDT)
    - Re: [AMBER] How to use mmpbsa.py for three-trajectory protocol? bin wang (Fri May 20 2011 - 08:23:06 PDT)
[AMBER] Problem of PB calculation when running mmpbsa.py bin wang (Fri May 20 2011 - 12:36:29 PDT)
- Re: [AMBER] Problem of PB calculation when running mmpbsa.py Bill Miller III (Fri May 20 2011 - 12:41:36 PDT)
  - Re: [AMBER] Problem of PB calculation when running mmpbsa.py. . Zheng, Zhong (Fri May 20 2011 - 13:06:15 PDT)
    - Re: [AMBER] Problem of PB calculation when running mmpbsa.py. . Jason Swails (Fri May 20 2011 - 13:11:47 PDT)
    - Re: [AMBER] Problem of PB calculation when running mmpbsa.py. . Ray Luo, Ph.D. (Fri May 20 2011 - 13:15:53 PDT)
    - Re: [AMBER] Problem of PB calculation when running mmpbsa.py. .. . Zheng, Zhong (Fri May 20 2011 - 14:03:30 PDT)
    - Re: [AMBER] Problem of PB calculation when running mmpbsa.py. .. . Ray Luo, Ph.D. (Fri May 20 2011 - 14:08:11 PDT)
    - Re: [AMBER] Problem of PB calculation when running mmpbsa.py. .. . Jason Swails (Fri May 20 2011 - 14:18:05 PDT)
    - Re: [AMBER] Problem of PB calculation when running mmpbsa.py. .. .. . Zheng, Zhong (Fri May 20 2011 - 14:46:54 PDT)
    - Re: [AMBER] Problem of PB calculation when running mmpbsa.py. .. . bin wang (Sat May 21 2011 - 13:02:34 PDT)
    - Re: [AMBER] Problem of PB calculation when running mmpbsa.py. .. . Jason Swails (Sat May 21 2011 - 13:08:43 PDT)
    - Re: [AMBER] Problem of PB calculation when running mmpbsa.py. .. . bin wang (Sat May 21 2011 - 13:42:38 PDT)
    - Re: [AMBER] Problem of PB calculation when running mmpbsa.py. .. . Ray Luo (Sat May 21 2011 - 16:28:39 PDT)
  - Re: [AMBER] Problem of PB calculation when running mmpbsa.py bin wang (Fri May 20 2011 - 13:07:54 PDT)
[AMBER] Post-processing trajectories: ntpr - ntwx George Tzotzos (Sat May 21 2011 - 08:28:01 PDT)
- Re: [AMBER] Post-processing trajectories: ntpr - ntwx Jason Swails (Sat May 21 2011 - 14:03:37 PDT)
[AMBER] Ambertools 1.5 make install error Andre Serobian (Sat May 21 2011 - 16:22:37 PDT)
- Re: [AMBER] Ambertools 1.5 make install error Vlad Cojocaru (Sun May 22 2011 - 00:46:47 PDT)
- Re: [AMBER] Ambertools 1.5 make install error Andre (Sun May 22 2011 - 03:04:15 PDT)
  - Re: [AMBER] Ambertools 1.5 make install error Marc van der Kamp (Tue May 24 2011 - 09:22:14 PDT)
- Re: [AMBER] Ambertools 1.5 make install error Andre Serobian (Tue May 24 2011 - 13:31:04 PDT)
- Re: [AMBER] Ambertools 1.5 make install error David A. Case (Wed May 25 2011 - 07:44:27 PDT)
[AMBER] Problems with calcein and antechamber Maria Federica Sanasi (Sun May 22 2011 - 03:35:00 PDT)
[AMBER] regarding calculation of interaction energies dhilip kumar ramalingam (Mon May 23 2011 - 00:19:38 PDT)
- Re: [AMBER] regarding calculation of interaction energies steinbrt.rci.rutgers.edu (Mon May 23 2011 - 00:29:21 PDT)
[AMBER] MMPBSA.py - entropy results Jesper Sørensen (Mon May 23 2011 - 02:37:27 PDT)
- Re: [AMBER] MMPBSA.py - entropy results Jason Swails (Mon May 23 2011 - 10:19:19 PDT)
  - Re: [AMBER] MMPBSA.py - entropy results Jesper Sørensen (Tue May 24 2011 - 02:27:36 PDT)
[AMBER] calculation of interaction energy using mmpbsa dhilip kumar ramalingam (Mon May 23 2011 - 04:21:51 PDT)
- Re: [AMBER] calculation of interaction energy using mmpbsa steinbrt.rci.rutgers.edu (Mon May 23 2011 - 04:30:33 PDT)
  - Re: [AMBER] calculation of interaction energy using mmpbsa dhilip kumar ramalingam (Mon May 23 2011 - 04:43:12 PDT)
[AMBER] Solvation Sindrila Dutta banik (Mon May 23 2011 - 05:56:42 PDT)
[AMBER] NEB calculation using amber 11 Buddhadev Maiti (Mon May 23 2011 - 10:14:13 PDT)
- Re: [AMBER] NEB calculation using amber 11 Carlos Simmerling (Mon May 23 2011 - 10:16:47 PDT)
- Re: [AMBER] NEB calculation using amber 11 Ross Walker (Mon May 23 2011 - 10:21:56 PDT)
[AMBER] Hvdw: Non polar contribution to solvation in MMPBSA with solvent layer Lekpa Duukori (Mon May 23 2011 - 10:24:47 PDT)
- Re: [AMBER] Hvdw: Non polar contribution to solvation in MMPBSA with solvent layer David A. Case (Tue May 24 2011 - 08:52:56 PDT)
  - Re: [AMBER] Hvdw: Non polar contribution to solvation in MMPBSA with solvent layer Lekpa Duukori (Tue May 24 2011 - 17:04:26 PDT)
[AMBER] NEB calculation using amber 11 Buddhadev Maiti (Mon May 23 2011 - 10:46:53 PDT)
- Re: [AMBER] NEB calculation using amber 11 Carlos Simmerling (Mon May 23 2011 - 10:48:57 PDT)
[AMBER] vacuum in Ewald Ignacio J. General (Mon May 23 2011 - 13:19:18 PDT)
- Re: [AMBER] vacuum in Ewald Ross Walker (Mon May 23 2011 - 13:46:47 PDT)
  - Re: [AMBER] vacuum in Ewald Ignacio J. General (Tue May 24 2011 - 07:44:27 PDT)
    - Re: [AMBER] vacuum in Ewald Ross Walker (Tue May 24 2011 - 09:30:22 PDT)
[AMBER] system extended beyond the virtual box Qian Wang (Mon May 23 2011 - 20:28:59 PDT)
- Re: [AMBER] system extended beyond the virtual box Ross Walker (Mon May 23 2011 - 20:42:27 PDT)
  - Re: [AMBER] system extended beyond the virtual box Qian Wang (Mon May 23 2011 - 21:18:00 PDT)
    - Re: [AMBER] system extended beyond the virtual box Ross Walker (Mon May 23 2011 - 22:06:12 PDT)
    - Re: [AMBER] system extended beyond the virtual box David Case (Tue May 31 2011 - 18:30:05 PDT)
- Re: [AMBER] system extended beyond the virtual box David A. Case (Wed May 25 2011 - 00:15:43 PDT)
[AMBER] Fw: Estiblish hanlu0366 (Mon May 23 2011 - 20:40:38 PDT)
- Re: [AMBER] Fw: Estiblish Ross Walker (Mon May 23 2011 - 20:46:28 PDT)
- Re: [AMBER] Fw: Estiblish David A. Case (Wed May 25 2011 - 00:15:32 PDT)
[AMBER] MM-PB/SA calculation problem 姜笑楠 (Mon May 23 2011 - 23:03:32 PDT)
- Re: [AMBER] MM-PB/SA calculation problem Ray Luo, Ph.D. (Tue May 24 2011 - 07:14:33 PDT)
  - Re: [AMBER] MM-PB/SA calculation problem Bill Miller III (Tue May 24 2011 - 12:41:37 PDT)
    - Re: [AMBER] MM-PB/SA calculation problem jiangxn (Tue May 24 2011 - 18:40:43 PDT)
[AMBER] Problem installing AMBER 11 (after installing AmberTools1.5) Marc van der Kamp (Tue May 24 2011 - 03:11:27 PDT)
- Re: [AMBER] Problem installing AMBER 11 (after installing AmberTools1.5) Daniel Roe (Tue May 24 2011 - 04:53:27 PDT)
  - Re: [AMBER] Problem installing AMBER 11 (after installing AmberTools1.5) Marc van der Kamp (Tue May 24 2011 - 05:03:50 PDT)
    - Re: [AMBER] Problem installing AMBER 11 (after installing AmberTools1.5) Jason Swails (Tue May 24 2011 - 05:38:05 PDT)
    - Re: [AMBER] Problem installing AMBER 11 (after installing AmberTools1.5) Marc van der Kamp (Tue May 24 2011 - 06:52:16 PDT)
    - Re: [AMBER] Problem installing AMBER 11 (after installing AmberTools1.5) Jason Swails (Tue May 24 2011 - 08:57:13 PDT)
[AMBER] Topology File Sindrila Dutta banik (Tue May 24 2011 - 07:21:58 PDT)
- [AMBER] PROBLEM IN TERMINAL RESIDUES: WRONG BONDS Sindrila Dutta banik (Tue May 24 2011 - 22:35:54 PDT)
  - Re: [AMBER] PROBLEM IN TERMINAL RESIDUES: WRONG BONDS David A. Case (Wed May 25 2011 - 07:07:51 PDT)
    - [AMBER] PROBLEM IN TERMINAL RESIDUES: WRONG BONDS Sindrila Dutta banik (Wed May 25 2011 - 09:10:00 PDT)
[AMBER] sander.MPI Bruno Rodrigues (Tue May 24 2011 - 12:21:52 PDT)
- Re: [AMBER] sander.MPI Jason Swails (Tue May 24 2011 - 13:11:16 PDT)
  - Re: [AMBER] sander.MPI Bruno Rodrigues (Tue May 24 2011 - 19:48:07 PDT)
    - Re: [AMBER] sander.MPI Bruno Rodrigues (Wed May 25 2011 - 05:18:02 PDT)
    - Re: [AMBER] sander.MPI Jason Swails (Wed May 25 2011 - 06:01:37 PDT)
    - Re: [AMBER] sander.MPI Ross Walker (Wed May 25 2011 - 09:42:49 PDT)
    - Re: [AMBER] sander.MPI Jason Swails (Wed May 25 2011 - 10:11:51 PDT)
    - Re: [AMBER] sander.MPI Bruno Rodrigues (Wed May 25 2011 - 12:04:27 PDT)
[AMBER] how are you? scott.pendley.gmail.com (Tue May 24 2011 - 13:06:24 PDT)
[AMBER] Size limit of traj file Jagur Lambix (Tue May 24 2011 - 14:34:42 PDT)
- Re: [AMBER] Size limit of traj file Jason Swails (Tue May 24 2011 - 18:57:52 PDT)
[AMBER] AMBER scaling and Hardware Specs Azat Mukhametov (Tue May 24 2011 - 18:15:09 PDT)
- Re: [AMBER] AMBER scaling and Hardware Specs Ross Walker (Tue May 24 2011 - 18:31:25 PDT)
- Re: [AMBER] AMBER scaling and Hardware Specs Carlos Simmerling (Tue May 24 2011 - 18:32:05 PDT)
  - Re: [AMBER] AMBER scaling and Hardware Specs Azat Mukhametov (Tue May 24 2011 - 18:47:55 PDT)
    - Re: [AMBER] AMBER scaling and Hardware Specs Jason Swails (Tue May 24 2011 - 18:55:03 PDT)
    - Re: [AMBER] AMBER scaling and Hardware Specs Azat Mukhametov (Tue May 24 2011 - 19:03:46 PDT)
    - Re: [AMBER] AMBER scaling and Hardware Specs David A. Case (Wed May 25 2011 - 02:10:00 PDT)
    - Re: [AMBER] AMBER scaling and Hardware Specs Ross Walker (Wed May 25 2011 - 09:29:45 PDT)
[AMBER] x86_64-alt-linux-gcc: cgen.o: No such file or directory make[1]: Leaving directory `/home/voronkov/amber11/AmberTools/src/nab' make: *** [serial] Error 2 Andrew Voronkov (Tue May 24 2011 - 23:05:08 PDT)
- Re: [AMBER] x86_64-alt-linux-gcc: cgen.o: No such file or directory make[1]: Leaving directory `/home/voronkov/amber11/AmberTools/src/nab' make: *** [serial] Error 2 David A. Case (Wed May 25 2011 - 02:30:47 PDT)
  - Re: [AMBER] x86_64-alt-linux-gcc: cgen.o: No such file or directory make[1]: Leaving directory `/home/voronkov/amber11/AmberTools/src/nab' make: *** [serial] Error 2 Andrew Voronkov (Thu May 26 2011 - 12:59:14 PDT)
    - Re: [AMBER] x86_64-alt-linux-gcc: cgen.o: No such file or directory make[1]: Leaving directory `/home/voronkov/amber11/AmberTools/src/nab' make: *** [serial] Error 2 Jason Swails (Thu May 26 2011 - 14:56:48 PDT)
    - Re: [AMBER] x86_64-alt-linux-gcc: cgen.o: No such file or directory make[1]: Leaving directory `/home/voronkov/amber11/AmberTools/src/nab' make: *** [serial] Error 2 David A. Case (Fri May 27 2011 - 18:38:33 PDT)
    - Re: [AMBER] x86_64-alt-linux-gcc: cgen.o: No such file or directory make[1]: Leaving directory `/home/voronkov/amber11/AmberTools/src/nab' make: *** [serial] Error 2 Andrew Voronkov (Sun May 29 2011 - 08:16:08 PDT)
    - Re: [AMBER] x86_64-alt-linux-gcc: cgen.o: No such file or directory make[1]: Leaving directory `/home/voronkov/amber11/AmberTools/src/nab' make: *** [serial] Error 2 case (Sun May 29 2011 - 10:45:23 PDT)
    - Re: [AMBER] x86_64-alt-linux-gcc: cgen.o: No such file or directory make[1]: Leaving directory `/home/voronkov/amber11/AmberTools/src/nab' make: *** [serial] Error 2 Andrew Voronkov (Mon May 30 2011 - 12:28:28 PDT)
[AMBER] Test results for amber-cuda, single node, single GPU, Tesla C2070 Paul Rigor (Wed May 25 2011 - 00:49:18 PDT)
- Re: [AMBER] Test results for amber-cuda, single node, single GPU, Tesla C2070 Ross Walker (Wed May 25 2011 - 09:38:44 PDT)
  - Re: [AMBER] Test results for amber-cuda, single node, single GPU, Tesla C2070 Jason Swails (Wed May 25 2011 - 10:27:27 PDT)
    - Re: [AMBER] Test results for amber-cuda, single node, single GPU, Tesla C2070 Scott Le Grand (Wed May 25 2011 - 10:54:24 PDT)
    - Re: [AMBER] Test results for amber-cuda, single node, single GPU, Tesla C2070 Paul Rigor (Wed May 25 2011 - 13:35:10 PDT)
    - Re: [AMBER] Test results for amber-cuda, single node, single GPU, Tesla C2070 Scott Le Grand (Wed May 25 2011 - 13:47:44 PDT)
    - Re: [AMBER] Test results for amber-cuda, single node, single GPU, Tesla C2070 Scott Le Grand (Wed May 25 2011 - 13:52:39 PDT)
    - Re: [AMBER] Test results for amber-cuda, single node, single GPU, Tesla C2070 Jason Swails (Wed May 25 2011 - 14:30:19 PDT)
    - Re: [AMBER] Test results for amber-cuda, single node, single GPU, Tesla C2070 Ross Walker (Wed May 25 2011 - 14:43:26 PDT)
    - Re: [AMBER] Test results for amber-cuda, single node, single GPU, Tesla C2070 Jason Swails (Wed May 25 2011 - 15:35:34 PDT)
    - Re: [AMBER] Test results for amber-cuda, single node, single GPU, Tesla C2070 Ross Walker (Wed May 25 2011 - 16:18:44 PDT)
    - Re: [AMBER] Test results for amber-cuda, single node, single GPU, Tesla C2070 Paul Rigor (Wed May 25 2011 - 17:53:37 PDT)
    - Re: [AMBER] Test results for amber-cuda, single node, single GPU, Tesla C2070 Paul Rigor (Wed May 25 2011 - 18:51:43 PDT)
    - Re: [AMBER] Test results for amber-cuda, single node, single GPU, Tesla C2070 Jason Swails (Wed May 25 2011 - 19:17:08 PDT)
    - Re: [AMBER] Test results for amber-cuda, single node, single GPU, Tesla C2070 Paul Rigor (Wed May 25 2011 - 19:25:56 PDT)
    - Re: [AMBER] Test results for amber-cuda, single node, single GPU, Tesla C2070 Paul Rigor (Wed May 25 2011 - 19:19:21 PDT)
    - Re: [AMBER] Test results for amber-cuda, single node, single GPU, Tesla C2070 Jason Swails (Wed May 25 2011 - 19:25:40 PDT)
    - Re: [AMBER] Test results for amber-cuda, single node, single GPU, Tesla C2070 Paul Rigor (Wed May 25 2011 - 19:41:32 PDT)
    - Re: [AMBER] Test results for amber-cuda, single node, single GPU, Tesla C2070 Jason Swails (Wed May 25 2011 - 19:54:07 PDT)
    - Re: [AMBER] Test results for amber-cuda, single node, single GPU, Tesla C2070 Paul Rigor (Wed May 25 2011 - 20:33:39 PDT)
    - Re: [AMBER] Test results for amber-cuda, single node, single GPU, Tesla C2070 Ross Walker (Wed May 25 2011 - 22:28:59 PDT)
    - Re: [AMBER] Test results for amber-cuda, single node, single GPU, Tesla C2070 Paul Rigor (Thu May 26 2011 - 23:34:27 PDT)
    - Re: [AMBER] Test results for amber-cuda, single node, single GPU, Tesla C2070 Ross Walker (Fri May 27 2011 - 09:02:22 PDT)
    - Re: [AMBER] Test results for amber-cuda, single node, single GPU, Tesla C2070 Jason Swails (Wed May 25 2011 - 19:12:22 PDT)
- Re: [AMBER] Test results for amber-cuda, single node, single GPU, Tesla C2070 Scott Le Grand (Wed May 25 2011 - 10:06:29 PDT)
[AMBER] disappearing atoms using softcore TI - amber 11 Zora Strelcova (Wed May 25 2011 - 06:32:55 PDT)
- Re: [AMBER] disappearing atoms using softcore TI - amber 11 Ignacio J. General (Wed May 25 2011 - 07:05:27 PDT)
- Re: [AMBER] disappearing atoms using softcore TI - amber 11 steinbrt.rci.rutgers.edu (Wed May 25 2011 - 07:10:36 PDT)
  - Re: [AMBER] disappearing atoms using softcore TI - amber 11 Zora Strelcova (Wed May 25 2011 - 12:44:34 PDT)
    - Re: [AMBER] disappearing atoms using softcore TI - amber 11 steinbrt.rci.rutgers.edu (Thu May 26 2011 - 00:28:58 PDT)
    - Re: [AMBER] disappearing atoms using softcore TI - amber 11 Zora Strelcova (Thu May 26 2011 - 00:48:51 PDT)
    - Re: [AMBER] disappearing atoms using softcore TI - amber 11 steinbrt.rci.rutgers.edu (Thu May 26 2011 - 01:16:32 PDT)
[AMBER] compilation with gcc 4.5.1 under openSuSE 11.4 64-bits JORGE IULEK (Wed May 25 2011 - 06:46:36 PDT)
- Re: [AMBER] compilation with gcc 4.5.1 under openSuSE 11.4 64-bits Vlad Cojocaru (Wed May 25 2011 - 07:15:42 PDT)
- Re: [AMBER] compilation with gcc 4.5.1 under openSuSE 11.4 64-bits David A. Case (Wed May 25 2011 - 08:11:35 PDT)
- Re: [AMBER] compilation with gcc 4.5.1 under openSuSE 11.4 64-bits JORGE IULEK (Wed May 25 2011 - 12:09:08 PDT)
  - Re: [AMBER] compilation with gcc 4.5.1 under openSuSE 11.4 64-bits Daniel Roe (Wed May 25 2011 - 12:59:29 PDT)
    - Re: [AMBER] compilation with gcc 4.5.1 under openSuSE 11.4 64-bits Jorge Iulek (Wed May 25 2011 - 15:51:49 PDT)
  - Re: [AMBER] compilation with gcc 4.5.1 under openSuSE 11.4 64-bits David A. Case (Wed May 25 2011 - 14:37:02 PDT)
    - Re: [AMBER] compilation with gcc 4.5.1 under openSuSE 11.4 64-bits Jorge Iulek (Wed May 25 2011 - 16:06:39 PDT)
    - Re: [AMBER] compilation with gcc 4.5.1 under openSuSE 11.4 64-bits David A. Case (Thu May 26 2011 - 01:59:12 PDT)
- Re: [AMBER] compilation with gcc 4.5.1 under openSuSE 11.4 64-bits JORGE IULEK (Wed May 25 2011 - 12:11:34 PDT)
  - Re: [AMBER] compilation with gcc 4.5.1 under openSuSE 11.4 64-bits Vlad Cojocaru (Wed May 25 2011 - 13:51:40 PDT)
    - Re: [AMBER] compilation with gcc 4.5.1 under openSuSE 11.4 64-bits Jorge Iulek (Wed May 25 2011 - 16:01:04 PDT)
[AMBER] Questions re: NEB on a large system patrick wintrode (Wed May 25 2011 - 07:49:02 PDT)
- Re: [AMBER] Questions re: NEB on a large system Carlos Simmerling (Wed May 25 2011 - 08:31:05 PDT)
[AMBER] PROBLEM IN TERMINAL RESIDUES: WRONG BONDS Sindrila Dutta banik (Wed May 25 2011 - 09:27:27 PDT)
- Re: [AMBER] PROBLEM IN TERMINAL RESIDUES: WRONG BONDS FyD (Thu May 26 2011 - 00:14:14 PDT)
[AMBER] CHAMBER Seibold, Stephen (Wed May 25 2011 - 10:18:25 PDT)
- Re: [AMBER] CHAMBER Ross Walker (Wed May 25 2011 - 10:45:08 PDT)
  - Re: [AMBER] CHAMBER Seibold, Stephen (Wed May 25 2011 - 11:18:00 PDT)
[AMBER] AmberTools 1.5 and Amber11 Massimiliano Porrini (Wed May 25 2011 - 11:35:30 PDT)
- Re: [AMBER] AmberTools 1.5 and Amber11 Daniel Roe (Wed May 25 2011 - 11:41:07 PDT)
- Re: [AMBER] AmberTools 1.5 and Amber11 Ben Roberts (Wed May 25 2011 - 11:41:19 PDT)
[AMBER] constrained atom minimization arikcohen (Wed May 25 2011 - 11:39:29 PDT)
- Re: [AMBER] constrained atom minimization David A. Case (Wed May 25 2011 - 14:30:33 PDT)
[AMBER] ibelly error qiaoyan (Wed May 25 2011 - 18:40:30 PDT)
- Re: [AMBER] ibelly error Jason Swails (Wed May 25 2011 - 19:21:42 PDT)
  - Re: [AMBER] ibelly error Marc van der Kamp (Thu May 26 2011 - 01:23:48 PDT)
- Re: [AMBER] ibelly error David A. Case (Thu May 26 2011 - 01:46:24 PDT)
[AMBER] In ff99SB, what does this SB stands for ? mish (Thu May 26 2011 - 04:46:57 PDT)
- Re: [AMBER] In ff99SB, what does this SB stands for ? Carlos Simmerling (Thu May 26 2011 - 04:55:02 PDT)
  - Re: [AMBER] In ff99SB, what does this SB stands for ? Jiri Sponer (Thu May 26 2011 - 05:01:22 PDT)
    - Re: [AMBER] In ff99SB, what does this SB stands for ? mish (Thu May 26 2011 - 06:40:05 PDT)
[AMBER] solvatebox George Tzotzos (Thu May 26 2011 - 06:20:25 PDT)
- Re: [AMBER] solvatebox Bill Ross (Sat Nov 06 2010 - 19:22:09 PDT)
  - Re: [AMBER] solvatebox M. L. Dodson (Sat Nov 06 2010 - 20:56:58 PDT)
- Re: [AMBER] solvatebox Bill Ross (Tue Dec 07 2010 - 10:26:36 PST)
- Re: [AMBER] solvatebox Carlos Simmerling (Thu May 26 2011 - 06:36:32 PDT)
  - Re: [AMBER] solvatebox George Tzotzos (Thu May 26 2011 - 06:44:18 PDT)
    - Re: [AMBER] solvatebox Carlos Simmerling (Thu May 26 2011 - 09:41:33 PDT)
    - Re: [AMBER] solvatebox George Tzotzos (Thu May 26 2011 - 12:38:07 PDT)
- Re: [AMBER] solvatebox Bill Ross (Thu May 26 2011 - 08:27:40 PDT)
- Re: [AMBER] solvatebox Bill Ross (Thu May 26 2011 - 08:34:30 PDT)
- Re: [AMBER] solvatebox Gustavo Seabra (Thu May 26 2011 - 08:39:07 PDT)
- Re: [AMBER] solvatebox Bill Ross (Thu May 26 2011 - 12:06:31 PDT)
  - Re: [AMBER] solvatebox Jason Swails (Fri May 27 2011 - 16:17:36 PDT)
    - Re: [AMBER] solvatebox M. L. Dodson (Fri May 27 2011 - 17:21:19 PDT)
- Re: [AMBER] solvatebox Bill Ross (Fri May 27 2011 - 21:44:48 PDT)
[AMBER] Equilibration step of tutorial 3 taking much longer than estimated run time Daniel Aiello (Thu May 26 2011 - 07:07:30 PDT)
- Re: [AMBER] Equilibration step of tutorial 3 taking much longer than estimated run time Daniel Roe (Thu May 26 2011 - 08:16:15 PDT)
  - Re: [AMBER] Equilibration step of tutorial 3 taking much longer than estimated run time Daniel Aiello (Thu May 26 2011 - 08:38:02 PDT)
- Re: [AMBER] Equilibration step of tutorial 3 taking much longer than estimated run time David A. Case (Thu May 26 2011 - 09:31:53 PDT)
  - Re: [AMBER] Equilibration step of tutorial 3 taking much longer than estimated run time Daniel Aiello (Thu May 26 2011 - 09:49:26 PDT)
    - Re: [AMBER] Equilibration step of tutorial 3 taking much longer than estimated run time Ross Walker (Thu May 26 2011 - 10:19:03 PDT)
[AMBER] watershell subrata paul (Thu May 26 2011 - 07:46:02 PDT)
- Re: [AMBER] watershell Daniel Roe (Thu May 26 2011 - 08:06:44 PDT)
[AMBER] CHAMBER Seibold, Stephen (Thu May 26 2011 - 11:20:03 PDT)
- Re: [AMBER] CHAMBER Mark Williamson (Fri May 27 2011 - 01:38:34 PDT)
  - Re: [AMBER] CHAMBER Seibold, Stephen (Sat May 28 2011 - 08:52:17 PDT)
[AMBER] RAM requirements Dmitry Osolodkin (Thu May 26 2011 - 14:08:18 PDT)
- Re: [AMBER] RAM requirements Jason Swails (Thu May 26 2011 - 21:01:19 PDT)
  - Re: [AMBER] RAM requirements Dmitry Osolodkin (Fri May 27 2011 - 04:21:05 PDT)
    - Re: [AMBER] RAM requirements Jason Swails (Fri May 27 2011 - 04:29:47 PDT)
  - Re: [AMBER] RAM requirements Robert Duke (Fri May 27 2011 - 08:05:40 PDT)
    - Re: [AMBER] RAM requirements Dmitry Osolodkin (Fri May 27 2011 - 11:01:29 PDT)
    - Re: [AMBER] RAM requirements Scott Le Grand (Fri May 27 2011 - 11:13:28 PDT)
    - Re: [AMBER] RAM requirements Robert Duke (Fri May 27 2011 - 16:09:01 PDT)
    - Re: [AMBER] RAM requirements Dmitry Osolodkin (Wed Jun 01 2011 - 09:36:07 PDT)
    - Re: [AMBER] RAM requirements Ross Walker (Wed Jun 01 2011 - 10:16:49 PDT)
    - Re: [AMBER] RAM requirements David A Case (Wed Jun 01 2011 - 10:29:51 PDT)
- Re: [AMBER] RAM requirements Robert Duke (Wed Jun 01 2011 - 10:25:29 PDT)
- Re: [AMBER] RAM requirements Robert Duke (Wed Jun 01 2011 - 10:29:21 PDT)
[AMBER] stripping of water Sangita Kachhap (Fri May 27 2011 - 00:13:15 PDT)
- Re: [AMBER] stripping of water Daniel Roe (Mon May 30 2011 - 05:41:06 PDT)
  - Re: [AMBER] stripping of water Sangita Kachhap (Mon May 30 2011 - 08:49:52 PDT)
[AMBER] rdf subrata paul (Fri May 27 2011 - 04:50:53 PDT)
- Re: [AMBER] rdf Lorenzo Gontrani (Fri May 27 2011 - 05:20:58 PDT)
  - Re: [AMBER] rdf subrata paul (Fri May 27 2011 - 06:35:15 PDT)
[AMBER] Defining molecules composed of new residues Brian Radak (Fri May 27 2011 - 07:02:25 PDT)
- Re: [AMBER] Defining molecules composed of new residues Jason Swails (Fri May 27 2011 - 09:03:44 PDT)
[AMBER] typo in parm99.dat? Thomas Gaillard (Fri May 27 2011 - 08:41:29 PDT)
- Re: [AMBER] typo in parm99.dat? Mark Williamson (Fri May 27 2011 - 08:56:16 PDT)
- Re: [AMBER] typo in parm99.dat? case (Sat May 28 2011 - 07:31:34 PDT)
[AMBER] AMBER11 Installation on FEDORA 15 Vivek Shankar Bharadwaj (Fri May 27 2011 - 10:00:21 PDT)
- Re: [AMBER] AMBER11 Installation on FEDORA 15 case (Sun May 29 2011 - 10:54:46 PDT)
  - Re: [AMBER] AMBER11 Installation on FEDORA 15 Vivek Shankar Bharadwaj (Mon May 30 2011 - 09:36:02 PDT)
    - Re: [AMBER] AMBER11 Installation on FEDORA 15 case (Mon May 30 2011 - 18:43:38 PDT)
    - Re: [AMBER] AMBER11 Installation on FEDORA 15 Vivek Shankar Bharadwaj (Tue May 31 2011 - 19:35:34 PDT)
    - Re: [AMBER] AMBER11 Installation on FEDORA 15 Daniel Roe (Tue May 31 2011 - 21:14:07 PDT)
    - Re: [AMBER] AMBER11 Installation on FEDORA 15 Vivek Shankar Bharadwaj (Wed Jun 01 2011 - 18:06:18 PDT)
    - Re: [AMBER] AMBER11 Installation on FEDORA 15 case (Wed Jun 01 2011 - 19:21:52 PDT)
[AMBER] problem with vector principal moitrayee.mbu.iisc.ernet.in (Fri May 27 2011 - 12:28:02 PDT)
- Re: [AMBER] problem with vector principal Daniel Roe (Mon May 30 2011 - 07:12:19 PDT)
  - [AMBER] problem with vector principal fatima chami (Tue Feb 21 2012 - 14:34:21 PST)
[AMBER] MMPBSA: protein-protein dimerisation George Tzotzos (Sat May 28 2011 - 02:03:26 PDT)
- Re: [AMBER] MMPBSA: protein-protein dimerisation Bill Miller III (Sat May 28 2011 - 04:57:37 PDT)
[AMBER] MMPBSA nmode warning Sangita Kachhap (Sat May 28 2011 - 02:41:11 PDT)
- Re: [AMBER] MMPBSA nmode warning Bill Miller III (Sat May 28 2011 - 04:59:21 PDT)
  - Re: [AMBER] MMPBSA nmode warning Sangita Kachhap (Sat May 28 2011 - 09:45:37 PDT)
    - Re: [AMBER] MMPBSA nmode warning Bill Miller III (Mon May 30 2011 - 18:53:56 PDT)
    - Re: [AMBER] MMPBSA nmode warning Sangita Kachhap (Tue May 31 2011 - 09:06:45 PDT)
    - Re: [AMBER] MMPBSA nmode warning Bill Miller III (Tue May 31 2011 - 09:09:58 PDT)
    - Re: [AMBER] MMPBSA nmode warning Jason Swails (Tue May 31 2011 - 09:15:08 PDT)
[AMBER] PROBLEM IN TERMINAL RESIDUES: WRONG BONDS Sindrila Dutta banik (Sat May 28 2011 - 22:03:04 PDT)
[AMBER] problems with AmberTools 1.5 compilation Anna Reymer (Sun May 29 2011 - 03:35:00 PDT)
- Re: [AMBER] problems with AmberTools 1.5 compilation Bruno Rodrigues (Sun May 29 2011 - 08:32:30 PDT)
  - Re: [AMBER] problems with AmberTools 1.5 compilation Jason Swails (Sun May 29 2011 - 08:57:20 PDT)
- Re: [AMBER] problems with AmberTools 1.5 compilation case (Sun May 29 2011 - 10:45:18 PDT)
  - Re: [AMBER] problems with AmberTools 1.5 compilation Bruno Rodrigues (Sun May 29 2011 - 13:30:30 PDT)
    - Re: [AMBER] problems with AmberTools 1.5 compilation Anna Reymer (Mon May 30 2011 - 04:17:49 PDT)
[AMBER] AMBER Shesh Nath (Mon May 30 2011 - 00:01:05 PDT)
- Re: [AMBER] AMBER case (Mon May 30 2011 - 05:55:46 PDT)
[AMBER] Where to send patches? Ake Sandgren (Mon May 30 2011 - 00:03:50 PDT)
- Re: [AMBER] Where to send patches? case (Mon May 30 2011 - 05:56:12 PDT)
  - Re: [AMBER] Where to send patches? Ake Sandgren (Wed Jun 01 2011 - 01:45:29 PDT)
[AMBER] compiling errors when using Intel compiler and AmberTools 1.5 Bongkeun Kim (Mon May 30 2011 - 03:20:34 PDT)
- Re: [AMBER] compiling errors when using Intel compiler and AmberTools 1.5 Daniel Roe (Mon May 30 2011 - 05:52:26 PDT)
  - Re: [AMBER] compiling errors when using Intel compiler and AmberTools 1.5 Bongkeun Kim (Mon May 30 2011 - 09:54:31 PDT)
[AMBER] H-bond analysis Wu Xu (Mon May 30 2011 - 05:01:51 PDT)
- Re: [AMBER] H-bond analysis Daniel Roe (Mon May 30 2011 - 06:19:43 PDT)
  - Re: [AMBER] H-bond analysis Wu Xu (Mon May 30 2011 - 15:25:46 PDT)
[AMBER] problem with running pmemd.mpi on cluster Zheng, Zhong (Mon May 30 2011 - 06:14:24 PDT)
- Re: [AMBER] problem with running pmemd.mpi on cluster Daniel Roe (Mon May 30 2011 - 06:27:19 PDT)
[AMBER] ptraj: rms George Tzotzos (Mon May 30 2011 - 08:45:56 PDT)
- Re: [AMBER] ptraj: rms Daniel Roe (Mon May 30 2011 - 08:56:59 PDT)
[AMBER] Analysis of secondary structure Alessio Atzori (Mon May 30 2011 - 12:21:56 PDT)
- Re: [AMBER] Analysis of secondary structure Daniel Roe (Mon May 30 2011 - 12:36:15 PDT)
[AMBER] Normal Mode Analysis Deák Robi (Mon May 30 2011 - 15:59:51 PDT)
- Re: [AMBER] Normal Mode Analysis case (Mon May 30 2011 - 18:32:47 PDT)
  - Re: [AMBER] Normal Mode Analysis Deák Robi (Tue May 31 2011 - 00:48:56 PDT)
[AMBER] hold H-bonds of ssRNA fixed Wu Xu (Mon May 30 2011 - 18:23:30 PDT)
- Re: [AMBER] hold H-bonds of ssRNA fixed Bill Ross (Mon May 30 2011 - 18:43:49 PDT)
  - Re: [AMBER] hold H-bonds of ssRNA fixed Wu Xu (Mon May 30 2011 - 19:17:12 PDT)
[AMBER] Restraints during relaxation Oliver Kuhn (Tue May 31 2011 - 04:40:13 PDT)
[AMBER] Restraints during relaxation - add Oliver Kuhn (Tue May 31 2011 - 06:03:22 PDT)
- Re: [AMBER] Restraints during relaxation - add Carlos Simmerling (Tue May 31 2011 - 11:41:19 PDT)
  - Re: [AMBER] Restraints during relaxation - add Oliver Kuhn (Tue May 31 2011 - 11:50:05 PDT)
[AMBER] AMBER Shesh Nath (Tue May 31 2011 - 06:15:45 PDT)
- Re: [AMBER] AMBER David A Case (Wed Jun 01 2011 - 05:49:23 PDT)
[AMBER] Configuration Checking souvik sur (Tue May 31 2011 - 06:41:47 PDT)
[AMBER] continue simulation with extended conformation Daniel Schaal (Tue May 31 2011 - 07:06:48 PDT)
- Re: [AMBER] continue simulation with extended conformation Carlos Simmerling (Tue May 31 2011 - 11:18:45 PDT)
[AMBER] protein scoop Aiko Matsumoto (Tue May 31 2011 - 08:50:36 PDT)
[AMBER] Fwd: RE: Ambertools1.5 installing problems. ning-shiuan.lee.yale.edu (Tue May 31 2011 - 12:03:57 PDT)
- Re: [AMBER] Fwd: RE: Ambertools1.5 installing problems. Daniel Roe (Tue May 31 2011 - 13:33:55 PDT)
[AMBER] MTK++/MCPB: Problem in converting prep to xml Naveen Samala (Tue May 31 2011 - 15:19:03 PDT)
[AMBER] XLEaP: Could not find type: Cl- Zheng (Tue May 31 2011 - 16:17:42 PDT)
- Re: [AMBER] XLEaP: Could not find type: Cl- Jason Swails (Tue May 31 2011 - 20:31:43 PDT)
[AMBER] Error message for cpptraj kurisaki (Tue May 31 2011 - 22:01:51 PDT)
- [AMBER] Alanine scanning with CYS Guenegou, Guillaume [ORDFR] (Wed Jun 01 2011 - 01:53:57 PDT)
  - [AMBER] Question about the influence of trajectory format (ioutfm) on results Lorenzo Gontrani (Wed Jun 01 2011 - 02:43:55 PDT)
    - Re: [AMBER] Question about the influence of trajectory format (ioutfm) on results David A Case (Wed Jun 01 2011 - 04:45:05 PDT)
  - Re: [AMBER] Alanine scanning with CYS Bill Miller III (Wed Jun 01 2011 - 03:48:13 PDT)
    - Re: [AMBER] Alanine scanning with CYS Guenegou, Guillaume [ORDFR] (Wed Jun 01 2011 - 04:42:05 PDT)
    - Re: [AMBER] Alanine scanning with CYS Bill Miller III (Wed Jun 01 2011 - 04:51:54 PDT)
- Re: [AMBER] Error message for cpptraj Daniel Roe (Wed Jun 01 2011 - 04:20:01 PDT)
[AMBER] Zotac GTX 580 3 GB german.erlenkamp.pharmazie.uni-halle.de (Wed Jun 01 2011 - 01:24:09 PDT)
- Re: [AMBER] Zotac GTX 580 3 GB Gould, Ian R (Wed Jun 01 2011 - 01:53:12 PDT)
  - Re: [AMBER] Zotac GTX 580 3 GB Gould, Ian R (Wed Jun 01 2011 - 01:54:25 PDT)
    - Re: [AMBER] Zotac GTX 580 3 GB Scott Le Grand (Wed Jun 01 2011 - 07:40:40 PDT)
    - Re: [AMBER] Zotac GTX 580 3 GB Gould, Ian R (Wed Jun 01 2011 - 08:09:47 PDT)
    - Re: [AMBER] Zotac GTX 580 3 GB Ross Walker (Wed Jun 01 2011 - 09:01:29 PDT)
    - Re: [AMBER] Zotac GTX 580 3 GB Ross Walker (Wed Jun 01 2011 - 08:57:39 PDT)
    - Re: [AMBER] Zotac GTX 580 3 GB Scott Le Grand (Wed Jun 01 2011 - 08:59:50 PDT)
    - Re: [AMBER] Zotac GTX 580 3 GB Ross Walker (Wed Jun 01 2011 - 10:20:17 PDT)
    - Re: [AMBER] Zotac GTX 580 3 GB Scott Le Grand (Wed Jun 01 2011 - 10:29:22 PDT)
[AMBER] Binary reported data were wrong.. Lorenzo Gontrani (Wed Jun 01 2011 - 02:48:11 PDT)
[AMBER] Sorry again..this is right Lorenzo Gontrani (Wed Jun 01 2011 - 02:52:43 PDT)
- Re: [AMBER] Sorry again..this is right David A Case (Wed Jun 01 2011 - 04:49:38 PDT)
  - Re: [AMBER] Sorry again..this is right Daniel Roe (Wed Jun 01 2011 - 07:02:11 PDT)
[AMBER] NMR restraints file format tong Zhu (Wed Jun 01 2011 - 03:07:57 PDT)
- Re: [AMBER] NMR restraints file format David A Case (Wed Jun 01 2011 - 04:53:32 PDT)
  - Re: [AMBER] NMR restraints file format Brendan Duggan (Wed Jun 01 2011 - 05:53:52 PDT)
[AMBER] Question about the influence of trajectory format (ioutfm) on results - part 2 Lorenzo Gontrani (Wed Jun 01 2011 - 03:11:53 PDT)
- Re: [AMBER] Question about the influence of trajectory format (ioutfm) on results - part 2 Jason Swails (Wed Jun 01 2011 - 06:00:09 PDT)
  - Re: [AMBER] Question about the influence of trajectory format (ioutfm) on results - part 2 Lorenzo Gontrani (Wed Jun 01 2011 - 08:34:18 PDT)
    - Re: [AMBER] Question about the influence of trajectory format (ioutfm) on results - part 2 David A Case (Wed Jun 01 2011 - 09:30:07 PDT)
[AMBER] pH-dependent folding simulation George Tzotzos (Wed Jun 01 2011 - 09:32:50 PDT)
- Re: [AMBER] pH-dependent folding simulation Adrian Roitberg (Wed Jun 01 2011 - 09:36:35 PDT)
  - Re: [AMBER] pH-dependent folding simulation George Tzotzos (Wed Jun 01 2011 - 10:25:29 PDT)
    - Re: [AMBER] pH-dependent folding simulation Adrian Roitberg (Wed Jun 01 2011 - 12:49:52 PDT)
    - Re: [AMBER] pH-dependent folding simulation George Tzotzos (Wed Jun 01 2011 - 13:25:24 PDT)
[AMBER] Bug - AMBER Atom type - iodine Mahmoud A. A. Ibrahim (Wed Jun 01 2011 - 10:30:11 PDT)
- Re: [AMBER] Bug - AMBER Atom type - iodine Ross Walker (Wed Jun 01 2011 - 10:37:35 PDT)
  - Re: [AMBER] Bug - AMBER Atom type - iodine Mahmoud A. A. Ibrahim (Wed Jun 01 2011 - 11:15:58 PDT)
    - Re: [AMBER] Bug - AMBER Atom type - iodine Mahmoud A. A. Ibrahim (Wed Jun 01 2011 - 11:23:35 PDT)
    - Re: [AMBER] Bug - AMBER Atom type - iodine David A Case (Wed Jun 01 2011 - 11:52:41 PDT)
[AMBER] CHAMBER and making PDB files Seibold, Stephen (Wed Jun 01 2011 - 10:34:55 PDT)
- Re: [AMBER] CHAMBER and making PDB files Ross Walker (Wed Jun 01 2011 - 10:49:55 PDT)
[AMBER] Delete Solvatebox Julian Zachmann (Wed Jun 01 2011 - 12:12:12 PDT)
- Re: [AMBER] Delete Solvatebox Bill Ross (Wed Jun 01 2011 - 12:19:39 PDT)
- Re: [AMBER] Delete Solvatebox Julian Zachmann (Wed Jun 01 2011 - 12:32:47 PDT)
[AMBER] residual dipolar coupling restraints Brendan Duggan (Wed Jun 01 2011 - 13:14:15 PDT)
- Re: [AMBER] residual dipolar coupling restraints case (Wed Jun 01 2011 - 19:09:21 PDT)
  - Re: [AMBER] residual dipolar coupling restraints Brendan Duggan (Tue Jun 07 2011 - 07:03:29 PDT)
[AMBER] sander terminates abruptly Praapti Jayaswal (Wed Jun 01 2011 - 21:01:36 PDT)
- Re: [AMBER] sander terminates abruptly Hirdesh Kumar (Thu Jun 02 2011 - 01:42:42 PDT)
  - Re: [AMBER] sander terminates abruptly Praapti Jayaswal (Thu Jun 02 2011 - 04:08:35 PDT)
    - Re: [AMBER] sander terminates abruptly Carlos Simmerling (Thu Jun 02 2011 - 04:15:18 PDT)
- Re: [AMBER] sander terminates abruptly Daniel Roe (Thu Jun 02 2011 - 04:17:00 PDT)
  - Re: [AMBER] sander terminates abruptly Praapti Jayaswal (Thu Jun 02 2011 - 21:39:41 PDT)
[AMBER] Energy Decomposition Error using Perl Script (#RECMAP + #LIGMAP != #COMPRI) Hirdesh Kumar (Thu Jun 02 2011 - 02:58:46 PDT)
- Re: [AMBER] Energy Decomposition Error using Perl Script (#RECMAP + #LIGMAP != #COMPRI) Bill Miller III (Thu Jun 02 2011 - 03:41:06 PDT)
  - Re: [AMBER] Energy Decomposition Error using Perl Script (#RECMAP + #LIGMAP != #COMPRI) Hirdesh Kumar (Thu Jun 02 2011 - 03:51:54 PDT)
[AMBER] AmberTools 1.5 installation problem Siavoush Dastmalchi (Thu Jun 02 2011 - 04:22:42 PDT)
- Re: [AMBER] AmberTools 1.5 installation problem Daniel Roe (Thu Jun 02 2011 - 04:45:59 PDT)
- Re: [AMBER] AmberTools 1.5 installation problem David A Case (Thu Jun 02 2011 - 05:16:36 PDT)
- Re: [AMBER] AmberTools 1.5 installation problem Siavoush Dastmalchi (Thu Jun 02 2011 - 08:21:16 PDT)
  - Re: [AMBER] AmberTools 1.5 installation problem David A Case (Thu Jun 02 2011 - 08:01:51 PDT)
- Re: [AMBER] AmberTools 1.5 installation problem Siavoush Dastmalchi (Thu Jun 02 2011 - 09:02:02 PDT)
  - Re: [AMBER] AmberTools 1.5 installation problem David A Case (Thu Jun 02 2011 - 08:42:41 PDT)
    - Re: [AMBER] AmberTools 1.5 installation problem Jason Swails (Thu Jun 02 2011 - 09:27:32 PDT)
- Re: [AMBER] AmberTools 1.5 installation problem Siavoush Dastmalchi (Thu Jun 02 2011 - 10:39:56 PDT)
[AMBER] ptraj: cluster George Tzotzos (Thu Jun 02 2011 - 05:45:27 PDT)
- Re: [AMBER] ptraj: cluster George Tzotzos (Thu Jun 02 2011 - 06:11:41 PDT)
- Re: [AMBER] ptraj: cluster Thomas Cheatham (Thu Jun 02 2011 - 06:36:10 PDT)
  - Re: [AMBER] ptraj: cluster George Tzotzos (Thu Jun 02 2011 - 06:51:10 PDT)
    - Re: [AMBER] ptraj: cluster Thomas Cheatham (Thu Jun 02 2011 - 07:21:37 PDT)
    - Re: [AMBER] ptraj: cluster George Tzotzos (Thu Jun 02 2011 - 07:50:05 PDT)
[AMBER] Force fields for DNA, what to choose? Anna Reymer (Thu Jun 02 2011 - 07:26:31 PDT)
- Re: [AMBER] Force fields for DNA, what to choose? David A Case (Thu Jun 02 2011 - 08:40:36 PDT)
- Re: [AMBER] Force fields for DNA, what to choose? Jiri Sponer (Thu Jun 02 2011 - 09:09:47 PDT)
[AMBER] simulation of small molecule with organic solvent and water Senthil Natesan (Thu Jun 02 2011 - 08:03:35 PDT)
- Re: [AMBER] simulation of small molecule with organic solvent and water aneesh cna (Thu Jun 02 2011 - 21:56:56 PDT)
  - Re: [AMBER] simulation of small molecule with organic solvent and water Senthil Natesan (Fri Jun 03 2011 - 07:12:05 PDT)
[AMBER] mmpbsa-bad atom (metal ions) 付婷 (Thu Jun 02 2011 - 17:59:26 PDT)
[AMBER] production run duration Xiao Chen (Thu Jun 02 2011 - 21:46:54 PDT)
- Re: [AMBER] production run duration Ben Roberts (Thu Jun 02 2011 - 22:02:36 PDT)
  - Re: [AMBER] production run duration Xiao Chen (Fri Jun 03 2011 - 01:53:44 PDT)
    - Re: [AMBER] production run duration Ben Roberts (Fri Jun 03 2011 - 08:45:07 PDT)
[AMBER] Choosing the number of replicas in NEB Chris Bryant (Fri Jun 03 2011 - 07:58:18 PDT)
- Re: [AMBER] Choosing the number of replicas in NEB Carlos Simmerling (Fri Jun 03 2011 - 09:27:02 PDT)
- Re: [AMBER] Choosing the number of replicas in NEB Ross Walker (Fri Jun 03 2011 - 09:32:23 PDT)
[AMBER] concerted effect of the backbone movement abhay.strubi.ox.ac.uk (Fri Jun 03 2011 - 08:11:03 PDT)
[AMBER] unexpected behavior of ambpdb Brian Radak (Fri Jun 03 2011 - 08:16:19 PDT)
- Re: [AMBER] unexpected behavior of ambpdb Marc van der Kamp (Fri Jun 03 2011 - 08:36:07 PDT)
- Re: [AMBER] unexpected behavior of ambpdb David A Case (Fri Jun 03 2011 - 09:54:40 PDT)
  - Re: [AMBER] unexpected behavior of ambpdb Brian Radak (Fri Jun 03 2011 - 10:15:40 PDT)
[AMBER] ptaj: contacts George Tzotzos (Fri Jun 03 2011 - 08:31:53 PDT)
[AMBER] RED Seibold, Stephen (Fri Jun 03 2011 - 14:11:43 PDT)
- Re: [AMBER] RED Paul S. Nerenberg (Fri Jun 03 2011 - 14:30:31 PDT)
- Re: [AMBER] RED FyD (Fri Jun 03 2011 - 15:58:07 PDT)
[AMBER] Problem related with the Ptraj Sindrila Dutta banik (Sat Jun 04 2011 - 04:14:08 PDT)
- Re: [AMBER] Problem related with the Ptraj Carlos Simmerling (Sat Jun 04 2011 - 04:17:38 PDT)
[AMBER] Simulating a periodic System about Molecular Crystal hanlu0366 (Sun Jun 05 2011 - 06:27:07 PDT)
- Re: [AMBER] Simulating a periodic System about Molecular Crystal case (Sun Jun 05 2011 - 07:26:22 PDT)
- Re: [AMBER] Simulating a periodic System about Molecular Crystal hanlu0366 (Sun Jun 05 2011 - 19:09:14 PDT)
- Re: [AMBER] Simulating a periodic System about Molecular Crystal hanlu0366 (Sun Jun 05 2011 - 20:34:12 PDT)
  - Re: [AMBER] Simulating a periodic System about Molecular Crystal David A Case (Mon Jun 06 2011 - 04:45:45 PDT)
[AMBER] PMEMD does not support intermolecular PRFs Maura Catherine Mooney (Sun Jun 05 2011 - 08:44:43 PDT)
- Re: [AMBER] PMEMD does not support intermolecular PRFs Ross Walker (Sun Jun 05 2011 - 22:12:55 PDT)
  - Re: [AMBER] PMEMD does not support intermolecular PRFs Maura Catherine Mooney (Mon Jun 06 2011 - 08:10:50 PDT)
    - Re: [AMBER] PMEMD does not support intermolecular PRFs Jason Swails (Mon Jun 06 2011 - 23:12:09 PDT)
    - Re: [AMBER] PMEMD does not support intermolecular PRFs Maura Catherine Mooney (Tue Jun 07 2011 - 05:22:15 PDT)
    - Re: [AMBER] PMEMD does not support intermolecular PRFs Jason Swails (Tue Jun 07 2011 - 08:08:26 PDT)
    - Re: [AMBER] PMEMD does not support intermolecular PRFs Jason Swails (Wed Jun 15 2011 - 14:28:16 PDT)
    - Re: [AMBER] PMEMD does not support intermolecular PRFs Maura Catherine Mooney (Thu Jun 16 2011 - 06:54:33 PDT)
    - Re: [AMBER] PMEMD does not support intermolecular PRFs David A Case (Thu Jun 16 2011 - 07:13:32 PDT)
    - Re: [AMBER] PMEMD does not support intermolecular PRFs Jason Swails (Thu Jun 16 2011 - 07:34:17 PDT)
    - Re: [AMBER] PMEMD does not support intermolecular PRFs Maura Catherine Mooney (Thu Jun 16 2011 - 07:39:25 PDT)
    - Re: [AMBER] PMEMD does not support intermolecular PRFs Jason Swails (Thu Jun 16 2011 - 07:44:24 PDT)
    - Re: [AMBER] PMEMD does not support intermolecular PRFs Maura Catherine Mooney (Thu Jun 16 2011 - 07:54:49 PDT)
    - Re: [AMBER] PMEMD does not support intermolecular PRFs Jason Swails (Thu Jun 16 2011 - 18:29:53 PDT)
    - Re: [AMBER] PMEMD does not support intermolecular PRFs Maura Catherine Mooney (Thu Jun 16 2011 - 19:05:22 PDT)
    - Re: [AMBER] PMEMD does not support intermolecular PRFs Jason Swails (Thu Jun 16 2011 - 23:37:56 PDT)
    - Re: [AMBER] PMEMD does not support intermolecular PRFs Maura Catherine Mooney (Fri Jun 17 2011 - 07:37:19 PDT)
[AMBER] prep files ATP-MG++ and for phosphorylated threonine Nitu Bansal (Sun Jun 05 2011 - 13:12:37 PDT)
- Re: [AMBER] prep files ATP-MG++ and for phosphorylated threonine Anselm Horn (Sun Jun 05 2011 - 14:15:04 PDT)
  - Re: [AMBER] prep files ATP-MG++ and for phosphorylated threonine Nitu Bansal (Mon Jun 06 2011 - 10:26:55 PDT)
    - Re: [AMBER] prep files ATP-MG++ and for phosphorylated threonine Anselm Horn (Mon Jun 06 2011 - 16:14:26 PDT)
- [AMBER] Problem with two jobs on one GPU Marek Maly (Mon Jun 06 2011 - 03:24:15 PDT)
  - Re: [AMBER] Problem with two jobs on one GPU Ross Walker (Mon Jun 06 2011 - 09:23:08 PDT)
    - Re: [AMBER] Problem with two jobs on one GPU Marek Maly (Wed Jun 08 2011 - 03:46:21 PDT)
  - Re: [AMBER] Problem with two jobs on one GPU Scott Le Grand (Mon Jun 06 2011 - 09:58:52 PDT)
[AMBER] Negative value of SASA calculated by surf command in cpptraj kurisaki (Sun Jun 05 2011 - 20:30:54 PDT)
- Re: [AMBER] Negative value of SASA calculated by surf command in cpptraj Daniel Roe (Sun Jun 05 2011 - 20:59:05 PDT)
  - Re: [AMBER] Negative value of SASA calculated by surf command in cpptraj kurisaki (Sun Jun 12 2011 - 19:29:19 PDT)
    - Re: [AMBER] Negative value of SASA calculated by surf command in cpptraj kurisaki (Sun Jun 12 2011 - 19:49:30 PDT)
[AMBER] Problem with make test.serial Amber 9 TH Chew (Mon Jun 06 2011 - 03:17:09 PDT)
- Re: [AMBER] Problem with make test.serial Amber 9 Jason Swails (Mon Jun 06 2011 - 05:58:28 PDT)
  - Re: [AMBER] Problem with make test.serial Amber 9 TH Chew (Mon Jun 06 2011 - 22:20:39 PDT)
[AMBER] Calculating energies Daniel Schaal (Mon Jun 06 2011 - 04:11:19 PDT)
- Re: [AMBER] Calculating energies Jason Swails (Mon Jun 06 2011 - 06:02:07 PDT)
[AMBER] Ligand Minimization with Simulated Annealing Julian Zachmann (Mon Jun 06 2011 - 07:24:51 PDT)
- Re: [AMBER] Ligand Minimization with Simulated Annealing Carlos Simmerling (Mon Jun 06 2011 - 07:28:11 PDT)
  - Re: [AMBER] Ligand Minimization with Simulated Annealing Julian Zachmann (Mon Jun 06 2011 - 07:42:00 PDT)
    - Re: [AMBER] Ligand Minimization with Simulated Annealing Carlos Simmerling (Mon Jun 06 2011 - 07:44:12 PDT)
    - Re: [AMBER] Ligand Minimization with Simulated Annealing Adrian Roitberg (Mon Jun 06 2011 - 07:45:29 PDT)
    - Re: [AMBER] Ligand Minimization with Simulated Annealing Kevin Hauser (Mon Jun 06 2011 - 10:10:41 PDT)
[AMBER] energy decomposition with mmpbsa.py victor ma (Mon Jun 06 2011 - 10:07:29 PDT)
- Re: [AMBER] energy decomposition with mmpbsa.py Bill Miller III (Mon Jun 06 2011 - 10:10:33 PDT)
  - Re: [AMBER] energy decomposition with mmpbsa.py victor ma (Mon Jun 06 2011 - 10:12:51 PDT)
    - Re: [AMBER] energy decomposition with mmpbsa.py Bill Miller III (Mon Jun 06 2011 - 10:14:58 PDT)
    - Re: [AMBER] energy decomposition with mmpbsa.py Hirdesh Kumar (Mon Jun 06 2011 - 20:28:00 PDT)
    - Re: [AMBER] energy decomposition with mmpbsa.py Bill Miller III (Mon Jun 06 2011 - 20:44:36 PDT)
[AMBER] Units of SMD Simulation Output Joseph Seemiller (Mon Jun 06 2011 - 13:16:44 PDT)
- Re: [AMBER] Units of SMD Simulation Output Dmitry Nilov (Mon Jun 06 2011 - 20:57:42 PDT)
[AMBER] ptraj error with *** glibc detected *** ptraj: free(): invalid next size (normal) Bongkeun Kim (Mon Jun 06 2011 - 13:30:03 PDT)
- Re: [AMBER] ptraj error with *** glibc detected *** ptraj: free(): invalid next size (normal) Daniel Roe (Tue Jun 07 2011 - 04:12:54 PDT)
  - Re: [AMBER] ptraj error with *** glibc detected *** ptraj: free(): invalid next size (normal) Bongkeun Kim (Tue Jun 07 2011 - 14:29:46 PDT)
    - Re: [AMBER] ptraj error with *** glibc detected *** ptraj: free(): invalid next size (normal) Daniel Roe (Wed Jun 08 2011 - 07:28:36 PDT)
    - Re: [AMBER] ptraj error with *** glibc detected *** ptraj: free(): invalid next size (normal) Bongkeun Kim (Thu Jun 09 2011 - 00:49:10 PDT)
    - Re: [AMBER] ptraj error with *** glibc detected *** ptraj: free(): invalid next size (normal) Daniel Roe (Thu Jun 09 2011 - 10:06:17 PDT)
    - Re: [AMBER] ptraj error with *** glibc detected *** ptraj: free(): invalid next size (normal) Bongkeun Kim (Thu Jun 09 2011 - 10:14:33 PDT)
    - Re: [AMBER] ptraj error with *** glibc detected *** ptraj: free(): invalid next size (normal) Bongkeun Kim (Thu Jun 09 2011 - 11:00:56 PDT)
    - Re: [AMBER] ptraj error with *** glibc detected *** ptraj: free(): invalid next size (normal) David A. Case (Fri Jun 10 2011 - 03:12:01 PDT)
    - Re: [AMBER] ptraj error with *** glibc detected *** ptraj: free(): invalid next size (normal) Bongkeun Kim (Fri Jun 10 2011 - 13:53:54 PDT)
    - Re: [AMBER] ptraj error with *** glibc detected *** ptraj: free(): invalid next size (normal) David A. Case (Sat Jun 11 2011 - 08:12:41 PDT)
[AMBER] rmsd calculation Xiao Chen (Tue Jun 07 2011 - 02:03:57 PDT)
- Re: [AMBER] rmsd calculation Thomas Gaillard (Tue Jun 07 2011 - 03:32:52 PDT)
  - Re: [AMBER] rmsd calculation Xiao Chen (Tue Jun 07 2011 - 04:04:09 PDT)
    - Re: [AMBER] rmsd calculation Daniel Roe (Tue Jun 07 2011 - 04:08:16 PDT)
    - Re: [AMBER] rmsd calculation Fredrick Devadoss (Tue Jun 07 2011 - 04:32:26 PDT)
  - [AMBER] MM-PBSA/GBSA of charged molecules Bernhard Poll (Tue Jun 07 2011 - 04:29:48 PDT)
    - Re: [AMBER] MM-PBSA/GBSA of charged molecules Ray Luo, Ph.D. (Tue Jun 07 2011 - 10:55:28 PDT)
- Re: [AMBER] rmsd calculation Daniel Roe (Tue Jun 07 2011 - 04:07:19 PDT)
  - Re: [AMBER] rmsd calculation Xiao Chen (Tue Jun 07 2011 - 21:55:53 PDT)
    - Re: [AMBER] rmsd calculation Daniel Roe (Wed Jun 08 2011 - 05:57:29 PDT)
- Re: [AMBER] rmsd calculation David A. Case (Tue Jun 07 2011 - 04:32:26 PDT)
  - Re: [AMBER] rmsd calculation Xiao Chen (Tue Jun 07 2011 - 21:48:43 PDT)
[AMBER] Loadin AMBER9 in linux souvik sur (Tue Jun 07 2011 - 03:08:00 PDT)
- Re: [AMBER] Loadin AMBER9 in linux TH Chew (Tue Jun 07 2011 - 03:11:23 PDT)
  - Re: [AMBER] Loadin AMBER9 in linux souvik sur (Tue Jun 07 2011 - 03:14:26 PDT)
  - Re: [AMBER] Loadin AMBER9 in linux souvik sur (Tue Jun 07 2011 - 03:44:19 PDT)
    - Re: [AMBER] Loadin AMBER9 in linux TH Chew (Tue Jun 07 2011 - 03:54:02 PDT)
    - Re: [AMBER] Loadin AMBER9 in linux Jason Swails (Tue Jun 07 2011 - 08:11:36 PDT)
    - Re: [AMBER] Loadin AMBER9 in linux souvik sur (Tue Jun 07 2011 - 10:15:31 PDT)
    - Re: [AMBER] Loadin AMBER9 in linux souvik sur (Tue Jun 07 2011 - 23:42:51 PDT)
    - Re: [AMBER] Loadin AMBER9 in linux TH Chew (Tue Jun 07 2011 - 23:47:29 PDT)
    - Re: [AMBER] Loadin AMBER9 in linux souvik sur (Wed Jun 08 2011 - 00:10:55 PDT)
    - Re: [AMBER] Loadin AMBER9 in linux TH Chew (Wed Jun 08 2011 - 00:17:32 PDT)
    - Re: [AMBER] Loadin AMBER9 in linux souvik sur (Wed Jun 08 2011 - 00:26:26 PDT)
    - Re: [AMBER] Loadin AMBER9 in linux TH Chew (Wed Jun 08 2011 - 00:45:12 PDT)
    - Re: [AMBER] Loadin AMBER9 in linux souvik sur (Wed Jun 08 2011 - 02:31:36 PDT)
    - Re: [AMBER] Loadin AMBER9 in linux TH Chew (Wed Jun 08 2011 - 05:56:56 PDT)
    - Re: [AMBER] Loadin AMBER9 in linux souvik sur (Wed Jun 08 2011 - 23:23:31 PDT)
    - Re: [AMBER] Loadin AMBER9 in linux TH Chew (Thu Jun 09 2011 - 06:49:59 PDT)
    - Re: [AMBER] Loadin AMBER9 in linux souvik sur (Fri Jun 10 2011 - 02:56:23 PDT)
    - Re: [AMBER] Loadin AMBER9 in linux David A. Case (Fri Jun 10 2011 - 03:08:45 PDT)
    - Re: [AMBER] Loadin AMBER9 in linux souvik sur (Fri Jun 10 2011 - 04:47:07 PDT)
    - Re: [AMBER] Loadin AMBER9 in linux TH Chew (Fri Jun 10 2011 - 07:07:39 PDT)
    - Re: [AMBER] Loadin AMBER9 in linux souvik sur (Sat Jun 11 2011 - 02:23:51 PDT)
    - Re: [AMBER] Loadin AMBER9 in linux TH Chew (Sat Jun 11 2011 - 02:32:24 PDT)
    - Re: [AMBER] Loadin AMBER9 in linux souvik sur (Sat Jun 11 2011 - 04:29:35 PDT)
    - Re: [AMBER] Loadin AMBER9 in linux TH Chew (Sat Jun 11 2011 - 22:30:56 PDT)
    - [AMBER] Leap question/suggestion for leap developers Sergio R Aragon (Sun Jun 12 2011 - 12:23:14 PDT)
    - Re: [AMBER] Leap question/suggestion for leap developers David A Case (Mon Jun 13 2011 - 05:37:40 PDT)
[AMBER] regarding pi-pi interaction Hirdesh Kumar (Tue Jun 07 2011 - 03:19:32 PDT)
- Re: [AMBER] regarding pi-pi interaction Jiri Sponer (Tue Jun 07 2011 - 03:28:00 PDT)
[AMBER] PTRAJ clustering Sander B. (Tue Jun 07 2011 - 07:40:12 PDT)
- Re: [AMBER] PTRAJ clustering Jianyin Shao (Tue Jun 07 2011 - 08:44:21 PDT)
  - Re: [AMBER] PTRAJ clustering Jianyin Shao (Tue Jun 07 2011 - 08:50:55 PDT)
  - Re: [AMBER] PTRAJ clustering Sander B. (Wed Jun 08 2011 - 01:11:42 PDT)
    - Re: [AMBER] PTRAJ clustering Jianyin Shao (Fri Jun 10 2011 - 23:51:57 PDT)
[AMBER] MMPBSA: general question George Tzotzos (Tue Jun 07 2011 - 09:51:12 PDT)
- Re: [AMBER] MMPBSA: general question Adrian Roitberg (Tue Jun 07 2011 - 10:01:15 PDT)
  - Re: [AMBER] MMPBSA: general question George Tzotzos (Tue Jun 07 2011 - 10:07:54 PDT)
[AMBER] Normal Mode Analysis David Cantu (Tue Jun 07 2011 - 16:08:48 PDT)
- Re: [AMBER] Normal Mode Analysis Dwight McGee (Tue Jun 07 2011 - 18:07:45 PDT)
  - Re: [AMBER] Normal Mode Analysis David Cantu (Wed Jun 08 2011 - 08:10:10 PDT)
    - Re: [AMBER] Normal Mode Analysis David A. Case (Wed Jun 08 2011 - 09:48:22 PDT)
    - Re: [AMBER] Normal Mode Analysis David Cantu (Mon Jun 13 2011 - 14:11:18 PDT)
    - Re: [AMBER] Normal Mode Analysis Jason Swails (Mon Jun 13 2011 - 14:59:15 PDT)
- [AMBER] Detection of residues within a sphere Guenegou, Guillaume [ORDFR] (Wed Jun 08 2011 - 05:40:53 PDT)
  - Re: [AMBER] Detection of residues within a sphere Daniel Roe (Wed Jun 08 2011 - 06:07:39 PDT)
    - Re: [AMBER] Detection of residues within a sphere Ignacio J. General (Wed Jun 08 2011 - 06:39:48 PDT)
[AMBER] Installation problem Shesh Nath (Tue Jun 07 2011 - 23:42:46 PDT)
- Re: [AMBER] Installation problem David A. Case (Thu Jun 09 2011 - 01:57:42 PDT)
[AMBER] non-bonded cutoff in the case of REMD in explicit solvent mish (Wed Jun 08 2011 - 01:20:10 PDT)
- Re: [AMBER] non-bonded cutoff in the case of REMD in explicit solvent Adrian Roitberg (Wed Jun 08 2011 - 01:28:06 PDT)
  - Re: [AMBER] non-bonded cutoff in the case of REMD in explicit solvent mish (Wed Jun 08 2011 - 01:55:11 PDT)
    - Re: [AMBER] non-bonded cutoff in the case of REMD in explicit solvent Adrian Roitberg (Wed Jun 08 2011 - 03:21:04 PDT)
    - Re: [AMBER] non-bonded cutoff in the case of REMD in explicit solvent Adrian Roitberg (Wed Jun 08 2011 - 03:21:17 PDT)
[AMBER] Does anyone know a screening program of hardware validity for GeForce GTX board? Hiromichi Tsurui (Wed Jun 08 2011 - 03:48:01 PDT)
- Re: [AMBER] Does anyone know a screening program of hardware validity for GeForce GTX board? Scott Le Grand (Wed Jun 08 2011 - 10:26:04 PDT)
- Re: [AMBER] Does anyone know a screening program of hardware validity for GeForce GTX board? Hiromichi Tsurui (Wed Jun 08 2011 - 18:11:44 PDT)
[AMBER] sander.mpi with amoeba? r smith (Wed Jun 08 2011 - 07:19:07 PDT)
- Re: [AMBER] sander.mpi with amoeba? David A. Case (Wed Jun 08 2011 - 14:15:09 PDT)
  - [AMBER] Structured water molecules with leap Guenegou, Guillaume [ORDFR] (Fri Jun 10 2011 - 06:39:48 PDT)
    - [AMBER] Alanine scanning Guenegou, Guillaume [ORDFR] (Fri Jun 10 2011 - 06:51:02 PDT)
    - Re: [AMBER] Alanine scanning Jason Swails (Fri Jun 10 2011 - 07:02:04 PDT)
    - Re: [AMBER] Alanine scanning Bill Miller III (Fri Jun 10 2011 - 07:01:53 PDT)
    - Re: [AMBER] Structured water molecules with leap David A Case (Mon Jun 13 2011 - 06:08:09 PDT)
[AMBER] water test with pmemd.amba r smith (Wed Jun 08 2011 - 08:26:38 PDT)
[AMBER] bin size for rdf subrata paul (Wed Jun 08 2011 - 09:23:05 PDT)
[AMBER] problem about entropy calculation caobb0214 (Wed Jun 08 2011 - 17:21:36 PDT)
- Re: [AMBER] problem about entropy calculation David A. Case (Thu Jun 09 2011 - 01:45:40 PDT)
- [AMBER] Estimation of free energy of solvation ? Marek Maly (Wed Jun 15 2011 - 07:19:37 PDT)
  - Re: [AMBER] Estimation of free energy of solvation ? Ignacio J. General (Wed Jun 15 2011 - 07:45:30 PDT)
    - Re: [AMBER] Estimation of free energy of solvation ? steinbrt.rci.rutgers.edu (Wed Jun 15 2011 - 07:58:10 PDT)
    - Re: [AMBER] Estimation of free energy of solvation ? Marek Maly (Wed Jun 15 2011 - 08:12:41 PDT)
    - Re: [AMBER] Estimation of free energy of solvation ? steinbrt.rci.rutgers.edu (Wed Jun 15 2011 - 08:36:21 PDT)
    - Re: [AMBER] Estimation of free energy of solvation ? Marek Maly (Wed Jun 15 2011 - 08:36:52 PDT)
    - Re: [AMBER] Estimation of free energy of solvation ? Marek Maly (Wed Jun 15 2011 - 07:46:15 PDT)
  - Re: [AMBER] Estimation of free energy of solvation ? Carlos Simmerling (Wed Jun 15 2011 - 08:35:02 PDT)
    - Re: [AMBER] Estimation of free energy of solvation ? Marek Maly (Wed Jun 15 2011 - 08:38:33 PDT)
[AMBER] Using PQR files produced by PDB2PQR as input for tleap/xleap Azat Mukhametov (Wed Jun 08 2011 - 19:35:42 PDT)
- Re: [AMBER] Using PQR files produced by PDB2PQR as input for tleap/xleap Daniel Sindhikara (Wed Jun 08 2011 - 19:50:00 PDT)
  - Re: [AMBER] Using PQR files produced by PDB2PQR as input for tleap/xleap Azat Mukhametov (Wed Jun 08 2011 - 19:57:15 PDT)
    - Re: [AMBER] Using PQR files produced by PDB2PQR as input for tleap/xleap Azat Mukhametov (Wed Jun 08 2011 - 23:56:53 PDT)
    - Re: [AMBER] Using PQR files produced by PDB2PQR as input for tleap/xleap Azat Mukhametov (Wed Jun 08 2011 - 23:57:53 PDT)
    - Re: [AMBER] Using PQR files produced by PDB2PQR as input for tleap/xleap Daniel Sindhikara (Thu Jun 09 2011 - 00:10:13 PDT)
    - Re: [AMBER] Using PQR files produced by PDB2PQR as input for tleap/xleap Azat Mukhametov (Thu Jun 09 2011 - 00:21:20 PDT)
    - Re: [AMBER] Using PQR files produced by PDB2PQR as input for tleap/xleap David A. Case (Thu Jun 09 2011 - 01:36:55 PDT)
    - Re: [AMBER] Using PQR files produced by PDB2PQR as input for tleap/xleap Azat Mukhametov (Thu Jun 09 2011 - 03:03:20 PDT)
    - Re: [AMBER] Using PQR files produced by PDB2PQR as input for tleap/xleap David A. Case (Thu Jun 09 2011 - 03:32:34 PDT)
    - Re: [AMBER] Using PQR files produced by PDB2PQR as input for tleap/xleap Jason Swails (Thu Jun 09 2011 - 09:47:10 PDT)
    - Re: [AMBER] Using PQR files produced by PDB2PQR as input fortleap/x leap. . Bashford, Donald (Thu Jun 09 2011 - 10:42:15 PDT)
    - Re: [AMBER] Using PQR files produced by PDB2PQR as input fortleap/x leap. . David A. Case (Fri Jun 10 2011 - 03:12:38 PDT)
[AMBER] Problem related to teh residue template and add ion Sindrila Dutta banik (Thu Jun 09 2011 - 03:47:16 PDT)
- Re: [AMBER] Problem related to teh residue template and add ion David A. Case (Thu Jun 09 2011 - 09:55:38 PDT)
  - [AMBER] Problem related to teh residue template and add ion Sindrila Dutta banik (Fri Jun 10 2011 - 08:18:13 PDT)
    - Re: [AMBER] Problem related to teh residue template and add ion Bill Ross (Thu Jun 09 2011 - 16:34:08 PDT)
[AMBER] problems ahout simulating a molecular crystal hanlu0366 (Thu Jun 09 2011 - 04:51:45 PDT)
- Re: [AMBER] problems ahout simulating a molecular crystal David A. Case (Thu Jun 09 2011 - 09:59:26 PDT)
- Re: [AMBER] problems ahout simulating a molecular crystal hanlu0366 (Fri Jun 10 2011 - 00:11:13 PDT)
  - Re: [AMBER] problems ahout simulating a molecular crystal David A. Case (Fri Jun 10 2011 - 03:11:49 PDT)
- Re: [AMBER] problems ahout simulating a molecular crystal hanlu0366 (Fri Jun 10 2011 - 05:55:30 PDT)
  - Re: [AMBER] problems ahout simulating a molecular crystal David A. Case (Sat Jun 11 2011 - 07:03:23 PDT)
- Re: [AMBER] problems ahout simulating a molecular crystal hanlu0366 (Mon Jun 13 2011 - 06:20:19 PDT)
  - Re: [AMBER] problems ahout simulating a molecular crystal David A Case (Mon Jun 13 2011 - 06:46:22 PDT)
- Re: [AMBER] problems ahout simulating a molecular crystal hanlu0366 (Tue Jun 21 2011 - 07:25:02 PDT)
  - Re: [AMBER] problems ahout simulating a molecular crystal David A Case (Tue Jun 21 2011 - 08:06:11 PDT)
[AMBER] Problem related to the residue template and add ion Sindrila Dutta banik (Thu Jun 09 2011 - 05:27:54 PDT)
[AMBER] re-image Bruno Rodrigues (Thu Jun 09 2011 - 06:28:19 PDT)
- Re: [AMBER] re-image Pablo I. D. Dans Puiggròs (Thu Jun 09 2011 - 06:34:54 PDT)
  - Re: [AMBER] re-image Bruno Rodrigues (Thu Jun 09 2011 - 06:47:30 PDT)
    - Re: [AMBER] re-image Pablo I. D. Dans Puiggròs (Thu Jun 09 2011 - 06:53:09 PDT)
    - Re: [AMBER] re-image Nadine Utz (Thu Jun 09 2011 - 07:04:25 PDT)
    - Re: [AMBER] re-image Bruno Rodrigues (Thu Jun 09 2011 - 07:34:26 PDT)
[AMBER] Antechamber Caterina Bianchi (Thu Jun 09 2011 - 07:09:57 PDT)
[AMBER] SANDER BOMB Xioling Chuang (Thu Jun 09 2011 - 07:41:29 PDT)
- Re: [AMBER] SANDER BOMB Ray Luo, Ph.D. (Thu Jun 09 2011 - 08:53:27 PDT)
[AMBER] CPPTRAJ- segmentation fault Xiao Chen (Thu Jun 09 2011 - 21:00:17 PDT)
- Re: [AMBER] CPPTRAJ- segmentation fault Daniel Roe (Fri Jun 10 2011 - 08:03:01 PDT)
[AMBER] ANTECHAMBER/RESP Caterina Bianchi (Fri Jun 10 2011 - 03:02:24 PDT)
- Re: [AMBER] ANTECHAMBER/RESP FyD (Sat Jun 11 2011 - 00:22:38 PDT)
[AMBER] Amber 10: Compilation error Kshatresh Dutta Dubey (Fri Jun 10 2011 - 04:51:34 PDT)
- Re: [AMBER] Amber 10: Compilation error David A. Case (Sat Jun 11 2011 - 06:56:59 PDT)
  - Re: [AMBER] Amber 10: Compilation error Kshatresh Dutta Dubey (Sun Jun 12 2011 - 21:09:56 PDT)
[AMBER] Free energy perturbation of Ca2+ ion Sergey Samsonov (Fri Jun 10 2011 - 06:50:37 PDT)
[AMBER] Question about INTRAmolecular restraint Lorenzo Gontrani (Fri Jun 10 2011 - 09:52:29 PDT)
- Re: [AMBER] Question about INTRAmolecular restraint Jason Swails (Fri Jun 10 2011 - 21:43:42 PDT)
  - Re: [AMBER] Question about INTRAmolecular restraint Lorenzo Gontrani (Sat Jun 11 2011 - 12:58:20 PDT)
[AMBER] Problems Compiling Amber10 Gordon Freeman (Fri Jun 10 2011 - 10:02:52 PDT)
- Re: [AMBER] Problems Compiling Amber10 Jason Swails (Fri Jun 10 2011 - 21:34:57 PDT)
[AMBER] running a MD with a innert gas Matias Factorovich (Fri Jun 10 2011 - 10:08:32 PDT)
- Re: [AMBER] running a MD with a innert gas Adrian Roitberg (Fri Jun 10 2011 - 10:09:26 PDT)
  - Re: [AMBER] running a MD with a innert gas case (Sat Jun 11 2011 - 10:58:37 PDT)
    - Re: [AMBER] running a MD with a innert gas Matias Factorovich (Sat Jun 11 2011 - 11:07:46 PDT)
[AMBER] Issues with Generating Prep File from Gaussian output using Antechamber Vivek Shankar Bharadwaj (Fri Jun 10 2011 - 13:44:22 PDT)
- Re: [AMBER] Issues with Generating Prep File from Gaussian output using Antechamber David A. Case (Sat Jun 11 2011 - 07:27:17 PDT)
[AMBER] Amber Compilation error Kshatresh Dutta Dubey (Fri Jun 10 2011 - 22:38:53 PDT)
- Re: [AMBER] Amber Compilation error Jason Swails (Fri Jun 10 2011 - 22:48:22 PDT)
[AMBER] Solution for frozen atom type hari krishna (Sat Jun 11 2011 - 02:07:39 PDT)
[AMBER] format error from mmpbsa.py Zhi Wang (Sat Jun 11 2011 - 14:01:38 PDT)
- Re: [AMBER] format error from mmpbsa.py Jason Swails (Sat Jun 11 2011 - 15:57:27 PDT)
  - Re: [AMBER] format error from mmpbsa.py Jason Swails (Sat Jun 11 2011 - 20:02:20 PDT)
    - Re: [AMBER] format error from mmpbsa.py Zhi Wang (Sun Jun 12 2011 - 01:31:05 PDT)
    - Re: [AMBER] format error from mmpbsa.py Zhi Wang (Sun Jun 12 2011 - 02:02:06 PDT)
    - Re: [AMBER] format error from mmpbsa.py Jason Swails (Sun Jun 12 2011 - 09:41:40 PDT)
    - Re: [AMBER] format error from mmpbsa.py zw258.cam.ac.uk (Mon Jun 13 2011 - 03:25:41 PDT)
    - Re: [AMBER] format error from mmpbsa.py Bill Miller III (Mon Jun 13 2011 - 03:44:24 PDT)
    - Re: [AMBER] format error from mmpbsa.py zw258.cam.ac.uk (Mon Jun 13 2011 - 05:18:30 PDT)
  - Re: [AMBER] format error from mmpbsa.py Mark Williamson (Mon Jun 13 2011 - 02:58:25 PDT)
[AMBER] Amber 11 and AmberTools 1.5 on Debian 6 Siavoush Dastmalchi (Sun Jun 12 2011 - 04:10:24 PDT)
- Re: [AMBER] Amber 11 and AmberTools 1.5 on Debian 6 Jiri Wiesner (Sun Jun 12 2011 - 07:59:46 PDT)
  - Re: [AMBER] Amber 11 and AmberTools 1.5 on Debian 6 Jason Swails (Sun Jun 12 2011 - 09:48:46 PDT)
[AMBER] About "Must have more residues than processors" Bin Wu (Sun Jun 12 2011 - 13:35:04 PDT)
- Re: [AMBER] About "Must have more residues than processors" Jason Swails (Sun Jun 12 2011 - 16:14:30 PDT)
  - Re: [AMBER] About "Must have more residues than processors" Ross Walker (Mon Jun 13 2011 - 07:36:46 PDT)
    - Re: [AMBER] About "Must have more residues than processors" Carlos Simmerling (Mon Jun 13 2011 - 07:41:07 PDT)
[AMBER] High-temperature output in REMD tdo.chem.ucsb.edu (Sun Jun 12 2011 - 18:16:44 PDT)
- Re: [AMBER] High-temperature output in REMD Jason Swails (Sun Jun 12 2011 - 21:25:03 PDT)
  - Re: [AMBER] High-temperature output in REMD Carlos Simmerling (Mon Jun 13 2011 - 06:19:29 PDT)
[AMBER] noesy and dip Program error when testing Amber11 Parallel Alison Lynton (Mon Jun 13 2011 - 00:53:16 PDT)
- Re: [AMBER] noesy and dip Program error when testing Amber11 Parallel David A Case (Mon Jun 13 2011 - 05:14:35 PDT)
  - Re: [AMBER] noesy and dip Program error when testing Amber11 Parallel Alison Lynton (Tue Jun 14 2011 - 19:24:29 PDT)
[AMBER] keyword ref Xiao Chen (Mon Jun 13 2011 - 03:39:23 PDT)
- Re: [AMBER] keyword ref Daniel Roe (Mon Jun 13 2011 - 07:55:33 PDT)
  - Re: [AMBER] keyword ref Xiao Chen (Tue Jun 14 2011 - 20:38:33 PDT)
    - Re: [AMBER] keyword ref Daniel Roe (Tue Jun 14 2011 - 20:58:50 PDT)
    - Re: [AMBER] keyword ref Xiao Chen (Tue Jun 14 2011 - 21:22:43 PDT)
[AMBER] Can Amoeba force field be used with divalent ions? Xioling Chuang (Mon Jun 13 2011 - 04:02:05 PDT)
- Re: [AMBER] Can Amoeba force field be used with divalent ions? David A Case (Mon Jun 13 2011 - 04:58:54 PDT)
- Re: [AMBER] Can Amoeba force field be used with divalent ions? Dian Jiao (Mon Jun 13 2011 - 08:37:08 PDT)
[AMBER] water test with pmemd.amba r smith (Mon Jun 13 2011 - 07:33:27 PDT)
[AMBER] Restart problems with pmemd.cuda Fabrício Bracht (Mon Jun 13 2011 - 08:42:04 PDT)
- Re: [AMBER] Restart problems with pmemd.cuda Ross Walker (Mon Jun 13 2011 - 09:08:52 PDT)
[AMBER] Problem related to the residue template and add ion Sindrila Dutta banik (Mon Jun 13 2011 - 09:01:36 PDT)
[AMBER] Antechamber Error David Cantu (Mon Jun 13 2011 - 14:09:42 PDT)
- Re: [AMBER] Antechamber Error case (Mon Jun 13 2011 - 19:17:51 PDT)
  - Re: [AMBER] Antechamber Error David Cantu (Tue Jun 21 2011 - 18:16:43 PDT)
    - Re: [AMBER] Antechamber Error David A Case (Wed Jun 22 2011 - 05:08:04 PDT)
    - Re: [AMBER] Antechamber Error Gustavo Seabra (Wed Jun 22 2011 - 06:24:45 PDT)
    - Re: [AMBER] Antechamber Error David Cantu (Wed Jun 22 2011 - 08:48:54 PDT)
    - Re: [AMBER] Antechamber Error David A Case (Wed Jun 22 2011 - 10:17:51 PDT)
    - Re: [AMBER] Antechamber Error David Cantu (Wed Jun 22 2011 - 15:11:31 PDT)
    - Re: [AMBER] Antechamber Error David A Case (Thu Jun 23 2011 - 05:11:15 PDT)
    - Re: [AMBER] Antechamber Error David Cantu (Thu Jun 23 2011 - 08:53:43 PDT)
[AMBER] Interpreting the distance covariance matrix Sajeewa Pemasinghe (Mon Jun 13 2011 - 15:48:39 PDT)
- [AMBER] Fwd: Interpreting the distance covariance matrix Sajeewa Pemasinghe (Tue Jun 14 2011 - 09:32:31 PDT)
  - Re: [AMBER] Fwd: Interpreting the distance covariance matrix Mariano Rech (Tue Jun 14 2011 - 14:40:01 PDT)
    - Re: [AMBER] Fwd: Interpreting the distance covariance matrix Mariano Rech (Tue Jun 14 2011 - 14:42:33 PDT)
    - Re: [AMBER] Fwd: Interpreting the distance covariance matrix Sajeewa Pemasinghe (Tue Jun 14 2011 - 16:48:05 PDT)
- Re: [AMBER] Interpreting the distance covariance matrix Sergio R Aragon (Tue Jun 14 2011 - 15:16:28 PDT)
  - Re: [AMBER] Interpreting the distance covariance matrix Sajeewa Pemasinghe (Tue Jun 14 2011 - 15:35:07 PDT)
    - Re: [AMBER] Interpreting the distance covariance matrix Sajeewa Pemasinghe (Tue Jun 14 2011 - 15:42:22 PDT)
    - Re: [AMBER] Interpreting the distance covariance matrix Sergio R Aragon (Tue Jun 14 2011 - 16:40:41 PDT)
    - Re: [AMBER] Interpreting the distance covariance matrix Sajeewa Pemasinghe (Tue Jun 14 2011 - 16:49:04 PDT)
    - Re: [AMBER] Interpreting the distance covariance matrix Mariano Rech (Tue Jun 14 2011 - 17:22:03 PDT)
    - Re: [AMBER] Interpreting the distance covariance matrix Sajeewa Pemasinghe (Tue Jun 14 2011 - 18:09:15 PDT)
[AMBER] Compile Python error Xioling Chuang (Mon Jun 13 2011 - 19:21:04 PDT)
- Re: [AMBER] Compile Python error Jason Swails (Mon Jun 13 2011 - 21:01:39 PDT)
  - Re: [AMBER] Compile Python error Xioling Chuang (Mon Jun 13 2011 - 21:22:50 PDT)
    - Re: [AMBER] Compile Python error Xioling Chuang (Mon Jun 13 2011 - 23:40:00 PDT)
    - Re: [AMBER] Compile Python error Jason Swails (Mon Jun 13 2011 - 23:53:27 PDT)
    - Re: [AMBER] Compile Python error Xioling Chuang (Tue Jun 14 2011 - 01:37:29 PDT)
    - Re: [AMBER] Compile Python error Jason Swails (Tue Jun 14 2011 - 07:04:18 PDT)
    - Re: [AMBER] Compile Python error Xioling Chuang (Tue Jun 14 2011 - 08:23:46 PDT)
[AMBER] PDB survey Eliac Brown (Mon Jun 13 2011 - 20:56:48 PDT)
[AMBER] secstruct analysis fatahiya (Tue Jun 14 2011 - 00:12:52 PDT)
- Re: [AMBER] secstruct analysis Adrian Roitberg (Tue Jun 14 2011 - 00:16:40 PDT)
  - Re: [AMBER] secstruct analysis fatahiya (Tue Jun 14 2011 - 00:52:24 PDT)
    - Re: [AMBER] secstruct analysis Adrian Roitberg (Tue Jun 14 2011 - 00:54:29 PDT)
    - Re: [AMBER] secstruct analysis fatahiya (Tue Jun 14 2011 - 01:14:36 PDT)
    - Re: [AMBER] secstruct analysis Daniel Roe (Tue Jun 14 2011 - 04:36:58 PDT)
Re: [AMBER] question about amber Ross Walker (Tue Jun 14 2011 - 01:33:08 PDT)
[AMBER] loadPdbUsingSeq command Antonija Tomić (Tue Jun 14 2011 - 02:26:00 PDT)
- Re: [AMBER] loadPdbUsingSeq command David A Case (Tue Jun 14 2011 - 05:00:14 PDT)
  - Re: [AMBER] loadPdbUsingSeq command Antonija Tomić (Tue Jun 14 2011 - 05:47:26 PDT)
    - Re: [AMBER] loadPdbUsingSeq command David A Case (Tue Jun 14 2011 - 06:27:41 PDT)
    - Re: [AMBER] loadPdbUsingSeq command David A Case (Tue Jun 14 2011 - 06:39:48 PDT)
    - Re: [AMBER] loadPdbUsingSeq command Bashford, Donald (Tue Jun 14 2011 - 08:23:00 PDT)
    - Re: [AMBER] loadPdbUsingSeq command Antonija Tomić (Wed Jun 15 2011 - 01:02:48 PDT)
    - Re: [AMBER] loadPdbUsingSeq command David A Case (Wed Jun 15 2011 - 04:40:51 PDT)
    - Re: [AMBER] loadPdbUsingSeq command Antonija Tomić (Thu Jun 16 2011 - 04:53:06 PDT)
[AMBER] Hairpin Shesh Nath (Tue Jun 14 2011 - 02:42:46 PDT)
- Re: [AMBER] Hairpin Hugh Heldenbrand (Tue Jun 14 2011 - 04:41:07 PDT)
[AMBER] Error While running RED III.4 hari krishna (Tue Jun 14 2011 - 03:02:41 PDT)
- Re: [AMBER] Error While running RED III.4 FyD (Tue Jun 14 2011 - 12:29:56 PDT)
  - Re: [AMBER] [q4md-fft] Re: Error While running RED III.4 Jason Swails (Fri Jun 17 2011 - 09:09:36 PDT)
[AMBER] Parallel compilation of AmberTools1.5 failed Xioling Chuang (Tue Jun 14 2011 - 20:24:28 PDT)
- Re: [AMBER] Parallel compilation of AmberTools1.5 failed Jason Swails (Tue Jun 14 2011 - 22:26:14 PDT)
  - Re: [AMBER] Parallel compilation of AmberTools1.5 failed Xioling Chuang (Tue Jun 14 2011 - 22:56:03 PDT)
    - Re: [AMBER] Parallel compilation of AmberTools1.5 failed Ross Walker (Wed Jun 15 2011 - 02:09:53 PDT)
- Re: [AMBER] Parallel compilation of AmberTools1.5 failed David A Case (Wed Jun 15 2011 - 05:07:43 PDT)
  - Re: [AMBER] Parallel compilation of AmberTools1.5 failed Xioling Chuang (Wed Jun 15 2011 - 22:06:59 PDT)
  - Re: [AMBER] Parallel compilation of AmberTools1.5 failed (2) Xioling Chuang (Thu Jun 16 2011 - 03:38:37 PDT)
    - Re: [AMBER] Parallel compilation of AmberTools1.5 failed (2) David A Case (Thu Jun 16 2011 - 05:03:34 PDT)
    - Re: [AMBER] Parallel compilation of AmberTools1.5 failed (2) Xioling Chuang (Thu Jun 16 2011 - 08:08:29 PDT)
[AMBER] Problem related to the load PDB Sindrila Dutta banik (Tue Jun 14 2011 - 22:47:57 PDT)
[AMBER] Problem related to the load PDB Sindrila Dutta banik (Tue Jun 14 2011 - 22:57:18 PDT)
- Re: [AMBER] Problem related to the load PDB/missing residues problem Sergio R Aragon (Tue Jun 14 2011 - 23:56:20 PDT)
- Re: [AMBER] Problem related to the load PDB Jason Swails (Fri Jun 17 2011 - 09:14:49 PDT)
[AMBER] Problem related to Missing amino acids in pdb Sindrila Dutta banik (Tue Jun 14 2011 - 23:06:31 PDT)
- Re: [AMBER] Problem related to Missing amino acids in pdb Sindrila Dutta banik (Tue Jun 14 2011 - 23:11:57 PDT)
- Re: [AMBER] Problem related to Missing amino acids in pdb David A Case (Wed Jun 15 2011 - 05:27:37 PDT)
[AMBER] hydration number subrata paul (Tue Jun 14 2011 - 23:38:26 PDT)
[AMBER] Bfactor calculation in cpptraj Xiao Chen (Wed Jun 15 2011 - 00:28:37 PDT)
- Re: [AMBER] Bfactor calculation in cpptraj Xiao Chen (Thu Jun 16 2011 - 01:26:44 PDT)
  - Re: [AMBER] Bfactor calculation in cpptraj Daniel Roe (Thu Jun 16 2011 - 07:44:40 PDT)
    - Re: [AMBER] Bfactor calculation in cpptraj Xiao Chen (Fri Jun 17 2011 - 02:54:51 PDT)
[AMBER] how to interprete x.ss file fatahiya (Wed Jun 15 2011 - 01:27:38 PDT)
- Re: [AMBER] how to interprete x.ss file Daniel Roe (Wed Jun 15 2011 - 09:52:22 PDT)
[AMBER] missing residue Jyotsna Bhat (Wed Jun 15 2011 - 01:34:52 PDT)
[AMBER] Restraint Minimization Pooja Khurana (Wed Jun 15 2011 - 03:01:19 PDT)
- Re: [AMBER] Restraint Minimization Carlos Simmerling (Wed Jun 15 2011 - 03:32:18 PDT)
  - Re: [AMBER] Restraint Minimization abc def (Wed Jun 15 2011 - 07:11:38 PDT)
    - Re: [AMBER] Restraint Minimization Carlos Simmerling (Wed Jun 15 2011 - 07:16:33 PDT)
    - Re: [AMBER] Restraint Minimization abc def (Wed Jun 15 2011 - 07:26:04 PDT)
    - Re: [AMBER] Restraint Minimization Carlos Simmerling (Wed Jun 15 2011 - 07:32:42 PDT)
    - Re: [AMBER] Restraint Minimization abc def (Wed Jun 15 2011 - 07:37:29 PDT)
    - Re: [AMBER] Restraint Minimization abc def (Wed Jun 15 2011 - 07:41:37 PDT)
    - Re: [AMBER] Restraint Minimization Dean Cuebas (Wed Jun 15 2011 - 18:34:41 PDT)
[AMBER] restraint simulation abhay.strubi.ox.ac.uk (Wed Jun 15 2011 - 03:51:29 PDT)
[AMBER] Installation Problem : Amber 9 souvik sur (Wed Jun 15 2011 - 05:41:21 PDT)
- Re: [AMBER] Installation Problem : Amber 9 David A Case (Wed Jun 15 2011 - 06:10:46 PDT)
  - Re: [AMBER] Installation Problem : Amber 9 souvik sur (Wed Jun 15 2011 - 23:06:36 PDT)
    - Re: [AMBER] Installation Problem : Amber 9 David A Case (Thu Jun 16 2011 - 05:13:09 PDT)
[AMBER] Amber Shesh Nath (Wed Jun 15 2011 - 05:34:36 PDT)
[AMBER] ptraj: Could not find target 300.000000 in any of the replica trajectories tdo.chem.ucsb.edu (Wed Jun 15 2011 - 06:49:23 PDT)
- Re: [AMBER] ptraj: Could not find target 300.000000 in any of the replica trajectories Carlos Simmerling (Wed Jun 15 2011 - 06:53:33 PDT)
  - Re: [AMBER] ptraj: Could not find target 300.000000 in any of the replica trajectories tdo.chem.ucsb.edu (Wed Jun 15 2011 - 06:57:43 PDT)
    - Re: [AMBER] ptraj: Could not find target 300.000000 in any of the replica trajectories Carlos Simmerling (Wed Jun 15 2011 - 07:01:39 PDT)
    - Re: [AMBER] ptraj: Could not find target 300.000000 in any of the replica trajectories tdo.chem.ucsb.edu (Wed Jun 15 2011 - 07:20:26 PDT)
[AMBER] System temperature Fernando Martín García (Wed Jun 15 2011 - 07:31:12 PDT)
- Re: [AMBER] System temperature Ross Walker (Wed Jun 15 2011 - 16:00:04 PDT)
  - Re: [AMBER] System temperature Fernando Martín García (Thu Jun 16 2011 - 02:00:29 PDT)
    - Re: [AMBER] System temperature Jason Swails (Fri Jun 17 2011 - 18:55:46 PDT)
    - Re: [AMBER] System temperature case (Sun Jun 19 2011 - 07:30:43 PDT)
    - Re: [AMBER] System temperature Fernando Martín García (Wed Jun 22 2011 - 05:09:53 PDT)
    - Re: [AMBER] System temperature Carlos Simmerling (Wed Jun 22 2011 - 10:57:32 PDT)
    - Re: [AMBER] System temperature Sergio R Aragon (Wed Jun 22 2011 - 11:47:25 PDT)
    - Re: [AMBER] System temperature Carlos Simmerling (Wed Jun 22 2011 - 11:51:03 PDT)
    - Re: [AMBER] System temperature Fernando Martín García (Fri Jun 24 2011 - 00:10:07 PDT)
    - Re: [AMBER] System temperature Adrian Roitberg (Fri Jun 24 2011 - 03:25:44 PDT)
    - Re: [AMBER] System temperature Fernando Martín García (Fri Jun 24 2011 - 03:47:01 PDT)
    - Re: [AMBER] System temperature Adrian Roitberg (Wed Jun 22 2011 - 11:53:31 PDT)
    - Re: [AMBER] System temperature Sergio R Aragon (Wed Jun 22 2011 - 12:25:32 PDT)
    - Re: [AMBER] System temperature Adrian Roitberg (Wed Jun 22 2011 - 12:35:43 PDT)
[AMBER] warning in ptraj check coordinates() Sajeewa Pemasinghe (Wed Jun 15 2011 - 09:17:21 PDT)
- [AMBER] Fwd: warning in ptraj check coordinates() Sajeewa Pemasinghe (Fri Jun 17 2011 - 11:21:49 PDT)
  - Re: [AMBER] Fwd: warning in ptraj check coordinates() Thomas Cheatham (Fri Jun 17 2011 - 11:30:09 PDT)
    - Re: [AMBER] Fwd: warning in ptraj check coordinates() Sajeewa Pemasinghe (Fri Jun 17 2011 - 11:53:09 PDT)
[AMBER] MPI_ABORT errorcode 1 for sander.MPI Erin Kelly (Wed Jun 15 2011 - 11:44:37 PDT)
- Re: [AMBER] MPI_ABORT errorcode 1 for sander.MPI David A Case (Wed Jun 15 2011 - 12:15:38 PDT)
  - Re: [AMBER] MPI_ABORT errorcode 1 for sander.MPI Erin Kelly (Wed Jun 15 2011 - 12:24:58 PDT)
    - Re: [AMBER] MPI_ABORT errorcode 1 for sander.MPI Erin Kelly (Wed Jun 15 2011 - 12:25:39 PDT)
    - Re: [AMBER] MPI_ABORT errorcode 1 for sander.MPI David A Case (Wed Jun 15 2011 - 12:46:36 PDT)
[AMBER] Methane with no surface area? Christoph Klein (Wed Jun 15 2011 - 12:45:39 PDT)
- Re: [AMBER] Methane with no surface area? David A Case (Thu Jun 16 2011 - 12:00:02 PDT)
[AMBER] MPI_ABORT errorcode 1 sander Erin Kelly (Wed Jun 15 2011 - 12:58:40 PDT)
- Re: [AMBER] MPI_ABORT errorcode 1 sander David A Case (Wed Jun 15 2011 - 13:40:01 PDT)
[AMBER] ptraj, alignment, and rmsd Michael Zimmermann (Wed Jun 15 2011 - 13:13:35 PDT)
- Re: [AMBER] ptraj, alignment, and rmsd Carlos Simmerling (Wed Jun 15 2011 - 13:17:06 PDT)
[AMBER] About difference between Sander and Pmemd Bin Wu (Wed Jun 15 2011 - 19:54:38 PDT)
- Re: [AMBER] About difference between Sander and Pmemd David A Case (Thu Jun 16 2011 - 04:48:01 PDT)
  - Re: [AMBER] About difference between Sander and Pmemd Bin Wu (Thu Jun 16 2011 - 18:24:54 PDT)
    - Re: [AMBER] About difference between Sander and Pmemd Jason Swails (Thu Jun 16 2011 - 23:48:20 PDT)
    - Re: [AMBER] About difference between Sander and Pmemd Bin Wu (Fri Jun 17 2011 - 07:07:22 PDT)
- Re: [AMBER] About difference between Sander and Pmemd Robert Duke (Thu Jun 16 2011 - 20:10:51 PDT)
- Re: [AMBER] About difference between Sander and Pmemd Robert Duke (Fri Jun 17 2011 - 09:16:11 PDT)
[AMBER] Installation of Amber 9 : Problem souvik sur (Wed Jun 15 2011 - 23:15:36 PDT)
- Re: [AMBER] Installation of Amber 9 : Problem Jason Swails (Fri Jun 17 2011 - 09:12:57 PDT)
[AMBER] Gromacs to Amber trajectory Raja Pandian (Thu Jun 16 2011 - 07:20:12 PDT)
- Re: [AMBER] Gromacs to Amber trajectory Lorenzo Gontrani (Thu Jun 16 2011 - 09:10:06 PDT)
[AMBER] Residue numbering Daniel Aiello (Thu Jun 16 2011 - 10:42:43 PDT)
- Re: [AMBER] Residue numbering Sergio R Aragon (Thu Jun 16 2011 - 12:01:29 PDT)
- Re: [AMBER] Residue numbering Jason Swails (Thu Jun 16 2011 - 12:15:23 PDT)
  - Re: [AMBER] Residue numbering Aiello, Daniel (Thu Jun 16 2011 - 12:50:15 PDT)
[AMBER] RDF Alexander Drozdetski (Thu Jun 16 2011 - 11:56:39 PDT)
- Re: [AMBER] RDF David A Case (Fri Jun 17 2011 - 04:46:50 PDT)
[AMBER] velocity auto correlation function; resident time; MD (Thu Jun 16 2011 - 13:00:23 PDT)
[AMBER] amber10 output Qian Wang (Thu Jun 16 2011 - 13:42:09 PDT)
- Re: [AMBER] amber10 output Anselm Horn (Thu Jun 16 2011 - 14:17:49 PDT)
  - Re: [AMBER] amber10 output Qian Wang (Thu Jun 16 2011 - 14:41:17 PDT)
    - Re: [AMBER] amber10 output Ben Roberts (Thu Jun 16 2011 - 14:48:08 PDT)
    - Re: [AMBER] amber10 output Qian Wang (Thu Jun 16 2011 - 15:15:42 PDT)
[AMBER] Nucleic residues with methylphosphonates Alexander Drozdetski (Thu Jun 16 2011 - 13:49:33 PDT)
- Re: [AMBER] Nucleic residues with methylphosphonates David Case (Thu Jun 16 2011 - 18:40:41 PDT)
- Re: [AMBER] Nucleic residues with methylphosphonates FyD (Thu Jun 16 2011 - 22:37:40 PDT)
[AMBER] velocity auto correlation function; resident time; MD (Thu Jun 16 2011 - 21:38:57 PDT)
- Re: [AMBER] velocity auto correlation function; resident time; Hannes Loeffler (Thu Jun 16 2011 - 23:58:40 PDT)
[AMBER] sleap never worked anymore since AT 1.2 Alan (Fri Jun 17 2011 - 01:45:01 PDT)
- Re: [AMBER] sleap never worked anymore since AT 1.2 David A Case (Tue Jun 21 2011 - 06:26:13 PDT)
  - Re: [AMBER] sleap never worked anymore since AT 1.2 Alan (Wed Jun 22 2011 - 01:50:43 PDT)
    - Re: [AMBER] sleap never worked anymore since AT 1.2 David A Case (Wed Jun 22 2011 - 05:10:42 PDT)
[AMBER] small inconsistencies in parm99.dat and parm94.dat Thomas Gaillard (Fri Jun 17 2011 - 02:43:23 PDT)
- Re: [AMBER] small inconsistencies in parm99.dat and parm94.dat David A Case (Tue Jun 21 2011 - 06:31:00 PDT)
[AMBER] Energy decomposition Guenegou, Guillaume [ORDFR] (Fri Jun 17 2011 - 06:25:56 PDT)
- Re: [AMBER] Energy decomposition Bill Miller III (Sat Jun 18 2011 - 05:17:40 PDT)
[AMBER] algorithm for rms Ada Sedova (Fri Jun 17 2011 - 07:36:27 PDT)
- Re: [AMBER] algorithm for rms Carlos Simmerling (Fri Jun 17 2011 - 07:38:26 PDT)
  - Re: [AMBER] algorithm for rms Ada Sedova (Fri Jun 17 2011 - 07:41:01 PDT)
    - Re: [AMBER] algorithm for rms Francesco Oteri (Fri Jun 17 2011 - 08:03:11 PDT)
    - Re: [AMBER] algorithm for rms Ada Sedova (Fri Jun 17 2011 - 08:08:22 PDT)
    - Re: [AMBER] algorithm for rms Ada Sedova (Fri Jun 17 2011 - 08:11:24 PDT)
    - Re: [AMBER] algorithm for rms Thomas Cheatham (Fri Jun 17 2011 - 08:20:18 PDT)
[AMBER] Amoeba with water and ion Xioling Chuang (Fri Jun 17 2011 - 23:07:10 PDT)
- Re: [AMBER] Amoeba with water and ion case (Sat Jun 18 2011 - 05:56:49 PDT)
  - [AMBER] Can I directly compare the PMF for two compounds with different size and chemical structures? Catein Catherine (Sat Jun 18 2011 - 21:55:37 PDT)
    - Re: [AMBER] Can I directly compare the PMF for two compounds with different size and chemical structures? Carlos Simmerling (Sun Jun 19 2011 - 03:10:46 PDT)
  - Re: [AMBER] Amoeba with water and ion Xioling Chuang (Sun Jun 19 2011 - 07:49:18 PDT)
[AMBER] Resp charge Takeshi Baba (Sat Jun 18 2011 - 01:18:51 PDT)
- Re: [AMBER] Resp charge Jason A. Ford-Green (Fri Feb 06 2009 - 12:38:29 PST)
- Re: [AMBER] Resp charge case (Sun Jun 19 2011 - 07:22:15 PDT)
[AMBER] Antechamber: Failure to calculate Mulliken partial charges using a Tripos MOL2 input file Joel Dockray (Sat Jun 18 2011 - 17:09:32 PDT)
- Re: [AMBER] Antechamber: Failure to calculate Mulliken partial charges using a Tripos MOL2 input file case (Sun Jun 19 2011 - 07:00:51 PDT)
[AMBER] ambertools.1.5 installation errors on Linux Francesco Pietra (Mon Jun 20 2011 - 01:15:48 PDT)
- Re: [AMBER] ambertools.1.5 installation errors on Linux David A Case (Mon Jun 20 2011 - 04:57:55 PDT)
[AMBER] Error compiling ambertools 1.5 Daniel Sindhikara (Mon Jun 20 2011 - 03:23:56 PDT)
- Re: [AMBER] Error compiling ambertools 1.5 David A Case (Mon Jun 20 2011 - 08:44:10 PDT)
  - Re: [AMBER] Error compiling ambertools 1.5 Daniel Sindhikara (Mon Jun 20 2011 - 19:57:38 PDT)
[AMBER] ambertools 1.2 compilation error on Debian Linux Francesco Pietra (Mon Jun 20 2011 - 07:36:58 PDT)
- Re: [AMBER] ambertools 1.2 compilation error on Debian Linux David A Case (Mon Jun 20 2011 - 08:39:13 PDT)
  - Re: [AMBER] ambertools 1.2 compilation error on Debian Linux Francesco Pietra (Mon Jun 20 2011 - 13:33:37 PDT)
[AMBER] problems with relaxing a phosphonamide parametrizated with Antechamber gloriarg (Mon Jun 20 2011 - 10:36:59 PDT)
[AMBER] AmberTools 1.5 gnu compilation fails under FC15 pamodeo (Mon Jun 20 2011 - 13:11:22 PDT)
- Re: [AMBER] AmberTools 1.5 gnu compilation fails under FC15 Ben Roberts (Mon Jun 20 2011 - 13:12:14 PDT)
  - Re: [AMBER] AmberTools 1.5 gnu compilation fails under FC15 Francesco Pietra (Mon Jun 20 2011 - 13:38:08 PDT)
[AMBER] Amoeba with water and ions (2)‏ Xioling Chuang (Mon Jun 20 2011 - 19:05:48 PDT)
- Re: [AMBER] Amoeba with water and ions (2)‏ David A Case (Tue Jun 21 2011 - 06:20:20 PDT)
[AMBER] How to prepare ATP with Antechamber? Azat Mukhametov (Tue Jun 21 2011 - 01:57:08 PDT)
- Re: [AMBER] How to prepare ATP with Antechamber? Takeshi Baba (Tue Jun 21 2011 - 02:05:03 PDT)
  - Re: [AMBER] How to prepare ATP with Antechamber? Azat Mukhametov (Tue Jun 21 2011 - 02:24:42 PDT)
[AMBER] Sirius software CHAMI F. (Tue Jun 21 2011 - 03:03:35 PDT)
- Re: [AMBER] Sirius software Ross Walker (Tue Jun 21 2011 - 08:35:26 PDT)
- Re: [AMBER] Sirius software CHAMI F. (Tue Jun 21 2011 - 09:28:01 PDT)
  - Re: [AMBER] Sirius software Sasha Buzko (Tue Jun 21 2011 - 10:21:11 PDT)
    - Re: [AMBER] Sirius software Joachim Reichelt (Wed Jun 22 2011 - 00:51:58 PDT)
    - Re: [AMBER] Sirius software George Tzotzos (Wed Jun 22 2011 - 01:55:54 PDT)
    - [AMBER] MMPBSA.py decomp Guenegou, Guillaume [ORDFR] (Wed Jun 22 2011 - 02:07:03 PDT)
    - Re: [AMBER] MMPBSA.py decomp Bill Miller III (Wed Jun 22 2011 - 03:47:29 PDT)
    - Re: [AMBER] Sirius software Sasha Buzko (Wed Jun 22 2011 - 10:23:10 PDT)
- Re: [AMBER] Sirius software CHAMI F. (Wed Jun 22 2011 - 03:11:58 PDT)
- Re: [AMBER] Sirius software CHAMI F. (Wed Jun 22 2011 - 05:31:33 PDT)
- Re: [AMBER] Sirius software CHAMI F. (Wed Jun 22 2011 - 17:17:40 PDT)
[AMBER] Request for Amber Heme parameter file Prajwal Nandekar (Tue Jun 21 2011 - 04:25:57 PDT)
[AMBER] intra- and interstrand interaction energies of DNA clwg (Tue Jun 21 2011 - 07:23:42 PDT)
[AMBER] MMPBSA-binding energy calculation baljinder (Tue Jun 21 2011 - 07:25:51 PDT)
- Re: [AMBER] MMPBSA-binding energy calculation Hirdesh Kumar (Tue Jun 21 2011 - 09:09:46 PDT)
  - Re: [AMBER] MMPBSA-binding energy calculation baljinder (Tue Jun 21 2011 - 10:17:58 PDT)
[AMBER] restraints file Massimiliano Porrini (Tue Jun 21 2011 - 08:51:51 PDT)
- Re: [AMBER] restraints file Jerome Golebiowski (Wed Jun 22 2011 - 00:29:39 PDT)
  - Re: [AMBER] restraints file Massimiliano Porrini (Wed Jun 22 2011 - 01:51:08 PDT)
[AMBER] regarding per residue decomposition of binding free energy using perl script Hirdesh Kumar (Tue Jun 21 2011 - 09:45:09 PDT)
[AMBER] Non-periodic behavior of NMR restraints upon restart in a periodic system Keith Yarem (Tue Jun 21 2011 - 09:57:00 PDT)
- Re: [AMBER] Non-periodic behavior of NMR restraints upon restart in a periodic system David A Case (Tue Jun 21 2011 - 10:54:25 PDT)
  - Re: [AMBER] Non-periodic behavior of NMR restraints upon restart in a periodic system Carlos Simmerling (Tue Jun 21 2011 - 10:59:02 PDT)
    - Re: [AMBER] Non-periodic behavior of NMR restraints upon restart in a periodic system Keith Yarem (Thu Sep 01 2011 - 11:23:03 PDT)
    - Re: [AMBER] Non-periodic behavior of NMR restraints upon restart in a periodic system Keith Yarem (Thu Sep 01 2011 - 11:40:54 PDT)
    - Re: [AMBER] Non-periodic behavior of NMR restraints upon restart in a periodic system InSuk Joung (Thu Sep 01 2011 - 12:16:56 PDT)
    - Re: [AMBER] Non-periodic behavior of NMR restraints upon restart in a periodic system Jason Swails (Thu Sep 01 2011 - 12:37:21 PDT)
[AMBER] Suggestion for minor user manual clarification Christoph Klein (Tue Jun 21 2011 - 11:13:53 PDT)
- Re: [AMBER] Suggestion for minor user manual clarification Carlos Simmerling (Tue Jun 21 2011 - 11:22:47 PDT)
  - Re: [AMBER] Suggestion for minor user manual clarification Christoph Klein (Tue Jun 21 2011 - 12:38:35 PDT)
- Re: [AMBER] Suggestion for minor user manual clarification David A Case (Thu Jun 23 2011 - 13:36:43 PDT)
[AMBER] Nmode calculations using Amber 8 manikanthan bhavaraju (Tue Jun 21 2011 - 12:29:14 PDT)
- [AMBER] Nmode calculations using Amber 8 manikanthan bhavaraju (Tue Jun 21 2011 - 17:19:52 PDT)
  - Re: [AMBER] Nmode calculations using Amber 8 Jason Swails (Wed Jun 22 2011 - 00:50:57 PDT)
[AMBER] trouble installing Amber 10 Jennifer L. Muzyka (Tue Jun 21 2011 - 13:45:41 PDT)
- Re: [AMBER] trouble installing Amber 10 David Case (Tue Jun 21 2011 - 19:39:59 PDT)
  - Re: [AMBER] trouble installing Amber 10 Jennifer L. Muzyka (Wed Jun 22 2011 - 06:17:34 PDT)
    - Re: [AMBER] trouble installing Amber 10 David A Case (Wed Jun 22 2011 - 06:41:54 PDT)
    - Re: [AMBER] trouble installing Amber 10 peker milas (Wed Jun 22 2011 - 06:53:53 PDT)
    - Re: [AMBER] trouble installing Amber 10 Jennifer L. Muzyka (Wed Jun 22 2011 - 08:06:09 PDT)
    - Re: [AMBER] trouble installing Amber 10 David A Case (Wed Jun 22 2011 - 08:47:54 PDT)
[AMBER] Vibrational entropy with NAB Emmanuel Baribefe Naziga (Tue Jun 21 2011 - 17:17:42 PDT)
- Re: [AMBER] Vibrational entropy with NAB Jason Swails (Wed Jun 22 2011 - 00:48:28 PDT)
- Re: [AMBER] Vibrational entropy with NAB David A Case (Wed Jun 22 2011 - 05:05:14 PDT)
  - Re: [AMBER] Vibrational entropy with NAB Emmanuel Baribefe Naziga (Wed Jun 22 2011 - 08:24:22 PDT)
    - Re: [AMBER] Vibrational entropy with NAB David A Case (Wed Jun 22 2011 - 08:56:58 PDT)
    - Re: [AMBER] Vibrational entropy with NAB Emmanuel Baribefe Naziga (Wed Jun 22 2011 - 09:51:11 PDT)
[AMBER] alanine mutagenisis in amber caobb0214 (Tue Jun 21 2011 - 17:44:25 PDT)
- [AMBER] Frequency analysis of small molecule, constructing heterocyclic ring systems Dean Cuebas (Tue Jun 21 2011 - 21:07:28 PDT)
- Re: [AMBER] alanine mutagenisis in amber Marc van der Kamp (Wed Jun 22 2011 - 00:18:11 PDT)
[AMBER] regarding per residue wise free energy decomposition Hirdesh Kumar (Tue Jun 21 2011 - 21:57:05 PDT)
- Re: [AMBER] regarding per residue wise free energy decomposition Bill Miller III (Thu Jun 23 2011 - 13:49:24 PDT)
  - Re: [AMBER] regarding per residue wise free energy decomposition Hirdesh Kumar (Fri Jun 24 2011 - 00:59:30 PDT)
    - Re: [AMBER] regarding per residue wise free energy decomposition Bill Miller III (Fri Jun 24 2011 - 05:30:09 PDT)
    - Re: [AMBER] regarding per residue wise free energy decomposition Hirdesh Kumar (Sun Jun 26 2011 - 22:49:03 PDT)
    - Re: [AMBER] regarding per residue wise free energy decomposition Bill Miller III (Wed Jun 29 2011 - 03:49:53 PDT)
    - Re: [AMBER] regarding per residue wise free energy decomposition Hirdesh Kumar (Mon Jul 04 2011 - 22:26:05 PDT)
[AMBER] Velocity autocorrelation function DEBOSTUTI GHOSHDASTIDAR (Wed Jun 22 2011 - 02:10:28 PDT)
[AMBER] energy of a single amino acid during minimization André C. Stiel (Wed Jun 22 2011 - 03:10:47 PDT)
[AMBER] forrtl: severe (64): input conversion error, unit 9 Alessio Atzori (Wed Jun 22 2011 - 04:10:56 PDT)
- Re: [AMBER] forrtl: severe (64): input conversion error, unit 9 Carlos Simmerling (Wed Jun 22 2011 - 04:14:50 PDT)
  - [AMBER] R: forrtl: severe (64): input conversion error, unit 9 Alessio Atzori (Wed Jun 22 2011 - 04:21:45 PDT)
    - Re: [AMBER] R: forrtl: severe (64): input conversion error, unit 9 Carlos Simmerling (Wed Jun 22 2011 - 12:01:55 PDT)
    - [AMBER] R: R: forrtl: severe (64): input conversion error, unit 9 Alessio Atzori (Wed Jun 22 2011 - 16:51:09 PDT)
[AMBER] ptraj cluster Katrine Kirkeby Skeby (Wed Jun 22 2011 - 04:21:58 PDT)
- Re: [AMBER] ptraj cluster Daniel Roe (Mon Jun 27 2011 - 22:09:38 PDT)
  - [AMBER] pairwise RMSD Mannan (Tue Jun 28 2011 - 01:26:53 PDT)
    - Re: [AMBER] pairwise RMSD Mariano Rech (Tue Jun 28 2011 - 02:35:12 PDT)
[AMBER] interaction energies of DNA clwg (Wed Jun 22 2011 - 08:24:54 PDT)
[AMBER] query regarding void volume calculation in protein-ligand complex Hirdesh Kumar (Wed Jun 22 2011 - 12:09:05 PDT)
[AMBER] AMBER 11 and Ambertools 1.5 Installs failing tests for mmpbsa_py Maria (Wed Jun 22 2011 - 14:18:47 PDT)
- Re: [AMBER] AMBER 11 and Ambertools 1.5 Installs failing tests for mmpbsa_py Jason Swails (Wed Jun 22 2011 - 20:25:29 PDT)
- Re: [AMBER] AMBER 11 and Ambertools 1.5 Installs failing tests for mmpbsa_py David A Case (Thu Jun 23 2011 - 05:07:15 PDT)
  - Re: [AMBER] AMBER 11 and Ambertools 1.5 Installs failing tests for mmpbsa_py Maria (Thu Jun 23 2011 - 06:58:26 PDT)
[AMBER] NMR chemical shift restraints for an intrinsically disordered peptide Thomas Evangelidis (Thu Jun 23 2011 - 02:32:06 PDT)
- Re: [AMBER] NMR chemical shift restraints for an intrinsically disordered peptide Jacopo Sgrignani (Thu Jun 23 2011 - 04:50:53 PDT)
- Re: [AMBER] NMR chemical shift restraints for an intrinsically disordered peptide David A Case (Thu Jun 23 2011 - 05:22:40 PDT)
  - Re: [AMBER] NMR chemical shift restraints for an intrinsically disordered peptide DEBOSTUTI GHOSHDASTIDAR (Thu Jun 23 2011 - 05:58:38 PDT)
    - Re: [AMBER] NMR chemical shift restraints for an intrinsically disordered peptide Thomas Evangelidis (Thu Jun 23 2011 - 09:22:28 PDT)
    - Re: [AMBER] NMR chemical shift restraints for an intrinsically disordered peptide David A Case (Thu Jun 23 2011 - 11:02:39 PDT)
[AMBER] mm_pbsa.pl with Fe(III) ion pirincn (Thu Jun 23 2011 - 05:38:54 PDT)
- Re: [AMBER] mm_pbsa.pl with Fe(III) ion Ray Luo, Ph.D. (Thu Jun 23 2011 - 10:47:50 PDT)
- Re: [AMBER] mm_pbsa.pl with Fe(III) ion pirincn (Thu Jun 23 2011 - 11:33:20 PDT)
[AMBER] DIELC constant for normal mode analyses in vacuum ? Marek Maly (Thu Jun 23 2011 - 05:55:04 PDT)
- Re: [AMBER] DIELC constant for normal mode analyses in vacuum ? Marek Maly (Thu Jun 23 2011 - 07:40:19 PDT)
  - Re: [AMBER] DIELC constant for normal mode analyses in vacuum ? David A Case (Thu Jun 23 2011 - 09:13:51 PDT)
    - Re: [AMBER] DIELC constant for normal mode analyses in vacuum ? Marek Maly (Thu Jun 23 2011 - 13:51:43 PDT)
    - Re: [AMBER] DIELC constant for normal mode analyses in vacuum ? David A. Case (Thu Jun 23 2011 - 19:35:40 PDT)
    - Re: [AMBER] DIELC constant for normal mode analyses in vacuum ? Toshifumi Yui (Fri Jun 24 2011 - 00:11:34 PDT)
    - Re: [AMBER] DIELC constant for normal mode analyses in vacuum ? Marek Maly (Fri Jun 24 2011 - 08:56:37 PDT)
[AMBER] AmberTools 1.5 + Amber 11 installation - bugfixes conflicts? Richard Owczarzy (Thu Jun 23 2011 - 07:17:59 PDT)
- Re: [AMBER] AmberTools 1.5 + Amber 11 installation - bugfixes conflicts? Jason Swails (Thu Jun 23 2011 - 13:02:53 PDT)
  - [AMBER] Amber11 Tests fail peter.stauffert.boehringer-ingelheim.com (Wed Jul 20 2011 - 11:41:39 PDT)
    - Re: [AMBER] Amber11 Tests fail David A Case (Wed Jul 20 2011 - 12:50:20 PDT)
    - Re: [AMBER] Amber11 Tests fail Mengjuei Hsieh (Wed Jul 20 2011 - 12:54:53 PDT)
    - Re: [AMBER] Amber11 Tests fail Jason Swails (Wed Jul 20 2011 - 13:52:09 PDT)
[AMBER] give_diff_runs balaji nagarajan (Thu Jun 23 2011 - 12:29:47 PDT)
- Re: [AMBER] give_diff_runs David A Case (Thu Jun 23 2011 - 13:07:03 PDT)
[AMBER] secondary structure plotting Jagur Lambix (Thu Jun 23 2011 - 13:45:44 PDT)
- Re: [AMBER] secondary structure plotting Brendan Duggan (Fri Jun 24 2011 - 07:51:13 PDT)
  - Re: [AMBER] secondary structure plotting Jagur Lambix (Fri Jun 24 2011 - 13:50:21 PDT)
[AMBER] single amino acid energies André C. Stiel (Fri Jun 24 2011 - 00:14:04 PDT)
- Re: [AMBER] single amino acid energies Bill Miller III (Fri Jun 24 2011 - 05:24:53 PDT)
  - Re: [AMBER] single amino acid energies André C. Stiel (Sat Jun 25 2011 - 03:22:00 PDT)
    - Re: [AMBER] single amino acid energies Jason Swails (Sat Jun 25 2011 - 13:27:52 PDT)
[AMBER] Sander Error Ali Faruqi (Fri Jun 24 2011 - 01:07:12 PDT)
- Re: [AMBER] Sander Error Kshatresh Dutta Dubey (Fri Jun 24 2011 - 01:12:06 PDT)
  - Re: [AMBER] Sander Error Ali Faruqi (Fri Jun 24 2011 - 07:33:17 PDT)
    - Re: [AMBER] Sander Error David A. Case (Fri Jun 24 2011 - 08:01:59 PDT)
    - Re: [AMBER] Sander Error Ali Faruqi (Sat Jun 25 2011 - 01:59:22 PDT)
    - Re: [AMBER] Sander Error David A. Case (Sat Jun 25 2011 - 07:52:10 PDT)
    - Re: [AMBER] Sander Error Ali Faruqi (Mon Jun 27 2011 - 01:20:21 PDT)
- Re: [AMBER] Sander Error Melissa Buskes (Fri Jun 22 2012 - 01:15:20 PDT)
[AMBER] tleap error in reading structure generated from GLYCAM web mish (Fri Jun 24 2011 - 01:58:11 PDT)
- Re: [AMBER] tleap error in reading structure generated from GLYCAM web Lachele Foley (Lists) (Fri Jun 24 2011 - 07:09:50 PDT)
  - Re: [AMBER] tleap error in reading structure generated from GLYCAM web mish (Fri Jun 24 2011 - 07:21:05 PDT)
[AMBER] Entropy Decomposition Daniel Aiello (Fri Jun 24 2011 - 08:08:39 PDT)
- Re: [AMBER] Entropy Decomposition David A. Case (Fri Jun 24 2011 - 08:57:27 PDT)
  - Re: [AMBER] Entropy Decomposition Daniel Aiello (Fri Jun 24 2011 - 10:43:33 PDT)
    - Re: [AMBER] Entropy Decomposition Balazs Jojart (Fri Jun 24 2011 - 13:56:02 PDT)
    - Re: [AMBER] Entropy Decomposition David A. Case (Fri Jun 24 2011 - 14:12:20 PDT)
    - Re: [AMBER] Entropy Decomposition Thomas Cheatham III (Fri Jun 24 2011 - 14:14:19 PDT)
    - Re: [AMBER] Entropy Decomposition Balazs Jojart (Fri Jun 24 2011 - 14:47:03 PDT)
    - Re: [AMBER] Entropy Decomposition Jason Swails (Fri Jun 24 2011 - 14:14:23 PDT)
[AMBER] Glycam Parameters for O-SIALIC ACID mish (Fri Jun 24 2011 - 08:21:00 PDT)
- Re: [AMBER] Glycam Parameters for O-SIALIC ACID Lachele Foley (Lists) (Fri Jun 24 2011 - 09:10:41 PDT)
- Re: [AMBER] Glycam Parameters for O-SIALIC ACID FyD (Fri Jun 24 2011 - 22:46:08 PDT)
  - Re: [AMBER] Glycam Parameters for O-SIALIC ACID Lachele Foley (Lists) (Sat Jun 25 2011 - 05:49:42 PDT)
    - Re: [AMBER] Glycam Parameters for O-SIALIC ACID mish (Sat Jun 25 2011 - 09:18:41 PDT)
    - Re: [AMBER] Glycam Parameters for O-SIALIC ACID Lachele Foley (Lists) (Mon Jun 27 2011 - 14:21:18 PDT)
    - Re: [AMBER] Glycam Parameters for O-SIALIC ACID mish (Tue Jun 28 2011 - 09:19:59 PDT)
    - Re: [AMBER] Glycam Parameters for O-SIALIC ACID Lachele Foley (Lists) (Tue Jun 28 2011 - 10:51:29 PDT)
[AMBER] About the coordinates of input or output files Aimin Guo (Fri Jun 24 2011 - 10:21:37 PDT)
- Re: [AMBER] About the coordinates of input or output files Thomas Cheatham III (Fri Jun 24 2011 - 13:39:21 PDT)
[AMBER] Question on the construction of a topology file lnedialkova.gmail.com (Fri Jun 24 2011 - 14:31:24 PDT)
- Re: [AMBER] Question on the construction of a topology file Daniel Roe (Mon Jun 27 2011 - 21:57:37 PDT)
[AMBER] Architecture/compiler is not supported Error! Ali Faruqi (Sat Jun 25 2011 - 03:36:53 PDT)
- Re: [AMBER] Architecture/compiler is not supported Error! David A. Case (Sat Jun 25 2011 - 07:49:17 PDT)
  - Re: [AMBER] Architecture/compiler is not supported Error! Ali Faruqi (Mon Jun 27 2011 - 01:21:21 PDT)
[AMBER] AMBER: error in reading namelist cntrl Antonio Peón López (Sat Jun 25 2011 - 14:14:50 PDT)
- Re: [AMBER] AMBER: error in reading namelist cntrl Jason Swails (Sat Jun 25 2011 - 17:34:22 PDT)
[AMBER] Prevent tleap to rearrange my ions? chicago.ecnu (Sun Jun 26 2011 - 03:18:13 PDT)
[AMBER] error running mmpbsa John S (Sun Jun 26 2011 - 14:26:54 PDT)
[AMBER] Error mmpbsa John S (Sun Jun 26 2011 - 20:29:24 PDT)
- Re: [AMBER] Error mmpbsa Bill Miller III (Mon Jun 27 2011 - 03:41:58 PDT)
  - Re: [AMBER] Error mmpbsa John S (Mon Jun 27 2011 - 19:44:53 PDT)
    - Re: [AMBER] Error mmpbsa Bill Miller III (Mon Jun 27 2011 - 20:01:41 PDT)
    - Re: [AMBER] Error mmpbsa John S (Thu Jun 30 2011 - 21:17:48 PDT)
    - Re: [AMBER] Error mmpbsa Ray Luo, Ph.D. (Thu Jun 30 2011 - 23:00:44 PDT)
    - Re: [AMBER] Error mmpbsa John S (Fri Jul 01 2011 - 07:21:01 PDT)
    - Re: [AMBER] Error mmpbsa Ray Luo, Ph.D. (Fri Jul 01 2011 - 07:57:41 PDT)
    - Re: [AMBER] Error mmpbsa John S (Fri Jul 01 2011 - 22:15:14 PDT)
[AMBER] Problems Compiling Amber11 Parallel GPU Alison Lynton (Sun Jun 26 2011 - 20:33:40 PDT)
- Re: [AMBER] Problems Compiling Amber11 Parallel GPU Ross Walker (Mon Jun 27 2011 - 08:08:59 PDT)
  - [AMBER] mmpbsa.py Guenegou, Guillaume [ORDFR] (Mon Jun 27 2011 - 08:38:38 PDT)
    - Re: [AMBER] mmpbsa.py Bill Miller III (Mon Jun 27 2011 - 13:08:56 PDT)
    - Re: [AMBER] mmpbsa.py Chris Chris (Mon Jun 27 2011 - 14:33:58 PDT)
    - Re: [AMBER] mmpbsa.py Jason Swails (Mon Jun 27 2011 - 16:41:32 PDT)
    - [AMBER] sleap/tleap mol2 features Guenegou, Guillaume [ORDFR] (Tue Jun 28 2011 - 02:03:46 PDT)
  - Re: [AMBER] Problems Compiling Amber11 Parallel GPU Alison Lynton (Mon Jun 27 2011 - 19:47:44 PDT)
[AMBER] how to assess the convergence of the clustering 475649770 (Sun Jun 26 2011 - 20:19:12 PDT)
- Re: [AMBER] how to assess the convergence of the clustering Thomas Cheatham III (Tue Jun 28 2011 - 14:36:56 PDT)
[AMBER] saving the first solvent shell molecules by Ptraj Zhu Tong (Mon Jun 27 2011 - 05:24:21 PDT)
- Re: [AMBER] saving the first solvent shell molecules by Ptraj Daniel Roe (Mon Jun 27 2011 - 21:41:55 PDT)
[AMBER] CHAMBER prmtop Manish (Mon Jun 27 2011 - 09:41:02 PDT)
- Re: [AMBER] CHAMBER prmtop Bill Ross (Tue Mar 01 2011 - 19:51:11 PST)
  - Re: [AMBER] CHAMBER prmtop colvin (Tue Mar 01 2011 - 19:58:06 PST)
    - Re: [AMBER] CHAMBER prmtop Ross Walker (Tue Mar 01 2011 - 20:30:08 PST)
    - Re: [AMBER] CHAMBER prmtop colvin (Tue Mar 01 2011 - 22:36:36 PST)
    - Re: [AMBER] CHAMBER prmtop Mark Williamson (Wed Mar 02 2011 - 09:48:02 PST)
    - Re: [AMBER] CHAMBER prmtop colvin (Thu Mar 03 2011 - 01:22:39 PST)
- Re: [AMBER] CHAMBER prmtop Bill Ross (Tue Mar 01 2011 - 20:05:29 PST)
- Re: [AMBER] CHAMBER prmtop Mark Williamson (Mon Jun 27 2011 - 11:27:17 PDT)
[AMBER] Steered Molecular Dynamics George Tzotzos (Mon Jun 27 2011 - 10:49:57 PDT)
- Re: [AMBER] Steered Molecular Dynamics Dmitry Nilov (Mon Jun 27 2011 - 13:06:01 PDT)
  - Re: [AMBER] Steered Molecular Dynamics George Tzotzos (Mon Jun 27 2011 - 13:33:46 PDT)
  - Re: [AMBER] Steered Molecular Dynamics George Tzotzos (Mon Jun 27 2011 - 13:40:14 PDT)
    - Re: [AMBER] Steered Molecular Dynamics Adrian Roitberg (Mon Jun 27 2011 - 13:58:31 PDT)
    - Re: [AMBER] Steered Molecular Dynamics George Tzotzos (Mon Jun 27 2011 - 14:14:39 PDT)
    - Re: [AMBER] Steered Molecular Dynamics Dwight McGee (Mon Jun 27 2011 - 14:38:30 PDT)
    - Re: [AMBER] Steered Molecular Dynamics George Tzotzos (Mon Jun 27 2011 - 14:56:26 PDT)
    - Re: [AMBER] Steered Molecular Dynamics George Tzotzos (Mon Jun 27 2011 - 15:18:23 PDT)
    - Re: [AMBER] Steered Molecular Dynamics Dmitry Nilov (Tue Jun 28 2011 - 00:34:42 PDT)
    - Re: [AMBER] Steered Molecular Dynamics George Tzotzos (Tue Jun 28 2011 - 01:40:30 PDT)
    - Re: [AMBER] Steered Molecular Dynamics Dmitry Nilov (Tue Jun 28 2011 - 02:07:08 PDT)
  - Re: [AMBER] Steered Molecular Dynamics Jason Swails (Mon Jun 27 2011 - 16:46:07 PDT)
[AMBER] Natural Language Angle Restraint Kevin Olsson (Mon Jun 27 2011 - 13:50:15 PDT)
- Re: [AMBER] Natural Language Angle Restraint Bill Ross (Mon Jun 27 2011 - 14:16:52 PDT)
[AMBER] netcdf Takeshi Baba (Mon Jun 27 2011 - 21:08:51 PDT)
- Re: [AMBER] netcdf Daniel Roe (Mon Jun 27 2011 - 21:23:37 PDT)
  - Re: [AMBER] netcdf Takeshi Baba (Tue Jun 28 2011 - 00:02:38 PDT)
[AMBER] Kinetic energy in mdout file is not identical to that calculated from mdvel file. kurisaki (Tue Jun 28 2011 - 01:19:29 PDT)
- Re: [AMBER] Kinetic energy in mdout file is not identical to that calculated from mdvel file. Carlos Simmerling (Tue Jun 28 2011 - 03:47:41 PDT)
  - Re: [AMBER] Kinetic energy in mdout file is not identical to that calculated from mdvel file. kurisaki (Tue Jun 28 2011 - 04:01:23 PDT)
    - Re: [AMBER] Kinetic energy in mdout file is not identical to that calculated from mdvel file. Carlos Simmerling (Tue Jun 28 2011 - 11:50:14 PDT)
    - Re: [AMBER] Kinetic energy in mdout file is not identical to that calculated from mdvel file. kurisaki (Thu Jun 30 2011 - 20:10:31 PDT)
[AMBER] I want to add amide group at the end of my peptide ? Esam Tolba (Tue Jun 28 2011 - 03:12:04 PDT)
[AMBER] software assistance Mr. Joseph S. Castle (Tue Jun 28 2011 - 06:05:57 PDT)
- Re: [AMBER] software assistance Jason Swails (Tue Jun 28 2011 - 10:54:18 PDT)
[AMBER] query with multocomponent system kaustubh joshi (Tue Jun 28 2011 - 07:49:29 PDT)
[AMBER] Inquiry about installing AMBER Mo Chen (Tue Jun 28 2011 - 08:33:19 PDT)
- Re: [AMBER] Inquiry about installing AMBER Bruno Rodrigues (Wed Jul 06 2011 - 04:41:40 PDT)
  - Re: [AMBER] Inquiry about installing AMBER Mo Chen (Wed Jul 06 2011 - 07:52:41 PDT)
[AMBER] Installation Problem Elisa Frezza (Tue Jun 28 2011 - 10:19:54 PDT)
- Re: [AMBER] Installation Problem Bill Ross (Mon Mar 18 2019 - 05:00:04 PDT)
  - Re: [AMBER] Installation Problem Gerardo Zerbetto De Palma (Mon Mar 18 2019 - 05:08:11 PDT)
  - Re: [AMBER] Installation Problem Bill Ross (Mon Mar 18 2019 - 05:18:51 PDT)
[AMBER] ff03 force field tsurma.umich.edu (Tue Jun 28 2011 - 11:07:19 PDT)
- Re: [AMBER] ff03 force field David A. Case (Tue Jun 28 2011 - 13:24:48 PDT)
  - Re: [AMBER] ff03 force field tsurma.umich.edu (Thu Jun 30 2011 - 09:27:04 PDT)
    - Re: [AMBER] ff03 force field case (Sun Jul 03 2011 - 09:59:17 PDT)
    - Re: [AMBER] ff03 force field tsurma.umich.edu (Wed Jul 06 2011 - 20:59:56 PDT)
    - Re: [AMBER] ff03 force field tsurma.umich.edu (Thu Jul 07 2011 - 14:08:07 PDT)
[AMBER] ptraj in parallel Fabrício Bracht (Tue Jun 28 2011 - 11:06:06 PDT)
- Re: [AMBER] ptraj in parallel Ross Walker (Tue Jun 28 2011 - 11:35:10 PDT)
[AMBER] Recompiling amber 8 on IBM manikanthan bhavaraju (Tue Jun 28 2011 - 13:54:30 PDT)
- Re: [AMBER] Recompiling amber 8 on IBM David Case (Wed Jun 29 2011 - 10:16:42 PDT)
[AMBER] Suggestions for additions to AmberTools Francesco Pietra (Tue Jun 28 2011 - 14:21:25 PDT)
[AMBER] Nmode with amber8 manikanthan bhavaraju (Tue Jun 28 2011 - 14:47:52 PDT)
[AMBER] RNA duplex Charles Johnson (Tue Jun 28 2011 - 17:33:45 PDT)
- Re: [AMBER] RNA duplex Raman Parkesh (Tue Jun 28 2011 - 17:50:51 PDT)
[AMBER] AMBER9- error in LEaP while learning MMPBSA tutorial Sheau Chen Lee (Tue Jun 28 2011 - 20:23:25 PDT)
- Re: [AMBER] AMBER9- error in LEaP while learning MMPBSA tutorial Ross Walker (Wed Jun 29 2011 - 02:02:41 PDT)
  - Re: [AMBER] AMBER9- error in LEaP while learning MMPBSA tutorial Sheau Chen Lee (Thu Jun 30 2011 - 00:28:58 PDT)
    - Re: [AMBER] AMBER9- error in LEaP while learning MMPBSA tutorial David A Case (Thu Jun 30 2011 - 05:29:31 PDT)
    - Re: [AMBER] AMBER9- error in LEaP while learning MMPBSA tutorial Sheau Chen Lee (Thu Jun 30 2011 - 20:41:51 PDT)
[AMBER] Uracil is not recognised as a nucleotide in Xleap - in FF99 hari krishna (Tue Jun 28 2011 - 23:50:40 PDT)
- Re: [AMBER] Uracil is not recognised as a nucleotide in Xleap - in FF99 Daniel Roe (Wed Jun 29 2011 - 08:53:18 PDT)
[AMBER] Sander Compilation Problem Ali Faruqi (Tue Jun 28 2011 - 23:51:14 PDT)
- Re: [AMBER] Sander Compilation Problem Jason Swails (Sun Jul 03 2011 - 12:14:47 PDT)
  - Re: [AMBER] Sander Compilation Problem Ali Faruqi (Sun Jul 03 2011 - 21:22:27 PDT)
[AMBER] NETCDF Installation Error Ali Faruqi (Wed Jun 29 2011 - 04:10:02 PDT)
- Re: [AMBER] NETCDF Installation Error David A Case (Thu Jun 30 2011 - 05:05:46 PDT)
  - Re: [AMBER] NETCDF Installation Error Ali Faruqi (Sat Jul 02 2011 - 01:59:06 PDT)
[AMBER] dist restraint e p (Wed Jun 29 2011 - 06:08:00 PDT)
- Re: [AMBER] dist restraint David A Case (Thu Jun 30 2011 - 05:10:04 PDT)
  - Re: [AMBER] dist restraint e p (Fri Jul 01 2011 - 20:10:04 PDT)
    - Re: [AMBER] dist restraint e p (Fri Jul 01 2011 - 22:03:00 PDT)
    - [AMBER] dist restraint e p (Fri Jul 01 2011 - 22:05:30 PDT)
    - Re: [AMBER] dist restraint case (Sat Jul 02 2011 - 06:00:18 PDT)
    - Re: [AMBER] dist restraint e p (Sat Jul 02 2011 - 22:22:11 PDT)
[AMBER] Problem in the energetics of the system Shake cannot be accomplished. hari krishna (Wed Jun 29 2011 - 08:06:24 PDT)
- Re: [AMBER] Problem in the energetics of the system Shake cannot be accomplished. Daniel Roe (Wed Jun 29 2011 - 08:45:13 PDT)
  - Re: [AMBER] Problem in the energetics of the system Shake cannot be accomplished. hari krishna (Wed Jun 29 2011 - 09:44:34 PDT)
[AMBER] Non-Standard Residues Problems David Cantu (Wed Jun 29 2011 - 10:38:36 PDT)
- Re: [AMBER] Non-Standard Residues Problems Carlos Simmerling (Wed Jun 29 2011 - 10:48:58 PDT)
- Re: [AMBER] Non-Standard Residues Problems Ben Roberts (Wed Jun 29 2011 - 10:50:25 PDT)
  - Re: [AMBER] Non-Standard Residues Problems David Cantu (Wed Jun 29 2011 - 12:36:49 PDT)
    - Re: [AMBER] Non-Standard Residues Problems David Cantu (Wed Jun 29 2011 - 15:14:40 PDT)
- Re: [AMBER] Non-Standard Residues Problems FyD (Thu Jun 30 2011 - 07:07:00 PDT)
  - Re: [AMBER] Non-Standard Residues Problems David Cantu (Thu Jun 30 2011 - 10:47:05 PDT)
    - Re: [AMBER] Non-Standard Residues Problems FyD (Thu Jun 30 2011 - 12:38:21 PDT)
    - Re: [AMBER] Non-Standard Residues Problems David Cantu (Thu Jun 30 2011 - 16:10:12 PDT)
    - Re: [AMBER] Non-Standard Residues Problems case (Thu Jun 30 2011 - 18:25:52 PDT)
    - Re: [AMBER] Non-Standard Residues Problems David Cantu (Thu Jun 30 2011 - 19:33:30 PDT)
    - Re: [AMBER] Non-Standard Residues Problems David A Case (Fri Jul 01 2011 - 04:59:18 PDT)
[AMBER] VMD-Chamber interface Mo Chen (Wed Jun 29 2011 - 13:20:19 PDT)
- Re: [AMBER] VMD-Chamber interface Adrian Roitberg (Wed Jun 29 2011 - 13:31:04 PDT)
- Re: [AMBER] VMD-Chamber interface Crowley, Michael (Wed Jun 29 2011 - 13:43:47 PDT)
  - Re: [AMBER] VMD-Chamber interface Mark Williamson (Thu Jun 30 2011 - 02:59:15 PDT)
- Re: [AMBER] VMD-Chamber interface Ross Walker (Thu Jun 30 2011 - 02:05:11 PDT)
[AMBER] Dihedral parameters for sp carbon in GAFF Hai Long (Wed Jun 29 2011 - 16:38:08 PDT)
[AMBER] Leap adds atoms to pdb (tutorial B1) Chirag Vora (Wed Jun 29 2011 - 22:48:48 PDT)
- Re: [AMBER] Leap adds atoms to pdb (tutorial B1) David A Case (Thu Jun 30 2011 - 05:22:06 PDT)
[AMBER] AMBER Workshop in Shanghai, China, August 22-26, 2011 Andreas Goetz (Thu Jun 30 2011 - 00:50:28 PDT)
[AMBER] Adding NH2 at the end of peptide Esam Tolba (Thu Jun 30 2011 - 03:51:55 PDT)
- Re: [AMBER] Adding NH2 at the end of peptide Carlos Simmerling (Thu Jun 30 2011 - 07:59:11 PDT)
[AMBER] MMPBSA Raja Pandian (Thu Jun 30 2011 - 03:56:01 PDT)
[AMBER] using Mg with ff99SB Irene Newhouse (Thu Jun 30 2011 - 14:24:20 PDT)
- Re: [AMBER] using Mg with ff99SB Takeshi Baba (Thu Jun 30 2011 - 18:12:46 PDT)
- Re: [AMBER] using Mg with ff99SB Irene Newhouse (Fri Jul 01 2011 - 01:43:25 PDT)
[AMBER] How Kinetic energy is can be converted to Temperature under the SHAKE constraint? kurisaki (Thu Jun 30 2011 - 19:18:43 PDT)
[AMBER] NBONH is greater than number of hydrogen for protein. kurisaki (Thu Jun 30 2011 - 20:23:22 PDT)
- Re: [AMBER] NBONH is greater than number of hydrogen for protein. kurisaki (Thu Jun 30 2011 - 20:42:47 PDT)
- Re: [AMBER] NBONH is greater than number of hydrogen for protein. David A Case (Fri Jul 01 2011 - 05:01:50 PDT)
[AMBER] Fwd: najmul arfin (Thu Jun 30 2011 - 22:21:32 PDT)
[AMBER] INSTALLATION ERROR ON RED HAT LINUX Rajabrata Bhuyan (Thu Jun 30 2011 - 23:13:28 PDT)
- Re: [AMBER] INSTALLATION ERROR ON RED HAT LINUX Ye MEI (Thu Jun 30 2011 - 23:45:00 PDT)
  - Re: [AMBER] INSTALLATION ERROR ON RED HAT LINUX Rajabrata Bhuyan (Fri Jul 08 2011 - 09:15:10 PDT)
    - Re: [AMBER] INSTALLATION ERROR ON RED HAT LINUX case (Fri Jul 08 2011 - 13:35:32 PDT)
[AMBER] APBS Daniel Aiello (Fri Jul 01 2011 - 07:06:23 PDT)
- Re: [AMBER] APBS Robert Konecny (Thu Jul 07 2011 - 10:48:21 PDT)
  - Re: [AMBER] APBS Daniel Aiello (Thu Jul 07 2011 - 11:05:07 PDT)
    - Re: [AMBER] APBS Robert Konecny (Thu Jul 07 2011 - 11:17:22 PDT)
    - Re: [AMBER] APBS Daniel Aiello (Thu Jul 07 2011 - 11:24:16 PDT)
[AMBER] MMPBSA.MPI running issue Ye Fan (Fri Jul 01 2011 - 09:00:33 PDT)
- Re: [AMBER] MMPBSA.MPI running issue Jason Swails (Fri Jul 01 2011 - 09:39:19 PDT)
  - Re: [AMBER] MMPBSA.MPI running issue Ye Fan (Fri Jul 01 2011 - 16:08:49 PDT)
    - Re: [AMBER] MMPBSA.MPI running issue Jason Swails (Sat Jul 02 2011 - 17:18:55 PDT)
    - Re: [AMBER] MMPBSA.MPI running issue Ye Fan (Tue Jul 05 2011 - 09:50:18 PDT)
    - Re: [AMBER] MMPBSA.MPI running issue Bill Miller III (Tue Jul 05 2011 - 09:57:29 PDT)
    - Re: [AMBER] MMPBSA.MPI running issue Ye Fan (Tue Jul 05 2011 - 12:53:29 PDT)
    - Re: [AMBER] MMPBSA.MPI running issue Bill Miller III (Tue Jul 05 2011 - 15:14:21 PDT)
    - Re: [AMBER] MMPBSA.MPI running issue Ye Fan (Wed Jul 06 2011 - 07:51:28 PDT)
    - Re: [AMBER] MMPBSA.MPI running issue Ye Fan (Fri Jul 15 2011 - 09:33:17 PDT)
    - Re: [AMBER] MMPBSA.MPI running issue Dwight McGee (Fri Jul 15 2011 - 09:47:07 PDT)
    - Re: [AMBER] MMPBSA.MPI running issue Ye Fan (Fri Jul 15 2011 - 12:27:08 PDT)
    - Re: [AMBER] MMPBSA.MPI running issue Jason Swails (Fri Jul 15 2011 - 15:20:41 PDT)
    - Re: [AMBER] MMPBSA.MPI running issue Ye Fan (Tue Jul 19 2011 - 10:39:59 PDT)
[AMBER] MPI cuda compilation error Fabrício Bracht (Fri Jul 01 2011 - 17:03:50 PDT)
- Re: [AMBER] MPI cuda compilation error filip fratev (Sat Jul 02 2011 - 02:46:29 PDT)
  - Re: [AMBER] MPI cuda compilation error Ross Walker (Sat Jul 02 2011 - 03:01:07 PDT)
    - Re: [AMBER] MPI cuda compilation error case (Sat Jul 02 2011 - 06:35:51 PDT)
    - Re: [AMBER] MPI cuda compilation error Fabrício Bracht (Sat Jul 02 2011 - 09:34:11 PDT)
    - Re: [AMBER] MPI cuda compilation error Ross Walker (Sat Jul 02 2011 - 11:31:34 PDT)
    - Re: [AMBER] MPI cuda compilation error Jason Swails (Sat Jul 02 2011 - 12:51:17 PDT)
    - Re: [AMBER] MPI cuda compilation error case (Sat Jul 02 2011 - 13:31:35 PDT)
    - Re: [AMBER] MPI cuda compilation error Fabrício Bracht (Sat Jul 02 2011 - 15:26:52 PDT)
[AMBER] /bin/sh /bin/dash Francesco Pietra (Sat Jul 02 2011 - 10:08:30 PDT)
- Re: [AMBER] /bin/sh /bin/dash Jason Swails (Sat Jul 02 2011 - 12:26:25 PDT)
  - Re: [AMBER] /bin/sh /bin/dash Francesco Pietra (Sat Jul 02 2011 - 23:11:21 PDT)
[AMBER] Multiple CPU and single GPU doubt Fabrício Bracht (Sat Jul 02 2011 - 15:36:26 PDT)
- Re: [AMBER] Multiple CPU and single GPU doubt Jason Swails (Sat Jul 02 2011 - 17:14:48 PDT)
- Re: [AMBER] Multiple CPU and single GPU doubt Ross Walker (Sun Jul 03 2011 - 04:59:50 PDT)
[AMBER] dist restraint e p (Sun Jul 03 2011 - 03:29:57 PDT)
- Re: [AMBER] dist restraint case (Sun Jul 03 2011 - 05:47:39 PDT)
  - Re: [AMBER] dist restraint e p (Sun Jul 03 2011 - 22:53:39 PDT)
    - Re: [AMBER] dist restraint case (Mon Jul 04 2011 - 05:53:40 PDT)
    - Re: [AMBER] dist restraint e p (Fri Jul 08 2011 - 22:18:21 PDT)
[AMBER] DNA simulation najmul arfin (Sun Jul 03 2011 - 22:55:38 PDT)
- Re: [AMBER] DNA simulation Jason Swails (Sun Jul 03 2011 - 23:30:55 PDT)
  - Re: [AMBER] DNA simulation Bruno Rodrigues (Wed Jul 06 2011 - 04:40:19 PDT)
[AMBER] Registration open - AMBER Workshop in Shanghai, China, August 22-26, 2011 Andreas Goetz (Mon Jul 04 2011 - 01:00:46 PDT)
[AMBER] MM-GBSA with QM data Aust, Susanne (Mon Jul 04 2011 - 02:04:17 PDT)
- Re: [AMBER] MM-GBSA with QM data Jason Swails (Mon Jul 04 2011 - 08:40:01 PDT)
[AMBER] amber Shesh Nath (Mon Jul 04 2011 - 03:08:34 PDT)
- Re: [AMBER] amber case (Mon Jul 04 2011 - 06:05:12 PDT)
- Re: [AMBER] amber manikanthan bhavaraju (Mon Jul 04 2011 - 11:47:37 PDT)
[AMBER] sander11 haris p (Mon Jul 04 2011 - 03:54:03 PDT)
- Re: [AMBER] sander11 Adrian Roitberg (Mon Jul 04 2011 - 03:56:23 PDT)
[AMBER] using sleap to load mol2 files case (Mon Jul 04 2011 - 06:15:03 PDT)
- Re: [AMBER] using sleap to load mol2 files Guenegou, Guillaume [ORDFR] (Tue Aug 09 2011 - 07:31:46 PDT)
[AMBER] continuing an mmpbsa run Chris Chris (Mon Jul 04 2011 - 06:29:20 PDT)
- Re: [AMBER] continuing an mmpbsa run Jason Swails (Mon Jul 04 2011 - 08:42:27 PDT)
[AMBER] reference for GLYCAM_06 force field subrata paul (Mon Jul 04 2011 - 22:14:34 PDT)
- Re: [AMBER] reference for GLYCAM_06 force field Sushil Mishra (Mon Jul 04 2011 - 22:49:47 PDT)
  - Re: [AMBER] reference for GLYCAM_06 force field Lachele Foley (Lists) (Tue Jul 05 2011 - 07:08:39 PDT)
[AMBER] sleap cannot deal with lipids? Tomoshi Kameda (Mon Jul 04 2011 - 23:09:32 PDT)
- Re: [AMBER] sleap cannot deal with lipids? Lachele Foley (Lists) (Tue Jul 05 2011 - 07:10:44 PDT)
  - Re: [AMBER] sleap cannot deal with lipids? Tomoshi Kameda (Tue Jul 05 2011 - 09:12:18 PDT)
    - Re: [AMBER] sleap cannot deal with lipids? Lachele Foley (Lists) (Tue Jul 05 2011 - 10:10:43 PDT)
    - Re: [AMBER] sleap cannot deal with lipids? Tomoshi Kameda (Tue Jul 05 2011 - 20:27:09 PDT)
    - Re: [AMBER] sleap cannot deal with lipids? David A Case (Wed Jul 06 2011 - 04:33:36 PDT)
    - Re: [AMBER] sleap cannot deal with lipids? Tomoshi Kameda (Wed Jul 06 2011 - 05:26:10 PDT)
    - Re: [AMBER] sleap cannot deal with lipids? Lachele Foley (Lists) (Wed Jul 06 2011 - 07:08:46 PDT)
[AMBER] Installation Problem souvik sur (Tue Jul 05 2011 - 00:00:02 PDT)
- Re: [AMBER] Installation Problem David A Case (Tue Jul 05 2011 - 04:54:19 PDT)
[AMBER] Intercalation site creation Pooja Khurana (Tue Jul 05 2011 - 03:48:59 PDT)
[AMBER] Running Amber 11 simulations using pmemd.cuda.MPI Baker D.J. (Tue Jul 05 2011 - 07:57:07 PDT)
- Re: [AMBER] Running Amber 11 simulations using pmemd.cuda.MPI Gould, Ian R (Tue Jul 05 2011 - 08:21:41 PDT)
  - Re: [AMBER] Running Amber 11 simulations using pmemd.cuda.MPI Baker D.J. (Tue Jul 05 2011 - 08:26:15 PDT)
    - Re: [AMBER] Running Amber 11 simulations using pmemd.cuda.MPI Gould, Ian R (Tue Jul 05 2011 - 08:32:03 PDT)
    - Re: [AMBER] Running Amber 11 simulations using pmemd.cuda.MPI Baker D.J. (Tue Jul 05 2011 - 08:42:00 PDT)
- Re: [AMBER] Running Amber 11 simulations using pmemd.cuda.MPI Ross Walker (Tue Jul 05 2011 - 08:57:44 PDT)
  - Re: [AMBER] Running Amber 11 simulations using pmemd.cuda.MPI Baker D.J. (Wed Jul 06 2011 - 08:45:56 PDT)
    - Re: [AMBER] Running Amber 11 simulations using pmemd.cuda.MPI Ross Walker (Wed Jul 06 2011 - 08:54:42 PDT)
    - Re: [AMBER] Running Amber 11 simulations using pmemd.cuda.MPI Scott Le Grand (Wed Jul 06 2011 - 10:34:36 PDT)
[AMBER] segmentation fault on tleap Giorgos Lamprinidis (Tue Jul 05 2011 - 08:32:14 PDT)
- Re: [AMBER] segmentation fault on tleap Daniel Roe (Tue Jul 05 2011 - 08:43:48 PDT)
  - Re: [AMBER] segmentation fault on tleap Giorgos Lamprinidis (Tue Jul 05 2011 - 08:48:03 PDT)
    - Re: [AMBER] segmentation fault on tleap Daniel Roe (Tue Jul 05 2011 - 09:20:02 PDT)
- Re: [AMBER] segmentation fault on tleap David A Case (Tue Jul 05 2011 - 09:02:40 PDT)
  - Re: [AMBER] segmentation fault on tleap Giorgos Lamprinidis (Wed Jul 06 2011 - 00:58:48 PDT)
[AMBER] amber11 openmpi installation problem mish (Tue Jul 05 2011 - 09:19:47 PDT)
[AMBER] install DFTB plus with Amber 11 Yubo Fan (Tue Jul 05 2011 - 09:39:44 PDT)
- Re: [AMBER] install DFTB plus with Amber 11 David A Case (Tue Jul 05 2011 - 09:52:39 PDT)
- Re: [AMBER] install DFTB plus with Amber 11 Gustavo Seabra (Tue Jul 05 2011 - 11:22:37 PDT)
  - Re: [AMBER] install DFTB plus with Amber 11 Yubo Fan (Wed Jul 06 2011 - 12:41:56 PDT)
    - Re: [AMBER] install DFTB plus with Amber 11 Gustavo Seabra (Wed Jul 06 2011 - 14:31:15 PDT)
[AMBER] About visualizing amber trajectory (periodic box) in VMD Mo Chen (Tue Jul 05 2011 - 11:08:11 PDT)
- Re: [AMBER] About visualizing amber trajectory (periodic box) in VMD Adrian Roitberg (Tue Jul 05 2011 - 11:12:40 PDT)
[AMBER] Fatal error in MPI_Init: Other MPI error Santosh Mogurampelly (Tue Jul 05 2011 - 11:30:19 PDT)
[AMBER] Large flcutions in the RMSD deviations upon changing the parameters values of gamma_ln, taup and timesteps ..How a small variation leads to such a larage change?? Rajesh Raju (Tue Jul 05 2011 - 16:27:58 PDT)
[AMBER] Amber11 Roy Lee (Tue Jul 05 2011 - 20:02:54 PDT)
- Re: [AMBER] Amber11 Ross Walker (Wed Jul 06 2011 - 08:28:31 PDT)
[AMBER] Error KIRTANA S (Tue Jul 05 2011 - 21:06:21 PDT)
[AMBER] AMBER Shesh Nath (Tue Jul 05 2011 - 23:36:20 PDT)
- Re: [AMBER] AMBER David A Case (Wed Jul 06 2011 - 04:40:42 PDT)
[AMBER] Problem related to the Potential Mean Force Sindrila Dutta banik (Tue Jul 05 2011 - 23:37:32 PDT)
[AMBER] MMPBSA_ERROR MAXNEI too short Raja Pandian (Wed Jul 06 2011 - 00:14:09 PDT)
- Re: [AMBER] MMPBSA_ERROR MAXNEI too short Ray Luo, Ph.D. (Wed Jul 06 2011 - 09:37:32 PDT)
[AMBER] Ala double mutation scans Jesper Sørensen (Wed Jul 06 2011 - 01:27:35 PDT)
- Re: [AMBER] Ala double mutation scans Dwight McGee (Wed Jul 06 2011 - 08:01:18 PDT)
  - Re: [AMBER] Ala double mutation scans Jesper Sørensen (Fri Jul 08 2011 - 00:24:42 PDT)
    - Re: [AMBER] Ala double mutation scans Jason Swails (Sat Jul 09 2011 - 07:58:12 PDT)
    - Re: [AMBER] Ala double mutation scans Jesper Sørensen (Sun Jul 10 2011 - 06:02:27 PDT)
    - Re: [AMBER] Ala double mutation scans Dwight McGee (Mon Jul 11 2011 - 10:36:58 PDT)
    - Re: [AMBER] Ala double mutation scans Jesper Sørensen (Tue Jul 12 2011 - 04:36:27 PDT)
[AMBER] Problems with density in aqueous solution tommaso.casalini.mail.polimi.it (Wed Jul 06 2011 - 03:05:11 PDT)
- Re: [AMBER] Problems with density in aqueous solution David A Case (Wed Jul 06 2011 - 04:47:13 PDT)
  - [AMBER] Radial distribution function tommaso.casalini.mail.polimi.it (Thu Oct 06 2011 - 02:31:48 PDT)
- Re: [AMBER] Problems with density in aqueous solution Bill Ross (Wed Jul 06 2011 - 12:22:23 PDT)
[AMBER] AmberTools installation error Jennifer L. Muzyka (Wed Jul 06 2011 - 05:08:58 PDT)
- Re: [AMBER] AmberTools installation error Jason Swails (Sat Jul 09 2011 - 08:00:51 PDT)
  - Re: [AMBER] AmberTools installation error Jennifer L. Muzyka (Wed Jul 20 2011 - 07:25:11 PDT)
    - Re: [AMBER] AmberTools installation error David A Case (Wed Jul 20 2011 - 07:57:28 PDT)
    - Re: [AMBER] AmberTools installation error Jennifer L. Muzyka (Wed Jul 20 2011 - 11:28:54 PDT)
    - Re: [AMBER] AmberTools installation error Jason Swails (Wed Jul 20 2011 - 20:33:39 PDT)
    - Re: [AMBER] AmberTools installation error Jennifer L. Muzyka (Thu Jul 21 2011 - 07:34:44 PDT)
    - Re: [AMBER] AmberTools installation error David A Case (Thu Jul 21 2011 - 08:00:01 PDT)
    - Re: [AMBER] AmberTools installation error Jason Swails (Thu Jul 21 2011 - 08:03:33 PDT)
[AMBER] AmberTools installation - Jennifer L. Muzyka (Wed Jul 06 2011 - 05:18:28 PDT)
- Re: [AMBER] AmberTools installation - David A Case (Wed Jul 06 2011 - 05:37:34 PDT)
  - Re: [AMBER] AmberTools installation - Jennifer L. Muzyka (Wed Jul 06 2011 - 06:02:42 PDT)
    - Re: [AMBER] AmberTools installation - David A Case (Wed Jul 06 2011 - 06:11:51 PDT)
Re: [AMBER] AmberTools1.5 &ff10 David A Case (Wed Jul 06 2011 - 05:27:38 PDT)
- Re: [AMBER] AmberTools1.5 &ff10 Takeshi Baba (Wed Jul 06 2011 - 05:51:11 PDT)
[AMBER] Different trajectories with large difference in RMSD with changing the parameters values of gamma_ln, taup, timesteps and extend of density equilibration Rajesh Raju (Wed Jul 06 2011 - 08:59:32 PDT)
- Re: [AMBER] Different trajectories with large difference in RMSD with changing the parameters values of gamma_ln, taup, timesteps and extend of density equilibration Adrian Roitberg (Wed Jul 06 2011 - 09:03:26 PDT)
  - Re: [AMBER] Different trajectories with large difference in RMSD with changing the parameters values of gamma_ln, taup, timesteps and extend of density equilibration Rajesh Raju (Wed Jul 06 2011 - 09:15:53 PDT)
[AMBER] ptraj analysis problems - protein leaving the box Daniel Scott (Wed Jul 06 2011 - 09:14:43 PDT)
- Re: [AMBER] ptraj analysis problems - protein leaving the box Daniel Roe (Wed Jul 06 2011 - 10:06:18 PDT)
[AMBER] scee=scnb=1 subrata paul (Wed Jul 06 2011 - 10:57:26 PDT)
- Re: [AMBER] scee=scnb=1 Ross Walker (Wed Jul 06 2011 - 11:02:12 PDT)
[AMBER] Amber11 using MPICH (parallel install problem) mish (Wed Jul 06 2011 - 11:21:35 PDT)
- Re: [AMBER] Amber11 using MPICH (parallel install problem) Ross Walker (Wed Jul 06 2011 - 11:32:25 PDT)
- Re: [AMBER] Amber11 using MPICH (parallel install problem) David A Case (Wed Jul 06 2011 - 12:36:13 PDT)
  - Re: [AMBER] Amber11 using MPICH (parallel install problem) mish (Thu Jul 07 2011 - 07:08:39 PDT)
    - Re: [AMBER] Amber11 using MPICH (parallel install problem) M. Shahid (Thu Jul 07 2011 - 07:15:25 PDT)
    - Re: [AMBER] Amber11 using MPICH (parallel install problem) Jason Swails (Thu Jul 07 2011 - 07:27:10 PDT)
[AMBER] Sander Problem souvik sur (Thu Jul 07 2011 - 02:08:52 PDT)
- Re: [AMBER] Sander Problem Hirdesh Kumar (Thu Jul 07 2011 - 02:24:41 PDT)
- Re: [AMBER] Sander Problem David A Case (Thu Jul 07 2011 - 04:46:32 PDT)
- Re: [AMBER] Sander Problem Jason Swails (Thu Jul 07 2011 - 07:28:44 PDT)
[AMBER] sander job crashed MUSTAFA BUGHIO (Thu Jul 07 2011 - 04:37:53 PDT)
- Re: [AMBER] sander job crashed Ben Roberts (Thu Jul 07 2011 - 17:02:30 PDT)
  - Re: [AMBER] sander job crashed MUSTAFA BUGHIO (Fri Jul 08 2011 - 01:02:23 PDT)
    - Re: [AMBER] sander job crashed Ben Roberts (Fri Jul 08 2011 - 04:59:23 PDT)
    - Re: [AMBER] sander job crashed MUSTAFA BUGHIO (Fri Jul 08 2011 - 07:44:35 PDT)
    - Re: [AMBER] sander job crashed MUSTAFA BUGHIO (Fri Jul 08 2011 - 07:50:07 PDT)
    - Re: [AMBER] sander job crashed Ben Roberts (Mon Jul 11 2011 - 08:24:21 PDT)
    - Re: [AMBER] sander job crashed MUSTAFA BUGHIO (Mon Jul 11 2011 - 11:09:57 PDT)
[AMBER] xleap problem Elisa Frezza (Thu Jul 07 2011 - 06:37:35 PDT)
- Re: [AMBER] xleap problem David A Case (Thu Jul 07 2011 - 07:24:06 PDT)
  - Re: [AMBER] xleap problem Elisa Frezza (Thu Jul 07 2011 - 07:40:43 PDT)
    - Re: [AMBER] xleap problem Elisa Frezza (Thu Jul 07 2011 - 08:13:06 PDT)
    - Re: [AMBER] xleap problem David A Case (Thu Jul 07 2011 - 08:22:51 PDT)
    - Re: [AMBER] xleap problem Elisa Frezza (Thu Jul 07 2011 - 08:26:20 PDT)
    - Re: [AMBER] xleap problem David A Case (Thu Jul 07 2011 - 10:01:43 PDT)
    - Re: [AMBER] xleap problem Elisa Frezza (Fri Jul 08 2011 - 05:51:26 PDT)
[AMBER] Amber help RUI_YAO (Thu Jul 07 2011 - 07:59:56 PDT)
- Re: [AMBER] Amber help Adrian Roitberg (Thu Jul 07 2011 - 08:01:11 PDT)
[AMBER] Energy Decomp with mm_pbsa.pl Daniel Aiello (Thu Jul 07 2011 - 09:58:11 PDT)
- Re: [AMBER] Energy Decomp with mm_pbsa.pl Dwight McGee (Thu Jul 07 2011 - 10:25:20 PDT)
  - Re: [AMBER] Energy Decomp with mm_pbsa.pl Daniel Aiello (Thu Jul 07 2011 - 10:26:37 PDT)
[AMBER] extra_pts.f tsurma.umich.edu (Thu Jul 07 2011 - 14:08:47 PDT)
- Re: [AMBER] extra_pts.f case (Fri Jul 08 2011 - 05:29:52 PDT)
  - Re: [AMBER] extra_pts.f tsurma.umich.edu (Fri Jul 08 2011 - 06:30:02 PDT)
    - Re: [AMBER] extra_pts.f case (Fri Jul 08 2011 - 15:07:22 PDT)
    - Re: [AMBER] extra_pts.f tsurma.umich.edu (Sun Jul 10 2011 - 13:47:37 PDT)
[AMBER] glib(c) error in mmpbsa KIRTANA S (Thu Jul 07 2011 - 14:57:59 PDT)
[AMBER] atom mapping in leaprc.parmCHI_YIL.bsc Niel Henriksen (Thu Jul 07 2011 - 16:05:42 PDT)
- Re: [AMBER] atom mapping in leaprc.parmCHI_YIL.bsc case (Sun Jul 10 2011 - 18:40:50 PDT)
[AMBER] deletion of one water molecule from .rst and prmtop files Hirdesh Kumar (Thu Jul 07 2011 - 22:18:26 PDT)
[AMBER] Creating hoogsteen basepaired DNA using NAB Andre Serobian (Fri Jul 08 2011 - 00:18:37 PDT)
- Re: [AMBER] Creating hoogsteen basepaired DNA using NAB case (Fri Jul 08 2011 - 05:41:39 PDT)
  - Re: [AMBER] Creating hoogsteen basepaired DNA using NAB Andre Serobian (Fri Jul 08 2011 - 18:38:01 PDT)
    - Re: [AMBER] Creating hoogsteen basepaired DNA using NAB case (Fri Jul 08 2011 - 20:08:23 PDT)
    - Re: [AMBER] Creating hoogsteen basepaired DNA using NAB Andre Serobian (Thu Jul 21 2011 - 21:26:26 PDT)
    - Re: [AMBER] Creating hoogsteen basepaired DNA using NAB David A Case (Fri Jul 22 2011 - 07:10:31 PDT)
    - Re: [AMBER] Creating hoogsteen basepaired DNA using NAB Andre Serobian (Fri Jul 22 2011 - 15:13:20 PDT)
    - Re: [AMBER] Creating hoogsteen basepaired DNA using NAB Andre Serobian (Thu Jul 28 2011 - 01:45:11 PDT)
[AMBER] Ligand parametrization Matteo Tiberti (Fri Jul 08 2011 - 03:30:42 PDT)
- Re: [AMBER] Ligand parametrization Thomas Gaillard (Fri Jul 08 2011 - 04:18:46 PDT)
[AMBER] minimization error Zhu Tong (Fri Jul 08 2011 - 05:55:24 PDT)
- Re: [AMBER] minimization error case (Fri Jul 08 2011 - 13:27:00 PDT)
[AMBER] XLEaP parameters for nonstandard residues Julia Blum (Fri Jul 08 2011 - 07:05:51 PDT)
- Re: [AMBER] XLEaP parameters for nonstandard residues Ilyas Yildirim (Fri Jul 08 2011 - 07:29:58 PDT)
  - Re: [AMBER] XLEaP parameters for nonstandard residues Julia Blum (Fri Jul 08 2011 - 09:26:04 PDT)
    - Re: [AMBER] XLEaP parameters for nonstandard residues Ilyas Yildirim (Fri Jul 08 2011 - 10:49:56 PDT)
    - Re: [AMBER] XLEaP parameters for nonstandard residues case (Fri Jul 08 2011 - 13:26:54 PDT)
    - Re: [AMBER] XLEaP parameters for nonstandard residues Julia Blum (Tue Jul 12 2011 - 06:31:28 PDT)
[AMBER] Different trajectories with different RMSD with changing the parameters of gamma_ln, taup, timesteps and extend of density equilibration Rajesh Raju (Fri Jul 08 2011 - 10:49:15 PDT)
- Re: [AMBER] Different trajectories with different RMSD with changing the parameters of gamma_ln, taup, timesteps and extend of density equilibration Daniel Roe (Fri Jul 08 2011 - 12:43:57 PDT)
  - Re: [AMBER] Different trajectories with different RMSD with changing the parameters of gamma_ln, taup, timesteps and extend of density equilibration Rajesh Raju (Fri Jul 08 2011 - 13:16:48 PDT)
  - Re: [AMBER] Different trajectories with different RMSD with changing the parameters of gamma_ln, taup, timesteps and extend of density equilibration Rajesh Raju (Fri Jul 08 2011 - 13:59:35 PDT)
  - Re: [AMBER] Different trajectories with different RMSD with changing the parameters of gamma_ln, taup, timesteps and extend of density equilibration Rajesh Raju (Fri Jul 08 2011 - 14:00:07 PDT)
- Re: [AMBER] Different trajectories with different RMSD with changing the parameters of gamma_ln, taup, timesteps and extend of density equilibration Thomas Cheatham III (Fri Jul 08 2011 - 14:49:34 PDT)
  - Re: [AMBER] Different trajectories with different RMSD with changing the parameters of gamma_ln, taup, timesteps and extend of density equilibration Rajesh Raju (Fri Jul 08 2011 - 15:46:56 PDT)
    - Re: [AMBER] Different trajectories with different RMSD with changing the parameters of gamma_ln, taup, timesteps and extend of density equilibration Thomas Cheatham III (Fri Jul 08 2011 - 16:11:59 PDT)
[AMBER] Missing Na+ type in ff10 in maksing topolgy file Rajesh Raju (Fri Jul 08 2011 - 17:15:25 PDT)
- Re: [AMBER] Missing Na+ type in ff10 in maksing topolgy file case (Fri Jul 08 2011 - 20:02:22 PDT)
[AMBER] ERROR - No pdb file generated using NAB Andre Serobian (Fri Jul 08 2011 - 21:08:18 PDT)
- Re: [AMBER] ERROR - No pdb file generated using NAB case (Sat Jul 09 2011 - 06:14:49 PDT)
[AMBER] sleap and ptraj output issue with terminal residues Kevin Wiehe (Fri Jul 08 2011 - 21:45:54 PDT)
- Re: [AMBER] sleap and ptraj output issue with terminal residues case (Sun Jul 10 2011 - 18:39:10 PDT)
[AMBER] Interaction - Constrain Eliac Brown (Sat Jul 09 2011 - 04:19:33 PDT)
- Re: [AMBER] Interaction - Constrain Carlos Simmerling (Sat Jul 09 2011 - 04:21:50 PDT)
[AMBER] Problem related to the residue template of zwiterionic state Sindrila Dutta banik (Sat Jul 09 2011 - 20:36:22 PDT)
- Re: [AMBER] Problem related to the residue template of zwiterionic state case (Sun Jul 10 2011 - 18:36:39 PDT)
[AMBER] About extracting partial atoms from a Amber trajectory file Mo Chen (Sun Jul 10 2011 - 08:47:59 PDT)
- Re: [AMBER] About extracting partial atoms from a Amber trajectory file Carlos Simmerling (Sun Jul 10 2011 - 08:53:17 PDT)
[AMBER] AMBER Shesh Nath (Sun Jul 10 2011 - 23:20:04 PDT)
- Re: [AMBER] AMBER Daniel Roe (Mon Jul 11 2011 - 04:17:17 PDT)
[AMBER] Heavy atom definition Eliac Brown (Mon Jul 11 2011 - 03:52:56 PDT)
[AMBER] Analysis the changes of secondary structure in MD trajectory qiao xue (Mon Jul 11 2011 - 05:45:31 PDT)
- Re: [AMBER] Analysis the changes of secondary structure in MD trajectory Carlos Simmerling (Mon Jul 11 2011 - 07:09:40 PDT)
[AMBER] ligand & protein with dist restraint e p (Mon Jul 11 2011 - 07:08:10 PDT)
- Re: [AMBER] ligand & protein with dist restraint Dmitry Nilov (Tue Jul 12 2011 - 04:30:35 PDT)
  - Re: [AMBER] ligand & protein with dist restraint e p (Tue Jul 12 2011 - 22:35:08 PDT)
    - Re: [AMBER] ligand & protein with dist restraint Dmitry Nilov (Tue Jul 12 2011 - 23:45:06 PDT)
    - Re: [AMBER] ligand & protein with dist restraint e p (Wed Jul 13 2011 - 02:05:34 PDT)
    - Re: [AMBER] ligand & protein with dist restraint Dmitry Nilov (Wed Jul 13 2011 - 02:54:12 PDT)
    - [AMBER] Aromatic bonds disappear during sdf creation with sleap Guenegou, Guillaume [ORDFR] (Wed Jul 27 2011 - 05:28:37 PDT)
[AMBER] cudaMemcpy GpuBuffer::Upload failed invalid argument Oliver Kuhn (Mon Jul 11 2011 - 08:32:56 PDT)
- Re: [AMBER] cudaMemcpy GpuBuffer::Upload failed invalid argument Ross Walker (Mon Jul 11 2011 - 09:12:18 PDT)
  - Re: [AMBER] cudaMemcpy GpuBuffer::Upload failed invalid argument Oliver Kuhn (Mon Jul 11 2011 - 10:24:45 PDT)
[AMBER] AmberTools manikanthan bhavaraju (Mon Jul 11 2011 - 13:26:15 PDT)
- Re: [AMBER] AmberTools Dwight McGee (Mon Jul 11 2011 - 14:44:57 PDT)
  - Re: [AMBER] AmberTools manikanthan bhavaraju (Tue Jul 12 2011 - 11:52:21 PDT)
[AMBER] Minimization Question Eliac Brown (Mon Jul 11 2011 - 18:18:41 PDT)
- Re: [AMBER] Minimization Question Bill Ross (Mon Jul 11 2011 - 19:15:35 PDT)
- Re: [AMBER] Minimization Question Bill Ross (Mon Jul 11 2011 - 19:25:12 PDT)
[AMBER] help xiao fugui (Mon Jul 11 2011 - 19:16:56 PDT)
[AMBER] regarding amber anal calculation dhilip kumar ramalingam (Mon Jul 11 2011 - 22:07:05 PDT)
- Re: [AMBER] regarding amber anal calculation Adrian Roitberg (Tue Jul 12 2011 - 00:37:32 PDT)
[AMBER] Please solve my problem e p (Tue Jul 12 2011 - 04:11:52 PDT)
- Re: [AMBER] Please solve my problem Adrian Roitberg (Tue Jul 12 2011 - 04:18:30 PDT)
  - Re: [AMBER] Please solve my problem e p (Tue Jul 12 2011 - 22:45:18 PDT)
- Re: [AMBER] Please solve my problem Carlos Simmerling (Tue Jul 12 2011 - 04:20:22 PDT)
  - Re: [AMBER] Please solve my problem e p (Tue Jul 12 2011 - 22:46:19 PDT)
[AMBER] Undefined symbols when compiling AMBER11 on Mac OSX 10.6 Daniel Sindhikara (Tue Jul 12 2011 - 04:35:05 PDT)
- Re: [AMBER] Undefined symbols when compiling AMBER11 on Mac OSX 10.6 Daniel Roe (Tue Jul 12 2011 - 05:07:08 PDT)
- Re: [AMBER] Undefined symbols when compiling AMBER11 on Mac OSX 10.6 David A Case (Tue Jul 12 2011 - 05:09:11 PDT)
- Re: [AMBER] Undefined symbols when compiling AMBER11 on Mac OSX 10.6 Takeshi Baba (Tue Jul 12 2011 - 07:42:12 PDT)
  - Re: [AMBER] Undefined symbols when compiling AMBER11 on Mac OSX 10.6 Daniel Sindhikara (Wed Jul 13 2011 - 04:01:11 PDT)
    - Re: [AMBER] Undefined symbols when compiling AMBER11 on Mac OSX 10.6 Takeshi Baba (Wed Jul 13 2011 - 04:28:03 PDT)
    - Re: [AMBER] Undefined symbols when compiling AMBER11 on Mac OSX 10.6 Daniel Sindhikara (Wed Jul 13 2011 - 19:44:45 PDT)
    - Re: [AMBER] Undefined symbols when compiling AMBER11 on Mac OSX 10.6 Takeshi Baba (Wed Jul 13 2011 - 22:10:25 PDT)
    - Re: [AMBER] Undefined symbols when compiling AMBER11 on Mac OSX 10.6 Daniel Sindhikara (Mon Jul 25 2011 - 00:10:37 PDT)
    - Re: [AMBER] Undefined symbols when compiling AMBER11 on Mac OSX 10.6 Takeshi Baba (Mon Jul 25 2011 - 01:04:52 PDT)
    - Re: [AMBER] Undefined symbols when compiling AMBER11 on Mac OSX 10.6 Daniel Sindhikara (Mon Jul 25 2011 - 01:26:29 PDT)
    - Re: [AMBER] Undefined symbols when compiling AMBER11 on Mac OSX 10.6 Jason Swails (Mon Jul 25 2011 - 18:32:17 PDT)
    - Re: [AMBER] Undefined symbols when compiling AMBER11 on Mac OSX 10.6 Daniel Sindhikara (Tue Jul 26 2011 - 02:41:23 PDT)
    - Re: [AMBER] Undefined symbols when compiling AMBER11 on Mac OSX 10.6 Takeshi Baba (Tue Jul 26 2011 - 18:53:13 PDT)
    - Re: [AMBER] Undefined symbols when compiling AMBER11 on Mac OSX 10.6 Daniel Sindhikara (Sun Jul 31 2011 - 22:56:25 PDT)
[AMBER] When and how is leap re-numbering residues? Jan-Philip Gehrcke (Tue Jul 12 2011 - 06:27:19 PDT)
- Re: [AMBER] When and how is leap re-numbering residues? David A Case (Wed Jul 13 2011 - 05:11:55 PDT)
  - Re: [AMBER] When and how is leap re-numbering residues? Jan-Philip Gehrcke (Wed Jul 13 2011 - 06:08:15 PDT)
[AMBER] AmberTools compilation problem Matteo Tiberti (Tue Jul 12 2011 - 07:54:35 PDT)
- Re: [AMBER] AmberTools compilation problem David A Case (Tue Jul 12 2011 - 09:29:41 PDT)
  - Re: [AMBER] AmberTools compilation problem Matteo Tiberti (Wed Jul 13 2011 - 01:40:02 PDT)
[AMBER] Antechamber trouble with COA-acyl chain Erin Kelly (Tue Jul 12 2011 - 07:59:28 PDT)
- Re: [AMBER] Antechamber trouble with COA-acyl chain Erin Kelly (Tue Jul 12 2011 - 09:19:24 PDT)
- Re: [AMBER] Antechamber trouble with COA-acyl chain David A Case (Tue Jul 12 2011 - 09:32:03 PDT)
  - Re: [AMBER] Antechamber trouble with COA-acyl chain Erin Kelly (Tue Jul 12 2011 - 09:37:15 PDT)
    - Re: [AMBER] Antechamber trouble with COA-acyl chain David A Case (Tue Jul 12 2011 - 11:43:34 PDT)
    - Re: [AMBER] Antechamber trouble with COA-acyl chain Erin Kelly (Tue Jul 12 2011 - 12:40:39 PDT)
    - Re: [AMBER] Antechamber trouble with COA-acyl chain David A Case (Tue Jul 12 2011 - 13:00:47 PDT)
    - Re: [AMBER] Antechamber trouble with COA-acyl chain Erin Kelly (Tue Jul 12 2011 - 13:22:50 PDT)
    - Re: [AMBER] Antechamber trouble with COA-acyl chain David A Case (Wed Jul 13 2011 - 05:15:18 PDT)
    - Re: [AMBER] Antechamber trouble with COA-acyl chain Erin Kelly (Wed Jul 13 2011 - 07:28:45 PDT)
    - Re: [AMBER] Antechamber trouble with COA-acyl chain Erin Kelly (Wed Jul 13 2011 - 07:53:48 PDT)
    - Re: [AMBER] Antechamber trouble with COA-acyl chain intra\\sa175950 (Wed Jul 13 2011 - 08:30:20 PDT)
    - Re: [AMBER-Developers] [AMBER] Antechamber trouble with COA-acyl chain David A Case (Wed Jul 13 2011 - 11:10:44 PDT)
    - Re: [AMBER] Antechamber trouble with COA-acyl chain Erin Kelly (Wed Jul 13 2011 - 12:59:03 PDT)
    - Re: [AMBER] Antechamber trouble with COA-acyl chain Erin Kelly (Wed Jul 13 2011 - 13:10:42 PDT)
    - Re: [AMBER] Antechamber trouble with COA-acyl chain case (Wed Jul 13 2011 - 14:58:30 PDT)
    - Re: [AMBER] Antechamber trouble with COA-acyl chain Erin Kelly (Wed Jul 13 2011 - 15:08:07 PDT)
    - Re: [AMBER] Antechamber trouble with COA-acyl chain Erin Kelly (Thu Jul 14 2011 - 07:07:46 PDT)
    - Re: [AMBER] Antechamber trouble with COA-acyl chain M. L. Dodson (Thu Jul 14 2011 - 08:28:36 PDT)
    - Re: [AMBER] Antechamber trouble with COA-acyl chain case (Wed Jul 13 2011 - 15:06:14 PDT)
- Re: [AMBER] Antechamber trouble with COA-acyl chain Dean Cuebas (Tue Jul 12 2011 - 13:04:04 PDT)
  - Re: [AMBER] Antechamber trouble with COA-acyl chain Erin Kelly (Tue Jul 12 2011 - 13:26:04 PDT)
[AMBER] zinc parameters Sel Ercan (Tue Jul 12 2011 - 10:00:56 PDT)
- Re: [AMBER] zinc parameters Ben Roberts (Tue Jul 12 2011 - 10:11:01 PDT)
  - Re: [AMBER] zinc parameters Oliver Kuhn (Tue Jul 12 2011 - 10:29:44 PDT)
- Re: [AMBER] zinc parameters Gustavo Seabra (Tue Jul 12 2011 - 11:42:32 PDT)
  - Re: [AMBER] zinc parameters Oliver Kuhn (Tue Jul 12 2011 - 12:08:48 PDT)
    - Re: [AMBER] zinc parameters Gustavo Seabra (Tue Jul 12 2011 - 22:19:53 PDT)
[AMBER] problem with type of pdb output. lawrence awadetsi (Tue Jul 12 2011 - 11:07:33 PDT)
- Re: [AMBER] problem with type of pdb output. Ben Roberts (Tue Jul 12 2011 - 11:51:50 PDT)
- Re: [AMBER] problem with type of pdb output. David A Case (Tue Jul 12 2011 - 12:46:49 PDT)
[AMBER] MMPBSA.py is crashing manikanthan bhavaraju (Tue Jul 12 2011 - 13:19:24 PDT)
- Re: [AMBER] MMPBSA.py is crashing Dwight McGee (Tue Jul 12 2011 - 13:43:54 PDT)
  - Re: [AMBER] MMPBSA.py is crashing manikanthan bhavaraju (Tue Jul 12 2011 - 14:07:26 PDT)
    - Re: [AMBER] MMPBSA.py is crashing Dwight McGee (Tue Jul 12 2011 - 18:35:38 PDT)
    - Re: [AMBER] MMPBSA.py is crashing Adrian Roitberg (Tue Jul 12 2011 - 23:53:41 PDT)
[AMBER] the picture of secstruct and the analysis of Hbond qiao xue (Tue Jul 12 2011 - 18:57:54 PDT)
- [AMBER] Steered MD using pmemd.cuda ? Marek Maly (Thu Jul 14 2011 - 09:51:21 PDT)
  - Re: [AMBER] Steered MD using pmemd.cuda ? Ross Walker (Thu Jul 14 2011 - 10:24:49 PDT)
    - Re: [AMBER] Steered MD using pmemd.cuda ? Marek Maly (Thu Jul 14 2011 - 10:19:21 PDT)
    - [AMBER] Discrepancy in Ca++ Vdw parameters ? Marek Maly (Sat Jul 16 2011 - 15:22:44 PDT)
[AMBER] Sander problem souvik sur (Tue Jul 12 2011 - 20:43:24 PDT)
- Re: [AMBER] Sander problem manikanthan bhavaraju (Tue Jul 12 2011 - 21:02:03 PDT)
[AMBER] Edit prmtop file Paul Mortenson (Wed Jul 13 2011 - 01:37:53 PDT)
- Re: [AMBER] Edit prmtop file Marc van der Kamp (Wed Jul 13 2011 - 01:48:59 PDT)
  - Re: [AMBER] Edit prmtop file Paul Mortenson (Wed Jul 13 2011 - 02:14:16 PDT)
    - Re: [AMBER] Edit prmtop file Marc van der Kamp (Wed Jul 13 2011 - 03:06:19 PDT)
- Re: [AMBER] Edit prmtop file Bill Ross (Wed Jul 13 2011 - 10:31:18 PDT)
[AMBER] number of solvent molecule around solute subrata paul (Wed Jul 13 2011 - 02:56:59 PDT)
- Re: [AMBER] number of solvent molecule around solute Adrian Roitberg (Wed Jul 13 2011 - 03:21:41 PDT)
[AMBER] MM_PBSA analysis warning Sangita Kachhap (Wed Jul 13 2011 - 04:30:09 PDT)
[AMBER] TR: Antechamber trouble with COA-acyl chain intra\\sa175950 (Wed Jul 13 2011 - 08:34:36 PDT)
- Re: [AMBER] TR: Antechamber trouble with COA-acyl chain Erin Kelly (Wed Jul 13 2011 - 08:56:34 PDT)
  - Re: [AMBER] TR: Antechamber trouble with COA-acyl chain intra\\sa175950 (Wed Jul 13 2011 - 09:03:23 PDT)
    - Re: [AMBER] TR: Antechamber trouble with COA-acyl chain Erin Kelly (Wed Jul 13 2011 - 10:43:44 PDT)
    - Re: [AMBER] TR: Antechamber trouble with COA-acyl chain Adrian Roitberg (Wed Jul 13 2011 - 10:47:21 PDT)
    - Re: [AMBER] TR: Antechamber trouble with COA-acyl chain Erin Kelly (Wed Jul 13 2011 - 10:51:06 PDT)
[AMBER] Regarding "Total unperturbed charge: -0.507900" on CYP1A1 Prajwal Nandekar (Wed Jul 13 2011 - 11:44:54 PDT)
- Re: [AMBER] Regarding "Total unperturbed charge: -0.507900" on CYP1A1 steinbrt.rci.rutgers.edu (Wed Jul 13 2011 - 13:26:07 PDT)
[AMBER] converting amber8 prmtop to amber11 manikanthan bhavaraju (Wed Jul 13 2011 - 12:38:45 PDT)
- Re: [AMBER] converting amber8 prmtop to amber11 Jason Swails (Wed Jul 13 2011 - 13:17:59 PDT)
[AMBER] How to make the picture of secstruct and the analysis of Hbond qiao xue (Wed Jul 13 2011 - 16:54:10 PDT)
- Re: [AMBER] How to make the picture of secstruct and the analysis of Hbond Daniel Roe (Thu Jul 14 2011 - 04:27:13 PDT)
  - Re: [AMBER] How to make the picture of secstruct and the analysis of Hbond qiao xue (Fri Jul 15 2011 - 20:21:04 PDT)
    - Re: [AMBER] How to make the picture of secstruct and the analysis of Hbond Daniel Roe (Mon Jul 18 2011 - 06:25:54 PDT)
    - Re: [AMBER] How to make the picture of secstruct and the analysis of Hbond qiao xue (Tue Jul 19 2011 - 19:01:48 PDT)
[AMBER] error: GBSA with mm_pbsa.pl manikanthan bhavaraju (Wed Jul 13 2011 - 20:35:25 PDT)
- Re: [AMBER] error: GBSA with mm_pbsa.pl Jason Swails (Sun Jul 17 2011 - 03:58:07 PDT)
  - Re: [AMBER] error: GBSA with mm_pbsa.pl manikanthan bhavaraju (Sun Jul 17 2011 - 22:01:42 PDT)
    - Re: [AMBER] error: GBSA with mm_pbsa.pl Jason Swails (Mon Jul 18 2011 - 07:44:58 PDT)
    - [AMBER] How to use nonlin option of APBS in MMPBSA.py? Wei Huang (Tue Jul 19 2011 - 10:03:38 PDT)
    - Re: [AMBER] How to use nonlin option of APBS in MMPBSA.py? Dwight McGee (Tue Jul 19 2011 - 10:31:32 PDT)
[AMBER] regarding hydrogen bonding dhilip kumar ramalingam (Thu Jul 14 2011 - 01:35:41 PDT)
- Re: [AMBER] regarding hydrogen bonding DEBOSTUTI GHOSHDASTIDAR (Thu Jul 14 2011 - 23:16:51 PDT)
[AMBER] renum water Jacopo Sgrignani (Thu Jul 14 2011 - 01:50:06 PDT)
[AMBER] installation of ambertools-- help Nyla Zaman (Thu Jul 14 2011 - 04:50:15 PDT)
- Re: [AMBER] installation of ambertools-- help David A Case (Thu Jul 14 2011 - 05:42:16 PDT)
  - Re: [AMBER] installation of ambertools-- help Nyla Zaman (Fri Jul 15 2011 - 02:57:22 PDT)
    - Re: [AMBER] installation of ambertools-- help waqasuddin.khan.iccs.edu (Fri Jul 15 2011 - 03:37:05 PDT)
    - Re: [AMBER] installation of ambertools-- help David A Case (Fri Jul 15 2011 - 05:30:48 PDT)
    - Re: [AMBER] installation of ambertools-- help Nyla Zaman (Sun Jul 17 2011 - 22:19:38 PDT)
    - Re: [AMBER] installation of ambertools-- help Daniel Roe (Mon Jul 18 2011 - 06:13:47 PDT)
- Re: [AMBER] installation of ambertools-- help Daniel Roe (Mon Jul 18 2011 - 05:31:43 PDT)
[AMBER] pmemd trajectory for mm_pbsa/gbsa analysis on sander Sangeetha B (Thu Jul 14 2011 - 07:38:40 PDT)
- Re: [AMBER] pmemd trajectory for mm_pbsa/gbsa analysis on sander David A Case (Thu Jul 14 2011 - 08:05:46 PDT)
[AMBER] Restrained MD Ozen, Aysegul (Thu Jul 14 2011 - 09:10:19 PDT)
- Re: [AMBER] Restrained MD Carlos Simmerling (Thu Jul 14 2011 - 14:22:21 PDT)
  - Re: [AMBER] Restrained MD Ozen, Aysegul (Fri Jul 15 2011 - 10:44:58 PDT)
- Re: [AMBER] Restrained MD Dmitry Nilov (Fri Jul 15 2011 - 01:45:46 PDT)
[AMBER] old prmtop and prmtop 7 Qian Wang (Thu Jul 14 2011 - 12:27:53 PDT)
- Re: [AMBER] old prmtop and prmtop 7 David A Case (Thu Jul 14 2011 - 13:15:23 PDT)
[AMBER] problem with running MMPBSA.py on a single frame Victor Ma (Thu Jul 14 2011 - 14:10:22 PDT)
[AMBER] problem with running MMPBSA.py on a single frame Victor Ma (Thu Jul 14 2011 - 14:33:27 PDT)
- Re: [AMBER] problem with running MMPBSA.py on a single frame Bill Miller III (Sun Jul 17 2011 - 09:49:39 PDT)
[AMBER] Diffusion George Tzotzos (Fri Jul 15 2011 - 05:18:17 PDT)
[AMBER] nonbond parameter for copper(Ⅱ) ion caobb0214 (Fri Jul 15 2011 - 17:29:27 PDT)
- Re: [AMBER] nonbond parameter for copper(Ⅱ) ion ros (Fri Jul 15 2011 - 18:58:06 PDT)
  - Re: [AMBER] nonbond parameter for copper(Ⅱ) ion Marek Maly (Sat Jul 16 2011 - 14:47:54 PDT)
    - Re: [AMBER] nonbond parameter for copper(Ⅱ) ion ros (Sat Jul 16 2011 - 15:35:56 PDT)
    - Re: [AMBER] nonbond parameter for copper(Ⅱ) ion Marek Maly (Sat Jul 16 2011 - 16:56:24 PDT)
[AMBER] Problem related to the Corelation Function Sindrila Dutta banik (Sat Jul 16 2011 - 07:20:53 PDT)
- Re: [AMBER] Problem related to the Corelation Function case (Sat Jul 16 2011 - 11:48:33 PDT)
  - [AMBER] Thanks Sindrila Dutta banik (Sat Jul 16 2011 - 22:43:41 PDT)
[AMBER] Problem related to the RMSD and Atomic fluctuation Sindrila Dutta banik (Sat Jul 16 2011 - 21:02:06 PDT)
- Re: [AMBER] Problem related to the RMSD and Atomic fluctuation case (Sun Jul 17 2011 - 18:51:40 PDT)
[AMBER] Error in unit 9 inpcrd file KIRTANA S (Sat Jul 16 2011 - 21:24:51 PDT)
- Re: [AMBER] Error in unit 9 inpcrd file case (Sun Jul 17 2011 - 18:40:39 PDT)
  - Re: [AMBER] Error in unit 9 inpcrd file KIRTANA S (Sun Jul 17 2011 - 19:36:23 PDT)
    - Re: [AMBER] Error in unit 9 inpcrd file jani vinod (Mon Jul 18 2011 - 02:00:53 PDT)
    - Re: [AMBER] Error in unit 9 inpcrd file case (Mon Jul 18 2011 - 04:50:10 PDT)
    - Re: [AMBER] Error in unit 9 inpcrd file KIRTANA S (Mon Jul 18 2011 - 10:21:42 PDT)
    - Re: [AMBER] Error in unit 9 inpcrd file David A Case (Mon Jul 18 2011 - 11:00:58 PDT)
    - Re: [AMBER] Error in unit 9 inpcrd file case (Mon Jul 18 2011 - 04:46:53 PDT)
- Re: [AMBER] Error in unit 9 inpcrd file KIRTANA S (Mon Jul 18 2011 - 11:44:46 PDT)
[AMBER] Problem related to the velocity correlation function Sindrila Dutta banik (Sat Jul 16 2011 - 22:48:16 PDT)
[AMBER] Tleap problem with save prmtop and inpcrd file. can someone give me advice? hai wei (Sun Jul 17 2011 - 00:27:21 PDT)
- Re: [AMBER] Tleap problem with save prmtop and inpcrd file. can someone give me advice? Jason Swails (Sun Jul 17 2011 - 03:55:09 PDT)
  - Re: [AMBER] Tleap problem with save prmtop and inpcrd file. can someone give me advice? hai wei (Sun Jul 17 2011 - 15:00:38 PDT)
    - Re: [AMBER] Tleap problem with save prmtop and inpcrd file. can someone give me advice? Jason Swails (Sun Jul 17 2011 - 15:04:43 PDT)
    - Re: [AMBER] Tleap problem with save prmtop and inpcrd file. can someone give me advice? hai wei (Sun Jul 17 2011 - 17:32:55 PDT)
    - Re: [AMBER] Tleap problem with save prmtop and inpcrd file. can someone give me advice? hai wei (Mon Jul 18 2011 - 15:51:52 PDT)
[AMBER] problem with ZAFF moitrayee.mbu.iisc.ernet.in (Sun Jul 17 2011 - 07:52:47 PDT)
- Re: [AMBER] problem with ZAFF Hashem Taha (Fri Aug 26 2011 - 07:19:49 PDT)
[AMBER] Imaging everything inside an octahedral box Daniel Kuroda (Sun Jul 17 2011 - 07:57:20 PDT)
- Re: [AMBER] Imaging everything inside an octahedral box Daniel Roe (Mon Jul 18 2011 - 06:52:14 PDT)
[AMBER] MMPBSA calculation in complex with Membrane 徐见容 (Sun Jul 17 2011 - 09:43:29 PDT)
- Re: [AMBER] MMPBSA calculation in complex with Membrane Bill Miller III (Sun Jul 17 2011 - 09:47:16 PDT)
- Re: [AMBER] MMPBSA calculation in complex with Membrane 徐见容 (Sun Jul 17 2011 - 10:19:49 PDT)
  - Re: [AMBER] MMPBSA calculation in complex with Membrane Bill Miller III (Sun Jul 17 2011 - 10:27:14 PDT)
- Re: [AMBER] MMPBSA calculation in complex with Membrane 徐见容 (Sun Jul 17 2011 - 10:48:34 PDT)
  - Re: [AMBER] MMPBSA calculation in complex with Membrane Bill Miller III (Sun Jul 17 2011 - 12:07:20 PDT)
- Re: [AMBER] MMPBSA calculation in complex with Membrane 徐见容 (Sun Jul 17 2011 - 14:12:26 PDT)
  - Re: [AMBER] MMPBSA calculation in complex with Membrane Bill Miller III (Sun Jul 17 2011 - 14:30:39 PDT)
- Re: [AMBER] MMPBSA calculation in complex with Membrane 徐见容 (Sun Jul 17 2011 - 16:33:59 PDT)
  - Re: [AMBER] MMPBSA calculation in complex with Membrane Bill Miller III (Sun Jul 17 2011 - 17:09:32 PDT)
[AMBER] using zaff parameters moitrayee.mbu.iisc.ernet.in (Sun Jul 17 2011 - 11:11:48 PDT)
[AMBER] /dat/slko DFTB files Somaye Badieyan (Sun Jul 17 2011 - 15:38:24 PDT)
- Re: [AMBER] /dat/slko DFTB files Gustavo Seabra (Sun Jul 17 2011 - 20:48:20 PDT)
[AMBER] Problem related to the Velocity correlation function Sindrila Dutta banik (Sun Jul 17 2011 - 21:31:45 PDT)
- [AMBER] Problem related to the Velocity correlation function Sindrila Dutta banik (Mon Jul 18 2011 - 05:01:40 PDT)
[AMBER] confusions about some thermodynamic properties of TIP3P water zhouhaibin2008.ok (Mon Jul 18 2011 - 01:30:47 PDT)
- Re: [AMBER] confusions about some thermodynamic properties of TIP3P water steinbrt.rci.rutgers.edu (Mon Jul 18 2011 - 02:02:01 PDT)
  - Re: [AMBER] confusions about some thermodynamic properties of TIP3P water zhouhaibin2008.ok (Mon Jul 18 2011 - 07:01:52 PDT)
[AMBER] Regarding umbrella sampling jani vinod (Mon Jul 18 2011 - 01:42:40 PDT)
[AMBER] Error with na_anal.c Chirag Vora (Mon Jul 18 2011 - 01:50:53 PDT)
- Re: [AMBER] Error with na_anal.c case (Mon Jul 18 2011 - 05:35:22 PDT)
  - Re: [AMBER] Error with na_anal.c Chirag Vora (Mon Jul 18 2011 - 06:07:57 PDT)
    - Re: [AMBER] Error with na_anal.c case (Mon Jul 18 2011 - 06:18:17 PDT)
[AMBER] Cuda compilation problem Fernando Martín García (Mon Jul 18 2011 - 02:14:35 PDT)
[AMBER] Count number of frames in any trajectory file Jan-Philip Gehrcke (Mon Jul 18 2011 - 07:45:37 PDT)
- Re: [AMBER] Count number of frames in any trajectory file Daniel Roe (Mon Jul 18 2011 - 08:32:05 PDT)
  - Re: [AMBER] Count number of frames in any trajectory file Jan-Philip Gehrcke (Mon Jul 18 2011 - 08:53:40 PDT)
    - Re: [AMBER] Count number of frames in any trajectory file Daniel Roe (Mon Jul 18 2011 - 10:10:11 PDT)
    - Re: [AMBER] Count number of frames in any trajectory file Jan-Philip Gehrcke (Mon Jul 18 2011 - 10:34:22 PDT)
  - Re: [AMBER] Count number of frames in any trajectory file Shafinaz Chowdhury (Mon Oct 15 2012 - 13:14:39 PDT)
    - Re: [AMBER] GPU accelerated - accelerated MD (Was: Count number of frames in any trajectory file) Ross Walker (Mon Oct 15 2012 - 13:44:07 PDT)
[AMBER] Related to the correlation function Sindrila Dutta banik (Mon Jul 18 2011 - 07:55:25 PDT)
- Re: [AMBER] Related to the correlation function case (Mon Jul 18 2011 - 08:07:52 PDT)
[AMBER] ptraj closest water George Tzotzos (Mon Jul 18 2011 - 09:00:59 PDT)
- Re: [AMBER] ptraj closest water Carlos Simmerling (Mon Jul 18 2011 - 09:06:46 PDT)
  - Re: [AMBER] ptraj closest water George Tzotzos (Mon Jul 18 2011 - 09:16:32 PDT)
    - Re: [AMBER] ptraj closest water Carlos Simmerling (Mon Jul 18 2011 - 09:24:11 PDT)
- Re: [AMBER] ptraj closest water Daniel Roe (Mon Jul 18 2011 - 09:19:20 PDT)
  - Re: [AMBER] ptraj closest water George Tzotzos (Mon Jul 18 2011 - 09:49:28 PDT)
    - Re: [AMBER] ptraj closest water Daniel Roe (Mon Jul 18 2011 - 10:23:07 PDT)
[AMBER] H++ protonation Massimiliano Porrini (Mon Jul 18 2011 - 09:34:23 PDT)
[AMBER] cluster MD trajectory by attribute Oliver Kuhn (Mon Jul 18 2011 - 11:01:23 PDT)
[AMBER] Periodicity in MD simulations Oliver Kuhn (Mon Jul 18 2011 - 11:17:35 PDT)
- Re: [AMBER] Periodicity in MD simulations Carlos Simmerling (Tue Jul 19 2011 - 07:42:53 PDT)
- Re: [AMBER] Periodicity in MD simulations Ignacio J. General (Tue Jul 19 2011 - 08:09:17 PDT)
- Re: [AMBER] Periodicity in MD simulations Daniel Roe (Tue Jul 19 2011 - 08:15:37 PDT)
  - Re: [AMBER] Periodicity in MD simulations Oliver Kuhn (Tue Jul 19 2011 - 22:30:43 PDT)
    - [AMBER] Fwd: Periodicity in MD simulations Oliver Kuhn (Tue Jul 19 2011 - 23:00:06 PDT)
    - [AMBER] Fwd: Periodicity in MD simulations Oliver Kuhn (Wed Jul 20 2011 - 00:43:39 PDT)
    - [AMBER] Fwd: Periodicity in MD simulations Oliver Kuhn (Wed Jul 20 2011 - 00:51:22 PDT)
    - Re: [AMBER] Fwd: Periodicity in MD simulations Ignacio J. General (Wed Jul 20 2011 - 06:29:36 PDT)
    - Re: [AMBER] Fwd: Periodicity in MD simulations Oliver Kuhn (Thu Jul 21 2011 - 01:56:18 PDT)
    - Re: [AMBER] Fwd: Periodicity in MD simulations Ross Walker (Thu Jul 21 2011 - 04:28:27 PDT)
    - Re: [AMBER] Fwd: Periodicity in MD simulations Oliver Kuhn (Thu Jul 21 2011 - 07:10:49 PDT)
[AMBER] H++ protonation Massimiliano Porrini (Mon Jul 18 2011 - 11:43:51 PDT)
- Re: [AMBER] H++ protonation Ramu Anandakrishnan (Mon Jul 18 2011 - 16:30:29 PDT)
[AMBER] confusions about some thermodynamic properties zhouhaibin2008.ok (Mon Jul 18 2011 - 17:42:13 PDT)
- Re: [AMBER] confusions about some thermodynamic properties case (Mon Jul 18 2011 - 19:40:49 PDT)
- Re: [AMBER] confusions about some thermodynamic properties steinbrt.rci.rutgers.edu (Tue Jul 19 2011 - 01:12:30 PDT)
[AMBER] Ligands and cofactors in enzymes David Cantu (Mon Jul 18 2011 - 21:54:50 PDT)
- Re: [AMBER] Ligands and cofactors in enzymes Dmitry Nilov (Mon Jul 18 2011 - 23:06:13 PDT)
- Re: [AMBER] Ligands and cofactors in enzymes Gustavo Seabra (Tue Jul 19 2011 - 03:58:31 PDT)
  - Re: [AMBER] Ligands and cofactors in enzymes David Cantu (Tue Jul 19 2011 - 07:31:38 PDT)
    - Re: [AMBER] Ligands and cofactors in enzymes Gustavo Seabra (Tue Jul 19 2011 - 08:37:02 PDT)
    - Re: [AMBER] Ligands and cofactors in enzymes David A Case (Tue Jul 19 2011 - 08:40:09 PDT)
    - Re: [AMBER] Ligands and cofactors in enzymes Gustavo Seabra (Tue Jul 19 2011 - 09:19:24 PDT)
    - Re: [AMBER] Ligands and cofactors in enzymes David Cantu (Tue Jul 19 2011 - 09:42:59 PDT)
[AMBER] PB calculation error when using MMPBSA.py zw258.cam.ac.uk (Tue Jul 19 2011 - 01:03:29 PDT)
- Re: [AMBER] PB calculation error when using MMPBSA.py Bill Miller III (Tue Jul 19 2011 - 03:28:33 PDT)
  - Re: [AMBER] PB calculation error when using MMPBSA.py zw258.cam.ac.uk (Tue Jul 19 2011 - 05:47:25 PDT)
    - Re: [AMBER] PB calculation error when using MMPBSA.py Bill Miller III (Tue Jul 19 2011 - 10:31:10 PDT)
    - Re: [AMBER] PB calculation error when using MMPBSA.py Bill Miller III (Tue Jul 19 2011 - 14:54:02 PDT)
    - Re: [AMBER] PB calculation error when using MMPBSA.py Zhi Wang (Tue Jul 19 2011 - 15:02:30 PDT)
    - Re: [AMBER] PB calculation error when using MMPBSA.py Bill Miller III (Tue Jul 19 2011 - 17:51:30 PDT)
    - Re: [AMBER] PB calculation error when using MMPBSA.py zw258.cam.ac.uk (Wed Jul 20 2011 - 01:01:45 PDT)
    - Re: [AMBER] PB calculation error when using MMPBSA.py Jason Swails (Wed Jul 20 2011 - 10:03:25 PDT)
    - Re: [AMBER] PB calculation error when using MMPBSA.py Zhi Wang (Wed Jul 20 2011 - 12:46:13 PDT)
    - Re: [AMBER] PB calculation error when using MMPBSA.py Mengjuei Hsieh (Wed Jul 20 2011 - 12:57:28 PDT)
    - Re: [AMBER] PB calculation error when using MMPBSA.py Bill Miller III (Wed Jul 20 2011 - 11:50:09 PDT)
[AMBER] Fwd: Cuda compilation problem Fernando Martín García (Tue Jul 19 2011 - 02:12:43 PDT)
[AMBER] Query about switch function using AMBER ff99SB forcefield and NAMD simulation code Madhurima Jana (Tue Jul 19 2011 - 04:42:07 PDT)
- Re: [AMBER] Query about switch function using AMBER ff99SB forcefield and NAMD simulation code Carlos Simmerling (Tue Jul 19 2011 - 08:16:05 PDT)
[AMBER] Error in ptraj trajin David Condon (Tue Jul 19 2011 - 06:11:03 PDT)
- Re: [AMBER] Error in ptraj trajin Daniel Roe (Tue Jul 19 2011 - 08:08:03 PDT)
  - Re: [AMBER] Error in ptraj trajin David Condon (Tue Jul 19 2011 - 10:28:09 PDT)
    - Re: [AMBER] Error in ptraj trajin Thomas Cheatham (Tue Jul 19 2011 - 10:53:56 PDT)
    - Re: [AMBER] Error in ptraj trajin David Condon (Tue Jul 19 2011 - 11:00:30 PDT)
[AMBER] Zero values for gbsur Daniel Aiello (Tue Jul 19 2011 - 06:36:33 PDT)
[AMBER] Fwd: cluster MD trajectory by attribute - solved Oliver Kuhn (Tue Jul 19 2011 - 07:20:38 PDT)
[AMBER] Discrepancy in Ca++ Vdw parameters considering two Amber data sources - please comment Marek Maly (Tue Jul 19 2011 - 07:33:58 PDT)
[AMBER] MMGBSA.py error Rajesh Raju (Tue Jul 19 2011 - 13:53:28 PDT)
- Re: [AMBER] MMGBSA.py error Bill Miller III (Tue Jul 19 2011 - 14:48:16 PDT)
  - Re: [AMBER] MMGBSA.py error Rajesh Raju (Tue Jul 19 2011 - 14:54:48 PDT)
    - Re: [AMBER] MMGBSA.py error Jason Swails (Tue Jul 19 2011 - 15:43:21 PDT)
[AMBER] Regarding umbrella sampling jani vinod (Tue Jul 19 2011 - 21:00:41 PDT)
- Re: [AMBER] Regarding umbrella sampling Daniel Sindhikara (Wed Jul 20 2011 - 06:26:46 PDT)
  - Re: [AMBER] Regarding umbrella sampling jani vinod (Thu Jul 21 2011 - 02:26:28 PDT)
Re: [AMBER] CUDA 4.0 Craig West (Tue Jul 19 2011 - 22:24:22 PDT)
- Re: [AMBER] CUDA 4.0 Jason Swails (Wed Jul 20 2011 - 09:58:31 PDT)
[AMBER] Amber test failure haris p (Tue Jul 19 2011 - 23:41:33 PDT)
- Re: [AMBER] Amber test failure peter.stauffert.boehringer-ingelheim.com (Wed Jul 20 2011 - 00:06:40 PDT)
[AMBER] adiabatic conformational map of carbohydrates Neha Gandhi (Wed Jul 20 2011 - 00:34:42 PDT)
[AMBER] Amber_CygWin_installation Carmen Di Giovanni (Wed Jul 20 2011 - 01:35:11 PDT)
- Re: [AMBER] Amber_CygWin_installation Daniel Roe (Wed Jul 20 2011 - 04:01:38 PDT)
[AMBER] protein-ligand-metal complex simulation Sangeetha B (Wed Jul 20 2011 - 03:25:17 PDT)
- [AMBER] protein-ligand-metal complex simulation Sangeetha B (Fri Jul 22 2011 - 03:18:40 PDT)
  - Re: [AMBER] protein-ligand-metal complex simulation David A Case (Fri Jul 22 2011 - 05:24:57 PDT)
[AMBER] CHARMM in AMBER Brian Radak (Wed Jul 20 2011 - 07:09:42 PDT)
- Re: [AMBER] CHARMM in AMBER David A Case (Wed Jul 20 2011 - 07:19:25 PDT)
- Re: [AMBER] CHARMM in AMBER Marc van der Kamp (Wed Jul 20 2011 - 08:16:31 PDT)
  - Re: [AMBER] CHARMM in AMBER Brian Radak (Wed Jul 20 2011 - 08:52:05 PDT)
    - Re: [AMBER] CHARMM in AMBER Marc van der Kamp (Wed Jul 20 2011 - 09:09:58 PDT)
    - Re: [AMBER] CHARMM in AMBER Brian Radak (Wed Jul 20 2011 - 09:21:09 PDT)
    - Re: [AMBER] CHARMM in AMBER Brian Radak (Wed Jul 20 2011 - 09:23:42 PDT)
    - Re: [AMBER] CHARMM in AMBER Brian Radak (Wed Jul 20 2011 - 13:14:12 PDT)
    - Re: [AMBER] CHARMM in AMBER Ross Walker (Wed Jul 20 2011 - 16:06:52 PDT)
    - Re: [AMBER] CHARMM in AMBER Brian Radak (Thu Jul 21 2011 - 06:05:26 PDT)
[AMBER] Urea box: artifacts or just a special distribution? Na Le Dang (Wed Jul 20 2011 - 08:57:58 PDT)
- Re: [AMBER] Urea box: artifacts or just a special distribution? David A Case (Wed Jul 20 2011 - 09:41:58 PDT)
- Re: [AMBER] Urea box: artifacts or just a special distribution? Bill Ross (Wed Jul 20 2011 - 12:27:47 PDT)
- Re: [AMBER] Urea box: artifacts or just a special distribution? Bill Ross (Wed Jul 20 2011 - 16:12:42 PDT)
  - Re: [AMBER] Urea box: artifacts or just a special distribution? Na Le Dang (Thu Jul 21 2011 - 07:53:23 PDT)
[AMBER] ions params for SPC/F water Bruno Rodrigues (Wed Jul 20 2011 - 20:39:50 PDT)
- Re: [AMBER] ions params for SPC/F water David A Case (Thu Jul 21 2011 - 05:43:21 PDT)
  - Re: [AMBER] ions params for SPC/F water Bruno Rodrigues (Thu Jul 21 2011 - 06:49:24 PDT)
- Re: [AMBER] ions params for SPC/F water Bill Ross (Fri Jul 22 2011 - 13:13:46 PDT)
[AMBER] REMD doubt : how to know the protein is not trapped in a conformation Rajeswari A. (Thu Jul 21 2011 - 04:17:02 PDT)
- Re: [AMBER] REMD doubt : how to know the protein is not trapped in a conformation Daniel Sindhikara (Thu Jul 21 2011 - 06:25:12 PDT)
  - Re: [AMBER] REMD doubt : how to know the protein is not trapped in a conformation Rajeswari A. (Thu Jul 21 2011 - 23:58:32 PDT)
[AMBER] Problem of creating trpcage TC5b amino acid sequence using "sequence" command Aimin (Thu Jul 21 2011 - 09:28:01 PDT)
- Re: [AMBER] Problem of creating trpcage TC5b amino acid sequence using "sequence" command Carlos Simmerling (Thu Jul 21 2011 - 09:34:56 PDT)
- Re: [AMBER] Problem of creating trpcage TC5b amino acid sequence using "sequence" command Emmanuel Baribefe Naziga (Thu Jul 21 2011 - 09:37:01 PDT)
  - Re: [AMBER] Problem of creating trpcage TC5b amino acid sequence using "sequence" command Aimin (Thu Jul 21 2011 - 09:58:46 PDT)
    - Re: [AMBER] Problem of creating trpcage TC5b amino acid sequence using "sequence" command Jason Swails (Thu Jul 21 2011 - 10:09:28 PDT)
    - Re: [AMBER] Problem of creating trpcage TC5b amino acid sequence using "sequence" command Aimin (Thu Jul 21 2011 - 10:19:23 PDT)
[AMBER] How to choose MMGBSA saltcon varaible value Rajesh Raju (Thu Jul 21 2011 - 16:37:49 PDT)
- Re: [AMBER] How to choose MMGBSA saltcon varaible value Jason Swails (Fri Jul 22 2011 - 07:24:06 PDT)
[AMBER] Error on installing AMBERTOOLS 1.5 ysjho (Thu Jul 21 2011 - 18:53:33 PDT)
[AMBER] problem with addIons in tleap Wei Chen (Thu Jul 21 2011 - 22:22:36 PDT)
- Re: [AMBER] problem with addIons in tleap Daniel Roe (Fri Jul 22 2011 - 04:19:28 PDT)
- Re: [AMBER] problem with addIons in tleap David A Case (Fri Jul 22 2011 - 05:15:40 PDT)
  - Re: [AMBER] problem with addIons in tleap Hirdesh Kumar (Fri Jul 22 2011 - 05:37:51 PDT)
    - Re: [AMBER] problem with addIons in tleap Wei Chen (Fri Jul 22 2011 - 11:25:04 PDT)
    - Re: [AMBER] problem with addIons in tleap Wei Chen (Fri Jul 22 2011 - 11:28:41 PDT)
- Re: [AMBER] problem with addIons in tleap Wei Chen (Fri Jul 22 2011 - 11:33:51 PDT)
  - Re: [AMBER] problem with addIons in tleap Thomas Cheatham III (Fri Jul 22 2011 - 12:33:59 PDT)
[AMBER] problem with xleap aneesh cna (Thu Jul 21 2011 - 23:55:52 PDT)
- Re: [AMBER] problem with xleap Daniel Roe (Fri Jul 22 2011 - 04:10:21 PDT)
  - Re: [AMBER] problem with xleap aneesh cna (Fri Jul 22 2011 - 05:30:41 PDT)
    - Re: [AMBER] problem with xleap Hirdesh Kumar (Fri Jul 22 2011 - 05:33:08 PDT)
[AMBER] ptraj can not read NC file. and not succeed in apply patch. hai wei (Fri Jul 22 2011 - 01:22:46 PDT)
- Re: [AMBER] ptraj can not read NC file. and not succeed in apply patch. Daniel Roe (Fri Jul 22 2011 - 04:05:44 PDT)
  - Re: [AMBER] ptraj can not read NC file. and not succeed in apply patch. hai wei (Sat Jul 23 2011 - 15:41:49 PDT)
[AMBER] MM_pbsa 刘金峰 (Fri Jul 22 2011 - 01:40:21 PDT)
- Re: [AMBER] MM_pbsa Ray Luo, Ph.D. (Fri Jul 22 2011 - 16:59:40 PDT)
  - Re: [AMBER] MM_pbsa 刘金峰 (Fri Jul 22 2011 - 17:29:25 PDT)
[AMBER] hbond vs time subrata paul (Fri Jul 22 2011 - 03:02:42 PDT)
[AMBER] H-bond vs. time Beale, John (Fri Jul 22 2011 - 03:06:46 PDT)
- Re: [AMBER] H-bond vs. time David A Case (Fri Jul 22 2011 - 05:20:11 PDT)
[AMBER] reproducing a simulation Xiao Chen (Fri Jul 22 2011 - 04:34:35 PDT)
- Re: [AMBER] reproducing a simulation Jason Swails (Fri Jul 22 2011 - 07:33:37 PDT)
  - Re: [AMBER] reproducing a simulation Xiao Chen (Sat Jul 23 2011 - 05:45:47 PDT)
    - Re: [AMBER] reproducing a simulation Jason Swails (Sat Jul 23 2011 - 09:34:13 PDT)
[AMBER] problem with unperturbed charge of the unit moitrayee.mbu.iisc.ernet.in (Fri Jul 22 2011 - 06:01:25 PDT)
[AMBER] ZAFF parameters: non integral charge moitrayee.mbu.iisc.ernet.in (Fri Jul 22 2011 - 06:27:50 PDT)
[AMBER] Make_Gnu_Win_error Carmen Di Giovanni (Fri Jul 22 2011 - 08:53:01 PDT)
- Re: [AMBER] Make_Gnu_Win_error Andreas Goetz (Sun Jul 24 2011 - 11:15:05 PDT)
- Re: [AMBER] Make_Gnu_Win_error Andreas Goetz (Wed Jul 27 2011 - 08:04:08 PDT)
[AMBER] sander.MPI is running on 8 nodes, but the output says it is running on 1 nodes M Kang (Fri Jul 22 2011 - 11:36:49 PDT)
- Re: [AMBER] sander.MPI is running on 8 nodes, but the output says it is running on 1 nodes Jason Swails (Fri Jul 22 2011 - 13:48:58 PDT)
[AMBER] Error compiling amber cuda Fabrício Bracht (Fri Jul 22 2011 - 14:30:31 PDT)
- Re: [AMBER] Error compiling amber cuda Fabrício Bracht (Fri Jul 22 2011 - 14:51:16 PDT)
- Re: [AMBER] Error compiling amber cuda Ross Walker (Fri Jul 22 2011 - 14:55:47 PDT)
  - Re: [AMBER] Error compiling amber cuda Fabrício Bracht (Fri Jul 22 2011 - 17:15:57 PDT)
    - Re: [AMBER] Error compiling amber cuda Jason Swails (Fri Jul 22 2011 - 18:38:31 PDT)
    - Re: [AMBER] Error compiling amber cuda Fabrício Bracht (Sat Jul 23 2011 - 07:29:37 PDT)
    - Re: [AMBER] Error compiling amber cuda Ross Walker (Sat Jul 23 2011 - 09:23:22 PDT)
    - Re: [AMBER] Error compiling amber cuda Fabrício Bracht (Sat Jul 23 2011 - 13:22:35 PDT)
    - Re: [AMBER] Error compiling amber cuda Fabrício Bracht (Mon Jul 25 2011 - 08:54:41 PDT)
    - Re: [AMBER] Error compiling amber cuda Ross Walker (Mon Jul 25 2011 - 09:53:25 PDT)
    - Re: [AMBER] Error compiling amber cuda Fabrício Bracht (Mon Jul 25 2011 - 10:10:32 PDT)
    - Re: [AMBER] Error compiling amber cuda Ross Walker (Mon Jul 25 2011 - 11:20:19 PDT)
    - Re: [AMBER] Error compiling amber cuda Fabrício Bracht (Mon Jul 25 2011 - 16:18:13 PDT)
    - Re: [AMBER] Error compiling amber cuda Jason Swails (Mon Jul 25 2011 - 18:26:57 PDT)
- Re: [AMBER] Error compiling amber cuda Ross Walker (Fri Jul 22 2011 - 16:38:58 PDT)
[AMBER] Problem with MMPBSA.py Seungyeul Yoo (Fri Jul 22 2011 - 15:15:18 PDT)
- Re: [AMBER] Problem with MMPBSA.py Jason Swails (Fri Jul 22 2011 - 18:30:41 PDT)
  - Re: [AMBER] Problem with MMPBSA.py Seungyeul Yoo (Fri Jul 22 2011 - 23:07:14 PDT)
    - Re: [AMBER] Problem with MMPBSA.py Bill Miller III (Sat Jul 23 2011 - 05:57:50 PDT)
    - Re: [AMBER] Problem with MMPBSA.py Seungyeul Yoo (Sat Jul 23 2011 - 08:05:08 PDT)
[AMBER] configure_error Carmen Di Giovanni (Tue Jul 19 2011 - 10:44:37 PDT)
- Re: [AMBER] configure_error Daniel Roe (Sat Jul 23 2011 - 10:50:04 PDT)
[AMBER] create walls amir abbasi (Sat Jul 23 2011 - 05:27:49 PDT)
- Re: [AMBER] create walls Jason Swails (Sat Jul 23 2011 - 09:22:03 PDT)
  - Re: [AMBER] create walls amir abbasi (Mon Jul 25 2011 - 04:07:51 PDT)
    - Re: [AMBER] create walls Jason Swails (Mon Jul 25 2011 - 18:17:20 PDT)
    - Re: [AMBER] create walls amir abbasi (Wed Jul 27 2011 - 06:36:56 PDT)
    - Re: [AMBER] create walls steinbrt.rci.rutgers.edu (Wed Jul 27 2011 - 07:51:51 PDT)
    - Re: [AMBER] create walls amir abbasi (Thu Jul 28 2011 - 01:15:13 PDT)
    - Re: [AMBER] create walls steinbrt.rci.rutgers.edu (Thu Jul 28 2011 - 03:56:49 PDT)
[AMBER] amber11 forcefield Roy Lee (Mon Jul 25 2011 - 02:13:34 PDT)
[AMBER] Cannot find MMPBSA.MPI Rajesh Raju (Mon Jul 25 2011 - 15:23:08 PDT)
- Re: [AMBER] Cannot find MMPBSA.MPI Jason Swails (Mon Jul 25 2011 - 18:15:51 PDT)
[AMBER] breaking down amber parameter file to create fragments of original molecule using tleap g t (Mon Jul 25 2011 - 19:49:44 PDT)
[AMBER] Failure kReduceSoluteCOM with GPU Fabrício Bracht (Mon Jul 25 2011 - 20:44:10 PDT)
- Re: [AMBER] Failure kReduceSoluteCOM with GPU Scott Brozell (Mon Jul 25 2011 - 23:27:37 PDT)
  - Re: [AMBER] Failure kReduceSoluteCOM with GPU Fabrício Bracht (Tue Jul 26 2011 - 06:07:28 PDT)
    - Re: [AMBER] Failure kReduceSoluteCOM with GPU Fabrício Bracht (Tue Jul 26 2011 - 16:04:27 PDT)
    - Re: [AMBER] Failure kReduceSoluteCOM with GPU Scott Brozell (Tue Jul 26 2011 - 23:55:01 PDT)
    - Re: [AMBER] Failure kReduceSoluteCOM with GPU Fabrício Bracht (Wed Jul 27 2011 - 08:52:31 PDT)
    - Re: [AMBER] Failure kReduceSoluteCOM with GPU Ross Walker (Wed Jul 27 2011 - 10:28:18 PDT)
    - Re: [AMBER] Failure kReduceSoluteCOM with GPU Fabrício Bracht (Wed Jul 27 2011 - 12:05:22 PDT)
    - Re: [AMBER] Failure kReduceSoluteCOM with GPU Ross Walker (Wed Jul 27 2011 - 14:57:12 PDT)
    - Re: [AMBER] Failure kReduceSoluteCOM with GPU Fabrício Bracht (Fri Jul 29 2011 - 10:42:33 PDT)
    - Re: [AMBER] Failure kReduceSoluteCOM with GPU Scott Le Grand (Sat Jul 30 2011 - 09:51:32 PDT)
    - Re: [AMBER] Failure kReduceSoluteCOM with GPU Ross Walker (Sat Jul 30 2011 - 13:15:22 PDT)
    - Re: [AMBER] Failure kReduceSoluteCOM with GPU Fabrício Bracht (Sat Jul 30 2011 - 19:26:25 PDT)
  - Re: [AMBER] Failure kReduceSoluteCOM with GPU Scott Le Grand (Mon Aug 01 2011 - 19:09:06 PDT)
    - Re: [AMBER] Failure kReduceSoluteCOM with GPU Ismail, Mohd F. (Tue Aug 09 2011 - 07:47:05 PDT)
    - Re: [AMBER] Failure kReduceSoluteCOM with GPU Scott Le Grand (Tue Aug 09 2011 - 09:03:23 PDT)
    - Re: [AMBER] Failure kReduceSoluteCOM with GPU Jason Swails (Tue Aug 09 2011 - 09:15:05 PDT)
    - Re: [AMBER] Failure kReduceSoluteCOM with GPU Scott Le Grand (Tue Aug 09 2011 - 10:28:34 PDT)
    - Re: [AMBER] Failure kReduceSoluteCOM with GPU Ismail, Mohd F. (Tue Aug 09 2011 - 11:14:33 PDT)
    - Re: [AMBER] Failure kReduceSoluteCOM with GPU Scott Le Grand (Tue Aug 09 2011 - 11:29:01 PDT)
[AMBER] MMPBSA.MPI running error problem Rajesh Raju (Mon Jul 25 2011 - 22:16:32 PDT)
- Re: [AMBER] MMPBSA.MPI running error problem Scott Brozell (Mon Jul 25 2011 - 23:37:18 PDT)
[AMBER] problem installing amber 10 Nyla Zaman (Mon Jul 25 2011 - 22:33:35 PDT)
- Re: [AMBER] problem installing amber 10 Scott Brozell (Mon Jul 25 2011 - 23:55:34 PDT)
- Re: [AMBER] problem installing amber 10 amir abbasi (Tue Jul 26 2011 - 01:42:57 PDT)
- Re: [AMBER] problem installing amber 10 Ali Faruqi (Tue Jul 26 2011 - 01:43:28 PDT)
  - Re: [AMBER] problem installing amber 10 Nyla Zaman (Tue Jul 26 2011 - 02:19:56 PDT)
    - Re: [AMBER] problem installing amber 10 Ali Faruqi (Tue Jul 26 2011 - 03:53:19 PDT)
    - Re: [AMBER] problem installing amber 10 amir abbasi (Tue Jul 26 2011 - 04:40:54 PDT)
    - Re: [AMBER] problem installing amber 10 Nyla Zaman (Tue Jul 26 2011 - 22:28:14 PDT)
    - Re: [AMBER] problem installing amber 10 Scott Brozell (Tue Jul 26 2011 - 23:59:23 PDT)
    - Re: [AMBER] problem installing amber 10 case (Tue Jul 26 2011 - 06:39:51 PDT)
[AMBER] Steered dynamics related questions Sergey Samsonov (Tue Jul 26 2011 - 02:32:22 PDT)
- Re: [AMBER] Steered dynamics related questions Adrian Roitberg (Tue Jul 26 2011 - 03:01:05 PDT)
  - Re: [AMBER] Steered dynamics related questions Sergey Samsonov (Tue Jul 26 2011 - 03:49:50 PDT)
    - Re: [AMBER] Steered dynamics related questions Dmitry Nilov (Tue Jul 26 2011 - 08:03:28 PDT)
  - Re: [AMBER] Steered dynamics related questions Bruno Rodrigues (Tue Jul 26 2011 - 12:15:45 PDT)
    - Re: [AMBER] Steered dynamics related questions Adrian Roitberg (Tue Jul 26 2011 - 12:21:17 PDT)
    - Re: [AMBER] Steered dynamics related questions Bruno Rodrigues (Tue Jul 26 2011 - 12:31:45 PDT)
    - Re: [AMBER] Steered dynamics related questions Daniel Roe (Tue Jul 26 2011 - 13:26:03 PDT)
- Re: [AMBER] Steered dynamics related questions Bill Ross (Tue Jul 26 2011 - 10:52:55 PDT)
  - Re: [AMBER] Steered dynamics related questions Sergey Samsonov (Thu Jul 28 2011 - 02:49:41 PDT)
[AMBER] Element definition amir abbasi (Tue Jul 26 2011 - 04:45:35 PDT)
[AMBER] belly energies Ignacio J. General (Tue Jul 26 2011 - 07:29:30 PDT)
[AMBER] selective qmshake? Brian Radak (Tue Jul 26 2011 - 08:57:10 PDT)
- Re: [AMBER] selective qmshake? Adrian Roitberg (Tue Jul 26 2011 - 09:03:43 PDT)
  - Re: [AMBER] selective qmshake? Vitor Felix (Tue Jul 26 2011 - 09:20:11 PDT)
- Re: [AMBER] selective qmshake? Ross Walker (Tue Jul 26 2011 - 09:40:40 PDT)
  - Re: [AMBER] selective qmshake? Brian Radak (Tue Jul 26 2011 - 11:29:50 PDT)
    - Re: [AMBER] selective qmshake? Jason Swails (Tue Jul 26 2011 - 16:57:29 PDT)
[AMBER] SYBYL to GAFF atom types David Cantu (Tue Jul 26 2011 - 09:36:52 PDT)
- Re: [AMBER] SYBYL to GAFF atom types case (Wed Jul 27 2011 - 06:57:56 PDT)
  - Re: [AMBER] SYBYL to GAFF atom types David Cantu (Wed Jul 27 2011 - 08:08:30 PDT)
[AMBER] vdW issues during TI Emmanuel Baribefe Naziga (Tue Jul 26 2011 - 11:11:57 PDT)
- Re: [AMBER] vdW issues during TI Niel Henriksen (Tue Jul 26 2011 - 15:00:58 PDT)
  - Re: [AMBER] vdW issues during TI Emmanuel Baribefe Naziga (Tue Jul 26 2011 - 17:14:01 PDT)
[AMBER] force field issues using AT15 Peter Varnai (Tue Jul 26 2011 - 14:11:19 PDT)
- Re: [AMBER] force field issues using AT15 Jason Swails (Tue Jul 26 2011 - 16:41:38 PDT)
  - Re: [AMBER] force field issues using AT15 Peter Varnai (Wed Jul 27 2011 - 05:26:58 PDT)
    - Re: [AMBER] force field issues using AT15 case (Wed Jul 27 2011 - 07:07:51 PDT)
    - Re: [AMBER] force field issues using AT15 Jason Swails (Wed Jul 27 2011 - 12:30:29 PDT)
[AMBER] CHARMM format to Amber format David Cantu (Tue Jul 26 2011 - 14:49:55 PDT)
- Re: [AMBER] CHARMM format to Amber format Jason Swails (Tue Jul 26 2011 - 16:26:46 PDT)
  - Re: [AMBER] CHARMM format to Amber format David Cantu (Wed Jul 27 2011 - 08:11:11 PDT)
    - Re: [AMBER] CHARMM format to Amber format Ross Walker (Wed Jul 27 2011 - 10:22:35 PDT)
    - Re: [AMBER] CHARMM format to Amber format David Cantu (Mon Aug 01 2011 - 09:59:36 PDT)
    - Re: [AMBER] CHARMM format to Amber format Ross Walker (Mon Aug 01 2011 - 10:30:03 PDT)
    - Re: [AMBER] CHARMM format to Amber format David Cantu (Mon Aug 01 2011 - 12:29:41 PDT)
[AMBER] Problem with MMPBSA.py Roman Osman (Tue Jul 26 2011 - 15:18:22 PDT)
- Re: [AMBER] Problem with MMPBSA.py Ray Luo, Ph.D. (Tue Jul 26 2011 - 15:21:05 PDT)
  - Re: [AMBER] Problem with MMPBSA.py Roman Osman (Tue Jul 26 2011 - 15:23:58 PDT)
    - Re: [AMBER] Problem with MMPBSA.py Ray Luo, Ph.D. (Tue Jul 26 2011 - 15:36:42 PDT)
    - Re: [AMBER] Problem with MMPBSA.py Jason Swails (Tue Jul 26 2011 - 16:23:36 PDT)
    - Re: [AMBER] Problem with MMPBSA.py Roman Osman (Tue Jul 26 2011 - 17:52:54 PDT)
    - Re: [AMBER] Problem with MMPBSA.py Roman Osman (Fri Jul 29 2011 - 11:53:34 PDT)
    - Re: [AMBER] Problem with MMPBSA.py Ray Luo, Ph.D. (Fri Jul 29 2011 - 15:51:22 PDT)
    - Re: [AMBER] Problem with MMPBSA.py Roman Osman (Sat Jul 30 2011 - 11:04:31 PDT)
[AMBER] Ptraj and glibc error Maura Catherine Mooney (Tue Jul 26 2011 - 17:34:37 PDT)
[AMBER] Problems installing AMBER 11 Carlos P Sosa (Tue Jul 26 2011 - 19:04:40 PDT)
- Re: [AMBER] Problems installing AMBER 11 Jason Swails (Tue Jul 26 2011 - 21:37:12 PDT)
  - Re: [AMBER] Problems installing AMBER 11 Carlos Sosa (Wed Jul 27 2011 - 10:25:39 PDT)
    - Re: [AMBER] Problems installing AMBER 11 Jason Swails (Wed Jul 27 2011 - 11:51:44 PDT)
[AMBER] (NAB issue) wc_helix : Problem in creating RNA structures Anjan Dwaraknath (Wed Jul 27 2011 - 03:03:52 PDT)
- Re: [AMBER] (NAB issue) wc_helix : Problem in creating RNA structures Anjan Dwaraknath (Wed Jul 27 2011 - 03:56:58 PDT)
- Re: [AMBER] (NAB issue) wc_helix : Problem in creating RNA structures case (Fri Jul 29 2011 - 07:32:07 PDT)
[AMBER] Script to run mm_pbsa.pl for ENTROPY calculation in parallel on workstation Azat Mukhametov (Wed Jul 27 2011 - 03:20:42 PDT)
- Re: [AMBER] Script to run mm_pbsa.pl for ENTROPY calculation in parallel on workstation Bill Miller III (Wed Jul 27 2011 - 03:26:50 PDT)
[AMBER] CHAMBER: problems reading bond parameters in charmm parameter file Patrick von Glehn (Wed Jul 27 2011 - 04:27:10 PDT)
[AMBER] Problem with removing Hydrogen in trajectory file using prtaj Devlina Chakravarty (Wed Jul 27 2011 - 05:23:17 PDT)
- Re: [AMBER] Problem with removing Hydrogen in trajectory file using prtaj Daniel Roe (Wed Jul 27 2011 - 06:04:40 PDT)
- Re: [AMBER] Problem with removing Hydrogen in trajectory file using prtaj Daniel Roe (Wed Jul 27 2011 - 06:07:41 PDT)
[AMBER] idecomp and res card Elisa Frezza (Wed Jul 27 2011 - 06:28:13 PDT)
- Re: [AMBER] idecomp and res card Jason Swails (Wed Jul 27 2011 - 12:33:09 PDT)
  - Re: [AMBER] idecomp and res card Elisa Frezza (Wed Jul 27 2011 - 12:36:31 PDT)
    - Re: [AMBER] idecomp and res card Jason Swails (Wed Jul 27 2011 - 14:52:14 PDT)
    - Re: [AMBER] idecomp and res card Elisa Frezza (Thu Jul 28 2011 - 01:21:22 PDT)
[AMBER] Problem related to the RMSD Sindrila Dutta banik (Wed Jul 27 2011 - 07:02:45 PDT)
- Re: [AMBER] Problem related to the RMSD Daniel Roe (Wed Jul 27 2011 - 10:52:24 PDT)
[AMBER] Changing the L-J parameter does not work? bkim.chem.ucsb.edu (Wed Jul 27 2011 - 09:58:41 PDT)
- Re: [AMBER] Changing the L-J parameter does not work? InSuk Joung (Wed Jul 27 2011 - 11:24:25 PDT)
  - Re: [AMBER] Changing the L-J parameter does not work? Bongkeun Kim (Wed Jul 27 2011 - 12:18:04 PDT)
    - Re: [AMBER] Changing the L-J parameter does not work? InSuk Joung (Wed Jul 27 2011 - 12:40:28 PDT)
    - Re: [AMBER] Changing the L-J parameter does not work? Bongkeun Kim (Wed Jul 27 2011 - 12:49:23 PDT)
    - Re: [AMBER] Changing the L-J parameter does not work? InSuk Joung (Wed Jul 27 2011 - 12:58:20 PDT)
    - Re: [AMBER] Changing the L-J parameter does not work? Bongkeun Kim (Wed Jul 27 2011 - 13:59:53 PDT)
[AMBER] nmropt on dihedral angles, are half harmonic restraints possible? Brian Radak (Wed Jul 27 2011 - 11:39:41 PDT)
- Re: [AMBER] nmropt on dihedral angles, are half harmonic restraints possible? case (Thu Jul 28 2011 - 07:33:52 PDT)
[AMBER] AMBER10 pimd failure on =>16 cores Andrew Petersen (Wed Jul 27 2011 - 14:22:02 PDT)
[AMBER] MMGBSA of Mg-containing ligand Irene Newhouse (Wed Jul 27 2011 - 14:57:02 PDT)
[AMBER] Oxygen Gaff Atom Type David Cantu (Wed Jul 27 2011 - 15:19:41 PDT)
- Re: [AMBER] Oxygen Gaff Atom Type David Case (Wed Jul 27 2011 - 16:24:32 PDT)
  - Re: [AMBER] Oxygen Gaff Atom Type David Cantu (Thu Jul 28 2011 - 10:29:10 PDT)
[AMBER] MMPBSA yielding different values when processed with .prepin and .lib file sunita gupta (Thu Jul 28 2011 - 01:14:41 PDT)
[AMBER] alpha 2-3 Sialyllactose in GLYCAM mish (Thu Jul 28 2011 - 02:29:40 PDT)
- Re: [AMBER] alpha 2-3 Sialyllactose in GLYCAM Oliver Grant (Thu Jul 28 2011 - 02:57:27 PDT)
[AMBER] hbond analysis subrata paul (Thu Jul 28 2011 - 02:51:11 PDT)
- Re: [AMBER] hbond analysis Bruno Rodrigues (Thu Jul 28 2011 - 09:45:10 PDT)
[AMBER] Problem related to the RMSD Sindrila Dutta banik (Thu Jul 28 2011 - 03:25:30 PDT)
- Re: [AMBER] Problem related to the RMSD Bruno Rodrigues (Wed Aug 03 2011 - 02:15:21 PDT)
[AMBER] Sorry Sindrila Dutta banik (Thu Jul 28 2011 - 03:29:38 PDT)
[AMBER] Energy or Temperature Fluctuation Sindrila Dutta banik (Thu Jul 28 2011 - 03:44:56 PDT)
- Re: [AMBER] Energy or Temperature Fluctuation Bruno Rodrigues (Wed Aug 03 2011 - 02:14:19 PDT)
[AMBER] sander problem lawrence awadetsi (Thu Jul 28 2011 - 10:48:38 PDT)
- Re: [AMBER] sander problem Carlos Simmerling (Thu Jul 28 2011 - 11:00:20 PDT)
  - Re: [AMBER] sander problem lawrence awadetsi (Thu Jul 28 2011 - 11:19:32 PDT)
    - Re: [AMBER] sander problem Carlos Simmerling (Thu Jul 28 2011 - 11:26:08 PDT)
Re: [AMBER] alpha 2-3 Sialyllactose in GLYCAM, Matthew Tessier (Thu Jul 28 2011 - 11:13:10 PDT)
- Re: [AMBER] alpha 2-3 Sialyllactose in GLYCAM, mish (Fri Jul 29 2011 - 01:06:48 PDT)
  - Re: [AMBER] alpha 2-3 Sialyllactose in GLYCAM, Dean Cuebas (Sat Jul 30 2011 - 15:58:53 PDT)
- Re: [AMBER] alpha 2-3 Sialyllactose in GLYCAM, Matthew Tessier (Fri Jul 29 2011 - 05:47:12 PDT)
[AMBER] Energy output when using ibelly Ignacio J. General (Thu Jul 28 2011 - 12:48:46 PDT)
- Re: [AMBER] Energy output when using ibelly Brian Radak (Thu Jul 28 2011 - 12:59:51 PDT)
- Re: [AMBER] Energy output when using ibelly Ross Walker (Thu Jul 28 2011 - 13:03:33 PDT)
  - Re: [AMBER] Energy output when using ibelly Ignacio J. General (Thu Jul 28 2011 - 13:16:34 PDT)
- Re: [AMBER] Energy output when using ibelly David Case (Thu Jul 28 2011 - 15:15:29 PDT)
  - Re: [AMBER] Energy output when using ibelly Ignacio J. General (Fri Jul 29 2011 - 07:13:38 PDT)
    - Re: [AMBER] Energy output when using ibelly case (Fri Jul 29 2011 - 07:44:43 PDT)
    - Re: [AMBER] Energy output when using ibelly Ignacio J. General (Fri Jul 29 2011 - 07:55:10 PDT)
    - Re: [AMBER] Energy output when using ibelly case (Fri Jul 29 2011 - 08:34:05 PDT)
    - Re: [AMBER] Energy output when using ibelly Jason Swails (Sat Jul 30 2011 - 14:17:58 PDT)
[AMBER] possible problem with periodic cell Bruno Rodrigues (Thu Jul 28 2011 - 14:01:32 PDT)
- Re: [AMBER] possible problem with periodic cell Bill Ross (Thu Jul 28 2011 - 14:34:08 PDT)
  - Re: [AMBER] possible problem with periodic cell Bruno Rodrigues (Thu Jul 28 2011 - 14:55:02 PDT)
[AMBER] AMBER/sander parallel performance problem Jyh-Shyong (Thu Jul 28 2011 - 17:00:27 PDT)
- Re: [AMBER] AMBER/sander parallel performance problem Niel Henriksen (Thu Jul 28 2011 - 17:16:49 PDT)
  - Re: [AMBER] AMBER/sander parallel performance problem Niel Henriksen (Thu Jul 28 2011 - 17:18:43 PDT)
- Re: [AMBER] AMBER/sander parallel performance problem case (Thu Jul 28 2011 - 17:18:43 PDT)
- Re: [AMBER] AMBER/sander parallel performance problem Ross Walker (Thu Jul 28 2011 - 17:29:10 PDT)
  - Re: [AMBER] AMBER/sander parallel performance problem Jyh-Shyong (Thu Jul 28 2011 - 19:15:03 PDT)
  - Re: [AMBER] AMBER/sander parallel performance problem Jyh-Shyong (Thu Jul 28 2011 - 17:57:06 PDT)
[AMBER] Volume of a Cavity Sindrila Dutta banik (Fri Jul 29 2011 - 03:08:31 PDT)
[AMBER] MMPBSA.py - cluster analysis George Tzotzos (Fri Jul 29 2011 - 06:21:25 PDT)
- Re: [AMBER] MMPBSA.py - cluster analysis Bill Miller III (Fri Jul 29 2011 - 06:56:17 PDT)
  - Re: [AMBER] MMPBSA.py - cluster analysis George Tzotzos (Fri Jul 29 2011 - 07:58:47 PDT)
    - Re: [AMBER] MMPBSA.py - cluster analysis Bill Miller III (Fri Jul 29 2011 - 08:09:29 PDT)
    - Re: [AMBER] MMPBSA.py - cluster analysis George Tzotzos (Fri Jul 29 2011 - 08:35:11 PDT)
    - Re: [AMBER] MMPBSA.py - cluster analysis Roman Osman (Fri Jul 29 2011 - 08:41:34 PDT)
[AMBER] question about possible failures during Amber10 and AmberTools1.2 Gordon Freeman (Fri Jul 29 2011 - 06:58:02 PDT)
- Re: [AMBER] question about possible failures during Amber10 and AmberTools1.2 Jason Swails (Sat Jul 30 2011 - 13:45:20 PDT)
[AMBER] distance and angle cutoff for hydrogen bond atila petrosian (Sat Jul 30 2011 - 05:04:08 PDT)
[AMBER] chiral restraints in AMBER David Condon (Sat Jul 30 2011 - 16:55:05 PDT)
- Re: [AMBER] chiral restraints in AMBER Ilyas Yildirim (Sat Jul 30 2011 - 20:39:21 PDT)
  - Re: [AMBER] chiral restraints in AMBER David Condon (Sun Jul 31 2011 - 04:40:48 PDT)
[AMBER] Parm .dat format and frcmod tdo.chem.ucsb.edu (Sat Jul 30 2011 - 23:29:32 PDT)
- Re: [AMBER] Parm .dat format and frcmod Thomas Gaillard (Sun Jul 31 2011 - 04:42:46 PDT)
[AMBER] Proble related to with dipole-dipole correlation function Sindrila Dutta banik (Sun Jul 31 2011 - 04:54:39 PDT)
- [AMBER] Proble related to with dipole-dipole correlation function Sindrila Dutta banik (Mon Aug 01 2011 - 04:55:42 PDT)
[AMBER] Protein-sugar interactions Thomas Exner (Mon Aug 01 2011 - 06:03:59 PDT)
- Re: [AMBER] Protein-sugar interactions David A Case (Mon Aug 01 2011 - 06:46:01 PDT)
  - Re: [AMBER] Protein-sugar interactions Lachele Foley (Lists) (Mon Aug 01 2011 - 08:27:29 PDT)
[AMBER] Announcement: Release of DOCK 6.5 Scott Brozell (Mon Aug 01 2011 - 07:11:33 PDT)
[AMBER] loadPdb segmentation fault Massimiliano Porrini (Mon Aug 01 2011 - 09:18:51 PDT)
- Re: [AMBER] loadPdb segmentation fault David A Case (Mon Aug 01 2011 - 09:50:03 PDT)
  - Re: [AMBER] loadPdb segmentation fault Massimiliano Porrini (Mon Aug 01 2011 - 10:09:20 PDT)
    - Re: [AMBER] loadPdb segmentation fault David A Case (Mon Aug 01 2011 - 13:03:45 PDT)
    - Re: [AMBER] loadPdb segmentation fault Jason Swails (Mon Aug 01 2011 - 13:53:57 PDT)
    - Re: [AMBER] loadPdb segmentation fault Massimiliano Porrini (Tue Aug 02 2011 - 13:42:10 PDT)
    - Re: [AMBER] loadPdb segmentation fault Jason Swails (Tue Aug 02 2011 - 20:08:45 PDT)
    - Re: [AMBER] loadPdb segmentation fault Jason Swails (Tue Aug 02 2011 - 21:38:22 PDT)
    - Re: [AMBER] loadPdb segmentation fault Massimiliano Porrini (Wed Aug 03 2011 - 03:08:30 PDT)
    - Re: [AMBER] loadPdb segmentation fault Jason Swails (Wed Aug 03 2011 - 06:43:33 PDT)
    - Re: [AMBER] loadPdb segmentation fault Massimiliano Porrini (Wed Aug 03 2011 - 08:08:18 PDT)
    - Re: [AMBER] loadPdb segmentation fault Jason Swails (Wed Aug 03 2011 - 09:15:17 PDT)
- Re: [AMBER] loadPdb segmentation fault Bill Ross (Wed Aug 03 2011 - 14:47:19 PDT)
[AMBER] About running sander parallel Aimin (Mon Aug 01 2011 - 11:04:36 PDT)
- Re: [AMBER] About running sander parallel Ross Walker (Mon Aug 01 2011 - 11:21:20 PDT)
  - Re: [AMBER] About running sander parallel Aimin (Mon Aug 01 2011 - 11:39:54 PDT)
  - Re: [AMBER] About running sander parallel Aimin (Mon Aug 01 2011 - 16:41:52 PDT)
    - Re: [AMBER] About running sander parallel Ross Walker (Mon Aug 01 2011 - 17:25:06 PDT)
    - Re: [AMBER] About running sander parallel Aimin (Mon Aug 01 2011 - 18:07:28 PDT)
    - Re: [AMBER] About running sander parallel Ross Walker (Mon Aug 01 2011 - 18:31:28 PDT)
    - Re: [AMBER] About running sander parallel Jason Swails (Mon Aug 01 2011 - 20:37:30 PDT)
    - Re: [AMBER] About running sander parallel Aimin (Tue Aug 02 2011 - 16:56:22 PDT)
    - Re: [AMBER] About running sander parallel Jason Swails (Tue Aug 02 2011 - 17:09:44 PDT)
[AMBER] MMGBSA error Irene Newhouse (Mon Aug 01 2011 - 14:00:16 PDT)
- Re: [AMBER] MMGBSA error Jason Swails (Mon Aug 01 2011 - 17:52:09 PDT)
[AMBER] Using NMR restraints during minimization Kamali Sripathi (Mon Aug 01 2011 - 14:57:50 PDT)
- Re: [AMBER] Using NMR restraints during minimization Jason Swails (Mon Aug 01 2011 - 20:41:11 PDT)
  - Re: [AMBER] Using NMR restraints during minimization Kamali Sripathi (Tue Aug 02 2011 - 04:31:33 PDT)
    - Re: [AMBER] Using NMR restraints during minimization Jason Swails (Tue Aug 02 2011 - 04:51:49 PDT)
    - Re: [AMBER] Using NMR restraints during minimization Kamali Sripathi (Tue Aug 02 2011 - 12:48:14 PDT)
    - Re: [AMBER] Using NMR restraints during minimization case (Tue Aug 02 2011 - 05:49:49 PDT)
    - Re: [AMBER] Using NMR restraints during minimization Kamali Sripathi (Tue Aug 02 2011 - 12:49:57 PDT)
[AMBER] ambpdb not installed Chirag Vora (Mon Aug 01 2011 - 20:58:53 PDT)
- Re: [AMBER] ambpdb not installed Bruno Rodrigues (Tue Aug 02 2011 - 02:07:30 PDT)
  - Re: [AMBER] ambpdb not installed Bruno Rodrigues (Tue Aug 02 2011 - 02:09:04 PDT)
    - Re: [AMBER] ambpdb not installed Chirag Vora (Tue Aug 02 2011 - 02:33:08 PDT)
- Re: [AMBER] ambpdb not installed Jason Swails (Tue Aug 02 2011 - 04:53:14 PDT)
[AMBER] QUASI-HARMONIC APPROXIMATION belal najjar (Mon Aug 01 2011 - 21:25:03 PDT)
- Re: [AMBER] QUASI-HARMONIC APPROXIMATION Bill Miller III (Tue Aug 02 2011 - 03:30:19 PDT)
  - Re: [AMBER] QUASI-HARMONIC APPROXIMATION belal najjar (Wed Aug 03 2011 - 18:16:27 PDT)
    - Re: [AMBER] QUASI-HARMONIC APPROXIMATION Bill Miller III (Thu Aug 04 2011 - 11:06:45 PDT)
    - Re: [AMBER] QUASI-HARMONIC APPROXIMATION belal najjar (Thu Aug 04 2011 - 18:24:14 PDT)
    - Re: [AMBER] QUASI-HARMONIC APPROXIMATION Bill Miller III (Sat Aug 06 2011 - 05:38:07 PDT)
- Re: [AMBER] QUASI-HARMONIC APPROXIMATION belal najjar (Wed Aug 10 2011 - 17:41:34 PDT)
[AMBER] 2011年7月20日 19:53:32 自动保存草稿 zhouhaibin2008.ok (Tue Aug 02 2011 - 01:20:53 PDT)
- Re: [AMBER] 2011年7月20日 19:53:32 自动保存草稿 Jason Swails (Tue Aug 02 2011 - 04:35:38 PDT)
  - [AMBER] Problems when I wanted to restart the MD production zhouhaibin2008.ok (Wed Aug 03 2011 - 18:26:35 PDT)
    - Re: [AMBER] Problems when I wanted to restart the MD production Jason Swails (Wed Aug 03 2011 - 19:31:04 PDT)
    - Re: [AMBER] Problems when I wanted to restart the MD production zhouhaibin2008.ok (Wed Aug 03 2011 - 19:49:09 PDT)
    - Re: [AMBER] Problems when I wanted to restart the MD production Bill Ross (Wed Aug 03 2011 - 22:48:40 PDT)
    - Re: [AMBER] Problems when I wanted to restart the MD production Jason Swails (Thu Aug 04 2011 - 07:44:32 PDT)
  - [AMBER] EPTOT shows big difference between the different force fields zhouhaibin2008.ok (Thu Aug 04 2011 - 17:33:00 PDT)
  - [AMBER] EPTOT shows big difference between the different force fields zhouhaibin2008.ok (Thu Aug 04 2011 - 20:58:14 PDT)
    - Re: [AMBER] EPTOT shows big difference between the different force fields Carlos Simmerling (Fri Aug 05 2011 - 03:25:21 PDT)
    - Re: [AMBER] EPTOT shows big difference between the different force fields Jason Swails (Fri Aug 05 2011 - 21:59:55 PDT)
    - Re: [AMBER] EPTOT shows big difference between the different force fields zhouhaibin2008.ok (Fri Aug 05 2011 - 22:41:06 PDT)
[AMBER] Movement of molecules to satisfy distance constraints David Condon (Tue Aug 02 2011 - 05:24:50 PDT)
- Re: [AMBER] Movement of molecules to satisfy distance constraints David A Case (Tue Aug 02 2011 - 09:26:31 PDT)
  - Re: [AMBER] Movement of molecules to satisfy distance constraints David Condon (Tue Aug 02 2011 - 10:35:46 PDT)
[AMBER] Fwd: Problem with MMPBSA.py Ray Luo, Ph.D. (Tue Aug 02 2011 - 09:08:36 PDT)
- Re: [AMBER] Problem with MMPBSA.py Osman, Roman (Sun Aug 21 2011 - 07:23:41 PDT)
  - Re: [AMBER] Problem with MMPBSA.py Seungyeul Yoo (Mon Aug 22 2011 - 08:27:19 PDT)
    - Re: [AMBER] Problem with MMPBSA.py Osman, Roman (Mon Aug 22 2011 - 09:12:37 PDT)
    - Re: [AMBER] Problem with MMPBSA.py Jan-Philip Gehrcke (Mon Aug 22 2011 - 09:42:58 PDT)
    - Re: [AMBER] Problem with MMPBSA.py Osman, Roman (Mon Aug 22 2011 - 09:52:14 PDT)
Re: [AMBER] [Amber] Amber vs ab initio Steven M. Graham (Tue Aug 02 2011 - 09:33:35 PDT)
- Re: [AMBER] [Amber] Amber vs ab initio David Cantu (Tue Aug 02 2011 - 19:33:36 PDT)
[AMBER] NAB for a mismatch RNA sequence Charles Johnson (Tue Aug 02 2011 - 10:37:56 PDT)
- Re: [AMBER] NAB for a mismatch RNA sequence David A Case (Wed Aug 03 2011 - 04:27:59 PDT)
  - Re: [AMBER] NAB for a mismatch RNA sequence Charles Johnson (Wed Aug 03 2011 - 06:37:03 PDT)
    - Re: [AMBER] NAB for a mismatch RNA sequence David A Case (Wed Aug 03 2011 - 07:03:34 PDT)
[AMBER] can non-bonded interactions be switched off? Jose Borreguero (Tue Aug 02 2011 - 11:39:34 PDT)
- Re: [AMBER] can non-bonded interactions be switched off? Ross Walker (Tue Aug 02 2011 - 11:57:52 PDT)
  - Re: [AMBER] can non-bonded interactions be switched off? Jose Borreguero (Tue Aug 02 2011 - 12:33:00 PDT)
[AMBER] Distorted waters in restrained mini Maura Catherine Mooney (Tue Aug 02 2011 - 14:48:00 PDT)
- Re: [AMBER] Distorted waters in restrained mini David Case (Tue Aug 02 2011 - 14:57:39 PDT)
  - Re: [AMBER] Distorted waters in restrained mini Maura Catherine Mooney (Tue Aug 02 2011 - 15:11:28 PDT)
    - Re: [AMBER] Distorted waters in restrained mini David Case (Tue Aug 02 2011 - 19:43:08 PDT)
    - Re: [AMBER] Distorted waters in restrained mini Maura Catherine Mooney (Wed Aug 03 2011 - 12:59:18 PDT)
    - Re: [AMBER] Distorted waters in restrained mini David A Case (Thu Aug 04 2011 - 05:11:22 PDT)
    - Re: [AMBER] Distorted waters in restrained mini Maura Catherine Mooney (Sun Aug 07 2011 - 15:55:13 PDT)
    - Re: [AMBER] Distorted waters in restrained mini Carlos Simmerling (Thu Aug 04 2011 - 05:18:04 PDT)
    - Re: [AMBER] Distorted waters in restrained mini Maura Catherine Mooney (Sun Aug 07 2011 - 15:34:31 PDT)
    - Re: [AMBER] Distorted waters in restrained mini David A Case (Mon Aug 08 2011 - 05:25:17 PDT)
    - Re: [AMBER] Distorted waters in restrained mini Maura Catherine Mooney (Mon Aug 08 2011 - 06:58:39 PDT)
    - Re: [AMBER] Distorted waters in restrained mini David A Case (Mon Aug 08 2011 - 07:12:32 PDT)
    - Re: [AMBER] Distorted waters in restrained mini Maura Catherine Mooney (Mon Aug 08 2011 - 07:27:24 PDT)
[AMBER] Electrostatci and van der Waals energy in Amber11 Okabe_Atsutoshi.takeda.co.jp (Tue Aug 02 2011 - 20:23:40 PDT)
[AMBER] MD stop but this job in cluster still run tien dung (Wed Aug 03 2011 - 01:51:58 PDT)
- Re: [AMBER] MD stop but this job in cluster still run Daniel Roe (Wed Aug 03 2011 - 11:02:21 PDT)
  - Re: [AMBER] MD stop but this job in cluster still run Jason Swails (Wed Aug 03 2011 - 11:25:54 PDT)
  - Re: [AMBER] MD stop but this job in cluster still run Ross Walker (Wed Aug 03 2011 - 11:26:54 PDT)
    - Re: [AMBER] MD stop but this job in cluster still run tien dung (Sat Aug 06 2011 - 17:00:41 PDT)
    - Re: [AMBER] MD stop but this job in cluster still run Marc van der Kamp (Sun Aug 07 2011 - 00:38:03 PDT)
[AMBER] Dipole-dipole correlation Function Sindrila Dutta banik (Wed Aug 03 2011 - 03:13:16 PDT)
- [AMBER] Dipole-dipole correlation Function Sindrila Dutta banik (Thu Aug 04 2011 - 09:49:15 PDT)
[AMBER] more info on using the Amber force field in NAMD David A Case (Wed Aug 03 2011 - 05:19:08 PDT)
- Re: [AMBER] more info on using the Amber force field in NAMD George Madalin Giambasu (Wed Aug 03 2011 - 07:35:41 PDT)
  - Re: [AMBER] more info on using the Amber force field in NAMD David A Case (Wed Aug 03 2011 - 08:17:17 PDT)
[AMBER] van der Waals atom parent list r smith (Wed Aug 03 2011 - 07:05:56 PDT)
[AMBER] "softcore potential" problem in TI calculation Victor Ma (Wed Aug 03 2011 - 07:29:11 PDT)
- Re: [AMBER] "softcore potential" problem in TI calculation steinbrt.rci.rutgers.edu (Wed Aug 03 2011 - 07:58:00 PDT)
  - Re: [AMBER] "softcore potential" problem in TI calculation Victor Ma (Wed Aug 03 2011 - 08:25:50 PDT)
[AMBER] convert netcdf to crd moitrayee.mbu.iisc.ernet.in (Wed Aug 03 2011 - 08:44:47 PDT)
- Re: [AMBER] convert netcdf to crd Daniel Roe (Wed Aug 03 2011 - 10:51:37 PDT)
[AMBER] AmberTools 1.5 top and cord files Molybdos Kirkimpolakis (Wed Aug 03 2011 - 15:03:18 PDT)
- Re: [AMBER] AmberTools 1.5 top and cord files Jason Swails (Wed Aug 03 2011 - 19:25:08 PDT)
  - Re: [AMBER] AmberTools 1.5 top and cord files Molybdos Kirkimpolakis (Wed Aug 03 2011 - 21:43:51 PDT)
    - Re: [AMBER] AmberTools 1.5 top and cord files Molybdos Kirkimpolakis (Thu Aug 04 2011 - 11:00:14 PDT)
    - Re: [AMBER] AmberTools 1.5 top and cord files Jason Swails (Fri Aug 05 2011 - 05:46:40 PDT)
[AMBER] simulating a protein-peptide complex Xiao Chen (Thu Aug 04 2011 - 00:00:12 PDT)
- Re: [AMBER] simulating a protein-peptide complex steinbrt.rci.rutgers.edu (Thu Aug 04 2011 - 00:51:26 PDT)
- Re: [AMBER] simulating a protein-peptide complex Carlos Simmerling (Thu Aug 04 2011 - 04:14:51 PDT)
  - Re: [AMBER] simulating a protein-peptide complex Xiao Chen (Fri Aug 05 2011 - 02:36:03 PDT)
    - Re: [AMBER] simulating a protein-peptide complex Carlos Simmerling (Fri Aug 05 2011 - 03:22:02 PDT)
    - [AMBER] questions about calculating thermodynamics properties of water model zhouhaibin2008.ok (Wed Aug 10 2011 - 08:05:10 PDT)
    - Re: [AMBER] questions about calculating thermodynamics properties of water model case (Fri Aug 12 2011 - 06:35:35 PDT)
[AMBER] Job Termination problem souvik sur (Thu Aug 04 2011 - 03:40:29 PDT)
[AMBER] 6 error: No torsion terms for ca-ca-ce-c2 Shulin Zhuang (Thu Aug 04 2011 - 09:03:51 PDT)
- Re: [AMBER] 6 error: No torsion terms for ca-ca-ce-c2 Jason Swails (Thu Aug 04 2011 - 09:25:24 PDT)
[AMBER] AmberTools 1.5 nmode error manikanthan bhavaraju (Thu Aug 04 2011 - 09:10:27 PDT)
- Re: [AMBER] AmberTools 1.5 nmode error Jason Swails (Thu Aug 04 2011 - 09:24:00 PDT)
[AMBER] Problem related to the correlation function Sindrila Dutta banik (Thu Aug 04 2011 - 09:59:57 PDT)
- Re: [AMBER] Problem related to the correlation function David A Case (Thu Aug 04 2011 - 11:10:38 PDT)
  - [AMBER] Problem related to the correlation function Sindrila Dutta banik (Fri Aug 05 2011 - 07:37:19 PDT)
    - [AMBER] Problem related to the correlation function Sindrila Dutta banik (Sat Aug 06 2011 - 09:15:39 PDT)
[AMBER] About Charge Assigning Method using Gaff Bin Wu (Thu Aug 04 2011 - 11:37:05 PDT)
- Re: [AMBER] About Charge Assigning Method using Gaff David A Case (Fri Aug 05 2011 - 06:36:09 PDT)
[AMBER] Nvidia M2070 Tesla ?? E. Nihal Korkmaz (Thu Aug 04 2011 - 13:19:50 PDT)
- Re: [AMBER] Nvidia M2070 Tesla ?? Ross Walker (Thu Aug 04 2011 - 13:32:59 PDT)
- Re: [AMBER] Nvidia M2070 Tesla ?? arikcohen (Thu Aug 04 2011 - 13:40:45 PDT)
[AMBER] Water residue and atom Numbering on Xleap David Cantu (Thu Aug 04 2011 - 15:42:37 PDT)
- Re: [AMBER] Water residue and atom Numbering on Xleap David Case (Thu Aug 04 2011 - 18:56:27 PDT)
[AMBER] 1st shell WITH solvent in ptraj Bruno Rodrigues (Thu Aug 04 2011 - 16:02:07 PDT)
- Re: [AMBER] 1st shell WITH solvent in ptraj Niel Henriksen (Thu Aug 04 2011 - 16:39:02 PDT)
  - Re: [AMBER] 1st shell WITH solvent in ptraj Bruno Rodrigues (Fri Aug 05 2011 - 05:53:57 PDT)
    - Re: [AMBER] 1st shell WITH solvent in ptraj Niel Henriksen (Fri Aug 05 2011 - 08:02:06 PDT)
[AMBER] How to know whether the sander is running parallel Aimin (Thu Aug 04 2011 - 16:50:44 PDT)
- Re: [AMBER] How to know whether the sander is running parallel David Case (Thu Aug 04 2011 - 19:02:47 PDT)
  - Re: [AMBER] How to know whether the sander is running parallel Aimin (Fri Aug 05 2011 - 09:39:27 PDT)
    - Re: [AMBER] How to know whether the sander is running parallel tdo.chem.ucsb.edu (Fri Aug 05 2011 - 09:47:39 PDT)
    - Re: [AMBER] How to know whether the sander is running parallel David A Case (Fri Aug 05 2011 - 09:49:26 PDT)
    - Re: [AMBER] How to know whether the sander is running parallel Aimin (Fri Aug 05 2011 - 10:03:44 PDT)
    - Re: [AMBER] How to know whether the sander is running parallel Jason Swails (Fri Aug 05 2011 - 11:50:29 PDT)
    - Re: [AMBER] How to know whether the sander is running parallel Aimin (Fri Aug 05 2011 - 13:41:50 PDT)
    - Re: [AMBER] How to know whether the sander is running parallel Jason Swails (Fri Aug 05 2011 - 19:23:55 PDT)
    - Re: [AMBER] How to know whether the sander is running parallel Aimin (Sat Aug 06 2011 - 20:54:57 PDT)
    - Re: [AMBER] How to know whether the sander is running parallel case (Sun Aug 07 2011 - 05:50:56 PDT)
[AMBER] dodecahedron box ? E. Nihal Korkmaz (Thu Aug 04 2011 - 23:08:38 PDT)
- Re: [AMBER] dodecahedron box ? Brian Radak (Thu Aug 25 2011 - 08:46:24 PDT)
[AMBER] how to scale energy barriers to get the harmonic constants in GAFF gloriarg (Fri Aug 05 2011 - 01:45:14 PDT)
[AMBER] Error in output file Aditya Padhi (Fri Aug 05 2011 - 02:55:38 PDT)
- Re: [AMBER] Error in output file Ross Walker (Fri Aug 05 2011 - 06:43:14 PDT)
  - Re: [AMBER] Error in output file Aditya Padhi (Mon Aug 08 2011 - 04:03:34 PDT)
[AMBER] Amoeba seems not work with free energy calculation li he (Fri Aug 05 2011 - 13:06:21 PDT)
- Re: [AMBER] Amoeba seems not work with free energy calculation case (Sat Aug 06 2011 - 13:09:30 PDT)
  - Re: [AMBER] Amoeba seems not work with free energy calculation li he (Wed Aug 10 2011 - 13:39:22 PDT)
[AMBER] About installation problems Mo Chen (Fri Aug 05 2011 - 14:34:32 PDT)
- Re: [AMBER] About installation problems Carlos Sosa (Fri Aug 05 2011 - 14:43:59 PDT)
- Re: [AMBER] About installation problems Mo Chen (Fri Aug 05 2011 - 15:38:31 PDT)
[AMBER] Amber 11 parallel installation problem 于丽影 Liying E\. Yu (Fri Aug 05 2011 - 18:30:16 PDT)
- Re: [AMBER] Amber 11 parallel installation problem Jason Swails (Fri Aug 05 2011 - 21:48:16 PDT)
- Re: [AMBER] Amber 11 parallel installation problem case (Sat Aug 06 2011 - 07:54:53 PDT)
[AMBER] Chemical shift restraints Siavoush Dastmalchi (Sat Aug 06 2011 - 04:30:51 PDT)
- Re: [AMBER] Chemical shift restraints case (Sat Aug 06 2011 - 08:02:08 PDT)
- Re: [AMBER] Chemical shift restraints Siavoush Dastmalchi (Sat Aug 06 2011 - 23:54:31 PDT)
  - Re: [AMBER] Chemical shift restraints case (Sun Aug 07 2011 - 05:38:05 PDT)
- Re: [AMBER] Chemical shift restraints Siavoush Dastmalchi (Sun Aug 07 2011 - 07:01:18 PDT)
  - Re: [AMBER] Chemical shift restraints case (Sun Aug 07 2011 - 11:14:50 PDT)
- Re: [AMBER] Chemical shift restraints Siavoush Dastmalchi (Sun Aug 07 2011 - 07:02:08 PDT)
- Re: [AMBER] Chemical shift restraints Siavoush Dastmalchi (Sun Aug 07 2011 - 07:05:16 PDT)
[AMBER] EQMMM modification Anglea A. (Sun Aug 07 2011 - 07:50:28 PDT)
- Re: [AMBER] EQMMM modification Jason Swails (Sun Aug 07 2011 - 19:55:32 PDT)
[AMBER] error in pmemd parallel installation hari krishna (Sun Aug 07 2011 - 23:08:52 PDT)
- Re: [AMBER] error in pmemd parallel installation David A Case (Mon Aug 08 2011 - 05:15:56 PDT)
  - Re: [AMBER] error in pmemd parallel installation hari krishna (Mon Aug 08 2011 - 05:42:29 PDT)
    - Re: [AMBER] error in pmemd parallel installation Daniel Roe (Mon Aug 08 2011 - 06:15:16 PDT)
    - Re: [AMBER] error in pmemd parallel installation hari krishna (Mon Aug 08 2011 - 06:27:12 PDT)
    - Re: [AMBER] error in pmemd parallel installation Jason Swails (Mon Aug 08 2011 - 06:34:24 PDT)
    - Re: [AMBER] error in pmemd parallel installation hari krishna (Mon Aug 08 2011 - 06:47:27 PDT)
    - Re: [AMBER] error in pmemd parallel installation Jason Swails (Mon Aug 08 2011 - 07:37:32 PDT)
[AMBER] free energy decomposition Sangita Kachhap (Mon Aug 08 2011 - 00:50:25 PDT)
- Re: [AMBER] free energy decomposition David A Case (Mon Aug 08 2011 - 05:17:56 PDT)
- Re: [AMBER] free energy decomposition Jason Swails (Mon Aug 08 2011 - 06:29:21 PDT)
  - Re: [AMBER] free energy decomposition Sangita Kachhap (Mon Aug 08 2011 - 09:06:46 PDT)
[AMBER] mmpbsa calculation using amber11 Siavoush Dastmalchi (Mon Aug 08 2011 - 04:43:14 PDT)
[AMBER] Problem related to the correlation function Sindrila Dutta banik (Mon Aug 08 2011 - 11:48:48 PDT)
[AMBER] DNA-22mer manikanthan bhavaraju (Mon Aug 08 2011 - 13:37:13 PDT)
- Re: [AMBER] DNA-22mer ros (Mon Aug 08 2011 - 13:44:35 PDT)
- Re: [AMBER] DNA-22mer Jason Swails (Mon Aug 08 2011 - 14:06:28 PDT)
- Re: [AMBER] DNA-22mer case (Fri Aug 12 2011 - 06:41:57 PDT)
  - Re: [AMBER] DNA-22mer Jason Swails (Fri Aug 12 2011 - 07:54:18 PDT)
    - Re: [AMBER] DNA-22mer manikanthan bhavaraju (Fri Aug 12 2011 - 15:27:40 PDT)
    - Re: [AMBER] DNA-22mer Bruno Rodrigues (Fri Aug 12 2011 - 16:00:14 PDT)
    - Re: [AMBER] DNA-22mer Daniel Roe (Sat Aug 13 2011 - 05:53:31 PDT)
    - Re: [AMBER] DNA-22mer Jason Swails (Sat Aug 13 2011 - 12:19:31 PDT)
    - Re: [AMBER] DNA-22mer manikanthan bhavaraju (Mon Aug 15 2011 - 11:09:28 PDT)
[AMBER] GAFF, Charges, and Cutoff Ismail, Mohd F. (Mon Aug 08 2011 - 14:19:11 PDT)
- Re: [AMBER] GAFF, Charges, and Cutoff Jason Swails (Mon Aug 08 2011 - 18:34:16 PDT)
  - Re: [AMBER] GAFF, Charges, and Cutoff Ismail, Mohd F. (Tue Aug 09 2011 - 07:53:55 PDT)
[AMBER] need suggestion about cutoff setyanto md (Mon Aug 08 2011 - 19:09:11 PDT)
- Re: [AMBER] need suggestion about cutoff Jason Swails (Mon Aug 08 2011 - 19:56:11 PDT)
  - Re: [AMBER] need suggestion about cutoff setyanto md (Tue Aug 09 2011 - 00:08:04 PDT)
    - Re: [AMBER] need suggestion about cutoff Catein Catherine (Tue Aug 09 2011 - 00:56:21 PDT)
    - Re: [AMBER] need suggestion about cutoff case (Tue Aug 09 2011 - 05:14:22 PDT)
    - [AMBER] Xleap installation problem kureeckal ramesh (Wed Aug 10 2011 - 05:36:41 PDT)
    - Re: [AMBER] Xleap installation problem Jason Swails (Wed Aug 10 2011 - 15:06:23 PDT)
    - [AMBER] Xleap installation problem kureeckal ramesh (Thu Aug 18 2011 - 00:13:42 PDT)
    - Re: [AMBER] Xleap installation problem Mark Williamson (Thu Aug 18 2011 - 01:58:21 PDT)
    - [AMBER] GBSA calculations for protein-protein complexes Catein Catherine (Tue Aug 09 2011 - 01:04:44 PDT)
    - Re: [AMBER] GBSA calculations for protein-protein complexes Carlos Simmerling (Tue Aug 09 2011 - 04:24:22 PDT)
    - Re: [AMBER] GBSA calculations for protein-protein complexes Catein Catherine (Tue Aug 09 2011 - 06:59:19 PDT)
    - Re: [AMBER] GBSA calculations for protein-protein complexes Carlos Simmerling (Tue Aug 09 2011 - 11:56:47 PDT)
    - Re: [AMBER] GBSA calculations with MgATP ligand Irene Newhouse (Tue Aug 09 2011 - 12:47:35 PDT)
    - Re: [AMBER] GBSA calculations with MgATP ligand Jason Swails (Tue Aug 09 2011 - 13:16:53 PDT)
    - Re: [AMBER] GBSA calculations with MgATP ligand Irene Newhouse (Tue Aug 09 2011 - 13:58:46 PDT)
    - Re: [AMBER] GBSA calculations with MgATP ligand filip fratev (Tue Aug 09 2011 - 19:16:35 PDT)
    - Re: [AMBER] GBSA calculations with MgATP ligand Irene Newhouse (Tue Aug 09 2011 - 19:37:24 PDT)
    - Re: [AMBER] GBSA calculations with MgATP ligand Jason Swails (Tue Aug 09 2011 - 19:43:38 PDT)
[AMBER] residuewise energy decomposition in Amber moitrayee.mbu.iisc.ernet.in (Mon Aug 08 2011 - 23:20:29 PDT)
- Re: [AMBER] residuewise energy decomposition in Amber Bill Miller III (Tue Aug 09 2011 - 04:43:08 PDT)
[AMBER] problem running with restraints Sangeetha B (Mon Aug 08 2011 - 23:22:01 PDT)
- [AMBER] problem running with restraints Sangeetha B (Mon Aug 08 2011 - 23:23:10 PDT)
- Re: [AMBER] problem running with restraints case (Tue Aug 09 2011 - 05:24:41 PDT)
  - Re: [AMBER] problem running with restraints Sangeetha B (Tue Aug 09 2011 - 06:33:19 PDT)
    - [AMBER] problem running with restraints Sangeetha B (Wed Aug 10 2011 - 05:33:44 PDT)
    - [AMBER] Fwd: problem running with restraints Sangeetha B (Thu Aug 11 2011 - 07:54:42 PDT)
[AMBER] MMPBSA.py - Entropy: Error message George Tzotzos (Tue Aug 09 2011 - 08:01:18 PDT)
- Re: [AMBER] MMPBSA.py - Entropy: Error message Bill Miller III (Tue Aug 09 2011 - 08:12:14 PDT)
  - Re: [AMBER] MMPBSA.py - Entropy: Error message George Tzotzos (Tue Aug 09 2011 - 08:31:26 PDT)
[AMBER] addition of massless particle to benzene that interacts only with massless particles in other benzene molecules Tan Yaw Sing (Tue Aug 09 2011 - 08:20:06 PDT)
- Re: [AMBER] addition of massless particle to benzene that interacts only with massless particles in other benzene molecules Jason Swails (Tue Aug 09 2011 - 09:25:10 PDT)
  - Re: [AMBER] addition of massless particle to benzene that interacts only with massless particles in other benzene molecules Carlos Simmerling (Tue Aug 09 2011 - 09:41:15 PDT)
    - [AMBER] Questions regarding Clustering in ptraj. Catein Catherine (Tue Aug 09 2011 - 10:30:55 PDT)
    - [AMBER] What is the physical meaning and good parameters for EXTDIEL and INDIEL and SURFTEN and SURFOFF in GBSA calculations? Catein Catherine (Tue Aug 09 2011 - 10:52:00 PDT)
    - Re: [AMBER] What is the physical meaning and good parameters for EXTDIEL and INDIEL and SURFTEN and SURFOFF in GBSA calculations? case (Thu Aug 11 2011 - 08:46:34 PDT)
- Re: [AMBER] addition of massless particle to benzene that interacts only with massless particles in other benzene molecules Dean Cuebas (Wed Aug 31 2011 - 08:09:24 PDT)
[AMBER] trouble compiling AmberTools 1.5 Jennifer L. Muzyka (Tue Aug 09 2011 - 11:16:55 PDT)
- Re: [AMBER] trouble compiling AmberTools 1.5 Jason Swails (Tue Aug 09 2011 - 11:38:07 PDT)
  - Re: [AMBER] trouble compiling AmberTools 1.5 Jennifer L. Muzyka (Tue Aug 09 2011 - 12:56:38 PDT)
[AMBER] mutating a residue to another residue on a protein structure George A. Khoury (Tue Aug 09 2011 - 13:48:33 PDT)
- Re: [AMBER] mutating a residue to another residue on a protein structure Jason Swails (Tue Aug 09 2011 - 14:04:41 PDT)
[AMBER] mol2 to PREP David Cantu (Tue Aug 09 2011 - 15:03:16 PDT)
- Re: [AMBER] mol2 to PREP tdo.chem.ucsb.edu (Tue Aug 09 2011 - 15:10:19 PDT)
- Re: [AMBER] mol2 to PREP Jason Swails (Tue Aug 09 2011 - 15:13:27 PDT)
  - Re: [AMBER] mol2 to PREP David Cantu (Tue Aug 09 2011 - 19:39:45 PDT)
[AMBER] PMEMD installation hari krishna (Wed Aug 10 2011 - 00:20:30 PDT)
- Re: [AMBER] PMEMD installation Ismail, Mohd F. (Wed Aug 10 2011 - 01:31:46 PDT)
  - [AMBER] Question about Tutorial 8 section 6: How to convert mdcrd to specific PDB files for clustering analysis with MMTSB? Catein Catherine (Wed Aug 10 2011 - 02:32:42 PDT)
    - Re: [AMBER] Question about Tutorial 8 section 6: How to convert mdcrd to specific PDB files for clustering analysis with MMTSB? Carlos Simmerling (Wed Aug 10 2011 - 04:19:38 PDT)
    - [AMBER] Can I use ptraj to cluster proteins based on residue contact map? Catein Catherine (Wed Aug 10 2011 - 09:54:21 PDT)
[AMBER] How to calculate the electrostatic contribution to "solvation free energy"? Jan-Philip Gehrcke (Wed Aug 10 2011 - 04:58:11 PDT)
- Re: [AMBER] How to calculate the electrostatic contribution to "solvation free energy"? Jason Swails (Wed Aug 10 2011 - 15:55:53 PDT)
  - Re: [AMBER] How to calculate the electrostatic contribution to "solvation free energy"? Jan-Philip Gehrcke (Thu Aug 11 2011 - 01:48:48 PDT)
    - Re: [AMBER] How to calculate the electrostatic contribution to "solvation free energy"? Jason Swails (Thu Aug 11 2011 - 06:52:49 PDT)
[AMBER] coordination number DEBOSTUTI GHOSHDASTIDAR (Wed Aug 10 2011 - 05:46:47 PDT)
- Re: [AMBER] coordination number Bruno Rodrigues (Wed Aug 10 2011 - 16:26:59 PDT)
[AMBER] Problem related to the correlation function Sindrila Dutta banik (Wed Aug 10 2011 - 05:53:22 PDT)
- Re: [AMBER] Problem related to the correlation function David Case (Wed Aug 10 2011 - 06:29:44 PDT)
[AMBER] Proble related to the correlation function Sindrila Dutta banik (Wed Aug 10 2011 - 06:02:54 PDT)
- Re: [AMBER] Proble related to the correlation function Jason Swails (Wed Aug 10 2011 - 15:57:26 PDT)
  - Re: [AMBER] Proble related to the correlation function Adrian Roitberg (Wed Aug 10 2011 - 16:01:44 PDT)
[AMBER] MMPBSA.py: Effect on ionic strength concentration on Delta G George Tzotzos (Wed Aug 10 2011 - 06:26:38 PDT)
- Re: [AMBER] MMPBSA.py: Effect on ionic strength concentration on Delta G Jason Swails (Wed Aug 10 2011 - 14:04:59 PDT)
  - Re: [AMBER] MMPBSA.py: Effect on ionic strength concentration on Delta G George Tzotzos (Wed Aug 10 2011 - 16:10:24 PDT)
    - Re: [AMBER] MMPBSA.py: Effect on ionic strength concentration on Delta G Jason Swails (Wed Aug 10 2011 - 20:13:14 PDT)
    - Re: [AMBER] MMPBSA.py: Effect on ionic strength concentration on Delta G George Tzotzos (Thu Aug 11 2011 - 04:17:42 PDT)
    - Re: [AMBER] MMPBSA.py: Effect on ionic strength concentration on Delta G Jason Swails (Thu Aug 11 2011 - 06:30:24 PDT)
    - Re: [AMBER] MMPBSA.py: Effect on ionic strength concentration on Delta G George Tzotzos (Thu Aug 11 2011 - 07:47:33 PDT)
    - Re: [AMBER] MMPBSA.py: Effect on ionic strength concentration on Delta G Jason Swails (Thu Aug 11 2011 - 08:19:29 PDT)
    - Re: [AMBER] MMPBSA.py: Effect on ionic strength concentration on Delta G George Tzotzos (Thu Aug 11 2011 - 08:22:31 PDT)
[AMBER] Cholesterol and Cholesteryl hemisuccinate TAEJIN KIM (Wed Aug 10 2011 - 11:43:07 PDT)
- Re: [AMBER] Cholesterol and Cholesteryl hemisuccinate Jason Swails (Wed Aug 10 2011 - 15:15:13 PDT)
[AMBER] could not find amber atom type F in forcefield 10 Rajesh Raju (Wed Aug 10 2011 - 14:52:49 PDT)
- Re: [AMBER] could not find amber atom type F in forcefield 10 Rajesh Raju (Wed Aug 10 2011 - 16:05:08 PDT)
[AMBER] rst to mdcrd Anglea A. (Wed Aug 10 2011 - 17:40:39 PDT)
- Re: [AMBER] rst to mdcrd Ozen, Aysegul (Wed Aug 10 2011 - 19:06:12 PDT)
  - [AMBER] How to extract selected residues from mdcrd to PDB file using ptraj? Catein Catherine (Wed Aug 10 2011 - 19:55:16 PDT)
    - Re: [AMBER] How to extract selected residues from mdcrd to PDB file using ptraj? Jason Swails (Wed Aug 10 2011 - 20:29:48 PDT)
    - Re: [AMBER] How to extract selected residues from mdcrd to PDB file using ptraj? Catein Catherine (Wed Aug 10 2011 - 21:06:41 PDT)
  - [AMBER] How to extract every 10th snapshot from mdcrd to PDB format? Catein Catherine (Wed Aug 10 2011 - 20:00:09 PDT)
    - Re: [AMBER] How to extract every 10th snapshot from mdcrd to PDB format? Jason Swails (Wed Aug 10 2011 - 20:17:05 PDT)
  - [AMBER] trying to make parallel Amber on Centos Irene Newhouse (Wed Aug 10 2011 - 20:01:42 PDT)
    - Re: [AMBER] trying to make parallel Amber on Centos Jason Swails (Wed Aug 10 2011 - 20:16:16 PDT)
  - Re: [AMBER] rst to mdcrd waqasuddin.khan.iccs.edu (Wed Aug 10 2011 - 20:40:01 PDT)
    - Re: [AMBER] rst to mdcrd Ross Walker (Wed Aug 10 2011 - 21:52:20 PDT)
    - Re: [AMBER] rst to mdcrd waqasuddin.khan.iccs.edu (Thu Aug 11 2011 - 06:16:59 PDT)
    - Re: [AMBER] rst to mdcrd Jason Swails (Thu Aug 11 2011 - 06:32:55 PDT)
[AMBER] nothing wtitten in .out file after heating Nyla Zaman (Wed Aug 10 2011 - 23:50:51 PDT)
- Re: [AMBER] nothing wtitten in .out file after heating case (Thu Aug 11 2011 - 08:56:16 PDT)
  - Re: [AMBER] nothing wtitten in .out file after heating M. L. Dodson (Thu Aug 11 2011 - 09:06:53 PDT)
    - Re: [AMBER] nothing wtitten in .out file after heating Jason Swails (Thu Aug 11 2011 - 09:57:42 PDT)
[AMBER] calculating distance between two atoms clwg (Thu Aug 11 2011 - 00:53:37 PDT)
- Re: [AMBER] calculating distance between two atoms steinbrt.rci.rutgers.edu (Thu Aug 11 2011 - 01:25:01 PDT)
- Re: [AMBER] calculating distance between two atoms Dean Cuebas (Thu Aug 11 2011 - 12:12:50 PDT)
[AMBER] espgen cannot generate esp file Reza Aditama (Thu Aug 11 2011 - 00:57:36 PDT)
[AMBER] Inpcrd file problem David Cantu (Thu Aug 11 2011 - 07:53:06 PDT)
- Re: [AMBER] Inpcrd file problem Daniel Roe (Thu Aug 11 2011 - 08:31:17 PDT)
  - Re: [AMBER] Inpcrd file problem David Cantu (Thu Aug 11 2011 - 08:57:34 PDT)
    - Re: [AMBER] Inpcrd file problem Daniel Roe (Thu Aug 11 2011 - 09:58:39 PDT)
    - Re: [AMBER] Inpcrd file problem David Cantu (Thu Aug 11 2011 - 10:27:47 PDT)
    - Re: [AMBER] Inpcrd file problem Ismail, Mohd F. (Thu Aug 11 2011 - 11:23:47 PDT)
    - Re: [AMBER] Inpcrd file problem Ismail, Mohd F. (Thu Aug 11 2011 - 12:11:22 PDT)
- Re: [AMBER] Inpcrd file problem Bill Ross (Thu Aug 11 2011 - 10:30:21 PDT)
  - Re: [AMBER] Inpcrd file problem David Cantu (Thu Aug 11 2011 - 10:48:25 PDT)
    - Re: [AMBER] Inpcrd file problem Daniel Roe (Thu Aug 11 2011 - 11:12:56 PDT)
    - Re: [AMBER] Inpcrd file problem David Cantu (Thu Aug 11 2011 - 12:35:47 PDT)
    - Re: [AMBER] Inpcrd file problem David Cantu (Thu Aug 11 2011 - 13:23:51 PDT)
    - Re: [AMBER] Inpcrd file problem Carlos Simmerling (Thu Aug 11 2011 - 13:32:36 PDT)
    - Re: [AMBER] Inpcrd file problem David Cantu (Thu Aug 11 2011 - 13:37:29 PDT)
    - Re: [AMBER] Inpcrd file problem Daniel Roe (Thu Aug 11 2011 - 13:53:11 PDT)
    - Re: [AMBER] Inpcrd file problem David Cantu (Thu Aug 11 2011 - 14:03:36 PDT)
    - Re: [AMBER] Inpcrd file problem David Cantu (Thu Aug 11 2011 - 14:07:37 PDT)
    - Re: [AMBER] Inpcrd file problem Jason Swails (Thu Aug 11 2011 - 14:12:10 PDT)
    - Re: [AMBER] Inpcrd file problem Thomas Cheatham (Thu Aug 11 2011 - 14:15:54 PDT)
    - Re: [AMBER] Inpcrd file problem David Cantu (Thu Aug 11 2011 - 14:21:22 PDT)
    - Re: [AMBER] Inpcrd file problem Jason Swails (Thu Aug 11 2011 - 14:09:16 PDT)
- Re: [AMBER] Inpcrd file problem Bill Ross (Thu Aug 11 2011 - 11:15:26 PDT)
[AMBER] leaprc Charles Johnson (Thu Aug 11 2011 - 10:11:54 PDT)
[AMBER] leaprc Charles Johnson (Thu Aug 11 2011 - 11:16:43 PDT)
- Re: [AMBER] leaprc Ismail, Mohd F. (Thu Aug 11 2011 - 11:22:17 PDT)
  - Re: [AMBER] leaprc Charles Johnson (Thu Aug 11 2011 - 12:27:44 PDT)
    - Re: [AMBER] leaprc Ismail, Mohd F. (Thu Aug 11 2011 - 13:00:28 PDT)
    - Re: [AMBER] leaprc Charles Johnson (Thu Aug 11 2011 - 13:04:02 PDT)
- Re: [AMBER] leaprc case (Thu Aug 11 2011 - 14:44:38 PDT)
  - Re: [AMBER] leaprc Charles Johnson (Fri Aug 12 2011 - 06:01:37 PDT)
    - Re: [AMBER] leaprc case (Sat Aug 13 2011 - 05:17:31 PDT)
[AMBER] GBSA E. Nihal Korkmaz (Thu Aug 11 2011 - 14:11:42 PDT)
- Re: [AMBER] GBSA Jason Swails (Thu Aug 11 2011 - 14:13:02 PDT)
[AMBER] unspecified launch failure launching kernel kCalculateMolecularVirial arikcohen (Thu Aug 11 2011 - 14:58:14 PDT)
- Re: [AMBER] unspecified launch failure launching kernel kCalculateMolecularVirial Scott Le Grand (Thu Aug 11 2011 - 15:03:59 PDT)
  - Re: [AMBER] unspecified launch failure launching kernel kCalculateMolecularVirial arikcohen (Thu Aug 11 2011 - 15:04:46 PDT)
    - Re: [AMBER] unspecified launch failure launching kernel kCalculateMolecularVirial Ross Walker (Thu Aug 11 2011 - 15:12:55 PDT)
    - Re: [AMBER] unspecified launch failure launching kernel kCalculateMolecularVirial arikcohen (Thu Aug 11 2011 - 15:19:25 PDT)
    - Re: [AMBER] unspecified launch failure launching kernel kCalculateMolecularVirial Ross Walker (Thu Aug 11 2011 - 15:28:05 PDT)
    - Re: [AMBER] unspecified launch failure launching kernel kCalculateMolecularVirial arikcohen (Thu Aug 11 2011 - 15:34:18 PDT)
    - Re: [AMBER] unspecified launch failure launching kernel kCalculateMolecularVirial arikcohen (Thu Aug 11 2011 - 15:53:58 PDT)
    - Re: [AMBER] unspecified launch failure launching kernel kCalculateMolecularVirial Ross Walker (Thu Aug 11 2011 - 16:06:36 PDT)
    - Re: [AMBER] unspecified launch failure launching kernel kCalculateMolecularVirial arikcohen (Thu Aug 11 2011 - 17:18:07 PDT)
    - Re: [AMBER] unspecified launch failure launching kernel kCalculateMolecularVirial Ross Walker (Thu Aug 11 2011 - 17:29:24 PDT)
    - Re: [AMBER] unspecified launch failure launching kernel kCalculateMolecularVirial Sangeetha B (Thu Aug 11 2011 - 21:24:18 PDT)
    - Re: [AMBER] unspecified launch failure launching kernel kCalculateMolecularVirial Ross Walker (Fri Aug 12 2011 - 09:02:24 PDT)
[AMBER] QM runs Maura Catherine Mooney (Thu Aug 11 2011 - 16:07:42 PDT)
- Re: [AMBER] QM runs Ross Walker (Thu Aug 11 2011 - 16:18:03 PDT)
  - Re: [AMBER] QM runs Maura Catherine Mooney (Fri Aug 12 2011 - 03:37:43 PDT)
    - Re: [AMBER] QM runs case (Fri Aug 12 2011 - 06:32:11 PDT)
[AMBER] loadpdb with GLYCAM_06 ? Yun Shi (Thu Aug 11 2011 - 20:42:52 PDT)
- Re: [AMBER] loadpdb with GLYCAM_06 ? Sushil Mishra (Thu Aug 11 2011 - 21:48:11 PDT)
  - [AMBER] PTRAJ; how to extract selected atoms from mdcrd to PDB file. Catein Catherine (Thu Aug 11 2011 - 23:34:27 PDT)
    - Re: [AMBER] PTRAJ; how to extract selected atoms from mdcrd to PDB file. Jason Swails (Fri Aug 12 2011 - 04:11:41 PDT)
- Re: [AMBER] loadpdb with GLYCAM_06 ? Oliver Grant (Fri Aug 12 2011 - 10:00:31 PDT)
  - Re: [AMBER] loadpdb with GLYCAM_06 ? Yun Shi (Fri Aug 12 2011 - 10:19:59 PDT)
    - Re: [AMBER] loadpdb with GLYCAM_06 ? Lachele Foley (Lists) (Fri Aug 12 2011 - 10:29:32 PDT)
    - Re: [AMBER] loadpdb with GLYCAM_06 ? Yun Shi (Fri Aug 12 2011 - 10:53:29 PDT)
    - Re: [AMBER] loadpdb with GLYCAM_06 ? Lachele Foley (Lists) (Fri Aug 12 2011 - 11:28:42 PDT)
    - Re: [AMBER] loadpdb with GLYCAM_06 ? Yun Shi (Fri Aug 12 2011 - 19:11:27 PDT)
    - Re: [AMBER] loadpdb with GLYCAM_06 ? Lachele Foley (Lists) (Fri Aug 12 2011 - 19:27:09 PDT)
    - Re: [AMBER] loadpdb with GLYCAM_06 ? Yun Shi (Fri Aug 12 2011 - 21:26:09 PDT)
    - Re: [AMBER] loadpdb with GLYCAM_06 ? Lachele Foley (Lists) (Sat Aug 13 2011 - 07:54:38 PDT)
    - Re: [AMBER] loadpdb with GLYCAM_06 ? Yun Shi (Sat Aug 13 2011 - 10:09:47 PDT)
    - Re: [AMBER] loadpdb with GLYCAM_06 ? Lachele Foley (Lists) (Sat Aug 13 2011 - 11:39:27 PDT)
    - Re: [AMBER] loadpdb with GLYCAM_06 ? Yun Shi (Mon Aug 15 2011 - 11:10:58 PDT)
    - Re: [AMBER] loadpdb with GLYCAM_06 ? Yun Shi (Mon Aug 15 2011 - 11:32:09 PDT)
    - Re: [AMBER] loadpdb with GLYCAM_06 ? Lachele Foley (Lists) (Mon Aug 15 2011 - 11:55:15 PDT)
    - Re: [AMBER] loadpdb with GLYCAM_06 ? Yun Shi (Tue Aug 16 2011 - 11:03:53 PDT)
    - [AMBER] Widom Method with amber Matias Factorovich (Tue Aug 16 2011 - 12:22:35 PDT)
    - Re: [AMBER] Widom Method with amber case (Tue Aug 16 2011 - 13:03:25 PDT)
    - Re: [AMBER] Widom Method with amber Bill Ross (Tue Aug 16 2011 - 16:02:54 PDT)
- Re: [AMBER] loadpdb with GLYCAM_06 ? Bill Ross (Sun Aug 14 2011 - 11:31:26 PDT)
[AMBER] Hot to compare to contact map instead of visually? Catein Catherine (Fri Aug 12 2011 - 00:45:42 PDT)
[AMBER] Non-identical prmtop files for PNEB William Cantara (Fri Aug 12 2011 - 05:52:21 PDT)
- Re: [AMBER] Non-identical prmtop files for PNEB Daniel Roe (Fri Aug 12 2011 - 10:07:21 PDT)
  - Re: [AMBER] Non-identical prmtop files for PNEB William Cantara (Fri Aug 12 2011 - 11:40:58 PDT)
[AMBER] residue list E. Nihal Korkmaz (Fri Aug 12 2011 - 15:47:15 PDT)
- Re: [AMBER] residue list Jason Swails (Fri Aug 12 2011 - 17:30:09 PDT)
  - [AMBER] Randomize trajectory frames Tai Chi For Me (Sat Aug 13 2011 - 17:21:17 PDT)
    - Re: [AMBER] Randomize trajectory frames Daniel Sindhikara (Sun Aug 14 2011 - 00:16:31 PDT)
    - Re: [AMBER] Randomize trajectory frames Dean Cuebas (Mon Aug 15 2011 - 21:30:33 PDT)
[AMBER] Binding energy with ff02ep Anglea A. (Fri Aug 12 2011 - 23:35:22 PDT)
[AMBER] Xmgr download link souvik sur (Sat Aug 13 2011 - 03:49:34 PDT)
- Re: [AMBER] Xmgr download link Marc van der Kamp (Sat Aug 13 2011 - 04:27:05 PDT)
[AMBER] error running mmpbsa.py Siavoush Dastmalchi (Sat Aug 13 2011 - 05:34:08 PDT)
- Re: [AMBER] error running mmpbsa.py Jason Swails (Sat Aug 13 2011 - 05:44:39 PDT)
[AMBER] question about the output of H-bond analysis by ptraj Ying Yang (Sat Aug 13 2011 - 05:07:37 PDT)
[AMBER] Amber11 re-compiling Anglea A. (Sat Aug 13 2011 - 05:58:21 PDT)
- Re: [AMBER] Amber11 re-compiling Jason Swails (Sat Aug 13 2011 - 06:15:04 PDT)
[AMBER] nmpimd heating Andrew Petersen (Sat Aug 13 2011 - 08:11:03 PDT)
- Re: [AMBER] nmpimd heating Francesco Paesani (Sat Aug 13 2011 - 16:07:14 PDT)
  - Re: [AMBER] nmpimd heating Andrew Petersen (Tue Aug 23 2011 - 07:19:13 PDT)
    - Re: [AMBER] nmpimd heating Francesco Paesani (Thu Aug 25 2011 - 08:43:18 PDT)
[AMBER] _mmpbsa_py_energy error durint PB calculations HIromichi Tsurui (Sun Aug 14 2011 - 04:30:49 PDT)
- Re: [AMBER] _mmpbsa_py_energy error durint PB calculations Jason Swails (Sun Aug 14 2011 - 07:20:48 PDT)
  - Re: [AMBER] _mmpbsa_py_energy error durint PB calculations 鶴井博理 (Mon Aug 15 2011 - 20:06:18 PDT)
    - Re: [AMBER] _mmpbsa_py_energy error durint PB calculations Ray Luo, Ph.D. (Mon Aug 15 2011 - 21:36:28 PDT)
    - Re: [AMBER] _mmpbsa_py_energy error durint PB calculations Jason Swails (Tue Aug 16 2011 - 04:20:48 PDT)
    - Re: [AMBER] _mmpbsa_py_energy error durint PB calculations 鶴井博理 (Tue Aug 16 2011 - 17:58:15 PDT)
    - Re: [AMBER] _mmpbsa_py_energy error durint PB calculations 鶴井博理 (Tue Aug 16 2011 - 17:02:09 PDT)
- Re: [AMBER] _mmpbsa_py_energy error durint PB calculations Hiromichi Tsurui (Sun Aug 14 2011 - 17:12:58 PDT)
  - Re: [AMBER] _mmpbsa_py_energy error durint PB calculations Jason Swails (Fri Aug 26 2011 - 18:49:44 PDT)
[AMBER] inter & intra-molecular interaction energies clwg (Sun Aug 14 2011 - 06:48:54 PDT)
[AMBER] Get access to my pictures and more Navanath Kumbhar (Sun Aug 14 2011 - 22:46:56 PDT)
[AMBER] No data for 0+2 PB PB 0 problem in Amber10 mm_pbsa sribone.fcq.unc.edu.ar (Mon Aug 15 2011 - 08:04:30 PDT)
- Re: [AMBER] No data for 0+2 PB PB 0 problem in Amber10 mm_pbsa Ray Luo, Ph.D. (Mon Aug 15 2011 - 13:48:50 PDT)
  - Re: [AMBER] No data for 0+2 PB PB 0 problem in Amber10 mm_pbsa sribone.fcq.unc.edu.ar (Tue Aug 16 2011 - 05:12:56 PDT)
    - Re: [AMBER] No data for 0+2 PB PB 0 problem in Amber10 mm_pbsa Jason Swails (Tue Aug 16 2011 - 06:02:58 PDT)
[AMBER] Amber Minimization MUSTAFA BUGHIO (Mon Aug 15 2011 - 09:31:33 PDT)
[AMBER] Software announcement: Release of PUPIL 1.4 Joan Torras (Mon Aug 15 2011 - 11:37:30 PDT)
[AMBER] Can one preserve heavy atom / hydrogen atom ordering in LEaP? Fenley, Andrew (Mon Aug 15 2011 - 12:05:19 PDT)
- Re: [AMBER] Can one preserve heavy atom / hydrogen atom ordering in LEaP? case (Tue Aug 16 2011 - 12:49:38 PDT)
- Re: [AMBER] Can one preserve heavy atom / hydrogen atom ordering in LEaP? Bill Ross (Tue Aug 16 2011 - 16:01:26 PDT)
- Re: [AMBER] Can one preserve heavy atom / hydrogen atom ordering in LEaP? Bill Ross (Tue Aug 16 2011 - 16:21:17 PDT)
[AMBER] pm6 parametes Anglea A. (Mon Aug 15 2011 - 17:28:58 PDT)
[AMBER] Old problem with restart Bruno Rodrigues (Mon Aug 15 2011 - 19:32:25 PDT)
- Re: [AMBER] Old problem with restart Jason Swails (Tue Aug 16 2011 - 04:16:11 PDT)
  - Re: [AMBER] Old problem with restart Marc van der Kamp (Tue Aug 16 2011 - 04:26:07 PDT)
    - Re: [AMBER] Old problem with restart Bruno Rodrigues (Tue Aug 16 2011 - 04:40:00 PDT)
    - Re: [AMBER] Old problem with restart Marc van der Kamp (Tue Aug 16 2011 - 04:56:45 PDT)
    - Re: [AMBER] Old problem with restart Bruno Rodrigues (Tue Aug 16 2011 - 13:22:40 PDT)
    - Re: [AMBER] Old problem with restart case (Tue Aug 16 2011 - 05:10:09 PDT)
    - Re: [AMBER] Old problem with restart Bruno Rodrigues (Tue Aug 16 2011 - 13:27:00 PDT)
    - Re: [AMBER] Old problem with restart Jason Swails (Tue Aug 16 2011 - 14:10:22 PDT)
- Re: [AMBER] Old problem with restart Bill Ross (Tue Aug 16 2011 - 16:07:44 PDT)
  - Re: [AMBER] Old problem with restart Bruno Rodrigues (Mon Aug 22 2011 - 16:03:32 PDT)
[AMBER] Fwd: simulating Modified residue of Cysteine attached to mercury madhumita das (Tue Aug 16 2011 - 04:24:54 PDT)
- Re: [AMBER] Fwd: simulating Modified residue of Cysteine attached to mercury case (Tue Aug 16 2011 - 12:53:31 PDT)
  - Re: [AMBER] Fwd: simulating Modified residue of Cysteine attached to mercury FyD (Sat Aug 20 2011 - 00:18:39 PDT)
[AMBER] again GLYCAM06 + 99SB + GAFF ? Yun Shi (Tue Aug 16 2011 - 11:34:59 PDT)
- Re: [AMBER] again GLYCAM06 + 99SB + GAFF ? Lachele Foley (Lists) (Tue Aug 16 2011 - 12:39:59 PDT)
  - Re: [AMBER] again GLYCAM06 + 99SB + GAFF ? Yun Shi (Fri Aug 19 2011 - 09:31:42 PDT)
    - Re: [AMBER] again GLYCAM06 + 99SB + GAFF ? Lachele Foley (Lists) (Fri Aug 19 2011 - 10:39:01 PDT)
    - Re: [AMBER] again GLYCAM06 + 99SB + GAFF ? Yun Shi (Fri Aug 19 2011 - 11:48:01 PDT)
    - Re: [AMBER] again GLYCAM06 + 99SB + GAFF ? Lachele Foley (Lists) (Fri Aug 19 2011 - 11:54:51 PDT)
    - Re: [AMBER] again GLYCAM06 + 99SB + GAFF ? Marek Maly (Mon Aug 22 2011 - 10:24:16 PDT)
    - Re: [AMBER] again GLYCAM06 + 99SB + GAFF ? FyD (Sat Aug 20 2011 - 00:07:05 PDT)
    - Re: [AMBER] again GLYCAM06 + 99SB + GAFF ? Yun Shi (Wed Aug 24 2011 - 16:21:23 PDT)
    - Re: [AMBER] again GLYCAM06 + 99SB + GAFF ? FyD (Wed Aug 24 2011 - 23:38:03 PDT)
    - Re: [AMBER] again GLYCAM06 + 99SB + GAFF ? Yun Shi (Thu Aug 25 2011 - 09:58:43 PDT)
    - Re: [AMBER] again GLYCAM06 + 99SB + GAFF ? Yun Shi (Thu Aug 25 2011 - 11:20:10 PDT)
    - Re: [AMBER] again GLYCAM06 + 99SB + GAFF ? Yun Shi (Thu Aug 25 2011 - 22:16:41 PDT)
    - Re: [AMBER] again GLYCAM06 + 99SB + GAFF ? FyD (Thu Aug 25 2011 - 23:56:29 PDT)
    - Re: [AMBER] again GLYCAM06 + 99SB + GAFF ? Yun Shi (Fri Aug 26 2011 - 18:15:09 PDT)
    - Re: [AMBER] again GLYCAM06 + 99SB + GAFF ? FyD (Fri Aug 26 2011 - 23:31:16 PDT)
    - Re: [AMBER] again GLYCAM06 + 99SB + GAFF ? FyD (Thu Aug 25 2011 - 23:37:29 PDT)
    - Re: [AMBER] again GLYCAM06 + 99SB + GAFF ? Yun Shi (Fri Aug 26 2011 - 11:08:06 PDT)
    - Re: [AMBER] again GLYCAM06 + 99SB + GAFF ? FyD (Sat Aug 27 2011 - 00:16:34 PDT)
    - Re: [AMBER] again GLYCAM06 + 99SB + GAFF ? Yun Shi (Tue Sep 06 2011 - 22:28:44 PDT)
    - Re: [AMBER] again GLYCAM06 + 99SB + GAFF ? FyD (Wed Sep 07 2011 - 23:57:43 PDT)
    - Re: [AMBER] again GLYCAM06 + 99SB + GAFF ? Yun Shi (Mon Sep 12 2011 - 23:32:47 PDT)
    - Re: [AMBER] again GLYCAM06 + 99SB + GAFF ? Yun Shi (Mon Sep 12 2011 - 23:55:50 PDT)
    - Re: [AMBER] again GLYCAM06 + 99SB + GAFF ? FyD (Tue Sep 13 2011 - 08:46:23 PDT)
    - Re: [AMBER] again GLYCAM06 + 99SB + GAFF ? Yun Shi (Thu Sep 15 2011 - 21:56:35 PDT)
    - Re: [AMBER] again GLYCAM06 + 99SB + GAFF ? FyD (Fri Sep 16 2011 - 03:42:46 PDT)
    - Re: [AMBER] again GLYCAM06 + 99SB + GAFF ? Yun Shi (Sun Sep 18 2011 - 21:38:55 PDT)
    - Re: [AMBER] again GLYCAM06 + 99SB + GAFF ? FyD (Mon Sep 19 2011 - 04:23:41 PDT)
    - Re: [AMBER] again GLYCAM06 + 99SB + GAFF ? Yun Shi (Tue Sep 20 2011 - 21:11:08 PDT)
    - Re: [AMBER] again GLYCAM06 + 99SB + GAFF ? FyD (Wed Sep 21 2011 - 00:08:17 PDT)
    - Re: [AMBER] again GLYCAM06 + 99SB + GAFF ? Yun Shi (Wed Sep 21 2011 - 07:41:36 PDT)
    - [AMBER] nmode analysis - different SCEE values in SANDMIN and NMODE output files ? Marek Maly (Wed Sep 21 2011 - 10:56:43 PDT)
    - Re: [AMBER] nmode analysis - different SCEE values in SANDMIN and NMODE output files ? Jason Swails (Wed Sep 21 2011 - 11:21:05 PDT)
    - Re: [AMBER] nmode analysis - different SCEE values in SANDMIN and NMODE output files ? Marek Maly (Wed Sep 21 2011 - 11:19:15 PDT)
    - Re: [AMBER] nmode analysis - different SCEE values in SANDMIN and NMODE output files ? Jason Swails (Wed Sep 21 2011 - 11:58:53 PDT)
    - Re: [AMBER] nmode analysis - different SCEE values in SANDMIN and NMODE output files ? Marek Maly (Wed Sep 21 2011 - 16:00:48 PDT)
    - Re: [AMBER] nmode analysis - different SCEE values in SANDMIN and NMODE output files ? Jason Swails (Wed Sep 21 2011 - 21:58:09 PDT)
    - Re: [AMBER] nmode analysis - different SCEE values in SANDMIN and NMODE output files ? Marek Maly (Thu Sep 22 2011 - 04:58:49 PDT)
    - Re: [AMBER] nmode analysis - different SCEE values in SANDMIN and NMODE output files ? Bill Ross (Wed Sep 21 2011 - 12:24:56 PDT)
    - Re: [AMBER] nmode analysis - different SCEE values in SANDMIN and NMODE output files ? Marek Maly (Wed Sep 21 2011 - 16:11:28 PDT)
    - Re: [AMBER] again GLYCAM06 + 99SB + GAFF ? FyD (Thu Sep 22 2011 - 00:12:38 PDT)
    - Re: [AMBER] again GLYCAM06 + 99SB + GAFF ? FyD (Tue Sep 13 2011 - 08:41:21 PDT)
    - Re: [AMBER] again GLYCAM06 + 99SB + GAFF ? FyD (Thu Aug 25 2011 - 23:15:38 PDT)
- Re: [AMBER] again GLYCAM06 + 99SB + GAFF ? Matthew Tessier (Wed Sep 21 2011 - 19:04:38 PDT)
[AMBER] Problems with MMPBSA and steered molecular dynamics Márcio Souza Damaso (Tue Aug 16 2011 - 13:21:13 PDT)
- Re: [AMBER] Problems with MMPBSA and steered molecular dynamics Jason Swails (Tue Aug 16 2011 - 14:13:58 PDT)
[AMBER] Amberlite error Irene Newhouse (Tue Aug 16 2011 - 13:58:11 PDT)
[AMBER] partial atomic charges parametarization in ff10 manikanthan bhavaraju (Tue Aug 16 2011 - 19:11:10 PDT)
- Re: [AMBER] partial atomic charges parametarization in ff10 Jason Swails (Tue Aug 16 2011 - 19:41:48 PDT)
[AMBER] General questions about POL3 and AMOEBA timings D.G. Sprous, PhD (Wed Aug 17 2011 - 08:18:31 PDT)
[AMBER] comments format within .mdin files Yun Shi (Wed Aug 17 2011 - 08:59:14 PDT)
- Re: [AMBER] comments format within .mdin files Ross Walker (Wed Aug 17 2011 - 09:51:33 PDT)
[AMBER] strategies to terminate and continue a MD run Yun Shi (Wed Aug 17 2011 - 09:03:41 PDT)
- Re: [AMBER] strategies to terminate and continue a MD run Jason Swails (Wed Aug 17 2011 - 10:40:00 PDT)
  - Re: [AMBER] strategies to terminate and continue a MD run Yun Shi (Wed Aug 17 2011 - 10:49:54 PDT)
    - Re: [AMBER] strategies to terminate and continue a MD run sribone.fcq.unc.edu.ar (Wed Aug 17 2011 - 11:38:10 PDT)
- Re: [AMBER] strategies to terminate and continue a MD run Bill Ross (Wed Aug 17 2011 - 13:15:27 PDT)
  - Re: [AMBER] strategies to terminate and continue a MD run Bruno Rodrigues (Thu Aug 18 2011 - 05:13:02 PDT)
[AMBER] Iron in CHAMBER: chemicalSymbolToZ() cannot map symbol: FE, to a Z value Patrick von Glehn (Wed Aug 17 2011 - 09:20:54 PDT)
- Re: [AMBER] Iron in CHAMBER: chemicalSymbolToZ() cannot map symbol: FE, to a Z value Ross Walker (Wed Aug 17 2011 - 09:44:47 PDT)
- Re: [AMBER] Iron in CHAMBER: chemicalSymbolToZ() cannot map symbol: FE, to a Z value Mark Williamson (Wed Aug 17 2011 - 10:44:15 PDT)
  - Re: [AMBER] Iron in CHAMBER: chemicalSymbolToZ() cannot map symbol: FE, to a Z value Jason Swails (Thu Aug 18 2011 - 07:49:53 PDT)
[AMBER] problem with NPT equilibration stage Jurica Novak (Wed Aug 17 2011 - 09:23:29 PDT)
- Re: [AMBER] problem with NPT equilibration stage Ross Walker (Wed Aug 17 2011 - 09:38:00 PDT)
[AMBER] How to specify a quantum region of a system Aimin (Wed Aug 17 2011 - 10:19:08 PDT)
- Re: [AMBER] How to specify a quantum region of a system Jason Swails (Wed Aug 17 2011 - 10:38:55 PDT)
  - Re: [AMBER] How to specify a quantum region of a system Ross Walker (Wed Aug 17 2011 - 13:38:02 PDT)
[AMBER] AmberTools installation difficulties on Mac OSX Jennifer L. Muzyka (Wed Aug 17 2011 - 13:33:49 PDT)
- Re: [AMBER] AmberTools installation difficulties on Mac OSX Jason Swails (Wed Aug 17 2011 - 15:00:26 PDT)
[AMBER] How to interpret GLYCAM prep file? Yun Shi (Wed Aug 17 2011 - 16:52:46 PDT)
- Re: [AMBER] How to interpret GLYCAM prep file? Bill Ross (Wed Aug 17 2011 - 18:34:32 PDT)
  - Re: [AMBER] How to interpret GLYCAM prep file? Lachele Foley (Lists) (Wed Aug 17 2011 - 19:09:57 PDT)
    - Re: [AMBER] How to interpret GLYCAM prep file? Yun Shi (Thu Aug 18 2011 - 11:03:47 PDT)
    - Re: [AMBER] How to interpret GLYCAM prep file? Lachele Foley (Lists) (Thu Aug 18 2011 - 11:54:29 PDT)
    - Re: [AMBER] How to interpret GLYCAM prep file? Yun Shi (Thu Aug 18 2011 - 12:18:05 PDT)
    - Re: [AMBER] How to interpret GLYCAM prep file? Lachele Foley (Lists) (Thu Aug 18 2011 - 12:47:01 PDT)
    - Re: [AMBER] How to interpret GLYCAM prep file? Yun Shi (Mon Aug 29 2011 - 16:03:10 PDT)
    - Re: [AMBER] How to interpret GLYCAM prep file? Lachele Foley (Lists) (Mon Aug 29 2011 - 16:56:12 PDT)
    - Re: [AMBER] How to interpret GLYCAM prep file? Yun Shi (Tue Aug 30 2011 - 13:24:57 PDT)
    - Re: [AMBER] How to interpret GLYCAM prep file? Lachele Foley (Lists) (Tue Aug 30 2011 - 14:01:19 PDT)
    - Re: [AMBER] How to interpret GLYCAM prep file? Yun Shi (Thu Sep 08 2011 - 23:38:15 PDT)
    - Re: [AMBER] How to interpret GLYCAM prep file? Lachele Foley (Lists) (Fri Sep 09 2011 - 07:52:18 PDT)
    - Re: [AMBER] How to interpret GLYCAM prep file? Yun Shi (Wed Sep 14 2011 - 16:49:42 PDT)
    - Re: [AMBER] How to interpret GLYCAM prep file? FyD (Thu Sep 15 2011 - 00:54:20 PDT)
    - Re: [AMBER] How to interpret GLYCAM prep file? Lachele Foley (Lists) (Thu Sep 15 2011 - 07:37:15 PDT)
[AMBER] Problem with AT 1.5 installation Emmanuel Baribefe Naziga (Wed Aug 17 2011 - 18:28:40 PDT)
- Re: [AMBER] Problem with AT 1.5 installation David Case (Wed Aug 17 2011 - 18:57:07 PDT)
  - Re: [AMBER] Problem with AT 1.5 installation Emmanuel Baribefe Naziga (Wed Aug 17 2011 - 19:52:19 PDT)
- Re: [AMBER] Problem with AT 1.5 installation Daniel Roe (Wed Aug 17 2011 - 20:17:14 PDT)
  - Re: [AMBER] Problem with AT 1.5 installation Emmanuel Baribefe Naziga (Wed Aug 17 2011 - 20:41:45 PDT)
[AMBER] Coordinate resetting cannot be accomplished, deviation is too large Danny Xu (Wed Aug 17 2011 - 19:13:05 PDT)
- Re: [AMBER] Coordinate resetting cannot be accomplished, deviation is too large Jason Swails (Wed Aug 17 2011 - 19:56:21 PDT)
  - Re: [AMBER] Coordinate resetting cannot be accomplished, deviation is too large Danny Xu (Wed Aug 17 2011 - 21:01:11 PDT)
  - [AMBER] Using iwrap with harmonic restraints Ozen, Aysegul (Thu Aug 18 2011 - 17:44:08 PDT)
    - Re: [AMBER] Using iwrap with harmonic restraints Jason Swails (Thu Aug 18 2011 - 17:50:55 PDT)
    - [AMBER] Questions about Amber Tutorials - A7 - Replica Exchange Simulations with AMBER 10 Catein Catherine (Thu Aug 18 2011 - 19:59:47 PDT)
    - Re: [AMBER] Questions about Amber Tutorials - A7 - Replica Exchange Simulations with AMBER 10 Daniel Sindhikara (Thu Aug 18 2011 - 21:31:34 PDT)
    - Re: [AMBER] Using iwrap with harmonic restraints Ozen, Aysegul (Mon Aug 22 2011 - 08:35:27 PDT)
    - Re: [AMBER] Using iwrap with harmonic restraints Ross Walker (Mon Aug 22 2011 - 10:33:07 PDT)
    - Re: [AMBER] Using iwrap with harmonic restraints Ozen, Aysegul (Mon Aug 22 2011 - 17:27:31 PDT)
    - Re: [AMBER] Using iwrap with harmonic restraints Ross Walker (Mon Aug 22 2011 - 18:30:11 PDT)
    - Re: [AMBER] Using iwrap with harmonic restraints Ozen, Aysegul (Tue Aug 23 2011 - 07:38:24 PDT)
    - Re: [AMBER] Using iwrap with harmonic restraints Ozen, Aysegul (Tue Aug 23 2011 - 07:58:05 PDT)
    - Re: [AMBER] Using iwrap with harmonic restraints Jason Swails (Tue Aug 23 2011 - 08:03:20 PDT)
- Re: [AMBER] Coordinate resetting cannot be accomplished, deviation is too large Daniel Roe (Wed Aug 17 2011 - 21:20:34 PDT)
  - Re: [AMBER] Coordinate resetting cannot be accomplished, deviation is too large Danny Xu (Wed Aug 17 2011 - 22:01:31 PDT)
    - Re: [AMBER] Coordinate resetting cannot be accomplished, deviation is too large Jason Swails (Thu Aug 18 2011 - 07:40:00 PDT)
[AMBER] pm6 parameters Anglea A. (Wed Aug 17 2011 - 21:44:46 PDT)
- Re: [AMBER] pm6 parameters Andreas Goetz (Thu Aug 18 2011 - 10:46:57 PDT)
[AMBER] Executing Parmchk madhumita das (Thu Aug 18 2011 - 03:25:17 PDT)
- Re: [AMBER] Executing Parmchk Jason Swails (Thu Aug 18 2011 - 07:36:06 PDT)
[AMBER] NOE constraints labeling marco.bartoloni.students.unibe.ch (Thu Aug 18 2011 - 03:55:32 PDT)
- Re: [AMBER] NOE constraints labeling David A Case (Thu Aug 18 2011 - 04:46:35 PDT)
[AMBER] test of the mailing list server David A Case (Thu Aug 18 2011 - 10:44:05 PDT)
[AMBER] molecule out box after reimage mirage . (Thu Aug 18 2011 - 15:47:25 PDT)
- Re: [AMBER] molecule out box after reimage Jason Swails (Thu Aug 18 2011 - 17:41:08 PDT)
[AMBER] Fwd: _mmpbsa_py_energy error durint PB calculations Ray Luo, Ph.D. (Thu Aug 18 2011 - 17:53:46 PDT)
[AMBER] Problem installing AmverTools 1.5 on Mac Alexej Grjasnow (Fri Aug 19 2011 - 01:49:13 PDT)
- Re: [AMBER] Problem installing AmverTools 1.5 on Mac Daniel Roe (Fri Aug 19 2011 - 09:30:46 PDT)
- Re: [AMBER] Problem installing AmverTools 1.5 on Mac Jason Swails (Fri Aug 19 2011 - 16:05:59 PDT)
[AMBER] ntr=1 nmropt=1 Fernando Martín García (Fri Aug 19 2011 - 02:40:12 PDT)
- Re: [AMBER] ntr=1 nmropt=1 Mark Williamson (Fri Aug 19 2011 - 03:16:34 PDT)
  - Re: [AMBER] ntr=1 nmropt=1 Fernando Martín García (Fri Aug 19 2011 - 03:33:44 PDT)
    - Re: [AMBER] ntr=1 nmropt=1 Mark Williamson (Fri Aug 19 2011 - 03:38:57 PDT)
    - Re: [AMBER] ntr=1 nmropt=1 Fernando Martín García (Fri Aug 19 2011 - 03:52:14 PDT)
- Re: [AMBER] ntr=1 nmropt=1 David A Case (Fri Aug 19 2011 - 05:00:12 PDT)
  - Re: [AMBER] ntr=1 nmropt=1 Fernando Martín García (Fri Aug 19 2011 - 06:37:46 PDT)
    - [AMBER] Any tutorial on 3D-RISM calculation with AMBER10? Catein Catherine (Fri Aug 19 2011 - 07:20:18 PDT)
    - Re: [AMBER] Any tutorial on 3D-RISM calculation with AMBER10? Tyler Luchko (Fri Aug 19 2011 - 11:10:47 PDT)
[AMBER] Amber 11 bugfix Jennifer L. Muzyka (Fri Aug 19 2011 - 07:46:42 PDT)
- Re: [AMBER] Amber 11 bugfix David A Case (Fri Aug 19 2011 - 07:51:37 PDT)
  - Re: [AMBER] Amber 11 bugfix Jennifer L. Muzyka (Fri Aug 19 2011 - 07:54:33 PDT)
    - Re: [AMBER] Amber 11 bugfix Jason Swails (Fri Aug 19 2011 - 08:04:54 PDT)
    - Re: [AMBER] Amber 11 bugfix/Cuda update filip fratev (Fri Aug 19 2011 - 10:20:44 PDT)
    - Re: [AMBER] Amber 11 bugfix/Cuda update Ismail, Mohd F. (Fri Aug 19 2011 - 10:23:16 PDT)
    - Re: [AMBER] Amber 11 bugfix/Cuda update Ross Walker (Fri Aug 19 2011 - 10:28:26 PDT)
    - Re: [AMBER] Amber 11 bugfix/cuda update filip fratev (Fri Aug 19 2011 - 10:33:31 PDT)
[AMBER] pmemd.cuda error Oliver Kuhn (Fri Aug 19 2011 - 07:59:11 PDT)
[AMBER] Major GPU Update Released Ross Walker (Fri Aug 19 2011 - 08:22:59 PDT)
- Re: [AMBER] Major GPU Update Released filip fratev (Fri Aug 19 2011 - 09:39:14 PDT)
- Re: [AMBER] Major GPU Update Released Ismail, Mohd F. (Fri Aug 19 2011 - 10:14:58 PDT)
  - Re: [AMBER] Major GPU Update Released Ross Walker (Fri Aug 19 2011 - 10:20:38 PDT)
    - Re: [AMBER] Major GPU Update Released Ismail, Mohd F. (Fri Aug 19 2011 - 10:47:46 PDT)
    - Re: [AMBER] Major GPU Update Released Ross Walker (Fri Aug 19 2011 - 11:02:12 PDT)
    - Re: [AMBER] Major GPU Update Released Ismail, Mohd F. (Fri Aug 19 2011 - 11:06:18 PDT)
    - Re: [AMBER] Major GPU Update Released filip fratev (Fri Aug 19 2011 - 16:08:43 PDT)
    - Re: [AMBER] Major GPU Update Released Scott Le Grand (Fri Aug 19 2011 - 16:37:50 PDT)
    - Re: [AMBER] Major GPU Update Released Levi Pierce (Sat Aug 20 2011 - 00:20:43 PDT)
    - Re: [AMBER] Major GPU Update Released Santosh Mogurampelly (Sat Aug 20 2011 - 02:39:06 PDT)
    - Re: [AMBER] Major GPU Update Released filip fratev (Sat Aug 20 2011 - 06:46:13 PDT)
    - Re: [AMBER] Major GPU Update Released Santosh Mogurampelly (Sat Aug 20 2011 - 21:39:00 PDT)
    - Re: [AMBER] Major GPU Update Released filip fratev (Sat Aug 20 2011 - 07:02:58 PDT)
    - Re: [AMBER] Major GPU Update Released filip fratev (Sat Aug 20 2011 - 07:16:55 PDT)
    - Re: [AMBER] Major GPU Update Released Ross Walker (Sat Aug 20 2011 - 08:40:46 PDT)
    - Re: [AMBER] Major GPU Update Released filip fratev (Sat Aug 20 2011 - 10:32:52 PDT)
    - Re: [AMBER] Major GPU Update Released Ismail, Mohd F. (Sat Aug 20 2011 - 11:13:46 PDT)
    - Re: [AMBER] Major GPU Update Released Danny Xu (Sat Aug 20 2011 - 12:51:46 PDT)
    - Re: [AMBER] Major GPU Update Released filip fratev (Sat Aug 20 2011 - 14:18:09 PDT)
    - Re: [AMBER] Major GPU Update Released filip fratev (Sat Aug 20 2011 - 14:15:08 PDT)
    - Re: [AMBER] Major GPU Update Released Scott Le Grand (Sat Aug 20 2011 - 16:04:04 PDT)
    - Re: [AMBER] Major GPU Update Released filip fratev (Sat Aug 20 2011 - 18:20:16 PDT)
    - Re: [AMBER] Major GPU Update Released Ross Walker (Sat Aug 20 2011 - 19:01:04 PDT)
    - Re: [AMBER] Major GPU Update Released Dmitry Mukha (Sun Aug 21 2011 - 10:13:31 PDT)
    - Re: [AMBER] Major GPU Update Released Jason Swails (Sun Aug 21 2011 - 10:17:34 PDT)
    - Re: [AMBER] Major GPU Update Released Dmitry Mukha (Sun Aug 21 2011 - 10:24:29 PDT)
    - Re: [AMBER] Major GPU Update Released Scott Le Grand (Sun Aug 21 2011 - 12:17:32 PDT)
    - Re: [AMBER] Major GPU Update Released Dmitry Mukha (Sun Aug 21 2011 - 13:27:36 PDT)
    - Re: [AMBER] Major GPU Update Released Scott Le Grand (Sun Aug 21 2011 - 13:34:35 PDT)
    - Re: [AMBER] Major GPU Update Released filip fratev (Sun Aug 21 2011 - 13:58:29 PDT)
    - Re: [AMBER] Major GPU Update Released Scott Le Grand (Sun Aug 21 2011 - 14:59:14 PDT)
    - Re: [AMBER] Major GPU Update Released Dmitry Mukha (Tue Aug 23 2011 - 06:51:52 PDT)
    - Re: [AMBER] Major GPU Update Released Scott Le Grand (Tue Aug 23 2011 - 08:43:28 PDT)
    - [AMBER] Is it possible to do REMD for a 12000 atom molecule? Catein Catherine (Tue Aug 23 2011 - 10:18:32 PDT)
    - Re: [AMBER] Is it possible to do REMD for a 12000 atom molecule? Carlos Simmerling (Tue Aug 23 2011 - 10:44:47 PDT)
    - Re: [AMBER] Is it possible to do REMD for a 12000 atom molecule? Adrian Roitberg (Tue Aug 23 2011 - 10:49:23 PDT)
    - [AMBER] Fwd: Is it possible to do REMD for a 12000 atom molecule? Dmitry Mukha (Tue Aug 23 2011 - 12:24:35 PDT)
    - Re: [AMBER] Fwd: Is it possible to do REMD for a 12000 atom molecule? Carlos Simmerling (Tue Aug 23 2011 - 12:26:41 PDT)
    - Re: [AMBER] Fwd: Is it possible to do REMD for a 12000 atom molecule? Dmitry Mukha (Tue Aug 23 2011 - 12:35:15 PDT)
    - Re: [AMBER] Fwd: Is it possible to do REMD for a 12000 atom molecule? Carlos Simmerling (Tue Aug 23 2011 - 12:38:22 PDT)
    - Re: [AMBER] Fwd: Is it possible to do REMD for a 12000 atom molecule? Adrian Roitberg (Tue Aug 23 2011 - 12:30:32 PDT)
    - Re: [AMBER] Fwd: Is it possible to do REMD for a 12000 atom molecule? Dmitry Mukha (Tue Aug 23 2011 - 12:39:27 PDT)
    - Re: [AMBER] Fwd: Is it possible to do REMD for a 12000 atom molecule? Carlos Simmerling (Tue Aug 23 2011 - 12:43:10 PDT)
    - Re: [AMBER] Fwd: Is it possible to do REMD for a 12000 atom molecule? Dmitry Mukha (Tue Aug 23 2011 - 12:59:16 PDT)
    - Re: [AMBER] Fwd: Is it possible to do REMD for a 12000 atom molecule? Adrian Roitberg (Tue Aug 23 2011 - 13:04:15 PDT)
    - Re: [AMBER] Fwd: Is it possible to do REMD for a 12000 atom molecule? Carlos Simmerling (Tue Aug 23 2011 - 13:06:18 PDT)
    - Re: [AMBER] Fwd: Is it possible to do REMD for a 12000 atom molecule? Dmitry Mukha (Tue Aug 23 2011 - 13:26:52 PDT)
    - Re: [AMBER] Fwd: Is it possible to do REMD for a 12000 atom molecule? Carlos Simmerling (Tue Aug 23 2011 - 13:32:43 PDT)
    - Re: [AMBER] Fwd: Is it possible to do REMD for a 12000 atom molecule? Jason Swails (Tue Aug 23 2011 - 14:18:28 PDT)
    - Re: [AMBER] Fwd: Is it possible to do REMD for a 12000 atom molecule? Ross Walker (Tue Aug 23 2011 - 14:11:53 PDT)
    - Re: [AMBER] Fwd: Is it possible to do REMD for a 12000 atom molecule? Carlos Simmerling (Tue Aug 23 2011 - 13:03:56 PDT)
    - Re: [AMBER] Is it possible to do REMD for a 12000 atom molecule? Catein Catherine (Tue Aug 23 2011 - 17:51:28 PDT)
    - Re: [AMBER] Is it possible to do REMD for a 12000 atom molecule? Carlos Simmerling (Tue Aug 23 2011 - 17:53:07 PDT)
    - Re: [AMBER] Major GPU Update Released Dmitry Mukha (Fri Aug 26 2011 - 09:41:42 PDT)
    - Re: [AMBER] Major GPU Update Released Scott Le Grand (Sat Aug 20 2011 - 19:18:59 PDT)
    - Re: [AMBER] Major GPU Update Released filip fratev (Sun Aug 21 2011 - 03:12:27 PDT)
- Re: [AMBER] Major GPU Update Released Ye MEI (Fri Aug 19 2011 - 10:39:38 PDT)
  - Re: [AMBER] Major GPU Update Released Ross Walker (Fri Aug 19 2011 - 10:44:26 PDT)
[AMBER] antechamber + CNT parameter Jagur Lambix (Fri Aug 19 2011 - 09:32:13 PDT)
- Re: [AMBER] antechamber + CNT parameter David A Case (Fri Aug 19 2011 - 09:54:02 PDT)
  - Re: [AMBER] antechamber + CNT parameter Jagur Lambix (Fri Aug 19 2011 - 10:17:47 PDT)
- Re: [AMBER] antechamber + CNT parameter Nadine Utz (Fri Aug 19 2011 - 10:14:59 PDT)
[AMBER] nmropt and restraint_wt Danny Xu (Fri Aug 19 2011 - 09:58:56 PDT)
- Re: [AMBER] nmropt and restraint_wt David A Case (Fri Aug 19 2011 - 11:15:34 PDT)
  - Re: [AMBER] nmropt and restraint_wt Danny Xu (Sat Aug 20 2011 - 08:15:52 PDT)
    - Re: [AMBER] nmropt and restraint_wt case (Sat Aug 20 2011 - 09:35:23 PDT)
    - Re: [AMBER] nmropt and restraint_wt Danny Xu (Sat Aug 20 2011 - 10:54:52 PDT)
    - Re: [AMBER] nmropt and restraint_wt Jason Swails (Sat Aug 20 2011 - 11:19:24 PDT)
[AMBER] TUTORIAL B3 - SECTION 6 George Tzotzos (Fri Aug 19 2011 - 11:12:33 PDT)
- Re: [AMBER] TUTORIAL B3 - SECTION 6 George Tzotzos (Fri Aug 19 2011 - 14:19:56 PDT)
  - Re: [AMBER] TUTORIAL B3 - SECTION 6 Jason Swails (Fri Aug 19 2011 - 15:51:19 PDT)
    - Re: [AMBER] TUTORIAL B3 - SECTION 6 George Tzotzos (Sat Aug 20 2011 - 04:12:58 PDT)
[AMBER] hbond atom mask in cpptraj mirage . (Fri Aug 19 2011 - 16:19:12 PDT)
- Re: [AMBER] hbond atom mask in cpptraj mirage . (Sat Aug 20 2011 - 10:50:12 PDT)
  - Re: [AMBER] hbond atom mask in cpptraj mirage . (Sat Aug 20 2011 - 16:16:46 PDT)
    - Re: [AMBER] hbond atom mask in cpptraj Daniel Roe (Mon Aug 22 2011 - 08:47:35 PDT)
    - Re: [AMBER] hbond atom mask in cpptraj mirage . (Mon Aug 22 2011 - 09:21:29 PDT)
- Re: [AMBER] hbond atom mask in cpptraj Jason Swails (Sat Aug 20 2011 - 11:27:30 PDT)
[AMBER] Creating new reaction coordinates Michael F. Bruist (Fri Aug 19 2011 - 16:59:03 PDT)
Re: [AMBER] [q4md-fft] General Question about Charge Derivation using RESP FyD (Sat Aug 20 2011 - 01:16:37 PDT)
- Re: [AMBER] [q4md-fft] General Question about Charge Derivation using RESP Ismail, Mohd F. (Tue Aug 23 2011 - 09:17:26 PDT)
  - Re: [AMBER] [q4md-fft] General Question about Charge Derivation using RESP FyD (Tue Aug 23 2011 - 23:41:58 PDT)
[AMBER] ptraj cluster George Tzotzos (Sat Aug 20 2011 - 04:08:29 PDT)
- Re: [AMBER] ptraj cluster Daniel Roe (Mon Aug 22 2011 - 09:08:49 PDT)
  - Re: [AMBER] ptraj cluster George Tzotzos (Mon Aug 22 2011 - 10:40:08 PDT)
[AMBER] fftw-2.1.5 and Fedora Dmitry Mukha (Sun Aug 21 2011 - 08:51:21 PDT)
- Re: [AMBER] fftw-2.1.5 and Fedora Dmitry Mukha (Tue Aug 23 2011 - 08:37:20 PDT)
[AMBER] Analysing the result after simulation souvik sur (Sun Aug 21 2011 - 22:27:08 PDT)
- Re: [AMBER] Analysing the result after simulation Kshatresh Dutta Dubey (Sun Aug 21 2011 - 23:00:38 PDT)
  - Re: [AMBER] Analysing the result after simulation souvik sur (Sun Aug 21 2011 - 23:27:17 PDT)
    - Re: [AMBER] Analysing the result after simulation Bruno Rodrigues (Mon Aug 22 2011 - 12:29:39 PDT)
- Re: [AMBER] Analysing the result after simulation TH Chew (Sun Aug 21 2011 - 23:01:07 PDT)
  - Re: [AMBER] Analysing the result after simulation souvik sur (Sun Aug 21 2011 - 23:27:38 PDT)
[AMBER] Error in mm_pbsa Esam Tolba (Mon Aug 22 2011 - 04:38:47 PDT)
- Re: [AMBER] Error in mm_pbsa Ray Luo, Ph.D. (Mon Aug 22 2011 - 04:58:07 PDT)
- Re: [AMBER] Error in mm_pbsa Ray Luo, Ph.D. (Mon Aug 22 2011 - 05:31:13 PDT)
  - Re: [AMBER] Error in mm_pbsa Chinh Su Tran To (Tue Jun 11 2013 - 02:09:38 PDT)
    - Re: [AMBER] Error in mm_pbsa Jason Swails (Tue Jun 11 2013 - 05:38:37 PDT)
    - Re: [AMBER] Error in mm_pbsa Chinh Su Tran To (Tue Jun 11 2013 - 20:56:09 PDT)
- Re: [AMBER] Error in mm_pbsa Mengjuei Hsieh (Mon Aug 22 2011 - 19:58:11 PDT)
[AMBER] problem with decomposition in mm-pbsa.pl moitrayee.mbu.iisc.ernet.in (Mon Aug 22 2011 - 06:00:41 PDT)
[AMBER] compilation problem with bugfix 1 to 17 Hongyu Miao (Mon Aug 22 2011 - 10:50:08 PDT)
- Re: [AMBER] compilation problem with bugfix 1 to 17 Jason Swails (Mon Aug 22 2011 - 12:32:54 PDT)
  - Re: [AMBER] compilation problem with bugfix 1 to 17 Hongyu Miao (Mon Aug 22 2011 - 13:49:21 PDT)
[AMBER] Is GB solvation possible with AT 1.5 sqm? Emmanuel Baribefe Naziga (Mon Aug 22 2011 - 12:45:31 PDT)
[AMBER] ESPGEN William Wei (Mon Aug 22 2011 - 14:23:20 PDT)
- Re: [AMBER] ESPGEN Jason Swails (Mon Aug 22 2011 - 14:30:52 PDT)
  - Re: [AMBER] ESPGEN William Wei (Tue Aug 23 2011 - 13:03:31 PDT)
    - Re: [AMBER] ESPGEN Jason Swails (Tue Aug 23 2011 - 14:21:13 PDT)
    - Re: [AMBER] ESPGEN Niel Henriksen (Tue Aug 23 2011 - 14:33:24 PDT)
    - Re: [AMBER] ESPGEN Jason Swails (Tue Aug 23 2011 - 14:40:30 PDT)
- Re: [AMBER] ESPGEN Niel Henriksen (Thu Aug 25 2011 - 14:40:17 PDT)
[AMBER] problem with mm_pbsa moitrayee.mbu.iisc.ernet.in (Mon Aug 22 2011 - 14:35:19 PDT)
- Re: [AMBER] problem with mm_pbsa Bill Miller III (Tue Aug 23 2011 - 10:54:27 PDT)
[AMBER] Error: Amber 11 and CUDA4.0 c00jsw00.nchc.narl.org.tw (Mon Aug 22 2011 - 21:59:53 PDT)
[AMBER] Error: Amber 11 and CUDA4.0 c00jsw00.nchc.narl.org.tw (Mon Aug 22 2011 - 22:01:35 PDT)
- Re: [AMBER] Error: Amber 11 and CUDA4.0 Ismail, Mohd F. (Mon Aug 22 2011 - 22:03:16 PDT)
- Re: [AMBER] Error: Amber 11 and CUDA4.0 Ross Walker (Mon Aug 22 2011 - 22:07:05 PDT)
  - Re: [AMBER] Error: Amber 11 and CUDA4.0 c00jsw00.nchc.narl.org.tw (Mon Aug 22 2011 - 22:27:12 PDT)
    - Re: [AMBER] Error: Amber 11 and CUDA4.0 Ross Walker (Mon Aug 22 2011 - 22:44:12 PDT)
[AMBER] MMPBSA not installed in amber11 vaibhav dixit (Tue Aug 23 2011 - 03:43:42 PDT)
- Re: [AMBER] MMPBSA not installed in amber11 Jason Swails (Tue Aug 23 2011 - 04:20:07 PDT)
  - Re: [AMBER] MMPBSA not installed in amber11 vaibhav dixit (Tue Aug 23 2011 - 06:06:58 PDT)
    - Re: [AMBER] MMPBSA not installed in amber11 Jason Swails (Tue Aug 23 2011 - 06:28:22 PDT)
    - Re: [AMBER] MMPBSA not installed in amber11 vaibhav dixit (Tue Aug 23 2011 - 06:49:00 PDT)
[AMBER] MD output files George Tzotzos (Tue Aug 23 2011 - 04:05:01 PDT)
- Re: [AMBER] MD output files Jason Swails (Tue Aug 23 2011 - 04:23:48 PDT)
[AMBER] AMBER11 GPGPU question Carlos Sosa (Tue Aug 23 2011 - 10:14:56 PDT)
[AMBER] GPGPU AMBER11 question Carlos P Sosa (Tue Aug 23 2011 - 11:30:14 PDT)
- Re: [AMBER] GPGPU AMBER11 question Carlos Sosa (Wed Aug 24 2011 - 14:17:36 PDT)
[AMBER] libstdc++, Fedora14, Amber11, pmemd.cuda Dmitry Mukha (Tue Aug 23 2011 - 12:15:43 PDT)
- Re: [AMBER] libstdc++, Fedora14, Amber11, pmemd.cuda Jason Swails (Tue Aug 23 2011 - 14:38:46 PDT)
  - Re: [AMBER] libstdc++, Fedora14, Amber11, pmemd.cuda Dmitry Mukha (Wed Aug 24 2011 - 05:46:00 PDT)
    - Re: [AMBER] libstdc++, Fedora14, Amber11, pmemd.cuda Jason Swails (Wed Aug 24 2011 - 07:39:40 PDT)
    - Re: [AMBER] libstdc++, Fedora14, Amber11, pmemd.cuda Dmitry Mukha (Wed Aug 24 2011 - 08:00:17 PDT)
    - Re: [AMBER] libstdc++, Fedora14, Amber11, pmemd.cuda Jason Swails (Wed Aug 24 2011 - 09:48:51 PDT)
    - Re: [AMBER] libstdc++, Fedora14, Amber11, pmemd.cuda Dmitry Mukha (Fri Aug 26 2011 - 06:07:45 PDT)
[AMBER] ptraj invalid writes Ben Gamari (Tue Aug 23 2011 - 13:10:02 PDT)
- Re: [AMBER] ptraj invalid writes Daniel Roe (Tue Aug 23 2011 - 14:48:32 PDT)
  - Re: [AMBER] ptraj invalid writes Ben Gamari (Thu Aug 25 2011 - 12:29:49 PDT)
[AMBER] About sudden simulation box twist Bin Wu (Tue Aug 23 2011 - 13:53:10 PDT)
- Re: [AMBER] About sudden simulation box twist Carlos Simmerling (Tue Aug 23 2011 - 13:58:16 PDT)
  - Re: [AMBER] About sudden simulation box twist Bin Wu (Tue Aug 23 2011 - 14:19:34 PDT)
    - Re: [AMBER] About sudden simulation box twist Adrian Roitberg (Tue Aug 23 2011 - 14:23:13 PDT)
    - Re: [AMBER] About sudden simulation box twist Bin Wu (Tue Aug 23 2011 - 14:39:23 PDT)
    - Re: [AMBER] About sudden simulation box twist Adrian Roitberg (Tue Aug 23 2011 - 14:40:55 PDT)
    - Re: [AMBER] About sudden simulation box twist Jason Swails (Tue Aug 23 2011 - 14:30:55 PDT)
    - Re: [AMBER] About sudden simulation box twist Bin Wu (Tue Aug 23 2011 - 15:43:52 PDT)
    - Re: [AMBER] About sudden simulation box twist Jason Swails (Tue Aug 23 2011 - 15:52:36 PDT)
    - Re: [AMBER] About sudden simulation box twist Bin Wu (Tue Aug 23 2011 - 16:42:02 PDT)
    - Re: [AMBER] About sudden simulation box twist Bin Wu (Wed Aug 24 2011 - 15:16:15 PDT)
    - Re: [AMBER] About sudden simulation box twist Thomas Cheatham III (Wed Aug 24 2011 - 15:23:29 PDT)
    - Re: [AMBER] About sudden simulation box twist Bin Wu (Wed Aug 24 2011 - 15:36:00 PDT)
    - Re: [AMBER] About sudden simulation box twist Thomas Cheatham III (Thu Aug 25 2011 - 13:36:08 PDT)
    - Re: [AMBER] About sudden simulation box twist Bin Wu (Thu Aug 25 2011 - 14:13:31 PDT)
[AMBER] antechamber error vaibhav dixit (Tue Aug 23 2011 - 21:33:57 PDT)
- Re: [AMBER] antechamber error Jason Swails (Wed Aug 24 2011 - 04:52:30 PDT)
  - Re: [AMBER] antechamber error vaibhav dixit (Wed Aug 24 2011 - 06:58:46 PDT)
    - Re: [AMBER] antechamber error David A Case (Wed Aug 24 2011 - 08:23:10 PDT)
    - Re: [AMBER] antechamber error vaibhav dixit (Thu Aug 25 2011 - 01:15:19 PDT)
    - Re: [AMBER] antechamber error Daniel Roe (Thu Aug 25 2011 - 04:19:32 PDT)
    - Re: [AMBER] antechamber error David A Case (Thu Aug 25 2011 - 07:16:54 PDT)
    - Re: [AMBER] antechamber error vaibhav dixit (Thu Aug 25 2011 - 22:50:43 PDT)
    - Re: [AMBER] antechamber error David A Case (Fri Aug 26 2011 - 05:35:54 PDT)
    - Re: [AMBER] antechamber error vaibhav dixit (Fri Aug 26 2011 - 22:34:45 PDT)
    - Re: [AMBER] antechamber error case (Sun Aug 28 2011 - 06:45:03 PDT)
    - Re: [AMBER] antechamber error vaibhav dixit (Mon Aug 29 2011 - 09:38:04 PDT)
[AMBER] How to make a graph of secondary structure? qiao xue (Wed Aug 24 2011 - 05:37:00 PDT)
[AMBER] Amber Shesh Nath (Wed Aug 24 2011 - 05:44:01 PDT)
- Re: [AMBER] Amber David A Case (Wed Aug 24 2011 - 06:17:17 PDT)
[AMBER] question about creating phantom residues moitrayee.mbu.iisc.ernet.in (Wed Aug 24 2011 - 11:30:56 PDT)
- Re: [AMBER] question about creating phantom residues Jason Swails (Wed Aug 24 2011 - 12:15:12 PDT)
[AMBER] mmgbsa.py energy decomposition problem Yi An (Wed Aug 24 2011 - 14:56:55 PDT)
- Re: [AMBER] mmgbsa.py energy decomposition problem Bill Miller III (Wed Aug 24 2011 - 15:27:17 PDT)
  - Re: [AMBER] mmgbsa.py energy decomposition problem Jason Swails (Wed Aug 24 2011 - 15:28:15 PDT)
[AMBER] MMPBSA free energy decomposition values and total binding free energy values Rajesh Raju (Wed Aug 24 2011 - 16:05:35 PDT)
[AMBER] Technical problems with running steered MD Sergey Samsonov (Thu Aug 25 2011 - 04:34:58 PDT)
- Re: [AMBER] Technical problems with running steered MD David A Case (Thu Aug 25 2011 - 07:21:36 PDT)
  - Re: [AMBER] Technical problems with running steered MD Sergey Samsonov (Thu Aug 25 2011 - 07:31:35 PDT)
    - Re: [AMBER] Technical problems with running steered MD David A Case (Thu Aug 25 2011 - 08:22:56 PDT)
    - Re: [AMBER] Technical problems with running steered MD Sergey Samsonov (Fri Aug 26 2011 - 00:20:31 PDT)
    - Re: [AMBER] Technical problems with running steered MD Jason Swails (Thu Aug 25 2011 - 09:01:54 PDT)
[AMBER] Dihedral of quadruple of centres of mass Massimiliano Porrini (Thu Aug 25 2011 - 07:34:33 PDT)
- Re: [AMBER] Dihedral of quadruple of centres of mass Daniel Roe (Thu Aug 25 2011 - 08:00:28 PDT)
  - Re: [AMBER] Dihedral of quadruple of centres of mass Massimiliano Porrini (Thu Aug 25 2011 - 08:22:43 PDT)
    - Re: [AMBER] Dihedral of quadruple of centres of mass Daniel Roe (Thu Aug 25 2011 - 09:17:57 PDT)
[AMBER] Jarzynski and PMEMD Sai Kumar Ramadugu (Thu Aug 25 2011 - 09:23:12 PDT)
- Re: [AMBER] Jarzynski and PMEMD Jason Swails (Thu Aug 25 2011 - 16:32:38 PDT)
[AMBER] Potential problem with CUDA version in release 18? Carlos P Sosa (Thu Aug 25 2011 - 10:26:39 PDT)
- Re: [AMBER] Potential problem with CUDA version in release 18? Ismail, Mohd F. (Thu Aug 25 2011 - 10:39:48 PDT)
[AMBER] Potential problem with CUDA version in release 18? Carlos P Sosa (Thu Aug 25 2011 - 11:04:19 PDT)
- Re: [AMBER] Potential problem with CUDA version in release 18? David A Case (Thu Aug 25 2011 - 11:53:32 PDT)
- Re: [AMBER] Potential problem with CUDA version in release 18? Ismail, Mohd F. (Thu Aug 25 2011 - 13:09:04 PDT)
  - Re: [AMBER] Potential problem with CUDA version in release 18? Carlos Sosa (Thu Aug 25 2011 - 13:14:09 PDT)
    - Re: [AMBER] Potential problem with CUDA version in release 18? Ross Walker (Thu Aug 25 2011 - 20:19:34 PDT)
    - Re: [AMBER] Potential problem with CUDA version in release 18? Carlos Sosa (Thu Aug 25 2011 - 21:11:02 PDT)
[AMBER] GPGPU AMBER11 question Carlos P Sosa (Thu Aug 25 2011 - 12:27:44 PDT)
- Re: [AMBER] GPGPU AMBER11 question Ross Walker (Thu Aug 25 2011 - 20:19:34 PDT)
  - Re: [AMBER] GPGPU AMBER11 question Carlos Sosa (Fri Aug 26 2011 - 08:21:28 PDT)
[AMBER] Ptraj and wrapping water molecules Sai Kumar Ramadugu (Thu Aug 25 2011 - 14:55:47 PDT)
- Re: [AMBER] Ptraj and wrapping water molecules Thomas Cheatham III (Thu Aug 25 2011 - 15:06:40 PDT)
  - Re: [AMBER] Ptraj and wrapping water molecules Ozen, Aysegul (Tue Aug 30 2011 - 12:07:49 PDT)
  - Re: [AMBER] Ptraj and wrapping water molecules Sai Kumar Ramadugu (Wed Aug 31 2011 - 13:32:23 PDT)
    - Re: [AMBER] Ptraj and wrapping water molecules InSuk Joung (Wed Aug 31 2011 - 13:53:47 PDT)
[AMBER] Calculating Cpu hours from output file Chris Bryant (Thu Aug 25 2011 - 15:02:03 PDT)
- Re: [AMBER] Calculating Cpu hours from output file Jason Swails (Thu Aug 25 2011 - 16:29:09 PDT)
  - Re: [AMBER] Calculating Cpu hours from output file Chris Bryant (Thu Aug 25 2011 - 19:13:04 PDT)
[AMBER] Amber11 on SGI Altix Bruno Rodrigues (Thu Aug 25 2011 - 16:12:41 PDT)
- Re: [AMBER] Amber11 on SGI Altix Bruno Rodrigues (Fri Aug 26 2011 - 04:50:18 PDT)
[AMBER] folding/unfolding or just local minimum trap? Chinh Su Tran To (Fri Aug 26 2011 - 03:16:11 PDT)
- Re: [AMBER] folding/unfolding or just local minimum trap? Carlos Simmerling (Fri Aug 26 2011 - 04:29:23 PDT)
  - Re: [AMBER] folding/unfolding or just local minimum trap? Chinh Su Tran To (Fri Aug 26 2011 - 05:51:57 PDT)
    - Re: [AMBER] folding/unfolding or just local minimum trap? Carlos Simmerling (Sat Aug 27 2011 - 06:26:27 PDT)
    - Re: [AMBER] folding/unfolding or just local minimum trap? Chinh Su Tran To (Sat Aug 27 2011 - 07:43:08 PDT)
[AMBER] postdoc positions in chemical physics Dr. Vitaly V. Chaban (Fri Aug 26 2011 - 07:36:59 PDT)
[AMBER] problem with Cadmium parameters and running minimization Hashem Taha (Fri Aug 26 2011 - 07:57:27 PDT)
- Re: [AMBER] problem with Cadmium parameters and running minimization Ben Roberts (Fri Aug 26 2011 - 08:01:37 PDT)
  - Re: [AMBER] problem with Cadmium parameters and running minimization Hashem Taha (Fri Aug 26 2011 - 08:10:48 PDT)
    - Re: [AMBER] problem with Cadmium parameters and running minimization Ben Roberts (Fri Aug 26 2011 - 08:13:37 PDT)
[AMBER] problem with TI calculation, help!! Victor Ma (Fri Aug 26 2011 - 09:19:15 PDT)
- Re: [AMBER] problem with TI calculation, help!! InSuk Joung (Fri Aug 26 2011 - 09:33:01 PDT)
- Re: [AMBER] problem with TI calculation, help!! Niel Henriksen (Fri Aug 26 2011 - 09:31:08 PDT)
  - Re: [AMBER] problem with TI calculation, help!! Victor Ma (Fri Aug 26 2011 - 09:39:15 PDT)
[AMBER] how to fill in missing parameters in tleap? Yun Shi (Fri Aug 26 2011 - 18:01:25 PDT)
- Re: [AMBER] how to fill in missing parameters in tleap? Jason Swails (Fri Aug 26 2011 - 18:48:33 PDT)
  - Re: [AMBER] how to fill in missing parameters in tleap? case (Sun Aug 28 2011 - 06:12:28 PDT)
    - Re: [AMBER] how to fill in missing parameters in tleap? Yun Shi (Mon Sep 05 2011 - 16:22:19 PDT)
    - Re: [AMBER] how to fill in missing parameters in tleap? Astrid Maaß (Tue Sep 06 2011 - 02:07:37 PDT)
    - Re: [AMBER] how to fill in missing parameters in tleap? Yun Shi (Tue Sep 06 2011 - 08:21:18 PDT)
    - Re: [AMBER] how to fill in missing parameters in tleap? Yun Shi (Tue Sep 06 2011 - 11:22:06 PDT)
    - Re: [AMBER] how to fill in missing parameters in tleap? Astrid Maaß (Wed Sep 07 2011 - 00:14:07 PDT)
    - Re: [AMBER] how to fill in missing parameters in tleap? Yun Shi (Thu Sep 08 2011 - 13:50:55 PDT)
    - Re: [AMBER] how to fill in missing parameters in tleap? Astrid Maaß (Thu Sep 08 2011 - 23:24:15 PDT)
    - Re: [AMBER] how to fill in missing parameters in tleap? Yun Shi (Thu Sep 08 2011 - 23:47:16 PDT)
    - Re: [AMBER] how to fill in missing parameters in tleap? Astrid Maaß (Fri Sep 09 2011 - 04:24:22 PDT)
    - Re: [AMBER] how to fill in missing parameters in tleap? Yun Shi (Fri Sep 09 2011 - 16:51:48 PDT)
    - Re: [AMBER] how to fill in missing parameters in tleap? Astrid Maaß (Mon Sep 12 2011 - 06:11:15 PDT)
    - Re: [AMBER] how to fill in missing parameters in tleap? Yun Shi (Wed Sep 14 2011 - 22:07:21 PDT)
- Re: [AMBER] how to fill in missing parameters in tleap? FyD (Fri Aug 26 2011 - 23:18:32 PDT)
[AMBER] NaN Error in mdout, restrt, mdcrd, mdvel files with pmemd.cuda Ismail, Mohd F. (Sat Aug 27 2011 - 13:13:50 PDT)
- Re: [AMBER] NaN Error in mdout, restrt, mdcrd, mdvel files with pmemd.cuda Ross Walker (Sat Aug 27 2011 - 16:48:31 PDT)
  - Re: [AMBER] NaN Error in mdout, restrt, mdcrd, mdvel files with pmemd.cuda Ismail, Mohd F. (Sun Aug 28 2011 - 12:38:39 PDT)
[AMBER] Error in pmemd.cuda: test.pmemd.cuda.pme zhenquan hu (Sun Aug 28 2011 - 04:44:36 PDT)
- Re: [AMBER] Error in pmemd.cuda: test.pmemd.cuda.pme Ross Walker (Sun Aug 28 2011 - 06:49:31 PDT)
- Re: [AMBER] Error in pmemd.cuda: test.pmemd.cuda.pme Zhenquan Hu (Sun Aug 28 2011 - 18:32:52 PDT)
  - Re: [AMBER] Error in pmemd.cuda: test.pmemd.cuda.pme Scott Le Grand (Sun Aug 28 2011 - 22:31:42 PDT)
[AMBER] ntf parameters in energy minimization Qin Zhang (Mon Aug 29 2011 - 10:24:51 PDT)
- Re: [AMBER] ntf parameters in energy minimization Jason Swails (Mon Aug 29 2011 - 12:45:50 PDT)
  - Re: [AMBER] ntf parameters in energy minimization Qin Zhang (Tue Aug 30 2011 - 12:19:02 PDT)
[AMBER] PBS script Bruno Rodrigues (Mon Aug 29 2011 - 13:05:41 PDT)
- Re: [AMBER] PBS script Jason Swails (Mon Aug 29 2011 - 13:34:25 PDT)
  - Re: [AMBER] PBS script Bruno Rodrigues (Mon Aug 29 2011 - 13:54:13 PDT)
    - Re: [AMBER] PBS script Jason Swails (Mon Aug 29 2011 - 13:59:57 PDT)
    - Re: [AMBER] PBS script Bruno Rodrigues (Mon Aug 29 2011 - 14:05:06 PDT)
    - Re: [AMBER] PBS script Bruno Rodrigues (Mon Aug 29 2011 - 15:13:53 PDT)
    - Re: [AMBER] PBS script Bruno Rodrigues (Mon Aug 29 2011 - 20:34:20 PDT)
    - Re: [AMBER] PBS script Ross Walker (Tue Aug 30 2011 - 07:37:00 PDT)
    - Re: [AMBER] PBS script Carlos Sosa (Tue Aug 30 2011 - 07:57:24 PDT)
    - Re: [AMBER] PBS script Bruno Rodrigues (Thu Sep 08 2011 - 21:38:58 PDT)
    - Re: [AMBER] PBS script Bruno Rodrigues (Thu Sep 08 2011 - 21:36:12 PDT)
[AMBER] MMPBSA.py parallel Jesper Sørensen (Mon Aug 29 2011 - 16:11:01 PDT)
- Re: [AMBER] MMPBSA.py parallel Bill Miller III (Mon Aug 29 2011 - 16:22:11 PDT)
  - Re: [AMBER] MMPBSA.py parallel Jesper Sørensen (Mon Aug 29 2011 - 16:53:50 PDT)
    - Re: [AMBER] MMPBSA.py parallel Jason Swails (Mon Aug 29 2011 - 19:32:55 PDT)
    - Re: [AMBER] MMPBSA.py parallel Jesper Sørensen (Mon Aug 29 2011 - 19:38:56 PDT)
[AMBER] two planes' dihedral angle caobb0214 (Mon Aug 29 2011 - 19:50:49 PDT)
- Re: [AMBER] two planes' dihedral angle Andrew Jewett (Mon Aug 29 2011 - 20:53:52 PDT)
[AMBER] mmpbsa issues Neha Gandhi (Mon Aug 29 2011 - 23:43:25 PDT)
- Re: [AMBER] mmpbsa issues sribone.fcq.unc.edu.ar (Tue Aug 30 2011 - 05:07:36 PDT)
  - Re: [AMBER] mmpbsa issues Jason Swails (Tue Aug 30 2011 - 07:58:27 PDT)
[AMBER] How to patch phosphate at the 3'-end Indrajit Deb (Tue Aug 30 2011 - 04:55:17 PDT)
- Re: [AMBER] How to patch phosphate at the 3'-end David A Case (Tue Aug 30 2011 - 13:21:54 PDT)
  - Re: [AMBER] How to patch phosphate at the 3'-end Hugh Heldenbrand (Tue Aug 30 2011 - 16:31:55 PDT)
[AMBER] LEaP for organic molecule Chidambar Kulkarni (Tue Aug 30 2011 - 05:17:33 PDT)
- Re: [AMBER] LEaP for organic molecule Daniel Roe (Tue Aug 30 2011 - 06:03:34 PDT)
[AMBER] cpptraj: 1) align using a certain region 2) calc rmsd for another region Jan-Philip Gehrcke (Tue Aug 30 2011 - 07:41:37 PDT)
- Re: [AMBER] cpptraj: 1) align using a certain region 2) calc rmsd for another region Jason Swails (Tue Aug 30 2011 - 08:04:18 PDT)
  - Re: [AMBER] cpptraj: 1) align using a certain region 2) calc rmsd for another region Jan-Philip Gehrcke (Wed Aug 31 2011 - 02:25:07 PDT)
[AMBER] sander compiled by which compiler can show full error mesage? xiaodong huang (Tue Aug 30 2011 - 14:17:37 PDT)
- Re: [AMBER] sander compiled by which compiler can show full error mesage? Ray Luo, Ph.D. (Tue Aug 30 2011 - 15:05:56 PDT)
  - Re: [AMBER] sander compiled by which compiler can show full error mesage? xiaodong huang (Tue Aug 30 2011 - 16:05:37 PDT)
    - Re: [AMBER] sander compiled by which compiler can show full error mesage? Jason Swails (Tue Aug 30 2011 - 16:30:03 PDT)
[AMBER] problem in installing xleap sonali dhindwal (Wed Aug 31 2011 - 00:37:25 PDT)
- Re: [AMBER] problem in installing xleap Hirdesh Kumar (Wed Aug 31 2011 - 00:45:36 PDT)
- Re: [AMBER] problem in installing xleap David A Case (Wed Aug 31 2011 - 05:29:10 PDT)
  - Re: [AMBER] problem in installing xleap Chirag Vora (Wed Aug 31 2011 - 06:31:03 PDT)
  - Re: [AMBER] problem in installing xleap sonali dhindwal (Wed Aug 31 2011 - 06:58:08 PDT)
    - Re: [AMBER] problem in installing xleap David A Case (Wed Aug 31 2011 - 11:20:11 PDT)
    - Re: [AMBER] problem in installing xleap sonali dhindwal (Wed Aug 31 2011 - 21:38:20 PDT)
    - Re: [AMBER] problem in installing xleap Ismail, Mohd F. (Wed Aug 31 2011 - 23:35:56 PDT)
    - Re: [AMBER] problem in installing xleap David A Case (Thu Sep 01 2011 - 05:07:57 PDT)
    - Re: [AMBER] problem in installing xleap sonali dhindwal (Fri Sep 02 2011 - 06:58:08 PDT)
    - Re: [AMBER] problem in installing xleap Ismail, Mohd F. (Fri Sep 02 2011 - 09:20:04 PDT)
    - Re: [AMBER] problem in installing xleap peker milas (Fri Sep 02 2011 - 10:21:38 PDT)
    - Re: [AMBER] problem in installing xleap sonali dhindwal (Sat Sep 03 2011 - 04:49:21 PDT)
    - Re: [AMBER] problem in installing xleap case (Sat Sep 03 2011 - 05:57:44 PDT)
    - Re: [AMBER] problem in installing xleap sonali dhindwal (Sat Sep 03 2011 - 07:08:30 PDT)
[AMBER] flip command in leap Peter Varnai (Wed Aug 31 2011 - 03:54:40 PDT)
- Re: [AMBER] flip command in leap FyD (Wed Aug 31 2011 - 08:35:17 PDT)
[AMBER] Calculation of Force during SMD Sai Kumar Ramadugu (Wed Aug 31 2011 - 16:04:09 PDT)
- Re: [AMBER] Calculation of Force during SMD Adrian Roitberg (Wed Aug 31 2011 - 16:09:02 PDT)
  - Re: [AMBER] Calculation of Force during SMD Sai Kumar Ramadugu (Wed Aug 31 2011 - 20:27:51 PDT)
[AMBER] cpptraj-segmentation fault Praapti Jayaswal (Wed Aug 31 2011 - 23:02:24 PDT)
- Re: [AMBER] cpptraj-segmentation fault Daniel Roe (Fri Sep 02 2011 - 15:30:14 PDT)
  - Re: [AMBER] cpptraj-segmentation fault Praapti Jayaswal (Sun Sep 04 2011 - 21:01:05 PDT)
    - Re: [AMBER] cpptraj-segmentation fault Daniel Roe (Mon Sep 05 2011 - 17:26:46 PDT)
    - Re: [AMBER] cpptraj-segmentation fault Praapti Jayaswal (Sun Sep 11 2011 - 23:58:39 PDT)
    - Re: [AMBER] cpptraj-segmentation fault Daniel Roe (Mon Sep 12 2011 - 05:52:38 PDT)
    - Re: [AMBER] cpptraj-segmentation fault Praapti Jayaswal (Mon Sep 12 2011 - 21:37:17 PDT)
    - Re: [AMBER] cpptraj-segmentation fault Daniel Roe (Thu Sep 15 2011 - 05:42:56 PDT)
    - Re: [AMBER] cpptraj-segmentation fault Praapti Jayaswal (Thu Sep 15 2011 - 21:19:40 PDT)
    - Re: [AMBER] cpptraj-segmentation fault Daniel Roe (Thu Sep 15 2011 - 22:10:27 PDT)
    - Re: [AMBER] cpptraj-segmentation fault Praapti Jayaswal (Mon Sep 19 2011 - 22:57:09 PDT)
    - Re: [AMBER] cpptraj-segmentation fault Daniel Roe (Tue Sep 20 2011 - 04:18:48 PDT)
[AMBER] CCA-Phe terminal using Antechamber Sindrila Dutta banik (Thu Sep 01 2011 - 05:39:46 PDT)
- Re: [AMBER] CCA-Phe terminal using Antechamber David A Case (Thu Sep 01 2011 - 07:33:11 PDT)
[AMBER] PTRAJ strange behavior peker milas (Thu Sep 01 2011 - 12:39:38 PDT)
[AMBER] Energy change KIRTANA S (Thu Sep 01 2011 - 13:09:19 PDT)
- Re: [AMBER] Energy change steinbrt.rci.rutgers.edu (Thu Sep 01 2011 - 23:43:24 PDT)
  - Re: [AMBER] Energy change KIRTANA S (Fri Sep 02 2011 - 10:43:55 PDT)
    - Re: [AMBER] Energy change Jason Swails (Fri Sep 02 2011 - 10:53:06 PDT)
    - Re: [AMBER] Energy change kirtana S (Sun Sep 04 2011 - 22:31:45 PDT)
    - Re: [AMBER] Energy change manikanthan bhavaraju (Mon Sep 05 2011 - 13:58:41 PDT)
    - Re: [AMBER] Energy change Bill Miller III (Mon Sep 05 2011 - 13:59:29 PDT)
[AMBER] solvateBox Ismail, Mohd F. (Thu Sep 01 2011 - 14:18:12 PDT)
- Re: [AMBER] solvateBox Jason Swails (Thu Sep 01 2011 - 18:49:07 PDT)
  - Re: [AMBER] solvateBox Jason Swails (Thu Sep 01 2011 - 18:54:44 PDT)
    - Re: [AMBER] solvateBox Ismail, Mohd F. (Thu Sep 01 2011 - 20:36:33 PDT)
    - Re: [AMBER] solvateBox Jason Swails (Thu Sep 01 2011 - 20:51:13 PDT)
    - Re: [AMBER] solvateBox Ismail, Mohd F. (Thu Sep 01 2011 - 21:02:52 PDT)
    - Re: [AMBER] solvateBox Jason Swails (Thu Sep 01 2011 - 22:42:52 PDT)
    - Re: [AMBER] solvateBox Ismail, Mohd F. (Fri Sep 02 2011 - 09:07:36 PDT)
[AMBER] Non standard residue parameterization madhumita das (Fri Sep 02 2011 - 03:20:19 PDT)
- [AMBER] writing box info to pdb file extracted from an mdcrd trajectory CHAMI F. (Fri Sep 02 2011 - 07:28:59 PDT)
  - Re: [AMBER] writing box info to pdb file extracted from an mdcrd trajectory Mark Williamson (Wed Sep 07 2011 - 06:51:42 PDT)
  - Re: [AMBER] writing box info to pdb file extracted from an mdcrd trajectory CHAMI F. (Wed Sep 07 2011 - 09:01:06 PDT)
- Re: [AMBER] Non standard residue parameterization Jason Swails (Fri Sep 02 2011 - 20:29:37 PDT)
  - Re: [AMBER] Non standard residue parameterization madhumita das (Mon Sep 05 2011 - 08:47:30 PDT)
    - Re: [AMBER] Non standard residue parameterization case (Mon Sep 05 2011 - 17:18:11 PDT)
    - Re: [AMBER] Non standard residue parameterization madhumita das (Mon Sep 05 2011 - 23:15:46 PDT)
    - Re: [AMBER] Non standard residue parameterization madhumita das (Mon Sep 05 2011 - 23:22:26 PDT)
    - Re: [AMBER] Non standard residue parameterization case (Tue Sep 06 2011 - 05:29:55 PDT)
- Re: [AMBER] Non standard residue parameterization Bill Ross (Mon Sep 05 2011 - 20:50:19 PDT)
[AMBER] Energy of solute molecule Mattei, Alessandra (Fri Sep 02 2011 - 10:31:35 PDT)
- Re: [AMBER] Energy of solute molecule Jason Swails (Fri Sep 02 2011 - 10:40:46 PDT)
  - Re: [AMBER] Energy of solute molecule Ignacio J. General (Mon Sep 05 2011 - 07:15:14 PDT)
    - Re: [AMBER] Energy of solute molecule Jason Swails (Mon Sep 05 2011 - 15:53:27 PDT)
[AMBER] Run Amber on a system with multiple GPUs peter.stauffert.boehringer-ingelheim.com (Fri Sep 02 2011 - 10:55:35 PDT)
- Re: [AMBER] Run Amber on a system with multiple GPUs Sasha Buzko (Fri Sep 02 2011 - 16:27:21 PDT)
[AMBER] some questions on GAFF su He (Fri Sep 02 2011 - 12:58:06 PDT)
- Re: [AMBER] some questions on GAFF Chirag Vora (Fri Sep 02 2011 - 13:13:07 PDT)
  - Re: [AMBER] some questions on GAFF su He (Fri Sep 02 2011 - 13:25:22 PDT)
[AMBER] SHAKE error help tsurma.umich.edu (Fri Sep 02 2011 - 19:28:08 PDT)
- Re: [AMBER] SHAKE error help Bill Ross (Fri Sep 02 2011 - 21:09:54 PDT)
- Re: [AMBER] SHAKE error help case (Sat Sep 03 2011 - 05:50:13 PDT)
  - Re: [AMBER] SHAKE error help tsurma.umich.edu (Sat Sep 03 2011 - 09:22:39 PDT)
    - Re: [AMBER] SHAKE error help case (Sat Sep 03 2011 - 11:05:41 PDT)
    - Re: [AMBER] SHAKE error help tsurma.umich.edu (Sat Sep 03 2011 - 14:35:49 PDT)
    - Re: [AMBER] SHAKE error help case (Mon Sep 05 2011 - 05:51:58 PDT)
    - Re: [AMBER] SHAKE error help tsurma.umich.edu (Tue Sep 06 2011 - 08:43:08 PDT)
    - Re: [AMBER] SHAKE error help tsurma.umich.edu (Mon Sep 05 2011 - 07:43:45 PDT)
  - Re: [AMBER] SHAKE error help tsurma.umich.edu (Fri Sep 09 2011 - 12:35:42 PDT)
    - Re: [AMBER] SHAKE error help case (Fri Sep 09 2011 - 14:43:43 PDT)
    - Re: [AMBER] SHAKE error help tsurma.umich.edu (Sat Sep 10 2011 - 11:49:10 PDT)
    - Re: [AMBER] SHAKE error help case (Sat Sep 10 2011 - 17:17:26 PDT)
    - Re: [AMBER] SHAKE error help tsurma.umich.edu (Wed Sep 14 2011 - 08:21:23 PDT)
    - [AMBER] sander.MPI tsurma.umich.edu (Tue Oct 25 2011 - 08:06:42 PDT)
    - Re: [AMBER] sander.MPI David A Case (Thu Oct 27 2011 - 05:15:13 PDT)
    - Re: [AMBER] sander.MPI tsurma.umich.edu (Thu Oct 27 2011 - 07:22:11 PDT)
[AMBER] antechamber error Soonmin Jang (Sat Sep 03 2011 - 01:45:47 PDT)
- Re: [AMBER] antechamber error case (Sat Sep 03 2011 - 05:59:25 PDT)
  - Re: [AMBER] antechamber error Jason Swails (Sat Sep 03 2011 - 08:46:05 PDT)
  - Re: [AMBER] antechamber error Soonmin Jang (Tue Sep 06 2011 - 07:04:50 PDT)
[AMBER] MM_PBSA triple trajectory approch Sangita Kachhap (Sat Sep 03 2011 - 05:00:33 PDT)
- Re: [AMBER] MM_PBSA triple trajectory approch Bill Miller III (Sat Sep 03 2011 - 05:19:17 PDT)
  - Re: [AMBER] MM_PBSA triple trajectory approch Sangita Kachhap (Sat Sep 03 2011 - 06:08:57 PDT)
    - Re: [AMBER] MM_PBSA triple trajectory approch Bill Miller III (Sat Sep 03 2011 - 06:14:27 PDT)
    - Re: [AMBER] MM_PBSA triple trajectory approch Jason Swails (Sat Sep 03 2011 - 08:23:55 PDT)
    - Re: [AMBER] MM_PBSA triple trajectory approch Sangita Kachhap (Sun Sep 04 2011 - 00:03:16 PDT)
[AMBER] Amber tools KIRTANA S (Sat Sep 03 2011 - 22:05:35 PDT)
- Re: [AMBER] Amber tools manikanthan bhavaraju (Sat Sep 03 2011 - 22:09:45 PDT)
- Re: [AMBER] Amber tools Jason Swails (Sat Sep 03 2011 - 23:04:11 PDT)
  - Re: [AMBER] Amber tools kirtana S (Sun Sep 04 2011 - 20:58:20 PDT)
    - Re: [AMBER] Amber tools case (Mon Sep 05 2011 - 17:12:47 PDT)
    - Re: [AMBER] Amber tools manikanthan bhavaraju (Tue Sep 06 2011 - 07:04:49 PDT)
[AMBER] NAB Module compilation error cpp failed Rajesh Raju (Mon Sep 05 2011 - 10:49:53 PDT)
- Re: [AMBER] NAB Module compilation error cpp failed Jason Swails (Mon Sep 05 2011 - 15:43:17 PDT)
[AMBER] NAB Module compilation error cpp failed Rajesh Raju (Mon Sep 05 2011 - 10:36:00 PDT)
[AMBER] Energy kirtana S (Mon Sep 05 2011 - 11:56:34 PDT)
- Re: [AMBER] Energy Bill Miller III (Mon Sep 05 2011 - 13:32:04 PDT)
  - Re: [AMBER] Energy kirtana S (Mon Sep 05 2011 - 13:51:15 PDT)
[AMBER] MMPBSA Ala scan error Jesper Sørensen (Sun Sep 04 2011 - 23:41:04 PDT)
- Re: [AMBER] MMPBSA Ala scan error Bill Miller III (Mon Sep 05 2011 - 13:53:29 PDT)
  - Re: [AMBER] MMPBSA Ala scan error Jesper Sørensen (Tue Sep 06 2011 - 01:16:25 PDT)
    - Re: [AMBER] MMPBSA Ala scan error Bill Miller III (Tue Sep 06 2011 - 04:31:49 PDT)
    - Re: [AMBER] MMPBSA Ala scan error Jesper Sørensen (Tue Sep 06 2011 - 12:14:28 PDT)
[AMBER] replace unit in leap tsurma.umich.edu (Sun Sep 04 2011 - 09:59:45 PDT)
[AMBER] replace unit in leap tsurma.umich.edu (Sun Sep 04 2011 - 10:56:05 PDT)
- Re: [AMBER] replace unit in leap case (Mon Sep 05 2011 - 17:11:46 PDT)
  - Re: [AMBER] replace unit in leap tsurma.umich.edu (Tue Sep 06 2011 - 08:41:00 PDT)
[AMBER] Sleap : amoeba and gaff Guenegou, Guillaume [JRDFR] (Mon Sep 05 2011 - 05:10:45 PDT)
- Re: [AMBER] Sleap : amoeba and gaff Wei Zhang (Mon Sep 05 2011 - 14:13:20 PDT)
[AMBER] problem while using Antechamber sonali dhindwal (Mon Sep 05 2011 - 07:21:24 PDT)
- Re: [AMBER] problem while using Antechamber case (Mon Sep 05 2011 - 17:16:34 PDT)
  - Re: [AMBER] problem while using Antechamber sonali dhindwal (Mon Sep 05 2011 - 22:19:17 PDT)
[AMBER] velocity modification in PMEMD, CUDA version Chen, Changjun (Mon Sep 05 2011 - 19:29:29 PDT)
- Re: [AMBER] velocity modification in PMEMD, CUDA version Ross Walker (Tue Sep 06 2011 - 20:10:29 PDT)
  - Re: [AMBER] velocity modification in PMEMD, CUDA version Chen, Changjun (Tue Sep 06 2011 - 20:15:42 PDT)
    - Re: [AMBER] velocity modification in PMEMD, CUDA version Jason Swails (Tue Sep 06 2011 - 22:34:27 PDT)
    - Re: [AMBER] velocity modification in PMEMD, CUDA version Chen, Changjun (Fri Sep 09 2011 - 03:04:15 PDT)
[AMBER] antechamber am1bcc stops with no error message Danny Xu (Mon Sep 05 2011 - 21:37:38 PDT)
- Re: [AMBER] antechamber am1bcc stops with no error message case (Sun Sep 11 2011 - 18:48:34 PDT)
  - [AMBER] Why cut=999.9 was used in Tutorial A7 for REMD calculation? Catein Catherine (Sun Sep 11 2011 - 23:30:13 PDT)
    - Re: [AMBER] Why cut=999.9 was used in Tutorial A7 for REMD calculation? Jason Swails (Mon Sep 12 2011 - 05:54:51 PDT)
    - Re: [AMBER] Why cut=999.9 was used in Tutorial A7 for REMD calculation? Catein Catherine (Mon Sep 12 2011 - 10:33:58 PDT)
[AMBER] Creating prmtop and inpcrd files Chidambar Kulkarni (Mon Sep 05 2011 - 23:57:53 PDT)
- Re: [AMBER] Creating prmtop and inpcrd files case (Tue Sep 06 2011 - 05:37:21 PDT)
  - Re: [AMBER] Creating prmtop and inpcrd files Chidambar Kulkarni (Tue Sep 06 2011 - 06:45:43 PDT)
    - Re: [AMBER] Creating prmtop and inpcrd files Jason Swails (Tue Sep 06 2011 - 08:44:43 PDT)
[AMBER] Is there any module which can calculate interaction energy, as ANAL in Amber 8? wrong string (Tue Sep 06 2011 - 01:09:06 PDT)
- Re: [AMBER] Is there any module which can calculate interaction energy, as ANAL in Amber 8? case (Tue Sep 06 2011 - 05:38:45 PDT)
  - [AMBER] How to use WHAM to analysis Replica Exchange Simulations Catein Catherine (Tue Sep 06 2011 - 07:20:41 PDT)
    - Re: [AMBER] How to use WHAM to analysis Replica Exchange Simulations Brian Radak (Tue Sep 06 2011 - 08:49:57 PDT)
    - Re: [AMBER] How to use WHAM to analysis Replica Exchange Simulations Daniel Sindhikara (Tue Sep 06 2011 - 15:28:54 PDT)
    - Re: [AMBER] How to use WHAM to analysis Replica Exchange Simulations Andrew Jewett (Tue Sep 06 2011 - 15:47:21 PDT)
[AMBER] problem with MM-PBSA Maryam Hamzehee (Tue Sep 06 2011 - 01:55:41 PDT)
- Re: [AMBER] problem with MM-PBSA Bill Miller III (Tue Sep 06 2011 - 04:39:22 PDT)
[AMBER] hydrogen boding and PBC Vijay Manickam Achari (Tue Sep 06 2011 - 03:19:02 PDT)
[AMBER] Amber for GPUs Baker D.J. (Tue Sep 06 2011 - 05:06:42 PDT)
[AMBER] How to Generate Structure with Correct Valence for an Unnatural Amino Acid in Position 1 George A. Khoury (Tue Sep 06 2011 - 07:00:43 PDT)
- Re: [AMBER] How to Generate Structure with Correct Valence for an Unnatural Amino Acid in Position 1 FyD (Tue Sep 06 2011 - 08:01:41 PDT)
- Re: [AMBER] How to Generate Structure with Correct Valence for an Unnatural Amino Acid in Position 1 case (Wed Sep 07 2011 - 12:41:32 PDT)
[AMBER] mbondi3 Peter Varnai (Tue Sep 06 2011 - 10:56:31 PDT)
- Re: [AMBER] mbondi3 Carlos Simmerling (Tue Sep 06 2011 - 11:38:25 PDT)
  - Re: [AMBER] mbondi3 Jason Swails (Tue Sep 06 2011 - 22:36:56 PDT)
    - Re: [AMBER] mbondi3 Peter Varnai (Wed Sep 07 2011 - 10:28:39 PDT)
    - Re: [AMBER] mbondi3 Jason Swails (Wed Sep 07 2011 - 12:48:41 PDT)
- Re: [AMBER] mbondi3 Mike NG (Sat Apr 28 2012 - 11:07:07 PDT)
  - Re: [AMBER] mbondi3 Jason Swails (Sat Apr 28 2012 - 13:32:21 PDT)
    - Re: [AMBER] mbondi3 Jesper Sørensen (Mon Apr 30 2012 - 00:11:51 PDT)
    - Re: [AMBER] mbondi3 Ray Luo, Ph.D. (Mon Apr 30 2012 - 09:02:53 PDT)
    - Re: [AMBER] mbondi3 Niel Henriksen (Mon Apr 30 2012 - 09:21:57 PDT)
    - [AMBER] Fwd: mbondi3 Ray Luo, Ph.D. (Mon Apr 30 2012 - 10:34:30 PDT)
    - Re: [AMBER] mbondi3 Qin Cai (Mon Apr 30 2012 - 12:30:12 PDT)
    - Re: [AMBER] mbondi3 Jesper Sørensen (Wed May 02 2012 - 08:05:41 PDT)
    - Re: [AMBER] mbondi3 Jason Swails (Wed May 02 2012 - 13:07:09 PDT)
    - Re: [AMBER] mbondi3 Jesper Soerensen (Wed May 02 2012 - 16:21:08 PDT)
    - Re: [AMBER] mbondi3 Jason Swails (Wed May 02 2012 - 17:00:14 PDT)
    - Re: [AMBER] mbondi3 Jesper Sørensen (Thu May 03 2012 - 08:56:02 PDT)
    - Re: [AMBER] mbondi3 Jesper Sørensen (Thu May 03 2012 - 14:08:09 PDT)
    - Re: [AMBER] mbondi3 case (Thu May 03 2012 - 19:14:00 PDT)
    - Re: [AMBER] mbondi3 Jesper Sørensen (Wed May 16 2012 - 15:26:49 PDT)
    - Re: [AMBER] mbondi3 Jason Swails (Sun May 20 2012 - 15:59:09 PDT)
    - Re: [AMBER] mbondi3 Jesper Sørensen (Wed May 23 2012 - 15:21:21 PDT)
    - Re: [AMBER] mbondi3 Jason Swails (Wed May 23 2012 - 17:25:42 PDT)
    - Re: [AMBER] mbondi3 David A. Case (Wed May 23 2012 - 18:44:28 PDT)
    - Re: [AMBER] mbondi3 Hai Nguyen (Tue May 01 2012 - 21:44:46 PDT)
[AMBER] moment of inertia John S (Tue Sep 06 2011 - 11:27:40 PDT)
- Re: [AMBER] moment of inertia peker milas (Tue Sep 06 2011 - 11:51:04 PDT)
[AMBER] umbrella sampling with amber10 Qian Wang (Tue Sep 06 2011 - 13:42:28 PDT)
[AMBER] results from independent simulations Wu Xu (Tue Sep 06 2011 - 17:37:25 PDT)
- Re: [AMBER] results from independent simulations Jason Swails (Wed Sep 07 2011 - 02:17:31 PDT)
  - Re: [AMBER] results from independent simulations Simon Becker (Wed Sep 07 2011 - 02:58:54 PDT)
    - Re: [AMBER] results from independent simulations Wu Xu (Wed Sep 07 2011 - 08:51:48 PDT)
    - Re: [AMBER] results from independent simulations Jason Swails (Wed Sep 07 2011 - 09:02:18 PDT)
    - Re: [AMBER] results from independent simulations Daniel Sindhikara (Wed Sep 07 2011 - 21:13:22 PDT)
    - Re: [AMBER] results from independent simulations Wu Xu (Thu Sep 08 2011 - 05:18:55 PDT)
- [AMBER] Sufficient CPU cores/GPU ratio ? Marek Maly (Tue Sep 13 2011 - 07:19:29 PDT)
  - Re: [AMBER] Sufficient CPU cores/GPU ratio ? dhilip kumar ramalingam (Tue Sep 13 2011 - 07:45:57 PDT)
    - Re: [AMBER] Sufficient CPU cores/GPU ratio ? Marek Maly (Tue Sep 13 2011 - 07:34:01 PDT)
  - Re: [AMBER] Sufficient CPU cores/GPU ratio ? Ross Walker (Tue Sep 13 2011 - 09:53:34 PDT)
    - Re: [AMBER] Sufficient CPU cores/GPU ratio ? Marek Maly (Tue Sep 13 2011 - 09:52:55 PDT)
    - Re: [AMBER] Sufficient CPU cores/GPU ratio ? Ross Walker (Tue Sep 13 2011 - 10:25:20 PDT)
    - Re: [AMBER] Sufficient CPU cores/GPU ratio ? Marek Maly (Tue Sep 13 2011 - 10:17:12 PDT)
    - Re: [AMBER] Sufficient CPU cores/GPU ratio ? Jodi Ann Hadden (Wed Sep 14 2011 - 08:50:21 PDT)
    - Re: [AMBER] Sufficient CPU cores/GPU ratio ? Marek Maly (Wed Sep 14 2011 - 17:15:32 PDT)
    - Re: [AMBER] Sufficient CPU cores/GPU ratio ? Scott Le Grand (Wed Sep 14 2011 - 17:51:33 PDT)
    - Re: [AMBER] Sufficient CPU cores/GPU ratio ? Marek Maly (Wed Sep 14 2011 - 18:01:15 PDT)
    - Re: [AMBER] Sufficient CPU cores/GPU ratio ? Gould, Ian R (Tue Sep 13 2011 - 11:04:32 PDT)
    - Re: [AMBER] Sufficient CPU cores/GPU ratio ? Marek Maly (Tue Sep 13 2011 - 11:00:47 PDT)
    - Re: [AMBER] Sufficient CPU cores/GPU ratio ? Ross Walker (Tue Sep 13 2011 - 11:40:56 PDT)
    - Re: [AMBER] Sufficient CPU cores/GPU ratio ? Marek Maly (Tue Sep 13 2011 - 11:41:28 PDT)
    - Re: [AMBER] Sufficient CPU cores/GPU ratio ? Scott Le Grand (Tue Sep 13 2011 - 11:15:27 PDT)
    - Re: [AMBER] Sufficient CPU cores/GPU ratio ? Marek Maly (Tue Sep 13 2011 - 11:06:09 PDT)
    - Re: [AMBER] Sufficient CPU cores/GPU ratio ? Scott Le Grand (Tue Sep 13 2011 - 12:50:30 PDT)
    - Re: [AMBER] Sufficient CPU cores/GPU ratio ? Marek Maly (Tue Sep 13 2011 - 13:47:09 PDT)
    - Re: [AMBER] Sufficient CPU cores/GPU ratio ? peter.stauffert.boehringer-ingelheim.com (Tue Sep 13 2011 - 10:57:29 PDT)
    - Re: [AMBER] Sufficient CPU cores/GPU ratio ? Marek Maly (Tue Sep 13 2011 - 10:50:02 PDT)
    - Re: [AMBER] Sufficient CPU cores/GPU ratio ? Ross Walker (Tue Sep 13 2011 - 11:40:56 PDT)
  - Re: [AMBER] Sufficient CPU cores/GPU ratio ? Jodi Ann Hadden (Fri Sep 16 2011 - 11:39:03 PDT)
    - Re: [AMBER] Sufficient CPU cores/GPU ratio ? Marek Maly (Sat Sep 17 2011 - 16:08:48 PDT)
    - Re: [AMBER] Sufficient CPU cores/GPU ratio ? Ross Walker (Sat Sep 17 2011 - 17:01:49 PDT)
    - Re: [AMBER] Sufficient CPU cores/GPU ratio ? Marek Maly (Sun Sep 18 2011 - 07:34:21 PDT)
  - Re: [AMBER] Sufficient CPU cores/GPU ratio ? Jodi Ann Hadden (Wed Sep 21 2011 - 10:54:08 PDT)
    - Re: [AMBER] Sufficient CPU cores/GPU ratio ? Marek Maly (Wed Sep 21 2011 - 11:10:06 PDT)
  - Re: [AMBER] Sufficient CPU cores/GPU ratio ? Jodi Ann Hadden (Tue Nov 29 2011 - 09:43:19 PST)
    - Re: [AMBER] Sufficient CPU cores/GPU ratio ? Scott Le Grand (Tue Nov 29 2011 - 13:16:01 PST)
    - Re: [AMBER] Sufficient CPU cores/GPU ratio ? Marek Maly (Tue Nov 29 2011 - 15:39:05 PST)
    - Re: [AMBER] Sufficient CPU cores/GPU ratio ? filip fratev (Wed Nov 30 2011 - 14:09:27 PST)
    - Re: [AMBER] Sufficient CPU cores/GPU ratio ? Ross Walker (Wed Nov 30 2011 - 14:31:00 PST)
    - Re: [AMBER] Sufficient CPU cores/GPU ratio ? Marek Maly (Wed Nov 30 2011 - 15:01:29 PST)
    - Re: [AMBER] Sufficient CPU cores/GPU ratio ? Marek Maly (Wed Nov 30 2011 - 14:39:37 PST)
[AMBER] Some question regarding force field for periodic system jun kit (Tue Sep 06 2011 - 21:24:02 PDT)
- Re: [AMBER] Some question regarding force field for periodic system Carlos Simmerling (Wed Sep 07 2011 - 04:09:38 PDT)
[AMBER] Minimum distance RANAJIT SHINDE (Wed Sep 07 2011 - 00:00:24 PDT)
[AMBER] Residence time aiswarya pawar (Wed Sep 07 2011 - 00:14:18 PDT)
- Re: [AMBER] Residence time Carlos Simmerling (Wed Sep 07 2011 - 04:08:13 PDT)
  - Re: [AMBER] Residence time aiswarya pawar (Wed Sep 07 2011 - 04:18:14 PDT)
    - Re: [AMBER] Residence time Carlos Simmerling (Wed Sep 07 2011 - 11:53:49 PDT)
[AMBER] Restrain of atoms during MD simulation Sindrila Dutta banik (Wed Sep 07 2011 - 00:37:16 PDT)
[AMBER] libmkl_ia32.a missing from MKL em64t Aaron Greenwood (Wed Sep 07 2011 - 09:57:33 PDT)
- Re: [AMBER] libmkl_ia32.a missing from MKL em64t case (Wed Sep 07 2011 - 12:57:56 PDT)
  - [AMBER] Serial Version of libFpbsa.a Aaron Greenwood (Fri Sep 16 2011 - 11:15:02 PDT)
    - Re: [AMBER] Serial Version of libFpbsa.a Ross Walker (Fri Sep 16 2011 - 11:27:37 PDT)
[AMBER] Proble related to correlation function Sindrila Dutta banik (Wed Sep 07 2011 - 10:51:17 PDT)
- Re: [AMBER] Proble related to correlation function InSuk Joung (Wed Sep 07 2011 - 11:26:16 PDT)
[AMBER] Format conversion aiswarya.pawar.gmail.com (Wed Sep 07 2011 - 11:18:12 PDT)
[AMBER] false positive on too large QM region? Brian Radak (Wed Sep 07 2011 - 14:37:58 PDT)
- Re: [AMBER] false positive on too large QM region? Gustavo Seabra (Wed Sep 07 2011 - 17:19:36 PDT)
[AMBER] MPI version of MMPBSA Siavoush Dastmalchi (Thu Sep 08 2011 - 00:35:59 PDT)
- Re: [AMBER] MPI version of MMPBSA Siavoush Dastmalchi (Thu Sep 08 2011 - 02:05:16 PDT)
  - Re: [AMBER] MPI version of MMPBSA Jason Swails (Thu Sep 08 2011 - 08:36:49 PDT)
[AMBER] Hydrogen Bonding Sara Ahmadi (Thu Sep 08 2011 - 04:22:34 PDT)
[AMBER] Parameters for Boron containing molecules gal.fradin.live.biu.ac.il (Thu Sep 08 2011 - 05:08:16 PDT)
- Re: [AMBER] Parameters for Boron containing molecules Jason Swails (Thu Sep 08 2011 - 08:39:58 PDT)
  - Re: [AMBER] Parameters for Boron containing molecules gal.fradin.live.biu.ac.il (Sat Sep 10 2011 - 21:57:43 PDT)
[AMBER] Fwd: false positive on too large QM region? Brian Radak (Thu Sep 08 2011 - 07:42:56 PDT)
- Re: [AMBER] Fwd: false positive on too large QM region? Gustavo Seabra (Thu Sep 08 2011 - 11:30:18 PDT)
  - Re: [AMBER] Fwd: false positive on too large QM region? Brian Radak (Thu Sep 08 2011 - 11:52:43 PDT)
    - Re: [AMBER] Fwd: false positive on too large QM region? Ross Walker (Thu Sep 08 2011 - 12:43:45 PDT)
    - Re: [AMBER] Fwd: false positive on too large QM region? Brian Radak (Thu Sep 08 2011 - 13:42:56 PDT)
    - Re: [AMBER] Fwd: false positive on too large QM region? Qiantao Wang (Thu Sep 08 2011 - 14:34:44 PDT)
    - Re: [AMBER] Fwd: false positive on too large QM region? Brian Radak (Tue Sep 13 2011 - 11:59:53 PDT)
    - Re: [AMBER] Fwd: false positive on too large QM region? Gustavo Seabra (Thu Sep 08 2011 - 13:13:22 PDT)
[AMBER] Water density/potential visualization Abhishek Mukhopadhyay (Thu Sep 08 2011 - 09:56:54 PDT)
- Re: [AMBER] Water density/potential visualization Ozen, Aysegul (Thu Sep 08 2011 - 10:57:03 PDT)
- Re: [AMBER] Water density/potential visualization Daniel Sindhikara (Thu Sep 08 2011 - 22:16:49 PDT)
[AMBER] turning on 1-2 and 1-3 interactions Steven Burger (Thu Sep 08 2011 - 10:46:26 PDT)
- Re: [AMBER] turning on 1-2 and 1-3 interactions Bill Ross (Thu Sep 08 2011 - 10:54:42 PDT)
- Re: [AMBER] turning on 1-2 and 1-3 interactions Jason Swails (Thu Sep 08 2011 - 11:54:22 PDT)
[AMBER] intermolecular interaction su He (Thu Sep 08 2011 - 13:02:17 PDT)
- Re: [AMBER] intermolecular interaction Jason Swails (Thu Sep 08 2011 - 21:00:41 PDT)
  - Re: [AMBER] intermolecular interaction su He (Fri Sep 09 2011 - 07:58:06 PDT)
[AMBER] SMD: restraints on the pulled apart interacting proteins Sergey Samsonov (Fri Sep 09 2011 - 07:39:36 PDT)
[AMBER] problems with prmtops & MMGBSA Irene Newhouse (Fri Sep 09 2011 - 18:05:58 PDT)
- Re: [AMBER] problems with prmtops & MMGBSA Romelia Salomon (Fri Sep 09 2011 - 18:23:54 PDT)
- Re: [AMBER] problems with prmtops & MMGBSA Jason Swails (Fri Sep 09 2011 - 20:12:44 PDT)
[AMBER] the result of pseudorotation angle clwg (Sat Sep 10 2011 - 01:31:08 PDT)
- Re: [AMBER] the result of pseudorotation angle case (Sat Sep 10 2011 - 06:01:47 PDT)
[AMBER] residue list kirtana S (Sun Sep 11 2011 - 19:40:52 PDT)
- Re: [AMBER] residue list Jason Swails (Sun Sep 11 2011 - 20:48:31 PDT)
[AMBER] vlimit exeeding problem Aparna P (Sun Sep 11 2011 - 23:46:33 PDT)
- Re: [AMBER] vlimit exeeding problem manikanthan bhavaraju (Mon Sep 12 2011 - 08:05:30 PDT)
  - Re: [AMBER] vlimit exeeding problem Aparna P (Mon Sep 12 2011 - 22:04:17 PDT)
    - Re: [AMBER] vlimit exeeding problem Ross Walker (Mon Sep 12 2011 - 22:16:19 PDT)
    - Re: [AMBER] vlimit exeeding problem Aparna P (Mon Sep 12 2011 - 22:46:22 PDT)
    - Re: [AMBER] vlimit exeeding problem Ross Walker (Mon Sep 12 2011 - 22:57:43 PDT)
    - Re: [AMBER] vlimit exeeding problem Aparna P (Tue Sep 13 2011 - 04:24:07 PDT)
[AMBER] QM-MM atoms input Shruti Koulgi (Mon Sep 12 2011 - 04:00:58 PDT)
- Re: [AMBER] QM-MM atoms input Shruti Koulgi (Mon Sep 12 2011 - 04:18:03 PDT)
- Re: [AMBER] QM-MM atoms input Marc van der Kamp (Mon Sep 12 2011 - 05:12:26 PDT)
- Re: [AMBER] QM-MM atoms input Jason Swails (Mon Sep 12 2011 - 06:00:13 PDT)
[AMBER] Aromatic bonds disappear during sdf creation with sleap Guenegou, Guillaume [JRDFR] (Mon Sep 12 2011 - 05:10:29 PDT)
- Re: [AMBER] Aromatic bonds disappear during sdf creation with sleap Jason Swails (Mon Sep 12 2011 - 05:58:43 PDT)
[AMBER] ptraj clustering George Tzotzos (Mon Sep 12 2011 - 08:02:40 PDT)
- Re: [AMBER] ptraj clustering Thomas Cheatham (Mon Sep 12 2011 - 12:13:35 PDT)
  - Re: [AMBER] ptraj clustering George Tzotzos (Mon Sep 12 2011 - 13:26:03 PDT)
    - Re: [AMBER] ptraj clustering Thomas Cheatham III (Mon Sep 12 2011 - 13:37:55 PDT)
[AMBER] pbsa kirtana S (Mon Sep 12 2011 - 08:56:44 PDT)
- Re: [AMBER] pbsa Ray Luo, Ph.D. (Mon Sep 12 2011 - 09:00:20 PDT)
  - Re: [AMBER] pbsa kirtana S (Mon Sep 12 2011 - 09:05:17 PDT)
    - [AMBER] Fwd: pbsa Ray Luo, Ph.D. (Mon Sep 12 2011 - 10:24:23 PDT)
    - Re: [AMBER] pbsa kirtana S (Mon Sep 12 2011 - 11:42:44 PDT)
    - Re: [AMBER] pbsa Jason Swails (Mon Sep 12 2011 - 12:22:37 PDT)
    - Re: [AMBER] pbsa kirtana S (Mon Sep 12 2011 - 19:01:17 PDT)
    - Re: [AMBER] pbsa Ray Luo, Ph.D. (Tue Sep 13 2011 - 11:50:31 PDT)
[AMBER] Amber 11 configure error with openmpi Lianhu Wei (Mon Sep 12 2011 - 10:14:33 PDT)
- Re: [AMBER] Amber 11 configure error with openmpi Jason Swails (Mon Sep 12 2011 - 10:23:48 PDT)
- Re: [AMBER] Amber 11 configure error with openmpi David A Case (Mon Sep 12 2011 - 13:34:10 PDT)
  - Re: [AMBER] Amber 11 configure error with openmpi Jason Swails (Mon Sep 12 2011 - 13:37:48 PDT)
    - Re: [AMBER] Amber 11 configure error with openmpi Lianhu Wei (Tue Sep 13 2011 - 07:49:36 PDT)
[AMBER] Residue transformation Fabrício Bracht (Mon Sep 12 2011 - 15:10:10 PDT)
- Re: [AMBER] Residue transformation Bruno Rodrigues (Mon Sep 12 2011 - 20:16:48 PDT)
  - Re: [AMBER] Residue transformation M. L. Dodson (Mon Sep 12 2011 - 20:52:35 PDT)
[AMBER] error using saveamberparm on pdb with nonstandard residues Darren Jindal (Mon Sep 12 2011 - 19:32:18 PDT)
- Re: [AMBER] error using saveamberparm on pdb with nonstandard residues David A Case (Tue Sep 13 2011 - 04:51:18 PDT)
[AMBER] Parameters from Jaguar output Kshatresh Dutta Dubey (Mon Sep 12 2011 - 22:09:29 PDT)
[AMBER] visualization of secstruc with e.g. gnuplot Nadine Utz (Tue Sep 13 2011 - 04:07:16 PDT)
- Re: [AMBER] visualization of secstruc with e.g. gnuplot steinbrt.rci.rutgers.edu (Tue Sep 13 2011 - 06:20:05 PDT)
  - Re: [AMBER] visualization of secstruc with e.g. gnuplot Anselm Horn (Tue Sep 13 2011 - 11:23:50 PDT)
[AMBER] Problem with mmpbsa Devlina Chakravarty (Tue Sep 13 2011 - 05:33:33 PDT)
- Re: [AMBER] Problem with mmpbsa Bill Miller III (Tue Sep 13 2011 - 05:50:37 PDT)
- Re: [AMBER] Problem with mmpbsa dhilip kumar ramalingam (Tue Sep 13 2011 - 05:50:09 PDT)
[AMBER] undefined reference Lars Skjærven (Tue Sep 13 2011 - 05:48:56 PDT)
- Re: [AMBER] undefined reference David A Case (Tue Sep 13 2011 - 06:45:10 PDT)
  - Re: [AMBER] undefined reference Lars Skjærven (Tue Sep 13 2011 - 07:03:39 PDT)
    - Re: [AMBER] undefined reference David A Case (Tue Sep 13 2011 - 10:01:42 PDT)
[AMBER] Fwd: amber Gustavo Seabra (Tue Sep 13 2011 - 06:59:55 PDT)
- Re: [AMBER] Fwd: amber steinbrt.rci.rutgers.edu (Tue Sep 13 2011 - 07:14:29 PDT)
[AMBER] Global Minimum in Simulated Annealing using SANDER Julian Zachmann (Tue Sep 13 2011 - 07:12:00 PDT)
- Re: [AMBER] Global Minimum in Simulated Annealing using SANDER steinbrt.rci.rutgers.edu (Tue Sep 13 2011 - 07:18:36 PDT)
[AMBER] October 20 deadline for ACS COMP division awards for junior faculty and graduate students Carlos Simmerling (Tue Sep 13 2011 - 10:46:56 PDT)
[AMBER] Compiling Amber11 on Blue Gene/P Garo Garabedyan (Tue Sep 13 2011 - 12:45:37 PDT)
- Re: [AMBER] Compiling Amber11 on Blue Gene/P Jed W Pitera (Tue Sep 13 2011 - 14:09:51 PDT)
  - Re: [AMBER] Compiling Amber11 on Blue Gene/P Garo Garabedyan (Tue Sep 13 2011 - 23:12:20 PDT)
    - Re: [AMBER] Compiling Amber11 on Blue Gene/P Garo Garabedyan (Wed Sep 14 2011 - 11:33:23 PDT)
    - Re: [AMBER] Compiling Amber11 on Blue Gene/P Ross Walker (Wed Sep 14 2011 - 12:20:45 PDT)
    - Re: [AMBER] Compiling Amber11 on Blue Gene/P Garo Garabedyan (Fri Sep 30 2011 - 01:18:53 PDT)
    - Re: [AMBER] Compiling Amber11 on Blue Gene/P Jason Swails (Fri Sep 30 2011 - 06:54:52 PDT)
[AMBER] Run amber on Cluster Lianhu Wei (Tue Sep 13 2011 - 12:46:17 PDT)
- Re: [AMBER] Run amber on Cluster Jason Swails (Tue Sep 13 2011 - 14:38:50 PDT)
  - Re: [AMBER] Run amber on Cluster Lianhu Wei (Wed Sep 14 2011 - 08:01:37 PDT)
    - Re: [AMBER] Run amber on Cluster Ross Walker (Wed Sep 14 2011 - 10:14:02 PDT)
    - Re: [AMBER] Run amber on Cluster Lianhu Wei (Wed Sep 14 2011 - 11:10:28 PDT)
[AMBER] MMGBSA binding free energy shows large change with saltcon parameter, but not for MMPBSA binding free energy value Rajesh Raju (Tue Sep 13 2011 - 16:48:12 PDT)
- Re: [AMBER] MMGBSA binding free energy shows large change with saltcon parameter, but not for MMPBSA binding free energy value David Case (Tue Sep 13 2011 - 16:59:58 PDT)
- Re: [AMBER] MMGBSA binding free energy shows large change with saltcon parameter, but not for MMPBSA binding free energy value Jason Swails (Tue Sep 13 2011 - 17:43:17 PDT)
  - Re: [AMBER] MMGBSA binding free energy shows large change with saltcon parameter, but not for MMPBSA binding free energy value Rajesh Raju (Tue Sep 13 2011 - 17:59:59 PDT)
    - Re: [AMBER] MMGBSA binding free energy shows large change with saltcon parameter, but not for MMPBSA binding free energy value Jason Swails (Tue Sep 13 2011 - 20:12:07 PDT)
[AMBER] TI and MM-GBSA results manikanthan bhavaraju (Tue Sep 13 2011 - 17:33:06 PDT)
- Re: [AMBER] TI and MM-GBSA results Ray Luo, Ph.D. (Wed Sep 14 2011 - 10:21:32 PDT)
  - Re: [AMBER] TI and MM-GBSA results manikanthan bhavaraju (Wed Sep 14 2011 - 10:46:04 PDT)
    - Re: [AMBER] TI and MM-GBSA results Jason Swails (Wed Sep 14 2011 - 10:49:33 PDT)
[AMBER] AMBER Shesh Nath (Wed Sep 14 2011 - 00:00:24 PDT)
- Re: [AMBER] AMBER Jason Swails (Wed Sep 14 2011 - 10:19:24 PDT)
[AMBER] Error in computing entropy! problem with number of frames in NMODE hongphuc nguyen (Wed Sep 14 2011 - 02:50:58 PDT)
- Re: [AMBER] Error in computing entropy! problem with number of frames in NMODE Bill Miller III (Wed Sep 14 2011 - 04:24:46 PDT)
  - Re: [AMBER] Error in computing entropy! problem with number of frames in NMODE hongphuc nguyen (Thu Sep 15 2011 - 20:12:42 PDT)
[AMBER] Running amber v11 over multiple gpus/nodes Baker D.J. (Wed Sep 14 2011 - 04:14:25 PDT)
- Re: [AMBER] Running amber v11 over multiple gpus/nodes peter.stauffert.boehringer-ingelheim.com (Wed Sep 14 2011 - 04:37:00 PDT)
  - Re: [AMBER] Running amber v11 over multiple gpus/nodes Baker D.J. (Wed Sep 14 2011 - 08:18:03 PDT)
    - Re: [AMBER] Running amber v11 over multiple gpus/nodes Ross Walker (Wed Sep 14 2011 - 10:55:03 PDT)
    - Re: [AMBER] Running amber v11 over multiple gpus/nodes Baker D.J. (Fri Sep 16 2011 - 00:47:39 PDT)
    - Re: [AMBER] Running amber v11 over multiple gpus/nodes Ross Walker (Fri Sep 16 2011 - 09:30:58 PDT)
[AMBER] hello Linda catherine (Wed Sep 14 2011 - 05:16:27 PDT)
- Re: [AMBER] hello steinbrt.rci.rutgers.edu (Wed Sep 14 2011 - 06:06:40 PDT)
  - [AMBER] How to extract time angle, time, Energy from for MBAR analysis? Catein Catherine (Wed Sep 14 2011 - 06:37:53 PDT)
    - Re: [AMBER] How to extract time angle, time, Energy from for MBAR analysis? Brian Radak (Wed Sep 14 2011 - 07:01:18 PDT)
    - [AMBER] Can we extract information from out file for MBAR analysis? Catein Catherine (Wed Sep 14 2011 - 10:50:20 PDT)
    - Re: [AMBER] Can we extract information from out file for MBAR analysis? Brian Radak (Wed Sep 14 2011 - 11:14:41 PDT)
    - Re: [AMBER] Can we extract information from out file for MBAR analysis for PMF analysis? Catein Catherine (Wed Sep 14 2011 - 11:36:11 PDT)
    - Re: [AMBER] Can we extract information from out file for MBAR analysis for PMF analysis? Brian Radak (Wed Sep 14 2011 - 12:33:50 PDT)
[AMBER] pulling DNA amir abbasi (Wed Sep 14 2011 - 05:38:39 PDT)
[AMBER] Need Help! (TMD - NSCM - IWRAP reg!) Fredrick Devadoss (Wed Sep 14 2011 - 06:51:22 PDT)
- Re: [AMBER] Need Help! (TMD - NSCM - IWRAP reg!) Jason Swails (Wed Sep 14 2011 - 07:14:20 PDT)
[AMBER] energy kirtana S (Wed Sep 14 2011 - 08:02:14 PDT)
- Re: [AMBER] energy Bill Miller III (Wed Sep 14 2011 - 09:00:13 PDT)
  - Re: [AMBER] energy kirtana S (Wed Sep 14 2011 - 09:40:21 PDT)
[AMBER] attachment for my previous mail Fredrick Devadoss (Wed Sep 14 2011 - 07:00:38 PDT)
[AMBER] benchmarking Tesla S2050 1U system Sidney Elmer (Wed Sep 14 2011 - 11:52:38 PDT)
- Re: [AMBER] benchmarking Tesla S2050 1U system Ross Walker (Wed Sep 14 2011 - 12:41:19 PDT)
  - Re: [AMBER] benchmarking Tesla S2050 1U system Sidney Elmer (Wed Sep 14 2011 - 15:55:23 PDT)
    - Re: [AMBER] benchmarking Tesla S2050 1U system Sidney Elmer (Thu Sep 15 2011 - 17:08:27 PDT)
[AMBER] Bond command using xleap or tleap Fabrício Bracht (Wed Sep 14 2011 - 12:53:09 PDT)
- Re: [AMBER] Bond command using xleap or tleap David A Case (Thu Sep 15 2011 - 11:51:01 PDT)
  - Re: [AMBER] Bond command using xleap or tleap Sidney Elmer (Thu Sep 15 2011 - 17:14:38 PDT)
  - Re: [AMBER] Bond command using xleap or tleap Bill Ross (Thu Sep 15 2011 - 17:39:59 PDT)
    - Re: [AMBER] Bond command using xleap or tleap Sidney Elmer (Fri Sep 16 2011 - 09:23:57 PDT)
    - Re: [AMBER] Bond command using xleap or tleap case (Sat Sep 17 2011 - 06:18:04 PDT)
  - Re: [AMBER] Bond command using xleap or tleap Bill Ross (Fri Sep 16 2011 - 15:10:30 PDT)
[AMBER] about Glycam_06g.dat and thiol-glycosidic linkage Yun Shi (Wed Sep 14 2011 - 15:53:43 PDT)
- Re: [AMBER] about Glycam_06g.dat and thiol-glycosidic linkage Lachele Foley (Lists) (Thu Sep 15 2011 - 08:32:33 PDT)
  - Re: [AMBER] about Glycam_06g.dat and thiol-glycosidic linkage Yun Shi (Thu Sep 15 2011 - 10:03:47 PDT)
    - Re: [AMBER] about Glycam_06g.dat and thiol-glycosidic linkage Lachele Foley (Lists) (Thu Sep 15 2011 - 10:41:01 PDT)
    - Re: [AMBER] about Glycam_06g.dat and thiol-glycosidic linkage Yun Shi (Thu Sep 15 2011 - 11:07:33 PDT)
    - Re: [AMBER] about Glycam_06g.dat and thiol-glycosidic linkage Lachele Foley (Lists) (Thu Sep 15 2011 - 11:39:44 PDT)
    - Re: [AMBER] about Glycam_06g.dat and thiol-glycosidic linkage Matthew Tessier (Thu Sep 15 2011 - 11:53:30 PDT)
    - Re: [AMBER] about Glycam_06g.dat and thiol-glycosidic linkage Yun Shi (Thu Sep 15 2011 - 15:30:28 PDT)
    - Re: [AMBER] about Glycam_06g.dat and thiol-glycosidic linkage Yun Shi (Fri Sep 16 2011 - 09:46:01 PDT)
    - Re: [AMBER] about Glycam_06g.dat and thiol-glycosidic linkage Matthew Tessier (Mon Sep 19 2011 - 07:41:30 PDT)
    - Re: [AMBER] about Glycam_06g.dat and thiol-glycosidic linkage Yun Shi (Mon Sep 19 2011 - 15:27:01 PDT)
    - Re: [AMBER] about Glycam_06g.dat and thiol-glycosidic linkage FyD (Tue Sep 20 2011 - 01:19:34 PDT)
    - Re: [AMBER] about Glycam_06g.dat and thiol-glycosidic linkage Matthew Tessier (Wed Sep 21 2011 - 06:46:14 PDT)
    - Re: [AMBER] about Glycam_06g.dat and thiol-glycosidic linkage FyD (Wed Sep 21 2011 - 23:45:31 PDT)
    - Re: [AMBER] about Glycam_06g.dat and thiol-glycosidic linkage Matthew Tessier (Thu Sep 22 2011 - 11:25:12 PDT)
    - Re: [AMBER] about Glycam_06g.dat and thiol-glycosidic linkage FyD (Fri Sep 23 2011 - 02:37:32 PDT)
    - Re: [AMBER] about Glycam_06g.dat and thiol-glycosidic linkage Karl N. Kirschner (Fri Sep 23 2011 - 03:10:57 PDT)
    - Re: [AMBER] about Glycam_06g.dat and thiol-glycosidic linkage FyD (Fri Sep 23 2011 - 05:12:44 PDT)
    - Re: [AMBER] about Glycam_06g.dat and thiol-glycosidic linkage Matthew Tessier (Fri Sep 23 2011 - 10:48:41 PDT)
    - Re: [AMBER] about Glycam_06g.dat and thiol-glycosidic linkage Yun Shi (Fri Sep 23 2011 - 22:26:22 PDT)
    - Re: [AMBER] about Glycam_06g.dat and thiol-glycosidic linkage FyD (Mon Sep 26 2011 - 04:51:12 PDT)
    - Re: [AMBER] about Glycam_06g.dat and thiol-glycosidic linkage Lachele Foley (Lists) (Thu Sep 15 2011 - 13:37:09 PDT)
[AMBER] inpcrd file fatahiya (Tue Sep 13 2011 - 23:47:04 PDT)
- Re: [AMBER] inpcrd file Emmanuel Baribefe Naziga (Wed Sep 14 2011 - 17:12:39 PDT)
[AMBER] Electrpostatic interaction vs Coulombic interaction Rilei Yu (Wed Sep 14 2011 - 17:48:08 PDT)
- Re: [AMBER] Electrpostatic interaction vs Coulombic interaction David Case (Wed Sep 14 2011 - 18:34:22 PDT)
  - Re: [AMBER] Electrpostatic interaction vs Coulombic interaction Rilei Yu (Wed Sep 14 2011 - 23:52:17 PDT)
[AMBER] MMPBSA.py 3DRISM error Jesper Soerensen (Wed Sep 14 2011 - 18:52:49 PDT)
- Re: [AMBER] MMPBSA.py 3DRISM error Jason Swails (Wed Sep 14 2011 - 19:09:18 PDT)
  - Re: [AMBER] MMPBSA.py 3DRISM error Jason Swails (Wed Sep 14 2011 - 19:15:25 PDT)
    - Re: [AMBER] MMPBSA.py 3DRISM error Jesper Soerensen (Fri Sep 23 2011 - 09:58:02 PDT)
    - Re: [AMBER] MMPBSA.py 3DRISM error Jason Swails (Sat Sep 24 2011 - 07:29:38 PDT)
- Re: [AMBER] MMPBSA.py 3DRISM error Jesper Soerensen (Wed Oct 05 2011 - 17:18:40 PDT)
  - Re: [AMBER] MMPBSA.py 3DRISM error Jason Swails (Thu Oct 06 2011 - 10:08:44 PDT)
    - Re: [AMBER] MMPBSA.py 3DRISM error Jesper Soerensen (Thu Oct 06 2011 - 10:47:24 PDT)
    - [AMBER] MMPBSA.py mask selections Jesper Soerensen (Wed Oct 12 2011 - 10:59:12 PDT)
    - Re: [AMBER] MMPBSA.py mask selections Jesper Soerensen (Wed Oct 12 2011 - 12:15:45 PDT)
    - [AMBER] MMPBSA.py -use-mdin. PB Bomb Jesper Soerensen (Wed Oct 12 2011 - 12:42:28 PDT)
    - [AMBER] MMPBSA.py - PB Bomb Jesper Soerensen (Mon Oct 17 2011 - 17:04:13 PDT)
    - Re: [AMBER] MMPBSA.py - PB Bomb Ray Luo, Ph.D. (Mon Oct 17 2011 - 17:09:25 PDT)
    - Re: [AMBER] MMPBSA.py - PB Bomb Jesper Soerensen (Tue Oct 18 2011 - 14:06:35 PDT)
    - [AMBER] PBSA grid output using MMPBSA.py Jesper Soerensen (Thu Oct 27 2011 - 15:29:10 PDT)
[AMBER] help ! zinc parameters Kk Zhu (Wed Sep 14 2011 - 19:48:36 PDT)
- Re: [AMBER] help ! zinc parameters FyD (Thu Sep 15 2011 - 00:23:58 PDT)
[AMBER] Print Dipole Moment in Centriod MD Wei Lin (Wed Sep 14 2011 - 20:56:20 PDT)
[AMBER] tleap command "set default Dielectric constant" not valid? Yongmei Wang (ywang) (Wed Sep 14 2011 - 21:33:29 PDT)
- Re: [AMBER] tleap command "set default Dielectric constant" not valid? David A Case (Thu Sep 15 2011 - 12:04:17 PDT)
  - Re: [AMBER] tleap command "set default Dielectric constant" not valid? Yongmei Wang (ywang) (Thu Sep 15 2011 - 12:13:22 PDT)
[AMBER] AMOEBA potentials Neha Gandhi (Thu Sep 15 2011 - 02:43:14 PDT)
- Re: [AMBER] AMOEBA potentials David A Case (Thu Sep 15 2011 - 12:08:01 PDT)
  - Re: [AMBER] AMOEBA potentials Neha Gandhi (Tue Oct 04 2011 - 02:41:08 PDT)
    - Re: [AMBER] AMOEBA potentials case (Tue Oct 04 2011 - 09:05:32 PDT)
    - Re: [AMBER] AMOEBA potentials Neha Gandhi (Wed Oct 05 2011 - 00:02:18 PDT)
    - Re: [AMBER] AMOEBA potentials David A Case (Thu Oct 06 2011 - 07:06:09 PDT)
    - Re: [AMBER] AMOEBA potentials Neha Gandhi (Thu Oct 06 2011 - 19:02:23 PDT)
    - Re: [AMBER] AMOEBA potentials David A Case (Fri Oct 07 2011 - 06:43:31 PDT)
[AMBER] MMPBSA.py energy decomposition inconsistencies Antje Wolf (Thu Sep 15 2011 - 05:13:17 PDT)
- Re: [AMBER] MMPBSA.py energy decomposition inconsistencies Jason Swails (Thu Sep 15 2011 - 07:15:29 PDT)
  - Re: [AMBER] MMPBSA.py energy decomposition inconsistencies Antje Wolf (Thu Sep 15 2011 - 08:34:24 PDT)
    - Re: [AMBER] MMPBSA.py energy decomposition inconsistencies Jason Swails (Thu Sep 15 2011 - 10:05:54 PDT)
    - Re: [AMBER] MMPBSA.py energy decomposition inconsistencies Antje Wolf (Thu Sep 15 2011 - 23:51:40 PDT)
    - Re: [AMBER] MMPBSA.py energy decomposition inconsistencies Jason Swails (Fri Sep 16 2011 - 07:03:30 PDT)
    - Re: [AMBER] MMPBSA.py energy decomposition inconsistencies Antje Wolf (Fri Sep 16 2011 - 09:13:21 PDT)
    - Re: [AMBER] MMPBSA.py energy decomposition inconsistencies Jason Swails (Fri Sep 16 2011 - 09:40:44 PDT)
[AMBER] X-PLOR formatted .psf in CHAMBER Marc van der Kamp (Thu Sep 15 2011 - 05:19:29 PDT)
- Re: [AMBER] X-PLOR formatted .psf in CHAMBER Thomas Cheatham (Thu Sep 15 2011 - 05:21:46 PDT)
  - Re: [AMBER] X-PLOR formatted .psf in CHAMBER Marc van der Kamp (Thu Sep 15 2011 - 06:26:14 PDT)
    - Re: [AMBER] X-PLOR formatted .psf in CHAMBER Marc van der Kamp (Thu Sep 15 2011 - 07:09:02 PDT)
[AMBER] radial distribution function Massimiliano Porrini (Thu Sep 15 2011 - 05:27:03 PDT)
- Re: [AMBER] radial distribution function Thomas Cheatham (Fri Sep 16 2011 - 06:13:47 PDT)
  - Re: [AMBER] radial distribution function Massimiliano Porrini (Sun Sep 18 2011 - 10:15:21 PDT)
    - Re: [AMBER] radial distribution function Thomas Cheatham III (Mon Sep 19 2011 - 16:04:23 PDT)
[AMBER] Dihedral parameters Chidambar Kulkarni (Thu Sep 15 2011 - 07:14:55 PDT)
- Re: [AMBER] Dihedral parameters Jason Swails (Thu Sep 15 2011 - 07:39:54 PDT)
  - Re: [AMBER] Dihedral parameters Chidambar Kulkarni (Thu Sep 15 2011 - 08:42:59 PDT)
    - Re: [AMBER] Dihedral parameters Jason Swails (Thu Sep 15 2011 - 10:07:42 PDT)
    - Re: [AMBER] Dihedral parameters Dean Cuebas (Thu Sep 15 2011 - 15:08:36 PDT)
    - Re: [AMBER] Dihedral parameters Chidambar Kulkarni (Thu Sep 15 2011 - 22:36:36 PDT)
[AMBER] Effect of SLI for Amber GPU calculations - AMD Bulldozers ? Marek Maly (Thu Sep 15 2011 - 09:52:13 PDT)
- Re: [AMBER] Effect of SLI for Amber GPU calculations - AMD Bulldozers ? Ross Walker (Thu Sep 15 2011 - 10:37:01 PDT)
  - Re: [AMBER] Effect of SLI for Amber GPU calculations - AMD Bulldozers ? Marek Maly (Thu Sep 15 2011 - 11:15:37 PDT)
- Re: [AMBER] Effect of SLI for Amber GPU calculations - AMD Bulldozers ? Scott Le Grand (Thu Sep 15 2011 - 12:05:50 PDT)
  - Re: [AMBER] Effect of SLI for Amber GPU calculations - AMD Bulldozers ? Marek Maly (Thu Sep 15 2011 - 11:59:51 PDT)
[AMBER] help ! zinc parameters Kk Zhu (Thu Sep 15 2011 - 23:46:06 PDT)
- Re: [AMBER] help ! zinc parameters Bill Ross (Fri Sep 16 2011 - 08:39:20 PDT)
  - Re: [AMBER] help ! zinc parameters Oteri Francesco (Fri Sep 16 2011 - 08:37:07 PDT)
    - Re: [AMBER] help ! zinc parameters zhukk (Mon Sep 19 2011 - 05:28:07 PDT)
  - Re: [AMBER] help ! zinc parameters zhukk (Mon Sep 19 2011 - 05:12:50 PDT)
- Re: [AMBER] help ! zinc parameters Ross Walker (Fri Sep 16 2011 - 09:18:15 PDT)
  - Re: [AMBER] help ! zinc parameters zhukk (Mon Sep 19 2011 - 05:25:39 PDT)
- Re: [AMBER] help ! zinc parameters Bill Ross (Mon Sep 19 2011 - 13:30:19 PDT)
  - Re: [AMBER] help ! zinc parameters FyD (Tue Sep 20 2011 - 02:14:09 PDT)
    - Re: [AMBER] help ! zinc parameters Kk Zhu (Wed Sep 21 2011 - 00:06:52 PDT)
    - Re: [AMBER] help ! zinc parameters FyD (Wed Sep 21 2011 - 08:02:16 PDT)
    - [AMBER] help ! zinc parameters Bruno Luís Pinto de Oliveira (Thu Sep 22 2011 - 06:07:20 PDT)
    - Re: [AMBER] help ! zinc parameters Baldoni Hector Armando (Thu Sep 22 2011 - 07:02:00 PDT)
[AMBER] Grid Aparna P (Fri Sep 16 2011 - 01:27:00 PDT)
- Re: [AMBER] Grid Thomas Cheatham (Fri Sep 16 2011 - 01:57:32 PDT)
[AMBER] FATAL: allocation failure in vector(), please help me to fix that problem hongphuc nguyen (Fri Sep 16 2011 - 01:26:55 PDT)
- Re: [AMBER] FATAL: allocation failure in vector(), please help me to fix that problem Bill Miller III (Fri Sep 16 2011 - 03:49:55 PDT)
[AMBER] Problems with parsing .PSF files by ptraj Marc van der Kamp (Fri Sep 16 2011 - 03:14:02 PDT)
[AMBER] Initial plateau of the radial distribution function Massimiliano Porrini (Fri Sep 16 2011 - 03:16:23 PDT)
[AMBER] ptraj Linda catherine (Fri Sep 16 2011 - 06:03:14 PDT)
- Re: [AMBER] ptraj Thomas Cheatham (Fri Sep 16 2011 - 06:25:44 PDT)
[AMBER] How to start with aiswarya.pawar.gmail.com (Fri Sep 16 2011 - 06:19:24 PDT)
- Re: [AMBER] How to start with Jason Swails (Fri Sep 16 2011 - 09:51:16 PDT)
[AMBER] help!!zinc parameters zhukk (Fri Sep 16 2011 - 08:16:17 PDT)
- Re: [AMBER] help!!zinc parameters steinbrt.rci.rutgers.edu (Fri Sep 16 2011 - 08:36:31 PDT)
  - Re: [AMBER] help!!zinc parameters zhukk (Mon Sep 19 2011 - 04:55:16 PDT)
[AMBER] unsubscribe Yongmei Wang (ywang) (Fri Sep 16 2011 - 09:48:03 PDT)
[AMBER] Radial distribution kirtana S (Fri Sep 16 2011 - 10:09:19 PDT)
[AMBER] AMBER expense David Condon (Fri Sep 16 2011 - 13:24:23 PDT)
- Re: [AMBER] AMBER expense steinbrt.rci.rutgers.edu (Fri Sep 16 2011 - 16:16:20 PDT)
  - Re: [AMBER] AMBER expense David Condon (Fri Sep 16 2011 - 17:08:34 PDT)
[AMBER] How to mutate nucleobases Rajesh Raju (Fri Sep 16 2011 - 13:42:13 PDT)
- Re: [AMBER] How to mutate nucleobases Sangita Kachhap (Sat Sep 17 2011 - 09:03:04 PDT)
  - Re: [AMBER] How to mutate nucleobases Rajesh Raju (Sat Sep 17 2011 - 09:41:08 PDT)
[AMBER] Difference between serial and parallel MMPBSA Osman, Roman (Fri Sep 16 2011 - 15:18:41 PDT)
- Re: [AMBER] Difference between serial and parallel MMPBSA Ray Luo, Ph.D. (Fri Sep 16 2011 - 20:33:19 PDT)
  - Re: [AMBER] Difference between serial and parallel MMPBSA Osman, Roman (Sat Sep 17 2011 - 08:23:38 PDT)
    - Re: [AMBER] Difference between serial and parallel MMPBSA Mengjuei Hsieh (Thu Sep 22 2011 - 12:58:45 PDT)
    - Re: [AMBER] Difference between serial and parallel MMPBSA Osman, Roman (Thu Sep 22 2011 - 13:07:26 PDT)
[AMBER] Problem with pme cuda :launching kernel kPMEGetGridWeights Himanshu Joshi (Fri Sep 16 2011 - 23:24:49 PDT)
- Re: [AMBER] Problem with pme cuda :launching kernel kPMEGetGridWeights Himanshu Joshi (Fri Sep 16 2011 - 23:29:40 PDT)
- Re: [AMBER] Problem with pme cuda :launching kernel kPMEGetGridWeights Ross Walker (Sat Sep 17 2011 - 16:50:40 PDT)
  - Re: [AMBER] Problem with pme cuda :launching kernel kPMEGetGridWeights Himanshu Joshi (Mon Sep 19 2011 - 02:29:31 PDT)
    - Re: [AMBER] Problem with pme cuda :launching kernel kPMEGetGridWeights Himanshu Joshi (Mon Sep 19 2011 - 03:49:05 PDT)
    - Re: [AMBER] Problem with pme cuda :launching kernel kPMEGetGridWeights Ross Walker (Mon Sep 19 2011 - 08:05:02 PDT)
    - Re: [AMBER] Problem with pme cuda :launching kernel kPMEGetGridWeights Ross Walker (Mon Sep 19 2011 - 08:00:27 PDT)
[AMBER] Dihedral Rotation David Condon (Sat Sep 17 2011 - 12:27:11 PDT)
- Re: [AMBER] Dihedral Rotation Niel Henriksen (Mon Sep 19 2011 - 19:40:58 PDT)
[AMBER] Serious error (or bug) with free energy decomposition MMPBSA.py..The binding free energy values differs in decomposition analysis.. Rajesh Raju (Sat Sep 17 2011 - 13:43:31 PDT)
- Re: [AMBER] Serious error (or bug) with free energy decomposition MMPBSA.py..The binding free energy values differs in decomposition analysis.. Bill Miller III (Sat Sep 17 2011 - 13:55:51 PDT)
  - Re: [AMBER] Serious error (or bug) with free energy decomposition MMPBSA.py..The binding free energy values differs in decomposition analysis.. Rajesh Raju (Sat Sep 17 2011 - 14:16:34 PDT)
- Re: [AMBER] Serious error (or bug) with free energy decomposition MMPBSA.py..The binding free energy values differs in decomposition analysis.. Jason Swails (Sun Sep 18 2011 - 02:21:57 PDT)
  - Re: [AMBER] Serious error (or bug) with free energy decomposition MMPBSA.py..The binding free energy values differs in decomposition analysis.. Rajesh Raju (Sun Sep 18 2011 - 11:34:22 PDT)
[AMBER] scaling factors in carbohydrate-protein interaction Yun Shi (Sat Sep 17 2011 - 15:43:52 PDT)
- Re: [AMBER] scaling factors in carbohydrate-protein interaction Lachele Foley (Lists) (Sat Sep 17 2011 - 19:22:31 PDT)
- Re: [AMBER] scaling factors in carbohydrate-protein interaction FyD (Sat Sep 17 2011 - 23:14:46 PDT)
  - Re: [AMBER] scaling factors in carbohydrate-protein interaction Lachele Foley (Lists) (Sun Sep 18 2011 - 15:12:36 PDT)
  - Re: [AMBER] scaling factors in carbohydrate-protein interaction Ross Walker (Sun Sep 18 2011 - 18:13:59 PDT)
    - Re: [AMBER] scaling factors in carbohydrate-protein interaction FyD (Tue Sep 20 2011 - 00:54:21 PDT)
[AMBER] rst or mdcrd file to view the structures? Chinh Su Tran To (Sun Sep 18 2011 - 22:34:54 PDT)
- Re: [AMBER] rst or mdcrd file to view the structures? steinbrt.rci.rutgers.edu (Mon Sep 19 2011 - 00:38:41 PDT)
  - Re: [AMBER] rst or mdcrd file to view the structures? Chinh Su Tran To (Mon Sep 19 2011 - 03:00:53 PDT)
    - Re: [AMBER] rst or mdcrd file to view the structures? steinbrt.rci.rutgers.edu (Mon Sep 19 2011 - 04:22:22 PDT)
    - Re: [AMBER] rst or mdcrd file to view the structures? Chinh Su Tran To (Mon Sep 19 2011 - 19:44:37 PDT)
- Re: [AMBER] rst or mdcrd file to view the structures? Bill Ross (Mon Sep 19 2011 - 20:36:33 PDT)
  - Re: [AMBER] rst or mdcrd file to view the structures? Chinh Su Tran To (Mon Sep 19 2011 - 22:47:38 PDT)
    - Re: [AMBER] rst or mdcrd file to view the structures? steinbrt.rci.rutgers.edu (Tue Sep 20 2011 - 00:25:51 PDT)
    - Re: [AMBER] rst or mdcrd file to view the structures? Chinh Su Tran To (Tue Sep 20 2011 - 00:54:30 PDT)
- Re: [AMBER] rst or mdcrd file to view the structures? Bill Ross (Tue Sep 20 2011 - 10:24:03 PDT)
  - Re: [AMBER] rst or mdcrd file to view the structures? Chinh Su Tran To (Tue Sep 20 2011 - 22:30:17 PDT)
[AMBER] Glycam06g and ff99SB cause the difference of DIHED (not attributed to the scaling factor) d944286.oz.nthu.edu.tw (Sun Sep 18 2011 - 22:50:38 PDT)
- Re: [AMBER] Glycam06g and ff99SB cause the difference of DIHED (not attributed to the scaling factor) mish (Sun Sep 18 2011 - 23:15:53 PDT)
  - Re: [AMBER] Glycam06g and ff99SB cause the difference of DIHED (not attributed to the scaling factor) Lachele Foley (Lists) (Mon Sep 19 2011 - 06:56:41 PDT)
[AMBER] ptraj: problem with distance and multi-atom masks Marc van der Kamp (Mon Sep 19 2011 - 02:32:47 PDT)
- Re: [AMBER] ptraj: problem with distance and multi-atom masks Daniel Roe (Mon Sep 19 2011 - 09:44:48 PDT)
  - Re: [AMBER] ptraj: problem with distance and multi-atom masks Marc van der Kamp (Tue Sep 20 2011 - 02:32:34 PDT)
    - Re: [AMBER] ptraj: problem with distance and multi-atom masks Daniel Roe (Tue Sep 20 2011 - 04:37:00 PDT)
    - Re: [AMBER] ptraj: problem with distance and multi-atom masks Marc van der Kamp (Tue Sep 20 2011 - 07:24:07 PDT)
[AMBER] help! zinc parameters Kk Zhu (Mon Sep 19 2011 - 05:46:05 PDT)
[AMBER] force field of molecular crystals jun kit (Mon Sep 19 2011 - 11:20:25 PDT)
- Re: [AMBER] force field of molecular crystals David A Case (Mon Sep 19 2011 - 12:00:07 PDT)
  - Re: [AMBER] force field of molecular crystals jun kit (Mon Sep 19 2011 - 12:05:20 PDT)
    - Re: [AMBER] force field of molecular crystals case (Mon Sep 19 2011 - 19:06:23 PDT)
[AMBER] Unit of the partial charge as given in the topology file Sindrila Dutta banik (Mon Sep 19 2011 - 11:47:26 PDT)
- Re: [AMBER] Unit of the partial charge as given in the topology file Jason Swails (Mon Sep 19 2011 - 11:56:29 PDT)
[AMBER] iAPBS 1.2.0 - APBS 1.0.0 - Amber11 compilation error Kenneth Tussey (Mon Sep 19 2011 - 13:47:21 PDT)
- Re: [AMBER] iAPBS 1.2.0 - APBS 1.0.0 - Amber11 compilation error Jason Swails (Mon Sep 19 2011 - 15:22:23 PDT)
  - Re: [AMBER] iAPBS 1.2.0 - APBS 1.0.0 - Amber11 compilation error Kenneth Tussey (Tue Sep 20 2011 - 13:12:07 PDT)
    - Re: [AMBER] iAPBS 1.2.0 - APBS 1.0.0 - Amber11 compilation error Jason Swails (Tue Sep 20 2011 - 14:50:51 PDT)
    - Re: [AMBER] iAPBS 1.2.0 - APBS 1.0.0 - Amber11 compilation error Kenneth Tussey (Tue Sep 20 2011 - 15:05:00 PDT)
    - Re: [AMBER] iAPBS 1.2.0 - APBS 1.0.0 - Amber11 compilation error Jason Swails (Tue Sep 20 2011 - 15:19:31 PDT)
    - Re: [AMBER] iAPBS 1.2.0 - APBS 1.0.0 - Amber11 compilation error Robert Konecny (Tue Sep 20 2011 - 20:22:46 PDT)
    - Re: [AMBER] iAPBS 1.2.0 - APBS 1.0.0 - Amber11 compilation error Jason Swails (Tue Sep 20 2011 - 21:39:16 PDT)
[AMBER] Self-Diffusion coefficient Bruno Rodrigues (Mon Sep 19 2011 - 14:43:31 PDT)
- Re: [AMBER] Self-Diffusion coefficient Thomas Cheatham III (Mon Sep 19 2011 - 15:50:20 PDT)
  - Re: [AMBER] Self-Diffusion coefficient Bruno Rodrigues (Tue Sep 20 2011 - 11:13:53 PDT)
[AMBER] How to build the surface of crystalline cellulose? bin wang (Mon Sep 19 2011 - 15:16:44 PDT)
[AMBER] How to build the surface of crystalline cellulose? bin wang (Mon Sep 19 2011 - 20:19:31 PDT)
- Re: [AMBER] How to build the surface of crystalline cellulose? Lachele Foley (Lists) (Wed Sep 21 2011 - 06:06:16 PDT)
[AMBER] new residue parameters transfer Yao Yao (Mon Sep 19 2011 - 22:37:30 PDT)
- Re: [AMBER] new residue parameters transfer David A Case (Tue Sep 20 2011 - 04:48:08 PDT)
- Re: [AMBER] new residue parameters transfer Yong Duan (Tue Sep 20 2011 - 05:46:13 PDT)
[AMBER] charges on ligand kamlesh sahu (Mon Sep 19 2011 - 22:58:18 PDT)
- Re: [AMBER] charges on ligand steinbrt.rci.rutgers.edu (Tue Sep 20 2011 - 00:32:47 PDT)
[AMBER] Automatic creation of charge and radius files for Delphi Jan-Philip Gehrcke (Tue Sep 20 2011 - 03:13:21 PDT)
[AMBER] topology and coordinate files madhumita das (Tue Sep 20 2011 - 04:14:58 PDT)
[AMBER] Instantaneous temperature in TI simulation Brian Radak (Tue Sep 20 2011 - 06:01:54 PDT)
- Re: [AMBER] Instantaneous temperature in TI simulation David A Case (Tue Sep 20 2011 - 07:33:55 PDT)
  - Re: [AMBER] Instantaneous temperature in TI simulation Brian Radak (Tue Sep 20 2011 - 07:59:36 PDT)
    - Re: [AMBER] Instantaneous temperature in TI simulation Brian Radak (Tue Sep 20 2011 - 11:23:48 PDT)
    - Re: [AMBER] Instantaneous temperature in TI simulation Qiantao Wang (Tue Sep 20 2011 - 12:33:51 PDT)
    - Re: [AMBER] Instantaneous temperature in TI simulation David A Case (Wed Sep 21 2011 - 04:52:54 PDT)
- Re: [AMBER] Instantaneous temperature in TI simulation Jason Swails (Tue Sep 20 2011 - 13:08:49 PDT)
- Re: [AMBER] Instantaneous temperature in TI simulation Brian Radak (Wed Sep 21 2011 - 06:40:07 PDT)
  - Re: [AMBER] Instantaneous temperature in TI simulation Qiantao Wang (Wed Sep 21 2011 - 12:43:09 PDT)
    - Re: [AMBER] Instantaneous temperature in TI simulation Brian Radak (Wed Sep 21 2011 - 13:44:41 PDT)
    - Re: [AMBER] Instantaneous temperature in TI simulation Qiantao Wang (Wed Sep 21 2011 - 14:12:01 PDT)
    - Re: [AMBER] Instantaneous temperature in TI simulation Qiantao Wang (Fri Sep 23 2011 - 12:08:41 PDT)
    - Re: [AMBER] Instantaneous temperature in TI simulation Qiantao Wang (Fri Sep 23 2011 - 12:25:06 PDT)
    - Re: [AMBER] Instantaneous temperature in TI simulation Brian Radak (Fri Sep 23 2011 - 13:07:58 PDT)
    - Re: [AMBER] Instantaneous temperature in TI simulation case (Sat Sep 24 2011 - 05:51:43 PDT)
    - Re: [AMBER] Instantaneous temperature in TI simulation Qiantao Wang (Sun Sep 25 2011 - 06:26:54 PDT)
    - Re: [AMBER] Instantaneous temperature in TI simulation Brian Radak (Mon Sep 26 2011 - 06:05:47 PDT)
    - Re: [AMBER] Instantaneous temperature in TI simulation Qiantao Wang (Wed Sep 28 2011 - 13:12:44 PDT)
Re: [AMBER] Glycam06g and ff99SB cause the difference of DIHED (notattributed to the scaling factor) d944286.oz.nthu.edu.tw (Tue Sep 20 2011 - 08:32:38 PDT)
[AMBER] tx/LEaP numlock. Ross Walker (Tue Sep 20 2011 - 09:38:01 PDT)
[AMBER] problem with TI calculations Victor Ma (Tue Sep 20 2011 - 12:08:03 PDT)
- Re: [AMBER] problem with TI calculations David A Case (Wed Sep 21 2011 - 04:50:38 PDT)
[AMBER] Xleap Installation Yao Yao (Tue Sep 20 2011 - 15:40:07 PDT)
- Re: [AMBER] Xleap Installation Ben Roberts (Wed Sep 21 2011 - 06:51:05 PDT)
[AMBER] Help needed for Amber SCC-DFTB code 杨立江 (Tue Sep 20 2011 - 22:45:23 PDT)
- Re: [AMBER] Help needed for Amber SCC-DFTB code Qiantao Wang (Wed Sep 21 2011 - 14:44:56 PDT)
[AMBER] Error: peek_ewald_inpcrd: SHOULD NOT BE HERE Hirdesh Kumar (Tue Sep 20 2011 - 23:07:50 PDT)
- Re: [AMBER] Error: peek_ewald_inpcrd: SHOULD NOT BE HERE case (Sun Sep 25 2011 - 14:03:34 PDT)
[AMBER] bug in respgen ? thomas.fox.boehringer-ingelheim.com (Wed Sep 21 2011 - 00:06:21 PDT)
- Re: [AMBER] bug in respgen ? FyD (Thu Sep 22 2011 - 00:25:43 PDT)
  - Re: [AMBER] bug in respgen ? thomas.fox.boehringer-ingelheim.com (Fri Sep 23 2011 - 05:59:04 PDT)
    - Re: [AMBER] bug in respgen ? FyD (Fri Sep 23 2011 - 07:27:13 PDT)
    - Re: [AMBER] bug in respgen ? thomas.fox.boehringer-ingelheim.com (Mon Sep 26 2011 - 00:00:06 PDT)
    - Re: [AMBER] bug in respgen ? FyD (Mon Sep 26 2011 - 03:19:08 PDT)
    - Re: [AMBER] bug in respgen ? FyD (Mon Sep 26 2011 - 04:33:35 PDT)
    - Re: [AMBER] bug in respgen ? David A Case (Wed Sep 28 2011 - 07:11:30 PDT)
    - Re: [AMBER] bug in respgen ? FyD (Wed Sep 28 2011 - 09:03:53 PDT)
    - Re: [AMBER] bug in respgen ? thomas.fox.boehringer-ingelheim.com (Fri Oct 07 2011 - 05:15:08 PDT)
[AMBER] Grid and SDF Lorenzo Gontrani (Wed Sep 21 2011 - 03:53:47 PDT)
[AMBER] Sleap and TIP4P BOX Guenegou, Guillaume [JRDFR] (Wed Sep 21 2011 - 04:42:51 PDT)
- Re: [AMBER] Sleap and TIP4P BOX David A Case (Wed Sep 21 2011 - 06:39:29 PDT)
  - Re: [AMBER] Sleap and TIP4P BOX Guenegou, Guillaume [JRDFR] (Wed Sep 21 2011 - 07:07:57 PDT)
    - Re: [AMBER] Sleap and TIP4P BOX David A Case (Thu Sep 22 2011 - 05:59:31 PDT)
    - Re: [AMBER] Sleap and TIP4P BOX Guenegou, Guillaume [JRDFR] (Fri Sep 23 2011 - 00:22:42 PDT)
    - Re: [AMBER] Sleap and TIP4P BOX David A Case (Fri Sep 23 2011 - 06:20:18 PDT)
    - Re: [AMBER] Sleap and TIP4P BOX Guenegou, Guillaume [JRDFR] (Fri Sep 23 2011 - 06:48:05 PDT)
[AMBER] Difficulties trying to derive charge for new acetylated serine Fabrício Bracht (Tue Sep 20 2011 - 22:36:32 PDT)
- Re: [AMBER] Difficulties trying to derive charge for new acetylated serine M. L. Dodson (Wed Sep 21 2011 - 06:18:28 PDT)
- Re: [AMBER] Difficulties trying to derive charge for new acetylated serine FyD (Wed Sep 21 2011 - 08:55:17 PDT)
[AMBER] Grid and SDF Lorenzo Gontrani (Wed Sep 21 2011 - 06:24:50 PDT)
[AMBER] SASA calculation in Amber Horacio Pérez-Sánchez (Wed Sep 21 2011 - 09:45:19 PDT)
- Re: [AMBER] SASA calculation in Amber Jason Swails (Wed Sep 21 2011 - 10:33:56 PDT)
[AMBER] Different Temps Coupling Yao Yao (Wed Sep 21 2011 - 10:35:56 PDT)
- Re: [AMBER] Different Temps Coupling Ross Walker (Wed Sep 21 2011 - 12:42:53 PDT)
[AMBER] RMSD fatahiya (Wed Sep 21 2011 - 23:13:02 PDT)
- Re: [AMBER] RMSD Aparna P (Thu Sep 22 2011 - 02:14:39 PDT)
- Re: [AMBER] RMSD Daniel Roe (Thu Sep 22 2011 - 04:42:56 PDT)
  - Re: [AMBER] RMSD fatahiya (Sun Sep 25 2011 - 22:00:59 PDT)
    - Re: [AMBER] RMSD Bruno Rodrigues (Mon Sep 26 2011 - 05:35:51 PDT)
    - Re: [AMBER] RMSD fatahiya (Mon Sep 26 2011 - 19:08:39 PDT)
    - Re: [AMBER] RMSD Daniel Roe (Tue Sep 27 2011 - 05:43:10 PDT)
[AMBER] GRID and SDF Lorenzo Gontrani (Thu Sep 22 2011 - 00:28:08 PDT)
[AMBER] Amber parmbsc0 souvik sur (Thu Sep 22 2011 - 00:35:03 PDT)
- Re: [AMBER] Amber parmbsc0 Nadine Utz (Thu Sep 22 2011 - 00:52:00 PDT)
- Re: [AMBER] Amber parmbsc0 Daniel Roe (Thu Sep 22 2011 - 04:58:12 PDT)
[AMBER] Grid and SDF Lorenzo Gontrani (Thu Sep 22 2011 - 00:40:41 PDT)
- Re: [AMBER] Grid and SDF Thomas Cheatham III (Thu Sep 22 2011 - 11:28:18 PDT)
[AMBER] Model building Aparna P (Thu Sep 22 2011 - 01:00:57 PDT)
- Re: [AMBER] Model building Daniel Roe (Thu Sep 22 2011 - 04:54:50 PDT)
  - Re: [AMBER] Model building Aparna P (Fri Sep 23 2011 - 01:05:29 PDT)
    - Re: [AMBER] Model building Daniel Roe (Fri Sep 23 2011 - 04:33:19 PDT)
    - Re: [AMBER] Model building Aparna P (Sat Sep 24 2011 - 21:31:03 PDT)
    - Re: [AMBER] Model building Aparna P (Mon Sep 26 2011 - 22:01:58 PDT)
    - Re: [AMBER] Model building Daniel Roe (Tue Sep 27 2011 - 04:47:16 PDT)
    - Re: [AMBER] Model building Aparna P (Thu Sep 29 2011 - 04:16:46 PDT)
    - Re: [AMBER] Model building Sangita Kachhap (Thu Sep 29 2011 - 10:54:09 PDT)
[AMBER] ICST truongco nguyen (Thu Sep 22 2011 - 02:10:49 PDT)
- Re: [AMBER] ICST David A Case (Thu Sep 22 2011 - 06:13:56 PDT)
[AMBER] Restart-Files in Sander Julian Zachmann (Thu Sep 22 2011 - 06:11:00 PDT)
- Re: [AMBER] Restart-Files in Sander Brian Radak (Thu Sep 22 2011 - 06:25:48 PDT)
[AMBER] Amber parmbsc0 vs ff99 souvik sur (Thu Sep 22 2011 - 06:41:45 PDT)
- Re: [AMBER] Amber parmbsc0 vs ff99 Brian Radak (Thu Sep 22 2011 - 06:50:40 PDT)
  - Re: [AMBER] Amber parmbsc0 vs ff99 Hugh Heldenbrand (Thu Sep 22 2011 - 08:02:40 PDT)
    - Re: [AMBER] Amber parmbsc0 vs ff99 Marek Maly (Thu Sep 22 2011 - 07:54:45 PDT)
    - Re: [AMBER] Amber parmbsc0 vs ff99 Jason Swails (Thu Sep 22 2011 - 08:22:10 PDT)
    - Re: [AMBER] Amber parmbsc0 vs ff99 Thomas Cheatham (Thu Sep 22 2011 - 08:15:16 PDT)
    - Re: [AMBER] Amber parmbsc0 vs ff99 Brian Radak (Thu Sep 22 2011 - 08:24:56 PDT)
    - Re: [AMBER] Amber parmbsc0 vs ff99 Marek Maly (Thu Sep 22 2011 - 08:43:12 PDT)
    - Re: [AMBER] Amber parmbsc0 vs ff99 Jason Swails (Thu Sep 22 2011 - 09:15:28 PDT)
    - Re: [AMBER] Amber parmbsc0 vs ff99 Marek Maly (Thu Sep 22 2011 - 09:06:56 PDT)
    - Re: [AMBER] Amber parmbsc0 vs ff99 Jiri Sponer (Thu Sep 22 2011 - 11:36:51 PDT)
[AMBER] GB protocol problems for large RNAs Kasprzak, Wojciech (NIH/NCI) [C] (Thu Sep 22 2011 - 09:02:28 PDT)
- Re: [AMBER] GB protocol problems for large RNAs Ross Walker (Thu Sep 22 2011 - 09:30:46 PDT)
[AMBER] sander/amoeba parameter format Andrew Petersen (Thu Sep 22 2011 - 09:53:40 PDT)
[AMBER] error when installing parallel sander / AmberTools1.5 Amber11 matheus froeyen (Thu Sep 22 2011 - 10:56:18 PDT)
- Re: [AMBER] error when installing parallel sander / AmberTools1.5 Amber11 Ross Walker (Thu Sep 22 2011 - 11:05:10 PDT)
  - Re: [AMBER] error when installing parallel sander / AmberTools1.5 Amber11 matheus froeyen (Fri Sep 23 2011 - 01:49:50 PDT)
- Re: [AMBER] error when installing parallel sander / AmberTools1.5 Amber11 K T (Thu Sep 22 2011 - 17:28:31 PDT)
  - Re: [AMBER] error when installing parallel sander / AmberTools1.5 Amber11 Jason Swails (Thu Sep 22 2011 - 17:43:14 PDT)
[AMBER] Large pressure fluctuations over the whole run Hernán Meier (Thu Sep 22 2011 - 16:14:54 PDT)
- Re: [AMBER] Large pressure fluctuations over the whole run Jason Swails (Thu Sep 22 2011 - 19:49:14 PDT)
  - Re: [AMBER] Large pressure fluctuations over the whole run Hernán Meier (Mon Sep 26 2011 - 15:04:51 PDT)
    - Re: [AMBER] Large pressure fluctuations over the whole run Adrian Roitberg (Mon Sep 26 2011 - 15:25:32 PDT)
    - Re: [AMBER] Large pressure fluctuations over the whole run case (Mon Sep 26 2011 - 19:19:59 PDT)
[AMBER] XH/pi (X=C, O, N) interactions and stacking interactions in AMBER Rajesh Raju (Thu Sep 22 2011 - 16:24:39 PDT)
- Re: [AMBER] XH/pi (X=C, O, N) interactions and stacking interactions in AMBER Jason Swails (Thu Sep 22 2011 - 16:42:37 PDT)
- Re: [AMBER] XH/pi (X=C, O, N) interactions and stacking interactions in AMBER Qiantao Wang (Fri Sep 23 2011 - 07:41:08 PDT)
  - Re: [AMBER] XH/pi (X=C, O, N) interactions and stacking interactions in AMBER Jiri Sponer (Fri Sep 23 2011 - 08:32:52 PDT)
[AMBER] AmberTools Parallel Compilation Issue Matteo Guglielmi (Thu Sep 22 2011 - 17:59:09 PDT)
- Re: [AMBER] AmberTools Parallel Compilation Issue Jason Swails (Thu Sep 22 2011 - 18:10:18 PDT)
  - Re: [AMBER] AmberTools Parallel Compilation Issue Matteo Guglielmi (Fri Sep 23 2011 - 02:06:56 PDT)
- Re: [AMBER] AmberTools Parallel Compilation Issue David A Case (Fri Sep 23 2011 - 06:15:59 PDT)
  - Re: [AMBER] AmberTools Parallel Compilation Issue Carlos Sosa (Fri Sep 23 2011 - 06:51:42 PDT)
    - Re: [AMBER] AmberTools Parallel Compilation Issue Matteo Guglielmi (Fri Sep 23 2011 - 08:21:53 PDT)
    - Re: [AMBER] AmberTools Parallel Compilation Issue Carlos Sosa (Fri Sep 23 2011 - 08:24:39 PDT)
    - Re: [AMBER] AmberTools Parallel Compilation Issue Matteo Guglielmi (Fri Sep 23 2011 - 12:06:59 PDT)
    - Re: [AMBER] AmberTools Parallel Compilation Issue Ross Walker (Fri Sep 23 2011 - 12:26:11 PDT)
    - Re: [AMBER] AmberTools Parallel Compilation Issue Matteo Guglielmi (Sat Sep 24 2011 - 08:03:03 PDT)
[AMBER] how to generate a correlation matrix for both protein and substrate atoms sunxi.comcast.net (Thu Sep 22 2011 - 22:08:13 PDT)
- Re: [AMBER] how to generate a correlation matrix for both protein and substrate atoms Daniel Roe (Fri Sep 23 2011 - 04:40:38 PDT)
Re: [AMBER] Grid and SDF - sorry for the mail spamming Lorenzo Gontrani (Thu Sep 22 2011 - 22:49:06 PDT)
[AMBER] problem with nmodes calculation-260-residue protein hongphuc nguyen (Fri Sep 23 2011 - 02:15:37 PDT)
- Re: [AMBER] problem with nmodes calculation-260-residue protein case (Sat Sep 24 2011 - 05:58:05 PDT)
[AMBER] RESP charge fitting shome sankar bhunia (Fri Sep 23 2011 - 04:22:37 PDT)
- Re: [AMBER] RESP charge fitting FyD (Fri Sep 23 2011 - 05:21:13 PDT)
[AMBER] hydrogen bonding Vijay Manickam Achari (Fri Sep 23 2011 - 05:17:06 PDT)
- Re: [AMBER] hydrogen bonding Daniel Roe (Fri Sep 23 2011 - 07:56:17 PDT)
  - Re: [AMBER] hydrogen bonding Vijay Manickam Achari (Fri Sep 23 2011 - 21:17:29 PDT)
[AMBER] load parmbsc0 and X-Ol for RNA David Condon (Fri Sep 23 2011 - 06:25:16 PDT)
- Re: [AMBER] load parmbsc0 and X-Ol for RNA David A Case (Fri Sep 23 2011 - 13:10:33 PDT)
  - Re: [AMBER] load parmbsc0 and X-Ol for RNA Catein Catherine (Fri Sep 23 2011 - 19:14:09 PDT)
    - [AMBER] How to recover rst or can I readin mdcrd for a MD by -c? Catein Catherine (Fri Sep 23 2011 - 19:18:57 PDT)
    - Re: [AMBER] How to recover rst or can I readin mdcrd for a MD by -c? Bruno Rodrigues (Sat Sep 24 2011 - 05:37:50 PDT)
    - Re: [AMBER] How to recover rst or can I readin mdcrd for a MD by -c? Catein Catherine (Sat Sep 24 2011 - 23:03:19 PDT)
  - Re: [AMBER] load parmbsc0 and X-Ol for RNA David Condon (Sun Sep 25 2011 - 14:03:06 PDT)
[AMBER] Antechamber Zachary Davis (Fri Sep 23 2011 - 10:17:38 PDT)
- Re: [AMBER] Antechamber case (Sun Sep 25 2011 - 14:09:14 PDT)
[AMBER] nmode calculations kirtana S (Fri Sep 23 2011 - 14:52:11 PDT)
- Re: [AMBER] nmode calculations Jason Swails (Sat Sep 24 2011 - 17:17:02 PDT)
  - Re: [AMBER] nmode calculations kirtana S (Sun Sep 25 2011 - 09:58:52 PDT)
    - Re: [AMBER] nmode calculations case (Sun Sep 25 2011 - 13:59:09 PDT)
[AMBER] Amber parmbsc0 force field souvik sur (Fri Sep 23 2011 - 21:25:11 PDT)
- Re: [AMBER] Amber parmbsc0 force field Bruno Rodrigues (Fri Sep 23 2011 - 22:22:44 PDT)
- Re: [AMBER] Amber parmbsc0 force field case (Sat Sep 24 2011 - 06:04:47 PDT)
  - Re: [AMBER] Amber parmbsc0 force field souvik sur (Sat Sep 24 2011 - 07:09:53 PDT)
    - Re: [AMBER] Amber parmbsc0 force field Jason Swails (Sat Sep 24 2011 - 07:33:29 PDT)
[AMBER] AmberTools 1.4 Installation on Mac OSX 10.6 George Tzotzos (Sat Sep 24 2011 - 02:41:03 PDT)
- Re: [AMBER] AmberTools 1.4 Installation on Mac OSX 10.6 George Tzotzos (Sat Sep 24 2011 - 04:08:22 PDT)
  - Re: [AMBER] AmberTools 1.4 Installation on Mac OSX 10.6 Daniel Roe (Sat Sep 24 2011 - 05:44:13 PDT)
  - Re: [AMBER] AmberTools 1.4 Installation on Mac OSX 10.6 Jason Swails (Sat Sep 24 2011 - 07:50:40 PDT)
    - Re: [AMBER] AmberTools 1.4 Installation on Mac OSX 10.6 Daniel Roe (Sat Sep 24 2011 - 08:48:53 PDT)
    - Re: [AMBER] AmberTools 1.4 Installation on Mac OSX 10.6 Jason Swails (Sat Sep 24 2011 - 17:13:04 PDT)
- Re: [AMBER] AmberTools 1.4 Installation on Mac OSX 10.6 Mengjuei Hsieh (Sat Sep 24 2011 - 08:31:23 PDT)
[AMBER] fixing rmsd values Massimiliano Porrini (Sun Sep 25 2011 - 08:22:13 PDT)
- Re: [AMBER] fixing rmsd values Niel Henriksen (Sun Sep 25 2011 - 08:47:23 PDT)
  - Re: [AMBER] fixing rmsd values Massimiliano Porrini (Mon Sep 26 2011 - 07:46:52 PDT)
    - Re: [AMBER] fixing rmsd values Bruno Rodrigues (Mon Sep 26 2011 - 08:54:25 PDT)
    - Re: [AMBER] fixing rmsd values Massimiliano Porrini (Mon Sep 26 2011 - 10:18:47 PDT)
    - Re: [AMBER] fixing rmsd values Niel Henriksen (Mon Sep 26 2011 - 10:29:22 PDT)
    - Re: [AMBER] fixing rmsd values InSuk Joung (Mon Sep 26 2011 - 10:29:35 PDT)
[AMBER] Problems of Hbond calculation qiao xue (Sun Sep 25 2011 - 19:30:33 PDT)
- Re: [AMBER] Problems of Hbond calculation Bruno Rodrigues (Mon Sep 26 2011 - 05:39:53 PDT)
[AMBER] Regarding Force field souvik sur (Sun Sep 25 2011 - 22:28:36 PDT)
- Re: [AMBER] Regarding Force field David A Case (Mon Sep 26 2011 - 05:03:26 PDT)
[AMBER] Solvent model charges off by factor of 18.2223 or typo? Daniel Sindhikara (Sun Sep 25 2011 - 23:57:08 PDT)
[AMBER] GAMESS to RESP input file shome sankar bhunia (Mon Sep 26 2011 - 03:46:25 PDT)
- Re: [AMBER] GAMESS to RESP input file FyD (Mon Sep 26 2011 - 04:58:34 PDT)
[AMBER] ambertool question !!! Алексей Раевский (Mon Sep 26 2011 - 11:22:14 PDT)
- Re: [AMBER] ambertool question !!! Brian Radak (Mon Sep 26 2011 - 11:36:16 PDT)
  - Re: [AMBER] ambertool question !!! Алексей Раевский (Mon Oct 03 2011 - 14:20:10 PDT)
- Re: [AMBER] ambertool question !!! Dmitry Nilov (Mon Sep 26 2011 - 12:11:28 PDT)
  - Re: [AMBER] ambertool question !!! Алексей Раевский (Mon Oct 03 2011 - 14:20:43 PDT)
    - Re: [AMBER] ambertool question !!! David Case (Mon Oct 03 2011 - 16:33:31 PDT)
    - Re: [AMBER] ambertool question !!! Алексей Раевский (Tue Oct 04 2011 - 00:21:58 PDT)
    - Re: [AMBER] ambertool question !!! Dmitry Nilov (Mon Oct 03 2011 - 20:54:30 PDT)
  - Re: [AMBER] ambertool question !!! Алексей Раевский (Sun Jan 15 2012 - 13:57:27 PST)
[AMBER] ambertool question !!! Алексей Раевский (Mon Sep 26 2011 - 11:23:58 PDT)
- [AMBER] MM/GBSA question - pairwise decomposition Anselm Horn (Mon Sep 26 2011 - 12:11:55 PDT)
[AMBER] Some common doubts about MMPBSA.py decomposition Rajesh Raju (Mon Sep 26 2011 - 12:24:36 PDT)
- Re: [AMBER] Some common doubts about MMPBSA.py decomposition Jason Swails (Mon Sep 26 2011 - 17:45:24 PDT)
- [AMBER] Some common doubts about MMPBSA.py decomposition Rajesh Raju (Mon Sep 26 2011 - 18:13:08 PDT)
[AMBER] dihedral parameters kirtana S (Mon Sep 26 2011 - 14:09:39 PDT)
- Re: [AMBER] dihedral parameters Jason Swails (Mon Sep 26 2011 - 18:08:39 PDT)
  - Re: [AMBER] dihedral parameters Chidambar Kulkarni (Mon Sep 26 2011 - 20:51:18 PDT)
    - Re: [AMBER] dihedral parameters Jason Swails (Tue Sep 27 2011 - 05:01:07 PDT)
    - Re: [AMBER] dihedral parameters Chidambar Kulkarni (Tue Sep 27 2011 - 09:09:05 PDT)
  - Re: [AMBER] dihedral parameters kirtana S (Tue Sep 27 2011 - 14:59:00 PDT)
[AMBER] thermodynamic integration on protein mutation Jorge Iulek (Mon Sep 26 2011 - 17:34:51 PDT)
- Re: [AMBER] thermodynamic integration on protein mutation case (Mon Sep 26 2011 - 19:22:06 PDT)
  - Re: [AMBER] thermodynamic integration on protein mutation Jorge Iulek (Tue Sep 27 2011 - 09:09:59 PDT)
[AMBER] Mol2 file creation Chidambar Kulkarni (Mon Sep 26 2011 - 20:57:36 PDT)
- Re: [AMBER] Mol2 file creation David A Case (Tue Sep 27 2011 - 04:53:35 PDT)
  - Re: [AMBER] Mol2 file creation Chidambar Kulkarni (Tue Sep 27 2011 - 09:05:04 PDT)
[AMBER] non-bond interaction Anglea A. (Tue Sep 27 2011 - 00:01:24 PDT)
- Re: [AMBER] non-bond interaction steinbrt.rci.rutgers.edu (Tue Sep 27 2011 - 00:07:12 PDT)
[AMBER] GB protocol problems for large RNAs (follow-up) Kasprzak, Wojciech (NIH/NCI) [C] (Tue Sep 27 2011 - 07:09:10 PDT)
- Re: [AMBER] GB protocol problems for large RNAs (follow-up) Ross Walker (Tue Sep 27 2011 - 09:13:32 PDT)
  - Re: [AMBER] GB protocol problems for large RNAs (follow-up) Carlos Simmerling (Tue Sep 27 2011 - 09:34:23 PDT)
  - Re: [AMBER] GB protocol problems for large RNAs (follow-up) Niel Henriksen (Tue Sep 27 2011 - 09:42:32 PDT)
    - Re: [AMBER] GB protocol problems for large RNAs (follow-up) David A Case (Tue Sep 27 2011 - 12:43:12 PDT)
- Re: [AMBER] GB protocol problems for large RNAs (follow-up) Thomas Gaillard (Tue Sep 27 2011 - 10:38:43 PDT)
[AMBER] giving acceptor mask in ptraj for hbond utility Bala subramanian (Tue Sep 27 2011 - 11:16:05 PDT)
- Re: [AMBER] giving acceptor mask in ptraj for hbond utility Daniel Roe (Tue Sep 27 2011 - 11:36:32 PDT)
[AMBER] Fwd: fixing rmsd values (follow-up) Massimiliano Porrini (Tue Sep 27 2011 - 11:44:14 PDT)
- Re: [AMBER] Fwd: fixing rmsd values (follow-up) Carlos Simmerling (Tue Sep 27 2011 - 11:51:37 PDT)
- Re: [AMBER] Fwd: fixing rmsd values (follow-up) Thomas Cheatham III (Tue Sep 27 2011 - 13:55:40 PDT)
  - Re: [AMBER] Fwd: fixing rmsd values (follow-up) Carlos Simmerling (Tue Sep 27 2011 - 14:14:33 PDT)
    - Re: [AMBER] Fwd: fixing rmsd values (follow-up) Bruno Rodrigues (Tue Sep 27 2011 - 14:39:47 PDT)
    - Re: [AMBER] Fwd: fixing rmsd values (follow-up) Massimiliano Porrini (Wed Sep 28 2011 - 04:26:29 PDT)
    - Re: [AMBER] Fwd: fixing rmsd values (follow-up) Massimiliano Porrini (Wed Sep 28 2011 - 11:10:52 PDT)
    - Re: [AMBER] Fwd: fixing rmsd values (follow-up) Mariano Rech (Wed Sep 28 2011 - 23:34:46 PDT)
    - Re: [AMBER] Fwd: fixing rmsd values (follow-up) Jason Swails (Thu Sep 29 2011 - 17:55:15 PDT)
[AMBER] Chromophore Building Yao Yao (Tue Sep 27 2011 - 12:34:19 PDT)
- Re: [AMBER] Chromophore Building M. L. Dodson (Tue Sep 27 2011 - 12:55:49 PDT)
[AMBER] Failure building Amber 11 parallel on AmberTools1.5 George Tzotzos (Tue Sep 27 2011 - 13:24:03 PDT)
- Re: [AMBER] Failure building Amber 11 parallel on AmberTools1.5 Jason Swails (Tue Sep 27 2011 - 17:26:16 PDT)
[AMBER] Parallel compile error of Amber11 kurisaki (Tue Sep 27 2011 - 20:30:52 PDT)
- Re: [AMBER] Parallel compile error of Amber11 Jason Swails (Tue Sep 27 2011 - 20:40:06 PDT)
  - Re: [AMBER] Parallel compile error of Amber11 kurisaki (Tue Sep 27 2011 - 23:29:01 PDT)
[AMBER] solvateBox or setBox or set box Neha Gandhi (Tue Sep 27 2011 - 23:36:29 PDT)
- Re: [AMBER] solvateBox or setBox or set box David A Case (Wed Sep 28 2011 - 05:17:24 PDT)
[AMBER] PMEMD job was aborted kurisaki (Wed Sep 28 2011 - 00:00:15 PDT)
- Re: [AMBER] PMEMD job was aborted Ross Walker (Wed Sep 28 2011 - 00:09:52 PDT)
  - Re: [AMBER] PMEMD job was aborted kurisaki (Wed Sep 28 2011 - 01:53:09 PDT)
[AMBER] sander outout using mdin=5 and idecomp=2 kurisaki (Wed Sep 28 2011 - 02:13:18 PDT)
- Re: [AMBER] sander outout using mdin=5 and idecomp=2 Jason Swails (Wed Sep 28 2011 - 05:58:29 PDT)
  - Re: [AMBER] sander outout using mdin=5 and idecomp=2 kurisaki (Wed Sep 28 2011 - 06:37:57 PDT)
  - Re: [AMBER] sander outout using mdin=5 and idecomp=2 kurisaki (Wed Sep 28 2011 - 07:01:13 PDT)
[AMBER] PCA Linda catherine (Wed Sep 28 2011 - 04:44:31 PDT)
- Re: [AMBER] PCA Jason Swails (Wed Sep 28 2011 - 22:31:11 PDT)
[AMBER] MMPBSA.py discrepancies in results George Tzotzos (Wed Sep 28 2011 - 06:20:28 PDT)
- Re: [AMBER] MMPBSA.py discrepancies in results Bill Miller III (Wed Sep 28 2011 - 06:27:31 PDT)
  - Re: [AMBER] MMPBSA.py discrepancies in results George Tzotzos (Wed Sep 28 2011 - 06:33:16 PDT)
    - Re: [AMBER] MMPBSA.py discrepancies in results Jason Swails (Wed Sep 28 2011 - 07:16:55 PDT)
    - Re: [AMBER] MMPBSA.py discrepancies in results George Tzotzos (Wed Sep 28 2011 - 07:43:42 PDT)
    - Re: [AMBER] MMPBSA.py discrepancies in results Jason Swails (Wed Sep 28 2011 - 08:23:33 PDT)
    - Re: [AMBER] MMPBSA.py discrepancies in results George Tzotzos (Wed Sep 28 2011 - 08:44:13 PDT)
    - Re: [AMBER] MMPBSA.py discrepancies in results Bill Miller III (Wed Sep 28 2011 - 09:03:04 PDT)
    - Re: [AMBER] MMPBSA.py discrepancies in results George Tzotzos (Wed Sep 28 2011 - 09:04:58 PDT)
    - Re: [AMBER] MMPBSA.py discrepancies in results Jason Swails (Wed Sep 28 2011 - 11:43:01 PDT)
    - Re: [AMBER] MMPBSA.py discrepancies in results George Tzotzos (Wed Sep 28 2011 - 14:43:57 PDT)
    - Re: [AMBER] MMPBSA.py discrepancies in results Jason Swails (Wed Sep 28 2011 - 15:22:06 PDT)
    - Re: [AMBER] MMPBSA.py discrepancies in results George Tzotzos (Thu Sep 29 2011 - 02:31:07 PDT)
    - Re: [AMBER] MMPBSA.py discrepancies in results Bill Miller III (Thu Sep 29 2011 - 04:16:04 PDT)
[AMBER] Announcing the NVIDIA MD SimCluster Program (Free test drives available) Ross Walker (Wed Sep 28 2011 - 14:29:36 PDT)
[AMBER] 1st DNA tutorial cannot save parameter Yao Yao (Wed Sep 28 2011 - 17:28:30 PDT)
- Re: [AMBER] 1st DNA tutorial cannot save parameter Ross Walker (Wed Sep 28 2011 - 21:49:17 PDT)
[AMBER] Survey Request - 10 minutes of your time please to help future AMBER development (http://surveys.nvidia.com/index.jsp?pi=f7d3e68a3e1b44841571e6ab4ce2f021) Ross Walker (Wed Sep 28 2011 - 19:01:08 PDT)
- Re: [AMBER] Survey Request - 10 minutes of your time please to help future AMBER development (http://surveys.nvidia.com/index.jsp?pi=f7d3e68a3e1b44841571e6ab4ce2f021) Jan-Philip Gehrcke (Thu Sep 29 2011 - 04:00:16 PDT)
  - Re: [AMBER] Survey Request - 10 minutes of your time please to help future AMBER development (http://surveys.nvidia.com/index.jsp?pi=f7d3e68a3e1b44841571e6ab4ce2f021) Ross Walker (Thu Sep 29 2011 - 07:38:08 PDT)
[AMBER] PNEB on GPUs William Cantara (Wed Sep 28 2011 - 20:20:30 PDT)
- Re: [AMBER] PNEB on GPUs Ross Walker (Wed Sep 28 2011 - 21:01:50 PDT)
  - Re: [AMBER] PNEB on GPUs Jason Swails (Wed Sep 28 2011 - 21:09:36 PDT)
    - Re: [AMBER] PNEB on GPUs Ross Walker (Wed Sep 28 2011 - 21:16:06 PDT)
    - Re: [AMBER] PNEB on GPUs Jason Swails (Wed Sep 28 2011 - 21:35:29 PDT)
    - Re: [AMBER] PNEB on GPUs Christina Bergonzo (Thu Sep 29 2011 - 05:25:59 PDT)
    - Re: [AMBER] PNEB on GPUs William Cantara (Thu Sep 29 2011 - 06:03:45 PDT)
    - Re: [AMBER] PNEB on GPUs Jason Swails (Thu Sep 29 2011 - 06:13:45 PDT)
    - Re: [AMBER] PNEB on GPUs William Cantara (Mon Oct 03 2011 - 17:33:21 PDT)
    - [AMBER] Energetic analysis with MMPBSA.py considering just one molecule ? Marek Maly (Thu Sep 29 2011 - 14:32:09 PDT)
    - Re: [AMBER] Energetic analysis with MMPBSA.py considering just one molecule ? Jason Swails (Thu Sep 29 2011 - 15:12:20 PDT)
    - Re: [AMBER] Energetic analysis with MMPBSA.py considering just one molecule ? Marek Maly (Thu Sep 29 2011 - 19:34:43 PDT)
    - Re: [AMBER] Energetic analysis with MMPBSA.py considering just one molecule ? Jason Swails (Thu Sep 29 2011 - 22:10:47 PDT)
    - Re: [AMBER] Energetic analysis with MMPBSA.py considering just one molecule ? Marek Maly (Fri Sep 30 2011 - 09:23:27 PDT)
    - Re: [AMBER] Energetic analysis with MMPBSA.py considering just one molecule ? Jason Swails (Fri Sep 30 2011 - 12:27:36 PDT)
    - Re: [AMBER] Energetic analysis with MMPBSA.py considering just one molecule ? Marek Maly (Fri Sep 30 2011 - 13:35:23 PDT)
    - Re: [AMBER] Energetic analysis with MMPBSA.py considering just one molecule ? Jason Swails (Fri Sep 30 2011 - 14:11:52 PDT)
    - Re: [AMBER] Energetic analysis with MMPBSA.py considering just one molecule ? Marek Maly (Fri Sep 30 2011 - 14:26:23 PDT)
    - Re: [AMBER] Energetic analysis with MMPBSA.py considering just one molecule ? Jason Swails (Fri Sep 30 2011 - 15:55:26 PDT)
    - Re: [AMBER] Energetic analysis with MMPBSA.py considering just one molecule ? Marek Maly (Fri Sep 30 2011 - 20:13:21 PDT)
- Re: [AMBER] PNEB on GPUs Jason Swails (Wed Sep 28 2011 - 21:02:32 PDT)
[AMBER] Parallel limit? Hu Ge (Wed Sep 28 2011 - 20:31:37 PDT)
- Re: [AMBER] Parallel limit? Ross Walker (Wed Sep 28 2011 - 20:45:38 PDT)
  - Re: [AMBER] Parallel limit? Jason Swails (Wed Sep 28 2011 - 21:14:09 PDT)
    - Re: [AMBER] Parallel limit? Ross Walker (Wed Sep 28 2011 - 21:20:28 PDT)
  - Re: [AMBER] Parallel limit? David A Case (Thu Sep 29 2011 - 05:32:26 PDT)
    - Re: [AMBER] Parallel limit? Scott Le Grand (Thu Sep 29 2011 - 10:02:54 PDT)
[AMBER] Parameter files :problem to save souvik sur (Wed Sep 28 2011 - 21:20:48 PDT)
- Re: [AMBER] Parameter files :problem to save Jason Swails (Wed Sep 28 2011 - 21:39:38 PDT)
- Re: [AMBER] Parameter files :problem to save Ross Walker (Wed Sep 28 2011 - 21:43:28 PDT)
- Re: [AMBER] Parameter files :problem to save Ross Walker (Wed Sep 28 2011 - 21:48:40 PDT)
[AMBER] Query regarding MMPBSA in Amber11 Hirdesh Kumar (Wed Sep 28 2011 - 21:47:34 PDT)
- Re: [AMBER] Query regarding MMPBSA in Amber11 Jason Swails (Wed Sep 28 2011 - 22:36:25 PDT)
  - Re: [AMBER] Query regarding MMPBSA in Amber11 Hirdesh Kumar (Thu Sep 29 2011 - 01:54:29 PDT)
    - Re: [AMBER] Query regarding MMPBSA in Amber11 Jason Swails (Thu Sep 29 2011 - 06:53:18 PDT)
    - Re: [AMBER] Query regarding MMPBSA in Amber11 Hirdesh Kumar (Thu Sep 29 2011 - 21:28:11 PDT)
    - Re: [AMBER] Query regarding MMPBSA in Amber11 Jason Swails (Thu Sep 29 2011 - 22:11:13 PDT)
[AMBER] Chirality restraints Rajeswari A. (Thu Sep 29 2011 - 00:06:40 PDT)
- Re: [AMBER] Chirality restraints David A Case (Thu Sep 29 2011 - 05:35:59 PDT)
  - Re: [AMBER] Chirality restraints Rajeswari A. (Thu Sep 29 2011 - 05:42:52 PDT)
[AMBER] sander mpi error when unfolding the protein Chinh Su Tran To (Thu Sep 29 2011 - 00:43:24 PDT)
- Re: [AMBER] sander mpi error when unfolding the protein steinbrt.rci.rutgers.edu (Thu Sep 29 2011 - 00:55:22 PDT)
  - Re: [AMBER] sander mpi error when unfolding the protein Chinh Su Tran To (Thu Sep 29 2011 - 01:10:59 PDT)
    - Re: [AMBER] sander mpi error when unfolding the protein steinbrt.rci.rutgers.edu (Thu Sep 29 2011 - 02:23:53 PDT)
    - Re: [AMBER] sander mpi error when unfolding the protein Chinh Su Tran To (Thu Sep 29 2011 - 03:00:46 PDT)
    - Re: [AMBER] sander mpi error when unfolding the protein Chinh Su Tran To (Sun Oct 09 2011 - 19:45:31 PDT)
[AMBER] GBSW AMBER Cindy Pembroke (Thu Sep 29 2011 - 00:52:16 PDT)
- Re: [AMBER] GBSW AMBER David A Case (Thu Sep 29 2011 - 05:37:30 PDT)
Re: [AMBER] On Cationic Dummy Atom francesco oteri (Thu Sep 29 2011 - 02:26:32 PDT)
- Re: [AMBER] On Cationic Dummy Atom Jason Swails (Thu Sep 29 2011 - 22:12:19 PDT)
[AMBER] AmberTools1.5 parallel implementation of mmpbsa.py - Incomplete installation? George Tzotzos (Thu Sep 29 2011 - 06:54:50 PDT)
- Re: [AMBER] AmberTools1.5 parallel implementation of mmpbsa.py - Incomplete installation? Bill Miller III (Thu Sep 29 2011 - 06:59:20 PDT)
  - Re: [AMBER] AmberTools1.5 parallel implementation of mmpbsa.py - Incomplete installation? George Tzotzos (Thu Sep 29 2011 - 07:07:51 PDT)
    - Re: [AMBER] AmberTools1.5 parallel implementation of mmpbsa.py - Incomplete installation? Jason Swails (Thu Sep 29 2011 - 07:18:31 PDT)
[AMBER] force field modification kirtana S (Thu Sep 29 2011 - 09:46:18 PDT)
[AMBER] how NOT to label terminal residue Victor Ma (Thu Sep 29 2011 - 13:54:44 PDT)
- Re: [AMBER] how NOT to label terminal residue Jason Swails (Thu Sep 29 2011 - 14:06:24 PDT)
  - Re: [AMBER] how NOT to label terminal residue Victor Ma (Thu Sep 29 2011 - 14:24:45 PDT)
    - Re: [AMBER] how NOT to label terminal residue David A Case (Fri Sep 30 2011 - 05:18:53 PDT)
[AMBER] From amber to gromacs madhumita das (Fri Sep 30 2011 - 01:31:44 PDT)
- Re: [AMBER] From amber to gromacs Ivan Gladich (Fri Sep 30 2011 - 05:02:04 PDT)
- Re: [AMBER] From amber to gromacs madhumita das (Fri Oct 14 2011 - 00:48:33 PDT)
  - Re: [AMBER] From amber to gromacs Alan (Fri Oct 14 2011 - 00:56:51 PDT)
[AMBER] Failure to compile AmberTools 1.5 on linux Francesco Pietra (Fri Sep 30 2011 - 02:43:18 PDT)
- Re: [AMBER] Failure to compile AmberTools 1.5 on linux FyD (Fri Sep 30 2011 - 04:57:53 PDT)
- Re: [AMBER] Failure to compile AmberTools 1.5 on linux David A Case (Fri Sep 30 2011 - 05:25:43 PDT)
  - Re: [AMBER] Failure to compile AmberTools 1.5 on linux Francesco Pietra (Fri Sep 30 2011 - 08:34:02 PDT)
[AMBER] Amber 10/ambertool Installation error Kshatresh Dutta Dubey (Fri Sep 30 2011 - 06:12:59 PDT)
- Re: [AMBER] Amber 10/ambertool Installation error Jason Swails (Fri Sep 30 2011 - 07:22:43 PDT)
[AMBER] Quick initial impressions of PNY water cooled GTX 580 and some numbers for the usual GPU benchmarks Gould, Ian R (Fri Sep 30 2011 - 08:15:36 PDT)
- Re: [AMBER] Quick initial impressions of PNY water cooled GTX 580 and some numbers for the usual GPU benchmarks Scott Le Grand (Fri Sep 30 2011 - 11:04:28 PDT)
[AMBER] MMPBSA: how to include only some residues Victor Ma (Fri Sep 30 2011 - 14:02:01 PDT)
- Re: [AMBER] MMPBSA: how to include only some residues Jason Swails (Fri Sep 30 2011 - 16:40:28 PDT)
  - Re: [AMBER] MMPBSA: how to include only some residues Victor Ma (Mon Oct 03 2011 - 12:30:22 PDT)
    - Re: [AMBER] MMPBSA: how to include only some residues Jason Swails (Mon Oct 03 2011 - 12:50:38 PDT)
    - Re: [AMBER] MMPBSA: how to include only some residues Victor Ma (Mon Oct 03 2011 - 13:08:49 PDT)
[AMBER] Parameters kirtana S (Fri Sep 30 2011 - 19:14:57 PDT)
[AMBER] Amber10 Shesh Nath (Fri Sep 30 2011 - 23:09:06 PDT)
- Re: [AMBER] Amber10 Jason Swails (Fri Sep 30 2011 - 23:31:55 PDT)
[AMBER] building topology for a big DNA/protein complex with tleap and sleap Giulia Palermo (Sat Oct 01 2011 - 03:05:49 PDT)
- Re: [AMBER] building topology for a big DNA/protein complex with tleap and sleap case (Sun Oct 02 2011 - 10:25:49 PDT)
[AMBER] Add extra force in sander.MPI Chicago Ji (Sat Oct 01 2011 - 11:23:39 PDT)
- Re: [AMBER] Add extra force in sander.MPI Jason Swails (Sat Oct 01 2011 - 12:20:02 PDT)
  - Re: [AMBER] Add extra force in sander.MPI Chicago Ji (Sun Oct 02 2011 - 02:54:47 PDT)
    - Re: [AMBER] Add extra force in sander.MPI case (Sun Oct 02 2011 - 10:31:58 PDT)
  - Re: [AMBER] Add extra force in sander.MPI case (Sun Oct 02 2011 - 10:49:34 PDT)
[AMBER] PLUMED for PATH COLLECTIVE VARIABLES Giulia Palermo (Sat Oct 01 2011 - 11:46:22 PDT)
- Re: [AMBER] PLUMED for PATH COLLECTIVE VARIABLES Ben Roberts (Sat Oct 01 2011 - 19:32:52 PDT)
[AMBER] Problem in compilng AmberTools1.5 on Mac OSX 10.7.1 Wei Huang (Sat Oct 01 2011 - 14:02:55 PDT)
[AMBER] bond lengths Aparna P (Sun Oct 02 2011 - 22:52:48 PDT)
- Re: [AMBER] bond lengths David A Case (Mon Oct 03 2011 - 04:40:15 PDT)
  - Re: [AMBER] bond lengths Aparna P (Mon Oct 03 2011 - 21:41:18 PDT)
[AMBER] problem with sulphur pancham lal gupta (Mon Oct 03 2011 - 03:39:57 PDT)
- Re: [AMBER] problem with sulphur FyD (Mon Oct 03 2011 - 04:31:34 PDT)
- Re: [AMBER] problem with sulphur Jason Swails (Mon Oct 03 2011 - 06:54:08 PDT)
  - Re: [AMBER] problem with sulphur David A Case (Mon Oct 03 2011 - 07:19:50 PDT)
    - Re: [AMBER] problem with sulphur Mark Williamson (Wed Oct 26 2011 - 05:20:50 PDT)
[AMBER] PDB file modification Asmita Gupta (Mon Oct 03 2011 - 07:26:53 PDT)
- Re: [AMBER] PDB file modification Victor Ma (Mon Oct 03 2011 - 08:05:15 PDT)
- Re: [AMBER] PDB file modification David A Case (Mon Oct 03 2011 - 09:03:26 PDT)
  - Re: [AMBER] PDB file modification Asmita Gupta (Mon Oct 03 2011 - 10:30:51 PDT)
    - Re: [AMBER] PDB file modification Jason Swails (Mon Oct 03 2011 - 10:53:54 PDT)
    - Re: [AMBER] PDB file modification David A Case (Mon Oct 03 2011 - 11:31:05 PDT)
[AMBER] MMPBSA.MPI: Entropy George Tzotzos (Mon Oct 03 2011 - 11:01:10 PDT)
- Re: [AMBER] MMPBSA.MPI: Entropy Jason Swails (Mon Oct 03 2011 - 12:47:57 PDT)
  - Re: [AMBER] MMPBSA.MPI: Entropy George Tzotzos (Tue Oct 04 2011 - 06:35:48 PDT)
    - Re: [AMBER] MMPBSA.MPI: Entropy Jason Swails (Tue Oct 04 2011 - 06:47:00 PDT)
    - Re: [AMBER] MMPBSA.MPI: Entropy George Tzotzos (Tue Oct 04 2011 - 07:04:54 PDT)
    - Re: [AMBER] MMPBSA.MPI: Entropy Jason Swails (Tue Oct 04 2011 - 08:28:14 PDT)
    - [AMBER] The recommended settings for PB analyses reasonably sensitive to istrng parameter and also suitable for charged systems Marek Maly (Tue Oct 04 2011 - 17:49:49 PDT)
[AMBER] Solvent accessible area kirtana S (Mon Oct 03 2011 - 14:03:50 PDT)
- Re: [AMBER] Solvent accessible area Jason Swails (Mon Oct 03 2011 - 18:02:54 PDT)
  - Re: [AMBER] Solvent accessible area kirtana S (Mon Oct 03 2011 - 21:57:38 PDT)
    - Re: [AMBER] Solvent accessible area Jason Swails (Mon Oct 03 2011 - 22:09:26 PDT)
    - Re: [AMBER] Solvent accessible area kirtana S (Mon Oct 03 2011 - 22:36:14 PDT)
    - Re: [AMBER] Solvent accessible area Jason Swails (Tue Oct 04 2011 - 06:47:48 PDT)
    - Re: [AMBER] Solvent accessible area kirtana S (Thu Oct 06 2011 - 14:22:52 PDT)
    - Re: [AMBER] Solvent accessible area Daniel Roe (Fri Oct 07 2011 - 05:34:03 PDT)
    - Re: [AMBER] Solvent accessible area kirtana S (Fri Oct 07 2011 - 08:28:35 PDT)
    - Re: [AMBER] Solvent accessible area Jason Swails (Fri Oct 07 2011 - 09:03:47 PDT)
[AMBER] Error with 99SBnmr force field Peter Eastman (Mon Oct 03 2011 - 16:18:27 PDT)
- Re: [AMBER] Error with 99SBnmr force field case (Tue Oct 04 2011 - 05:27:35 PDT)
[AMBER] Illegal atomic numbers in nucleic10.lib Peter Eastman (Mon Oct 03 2011 - 16:57:17 PDT)
- Re: [AMBER] Illegal atomic numbers in nucleic10.lib Jason Swails (Mon Oct 03 2011 - 19:33:43 PDT)
  - Re: [AMBER] Illegal atomic numbers in nucleic10.lib Ross Walker (Mon Oct 03 2011 - 19:41:27 PDT)
    - Re: [AMBER] Illegal atomic numbers in nucleic10.lib Jason Swails (Mon Oct 03 2011 - 19:51:52 PDT)
    - Re: [AMBER] Illegal atomic numbers in nucleic10.lib Peter Eastman (Tue Oct 04 2011 - 09:58:17 PDT)
    - Re: [AMBER] Illegal atomic numbers in nucleic10.lib Ross Walker (Tue Oct 04 2011 - 10:16:54 PDT)
    - Re: [AMBER] Illegal atomic numbers in nucleic10.lib Peter Eastman (Tue Oct 04 2011 - 10:25:44 PDT)
    - Re: [AMBER] Illegal atomic numbers in nucleic10.lib Jason Swails (Tue Oct 04 2011 - 10:31:01 PDT)
    - Re: [AMBER] Illegal atomic numbers in nucleic10.lib Ross Walker (Tue Oct 04 2011 - 10:44:26 PDT)
    - Re: [AMBER] Illegal atomic numbers in nucleic10.lib Jason Swails (Tue Oct 04 2011 - 10:47:13 PDT)
    - Re: [AMBER] Illegal atomic numbers in nucleic10.lib Jason Swails (Tue Oct 04 2011 - 10:34:12 PDT)
    - Re: [AMBER] Illegal atomic numbers in nucleic10.lib Peter Eastman (Tue Oct 04 2011 - 11:13:08 PDT)
    - Re: [AMBER] Illegal atomic numbers in nucleic10.lib Jason Swails (Tue Oct 04 2011 - 13:41:35 PDT)
[AMBER] TMD for a large conformation change William Cantara (Mon Oct 03 2011 - 17:52:39 PDT)
[AMBER] MMPBSA input error for INP Niel Henriksen (Mon Oct 03 2011 - 19:33:20 PDT)
- Re: [AMBER] MMPBSA input error for INP Jason Swails (Mon Oct 03 2011 - 19:48:33 PDT)
  - Re: [AMBER] MMPBSA input error for INP Niel Henriksen (Mon Oct 03 2011 - 19:51:18 PDT)
[AMBER] A Gentle Reminder: Survey Request - 10 minutes of your time please to help future AMBER development (http://surveys.nvidia.com/index.jsp?pi=f7d3e68a3e1b44841571e6ab4ce2f021) Ross Walker (Mon Oct 03 2011 - 19:39:22 PDT)
[AMBER] Calculating the force applied to a restrained point Ali M. Naserian-Nik (Tue Oct 04 2011 - 00:49:01 PDT)
- Re: [AMBER] Calculating the force applied to a restrained point Jason Swails (Tue Oct 04 2011 - 06:51:59 PDT)
  - Re: [AMBER] Calculating the force applied to a restrained point Daniel Sindhikara (Tue Oct 04 2011 - 07:29:38 PDT)
    - Re: [AMBER] Calculating the force applied to a restrained point Ali M. Naserian-Nik (Tue Oct 04 2011 - 12:10:54 PDT)
    - Re: [AMBER] Calculating the force applied to a restrained point Jason Swails (Tue Oct 04 2011 - 12:28:38 PDT)
[AMBER] Small inquiry regarding MMPBSA.py code Jan-Philip Gehrcke (Tue Oct 04 2011 - 10:00:55 PDT)
- Re: [AMBER] Small inquiry regarding MMPBSA.py code Jason Swails (Tue Oct 04 2011 - 10:39:32 PDT)
  - Re: [AMBER] Small inquiry regarding MMPBSA.py code Jan-Philip Gehrcke (Tue Oct 04 2011 - 11:42:14 PDT)
[AMBER] Ordering of torsion definitions Peter Eastman (Tue Oct 04 2011 - 10:06:20 PDT)
- Re: [AMBER] Ordering of torsion definitions Ross Walker (Tue Oct 04 2011 - 10:41:05 PDT)
- Re: [AMBER] Ordering of torsion definitions Bill Ross (Tue Oct 04 2011 - 11:05:31 PDT)
  - Re: [AMBER] Ordering of torsion definitions Peter Eastman (Tue Oct 04 2011 - 11:17:01 PDT)
- Re: [AMBER] Ordering of torsion definitions Bill Ross (Tue Oct 04 2011 - 11:50:07 PDT)
  - Re: [AMBER] Ordering of torsion definitions Peter Eastman (Tue Oct 04 2011 - 11:56:16 PDT)
    - Re: [AMBER] Ordering of torsion definitions Ross Walker (Tue Oct 04 2011 - 12:05:51 PDT)
- Re: [AMBER] Ordering of torsion definitions Bill Ross (Tue Oct 04 2011 - 13:06:53 PDT)
  - Re: [AMBER] Ordering of torsion definitions Peter Eastman (Tue Oct 04 2011 - 13:14:36 PDT)
    - [AMBER] Creating periodic solvent box Dean Cuebas (Tue Oct 04 2011 - 13:35:03 PDT)
    - Re: [AMBER] Creating periodic solvent box Jason Swails (Tue Oct 04 2011 - 13:43:45 PDT)
    - Re: [AMBER] Creating periodic solvent box Dean Cuebas (Tue Oct 04 2011 - 15:21:16 PDT)
- Re: [AMBER] Ordering of torsion definitions Bill Ross (Tue Oct 04 2011 - 15:52:22 PDT)
[AMBER] MMPBSA calculation Sangita Kachhap (Tue Oct 04 2011 - 10:14:20 PDT)
- Re: [AMBER] MMPBSA calculation Jason Swails (Tue Oct 04 2011 - 10:42:05 PDT)
  - Re: [AMBER] MMPBSA calculation Sangita Kachhap (Tue Oct 04 2011 - 11:06:43 PDT)
    - Re: [AMBER] MMPBSA calculation Jason Swails (Tue Oct 04 2011 - 11:29:53 PDT)
    - Re: [AMBER] MMPBSA calculation Sangita Kachhap (Tue Oct 04 2011 - 21:13:54 PDT)
[AMBER] pmemd.cuda and nonzero gbsa E. Nihal Korkmaz (Tue Oct 04 2011 - 11:25:32 PDT)
- Re: [AMBER] pmemd.cuda and nonzero gbsa Ross Walker (Tue Oct 04 2011 - 11:43:07 PDT)
  - Re: [AMBER] pmemd.cuda and nonzero gbsa Jason Swails (Tue Oct 04 2011 - 12:12:13 PDT)
  - Re: [AMBER] pmemd.cuda and nonzero gbsa E. Nihal Korkmaz (Tue Oct 04 2011 - 12:22:29 PDT)
  - Re: [AMBER] pmemd.cuda and nonzero gbsa Scott Le Grand (Tue Oct 04 2011 - 12:33:34 PDT)
    - Re: [AMBER] pmemd.cuda and nonzero gbsa Jason Swails (Tue Oct 04 2011 - 12:38:50 PDT)
    - Re: [AMBER] pmemd.cuda and nonzero gbsa Scott Le Grand (Tue Oct 04 2011 - 12:52:45 PDT)
[AMBER] Self assembled surface. ros (Tue Oct 04 2011 - 15:41:22 PDT)
[AMBER] Using ff10 with ildn or nmr Peter Eastman (Tue Oct 04 2011 - 15:49:52 PDT)
- Re: [AMBER] Using ff10 with ildn or nmr Jason Swails (Tue Oct 04 2011 - 16:18:35 PDT)
- Re: [AMBER] Using ff10 with ildn or nmr David A. Case (Tue Oct 04 2011 - 16:35:35 PDT)
[AMBER] message during pbsa energy calculation Jorge Iulek (Tue Oct 04 2011 - 16:17:17 PDT)
- Re: [AMBER] message during pbsa energy calculation Jason Swails (Tue Oct 04 2011 - 16:20:43 PDT)
- Re: [AMBER] message during pbsa energy calculation JORGE IULEK (Wed Oct 05 2011 - 05:28:09 PDT)
[AMBER] How to Calculate SASA with Amber? qiao xue (Wed Oct 05 2011 - 03:53:54 PDT)
- Re: [AMBER] How to Calculate SASA with Amber? Jason Swails (Wed Oct 05 2011 - 07:43:04 PDT)
- Re: [AMBER] How to Calculate SASA with Amber? Daniel Roe (Thu Oct 06 2011 - 07:32:59 PDT)
  - Re: [AMBER] How to Calculate SASA with Amber? qiao xue (Sun Oct 09 2011 - 16:53:53 PDT)
    - Re: [AMBER] How to Calculate SASA with Amber? Daniel Roe (Mon Oct 10 2011 - 12:55:39 PDT)
    - Re: [AMBER] How to Calculate SASA with Amber? Oliver Grant (Tue Oct 11 2011 - 02:13:10 PDT)
- Re: [AMBER] How to Calculate SASA with Amber? Shafinaz Chowdhury (Tue Jul 24 2012 - 13:40:56 PDT)
  - Re: [AMBER] How to Calculate SASA with Amber? Daniel Roe (Tue Jul 24 2012 - 15:46:47 PDT)
    - Re: [AMBER] How to Calculate SASA with Amber? Daniel Roe (Tue Jul 24 2012 - 15:47:54 PDT)
[AMBER] MMPBSA.py.MPI problems: L-J-parameters, bad file descriptors, MMPBSA hangup due to sander failure Jan-Philip Gehrcke (Wed Oct 05 2011 - 03:54:16 PDT)
- Re: [AMBER] MMPBSA.py.MPI problems: L-J-parameters, bad file descriptors, MMPBSA hangup due to sander failure Jan-Philip Gehrcke (Wed Oct 05 2011 - 06:54:15 PDT)
- Re: [AMBER] MMPBSA.py.MPI problems: L-J-parameters, bad file descriptors, MMPBSA hangup due to sander failure Jason Swails (Wed Oct 05 2011 - 07:40:45 PDT)
  - Re: [AMBER] MMPBSA.py.MPI problems: L-J-parameters, bad file descriptors, MMPBSA hangup due to sander failure Jan-Philip Gehrcke (Wed Oct 05 2011 - 09:16:45 PDT)
    - Re: [AMBER] MMPBSA.py.MPI problems: L-J-parameters, bad file descriptors, MMPBSA hangup due to sander failure Jan-Philip Gehrcke (Fri Oct 07 2011 - 02:45:48 PDT)
    - Re: [AMBER] MMPBSA.py.MPI problems: L-J-parameters, bad file descriptors, MMPBSA hangup due to sander failure Jason Swails (Fri Oct 07 2011 - 08:53:12 PDT)
    - Re: [AMBER] MMPBSA.py.MPI problems: L-J-parameters, bad file descriptors, MMPBSA hangup due to sander failure Jan-Philip Gehrcke (Tue Oct 11 2011 - 02:22:40 PDT)
[AMBER] MMPBSA.py: no value inserted for "Residues to print": left as "RES EDIT" Jan-Philip Gehrcke (Wed Oct 05 2011 - 07:32:45 PDT)
[AMBER] AMBER parameters for the acetylated lysine Gorka lasso (Wed Oct 05 2011 - 08:19:35 PDT)
- Re: [AMBER] AMBER parameters for the acetylated lysine FyD (Thu Oct 06 2011 - 22:55:31 PDT)
- Re: [AMBER] AMBER parameters for the acetylated lysine Ramu Anandakrishnan (Fri Oct 07 2011 - 04:51:11 PDT)
[AMBER] HO atom type van der Waals (GLYCAM) Matthew Tessier (Wed Oct 05 2011 - 10:44:58 PDT)
[AMBER] not too many MD simulations of protein-ligand system? Yun Shi (Wed Oct 05 2011 - 12:50:54 PDT)
- Re: [AMBER] not too many MD simulations of protein-ligand system? Carlos Simmerling (Wed Oct 05 2011 - 16:48:14 PDT)
  - Re: [AMBER] not too many MD simulations of protein-ligand system? Yun Shi (Wed Oct 05 2011 - 17:07:13 PDT)
  - Re: [AMBER] not too many MD simulations of protein-ligand system? ros (Wed Oct 05 2011 - 18:23:09 PDT)
[AMBER] QMMMMD Tutorial Question Yao Yao (Wed Oct 05 2011 - 14:52:09 PDT)
- Re: [AMBER] QMMMMD Tutorial Question Ross Walker (Wed Oct 05 2011 - 14:59:42 PDT)
[AMBER] Total Energy Autocorrelation Function Yao Yao (Wed Oct 05 2011 - 19:40:37 PDT)
- [AMBER] Total Energy Autocorrelation Function Yao Yao (Thu Oct 06 2011 - 10:06:45 PDT)
  - Re: [AMBER] Total Energy Autocorrelation Function Jason Swails (Thu Oct 06 2011 - 10:09:20 PDT)
    - Re: [AMBER] Total Energy Autocorrelation Function Yao Yao (Thu Oct 06 2011 - 10:30:28 PDT)
[AMBER] MMPBSA error Soumya Lipsa Rath (Thu Oct 06 2011 - 03:03:31 PDT)
[AMBER] iron sulphur cluster parameters francesco oteri (Thu Oct 06 2011 - 06:10:39 PDT)
[AMBER] Reg:QM region + cutoff larger than box dimension kaustubh joshi (Thu Oct 06 2011 - 07:46:29 PDT)
- Re: [AMBER] Reg:QM region + cutoff larger than box dimension Brian Radak (Thu Oct 06 2011 - 08:02:44 PDT)
  - Re: [AMBER] Reg:QM region + cutoff larger than box dimension kaustubh joshi (Thu Oct 06 2011 - 08:42:58 PDT)
    - Re: [AMBER] Reg:QM region + cutoff larger than box dimension Brian Radak (Thu Oct 06 2011 - 08:56:58 PDT)
    - Re: [AMBER] Reg:QM region + cutoff larger than box dimension Ross Walker (Thu Oct 06 2011 - 09:18:03 PDT)
    - Re: [AMBER] Reg:QM region + cutoff larger than box dimension Brian Radak (Thu Oct 06 2011 - 09:42:09 PDT)
    - Re: [AMBER] Reg:QM region + cutoff larger than box dimension Ross Walker (Thu Oct 06 2011 - 10:11:19 PDT)
    - Re: [AMBER] Reg:QM region + cutoff larger than box dimension Brian Radak (Thu Oct 06 2011 - 10:31:05 PDT)
- Re: [AMBER] Reg:QM region + cutoff larger than box dimension Ross Walker (Thu Oct 06 2011 - 09:50:52 PDT)
[AMBER] Parallel Amber11 Installation Error David Cantu (Thu Oct 06 2011 - 15:26:28 PDT)
- Re: [AMBER] Parallel Amber11 Installation Error Jason Swails (Thu Oct 06 2011 - 16:40:04 PDT)
  - Re: [AMBER] Parallel Amber11 Installation Error David Cantu (Thu Oct 06 2011 - 18:25:26 PDT)
    - Re: [AMBER] Parallel Amber11 Installation Error David A Case (Fri Oct 07 2011 - 06:37:17 PDT)
    - Re: [AMBER] Parallel Amber11 Installation Error David Cantu (Sat Oct 08 2011 - 11:28:23 PDT)
[AMBER] MMPBSA.MPI: IOError: [Errno 9] Bad file descriptor George Tzotzos (Thu Oct 06 2011 - 15:45:32 PDT)
- Re: [AMBER] MMPBSA.MPI: IOError: [Errno 9] Bad file descriptor Jan-Philip Gehrcke (Fri Oct 07 2011 - 05:20:23 PDT)
  - Re: [AMBER] MMPBSA.MPI: IOError: [Errno 9] Bad file descriptor George Tzotzos (Fri Oct 07 2011 - 08:07:18 PDT)
  - Re: [AMBER] MMPBSA.MPI: IOError: [Errno 9] Bad file descriptor Jason Swails (Fri Oct 07 2011 - 08:20:29 PDT)
[AMBER] Problem installing on a mac Lion 10.7 using gcc 4.2 Gamal Akabani (Thu Oct 06 2011 - 16:01:44 PDT)
- Re: [AMBER] Problem installing on a mac Lion 10.7 using gcc 4.2 Jason Swails (Sun Oct 09 2011 - 06:07:28 PDT)
[AMBER] MMPBSA on a protein-protein complex when protein contains non-protein Irene Newhouse (Thu Oct 06 2011 - 16:09:53 PDT)
- Re: [AMBER] MMPBSA on a protein-protein complex when protein contains non-protein Jason Swails (Thu Oct 06 2011 - 17:06:33 PDT)
[AMBER] Amber 11, AmberTools 1.5 installation problem #MAZIAR SOLEYMANI ARDEJANI# (Fri Oct 07 2011 - 03:29:18 PDT)
- Re: [AMBER] Amber 11, AmberTools 1.5 installation problem David A Case (Fri Oct 07 2011 - 06:56:21 PDT)
- Re: [AMBER] Amber 11, AmberTools 1.5 installation problem Tru Huynh (Tue Oct 11 2011 - 23:57:51 PDT)
[AMBER] oct or cubic box? Yun Shi (Fri Oct 07 2011 - 11:15:18 PDT)
- Re: [AMBER] oct or cubic box? David A Case (Fri Oct 07 2011 - 12:45:24 PDT)
- Re: [AMBER] oct or cubic box? Bill Ross (Fri Oct 07 2011 - 14:30:39 PDT)
- [AMBER] 回复： oct or cubic box? li li (Sun Oct 09 2011 - 17:03:54 PDT)
  - Re: [AMBER] 回复： oct or cubic box? Thomas Cheatham (Sun Oct 09 2011 - 17:55:36 PDT)
[AMBER] ptraj clustering error Rajesh Raju (Fri Oct 07 2011 - 12:08:59 PDT)
- Re: [AMBER] ptraj clustering error Thomas Cheatham III (Fri Oct 07 2011 - 12:25:16 PDT)
  - Re: [AMBER] ptraj clustering error Rajesh Raju (Fri Oct 07 2011 - 12:47:24 PDT)
[AMBER] Interaction Energy in QMMMMD Yao Yao (Fri Oct 07 2011 - 12:27:30 PDT)
- Re: [AMBER] Interaction Energy in QMMMMD Qiantao Wang (Fri Oct 07 2011 - 13:17:10 PDT)
  - [AMBER] Interaction Energy in QMMMMD Yao Yao (Mon Oct 10 2011 - 12:44:20 PDT)
    - Re: [AMBER] Interaction Energy in QMMMMD Gustavo Seabra (Tue Oct 11 2011 - 11:18:39 PDT)
[AMBER] Gromacs Make Index in AMBER Yao Yao (Fri Oct 07 2011 - 15:56:47 PDT)
- Re: [AMBER] Gromacs Make Index in AMBER Jason Swails (Fri Oct 07 2011 - 17:00:27 PDT)
[AMBER] Fw: Gromacs Make Index in AMBER Yao Yao (Fri Oct 07 2011 - 17:13:29 PDT)
- Re: [AMBER] Fw: Gromacs Make Index in AMBER Yun Shi (Sat Oct 08 2011 - 08:58:27 PDT)
  - Re: [AMBER] Fw: Gromacs Make Index in AMBER Jason Swails (Sat Oct 08 2011 - 09:59:41 PDT)
[AMBER] FEP E. Nihal Korkmaz (Sun Oct 09 2011 - 15:35:36 PDT)
- Re: [AMBER] FEP Jason Swails (Sun Oct 09 2011 - 18:14:53 PDT)
  - Re: [AMBER] FEP E. Nihal Korkmaz (Sun Oct 09 2011 - 19:15:37 PDT)
    - Re: [AMBER] FEP Adrian Roitberg (Sun Oct 09 2011 - 19:26:38 PDT)
    - Re: [AMBER] FEP steinbrt.rci.rutgers.edu (Mon Oct 10 2011 - 01:32:08 PDT)
[AMBER] residue stripping in ptraj Praapti Jayaswal (Sun Oct 09 2011 - 22:11:15 PDT)
- Re: [AMBER] residue stripping in ptraj Daniel Roe (Mon Oct 10 2011 - 05:20:50 PDT)
- Re: [AMBER] residue stripping in ptraj Thomas Cheatham III (Tue Oct 11 2011 - 13:11:03 PDT)
[AMBER] "Frontiers in Biomolecular Simulation" - Heraeus conference in Germany, Jan. 22.-25. 2012 steinbrt.rci.rutgers.edu (Mon Oct 10 2011 - 07:34:54 PDT)
[AMBER] Turning off non-bonded interactions for specific atomtype pairs Marc van der Kamp (Tue Oct 11 2011 - 01:42:49 PDT)
- Re: [AMBER] Turning off non-bonded interactions for specific atomtype pairs Marc van der Kamp (Tue Oct 11 2011 - 01:49:27 PDT)
  - Re: [AMBER] Turning off non-bonded interactions for specific atomtype pairs Jason Swails (Tue Oct 11 2011 - 14:46:00 PDT)
- Re: [AMBER] Turning off non-bonded interactions for specific atomtype pairs Qiantao Wang (Tue Oct 11 2011 - 08:06:02 PDT)
- Re: [AMBER] Turning off non-bonded interactions for specific atomtype pairs Jason Swails (Tue Oct 11 2011 - 17:59:50 PDT)
  - Re: [AMBER] Turning off non-bonded interactions for specific atomtype pairs Marc van der Kamp (Wed Oct 12 2011 - 06:21:46 PDT)
    - Re: [AMBER] Turning off non-bonded interactions for specific atomtype pairs Qiantao Wang (Wed Oct 12 2011 - 07:21:55 PDT)
    - Re: [AMBER] Turning off non-bonded interactions for specific atomtype pairs Jason Swails (Wed Oct 12 2011 - 10:27:28 PDT)
    - Re: [AMBER] Turning off non-bonded interactions for specific atomtype pairs Marc van der Kamp (Thu Oct 13 2011 - 03:17:28 PDT)
[AMBER] ff99-ildn frcmod validation question D.G. Sprous, PhD (Tue Oct 11 2011 - 05:12:01 PDT)
[AMBER] regarding qmmm simulation jani vinod (Tue Oct 11 2011 - 05:30:16 PDT)
- Re: [AMBER] regarding qmmm simulation Ross Walker (Tue Oct 11 2011 - 09:06:09 PDT)
  - Re: [AMBER] regarding qmmm simulation jani vinod (Wed Oct 12 2011 - 05:51:45 PDT)
    - Re: [AMBER] regarding qmmm simulation Ross Walker (Wed Oct 12 2011 - 09:29:57 PDT)
[AMBER] mmtsb problem Sel Ercan (Tue Oct 11 2011 - 06:03:19 PDT)
- [AMBER] mmtsb problem Sel Ercan (Wed Oct 12 2011 - 00:08:46 PDT)
[AMBER] MMPBSA.py: error during parsing of _MMPBSA_complex_gb.mdout Jan-Philip Gehrcke (Tue Oct 11 2011 - 06:20:14 PDT)
- Re: [AMBER] MMPBSA.py: error during parsing of _MMPBSA_complex_gb.mdout Jason Swails (Tue Oct 11 2011 - 06:54:51 PDT)
  - Re: [AMBER] MMPBSA.py: error during parsing of _MMPBSA_complex_gb.mdout Jan-Philip Gehrcke (Tue Oct 18 2011 - 10:03:37 PDT)
    - Re: [AMBER] MMPBSA.py: error during parsing of _MMPBSA_complex_gb.mdout Jason Swails (Tue Oct 18 2011 - 11:08:31 PDT)
    - Re: [AMBER] MMPBSA.py: error during parsing of _MMPBSA_complex_gb.mdout Jan-Philip Gehrcke (Tue Oct 25 2011 - 08:30:40 PDT)
    - Re: [AMBER] MMPBSA.py: error during parsing of _MMPBSA_complex_gb.mdout Jason Swails (Tue Oct 25 2011 - 09:04:55 PDT)
    - Re: [AMBER] MMPBSA.py: error during parsing of _MMPBSA_complex_gb.mdout Jan-Philip Gehrcke (Wed Oct 26 2011 - 02:00:58 PDT)
    - Re: [AMBER] MMPBSA.py: error during parsing of _MMPBSA_complex_gb.mdout Jason Swails (Wed Oct 26 2011 - 07:46:14 PDT)
[AMBER] Antechamber/SQM Chidambar Kulkarni (Tue Oct 11 2011 - 09:13:07 PDT)
- Re: [AMBER] Antechamber/SQM David A Case (Tue Oct 11 2011 - 10:18:54 PDT)
  - Re: [AMBER] Antechamber/SQM Chidambar Kulkarni (Tue Oct 11 2011 - 21:29:14 PDT)
    - Re: [AMBER] Antechamber/SQM David A Case (Wed Oct 12 2011 - 05:17:31 PDT)
    - Re: [AMBER] Antechamber/SQM Chidambar Kulkarni (Wed Oct 12 2011 - 07:26:53 PDT)
[AMBER] 3D-RISM bugfix for polar/apolar decomposition Tyler Luchko (Tue Oct 11 2011 - 11:49:36 PDT)
[AMBER] LMOD error and questions Sarah Edwards (Tue Oct 11 2011 - 11:54:41 PDT)
- Re: [AMBER] LMOD error and questions Daniel Roe (Tue Oct 11 2011 - 13:27:52 PDT)
[AMBER] Question regarding HAS_10_12 flag in PMEMD (LINMIN Failure) brian_jo.berkeley.edu (Tue Oct 11 2011 - 17:30:21 PDT)
- Re: [AMBER] Question regarding HAS_10_12 flag in PMEMD (LINMIN Failure) Duke, Robert E Jr (Tue Oct 11 2011 - 17:55:46 PDT)
  - Re: [AMBER] Question regarding HAS_10_12 flag in PMEMD (LINMIN Failure) brian_jo.berkeley.edu (Tue Oct 11 2011 - 18:06:20 PDT)
    - Re: [AMBER] Question regarding HAS_10_12 flag in PMEMD (LINMIN Failure) Ross Walker (Tue Oct 11 2011 - 19:19:21 PDT)
- Re: [AMBER] Question regarding HAS_10_12 flag in PMEMD (LINMIN Failure) Jason Swails (Tue Oct 11 2011 - 18:04:26 PDT)
[AMBER] please help me pancham lal gupta (Wed Oct 12 2011 - 06:04:25 PDT)
- Re: [AMBER] please help me steinbrt.rci.rutgers.edu (Wed Oct 12 2011 - 06:39:17 PDT)
- Re: [AMBER] please help me Brian Radak (Wed Oct 12 2011 - 06:47:31 PDT)
- Re: [AMBER] please help me Nej Pir (Wed Oct 12 2011 - 06:53:02 PDT)
[AMBER] extract trajectory and average structure najmul arfin (Wed Oct 12 2011 - 07:13:13 PDT)
- Re: [AMBER] extract trajectory and average structure Jason Swails (Wed Oct 12 2011 - 10:38:48 PDT)
[AMBER] extract trajectory and average structure najmul arfin (Wed Oct 12 2011 - 07:17:00 PDT)
[AMBER] proteins with Ff10 + igb=7 Abhishek Singh (Wed Oct 12 2011 - 08:15:03 PDT)
- Re: [AMBER] proteins with Ff10 + igb=7 Carlos Simmerling (Wed Oct 12 2011 - 08:55:59 PDT)
  - Re: [AMBER] proteins with Ff10 + igb=7 Abhishek Singh (Wed Oct 12 2011 - 10:32:14 PDT)
    - Re: [AMBER] proteins with Ff10 + igb=7 Carlos Simmerling (Wed Oct 12 2011 - 10:36:45 PDT)
    - Re: [AMBER] proteins with Ff10 + igb=7 Abhishek Singh (Wed Oct 12 2011 - 10:41:32 PDT)
  - Re: [AMBER] proteins with Ff10 + igb=7 Jason Swails (Wed Oct 12 2011 - 10:37:50 PDT)
- Re: [AMBER] proteins with Ff10 + igb=7 David A Case (Wed Oct 12 2011 - 09:23:41 PDT)
[AMBER] chiral restraints kirtana S (Wed Oct 12 2011 - 11:05:35 PDT)
- Re: [AMBER] chiral restraints Jason Swails (Wed Oct 12 2011 - 17:42:08 PDT)
[AMBER] New to AMBER, installation issues Matthew D Antalek (Wed Oct 12 2011 - 12:06:02 PDT)
- Re: [AMBER] New to AMBER, installation issues Carlos Sosa (Wed Oct 12 2011 - 12:17:23 PDT)
  - Re: [AMBER] New to AMBER, installation issues Matthew D Antalek (Wed Oct 12 2011 - 12:26:36 PDT)
    - Re: [AMBER] New to AMBER, installation issues peker milas (Wed Oct 12 2011 - 13:11:06 PDT)
    - Re: [AMBER] New to AMBER, installation issues Jason Swails (Wed Oct 12 2011 - 13:50:22 PDT)
    - Re: [AMBER] New to AMBER, installation issues Matthew D Antalek (Wed Oct 12 2011 - 14:07:56 PDT)
    - Re: [AMBER] New to AMBER, installation issues Jason Swails (Wed Oct 12 2011 - 14:16:04 PDT)
- Re: [AMBER] New to AMBER, installation issues Bill Ross (Wed Oct 12 2011 - 14:29:03 PDT)
  - Re: [AMBER] New to AMBER, installation issues Matthew D Antalek (Wed Oct 12 2011 - 20:31:45 PDT)
    - Re: [AMBER] New to AMBER, installation issues peker milas (Wed Oct 12 2011 - 23:36:55 PDT)
    - Re: [AMBER] New to AMBER, installation issues David A Case (Thu Oct 13 2011 - 07:17:17 PDT)
[AMBER] About SMD simulation restart file Mo Chen (Wed Oct 12 2011 - 13:26:29 PDT)
- Re: [AMBER] About SMD simulation restart file Adrian Roitberg (Wed Oct 12 2011 - 13:30:09 PDT)
  - Re: [AMBER] About SMD simulation restart file Mo Chen (Wed Oct 12 2011 - 13:39:12 PDT)
    - Re: [AMBER] About SMD simulation restart file Adrian Roitberg (Wed Oct 12 2011 - 13:48:10 PDT)
    - Re: [AMBER] About SMD simulation restart file Chinh Su Tran To (Sun Oct 16 2011 - 22:12:01 PDT)
    - Re: [AMBER] About SMD simulation restart file Jason Swails (Sun Oct 16 2011 - 22:58:43 PDT)
    - Re: [AMBER] About SMD simulation restart file Chinh Su Tran To (Sun Oct 16 2011 - 23:29:44 PDT)
    - Re: [AMBER] About SMD simulation restart file Jason Swails (Mon Oct 17 2011 - 03:56:05 PDT)
- Re: [AMBER] About SMD simulation restart file Bill Ross (Wed Oct 12 2011 - 14:43:31 PDT)
  - Re: [AMBER] About SMD simulation restart file Mo Chen (Wed Oct 12 2011 - 18:26:59 PDT)
  - Re: [AMBER] About SMD simulation restart file Antje Wolf (Wed Oct 12 2011 - 23:18:14 PDT)
    - Re: [AMBER] About SMD simulation restart file Jason Swails (Thu Oct 13 2011 - 07:29:12 PDT)
- Re: [AMBER] About SMD simulation restart file Bill Ross (Thu Oct 13 2011 - 14:49:53 PDT)
  - Re: [AMBER] About SMD simulation restart file Antje Wolf (Fri Oct 14 2011 - 06:09:32 PDT)
    - Re: [AMBER] About SMD simulation restart file Brian Radak (Fri Oct 14 2011 - 06:18:22 PDT)
    - Re: [AMBER] About SMD simulation restart file Marc van der Kamp (Fri Oct 14 2011 - 06:19:30 PDT)
- Re: [AMBER] About SMD simulation restart file Bill Ross (Fri Oct 14 2011 - 17:06:54 PDT)
- Re: [AMBER] About SMD simulation restart file Bill Ross (Fri Oct 14 2011 - 17:10:34 PDT)
  - Re: [AMBER] About SMD simulation restart file Jason Swails (Fri Oct 14 2011 - 20:56:05 PDT)
- Re: [AMBER] About SMD simulation restart file Bill Ross (Fri Oct 14 2011 - 21:01:20 PDT)
  - Re: [AMBER] About SMD simulation restart file Jason Swails (Fri Oct 14 2011 - 21:50:08 PDT)
[AMBER] Can we avoid output the distance between closed atoms in the same residue: question for usage of checkoverlap in PTRAJ. kurisaki (Wed Oct 12 2011 - 23:31:15 PDT)
[AMBER] PMEMD command Chinh Su Tran To (Thu Oct 13 2011 - 00:18:24 PDT)
- Re: [AMBER] PMEMD command Chinh Su Tran To (Thu Oct 13 2011 - 02:28:43 PDT)
Re: [AMBER] Turning off non-bonded interactions for specificatomtype pairs CHAMI F. (Thu Oct 13 2011 - 04:03:45 PDT)
- Re: [AMBER] Turning off non-bonded interactions for specificatomtype pairs Jason Swails (Thu Oct 13 2011 - 05:45:03 PDT)
[AMBER] SASA calculate Tong Zhu (Thu Oct 13 2011 - 06:36:19 PDT)
- Re: [AMBER] SASA calculate Ilyas Yildirim (Thu Oct 13 2011 - 06:48:04 PDT)
[AMBER] One more Gentle Reminder: Survey Request - 10 minutes of your time please to help future AMBER development (http://surveys.nvidia.com/index.jsp?pi=f7d3e68a3e1b44841571e6ab4ce2f021) Ross Walker (Thu Oct 13 2011 - 10:33:34 PDT)
[AMBER] About pmemd and pmemd.MPI Mo Chen (Thu Oct 13 2011 - 12:27:34 PDT)
- Re: [AMBER] About pmemd and pmemd.MPI Jason Swails (Thu Oct 13 2011 - 12:40:37 PDT)
  - Re: [AMBER] About pmemd and pmemd.MPI Mo Chen (Thu Oct 13 2011 - 12:44:39 PDT)
    - Re: [AMBER] About pmemd and pmemd.MPI Jason Swails (Thu Oct 13 2011 - 12:46:03 PDT)
    - Re: [AMBER] About pmemd and pmemd.MPI Mo Chen (Thu Oct 13 2011 - 12:47:30 PDT)
    - Re: [AMBER] About pmemd and pmemd.MPI Mo Chen (Fri Oct 21 2011 - 20:57:31 PDT)
    - Re: [AMBER] About pmemd and pmemd.MPI Ross Walker (Fri Oct 21 2011 - 21:14:50 PDT)
    - Re: [AMBER] About pmemd and pmemd.MPI Ross Walker (Thu Oct 13 2011 - 12:59:25 PDT)
    - Re: [AMBER] About pmemd and pmemd.MPI Mo Chen (Thu Oct 13 2011 - 13:07:05 PDT)
- Re: [AMBER] About pmemd and pmemd.MPI Ross Walker (Thu Oct 13 2011 - 12:44:27 PDT)
[AMBER] safemem.o error while compiling Ambertools 1.5 Josmar R. da Rocha (Thu Oct 13 2011 - 15:35:25 PDT)
- Re: [AMBER] safemem.o error while compiling Ambertools 1.5 Tyler Luchko (Thu Oct 13 2011 - 16:05:46 PDT)
  - Re: [AMBER] safemem.o error while compiling Ambertools 1.5 Josmar R. da Rocha (Thu Oct 13 2011 - 20:34:22 PDT)
    - Re: [AMBER] safemem.o error while compiling Ambertools 1.5 Andrew Voronkov (Thu Nov 03 2011 - 02:53:42 PDT)
    - Re: [AMBER] safemem.o error while compiling Ambertools 1.5 Josmar R. da Rocha (Thu Nov 03 2011 - 06:49:34 PDT)
- Re: [AMBER] safemem.o error while compiling Ambertools 1.5 Jason Swails (Thu Oct 13 2011 - 16:07:34 PDT)
[AMBER] sander pb focusing error Niel Henriksen (Thu Oct 13 2011 - 20:17:06 PDT)
[AMBER] Inquiry about Amber installation Mo Chen (Thu Oct 13 2011 - 20:21:09 PDT)
- Re: [AMBER] Inquiry about Amber installation Jason Swails (Fri Oct 14 2011 - 03:20:20 PDT)
  - Re: [AMBER] Inquiry about Amber installation Niel Henriksen (Fri Oct 14 2011 - 06:36:03 PDT)
    - Re: [AMBER] Inquiry about Amber installation Mo Chen (Fri Oct 14 2011 - 11:20:34 PDT)
  - Re: [AMBER] Inquiry about Amber installation Mo Chen (Fri Oct 14 2011 - 11:20:16 PDT)
    - Re: [AMBER] Inquiry about Amber installation Jason Swails (Fri Oct 14 2011 - 12:48:45 PDT)
    - Re: [AMBER] Inquiry about Amber installation Mo Chen (Fri Oct 14 2011 - 13:25:44 PDT)
    - Re: [AMBER] Inquiry about Amber installation Jason Swails (Fri Oct 14 2011 - 15:59:40 PDT)
    - Re: [AMBER] Inquiry about Amber installation Mo Chen (Fri Oct 14 2011 - 16:47:40 PDT)
[AMBER] Poisson-Boltzmann/GB Solvents with FF02 Neha Gandhi (Thu Oct 13 2011 - 22:50:32 PDT)
[AMBER] changes in secstruct command Antje Wolf (Fri Oct 14 2011 - 03:42:34 PDT)
- [AMBER] changes in secstruct command Antje Wolf (Fri Oct 14 2011 - 03:45:28 PDT)
- Re: [AMBER] changes in secstruct command Daniel Roe (Fri Oct 14 2011 - 04:48:08 PDT)
[AMBER] GB simulation on GPU freezes E. Nihal Korkmaz (Fri Oct 14 2011 - 10:55:24 PDT)
- Re: [AMBER] GB simulation on GPU freezes Scott Le Grand (Fri Oct 14 2011 - 11:05:37 PDT)
  - Re: [AMBER] GB simulation on GPU freezes E. Nihal Korkmaz (Fri Oct 14 2011 - 11:17:00 PDT)
    - Re: [AMBER] GB simulation on GPU freezes E. Nihal Korkmaz (Fri Oct 14 2011 - 11:29:20 PDT)
    - Re: [AMBER] GB simulation on GPU freezes Ross Walker (Fri Oct 14 2011 - 12:15:59 PDT)
    - Re: [AMBER] GB simulation on GPU freezes E. Nihal Korkmaz (Fri Oct 14 2011 - 12:28:12 PDT)
    - Re: [AMBER] GB simulation on GPU freezes Ross Walker (Fri Oct 14 2011 - 14:55:30 PDT)
    - Re: [AMBER] GB simulation on GPU freezes Scott Le Grand (Fri Oct 14 2011 - 15:29:39 PDT)
    - Re: [AMBER] GB simulation on GPU freezes E. Nihal Korkmaz (Fri Oct 14 2011 - 16:15:41 PDT)
    - Re: [AMBER] GB simulation on GPU freezes E. Nihal Korkmaz (Mon Oct 17 2011 - 13:46:44 PDT)
    - Re: [AMBER] GB simulation on GPU freezes Scott Le Grand (Mon Oct 17 2011 - 14:49:18 PDT)
    - Re: [AMBER] GB simulation on GPU freezes Ross Walker (Mon Oct 17 2011 - 15:24:45 PDT)
    - Re: [AMBER] GB simulation on GPU freezes E. Nihal Korkmaz (Mon Oct 17 2011 - 19:08:13 PDT)
    - Re: [AMBER] GB simulation on GPU freezes E. Nihal Korkmaz (Tue Oct 18 2011 - 01:08:12 PDT)
[AMBER] QMMMMD blowup Yao Yao (Fri Oct 14 2011 - 12:58:35 PDT)
- Re: [AMBER] QMMMMD blowup Adrian Roitberg (Fri Oct 14 2011 - 13:13:23 PDT)
- Re: [AMBER] QMMMMD blowup David A. Case (Fri Oct 14 2011 - 13:22:57 PDT)
  - [AMBER] QMMMMD blowup STILL Yao Yao (Fri Oct 14 2011 - 20:56:07 PDT)
    - Re: [AMBER] QMMMMD blowup STILL Ross Walker (Sat Oct 15 2011 - 09:09:31 PDT)
[AMBER] sander bug? Yao Yao (Fri Oct 14 2011 - 15:24:16 PDT)
- Re: [AMBER] sander bug? Adrian Roitberg (Fri Oct 14 2011 - 15:27:29 PDT)
  - Re: [AMBER] sander bug? Jason Swails (Fri Oct 14 2011 - 16:00:41 PDT)
[AMBER] converting Amber trajectories to Gromacs XTC mish (Sat Oct 15 2011 - 03:52:40 PDT)
- Re: [AMBER] converting Amber trajectories to Gromacs XTC Oliver Grant (Sat Oct 15 2011 - 07:42:55 PDT)
  - Re: [AMBER] converting Amber trajectories to Gromacs XTC Marc van der Kamp (Sat Oct 15 2011 - 10:03:24 PDT)
[AMBER] xleap problem souvik sur (Sat Oct 15 2011 - 04:16:34 PDT)
- Re: [AMBER] xleap problem David A. Case (Sat Oct 15 2011 - 08:50:31 PDT)
[AMBER] How to make the library of PNA-DNA duplex souvik sur (Sat Oct 15 2011 - 04:57:10 PDT)
- Re: [AMBER] How to make the library of PNA-DNA duplex FyD (Sun Oct 16 2011 - 06:51:10 PDT)
[AMBER] relative binding free energy calculation leila karami (Sat Oct 15 2011 - 07:00:59 PDT)
- Re: [AMBER] relative binding free energy calculation David A. Case (Sat Oct 15 2011 - 08:54:36 PDT)
[AMBER] problem in interpreting RMSDs Sajeewa Pemasinghe (Sat Oct 15 2011 - 09:15:21 PDT)
- Re: [AMBER] problem in interpreting RMSDs Jason Swails (Sat Oct 15 2011 - 09:59:49 PDT)
[AMBER] SASA calculation: removing water and ion problem. Ouaray Z. (Sun Oct 16 2011 - 06:14:36 PDT)
- Re: [AMBER] SASA calculation: removing water and ion problem. Sangita Kachhap (Sun Oct 16 2011 - 07:21:53 PDT)
  - Re: [AMBER] SASA calculation: removing water and ion problem. Ouaray Z. (Sun Oct 16 2011 - 09:16:58 PDT)
    - Re: [AMBER] SASA calculation: removing water and ion problem. David Case (Sun Oct 16 2011 - 09:59:58 PDT)
    - Re: [AMBER] SASA calculation: removing water and ion problem. Jason Swails (Mon Oct 17 2011 - 04:05:27 PDT)
[AMBER] Self-assembled monolayers ros (Sun Oct 16 2011 - 09:19:53 PDT)
[AMBER] Solvent accessible area kirtana S (Sun Oct 16 2011 - 09:38:58 PDT)
[AMBER] subscription! Dr. Alaa El-Din A. Gawad (Fri Oct 14 2011 - 13:09:22 PDT)
[AMBER] AmberTools-1.5 installation Dr. Alaa El-Din A. Gawad (Fri Oct 14 2011 - 13:07:04 PDT)
- Re: [AMBER] AmberTools-1.5 installation David A. Case (Sun Oct 16 2011 - 13:58:44 PDT)
  - Re: [AMBER] AmberTools-1.5 installation Dr. Alaa El-Din A. Abdel-Gawad (Tue Oct 18 2011 - 02:05:14 PDT)
    - Re: [AMBER] AmberTools-1.5 installation David A Case (Tue Oct 18 2011 - 05:08:15 PDT)
    - Re: [AMBER] AmberTools-1.5 installation Jason Swails (Tue Oct 18 2011 - 06:42:42 PDT)
    - Re: [AMBER] AmberTools-1.5 installation Dr. Alaa El-Din A. Abdel-Gawad (Thu Oct 20 2011 - 01:40:03 PDT)
    - Re: [AMBER] AmberTools-1.5 installation Jan-Philip Gehrcke (Thu Oct 20 2011 - 03:51:26 PDT)
    - Re: [AMBER] AmberTools-1.5 installation Dr. Alaa El-Din A. Abdel-Gawad (Sat Oct 22 2011 - 02:38:34 PDT)
    - Re: [AMBER] AmberTools-1.5 installation Jason Swails (Sat Oct 22 2011 - 06:41:02 PDT)
    - Re: [AMBER] AmberTools-1.5 installation Dr. Alaa El-Din A. Abdel-Gawad (Sun Oct 23 2011 - 01:35:57 PDT)
    - Re: [AMBER] AmberTools-1.5 installation Jason Swails (Sun Oct 23 2011 - 21:19:14 PDT)
[AMBER] Judje error Алексей Раевский (Sun Oct 16 2011 - 15:19:37 PDT)
- Re: [AMBER] Judje error David A. Case (Sun Oct 16 2011 - 18:24:52 PDT)
  - Re: [AMBER] Judje error Алексей Раевский (Sun Oct 16 2011 - 22:49:26 PDT)
[AMBER] Energy calculateion from MD trajectory: can we skip the minimization? kurisaki (Sun Oct 16 2011 - 23:58:17 PDT)
- Re: [AMBER] Energy calculateion from MD trajectory: can we skip the minimization? Jason Swails (Mon Oct 17 2011 - 03:59:43 PDT)
  - Re: [AMBER] Energy calculateion from MD trajectory: can we skip the minimization? kurisaki (Mon Oct 17 2011 - 04:32:09 PDT)
- [AMBER] PMEMD conditions for solvent bulk characterization? Dean Cuebas (Mon Oct 17 2011 - 15:05:31 PDT)
  - Re: [AMBER] PMEMD conditions for solvent bulk characterization? David A. Case (Mon Oct 17 2011 - 18:32:10 PDT)
    - Re: [AMBER] PMEMD conditions for solvent bulk characterization? Dean Cuebas (Mon Oct 17 2011 - 20:22:05 PDT)
Re: [AMBER] Trouble with Installation of AmberTools 1.5 Ben Ahmady (Mon Oct 17 2011 - 09:11:53 PDT)
- Re: [AMBER] Trouble with Installation of AmberTools 1.5 Tyler Luchko (Mon Oct 17 2011 - 09:19:29 PDT)
  - Re: [AMBER] Installation of AmberTools 1.5 (and Amber 11) Ben Ahmady (Tue Oct 18 2011 - 10:41:34 PDT)
    - Re: [AMBER] Installation of AmberTools 1.5 (and Amber 11) Jason Swails (Tue Oct 18 2011 - 11:02:46 PDT)
    - Re: [AMBER] Installation of AmberTools 1.5 (and Amber 11) Ben Ahmady (Tue Oct 18 2011 - 11:08:04 PDT)
[AMBER] Help on self-assembled mono layer ros (Mon Oct 17 2011 - 11:58:02 PDT)
[AMBER] solvents in AMBER Yao Yao (Mon Oct 17 2011 - 13:36:02 PDT)
Re: [AMBER] vmd-l: AMBER prmtop and traj to pqr - radii error Jesper Soerensen (Mon Oct 17 2011 - 16:58:53 PDT)
[AMBER] Force field parameters for polyethene 陶晓芳 (Mon Oct 17 2011 - 20:18:20 PDT)
- Re: [AMBER] Force field parameters for polyethene David A Case (Tue Oct 18 2011 - 05:03:08 PDT)
  - Re: [AMBER] Force field parameters for polyethene 陶晓芳 (Tue Oct 18 2011 - 19:31:15 PDT)
- Re: [AMBER] Force field parameters for polyethene FyD (Tue Oct 18 2011 - 23:59:22 PDT)
  - Re: [AMBER] Force field parameters for polyethene 陶晓芳 (Thu Oct 20 2011 - 00:47:07 PDT)
[AMBER] sander pbsa and imin = 5 problem Niel Henriksen (Mon Oct 17 2011 - 20:27:18 PDT)
- Re: [AMBER] sander pbsa and imin = 5 problem Ray Luo, Ph.D. (Mon Oct 17 2011 - 20:54:29 PDT)
  - Re: [AMBER] sander pbsa and imin = 5 problem Niel Henriksen (Mon Oct 17 2011 - 21:26:23 PDT)
  - Re: [AMBER] sander pbsa and imin = 5 problem Niel Henriksen (Mon Oct 17 2011 - 22:23:35 PDT)
[AMBER] error "reset fillratio to a larger number 2.000" in mm_pbsa calculation Prajwal Nandekar (Mon Oct 17 2011 - 23:14:54 PDT)
- Re: [AMBER] error "reset fillratio to a larger number 2.000" in mm_pbsa calculation Bill Miller III (Tue Oct 18 2011 - 04:01:29 PDT)
[AMBER] Amber 10 compile error Kijeong Kwac (Tue Oct 18 2011 - 08:25:11 PDT)
[AMBER] Is Amber a 32-bit or 64-bit program? Jiaqi Jin (Tue Oct 18 2011 - 14:58:57 PDT)
- Re: [AMBER] Is Amber a 32-bit or 64-bit program? Ismail, Mohd F. (Tue Oct 18 2011 - 15:15:11 PDT)
  - Re: [AMBER] Is Amber a 32-bit or 64-bit program? Matthew D Antalek (Tue Oct 18 2011 - 17:14:58 PDT)
[AMBER] Material including Boron, "ATTN need revision" Hoshin Kim (Tue Oct 18 2011 - 16:51:14 PDT)
[AMBER] Amber Tools 1.5 installation Matthew D Antalek (Tue Oct 18 2011 - 17:10:50 PDT)
- Re: [AMBER] Amber Tools 1.5 installation David A. Case (Tue Oct 18 2011 - 19:26:50 PDT)
  - Re: [AMBER] Amber Tools 1.5 installation Matthew D Antalek (Tue Oct 18 2011 - 20:12:51 PDT)
    - Re: [AMBER] Amber Tools 1.5 installation Matthew D Antalek (Wed Oct 19 2011 - 05:05:10 PDT)
[AMBER] AMBER10 Shesh Nath (Tue Oct 18 2011 - 23:26:41 PDT)
- [AMBER] Fwd: AMBER10 Shesh Nath (Thu Oct 20 2011 - 08:47:49 PDT)
[AMBER] Applying Bugfixes Amber11 Matthew D Antalek (Wed Oct 19 2011 - 15:46:07 PDT)
- Re: [AMBER] Applying Bugfixes Amber11 Niel Henriksen (Wed Oct 19 2011 - 15:51:00 PDT)
  - Re: [AMBER] Applying Bugfixes Amber11 Matthew D Antalek (Wed Oct 19 2011 - 16:02:40 PDT)
    - [AMBER] AmberTools 1.5 compilation error Sasha Buzko (Wed Oct 19 2011 - 16:21:55 PDT)
    - Re: [AMBER] AmberTools 1.5 compilation error Sasha Buzko (Wed Oct 19 2011 - 16:34:54 PDT)
    - Re: [AMBER] AmberTools 1.5 compilation error Ben Roberts (Wed Oct 19 2011 - 16:45:56 PDT)
    - Re: [AMBER] AmberTools 1.5 compilation error Jason Swails (Wed Oct 19 2011 - 17:00:46 PDT)
    - Re: [AMBER] AmberTools 1.5 compilation error Sasha Buzko (Wed Oct 19 2011 - 17:57:49 PDT)
[AMBER] Inquiry about the cutoff (cut, vdw_cutoff, es_cutoff) settings of PMEMD Mo Chen (Wed Oct 19 2011 - 19:18:46 PDT)
- Re: [AMBER] Inquiry about the cutoff (cut, vdw_cutoff, es_cutoff) settings of PMEMD Mo Chen (Wed Oct 19 2011 - 19:59:26 PDT)
- Re: [AMBER] Inquiry about the cutoff (cut, vdw_cutoff, es_cutoff) settings of PMEMD Ross Walker (Thu Oct 20 2011 - 00:32:00 PDT)
  - Re: [AMBER] Inquiry about the cutoff (cut, vdw_cutoff, es_cutoff) settings of PMEMD Mo Chen (Thu Oct 20 2011 - 09:27:58 PDT)
[AMBER] Failure minimizing pamr7 files from A1 tutorial with NAMD=CUDA Francesco Pietra (Wed Oct 19 2011 - 23:32:13 PDT)
- Re: [AMBER] Failure minimizing pamr7 files from A1 tutorial with NAMD=CUDA Ross Walker (Thu Oct 20 2011 - 00:13:07 PDT)
  - Re: [AMBER] Failure minimizing pamr7 files from A1 tutorial with NAMD=CUDA Francesco Pietra (Thu Oct 20 2011 - 01:02:36 PDT)
    - Re: [AMBER] Failure minimizing pamr7 files from A1 tutorial with NAMD=CUDA Ross Walker (Thu Oct 20 2011 - 01:17:43 PDT)
    - Re: [AMBER] Failure minimizing pamr7 files from A1 tutorial with NAMD=CUDA Francesco Pietra (Thu Oct 20 2011 - 03:24:39 PDT)
    - Re: [AMBER] Failure minimizing pamr7 files from A1 tutorial with NAMD=CUDA Ismail, Mohd F. (Thu Oct 20 2011 - 09:14:37 PDT)
    - Re: [AMBER] Failure minimizing pamr7 files from A1 tutorial with NAMD=CUDA Francesco Pietra (Thu Oct 20 2011 - 13:29:26 PDT)
    - Re: [AMBER] Failure minimizing pamr7 files from A1 tutorial with NAMD=CUDA Ross Walker (Thu Oct 20 2011 - 09:39:50 PDT)
    - Re: [AMBER] Failure minimizing pamr7 files from A1 tutorial with NAMD=CUDA Francesco Pietra (Thu Oct 20 2011 - 13:26:42 PDT)
[AMBER] please help me pancham lal gupta (Thu Oct 20 2011 - 02:59:57 PDT)
[AMBER] Sander.MPI parallel run Lianhu Wei (Thu Oct 20 2011 - 09:04:26 PDT)
- Re: [AMBER] Sander.MPI parallel run Ross Walker (Thu Oct 20 2011 - 09:33:14 PDT)
  - Re: [AMBER] Sander.MPI parallel run Lianhu Wei (Thu Oct 27 2011 - 12:08:11 PDT)
    - Re: [AMBER] Sander.MPI parallel run Jason Swails (Thu Oct 27 2011 - 12:32:20 PDT)
    - Re: [AMBER] Sander.MPI parallel run Ross Walker (Thu Oct 27 2011 - 12:44:56 PDT)
    - Re: [AMBER] Sander.MPI parallel run Lianhu Wei (Thu Oct 27 2011 - 13:02:59 PDT)
    - Re: [AMBER] Sander.MPI parallel run Jason Swails (Thu Oct 27 2011 - 13:21:21 PDT)
    - Re: [AMBER] Sander.MPI parallel run Lianhu Wei (Fri Oct 28 2011 - 07:33:04 PDT)
    - Re: [AMBER] Sander.MPI parallel run Ross Walker (Fri Oct 28 2011 - 09:20:36 PDT)
[AMBER] Error using set default PBradii bondi in tleap with pmemd.cuda or sander Fabrício Bracht (Thu Oct 20 2011 - 21:05:04 PDT)
- Re: [AMBER] Error using set default PBradii bondi in tleap with pmemd.cuda or sander Jason Swails (Thu Oct 20 2011 - 21:12:42 PDT)
  - Re: [AMBER] Error using set default PBradii bondi in tleap with pmemd.cuda or sander Fabrício Bracht (Thu Oct 20 2011 - 21:51:41 PDT)
[AMBER] crash due to ewald Jorgen Simonsen (Fri Oct 21 2011 - 05:17:42 PDT)
- Re: [AMBER] crash due to ewald steinbrt.rci.rutgers.edu (Fri Oct 21 2011 - 05:33:37 PDT)
  - Re: [AMBER] crash due to ewald Jason Swails (Fri Oct 21 2011 - 06:37:00 PDT)
    - Re: [AMBER] crash due to ewald Jorgen Simonsen (Fri Oct 21 2011 - 06:59:44 PDT)
    - Re: [AMBER] crash due to ewald Jason Swails (Fri Oct 21 2011 - 07:38:57 PDT)
[AMBER] errors when add Zn ions Yunjie Zhao (Fri Oct 21 2011 - 05:37:15 PDT)
- Re: [AMBER] errors when add Zn ions Jason Swails (Fri Oct 21 2011 - 09:59:07 PDT)
- Re: [AMBER] errors when add Zn ions Daniel Roe (Fri Oct 21 2011 - 10:35:56 PDT)
[AMBER] PB parameters: SURFTEN/SURFOFF Qiong Zhang (Sat Oct 22 2011 - 13:56:33 PDT)
- Re: [AMBER] PB parameters: SURFTEN/SURFOFF Ray Luo, Ph.D. (Sat Oct 22 2011 - 21:19:01 PDT)
  - Re: [AMBER] PB parameters: SURFTEN/SURFOFF Qiong Zhang (Sat Oct 22 2011 - 22:41:17 PDT)
    - Re: [AMBER] PB parameters: SURFTEN/SURFOFF Jason Swails (Sun Oct 23 2011 - 21:21:22 PDT)
    - Re: [AMBER] PB parameters: SURFTEN/SURFOFF Qiong Zhang (Mon Oct 24 2011 - 12:50:20 PDT)
    - Re: [AMBER] PB parameters: SURFTEN/SURFOFF Jason Swails (Mon Oct 24 2011 - 13:20:34 PDT)
    - Re: [AMBER] PB parameters: SURFTEN/SURFOFF Qiong Zhang (Mon Oct 24 2011 - 14:04:30 PDT)
[AMBER] how to get tetramer coordinate of Melittin Form PDB ID:2MLT. hai wei (Sat Oct 22 2011 - 18:36:27 PDT)
- Re: [AMBER] how to get tetramer coordinate of Melittin Form PDB ID:2MLT. Hector A. Baldoni (Tue Oct 25 2011 - 15:23:54 PDT)
  - Re: [AMBER] how to get tetramer coordinate of Melittin Form PDB ID:2MLT. hai wei (Sun Oct 30 2011 - 01:58:16 PDT)
[AMBER] for mm_pbsa.pl, when MS=0, PB does not work, GB works Qiong Zhang (Sat Oct 22 2011 - 22:46:27 PDT)
- Re: [AMBER] for mm_pbsa.pl, when MS=0, PB does not work, GB works Ray Luo, Ph.D. (Sun Oct 23 2011 - 08:23:02 PDT)
  - Re: [AMBER] for mm_pbsa.pl, when MS=0, PB does not work, GB works Qiong Zhang (Sun Oct 23 2011 - 08:26:10 PDT)
[AMBER] AMBER, haris p has invited you to open a Gmail account haris p (Sun Oct 23 2011 - 00:58:40 PDT)
[AMBER] Polarization term in Energy Anglea A. (Sun Oct 23 2011 - 06:55:38 PDT)
- Re: [AMBER] Polarization term in Energy David A Case (Tue Oct 25 2011 - 05:42:14 PDT)
[AMBER] ATP+Mg Алексей Раевский (Mon Oct 24 2011 - 00:59:38 PDT)
- Re: [AMBER] ATP+Mg Gannett, Peter (Mon Oct 24 2011 - 04:18:04 PDT)
  - Re: [AMBER] ATP+Mg Алексей Раевский (Mon Oct 24 2011 - 05:30:02 PDT)
    - Re: [AMBER] ATP+Mg Gannett, Peter (Mon Oct 24 2011 - 05:34:06 PDT)
    - Re: [AMBER] ATP+Mg filip fratev (Mon Oct 24 2011 - 05:51:55 PDT)
    - Re: [AMBER] ATP+Mg Алексей Раевский (Mon Oct 24 2011 - 06:08:55 PDT)
- Re: [AMBER] ATP+Mg FyD (Wed Oct 26 2011 - 08:50:10 PDT)
[AMBER] How to use "impose" command in ptraj to rotate dihedral angle mish (Mon Oct 24 2011 - 02:49:49 PDT)
- Re: [AMBER] How to use "impose" command in ptraj to rotate dihedral angle Sai Kumar Ramadugu (Tue Oct 25 2011 - 08:23:24 PDT)
[AMBER] Minor RNA bases gunajyoti das (Mon Oct 24 2011 - 05:04:47 PDT)
- Re: [AMBER] Minor RNA bases David A Case (Mon Oct 24 2011 - 13:20:27 PDT)
[AMBER] does CHECKOVERLAP check image cell? kurisaki (Mon Oct 24 2011 - 05:14:44 PDT)
- Re: [AMBER] does CHECKOVERLAP check image cell? Thomas Cheatham III (Wed Oct 26 2011 - 13:44:09 PDT)
  - Re: [AMBER] does CHECKOVERLAP check image cell? kurisaki (Wed Oct 26 2011 - 18:33:41 PDT)
[AMBER] Final chance to win a C2070 - Survey ends at midnight PDT tonight Monday Oct 24th 2011. Survey Request - 10 minutes of your time please to help future AMBER development (http://surveys.nvidia.com/index.jsp?pi=f7d3e68a3e1b44841571e6ab4ce2f021) Ross Walker (Mon Oct 24 2011 - 09:24:57 PDT)
Re: [AMBER] Final chance to win a C2070 - Survey ends at midnight PDT tonight Monday Oct 24th 2011. Survey Request - 10 minutes of your time please to help future AMBER development (http://surveys.nvidia.com/index.jsp?pi=f7d3e68a3e1b44841571e6ab4ce2f peker milas (Mon Oct 24 2011 - 09:26:42 PDT)
- Re: [AMBER] Final chance to win a C2070 - Survey ends at midnight PDT tonight Monday Oct 24th 2011. Survey Request - 10 minutes of your time please to help future AMBER development (http://surveys.nvidia.com/index.jsp?pi=f7d3e68a3e1b44841571e6ab4ce2f Ross Walker (Mon Oct 24 2011 - 09:36:35 PDT)
  - Re: [AMBER] Final chance to win a C2070 - Survey ends at midnight PDT tonight Monday Oct 24th 2011. Survey Request - 10 minutes of your time please to help future AMBER development (http://surveys.nvidia.com/index.jsp?pi=f7d3e68a3e1b44841571e6ab4ce2f Crowley, Michael (Mon Oct 24 2011 - 09:41:31 PDT)
Re: [AMBER] GPU Survey link: http://surveys.nvidia.com/index.jsp?pi=f7d3e68a3e1b44841571e6ab4ce2f021 Ross Walker (Mon Oct 24 2011 - 09:55:46 PDT)
[AMBER] please help me pancham lal gupta (Mon Oct 24 2011 - 20:08:06 PDT)
- Re: [AMBER] please help me David A Case (Tue Oct 25 2011 - 05:29:06 PDT)
  - Re: [AMBER] please help me pancham lal gupta (Wed Nov 02 2011 - 03:21:42 PDT)
    - Re: [AMBER] please help me David A Case (Wed Nov 02 2011 - 04:49:17 PDT)
[AMBER] Ambertools1.5, mmpbsa.py. PB Bomb in pb_atmlist(): maxnba too short Qiong Zhang (Tue Oct 25 2011 - 02:07:55 PDT)
- Re: [AMBER] Ambertools1.5, mmpbsa.py. PB Bomb in pb_atmlist(): maxnba too short Qiong Zhang (Tue Oct 25 2011 - 02:15:40 PDT)
- Re: [AMBER] Ambertools1.5, mmpbsa.py. PB Bomb in pb_atmlist(): maxnba too short Qiong Zhang (Tue Oct 25 2011 - 05:13:37 PDT)
  - Re: [AMBER] Ambertools1.5, mmpbsa.py. PB Bomb in pb_atmlist(): maxnba too short Ray Luo, Ph.D. (Tue Oct 25 2011 - 09:31:25 PDT)
    - Re: [AMBER] Ambertools1.5, mmpbsa.py. PB Bomb in pb_atmlist(): maxnba too short Qiong Zhang (Tue Oct 25 2011 - 09:56:28 PDT)
    - [AMBER] Building parallel Amber11 on CRAY XD1 Dean Cuebas (Tue Oct 25 2011 - 11:30:31 PDT)
    - Re: [AMBER] Building parallel Amber11 on CRAY XD1 Ross Walker (Tue Oct 25 2011 - 11:57:00 PDT)
    - Re: [AMBER] Building parallel Amber11 on CRAY XD1 Dean Cuebas (Fri Oct 28 2011 - 13:13:43 PDT)
[AMBER] REMD: mismatches in potential energy values Mariarosaria Ferraro (Tue Oct 25 2011 - 03:24:22 PDT)
- Re: [AMBER] REMD: mismatches in potential energy values Jason Swails (Tue Oct 25 2011 - 06:28:57 PDT)
[AMBER] ERROR: max pairlist cutoff must be less than unit cell max sphere radius! Ashutosh Shandilya (Tue Oct 25 2011 - 06:04:20 PDT)
- Re: [AMBER] ERROR: max pairlist cutoff must be less than unit cell max sphere radius! Ross Walker (Tue Oct 25 2011 - 09:29:48 PDT)
  - Re: [AMBER] ERROR: max pairlist cutoff must be less than unit cell max sphere radius! Ashutosh Shandilya (Thu Oct 27 2011 - 01:36:01 PDT)
    - Re: [AMBER] ERROR: max pairlist cutoff must be less than unit cell max sphere radius! Ashutosh Shandilya (Thu Oct 27 2011 - 01:39:05 PDT)
    - Re: [AMBER] ERROR: max pairlist cutoff must be less than unit cell max sphere radius! Ross Walker (Thu Oct 27 2011 - 10:20:14 PDT)
[AMBER] reimage method and hbond analysis mirage . (Wed Oct 26 2011 - 00:02:47 PDT)
[AMBER] quasi-harmonic analysis Neha Gandhi (Wed Oct 26 2011 - 01:50:48 PDT)
- Re: [AMBER] quasi-harmonic analysis Collu, Francesca (DCB) (Wed Oct 26 2011 - 01:56:03 PDT)
  - Re: [AMBER] quasi-harmonic analysis Neha Gandhi (Wed Oct 26 2011 - 02:53:24 PDT)
    - Re: [AMBER] quasi-harmonic analysis Hannes Loeffler (Wed Oct 26 2011 - 03:25:40 PDT)
    - Re: [AMBER] quasi-harmonic analysis c00jsw00.nchc.narl.org.tw (Wed Oct 26 2011 - 04:00:47 PDT)
[AMBER] Molecular velocity from molecular trajectories tommaso.casalini.mail.polimi.it (Wed Oct 26 2011 - 02:51:53 PDT)
- Re: [AMBER] Molecular velocity from molecular trajectories Daniel Roe (Wed Oct 26 2011 - 06:24:13 PDT)
[AMBER] box information in .inpcrd and .rst files Giovanni Pavan (Wed Oct 26 2011 - 04:35:59 PDT)
- Re: [AMBER] box information in .inpcrd and .rst files David A Case (Thu Oct 27 2011 - 05:10:02 PDT)
  - Re: [AMBER] box information in .inpcrd and .rst files Pavan Giovanni (Thu Oct 27 2011 - 08:44:27 PDT)
- Re: [AMBER] box information in .inpcrd and .rst files Bill Ross (Thu Oct 27 2011 - 15:30:19 PDT)
[AMBER] pseudorotation phase angle for RNA Charles Johnson (Wed Oct 26 2011 - 08:50:56 PDT)
- Re: [AMBER] pseudorotation phase angle for RNA David A Case (Thu Oct 27 2011 - 05:03:40 PDT)
[AMBER] Amber on IBM Power7 or Opteron 6200 series? Gustavo Seabra (Wed Oct 26 2011 - 09:17:53 PDT)
- Re: [AMBER] Amber on IBM Power7 or Opteron 6200 series? Carlos Sosa (Wed Oct 26 2011 - 09:24:46 PDT)
  - Re: [AMBER] Amber on IBM Power7 or Opteron 6200 series? Gustavo Seabra (Wed Oct 26 2011 - 10:14:24 PDT)
    - Re: [AMBER] Amber on IBM Power7 or Opteron 6200 series? Ross Walker (Wed Oct 26 2011 - 10:20:58 PDT)
[AMBER] input conformations for RESP procedure for modified amino? jzintsma.nd.edu (Wed Oct 26 2011 - 10:04:20 PDT)
- Re: [AMBER] input conformations for RESP procedure for modified amino? FyD (Thu Oct 27 2011 - 01:52:35 PDT)
[AMBER] pseudorotation phase angle for RNA Charles Johnson (Wed Oct 26 2011 - 13:57:28 PDT)
- Re: [AMBER] pseudorotation phase angle for RNA Ilyas Yildirim (Thu Oct 27 2011 - 01:37:34 PDT)
  - Re: [AMBER] pseudorotation phase angle for RNA David A Case (Thu Oct 27 2011 - 05:05:23 PDT)
[AMBER] About defining force direction in SMD simulation Mo Chen (Wed Oct 26 2011 - 15:25:02 PDT)
- Re: [AMBER] About defining force direction in SMD simulation Jason Swails (Wed Oct 26 2011 - 20:52:17 PDT)
  - Re: [AMBER] About defining force direction in SMD simulation Mo Chen (Wed Oct 26 2011 - 22:24:01 PDT)
    - Re: [AMBER] About defining force direction in SMD simulation Mo Chen (Wed Oct 26 2011 - 22:46:36 PDT)
    - Re: [AMBER] About defining force direction in SMD simulation Jason Swails (Thu Oct 27 2011 - 06:02:09 PDT)
[AMBER] prmtop details Yao Yao (Wed Oct 26 2011 - 17:10:10 PDT)
- Re: [AMBER] prmtop details Alessandro Nascimento (Wed Oct 26 2011 - 17:13:01 PDT)
- Re: [AMBER] prmtop details Jason Swails (Wed Oct 26 2011 - 18:21:54 PDT)
- Re: [AMBER] prmtop details Jason Swails (Wed Oct 26 2011 - 19:50:12 PDT)
[AMBER] molecule out box and correct hbond analysis mirage . (Thu Oct 27 2011 - 01:27:54 PDT)
- Re: [AMBER] molecule out box and correct hbond analysis Daniel Roe (Thu Oct 27 2011 - 07:15:47 PDT)
  - Re: [AMBER] molecule out box and correct hbond analysis mirage . (Thu Oct 27 2011 - 08:39:47 PDT)
    - Re: [AMBER] molecule out box and correct hbond analysis Daniel Roe (Thu Oct 27 2011 - 09:20:23 PDT)
    - [AMBER] Nudged Elastic Band (NEB) with torque PBS system c00jsw00.nchc.narl.org.tw (Thu Oct 27 2011 - 09:47:48 PDT)
    - Re: [AMBER] Nudged Elastic Band (NEB) with torque PBS system Jason Swails (Thu Oct 27 2011 - 09:55:03 PDT)
    - Re: [AMBER] Nudged Elastic Band (NEB) with torque PBS system Carlos Simmerling (Thu Oct 27 2011 - 10:01:36 PDT)
    - Re: [AMBER] Nudged Elastic Band (NEB) with torque PBS system c00jsw00.nchc.narl.org.tw (Mon Oct 31 2011 - 00:02:26 PDT)
    - Re: [AMBER] Nudged Elastic Band (NEB) with torque PBS system Daniel Roe (Mon Oct 31 2011 - 05:09:57 PDT)
    - Re: [AMBER] Nudged Elastic Band (NEB) with torque PBS system c00jsw00.nchc.narl.org.tw (Wed Nov 09 2011 - 22:44:53 PST)
    - Re: [AMBER] Nudged Elastic Band (NEB) with torque PBS system Daniel Roe (Thu Nov 10 2011 - 05:51:36 PST)
    - Re: [AMBER] molecule out box and correct hbond analysis Bruno Rodrigues (Tue Nov 01 2011 - 04:56:00 PDT)
[AMBER] E-mail change Maciej Masłyk (Thu Oct 27 2011 - 05:47:39 PDT)
- Re: [AMBER] E-mail change Jason Swails (Thu Oct 27 2011 - 06:03:32 PDT)
[AMBER] distribution of selected water kirtana S (Thu Oct 27 2011 - 10:10:20 PDT)
- Re: [AMBER] distribution of selected water Bruno Rodrigues (Tue Nov 01 2011 - 03:26:42 PDT)
  - Re: [AMBER] distribution of selected water Jason Swails (Tue Nov 01 2011 - 07:19:46 PDT)
    - Re: [AMBER] distribution of selected water Bruno Rodrigues (Tue Nov 01 2011 - 07:39:03 PDT)
    - Re: [AMBER] distribution of selected water Jason Swails (Tue Nov 01 2011 - 07:41:33 PDT)
    - Re: [AMBER] distribution of selected water Bruno Rodrigues (Tue Nov 01 2011 - 07:51:32 PDT)
    - Re: [AMBER] distribution of selected water Daniel Roe (Tue Nov 01 2011 - 08:55:13 PDT)
    - Re: [AMBER] distribution of selected water Daniel Roe (Tue Nov 01 2011 - 07:44:21 PDT)
[AMBER] Query for using Curves+ from Amber trajectories souvik sur (Thu Oct 27 2011 - 23:19:49 PDT)
- Re: [AMBER] Query for using Curves+ from Amber trajectories Osman, Roman (Fri Oct 28 2011 - 07:11:36 PDT)
[AMBER] Bug in nmode Ake Sandgren (Fri Oct 28 2011 - 01:15:51 PDT)
- Re: [AMBER] Bug in nmode David A Case (Fri Oct 28 2011 - 06:51:21 PDT)
[AMBER] compiling amber11 (sander) on Blue Gene/P piotr zarzycki (Fri Oct 28 2011 - 01:56:37 PDT)
[AMBER] Salt in explicit water Beale, John (Fri Oct 28 2011 - 02:01:20 PDT)
- Re: [AMBER] Salt in explicit water Daniel Roe (Fri Oct 28 2011 - 04:16:31 PDT)
[AMBER] Specifying a gcc compiler for amber tools installation Sai Kumar Ramadugu (Fri Oct 28 2011 - 10:21:50 PDT)
- Re: [AMBER] Specifying a gcc compiler for amber tools installation Jason Swails (Fri Oct 28 2011 - 13:01:46 PDT)
  - Re: [AMBER] Specifying a gcc compiler for amber tools installation Daniel Roe (Fri Oct 28 2011 - 14:27:12 PDT)
[AMBER] 1st DNA Tutorial Pressure Yao Yao (Fri Oct 28 2011 - 11:58:34 PDT)
- Re: [AMBER] 1st DNA Tutorial Pressure Ross Walker (Fri Oct 28 2011 - 12:09:15 PDT)
[AMBER] iron sulphur cluster parametrization Francesco Oteri (Sat Oct 29 2011 - 01:39:52 PDT)
- Re: [AMBER] iron sulphur cluster parametrization case (Sat Oct 29 2011 - 07:27:04 PDT)
  - Re: [AMBER] iron sulphur cluster parametrization Francesco Oteri (Sat Oct 29 2011 - 13:35:04 PDT)
    - Re: [AMBER] iron sulphur cluster parametrization David Case (Mon Oct 31 2011 - 18:00:09 PDT)
- Re: [AMBER] iron sulphur cluster parametrization FyD (Tue Nov 01 2011 - 01:10:26 PDT)
  - Re: [AMBER] iron sulphur cluster parametrization Francesco Oteri (Tue Nov 01 2011 - 03:29:13 PDT)
    - Re: [AMBER] iron sulphur cluster parametrization FyD (Tue Nov 01 2011 - 04:19:18 PDT)
    - Re: [AMBER] iron sulphur cluster parametrization Ilyas Yildirim (Tue Nov 01 2011 - 04:25:42 PDT)
    - Re: [AMBER] iron sulphur cluster parametrization Francesco Oteri (Tue Nov 01 2011 - 04:46:51 PDT)
    - Re: [AMBER] iron sulphur cluster parametrization Francesco Oteri (Tue Nov 01 2011 - 05:03:02 PDT)
    - Re: [AMBER] iron sulphur cluster parametrization FyD (Tue Nov 01 2011 - 07:03:17 PDT)
[AMBER] Problems with AmberTools compilation under Debian James Starlight (Sat Oct 29 2011 - 10:42:29 PDT)
- Re: [AMBER] Problems with AmberTools compilation under Debian Daniel Roe (Sat Oct 29 2011 - 13:21:59 PDT)
  - Re: [AMBER] Problems with AmberTools compilation under Debian James Starlight (Sun Oct 30 2011 - 00:45:33 PDT)
    - Re: [AMBER] Problems with AmberTools compilation under Debian James Starlight (Sun Oct 30 2011 - 06:53:30 PDT)
    - Re: [AMBER] Problems with AmberTools compilation under Debian Daniel Roe (Sun Oct 30 2011 - 07:00:02 PDT)
    - Re: [AMBER] Problems with AmberTools compilation under Debian James Starlight (Sun Oct 30 2011 - 08:33:27 PDT)
    - Re: [AMBER] Problems with AmberTools compilation under Debian James Starlight (Mon Oct 31 2011 - 00:42:02 PDT)
    - Re: [AMBER] Problems with AmberTools compilation under Debian Daniel Roe (Mon Oct 31 2011 - 05:22:31 PDT)
    - Re: [AMBER] Problems with AmberTools compilation under Debian James Starlight (Mon Oct 31 2011 - 06:23:56 PDT)
    - Re: [AMBER] Problems with AmberTools compilation under Debian Jason Swails (Mon Oct 31 2011 - 06:57:44 PDT)
    - Re: [AMBER] Problems with AmberTools compilation under Debian James Starlight (Mon Oct 31 2011 - 07:11:51 PDT)
    - Re: [AMBER] Problems with AmberTools compilation under Debian James Starlight (Tue Nov 01 2011 - 00:05:18 PDT)
    - Re: [AMBER] Problems with AmberTools compilation under Debian David A Case (Tue Nov 01 2011 - 05:01:50 PDT)
    - Re: [AMBER] Problems with AmberTools compilation under Debian James Starlight (Tue Nov 01 2011 - 05:04:35 PDT)
[AMBER] 1JFF Antechamber, LEaP problems Matthew D Antalek (Sat Oct 29 2011 - 14:51:07 PDT)
- Re: [AMBER] 1JFF Antechamber, LEaP problems Jason Swails (Sat Oct 29 2011 - 15:03:23 PDT)
  - Re: [AMBER] 1JFF Antechamber, LEaP problems Matthew D Antalek (Sat Oct 29 2011 - 15:12:07 PDT)
    - Re: [AMBER] 1JFF Antechamber, LEaP problems Jason Swails (Sat Oct 29 2011 - 15:52:58 PDT)
    - Re: [AMBER] 1JFF Antechamber, LEaP problems Matthew D Antalek (Wed Nov 02 2011 - 14:23:38 PDT)
    - Re: [AMBER] 1JFF Antechamber, LEaP problems Jason Swails (Wed Nov 02 2011 - 14:36:17 PDT)
    - Re: [AMBER] 1JFF Antechamber, LEaP problems Matthew D Antalek (Wed Nov 02 2011 - 14:54:35 PDT)
    - Re: [AMBER] 1JFF Antechamber, LEaP problems Matthew D Antalek (Wed Nov 02 2011 - 15:37:37 PDT)
    - Re: [AMBER] 1JFF Antechamber, LEaP problems case (Wed Nov 02 2011 - 18:51:08 PDT)
    - Re: [AMBER] 1JFF Antechamber, LEaP problems FyD (Thu Nov 03 2011 - 01:34:31 PDT)
    - Re: [AMBER] 1JFF Antechamber, LEaP problems Matthew D Antalek (Sun Nov 06 2011 - 18:47:45 PST)
    - Re: [AMBER] 1JFF Antechamber, LEaP problems FyD (Mon Nov 07 2011 - 07:16:30 PST)
    - Re: [AMBER] 1JFF Antechamber, LEaP problems case (Wed Nov 02 2011 - 18:59:07 PDT)
[AMBER] position restraints on heavy atoms or all? Yun Shi (Sat Oct 29 2011 - 17:04:16 PDT)
- Re: [AMBER] position restraints on heavy atoms or all? Brian Radak (Mon Oct 31 2011 - 06:09:32 PDT)
[AMBER] tutorial A6 leila karami (Sun Oct 30 2011 - 03:21:18 PDT)
- Re: [AMBER] tutorial A6 Jason Swails (Sun Oct 30 2011 - 09:37:13 PDT)
[AMBER] tutorial A6 leila karami (Sun Oct 30 2011 - 03:40:42 PDT)
- Re: [AMBER] tutorial A6 David A Case (Mon Oct 31 2011 - 05:24:19 PDT)
[AMBER] Periodic Box in igb mode Davood Norouzi (Sun Oct 30 2011 - 05:26:06 PDT)
- Re: [AMBER] Periodic Box in igb mode David A Case (Mon Oct 31 2011 - 05:25:21 PDT)
[AMBER] Atom ordering after LEAP Gonzalo Jimenez (Sun Oct 30 2011 - 06:47:58 PDT)
- Re: [AMBER] Atom ordering after LEAP Jason Swails (Sun Oct 30 2011 - 14:04:45 PDT)
  - Re: [AMBER] Atom ordering after LEAP steinbrt.rci.rutgers.edu (Mon Oct 31 2011 - 01:33:41 PDT)
- Re: [AMBER] Atom ordering after LEAP David A Case (Mon Oct 31 2011 - 05:29:11 PDT)
  - Re: [AMBER] Atom ordering after LEAP Jason Swails (Mon Oct 31 2011 - 06:45:22 PDT)
    - Re: [AMBER] Atom ordering after LEAP Jason Swails (Mon Oct 31 2011 - 06:46:08 PDT)
[AMBER] parameters for anchor-modified glycopeptides Urszula Uciechowska (Sun Oct 30 2011 - 10:10:35 PDT)
- Re: [AMBER] parameters for anchor-modified glycopeptides David A Case (Mon Oct 31 2011 - 05:35:20 PDT)
- Re: [AMBER] parameters for anchor-modified glycopeptides FyD (Mon Oct 31 2011 - 09:59:29 PDT)
  - Re: [AMBER] parameters for anchor-modified glycopeptides Urszula Uciechowska (Tue Nov 01 2011 - 01:49:48 PDT)
    - Re: [AMBER] parameters for anchor-modified glycopeptides FyD (Tue Nov 01 2011 - 04:35:00 PDT)
    - Re: [AMBER] parameters for anchor-modified glycopeptides Urszula Uciechowska (Tue Nov 01 2011 - 06:27:02 PDT)
    - Re: [AMBER] parameters for anchor-modified glycopeptides FyD (Tue Nov 01 2011 - 07:11:09 PDT)
    - Re: [AMBER] parameters for anchor-modified glycopeptides Urszula Uciechowska (Tue Nov 01 2011 - 07:53:03 PDT)
    - Re: [AMBER] parameters for anchor-modified glycopeptides FyD (Wed Nov 02 2011 - 01:10:38 PDT)
    - Re: [AMBER] parameters for anchor-modified glycopeptides Urszula Uciechowska (Wed Nov 02 2011 - 05:15:50 PDT)
    - Re: [AMBER] parameters for anchor-modified glycopeptides FyD (Wed Nov 02 2011 - 05:40:47 PDT)
    - Re: [AMBER] parameters for anchor-modified glycopeptides Urszula Uciechowska (Fri Nov 04 2011 - 02:29:32 PDT)
    - Re: [AMBER] parameters for anchor-modified glycopeptides FyD (Fri Nov 04 2011 - 04:16:33 PDT)
    - Re: [AMBER] parameters for anchor-modified glycopeptides Urszula Uciechowska (Mon Nov 07 2011 - 01:58:39 PST)
    - Re: [AMBER] parameters for anchor-modified glycopeptides FyD (Mon Nov 07 2011 - 06:15:01 PST)
- Re: [AMBER] parameters for anchor-modified glycopeptides Bill Ross (Mon Nov 07 2011 - 11:23:51 PST)
  - Re: [AMBER] parameters for anchor-modified glycopeptides FyD (Tue Nov 08 2011 - 00:41:11 PST)
[AMBER] umbrella sampling amber11 Elisa Frezza (Sun Oct 30 2011 - 14:40:50 PDT)
- Re: [AMBER] umbrella sampling amber11 Jason Swails (Sun Oct 30 2011 - 14:55:40 PDT)
  - Re: [AMBER] umbrella sampling amber11 Elisa Frezza (Mon Oct 31 2011 - 03:55:23 PDT)
    - Re: [AMBER] umbrella sampling amber11 Jason Swails (Mon Oct 31 2011 - 06:37:43 PDT)
    - Re: [AMBER] umbrella sampling amber11 Elisa Frezza (Mon Oct 31 2011 - 07:31:56 PDT)
[AMBER] how to load atom type for divalent ions in leaprc.ff10? Victor Ma (Mon Oct 31 2011 - 08:56:49 PDT)
- Re: [AMBER] how to load atom type for divalent ions in leaprc.ff10? David A Case (Tue Nov 01 2011 - 05:14:08 PDT)
  - Re: [AMBER] how to load atom type for divalent ions in leaprc.ff10? Victor Ma (Tue Nov 01 2011 - 08:28:15 PDT)
    - Re: [AMBER] how to load atom type for divalent ions in leaprc.ff10? David A Case (Tue Nov 01 2011 - 08:51:07 PDT)
    - Re: [AMBER] how to load atom type for divalent ions in leaprc.ff10? Victor Ma (Tue Nov 01 2011 - 11:09:51 PDT)
    - Re: [AMBER] how to load atom type for divalent ions in leaprc.ff10? Victor Ma (Tue Nov 08 2011 - 09:23:00 PST)
    - Re: [AMBER] how to load atom type for divalent ions in leaprc.ff10? Jason Swails (Tue Nov 08 2011 - 20:32:33 PST)
[AMBER] Issue with running sander with SHAKE Breuer, Marian (Mon Oct 31 2011 - 11:07:37 PDT)
- Re: [AMBER] Issue with running sander with SHAKE David A Case (Tue Nov 01 2011 - 05:22:13 PDT)
  - Re: [AMBER] Issue with running sander with SHAKE Breuer, Marian (Tue Nov 01 2011 - 10:37:06 PDT)
    - Re: [AMBER] Issue with running sander with SHAKE Jason Swails (Tue Nov 01 2011 - 14:49:23 PDT)
    - Re: [AMBER] Issue with running sander with SHAKE Breuer, Marian (Tue Nov 01 2011 - 15:49:36 PDT)
    - Re: [AMBER] Issue with running sander with SHAKE case (Tue Nov 01 2011 - 18:48:21 PDT)
    - Re: [AMBER] Issue with running sander with SHAKE Jason Swails (Tue Nov 01 2011 - 22:36:44 PDT)
    - Re: [AMBER] Issue with running sander with SHAKE Breuer, Marian (Fri Nov 04 2011 - 10:10:48 PDT)
    - Re: [AMBER] Issue with running sander with SHAKE David A Case (Fri Nov 04 2011 - 10:39:14 PDT)
    - Re: [AMBER] Issue with running sander with SHAKE Breuer, Marian (Sat Nov 05 2011 - 15:52:12 PDT)
    - Re: [AMBER] Issue with running sander with SHAKE Andrew Voronkov (Sat Nov 26 2011 - 00:38:58 PST)
    - Re: [AMBER] Issue with running sander with SHAKE Andrew Voronkov (Sat Nov 26 2011 - 09:45:59 PST)
    - Re: [AMBER] Issue with running sander with SHAKE David A Case (Tue Nov 29 2011 - 06:42:14 PST)
    - Re: [AMBER] Issue with running sander with SHAKE Andrew Voronkov (Tue Nov 29 2011 - 11:52:05 PST)
    - Re: [AMBER] Issue with running sander with SHAKE David A Case (Tue Nov 29 2011 - 12:15:32 PST)
[AMBER] cutoff in amber cuda Neha Gandhi (Mon Oct 31 2011 - 19:23:34 PDT)
- Re: [AMBER] cutoff in amber cuda Jason Swails (Tue Nov 01 2011 - 07:09:34 PDT)
  - Re: [AMBER] cutoff in amber cuda Ross Walker (Tue Nov 01 2011 - 08:58:53 PDT)
[AMBER] Measurement of distance between residues forming Hydrogen bond Aditya Padhi (Tue Nov 01 2011 - 01:56:05 PDT)
- Re: [AMBER] Measurement of distance between residues forming Hydrogen bond Jason Swails (Tue Nov 01 2011 - 07:15:09 PDT)
- Re: [AMBER] Measurement of distance between residues forming Hydrogen bond Daniel Roe (Tue Nov 01 2011 - 07:35:04 PDT)
[AMBER] Problems with XLEAP James Starlight (Tue Nov 01 2011 - 03:44:07 PDT)
- Re: [AMBER] Problems with XLEAP Pavan Giovanni (Tue Nov 01 2011 - 03:51:15 PDT)
  - Re: [AMBER] Problems with XLEAP James Starlight (Tue Nov 01 2011 - 04:17:38 PDT)
    - Re: [AMBER] Problems with XLEAP Pavan Giovanni (Tue Nov 01 2011 - 04:33:40 PDT)
    - Re: [AMBER] Problems with XLEAP James Starlight (Tue Nov 01 2011 - 04:56:24 PDT)
    - Re: [AMBER] Problems with XLEAP James Starlight (Tue Nov 01 2011 - 06:06:55 PDT)
    - Re: [AMBER] Problems with XLEAP David A Case (Tue Nov 01 2011 - 07:34:08 PDT)
    - Re: [AMBER] Problems with XLEAP James Starlight (Tue Nov 01 2011 - 07:47:34 PDT)
    - Re: [AMBER] Problems with XLEAP David A Case (Tue Nov 01 2011 - 08:56:05 PDT)
    - Re: [AMBER] Problems with XLEAP James Starlight (Wed Nov 02 2011 - 04:44:20 PDT)
    - Re: [AMBER] Problems with XLEAP David A Case (Wed Nov 02 2011 - 06:50:02 PDT)
    - Re: [AMBER] Problems with XLEAP James Starlight (Mon Nov 07 2011 - 04:52:10 PST)
    - Re: [AMBER] Problems with XLEAP Jason Swails (Mon Nov 07 2011 - 05:44:47 PST)
[AMBER] RMSD of one atom Esam Tolba (Tue Nov 01 2011 - 10:31:41 PDT)
- Re: [AMBER] RMSD of one atom Adrian Roitberg (Tue Nov 01 2011 - 10:34:43 PDT)
- Re: [AMBER] RMSD of one atom Thomas Cheatham III (Tue Nov 01 2011 - 10:38:04 PDT)
[AMBER] PB Bomb in pb_atmlist(): maxnba too short manikanthan bhavaraju (Tue Nov 01 2011 - 11:47:30 PDT)
- Re: [AMBER] PB Bomb in pb_atmlist(): maxnba too short manikanthan bhavaraju (Tue Nov 01 2011 - 12:41:04 PDT)
  - Re: [AMBER] PB Bomb in pb_atmlist(): maxnba too short Ray Luo, Ph.D. (Tue Nov 01 2011 - 17:50:50 PDT)
    - Re: [AMBER] PB Bomb in pb_atmlist(): maxnba too short manikanthan bhavaraju (Tue Nov 01 2011 - 17:58:03 PDT)
    - Re: [AMBER] PB Bomb in pb_atmlist(): maxnba too short Ray Luo, Ph.D. (Tue Nov 01 2011 - 18:02:53 PDT)
    - Re: [AMBER] PB Bomb in pb_atmlist(): maxnba too short manikanthan bhavaraju (Tue Nov 01 2011 - 18:06:53 PDT)
    - Re: [AMBER] PB Bomb in pb_atmlist(): maxnba too short Ray Luo, Ph.D. (Tue Nov 01 2011 - 21:04:04 PDT)
- Re: [AMBER] PB Bomb in pb_atmlist(): maxnba too short Ray Luo, Ph.D. (Wed Nov 02 2011 - 17:10:08 PDT)
[AMBER] AmberTools 1.5 build fails due to undefined symbols in libnetcdf.a Jan-Philip Gehrcke (Tue Nov 01 2011 - 13:45:51 PDT)
- Re: [AMBER] AmberTools 1.5 build fails due to undefined symbols in libnetcdf.a Jan-Philip Gehrcke (Tue Nov 01 2011 - 14:38:21 PDT)
- Re: [AMBER] AmberTools 1.5 build fails due to undefined symbols in libnetcdf.a Ross Walker (Tue Nov 01 2011 - 14:49:01 PDT)
  - Re: [AMBER] AmberTools 1.5 build fails due to undefined symbols in libnetcdf.a Jan-Philip Gehrcke (Tue Nov 01 2011 - 15:52:04 PDT)
    - Re: [AMBER] AmberTools 1.5 build fails due to undefined symbols in libnetcdf.a Jason Swails (Tue Nov 01 2011 - 16:20:28 PDT)
- Re: [AMBER] AmberTools 1.5 build fails due to undefined symbols in libnetcdf.a Daniel Roe (Tue Nov 01 2011 - 19:41:12 PDT)
  - Re: [AMBER] AmberTools 1.5 build fails due to undefined symbols in libnetcdf.a Jan-Philip Gehrcke (Wed Nov 02 2011 - 03:48:29 PDT)
    - Re: [AMBER] AmberTools 1.5 build fails due to undefined symbols in libnetcdf.a Jan-Philip Gehrcke (Wed Nov 02 2011 - 08:07:17 PDT)
    - Re: [AMBER] AmberTools 1.5 build fails due to undefined symbols in libnetcdf.a Jason Swails (Wed Nov 02 2011 - 08:12:21 PDT)
    - Re: [AMBER] AmberTools 1.5 build fails due to undefined symbols in libnetcdf.a Jan-Philip Gehrcke (Wed Nov 02 2011 - 08:18:10 PDT)
    - Re: [AMBER] AmberTools 1.5 build fails due to undefined symbols in libnetcdf.a Jan-Philip Gehrcke (Thu Nov 03 2011 - 06:59:42 PDT)
    - Re: [AMBER] AmberTools 1.5 build fails due to undefined symbols in libnetcdf.a Daniel Roe (Thu Nov 03 2011 - 07:43:55 PDT)
    - Re: [AMBER] AmberTools 1.5 build fails due to undefined symbols in libnetcdf.a Jan-Philip Gehrcke (Fri Nov 04 2011 - 05:47:46 PDT)
    - Re: [AMBER] AmberTools 1.5 build fails due to undefined symbols in libnetcdf.a Jason Swails (Thu Nov 03 2011 - 08:14:38 PDT)
[AMBER] Minimization in sander Anglea A. (Wed Nov 02 2011 - 01:49:13 PDT)
- Re: [AMBER] Minimization in sander David A Case (Wed Nov 02 2011 - 04:47:06 PDT)
  - Re: [AMBER] Minimization in sander Anglea A. (Wed Nov 02 2011 - 05:22:01 PDT)
    - Re: [AMBER] Minimization in sander David A Case (Wed Nov 02 2011 - 06:58:38 PDT)
    - Re: [AMBER] Minimization in sander Anglea A. (Thu Nov 03 2011 - 04:45:10 PDT)
    - Re: [AMBER] Minimization in sander David A Case (Thu Nov 03 2011 - 05:24:46 PDT)
[AMBER] Softcore TI. Peter Winn (Wed Nov 02 2011 - 05:36:16 PDT)
- Re: [AMBER] Softcore TI. steinbrt.rci.rutgers.edu (Wed Nov 02 2011 - 07:15:24 PDT)
  - Re: [AMBER] Softcore TI. Ross Walker (Wed Nov 02 2011 - 07:37:08 PDT)
    - Re: [AMBER] Softcore TI. Peter Winn (Wed Nov 02 2011 - 07:57:29 PDT)
    - Re: [AMBER] Softcore TI. steinbrt.rci.rutgers.edu (Wed Nov 02 2011 - 08:51:39 PDT)
    - Re: [AMBER] Softcore TI. now with data! steinbrt.rci.rutgers.edu (Thu Nov 03 2011 - 03:39:47 PDT)
[AMBER] test_amber_cuda.sh requires small fix Jan-Philip Gehrcke (Wed Nov 02 2011 - 08:13:39 PDT)
- Re: [AMBER] test_amber_cuda.sh requires small fix Jason Swails (Wed Nov 02 2011 - 10:27:41 PDT)
  - Re: [AMBER] test_amber_cuda.sh requires small fix Ross Walker (Wed Nov 02 2011 - 11:14:27 PDT)
    - Re: [AMBER] test_amber_cuda.sh requires small fix Jan-Philip Gehrcke (Wed Nov 02 2011 - 11:24:07 PDT)
    - Re: [AMBER] test_amber_cuda.sh requires small fix Jason Swails (Wed Nov 02 2011 - 12:03:27 PDT)
    - Re: [AMBER] test_amber_cuda.sh requires small fix case (Wed Nov 02 2011 - 18:41:33 PDT)
[AMBER] sander simulated annealing Charles Johnson (Wed Nov 02 2011 - 08:53:50 PDT)
- Re: [AMBER] sander simulated annealing Brian Radak (Wed Nov 02 2011 - 09:24:45 PDT)
  - Re: [AMBER] sander simulated annealing Charles Johnson (Wed Nov 02 2011 - 09:32:02 PDT)
    - Re: [AMBER] sander simulated annealing Brian Radak (Wed Nov 02 2011 - 10:02:13 PDT)
- Re: [AMBER] sander simulated annealing David A Case (Wed Nov 02 2011 - 10:18:46 PDT)
[AMBER] post MD energy calculations peker milas (Wed Nov 02 2011 - 09:39:19 PDT)
- Re: [AMBER] post MD energy calculations David A Case (Wed Nov 02 2011 - 10:24:03 PDT)
  - Re: [AMBER] post MD energy calculations peker milas (Wed Nov 02 2011 - 10:35:05 PDT)
[AMBER] Creating i-motif (cruciform DNA) using NAB?? raghav singh (Wed Nov 02 2011 - 11:17:46 PDT)
[AMBER] using AmberTools on Desmond trajectories Ozen, Aysegul (Wed Nov 02 2011 - 15:48:52 PDT)
- Re: [AMBER] using AmberTools on Desmond trajectories Thomas Cheatham III (Wed Nov 02 2011 - 16:16:09 PDT)
- Re: [AMBER] using AmberTools on Desmond trajectories Bill Ross (Wed Nov 02 2011 - 17:35:17 PDT)
[AMBER] Some questions in cluster output qiao xue (Wed Nov 02 2011 - 19:52:31 PDT)
[AMBER] problems in reading molecule in tleap/xleap Urszula Uciechowska (Thu Nov 03 2011 - 05:28:20 PDT)
- Re: [AMBER] problems in reading molecule in tleap/xleap David A Case (Thu Nov 03 2011 - 11:06:36 PDT)
  - Re: [AMBER] problems in reading molecule in tleap/xleap Urszula Uciechowska (Fri Nov 04 2011 - 01:57:32 PDT)
    - Re: [AMBER] problems in reading molecule in tleap/xleap David A Case (Fri Nov 04 2011 - 07:16:44 PDT)
    - Re: [AMBER] problems in reading molecule in tleap/xleap FyD (Sat Nov 05 2011 - 00:17:58 PDT)
- Re: [AMBER] problems in reading molecule in tleap/xleap FyD (Tue Nov 08 2011 - 03:39:52 PST)
- Re: [AMBER] problems in reading molecule in tleap/xleap FyD (Tue Nov 08 2011 - 06:07:47 PST)
- Re: [AMBER] problems in reading molecule in tleap/xleap David A Case (Wed Nov 09 2011 - 07:02:11 PST)
[AMBER] sander error Charles Johnson (Thu Nov 03 2011 - 07:24:08 PDT)
- Re: [AMBER] sander error Ben Roberts (Thu Nov 03 2011 - 08:24:18 PDT)
  - Re: [AMBER] sander error Charles Johnson (Thu Nov 03 2011 - 10:06:17 PDT)
    - Re: [AMBER] sander error Ben Roberts (Thu Nov 03 2011 - 10:15:54 PDT)
    - Re: [AMBER] sander error Charles Johnson (Thu Nov 03 2011 - 10:20:07 PDT)
    - Re: [AMBER] sander error Ben Roberts (Thu Nov 03 2011 - 10:50:46 PDT)
    - Re: [AMBER] sander error Charles Johnson (Thu Nov 03 2011 - 10:57:29 PDT)
    - Re: [AMBER] sander error Ben Roberts (Thu Nov 03 2011 - 11:00:08 PDT)
    - Re: [AMBER] sander error David A Case (Thu Nov 03 2011 - 11:06:53 PDT)
    - Re: [AMBER] sander error Charles Johnson (Thu Nov 03 2011 - 11:11:51 PDT)
    - Re: [AMBER] sander error Ben Roberts (Thu Nov 03 2011 - 15:11:30 PDT)
    - Re: [AMBER] sander error David A Case (Fri Nov 04 2011 - 10:48:20 PDT)
[AMBER] Minimization problems. same box different water model Brian Radak (Thu Nov 03 2011 - 08:52:19 PDT)
- Re: [AMBER] Minimization problems. same box different water model David A Case (Thu Nov 03 2011 - 10:52:13 PDT)
  - Re: [AMBER] Minimization problems. same box different water model Brian Radak (Thu Nov 03 2011 - 11:23:09 PDT)
    - Re: [AMBER] Minimization problems. same box different water model David A Case (Fri Nov 04 2011 - 07:10:47 PDT)
[AMBER] Two LMOD questions Sarah Edwards (Thu Nov 03 2011 - 12:11:23 PDT)
- Re: [AMBER] Two LMOD questions Daniel Roe (Thu Nov 03 2011 - 14:57:29 PDT)
  - Re: [AMBER] Two LMOD questions David A Case (Fri Nov 04 2011 - 07:20:28 PDT)
    - Re: [AMBER] Two LMOD questions Sarah Edwards (Fri Nov 04 2011 - 14:39:19 PDT)
[AMBER] bashrc problems Andrew Voronkov (Fri Nov 04 2011 - 04:08:29 PDT)
- Re: [AMBER] bashrc problems Jan-Philip Gehrcke (Fri Nov 04 2011 - 04:38:07 PDT)
  - Re: [AMBER] bashrc problems James Starlight (Fri Nov 04 2011 - 05:52:15 PDT)
    - Re: [AMBER] bashrc problems Jan-Philip Gehrcke (Fri Nov 04 2011 - 06:03:39 PDT)
    - Re: [AMBER] bashrc problems James Starlight (Fri Nov 04 2011 - 06:47:44 PDT)
    - Re: [AMBER] bashrc problems Ross Walker (Fri Nov 04 2011 - 11:31:40 PDT)
    - Re: [AMBER] bashrc problems Andrew Voronkov (Sun Nov 06 2011 - 07:14:55 PST)
    - Re: [AMBER] bashrc problems Ben Roberts (Sun Nov 13 2011 - 19:53:12 PST)
[AMBER] Installation of MMPBSA.MPI should be clarified Jan-Philip Gehrcke (Fri Nov 04 2011 - 07:37:29 PDT)
- Re: [AMBER] Installation of MMPBSA.MPI should be clarified Jason Swails (Fri Nov 04 2011 - 09:23:12 PDT)
[AMBER] directional pressure variation Giovanni Pavan (Fri Nov 04 2011 - 08:08:05 PDT)
[AMBER] MMPBSA.py: DELTA section missing in FINAL_DECOMP_MMPBSA.dat for dec_verbose=3 Jan-Philip Gehrcke (Fri Nov 04 2011 - 09:47:32 PDT)
- Re: [AMBER] MMPBSA.py: DELTA section missing in FINAL_DECOMP_MMPBSA.dat for dec_verbose=3 Jason Swails (Fri Nov 04 2011 - 13:00:41 PDT)
  - Re: [AMBER] MMPBSA.py: DELTA section missing in FINAL_DECOMP_MMPBSA.dat for dec_verbose=3 Jan-Philip Gehrcke (Fri Nov 04 2011 - 13:53:05 PDT)
    - Re: [AMBER] MMPBSA.py: DELTA section missing in FINAL_DECOMP_MMPBSA.dat for dec_verbose=3 Jason Swails (Fri Nov 04 2011 - 14:28:40 PDT)
[AMBER] Segmentation fault in ptraj clustering Seungyeul Yoo (Fri Nov 04 2011 - 12:17:56 PDT)
[AMBER] crashed run and time estimate Yao Yao (Fri Nov 04 2011 - 17:52:52 PDT)
- Re: [AMBER] crashed run and time estimate Ross Walker (Fri Nov 04 2011 - 22:49:25 PDT)
[AMBER] Visualization of Cluster analysis results wrong string (Fri Nov 04 2011 - 22:42:47 PDT)
[AMBER] About RESP fitting gunajyoti das (Sat Nov 05 2011 - 05:36:52 PDT)
- Re: [AMBER] About RESP fitting case (Sat Nov 05 2011 - 07:07:53 PDT)
  - Re: [AMBER] About RESP fitting FyD (Sun Nov 06 2011 - 03:02:32 PST)
[AMBER] Some questions of cluster analysis qiao xue (Sat Nov 05 2011 - 08:31:50 PDT)
- Re: [AMBER] Some questions of cluster analysis Thomas Cheatham (Sun Nov 06 2011 - 14:48:20 PST)
[AMBER] mm_pbsa error Esam Tolba (Sat Nov 05 2011 - 09:27:28 PDT)
- Re: [AMBER] mm_pbsa error Ray Luo, Ph.D. (Sat Nov 05 2011 - 14:08:14 PDT)
[AMBER] anisotropic NPT simulation Giovanni Pavan (Sat Nov 05 2011 - 11:16:30 PDT)
- Re: [AMBER] anisotropic NPT simulation Benjamin D Madej (Sat Nov 05 2011 - 17:53:26 PDT)
[AMBER] 256 CPUs restriction in AmberMD? Garo Garabedyan (Sun Nov 06 2011 - 13:06:57 PST)
- Re: [AMBER] 256 CPUs restriction in AmberMD? case (Sun Nov 06 2011 - 18:10:28 PST)
[AMBER] How to keep Graphene sheet fixed during MD simulation. hai wei (Sun Nov 06 2011 - 15:51:06 PST)
- Re: [AMBER] How to keep Graphene sheet fixed during MD simulation. case (Sun Nov 06 2011 - 18:15:35 PST)
  - Re: [AMBER] How to keep Graphene sheet fixed during MD simulation. hai wei (Sun Nov 06 2011 - 19:10:44 PST)
    - Re: [AMBER] How to keep Graphene sheet fixed during MD simulation. hai wei (Sun Nov 06 2011 - 22:30:12 PST)
    - Re: [AMBER] How to keep Graphene sheet fixed during MD simulation. hai wei (Sun Nov 06 2011 - 23:02:24 PST)
    - Re: [AMBER] How to keep Graphene sheet fixed during MD simulation. Jason Swails (Mon Nov 07 2011 - 05:42:27 PST)
    - Re: [AMBER] How to keep Graphene sheet fixed during MD simulation. David A Case (Mon Nov 07 2011 - 06:08:58 PST)
    - Re: [AMBER] How to keep Graphene sheet fixed during MD simulation. hai wei (Mon Nov 07 2011 - 15:24:59 PST)
    - Re: [AMBER] How to keep Graphene sheet fixed during MD simulation. Jason Swails (Mon Nov 07 2011 - 17:00:24 PST)
    - Re: [AMBER] How to keep Graphene sheet fixed during MD simulation. hai wei (Mon Nov 07 2011 - 19:14:54 PST)
    - Re: [AMBER] How to keep Graphene sheet fixed during MD simulation. David A Case (Mon Nov 07 2011 - 06:08:00 PST)
[AMBER] About Mn2+ parameters in amber 刘吉元 (Sun Nov 06 2011 - 20:14:48 PST)
[AMBER] Installation of amber11 on the latest Ubuntu 64bit Qinghua Liao (Sun Nov 06 2011 - 23:43:00 PST)
- [AMBER] Installation of amber11 on the latest Ubuntu 64bit Qinghua Liao (Mon Nov 07 2011 - 05:19:46 PST)
  - Re: [AMBER] Installation of amber11 on the latest Ubuntu 64bit Jason Swails (Mon Nov 07 2011 - 05:37:38 PST)
    - Re: [AMBER] Installation of amber11 on the latest Ubuntu 64bit Jan-Philip Gehrcke (Mon Nov 07 2011 - 05:55:19 PST)
    - Re: [AMBER] Installation of amber11 on the latest Ubuntu 64bit Qinghua Liao (Mon Nov 07 2011 - 06:38:17 PST)
    - Re: [AMBER] Installation of amber11 on the latest Ubuntu 64bit Jan-Philip Gehrcke (Mon Nov 07 2011 - 07:55:35 PST)
    - Re: [AMBER] Installation of amber11 on the latest Ubuntu 64bit Qinghua Liao (Mon Nov 07 2011 - 14:20:56 PST)
    - Re: [AMBER] Installation of amber11 on the latest Ubuntu 64bit Qinghua Liao (Mon Nov 07 2011 - 06:33:42 PST)
- Re: [AMBER] Installation of amber11 on the latest Ubuntu 64bit David A Case (Mon Nov 07 2011 - 06:26:56 PST)
  - Re: [AMBER] Installation of amber11 on the latest Ubuntu 64bit Qinghua Liao (Mon Nov 07 2011 - 07:29:55 PST)
    - Re: [AMBER] Installation of amber11 on the latest Ubuntu 64bit Jason Swails (Mon Nov 07 2011 - 07:53:57 PST)
[AMBER] problem of installation of amber 11 on ubuntu Qinghua Liao (Mon Nov 07 2011 - 00:10:28 PST)
- [AMBER] problem of installation of amber 11 on ubuntu Qinghua Liao (Mon Nov 07 2011 - 05:22:34 PST)
  - Re: [AMBER] problem of installation of amber 11 on ubuntu Jason Swails (Mon Nov 07 2011 - 05:45:55 PST)
    - Re: [AMBER] problem of installation of amber 11 on ubuntu Qinghua Liao (Mon Nov 07 2011 - 06:24:33 PST)
- Re: [AMBER] problem of installation of amber 11 on ubuntu David A Case (Mon Nov 07 2011 - 06:34:20 PST)
  - Re: [AMBER] problem of installation of amber 11 on ubuntu Qinghua Liao (Mon Nov 07 2011 - 07:07:51 PST)
    - Re: [AMBER] problem of installation of amber 11 on ubuntu Jason Swails (Mon Nov 07 2011 - 07:58:32 PST)
[AMBER] Protein structure heating into a mess Xiaozhou Li (Mon Nov 07 2011 - 09:18:13 PST)
- Re: [AMBER] Protein structure heating into a mess DEBOSTUTI GHOSHDASTIDAR (Mon Nov 07 2011 - 09:27:54 PST)
  - Re: [AMBER] Protein structure heating into a mess DEBOSTUTI GHOSHDASTIDAR (Mon Nov 07 2011 - 09:28:38 PST)
    - Re: [AMBER] Protein structure heating into a mess Xiaozhou Li (Mon Nov 07 2011 - 09:33:43 PST)
[AMBER] addles "old coordinate file not specified" Jennifer Brookes (Mon Nov 07 2011 - 09:25:50 PST)
- Re: [AMBER] addles "old coordinate file not specified" Carlos Simmerling (Mon Nov 07 2011 - 09:29:18 PST)
  - Re: [AMBER] addles "old coordinate file not specified" Jennifer Brookes (Mon Nov 07 2011 - 10:01:28 PST)
    - Re: [AMBER] addles "old coordinate file not specified" Carlos Simmerling (Mon Nov 07 2011 - 10:37:50 PST)
    - Re: [AMBER] addles "old coordinate file not specified" Jennifer Brookes (Mon Nov 07 2011 - 12:13:03 PST)
    - Re: [AMBER] addles "old coordinate file not specified" Carlos Simmerling (Tue Nov 08 2011 - 07:17:00 PST)
    - Re: [AMBER] addles "old coordinate file not specified" Jenny C Brookes (Tue Nov 08 2011 - 08:10:59 PST)
    - Re: [AMBER] addles "old coordinate file not specified" Carlos Simmerling (Tue Nov 08 2011 - 09:19:39 PST)
    - Re: [AMBER] addles "old coordinate file not specified" Jenny C Brookes (Tue Nov 08 2011 - 10:16:41 PST)
    - Re: [AMBER] addles "old coordinate file not specified" Carlos Simmerling (Wed Nov 09 2011 - 06:36:29 PST)
    - Re: [AMBER] addles "old coordinate file not specified" Jennifer Brookes (Wed Nov 09 2011 - 06:50:51 PST)
    - Re: [AMBER] addles "old coordinate file not specified" Carlos Simmerling (Wed Nov 09 2011 - 06:53:16 PST)
- Re: [AMBER] addles "old coordinate file not specified" Bill Ross (Tue Nov 08 2011 - 08:42:05 PST)
  - Re: [AMBER] addles "old coordinate file not specified" Jennifer Brookes (Tue Nov 08 2011 - 10:11:15 PST)
    - Re: [AMBER] addles "old coordinate file not specified" David A Case (Wed Nov 09 2011 - 07:07:49 PST)
    - Re: [AMBER] addles "old coordinate file not specified" Jenny C Brookes (Wed Nov 09 2011 - 08:06:04 PST)
    - Re: [AMBER] addles "old coordinate file not specified" Jan-Philip Gehrcke (Wed Nov 09 2011 - 08:34:30 PST)
    - Re: [AMBER] addles "old coordinate file not specified" Jennifer Brookes (Wed Nov 09 2011 - 14:49:52 PST)
- Re: [AMBER] addles "old coordinate file not specified" Bill Ross (Tue Nov 08 2011 - 15:15:19 PST)
- Re: [AMBER] addles "old coordinate file not specified" Bill Ross (Wed Nov 09 2011 - 08:39:17 PST)
[AMBER] About defining of a modified cytosine which is covalently bonded to the sulfer of cysteine Jin Yang (Mon Nov 07 2011 - 11:16:50 PST)
- Re: [AMBER] About defining of a modified cytosine which is covalently bonded to the sulfer of cysteine FyD (Tue Nov 08 2011 - 02:43:32 PST)
  - Re: [AMBER] About defining of a modified cytosine which is covalently bonded to the sulfer of cysteine Jin Yang (Thu Nov 10 2011 - 07:36:31 PST)
[AMBER] separate build and install dirs? Michael Sternberg (Mon Nov 07 2011 - 15:01:19 PST)
- Re: [AMBER] separate build and install dirs? Ben Roberts (Mon Nov 07 2011 - 15:18:15 PST)
  - Re: [AMBER] separate build and install dirs? Michael Sternberg (Wed Nov 09 2011 - 09:31:02 PST)
    - [AMBER] Passing the free-format flag to files in sander and nmode case (Wed Nov 09 2011 - 19:08:55 PST)
    - Re: [AMBER] Passing the free-format flag to files in sander and nmode Jason Swails (Wed Nov 09 2011 - 21:51:49 PST)
    - Re: [AMBER] Passing the free-format flag to files in sander and nmode Michael Sternberg (Thu Nov 10 2011 - 00:03:25 PST)
    - Re: [AMBER] Passing the free-format flag to files in sander and nmode case (Thu Nov 10 2011 - 05:17:26 PST)
    - Re: [AMBER] global build; was: Passing the free-format flag to files in sander and nmode Michael Sternberg (Fri Nov 11 2011 - 07:42:36 PST)
    - Re: [AMBER] Passing the free-format flag to files in sander and nmode Jason Swails (Thu Nov 10 2011 - 06:33:46 PST)
    - Re: [AMBER] Passing the free-format flag to files in sander and nmode Michael Sternberg (Fri Nov 11 2011 - 08:01:50 PST)
- Re: [AMBER] separate build and install dirs? Bill Ross (Wed Nov 09 2011 - 10:34:06 PST)
  - Re: [AMBER] separate build and install dirs? Michael Sternberg (Wed Nov 09 2011 - 12:49:03 PST)
[AMBER] AMBER Survey C2075 Winners Ross Walker (Mon Nov 07 2011 - 16:36:28 PST)
[AMBER] AMBER9 in GPU Vijay Manickam Achari (Mon Nov 07 2011 - 20:01:29 PST)
- Re: [AMBER] AMBER9 in GPU Jason Swails (Mon Nov 07 2011 - 20:09:29 PST)
[AMBER] entropy calculation Sangita Kachhap (Mon Nov 07 2011 - 22:27:38 PST)
- Re: [AMBER] entropy calculation Jason Swails (Mon Nov 07 2011 - 22:39:48 PST)
  - Re: [AMBER] entropy calculation Sangita Kachhap (Tue Nov 08 2011 - 01:05:25 PST)
    - Re: [AMBER] entropy calculation Bill Miller III (Tue Nov 08 2011 - 04:13:00 PST)
    - Re: [AMBER] entropy calculation Sangita Kachhap (Tue Nov 08 2011 - 04:31:33 PST)
[AMBER] Recent mails Marc Baaden (Mon Nov 07 2011 - 23:48:20 PST)
[AMBER] apologies for an error Marc Baaden (Mon Nov 07 2011 - 23:58:17 PST)
[AMBER] MN2+ ion protein can't be dealed with MCPB 刘吉元 (Tue Nov 08 2011 - 06:19:33 PST)
- Re: [AMBER] MN2+ ion protein can't be dealed with MCPB case (Thu Nov 10 2011 - 06:24:14 PST)
[AMBER] Membrane building madhumita das (Tue Nov 08 2011 - 09:05:32 PST)
- Re: [AMBER] Membrane building David A Case (Wed Nov 09 2011 - 07:13:08 PST)
  - Re: [AMBER] Membrane building madhumita das (Sat Nov 19 2011 - 04:00:50 PST)
    - Re: [AMBER] Membrane building Vlad Cojocaru (Sat Nov 19 2011 - 05:22:38 PST)
    - Re: [AMBER] Membrane building Benjamin Madej (Sat Nov 19 2011 - 13:18:48 PST)
[AMBER] problem in solvation Senthil Natesan (Tue Nov 08 2011 - 09:24:50 PST)
- Re: [AMBER] problem in solvation Jan-Philip Gehrcke (Tue Nov 08 2011 - 10:06:18 PST)
  - Re: [AMBER] problem in solvation Senthil Natesan (Tue Nov 08 2011 - 10:18:42 PST)
    - Re: [AMBER] problem in solvation Brian Radak (Tue Nov 08 2011 - 10:54:29 PST)
    - Re: [AMBER] problem in solvation Senthil Natesan (Tue Nov 08 2011 - 11:04:01 PST)
    - Re: [AMBER] problem in solvation Brian Radak (Tue Nov 08 2011 - 11:49:26 PST)
- Re: [AMBER] problem in solvation Bill Ross (Tue Nov 08 2011 - 14:29:12 PST)
  - Re: [AMBER] problem in solvation Senthil Natesan (Tue Nov 08 2011 - 14:51:00 PST)
- Re: [AMBER] problem in solvation Bill Ross (Tue Nov 08 2011 - 15:05:19 PST)
  - Re: [AMBER] problem in solvation Jan-Philip Gehrcke (Wed Nov 09 2011 - 02:21:28 PST)
    - Re: [AMBER] problem in solvation Senthil Natesan (Wed Nov 09 2011 - 04:59:39 PST)
    - Re: [AMBER] problem in solvation David A Case (Wed Nov 09 2011 - 07:22:19 PST)
    - Re: [AMBER] problem in solvation Jan-Philip Gehrcke (Wed Nov 09 2011 - 07:38:05 PST)
    - Re: [AMBER] problem in solvation Jan-Philip Gehrcke (Wed Nov 09 2011 - 07:52:06 PST)
    - Re: [AMBER] problem in solvation David A Case (Wed Nov 09 2011 - 13:30:31 PST)
    - Re: [AMBER] problem in solvation Jason Swails (Wed Nov 09 2011 - 13:55:40 PST)
    - Re: [AMBER] problem in solvation Senthil Natesan (Wed Nov 09 2011 - 14:20:30 PST)
    - Re: [AMBER] problem in solvation Senthil Natesan (Wed Nov 09 2011 - 11:11:50 PST)
- Re: [AMBER] problem in solvation Bill Ross (Tue Nov 08 2011 - 15:08:30 PST)
- Re: [AMBER] problem in solvation Bill Ross (Tue Nov 08 2011 - 15:13:03 PST)
- Re: [AMBER] problem in solvation Bill Ross (Wed Nov 09 2011 - 06:37:36 PST)
- Re: [AMBER] problem in solvation Bill Ross (Wed Nov 09 2011 - 08:25:10 PST)
  - Re: [AMBER] problem in solvation Senthil Natesan (Wed Nov 09 2011 - 11:22:42 PST)
- Re: [AMBER] problem in solvation Bill Ross (Wed Nov 09 2011 - 08:53:10 PST)
- Re: [AMBER] problem in solvation Bill Ross (Wed Nov 09 2011 - 14:22:12 PST)
[AMBER] AmberTools1.5 install problems on Mac OS X 10.7.2 Frank Barry (Tue Nov 08 2011 - 12:30:58 PST)
- Re: [AMBER] AmberTools1.5 install problems on Mac OS X 10.7.2 Jason Swails (Tue Nov 08 2011 - 14:47:00 PST)
  - Re: [AMBER] AmberTools1.5 install problems on Mac OS X 10.7.2 Frank Barry (Tue Nov 08 2011 - 17:01:56 PST)
    - Re: [AMBER] AmberTools1.5 install problems on Mac OS X 10.7.2 Jason Swails (Tue Nov 08 2011 - 20:23:23 PST)
[AMBER] Questions about LEaP: atom connect and delete hydrogen Tales Yuan (Tue Nov 08 2011 - 19:06:03 PST)
- Re: [AMBER] Questions about LEaP: atom connect and delete hydrogen Jason Swails (Tue Nov 08 2011 - 20:27:15 PST)
  - Re: [AMBER] Questions about LEaP: atom connect and delete hydrogen Tales Yuan (Wed Nov 09 2011 - 05:35:26 PST)
[AMBER] calculate residue wise SASA Xiao Chen (Tue Nov 08 2011 - 21:08:13 PST)
- Re: [AMBER] calculate residue wise SASA Daniel Roe (Tue Nov 08 2011 - 22:23:06 PST)
  - Re: [AMBER] calculate residue wise SASA Xiao Chen (Wed Nov 09 2011 - 01:17:36 PST)
    - Re: [AMBER] calculate residue wise SASA Jason Swails (Wed Nov 09 2011 - 08:34:25 PST)
[AMBER] problem with pmemd.cuda Giovanni Pavan (Wed Nov 09 2011 - 01:07:57 PST)
- Re: [AMBER] problem with pmemd.cuda Ross Walker (Wed Nov 09 2011 - 09:10:44 PST)
  - Re: [AMBER] problem with pmemd.cuda Pavan Giovanni (Wed Nov 09 2011 - 11:06:46 PST)
  - Re: [AMBER] problem with pmemd.cuda Scott Le Grand (Wed Nov 09 2011 - 12:50:23 PST)
- Re: [AMBER] problem with pmemd.cuda Scott Le Grand (Wed Nov 09 2011 - 16:17:23 PST)
  - [AMBER] R: problem with pmemd.cuda Giovanni Pavan (Thu Nov 10 2011 - 01:00:23 PST)
    - Re: [AMBER] R: problem with pmemd.cuda case (Thu Nov 10 2011 - 05:22:43 PST)
    - Re: [AMBER] R: problem with pmemd.cuda Scott Le Grand (Thu Nov 10 2011 - 15:23:08 PST)
    - Re: [AMBER] R: problem with pmemd.cuda Pavan Giovanni (Fri Nov 11 2011 - 10:36:45 PST)
    - Re: [AMBER] R: problem with pmemd.cuda Ross Walker (Thu Nov 10 2011 - 20:53:49 PST)
[AMBER] AMBER Shesh Nath (Wed Nov 09 2011 - 02:20:28 PST)
[AMBER] Different print behavior for mdcrd and ncsu modules Brian Radak (Wed Nov 09 2011 - 06:56:43 PST)
- Re: [AMBER] Different print behavior for mdcrd and ncsu modules David A Case (Thu Nov 10 2011 - 08:22:19 PST)
[AMBER] PLUMED release 1.3 available Massimiliano Bonomi (Wed Nov 09 2011 - 07:11:50 PST)
[AMBER] help with antechamber jun kit (Wed Nov 09 2011 - 10:45:01 PST)
- Re: [AMBER] help with antechamber case (Wed Nov 09 2011 - 19:15:01 PST)
  - Re: [AMBER] help with antechamber jun kit (Sun Nov 20 2011 - 12:32:38 PST)
    - Re: [AMBER] help with antechamber David A Case (Mon Nov 21 2011 - 08:50:28 PST)
    - Re: [AMBER] help with antechamber jun kit (Tue Nov 22 2011 - 14:16:45 PST)
    - Re: [AMBER] help with antechamber jun kit (Tue Nov 22 2011 - 18:14:42 PST)
[AMBER] problem of generating prmtop and inpcrd files of a small molecule attached with several amino acids Qinghua Liao (Thu Nov 10 2011 - 05:20:43 PST)
- Re: [AMBER] problem of generating prmtop and inpcrd files of a small molecule attached with several amino acids David A Case (Thu Nov 10 2011 - 08:21:12 PST)
  - Re: [AMBER] problem of generating prmtop and inpcrd files of a small molecule attached with several amino acids Qinghua Liao (Thu Nov 10 2011 - 11:00:32 PST)
  - Re: [AMBER] problem of generating prmtop and inpcrd files of a small molecule attached with several amino acids Qinghua Liao (Fri Nov 11 2011 - 03:06:00 PST)
    - Re: [AMBER] problem of generating prmtop and inpcrd files of a small molecule attached with several amino acids case (Fri Nov 11 2011 - 04:56:48 PST)
Re: [AMBER] problems in reading linrary/tleap case (Thu Nov 10 2011 - 06:21:13 PST)
- Re: [AMBER] problems in reading linrary/tleap FyD (Thu Nov 10 2011 - 09:59:26 PST)
[AMBER] Xleap pdb editing James Starlight (Thu Nov 10 2011 - 07:47:15 PST)
- Re: [AMBER] Xleap pdb editing David A Case (Thu Nov 10 2011 - 08:18:46 PST)
  - Re: [AMBER] Xleap pdb editing James Starlight (Thu Nov 10 2011 - 10:31:42 PST)
    - Re: [AMBER] Xleap pdb editing David A Case (Thu Nov 10 2011 - 10:57:58 PST)
    - Re: [AMBER] Xleap pdb editing James Starlight (Thu Nov 10 2011 - 11:48:23 PST)
    - Re: [AMBER] Xleap pdb editing David A Case (Thu Nov 10 2011 - 13:38:15 PST)
[AMBER] any fix so that I can compile AmberTools with gfortran 4.6.1? Jose Borreguero (Thu Nov 10 2011 - 08:30:06 PST)
[AMBER] leap cannot read MOL2 file that it has written before: small fix suggested Jan-Philip Gehrcke (Thu Nov 10 2011 - 11:26:20 PST)
- Re: [AMBER] leap cannot read MOL2 file that it has written before: small fix suggested M. L. Dodson (Thu Nov 10 2011 - 13:09:35 PST)
  - Re: [AMBER] leap cannot read MOL2 file that it has written before: small fix suggested M. L. Dodson (Thu Nov 10 2011 - 13:30:19 PST)
    - Re: [AMBER] leap cannot read MOL2 file that it has written before: small fix suggested M. L. Dodson (Thu Nov 10 2011 - 13:50:09 PST)
    - Re: [AMBER] leap cannot read MOL2 file that it has written before: small fix suggested Jan-Philip Gehrcke (Thu Nov 10 2011 - 14:32:30 PST)
    - Re: [AMBER] leap cannot read MOL2 file that it has written before: small fix suggested Jan-Philip Gehrcke (Thu Nov 10 2011 - 14:35:12 PST)
    - Re: [AMBER] leap cannot read MOL2 file that it has written before: small fix suggested M. L. Dodson (Thu Nov 10 2011 - 15:35:10 PST)
    - Re: [AMBER] leap cannot read MOL2 file that it has written before: small fix suggested Jan-Philip Gehrcke (Fri Nov 11 2011 - 02:00:09 PST)
    - Re: [AMBER] leap cannot read MOL2 file that it has written before: small fix suggested M. L. Dodson (Fri Nov 11 2011 - 07:00:38 PST)
    - Re: [AMBER] leap cannot read MOL2 file that it has written before: small fix suggested Jan-Philip Gehrcke (Tue Nov 15 2011 - 03:48:13 PST)
    - Re: [AMBER] leap cannot read MOL2 file that it has written before: small fix suggested David A Case (Tue Nov 15 2011 - 04:44:56 PST)
[AMBER] ZAFF parametrization problem , parameters not saved, could not find bond parameters Andrew Voronkov (Thu Nov 10 2011 - 13:21:21 PST)
[AMBER] AMBER 11 (Problem with the input format) Fernando Blanco (Fri Nov 11 2011 - 04:40:30 PST)
- Re: [AMBER] AMBER 11 (Problem with the input format) case (Fri Nov 11 2011 - 04:59:23 PST)
  - Re: [AMBER] AMBER 11 (Problem with the input format) Fernando Blanco (Fri Nov 11 2011 - 05:09:44 PST)
    - Re: [AMBER] AMBER 11 (Problem with the input format) Jason Swails (Fri Nov 11 2011 - 10:13:12 PST)
  - Re: [AMBER] AMBER 11 (Problem with the input format) Fernando Blanco (Fri Nov 11 2011 - 05:12:56 PST)
[AMBER] MKL: lib dir name changed for 64bit version Michael Sternberg (Fri Nov 11 2011 - 07:50:23 PST)
[AMBER] Phi/psi to free energies Lekpa Duukori (Fri Nov 11 2011 - 08:23:36 PST)
- Re: [AMBER] Phi/psi to free energies Ben Roberts (Thu Nov 17 2011 - 10:39:55 PST)
[AMBER] bad atom type: Br Hector A. Baldoni (Fri Nov 11 2011 - 13:17:17 PST)
- Re: [AMBER] bad atom type: Br Jason Swails (Fri Nov 11 2011 - 19:20:41 PST)
  - Re: [AMBER] bad atom type: Br Baldoni Hector Armando (Sun Nov 13 2011 - 08:24:18 PST)
[AMBER] Problems of generating prmtop and inpcrd files for ligand-receptor with two Mg2+ ions --please help Crystal.CHIA-YU Ku (Fri Nov 11 2011 - 13:48:18 PST)
- Re: [AMBER] Problems of generating prmtop and inpcrd files for ligand-receptor with two Mg2+ ions --please help case (Fri Nov 11 2011 - 15:05:32 PST)
  - Re: [AMBER] Problems of generating prmtop and inpcrd files for ligand-receptor with two Mg2+ ions --please help Crystal.CHIA-YU Ku (Fri Nov 11 2011 - 17:47:51 PST)
    - Re: [AMBER] Problems of generating prmtop and inpcrd files for ligand-receptor with two Mg2+ ions --please help case (Fri Nov 11 2011 - 19:36:39 PST)
    - Re: [AMBER] Problems of generating prmtop and inpcrd files for ligand-receptor with two Mg2+ ions --please help Crystal.CHIA-YU Ku (Mon Nov 14 2011 - 11:52:12 PST)
    - Re: [AMBER] Problems of generating prmtop and inpcrd files for ligand-receptor with two Mg2+ ions --please help case (Mon Nov 14 2011 - 14:29:27 PST)
    - Re: [AMBER] Problems of generating prmtop and inpcrd files for ligand-receptor with two Mg2+ ions --please help Crystal.CHIA-YU Ku (Mon Nov 14 2011 - 16:33:02 PST)
    - Re: [AMBER] Problems of generating prmtop and inpcrd files for ligand-receptor with two Mg2+ ions --please help David A Case (Tue Nov 15 2011 - 05:26:06 PST)
    - Re: [AMBER] Problems of generating prmtop and inpcrd files for ligand-receptor with two Mg2+ ions --please help Crystal.CHIA-YU Ku (Tue Nov 15 2011 - 14:24:00 PST)
    - Re: [AMBER] Problems of generating prmtop and inpcrd files for ligand-receptor with two Mg2+ ions --please help case (Tue Nov 15 2011 - 17:59:16 PST)
- Re: [AMBER] Problems of generating prmtop and inpcrd files for ligand-receptor with two Mg2+ ions --please help Crystal.CHIA-YU Ku (Mon Nov 14 2011 - 14:42:43 PST)
  - Re: [AMBER] Problems of generating prmtop and inpcrd files for ligand-receptor with two Mg2+ ions --please help David A Case (Tue Nov 15 2011 - 05:29:02 PST)
    - Re: [AMBER] Problems of generating prmtop and inpcrd files for ligand-receptor with two Mg2+ ions --please help Crystal.CHIA-YU Ku (Tue Nov 15 2011 - 15:42:58 PST)
    - Re: [AMBER] Problems of generating prmtop and inpcrd files for ligand-receptor with two Mg2+ ions --please help case (Tue Nov 15 2011 - 18:06:41 PST)
    - Re: [AMBER] Problems of generating prmtop and inpcrd files for ligand-receptor with two Mg2+ ions --please help Crystal.CHIA-YU Ku (Wed Nov 16 2011 - 11:08:18 PST)
    - Re: [AMBER] Problems of generating prmtop and inpcrd files for ligand-receptor with two Mg2+ ions --please help David A Case (Wed Nov 16 2011 - 13:24:06 PST)
    - Re: [AMBER] Problems of generating prmtop and inpcrd files for ligand-receptor with two Mg2+ ions --please help Crystal.CHIA-YU Ku (Fri Nov 18 2011 - 14:21:07 PST)
  - Re: [AMBER] Problems of generating prmtop and inpcrd files for ligand-receptor with two Mg2+ ions --please help Irene Newhouse (Tue Nov 15 2011 - 11:26:15 PST)
- Re: [AMBER] Problems of generating prmtop and inpcrd files for ligand-receptor with two Mg2+ ions --please help David A Case (Thu Nov 17 2011 - 08:33:26 PST)
  - Re: [AMBER] Problems of generating prmtop and inpcrd files for ligand-receptor with two Mg2+ ions --please help Crystal.CHIA-YU Ku (Thu Nov 17 2011 - 16:32:03 PST)
    - Re: [AMBER] Problems of generating prmtop and inpcrd files for ligand-receptor with two Mg2+ ions --please help David A. Case (Thu Nov 17 2011 - 19:26:42 PST)
    - Re: [AMBER] Problems of generating prmtop and inpcrd files for ligand-receptor with two Mg2+ ions --please help Crystal.CHIA-YU Ku (Fri Nov 18 2011 - 17:12:24 PST)
    - Re: [AMBER] Problems of generating prmtop and inpcrd files for ligand-receptor with two Mg2+ ions --please help David A. Case (Fri Nov 18 2011 - 21:13:26 PST)
    - Re: [AMBER] Problems of generating prmtop and inpcrd files for ligand-receptor with two Mg2+ ions --please help Crystal.CHIA-YU Ku (Mon Nov 21 2011 - 17:40:38 PST)
  - Re: [AMBER] Problems of generating prmtop and inpcrd files for ligand-receptor with two Mg2+ ions --please help FyD (Fri Nov 18 2011 - 08:31:24 PST)
[AMBER] comparison failures in the Amber11 and AT15 test bin wang (Fri Nov 11 2011 - 15:20:25 PST)
- Re: [AMBER] comparison failures in the Amber11 and AT15 test Jason Swails (Fri Nov 11 2011 - 19:22:41 PST)
  - Re: [AMBER] comparison failures in the Amber11 and AT15 test bin wang (Mon Nov 14 2011 - 11:16:56 PST)
[AMBER] question about MMPBSA.py Sidney Elmer (Fri Nov 11 2011 - 15:42:18 PST)
- Re: [AMBER] question about MMPBSA.py Jason Swails (Fri Nov 11 2011 - 19:18:46 PST)
[AMBER] msd subrata paul (Fri Nov 11 2011 - 22:34:06 PST)
- Re: [AMBER] msd Bruno Rodrigues (Mon Nov 14 2011 - 05:28:21 PST)
[AMBER] mpirun leila karami (Sat Nov 12 2011 - 06:22:42 PST)
- Re: [AMBER] mpirun case (Sat Nov 12 2011 - 08:04:34 PST)
[AMBER] mpirun leila karami (Sat Nov 12 2011 - 07:01:35 PST)
- Re: [AMBER] mpirun Jason Swails (Sat Nov 12 2011 - 07:52:45 PST)
- Re: [AMBER] mpirun case (Sat Nov 12 2011 - 08:05:16 PST)
- Re: [AMBER] mpirun Sudeep Narayan Banerjee (Mon Nov 14 2011 - 21:50:52 PST)
[AMBER] Discrepancy of GBSA results Anglea A. (Sat Nov 12 2011 - 07:20:23 PST)
- Re: [AMBER] Discrepancy of GBSA results Carlos Simmerling (Sat Nov 12 2011 - 07:22:21 PST)
- Re: [AMBER] Discrepancy of GBSA results Adrian Roitberg (Sat Nov 12 2011 - 07:44:26 PST)
[AMBER] building a polymer and running antechamber on it Changwoo Do (Sat Nov 12 2011 - 10:14:13 PST)
- Re: [AMBER] building a polymer and running antechamber on it FyD (Tue Nov 15 2011 - 04:13:14 PST)
[AMBER] Calculate charges using better method/basis set? Ismail, Mohd F. (Sat Nov 12 2011 - 10:22:20 PST)
- Re: [AMBER] Calculate charges using better method/basis set? Dr. Vitaly V. Chaban (Sun Nov 13 2011 - 12:52:17 PST)
  - Re: [AMBER] Calculate charges using better method/basis set? Adrian Roitberg (Sun Nov 13 2011 - 12:55:31 PST)
    - Re: [AMBER] Calculate charges using better method/basis set? Ismail, Mohd F. (Mon Nov 14 2011 - 08:29:49 PST)
    - Re: [AMBER] Calculate charges using better method/basis set? Dr. Vitaly V. Chaban (Mon Nov 14 2011 - 10:21:49 PST)
  - Re: [AMBER] Calculate charges using better method/basis set? Dr. Vitaly V. Chaban (Sun Nov 13 2011 - 12:54:57 PST)
  - Re: [AMBER] Calculate charges using better method/basis set? Ross Walker (Mon Nov 14 2011 - 09:23:43 PST)
    - Re: [AMBER] Calculate charges using better method/basis set? Dr. Vitaly V. Chaban (Mon Nov 14 2011 - 10:26:11 PST)
    - Re: [AMBER] Calculate charges using better method/basis set? Adrian Roitberg (Mon Nov 14 2011 - 10:33:27 PST)
    - Re: [AMBER] Calculate charges using better method/basis set? Ross Walker (Mon Nov 14 2011 - 10:36:14 PST)
    - Re: [AMBER] Calculate charges using better method/basis set? Brian Radak (Mon Nov 14 2011 - 10:54:07 PST)
    - Re: [AMBER] Calculate charges using better method/basis set? Ismail, Mohd F. (Wed Nov 16 2011 - 07:10:34 PST)
    - Re: [AMBER] Calculate charges using better method/basis set? Karl N. Kirschner (Wed Nov 16 2011 - 07:53:13 PST)
    - Re: [AMBER] Calculate charges using better method/basis set? Ismail, Mohd F. (Wed Nov 16 2011 - 11:03:04 PST)
[AMBER] MMPBSA - running dynamics Fernando Blanco (Sat Nov 12 2011 - 11:16:06 PST)
[AMBER] MN2+ ion protein can't be dealed with MCPB 刘吉元 (Sun Nov 13 2011 - 01:33:41 PST)
[AMBER] how to use ptraj to convert trajectory files? Yun Shi (Sun Nov 13 2011 - 11:06:14 PST)
- Re: [AMBER] how to use ptraj to convert trajectory files? Jan-Philip Gehrcke (Sun Nov 13 2011 - 12:45:59 PST)
[AMBER] Ca(2+) LJ parameters Dr. Vitaly V. Chaban (Sun Nov 13 2011 - 12:40:53 PST)
- Re: [AMBER] Ca(2+) LJ parameters case (Sun Nov 13 2011 - 17:09:14 PST)
  - Re: [AMBER] Ca(2+) LJ parameters ros (Sun Nov 13 2011 - 19:29:47 PST)
[AMBER] 16 microsecond MD run David Condon (Sun Nov 13 2011 - 15:30:45 PST)
[AMBER] MCPB settings file 刘吉元 (Sun Nov 13 2011 - 21:47:57 PST)
- Re: [AMBER] MCPB settings file Ben Roberts (Mon Nov 14 2011 - 08:12:12 PST)
  - Re: [AMBER] MCPB settings file Ben Roberts (Mon Nov 14 2011 - 15:37:05 PST)
- Re: [AMBER] MCPB settings file JiYuan Liu (Thu Nov 17 2011 - 21:59:13 PST)
  - Re: [AMBER] MCPB settings file Ben Roberts (Fri Nov 18 2011 - 09:01:38 PST)
- Re: [AMBER] MCPB settings file JiYuan Liu (Sun Nov 20 2011 - 06:38:02 PST)
  - Re: [AMBER] MCPB settings file Ben Roberts (Tue Nov 22 2011 - 20:24:01 PST)
- Re: [AMBER] MCPB settings file JiYuan Liu (Tue Nov 22 2011 - 06:58:35 PST)
[AMBER] Compiling trouble of AmberTools with intel compiler v12.1.0. K. Uebayashi (Sun Nov 13 2011 - 22:51:29 PST)
- Re: [AMBER] Compiling trouble of AmberTools with intel compiler v12.1.0. Mark Williamson (Tue Nov 15 2011 - 07:04:56 PST)
  - [AMBER] [SOLVED] Compiling trouble of AmberTools with intel compiler v12.1.0. Jose Borreguero (Tue Nov 15 2011 - 07:07:37 PST)
  - Re: [AMBER] Compiling trouble of AmberTools with intel compiler v12.1.0. K. Uebayashi (Wed Nov 16 2011 - 22:06:13 PST)
[AMBER] Pre-equilibrium of REMD simulations ÏéÇ« ¿× (Mon Nov 14 2011 - 06:15:57 PST)
- Re: [AMBER] Pre-equilibrium of REMD simulations Carlos Simmerling (Mon Nov 14 2011 - 06:17:52 PST)
[AMBER] "force field" vs. "potential" Jan-Philip Gehrcke (Mon Nov 14 2011 - 11:15:47 PST)
- Re: [AMBER] "force field" vs. "potential" Dr. Vitaly V. Chaban (Mon Nov 14 2011 - 11:19:20 PST)
- Re: [AMBER] "force field" vs. "potential" Ross Walker (Mon Nov 14 2011 - 11:24:28 PST)
  - Re: [AMBER] "force field" vs. "potential" Jan-Philip Gehrcke (Tue Nov 15 2011 - 03:43:09 PST)
    - Re: [AMBER] "force field" vs. "potential" Brian Radak (Tue Nov 15 2011 - 06:03:39 PST)
[AMBER] problems of MMPBSA.py.MPI Qinghua Liao (Mon Nov 14 2011 - 12:54:03 PST)
- Re: [AMBER] problems of MMPBSA.py.MPI Jason Swails (Mon Nov 14 2011 - 14:58:59 PST)
  - Re: [AMBER] problems of MMPBSA.py.MPI Qinghua Liao (Mon Nov 14 2011 - 23:37:34 PST)
[AMBER] QMMM SCC-DFTB: ERROR ON EWEVGE (Eigenvalue solver) Emmanuel Baribefe Naziga (Mon Nov 14 2011 - 15:39:13 PST)
- Re: [AMBER] QMMM SCC-DFTB: ERROR ON EWEVGE (Eigenvalue solver) Brian Radak (Tue Nov 15 2011 - 05:49:51 PST)
  - Re: [AMBER] QMMM SCC-DFTB: ERROR ON EWEVGE (Eigenvalue solver) Emmanuel Baribefe Naziga (Tue Nov 15 2011 - 09:01:49 PST)
    - Re: [AMBER] QMMM SCC-DFTB: ERROR ON EWEVGE (Eigenvalue solver) Adrian Roitberg (Tue Nov 15 2011 - 09:06:44 PST)
    - Re: [AMBER] QMMM SCC-DFTB: ERROR ON EWEVGE (Eigenvalue solver) Emmanuel Baribefe Naziga (Tue Nov 15 2011 - 10:12:11 PST)
    - Re: [AMBER] QMMM SCC-DFTB: ERROR ON EWEVGE (Eigenvalue solver) Brian Radak (Tue Nov 15 2011 - 10:21:36 PST)
    - Re: [AMBER] QMMM SCC-DFTB: ERROR ON EWEVGE (Eigenvalue solver) Emmanuel Baribefe Naziga (Tue Nov 15 2011 - 10:32:36 PST)
- Re: [AMBER] QMMM SCC-DFTB: ERROR ON EWEVGE (Eigenvalue solver) Gustavo Seabra (Tue Nov 15 2011 - 10:54:43 PST)
[AMBER] How MCPB add ligand with a small molecule in *_siderchain.bcl 刘吉元 (Mon Nov 14 2011 - 19:15:37 PST)
- Re: [AMBER] How MCPB add ligand with a small molecule in *_siderchain.bcl Ben Roberts (Thu Nov 17 2011 - 15:26:35 PST)
[AMBER] Building non standard DNA residue Buddhadev Maiti (Mon Nov 14 2011 - 20:36:14 PST)
- Re: [AMBER] Building non standard DNA residue FyD (Tue Nov 15 2011 - 04:06:17 PST)
[AMBER] Installing AMBER9 in SGI_ALTIX-XE1300 - need some help Vijay Manickam Achari (Tue Nov 15 2011 - 00:55:58 PST)
- Re: [AMBER] Installing AMBER9 in SGI_ALTIX-XE1300 - need some help David A Case (Tue Nov 15 2011 - 04:53:18 PST)
  - Re: [AMBER] Installing AMBER9 in SGI_ALTIX-XE1300 - need some help Vijay Manickam Achari (Wed Nov 16 2011 - 00:08:44 PST)
    - Re: [AMBER] Installing AMBER9 in SGI_ALTIX-XE1300 - need some help David A Case (Wed Nov 16 2011 - 06:19:11 PST)
[AMBER] dummny atoms in .prep file Andrew Voronkov (Tue Nov 15 2011 - 01:57:55 PST)
- Re: [AMBER] dummny atoms in .prep file Jason Swails (Wed Nov 16 2011 - 12:15:14 PST)
[AMBER] ambertools 1.5 compiling ERROR: Return type mismatch of function 'cgalf' at (1) (REAL(8)/REAL(4)) Jose Borreguero (Tue Nov 15 2011 - 05:44:22 PST)
- Re: [AMBER] ambertools 1.5 compiling ERROR: Return type mismatch of function 'cgalf' at (1) (REAL(8)/REAL(4)) David A Case (Tue Nov 15 2011 - 08:08:06 PST)
  - Re: [AMBER] ambertools 1.5 compiling ERROR: Return type mismatch of function 'cgalf' at (1) (REAL(8)/REAL(4)) Jose Borreguero (Tue Nov 15 2011 - 08:15:14 PST)
[AMBER] Minimization of only certain atoms David Condon (Tue Nov 15 2011 - 06:51:51 PST)
- Re: [AMBER] Minimization of only certain atoms Brian Radak (Tue Nov 15 2011 - 10:17:57 PST)
  - Re: [AMBER] Minimization of only certain atoms Jason Swails (Tue Nov 15 2011 - 15:55:26 PST)
    - Re: [AMBER] Minimization of only certain atoms David Condon (Wed Nov 16 2011 - 06:30:56 PST)
[AMBER] Charge method Changwoo Do (Tue Nov 15 2011 - 12:27:04 PST)
- Re: [AMBER] Charge method Dr. Vitaly V. Chaban (Tue Nov 15 2011 - 14:17:21 PST)
  - Re: [AMBER] Charge method Dr. Vitaly V. Chaban (Tue Nov 15 2011 - 14:18:55 PST)
    - Re: [AMBER] Charge method Changwoo Do (Tue Nov 15 2011 - 14:45:01 PST)
    - Re: [AMBER] Charge method Dr. Vitaly V. Chaban (Tue Nov 15 2011 - 20:30:38 PST)
[AMBER] problem in leap Qinghua Liao (Wed Nov 16 2011 - 01:16:29 PST)
- Re: [AMBER] problem in leap David A Case (Wed Nov 16 2011 - 06:26:00 PST)
  - Re: [AMBER] problem in leap Qinghua Liao (Wed Nov 16 2011 - 12:17:34 PST)
[AMBER] MMPBSA - ptraj for RMSD Fernando Blanco (Wed Nov 16 2011 - 03:05:27 PST)
- Re: [AMBER] MMPBSA - ptraj for RMSD Daniel Roe (Wed Nov 16 2011 - 05:14:59 PST)
[AMBER] mpirun leila karami (Wed Nov 16 2011 - 03:12:39 PST)
- Re: [AMBER] mpirun David A Case (Wed Nov 16 2011 - 06:28:12 PST)
[AMBER] compilation openmpi FAIL for AMBER9 Vijay Manickam Achari (Wed Nov 16 2011 - 03:36:40 PST)
[AMBER] Compilation fail of amberTools 1.2 for amber10 support Jose Borreguero (Wed Nov 16 2011 - 06:15:34 PST)
- Re: [AMBER] Compilation fail of amberTools 1.2 for amber10 support David A Case (Wed Nov 16 2011 - 06:42:45 PST)
  - [AMBER] [SOLVED] Re: Compilation fail of amberTools 1.2 for amber10 support Jose Borreguero (Wed Nov 16 2011 - 08:20:06 PST)
[AMBER] H-Bond problem najmul arfin (Wed Nov 16 2011 - 08:24:50 PST)
- Re: [AMBER] H-Bond problem David A Case (Wed Nov 16 2011 - 13:33:24 PST)
[AMBER] pulling the ligand in different directions Sai Kumar Ramadugu (Wed Nov 16 2011 - 10:09:34 PST)
[AMBER] Parameters for Ionic liquids in AMBER Ganesh Kamath (Wed Nov 16 2011 - 12:48:47 PST)
- Re: [AMBER] Parameters for Ionic liquids in AMBER Jones de Andrade (Wed Nov 16 2011 - 13:20:04 PST)
  - Re: [AMBER] Parameters for Ionic liquids in AMBER Ganesh Kamath (Wed Nov 16 2011 - 13:27:21 PST)
- Re: [AMBER] Parameters for Ionic liquids in AMBER case (Wed Nov 16 2011 - 18:53:15 PST)
[AMBER] ncsu_pmd and ncsu_smd Sai Kumar Ramadugu (Wed Nov 16 2011 - 17:26:25 PST)
- Re: [AMBER] ncsu_pmd and ncsu_smd Brian Radak (Thu Nov 17 2011 - 06:10:59 PST)
[AMBER] how to calculate interaction surface in time Tomáš Kučera (Thu Nov 17 2011 - 03:03:08 PST)
[AMBER] question to R.E.D server Urszula Uciechowska (Thu Nov 17 2011 - 05:20:26 PST)
- Re: [AMBER] question to R.E.D server intra\\sa175950 (Thu Nov 17 2011 - 07:22:38 PST)
[AMBER] Got a mistake with 3H68_OH_large.bcl 刘吉元 (Thu Nov 17 2011 - 05:54:18 PST)
- Re: [AMBER] Got a mistake with 3H68_OH_large.bcl Ben Roberts (Thu Nov 17 2011 - 15:24:18 PST)
[AMBER] Spherical Coordinates & Pulling Ligand Sai Kumar Ramadugu (Thu Nov 17 2011 - 09:09:25 PST)
[AMBER] Differentially restraining backbone and sidechain atoms from Chamber generated prmtop Joshua Adelman (Thu Nov 17 2011 - 11:09:32 PST)
- Re: [AMBER] Differentially restraining backbone and sidechain atoms from Chamber generated prmtop Mark Williamson (Fri Nov 18 2011 - 01:52:51 PST)
  - Re: [AMBER] Differentially restraining backbone and sidechain atoms from Chamber generated prmtop Joshua Adelman (Fri Nov 18 2011 - 05:46:25 PST)
    - Re: [AMBER] Differentially restraining backbone and sidechain atoms from Chamber generated prmtop Jason Swails (Fri Nov 18 2011 - 10:27:50 PST)
Re: [AMBER] large.bcl bug in MCPB Ben Roberts (Thu Nov 17 2011 - 15:19:48 PST)
[AMBER] compiling pmemd in amber9 Vijay Manickam Achari (Thu Nov 17 2011 - 17:08:00 PST)
- Re: [AMBER] compiling pmemd in amber9 David A. Case (Thu Nov 17 2011 - 19:31:45 PST)
  - Re: [AMBER] compiling pmemd in amber9 Vijay Manickam Achari (Tue Dec 06 2011 - 02:50:37 PST)
    - Re: [AMBER] compiling pmemd in amber9 David A Case (Tue Dec 06 2011 - 05:41:06 PST)
    - Re: [AMBER] compiling pmemd in amber9 Vijay Manickam Achari (Tue Dec 06 2011 - 19:22:30 PST)
    - Re: [AMBER] compiling pmemd in amber9 David A Case (Wed Dec 07 2011 - 05:39:07 PST)
- [AMBER] 2 traj approach using MMPBSA.py ? Marek Maly (Fri Nov 18 2011 - 08:34:54 PST)
  - Re: [AMBER] 2 traj approach using MMPBSA.py ? Marek Maly (Mon Nov 21 2011 - 03:04:23 PST)
- Re: [AMBER] compiling pmemd in amber9 Ross Walker (Fri Nov 18 2011 - 10:28:05 PST)
[AMBER] Select cuda ID device in PMEMD Gonzalo Jimenez (Thu Nov 17 2011 - 19:14:34 PST)
- Re: [AMBER] Select cuda ID device in PMEMD Gonzalo Jimenez (Thu Nov 17 2011 - 19:43:48 PST)
  - Re: [AMBER] Select cuda ID device in PMEMD Jason Swails (Thu Nov 17 2011 - 20:55:17 PST)
    - Re: [AMBER] Select cuda ID device in PMEMD Gonzalo Jimenez (Thu Nov 17 2011 - 21:04:26 PST)
    - Re: [AMBER] Select cuda ID device in PMEMD Ross Walker (Thu Nov 17 2011 - 21:19:22 PST)
    - Re: [AMBER] Select cuda ID device in PMEMD Gonzalo Jimenez (Thu Nov 17 2011 - 22:19:15 PST)
  - Re: [AMBER] Select cuda ID device in PMEMD Ross Walker (Thu Nov 17 2011 - 21:10:13 PST)
- Re: [AMBER] Select cuda ID device in PMEMD Gonzalo Jimenez (Thu Nov 17 2011 - 23:05:24 PST)
  - Re: [AMBER] Select cuda ID device in PMEMD Ross Walker (Fri Nov 18 2011 - 09:41:13 PST)
Re: [AMBER] How MCPB add ligand with a small molecule in*_siderchain.bcl JiYuan Liu (Thu Nov 17 2011 - 22:17:24 PST)
- Re: [AMBER] How MCPB add ligand with a small molecule in*_siderchain.bcl JiYuan Liu (Sat Nov 19 2011 - 19:55:15 PST)
  - Re: [AMBER] How MCPB add ligand with a small molecule in*_siderchain.bcl Ben Roberts (Tue Nov 22 2011 - 20:00:42 PST)
- Re: [AMBER] How MCPB add ligand with a small molecule in*_siderchain.bcl JiYuan Liu (Mon Nov 21 2011 - 05:12:52 PST)
- Re: [AMBER] How MCPB add ligand with a small molecule in*_siderchain.bcl JiYuan Liu (Mon Nov 21 2011 - 18:20:11 PST)
  - Re: [AMBER] How MCPB add ligand with a small molecule in*_siderchain.bcl Ben Roberts (Tue Nov 22 2011 - 20:06:56 PST)
- Re: [AMBER] How MCPB add ligand with a small molecule in*_siderchain.bcl JiYuan Liu (Tue Nov 22 2011 - 06:54:18 PST)
  - Re: [AMBER] How MCPB add ligand with a small molecule in*_siderchain.bcl Ben Roberts (Tue Nov 22 2011 - 20:11:02 PST)
[AMBER] Can't get the correct gaussian input name after runed *_sidechain.bcl in MCPB JiYuan Liu (Thu Nov 17 2011 - 23:12:33 PST)
- Re: [AMBER] Can't get the correct gaussian input name after runed *_sidechain.bcl in MCPB Martin Peters (Fri Nov 18 2011 - 09:15:51 PST)
[AMBER] bonds problem in leap Qinghua Liao (Fri Nov 18 2011 - 05:32:16 PST)
[AMBER] Segmentation fault - LeAP - Ring structure Volker Lesch (Fri Nov 18 2011 - 05:45:33 PST)
- Re: [AMBER] Segmentation fault - LeAP - Ring structure David A Case (Fri Nov 18 2011 - 07:55:47 PST)
- Re: [AMBER] Segmentation fault - LeAP - Ring structure Jason Swails (Fri Nov 18 2011 - 07:59:43 PST)
- Re: [AMBER] Segmentation fault - LeAP - Ring structure David A. Case (Fri Nov 18 2011 - 21:18:25 PST)
[AMBER] problems with MCBP parametrization Andrew Voronkov (Fri Nov 18 2011 - 06:57:39 PST)
- Re: [AMBER] problems with MCBP parametrization Martin Peters (Fri Nov 18 2011 - 09:20:50 PST)
  - Re: [AMBER] problems with MCBP parametrization Andrew Voronkov (Mon Nov 21 2011 - 08:07:19 PST)
- Re: [AMBER] problems with MCBP parametrization Yang, Yue (Fri Nov 18 2011 - 12:25:41 PST)
[AMBER] how to add new groups to all_amino94.in Li, Yawen (MU-Student) (Fri Nov 18 2011 - 09:20:33 PST)
- Re: [AMBER] how to add new groups to all_amino94.in FyD (Sat Nov 19 2011 - 01:37:24 PST)
- Re: [AMBER] how to add new groups to all_amino94.in Jason Swails (Sat Nov 19 2011 - 13:26:15 PST)
  - Re: [AMBER] how to add new groups to all_amino94.in FyD (Sun Nov 20 2011 - 08:02:29 PST)
    - Re: [AMBER] how to add new groups to all_amino94.in M. L. Dodson (Sun Nov 20 2011 - 08:59:20 PST)
    - Re: [AMBER] how to add new groups to all_amino94.in Jason Swails (Sun Nov 20 2011 - 10:20:03 PST)
    - Re: [AMBER] how to add new groups to all_amino94.in FyD (Mon Nov 21 2011 - 00:09:51 PST)
    - Re: [AMBER] how to add new groups to all_amino94.in M. L. Dodson (Sun Nov 20 2011 - 09:03:30 PST)
    - Re: [AMBER] how to add new groups to all_amino94.in M. L. Dodson (Sun Nov 20 2011 - 11:03:25 PST)
[AMBER] generating frcmod files Soma Ghosh (Fri Nov 18 2011 - 09:51:07 PST)
- Re: [AMBER] generating frcmod files David A. Case (Fri Nov 18 2011 - 21:11:37 PST)
[AMBER] atom type requested that does not appear in the prep file arikcohen (Fri Nov 18 2011 - 16:25:09 PST)
- Re: [AMBER] atom type requested that does not appear in the prep file Bill Ross (Fri Nov 18 2011 - 16:57:40 PST)
  - Re: [AMBER] atom type requested that does not appear in the prep file arikcohen (Fri Nov 18 2011 - 17:01:06 PST)
[AMBER] Order parameter subrata paul (Sat Nov 19 2011 - 05:48:26 PST)
- Re: [AMBER] Order parameter David A. Case (Sat Nov 19 2011 - 07:31:06 PST)
[AMBER] binding energy calculated by mm_pbsa.pl Qinghua Liao (Sun Nov 20 2011 - 00:10:18 PST)
- Re: [AMBER] binding energy calculated by mm_pbsa.pl Ray Luo, Ph.D. (Sun Nov 20 2011 - 07:00:59 PST)
  - Re: [AMBER] binding energy calculated by mm_pbsa.pl Qinghua Liao (Sun Nov 20 2011 - 07:34:32 PST)
    - Re: [AMBER] binding energy calculated by mm_pbsa.pl Ray Luo, Ph.D. (Mon Nov 21 2011 - 10:08:26 PST)
    - Re: [AMBER] binding energy calculated by mm_pbsa.pl Qinghua Liao (Mon Nov 21 2011 - 23:23:17 PST)
[AMBER] polymer blend Changwoo Do (Sun Nov 20 2011 - 09:45:07 PST)
[AMBER] how to speed up nmode calculation using MMPBSA.MPI? Josmar R. da Rocha (Sun Nov 20 2011 - 18:51:03 PST)
- Re: [AMBER] how to speed up nmode calculation using MMPBSA.MPI? Jason Swails (Sun Nov 20 2011 - 20:45:56 PST)
  - Re: [AMBER] how to speed up nmode calculation using MMPBSA.MPI? Josmar R. da Rocha (Tue Nov 22 2011 - 04:33:48 PST)
Re: [AMBER] Can't get the correct gaussian input name after runed*_sidechain.bcl in MCPB JiYuan Liu (Sun Nov 20 2011 - 20:33:30 PST)
- Re: [AMBER] Can't get the correct gaussian input name after runed*_sidechain.bcl in MCPB Martin Peters (Mon Nov 21 2011 - 00:43:24 PST)
[AMBER] dynamics of isotopically labelled proteins vaibhav dixit (Mon Nov 21 2011 - 00:27:17 PST)
- Re: [AMBER] dynamics of isotopically labelled proteins Jason Swails (Mon Nov 21 2011 - 06:00:00 PST)
  - Re: [AMBER] dynamics of isotopically labelled proteins vaibhav dixit (Mon Nov 21 2011 - 07:34:11 PST)
    - Re: [AMBER] dynamics of isotopically labelled proteins Francesco Paesani (Mon Nov 21 2011 - 08:18:57 PST)
    - Re: [AMBER] dynamics of isotopically labelled proteins vaibhav dixit (Mon Nov 21 2011 - 08:33:04 PST)
[AMBER] Stability of water force fields Bruno Rodrigues (Mon Nov 21 2011 - 04:30:21 PST)
- Re: [AMBER] Stability of water force fields David A Case (Mon Nov 21 2011 - 09:04:46 PST)
  - Re: [AMBER] Stability of water force fields Bruno Rodrigues (Mon Nov 21 2011 - 09:32:40 PST)
    - Re: [AMBER] Stability of water force fields David A Case (Tue Nov 22 2011 - 05:35:42 PST)
    - Re: [AMBER] Stability of water force fields Jiri Sponer (Tue Nov 22 2011 - 05:35:54 PST)
Re: [AMBER] Can't get the correct gaussian input name afterruned*_sidechain.bcl in MCPB JiYuan Liu (Mon Nov 21 2011 - 05:05:55 PST)
- Re: [AMBER] Can't get the correct gaussian input name afterruned*_sidechain.bcl in MCPB Ben Roberts (Tue Nov 22 2011 - 19:40:57 PST)
[AMBER] installation of amberTools on lion fails Jorgen Simonsen (Mon Nov 21 2011 - 06:47:36 PST)
- Re: [AMBER] installation of amberTools on lion fails Jason Swails (Mon Nov 21 2011 - 07:04:39 PST)
  - Re: [AMBER] installation of amberTools on lion fails Gustavo Seabra (Mon Nov 21 2011 - 07:16:01 PST)
    - Re: [AMBER] installation of amberTools on lion fails Jason Swails (Mon Nov 21 2011 - 08:07:12 PST)
    - Re: [AMBER] installation of amberTools on lion fails Gustavo Seabra (Mon Nov 21 2011 - 08:14:42 PST)
    - Re: [AMBER] installation of amberTools on lion fails Jason Swails (Mon Nov 21 2011 - 11:12:06 PST)
    - Re: [AMBER] installation of amberTools on lion fails Jorgen Simonsen (Mon Nov 21 2011 - 10:25:39 PST)
    - Re: [AMBER] installation of amberTools on lion fails Jason Swails (Mon Nov 21 2011 - 11:09:20 PST)
    - Re: [AMBER] installation of amberTools on lion fails Jorgen Simonsen (Mon Nov 21 2011 - 11:32:55 PST)
    - Re: [AMBER] installation of amberTools on lion fails Jason Swails (Mon Nov 21 2011 - 11:40:11 PST)
    - Re: [AMBER] installation of amberTools on lion fails Jorgen Simonsen (Mon Nov 21 2011 - 12:01:07 PST)
    - Re: [AMBER] installation of amberTools on lion fails Jason Swails (Mon Nov 21 2011 - 12:21:11 PST)
    - Re: [AMBER] installation of amberTools on lion fails Jorgen Simonsen (Mon Nov 21 2011 - 12:41:22 PST)
    - Re: [AMBER] installation of amberTools on lion fails Jason Swails (Mon Nov 21 2011 - 13:03:22 PST)
  - Re: [AMBER] installation of amberTools on lion fails Jorgen Simonsen (Mon Nov 21 2011 - 07:37:19 PST)
    - Re: [AMBER] installation of amberTools on lion fails Jason Swails (Mon Nov 21 2011 - 08:06:59 PST)
[AMBER] amber99sb in AMBER vs amber99sb in GROMACS or NAMD Thomas Evangelidis (Mon Nov 21 2011 - 12:00:50 PST)
- Re: [AMBER] amber99sb in AMBER vs amber99sb in GROMACS or NAMD George M Giambasu (Mon Nov 21 2011 - 12:58:59 PST)
  - Re: [AMBER] amber99sb in AMBER vs amber99sb in GROMACS or NAMD Oliver Grant (Tue Nov 22 2011 - 02:01:43 PST)
[AMBER] How to repair defect RNA residues? Crystal.CHIA-YU Ku (Mon Nov 21 2011 - 18:38:19 PST)
- Re: [AMBER] How to repair defect RNA residues? Jason Swails (Tue Nov 22 2011 - 03:53:13 PST)
  - Re: [AMBER] How to repair defect RNA residues? Crystal.CHIA-YU Ku (Tue Nov 22 2011 - 14:41:32 PST)
    - Re: [AMBER] How to repair defect RNA residues? Jason Swails (Wed Nov 23 2011 - 08:38:22 PST)
    - Re: [AMBER] How to repair defect RNA residues? Crystal.CHIA-YU Ku (Wed Nov 23 2011 - 16:05:07 PST)
    - Re: [AMBER] How to repair defect RNA residues? case (Thu Nov 24 2011 - 11:05:59 PST)
    - Re: [AMBER] How to repair defect RNA residues? Crystal.CHIA-YU Ku (Fri Dec 02 2011 - 14:25:34 PST)
[AMBER] How to use strip mask and receptor mask in the new mmpbsa.py? bin wang (Mon Nov 21 2011 - 18:40:24 PST)
- Re: [AMBER] How to use strip mask and receptor mask in the new mmpbsa.py? Jason Swails (Tue Nov 22 2011 - 04:07:03 PST)
  - Re: [AMBER] How to use strip mask and receptor mask in the new mmpbsa.py? bin wang (Tue Nov 29 2011 - 12:43:34 PST)
[AMBER] mpirun leila karami (Tue Nov 22 2011 - 01:31:27 PST)
- Re: [AMBER] mpirun Jason Swails (Tue Nov 22 2011 - 04:13:50 PST)
[AMBER] clustering analysis in ptraj takes too long time liu junjun (Tue Nov 22 2011 - 02:07:00 PST)
- Re: [AMBER] clustering analysis in ptraj takes too long time Alex Rodriguez (Tue Nov 22 2011 - 05:08:33 PST)
  - Re: [AMBER] clustering analysis in ptraj takes too long time liu junjun (Tue Nov 22 2011 - 05:49:51 PST)
  - Re: [AMBER] clustering analysis in ptraj takes too long time Daniel Roe (Tue Nov 22 2011 - 10:07:44 PST)
[AMBER] AmberTools 1.5 compilation: Error importing cpinutil.py python modules! cpinutil will not work Vlad Cojocaru (Tue Nov 22 2011 - 02:27:22 PST)
- Re: [AMBER] AmberTools 1.5 compilation: Error importing cpinutil.py python modules! cpinutil will not work Jason Swails (Tue Nov 22 2011 - 04:20:38 PST)
  - Re: [AMBER] AmberTools 1.5 compilation: Error importing cpinutil.py python modules! cpinutil will not work Vlad Cojocaru (Tue Nov 22 2011 - 06:00:02 PST)
    - Re: [AMBER] AmberTools 1.5 compilation: Error importing cpinutil.py python modules! cpinutil will not work Vlad Cojocaru (Tue Nov 22 2011 - 06:28:24 PST)
    - Re: [AMBER] AmberTools 1.5 compilation: Error importing cpinutil.py python modules! cpinutil will not work Jason Swails (Tue Nov 22 2011 - 07:27:13 PST)
    - Re: [AMBER] AmberTools 1.5 compilation: Error importing cpinutil.py python modules! cpinutil will not work Vlad Cojocaru (Tue Nov 22 2011 - 08:02:02 PST)
    - Re: [AMBER] AmberTools 1.5 compilation: Error importing cpinutil.py python modules! cpinutil will not work Jason Swails (Tue Nov 22 2011 - 10:26:35 PST)
    - Re: [AMBER] AmberTools 1.5 compilation: Error importing cpinutil.py python modules! cpinutil will not work Vlad Cojocaru (Tue Nov 22 2011 - 11:11:11 PST)
    - Re: [AMBER] AmberTools 1.5 compilation: Error importing cpinutil.py python modules! cpinutil will not work Vlad Cojocaru (Tue Nov 22 2011 - 11:16:02 PST)
  - [AMBER] Error on PCA Elisabeth Widjajakusuma (Tue Nov 22 2011 - 06:00:13 PST)
    - Re: [AMBER] Error on PCA David A Case (Tue Nov 22 2011 - 07:51:24 PST)
    - Re: [AMBER] Error on PCA Elisabeth Widjajakusuma (Tue Nov 22 2011 - 08:16:26 PST)
[AMBER] frcmod file for metal-amino acid complex Soma Ghosh (Tue Nov 22 2011 - 03:42:12 PST)
- Re: [AMBER] frcmod file for metal-amino acid complex Jason Swails (Tue Nov 22 2011 - 04:26:45 PST)
- Re: [AMBER] frcmod file for metal-amino acid complex David A Case (Tue Nov 22 2011 - 05:20:14 PST)
  - [AMBER] MCPB execution error Soma Ghosh (Sun Nov 27 2011 - 22:01:31 PST)
    - [AMBER] MCPB execution error (repeat mail) Soma Ghosh (Tue Nov 29 2011 - 06:36:45 PST)
    - Re: [AMBER] MCPB execution error Martin Peters (Thu Dec 01 2011 - 14:15:53 PST)
    - Re: [AMBER] MCPB execution error Soma Ghosh (Thu Dec 01 2011 - 22:24:29 PST)
    - Re: [AMBER] MCPB execution error Soma Ghosh (Mon Dec 05 2011 - 21:31:59 PST)
    - Re: [AMBER] MCPB execution error Ben Roberts (Tue Dec 06 2011 - 08:53:36 PST)
    - Re: [AMBER] MCPB execution error Soma Ghosh (Tue Dec 06 2011 - 22:23:31 PST)
    - Re: [AMBER] MCPB execution error Soma Ghosh (Sun Dec 11 2011 - 20:05:48 PST)
    - Re: [AMBER] MCPB execution error Ben Roberts (Sun Dec 11 2011 - 20:12:14 PST)
    - Re: [AMBER] MCPB execution error Ben Roberts (Sun Dec 11 2011 - 20:17:10 PST)
    - Re: [AMBER] MCPB execution error Soma Ghosh (Sun Dec 11 2011 - 20:54:10 PST)
    - Re: [AMBER] MCPB execution error Martin Peters (Mon Dec 12 2011 - 13:23:47 PST)
    - Re: [AMBER] MCPB execution error Soma Ghosh (Mon Dec 12 2011 - 19:30:54 PST)
[AMBER] how to obtain NOEs from MD trajectory ? Jose Borreguero (Tue Nov 22 2011 - 06:22:18 PST)
- Re: [AMBER] how to obtain NOEs from MD trajectory ? David A Case (Tue Nov 22 2011 - 07:48:22 PST)
[AMBER] makeDIST_RST error Charles Johnson (Tue Nov 22 2011 - 08:46:15 PST)
- Re: [AMBER] makeDIST_RST error David A Case (Tue Nov 22 2011 - 11:23:00 PST)
[AMBER] compilation of Amber Tools 1.5 with GCC 4.6.2 with "-nopython" Vlad Cojocaru (Tue Nov 22 2011 - 12:55:55 PST)
- Re: [AMBER] compilation of Amber Tools 1.5 with GCC 4.6.2 with "-nopython" Tyler Luchko (Tue Nov 22 2011 - 13:07:00 PST)
- Re: [AMBER] compilation of Amber Tools 1.5 with GCC 4.6.2 with "-nopython" Vlad Cojocaru (Tue Nov 22 2011 - 14:38:59 PST)
[AMBER] How to fix the installation problem of mopac Crystal.CHIA-YU Ku (Tue Nov 22 2011 - 16:53:59 PST)
- Re: [AMBER] How to fix the installation problem of mopac David A Case (Wed Nov 23 2011 - 05:05:21 PST)
  - Re: [AMBER] How to fix the installation problem of mopac Crystal.CHIA-YU Ku (Wed Nov 23 2011 - 14:38:12 PST)
    - Re: [AMBER] How to fix the installation problem of mopac case (Thu Nov 24 2011 - 07:12:41 PST)
    - Re: [AMBER] How to fix the installation problem of mopac Crystal.CHIA-YU Ku (Fri Dec 02 2011 - 14:18:13 PST)
Re: [AMBER] How MCPB add ligand with a small moleculein*_siderchain.bcl JiYuan Liu (Tue Nov 22 2011 - 20:24:26 PST)
- Re: [AMBER] How MCPB add ligand with a small moleculein*_siderchain.bcl JiYuan Liu (Wed Nov 23 2011 - 09:00:56 PST)
  - Re: [AMBER] How MCPB add ligand with a small moleculein*_siderchain.bcl Ben Roberts (Fri Nov 25 2011 - 07:24:51 PST)
[AMBER] ICST-Amber Install co nguyentruong (Wed Nov 23 2011 - 01:14:07 PST)
- Re: [AMBER] ICST-Amber Install co nguyentruong (Wed Nov 23 2011 - 01:16:18 PST)
  - Re: [AMBER] ICST-Amber Install Jason Swails (Wed Nov 23 2011 - 22:21:31 PST)
    - Re: [AMBER] ICST-Amber Install co nguyentruong (Thu Nov 24 2011 - 04:57:38 PST)
    - Re: [AMBER] ICST-Amber Install Jason Swails (Thu Nov 24 2011 - 08:45:17 PST)
    - Re: [AMBER] ICST-Amber Install co nguyentruong (Thu Nov 24 2011 - 11:31:52 PST)
[AMBER] MD of a Ca2+ dependent interaction Juan Carlos (Wed Nov 23 2011 - 04:13:55 PST)
[AMBER] parameters in mm/pbsa calculations Qinghua Liao (Wed Nov 23 2011 - 04:45:42 PST)
- Re: [AMBER] parameters in mm/pbsa calculations Bill Miller III (Wed Nov 23 2011 - 04:53:56 PST)
  - Re: [AMBER] parameters in mm/pbsa calculations Qinghua Liao (Wed Nov 23 2011 - 05:08:56 PST)
    - Re: [AMBER] parameters in mm/pbsa calculations Bill Miller III (Wed Nov 23 2011 - 05:13:21 PST)
    - Re: [AMBER] parameters in mm/pbsa calculations Qinghua Liao (Wed Nov 23 2011 - 05:57:20 PST)
    - Re: [AMBER] parameters in mm/pbsa calculations Ray Luo, Ph.D. (Wed Nov 23 2011 - 10:31:14 PST)
[AMBER] alpha helix structure consist of Alanine Tong Zhu (Wed Nov 23 2011 - 06:47:45 PST)
- Re: [AMBER] alpha helix structure consist of Alanine Carlos Simmerling (Wed Nov 23 2011 - 08:57:53 PST)
- Re: [AMBER] alpha helix structure consist of Alanine Bill Ross (Wed Nov 23 2011 - 11:11:00 PST)
[AMBER] BUG in NAB file nabgrm.y Chris Whittleston (Wed Nov 23 2011 - 08:48:49 PST)
- Re: [AMBER] BUG in NAB file nabgrm.y case (Thu Nov 24 2011 - 08:03:36 PST)
  - Re: [AMBER] BUG in NAB file nabgrm.y Chris Whittleston (Fri Nov 25 2011 - 02:48:20 PST)
[AMBER] CCYX not recognized by ff03 in tleap Raik Grünberg (Wed Nov 23 2011 - 13:13:07 PST)
- Re: [AMBER] CCYX not recognized by ff03 in tleap Jason Swails (Wed Nov 23 2011 - 13:58:20 PST)
  - Re: [AMBER] CCYX not recognized by ff03 in tleap Raik Grünberg (Wed Nov 23 2011 - 20:59:43 PST)
    - Re: [AMBER] CCYX not recognized by ff03 in tleap Jason Swails (Wed Nov 23 2011 - 21:47:58 PST)
    - Re: [AMBER] CCYX not recognized by ff03 in tleap Raik Grünberg (Thu Nov 24 2011 - 07:53:01 PST)
[AMBER] combination of CHAMBER prmtop and pmemd.cuda is causing serious instability Marc van der Kamp (Thu Nov 24 2011 - 02:10:05 PST)
- Re: [AMBER] combination of CHAMBER prmtop and pmemd.cuda is causing serious instability Marc van der Kamp (Thu Nov 24 2011 - 04:20:24 PST)
  - Re: [AMBER] combination of CHAMBER prmtop and pmemd.cuda is causing serious instability Mark Williamson (Thu Nov 24 2011 - 05:30:55 PST)
    - Re: [AMBER] combination of CHAMBER prmtop and pmemd.cuda is causing serious instability Marc van der Kamp (Thu Nov 24 2011 - 09:16:39 PST)
    - Re: [AMBER] combination of CHAMBER prmtop and pmemd.cuda is causing serious instability Marc van der Kamp (Tue Nov 29 2011 - 07:07:47 PST)
    - Re: [AMBER] combination of CHAMBER prmtop and pmemd.cuda is causing serious instability Scott Le Grand (Tue Nov 29 2011 - 09:51:36 PST)
    - Re: [AMBER] combination of CHAMBER prmtop and pmemd.cuda is causing serious instability Scott Le Grand (Tue Nov 29 2011 - 09:53:20 PST)
    - Re: [AMBER] combination of CHAMBER prmtop and pmemd.cuda is causing serious instability Ross Walker (Tue Nov 29 2011 - 10:23:55 PST)
    - Re: [AMBER] combination of CHAMBER prmtop and pmemd.cuda is causing serious instability Marc van der Kamp (Wed Nov 30 2011 - 05:36:40 PST)
    - Re: [AMBER] combination of CHAMBER prmtop and pmemd.cuda is causing serious instability Marc van der Kamp (Wed Nov 30 2011 - 09:27:00 PST)
    - Re: [AMBER] combination of CHAMBER prmtop and pmemd.cuda is causing serious instability Marc van der Kamp (Wed Nov 30 2011 - 09:51:56 PST)
    - Re: [AMBER] combination of CHAMBER prmtop and pmemd.cuda is causing serious instability Scott Le Grand (Wed Nov 30 2011 - 21:12:40 PST)
    - Re: [AMBER] combination of CHAMBER prmtop and pmemd.cuda is causing serious instability Marc van der Kamp (Thu Dec 01 2011 - 05:55:34 PST)
    - Re: [AMBER] combination of CHAMBER prmtop and pmemd.cuda is causing serious instability Ross Walker (Thu Dec 01 2011 - 09:15:12 PST)
    - Re: [AMBER] combination of CHAMBER prmtop and pmemd.cuda is causing serious instability Scott Le Grand (Thu Dec 01 2011 - 09:23:28 PST)
    - Re: [AMBER] combination of CHAMBER prmtop and pmemd.cuda is causing serious instability Marc van der Kamp (Mon Dec 19 2011 - 01:53:36 PST)
    - Re: [AMBER] combination of CHAMBER prmtop and pmemd.cuda is causing serious instability Ross Walker (Mon Dec 19 2011 - 09:31:07 PST)
    - Re: [AMBER] combination of CHAMBER prmtop and pmemd.cuda is causing serious instability Marc van der Kamp (Tue Dec 20 2011 - 02:03:05 PST)
    - Re: [AMBER] combination of CHAMBER prmtop and pmemd.cuda is causing serious instability Mark Williamson (Tue Dec 20 2011 - 02:22:59 PST)
    - Re: [AMBER] combination of CHAMBER prmtop and pmemd.cuda is causing serious instability Mark Williamson (Tue Dec 20 2011 - 04:18:22 PST)
    - [AMBER] MM_PBSA Toshifumi Yui (Tue Dec 20 2011 - 05:41:00 PST)
    - Re: [AMBER] MM_PBSA Jason Swails (Tue Dec 20 2011 - 13:21:56 PST)
    - Re: [AMBER] MM_PBSA Toshifumi Yui (Tue Dec 20 2011 - 17:31:30 PST)
    - Re: [AMBER] MM_PBSA Jason Swails (Tue Dec 20 2011 - 20:11:15 PST)
    - Re: [AMBER] MM_PBSA Toshifumi Yui (Wed Dec 21 2011 - 01:25:51 PST)
    - Re: [AMBER] combination of CHAMBER prmtop and pmemd.cuda is causing serious instability Marc van der Kamp (Tue Dec 20 2011 - 08:20:19 PST)
    - Re: [AMBER] combination of CHAMBER prmtop and pmemd.cuda is causing serious instability Mark Williamson (Tue Dec 20 2011 - 11:23:02 PST)
    - Re: [AMBER] combination of CHAMBER prmtop and pmemd.cuda is causing serious instability Marc van der Kamp (Wed Dec 21 2011 - 02:07:23 PST)
    - Re: [AMBER] combination of CHAMBER prmtop and pmemd.cuda is causing serious instability Mark Williamson (Wed Dec 21 2011 - 04:29:34 PST)
    - Re: [AMBER] combination of CHAMBER prmtop and pmemd.cuda is causing serious instability Scott Le Grand (Wed Dec 21 2011 - 07:34:26 PST)
    - Re: [AMBER] combination of CHAMBER prmtop and pmemd.cuda is causing serious instability Marc van der Kamp (Wed Jan 11 2012 - 08:53:08 PST)
    - Re: [AMBER] combination of CHAMBER prmtop and pmemd.cuda is causing serious instability Joshua Adelman (Wed Jan 11 2012 - 08:58:47 PST)
    - Re: [AMBER] combination of CHAMBER prmtop and pmemd.cuda is causing serious instability Ross Walker (Wed Jan 11 2012 - 10:42:11 PST)
    - Re: [AMBER] combination of CHAMBER prmtop and pmemd.cuda is causing serious instability Joshua Adelman (Wed Jan 11 2012 - 10:51:40 PST)
    - Re: [AMBER] combination of CHAMBER prmtop and pmemd.cuda is causing serious instability Scott Le Grand (Wed Jan 11 2012 - 16:14:21 PST)
    - Re: [AMBER] combination of CHAMBER prmtop and pmemd.cuda is causing serious instability Scott Le Grand (Wed Jan 11 2012 - 19:03:17 PST)
    - Re: [AMBER] combination of CHAMBER prmtop and pmemd.cuda is causing serious instability Scott Le Grand (Thu Jan 12 2012 - 07:47:47 PST)
    - Re: [AMBER] combination of CHAMBER prmtop and pmemd.cuda is causing serious instability Ben Roberts (Thu Jan 12 2012 - 07:53:30 PST)
    - Re: [AMBER] combination of CHAMBER prmtop and pmemd.cuda is causing serious instability Scott Le Grand (Thu Jan 12 2012 - 16:45:50 PST)
    - Re: [AMBER] combination of CHAMBER prmtop and pmemd.cuda is causing serious instability Ben Roberts (Sat Jan 21 2012 - 09:23:25 PST)
    - Re: [AMBER] combination of CHAMBER prmtop and pmemd.cuda is causing serious instability Marc van der Kamp (Thu Jan 12 2012 - 07:54:06 PST)
    - Re: [AMBER] combination of CHAMBER prmtop and pmemd.cuda is causing serious instability Marc van der Kamp (Mon Jan 23 2012 - 06:00:23 PST)
    - Re: [AMBER] combination of CHAMBER prmtop and pmemd.cuda is causing serious instability Joshua Adelman (Thu Dec 01 2011 - 06:13:55 PST)
    - Re: [AMBER] combination of CHAMBER prmtop and pmemd.cuda is causing serious instability Ross Walker (Thu Dec 01 2011 - 07:07:41 PST)
    - Re: [AMBER] combination of CHAMBER prmtop and pmemd.cuda is causing serious instability Scott Le Grand (Thu Dec 01 2011 - 08:05:13 PST)
[AMBER] Fwd: problems with MCBP parametrization Andrew Voronkov (Thu Nov 24 2011 - 12:28:16 PST)
- Re: [AMBER] Fwd: problems with MCBP parametrization Ben Roberts (Fri Nov 25 2011 - 07:21:03 PST)
[AMBER] q4md-forcefieldtools.org announcement FyD (Thu Nov 24 2011 - 12:51:26 PST)
[AMBER] General Amber FF Parameters Caglar Bayar (Thu Nov 24 2011 - 14:08:47 PST)
- Re: [AMBER] General Amber FF Parameters Bill Ross (Thu Nov 24 2011 - 14:26:23 PST)
- Re: [AMBER] General Amber FF Parameters Jason Swails (Thu Nov 24 2011 - 20:26:45 PST)
[AMBER] 2-d PMF calculation with REMD caobb0214 (Thu Nov 24 2011 - 21:12:27 PST)
- Re: [AMBER] 2-d PMF calculation with REMD Daniel Sindhikara (Thu Nov 24 2011 - 22:20:54 PST)
- Re: [AMBER] 2-d PMF calculation with REMD Yong Duan (Fri Nov 25 2011 - 10:40:07 PST)
[AMBER] Problem running Ptraj with CHARMM psf and dcd trajectory file Puspita Halder (Thu Nov 24 2011 - 22:28:07 PST)
- Re: [AMBER] Problem running Ptraj with CHARMM psf and dcd trajectory file Daniel Roe (Mon Nov 28 2011 - 08:09:26 PST)
- Re: [AMBER] Problem running Ptraj with CHARMM psf and dcd trajectory file Puspita Halder (Tue Nov 29 2011 - 21:08:36 PST)
  - Re: [AMBER] Problem running Ptraj with CHARMM psf and dcd trajectory file Daniel Roe (Thu Dec 01 2011 - 13:10:29 PST)
[AMBER] Parameters for heme C Konrad Hinsen (Fri Nov 25 2011 - 02:31:38 PST)
[AMBER] Sander kanika sharma (Fri Nov 25 2011 - 03:09:23 PST)
- Re: [AMBER] Sander case (Fri Nov 25 2011 - 05:10:36 PST)
[AMBER] MMPBSA M. Reza Ganjalikhany (Fri Nov 25 2011 - 04:47:37 PST)
- Re: [AMBER] MMPBSA Jason Swails (Fri Nov 25 2011 - 08:27:47 PST)
  - Re: [AMBER] MMPBSA M. Reza Ganjalikhany (Fri Nov 25 2011 - 12:41:08 PST)
[AMBER] question on antechamber generating parameters for a charged ligand fn1.rice.edu (Fri Nov 25 2011 - 06:17:42 PST)
- Re: [AMBER] question on antechamber generating parameters for a charged ligand Dmitry Nilov (Fri Nov 25 2011 - 06:36:26 PST)
  - Re: [AMBER] question on antechamber generating parameters for a charged ligand fn1.rice.edu (Fri Nov 25 2011 - 06:53:24 PST)
    - Re: [AMBER] question on antechamber generating parameters for a charged ligand ros (Fri Nov 25 2011 - 07:17:05 PST)
    - Re: [AMBER] question on antechamber generating parameters for a charged ligand fn1.rice.edu (Fri Nov 25 2011 - 07:25:33 PST)
    - Re: [AMBER] question on antechamber generating parameters for a charged ligand Dmitry Nilov (Fri Nov 25 2011 - 07:24:22 PST)
    - Re: [AMBER] question on antechamber generating parameters for a charged ligand fn1.rice.edu (Fri Nov 25 2011 - 07:33:12 PST)
    - Re: [AMBER] question on antechamber generating parameters for a charged ligand Dmitry Nilov (Fri Nov 25 2011 - 07:39:16 PST)
    - Re: [AMBER] question on antechamber generating parameters for a charged ligand case (Fri Nov 25 2011 - 09:14:37 PST)
    - Re: [AMBER] question on antechamber generating parameters for a charged ligand Dean Cuebas (Sat Nov 26 2011 - 14:02:16 PST)
    - Re: [AMBER] question on antechamber generating parameters for a charged ligand fn1.rice.edu (Sat Nov 26 2011 - 14:36:08 PST)
[AMBER] top2mol2 charges output in mol2 Jio M (Fri Nov 25 2011 - 08:19:32 PST)
- Re: [AMBER] top2mol2 charges output in mol2 case (Fri Nov 25 2011 - 09:27:32 PST)
  - Re: [AMBER] top2mol2 charges output in mol2 Jio M (Fri Nov 25 2011 - 11:49:30 PST)
    - [AMBER] fwd: top2mol2 charges output in mol2: no reply Jio M (Sun Nov 27 2011 - 21:58:34 PST)
    - Re: [AMBER] top2mol2 charges output in mol2 David A Case (Mon Nov 28 2011 - 06:44:42 PST)
- Re: [AMBER] top2mol2 charges output in mol2 Jio M (Tue Nov 29 2011 - 02:55:08 PST)
[AMBER] ANTECHAMBER: fatal error George Tzotzos (Sat Nov 26 2011 - 10:13:37 PST)
- Re: [AMBER] ANTECHAMBER: fatal error George Tzotzos (Sat Nov 26 2011 - 11:10:37 PST)
  - Re: [AMBER] ANTECHAMBER: fatal error Yong Duan (Sat Nov 26 2011 - 12:36:44 PST)
    - Re: [AMBER] ANTECHAMBER: fatal error George Tzotzos (Sat Nov 26 2011 - 13:51:57 PST)
- Re: [AMBER] ANTECHAMBER: fatal error David A Case (Tue Nov 29 2011 - 06:44:13 PST)
[AMBER] cutoff distance again Yun Shi (Sat Nov 26 2011 - 11:09:38 PST)
- Re: [AMBER] cutoff distance again David A Case (Mon Nov 28 2011 - 06:31:19 PST)
[AMBER] Fwd: Issue with running sander with SHAKE Andrew Voronkov (Sat Nov 26 2011 - 12:22:22 PST)
- Re: [AMBER] Fwd: Issue with running sander with SHAKE Yong Duan (Sat Nov 26 2011 - 12:28:32 PST)
  - Re: [AMBER] Fwd: Issue with running sander with SHAKE Andrew Voronkov (Sun Nov 27 2011 - 01:00:17 PST)
    - Re: [AMBER] Fwd: Issue with running sander with SHAKE Yong Duan (Sun Nov 27 2011 - 11:02:57 PST)
  - Re: [AMBER] Fwd: Issue with running sander with SHAKE Andrew Voronkov (Sun Nov 27 2011 - 11:51:25 PST)
[AMBER] Using nrespa with NPT Sasha Perkins (Sat Nov 26 2011 - 14:40:33 PST)
- Re: [AMBER] Using nrespa with NPT Jason Swails (Sun Nov 27 2011 - 02:16:18 PST)
  - Re: [AMBER] Using nrespa with NPT Sasha Perkins (Sun Nov 27 2011 - 08:58:10 PST)
Re: [AMBER] Using nrespa with NPT Bill Ross (Sat Nov 26 2011 - 14:46:45 PST)
[AMBER] running of the sander in background in parallel state leila karami (Sun Nov 27 2011 - 03:30:09 PST)
- Re: [AMBER] running of the sander in background in parallel state Ross Walker (Mon Nov 28 2011 - 10:16:48 PST)
  - Re: [AMBER] running of the sander in background in parallel state Brian Radak (Mon Nov 28 2011 - 14:26:21 PST)
[AMBER] how to prepare 4:4:1 methanol–chloroform–water mixture rameshwar prajapati (Sun Nov 27 2011 - 09:35:00 PST)
- [AMBER] R: how to prepare 4:4:1 methanol-chloroform-water mixture Giovanni Pavan (Mon Nov 28 2011 - 01:22:14 PST)
  - Re: [AMBER] R: how to prepare 4:4:1 methanol-chloroform-water mixture rameshwar prajapati (Mon Nov 28 2011 - 03:45:41 PST)
[AMBER] adding a phosphate group to a protein Petit, Chad (Sun Nov 27 2011 - 18:07:09 PST)
- Re: [AMBER] adding a phosphate group to a protein Marc van der Kamp (Mon Nov 28 2011 - 01:08:14 PST)
[AMBER] Calculation of free energy of solvation M. Reza Ganjalikhany (Sun Nov 27 2011 - 20:29:05 PST)
- Re: [AMBER] Calculation of free energy of solvation Jason Swails (Sun Nov 27 2011 - 20:52:23 PST)
[AMBER] antechamber solvent Алексей Раевский (Mon Nov 28 2011 - 02:11:05 PST)
- Re: [AMBER] antechamber solvent David A Case (Mon Nov 28 2011 - 06:38:05 PST)
  - Re: [AMBER] antechamber solvent Алексей Раевский (Mon Nov 28 2011 - 07:51:08 PST)
[AMBER] NVIDIA GPU Event at Imperial College London Gould, Ian R (Mon Nov 28 2011 - 02:59:48 PST)
Re: [AMBER] How MCPB add ligand with a smallmoleculein*_siderchain.bcl JiYuan Liu (Mon Nov 28 2011 - 04:26:24 PST)
- Re: [AMBER] How MCPB add ligand with a smallmoleculein*_siderchain.bcl Ben Roberts (Mon Nov 28 2011 - 07:57:43 PST)
[AMBER] glibc error while running Xleap Vlad Cojocaru (Mon Nov 28 2011 - 04:53:04 PST)
- Re: [AMBER] glibc error while running Xleap David A Case (Tue Nov 29 2011 - 06:48:26 PST)
  - Re: [AMBER] glibc error while running Xleap Vlad Cojocaru (Tue Nov 29 2011 - 07:03:55 PST)
    - Re: [AMBER] glibc error while running Xleap David A Case (Tue Nov 29 2011 - 08:38:25 PST)
    - Re: [AMBER] glibc error while running Xleap Vlad Cojocaru (Wed Nov 30 2011 - 01:42:56 PST)
    - Re: [AMBER] glibc error while running Xleap Vlad Cojocaru (Wed Nov 30 2011 - 02:04:42 PST)
    - Re: [AMBER] glibc error while running Xleap David A Case (Wed Nov 30 2011 - 05:13:04 PST)
    - Re: [AMBER] glibc error while running Xleap Vlad Cojocaru (Wed Nov 30 2011 - 09:17:27 PST)
[AMBER] pdb file with a covalently linked nerve agent Urszula Uciechowska (Mon Nov 28 2011 - 05:45:49 PST)
- Re: [AMBER] pdb file with a covalently linked nerve agent David A Case (Mon Nov 28 2011 - 10:04:32 PST)
[AMBER] Restarting an MD run Beale, John (Mon Nov 28 2011 - 05:56:29 PST)
- Re: [AMBER] Restarting an MD run Jason Swails (Mon Nov 28 2011 - 06:13:17 PST)
- Re: [AMBER] Restarting an MD run Carlos Simmerling (Mon Nov 28 2011 - 06:13:44 PST)
Re: [AMBER] How MCPB add ligand with asmallmoleculein*_siderchain.bcl JiYuan Liu (Mon Nov 28 2011 - 09:34:26 PST)
- Re: [AMBER] How MCPB add ligand with asmallmoleculein*_siderchain.bcl Ben Roberts (Mon Nov 28 2011 - 15:16:47 PST)
[AMBER] mdrun continuation Yao Yao (Mon Nov 28 2011 - 18:52:15 PST)
- Re: [AMBER] mdrun continuation David A Case (Tue Nov 29 2011 - 04:45:37 PST)
Re: [AMBER] How MCPB add ligand withasmallmoleculein*_siderchain.bcl JiYuan Liu (Mon Nov 28 2011 - 19:47:18 PST)
- Re: [AMBER] How MCPB add ligand withasmallmoleculein*_siderchain.bcl Ben Roberts (Tue Nov 29 2011 - 07:10:23 PST)
- Re: [AMBER] How MCPB add ligand withasmallmoleculein*_siderchain.bcl JiYuan Liu (Tue Nov 29 2011 - 09:03:42 PST)
  - Re: [AMBER] How MCPB add ligand withasmallmoleculein*_siderchain.bcl Ben Roberts (Fri Dec 02 2011 - 07:23:19 PST)
[AMBER] REMD umbrella sampling caobb0214 (Mon Nov 28 2011 - 20:13:47 PST)
- Re: [AMBER] REMD umbrella sampling Daniel Sindhikara (Tue Nov 29 2011 - 01:48:23 PST)
  - Re: [AMBER] REMD umbrella sampling Adrian Roitberg (Tue Nov 29 2011 - 04:31:05 PST)
[AMBER] atom types error Urszula Uciechowska (Mon Nov 28 2011 - 23:15:29 PST)
- Re: [AMBER] atom types error FyD (Tue Nov 29 2011 - 02:57:03 PST)
[AMBER] ptraj atomic fluctuation analysis Asmita Gupta (Tue Nov 29 2011 - 04:54:18 PST)
- Re: [AMBER] ptraj atomic fluctuation analysis Thomas Cheatham III (Tue Nov 29 2011 - 09:50:28 PST)
[AMBER] sp3d hybridization Lee Lior (Tue Nov 29 2011 - 05:21:02 PST)
- Re: [AMBER] sp3d hybridization Jason Swails (Tue Nov 29 2011 - 06:23:00 PST)
[AMBER] leap problem: TER cards disappearing thomas.fox.boehringer-ingelheim.com (Tue Nov 29 2011 - 06:33:40 PST)
- Re: [AMBER] leap problem: TER cards disappearing David A Case (Tue Nov 29 2011 - 08:59:35 PST)
[AMBER] amber - TUTORIAL A9 Atila Petrosian (Tue Nov 29 2011 - 06:56:52 PST)
- Re: [AMBER] amber - TUTORIAL A9 steinbrt.rci.rutgers.edu (Wed Nov 30 2011 - 04:29:34 PST)
  - Re: [AMBER] amber - TUTORIAL A9 Atila Petrosian (Wed Nov 30 2011 - 05:49:20 PST)
    - Re: [AMBER] amber - TUTORIAL A9 steinbrt.rci.rutgers.edu (Wed Nov 30 2011 - 08:20:53 PST)
    - Re: [AMBER] amber - TUTORIAL A9 Atila Petrosian (Sat Dec 03 2011 - 04:25:04 PST)
    - Re: [AMBER] amber - TUTORIAL A9 steinbrt.rci.rutgers.edu (Sun Dec 04 2011 - 11:54:16 PST)
[AMBER] cis conformation of amino acid Yun Shi (Tue Nov 29 2011 - 08:56:44 PST)
- Re: [AMBER] cis conformation of amino acid David A Case (Tue Nov 29 2011 - 10:15:45 PST)
[AMBER] chlorine naming question and parametrization Andrew Voronkov (Tue Nov 29 2011 - 11:53:35 PST)
- Re: [AMBER] chlorine naming question and parametrization Jason Swails (Thu Dec 01 2011 - 19:29:08 PST)
[AMBER] antechamber error kureeckal ramesh (Tue Nov 29 2011 - 22:30:14 PST)
- Re: [AMBER] antechamber error David A Case (Wed Nov 30 2011 - 05:08:22 PST)
[AMBER] error by running MMPBSa Urszula Uciechowska (Wed Nov 30 2011 - 05:16:40 PST)
- Re: [AMBER] error by running MMPBSa Jason Swails (Wed Nov 30 2011 - 05:58:23 PST)
  - Re: [AMBER] error by running MMPBSa Urszula Uciechowska (Wed Nov 30 2011 - 06:12:31 PST)
    - [AMBER] Fwd: error by running MMPBSa Ray Luo, Ph.D. (Wed Nov 30 2011 - 09:42:40 PST)
[AMBER] D-N-Sulfate-glucosamine net charge Massimiliano Porrini (Wed Nov 30 2011 - 11:23:58 PST)
- Re: [AMBER] D-N-Sulfate-glucosamine net charge Matthew Tessier (Wed Nov 30 2011 - 13:07:40 PST)
- Re: [AMBER] D-N-Sulfate-glucosamine net charge FyD (Wed Nov 30 2011 - 23:40:45 PST)
[AMBER] CUDA NaN error occuring at "wrapping first mol" Bill Sinko (Wed Nov 30 2011 - 15:54:31 PST)
- Re: [AMBER] CUDA NaN error occuring at "wrapping first mol" Ross Walker (Wed Nov 30 2011 - 17:26:29 PST)
  - Re: [AMBER] CUDA NaN error occuring at "wrapping first mol" Ross Walker (Wed Nov 30 2011 - 20:01:28 PST)
    - Re: [AMBER] CUDA NaN error occuring at "wrapping first mol" Bill Sinko (Thu Dec 01 2011 - 16:20:30 PST)
    - Re: [AMBER] CUDA NaN error occuring at "wrapping first mol" Scott Le Grand (Thu Dec 01 2011 - 16:32:09 PST)
- [AMBER] R: CUDA NaN error occuring at "wrapping first mol" Giovanni Pavan (Thu Dec 01 2011 - 01:20:08 PST)
[AMBER] Fwd: error by running MMPBSa Ray Luo, Ph.D. (Wed Nov 30 2011 - 15:59:28 PST)
- Re: [AMBER] Fwd: error by running MMPBSa Qin Cai (Wed Nov 30 2011 - 17:25:53 PST)
[AMBER] error in MD simulation kureeckal ramesh (Wed Nov 30 2011 - 19:42:29 PST)
- Re: [AMBER] error in MD simulation Ross Walker (Wed Nov 30 2011 - 20:09:25 PST)
  - Re: [AMBER] error in MD simulation kureeckal ramesh (Wed Nov 30 2011 - 21:24:53 PST)
    - Re: [AMBER] error in MD simulation Yong Duan (Wed Nov 30 2011 - 22:31:14 PST)
[AMBER] will AM1-BCC good enough for GAFF lipids? Albert (Wed Nov 30 2011 - 23:02:19 PST)
- Re: [AMBER] will AM1-BCC good enough for GAFF lipids? FyD (Thu Dec 01 2011 - 00:06:09 PST)
  - Re: [AMBER] will AM1-BCC good enough for GAFF lipids? Albert (Thu Dec 01 2011 - 00:14:26 PST)
  - Re: [AMBER] will AM1-BCC good enough for GAFF lipids? Albert (Thu Dec 01 2011 - 00:37:16 PST)
    - Re: [AMBER] will AM1-BCC good enough for GAFF lipids? FyD (Thu Dec 01 2011 - 01:01:40 PST)
  - Re: [AMBER] will AM1-BCC good enough for GAFF lipids? Albert (Thu Dec 01 2011 - 15:36:50 PST)
    - Re: [AMBER] will AM1-BCC good enough for GAFF lipids? FyD (Fri Dec 02 2011 - 00:02:10 PST)
    - Re: [AMBER] will AM1-BCC good enough for GAFF lipids? Albert (Fri Dec 02 2011 - 01:03:47 PST)
    - Re: [AMBER] will AM1-BCC good enough for GAFF lipids? Vlad Cojocaru (Fri Dec 02 2011 - 01:58:17 PST)
    - Re: [AMBER] will AM1-BCC good enough for GAFF lipids? Vlad Cojocaru (Fri Dec 02 2011 - 02:03:15 PST)
    - Re: [AMBER] will AM1-BCC good enough for GAFF lipids? Albert (Fri Dec 02 2011 - 05:43:13 PST)
[AMBER] NAB possibility for automatic creation of initial configurations of unusual DNA/RNA "duplexes" ? Marek Maly (Thu Dec 01 2011 - 02:53:53 PST)
- Re: [AMBER] NAB possibility for automatic creation of initial configurations of unusual DNA/RNA "duplexes" ? David A Case (Fri Dec 02 2011 - 04:59:32 PST)
  - Re: [AMBER] NAB possibility for automatic creation of initial configurations of unusual DNA/RNA "duplexes" ? Marek Maly (Fri Dec 02 2011 - 05:36:11 PST)
[AMBER] atom types error Urszula Uciechowska (Thu Dec 01 2011 - 03:36:06 PST)
- Re: [AMBER] atom types error FyD (Thu Dec 01 2011 - 04:20:53 PST)
  - Re: [AMBER] atom types error Urszula Uciechowska (Thu Dec 01 2011 - 05:25:32 PST)
    - Re: [AMBER] atom types error FyD (Thu Dec 01 2011 - 06:21:22 PST)
[AMBER] error in reading mol2 file by tleap kureeckal ramesh (Thu Dec 01 2011 - 20:17:18 PST)
- Re: [AMBER] error in reading mol2 file by tleap David A Case (Fri Dec 02 2011 - 05:01:31 PST)
[AMBER] single longer simulation Vs multiple shorter simulation Bala subramanian (Thu Dec 01 2011 - 23:18:38 PST)
- Re: [AMBER] single longer simulation Vs multiple shorter simulation Jason Swails (Fri Dec 02 2011 - 06:42:57 PST)
[AMBER] ptraj issues Nyla Zaman (Fri Dec 02 2011 - 00:58:17 PST)
- Re: [AMBER] ptraj issues Daniel Roe (Fri Dec 02 2011 - 06:37:28 PST)
[AMBER] charge groups of a ligand Thomas Evangelidis (Fri Dec 02 2011 - 06:44:29 PST)
- Re: [AMBER] charge groups of a ligand David A Case (Fri Dec 02 2011 - 08:24:29 PST)
  - Re: [AMBER] charge groups of a ligand Thomas Evangelidis (Fri Dec 02 2011 - 11:25:41 PST)
    - Re: [AMBER] charge groups of a ligand David A Case (Fri Dec 02 2011 - 12:52:24 PST)
[AMBER] At line 2763 of file _ew_setup.f Jorgen Simonsen (Fri Dec 02 2011 - 07:03:20 PST)
- Re: [AMBER] At line 2763 of file _ew_setup.f Jason Swails (Fri Dec 02 2011 - 07:32:20 PST)
- Re: [AMBER] At line 2763 of file _ew_setup.f Brian Radak (Fri Dec 02 2011 - 07:35:46 PST)
  - Re: [AMBER] At line 2763 of file _ew_setup.f Jason Swails (Fri Dec 02 2011 - 07:37:52 PST)
    - Re: [AMBER] At line 2763 of file _ew_setup.f Jorgen Simonsen (Fri Dec 02 2011 - 07:53:45 PST)
    - Re: [AMBER] At line 2763 of file _ew_setup.f Jason Swails (Fri Dec 02 2011 - 07:57:18 PST)
- Re: [AMBER] At line 2763 of file _ew_setup.f Bill Ross (Fri Dec 02 2011 - 15:02:34 PST)
[AMBER] Glutathione with disufide-bond german.erlenkamp.pharmazie.uni-halle.de (Fri Dec 02 2011 - 07:08:07 PST)
[AMBER] Two bugs in MCPB JiYuan Liu (Thu Dec 01 2011 - 04:45:40 PST)
- Re: [AMBER] Two bugs in MCPB JiYuan Liu (Sun Dec 04 2011 - 22:12:22 PST)
[AMBER] Hybridization Question Sasha Perkins (Fri Dec 02 2011 - 16:48:09 PST)
- Re: [AMBER] Hybridization Question case (Sat Dec 03 2011 - 06:34:17 PST)
- Re: [AMBER] Hybridization Question Bill Ross (Sat Dec 03 2011 - 12:12:34 PST)
[AMBER] amber11, AmberTools 1.5 installation problem on Suse 10 M. Shahid (Sat Dec 03 2011 - 03:43:55 PST)
- Re: [AMBER] amber11, AmberTools 1.5 installation problem on Suse 10 case (Sat Dec 03 2011 - 06:39:59 PST)
[AMBER] constant pressure kirtana S (Sat Dec 03 2011 - 11:42:44 PST)
- Re: [AMBER] constant pressure case (Sat Dec 03 2011 - 15:07:15 PST)
  - Re: [AMBER] constant pressure kirtana S (Sat Dec 03 2011 - 16:02:00 PST)
    - Re: [AMBER] constant pressure Yong Duan (Sun Dec 04 2011 - 00:42:53 PST)
    - Re: [AMBER] constant pressure kirtana S (Sun Dec 04 2011 - 10:22:49 PST)
    - Re: [AMBER] constant pressure Yong Duan (Sun Dec 04 2011 - 10:52:50 PST)
    - Re: [AMBER] constant pressure Brian Radak (Sun Dec 04 2011 - 11:14:24 PST)
    - Re: [AMBER] constant pressure kirtana S (Sun Dec 04 2011 - 11:52:54 PST)
    - Re: [AMBER] constant pressure Yong Duan (Sun Dec 04 2011 - 12:43:32 PST)
    - Re: [AMBER] constant pressure kirtana S (Sun Dec 04 2011 - 12:59:21 PST)
    - Re: [AMBER] constant pressure Yong Duan (Sun Dec 04 2011 - 13:04:16 PST)
    - Re: [AMBER] constant pressure kirtana S (Sun Dec 04 2011 - 19:27:29 PST)
    - Re: [AMBER] constant pressure Yong Duan (Sun Dec 04 2011 - 22:04:26 PST)
    - Re: [AMBER] constant pressure kirtana S (Sun Dec 04 2011 - 22:18:17 PST)
    - Re: [AMBER] constant pressure Yong Duan (Sun Dec 04 2011 - 23:14:50 PST)
    - Re: [AMBER] constant pressure David A Case (Mon Dec 05 2011 - 05:19:08 PST)
    - Re: [AMBER] constant pressure kirtana S (Mon Dec 05 2011 - 15:18:11 PST)
    - Re: [AMBER] constant pressure Yong Duan (Mon Dec 05 2011 - 21:28:17 PST)
- Re: [AMBER] constant pressure Bill Ross (Sun Dec 04 2011 - 12:02:43 PST)
  - Re: [AMBER] constant pressure kirtana S (Sun Dec 04 2011 - 12:21:13 PST)
- Re: [AMBER] constant pressure Bill Ross (Sun Dec 04 2011 - 12:36:55 PST)
  - Re: [AMBER] constant pressure kirtana S (Sun Dec 04 2011 - 12:46:04 PST)
- Re: [AMBER] constant pressure Bill Ross (Sun Dec 04 2011 - 14:10:43 PST)
- Re: [AMBER] constant pressure Bill Ross (Sun Dec 04 2011 - 14:13:04 PST)
- Re: [AMBER] constant pressure Bill Ross (Sun Dec 04 2011 - 14:31:42 PST)
- Re: [AMBER] constant pressure Bill Ross (Sun Dec 04 2011 - 20:10:05 PST)
  - Re: [AMBER] constant pressure kirtana S (Sun Dec 04 2011 - 20:28:57 PST)
- Re: [AMBER] constant pressure Bill Ross (Sun Dec 04 2011 - 21:07:14 PST)
- Re: [AMBER] constant pressure Bill Ross (Mon Dec 05 2011 - 23:46:45 PST)
[AMBER] problem setting drms to low values Attilio Vittorio Vargiu (Sat Dec 03 2011 - 23:31:53 PST)
- Re: [AMBER] problem setting drms to low values David A Case (Mon Dec 05 2011 - 05:22:30 PST)
  - Re: [AMBER] problem setting drms to low values Attilio Vittorio Vargiu (Mon Dec 05 2011 - 14:52:21 PST)
    - Re: [AMBER] problem setting drms to low values Attilio Vittorio Vargiu (Wed Dec 07 2011 - 11:15:48 PST)
    - Re: [AMBER] problem setting drms to low values Attilio Vittorio Vargiu (Thu Dec 08 2011 - 09:14:16 PST)
    - Re: [AMBER] problem setting drms to low values David A Case (Thu Dec 08 2011 - 10:41:55 PST)
    - Re: [AMBER] problem setting drms to low values Attilio Vittorio Vargiu (Thu Dec 08 2011 - 11:17:11 PST)
[AMBER] relative binding free energy - tutorial a9 leila karami (Sat Dec 03 2011 - 23:48:51 PST)
- Re: [AMBER] relative binding free energy - tutorial a9 steinbrt.rci.rutgers.edu (Sun Dec 04 2011 - 11:57:54 PST)
  - Re: [AMBER] relative binding free energy - tutorial a9 leila karami (Mon Dec 05 2011 - 01:48:08 PST)
    - Re: [AMBER] relative binding free energy - tutorial a9 steinbrt.rci.rutgers.edu (Mon Dec 05 2011 - 04:19:22 PST)
[AMBER] amber - TUTORIAL A9 Atila Petrosian (Sun Dec 04 2011 - 04:20:48 PST)
- Re: [AMBER] amber - TUTORIAL A9 steinbrt.rci.rutgers.edu (Sun Dec 04 2011 - 12:02:04 PST)
  - [AMBER] TI in Amber and the TUTORIAL A9 Marek Maly (Sun Dec 04 2011 - 15:42:49 PST)
    - Re: [AMBER] TI in Amber and the TUTORIAL A9 steinbrt.rci.rutgers.edu (Mon Dec 05 2011 - 04:05:41 PST)
    - Re: [AMBER] TI in Amber and the TUTORIAL A9 Marek Maly (Mon Dec 05 2011 - 15:38:28 PST)
    - Re: [AMBER] TI in Amber and the TUTORIAL A9 steinbrt.rci.rutgers.edu (Tue Dec 06 2011 - 01:41:53 PST)
    - Re: [AMBER] TI in Amber and the TUTORIAL A9 Marek Maly (Thu Dec 08 2011 - 13:48:18 PST)
    - Re: [AMBER] TI in Amber and the TUTORIAL A9 Marek Maly (Fri Dec 09 2011 - 10:44:21 PST)
    - Re: [AMBER] TI in Amber and the TUTORIAL A9 steinbrt.rci.rutgers.edu (Fri Dec 09 2011 - 12:27:24 PST)
    - Re: [AMBER] TI in Amber and the TUTORIAL A9 Marek Maly (Sat Dec 10 2011 - 09:04:51 PST)
[AMBER] RMSD ptaj difficulty vaibhav dixit (Sun Dec 04 2011 - 21:18:25 PST)
- Re: [AMBER] RMSD ptaj difficulty Thomas Cheatham (Sun Dec 04 2011 - 21:32:27 PST)
  - Re: [AMBER] RMSD ptaj difficulty vaibhav dixit (Sun Dec 04 2011 - 22:38:00 PST)
    - Re: [AMBER] RMSD ptaj difficulty Daniel Roe (Mon Dec 05 2011 - 07:12:37 PST)
  - Re: [AMBER] RMSD ptaj difficulty vaibhav dixit (Sun Dec 04 2011 - 22:38:47 PST)
[AMBER] Problem with running antechamber on a small molecule Devlina Chakravarty (Mon Dec 05 2011 - 02:53:36 PST)
- Re: [AMBER] Problem with running antechamber on a small molecule Ashutosh Shandilya (Mon Dec 05 2011 - 03:02:03 PST)
[AMBER] atom types for pyridine ... Urszula Uciechowska (Mon Dec 05 2011 - 03:28:09 PST)
- Re: [AMBER] atom types for pyridine ... David A Case (Mon Dec 05 2011 - 05:34:10 PST)
- Re: [AMBER] atom types for pyridine ... FyD (Mon Dec 05 2011 - 22:24:07 PST)
- Re: [AMBER] atom types for pyridine ... FyD (Mon Dec 05 2011 - 22:36:42 PST)
  - Re: [AMBER] atom types for pyridine ... Urszula Uciechowska (Tue Dec 06 2011 - 02:04:57 PST)
    - Re: [AMBER] atom types for pyridine ... FyD (Tue Dec 06 2011 - 08:30:48 PST)
[AMBER] rdf-center of mass subrata paul (Mon Dec 05 2011 - 05:45:16 PST)
[AMBER] AMBER11, pmemd.cuda: the system crashed. Chinh Su Tran To (Mon Dec 05 2011 - 19:33:22 PST)
- Re: [AMBER] AMBER11, pmemd.cuda: the system crashed. Scott Le Grand (Mon Dec 05 2011 - 20:35:41 PST)
- Re: [AMBER] AMBER11, pmemd.cuda: the system crashed. Ross Walker (Mon Dec 05 2011 - 21:01:15 PST)
  - Re: [AMBER] AMBER11, pmemd.cuda: the system crashed. Chinh Su Tran To (Mon Dec 05 2011 - 21:18:38 PST)
  - Re: [AMBER] AMBER11, pmemd.cuda: the system crashed. Chinh Su Tran To (Mon Dec 12 2011 - 20:04:10 PST)
    - Re: [AMBER] AMBER11, pmemd.cuda: the system crashed. Ross Walker (Mon Dec 12 2011 - 20:09:36 PST)
    - Re: [AMBER] AMBER11, pmemd.cuda: the system crashed. Chinh Su Tran To (Tue Dec 13 2011 - 20:03:50 PST)
    - Re: [AMBER] AMBER11, pmemd.cuda: the system crashed. Ross Walker (Wed Dec 14 2011 - 14:06:52 PST)
    - Re: [AMBER] AMBER11, pmemd.cuda: the system crashed. Chinh Su Tran To (Wed Dec 14 2011 - 19:19:46 PST)
    - Re: [AMBER] AMBER11, pmemd.cuda: the system crashed. Chinh Su Tran To (Wed Jan 11 2012 - 00:04:48 PST)
    - Re: [AMBER] AMBER11, pmemd.cuda: the system crashed. Scott Le Grand (Wed Jan 11 2012 - 08:40:03 PST)
    - Re: [AMBER] AMBER11, pmemd.cuda: the system crashed. Chinh Su Tran To (Thu Jan 12 2012 - 21:23:57 PST)
[AMBER] mmView - a tool for mmCIF exploration Daniel Svozil (Tue Dec 06 2011 - 03:32:39 PST)
[AMBER] How to turn off non-bonded interactions between non-bonded atoms? Marc van der Kamp (Tue Dec 06 2011 - 08:15:41 PST)
- Re: [AMBER] How to turn off non-bonded interactions between non-bonded atoms? Jason Swails (Tue Dec 06 2011 - 09:03:01 PST)
  - Re: [AMBER] How to turn off non-bonded interactions between non-bonded atoms? Marc van der Kamp (Tue Dec 06 2011 - 09:16:10 PST)
    - Re: [AMBER] How to turn off non-bonded interactions between non-bonded atoms? Jason Swails (Tue Dec 06 2011 - 11:50:56 PST)
    - Re: [AMBER] How to turn off non-bonded interactions between non-bonded atoms? Marc van der Kamp (Tue Dec 06 2011 - 12:35:04 PST)
    - Re: [AMBER] How to turn off non-bonded interactions between non-bonded atoms? Jason Swails (Tue Dec 06 2011 - 17:07:23 PST)
    - Re: [AMBER] How to turn off non-bonded interactions between non-bonded atoms? Marc van der Kamp (Wed Dec 07 2011 - 02:15:26 PST)
    - Re: [AMBER] How to turn off non-bonded interactions between non-bonded atoms? Jason Swails (Wed Dec 07 2011 - 05:42:42 PST)
    - Re: [AMBER] How to turn off non-bonded interactions between non-bonded atoms? David A Case (Thu Dec 08 2011 - 04:53:17 PST)
    - Re: [AMBER] How to turn off non-bonded interactions between non-bonded atoms? Marc van der Kamp (Thu Dec 08 2011 - 06:43:28 PST)
    - Re: [AMBER] How to turn off non-bonded interactions between non-bonded atoms? Ross Walker (Thu Dec 08 2011 - 08:59:14 PST)
    - Re: [AMBER] How to turn off non-bonded interactions between non-bonded atoms? Marc van der Kamp (Thu Dec 08 2011 - 09:48:13 PST)
    - Re: [AMBER] How to turn off non-bonded interactions between non-bonded atoms? Yong Duan (Thu Dec 08 2011 - 14:48:40 PST)
Re: [AMBER] atom types for pyridine II... FyD (Tue Dec 06 2011 - 08:37:04 PST)
- Re: [AMBER] atom types for pyridine II... Urszula Uciechowska (Wed Dec 07 2011 - 01:46:06 PST)
  - Re: [AMBER] atom types for pyridine II... FyD (Wed Dec 07 2011 - 06:23:34 PST)
[AMBER] Doubt in atomicfluct usage Asmita Gupta (Tue Dec 06 2011 - 09:50:50 PST)
[AMBER] Minimization and Heating error kirtana S (Tue Dec 06 2011 - 09:50:57 PST)
- Re: [AMBER] Minimization and Heating error Yong Duan (Tue Dec 06 2011 - 11:04:46 PST)
  - Re: [AMBER] Minimization and Heating error kirtana S (Tue Dec 06 2011 - 11:27:02 PST)
    - Re: [AMBER] Minimization and Heating error Yong Duan (Tue Dec 06 2011 - 11:56:14 PST)
    - Re: [AMBER] Minimization and Heating error kirtana S (Tue Dec 06 2011 - 12:06:44 PST)
- Re: [AMBER] Minimization and Heating error Sangita Kachhap (Wed Dec 07 2011 - 00:13:52 PST)
  - Re: [AMBER] Minimization and Heating error kirtana S (Wed Dec 07 2011 - 12:32:31 PST)
- Re: [AMBER] Minimization and Heating error Bill Ross (Wed Dec 07 2011 - 15:19:53 PST)
  - Re: [AMBER] Minimization and Heating error kirtana S (Wed Dec 07 2011 - 15:45:21 PST)
- Re: [AMBER] Minimization and Heating error Bill Ross (Wed Dec 07 2011 - 17:37:49 PST)
[AMBER] Doubt in atomicfluct usage Asmita Gupta (Tue Dec 06 2011 - 09:57:56 PST)
[AMBER] Adaptively Biased Molecular Dynamics Aron Broom (Tue Dec 06 2011 - 15:39:31 PST)
- Re: [AMBER] Adaptively Biased Molecular Dynamics case (Tue Dec 06 2011 - 17:51:42 PST)
  - Re: [AMBER] Adaptively Biased Molecular Dynamics Aron Broom (Tue Dec 06 2011 - 17:58:59 PST)
[AMBER] which force field to choose for implicit solvent simulation? Jose Borreguero (Wed Dec 07 2011 - 08:43:13 PST)
- Re: [AMBER] which force field to choose for implicit solvent simulation? Carlos Simmerling (Wed Dec 07 2011 - 10:17:23 PST)
  - Re: [AMBER] which force field to choose for implicit solvent simulation? Jose Borreguero (Wed Dec 07 2011 - 11:12:29 PST)
  - Re: [AMBER] which force field to choose for implicit solvent simulation? David A Case (Thu Dec 08 2011 - 05:00:07 PST)
    - Re: [AMBER] which force field to choose for implicit solvent simulation? Carlos Simmerling (Thu Dec 08 2011 - 05:11:54 PST)
[AMBER] Has charged system correction term been implemented in PME? Surya Prakash Tiwari (Wed Dec 07 2011 - 20:16:16 PST)
- Re: [AMBER] Has charged system correction term been implemented in PME? David A Case (Thu Dec 08 2011 - 05:57:13 PST)
[AMBER] AMBER GPU event in London 14th of December Cancellation Gould, Ian R (Thu Dec 08 2011 - 08:07:02 PST)
[AMBER] Order of ff99SB and GLYCAM when using xleap Sai Kumar Ramadugu (Thu Dec 08 2011 - 09:07:19 PST)
- Re: [AMBER] Order of ff99SB and GLYCAM when using xleap Lachele Foley (Lists) (Thu Dec 08 2011 - 09:22:38 PST)
  - Re: [AMBER] Order of ff99SB and GLYCAM when using xleap Sai Kumar Ramadugu (Thu Dec 08 2011 - 11:59:27 PST)
    - Re: [AMBER] Order of ff99SB and GLYCAM when using xleap Aron Broom (Thu Dec 08 2011 - 12:29:39 PST)
    - Re: [AMBER] Order of ff99SB and GLYCAM when using xleap Sai Kumar Ramadugu (Thu Dec 08 2011 - 16:46:31 PST)
    - Re: [AMBER] Order of ff99SB and GLYCAM when using xleap Lachele Foley (Lists) (Thu Dec 08 2011 - 17:27:49 PST)
    - Re: [AMBER] Order of ff99SB and GLYCAM when using xleap Lachele Foley (Lists) (Thu Dec 15 2011 - 10:04:28 PST)
[AMBER] FATAL: Could not read velocities from step3.crd Urszula Uciechowska (Fri Dec 09 2011 - 01:54:11 PST)
- [AMBER] assigning a primed atom Toshifumi Yui (Fri Dec 09 2011 - 02:27:47 PST)
  - Re: [AMBER] assigning a primed atom Daniel Roe (Fri Dec 09 2011 - 04:33:28 PST)
  - Re: [AMBER] assigning a primed atom Thomas Cheatham (Sat Dec 10 2011 - 11:04:40 PST)
- Re: [AMBER] FATAL: Could not read velocities from step3.crd David A Case (Fri Dec 09 2011 - 07:38:03 PST)
- Re: [AMBER] FATAL: Could not read velocities from step3.crd Bill Ross (Fri Dec 09 2011 - 12:02:25 PST)
[AMBER] Amber11 compile yukio (Fri Dec 09 2011 - 02:55:33 PST)
- Re: [AMBER] Amber11 compile Daniel Roe (Fri Dec 09 2011 - 04:36:19 PST)
  - Re: [AMBER] Amber11 compile yukio (Fri Dec 09 2011 - 06:42:52 PST)
[AMBER] problems with getting right parameters ... Urszula Uciechowska (Fri Dec 09 2011 - 03:58:59 PST)
- Re: [AMBER] problems with getting right parameters ... FyD (Fri Dec 09 2011 - 05:11:05 PST)
[AMBER] single -step transformation TI calculation Victor Ma (Fri Dec 09 2011 - 12:19:01 PST)
- Re: [AMBER] single -step transformation TI calculation steinbrt.rci.rutgers.edu (Fri Dec 09 2011 - 12:37:08 PST)
  - Re: [AMBER] single -step transformation TI calculation Victor Ma (Fri Dec 09 2011 - 13:18:22 PST)
    - Re: [AMBER] single -step transformation TI calculation steinbrt.rci.rutgers.edu (Sat Dec 10 2011 - 03:14:50 PST)
    - Re: [AMBER] single -step transformation TI calculation Victor Ma (Sun Dec 11 2011 - 09:07:41 PST)
    - Re: [AMBER] single -step transformation TI calculation Victor Ma (Fri Dec 16 2011 - 09:23:30 PST)
    - Re: [AMBER] single -step transformation TI calculation steinbrt.rci.rutgers.edu (Fri Dec 16 2011 - 09:44:13 PST)
    - Re: [AMBER] single -step transformation TI calculation Victor Ma (Fri Dec 16 2011 - 14:43:31 PST)
    - Re: [AMBER] single -step transformation TI calculation steinbrt.rci.rutgers.edu (Sat Dec 17 2011 - 02:46:21 PST)
[AMBER] ATTN GLYCAM users: CY atom type work around Jodi Ann Hadden (Fri Dec 09 2011 - 16:50:07 PST)
- Re: [AMBER] ATTN GLYCAM users: CY atom type work around Aron Broom (Fri Dec 09 2011 - 17:26:15 PST)
  - Re: [AMBER] ATTN GLYCAM users: CY atom type work around Lachele Foley (Lists) (Fri Dec 09 2011 - 17:28:48 PST)
    - Re: [AMBER] ATTN GLYCAM users: CY atom type work around Aron Broom (Fri Dec 09 2011 - 17:34:38 PST)
    - Re: [AMBER] ATTN GLYCAM users: CY atom type work around Lachele Foley (Lists) (Fri Dec 09 2011 - 17:41:50 PST)
- Re: [AMBER] ATTN GLYCAM users: CY atom type work around Lachele Foley (Lists) (Thu Dec 15 2011 - 07:29:43 PST)
[AMBER] Problem with GDP parameters generation neeru sharma (Sat Dec 10 2011 - 01:33:44 PST)
- Re: [AMBER] Problem with GDP parameters generation Marc van der Kamp (Sat Dec 10 2011 - 03:08:40 PST)
  - Re: [AMBER] Problem with GDP parameters generation Marc van der Kamp (Sat Dec 10 2011 - 03:10:48 PST)
    - Re: [AMBER] Problem with GDP parameters generation neeru sharma (Sat Dec 10 2011 - 05:53:05 PST)
- Re: [AMBER] Problem with GDP parameters generation case (Sat Dec 10 2011 - 06:33:12 PST)
  - Re: [AMBER] Problem with GDP parameters generation neeru sharma (Sat Dec 10 2011 - 06:51:48 PST)
    - Re: [AMBER] Problem with GDP parameters generation David A Case (Mon Dec 12 2011 - 05:52:51 PST)
    - Re: [AMBER] Problem with GDP parameters generation neeru sharma (Mon Dec 12 2011 - 07:14:44 PST)
- Re: [AMBER] Problem with GDP parameters generation FyD (Sun Dec 11 2011 - 11:09:42 PST)
[AMBER] Need GDP parameters for ff03 neeru sharma (Sun Dec 11 2011 - 05:35:15 PST)
- Re: [AMBER] Need GDP parameters for ff03 Carlos Simmerling (Sun Dec 11 2011 - 05:43:11 PST)
  - Re: [AMBER] Need GDP parameters for ff03 neeru sharma (Sun Dec 11 2011 - 05:47:21 PST)
    - Re: [AMBER] Need GDP parameters for ff03 Jason Swails (Sun Dec 11 2011 - 06:39:27 PST)
    - Re: [AMBER] Need GDP parameters for ff03 neeru sharma (Sun Dec 11 2011 - 08:39:50 PST)
- Re: [AMBER] Need GDP parameters for ff03 FyD (Sun Dec 11 2011 - 11:24:24 PST)
  - Re: [AMBER] Need GDP parameters for ff03 neeru sharma (Sun Dec 11 2011 - 19:37:32 PST)
    - Re: [AMBER] Need GDP parameters for ff03 FyD (Mon Dec 12 2011 - 01:58:52 PST)
    - Re: [AMBER] Need GDP parameters for ff03 neeru sharma (Mon Dec 12 2011 - 02:14:59 PST)
[AMBER] Force field Siti Mohamad (Sun Dec 11 2011 - 22:57:51 PST)
- Re: [AMBER] Force field Aron Broom (Sun Dec 11 2011 - 23:23:07 PST)
[AMBER] how many cores should be used in MMPBSA.py.MPI calculations at most Qinghua Liao (Mon Dec 12 2011 - 01:31:26 PST)
- Re: [AMBER] how many cores should be used in MMPBSA.py.MPI calculations at most Bill Miller III (Mon Dec 12 2011 - 04:36:03 PST)
  - Re: [AMBER] how many cores should be used in MMPBSA.py.MPI calculations at most Qinghua Liao (Mon Dec 12 2011 - 04:42:06 PST)
[AMBER] MD stopped for unknown reason in the TI soft core potential run with solvateCap solvation option Ying-Chieh Sun (Mon Dec 12 2011 - 02:13:13 PST)
[AMBER] Units/Typos in MDL file format Daniel Sindhikara (Mon Dec 12 2011 - 03:49:53 PST)
- Re: [AMBER] Units/Typos in MDL file format Tyler Luchko (Tue Dec 13 2011 - 14:23:40 PST)
[AMBER] gaff+charmm36 in amber vs namd Jio M (Mon Dec 12 2011 - 04:07:26 PST)
[AMBER] parameters in mm/pbsa calculations using python and perl versions Qinghua Liao (Mon Dec 12 2011 - 06:00:14 PST)
- Re: [AMBER] parameters in mm/pbsa calculations using python and perl versions Jason Swails (Mon Dec 12 2011 - 13:21:54 PST)
  - Re: [AMBER] parameters in mm/pbsa calculations using python and perl versions Qinghua Liao (Mon Dec 12 2011 - 23:43:26 PST)
[AMBER] CUDA PMEMD on Longhorn: MPI_Win_free fatal error Ben Roberts (Mon Dec 12 2011 - 10:00:36 PST)
- Re: [AMBER] CUDA PMEMD on Longhorn: MPI_Win_free fatal error Scott Le Grand (Mon Dec 12 2011 - 10:25:09 PST)
- Re: [AMBER] CUDA PMEMD on Longhorn: MPI_Win_free fatal error Ross Walker (Mon Dec 12 2011 - 10:51:03 PST)
  - Re: [AMBER] CUDA PMEMD on Longhorn: MPI_Win_free fatal error Ben Roberts (Mon Dec 12 2011 - 13:19:14 PST)
    - Re: [AMBER] CUDA PMEMD on Longhorn: MPI_Win_free fatal error Ben Roberts (Fri Dec 30 2011 - 16:08:40 PST)
    - Re: [AMBER] CUDA PMEMD on Longhorn: MPI_Win_free fatal error Ben Roberts (Fri Dec 30 2011 - 16:14:02 PST)
    - Re: [AMBER] CUDA PMEMD on Longhorn: MPI_Win_free fatal error Ross Walker (Fri Dec 30 2011 - 17:01:50 PST)
    - Re: [AMBER] CUDA PMEMD on Longhorn: MPI_Win_free fatal error Ben Roberts (Fri Dec 30 2011 - 17:16:10 PST)
    - Re: [AMBER] CUDA PMEMD on Longhorn: MPI_Win_free fatal error Ben Roberts (Tue Jan 03 2012 - 13:10:29 PST)
    - Re: [AMBER] CUDA PMEMD on Longhorn: MPI_Win_free fatal error Ross Walker (Tue Jan 03 2012 - 13:18:59 PST)
    - Re: [AMBER] CUDA PMEMD on Longhorn: MPI_Win_free fatal error Ben Roberts (Tue Jan 03 2012 - 16:24:18 PST)
[AMBER] 2D RMS David Condon (Mon Dec 12 2011 - 15:52:57 PST)
- Re: [AMBER] 2D RMS Thomas Cheatham III (Mon Dec 12 2011 - 16:23:05 PST)
- Re: [AMBER] 2D RMS Ilyas Yildirim (Mon Dec 12 2011 - 16:35:10 PST)
  - Re: [AMBER] 2D RMS David Condon (Tue Dec 13 2011 - 07:47:49 PST)
[AMBER] removing few side waters (thin layer) in membranes Jio M (Tue Dec 13 2011 - 03:58:22 PST)
[AMBER] vlimit exceeded issue Xiaozhou Li (Tue Dec 13 2011 - 06:23:31 PST)
- Re: [AMBER] vlimit exceeded issue Brian Radak (Tue Dec 13 2011 - 07:04:20 PST)
  - Re: [AMBER] vlimit exceeded issue Xiaozhou Li (Tue Dec 13 2011 - 07:41:06 PST)
    - Re: [AMBER] vlimit exceeded issue Ismail, Mohd F. (Tue Dec 13 2011 - 07:53:33 PST)
    - Re: [AMBER] vlimit exceeded issue Aron Broom (Tue Dec 13 2011 - 07:56:35 PST)
    - Re: [AMBER] vlimit exceeded issue Xiaozhou Li (Tue Dec 13 2011 - 08:43:14 PST)
    - Re: [AMBER] vlimit exceeded issue Aron Broom (Tue Dec 13 2011 - 09:13:39 PST)
    - Re: [AMBER] vlimit exceeded issue Xiaozhou Li (Fri Dec 16 2011 - 02:46:22 PST)
- Re: [AMBER] vlimit exceeded issue David A Case (Tue Dec 13 2011 - 08:32:17 PST)
Re: [AMBER] Meeting Request from BSM (Agenda: Risk Free & Cost Effective IT Solutions & Staff Augmentation) Justin L. Elliott | BSM (Tue Dec 13 2011 - 08:51:52 PST)
[AMBER] The charge is wrong when the ligand together with the large model in MCPB JiYuan Liu (Mon Dec 12 2011 - 22:51:12 PST)
- Re: [AMBER] The charge is wrong when the ligand together with the large model in MCPB Ben Roberts (Wed Dec 14 2011 - 12:48:38 PST)
[AMBER] Generation of .mol2 file Chidambar Kulkarni (Wed Dec 14 2011 - 10:13:18 PST)
- Re: [AMBER] Generation of .mol2 file David A Case (Wed Dec 14 2011 - 11:13:15 PST)
  - Re: [AMBER] Generation of .mol2 file Chidambar Kulkarni (Wed Dec 14 2011 - 11:34:27 PST)
[AMBER] problems of simulation using pmemd Qinghua Liao (Wed Dec 14 2011 - 13:31:48 PST)
- Re: [AMBER] problems of simulation using pmemd Jason Swails (Wed Dec 14 2011 - 13:55:42 PST)
  - Re: [AMBER] problems of simulation using pmemd Qinghua Liao (Thu Dec 15 2011 - 00:16:24 PST)
[AMBER] AMBER GPU jobs Neha Gandhi (Wed Dec 14 2011 - 18:59:17 PST)
- Re: [AMBER] AMBER GPU jobs Ross Walker (Wed Dec 14 2011 - 21:37:54 PST)
[AMBER] TI + solvateCap work in Amber11? Ying-Chieh Sun (Wed Dec 14 2011 - 20:42:45 PST)
[AMBER] MMPBSA.py Rajesh Singh (Wed Dec 14 2011 - 22:42:04 PST)
[AMBER] : Error in MMPBSA Rajesh Singh (Wed Dec 14 2011 - 23:00:08 PST)
- Re: [AMBER] : Error in MMPBSA Jason Swails (Thu Dec 15 2011 - 04:44:44 PST)
[AMBER] Regarding low %CPU efficiency while running production MD abinayar.imsc.res.in (Thu Dec 15 2011 - 03:57:42 PST)
- Re: [AMBER] Regarding low %CPU efficiency while running production MD Jason Swails (Thu Dec 15 2011 - 04:32:24 PST)
  - Re: [AMBER] Regarding low %CPU efficiency while running production MD abinayar.imsc.res.in (Thu Dec 15 2011 - 04:57:09 PST)
    - Re: [AMBER] Regarding low %CPU efficiency while running production MD Jason Swails (Thu Dec 15 2011 - 06:32:32 PST)
    - Re: [AMBER] Regarding low %CPU efficiency while running production MD abinayar.imsc.res.in (Thu Dec 15 2011 - 20:40:23 PST)
    - Re: [AMBER] Regarding low %CPU efficiency while running production MD abinayar.imsc.res.in (Sat Dec 17 2011 - 02:13:37 PST)
    - Re: [AMBER] Regarding low %CPU efficiency while running production MD case (Sat Dec 17 2011 - 07:15:18 PST)
[AMBER] MTK++ and MCPB patch released Ben Roberts (Thu Dec 15 2011 - 07:08:33 PST)
- Re: [AMBER] MTK++ and MCPB patch released JiYuan Liu (Mon Dec 19 2011 - 18:37:27 PST)
  - Re: [AMBER] MTK++ and MCPB patch released Martin Peters (Tue Dec 20 2011 - 01:08:16 PST)
    - Re: [AMBER] MTK++ and MCPB patch released JiYuan Liu (Tue Dec 20 2011 - 05:04:37 PST)
    - Re: [AMBER] MTK++ and MCPB patch released Martin Peters (Tue Dec 20 2011 - 05:31:27 PST)
    - Re: [AMBER] MTK++ and MCPB patch released JiYuan Liu (Tue Dec 20 2011 - 18:24:32 PST)
    - Re: [AMBER] MTK++ and MCPB patch released Martin Peters (Thu Dec 22 2011 - 02:38:06 PST)
    - Re: [AMBER] MTK++ and MCPB patch released JiYuan Liu (Thu Dec 22 2011 - 04:41:45 PST)
    - Re: [AMBER] MTK++ and MCPB patch released Martin Peters (Thu Dec 22 2011 - 05:08:19 PST)
    - Re: [AMBER] MTK++ and MCPB patch released JiYuan Liu (Thu Dec 22 2011 - 06:06:19 PST)
    - Re: [AMBER] MTK++ and MCPB patch released Martin Peters (Thu Dec 22 2011 - 07:54:20 PST)
    - Re: [AMBER] MTK++ and MCPB patch released JiYuan Liu (Sat Dec 24 2011 - 02:58:03 PST)
    - Re: [AMBER] MTK++ and MCPB patch released Ben Roberts (Sat Dec 24 2011 - 08:20:23 PST)
    - Re: [AMBER] MTK++ and MCPB patch released JiYuan Liu (Tue Dec 27 2011 - 20:35:15 PST)
[AMBER] problems of mm/pbsa calculations Qinghua Liao (Thu Dec 15 2011 - 08:21:02 PST)
- Re: [AMBER] problems of mm/pbsa calculations Jason Swails (Thu Dec 15 2011 - 10:50:53 PST)
  - Re: [AMBER] problems of mm/pbsa calculations Qinghua Liao (Thu Dec 15 2011 - 12:44:02 PST)
    - Re: [AMBER] problems of mm/pbsa calculations Jason Swails (Thu Dec 15 2011 - 13:30:22 PST)
    - Re: [AMBER] problems of mm/pbsa calculations Qinghua Liao (Thu Dec 15 2011 - 22:56:14 PST)
    - Re: [AMBER] problems of mm/pbsa calculations Jason Swails (Fri Dec 16 2011 - 05:57:52 PST)
[AMBER] What's the combine rules for OPLS force field in AMBER? Guoxiong Su (Thu Dec 15 2011 - 09:08:09 PST)
- Re: [AMBER] What's the combine rules for OPLS force field in AMBER? Bill Ross (Thu Dec 15 2011 - 13:48:27 PST)
  - Re: [AMBER] What's the combine rules for OPLS force field in AMBER? Guoxiong Su (Thu Dec 15 2011 - 14:13:49 PST)
- Re: [AMBER] What's the combine rules for OPLS force field in AMBER? Bill Ross (Thu Dec 15 2011 - 17:55:08 PST)
- Re: [AMBER] What's the combine rules for OPLS force field in AMBER? case (Thu Dec 15 2011 - 19:43:02 PST)
[AMBER] MMPBSA tutorial question Dario Mizraji (Thu Dec 15 2011 - 23:14:28 PST)
[AMBER] sourcing solvents.cmd quits xleap/tleap Jio M (Thu Dec 15 2011 - 23:24:59 PST)
- Re: [AMBER] sourcing solvents.cmd quits xleap/tleap case (Fri Dec 16 2011 - 05:07:35 PST)
  - Re: [AMBER] sourcing solvents.cmd quits xleap/tleap Jio M (Fri Dec 16 2011 - 05:28:19 PST)
[AMBER] segmentation fault using GPUs Ouaray Z. (Fri Dec 16 2011 - 03:38:36 PST)
- Re: [AMBER] segmentation fault using GPUs Marc van der Kamp (Fri Dec 16 2011 - 04:10:22 PST)
[AMBER] Measuring the distance in Amber 11 Esam Tolba (Fri Dec 16 2011 - 05:43:14 PST)
- Re: [AMBER] Measuring the distance in Amber 11 Daniel Roe (Fri Dec 16 2011 - 06:52:49 PST)
  - Re: [AMBER] Measuring the distance in Amber 11 Esam Tolba (Fri Dec 16 2011 - 07:41:07 PST)
[AMBER] Change center of water box Ngo Son Tung (Fri Dec 16 2011 - 07:11:32 PST)
[AMBER] Sander.MPI speed vs cpu x node Changwoo Do (Fri Dec 16 2011 - 08:58:23 PST)
- Re: [AMBER] Sander.MPI speed vs cpu x node Aron Broom (Fri Dec 16 2011 - 09:08:05 PST)
- Re: [AMBER] Sander.MPI speed vs cpu x node Andrew Petersen (Fri Dec 16 2011 - 09:28:42 PST)
- Re: [AMBER] Sander.MPI speed vs cpu x node Jason Swails (Fri Dec 16 2011 - 09:48:31 PST)
  - Re: [AMBER] Sander.MPI speed vs cpu x node Changwoo Do (Fri Dec 16 2011 - 12:31:26 PST)
[AMBER] Non-standard Serine Residue Chris Bryant (Fri Dec 16 2011 - 12:59:45 PST)
- Re: [AMBER] Non-standard Serine Residue case (Fri Dec 16 2011 - 18:22:00 PST)
  - Re: [AMBER] Non-standard Serine Residue Chris Bryant (Sat Dec 17 2011 - 07:48:20 PST)
- Re: [AMBER] Non-standard Serine Residue FyD (Sun Dec 18 2011 - 06:53:45 PST)
[AMBER] big difference of binding energy generated by python and perl mm/pbsa respectively Qinghua Liao (Fri Dec 16 2011 - 14:21:02 PST)
- Re: [AMBER] big difference of binding energy generated by python and perl mm/pbsa respectively Ngo Son Tung (Fri Dec 16 2011 - 15:09:47 PST)
  - Re: [AMBER] big difference of binding energy generated by python and perl mm/pbsa respectively Qinghua Liao (Sat Dec 17 2011 - 14:43:36 PST)
- Re: [AMBER] big difference of binding energy generated by python and perl mm/pbsa respectively Jason Swails (Sat Dec 17 2011 - 15:32:17 PST)
  - Re: [AMBER] big difference of binding energy generated by python and perl mm/pbsa respectively Qinghua Liao (Tue Dec 20 2011 - 01:49:33 PST)
[AMBER] how to build Polyethylene terephthalate (PET) surface? Albert (Fri Dec 16 2011 - 16:47:49 PST)
[AMBER] Strange keyword generated by antechamber to cause fail when use mopac Crystal.CHIA-YU Ku (Fri Dec 16 2011 - 16:59:37 PST)
- Re: [AMBER] Strange keyword generated by antechamber to cause fail when use mopac case (Fri Dec 16 2011 - 18:26:00 PST)
  - Re: [AMBER] Strange keyword generated by antechamber to cause fail when use mopac Crystal.CHIA-YU Ku (Thu Dec 22 2011 - 14:32:19 PST)
[AMBER] MMTSB fatahiya (Sat Dec 17 2011 - 01:09:41 PST)
- Re: [AMBER] MMTSB case (Sat Dec 17 2011 - 07:04:44 PST)
[AMBER] installation problem of amber9 in ubuntu 10.04 Madhurima Jana (Sat Dec 17 2011 - 02:09:42 PST)
- Re: [AMBER] installation problem of amber9 in ubuntu 10.04 case (Sat Dec 17 2011 - 07:10:25 PST)
[AMBER] Amber 11 error Esam Tolba (Sat Dec 17 2011 - 11:16:54 PST)
- Re: [AMBER] Amber 11 error Bill Ross (Sat Dec 17 2011 - 11:45:03 PST)
  - Re: [AMBER] Amber 11 error Esam Tolba (Sat Dec 17 2011 - 13:35:52 PST)
[AMBER] RMSD value Esam Tolba (Sat Dec 17 2011 - 13:40:50 PST)
- Re: [AMBER] RMSD value Daniel Roe (Sun Dec 18 2011 - 06:27:03 PST)
  - Re: [AMBER] RMSD value Esam Tolba (Sun Dec 18 2011 - 08:42:40 PST)
    - Re: [AMBER] RMSD value Jason Swails (Mon Dec 19 2011 - 07:29:52 PST)
[AMBER] error in measuring distances in amber 11 Esam Tolba (Sun Dec 18 2011 - 08:46:09 PST)
- Re: [AMBER] error in measuring distances in amber 11 Jason Swails (Mon Dec 19 2011 - 07:34:28 PST)
- Re: [AMBER] error in measuring distances in amber 11 Thomas Cheatham (Mon Dec 19 2011 - 08:16:37 PST)
[AMBER] RMDS vs. time problem vaibhav dixit (Sun Dec 18 2011 - 23:07:35 PST)
- Re: [AMBER] RMDS vs. time problem Sangita Kachhap (Mon Dec 19 2011 - 03:42:31 PST)
  - Re: [AMBER] RMDS vs. time problem vaibhav dixit (Mon Dec 19 2011 - 05:19:48 PST)
[AMBER] Phosphotyrosine connectivity problem Sangeetha B (Mon Dec 19 2011 - 00:41:42 PST)
- Re: [AMBER] Phosphotyrosine connectivity problem Soumya Lipsa Rath (Mon Dec 19 2011 - 01:01:22 PST)
  - Re: [AMBER] Phosphotyrosine connectivity problem Sangeetha B (Mon Dec 19 2011 - 01:19:22 PST)
    - Re: [AMBER] Phosphotyrosine connectivity problem Soumya Lipsa Rath (Mon Dec 19 2011 - 01:48:18 PST)
    - Re: [AMBER] Phosphotyrosine connectivity problem Sangeetha B (Mon Dec 19 2011 - 03:48:51 PST)
  - Re: [AMBER] Phosphotyrosine connectivity problem Marc van der Kamp (Mon Dec 19 2011 - 01:48:42 PST)
- Re: [AMBER] Phosphotyrosine connectivity problem David A Case (Mon Dec 19 2011 - 05:14:24 PST)
  - Re: [AMBER] Phosphotyrosine connectivity problem Sangeetha B (Mon Dec 19 2011 - 19:37:03 PST)
[AMBER] problem in writing pdb with ambpdb Jio M (Mon Dec 19 2011 - 02:38:53 PST)
- Re: [AMBER] problem in writing pdb with ambpdb Marc van der Kamp (Mon Dec 19 2011 - 02:52:52 PST)
  - Re: [AMBER] problem in writing pdb with ambpdb Jio M (Mon Dec 19 2011 - 03:18:09 PST)
    - [AMBER] R: problem in writing pdb with ambpdb Giovanni Pavan (Mon Dec 19 2011 - 03:26:44 PST)
- Re: [AMBER] problem in writing pdb with ambpdb Astrid Maaß (Mon Dec 19 2011 - 04:14:55 PST)
- Re: [AMBER] problem in writing pdb with ambpdb Jio M (Mon Dec 19 2011 - 04:55:36 PST)
- Re: [AMBER] problem in writing pdb with ambpdb David A Case (Mon Dec 19 2011 - 05:20:38 PST)
  - Re: [AMBER] problem in writing pdb with ambpdb Jio M (Mon Dec 19 2011 - 07:50:06 PST)
[AMBER] dihedral analysis Shirin Jamshidi (Mon Dec 19 2011 - 09:05:55 PST)
[AMBER] water in enzyme active site Shirin Jamshidi (Mon Dec 19 2011 - 09:10:24 PST)
[AMBER] Prepping PDB files for amber Jeffrey Thalhammer (Mon Dec 19 2011 - 13:16:47 PST)
- Re: [AMBER] Prepping PDB files for amber Lachele Foley (Lists) (Mon Dec 19 2011 - 13:39:10 PST)
  - Re: [AMBER] Prepping PDB files for amber Jeffrey Thalhammer (Mon Dec 19 2011 - 14:22:25 PST)
    - Re: [AMBER] Prepping PDB files for amber Lachele Foley (Lists) (Mon Dec 19 2011 - 14:34:47 PST)
    - Re: [AMBER] Prepping PDB files for amber Jan-Philip Gehrcke (Mon Dec 19 2011 - 15:18:51 PST)
    - Re: [AMBER] Prepping PDB files for amber Thomas Gaillard (Mon Dec 19 2011 - 16:56:34 PST)
    - Re: [AMBER] Prepping PDB files for amber Jan-Philip Gehrcke (Mon Dec 19 2011 - 23:58:07 PST)
    - Re: [AMBER] Prepping PDB files for amber Lachele Foley (Lists) (Tue Dec 20 2011 - 12:45:13 PST)
- Re: [AMBER] Prepping PDB files for amber Jason Swails (Mon Dec 19 2011 - 16:26:36 PST)
  - Re: [AMBER] Prepping PDB files for amber Jeffrey Thalhammer (Mon Dec 19 2011 - 22:15:00 PST)
- Re: [AMBER] Prepping PDB files for amber Bill Ross (Mon Dec 19 2011 - 17:04:49 PST)
- Re: [AMBER] Prepping PDB files for amber David A Case (Tue Dec 20 2011 - 12:33:57 PST)
[AMBER] pmemd.cuda: bugfix.20 failed HUNKs Marc van der Kamp (Tue Dec 20 2011 - 01:09:08 PST)
- Re: [AMBER] pmemd.cuda: bugfix.20 failed HUNKs Marc van der Kamp (Tue Dec 20 2011 - 01:53:49 PST)
Re: [AMBER] problem in writing pdb with ambpdb:test case attached David A Case (Tue Dec 20 2011 - 05:50:41 PST)
- [AMBER] How many nodes to be used is best for AMBER parallel calculation? Catein Catherine (Tue Dec 20 2011 - 06:54:52 PST)
  - Re: [AMBER] How many nodes to be used is best for AMBER parallel calculation? Jason Swails (Tue Dec 20 2011 - 12:35:10 PST)
    - Re: [AMBER] How many nodes to be used is best for AMBER parallel calculation? Ilyas Yildirim (Tue Dec 20 2011 - 12:55:03 PST)
- Re: [AMBER] problem in writing pdb with ambpdb:test case attached Jio M (Tue Dec 20 2011 - 07:31:52 PST)
  - Re: [AMBER] problem in writing pdb with ambpdb:test case attached Jason Swails (Tue Dec 20 2011 - 21:07:02 PST)
[AMBER] : Membrane Dynamics Rajesh Singh (Tue Dec 20 2011 - 07:56:31 PST)
- [AMBER] leap mis-specified improper dihedral Dean Cuebas (Tue Dec 20 2011 - 10:23:02 PST)
  - Re: [AMBER] leap mis-specified improper dihedral David A Case (Tue Dec 20 2011 - 12:18:17 PST)
  - Re: [AMBER] leap mis-specified improper dihedral Bill Ross (Tue Dec 20 2011 - 16:15:31 PST)
    - Re: [AMBER] leap mis-specified improper dihedral FyD (Tue Dec 20 2011 - 23:22:44 PST)
    - Re: [AMBER] leap mis-specified improper dihedral Dean Cuebas (Tue Dec 20 2011 - 22:34:23 PST)
- Re: [AMBER] : Membrane Dynamics Albert (Tue Dec 20 2011 - 15:54:49 PST)
  - Re: [AMBER] : Membrane Dynamics Carlos Simmerling (Tue Dec 20 2011 - 16:03:20 PST)
    - Re: [AMBER] : Membrane Dynamics Aron Broom (Tue Dec 20 2011 - 16:07:25 PST)
    - Re: [AMBER] : Membrane Dynamics Albert (Tue Dec 20 2011 - 16:29:24 PST)
    - Re: [AMBER] : Membrane Dynamics Vlad Cojocaru (Tue Dec 20 2011 - 22:37:27 PST)
    - Re: [AMBER] : Membrane Dynamics Albert (Tue Dec 20 2011 - 23:41:48 PST)
    - Re: [AMBER] : Membrane Dynamics Albert (Tue Dec 20 2011 - 16:21:29 PST)
    - Re: [AMBER] : Membrane Dynamics Jason Swails (Tue Dec 20 2011 - 20:22:51 PST)
[AMBER] studying the pH-dependent stability of a "large" homodimeric protein Jan-Philip Gehrcke (Tue Dec 20 2011 - 08:15:55 PST)
- Re: [AMBER] studying the pH-dependent stability of a "large" homodimeric protein Adrian Roitberg (Tue Dec 20 2011 - 10:18:27 PST)
  - Re: [AMBER] studying the pH-dependent stability of a "large" homodimeric protein Kshatresh Dutta Dubey (Tue Dec 20 2011 - 17:19:34 PST)
    - Re: [AMBER] studying the pH-dependent stability of a "large" homodimeric protein Jason Swails (Tue Dec 20 2011 - 21:03:40 PST)
  - Re: [AMBER] studying the pH-dependent stability of a "large" homodimeric protein Jan-Philip Gehrcke (Tue Jan 03 2012 - 07:45:16 PST)
[AMBER] antechamber for boron DEBOSTUTI GHOSHDASTIDAR (Tue Dec 20 2011 - 09:36:46 PST)
[AMBER] ptraj: Hbonds George Tzotzos (Tue Dec 20 2011 - 09:38:10 PST)
[AMBER] About interaction energy over time Mo Chen (Tue Dec 20 2011 - 13:44:18 PST)
- Re: [AMBER] About interaction energy over time steinbrt.rci.rutgers.edu (Wed Dec 21 2011 - 01:12:29 PST)
[AMBER] mtkpp: parameters in metals.frcmod Patrick G Blachly (Tue Dec 20 2011 - 20:59:39 PST)
- Re: [AMBER] mtkpp: parameters in metals.frcmod Ben Roberts (Wed Dec 21 2011 - 08:03:11 PST)
  - Re: [AMBER] mtkpp: parameters in metals.frcmod Patrick G Blachly (Wed Dec 21 2011 - 20:45:46 PST)
    - Re: [AMBER] mtkpp: parameters in metals.frcmod ros (Thu Dec 22 2011 - 07:19:25 PST)
    - Re: [AMBER] mtkpp: parameters in metals.frcmod Ben Roberts (Thu Dec 22 2011 - 07:24:06 PST)
    - Re: [AMBER] mtkpp: parameters in metals.frcmod Martin Peters (Thu Dec 22 2011 - 07:34:59 PST)
    - Re: [AMBER] mtkpp: parameters in metals.frcmod Patrick G Blachly (Tue Jan 10 2012 - 14:52:05 PST)
[AMBER] Amber:SANDER BOMB:volume of ucell too big, too many subcells shradhey gupta (Tue Dec 20 2011 - 22:10:17 PST)
- Re: [AMBER] Amber:SANDER BOMB:volume of ucell too big, too many subcells David A Case (Wed Dec 21 2011 - 05:33:04 PST)
[AMBER] Amber:SANDER BOMB:volume of ucell too big, too many subcells shradhey gupta (Tue Dec 20 2011 - 22:23:59 PST)
[AMBER] High Molarity solutions Hemant Gangwar (Wed Dec 21 2011 - 01:58:28 PST)
[AMBER] Eptot is positive Junjian Miao (Wed Dec 21 2011 - 18:31:54 PST)
- Re: [AMBER] Eptot is positive steinbrt.rci.rutgers.edu (Thu Dec 22 2011 - 00:11:51 PST)
- Re: [AMBER] Eptot is positive Junjian Miao (Thu Dec 22 2011 - 23:17:41 PST)
[AMBER] AMBER parameters for caffeine molecule Bhanita Sharma (Wed Dec 21 2011 - 21:26:58 PST)
- Re: [AMBER] AMBER parameters for caffeine molecule Ashutosh Shandilya (Wed Dec 21 2011 - 21:37:08 PST)
- Re: [AMBER] AMBER parameters for caffeine molecule arikcohen (Wed Dec 21 2011 - 22:58:47 PST)
- Re: [AMBER] AMBER parameters for caffeine molecule FyD (Thu Dec 22 2011 - 23:39:24 PST)
[AMBER] problems of results of decomposition Qinghua Liao (Thu Dec 22 2011 - 02:16:02 PST)
[AMBER] Restart file for pmemd not showing all information Sasha Perkins (Thu Dec 22 2011 - 08:48:17 PST)
- Re: [AMBER] Restart file for pmemd not showing all information Ross Walker (Thu Dec 22 2011 - 09:10:24 PST)
  - Re: [AMBER] Restart file for pmemd not showing all information Sasha Perkins (Thu Dec 22 2011 - 13:54:55 PST)
    - Re: [AMBER] Restart file for pmemd not showing all information Dean Cuebas (Sat Dec 24 2011 - 13:02:15 PST)
    - Re: [AMBER] Restart file for pmemd not showing all information Duke, Robert E Jr (Sat Dec 24 2011 - 13:11:29 PST)
- Re: [AMBER] Restart file for pmemd not showing all information Bill Ross (Sat Dec 24 2011 - 13:26:25 PST)
  - Re: [AMBER] Restart file for pmemd not showing all information Duke, Robert E Jr (Sat Dec 24 2011 - 14:29:41 PST)
  - Re: [AMBER] Restart file for pmemd not showing all information filip fratev (Sun Dec 25 2011 - 03:30:29 PST)
    - Re: [AMBER] Restart file for pmemd not showing all information Duke, Robert E Jr (Sun Dec 25 2011 - 11:03:33 PST)
    - Re: [AMBER] Restart file for pmemd not showing all information filip fratev (Sun Dec 25 2011 - 12:46:15 PST)
    - Re: [AMBER] Restart file for pmemd not showing all information Duke, Robert E Jr (Sun Dec 25 2011 - 12:52:05 PST)
- Re: [AMBER] Restart file for pmemd not showing all information filip fratev (Sun Dec 25 2011 - 13:48:51 PST)
  - Re: [AMBER] Restart file for pmemd not showing all information Duke, Robert E Jr (Sun Dec 25 2011 - 14:30:19 PST)
    - Re: [AMBER] Restart file for pmemd not showing all information Dean Cuebas (Tue Dec 27 2011 - 12:29:01 PST)
    - Re: [AMBER] Restart file for pmemd not showing all information filip fratev (Tue Feb 14 2012 - 08:38:57 PST)
    - Re: [AMBER] Restart file for pmemd not showing all information Sasha Perkins (Tue Feb 14 2012 - 08:54:23 PST)
    - Re: [AMBER] Restart file for pmemd not showing all information Ismail, Mohd F. (Tue Feb 14 2012 - 09:33:26 PST)
    - Re: [AMBER] Restart file for pmemd not showing all information Aron Broom (Tue Feb 14 2012 - 09:40:59 PST)
    - Re: [AMBER] Restart file for pmemd not showing all information David A Case (Tue Feb 14 2012 - 12:04:56 PST)
    - Re: [AMBER] Restart file for pmemd not showing all information filip fratev (Tue Feb 14 2012 - 17:28:31 PST)
    - Re: [AMBER] Restart file for pmemd not showing all information case (Tue Feb 14 2012 - 18:52:58 PST)
    - Re: [AMBER] Restart file for pmemd not showing all information filip fratev (Tue Feb 14 2012 - 19:15:16 PST)
    - Re: [AMBER] Restart file for pmemd not showing all information Aron Broom (Tue Feb 14 2012 - 19:33:47 PST)
  - Re: [AMBER] Restart file for pmemd not showing all information Duke, Robert E Jr (Tue Dec 27 2011 - 18:25:34 PST)
Re: [AMBER] carborane_and_icosohedral_boron Raman Parkesh (Thu Dec 22 2011 - 08:50:12 PST)
[AMBER] problem with charge on iron in heme cysteine system pancham lal gupta (Thu Dec 22 2011 - 23:57:26 PST)
- Re: [AMBER] problem with charge on iron in heme cysteine system case (Fri Dec 23 2011 - 06:50:51 PST)
[AMBER] PMEMD installation error hari krishna (Fri Dec 23 2011 - 04:41:16 PST)
- Re: [AMBER] PMEMD installation error Jason Swails (Fri Dec 23 2011 - 06:46:09 PST)
- Re: [AMBER] PMEMD installation error case (Fri Dec 23 2011 - 07:00:33 PST)
- [AMBER] PMEMD installation error hari krishna (Tue Jan 03 2012 - 21:05:45 PST)
  - Re: [AMBER] PMEMD installation error David A Case (Mon Jan 09 2012 - 05:52:19 PST)
  - Re: [AMBER] PMEMD installation error hari krishna (Mon Jan 09 2012 - 21:30:30 PST)
[AMBER] cpptraj -- doesn't like reading Amber restart files with more than 99, 999 atoms Ben Roberts (Fri Dec 23 2011 - 08:25:29 PST)
- Re: [AMBER] cpptraj -- doesn't like reading Amber restart files with more than 99, 999 atoms Daniel Roe (Fri Dec 23 2011 - 08:42:43 PST)
  - Re: [AMBER] cpptraj -- doesn't like reading Amber restart files with more than 99, 999 atoms Daniel Roe (Fri Dec 23 2011 - 09:46:15 PST)
    - Re: [AMBER] cpptraj -- doesn't like reading Amber restart files with more than 99, 999 atoms Ben Roberts (Fri Dec 23 2011 - 10:21:01 PST)
[AMBER] Bad atom type error in MMPBSA hari krishna (Sat Dec 24 2011 - 04:03:48 PST)
- Re: [AMBER] Bad atom type error in MMPBSA Jason Swails (Sat Dec 24 2011 - 06:19:01 PST)
[AMBER] Create a parameters and topology files! john Kerk (Sun Dec 25 2011 - 00:35:57 PST)
- Re: [AMBER] Create a parameters and topology files! Ben Roberts (Mon Dec 26 2011 - 06:25:37 PST)
[AMBER] Fw: Restart file for pmemd not showing all information filip fratev (Sun Dec 25 2011 - 13:47:21 PST)
[AMBER] Error in output file Aditya Padhi (Sun Dec 25 2011 - 23:02:38 PST)
- Re: [AMBER] Error in output file Jason Swails (Mon Dec 26 2011 - 19:52:41 PST)
[AMBER] simulation replication kanika singal (Mon Dec 26 2011 - 02:38:08 PST)
- Re: [AMBER] simulation replication Carlos Simmerling (Mon Dec 26 2011 - 04:32:10 PST)
[AMBER] Fwd: WARNING in ptraj(): No input trajectories specified (trajin), aborting... rosy stone (Mon Dec 26 2011 - 21:52:17 PST)
- Re: [AMBER] Fwd: WARNING in ptraj(): No input trajectories specified (trajin), aborting... DEBOSTUTI GHOSHDASTIDAR (Mon Dec 26 2011 - 22:12:09 PST)
  - [AMBER] Fwd: Fwd: WARNING in ptraj(): No input trajectories specified (trajin), aborting... rosy stone (Tue Dec 27 2011 - 02:03:39 PST)
    - Re: [AMBER] Fwd: Fwd: WARNING in ptraj(): No input trajectories specified (trajin), aborting... case (Tue Dec 27 2011 - 05:42:38 PST)
    - [AMBER] Fwd: Fwd: Fwd: WARNING in ptraj(): No input trajectories specified (trajin), aborting... rosy stone (Tue Dec 27 2011 - 21:06:20 PST)
    - Re: [AMBER] Fwd: Fwd: Fwd: WARNING in ptraj(): No input trajectories specified (trajin), aborting... case (Wed Dec 28 2011 - 06:29:48 PST)
    - [AMBER] Fwd: Fwd: Fwd: Fwd: WARNING in ptraj(): No input trajectories specified (trajin), aborting... rosy stone (Wed Dec 28 2011 - 22:27:51 PST)
    - Re: [AMBER] Fwd: Fwd: Fwd: Fwd: WARNING in ptraj(): No input trajectories specified (trajin), aborting... David A Case (Thu Dec 29 2011 - 07:32:51 PST)
    - Re: [AMBER] Fwd: Fwd: Fwd: Fwd: WARNING in ptraj(): No input trajectories specified (trajin), aborting... Daniel Roe (Thu Dec 29 2011 - 07:49:24 PST)
[AMBER] installation error in AmberTools1.5 Asmita Gupta (Tue Dec 27 2011 - 03:13:40 PST)
- Re: [AMBER] installation error in AmberTools1.5 Jason Swails (Tue Dec 27 2011 - 05:07:04 PST)
  - Re: [AMBER] installation error in AmberTools1.5 Asmita Gupta (Tue Dec 27 2011 - 08:38:38 PST)
    - Re: [AMBER] installation error in AmberTools1.5 Jason Swails (Tue Dec 27 2011 - 17:34:51 PST)
[AMBER] SMD multiple restraints problem? Hu Ge (Tue Dec 27 2011 - 06:34:29 PST)
[AMBER] Entropy: quasi harmonic vs NMode - Weird results George Tzotzos (Tue Dec 27 2011 - 07:57:39 PST)
- Re: [AMBER] Entropy: quasi harmonic vs NMode - Weird results Jason Swails (Tue Dec 27 2011 - 09:18:24 PST)
[AMBER] PMEMD parallelization on Ubuntu Lucid David Condon (Tue Dec 27 2011 - 09:20:26 PST)
- Re: [AMBER] PMEMD parallelization on Ubuntu Lucid Jason Swails (Tue Dec 27 2011 - 15:00:18 PST)
  - Re: [AMBER] PMEMD parallelization on Ubuntu Lucid David Condon (Tue Dec 27 2011 - 15:42:41 PST)
    - Re: [AMBER] PMEMD parallelization on Ubuntu Lucid Jason Swails (Tue Dec 27 2011 - 17:29:17 PST)
    - Re: [AMBER] PMEMD parallelization on Ubuntu Lucid Mark Williamson (Mon Jan 09 2012 - 06:52:12 PST)
[AMBER] nonbond parameters for copper gaoya (Tue Dec 27 2011 - 21:21:11 PST)
- Re: [AMBER] nonbond parameters for copper ros (Tue Dec 27 2011 - 21:34:41 PST)
  - Re: [AMBER] nonbond parameters for copper gaoya (Tue Dec 27 2011 - 21:40:24 PST)
    - Re: [AMBER] nonbond parameters for copper ros (Tue Dec 27 2011 - 21:55:04 PST)
    - Re: [AMBER] nonbond parameters for copper gaoya (Tue Dec 27 2011 - 22:00:03 PST)
[AMBER] chamber - Fortran runtime error colvin (Tue Dec 27 2011 - 23:27:19 PST)
[AMBER] ambertools 1.5 subrata paul (Wed Dec 28 2011 - 01:18:38 PST)
- Re: [AMBER] ambertools 1.5 Reza Aditama (Wed Dec 28 2011 - 02:46:35 PST)
  - Re: [AMBER] ambertools 1.5 subrata paul (Wed Dec 28 2011 - 22:48:54 PST)
    - Re: [AMBER] ambertools 1.5 Jason Swails (Thu Dec 29 2011 - 07:19:09 PST)
- Re: [AMBER] ambertools 1.5 case (Wed Dec 28 2011 - 06:36:54 PST)
[AMBER] Which method is the best way to solve metalloprotein?MCPB or Only consider Electrostatic and VDW JiYuan Liu (Wed Dec 28 2011 - 06:58:01 PST)
- Re: [AMBER] Which method is the best way to solve metalloprotein?MCPB or Only consider Electrostatic and VDW Jacopo Sgrignani (Wed Dec 28 2011 - 08:25:54 PST)
  - Re: [AMBER] Which method is the best way to solve metalloprotein?MCPB or Only consider Electrostatic and VDW JiYuan Liu (Thu Dec 29 2011 - 05:22:54 PST)
    - Re: [AMBER] Which method is the best way to solve metalloprotein?MCPB or Only consider Electrostatic and VDW Ben Roberts (Thu Dec 29 2011 - 06:58:52 PST)
    - Re: [AMBER] Which method is the best way to solve metalloprotein?MCPB or Only consider Electrostatic and VDW JiYuan Liu (Fri Dec 30 2011 - 05:03:09 PST)
    - Re: [AMBER] Which method is the best way to solve metalloprotein?MCPB or Only consider Electrostatic and VDW Ben Roberts (Fri Dec 30 2011 - 06:12:34 PST)
    - Re: [AMBER] Which method is the best way to solve metalloprotein?MCPB or Only consider Electrostatic and VDW JiYuan Liu (Fri Dec 30 2011 - 06:37:37 PST)
    - Re: [AMBER] Which method is the best way to solve metalloprotein?MCPB or Only consider Electrostatic and VDW Ben Roberts (Fri Dec 30 2011 - 06:57:36 PST)
    - Re: [AMBER] Which method is the best way to solve metalloprotein?MCPB or Only consider Electrostatic and VDW JiYuan Liu (Fri Dec 30 2011 - 07:12:08 PST)
    - Re: [AMBER] Which method is the best way to solve metalloprotein?MCPB or Only consider Electrostatic and VDW Ben Roberts (Fri Dec 30 2011 - 07:20:16 PST)
    - Re: [AMBER] Which method is the best way to solve metalloprotein?MCPB or Only consider Electrostatic and VDW JiYuan Liu (Fri Dec 30 2011 - 20:02:35 PST)
    - Re: [AMBER] Which method is the best way to solve metalloprotein?MCPB or Only consider Electrostatic and VDW JiYuan Liu (Wed Jan 04 2012 - 00:07:08 PST)
    - Re: [AMBER] Which method is the best way to solve metalloprotein?MCPB or Only consider Electrostatic and VDW Ben Roberts (Thu Jan 12 2012 - 05:55:49 PST)
    - Re: [AMBER] Which method is the best way to solve metalloprotein?MCPB or Only consider Electrostatic and VDW JiYuan Liu (Tue Feb 28 2012 - 01:16:04 PST)
    - Re: [AMBER] Which method is the best way to solve metalloprotein?MCPB or Only consider Electrostatic and VDW Ben Roberts (Mon Mar 19 2012 - 01:30:42 PDT)
    - Re: [AMBER] Which method is the best way to solve metalloprotein?MCPB or Only consider Electrostatic and VDW JiYuan Liu (Mon Mar 19 2012 - 05:51:51 PDT)
    - Re: [AMBER] Which method is the best way to solve metalloprotein?MCPB or Only consider Electrostatic and VDW FyD (Tue Mar 20 2012 - 09:26:58 PDT)
[AMBER] atomic radii for PBSA Qiong Zhang (Wed Dec 28 2011 - 08:58:49 PST)
[AMBER] Undefined reference netcdf in 'patched'/updated AmberTools 1.5/ pmemd.cuda compilation. Danni L Harris (Wed Dec 28 2011 - 14:26:42 PST)
- Re: [AMBER] Undefined reference netcdf in 'patched'/updated AmberTools 1.5/ pmemd.cuda compilation. Jason Swails (Wed Dec 28 2011 - 16:42:25 PST)
[AMBER] resending -- chamber-fortran runtime error colvin (Wed Dec 28 2011 - 16:38:53 PST)
- Re: [AMBER] resending -- chamber-fortran runtime error Scott Brozell (Wed Dec 28 2011 - 19:23:58 PST)
- Re: [AMBER] resending -- chamber-fortran runtime error case (Wed Dec 28 2011 - 20:42:33 PST)
[AMBER] problem extracting AmberTools-1.5.tar.bz2 file Puspita Halder (Wed Dec 28 2011 - 21:49:15 PST)
- Re: [AMBER] problem extracting AmberTools-1.5.tar.bz2 file Jason Swails (Thu Dec 29 2011 - 07:21:06 PST)
- Re: [AMBER] problem extracting AmberTools-1.5.tar.bz2 file David A Case (Thu Dec 29 2011 - 07:29:12 PST)
[AMBER] error in crd file due to lack of disk space Ashutosh Shandilya (Wed Dec 28 2011 - 23:23:07 PST)
- Re: [AMBER] error in crd file due to lack of disk space David A Case (Thu Dec 29 2011 - 07:36:11 PST)
[AMBER] Leap: addions George Tzotzos (Thu Dec 29 2011 - 02:27:37 PST)
- Re: [AMBER] Leap: addions Jason Swails (Thu Dec 29 2011 - 07:25:59 PST)
  - Re: [AMBER] Leap: addions George Tzotzos (Thu Dec 29 2011 - 07:41:43 PST)
    - Re: [AMBER] Leap: addions Jason Swails (Thu Dec 29 2011 - 08:47:52 PST)
[AMBER] sander.rism3d 민병진 (Thu Dec 29 2011 - 04:00:45 PST)
- Re: [AMBER] sander.rism3d Jason Swails (Thu Dec 29 2011 - 07:22:51 PST)
- Re: [AMBER] sander.rism3d David A Case (Thu Dec 29 2011 - 07:43:58 PST)
  - Re: [AMBER] sander.rism3d Tyler Luchko (Thu Dec 29 2011 - 08:18:40 PST)
[AMBER] Chloroform in Amber, a rigid model? Robert Woodwhite (Thu Dec 29 2011 - 15:29:49 PST)
- Re: [AMBER] Chloroform in Amber, a rigid model? Jason Swails (Thu Dec 29 2011 - 21:45:15 PST)
  - Re: [AMBER] Chloroform in Amber, a rigid model? Robert Woodwhite (Fri Dec 30 2011 - 09:43:39 PST)
    - Re: [AMBER] Chloroform in Amber, a rigid model? case (Fri Dec 30 2011 - 10:27:26 PST)
    - Re: [AMBER] Chloroform in Amber, a rigid model? Robert Woodwhite (Fri Dec 30 2011 - 11:19:16 PST)
    - Re: [AMBER] Chloroform in Amber, a rigid model? case (Mon Jan 02 2012 - 19:36:39 PST)
[AMBER] free energy calculation: turn off the VDW interaction between ligand and protein Bing Xiong (Fri Dec 30 2011 - 16:42:17 PST)
- Re: [AMBER] free energy calculation: turn off the VDW interaction between ligand and protein case (Fri Dec 30 2011 - 17:19:35 PST)
- Re: [AMBER] free energy calculation: turn off the VDW interaction between ligand and protein bxiong (Sun Jan 01 2012 - 22:32:53 PST)
  - Re: [AMBER] free energy calculation: turn off the VDW interaction between ligand and protein steinbrt.rci.rutgers.edu (Mon Jan 02 2012 - 03:52:27 PST)
  - Re: [AMBER] free energy calculation: turn off the VDW interactionbetween ligand and protein Bing Xiong (Tue Jan 03 2012 - 16:21:49 PST)
    - Re: [AMBER] free energy calculation: turn off the VDW interactionbetween ligand and protein steinbrt.rci.rutgers.edu (Wed Jan 04 2012 - 01:45:30 PST)
- Re: [AMBER] free energy calculation: turn off the VDW interaction between ligand and protein bxiong (Wed Jan 04 2012 - 16:31:32 PST)
  - Re: [AMBER] free energy calculation: turn off the VDW interaction between ligand and protein steinbrt.rci.rutgers.edu (Thu Jan 05 2012 - 01:49:15 PST)
    - Re: [AMBER] free energy calculation: turn off the VDW interaction between ligand and protein Marek Maly (Fri Jan 06 2012 - 07:57:52 PST)
    - Re: [AMBER] free energy calculation: turn off the VDW interaction between ligand and protein steinbrt.rci.rutgers.edu (Fri Jan 06 2012 - 08:06:51 PST)
    - Re: [AMBER] free energy calculation: turn off the VDW interaction between ligand and protein Marek Maly (Mon Jan 23 2012 - 16:17:13 PST)
    - Re: [AMBER] free energy calculation: turn off the VDW interaction between ligand and protein steinbrt.rci.rutgers.edu (Thu Jan 26 2012 - 07:43:28 PST)
    - Re: [AMBER] free energy calculation: turn off the VDW interaction between ligand and protein Marek Maly (Thu Jan 26 2012 - 08:34:59 PST)
    - Re: [AMBER] free energy calculation: turn off the VDW interaction between ligand and protein steinbrt.rci.rutgers.edu (Thu Jan 26 2012 - 09:18:03 PST)
    - Re: [AMBER] free energy calculation: turn off the VDW interaction between ligand and protein Marek Maly (Thu Jan 26 2012 - 09:30:53 PST)
[AMBER] Solvate a system in AMBER 11. Sudarshan Debnath (Sat Dec 31 2011 - 07:35:22 PST)
- Re: [AMBER] Solvate a system in AMBER 11. Daniel Sindhikara (Sat Dec 31 2011 - 17:27:32 PST)
Re: [AMBER] Regarding solvating a protein using amber Daniel Sindhikara (Sun Jan 01 2012 - 22:30:50 PST)
[AMBER] Using antechamber -Heme molecule יוכבד (Mon Jan 02 2012 - 03:24:26 PST)
- Re: [AMBER-Developers] [AMBER] Using antechamber -Heme molecule case (Mon Jan 02 2012 - 06:20:19 PST)
[AMBER] Ser/Thr phosphorylation support in AMBER-11 Michael Petukhov (Mon Jan 02 2012 - 09:58:24 PST)
- Re: [AMBER] Ser/Thr phosphorylation support in AMBER-11 steinbrt.rci.rutgers.edu (Mon Jan 02 2012 - 10:06:14 PST)
  - [AMBER] The per-partes ligand decoupling as the alternative to simultaneous decouplig of all ligand atoms with use of restraints ? Marek Maly (Mon Jan 02 2012 - 17:07:23 PST)
    - Re: [AMBER] The per-partes ligand decoupling as the alternative to simultaneous decouplig of all ligand atoms with use of restraints ? case (Mon Jan 02 2012 - 19:38:18 PST)
    - Re: [AMBER] The per-partes ligand decoupling as the alternative to simultaneous decouplig of all ligand atoms with use of restraints ? Adrian Roitberg (Tue Jan 03 2012 - 07:22:59 PST)
    - Re: [AMBER] The per-partes ligand decoupling as the alternative to simultaneous decouplig of all ligand atoms with use of restraints ? steinbrt.rci.rutgers.edu (Tue Jan 03 2012 - 01:26:37 PST)
    - Re: [AMBER] The per-partes ligand decoupling as the alternative to simultaneous decouplig of all ligand atoms with use of restraints ? Marek Maly (Tue Jan 03 2012 - 10:33:43 PST)
[AMBER] How to set the dist.RST file in SMD using Amber11? 潘显超 (Mon Jan 02 2012 - 23:12:00 PST)
[AMBER] rounding issue Dmitry Mukha (Tue Jan 03 2012 - 07:49:41 PST)
- Re: [AMBER] rounding issue Adrian Roitberg (Tue Jan 03 2012 - 07:54:37 PST)
  - Re: [AMBER] rounding issue Dmitry Mukha (Tue Jan 03 2012 - 08:07:36 PST)
- Re: [AMBER] rounding issue Ross Walker (Tue Jan 03 2012 - 10:50:48 PST)
  - Re: [AMBER] rounding issue Dmitry Mukha (Wed Jan 04 2012 - 00:04:21 PST)
    - Re: [AMBER] rounding issue Jason Swails (Wed Jan 04 2012 - 07:49:13 PST)
[AMBER] Free Energy Calculations of Potassium and Chloride Sai Kumar Ramadugu (Tue Jan 03 2012 - 11:58:51 PST)
- Re: [AMBER] Free Energy Calculations of Potassium and Chloride steinbrt.rci.rutgers.edu (Tue Jan 03 2012 - 12:37:44 PST)
  - Re: [AMBER] Free Energy Calculations of Potassium and Chloride Sai Kumar Ramadugu (Wed Jan 04 2012 - 12:27:29 PST)
    - Re: [AMBER] Free Energy Calculations of Potassium and Chloride Sai Kumar Ramadugu (Thu Jan 12 2012 - 11:06:15 PST)
    - Re: [AMBER] Free Energy Calculations of Potassium and Chloride steinbrt.rci.rutgers.edu (Fri Jan 13 2012 - 05:28:31 PST)
    - Re: [AMBER] Free Energy Calculations of Potassium and Chloride Sai Kumar Ramadugu (Wed Jan 18 2012 - 09:32:34 PST)
    - Re: [AMBER] Free Energy Calculations of Potassium and Chloride steinbrt.rci.rutgers.edu (Wed Jan 18 2012 - 10:15:25 PST)
    - Re: [AMBER] Free Energy Calculations of Potassium and Chloride Sai Kumar Ramadugu (Wed Jan 18 2012 - 10:43:25 PST)
    - Re: [AMBER] Free Energy Calculations of Potassium and Chloride steinbrt.rci.rutgers.edu (Wed Jan 18 2012 - 10:54:59 PST)
    - Re: [AMBER] Free Energy Calculations of Potassium and Chloride Sai Kumar Ramadugu (Wed Jan 18 2012 - 11:14:44 PST)
    - Re: [AMBER] Free Energy Calculations of Potassium and Chloride steinbrt.rci.rutgers.edu (Thu Jan 19 2012 - 02:49:18 PST)
    - Re: [AMBER] Free Energy Calculations of Potassium and Chloride Sai Kumar Ramadugu (Thu Jan 19 2012 - 11:22:39 PST)
    - Re: [AMBER] Free Energy Calculations of Potassium and Chloride David A Case (Thu Jan 19 2012 - 12:53:25 PST)
    - Re: [AMBER] Free Energy Calculations of Potassium and Chloride Sai Kumar Ramadugu (Wed Jan 25 2012 - 10:14:01 PST)
    - Re: [AMBER] Free Energy Calculations of Potassium and Chloride David A Case (Thu Jan 26 2012 - 05:07:41 PST)
    - Re: [AMBER] Free Energy Calculations of Potassium and Chloride Sai Kumar Ramadugu (Tue Jan 24 2012 - 14:58:37 PST)
    - Re: [AMBER] Free Energy Calculations of Potassium and Chloride steinbrt.rci.rutgers.edu (Thu Jan 26 2012 - 07:39:31 PST)
    - Re: [AMBER] Free Energy Calculations of Potassium and Chloride Sai Kumar Ramadugu (Mon Jan 30 2012 - 14:14:07 PST)
    - Re: [AMBER] Free Energy Calculations of Potassium and Chloride steinbrt.rci.rutgers.edu (Tue Jan 31 2012 - 00:25:50 PST)
    - Re: [AMBER] Free Energy Calculations of Potassium and Chloride Sai Kumar Ramadugu (Tue Jan 31 2012 - 09:16:00 PST)
[AMBER] how to set the dist.RST file in SMD using Amber11? pxc.cqu.edu.cn (Tue Jan 03 2012 - 17:20:56 PST)
- Re: [AMBER] how to set the dist.RST file in SMD using Amber11? Adrian Roitberg (Tue Jan 03 2012 - 17:50:50 PST)
Re: [AMBER] chamber-fortran runtime error colvin (Wed Jan 04 2012 - 01:23:45 PST)
[AMBER] Error while compiling AMBER11 Lucas A. Defelipe (Wed Jan 04 2012 - 08:17:30 PST)
- Re: [AMBER] Error while compiling AMBER11 Jason Swails (Wed Jan 04 2012 - 11:57:31 PST)
- Re: [AMBER] Error while compiling AMBER11 Jason Swails (Wed Jan 04 2012 - 12:56:14 PST)
[AMBER] ptaj: RMSD George Tzotzos (Wed Jan 04 2012 - 10:15:38 PST)
- Re: [AMBER] ptaj: RMSD vaibhav dixit (Wed Jan 04 2012 - 22:00:31 PST)
- Re: [AMBER] ptaj: RMSD Astrid Maaß (Fri Jan 06 2012 - 05:49:13 PST)
  - Re: [AMBER] ptaj: RMSD George Tzotzos (Fri Jan 06 2012 - 10:15:16 PST)
[AMBER] Deleting Cymal-6 from PDB Chris Bryant (Wed Jan 04 2012 - 10:20:52 PST)
[AMBER] Problem with oxygens bonded to three atoms in metal clusters Ben Roberts (Wed Jan 04 2012 - 14:03:50 PST)
- Re: [AMBER] Problem with oxygens bonded to three atoms in metal clusters Ben Roberts (Wed Jan 04 2012 - 14:53:54 PST)
  - Re: [AMBER] Problem with oxygens bonded to three atoms in metal clusters Brian Radak (Thu Jan 05 2012 - 13:00:32 PST)
    - Re: [AMBER] Problem with oxygens bonded to three atoms in metal clusters Ben Roberts (Thu Jan 05 2012 - 13:25:27 PST)
[AMBER] Solvation of a system in AMBER11. Sudarshan Debnath (Wed Jan 04 2012 - 20:19:37 PST)
- Re: [AMBER] Solvation of a system in AMBER11. Daniel Sindhikara (Wed Jan 04 2012 - 20:39:55 PST)
[AMBER] Problem with generating topology file using tleap Devlina Chakravarty (Thu Jan 05 2012 - 00:19:14 PST)
- Re: [AMBER] Problem with generating topology file using tleap Sangita Kachhap (Thu Jan 05 2012 - 06:41:52 PST)
- Re: [AMBER] R.E.D. Server / Antechamber problem Ben Ahmady (Thu Jan 05 2012 - 09:53:50 PST)
  - Re: [AMBER] R.E.D. Server / Antechamber problem FyD (Fri Jan 06 2012 - 00:52:59 PST)
    - Re: [AMBER] R.E.D. Server / Antechamber problem Ben Ahmady (Fri Jan 06 2012 - 12:28:31 PST)
    - Re: [AMBER] R.E.D. Server / Antechamber problem FyD (Sat Jan 07 2012 - 00:32:14 PST)
[AMBER] Solvation of a system in AMBER11. Sudarshan Debnath (Thu Jan 05 2012 - 04:52:07 PST)
- Re: [AMBER] Solvation of a system in AMBER11. Daniel Sindhikara (Thu Jan 05 2012 - 16:32:15 PST)
  - Re: [AMBER] Solvation of a system in AMBER11. Tyler Luchko (Thu Jan 05 2012 - 16:46:41 PST)
[AMBER] Origin of calculated system temperature (in mdout file) Jan-Philip Gehrcke (Thu Jan 05 2012 - 09:01:56 PST)
- Re: [AMBER] Origin of calculated system temperature (in mdout file) Brian Radak (Thu Jan 05 2012 - 12:50:10 PST)
  - Re: [AMBER] Origin of calculated system temperature (in mdout file) Jan-Philip Gehrcke (Fri Jan 06 2012 - 07:05:21 PST)
    - Re: [AMBER] Origin of calculated system temperature (in mdout file) David A. Case (Sat Jan 07 2012 - 09:39:14 PST)
[AMBER] Problem with clashing solvent molecules with solvateoct Gonzalo Jimenez Oses (Thu Jan 05 2012 - 09:07:33 PST)
- Re: [AMBER] Problem with clashing solvent molecules with solvateoct Daniel Sindhikara (Thu Jan 05 2012 - 21:48:16 PST)
[AMBER] Problem with PB calculation using ff99SBildn: PB Bomb in pb_aaradi(): No radius assigned for atom Ryan Pavlovicz (Thu Jan 05 2012 - 09:53:31 PST)
- Re: [AMBER] Problem with PB calculation using ff99SBildn: PB Bomb in pb_aaradi(): No radius assigned for atom Ray Luo, Ph.D. (Thu Jan 05 2012 - 15:01:50 PST)
[AMBER] Gas Phase Simulations in PMEMD Aron Broom (Thu Jan 05 2012 - 13:20:34 PST)
- Re: [AMBER] Gas Phase Simulations in PMEMD George M Giambasu (Thu Jan 05 2012 - 13:29:47 PST)
  - Re: [AMBER] Gas Phase Simulations in PMEMD Aron Broom (Thu Jan 05 2012 - 13:55:10 PST)
    - Re: [AMBER] Gas Phase Simulations in PMEMD Ross Walker (Thu Jan 05 2012 - 14:15:07 PST)
    - Re: [AMBER] Gas Phase Simulations in PMEMD Aron Broom (Fri Jan 13 2012 - 21:21:43 PST)
[AMBER] SANDER NMR violations Charles Johnson (Thu Jan 05 2012 - 13:40:21 PST)
- Re: [AMBER] SANDER NMR violations David A. Case (Sat Jan 07 2012 - 09:44:03 PST)
[AMBER] calculation of spectral density Mahendra B Thapa (Thu Jan 05 2012 - 14:51:35 PST)
- Re: [AMBER] calculation of spectral density David A. Case (Sat Jan 07 2012 - 09:46:56 PST)
- Re: [AMBER] calculation of spectral density Hector A. Baldoni (Sat Jan 07 2012 - 15:23:01 PST)
[AMBER] Ambertools installation. Sudarshan Debnath (Thu Jan 05 2012 - 23:10:20 PST)
- Re: [AMBER] Ambertools installation. Tyler Luchko (Sun Jan 08 2012 - 14:40:24 PST)
[AMBER] No leap in ambertool11 nicholus bhattacharjee (Fri Jan 06 2012 - 05:36:11 PST)
- Re: [AMBER] No leap in ambertool11 Ben Roberts (Fri Jan 06 2012 - 08:02:57 PST)
[AMBER] installation subrata paul (Sat Jan 07 2012 - 02:55:05 PST)
- Re: [AMBER] installation David A. Case (Sat Jan 07 2012 - 09:51:01 PST)
  - Re: [AMBER] installation Jason Swails (Sat Jan 07 2012 - 10:13:29 PST)
[AMBER] system breaks during simulation moitrayee.mbu.iisc.ernet.in (Sat Jan 07 2012 - 11:20:16 PST)
- Re: [AMBER] system breaks during simulation Ben Roberts (Sat Jan 07 2012 - 11:28:45 PST)
- Re: [AMBER] system breaks during simulation Francesco Oteri (Sat Jan 07 2012 - 11:29:44 PST)
[AMBER] clarification regarding the charge on the cluster in MCPB kanika singal (Mon Jan 09 2012 - 01:15:49 PST)
[AMBER] gpu information Elisa Frezza (Mon Jan 09 2012 - 07:01:14 PST)
- Re: [AMBER] gpu information Adrian Roitberg (Mon Jan 09 2012 - 07:03:18 PST)
  - Re: [AMBER] gpu information Elisa Frezza (Mon Jan 09 2012 - 07:39:43 PST)
[AMBER] Problems with amber topology in NAMD Osman, Roman (Mon Jan 09 2012 - 09:38:11 PST)
- Re: [AMBER] Problems with amber topology in NAMD Adrian Roitberg (Mon Jan 09 2012 - 09:41:33 PST)
  - Re: [AMBER] Problems with amber topology in NAMD Ben Roberts (Mon Jan 09 2012 - 09:44:39 PST)
    - Re: [AMBER] Problems with amber topology in NAMD Osman, Roman (Mon Jan 09 2012 - 10:16:59 PST)
    - Re: [AMBER] Problems with amber topology in NAMD George M Giambasu (Mon Jan 09 2012 - 10:26:26 PST)
  - Re: [AMBER] Problems with amber topology in NAMD Osman, Roman (Mon Jan 09 2012 - 09:46:55 PST)
  - Re: [AMBER] Problems with amber topology in NAMD Aron Broom (Mon Jan 09 2012 - 10:02:25 PST)
[AMBER] antechamber parameter file issues? Thomas Pochapsky (Mon Jan 09 2012 - 10:15:40 PST)
- Re: [AMBER] antechamber parameter file issues? Ben Roberts (Mon Jan 09 2012 - 10:24:57 PST)
  - Re: [AMBER] antechamber parameter file issues? Thomas Pochapsky (Mon Jan 09 2012 - 11:03:00 PST)
  - Re: [AMBER] antechamber parameter file issues? Thomas Pochapsky (Thu Jan 12 2012 - 07:55:24 PST)
    - Re: [AMBER] antechamber parameter file issues? FyD (Thu Jan 12 2012 - 12:49:38 PST)
    - Re: [AMBER] antechamber parameter file issues? David A Case (Fri Jan 13 2012 - 05:12:08 PST)
    - Re: [AMBER] antechamber parameter file issues? case (Fri Jan 13 2012 - 18:46:00 PST)
    - Re: [AMBER] antechamber parameter file issues? Dean Cuebas (Sat Jan 14 2012 - 11:37:22 PST)
    - Re: [AMBER] antechamber parameter file issues? case (Sat Jan 14 2012 - 14:01:36 PST)
    - Re: [AMBER] antechamber parameter file issues? FyD (Sun Jan 15 2012 - 02:31:38 PST)
    - Re: [AMBER] antechamber parameter file issues? case (Sun Jan 15 2012 - 08:33:34 PST)
    - Re: [AMBER] antechamber parameter file issues? FyD (Sun Jan 15 2012 - 02:17:22 PST)
[AMBER] problem with ester bond between side chains moitrayee.mbu.iisc.ernet.in (Tue Jan 10 2012 - 02:33:17 PST)
[AMBER] improper torsions in old prep form Andrew Voronkov (Tue Jan 10 2012 - 05:09:15 PST)
- Re: [AMBER] improper torsions in old prep form David A Case (Tue Jan 10 2012 - 06:59:28 PST)
- Re: [AMBER] improper torsions in old prep form Bill Ross (Tue Jan 10 2012 - 12:00:52 PST)
[AMBER] installation amber10 subrata paul (Tue Jan 10 2012 - 05:46:11 PST)
- Re: [AMBER] installation amber10 David A Case (Tue Jan 10 2012 - 07:01:28 PST)
[AMBER] i7 extreme for Amber GPU computing? Raik Grünberg (Tue Jan 10 2012 - 12:34:32 PST)
- Re: [AMBER] i7 extreme for Amber GPU computing? Aron Broom (Tue Jan 10 2012 - 14:39:24 PST)
  - Re: [AMBER] i7 extreme for Amber GPU computing? filip fratev (Tue Jan 10 2012 - 15:24:14 PST)
    - Re: [AMBER] i7 extreme for Amber GPU computing? filip fratev (Tue Jan 10 2012 - 15:29:38 PST)
    - Re: [AMBER] i7 extreme for Amber GPU computing? Aron Broom (Tue Jan 10 2012 - 21:14:33 PST)
    - Re: [AMBER] i7 extreme for Amber GPU computing? Jan-Philip Gehrcke (Wed Jan 11 2012 - 02:05:24 PST)
    - Re: [AMBER] i7 extreme for Amber GPU computing? Ross Walker (Wed Jan 11 2012 - 07:03:53 PST)
    - Re: [AMBER] i7 extreme for Amber GPU computing? Jan-Philip Gehrcke (Wed Jan 11 2012 - 07:51:29 PST)
[AMBER] Solvation of a system in Amber11 Sudarshan Debnath (Tue Jan 10 2012 - 22:07:25 PST)
- Re: [AMBER] Solvation of a system in Amber11 Tyler Luchko (Tue Jan 10 2012 - 22:38:57 PST)
[AMBER] Amber 11 installation problem R. K. Kar (Wed Jan 11 2012 - 00:19:59 PST)
- Re: [AMBER] Amber 11 installation problem R. K. Kar (Wed Jan 11 2012 - 03:50:41 PST)
  - Re: [AMBER] Amber 11 installation problem David A Case (Wed Jan 11 2012 - 04:34:56 PST)
- Re: [AMBER] Amber 11 installation problem Tales Yuan (Wed Jan 11 2012 - 17:23:51 PST)
[AMBER] bad atom type: f Rajesh Singh (Wed Jan 11 2012 - 08:57:49 PST)
- Re: [AMBER] bad atom type: f Bill Miller III (Wed Jan 11 2012 - 09:08:14 PST)
  - Re: [AMBER] bad atom type: f Jason Swails (Wed Jan 11 2012 - 13:38:43 PST)
    - Re: [AMBER] bad atom type: f Rajesh Singh (Thu Jan 12 2012 - 08:19:07 PST)
[AMBER] q4md: When using red, it outputs incorrect primary amine geometry as tetrahedral instead of trigonal planar g t (Thu Jan 12 2012 - 03:23:51 PST)
[AMBER] rism1d solvent models Meli Massimiliano (Thu Jan 12 2012 - 07:27:39 PST)
- Re: [AMBER] rism1d solvent models Tyler Luchko (Thu Jan 12 2012 - 08:19:19 PST)
  - Re: [AMBER] rism1d solvent models Meli Massimiliano (Thu Jan 12 2012 - 09:32:30 PST)
[AMBER] closest water George Tzotzos (Thu Jan 12 2012 - 09:29:18 PST)
- Re: [AMBER] closest water Daniel Roe (Thu Jan 12 2012 - 10:21:16 PST)
  - Re: [AMBER] closest water George Tzotzos (Thu Jan 12 2012 - 10:57:28 PST)
[AMBER] Fwd: Re: [q4md-fft] When using red, it outputs incorrect primary amine geometry as tetrahedral instead of trigonal planar FyD (Thu Jan 12 2012 - 09:57:01 PST)
- Re: [AMBER] Fwd: Re: [q4md-fft] When using red, it outputs incorrect primary amine geometry as tetrahedral instead of trigonal planar g t (Thu Jan 12 2012 - 10:14:30 PST)
[AMBER] Chirality restraints in Simulated Annealing Josmar R. da Rocha (Thu Jan 12 2012 - 14:07:38 PST)
[AMBER] Running NAB Aleksandra Skoric (Thu Jan 12 2012 - 14:25:40 PST)
- Re: [AMBER] Running NAB Jason Swails (Thu Jan 12 2012 - 19:32:57 PST)
[AMBER] PES for dialanine Ye MEI (Thu Jan 12 2012 - 19:25:51 PST)
- Re: [AMBER] PES for dialanine Daniel Roe (Fri Jan 13 2012 - 05:15:30 PST)
- Re: [AMBER] PES for dialanine Ye MEI (Fri Jan 13 2012 - 06:04:00 PST)
  - Re: [AMBER] PES for dialanine Carlos Simmerling (Fri Jan 13 2012 - 06:32:46 PST)
- Re: [AMBER] PES for dialanine Ye MEI (Fri Jan 13 2012 - 07:11:09 PST)
[AMBER] AMBERTOOL1.5 installation Hirdesh Kumar (Fri Jan 13 2012 - 00:43:14 PST)
- Re: [AMBER] AMBERTOOL1.5 installation Ben Roberts (Fri Jan 13 2012 - 05:49:35 PST)
  - Re: [AMBER] AMBERTOOL1.5 installation Hirdesh Kumar (Fri Jan 13 2012 - 05:55:07 PST)
[AMBER] Problem with xleap installation Cristina Airoldi (Fri Jan 13 2012 - 02:20:12 PST)
- Re: [AMBER] Problem with xleap installation Ye MEI (Fri Jan 13 2012 - 02:34:44 PST)
  - Re: [AMBER] Problem with xleap installation Cristina Airoldi (Fri Jan 13 2012 - 02:55:09 PST)
    - Re: [AMBER] Problem with xleap installation Cristina Airoldi (Fri Jan 13 2012 - 05:31:23 PST)
    - Re: [AMBER] Problem with xleap installation Josmar R. da Rocha (Fri Jan 13 2012 - 06:01:23 PST)
    - Re: [AMBER] Problem with xleap installation Cristina Airoldi (Fri Jan 13 2012 - 06:51:20 PST)
[AMBER] tleap/xleap segmenatation fault Marina Grabar Branilović (Fri Jan 13 2012 - 05:30:21 PST)
- Re: [AMBER] tleap/xleap segmenatation fault Ben Roberts (Fri Jan 13 2012 - 05:48:34 PST)
  - Re: [AMBER] tleap/xleap segmenatation fault Marina Grabar Branilović (Mon Jan 16 2012 - 03:13:13 PST)
[AMBER] Issue with HowToCompileAmberTools1.5AndAMBER11WithUbuntu10.04.3LTS.html Jan-Philip Gehrcke (Fri Jan 13 2012 - 06:34:06 PST)
- Re: [AMBER] Issue with HowToCompileAmberTools1.5AndAMBER11WithUbuntu10.04.3LTS.html Jan-Philip Gehrcke (Fri Jan 13 2012 - 06:46:53 PST)
  - Re: [AMBER] Issue with HowToCompileAmberTools1.5AndAMBER11WithUbuntu10.04.3LTS.html Mark Williamson (Fri Jan 13 2012 - 06:53:46 PST)
[AMBER] Upcoming of Amber Workshop in USA manikanthan bhavaraju (Fri Jan 13 2012 - 09:45:25 PST)
[AMBER] ACE and NME caps Chris Bryant (Fri Jan 13 2012 - 11:53:57 PST)
- Re: [AMBER] ACE and NME caps FyD (Fri Jan 13 2012 - 23:27:59 PST)
  - Re: [AMBER] ACE and NME caps Chris Bryant (Wed Jan 18 2012 - 11:18:42 PST)
- Re: [AMBER] ACE and NME caps FyD (Wed Jan 18 2012 - 22:12:40 PST)
  - Re: [AMBER] ACE and NME caps FyD (Wed Jan 18 2012 - 23:13:23 PST)
    - Re: [AMBER] ACE and NME caps FyD (Thu Jan 19 2012 - 00:50:30 PST)
    - Re: [AMBER] ACE and NME caps Chris Bryant (Thu Jan 19 2012 - 06:35:30 PST)
- Re: [AMBER] ACE and NME caps FyD (Tue Jan 24 2012 - 03:08:03 PST)
- Re: [AMBER] ACE and NME caps FyD (Mon Jan 30 2012 - 23:48:25 PST)
[AMBER] water molecules within a distance cutoff; ptraj analysis kanika singal (Fri Jan 13 2012 - 23:57:14 PST)
- Re: [AMBER] water molecules within a distance cutoff; ptraj analysis Jason Swails (Sat Jan 14 2012 - 06:49:51 PST)
[AMBER] Water considered in Amber11. Sudarshan Debnath (Sat Jan 14 2012 - 00:44:25 PST)
- Re: [AMBER] Water considered in Amber11. Jason Swails (Sat Jan 14 2012 - 06:31:21 PST)
[AMBER] Question related to the Force Field and water Sindrila Dutta banik (Sat Jan 14 2012 - 00:56:05 PST)
- Re: [AMBER] Question related to the Force Field and water case (Sat Jan 14 2012 - 06:07:03 PST)
[AMBER] strip water and save new trajectory Hirdesh Kumar (Sat Jan 14 2012 - 06:27:49 PST)
- Re: [AMBER] strip water and save new trajectory Jason Swails (Sat Jan 14 2012 - 06:37:06 PST)
  - Re: [AMBER] strip water and save new trajectory Hirdesh Kumar (Sun Jan 15 2012 - 20:36:53 PST)
[AMBER] Question related to the B factor Sindrila Dutta banik (Sat Jan 14 2012 - 09:03:19 PST)
- Re: [AMBER] Question related to the B factor Bill Ross (Sat Jan 14 2012 - 11:25:36 PST)
  - [AMBER] Question related to the B factor Sindrila Dutta banik (Mon Jan 16 2012 - 09:43:15 PST)
    - Re: [AMBER] Question related to the B factor Adrian Roitberg (Mon Jan 16 2012 - 09:54:20 PST)
    - Re: [AMBER] Question related to the B factor Bill Ross (Mon Jan 16 2012 - 11:46:27 PST)
[AMBER] mpi4py installation for mmpbsa_py Vlad Cojocaru (Sat Jan 14 2012 - 14:39:58 PST)
- Re: [AMBER] mpi4py installation for mmpbsa_py Jason Swails (Sat Jan 14 2012 - 16:59:34 PST)
[AMBER] Using glycam06 under Amber8 john Kerk (Sun Jan 15 2012 - 10:45:19 PST)
- Re: [AMBER] Using glycam06 under Amber8 Lachele Foley (Lists) (Sun Jan 15 2012 - 11:07:58 PST)
  - Re: [AMBER] Using glycam06 under Amber8 john Kerk (Sun Jan 15 2012 - 23:42:00 PST)
    - Re: [AMBER] Using glycam06 under Amber8 Lachele Foley (Lists) (Mon Jan 16 2012 - 10:52:14 PST)
[AMBER] nab string functions M. L. Dodson (Sun Jan 15 2012 - 16:34:33 PST)
- Re: [AMBER] nab string functions Daniel Roe (Sun Jan 15 2012 - 16:55:33 PST)
  - Re: [AMBER] nab string functions M. L. Dodson (Sun Jan 15 2012 - 17:17:31 PST)
    - Re: [AMBER] nab string functions Daniel Roe (Sun Jan 15 2012 - 17:51:03 PST)
  - Re: [AMBER] nab string functions M. L. Dodson (Sun Jan 15 2012 - 17:24:48 PST)
- Re: [AMBER] nab string functions David A Case (Mon Jan 16 2012 - 05:51:20 PST)
[AMBER] Calculate the cosine content of PC surasak chunsrivirot (Mon Jan 16 2012 - 02:44:20 PST)
- Re: [AMBER] Calculate the cosine content of PC Ben Roberts (Sat Jan 21 2012 - 09:31:45 PST)
  - Re: [AMBER] Calculate the cosine content of PC surasak chunsrivirot (Thu Jan 26 2012 - 19:57:46 PST)
[AMBER] Problem regarding Molecular Dynamics simulation of DNA using Parmbsc0 and ff99sb Muhammad Khaled Tumbi (Tue Jan 17 2012 - 05:12:51 PST)
- Re: [AMBER] Problem regarding Molecular Dynamics simulation of DNA using Parmbsc0 and ff99sb steinbrt.rci.rutgers.edu (Tue Jan 17 2012 - 06:31:01 PST)
- Re: [AMBER] Problem regarding Molecular Dynamics simulation of DNA using Parmbsc0 and ff99sb Thomas Cheatham III (Tue Jan 17 2012 - 14:49:21 PST)
[AMBER] Conversion of binary velocity files to pdb style Ganesh Kamath (Tue Jan 17 2012 - 09:22:14 PST)
[AMBER] :How to get 1PLC_mod.pdb from 1PLC.pdb [TUTORIAL A1 - SECTION 1] Mahendra B Thapa (Tue Jan 17 2012 - 14:24:19 PST)
- Re: [AMBER] :How to get 1PLC_mod.pdb from 1PLC.pdb [TUTORIAL A1 - SECTION 1] case (Tue Jan 17 2012 - 18:14:10 PST)
[AMBER] MCPB : addFragment in case of CYM kanika singal (Tue Jan 17 2012 - 22:50:08 PST)
- Re: [AMBER] MCPB : addFragment in case of CYM Ben Roberts (Sat Jan 21 2012 - 09:38:50 PST)
[AMBER] chamber segfault Hannes Loeffler (Wed Jan 18 2012 - 02:44:12 PST)
- Re: [AMBER] chamber segfault Jason Swails (Wed Jan 18 2012 - 06:02:00 PST)
  - Re: [AMBER] chamber segfault Hannes Loeffler (Wed Jan 18 2012 - 06:38:32 PST)
[AMBER] Minimization problem for a homotrimer of small molecules Baptiste Legrand (Wed Jan 18 2012 - 03:22:36 PST)
- Re: [AMBER] Minimization problem for a homotrimer of small molecules Jason Swails (Wed Jan 18 2012 - 06:08:03 PST)
  - Re: [AMBER] Minimization problem for a homotrimer of small molecules Baptiste Legrand (Wed Jan 18 2012 - 06:41:53 PST)
    - Re: [AMBER] Minimization problem for a homotrimer of small molecules Jason Swails (Wed Jan 18 2012 - 07:55:09 PST)
    - [AMBER] Problem with magnesium ions using FF10 in leap Jesper Sørensen (Wed Jan 18 2012 - 08:05:56 PST)
    - Re: [AMBER] Problem with magnesium ions using FF10 in leap Jesper Sørensen (Wed Jan 18 2012 - 08:33:50 PST)
    - Re: [AMBER] Problem with magnesium ions using FF10 in leap David A Case (Wed Jan 18 2012 - 08:49:28 PST)
    - Re: [AMBER] Problem with magnesium ions using FF10 in leap Jesper Sørensen (Wed Jan 18 2012 - 09:17:39 PST)
    - Re: [AMBER] Problem with magnesium ions using FF10 in leap Jason Swails (Wed Jan 18 2012 - 10:40:39 PST)
    - Re: [AMBER] Problem with magnesium ions using FF10 in leap David A Case (Wed Jan 18 2012 - 12:19:43 PST)
    - Re: [AMBER] Problem with magnesium ions using FF10 in leap Jesper Sørensen (Wed Jan 18 2012 - 12:42:58 PST)
[AMBER] nmode error Urszula Uciechowska (Wed Jan 18 2012 - 03:42:30 PST)
- Re: [AMBER] nmode error Cenk $Jenk$ Andac (Wed Jan 18 2012 - 05:19:42 PST)
[AMBER] Adjusting density Beale, John (Wed Jan 18 2012 - 05:28:31 PST)
- Re: [AMBER] Adjusting density Brian Radak (Wed Jan 18 2012 - 05:45:42 PST)
  - Re: [AMBER] Adjusting density Jason Swails (Wed Jan 18 2012 - 05:53:06 PST)
- Re: [AMBER] Adjusting density Hugh Heldenbrand (Wed Jan 18 2012 - 05:51:04 PST)
[AMBER] AmberTools Installation Error Hevener, Kirk (Wed Jan 18 2012 - 08:59:15 PST)
- Re: [AMBER] AmberTools Installation Error Jason Swails (Wed Jan 18 2012 - 10:38:07 PST)
  - Re: [AMBER] AmberTools Installation Error Hevener, Kirk (Thu Jan 19 2012 - 06:00:40 PST)
    - Re: [AMBER] AmberTools Installation Error Jason Swails (Thu Jan 19 2012 - 06:45:49 PST)
Re: [AMBER] FW: :How to get 1PLC_mod.pdb from 1PLC.pdb [TUTORIAL A1 - SECTION 1] Mahendra B Thapa (Wed Jan 18 2012 - 10:25:21 PST)
- Re: [AMBER] FW: :How to get 1PLC_mod.pdb from 1PLC.pdb [TUTORIAL A1 - SECTION 1] Jason Swails (Wed Jan 18 2012 - 11:43:26 PST)
Re: [AMBER] FW: FW: :How to get 1PLC_mod.pdb from 1PLC.pdb [TUTORIAL A1 - SECTION 1] Mahendra B Thapa (Wed Jan 18 2012 - 12:10:26 PST)
- Re: [AMBER] FW: FW: :How to get 1PLC_mod.pdb from 1PLC.pdb [TUTORIAL A1 - SECTION 1] David A Case (Thu Jan 19 2012 - 04:43:26 PST)
[AMBER] simulation with implicit solvent runs longer than explicit? Victor Ma (Wed Jan 18 2012 - 13:48:01 PST)
- Re: [AMBER] simulation with implicit solvent runs longer than explicit? Aron Broom (Wed Jan 18 2012 - 14:01:35 PST)
  - Re: [AMBER] simulation with implicit solvent runs longer than explicit? Victor Ma (Wed Jan 18 2012 - 14:11:21 PST)
    - Re: [AMBER] simulation with implicit solvent runs longer than explicit? Adrian Roitberg (Wed Jan 18 2012 - 14:22:16 PST)
    - Re: [AMBER] simulation with implicit solvent runs longer than explicit? Victor Ma (Wed Jan 18 2012 - 14:40:31 PST)
    - Re: [AMBER] simulation with implicit solvent runs longer than explicit? Adrian Roitberg (Wed Jan 18 2012 - 14:22:35 PST)
[AMBER] amber hangs on minimization Jorgen Simonsen (Thu Jan 19 2012 - 01:04:08 PST)
- Re: [AMBER] amber hangs on minimization David A Case (Thu Jan 19 2012 - 04:49:11 PST)
  - Re: [AMBER] amber hangs on minimization Jorgen Simonsen (Thu Jan 19 2012 - 05:10:26 PST)
    - Re: [AMBER] amber hangs on minimization David A Case (Thu Jan 19 2012 - 06:12:12 PST)
[AMBER] Glycine in QM region Fernando Martín García (Thu Jan 19 2012 - 02:36:18 PST)
[AMBER] error message for installing amber 10 Per Jr. Greisen (Thu Jan 19 2012 - 03:46:24 PST)
- Re: [AMBER] error message for installing amber 10 David A Case (Thu Jan 19 2012 - 05:16:03 PST)
- Re: [AMBER] error message for installing amber 10 Terry (Thu Jan 19 2012 - 05:30:17 PST)
  - Re: [AMBER] error message for installing amber 10 Per Jr. Greisen (Thu Jan 19 2012 - 05:57:04 PST)
    - Re: [AMBER] error message for installing amber 10 David A Case (Thu Jan 19 2012 - 06:15:10 PST)
[AMBER] MMPBSA analysis vaibhav dixit (Thu Jan 19 2012 - 04:44:58 PST)
[AMBER] negative DeltaGsolv in MMPBSA vaibhav dixit (Thu Jan 19 2012 - 07:49:42 PST)
[AMBER] Amber11 tests fail Massimiliano Porrini (Thu Jan 19 2012 - 10:05:10 PST)
- Re: [AMBER] Amber11 tests fail David A Case (Thu Jan 19 2012 - 11:06:04 PST)
  - Re: [AMBER] Amber11 tests fail Massimiliano Porrini (Thu Jan 19 2012 - 11:20:44 PST)
    - Re: [AMBER] Amber11 tests fail Jason Swails (Thu Jan 19 2012 - 11:33:47 PST)
    - Re: [AMBER] Amber11 tests fail Massimiliano Porrini (Fri Jan 20 2012 - 05:52:48 PST)
    - Re: [AMBER] Amber11 tests fail Jason Swails (Fri Jan 20 2012 - 06:20:19 PST)
    - Re: [AMBER] Amber11 tests fail Massimiliano Porrini (Fri Jan 20 2012 - 10:17:11 PST)
    - Re: [AMBER] Amber11 tests fail Jason Swails (Fri Jan 20 2012 - 11:54:14 PST)
- Re: [AMBER] Amber11 tests fail Massimiliano Porrini (Sat Jan 21 2012 - 04:33:50 PST)
- Re: [AMBER] Amber11 tests fail Massimiliano Porrini (Sat Jan 21 2012 - 04:35:22 PST)
  - Re: [AMBER] Amber11 tests fail Jason Swails (Sat Jan 21 2012 - 07:28:41 PST)
    - Re: [AMBER] Amber11 tests fail Massimiliano Porrini (Sun Jan 22 2012 - 01:56:09 PST)
    - Re: [AMBER] Amber11 tests fail Massimiliano Porrini (Tue Jan 24 2012 - 03:52:46 PST)
    - Re: [AMBER] Amber11 tests fail Massimiliano Porrini (Wed Jan 25 2012 - 11:53:37 PST)
    - Re: [AMBER] Amber11 tests fail Jason Swails (Wed Jan 25 2012 - 12:07:46 PST)
    - Re: [AMBER] Amber11 tests fail Massimiliano Porrini (Thu Jan 26 2012 - 04:03:22 PST)
    - Re: [AMBER] Amber11 tests fail Jason Swails (Thu Jan 26 2012 - 05:21:27 PST)
    - Re: [AMBER] Amber11 tests fail Massimiliano Porrini (Thu Jan 26 2012 - 05:27:41 PST)
    - Re: [AMBER] Amber11 tests fail Jason Swails (Thu Jan 26 2012 - 06:46:34 PST)
    - Re: [AMBER] Amber11 tests fail Massimiliano Porrini (Thu Jan 26 2012 - 09:06:34 PST)
    - Re: [AMBER] Amber11 tests fail Jason Swails (Thu Jan 26 2012 - 10:20:07 PST)
    - Re: [AMBER] Amber11 tests fail Massimiliano Porrini (Thu Jan 26 2012 - 11:04:30 PST)
    - Re: [AMBER] Amber11 tests fail Jason Swails (Thu Jan 26 2012 - 12:12:11 PST)
[AMBER] MCPB: error Pls help kanika singal (Fri Jan 20 2012 - 06:46:27 PST)
- Re: [AMBER] MCPB: error Pls help Martin Peters (Fri Jan 20 2012 - 07:56:45 PST)
[AMBER] MD trajectory extraction using ptraj Lianhu Wei (Fri Jan 20 2012 - 07:25:09 PST)
- Re: [AMBER] MD trajectory extraction using ptraj Daniel Roe (Fri Jan 20 2012 - 07:50:39 PST)
  - Re: [AMBER] MD trajectory extraction using ptraj Lianhu Wei (Fri Jan 20 2012 - 09:10:48 PST)
  - Re: [AMBER] MD trajectory extraction using ptraj Lianhu Wei (Fri Jan 20 2012 - 11:54:56 PST)
[AMBER] which fitting methods should I use for OPLS FF? Albert (Fri Jan 20 2012 - 22:23:03 PST)
[AMBER] MCPB: error Pls help kanika singal (Sat Jan 21 2012 - 02:18:56 PST)
- Re: [AMBER] MCPB: error Pls help kanika singal (Sat Jan 21 2012 - 23:26:48 PST)
  - Re: [AMBER] MCPB: error Pls help Ben Roberts (Mon Jan 23 2012 - 12:06:32 PST)
[AMBER] positive van der Waal energy and comparison Jio M (Sat Jan 21 2012 - 02:34:13 PST)
- Re: [AMBER] positive van der Waal energy and comparison David A Case (Thu Jan 26 2012 - 05:13:39 PST)
[AMBER] ptraj contacts output query Rajeswari A. (Sat Jan 21 2012 - 04:04:41 PST)
Re: [AMBER] [q4md-fft] which fitting methods should I use for OPLS FF? FyD (Sat Jan 21 2012 - 09:03:37 PST)
[AMBER] Amber for monolayer Sindrila Dutta banik (Sat Jan 21 2012 - 19:40:41 PST)
[AMBER] installation subrata paul (Sun Jan 22 2012 - 08:27:37 PST)
- Re: [AMBER] installation case (Sun Jan 22 2012 - 12:36:00 PST)
  - Re: [AMBER] installation mehdi bagherpoor (Sun Jan 22 2012 - 12:45:20 PST)
[AMBER] md.crd file is very large! john Kerk (Mon Jan 23 2012 - 00:22:25 PST)
- Re: [AMBER] md.crd file is very large! Daniel Sindhikara (Mon Jan 23 2012 - 00:32:54 PST)
  - Re: [AMBER] md.crd file is very large! john Kerk (Mon Jan 23 2012 - 01:10:53 PST)
    - Re: [AMBER] md.crd file is very large! Daniel Sindhikara (Mon Jan 23 2012 - 01:18:24 PST)
    - Re: [AMBER] md.crd file is very large! Jason Swails (Mon Jan 23 2012 - 07:22:37 PST)
[AMBER] adding hydrogens to protein crystal structure abinayar.imsc.res.in (Mon Jan 23 2012 - 04:43:45 PST)
- Re: [AMBER] adding hydrogens to protein crystal structure Daniel Roe (Mon Jan 23 2012 - 06:22:58 PST)
[AMBER] superimpose on first snapshot Simon Becker (Mon Jan 23 2012 - 06:05:03 PST)
- Re: [AMBER] superimpose on first snapshot Daniel Roe (Mon Jan 23 2012 - 08:02:31 PST)
  - Re: [AMBER] superimpose on first snapshot Simon Becker (Mon Jan 23 2012 - 23:35:37 PST)
[AMBER] Molecular Modelling Workshop 2012 in Erlangen, Germany Harald Lanig (Mon Jan 23 2012 - 08:15:17 PST)
[AMBER] AmberTools 1.5 & Centos6 Irene Newhouse (Mon Jan 23 2012 - 11:49:36 PST)
- Re: [AMBER] AmberTools 1.5 & Centos6 Jason Swails (Mon Jan 23 2012 - 13:35:43 PST)
  - Re: [AMBER] AmberTools 1.5 & Centos6 Irene Newhouse (Tue Jan 24 2012 - 09:22:21 PST)
    - Re: [AMBER] AmberTools 1.5 & Centos6 Jason Swails (Tue Jan 24 2012 - 10:16:44 PST)
    - Re: [AMBER] AmberTools 1.5 & Centos6 Irene Newhouse (Tue Jan 24 2012 - 11:24:34 PST)
    - Re: [AMBER] AmberTools 1.5 & Centos6 Irene Newhouse (Tue Jan 24 2012 - 11:43:41 PST)
    - Re: [AMBER] AmberTools 1.5 & Centos6 Irene Newhouse (Tue Jan 24 2012 - 12:01:52 PST)
    - Re: [AMBER] AmberTools 1.5 & Centos6 Ismail, Mohd F. (Tue Jan 24 2012 - 12:08:13 PST)
    - Re: [AMBER] AmberTools 1.5 & Centos6 Jason Swails (Tue Jan 24 2012 - 12:32:05 PST)
    - Re: [AMBER] AmberTools 1.5 & Centos6 Irene Newhouse (Tue Jan 24 2012 - 13:08:10 PST)
    - Re: [AMBER] AmberTools 1.5 & Centos6 Daniel Roe (Tue Jan 24 2012 - 13:22:11 PST)
    - Re: [AMBER] AmberTools 1.5 & Centos6 Irene Newhouse (Wed Jan 25 2012 - 09:48:40 PST)
    - [AMBER] Building of Amber/APBS module peter.stauffert.boehringer-ingelheim.com (Fri Jan 27 2012 - 12:28:52 PST)
    - Re: [AMBER] Building of Amber/APBS module Jason Swails (Fri Jan 27 2012 - 13:28:16 PST)
[AMBER] Steered Molecular Dynamics: some questions George Tzotzos (Tue Jan 24 2012 - 05:40:57 PST)
- Re: [AMBER] Steered Molecular Dynamics: some questions Dwight McGee (Tue Jan 24 2012 - 18:06:57 PST)
  - Re: [AMBER] Steered Molecular Dynamics: some questions George Tzotzos (Tue Jan 24 2012 - 23:39:21 PST)
  - Re: [AMBER] Steered Molecular Dynamics: some questions George Tzotzos (Tue Jan 31 2012 - 09:44:23 PST)
    - Re: [AMBER] Steered Molecular Dynamics: some questions Dwight McGee (Tue Jan 31 2012 - 11:15:31 PST)
[AMBER] energy decomposition equation Anglea A. (Tue Jan 24 2012 - 08:53:13 PST)
- Re: [AMBER] energy decomposition equation Jason Swails (Tue Jan 24 2012 - 10:25:31 PST)
[AMBER] creating input files for a protein connected to a fatty acid chain - angle parameters missing error Amir Marcovitz (Tue Jan 24 2012 - 13:06:37 PST)
- Re: [AMBER] creating input files for a protein connected to a fatty acid chain - angle parameters missing error FyD (Tue Jan 24 2012 - 23:42:09 PST)
[AMBER] GBSA decomposition per reside SANCHEZ MURCIA, PEDRO ALEJANDRO (Tue Jan 24 2012 - 13:48:58 PST)
[AMBER] GBSA decomposition per reside SANCHEZ MURCIA, PEDRO ALEJANDRO (Tue Jan 24 2012 - 13:49:18 PST)
[AMBER] GBSA decomposition per reside SANCHEZ MURCIA, PEDRO ALEJANDRO (Tue Jan 24 2012 - 13:53:09 PST)
[AMBER] [qm2_pm6_hof_module.o] Error 1 Carlos Sosa (Tue Jan 24 2012 - 14:11:51 PST)
- Re: [AMBER] [qm2_pm6_hof_module.o] Error 1 case (Wed Jan 25 2012 - 04:52:10 PST)
[AMBER] velocities in restart files taken from ptraj Sidney Elmer (Tue Jan 24 2012 - 16:14:02 PST)
- Re: [AMBER] velocities in restart files taken from ptraj Bill Ross (Tue Jan 24 2012 - 16:29:05 PST)
  - Re: [AMBER] velocities in restart files taken from ptraj Sidney Elmer (Tue Jan 24 2012 - 17:23:42 PST)
    - Re: [AMBER] velocities in restart files taken from ptraj Jason Swails (Tue Jan 24 2012 - 20:37:50 PST)
    - Re: [AMBER] velocities in restart files taken from ptraj Bill Ross (Tue Jan 24 2012 - 21:10:40 PST)
- Re: [AMBER] velocities in restart files taken from ptraj Thomas Cheatham (Tue Jan 24 2012 - 17:28:51 PST)
[AMBER] anal in parallel Jio M (Wed Jan 25 2012 - 02:43:17 PST)
- Re: [AMBER] anal in parallel David A Case (Wed Jan 25 2012 - 04:50:47 PST)
[AMBER] analysis in all simulation time Atila Petrosian (Wed Jan 25 2012 - 02:44:40 PST)
- Re: [AMBER] analysis in all simulation time Marc van der Kamp (Wed Jan 25 2012 - 02:56:36 PST)
  - Re: [AMBER] analysis in all simulation time Atila Petrosian (Wed Jan 25 2012 - 03:09:46 PST)
    - Re: [AMBER] analysis in all simulation time Marc van der Kamp (Wed Jan 25 2012 - 04:00:33 PST)
[AMBER] temperature and pressure coupling shahab shariati (Wed Jan 25 2012 - 03:53:45 PST)
- Re: [AMBER] temperature and pressure coupling Marc van der Kamp (Wed Jan 25 2012 - 04:03:29 PST)
[AMBER] peptide+sugar Urszula Uciechowska (Wed Jan 25 2012 - 04:44:51 PST)
- Re: [AMBER] peptide+sugar FyD (Wed Jan 25 2012 - 07:22:05 PST)
[AMBER] solvation in a cubic box shahab shariati (Wed Jan 25 2012 - 05:11:49 PST)
- Re: [AMBER] solvation in a cubic box David A Case (Wed Jan 25 2012 - 06:39:18 PST)
[AMBER] Problem related to the order parameter Sindrila Dutta banik (Wed Jan 25 2012 - 07:47:23 PST)
[AMBER] installation of sander.MPI Jorgen Simonsen (Wed Jan 25 2012 - 09:18:15 PST)
- Re: [AMBER] installation of sander.MPI Jason Swails (Wed Jan 25 2012 - 09:56:13 PST)
  - Re: [AMBER] installation of sander.MPI Jorgen Simonsen (Wed Jan 25 2012 - 11:09:46 PST)
    - Re: [AMBER] installation of sander.MPI Jason Swails (Wed Jan 25 2012 - 11:23:34 PST)
    - Re: [AMBER] installation of sander.MPI Jorgen Simonsen (Wed Jan 25 2012 - 11:48:16 PST)
    - Re: [AMBER] installation of sander.MPI Jason Swails (Wed Jan 25 2012 - 12:16:22 PST)
    - Re: [AMBER] installation of sander.MPI Jorgen Simonsen (Wed Jan 25 2012 - 12:38:58 PST)
    - Re: [AMBER] installation of sander.MPI Ross Walker (Wed Jan 25 2012 - 15:10:22 PST)
    - Re: [AMBER] installation of sander.MPI Jorgen Simonsen (Thu Jan 26 2012 - 06:19:16 PST)
    - Re: [AMBER] installation of sander.MPI David A Case (Thu Jan 26 2012 - 07:20:24 PST)
    - Re: [AMBER] installation of sander.MPI Jason Swails (Wed Jan 25 2012 - 12:04:31 PST)
    - Re: [AMBER] installation of sander.MPI Jorgen Simonsen (Wed Jan 25 2012 - 12:10:51 PST)
[AMBER] Review MD sampling techniques Thomas Exner (Wed Jan 25 2012 - 09:57:55 PST)
- Re: [AMBER] Review MD sampling techniques Matthew Zwier (Thu Jan 26 2012 - 05:20:56 PST)
[AMBER] divcon: error while loading shared libraries: libvml.so: cannot open shared object file rainy908 (Wed Jan 25 2012 - 11:21:16 PST)
- Re: [AMBER] divcon: error while loading shared libraries: libvml.so: cannot open shared object file rainy908 (Wed Jan 25 2012 - 11:25:54 PST)
- Re: [AMBER] divcon: error while loading shared libraries: libvml.so: cannot open shared object file FyD (Thu Jan 26 2012 - 00:06:21 PST)
[AMBER] Workshop and Tutorial Announcement: State-of-the-Art Algorithms for Molecular Dynamics, April 30th to May 4th 2012, Edinburgh UK Ross Walker (Wed Jan 25 2012 - 11:38:24 PST)
[AMBER] Cannot find $AMBERHOME/test/antechamber bin wang (Wed Jan 25 2012 - 13:28:03 PST)
- Re: [AMBER] Cannot find $AMBERHOME/test/antechamber Jason Swails (Wed Jan 25 2012 - 16:56:37 PST)
[AMBER] problem python compiling when install AmberTools 1.5 setyanto md (Thu Jan 26 2012 - 06:28:18 PST)
- Re: [AMBER] problem python compiling when install AmberTools 1.5 Jason Swails (Thu Jan 26 2012 - 06:45:55 PST)
  - Re: [AMBER] problem python compiling when install AmberTools 1.5 setyanto md (Thu Jan 26 2012 - 07:13:30 PST)
    - Re: [AMBER] problem python compiling when install AmberTools 1.5 Jason Swails (Thu Jan 26 2012 - 09:04:46 PST)
[AMBER] makeDIST_RST command problem Olena Dobrovolska (Thu Jan 26 2012 - 08:39:05 PST)
- Re: [AMBER] makeDIST_RST command problem David A Case (Thu Jan 26 2012 - 13:34:51 PST)
  - Re: [AMBER] makeDIST_RST command problem Olena Dobrovolska (Fri Jan 27 2012 - 06:00:55 PST)
    - Re: [AMBER] makeDIST_RST command problem David A Case (Fri Jan 27 2012 - 11:58:58 PST)
    - Re: [AMBER] makeDIST_RST command problem Olena Dobrovolska (Mon Jan 30 2012 - 08:59:55 PST)
    - Re: [AMBER] makeDIST_RST command problem David A Case (Mon Jan 30 2012 - 14:37:28 PST)
    - Re: [AMBER] makeDIST_RST command problem Olena Dobrovolska (Tue Jan 31 2012 - 01:11:24 PST)
    - Re: [AMBER] makeDIST_RST command problem David A Case (Tue Jan 31 2012 - 04:47:42 PST)
    - Re: [AMBER] makeDIST_RST command problem Olena Dobrovolska (Tue Jan 31 2012 - 05:03:05 PST)
    - Re: [AMBER] makeDIST_RST command problem David A Case (Tue Jan 31 2012 - 06:35:39 PST)
    - Re: [AMBER] makeDIST_RST command problem Olena Dobrovolska (Tue Jan 31 2012 - 07:33:09 PST)
    - Re: [AMBER] makeDIST_RST command problem case (Tue Jan 31 2012 - 18:33:47 PST)
    - Re: [AMBER] makeDIST_RST command problem Olena Dobrovolska (Thu Feb 02 2012 - 08:13:42 PST)
[AMBER] Splitting cyclic molecule into QM and MM parts Dmitry Nilov (Fri Jan 27 2012 - 05:12:33 PST)
- Re: [AMBER] Splitting cyclic molecule into QM and MM parts Brian Radak (Fri Jan 27 2012 - 07:51:09 PST)
  - Re: [AMBER] Splitting cyclic molecule into QM and MM parts Dmitry Nilov (Sat Jan 28 2012 - 01:33:53 PST)
    - Re: [AMBER] Splitting cyclic molecule into QM and MM parts Brian Radak (Sat Jan 28 2012 - 13:50:34 PST)
[AMBER] compiler-dependent error: "Invalid atom or grouping specified in restraint." Jan-Philip Gehrcke (Fri Jan 27 2012 - 05:51:27 PST)
- Re: [AMBER] compiler-dependent error: "Invalid atom or grouping specified in restraint." Jason Swails (Fri Jan 27 2012 - 07:28:24 PST)
  - Re: [AMBER] compiler-dependent error: "Invalid atom or grouping specified in restraint." Jan-Philip Gehrcke (Fri Jan 27 2012 - 08:06:25 PST)
    - Re: [AMBER] compiler-dependent error: "Invalid atom or grouping specified in restraint." Jason Swails (Fri Jan 27 2012 - 10:15:12 PST)
    - Re: [AMBER] compiler-dependent error: "Invalid atom or grouping specified in restraint." Jan-Philip Gehrcke (Mon Jan 30 2012 - 08:21:25 PST)
    - Re: [AMBER] compiler-dependent error: "Invalid atom or grouping specified in restraint." David A Case (Mon Jan 30 2012 - 14:32:09 PST)
    - Re: [AMBER] compiler-dependent error: "Invalid atom or grouping specified in restraint." Jan-Philip Gehrcke (Tue Jan 31 2012 - 02:49:47 PST)
- Re: [AMBER] compiler-dependent error: "Invalid atom or grouping specified in restraint." David A Case (Thu Feb 16 2012 - 06:33:07 PST)
  - Re: [AMBER] compiler-dependent error: "Invalid atom or grouping specified in restraint." Jan-Philip Gehrcke (Mon Feb 20 2012 - 11:17:49 PST)
    - Re: [AMBER] compiler-dependent error: "Invalid atom or grouping specified in restraint." Jan-Philip Gehrcke (Fri Mar 09 2012 - 06:28:38 PST)
    - Re: [AMBER] compiler-dependent error: "Invalid atom or grouping specified in restraint." David A. Case (Sun Mar 11 2012 - 10:54:23 PDT)
    - Re: [AMBER] compiler-dependent error: "Invalid atom or grouping specified in restraint." Jason Swails (Sun Mar 11 2012 - 14:42:36 PDT)
[AMBER] antechamber and parm.frosst thomas.fox.boehringer-ingelheim.com (Fri Jan 27 2012 - 07:19:33 PST)
[AMBER] Building Wrapped DNA in NAB Ian Slaymaker (Fri Jan 27 2012 - 09:56:55 PST)
- Re: [AMBER] Building Wrapped DNA in NAB David A Case (Wed Feb 15 2012 - 12:32:04 PST)
[AMBER] Editing structure via Xleap James Starlight (Fri Jan 27 2012 - 10:28:06 PST)
- Re: [AMBER] Editing structure via Xleap David A Case (Fri Jan 27 2012 - 12:21:18 PST)
- Re: [AMBER] Editing structure via Xleap Dean Cuebas (Fri Jan 27 2012 - 12:55:31 PST)
- Re: [AMBER] Editing structure via Xleap FyD (Fri Jan 27 2012 - 23:19:35 PST)
  - Re: [AMBER] Editing structure via Xleap James Starlight (Sat Jan 28 2012 - 00:44:11 PST)
    - Re: [AMBER] Editing structure via Xleap case (Sat Jan 28 2012 - 06:39:31 PST)
    - Re: [AMBER] Editing structure via Xleap FyD (Sat Jan 28 2012 - 09:03:28 PST)
    - Re: [AMBER] Editing structure via Xleap Bill Ross (Sun Jan 29 2012 - 11:07:57 PST)
[AMBER] NMODE list index out of range error Sangeetha B (Fri Jan 27 2012 - 22:43:41 PST)
- Re: [AMBER] NMODE list index out of range error Jason Swails (Sat Jan 28 2012 - 07:42:42 PST)
  - Re: [AMBER] NMODE list index out of range error Sangeetha B (Mon Jan 30 2012 - 20:26:18 PST)
  - Re: [AMBER] NMODE list index out of range error Sangeetha B (Wed Feb 01 2012 - 20:18:27 PST)
    - [AMBER] Fwd: NMODE list index out of range error Sangeetha B (Tue Feb 07 2012 - 03:52:42 PST)
    - Re: [AMBER] Fwd: NMODE list index out of range error Jason Swails (Tue Feb 07 2012 - 08:51:16 PST)
    - Re: [AMBER] Fwd: NMODE list index out of range error Jason Swails (Tue Feb 07 2012 - 12:05:16 PST)
    - Re: [AMBER] Fwd: NMODE list index out of range error Sangeetha B (Wed Feb 08 2012 - 06:35:30 PST)
    - Re: [AMBER] Fwd: NMODE list index out of range error Jason Swails (Thu Feb 09 2012 - 12:20:03 PST)
[AMBER] problem with SASA calculation Maryam Hamzehee (Sat Jan 28 2012 - 01:21:42 PST)
- Re: [AMBER] problem with SASA calculation case (Sat Jan 28 2012 - 06:47:57 PST)
- Re: [AMBER] problem with SASA calculation Daniel Roe (Sat Jan 28 2012 - 07:29:22 PST)
  - Re: [AMBER] problem with SASA calculation case (Sat Jan 28 2012 - 09:43:58 PST)
- Re: [AMBER] problem with SASA calculation Jason Swails (Sat Jan 28 2012 - 07:32:56 PST)
- Re: [AMBER] problem with SASA calculation Maryam Hamzehee (Sun Jan 29 2012 - 05:31:15 PST)
- Re: [AMBER] problem with SASA calculation Maryam Hamzehee (Mon Jan 30 2012 - 03:23:38 PST)
[AMBER] loading of fullerene2160 gargi borgohai (Sat Jan 28 2012 - 09:49:03 PST)
- Re: [AMBER] loading of fullerene2160 FyD (Sun Jan 29 2012 - 10:09:04 PST)
[AMBER] Can I set the direction of the pulling force? Qian Wang (Sat Jan 28 2012 - 10:58:36 PST)
- Re: [AMBER] Can I set the direction of the pulling force? Brian Radak (Sat Jan 28 2012 - 14:24:04 PST)
  - Re: [AMBER] Can I set the direction of the pulling force? Qian Wang (Sat Jan 28 2012 - 14:37:54 PST)
    - Re: [AMBER] Can I set the direction of the pulling force? Brian Radak (Sat Jan 28 2012 - 14:52:20 PST)
[AMBER] syntax error in ambpdb leila karami (Sun Jan 29 2012 - 03:01:38 PST)
- Re: [AMBER] syntax error in ambpdb mehdi bagherpoor (Sun Jan 29 2012 - 08:52:36 PST)
  - Re: [AMBER] syntax error in ambpdb Bill Ross (Sun Jan 29 2012 - 11:40:13 PST)
- Re: [AMBER] syntax error in ambpdb case (Sun Jan 29 2012 - 09:05:23 PST)
[AMBER] Preparation of the topology file by means of Antechamber James Starlight (Sun Jan 29 2012 - 09:12:21 PST)
- Re: [AMBER] Preparation of the topology file by means of Antechamber Jason Swails (Mon Jan 30 2012 - 07:40:54 PST)
  - Re: [AMBER] Preparation of the topology file by means of Antechamber James Starlight (Mon Jan 30 2012 - 22:11:44 PST)
    - Re: [AMBER] Preparation of the topology file by means of Antechamber FyD (Mon Jan 30 2012 - 23:58:32 PST)
[AMBER] loading of fullerene2160 gargi borgohai (Sun Jan 29 2012 - 20:49:41 PST)
- Re: [AMBER] loading of fullerene2160 FyD (Sun Jan 29 2012 - 22:26:59 PST)
[AMBER] clustering in ptraj doesn't create mdrcd and pdb files Andrew Voronkov (Mon Jan 30 2012 - 02:29:29 PST)
[AMBER] fortran error during installation Mettu, Ramgopal (Mon Jan 30 2012 - 17:16:44 PST)
- Re: [AMBER] fortran error during installation Bill Ross (Mon Jan 30 2012 - 17:27:26 PST)
  - Re: [AMBER] fortran error during installation Mettu, Ramgopal (Mon Jan 30 2012 - 18:35:16 PST)
    - Re: [AMBER] fortran error during installation Jason Swails (Mon Jan 30 2012 - 19:53:15 PST)
    - Re: [AMBER] fortran error during installation Mettu, Ramgopal (Tue Jan 31 2012 - 07:36:26 PST)
    - Re: [AMBER] fortran error during installation case (Tue Jan 31 2012 - 18:28:59 PST)
[AMBER] antechamber doesn't create mol2 file Dian Jiao (Mon Jan 30 2012 - 22:01:27 PST)
- Re: [AMBER] antechamber doesn't create mol2 file FyD (Tue Jan 31 2012 - 00:06:59 PST)
- Re: [AMBER] antechamber doesn't create mol2 file FyD (Tue Jan 31 2012 - 22:17:03 PST)
- Re: [AMBER] antechamber doesn't create mol2 file FyD (Fri Feb 03 2012 - 00:04:42 PST)
- Re: [AMBER] antechamber doesn't create mol2 file FyD (Fri Feb 10 2012 - 00:03:26 PST)
[AMBER] AMBER9 Urszula Uciechowska (Tue Jan 31 2012 - 00:25:45 PST)
- Re: [AMBER] AMBER9 David A Case (Tue Jan 31 2012 - 04:51:06 PST)
[AMBER] Problem during pnetcdf build on CentOS 5 Jan-Philip Gehrcke (Tue Jan 31 2012 - 02:47:41 PST)
- Re: [AMBER] Problem during pnetcdf build on CentOS 5 David A Case (Tue Jan 31 2012 - 05:01:46 PST)
[AMBER] ptraj.MPI Sel Ercan (Tue Jan 31 2012 - 03:55:12 PST)
- Re: [AMBER] ptraj.MPI David A Case (Tue Jan 31 2012 - 05:03:27 PST)
  - Re: [AMBER] ptraj.MPI Sel Ercan (Tue Jan 31 2012 - 08:41:13 PST)
    - Re: [AMBER] ptraj.MPI case (Tue Jan 31 2012 - 18:35:32 PST)
    - Re: [AMBER] ptraj.MPI Jason Swails (Tue Jan 31 2012 - 19:22:03 PST)
[AMBER] Constant pH George Tzotzos (Tue Jan 31 2012 - 04:26:04 PST)
- Re: [AMBER] Constant pH Jason Swails (Tue Jan 31 2012 - 05:00:15 PST)
  - Re: [AMBER] Constant pH George Tzotzos (Tue Jan 31 2012 - 05:08:20 PST)
    - Re: [AMBER] Constant pH Jason Swails (Tue Jan 31 2012 - 07:14:51 PST)
[AMBER] Ambiguous C0 atom type Vlastimil Zíma (Tue Jan 31 2012 - 05:23:47 PST)
- Re: [AMBER] Ambiguous C0 atom type David A Case (Tue Jan 31 2012 - 06:45:46 PST)
[AMBER] how to obtain prmtop and inpcrd files truely from initial pdb file? leila karami (Tue Jan 31 2012 - 06:09:07 PST)
- Re: [AMBER] how to obtain prmtop and inpcrd files truely from initial pdb file? steinbrt.rci.rutgers.edu (Tue Jan 31 2012 - 07:25:57 PST)
[AMBER] SMD: Segmentation fault George Tzotzos (Tue Jan 31 2012 - 10:32:28 PST)
[AMBER] MMPBSA problem Urszula Uciechowska (Tue Jan 31 2012 - 22:26:33 PST)
- Re: [AMBER] MMPBSA problem mish (Tue Jan 31 2012 - 22:41:30 PST)
  - Re: [AMBER] MMPBSA problem Urszula Uciechowska (Tue Jan 31 2012 - 23:36:18 PST)
    - Re: [AMBER] MMPBSA problem Sushil Mishra (Tue Jan 31 2012 - 23:53:00 PST)
    - Re: [AMBER] MMPBSA problem Urszula Uciechowska (Wed Feb 01 2012 - 00:02:35 PST)
    - Re: [AMBER] MMPBSA problem mish (Wed Feb 01 2012 - 00:49:18 PST)
[AMBER] about using MMPBSA Tan and Luo method in AMBER 11: discrepancy in ECAVITY values Therese Malliavin (Wed Feb 01 2012 - 00:48:36 PST)
- [AMBER] Fwd: about using MMPBSA Tan and Luo method in AMBER 11: discrepancy in ECAVITY values Ray Luo, Ph.D. (Wed Feb 01 2012 - 09:49:57 PST)
  - Re: [AMBER] Fwd: about using MMPBSA Tan and Luo method in AMBER 11: discrepancy in ECAVITY values Qin Cai (Thu Feb 02 2012 - 12:33:57 PST)
  - Re: [AMBER] Fwd: about using MMPBSA Tan and Luo method in AMBER 11: discrepancy in ECAVITY values Qin Cai (Thu Feb 02 2012 - 12:49:51 PST)
    - Re: [AMBER] Fwd: about using MMPBSA Tan and Luo method in AMBER 11: discrepancy in ECAVITY values Jason Swails (Thu Feb 02 2012 - 15:35:40 PST)
  - Re: [AMBER] about using MMPBSA Tan and Luo method in AMBER 11: discrepancy in ECAVITY values Fulle.uni-duesseldorf.de (Fri Feb 03 2012 - 09:26:08 PST)
[AMBER] tLEaP Алексей Раевский (Wed Feb 01 2012 - 02:38:05 PST)
- Re: [AMBER] tLEaP David A Case (Wed Feb 01 2012 - 05:53:03 PST)
- Re: [AMBER] tLEaP FyD (Wed Feb 01 2012 - 09:20:20 PST)
[AMBER] Fw: rmsd input file Sel Ercan (Wed Feb 01 2012 - 02:47:36 PST)
[AMBER] parm.frosst parameters thomas.fox.boehringer-ingelheim.com (Wed Feb 01 2012 - 07:32:24 PST)
- Re: [AMBER] parm.frosst parameters case (Sun Feb 05 2012 - 06:11:48 PST)
  - Re: [AMBER] parm.frosst parameters Guanglei Cui (Tue Feb 07 2012 - 10:16:17 PST)
    - Re: [AMBER] parm.frosst parameters Jason Swails (Tue Feb 07 2012 - 10:32:45 PST)
    - Re: [AMBER] parm.frosst parameters thomas.fox.boehringer-ingelheim.com (Tue Feb 14 2012 - 07:49:18 PST)
    - Re: [AMBER] parm.frosst parameters Jason Swails (Tue Feb 14 2012 - 15:13:10 PST)
    - Re: [AMBER] parm.frosst parameters David A. Case (Tue Feb 07 2012 - 16:57:04 PST)
    - Re: [AMBER] parm.frosst parameters Guanglei Cui (Wed Feb 08 2012 - 07:30:07 PST)
    - Re: [AMBER] parm.frosst parameters Cen Gao (Wed Feb 08 2012 - 19:22:44 PST)
[AMBER] other makeDIST_RST issues Thomas Pochapsky (Wed Feb 01 2012 - 08:34:24 PST)
- Re: [AMBER] other makeDIST_RST issues David A Case (Wed Feb 01 2012 - 09:24:49 PST)
  - Re: [AMBER] other makeDIST_RST issues Thomas Pochapsky (Fri Feb 10 2012 - 08:27:58 PST)
    - Re: [AMBER] other makeDIST_RST issues David A Case (Fri Feb 10 2012 - 11:33:41 PST)
[AMBER] Problems in ions in Amber11 TAEJIN KIM (Wed Feb 01 2012 - 11:11:30 PST)
- Re: [AMBER] Problems in ions in Amber11 InSuk Joung (Wed Feb 01 2012 - 11:19:05 PST)
  - Re: [AMBER] Problems in ions in Amber11 TAEJIN KIM (Thu Feb 02 2012 - 15:23:06 PST)
    - Re: [AMBER] Problems in ions in Amber11 Thomas Cheatham III (Thu Feb 02 2012 - 15:35:38 PST)
    - Re: [AMBER] Problems in ions in Amber11 Bill Ross (Thu Feb 02 2012 - 15:42:50 PST)
[AMBER] Multiple frcmod files in tleap: Do parameters come from the last frcmod file loaded? Joel Dockray (Wed Feb 01 2012 - 11:16:49 PST)
- Re: [AMBER] Multiple frcmod files in tleap: Do parameters come from the last frcmod file loaded? FyD (Wed Feb 01 2012 - 12:39:30 PST)
  - Re: [AMBER] Multiple frcmod files in tleap: Do parameters come from the last frcmod file loaded? Jason Swails (Wed Feb 01 2012 - 19:35:50 PST)
[AMBER] need KDO prep file Camille Sultana (Wed Feb 01 2012 - 17:06:22 PST)
- Re: [AMBER] need KDO prep file Camille Sultana (Wed Feb 01 2012 - 17:14:58 PST)
- Re: [AMBER] need KDO prep file Lachele Foley (Lists) (Wed Feb 01 2012 - 17:16:59 PST)
- Re: [AMBER] need KDO prep file FyD (Wed Feb 01 2012 - 23:34:59 PST)
  - Re: [AMBER] need KDO prep file Lachele Foley (Lists) (Thu Feb 02 2012 - 09:11:22 PST)
    - Re: [AMBER] need KDO prep file Camille Sultana (Thu Feb 02 2012 - 13:53:27 PST)
    - Re: [AMBER] need KDO prep file Lachele Foley (Lists) (Thu Feb 02 2012 - 16:43:02 PST)
    - Re: [AMBER] need KDO prep file Lachele Foley (Lists) (Mon Feb 06 2012 - 11:59:26 PST)
    - Re: [AMBER] need KDO prep file FyD (Thu Feb 02 2012 - 23:42:57 PST)
[AMBER] [Fwd: Problems with ff99SB force field reading] vladanstefanovic.kg.ac.rs (Thu Feb 02 2012 - 08:05:59 PST)
- Re: [AMBER] [Fwd: Problems with ff99SB force field reading] Jason Swails (Thu Feb 02 2012 - 08:40:17 PST)
  - Re: [AMBER] [Fwd: Problems with ff99SB force field reading] vladanstefanovic.kg.ac.rs (Fri Feb 03 2012 - 01:23:15 PST)
    - [AMBER] Any references on studying energy landscape of a protein by AMBER Catein Catherine (Fri Feb 03 2012 - 01:34:49 PST)
    - Re: [AMBER] Any references on studying energy landscape of a protein by AMBER Jason Swails (Fri Feb 03 2012 - 11:23:24 PST)
- Re: [AMBER] [Fwd: Problems with ff99SB force field reading] David A Case (Thu Feb 02 2012 - 10:46:55 PST)
[AMBER] Ptraj - Multimodel PDB Segmentation Fault... Cihan Aydin (Thu Feb 02 2012 - 20:12:03 PST)
- Re: [AMBER] Ptraj - Multimodel PDB Segmentation Fault... Daniel Roe (Fri Feb 03 2012 - 05:23:04 PST)
[AMBER] AMBER11 installation Hirdesh Kumar (Thu Feb 02 2012 - 21:53:43 PST)
- Re: [AMBER] AMBER11 installation rameshwar prajapati (Thu Feb 02 2012 - 22:13:56 PST)
- Re: [AMBER] AMBER11 installation Jason Swails (Thu Feb 02 2012 - 22:19:47 PST)
  - Re: [AMBER] AMBER11 installation Hirdesh Kumar (Thu Feb 02 2012 - 22:39:53 PST)
[AMBER] regarding QM/MM simulation jani vinod (Fri Feb 03 2012 - 03:32:03 PST)
- Re: [AMBER] regarding QM/MM simulation Marc van der Kamp (Fri Feb 03 2012 - 04:29:26 PST)
  - Re: [AMBER] regarding QM/MM simulation Adrian Roitberg (Fri Feb 03 2012 - 05:02:39 PST)
    - Re: [AMBER] regarding QM/MM simulation jani vinod (Sun Feb 05 2012 - 03:52:31 PST)
[AMBER] error in .rst file creation abinayar.imsc.res.in (Fri Feb 03 2012 - 03:51:22 PST)
- Re: [AMBER] error in .rst file creation Daniel Roe (Fri Feb 03 2012 - 05:28:06 PST)
- Re: [AMBER] error in .rst file creation David A Case (Fri Feb 03 2012 - 05:58:30 PST)
[AMBER] PMEMD.CUDA.MPI PME tests/Benchmarks Martin Peters (Fri Feb 03 2012 - 07:08:46 PST)
- Re: [AMBER] PMEMD.CUDA.MPI PME tests/Benchmarks Ross Walker (Fri Feb 03 2012 - 16:15:15 PST)
  - Re: [AMBER] PMEMD.CUDA.MPI PME tests/Benchmarks Martin Peters (Tue Feb 07 2012 - 01:07:23 PST)
    - Re: [AMBER] PMEMD.CUDA.MPI PME tests/Benchmarks Ross Walker (Tue Feb 07 2012 - 06:45:53 PST)
    - Re: [AMBER] PMEMD.CUDA.MPI PME tests/Benchmarks Scott Le Grand (Tue Feb 07 2012 - 07:52:49 PST)
    - Re: [AMBER] PMEMD.CUDA.MPI PME tests/Benchmarks Martin Peters (Tue Feb 07 2012 - 08:05:34 PST)
    - Re: [AMBER] PMEMD.CUDA.MPI PME tests/Benchmarks Scott Le Grand (Tue Feb 07 2012 - 11:31:21 PST)
[AMBER] fail to compile Amber 9 with intel/10.1 + openmpi/1.2.4 Yubo Fan (Fri Feb 03 2012 - 08:03:51 PST)
- Re: [AMBER] fail to compile Amber 9 with intel/10.1 + openmpi/1.2.4 Daniel Roe (Fri Feb 03 2012 - 10:11:26 PST)
  - Re: [AMBER] fail to compile Amber 9 with intel/10.1 + openmpi/1.2.4 Yubo Fan (Fri Feb 03 2012 - 13:13:23 PST)
    - Re: [AMBER] fail to compile Amber 9 with intel/10.1 + openmpi/1.2.4 Jason Swails (Fri Feb 03 2012 - 16:09:09 PST)
[AMBER] ptraj to make NMR structure ensemble Charles Johnson (Fri Feb 03 2012 - 11:26:55 PST)
[AMBER] Amber11 Installation Error Hirdesh Kumar (Sat Feb 04 2012 - 00:35:26 PST)
- Re: [AMBER] Amber11 Installation Error case (Sat Feb 04 2012 - 07:07:08 PST)
[AMBER] Fwd: Re: : about using MMPBSA Tan and Luo method in AMBER 11: discrepancy in ECAVITY values Holger Gohlke (Sat Feb 04 2012 - 01:34:53 PST)
[AMBER] Deprotonated Tyrosine Thomas Exner (Sat Feb 04 2012 - 07:35:21 PST)
- Re: [AMBER] Deprotonated Tyrosine Aron Broom (Sat Feb 04 2012 - 08:45:00 PST)
- Re: [AMBER] Deprotonated Tyrosine FyD (Sun Feb 05 2012 - 00:04:46 PST)
  - Re: [AMBER] Deprotonated Tyrosine Albert (Sun Feb 05 2012 - 00:16:17 PST)
    - Re: [AMBER] Deprotonated Tyrosine Barbault Florent (Sun Feb 05 2012 - 00:33:07 PST)
    - Re: [AMBER] Deprotonated Tyrosine FyD (Sun Feb 05 2012 - 02:13:16 PST)
    - Re: [AMBER] Deprotonated Tyrosine Thomas Exner (Sun Feb 05 2012 - 03:21:49 PST)
    - Re: [AMBER] Deprotonated Tyrosine FyD (Sun Feb 05 2012 - 11:15:05 PST)
    - Re: [AMBER] Deprotonated Tyrosine Markus Kaukonen (Sun Feb 05 2012 - 11:37:29 PST)
    - Re: [AMBER] Deprotonated Tyrosine Irene Newhouse (Sun Feb 05 2012 - 16:14:14 PST)
[AMBER] RNA/Protein Interaction amir abbasi (Sat Feb 04 2012 - 13:53:39 PST)
- Re: [AMBER] RNA/Protein Interaction amirhossein taghavi (Sun Feb 05 2012 - 07:13:19 PST)
- Re: [AMBER] RNA/Protein Interaction Amir Abbasi (Mon Feb 06 2012 - 02:05:27 PST)
  - Re: [AMBER] RNA/Protein Interaction Vlad Cojocaru (Mon Feb 06 2012 - 02:14:44 PST)
[AMBER] mmpbsa Sel Ercan (Sat Feb 04 2012 - 17:05:08 PST)
- Re: [AMBER] mmpbsa case (Sun Feb 05 2012 - 09:44:27 PST)
  - Re: [AMBER] mmpbsa Jason Swails (Sun Feb 05 2012 - 10:08:34 PST)
    - Re: [AMBER] mmpbsa Sel Ercan (Sun Feb 05 2012 - 13:25:03 PST)
[AMBER] GL4 at C-terminal kurisaki (Sun Feb 05 2012 - 04:56:36 PST)
- Re: [AMBER] GL4 at C-terminal Jason Swails (Sun Feb 05 2012 - 10:16:57 PST)
  - Re: [AMBER] GL4 at C-terminal kurisaki (Sun Feb 05 2012 - 16:43:48 PST)
- Re: [AMBER] GL4 at C-terminal FyD (Sun Feb 05 2012 - 11:26:58 PST)
  - Re: [AMBER] GL4 at C-terminal kurisaki (Sun Feb 05 2012 - 16:47:38 PST)
[AMBER] Fwd: [q4md-fft] Constraint during geometry optimization FyD (Sun Feb 05 2012 - 11:21:06 PST)
[AMBER] MMPBSA entropy calculations ASSERTion ' ier == 0 ' failed in nmode.f at line 114. ? Urszula Uciechowska (Sun Feb 05 2012 - 12:50:54 PST)
- Re: [AMBER] MMPBSA entropy calculations ASSERTion ' ier == 0 ' failed in nmode.f at line 114. ? David A Case (Mon Feb 06 2012 - 05:10:58 PST)
  - Re: [AMBER] MMPBSA entropy calculations ASSERTion ' ier == 0 ' failed in nmode.f at line 114. ? Ake Sandgren (Mon Feb 06 2012 - 05:40:20 PST)
    - Re: [AMBER] MMPBSA entropy calculations ASSERTion ' ier == 0 ' failed in nmode.f at line 114. ? David A Case (Mon Feb 06 2012 - 11:31:06 PST)
[AMBER] Error during extending the simulations... Rajendra Sharma (Sun Feb 05 2012 - 18:06:16 PST)
- [AMBER] How to calculate conformational entropy for a protein using AMBER? Catein Catherine (Sun Feb 05 2012 - 19:38:01 PST)
- Re: [AMBER] Error during extending the simulations... Jason Swails (Mon Feb 06 2012 - 14:55:07 PST)
[AMBER] cygwin-ambertools Алексей Раевский (Mon Feb 06 2012 - 00:08:39 PST)
- Re: [AMBER] cygwin-ambertools David A Case (Mon Feb 06 2012 - 05:14:09 PST)
[AMBER] compilation of amber 11 + amber tools 1.5 with intel 12.1.2 Vlad Cojocaru (Mon Feb 06 2012 - 02:13:41 PST)
- Re: [AMBER] compilation of amber 11 + amber tools 1.5 with intel 12.1.2 Vlad Cojocaru (Mon Feb 06 2012 - 02:58:59 PST)
  - Re: [AMBER] compilation of amber 11 + amber tools 1.5 with intel 12.1.2 Jan-Philip Gehrcke (Mon Feb 06 2012 - 03:18:43 PST)
[AMBER] Error in running energy minimization DEBOSTUTI GHOSHDASTIDAR (Mon Feb 06 2012 - 03:12:11 PST)
- Re: [AMBER] Error in running energy minimization David A Case (Mon Feb 06 2012 - 05:26:30 PST)
[AMBER] NAB+fortran Daniel Hollas (Mon Feb 06 2012 - 03:20:09 PST)
- Re: [AMBER] NAB+fortran David A. Case (Thu Feb 09 2012 - 08:44:56 PST)
[AMBER] Charge calculation using RESP: MCPB kanika singal (Mon Feb 06 2012 - 04:06:04 PST)
- Re: [AMBER] Charge calculation using RESP: MCPB Martin Peters (Tue Feb 07 2012 - 06:07:54 PST)
[AMBER] a general question about membrane simulation Albert (Mon Feb 06 2012 - 05:11:34 PST)
[AMBER] loading of fullerene2160 gargi borgohai (Mon Feb 06 2012 - 05:15:50 PST)
- Re: [AMBER] loading of fullerene2160 FyD (Mon Feb 06 2012 - 06:27:19 PST)
[AMBER] How to set the existing waters to be the cap molecules? liu junjun (Mon Feb 06 2012 - 06:22:49 PST)
- Re: [AMBER] How to set the existing waters to be the cap molecules? David A Case (Mon Feb 06 2012 - 11:35:40 PST)
  - Re: [AMBER] How to set the existing waters to be the cap molecules? liu junjun (Mon Feb 06 2012 - 18:29:05 PST)
    - Re: [AMBER] How to set the existing waters to be the cap molecules? David A. Case (Tue Feb 07 2012 - 17:06:18 PST)
[AMBER] pmemd test failure when compiling with intel 12.1.2 Vlad Cojocaru (Mon Feb 06 2012 - 07:22:52 PST)
- Re: [AMBER] pmemd test failure when compiling with intel 12.1.2 Jason Swails (Mon Feb 06 2012 - 08:04:27 PST)
  - Re: [AMBER] pmemd test failure when compiling with intel 12.1.2 Vlad Cojocaru (Mon Feb 06 2012 - 08:17:42 PST)
    - Re: [AMBER] pmemd test failure when compiling with intel 12.1.2 David A Case (Mon Feb 06 2012 - 11:37:51 PST)
    - Re: [AMBER] pmemd test failure when compiling with intel 12.1.2 Vlad Cojocaru (Mon Feb 06 2012 - 11:43:52 PST)
[AMBER] TI: error in reading namelist cntrl leila karami (Mon Feb 06 2012 - 07:36:18 PST)
- Re: [AMBER] TI: error in reading namelist cntrl Jason Swails (Mon Feb 06 2012 - 07:57:36 PST)
  - Re: [AMBER] TI: error in reading namelist cntrl leila karami (Mon Feb 06 2012 - 10:13:27 PST)
    - Re: [AMBER] TI: error in reading namelist cntrl leila karami (Tue Feb 07 2012 - 00:08:32 PST)
    - Re: [AMBER] TI: error in reading namelist cntrl steinbrt.rci.rutgers.edu (Tue Feb 07 2012 - 01:04:09 PST)
    - Re: [AMBER] TI: error in reading namelist cntrl leila karami (Tue Feb 07 2012 - 01:33:05 PST)
    - Re: [AMBER] TI: error in reading namelist cntrl steinbrt.rci.rutgers.edu (Tue Feb 07 2012 - 02:36:50 PST)
    - Re: [AMBER] TI: error in reading namelist cntrl leila karami (Tue Feb 07 2012 - 04:09:36 PST)
    - Re: [AMBER] TI: error in reading namelist cntrl steinbrt.rci.rutgers.edu (Tue Feb 07 2012 - 04:44:55 PST)
    - Re: [AMBER] TI: error in reading namelist cntrl leila karami (Tue Feb 07 2012 - 04:59:42 PST)
    - Re: [AMBER] TI: error in reading namelist cntrl steinbrt.rci.rutgers.edu (Tue Feb 07 2012 - 05:13:57 PST)
    - Re: [AMBER] TI: error in reading namelist cntrl leila karami (Tue Feb 07 2012 - 06:05:51 PST)
    - Re: [AMBER] TI: error in reading namelist cntrl steinbrt.rci.rutgers.edu (Tue Feb 07 2012 - 07:32:06 PST)
[AMBER] HTML page explaining mm_pbsa.pl error messages available Nadine Homeyer (Mon Feb 06 2012 - 08:50:25 PST)
- Re: [AMBER] HTML page explaining mm_pbsa.pl error messages available Adrian Roitberg (Mon Feb 06 2012 - 09:17:05 PST)
[AMBER] force field Hydroxide ion iccy liu (Mon Feb 06 2012 - 10:59:25 PST)
- Re: [AMBER] force field Hydroxide ion Brian Radak (Mon Feb 06 2012 - 11:09:58 PST)
[AMBER] ante-MMPBSA error message:additional OXT atom Shuyi Cao (Mon Feb 06 2012 - 18:03:51 PST)
- Re: [AMBER] ante-MMPBSA error message:additional OXT atom liu junjun (Mon Feb 06 2012 - 18:35:48 PST)
  - Re: [AMBER] ante-MMPBSA error message:additional OXT atom Shuyi Cao (Mon Feb 06 2012 - 18:40:47 PST)
- Re: [AMBER] ante-MMPBSA error message:additional OXT atom Jason Swails (Mon Feb 06 2012 - 20:27:13 PST)
  - Re: [AMBER] ante-MMPBSA error message:additional OXT atom Shuyi Cao (Tue Feb 07 2012 - 08:25:42 PST)
    - Re: [AMBER] ante-MMPBSA error message:additional OXT atom Jason Swails (Tue Feb 07 2012 - 08:42:18 PST)
[AMBER] Compile Amber 11 with IPP instead of OpenMPI Yubo Fan (Mon Feb 06 2012 - 19:37:57 PST)
- Re: [AMBER] Compile Amber 11 with IPP instead of OpenMPI David A Case (Tue Feb 07 2012 - 04:48:16 PST)
- Re: [AMBER] Compile Amber 11 with IPP instead of OpenMPI David A Case (Tue Feb 07 2012 - 04:49:51 PST)
[AMBER] Does AMBER ignore CONECT information in pdb input? Chinh Su Tran To (Mon Feb 06 2012 - 20:05:04 PST)
- Re: [AMBER] Does AMBER ignore CONECT information in pdb input? Aron Broom (Mon Feb 06 2012 - 20:18:26 PST)
  - Re: [AMBER] Does AMBER ignore CONECT information in pdb input? Chinh Su Tran To (Mon Feb 06 2012 - 21:24:36 PST)
    - Re: [AMBER] Does AMBER ignore CONECT information in pdb input? Chinh Su Tran To (Mon Feb 06 2012 - 21:25:59 PST)
    - Re: [AMBER] Does AMBER ignore CONECT information in pdb input? steinbrt.rci.rutgers.edu (Tue Feb 07 2012 - 01:00:00 PST)
    - Re: [AMBER] Does AMBER ignore CONECT information in pdb input? Chinh Su Tran To (Tue Feb 07 2012 - 02:58:00 PST)
- Re: [AMBER] Does AMBER ignore CONECT information in pdb input? Jason Swails (Mon Feb 06 2012 - 20:32:52 PST)
[AMBER] tleap: added ions are in close vicinity to protein Hirdesh Kumar (Mon Feb 06 2012 - 21:27:45 PST)
- Re: [AMBER] tleap: added ions are in close vicinity to protein David A Case (Tue Feb 07 2012 - 04:53:55 PST)
  - Re: [AMBER] tleap: added ions are in close vicinity to protein Hirdesh Kumar (Tue Feb 07 2012 - 04:59:39 PST)
[AMBER] Problems about dihedral restraint in umbrella sampling jylu (Mon Feb 06 2012 - 22:44:10 PST)
- [AMBER] per-residue RMSF without B-factor, what is the unit of these values, could be as large as 5000? Catein Catherine (Mon Feb 06 2012 - 23:48:11 PST)
  - Re: [AMBER] per-residue RMSF without B-factor, what is the unit of these values, could be as large as 5000? Jason Swails (Tue Feb 07 2012 - 21:27:04 PST)
[AMBER] query on .inpcrd file format abinayar.imsc.res.in (Tue Feb 07 2012 - 01:25:00 PST)
- Re: [AMBER] query on .inpcrd file format Marc van der Kamp (Tue Feb 07 2012 - 01:55:24 PST)
[AMBER] Sander with NMROPT Rahul Banerjee (Tue Feb 07 2012 - 07:19:54 PST)
- Re: [AMBER] Sander with NMROPT Jason Swails (Tue Feb 07 2012 - 08:46:46 PST)
  - Re: [AMBER] Sander with NMROPT Carlos Simmerling (Tue Feb 07 2012 - 09:28:33 PST)
[AMBER] Force Field Parameterization -- Torsion Potentials Ryan Pavlovicz (Tue Feb 07 2012 - 07:40:05 PST)
- Re: [AMBER] Force Field Parameterization -- Torsion Potentials Karl N. Kirschner (Wed Feb 08 2012 - 05:11:55 PST)
  - Re: [AMBER] Force Field Parameterization -- Torsion Potentials Ryan Pavlovicz (Wed Feb 08 2012 - 09:14:45 PST)
    - Re: [AMBER] Force Field Parameterization -- Torsion Potentials Karl N. Kirschner (Thu Feb 09 2012 - 01:25:48 PST)
    - Re: [AMBER] Force Field Parameterization -- Torsion Potentials Ismail, Mohd F. (Tue Mar 13 2012 - 15:08:48 PDT)
    - Re: [AMBER] Force Field Parameterization -- Torsion Potentials Ismail, Mohd F. (Tue Mar 13 2012 - 15:14:08 PDT)
    - Re: [AMBER] Force Field Parameterization -- Torsion Potentials Karl N. Kirschner (Wed Mar 14 2012 - 04:53:23 PDT)
    - Re: [AMBER] Force Field Parameterization -- Torsion Potentials Ismail, Mohd F. (Thu Mar 15 2012 - 22:31:02 PDT)
    - Re: [AMBER] Force Field Parameterization -- Torsion Potentials Karl N. Kirschner (Mon Mar 19 2012 - 05:50:46 PDT)
  - Re: [AMBER] Force Field Parameterization -- Torsion Potentials Ryan Pavlovicz (Fri Feb 10 2012 - 10:10:38 PST)
  - Re: [AMBER] Force Field Parameterization -- Torsion Potentials Ryan Pavlovicz (Fri Feb 10 2012 - 14:26:25 PST)
- Re: [AMBER] Force Field Parameterization -- Torsion Potentials Lorenzo Gontrani (Thu Feb 09 2012 - 00:47:43 PST)
  - Re: [AMBER] Force Field Parameterization -- Torsion Potentials FyD (Thu Feb 09 2012 - 03:59:50 PST)
  - Re: [AMBER] Force Field Parameterization -- Torsion Potentials Ryan Pavlovicz (Fri Feb 10 2012 - 14:18:44 PST)
[AMBER] AMBER minimization Olena Dobrovolska (Tue Feb 07 2012 - 08:19:43 PST)
- Re: [AMBER] AMBER minimization David A. Case (Tue Feb 07 2012 - 16:56:54 PST)
  - Re: [AMBER] AMBER minimization Olena Dobrovolska (Wed Feb 08 2012 - 04:19:21 PST)
    - Re: [AMBER] AMBER minimization David A. Case (Wed Feb 08 2012 - 05:38:27 PST)
    - Re: [AMBER] AMBER minimization Olena Dobrovolska (Wed Feb 08 2012 - 10:12:01 PST)
    - Re: [AMBER] AMBER minimization David A. Case (Wed Feb 08 2012 - 10:31:38 PST)
    - Re: [AMBER] AMBER minimization Olena Dobrovolska (Thu Feb 09 2012 - 03:04:52 PST)
    - Re: [AMBER] AMBER minimization David A Case (Thu Feb 09 2012 - 08:34:06 PST)
[AMBER] Charge calculation using RESP: MCPB kanika singal (Tue Feb 07 2012 - 08:45:54 PST)
[AMBER] Stripping hydrogens etc. from the prmtop? Cihan Aydin (Tue Feb 07 2012 - 12:43:01 PST)
- Re: [AMBER] Stripping hydrogens etc. from the prmtop? David A. Case (Tue Feb 07 2012 - 17:03:22 PST)
  - Re: [AMBER] Stripping hydrogens etc. from the prmtop? Cihan Aydin (Tue Feb 07 2012 - 17:41:38 PST)
- Re: [AMBER] Stripping hydrogens etc. from the prmtop? Jason Swails (Tue Feb 07 2012 - 21:17:54 PST)
[AMBER] error in tleap execution of loadpdb molguin.miners.utep.edu (Tue Feb 07 2012 - 22:09:48 PST)
- Re: [AMBER] error in tleap execution of loadpdb Aron Broom (Tue Feb 07 2012 - 22:33:16 PST)
  - Re: [AMBER] error in tleap execution of loadpdb molguin.miners.utep.edu (Wed Feb 08 2012 - 21:02:57 PST)
[AMBER] Problem with leaprc.ff99SB file sourcing vladanstefanovic.kg.ac.rs (Wed Feb 08 2012 - 02:11:57 PST)
- Re: [AMBER] Problem with leaprc.ff99SB file sourcing David A. Case (Wed Feb 08 2012 - 05:52:26 PST)
  - Re: [AMBER] Problem with leaprc.ff99SB file sourcing vladanstefanovic.kg.ac.rs (Wed Feb 08 2012 - 07:22:44 PST)
    - Re: [AMBER] Problem with leaprc.ff99SB file sourcing David A. Case (Wed Feb 08 2012 - 08:53:46 PST)
[AMBER] Error in running energy minimization DEBOSTUTI GHOSHDASTIDAR (Wed Feb 08 2012 - 02:18:47 PST)
- Re: [AMBER] Error in running energy minimization Brian Radak (Wed Feb 08 2012 - 05:54:48 PST)
  - Re: [AMBER] Error in running energy minimization DEBOSTUTI GHOSHDASTIDAR (Thu Feb 09 2012 - 02:42:53 PST)
    - Re: [AMBER] Error in running energy minimization David A Case (Thu Feb 09 2012 - 08:32:38 PST)
[AMBER] what do reprocessing steps do in md simulation? khaled bodoor (Wed Feb 08 2012 - 04:13:55 PST)
- Re: [AMBER] what do reprocessing steps do in md simulation? Irene Newhouse (Wed Feb 08 2012 - 09:12:39 PST)
[AMBER] about Ewald error estimate leila karami (Wed Feb 08 2012 - 04:19:55 PST)
- Re: [AMBER] about Ewald error estimate case (Sat Feb 11 2012 - 09:05:43 PST)
  - Re: [AMBER] about Ewald error estimate leila karami (Sun Feb 12 2012 - 00:02:56 PST)
    - Re: [AMBER] about Ewald error estimate case (Sun Feb 12 2012 - 04:41:12 PST)
[AMBER] installation subrata paul (Wed Feb 08 2012 - 05:01:56 PST)
- Re: [AMBER] installation David A. Case (Wed Feb 08 2012 - 08:30:00 PST)
  - Re: [AMBER] installation subrata paul (Wed Feb 08 2012 - 20:58:09 PST)
    - Re: [AMBER] installation David A Case (Thu Feb 09 2012 - 08:29:36 PST)
    - Re: [AMBER] installation subrata paul (Thu Feb 09 2012 - 21:33:12 PST)
    - Re: [AMBER] installation David A Case (Fri Feb 10 2012 - 05:48:18 PST)
    - Re: [AMBER] installation subrata paul (Fri Feb 10 2012 - 21:11:06 PST)
    - Re: [AMBER] installation case (Sat Feb 11 2012 - 09:02:43 PST)
    - Re: [AMBER] installation subrata paul (Sun Feb 12 2012 - 20:56:51 PST)
    - Re: [AMBER] installation David A Case (Mon Feb 13 2012 - 04:51:05 PST)
    - Re: [AMBER] installation subrata paul (Mon Feb 13 2012 - 06:32:15 PST)
Re: [AMBER] p2n file connectivity issue Steven M. Graham (Wed Feb 08 2012 - 08:00:48 PST)
- Re: [AMBER] [q4md-fft] Re: p2n file connectivity issue FyD (Wed Feb 08 2012 - 10:02:44 PST)
[AMBER] unit for SD in MMPBSa Urszula Uciechowska (Thu Feb 09 2012 - 00:33:22 PST)
[AMBER] SD unit Urszula Uciechowska (Thu Feb 09 2012 - 02:49:55 PST)
- Re: [AMBER] SD unit Bill Miller III (Thu Feb 09 2012 - 04:20:09 PST)
[AMBER] How to create a script to add two integers in bash shenna shearin (Thu Feb 09 2012 - 11:26:09 PST)
- Re: [AMBER] How to create a script to add two integers in bash Lachele Foley (Lists) (Thu Feb 09 2012 - 12:06:57 PST)
- Re: [AMBER] How to create a script to add two integers in bash Jason Swails (Thu Feb 09 2012 - 12:16:00 PST)
  - Re: [AMBER] How to create a script to add two integers in bash Mariano Rech (Thu Feb 09 2012 - 12:45:34 PST)
[AMBER] Fwd: Residue Decomposition Sander Error Hirdesh Kumar (Thu Feb 09 2012 - 20:33:37 PST)
[AMBER] Announcement: 2012 summer intern position at GSK Guanglei Cui (Fri Feb 10 2012 - 12:59:32 PST)
- Re: [AMBER] Announcement: 2012 summer intern position at GSK Ganesh Kamath (Fri Feb 10 2012 - 13:05:19 PST)
  - Re: [AMBER] Announcement: 2012 summer intern position at GSK Guanglei Cui (Fri Feb 10 2012 - 13:13:27 PST)
- Re: [AMBER] Announcement: 2012 summer intern position at GSK 肖立 (Sun Mar 25 2012 - 16:24:55 PDT)
[AMBER] a question about double bond in R.E.D Albert (Sat Feb 11 2012 - 21:52:02 PST)
- [AMBER] [q4md-fft] a question about double bond in R.E.D FyD (Sun Feb 12 2012 - 00:04:52 PST)
[AMBER] md stopping in TI calculation leila karami (Sun Feb 12 2012 - 04:11:06 PST)
- Re: [AMBER] md stopping in TI calculation case (Sun Feb 12 2012 - 04:45:52 PST)
  - Re: [AMBER] md stopping in TI calculation leila karami (Sun Feb 12 2012 - 06:17:24 PST)
    - Re: [AMBER] md stopping in TI calculation case (Sun Feb 12 2012 - 18:45:55 PST)
    - Re: [AMBER] md stopping in TI calculation leila karami (Mon Feb 13 2012 - 02:21:18 PST)
    - Re: [AMBER] md stopping in TI calculation steinbrt.rci.rutgers.edu (Mon Feb 13 2012 - 03:32:21 PST)
    - Re: [AMBER] md stopping in TI calculation David A Case (Mon Feb 13 2012 - 11:12:42 PST)
- Re: [AMBER] md stopping in TI calculation leila karami (Mon Feb 13 2012 - 23:23:52 PST)
  - Re: [AMBER] md stopping in TI calculation steinbrt.rci.rutgers.edu (Tue Feb 14 2012 - 00:28:33 PST)
    - Re: [AMBER] md stopping in TI calculation leila karami (Tue Feb 14 2012 - 01:12:08 PST)
    - Re: [AMBER] md stopping in TI calculation steinbrt.rci.rutgers.edu (Tue Feb 14 2012 - 04:07:24 PST)
[AMBER] md stopping in TI calculation leila karami (Sun Feb 12 2012 - 06:07:46 PST)
[AMBER] bond breaking amir abbasi (Sun Feb 12 2012 - 10:38:26 PST)
- Re: [AMBER] bond breaking Jason Swails (Sun Feb 12 2012 - 13:02:13 PST)
[AMBER] Generating topology files for non standard amino acid residue Matthew D Antalek (Sun Feb 12 2012 - 18:41:19 PST)
- Re: [AMBER] Generating topology files for non standard amino acid residue Aron Broom (Sun Feb 12 2012 - 19:09:28 PST)
- Re: [AMBER] Generating topology files for non standard amino acid residue Jason Swails (Sun Feb 12 2012 - 19:40:31 PST)
  - Re: [AMBER] Generating topology files for non standard amino acid residue Aron Broom (Sun Feb 12 2012 - 19:50:33 PST)
    - Re: [AMBER] Generating topology files for non standard amino acid residue Matthew D Antalek (Sun Feb 12 2012 - 20:00:45 PST)
    - Re: [AMBER] Generating topology files for non standard amino acid residue Matthew D Antalek (Mon Feb 13 2012 - 20:55:34 PST)
    - Re: [AMBER] Generating topology files for non standard amino acid residue Aron Broom (Tue Feb 14 2012 - 05:43:15 PST)
    - Re: [AMBER] Generating topology files for non standard amino acid residue FyD (Tue Feb 14 2012 - 08:10:21 PST)
    - Re: [AMBER] Generating topology files for non standard amino acid residue Matthew D Antalek (Tue Feb 14 2012 - 11:44:05 PST)
    - Re: [AMBER] Generating topology files for non standard amino acid residue Aron Broom (Tue Feb 14 2012 - 19:25:44 PST)
[AMBER] Amber 12 & Amoeba Ismail, Mohd F. (Sun Feb 12 2012 - 20:18:47 PST)
- Re: [AMBER] Amber 12 & Amoeba Jason Swails (Sun Feb 12 2012 - 20:54:09 PST)
[AMBER] AMBER QM/MM Coordinate resetting (SHAKE) cannot be accomplished tonghf (Sun Feb 12 2012 - 21:08:26 PST)
- Re: [AMBER] AMBER QM/MM Coordinate resetting (SHAKE) cannot be accomplished Marc van der Kamp (Mon Feb 13 2012 - 01:27:58 PST)
[AMBER] use Restrain mask function in PMEMD Muhammad Khaled Tumbi (Mon Feb 13 2012 - 01:15:49 PST)
- Re: [AMBER] use Restrain mask function in PMEMD David A Case (Mon Feb 13 2012 - 04:53:54 PST)
[AMBER] dicrepancy of percentage nonbonded calculation between 2 and 1 node setyanto md (Mon Feb 13 2012 - 02:31:31 PST)
- Re: [AMBER] dicrepancy of percentage nonbonded calculation between 2 and 1 node David A Case (Mon Feb 13 2012 - 04:59:03 PST)
  - Re: [AMBER] dicrepancy of percentage nonbonded calculation between 2 and 1 node setyanto md (Tue Feb 14 2012 - 21:43:14 PST)
[AMBER] MMPBSA query Soumya Lipsa Rath (Mon Feb 13 2012 - 04:20:31 PST)
- Re: [AMBER] MMPBSA query David A Case (Mon Feb 13 2012 - 05:04:14 PST)
[AMBER] Water models in prmtop files Peter Eastman (Mon Feb 13 2012 - 11:33:09 PST)
- Re: [AMBER] Water models in prmtop files David A Case (Mon Feb 13 2012 - 13:22:37 PST)
  - Re: [AMBER] Water models in prmtop files Peter Eastman (Mon Feb 13 2012 - 15:42:33 PST)
    - Re: [AMBER] Water models in prmtop files Brian Radak (Tue Feb 14 2012 - 08:46:35 PST)
    - Re: [AMBER] Water models in prmtop files David A Case (Tue Feb 14 2012 - 12:06:55 PST)
[AMBER] Problem with ampdb and ptraj Andrianopsyah Mas Jaya Putra (Mon Feb 13 2012 - 21:33:38 PST)
- Re: [AMBER] Problem with ampdb and ptraj David A Case (Tue Feb 14 2012 - 04:55:51 PST)
[AMBER] using AMBER in GPU & MPI environment 홍종희 (Mon Feb 13 2012 - 23:45:46 PST)
- Re: [AMBER] using AMBER in GPU & MPI environment Jason Swails (Tue Feb 14 2012 - 16:03:09 PST)
[AMBER] Query on Antechmaber Charge distribution Dilraj LAMA (Tue Feb 14 2012 - 00:13:53 PST)
- Re: [AMBER] Query on Antechmaber Charge distribution David A Case (Tue Feb 14 2012 - 04:49:33 PST)
[AMBER] simulation without solvent Atila Petrosian (Tue Feb 14 2012 - 00:19:37 PST)
- Re: [AMBER] simulation without solvent steinbrt.rci.rutgers.edu (Tue Feb 14 2012 - 00:31:29 PST)
- Re: [AMBER] simulation without solvent David A Case (Tue Feb 14 2012 - 04:46:43 PST)
[AMBER] MMPBSA results and huge SD Urszula Uciechowska (Tue Feb 14 2012 - 01:14:21 PST)
- Re: [AMBER] MMPBSA results and huge SD mish (Tue Feb 14 2012 - 01:26:20 PST)
  - Re: [AMBER] MMPBSA results and huge SD Urszula Uciechowska (Tue Feb 14 2012 - 02:04:28 PST)
    - Re: [AMBER] MMPBSA results and huge SD mish (Tue Feb 14 2012 - 02:47:18 PST)
    - Re: [AMBER] MMPBSA results and huge SD Cenk $Jenk$ Andac (Tue Feb 14 2012 - 07:38:40 PST)
- Re: [AMBER] MMPBSA results and huge SD Jason Swails (Tue Feb 14 2012 - 15:56:02 PST)
- Re: [AMBER] MMPBSA results and huge SD Massimiliano Porrini (Mon Jul 09 2012 - 06:35:51 PDT)
  - Re: [AMBER] MMPBSA results and huge SD Jason Swails (Mon Jul 09 2012 - 09:06:01 PDT)
[AMBER] ptraj analysis Giachetti Andrea - CERM (Tue Feb 14 2012 - 06:54:25 PST)
- Re: [AMBER] ptraj analysis Daniel Roe (Tue Feb 14 2012 - 07:24:11 PST)
  - Re: [AMBER] ptraj analysis Giachetti Andrea - CERM (Tue Feb 14 2012 - 07:40:06 PST)
    - Re: [AMBER] ptraj analysis Daniel Roe (Tue Feb 14 2012 - 07:56:31 PST)
    - [AMBER] Amber 11/12 and Kepler filip fratev (Tue Feb 14 2012 - 08:25:20 PST)
    - Re: [AMBER] Amber 11/12 and Kepler Ross Walker (Tue Feb 14 2012 - 09:18:01 PST)
[AMBER] Rupture of GlcNAc C-H bonds with AMBER8 Sebastian Enck (Tue Feb 14 2012 - 09:09:10 PST)
- Re: [AMBER] Rupture of GlcNAc C-H bonds with AMBER8 Lachele Foley (Lists) (Tue Feb 14 2012 - 10:25:59 PST)
- Re: [AMBER] Rupture of GlcNAc C-H bonds with AMBER8 Sebastian Enck (Tue Feb 14 2012 - 17:16:27 PST)
  - Re: [AMBER] Rupture of GlcNAc C-H bonds with AMBER8 Lachele Foley (Lists) (Tue Feb 14 2012 - 17:44:56 PST)
    - Re: [AMBER] Rupture of GlcNAc C-H bonds with AMBER8 case (Tue Feb 14 2012 - 19:08:05 PST)
    - Re: [AMBER] Rupture of GlcNAc C-H bonds with AMBER8 Aron Broom (Tue Feb 14 2012 - 19:30:57 PST)
- Re: [AMBER] Rupture of GlcNAc C-H bonds with AMBER8 Sebastian Enck (Wed Feb 15 2012 - 15:37:54 PST)
  - Re: [AMBER] Rupture of GlcNAc C-H bonds with AMBER8 Lachele Foley (Lists) (Wed Feb 15 2012 - 18:53:21 PST)
[AMBER] energy decomposition for the surface term Junmei Wang (Tue Feb 14 2012 - 19:17:33 PST)
[AMBER] iwrap concern Dilraj LAMA (Wed Feb 15 2012 - 01:14:29 PST)
- Re: [AMBER] iwrap concern David A Case (Wed Feb 15 2012 - 05:23:49 PST)
[AMBER] ff03.r1 issue Dmitry Mukha (Wed Feb 15 2012 - 01:31:55 PST)
- Re: [AMBER] ff03.r1 issue Aron Broom (Wed Feb 15 2012 - 05:43:08 PST)
- Re: [AMBER] ff03.r1 issue David A Case (Wed Feb 15 2012 - 07:40:00 PST)
[AMBER] To account for the protonation states of amino acids at a constant pH abinayar.imsc.res.in (Wed Feb 15 2012 - 03:49:01 PST)
- Re: [AMBER] To account for the protonation states of amino acids at a constant pH David A Case (Wed Feb 15 2012 - 12:34:54 PST)
  - Re: [AMBER] To account for the protonation states of amino acids at a constant pH abinayar.imsc.res.in (Wed Feb 15 2012 - 21:01:37 PST)
    - Re: [AMBER] To account for the protonation states of amino acids at a constant pH Aron Broom (Wed Feb 15 2012 - 21:22:36 PST)
    - Re: [AMBER] To account for the protonation states of amino acids at a constant pH Jason Swails (Fri Feb 17 2012 - 04:56:08 PST)
  - [AMBER] Issues with hydrogens using glycam force field in Amber 10 tommaso.casalini.mail.polimi.it (Fri Feb 17 2012 - 03:35:00 PST)
    - Re: [AMBER] Issues with hydrogens using glycam force field in Amber 10 Lachele Foley (Lists) (Fri Feb 17 2012 - 08:04:25 PST)
    - Re: [AMBER] Issues with hydrogens using glycam force field in Amber 10 tommaso.casalini.mail.polimi.it (Fri Feb 17 2012 - 09:09:46 PST)
    - Re: [AMBER] Issues with hydrogens using glycam force field in Amber 10 Karl N. Kirschner (Fri Feb 17 2012 - 17:18:11 PST)
    - Re: [AMBER] Issues with hydrogens using glycam force field in Amber 10 Lachele Foley (Lists) (Fri Feb 17 2012 - 19:07:37 PST)
    - Re: [AMBER] Issues with hydrogens using glycam force field in Amber 10 tommaso.casalini.mail.polimi.it (Sat Feb 18 2012 - 03:57:52 PST)
    - Re: [AMBER] Issues with hydrogens using glycam force field in Amber 10 tommaso.casalini.mail.polimi.it (Sat Feb 18 2012 - 07:03:07 PST)
    - Re: [AMBER-Developers] [AMBER] Issues with hydrogens using glycam force field in Amber 10 David A Case (Mon Feb 20 2012 - 06:13:48 PST)
    - Re: [AMBER] Issues with hydrogens using glycam force field in Amber 10 tommaso.casalini.mail.polimi.it (Mon Feb 20 2012 - 06:54:30 PST)
    - Re: [AMBER] Issues with hydrogens using glycam force field in Amber 10 Lachele Foley (Lists) (Mon Feb 20 2012 - 08:08:43 PST)
    - Re: [AMBER] Issues with hydrogens using glycam force field in Amber 10 Lachele Foley (Lists) (Mon Feb 20 2012 - 09:00:21 PST)
    - Re: [AMBER] Issues with hydrogens using glycam force field in Amber 10 Bill Ross (Tue Feb 21 2012 - 09:07:23 PST)
[AMBER] Change the residue number in pdb file Olena Dobrovolska (Wed Feb 15 2012 - 05:46:27 PST)
- Re: [AMBER] Change the residue number in pdb file Jan-Philip Gehrcke (Wed Feb 15 2012 - 06:46:51 PST)
- Re: [AMBER] Change the residue number in pdb file David A Case (Wed Feb 15 2012 - 07:42:19 PST)
[AMBER] MD simulation of protein with Calcium ion in explicit solvent Quentin Delettre (Wed Feb 15 2012 - 07:02:27 PST)
- Re: [AMBER] MD simulation of protein with Calcium ion in explicit solvent Aron Broom (Wed Feb 15 2012 - 07:17:46 PST)
- Re: [AMBER] MD simulation of protein with Calcium ion in explicit solvent Brian Radak (Wed Feb 15 2012 - 07:22:54 PST)
  - Re: [AMBER] MD simulation of protein with Calcium ion in explicit solvent Aron Broom (Wed Feb 15 2012 - 07:34:49 PST)
Re: [AMBER] building wrapped DNA in NAB David A Case (Wed Feb 15 2012 - 13:31:42 PST)
[AMBER] potential of mean force kirtana S (Wed Feb 15 2012 - 14:34:27 PST)
- Re: [AMBER] potential of mean force Ben Roberts (Wed Feb 15 2012 - 14:41:25 PST)
- Re: [AMBER] potential of mean force Aron Broom (Wed Feb 15 2012 - 14:43:54 PST)
  - Re: [AMBER] potential of mean force kirtana S (Sat Feb 25 2012 - 22:05:17 PST)
    - Re: [AMBER] potential of mean force M. L. Dodson (Sun Feb 26 2012 - 05:46:51 PST)
    - Re: [AMBER] potential of mean force kirtana S (Sun Feb 26 2012 - 12:46:55 PST)
    - Re: [AMBER] potential of mean force M. L. Dodson (Sun Feb 26 2012 - 14:17:06 PST)
    - [AMBER] Enquiry about MM/PBSA energy Catein Catherine (Sun Feb 26 2012 - 23:17:48 PST)
    - Re: [AMBER] Enquiry about MM/PBSA energy Jason Swails (Mon Feb 27 2012 - 08:27:00 PST)
    - [AMBER] How to convert mdcrd for GROMACS analysis? Catein Catherine (Tue Feb 28 2012 - 01:01:11 PST)
    - Re: [AMBER] How to convert mdcrd for GROMACS analysis? Lorenzo Gontrani (Tue Feb 28 2012 - 01:20:05 PST)
    - [AMBER] MMPBSA and explicit ions: what should I do? tommaso.casalini.mail.polimi.it (Thu Mar 01 2012 - 02:21:51 PST)
    - Re: [AMBER] MMPBSA and explicit ions: what should I do? David A Case (Thu Mar 01 2012 - 05:11:42 PST)
    - [AMBER] MMPBSA issue: incosistency within internal potential error tommaso.casalini.mail.polimi.it (Thu Mar 01 2012 - 07:30:36 PST)
    - Re: [AMBER] How to convert mdcrd for GROMACS analysis? Francesco Oteri (Tue Feb 28 2012 - 01:21:18 PST)
[AMBER] GFP Chromophore 1EMB.pdb, Yasuo Kurita (Wed Feb 15 2012 - 22:59:17 PST)
- Re: [AMBER] GFP Chromophore 1EMB.pdb, David A Case (Thu Feb 16 2012 - 05:30:26 PST)
- Re: [AMBER] GFP Chromophore 1EMB.pdb, FyD (Thu Feb 16 2012 - 05:43:02 PST)
[AMBER] Amber 12 Artem Zhmurov (Wed Feb 15 2012 - 23:45:11 PST)
- Re: [AMBER] Amber 12 David A Case (Thu Feb 16 2012 - 05:31:28 PST)
[AMBER] Problem with rst file retrieval komal soni (Thu Feb 16 2012 - 03:01:01 PST)
- Re: [AMBER] Problem with rst file retrieval David A Case (Thu Feb 16 2012 - 05:32:26 PST)
[AMBER] How to handle with two Zn2+ when calculates the free binding energy by mmpbsa.py in metalloprotein JiYuan Liu (Thu Feb 16 2012 - 05:56:11 PST)
[AMBER] How to handle with two Zn2+ when calculates the free binding energy by mmpbsa.py in metalloprotein JiYuan Liu (Thu Feb 16 2012 - 06:16:51 PST)
Re: [AMBER] FW: calculation of spectral density Mahendra B Thapa (Thu Feb 16 2012 - 12:11:34 PST)
- Re: [AMBER] FW: calculation of spectral density David A Case (Mon Feb 20 2012 - 06:40:58 PST)
[AMBER] format plotmtv and plotmtv for ubuntu 11.04 setyanto md (Thu Feb 16 2012 - 19:17:08 PST)
- Re: [AMBER] format plotmtv and plotmtv for ubuntu 11.04 Jason Swails (Wed Feb 29 2012 - 14:10:33 PST)
[AMBER] Radii issue with mbondi2 + leaprc.parmCHI_YIL.bsc for RNA Hai Nguyen (Thu Feb 16 2012 - 20:38:56 PST)
- Re: [AMBER] Radii issue with mbondi2 + leaprc.parmCHI_YIL.bsc for RNA Jason Swails (Fri Feb 17 2012 - 04:49:11 PST)
  - Re: [AMBER] Radii issue with mbondi2 + leaprc.parmCHI_YIL.bsc for RNA Mike NG (Fri Feb 17 2012 - 07:47:44 PST)
    - Re: [AMBER] Radii issue with mbondi2 + leaprc.parmCHI_YIL.bsc for RNA Niel Henriksen (Fri Feb 17 2012 - 08:12:46 PST)
    - Re: [AMBER] Radii issue with mbondi2 + leaprc.parmCHI_YIL.bsc for RNA Ilyas Yildirim (Fri Feb 17 2012 - 09:06:15 PST)
    - Re: [AMBER] Radii issue with mbondi2 + leaprc.parmCHI_YIL.bsc for RNA Mike NG (Fri Feb 17 2012 - 11:49:01 PST)
    - Re: [AMBER-Developers] [AMBER] Radii issue with mbondi2 + leaprc.parmCHI_YIL.bsc for RNA David A Case (Mon Feb 20 2012 - 06:07:17 PST)
[AMBER] restraints in igb simulation Danny Xu (Thu Feb 16 2012 - 22:21:39 PST)
- Re: [AMBER] restraints in igb simulation Jason Swails (Fri Feb 17 2012 - 04:52:07 PST)
  - Re: [AMBER] restraints in igb simulation Aron Broom (Fri Feb 17 2012 - 05:24:13 PST)
  - Re: [AMBER] restraints in igb simulation Danny Xu (Fri Feb 17 2012 - 15:39:56 PST)
    - Re: [AMBER] restraints in igb simulation Danny Xu (Fri Feb 17 2012 - 15:44:32 PST)
    - Re: [AMBER] restraints in igb simulation M. L. Dodson (Fri Feb 17 2012 - 16:03:06 PST)
    - Re: [AMBER] restraints in igb simulation Aron Broom (Fri Feb 17 2012 - 19:04:46 PST)
    - Re: [AMBER] restraints in igb simulation Danny Xu (Fri Feb 17 2012 - 20:43:58 PST)
    - Re: [AMBER] restraints in igb simulation M. L. Dodson (Fri Feb 17 2012 - 21:23:20 PST)
    - [AMBER] Fwd: restraints in igb simulation M. L. Dodson (Fri Feb 17 2012 - 21:27:23 PST)
    - Re: [AMBER] restraints in igb simulation Aron Broom (Fri Feb 17 2012 - 21:25:56 PST)
- Re: [AMBER] restraints in igb simulation Daniel Roe (Fri Feb 17 2012 - 09:03:09 PST)
  - Re: [AMBER] restraints in igb simulation Danny Xu (Fri Feb 17 2012 - 15:34:46 PST)
    - Re: [AMBER] restraints in igb simulation Aron Broom (Fri Feb 17 2012 - 15:38:25 PST)
[AMBER] GFP chromophore 1EMB.pdb(detail) Yasuo Kurita (Fri Feb 17 2012 - 03:25:16 PST)
- Re: [AMBER] GFP chromophore 1EMB.pdb(detail) FyD (Fri Feb 17 2012 - 22:56:20 PST)
[AMBER] G09 incompatibility with ANTECHAMBER for RESP charges lfelberg.uchicago.edu (Fri Feb 17 2012 - 08:25:58 PST)
- Re: [AMBER] G09 incompatibility with ANTECHAMBER for RESP charges FyD (Fri Feb 17 2012 - 23:47:13 PST)
[AMBER] Entropy analysis Amir Abbasi (Fri Feb 17 2012 - 12:56:46 PST)
[AMBER] NVT and NPT simulation Atila Petrosian (Sat Feb 18 2012 - 03:02:31 PST)
- Re: [AMBER] NVT and NPT simulation Atila Petrosian (Sat Feb 18 2012 - 03:39:40 PST)
  - Re: [AMBER] NVT and NPT simulation Aron Broom (Sat Feb 18 2012 - 06:11:43 PST)
    - Re: [AMBER] NVT and NPT simulation Daniel Roe (Sat Feb 18 2012 - 07:47:28 PST)
    - Re: [AMBER] NVT and NPT simulation Brian Radak (Mon Feb 20 2012 - 06:30:42 PST)
[AMBER] TI_All non-softcore atoms must be identical in both systems leila karami (Sun Feb 19 2012 - 03:52:18 PST)
- Re: [AMBER] TI_All non-softcore atoms must be identical in both systems steinbrt.rci.rutgers.edu (Sun Feb 19 2012 - 05:05:55 PST)
  - Re: [AMBER] TI_All non-softcore atoms must be identical in both systems leila karami (Sun Feb 19 2012 - 06:20:34 PST)
    - Re: [AMBER] TI_All non-softcore atoms must be identical in both systems steinbrt.rci.rutgers.edu (Sun Feb 19 2012 - 07:03:55 PST)
    - Re: [AMBER] TI_All non-softcore atoms must be identical in both systems leila karami (Sun Feb 19 2012 - 07:42:29 PST)
    - Re: [AMBER] TI_All non-softcore atoms must be identical in both systems steinbrt.rci.rutgers.edu (Mon Feb 20 2012 - 00:31:45 PST)
[AMBER] Ligands fly away from binding pocket tian zhu (Sun Feb 19 2012 - 15:30:35 PST)
- Re: [AMBER] Ligands fly away from binding pocket Aron Broom (Sun Feb 19 2012 - 20:16:36 PST)
[AMBER] problem with atom type pancham lal gupta (Sun Feb 19 2012 - 23:50:58 PST)
- Re: [AMBER] problem with atom type David A Case (Mon Feb 20 2012 - 05:36:00 PST)
  - Re: [AMBER] problem with atom type pancham lal gupta (Mon Feb 20 2012 - 09:09:37 PST)
    - Re: [AMBER] problem with atom type David A Case (Tue Feb 21 2012 - 05:00:43 PST)
[AMBER] Antechamber Beale, John (Mon Feb 20 2012 - 02:04:32 PST)
- Re: [AMBER] Antechamber David A Case (Mon Feb 20 2012 - 05:41:03 PST)
[AMBER] Calculating Binding Energy Ravleen, KAUR (Mon Feb 20 2012 - 03:06:02 PST)
- Re: [AMBER] Calculating Binding Energy Aron Broom (Mon Feb 20 2012 - 07:43:26 PST)
[AMBER] Protonated state of GLU, CYS Ngo Son Tung (Mon Feb 20 2012 - 07:11:45 PST)
[AMBER] Problem building octahedral coordinated ligands in LEaP Cannon, John F. (Mon Feb 20 2012 - 08:27:38 PST)
- Re: [AMBER] Problem building octahedral coordinated ligands in LEaP Tom Joseph (Mon Feb 20 2012 - 10:21:48 PST)
  - Re: [AMBER] Problem building octahedral coordinated ligands in LEaP Jesper Sørensen (Mon Feb 20 2012 - 10:38:54 PST)
  - Re: [AMBER] Problem building octahedral coordinated ligands in LEaP Cannon, John F. (Mon Feb 20 2012 - 12:30:27 PST)
    - Re: [AMBER] Problem building octahedral coordinated ligands in LEaP Jesper Sørensen (Mon Feb 20 2012 - 12:50:21 PST)
[AMBER] wrapping first molecule.. again Dmitry Mukha (Mon Feb 20 2012 - 09:46:36 PST)
- Re: [AMBER] wrapping first molecule.. again Aron Broom (Mon Feb 20 2012 - 10:37:55 PST)
  - Re: [AMBER] wrapping first molecule.. again Jan-Philip Gehrcke (Mon Feb 20 2012 - 10:52:11 PST)
  - Re: [AMBER] wrapping first molecule.. again Dmitry Mukha (Mon Feb 20 2012 - 10:54:52 PST)
    - Re: [AMBER] wrapping first molecule.. again Aron Broom (Mon Feb 20 2012 - 12:40:00 PST)
    - Re: [AMBER] wrapping first molecule.. again Dmitry Mukha (Tue Feb 21 2012 - 00:09:41 PST)
[AMBER] problem in getting required snapshots Mahendra B Thapa (Mon Feb 20 2012 - 13:05:28 PST)
- Re: [AMBER] problem in getting required snapshots Adrian Roitberg (Mon Feb 20 2012 - 13:09:16 PST)
  - Re: [AMBER] problem in getting required snapshots Aron Broom (Mon Feb 20 2012 - 13:26:14 PST)
- Re: [AMBER] problem in getting required snapshots Daniel Roe (Tue Feb 21 2012 - 04:20:04 PST)
[AMBER] Mixing GAFF and OPLS force field Guoxiong Su (Mon Feb 20 2012 - 13:56:20 PST)
- Re: [AMBER] Mixing GAFF and OPLS force field Thomas Schlesier (Tue Feb 21 2012 - 06:38:48 PST)
  - Re: [AMBER] Mixing GAFF and OPLS force field Guoxiong Su (Tue Feb 21 2012 - 08:31:10 PST)
- Re: [AMBER] Mixing GAFF and OPLS force field FyD (Tue Feb 21 2012 - 08:27:25 PST)
  - Re: [AMBER] Mixing GAFF and OPLS force field Guoxiong Su (Tue Feb 21 2012 - 08:55:53 PST)
    - Re: [AMBER] Mixing GAFF and OPLS force field FyD (Tue Feb 21 2012 - 09:14:47 PST)
    - Re: [AMBER] Mixing GAFF and OPLS force field Thomas Schlesier (Tue Feb 21 2012 - 09:17:46 PST)
    - Re: [AMBER] Mixing GAFF and OPLS force field FyD (Wed Feb 22 2012 - 00:12:12 PST)
    - Re: [AMBER] Mixing GAFF and OPLS force field Guoxiong Su (Wed Feb 22 2012 - 12:19:15 PST)
[AMBER] ions Carlos Romero (Mon Feb 20 2012 - 18:21:31 PST)
- Re: [AMBER] ions case (Thu Feb 23 2012 - 18:51:29 PST)
  - Re: [AMBER] ions Carlos Romero (Thu Feb 23 2012 - 22:32:33 PST)
    - Re: [AMBER] ions David A Case (Fri Feb 24 2012 - 04:47:39 PST)
    - Re: [AMBER] ions Carlos Romero (Fri Feb 24 2012 - 14:45:27 PST)
[AMBER] The charge of metal center is not integer which handled with MCPB JiYuan Liu (Mon Feb 20 2012 - 22:15:41 PST)
- Re: [AMBER] The charge of metal center is not integer which handled with MCPB FyD (Mon Feb 20 2012 - 23:35:39 PST)
[AMBER] partial atomic charges Mary Varughese (Tue Feb 21 2012 - 01:40:54 PST)
- Re: [AMBER] partial atomic charges David A Case (Tue Feb 21 2012 - 05:06:46 PST)
  - Re: [AMBER] partial atomic charges Mary Varughese (Tue Feb 21 2012 - 10:42:11 PST)
- Re: [AMBER] partial atomic charges FyD (Tue Feb 21 2012 - 08:30:04 PST)
[AMBER] mutation of the one base pair by leap leila karami (Tue Feb 21 2012 - 02:01:16 PST)
- Re: [AMBER] mutation of the one base pair by leap case (Thu Feb 23 2012 - 18:48:47 PST)
  - Re: [AMBER] mutation of the one base pair by leap Vlad Cojocaru (Thu Feb 23 2012 - 23:00:25 PST)
[AMBER] [Fwd: Protonated state of GLU, CYS] Ngo Son Tung (Tue Feb 21 2012 - 02:11:43 PST)
- Re: [AMBER] [Fwd: Protonated state of GLU, CYS] David A Case (Tue Feb 21 2012 - 05:19:04 PST)
  - Re: [AMBER] [Fwd: Protonated state of GLU, CYS] Ngo Son Tung (Tue Feb 21 2012 - 05:57:58 PST)
    - Re: [AMBER] [Fwd: Protonated state of GLU, CYS] Jason Swails (Tue Feb 21 2012 - 20:01:44 PST)
    - Re: [AMBER] [Fwd: Protonated state of GLU, CYS] Ngo Son Tung (Wed Feb 22 2012 - 07:47:46 PST)
[AMBER] Charges Beale, John (Tue Feb 21 2012 - 02:11:32 PST)
- Re: [AMBER] Charges David A Case (Tue Feb 21 2012 - 05:11:59 PST)
[AMBER] deletion of hydrogen atoms of pdb file Atila Petrosian (Tue Feb 21 2012 - 02:37:44 PST)
- Re: [AMBER] deletion of hydrogen atoms of pdb file David A Case (Tue Feb 21 2012 - 05:27:13 PST)
  - Re: [AMBER] deletion of hydrogen atoms of pdb file Jason Swails (Tue Feb 21 2012 - 20:05:11 PST)
[AMBER] Issue with mmpbsa Nick Rakowski (Tue Feb 21 2012 - 05:58:22 PST)
- Re: [AMBER] Issue with mmpbsa Jason Swails (Tue Feb 21 2012 - 14:41:24 PST)
  - Re: [AMBER] Issue with mmpbsa Nick Rakowski (Tue Feb 21 2012 - 23:43:05 PST)
    - Re: [AMBER] Issue with mmpbsa Bill Miller III (Fri Feb 24 2012 - 12:49:58 PST)
[AMBER] Faking Vacuum Simulations with a GPU Aron Broom (Tue Feb 21 2012 - 06:56:03 PST)
- [AMBER] R: Faking Vacuum Simulations with a GPU Giovanni Pavan (Tue Feb 21 2012 - 07:17:20 PST)
- Re: [AMBER] Faking Vacuum Simulations with a GPU David A Case (Thu Feb 23 2012 - 11:09:57 PST)
  - Re: [AMBER] Faking Vacuum Simulations with a GPU Aron Broom (Sat Feb 25 2012 - 21:44:36 PST)
Re: [AMBER] R: Faking Vacuum Simulations with a GPU Aron Broom (Tue Feb 21 2012 - 07:55:58 PST)
[AMBER] errors on testing pbsa Yubo Fan (Tue Feb 21 2012 - 08:26:17 PST)
- [AMBER] Fwd: errors on testing pbsa Ray Luo, Ph.D. (Tue Feb 21 2012 - 10:32:02 PST)
  - Re: [AMBER] Fwd: errors on testing pbsa Jason Swails (Tue Feb 21 2012 - 14:43:06 PST)
  - Re: [AMBER] Fwd: errors on testing pbsa Qin Cai (Tue Feb 21 2012 - 14:47:43 PST)
  - [AMBER] Use of tabulated potentials in Amber ? Marek Maly (Thu Feb 23 2012 - 08:53:50 PST)
    - Re: [AMBER] Use of tabulated potentials in Amber ? Adrian Roitberg (Thu Feb 23 2012 - 09:09:24 PST)
[AMBER] Problem with vector principal fatima chami (Tue Feb 21 2012 - 14:41:41 PST)
- Re: [AMBER] Problem with vector principal Daniel Roe (Tue Feb 21 2012 - 21:42:51 PST)
[AMBER] Using Antechamber in order to make prmtop and inpcrd Aditya Setiajid (Tue Feb 21 2012 - 20:20:56 PST)
- Re: [AMBER] Using Antechamber in order to make prmtop and inpcrd FyD (Tue Feb 21 2012 - 22:10:59 PST)
  - Re: [AMBER] Using Antechamber in order to make prmtop and inpcrd Aditya Setiajid (Tue Feb 21 2012 - 22:51:38 PST)
- Re: [AMBER] Using Antechamber in order to make prmtop and inpcrd FyD (Wed Feb 22 2012 - 01:11:01 PST)
  - Re: [AMBER] Using Antechamber in order to make prmtop and inpcrd Muhammad Aditya Setiajid (Wed Feb 22 2012 - 03:41:19 PST)
  - Re: [AMBER] Using Antechamber in order to make prmtop and inpcrd Aditya Setiajid (Sun Feb 26 2012 - 23:39:58 PST)
[AMBER] Release of the R.E.D. III.5 tools FyD (Wed Feb 22 2012 - 02:46:40 PST)
[AMBER] QM/MM atoms Fernando Martín García (Wed Feb 22 2012 - 07:55:34 PST)
[AMBER] ATP minimization Sangita Kachhap (Wed Feb 22 2012 - 09:32:04 PST)
- Re: [AMBER] ATP minimization FyD (Wed Feb 22 2012 - 09:49:59 PST)
  - Re: [AMBER] ATP minimization Sangita Kachhap (Wed Feb 22 2012 - 10:15:59 PST)
    - Re: [AMBER] ATP minimization FyD (Wed Feb 22 2012 - 10:22:38 PST)
    - Re: [AMBER] ATP minimization Sangita Kachhap (Sun Feb 26 2012 - 09:16:57 PST)
    - Re: [AMBER] ATP minimization FyD (Mon Feb 27 2012 - 00:22:15 PST)
    - Re: [AMBER] ATP minimization Sangita Kachhap (Tue Feb 28 2012 - 03:20:03 PST)
    - Re: [AMBER] ATP minimization FyD (Tue Feb 28 2012 - 06:37:16 PST)
    - Re: [AMBER] ATP minimization Sangita Kachhap (Mon Mar 05 2012 - 21:58:33 PST)
    - Re: [AMBER] ATP minimization FyD (Tue Mar 06 2012 - 01:17:28 PST)
[AMBER] restraining membrane diffusion Jose Borreguero (Wed Feb 22 2012 - 12:09:00 PST)
[AMBER] Electrostatic calculation using Amber partial charge. SENTHIL KUMAR (Wed Feb 22 2012 - 23:56:01 PST)
- Re: [AMBER] Electrostatic calculation using Amber partial charge. David A Case (Thu Feb 23 2012 - 06:08:26 PST)
  - Re: [AMBER] Electrostatic calculation using Amber partial charge. BERGY (Thu Feb 23 2012 - 20:23:13 PST)
[AMBER] Polarization and normal Ewald Summation Volker Lesch (Thu Feb 23 2012 - 06:06:15 PST)
- Re: [AMBER] Polarization and normal Ewald Summation David A Case (Thu Feb 23 2012 - 08:30:30 PST)
[AMBER] problem in output file of the awk script in tutorial A6 shahab shariati (Thu Feb 23 2012 - 07:21:02 PST)
- Re: [AMBER] problem in output file of the awk script in tutorial A6 David A Case (Thu Feb 23 2012 - 11:07:44 PST)
  - Re: [AMBER] problem in output file of the awk script in tutorial A6 g t (Thu Mar 22 2012 - 00:24:30 PDT)
[AMBER] MMPBSA.py troubleshooting Åge Skjevik (Thu Feb 23 2012 - 09:49:13 PST)
- Re: [AMBER] MMPBSA.py troubleshooting Bill Miller III (Fri Feb 24 2012 - 12:45:52 PST)
[AMBER] CUDA version for Amber 11? Mettu, Ramgopal (Thu Feb 23 2012 - 14:09:35 PST)
- Re: [AMBER] CUDA version for Amber 11? Ross Walker (Thu Feb 23 2012 - 15:34:49 PST)
  - Re: [AMBER] CUDA version for Amber 11? Mettu, Ramgopal (Thu Feb 23 2012 - 20:22:54 PST)
    - Re: [AMBER] CUDA version for Amber 11? Ross Walker (Thu Feb 23 2012 - 20:37:53 PST)
    - Re: [AMBER] CUDA version for Amber 11? Mettu, Ramgopal (Thu Feb 23 2012 - 20:45:48 PST)
    - Re: [AMBER] CUDA version for Amber 11? Ismail, Mohd F. (Fri Feb 24 2012 - 06:24:15 PST)
    - Re: [AMBER] CUDA version for Amber 11? Mettu, Ramgopal (Fri Feb 24 2012 - 08:36:39 PST)
    - Re: [AMBER] CUDA version for Amber 11? Scott Le Grand (Fri Feb 24 2012 - 09:16:22 PST)
    - Re: [AMBER] CUDA version for Amber 11? Mettu, Ramgopal (Mon Feb 27 2012 - 07:37:34 PST)
    - Re: [AMBER] CUDA version for Amber 11? Scott Le Grand (Mon Feb 27 2012 - 07:45:11 PST)
    - Re: [AMBER] CUDA version for Amber 11? Jan-Philip Gehrcke (Mon Feb 27 2012 - 07:57:39 PST)
    - Re: [AMBER] CUDA version for Amber 11? Ross Walker (Mon Feb 27 2012 - 08:44:27 PST)
    - Re: [AMBER] CUDA version for Amber 11? Ross Walker (Mon Feb 27 2012 - 08:48:03 PST)
    - Re: [AMBER] CUDA version for Amber 11? Jan-Philip Gehrcke (Mon Feb 27 2012 - 08:58:32 PST)
    - Re: [AMBER] CUDA version for Amber 11? Scott Le Grand (Mon Feb 27 2012 - 10:15:41 PST)
    - Re: [AMBER] CUDA version for Amber 11? Mettu, Ramgopal (Mon Feb 27 2012 - 11:24:13 PST)
    - Re: [AMBER] CUDA version for Amber 11? Scott Le Grand (Mon Feb 27 2012 - 11:37:15 PST)
[AMBER] same simulation using different random seeds on GPU Oliver Kuhn (Fri Feb 24 2012 - 08:37:16 PST)
- Re: [AMBER] same simulation using different random seeds on GPU Cannon, John F. (Fri Feb 24 2012 - 08:43:11 PST)
  - Re: [AMBER] same simulation using different random seeds on GPU Oliver Kuhn (Fri Feb 24 2012 - 08:50:29 PST)
  - Re: [AMBER] same simulation using different random seeds on GPU Aron Broom (Fri Feb 24 2012 - 08:53:10 PST)
- Re: [AMBER] same simulation using different random seeds on GPU Ross Walker (Fri Feb 24 2012 - 09:01:59 PST)
  - Re: [AMBER] same simulation using different random seeds on GPU Oliver Kuhn (Fri Feb 24 2012 - 09:22:50 PST)
  - Re: [AMBER] same simulation using different random seeds on GPU Oliver Kuhn (Sun Feb 26 2012 - 02:09:18 PST)
    - Re: [AMBER] same simulation using different random seeds on GPU Jason Swails (Sun Feb 26 2012 - 10:09:18 PST)
Re: [AMBER] FW: problem in getting required snapshots Mahendra B Thapa (Fri Feb 24 2012 - 09:11:46 PST)
[AMBER] Constant Temperature amir abbasi (Fri Feb 24 2012 - 11:35:22 PST)
- Re: [AMBER] Constant Temperature Jason Swails (Fri Feb 24 2012 - 12:25:12 PST)
  - Re: [AMBER] Constant Temperature Aron Broom (Fri Feb 24 2012 - 12:39:06 PST)
- Re: [AMBER] Constant Temperature David A Case (Fri Feb 24 2012 - 12:37:41 PST)
  - Re: [AMBER] Constant Temperature amir abbasi (Fri Feb 24 2012 - 12:48:29 PST)
    - Re: [AMBER] Constant Temperature Daniel Roe (Fri Feb 24 2012 - 12:54:05 PST)
    - Re: [AMBER] Constant Temperature amir abbasi (Fri Feb 24 2012 - 13:05:32 PST)
Re: [AMBER] [q4md-fft] How to show charge values using Jmol? FyD (Fri Feb 24 2012 - 23:09:44 PST)
- Re: [AMBER] [q4md-fft] How to show charge values using Jmol? FyD (Fri Feb 24 2012 - 23:26:14 PST)
Re: [AMBER] [Contact q4md] HF/6-31++g(2d, 2p) option for anionic fragments in GLYCAM06 FyD (Sat Feb 25 2012 - 00:26:19 PST)
[AMBER] Comaring energy values after restart Dilraj LAMA (Sat Feb 25 2012 - 00:32:33 PST)
- Re: [AMBER] Comaring energy values after restart Daniel Roe (Sat Feb 25 2012 - 05:23:57 PST)
- Re: [AMBER] Comaring energy values after restart case (Sat Feb 25 2012 - 06:26:11 PST)
  - Re: [AMBER] Comaring energy values after restart Jason Swails (Sat Feb 25 2012 - 14:32:37 PST)
  - Re: [AMBER] Comaring energy values after restart Daniel Roe (Sun Feb 26 2012 - 05:52:11 PST)
- Re: [AMBER] Comaring energy values after restart Dilraj LAMA (Sun Feb 26 2012 - 02:36:08 PST)
[AMBER] md sticking! amir abbasi (Sat Feb 25 2012 - 05:38:53 PST)
- Re: [AMBER] md sticking! case (Sat Feb 25 2012 - 06:33:37 PST)
  - Re: [AMBER] md sticking! amir abbasi (Sat Feb 25 2012 - 07:41:13 PST)
    - Re: [AMBER] md sticking! case (Sat Feb 25 2012 - 08:42:39 PST)
    - Re: [AMBER] md sticking! amir abbasi (Sun Feb 26 2012 - 03:21:40 PST)
    - Re: [AMBER] md sticking! amir abbasi (Tue Feb 28 2012 - 05:56:51 PST)
    - Re: [AMBER] md sticking! Ross Walker (Tue Feb 28 2012 - 09:45:57 PST)
    - Re: [AMBER] md sticking! amir abbasi (Sat Mar 03 2012 - 04:37:25 PST)
    - [AMBER] Test if MD converged or not. Catein Catherine (Sun Feb 26 2012 - 23:08:02 PST)
    - Re: [AMBER] Test if MD converged or not. Carlos Simmerling (Mon Feb 27 2012 - 04:03:34 PST)
    - Re: [AMBER] Test if MD converged or not. g t (Thu Mar 22 2012 - 00:14:36 PDT)
[AMBER] Simulation set up John S (Sun Feb 26 2012 - 01:04:17 PST)
[AMBER] Calculation of backbone torsion angles souvik sur (Mon Feb 27 2012 - 04:10:49 PST)
- Re: [AMBER] Calculation of backbone torsion angles Carlos Simmerling (Mon Feb 27 2012 - 04:23:17 PST)
- Re: [AMBER] Calculation of backbone torsion angles Rajendra P. OJHA (Mon Feb 27 2012 - 22:48:01 PST)
[AMBER] Is there a membrane tutorial for Amber? Arthur Roberts (Mon Feb 27 2012 - 14:34:28 PST)
- Re: [AMBER] Is there a membrane tutorial for Amber? Vlad Cojocaru (Mon Feb 27 2012 - 22:59:28 PST)
  - Re: [AMBER] Is there a membrane tutorial for Amber? David A Case (Tue Feb 28 2012 - 04:57:12 PST)
    - Re: [AMBER] Is there a membrane tutorial for Amber? Ross Walker (Tue Feb 28 2012 - 09:43:24 PST)
[AMBER] Calculate the volume of a protein from the trajectory surasak chunsrivirot (Mon Feb 27 2012 - 23:41:08 PST)
- Re: [AMBER] Calculate the volume of a protein from the trajectory Brian Radak (Tue Feb 28 2012 - 06:24:24 PST)
  - Re: [AMBER] Calculate the volume of a protein from the trajectory George M Giambasu (Tue Feb 28 2012 - 06:30:58 PST)
    - Re: [AMBER] Calculate the volume of a protein from the trajectory Tyler Luchko (Tue Feb 28 2012 - 10:07:52 PST)
    - Re: [AMBER] Calculate the volume of a protein from the trajectory surasak chunsrivirot (Wed Feb 29 2012 - 02:15:24 PST)
  - Re: [AMBER] Calculate the volume of a protein from the trajectory Cannon, John F. (Tue Feb 28 2012 - 06:31:21 PST)
- Re: [AMBER] Calculate the volume of a protein from the trajectory Mark Williamson (Tue Feb 28 2012 - 06:34:19 PST)
  - [AMBER] Clustering and minimization Bernhard (Tue Feb 28 2012 - 08:07:35 PST)
[AMBER] Cosine content of PCA analysis Catein Catherine (Tue Feb 28 2012 - 00:58:12 PST)
- Re: [AMBER] Cosine content of PCA analysis Fernando Martín García (Tue Feb 28 2012 - 02:35:38 PST)
[AMBER] How to calculate cosine content of PCA analysis? Catein Catherine (Tue Feb 28 2012 - 00:58:54 PST)
[AMBER] when will Amber 12 be released? Albert (Tue Feb 28 2012 - 01:09:10 PST)
- Re: [AMBER] when will Amber 12 be released? Scott Brozell (Tue Feb 28 2012 - 01:47:02 PST)
  - Re: [AMBER] when will Amber 12 be released? Albert (Tue Feb 28 2012 - 05:07:58 PST)
    - Re: [AMBER] when will Amber 12 be released? Ross Walker (Tue Feb 28 2012 - 09:41:08 PST)
    - Re: [AMBER] when will Amber 12 be released? Albert (Tue Feb 28 2012 - 10:10:21 PST)
    - Re: [AMBER] when will Amber 12 be released? Ross Walker (Tue Feb 28 2012 - 13:50:38 PST)
[AMBER] implicit and explicit amir abbasi (Tue Feb 28 2012 - 05:34:06 PST)
- Re: [AMBER] implicit and explicit Carlos Simmerling (Sun Mar 04 2012 - 04:35:12 PST)
[AMBER] PTRAJ H-bond analysis for protein and ligand Swati Adlakha (Tue Feb 28 2012 - 05:44:18 PST)
[AMBER] 2D PMFs with multiple constraints Sampson C.M. (Tue Feb 28 2012 - 07:28:00 PST)
- Re: [AMBER] 2D PMFs with multiple constraints Adrian Roitberg (Tue Feb 28 2012 - 07:30:24 PST)
  - Re: [AMBER] 2D PMFs with multiple constraints Aron Broom (Tue Feb 28 2012 - 09:47:57 PST)
[AMBER] Help with solvating organic molecule with input .prmtop file Andy Ballard (Tue Feb 28 2012 - 07:55:42 PST)
- Re: [AMBER] Help with solvating organic molecule with input .prmtop file David A Case (Wed Feb 29 2012 - 05:04:25 PST)
  - Re: [AMBER] Help with solvating organic molecule with input .prmtop file Jason Swails (Wed Feb 29 2012 - 14:04:03 PST)
    - Re: [AMBER] Help with solvating organic molecule with input .prmtop file Andy Ballard (Thu Mar 01 2012 - 09:28:23 PST)
    - Re: [AMBER] Help with solvating organic molecule with input .prmtop file Jason Swails (Thu Mar 01 2012 - 12:33:32 PST)
[AMBER] Embed Shell Scripting in ptraj script Ismail, Mohd F. (Tue Feb 28 2012 - 09:48:13 PST)
- Re: [AMBER] Embed Shell Scripting in ptraj script Adrian Roitberg (Tue Feb 28 2012 - 09:53:27 PST)
- Re: [AMBER] Embed Shell Scripting in ptraj script Thomas Cheatham III (Tue Feb 28 2012 - 09:54:14 PST)
  - Re: [AMBER] Embed Shell Scripting in ptraj script Ismail, Mohd F. (Tue Feb 28 2012 - 10:03:24 PST)
    - Re: [AMBER] Embed Shell Scripting in ptraj script g t (Wed Feb 29 2012 - 04:59:32 PST)
[AMBER] is there any tools that can convert Desmond .cms to Amber format? Albert (Tue Feb 28 2012 - 11:06:55 PST)
[AMBER] strip and use of distance-based mask Nanna Holmgaard List (Tue Feb 28 2012 - 11:52:02 PST)
- Re: [AMBER] strip and use of distance-based mask Daniel Roe (Tue Feb 28 2012 - 14:48:36 PST)
  - Re: [AMBER] strip and use of distance-based mask Nanna Holmgaard List (Tue Feb 28 2012 - 22:42:29 PST)
    - Re: [AMBER] strip and use of distance-based mask Daniel Roe (Wed Feb 29 2012 - 06:10:06 PST)
    - Re: [AMBER] strip and use of distance-based mask Nanna Holmgaard List (Wed Feb 29 2012 - 08:32:48 PST)
    - Re: [AMBER] strip and use of distance-based mask Daniel Roe (Wed Feb 29 2012 - 09:23:19 PST)
    - Re: [AMBER] strip and use of distance-based mask Nanna Holmgaard List (Wed Feb 29 2012 - 12:41:06 PST)
[AMBER] bad atom type Osman, Roman (Tue Feb 28 2012 - 14:59:05 PST)
- Re: [AMBER] bad atom type Dwight McGee (Tue Feb 28 2012 - 15:33:31 PST)
  - Re: [AMBER] bad atom type Osman, Roman (Tue Feb 28 2012 - 16:08:40 PST)
    - Re: [AMBER] bad atom type Jason Swails (Tue Feb 28 2012 - 17:53:34 PST)
    - Re: [AMBER] bad atom type Osman, Roman (Wed Feb 29 2012 - 09:11:45 PST)
[AMBER] About the source file regarding SMD calculations Mo Chen (Tue Feb 28 2012 - 15:08:57 PST)
- Re: [AMBER] About the source file regarding SMD calculations Aron Broom (Tue Feb 28 2012 - 18:32:22 PST)
  - Re: [AMBER] About the source file regarding SMD calculations Mo Chen (Tue Feb 28 2012 - 18:38:10 PST)
[AMBER] how to cite ambertool setyanto md (Tue Feb 28 2012 - 20:59:10 PST)
- Re: [AMBER] how to cite ambertool David A Case (Wed Feb 29 2012 - 05:07:11 PST)
[AMBER] simulation in lipid rukman kesh (Tue Feb 28 2012 - 21:38:44 PST)
[AMBER] mm_pbsa error: Flag "RADII" not found in PARM file g t (Wed Feb 29 2012 - 04:32:06 PST)
- Re: [AMBER] mm_pbsa error: Flag "RADII" not found in PARM file Jason Swails (Wed Feb 29 2012 - 13:59:09 PST)
  - Re: [AMBER] mm_pbsa error: Flag "RADII" not found in PARM file g t (Thu Mar 01 2012 - 06:40:24 PST)
    - Re: [AMBER] mm_pbsa error: Flag "RADII" not found in PARM file g t (Thu Mar 01 2012 - 06:59:07 PST)
    - Re: [AMBER] mm_pbsa error: Flag "RADII" not found in PARM file Jason Swails (Thu Mar 01 2012 - 07:24:57 PST)
    - Re: [AMBER] mm_pbsa error: Flag "RADII" not found in PARM file g t (Thu Mar 01 2012 - 08:32:45 PST)
[AMBER] problem with MMPBSA script kureeckal ramesh (Thu Mar 01 2012 - 00:52:39 PST)
- Re: [AMBER] problem with MMPBSA script Nadine.Homeyer.uni-duesseldorf.de (Thu Mar 01 2012 - 01:51:57 PST)
  - [AMBER] error in sander_com.1.out kureeckal ramesh (Thu Mar 01 2012 - 02:30:54 PST)
    - Re: [AMBER] error in sander_com.1.out Nadine.Homeyer.uni-duesseldorf.de (Thu Mar 01 2012 - 03:12:05 PST)
    - [AMBER] error in AMBER while generatting prmtop and ipcrd kureeckal ramesh (Mon Apr 23 2012 - 01:56:11 PDT)
    - Re: [AMBER] error in AMBER while generatting prmtop and ipcrd David A Case (Mon Apr 23 2012 - 09:51:57 PDT)
- Re: [AMBER] problem with MMPBSA script David A Case (Thu Mar 01 2012 - 05:14:41 PST)
[AMBER] slow : amber job akshar bhosale (Thu Mar 01 2012 - 09:44:09 PST)
- Re: [AMBER] slow : amber job Aron Broom (Thu Mar 01 2012 - 10:02:55 PST)
- Re: [AMBER] slow : amber job Cannon, John F. (Thu Mar 01 2012 - 10:27:29 PST)
  - Re: [AMBER] slow : amber job akshar bhosale (Fri Mar 02 2012 - 19:14:20 PST)
    - Re: [AMBER] slow : amber job Jason Swails (Sat Mar 03 2012 - 04:34:23 PST)
    - Re: [AMBER] slow : amber job akshar bhosale (Sat Mar 03 2012 - 10:26:45 PST)
    - Re: [AMBER] slow : amber job Carlos Simmerling (Sat Mar 03 2012 - 10:35:22 PST)
    - Re: [AMBER] slow : amber job akshar bhosale (Sat Mar 03 2012 - 19:21:33 PST)
    - Re: [AMBER] slow : amber job Aron Broom (Sat Mar 03 2012 - 20:03:51 PST)
[AMBER] ABMD in pmemd.cuda in AMBER 12 Aron Broom (Thu Mar 01 2012 - 10:08:52 PST)
- Re: [AMBER] ABMD in pmemd.cuda in AMBER 12 Jason Swails (Thu Mar 01 2012 - 10:18:17 PST)
  - Re: [AMBER] ABMD in pmemd.cuda in AMBER 12 M. L. Dodson (Thu Mar 01 2012 - 10:43:37 PST)
    - Re: [AMBER] ABMD in pmemd.cuda in AMBER 12 Jason Swails (Thu Mar 01 2012 - 12:35:47 PST)
  - Re: [AMBER] ABMD in pmemd.cuda in AMBER 12 Aron Broom (Thu Mar 01 2012 - 10:45:37 PST)
    - Re: [AMBER] ABMD in pmemd.cuda in AMBER 12 Ross Walker (Thu Mar 01 2012 - 13:33:38 PST)
    - [AMBER] Question about Simulated Annealing procedure filip fratev (Sun Mar 04 2012 - 18:29:13 PST)
    - Re: [AMBER] Question about Simulated Annealing procedure Carlos Simmerling (Mon Mar 05 2012 - 05:19:43 PST)
    - Re: [AMBER] Question about Simulated Annealing procedure filip fratev (Mon Mar 05 2012 - 06:08:35 PST)
    - Re: [AMBER] ABMD in pmemd.cuda in AMBER 12 Aron Broom (Mon Mar 26 2012 - 10:39:36 PDT)
[AMBER] Problem in creating topology of NAD Ashutosh Shandilya (Thu Mar 01 2012 - 22:50:06 PST)
- Re: [AMBER] Problem in creating topology of NAD Ashutosh Shandilya (Thu Mar 01 2012 - 22:55:25 PST)
  - Re: [AMBER] Problem in creating topology of NAD FyD (Thu Mar 01 2012 - 23:18:29 PST)
- Re: [AMBER] Problem in creating topology of NAD FyD (Thu Mar 01 2012 - 23:05:26 PST)
[AMBER] top and crd file error kanika sharma (Thu Mar 01 2012 - 22:59:03 PST)
- Re: [AMBER] top and crd file error Aron Broom (Thu Mar 01 2012 - 23:13:01 PST)
  - Re: [AMBER] top and crd file error kanika sharma (Thu Mar 01 2012 - 23:22:07 PST)
    - Re: [AMBER] top and crd file error Aron Broom (Thu Mar 01 2012 - 23:34:47 PST)
[AMBER] Distance plot Beale, John (Fri Mar 02 2012 - 05:57:35 PST)
- Re: [AMBER] Distance plot Cannon, John F. (Fri Mar 02 2012 - 06:42:27 PST)
  - Re: [AMBER] Distance plot Beale, John (Fri Mar 02 2012 - 06:50:18 PST)
[AMBER] AMBER force calculations David Condon (Fri Mar 02 2012 - 06:25:10 PST)
- Re: [AMBER] AMBER force calculations Brian Radak (Fri Mar 02 2012 - 06:47:43 PST)
  - Re: [AMBER] AMBER force calculations David Condon (Fri Mar 16 2012 - 13:03:29 PDT)
    - Re: [AMBER] AMBER force calculations Brian Radak (Fri Mar 16 2012 - 13:10:53 PDT)
    - Re: [AMBER] AMBER force calculations David Condon (Fri Mar 16 2012 - 13:30:45 PDT)
    - Re: [AMBER] AMBER force calculations Jason Swails (Fri Mar 16 2012 - 15:01:19 PDT)
[AMBER] Defining sulfonyl halide atom type Chris Bryant (Fri Mar 02 2012 - 09:03:08 PST)
- Re: [AMBER] Defining sulfonyl halide atom type FyD (Sat Mar 03 2012 - 10:39:04 PST)
[AMBER] control_rmsd_in TMD neha sree (Fri Mar 02 2012 - 11:57:42 PST)
[AMBER] MMPB(GB)SA: two questions George Tzotzos (Sat Mar 03 2012 - 05:05:05 PST)
- Re: [AMBER] MMPB(GB)SA: two questions Cannon, John F. (Mon Mar 05 2012 - 05:37:16 PST)
  - Re: [AMBER] MMPB(GB)SA: two questions George Tzotzos (Mon Mar 05 2012 - 09:23:06 PST)
[AMBER] PDB trajectory format Dmitry Osolodkin (Sat Mar 03 2012 - 08:10:46 PST)
- Re: [AMBER] PDB trajectory format Aron Broom (Sat Mar 03 2012 - 08:45:16 PST)
- Re: [AMBER] PDB trajectory format Daniel Roe (Sat Mar 03 2012 - 10:53:39 PST)
  - Re: [AMBER] PDB trajectory format Dmitry Osolodkin (Thu Mar 15 2012 - 09:15:21 PDT)
    - Re: [AMBER] PDB trajectory format Daniel Roe (Thu Mar 15 2012 - 09:46:40 PDT)
    - Re: [AMBER] PDB trajectory format Dmitry Osolodkin (Fri Mar 16 2012 - 08:08:48 PDT)
    - Re: [AMBER] PDB trajectory format Daniel Roe (Fri Mar 16 2012 - 08:43:20 PDT)
    - Re: [AMBER] PDB trajectory format Dmitry Osolodkin (Fri Mar 16 2012 - 09:11:26 PDT)
    - Re: [AMBER] PDB trajectory format Daniel Roe (Fri Mar 16 2012 - 09:30:34 PDT)
[AMBER] using GAFF with TIP3P model for simulation of solvated organic molecule Andy Ballard (Sun Mar 04 2012 - 12:19:22 PST)
- Re: [AMBER] using GAFF with TIP3P model for simulation of solvated organic molecule Jason Swails (Sun Mar 04 2012 - 17:46:13 PST)
[AMBER] different residues use different force to restrict xiaojiong (Sun Mar 04 2012 - 17:41:16 PST)
- Re: [AMBER] different residues use different force to restrict David A Case (Mon Mar 05 2012 - 05:15:04 PST)
[AMBER] MM-PBSA: different dielectric constants for ligand and receptor? Antonija Tomić (Mon Mar 05 2012 - 02:07:38 PST)
- Re: [AMBER] MM-PBSA: different dielectric constants for ligand and receptor? David A Case (Mon Mar 05 2012 - 05:20:10 PST)
[AMBER] Free Energy Calculate mehdi bagherpoor (Mon Mar 05 2012 - 04:41:05 PST)
- Re: [AMBER] Free Energy Calculate David A Case (Mon Mar 05 2012 - 05:24:28 PST)
[AMBER] Error in amber output files souvik sur (Mon Mar 05 2012 - 05:19:40 PST)
- Re: [AMBER] Error in amber output files Jason Swails (Mon Mar 05 2012 - 13:34:51 PST)
  - Re: [AMBER] Error in amber output files souvik sur (Mon Mar 05 2012 - 21:11:01 PST)
    - Re: [AMBER] Error in amber output files David A Case (Tue Mar 06 2012 - 04:50:08 PST)
    - Re: [AMBER] Error in amber output files Jason Swails (Tue Mar 06 2012 - 07:44:32 PST)
[AMBER] ./nab -c dna3.nab,nab2c failed! Yudong Sun (Mon Mar 05 2012 - 06:40:03 PST)
- Re: [AMBER] ./nab -c dna3.nab,nab2c failed! David A Case (Mon Mar 05 2012 - 06:54:20 PST)
[AMBER] Alkali and Halide Monovalent Ion : paper CHAMI F. (Mon Mar 05 2012 - 09:18:17 PST)
- Re: [AMBER] Alkali and Halide Monovalent Ion : paper Brian Radak (Mon Mar 05 2012 - 09:28:40 PST)
- Re: [AMBER] Alkali and Halide Monovalent Ion : paper CHAMI F. (Tue Mar 06 2012 - 07:27:17 PST)
  - Re: [AMBER-Developers] [AMBER] Alkali and Halide Monovalent Ion : paper David A Case (Tue Mar 06 2012 - 09:42:15 PST)
[AMBER] turning off solute-solvent interactions Andy Ballard (Mon Mar 05 2012 - 13:22:17 PST)
- Re: [AMBER] turning off solute-solvent interactions Brian Radak (Mon Mar 05 2012 - 14:01:27 PST)
[AMBER] Modified phosphotyrosine parameters Ilya Belalov (Mon Mar 05 2012 - 17:32:44 PST)
- Re: [AMBER] Modified phosphotyrosine parameters FyD (Tue Mar 06 2012 - 02:18:37 PST)
[AMBER] Parameters Maxier Acosta (Mon Mar 05 2012 - 20:27:45 PST)
- Re: [AMBER] Parameters FyD (Tue Mar 06 2012 - 01:48:22 PST)
  - Re: [AMBER] Parameters setyanto md (Wed Mar 07 2012 - 21:18:55 PST)
[AMBER] performance dependency on OS amir abbasi (Tue Mar 06 2012 - 02:41:18 PST)
- Re: [AMBER] performance dependency on OS steinbrt.rci.rutgers.edu (Tue Mar 06 2012 - 02:56:09 PST)
[AMBER] SASA Plot Beale, John (Tue Mar 06 2012 - 03:08:06 PST)
- Re: [AMBER] SASA Plot Rajeswari A. (Tue Mar 06 2012 - 03:31:04 PST)
- Re: [AMBER] SASA Plot Daniel Roe (Tue Mar 06 2012 - 04:05:16 PST)
- Re: [AMBER] SASA Plot Bruno Luís Pinto de Oliveira (Tue Mar 06 2012 - 07:00:49 PST)
  - Re: [AMBER] SASA Plot setyanto md (Wed Mar 07 2012 - 00:51:29 PST)
    - Re: [AMBER] SASA Plot Daniel Roe (Wed Mar 07 2012 - 09:27:56 PST)
    - Re: [AMBER] SASA Plot setyanto md (Wed Mar 07 2012 - 21:05:23 PST)
[AMBER] correct inconsistencies in [DR]NA_CI.lib Thomas Gaillard (Tue Mar 06 2012 - 08:57:36 PST)
- Re: [AMBER] correct inconsistencies in [DR]NA_CI.lib Jason Swails (Tue Mar 06 2012 - 20:38:09 PST)
[AMBER] Assignment of partial charge to a molecule gargi borgohai (Tue Mar 06 2012 - 10:05:07 PST)
- Re: [AMBER] Assignment of partial charge to a molecule Aron Broom (Tue Mar 06 2012 - 10:18:47 PST)
[AMBER] RED resp step failed Albert (Tue Mar 06 2012 - 11:38:11 PST)
- Re: [AMBER] RED resp step failed Ismail, Mohd F. (Tue Mar 06 2012 - 13:41:45 PST)
  - Re: [AMBER] RED resp step failed Albert (Wed Mar 07 2012 - 22:24:46 PST)
    - Re: [AMBER] [q4md-fft] Re: RED resp step failed FyD (Wed Mar 07 2012 - 23:30:59 PST)
[AMBER] Residual Dipolar Coupling Rahul Banerjee (Tue Mar 06 2012 - 13:32:27 PST)
- Re: [AMBER] Residual Dipolar Coupling case (Wed Mar 07 2012 - 05:04:23 PST)
[AMBER] Dedication from Ibrahim - Manchester/Minia Mahmoud Ibrahim (Tue Mar 06 2012 - 14:17:57 PST)
- Re: [AMBER] Dedication from Ibrahim - Manchester/Minia David A Case (Wed Mar 07 2012 - 12:01:38 PST)
[AMBER] cluster configuration help Sangeetha B (Tue Mar 06 2012 - 19:27:09 PST)
- [AMBER] cluster configuration help Sangeetha B (Fri Mar 09 2012 - 09:16:42 PST)
- Re: [AMBER] cluster configuration help Thomas Cheatham (Sat Mar 10 2012 - 10:24:33 PST)
  - Re: [AMBER] cluster configuration help Sangeetha B (Sun Mar 11 2012 - 08:11:30 PDT)
[AMBER] MMGBSA residue-wise decomposition Rajeswari A. (Tue Mar 06 2012 - 21:18:28 PST)
- [AMBER] MMGBSA residue-wise decomposition Rajeswari A. (Wed Mar 07 2012 - 21:10:52 PST)
  - [AMBER] MMGBSA residue-wise decomposition Rajeswari A. (Tue Mar 13 2012 - 04:42:53 PDT)
    - Re: [AMBER] MMGBSA residue-wise decomposition Carlos Simmerling (Wed Mar 14 2012 - 06:05:01 PDT)
- Re: [AMBER] MMGBSA residue-wise decomposition Jason Swails (Wed Mar 14 2012 - 06:34:40 PDT)
  - Re: [AMBER] MMGBSA residue-wise decomposition Rajeswari A. (Wed Mar 14 2012 - 23:58:35 PDT)
    - Re: [AMBER] MMGBSA residue-wise decomposition Jason Swails (Thu Mar 15 2012 - 07:10:50 PDT)
[AMBER] how to keep atom restrained in R.E.D? Albert (Tue Mar 06 2012 - 22:45:37 PST)
- Re: [AMBER] [q4md-fft] how to keep atom restrained in R.E.D? FyD (Wed Mar 07 2012 - 01:01:44 PST)
[AMBER] Fwd: SASA Plot João Ribeiro (Wed Mar 07 2012 - 02:16:53 PST)
[AMBER] covert CHARMM format PDB file to AMBER formart Tong Zhu (Wed Mar 07 2012 - 02:25:05 PST)
- Re: [AMBER] covert CHARMM format PDB file to AMBER formart c00jsw00.nchc.narl.org.tw (Wed Mar 07 2012 - 03:11:32 PST)
- Re: [AMBER] covert CHARMM format PDB file to AMBER formart case (Wed Mar 07 2012 - 05:09:19 PST)
[AMBER] AM1 Jacopo Sgrignani (Wed Mar 07 2012 - 03:17:51 PST)
- Re: [AMBER] AM1 Brian Radak (Wed Mar 07 2012 - 07:33:33 PST)
  - Re: [AMBER] AM1 Jacopo Sgrignani (Wed Mar 07 2012 - 23:23:57 PST)
[AMBER] GPU performance and GPU Direct steinbrt.rci.rutgers.edu (Wed Mar 07 2012 - 05:26:53 PST)
- Re: [AMBER] GPU performance and GPU Direct Gould, Ian R (Wed Mar 07 2012 - 06:14:08 PST)
- Re: [AMBER] Best way to implement PBC Ben Ahmady (Wed Mar 07 2012 - 07:26:35 PST)
  - Re: [AMBER] Best way to implement PBC steinbrt.rci.rutgers.edu (Wed Mar 07 2012 - 13:22:35 PST)
[AMBER] cpptraj surf Segmentation fault Guillermo Mulliert Carlín (Wed Mar 07 2012 - 07:51:07 PST)
- Re: [AMBER] cpptraj surf Segmentation fault Daniel Roe (Wed Mar 07 2012 - 08:12:46 PST)
[AMBER] non-linear PB solver within MMPBSA: questions regarding EEL, eneopt and cutnb Jan-Philip Gehrcke (Wed Mar 07 2012 - 08:23:32 PST)
- Re: [AMBER] non-linear PB solver within MMPBSA: questions regarding EEL, eneopt and cutnb Jason Swails (Sat Mar 10 2012 - 13:36:04 PST)
[AMBER] Dihedral analysis Ibrahim Moustafa (Wed Mar 07 2012 - 10:05:00 PST)
- Re: [AMBER] Dihedral analysis Niel Henriksen (Thu Mar 08 2012 - 06:10:26 PST)
  - Re: [AMBER] Dihedral analysis Ibrahim Moustafa (Thu Mar 08 2012 - 08:06:33 PST)
    - Re: [AMBER] Dihedral analysis CHAMI F. (Thu Mar 08 2012 - 08:47:45 PST)
    - Re: [AMBER] Dihedral analysis g t (Tue Mar 13 2012 - 10:41:45 PDT)
[AMBER] Velocity kirtana S (Wed Mar 07 2012 - 11:02:32 PST)
- Re: [AMBER] Velocity Adrian Roitberg (Wed Mar 07 2012 - 11:05:50 PST)
[AMBER] SHAKE not available for parallel runs CHAMI F. (Wed Mar 07 2012 - 12:30:51 PST)
- Re: [AMBER] SHAKE not available for parallel runs case (Wed Mar 07 2012 - 14:55:54 PST)
[AMBER] Question about output files lnedialkova.gmail.com (Wed Mar 07 2012 - 14:18:42 PST)
- Re: [AMBER] Question about output files case (Wed Mar 07 2012 - 14:59:08 PST)
[AMBER] Comparison of the results manikanthan bhavaraju (Wed Mar 07 2012 - 14:23:54 PST)
- [AMBER] Fwd: Comparison of the results manikanthan bhavaraju (Wed Mar 07 2012 - 22:31:48 PST)
- Re: [AMBER] Comparison of the results Jason Swails (Thu Mar 08 2012 - 14:00:20 PST)
  - Re: [AMBER] Comparison of the results manikanthan bhavaraju (Thu Mar 08 2012 - 14:19:50 PST)
[AMBER] Harmonic Restraint in pmemd.cuda Aron Broom (Wed Mar 07 2012 - 15:01:37 PST)
- Re: [AMBER] Harmonic Restraint in pmemd.cuda Adrian Roitberg (Wed Mar 07 2012 - 15:10:07 PST)
  - Re: [AMBER] Harmonic Restraint in pmemd.cuda Aron Broom (Wed Mar 07 2012 - 15:14:40 PST)
    - Re: [AMBER] Harmonic Restraint in pmemd.cuda Adrian Roitberg (Wed Mar 07 2012 - 15:16:33 PST)
[AMBER] How to get the information of hydrophobic contact? qiao xue (Wed Mar 07 2012 - 19:03:48 PST)
- Re: [AMBER] How to get the information of hydrophobic contact? g t (Tue Mar 13 2012 - 10:39:44 PDT)
[AMBER] Viewing with VMD bonds set by the "bond" command Francesco Pietra (Wed Mar 07 2012 - 23:59:23 PST)
- Re: [AMBER] Viewing with VMD bonds set by the "bond" command Lorenzo Gontrani (Thu Mar 08 2012 - 00:42:00 PST)
  - Re: [AMBER] Viewing with VMD bonds set by the "bond" command Francesco Pietra (Thu Mar 08 2012 - 01:48:48 PST)
    - Re: [AMBER] Viewing with VMD bonds set by the "bond" command Lorenzo Gontrani (Thu Mar 08 2012 - 02:21:57 PST)
    - Re: [AMBER] Viewing with VMD bonds set by the "bond" command Francesco Pietra (Thu Mar 08 2012 - 03:01:34 PST)
    - Re: [AMBER] Viewing with VMD bonds set by the "bond" command FyD (Thu Mar 08 2012 - 03:22:40 PST)
    - Re: [AMBER] Viewing with VMD bonds set by the "bond" command Francesco Pietra (Thu Mar 08 2012 - 03:30:29 PST)
    - Re: [AMBER] Viewing with VMD bonds set by the "bond" command FyD (Thu Mar 08 2012 - 03:48:31 PST)
    - Re: [AMBER] Viewing with VMD bonds set by the "bond" command francesco oteri (Thu Mar 08 2012 - 06:27:46 PST)
    - Re: [AMBER] Viewing with VMD bonds set by the "bond" command Francesco Pietra (Thu Mar 08 2012 - 10:27:58 PST)
    - [AMBER] Fwd: vmd-l: Re: Viewing with VMD bonds set by the "bond" command Francesco Pietra (Thu Mar 08 2012 - 23:39:17 PST)
    - Re: [AMBER] Viewing with VMD bonds set by the "bond" command FyD (Fri Mar 09 2012 - 10:10:27 PST)
[AMBER] Base stacking amir abbasi (Thu Mar 08 2012 - 03:13:51 PST)
- Re: [AMBER] Base stacking amirhossein taghavi (Thu Mar 08 2012 - 09:17:06 PST)
- Re: [AMBER] Base stacking amirhossein taghavi (Thu Mar 08 2012 - 09:18:27 PST)
  - Re: [AMBER] Base stacking amir abbasi (Thu Mar 08 2012 - 10:11:12 PST)
    - Re: [AMBER] Base stacking Ilyas Yildirim (Thu Mar 08 2012 - 10:39:13 PST)
    - Re: [AMBER] Base stacking francesco oteri (Thu Mar 08 2012 - 11:00:49 PST)
    - Re: [AMBER] Base stacking amir abbasi (Thu Mar 08 2012 - 11:10:11 PST)
    - Re: [AMBER] Base stacking amirhossein taghavi (Fri Mar 09 2012 - 07:33:51 PST)
[AMBER] How to convert multiple mdcrd files to single files with minimium size? Catein Catherine (Thu Mar 08 2012 - 07:47:26 PST)
- Re: [AMBER] How to convert multiple mdcrd files to single files with minimium size? Marc van der Kamp (Thu Mar 08 2012 - 07:53:35 PST)
  - Re: [AMBER] How to convert multiple mdcrd files to single files with minimium size? Aron Broom (Thu Mar 08 2012 - 08:08:47 PST)
[AMBER] NAB segmentation fault Michael F. Bruist (Thu Mar 08 2012 - 08:03:12 PST)
- Re: [AMBER] NAB segmentation fault David A. Case (Sun Mar 11 2012 - 10:57:16 PDT)
  - Re: [AMBER] NAB segmentation fault Michael F. Bruist (Mon Mar 12 2012 - 11:34:46 PDT)
    - Re: [AMBER] NAB segmentation fault David A. Case (Tue Mar 13 2012 - 00:28:08 PDT)
    - Re: [AMBER] NAB segmentation fault Michael F. Bruist (Fri Mar 16 2012 - 09:32:33 PDT)
- Re: [AMBER] NAB segmentation fault Brian Wolfe (Tue Mar 20 2012 - 17:34:19 PDT)
  - Re: [AMBER] NAB segmentation fault case (Tue Mar 20 2012 - 18:26:52 PDT)
[AMBER] saltconc and string parameters in MM/PB(GB)SA mish (Thu Mar 08 2012 - 09:34:00 PST)
- Re: [AMBER] saltconc and string parameters in MM/PB(GB)SA Thomas Cheatham III (Thu Mar 08 2012 - 10:00:30 PST)
  - Re: [AMBER] saltconc and string parameters in MM/PB(GB)SA mish (Thu Mar 08 2012 - 11:10:10 PST)
    - Re: [AMBER] saltconc and string parameters in MM/PB(GB)SA Aron Broom (Thu Mar 08 2012 - 11:21:44 PST)
[AMBER] Can I use Amber 10 PRMTOP with Amber 11? Kasprzak, Wojciech (NIH/NCI) [C] (Thu Mar 08 2012 - 10:40:32 PST)
- Re: [AMBER] Can I use Amber 10 PRMTOP with Amber 11? Jason Swails (Thu Mar 08 2012 - 12:41:53 PST)
[AMBER] Mac OSX 10.7 George Tzotzos (Thu Mar 08 2012 - 11:05:05 PST)
- Re: [AMBER] Mac OSX 10.7 Jason Swails (Thu Mar 08 2012 - 12:36:00 PST)
[AMBER] Hydrogen bond analysis tdo.chem.ucsb.edu (Thu Mar 08 2012 - 23:48:00 PST)
- Re: [AMBER] Hydrogen bond analysis Daniel Roe (Fri Mar 09 2012 - 04:34:41 PST)
[AMBER] separated thermostat in AMBER mjyang (Fri Mar 09 2012 - 05:25:57 PST)
- Re: [AMBER] separated thermostat in AMBER David A Case (Fri Mar 09 2012 - 06:54:24 PST)
[AMBER] Job Opening at Simbios/Stanford University Ross Walker (Fri Mar 09 2012 - 13:19:54 PST)
[AMBER] Energy and Coordinate Outputs David Minh (Fri Mar 09 2012 - 13:47:53 PST)
- Re: [AMBER] Energy and Coordinate Outputs David Case (Fri Mar 09 2012 - 17:37:45 PST)
  - Re: [AMBER] Energy and Coordinate Outputs David Minh (Fri Mar 09 2012 - 18:26:39 PST)
    - Re: [AMBER] Energy and Coordinate Outputs David A. Case (Sat Mar 10 2012 - 10:13:00 PST)
    - Re: [AMBER] Energy and Coordinate Outputs David Minh (Mon Mar 12 2012 - 08:55:38 PDT)
    - Re: [AMBER] Energy and Coordinate Outputs Jason Swails (Tue Mar 13 2012 - 15:22:11 PDT)
    - Re: [AMBER] Energy and Coordinate Outputs David A. Case (Wed Mar 14 2012 - 14:15:58 PDT)
    - Re: [AMBER] Energy and Coordinate Outputs David Minh (Sat Mar 17 2012 - 05:03:28 PDT)
- [AMBER] Amber10 paralel installation Shaandar Nyamtulga (Fri Mar 09 2012 - 19:06:01 PST)
  - Re: [AMBER] Amber10 paralel installation Jason Swails (Sat Mar 10 2012 - 13:08:21 PST)
- Re: [AMBER] Energy and Coordinate Outputs David A. Case (Wed Mar 14 2012 - 14:49:53 PDT)
[AMBER] Amber11 Intel compiler version 12 make parallel fail Andrew Petersen (Fri Mar 09 2012 - 14:34:32 PST)
- Re: [AMBER] Amber11 Intel compiler version 12 make parallel fail David Case (Fri Mar 09 2012 - 17:44:03 PST)
[AMBER] asking about mden setyanto md (Sun Mar 11 2012 - 22:33:57 PDT)
- Re: [AMBER] asking about mden Ben Roberts (Sun Mar 11 2012 - 23:35:11 PDT)
  - Re: [AMBER] asking about mden setyanto md (Mon Mar 12 2012 - 03:26:43 PDT)
[AMBER] April 3 deadline for application for ACS computational chemistry awards for the Fall 2012 national meeting Carlos Simmerling (Mon Mar 12 2012 - 10:02:19 PDT)
[AMBER] binding free energy kirtana S (Tue Mar 13 2012 - 00:35:19 PDT)
- Re: [AMBER] binding free energy Sushil Mishra (Tue Mar 13 2012 - 00:55:33 PDT)
- Re: [AMBER] binding free energy David A. Case (Wed Mar 14 2012 - 14:16:20 PDT)
- Re: [AMBER] binding free energy David A. Case (Wed Mar 14 2012 - 14:49:23 PDT)
- Re: [AMBER] binding free energy David A Case (Thu Mar 15 2012 - 05:51:43 PDT)
[AMBER] Use of SLEF1 force field in Amber Gonzalo Jimenez (Tue Mar 13 2012 - 00:56:54 PDT)
- Re: [AMBER] Use of SLEF1 force field in Amber CHAMI F. (Wed Mar 14 2012 - 11:52:05 PDT)
  - Re: [AMBER] Use of SLEF1 force field in Amber Gonzalo Jimenez (Wed Mar 14 2012 - 16:40:40 PDT)
[AMBER] tleap and water molecules Enrico Caldarulo (Tue Mar 13 2012 - 03:05:36 PDT)
- [AMBER] R: tleap and water molecules Giovanni Pavan (Tue Mar 13 2012 - 03:19:05 PDT)
[AMBER] Replica Exchange Rajendra Sharma (Tue Mar 13 2012 - 08:08:06 PDT)
- Re: [AMBER] Replica Exchange Dmitry Mukha (Tue Mar 13 2012 - 13:34:23 PDT)
  - Re: [AMBER] Replica Exchange Rajendra Sharma (Wed Mar 14 2012 - 08:22:38 PDT)
    - Re: [AMBER] Replica Exchange Indrajit Deb (Wed Mar 14 2012 - 08:29:19 PDT)
    - Re: [AMBER] Replica Exchange Carlos Simmerling (Wed Mar 14 2012 - 08:29:16 PDT)
    - Re: [AMBER] Replica Exchange Alex Rodriguez (Wed Mar 14 2012 - 08:32:40 PDT)
    - Re: [AMBER] Replica Exchange Logan Ahlstrom (Wed Mar 14 2012 - 08:34:59 PDT)
    - Re: [AMBER] Replica Exchange Adrian Roitberg (Wed Mar 14 2012 - 08:40:46 PDT)
[AMBER] MMPBSA George Tzotzos (Tue Mar 13 2012 - 10:06:14 PDT)
- Re: [AMBER] MMPBSA Aron Broom (Tue Mar 13 2012 - 10:13:04 PDT)
  - Re: [AMBER] MMPBSA George Tzotzos (Tue Mar 13 2012 - 10:26:43 PDT)
    - Re: [AMBER] MMPBSA Dmitry Mukha (Tue Mar 13 2012 - 12:19:19 PDT)
    - Re: [AMBER] MMPBSA George Tzotzos (Tue Mar 13 2012 - 12:28:12 PDT)
    - Re: [AMBER] MMPBSA Dmitry Mukha (Tue Mar 13 2012 - 13:15:21 PDT)
    - Re: [AMBER] MMPBSA George Tzotzos (Tue Mar 13 2012 - 13:43:36 PDT)
[AMBER] MMPBSA George Tzotzos (Tue Mar 13 2012 - 10:08:47 PDT)
[AMBER] PBSA sprob question Jesper Sørensen (Tue Mar 13 2012 - 13:49:09 PDT)
- Re: [AMBER] PBSA sprob question Qin Cai (Tue Mar 13 2012 - 15:13:42 PDT)
  - Re: [AMBER] PBSA sprob question Jesper Sørensen (Tue Mar 13 2012 - 15:58:18 PDT)
    - Re: [AMBER] PBSA sprob question Qin Cai (Tue Mar 13 2012 - 16:46:48 PDT)
    - Re: [AMBER] PBSA sprob question Jesper Sørensen (Wed Mar 14 2012 - 08:57:50 PDT)
[AMBER] Extra Bonds For Water Kyle Greenway (Tue Mar 13 2012 - 15:37:33 PDT)
- Re: [AMBER] Extra Bonds For Water Adrian Roitberg (Tue Mar 13 2012 - 15:44:59 PDT)
[AMBER] ptraj: Sort trajectory based on protein-ligand distance tdo.chem.ucsb.edu (Tue Mar 13 2012 - 18:27:05 PDT)
- Re: [AMBER] ptraj: Sort trajectory based on protein-ligand distance g t (Wed Mar 14 2012 - 11:37:31 PDT)
[AMBER] The value of Delta G is positive after MMPBSA calculation for metalloprotein JiYuan Liu (Tue Mar 13 2012 - 20:02:24 PDT)
[AMBER] Amber 10 parallel installation error Shaandar Nyamtulga (Wed Mar 14 2012 - 00:19:03 PDT)
- Re: [AMBER] Amber 10 parallel installation error David A Case (Fri Mar 16 2012 - 05:20:17 PDT)
[AMBER] antechamber error Syed Tarique Moin (Wed Mar 14 2012 - 03:59:45 PDT)
- Re: [AMBER] antechamber error David A Case (Fri Mar 16 2012 - 05:16:22 PDT)
[AMBER] both parallel and serial amir abbasi (Wed Mar 14 2012 - 06:57:34 PDT)
- Re: [AMBER] both parallel and serial Jason Swails (Wed Mar 14 2012 - 07:10:59 PDT)
[AMBER] Amber10 parallel installation test example run error Shaandar Nyamtulga (Wed Mar 14 2012 - 20:50:37 PDT)
- Re: [AMBER] Amber10 parallel installation test example run error Daniel Roe (Thu Mar 15 2012 - 03:16:25 PDT)
[AMBER] Amber10 parallel installation test error Shaandar Nyamtulga (Wed Mar 14 2012 - 22:48:45 PDT)
- Re: [AMBER] Amber10 parallel installation test error David A Case (Thu Mar 15 2012 - 12:29:09 PDT)
[AMBER] simulation with metal-containing ligands Fati (Thu Mar 15 2012 - 05:01:04 PDT)
[AMBER] Announcement: Large biomolecule benchmark report Hannes Loeffler (Thu Mar 15 2012 - 05:50:10 PDT)
[AMBER] puting restrains Urszula Uciechowska (Thu Mar 15 2012 - 06:24:26 PDT)
- Re: [AMBER] puting restrains Brian Radak (Thu Mar 15 2012 - 06:59:11 PDT)
  - [AMBER] Is it possible to cluster several mdcrd files based on a dihedral angles of a particular residues? Catein Catherine (Thu Mar 15 2012 - 07:16:56 PDT)
  - Re: [AMBER] puting restrains Urszula Uciechowska (Fri Mar 16 2012 - 04:01:13 PDT)
[AMBER] rigid body simulation Qian Wang (Thu Mar 15 2012 - 08:19:06 PDT)
- Re: [AMBER] rigid body simulation David A Case (Thu Mar 15 2012 - 12:30:40 PDT)
  - Re: [AMBER] rigid body simulation Ilyas Yildirim (Thu Mar 15 2012 - 12:36:48 PDT)
[AMBER] restrain water in a solvatecap Yi An (Thu Mar 15 2012 - 10:05:22 PDT)
- [AMBER] restrain water in a solvatecap Yi An (Mon Mar 19 2012 - 13:01:44 PDT)
  - Re: [AMBER] restrain water in a solvatecap liu junjun (Mon Mar 19 2012 - 20:40:22 PDT)
[AMBER] on the AMBER advanced tutorial 3 MM-PBSA Wholly Peach (Thu Mar 15 2012 - 17:18:01 PDT)
- Re: [AMBER] on the AMBER advanced tutorial 3 MM-PBSA Bill Miller III (Sat Mar 17 2012 - 11:19:03 PDT)
  - Re: [AMBER] on the AMBER advanced tutorial 3 MM-PBSA Aron Broom (Sat Mar 17 2012 - 11:40:25 PDT)
[AMBER] the problem of RAMD xiaojiong (Fri Mar 16 2012 - 02:02:50 PDT)
- Re: [AMBER] the problem of RAMD Vlad Cojocaru (Fri Mar 16 2012 - 03:52:47 PDT)
[AMBER] MMPBSA, in parallel? Fernando Blanco (Fri Mar 16 2012 - 05:30:17 PDT)
- Re: [AMBER] MMPBSA, in parallel? Jason Swails (Fri Mar 16 2012 - 06:41:07 PDT)
[AMBER] mpi-allreduce in AMBER11 Carlos Sosa (Fri Mar 16 2012 - 06:23:16 PDT)
- Re: [AMBER] mpi-allreduce in AMBER11 Jason Swails (Fri Mar 16 2012 - 06:38:40 PDT)
  - Re: [AMBER] mpi-allreduce in AMBER11 Carlos Sosa (Fri Mar 16 2012 - 09:36:59 PDT)
[AMBER] Amber for Cuda on Mac OSX George Tzotzos (Fri Mar 16 2012 - 07:35:38 PDT)
- Re: [AMBER] Amber for Cuda on Mac OSX Jason Swails (Fri Mar 16 2012 - 12:03:52 PDT)
[AMBER] MMPBSA.py - Internal energy George Tzotzos (Fri Mar 16 2012 - 11:58:40 PDT)
- Re: [AMBER] MMPBSA.py - Internal energy Jason Swails (Fri Mar 16 2012 - 12:05:58 PDT)
  - Re: [AMBER] MMPBSA.py - Internal energy George Tzotzos (Fri Mar 16 2012 - 12:13:40 PDT)
[AMBER] Implicit MD run Aditya Padhi (Fri Mar 16 2012 - 21:29:00 PDT)
- [AMBER] No Na molecule type for genion Wholly Peach (Fri Mar 16 2012 - 22:45:32 PDT)
  - Re: [AMBER] No Na molecule type for genion raghav singh (Fri Mar 16 2012 - 22:57:05 PDT)
  - Re: [AMBER] No Na molecule type for genion M. L. Dodson (Sat Mar 17 2012 - 06:40:06 PDT)
- Re: [AMBER] Implicit MD run Aron Broom (Fri Mar 16 2012 - 22:53:08 PDT)
  - Re: [AMBER] Implicit MD run Aditya Padhi (Fri Mar 16 2012 - 22:57:20 PDT)
    - Re: [AMBER] Implicit MD run Aron Broom (Fri Mar 16 2012 - 23:06:13 PDT)
    - Re: [AMBER] Implicit MD run Aditya Padhi (Fri Mar 16 2012 - 23:19:21 PDT)
    - Re: [AMBER] Implicit MD run Carlos Simmerling (Sat Mar 17 2012 - 04:20:00 PDT)
    - Re: [AMBER] Implicit MD run Aditya Padhi (Sun Mar 18 2012 - 21:30:51 PDT)
    - Re: [AMBER] Implicit MD run Carlos Simmerling (Mon Mar 19 2012 - 03:30:27 PDT)
    - Re: [AMBER] Implicit MD run Aditya Padhi (Mon Mar 19 2012 - 04:11:35 PDT)
    - Re: [AMBER] Implicit MD run Carlos Simmerling (Mon Mar 19 2012 - 05:42:34 PDT)
    - Re: [AMBER] Implicit MD run Aditya Padhi (Mon Mar 19 2012 - 22:52:57 PDT)
    - Re: [AMBER] Implicit MD run Carlos Simmerling (Tue Mar 20 2012 - 04:02:13 PDT)
    - Re: [AMBER] Implicit MD run Aditya Padhi (Tue Mar 20 2012 - 04:12:04 PDT)
[AMBER] PB with inp=2 doesn't recognize ff10 atom types? David Minh (Sat Mar 17 2012 - 11:10:45 PDT)
- [AMBER] Fwd: PB with inp=2 doesn't recognize ff10 atom types? Ray Luo, Ph.D. (Sat Mar 17 2012 - 19:33:14 PDT)
  - Re: [AMBER] PB with inp=2 doesn't recognize ff10 atom types? Qin Cai (Mon Mar 19 2012 - 15:15:38 PDT)
[AMBER] Amber8 and RAMD xiaojiong (Sun Mar 18 2012 - 01:59:00 PDT)
- Re: [AMBER] Amber8 and RAMD Vlad Cojocaru (Sun Mar 18 2012 - 02:54:15 PDT)
[AMBER] is GB/SA suitable for nonaqueous solvent? Junjian Miao (Sun Mar 18 2012 - 07:21:42 PDT)
- Re: [AMBER] is GB/SA suitable for nonaqueous solvent? Carlos Simmerling (Sun Mar 18 2012 - 07:25:35 PDT)
- Re: [AMBER] is GB/SA suitable for nonaqueous solvent? Dean Cuebas (Mon Mar 19 2012 - 09:51:28 PDT)
  - Re: [AMBER] is GB/SA suitable for nonaqueous solvent? Alex Rodriguez (Mon Mar 19 2012 - 10:25:15 PDT)
[AMBER] Problems with tetrahedral Al in antechamber Gonzalo Jimenez (Mon Mar 19 2012 - 01:44:19 PDT)
- Re: [AMBER] Problems with tetrahedral Al in antechamber case (Mon Mar 19 2012 - 05:11:32 PDT)
[AMBER] Problems with tetrahedral Al in antechamber Gonzalo Jimenez (Mon Mar 19 2012 - 02:16:35 PDT)
[AMBER] To generate more than one structure using ptraj Souvik Sur (Mon Mar 19 2012 - 06:36:31 PDT)
- Re: [AMBER] To generate more than one structure using ptraj Jason Swails (Mon Mar 19 2012 - 08:17:12 PDT)
  - Re: [AMBER] To generate more than one structure using ptraj Souvik Sur (Mon Mar 19 2012 - 22:56:44 PDT)
    - Re: [AMBER] To generate more than one structure using ptraj Jason Swails (Tue Mar 20 2012 - 10:04:48 PDT)
[AMBER] charges for ion and surrounding residues at the active site JORGE IULEK (Mon Mar 19 2012 - 12:51:05 PDT)
[AMBER] How to calculate the energy contributed by hydrogen bonds? bin wang (Mon Mar 19 2012 - 14:00:51 PDT)
- Re: [AMBER] How to calculate the energy contributed by hydrogen bonds? Jason Swails (Mon Mar 19 2012 - 19:27:01 PDT)
  - Re: [AMBER] How to calculate the energy contributed by hydrogen bonds? bin wang (Tue Mar 20 2012 - 07:17:29 PDT)
    - Re: [AMBER] How to calculate the energy contributed by hydrogen bonds? Jason Swails (Tue Mar 20 2012 - 10:01:24 PDT)
    - Re: [AMBER] How to calculate the energy contributed by hydrogen bonds? bin wang (Wed Mar 21 2012 - 20:58:22 PDT)
[AMBER] charges for ion and surrounding residues at the active site Jorge Iulek (Mon Mar 19 2012 - 17:33:10 PDT)
- Re: [AMBER] charges for ion and surrounding residues at the active site FyD (Tue Mar 20 2012 - 04:55:07 PDT)
  - Re: [AMBER] charges for ion and surrounding residues at the active site Jorge Iulek (Tue Mar 20 2012 - 17:28:36 PDT)
    - Re: [AMBER] charges for ion and surrounding residues at the active site FyD (Wed Mar 21 2012 - 00:02:44 PDT)
    - Re: [AMBER] charges for ion and surrounding residues at the active site Jorge Iulek (Wed Mar 21 2012 - 09:07:08 PDT)
[AMBER] organics solvent radius setyanto md (Mon Mar 19 2012 - 23:04:23 PDT)
[AMBER] MD and RAMD xiaojiong (Tue Mar 20 2012 - 00:12:20 PDT)
- Re: [AMBER] MD and RAMD Vlad Cojocaru (Tue Mar 20 2012 - 00:59:52 PDT)
[AMBER] Is there some constrains required for the REMD simulation on disaccharide in Amber11? 黄恋琦 (Tue Mar 20 2012 - 00:42:05 PDT)
[AMBER] Fast ibelly? David Minh (Tue Mar 20 2012 - 08:29:00 PDT)
- Re: [AMBER] Fast ibelly? Ross Walker (Tue Mar 20 2012 - 10:09:47 PDT)
  - Re: [AMBER] Fast ibelly? David Minh (Tue Mar 20 2012 - 11:10:15 PDT)
    - Re: [AMBER] Fast ibelly? Ross Walker (Tue Mar 20 2012 - 11:31:10 PDT)
    - Re: [AMBER] Fast ibelly? David A Case (Tue Mar 20 2012 - 13:22:15 PDT)
    - Re: [AMBER] Fast ibelly? David Minh (Wed Mar 21 2012 - 07:22:59 PDT)
[AMBER] GBSA - surface tension question for calculation of ΔGnonpolar g t (Tue Mar 20 2012 - 10:34:48 PDT)
- Re: [AMBER] GBSA - surface tension question for calculation of ΔGnonpolar Carlos Simmerling (Tue Mar 20 2012 - 10:44:37 PDT)
  - Re: [AMBER] GBSA - surface tension question for calculation of ΔGnonpolar g t (Tue Mar 20 2012 - 16:02:06 PDT)
    - Re: [AMBER] GBSA - surface tension question for calculation of ΔGnonpolar Carlos Simmerling (Wed Mar 21 2012 - 04:08:30 PDT)
    - Re: [AMBER] GBSA - surface tension question for calculation of ΔGnonpolar g t (Wed Mar 21 2012 - 23:18:34 PDT)
[AMBER] disulfide bond warnings George Tzotzos (Tue Mar 20 2012 - 11:30:29 PDT)
- Re: [AMBER] disulfide bond warnings Jason Swails (Tue Mar 20 2012 - 16:01:09 PDT)
  - Re: [AMBER] disulfide bond warnings George Tzotzos (Tue Mar 20 2012 - 16:19:41 PDT)
    - Re: [AMBER] disulfide bond warnings Jason Swails (Tue Mar 20 2012 - 18:45:32 PDT)
[AMBER] Water coordinated with transition metal ashwini gupta (Tue Mar 20 2012 - 23:36:40 PDT)
- Re: [AMBER] Water coordinated with transition metal Ben Roberts (Wed Mar 21 2012 - 00:21:35 PDT)
  - Re: [AMBER] Water coordinated with transition metal ashwini gupta (Wed Mar 21 2012 - 02:09:04 PDT)
    - Re: [AMBER] Water coordinated with transition metal Ben Roberts (Wed Mar 21 2012 - 02:40:50 PDT)
    - Re: [AMBER] Water coordinated with transition metal ashwini gupta (Wed Mar 21 2012 - 03:33:29 PDT)
    - Re: [AMBER] Water coordinated with transition metal Ben Roberts (Wed Mar 21 2012 - 03:41:10 PDT)
    - Re: [AMBER] Water coordinated with transition metal ashwini gupta (Wed Mar 21 2012 - 04:40:32 PDT)
[AMBER] About ANAL problem: Amber 王伟 (Wed Mar 21 2012 - 04:16:23 PDT)
- Re: [AMBER] About ANAL problem: Amber David A Case (Wed Mar 21 2012 - 04:55:01 PDT)
  - Re: [AMBER] About ANAL problem: Amber Soumya Lipsa Rath (Wed Mar 21 2012 - 23:25:36 PDT)
    - Re: [AMBER] About ANAL problem: Amber David A Case (Thu Mar 22 2012 - 05:14:10 PDT)
    - Re: [AMBER] About ANAL problem: Amber 王伟 (Sat Mar 24 2012 - 00:41:00 PDT)
  - Re: [AMBER] About ANAL problem: Amber 王伟 (Thu Mar 22 2012 - 06:14:43 PDT)
[AMBER] Amber 11 Compilation Error (again!) Adam Jion (Wed Mar 21 2012 - 04:57:37 PDT)
- Re: [AMBER] Amber 11 Compilation Error (again!) Jason Swails (Wed Mar 21 2012 - 05:16:25 PDT)
[AMBER] Converting Gromacs coordinate file to Amber input files for molecular dynamics Adam Jion (Wed Mar 21 2012 - 10:00:23 PDT)
- Re: [AMBER] Converting Gromacs coordinate file to Amber input files formolecular dynamics Vlad Cojocaru (Wed Mar 21 2012 - 10:10:52 PDT)
- Re: [AMBER] Converting Gromacs coordinate file to Amber input files for molecular dynamics Alex Rodriguez (Wed Mar 21 2012 - 10:13:23 PDT)
[AMBER] External Force Method in pmemd.cuda Ismail, Mohd F. (Wed Mar 21 2012 - 10:28:43 PDT)
- Re: [AMBER] External Force Method in pmemd.cuda Jason Swails (Wed Mar 21 2012 - 10:35:52 PDT)
  - Re: [AMBER] External Force Method in pmemd.cuda Ismail, Mohd F. (Wed Mar 21 2012 - 10:46:59 PDT)
[AMBER] Problem in Amber installation vishal Nemaysh (Thu Mar 22 2012 - 01:06:08 PDT)
- Re: [AMBER] Problem in Amber installation David A Case (Thu Mar 22 2012 - 05:18:32 PDT)
  - Re: [AMBER] Problem in Amber installation Jason Swails (Thu Mar 22 2012 - 06:09:39 PDT)
    - Re: [AMBER] Problem in Amber installation vishal Nemaysh (Wed Mar 28 2012 - 22:01:57 PDT)
    - Re: [AMBER] Problem in Amber installation Jason Swails (Thu Mar 29 2012 - 04:49:37 PDT)
    - Re: [AMBER] Problem in Amber installation setyanto md (Fri Mar 30 2012 - 02:21:57 PDT)
    - Re: [AMBER] Problem in Amber installation Jason Swails (Fri Mar 30 2012 - 07:09:11 PDT)
    - Re: [AMBER] Problem in Amber installation setyanto md (Mon Apr 02 2012 - 01:11:55 PDT)
[AMBER] Non - integral charge o unperturbed unit ashwini gupta (Thu Mar 22 2012 - 03:08:44 PDT)
- Re: [AMBER] Non - integral charge o unperturbed unit FyD (Fri Mar 23 2012 - 07:58:26 PDT)
[AMBER] Is it possible to just calculate translational and rotational entropy? Tan Yaw Sing (Thu Mar 22 2012 - 03:57:57 PDT)
- Re: [AMBER] Is it possible to just calculate translational and rotational entropy? David A Case (Thu Mar 22 2012 - 05:23:10 PDT)
[AMBER] amber parameters for cytochrome c Gurunath Katagi (Thu Mar 22 2012 - 19:42:03 PDT)
- Re: [AMBER] amber parameters for cytochrome c Jason Swails (Sat Mar 24 2012 - 08:49:23 PDT)
[AMBER] atom type of Sulphur in CYS/CYM (MCPB) ashwini gupta (Thu Mar 22 2012 - 23:39:03 PDT)
- Re: [AMBER] atom type of Sulphur in CYS/CYM (MCPB) Tong Zhu (Fri Mar 23 2012 - 02:12:32 PDT)
  - Re: [AMBER] atom type of Sulphur in CYS/CYM (MCPB) Ben Roberts (Sun Mar 25 2012 - 11:02:04 PDT)
    - Re: [AMBER] atom type of Sulphur in CYS/CYM (MCPB) ashwini gupta (Sun Mar 25 2012 - 21:33:53 PDT)
[AMBER] Amber10 parallel installation test example Shaandar Nyamtulga (Fri Mar 23 2012 - 01:08:31 PDT)
- Re: [AMBER] Amber10 parallel installation test example David A Case (Fri Mar 23 2012 - 05:21:38 PDT)
[AMBER] esp and resp comparison jun kit (Fri Mar 23 2012 - 01:23:49 PDT)
- Re: [AMBER] esp and resp comparison FyD (Fri Mar 23 2012 - 08:01:27 PDT)
[AMBER] parameters for Lys-sugar Urszula Uciechowska (Fri Mar 23 2012 - 05:15:38 PDT)
- Re: [AMBER] parameters for Lys-sugar FyD (Fri Mar 23 2012 - 08:06:35 PDT)
  - Re: [AMBER] parameters for Lys-sugar Lachele Foley (Lists) (Fri Mar 23 2012 - 08:11:15 PDT)
    - Re: [AMBER] parameters for Lys-sugar Urszula Uciechowska (Fri Mar 23 2012 - 08:26:19 PDT)
    - Re: [AMBER] parameters for Lys-sugar FyD (Fri Mar 23 2012 - 09:11:51 PDT)
    - Re: [AMBER] parameters for Lys-sugar Lachele Foley (Lists) (Fri Mar 23 2012 - 11:01:27 PDT)
    - Re: [AMBER] parameters for Lys-sugar Lachele Foley (Lists) (Fri Mar 23 2012 - 12:39:04 PDT)
    - Re: [AMBER] parameters for Lys-sugar FyD (Sat Mar 24 2012 - 01:14:17 PDT)
    - Re: [AMBER] parameters for Lys-sugar Lachele Foley (Lists) (Sat Mar 24 2012 - 08:10:20 PDT)
    - Re: [AMBER] parameters for Lys-sugar Urszula Uciechowska (Sat Mar 24 2012 - 13:41:00 PDT)
    - Re: [AMBER] parameters for Lys-sugar Lachele Foley (Lists) (Sun Mar 25 2012 - 13:10:23 PDT)
    - Re: [AMBER] parameters for Lys-sugar Urszula Uciechowska (Sat Mar 24 2012 - 13:52:42 PDT)
- Re: [AMBER] parameters for Lys-sugar Urszula Uciechowska (Mon Apr 23 2012 - 03:38:24 PDT)
  - Re: [AMBER] parameters for Lys-sugar FyD (Mon Apr 23 2012 - 09:26:41 PDT)
    - Re: [AMBER] parameters for Lys-sugar Lachele Foley (Lists) (Mon Apr 23 2012 - 13:05:31 PDT)
    - Re: [AMBER] parameters for Lys-sugar Jan-Philip Gehrcke (Wed Apr 25 2012 - 04:48:51 PDT)
    - Re: [AMBER] parameters for Lys-sugar Lachele Foley (Lists) (Tue Jun 26 2012 - 09:56:48 PDT)
    - Re: [AMBER] parameters for Lys-sugar Urszula Uciechowska (Tue Jun 26 2012 - 10:58:43 PDT)
[AMBER] Problems compiling pmemd.cuda - undefined reference to ... Adam Jion (Fri Mar 23 2012 - 07:15:28 PDT)
- Re: [AMBER] Problems compiling pmemd.cuda - undefined reference to ... Ross Walker (Fri Mar 23 2012 - 09:17:06 PDT)
  - Re: [AMBER] Problems compiling pmemd.cuda - undefined reference to ... Adam Jion (Fri Mar 23 2012 - 10:22:40 PDT)
    - Re: [AMBER] Problems compiling pmemd.cuda - undefined reference to ... Daniel Roe (Fri Mar 23 2012 - 11:10:19 PDT)
    - Re: [AMBER] Problems compiling pmemd.cuda - undefined reference to ... Jason Swails (Sat Mar 24 2012 - 09:06:43 PDT)
[AMBER] About ANAL problem: Amber 王伟 (Fri Mar 23 2012 - 07:37:32 PDT)
[AMBER] Conflict between AmberTools 1.5 and Cuda Adam Jion (Fri Mar 23 2012 - 08:18:55 PDT)
- Re: [AMBER] Conflict between AmberTools 1.5 and Cuda Daniel Roe (Fri Mar 23 2012 - 09:16:55 PDT)
- Re: [AMBER] Conflict between AmberTools 1.5 and Cuda Ross Walker (Fri Mar 23 2012 - 09:19:07 PDT)
  - Re: [AMBER] Conflict between AmberTools 1.5 and Cuda Adam Jion (Fri Mar 23 2012 - 10:09:32 PDT)
    - Re: [AMBER] Conflict between AmberTools 1.5 and Cuda David A Case (Fri Mar 23 2012 - 11:11:32 PDT)
    - Re: [AMBER] Conflict between AmberTools 1.5 and Cuda Adam Jion (Sat Mar 24 2012 - 04:26:21 PDT)
    - Re: [AMBER] Conflict between AmberTools 1.5 and Cuda Jan-Philip Gehrcke (Sat Mar 24 2012 - 05:23:38 PDT)
  - [AMBER] GTX680 filip fratev (Fri Mar 23 2012 - 11:37:02 PDT)
    - Re: [AMBER] GTX680 Ross Walker (Fri Mar 23 2012 - 11:49:15 PDT)
    - Re: [AMBER] GTX680 Scott Le Grand (Fri Mar 23 2012 - 11:57:00 PDT)
    - Re: [AMBER] GTX680 Scott Le Grand (Wed Mar 28 2012 - 09:33:39 PDT)
    - Re: [AMBER] GTX680 Aron Broom (Wed Mar 28 2012 - 09:54:11 PDT)
    - Re: [AMBER] GTX680 Scott Le Grand (Wed Mar 28 2012 - 10:07:57 PDT)
    - Re: [AMBER] GTX680 Aron Broom (Wed Mar 28 2012 - 10:30:30 PDT)
    - Re: [AMBER] GTX680 Scott Le Grand (Wed Mar 28 2012 - 10:40:40 PDT)
    - Re: [AMBER] GTX680 Aron Broom (Wed Mar 28 2012 - 10:45:45 PDT)
    - Re: [AMBER] GTX680 Ross Walker (Wed Mar 28 2012 - 13:39:14 PDT)
    - Re: [AMBER] GTX680 Aron Broom (Wed Mar 28 2012 - 15:11:26 PDT)
    - Re: [AMBER] GTX680 Fenley, Andrew (Wed Mar 28 2012 - 19:33:53 PDT)
    - Re: [AMBER] GTX680 Scott Le Grand (Thu Mar 29 2012 - 08:39:21 PDT)
[AMBER] ANAL 王伟 (Sat Mar 24 2012 - 00:57:41 PDT)
[AMBER] Error Compiling pmemd.cuda.MPI (i.e. Multiple GPUs) Adam Jion (Sat Mar 24 2012 - 06:03:58 PDT)
- Re: [AMBER] Error Compiling pmemd.cuda.MPI (i.e. Multiple GPUs) Jason Swails (Sat Mar 24 2012 - 08:17:58 PDT)
  - Re: [AMBER] Error Compiling pmemd.cuda.MPI (i.e. Multiple GPUs) Adam Jion (Sat Mar 24 2012 - 09:38:16 PDT)
    - Re: [AMBER] Error Compiling pmemd.cuda.MPI (i.e. Multiple GPUs) Scott Le Grand (Sat Mar 24 2012 - 09:49:42 PDT)
    - Re: [AMBER] Error Compiling pmemd.cuda.MPI (i.e. Multiple GPUs) Jason Swails (Sat Mar 24 2012 - 10:06:02 PDT)
    - Re: [AMBER] Error Compiling pmemd.cuda.MPI (i.e. Multiple GPUs) Adam Jion (Sat Mar 24 2012 - 10:29:09 PDT)
  - Re: [AMBER] Error Compiling pmemd.cuda.MPI (i.e. Multiple GPUs) Adam Jion (Sat Mar 24 2012 - 17:12:48 PDT)
    - Re: [AMBER] Error Compiling pmemd.cuda.MPI (i.e. Multiple GPUs) Jason Swails (Sat Mar 24 2012 - 17:15:42 PDT)
    - Re: [AMBER] Error Compiling pmemd.cuda.MPI (i.e. Multiple GPUs) Adam Jion (Sat Mar 24 2012 - 17:45:47 PDT)
    - Re: [AMBER] Error Compiling pmemd.cuda.MPI (i.e. Multiple GPUs) Jason Swails (Sat Mar 24 2012 - 19:33:37 PDT)
    - Re: [AMBER] Error Compiling pmemd.cuda.MPI (i.e. Multiple GPUs) Adam Jion (Sat Mar 24 2012 - 20:28:04 PDT)
[AMBER] ptraj atomicfluct George Tzotzos (Sat Mar 24 2012 - 14:12:11 PDT)
- Re: [AMBER] ptraj atomicfluct Thomas Cheatham (Sat Mar 24 2012 - 14:26:16 PDT)
  - Re: [AMBER] ptraj atomicfluct George Tzotzos (Sat Mar 24 2012 - 14:54:48 PDT)
[AMBER] Problems testing pmemd.cuda.MPI Adam Jion (Sat Mar 24 2012 - 19:21:02 PDT)
- Re: [AMBER] Problems testing pmemd.cuda.MPI Ben Roberts (Sun Mar 25 2012 - 16:14:18 PDT)
[AMBER] ANAL 王伟 (Sat Mar 24 2012 - 20:17:43 PDT)
[AMBER] ANAL wei wang (Sat Mar 24 2012 - 20:32:47 PDT)
[AMBER] About ANAL wei wang (Sun Mar 25 2012 - 02:33:33 PDT)
- Re: [AMBER] About ANAL David A. Case (Sun Mar 25 2012 - 07:47:38 PDT)
[AMBER] Problems with pmemd.cuda.mpi (again!) Adam Jion (Sun Mar 25 2012 - 04:51:53 PDT)
- Re: [AMBER] Problems with pmemd.cuda.mpi (again!) Ross Walker (Sun Mar 25 2012 - 07:03:48 PDT)
  - Re: [AMBER] Problems with pmemd.cuda.mpi (again!) Adam Jion (Sun Mar 25 2012 - 07:34:28 PDT)
    - Re: [AMBER] Problems with pmemd.cuda.mpi (again!) Jason Swails (Sun Mar 25 2012 - 08:24:26 PDT)
    - Re: [AMBER] Problems with pmemd.cuda.mpi (again!) Adam Jion (Sun Mar 25 2012 - 09:58:48 PDT)
- Re: [AMBER] Problems with pmemd.cuda.mpi (again!) Jason Swails (Mon Mar 26 2012 - 07:24:35 PDT)
  - Re: [AMBER] Problems with pmemd.cuda.mpi (again!) Adam Jion (Mon Mar 26 2012 - 09:13:05 PDT)
    - Re: [AMBER] Problems with pmemd.cuda.mpi (again!) Jason Swails (Mon Mar 26 2012 - 09:51:13 PDT)
    - Re: [AMBER] Problems with pmemd.cuda.mpi (again!) Adam Jion (Mon Mar 26 2012 - 10:25:30 PDT)
[AMBER] MP2 for RESP Tong Zhu (Mon Mar 26 2012 - 01:46:36 PDT)
- Re: [AMBER] MP2 for RESP Ben Roberts (Mon Mar 26 2012 - 13:26:07 PDT)
[AMBER] amber12 Elisa Frezza (Mon Mar 26 2012 - 02:26:39 PDT)
- Re: [AMBER] amber12 Jason Swails (Mon Mar 26 2012 - 08:32:45 PDT)
  - Re: [AMBER] amber12 Ross Walker (Mon Mar 26 2012 - 09:35:22 PDT)
    - Re: [AMBER] amber12 Elisa Frezza (Tue Mar 27 2012 - 05:35:44 PDT)
    - Re: [AMBER] amber12 Jason Swails (Tue Mar 27 2012 - 06:16:40 PDT)
[AMBER] Fwd: V limit RAMON (Mon Mar 26 2012 - 07:21:46 PDT)
- Re: [AMBER] Fwd: V limit David A Case (Thu Mar 29 2012 - 09:18:59 PDT)
  - Re: [AMBER] Fwd: V limit Ross Walker (Thu Mar 29 2012 - 11:47:37 PDT)
    - Re: [AMBER] Fwd: V limit Jason Swails (Thu Mar 29 2012 - 12:04:41 PDT)
    - Re: [AMBER] Fwd: V limit David A Case (Thu Mar 29 2012 - 13:20:05 PDT)
[AMBER] cpptraj hbond George Tzotzos (Mon Mar 26 2012 - 07:26:28 PDT)
- Re: [AMBER] cpptraj hbond George Tzotzos (Mon Mar 26 2012 - 11:13:55 PDT)
  - Re: [AMBER] cpptraj hbond Daniel Roe (Mon Mar 26 2012 - 12:06:57 PDT)
    - Re: [AMBER] cpptraj hbond George Tzotzos (Mon Mar 26 2012 - 12:10:43 PDT)
[AMBER] Amber and Short Bonds Aronica, Pietro (Mon Mar 26 2012 - 08:04:45 PDT)
- Re: [AMBER] Amber and Short Bonds Ross Walker (Mon Mar 26 2012 - 09:44:30 PDT)
  - Re: [AMBER] Amber and Short Bonds Aronica, Pietro (Mon Mar 26 2012 - 10:05:41 PDT)
    - Re: [AMBER] Amber and Short Bonds Jason Swails (Mon Mar 26 2012 - 13:15:55 PDT)
    - Re: [AMBER] Amber and Short Bonds Thomas Cheatham (Mon Mar 26 2012 - 13:21:22 PDT)
    - Re: [AMBER] Amber and Short Bonds Aronica, Pietro (Mon Mar 26 2012 - 16:18:35 PDT)
    - Re: [AMBER] Amber and Short Bonds Jason Swails (Mon Mar 26 2012 - 16:47:36 PDT)
    - Re: [AMBER] Amber and Short Bonds Aronica, Pietro (Mon Mar 26 2012 - 17:02:02 PDT)
    - Re: [AMBER] Amber and Short Bonds Adrian Roitberg (Mon Mar 26 2012 - 17:08:47 PDT)
    - Re: [AMBER] Amber and Short Bonds Aronica, Pietro (Tue Mar 27 2012 - 05:24:43 PDT)
    - Re: [AMBER] Amber and Short Bonds Jason Swails (Tue Mar 27 2012 - 05:59:12 PDT)
[AMBER] TUTORIAL A1: Protein that Contains Non-Standard Residues Bala subramanian (Mon Mar 26 2012 - 08:23:49 PDT)
- Re: [AMBER] TUTORIAL A1: Protein that Contains Non-Standard Residues Ross Walker (Mon Mar 26 2012 - 09:37:02 PDT)
  - Re: [AMBER] TUTORIAL A1: Protein that Contains Non-Standard Residues Bala subramanian (Mon Mar 26 2012 - 12:05:29 PDT)
- Re: [AMBER] TUTORIAL A1: Protein that Contains Non-Standard Residues FyD (Tue Mar 27 2012 - 06:30:52 PDT)
- Re: [AMBER] TUTORIAL A1: Protein that Contains Non-Standard Residues sudipta (Thu Jun 14 2012 - 13:20:31 PDT)
[AMBER] compiling failure on ibm Yubo Fan (Mon Mar 26 2012 - 11:44:03 PDT)
- Re: [AMBER] compiling failure on ibm Scott Brozell (Mon Mar 26 2012 - 12:20:00 PDT)
- Re: [AMBER] compiling failure on ibm Jason Swails (Mon Mar 26 2012 - 12:51:48 PDT)
  - Re: [AMBER] compiling failure on ibm Yubo Fan (Mon Mar 26 2012 - 13:50:06 PDT)
[AMBER] Another question about Amber 12 Tong Zhu (Mon Mar 26 2012 - 18:04:31 PDT)
- Re: [AMBER] Another question about Amber 12 Ross Walker (Tue Mar 27 2012 - 10:25:43 PDT)
  - Re: [AMBER] Another question about Amber 12 Tong Zhu (Wed Mar 28 2012 - 18:51:25 PDT)
[AMBER] glycine sidechain contribution in MM-GBSA decompostion caobb0214 (Mon Mar 26 2012 - 18:05:04 PDT)
- Re: [AMBER] glycine sidechain contribution in MM-GBSA decompostion Carlos Simmerling (Mon Mar 26 2012 - 18:08:33 PDT)
  - Re: [AMBER] glycine sidechain contribution in MM-GBSA decompostion caobb0214 (Mon Mar 26 2012 - 18:56:22 PDT)
    - Re: [AMBER] glycine sidechain contribution in MM-GBSA decompostion Jason Swails (Mon Mar 26 2012 - 21:52:10 PDT)
    - Re: [AMBER] glycine sidechain contribution in MM-GBSA decompostion Carlos Simmerling (Tue Mar 27 2012 - 03:01:13 PDT)
[AMBER] ptraj removes my ligands DENILSON FERREIRA DE OLIVEIRA (Mon Mar 26 2012 - 19:22:48 PDT)
- Re: [AMBER] ptraj removes my ligands Daniel Roe (Mon Mar 26 2012 - 21:10:01 PDT)
- Re: [AMBER] ptraj removes my ligands Daniel Roe (Fri Mar 30 2012 - 11:36:23 PDT)
  - Re: [AMBER] ptraj removes my ligands denilson.dqi.ufla.br (Mon Apr 02 2012 - 06:55:33 PDT)
[AMBER] assignment of partial charge to fullerene2160 gargi borgohai (Tue Mar 27 2012 - 00:15:21 PDT)
- Re: [AMBER] assignment of partial charge to fullerene2160 steinbrt.rci.rutgers.edu (Tue Mar 27 2012 - 01:05:44 PDT)
- Re: [AMBER] assignment of partial charge to fullerene2160 FyD (Tue Mar 27 2012 - 05:55:04 PDT)
[AMBER] angle restraint Elisa Frezza (Tue Mar 27 2012 - 02:28:46 PDT)
[AMBER] AmberGS forcefield steinbrt.rci.rutgers.edu (Tue Mar 27 2012 - 07:57:05 PDT)
- Re: [AMBER] AmberGS forcefield Carlos Simmerling (Tue Mar 27 2012 - 08:17:19 PDT)
  - [AMBER] Odd coordinate writing problem in pmemd.MPI steinbrt.rci.rutgers.edu (Thu Apr 05 2012 - 05:49:40 PDT)
    - Re: [AMBER] Odd coordinate writing problem in pmemd.MPI David A Case (Thu Apr 05 2012 - 06:55:32 PDT)
    - Re: [AMBER] Odd coordinate writing problem in pmemd.MPI David A Case (Thu Apr 05 2012 - 07:33:37 PDT)
    - Re: [AMBER] Odd coordinate writing problem in pmemd.MPI Aron Broom (Thu Apr 05 2012 - 07:49:43 PDT)
    - Re: [AMBER] Odd coordinate writing problem in pmemd.MPI steinbrt.rci.rutgers.edu (Thu Apr 05 2012 - 07:58:48 PDT)
    - Re: [AMBER] Odd coordinate writing problem in pmemd.MPI Aron Broom (Thu Apr 05 2012 - 08:02:22 PDT)
    - Re: [AMBER] Odd coordinate writing problem in pmemd.MPI Ross Walker (Thu Apr 05 2012 - 09:42:55 PDT)
    - Re: [AMBER] Odd coordinate writing problem in pmemd.MPI steinbrt.rci.rutgers.edu (Thu Apr 05 2012 - 13:33:05 PDT)
    - Re: [AMBER] Odd coordinate writing problem in pmemd.MPI SOLVED steinbrt.rci.rutgers.edu (Wed Apr 11 2012 - 06:20:39 PDT)
[AMBER] COM Olena Dobrovolska (Tue Mar 27 2012 - 08:01:27 PDT)
- Re: [AMBER] COM David A. Case (Wed Mar 28 2012 - 07:53:38 PDT)
  - Re: [AMBER] COM Olena Dobrovolska (Wed Mar 28 2012 - 08:40:02 PDT)
    - Re: [AMBER] COM David A. Case (Wed Mar 28 2012 - 12:25:45 PDT)
[AMBER] Segmentation fault Agostino Bruno (Wed Mar 28 2012 - 08:33:15 PDT)
- Re: [AMBER] Segmentation fault Ben Roberts (Wed Mar 28 2012 - 13:22:06 PDT)
  - Re: [AMBER] Segmentation fault Agostino Bruno (Thu Mar 29 2012 - 01:06:09 PDT)
[AMBER] how to measure atom distance in md trajectories using ptraj program Bala Subramani (Wed Mar 28 2012 - 10:26:21 PDT)
- Re: [AMBER] how to measure atom distance in md trajectories using ptraj program Daniel Roe (Wed Mar 28 2012 - 10:33:39 PDT)
  - Re: [AMBER] how to measure atom distance in md trajectories using ptraj program Bala Subramani (Wed Mar 28 2012 - 11:25:41 PDT)
    - Re: [AMBER] how to measure atom distance in md trajectories using ptraj program Daniel Roe (Wed Mar 28 2012 - 12:37:04 PDT)
- Re: [AMBER] how to measure atom distance in md trajectories using ptraj program Jason Swails (Wed Mar 28 2012 - 12:23:30 PDT)
[AMBER] error in nmode calculations manikanthan bhavaraju (Wed Mar 28 2012 - 11:41:04 PDT)
- Re: [AMBER] error in nmode calculations Bill Miller III (Wed Mar 28 2012 - 12:05:14 PDT)
  - Re: [AMBER] error in nmode calculations Cannon, John F. (Wed Mar 28 2012 - 13:11:03 PDT)
    - Re: [AMBER] error in nmode calculations manikanthan bhavaraju (Wed Mar 28 2012 - 14:18:06 PDT)
    - Re: [AMBER] error in nmode calculations Jason Swails (Wed Mar 28 2012 - 14:46:54 PDT)
- Re: [AMBER] error in nmode calculations David A. Case (Thu Mar 29 2012 - 06:09:53 PDT)
[AMBER] Problem with installation of MTKPP setyanto md (Wed Mar 28 2012 - 19:33:09 PDT)
- Re: [AMBER] Problem with installation of MTKPP Martin Peters (Thu Mar 29 2012 - 01:41:58 PDT)
  - Re: [AMBER] Problem with installation of MTKPP setyanto md (Thu Mar 29 2012 - 03:55:07 PDT)
[AMBER] how to merge 10 trajectory files BALASUBRAMANI G L (Wed Mar 28 2012 - 21:35:42 PDT)
- Re: [AMBER] how to merge 10 trajectory files Ben Roberts (Wed Mar 28 2012 - 21:42:41 PDT)
[AMBER] rfree: Error decoding variable 1 3 from: Elisa Frezza (Thu Mar 29 2012 - 06:04:47 PDT)
- Re: [AMBER] rfree: Error decoding variable 1 3 from: Jason Swails (Thu Mar 29 2012 - 06:33:42 PDT)
  - Re: [AMBER] rfree: Error decoding variable 1 3 from: Elisa Frezza (Thu Mar 29 2012 - 06:46:30 PDT)
    - Re: [AMBER] rfree: Error decoding variable 1 3 from: David A Case (Thu Mar 29 2012 - 07:47:25 PDT)
    - Re: [AMBER] rfree: Error decoding variable 1 3 from: Jason Swails (Thu Mar 29 2012 - 11:42:44 PDT)
    - Re: [AMBER] rfree: Error decoding variable 1 3 from: Elisa Frezza (Sun Apr 01 2012 - 09:53:03 PDT)
    - Re: [AMBER] rfree: Error decoding variable 1 3 from: Jason Swails (Sun Apr 01 2012 - 11:11:43 PDT)
    - Re: [AMBER] rfree: Error decoding variable 1 3 from: Elisa Frezza (Sun Apr 01 2012 - 11:18:20 PDT)
    - Re: [AMBER] rfree: Error decoding variable 1 3 from: Jason Swails (Sun Apr 01 2012 - 11:36:58 PDT)
    - Re: [AMBER] rfree: Error decoding variable 1 3 from: Elisa Frezza (Sun Apr 01 2012 - 12:19:55 PDT)
    - Re: [AMBER] rfree: Error decoding variable 1 3 from: Elisa Frezza (Sun Apr 01 2012 - 13:28:24 PDT)
    - Re: [AMBER] rfree: Error decoding variable 1 3 from: Niel Henriksen (Sun Apr 01 2012 - 14:03:35 PDT)
    - Re: [AMBER] rfree: Error decoding variable 1 3 from: Jason Swails (Sun Apr 01 2012 - 14:04:32 PDT)
    - Re: [AMBER] rfree: Error decoding variable 1 3 from: Niel Henriksen (Sun Apr 01 2012 - 14:12:59 PDT)
    - Re: [AMBER] rfree: Error decoding variable 1 3 from: Elisa Frezza (Thu Apr 05 2012 - 02:06:44 PDT)
    - Re: [AMBER] rfree: Error decoding variable 1 3 from: Niel Henriksen (Thu Apr 05 2012 - 07:49:49 PDT)
    - Re: [AMBER] rfree: Error decoding variable 1 3 from: Elisa Frezza (Wed Apr 11 2012 - 01:03:45 PDT)
    - Re: [AMBER] rfree: Error decoding variable 1 3 from: David A Case (Wed Apr 11 2012 - 05:06:04 PDT)
    - Re: [AMBER] rfree: Error decoding variable 1 3 from: Elisa Frezza (Wed Apr 11 2012 - 05:34:50 PDT)
    - Re: [AMBER] rfree: Error decoding variable 1 3 from: David A Case (Wed Apr 11 2012 - 07:16:18 PDT)
    - Re: [AMBER] rfree: Error decoding variable 1 3 from: Elisa Frezza (Wed Apr 11 2012 - 07:33:30 PDT)
    - Re: [AMBER] rfree: Error decoding variable 1 3 from: Niel Henriksen (Wed Apr 11 2012 - 07:46:36 PDT)
    - Re: [AMBER] rfree: Error decoding variable 1 3 from: Elisa Frezza (Wed Apr 11 2012 - 07:58:14 PDT)
    - Re: [AMBER] rfree: Error decoding variable 1 3 from: Niel Henriksen (Wed Apr 11 2012 - 08:08:21 PDT)
    - Re: [AMBER] rfree: Error decoding variable 1 3 from: David A Case (Thu Apr 12 2012 - 05:45:33 PDT)
    - Re: [AMBER] rfree: Error decoding variable 1 3 from: Jason Swails (Thu Apr 12 2012 - 05:53:35 PDT)
    - Re: [AMBER] rfree: Error decoding variable 1 3 from: David A Case (Thu Apr 12 2012 - 07:48:39 PDT)
    - Re: [AMBER] rfree: Error decoding variable 1 3 from: Elisa Frezza (Thu Apr 12 2012 - 08:05:16 PDT)
    - Re: [AMBER] rfree: Error decoding variable 1 3 from: David A Case (Thu Apr 12 2012 - 08:25:11 PDT)
    - Re: [AMBER] rfree: Error decoding variable 1 3 from: Elisa Frezza (Thu Apr 12 2012 - 08:38:29 PDT)
    - Re: [AMBER] rfree: Error decoding variable 1 3 from: Niel Henriksen (Thu Apr 12 2012 - 08:42:51 PDT)
    - Re: [AMBER] rfree: Error decoding variable 1 3 from: Elisa Frezza (Thu Apr 12 2012 - 08:54:32 PDT)
    - Re: [AMBER] rfree: Error decoding variable 1 3 from: Niel Henriksen (Wed Apr 11 2012 - 06:53:03 PDT)
    - Re: [AMBER] rfree: Error decoding variable 1 3 from: Elisa Frezza (Wed Apr 11 2012 - 07:30:42 PDT)
[AMBER] Particles moving outside of simulation box for pmemd.cuda.mpi Adam Jion (Thu Mar 29 2012 - 17:05:16 PDT)
- Re: [AMBER] Particles moving outside of simulation box for pmemd.cuda.mpi Aron Broom (Thu Mar 29 2012 - 17:35:33 PDT)
- Re: [AMBER] Particles moving outside of simulation box for pmemd.cuda.mpi Ben Roberts (Thu Mar 29 2012 - 17:38:00 PDT)
  - Re: [AMBER] Particles moving outside of simulation box for pmemd.cuda.mpi Adam Jion (Fri Mar 30 2012 - 04:08:07 PDT)
    - Re: [AMBER] Particles moving outside of simulation box for pmemd.cuda.mpi Ross Walker (Fri Mar 30 2012 - 10:34:17 PDT)
- Re: [AMBER] Particles moving outside of simulation box for pmemd.cuda.mpi Ross Walker (Tue Apr 03 2012 - 16:14:19 PDT)
  - Re: [AMBER] Particles moving outside of simulation box for pmemd.cuda.mpi Adam Jion (Wed Apr 04 2012 - 00:13:01 PDT)
    - Re: [AMBER] Particles moving outside of simulation box for pmemd.cuda.mpi David A Case (Wed Apr 04 2012 - 06:11:50 PDT)
[AMBER] Amber10 parallel test example run error Shaandar Nyamtulga (Thu Mar 29 2012 - 23:25:32 PDT)
- Re: [AMBER] Amber10 parallel test example run error Shaandar Nyamtulga (Fri Mar 30 2012 - 01:04:16 PDT)
  - [AMBER] Amber10 parallel test Shaandar Nyamtulga (Thu May 03 2012 - 22:34:11 PDT)
    - Re: [AMBER] Amber10 parallel test David A Case (Fri May 04 2012 - 05:14:13 PDT)
[AMBER] Asking About Differences between amber force field ff10 and ff03 setyanto md (Fri Mar 30 2012 - 02:50:59 PDT)
- Re: [AMBER] Asking About Differences between amber force field ff10 and ff03 Aron Broom (Fri Mar 30 2012 - 07:21:30 PDT)
- Re: [AMBER] Asking About Differences between amber force field ff10 and ff03 David A Case (Fri Mar 30 2012 - 09:27:54 PDT)
  - Re: [AMBER] Asking About Differences between amber force field ff10 and ff03 setyanto md (Mon Apr 02 2012 - 01:30:42 PDT)
    - Re: [AMBER] Asking About Differences between amber force field ff10 and ff03 David A Case (Mon Apr 02 2012 - 05:14:32 PDT)
[AMBER] Fast moving system in targeted MD Thomas Exner (Fri Mar 30 2012 - 05:16:18 PDT)
[AMBER] Large Energy Jump in TMD simulation - Regarding Fredrick Devadoss (Fri Mar 30 2012 - 05:19:56 PDT)
- Re: [AMBER] Large Energy Jump in TMD simulation - Regarding Carlos Simmerling (Fri Mar 30 2012 - 05:52:35 PDT)
  - Re: [AMBER] Large Energy Jump in TMD simulation - Regarding Fredrick Devadoss (Fri Mar 30 2012 - 06:34:11 PDT)
    - Re: [AMBER] Large Energy Jump in TMD simulation - Regarding Carlos Simmerling (Fri Mar 30 2012 - 06:41:13 PDT)
    - Re: [AMBER] Large Energy Jump in TMD simulation - Regarding Fredrick Devadoss (Fri Mar 30 2012 - 06:49:21 PDT)
    - Re: [AMBER] Large Energy Jump in TMD simulation - Regarding Carlos Simmerling (Fri Mar 30 2012 - 08:57:53 PDT)
    - Re: [AMBER] Large Energy Jump in TMD simulation - Regarding Fredrick Devadoss (Fri Mar 30 2012 - 11:06:02 PDT)
    - Re: [AMBER] Large Energy Jump in TMD simulation - Regarding Jason Swails (Fri Mar 30 2012 - 12:25:40 PDT)
    - Re: [AMBER] Large Energy Jump in TMD simulation - Regarding Fredrick Devadoss (Fri Mar 30 2012 - 15:15:50 PDT)
    - Re: [AMBER] Large Energy Jump in TMD simulation - Regarding Jason Swails (Fri Mar 30 2012 - 15:51:50 PDT)
    - [AMBER] How to set VMD_PLUGIN_PATH ? (in order to analysis mdcrd by GROMACS directly) Catein Catherine (Sat Mar 31 2012 - 21:11:32 PDT)
    - Re: [AMBER] How to set VMD_PLUGIN_PATH ? (in order to analysis mdcrd by GROMACS directly) Jason Swails (Sun Apr 01 2012 - 08:46:03 PDT)
    - Re: [AMBER] Large Energy Jump in TMD simulation - Regarding Carlos Simmerling (Tue Apr 03 2012 - 08:21:07 PDT)
    - Re: [AMBER] Large Energy Jump in TMD simulation - Regarding Fredrick Devadoss (Wed Apr 04 2012 - 02:53:39 PDT)
    - Re: [AMBER] Large Energy Jump in TMD simulation - Regarding Carlos Simmerling (Wed Apr 04 2012 - 03:00:36 PDT)
    - Re: [AMBER] Large Energy Jump in TMD simulation - Regarding Fredrick Devadoss (Wed Apr 04 2012 - 03:09:18 PDT)
    - Re: [AMBER] Large Energy Jump in TMD simulation - Regarding Carlos Simmerling (Wed Apr 04 2012 - 04:55:49 PDT)
    - Re: [AMBER] Large Energy Jump in TMD simulation - Regarding Fredrick Devadoss (Wed Apr 04 2012 - 05:39:04 PDT)
    - Re: [AMBER] Large Energy Jump in TMD simulation - Regarding Carlos Simmerling (Wed Apr 04 2012 - 07:47:21 PDT)
    - Re: [AMBER] Large Energy Jump in TMD simulation - Regarding Fredrick Devadoss (Wed Apr 04 2012 - 05:34:52 PDT)
    - Re: [AMBER] Large Energy Jump in TMD simulation - Regarding Carlos Simmerling (Thu Apr 12 2012 - 05:22:05 PDT)
    - Re: [AMBER] Large Energy Jump in TMD simulation - Regarding Fredrick Devadoss (Tue Apr 17 2012 - 02:51:56 PDT)
[AMBER] Issue with running sander 板垣哲彦 (Fri Mar 30 2012 - 05:37:21 PDT)
- Re: [AMBER] Issue with running sander Jason Swails (Fri Mar 30 2012 - 07:13:14 PDT)
- Re: [AMBER] Issue with running sander David A Case (Fri Mar 30 2012 - 09:39:47 PDT)
  - Re: [AMBER] Issue with running sander Jason Swails (Fri Mar 30 2012 - 10:56:15 PDT)
[AMBER] Query on error abinayar.imsc.res.in (Fri Mar 30 2012 - 05:39:19 PDT)
[AMBER] Query on error :Atom does not have a type abinayar.imsc.res.in (Fri Mar 30 2012 - 05:52:49 PDT)
- Re: [AMBER] Query on error :Atom does not have a type Jason Swails (Fri Mar 30 2012 - 07:15:33 PDT)
[AMBER] Which methodology could estimate the binding affinity of zinc containing metalloprotei(wrong string) �Cligand complex accurately? JiYuan Liu (Fri Mar 30 2012 - 08:00:35 PDT)
[AMBER] ptraj: SegFault during SOM clustering Anselm Horn (Fri Mar 30 2012 - 09:47:34 PDT)
- [AMBER] SOM clustering Anselm Horn (Wed Apr 11 2012 - 00:51:24 PDT)
[AMBER] test failure in the AMBERTOOL installation Acoot Brett (Sat Mar 31 2012 - 23:26:34 PDT)
- [AMBER] Can anyone point out whether my ambertools and amber test failures are significant Acoot Brett (Sun Apr 01 2012 - 04:17:39 PDT)
  - Re: [AMBER] Can anyone point out whether my ambertools and amber test failures are significant Jason Swails (Sun Apr 01 2012 - 08:54:05 PDT)
    - [AMBER] on my AMBER AND AMBERTOOLS installation test failures Acoot Brett (Mon Apr 02 2012 - 20:56:57 PDT)
- Re: [AMBER] test failure in the AMBERTOOL installation Ben Roberts (Sun Apr 01 2012 - 14:01:17 PDT)
[AMBER] debug energy into individual atoms Jorgen Simonsen (Sun Apr 01 2012 - 14:16:39 PDT)
- [AMBER] a question related to force field Acoot Brett (Sun Apr 01 2012 - 14:59:39 PDT)
  - Re: [AMBER] a question related to force field Carlos Simmerling (Sun Apr 01 2012 - 15:02:02 PDT)
    - Re: [AMBER] a question related to force field Acoot Brett (Sun Apr 01 2012 - 15:09:46 PDT)
  - Re: [AMBER] a question related to force field Ben Roberts (Sun Apr 01 2012 - 15:08:32 PDT)
  - Re: [AMBER] a question related to force field M. L. Dodson (Sun Apr 01 2012 - 15:09:26 PDT)
  - Re: [AMBER] a question related to force field FyD (Sun Apr 01 2012 - 22:24:37 PDT)
[AMBER] generating non-standard residue ashwini gupta (Sun Apr 01 2012 - 22:22:32 PDT)
- Re: [AMBER] generating non-standard residue FyD (Sun Apr 01 2012 - 22:29:05 PDT)
[AMBER] error in making prmtop & inpcrd for ligand-protein complex Aditya Setiajid (Sun Apr 01 2012 - 23:33:08 PDT)
- Re: [AMBER] error in making prmtop & inpcrd for ligand-protein complex David A Case (Mon Apr 02 2012 - 05:08:56 PDT)
  - Re: [AMBER] error in making prmtop & inpcrd for ligand-protein complex Aditya Setiajid (Mon Apr 02 2012 - 06:39:35 PDT)
    - Re: [AMBER] error in making prmtop & inpcrd for ligand-protein complex steinbrt.rci.rutgers.edu (Mon Apr 02 2012 - 06:50:45 PDT)
    - Re: [AMBER] error in making prmtop & inpcrd for ligand-protein complex Aditya Setiajid (Mon Apr 02 2012 - 19:32:03 PDT)
    - Re: [AMBER] error in making prmtop & inpcrd for ligand-protein complex Jason Swails (Mon Apr 02 2012 - 20:41:35 PDT)
[AMBER] MM-PBSA Question Hoshin Kim (Mon Apr 02 2012 - 02:08:47 PDT)
[AMBER] Error: unspecified launch failure launching kernel kReduceForces Giovanni Pavan (Mon Apr 02 2012 - 03:34:00 PDT)
- Re: [AMBER] Error: unspecified launch failure launching kernel kReduceForces Aron Broom (Mon Apr 02 2012 - 06:47:23 PDT)
  - [AMBER] R: Error: unspecified launch failure launching kernel kReduceForces Giovanni Pavan (Mon Apr 02 2012 - 08:13:42 PDT)
    - Re: [AMBER] R: Error: unspecified launch failure launching kernel kReduceForces Ross Walker (Wed Apr 11 2012 - 09:23:06 PDT)
- Re: [AMBER] Error: unspecified launch failure launching kernel kReduceForces Ross Walker (Mon Apr 02 2012 - 09:36:38 PDT)
  - Re: [AMBER] Error: unspecified launch failure launching kernel kReduceForces Aron Broom (Mon Apr 02 2012 - 09:43:21 PDT)
    - Re: [AMBER] Error: unspecified launch failure launching kernel kReduceForces Ross Walker (Mon Apr 02 2012 - 09:56:55 PDT)
    - Re: [AMBER] Error: unspecified launch failure launching kernel kReduceForces Aron Broom (Mon Apr 02 2012 - 10:57:26 PDT)
    - Re: [AMBER] Error: unspecified launch failure launching kernel kReduceForces Scott Le Grand (Wed Apr 11 2012 - 08:57:43 PDT)
    - [AMBER] Ambertools12 cygwin install keeps asking for csh????? Dean Cuebas (Wed Apr 11 2012 - 11:28:08 PDT)
    - Re: [AMBER] Ambertools12 cygwin install keeps asking for csh????? Dean Cuebas (Wed Apr 11 2012 - 11:59:59 PDT)
  - [AMBER] R: Error: unspecified launch failure launching kernel kReduceForces Giovanni Pavan (Wed Apr 11 2012 - 08:39:22 PDT)
[AMBER] AmberTools-1.5 installation problems Genzo Tanaka (Mon Apr 02 2012 - 04:16:51 PDT)
- Re: [AMBER] AmberTools-1.5 installation problems David A Case (Mon Apr 02 2012 - 05:19:13 PDT)
  - Re: [AMBER] AmberTools-1.5 installation problems Genzo Tanaka (Mon Apr 02 2012 - 14:30:08 PDT)
    - Re: [AMBER] AmberTools-1.5 installation problems case (Mon Apr 02 2012 - 15:06:15 PDT)
[AMBER] Exporting and Boxing Amber Trajectories by Frame Adam Jion (Mon Apr 02 2012 - 04:38:48 PDT)
- Re: [AMBER] Exporting and Boxing Amber Trajectories by Frame Jason Swails (Mon Apr 02 2012 - 05:30:16 PDT)
[AMBER] Use of PCASuite in analyzing DNA-MD trajectories Muhammad Khaled Tumbi (Mon Apr 02 2012 - 11:53:17 PDT)
- Re: [AMBER] Use of PCASuite in analyzing DNA-MD trajectories francesco oteri (Mon Apr 02 2012 - 23:50:41 PDT)
[AMBER] metal site Per Jr. Greisen (Mon Apr 02 2012 - 13:09:25 PDT)
- Re: [AMBER] metal site Jason Swails (Mon Apr 02 2012 - 20:51:34 PDT)
- Re: [AMBER] metal site FyD (Tue Apr 03 2012 - 03:01:20 PDT)
[AMBER] Setting the cut-off and size of box Pengzhi (Mon Apr 02 2012 - 16:29:00 PDT)
- Re: [AMBER] Setting the cut-off and size of box case (Mon Apr 02 2012 - 18:19:27 PDT)
- Re: [AMBER] Setting the cut-off and size of box Pengzhi (Mon Apr 02 2012 - 19:59:58 PDT)
  - Re: [AMBER] Setting the cut-off and size of box case (Tue Apr 03 2012 - 19:53:48 PDT)
[AMBER] Amber GPU test fails Mohammad Ashraf Bhuiyan (Mon Apr 02 2012 - 17:44:07 PDT)
- Re: [AMBER] Amber GPU test fails Jason Swails (Mon Apr 02 2012 - 20:53:42 PDT)
  - [AMBER] how where to read the amber and amber test failure diff files Acoot Brett (Mon Apr 02 2012 - 22:58:09 PDT)
    - [AMBER] on "-v" in mdrun Acoot Brett (Mon Apr 02 2012 - 23:14:36 PDT)
- Re: [AMBER] Amber GPU test fails Ross Walker (Mon Apr 02 2012 - 21:08:07 PDT)
[AMBER] "Possible Failures" in Amber 11 and Amber tools tests Dureid El-Moghraby (Tue Apr 03 2012 - 03:27:49 PDT)
[AMBER] Inconsistent Internal energy from monomer to dimer Josep Maria Campanera Alsina (Tue Apr 03 2012 - 04:15:55 PDT)
- Re: [AMBER] Inconsistent Internal energy from monomer to dimer Carlos Simmerling (Tue Apr 03 2012 - 04:25:32 PDT)
- Re: [AMBER] Inconsistent Internal energy from monomer to dimer Josep Maria Campanera Alsina (Wed Apr 04 2012 - 00:40:56 PDT)
  - Re: [AMBER] Inconsistent Internal energy from monomer to dimer Carlos Simmerling (Wed Apr 04 2012 - 02:37:37 PDT)
    - Re: [AMBER] Inconsistent Internal energy from monomer to dimer Jason Swails (Wed Apr 04 2012 - 07:33:40 PDT)
- Re: [AMBER] Inconsistent Internal energy from monomer to dimer Josep Maria Campanera Alsina (Thu Apr 05 2012 - 04:11:13 PDT)
  - Re: [AMBER] Inconsistent Internal energy from monomer to dimer Carlos Simmerling (Thu Apr 05 2012 - 07:49:43 PDT)
- Re: [AMBER] Inconsistent Internal energy from monomer to dimer Josep Maria Campanera Alsina (Sat Apr 07 2012 - 02:51:02 PDT)
  - Re: [AMBER] Inconsistent Internal energy from monomer to dimer Carlos Simmerling (Sat Apr 07 2012 - 04:06:27 PDT)
[AMBER] RE GPU test fails Mohammad Ashraf Bhuiyan (Tue Apr 03 2012 - 10:39:57 PDT)
- Re: [AMBER] RE GPU test fails Ross Walker (Tue Apr 03 2012 - 11:35:57 PDT)
Re: [AMBER] GPU test fails Mohammad Ashraf Bhuiyan (Tue Apr 03 2012 - 12:49:43 PDT)
- Re: [AMBER] GPU test fails Ross Walker (Tue Apr 03 2012 - 13:00:57 PDT)
[AMBER] error with chamber Albert (Tue Apr 03 2012 - 13:15:22 PDT)
- Re: [AMBER] error with chamber Crowley, Michael (Tue Apr 03 2012 - 13:18:00 PDT)
  - Re: [AMBER] error with chamber Albert (Tue Apr 03 2012 - 13:21:02 PDT)
    - Re: [AMBER] error with chamber Crowley, Michael (Tue Apr 03 2012 - 13:25:55 PDT)
    - Re: [AMBER] error with chamber Albert (Tue Apr 03 2012 - 13:28:54 PDT)
    - Re: [AMBER] error with chamber Crowley, Michael (Tue Apr 03 2012 - 13:35:36 PDT)
    - Re: [AMBER] error with chamber Albert (Tue Apr 03 2012 - 13:39:27 PDT)
    - Re: [AMBER] error with chamber Crowley, Michael (Tue Apr 03 2012 - 13:47:27 PDT)
    - Re: [AMBER] error with chamber Joshua Adelman (Tue Apr 03 2012 - 15:08:31 PDT)
[AMBER] distance dependent dielectric constant kanika sharma (Wed Apr 04 2012 - 05:42:17 PDT)
- Re: [AMBER] distance dependent dielectric constant David A Case (Wed Apr 04 2012 - 06:10:15 PDT)
- [AMBER] distance dependent dielectric constant kanika sharma (Wed Apr 04 2012 - 22:46:15 PDT)
  - [AMBER] on the protonation of the HIS, etc Acoot Brett (Thu Apr 05 2012 - 04:08:46 PDT)
    - Re: [AMBER] on the protonation of the HIS, etc Marc van der Kamp (Thu Apr 05 2012 - 04:14:37 PDT)
  - Re: [AMBER] distance dependent dielectric constant David A Case (Thu Apr 05 2012 - 05:24:22 PDT)
[AMBER] Announcement: release of Amber12 and AmberTools12 David A Case (Wed Apr 04 2012 - 07:09:32 PDT)
[AMBER] close PME in AMBER 10 Qian Wang (Wed Apr 04 2012 - 10:17:08 PDT)
- Re: [AMBER] close PME in AMBER 10 Jason Swails (Wed Apr 04 2012 - 10:36:52 PDT)
[AMBER] AMBERHOME is not recognized by ./configure Genzo Tanaka (Wed Apr 04 2012 - 15:15:12 PDT)
- Re: [AMBER] AMBERHOME is not recognized by ./configure Ben Roberts (Wed Apr 04 2012 - 15:24:02 PDT)
- Re: [AMBER] AMBERHOME is not recognized by ./configure Jason Swails (Wed Apr 04 2012 - 21:11:19 PDT)
  - Re: [AMBER] AMBERHOME is not recognized by ./configure Genzo Tanaka (Thu Apr 05 2012 - 14:04:21 PDT)
[AMBER] Fwd: error in making prmtop & inpcrd for ligand-protein complex Muhammad Aditya Setiajid (Wed Apr 04 2012 - 20:39:11 PDT)
- Re: [AMBER] Fwd: error in making prmtop & inpcrd for ligand-protein complex Jason Swails (Wed Apr 04 2012 - 21:17:01 PDT)
[AMBER] ion parameters in simulations with nucleic acids Vlad Cojocaru (Thu Apr 05 2012 - 04:54:12 PDT)
- Re: [AMBER] ion parameters in simulations with nucleic acids Thomas Cheatham III (Tue Apr 10 2012 - 11:44:57 PDT)
  - Re: [AMBER] ion parameters in simulations with nucleic acids Vlad Cojocaru (Tue Apr 10 2012 - 14:51:57 PDT)
[AMBER] using both the ILDN and NMR-based modifications of ff99SB Vlad Cojocaru (Thu Apr 05 2012 - 05:42:38 PDT)
- Re: [AMBER] using both the ILDN and NMR-based modifications of ff99SB David A Case (Thu Apr 05 2012 - 06:53:18 PDT)
  - Re: [AMBER] using both the ILDN and NMR-based modifications of ff99SB Vlad Cojocaru (Thu Apr 05 2012 - 06:58:42 PDT)
    - Re: [AMBER] using both the ILDN and NMR-based modifications of ff99SB Carlos Simmerling (Thu Apr 05 2012 - 08:07:21 PDT)
    - Re: [AMBER] using both the ILDN and NMR-based modifications of ff99SB Jason Swails (Thu Apr 05 2012 - 14:18:12 PDT)
[AMBER] how to add a electric field? Xianwei Wang (Thu Apr 05 2012 - 05:59:19 PDT)
- [AMBER] cygwin xleap cannot open display Acoot Brett (Thu Apr 05 2012 - 06:35:36 PDT)
  - Re: [AMBER] cygwin xleap cannot open display David A Case (Thu Apr 05 2012 - 07:32:13 PDT)
[AMBER] Fwd: Problem? krati sharma (Fri Apr 06 2012 - 02:58:43 PDT)
[AMBER] Further question on protonation state of histidine Acoot Brett (Fri Apr 06 2012 - 04:25:04 PDT)
- Re: [AMBER] Further question on protonation state of histidine Brian Radak (Fri Apr 06 2012 - 06:02:38 PDT)
- Re: [AMBER] Further question on protonation state of histidine Rajendra Sharma (Fri Apr 06 2012 - 06:12:00 PDT)
- Re: [AMBER] Further question on protonation state of histidine David A Case (Fri Apr 06 2012 - 06:28:59 PDT)
  - [AMBER] question on protonation state of histidine Acoot Brett (Fri Apr 06 2012 - 15:48:27 PDT)
    - Re: [AMBER] question on protonation state of histidine Dean Cuebas (Fri Apr 06 2012 - 19:16:07 PDT)
    - Re: [AMBER] question on protonation state of histidine Acoot Brett (Fri Apr 06 2012 - 19:33:52 PDT)
    - Re: [AMBER] question on protonation state of histidine Jason Swails (Fri Apr 06 2012 - 23:49:41 PDT)
    - Re: [AMBER] question on protonation state of histidine case (Sat Apr 07 2012 - 13:42:18 PDT)
  - [AMBER] PDB file conversion server to meet the atom type requirement Acoot Brett (Sat Apr 07 2012 - 02:15:45 PDT)
    - Re: [AMBER] PDB file conversion server to meet the atom type requirement M. L. Dodson (Sat Apr 07 2012 - 05:21:25 PDT)
    - Re: [AMBER] PDB file conversion server to meet the atom type requirement case (Sat Apr 07 2012 - 13:58:56 PDT)
    - [AMBER] an error message in installation of AMBERTOOLS12 Acoot Brett (Sat Apr 07 2012 - 17:52:30 PDT)
    - Re: [AMBER] an error message in installation of AMBERTOOLS12 Jason Swails (Sun Apr 08 2012 - 04:45:24 PDT)
    - [AMBER] the command to make the sander running visible Acoot Brett (Sun Apr 08 2012 - 05:13:45 PDT)
    - Re: [AMBER] the command to make the sander running visible Acoot Brett (Sun Apr 08 2012 - 06:10:02 PDT)
    - Re: [AMBER] the command to make the sander running visible Fredrick Devadoss (Sun Apr 08 2012 - 07:27:27 PDT)
    - Re: [AMBER] the command to make the sander running visible Aron Broom (Sun Apr 08 2012 - 07:28:02 PDT)
    - Re: [AMBER] the command to make the sander running visible Adrian Roitberg (Sun Apr 08 2012 - 07:37:06 PDT)
    - Re: [AMBER] the command to make the sander running visible Acoot Brett (Sun Apr 08 2012 - 15:29:00 PDT)
    - Re: [AMBER] the command to make the sander running visible Adrian Roitberg (Sun Apr 08 2012 - 15:43:26 PDT)
    - [AMBER] sander minimization *.i file for protein complex Acoot Brett (Sun Apr 08 2012 - 19:10:33 PDT)
    - [AMBER] sander minimization mini.in file for protein complex Acoot Brett (Sun Apr 08 2012 - 19:40:23 PDT)
    - Re: [AMBER] sander minimization mini.in file for protein complex David A Case (Mon Apr 09 2012 - 05:37:21 PDT)
    - Re: [AMBER] sander minimization mini.in file for protein complex Anselm Horn (Mon Apr 09 2012 - 05:42:27 PDT)
[AMBER] What is major difference between Amber11 and Amber12 K. Uebayashi (Fri Apr 06 2012 - 07:06:48 PDT)
- Re: [AMBER] What is major difference between Amber11 and Amber12 David A Case (Fri Apr 06 2012 - 09:14:38 PDT)
- Re: [AMBER] What is major difference between Amber11 and Amber12 Ross Walker (Fri Apr 06 2012 - 09:58:45 PDT)
[AMBER] binding energy calculations kirtana S (Fri Apr 06 2012 - 10:41:53 PDT)
- Re: [AMBER] binding energy calculations case (Fri Apr 06 2012 - 18:04:59 PDT)
  - Re: [AMBER] binding energy calculations kirtana S (Fri Apr 06 2012 - 22:35:47 PDT)
    - Re: [AMBER] binding energy calculations Aron Broom (Fri Apr 06 2012 - 22:55:47 PDT)
    - Re: [AMBER] binding energy calculations kirtana S (Sat Apr 07 2012 - 11:57:41 PDT)
    - Re: [AMBER] binding energy calculations Jason Swails (Sat Apr 07 2012 - 12:09:03 PDT)
    - Re: [AMBER] binding energy calculations kirtana S (Mon Apr 09 2012 - 13:25:06 PDT)
    - Re: [AMBER] binding energy calculations David A Case (Mon Apr 09 2012 - 13:38:44 PDT)
    - Re: [AMBER] binding energy calculations kirtana S (Mon Apr 09 2012 - 18:33:25 PDT)
    - Re: [AMBER] binding energy calculations Jason Swails (Mon Apr 09 2012 - 21:33:49 PDT)
    - Re: [AMBER] binding energy calculations kirtana S (Tue Apr 10 2012 - 10:04:29 PDT)
    - Re: [AMBER] binding energy calculations Jason Swails (Tue Apr 10 2012 - 14:14:18 PDT)
[AMBER] How can I fix two ends of DNA? mehdi bagherpoor (Sun Apr 08 2012 - 03:20:42 PDT)
- Re: [AMBER] How can I fix two ends of DNA? case (Sun Apr 08 2012 - 11:25:02 PDT)
- Re: [AMBER] How can I fix two ends of DNA? Jason Swails (Sun Apr 08 2012 - 20:08:09 PDT)
  - Re: [AMBER] How can I fix two ends of DNA? mehdi bagherpoor (Mon Apr 09 2012 - 16:08:50 PDT)
    - Re: [AMBER] How can I fix two ends of DNA? Jason Swails (Mon Apr 09 2012 - 21:40:52 PDT)
    - [AMBER] How to overcome the limitation of file size when using ptraj? Catein Catherine (Tue Apr 10 2012 - 00:29:16 PDT)
    - [AMBER] installation of Amber 12 under Cygwin Acoot Brett (Tue Apr 10 2012 - 04:40:11 PDT)
    - Re: [AMBER] installation of Amber 12 under Cygwin David A Case (Tue Apr 10 2012 - 04:55:48 PDT)
    - Re: [AMBER] How to overcome the limitation of file size when using ptraj? David A Case (Tue Apr 10 2012 - 04:55:22 PDT)
[AMBER] Ligand and receptor separated when setting iwrap=1 Liu Denis (Sun Apr 08 2012 - 07:39:10 PDT)
- Re: [AMBER] Ligand and receptor separated when setting iwrap=1 Brian Radak (Sun Apr 08 2012 - 11:48:55 PDT)
  - Re: [AMBER] Ligand and receptor separated when setting iwrap=1 Liu Denis (Sun Apr 08 2012 - 23:55:32 PDT)
[AMBER] GB and Dielectric constant kanika sharma (Mon Apr 09 2012 - 04:49:29 PDT)
- Re: [AMBER] GB and Dielectric constant Carlos Simmerling (Mon Apr 09 2012 - 05:04:42 PDT)
- Re: [AMBER] GB and Dielectric constant David A Case (Mon Apr 09 2012 - 05:41:24 PDT)
  - Re: [AMBER] GB and Dielectric constant kanika sharma (Mon Apr 09 2012 - 05:51:55 PDT)
[AMBER] query regarding gaussian and antechamber jun kit (Mon Apr 09 2012 - 08:57:32 PDT)
- Re: [AMBER] query regarding gaussian and antechamber Jason Swails (Mon Apr 09 2012 - 09:50:02 PDT)
[AMBER] GB/SA Aron Broom (Mon Apr 09 2012 - 09:15:55 PDT)
- Re: [AMBER] GB/SA Jason Swails (Mon Apr 09 2012 - 10:10:30 PDT)
  - Re: [AMBER] GB/SA Aron Broom (Mon Apr 09 2012 - 10:27:04 PDT)
    - Re: [AMBER] GB/SA Carlos Simmerling (Mon Apr 09 2012 - 12:47:58 PDT)
    - Re: [AMBER] GB/SA Aron Broom (Mon Apr 09 2012 - 16:16:28 PDT)
    - Re: [AMBER] GB/SA Jason Swails (Mon Apr 09 2012 - 21:25:56 PDT)
[AMBER] crystallographic artifacts ashwini gupta (Mon Apr 09 2012 - 23:33:54 PDT)
[AMBER] PBC Fernando Martín García (Tue Apr 10 2012 - 03:40:51 PDT)
- Re: [AMBER] PBC David A Case (Tue Apr 10 2012 - 04:58:51 PDT)
  - Re: [AMBER] PBC Fernando Martín García (Tue Apr 10 2012 - 05:07:05 PDT)
[AMBER] is there any tutorial for membrane protein simulations for Amber 12? Albert (Tue Apr 10 2012 - 05:52:25 PDT)
- Re: [AMBER] is there any tutorial for membrane protein simulations for Amber 12? Benjamin D Madej (Tue Apr 10 2012 - 08:58:34 PDT)
  - Re: [AMBER] is there any tutorial for membrane protein simulations for Amber 12? Albert (Tue Apr 10 2012 - 09:06:16 PDT)
    - Re: [AMBER] is there any tutorial for membrane protein simulations for Amber 12? Aron Broom (Tue Apr 10 2012 - 09:22:33 PDT)
    - Re: [AMBER] is there any tutorial for membrane protein simulations for Amber 12? Ross Walker (Tue Apr 10 2012 - 09:42:48 PDT)
    - Re: [AMBER] is there any tutorial for membrane protein simulations for Amber 12? Aron Broom (Tue Apr 10 2012 - 09:47:40 PDT)
- Re: [AMBER] is there any tutorial for membrane protein simulations for Amber 12? Ross Walker (Tue Apr 10 2012 - 09:15:31 PDT)
  - Re: [AMBER] is there any tutorial for membrane protein simulations for Amber 12? Albert (Tue Apr 10 2012 - 09:22:47 PDT)
[AMBER] Units of the output file. Arthur Roberts (Tue Apr 10 2012 - 05:54:54 PDT)
- Re: [AMBER] Units of the output file. steinbrt.rci.rutgers.edu (Tue Apr 10 2012 - 06:06:32 PDT)
  - Re: [AMBER] Units of the output file. David A Case (Tue Apr 10 2012 - 10:22:35 PDT)
[AMBER] Could not read velocities from restart file David Condon (Tue Apr 10 2012 - 06:13:57 PDT)
- [AMBER] AMBER 99SB force field used by GROMACS Acoot Brett (Tue Apr 10 2012 - 06:25:12 PDT)
  - Re: [AMBER] AMBER 99SB force field used by GROMACS Adrian Roitberg (Tue Apr 10 2012 - 06:26:18 PDT)
    - Re: [AMBER] AMBER 99SB force field used by GROMACS steinbrt.rci.rutgers.edu (Tue Apr 10 2012 - 07:18:40 PDT)
  - Re: [AMBER] AMBER 99SB force field used by GROMACS Lorenzo Gontrani (Tue Apr 10 2012 - 07:39:51 PDT)
    - Re: [AMBER] AMBER 99SB force field used by GROMACS Acoot Brett (Tue Apr 10 2012 - 22:03:22 PDT)
- Re: [AMBER] Could not read velocities from restart file steinbrt.rci.rutgers.edu (Tue Apr 10 2012 - 07:08:14 PDT)
  - Re: [AMBER] Could not read velocities from restart file David Condon (Tue Apr 10 2012 - 11:16:40 PDT)
    - Re: [AMBER] Could not read velocities from restart file Aron Broom (Tue Apr 10 2012 - 11:18:54 PDT)
    - Re: [AMBER] Could not read velocities from restart file Ross Walker (Tue Apr 10 2012 - 11:41:49 PDT)
    - Re: [AMBER] Could not read velocities from restart file David Condon (Tue Apr 10 2012 - 11:59:02 PDT)
    - Re: [AMBER] Could not read velocities from restart file Ross Walker (Tue Apr 10 2012 - 13:20:38 PDT)
    - Re: [AMBER] Could not read velocities from restart file Aron Broom (Tue Apr 10 2012 - 13:33:47 PDT)
    - Re: [AMBER] Could not read velocities from restart file Ross Walker (Tue Apr 10 2012 - 15:31:43 PDT)
    - Re: [AMBER] Could not read velocities from restart file Ross Walker (Tue Apr 10 2012 - 15:49:33 PDT)
    - Re: [AMBER] Could not read velocities from restart file David Condon (Wed Apr 11 2012 - 06:06:35 PDT)
    - Re: [AMBER] Could not read velocities from restart file Aron Broom (Wed Apr 11 2012 - 06:24:31 PDT)
    - Re: [AMBER] Could not read velocities from restart file David Condon (Wed Apr 11 2012 - 11:45:15 PDT)
    - Re: [AMBER] Could not read velocities from restart file Ross Walker (Wed Apr 11 2012 - 12:37:04 PDT)
    - Re: [AMBER] Could not read velocities from restart file David Condon (Wed Apr 11 2012 - 18:04:40 PDT)
    - [AMBER] which methods calculate the binding energy most accurate Acoot Brett (Wed Apr 11 2012 - 18:21:14 PDT)
    - Re: [AMBER] which methods calculate the binding energy most accurate Aron Broom (Wed Apr 11 2012 - 21:49:09 PDT)
    - Re: [AMBER] Could not read velocities from restart file David A Case (Tue Apr 10 2012 - 13:20:24 PDT)
    - Re: [AMBER] Could not read velocities from restart file Ross Walker (Tue Apr 10 2012 - 13:59:26 PDT)
    - Re: [AMBER] Could not read velocities from restart file Bill Ross (Tue Apr 10 2012 - 15:09:48 PDT)
    - Re: [AMBER] Could not read velocities from restart file Ross Walker (Tue Apr 10 2012 - 15:24:05 PDT)
    - Re: [AMBER] Could not read velocities from restart file Bill Ross (Tue Apr 10 2012 - 15:42:48 PDT)
[AMBER] 2FE-2S cluster proteins topology and parameters files Angelo Gallo CERM (Tue Apr 10 2012 - 09:49:46 PDT)
- Re: [AMBER] 2FE-2S cluster proteins topology and parameters files Markus Kaukonen (Tue Apr 10 2012 - 23:30:00 PDT)
[AMBER] Calculating B-factor in ptraj mish (Tue Apr 10 2012 - 10:55:28 PDT)
- Re: [AMBER] Calculating B-factor in ptraj Gonzalo Jimenez (Tue Apr 10 2012 - 11:16:04 PDT)
  - Re: [AMBER] Calculating B-factor in ptraj mish (Tue Apr 10 2012 - 11:27:27 PDT)
[AMBER] Residue mismatch - Amber11 sławek bojarowski (Tue Apr 10 2012 - 14:47:18 PDT)
- Re: [AMBER] Residue mismatch - Amber11 Jason Swails (Tue Apr 10 2012 - 20:14:03 PDT)
[AMBER] how does frcmod work specifially. rdparm Knips, Alexander (Wed Apr 11 2012 - 05:05:42 PDT)
- Re: [AMBER] how does frcmod work specifially. rdparm David A Case (Wed Apr 11 2012 - 07:12:57 PDT)
[AMBER] nmode list index out of range manikanthan bhavaraju (Wed Apr 11 2012 - 06:34:46 PDT)
- Re: [AMBER] nmode list index out of range Jason Swails (Wed Apr 11 2012 - 12:00:23 PDT)
  - Re: [AMBER] nmode list index out of range manikanthan bhavaraju (Wed Apr 11 2012 - 12:28:44 PDT)
[AMBER] Fwd: no info contained in Residues to print section - MMPBSA.py Alfredo Quevedo (Wed Apr 11 2012 - 07:03:01 PDT)
- Re: [AMBER] Fwd: no info contained in Residues to print section - MMPBSA.py Jason Swails (Wed Apr 11 2012 - 11:31:47 PDT)
[AMBER] Error: Could not parse GB output files! Check for missing values (*********). zhangaidi (Wed Apr 11 2012 - 07:24:50 PDT)
- Re: [AMBER] Error: Could not parse GB output files! Check for missing values (*********). Jason Swails (Wed Apr 11 2012 - 11:58:03 PDT)
[AMBER] Error: Could not parse GB output files! Check for missing values (*********). zhangaidi (Wed Apr 11 2012 - 07:35:40 PDT)
[AMBER] about sander and pmemd bmartini (Wed Apr 11 2012 - 10:03:15 PDT)
- Re: [AMBER] about sander and pmemd David A Case (Wed Apr 11 2012 - 11:26:14 PDT)
Re: [AMBER] AMBER Digest, Vol 121, Issue 2 Alfredo Quevedo (Wed Apr 11 2012 - 12:33:10 PDT)
[AMBER] MMPBSA error Kumar, Sonu (Wed Apr 11 2012 - 14:24:47 PDT)
- Re: [AMBER] MMPBSA error Jason Swails (Thu Apr 12 2012 - 05:56:23 PDT)
  - Re: [AMBER] MMPBSA error Kumar, Sonu (Tue Apr 17 2012 - 03:51:40 PDT)
    - Re: [AMBER] MMPBSA error Jan-Philip Gehrcke (Tue Apr 17 2012 - 05:28:02 PDT)
    - Re: [AMBER] MMPBSA error Jan-Philip Gehrcke (Tue Apr 17 2012 - 05:40:58 PDT)
    - Re: [AMBER] MMPBSA error Jason Swails (Tue Apr 17 2012 - 07:07:27 PDT)
    - Re: [AMBER] MMPBSA error Kumar, Sonu (Tue Apr 17 2012 - 07:17:14 PDT)
[AMBER] parameters for Lys-sugar P2N file Urszula Uciechowska (Thu Apr 12 2012 - 01:48:53 PDT)
- Re: [AMBER] parameters for Lys-sugar P2N file Urszula Uciechowska (Sun Mar 25 2012 - 23:52:33 PDT)
  - Re: [AMBER] parameters for Lys-sugar P2N file FyD (Mon Mar 26 2012 - 05:47:17 PDT)
    - Re: [AMBER] parameters for Lys-sugar P2N file Urszula Uciechowska (Wed Apr 11 2012 - 09:33:52 PDT)
- Re: [AMBER] parameters for Lys-sugar P2N file FyD (Thu Apr 12 2012 - 05:13:55 PDT)
[AMBER] Query regarding Amber 11 Somnath Nandy (Thu Apr 12 2012 - 05:39:42 PDT)
[AMBER] Query regarding Amber Installation Somnath Nandy (Thu Apr 12 2012 - 06:02:53 PDT)
- Re: [AMBER] Query regarding Amber Installation David A Case (Thu Apr 12 2012 - 07:52:31 PDT)
- Re: [AMBER] Query regarding Amber Installation Somnath Nandy (Fri Apr 13 2012 - 04:09:40 PDT)
  - Re: [AMBER] Query regarding Amber Installation Jason Swails (Sat Apr 14 2012 - 09:05:12 PDT)
[AMBER] MMPBSA.py.MPI calls sander instead of sander.MPI Alfredo Quevedo (Thu Apr 12 2012 - 06:12:01 PDT)
- Re: [AMBER] MMPBSA.py.MPI calls sander instead of sander.MPI Jason Swails (Thu Apr 12 2012 - 06:23:01 PDT)
[AMBER] Fwd: [q4md-fft] Re: parameters for Lys-sugar P2N file FyD (Thu Apr 12 2012 - 07:44:15 PDT)
[AMBER] how to use Amber99SB-ILDN in Amber11? Albert (Thu Apr 12 2012 - 11:28:57 PDT)
- Re: [AMBER] how to use Amber99SB-ILDN in Amber11? David A Case (Thu Apr 12 2012 - 12:26:35 PDT)
[AMBER] closest command Qiong Zhang (Thu Apr 12 2012 - 14:30:55 PDT)
- Re: [AMBER] closest command Daniel Roe (Thu Apr 12 2012 - 16:02:01 PDT)
  - Re: [AMBER] closest command Qiong Zhang (Thu Apr 12 2012 - 18:29:44 PDT)
    - Re: [AMBER] closest command Daniel Roe (Fri Apr 13 2012 - 04:33:32 PDT)
    - Re: [AMBER] closest command Qiong Zhang (Fri Apr 13 2012 - 05:51:24 PDT)
    - Re: [AMBER] closest command Daniel Roe (Fri Apr 13 2012 - 06:45:15 PDT)
    - Re: [AMBER] closest command Qiong Zhang (Fri Apr 13 2012 - 08:41:05 PDT)
[AMBER] MMPBSA error in segmentation fault Aditya Setiajid (Fri Apr 13 2012 - 01:05:16 PDT)
- Re: [AMBER] MMPBSA error in segmentation fault Bill Miller III (Fri Apr 13 2012 - 05:48:10 PDT)
  - Re: [AMBER] MMPBSA error in segmentation fault Aditya Setiajid (Fri Apr 13 2012 - 23:03:28 PDT)
    - Re: [AMBER] MMPBSA error in segmentation fault Bill Miller III (Sat Apr 14 2012 - 05:07:38 PDT)
    - [AMBER] Fw: MMPBSA error in segmentation fault Aditya Setiajid (Sun Apr 15 2012 - 06:56:39 PDT)
    - Re: [AMBER] Fw: MMPBSA error in segmentation fault Jason Swails (Sun Apr 15 2012 - 07:49:26 PDT)
[AMBER] pcacovar in ptraj Bala Subramani (Fri Apr 13 2012 - 04:15:08 PDT)
[AMBER] Electrostatic potential calculation Sudarshan Debnath (Fri Apr 13 2012 - 07:17:04 PDT)
[AMBER] installing Amber12 in parallel Marc van der Kamp (Fri Apr 13 2012 - 07:39:42 PDT)
- Re: [AMBER] installing Amber12 in parallel case (Fri Apr 13 2012 - 20:01:08 PDT)
  - Re: [AMBER] installing Amber12 in parallel Marc van der Kamp (Mon Apr 16 2012 - 01:56:33 PDT)
[AMBER] Can MMPBSA calculate the binding energy in organic solvent? Liu Denis (Fri Apr 13 2012 - 08:20:33 PDT)
[AMBER] Error compiling pmemd.cuda.MPI Alfredo Quevedo (Fri Apr 13 2012 - 08:51:17 PDT)
- Re: [AMBER] Error compiling pmemd.cuda.MPI Ross Walker (Fri Apr 13 2012 - 09:21:49 PDT)
- Re: [AMBER] Error compiling pmemd.cuda.MPI Alfredo Quevedo (Fri Apr 13 2012 - 12:21:11 PDT)
  - Re: [AMBER] Error compiling pmemd.cuda.MPI Ross Walker (Fri Apr 13 2012 - 12:46:04 PDT)
[AMBER] reduce and trim function Mahendra B Thapa (Fri Apr 13 2012 - 09:17:32 PDT)
- Re: [AMBER] reduce and trim function Jason Swails (Fri Apr 13 2012 - 15:25:01 PDT)
[AMBER] Electrostatic potential calculation Sudarshan Debnath (Fri Apr 13 2012 - 09:50:53 PDT)
- Re: [AMBER] Electrostatic potential calculation case (Fri Apr 13 2012 - 20:09:17 PDT)
[AMBER] how to restrain the ligand in minimization and NVT equilibration step? Albert (Fri Apr 13 2012 - 10:17:39 PDT)
- Re: [AMBER] how to restrain the ligand in minimization and NVT equilibration step? Carlos Simmerling (Fri Apr 13 2012 - 10:21:34 PDT)
[AMBER] Error loading Glycam_06 parameters in xLEaP / tleap Kepa K. Burusco (Fri Apr 13 2012 - 10:25:59 PDT)
- Re: [AMBER] Error loading Glycam_06 parameters in xLEaP / tleap Lachele Foley (Lists) (Fri Apr 13 2012 - 10:37:51 PDT)
  - Re: [AMBER] Error loading Glycam_06 parameters in xLEaP / tleap Kepa K. Burusco (Mon Apr 16 2012 - 03:19:42 PDT)
[AMBER] is it possible strip off restrain linearly? Albert (Fri Apr 13 2012 - 11:28:20 PDT)
- Re: [AMBER] is it possible strip off restrain linearly? Jason Swails (Fri Apr 13 2012 - 15:26:37 PDT)
[AMBER] NVT error Albert (Fri Apr 13 2012 - 11:45:04 PDT)
- Re: [AMBER] NVT error case (Fri Apr 13 2012 - 20:16:45 PDT)
[AMBER] Problem with mdnab: ERROR in RATTLE Andrey (Fri Apr 13 2012 - 12:57:19 PDT)
- Re: [AMBER] Problem with mdnab: ERROR in RATTLE case (Sat Apr 14 2012 - 11:04:34 PDT)
  - Re: [AMBER] Problem with mdnab: ERROR in RATTLE Andrey (Tue Apr 17 2012 - 07:20:42 PDT)
    - Re: [AMBER] Problem with mdnab: ERROR in RATTLE case (Tue Apr 17 2012 - 16:35:47 PDT)
    - Re: [AMBER] Problem with mdnab: ERROR in RATTLE David A Case (Wed Apr 18 2012 - 04:46:12 PDT)
    - Re: [AMBER] Problem with mdnab: ERROR in RATTLE Andrey (Mon Apr 23 2012 - 01:25:56 PDT)
[AMBER] Problem with MCPB moitrayee.mbu.iisc.ernet.in (Fri Apr 13 2012 - 15:33:37 PDT)
- Re: [AMBER] Problem with MCPB Ben Roberts (Sun Apr 15 2012 - 03:10:16 PDT)
  - Re: [AMBER] Problem with MCPB Ben Roberts (Sun Apr 15 2012 - 03:46:53 PDT)
    - Re: [AMBER] Problem with MCPB moitrayee.mbu.iisc.ernet.in (Sun Apr 15 2012 - 09:11:48 PDT)
[AMBER] saveamberparm in xleap does not recognize atom type F Genzo Tanaka (Fri Apr 13 2012 - 16:01:36 PDT)
- Re: [AMBER] saveamberparm in xleap does not recognize atom type F case (Fri Apr 13 2012 - 20:22:43 PDT)
  - Re: [AMBER] saveamberparm in xleap does not recognize atom type F Genzo Tanaka (Mon Apr 16 2012 - 09:13:13 PDT)
    - Re: [AMBER] saveamberparm in xleap does not recognize atom type F David A Case (Tue Apr 17 2012 - 05:04:15 PDT)
[AMBER] : wrong charge calculation by xleap Sharma, Purshotam (Fri Apr 13 2012 - 17:52:02 PDT)
- Re: [AMBER] : wrong charge calculation by xleap raghav singh (Fri Apr 13 2012 - 19:48:55 PDT)
  - Re: [AMBER] : wrong charge calculation by xleap Sharma, Purshotam (Fri Apr 13 2012 - 20:49:01 PDT)
- Re: [AMBER] : wrong charge calculation by xleap case (Fri Apr 13 2012 - 20:26:50 PDT)
  - Re: [AMBER] : wrong charge calculation by xleap Sharma, Purshotam (Fri Apr 13 2012 - 20:46:29 PDT)
    - Re: [AMBER] : wrong charge calculation by xleap Bill Ross (Fri Apr 13 2012 - 22:21:46 PDT)
    - Re: [AMBER] : wrong charge calculation by xleap Sharma, Purshotam (Fri Apr 13 2012 - 22:51:05 PDT)
[AMBER] restrain syntax Albert (Fri Apr 13 2012 - 21:42:41 PDT)
- Re: [AMBER] restrain syntax Jason Swails (Sat Apr 14 2012 - 08:56:50 PDT)
[AMBER] Electrostatic potential calculation Sudarshan Debnath (Fri Apr 13 2012 - 21:43:31 PDT)
- Re: [AMBER] Electrostatic potential calculation Ray Luo, Ph.D. (Fri Apr 13 2012 - 22:54:33 PDT)
[AMBER] strange output information Albert (Fri Apr 13 2012 - 23:18:13 PDT)
- [AMBER] Ambertools 12 installation: Help needed Acoot Brett (Sat Apr 14 2012 - 02:43:19 PDT)
  - Re: [AMBER] Ambertools 12 installation: Help needed case (Sat Apr 14 2012 - 06:32:21 PDT)
- Re: [AMBER] strange output information Carlos Simmerling (Sat Apr 14 2012 - 04:25:17 PDT)
  - Re: [AMBER] strange output information Albert (Sat Apr 14 2012 - 04:40:36 PDT)
[AMBER] what's the amber efficiency? Albert (Sat Apr 14 2012 - 04:45:57 PDT)
- Re: [AMBER] what's the amber efficiency? case (Sat Apr 14 2012 - 06:37:05 PDT)
- Re: [AMBER] what's the amber efficiency? Scott Le Grand (Sat Apr 14 2012 - 09:03:49 PDT)
Re: [AMBER] [amber] error: could not parse gb output files! check for missing values (*********). zhangaidi (Sat Apr 14 2012 - 04:57:24 PDT)
- Re: [AMBER] [amber] error: could not parse gb output files! check for missing values (*********). Jason Swails (Sat Apr 14 2012 - 08:54:44 PDT)
[AMBER] Electrostatic potential calculation Sudarshan Debnath (Sat Apr 14 2012 - 06:03:52 PDT)
- Re: [AMBER] Electrostatic potential calculation case (Sat Apr 14 2012 - 06:38:17 PDT)
  - Re: [AMBER] Electrostatic potential calculation Ray Luo, Ph.D. (Sat Apr 14 2012 - 14:36:34 PDT)
[AMBER] Amber12 compile with "intel" err. javacfish (Sat Apr 14 2012 - 07:48:05 PDT)
- [AMBER] my ambertools 12 test Acoot Brett (Sat Apr 14 2012 - 08:42:55 PDT)
  - Re: [AMBER] my ambertools 12 test M. L. Dodson (Sat Apr 14 2012 - 08:50:10 PDT)
- Re: [AMBER] Amber12 compile with "intel" err. Jason Swails (Sat Apr 14 2012 - 08:47:39 PDT)
  - [AMBER] reply： Amber12 compile with "intel" err. javacfish (Sat Apr 14 2012 - 12:57:36 PDT)
- Re: [AMBER] Amber12 compile with "intel" err. case (Sat Apr 14 2012 - 10:55:38 PDT)
  - Re: [AMBER] Amber12 compile with "intel" err. Jason Swails (Sat Apr 14 2012 - 12:40:58 PDT)
    - [AMBER] 回复： Amber12 compile with "intel" err. javacfish (Sat Apr 14 2012 - 12:55:21 PDT)
[AMBER] Problem with gaussian input file generation moitrayee.mbu.iisc.ernet.in (Sat Apr 14 2012 - 13:27:17 PDT)
[AMBER] abertools12 installation failure Francesco Pietra (Sun Apr 15 2012 - 00:53:03 PDT)
- [AMBER] Fwd: abertools12 installation failure Francesco Pietra (Sun Apr 15 2012 - 01:10:21 PDT)
- Re: [AMBER] abertools12 installation failure Jason Swails (Sun Apr 15 2012 - 08:22:21 PDT)
  - Re: [AMBER] abertools12 installation failure Francesco Pietra (Sun Apr 15 2012 - 10:07:45 PDT)
    - Re: [AMBER] abertools12 installation failure Jason Swails (Sun Apr 15 2012 - 17:44:51 PDT)
- Re: [AMBER] abertools12 installation failure case (Sun Apr 15 2012 - 13:37:17 PDT)
  - Re: [AMBER] abertools12 installation failure Francesco Pietra (Mon Apr 16 2012 - 00:37:25 PDT)
- [AMBER] 回复： abertools12 installation failure javacfish (Mon Apr 16 2012 - 00:28:08 PDT)
- Re: [AMBER] abertools12 installation failure Jason Swails (Wed Apr 18 2012 - 09:54:14 PDT)
Re: [AMBER] FW: reduce and trim function Mahendra B Thapa (Sun Apr 15 2012 - 14:49:49 PDT)
- Re: [AMBER] FW: reduce and trim function case (Sun Apr 15 2012 - 19:25:57 PDT)
[AMBER] Partitioning issue of sander 板垣哲彦 (Sun Apr 15 2012 - 19:00:14 PDT)
- Re: [AMBER] Partitioning issue of sander Jason Swails (Sun Apr 15 2012 - 20:56:54 PDT)
- Re: [AMBER] Partitioning issue of sander David A Case (Mon Apr 16 2012 - 06:10:08 PDT)
- Re: [AMBER] Partitioning issue of sander 板垣哲彦 (Tue Apr 17 2012 - 05:30:59 PDT)
  - Re: [AMBER] Partitioning issue of sander David A Case (Tue Apr 17 2012 - 06:20:05 PDT)
    - Re: [AMBER] Partitioning issue of sander Jason Swails (Tue Apr 17 2012 - 08:53:03 PDT)
[AMBER] parallelization of paramfit in ambertools12 Francesco Pietra (Mon Apr 16 2012 - 00:47:16 PDT)
- Re: [AMBER] parallelization of paramfit in ambertools12 Robin Betz (Mon Apr 16 2012 - 15:13:05 PDT)
  - Re: [AMBER] parallelization of paramfit in ambertools12 Francesco Pietra (Mon Apr 16 2012 - 22:28:02 PDT)
    - Re: [AMBER] parallelization of paramfit in ambertools12 Robin Betz (Mon Apr 16 2012 - 23:00:51 PDT)
    - Re: [AMBER] parallelization of paramfit in ambertools12 Sidney Elmer (Tue Apr 17 2012 - 00:38:06 PDT)
    - Re: [AMBER] parallelization of paramfit in ambertools12 Robin Betz (Tue Apr 17 2012 - 11:28:18 PDT)
[AMBER] error installing Amber12-gpu version Vijay Manickam Achari (Mon Apr 16 2012 - 01:25:09 PDT)
- Re: [AMBER] error installing Amber12-gpu version javacfish (Mon Apr 16 2012 - 02:15:10 PDT)
  - Re: [AMBER] error installing Amber12-gpu version Vijay Manickam Achari (Mon Apr 16 2012 - 05:48:37 PDT)
    - Re: [AMBER] error installing Amber12-gpu version David A Case (Mon Apr 16 2012 - 06:19:59 PDT)
    - Re: [AMBER] error installing Amber12-gpu version Jason Swails (Mon Apr 16 2012 - 11:53:46 PDT)
    - Re: [AMBER] error installing Amber12-gpu version Vijay Manickam Achari (Tue Apr 17 2012 - 09:06:41 PDT)
    - Re: [AMBER] error installing Amber12-gpu version Jason Swails (Tue Apr 17 2012 - 11:38:19 PDT)
    - Re: [AMBER] error installing Amber12-gpu version Vijay Manickam Achari (Tue Apr 17 2012 - 19:37:59 PDT)
    - Re: [AMBER] error installing Amber12-gpu version Aron Broom (Tue Apr 17 2012 - 19:49:10 PDT)
    - Re: [AMBER] error installing Amber12-gpu version Thomas Cheatham (Tue Apr 17 2012 - 20:04:34 PDT)
    - Re: [AMBER] error installing Amber12-gpu version Vijay Manickam Achari (Wed Apr 18 2012 - 00:11:39 PDT)
    - Re: [AMBER] error installing Amber12-gpu version David A Case (Wed Apr 18 2012 - 04:52:39 PDT)
    - Re: [AMBER] error installing Amber12-gpu version Vijay Manickam Achari (Fri Apr 20 2012 - 05:19:55 PDT)
    - Re: [AMBER] error installing Amber12-gpu version Jan-Philip Gehrcke (Wed Apr 18 2012 - 01:18:32 PDT)
    - Re: [AMBER] error installing Amber12-gpu version Vijay Manickam Achari (Wed Apr 18 2012 - 07:49:41 PDT)
    - Re: [AMBER] error installing Amber12-gpu version Vijay Manickam Achari (Tue Apr 17 2012 - 00:58:30 PDT)
[AMBER] AMBER USER José Guilherme Vilhena Albuquerque d'Orey (Mon Apr 16 2012 - 03:03:00 PDT)
[AMBER] MICA SURFACE José Guilherme Vilhena Albuquerque d'Orey (Mon Apr 16 2012 - 03:04:25 PDT)
[AMBER] when will the membrane protein simulation tutorial be available? Albert (Mon Apr 16 2012 - 06:05:39 PDT)
- Re: [AMBER] when will the membrane protein simulation tutorial be available? Benjamin D Madej (Mon Apr 16 2012 - 20:05:02 PDT)
[AMBER] Good cluster configuration for running PMEMD.MPI? Juan Carlos Muñoz García (Mon Apr 16 2012 - 06:19:56 PDT)
- Re: [AMBER] Good cluster configuration for running PMEMD.MPI? Jason Swails (Mon Apr 16 2012 - 14:37:10 PDT)
  - Re: [AMBER] Good cluster configuration for running PMEMD.MPI? Matthew Zwier (Tue Apr 17 2012 - 06:00:08 PDT)
[AMBER] Electrostatic potential calculation Sudarshan Debnath (Mon Apr 16 2012 - 06:47:57 PDT)
- Re: [AMBER] Electrostatic potential calculation Ray Luo, Ph.D. (Mon Apr 16 2012 - 07:12:50 PDT)
[AMBER] problem with "make test.parallel" for AMBER12 Marc van der Kamp (Mon Apr 16 2012 - 07:15:21 PDT)
- Re: [AMBER] problem with "make test.parallel" for AMBER12 Jason Swails (Mon Apr 16 2012 - 12:05:15 PDT)
  - Re: [AMBER] problem with "make test.parallel" for AMBER12 Marc van der Kamp (Tue Apr 17 2012 - 01:34:10 PDT)
[AMBER] Error while running mm_pbsa.pl Prashant Kumar (Mon Apr 16 2012 - 08:30:14 PDT)
- Re: [AMBER] Error while running mm_pbsa.pl Ray Luo, Ph.D. (Mon Apr 16 2012 - 09:33:09 PDT)
[AMBER] AMBER12 QM/MM: is d-orbital code going to be parallelized? Marc van der Kamp (Mon Apr 16 2012 - 08:57:39 PDT)
- Re: [AMBER] AMBER12 QM/MM: is d-orbital code going to be parallelized? filip fratev (Mon Apr 16 2012 - 09:26:03 PDT)
  - Re: [AMBER] AMBER12 QM/MM: is d-orbital code going to be parallelized? David A Case (Mon Apr 16 2012 - 10:08:54 PDT)
    - Re: [AMBER] AMBER12 QM/MM: is d-orbital code going to be parallelized? Andreas Goetz (Thu Apr 19 2012 - 12:50:42 PDT)
    - Re: [AMBER] AMBER12 QM/MM: is d-orbital code going to be parallelized? filip fratev (Thu Apr 19 2012 - 22:30:55 PDT)
    - Re: [AMBER] AMBER12 QM/MM: is d-orbital code going to be parallelized? filip fratev (Fri Apr 20 2012 - 20:35:25 PDT)
    - [AMBER] QM/MM ATP-Mg2+ system filip fratev (Sun Apr 22 2012 - 15:55:07 PDT)
    - Re: [AMBER] QM/MM ATP-Mg2+ system Brian Radak (Mon Apr 23 2012 - 09:03:39 PDT)
    - Re: [AMBER] QM/MM ATP-Mg2+ system Yang, Yue (Mon Apr 23 2012 - 16:26:06 PDT)
    - Re: [AMBER] QM/MM ATP-Mg2+ system filip fratev (Tue Apr 24 2012 - 13:48:07 PDT)
  - Re: [AMBER] AMBER12 QM/MM: is d-orbital code going to be parallelized? Brian Radak (Mon Apr 16 2012 - 10:34:57 PDT)
    - Re: [AMBER] AMBER12 QM/MM: is d-orbital code going to be parallelized? Marc van der Kamp (Tue Apr 17 2012 - 02:23:43 PDT)
[AMBER] Need help with MMPBSA.MPI Victor Ma (Mon Apr 16 2012 - 09:12:31 PDT)
- Re: [AMBER] Need help with MMPBSA.MPI Bill Miller III (Mon Apr 16 2012 - 09:21:59 PDT)
  - Re: [AMBER] Need help with MMPBSA.MPI Victor Ma (Mon Apr 16 2012 - 09:31:36 PDT)
    - Re: [AMBER] Need help with MMPBSA.MPI Bill Miller III (Mon Apr 16 2012 - 13:49:38 PDT)
[AMBER] forcefield modifications Knips, Alexander (Mon Apr 16 2012 - 09:23:25 PDT)
- Re: [AMBER] forcefield modifications David A Case (Mon Apr 16 2012 - 09:59:23 PDT)
[AMBER] problem converting AmbertoDesmond Albert (Mon Apr 16 2012 - 11:54:11 PDT)
- Re: [AMBER] problem converting AmbertoDesmond David A Case (Mon Apr 16 2012 - 12:30:49 PDT)
  - Re: [AMBER] problem converting AmbertoDesmond Albert (Mon Apr 16 2012 - 14:15:15 PDT)
  - Re: [AMBER] problem converting AmbertoDesmond Albert (Mon Apr 16 2012 - 23:03:43 PDT)
    - Re: [AMBER] problem converting AmbertoDesmond David A Case (Tue Apr 17 2012 - 04:43:18 PDT)
    - Re: [AMBER] problem converting AmbertoDesmond Bill Ross (Tue Apr 17 2012 - 16:54:03 PDT)
[AMBER] "closest" command in cpptraj Alfredo Quevedo (Mon Apr 16 2012 - 12:57:11 PDT)
- Re: [AMBER] "closest" command in cpptraj Daniel Roe (Mon Apr 16 2012 - 14:25:54 PDT)
[AMBER] AmberTools12 Installation Error Senthil Natesan (Mon Apr 16 2012 - 12:59:20 PDT)
- Re: [AMBER] AmberTools12 Installation Error Jason Swails (Mon Apr 16 2012 - 14:45:14 PDT)
  - Re: [AMBER] AmberTools12 Installation Error - [SOLVED] Senthil Natesan (Mon Apr 16 2012 - 17:40:28 PDT)
[AMBER] sander error during GB calculations Qiong Zhang (Mon Apr 16 2012 - 19:09:28 PDT)
- Re: [AMBER] sander error during GB calculations Qiong Zhang (Mon Apr 16 2012 - 19:15:40 PDT)
[AMBER] Creating input file for Protein-protein simulation Tommy Yap (Tue Apr 17 2012 - 00:51:41 PDT)
- Re: [AMBER] Creating input file for Protein-protein simulation filip fratev (Tue Apr 17 2012 - 10:14:36 PDT)
  - Re: [AMBER] Creating input file for Protein-protein simulation Tommy Yap (Tue Apr 17 2012 - 20:09:54 PDT)
    - Re: [AMBER] Creating input file for Protein-protein simulation David A Case (Wed Apr 18 2012 - 04:56:42 PDT)
Re: [AMBER] :Re: "closest" command in cpptraj Alfredo Quevedo (Tue Apr 17 2012 - 05:44:20 PDT)
- Re: [AMBER] :Re: "closest" command in cpptraj Daniel Roe (Tue Apr 17 2012 - 06:14:43 PDT)
  - Re: [AMBER] :Re: "closest" command in cpptraj Alfredo Quevedo (Tue Apr 17 2012 - 07:22:32 PDT)
    - Re: [AMBER] :Re: "closest" command in cpptraj Daniel Roe (Tue Apr 17 2012 - 07:35:40 PDT)
    - Re: [AMBER] :Re: "closest" command in cpptraj Alfredo Quevedo (Tue Apr 17 2012 - 07:37:00 PDT)
    - Re: [AMBER] :Re: "closest" command in cpptraj Daniel Roe (Tue Apr 17 2012 - 08:05:00 PDT)
    - Re: [AMBER] :Re: "closest" command in cpptraj Alfredo Quevedo (Tue Apr 17 2012 - 08:18:21 PDT)
  - Re: [AMBER] :Re: "closest" command in cpptraj Thomas Evangelidis (Tue Apr 17 2012 - 07:29:51 PDT)
[AMBER] P2N file error from RED Urszula Uciechowska (Tue Apr 17 2012 - 05:59:11 PDT)
- Re: [AMBER] P2N file error from RED FyD (Tue Apr 17 2012 - 06:37:27 PDT)
  - Re: [AMBER] P2N file error from RED Urszula Uciechowska (Fri Apr 20 2012 - 00:57:43 PDT)
    - Re: [AMBER] P2N file error from RED Per Jr. Greisen (Fri Apr 20 2012 - 01:04:37 PDT)
    - Re: [AMBER] P2N file error from RED Urszula Uciechowska (Fri Apr 20 2012 - 01:22:51 PDT)
    - Re: [AMBER] P2N file error from RED FyD (Fri Apr 20 2012 - 02:10:02 PDT)
[AMBER] Using Antechamber to generate RESP prepi file Lianhu Wei (Tue Apr 17 2012 - 14:12:29 PDT)
- Re: [AMBER] Using Antechamber to generate RESP prepi file FyD (Wed Apr 18 2012 - 00:43:09 PDT)
  - Re: [AMBER] Using Antechamber to generate RESP prepi file Lianhu Wei (Wed Apr 18 2012 - 06:34:30 PDT)
    - Re: [AMBER] Using Antechamber to generate RESP prepi file FyD (Wed Apr 18 2012 - 09:47:55 PDT)
    - Re: [AMBER] Using Antechamber to generate RESP prepi file Lianhu Wei (Wed Apr 18 2012 - 12:27:42 PDT)
    - Re: [AMBER] Using Antechamber to generate RESP prepi file FyD (Thu Apr 19 2012 - 03:02:18 PDT)
    - Re: [AMBER] Using Antechamber to generate RESP prepi file Lianhu Wei (Thu Apr 19 2012 - 08:33:46 PDT)
[AMBER] Why RMSD goes fast to 5 angstrom? Shulin Zhuang (Tue Apr 17 2012 - 19:26:20 PDT)
- Re: [AMBER] Why RMSD goes fast to 5 angstrom? Aron Broom (Tue Apr 17 2012 - 19:40:58 PDT)
- Re: [AMBER] Why RMSD goes fast to 5 angstrom? Jason Swails (Tue Apr 17 2012 - 20:23:25 PDT)
  - Re: [AMBER] Why RMSD goes fast to 5 angstrom? steinbrt.rci.rutgers.edu (Wed Apr 18 2012 - 00:21:30 PDT)
    - Re: [AMBER] Why RMSD goes fast to 5 angstrom? Jason Swails (Wed Apr 18 2012 - 05:16:10 PDT)
    - Re: [AMBER] Why RMSD goes fast to 5 angstrom? Shulin Zhuang (Wed Apr 18 2012 - 05:42:03 PDT)
[AMBER] About restraint Jun Wang (Tue Apr 17 2012 - 19:33:09 PDT)
- Re: [AMBER] About restraint Aron Broom (Tue Apr 17 2012 - 19:47:06 PDT)
  - Re: [AMBER] About restraint Thomas Cheatham (Tue Apr 17 2012 - 20:30:03 PDT)
[AMBER] Fwd: Why RMSD goes fast to 5 angstrom? Shulin Zhuang (Tue Apr 17 2012 - 20:14:04 PDT)
[AMBER] how to improve GPU running? Albert (Tue Apr 17 2012 - 23:24:54 PDT)
- Re: [AMBER] how to improve GPU running? steinbrt.rci.rutgers.edu (Wed Apr 18 2012 - 00:36:38 PDT)
  - Re: [AMBER] how to improve GPU running? Albert (Wed Apr 18 2012 - 03:52:39 PDT)
    - Re: [AMBER] how to improve GPU running? steinbrt.rci.rutgers.edu (Wed Apr 18 2012 - 04:10:10 PDT)
    - Re: [AMBER] how to improve GPU running? Ross Walker (Wed Apr 18 2012 - 04:10:37 PDT)
    - Re: [AMBER] how to improve GPU running? Ross Walker (Wed Apr 18 2012 - 04:28:33 PDT)
- Re: [AMBER] how to improve GPU running? Scott Le Grand (Wed Apr 18 2012 - 04:55:06 PDT)
[AMBER] problem installing AmberTools 12 on Mac OS X Lion Sidney Elmer (Wed Apr 18 2012 - 01:11:01 PDT)
- [AMBER] on The Nudged Elastic Band Approach (Tutorial 5) Acoot Brett (Wed Apr 18 2012 - 02:42:17 PDT)
  - Re: [AMBER] on The Nudged Elastic Band Approach (Tutorial 5) Carlos Simmerling (Fri Apr 20 2012 - 05:01:17 PDT)
    - Re: [AMBER] on The Nudged Elastic Band Approach (Tutorial 5) Aron Broom (Fri Apr 20 2012 - 07:21:32 PDT)
- Re: [AMBER] problem installing AmberTools 12 on Mac OS X Lion Sidney Elmer (Wed Apr 18 2012 - 11:11:14 PDT)
[AMBER] Use effective core potential in amber QM/MM calculation with Gaussian Tong Zhu (Wed Apr 18 2012 - 02:46:43 PDT)
[AMBER] Dielectric constant and scaled charges Lorenzo Gontrani (Wed Apr 18 2012 - 03:34:09 PDT)
- Re: [AMBER] Dielectric constant and scaled charges David A Case (Wed Apr 18 2012 - 05:09:24 PDT)
Re: [AMBER] About Restraint Jun Wang (Wed Apr 18 2012 - 07:48:14 PDT)
[AMBER] SCEE and SCNB GLYCAM_06 values with amber11 top crd files Kepa K. Burusco (Wed Apr 18 2012 - 10:55:09 PDT)
- Re: [AMBER] SCEE and SCNB GLYCAM_06 values with amber11 top crd files David A Case (Wed Apr 18 2012 - 12:10:00 PDT)
- Re: [AMBER] SCEE and SCNB GLYCAM_06 values with amber11 top crd files Lachele Foley (Lists) (Wed Apr 18 2012 - 12:23:03 PDT)
[AMBER] Amber11: running ptraj bmartini (Wed Apr 18 2012 - 11:26:38 PDT)
- Re: [AMBER] Amber11: running ptraj Thomas Cheatham III (Wed Apr 18 2012 - 11:37:24 PDT)
  - Re: [AMBER] Amber11: running ptraj bmartini (Wed Apr 18 2012 - 11:45:42 PDT)
- [AMBER] running the on-line tutorial B1 (DNA) by Amber 12 Acoot Brett (Fri Apr 20 2012 - 04:21:52 PDT)
  - [AMBER] Fw: running the on-line tutorial B1 (DNA) by Amber 12 Acoot Brett (Fri Apr 20 2012 - 05:16:25 PDT)
  - Re: [AMBER] running the on-line tutorial B1 (DNA) by Amber 12 David A Case (Fri Apr 20 2012 - 05:36:06 PDT)
- [AMBER] implicit MD and explicit MD Acoot Brett (Sat Apr 21 2012 - 08:26:32 PDT)
  - Re: [AMBER] implicit MD and explicit MD Carlos Simmerling (Sat Apr 21 2012 - 12:14:34 PDT)
[AMBER] why no periodic information? Albert (Wed Apr 18 2012 - 12:16:04 PDT)
- Re: [AMBER] why no periodic information? Aron Broom (Wed Apr 18 2012 - 12:21:16 PDT)
  - Re: [AMBER] why no periodic information? Albert (Wed Apr 18 2012 - 12:29:01 PDT)
  - Re: [AMBER] why no periodic information? Albert (Wed Apr 18 2012 - 12:29:20 PDT)
    - Re: [AMBER] why no periodic information? Aron Broom (Wed Apr 18 2012 - 12:36:06 PDT)
    - Re: [AMBER] why no periodic information? Albert (Wed Apr 18 2012 - 12:39:04 PDT)
  - Re: [AMBER] why no periodic information? Brian Radak (Wed Apr 18 2012 - 12:35:01 PDT)
    - Re: [AMBER] why no periodic information? Aron Broom (Wed Apr 18 2012 - 12:47:44 PDT)
    - Re: [AMBER] why no periodic information? Albert (Wed Apr 18 2012 - 12:48:29 PDT)
    - Re: [AMBER] why no periodic information? Albert (Wed Apr 18 2012 - 13:01:58 PDT)
[AMBER] problem in tleap with head and tail atom assignment Cramariuc Oana (Wed Apr 18 2012 - 13:10:34 PDT)
- Re: [AMBER] problem in tleap with head and tail atom assignment Jason Swails (Wed Apr 18 2012 - 14:27:53 PDT)
- Re: [AMBER] problem in tleap with head and tail atom assignment FyD (Thu Apr 19 2012 - 03:14:32 PDT)
  - Re: [AMBER] problem in tleap with head and tail atom assignment Cramariuc Oana (Thu Apr 19 2012 - 04:44:14 PDT)
[AMBER] NUCGEN and FORCE Field disfunction VladanStefanovic.kg.ac.rs (Thu Apr 19 2012 - 03:00:16 PDT)
- Re: [AMBER] NUCGEN and FORCE Field disfunction David A Case (Thu Apr 19 2012 - 04:55:10 PDT)
- Re: [AMBER] NUCGEN and FORCE Field disfunction Jason Swails (Thu Apr 19 2012 - 04:55:48 PDT)
[AMBER] How can I exert external force in the end of DNA? mehdi bagherpoor (Thu Apr 19 2012 - 07:13:01 PDT)
- Re: [AMBER] How can I exert external force in the end of DNA? Bahareh honarparvar (Thu Apr 19 2012 - 08:30:51 PDT)
- Re: [AMBER] How can I exert external force in the end of DNA? ros (Thu Apr 19 2012 - 08:36:33 PDT)
[AMBER] xleap pdb file loading problem. DoYong Kim (Thu Apr 19 2012 - 08:53:10 PDT)
- Re: [AMBER] xleap pdb file loading problem. David A Case (Thu Apr 19 2012 - 11:47:55 PDT)
- Re: [AMBER] xleap pdb file loading problem. DoYong Kim (Fri Apr 20 2012 - 12:49:59 PDT)
  - Re: [AMBER] xleap pdb file loading problem. Jason Swails (Sat Apr 21 2012 - 07:29:56 PDT)
[AMBER] cpptraj, ptraj and time interval Fabrício Bracht (Thu Apr 19 2012 - 10:15:07 PDT)
- Re: [AMBER] cpptraj, ptraj and time interval Liu Denis (Thu Apr 19 2012 - 17:38:39 PDT)
  - Re: [AMBER] cpptraj, ptraj and time interval Fabrício Bracht (Fri Apr 20 2012 - 07:25:52 PDT)
    - Re: [AMBER] cpptraj, ptraj and time interval Jan-Philip Gehrcke (Fri Apr 20 2012 - 08:15:04 PDT)
    - Re: [AMBER] cpptraj, ptraj and time interval Fabrício Bracht (Fri Apr 20 2012 - 11:23:56 PDT)
    - Re: [AMBER] cpptraj, ptraj and time interval David A Case (Fri Apr 20 2012 - 13:05:02 PDT)
    - Re: [AMBER] cpptraj, ptraj and time interval Jason Swails (Sat Apr 21 2012 - 07:25:06 PDT)
- Re: [AMBER] cpptraj, ptraj and time interval Daniel Roe (Thu Apr 19 2012 - 17:41:49 PDT)
[AMBER] About force constant in umbrella sampling Mo Chen (Thu Apr 19 2012 - 10:46:34 PDT)
- Re: [AMBER] About force constant in umbrella sampling Brian Radak (Thu Apr 19 2012 - 11:11:38 PDT)
[AMBER] Amber 12 - Check for updates failed Shaw, Sharon (Thu Apr 19 2012 - 12:08:26 PDT)
- Re: [AMBER] Amber 12 - Check for updates failed Jason Swails (Thu Apr 19 2012 - 12:24:55 PDT)
  - Re: [AMBER] Amber 12 - Check for updates failed Shaw, Sharon (Thu Apr 19 2012 - 12:37:06 PDT)
  - Re: [AMBER] Amber 12 - Check for updates failed Shaw, Sharon (Thu Apr 19 2012 - 13:48:05 PDT)
[AMBER] ★what's new?◆amber◆ ZhaoLei (Thu Apr 19 2012 - 12:12:48 PDT)
[AMBER] Bug? Antechamber, Ambertools-1.4 Lianhu Wei (Thu Apr 19 2012 - 13:11:46 PDT)
Re: [AMBER] Old version Thales Kronenberger (Thu Apr 19 2012 - 13:18:36 PDT)
- Re: [AMBER] Old version case (Thu Apr 19 2012 - 17:52:32 PDT)
  - Re: [AMBER] Old version Alan (Fri Apr 20 2012 - 00:54:41 PDT)
[AMBER] How to determine the protonation state of phosphorylated residue in a protein? Rajendra Sharma (Thu Apr 19 2012 - 17:08:00 PDT)
- Re: [AMBER] How to determine the protonation state of phosphorylated residue in a protein? Jason Swails (Sun Apr 22 2012 - 15:31:10 PDT)
[AMBER] The error of installing mpi4py in ambertools12 for MMPBSA parallel JiYuan Liu (Fri Apr 20 2012 - 21:13:02 PDT)
- Re: [AMBER] The error of installing mpi4py in ambertools12 for MMPBSA parallel Jason Swails (Fri Apr 20 2012 - 08:47:57 PDT)
[AMBER] Some problem with building Non-standard residue Nicholus Bhattacharjee (Thu Apr 19 2012 - 23:14:30 PDT)
[AMBER] QM/MM and water box type Fernando Martín García (Fri Apr 20 2012 - 01:07:26 PDT)
- Re: [AMBER] QM/MM and water box type Qiantao Wang (Fri Apr 20 2012 - 10:59:33 PDT)
[AMBER] Confusion in adding TER cards Asmita Gupta (Fri Apr 20 2012 - 04:05:24 PDT)
- Re: [AMBER] Confusion in adding TER cards David A Case (Fri Apr 20 2012 - 13:13:28 PDT)
[AMBER] MM/PBSA calculations mish (Fri Apr 20 2012 - 05:06:28 PDT)
- Re: [AMBER] MM/PBSA calculations Ray Luo, Ph.D. (Fri Apr 20 2012 - 16:46:29 PDT)
[AMBER] imin = 5, expected numerical error when re-calculating energy Brian Radak (Fri Apr 20 2012 - 07:46:13 PDT)
- Re: [AMBER] imin = 5, expected numerical error when re-calculating energy Jason Swails (Fri Apr 20 2012 - 08:41:45 PDT)
  - Re: [AMBER] imin = 5, expected numerical error when re-calculating energy Brian Radak (Fri Apr 20 2012 - 09:03:41 PDT)
[AMBER] (GPU) preformance of amber 12 István Lőrincz (Fri Apr 20 2012 - 08:33:37 PDT)
- Re: [AMBER] (GPU) preformance of amber 12 Scott Le Grand (Fri Apr 20 2012 - 09:44:09 PDT)
  - Re: [AMBER] (GPU) preformance of amber 12 István Lőrincz (Mon Apr 23 2012 - 03:37:34 PDT)
    - Re: [AMBER] (GPU) preformance of amber 12 Ross Walker (Mon Apr 23 2012 - 19:13:30 PDT)
[AMBER] error Building proper torsion parameters. zhangaidi (Fri Apr 20 2012 - 10:52:29 PDT)
- Re: [AMBER] error Building proper torsion parameters. David A Case (Fri Apr 20 2012 - 12:56:49 PDT)
[AMBER] external force in the end of DNA strands mehdi bagherpoor (Fri Apr 20 2012 - 16:15:44 PDT)
- [AMBER] constant pH titration Acoot Brett (Fri Apr 20 2012 - 23:38:58 PDT)
  - [AMBER] using AMBER forcefield by GROMACS Acoot Brett (Sat Apr 21 2012 - 04:24:07 PDT)
    - Re: [AMBER] using AMBER forcefield by GROMACS Francesco Oteri (Sat Apr 21 2012 - 04:31:03 PDT)
    - Re: [AMBER] using AMBER forcefield by GROMACS Acoot Brett (Sat Apr 21 2012 - 04:36:48 PDT)
    - Re: [AMBER] using AMBER forcefield by GROMACS Jason Swails (Sat Apr 21 2012 - 07:21:01 PDT)
  - Re: [AMBER] constant pH titration Jason Swails (Sat Apr 21 2012 - 07:08:17 PDT)
[AMBER] using two GPUs Vijay Manickam Achari (Fri Apr 20 2012 - 17:39:33 PDT)
- Re: [AMBER] using two GPUs Robert Crovella (Fri Apr 20 2012 - 19:07:32 PDT)
  - Re: [AMBER] using two GPUs David Jones (Fri Apr 20 2012 - 19:23:30 PDT)
  - Re: [AMBER] using two GPUs Vijay Manickam Achari (Fri Apr 20 2012 - 20:14:51 PDT)
    - Re: [AMBER] using two GPUs Robert Crovella (Sat Apr 21 2012 - 05:50:31 PDT)
    - Re: [AMBER] using two GPUs Jason Swails (Sat Apr 21 2012 - 07:18:02 PDT)
    - Re: [AMBER] using two GPUs Vijay Manickam Achari (Mon Apr 23 2012 - 22:16:49 PDT)
    - Re: [AMBER] using two GPUs Robert Crovella (Tue Apr 24 2012 - 07:39:49 PDT)
    - Re: [AMBER] using two GPUs Vijay Manickam Achari (Tue Apr 24 2012 - 22:34:52 PDT)
    - Re: [AMBER] using two GPUs Jason Swails (Wed Apr 25 2012 - 09:05:13 PDT)
    - Re: [AMBER] using two GPUs Vijay Manickam Achari (Wed Apr 25 2012 - 11:41:59 PDT)
    - Re: [AMBER] using two GPUs Jason Swails (Wed Apr 25 2012 - 11:44:31 PDT)
    - Re: [AMBER] using two GPUs Vijay Manickam Achari (Wed Apr 25 2012 - 17:57:04 PDT)
    - Re: [AMBER] using two GPUs Robert Crovella (Tue May 01 2012 - 12:15:05 PDT)
    - Re: [AMBER] using two GPUs Shaw, Sharon (Tue May 01 2012 - 12:21:25 PDT)
    - Re: [AMBER] using two GPUs Scott Le Grand (Tue May 01 2012 - 14:57:40 PDT)
    - Re: [AMBER] using two GPUs Ross Walker (Wed May 02 2012 - 05:38:20 PDT)
    - Re: [AMBER] using two GPUs Vijay Manickam Achari (Wed May 02 2012 - 16:37:46 PDT)
    - [AMBER] using two GPUs Vijay Manickam Achari (Wed May 02 2012 - 20:55:34 PDT)
    - Re: [AMBER] using two GPUs Ross Walker (Thu May 03 2012 - 01:41:45 PDT)
- [AMBER] addions command in the xleap Acoot Brett (Fri Apr 20 2012 - 21:57:28 PDT)
  - Re: [AMBER] addions command in the xleap Aron Broom (Sat Apr 21 2012 - 05:14:53 PDT)
[AMBER] is membrane protein simulation tutorial ready? Albert (Sat Apr 21 2012 - 12:14:22 PDT)
- Re: [AMBER] is membrane protein simulation tutorial ready? Jason Swails (Sat Apr 21 2012 - 13:32:50 PDT)
[AMBER] Installation problem for Ambertools 12 on Mac OS X Lion Richard Lonsdale (Sun Apr 22 2012 - 00:26:46 PDT)
- Re: [AMBER] Installation problem for Ambertools 12 on Mac OS X Lion Jason Swails (Sun Apr 22 2012 - 07:28:46 PDT)
  - Re: [AMBER] Installation problem for Ambertools 12 on Mac OS X Lion Richard Lonsdale (Sun Apr 22 2012 - 11:10:21 PDT)
    - Re: [AMBER] Installation problem for Ambertools 12 on Mac OS X Lion David Case (Sun Apr 22 2012 - 12:47:35 PDT)
    - Re: [AMBER] Installation problem for Ambertools 12 on Mac OS X Lion Richard Lonsdale (Sun Apr 22 2012 - 13:51:42 PDT)
- Re: [AMBER] Installation problem for Ambertools 12 on Mac OS X Lion Jason Swails (Sun Apr 22 2012 - 16:21:13 PDT)
  - Re: [AMBER] Installation problem for Ambertools 12 on Mac OS X Lion David A Case (Mon Apr 23 2012 - 05:22:21 PDT)
    - Re: [AMBER] Installation problem for Ambertools 12 on Mac OS X Lion Jason Swails (Mon Apr 23 2012 - 05:57:26 PDT)
[AMBER] Where can I find silhouette.pl? Irene Newhouse (Sun Apr 22 2012 - 01:54:05 PDT)
[AMBER] amber 10 nmode error. xmzpzengs (Mon Apr 23 2012 - 01:26:04 PDT)
[AMBER] H-Bonding and Amber's Shake algorithm Adam Jion (Mon Apr 23 2012 - 03:33:38 PDT)
- Re: [AMBER] H-Bonding and Amber's Shake algorithm David A Case (Mon Apr 23 2012 - 05:24:35 PDT)
[AMBER] RMSD analysis for cyclo-tetra-peptide mcj452500 (Mon Apr 23 2012 - 04:08:42 PDT)
- Re: [AMBER] RMSD analysis for cyclo-tetra-peptide Carlos Simmerling (Mon Apr 23 2012 - 04:44:56 PDT)
Re: [AMBER] [amber] error building proper torsion parameters. 本人 (Mon Apr 23 2012 - 08:02:37 PDT)
- Re: [AMBER] [amber] error building proper torsion parameters. David A Case (Mon Apr 23 2012 - 09:47:45 PDT)
- Re: [AMBER] [amber] error building proper torsion parameters. 本人 (Wed Apr 25 2012 - 00:45:05 PDT)
  - Re: [AMBER] [amber] error building proper torsion parameters. David A Case (Wed Apr 25 2012 - 05:30:37 PDT)
[AMBER] Problems with atom type in sidechain.bcl Fabrício Bracht (Mon Apr 23 2012 - 08:21:42 PDT)
- Re: [AMBER] Problems with atom type in sidechain.bcl Yang, Yue (Mon Apr 23 2012 - 16:31:32 PDT)
[AMBER] Huge discrepancy in el part of "solvation energy" using Thermodynamic Integration Marek Maly (Mon Apr 23 2012 - 09:55:26 PDT)
- Re: [AMBER] Huge discrepancy in el part of "solvation energy" using Thermodynamic Integration Marek Maly (Tue May 01 2012 - 20:12:18 PDT)
  - Re: [AMBER] Huge discrepancy in el part of "solvation energy" using Thermodynamic Integration case (Sat May 05 2012 - 06:45:09 PDT)
    - Re: [AMBER] Huge discrepancy in el part of "solvation energy" using Thermodynamic Integration Marek Maly (Sun May 06 2012 - 09:15:01 PDT)
    - Re: [AMBER] Huge discrepancy in el part of "solvation energy" using Thermodynamic Integration David Case (Sun May 06 2012 - 14:13:53 PDT)
    - Re: [AMBER] Huge discrepancy in el part of "solvation energy" using Thermodynamic Integration Marek Maly (Sun May 06 2012 - 14:16:29 PDT)
[AMBER] AMBER12 build on Linux x86_64 Shaw, Sharon (Mon Apr 23 2012 - 11:41:36 PDT)
- Re: [AMBER] AMBER12 build on Linux x86_64 Matthew Zwier (Mon Apr 23 2012 - 12:16:41 PDT)
  - Re: [AMBER] AMBER12 build on Linux x86_64 Jason Swails (Mon Apr 23 2012 - 12:31:21 PDT)
    - Re: [AMBER] AMBER12 build on Linux x86_64 Shaw, Sharon (Mon Apr 23 2012 - 13:51:14 PDT)
    - Re: [AMBER] AMBER12 build on Linux x86_64 Jason Swails (Mon Apr 23 2012 - 15:27:50 PDT)
    - Re: [AMBER] AMBER12 build on Linux x86_64 case (Mon Apr 23 2012 - 18:11:15 PDT)
    - Re: [AMBER] AMBER12 build on Linux x86_64 Shaw, Sharon (Tue Apr 24 2012 - 08:00:37 PDT)
    - Re: [AMBER] AMBER12 build on Linux x86_64 Jason Swails (Tue Apr 24 2012 - 08:32:27 PDT)
    - Re: [AMBER] AMBER12 build on Linux x86_64 Jason Swails (Tue Apr 24 2012 - 08:33:30 PDT)
    - Re: [AMBER] AMBER12 build on Linux x86_64 Shaw, Sharon (Tue Apr 24 2012 - 13:11:07 PDT)
[AMBER] AMBER 11 sander segmentation fault Shuyi Cao (Mon Apr 23 2012 - 16:32:21 PDT)
- Re: [AMBER] AMBER 11 sander segmentation fault case (Mon Apr 23 2012 - 18:24:18 PDT)
Re: [AMBER] Amber using Gaussian input ashley chen (Mon Apr 23 2012 - 23:51:45 PDT)
- Re: [AMBER] Amber using Gaussian input Scott Brozell (Tue Apr 24 2012 - 00:51:32 PDT)
[AMBER] Amber 12 Installation errors relevant to fftw3 Shulin Zhuang (Tue Apr 24 2012 - 02:15:05 PDT)
- Re: [AMBER] Amber 12 Installation errors relevant to fftw3 David A Case (Tue Apr 24 2012 - 05:31:38 PDT)
  - Re: [AMBER] Amber 12 Installation errors relevant to fftw3 Shulin Zhuang (Tue Apr 24 2012 - 18:08:07 PDT)
    - Re: [AMBER] Amber 12 Installation errors relevant to fftw3 David A Case (Wed Apr 25 2012 - 05:12:20 PDT)
    - Re: [AMBER] Amber 12 Installation errors relevant to fftw3 Shulin Zhuang (Wed Apr 25 2012 - 17:23:32 PDT)
    - Re: [AMBER] Amber 12 Installation errors relevant to fftw3 Jason Swails (Wed Apr 25 2012 - 17:37:50 PDT)
    - Re: [AMBER] Amber 12 Installation errors relevant to fftw3 Shulin Zhuang (Wed Apr 25 2012 - 17:49:21 PDT)
    - Re: [AMBER] Amber 12 Installation errors relevant to fftw3 case (Wed Apr 25 2012 - 19:30:22 PDT)
    - Re: [AMBER] Amber 12 Installation errors relevant to fftw3 Jason Swails (Thu Apr 26 2012 - 07:29:10 PDT)
    - Re: [AMBER] Amber 12 Installation errors relevant to fftw3 M. L. Dodson (Thu Apr 26 2012 - 08:32:44 PDT)
    - Re: [AMBER] Amber 12 Installation errors relevant to fftw3 David A Case (Thu Apr 26 2012 - 12:25:23 PDT)
    - Re: [AMBER] Amber 12 Installation errors relevant to fftw3 Shulin Zhuang (Fri Apr 27 2012 - 23:21:31 PDT)
    - Re: [AMBER] Amber 12 Installation errors relevant to fftw3 M. L. Dodson (Sat Apr 28 2012 - 06:10:06 PDT)
    - Re: [AMBER] Amber 12 Installation errors relevant to fftw3 Shulin Zhuang (Tue May 01 2012 - 18:53:32 PDT)
[AMBER] Entropy: nmode and quasi-harmonic approximation George Tzotzos (Tue Apr 24 2012 - 02:24:15 PDT)
- Re: [AMBER] Entropy: nmode and quasi-harmonic approximation Hannes Loeffler (Tue Apr 24 2012 - 02:58:16 PDT)
  - Re: [AMBER] Entropy: nmode and quasi-harmonic approximation George Tzotzos (Tue Apr 24 2012 - 04:50:46 PDT)
[AMBER] error in parallel amber 11 installation Asmita Gupta (Tue Apr 24 2012 - 02:43:06 PDT)
- Re: [AMBER] error in parallel amber 11 installation David A Case (Tue Apr 24 2012 - 05:41:26 PDT)
  - Re: [AMBER] error in parallel amber 11 installation Jason Swails (Tue Apr 24 2012 - 06:10:29 PDT)
    - Re: [AMBER] error in parallel amber 11 installation Asmita Gupta (Wed Apr 25 2012 - 01:31:00 PDT)
    - Re: [AMBER] error in parallel amber 11 installation David A Case (Wed Apr 25 2012 - 05:22:04 PDT)
    - Re: [AMBER] error in parallel amber 11 installation Asmita Gupta (Thu Apr 26 2012 - 05:24:36 PDT)
[AMBER] Protein nanoparticle interaction Navin Jain (Tue Apr 24 2012 - 02:56:55 PDT)
- Re: [AMBER] Protein nanoparticle interaction Ben Roberts (Tue Apr 24 2012 - 19:42:58 PDT)
[AMBER] AM1 scalability Jacopo Sgrignani (Tue Apr 24 2012 - 08:12:00 PDT)
- Re: [AMBER] AM1 scalability Marc van der Kamp (Tue Apr 24 2012 - 08:29:45 PDT)
[AMBER] For atom: .R<Na+ 127>.A<Na+ 1> Could not find type: Na+ George Tzotzos (Tue Apr 24 2012 - 10:59:01 PDT)
- Re: [AMBER] For atom: .R<Na+ 127>.A<Na+ 1> Could not find type: Na+ InSuk Joung (Tue Apr 24 2012 - 12:03:18 PDT)
 - Re: [AMBER] For atom: .R<Na+ 127>.A<Na+ 1> Could not find type: Na+ George Tzotzos (Tue Apr 24 2012 - 12:39:07 PDT)
[AMBER] Trouble installing AmberTools 1.5 on mac Andrew Ritchie (Tue Apr 24 2012 - 11:05:33 PDT)
- Re: [AMBER] Trouble installing AmberTools 1.5 on mac Jason Swails (Tue Apr 24 2012 - 14:29:38 PDT)
[AMBER] AMBER12 installation error Peter Fojan (Wed Apr 25 2012 - 01:29:13 PDT)
- Re: [AMBER] AMBER12 installation error David A Case (Wed Apr 25 2012 - 05:16:15 PDT)
  - Re: [AMBER] AMBER12 installation error Peter Fojan (Wed Apr 25 2012 - 05:45:32 PDT)
    - Re: [AMBER] AMBER12 installation error Jason Swails (Wed Apr 25 2012 - 09:08:09 PDT)
    - Re: [AMBER] AMBER12 installation error Peter Fojan (Wed Apr 25 2012 - 09:57:40 PDT)
[AMBER] add_pdb colvin (Wed Apr 25 2012 - 02:12:21 PDT)
- Re: [AMBER] add_pdb David A Case (Wed Apr 25 2012 - 05:26:51 PDT)
  - Re: [AMBER] add_pdb colvin (Wed Apr 25 2012 - 17:02:06 PDT)
    - Re: [AMBER] add_pdb Jason Swails (Wed Apr 25 2012 - 17:06:12 PDT)
    - Re: [AMBER] add_pdb colvin (Wed Apr 25 2012 - 17:39:58 PDT)
    - Re: [AMBER] add_pdb Jason Swails (Wed Apr 25 2012 - 18:36:47 PDT)
    - Re: [AMBER] add_pdb case (Wed Apr 25 2012 - 19:21:28 PDT)
    - Re: [AMBER] add_pdb colvin (Thu Apr 26 2012 - 01:39:46 PDT)
    - Re: [AMBER] add_pdb Jason Swails (Thu Apr 26 2012 - 05:56:20 PDT)
[AMBER] ff12SB with Na+ ion Tong Zhu (Wed Apr 25 2012 - 03:56:33 PDT)
- Re: [AMBER] ff12SB with Na+ ion Marc van der Kamp (Wed Apr 25 2012 - 04:10:38 PDT)
[AMBER] QM/MM simulation ashwini gupta (Wed Apr 25 2012 - 05:19:36 PDT)
- Re: [AMBER] QM/MM simulation Brian Radak (Wed Apr 25 2012 - 06:11:33 PDT)
- Re: [AMBER] QM/MM simulation bharat gupta (Wed Jun 29 2016 - 01:44:46 PDT)
  - Re: [AMBER] QM/MM simulation Marc van der Kamp (Wed Jun 29 2016 - 02:09:09 PDT)
  - Re: [AMBER] QM/MM simulation Gustavo Seabra (Wed Jun 29 2016 - 06:54:42 PDT)
[AMBER] is it possible to convert gromacs MD system into Amber? Albert (Wed Apr 25 2012 - 06:13:50 PDT)
- Re: [AMBER] is it possible to convert gromacs MD system into Amber? Jason Swails (Wed Apr 25 2012 - 09:09:03 PDT)
[AMBER] Angle restrained minimization Ashutosh Shandilya (Wed Apr 25 2012 - 06:39:52 PDT)
- Re: [AMBER] Angle restrained minimization David A Case (Wed Apr 25 2012 - 09:41:29 PDT)
[AMBER] computational scanning Hector A. Baldoni (Wed Apr 25 2012 - 08:06:57 PDT)
- Re: [AMBER] computational scanning Carlos Simmerling (Wed Apr 25 2012 - 08:11:13 PDT)
- Re: [AMBER] computational scanning Gould, Ian R (Wed Apr 25 2012 - 08:15:45 PDT)
[AMBER] Lmode_in_Amber11 JAIME RUBIO MARTINEZ (Wed Apr 25 2012 - 11:08:18 PDT)
- Re: [AMBER] Lmode_in_Amber11 case (Wed Apr 25 2012 - 14:25:47 PDT)
  - Re: [AMBER] Lmode_in_Amber11 JAIME RUBIO MARTINEZ (Thu Apr 26 2012 - 01:07:26 PDT)
  - Re: [AMBER] Lmode_in_Amber11 JAIME RUBIO MARTINEZ (Thu Apr 26 2012 - 01:09:15 PDT)
    - Re: [AMBER] Lmode_in_Amber11 David A Case (Thu Apr 26 2012 - 05:19:03 PDT)
[AMBER] 1-4 EEL meaning Camille Sultana (Wed Apr 25 2012 - 11:21:08 PDT)
- Re: [AMBER] 1-4 EEL meaning Thomas Cheatham (Wed Apr 25 2012 - 11:34:24 PDT)
  - Re: [AMBER] 1-4 EEL meaning Camille Sultana (Wed Apr 25 2012 - 15:02:30 PDT)
    - Re: [AMBER] 1-4 EEL meaning Jason Swails (Wed Apr 25 2012 - 15:23:54 PDT)
[AMBER] the real binding free energy bmartini (Wed Apr 25 2012 - 19:34:21 PDT)
- Re: [AMBER] the real binding free energy David A Case (Thu Apr 26 2012 - 05:26:16 PDT)
[AMBER] problems installing pmedm.cuda Peter Fojan (Thu Apr 26 2012 - 00:39:35 PDT)
- Re: [AMBER] problems installing pmedm.cuda Jason Swails (Thu Apr 26 2012 - 05:58:12 PDT)
  - Re: [AMBER] problems installing pmedm.cuda Jason Swails (Thu Apr 26 2012 - 06:52:02 PDT)
    - Re: [AMBER] problems installing pmedm.cuda Peter Fojan (Thu Apr 26 2012 - 07:19:37 PDT)
Re: [AMBER] parameters for Lys-sugar leap errors Urszula Uciechowska (Thu Apr 26 2012 - 02:41:01 PDT)
- Re: [AMBER] parameters for Lys-sugar leap errors Lachele Foley (Lists) (Thu Apr 26 2012 - 07:17:48 PDT)
  - Re: [AMBER] parameters for Lys-sugar leap errors Lachele Foley (Lists) (Thu Apr 26 2012 - 07:19:29 PDT)
- Re: [AMBER] parameters for Lys-sugar leap errors FyD (Thu Apr 26 2012 - 08:36:39 PDT)
[AMBER] creating a box of fixed size Bala subramanian (Thu Apr 26 2012 - 02:44:55 PDT)
- Re: [AMBER] creating a box of fixed size francesco oteri (Thu Apr 26 2012 - 06:34:25 PDT)
  - Re: [AMBER] creating a box of fixed size Lorenzo Gontrani (Thu Apr 26 2012 - 06:55:48 PDT)
[AMBER] sander and pmemd xiaojiong (Thu Apr 26 2012 - 04:56:18 PDT)
- Re: [AMBER] sander and pmemd Ross Walker (Thu Apr 26 2012 - 06:53:33 PDT)
[AMBER] "Spiderweb" jun kit (Thu Apr 26 2012 - 06:52:19 PDT)
- Re: [AMBER] "Spiderweb" Ross Walker (Thu Apr 26 2012 - 06:59:00 PDT)
- Re: [AMBER] "Spiderweb" FyD (Thu Apr 26 2012 - 08:57:31 PDT)
  - [AMBER] problems with added hydrogens to non standard residue Urszula Uciechowska (Mon May 14 2012 - 01:26:00 PDT)
    - Re: [AMBER] problems with added hydrogens to non standard residue FyD (Mon May 14 2012 - 03:40:03 PDT)
    - Re: [AMBER] problems with added hydrogens to non standard residue Urszula Uciechowska (Mon May 14 2012 - 04:43:30 PDT)
    - Re: [AMBER] problems with added hydrogens to non standard residue Renata KWIECIEN (Mon May 14 2012 - 05:26:41 PDT)
    - Re: [AMBER] problems with added hydrogens to non standard residue FyD (Tue May 15 2012 - 00:07:44 PDT)
    - Re: [AMBER] problems with added hydrogens to non standard residue Urszula Uciechowska (Tue May 15 2012 - 04:47:53 PDT)
    - Re: [AMBER] problems with added hydrogens to non standard residue case (Tue May 15 2012 - 06:07:55 PDT)
    - Re: [AMBER] problems with added hydrogens to non standard residue Urszula Uciechowska (Tue May 15 2012 - 06:27:14 PDT)
    - Re: [AMBER] problems with added hydrogens to non standard residue FyD (Tue May 15 2012 - 06:42:45 PDT)
    - Re: [AMBER] problems with added hydrogens to non standard residue Urszula Uciechowska (Tue May 15 2012 - 07:28:41 PDT)
    - Re: [AMBER] problems with added hydrogens to non standard residue FyD (Wed May 16 2012 - 06:19:52 PDT)
    - [AMBER] Coordinate resetting (SHAKE) cannot be accomplished, deviation is too large Urszula Uciechowska (Wed May 16 2012 - 03:26:36 PDT)
    - [AMBER] 1-4 scale factors Urszula Uciechowska (Wed May 16 2012 - 04:01:39 PDT)
    - Re: [AMBER] 1-4 scale factors Lachele Foley (Lists) (Wed May 16 2012 - 10:19:25 PDT)
    - Re: [AMBER] 1-4 scale factors Urszula Uciechowska (Wed May 16 2012 - 22:27:25 PDT)
    - Re: [AMBER] 1-4 scale factors FyD (Wed May 16 2012 - 22:58:27 PDT)
    - Re: [AMBER] 1-4 scale factors Urszula Uciechowska (Thu May 17 2012 - 04:56:50 PDT)
    - Re: [AMBER] 1-4 scale factors FyD (Fri May 18 2012 - 23:30:29 PDT)
    - Re: [AMBER] 1-4 scale factors Karl N. Kirschner (Mon May 21 2012 - 00:31:40 PDT)
    - Re: [AMBER] 1-4 scale factors Jason Swails (Wed May 23 2012 - 02:49:36 PDT)
    - Re: [AMBER] 1-4 scale factors Lachele Foley (Lists) (Thu May 17 2012 - 12:21:01 PDT)
    - Re: [AMBER] 1-4 scale factors FyD (Wed May 16 2012 - 12:30:50 PDT)
    - Re: [AMBER] 1-4 scale factors Urszula Uciechowska (Wed May 16 2012 - 14:49:48 PDT)
    - Re: [AMBER] 1-4 scale factors Lachele Foley (Lists) (Wed May 16 2012 - 15:12:32 PDT)
    - Re: [AMBER] Coordinate resetting (SHAKE) cannot be accomplished, deviation is too large case (Wed May 16 2012 - 15:05:27 PDT)
    - Re: [AMBER] Coordinate resetting (SHAKE) cannot be accomplished, deviation is too large Hai Nguyen (Wed May 16 2012 - 16:04:48 PDT)
[AMBER] is lipid 11 FF compatible with GAFF? Albert (Thu Apr 26 2012 - 09:21:34 PDT)
- Re: [AMBER] is lipid 11 FF compatible with GAFF? Benjamin D Madej (Thu Apr 26 2012 - 11:10:08 PDT)
  - Re: [AMBER] is lipid 11 FF compatible with GAFF? Albert (Thu Apr 26 2012 - 11:30:01 PDT)
[AMBER] Radii in prmtop Jesper Sørensen (Thu Apr 26 2012 - 09:51:48 PDT)
- Re: [AMBER] Radii in prmtop Carlos Simmerling (Thu Apr 26 2012 - 09:55:21 PDT)
  - Re: [AMBER] Radii in prmtop Jesper Sørensen (Thu Apr 26 2012 - 11:06:18 PDT)
    - Re: [AMBER] Radii in prmtop Jason Swails (Thu Apr 26 2012 - 12:18:33 PDT)
    - Re: [AMBER] Radii in prmtop Jesper Sørensen (Thu Apr 26 2012 - 12:56:51 PDT)
    - Re: [AMBER] Radii in prmtop Jason Swails (Thu Apr 26 2012 - 13:24:16 PDT)
    - Re: [AMBER] Radii in prmtop case (Thu Apr 26 2012 - 18:46:26 PDT)
    - Re: [AMBER] Radii in prmtop Jesper Sørensen (Sat Apr 28 2012 - 14:38:30 PDT)
    - Re: [AMBER] Radii in prmtop case (Sat Apr 28 2012 - 19:25:42 PDT)
    - Re: [AMBER] Radii in prmtop Jesper Sørensen (Sun Apr 29 2012 - 11:19:41 PDT)
    - Re: [AMBER] Radii in prmtop case (Sun Apr 29 2012 - 14:48:48 PDT)
    - Re: [AMBER] Radii in prmtop Ray Luo (Sun Apr 29 2012 - 14:52:10 PDT)
    - Re: [AMBER] Radii in prmtop Jesper Sørensen (Sun Apr 29 2012 - 23:42:00 PDT)
    - Re: [AMBER] Radii in prmtop Daniel Roe (Mon Apr 30 2012 - 07:52:38 PDT)
    - Re: [AMBER] Radii in prmtop Jesper Sørensen (Wed May 02 2012 - 07:59:56 PDT)
[AMBER] GTP parameter set for RNA luca codutti (Thu Apr 26 2012 - 11:28:31 PDT)
- Re: [AMBER] GTP parameter set for RNA Jacopo Sgrignani (Thu Apr 26 2012 - 12:28:47 PDT)
  - Re: [AMBER] GTP parameter set for RNA luca codutti (Fri Apr 27 2012 - 01:00:57 PDT)
  - Re: [AMBER] GTP parameter set for RNA luca codutti (Fri Apr 27 2012 - 07:28:22 PDT)
    - Re: [AMBER] GTP parameter set for RNA Jason Swails (Fri Apr 27 2012 - 08:12:20 PDT)
    - Re: [AMBER] GTP parameter set for RNA luca codutti (Fri Apr 27 2012 - 08:22:19 PDT)
[AMBER] GLYCAM 06h and 06EPb Lachele Foley (Lists) (Thu Apr 26 2012 - 11:38:39 PDT)
[AMBER] Creating a concatenated coordinate file for LES Sajeewa Pemasinghe (Thu Apr 26 2012 - 14:38:15 PDT)
[AMBER] Creating a concatenated coordinate file for LES Sajeewa Pemasinghe (Thu Apr 26 2012 - 19:01:22 PDT)
- [AMBER] Fwd: Creating a concatenated coordinate file for LES Sajeewa Pemasinghe (Sun Apr 29 2012 - 06:50:31 PDT)
- Re: [AMBER] Creating a concatenated coordinate file for LES Carlos Simmerling (Mon Apr 30 2012 - 09:24:33 PDT)
[AMBER] Angle restraints Komal Soni (Fri Apr 27 2012 - 06:14:15 PDT)
- Re: [AMBER] Angle restraints David A Case (Fri Apr 27 2012 - 07:10:47 PDT)
[AMBER] Problem with molegro file Chris Chris (Fri Apr 27 2012 - 09:52:31 PDT)
- Re: [AMBER] Problem with molegro file case (Sat Apr 28 2012 - 06:56:19 PDT)
- Re: [AMBER] Problem with molegro file FyD (Sun Apr 29 2012 - 00:16:39 PDT)
[AMBER] IBM compiler for Amber12? Albert (Fri Apr 27 2012 - 10:02:13 PDT)
- [AMBER] calculation mean B factor of a PDB file Acoot Brett (Sat Apr 28 2012 - 02:42:28 PDT)
  - Re: [AMBER] calculation mean B factor of a PDB file Daniel Roe (Sat Apr 28 2012 - 06:36:23 PDT)
[AMBER] amber 12 with intel compiler failed Albert (Fri Apr 27 2012 - 12:34:49 PDT)
- Re: [AMBER] amber 12 with intel compiler failed Jason Swails (Fri Apr 27 2012 - 12:41:17 PDT)
  - Re: [AMBER] amber 12 with intel compiler failed Albert (Fri Apr 27 2012 - 13:13:04 PDT)
  - Re: [AMBER] amber 12 with intel compiler failed Albert (Fri Apr 27 2012 - 13:23:30 PDT)
    - Re: [AMBER] amber 12 with intel compiler failed Jason Swails (Fri Apr 27 2012 - 13:27:17 PDT)
[AMBER] water cap simulation Yi An (Fri Apr 27 2012 - 14:08:03 PDT)
- Re: [AMBER] water cap simulation case (Sat Apr 28 2012 - 07:00:20 PDT)
  - Re: [AMBER] water cap simulation anyiphysics.gmail.com (Mon Apr 30 2012 - 12:48:49 PDT)
[AMBER] Electrostatic potential calculation Sudarshan Debnath (Sat Apr 28 2012 - 05:13:08 PDT)
- Re: [AMBER] Electrostatic potential calculation Ray Luo, Ph.D. (Sat Apr 28 2012 - 21:05:32 PDT)
[AMBER] preparation of silver metal parameter file Navin Jain (Sat Apr 28 2012 - 06:05:40 PDT)
- Re: [AMBER] preparation of silver metal parameter file Jason Swails (Sat Apr 28 2012 - 09:50:45 PDT)
- Re: [AMBER] preparation of silver metal parameter file FyD (Sun Apr 29 2012 - 00:21:13 PDT)
[AMBER] Problems with atom type in sidechain.bcl Fabrício Bracht (Sat Apr 28 2012 - 08:03:21 PDT)
- Re: [AMBER] Problems with atom type in sidechain.bcl ashwini gupta (Sat Apr 28 2012 - 22:15:20 PDT)
[AMBER] multiple GPU compile failed for Amber12 Albert (Sat Apr 28 2012 - 11:13:44 PDT)
- Re: [AMBER] multiple GPU compile failed for Amber12 Jason Swails (Sat Apr 28 2012 - 13:24:42 PDT)
  - Re: [AMBER] multiple GPU compile failed for Amber12 Albert (Sat Apr 28 2012 - 21:24:02 PDT)
[AMBER] calculation parallel xiaojiong (Sat Apr 28 2012 - 17:59:56 PDT)
- Re: [AMBER] calculation parallel Ben Roberts (Sat Apr 28 2012 - 22:58:30 PDT)
[AMBER] the problem of charge xiaojiong (Sat Apr 28 2012 - 18:03:08 PDT)
- Re: [AMBER] the problem of charge Ben Roberts (Sat Apr 28 2012 - 22:52:23 PDT)
- Re: [AMBER] the problem of charge FyD (Sun Apr 29 2012 - 00:40:51 PDT)
  - Re: [AMBER] the problem of charge FyD (Sun Apr 29 2012 - 03:52:45 PDT)
[AMBER] testing amber12 fails Vijay Manickam Achari (Sun Apr 29 2012 - 01:17:47 PDT)
- Re: [AMBER] testing amber12 fails case (Sun Apr 29 2012 - 05:19:58 PDT)
[AMBER] how can apply external force to DNA residues? mehdi bagherpoor (Sun Apr 29 2012 - 01:51:16 PDT)
[AMBER] is there a second methods to use CHARMM FF in amber? Albert (Sun Apr 29 2012 - 22:42:35 PDT)
- Re: [AMBER] is there a second methods to use CHARMM FF in amber? Marc van der Kamp (Mon Apr 30 2012 - 01:20:55 PDT)
  - Re: [AMBER] is there a second methods to use CHARMM FF in amber? Albert (Mon Apr 30 2012 - 12:29:10 PDT)
[AMBER] MPI with options "-ip" and "-axSTPW" kurisaki (Mon Apr 30 2012 - 02:33:37 PDT)
- Re: [AMBER] MPI with options "-ip" and "-axSTPW" Ben Roberts (Mon Apr 30 2012 - 03:10:50 PDT)
  - Re: [AMBER] MPI with options "-ip" and "-axSTPW" kurisaki (Mon Apr 30 2012 - 03:18:22 PDT)
[AMBER] RAMD simulations Agostino Bruno (Mon Apr 30 2012 - 06:54:18 PDT)
- Re: [AMBER] RAMD simulations Vlad Cojocaru (Mon Apr 30 2012 - 07:23:30 PDT)
- Re: [AMBER] RAMD simulations Jacopo Sgrignani (Mon Apr 30 2012 - 07:28:21 PDT)
[AMBER] input format for qms Genzo Tanaka (Mon Apr 30 2012 - 09:16:36 PDT)
- Re: [AMBER] input format for qms Genzo Tanaka (Mon Apr 30 2012 - 20:48:39 PDT)
  - Re: [AMBER] input format for qms Jason Swails (Tue May 01 2012 - 03:26:27 PDT)
[AMBER] error in decomposition analysis using ambertools 1.5 manikanthan bhavaraju (Mon Apr 30 2012 - 14:25:30 PDT)
- Re: [AMBER] error in decomposition analysis using ambertools 1.5 Jason Swails (Mon Apr 30 2012 - 15:11:46 PDT)
  - Re: [AMBER] error in decomposition analysis using ambertools 1.5 manikanthan bhavaraju (Mon Apr 30 2012 - 16:09:07 PDT)
    - Re: [AMBER] error in decomposition analysis using ambertools 1.5 Jason Swails (Mon Apr 30 2012 - 17:12:49 PDT)
    - Re: [AMBER] error in decomposition analysis using ambertools 1.5 manikanthan bhavaraju (Mon Apr 30 2012 - 18:13:24 PDT)
    - Re: [AMBER] error in decomposition analysis using ambertools 1.5 Jason Swails (Tue May 01 2012 - 08:41:05 PDT)
    - Re: [AMBER] error in decomposition analysis using ambertools 1.5 Kumar, Sonu (Wed May 02 2012 - 03:46:08 PDT)
    - Re: [AMBER] error in decomposition analysis using ambertools 1.5 Jason Swails (Wed May 02 2012 - 12:57:39 PDT)
    - Re: [AMBER] error in decomposition analysis using ambertools 1.5 Kumar, Sonu (Wed May 02 2012 - 14:13:10 PDT)
    - Re: [AMBER] error in decomposition analysis using ambertools 1.5 Jason Swails (Wed May 02 2012 - 16:42:23 PDT)
Re: [AMBER] FW: FW: reduce and trim function Mahendra B Thapa (Mon Apr 30 2012 - 15:17:58 PDT)
[AMBER] getting metal ions coordinates of nmr structures of a protein Mahendra B Thapa (Mon Apr 30 2012 - 16:11:36 PDT)
- Re: [AMBER] getting metal ions coordinates of nmr structures of a protein Daniel Sindhikara (Mon Apr 30 2012 - 18:48:44 PDT)
[AMBER] Some problem with building Non-standard residue Nicholus Bhattacharjee (Tue May 01 2012 - 04:43:49 PDT)
- Re: [AMBER] Some problem with building Non-standard residue FyD (Wed May 02 2012 - 02:25:32 PDT)
  - Re: [AMBER] Some problem with building Non-standard residue Nicholus Bhattacharjee (Thu May 03 2012 - 23:04:29 PDT)
    - Re: [AMBER] Some problem with building Non-standard residue FyD (Fri May 04 2012 - 06:14:49 PDT)
[AMBER] anisotropic pressure in bilayer simulation Vijay Manickam Achari (Wed May 02 2012 - 04:26:22 PDT)
- Re: [AMBER] anisotropic pressure in bilayer simulation Ross Walker (Wed May 02 2012 - 06:31:18 PDT)
  - Re: [AMBER] anisotropic pressure in bilayer simulation Benjamin D Madej (Wed May 02 2012 - 09:11:21 PDT)
[AMBER] what's the difference between sandar.MPI and sander.LES.MPI ? Albert (Wed May 02 2012 - 05:26:45 PDT)
- Re: [AMBER] what's the difference between sandar.MPI and sander.LES.MPI ? Ross Walker (Wed May 02 2012 - 05:40:08 PDT)
[AMBER] Electrostatic potential calculation Sudarshan Debnath (Wed May 02 2012 - 05:54:08 PDT)
- [AMBER] Fwd: Electrostatic potential calculation Ray Luo, Ph.D. (Wed May 02 2012 - 10:13:00 PDT)
  - Re: [AMBER] Electrostatic potential calculation Qin Cai (Wed May 02 2012 - 13:06:21 PDT)
[AMBER] Umbrella sampling using GPU acceleration Massimiliano Porrini (Wed May 02 2012 - 06:22:41 PDT)
- Re: [AMBER] Umbrella sampling using GPU acceleration Ross Walker (Wed May 02 2012 - 06:28:35 PDT)
[AMBER] Energy Differences between mmpbsa_py_energy and sander outputs Damodaran, Komath (Wed May 02 2012 - 13:45:36 PDT)
[AMBER] RESP structure optimization for larger ligand Robin Betz (Wed May 02 2012 - 15:44:09 PDT)
- Re: [AMBER] RESP structure optimization for larger ligand Dean Cuebas (Thu May 03 2012 - 09:19:42 PDT)
- Re: [AMBER] RESP structure optimization for larger ligand FyD (Fri May 04 2012 - 01:33:40 PDT)
[AMBER] a question about ensemble Albert (Wed May 02 2012 - 22:33:10 PDT)
- Re: [AMBER] a question about ensemble Benjamin D Madej (Thu May 03 2012 - 12:40:14 PDT)
- Re: [AMBER] a question about ensemble case (Thu May 03 2012 - 12:40:57 PDT)
[AMBER] Max Pairlist Cutoff issue Agostino Bruno (Wed May 02 2012 - 23:50:35 PDT)
- Re: [AMBER] Max Pairlist Cutoff issue Aron Broom (Thu May 03 2012 - 09:06:30 PDT)
  - Re: [AMBER] Max Pairlist Cutoff issue Ben Roberts (Sat May 05 2012 - 23:16:48 PDT)
[AMBER] adding/deleting water molecules in leap Bala subramanian (Thu May 03 2012 - 04:33:13 PDT)
- Re: [AMBER] adding/deleting water molecules in leap Simon Becker (Thu May 03 2012 - 04:56:05 PDT)
- Re: [AMBER] adding/deleting water molecules in leap Jason Swails (Thu May 03 2012 - 15:59:55 PDT)
  - Re: [AMBER] adding/deleting water molecules in leap Jason Swails (Thu May 03 2012 - 18:15:23 PDT)
[AMBER] CHAMBER with RNA Sean Law (Thu May 03 2012 - 08:16:22 PDT)
- Re: [AMBER] CHAMBER with RNA Mark Williamson (Tue May 08 2012 - 04:11:15 PDT)
  - Re: [AMBER] CHAMBER with RNA BERGY (Fri Jun 29 2012 - 00:28:15 PDT)
[AMBER] Amber 11, Amber-Tools 1.5 and Amber-Tools 12 respgen Bug Marko Wehle (Thu May 03 2012 - 09:58:07 PDT)
- Re: [AMBER] Amber 11, Amber-Tools 1.5 and Amber-Tools 12 respgen Bug FyD (Fri May 04 2012 - 01:04:13 PDT)
- Re: [AMBER] Amber 11, Amber-Tools 1.5 and Amber-Tools 12 respgen Bug Marko Wehle (Fri May 04 2012 - 08:38:18 PDT)
  - Re: [AMBER] Amber 11, Amber-Tools 1.5 and Amber-Tools 12 respgen Bug FyD (Sat May 05 2012 - 01:15:31 PDT)
  - Re: [AMBER] Amber 11, Amber-Tools 1.5 and Amber-Tools 12 respgen Bug case (Sat May 05 2012 - 06:28:02 PDT)
[AMBER] Building Amber 12 & python Shaw, Sharon (Thu May 03 2012 - 12:58:17 PDT)
- Re: [AMBER] Building Amber 12 & python case (Thu May 03 2012 - 13:57:58 PDT)
  - Re: [AMBER] Building Amber 12 & python Shaw, Sharon (Fri May 04 2012 - 11:59:30 PDT)
[AMBER] MCPB espgen error Fabrício Bracht (Thu May 03 2012 - 14:00:58 PDT)
- [AMBER] MCPB espgen error Fabrício Bracht (Mon May 07 2012 - 07:19:36 PDT)
  - Re: [AMBER] MCPB espgen error Ben Roberts (Mon May 07 2012 - 13:28:56 PDT)
    - Re: [AMBER] MCPB espgen error Fabrício Bracht (Mon May 07 2012 - 13:36:52 PDT)
  - Re: [AMBER] MCPB espgen error FyD (Mon May 07 2012 - 13:56:55 PDT)
    - Re: [AMBER] MCPB espgen error Fabrício Bracht (Mon May 07 2012 - 21:12:44 PDT)
    - Re: [AMBER] MCPB espgen error Robin Betz (Tue May 08 2012 - 11:23:36 PDT)
    - Re: [AMBER] MCPB espgen error Fabrício Bracht (Wed May 09 2012 - 05:40:14 PDT)
    - Re: [AMBER] MCPB espgen error Fabrício Bracht (Thu May 10 2012 - 05:40:56 PDT)
    - Re: [AMBER] MCPB espgen error Robin Betz (Mon May 14 2012 - 17:14:35 PDT)
    - Re: [AMBER] MCPB espgen error Fabrício Bracht (Tue May 15 2012 - 10:27:05 PDT)
    - Re: [AMBER] MCPB espgen error Fabrício Bracht (Sat May 19 2012 - 07:18:02 PDT)
    - Re: [AMBER] MCPB espgen error FyD (Sat May 19 2012 - 08:52:14 PDT)
    - Re: [AMBER] MCPB espgen error Fabrício Bracht (Tue May 29 2012 - 19:54:48 PDT)
    - Re: [AMBER] MCPB espgen error FyD (Tue May 29 2012 - 22:42:39 PDT)
    - Re: [AMBER] MCPB espgen error Fabrício Bracht (Thu May 31 2012 - 09:42:14 PDT)
    - Re: [AMBER] MCPB espgen error FyD (Thu May 31 2012 - 12:37:52 PDT)
[AMBER] am1d problem Gabriel Jara (Thu May 03 2012 - 15:10:38 PDT)
- Re: [AMBER] am1d problem Andreas Goetz (Mon May 07 2012 - 13:40:35 PDT)
- Re: [AMBER] am1d problem Gabriel Jara (Fri May 11 2012 - 17:36:47 PDT)
  - Re: [AMBER] am1d problem Andreas Goetz (Sat May 12 2012 - 03:15:37 PDT)
- Re: [AMBER] am1d problem Gabriel Jara (Wed May 16 2012 - 18:02:25 PDT)
  - Re: [AMBER] am1d problem Brian Radak (Wed May 30 2012 - 19:15:48 PDT)
- Re: [AMBER] am1d problem Gabriel Jara (Fri Jun 01 2012 - 07:21:04 PDT)
[AMBER] Fwd: question pooja chahal (Thu May 03 2012 - 22:15:23 PDT)
- Re: [AMBER] Fwd: question David A Case (Fri May 04 2012 - 05:09:06 PDT)
[AMBER] question pooja chahal (Thu May 03 2012 - 22:16:58 PDT)
- Re: [AMBER] question mish (Thu May 03 2012 - 22:49:22 PDT)
- Re: [AMBER] question steinbrt.rci.rutgers.edu (Fri May 04 2012 - 00:24:38 PDT)
[AMBER] ptraj closest water script problem Andre Serobian (Fri May 04 2012 - 02:32:21 PDT)
- Re: [AMBER] ptraj closest water script problem Thomas Cheatham (Fri May 04 2012 - 02:39:28 PDT)
  - [AMBER] mmpbsa problem . mirage (Fri May 04 2012 - 03:01:47 PDT)
    - Re: [AMBER] mmpbsa problem Ray Luo, Ph.D. (Fri May 04 2012 - 06:27:03 PDT)
  - Re: [AMBER] ptraj closest water script problem Daniel Roe (Fri May 04 2012 - 03:39:28 PDT)
    - Re: [AMBER] ptraj closest water script problem Andre Serobian (Sun May 06 2012 - 20:59:26 PDT)
[AMBER] Why not AmberTools12 bugfix.all Alan (Fri May 04 2012 - 04:15:37 PDT)
- Re: [AMBER] Why not AmberTools12 bugfix.all Alan (Fri May 04 2012 - 04:25:01 PDT)
  - Re: [AMBER] Why not AmberTools12 bugfix.all Jason Swails (Fri May 04 2012 - 06:21:02 PDT)
[AMBER] add H-atoms automatic in tleap Zhou Gong (Fri May 04 2012 - 07:52:34 PDT)
- Re: [AMBER] add H-atoms automatic in tleap David A Case (Fri May 04 2012 - 11:39:45 PDT)
  - [AMBER] 答复: add H-atoms automatic in tleap Zhou Gong (Sat May 05 2012 - 07:59:16 PDT)
    - Re: [AMBER] 答复: add H-atoms automatic in tleap case (Sat May 05 2012 - 18:41:53 PDT)
    - [AMBER] 答复: 答复: add H-atoms automatic in tleap Zhou Gong (Sat May 05 2012 - 19:06:01 PDT)
    - Re: [AMBER] : add H-atoms automatic in tleap FyD (Sun May 06 2012 - 01:40:00 PDT)
    - Re: [AMBER] 答复: 答复: add H-atoms automatic in tleap case (Sun May 06 2012 - 04:48:39 PDT)
    - [AMBER] 答复: 答复: 答复: add H-atoms automatic in tleap Zhou Gong (Sun May 06 2012 - 07:47:16 PDT)
[AMBER] A1. Conversion of Gaussian output into mol 2 file Debolina Mitra (Sun May 06 2012 - 06:23:51 PDT)
- Re: [AMBER] A1. Conversion of Gaussian output into mol 2 file case (Sun May 06 2012 - 08:17:23 PDT)
- Re: [AMBER] A1. Conversion of Gaussian output into mol 2 file Nadine Homeyer (Sun May 06 2012 - 23:23:55 PDT)
- Re: [AMBER] A1. Conversion of Gaussian output into mol 2 file FyD (Sun May 06 2012 - 23:49:50 PDT)
[AMBER] Decoupling of the restrained ligand using Thermodynamic Integration in Amber ? Marek Maly (Sun May 06 2012 - 18:26:46 PDT)
- Re: [AMBER] Decoupling of the restrained ligand using Thermodynamic Integration in Amber ? steinbrt.rci.rutgers.edu (Mon May 07 2012 - 00:49:31 PDT)
  - Re: [AMBER] Decoupling of the restrained ligand using Thermodynamic Integration in Amber ? Marek Maly (Mon May 07 2012 - 08:05:03 PDT)
    - Re: [AMBER] Decoupling of the restrained ligand using Thermodynamic Integration in Amber ? steinbrt.rci.rutgers.edu (Tue May 08 2012 - 09:40:14 PDT)
    - Re: [AMBER] Decoupling of the restrained ligand using Thermodynamic Integration in Amber ? Marek Maly (Wed May 09 2012 - 07:38:11 PDT)
    - Re: [AMBER] Decoupling of the restrained ligand using Thermodynamic Integration in Amber ? steinbrt.rci.rutgers.edu (Wed May 09 2012 - 08:08:52 PDT)
    - Re: [AMBER] Decoupling of the restrained ligand using Thermodynamic Integration in Amber ? Marek Maly (Wed May 09 2012 - 08:43:13 PDT)
    - Re: [AMBER] Decoupling of the restrained ligand using Thermodynamic Integration in Amber ? steinbrt.rci.rutgers.edu (Thu May 10 2012 - 00:33:34 PDT)
    - Re: [AMBER] Decoupling of the restrained ligand using Thermodynamic Integration in Amber ? Marek Maly (Thu May 10 2012 - 15:32:02 PDT)
    - Re: [AMBER] Visualizing ptraj eigenvectors steinbrt.rci.rutgers.edu (Tue May 22 2012 - 02:57:28 PDT)
[AMBER] include/fftw3.h(370): error: identifier "__float128" is undefined Mark Rance (Sun May 06 2012 - 20:56:45 PDT)
- Re: [AMBER] include/fftw3.h(370): error: identifier "__float128" is undefined David A Case (Mon May 07 2012 - 05:10:00 PDT)
  - Re: [AMBER] include/fftw3.h(370): error: identifier "__float128" is undefined tluchko (Fri May 11 2012 - 08:13:31 PDT)
    - Re: [AMBER] include/fftw3.h(370): error: identifier "__float128" is undefined Mark Rance (Fri May 11 2012 - 12:51:48 PDT)
    - Re: [AMBER] include/fftw3.h(370): error: identifier "__float128" is undefined David A Case (Fri May 11 2012 - 13:07:17 PDT)
    - Re: [AMBER] include/fftw3.h(370): error: identifier "__float128" is undefined Mark Rance (Fri May 11 2012 - 14:52:52 PDT)
    - Re: [AMBER] include/fftw3.h(370): error: identifier "__float128" is undefined Jason Swails (Fri May 11 2012 - 16:22:44 PDT)
    - Re: [AMBER] include/fftw3.h(370): error: identifier "__float128" is undefined Mark Rance (Sun May 13 2012 - 15:56:07 PDT)
    - Re: [AMBER] include/fftw3.h(370): error: identifier "__float128" is undefined Jason Swails (Sun May 13 2012 - 19:21:32 PDT)
    - Re: [AMBER] include/fftw3.h(370): error: identifier "__float128" is undefined Mark Rance (Mon May 14 2012 - 12:07:59 PDT)
    - Re: [AMBER] include/fftw3.h(370): error: identifier "__float128" is undefined tluchko (Mon May 14 2012 - 13:36:12 PDT)
[AMBER] strange CUDA MD output in VMD Albert (Sun May 06 2012 - 23:22:41 PDT)
- Re: [AMBER] strange CUDA MD output in VMD Daniel Roe (Mon May 07 2012 - 04:52:52 PDT)
  - Re: [AMBER] strange CUDA MD output in VMD Albert (Mon May 07 2012 - 06:52:57 PDT)
[AMBER] MMPBSA calculation of large proteins Jyotsna Bhat (Sun May 06 2012 - 23:58:16 PDT)
- Re: [AMBER] MMPBSA calculation of large proteins Jason Swails (Mon May 07 2012 - 07:14:04 PDT)
  - Re: [AMBER] MMPBSA calculation of large proteins Jyotsna Bhat (Mon May 07 2012 - 09:31:30 PDT)
    - Re: [AMBER] MMPBSA calculation of large proteins Ray Luo, Ph.D. (Mon May 07 2012 - 10:15:32 PDT)
    - Re: [AMBER] MMPBSA calculation of large proteins Jyotsna Bhat (Tue May 08 2012 - 03:02:40 PDT)
    - Re: [AMBER] MMPBSA calculation of large proteins Ray Luo, Ph.D. (Tue May 08 2012 - 09:39:13 PDT)
    - Re: [AMBER] MMPBSA calculation of large proteins Jyotsna Bhat (Tue May 08 2012 - 22:05:21 PDT)
    - Re: [AMBER] MMPBSA calculation of large proteins Bill Miller III (Wed May 09 2012 - 06:07:18 PDT)
    - Re: [AMBER] MMPBSA calculation of large proteins Jyotsna Bhat (Wed May 09 2012 - 07:57:49 PDT)
    - Re: [AMBER] MMPBSA calculation of large proteins Ray Luo (Wed May 09 2012 - 09:51:04 PDT)
[AMBER] Homotrimeric structure not holding together during equilibration steps an MD simulations. Emilio Lence (Mon May 07 2012 - 03:38:47 PDT)
- Re: [AMBER] Homotrimeric structure not holding together during equilibration steps an MD simulations. Carlos Simmerling (Mon May 07 2012 - 04:13:54 PDT)
[AMBER] PLEASE GIVE SOME SUGGESTION jit mukherjee (Mon May 07 2012 - 05:14:44 PDT)
- Re: [AMBER] PLEASE GIVE SOME SUGGESTION steinbrt.rci.rutgers.edu (Mon May 07 2012 - 06:02:06 PDT)
  - Re: [AMBER] PLEASE GIVE SOME SUGGESTION jit mukherjee (Mon May 07 2012 - 10:08:21 PDT)
    - Re: [AMBER] PLEASE GIVE SOME SUGGESTION David A Case (Mon May 07 2012 - 10:40:14 PDT)
    - Re: [AMBER] PLEASE GIVE SOME SUGGESTION jit mukherjee (Mon May 07 2012 - 13:10:04 PDT)
    - Re: [AMBER] PLEASE GIVE SOME SUGGESTION jit mukherjee (Mon May 07 2012 - 19:18:18 PDT)
    - Re: [AMBER] PLEASE GIVE SOME SUGGESTION David A Case (Tue May 08 2012 - 05:19:32 PDT)
    - Re: [AMBER] PLEASE GIVE SOME SUGGESTION jit mukherjee (Tue May 08 2012 - 20:40:48 PDT)
    - Re: [AMBER] PLEASE GIVE SOME SUGGESTION steinbrt.rci.rutgers.edu (Wed May 09 2012 - 00:55:07 PDT)
- Re: [AMBER] PLEASE GIVE SOME SUGGESTION Jyotsna Bhat (Mon May 07 2012 - 21:25:48 PDT)
[AMBER] intel compiler still doesn't work for MPI Albert (Mon May 07 2012 - 12:09:37 PDT)
- Re: [AMBER] intel compiler still doesn't work for MPI Jason Swails (Mon May 07 2012 - 12:43:06 PDT)
  - Re: [AMBER] intel compiler still doesn't work for MPI Albert (Mon May 07 2012 - 13:07:21 PDT)
[AMBER] error when using PMEMD Chris Chris (Mon May 07 2012 - 12:22:06 PDT)
- Re: [AMBER] error when using PMEMD Jason Swails (Mon May 07 2012 - 12:44:00 PDT)
[AMBER] CUDA running error Albert (Mon May 07 2012 - 13:31:15 PDT)
- [AMBER] CUDA running error Albert (Mon May 07 2012 - 22:19:07 PDT)
  - Re: [AMBER] CUDA running error Ross Walker (Tue May 08 2012 - 09:57:24 PDT)
    - Re: [AMBER] CUDA running error Albert (Tue May 08 2012 - 10:11:31 PDT)
    - Re: [AMBER] CUDA running error Ross Walker (Tue May 08 2012 - 10:24:30 PDT)
    - Re: [AMBER] CUDA running error Albert (Tue May 08 2012 - 10:41:44 PDT)
    - Re: [AMBER] CUDA running error Ross Walker (Tue May 08 2012 - 10:48:52 PDT)
    - Re: [AMBER] CUDA running error Albert (Tue May 08 2012 - 10:50:56 PDT)
[AMBER] error with torus in ffgbsa Charlotte Siska (Mon May 07 2012 - 15:31:29 PDT)
- Re: [AMBER] error with torus in ffgbsa case (Mon May 07 2012 - 18:26:16 PDT)
[AMBER] About the system temperature of QMMM simulations (amber12+ Terachem V1.5 ) Yeng-Tseng Wang (Mon May 07 2012 - 18:05:55 PDT)
- Re: [AMBER] About the system temperature of QMMM simulations (amber12+ Terachem V1.5 ) Brian Radak (Tue May 08 2012 - 05:32:07 PDT)
  - Re: [AMBER] About the system temperature of QMMM simulations (amber12+ Terachem V1.5 ) c00jsw00.nchc.narl.org.tw (Tue May 08 2012 - 10:35:41 PDT)
    - Re: [AMBER] About the system temperature of QMMM simulations (amber12+ Terachem V1.5 ) Brian Radak (Tue May 08 2012 - 11:10:50 PDT)
    - Re: [AMBER] About the system temperature of QMMM simulations (amber12+ Terachem V1.5 ) Yeng-Tseng Wang (Wed May 16 2012 - 01:59:15 PDT)
[AMBER] help with pmemd .in file Chris Chris (Mon May 07 2012 - 18:15:58 PDT)
- Re: [AMBER] help with pmemd .in file Niel Henriksen (Mon May 07 2012 - 18:24:09 PDT)
- Re: [AMBER] help with pmemd .in file Jason Swails (Mon May 07 2012 - 18:27:58 PDT)
  - Re: [AMBER] help with pmemd .in file Chris Chris (Mon May 07 2012 - 18:30:43 PDT)
  - Re: [AMBER] help with pmemd .in file Chris Chris (Mon May 07 2012 - 18:43:13 PDT)
    - Re: [AMBER] help with pmemd .in file Niel Henriksen (Mon May 07 2012 - 18:52:49 PDT)
    - Re: [AMBER] help with pmemd .in file David A Case (Tue May 08 2012 - 05:15:36 PDT)
    - Re: [AMBER] help with pmemd .in file Chris Chris (Tue May 08 2012 - 09:23:17 PDT)
    - Re: [AMBER] help with pmemd .in file Ross Walker (Tue May 08 2012 - 09:42:36 PDT)
    - Re: [AMBER] help with pmemd .in file Chris Chris (Tue May 08 2012 - 21:49:28 PDT)
[AMBER] About the system temperature of QMMM simulations (amber12+ Terachem V1.5 ) c00jsw00.nchc.narl.org.tw (Mon May 07 2012 - 10:20:07 PDT)
[AMBER] Sander Error Melissa Buskes (Mon May 07 2012 - 22:27:40 PDT)
- Re: [AMBER] Sander Error David A Case (Tue May 08 2012 - 05:25:04 PDT)
- [AMBER] Sander Error Melissa Buskes (Tue May 08 2012 - 16:19:03 PDT)
  - Re: [AMBER] Sander Error Ben Roberts (Tue May 08 2012 - 16:47:58 PDT)
[AMBER] CUDA test failed Albert (Mon May 07 2012 - 23:44:15 PDT)
[AMBER] strange CUDA benchmark Albert (Tue May 08 2012 - 01:36:01 PDT)
- Re: [AMBER] strange CUDA benchmark Ross Walker (Tue May 08 2012 - 09:50:51 PDT)
  - Re: [AMBER] strange CUDA benchmark Albert (Tue May 08 2012 - 10:01:43 PDT)
    - Re: [AMBER] strange CUDA benchmark Jason Swails (Tue May 08 2012 - 10:10:35 PDT)
    - Re: [AMBER] strange CUDA benchmark Albert (Tue May 08 2012 - 10:14:44 PDT)
[AMBER] apply an external force between two residue mehdi bagherpoor (Tue May 08 2012 - 02:08:04 PDT)
[AMBER] high value in MMPBSA xiaojiong (Tue May 08 2012 - 02:34:20 PDT)
- Re: [AMBER] high value in MMPBSA Bill Miller III (Tue May 08 2012 - 04:51:08 PDT)
- Re: [AMBER] high value in MMPBSA 21119012 (Tue May 08 2012 - 08:56:12 PDT)
- Re: [AMBER] high value in MMPBSA Ray Luo, Ph.D. (Tue May 08 2012 - 09:43:49 PDT)
[AMBER] charmmlipid2amber.x error Albert (Tue May 08 2012 - 02:39:37 PDT)
- Re: [AMBER] charmmlipid2amber.x error David A Case (Tue May 08 2012 - 05:28:11 PDT)
  - Re: [AMBER] charmmlipid2amber.x error Albert (Tue May 08 2012 - 05:32:52 PDT)
  - Re: [AMBER] charmmlipid2amber.x error Albert (Tue May 08 2012 - 06:47:47 PDT)
    - Re: [AMBER] charmmlipid2amber.x error Ross Walker (Tue May 08 2012 - 09:46:18 PDT)
    - Re: [AMBER] charmmlipid2amber.x error Albert (Tue May 08 2012 - 10:06:00 PDT)
- Re: [AMBER] charmmlipid2amber.x error Benjamin D Madej (Tue May 08 2012 - 11:36:14 PDT)
  - Re: [AMBER] charmmlipid2amber.x error Albert (Tue May 08 2012 - 11:47:17 PDT)
  - Re: [AMBER] charmmlipid2amber.x error Albert (Tue May 08 2012 - 11:58:31 PDT)
    - Re: [AMBER] charmmlipid2amber.x error Benjamin D Madej (Tue May 08 2012 - 12:10:39 PDT)
    - Re: [AMBER] charmmlipid2amber.x error Albert (Tue May 08 2012 - 12:25:06 PDT)
    - Re: [AMBER] charmmlipid2amber.x error Benjamin D Madej (Tue May 08 2012 - 12:44:40 PDT)
    - Re: [AMBER] charmmlipid2amber.x error Albert (Wed May 09 2012 - 02:00:46 PDT)
    - Re: [AMBER] charmmlipid2amber.x error Albert (Wed May 09 2012 - 02:01:37 PDT)
    - Re: [AMBER] charmmlipid2amber.x error Albert (Wed May 09 2012 - 02:23:22 PDT)
    - Re: [AMBER] charmmlipid2amber.x error David A Case (Wed May 09 2012 - 04:43:52 PDT)
    - Re: [AMBER] charmmlipid2amber.x error Albert (Wed May 09 2012 - 05:55:20 PDT)
[AMBER] job terminate abnormally Albert (Tue May 08 2012 - 07:16:25 PDT)
- Re: [AMBER] job terminate abnormally Marc van der Kamp (Tue May 08 2012 - 07:27:54 PDT)
  - Re: [AMBER] job terminate abnormally Jason Swails (Tue May 08 2012 - 07:30:24 PDT)
    - Re: [AMBER] job terminate abnormally Jason Swails (Tue May 08 2012 - 07:37:51 PDT)
    - Re: [AMBER] job terminate abnormally Albert (Tue May 08 2012 - 08:03:48 PDT)
[AMBER] Error while loading file in VMD kirtana S (Tue May 08 2012 - 07:26:42 PDT)
[AMBER] error in SMD mehdi bagherpoor (Tue May 08 2012 - 08:41:56 PDT)
- Re: [AMBER] error in SMD David A Case (Tue May 08 2012 - 10:01:14 PDT)
- Re: [AMBER] error in SMD mehdi bagherpoor (Tue May 08 2012 - 23:15:22 PDT)
[AMBER] non-polar solvation energies decomposed in PB Qiong Zhang (Tue May 08 2012 - 09:19:22 PDT)
- Re: [AMBER] non-polar solvation energies decomposed in PB Jason Swails (Tue May 08 2012 - 12:26:27 PDT)
  - Re: [AMBER] non-polar solvation energies decomposed in PB Qiong Zhang (Tue May 08 2012 - 13:16:10 PDT)
[AMBER] Zinc ion with five coordination bonds Jagur Lambix (Tue May 08 2012 - 10:53:19 PDT)
- [AMBER] Zinc ion with five coordination bonds Jagur Lambix (Tue May 08 2012 - 13:15:10 PDT)
  - Re: [AMBER] Zinc ion with five coordination bonds FyD (Wed May 09 2012 - 04:31:25 PDT)
[AMBER] inconsistent results in MMPBSA w/o energy decomposition Victor Ma (Tue May 08 2012 - 11:29:53 PDT)
- Re: [AMBER] inconsistent results in MMPBSA w/o energy decomposition Bill Miller III (Tue May 08 2012 - 11:35:48 PDT)
  - Re: [AMBER] inconsistent results in MMPBSA w/o energy decomposition Victor Ma (Tue May 08 2012 - 11:50:12 PDT)
- Re: [AMBER] inconsistent results in MMPBSA w/o energy decomposition Jason Swails (Tue May 08 2012 - 11:42:04 PDT)
  - Re: [AMBER] inconsistent results in MMPBSA w/o energy decomposition Victor Ma (Tue May 08 2012 - 11:52:19 PDT)
    - Re: [AMBER] inconsistent results in MMPBSA w/o energy decomposition Bill Miller III (Tue May 08 2012 - 11:56:52 PDT)
[AMBER] Purchasing -challenged researcher seeks help on GPU purchase David Cowburn (Tue May 08 2012 - 11:50:12 PDT)
- Re: [AMBER] Purchasing -challenged researcher seeks help on GPU purchase Ross Walker (Tue May 08 2012 - 11:58:11 PDT)
[AMBER] qmmmmask Jacopo Sgrignani (Tue May 08 2012 - 13:45:16 PDT)
- Re: [AMBER] qmmmmask Ben Roberts (Tue May 08 2012 - 14:20:07 PDT)
  - Re: [AMBER] qmmmmask Brian Radak (Wed May 09 2012 - 11:21:04 PDT)
    - Re: [AMBER] qmmmmask Jacopo Sgrignani (Wed May 09 2012 - 11:49:59 PDT)
[AMBER] remd simulation Nadeem Ahmad Vellore (Tue May 08 2012 - 15:43:15 PDT)
- Re: [AMBER] remd simulation Carlos Simmerling (Wed May 09 2012 - 04:56:40 PDT)
  - Re: [AMBER] remd simulation Daniel Roe (Wed May 09 2012 - 05:26:34 PDT)
[AMBER] vdW parameters for cations Jesper Sørensen (Tue May 08 2012 - 22:20:57 PDT)
- Re: [AMBER] vdW parameters for cations Jesper Sørensen (Wed May 09 2012 - 10:58:37 PDT)
[AMBER] SA Bomb in sa_arc(): Allocation aborted jyoti alyan (Tue May 08 2012 - 23:53:50 PDT)
- Re: [AMBER] SA Bomb in sa_arc(): Allocation aborted Bill Miller III (Wed May 09 2012 - 06:08:50 PDT)
  - Re: [AMBER] SA Bomb in sa_arc(): Allocation aborted Ray Luo, Ph.D. (Wed May 09 2012 - 09:29:31 PDT)
[AMBER] My email Asma Abro 28-FBAS/MSBI/F09 (Wed May 09 2012 - 00:32:21 PDT)
[AMBER] bug.7 for Amber 12 has some problem Albert (Wed May 09 2012 - 02:52:06 PDT)
- Re: [AMBER] bug.7 for Amber 12 has some problem Jason Swails (Wed May 09 2012 - 04:13:17 PDT)
  - Re: [AMBER] bug.7 for Amber 12 has some problem Albert (Wed May 09 2012 - 05:42:53 PDT)
[AMBER] how to specify CUDA devices? Albert (Wed May 09 2012 - 05:47:44 PDT)
- Re: [AMBER] how to specify CUDA devices? Jason Swails (Wed May 09 2012 - 06:36:10 PDT)
[AMBER] Problems doing MD on protein complex Chris Chris (Wed May 09 2012 - 08:29:22 PDT)
- Re: [AMBER] Problems doing MD on protein complex Dean Cuebas (Wed May 09 2012 - 11:40:26 PDT)
  - Re: [AMBER] Problems doing MD on protein complex Chris Chris (Wed May 09 2012 - 14:58:45 PDT)
[AMBER] how much dyne/cm should we use for lipids? Albert (Wed May 09 2012 - 08:54:49 PDT)
[AMBER] Question on Entropy and MMPBSA calculation Kumar, Sonu (Wed May 09 2012 - 09:09:57 PDT)
- Re: [AMBER] Question on Entropy and MMPBSA calculation Jason Swails (Wed May 09 2012 - 12:18:58 PDT)
[AMBER] Zinc ion with five coordination bonds Jagur Lambix (Wed May 09 2012 - 09:58:21 PDT)
[AMBER] different files for protein-protein complex? Asmita Gupta (Wed May 09 2012 - 10:09:12 PDT)
[AMBER] is NPAT available in Amber 12? Albert (Wed May 09 2012 - 10:57:56 PDT)
[AMBER] job error Albert (Wed May 09 2012 - 12:07:58 PDT)
- Re: [AMBER] job error Jason Swails (Wed May 09 2012 - 12:26:44 PDT)
  - Re: [AMBER] job error Albert (Wed May 09 2012 - 12:36:26 PDT)
    - Re: [AMBER] job error Jason Swails (Wed May 09 2012 - 12:41:17 PDT)
    - Re: [AMBER] job error Albert (Wed May 09 2012 - 12:48:36 PDT)
    - Re: [AMBER] job error David A Case (Wed May 09 2012 - 13:31:01 PDT)
    - Re: [AMBER] job error Bill Ross (Wed May 09 2012 - 13:36:27 PDT)
    - Re: [AMBER] job error Albert (Wed May 09 2012 - 23:27:49 PDT)
    - Re: [AMBER] job error Marc van der Kamp (Thu May 10 2012 - 00:30:16 PDT)
    - Re: [AMBER] job error Albert (Thu May 10 2012 - 00:33:02 PDT)
    - Re: [AMBER] job error Albert (Thu May 10 2012 - 00:40:15 PDT)
    - Re: [AMBER] job error Marc van der Kamp (Thu May 10 2012 - 01:19:35 PDT)
    - Re: [AMBER] job error Bill Ross (Wed May 09 2012 - 13:29:33 PDT)
[AMBER] MM-RISM and per residue energy decomposition Lucas A. Defelipe (Wed May 09 2012 - 13:30:16 PDT)
- Re: [AMBER] MM-RISM and per residue energy decomposition Dwight McGee (Wed May 09 2012 - 13:40:00 PDT)
[AMBER] Energy Differences between mmpbsa_py_energy and sander outputs (reposting) Damodaran, Komath (Wed May 09 2012 - 16:01:16 PDT)
- Re: [AMBER] Energy Differences between mmpbsa_py_energy and sander outputs (reposting) Bill Miller III (Fri May 11 2012 - 08:19:43 PDT)
[AMBER] question about cpptraj surf command Sidney Elmer (Wed May 09 2012 - 17:33:25 PDT)
- Re: [AMBER] question about cpptraj surf command Daniel Roe (Wed May 09 2012 - 17:41:29 PDT)
  - Re: [AMBER] question about cpptraj surf command Sidney Elmer (Wed May 09 2012 - 17:56:37 PDT)
    - Re: [AMBER] question about cpptraj surf command Daniel Roe (Thu May 10 2012 - 06:44:01 PDT)
[AMBER] how to assign SS bond? Albert (Thu May 10 2012 - 00:05:00 PDT)
- Re: [AMBER] how to assign SS bond? Albert (Thu May 10 2012 - 00:13:03 PDT)
[AMBER] Umbrella sampling mehdi bagherpoor (Thu May 10 2012 - 00:58:48 PDT)
- Re: [AMBER] Umbrella sampling ros (Thu May 10 2012 - 07:43:17 PDT)
[AMBER] AM1-DH+ marawan hussain (Thu May 10 2012 - 01:03:13 PDT)
- Re: [AMBER] AM1-DH+ Andreas Goetz (Thu May 10 2012 - 12:08:09 PDT)
[AMBER] Amber11 using openmpi (parallel install problem) yjzhao.wh.gmail.com (Thu May 10 2012 - 02:45:39 PDT)
- Re: [AMBER] Amber11 using openmpi (parallel install problem) David A Case (Thu May 10 2012 - 04:41:21 PDT)
[AMBER] Electrostatic potential calculation Sudarshan Debnath (Thu May 10 2012 - 10:34:33 PDT)
- Re: [AMBER] Electrostatic potential calculation Ray Luo, Ph.D. (Thu May 10 2012 - 10:37:52 PDT)
[AMBER] parameters for Zinc ion with five coordination bonds. Jagur Lambix (Thu May 10 2012 - 13:12:56 PDT)
- Re: [AMBER] parameters for Zinc ion with five coordination bonds. Ben Roberts (Thu May 10 2012 - 15:50:48 PDT)
- Re: [AMBER] parameters for Zinc ion with five coordination bonds. Hector A. Baldoni (Thu May 10 2012 - 17:04:39 PDT)
[AMBER] how can we add ACE and NME to to the cap protein terminal? Albert (Thu May 10 2012 - 13:12:44 PDT)
- Re: [AMBER] how can we add ACE and NME to to the cap protein terminal? case (Thu May 10 2012 - 15:05:53 PDT)
  - Re: [AMBER] how can we add ACE and NME to to the cap protein terminal? Albert (Thu May 10 2012 - 21:48:58 PDT)
    - Re: [AMBER] how can we add ACE and NME to to the cap protein terminal? tdo.chem.ucsb.edu (Thu May 10 2012 - 22:40:42 PDT)
    - Re: [AMBER] how can we add ACE and NME to to the cap protein terminal? David A Case (Fri May 11 2012 - 04:52:14 PDT)
    - Re: [AMBER] how can we add ACE and NME to to the cap protein terminal? Albert (Fri May 11 2012 - 06:40:06 PDT)
    - Re: [AMBER] how can we add ACE and NME to to the cap protein terminal? Sajeewa Pemasinghe (Fri May 11 2012 - 08:18:28 PDT)
    - Re: [AMBER] how can we add ACE and NME to to the cap protein terminal? Albert (Fri May 11 2012 - 11:03:32 PDT)
[AMBER] Problem with the binding free energy from MMPBSA decomposed energies Qiong Zhang (Thu May 10 2012 - 13:17:09 PDT)
- Re: [AMBER] Problem with the binding free energy from MMPBSA decomposed energies Qiong Zhang (Fri May 11 2012 - 07:54:37 PDT)
Re: [AMBER] FW: getting metal ions coordinates of nmr structures of a protein Mahendra B Thapa (Thu May 10 2012 - 15:22:46 PDT)
- Re: [AMBER] FW: getting metal ions coordinates of nmr structures of a protein Daniel Sindhikara (Thu May 10 2012 - 18:45:25 PDT)
  - [AMBER] How to generate single mismatch DNA duplex using NAB natty yoshisawa (Thu May 10 2012 - 20:43:30 PDT)
    - Re: [AMBER] How to generate single mismatch DNA duplex using NAB case (Sat May 12 2012 - 10:48:45 PDT)
    - Re: [AMBER] How to generate single mismatch DNA duplex using NAB M. L. Dodson (Sat May 12 2012 - 12:40:13 PDT)
    - Re: [AMBER] How to generate single mismatch DNA duplex using NAB natty yoshisawa (Sun May 13 2012 - 20:30:05 PDT)
    - Re: [AMBER] How to generate single mismatch DNA duplex using NAB Charles Johnson (Mon May 14 2012 - 05:41:19 PDT)
    - [AMBER] Large standard deviation of entropy obtained from NMODE Xioling Chuang (Sat May 12 2012 - 21:40:36 PDT)
    - Re: [AMBER] Large standard deviation of entropy obtained from NMODE Jason Swails (Mon May 14 2012 - 01:11:19 PDT)
    - Re: [AMBER] Large standard deviation of entropy obtained from NMODE Xioling Chuang (Tue May 15 2012 - 18:33:38 PDT)
[AMBER] regarding REMD Dilraj LAMA (Fri May 11 2012 - 00:17:55 PDT)
- Re: [AMBER] regarding REMD Jason Swails (Fri May 11 2012 - 05:51:54 PDT)
  - Re: [AMBER] regarding REMD Carlos Simmerling (Fri May 11 2012 - 07:38:38 PDT)
    - Re: [AMBER] regarding REMD David A Case (Fri May 11 2012 - 10:40:02 PDT)
    - Re: [AMBER] regarding REMD Carlos Simmerling (Fri May 11 2012 - 10:59:08 PDT)
    - Re: [AMBER] regarding REMD Jason Swails (Fri May 11 2012 - 12:28:57 PDT)
[AMBER] lipid11 problem with leap Tales Yuan (Fri May 11 2012 - 00:32:49 PDT)
- [AMBER] lipid11 problem with leap Tales Yuan (Fri May 11 2012 - 00:39:14 PDT)
[AMBER] Problem regarding antechamber Asma Abro 28-FBAS/MSBI/F09 (Fri May 11 2012 - 01:13:48 PDT)
- Re: [AMBER] Problem regarding antechamber David A Case (Fri May 11 2012 - 05:03:12 PDT)
  - Re: [AMBER] Problem regarding antechamber Asma Abro 28-FBAS/MSBI/F09 (Fri May 11 2012 - 08:10:43 PDT)
    - Re: [AMBER] Problem regarding antechamber David A Case (Fri May 11 2012 - 10:45:45 PDT)
    - Re: [AMBER] Problem regarding antechamber Asma Abro 28-FBAS/MSBI/F09 (Fri May 11 2012 - 23:25:36 PDT)
    - Re: [AMBER] Problem regarding antechamber Asma Abro 28-FBAS/MSBI/F09 (Tue May 15 2012 - 03:25:14 PDT)
    - Re: [AMBER] Problem regarding antechamber case (Tue May 15 2012 - 05:59:34 PDT)
    - Re: [AMBER] Problem regarding antechamber Asma Abro 28-FBAS/MSBI/F09 (Tue May 15 2012 - 21:05:27 PDT)
    - Re: [AMBER] Problem regarding antechamber Asma Abro 28-FBAS/MSBI/F09 (Tue May 15 2012 - 22:09:28 PDT)
    - Re: [AMBER] Problem regarding antechamber Asma Abro 28-FBAS/MSBI/F09 (Tue May 15 2012 - 22:32:49 PDT)
    - Re: [AMBER] Problem regarding antechamber case (Tue May 15 2012 - 22:52:39 PDT)
    - Re: [AMBER] Problem regarding antechamber Asma Abro 28-FBAS/MSBI/F09 (Tue May 15 2012 - 23:17:34 PDT)
    - Re: [AMBER] Problem regarding antechamber Asma Abro 28-FBAS/MSBI/F09 (Wed May 16 2012 - 00:44:35 PDT)
    - Re: [AMBER] Problem regarding antechamber FyD (Wed May 16 2012 - 01:29:11 PDT)
    - Re: [AMBER] Problem regarding antechamber Asma Abro 28-FBAS/MSBI/F09 (Thu May 31 2012 - 02:22:32 PDT)
    - Re: [AMBER] Problem regarding antechamber FyD (Thu May 31 2012 - 02:51:27 PDT)
[AMBER] slow AMBER on my machine Cao Yang (Fri May 11 2012 - 01:42:17 PDT)
- Re: [AMBER] slow AMBER on my machine David A Case (Fri May 11 2012 - 05:06:45 PDT)
[AMBER] lipid11 force filed problem with tleap Tales Yuan (Fri May 11 2012 - 02:00:57 PDT)
[AMBER] sander.MPI error George Tzotzos (Fri May 11 2012 - 02:30:12 PDT)
- Re: [AMBER] sander.MPI error Jason Swails (Fri May 11 2012 - 05:29:23 PDT)
  - Re: [AMBER] sander.MPI error George Tzotzos (Fri May 11 2012 - 05:32:47 PDT)
    - Re: [AMBER] sander.MPI error Jason Swails (Fri May 11 2012 - 05:40:38 PDT)
    - Re: [AMBER] sander.MPI error George Tzotzos (Fri May 11 2012 - 06:02:35 PDT)
    - Re: [AMBER] sander.MPI error Marc van der Kamp (Fri May 11 2012 - 06:13:39 PDT)
    - Re: [AMBER] sander.MPI error George Tzotzos (Fri May 11 2012 - 06:26:22 PDT)
    - Re: [AMBER] sander.MPI error Jason Swails (Fri May 11 2012 - 12:23:50 PDT)
[AMBER] Difference in PB results of mmpbsa and mmpbsa.mpi amin.imtech.res.in (Fri May 11 2012 - 02:52:17 PDT)
- Re: [AMBER] Difference in PB results of mmpbsa and mmpbsa.mpi Bill Miller III (Fri May 11 2012 - 05:14:47 PDT)
[AMBER] does LIPID11 require surface tension ? Vlad Cojocaru (Fri May 11 2012 - 03:03:00 PDT)
[AMBER] lipid11 force filed question Tales Yuan (Fri May 11 2012 - 03:19:58 PDT)
- Re: [AMBER] lipid11 force filed question Jason Swails (Fri May 11 2012 - 05:34:26 PDT)
  - Re: [AMBER] lipid11 force filed question Tales Yuan (Fri May 11 2012 - 05:43:53 PDT)
    - Re: [AMBER] lipid11 force filed question Jason Swails (Fri May 11 2012 - 05:53:46 PDT)
  - Re: [AMBER] lipid11 force filed question Albert (Fri May 11 2012 - 06:58:39 PDT)
    - Re: [AMBER] lipid11 force filed question Vlad Cojocaru (Fri May 11 2012 - 07:14:24 PDT)
    - Re: [AMBER] lipid11 force filed question Albert (Fri May 11 2012 - 07:20:30 PDT)
    - Re: [AMBER] lipid11 force filed question Ross Walker (Fri May 11 2012 - 10:08:47 PDT)
    - Re: [AMBER] lipid11 force filed question Gould, Ian R (Fri May 11 2012 - 10:14:16 PDT)
    - Re: [AMBER] lipid11 force filed question Albert (Fri May 11 2012 - 10:20:11 PDT)
    - Re: [AMBER] lipid11 force filed question Ross Walker (Fri May 11 2012 - 10:07:47 PDT)
    - Re: [AMBER] lipid11 force filed question Albert (Fri May 11 2012 - 10:58:31 PDT)
- Re: [AMBER] lipid11 force filed question Ross Walker (Fri May 11 2012 - 08:12:52 PDT)
  - Re: [AMBER] lipid11 force filed question Albert (Fri May 11 2012 - 08:52:42 PDT)
    - Re: [AMBER] lipid11 force filed question Ross Walker (Fri May 11 2012 - 10:10:49 PDT)
  - Re: [AMBER] lipid11 force filed question Tales Yuan (Fri May 11 2012 - 09:11:01 PDT)
    - Re: [AMBER] lipid11 force filed question Daniel Roe (Fri May 11 2012 - 09:17:40 PDT)
    - Re: [AMBER] lipid11 force filed question Tales Yuan (Fri May 11 2012 - 09:24:37 PDT)
    - Re: [AMBER] lipid11 force filed question Daniel Roe (Mon May 21 2012 - 04:09:00 PDT)
    - Re: [AMBER] lipid11 force filed question Ross Walker (Mon May 21 2012 - 12:23:49 PDT)
    - Re: [AMBER] lipid11 force filed question Daniel Roe (Mon May 21 2012 - 16:26:45 PDT)
    - Re: [AMBER] lipid11 force filed question Ross Walker (Fri May 11 2012 - 10:15:59 PDT)
    - Re: [AMBER] lipid11 force filed question Tales Yuan (Fri May 11 2012 - 10:36:18 PDT)
    - Re: [AMBER] lipid11 force filed question Benjamin D Madej (Fri May 11 2012 - 12:21:47 PDT)
[AMBER] Quantification of forces Soumya Lipsa Rath (Fri May 11 2012 - 03:56:54 PDT)
- Re: [AMBER] Quantification of forces steinbrt.rci.rutgers.edu (Fri May 11 2012 - 04:32:30 PDT)
[AMBER] RNA xleap Charles Johnson (Fri May 11 2012 - 09:18:53 PDT)
- Re: [AMBER] RNA xleap David A Case (Fri May 11 2012 - 10:49:35 PDT)
  - Re: [AMBER] RNA xleap Charles Johnson (Fri May 11 2012 - 11:07:54 PDT)
    - Re: [AMBER] RNA xleap David A Case (Fri May 11 2012 - 11:30:13 PDT)
[AMBER] apply an external force mehdi bagherpoor (Sat May 12 2012 - 07:18:11 PDT)
- Re: [AMBER] apply an external force ros (Sat May 12 2012 - 07:57:43 PDT)
  - Re: [AMBER] apply an external force case (Sat May 12 2012 - 10:46:24 PDT)
[AMBER] Placing molecules randomly in a simulation box Massimiliano Porrini (Sat May 12 2012 - 11:09:25 PDT)
- Re: [AMBER] Placing molecules randomly in a simulation box Lachele Foley (Lists) (Sat May 12 2012 - 18:48:58 PDT)
  - Re: [AMBER] Placing molecules randomly in a simulation box Dickson, Callum (Mon May 14 2012 - 03:14:13 PDT)
    - Re: [AMBER] Placing molecules randomly in a simulation box Marek Maly (Mon May 14 2012 - 04:36:17 PDT)
    - Re: [AMBER] Placing molecules randomly in a simulation box Massimiliano Porrini (Mon May 14 2012 - 04:58:18 PDT)
[AMBER] bi-layer membrane system shrink with NPgamaT Albert (Sun May 13 2012 - 23:49:44 PDT)
- Re: [AMBER] bi-layer membrane system shrink with NPgamaT Åge Skjevik (Mon May 14 2012 - 00:40:56 PDT)
  - Re: [AMBER] bi-layer membrane system shrink with NPgamaT Albert (Mon May 14 2012 - 00:46:03 PDT)
[AMBER] qmmm_EXTERN/ tests failing Marc van der Kamp (Mon May 14 2012 - 00:58:52 PDT)
- Re: [AMBER] qmmm_EXTERN/ tests failing Jason Swails (Mon May 14 2012 - 06:12:23 PDT)
  - Re: [AMBER] qmmm_EXTERN/ tests failing Marc van der Kamp (Mon May 14 2012 - 09:39:34 PDT)
    - Re: [AMBER] qmmm_EXTERN/ tests failing Jason Swails (Mon May 14 2012 - 12:41:14 PDT)
    - Re: [AMBER] qmmm_EXTERN/ tests failing Andreas Goetz (Mon May 14 2012 - 12:52:59 PDT)
    - Re: [AMBER] qmmm_EXTERN/ tests failing Marc van der Kamp (Tue May 15 2012 - 01:36:14 PDT)
    - Re: [AMBER] qmmm_EXTERN/ tests failing Marc van der Kamp (Tue May 15 2012 - 02:03:53 PDT)
    - Re: [AMBER] qmmm_EXTERN/ tests failing Andreas Goetz (Sun Jul 22 2012 - 14:18:50 PDT)
[AMBER] printing out total energy in sander with high precision (more digits) Marc van der Kamp (Mon May 14 2012 - 01:53:52 PDT)
- Re: [AMBER] printing out total energy in sander with high precision (more digits) Mark Williamson (Mon May 14 2012 - 02:40:03 PDT)
  - Re: [AMBER] printing out total energy in sander with high precision (more digits) Marc van der Kamp (Mon May 14 2012 - 02:56:21 PDT)
    - Re: [AMBER] printing out total energy in sander with high precision (more digits) Mark Williamson (Mon May 14 2012 - 03:21:56 PDT)
- Re: [AMBER] printing out total energy in sander with high precision (more digits) Jason Swails (Mon May 14 2012 - 05:52:32 PDT)
  - Re: [AMBER] printing out total energy in sander with high precision (more digits) Marc van der Kamp (Mon May 14 2012 - 05:56:15 PDT)
[AMBER] Amber 12 parallel compilation error Fernando Martín García (Mon May 14 2012 - 03:46:18 PDT)
- Re: [AMBER] Amber 12 parallel compilation error Fernando Martín García (Mon May 14 2012 - 03:53:56 PDT)
[AMBER] Not able to apply bugfix on Amber 11 HIMANSHU JOSHI (Mon May 14 2012 - 03:48:22 PDT)
- Re: [AMBER] Not able to apply bugfix on Amber 11 Jason Swails (Mon May 14 2012 - 05:47:22 PDT)
  - Re: [AMBER] Not able to apply bugfix on Amber 11 HIMANSHU JOSHI (Mon May 14 2012 - 07:15:33 PDT)
    - Re: [AMBER] Not able to apply bugfix on Amber 11 Jason Swails (Mon May 14 2012 - 08:13:05 PDT)
[AMBER] ACPYPE error Albert (Mon May 14 2012 - 06:01:07 PDT)
- Re: [AMBER] ACPYPE error Alan (Mon May 14 2012 - 06:45:04 PDT)
[AMBER] NetCDF Restart Files - Amber 12 Lucas A. Defelipe (Mon May 14 2012 - 06:26:05 PDT)
- Re: [AMBER] NetCDF Restart Files - Amber 12 Jason Swails (Mon May 14 2012 - 06:35:59 PDT)
  - Re: [AMBER] NetCDF Restart Files - Amber 12 Daniel Roe (Mon May 14 2012 - 08:30:36 PDT)
[AMBER] problem installing AMBER12 on MacOSX Robert Oswald (Mon May 14 2012 - 08:06:38 PDT)
- Re: [AMBER] problem installing AMBER12 on MacOSX Jason Swails (Mon May 14 2012 - 08:11:59 PDT)
  - Re: [AMBER] problem installing AMBER12 on MacOSX Robert Oswald (Mon May 14 2012 - 08:23:31 PDT)
    - Re: [AMBER] problem installing AMBER12 on MacOSX Jason Swails (Mon May 14 2012 - 08:38:25 PDT)
- Re: [AMBER] problem installing AMBER12 on MacOSX Philip Winter (Wed May 23 2012 - 13:05:27 PDT)
  - Re: [AMBER] problem installing AMBER12 on MacOSX David A Case (Thu May 24 2012 - 04:57:48 PDT)
    - Re: [AMBER] problem installing AMBER12 on MacOSX Jason Swails (Fri May 25 2012 - 19:22:42 PDT)
    - Re: [AMBER] problem installing AMBER12 on MacOSX David Watson (Fri May 25 2012 - 20:35:34 PDT)
[AMBER] Errrors in mm_pbsa.pl Souvik Sur (Mon May 14 2012 - 09:05:32 PDT)
- Re: [AMBER] Errrors in mm_pbsa.pl Ray Luo, Ph.D. (Mon May 14 2012 - 11:05:14 PDT)
[AMBER] How does radial work? Alan (Mon May 14 2012 - 09:27:22 PDT)
[AMBER] Periodicity errors in pymdsapb Genzo Tanaka (Mon May 14 2012 - 09:57:46 PDT)
- Re: [AMBER] Periodicity errors in pymdsapb Genzo Tanaka (Mon May 14 2012 - 10:07:44 PDT)
- Re: [AMBER] Periodicity errors in pymdsapb case (Mon May 14 2012 - 14:54:04 PDT)
  - Re: [AMBER] Periodicity errors in pymdsapb Genzo Tanaka (Tue May 15 2012 - 08:36:43 PDT)
    - Re: [AMBER] Periodicity errors in pymdsapb Jason Swails (Tue May 15 2012 - 08:57:58 PDT)
    - [AMBER] charge and ionization state at pH 6.5 Acoot Brett (Wed May 16 2012 - 04:11:30 PDT)
    - Re: [AMBER] charge and ionization state at pH 6.5 case (Wed May 16 2012 - 15:07:14 PDT)
    - Re: [AMBER] charge and ionization state at pH 6.5 Marek Maly (Wed May 16 2012 - 16:15:49 PDT)
    - Re: [AMBER] Periodicity errors in pymdsapb Genzo Tanaka (Thu May 17 2012 - 09:02:31 PDT)
    - Re: [AMBER] Periodicity errors in pymdsapb Bill Miller III (Fri May 18 2012 - 11:38:41 PDT)
    - Re: [AMBER] Periodicity errors in pymdsapb Genzo Tanaka (Tue May 22 2012 - 09:19:05 PDT)
[AMBER] Bug? Zero decomposed vdw and ele energies for explicit water molecules in the decomposed PB calculation. Qiong Zhang (Mon May 14 2012 - 11:45:40 PDT)
[AMBER] Fwd: Bug? Zero decomposed vdw and ele energies for explicit water molecules in the decomposed PB calculation. Ray Luo, Ph.D. (Mon May 14 2012 - 15:00:37 PDT)
- Re: [AMBER] Bug? Zero decomposed vdw and ele energies for explicit water molecules in the decomposed PB calculation. Qiong Zhang (Mon May 14 2012 - 19:48:44 PDT)
- Re: [AMBER] Fwd: Bug? Zero decomposed vdw and ele energies for explicit water molecules in the decomposed PB calculation. Qin Cai (Wed May 16 2012 - 10:46:07 PDT)
[AMBER] Antechamber Error Pedro Swagger (Mon May 14 2012 - 15:01:50 PDT)
- Re: [AMBER] Antechamber Error case (Mon May 14 2012 - 15:41:31 PDT)
[AMBER] How to implement a new energy function in AMBER Xin Geng (Mon May 14 2012 - 15:55:10 PDT)
- Re: [AMBER] How to implement a new energy function in AMBER Jason Swails (Mon May 14 2012 - 17:10:10 PDT)
  - Re: [AMBER] How to implement a new energy function in AMBER Xin Geng (Mon May 14 2012 - 18:01:40 PDT)
    - Re: [AMBER] How to implement a new energy function in AMBER Jason Swails (Mon May 14 2012 - 19:22:58 PDT)
    - Re: [AMBER] How to implement a new energy function in AMBER Xin Geng (Wed May 16 2012 - 10:04:12 PDT)
    - Re: [AMBER] How to implement a new energy function in AMBER Xin Geng (Thu May 17 2012 - 16:41:27 PDT)
[AMBER] Build B form RNA by NAB? Hai Nguyen (Mon May 14 2012 - 22:36:19 PDT)
- Re: [AMBER] Build B form RNA by NAB? Hai Nguyen (Sat May 19 2012 - 09:01:30 PDT)
  - Re: [AMBER] Build B form RNA by NAB? Vlad Cojocaru (Sat May 19 2012 - 09:48:19 PDT)
    - Re: [AMBER] Build B form RNA by NAB? Hai Nguyen (Sun May 20 2012 - 08:09:56 PDT)
[AMBER] mpi problem Syed Tarique Moin (Mon May 14 2012 - 23:04:29 PDT)
- Re: [AMBER] mpi problem Jason Swails (Tue May 15 2012 - 00:53:09 PDT)
  - Re: [AMBER] mpi problem Syed Tarique Moin (Tue May 15 2012 - 03:29:23 PDT)
    - Re: [AMBER] mpi problem Jason Swails (Tue May 15 2012 - 07:42:02 PDT)
    - Re: [AMBER] mpi problem Syed Tarique Moin (Tue May 15 2012 - 22:29:07 PDT)
    - Re: [AMBER] mpi problem Syed Tarique Moin (Fri May 18 2012 - 00:30:15 PDT)
[AMBER] problem in reading pdb file Asmita Gupta (Tue May 15 2012 - 00:18:42 PDT)
- Re: [AMBER] problem in reading pdb file case (Tue May 15 2012 - 01:18:03 PDT)
  - Re: [AMBER] problem in reading pdb file Asmita Gupta (Tue May 15 2012 - 01:37:47 PDT)
    - Re: [AMBER] problem in reading pdb file case (Tue May 15 2012 - 03:26:15 PDT)
  - Re: [AMBER] problem in reading pdb file Claire Shoemake (Tue May 15 2012 - 14:53:06 PDT)
[AMBER] sleap/tleap differences for parmbsc0 DNA C.M. Baker (Tue May 15 2012 - 02:46:22 PDT)
- Re: [AMBER] sleap/tleap differences for parmbsc0 DNA case (Tue May 15 2012 - 03:53:03 PDT)
  - Re: [AMBER] sleap/tleap differences for parmbsc0 DNA C.M. Baker (Wed May 16 2012 - 04:38:03 PDT)
    - Re: [AMBER] sleap/tleap differences for parmbsc0 DNA Jason Swails (Sun May 20 2012 - 15:56:24 PDT)
[AMBER] MMPBSA.py problem marawan hussain (Tue May 15 2012 - 17:13:13 PDT)
- Re: [AMBER] MMPBSA.py problem Bill Miller III (Tue May 15 2012 - 17:39:56 PDT)
- Re: [AMBER] MMPBSA.py problem Jason Swails (Tue May 15 2012 - 19:02:47 PDT)
  - Re: [AMBER] MMPBSA.py problem marawan hussain (Tue May 15 2012 - 20:22:06 PDT)
  - Re: [AMBER] MMPBSA.py problem marawan hussain (Tue May 15 2012 - 21:05:38 PDT)
    - Re: [AMBER] MMPBSA.py problem case (Tue May 15 2012 - 22:45:25 PDT)
[AMBER] Amber 12 cuda test failed Fernando Martín García (Wed May 16 2012 - 00:32:39 PDT)
- Re: [AMBER] Amber 12 cuda test failed Ross Walker (Wed May 16 2012 - 08:19:10 PDT)
  - Re: [AMBER] Amber 12 cuda test failed Fernando Martín García (Wed May 16 2012 - 23:55:12 PDT)
[AMBER] Electrostatic potential calculation. Sudarshan Debnath (Wed May 16 2012 - 02:54:59 PDT)
[AMBER] Several types of extra point charges in sander? Олег Титов (Wed May 16 2012 - 03:10:25 PDT)
- Re: [AMBER] Several types of extra point charges in sander? Jason Swails (Sun May 20 2012 - 15:50:06 PDT)
[AMBER] Is the performance issue of CUDA 4.1 compilers resolved in CUDA 4.2 compilers? Jan-Philip Gehrcke (Wed May 16 2012 - 04:45:27 PDT)
- Re: [AMBER] Is the performance issue of CUDA 4.1 compilers resolved in CUDA 4.2 compilers? filip fratev (Wed May 16 2012 - 04:54:29 PDT)
  - Re: [AMBER] Is the performance issue of CUDA 4.1 compilers resolved in CUDA 4.2 compilers? Ross Walker (Wed May 16 2012 - 08:19:04 PDT)
- Re: [AMBER] Is the performance issue of CUDA 4.1 compilers resolved in CUDA 4.2 compilers? Scott Le Grand (Wed May 16 2012 - 09:19:48 PDT)
[AMBER] new Mg parameters Asmita Gupta (Wed May 16 2012 - 11:01:50 PDT)
- Re: [AMBER] new Mg parameters Jesper Sørensen (Wed May 16 2012 - 11:51:13 PDT)
  - Re: [AMBER] new Mg parameters Thomas Cheatham III (Wed May 16 2012 - 12:03:42 PDT)
    - Re: [AMBER] new Mg parameters Jesper Sørensen (Wed May 16 2012 - 12:16:06 PDT)
    - Re: [AMBER] new Mg parameters Jiri Sponer (Thu May 17 2012 - 12:19:46 PDT)
    - Re: [AMBER] new Mg parameters Jesper Sørensen (Thu May 17 2012 - 12:39:22 PDT)
    - Re: [AMBER] new Mg parameters Jiri Sponer (Thu May 17 2012 - 12:54:44 PDT)
    - Re: [AMBER] new Mg parameters Asmita Gupta (Fri May 18 2012 - 04:26:01 PDT)
    - Re: [AMBER] new Mg parameters Jiri Sponer (Fri May 18 2012 - 04:59:31 PDT)
    - Re: [AMBER] new Mg parameters Jesper Sørensen (Fri May 18 2012 - 09:49:21 PDT)
    - Re: [AMBER] new Mg parameters Asmita Gupta (Fri May 18 2012 - 11:35:27 PDT)
[AMBER] Electrostatic potential calculation Sudarshan Debnath (Wed May 16 2012 - 20:09:50 PDT)
- Re: [AMBER] Electrostatic potential calculation Ray Luo, Ph.D. (Thu May 17 2012 - 09:57:05 PDT)
[AMBER] how to calculate the volume of our system? Albert (Thu May 17 2012 - 00:13:06 PDT)
- Re: [AMBER] how to calculate the volume of our system? David A Case (Thu May 17 2012 - 05:11:31 PDT)
  - Re: [AMBER] how to calculate the volume of our system? Albert (Thu May 17 2012 - 08:17:33 PDT)
[AMBER] cpptraj-secstruct colvin (Thu May 17 2012 - 01:06:30 PDT)
- Re: [AMBER] cpptraj-secstruct Daniel Roe (Thu May 17 2012 - 04:17:02 PDT)
- Re: [AMBER] cpptraj-secstruct Daniel Roe (Tue May 22 2012 - 11:41:29 PDT)
  - Re: [AMBER] cpptraj-secstruct colvin (Wed May 23 2012 - 01:06:01 PDT)
    - Re: [AMBER] cpptraj-secstruct Marc van der Kamp (Wed May 23 2012 - 01:10:50 PDT)
    - Re: [AMBER] cpptraj-secstruct colvin (Wed May 23 2012 - 02:00:50 PDT)
[AMBER] Force.dat file from pbsa calculation tommaso.casalini.mail.polimi.it (Thu May 17 2012 - 05:04:26 PDT)
[AMBER] Electrostatic potential calculation Sudarshan Debnath (Thu May 17 2012 - 08:45:49 PDT)
- Re: [AMBER] Electrostatic potential calculation Ray Luo, Ph.D. (Thu May 17 2012 - 09:52:46 PDT)
[AMBER] Failure in mol surf in pymdpbsa Genzo Tanaka (Thu May 17 2012 - 09:08:10 PDT)
- [AMBER] Failure in mol surf in pymdpbsa Genzo Tanaka (Tue May 22 2012 - 12:25:19 PDT)
[AMBER] Iron-Sulfur Cluster Wilson, Katie (Thu May 17 2012 - 12:14:41 PDT)
- Re: [AMBER] Iron-Sulfur Cluster francesco oteri (Thu May 17 2012 - 15:51:22 PDT)
  - Re: [AMBER] Iron-Sulfur Cluster Wilson, Katie (Fri May 25 2012 - 08:06:29 PDT)
    - Re: [AMBER] Iron-Sulfur Cluster francesco oteri (Fri May 25 2012 - 09:45:48 PDT)
[AMBER] prmtop generated from chamber colvin (Thu May 17 2012 - 20:38:54 PDT)
- Re: [AMBER] prmtop generated from chamber Marc van der Kamp (Fri May 18 2012 - 00:43:29 PDT)
- Re: [AMBER] prmtop generated from chamber Ross Walker (Fri May 18 2012 - 10:14:26 PDT)
[AMBER] Electrostatic potential calculation Sudarshan Debnath (Thu May 17 2012 - 22:11:00 PDT)
[AMBER] The QMMM_MD err calculation of amber12+ gamessUS javacfish (Fri May 18 2012 - 02:52:12 PDT)
- Re: [AMBER] The QMMM_MD err calculation of amber12+ gamessUS Andreas Goetz (Wed May 23 2012 - 13:22:53 PDT)
[AMBER] Electrostatic potential calculation Sudarshan Debnath (Fri May 18 2012 - 05:59:00 PDT)
- Re: [AMBER] Electrostatic potential calculation Ray Luo, Ph.D. (Fri May 18 2012 - 09:41:02 PDT)
[AMBER] Output from pairwise decomposition with MMPBSA.py(.MPI) Åge Skjevik (Fri May 18 2012 - 06:01:26 PDT)
- Re: [AMBER] Output from pairwise decomposition with MMPBSA.py(.MPI) Bill Miller III (Fri May 18 2012 - 06:11:30 PDT)
  - Re: [AMBER] Output from pairwise decomposition with MMPBSA.py(.MPI) Åge Skjevik (Fri May 18 2012 - 07:07:17 PDT)
    - Re: [AMBER] Output from pairwise decomposition with MMPBSA.py(.MPI) Bill Miller III (Fri May 18 2012 - 08:36:07 PDT)
    - Re: [AMBER] Output from pairwise decomposition with MMPBSA.py(.MPI) Åge Skjevik (Fri May 18 2012 - 10:53:09 PDT)
    - Re: [AMBER] Output from pairwise decomposition with MMPBSA.py(.MPI) Bill Miller III (Fri May 18 2012 - 11:02:56 PDT)
    - Re: [AMBER] Output from pairwise decomposition with MMPBSA.py(.MPI) Åge Skjevik (Mon May 21 2012 - 14:56:46 PDT)
    - Re: [AMBER] Output from pairwise decomposition with MMPBSA.py(.MPI) Bill Miller III (Mon May 21 2012 - 15:33:06 PDT)
[AMBER] High Electrostatic Interaction Khaled Barakat (Fri May 18 2012 - 07:54:39 PDT)
[AMBER] sander error in the decomposed MMGBSA using Ambertools12 and Amber11 Qiong Zhang (Fri May 18 2012 - 11:29:30 PDT)
- Re: [AMBER] sander error in the decomposed MMGBSA using Ambertools12 and Amber11 Bill Miller III (Fri May 18 2012 - 11:35:56 PDT)
  - Re: [AMBER] sander error in the decomposed MMGBSA using Ambertools12 and Amber11 Qiong Zhang (Fri May 18 2012 - 11:38:44 PDT)
  - Re: [AMBER] sander error in the decomposed MMGBSA using Ambertools12 and Amber11 Qiong Zhang (Fri May 18 2012 - 11:43:11 PDT)
    - Re: [AMBER] sander error in the decomposed MMGBSA using Ambertools12 and Amber11 Bill Miller III (Fri May 18 2012 - 11:49:47 PDT)
    - Re: [AMBER] sander error in the decomposed MMGBSA using Ambertools12 and Amber11 Qiong Zhang (Fri May 18 2012 - 11:56:54 PDT)
    - Re: [AMBER] sander error in the decomposed MMGBSA using Ambertools12 and Amber11 Bill Miller III (Fri May 18 2012 - 12:02:15 PDT)
    - Re: [AMBER] sander error in the decomposed MMGBSA using Ambertools12 and Amber11 Qiong Zhang (Fri May 18 2012 - 12:14:37 PDT)
    - Re: [AMBER] sander error in the decomposed MMGBSA using Ambertools12 and Amber11 Bill Miller III (Fri May 18 2012 - 12:46:13 PDT)
    - Re: [AMBER] sander error in the decomposed MMGBSA using Ambertools12 and Amber11 Qiong Zhang (Fri May 18 2012 - 12:52:17 PDT)
    - Re: [AMBER] sander error in the decomposed MMGBSA using Ambertools12 and Amber11 Qiong Zhang (Fri May 18 2012 - 12:57:15 PDT)
    - Re: [AMBER] sander error in the decomposed MMGBSA using Ambertools12 and Amber11 Bill Miller III (Fri May 18 2012 - 14:06:50 PDT)
    - Re: [AMBER] sander error in the decomposed MMGBSA using Ambertools12 and Amber11 Qiong Zhang (Fri May 18 2012 - 14:37:01 PDT)
    - Re: [AMBER] sander error in the decomposed MMGBSA using Ambertools12 and Amber11 Bill Miller III (Fri May 18 2012 - 17:20:53 PDT)
    - Re: [AMBER] sander error in the decomposed MMGBSA using Ambertools12 and Amber11 Qiong Zhang (Fri May 18 2012 - 20:00:09 PDT)
    - Re: [AMBER] sander error in the decomposed MMGBSA using Ambertools12 and Amber11 Bill Miller III (Sat May 19 2012 - 06:55:47 PDT)
    - Re: [AMBER] sander error in the decomposed MMGBSA using Ambertools12 and Amber11 Qiong Zhang (Sat May 19 2012 - 07:45:58 PDT)
    - Re: [AMBER] sander error in the decomposed MMGBSA using Ambertools12 and Amber11 Qiong Zhang (Sat May 19 2012 - 07:55:37 PDT)
    - Re: [AMBER] sander error in the decomposed MMGBSA using Ambertools12 and Amber11 Qiong Zhang (Sat May 19 2012 - 08:01:59 PDT)
    - Re: [AMBER] sander error in the decomposed MMGBSA using Ambertools12 and Amber11 Jason Swails (Sun May 20 2012 - 18:35:26 PDT)
    - Re: [AMBER] sander error in the decomposed MMGBSA using Ambertools12 and Amber11 Qiong Zhang (Sun May 20 2012 - 19:49:01 PDT)
    - Re: [AMBER] sander error in the decomposed MMGBSA using Ambertools12 and Amber11 Qiong Zhang (Mon May 21 2012 - 17:43:27 PDT)
- Re: [AMBER] sander error in the decomposed MMGBSA using Ambertools12 and Amber11 Qiong Zhang (Tue May 22 2012 - 07:28:53 PDT)
  - Re: [AMBER] sander error in the decomposed MMGBSA using Ambertools12 and Amber11 Bill Miller III (Tue May 22 2012 - 18:40:01 PDT)
    - Re: [AMBER] sander error in the decomposed MMGBSA using Ambertools12 and Amber11 Qiong Zhang (Tue May 22 2012 - 19:04:27 PDT)
[AMBER] was the bug fixed for tleap? Albert (Fri May 18 2012 - 11:43:17 PDT)
- Re: [AMBER] was the bug fixed for tleap? Benjamin D Madej (Fri May 18 2012 - 17:03:27 PDT)
  - Re: [AMBER] was the bug fixed for tleap? Albert (Wed May 23 2012 - 00:23:59 PDT)
    - Re: [AMBER] was the bug fixed for tleap? Åge Skjevik (Wed May 23 2012 - 04:37:21 PDT)
[AMBER] Electrostatic potential calculation Sudarshan Debnath (Fri May 18 2012 - 12:29:45 PDT)
- Re: [AMBER] Electrostatic potential calculation David A Case (Fri May 18 2012 - 13:02:17 PDT)
[AMBER] pmemd.cuda for JAC benchmark Mohammad Ashraf Bhuiyan (Fri May 18 2012 - 13:26:31 PDT)
- Re: [AMBER] pmemd.cuda for JAC benchmark case (Sat May 19 2012 - 10:45:48 PDT)
[AMBER] Electrostatic potential calculation Sudarshan Debnath (Fri May 18 2012 - 21:33:18 PDT)
- Re: [AMBER] Electrostatic potential calculation Jan-Philip Gehrcke (Sat May 19 2012 - 03:48:48 PDT)
[AMBER] Electrostatic potential calculation Sudarshan Debnath (Fri May 18 2012 - 21:50:10 PDT)
[AMBER] Problem Installing Amber on Mac OSX Lion Arthur Roberts (Sat May 19 2012 - 17:45:53 PDT)
- Re: [AMBER] Problem Installing Amber on Mac OSX Lion case (Sun May 20 2012 - 04:52:49 PDT)
  - Re: [AMBER] Problem Installing Amber on Mac OSX Lion Arthur Roberts (Sun May 20 2012 - 16:12:33 PDT)
    - Re: [AMBER] Problem Installing Amber on Mac OSX Lion Jason Swails (Sun May 20 2012 - 18:50:54 PDT)
    - Re: [AMBER] Problem Installing Amber on Mac OSX Lion Arthur Roberts (Sun May 20 2012 - 19:28:28 PDT)
    - Re: [AMBER] Problem Installing Amber on Mac OSX Lion Jason Swails (Thu May 31 2012 - 13:01:43 PDT)
    - Re: [AMBER] Problem Installing Amber on Mac OSX Lion Jason Swails (Thu May 31 2012 - 13:02:45 PDT)
[AMBER] Electrostatic potential calculation Sudarshan Debnath (Sun May 20 2012 - 02:27:58 PDT)
- Re: [AMBER] Electrostatic potential calculation Jan-Philip Gehrcke (Mon May 21 2012 - 04:43:41 PDT)
Re: [AMBER] Problem Installing Amber on Mac OSX Lion (lenin) Julio Dominguez (Sun May 20 2012 - 16:08:53 PDT)
[AMBER] MMPBSA-CalcError marawan hussain (Sun May 20 2012 - 19:00:46 PDT)
- Re: [AMBER] MMPBSA-CalcError Bill Miller III (Sun May 20 2012 - 19:14:50 PDT)
  - Re: [AMBER] MMPBSA-CalcError marawan hussain (Sun May 20 2012 - 19:30:14 PDT)
    - Re: [AMBER] MMPBSA-CalcError Bill Miller III (Sun May 20 2012 - 19:32:43 PDT)
[AMBER] Electrostatic potential calculation Sudarshan Debnath (Mon May 21 2012 - 01:20:52 PDT)
- Re: [AMBER] Electrostatic potential calculation Qin Cai (Mon May 21 2012 - 13:44:36 PDT)
[AMBER] setting gcc compiler Alan (Mon May 21 2012 - 05:49:03 PDT)
- Re: [AMBER] setting gcc compiler David A. Case (Mon May 21 2012 - 18:02:35 PDT)
  - Re: [AMBER] setting gcc compiler Alan (Tue May 22 2012 - 01:44:01 PDT)
[AMBER] Amber tools 12 and esp visualization in VMD and PyMol Sudarshan Debnath (Mon May 21 2012 - 12:11:04 PDT)
- Re: [AMBER] Amber tools 12 and esp visualization in VMD and PyMol Ray Luo, Ph.D. (Mon May 21 2012 - 17:55:59 PDT)
- Re: [AMBER] Amber tools 12 and esp visualization in VMD and PyMol Ray Luo, Ph.D. (Wed May 23 2012 - 11:14:33 PDT)
  - [AMBER] Amber tools 12 and esp visualization in VMD and PyMol Sudarshan Debnath (Wed May 23 2012 - 22:24:34 PDT)
  - [AMBER] Electrostatic potential and forces computation tommaso.casalini.mail.polimi.it (Thu May 24 2012 - 06:52:14 PDT)
    - Re: [AMBER] Electrostatic potential and forces computation Ray Luo, Ph.D. (Thu May 24 2012 - 09:35:38 PDT)
    - Re: [AMBER] Electrostatic potential and forces computation Qin Cai (Thu May 24 2012 - 14:36:18 PDT)
    - Re: [AMBER] Electrostatic potential and forces computation tommaso.casalini.mail.polimi.it (Fri May 25 2012 - 08:20:18 PDT)
    - [AMBER] Fwd: Electrostatic potential and forces computation Ray Luo, Ph.D. (Fri May 25 2012 - 10:11:39 PDT)
    - Re: [AMBER] Electrostatic potential and forces computation Qin Cai (Sat May 26 2012 - 22:25:17 PDT)
    - Re: [AMBER] Electrostatic potential and forces computation Ray Luo, Ph.D. (Sun May 27 2012 - 06:25:55 PDT)
    - Re: [AMBER] Electrostatic potential and forces computation tommaso.casalini.mail.polimi.it (Tue May 29 2012 - 01:56:49 PDT)
[AMBER] add new functions into Amber10 Xin Geng (Mon May 21 2012 - 12:59:51 PDT)
- Re: [AMBER] add new functions into Amber10 David A. Case (Mon May 21 2012 - 18:29:14 PDT)
[AMBER] amber99tor and amber99ez force field Indrajit Deb (Mon May 21 2012 - 13:21:43 PDT)
- Re: [AMBER] amber99tor and amber99ez force field David Condon (Mon May 21 2012 - 14:21:00 PDT)
  - Re: [AMBER] amber99tor and amber99ez force field Indrajit Deb (Mon May 21 2012 - 14:43:10 PDT)
    - Re: [AMBER] amber99tor and amber99ez force field David Condon (Mon May 21 2012 - 15:04:09 PDT)
    - Re: [AMBER] amber99tor and amber99ez force field Indrajit Deb (Mon May 21 2012 - 15:06:06 PDT)
    - Re: [AMBER] amber99tor and amber99ez force field Indrajit Deb (Mon May 21 2012 - 15:17:01 PDT)
    - Re: [AMBER] amber99tor and amber99ez force field David Condon (Mon May 21 2012 - 16:48:49 PDT)
    - Re: [AMBER] amber99tor and amber99ez force field Indrajit Deb (Mon May 21 2012 - 23:35:21 PDT)
[AMBER] OT -- Have a Model Setup Wish List? Lachele Foley (Lists) (Mon May 21 2012 - 18:03:48 PDT)
[AMBER] antechamber problem anyiphysics.gmail.com (Mon May 21 2012 - 20:11:10 PDT)
- Re: [AMBER] antechamber problem Bill Ross (Mon May 21 2012 - 20:23:42 PDT)
- Re: [AMBER] antechamber problem David A. Case (Tue May 22 2012 - 03:54:28 PDT)
[AMBER] where's http://ambermd.org/bugfixes/11.0/bugfix.all? Alan (Tue May 22 2012 - 04:03:11 PDT)
- Re: [AMBER] where's http://ambermd.org/bugfixes/11.0/bugfix.all? David A. Case (Tue May 22 2012 - 18:04:47 PDT)
  - Re: [AMBER] where's http://ambermd.org/bugfixes/11.0/bugfix.all? Alan (Wed May 23 2012 - 01:41:02 PDT)
[AMBER] High Electrostatic interaction Khaled Barakat (Tue May 22 2012 - 07:41:25 PDT)
[AMBER] how to use self compiled Ambertools1.5 and Amber11 on the cluster Qiong Zhang (Tue May 22 2012 - 07:59:40 PDT)
- Re: [AMBER] how to use self compiled Ambertools1.5 and Amber11 on the cluster Jan-Philip Gehrcke (Tue May 22 2012 - 08:21:14 PDT)
  - Re: [AMBER] how to use self compiled Ambertools1.5 and Amber11 on the cluster Qiong Zhang (Tue May 22 2012 - 08:52:41 PDT)
    - Re: [AMBER] how to use self compiled Ambertools1.5 and Amber11 on the cluster Jan-Philip Gehrcke (Tue May 22 2012 - 09:25:39 PDT)
    - Re: [AMBER] how to use self compiled Ambertools1.5 and Amber11 on the cluster Qiong Zhang (Tue May 22 2012 - 10:05:07 PDT)
    - Re: [AMBER] how to use self compiled Ambertools1.5 and Amber11 on the cluster Jan-Philip Gehrcke (Tue May 22 2012 - 10:11:28 PDT)
    - Re: [AMBER] how to use self compiled Ambertools1.5 and Amber11 on the cluster Qiong Zhang (Tue May 22 2012 - 10:15:59 PDT)
[AMBER] cuda.a(kNLRadixSort. o): undefined reference to symbol '__cxa_pure_virtual Mark Rance (Tue May 22 2012 - 10:18:36 PDT)
[AMBER] refc error with PMEMD.MPI g t (Tue May 22 2012 - 10:55:41 PDT)
- Re: [AMBER] refc error with PMEMD.MPI David A. Case (Tue May 22 2012 - 18:10:59 PDT)
  - Re: [AMBER] refc error with PMEMD.MPI g t (Wed May 23 2012 - 09:56:57 PDT)
[AMBER] creating a primitive object such as a cylinder in amber g t (Tue May 22 2012 - 10:58:58 PDT)
[AMBER] MM-PBSA ATP binding Alejandro Blanco (Tue May 22 2012 - 15:54:15 PDT)
- Re: [AMBER] MM-PBSA ATP binding Bill Miller III (Tue May 22 2012 - 18:16:42 PDT)
[AMBER] ammonia parameters Sajeewa Pemasinghe (Tue May 22 2012 - 16:00:56 PDT)
[AMBER] MMPBSA.py issues marawan hussain (Tue May 22 2012 - 18:24:39 PDT)
- Re: [AMBER] MMPBSA.py issues Jason Swails (Wed May 23 2012 - 03:02:56 PDT)
  - Re: [AMBER] MMPBSA.py issues David A. Case (Wed May 23 2012 - 04:04:24 PDT)
[AMBER] simulation with special amino acid yjzhao.wh.gmail.com (Tue May 22 2012 - 19:38:00 PDT)
- Re: [AMBER] simulation with special amino acid David A. Case (Wed May 23 2012 - 04:09:07 PDT)
  - Re: [AMBER] simulation with special amino acid Yunjie Zhao (Wed May 23 2012 - 04:47:29 PDT)
[AMBER] High Electrostatic Energy in MMPBSA analysis Khaled Barakat (Tue May 22 2012 - 19:41:29 PDT)
- Re: [AMBER] High Electrostatic Energy in MMPBSA analysis Ray Luo, Ph.D. (Wed May 23 2012 - 10:03:34 PDT)
[AMBER] Amber tools 12 and esp visualization in VMD and PyMol Sudarshan Debnath (Tue May 22 2012 - 21:23:45 PDT)
- Re: [AMBER] Amber tools 12 and esp visualization in VMD and PyMol Ray Luo, Ph.D. (Wed May 23 2012 - 10:09:27 PDT)
[AMBER] how can i introduce Zn2+ in amber Sanjib Paul (Wed May 23 2012 - 00:17:45 PDT)
- Re: [AMBER] how can i introduce Zn2+ in amber David A. Case (Wed May 23 2012 - 04:10:30 PDT)
[AMBER] convert error Albert (Wed May 23 2012 - 00:38:57 PDT)
[AMBER] how to introduce Zn2+ in amber Sanjib Paul (Wed May 23 2012 - 01:50:28 PDT)
- Re: [AMBER] how to introduce Zn2+ in amber Marc van der Kamp (Wed May 23 2012 - 02:01:10 PDT)
- Re: [AMBER] how to introduce Zn2+ in amber Urszula Uciechowska (Wed May 23 2012 - 02:17:02 PDT)
  - Re: [AMBER] how to introduce Zn2+ in amber Sanjib Paul (Wed May 23 2012 - 21:45:11 PDT)
[AMBER] periodic box blow up kamlesh sahu (Wed May 23 2012 - 02:23:48 PDT)
- Re: [AMBER] periodic box blow up David A. Case (Wed May 23 2012 - 04:17:38 PDT)
  - Re: [AMBER] periodic box blow up kamlesh sahu (Wed May 23 2012 - 23:55:14 PDT)
[AMBER] Amber tools 12 and esp visualization in VMD and PyMol Sudarshan Debnath (Wed May 23 2012 - 05:30:31 PDT)
[AMBER] openf90 seg-faults during compilation Fluder, Eugene (Wed May 23 2012 - 06:04:57 PDT)
[AMBER] Amber tools 12 and esp visualization in VMD and PyMol Sudarshan Debnath (Wed May 23 2012 - 06:10:18 PDT)
- Re: [AMBER] Amber tools 12 and esp visualization in VMD and PyMol Jan-Philip Gehrcke (Wed May 23 2012 - 09:20:52 PDT)
  - Re: [AMBER] Visualisation of periodic boundary conditions within VMD Ben Ahmady (Wed May 23 2012 - 09:45:54 PDT)
    - Re: [AMBER] Visualisation of periodic boundary conditions within VMD Jason Swails (Tue May 29 2012 - 09:59:38 PDT)
[AMBER] DNA capping Mithun Biswas (Wed May 23 2012 - 07:54:03 PDT)
- Re: [AMBER] DNA capping FyD (Thu May 24 2012 - 23:31:25 PDT)
  - Re: [AMBER] DNA capping David A Case (Fri May 25 2012 - 04:46:58 PDT)
[AMBER] Antechamber Atom Types Sarah Edwards (Wed May 23 2012 - 14:43:07 PDT)
- Re: [AMBER] Antechamber Atom Types David A. Case (Wed May 23 2012 - 18:42:59 PDT)
[AMBER] problem with mol2 to pdb conversion Chris Chris (Mon May 21 2012 - 20:46:04 PDT)
- Re: [AMBER] problem with mol2 to pdb conversion g t (Thu May 24 2012 - 01:24:44 PDT)
  - Re: [AMBER] problem with mol2 to pdb conversion Marc van der Kamp (Thu May 24 2012 - 04:40:48 PDT)
    - Re: [AMBER] problem with mol2 to pdb conversion George Tzotzos (Thu May 24 2012 - 06:06:25 PDT)
[AMBER] Hydrogen bond energy calculation Aditya Padhi (Wed May 23 2012 - 20:55:35 PDT)
Re: [AMBER] AMBER Digest, Vol 162, Issue 3 jit mukherjee (Wed May 23 2012 - 21:37:56 PDT)
- Re: [AMBER] AMBER Digest, Vol 162, Issue 3 Julio Dominguez (Thu May 24 2012 - 08:48:15 PDT)
  - Re: [AMBER] AMBER Digest, Vol 162, Issue 3 Jason Swails (Mon May 28 2012 - 15:41:54 PDT)
[AMBER] SIMMULATION OF CARBON NANOTUBE jit mukherjee (Wed May 23 2012 - 21:52:50 PDT)
- Re: [AMBER] SIMMULATION OF CARBON NANOTUBE FyD (Thu May 24 2012 - 23:18:32 PDT)
  - Re: [AMBER] SIMMULATION OF CARBON NANOTUBE Markus Kaukonen (Thu May 24 2012 - 23:44:49 PDT)
- Re: [AMBER] SIMMULATION OF CARBON NANOTUBE jit mukherjee (Fri May 25 2012 - 12:35:11 PDT)
[AMBER] Problem in Amber11 Compilation HIMANSHU JOSHI (Wed May 23 2012 - 22:07:00 PDT)
- Re: [AMBER] Problem in Amber11 Compilation David A Case (Thu May 24 2012 - 05:06:10 PDT)
[AMBER] Solvation of surfactant molecules Debolina Mitra (Thu May 24 2012 - 01:19:44 PDT)
- Re: [AMBER] Solvation of surfactant molecules FyD (Thu May 24 2012 - 23:33:49 PDT)
[AMBER] Generate Gaussian file in antechamber Debolina Mitra (Thu May 24 2012 - 01:33:08 PDT)
[AMBER] Amber tools 12 and esp visualization in VMD and PyMol Sudarshan Debnath (Thu May 24 2012 - 04:00:09 PDT)
[AMBER] Amber tools 12 and esp visualization in VMD and PyMol Sudarshan Debnath (Thu May 24 2012 - 02:30:10 PDT)
[AMBER] large deviation on entropy value using ambertools1.5 manikanthan bhavaraju (Thu May 24 2012 - 21:30:34 PDT)
- [AMBER] large deviation on entropy value using ambertools1.5 manikanthan bhavaraju (Sat May 26 2012 - 08:20:08 PDT)
  - Re: [AMBER] large deviation on entropy value using ambertools1.5 Bill Miller III (Mon May 28 2012 - 06:55:41 PDT)
    - Re: [AMBER] large deviation on entropy value using ambertools1.5 Cao Yang (Mon May 28 2012 - 23:52:46 PDT)
    - Re: [AMBER] large deviation on entropy value using ambertools1.5 Jason Swails (Tue May 29 2012 - 06:42:48 PDT)
    - Re: [AMBER] large deviation on entropy value using ambertools1.5 Jason Swails (Tue May 29 2012 - 10:28:39 PDT)
    - Re: [AMBER] large deviation on entropy value using ambertools1.5 Cao Yang (Tue May 29 2012 - 19:07:13 PDT)
    - Re: [AMBER] large deviation on entropy value using ambertools1.5 Jason Swails (Tue May 29 2012 - 19:34:23 PDT)
    - Re: [AMBER] large deviation on entropy value using ambertools1.5 Cao Yang (Tue May 29 2012 - 19:45:47 PDT)
    - Re: [AMBER] large deviation on entropy value using ambertools1.5 Jason Swails (Tue May 29 2012 - 20:30:01 PDT)
    - Re: [AMBER] large deviation on entropy value using ambertools1.5 Cao Yang (Tue May 29 2012 - 21:49:45 PDT)
    - Re: [AMBER] large deviation on entropy value using ambertools1.5 Jason Swails (Tue May 29 2012 - 22:06:23 PDT)
    - Re: [AMBER] large deviation on entropy value using ambertools1.5 Cao Yang (Wed May 30 2012 - 05:11:43 PDT)
    - Re: [AMBER] large deviation on entropy value using ambertools1.5 Jason Swails (Wed May 30 2012 - 05:44:48 PDT)
[AMBER] Reallocation of memory space Debolina Mitra (Fri May 25 2012 - 02:39:09 PDT)
- [AMBER] Reallocation of memory space Debolina Mitra (Mon May 28 2012 - 23:23:17 PDT)
- [AMBER] Reallocation of memory space Debolina Mitra (Mon Jun 04 2012 - 05:38:32 PDT)
[AMBER] AM1/D - ATP+PROTEIN Fernando Martín García (Fri May 25 2012 - 03:22:47 PDT)
- Re: [AMBER] AM1/D - ATP+PROTEIN Brian Radak (Fri May 25 2012 - 06:02:46 PDT)
  - Re: [AMBER] AM1/D - ATP+PROTEIN Fernando Martín García (Fri May 25 2012 - 07:07:11 PDT)
[AMBER] Problem regarding CaDA Sanjib Paul (Fri May 25 2012 - 03:30:05 PDT)
- Re: [AMBER] Problem regarding CaDA Marc van der Kamp (Fri May 25 2012 - 03:36:18 PDT)
[AMBER] manual prmtop file editing for free energy calculation Audrius Laurynėnas (Fri May 25 2012 - 04:16:42 PDT)
- Re: [AMBER] manual prmtop file editing for free energy calculation Brian Radak (Fri May 25 2012 - 06:17:33 PDT)
  - Re: [AMBER] manual prmtop file editing for free energy calculation Jason Swails (Sat May 26 2012 - 16:14:55 PDT)
[AMBER] input card for relative permittivity Bala subramanian (Fri May 25 2012 - 05:39:53 PDT)
[AMBER] pnetcdf.h missing in compiling of ptraj.MPI Yubo Fan (Fri May 25 2012 - 13:47:06 PDT)
- Re: [AMBER] pnetcdf.h missing in compiling of ptraj.MPI Jason Swails (Fri May 25 2012 - 19:26:52 PDT)
[AMBER] Two Dimensional Periodic Boundary Conditions Zubin Kuvadia (Fri May 25 2012 - 14:10:01 PDT)
- [AMBER] How can we make sure we have the extent of conformational sampling is enough? Catein Catherine (Fri May 25 2012 - 19:10:32 PDT)
[AMBER] How to calculate entropy lost upon binding? Catein Catherine (Fri May 25 2012 - 19:16:10 PDT)
[AMBER] Saving the original position of atoms on using LEaP Francesco Pietra (Sat May 26 2012 - 07:13:12 PDT)
- Re: [AMBER] Saving the original position of atoms on using LEaP case (Sun May 27 2012 - 06:25:50 PDT)
[AMBER] Can AMBER do Go model? Catein Catherine (Sat May 26 2012 - 08:14:09 PDT)
[AMBER] relaxation time kirtana S (Sat May 26 2012 - 23:59:50 PDT)
- Re: [AMBER] relaxation time Jason Swails (Sun May 27 2012 - 16:57:03 PDT)
  - [AMBER] why is internal energy not taken into account for G gas? Xioling Chuang (Sun May 27 2012 - 23:02:13 PDT)
    - Re: [AMBER] why is internal energy not taken into account for G gas? Bill Miller III (Mon May 28 2012 - 04:53:02 PDT)
    - Re: [AMBER] why is internal energy not taken into account for G gas? Jason Swails (Mon May 28 2012 - 15:31:43 PDT)
    - Re: [AMBER] why is internal energy not taken into account for G gas? Xioling Chuang (Tue May 29 2012 - 19:03:45 PDT)
[AMBER] Problem regarding CaDA Sanjib Paul (Sun May 27 2012 - 03:27:56 PDT)
[AMBER] How to get a reliable RMSF value? aa aa (Sun May 27 2012 - 23:31:03 PDT)
- Re: [AMBER] How to get a reliable RMSF value? Jason Swails (Tue May 29 2012 - 09:45:20 PDT)
Re: [AMBER] Help! Assigned Bond types are wrong ashley chen (Sun May 27 2012 - 23:58:47 PDT)
- Re: [AMBER] Help! Assigned Bond types are wrong Marc van der Kamp (Mon May 28 2012 - 00:59:14 PDT)
- Re: [AMBER] Help! Assigned Bond types are wrong case (Mon May 28 2012 - 06:11:46 PDT)
[AMBER] conformational entropy of a peptide - how to calculate with AMBER? aa aa (Mon May 28 2012 - 01:37:19 PDT)
[AMBER] Compile Amber 12 with IBM compilers Yubo Fan (Mon May 28 2012 - 08:33:28 PDT)
- Re: [AMBER] Compile Amber 12 with IBM compilers case (Mon May 28 2012 - 13:45:35 PDT)
  - Re: [AMBER] Compile Amber 12 with IBM compilers Yubo Fan (Mon May 28 2012 - 18:48:56 PDT)
    - Re: [AMBER] Compile Amber 12 with IBM compilers David A Case (Tue May 29 2012 - 04:48:50 PDT)
[AMBER] How to resume production phase simulation from power failure? bin wang (Mon May 28 2012 - 08:54:59 PDT)
- Re: [AMBER] How to resume production phase simulation from power failure? case (Mon May 28 2012 - 13:49:06 PDT)
  - Re: [AMBER] How to resume production phase simulation from power failure? bin wang (Tue May 29 2012 - 06:40:22 PDT)
[AMBER] Volume fraction John S (Mon May 28 2012 - 12:36:43 PDT)
Re: [AMBER] Help! Assigned Bond types may be wrong ashley chen (Mon May 28 2012 - 21:07:45 PDT)
- Re: [AMBER] Help! Assigned Bond types may be wrong David A Case (Tue May 29 2012 - 04:53:01 PDT)
[AMBER] simmulation of carbon nanotube jit mukherjee (Mon May 28 2012 - 21:18:20 PDT)
[AMBER] Looping over a trajectory Lee-Ping Wang (Tue May 29 2012 - 00:27:22 PDT)
- Re: [AMBER] Looping over a trajectory David A Case (Tue May 29 2012 - 05:00:39 PDT)
  - Re: [AMBER] Looping over a trajectory Lee-Ping Wang (Tue May 29 2012 - 10:29:48 PDT)
    - Re: [AMBER] Looping over a trajectory Jason Swails (Tue May 29 2012 - 10:33:22 PDT)
    - Re: [AMBER] Looping over a trajectory Lee-Ping Wang (Tue May 29 2012 - 10:53:23 PDT)
    - Re: [AMBER] Looping over a trajectory Jason Swails (Tue May 29 2012 - 11:06:37 PDT)
    - Re: [AMBER] Looping over a trajectory Lee-Ping Wang (Tue May 29 2012 - 11:18:15 PDT)
    - Re: [AMBER] Looping over a trajectory Jason Swails (Tue May 29 2012 - 11:41:00 PDT)
    - Re: [AMBER] Looping over a trajectory Lee-Ping Wang (Wed Jul 04 2012 - 12:48:01 PDT)
[AMBER] Can I use “-rewrite-output” option in redoing the free energy calculation Cao Yang (Tue May 29 2012 - 02:59:16 PDT)
- Re: [AMBER] Can I use “-rewrite-output” option in redoing the free energy calculation Bill Miller III (Tue May 29 2012 - 04:55:03 PDT)
  - Re: [AMBER] Can I use “-rewrite-output” option in redoing the free energy calculation Jason Swails (Tue May 29 2012 - 10:16:53 PDT)
[AMBER] High standard deviation in entropy and decomping calculation Cao Yang (Tue May 29 2012 - 05:53:53 PDT)
- Re: [AMBER] High standard deviation in entropy and decomping calculation Bill Miller III (Tue May 29 2012 - 05:58:02 PDT)
- Re: [AMBER] High standard deviation in entropy and decomping calculation Jason Swails (Tue May 29 2012 - 10:50:38 PDT)
[AMBER] multi-threading cpu's or no multi-threading Jonathan Gough (Tue May 29 2012 - 15:40:05 PDT)
- Re: [AMBER] multi-threading cpu's or no multi-threading Jason Swails (Tue May 29 2012 - 18:25:01 PDT)
  - Re: [AMBER] multi-threading cpu's or no multi-threading Jonathan Gough (Tue May 29 2012 - 19:25:33 PDT)
    - Re: [AMBER] multi-threading cpu's or no multi-threading Jason Swails (Tue May 29 2012 - 19:33:07 PDT)
[AMBER] Problem regarding simulation of bio-molecules using AMBER 9 somedatta pal (Wed May 30 2012 - 03:41:59 PDT)
- Re: [AMBER] Problem regarding simulation of bio-molecules using AMBER 9 David A Case (Wed May 30 2012 - 04:51:08 PDT)
[AMBER] Trouble compiling cuda, need help. Jonathan Gough (Wed May 30 2012 - 05:25:39 PDT)
- Re: [AMBER] Trouble compiling cuda, need help. Jason Swails (Wed May 30 2012 - 06:06:55 PDT)
  - Re: [AMBER] Trouble compiling cuda, need help. Jonathan Gough (Wed May 30 2012 - 06:08:06 PDT)
    - [AMBER] How AMBER process the energy of hydrogen bond Acoot Brett (Wed May 30 2012 - 23:40:41 PDT)
    - Re: [AMBER] How AMBER process the energy of hydrogen bond Brian Radak (Thu May 31 2012 - 04:33:21 PDT)
- Re: [AMBER] Trouble compiling cuda, need help. Ross Walker (Wed May 30 2012 - 09:23:53 PDT)
  - Re: [AMBER] Trouble compiling cuda, need help. Jonathan Gough (Wed May 30 2012 - 09:29:44 PDT)
    - Re: [AMBER] Trouble compiling cuda, need help. Ross Walker (Wed May 30 2012 - 09:39:14 PDT)
    - Re: [AMBER] Trouble compiling cuda, need help. Jonathan Gough (Wed May 30 2012 - 09:54:23 PDT)
    - Re: [AMBER] Trouble compiling cuda, need help. David A Case (Wed May 30 2012 - 11:09:08 PDT)
    - Re: [AMBER] Trouble compiling cuda, need help. Jonathan Gough (Wed May 30 2012 - 11:27:08 PDT)
    - Re: [AMBER] Trouble compiling cuda, need help. Jonathan Gough (Wed May 30 2012 - 11:44:19 PDT)
    - Re: [AMBER] Trouble compiling cuda, need help. Ross Walker (Wed May 30 2012 - 11:59:20 PDT)
    - Re: [AMBER] Trouble compiling cuda, need help. Jonathan Gough (Wed May 30 2012 - 12:20:12 PDT)
    - Re: [AMBER] Trouble compiling cuda, need help. Scott Le Grand (Wed May 30 2012 - 15:43:31 PDT)
    - Re: [AMBER] Trouble compiling cuda, need help. case (Wed May 30 2012 - 20:38:45 PDT)
    - [AMBER] Problem with NAB: "Residue g not in library rna.amber94.rlb." Romelia Salomon (Tue Jun 05 2012 - 10:30:12 PDT)
    - Re: [AMBER] Problem with NAB: "Residue g not in library rna.amber94.rlb." David A. Case (Tue Jun 05 2012 - 10:50:47 PDT)
    - Re: [AMBER] Problem with NAB: "Residue g not in library rna.amber94.rlb." Romelia Salomon (Tue Jun 05 2012 - 11:17:31 PDT)
    - Re: [AMBER] Problem with NAB: "Residue g not in library rna.amber94.rlb." cieplak.cgl.ucsf.edu (Tue Jun 05 2012 - 13:07:06 PDT)
    - Re: [AMBER] Problem with NAB: "Residue g not in library rna.amber94.rlb." Romelia Salomon (Tue Jun 05 2012 - 15:07:11 PDT)
[AMBER] problem with solute that breaks up Massimiliano Porrini (Wed May 30 2012 - 05:46:16 PDT)
- Re: [AMBER] problem with solute that breaks up David A Case (Wed May 30 2012 - 07:45:36 PDT)
  - Re: [AMBER] problem with solute that breaks up Massimiliano Porrini (Wed May 30 2012 - 11:05:03 PDT)
    - Re: [AMBER] problem with solute that breaks up Jason Swails (Wed May 30 2012 - 15:03:06 PDT)
    - Re: [AMBER] problem with solute that breaks up Massimiliano Porrini (Thu May 31 2012 - 04:55:15 PDT)
  - [AMBER] Heme force field hwchem chem (Wed May 30 2012 - 17:48:51 PDT)
    - Re: [AMBER] Heme force field Mark Williamson (Thu May 31 2012 - 03:16:46 PDT)
    - Re: [AMBER] Heme force field Yue (Thu May 31 2012 - 18:40:10 PDT)
- Re: [AMBER] problem with solute that breaks up Thomas Cheatham (Wed May 30 2012 - 15:09:22 PDT)
  - Re: [AMBER] problem with solute that breaks up gaoya (Thu May 31 2012 - 22:20:54 PDT)
[AMBER] Amber 12 on x86_64 CentOS 5 Kevin Parkes (Wed May 30 2012 - 05:48:40 PDT)
- Re: [AMBER] Amber 12 on x86_64 CentOS 5 Jason Swails (Wed May 30 2012 - 06:04:45 PDT)
  - Re: [AMBER] Amber 12 on x86_64 CentOS 5 Kevin Parkes (Wed May 30 2012 - 06:25:54 PDT)
    - Re: [AMBER] Amber 12 on x86_64 CentOS 5 Jason Swails (Wed May 30 2012 - 08:01:51 PDT)
    - Re: [AMBER] Amber 12 on x86_64 CentOS 5 Kevin Parkes (Thu May 31 2012 - 06:21:55 PDT)
    - Re: [AMBER] Amber 12 on x86_64 CentOS 5 - SOLVED Kevin Parkes (Fri Jun 01 2012 - 02:59:03 PDT)
[AMBER] how long does cuda test usually take? Jonathan Gough (Wed May 30 2012 - 13:23:09 PDT)
- Re: [AMBER] how long does cuda test usually take? Jason Swails (Wed May 30 2012 - 13:49:19 PDT)
  - Re: [AMBER] how long does cuda test usually take? Jonathan Gough (Wed May 30 2012 - 13:52:15 PDT)
    - Re: [AMBER] how long does cuda test usually take? Scott Le Grand (Wed May 30 2012 - 14:55:47 PDT)
    - Re: [AMBER] how long does cuda test usually take? Jonathan Gough (Wed May 30 2012 - 17:48:46 PDT)
[AMBER] Cuda-enabled amber 11 installation error Rajeswari A. (Thu May 31 2012 - 00:33:04 PDT)
- Re: [AMBER] Cuda-enabled amber 11 installation error case (Thu May 31 2012 - 04:33:57 PDT)
  - Re: [AMBER] Cuda-enabled amber 11 installation error Rajeswari A. (Thu May 31 2012 - 06:36:44 PDT)
[AMBER] Loading charged Peptide in tleap Thorsten Pisternick (Thu May 31 2012 - 01:52:31 PDT)
- Re: [AMBER] Loading charged Peptide in tleap case (Thu May 31 2012 - 04:28:02 PDT)
[AMBER] ptraj Hbond analysis shradhey gupta (Thu May 31 2012 - 04:51:14 PDT)
[AMBER] ptraj Hbond analysis shradhey gupta (Thu May 31 2012 - 06:51:00 PDT)
[AMBER] ptraj Hbond analysis shradhey gupta (Thu May 31 2012 - 06:53:26 PDT)
[AMBER] ptraj Hbond analysis shradhey gupta (Thu May 31 2012 - 06:55:04 PDT)
[AMBER] mm_pbsa.pl analysis bmartini (Thu May 31 2012 - 08:52:27 PDT)
[AMBER] MMPBSA error in AmberTools 12 --- TrajError: Solvated topology 0 has IFBOX == 0 Cao Yang (Thu May 31 2012 - 10:02:48 PDT)
- Re: [AMBER] MMPBSA error in AmberTools 12 --- TrajError: Solvated topology 0 has IFBOX == 0 Bill Miller III (Thu May 31 2012 - 10:20:26 PDT)
  - Re: [AMBER] MMPBSA error in AmberTools 12 --- TrajError: Solvated topology 0 has IFBOX == 0 Cao Yang (Thu May 31 2012 - 18:05:31 PDT)
    - Re: [AMBER] MMPBSA error in AmberTools 12 --- TrajError: Solvated topology 0 has IFBOX == 0 Bill Miller III (Thu May 31 2012 - 18:43:47 PDT)
    - Re: [AMBER] MMPBSA error in AmberTools 12 --- TrajError: Solvated topology 0 has IFBOX == 0 Jason Swails (Thu May 31 2012 - 19:02:00 PDT)
    - Re: [AMBER] MMPBSA error in AmberTools 12 --- TrajError: Solvated topology 0 has IFBOX == 0 Cao Yang (Thu May 31 2012 - 19:13:06 PDT)
    - Re: [AMBER] MMPBSA error in AmberTools 12 --- TrajError: Solvated topology 0 has IFBOX == 0 Jason Swails (Thu May 31 2012 - 20:36:26 PDT)
    - Re: [AMBER] MMPBSA error in AmberTools 12 --- TrajError: Solvated topology 0 has IFBOX == 0 Cao Yang (Thu May 31 2012 - 20:50:54 PDT)
    - Re: [AMBER] MMPBSA error in AmberTools 12 --- TrajError: Solvated topology 0 has IFBOX == 0 Jason Swails (Fri Jun 01 2012 - 05:51:01 PDT)
    - Re: [AMBER] MMPBSA error in AmberTools 12 --- TrajError: Solvated topology 0 has IFBOX == 0 Cao Yang (Fri Jun 01 2012 - 06:03:50 PDT)
    - Re: [AMBER] MMPBSA error in AmberTools 12 --- TrajError: Solvated topology 0 has IFBOX == 0 Jason Swails (Fri Jun 01 2012 - 06:22:54 PDT)
    - Re: [AMBER] MMPBSA error in AmberTools 12 --- TrajError: Solvated topology 0 has IFBOX == 0 Cao Yang (Fri Jun 01 2012 - 06:42:30 PDT)
[AMBER] Ptraj and new netcdf Restart files Joshua Adelman (Thu May 31 2012 - 10:55:05 PDT)
- [AMBER] base pairs missing from nastruct analysis of canonical B-DNA dodecamer Dean Cuebas (Thu May 31 2012 - 12:00:09 PDT)
  - Re: [AMBER] base pairs missing from nastruct analysis of canonical B-DNA dodecamer Daniel Roe (Thu May 31 2012 - 13:55:25 PDT)
- Re: [AMBER] Ptraj and new netcdf Restart files Jason Swails (Thu May 31 2012 - 12:16:29 PDT)
[AMBER] problem with running equilibration MD in an LES system Sajeewa Pemasinghe (Thu May 31 2012 - 13:39:02 PDT)
- [AMBER] Fwd: problem with running equilibration MD in an LES system Sajeewa Pemasinghe (Thu May 31 2012 - 13:58:06 PDT)
  - [AMBER] Fwd: problem with running equilibration MD in an LES system Sajeewa Pemasinghe (Fri Jun 01 2012 - 05:58:51 PDT)
    - Re: [AMBER] Fwd: problem with running equilibration MD in an LES system David A Case (Fri Jun 01 2012 - 06:47:18 PDT)
    - Re: [AMBER] Fwd: problem with running equilibration MD in an LES system Sajeewa Pemasinghe (Fri Jun 01 2012 - 07:43:18 PDT)
    - Re: [AMBER] Fwd: problem with running equilibration MD in an LES system David A Case (Fri Jun 01 2012 - 08:42:19 PDT)
    - Re: [AMBER] Fwd: problem with running equilibration MD in an LES system Brian Radak (Fri Jun 01 2012 - 15:51:40 PDT)
    - Re: [AMBER] Fwd: problem with running equilibration MD in an LES system Sajeewa Pemasinghe (Fri Jun 01 2012 - 18:51:27 PDT)
    - [AMBER] Fwd: Fwd: problem with running equilibration MD in an LES system Sajeewa Pemasinghe (Mon Jun 04 2012 - 09:25:23 PDT)
    - Re: [AMBER] Fwd: Fwd: problem with running equilibration MD in an LES system Carlos Simmerling (Mon Jun 04 2012 - 09:44:10 PDT)
    - Re: [AMBER] Fwd: Fwd: problem with running equilibration MD in an LES system Sajeewa Pemasinghe (Mon Jun 04 2012 - 10:15:21 PDT)
[AMBER] Trouble calculating free energy bmartini (Thu May 31 2012 - 20:14:57 PDT)
- Re: [AMBER] Trouble calculating free energy steinbrt.rci.rutgers.edu (Fri Jun 01 2012 - 01:04:12 PDT)
- Re: [AMBER] Trouble calculating free energy Aldo Segura (Fri Jun 01 2012 - 22:48:34 PDT)
[AMBER] cuda errors Jonathan Gough (Thu May 31 2012 - 21:13:22 PDT)
- Re: [AMBER] cuda errors Ross Walker (Thu May 31 2012 - 21:35:26 PDT)
  - Re: [AMBER] cuda errors Jonathan Gough (Fri Jun 01 2012 - 08:21:24 PDT)
[AMBER] ptraj Hbond analysis shradhey gupta (Thu May 31 2012 - 21:55:09 PDT)
[AMBER] ptraj Hbond analysis shradhey gupta (Thu May 31 2012 - 21:56:20 PDT)
- Re: [AMBER] ptraj Hbond analysis Thomas Cheatham (Mon Jun 04 2012 - 12:01:35 PDT)
[AMBER] MMPBSA_Error: Could not find necessary program [sander] Cao Yang (Fri Jun 01 2012 - 00:58:05 PDT)
- Re: [AMBER] MMPBSA_Error: Could not find necessary program [sander] Jason Swails (Fri Jun 01 2012 - 05:40:44 PDT)
  - Re: [AMBER] MMPBSA_Error: Could not find necessary program [sander] Cao Yang (Fri Jun 01 2012 - 06:29:34 PDT)
    - Re: [AMBER] MMPBSA_Error: Could not find necessary program [sander] Bill Miller III (Fri Jun 01 2012 - 07:46:28 PDT)
[AMBER] chloride ions outside the box Francesco Pietra (Fri Jun 01 2012 - 01:53:26 PDT)
[AMBER] Effect of Temperature Soumya Lipsa Rath (Fri Jun 01 2012 - 04:15:29 PDT)
- Re: [AMBER] Effect of Temperature Jason Swails (Fri Jun 01 2012 - 05:57:29 PDT)
  - Re: [AMBER] Effect of Temperature Soumya Lipsa Rath (Fri Jun 01 2012 - 20:19:27 PDT)
- Re: [AMBER] Effect of Temperature Hai Nguyen (Fri Jun 01 2012 - 20:49:07 PDT)
  - Re: [AMBER] Effect of Temperature Soumya Lipsa Rath (Fri Jun 01 2012 - 20:57:53 PDT)
[AMBER] cuda parallel - can't find mpi.h Jonathan Gough (Fri Jun 01 2012 - 08:45:28 PDT)
- Re: [AMBER] cuda parallel - can't find mpi.h Jason Swails (Fri Jun 01 2012 - 09:16:20 PDT)
- Re: [AMBER] cuda parallel - can't find mpi.h Ross Walker (Fri Jun 01 2012 - 09:19:33 PDT)
  - Re: [AMBER] cuda parallel - can't find mpi.h Jonathan Gough (Fri Jun 01 2012 - 09:40:54 PDT)
  - Re: [AMBER] cuda parallel - can't find mpi.h David A Case (Fri Jun 01 2012 - 09:49:34 PDT)
[AMBER] Configurational bias Monte Carlo Benjamin Haley (Fri Jun 01 2012 - 09:19:01 PDT)
- Re: [AMBER] Configurational bias Monte Carlo David A Case (Fri Jun 01 2012 - 09:50:29 PDT)
- Re: [AMBER] Configurational bias Monte Carlo Jason Swails (Fri Jun 01 2012 - 10:22:25 PDT)
[AMBER] No C-terminal GLH in aminoct*.in Marc van der Kamp (Fri Jun 01 2012 - 10:01:02 PDT)
- Re: [AMBER] No C-terminal GLH in aminoct*.in Jason Swails (Fri Jun 01 2012 - 10:27:33 PDT)
  - Re: [AMBER] No C-terminal GLH in aminoct*.in FyD (Sat Jun 02 2012 - 23:18:16 PDT)
    - Re: [AMBER] No C-terminal GLH in aminoct*.in Marc van der Kamp (Tue Jun 05 2012 - 08:46:21 PDT)
    - Re: [AMBER] No C-terminal GLH in aminoct*.in Jason Swails (Tue Jun 05 2012 - 10:29:40 PDT)
    - Re: [AMBER] No C-terminal GLH in aminoct*.in Marc van der Kamp (Wed Jun 06 2012 - 00:29:17 PDT)
    - Re: [AMBER] No C-terminal GLH in aminoct*.in FyD (Wed Jun 06 2012 - 02:20:33 PDT)
    - Re: [AMBER] No C-terminal GLH in aminoct*.in FyD (Tue Jun 05 2012 - 23:22:32 PDT)
[AMBER] is there a batch queue app? Jonathan Gough (Fri Jun 01 2012 - 11:58:12 PDT)
- Re: [AMBER] is there a batch queue app? Scott Le Grand (Fri Jun 01 2012 - 12:06:17 PDT)
  - Re: [AMBER] is there a batch queue app? Jason Swails (Fri Jun 01 2012 - 12:22:32 PDT)
  - Re: [AMBER] is there a batch queue app? Anselm Horn (Fri Jun 01 2012 - 13:02:17 PDT)
    - Re: [AMBER] is there a batch queue app? Jonathan Gough (Fri Jun 01 2012 - 13:56:05 PDT)
    - Re: [AMBER] is there a batch queue app? Jonathan Gough (Tue Jun 05 2012 - 14:38:42 PDT)
[AMBER] rocks cluster: MD is much slower when using more than one node Junmei Wang (Fri Jun 01 2012 - 13:15:56 PDT)
- Re: [AMBER] rocks cluster: MD is much slower when using more than one node Dmitry Mukha (Sat Jun 02 2012 - 02:35:38 PDT)
- Re: [AMBER] rocks cluster: MD is much slower when using more than one node case (Sat Jun 02 2012 - 06:06:10 PDT)
  - Re: [AMBER] rocks cluster: MD is much slower when using more than one node Junmei Wang (Sat Jun 02 2012 - 07:11:34 PDT)
    - Re: [AMBER] rocks cluster: MD is much slower when using more than one node Matthew Zwier (Sun Jun 03 2012 - 06:08:09 PDT)
[AMBER] decomposition of potential of mean force into free energy contribution caobb0214 (Fri Jun 01 2012 - 21:50:22 PDT)
[AMBER] ptraj Hbond analysis shradhey gupta (Fri Jun 01 2012 - 22:51:36 PDT)
[AMBER] Trouble calculating free energy bmartini (Sat Jun 02 2012 - 06:43:14 PDT)
[AMBER] inpcrd Dr. Vitaly V. Chaban (Sun Jun 03 2012 - 12:08:29 PDT)
- Re: [AMBER] inpcrd Daniel Roe (Sun Jun 03 2012 - 13:04:23 PDT)
  - Re: [AMBER] inpcrd Dr. Vitaly V. Chaban (Sun Jun 03 2012 - 14:24:51 PDT)
    - [AMBER] how to change the namme of the terminal OXT so that it can be recoginized by MOLMOL Acoot Brett (Sun Jun 03 2012 - 23:57:53 PDT)
    - Re: [AMBER] how to change the namme of the terminal OXT so that it can be recoginized by MOLMOL steinbrt.rci.rutgers.edu (Mon Jun 04 2012 - 00:25:58 PDT)
    - Re: [AMBER] how to change the namme of the terminal OXT so that it can be recoginized by MOLMOL David A Case (Mon Jun 04 2012 - 04:55:03 PDT)
[AMBER] Distance constraints not working.. Kumar, Sonu (Mon Jun 04 2012 - 01:35:37 PDT)
- Re: [AMBER] Distance constraints not working.. David A Case (Mon Jun 04 2012 - 04:57:17 PDT)
  - Re: [AMBER] Distance constraints not working.. Kumar, Sonu (Mon Jun 04 2012 - 09:53:58 PDT)
    - Re: [AMBER] Distance constraints not working.. Adrian Roitberg (Mon Jun 04 2012 - 09:58:49 PDT)
[AMBER] Problem in parameter file generation Asma Abro 28-FBAS/MSBI/F09 (Mon Jun 04 2012 - 02:47:19 PDT)
- Re: [AMBER] Problem in parameter file generation Alex Rodriguez (Mon Jun 04 2012 - 02:54:25 PDT)
  - Re: [AMBER] Problem in parameter file generation Asma Abro 28-FBAS/MSBI/F09 (Mon Jun 04 2012 - 03:02:35 PDT)
    - Re: [AMBER] Problem in parameter file generation Alex Rodriguez (Mon Jun 04 2012 - 03:09:36 PDT)
    - Re: [AMBER] Problem in parameter file generation Asma Abro 28-FBAS/MSBI/F09 (Mon Jun 04 2012 - 03:22:32 PDT)
    - Re: [AMBER] Problem in parameter file generation Alex Rodriguez (Mon Jun 04 2012 - 03:30:17 PDT)
    - Re: [AMBER] Problem in parameter file generation Asma Abro 28-FBAS/MSBI/F09 (Mon Jun 04 2012 - 03:33:19 PDT)
[AMBER] Antechamber problem monica.imtech.res.in (Mon Jun 04 2012 - 08:57:03 PDT)
- Re: [AMBER] Antechamber problem David A Case (Mon Jun 04 2012 - 09:49:32 PDT)
[AMBER] compiling parallel on centOS5 - rocks with intel Jonathan Gough (Mon Jun 04 2012 - 10:54:44 PDT)
- Re: [AMBER] compiling parallel on centOS5 - rocks with intel David A Case (Mon Jun 04 2012 - 11:54:32 PDT)
  - Re: [AMBER] compiling parallel on centOS5 - rocks with intel Jonathan Gough (Mon Jun 04 2012 - 12:17:20 PDT)
    - Re: [AMBER] compiling parallel on centOS5 - rocks with intel Jason Swails (Mon Jun 04 2012 - 13:20:22 PDT)
    - Re: [AMBER] compiling parallel on centOS5 - rocks with intel Jonathan Gough (Mon Jun 04 2012 - 13:38:19 PDT)
    - Re: [AMBER] compiling parallel on centOS5 - rocks with intel Jason Swails (Mon Jun 04 2012 - 16:16:25 PDT)
    - Re: [AMBER] compiling parallel on centOS5 - rocks with intel Jonathan Gough (Mon Jun 04 2012 - 16:33:06 PDT)
    - Re: [AMBER] compiling parallel on centOS5 - rocks with intel Jason Swails (Mon Jun 04 2012 - 17:45:49 PDT)
[AMBER] nvidia GTX 550 Ti Michael Mayo (Mon Jun 04 2012 - 20:52:47 PDT)
- Re: [AMBER] nvidia GTX 550 Ti Scott Le Grand (Tue Jun 05 2012 - 08:02:38 PDT)
[AMBER] Small molecule simulations Chris Chris (Mon Jun 04 2012 - 21:37:51 PDT)
- Re: [AMBER] Small molecule simulations Dr. Vitaly V. Chaban (Mon Jun 04 2012 - 22:17:48 PDT)
- Re: [AMBER] Small molecule simulations bmartini (Mon Jun 04 2012 - 22:11:36 PDT)
[AMBER] Error in minimization Asma Abro 28-FBAS/MSBI/F09 (Mon Jun 04 2012 - 23:24:49 PDT)
- Re: [AMBER] Error in minimization Ben Roberts (Tue Jun 05 2012 - 00:26:05 PDT)
  - Re: [AMBER] Error in minimization Asma Abro 28-FBAS/MSBI/F09 (Tue Jun 05 2012 - 00:37:00 PDT)
    - Re: [AMBER] Error in minimization Daniel Roe (Tue Jun 05 2012 - 04:18:32 PDT)
    - Re: [AMBER] Error in minimization Asma Abro 28-FBAS/MSBI/F09 (Tue Jun 05 2012 - 21:28:18 PDT)
    - Re: [AMBER] Error in minimization Asma Abro 28-FBAS/MSBI/F09 (Wed Jun 06 2012 - 00:32:41 PDT)
    - [AMBER] Error in new installation. Catein Catherine (Wed Jun 06 2012 - 02:09:08 PDT)
    - Re: [AMBER] Error in new installation. Jason Swails (Wed Jun 06 2012 - 06:39:27 PDT)
    - Re: [AMBER] Error in minimization Jason Swails (Wed Jun 06 2012 - 06:40:14 PDT)
    - Re: [AMBER] Error in minimization Asma Abro 28-FBAS/MSBI/F09 (Wed Jun 06 2012 - 21:18:58 PDT)
    - Re: [AMBER] Error in minimization David A Case (Thu Jun 07 2012 - 04:49:58 PDT)
    - Re: [AMBER] Error in minimization Asma Abro 28-FBAS/MSBI/F09 (Thu Jun 07 2012 - 22:20:17 PDT)
    - Re: [AMBER] Error in minimization Asma Abro 28-FBAS/MSBI/F09 (Thu Jun 07 2012 - 22:49:36 PDT)
    - Re: [AMBER] Error in minimization Jason Swails (Fri Jun 08 2012 - 04:09:54 PDT)
    - Re: [AMBER] Error in minimization David A Case (Fri Jun 08 2012 - 05:20:22 PDT)
    - Re: [AMBER] Error in minimization Asma Abro 28-FBAS/MSBI/F09 (Fri Jun 08 2012 - 10:25:16 PDT)
    - Re: [AMBER] Error in minimization Asma Abro 28-FBAS/MSBI/F09 (Sun Jun 10 2012 - 22:10:27 PDT)
    - Re: [AMBER] Error in minimization Daniel Sindhikara (Sun Jun 10 2012 - 22:20:39 PDT)
    - Re: [AMBER] Error in minimization Asma Abro 28-FBAS/MSBI/F09 (Sun Jun 10 2012 - 22:24:54 PDT)
    - Re: [AMBER] Error in minimization Daniel Sindhikara (Sun Jun 10 2012 - 23:29:21 PDT)
    - Re: [AMBER] Error in minimization Ben Roberts (Mon Jun 11 2012 - 16:56:42 PDT)
    - Re: [AMBER] Error in minimization Asma Abro 28-FBAS/MSBI/F09 (Tue Jun 12 2012 - 04:00:29 PDT)
[AMBER] Amber11 Installation Problem arun kumar (Tue Jun 05 2012 - 00:46:47 PDT)
- Re: [AMBER] Amber11 Installation Problem Rajeswari A. (Tue Jun 05 2012 - 03:58:14 PDT)
  - Re: [AMBER] Amber11 Installation Problem Daniel Roe (Tue Jun 05 2012 - 04:16:57 PDT)
- Re: [AMBER] Amber11 Installation Problem Jason Swails (Tue Jun 05 2012 - 06:47:10 PDT)
  - [AMBER] Amber11 Installation Problem arun kumar (Tue Jun 05 2012 - 23:35:20 PDT)
    - Re: [AMBER] Amber11 Installation Problem Jason Swails (Wed Jun 06 2012 - 04:20:42 PDT)
    - Re: [AMBER] Amber11 Installation Problem arun kumar (Wed Jun 06 2012 - 05:51:10 PDT)
    - Re: [AMBER] Amber11 Installation Problem Jason Swails (Wed Jun 06 2012 - 06:22:51 PDT)
[AMBER] DMSO parameters Yun Shi (Tue Jun 05 2012 - 15:07:38 PDT)
- Re: [AMBER] DMSO parameters Dr. Vitaly V. Chaban (Tue Jun 05 2012 - 17:05:32 PDT)
[AMBER] MMPBSA.py - problem with complex.prmtop colvin (Wed Jun 06 2012 - 01:49:25 PDT)
- Re: [AMBER] MMPBSA.py - problem with complex.prmtop Bill Miller III (Wed Jun 06 2012 - 04:53:13 PDT)
  - Re: [AMBER] MMPBSA.py - problem with complex.prmtop colvin (Wed Jun 06 2012 - 20:01:32 PDT)
    - Re: [AMBER] MMPBSA.py - problem with complex.prmtop colvin (Tue Nov 27 2012 - 01:16:44 PST)
    - Re: [AMBER] MMPBSA.py - problem with complex.prmtop Jason Swails (Tue Nov 27 2012 - 04:54:39 PST)
[AMBER] center of mass. Subrata Paul (Wed Jun 06 2012 - 04:27:22 PDT)
[AMBER] Sander MMPBSA (EPB) Differences between Amber10 and Amber11 Damodaran, Komath (Wed Jun 06 2012 - 08:18:00 PDT)
- Re: [AMBER] Sander MMPBSA (EPB) Differences between Amber10 and Amber11 Bill Miller III (Wed Jun 06 2012 - 08:32:09 PDT)
- Re: [AMBER] Sander MMPBSA (EPB) Differences between Amber10 and Amber11 Damodaran, Komath (Thu Jun 07 2012 - 09:09:16 PDT)
  - Re: [AMBER] Sander MMPBSA (EPB) Differences between Amber10 and Amber11 Ray Luo, Ph.D. (Thu Jun 07 2012 - 09:52:12 PDT)
- Re: [AMBER] Sander MMPBSA (EPB) Differences between Amber10 and Amber11 Ray Luo, Ph.D. (Thu Jun 07 2012 - 15:02:28 PDT)
- Re: [AMBER] Sander MMPBSA (EPB) Differences between Amber10 and Amber11 Ray Luo, Ph.D. (Thu Jun 07 2012 - 16:32:10 PDT)
[AMBER] Convergence problems with rism1d and water model other than SPC Fabrício Bracht (Wed Jun 06 2012 - 10:26:23 PDT)
- [AMBER] Convergence problems with rism1d and water model other than SPC Fabrício Bracht (Wed Jun 06 2012 - 10:33:57 PDT)
  - Re: [AMBER] Convergence problems with rism1d and water model other than SPC tluchko (Wed Jun 06 2012 - 12:10:43 PDT)
[AMBER] Why calcualted energy difference betwwen MM-PBSA and MM-GBSA is so large Delwar Hossain (Wed Jun 06 2012 - 13:01:20 PDT)
[AMBER] restraining residues with a gpu cluster Tom Patapoff (Wed Jun 06 2012 - 17:50:18 PDT)
- Re: [AMBER] restraining residues with a gpu cluster case (Wed Jun 06 2012 - 19:10:24 PDT)
[AMBER] Removing finite number of solvent particles from simulation box Adam Jion (Wed Jun 06 2012 - 18:12:44 PDT)
- Re: [AMBER] Removing finite number of solvent particles from simulation box Jason Swails (Wed Jun 06 2012 - 19:31:01 PDT)
  - Re: [AMBER] Removing finite number of solvent particles from simulation box Jason Swails (Wed Jun 06 2012 - 19:31:25 PDT)
    - Re: [AMBER] Removing finite number of solvent particles from simulation box Adam Jion (Wed Jun 06 2012 - 21:49:22 PDT)
    - Re: [AMBER] Removing finite number of solvent particles from simulation box Jason Swails (Thu Jun 07 2012 - 07:23:30 PDT)
[AMBER] Problems installing AmberTools12 on Ubuntu Adam Jion (Thu Jun 07 2012 - 01:47:19 PDT)
- Re: [AMBER] Problems installing AmberTools12 on Ubuntu Jason Swails (Thu Jun 07 2012 - 07:40:23 PDT)
  - Re: [AMBER] Problems installing AmberTools12 on Ubuntu Adam Jion (Thu Jun 07 2012 - 18:22:42 PDT)
    - Re: [AMBER] Problems installing AmberTools12 on Ubuntu Jason Swails (Thu Jun 07 2012 - 18:31:07 PDT)
    - Re: [AMBER] Problems installing AmberTools12 on Ubuntu Adam Jion (Thu Jun 07 2012 - 18:41:55 PDT)
    - Re: [AMBER] Problems installing AmberTools12 on Ubuntu Jason Swails (Thu Jun 07 2012 - 19:16:45 PDT)
    - Re: [AMBER] Problems installing AmberTools12 on Ubuntu Adam Jion (Thu Jun 07 2012 - 19:32:29 PDT)
    - Re: [AMBER] Problems installing AmberTools12 on Ubuntu Jason Swails (Fri Jun 08 2012 - 04:05:23 PDT)
[AMBER] ptraj behaves differently on Mac and Linux Benjamin Stauch (Thu Jun 07 2012 - 02:23:33 PDT)
- Re: [AMBER] ptraj behaves differently on Mac and Linux Daniel Roe (Thu Jun 07 2012 - 06:24:29 PDT)
[AMBER] up coming workshop? Albert (Thu Jun 07 2012 - 10:06:55 PDT)
- Re: [AMBER] up coming workshop? Ross Walker (Thu Jun 07 2012 - 13:37:01 PDT)
  - Re: [AMBER] up coming workshop? Albert (Fri Jun 08 2012 - 00:17:11 PDT)
  - Re: [AMBER] up coming workshop? Albert (Fri Jun 08 2012 - 02:51:44 PDT)
[AMBER] what version of xcode are you using? Jonathan Gough (Thu Jun 07 2012 - 11:38:13 PDT)
- Re: [AMBER] what version of xcode are you using? Jason Swails (Thu Jun 07 2012 - 12:04:36 PDT)
  - Re: [AMBER] what version of xcode are you using? Jonathan Gough (Fri Jun 08 2012 - 04:56:01 PDT)
    - Re: [AMBER] what version of xcode are you using? Jason Swails (Fri Jun 08 2012 - 05:01:19 PDT)
    - Re: [AMBER] what version of xcode are you using? Jonathan Gough (Fri Jun 08 2012 - 05:05:46 PDT)
    - Re: [AMBER] what version of xcode are you using? Jonathan Gough (Fri Jun 08 2012 - 05:51:06 PDT)
    - Re: [AMBER] what version of xcode are you using? Jason Swails (Fri Jun 08 2012 - 06:25:17 PDT)
    - Re: [AMBER] what version of xcode are you using? Jonathan Gough (Fri Jun 08 2012 - 06:59:03 PDT)
    - Re: [AMBER] what version of xcode are you using? Jason Swails (Fri Jun 08 2012 - 08:06:30 PDT)
    - Re: [AMBER] what version of xcode are you using? Jonathan Gough (Fri Jun 08 2012 - 08:28:04 PDT)
    - Re: [AMBER] what version of xcode are you using? Jason Swails (Fri Jun 08 2012 - 08:34:22 PDT)
    - Re: [AMBER] what version of xcode are you using? Jonathan Gough (Fri Jun 08 2012 - 08:36:22 PDT)
[AMBER] Entropy from MMPBSA.py and MM_PBSA.pl Nan Li (Thu Jun 07 2012 - 11:57:18 PDT)
- Re: [AMBER] Entropy from MMPBSA.py and MM_PBSA.pl Jason Swails (Thu Jun 07 2012 - 12:06:44 PDT)
  - Re: [AMBER] Entropy from MMPBSA.py and MM_PBSA.pl Nan Li (Thu Jun 07 2012 - 12:09:52 PDT)
    - Re: [AMBER] Entropy from MMPBSA.py and MM_PBSA.pl Jason Swails (Thu Jun 07 2012 - 13:10:54 PDT)
    - Re: [AMBER] Entropy from MMPBSA.py and MM_PBSA.pl Nan Li (Fri Jun 08 2012 - 09:01:15 PDT)
    - Re: [AMBER] Entropy from MMPBSA.py and MM_PBSA.pl Jason Swails (Fri Jun 08 2012 - 09:03:16 PDT)
    - Re: [AMBER] Entropy from MMPBSA.py and MM_PBSA.pl Nan Li (Fri Jun 08 2012 - 09:17:21 PDT)
- Re: [AMBER] Entropy from MMPBSA.py and MM_PBSA.pl Nadine.Homeyer.uni-duesseldorf.de (Sat Jun 09 2012 - 00:58:02 PDT)
[AMBER] FactorIX test: CUDA + MPI + ntt=2 => never ends Gerald Monard (Thu Jun 07 2012 - 14:06:44 PDT)
[AMBER] GBSA for simulation of disordered proteins Bashford, Donald (Thu Jun 07 2012 - 19:07:20 PDT)
[AMBER] unfolding with iwrap=1, 500K heating is enough? Chinh Su Tran To (Thu Jun 07 2012 - 20:17:15 PDT)
- Re: [AMBER] unfolding with iwrap=1, 500K heating is enough? Carlos Simmerling (Fri Jun 08 2012 - 02:57:06 PDT)
  - Re: [AMBER] unfolding with iwrap=1, 500K heating is enough? Chinh Su Tran To (Sun Jun 10 2012 - 23:52:01 PDT)
    - Re: [AMBER] unfolding with iwrap=1, 500K heating is enough? Carlos Simmerling (Thu Jun 14 2012 - 08:58:18 PDT)
    - Re: [AMBER] unfolding with iwrap=1, 500K heating is enough? Chinh Su Tran To (Sun Jun 17 2012 - 20:05:40 PDT)
    - Re: [AMBER] unfolding with iwrap=1, 500K heating is enough? Jason Swails (Mon Jun 18 2012 - 06:40:04 PDT)
    - [AMBER] hydrogen bond analysis Urszula Uciechowska (Fri Jun 22 2012 - 04:48:55 PDT)
    - Re: [AMBER] hydrogen bond analysis Daniel Roe (Fri Jun 22 2012 - 06:15:58 PDT)
[AMBER] REMD equilibration Soumya Lipsa Rath (Thu Jun 07 2012 - 20:58:31 PDT)
- Re: [AMBER] REMD equilibration Carlos Simmerling (Fri Jun 08 2012 - 02:59:51 PDT)
  - Re: [AMBER] REMD equilibration Soumya Lipsa Rath (Fri Jun 08 2012 - 21:10:36 PDT)
    - Re: [AMBER] REMD equilibration Daniel Sindhikara (Sat Jun 09 2012 - 02:56:03 PDT)
- Re: [AMBER] REMD equilibration Hai Nguyen (Sat Jun 09 2012 - 21:48:56 PDT)
  - Re: [AMBER] REMD equilibration Soumya Lipsa Rath (Sun Jun 10 2012 - 23:15:32 PDT)
    - Re: [AMBER] REMD equilibration Carlos Simmerling (Thu Jun 14 2012 - 11:11:34 PDT)
    - Re: [AMBER] REMD equilibration Daniel Sindhikara (Thu Jun 14 2012 - 18:36:05 PDT)
    - Re: [AMBER] REMD equilibration Soumya Lipsa Rath (Thu Jun 14 2012 - 20:33:15 PDT)
    - Re: [AMBER] REMD equilibration Daniel Sindhikara (Fri Jun 15 2012 - 02:25:51 PDT)
    - Re: [AMBER] REMD equilibration Daniel Roe (Fri Jun 15 2012 - 06:29:03 PDT)
    - Re: [AMBER] REMD equilibration Soumya Lipsa Rath (Fri Jun 15 2012 - 07:08:20 PDT)
    - Re: [AMBER] REMD equilibration Carlos Simmerling (Fri Jun 15 2012 - 08:09:05 PDT)
    - Re: [AMBER] REMD equilibration Soumya Lipsa Rath (Fri Jun 15 2012 - 22:33:36 PDT)
    - Re: [AMBER] REMD equilibration Carlos Simmerling (Sat Jun 16 2012 - 04:03:10 PDT)
    - Re: [AMBER] REMD equilibration Soumya Lipsa Rath (Sat Jun 16 2012 - 05:05:36 PDT)
    - Re: [AMBER] REMD equilibration Carlos Simmerling (Fri Jun 15 2012 - 03:38:11 PDT)
    - Re: [AMBER] REMD equilibration Jason Swails (Fri Jun 15 2012 - 06:08:21 PDT)
[AMBER] Generation of ESP files Debolina Mitra (Thu Jun 07 2012 - 23:26:14 PDT)
- Re: [AMBER] Generation of ESP files intra\\sa175950 (Fri Jun 08 2012 - 01:33:03 PDT)
- [AMBER] partial charge, charge radius and epsilon Acoot Brett (Fri Jun 08 2012 - 04:45:24 PDT)
  - Re: [AMBER] partial charge, charge radius and epsilon Jason Swails (Fri Jun 08 2012 - 06:36:23 PDT)
[AMBER] FIX for Mac OS X Lion with Xcode 4.3.2 Jason Swails (Fri Jun 08 2012 - 05:21:26 PDT)
- Re: [AMBER] FIX for Mac OS X Lion with Xcode 4.3.2 David A Case (Fri Jun 08 2012 - 07:11:47 PDT)
  - Re: [AMBER] FIX for Mac OS X Lion with Xcode 4.3.2 Jason Swails (Fri Jun 08 2012 - 08:04:23 PDT)
- Re: [AMBER] FIX for Mac OS X Lion with Xcode 4.3.2 Jonathan Gough (Fri Jun 08 2012 - 12:10:47 PDT)
  - Re: [AMBER] FIX for Mac OS X Lion with Xcode 4.3.2 David A Case (Fri Jun 08 2012 - 13:18:26 PDT)
[AMBER] Problems matching atom names to PREP files Chris Whittleston (Fri Jun 08 2012 - 05:35:34 PDT)
- Re: [AMBER] Problems matching atom names to PREP files Daniel Roe (Fri Jun 08 2012 - 06:23:01 PDT)
- Re: [AMBER] Problems matching atom names to PREP files FyD (Fri Jun 08 2012 - 07:06:34 PDT)
- Re: [AMBER] Problems matching atom names to PREP files Bill Ross (Fri Jun 08 2012 - 14:16:19 PDT)
[AMBER] LEaP misplaces ions Francesco Pietra (Sat Jun 09 2012 - 01:29:20 PDT)
- [AMBER] Fwd: LEaP misplaces ions Francesco Pietra (Sat Jun 09 2012 - 01:48:35 PDT)
- Re: [AMBER] LEaP misplaces ions Bill Ross (Sat Jun 09 2012 - 09:51:30 PDT)
  - Re: [AMBER] LEaP misplaces ions Jason Swails (Sat Jun 09 2012 - 10:26:15 PDT)
    - Re: [AMBER] LEaP misplaces ions Francesco Pietra (Sat Jun 09 2012 - 23:09:44 PDT)
    - Re: [AMBER] LEaP misplaces ions Robin Betz (Sun Jun 10 2012 - 00:11:01 PDT)
    - Re: [AMBER] LEaP misplaces ions Francesco Pietra (Sun Jun 10 2012 - 03:37:23 PDT)
  - Re: [AMBER] LEaP misplaces ions Francesco Pietra (Sat Jun 09 2012 - 10:36:29 PDT)
    - Re: [AMBER] LEaP misplaces ions Bill Ross (Sat Jun 09 2012 - 10:45:05 PDT)
[AMBER] Mac OS X Lion workaround Jason Swails (Sat Jun 09 2012 - 13:48:52 PDT)
- Re: [AMBER] Mac OS X Lion workaround Jason Swails (Mon Jun 11 2012 - 03:35:15 PDT)
[AMBER] protein misplaced into the water box Francesco Pietra (Mon Jun 11 2012 - 00:17:48 PDT)
- Re: [AMBER] protein misplaced into the water box Bill Ross (Mon Jun 11 2012 - 14:08:44 PDT)
  - Re: [AMBER] protein misplaced into the water box Francesco Pietra (Tue Jun 12 2012 - 02:25:12 PDT)
    - Re: [AMBER] protein misplaced into the water box Bill Ross (Tue Jun 12 2012 - 15:52:44 PDT)
[AMBER] MMPBSA calculation reproducibility Sangita Kachhap (Mon Jun 11 2012 - 02:08:26 PDT)
- Re: [AMBER] MMPBSA calculation reproducibility Ray Luo, Ph.D. (Mon Jun 11 2012 - 08:46:36 PDT)
  - Re: [AMBER] MMPBSA calculation reproducibility Sangita Kachhap (Mon Jun 11 2012 - 11:56:33 PDT)
    - Re: [AMBER] MMPBSA calculation reproducibility Ray Luo, Ph.D. (Mon Jun 11 2012 - 12:27:38 PDT)
[AMBER] Amber12 Compilation Error in CENTOS 4.5 BERGY (Mon Jun 11 2012 - 02:41:15 PDT)
- [AMBER] How to get starting geometry for <10 AA peptides? Catein Catherine (Mon Jun 11 2012 - 03:09:06 PDT)
 - Re: [AMBER] How to get starting geometry for <10 AA peptides? Jonathan Gough (Mon Jun 11 2012 - 03:39:18 PDT)
[AMBER] FF param William Henry BISSON (Mon Jun 11 2012 - 03:48:27 PDT)
- Re: [AMBER] FF param Giulia (Mon Jun 11 2012 - 04:45:37 PDT)
[AMBER] FF12SB + GLYCAM_06h + Fluorine Kevin Parkes (Mon Jun 11 2012 - 07:18:52 PDT)
- Re: [AMBER] FF12SB + GLYCAM_06h + Fluorine Lachele Foley (Lists) (Mon Jun 11 2012 - 09:00:32 PDT)
  - Re: [AMBER] FF12SB + GLYCAM_06h + Fluorine Kevin Parkes (Tue Jun 12 2012 - 03:47:47 PDT)
    - Re: [AMBER] FF12SB + GLYCAM_06h + Fluorine David A Case (Tue Jun 12 2012 - 07:51:25 PDT)
[AMBER] QM/MM minimization Ewa Chudyk (Mon Jun 11 2012 - 08:17:43 PDT)
- Re: [AMBER] QM/MM minimization Pansy Patel (Thu Sep 10 2009 - 07:09:48 PDT)
- Re: [AMBER] QM/MM minimization Adrian Roitberg (Mon Jun 11 2012 - 08:38:14 PDT)
[AMBER] Bug in resp or respgen? using intra-molecular-charge-constraints... Marko Wehle (Mon Jun 11 2012 - 11:39:11 PDT)
- Re: [AMBER] Bug in resp or respgen? using intra-molecular-charge-constraints... FyD (Mon Jun 11 2012 - 23:54:31 PDT)
- Re: [AMBER] Bug in resp or respgen? using intra-molecular-charge-constraints... Marko Wehle (Tue Jun 12 2012 - 13:29:20 PDT)
  - Re: [AMBER] Bug in resp or respgen? using intra-molecular-charge-constraints... FyD (Wed Jun 13 2012 - 00:28:12 PDT)
[AMBER] mmpbsa kirtana S (Mon Jun 11 2012 - 12:14:39 PDT)
- Re: [AMBER] mmpbsa case (Mon Jun 11 2012 - 18:48:04 PDT)
  - Re: [AMBER] mmpbsa kirtana S (Tue Jun 12 2012 - 09:18:06 PDT)
    - Re: [AMBER] mmpbsa David A Case (Tue Jun 12 2012 - 10:50:36 PDT)
    - Re: [AMBER] mmpbsa Jason Swails (Tue Jun 12 2012 - 12:59:56 PDT)
    - Re: [AMBER] mmpbsa kirtana S (Wed Jun 13 2012 - 09:36:36 PDT)
    - Re: [AMBER] mmpbsa David A Case (Thu Jun 14 2012 - 05:11:55 PDT)
[AMBER] QM/MM periodic boundary conditions in Amber Ivan Ufimtsev (Mon Jun 11 2012 - 13:00:17 PDT)
- Re: [AMBER] QM/MM periodic boundary conditions in Amber Ross Walker (Mon Jun 11 2012 - 14:47:34 PDT)
- Re: [AMBER] QM/MM periodic boundary conditions in Amber case (Mon Jun 11 2012 - 18:37:16 PDT)
[AMBER] parameters and charges for R and S Configurations Jio M (Mon Jun 11 2012 - 13:50:33 PDT)
- [AMBER] Fw: parameters and charges for R and S Configurations Jio M (Mon Jun 11 2012 - 14:36:08 PDT)
- Re: [AMBER] parameters and charges for R and S Configurations FyD (Mon Jun 11 2012 - 23:39:12 PDT)
  - Re: [AMBER] parameters and charges for R and S Configurations Jio M (Tue Jun 12 2012 - 01:35:29 PDT)
[AMBER] ptraj: combine pdb's to mdcrd Do-Yong Kim (Mon Jun 11 2012 - 15:45:45 PDT)
- Re: [AMBER] ptraj: combine pdb's to mdcrd Jason Swails (Tue Jun 12 2012 - 19:21:32 PDT)
[AMBER] Abnormally Slow NMode entropy calculation Cao Yang (Mon Jun 11 2012 - 21:02:40 PDT)
- Re: [AMBER] Abnormally Slow NMode entropy calculation Jason Swails (Tue Jun 12 2012 - 04:16:54 PDT)
- [AMBER] long range LJ correction; surface tension; trajectory MD (Thu Jun 14 2012 - 23:53:28 PDT)
  - Re: [AMBER] long range LJ correction; surface tension; trajectory Carlos Simmerling (Fri Jun 15 2012 - 03:41:09 PDT)
    - Re: [AMBER] long range LJ correction; surface tension; trajectory MD (Mon Jun 18 2012 - 03:24:36 PDT)
[AMBER] Value of internal dielectric constant ? for per residue decomposition free energy calculation using MMGBSA method Jignesh Patel (Tue Jun 12 2012 - 04:13:49 PDT)
- Re: [AMBER] Value of internal dielectric constant ? for per residue decomposition free energy calculation using MMGBSA method Jason Swails (Tue Jun 12 2012 - 04:25:02 PDT)
  - Re: [AMBER] Value of internal dielectric constant ? for per residue decomposition free energy calculation using MMGBSA method Jignesh Patel (Tue Jun 12 2012 - 10:16:57 PDT)
[AMBER] diffusion coefficient Subrata Paul (Tue Jun 12 2012 - 04:45:39 PDT)
[AMBER] Amber cuda test failure jani vinod (Tue Jun 12 2012 - 05:19:36 PDT)
[AMBER] The VDWAALS is huge in MMPBSA calculation. qiao xue (Tue Jun 12 2012 - 23:03:30 PDT)
- Re: [AMBER] The VDWAALS is huge in MMPBSA calculation. Bill Miller III (Tue Jun 12 2012 - 23:07:19 PDT)
  - Re: [AMBER] The VDWAALS is huge in MMPBSA calculation. qiao xue (Tue Jun 12 2012 - 23:32:08 PDT)
    - Re: [AMBER] The VDWAALS is huge in MMPBSA calculation. Bill Miller III (Wed Jun 13 2012 - 04:53:23 PDT)
    - Re: [AMBER] The VDWAALS is huge in MMPBSA calculation. Cao Yang (Wed Jun 13 2012 - 20:11:42 PDT)
    - Re: [AMBER] The VDWAALS is huge in MMPBSA calculation. qiao xue (Fri Jun 15 2012 - 05:01:06 PDT)
    - Re: [AMBER] The VDWAALS is huge in MMPBSA calculation. Bill Miller III (Fri Jun 15 2012 - 05:08:20 PDT)
    - Re: [AMBER] The VDWAALS is huge in MMPBSA calculation. qiao xue (Fri Jun 15 2012 - 05:25:38 PDT)
    - Re: [AMBER] The VDWAALS is huge in MMPBSA calculation. Jason Swails (Fri Jun 15 2012 - 06:06:41 PDT)
[AMBER] what is vlimit error? Sanjib Paul (Tue Jun 12 2012 - 23:19:38 PDT)
- Re: [AMBER] what is vlimit error? Scott Brozell (Wed Jun 13 2012 - 00:33:14 PDT)
  - Re: [AMBER] what is vlimit error? David A Case (Wed Jun 13 2012 - 04:59:09 PDT)
    - Re: [AMBER] what is vlimit error? Scott Brozell (Thu Jun 14 2012 - 01:05:45 PDT)
[AMBER] where is velocity information? Albert (Tue Jun 12 2012 - 23:31:40 PDT)
- Re: [AMBER] where is velocity information? Brian Radak (Wed Jun 13 2012 - 06:26:39 PDT)
[AMBER] how to assign bond order for the output of RED .mol2? Albert (Tue Jun 12 2012 - 23:35:43 PDT)
- Re: [AMBER] how to assign bond order for the output of RED .mol2? FyD (Wed Jun 13 2012 - 00:38:32 PDT)
- Re: [AMBER] how to assign bond order for the output of RED .mol2? FyD (Wed Jun 13 2012 - 00:42:45 PDT)
[AMBER] A small point of confusion in 3DRISM outfiles Daniel Sindhikara (Wed Jun 13 2012 - 02:54:31 PDT)
- Re: [AMBER] A small point of confusion in 3DRISM outfiles Tyler Luchko (Wed Jun 13 2012 - 05:48:53 PDT)
[AMBER] calculation the entropy of a membrane DPPC-protein-ligand complex xiaojiong (Wed Jun 13 2012 - 06:37:08 PDT)
[AMBER] unit of energy Nan Li (Wed Jun 13 2012 - 08:41:24 PDT)
[AMBER] ptraj cannot handle large crd file vishal kumar Jaiswal (Wed Jun 13 2012 - 11:01:12 PDT)
- Re: [AMBER] ptraj cannot handle large crd file vishal kumar Jaiswal (Wed Jun 13 2012 - 11:39:32 PDT)
- Re: [AMBER] ptraj cannot handle large crd file Daniel Roe (Wed Jun 13 2012 - 11:58:47 PDT)
[AMBER] Regarding running PME simulation on GPU jani vinod (Thu Jun 14 2012 - 04:17:55 PDT)
- Re: [AMBER] Regarding running PME simulation on GPU Ross Walker (Thu Jun 14 2012 - 04:41:49 PDT)
  - Re: [AMBER] Regarding running PME simulation on GPU jani vinod (Sun Jun 17 2012 - 19:29:56 PDT)
[AMBER] whether it is proper to strip DPPCs xiaojiong (Thu Jun 14 2012 - 05:30:26 PDT)
[AMBER] strange POPC under lipids 11 FF Albert (Thu Jun 14 2012 - 06:17:20 PDT)
- Re: [AMBER] strange POPC under lipids 11 FF Ross Walker (Thu Jun 14 2012 - 07:09:00 PDT)
  - [AMBER] R: strange POPC under lipids 11 FF Giovanni Pavan (Fri Jun 15 2012 - 01:00:35 PDT)
    - Re: [AMBER] R: strange POPC under lipids 11 FF Ross Walker (Fri Jun 15 2012 - 02:26:20 PDT)
    - Re: [AMBER] R: strange POPC under lipids 11 FF Albert (Fri Jun 15 2012 - 02:48:54 PDT)
    - Re: [AMBER] R: strange POPC under lipids 11 FF Ross Walker (Fri Jun 15 2012 - 03:02:54 PDT)
    - Re: [AMBER] R: strange POPC under lipids 11 FF Albert (Fri Jun 15 2012 - 03:28:45 PDT)
    - Re: [AMBER] R: strange POPC under lipids 11 FF Ross Walker (Fri Jun 15 2012 - 03:38:32 PDT)
    - Re: [AMBER] R: strange POPC under lipids 11 FF Albert (Fri Jun 15 2012 - 03:35:38 PDT)
    - Re: [AMBER] R: strange POPC under lipids 11 FF Ross Walker (Fri Jun 15 2012 - 15:56:27 PDT)
    - Re: [AMBER] R: strange POPC under lipids 11 FF Albert (Fri Jun 15 2012 - 11:07:08 PDT)
    - Re: [AMBER] R: strange POPC under lipids 11 FF Ross Walker (Fri Jun 15 2012 - 15:33:37 PDT)
    - Re: [AMBER] R: strange POPC under lipids 11 FF David A. Case (Sat Jun 16 2012 - 09:20:17 PDT)
    - Re: [AMBER] R: strange POPC under lipids 11 FF Ross Walker (Sat Jun 16 2012 - 09:56:02 PDT)
    - Re: [AMBER] R: strange POPC under lipids 11 FF Adrian Roitberg (Fri Jun 15 2012 - 06:46:23 PDT)
    - Re: [AMBER] R: strange POPC under lipids 11 FF Tales Yuan (Sat Jun 16 2012 - 10:39:22 PDT)
    - [AMBER] R: R: strange POPC under lipids 11 FF Giovanni Pavan (Fri Jun 15 2012 - 06:41:53 PDT)
    - Re: [AMBER] R: R: strange POPC under lipids 11 FF Marek Maly (Fri Jun 15 2012 - 07:05:22 PDT)
    - Re: [AMBER] R: R: strange POPC under lipids 11 FF Ross Walker (Fri Jun 15 2012 - 15:43:30 PDT)
    - Re: [AMBER] R: R: strange POPC under lipids 11 FF Marek Maly (Sat Jun 16 2012 - 03:19:23 PDT)
    - Re: [AMBER] R: R: strange POPC under lipids 11 FF Benjamin D Madej (Sat Jun 16 2012 - 09:59:45 PDT)
    - Re: [AMBER] R: strange POPC under lipids 11 FF Vlad Cojocaru (Sat Jun 16 2012 - 00:05:59 PDT)
    - Re: [AMBER] R: strange POPC under lipids 11 FF Ross Walker (Sat Jun 16 2012 - 09:28:00 PDT)
    - Re: [AMBER] R: strange POPC under lipids 11 FF Vlad Cojocaru (Sat Jun 16 2012 - 09:57:04 PDT)
    - Re: [AMBER] R: strange POPC under lipids 11 FF Albert (Sat Jun 16 2012 - 10:01:33 PDT)
    - Re: [AMBER] R: strange POPC under lipids 11 FF Vlad Cojocaru (Sat Jun 16 2012 - 10:19:15 PDT)
    - Re: [AMBER] R: strange POPC under lipids 11 FF Benjamin D Madej (Sat Jun 16 2012 - 10:37:09 PDT)
    - Re: [AMBER] R: strange POPC under lipids 11 FF Tales Yuan (Sat Jun 16 2012 - 10:49:02 PDT)
    - Re: [AMBER] R: strange POPC under lipids 11 FF Benjamin D Madej (Sat Jun 16 2012 - 11:17:28 PDT)
    - Re: [AMBER] R: strange POPC under lipids 11 FF Albert (Sat Jun 16 2012 - 12:15:53 PDT)
[AMBER] acpye for CHARMM? Albert (Thu Jun 14 2012 - 08:18:54 PDT)
- Re: [AMBER] acpye for CHARMM? Alan (Fri Jun 15 2012 - 04:11:17 PDT)
[AMBER] Leap. Error messages on renaming ASP to AS4 etc. George Tzotzos (Thu Jun 14 2012 - 08:52:13 PDT)
- Re: [AMBER] Leap. Error messages on renaming ASP to AS4 etc. Dwight McGee (Thu Jun 14 2012 - 09:43:05 PDT)
  - Re: [AMBER] Leap. Error messages on renaming ASP to AS4 etc. George Tzotzos (Thu Jun 14 2012 - 12:10:41 PDT)
    - Re: [AMBER] Leap. Error messages on renaming ASP to AS4 etc. Marc van der Kamp (Thu Jun 14 2012 - 12:27:38 PDT)
    - Re: [AMBER] Leap. Error messages on renaming ASP to AS4 etc. Jason Swails (Thu Jun 14 2012 - 12:37:19 PDT)
    - Re: [AMBER] Leap. Error messages on renaming ASP to AS4 etc. George Tzotzos (Thu Jun 14 2012 - 13:10:04 PDT)
    - Re: [AMBER] Leap. Error messages on renaming ASP to AS4 etc. Marc van der Kamp (Thu Jun 14 2012 - 13:28:42 PDT)
    - Re: [AMBER] Leap. Error messages on renaming ASP to AS4 etc. David A Case (Thu Jun 14 2012 - 13:23:11 PDT)
    - Re: [AMBER] Leap. Error messages on renaming ASP to AS4 etc. Jason Swails (Thu Jun 14 2012 - 13:55:49 PDT)
    - Re: [AMBER] Leap. Error messages on renaming ASP to AS4 etc. George Tzotzos (Thu Jun 14 2012 - 14:10:46 PDT)
    - Re: [AMBER] Leap. Error messages on renaming ASP to AS4 etc. Jason Swails (Thu Jun 14 2012 - 14:37:12 PDT)
[AMBER] Help with Zn parameters after MCPB parameterization Fabrício Bracht (Thu Jun 14 2012 - 09:44:04 PDT)
- Re: [AMBER] Help with Zn parameters after MCPB parameterization Ben Roberts (Thu Jun 14 2012 - 13:37:00 PDT)
[AMBER] force field library for protonated cytosine Asmita Gupta (Thu Jun 14 2012 - 11:24:32 PDT)
- Re: [AMBER] force field library for protonated cytosine Jason Swails (Thu Jun 14 2012 - 12:00:28 PDT)
- Re: [AMBER] force field library for protonated cytosine David A Case (Thu Jun 14 2012 - 13:09:57 PDT)
- Re: [AMBER] force field library for protonated cytosine FyD (Fri Jun 15 2012 - 11:52:03 PDT)
  - Re: [AMBER] force field library for protonated cytosine Asmita Gupta (Mon Jun 25 2012 - 10:28:18 PDT)
    - Re: [AMBER] force field library for protonated cytosine David A Case (Mon Jun 25 2012 - 11:16:01 PDT)
    - Re: [AMBER] force field library for protonated cytosine Asmita Gupta (Mon Jun 25 2012 - 11:42:22 PDT)
    - Re: [AMBER] force field library for protonated cytosine case (Mon Jun 25 2012 - 15:12:37 PDT)
    - Re: [AMBER] force field library for protonated cytosine Jio M (Thu Jun 28 2012 - 09:04:15 PDT)
    - Re: [AMBER] force field library for protonated cytosine David A Case (Thu Jun 28 2012 - 10:50:04 PDT)
    - Re: [AMBER] force field library for protonated cytosine FyD (Tue Jun 26 2012 - 00:35:09 PDT)
[AMBER] Facing problem on TUTORIAL A1 sudipta (Thu Jun 14 2012 - 15:29:29 PDT)
- Re: [AMBER] Facing problem on TUTORIAL A1 steinbrt.rci.rutgers.edu (Fri Jun 15 2012 - 00:10:52 PDT)
  - Re: [AMBER] Facing problem on TUTORIAL A1 sudipta (Fri Jun 15 2012 - 12:05:30 PDT)
    - Re: [AMBER] Facing problem on TUTORIAL A1 steinbrt.rci.rutgers.edu (Sun Jun 17 2012 - 07:56:10 PDT)
[AMBER] undefined reference error in compiling Xin Geng (Thu Jun 14 2012 - 17:52:18 PDT)
- Re: [AMBER] undefined reference error in compiling Ben Roberts (Thu Jun 14 2012 - 18:12:45 PDT)
- Re: [AMBER] undefined reference error in compiling Jason Swails (Thu Jun 14 2012 - 18:12:51 PDT)
- Re: [AMBER] undefined reference error in compiling case (Thu Jun 14 2012 - 18:35:33 PDT)
  - Re: [AMBER] undefined reference error in compiling Xin Geng (Fri Jun 15 2012 - 10:36:02 PDT)
    - Re: [AMBER] undefined reference error in compiling Jason Swails (Fri Jun 15 2012 - 10:58:04 PDT)
    - Re: [AMBER] undefined reference error in compiling David A. Case (Fri Jun 15 2012 - 18:24:38 PDT)
    - Re: [AMBER] undefined reference error in compiling Jason Swails (Fri Jun 15 2012 - 19:55:28 PDT)
    - Re: [AMBER] undefined reference error in compiling Xin Geng (Mon Jun 18 2012 - 13:34:10 PDT)
[AMBER] GPU kernel error Fernando Martín García (Fri Jun 15 2012 - 03:01:19 PDT)
- Re: [AMBER] GPU kernel error Scott Le Grand (Fri Jun 15 2012 - 05:22:07 PDT)
  - Re: [AMBER] GPU kernel error Fernando Martín García (Fri Jun 15 2012 - 05:39:18 PDT)
- Re: [AMBER] GPU kernel error Ross Walker (Fri Jun 15 2012 - 15:33:37 PDT)
  - Re: [AMBER] GPU kernel error Dmitry Mukha (Sun Jun 17 2012 - 05:53:56 PDT)
    - Re: [AMBER] GPU kernel error Ross Walker (Sun Jun 17 2012 - 08:25:21 PDT)
    - Re: [AMBER] GPU kernel error Dmitry Mukha (Sun Jun 17 2012 - 08:56:11 PDT)
    - Re: [AMBER] GPU kernel error Dmitry Mukha (Mon Jun 18 2012 - 23:27:19 PDT)
    - Re: [AMBER] GPU kernel error Ross Walker (Tue Jun 19 2012 - 10:02:44 PDT)
- Re: [AMBER] GPU kernel error Adam Jion (Tue Jun 19 2012 - 22:51:36 PDT)
[AMBER] Error with box parameters Карлов Дмитрий (Fri Jun 15 2012 - 03:42:11 PDT)
- Re: [AMBER] Error with box parameters David A Case (Fri Jun 15 2012 - 05:21:03 PDT)
[AMBER] Fail to read hem parameters written by P. Rydberg 崔颖璐 (Fri Jun 15 2012 - 05:08:07 PDT)
- Re: [AMBER] Fail to read hem parameters written by P. Rydberg Mark Williamson (Fri Jun 15 2012 - 05:39:35 PDT)
  - Re: [AMBER] Fail to read hem parameters written by P. Rydberg 崔颖璐 (Mon Jun 18 2012 - 06:13:38 PDT)
[AMBER] why cut off is so small for CUDA running? Albert (Fri Jun 15 2012 - 05:18:00 PDT)
- Re: [AMBER] why cut off is so small for CUDA running? Daniel Roe (Fri Jun 15 2012 - 06:07:48 PDT)
- Re: [AMBER] why cut off is so small for CUDA running? Scott Le Grand (Sun Jun 17 2012 - 18:14:55 PDT)
  - Re: [AMBER] why cut off is so small for CUDA running? Martin Andersson (Tue Jun 19 2012 - 04:45:45 PDT)
    - Re: [AMBER] why cut off is so small for CUDA running? Ross Walker (Tue Jun 19 2012 - 09:34:58 PDT)
- Re: [AMBER] why cut off is so small for CUDA running? Ross Walker (Sun Jun 17 2012 - 21:47:47 PDT)
[AMBER] chiral Sulfur atom Yun Shi (Fri Jun 15 2012 - 15:30:00 PDT)
- Re: [AMBER] chiral Sulfur atom FyD (Fri Jun 15 2012 - 23:51:11 PDT)
[AMBER] MMPBSA.py Delwar Hossain (Fri Jun 15 2012 - 16:05:07 PDT)
- Re: [AMBER] MMPBSA.py manikanthan bhavaraju (Fri Jun 15 2012 - 16:44:07 PDT)
- Re: [AMBER] MMPBSA.py Jason Swails (Fri Jun 15 2012 - 20:06:21 PDT)
[AMBER] umbrella sampling -- centroid or center of mass Junjian Miao (Fri Jun 15 2012 - 06:24:53 PDT)
- Re: [AMBER] umbrella sampling -- centroid or center of mass David A. Case (Fri Jun 15 2012 - 18:21:13 PDT)
[AMBER] Job running problem in sander Souvik Sur (Fri Jun 15 2012 - 22:34:43 PDT)
- Re: [AMBER] Job running problem in sander Daniel Roe (Sat Jun 16 2012 - 04:52:56 PDT)
[AMBER] Cuda performance HIMANSHU JOSHI (Sat Jun 16 2012 - 03:26:25 PDT)
- Re: [AMBER] Cuda performance Ross Walker (Sat Jun 16 2012 - 09:29:50 PDT)
  - Re: [AMBER] Cuda performance HIMANSHU JOSHI (Sun Jun 17 2012 - 00:29:03 PDT)
[AMBER] duplicating - multiplying input files to create dimer etc. Jonathan Gough (Sat Jun 16 2012 - 13:45:30 PDT)
- Re: [AMBER] duplicating - multiplying input files to create dimer etc. Jason Swails (Sat Jun 16 2012 - 15:34:56 PDT)
  - Re: [AMBER] duplicating - multiplying input files to create dimer etc. Jonathan Gough (Sat Jun 16 2012 - 15:41:52 PDT)
[AMBER] MMPBSA.py.MPI Delwar Hossain (Sat Jun 16 2012 - 20:30:01 PDT)
- Re: [AMBER] MMPBSA.py.MPI Bill Miller III (Sat Jun 16 2012 - 20:38:19 PDT)
[AMBER] Problem of Force filed (Calculate the dihedral parameter) Takeshi Baba (Sat Jun 16 2012 - 21:01:24 PDT)
- Re: [AMBER] Problem of Force filed (Calculate the dihedral parameter) Adrian Roitberg (Sat Jun 16 2012 - 22:31:16 PDT)
[AMBER] C- and N-terminal amino acids in AmberTools 1.4 Kamali Sripathi (Sun Jun 17 2012 - 12:51:07 PDT)
- Re: [AMBER] C- and N-terminal amino acids in AmberTools 1.4 Jason Swails (Sun Jun 17 2012 - 13:59:10 PDT)
  - Re: [AMBER] C- and N-terminal amino acids in AmberTools 1.4 Kamali Sripathi (Sun Jun 17 2012 - 16:55:31 PDT)
[AMBER] Ion clumping in large protein-RNA systems Kamali Sripathi (Sun Jun 17 2012 - 14:28:52 PDT)
- Re: [AMBER] Ion clumping in large protein-RNA systems Daniel Sindhikara (Sun Jun 17 2012 - 18:32:23 PDT)
  - Re: [AMBER] Ion clumping in large protein-RNA systems Kamali Sripathi (Mon Jun 18 2012 - 05:03:27 PDT)
- Re: [AMBER] Ion clumping in large protein-RNA systems Thomas Cheatham (Tue Jun 19 2012 - 06:16:41 PDT)
  - Re: [AMBER] Ion clumping in large protein-RNA systems Kamali Sripathi (Tue Jun 19 2012 - 07:55:14 PDT)
    - Re: [AMBER] Ion clumping in large protein-RNA systems Robin Betz (Tue Jun 19 2012 - 08:09:59 PDT)
    - Re: [AMBER] Ion clumping in large protein-RNA systems Kamali Sripathi (Fri Jun 22 2012 - 11:51:02 PDT)
    - Re: [AMBER] Ion clumping in large protein-RNA systems Kevin Hauser (Fri Jun 22 2012 - 13:38:01 PDT)
    - Re: [AMBER] Ion clumping in large protein-RNA systems Kamali Sripathi (Thu Jul 05 2012 - 07:41:49 PDT)
    - Re: [AMBER] Ion clumping in large protein-RNA systems Kevin Hauser (Thu Jul 05 2012 - 08:16:06 PDT)
    - Re: [AMBER] Ion clumping in large protein-RNA systems Kamali Sripathi (Fri Jul 06 2012 - 07:06:35 PDT)
[AMBER] How to calculate distance between Center of Axis (DNA) to Center of Mass of Ligand in ptraj Muhammad Khaled Tumbi (Sun Jun 17 2012 - 23:47:00 PDT)
[AMBER] Atom type for oxygen bound to Phosphate Dilraj LAMA (Mon Jun 18 2012 - 04:25:12 PDT)
- Re: [AMBER] Atom type for oxygen bound to Phosphate David A. Case (Mon Jun 18 2012 - 05:02:47 PDT)
- Re: [AMBER] Atom type for oxygen bound to Phosphate FyD (Mon Jun 18 2012 - 05:07:07 PDT)
  - Re: [AMBER] Atom type for oxygen bound to Phosphate FyD (Mon Jun 18 2012 - 07:14:06 PDT)
[AMBER] POPE lipids is too 'ordered' Albert (Mon Jun 18 2012 - 07:02:29 PDT)
- Re: [AMBER] POPE lipids is too 'ordered' Benjamin D Madej (Mon Jun 18 2012 - 09:28:46 PDT)
  - Re: [AMBER] POPE lipids is too 'ordered' Albert (Mon Jun 18 2012 - 11:16:09 PDT)
    - Re: [AMBER] POPE lipids is too 'ordered' Benjamin D Madej (Mon Jun 18 2012 - 11:25:02 PDT)
    - Re: [AMBER] POPE lipids is too 'ordered' Albert (Mon Jun 18 2012 - 11:27:12 PDT)
    - Re: [AMBER] POPE lipids is too 'ordered' Albert (Tue Jun 19 2012 - 05:14:38 PDT)
    - Re: [AMBER] POPE lipids is too 'ordered' Hannes Loeffler (Tue Jun 19 2012 - 05:50:54 PDT)
    - Re: [AMBER] POPE lipids is too 'ordered' Hannes Loeffler (Tue Jun 19 2012 - 05:32:44 PDT)
    - Re: [AMBER] POPE lipids is too 'ordered' Albert (Tue Jun 19 2012 - 05:42:18 PDT)
[AMBER] modeling GDP Brandon Sim (Mon Jun 18 2012 - 11:43:52 PDT)
- Re: [AMBER] modeling GDP David A. Case (Mon Jun 18 2012 - 14:27:37 PDT)
  - Re: [AMBER] modeling GDP Brandon Sim (Mon Jun 18 2012 - 15:38:47 PDT)
    - Re: [AMBER] modeling GDP David A. Case (Tue Jun 19 2012 - 01:24:13 PDT)
    - Re: [AMBER] modeling GDP Brandon Sim (Tue Jun 19 2012 - 22:23:09 PDT)
    - Re: [AMBER] modeling GDP FyD (Wed Jun 20 2012 - 00:34:42 PDT)
- Re: [AMBER] modeling GDP FyD (Mon Jun 18 2012 - 15:31:32 PDT)
[AMBER] NaN with GTX580 pmemd.cuda simulation with and without iwrap = 1 Fabrício Bracht (Mon Jun 18 2012 - 12:10:37 PDT)
- [AMBER] NaN with GTX580 pmemd.cuda simulation with and without iwrap = 1 Fabrício Bracht (Sat Jun 23 2012 - 06:43:48 PDT)
  - Re: [AMBER] NaN with GTX580 pmemd.cuda simulation with and without iwrap = 1 Ben Roberts (Sat Jun 23 2012 - 21:17:24 PDT)
    - Re: [AMBER] NaN with GTX580 pmemd.cuda simulation with and without iwrap = 1 Fabrício Bracht (Sun Jun 24 2012 - 08:23:45 PDT)
    - Re: [AMBER] NaN with GTX580 pmemd.cuda simulation with and without iwrap = 1 Fabrício Bracht (Tue Jun 26 2012 - 16:57:51 PDT)
    - Re: [AMBER] NaN with GTX580 pmemd.cuda simulation with and without iwrap = 1 case (Tue Jun 26 2012 - 18:21:44 PDT)
    - Re: [AMBER] NaN with GTX580 pmemd.cuda simulation with and without iwrap = 1 Bill Ross (Wed Jun 27 2012 - 14:34:04 PDT)
    - Re: [AMBER] NaN with GTX580 pmemd.cuda simulation with and without iwrap = 1 Fabrício Bracht (Thu Jun 28 2012 - 05:01:13 PDT)
    - Re: [AMBER] NaN with GTX580 pmemd.cuda simulation with and without iwrap = 1 David A Case (Thu Jun 28 2012 - 07:39:14 PDT)
    - Re: [AMBER] NaN with GTX580 pmemd.cuda simulation with and without iwrap = 1 Fabrício Bracht (Thu Jun 28 2012 - 12:09:21 PDT)
    - Re: [AMBER] NaN with GTX580 pmemd.cuda simulation with and without iwrap = 1 Ross Walker (Thu Jun 28 2012 - 12:28:41 PDT)
    - Re: [AMBER] NaN with GTX580 pmemd.cuda simulation with and without iwrap = 1 Fabrício Bracht (Thu Jun 28 2012 - 13:29:04 PDT)
    - Re: [AMBER] NaN with GTX580 pmemd.cuda simulation with and without iwrap = 1 Ross Walker (Thu Jun 28 2012 - 14:05:55 PDT)
    - Re: [AMBER] NaN with GTX580 pmemd.cuda simulation with and without iwrap = 1 Fabrício Bracht (Thu Jun 28 2012 - 14:43:24 PDT)
    - Re: [AMBER] NaN with GTX580 pmemd.cuda simulation with and without iwrap = 1 Fabrício Bracht (Wed Jul 04 2012 - 11:20:16 PDT)
    - Re: [AMBER] NaN with GTX580 pmemd.cuda simulation with and without iwrap = 1 Ben Roberts (Wed Jul 04 2012 - 17:04:46 PDT)
    - Re: [AMBER] NaN with GTX580 pmemd.cuda simulation with and without iwrap = 1 Fabrício Bracht (Thu Jul 05 2012 - 13:42:09 PDT)
    - Re: [AMBER] NaN with GTX580 pmemd.cuda simulation with and without iwrap = 1 Ben Roberts (Thu Jul 05 2012 - 14:48:27 PDT)
    - Re: [AMBER] NaN with GTX580 pmemd.cuda simulation with and without iwrap = 1 Jason Swails (Thu Jul 05 2012 - 15:19:29 PDT)
    - [AMBER] How to combine mdcrd and netcdf files to one single netcdf file? Catein Catherine (Thu Jul 05 2012 - 15:47:03 PDT)
    - Re: [AMBER] How to combine mdcrd and netcdf files to one single netcdf file? case (Thu Jul 05 2012 - 16:26:47 PDT)
    - [AMBER] What is the typical stimulation time? Catein Catherine (Thu Jul 05 2012 - 17:44:23 PDT)
    - Re: [AMBER] What is the typical stimulation time? Carlos Simmerling (Thu Jul 05 2012 - 17:49:17 PDT)
    - Re: [AMBER] What is the typical stimulation time? Baldoni Hector Armando (Thu Jul 05 2012 - 18:45:22 PDT)
    - Re: [AMBER] What is the typical stimulation time? Dr. Vitaly V. G. Chaban (Thu Jul 05 2012 - 18:55:18 PDT)
    - Re: [AMBER] What is the typical stimulation time? Ganesh Kamath (Thu Jul 05 2012 - 19:06:46 PDT)
    - Re: [AMBER] What is the typical stimulation time? Dr. Vitaly V. G. Chaban (Thu Jul 05 2012 - 19:25:24 PDT)
    - Re: [AMBER] What is the typical stimulation time? steinbrt.rci.rutgers.edu (Fri Jul 06 2012 - 02:51:28 PDT)
    - Re: [AMBER] What is the typical stimulation time? Ross Walker (Fri Jul 06 2012 - 09:23:09 PDT)
    - Re: [AMBER] What is the typical stimulation time? Carlos Simmerling (Fri Jul 06 2012 - 10:48:20 PDT)
    - Re: [AMBER] What is the typical stimulation time? George Tzotzos (Fri Jul 06 2012 - 11:18:34 PDT)
    - Re: [AMBER] What is the typical stimulation time? Carlos Simmerling (Fri Jul 06 2012 - 11:21:55 PDT)
    - Re: [AMBER] What is the typical stimulation time? Ross Walker (Sat Jul 07 2012 - 21:19:40 PDT)
    - Re: [AMBER] What is the typical stimulation time? Ilyas Yildirim (Fri Jul 06 2012 - 12:04:16 PDT)
    - Re: [AMBER] What is the typical stimulation time? George Tzotzos (Sat Jul 07 2012 - 04:37:39 PDT)
    - Re: [AMBER] What is the typical stimulation time? Ilyas Yildirim (Sat Jul 07 2012 - 10:34:33 PDT)
    - [AMBER] How to read netcdf files to ptraj? Catein Catherine (Thu Jul 12 2012 - 21:54:57 PDT)
    - Re: [AMBER] How to read netcdf files to ptraj? Daniel Roe (Thu Jul 12 2012 - 22:05:24 PDT)
    - Re: [AMBER] How to read netcdf files to ptraj? Catein Catherine (Thu Jul 12 2012 - 22:39:43 PDT)
    - Re: [AMBER] How to read netcdf files to ptraj? Daniel Roe (Fri Jul 13 2012 - 07:09:56 PDT)
    - Re: [AMBER] NaN with GTX580 pmemd.cuda simulation with and without iwrap = 1 Fabrício Bracht (Fri Jul 06 2012 - 10:56:20 PDT)
    - Re: [AMBER] NaN with GTX580 pmemd.cuda simulation with and without iwrap = 1 Ben Roberts (Sat Jul 07 2012 - 02:28:30 PDT)
    - Re: [AMBER] NaN with GTX580 pmemd.cuda simulation with and without iwrap = 1 Fabrício Bracht (Sat Jul 07 2012 - 23:41:35 PDT)
    - Re: [AMBER] NaN with GTX580 pmemd.cuda simulation with and without iwrap = 1 Jason Swails (Sun Jul 08 2012 - 10:46:53 PDT)
    - Re: [AMBER] NaN with GTX580 pmemd.cuda simulation with and without iwrap = 1 Fabrício Bracht (Wed Jul 11 2012 - 11:28:57 PDT)
    - Re: [AMBER] NaN with GTX580 pmemd.cuda simulation with and without iwrap = 1 Jason Swails (Wed Jul 11 2012 - 12:03:29 PDT)
    - Re: [AMBER] NaN with GTX580 pmemd.cuda simulation with and without iwrap = 1 Fabrício Bracht (Wed Jul 11 2012 - 12:44:39 PDT)
    - Re: [AMBER] NaN with GTX580 pmemd.cuda simulation with and without iwrap = 1 Jason Swails (Wed Jul 11 2012 - 12:54:40 PDT)
    - Re: [AMBER] NaN with GTX580 pmemd.cuda simulation with and without iwrap = 1 Fabrício Bracht (Wed Jul 11 2012 - 17:22:47 PDT)
    - Re: [AMBER] NaN with GTX580 pmemd.cuda simulation with and without iwrap = 1 Jason Swails (Wed Jul 11 2012 - 21:00:07 PDT)
    - Re: [AMBER] NaN with GTX580 pmemd.cuda simulation with and without iwrap = 1 Jason Swails (Thu Jun 28 2012 - 13:44:07 PDT)
[AMBER] Script error to restart MD automatically Tommy Yap (Mon Jun 18 2012 - 20:06:05 PDT)
- Re: [AMBER] Script error to restart MD automatically Niel Henriksen (Mon Jun 18 2012 - 20:58:36 PDT)
  - Re: [AMBER] Script error to restart MD automatically Tommy Yap (Mon Jun 18 2012 - 21:49:32 PDT)
    - Re: [AMBER] Script error to restart MD automatically Anselm Horn (Tue Jun 19 2012 - 00:05:01 PDT)
    - Re: [AMBER] Script error to restart MD automatically Tommy Yap (Tue Jun 19 2012 - 00:40:04 PDT)
    - Re: [AMBER] Script error to restart MD automatically Adrian Roitberg (Tue Jun 19 2012 - 06:03:49 PDT)
[AMBER] MMPBSA problem marawan hussain (Mon Jun 18 2012 - 21:57:41 PDT)
- Re: [AMBER] MMPBSA problem Bill Miller III (Tue Jun 19 2012 - 18:59:39 PDT)
[AMBER] RESP charges for single nucleic acid residue Yun Shi (Mon Jun 18 2012 - 22:15:16 PDT)
[AMBER] ptraj vector error Albert (Tue Jun 19 2012 - 01:04:40 PDT)
- Re: [AMBER] ptraj vector error Marc van der Kamp (Tue Jun 19 2012 - 01:18:52 PDT)
  - Re: [AMBER] ptraj vector error Albert (Tue Jun 19 2012 - 02:13:09 PDT)
    - Re: [AMBER] ptraj vector error Marc van der Kamp (Tue Jun 19 2012 - 02:47:36 PDT)
    - Re: [AMBER] ptraj vector error Albert (Tue Jun 19 2012 - 04:42:03 PDT)
[AMBER] Slow jobs Cao Yang (Tue Jun 19 2012 - 03:52:20 PDT)
- Re: [AMBER] Slow jobs Ross Walker (Tue Jun 19 2012 - 09:22:57 PDT)
[AMBER] Atom type for oxygen bound to Phosphate Dilraj LAMA (Tue Jun 19 2012 - 06:03:03 PDT)
[AMBER] Bad atom MN in free energy decomposition with MMPBSA.py Cao Yang (Tue Jun 19 2012 - 07:26:08 PDT)
[AMBER] PB Bomb in epsmap(): epsy out of range Xiao Ba (Tue Jun 19 2012 - 14:37:12 PDT)
- Re: [AMBER] PB Bomb in epsmap(): epsy out of range Ray Luo, Ph.D. (Tue Jun 19 2012 - 14:47:04 PDT)
[AMBER] problem with solvateShell command Sajeewa Pemasinghe (Tue Jun 19 2012 - 14:53:22 PDT)
- Re: [AMBER] problem with solvateShell command Bill Ross (Tue Jun 19 2012 - 16:31:31 PDT)
  - Re: [AMBER] problem with solvateShell command Sajeewa Pemasinghe (Tue Jun 19 2012 - 19:02:47 PDT)
[AMBER] Sander output Error Souvik Sur (Tue Jun 19 2012 - 21:53:32 PDT)
- Re: [AMBER] Sander output Error Jason Swails (Tue Jun 19 2012 - 22:01:45 PDT)
[AMBER] Switching-off the partial charges Adam Jion (Tue Jun 19 2012 - 22:56:08 PDT)
- Re: [AMBER] Switching-off the partial charges Daniel Sindhikara (Tue Jun 19 2012 - 23:17:30 PDT)
  - Re: [AMBER] Switching-off the partial charges steinbrt.rci.rutgers.edu (Wed Jun 20 2012 - 00:54:00 PDT)
- Re: [AMBER] Switching-off the partial charges David A. Case (Tue Jun 19 2012 - 23:43:39 PDT)
[AMBER] problem during heating up the system Sanjib Paul (Wed Jun 20 2012 - 03:13:42 PDT)
- Re: [AMBER] problem during heating up the system chirag740.gmail.com (Wed Jun 20 2012 - 04:50:40 PDT)
  - Re: [AMBER] problem during heating up the system Sanjib Paul (Wed Jun 20 2012 - 05:09:36 PDT)
- Re: [AMBER] problem during heating up the system David A. Case (Wed Jun 20 2012 - 05:13:03 PDT)
[AMBER] Constant pH simulation at pH 7 Nicholus Bhattacharjee (Wed Jun 20 2012 - 06:00:18 PDT)
- Re: [AMBER] Constant pH simulation at pH 7 Jason Swails (Wed Jun 20 2012 - 06:44:50 PDT)
[AMBER] Entropy calculations with mm_pbsa.pl using amber12 manikanthan bhavaraju (Wed Jun 20 2012 - 08:43:36 PDT)
[AMBER] Problem while running MMPBSA qiqi (Wed Jun 20 2012 - 09:08:51 PDT)
- Re: [AMBER] Problem while running MMPBSA Jason Swails (Wed Jun 20 2012 - 10:19:53 PDT)
  - Re: [AMBER] Problem while running MMPBSA qiqi (Wed Jun 20 2012 - 10:32:31 PDT)
    - Re: [AMBER] Problem while running MMPBSA Jason Swails (Wed Jun 20 2012 - 11:08:58 PDT)
    - Re: [AMBER] Problem while running MMPBSA qiqi (Fri Jun 22 2012 - 13:33:26 PDT)
    - Re: [AMBER] Problem while running MMPBSA Jason Swails (Fri Jun 22 2012 - 16:26:24 PDT)
    - Re: [AMBER] Problem while running MMPBSA qiqi (Mon Jun 25 2012 - 08:33:43 PDT)
    - Re: [AMBER] Problem while running MMPBSA Jason Swails (Mon Jun 25 2012 - 10:09:22 PDT)
    - Re: [AMBER] Problem while running MMPBSA qiqi (Thu Jun 28 2012 - 06:53:41 PDT)
    - Re: [AMBER] Problem while running MMPBSA Jason Swails (Sun Jul 01 2012 - 19:18:11 PDT)
    - Re: [AMBER] Problem while running MMPBSA qiqi (Mon Jul 02 2012 - 12:37:15 PDT)
    - Re: [AMBER] Problem while running MMPBSA Jason Swails (Tue Jul 03 2012 - 20:31:01 PDT)
    - Re: [AMBER] Problem while running MMPBSA qiqi (Thu Jul 05 2012 - 07:32:58 PDT)
    - Re: [AMBER] Problem while running MMPBSA Jason Swails (Thu Jul 05 2012 - 08:28:50 PDT)
    - Re: [AMBER] Problem while running MMPBSA qiqi (Mon Jul 09 2012 - 14:05:00 PDT)
    - Re: [AMBER] Problem while running MMPBSA Ray Luo (Mon Jul 09 2012 - 15:58:16 PDT)
    - Re: [AMBER] Problem while running MMPBSA qiqi (Tue Jul 10 2012 - 06:26:54 PDT)
    - Re: [AMBER] Problem while running MMPBSA Jan-Philip Gehrcke (Tue Jul 10 2012 - 07:16:35 PDT)
- Re: [AMBER] Problem while running MMPBSA qiqi (Fri Jun 29 2012 - 13:08:44 PDT)
[AMBER] MMPBSA.py.MPI and MMPBSA.py Delwar Hossain (Wed Jun 20 2012 - 12:24:51 PDT)
- Re: [AMBER] MMPBSA.py.MPI and MMPBSA.py Jason Swails (Wed Jun 20 2012 - 12:53:32 PDT)
[AMBER] Error in writing of coordinate file after simulation Ashutosh Shandilya (Wed Jun 20 2012 - 12:34:12 PDT)
- Re: [AMBER] Error in writing of coordinate file after simulation Daniel Roe (Thu Jun 21 2012 - 04:39:49 PDT)
- Re: [AMBER] Error in writing of coordinate file after simulation Ashutosh Shandilya (Thu Jul 12 2012 - 11:17:08 PDT)
  - Re: [AMBER] Error in writing of coordinate file after simulation Daniel Roe (Fri Jul 13 2012 - 11:08:21 PDT)
[AMBER] rdf/count of ions around a protein E. Nihal Korkmaz (Wed Jun 20 2012 - 13:40:42 PDT)
Re: [AMBER] Problem with installing Amber 12 CUDA GPU version (NetCDF error) Ross Walker (Wed Jun 20 2012 - 17:08:19 PDT)
[AMBER] strange ion location Albert (Wed Jun 20 2012 - 23:56:01 PDT)
- [AMBER] strange ion location Albert (Thu Jun 21 2012 - 06:22:07 PDT)
[AMBER] Specifying disulfide bonds in a protein model Beale, John (Thu Jun 21 2012 - 02:18:09 PDT)
- Re: [AMBER] Specifying disulfide bonds in a protein model Anselm Horn (Thu Jun 21 2012 - 03:45:22 PDT)
- Re: [AMBER] Specifying disulfide bonds in a protein model David A. Case (Thu Jun 21 2012 - 04:36:30 PDT)
- [AMBER] How to explain this phenomenon is production MD Acoot Brett (Thu Jun 21 2012 - 23:31:17 PDT)
  - Re: [AMBER] How to explain this phenomenon is production MD steinbrt.rci.rutgers.edu (Fri Jun 22 2012 - 00:35:31 PDT)
    - Re: [AMBER] How to explain this phenomenon is production MD Acoot Brett (Sat Jun 23 2012 - 01:51:01 PDT)
    - Re: [AMBER] How to explain this phenomenon is production MD steinbrt.rci.rutgers.edu (Sat Jun 23 2012 - 03:40:38 PDT)
    - Re: [AMBER] How to explain this phenomenon is production MD Acoot Brett (Sat Jun 23 2012 - 18:12:33 PDT)
    - Re: [AMBER] How to explain this phenomenon is production MD steinbrt.rci.rutgers.edu (Sun Jun 24 2012 - 10:42:36 PDT)
[AMBER] TI calculation Amber 12 Anna Bauß (Thu Jun 21 2012 - 02:42:53 PDT)
- Re: [AMBER] TI calculation Amber 12 steinbrt.rci.rutgers.edu (Thu Jun 21 2012 - 04:01:07 PDT)
  - Re: [AMBER] TI calculation Amber 12 Anna Bauß (Thu Jun 21 2012 - 04:31:35 PDT)
    - Re: [AMBER] TI calculation Amber 12 steinbrt.rci.rutgers.edu (Thu Jun 21 2012 - 04:48:10 PDT)
    - Re: [AMBER] TI calculation Amber 12 Anna Bauß (Thu Jun 21 2012 - 05:53:54 PDT)
    - Re: [AMBER] TI calculation Amber 12 steinbrt.rci.rutgers.edu (Thu Jun 21 2012 - 07:12:45 PDT)
- Re: [AMBER] TI calculation Amber 12 Anna Bauß (Mon Jul 02 2012 - 02:36:30 PDT)
  - Re: [AMBER] TI calculation Amber 12 steinbrt.rci.rutgers.edu (Mon Jul 02 2012 - 02:54:39 PDT)
  - Re: [AMBER] TI calculation Amber 12 David A Case (Mon Jul 02 2012 - 04:40:02 PDT)
    - Re: [AMBER] TI calculation Amber 12 Anna Bauß (Mon Jul 02 2012 - 04:47:43 PDT)
    - Re: [AMBER] TI calculation Amber 12 steinbrt.rci.rutgers.edu (Mon Jul 02 2012 - 04:58:33 PDT)
    - Re: [AMBER] TI calculation Amber 12 Anna Bauß (Mon Jul 02 2012 - 05:07:34 PDT)
[AMBER] Solvent box specification for sander Brandon Sim (Thu Jun 21 2012 - 05:31:01 PDT)
- Re: [AMBER] Solvent box specification for sander Brian Radak (Thu Jun 21 2012 - 06:17:30 PDT)
- Re: [AMBER] Solvent box specification for sander Jason Swails (Thu Jun 21 2012 - 06:47:01 PDT)
  - Re: [AMBER] Solvent box specification for sander Brandon Sim (Thu Jun 21 2012 - 08:37:17 PDT)
    - Re: [AMBER] Solvent box specification for sander Jason Swails (Thu Jun 21 2012 - 08:48:49 PDT)
    - Re: [AMBER] Solvent box specification for sander Brandon Sim (Thu Jun 21 2012 - 10:33:47 PDT)
    - Re: [AMBER] Solvent box specification for sander Jason Swails (Thu Jun 21 2012 - 10:41:20 PDT)
[AMBER] Issues with library location on compiling AmberTools12 Francesco Pietra (Thu Jun 21 2012 - 11:57:59 PDT)
- Re: [AMBER] Issues with library location on compiling AmberTools12 David A. Case (Fri Jun 22 2012 - 15:41:14 PDT)
  - Re: [AMBER] Issues with library location on compiling AmberTools12 Francesco Pietra (Fri Jun 22 2012 - 22:21:37 PDT)
[AMBER] R: strange POPC under lipids 11 FF J B (Thu Jun 21 2012 - 15:05:40 PDT)
- Re: [AMBER] R: strange POPC under lipids 11 FF Albert (Thu Jun 21 2012 - 22:41:02 PDT)
- Re: [AMBER] R: strange POPC under lipids 11 FF Vlad Cojocaru (Thu Jun 21 2012 - 22:45:01 PDT)
  - Re: [AMBER] R: strange POPC under lipids 11 FF Albert (Thu Jun 21 2012 - 22:51:50 PDT)
    - Re: [AMBER] R: strange POPC under lipids 11 FF Vlad Cojocaru (Thu Jun 21 2012 - 22:58:13 PDT)
- [AMBER] R: strange POPC under lipids 11 FF J B (Thu Jun 21 2012 - 23:14:16 PDT)
  - Re: [AMBER] R: strange POPC under lipids 11 FF Gould, Ian R (Fri Jun 22 2012 - 01:50:25 PDT)
    - Re: [AMBER] R: strange POPC under lipids 11 FF Albert (Fri Jun 22 2012 - 01:50:32 PDT)
    - Re: [AMBER] R: strange POPC under lipids 11 FF Vlad Cojocaru (Fri Jun 22 2012 - 02:53:56 PDT)
    - Re: [AMBER] R: strange POPC under lipids 11 FF Benjamin Madej (Mon Jun 25 2012 - 10:14:56 PDT)
    - Re: [AMBER] R: strange POPC under lipids 11 FF Albert (Mon Jun 25 2012 - 10:52:42 PDT)
    - Re: [AMBER] R: strange POPC under lipids 11 FF Benjamin Madej (Mon Jun 25 2012 - 11:33:08 PDT)
[AMBER] idea of RMSD calculation in AMBER Sajeewa Pemasinghe (Thu Jun 21 2012 - 15:36:36 PDT)
- Re: [AMBER] idea of RMSD calculation in AMBER Carlos Simmerling (Thu Jun 21 2012 - 15:52:18 PDT)
[AMBER] C-H...O hydrogen bonds? Schubert Mario (Thu Jun 21 2012 - 15:56:00 PDT)
- Re: [AMBER] C-H...O hydrogen bonds? Daniel Roe (Fri Jun 22 2012 - 06:10:00 PDT)
[AMBER] SOLVED Fwd: Issues with library location on compiling AmberTools12 Francesco Pietra (Thu Jun 21 2012 - 22:48:30 PDT)
[AMBER] ERROR: max pairlist cutoff must be less than unit cell max sphere radius! Elisa Frezza (Fri Jun 22 2012 - 03:36:04 PDT)
- Re: [AMBER] ERROR: max pairlist cutoff must be less than unit cell max sphere radius! Daniel Roe (Fri Jun 22 2012 - 06:06:57 PDT)
  - Re: [AMBER] ERROR: max pairlist cutoff must be less than unit cell max sphere radius! Elisa Frezza (Fri Jun 22 2012 - 06:11:03 PDT)
    - Re: [AMBER] ERROR: max pairlist cutoff must be less than unit cell max sphere radius! Daniel Roe (Fri Jun 22 2012 - 06:17:53 PDT)
    - Re: [AMBER] ERROR: max pairlist cutoff must be less than unit cell max sphere radius! Elisa Frezza (Fri Jun 22 2012 - 06:38:18 PDT)
    - Re: [AMBER] ERROR: max pairlist cutoff must be less than unit cell max sphere radius! Daniel Roe (Fri Jun 22 2012 - 08:38:31 PDT)
- Re: [AMBER] ERROR: max pairlist cutoff must be less than unit cell max sphere radius! David A Case (Mon Jun 25 2012 - 04:58:56 PDT)
[AMBER] warning during nmode calulation - Not all of your snapshots minimized within tolerable limits for nmode Sangita Kachhap (Fri Jun 22 2012 - 03:55:28 PDT)
- Re: [AMBER] warning during nmode calulation - Not all of your snapshots minimized within tolerable limits for nmode Bill Miller III (Fri Jun 22 2012 - 11:11:53 PDT)
  - Re: [AMBER] warning during nmode calulation - Not all of your snapshots minimized within tolerable limits for nmode Sangita Kachhap (Thu Jun 28 2012 - 02:28:09 PDT)
[AMBER] R: strange POPC under lipids 11 FF Joakim Jämbeck (Fri Jun 22 2012 - 04:10:07 PDT)
- Re: [AMBER] R: strange POPC under lipids 11 FF Vlad Cojocaru (Fri Jun 22 2012 - 05:44:29 PDT)
  - Re: [AMBER] strange POPC under lipids 11 FF Vítor Félix (Fri Jun 22 2012 - 05:51:11 PDT)
[AMBER] vacuum simulation fails using pmemd g t (Fri Jun 22 2012 - 04:12:04 PDT)
- Re: [AMBER] vacuum simulation fails using pmemd Jason Swails (Fri Jun 22 2012 - 08:14:48 PDT)
  - Re: [AMBER] vacuum simulation fails using pmemd g t (Sat Jun 23 2012 - 10:48:44 PDT)
[AMBER] is the 'image' behavior of cpptraj's 'distance' command correct? Jan-Philip Gehrcke (Fri Jun 22 2012 - 08:07:08 PDT)
- Re: [AMBER] is the 'image' behavior of cpptraj's 'distance' command correct? Daniel Roe (Fri Jun 22 2012 - 08:19:11 PDT)
  - Re: [AMBER] is the 'image' behavior of cpptraj's 'distance' command correct? Jan-Philip Gehrcke (Mon Jun 25 2012 - 02:59:06 PDT)
[AMBER] AMBER GPU "Success Stories" mark94025.comcast.net (Fri Jun 22 2012 - 08:35:50 PDT)
[AMBER] Question on Ig=-1 usage Dilraj LAMA (Sat Jun 23 2012 - 01:05:55 PDT)
- Re: [AMBER] Question on Ig=-1 usage David A. Case (Sat Jun 23 2012 - 06:33:28 PDT)
- [AMBER] Regarding mmpbsa.py dilrajl.bii.a-star.edu.sg (Mon May 13 2013 - 03:55:57 PDT)
  - Re: [AMBER] Regarding mmpbsa.py David A Case (Mon May 13 2013 - 04:54:25 PDT)
  - Re: [AMBER] Regarding mmpbsa.py Jason Swails (Mon May 13 2013 - 05:00:28 PDT)
  - [AMBER] rmsd vs rmsf nguyentb.bii.a-star.edu.sg (Tue May 21 2013 - 02:36:08 PDT)
    - Re: [AMBER] rmsd vs rmsf Carlos Simmerling (Tue May 21 2013 - 04:17:08 PDT)
    - Re: [AMBER] rmsd vs rmsf Jason Swails (Tue May 21 2013 - 04:36:55 PDT)
    - Re: [AMBER] rmsd vs rmsf nguyentb.bii.a-star.edu.sg (Tue May 21 2013 - 05:30:08 PDT)
  - [AMBER] pairwise decomposition using mmpbsa.py dilrajl.bii.a-star.edu.sg (Wed May 22 2013 - 05:34:45 PDT)
    - Re: [AMBER] pairwise decomposition using mmpbsa.py Jason Swails (Wed May 22 2013 - 05:52:38 PDT)
  - [AMBER] RMSD calculation between trajectories dilrajl.bii.a-star.edu.sg (Tue May 28 2013 - 05:42:42 PDT)
    - Re: [AMBER] RMSD calculation between trajectories Niel Henriksen (Tue May 28 2013 - 05:59:50 PDT)
    - Re: [AMBER] RMSD calculation between trajectories Niel Henriksen (Tue May 28 2013 - 06:13:30 PDT)
    - Re: [AMBER] RMSD calculation between trajectories Daniel Roe (Tue May 28 2013 - 07:24:01 PDT)
    - Re: [AMBER] RMSD calculation between trajectories dilrajl.bii.a-star.edu.sg (Wed May 29 2013 - 05:10:58 PDT)
    - Re: [AMBER] RMSD calculation between trajectories Daniel Roe (Wed May 29 2013 - 07:11:18 PDT)
    - Re: [AMBER] RMSD calculation between trajectories dilrajl.bii.a-star.edu.sg (Thu May 30 2013 - 05:27:31 PDT)
    - Re: [AMBER] RMSD calculation between trajectories Daniel Roe (Thu May 30 2013 - 05:56:56 PDT)
- [AMBER] Comparing Enthalpy change and energy decomposition values dilrajl.bii.a-star.edu.sg (Fri Aug 23 2013 - 03:41:59 PDT)
[AMBER] How does 'restraint' work in Amber? Adam Jion (Sat Jun 23 2012 - 02:04:29 PDT)
- Re: [AMBER] How does 'restraint' work in Amber? vishal kumar Jaiswal (Sat Jun 23 2012 - 02:40:50 PDT)
  - Re: [AMBER] How does 'restraint' work in Amber? vishal kumar Jaiswal (Sat Jun 23 2012 - 02:56:11 PDT)
[AMBER] Mn2+ parameter Indrajit Deb (Sat Jun 23 2012 - 05:23:04 PDT)
[AMBER] Making a complex Saaz Sakrikar (Sat Jun 23 2012 - 05:51:40 PDT)
- Re: [AMBER] Making a complex David A. Case (Sat Jun 23 2012 - 06:37:29 PDT)
  - Re: [AMBER] Making a complex Saaz Sakrikar (Thu Aug 02 2012 - 04:00:49 PDT)
    - Re: [AMBER] Making a complex David A Case (Thu Aug 02 2012 - 05:00:52 PDT)
[AMBER] Fwd: Mn2+ parameter and crystal water Indrajit Deb (Sat Jun 23 2012 - 12:32:03 PDT)
- Re: [AMBER] Fwd: Mn2+ parameter and crystal water David A Case (Mon Jun 25 2012 - 04:42:31 PDT)
  - Re: [AMBER] Fwd: Mn2+ parameter and crystal water Indrajit Deb (Tue Jun 26 2012 - 00:45:28 PDT)
[AMBER] the problem of cpptraj xiaojiong (Sun Jun 24 2012 - 06:06:26 PDT)
- Re: [AMBER] the problem of cpptraj Jason Swails (Sun Jun 24 2012 - 07:43:42 PDT)
[AMBER] Pressure Regulaton Under Position Restraint Adam Jion (Sun Jun 24 2012 - 10:06:45 PDT)
- Re: [AMBER] Pressure Regulaton Under Position Restraint David A Case (Mon Jun 25 2012 - 04:40:54 PDT)
[AMBER] Re [amber] north/sout energy difference Steven M. Graham (Sun Jun 24 2012 - 10:53:23 PDT)
- Re: [AMBER] Re [amber] north/sout energy difference Jiri Sponer (Sun Jun 24 2012 - 12:39:26 PDT)
[AMBER] Problem in MM-PBSA decomp module moitrayee.mbu.iisc.ernet.in (Sun Jun 24 2012 - 11:57:13 PDT)
- Re: [AMBER] Problem in MM-PBSA decomp module Jason Swails (Sun Jun 24 2012 - 14:24:35 PDT)
[AMBER] problem in antechamber jit mukherjee (Mon Jun 25 2012 - 01:30:20 PDT)
- Re: [AMBER] problem in antechamber David A Case (Mon Jun 25 2012 - 04:35:21 PDT)
[AMBER] Doubt about ligand preparation in Gaussian and tleap Jitesh Doshi (Mon Jun 25 2012 - 06:50:14 PDT)
- Re: [AMBER] Doubt about ligand preparation in Gaussian and tleap David A Case (Mon Jun 25 2012 - 08:30:12 PDT)
- Re: [AMBER] Doubt about ligand preparation in Gaussian and tleap FyD (Tue Jun 26 2012 - 00:03:43 PDT)
[AMBER] binding energy of duplex DNA by mm-pbsa barb fr (Mon Jun 25 2012 - 07:28:04 PDT)
- Re: [AMBER] binding energy of duplex DNA by mm-pbsa David A Case (Mon Jun 25 2012 - 08:38:16 PDT)
  - Re: [AMBER] binding energy of duplex DNA by mm-pbsa Ilyas Yildirim (Mon Jun 25 2012 - 08:51:52 PDT)
  - Re: [AMBER] binding energy of duplex DNA by mm-pbsa cieplak.cgl.ucsf.edu (Tue Jun 26 2012 - 14:24:45 PDT)
[AMBER] problem in running LES calculation with a solvated shell system Sajeewa Pemasinghe (Mon Jun 25 2012 - 09:30:37 PDT)
- [AMBER] Fwd: problem in running LES calculation with a solvated shell system Sajeewa Pemasinghe (Mon Jun 25 2012 - 21:08:10 PDT)
- Re: [AMBER] problem in running LES calculation with a solvated shell system Carlos Simmerling (Tue Jun 26 2012 - 02:49:13 PDT)
  - Re: [AMBER] problem in running LES calculation with a solvated shell system Sajeewa Pemasinghe (Tue Jun 26 2012 - 05:29:36 PDT)
    - Re: [AMBER] problem in running LES calculation with a solvated shell system Carlos Simmerling (Tue Jun 26 2012 - 06:13:21 PDT)
[AMBER] REMD structure failure Do Yong Kim (Mon Jun 25 2012 - 09:48:02 PDT)
- Re: [AMBER] REMD structure failure Carlos Simmerling (Mon Jun 25 2012 - 09:50:59 PDT)
[AMBER] AmberTools 12 pbsa: missing newline character in OpenDX output Jan-Philip Gehrcke (Mon Jun 25 2012 - 10:33:59 PDT)
- [AMBER] Fwd: AmberTools 12 pbsa: missing newline character in OpenDX output Ray Luo, Ph.D. (Mon Jun 25 2012 - 10:44:07 PDT)
  - Re: [AMBER] Fwd: AmberTools 12 pbsa: missing newline character in OpenDX output (patched gen_dx_file.F90 attached) Jan-Philip Gehrcke (Mon Jul 09 2012 - 11:57:21 PDT)
    - Re: [AMBER] Fwd: AmberTools 12 pbsa: missing newline character in OpenDX output (patched gen_dx_file.F90 attached) Jason Swails (Mon Jul 09 2012 - 13:04:10 PDT)
    - Re: [AMBER] Fwd: AmberTools 12 pbsa: missing newline character in OpenDX output (patched gen_dx_file.F90 attached) Jan-Philip Gehrcke (Tue Jul 10 2012 - 00:20:21 PDT)
    - Re: [AMBER] Fwd: AmberTools 12 pbsa: missing newline character in OpenDX output (patched gen_dx_file.F90 attached) Ray Luo, Ph.D. (Tue Jul 10 2012 - 08:15:09 PDT)
    - Re: [AMBER] Fwd: AmberTools 12 pbsa: missing newline character in OpenDX output (patched gen_dx_file.F90 attached) Ray Luo (Mon Jul 09 2012 - 13:19:01 PDT)
[AMBER] valence not found for for [Na+ ] Mahendra B Thapa (Mon Jun 25 2012 - 12:41:26 PDT)
- Re: [AMBER] valence not found for for [Na+ ] Daniel Roe (Mon Jun 25 2012 - 19:35:20 PDT)
[AMBER] creating a bellymask which includes residues at a given distance from a point Sajeewa Pemasinghe (Mon Jun 25 2012 - 12:56:27 PDT)
- Re: [AMBER] creating a bellymask which includes residues at a given distance from a point Jason Swails (Mon Jun 25 2012 - 13:15:00 PDT)
[AMBER] using bellymask and group specification together Sajeewa Pemasinghe (Mon Jun 25 2012 - 14:29:36 PDT)
- Re: [AMBER] using bellymask and group specification together case (Mon Jun 25 2012 - 18:03:22 PDT)
[AMBER] Reading velocities from netcdf file Hemant Gangwar (Tue Jun 26 2012 - 00:31:06 PDT)
- [AMBER] Reading velocities from netcdf file Hemant Gangwar (Tue Jun 26 2012 - 02:22:28 PDT)
[AMBER] problem in the bondtype judgement step in antechamber jit mukherjee (Tue Jun 26 2012 - 00:30:57 PDT)
- Re: [AMBER] problem in the bondtype judgement step in antechamber FyD (Tue Jun 26 2012 - 01:27:53 PDT)
  - Re: [AMBER] problem in the bondtype judgement step in antechamber jit mukherjee (Tue Jun 26 2012 - 02:41:43 PDT)
[AMBER] Can we change BUFFER_SIZE (1024) ? kurisaki (Tue Jun 26 2012 - 00:42:24 PDT)
- Re: [AMBER] Can we change BUFFER_SIZE (1024) ? Jason Swails (Tue Jun 26 2012 - 07:13:34 PDT)
  - Re: [AMBER] Can we change BUFFER_SIZE (1024) ? kurisaki (Tue Jun 26 2012 - 19:42:04 PDT)
[AMBER] Fwd: HIMANSHU JOSHI (Tue Jun 26 2012 - 03:22:00 PDT)
[AMBER] PTRAJ not able to read netcdf format HIMANSHU JOSHI (Tue Jun 26 2012 - 03:25:09 PDT)
- Re: [AMBER] PTRAJ not able to read netcdf format Jason Swails (Tue Jun 26 2012 - 07:08:01 PDT)
[AMBER] Implicit solvent (GB options) with GLYCAM_06h Kepa K. Burusco (Tue Jun 26 2012 - 04:11:49 PDT)
- Re: [AMBER] Implicit solvent (GB options) with GLYCAM_06h Lachele Foley (Lists) (Tue Jun 26 2012 - 09:53:59 PDT)
  - Re: [AMBER] Implicit solvent (GB options) with GLYCAM_06h Kepa K. Burusco (Tue Jun 26 2012 - 11:27:03 PDT)
[AMBER] calculation of the average structure Olena Dobrovolska (Tue Jun 26 2012 - 05:15:02 PDT)
- Re: [AMBER] calculation of the average structure Jason Swails (Tue Jun 26 2012 - 06:55:39 PDT)
  - Re: [AMBER] calculation of the average structure Olena Dobrovolska (Tue Jun 26 2012 - 08:00:24 PDT)
    - Re: [AMBER] calculation of the average structure Jason Swails (Tue Jun 26 2012 - 08:14:46 PDT)
[AMBER] using "append" in trajout Mahendra B Thapa (Tue Jun 26 2012 - 09:46:23 PDT)
- Re: [AMBER] using "append" in trajout Daniel Roe (Wed Jun 27 2012 - 05:51:56 PDT)
[AMBER] implicit GB model for membrane simulation houcemeddine othman (Tue Jun 26 2012 - 16:11:59 PDT)
- Re: [AMBER] implicit GB model for membrane simulation Ray Luo, Ph.D. (Tue Jun 26 2012 - 16:30:53 PDT)
[AMBER] AMBER Error: unable to achieve consistency Asma Abro 28-FBAS/MSBI/F09 (Tue Jun 26 2012 - 20:40:12 PDT)
- Re: [AMBER] AMBER Error: unable to achieve consistency Ross Walker (Tue Jun 26 2012 - 21:42:00 PDT)
  - Re: [AMBER] AMBER Error: unable to achieve consistency Asma Abro 28-FBAS/MSBI/F09 (Tue Jun 26 2012 - 22:19:27 PDT)
    - Re: [AMBER] AMBER Error: unable to achieve consistency Asma Abro 28-FBAS/MSBI/F09 (Tue Jun 26 2012 - 22:20:21 PDT)
    - Re: [AMBER] AMBER Error: unable to achieve consistency Asma Abro 28-FBAS/MSBI/F09 (Tue Jun 26 2012 - 23:45:40 PDT)
- Re: [AMBER] AMBER Error: unable to achieve consistency Jodi Ann Hadden (Wed Jun 27 2012 - 08:32:28 PDT)
  - Re: [AMBER] AMBER Error: unable to achieve consistency Asma Abro 28-FBAS/MSBI/F09 (Wed Jun 27 2012 - 21:57:27 PDT)
- Re: [AMBER] AMBER Error: unable to achieve consistency Jodi Ann Hadden (Thu Jun 28 2012 - 07:06:08 PDT)
  - Re: [AMBER] AMBER Error: unable to achieve consistency David A Case (Thu Jun 28 2012 - 07:42:50 PDT)
    - Re: [AMBER] AMBER Error: unable to achieve consistency Asma Abro 28-FBAS/MSBI/F09 (Thu Jun 28 2012 - 20:51:15 PDT)
[AMBER] APPEND option does not work in TRAJOUT of CPPTRAJ kurisaki (Tue Jun 26 2012 - 23:36:37 PDT)
- Re: [AMBER] APPEND option does not work in TRAJOUT of CPPTRAJ kurisaki (Tue Jun 26 2012 - 23:45:00 PDT)
  - Re: [AMBER] APPEND option does not work in TRAJOUT of CPPTRAJ Jason Swails (Wed Jun 27 2012 - 04:20:31 PDT)
[AMBER] PMEMD CUPA MPI STOP WRITING OUTPUT IN RUNNIG STATUS HIMANSHU JOSHI (Tue Jun 26 2012 - 23:55:22 PDT)
- Re: [AMBER] PMEMD CUPA MPI STOP WRITING OUTPUT IN RUNNIG STATUS Ross Walker (Wed Jun 27 2012 - 09:11:24 PDT)
  - Re: [AMBER] PMEMD CUPA MPI STOP WRITING OUTPUT IN RUNNIG STATUS HIMANSHU JOSHI (Wed Jun 27 2012 - 10:36:22 PDT)
[AMBER] MMPBSA calculation of DNA solvation Soumya Lipsa Rath (Wed Jun 27 2012 - 02:49:42 PDT)
- Re: [AMBER] MMPBSA calculation of DNA solvation David A Case (Wed Jun 27 2012 - 04:58:36 PDT)
[AMBER] gaff.dat column and preference to frcmod file params Jio M (Wed Jun 27 2012 - 04:24:53 PDT)
- Re: [AMBER] gaff.dat column and preference to frcmod file params David A Case (Wed Jun 27 2012 - 05:05:38 PDT)
  - Re: [AMBER] gaff.dat column and preference to frcmod file params Jio M (Wed Jun 27 2012 - 05:27:58 PDT)
    - [AMBER] a question on molecular dynamics simulation of key residue mutated protein Acoot Brett (Wed Jun 27 2012 - 16:42:22 PDT)
    - Re: [AMBER] a question on molecular dynamics simulation of key residue mutated protein Carlos Simmerling (Wed Jun 27 2012 - 16:51:21 PDT)
    - [AMBER] Which server can give the series of PDB files for the energy equivalent conformations Acoot Brett (Wed Jun 27 2012 - 17:30:16 PDT)
[AMBER] tleap adds in "missing" terminal hydrogens - how to stop? Brandon Sim (Wed Jun 27 2012 - 12:09:48 PDT)
- Re: [AMBER] tleap adds in "missing" terminal hydrogens - how to stop? Brandon Sim (Wed Jun 27 2012 - 12:10:20 PDT)
  - Re: [AMBER] tleap adds in "missing" terminal hydrogens - how to stop? Brandon Sim (Wed Jun 27 2012 - 12:11:53 PDT)
- Re: [AMBER] tleap adds in "missing" terminal hydrogens - how to stop? David A Case (Wed Jun 27 2012 - 12:51:22 PDT)
  - Re: [AMBER] tleap adds in "missing" terminal hydrogens - how to stop? Brandon Sim (Wed Jun 27 2012 - 13:12:50 PDT)
    - Re: [AMBER] tleap adds in "missing" terminal hydrogens - how to stop? case (Wed Jun 27 2012 - 17:44:21 PDT)
    - Re: [AMBER] tleap adds in "missing" terminal hydrogens - how to stop? Jason Swails (Wed Jun 27 2012 - 19:59:48 PDT)
    - Re: [AMBER] tleap adds in "missing" terminal hydrogens - how to stop? Brandon Sim (Wed Jun 27 2012 - 20:19:08 PDT)
    - Re: [AMBER] tleap adds in "missing" terminal hydrogens - how to stop? Jason Swails (Wed Jun 27 2012 - 20:39:43 PDT)
    - Re: [AMBER] tleap adds in "missing" terminal hydrogens - how to stop? Brandon Sim (Wed Jun 27 2012 - 23:51:42 PDT)
[AMBER] MMPBSA.py gbsa unrecognized E. Nihal Korkmaz (Wed Jun 27 2012 - 13:39:09 PDT)
- Re: [AMBER] MMPBSA.py gbsa unrecognized Jason Swails (Wed Jun 27 2012 - 14:14:09 PDT)
  - Re: [AMBER] MMPBSA.py gbsa unrecognized E. Nihal Korkmaz (Tue Aug 21 2012 - 21:19:33 PDT)
    - Re: [AMBER] MMPBSA.py gbsa unrecognized Jason Swails (Tue Aug 21 2012 - 21:44:32 PDT)
[AMBER] all_prot_nucleic10.lib file in amber12 Asmita Gupta (Wed Jun 27 2012 - 23:44:29 PDT)
- Re: [AMBER] all_prot_nucleic10.lib file in amber12 FyD (Wed Jun 27 2012 - 23:57:53 PDT)
- Re: [AMBER] all_prot_nucleic10.lib file in amber12 FyD (Wed Jul 04 2012 - 01:16:10 PDT)
  - Re: [AMBER] [q4md-fft] Re: all_prot_nucleic10.lib file in amber12 Jason Swails (Wed Jul 04 2012 - 09:26:46 PDT)
    - Re: [AMBER] [q4md-fft] Re: all_prot_nucleic10.lib file in amber12 FyD (Fri Jul 06 2012 - 23:12:37 PDT)
[AMBER] Monitoring formation of Water bridges in ptraj Andre Serobian (Wed Jun 27 2012 - 23:46:45 PDT)
[AMBER] set box problem Jio M (Thu Jun 28 2012 - 08:46:55 PDT)
- [AMBER] Fw: set box problem Jio M (Fri Jun 29 2012 - 06:00:23 PDT)
  - Re: [AMBER] Fw: set box problem David A Case (Fri Jun 29 2012 - 06:46:55 PDT)
    - Re: [AMBER] Fw: set box problem David A Case (Fri Jun 29 2012 - 09:02:01 PDT)
- [AMBER] set box problem: not solved Jio M (Fri Jun 29 2012 - 06:19:46 PDT)
[AMBER] Low POPC area per lipid - LIPID11 James Murdock (Thu Jun 28 2012 - 11:47:17 PDT)
- Re: [AMBER] Low POPC area per lipid - LIPID11 Ross Walker (Thu Jun 28 2012 - 12:34:14 PDT)
[AMBER] rmsd Wilson, Katie (Thu Jun 28 2012 - 12:22:12 PDT)
- Re: [AMBER] rmsd Carlos Simmerling (Thu Jun 28 2012 - 12:25:10 PDT)
  - Re: [AMBER] rmsd Wilson, Katie (Thu Jun 28 2012 - 12:43:26 PDT)
    - Re: [AMBER] rmsd Carlos Simmerling (Thu Jun 28 2012 - 12:45:10 PDT)
    - Re: [AMBER] rmsd Wilson, Katie (Thu Jun 28 2012 - 12:52:32 PDT)
    - Re: [AMBER] rmsd Carlos Simmerling (Thu Jun 28 2012 - 12:53:32 PDT)
    - Re: [AMBER] rmsd Wilson, Katie (Thu Jun 28 2012 - 14:20:09 PDT)
    - Re: [AMBER] rmsd Niel Henriksen (Thu Jun 28 2012 - 14:33:34 PDT)
[AMBER] REMD trajectories: Ts -> replicas panecka.icm.edu.pl (Thu Jun 28 2012 - 13:42:35 PDT)
[AMBER] Prepgen omits information about half of the atoms Maria Minakova (Thu Jun 28 2012 - 14:25:15 PDT)
- Re: [AMBER] Prepgen omits information about half of the atoms Ross Walker (Thu Jun 28 2012 - 14:48:44 PDT)
[AMBER] Re [amber] north/sout energy difference Steven M. Graham (Thu Jun 28 2012 - 15:09:38 PDT)
- Re: [AMBER] Re [amber] north/sout energy difference Ilyas Yildirim (Thu Jun 28 2012 - 15:25:52 PDT)
  - Re: [AMBER] Re [amber] north/sout energy difference Steven M. Graham (Fri Jun 29 2012 - 10:03:25 PDT)
    - Re: [AMBER] Re [amber] north/sout energy difference Ilyas Yildirim (Fri Jun 29 2012 - 10:40:33 PDT)
[AMBER] How to estimate Tm of DNA duplex? Xioling Chuang (Fri Jun 29 2012 - 01:19:01 PDT)
[AMBER] sander termination upon reaching end temperature Brandon Sim (Fri Jun 29 2012 - 02:17:05 PDT)
- Re: [AMBER] sander termination upon reaching end temperature Vishal Kumar Jaiswal (Fri Jun 29 2012 - 02:46:43 PDT)
  - Re: [AMBER] sander termination upon reaching end temperature Brandon Sim (Fri Jun 29 2012 - 03:14:59 PDT)
    - Re: [AMBER] sander termination upon reaching end temperature Carlos Simmerling (Fri Jun 29 2012 - 03:24:38 PDT)
    - Re: [AMBER] sander termination upon reaching end temperature Brandon Sim (Fri Jun 29 2012 - 03:39:01 PDT)
    - Re: [AMBER] sander termination upon reaching end temperature Carlos Simmerling (Fri Jun 29 2012 - 03:42:40 PDT)
    - Re: [AMBER] sander termination upon reaching end temperature Vishal Kumar Jaiswal (Fri Jun 29 2012 - 04:42:42 PDT)
    - Re: [AMBER] sander termination upon reaching end temperature Vishal Kumar Jaiswal (Fri Jun 29 2012 - 04:43:25 PDT)
    - Re: [AMBER] sander termination upon reaching end temperature Carlos Simmerling (Fri Jun 29 2012 - 04:48:57 PDT)
    - Re: [AMBER] sander termination upon reaching end temperature Brandon Sim (Fri Jun 29 2012 - 15:05:59 PDT)
    - Re: [AMBER] sander termination upon reaching end temperature Ross Walker (Fri Jun 29 2012 - 15:23:35 PDT)
    - [AMBER] How to call up ptraj in supercomputer facilities? should I use mpi? Catein Catherine (Sat Jun 30 2012 - 03:28:30 PDT)
    - Re: [AMBER] How to call up ptraj in supercomputer facilities? should I use mpi? Ben Roberts (Sat Jun 30 2012 - 22:43:03 PDT)
    - Re: [AMBER] How to call up ptraj in supercomputer facilities? should I use mpi? Jason Swails (Sun Jul 01 2012 - 08:23:24 PDT)
    - Re: [AMBER] How to call up ptraj in supercomputer facilities? should I use mpi? Catein Catherine (Sun Jul 01 2012 - 23:41:59 PDT)
    - Re: [AMBER] sander termination upon reaching end temperature Brandon Sim (Sat Jun 30 2012 - 15:06:49 PDT)
- Re: [AMBER] sander termination upon reaching end temperature Carlos Simmerling (Fri Jun 29 2012 - 02:59:27 PDT)
[AMBER] no hydrogen added with xleap houcemeddine othman (Fri Jun 29 2012 - 04:25:11 PDT)
- Re: [AMBER] no hydrogen added with xleap Vishal Kumar Jaiswal (Fri Jun 29 2012 - 04:30:22 PDT)
  - Re: [AMBER] no hydrogen added with xleap houcemeddine othman (Fri Jun 29 2012 - 05:05:05 PDT)
- Re: [AMBER] no hydrogen added with xleap David A Case (Fri Jun 29 2012 - 05:24:45 PDT)
[AMBER] update for POPE test Albert (Fri Jun 29 2012 - 05:28:44 PDT)
- [AMBER] update for POPE test Albert (Fri Jun 29 2012 - 05:32:16 PDT)
  - Re: [AMBER] update for POPE test Vlad Cojocaru (Fri Jun 29 2012 - 05:52:57 PDT)
    - Re: [AMBER] update for POPE test Sarah Witzke (Fri Jun 29 2012 - 05:55:35 PDT)
  - Re: [AMBER] update for POPE test Åge Skjevik (Fri Jun 29 2012 - 05:56:31 PDT)
    - Re: [AMBER] update for POPE test Albert (Fri Jun 29 2012 - 07:16:46 PDT)
    - Re: [AMBER] update for POPE test Åge Skjevik (Fri Jun 29 2012 - 07:40:36 PDT)
    - [AMBER] Salt concentration: general question Anselm Horn (Sat Jun 30 2012 - 07:20:06 PDT)
    - Re: [AMBER] Salt concentration: general question Carlos Simmerling (Sat Jun 30 2012 - 07:52:19 PDT)
[AMBER] atom type specification for chlorine Sanjib Paul (Fri Jun 29 2012 - 07:05:45 PDT)
- Re: [AMBER] atom type specification for chlorine case (Sat Jun 30 2012 - 05:27:35 PDT)
[AMBER] trajectory imaging results in structural clashes in protein-ligand complexes Harald Lanig (Fri Jun 29 2012 - 07:42:12 PDT)
- Re: [AMBER] trajectory imaging results in structural clashes in protein-ligand complexes Carlos Simmerling (Fri Jun 29 2012 - 07:43:37 PDT)
  - Re: [AMBER] trajectory imaging results in structural clashes in protein-ligand complexes Harald Lanig (Mon Jul 02 2012 - 05:11:30 PDT)
- Re: [AMBER] trajectory imaging results in structural clashes in protein-ligand complexes Fredrick Devadoss (Mon Jul 02 2012 - 06:40:22 PDT)
  - Re: [AMBER] trajectory imaging results in structural clashes in protein-ligand complexes Jason Swails (Mon Jul 02 2012 - 06:48:50 PDT)
- Re: [AMBER] trajectory imaging results in structural clashes in protein-ligand complexes Harald Lanig (Mon Jul 02 2012 - 09:40:38 PDT)
  - Re: [AMBER] trajectory imaging results in structural clashes in protein-ligand complexes Daniel Roe (Fri Jul 13 2012 - 09:50:51 PDT)
Re: [AMBER] Fw: set box problem Jio M (Fri Jun 29 2012 - 20:29:10 PDT)
[AMBER] Amber: mm_pbsa.pl rajeevy.iitk.ac.in (Sat Jun 30 2012 - 03:36:00 PDT)
- Re: [AMBER] Amber: mm_pbsa.pl Ray Luo, Ph.D. (Sat Jun 30 2012 - 07:26:43 PDT)
  - Re: [AMBER] Amber: mm_pbsa.pl rajeevy.iitk.ac.in (Sun Jul 01 2012 - 00:10:01 PDT)
    - Re: [AMBER] Amber: mm_pbsa.pl Ray Luo, Ph.D. (Sun Jul 01 2012 - 07:41:58 PDT)
    - Re: [AMBER] Amber: mm_pbsa.pl rajeevy.iitk.ac.in (Mon Jul 02 2012 - 07:36:42 PDT)
    - Re: [AMBER] Amber: mm_pbsa.pl Jason Swails (Mon Jul 02 2012 - 07:41:56 PDT)
    - Re: [AMBER] Amber: mm_pbsa.pl rajeevy.iitk.ac.in (Tue Jul 03 2012 - 07:03:00 PDT)
    - Re: [AMBER] Amber: mm_pbsa.pl Jason Swails (Tue Jul 03 2012 - 07:36:21 PDT)
    - Re: [AMBER] Amber: mm_pbsa.pl rajeevy.iitk.ac.in (Tue Jul 03 2012 - 23:24:42 PDT)
    - Re: [AMBER] Amber: mm_pbsa.pl case (Wed Jul 04 2012 - 05:54:58 PDT)
    - Re: [AMBER] Amber: mm_pbsa.pl rajeevy.iitk.ac.in (Wed Jul 04 2012 - 07:54:10 PDT)
    - Re: [AMBER] Amber: mm_pbsa.pl Jason Swails (Wed Jul 04 2012 - 12:41:53 PDT)
    - Re: [AMBER] Amber: mm_pbsa.pl rajeevy.iitk.ac.in (Mon Jul 09 2012 - 05:25:45 PDT)
    - Re: [AMBER] Amber: mm_pbsa.pl Jason Swails (Mon Jul 09 2012 - 08:43:40 PDT)
    - Re: [AMBER] Amber: mm_pbsa.pl Ray Luo (Mon Jul 09 2012 - 16:09:14 PDT)
    - Re: [AMBER] Amber: mm_pbsa.pl Qin Cai (Mon Jul 09 2012 - 17:40:45 PDT)
    - Re: [AMBER] Amber: mm_pbsa.pl rajeevy.iitk.ac.in (Mon Jul 09 2012 - 21:40:00 PDT)
    - Re: [AMBER] Amber: mm_pbsa.pl Ray Luo, Ph.D. (Tue Jul 10 2012 - 08:05:20 PDT)
[AMBER] failure about pmemd.cuda caobb0214 (Sat Jun 30 2012 - 20:27:10 PDT)
- Re: [AMBER] failure about pmemd.cuda case (Sun Jul 01 2012 - 05:21:38 PDT)
[AMBER] complex of protein dimer and two ligands simulated MMPBSA.py error kamlesh sahu (Mon Jul 02 2012 - 01:19:28 PDT)
- Re: [AMBER] complex of protein dimer and two ligands simulated MMPBSA.py error Jason Swails (Mon Jul 02 2012 - 06:43:54 PDT)
  - Re: [AMBER] complex of protein dimer and two ligands simulated MMPBSA.py error kamlesh sahu (Tue Jul 03 2012 - 00:48:34 PDT)
  - Re: [AMBER] complex of protein dimer and two ligands simulated MMPBSA.py error kamlesh sahu (Mon Jul 23 2012 - 00:51:47 PDT)
    - Re: [AMBER] complex of protein dimer and two ligands simulated MMPBSA.py error Jason Swails (Mon Jul 23 2012 - 04:51:22 PDT)
    - Re: [AMBER] complex of protein dimer and two ligands simulated MMPBSA.py error kamlesh sahu (Mon Jul 23 2012 - 17:58:20 PDT)
    - [AMBER] Fwd: complex of protein dimer and two ligands simulated MMPBSA.py error kamlesh sahu (Mon Jul 23 2012 - 18:41:17 PDT)
    - Re: [AMBER] Fwd: complex of protein dimer and two ligands simulated MMPBSA.py error Jason Swails (Mon Jul 23 2012 - 19:27:49 PDT)
    - Re: [AMBER] Fwd: complex of protein dimer and two ligands simulated MMPBSA.py error kamlesh sahu (Mon Jul 23 2012 - 19:42:44 PDT)
    - Re: [AMBER] Fwd: complex of protein dimer and two ligands simulated MMPBSA.py error Jason Swails (Mon Jul 23 2012 - 20:39:03 PDT)
[AMBER] Error on REMD trajectory analysis Dilraj LAMA (Mon Jul 02 2012 - 05:11:17 PDT)
[AMBER] Error in post-processing REMD trajectory Dilraj LAMA (Mon Jul 02 2012 - 05:13:00 PDT)
- Re: [AMBER] Error in post-processing REMD trajectory Jason Swails (Mon Jul 02 2012 - 08:52:49 PDT)
[AMBER] error to run pmemd.MPI on Opteron CPU Yubo Fan (Mon Jul 02 2012 - 22:52:30 PDT)
- Re: [AMBER] error to run pmemd.MPI on Opteron CPU David A Case (Tue Jul 03 2012 - 04:54:59 PDT)
  - Re: [AMBER] error to run pmemd.MPI on Opteron CPU Jason Swails (Tue Jul 03 2012 - 05:02:16 PDT)
    - Re: [AMBER] error to run pmemd.MPI on Opteron CPU Yubo Fan (Thu Jul 05 2012 - 08:05:09 PDT)
[AMBER] Script to restore resid numbering Francesco Pietra (Tue Jul 03 2012 - 00:49:03 PDT)
[AMBER] Constraint simulations Rajendra Sharma (Wed Jul 04 2012 - 00:21:24 PDT)
- Re: [AMBER] Constraint simulations Jason Swails (Wed Jul 04 2012 - 09:21:11 PDT)
[AMBER] Thermodynamic integration with polarizable force field VAN DAMME Steven (Wed Jul 04 2012 - 05:56:27 PDT)
- Re: [AMBER] Thermodynamic integration with polarizable force field case (Wed Jul 04 2012 - 09:24:01 PDT)
[AMBER] velocities and irest=0 in Amber 11/12 Jan-Philip Gehrcke (Wed Jul 04 2012 - 08:33:46 PDT)
- Re: [AMBER] velocities and irest=0 in Amber 11/12 Jason Swails (Wed Jul 04 2012 - 09:28:38 PDT)
  - Re: [AMBER] velocities and irest=0 in Amber 11/12 Jan-Philip Gehrcke (Wed Jul 04 2012 - 09:46:59 PDT)
    - Re: [AMBER] velocities and irest=0 in Amber 11/12 Jan-Philip Gehrcke (Wed Jul 04 2012 - 09:55:58 PDT)
    - Re: [AMBER] velocities and irest=0 in Amber 11/12 Jason Swails (Wed Jul 04 2012 - 11:52:42 PDT)
    - Re: [AMBER] velocities and irest=0 in Amber 11/12 Jan-Philip Gehrcke (Thu Jul 05 2012 - 05:13:25 PDT)
[AMBER] ff12SB manikanthan bhavaraju (Wed Jul 04 2012 - 12:04:44 PDT)
- Re: [AMBER] ff12SB Carlos Simmerling (Wed Jul 04 2012 - 12:09:07 PDT)
[AMBER] MMPBSA calculation problem 刘金峰 (Wed Jul 04 2012 - 22:17:46 PDT)
[AMBER] AMBER 12 benchmarks Hannes Loeffler (Thu Jul 05 2012 - 05:54:37 PDT)
- Re: [AMBER] AMBER 12 benchmarks Jan-Philip Gehrcke (Thu Jul 05 2012 - 06:06:09 PDT)
  - Re: [AMBER] AMBER 12 benchmarks Hannes Loeffler (Thu Jul 05 2012 - 08:49:38 PDT)
    - Re: [AMBER] AMBER 12 benchmarks Jason Swails (Thu Jul 05 2012 - 10:02:42 PDT)
    - Re: [AMBER] AMBER 12 benchmarks Hannes Loeffler (Wed Jul 11 2012 - 01:27:14 PDT)
- Re: [AMBER] AMBER 12 benchmarks Albert (Thu Jul 05 2012 - 06:54:23 PDT)
  - Re: [AMBER] AMBER 12 benchmarks Hannes Loeffler (Thu Jul 05 2012 - 08:56:20 PDT)
  - Re: [AMBER] AMBER 12 benchmarks Ross Walker (Thu Jul 05 2012 - 09:28:02 PDT)
    - Re: [AMBER] AMBER 12 benchmarks Albert (Thu Jul 05 2012 - 09:56:00 PDT)
- Re: [AMBER] AMBER 12 benchmarks Ross Walker (Thu Jul 05 2012 - 09:23:14 PDT)
  - Re: [AMBER] AMBER 12 benchmarks Hannes Loeffler (Wed Jul 11 2012 - 01:25:38 PDT)
[AMBER] CUDA MPI failed in Ubuntu Albert (Thu Jul 05 2012 - 08:38:26 PDT)
[AMBER] entropy calculations bmartini (Thu Jul 05 2012 - 09:50:49 PDT)
- Re: [AMBER] entropy calculations Jason Swails (Thu Jul 05 2012 - 10:05:16 PDT)
  - Re: [AMBER] entropy calculations bmartini (Thu Jul 05 2012 - 12:05:26 PDT)
    - Re: [AMBER] entropy calculations Jason Swails (Thu Jul 05 2012 - 12:29:24 PDT)
    - Re: [AMBER] entropy calculations bmartini (Fri Jul 06 2012 - 09:48:39 PDT)
    - Re: [AMBER] entropy calculations Jason Swails (Fri Jul 06 2012 - 11:05:09 PDT)
[AMBER] Difficulty using ptraj to generate pdb frames from .mdcrd trajectory Gordon S Freeman (Thu Jul 05 2012 - 12:23:42 PDT)
- Re: [AMBER] Difficulty using ptraj to generate pdb frames from .mdcrd trajectory Daniel Roe (Tue Jul 10 2012 - 07:24:40 PDT)
  - Re: [AMBER] Difficulty using ptraj to generate pdb frames from .mdcrd trajectory Gordon S Freeman (Tue Jul 10 2012 - 15:15:14 PDT)
    - Re: [AMBER] Difficulty using ptraj to generate pdb frames from .mdcrd trajectory Jason Swails (Thu Jul 12 2012 - 12:27:19 PDT)
    - Re: [AMBER] Difficulty using ptraj to generate pdb frames from .mdcrd trajectory Thomas Cheatham (Thu Jul 12 2012 - 12:34:37 PDT)
    - Re: [AMBER] Difficulty using ptraj to generate pdb frames from .mdcrd trajectory Daniel Roe (Fri Jul 13 2012 - 06:59:46 PDT)
[AMBER] Force field for bend DNA sudipta (Thu Jul 05 2012 - 17:07:00 PDT)
[AMBER] Polarizable vs Fixed Charge FF Nikolay Igorovich Rodionov (Fri Jul 06 2012 - 07:11:28 PDT)
[AMBER] different RMSF between CPU and GPU Massimiliano Porrini (Fri Jul 06 2012 - 12:37:17 PDT)
- Re: [AMBER] different RMSF between CPU and GPU Ross Walker (Fri Jul 06 2012 - 14:51:14 PDT)
  - Re: [AMBER] different RMSF between CPU and GPU Massimiliano Porrini (Sat Jul 07 2012 - 11:57:19 PDT)
    - Re: [AMBER] different RMSF between CPU and GPU Ross Walker (Sat Jul 07 2012 - 21:21:57 PDT)
[AMBER] protonated nucleic acid residues Timothy Robbins (trobbins) (Fri Jul 06 2012 - 14:13:32 PDT)
- Re: [AMBER] protonated nucleic acid residues Jason Swails (Fri Jul 06 2012 - 15:40:32 PDT)
[AMBER] Fwd: Protein aggregation energy calculation Binwu Zhao (Sat Jul 07 2012 - 14:54:32 PDT)
- Re: [AMBER] Fwd: Protein aggregation energy calculation Jason Swails (Sat Jul 07 2012 - 18:50:25 PDT)
[AMBER] I can prepare Na+ parameter files under LEAPRC.CONSTPH. kurisaki (Sun Jul 08 2012 - 01:22:39 PDT)
- Re: [AMBER] I can prepare Na+ parameter files under LEAPRC.CONSTPH. Jason Swails (Sun Jul 08 2012 - 09:09:02 PDT)
  - Re: [AMBER] I can prepare Na+ parameter files under LEAPRC.CONSTPH. kurisaki (Sun Jul 08 2012 - 18:07:38 PDT)
    - Re: [AMBER] I can prepare Na+ parameter files under LEAPRC.CONSTPH. Jason Swails (Sun Jul 08 2012 - 18:58:22 PDT)
    - Re: [AMBER] I can prepare Na+ parameter files under LEAPRC.CONSTPH. kurisaki (Sun Jul 08 2012 - 19:08:38 PDT)
[AMBER] MMPBSA: dubious results George Tzotzos (Mon Jul 09 2012 - 04:18:49 PDT)
- Re: [AMBER] MMPBSA: dubious results Jason Swails (Mon Jul 09 2012 - 08:50:07 PDT)
  - Re: [AMBER] MMPBSA: dubious results George Tzotzos (Mon Jul 09 2012 - 10:37:04 PDT)
    - Re: [AMBER] MMPBSA: dubious results Jason Swails (Mon Jul 09 2012 - 13:03:13 PDT)
    - Re: [AMBER] MMPBSA: dubious results George Tzotzos (Mon Jul 09 2012 - 13:34:31 PDT)
- Re: [AMBER] MMPBSA: dubious results Damodaran, Komath (Mon Jul 09 2012 - 13:24:52 PDT)
  - Re: [AMBER] MMPBSA: dubious results George Tzotzos (Fri Jul 13 2012 - 11:34:21 PDT)
    - Re: [AMBER] MMPBSA: dubious results Jason Swails (Fri Jul 13 2012 - 19:04:46 PDT)
[AMBER] Compiling Amber12 on the Cray XK6 (Jaguar) Gustavo Seabra (Mon Jul 09 2012 - 12:43:37 PDT)
- Re: [AMBER] Compiling Amber12 on the Cray XK6 (Jaguar) Jason Swails (Mon Jul 09 2012 - 12:52:43 PDT)
  - Re: [AMBER] Compiling Amber12 on the Cray XK6 (Jaguar) Gustavo Seabra (Mon Jul 09 2012 - 13:03:12 PDT)
[AMBER] amd.log file Milo Westler (Mon Jul 09 2012 - 12:48:06 PDT)
- Re: [AMBER] amd.log file Nadeem A. Vellore (Mon Jul 09 2012 - 14:03:26 PDT)
  - Re: [AMBER] amd.log file Milo Westler (Mon Jul 09 2012 - 17:32:31 PDT)
[AMBER] Updated free GPU test drives for AMBER Ross Walker (Mon Jul 09 2012 - 21:56:17 PDT)
Re: [AMBER] cpptraj-secstruct N-terminal proline colvin (Tue Jul 10 2012 - 01:06:16 PDT)
- Re: [AMBER] cpptraj-secstruct N-terminal proline Daniel Roe (Tue Jul 10 2012 - 07:15:39 PDT)
- Re: [AMBER] cpptraj-secstruct N-terminal proline David A. Case (Tue Jul 10 2012 - 14:55:22 PDT)
  - Re: [AMBER] cpptraj-secstruct N-terminal proline colvin (Tue Jul 10 2012 - 18:36:44 PDT)
[AMBER] Installation Amber 12 using cygwin on windows 7 64 bit Mohammad Jane Alam (Tue Jul 10 2012 - 07:54:36 PDT)
- Re: [AMBER] Installation Amber 12 using cygwin on windows 7 64 bit Daniel Roe (Tue Jul 10 2012 - 08:44:43 PDT)
[AMBER] MMPBSA.py decomposition option Damodaran, Komath (Tue Jul 10 2012 - 09:06:31 PDT)
- Re: [AMBER] MMPBSA.py decomposition option Hannes Kopitz (Tue Jul 10 2012 - 20:45:05 PDT)
[AMBER] Aqueous Ionic Grouping Problems Eckler, Logan, H (Tue Jul 10 2012 - 14:23:59 PDT)
- Re: [AMBER] Aqueous Ionic Grouping Problems David A. Case (Tue Jul 10 2012 - 15:01:04 PDT)
[AMBER] installing amber12 huseyin istanbullu (Wed Jul 11 2012 - 01:57:42 PDT)
- Re: [AMBER] installing amber12 huseyin istanbullu (Wed Jul 11 2012 - 02:17:00 PDT)
  - Re: [AMBER] installing amber12 Jason Swails (Wed Jul 11 2012 - 05:07:42 PDT)
[AMBER] Met92 not bound to Cu atom in TUTORIAL-A1(simple version) Mahendra B Thapa (Wed Jul 11 2012 - 13:50:55 PDT)
[AMBER] Bug? tleap of AmberTools12 cannot deal with branch carbohydrates contain sialic acid Tomoshi Kameda (Wed Jul 11 2012 - 16:21:46 PDT)
- Re: [AMBER] Bug? tleap of AmberTools12 cannot deal with branch carbohydrates contain sialic acid Jodi Ann Hadden (Thu Jul 12 2012 - 05:19:07 PDT)
  - Re: [AMBER] Bug? tleap of AmberTools12 cannot deal with branch carbohydrates contain sialic acid Tomoshi Kameda (Fri Jul 13 2012 - 23:54:44 PDT)
[AMBER] Error: Error in box coord line of trajectory (AMBER 12.0) - MM/PBSA per residue decomposition Ashley Ferraro (Wed Jul 11 2012 - 17:25:56 PDT)
[AMBER] Bug? tleap of AmberTools12 cannot deal with branch carbohydrates contain sialic acid Tomoshi Kameda (Wed Jul 11 2012 - 23:58:49 PDT)
[AMBER] Ptraj discrepancy C.M.Sampson (Thu Jul 12 2012 - 02:56:49 PDT)
- Re: [AMBER] Ptraj discrepancy David A. Case (Thu Jul 12 2012 - 04:48:28 PDT)
  - Re: [AMBER] Ptraj discrepancy C.M.Sampson (Thu Jul 12 2012 - 06:01:48 PDT)
Re: [AMBER] installing Amber12 Jason Swails (Thu Jul 12 2012 - 05:03:30 PDT)
Re: [AMBER] Protein aggregation energy calculation(Binwu Zhao) Binwu Zhao (Thu Jul 12 2012 - 11:28:21 PDT)
[AMBER] frcmod file to include Urey Bradley angle terms Scott Pendley (Thu Jul 12 2012 - 11:44:49 PDT)
- Re: [AMBER] frcmod file to include Urey Bradley angle terms Jason Swails (Thu Jul 12 2012 - 12:03:29 PDT)
[AMBER] Sulfotyrosine force field Pedro Swagger (Thu Jul 12 2012 - 12:56:45 PDT)
- Re: [AMBER] Sulfotyrosine force field David Case (Thu Jul 12 2012 - 13:19:33 PDT)
- Re: [AMBER] Sulfotyrosine force field FyD (Fri Jul 13 2012 - 00:03:07 PDT)
  - Re: [AMBER] Sulfotyrosine force field Jio M (Fri Jul 13 2012 - 00:15:25 PDT)
[AMBER] atoms on phosphonic acid groups collapse during minimization Maria Minakova (Thu Jul 12 2012 - 15:23:28 PDT)
- Re: [AMBER] atoms on phosphonic acid groups collapse during minimization Dr. Vitaly V. G. Chaban (Thu Jul 12 2012 - 16:05:42 PDT)
  - Re: [AMBER] atoms on phosphonic acid groups collapse during minimization Bill Ross (Thu Jul 12 2012 - 16:20:21 PDT)
    - Re: [AMBER] atoms on phosphonic acid groups collapse during minimization Maria Minakova (Thu Jul 12 2012 - 16:30:03 PDT)
    - Re: [AMBER] atoms on phosphonic acid groups collapse during minimization Bill Ross (Thu Jul 12 2012 - 17:15:40 PDT)
    - Re: [AMBER] atoms on phosphonic acid groups collapse during minimization Bill Ross (Thu Jul 12 2012 - 17:24:47 PDT)
    - Re: [AMBER] atoms on phosphonic acid groups collapse during minimization Maria Minakova (Mon Jul 30 2012 - 14:16:03 PDT)
    - Re: [AMBER] atoms on phosphonic acid groups collapse during minimization Jason Swails (Mon Jul 30 2012 - 15:25:15 PDT)
- Re: [AMBER] atoms on phosphonic acid groups collapse during minimization Dr. Vitaly V. G. Chaban (Thu Jul 12 2012 - 17:26:28 PDT)
[AMBER] AMBER11_CUDA issue with binary restart HIMANSHU JOSHI (Thu Jul 12 2012 - 22:47:03 PDT)
- Re: [AMBER] AMBER11_CUDA issue with binary restart Ross Walker (Fri Jul 13 2012 - 06:53:08 PDT)
[AMBER] system out of pbc box Albert (Fri Jul 13 2012 - 00:57:42 PDT)
[AMBER] lipid params Jio M (Fri Jul 13 2012 - 01:35:31 PDT)
- Re: [AMBER] lipid params Vlad Cojocaru (Fri Jul 13 2012 - 01:53:23 PDT)
  - Re: [AMBER] lipid params Jio M (Fri Jul 13 2012 - 02:10:01 PDT)
    - Re: [AMBER] lipid params Gould, Ian R (Fri Jul 13 2012 - 02:17:54 PDT)
    - Re: [AMBER] lipid params Jio M (Fri Jul 13 2012 - 02:42:39 PDT)
    - [AMBER] lipid params and paper Gould, Ian R (Tue Aug 07 2012 - 05:08:54 PDT)
    - Re: [AMBER] lipid params and paper Albert (Tue Aug 07 2012 - 05:11:51 PDT)
    - Re: [AMBER] lipid params and paper Igor Marques (Mon Sep 10 2012 - 02:26:09 PDT)
    - Re: [AMBER] lipid params and paper FyD (Mon Sep 10 2012 - 23:16:17 PDT)
    - Re: [AMBER] lipid params and paper Gould, Ian R (Tue Sep 11 2012 - 07:36:02 PDT)
- Re: [AMBER] lipid params Ross Walker (Fri Jul 13 2012 - 06:43:00 PDT)
  - Re: [AMBER] lipid params Jio M (Fri Jul 13 2012 - 07:00:56 PDT)
- Re: [AMBER] lipid params Benjamin Madej (Fri Jul 13 2012 - 12:14:46 PDT)
  - Re: [AMBER] lipid params Jio M (Sat Jul 14 2012 - 00:57:58 PDT)
    - Re: [AMBER] lipid params Benjamin Madej (Mon Jul 16 2012 - 14:54:29 PDT)
    - Re: [AMBER] lipid params Jio M (Tue Jul 17 2012 - 03:14:35 PDT)
[AMBER] PB with inp=2 doesn't recognize ff10 atom types? (Amber Archive Mar 2012) Miguel Ortiz Lombardia (Fri Jul 13 2012 - 05:21:40 PDT)
[AMBER] benzene-sulfonate (atom type for Sulfur) Jio M (Fri Jul 13 2012 - 05:37:56 PDT)
- Re: [AMBER] benzene-sulfonate (atom type for Sulfur) FyD (Fri Jul 13 2012 - 09:01:43 PDT)
  - Re: [AMBER] benzene-sulfonate (atom type for Sulfur) Jio M (Fri Jul 13 2012 - 23:31:53 PDT)
    - Re: [AMBER] benzene-sulfonate (atom type for Sulfur) FyD (Sat Jul 14 2012 - 02:15:46 PDT)
    - Re: [AMBER] benzene-sulfonate (atom type for Sulfur) Jio M (Sat Jul 14 2012 - 02:25:28 PDT)
    - Re: [AMBER] benzene-sulfonate (atom type for Sulfur) FyD (Sat Jul 14 2012 - 03:11:33 PDT)
    - Re: [AMBER] benzene-sulfonate (atom type for Sulfur) Jio M (Sat Jul 14 2012 - 03:30:51 PDT)
[AMBER] no restart file from pmemd.cuda in Amber 11 Seren Soner (Fri Jul 13 2012 - 06:44:02 PDT)
- Re: [AMBER] no restart file from pmemd.cuda in Amber 11 Ross Walker (Fri Jul 13 2012 - 06:57:53 PDT)
  - Re: [AMBER] no restart file from pmemd.cuda in Amber 11 Seren Soner (Fri Jul 13 2012 - 07:03:53 PDT)
[AMBER] Amber12 qm_ewald DJH71.pitt.edu (Fri Jul 13 2012 - 09:01:39 PDT)
- Re: [AMBER] Amber12 qm_ewald Brian Radak (Fri Jul 13 2012 - 09:17:32 PDT)
[AMBER] http://archive.ambermd.org/201206/0014.html Osman, Roman (Fri Jul 13 2012 - 09:42:35 PDT)
[AMBER] can Amber run in Anton? Albert (Fri Jul 13 2012 - 11:01:10 PDT)
- Re: [AMBER] can Amber run in Anton? case (Fri Jul 13 2012 - 17:59:08 PDT)
  - Re: [AMBER] can Amber run in Anton? Dr. Vitaly V. G. Chaban (Fri Jul 13 2012 - 19:02:53 PDT)
[AMBER] npt stacked with CUDA running Albert (Fri Jul 13 2012 - 13:15:03 PDT)
- Re: [AMBER] npt stacked with CUDA running case (Fri Jul 13 2012 - 18:10:12 PDT)
  - Re: [AMBER] npt stacked with CUDA running Albert (Fri Jul 13 2012 - 22:48:15 PDT)
  - Re: [AMBER] npt stacked with CUDA running Albert (Fri Jul 13 2012 - 22:58:13 PDT)
[AMBER] Amber10 and AmberTools12 compatibility vaibhav dixit (Fri Jul 13 2012 - 22:32:23 PDT)
- Re: [AMBER] Amber10 and AmberTools12 compatibility David Case (Sat Jul 14 2012 - 05:31:15 PDT)
  - Re: [AMBER] Amber10 and AmberTools12 compatibility vaibhav dixit (Sat Jul 14 2012 - 08:17:45 PDT)
    - Re: [AMBER] Amber10 and AmberTools12 compatibility Jason Swails (Sat Jul 14 2012 - 15:08:26 PDT)
[AMBER] ambertool12 installation in Cygwin 钟舜 (Sat Jul 14 2012 - 19:22:33 PDT)
- Re: [AMBER] ambertool12 installation in Cygwin case (Sun Jul 15 2012 - 06:04:43 PDT)
  - Re: [AMBER] ambertool12 installation in Cygwin Jason Swails (Sun Jul 15 2012 - 15:32:31 PDT)
[AMBER] problem to attach n terminal residue to protein Sanjib Paul (Sun Jul 15 2012 - 00:21:38 PDT)
- Re: [AMBER] problem to attach n terminal residue to protein case (Sun Jul 15 2012 - 06:08:45 PDT)
  - Re: [AMBER] problem to attach n terminal residue to protein Sanjib Paul (Mon Jul 16 2012 - 03:36:38 PDT)
    - Re: [AMBER] problem to attach n terminal residue to protein Sanjib Paul (Mon Jul 16 2012 - 03:38:52 PDT)
[AMBER] Global Minimum? jit mukherjee (Sun Jul 15 2012 - 02:56:29 PDT)
- Re: [AMBER] Global Minimum? steinbrt.rci.rutgers.edu (Sun Jul 15 2012 - 05:38:00 PDT)
- Re: [AMBER] Global Minimum? Carlos Simmerling (Sun Jul 15 2012 - 06:03:37 PDT)
  - Re: [AMBER] Global Minimum? jit mukherjee (Sun Jul 15 2012 - 08:38:36 PDT)
    - Re: [AMBER] Global Minimum? Dr. Vitaly V. G. Chaban (Sun Jul 15 2012 - 08:44:14 PDT)
    - Re: [AMBER] Global Minimum? jit mukherjee (Sun Jul 15 2012 - 08:47:48 PDT)
    - Re: [AMBER] Global Minimum? jit mukherjee (Sun Jul 15 2012 - 09:45:13 PDT)
    - Re: [AMBER] Global Minimum? Dr. Vitaly V. G. Chaban (Sun Jul 15 2012 - 10:44:49 PDT)
    - Re: [AMBER] Global Minimum? jit mukherjee (Sun Jul 15 2012 - 21:21:51 PDT)
    - Re: [AMBER] Global Minimum? Dr. Vitaly V. G. Chaban (Sun Jul 15 2012 - 21:44:03 PDT)
[AMBER] parameters reading Yun Shi (Sun Jul 15 2012 - 15:42:38 PDT)
- Re: [AMBER] parameters reading Jason Swails (Sun Jul 15 2012 - 17:02:51 PDT)
[AMBER] what do the preceding "E" and "B" mean in rdparm dihedral prints Yun Shi (Sun Jul 15 2012 - 19:38:51 PDT)
- Re: [AMBER] what do the preceding "E" and "B" mean in rdparm dihedral prints Jason Swails (Sun Jul 15 2012 - 20:23:06 PDT)
[AMBER] installing on ubuntu 12.04 LTS 64 bit huseyin istanbullu (Mon Jul 16 2012 - 01:31:53 PDT)
- Re: [AMBER] installing on ubuntu 12.04 LTS 64 bit Jason Swails (Mon Jul 16 2012 - 04:47:43 PDT)
  - Re: [AMBER] installing on ubuntu 12.04 LTS 64 bit Catein Catherine (Mon Jul 16 2012 - 06:19:38 PDT)
    - [AMBER] Error in ptraj after using iwrap=1, even using center and image origin Catein Catherine (Tue Jul 17 2012 - 20:18:42 PDT)
    - Re: [AMBER] Error in ptraj after using iwrap=1, even using center and image origin Daniel Roe (Wed Jul 18 2012 - 07:02:33 PDT)
    - Re: [AMBER] Error in ptraj after using iwrap=1, even using center and image origin Catein Catherine (Wed Jul 18 2012 - 08:14:32 PDT)
    - Re: [AMBER] Error in ptraj after using iwrap=1, even using center and image origin Marc van der Kamp (Wed Jul 18 2012 - 08:36:10 PDT)
    - [AMBER] Error in ptraj analysis after using iwrap=1 Catein Catherine (Mon Jul 16 2012 - 06:25:55 PDT)
    - Re: [AMBER] Error in ptraj analysis after using iwrap=1 Daniel Roe (Thu Jul 26 2012 - 19:02:50 PDT)
    - Re: [AMBER] Error in ptraj analysis after using iwrap=1 Catein Catherine (Fri Jul 27 2012 - 10:10:30 PDT)
    - Re: [AMBER] Error in ptraj analysis after using iwrap=1 Jason Swails (Fri Jul 27 2012 - 10:35:53 PDT)
    - [AMBER] How to install bugfix.16 specifically? Catein Catherine (Sun Jul 29 2012 - 21:29:10 PDT)
    - Re: [AMBER] How to install bugfix.16 specifically? Catein Catherine (Sun Jul 29 2012 - 23:37:53 PDT)
    - Re: [AMBER] How to install bugfix.16 specifically? Jason Swails (Mon Jul 30 2012 - 03:32:32 PDT)
    - Re: [AMBER] How to install bugfix.16 specifically? Catein Catherine (Mon Jul 30 2012 - 04:31:24 PDT)
    - Re: [AMBER] How to install bugfix.16 specifically? Jason Swails (Mon Jul 30 2012 - 06:14:31 PDT)
    - Re: [AMBER] How to install bugfix.16 specifically? Catein Catherine (Mon Jul 30 2012 - 07:16:47 PDT)
    - [AMBER] After autoimage, rms jump Catein Catherine (Tue Jul 31 2012 - 00:17:12 PDT)
    - Re: [AMBER] After autoimage, rms jump Daniel Roe (Tue Jul 31 2012 - 06:53:53 PDT)
    - Re: [AMBER] After autoimage, rms jump Daniel Roe (Tue Jul 31 2012 - 09:22:31 PDT)
    - [AMBER] cpptraj: autoimage + anchor works very well. Catein Catherine (Tue Jul 31 2012 - 20:23:37 PDT)
[AMBER] AMBER12 - ninterface for double bilayer system James Murdock (Mon Jul 16 2012 - 03:30:52 PDT)
- Re: [AMBER] AMBER12 - ninterface for double bilayer system Ross Walker (Mon Jul 16 2012 - 10:58:33 PDT)
  - Re: [AMBER] AMBER12 - ninterface for double bilayer system Benjamin Madej (Mon Jul 16 2012 - 16:26:32 PDT)
    - Re: [AMBER] AMBER12 - ninterface for double bilayer system Albert (Mon Jul 16 2012 - 22:09:37 PDT)
    - Re: [AMBER] AMBER12 - ninterface for double bilayer system Benjamin Madej (Tue Jul 17 2012 - 16:30:57 PDT)
    - Re: [AMBER] AMBER12 - ninterface for double bilayer system Albert (Tue Jul 17 2012 - 22:52:45 PDT)
    - Re: [AMBER] AMBER12 - ninterface for double bilayer system Benjamin D Madej (Tue Jul 24 2012 - 07:36:51 PDT)
[AMBER] Quantification of fraction of Helicity. Rajendra Sharma (Mon Jul 16 2012 - 04:08:51 PDT)
[AMBER] AMBER GPU Bench mark procedure Ravi Teja (Mon Jul 16 2012 - 04:41:52 PDT)
- Re: [AMBER] AMBER GPU Bench mark procedure Ross Walker (Mon Jul 16 2012 - 09:30:05 PDT)
[AMBER] problem in minimization jit mukherjee (Mon Jul 16 2012 - 08:23:21 PDT)
- Re: [AMBER] problem in minimization Dr. Vitaly V. G. Chaban (Mon Jul 16 2012 - 08:30:34 PDT)
  - Re: [AMBER] problem in minimization steinbrt.rci.rutgers.edu (Mon Jul 16 2012 - 09:23:13 PDT)
    - Re: [AMBER] problem in minimization jit mukherjee (Mon Jul 16 2012 - 09:35:00 PDT)
- Re: [AMBER] problem in minimization Jason Swails (Mon Jul 16 2012 - 09:16:07 PDT)
[AMBER] pi-pi stacking interaction and hydrogen bonding with amber jit mukherjee (Mon Jul 16 2012 - 09:37:31 PDT)
- Re: [AMBER] pi-pi stacking interaction and hydrogen bonding with amber Jiri Sponer (Mon Jul 16 2012 - 09:47:58 PDT)
  - Re: [AMBER] pi-pi stacking interaction and hydrogen bonding with amber jit mukherjee (Mon Jul 16 2012 - 10:59:22 PDT)
    - Re: [AMBER] pi-pi stacking interaction and hydrogen bonding with amber Dr. Vitaly V. G. Chaban (Mon Jul 16 2012 - 11:21:48 PDT)
    - Re: [AMBER] pi-pi stacking interaction and hydrogen bonding with amber Dean Cuebas (Mon Jul 16 2012 - 11:23:18 PDT)
    - Re: [AMBER] pi-pi stacking interaction and hydrogen bonding with amber jit mukherjee (Mon Jul 16 2012 - 12:13:21 PDT)
    - Re: [AMBER] pi-pi stacking interaction and hydrogen bonding with amber jit mukherjee (Mon Jul 16 2012 - 21:25:07 PDT)
    - Re: [AMBER] pi-pi stacking interaction and hydrogen bonding with amber Bill Ross (Mon Jul 16 2012 - 22:17:37 PDT)
    - Re: [AMBER] pi-pi stacking interaction and hydrogen bonding with amber jit mukherjee (Tue Jul 17 2012 - 01:42:37 PDT)
    - Re: [AMBER] pi-pi stacking interaction and hydrogen bonding with amber Gustavo Seabra (Tue Jul 17 2012 - 07:08:15 PDT)
    - Re: [AMBER] pi-pi stacking interaction and hydrogen bonding with amber Jiri Sponer (Tue Jul 17 2012 - 07:33:05 PDT)
    - Re: [AMBER] pi-pi stacking interaction and hydrogen bonding with amber Gustavo Seabra (Tue Jul 17 2012 - 07:38:49 PDT)
    - Re: [AMBER] pi-pi stacking interaction and hydrogen bonding with amber jit mukherjee (Tue Jul 17 2012 - 07:43:27 PDT)
    - Re: [AMBER] pi-pi stacking interaction and hydrogen bonding with amber Jiri Sponer (Tue Jul 17 2012 - 07:49:13 PDT)
    - Re: [AMBER] pi-pi stacking interaction and hydrogen bonding with amber jit mukherjee (Tue Jul 17 2012 - 21:32:34 PDT)
    - Re: [AMBER] pi-pi stacking interaction and hydrogen bonding with amber steinbrt.rci.rutgers.edu (Wed Jul 18 2012 - 00:47:54 PDT)
    - Re: [AMBER] pi-pi stacking interaction and hydrogen bonding with amber Alessandro Contini (Wed Jul 18 2012 - 01:00:52 PDT)
    - Re: [AMBER] pi-pi stacking interaction and hydrogen bonding with amber Jiri Sponer (Wed Jul 18 2012 - 02:53:32 PDT)
    - Re: [AMBER] pi-pi stacking interaction and hydrogen bonding with amber jit mukherjee (Wed Jul 18 2012 - 22:14:02 PDT)
    - Re: [AMBER] pi-pi stacking interaction and hydrogen bonding with amber Jason Swails (Thu Jul 19 2012 - 20:09:42 PDT)
    - Re: [AMBER] pi-pi stacking interaction and hydrogen bonding with amber Jiri Sponer (Tue Jul 17 2012 - 07:44:38 PDT)
[AMBER] GPU bugs for Amber 12? Albert (Mon Jul 16 2012 - 09:42:42 PDT)
- Re: [AMBER] GPU bugs for Amber 12? Ross Walker (Mon Jul 16 2012 - 10:54:48 PDT)
  - Re: [AMBER] GPU bugs for Amber 12? Albert (Mon Jul 16 2012 - 11:53:44 PDT)
- Re: [AMBER] GPU bugs for Amber 12? Scott Le Grand (Mon Jul 16 2012 - 10:56:35 PDT)
  - Re: [AMBER] GPU bugs for Amber 12? Albert (Mon Jul 16 2012 - 11:17:17 PDT)
[AMBER] Dihedral parameters assignment by tleap Yun Shi (Mon Jul 16 2012 - 09:59:48 PDT)
- Re: [AMBER] Dihedral parameters assignment by tleap David A Case (Mon Jul 16 2012 - 11:31:48 PDT)
  - Re: [AMBER] Dihedral parameters assignment by tleap Yun Shi (Mon Jul 16 2012 - 13:03:21 PDT)
    - Re: [AMBER] Dihedral parameters assignment by tleap Jason Swails (Mon Jul 16 2012 - 13:59:02 PDT)
[AMBER] Parmtop files for TI Softcore Potentials Kepa K. Burusco (Mon Jul 16 2012 - 11:30:24 PDT)
- Re: [AMBER] Parmtop files for TI Softcore Potentials Marek Maly (Mon Jul 16 2012 - 12:18:45 PDT)
  - Re: [AMBER] Parmtop files for TI Softcore Potentials steinbrt.rci.rutgers.edu (Mon Jul 16 2012 - 23:48:49 PDT)
[AMBER] Continuation of thread regarding problems with Zinc parameterization with MCPB (Apparently solved) Fabrício Bracht (Mon Jul 16 2012 - 13:24:48 PDT)
[AMBER] Langevin Dynamics Qian Wang (Mon Jul 16 2012 - 15:55:53 PDT)
- Re: [AMBER] Langevin Dynamics Jason Swails (Mon Jul 16 2012 - 18:29:10 PDT)
- Re: [AMBER] Langevin Dynamics David A Case (Tue Jul 17 2012 - 04:50:18 PDT)
  - Re: [AMBER] Langevin Dynamics Qian Wang (Tue Jul 17 2012 - 08:05:13 PDT)
[AMBER] Polarization Nikolay Igorovich Rodionov (Mon Jul 16 2012 - 17:10:09 PDT)
- Re: [AMBER] Polarization David A Case (Tue Jul 17 2012 - 04:52:46 PDT)
[AMBER] Problem with MMPBSA using a solvated structure topology Osman, Roman (Mon Jul 16 2012 - 18:57:12 PDT)
- Re: [AMBER] Problem with MMPBSA using a solvated structure topology Jason Swails (Mon Jul 16 2012 - 19:21:18 PDT)
- Re: [AMBER] Problem with MMPBSA using a solvated structure topology Osman, Roman (Tue Jul 17 2012 - 05:53:03 PDT)
  - Re: [AMBER] Problem with MMPBSA using a solvated structure topology Jason Swails (Tue Jul 17 2012 - 06:03:15 PDT)
[AMBER] MMPBSA.py Delwar Hossain (Mon Jul 16 2012 - 19:55:46 PDT)
- Re: [AMBER] MMPBSA.py Bill Miller III (Tue Jul 17 2012 - 03:48:52 PDT)
[AMBER] Two md.in files in manual and tutorials when running SMD 崔颖璐 (Tue Jul 17 2012 - 00:35:51 PDT)
[AMBER] Defining bonds between calcium and protein Zalikha Ibrahim (Tue Jul 17 2012 - 01:02:16 PDT)
- Re: [AMBER] Defining bonds between calcium and protein David A Case (Tue Jul 17 2012 - 05:02:22 PDT)
  - Re: [AMBER] Defining bonds between calcium and protein Zalikha Ibrahim (Tue Jul 17 2012 - 19:08:17 PDT)
[AMBER] MMPBSA Entropies: N-mode and Quasi Harmonic calculations George Tzotzos (Tue Jul 17 2012 - 04:38:16 PDT)
- Re: [AMBER] MMPBSA Entropies: N-mode and Quasi Harmonic calculations Jason Swails (Tue Jul 17 2012 - 05:58:46 PDT)
[AMBER] Amber 11: iwrap=1 separates two RNA chains Kasprzak, Wojciech (NIH/NCI) [C] (Tue Jul 17 2012 - 07:30:44 PDT)
- Re: [AMBER] Amber 11: iwrap=1 separates two RNA chains Jason Swails (Tue Jul 17 2012 - 08:02:06 PDT)
[AMBER] How to convert AMBER atom type to CYANA Rahul Banerjee (Tue Jul 17 2012 - 15:18:19 PDT)
- Re: [AMBER] How to convert AMBER atom type to CYANA case (Tue Jul 17 2012 - 17:38:18 PDT)
  - Re: [AMBER] How to convert AMBER atom type to CYANA Rahul Banerjee (Wed Jul 18 2012 - 07:23:33 PDT)
    - Re: [AMBER] How to convert AMBER atom type to CYANA David A Case (Wed Jul 18 2012 - 09:38:50 PDT)
    - Re: [AMBER] How to convert AMBER atom type to CYANA Hector A. Baldoni (Thu Jul 19 2012 - 07:52:53 PDT)
[AMBER] RNA chi torsion corrections Asmita Gupta (Wed Jul 18 2012 - 03:06:21 PDT)
- Re: [AMBER] RNA chi torsion corrections Jiri Sponer (Wed Jul 18 2012 - 03:40:14 PDT)
- Re: [AMBER] RNA chi torsion corrections Ilyas Yildirim (Wed Jul 18 2012 - 08:41:45 PDT)
[AMBER] Help with amber12 at ORNL Foertter, Fernanda S. (Wed Jul 18 2012 - 08:31:19 PDT)
- Re: [AMBER] Help with amber12 at ORNL David A Case (Wed Jul 18 2012 - 10:02:38 PDT)
  - Re: [AMBER] Help with amber12 at ORNL Foertter, Fernanda S. (Wed Jul 18 2012 - 10:37:24 PDT)
    - Re: [AMBER] Help with amber12 at ORNL David A Case (Wed Jul 18 2012 - 13:08:58 PDT)
Re: [AMBER] Installation of Amber in Cygwin Jason Swails (Wed Jul 18 2012 - 12:35:04 PDT)
- Re: [AMBER] Installation of Amber in Cygwin Daniel Roe (Wed Jul 18 2012 - 12:37:40 PDT)
- Re: [AMBER] Installation of Amber in Cygwin 钟舜 (Wed Jul 18 2012 - 19:38:46 PDT)
  - Re: [AMBER] Installation of Amber in Cygwin Jason Swails (Wed Jul 18 2012 - 19:42:02 PDT)
- Re: [AMBER] Installation of Amber in Cygwin Jason Swails (Thu Jul 19 2012 - 05:36:20 PDT)
  - [AMBER] Any parameters can be used to model a transmembrane protein? Catein Catherine (Thu Jul 19 2012 - 06:24:09 PDT)
    - Re: [AMBER] Any parameters can be used to model a transmembrane protein? Benjamin D Madej (Tue Jul 24 2012 - 08:02:45 PDT)
  - Re: [AMBER] Installation of Amber in Cygwin 钟舜 (Thu Jul 19 2012 - 17:48:40 PDT)
    - Re: [AMBER] Installation of Amber in Cygwin Daniel Roe (Thu Jul 19 2012 - 17:55:45 PDT)
[AMBER] Difference between "jar=1" and "ncsu_smd" when running SMD simulations 崔颖璐 (Wed Jul 18 2012 - 19:11:55 PDT)
- Re: [AMBER] Difference between "jar=1" and "ncsu_smd" when running SMD simulations Jason Swails (Wed Jul 18 2012 - 19:37:58 PDT)
  - Re: [AMBER] Difference between "jar=1" and "ncsu_smd" when running SMD simulations Jason Swails (Wed Jul 18 2012 - 19:39:29 PDT)
    - Re: [AMBER] Difference between "jar=1" and "ncsu_smd" when running SMD simulations 崔颖璐 (Thu Jul 19 2012 - 00:21:15 PDT)
[AMBER] ZAFF parameters Siavoush Dastmalchi (Wed Jul 18 2012 - 22:33:26 PDT)
- Re: [AMBER] ZAFF parameters Siavoush Dastmalchi (Sun Jul 29 2012 - 05:15:39 PDT)
  - [AMBER] Simple question about Amber version scanya.interia.eu (Mon Jul 30 2012 - 05:41:46 PDT)
    - Re: [AMBER] Simple question about Amber version Daniel Roe (Mon Jul 30 2012 - 06:34:18 PDT)
  - Re: [AMBER] ZAFF parameters Tong Zhu (Tue Jul 31 2012 - 00:44:13 PDT)
    - Re: [AMBER] ZAFF parameters Jason Swails (Tue Jul 31 2012 - 08:13:48 PDT)
[AMBER] error with ambertools12 and amber10 installation vaibhav dixit (Thu Jul 19 2012 - 04:39:06 PDT)
- Re: [AMBER] error with ambertools12 and amber10 installation David A Case (Thu Jul 19 2012 - 08:33:00 PDT)
  - Re: [AMBER] error with ambertools12 and amber10 installation vaibhav dixit (Fri Jul 20 2012 - 04:13:33 PDT)
    - Re: [AMBER] error with ambertools12 and amber10 installation David A Case (Fri Jul 20 2012 - 05:29:29 PDT)
    - Re: [AMBER] error with ambertools12 and amber10 installation vaibhav dixit (Wed Jul 25 2012 - 02:24:11 PDT)
    - Re: [AMBER] error with ambertools12 and amber10 installation David A. Case (Wed Jul 25 2012 - 04:34:50 PDT)
[AMBER] Question concerning TI using soft core potential Wook Lee (Thu Jul 19 2012 - 07:04:21 PDT)
- Re: [AMBER] Question concerning TI using soft core potential steinbrt.rci.rutgers.edu (Thu Jul 19 2012 - 07:19:05 PDT)
  - Re: [AMBER] Question concerning TI using soft core potential Wook Lee (Thu Jul 19 2012 - 08:19:49 PDT)
    - Re: [AMBER] Question concerning TI using soft core potential steinbrt.rci.rutgers.edu (Thu Jul 19 2012 - 08:36:52 PDT)
    - Re: [AMBER] Question concerning TI using soft core potential Wook Lee (Sat Jul 21 2012 - 06:33:16 PDT)
    - Re: [AMBER] Question concerning TI using soft core potential steinbrt.rci.rutgers.edu (Sat Jul 21 2012 - 10:16:54 PDT)
    - Re: [AMBER] Question concerning TI using soft core potential Wook Lee (Mon Jul 23 2012 - 05:30:29 PDT)
    - Re: [AMBER] Question concerning TI using soft core potential steinbrt.rci.rutgers.edu (Mon Jul 23 2012 - 06:00:02 PDT)
    - Re: [AMBER] Question concerning TI using soft core potential Wook Lee (Mon Jul 23 2012 - 06:31:49 PDT)
    - Re: [AMBER] Question concerning TI using soft core potential Wook Lee (Mon Jul 23 2012 - 06:18:46 PDT)
    - Re: [AMBER] Question concerning TI using soft core potential David A Case (Mon Jul 23 2012 - 06:31:09 PDT)
    - Re: [AMBER] Question concerning TI using soft core potential David A Case (Thu Jul 19 2012 - 12:07:57 PDT)
    - Re: [AMBER] Question concerning TI using soft core potential Wook Lee (Sat Jul 21 2012 - 06:35:08 PDT)
[AMBER] Interaction energy between residue pairs Fabrício Bracht (Thu Jul 19 2012 - 14:47:25 PDT)
- Re: [AMBER] Interaction energy between residue pairs Irene Newhouse (Thu Jul 19 2012 - 15:21:06 PDT)
  - Re: [AMBER] Interaction energy between residue pairs Jason Swails (Thu Jul 19 2012 - 18:57:11 PDT)
    - Re: [AMBER] Interaction energy between residue pairs Carlos Simmerling (Thu Jul 19 2012 - 19:02:14 PDT)
    - Re: [AMBER] Interaction energy between residue pairs Jason Swails (Thu Jul 19 2012 - 19:37:43 PDT)
    - Re: [AMBER] Interaction energy between residue pairs Fabrício Bracht (Thu Jul 19 2012 - 19:58:46 PDT)
    - Re: [AMBER] Interaction energy between residue pairs Jason Swails (Thu Jul 19 2012 - 20:06:04 PDT)
- Re: [AMBER] Interaction energy between residue pairs Carlos Simmerling (Thu Jul 19 2012 - 16:25:12 PDT)
[AMBER] GBIS and SASA Aron Broom (Thu Jul 19 2012 - 15:03:29 PDT)
- Re: [AMBER] GBIS and SASA case (Thu Jul 19 2012 - 18:43:41 PDT)
  - Re: [AMBER] GBIS and SASA Aron Broom (Thu Jul 19 2012 - 21:31:21 PDT)
[AMBER] how to make statistics of solvent molecules? Albert (Fri Jul 20 2012 - 00:52:31 PDT)
- [AMBER] how to make statistics of solvent molecules? Daniel Roe (Fri Jul 20 2012 - 09:33:06 PDT)
  - Re: [AMBER] how to make statistics of solvent molecules? Albert (Fri Jul 20 2012 - 22:07:52 PDT)
[AMBER] Amber Error hclengineer niper (Fri Jul 20 2012 - 04:26:37 PDT)
- Re: [AMBER] Amber Error David A Case (Fri Jul 20 2012 - 05:37:03 PDT)
- [AMBER] Amber Error hclengineer niper (Mon Jul 23 2012 - 00:38:14 PDT)
  - Re: [AMBER] Amber Error David A Case (Mon Jul 23 2012 - 04:48:48 PDT)
[AMBER] LEaP problems with non-standard residue Francesco Pietra (Fri Jul 20 2012 - 06:57:25 PDT)
[AMBER] Iwrap=1 and imaging revisited Kasprzak, Wojciech (NIH/NCI) [C] (Fri Jul 20 2012 - 08:05:01 PDT)
- Re: [AMBER] Iwrap=1 and imaging revisited Daniel Roe (Mon Jul 23 2012 - 08:16:21 PDT)
[AMBER] TI calculation with amber and finite size correction for PME manikanthan bhavaraju (Fri Jul 20 2012 - 14:02:54 PDT)
- [AMBER] TI calculation with amber and finite size correction for PME manikanthan bhavaraju (Fri Jul 20 2012 - 22:17:06 PDT)
  - Re: [AMBER] TI calculation with amber and finite size correction for PME case (Sat Jul 21 2012 - 06:22:54 PDT)
    - [AMBER] Any AMBER's reference article on modeling transmembrane proteins? Catein Catherine (Sat Jul 21 2012 - 09:20:51 PDT)
[AMBER] Restrained minimization pancham lal gupta (Sat Jul 21 2012 - 10:31:00 PDT)
- Re: [AMBER] Restrained minimization Jason Swails (Sat Jul 21 2012 - 14:52:01 PDT)
[AMBER] stripping number of residues (>20K) problem Jio M (Sun Jul 22 2012 - 02:48:44 PDT)
- Re: [AMBER] stripping number of residues (>20K) problem case (Sun Jul 22 2012 - 05:16:32 PDT)
  - Re: [AMBER] stripping number of residues (>20K) problem Jio M (Sun Jul 22 2012 - 06:46:10 PDT)
    - Re: [AMBER] stripping number of residues (>20K) problem Jason Swails (Sun Jul 22 2012 - 11:12:35 PDT)
    - Re: [AMBER] stripping number of residues (>20K) problem Jio M (Mon Jul 23 2012 - 01:54:11 PDT)
  - [AMBER] Difficult Problem: iwrap=1 and ptraj for a protein complex. Catein Catherine (Sun Jul 22 2012 - 19:36:59 PDT)
    - Re: [AMBER] Difficult Problem: iwrap=1 and ptraj for a protein complex. Daniel Roe (Mon Jul 23 2012 - 09:08:34 PDT)
  - Re: [AMBER] stripping number of residues (>20K) problem Daniel Roe (Mon Jul 23 2012 - 07:32:34 PDT)
- Re: [AMBER] stripping number of residues (>20K) problem Jio M (Wed Jul 25 2012 - 03:57:26 PDT)
  - Re: [AMBER] stripping number of residues (>20K) problem Jio M (Wed Jul 25 2012 - 22:51:38 PDT)
  - Re: [AMBER] stripping number of residues (>20K) problem Daniel Roe (Thu Jul 26 2012 - 07:10:20 PDT)
[AMBER] Question about corrections to the quasi-harmonic approximation zhouhaibin2008.ok (Sun Jul 22 2012 - 08:39:26 PDT)
- Re: [AMBER] Question about corrections to the quasi-harmonic approximation David A Case (Mon Jul 23 2012 - 06:31:47 PDT)
[AMBER] problem with testing water movement during md simulation Danny Blue (Sun Jul 22 2012 - 09:44:27 PDT)
- Re: [AMBER] problem with testing water movement during md simulation Joshua Adelman (Sun Jul 22 2012 - 11:27:23 PDT)
[AMBER] PMF of a salt bridge. Rajendra Sharma (Sun Jul 22 2012 - 12:03:08 PDT)
- Re: [AMBER] PMF of a salt bridge. Aron Broom (Sun Jul 22 2012 - 13:14:38 PDT)
- Re: [AMBER] PMF of a salt bridge. Kevin Hauser (Sun Jul 22 2012 - 16:28:38 PDT)
[AMBER] KeyError: 'Total' at parsing MMPBSA results Miguel Ortiz Lombardía (Mon Jul 23 2012 - 01:01:45 PDT)
- Re: [AMBER] KeyError: 'Total' at parsing MMPBSA results Jason Swails (Mon Jul 23 2012 - 04:41:41 PDT)
  - Re: [AMBER] KeyError: 'Total' at parsing MMPBSA results Miguel Ortiz Lombardía (Mon Jul 23 2012 - 05:56:25 PDT)
    - Re: [AMBER] KeyError: 'Total' at parsing MMPBSA results Jason Swails (Mon Jul 23 2012 - 08:43:07 PDT)
    - Re: [AMBER] KeyError: 'Total' at parsing MMPBSA results Miguel Ortiz Lombardía (Mon Jul 23 2012 - 09:08:15 PDT)
    - Re: [AMBER] KeyError: 'Total' at parsing MMPBSA results Jason Swails (Mon Jul 23 2012 - 09:17:02 PDT)
[AMBER] problem in installing sander.MPI devawati dutta (Mon Jul 23 2012 - 02:12:50 PDT)
- Re: [AMBER] problem in installing sander.MPI Miguel Ortiz Lombardía (Mon Jul 23 2012 - 02:28:08 PDT)
- Re: [AMBER] problem in installing sander.MPI David A Case (Mon Jul 23 2012 - 04:51:25 PDT)
[AMBER] Regarding creating a leap input file aneesh cna (Mon Jul 23 2012 - 05:25:32 PDT)
- Re: [AMBER] Regarding creating a leap input file David A Case (Mon Jul 23 2012 - 06:26:27 PDT)
[AMBER] pbsa: unit of the electrostatic potential values written to DX file Jan-Philip Gehrcke (Mon Jul 23 2012 - 08:43:20 PDT)
- [AMBER] Fwd: pbsa: unit of the electrostatic potential values written to DX file Ray Luo, Ph.D. (Mon Jul 23 2012 - 09:59:21 PDT)
  - Re: [AMBER] Fwd: pbsa: unit of the electrostatic potential values written to DX file Jan-Philip Gehrcke (Tue Jul 24 2012 - 01:55:15 PDT)
    - Re: [AMBER] Fwd: pbsa: unit of the electrostatic potential values written to DX file Ray Luo, Ph.D. (Tue Jul 24 2012 - 11:09:44 PDT)
[AMBER] Problem with MMPBSA.py.MPI sudipta (Mon Jul 23 2012 - 13:03:06 PDT)
- Re: [AMBER] Problem with MMPBSA.py.MPI Miguel Ortiz Lombardia (Mon Jul 23 2012 - 14:03:15 PDT)
  - Re: [AMBER] Problem with MMPBSA.py.MPI sudipta (Mon Jul 23 2012 - 14:11:15 PDT)
- Re: [AMBER] Problem with MMPBSA.py.MPI Jason Swails (Mon Jul 23 2012 - 14:32:01 PDT)
  - Re: [AMBER] Problem with MMPBSA.py.MPI sudipta (Mon Jul 23 2012 - 14:38:59 PDT)
    - Re: [AMBER] Problem with MMPBSA.py.MPI Ray Luo, Ph.D. (Mon Jul 23 2012 - 14:54:44 PDT)
    - Re: [AMBER] Problem with MMPBSA.py.MPI sudipta (Mon Jul 23 2012 - 15:01:00 PDT)
    - Re: [AMBER] Problem with MMPBSA.py.MPI Ray Luo, Ph.D. (Mon Jul 23 2012 - 15:09:45 PDT)
    - Re: [AMBER] Problem with MMPBSA.py.MPI sudipta (Mon Jul 23 2012 - 16:09:00 PDT)
    - Re: [AMBER] Problem with MMPBSA.py.MPI Jason Swails (Mon Jul 23 2012 - 16:21:37 PDT)
    - Re: [AMBER] Problem with MMPBSA.py.MPI Ray Luo, Ph.D. (Mon Jul 23 2012 - 16:42:38 PDT)
    - Re: [AMBER] Problem with MMPBSA.py.MPI sudipta (Mon Jul 23 2012 - 17:35:32 PDT)
[AMBER] the meaning of variables used in source file force.f Xin Geng (Mon Jul 23 2012 - 15:22:24 PDT)
- Re: [AMBER] the meaning of variables used in source file force.f Jason Swails (Mon Jul 23 2012 - 16:03:28 PDT)
[AMBER] Error: periodicity of dihedral is zero Francesco Pietra (Tue Jul 24 2012 - 01:26:01 PDT)
- Re: [AMBER] Error: periodicity of dihedral is zero Jason Swails (Tue Jul 24 2012 - 05:16:20 PDT)
  - Re: [AMBER] Error: periodicity of dihedral is zero Francesco Pietra (Tue Jul 24 2012 - 08:44:22 PDT)
    - Re: [AMBER] Error: periodicity of dihedral is zero David A. Case (Tue Jul 24 2012 - 14:43:41 PDT)
    - Re: [AMBER] Error: periodicity of dihedral is zero Lorenzo Gontrani (Wed Jul 25 2012 - 09:56:38 PDT)
    - Re: [AMBER] Error: periodicity of dihedral is zero Jason Swails (Wed Jul 25 2012 - 12:06:24 PDT)
    - Re: [AMBER] Error: periodicity of dihedral is zero Francesco Pietra (Wed Jul 25 2012 - 22:58:19 PDT)
[AMBER] problem in parallel testing devawati dutta (Tue Jul 24 2012 - 03:51:30 PDT)
- Re: [AMBER] problem in parallel testing steinbrt.rci.rutgers.edu (Tue Jul 24 2012 - 03:57:33 PDT)
  - Re: [AMBER] problem in parallel testing David A. Case (Tue Jul 24 2012 - 05:41:33 PDT)
[AMBER] pbsa: how to increase the sampling volume (grid dimensions)? Jan-Philip Gehrcke (Tue Jul 24 2012 - 10:13:00 PDT)
- Re: [AMBER] pbsa: how to increase the sampling volume (grid dimensions)? Jan-Philip Gehrcke (Mon Aug 20 2012 - 03:24:49 PDT)
  - Re: [AMBER] pbsa: how to increase the sampling volume (grid dimensions)? Ray Luo (Wed Aug 22 2012 - 07:25:49 PDT)
    - Re: [AMBER] pbsa: how to increase the sampling volume (grid dimensions)? Jan-Philip Gehrcke (Wed Sep 12 2012 - 10:32:18 PDT)
    - Re: [AMBER] pbsa: how to increase the sampling volume (grid dimensions)? Ray Luo, Ph.D. (Wed Sep 12 2012 - 10:39:02 PDT)
    - Re: [AMBER] pbsa: how to increase the sampling volume (grid dimensions)? Jan-Philip Gehrcke (Wed Sep 12 2012 - 10:43:11 PDT)
    - [AMBER] amber12 new installation issue Su, Shiquan (Wed Sep 12 2012 - 12:38:28 PDT)
    - Re: [AMBER] amber12 new installation issue Ross Walker (Wed Sep 12 2012 - 12:52:44 PDT)
    - Re: [AMBER] amber12 new installation issue Robin Betz (Fri Sep 14 2012 - 14:11:35 PDT)
    - Re: [AMBER] amber12 new installation issue Su, Shiquan (Fri Sep 14 2012 - 15:15:26 PDT)
  - Re: [AMBER] pbsa: how to increase the sampling volume (grid dimensions)? Jan-Philip Gehrcke (Wed Sep 12 2012 - 09:41:59 PDT)
    - Re: [AMBER] pbsa: how to increase the sampling volume (grid dimensions)? Ray Luo, Ph.D. (Wed Sep 12 2012 - 10:10:37 PDT)
    - Re: [AMBER] pbsa: how to increase the sampling volume (grid dimensions)? Jan-Philip Gehrcke (Wed Sep 12 2012 - 10:23:18 PDT)
[AMBER] xLeap and Windows questions Mickey Richards (Tue Jul 24 2012 - 11:56:33 PDT)
- Re: [AMBER] xLeap and Windows questions Daniel Roe (Tue Jul 24 2012 - 15:59:30 PDT)
  - Re: [AMBER] xLeap and Windows questions Mickey Richards (Tue Jul 24 2012 - 17:19:57 PDT)
    - Re: [AMBER] xLeap and Windows questions Jason Swails (Wed Jul 25 2012 - 06:39:20 PDT)
    - Re: [AMBER] xLeap and Windows questions Mickey Richards (Wed Jul 25 2012 - 08:21:20 PDT)
[AMBER] install amber10 error onfiguring netcdf; (may be time-consuming) ./configure: line 22350: type: mpic++: not found NETCDF configure succeeded. Jorgen Simonsen (Tue Jul 24 2012 - 14:34:32 PDT)
- Re: [AMBER] install amber10 error onfiguring netcdf; (may be time-consuming) ./configure: line 22350: type: mpic++: not found NETCDF configure succeeded. Daniel Roe (Tue Jul 24 2012 - 15:44:00 PDT)
  - Re: [AMBER] install amber10 error onfiguring netcdf; (may be time-consuming) ./configure: line 22350: type: mpic++: not found NETCDF configure succeeded. Jorgen Simonsen (Tue Jul 24 2012 - 17:50:52 PDT)
    - [AMBER] Fwd: install amber10 error onfiguring netcdf; (may be time-consuming) ./configure: line 22350: type: mpic++: not found NETCDF configure succeeded. Jorgen Simonsen (Tue Jul 24 2012 - 23:00:04 PDT)
[AMBER] internal dielectric constant in MMPBSA Qiong Zhang (Tue Jul 24 2012 - 18:12:11 PDT)
- Re: [AMBER] internal dielectric constant in MMPBSA Qiong Zhang (Wed Jul 25 2012 - 06:15:21 PDT)
  - Re: [AMBER] internal dielectric constant in MMPBSA Jason Swails (Wed Jul 25 2012 - 07:11:16 PDT)
    - Re: [AMBER] internal dielectric constant in MMPBSA Qiong Zhang (Wed Jul 25 2012 - 07:36:40 PDT)
    - Re: [AMBER] internal dielectric constant in MMPBSA Ray Luo, Ph.D. (Wed Jul 25 2012 - 09:44:35 PDT)
[AMBER] RDF calculation Bhanita Sharma (Tue Jul 24 2012 - 23:40:27 PDT)
[AMBER] "Error: unknown flag: -rismmpi" Daniel Sindhikara (Wed Jul 25 2012 - 00:07:09 PDT)
- Re: [AMBER] "Error: unknown flag: -rismmpi" Tyler Luchko (Wed Jul 25 2012 - 06:16:55 PDT)
  - Re: [AMBER] "Error: unknown flag: -rismmpi" Daniel Sindhikara (Wed Jul 25 2012 - 19:10:25 PDT)
[AMBER] MMPBSA per-residue decomposition: how is the polar solvation contribution calculated? Jan-Philip Gehrcke (Wed Jul 25 2012 - 03:07:12 PDT)
- Re: [AMBER] MMPBSA per-residue decomposition: how is the polar solvation contribution calculated? Ray Luo, Ph.D. (Wed Jul 25 2012 - 10:30:36 PDT)
  - Re: [AMBER] MMPBSA per-residue decomposition: how is the polar solvation contribution calculated? Jan-Philip Gehrcke (Thu Jul 26 2012 - 03:51:58 PDT)
[AMBER] Bending force constant in kcal/mol/rad2 from bending frequency(cm-1) arup pathak (Wed Jul 25 2012 - 04:56:19 PDT)
[AMBER] FW: Re: How to Calculate SASA with Amber? Shafinaz Chowdhury (Wed Jul 25 2012 - 09:09:40 PDT)
- Re: [AMBER] FW: Re: How to Calculate SASA with Amber? Daniel Roe (Wed Jul 25 2012 - 09:18:28 PDT)
  - Re: [AMBER] FW: Re: How to Calculate SASA with Amber? E. Nihal Korkmaz (Sun Aug 19 2012 - 20:49:25 PDT)
    - Re: [AMBER] FW: Re: How to Calculate SASA with Amber? E. Nihal Korkmaz (Sun Aug 19 2012 - 20:52:24 PDT)
    - Re: [AMBER] FW: Re: How to Calculate SASA with Amber? Ross Walker (Sun Aug 19 2012 - 20:58:49 PDT)
    - Re: [AMBER] FW: Re: How to Calculate SASA with Amber? Jason Swails (Sun Aug 19 2012 - 20:59:38 PDT)
    - Re: [AMBER] FW: Re: How to Calculate SASA with Amber? Daniel Roe (Sun Aug 19 2012 - 21:20:56 PDT)
[AMBER] installation of amber10 Jorgen Simonsen (Wed Jul 25 2012 - 09:18:18 PDT)
- Re: [AMBER] installation of amber10 Daniel Roe (Wed Jul 25 2012 - 09:30:19 PDT)
  - Re: [AMBER] installation of amber10 Jorgen Simonsen (Wed Jul 25 2012 - 10:15:46 PDT)
    - Re: [AMBER] installation of amber10 Jorgen Simonsen (Wed Jul 25 2012 - 10:35:41 PDT)
    - Re: [AMBER] installation of amber10 Jason Swails (Wed Jul 25 2012 - 12:09:10 PDT)
    - Re: [AMBER] installation of amber10 Jorgen Simonsen (Wed Jul 25 2012 - 20:00:58 PDT)
    - Re: [AMBER] installation of amber10 Jason Swails (Wed Jul 25 2012 - 20:27:40 PDT)
    - Re: [AMBER] installation of amber10 Jorgen Simonsen (Thu Jul 26 2012 - 18:34:46 PDT)
[AMBER] Bfactor for binding site waters Senthil Natesan (Wed Jul 25 2012 - 09:26:36 PDT)
- Re: [AMBER] Bfactor for binding site waters Thomas Cheatham III (Wed Jul 25 2012 - 14:36:58 PDT)
  - Re: [AMBER] Bfactor for binding site waters Senthil Natesan (Thu Jul 26 2012 - 07:40:05 PDT)
[AMBER] internal dielectric constant in MMPBSA Qiong Zhang (Wed Jul 25 2012 - 09:58:22 PDT)
[AMBER] Molecular Surface from MMPBSA Damodaran, Komath (Wed Jul 25 2012 - 10:58:41 PDT)
- Re: [AMBER] Molecular Surface from MMPBSA David A. Case (Thu Jul 26 2012 - 05:00:05 PDT)
  - Re: [AMBER] Molecular Surface from MMPBSA Ray Luo, Ph.D. (Thu Jul 26 2012 - 09:40:50 PDT)
[AMBER] TI with softcore at lambda=0 or 1? Liu Denis (Wed Jul 25 2012 - 19:58:18 PDT)
- Re: [AMBER] TI with softcore at lambda=0 or 1? steinbrt.rci.rutgers.edu (Thu Jul 26 2012 - 00:31:37 PDT)
  - Re: [AMBER] TI with softcore at lambda=0 or 1? Liu Denis (Thu Jul 26 2012 - 01:11:40 PDT)
  - Re: [AMBER] TI with softcore at lambda=0 or 1? Liu Denis (Wed Aug 08 2012 - 10:01:14 PDT)
    - Re: [AMBER] TI with softcore at lambda=0 or 1? steinbrt.rci.rutgers.edu (Thu Aug 09 2012 - 01:05:12 PDT)
    - Re: [AMBER] TI with softcore at lambda=0 or 1? Liu Denis (Thu Aug 09 2012 - 06:37:15 PDT)
    - Re: [AMBER] TI with softcore at lambda=0 or 1? steinbrt.rci.rutgers.edu (Thu Aug 09 2012 - 08:08:40 PDT)
    - Re: [AMBER] TI with softcore at lambda=0 or 1? Liu Denis (Sat Aug 11 2012 - 09:37:36 PDT)
    - Re: [AMBER] TI with softcore at lambda=0 or 1? case (Sun Aug 12 2012 - 05:55:20 PDT)
- Re: [AMBER] TI with softcore at lambda=0 or 1? Liu Denis (Sun Aug 12 2012 - 08:01:33 PDT)
  - Re: [AMBER] TI with softcore at lambda=0 or 1? David A Case (Tue Aug 14 2012 - 05:22:53 PDT)
    - Re: [AMBER] TI with softcore at lambda=0 or 1? Liu Denis (Tue Aug 14 2012 - 18:29:16 PDT)
[AMBER] RDF considering center of mass Bhanita Sharma (Wed Jul 25 2012 - 21:47:31 PDT)
[AMBER] Amber12 issue with SMD protocol Agostino Bruno (Thu Jul 26 2012 - 03:05:25 PDT)
- Re: [AMBER] Amber12 issue with SMD protocol Jan-Philip Gehrcke (Thu Jul 26 2012 - 03:18:33 PDT)
  - Re: [AMBER] Amber12 issue with SMD protocol Jason Swails (Thu Jul 26 2012 - 05:12:09 PDT)
    - Re: [AMBER] Amber12 issue with SMD protocol Jan-Philip Gehrcke (Thu Jul 26 2012 - 06:14:08 PDT)
    - Re: [AMBER] Amber12 issue with SMD protocol David Case (Thu Jul 26 2012 - 09:02:30 PDT)
    - Re: [AMBER] Amber12 issue with SMD protocol Niel Henriksen (Thu Jul 26 2012 - 09:14:24 PDT)
    - Re: [AMBER] Amber12 issue with SMD protocol Jason Swails (Thu Jul 26 2012 - 12:02:41 PDT)
[AMBER] Bugfix 16: New cpptraj action, AutoImage Daniel Roe (Thu Jul 26 2012 - 07:36:42 PDT)
[AMBER] radgyr command ? Marek Maly (Thu Jul 26 2012 - 09:30:13 PDT)
- Re: [AMBER] radgyr command ? Daniel Roe (Thu Jul 26 2012 - 20:45:06 PDT)
  - Re: [AMBER] radgyr command ? Marek Maly (Fri Jul 27 2012 - 05:50:24 PDT)
[AMBER] aMD issues: sander vs. pmemd vs. pmemd.cuda Niel Henriksen (Thu Jul 26 2012 - 13:24:36 PDT)
- Re: [AMBER] aMD issues: sander vs. pmemd vs. pmemd.cuda Romelia Salomon (Thu Jul 26 2012 - 17:02:24 PDT)
- Re: [AMBER] aMD issues: sander vs. pmemd vs. pmemd.cuda Romelia Salomon (Thu Jul 26 2012 - 17:39:02 PDT)
[AMBER] Diverging sander.MPI results according to core allocation Bashford, Donald (Thu Jul 26 2012 - 15:25:11 PDT)
- Re: [AMBER] Diverging sander.MPI results according to core allocation Jason Swails (Thu Aug 02 2012 - 20:41:41 PDT)
  - Re: [AMBER] Diverging sander.MPI results according to core allocation Bashford, Donald (Fri Aug 03 2012 - 12:12:10 PDT)
    - Re: [AMBER] Diverging sander.MPI results according to core allocation Jason Swails (Fri Aug 03 2012 - 13:22:55 PDT)
[AMBER] Bug in PM6: Halogens (?) DJH71.pitt.edu (Wed Jul 25 2012 - 12:31:09 PDT)
- Re: [AMBER] Bug in PM6: Halogens (?) Qiantao Wang (Fri Jul 27 2012 - 10:31:38 PDT)
  - Re: [AMBER] Bug in PM6: Halogens (?) Andreas Goetz (Fri Jul 27 2012 - 20:29:32 PDT)
    - Re: [AMBER] Bug in PM6: Halogens (?) DJH71.pitt.edu (Tue Jul 31 2012 - 10:15:40 PDT)
[AMBER] compilation aborted for pme_setup.f90 (code 1) Jorgen Simonsen (Thu Jul 26 2012 - 20:11:17 PDT)
- Re: [AMBER] compilation aborted for pme_setup.f90 (code 1) David A Case (Fri Jul 27 2012 - 08:34:23 PDT)
[AMBER] iAPBS huseyin istanbullu (Fri Jul 27 2012 - 05:53:53 PDT)
- Re: [AMBER] iAPBS Robert Konecny (Fri Jul 27 2012 - 08:19:49 PDT)
- Re: [AMBER] iAPBS David A Case (Fri Jul 27 2012 - 08:37:59 PDT)
[AMBER] trajin lastframe keyword problem Marek Maly (Fri Jul 27 2012 - 09:01:19 PDT)
- Re: [AMBER] trajin lastframe keyword problem Daniel Roe (Fri Jul 27 2012 - 09:45:41 PDT)
  - Re: [AMBER] trajin lastframe keyword problem Marek Maly (Fri Jul 27 2012 - 09:51:55 PDT)
[AMBER] GAFF c2-c data lacking? Francesco Pietra (Sun Jul 29 2012 - 07:31:26 PDT)
- [AMBER] Fwd: GAFF c2-c data lacking? Francesco Pietra (Sun Jul 29 2012 - 08:02:49 PDT)
[AMBER] mm_pbsa (.pl) calculations for a complex composed of 11 chains and 6 ligand molecules Naeem Attari (Mon Jul 30 2012 - 04:58:31 PDT)
- Re: [AMBER] mm_pbsa (.pl) calculations for a complex composed of 11 chains and 6 ligand molecules Anselm Horn (Tue Jul 31 2012 - 04:46:36 PDT)
[AMBER] problem in converting rst-file to pdb using cpptraj Mahendra B Thapa (Mon Jul 30 2012 - 09:32:24 PDT)
- Re: [AMBER] problem in converting rst-file to pdb using cpptraj Daniel Roe (Mon Jul 30 2012 - 10:43:04 PDT)
[AMBER] NPT equilibration error: ASSERTion 'e' failed in nonbond_list.F90 at line 849 Maria Minakova (Mon Jul 30 2012 - 12:32:34 PDT)
- Re: [AMBER] NPT equilibration error: ASSERTion 'e' failed in nonbond_list.F90 at line 849 Dr. Vitaly V. G. Chaban (Mon Jul 30 2012 - 14:39:51 PDT)
  - Re: [AMBER] NPT equilibration error: ASSERTion 'e' failed in nonbond_list.F90 at line 849 Dr. Vitaly V. G. Chaban (Mon Jul 30 2012 - 14:53:44 PDT)
    - Re: [AMBER] NPT equilibration error: ASSERTion 'e' failed in nonbond_list.F90 at line 849 Maria Minakova (Thu Aug 02 2012 - 12:11:17 PDT)
[AMBER] compiling amber on Ranger/Teragrid Pawel (Mon Jul 30 2012 - 13:36:09 PDT)
- Re: [AMBER] compiling amber on Ranger/Teragrid Ross Walker (Mon Jul 30 2012 - 14:03:56 PDT)
[AMBER] Using CHAMBER with implicit solvent CHARMM force field Anna Tarakanova (Mon Jul 30 2012 - 14:36:05 PDT)
- Re: [AMBER] Using CHAMBER with implicit solvent CHARMM force field Marc van der Kamp (Tue Jul 31 2012 - 00:54:35 PDT)
[AMBER] mobility of protein from MD trajectories kamlesh sahu (Mon Jul 30 2012 - 19:42:32 PDT)
[AMBER] Bug in AmberTools12 cpptraj? 'trajout onlyframes' doesn't work Marc van der Kamp (Tue Jul 31 2012 - 06:24:01 PDT)
- Re: [AMBER] Bug in AmberTools12 cpptraj? 'trajout onlyframes' doesn't work Marc van der Kamp (Tue Jul 31 2012 - 06:46:12 PDT)
  - Re: [AMBER] Bug in AmberTools12 cpptraj? 'trajout onlyframes' doesn't work Daniel Roe (Tue Jul 31 2012 - 06:49:50 PDT)
    - Re: [AMBER] Bug in AmberTools12 cpptraj? 'trajout onlyframes' doesn't work Marc van der Kamp (Tue Jul 31 2012 - 07:08:49 PDT)
    - Re: [AMBER] Bug in AmberTools12 cpptraj? 'trajout onlyframes' doesn't work Daniel Roe (Tue Jul 31 2012 - 07:18:37 PDT)
    - Re: [AMBER] Bug in AmberTools12 cpptraj? 'trajout onlyframes' doesn't work Marc van der Kamp (Tue Jul 31 2012 - 08:38:18 PDT)
    - Re: [AMBER] Bug in AmberTools12 cpptraj? 'trajout onlyframes' doesn't work Daniel Roe (Tue Jul 31 2012 - 08:52:42 PDT)
    - Re: [AMBER] Bug in AmberTools12 cpptraj? 'trajout onlyframes' doesn't work Jason Swails (Tue Jul 31 2012 - 09:16:45 PDT)
    - Re: [AMBER] Bug in AmberTools12 cpptraj? 'trajout onlyframes' doesn't work Marc van der Kamp (Tue Jul 31 2012 - 09:24:32 PDT)
[AMBER] Creating AMBER files from implicit solvent CHARMM19 force field Anna Tarakanova (Tue Jul 31 2012 - 08:52:41 PDT)
- Re: [AMBER] Creating AMBER files from implicit solvent CHARMM19 force field David A. Case (Tue Jul 31 2012 - 14:40:19 PDT)
[AMBER] Problems parameterizing water/ZN active site with MKT++ Fabrício Bracht (Tue Jul 31 2012 - 12:36:56 PDT)
- Re: [AMBER] Problems parameterizing water/ZN active site with MKT++ Ben Roberts (Sat Aug 04 2012 - 22:19:53 PDT)
  - Re: [AMBER] Problems parameterizing water/ZN active site with MKT++ Fabrício Bracht (Sun Aug 05 2012 - 07:39:03 PDT)
    - Re: [AMBER] Problems parameterizing water/ZN active site with MKT++ Ben Roberts (Sun Aug 05 2012 - 17:43:37 PDT)
    - Re: [AMBER] Problems parameterizing water/ZN active site with MKT++ Fabrício Bracht (Fri Aug 10 2012 - 05:47:02 PDT)
    - Re: [AMBER] Problems parameterizing water/ZN active site with MKT++ Ben Roberts (Sun Aug 12 2012 - 02:48:08 PDT)
    - Re: [AMBER] Problems parameterizing water/ZN active site with MKT++ Ben Roberts (Mon Aug 13 2012 - 01:19:10 PDT)
    - Re: [AMBER] Problems parameterizing water/ZN active site with MKT++ Fabrício Bracht (Tue Aug 14 2012 - 10:55:43 PDT)
    - Re: [AMBER] Problems parameterizing water/ZN active site with MKT++ Ben Roberts (Tue Aug 14 2012 - 14:27:23 PDT)
[AMBER] how to include derived charges in AMBER Sanjib Paul (Tue Jul 31 2012 - 23:52:02 PDT)
[AMBER] laptop GPU support Thomas Evangelidis (Wed Aug 01 2012 - 03:08:52 PDT)
- [AMBER] AMBER on GPU: What is the maximum no. of nodes tested? Catein Catherine (Wed Aug 01 2012 - 03:40:19 PDT)
  - Re: [AMBER] AMBER on GPU: What is the maximum no. of nodes tested? Scott Le Grand (Thu Aug 02 2012 - 08:00:08 PDT)
- Re: [AMBER] laptop GPU support Jason Swails (Wed Aug 01 2012 - 05:29:10 PDT)
  - Re: [AMBER] laptop GPU support Benjamin D Madej (Wed Aug 01 2012 - 11:14:05 PDT)
    - Re: [AMBER] laptop GPU support Scott Le Grand (Thu Aug 02 2012 - 08:04:43 PDT)
[AMBER] Problem in Amber12 and Amber12tools parallel installation in mac OS X 10.5 Prabu Manoharan (Wed Aug 01 2012 - 06:01:02 PDT)
- Re: [AMBER] Problem in Amber12 and Amber12tools parallel installation in mac OS X 10.5 Jason Swails (Wed Aug 01 2012 - 06:10:20 PDT)
- Re: [AMBER] Problem in Amber12 and Amber12tools parallel installation in mac OS X 10.5 David A Case (Wed Aug 01 2012 - 07:08:29 PDT)
  - Re: [AMBER] Problem in Amber12 and Amber12tools parallel installation in mac OS X 10.5 Prabu Manoharan (Thu Aug 02 2012 - 05:48:32 PDT)
    - Re: [AMBER] Problem in Amber12 and Amber12tools parallel installation in mac OS X 10.5 David A Case (Thu Aug 02 2012 - 07:41:59 PDT)
[AMBER] receptor nmode calculation using amber12 mmpbsa.pl manikanthan bhavaraju (Wed Aug 01 2012 - 10:36:55 PDT)
- Re: [AMBER] receptor nmode calculation using amber12 mmpbsa.pl Jason Swails (Wed Aug 01 2012 - 10:52:32 PDT)
[AMBER] non polar solvation energy kirtana S (Wed Aug 01 2012 - 12:26:03 PDT)
[AMBER] large difference between MMGBSA and MMPBSA free energy Kong, Ren (Wed Aug 01 2012 - 12:26:02 PDT)
- Re: [AMBER] large difference between MMGBSA and MMPBSA free energy Ray Luo, Ph.D. (Wed Aug 01 2012 - 12:38:44 PDT)
  - Re: [AMBER] large difference between MMGBSA and MMPBSA free energy Kong, Ren (Wed Aug 01 2012 - 13:45:36 PDT)
    - Re: [AMBER] large difference between MMGBSA and MMPBSA free energy Ray Luo, Ph.D. (Wed Aug 01 2012 - 14:45:45 PDT)
[AMBER] frcmod and lib files fro Cadmium Mahendra B Thapa (Wed Aug 01 2012 - 13:08:54 PDT)
- Re: [AMBER] frcmod and lib files fro Cadmium Kong, Ren (Wed Aug 01 2012 - 13:39:20 PDT)
Re: [AMBER] FW: problem in converting rst-file to pdb using cpptraj Mahendra B Thapa (Wed Aug 01 2012 - 14:18:58 PDT)
[AMBER] make test query vaibhav dixit (Thu Aug 02 2012 - 02:40:39 PDT)
[AMBER] Restarting PMEMD calculation after server shutdown Saaz Sakrikar (Thu Aug 02 2012 - 04:07:15 PDT)
- Re: [AMBER] Restarting PMEMD calculation after server shutdown David A Case (Thu Aug 02 2012 - 05:05:01 PDT)
  - Re: [AMBER] Restarting PMEMD calculation after server shutdown Jason Swails (Thu Aug 02 2012 - 05:17:38 PDT)
[AMBER] Looking for parameters for a metal-organic compound Kat Russell (Thu Aug 02 2012 - 11:10:08 PDT)
Re: [AMBER] FW: frcmod and lib files fro Cadmium Mahendra B Thapa (Thu Aug 02 2012 - 14:07:11 PDT)
[AMBER] Amber force field for PNIPAM Ganesh Kamath (Thu Aug 02 2012 - 16:36:10 PDT)
- Re: [AMBER] Amber force field for PNIPAM Vishal Maingi (Fri Aug 03 2012 - 03:25:18 PDT)
[AMBER] Switch-off PBC in md-GPU Adam Jion (Fri Aug 03 2012 - 03:42:18 PDT)
- Re: [AMBER] Switch-off PBC in md-GPU David A Case (Fri Aug 03 2012 - 05:17:07 PDT)
[AMBER] problem for MMPBSA.py in AmberTools12 zhenquan hu (Fri Aug 03 2012 - 06:49:15 PDT)
- Re: [AMBER] problem for MMPBSA.py in AmberTools12 Bill Miller III (Fri Aug 03 2012 - 07:17:10 PDT)
- Re: [AMBER] problem for MMPBSA.py in AmberTools12 zhenquan hu (Sun Aug 05 2012 - 23:48:40 PDT)
[AMBER] TI run energy does not conserve Pin-Chih Su (Henry Su) (Fri Aug 03 2012 - 10:44:03 PDT)
- Re: [AMBER] TI run energy does not conserve Brian Radak (Fri Aug 03 2012 - 11:44:40 PDT)
  - Re: [AMBER] TI run energy does not conserve Pin-Chih Su (Henry Su) (Mon Aug 06 2012 - 15:51:54 PDT)
    - Re: [AMBER] TI run energy does not conserve Brian Radak (Tue Aug 07 2012 - 07:09:53 PDT)
    - Re: [AMBER] TI run energy does not conserve Pin-Chih Su (Henry Su) (Wed Aug 08 2012 - 15:02:55 PDT)
    - Re: [AMBER] TI run energy does not conserve Brian Radak (Thu Aug 09 2012 - 07:30:48 PDT)
    - Re: [AMBER] TI run energy does not conserve psu4.uic.edu (Fri Aug 10 2012 - 00:16:10 PDT)
    - Re: [AMBER] TI run energy does not conserve Brian Radak (Fri Aug 10 2012 - 06:20:51 PDT)
- Re: [AMBER] TI run energy does not conserve psu4.uic.edu (Fri Aug 10 2012 - 13:41:22 PDT)
  - Re: [AMBER] TI run energy does not conserve Brian Radak (Sun Aug 12 2012 - 12:14:34 PDT)
[AMBER] to draw vector along the axis Sangita Kachhap (Fri Aug 03 2012 - 10:54:53 PDT)
[AMBER] Reflective Boundary Conditions Adam Jion (Fri Aug 03 2012 - 21:17:50 PDT)
- Re: [AMBER] Reflective Boundary Conditions case (Sun Aug 05 2012 - 07:13:30 PDT)
  - Re: [AMBER] Reflective Boundary Conditions Dr. Vitaly V. G. Chaban (Sun Aug 05 2012 - 13:16:27 PDT)
    - [AMBER] Extreme large scale movement of a residue Acoot Brett (Mon Aug 06 2012 - 03:38:42 PDT)
[AMBER] non integer charge in antechamber generated mol2 file Raik Grünberg (Sat Aug 04 2012 - 17:32:59 PDT)
- Re: [AMBER] non integer charge in antechamber generated mol2 file Raik Grünberg (Sat Aug 04 2012 - 19:38:18 PDT)
- Re: [AMBER] non integer charge in antechamber generated mol2 file case (Mon Aug 06 2012 - 18:28:13 PDT)
  - Re: [AMBER] non integer charge in antechamber generated mol2 file Raik Grünberg (Wed Aug 08 2012 - 10:41:14 PDT)
    - Re: [AMBER] non integer charge in antechamber generated mol2 file case (Fri Aug 10 2012 - 05:35:41 PDT)
    - Re: [AMBER] non integer charge in antechamber generated mol2 file Raik Grünberg (Fri Aug 10 2012 - 20:28:42 PDT)
- Re: [AMBER] non integer charge in antechamber generated mol2 file FyD (Thu Aug 09 2012 - 08:53:54 PDT)
  - Re: [AMBER] non integer charge in antechamber generated mol2 file Raik Grünberg (Fri Aug 10 2012 - 20:43:02 PDT)
    - Re: [AMBER] non integer charge in antechamber generated mol2 file FyD (Mon Aug 13 2012 - 09:35:31 PDT)
[AMBER] angles and dihedrals for lone pairs Ivanov, Maxim (Sun Aug 05 2012 - 16:39:47 PDT)
- Re: [AMBER] angles and dihedrals for lone pairs case (Mon Aug 06 2012 - 06:06:17 PDT)
  - Re: [AMBER] angles and dihedrals for lone pairs Ivanov, Maxim (Tue Aug 07 2012 - 15:19:48 PDT)
    - Re: [AMBER] angles and dihedrals for lone pairs case (Tue Aug 07 2012 - 18:52:12 PDT)
[AMBER] TMD setup Manish Datt (Mon Aug 06 2012 - 01:46:14 PDT)
- Re: [AMBER] TMD setup Simon Becker (Mon Aug 06 2012 - 02:15:29 PDT)
[AMBER] charge derivation for simulations in organic solvents Igor Pochorovski (Mon Aug 06 2012 - 07:53:31 PDT)
- Re: [AMBER] charge derivation for simulations in organic solvents Dr. Vitaly V. G. Chaban (Mon Aug 06 2012 - 07:58:22 PDT)
- Re: [AMBER] charge derivation for simulations in organic solvents Dr. Vitaly V. G. Chaban (Mon Aug 06 2012 - 08:18:06 PDT)
[AMBER] Amber12 parallel running issues Prabu Manoharan (Mon Aug 06 2012 - 10:00:50 PDT)
- Re: [AMBER] Amber12 parallel running issues Miguel Ortiz Lombardia (Mon Aug 06 2012 - 11:50:37 PDT)
[AMBER] Aspartate and Glutamate naming in PDB Zalikha Ibrahim (Mon Aug 06 2012 - 18:21:05 PDT)
- Re: [AMBER] Aspartate and Glutamate naming in PDB Carlos Simmerling (Mon Aug 06 2012 - 18:23:41 PDT)
  - Re: [AMBER] Aspartate and Glutamate naming in PDB Zalikha Ibrahim (Mon Aug 06 2012 - 18:39:29 PDT)
    - Re: [AMBER] Aspartate and Glutamate naming in PDB Carlos Simmerling (Tue Aug 07 2012 - 04:43:27 PDT)
    - [AMBER] MMPBSA, nonpolar solvation free energy inp=1 versus inp=2 Vlad Cojocaru (Tue Aug 07 2012 - 10:04:50 PDT)
    - Re: [AMBER] MMPBSA, nonpolar solvation free energy inp=1 versus inp=2 Ray Luo, Ph.D. (Tue Aug 07 2012 - 15:22:58 PDT)
    - Re: [AMBER] MMPBSA, nonpolar solvation free energy inp=1 versus inp=2 Vlad Cojocaru (Tue Aug 07 2012 - 22:45:05 PDT)
[AMBER] myristoyl lipid11/12 (DMPC) Vishal Maingi (Tue Aug 07 2012 - 01:48:36 PDT)
- Re: [AMBER] myristoyl lipid11/12 (DMPC) Vishal Maingi (Tue Aug 07 2012 - 06:15:59 PDT)
[AMBER] MMPSA: PB Bomb in pb_aaradi(): ... Vlad Cojocaru (Tue Aug 07 2012 - 06:03:12 PDT)
- Re: [AMBER] MMPSA: PB Bomb in pb_aaradi(): ... Jason Swails (Tue Aug 07 2012 - 06:34:54 PDT)
  - Re: [AMBER] MMPSA: PB Bomb in pb_aaradi(): ... Vlad Cojocaru (Tue Aug 07 2012 - 06:53:57 PDT)
    - Re: [AMBER] MMPSA: PB Bomb in pb_aaradi(): ... Jason Swails (Tue Aug 07 2012 - 07:21:39 PDT)
    - Re: [AMBER] MMPSA: PB Bomb in pb_aaradi(): ... Niel Henriksen (Tue Aug 07 2012 - 07:30:07 PDT)
    - Re: [AMBER] MMPSA: PB Bomb in pb_aaradi(): ... Ray Luo, Ph.D. (Tue Aug 07 2012 - 15:16:18 PDT)
    - Re: [AMBER] MMPSA: PB Bomb in pb_aaradi(): ... Vlad Cojocaru (Tue Aug 07 2012 - 07:32:57 PDT)
    - Re: [AMBER] MMPSA: PB Bomb in pb_aaradi(): ... Jason Swails (Tue Aug 07 2012 - 07:49:29 PDT)
    - Re: [AMBER] MMPSA: PB Bomb in pb_aaradi(): ... Vlad Cojocaru (Tue Aug 07 2012 - 07:58:25 PDT)
    - Re: [AMBER] MMPSA: PB Bomb in pb_aaradi(): ... Ray Luo, Ph.D. (Tue Aug 07 2012 - 15:17:15 PDT)
    - Re: [AMBER] MMPSA: PB Bomb in pb_aaradi(): ... Ray Luo, Ph.D. (Tue Aug 07 2012 - 15:15:38 PDT)
  - Re: [AMBER] MMPSA: PB Bomb in pb_aaradi(): ... psu4.uic.edu (Fri Oct 11 2013 - 10:39:56 PDT)
    - Re: [AMBER] MMPSA: PB Bomb in pb_aaradi(): ... Ray Luo, Ph.D. (Fri Oct 11 2013 - 10:59:11 PDT)
[AMBER] Looking for parameters Kat Russell (Tue Aug 07 2012 - 08:22:51 PDT)
- Re: [AMBER] Looking for parameters FyD (Thu Aug 09 2012 - 09:54:38 PDT)
[AMBER] AMBER 12 Documentation detail missing Aron Broom (Tue Aug 07 2012 - 11:42:21 PDT)
[AMBER] Test message please ignore Ross Walker (Tue Aug 07 2012 - 22:21:36 PDT)
[AMBER] Restraint problem Fernando Martín García (Wed Aug 08 2012 - 02:53:15 PDT)
- Re: [AMBER] Restraint problem Jérôme Golebiowski (Wed Aug 08 2012 - 03:13:51 PDT)
  - Re: [AMBER] Restraint problem Fernando Martín García (Wed Aug 08 2012 - 03:35:03 PDT)
    - Re: [AMBER] Restraint problem Anselm Horn (Wed Aug 08 2012 - 04:27:22 PDT)
    - Re: [AMBER] Restraint problem Jason Swails (Wed Aug 08 2012 - 05:09:53 PDT)
    - Re: [AMBER] Restraint problem Fernando Martín García (Wed Aug 08 2012 - 05:27:38 PDT)
- Re: [AMBER] Restraint problem case (Wed Aug 08 2012 - 06:30:05 PDT)
  - Re: [AMBER] Restraint problem Fernando Martín García (Fri Aug 10 2012 - 02:59:43 PDT)
[AMBER] polarizable force field 旭东肖 (Wed Aug 08 2012 - 06:46:13 PDT)
- Re: [AMBER] polarizable force field Yong Duan (Wed Aug 08 2012 - 15:19:55 PDT)
  - Re: [AMBER] polarizable force field 旭东肖 (Wed Aug 08 2012 - 18:18:18 PDT)
[AMBER] how to make a certain ionic concentration for the system? Kong, Ren (Wed Aug 08 2012 - 09:29:50 PDT)
- Re: [AMBER] how to make a certain ionic concentration for the system? Brian Radak (Wed Aug 08 2012 - 12:26:09 PDT)
  - Re: [AMBER] how to make a certain ionic concentration for the system? Kong, Ren (Thu Aug 09 2012 - 09:45:28 PDT)
- Re: [AMBER] how to make a certain ionic concentration for the system? Aron Broom (Wed Aug 08 2012 - 12:27:48 PDT)
  - Re: [AMBER] how to make a certain ionic concentration for the system? Kong, Ren (Thu Aug 09 2012 - 09:46:19 PDT)
[AMBER] question about calculation of PMF with WHAM Yan Li (Wed Aug 08 2012 - 10:07:37 PDT)
- Re: [AMBER] question about calculation of PMF with WHAM Brian Radak (Wed Aug 08 2012 - 13:11:19 PDT)
  - Re: [AMBER] question about calculation of PMF with WHAM Yan Li (Wed Aug 08 2012 - 18:43:02 PDT)
    - Re: [AMBER] question about calculation of PMF with WHAM Daniel Sindhikara (Thu Aug 09 2012 - 18:40:00 PDT)
[AMBER] Starting and ending temperatures for REMD Sajeewa Pemasinghe (Wed Aug 08 2012 - 10:26:56 PDT)
[AMBER] resp charge calculation jit mukherjee (Wed Aug 08 2012 - 17:44:13 PDT)
- Re: [AMBER] resp charge calculation FyD (Thu Aug 09 2012 - 09:45:31 PDT)
[AMBER] Have any one used the Nmode to calculate the entropy? Kong, Ren (Thu Aug 09 2012 - 09:59:26 PDT)
- Re: [AMBER] Have any one used the Nmode to calculate the entropy? Jason Swails (Thu Aug 09 2012 - 10:35:03 PDT)
  - Re: [AMBER] Have any one used the Nmode to calculate the entropy? Matthew Tessier (Thu Aug 09 2012 - 12:12:46 PDT)
    - Re: [AMBER] Have any one used the Nmode to calculate the entropy? Matthew Tessier (Mon Aug 20 2012 - 08:42:43 PDT)
[AMBER] How to save Eigenvectors of modes using MMPBSA.py script? habi (Thu Aug 09 2012 - 10:36:46 PDT)
[AMBER] How to recover box information from pdb with truncated octahedron solvent? Liu Denis (Thu Aug 09 2012 - 21:24:03 PDT)
[AMBER] Problem while using acdoctor command Sumra Wajid Abbasi 30-FBAS/MSBI/F09 (Thu Aug 09 2012 - 23:09:15 PDT)
- Re: [AMBER] Problem while using acdoctor command David A Case (Tue Aug 14 2012 - 05:30:01 PDT)
[AMBER] Errors during minimization (rfree: Error decoding variable 1 3) Zalikha Ibrahim (Fri Aug 10 2012 - 01:01:52 PDT)
- Re: [AMBER] Errors during minimization (rfree: Error decoding variable 1 3) Terry (Fri Aug 10 2012 - 01:06:01 PDT)
  - Re: [AMBER] Errors during minimization (rfree: Error decoding variable 1 3) Jason Swails (Fri Aug 10 2012 - 05:40:15 PDT)
[AMBER] unique atom names Chris Chris (Fri Aug 10 2012 - 08:56:49 PDT)
- Re: [AMBER] unique atom names case (Fri Aug 10 2012 - 17:54:37 PDT)
[AMBER] specific atom restraint Thanh Binh NGUYEN (Fri Aug 10 2012 - 09:09:47 PDT)
- Re: [AMBER] specific atom restraint Jason Swails (Fri Aug 10 2012 - 10:04:38 PDT)
  - Re: [AMBER] specific atom restraint Thanh Binh NGUYEN (Fri Aug 10 2012 - 20:08:55 PDT)
[AMBER] Installation of Amber11 Meena Singh (Sat Aug 11 2012 - 03:32:49 PDT)
- Re: [AMBER] Installation of Amber11 case (Sat Aug 11 2012 - 05:57:31 PDT)
[AMBER] Production md ariana karakutuk (Mon Aug 13 2012 - 03:06:04 PDT)
- Re: [AMBER] Production md case (Mon Aug 13 2012 - 05:35:01 PDT)
  - Re: [AMBER] Production md ariana karakutuk (Tue Aug 14 2012 - 00:19:56 PDT)
    - Re: [AMBER] Production md David A Case (Tue Aug 14 2012 - 05:09:23 PDT)
    - Re: [AMBER] Production md ariana karakutuk (Thu Aug 16 2012 - 00:55:01 PDT)
    - Re: [AMBER] Production md David A Case (Thu Aug 16 2012 - 05:08:34 PDT)
[AMBER] Internal energy linear increase with temperature Binwu Zhao (Mon Aug 13 2012 - 08:01:19 PDT)
- Re: [AMBER] Internal energy linear increase with temperature David A Case (Mon Aug 13 2012 - 08:16:19 PDT)
[AMBER] General question George Tzotzos (Mon Aug 13 2012 - 13:42:02 PDT)
- Re: [AMBER] General question Jason Swails (Mon Aug 13 2012 - 19:08:01 PDT)
  - Re: [AMBER] General question Gould, Ian R (Tue Aug 14 2012 - 01:06:37 PDT)
    - Re: [AMBER] General question George Tzotzos (Tue Aug 14 2012 - 01:12:50 PDT)
[AMBER] Query about how to run ambertools12 after installing it Yousef Elsyid (Tue Aug 14 2012 - 05:04:38 PDT)
- Re: [AMBER] Query about how to run ambertools12 after installing it David A Case (Tue Aug 14 2012 - 06:40:44 PDT)
[AMBER] RMS fit Eliac Brown (Tue Aug 14 2012 - 07:45:13 PDT)
- Re: [AMBER] RMS fit Daniel Roe (Tue Aug 14 2012 - 08:04:10 PDT)
  - Re: [AMBER] RMS fit Eliac Brown (Tue Aug 14 2012 - 10:06:03 PDT)
    - Re: [AMBER] RMS fit Jason Swails (Tue Aug 14 2012 - 10:29:29 PDT)
    - Re: [AMBER] RMS fit Daniel Roe (Tue Aug 14 2012 - 10:35:30 PDT)
    - [AMBER] More RMS fit George Tzotzos (Thu Aug 23 2012 - 05:28:05 PDT)
    - [AMBER] RECALL More RMS fit George Tzotzos (Thu Aug 23 2012 - 05:34:47 PDT)
[AMBER] Problems when using cpptraj for reimaging when INPCRD file is one of the input frames Marek Maly (Tue Aug 14 2012 - 11:57:52 PDT)
- Re: [AMBER] Problems when using cpptraj for reimaging when INPCRD file is one of the input frames Daniel Roe (Tue Aug 14 2012 - 15:30:33 PDT)
  - Re: [AMBER] Problems when using cpptraj for reimaging when INPCRD file is one of the input frames Marek Maly (Wed Aug 15 2012 - 03:11:31 PDT)
    - Re: [AMBER] Problems when using cpptraj for reimaging when INPCRD file is one of the input frames Daniel Roe (Wed Aug 15 2012 - 10:49:18 PDT)
    - Re: [AMBER] Problems when using cpptraj for reimaging when INPCRD file is one of the input frames Marek Maly (Wed Aug 15 2012 - 11:21:08 PDT)
    - Re: [AMBER] Problems when using cpptraj for reimaging when INPCRD file is one of the input frames Daniel Roe (Wed Aug 15 2012 - 12:55:50 PDT)
    - Re: [AMBER] Problems when using cpptraj for reimaging when INPCRD file is one of the input frames Daniel Roe (Wed Aug 15 2012 - 13:29:34 PDT)
    - Re: [AMBER] Problems when using cpptraj for reimaging when INPCRD file is one of the input frames Marek Maly (Wed Aug 15 2012 - 13:33:39 PDT)
    - Re: [AMBER] Problems when using cpptraj for reimaging when INPCRD file is one of the input frames Daniel Roe (Fri Aug 17 2012 - 06:58:21 PDT)
    - Re: [AMBER] Problems when using cpptraj for reimaging when INPCRD file is one of the input frames Marek Maly (Fri Aug 17 2012 - 06:59:57 PDT)
[AMBER] which part of source code implementing GB/SA simulations? Xin Geng (Tue Aug 14 2012 - 16:26:47 PDT)
- Re: [AMBER] which part of source code implementing GB/SA simulations? case (Tue Aug 14 2012 - 19:30:49 PDT)
  - Re: [AMBER] which part of source code implementing GB/SA simulations? Xin Geng (Tue Aug 14 2012 - 20:48:24 PDT)
[AMBER] which part of source code implementing GB/SA simulations? Xin Geng (Tue Aug 14 2012 - 20:42:10 PDT)
[AMBER] job in multiple GPUs Vijay Manickam Achari (Tue Aug 14 2012 - 21:41:40 PDT)
[AMBER] Fatal error (Could not read velocities) during heating Zalikha Ibrahim (Wed Aug 15 2012 - 02:09:51 PDT)
- Re: [AMBER] Fatal error (Could not read velocities) during heating David A Case (Wed Aug 15 2012 - 05:00:34 PDT)
  - Re: [AMBER] Fatal error (Could not read velocities) during heating Jason Swails (Wed Aug 15 2012 - 06:02:57 PDT)
[AMBER] Temperature regulation in HREMD Brian Radak (Wed Aug 15 2012 - 06:39:31 PDT)
- Re: [AMBER] Temperature regulation in HREMD dani sd (Wed Aug 15 2012 - 11:39:59 PDT)
  - Re: [AMBER] Temperature regulation in HREMD Carlos Simmerling (Wed Aug 15 2012 - 12:58:45 PDT)
    - Re: [AMBER] Temperature regulation in HREMD dani sd (Wed Aug 15 2012 - 13:29:58 PDT)
[AMBER] PRMTOP TO PSF manikanthan bhavaraju (Wed Aug 15 2012 - 11:34:29 PDT)
- Re: [AMBER] PRMTOP TO PSF case (Wed Aug 15 2012 - 18:16:09 PDT)
[AMBER] meaning of "tolerance" in REMD Sajeewa Pemasinghe (Wed Aug 15 2012 - 11:12:48 PDT)
- [AMBER] Fwd: meaning of "tolerance" in REMD Sajeewa Pemasinghe (Thu Aug 16 2012 - 11:02:54 PDT)
  - Re: [AMBER] Fwd: meaning of "tolerance" in REMD Brian Radak (Thu Aug 16 2012 - 11:53:12 PDT)
    - Re: [AMBER] Fwd: meaning of "tolerance" in REMD Sajeewa Pemasinghe (Thu Aug 16 2012 - 14:38:43 PDT)
    - Re: [AMBER] Fwd: meaning of "tolerance" in REMD Niel Henriksen (Thu Aug 16 2012 - 14:46:53 PDT)
    - Re: [AMBER] Fwd: meaning of "tolerance" in REMD Jason Swails (Thu Aug 16 2012 - 15:56:07 PDT)
[AMBER] amber10 install Qian Wang (Wed Aug 15 2012 - 13:31:00 PDT)
- Re: [AMBER] amber10 install case (Wed Aug 15 2012 - 18:22:58 PDT)
  - Re: [AMBER] amber10 install Qian Wang (Thu Aug 16 2012 - 07:18:40 PDT)
    - Re: [AMBER] amber10 install David A Case (Thu Aug 16 2012 - 07:25:40 PDT)
    - Re: [AMBER] amber10 install Qian Wang (Thu Aug 16 2012 - 07:33:16 PDT)
[AMBER] how to predict time for MMPBSA decomp analysis vaibhav dixit (Wed Aug 15 2012 - 22:45:23 PDT)
- Re: [AMBER] how to predict time for MMPBSA decomp analysis Jason Swails (Thu Aug 16 2012 - 07:34:26 PDT)
  - Re: [AMBER] how to predict time for MMPBSA decomp analysis vaibhav dixit (Thu Aug 16 2012 - 08:59:49 PDT)
    - Re: [AMBER] how to predict time for MMPBSA decomp analysis vaibhav dixit (Mon Aug 20 2012 - 22:03:13 PDT)
    - Re: [AMBER] how to predict time for MMPBSA decomp analysis Soumya Lipsa Rath (Mon Aug 20 2012 - 22:57:54 PDT)
    - Re: [AMBER] how to predict time for MMPBSA decomp analysis vaibhav dixit (Tue Oct 09 2012 - 23:25:06 PDT)
    - Re: [AMBER] how to predict time for MMPBSA decomp analysis Jiri Sponer (Tue Aug 21 2012 - 00:44:00 PDT)
[AMBER] MBAR calculation Liu Denis (Thu Aug 16 2012 - 08:33:21 PDT)
- Re: [AMBER] MBAR calculation Brian Radak (Thu Aug 16 2012 - 08:50:57 PDT)
[AMBER] Help with ncsu_abmd flooding mode Fabrício Bracht (Thu Aug 16 2012 - 14:15:09 PDT)
- [AMBER] Help with ncsu_abmd flooding mode Fabrício Bracht (Mon Aug 27 2012 - 08:17:00 PDT)
  - Re: [AMBER] Help with ncsu_abmd flooding mode Brian Radak (Mon Aug 27 2012 - 09:08:15 PDT)
    - Re: [AMBER] Help with ncsu_abmd flooding mode Fabrício Bracht (Mon Aug 27 2012 - 10:48:17 PDT)
    - Re: [AMBER] Help with ncsu_abmd flooding mode Jason Swails (Mon Aug 27 2012 - 11:16:26 PDT)
    - Re: [AMBER] Help with ncsu_abmd flooding mode M. L. Dodson (Mon Aug 27 2012 - 14:05:12 PDT)
[AMBER] Zn atom flying off moitrayee.mbu.iisc.ernet.in (Fri Aug 17 2012 - 06:55:18 PDT)
[AMBER] nmode - calculation of vibrational frequencies Svetlana Oard (Fri Aug 17 2012 - 09:04:33 PDT)
- Re: [AMBER] nmode - calculation of vibrational frequencies case (Tue Aug 21 2012 - 18:39:40 PDT)
  - Re: [AMBER] nmode - calculation of vibrational frequencies Svetlana Oard (Thu Aug 23 2012 - 09:53:09 PDT)
[AMBER] Calculating Energy of an atom selection Aron Broom (Fri Aug 17 2012 - 14:19:28 PDT)
[AMBER] COM coordinates Vishal Maingi (Fri Aug 17 2012 - 15:57:38 PDT)
- Re: [AMBER] COM coordinates Vishal Maingi (Tue Aug 21 2012 - 02:12:39 PDT)
- Re: [AMBER] COM coordinates Daniel Roe (Tue Aug 21 2012 - 14:00:56 PDT)
  - Re: [AMBER] COM coordinates Vishal Maingi (Tue Aug 21 2012 - 23:59:25 PDT)
[AMBER] where is the subroutine amflsh in Amber10? Xin Geng (Sat Aug 18 2012 - 15:50:38 PDT)
- Re: [AMBER] where is the subroutine amflsh in Amber10? case (Sun Aug 19 2012 - 06:08:00 PDT)
[AMBER] Flag for saving particular residues. HIMANSHU JOSHI (Sat Aug 18 2012 - 23:04:58 PDT)
- Re: [AMBER] Flag for saving particular residues. case (Sun Aug 19 2012 - 08:18:01 PDT)
  - [AMBER] Error message in cpptraj when running at single node in supercomputer using mpirun Catein Catherine (Sun Aug 19 2012 - 18:53:31 PDT)
    - Re: [AMBER] Error message in cpptraj when running at single node in supercomputer using mpirun Jason Swails (Sun Aug 19 2012 - 21:07:09 PDT)
    - Re: [AMBER] Error message in cpptraj when running at single node in supercomputer using mpirun Catein Catherine (Sun Aug 19 2012 - 23:57:23 PDT)
[AMBER] Accelerated Molecular Dynamics in Amber12 Soumya Lipsa Rath (Sun Aug 19 2012 - 22:15:11 PDT)
- Re: [AMBER] Accelerated Molecular Dynamics in Amber12 Ross Walker (Sun Aug 19 2012 - 23:06:13 PDT)
  - [AMBER] How to get the averaged structure of each cluster with cpptraj? Catein Catherine (Mon Aug 20 2012 - 00:01:14 PDT)
    - Re: [AMBER] How to get the averaged structure of each cluster with cpptraj? Daniel Roe (Mon Aug 20 2012 - 06:41:47 PDT)
  - Re: [AMBER] Accelerated Molecular Dynamics in Amber12 Soumya Lipsa Rath (Mon Aug 20 2012 - 00:04:04 PDT)
Re: [AMBER] Internal energy linear increase with temperature (David A Case) Binwu Zhao (Mon Aug 20 2012 - 12:56:02 PDT)
- Re: [AMBER] Internal energy linear increase with temperature (David A Case) David A Case (Mon Aug 20 2012 - 13:40:43 PDT)
[AMBER] pmemd.cuda and nmropt Larry Olson (Mon Aug 20 2012 - 14:08:46 PDT)
- Re: [AMBER] pmemd.cuda and nmropt Ross Walker (Mon Aug 20 2012 - 14:20:50 PDT)
[AMBER] transition metal system works on pmemd crashes on pmemd.cuda Patrick von Glehn (Mon Aug 20 2012 - 16:37:41 PDT)
- Re: [AMBER] transition metal system works on pmemd crashes on pmemd.cuda Scott Le Grand (Mon Aug 20 2012 - 19:35:09 PDT)
  - Re: [AMBER] transition metal system works on pmemd crashes on pmemd.cuda Patrick von Glehn (Wed Aug 22 2012 - 07:28:50 PDT)
    - Re: [AMBER] transition metal system works on pmemd crashes on pmemd.cuda Jason Swails (Wed Aug 22 2012 - 07:50:05 PDT)
    - Re: [AMBER] transition metal system works on pmemd crashes on pmemd.cuda Patrick von Glehn (Tue Sep 04 2012 - 10:27:04 PDT)
    - Re: [AMBER] transition metal system works on pmemd crashes on pmemd.cuda Scott Le Grand (Tue Sep 04 2012 - 11:44:21 PDT)
    - Re: [AMBER] transition metal system works on pmemd crashes on pmemd.cuda Marc van der Kamp (Tue Sep 04 2012 - 13:08:38 PDT)
    - Re: [AMBER] transition metal system works on pmemd crashes on pmemd.cuda Scott Le Grand (Tue Sep 04 2012 - 13:15:26 PDT)
    - Re: [AMBER] transition metal system works on pmemd crashes on pmemd.cuda Marc van der Kamp (Tue Sep 04 2012 - 13:21:02 PDT)
    - Re: [AMBER] transition metal system works on pmemd crashes on pmemd.cuda Marc van der Kamp (Tue Sep 04 2012 - 13:31:42 PDT)
    - Re: [AMBER] transition metal system works on pmemd crashes on pmemd.cuda Scott Le Grand (Tue Sep 04 2012 - 14:34:26 PDT)
    - Re: [AMBER] transition metal system works on pmemd crashes on pmemd.cuda Marc van der Kamp (Wed Sep 05 2012 - 04:18:58 PDT)
    - Re: [AMBER] transition metal system works on pmemd crashes on pmemd.cuda Scott Le Grand (Wed Sep 05 2012 - 05:50:16 PDT)
    - Re: [AMBER] transition metal system works on pmemd crashes on pmemd.cuda Patrick von Glehn (Mon Sep 10 2012 - 08:18:16 PDT)
    - Re: [AMBER] transition metal system works on pmemd crashes on pmemd.cuda Scott Le Grand (Tue Sep 11 2012 - 10:19:45 PDT)
    - Re: [AMBER] transition metal system works on pmemd crashes on pmemd.cuda Scott Le Grand (Wed Sep 12 2012 - 09:15:24 PDT)
[AMBER] AMBER alanine scan with chlorine Mannan (Tue Aug 21 2012 - 02:31:50 PDT)
- Re: [AMBER] AMBER alanine scan with chlorine Bill Miller III (Tue Aug 21 2012 - 04:04:28 PDT)
[AMBER] Recommendations for Amber on AMD Bulldozer Jan-Philip Gehrcke (Tue Aug 21 2012 - 05:02:52 PDT)
- Re: [AMBER] Recommendations for Amber on AMD Bulldozer Ross Walker (Tue Aug 21 2012 - 07:56:49 PDT)
  - Re: [AMBER] Recommendations for Amber on AMD Bulldozer Jan-Philip Gehrcke (Tue Aug 21 2012 - 10:17:42 PDT)
[AMBER] amber10 install (mpi) Qian Wang (Tue Aug 21 2012 - 14:11:22 PDT)
- Re: [AMBER] amber10 install (mpi) Jason Swails (Tue Aug 21 2012 - 14:18:50 PDT)
  - Re: [AMBER] amber10 install (mpi) Qian Wang (Tue Aug 21 2012 - 14:39:42 PDT)
    - Re: [AMBER] amber10 install (mpi) Jason Swails (Tue Aug 21 2012 - 15:05:40 PDT)
    - Re: [AMBER] amber10 install (mpi) Qian Wang (Tue Aug 21 2012 - 15:14:28 PDT)
    - Re: [AMBER] amber10 install (mpi) Jason Swails (Tue Aug 21 2012 - 16:20:43 PDT)
    - Re: [AMBER] amber10 install (mpi) case (Tue Aug 21 2012 - 18:26:47 PDT)
    - Re: [AMBER] amber10 install (mpi) Qian Wang (Wed Aug 22 2012 - 07:41:09 PDT)
[AMBER] area per lipid popc membrane Fabrício Bracht (Tue Aug 21 2012 - 14:25:28 PDT)
- Re: [AMBER] area per lipid popc membrane Benjamin D Madej (Wed Aug 22 2012 - 10:51:37 PDT)
  - Re: [AMBER] area per lipid popc membrane Fabrício Bracht (Wed Aug 22 2012 - 15:39:26 PDT)
    - Re: [AMBER] area per lipid popc membrane Benjamin D Madej (Wed Aug 22 2012 - 16:20:55 PDT)
    - Re: [AMBER] area per lipid popc membrane jojartb.jgypk.u-szeged.hu (Wed Aug 22 2012 - 22:19:14 PDT)
    - Re: [AMBER] area per lipid popc membrane Albert (Wed Aug 22 2012 - 22:52:19 PDT)
    - Re: [AMBER] area per lipid popc membrane Dickson, Callum (Thu Aug 23 2012 - 02:12:14 PDT)
[AMBER] Is there any guide/tutorial/review to decide input format for MD based on system under consideration vaibhav dixit (Tue Aug 21 2012 - 22:46:34 PDT)
[AMBER] How to derive dihedral angle force constants by MCPB JiYuan Liu (Wed Aug 22 2012 - 01:20:28 PDT)
- Re: [AMBER] How to derive dihedral angle force constants by MCPB Ben Roberts (Wed Aug 22 2012 - 15:50:15 PDT)
[AMBER] Diffenent EPB in MMPBSA result with Liu Denis (Wed Aug 22 2012 - 02:03:56 PDT)
- Re: [AMBER] Diffenent EPB in MMPBSA result with Liu Denis (Wed Aug 22 2012 - 10:18:45 PDT)
  - Re: [AMBER] Diffenent EPB in MMPBSA result with Miguel Ortiz Lombardia (Wed Aug 22 2012 - 10:26:13 PDT)
  - Re: [AMBER] Diffenent EPB in MMPBSA result with Qin Cai (Thu Aug 23 2012 - 10:21:24 PDT)
    - Re: [AMBER] Diffenent EPB in MMPBSA result with Qin Cai (Fri Aug 31 2012 - 11:35:13 PDT)
[AMBER] NPT at high pressure Francesco Pietra (Wed Aug 22 2012 - 06:33:30 PDT)
- Re: [AMBER] NPT at high pressure Jason Swails (Wed Aug 22 2012 - 07:19:46 PDT)
  - Re: [AMBER] NPT at high pressure Francesco Pietra (Wed Aug 22 2012 - 07:36:37 PDT)
[AMBER] Amber 12 cuda test suite: some tests 'hang' Jan-Philip Gehrcke (Wed Aug 22 2012 - 08:00:35 PDT)
- Re: [AMBER] Amber 12 cuda test suite: some tests 'hang' Ross Walker (Wed Aug 22 2012 - 08:08:47 PDT)
  - Re: [AMBER] Amber 12 cuda test suite: some tests 'hang' Jan-Philip Gehrcke (Wed Aug 22 2012 - 08:25:47 PDT)
    - Re: [AMBER] Amber 12 cuda test suite: some tests 'hang' Ross Walker (Wed Aug 22 2012 - 09:04:14 PDT)
    - Re: [AMBER] Amber 12 cuda test suite: some tests 'hang' Jan-Philip Gehrcke (Wed Aug 22 2012 - 11:35:23 PDT)
    - Re: [AMBER] Amber 12 cuda test suite: some tests 'hang' Ross Walker (Wed Aug 22 2012 - 12:20:22 PDT)
    - Re: [AMBER] Amber 12 cuda test suite: some tests 'hang' Jan-Philip Gehrcke (Wed Aug 22 2012 - 14:11:31 PDT)
    - Re: [AMBER] Amber 12 cuda test suite: some tests 'hang' Robert Crovella (Fri Aug 24 2012 - 06:58:32 PDT)
- Re: [AMBER] Amber 12 cuda test suite: some tests 'hang' Scott Le Grand (Wed Aug 22 2012 - 08:53:16 PDT)
  - Re: [AMBER] Amber 12 cuda test suite: some tests 'hang' Jan-Philip Gehrcke (Wed Aug 22 2012 - 08:57:02 PDT)
- Re: [AMBER] Amber 12 cuda test suite: some tests 'hang' Alessandro Contini (Thu Jan 31 2013 - 08:45:40 PST)
  - Re: [AMBER] Amber 12 cuda test suite: some tests 'hang' Jason Swails (Thu Jan 31 2013 - 09:24:54 PST)
    - Re: [AMBER] Amber 12 cuda test suite: some tests 'hang' Ross Walker (Thu Jan 31 2013 - 10:16:50 PST)
    - Re: [AMBER] Amber 12 cuda test suite: some tests 'hang' Scott Le Grand (Thu Jan 31 2013 - 10:24:35 PST)
    - Re: [AMBER] Amber 12 cuda test suite: some tests 'hang' Alessandro Contini (Thu Jan 31 2013 - 12:11:54 PST)
[AMBER] protein+DNA simulation najmul arfin (Wed Aug 22 2012 - 11:40:18 PDT)
- Re: [AMBER] protein+DNA simulation Thomas Cheatham III (Wed Aug 22 2012 - 15:17:41 PDT)
- Re: [AMBER] protein+DNA simulation Dean Cuebas (Thu Aug 23 2012 - 09:50:45 PDT)
[AMBER] Help about the igb Elaine Cheung (Wed Aug 22 2012 - 11:56:44 PDT)
- Re: [AMBER] Help about the igb Carlos Simmerling (Wed Aug 22 2012 - 15:28:26 PDT)
  - Re: [AMBER] Help about the igb Elaine Cheung (Wed Aug 22 2012 - 18:51:39 PDT)
    - Re: [AMBER] Help about the igb Carlos Simmerling (Sat Aug 25 2012 - 04:55:27 PDT)
    - [AMBER] Can we use Ambertools analysis MD from GROMACS Acoot Brett (Mon Aug 27 2012 - 01:52:30 PDT)
    - Re: [AMBER] Can we use Ambertools analysis MD from GROMACS Jason Swails (Mon Aug 27 2012 - 04:02:25 PDT)
    - Re: [AMBER] Can we use Ambertools analysis MD from GROMACS Pawel (Mon Aug 27 2012 - 05:47:58 PDT)
    - Re: [AMBER] Help about the igb Elaine Cheung (Mon Aug 27 2012 - 08:22:50 PDT)
[AMBER] problem w/ radial results E. Nihal Korkmaz (Wed Aug 22 2012 - 14:23:04 PDT)
- Re: [AMBER] problem w/ radial results Thomas Cheatham III (Wed Aug 22 2012 - 14:56:37 PDT)
[AMBER] loading of a mutant protein in XLEaP gargi borgohai (Wed Aug 22 2012 - 23:32:57 PDT)
- Re: [AMBER] loading of a mutant protein in XLEaP Jason Swails (Thu Aug 23 2012 - 07:33:55 PDT)
[AMBER] ptraj: msd with diffusion command Bala subramanian (Thu Aug 23 2012 - 07:41:45 PDT)
- Re: [AMBER] ptraj: msd with diffusion command Daniel Roe (Thu Aug 23 2012 - 12:09:58 PDT)
  - Re: [AMBER] ptraj: msd with diffusion command Dmitry Mukha (Sat Aug 25 2012 - 08:59:06 PDT)
    - Re: [AMBER] ptraj: msd with diffusion command Bala subramanian (Fri Aug 31 2012 - 10:47:14 PDT)
    - Re: [AMBER] ptraj: msd with diffusion command Bala subramanian (Sat Sep 01 2012 - 09:40:07 PDT)
[AMBER] amber 12 installation error Shuyi Cao (Thu Aug 23 2012 - 09:04:22 PDT)
- Re: [AMBER] amber 12 installation error Jason Swails (Thu Aug 23 2012 - 10:58:17 PDT)
[AMBER] failed to config serial amber 12 on IBM POWER7 Yubo Fan (Thu Aug 23 2012 - 09:49:52 PDT)
[AMBER] Different Properties Value with Tesla vs GeForce GPUs Ismail, Mohd F. (Thu Aug 23 2012 - 10:40:50 PDT)
[AMBER] AMBER Workshop Announcement - Oct 8th to 12th - Lausanne Switzerland Ross Walker (Thu Aug 23 2012 - 11:05:14 PDT)
- Re: [AMBER] AMBER Workshop Announcement - Oct 8th to 12th - Lausanne Switzerland Albert (Thu Aug 23 2012 - 11:08:16 PDT)
  - Re: [AMBER] AMBER Workshop Announcement - Oct 8th to 12th - Lausanne Switzerland Ross Walker (Thu Aug 23 2012 - 11:16:35 PDT)
    - Re: [AMBER] AMBER Workshop Announcement - Oct 8th to 12th - Lausanne Switzerland Albert (Fri Aug 24 2012 - 01:47:01 PDT)
- Re: [AMBER] AMBER Workshop Announcement - Oct 8th to 12th - Lausanne Switzerland Jonathan Gough (Mon Sep 17 2012 - 10:35:36 PDT)
  - Re: [AMBER] AMBER Workshop Announcement - Oct 8th to 12th - Lausanne Switzerland Adrian Roitberg (Mon Sep 17 2012 - 14:32:56 PDT)
[AMBER] parallel installation problem: Amber11+AmberTools1.4 on a linux cluster Alfred Zheng (Thu Aug 23 2012 - 17:14:00 PDT)
- Re: [AMBER] parallel installation problem: Amber11+AmberTools1.4 on a linux cluster Jason Swails (Thu Aug 23 2012 - 18:08:05 PDT)
[AMBER] about ions Carlos Romero (Thu Aug 23 2012 - 22:50:34 PDT)
- Re: [AMBER] about ions David A Case (Fri Aug 24 2012 - 05:52:28 PDT)
  - Re: [AMBER] about ions Carlos Romero (Fri Aug 24 2012 - 17:44:37 PDT)
    - Re: [AMBER] about ions Jason Swails (Fri Aug 24 2012 - 19:57:04 PDT)
    - Re: [AMBER] about ions Carlos Romero (Sun Aug 26 2012 - 16:55:19 PDT)
[AMBER] failed to config serial amber 12 on IBM POWER7 Yubo Fan (Thu Aug 23 2012 - 23:40:45 PDT)
- Re: [AMBER] failed to config serial amber 12 on IBM POWER7 David A Case (Fri Aug 24 2012 - 06:09:10 PDT)
[AMBER] cpptraj surf George Tzotzos (Fri Aug 24 2012 - 06:22:01 PDT)
- Re: [AMBER] cpptraj surf Daniel Roe (Fri Aug 24 2012 - 07:37:37 PDT)
  - Re: [AMBER] cpptraj surf George Tzotzos (Fri Aug 24 2012 - 08:28:55 PDT)
    - Re: [AMBER] cpptraj surf Jason Swails (Fri Aug 24 2012 - 08:47:59 PDT)
    - Re: [AMBER] cpptraj surf George Tzotzos (Fri Aug 24 2012 - 09:21:22 PDT)
    - Re: [AMBER] cpptraj surf Daniel Roe (Fri Aug 24 2012 - 09:32:36 PDT)
    - Re: [AMBER] cpptraj surf George Tzotzos (Fri Aug 24 2012 - 09:52:46 PDT)
    - Re: [AMBER] cpptraj surf Jason Swails (Fri Aug 24 2012 - 10:42:25 PDT)
    - [AMBER] CPPTRAJ: Is it a program that requires a large memory? Catein Catherine (Mon Aug 27 2012 - 00:06:42 PDT)
    - Re: [AMBER] CPPTRAJ: Is it a program that requires a large memory? Jason Swails (Mon Aug 27 2012 - 03:59:52 PDT)
    - Re: [AMBER] CPPTRAJ: Is it a program that requires a large memory? Daniel Roe (Mon Aug 27 2012 - 18:02:21 PDT)
[AMBER] parallel constraints SMD e g (Fri Aug 24 2012 - 08:39:59 PDT)
- Re: [AMBER] parallel constraints SMD Jason Swails (Fri Aug 24 2012 - 08:51:19 PDT)
  - Re: [AMBER] parallel constraints SMD e g (Fri Aug 24 2012 - 12:38:03 PDT)
[AMBER] Can electrostatic potential of GBSA be visualized? Liu Denis (Sat Aug 25 2012 - 06:28:49 PDT)
[AMBER] parallel run error najmul arfin (Sun Aug 26 2012 - 22:04:43 PDT)
- Re: [AMBER] parallel run error Jason Swails (Mon Aug 27 2012 - 03:52:14 PDT)
[AMBER] Decomposing the free energy contributions to the binding free energy Deák Robert (Mon Aug 27 2012 - 00:55:17 PDT)
- Re: [AMBER] Decomposing the free energy contributions to the binding free energy Liu Denis (Mon Aug 27 2012 - 09:47:12 PDT)
  - Re: [AMBER] Decomposing the free energy contributions to the binding free energy Deák Robert (Mon Aug 27 2012 - 12:52:12 PDT)
    - Re: [AMBER] Decomposing the free energy contributions to the binding free energy Liu Denis (Mon Aug 27 2012 - 17:51:39 PDT)
    - Re: [AMBER] Decomposing the free energy contributions to the binding free energy Deák Robert (Tue Aug 28 2012 - 03:12:03 PDT)
    - Re: [AMBER] Decomposing the free energy contributions to the binding free energy Jason Swails (Tue Aug 28 2012 - 07:05:19 PDT)
[AMBER] GDP and MG parameters Vlad Cojocaru (Mon Aug 27 2012 - 01:21:56 PDT)
- Re: [AMBER] GDP and MG parameters George M Giambasu (Mon Aug 27 2012 - 09:40:18 PDT)
- Re: [AMBER] GDP and MG parameters FyD (Tue Aug 28 2012 - 03:15:54 PDT)
  - Re: [AMBER] GDP and MG parameters Vlad Cojocaru (Tue Aug 28 2012 - 04:09:22 PDT)
    - Re: [AMBER] GDP and MG parameters FyD (Tue Aug 28 2012 - 09:17:17 PDT)
    - Re: [AMBER] GDP and MG parameters Vlad Cojocaru (Tue Aug 28 2012 - 11:42:22 PDT)
[AMBER] Particles diffuse very far away from each other ariana karakutuk (Mon Aug 27 2012 - 22:11:07 PDT)
- Re: [AMBER] Particles diffuse very far away from each other Jason Swails (Mon Aug 27 2012 - 23:12:40 PDT)
[AMBER] help about TMD 燕燕朱 (Tue Aug 28 2012 - 05:10:49 PDT)
- Re: [AMBER] help about TMD David A Case (Tue Aug 28 2012 - 06:19:25 PDT)
[AMBER] How can I get a average structure? Sanjib Paul (Tue Aug 28 2012 - 07:05:47 PDT)
- Re: [AMBER] How can I get a average structure? Jason Swails (Tue Aug 28 2012 - 07:13:18 PDT)
  - [AMBER] Can we use autoimage of cpptraj in AMBER 12? Catein Catherine (Tue Aug 28 2012 - 07:31:14 PDT)
    - Re: [AMBER] Can we use autoimage of cpptraj in AMBER 12? Jason Swails (Tue Aug 28 2012 - 07:41:25 PDT)
  - Re: [AMBER] How can I get a average structure? Sanjib Paul (Tue Aug 28 2012 - 08:33:41 PDT)
    - Re: [AMBER] How can I get a average structure? Daniel Roe (Tue Aug 28 2012 - 09:12:52 PDT)
    - Re: [AMBER] How can I get a average structure? Sanjib Paul (Tue Aug 28 2012 - 09:39:24 PDT)
[AMBER] Dummy atom and PMEMD Ali M. Naserian-Nik (Tue Aug 28 2012 - 07:21:57 PDT)
- Re: [AMBER] Dummy atom and PMEMD case (Tue Aug 28 2012 - 17:35:08 PDT)
  - Re: [AMBER] Dummy atom and PMEMD Ali M. Naserian-Nik (Tue Aug 28 2012 - 22:57:06 PDT)
    - Re: [AMBER] Dummy atom and PMEMD David A Case (Thu Aug 30 2012 - 10:04:53 PDT)
    - Re: [AMBER] Dummy atom and PMEMD Ali M. Naserian-Nik (Thu Aug 30 2012 - 11:29:31 PDT)
    - Re: [AMBER] Dummy atom and PMEMD Jason Swails (Thu Aug 30 2012 - 11:48:05 PDT)
    - Re: [AMBER] Dummy atom and PMEMD Ali M. Naserian-Nik (Thu Aug 30 2012 - 12:21:08 PDT)
    - Re: [AMBER] Dummy atom and PMEMD Jason Swails (Thu Aug 30 2012 - 13:05:11 PDT)
    - Re: [AMBER] Dummy atom and PMEMD Ali M. Naserian-Nik (Fri Aug 31 2012 - 00:20:57 PDT)
    - Re: [AMBER] Dummy atom and PMEMD David A Case (Fri Aug 31 2012 - 05:08:45 PDT)
[AMBER] Problem regarding imin = 5 Sanjib Paul (Tue Aug 28 2012 - 10:50:09 PDT)
- Re: [AMBER] Problem regarding imin = 5 Carlos Simmerling (Tue Aug 28 2012 - 10:53:35 PDT)
- Re: [AMBER] Problem regarding imin = 5 Sanjib Paul (Tue Aug 28 2012 - 10:54:09 PDT)
  - Re: [AMBER] Problem regarding imin = 5 Sanjib Paul (Tue Aug 28 2012 - 10:56:54 PDT)
[AMBER] MPI version of Amber on CPU provide different results in each run Mohammad Ashraf Bhuiyan (Tue Aug 28 2012 - 16:46:47 PDT)
- Re: [AMBER] MPI version of Amber on CPU provide different results in each run Liu Denis (Tue Aug 28 2012 - 18:02:05 PDT)
[AMBER] "QMMM of protein-ligand complex: Unable to achieve self consistency" and "bond stretch too far" psu4.uic.edu (Tue Aug 28 2012 - 16:48:31 PDT)
[AMBER] Adding water molecules directly into files Adam Jion (Tue Aug 28 2012 - 21:04:15 PDT)
- Re: [AMBER] Adding water molecules directly into files Liu Denis (Tue Aug 28 2012 - 21:10:00 PDT)
  - Re: [AMBER] Adding water molecules directly into files Jason Swails (Tue Aug 28 2012 - 21:24:58 PDT)
    - [AMBER] How to combine RMSF profiles? Catein Catherine (Tue Aug 28 2012 - 22:49:05 PDT)
    - Re: [AMBER] How to combine RMSF profiles? Jason Swails (Wed Aug 29 2012 - 07:38:46 PDT)
    - Re: [AMBER] How to combine RMSF profiles? Catein Catherine (Wed Aug 29 2012 - 20:10:43 PDT)
    - Re: [AMBER] How to combine RMSF profiles? Jason Swails (Wed Aug 29 2012 - 21:48:56 PDT)
    - Re: [AMBER] How to combine RMSF profiles? Carlos Simmerling (Wed Aug 29 2012 - 07:48:11 PDT)
    - Re: [AMBER] Adding water molecules directly into files Marc van der Kamp (Wed Aug 29 2012 - 01:40:29 PDT)
[AMBER] mpi4py import error mesage is improvable Jan-Philip Gehrcke (Wed Aug 29 2012 - 02:20:46 PDT)
- Re: [AMBER] mpi4py import error mesage is improvable Jason Swails (Wed Aug 29 2012 - 07:25:28 PDT)
[AMBER] Amber 12: CalcError in mmpbsa_py_energy and sander Jan-Philip Gehrcke (Wed Aug 29 2012 - 05:11:28 PDT)
- Re: [AMBER] Amber 12: CalcError in mmpbsa_py_energy and sander Jason Swails (Wed Aug 29 2012 - 07:17:17 PDT)
  - Re: [AMBER] Amber 12: CalcError in mmpbsa_py_energy and sander Jan-Philip Gehrcke (Fri Aug 31 2012 - 06:50:32 PDT)
    - Re: [AMBER] Amber 12: CalcError in mmpbsa_py_energy and sander Jason Swails (Fri Aug 31 2012 - 07:26:01 PDT)
    - Re: [AMBER] Amber 12: CalcError in mmpbsa_py_energy and sander Jan-Philip Gehrcke (Fri Aug 31 2012 - 07:58:31 PDT)
    - Re: [AMBER] Amber 12: CalcError in mmpbsa_py_energy and sander Jason Swails (Fri Aug 31 2012 - 08:43:24 PDT)
    - Re: [AMBER] Amber 12: CalcError in mmpbsa_py_energy and sander Jan-Philip Gehrcke (Fri Aug 31 2012 - 08:56:49 PDT)
    - Re: [AMBER] Amber 12: CalcError in mmpbsa_py_energy and sander Ray Luo, Ph.D. (Fri Aug 31 2012 - 09:55:12 PDT)
[AMBER] problem to perform nmode analysis Sanjib Paul (Wed Aug 29 2012 - 05:41:06 PDT)
- Re: [AMBER] problem to perform nmode analysis Sanjib Paul (Wed Aug 29 2012 - 05:57:21 PDT)
- Re: [AMBER] problem to perform nmode analysis David A Case (Wed Aug 29 2012 - 08:03:32 PDT)
  - Re: [AMBER] problem to perform nmode analysis Jason Swails (Wed Aug 29 2012 - 08:28:18 PDT)
    - Re: [AMBER] problem to perform nmode analysis Sanjib Paul (Wed Aug 29 2012 - 08:39:33 PDT)
[AMBER] CPPTRAJ hbond command Samuel Genheden (Wed Aug 29 2012 - 07:35:01 PDT)
- Re: [AMBER] CPPTRAJ hbond command Daniel Roe (Wed Aug 29 2012 - 09:50:32 PDT)
[AMBER] group specification for different force constants for different groups Sajeewa Pemasinghe (Wed Aug 29 2012 - 10:06:36 PDT)
- Re: [AMBER] group specification for different force constants for different groups Jason Swails (Wed Aug 29 2012 - 10:41:09 PDT)
[AMBER] keeping parts of a protein virtually frozen in MD with pmemd Sajeewa Pemasinghe (Wed Aug 29 2012 - 11:28:53 PDT)
[AMBER] Amber12 Configuring NetCDF or fftw3 or MTK++ hang Yu Chen (Wed Aug 29 2012 - 13:26:56 PDT)
- Re: [AMBER] Amber12 Configuring NetCDF or fftw3 or MTK++ hang Jason Swails (Wed Aug 29 2012 - 14:16:21 PDT)
- Re: [AMBER] Amber12 Configuring NetCDF or fftw3 or MTK++ hang Ben Roberts (Wed Aug 29 2012 - 15:54:50 PDT)
  - Re: [AMBER] Amber12 Configuring NetCDF or fftw3 or MTK++ hang Yu Chen (Thu Aug 30 2012 - 08:19:17 PDT)
    - Re: [AMBER] Amber12 Configuring NetCDF or fftw3 or MTK++ hang Jason Swails (Thu Aug 30 2012 - 08:29:34 PDT)
    - Re: [AMBER] Amber12 Configuring NetCDF or fftw3 or MTK++ hang Yu Chen (Sat Sep 01 2012 - 20:30:25 PDT)
[AMBER] Installation problem of AmberTools of AMBER11 Sanjib Paul (Wed Aug 29 2012 - 23:01:30 PDT)
- Re: [AMBER] Installation problem of AmberTools of AMBER11 David A Case (Thu Aug 30 2012 - 05:16:47 PDT)
  - Re: [AMBER] Installation problem of AmberTools of AMBER11 Sanjib Paul (Thu Aug 30 2012 - 06:17:47 PDT)
    - Re: [AMBER] Installation problem of AmberTools of AMBER11 Jason Swails (Thu Aug 30 2012 - 07:34:55 PDT)
    - Re: [AMBER] Installation problem of AmberTools of AMBER11 Sanjib Paul (Thu Aug 30 2012 - 09:33:45 PDT)
    - Re: [AMBER] Installation problem of AmberTools of AMBER11 Jason Swails (Thu Aug 30 2012 - 10:10:28 PDT)
    - Re: [AMBER] Installation problem of AmberTools of AMBER11 Sanjib Paul (Thu Aug 30 2012 - 11:58:38 PDT)
    - Re: [AMBER] Installation problem of AmberTools of AMBER11 Jason Swails (Thu Aug 30 2012 - 13:03:27 PDT)
    - Re: [AMBER] Installation problem of AmberTools of AMBER11 Sanjib Paul (Thu Aug 30 2012 - 21:43:04 PDT)
    - Re: [AMBER] Installation problem of AmberTools of AMBER11 David A Case (Fri Aug 31 2012 - 05:13:18 PDT)
    - Re: [AMBER] Installation problem of AmberTools of AMBER11 Sanjib Paul (Sat Sep 01 2012 - 05:25:29 PDT)
    - Re: [AMBER] Installation problem of AmberTools of AMBER11 Jason Swails (Sat Sep 01 2012 - 12:55:51 PDT)
    - Re: [AMBER] Installation problem of AmberTools of AMBER11 Sanjib Paul (Mon Sep 03 2012 - 03:16:16 PDT)
[AMBER] Bacteriochlorophyll parameters from Ceccarelli et al.? Marc van der Kamp (Thu Aug 30 2012 - 08:33:32 PDT)
[AMBER] RESP charge derivation shomesankar bhunia (Thu Aug 30 2012 - 11:49:34 PDT)
- Re: [AMBER] RESP charge derivation Jason Swails (Thu Aug 30 2012 - 11:55:57 PDT)
  - Re: [AMBER] RESP charge derivation shomesankar bhunia (Thu Aug 30 2012 - 12:04:44 PDT)
    - Re: [AMBER] RESP charge derivation Jason Swails (Thu Aug 30 2012 - 12:21:56 PDT)
    - Re: [AMBER] RESP charge derivation shomesankar bhunia (Thu Aug 30 2012 - 21:02:45 PDT)
    - Re: [AMBER] RESP charge derivation shomesankar bhunia (Thu Aug 30 2012 - 22:51:40 PDT)
    - Re: [AMBER] RESP charge derivation FyD (Thu Aug 30 2012 - 23:06:10 PDT)
    - Re: [AMBER] RESP charge derivation shomesankar bhunia (Thu Aug 30 2012 - 23:13:53 PDT)
    - Re: [AMBER] RESP charge derivation shomesankar bhunia (Fri Aug 31 2012 - 13:16:15 PDT)
    - Re: [AMBER] RESP charge derivation FyD (Fri Aug 31 2012 - 22:16:16 PDT)
- Re: [AMBER] RESP charge derivation FyD (Mon Sep 03 2012 - 22:56:20 PDT)
- Re: [AMBER] RESP charge derivation FyD (Tue Sep 04 2012 - 02:51:58 PDT)
[AMBER] Segmentation Fault in Tleap Deepak Ojha (Thu Aug 30 2012 - 14:19:37 PDT)
- Re: [AMBER] Segmentation Fault in Tleap Jason Swails (Thu Aug 30 2012 - 16:52:28 PDT)
[AMBER] ions concenration Carlos Romero (Thu Aug 30 2012 - 18:30:17 PDT)
- Re: [AMBER] ions concenration Daniel Sindhikara (Fri Aug 31 2012 - 07:32:39 PDT)
  - Re: [AMBER] ions concenration Marek Maly (Fri Aug 31 2012 - 08:07:43 PDT)
    - Re: [AMBER] ions concenration Carlos Romero (Fri Aug 31 2012 - 10:13:16 PDT)
    - Re: [AMBER] ions concenration Marek Maly (Mon Sep 03 2012 - 05:07:56 PDT)
    - Re: [AMBER] ions concenration Carlos Romero (Mon Sep 03 2012 - 13:24:20 PDT)
  - Re: [AMBER] ions concenration Carlos Romero (Fri Aug 31 2012 - 08:40:00 PDT)
[AMBER] How to choose a particular region to minimization? Thanh Binh NGUYEN (Thu Aug 30 2012 - 23:55:02 PDT)
- Re: [AMBER] How to choose a particular region to minimization? Marc van der Kamp (Fri Aug 31 2012 - 03:49:06 PDT)
  - Re: [AMBER] How to choose a particular region to minimization? Thanh Binh NGUYEN (Fri Aug 31 2012 - 04:09:50 PDT)
    - Re: [AMBER] How to choose a particular region to minimization? Jason Swails (Fri Aug 31 2012 - 07:31:26 PDT)
[AMBER] newbie question: simulating miRNA Michiel de Hoon (Fri Aug 31 2012 - 07:30:25 PDT)
- Re: [AMBER] newbie question: simulating miRNA Niel Henriksen (Fri Aug 31 2012 - 08:47:10 PDT)
  - Re: [AMBER] newbie question: simulating miRNA David A Case (Fri Aug 31 2012 - 12:44:25 PDT)
    - Re: [AMBER] newbie question: simulating miRNA Niel Henriksen (Fri Aug 31 2012 - 12:53:59 PDT)
  - Re: [AMBER] newbie question: simulating miRNA Michiel de Hoon (Fri Aug 31 2012 - 20:10:04 PDT)
[AMBER] ERROR: max pairlist cutoff must be less than unit cell max sphere radius! Gabriel Jara (Fri Aug 31 2012 - 07:39:51 PDT)
- Re: [AMBER] ERROR: max pairlist cutoff must be less than unit cell max sphere radius! Brian Radak (Fri Aug 31 2012 - 07:50:06 PDT)
[AMBER] Surface Energy John S (Sat Sep 01 2012 - 07:51:19 PDT)
[AMBER] Lipid bilayer coarse-grained simulations Bharath K. Srikanth (Sat Sep 01 2012 - 23:20:33 PDT)
- Re: [AMBER] Lipid bilayer coarse-grained simulations Jason Swails (Sun Sep 02 2012 - 08:06:27 PDT)
- Re: [AMBER] Lipid bilayer coarse-grained simulations jojartb.jgypk.u-szeged.hu (Sun Sep 02 2012 - 11:10:43 PDT)
  - Re: [AMBER] Lipid bilayer coarse-grained simulations Benjamin D Madej (Wed Sep 05 2012 - 08:42:33 PDT)
[AMBER] parallel error najmul arfin (Sun Sep 02 2012 - 01:39:50 PDT)
[AMBER] parallel error with NVT file najmul arfin (Sun Sep 02 2012 - 01:51:21 PDT)
[AMBER] finding global minimum jit mukherjee (Sun Sep 02 2012 - 04:05:58 PDT)
- Re: [AMBER] finding global minimum Scott Le Grand (Sun Sep 02 2012 - 08:15:01 PDT)
[AMBER] RESP charges for HHCC motif with Zn2+ ion Sangeetha B (Sun Sep 02 2012 - 06:23:20 PDT)
- Re: [AMBER] RESP charges for HHCC motif with Zn2+ ion FyD (Mon Sep 03 2012 - 11:42:18 PDT)
[AMBER] MMPBSA energy decomposition George Tzotzos (Sun Sep 02 2012 - 08:16:07 PDT)
- Re: [AMBER] MMPBSA energy decomposition Jason Swails (Sun Sep 02 2012 - 09:33:09 PDT)
[AMBER] problem in inter molecular RDF Subrata Paul (Mon Sep 03 2012 - 03:57:37 PDT)
- [AMBER] Fwd: problem in inter molecular RDF Subrata Paul (Tue Sep 04 2012 - 23:26:13 PDT)
  - Re: [AMBER] Fwd: problem in inter molecular RDF francesco oteri (Wed Sep 05 2012 - 00:18:31 PDT)
- Re: [AMBER] problem in inter molecular RDF Thomas Cheatham III (Wed Sep 05 2012 - 09:51:52 PDT)
  - Re: [AMBER] problem in inter molecular RDF Subrata Paul (Wed Sep 05 2012 - 11:53:33 PDT)
[AMBER] GPU related update to Amber12 case (Mon Sep 03 2012 - 05:40:39 PDT)
[AMBER] Announcement: Major GPU Update Ross Walker (Mon Sep 03 2012 - 13:52:58 PDT)
- Re: [AMBER] Announcement: Major GPU Update Jason Swails (Mon Sep 03 2012 - 06:00:54 PDT)
- Re: [AMBER] Announcement: Major GPU Update Ye MEI (Mon Sep 03 2012 - 06:13:18 PDT)
  - Re: [AMBER] Announcement: Major GPU Update Ross Walker (Mon Sep 03 2012 - 14:23:16 PDT)
[AMBER] How can I get restart file for every step. Sanjib Paul (Mon Sep 03 2012 - 11:13:58 PDT)
- Re: [AMBER] How can I get restart file for every step. Jason Swails (Mon Sep 03 2012 - 14:53:57 PDT)
- Re: [AMBER] How can I get restart file for every step. case (Mon Sep 03 2012 - 17:44:09 PDT)
  - Re: [AMBER] How can I get restart file for every step. Sanjib Paul (Tue Sep 04 2012 - 07:40:14 PDT)
    - Re: [AMBER] How can I get restart file for every step. David A Case (Tue Sep 04 2012 - 08:00:41 PDT)
[AMBER] AMBER weird performance marawan hussain (Mon Sep 03 2012 - 18:22:59 PDT)
[AMBER] output error Subrata Paul (Mon Sep 03 2012 - 20:40:09 PDT)
- Re: [AMBER] output error Bill Ross (Mon Sep 03 2012 - 21:27:08 PDT)
  - Re: [AMBER] output error Subrata Paul (Mon Sep 03 2012 - 21:55:45 PDT)
- Re: [AMBER] output error Jason Swails (Tue Sep 04 2012 - 13:40:39 PDT)
  - Re: [AMBER] output error Subrata Paul (Tue Sep 04 2012 - 21:52:54 PDT)
[AMBER] forcefield for dipeptide Mary Varughese (Tue Sep 04 2012 - 01:40:04 PDT)
- Re: [AMBER] forcefield for dipeptide FyD (Tue Sep 04 2012 - 02:55:40 PDT)
  - Re: [AMBER] forcefield for dipeptide Mary Varughese (Fri Sep 07 2012 - 09:59:02 PDT)
    - Re: [AMBER] forcefield for dipeptide FyD (Sat Sep 08 2012 - 00:10:45 PDT)
    - Re: [AMBER] forcefield for dipeptide Mary Varughese (Sun Sep 09 2012 - 07:09:27 PDT)
[AMBER] using igb=7 jit mukherjee (Tue Sep 04 2012 - 01:48:36 PDT)
[AMBER] Amber : System must be very inhomogeneous. najmul arfin (Tue Sep 04 2012 - 04:12:52 PDT)
- Re: [AMBER] Amber : System must be very inhomogeneous. Dr. Vitaly Chaban (Tue Sep 04 2012 - 05:52:37 PDT)
  - Re: [AMBER] Amber : System must be very inhomogeneous. najmul arfin (Tue Sep 04 2012 - 06:46:38 PDT)
    - Re: [AMBER] Amber : System must be very inhomogeneous. Dr. Vitaly Chaban (Tue Sep 04 2012 - 06:57:35 PDT)
[AMBER] using igb=7 jit mukherjee (Tue Sep 04 2012 - 08:41:35 PDT)
- Re: [AMBER] using igb=7 Carlos Simmerling (Tue Sep 04 2012 - 08:44:45 PDT)
  - Re: [AMBER] using igb=7 jit mukherjee (Tue Sep 04 2012 - 10:01:10 PDT)
    - Re: [AMBER] using igb=7 Carlos Simmerling (Tue Sep 04 2012 - 12:43:23 PDT)
    - Re: [AMBER] using igb=7 David A Case (Wed Sep 05 2012 - 05:34:34 PDT)
    - Re: [AMBER] using igb=7 Thomas Gaillard (Wed Sep 05 2012 - 03:35:55 PDT)
    - Re: [AMBER] using igb=7 Hai Nguyen (Wed Sep 05 2012 - 09:58:19 PDT)
    - Re: [AMBER] using igb=7 jit mukherjee (Wed Sep 05 2012 - 10:28:56 PDT)
    - Re: [AMBER] using igb=7 Hai Nguyen (Wed Sep 05 2012 - 15:00:18 PDT)
[AMBER] Compiling ptraj in parallel Gustavo Seabra (Tue Sep 04 2012 - 10:12:55 PDT)
- Re: [AMBER] Compiling ptraj in parallel David A Case (Tue Sep 04 2012 - 11:16:05 PDT)
  - Re: [AMBER] Compiling ptraj in parallel Gustavo Seabra (Wed Sep 05 2012 - 19:36:15 PDT)
    - Re: [AMBER] Compiling ptraj in parallel Daniel Roe (Wed Sep 05 2012 - 21:03:31 PDT)
    - Re: [AMBER] Compiling ptraj in parallel Gustavo Seabra (Thu Sep 06 2012 - 03:44:32 PDT)
[AMBER] Antibiotics Parameters Shahoei, Seyyedehrezvan (Tue Sep 04 2012 - 17:14:00 PDT)
- Re: [AMBER] Antibiotics Parameters FyD (Wed Sep 05 2012 - 00:15:48 PDT)
  - Re: [AMBER] Antibiotics Parameters Shahoei, Seyyedehrezvan (Fri Sep 07 2012 - 18:38:03 PDT)
    - Re: [AMBER] Antibiotics Parameters FyD (Sat Sep 08 2012 - 08:10:22 PDT)
    - Re: [AMBER] Antibiotics Parameters Shahoei, Seyyedehrezvan (Fri Sep 14 2012 - 09:39:02 PDT)
    - Re: [AMBER] Antibiotics Parameters FyD (Sat Sep 15 2012 - 05:51:35 PDT)
- Re: [AMBER] Antibiotics Parameters David A Case (Wed Sep 05 2012 - 05:35:45 PDT)
[AMBER] ips=4 and pmemd.cuda Martin Andersson (Wed Sep 05 2012 - 01:23:47 PDT)
- Re: [AMBER] ips=4 and pmemd.cuda David A Case (Wed Sep 05 2012 - 05:37:57 PDT)
[AMBER] CUDA-SPFP code and Hardware Version 1.3? Thomas Zeiser (Wed Sep 05 2012 - 03:58:53 PDT)
- Re: [AMBER] CUDA-SPFP code and Hardware Version 1.3? Jason Swails (Wed Sep 05 2012 - 05:07:08 PDT)
  - Re: [AMBER] CUDA-SPFP code and Hardware Version 1.3? Thomas Zeiser (Wed Sep 05 2012 - 13:25:24 PDT)
    - Re: [AMBER] CUDA-SPFP code and Hardware Version 1.3? Ross Walker (Thu Sep 06 2012 - 16:45:12 PDT)
    - Re: [AMBER] CUDA-SPFP code and Hardware Version 1.3? Thomas Zeiser (Wed Sep 12 2012 - 01:57:38 PDT)
[AMBER] Problem in nmode analysis by NAB Sanjib Paul (Wed Sep 05 2012 - 05:59:53 PDT)
- Re: [AMBER] Problem in nmode analysis by NAB Jason Swails (Wed Sep 05 2012 - 06:17:12 PDT)
  - Re: [AMBER] Problem in nmode analysis by NAB Sanjib Paul (Thu Sep 06 2012 - 03:59:54 PDT)
    - Re: [AMBER] Problem in nmode analysis by NAB Bill Miller III (Thu Sep 06 2012 - 05:18:28 PDT)
    - Re: [AMBER] Problem in nmode analysis by NAB Sanjib Paul (Thu Sep 06 2012 - 05:39:53 PDT)
[AMBER] problem with SCNB & SCEE Subrata Paul (Wed Sep 05 2012 - 06:36:56 PDT)
- Re: [AMBER] problem with SCNB & SCEE Jason Swails (Wed Sep 05 2012 - 12:55:23 PDT)
[AMBER] Minimization problem on Amber 12.1 GPU version Tim Travers (Wed Sep 05 2012 - 09:20:43 PDT)
- Re: [AMBER] Minimization problem on Amber 12.1 GPU version Scott Le Grand (Wed Sep 05 2012 - 10:31:29 PDT)
[AMBER] visualizing normal mode jit mukherjee (Wed Sep 05 2012 - 09:57:20 PDT)
[AMBER] ntt 2 vs 3 on GPU using latest Amber 12 updates Tim Travers (Wed Sep 05 2012 - 10:06:55 PDT)
- Re: [AMBER] ntt 2 vs 3 on GPU using latest Amber 12 updates Scott Le Grand (Wed Sep 05 2012 - 10:32:19 PDT)
[AMBER] Adding a ROH to a oligosaccharide Pedro Swagger (Wed Sep 05 2012 - 12:44:56 PDT)
- Re: [AMBER] Adding a ROH to a oligosaccharide Lachele Foley (Lists) (Wed Sep 05 2012 - 12:58:05 PDT)
  - Re: [AMBER] Adding a ROH to a oligosaccharide Pedro Swagger (Wed Sep 05 2012 - 13:28:01 PDT)
    - Re: [AMBER] Adding a ROH to a oligosaccharide Lachele Foley (Lists) (Wed Sep 05 2012 - 13:30:40 PDT)
    - Re: [AMBER] Adding a ROH to a oligosaccharide Pedro Swagger (Wed Sep 05 2012 - 13:36:57 PDT)
    - Re: [AMBER] Adding a ROH to a oligosaccharide Lachele Foley (Lists) (Wed Sep 05 2012 - 14:44:10 PDT)
    - Re: [AMBER] Adding a ROH to a oligosaccharide Pedro Swagger (Thu Sep 06 2012 - 08:49:12 PDT)
    - Re: [AMBER] Adding a ROH to a oligosaccharide Lachele Foley (Lists) (Thu Sep 06 2012 - 09:18:47 PDT)
    - Re: [AMBER] Adding a ROH to a oligosaccharide Pedro Swagger (Thu Sep 06 2012 - 09:44:15 PDT)
    - Re: [AMBER] Adding a ROH to a oligosaccharide Pedro Swagger (Thu Sep 06 2012 - 09:48:59 PDT)
    - Re: [AMBER] Adding a ROH to a oligosaccharide Lachele Foley (Lists) (Thu Sep 06 2012 - 09:51:08 PDT)
- Re: [AMBER] Adding a ROH to a oligosaccharide David A Case (Wed Sep 05 2012 - 13:15:38 PDT)
  - Re: [AMBER] Adding a ROH to a oligosaccharide Lachele Foley (Lists) (Wed Sep 05 2012 - 13:24:52 PDT)
[AMBER] xleap and tleap do not recognize Na+ they themselves added Chris Chris (Wed Sep 05 2012 - 17:47:55 PDT)
- Re: [AMBER] xleap and tleap do not recognize Na+ they themselves added David A. Case (Wed Sep 05 2012 - 18:29:26 PDT)
[AMBER] presumed problem with SHAKEH: disappears on passing from CUDA version to normal Sander Emanuele Monza (Thu Sep 06 2012 - 02:08:13 PDT)
- Re: [AMBER] presumed problem with SHAKEH: disappears on passing from CUDA version to normal Sander Scott Le Grand (Thu Sep 06 2012 - 09:07:27 PDT)
- [AMBER] presumed problem with SHAKEH: disappears on passing from CUDA version to normal Sander Emanuele Monza (Fri Sep 07 2012 - 06:02:16 PDT)
  - Re: [AMBER] presumed problem with SHAKEH: disappears on passing from CUDA version to normal Sander Jason Swails (Fri Sep 07 2012 - 07:57:03 PDT)
[AMBER] RESP-charge fitting. shomesankar bhunia (Thu Sep 06 2012 - 05:57:46 PDT)
- Re: [AMBER] RESP-charge fitting. Marc van der Kamp (Thu Sep 06 2012 - 06:00:18 PDT)
  - Re: [AMBER] RESP-charge fitting. shomesankar bhunia (Thu Sep 06 2012 - 06:14:01 PDT)
    - Re: [AMBER] RESP-charge fitting. shomesankar bhunia (Thu Sep 06 2012 - 06:17:23 PDT)
    - Re: [AMBER] RESP-charge fitting. FyD (Thu Sep 06 2012 - 11:48:23 PDT)
    - Re: [AMBER] RESP-charge fitting. shomesankar bhunia (Thu Sep 06 2012 - 12:10:47 PDT)
    - Re: [AMBER] RESP-charge fitting. shomesankar bhunia (Thu Sep 06 2012 - 19:00:42 PDT)
    - Re: [AMBER] RESP-charge fitting. FyD (Thu Sep 06 2012 - 23:20:10 PDT)
    - Re: [AMBER] RESP-charge fitting. shomesankar bhunia (Thu Sep 06 2012 - 23:42:50 PDT)
    - Re: [AMBER] RESP-charge fitting. FyD (Thu Sep 06 2012 - 23:49:38 PDT)
    - Re: [AMBER] RESP-charge fitting. shomesankar bhunia (Fri Sep 07 2012 - 00:12:45 PDT)
[AMBER] water radial distribution function experimental data 旭东肖 (Thu Sep 06 2012 - 07:07:23 PDT)
[AMBER] PCA analysis Sangita Kachhap (Thu Sep 06 2012 - 08:53:14 PDT)
- Re: [AMBER] PCA analysis Daniel Roe (Thu Sep 06 2012 - 09:09:16 PDT)
  - Re: [AMBER] PCA analysis Sangita Kachhap (Thu Sep 06 2012 - 21:09:19 PDT)
    - Re: [AMBER] PCA analysis Daniel Roe (Fri Sep 07 2012 - 14:23:21 PDT)
[AMBER] nividia GTX 690 and pmed.cuda Jonathan Gough (Thu Sep 06 2012 - 08:58:30 PDT)
- Re: [AMBER] nividia GTX 690 and pmed.cuda Scott Le Grand (Thu Sep 06 2012 - 09:03:22 PDT)
[AMBER] Unable to correctly identify element N1 Hakansson P. (Thu Sep 06 2012 - 15:57:06 PDT)
[AMBER] Amber12 Question Buback, Clayton (S&T-Student) (Thu Sep 06 2012 - 17:15:13 PDT)
- Re: [AMBER] Amber12 Question David A. Case (Fri Sep 07 2012 - 07:14:28 PDT)
[AMBER] RESP shomesankar bhunia (Thu Sep 06 2012 - 23:07:32 PDT)
- Re: [AMBER] RESP FyD (Thu Sep 06 2012 - 23:40:58 PDT)
[AMBER] mechanical unfolding of nucleic acids Asmita Gupta (Thu Sep 06 2012 - 23:17:13 PDT)
[AMBER] Using mopac in antechamber with Amber11/AmberTools 1.5 Baptiste Legrand (Fri Sep 07 2012 - 02:42:55 PDT)
- Re: [AMBER] Using mopac in antechamber with Amber11/AmberTools 1.5 David A. Case (Fri Sep 07 2012 - 07:20:42 PDT)
  - Re: [AMBER] Using mopac in antechamber with Amber11/AmberTools 1.5 Baptiste Legrand (Fri Sep 07 2012 - 08:30:18 PDT)
    - Re: [AMBER] Using mopac in antechamber with Amber11/AmberTools 1.5 David Case (Fri Sep 07 2012 - 08:46:43 PDT)
    - Re: [AMBER] Using mopac in antechamber with Amber11/AmberTools 1.5 Baptiste Legrand (Fri Sep 07 2012 - 09:11:45 PDT)
[AMBER] installing RESP shomesankar bhunia (Fri Sep 07 2012 - 04:27:23 PDT)
- Re: [AMBER] installing RESP FyD (Fri Sep 07 2012 - 04:49:30 PDT)
  - Re: [AMBER] installing RESP shomesankar bhunia (Fri Sep 07 2012 - 05:45:29 PDT)
[AMBER] changing isotope in QM/MM simulation Hakansson P. (Fri Sep 07 2012 - 08:49:48 PDT)
- Re: [AMBER] changing isotope in QM/MM simulation Andreas Goetz (Mon Sep 10 2012 - 13:32:59 PDT)
[AMBER] SASA and temperature Aron Broom (Fri Sep 07 2012 - 10:05:10 PDT)
[AMBER] Small differences in cuda calculations Jonathan Gough (Fri Sep 07 2012 - 10:13:23 PDT)
- Re: [AMBER] Small differences in cuda calculations Scott Le Grand (Fri Sep 07 2012 - 10:18:30 PDT)
  - Re: [AMBER] Small differences in cuda calculations Jonathan Gough (Fri Sep 07 2012 - 10:23:22 PDT)
[AMBER] Molcular dynamics shomesankar bhunia (Sat Sep 08 2012 - 02:08:55 PDT)
- Re: [AMBER] Molcular dynamics David A. Case (Sat Sep 08 2012 - 06:38:41 PDT)
  - Re: [AMBER] Molcular dynamics shomesankar bhunia (Sat Sep 08 2012 - 08:46:23 PDT)
[AMBER] RESP_charge _derivation shomesankar bhunia (Sat Sep 08 2012 - 03:35:04 PDT)
- Re: [AMBER] RESP_charge _derivation FyD (Sat Sep 08 2012 - 23:02:55 PDT)
  - Re: [AMBER] RESP_charge _derivation Shomesankar Bhunia (Mon Sep 10 2012 - 12:49:39 PDT)
    - Re: [AMBER] RESP_charge _derivation FyD (Mon Sep 10 2012 - 22:21:46 PDT)
    - Re: [AMBER] RESP_charge _derivation Shomesankar Bhunia (Tue Sep 11 2012 - 03:37:04 PDT)
[AMBER] help amber rdf Yanyan ZHU (Sat Sep 08 2012 - 18:44:10 PDT)
- Re: [AMBER] help amber rdf Daniel Roe (Sat Sep 08 2012 - 21:09:26 PDT)
[AMBER] Using ff12SB force field in amber10 H. Chen (Sun Sep 09 2012 - 01:05:43 PDT)
- Re: [AMBER] Using ff12SB force field in amber10 David A. Case (Sun Sep 09 2012 - 14:36:43 PDT)
[AMBER] igb=7, 8 incompatible with the ILDN modifications of ff99SB Vlad Cojocaru (Mon Sep 10 2012 - 01:49:28 PDT)
- Re: [AMBER] igb=7, 8 incompatible with the ILDN modifications of ff99SB Carlos Simmerling (Mon Sep 10 2012 - 05:57:52 PDT)
  - Re: [AMBER] igb=7, 8 incompatible with the ILDN modifications of ff99SB Vlad Cojocaru (Mon Sep 10 2012 - 06:20:48 PDT)
    - Re: [AMBER] igb=7, 8 incompatible with the ILDN modifications of ff99SB Carlos Simmerling (Mon Sep 10 2012 - 06:25:54 PDT)
    - Re: [AMBER] igb=7, 8 incompatible with the ILDN modifications of ff99SB Vlad Cojocaru (Tue Sep 11 2012 - 06:14:32 PDT)
    - Re: [AMBER] igb=7, 8 incompatible with the ILDN modifications of ff99SB Jason Swails (Tue Sep 11 2012 - 06:50:12 PDT)
    - Re: [AMBER] igb=7, 8 incompatible with the ILDN modifications of ff99SB Vlad Cojocaru (Tue Sep 11 2012 - 07:15:29 PDT)
    - Re: [AMBER] igb=7, 8 incompatible with the ILDN modifications of ff99SB Vlad Cojocaru (Thu Oct 24 2013 - 07:35:17 PDT)
    - Re: [AMBER] igb=7, 8 incompatible with the ILDN modifications of ff99SB Jason Swails (Thu Oct 24 2013 - 07:52:44 PDT)
    - Re: [AMBER] igb=7, 8 incompatible with the ILDN modifications of ff99SB Hai Nguyen (Thu Sep 20 2012 - 14:25:46 PDT)
  - [AMBER] TI on Crambin, lacking bond in backbone Anna Bauß (Tue Sep 11 2012 - 02:18:24 PDT)
    - Re: [AMBER] TI on Crambin, lacking bond in backbone David A Case (Tue Sep 11 2012 - 05:24:44 PDT)
- Re: [AMBER] igb=7, 8 incompatible with the ILDN modifications of ff99SB Hai Nguyen (Thu Sep 20 2012 - 14:20:53 PDT)
[AMBER] visualizing normal modes jit mukherjee (Mon Sep 10 2012 - 02:31:10 PDT)
- Re: [AMBER] visualizing normal modes case (Mon Sep 10 2012 - 06:03:54 PDT)
[AMBER] point mutation - residue swap Jonathan Gough (Mon Sep 10 2012 - 10:24:55 PDT)
- Re: [AMBER] point mutation - residue swap Carlos Simmerling (Mon Sep 10 2012 - 10:30:47 PDT)
- [AMBER] RE : point mutation - residue swap ABEL Stephane 175950 (Mon Sep 10 2012 - 10:34:42 PDT)
  - Re: [AMBER] RE : point mutation - residue swap Jonathan Gough (Mon Sep 10 2012 - 10:39:23 PDT)
- Re: [AMBER] point mutation - residue swap FyD (Mon Sep 10 2012 - 11:48:04 PDT)
  - Re: [AMBER] point mutation - residue swap Carlos Simmerling (Mon Sep 10 2012 - 12:01:01 PDT)
    - Re: [AMBER] point mutation - residue swap Carlos Simmerling (Mon Sep 10 2012 - 12:17:16 PDT)
    - [AMBER] RE : point mutation - residue swap ABEL Stephane 175950 (Mon Sep 10 2012 - 12:38:25 PDT)
    - Re: [AMBER] point mutation - residue swap Carmenza Martinez (Mon Sep 10 2012 - 12:39:51 PDT)
    - Re: [AMBER] point mutation - residue swap Carmenza Martinez (Mon Sep 10 2012 - 12:43:27 PDT)
    - Re: [AMBER] point mutation - residue swap Jonathan Gough (Mon Sep 10 2012 - 13:30:36 PDT)
    - Re: [AMBER] point mutation - residue swap Aron Broom (Mon Sep 10 2012 - 14:53:45 PDT)
    - Re: [AMBER] point mutation - residue swap Carlos Simmerling (Mon Sep 10 2012 - 15:24:42 PDT)
    - Re: [AMBER] point mutation - residue swap Aron Broom (Mon Sep 10 2012 - 17:32:45 PDT)
    - Re: [AMBER] point mutation - residue swap vaibhav dixit (Mon Sep 10 2012 - 19:52:42 PDT)
    - Re: [AMBER] point mutation - residue swap Aron Broom (Mon Sep 10 2012 - 20:35:06 PDT)
    - Re: [AMBER] point mutation - residue swap Bill Ross (Mon Sep 10 2012 - 20:41:34 PDT)
    - Re: [AMBER] point mutation - residue swap Carlos Simmerling (Tue Sep 11 2012 - 02:50:52 PDT)
    - Re: [AMBER] point mutation - residue swap vaibhav dixit (Tue Sep 11 2012 - 03:06:11 PDT)
    - Re: [AMBER] point mutation - residue swap FyD (Tue Sep 11 2012 - 05:49:12 PDT)
    - Re: [AMBER] point mutation - residue swap Carlos Simmerling (Wed Sep 12 2012 - 10:20:15 PDT)
    - Re: [AMBER] point mutation - residue swap Rupesh K. Nanjunda (Wed Sep 12 2012 - 10:25:09 PDT)
    - Re: [AMBER] point mutation - residue swap FyD (Tue Sep 11 2012 - 00:24:53 PDT)
    - Re: [AMBER] point mutation - residue swap vaibhav dixit (Tue Sep 11 2012 - 01:29:29 PDT)
    - Re: [AMBER] point mutation - residue swap Carlos Simmerling (Wed Sep 12 2012 - 10:18:07 PDT)
[AMBER] cannot open input file during analysis Zalikha Ibrahim (Mon Sep 10 2012 - 15:12:31 PDT)
- Re: [AMBER] cannot open input file during analysis Jason Swails (Wed Sep 12 2012 - 05:33:42 PDT)
[AMBER] My input file Chris Chris (Mon Sep 10 2012 - 15:31:54 PDT)
- Re: [AMBER] My input file Ross Walker (Mon Sep 10 2012 - 13:49:23 PDT)
[AMBER] about md.out file thank you 黎永秀 (Mon Sep 10 2012 - 19:33:27 PDT)
- Re: [AMBER] about md.out file thank you zhouhaibin2008.ok (Mon Sep 10 2012 - 20:51:42 PDT)
[AMBER] Help for RDF Yanyan ZHU (Mon Sep 10 2012 - 19:48:05 PDT)
[AMBER] About error of min_qmmm.out JiYuan Liu (Mon Sep 10 2012 - 23:08:51 PDT)
- Re: [AMBER] About error of min_qmmm.out Andreas Goetz (Tue Sep 11 2012 - 10:04:19 PDT)
[AMBER] POL3 water model run error... 旭东肖 (Tue Sep 11 2012 - 03:34:32 PDT)
- Re: [AMBER] POL3 water model run error... David A Case (Fri Sep 14 2012 - 07:05:00 PDT)
[AMBER] NTB does not work for trajectory analysis with IMIN=5 kurisaki (Tue Sep 11 2012 - 05:20:27 PDT)
- Re: [AMBER] NTB does not work for trajectory analysis with IMIN=5 Jason Swails (Tue Sep 11 2012 - 05:45:38 PDT)
  - Re: [AMBER] NTB does not work for trajectory analysis with IMIN=5 kurisaki (Tue Sep 11 2012 - 06:08:08 PDT)
    - Re: [AMBER] NTB does not work for trajectory analysis with IMIN=5 Jason Swails (Tue Sep 11 2012 - 06:53:18 PDT)
    - Re: [AMBER] NTB does not work for trajectory analysis with IMIN=5 Daniel Roe (Tue Sep 11 2012 - 07:01:01 PDT)
    - Re: [AMBER] NTB does not work for trajectory analysis with IMIN=5 kurisaki (Tue Sep 11 2012 - 18:32:40 PDT)
    - Re: [AMBER] NTB does not work for trajectory analysis with IMIN=5 Daniel Roe (Wed Sep 12 2012 - 07:35:01 PDT)
[AMBER] Probably simple but, I'm stuck. Jonathan Gough (Tue Sep 11 2012 - 10:43:14 PDT)
- Re: [AMBER] Probably simple but, I'm stuck. Carmenza Martinez (Tue Sep 11 2012 - 11:03:55 PDT)
  - Re: [AMBER] Probably simple but, I'm stuck. Jonathan Gough (Tue Sep 11 2012 - 11:06:40 PDT)
  - Re: [AMBER] Probably simple but, I'm stuck. Sasha Buzko (Tue Sep 11 2012 - 11:07:39 PDT)
    - Re: [AMBER] Probably simple but, I'm stuck. Jonathan Gough (Tue Sep 11 2012 - 11:10:06 PDT)
    - Re: [AMBER] Probably simple but, I'm stuck. Jason Swails (Tue Sep 11 2012 - 11:31:20 PDT)
    - Re: [AMBER] Probably simple but, I'm stuck. Bill Ross (Tue Sep 11 2012 - 14:03:17 PDT)
- Re: [AMBER] Probably simple but, I'm stuck. case (Tue Sep 11 2012 - 17:24:27 PDT)
  - Re: [AMBER] Probably simple but, I'm stuck. Jonathan Gough (Wed Sep 12 2012 - 05:08:15 PDT)
    - Re: [AMBER] Probably simple but, I'm stuck. Jason Swails (Wed Sep 12 2012 - 05:31:43 PDT)
[AMBER] Problem (perhaps) with new precision model Fabrício Bracht (Tue Sep 11 2012 - 16:23:17 PDT)
- Re: [AMBER] Problem (perhaps) with new precision model Scott Le Grand (Tue Sep 11 2012 - 16:47:43 PDT)
- [AMBER] Problem with "make install" after "./configure -mpi -cuda gnu" Su, Shiquan (Wed Oct 03 2012 - 12:57:54 PDT)
  - Re: [AMBER] Problem with "make install" after "./configure -mpi -cuda gnu" Jason Swails (Wed Oct 03 2012 - 18:33:04 PDT)
    - Re: [AMBER] Problem with "make install" after "./configure -mpi -cuda gnu" Su, Shiquan (Thu Oct 04 2012 - 10:21:25 PDT)
    - Re: [AMBER] Problem with "make install" after "./configure -mpi -cuda gnu" Jason Swails (Thu Oct 04 2012 - 11:42:50 PDT)
    - Re: [AMBER] Problem with "make install" after "./configure -mpi -cuda gnu" Tru Huynh (Fri Oct 05 2012 - 00:42:03 PDT)
    - Re: [AMBER] Problem with "make install" after "./configure -mpi -cuda gnu" David A Case (Fri Oct 05 2012 - 05:13:04 PDT)
    - Re: [AMBER] Problem with "make install" after "./configure -mpi -cuda gnu" Su, Shiquan (Sun Oct 07 2012 - 14:35:48 PDT)
    - Re: [AMBER] Problem with "make install" after "./configure -mpi -cuda gnu" Jason Swails (Mon Oct 08 2012 - 03:37:18 PDT)
    - Re: [AMBER] Problem with "make install" after "./configure -mpi -cuda gnu" Tru Huynh (Mon Oct 08 2012 - 06:27:14 PDT)
    - [AMBER] Problem with "make install" after "./configure intel" Su, Shiquan (Tue Nov 13 2012 - 13:16:33 PST)
    - Re: [AMBER] Problem with "make install" after "./configure intel" Daniel Roe (Tue Nov 13 2012 - 13:25:59 PST)
Re: [AMBER] Using ff12SB force field in amber10 (David A. Case) H. Chen (Tue Sep 11 2012 - 18:04:33 PDT)
[AMBER] help about rdf Yanyan ZHU (Tue Sep 11 2012 - 18:36:12 PDT)
- Re: [AMBER] help about rdf Daniel Roe (Wed Sep 12 2012 - 08:18:54 PDT)
[AMBER] help for TMD Yanyan ZHU (Tue Sep 11 2012 - 20:41:03 PDT)
- Re: [AMBER] help for TMD Jason Swails (Wed Sep 12 2012 - 05:25:56 PDT)
[AMBER] Error in converstion of pdb to mol2 Anogna (Wed Sep 12 2012 - 01:09:47 PDT)
- Re: [AMBER] Error in converstion of pdb to mol2 David A Case (Wed Sep 12 2012 - 05:48:31 PDT)
  - Re: [AMBER] Error in converstion of pdb to mol2 Anogna (Wed Sep 12 2012 - 23:03:12 PDT)
    - Re: [AMBER] Error in converstion of pdb to mol2 Jason Swails (Thu Sep 13 2012 - 04:47:24 PDT)
    - Re: [AMBER] Error in converstion of pdb to mol2 Anogna (Thu Sep 13 2012 - 22:18:06 PDT)
    - Re: [AMBER] Error in converstion of pdb to mol2 David A Case (Fri Sep 14 2012 - 06:59:50 PDT)
[AMBER] presumed problem with SHAKEH: disappears on passing from CUDA version to normal Sander Emanuele Monza (Wed Sep 12 2012 - 02:19:19 PDT)
- Re: [AMBER] presumed problem with SHAKEH: disappears on passing from CUDA version to normal Sander Jason Swails (Wed Sep 12 2012 - 03:24:59 PDT)
- Re: [AMBER] presumed problem with SHAKEH: disappears on passing from CUDA version to normal Sander Scott Le Grand (Wed Sep 12 2012 - 07:21:29 PDT)
  - Re: [AMBER] presumed problem with SHAKEH: disappears on passing from CUDA version to normal Sander Jason Swails (Wed Sep 12 2012 - 08:36:56 PDT)
[AMBER] Cpptraj - Autoimage Fernando Martín García (Wed Sep 12 2012 - 06:11:14 PDT)
- Re: [AMBER] Cpptraj - Autoimage Daniel Roe (Wed Sep 12 2012 - 08:14:36 PDT)
  - Re: [AMBER] Cpptraj - Autoimage Fernando Martín García (Wed Sep 12 2012 - 23:28:45 PDT)
    - Re: [AMBER] Cpptraj - Autoimage Thomas Cheatham III (Thu Sep 13 2012 - 12:17:55 PDT)
[AMBER] Antechamber Buback, Clayton (S&T-Student) (Wed Sep 12 2012 - 12:25:39 PDT)
- Re: [AMBER] Antechamber David A Case (Thu Sep 13 2012 - 05:56:37 PDT)
  - Re: [AMBER] Antechamber Buback, Clayton (S&T-Student) (Tue Sep 18 2012 - 10:34:07 PDT)
    - Re: [AMBER] Antechamber David A Case (Thu Sep 20 2012 - 05:54:42 PDT)
    - Re: [AMBER] Antechamber Buback, Clayton (S&T-Student) (Wed Sep 26 2012 - 12:24:57 PDT)
    - Re: [AMBER] Antechamber David A Case (Wed Sep 26 2012 - 15:08:20 PDT)
[AMBER] meaning of columns in hbond output Yubo Fan (Wed Sep 12 2012 - 14:44:05 PDT)
- Re: [AMBER] meaning of columns in hbond output Daniel Roe (Wed Sep 12 2012 - 17:05:31 PDT)
[AMBER] to buy amber package KUMAR K M (10PHD0309) (Wed Sep 12 2012 - 21:51:27 PDT)
- Re: [AMBER] to buy amber package Jason Swails (Thu Sep 13 2012 - 04:45:55 PDT)
[AMBER] random number generator in pmemd.CUDA ? Marek Maly (Thu Sep 13 2012 - 01:10:52 PDT)
- Re: [AMBER] random number generator in pmemd.CUDA ? Jason Swails (Thu Sep 13 2012 - 04:27:13 PDT)
  - Re: [AMBER] random number generator in pmemd.CUDA ? Marek Maly (Thu Sep 13 2012 - 04:27:44 PDT)
[AMBER] MMPBSA.pl masks Chiara Pallara (Thu Sep 13 2012 - 05:24:39 PDT)
- Re: [AMBER] MMPBSA.pl masks Jason Swails (Thu Sep 13 2012 - 07:56:52 PDT)
  - Re: [AMBER] MMPBSA.pl masks Chiara Pallara (Thu Sep 13 2012 - 08:00:49 PDT)
    - Re: [AMBER] MMPBSA.pl masks Jason Swails (Thu Sep 13 2012 - 08:17:48 PDT)
    - Re: [AMBER] MMPBSA.pl masks Chiara Pallara (Thu Sep 13 2012 - 08:30:09 PDT)
    - Re: [AMBER] MMPBSA.pl masks Jason Swails (Thu Sep 13 2012 - 08:43:45 PDT)
[AMBER] constant-pH REMD Cheng-I Lee (Thu Sep 13 2012 - 06:36:17 PDT)
- Re: [AMBER] constant-pH REMD Jason Swails (Thu Sep 13 2012 - 07:38:21 PDT)
[AMBER] Help for rdf Yanyan ZHU (Thu Sep 13 2012 - 20:23:19 PDT)
- Re: [AMBER] Help for rdf Daniel Roe (Fri Sep 14 2012 - 15:36:04 PDT)
[AMBER] MMPBSA: standard deviation George Tzotzos (Fri Sep 14 2012 - 01:28:07 PDT)
- Re: [AMBER] MMPBSA: standard deviation Hannes Loeffler (Fri Sep 14 2012 - 01:58:43 PDT)
- Re: [AMBER] MMPBSA: standard deviation Jason Swails (Fri Sep 14 2012 - 04:43:39 PDT)
[AMBER] NMODE calculation using mmpbsa.py Dilraj LAMA (Fri Sep 14 2012 - 01:54:37 PDT)
- Re: [AMBER] NMODE calculation using mmpbsa.py Bill Miller III (Fri Sep 14 2012 - 04:15:28 PDT)
- Re: [AMBER] NMODE calculation using mmpbsa.py Dilraj LAMA (Sat Sep 15 2012 - 02:13:38 PDT)
[AMBER] GAFFLipid Parameters Gould, Ian R (Fri Sep 14 2012 - 04:21:36 PDT)
- Re: [AMBER] GAFFLipid Parameters Albert (Fri Sep 14 2012 - 05:39:25 PDT)
  - Re: [AMBER] GAFFLipid Parameters Dickson, Callum (Fri Sep 14 2012 - 06:10:54 PDT)
    - Re: [AMBER] GAFFLipid Parameters Albert (Fri Sep 14 2012 - 06:29:37 PDT)
    - Re: [AMBER] GAFFLipid Parameters Dickson, Callum (Fri Sep 14 2012 - 06:36:35 PDT)
    - Re: [AMBER] GAFFLipid Parameters Adrian Roitberg (Fri Sep 14 2012 - 06:39:11 PDT)
    - Re: [AMBER] GAFFLipid Parameters Dickson, Callum (Fri Sep 14 2012 - 06:44:57 PDT)
    - Re: [AMBER] GAFFLipid Parameters Adrian Roitberg (Fri Sep 14 2012 - 06:48:51 PDT)
    - Re: [AMBER] GAFFLipid Parameters Gould, Ian R (Fri Sep 14 2012 - 06:43:26 PDT)
    - Re: [AMBER] GAFFLipid Parameters Albert (Fri Sep 14 2012 - 07:13:21 PDT)
    - Re: [AMBER] GAFFLipid Parameters Ross Walker (Fri Sep 14 2012 - 09:01:05 PDT)
    - Re: [AMBER] GAFFLipid Parameters Albert (Wed Sep 19 2012 - 04:43:44 PDT)
[AMBER] query antechamber-reg Revthi Sanker (Fri Sep 14 2012 - 06:05:46 PDT)
- Re: [AMBER] query antechamber-reg David A Case (Fri Sep 14 2012 - 06:58:15 PDT)
- Re: [AMBER] query antechamber-reg Revthi Sanker (Fri Sep 14 2012 - 23:59:22 PDT)
  - Re: [AMBER] query antechamber-reg David A Case (Sat Sep 22 2012 - 05:51:58 PDT)
[AMBER] performance of pmed.cuda.MPI Jonathan Gough (Fri Sep 14 2012 - 11:40:33 PDT)
- Re: [AMBER] performance of pmed.cuda.MPI Scott Le Grand (Fri Sep 14 2012 - 11:46:28 PDT)
  - Re: [AMBER] performance of pmed.cuda.MPI Jonathan Gough (Fri Sep 14 2012 - 11:50:07 PDT)
  - Re: [AMBER] performance of pmed.cuda.MPI Tru Huynh (Thu Sep 20 2012 - 23:54:54 PDT)
    - Re: [AMBER] performance of pmed.cuda.MPI Gould, Ian R (Fri Sep 21 2012 - 01:04:58 PDT)
    - Re: [AMBER] performance of pmed.cuda.MPI Ross Walker (Fri Sep 21 2012 - 09:56:27 PDT)
    - Re: [AMBER] performance of pmed.cuda.MPI Jonathan Gough (Fri Sep 21 2012 - 10:09:11 PDT)
    - Re: [AMBER] performance of pmed.cuda.MPI Gould, Ian R (Fri Sep 21 2012 - 10:18:05 PDT)
    - Re: [AMBER] performance of pmed.cuda.MPI Ross Walker (Fri Sep 21 2012 - 10:22:28 PDT)
    - Re: [AMBER] performance of pmed.cuda.MPI Jonathan Gough (Fri Sep 21 2012 - 10:44:13 PDT)
    - Re: [AMBER] performance of pmed.cuda.MPI Ross Walker (Fri Sep 21 2012 - 10:51:01 PDT)
    - Re: [AMBER] performance of pmed.cuda.MPI Jonathan Gough (Fri Sep 21 2012 - 11:09:46 PDT)
    - Re: [AMBER] performance of pmed.cuda.MPI Ross Walker (Fri Sep 21 2012 - 11:15:12 PDT)
    - Re: [AMBER] performance of pmed.cuda.MPI Jonathan Gough (Fri Sep 21 2012 - 11:19:03 PDT)
    - Re: [AMBER] performance of pmed.cuda.MPI Tru Huynh (Sun Sep 23 2012 - 13:18:57 PDT)
[AMBER] Angle parameters not going after tleap Fabrício Bracht (Fri Sep 14 2012 - 12:49:47 PDT)
- Re: [AMBER] Angle parameters not going after tleap Ross Walker (Fri Sep 14 2012 - 12:59:39 PDT)
  - Re: [AMBER] Angle parameters not going after tleap Fabrício Bracht (Fri Sep 14 2012 - 13:10:38 PDT)
    - Re: [AMBER] Angle parameters not going after tleap Fabrício Bracht (Fri Sep 14 2012 - 13:13:21 PDT)
    - Re: [AMBER] Angle parameters not going after tleap Fabrício Bracht (Fri Sep 14 2012 - 13:16:54 PDT)
    - Re: [AMBER] Angle parameters not going after tleap Ben Roberts (Fri Sep 14 2012 - 13:35:53 PDT)
- Re: [AMBER] Angle parameters not going after tleap Jason Swails (Fri Sep 14 2012 - 13:35:33 PDT)
  - Re: [AMBER] Angle parameters not going after tleap Fabrício Bracht (Fri Sep 14 2012 - 13:51:14 PDT)
    - Re: [AMBER] Angle parameters not going after tleap Fabrício Bracht (Fri Sep 14 2012 - 14:09:47 PDT)
    - Re: [AMBER] Angle parameters not going after tleap Fabrício Bracht (Fri Sep 14 2012 - 15:14:15 PDT)
    - Re: [AMBER] Angle parameters not going after tleap Ben Roberts (Fri Sep 14 2012 - 17:06:53 PDT)
    - Re: [AMBER] Angle parameters not going after tleap Fabrício Bracht (Sun Sep 16 2012 - 07:25:08 PDT)
[AMBER] Antechamber Buback, Clayton (S&T-Student) (Fri Sep 14 2012 - 13:52:34 PDT)
- Re: [AMBER] Antechamber David A Case (Sat Sep 15 2012 - 08:45:44 PDT)
[AMBER] Atomtype for negatively charged O Jesper Sørensen (Fri Sep 14 2012 - 16:37:06 PDT)
- [AMBER] Atomtype for negatively charged O, part 2 Jesper Sørensen (Mon Sep 17 2012 - 09:47:59 PDT)
  - Re: [AMBER] Atomtype for negatively charged O, part 2 FyD (Mon Sep 17 2012 - 23:26:59 PDT)
    - Re: [AMBER] Atomtype for negatively charged O, part 2 Brent Krueger (Tue Sep 18 2012 - 04:22:10 PDT)
    - Re: [AMBER] Atomtype for negatively charged O, part 2 Jesper Sørensen (Tue Sep 18 2012 - 15:44:40 PDT)
    - Re: [AMBER] Atomtype for negatively charged O, part 2 FyD (Wed Sep 19 2012 - 12:39:39 PDT)
    - Re: [AMBER] Atomtype for negatively charged O, part 2 Jesper Sørensen (Wed Sep 19 2012 - 12:56:37 PDT)
    - Re: [AMBER] Atomtype for negatively charged O, part 2 FyD (Wed Sep 19 2012 - 22:03:19 PDT)
[AMBER] query- antechamber Revthi Sanker (Fri Sep 14 2012 - 23:55:28 PDT)
Re: [AMBER] AMBER Digest, Vol 274, Issue 1 Dilraj LAMA (Sat Sep 15 2012 - 02:10:56 PDT)
- Re: [AMBER] AMBER Digest, Vol 274, Issue 1 Jason Swails (Sat Sep 15 2012 - 05:48:37 PDT)
[AMBER] Problem in inpcrd file while running minimization Jitesh Doshi (Sat Sep 15 2012 - 03:14:07 PDT)
- Re: [AMBER] Problem in inpcrd file while running minimization Jason Swails (Sat Sep 15 2012 - 04:46:23 PDT)
  - Re: [AMBER] Problem in inpcrd file while running minimization Jitesh Doshi (Sat Sep 15 2012 - 05:11:48 PDT)
[AMBER] GAMESS_RESP Shomesankar Bhunia (Sat Sep 15 2012 - 05:15:25 PDT)
- Re: [AMBER] GAMESS_RESP FyD (Sat Sep 15 2012 - 06:00:23 PDT)
  - Re: [AMBER] GAMESS_RESP Shomesankar Bhunia (Sat Sep 15 2012 - 10:08:21 PDT)
    - Re: [AMBER] GAMESS_RESP FyD (Sun Sep 16 2012 - 00:54:08 PDT)
    - Re: [AMBER] GAMESS_RESP Shomesankar Bhunia (Sun Sep 16 2012 - 21:27:07 PDT)
[AMBER] GAMESS Shomesankar Bhunia (Sat Sep 15 2012 - 05:23:27 PDT)
- Re: [AMBER] GAMESS Daniel Sindhikara (Sat Sep 15 2012 - 17:39:08 PDT)
- Re: [AMBER] GAMESS FyD (Sun Sep 16 2012 - 01:17:25 PDT)
[AMBER] meaning of various columns of closest output in cpptraj Asmita Gupta (Sat Sep 15 2012 - 10:07:25 PDT)
- Re: [AMBER] meaning of various columns of closest output in cpptraj Daniel Roe (Sat Sep 15 2012 - 14:42:14 PDT)
[AMBER] prmtop_inpcrd_ error Shomesankar Bhunia (Sat Sep 15 2012 - 12:51:16 PDT)
- Re: [AMBER] prmtop_inpcrd_ error David A Case (Sun Sep 16 2012 - 09:35:07 PDT)
  - Re: [AMBER] prmtop_inpcrd_ error Shomesankar Bhunia (Sun Sep 16 2012 - 21:28:51 PDT)
[AMBER] will ACEMD accelerate Amber? Albert (Sun Sep 16 2012 - 01:22:54 PDT)
- Re: [AMBER] will ACEMD accelerate Amber? Ross Walker (Sun Sep 16 2012 - 10:51:26 PDT)
[AMBER] hello. 이상민 (Sun Sep 16 2012 - 21:02:17 PDT)
[AMBER] can DSSP program give more information vaibhav dixit (Mon Sep 17 2012 - 00:04:08 PDT)
- Re: [AMBER] can DSSP program give more information Daniel Roe (Mon Sep 17 2012 - 05:38:23 PDT)
  - Re: [AMBER] can DSSP program give more information vaibhav dixit (Mon Sep 17 2012 - 20:41:30 PDT)
    - Re: [AMBER] can DSSP program give more information Daniel Roe (Tue Sep 18 2012 - 06:04:19 PDT)
    - Re: [AMBER] can DSSP program give more information vaibhav dixit (Wed Sep 19 2012 - 23:14:48 PDT)
    - Re: [AMBER] can DSSP program give more information vaibhav dixit (Wed Sep 19 2012 - 23:19:24 PDT)
    - Re: [AMBER] can DSSP program give more information Daniel Roe (Thu Sep 20 2012 - 07:17:51 PDT)
    - Re: [AMBER] can DSSP program give more information vaibhav dixit (Mon Sep 24 2012 - 04:48:45 PDT)
[AMBER] help for sending figures Yanyan ZHU (Mon Sep 17 2012 - 01:18:30 PDT)
- Re: [AMBER] help for sending figures Daniel Roe (Mon Sep 17 2012 - 05:31:15 PDT)
[AMBER] MMPBSA per-residue Soumya Lipsa Rath (Mon Sep 17 2012 - 01:43:03 PDT)
- Re: [AMBER] MMPBSA per-residue Bill Miller III (Mon Sep 17 2012 - 06:13:16 PDT)
  - Re: [AMBER] MMPBSA per-residue Soumya Lipsa Rath (Mon Sep 17 2012 - 06:58:37 PDT)
  - Re: [AMBER] MMPBSA per-residue Åge Skjevik (Thu Sep 20 2012 - 08:08:27 PDT)
[AMBER] PMEMD and Steered MD Ali M. Naserian-Nik (Mon Sep 17 2012 - 02:42:51 PDT)
[AMBER] AMBER12 Manual: igb=8 in pmemd Marc van der Kamp (Mon Sep 17 2012 - 03:16:20 PDT)
- Re: [AMBER] AMBER12 Manual: igb=8 in pmemd Jason Swails (Mon Sep 17 2012 - 09:03:02 PDT)
[AMBER] Periodicity error in parmtop file Shomesankar Bhunia (Mon Sep 17 2012 - 03:27:44 PDT)
- Re: [AMBER] Periodicity error in parmtop file Carlos Simmerling (Mon Sep 17 2012 - 03:39:08 PDT)
  - Re: [AMBER] Periodicity error in parmtop file Shomesankar Bhunia (Mon Sep 17 2012 - 04:01:20 PDT)
    - Re: [AMBER] Periodicity error in parmtop file David A Case (Mon Sep 17 2012 - 08:40:57 PDT)
    - Re: [AMBER] Periodicity error in parmtop file Jason Swails (Mon Sep 17 2012 - 09:00:59 PDT)
    - Re: [AMBER] Periodicity error in parmtop file Shomesankar Bhunia (Tue Sep 18 2012 - 01:12:49 PDT)
    - Re: [AMBER] Periodicity error in parmtop file Jason Swails (Tue Sep 18 2012 - 06:05:20 PDT)
    - Re: [AMBER] Periodicity error in parmtop file Shomesankar Bhunia (Tue Sep 18 2012 - 00:33:06 PDT)
    - Re: [AMBER] Periodicity error in parmtop file Shomesankar Bhunia (Tue Sep 18 2012 - 00:44:45 PDT)
[AMBER] pyroglutamic acid parameters houcemeddine othman (Mon Sep 17 2012 - 03:44:38 PDT)
[AMBER] Antechamber: generating prep file Rajeswari A. (Mon Sep 17 2012 - 06:38:57 PDT)
- Re: [AMBER] Antechamber: generating prep file David A Case (Mon Sep 17 2012 - 09:19:19 PDT)
  - Re: [AMBER] Antechamber: generating prep file Rajeswari A. (Tue Sep 18 2012 - 00:30:17 PDT)
[AMBER] Question with mass weighted covariance matrix in ptraj Ganesh Kamath (Mon Sep 17 2012 - 12:55:07 PDT)
- Re: [AMBER] Question with mass weighted covariance matrix in ptraj Daniel Roe (Mon Sep 17 2012 - 15:53:34 PDT)
  - Re: [AMBER] Question with mass weighted covariance matrix in ptraj Ganesh Kamath (Mon Sep 17 2012 - 17:12:22 PDT)
[AMBER] Error with umbrella sampling Fabrício Bracht (Mon Sep 17 2012 - 13:01:02 PDT)
- Re: [AMBER] Error with umbrella sampling Brian Radak (Mon Sep 17 2012 - 13:27:45 PDT)
  - Re: [AMBER] Error with umbrella sampling Fabrício Bracht (Mon Sep 17 2012 - 13:54:23 PDT)
    - Re: [AMBER] Error with umbrella sampling David A Case (Tue Sep 18 2012 - 15:32:07 PDT)
- Re: [AMBER] Error with umbrella sampling David A Case (Tue Sep 18 2012 - 18:32:32 PDT)
  - Re: [AMBER] Error with umbrella sampling Fabrício Bracht (Tue Sep 18 2012 - 19:25:37 PDT)
    - Re: [AMBER] Error with umbrella sampling Jason Swails (Tue Sep 18 2012 - 19:55:20 PDT)
    - Re: [AMBER] Error with umbrella sampling Fabrício Bracht (Tue Sep 18 2012 - 22:26:43 PDT)
    - Re: [AMBER] Error with umbrella sampling Mo Chen (Tue Sep 18 2012 - 22:41:16 PDT)
    - Re: [AMBER] Error with umbrella sampling Jason Swails (Wed Sep 19 2012 - 06:53:36 PDT)
    - Re: [AMBER] Error with umbrella sampling Fabrício Bracht (Wed Sep 19 2012 - 10:21:33 PDT)
    - Re: [AMBER] Error with umbrella sampling Niel Henriksen (Wed Sep 19 2012 - 10:24:57 PDT)
    - Re: [AMBER] Error with umbrella sampling Jason Swails (Wed Sep 19 2012 - 10:47:30 PDT)
    - Re: [AMBER] Error with umbrella sampling Fabrício Bracht (Wed Sep 19 2012 - 12:12:34 PDT)
[AMBER] cudaMemcpy GpuBuffer error in pmemd.cuda Fabrício Bracht (Mon Sep 17 2012 - 13:46:27 PDT)
- Re: [AMBER] cudaMemcpy GpuBuffer error in pmemd.cuda M. L. Dodson (Mon Sep 17 2012 - 14:28:09 PDT)
  - Re: [AMBER] cudaMemcpy GpuBuffer error in pmemd.cuda Fabrício Bracht (Mon Sep 17 2012 - 14:55:02 PDT)
    - Re: [AMBER] cudaMemcpy GpuBuffer error in pmemd.cuda Fabrício Bracht (Tue Sep 18 2012 - 10:37:59 PDT)
    - Re: [AMBER] cudaMemcpy GpuBuffer error in pmemd.cuda Fabrício Bracht (Thu Sep 20 2012 - 08:39:43 PDT)
    - Re: [AMBER] cudaMemcpy GpuBuffer error in pmemd.cuda Ross Walker (Thu Sep 20 2012 - 10:08:57 PDT)
    - Re: [AMBER] cudaMemcpy GpuBuffer error in pmemd.cuda Fabrício Bracht (Thu Sep 20 2012 - 14:36:13 PDT)
    - Re: [AMBER] cudaMemcpy GpuBuffer error in pmemd.cuda Ross Walker (Thu Sep 20 2012 - 14:45:22 PDT)
    - Re: [AMBER] cudaMemcpy GpuBuffer error in pmemd.cuda Fabrício Bracht (Thu Sep 20 2012 - 15:04:53 PDT)
[AMBER] why in TI softcore potential part, 0.01 < clamda < 0.99 ? psu4.uic.edu (Mon Sep 17 2012 - 16:25:22 PDT)
- Re: [AMBER] why in TI softcore potential part, 0.01 < clamda < 0.99 ? Jason Swails (Mon Sep 17 2012 - 20:28:48 PDT)
 - Re: [AMBER] why in TI softcore potential part, 0.01 < clamda < 0.99 ? Brian Radak (Tue Sep 18 2012 - 06:11:34 PDT)
 - Re: [AMBER] why in TI softcore potential part, 0.01 < clamda < 0.99 ? psu4.uic.edu (Mon Sep 24 2012 - 11:08:25 PDT)
[AMBER] help for rdf Yanyan ZHU (Mon Sep 17 2012 - 18:49:25 PDT)
- Re: [AMBER] help for rdf Daniel Roe (Mon Sep 17 2012 - 19:39:18 PDT)
[AMBER] question about nmode 이상민 (Mon Sep 17 2012 - 23:00:47 PDT)
- Re: [AMBER] question about nmode David A Case (Thu Sep 20 2012 - 05:52:05 PDT)
[AMBER] Error while preparing Docked complex for Minimization Sumra Wajid Abbasi 30-FBAS/MSBI/F09 (Tue Sep 18 2012 - 00:15:22 PDT)
- Re: [AMBER] Error while preparing Docked complex for Minimization Daniel Roe (Tue Sep 18 2012 - 04:56:56 PDT)
  - Re: [AMBER] Error while preparing Docked complex for Minimization Sumra Wajid Abbasi 30-FBAS/MSBI/F09 (Tue Sep 18 2012 - 06:05:49 PDT)
[AMBER] help for analysising my pictures Yanyan ZHU (Tue Sep 18 2012 - 00:43:51 PDT)
[AMBER] Monitoring Torsion Angles during MD Simulations Γιώργος Λαμπρινίδης (Tue Sep 18 2012 - 04:40:28 PDT)
- Re: [AMBER] Monitoring Torsion Angles during MD Simulations Dickson, Callum (Tue Sep 18 2012 - 05:48:05 PDT)
  - Re: [AMBER] Monitoring Torsion Angles during MD Simulations Daniel Sindhikara (Tue Sep 18 2012 - 05:58:03 PDT)
  - Re: [AMBER] Monitoring Torsion Angles during MD Simulations Giorgos Lamprinidis (Tue Sep 18 2012 - 06:05:57 PDT)
[AMBER] assigning FFT grids Brian Radak (Tue Sep 18 2012 - 07:25:11 PDT)
- Re: [AMBER] assigning FFT grids Matthew Zwier (Tue Sep 18 2012 - 12:54:41 PDT)
[AMBER] Tesla or GTX? Albert (Tue Sep 18 2012 - 07:36:00 PDT)
- Re: [AMBER] Tesla or GTX? Ross Walker (Tue Sep 18 2012 - 09:15:29 PDT)
  - Re: [AMBER] Tesla or GTX? Albert (Tue Sep 18 2012 - 09:44:49 PDT)
[AMBER] TI input files: tleap adds unwanted hydrogen to a residue Kepa K. Burusco (Tue Sep 18 2012 - 11:51:30 PDT)
- Re: [AMBER] TI input files: tleap adds unwanted hydrogen to a residue Jason Swails (Tue Sep 18 2012 - 12:41:01 PDT)
[AMBER] About Langevin dynamics algarithm Mo Chen (Tue Sep 18 2012 - 12:28:44 PDT)
- Re: [AMBER] About Langevin dynamics algarithm Brian Radak (Tue Sep 18 2012 - 12:50:21 PDT)
- Re: [AMBER] About Langevin dynamics algarithm David A Case (Thu Sep 20 2012 - 05:56:11 PDT)
  - Re: [AMBER] About Langevin dynamics algarithm Mo Chen (Thu Sep 20 2012 - 09:10:22 PDT)
    - Re: [AMBER] About Langevin dynamics algarithm Mo Chen (Thu Sep 20 2012 - 09:40:09 PDT)
    - Re: [AMBER] About Langevin dynamics algarithm Brian Radak (Thu Sep 20 2012 - 10:03:32 PDT)
    - Re: [AMBER] About Langevin dynamics algarithm Mo Chen (Thu Sep 20 2012 - 10:17:09 PDT)
    - Re: [AMBER] About Langevin dynamics algarithm Brian Radak (Thu Sep 20 2012 - 11:06:34 PDT)
    - Re: [AMBER] About Langevin dynamics algarithm Mo Chen (Thu Sep 20 2012 - 12:49:50 PDT)
    - Re: [AMBER] About Langevin dynamics algarithm Brian Radak (Thu Sep 20 2012 - 13:19:55 PDT)
[AMBER] nvidia settings cuda jobs with pbs? Jonathan Gough (Tue Sep 18 2012 - 14:44:38 PDT)
- Re: [AMBER] nvidia settings cuda jobs with pbs? Robert Crovella (Wed Sep 19 2012 - 12:20:38 PDT)
  - Re: [AMBER] nvidia settings cuda jobs with pbs? Jonathan Gough (Wed Sep 19 2012 - 13:06:00 PDT)
[AMBER] amber 12 installation bmartini (Tue Sep 18 2012 - 19:00:29 PDT)
- Re: [AMBER] amber 12 installation Ross Walker (Tue Sep 18 2012 - 19:21:01 PDT)
[AMBER] General question about AmberTools with older Amber Zalikha Ibrahim (Tue Sep 18 2012 - 19:07:07 PDT)
- Re: [AMBER] General question about AmberTools with older Amber Ross Walker (Tue Sep 18 2012 - 19:23:50 PDT)
[AMBER] notes on mountain lion istall and a question Jonathan Gough (Tue Sep 18 2012 - 19:15:40 PDT)
- Re: [AMBER] notes on mountain lion istall and a question Ross Walker (Tue Sep 18 2012 - 19:32:14 PDT)
[AMBER] rdf1.gif Yanyan ZHU (Tue Sep 18 2012 - 19:57:03 PDT)
[AMBER] vlimit exceeded for step 0 rosy stone (Tue Sep 18 2012 - 22:32:36 PDT)
- Re: [AMBER] vlimit exceeded for step 0 Daniel Roe (Wed Sep 19 2012 - 04:58:17 PDT)
[AMBER] IDECOMP does not work with NTB>0 and IMIN=5 ? kurisaki (Wed Sep 19 2012 - 00:50:14 PDT)
- Re: [AMBER] IDECOMP does not work with NTB>0 and IMIN=5 ? kurisaki (Wed Sep 19 2012 - 19:00:06 PDT)
[AMBER] Loading across GPUs Adam Jion (Wed Sep 19 2012 - 02:57:38 PDT)
- Re: [AMBER] Loading across GPUs Jason Swails (Wed Sep 19 2012 - 05:50:22 PDT)
  - Re: [AMBER] Loading across GPUs Scott Le Grand (Wed Sep 19 2012 - 11:18:16 PDT)
    - Re: [AMBER] Loading across GPUs Duke, Robert E Jr (Wed Sep 19 2012 - 12:01:29 PDT)
    - Re: [AMBER] Loading across GPUs Duke, Robert E Jr (Wed Sep 19 2012 - 12:03:41 PDT)
    - Re: [AMBER] Loading across GPUs Scott Le Grand (Wed Sep 19 2012 - 14:38:55 PDT)
    - Re: [AMBER] Loading across GPUs Duke, Robert E Jr (Wed Sep 19 2012 - 15:30:20 PDT)
[AMBER] Amber tutorial Chiara Pallara (Wed Sep 19 2012 - 05:03:17 PDT)
- Re: [AMBER] Amber tutorial Jason Swails (Wed Sep 19 2012 - 05:20:34 PDT)
[AMBER] need help to generate parameter file for a small molecule which is covalently bound to the main chain of the protein ARP ARP (Wed Sep 19 2012 - 05:21:52 PDT)
- Re: [AMBER] need help to generate parameter file for a small molecule which is covalently bound to the main chain of the protein FyD (Wed Sep 19 2012 - 12:42:17 PDT)
[AMBER] Questions regarding MMPBSA.py Dilraj LAMA (Wed Sep 19 2012 - 05:27:12 PDT)
- Re: [AMBER] Questions regarding MMPBSA.py Bill Miller III (Wed Sep 19 2012 - 06:04:17 PDT)
- Re: [AMBER] Questions regarding MMPBSA.py Jason Swails (Wed Sep 19 2012 - 06:48:16 PDT)
[AMBER] MMPBSA.py on single snapshot Kasam, Vinod (Wed Sep 19 2012 - 13:44:14 PDT)
- Re: [AMBER] MMPBSA.py on single snapshot Jason Swails (Wed Sep 19 2012 - 14:20:59 PDT)
  - Re: [AMBER] MMPBSA.py on single snapshot Kasam, Vinod (Wed Sep 19 2012 - 15:25:13 PDT)
[AMBER] NMR pmemd.cuda input error Larry Olson (Wed Sep 19 2012 - 13:57:37 PDT)
- Re: [AMBER] NMR pmemd.cuda input error Jason Swails (Wed Sep 19 2012 - 14:18:01 PDT)
[AMBER] IMIN=5 does not work with IDECOMP>0 under NTB=1? kurisaki (Wed Sep 19 2012 - 19:49:00 PDT)
- Re: [AMBER] IMIN=5 does not work with IDECOMP>0 under NTB=1? Jason Swails (Wed Sep 19 2012 - 20:27:03 PDT)
[AMBER] performance marawan hussain (Wed Sep 19 2012 - 20:43:40 PDT)
- Re: [AMBER] performance Jason Swails (Wed Sep 19 2012 - 20:59:39 PDT)
  - Re: [AMBER] performance marawan hussain (Wed Sep 19 2012 - 22:50:50 PDT)
    - Re: [AMBER] performance Jason Swails (Thu Sep 20 2012 - 04:33:44 PDT)
    - Re: [AMBER] performance Ross Walker (Thu Sep 20 2012 - 09:58:34 PDT)
[AMBER] RDF Yanyan MENG (Thu Sep 20 2012 - 00:01:06 PDT)
- Re: [AMBER] RDF Daniel Roe (Thu Sep 20 2012 - 08:50:26 PDT)
[AMBER] MMPBSA.py per-residue decomposition Chiara Pallara (Thu Sep 20 2012 - 01:19:35 PDT)
- Re: [AMBER] MMPBSA.py per-residue decomposition Jason Swails (Thu Sep 20 2012 - 04:38:56 PDT)
  - Re: [AMBER] MMPBSA.py per-residue decomposition Chiara Pallara (Fri Sep 21 2012 - 02:06:00 PDT)
[AMBER] modified nucleotide Krisztina Feher (Thu Sep 20 2012 - 04:28:34 PDT)
- Re: [AMBER] modified nucleotide FyD (Thu Sep 20 2012 - 08:53:53 PDT)
  - Re: [AMBER] modified nucleotide Carlos Simmerling (Thu Sep 20 2012 - 08:59:39 PDT)
    - Re: [AMBER] modified nucleotide Krisztina Feher (Thu Sep 20 2012 - 12:32:16 PDT)
  - Re: [AMBER] modified nucleotide Krisztina Feher (Thu Sep 20 2012 - 12:22:55 PDT)
    - Re: [AMBER] modified nucleotide FyD (Thu Sep 20 2012 - 13:04:21 PDT)
[AMBER] How can I use mixing SCEE values in NAB? 양지현 (Thu Sep 20 2012 - 04:58:45 PDT)
- Re: [AMBER] How can I use mixing SCEE values in NAB? Jason Swails (Thu Sep 20 2012 - 07:06:04 PDT)
[AMBER] Difference of results between MMPBSA.py and NAB. Sangmin Lee (Thu Sep 20 2012 - 06:17:30 PDT)
- Re: [AMBER] Difference of results between MMPBSA.py and NAB. Jason Swails (Thu Sep 20 2012 - 06:39:49 PDT)
[AMBER] Difference of results between MMPBSA.py and NAB.(adjusted datas) Sangmin Lee (Thu Sep 20 2012 - 07:13:45 PDT)
- Re: [AMBER] Difference of results between MMPBSA.py and NAB.(adjusted datas) Jason Swails (Thu Sep 20 2012 - 07:41:57 PDT)
[AMBER] PMEMD and Steered MD with an Additional Restraint Ali M. Naserian-Nik (Thu Sep 20 2012 - 09:45:12 PDT)
- Re: [AMBER] PMEMD and Steered MD with an Additional Restraint Jason Swails (Thu Sep 20 2012 - 10:25:20 PDT)
[AMBER] PM3 instead of AM1 in ANTECHAMBER? Shahoei, Seyyedehrezvan (Thu Sep 20 2012 - 10:21:58 PDT)
- Re: [AMBER] PM3 instead of AM1 in ANTECHAMBER? David A Case (Thu Sep 20 2012 - 13:20:01 PDT)
[AMBER] Create a solution davide.savy.unina.it (Thu Sep 20 2012 - 12:24:03 PDT)
- Re: [AMBER] Create a solution Jason Swails (Thu Sep 20 2012 - 12:33:00 PDT)
- Re: [AMBER] Create a solution David A Case (Thu Sep 20 2012 - 13:23:02 PDT)
[AMBER] performance marawan hussain (Thu Sep 20 2012 - 18:14:17 PDT)
[AMBER] performance marawan hussain (Thu Sep 20 2012 - 18:14:56 PDT)
- Re: [AMBER] performance Jason Swails (Thu Sep 20 2012 - 20:49:54 PDT)
[AMBER] performance marawan hussain (Thu Sep 20 2012 - 22:51:22 PDT)
- Re: [AMBER] performance Jason Swails (Fri Sep 21 2012 - 05:28:29 PDT)
[AMBER] Fermi and Kepler cards running in parallel Adam Jion (Fri Sep 21 2012 - 17:02:23 PDT)
- Re: [AMBER] Fermi and Kepler cards running in parallel Jason Swails (Fri Sep 21 2012 - 22:00:21 PDT)
  - Re: [AMBER] Fermi and Kepler cards running in parallel Ross Walker (Sat Sep 22 2012 - 10:30:28 PDT)
[AMBER] performance marawan hussain (Sat Sep 22 2012 - 19:53:45 PDT)
- Re: [AMBER] performance Jason Swails (Sat Sep 22 2012 - 20:15:13 PDT)
[AMBER] performance marawan hussain (Sat Sep 22 2012 - 20:32:56 PDT)
[AMBER] vlimit exceeded for step 0; vmax********** rosy stone (Sat Sep 22 2012 - 23:32:19 PDT)
- Re: [AMBER] vlimit exceeded for step 0; vmax********** Jason Swails (Sun Sep 23 2012 - 00:13:56 PDT)
[AMBER] MTK++ Error: no active site found Francesco Pietra (Sun Sep 23 2012 - 03:08:31 PDT)
- Re: [AMBER] MTK++ Error: no active site found Ben Roberts (Sun Sep 23 2012 - 14:24:53 PDT)
  - Re: [AMBER] MTK++ Error: no active site found Francesco Pietra (Sun Sep 23 2012 - 15:19:37 PDT)
    - Re: [AMBER] MTK++ Error: no active site found Ben Roberts (Sun Sep 23 2012 - 21:43:47 PDT)
    - Re: [AMBER] MTK++ Error: no active site found Francesco Pietra (Sun Sep 23 2012 - 23:47:04 PDT)
    - [AMBER] Fwd: MTK++ Error: no active site found Francesco Pietra (Mon Sep 24 2012 - 02:40:44 PDT)
    - Re: [AMBER] MTK++ Error: no active site found Ben Roberts (Tue Sep 25 2012 - 17:02:50 PDT)
    - Re: [AMBER] MTK++ Error: no active site found Francesco Pietra (Tue Sep 25 2012 - 22:16:23 PDT)
    - Re: [AMBER] MTK++ Error: no active site found Ben Roberts (Wed Sep 26 2012 - 14:10:03 PDT)
[AMBER] cuda Mary Varughese (Sun Sep 23 2012 - 21:03:07 PDT)
- Re: [AMBER] cuda filip fratev (Sun Sep 23 2012 - 22:38:54 PDT)
  - Re: [AMBER] cuda Mary Varughese (Mon Sep 24 2012 - 07:41:35 PDT)
    - Re: [AMBER] cuda Deák Robert (Mon Sep 24 2012 - 07:57:13 PDT)
    - Re: [AMBER] cuda Ross Walker (Mon Sep 24 2012 - 09:08:06 PDT)
    - Re: [AMBER] cuda Mary Varughese (Mon Sep 24 2012 - 10:52:24 PDT)
    - Re: [AMBER] cuda Daniel Roe (Mon Sep 24 2012 - 11:56:35 PDT)
    - Re: [AMBER] cuda Robert Crovella (Mon Sep 24 2012 - 15:17:42 PDT)
    - Re: [AMBER] cuda Mary Varughese (Mon Sep 24 2012 - 21:48:23 PDT)
    - Re: [AMBER] cuda Jason Swails (Tue Sep 25 2012 - 04:30:15 PDT)
    - Re: [AMBER] cuda Mary Varughese (Fri Sep 28 2012 - 09:22:49 PDT)
- Re: [AMBER] cuda Deák Robert (Mon Sep 24 2012 - 01:24:42 PDT)
[AMBER] Problem in nmode analysis of single water molecule by MMPBSA.py Sanjib Paul (Mon Sep 24 2012 - 04:20:11 PDT)
- Re: [AMBER] Problem in nmode analysis of single water molecule by MMPBSA.py Jason Swails (Mon Sep 24 2012 - 04:33:44 PDT)
  - Re: [AMBER] Problem in nmode analysis of single water molecule by MMPBSA.py David A Case (Mon Sep 24 2012 - 06:05:12 PDT)
[AMBER] bugfix9 Nadeem A. Vellore (Mon Sep 24 2012 - 13:15:25 PDT)
- Re: [AMBER] bugfix9 Jason Swails (Mon Sep 24 2012 - 14:33:23 PDT)
[AMBER] Could not open mdcrd file with mode (r) Zalikha Ibrahim (Mon Sep 24 2012 - 16:56:40 PDT)
- Re: [AMBER] Could not open mdcrd file with mode (r) Daniel Roe (Mon Sep 24 2012 - 19:56:17 PDT)
  - Re: [AMBER] Could not open mdcrd file with mode (r) Bill Ross (Mon Sep 24 2012 - 20:13:27 PDT)
    - Re: [AMBER] Could not open mdcrd file with mode (r) Zalikha Ibrahim (Tue Sep 25 2012 - 01:31:19 PDT)
    - Re: [AMBER] Could not open mdcrd file with mode (r) Jason Swails (Tue Sep 25 2012 - 04:24:20 PDT)
    - Re: [AMBER] Could not open mdcrd file with mode (r) Bill Ross (Tue Sep 25 2012 - 16:56:29 PDT)
    - Re: [AMBER] Could not open mdcrd file with mode (r) Gannett, Peter (Tue Sep 25 2012 - 17:34:42 PDT)
    - Re: [AMBER] Could not open mdcrd file with mode (r) Zalikha Ibrahim (Wed Sep 26 2012 - 02:30:22 PDT)
    - Re: [AMBER] Could not open mdcrd file with mode (r) Zalikha Ibrahim (Wed Sep 26 2012 - 02:19:04 PDT)
    - Re: [AMBER] Could not open mdcrd file with mode (r) Daniel Roe (Wed Sep 26 2012 - 07:36:54 PDT)
    - Re: [AMBER] Could not open mdcrd file with mode (r) Zalikha Ibrahim (Wed Sep 26 2012 - 19:53:24 PDT)
    - Re: [AMBER] Could not open mdcrd file with mode (r) Jason Swails (Thu Sep 27 2012 - 04:27:48 PDT)
    - Re: [AMBER] Could not open mdcrd file with mode (r) Bill Ross (Tue Sep 25 2012 - 16:48:22 PDT)
    - Re: [AMBER] Could not open mdcrd file with mode (r) Zalikha Ibrahim (Wed Sep 26 2012 - 02:24:16 PDT)
    - Re: [AMBER] Could not open mdcrd file with mode (r) Bill Ross (Thu Sep 27 2012 - 15:08:53 PDT)
    - [AMBER] Problem with PM6 in sqm Wei Lin (Thu Sep 27 2012 - 16:45:24 PDT)
    - Re: [AMBER] Problem with PM6 in sqm Gerald Monard (Fri Sep 28 2012 - 01:58:06 PDT)
    - Re: [AMBER] Problem with PM6 in sqm Gerald Monard (Fri Sep 28 2012 - 07:09:26 PDT)
    - Re: [AMBER] Problem with PM6 in sqm Matthew Zwier (Fri Sep 28 2012 - 08:50:40 PDT)
    - Re: [AMBER] Problem with PM6 in sqm Wei Lin (Fri Sep 28 2012 - 10:00:08 PDT)
    - Re: [AMBER] Problem with PM6 in sqm Brian Radak (Fri Sep 28 2012 - 10:54:09 PDT)
    - Re: [AMBER] Problem with PM6 in sqm Andreas Goetz (Fri Sep 28 2012 - 15:10:35 PDT)
    - Re: [AMBER] Could not open mdcrd file with mode (r) Zalikha Ibrahim (Sun Sep 30 2012 - 01:14:33 PDT)
[AMBER] help for TMD Yanyan ZHU (Mon Sep 24 2012 - 18:56:00 PDT)
[AMBER] puzzles about TMD Yanyan ZHU (Tue Sep 25 2012 - 01:50:43 PDT)
[AMBER] thioester-containing proteins (backbone with side chain ) 甄云梅 (Tue Sep 25 2012 - 04:42:26 PDT)
- Re: [AMBER] thioester-containing proteins (backbone with side chain ) FyD (Tue Sep 25 2012 - 06:02:25 PDT)
[AMBER] Read scee and scnb from topology file in NAB Sangmin Lee (Tue Sep 25 2012 - 05:14:14 PDT)
- Re: [AMBER] Read scee and scnb from topology file in NAB Jason Swails (Thu Sep 27 2012 - 07:01:23 PDT)
[AMBER] simulation h a (Tue Sep 25 2012 - 10:02:10 PDT)
[AMBER] Problem with installation amber 9/tleap Deepak Ojha (Tue Sep 25 2012 - 12:13:30 PDT)
- Re: [AMBER] Problem with installation amber 9/tleap Ross Walker (Tue Sep 25 2012 - 12:28:34 PDT)
[AMBER] Centering a multimeric protein with solvateOct Jonathan Sheehan (Tue Sep 25 2012 - 12:39:10 PDT)
- Re: [AMBER] Centering a multimeric protein with solvateOct Jonathan Sheehan (Thu Oct 04 2012 - 12:24:29 PDT)
  - Re: [AMBER] Centering a multimeric protein with solvateOct Bill Ross (Sat Oct 06 2012 - 15:09:05 PDT)
    - Re: [AMBER] Centering a multimeric protein with solvateOct Jonathan Sheehan (Sat Oct 06 2012 - 18:07:47 PDT)
[AMBER] Running Free Energy calculations for Substrate Binding Vivek Shankar Bharadwaj (Tue Sep 25 2012 - 11:59:04 PDT)
[AMBER] AMBER-Gaussian QM/MM marawan hussain (Tue Sep 25 2012 - 23:48:52 PDT)
- Re: [AMBER] AMBER-Gaussian QM/MM Andreas Goetz (Wed Sep 26 2012 - 11:16:38 PDT)
[AMBER] using antechamber to parapetrize non standard amino acid houcemeddine othman (Wed Sep 26 2012 - 02:35:40 PDT)
- Re: [AMBER] using antechamber to parapetrize non standard amino acid FyD (Wed Sep 26 2012 - 06:49:28 PDT)
[AMBER] Problem related to the RED Tools Sindrila Dutta banik (Wed Sep 26 2012 - 02:46:20 PDT)
[AMBER] problem install Amber in MacOS Albert (Wed Sep 26 2012 - 06:00:07 PDT)
- Re: [AMBER] problem install Amber in MacOS Daniel Roe (Wed Sep 26 2012 - 06:52:36 PDT)
Re: [AMBER] [q4md-fft] Problem related to the installation of RED FyD (Wed Sep 26 2012 - 06:42:12 PDT)
- [AMBER] [q4md-fft] Problem related to the installation of RED Sindrila Dutta banik (Thu Sep 27 2012 - 02:56:45 PDT)
  - Re: [AMBER] [q4md-fft] Problem related to the installation of RED FyD (Thu Sep 27 2012 - 03:24:13 PDT)
[AMBER] dipole printing in mdout file Sanjib Paul (Wed Sep 26 2012 - 06:46:35 PDT)
[AMBER] Running TI calculations on sander.MPI Vivek Shankar Bharadwaj (Wed Sep 26 2012 - 10:03:31 PDT)
- Re: [AMBER] Running TI calculations on sander.MPI David A Case (Wed Sep 26 2012 - 11:04:56 PDT)
  - Re: [AMBER] Running TI calculations on sander.MPI Vivek Shankar Bharadwaj (Wed Sep 26 2012 - 11:56:59 PDT)
[AMBER] questions about Accelerated MD Thomas Evangelidis (Wed Sep 26 2012 - 11:17:59 PDT)
- Re: [AMBER] questions about Accelerated MD Romelia Salomon (Wed Sep 26 2012 - 15:27:03 PDT)
  - Re: [AMBER] questions about Accelerated MD Thomas Evangelidis (Sun Nov 18 2012 - 13:48:51 PST)
    - Re: [AMBER] questions about Accelerated MD Romelia Salomon (Mon Nov 19 2012 - 08:35:36 PST)
    - Re: [AMBER] questions about Accelerated MD Thomas Evangelidis (Mon Nov 19 2012 - 08:46:54 PST)
    - Re: [AMBER] questions about Accelerated MD Romelia Salomon (Mon Nov 19 2012 - 10:20:25 PST)
    - Re: [AMBER] questions about Accelerated MD Thomas Evangelidis (Mon Nov 19 2012 - 11:39:52 PST)
    - Re: [AMBER] questions about Accelerated MD Romelia Salomon (Mon Nov 19 2012 - 13:47:10 PST)
    - Re: [AMBER] questions about Accelerated MD Thomas Evangelidis (Thu Nov 22 2012 - 13:47:22 PST)
[AMBER] REMD simulation gargi borgohai (Wed Sep 26 2012 - 22:46:08 PDT)
- Re: [AMBER] REMD simulation Carlos Simmerling (Thu Sep 27 2012 - 03:09:19 PDT)
[AMBER] MMPBSA error DEBOSTUTI GHOSHDASTIDAR (Thu Sep 27 2012 - 03:32:07 PDT)
- Re: [AMBER] MMPBSA error Jason Swails (Thu Sep 27 2012 - 04:30:22 PDT)
[AMBER] Minimizations and Equilibrations for TI Vivek Shankar Bharadwaj (Thu Sep 27 2012 - 08:20:31 PDT)
- Re: [AMBER] Minimizations and Equilibrations for TI Brian Radak (Thu Sep 27 2012 - 08:49:16 PDT)
  - Re: [AMBER] Minimizations and Equilibrations for TI Vivek Shankar Bharadwaj (Thu Sep 27 2012 - 09:22:13 PDT)
[AMBER] TI and number of solvent molecules Fabrício Bracht (Thu Sep 27 2012 - 10:34:55 PDT)
- Re: [AMBER] TI and number of solvent molecules Jason Swails (Thu Sep 27 2012 - 10:48:37 PDT)
- Re: [AMBER] TI and number of solvent molecules Niel Henriksen (Thu Sep 27 2012 - 10:55:09 PDT)
[AMBER] Large trajectory for cluster analysis in ptraj Kira Armacost (Thu Sep 27 2012 - 11:29:56 PDT)
- Re: [AMBER] Large trajectory for cluster analysis in ptraj Daniel Roe (Thu Sep 27 2012 - 13:25:30 PDT)
  - Re: [AMBER] Large trajectory for cluster analysis in ptraj Kira Armacost (Thu Sep 27 2012 - 13:33:38 PDT)
    - Re: [AMBER] Large trajectory for cluster analysis in ptraj Daniel Roe (Thu Sep 27 2012 - 13:39:47 PDT)
    - Re: [AMBER] Large trajectory for cluster analysis in ptraj Kira Armacost (Thu Sep 27 2012 - 20:08:32 PDT)
    - Re: [AMBER] Large trajectory for cluster analysis in ptraj Daniel Roe (Thu Sep 27 2012 - 20:29:03 PDT)
    - Re: [AMBER] Large trajectory for cluster analysis in ptraj Kira Armacost (Sat Sep 29 2012 - 14:42:36 PDT)
  - Re: [AMBER] Large trajectory for cluster analysis in ptraj Ganesh Kamath (Thu Sep 27 2012 - 20:24:56 PDT)
    - Re: [AMBER] Large trajectory for cluster analysis in ptraj Daniel Roe (Thu Sep 27 2012 - 20:34:20 PDT)
[AMBER] cudaMemcpy GpuBuffer::Download failed unspecified launch failure Gerald Monard (Thu Sep 27 2012 - 14:45:32 PDT)
- Re: [AMBER] cudaMemcpy GpuBuffer::Download failed unspecified launch failure filip fratev (Fri Jan 10 2014 - 01:48:49 PST)
  - Re: [AMBER] cudaMemcpy GpuBuffer::Download failed unspecified launch failure filip fratev (Fri Jan 10 2014 - 03:13:44 PST)
    - Re: [AMBER] cudaMemcpy GpuBuffer::Download failed unspecified launch failure Ross Walker (Fri Jan 10 2014 - 07:36:03 PST)
    - Re: [AMBER] cudaMemcpy GpuBuffer::Download failed unspecified launch failure filip fratev (Sat Jan 11 2014 - 06:58:37 PST)
    - Re: [AMBER] cudaMemcpy GpuBuffer::Download failed unspecified launch failure filip fratev (Sat Jan 11 2014 - 13:27:04 PST)
    - Re: [AMBER] cudaMemcpy GpuBuffer::Download failed unspecified launch failure filip fratev (Mon Jan 13 2014 - 13:18:56 PST)
    - Re: [AMBER] cudaMemcpy GpuBuffer::Download failed unspecified launch failure Ross Walker (Mon Jan 13 2014 - 13:28:41 PST)
    - Re: [AMBER] cudaMemcpy GpuBuffer::Download failed unspecified launch failure filip fratev (Thu Jan 30 2014 - 08:32:55 PST)
[AMBER] Molecular Dynamic production Anogna (Thu Sep 27 2012 - 23:29:42 PDT)
- Re: [AMBER] Molecular Dynamic production Jason Swails (Fri Sep 28 2012 - 05:32:01 PDT)
- Re: [AMBER] Molecular Dynamic production David A Case (Sat Sep 29 2012 - 14:40:45 PDT)
  - Re: [AMBER] Molecular Dynamic production Anogna (Mon Oct 01 2012 - 22:51:28 PDT)
    - Re: [AMBER] Molecular Dynamic production Jason Swails (Tue Oct 02 2012 - 04:42:15 PDT)
[AMBER] patching AmberTools 12 failed Francesco Pietra (Fri Sep 28 2012 - 02:36:34 PDT)
- [AMBER] Fwd: patching AmberTools 12 failed Francesco Pietra (Fri Sep 28 2012 - 02:53:18 PDT)
- Re: [AMBER] patching AmberTools 12 failed Jason Swails (Fri Sep 28 2012 - 05:29:26 PDT)
  - Re: [AMBER] patching AmberTools 12 failed Francesco Pietra (Fri Sep 28 2012 - 10:54:37 PDT)
    - Re: [AMBER] patching AmberTools 12 failed Jason Swails (Fri Sep 28 2012 - 11:38:29 PDT)
    - Re: [AMBER] patching AmberTools 12 failed Francesco Pietra (Fri Sep 28 2012 - 13:30:43 PDT)
[AMBER] the origin of ELEC DV/DL in the case of softcore TI calculation of the solute with no charge by crgmask hironori.kokubo.takeda.com (Fri Sep 28 2012 - 03:49:33 PDT)
- Re: [AMBER] the origin of ELEC DV/DL in the case of softcore TI calculation of the solute with no charge by crgmask David A Case (Thu Oct 04 2012 - 07:16:44 PDT)
  - Re: [AMBER] the origin of ELEC DV/DL in the case of softcore TIcalculation of the solute with no charge by crgmask hironori.kokubo.takeda.com (Thu Oct 04 2012 - 20:27:07 PDT)
    - Re: [AMBER] the origin of ELEC DV/DL in the case of softcore TIcalculation of the solute with no charge by crgmask David A Case (Thu Oct 11 2012 - 07:45:40 PDT)
    - Re: [AMBER] the origin of ELEC DV/DL in the case of softcoreTIcalculation of the solute with no charge by crgmask hironori.kokubo.takeda.com (Sun Oct 14 2012 - 23:11:49 PDT)
[AMBER] How to equilibrate only protons, and only side chain Sindrila Dutta banik (Fri Sep 28 2012 - 05:54:32 PDT)
- Re: [AMBER] How to equilibrate only protons, and only side chain Carlos Simmerling (Fri Sep 28 2012 - 06:05:22 PDT)
[AMBER] test errors in cuda-enabled amber12 崔幼恬 (Fri Sep 28 2012 - 08:49:19 PDT)
- Re: [AMBER] test errors in cuda-enabled amber12 Ross Walker (Fri Sep 28 2012 - 08:57:59 PDT)
[AMBER] Softcore potentials in TI calculations Vivek Shankar Bharadwaj (Fri Sep 28 2012 - 09:15:04 PDT)
[AMBER] TI Softcore potentials and SHAKE Kepa K. Burusco (Fri Sep 28 2012 - 10:27:36 PDT)
- Re: [AMBER] TI Softcore potentials and SHAKE Brian Radak (Fri Sep 28 2012 - 11:04:02 PDT)
  - Re: [AMBER] TI Softcore potentials and SHAKE Kepa K. Burusco (Sun Sep 30 2012 - 16:12:10 PDT)
    - Re: [AMBER] TI Softcore potentials and SHAKE David A Case (Sun Sep 30 2012 - 18:49:36 PDT)
    - Re: [AMBER] TI Softcore potentials and SHAKE Kepa K. Burusco (Mon Oct 01 2012 - 03:17:52 PDT)
    - Re: [AMBER] TI Softcore potentials and SHAKE David A Case (Mon Oct 01 2012 - 05:25:21 PDT)
    - Re: [AMBER] TI Softcore potentials and SHAKE Kepa K. Burusco (Mon Oct 01 2012 - 09:02:03 PDT)
[AMBER] error while using chamber (AmberTools1.5) to convert charmm psf and pdb to amber crd and top duanbg (Fri Sep 28 2012 - 17:37:28 PDT)
[AMBER] single residue energy contribution André C. Stiel (Sat Sep 29 2012 - 01:09:56 PDT)
- Re: [AMBER] single residue energy contribution kurisaki (Sat Sep 29 2012 - 02:29:33 PDT)
  - [AMBER] Installation problem of AMBER12 Catein Catherine (Sat Sep 29 2012 - 07:09:13 PDT)
    - Re: [AMBER] Installation problem of AMBER12 Jan-Philip Gehrcke (Sat Sep 29 2012 - 08:49:45 PDT)
[AMBER] Molecular Dynamic production Anogna (Sat Sep 29 2012 - 01:53:35 PDT)
[AMBER] Installation of Parallel version of Amber Sindrila Dutta banik (Sat Sep 29 2012 - 03:47:09 PDT)
- Re: [AMBER] Installation of Parallel version of Amber David A Case (Sat Sep 29 2012 - 14:46:48 PDT)
[AMBER] Problem related to the parallel installation og Amber11 Sindrila Dutta banik (Sun Sep 30 2012 - 09:36:23 PDT)
- Re: [AMBER] Problem related to the parallel installation og Amber11 Ben Roberts (Sun Sep 30 2012 - 14:15:10 PDT)
  - Re: [AMBER] Problem related to the parallel installation og Amber11 David A Case (Sun Sep 30 2012 - 19:02:43 PDT)
    - Re: [AMBER] Problem related to the parallel installation og Amber11 Ben Roberts (Sun Sep 30 2012 - 20:55:32 PDT)
    - Re: [AMBER] Problem related to the parallel installation of Amber11 Sindrila Dutta banik (Mon Oct 01 2012 - 02:11:47 PDT)
    - Re: [AMBER] Problem related to the parallel installation of Amber11 Jason Swails (Mon Oct 01 2012 - 04:25:52 PDT)
    - Re: [AMBER] Problem related to the parallel installation of Amber11 Sindrila Dutta banik (Mon Oct 01 2012 - 10:39:24 PDT)
    - Re: [AMBER] Problem related to the parallel installation of Amber11 Jason Swails (Mon Oct 01 2012 - 11:04:19 PDT)
    - [AMBER] Problem related to the parallel installation of Amber11 Sindrila Dutta banik (Mon Oct 01 2012 - 11:49:35 PDT)
    - Re: [AMBER] Problem related to the parallel installation of Amber11 Jason Swails (Mon Oct 01 2012 - 12:14:54 PDT)
    - [AMBER] Problem related to the parallel installation of Amber11 Sindrila Dutta banik (Mon Oct 01 2012 - 12:57:42 PDT)
    - Re: [AMBER] Problem related to the parallel installation of Amber11 Jason Swails (Mon Oct 01 2012 - 13:10:09 PDT)
    - [AMBER] Problem related to the parallel installation of Amber11 Sindrila Dutta banik (Mon Oct 01 2012 - 13:21:16 PDT)
[AMBER] different Partial charges for CYM in amino94.xml (MCPB) and all_amino94.lib (leap) Sangeetha B (Mon Oct 01 2012 - 00:30:48 PDT)
[AMBER] MMPBSA error BERGY (Mon Oct 01 2012 - 02:15:17 PDT)
- Re: [AMBER] MMPBSA error Jason Swails (Mon Oct 01 2012 - 04:23:46 PDT)
- Re: [AMBER] MMPBSA error Nadine Homeyer (Mon Oct 01 2012 - 05:49:38 PDT)
[AMBER] Release of the R.E.D.-III.52 tools FyD (Mon Oct 01 2012 - 02:32:02 PDT)
[AMBER] Antechamber + SQM/DFTB Edgar Mixcoha (Mon Oct 01 2012 - 03:12:14 PDT)
- Re: [AMBER] Antechamber + SQM/DFTB David A Case (Mon Oct 01 2012 - 05:32:28 PDT)
  - Re: [AMBER] Antechamber + SQM/DFTB Edgar Mixcoha (Mon Oct 01 2012 - 06:56:52 PDT)
[AMBER] parallel MMPBSA: no of cores versus no of frames analyzed Vlad Cojocaru (Mon Oct 01 2012 - 09:10:47 PDT)
- Re: [AMBER] parallel MMPBSA: no of cores versus no of frames analyzed Jason Swails (Mon Oct 01 2012 - 09:32:04 PDT)
  - Re: [AMBER] parallel MMPBSA: no of cores versus no of frames analyzed Vlad Cojocaru (Mon Oct 01 2012 - 09:39:06 PDT)
    - Re: [AMBER] parallel MMPBSA: no of cores versus no of frames analyzed Jason Swails (Mon Oct 01 2012 - 10:18:21 PDT)
[AMBER] effect neutralizing ions on value of "saltcon" in generalized Born model Sajeewa Pemasinghe (Mon Oct 01 2012 - 13:36:09 PDT)
- Re: [AMBER] effect neutralizing ions on value of "saltcon" in generalized Born model Brian Radak (Mon Oct 01 2012 - 13:58:22 PDT)
[AMBER] X11 problems on Mac OS X 10.8 Julio Dominguez (Mon Oct 01 2012 - 13:59:59 PDT)
- Re: [AMBER] X11 problems on Mac OS X 10.8 Jason Swails (Mon Oct 01 2012 - 16:14:17 PDT)
- Re: [AMBER] X11 problems on Mac OS X 10.8 Julio Dominguez (Tue Oct 02 2012 - 15:09:29 PDT)
  - Re: [AMBER] X11 problems on Mac OS X 10.8 David A Case (Tue Oct 02 2012 - 18:01:37 PDT)
    - Re: [AMBER] X11 problems on Mac OS X 10.8 Jonathan Gough (Tue Oct 02 2012 - 19:36:45 PDT)
    - Re: [AMBER] X11 problems on Mac OS X 10.8 David A Case (Wed Oct 03 2012 - 04:49:30 PDT)
- Re: [AMBER] X11 problems on Mac OS X 10.8 Julio Dominguez (Wed Oct 03 2012 - 19:47:31 PDT)
  - Re: [AMBER] X11 problems on Mac OS X 10.8 Jonathan Gough (Thu Oct 04 2012 - 08:08:32 PDT)
    - Re: [AMBER] X11 problems on Mac OS X 10.8 Jason Swails (Thu Oct 04 2012 - 09:02:56 PDT)
    - Re: [AMBER] X11 problems on Mac OS X 10.8 David A Case (Thu Oct 04 2012 - 09:30:29 PDT)
    - Re: [AMBER] X11 problems on Mac OS X 10.8 Jonathan Gough (Thu Oct 04 2012 - 10:24:51 PDT)
- Re: [AMBER] X11 problems on Mac OS X 10.8 Maria Ana Castro (Tue Oct 16 2012 - 08:11:51 PDT)
  - Re: [AMBER] X11 problems on Mac OS X 10.8 David A Case (Tue Oct 16 2012 - 18:38:01 PDT)
[AMBER] Difference between ntx5 and ntx 7 Sindrila Dutta banik (Mon Oct 01 2012 - 23:01:14 PDT)
- Re: [AMBER] Difference between ntx5 and ntx 7 Jason Swails (Tue Oct 02 2012 - 04:36:44 PDT)
[AMBER] different between PBSA and MMPBSA ? setyanto md (Tue Oct 02 2012 - 02:00:20 PDT)
- Re: [AMBER] different between PBSA and MMPBSA ? setyanto md (Tue Oct 02 2012 - 02:59:49 PDT)
- Re: [AMBER] different between PBSA and MMPBSA ? Jason Swails (Tue Oct 02 2012 - 04:31:00 PDT)
  - Re: [AMBER] different between PBSA and MMPBSA ? setyanto md (Tue Oct 02 2012 - 04:41:26 PDT)
    - Re: [AMBER] different between PBSA and MMPBSA ? Jason Swails (Tue Oct 02 2012 - 04:45:54 PDT)
    - Re: [AMBER] different between PBSA and MMPBSA ? David A Case (Tue Oct 02 2012 - 05:25:30 PDT)
    - Re: [AMBER] different between PBSA and MMPBSA ? setyanto md (Mon Oct 08 2012 - 01:05:34 PDT)
    - Re: [AMBER] different between PBSA and MMPBSA ? Jason Swails (Mon Oct 08 2012 - 03:26:37 PDT)
    - Re: [AMBER] different between PBSA and MMPBSA ? setyanto md (Mon Oct 08 2012 - 04:01:13 PDT)
[AMBER] error while using chamber (AmberTools1.5) to convert charmm psf and pdb to amber crd and top duanbg (Tue Oct 02 2012 - 20:05:09 PDT)
[AMBER] To which ensemble does generalized Born trajectory fall? Sajeewa Pemasinghe (Tue Oct 02 2012 - 20:43:44 PDT)
- Re: [AMBER] To which ensemble does generalized Born trajectory fall? David A Case (Wed Oct 03 2012 - 04:56:17 PDT)
  - Re: [AMBER] To which ensemble does generalized Born trajectory fall? Sajeewa Pemasinghe (Wed Oct 03 2012 - 06:31:03 PDT)
[AMBER] Setting the random seed in Langevin dynamics Sajeewa Pemasinghe (Tue Oct 02 2012 - 20:57:37 PDT)
- Re: [AMBER] Setting the random seed in Langevin dynamics Deák Robert (Wed Oct 03 2012 - 02:54:52 PDT)
  - Re: [AMBER] Setting the random seed in Langevin dynamics Sajeewa Pemasinghe (Wed Oct 03 2012 - 06:19:55 PDT)
    - Re: [AMBER] Setting the random seed in Langevin dynamics Adrian Roitberg (Wed Oct 03 2012 - 06:25:00 PDT)
    - Re: [AMBER] Setting the random seed in Langevin dynamics Sajeewa Pemasinghe (Wed Oct 03 2012 - 06:38:18 PDT)
    - Re: [AMBER] Setting the random seed in Langevin dynamics Deák Robert (Wed Oct 03 2012 - 07:25:50 PDT)
    - Re: [AMBER] Setting the random seed in Langevin dynamics Sajeewa Pemasinghe (Wed Oct 03 2012 - 08:53:53 PDT)
Re: [AMBER] AMBER Digest, Vol 292, Issue 2 Julio Dominguez (Tue Oct 02 2012 - 21:03:57 PDT)
[AMBER] unable to find mopac charges Anogna (Wed Oct 03 2012 - 03:03:53 PDT)
- Re: [AMBER] unable to find mopac charges David A Case (Wed Oct 03 2012 - 04:58:18 PDT)
  - Re: [AMBER] unable to find mopac charges Anogna (Thu Oct 04 2012 - 23:55:20 PDT)
    - Re: [AMBER] unable to find mopac charges Jason Swails (Fri Oct 05 2012 - 04:59:54 PDT)
    - Re: [AMBER] unable to find mopac charges David A Case (Fri Oct 05 2012 - 05:07:58 PDT)
    - Re: [AMBER] unable to find mopac charges Anogna (Wed Oct 10 2012 - 03:39:36 PDT)
    - Re: [AMBER] unable to find mopac charges Jason Swails (Wed Oct 10 2012 - 05:42:29 PDT)
    - Re: [AMBER] unable to find mopac charges David A Case (Wed Oct 10 2012 - 05:47:53 PDT)
    - Re: [AMBER] unable to find mopac charges Anogna (Wed Oct 10 2012 - 23:07:45 PDT)
    - Re: [AMBER] unable to find mopac charges Jason Swails (Thu Oct 11 2012 - 01:22:20 PDT)
    - Re: [AMBER] unable to find mopac charges David A Case (Thu Oct 11 2012 - 05:00:01 PDT)
    - Re: [AMBER] unable to find mopac charges Anselm Horn (Mon Oct 15 2012 - 00:07:38 PDT)
[AMBER] vlimit exceeded on step.. error Jitesh Doshi (Wed Oct 03 2012 - 06:19:52 PDT)
- Re: [AMBER] vlimit exceeded on step.. error David A Case (Wed Oct 03 2012 - 06:53:42 PDT)
  - Re: [AMBER] vlimit exceeded on step.. error Jitesh Doshi (Thu Oct 04 2012 - 23:44:22 PDT)
    - Re: [AMBER] vlimit exceeded on step.. error David A Case (Fri Oct 05 2012 - 04:58:43 PDT)
    - Re: [AMBER] vlimit exceeded on step.. error Jitesh Doshi (Fri Oct 05 2012 - 05:11:37 PDT)
    - Re: [AMBER] vlimit exceeded on step.. error Jitesh Doshi (Tue Oct 09 2012 - 04:18:50 PDT)
    - Re: [AMBER] vlimit exceeded on step.. error Daniel Roe (Tue Oct 09 2012 - 09:05:55 PDT)
    - Re: [AMBER] vlimit exceeded on step.. error Jitesh Doshi (Wed Oct 10 2012 - 03:19:16 PDT)
    - Re: [AMBER] vlimit exceeded on step.. error David A Case (Wed Oct 10 2012 - 04:16:51 PDT)
    - Re: [AMBER] vlimit exceeded on step.. error Jitesh Doshi (Wed Oct 10 2012 - 05:24:00 PDT)
    - Re: [AMBER] vlimit exceeded on step.. error Anna Bauß (Thu Oct 11 2012 - 01:43:38 PDT)
    - Re: [AMBER] vlimit exceeded on step.. error Jitesh Doshi (Thu Oct 18 2012 - 04:39:35 PDT)
[AMBER] Problem related to the trajectory analysis Sindrila Dutta banik (Wed Oct 03 2012 - 11:20:10 PDT)
- Re: [AMBER] Problem related to the trajectory analysis Jason Swails (Wed Oct 03 2012 - 18:38:23 PDT)
[AMBER] TI with shake Abhishek Mukhopadhyay (Wed Oct 03 2012 - 14:37:28 PDT)
[AMBER] Problem in Installing Amber12/Tools in parallel Sajeewa Pemasinghe (Wed Oct 03 2012 - 23:40:55 PDT)
- Re: [AMBER] Problem in Installing Amber12/Tools in parallel Jason Swails (Thu Oct 04 2012 - 05:12:16 PDT)
[AMBER] simulation box shape changed Syed Tarique Moin (Wed Oct 03 2012 - 23:46:41 PDT)
- Re: [AMBER] simulation box shape changed Jason Swails (Thu Oct 04 2012 - 04:44:00 PDT)
  - Re: [AMBER] simulation box shape changed Syed Tarique Moin (Thu Oct 11 2012 - 02:10:47 PDT)
[AMBER] Problem related to the analysis of mdcrd Sindrila Dutta banik (Wed Oct 03 2012 - 23:48:59 PDT)
- Re: [AMBER] Problem related to the analysis of mdcrd Daniel Roe (Thu Oct 04 2012 - 07:39:29 PDT)
[AMBER] Obtain trajectory in NAB Sangmin Lee (Thu Oct 04 2012 - 01:13:46 PDT)
- Re: [AMBER] Obtain trajectory in NAB David A Case (Thu Oct 04 2012 - 07:10:02 PDT)
- Re: [AMBER] Obtain trajectory in NAB Sangmin Lee (Thu Oct 04 2012 - 22:17:58 PDT)
[AMBER] PairwiseDistance file location vaibhav dixit (Thu Oct 04 2012 - 01:28:11 PDT)
- Re: [AMBER] PairwiseDistance file location Daniel Roe (Thu Oct 04 2012 - 07:35:35 PDT)
  - Re: [AMBER] PairwiseDistance file location vaibhav dixit (Thu Oct 04 2012 - 22:10:40 PDT)
    - Re: [AMBER] PairwiseDistance file location Daniel Roe (Fri Oct 05 2012 - 10:47:55 PDT)
    - Re: [AMBER] PairwiseDistance file location vaibhav dixit (Fri Oct 05 2012 - 18:58:53 PDT)
[AMBER] What does the word 'DIPGRP - 1' mean? Sanjib Paul (Thu Oct 04 2012 - 05:50:37 PDT)
[AMBER] How do I generate prmtop files with bondi radii? Sajeewa Pemasinghe (Thu Oct 04 2012 - 15:20:36 PDT)
- Re: [AMBER] How do I generate prmtop files with bondi radii? Jason Swails (Thu Oct 04 2012 - 15:28:08 PDT)
  - Re: [AMBER] How do I generate prmtop files with bondi radii? Sajeewa Pemasinghe (Thu Oct 04 2012 - 15:52:22 PDT)
[AMBER] Meaning of setting gbsa=0 in generalized Born calculations Sajeewa Pemasinghe (Thu Oct 04 2012 - 21:01:50 PDT)
- Re: [AMBER] Meaning of setting gbsa=0 in generalized Born calculations Jason Swails (Fri Oct 05 2012 - 04:45:19 PDT)
  - Re: [AMBER] Meaning of setting gbsa=0 in generalized Born calculations Carlos Simmerling (Fri Oct 05 2012 - 04:48:26 PDT)
    - Re: [AMBER] Meaning of setting gbsa=0 in generalized Born calculations Jason Swails (Fri Oct 05 2012 - 07:27:42 PDT)
    - Re: [AMBER] Meaning of setting gbsa=0 in generalized Born calculations Sajeewa Pemasinghe (Fri Oct 05 2012 - 07:48:36 PDT)
[AMBER] calculating intramolecular hydrogen bonding Vijay Manickam Achari (Fri Oct 05 2012 - 00:29:22 PDT)
- Re: [AMBER] calculating intramolecular hydrogen bonding Daniel Roe (Fri Oct 05 2012 - 10:43:11 PDT)
  - Re: [AMBER] calculating intramolecular hydrogen bonding Vijay Manickam Achari (Mon Oct 15 2012 - 01:19:08 PDT)
    - Re: [AMBER] calculating intramolecular hydrogen bonding Daniel Roe (Wed Oct 17 2012 - 06:57:44 PDT)
[AMBER] phosphate moiety & igb model Marc van der Kamp (Fri Oct 05 2012 - 03:10:21 PDT)
- Re: [AMBER] phosphate moiety & igb model Carlos Simmerling (Fri Oct 05 2012 - 04:43:50 PDT)
[AMBER] aMD with implicit solvent? Marc van der Kamp (Fri Oct 05 2012 - 08:30:52 PDT)
[AMBER] diff. between avg/rep structures & connectivity problem in PDB files vaibhav dixit (Sun Oct 07 2012 - 02:24:02 PDT)
- Re: [AMBER] diff. between avg/rep structures & connectivity problem in PDB files Daniel Roe (Mon Oct 08 2012 - 07:39:42 PDT)
  - Re: [AMBER] diff. between avg/rep structures & connectivity problem in PDB files vaibhav dixit (Mon Oct 08 2012 - 08:15:44 PDT)
[AMBER] Distance calculations with ptraj Kira Armacost (Sun Oct 07 2012 - 12:23:43 PDT)
- Re: [AMBER] Distance calculations with ptraj Daniel Roe (Mon Oct 08 2012 - 07:28:49 PDT)
  - Re: [AMBER] Distance calculations with ptraj Kira Armacost (Mon Oct 08 2012 - 13:18:03 PDT)
    - Re: [AMBER] Distance calculations with ptraj Daniel Roe (Mon Oct 08 2012 - 15:07:15 PDT)
[AMBER] Umbrella Sampling with Z-axis as Reaction Coordinate Dail Chapman (Sun Oct 07 2012 - 16:57:08 PDT)
- Re: [AMBER] Umbrella Sampling with Z-axis as Reaction Coordinate Jason Swails (Mon Oct 08 2012 - 03:38:44 PDT)
- Re: [AMBER] Umbrella Sampling with Z-axis as Reaction Coordinate Dail Chapman (Sun Oct 14 2012 - 22:23:00 PDT)
[AMBER] Estimating time in AMD Soumya Lipsa Rath (Sun Oct 07 2012 - 22:08:04 PDT)
- Re: [AMBER] Estimating time in AMD Romelia Salomon (Mon Oct 08 2012 - 01:25:49 PDT)
  - Re: [AMBER] Estimating time in AMD Adrian Roitberg (Mon Oct 08 2012 - 02:10:48 PDT)
    - Re: [AMBER] Estimating time in AMD Soumya Lipsa Rath (Mon Oct 08 2012 - 07:19:30 PDT)
  - Re: [AMBER] Estimating time in AMD Soumya Lipsa Rath (Mon Oct 08 2012 - 02:31:46 PDT)
  - Re: [AMBER] Estimating time in AMD Thomas Evangelidis (Sat Mar 02 2013 - 05:48:07 PST)
[AMBER] missing bonds and angles Mary Varughese (Sun Oct 07 2012 - 22:36:17 PDT)
[AMBER] Reference for the AMBER12SB force field ABEL Stephane 175950 (Mon Oct 08 2012 - 04:13:57 PDT)
- Re: [AMBER] Reference for the AMBER12SB force field Carlos Simmerling (Mon Oct 08 2012 - 04:57:33 PDT)
  - [AMBER] RE : Reference for the AMBER12SB force field ABEL Stephane 175950 (Mon Oct 08 2012 - 05:05:02 PDT)
    - Re: [AMBER] RE : Reference for the AMBER12SB force field Carlos Simmerling (Thu Oct 11 2012 - 04:28:58 PDT)
    - [AMBER] RE : RE : Reference for the AMBER12SB force field ABEL Stephane 175950 (Thu Oct 11 2012 - 04:36:44 PDT)
[AMBER] Asterisks in the restart file Cao Yang (Mon Oct 08 2012 - 05:08:41 PDT)
- Re: [AMBER] Asterisks in the restart file David A Case (Mon Oct 08 2012 - 05:43:29 PDT)
- Re: [AMBER] Asterisks in the restart file Ross Walker (Mon Oct 08 2012 - 05:44:25 PDT)
[AMBER] Reg: error in equilibration subramanian boopathi (Mon Oct 08 2012 - 05:09:02 PDT)
- Re: [AMBER] Reg: error in equilibration David A Case (Mon Oct 08 2012 - 05:47:49 PDT)
[AMBER] idecomp and so on.... André C. Stiel (Mon Oct 08 2012 - 09:52:36 PDT)
- Re: [AMBER] idecomp and so on.... Jason Swails (Mon Oct 08 2012 - 14:40:49 PDT)
  - Re: [AMBER] idecomp and so on.... André C. Stiel (Tue Oct 09 2012 - 09:35:56 PDT)
    - Re: [AMBER] idecomp and so on.... Jason Swails (Tue Oct 09 2012 - 12:26:07 PDT)
    - Re: [AMBER] idecomp and so on.... André C. Stiel (Tue Oct 09 2012 - 13:59:12 PDT)
    - Re: [AMBER] idecomp and so on.... Jason Swails (Tue Oct 09 2012 - 14:11:49 PDT)
[AMBER] Errors in Amber12 installation Sajeewa Pemasinghe (Mon Oct 08 2012 - 11:28:04 PDT)
- Re: [AMBER] Errors in Amber12 installation Ross Walker (Mon Oct 08 2012 - 13:26:49 PDT)
  - Re: [AMBER] Errors in Amber12 installation Sajeewa Pemasinghe (Mon Oct 08 2012 - 19:11:21 PDT)
- Re: [AMBER] Errors in Amber12 installation David A Case (Mon Oct 08 2012 - 13:33:19 PDT)
  - Re: [AMBER] Errors in Amber12 installation Ben Roberts (Mon Oct 08 2012 - 16:46:09 PDT)
    - Re: [AMBER] Errors in Amber12 installation Sajeewa Pemasinghe (Mon Oct 08 2012 - 17:30:25 PDT)
    - Re: [AMBER] Errors in Amber12 installation Ben Roberts (Mon Oct 08 2012 - 18:57:18 PDT)
    - Re: [AMBER] Errors in Amber12 installation Sajeewa Pemasinghe (Mon Oct 08 2012 - 19:09:52 PDT)
  - Re: [AMBER] Errors in Amber12 installation Sajeewa Pemasinghe (Mon Oct 08 2012 - 19:10:58 PDT)
[AMBER] Queastions Regarding Tutorial A11 NCSU Method Γιώργος Λαμπρινίδης (Mon Oct 08 2012 - 12:48:17 PDT)
- Re: [AMBER] Queastions Regarding Tutorial A11 NCSU Method Jason Swails (Mon Oct 08 2012 - 14:26:44 PDT)
  - Re: [AMBER] Queastions Regarding Tutorial A11 NCSU Method Γιώργος Λαμπρινίδης (Mon Oct 08 2012 - 23:43:48 PDT)
[AMBER] Can not find dhfr containing 23,558 atoms in AMBER 陶晓芳 (Mon Oct 08 2012 - 20:18:53 PDT)
- Re: [AMBER] Can not find dhfr containing 23,558 atoms in AMBER Ross Walker (Tue Oct 09 2012 - 01:11:59 PDT)
[AMBER] Problems in Amber12 parallel installation Sajeewa Pemasinghe (Mon Oct 08 2012 - 20:38:34 PDT)
- Re: [AMBER] Problems in Amber12 parallel installation David A Case (Tue Oct 09 2012 - 07:26:32 PDT)
  - Re: [AMBER] Problems in Amber12 parallel installation Sajeewa Pemasinghe (Tue Oct 09 2012 - 11:56:45 PDT)
[AMBER] Problem related to the Amber11 installation in user account Sindrila Dutta banik (Mon Oct 08 2012 - 21:39:46 PDT)
- Re: [AMBER] Problem related to the Amber11 installation in user account Jason Swails (Tue Oct 09 2012 - 00:22:37 PDT)
  - [AMBER] Problem related to the Amber11 installation in user account Sindrila Dutta banik (Tue Oct 09 2012 - 00:59:16 PDT)
    - Re: [AMBER] Problem related to the Amber11 installation in user account Jason Swails (Tue Oct 09 2012 - 01:06:30 PDT)
    - Re: [AMBER] Problem related to the Amber11 installation in user account Sindrila Dutta banik (Tue Oct 09 2012 - 01:25:52 PDT)
    - Re: [AMBER] Problem related to the Amber11 installation in user account Jason Swails (Tue Oct 09 2012 - 02:03:25 PDT)
    - [AMBER] Problem related to the Amber11 installation in user account Sindrila Dutta banik (Tue Oct 09 2012 - 02:19:36 PDT)
    - Re: [AMBER] Problem related to the Amber11 installation in user account Jason Swails (Tue Oct 09 2012 - 05:15:53 PDT)
    - [AMBER] QM method Mannan (Tue Oct 09 2012 - 06:24:04 PDT)
    - Re: [AMBER] QM method Brian Radak (Tue Oct 09 2012 - 08:45:20 PDT)
    - Re: [AMBER] QM method FyD (Tue Oct 09 2012 - 09:03:48 PDT)
[AMBER] Arsenic VDW parameters zhukk (Tue Oct 09 2012 - 01:11:34 PDT)
[AMBER] how to create crd file from my tra file? Esam Tolba (Tue Oct 09 2012 - 02:07:26 PDT)
- Re: [AMBER] how to create crd file from my tra file? Daniel Roe (Tue Oct 09 2012 - 09:00:02 PDT)
[AMBER] difference in amino94.xml (MCPB) and all_amino94.lib (leap) for CYM Sangeetha B (Tue Oct 09 2012 - 03:59:19 PDT)
- Re: [AMBER] difference in amino94.xml (MCPB) and all_amino94.lib (leap) for CYM Jason Swails (Tue Oct 09 2012 - 04:47:48 PDT)
  - Re: [AMBER] difference in amino94.xml (MCPB) and all_amino94.lib (leap) for CYM Ben Roberts (Tue Oct 09 2012 - 13:14:52 PDT)
    - Re: [AMBER] difference in amino94.xml (MCPB) and all_amino94.lib (leap) for CYM Sangeetha B (Wed Oct 10 2012 - 04:14:40 PDT)
  - Re: [AMBER] difference in amino94.xml (MCPB) and all_amino94.lib (leap) for CYM Sangeetha B (Wed Oct 10 2012 - 04:27:22 PDT)
[AMBER] Question regarding COM and atom pulling Fabrício Bracht (Tue Oct 09 2012 - 10:11:25 PDT)
- Re: [AMBER] Question regarding COM and atom pulling Jason Swails (Tue Oct 09 2012 - 12:54:09 PDT)
[AMBER] Basis of sander of Amber11 and Amber9 Sindrila Dutta banik (Tue Oct 09 2012 - 13:12:27 PDT)
- Re: [AMBER] Basis of sander of Amber11 and Amber9 David A Case (Wed Oct 10 2012 - 05:49:05 PDT)
[AMBER] NVE ensemble for solvation marawan hussain (Tue Oct 09 2012 - 17:12:04 PDT)
- Re: [AMBER] NVE ensemble for solvation David A Case (Wed Oct 10 2012 - 04:08:50 PDT)
[AMBER] Using NMR restraints for G-Quadruplex structure Rajiv (Tue Oct 09 2012 - 23:07:48 PDT)
- Re: [AMBER] Using NMR restraints for G-Quadruplex structure David A Case (Wed Oct 10 2012 - 04:11:37 PDT)
[AMBER] spce water Elisa Frezza (Wed Oct 10 2012 - 02:02:06 PDT)
- Re: [AMBER] spce water David A Case (Wed Oct 10 2012 - 04:13:36 PDT)
  - Re: [AMBER] spce water Elisa Frezza (Wed Oct 10 2012 - 04:40:51 PDT)
[AMBER] Problem related to the radial distribution function Sindrila Dutta banik (Wed Oct 10 2012 - 04:55:31 PDT)
- Re: [AMBER] Problem related to the radial distribution function Daniel Roe (Wed Oct 10 2012 - 10:41:53 PDT)
[AMBER] no prmtop created with closest Andre Serobian (Wed Oct 10 2012 - 19:26:46 PDT)
- Re: [AMBER] no prmtop created with closest Daniel Roe (Wed Oct 10 2012 - 21:56:45 PDT)
  - Re: [AMBER] no prmtop created with closest Andre Serobian (Wed Oct 10 2012 - 22:33:47 PDT)
[AMBER] angle between axes of two helices vaibhav dixit (Wed Oct 10 2012 - 22:24:38 PDT)
[AMBER] Non-polar solvation free energy in AMBER11 MMPBSA.py Tong Zhu (Wed Oct 10 2012 - 23:55:07 PDT)
- Re: [AMBER] Non-polar solvation free energy in AMBER11 MMPBSA.py Ray Luo, Ph.D. (Thu Oct 11 2012 - 14:25:38 PDT)
- Re: [AMBER] Non-polar solvation free energy in AMBER11 MMPBSA.py Ray Luo, Ph.D. (Fri Oct 12 2012 - 10:25:22 PDT)
[AMBER] about salt concentration Thomas Evangelidis (Thu Oct 11 2012 - 02:23:28 PDT)
[AMBER] pmemd installation error mehdi bagherpoor (Thu Oct 11 2012 - 04:10:30 PDT)
- Re: [AMBER] pmemd installation error Jason Swails (Thu Oct 11 2012 - 05:11:42 PDT)
- [AMBER] problem with antechamber and ESP Rebeca García Fandiño (Thu Oct 11 2012 - 05:31:12 PDT)
  - Re: [AMBER] problem with antechamber and ESP David A Case (Thu Oct 11 2012 - 06:57:25 PDT)
[AMBER] restraint and NMR Elisa Frezza (Thu Oct 11 2012 - 04:38:59 PDT)
[AMBER] How to express a right-handed amino acid in leap Changqing Yan (Thu Oct 11 2012 - 05:36:49 PDT)
- Re: [AMBER] How to express a right-handed amino acid in leap Jason Swails (Thu Oct 11 2012 - 07:03:04 PDT)
[AMBER] Average structure of trajectories as pdb file? Esam Tolba (Thu Oct 11 2012 - 06:44:01 PDT)
- Re: [AMBER] Average structure of trajectories as pdb file? Daniel Roe (Thu Oct 11 2012 - 07:40:37 PDT)
[AMBER] problem restraint Elisa Frezza (Thu Oct 11 2012 - 06:53:45 PDT)
- Re: [AMBER] problem restraint Jason Swails (Thu Oct 11 2012 - 07:30:43 PDT)
  - Re: [AMBER] problem restraint Elisa Frezza (Thu Oct 11 2012 - 07:45:43 PDT)
  - Re: [AMBER] problem restraint Elisa Frezza (Thu Oct 11 2012 - 07:51:17 PDT)
    - Re: [AMBER] problem restraint Jason Swails (Thu Oct 11 2012 - 08:10:06 PDT)
    - Re: [AMBER] problem restraint Elisa Frezza (Thu Oct 11 2012 - 08:12:04 PDT)
[AMBER] clustering the trajectories Esam Tolba (Thu Oct 11 2012 - 07:37:05 PDT)
- Re: [AMBER] clustering the trajectories Daniel Roe (Thu Oct 11 2012 - 07:43:10 PDT)
  - Re: [AMBER] clustering the trajectories Esam Tolba (Wed Oct 17 2012 - 01:44:51 PDT)
    - Re: [AMBER] clustering the trajectories David A Case (Wed Oct 17 2012 - 06:26:56 PDT)
    - Re: [AMBER] clustering the trajectories Esam Tolba (Wed Oct 17 2012 - 12:49:09 PDT)
    - Re: [AMBER] clustering the trajectories Daniel Roe (Wed Oct 17 2012 - 13:09:42 PDT)
    - Re: [AMBER] clustering the trajectories Esam Tolba (Thu Oct 18 2012 - 00:38:24 PDT)
    - Re: [AMBER] clustering the trajectories Daniel Roe (Thu Oct 18 2012 - 08:57:52 PDT)
[AMBER] NMR restraints based on order parameters Guanglei Cui (Thu Oct 11 2012 - 07:42:45 PDT)
[AMBER] TI problem Fabrício Bracht (Thu Oct 11 2012 - 11:15:04 PDT)
- Re: [AMBER] TI problem David A Case (Thu Oct 11 2012 - 18:37:14 PDT)
  - Re: [AMBER] TI problem Fabrício Bracht (Fri Oct 12 2012 - 06:12:53 PDT)
    - Re: [AMBER] TI problem David A Case (Fri Oct 12 2012 - 08:13:00 PDT)
[AMBER] completing C-term atoms after strip in ptraj Nihal Korkmaz (Thu Oct 11 2012 - 16:53:56 PDT)
- Re: [AMBER] completing C-term atoms after strip in ptraj Jason Swails (Thu Oct 11 2012 - 23:38:08 PDT)
  - Re: [AMBER] completing C-term atoms after strip in ptraj Nihal Korkmaz (Fri Oct 12 2012 - 11:48:36 PDT)
- Re: [AMBER] completing C-term atoms after strip in ptraj David A Case (Fri Oct 12 2012 - 04:56:18 PDT)
[AMBER] error while using chamber (AmberTools1.5) to convert charmm psf and pdb to amber crd and top baogen duan (Thu Oct 11 2012 - 19:16:03 PDT)
[AMBER] bad atom type: cl error in MMPBSA decomp vaibhav dixit (Fri Oct 12 2012 - 02:43:39 PDT)
- Re: [AMBER] bad atom type: cl error in MMPBSA decomp Bill Miller III (Fri Oct 12 2012 - 05:12:05 PDT)
[AMBER] forefield for Pyridoxal 5-phosphate BALA SUBRAMANI G L (Fri Oct 12 2012 - 07:39:35 PDT)
- Re: [AMBER] forefield for Pyridoxal 5-phosphate FyD (Fri Oct 12 2012 - 13:02:08 PDT)
[AMBER] AmberTools 12 Build Issue Mark Zottola (Fri Oct 12 2012 - 07:57:54 PDT)
- Re: [AMBER] AmberTools 12 Build Issue Jason Swails (Fri Oct 12 2012 - 08:23:46 PDT)
[AMBER] XLeap Install Issue Mark Zottola (Fri Oct 12 2012 - 10:32:52 PDT)
- Re: [AMBER] XLeap Install Issue Jason Swails (Fri Oct 12 2012 - 16:47:40 PDT)
  - Re: [AMBER] XLeap Install Issue Mark Zottola (Fri Oct 12 2012 - 18:11:00 PDT)
    - Re: [AMBER] XLeap Install Issue Bill Ross (Fri Oct 12 2012 - 18:58:41 PDT)
    - Re: [AMBER] XLeap Install Issue David A Case (Sat Oct 13 2012 - 06:05:18 PDT)
[AMBER] Part 2 of xleap Mark Zottola (Fri Oct 12 2012 - 10:57:45 PDT)
[AMBER] Notes and warnings in the generalized Born calculation Sajeewa Pemasinghe (Fri Oct 12 2012 - 11:24:45 PDT)
- [AMBER] Fwd: Notes and warnings in the generalized Born calculation Sajeewa Pemasinghe (Fri Oct 12 2012 - 14:23:48 PDT)
  - Re: [AMBER] Fwd: Notes and warnings in the generalized Born calculation Carlos Simmerling (Fri Oct 12 2012 - 14:26:55 PDT)
    - Re: [AMBER] Fwd: Notes and warnings in the generalized Born calculation Sajeewa Pemasinghe (Fri Oct 12 2012 - 18:37:02 PDT)
  - Re: [AMBER] Fwd: Notes and warnings in the generalized Born calculation David A Case (Fri Oct 12 2012 - 17:48:35 PDT)
    - Re: [AMBER] Fwd: Notes and warnings in the generalized Born calculation Sajeewa Pemasinghe (Fri Oct 12 2012 - 18:36:20 PDT)
- Re: [AMBER] Notes and warnings in the generalized Born calculation Jason Swails (Fri Oct 12 2012 - 17:12:25 PDT)
  - Re: [AMBER] Notes and warnings in the generalized Born calculation Sajeewa Pemasinghe (Fri Oct 12 2012 - 18:35:39 PDT)
[AMBER] problems with the keyword "append" in trajout command... Shashidhar Rao (Fri Oct 12 2012 - 11:46:24 PDT)
- Re: [AMBER] problems with the keyword "append" in trajout command... Jason Swails (Sat Oct 13 2012 - 11:39:43 PDT)
[AMBER] about results Carlos Romero (Fri Oct 12 2012 - 18:28:18 PDT)
- [AMBER] on salt bridge affinity by AMBER Acoot Brett (Fri Oct 12 2012 - 20:28:31 PDT)
  - Re: [AMBER] on salt bridge affinity by AMBER Carlos Simmerling (Sat Oct 13 2012 - 06:08:02 PDT)
[AMBER] How Can I modify a amino acid in Amber? Changqing Yan (Fri Oct 12 2012 - 19:17:02 PDT)
- Re: [AMBER] How Can I modify a amino acid in Amber? Sajeewa Pemasinghe (Sat Oct 13 2012 - 00:48:49 PDT)
  - Re: [AMBER] How Can I modify a amino acid in Amber? FyD (Sat Oct 13 2012 - 03:42:41 PDT)
    - Re: [AMBER] How Can I modify a amino acid in Amber? Sajeewa Pemasinghe (Sat Oct 13 2012 - 05:33:52 PDT)
- Re: [AMBER] How Can I modify a amino acid in Amber? Changqing Yan (Sun Oct 14 2012 - 20:11:17 PDT)
  - Re: [AMBER] How Can I modify a amino acid in Amber? FyD (Sun Oct 14 2012 - 22:22:59 PDT)
[AMBER] glycoprotein yanyuna (Sat Oct 13 2012 - 23:27:26 PDT)
- Re: [AMBER] glycoprotein Lachele Foley (Lists) (Sun Oct 14 2012 - 09:24:53 PDT)
[AMBER] Input files for MMPBSA Tommy Yap (Sun Oct 14 2012 - 19:54:24 PDT)
- Re: [AMBER] Input files for MMPBSA Jason Swails (Mon Oct 15 2012 - 04:52:56 PDT)
  - Re: [AMBER] Input files for MMPBSA Tommy Yap (Mon Oct 15 2012 - 18:59:35 PDT)
    - Re: [AMBER] Input files for MMPBSA Jason Swails (Tue Oct 16 2012 - 04:25:43 PDT)
[AMBER] glycoprotein yanyuna (Sun Oct 14 2012 - 19:59:01 PDT)
- Re: [AMBER] glycoprotein Lachele Foley (Lists) (Sun Oct 14 2012 - 20:54:55 PDT)
[AMBER] RESTARTED DUE TO LINMIN FAILURE Chris Chris (Sun Oct 14 2012 - 21:55:55 PDT)
- Re: [AMBER] RESTARTED DUE TO LINMIN FAILURE Jason Swails (Mon Oct 15 2012 - 05:05:55 PDT)
[AMBER] a question about replica exchange Albert (Sun Oct 14 2012 - 23:19:36 PDT)
- Re: [AMBER] a question about replica exchange Carlos Simmerling (Mon Oct 15 2012 - 03:12:10 PDT)
[AMBER] problem with calculating decomposition energy Maryam Hamzehee (Sun Oct 14 2012 - 23:23:27 PDT)
- Re: [AMBER] problem with calculating decomposition energy Jason Swails (Mon Oct 15 2012 - 04:50:34 PDT)
[AMBER] performance of pmemd.cuda.MPI vs pmemd.cuda both running on single GPU pavel.banas.upol.cz (Mon Oct 15 2012 - 00:22:33 PDT)
- Re: [AMBER] performance of pmemd.cuda.MPI vs pmemd.cuda both running on single GPU Niel Henriksen (Mon Oct 15 2012 - 09:39:12 PDT)
  - Re: [AMBER] performance of pmemd.cuda.MPI vs pmemd.cuda both running on single GPU Scott Le Grand (Mon Oct 15 2012 - 10:56:46 PDT)
- Re: [AMBER] performance of pmemd.cuda.MPI vs pmemd.cuda both running on single GPU pavel.banas.upol.cz (Mon Oct 15 2012 - 11:25:17 PDT)
  - Re: [AMBER] performance of pmemd.cuda.MPI vs pmemd.cuda both running on single GPU Niel Henriksen (Mon Oct 15 2012 - 12:07:39 PDT)
  - Re: [AMBER] performance of pmemd.cuda.MPI vs pmemd.cuda both running on single GPU Jason Swails (Mon Oct 15 2012 - 12:38:16 PDT)
    - Re: [AMBER] performance of pmemd.cuda.MPI vs pmemd.cuda both running on single GPU Niel Henriksen (Mon Oct 15 2012 - 12:58:48 PDT)
    - Re: [AMBER] performance of pmemd.cuda.MPI vs pmemd.cuda both running on single GPU Niel Henriksen (Tue Oct 16 2012 - 10:06:17 PDT)
- Re: [AMBER] performance of pmemd.cuda.MPI vs pmemd.cuda both running on single GPU pavel.banas.upol.cz (Tue Oct 16 2012 - 13:57:04 PDT)
[AMBER] umbrella sampling Elisa Frezza (Mon Oct 15 2012 - 00:32:26 PDT)
- Re: [AMBER] umbrella sampling Jason Swails (Mon Oct 15 2012 - 05:07:24 PDT)
  - Re: [AMBER] umbrella sampling Elisa Frezza (Mon Oct 15 2012 - 05:13:28 PDT)
[AMBER] NPA charge for the ligand Mu Xia (Mon Oct 15 2012 - 00:58:30 PDT)
- Re: [AMBER] NPA charge for the ligand FyD (Mon Oct 15 2012 - 01:37:11 PDT)
[AMBER] glyco yanyuna (Mon Oct 15 2012 - 01:59:46 PDT)
- Re: [AMBER] glyco Lachele Foley (Lists) (Mon Oct 15 2012 - 17:26:50 PDT)
  - Re: [AMBER] glyco yanyuna (Mon Oct 15 2012 - 19:58:57 PDT)
    - Re: [AMBER] glyco Lachele Foley (Lists) (Wed Oct 17 2012 - 18:27:22 PDT)
[AMBER] How dose ptraj calculate diffusion Alan (Mon Oct 15 2012 - 04:56:51 PDT)
- Re: [AMBER] How dose ptraj calculate diffusion Daniel Roe (Mon Oct 15 2012 - 14:23:57 PDT)
[AMBER] RESP charge of the ligand Mu Xia (Mon Oct 15 2012 - 07:08:17 PDT)
- Re: [AMBER] RESP charge of the ligand FyD (Tue Oct 16 2012 - 01:44:50 PDT)
[AMBER] Maintaining Chain ID Brown, Kyle (Mon Oct 15 2012 - 10:26:52 PDT)
- Re: [AMBER] Maintaining Chain ID David A Case (Mon Oct 15 2012 - 12:45:36 PDT)
  - Re: [AMBER] Maintaining Chain ID Daniel Roe (Wed Oct 17 2012 - 07:04:15 PDT)
    - [AMBER] Accelerated MD Shafinaz Chowdhury (Mon Dec 03 2012 - 10:43:03 PST)
    - Re: [AMBER] Accelerated MD Romelia Salomon (Mon Dec 03 2012 - 12:01:37 PST)
[AMBER] job failed for REMD in cluster Albert (Mon Oct 15 2012 - 11:48:04 PDT)
- Re: [AMBER] job failed for REMD in cluster Albert (Mon Oct 15 2012 - 11:53:49 PDT)
  - Re: [AMBER] job failed for REMD in cluster Carlos Simmerling (Mon Oct 15 2012 - 12:01:47 PDT)
    - Re: [AMBER] job failed for REMD in cluster Ross Walker (Mon Oct 15 2012 - 12:07:41 PDT)
    - Re: [AMBER] job failed for REMD in cluster David A Case (Mon Oct 15 2012 - 12:53:18 PDT)
    - Re: [AMBER] job failed for REMD in cluster Jason Swails (Mon Oct 15 2012 - 13:09:01 PDT)
    - Re: [AMBER] job failed for REMD in cluster Scott Le Grand (Mon Oct 15 2012 - 13:47:04 PDT)
  - Re: [AMBER] job failed for REMD in cluster Jason Swails (Mon Oct 15 2012 - 12:47:14 PDT)
- Re: [AMBER] job failed for REMD in cluster Ross Walker (Mon Oct 15 2012 - 12:06:32 PDT)
[AMBER] details of energy values for individual frames in MMPBSA.py calculations... Shashidhar Rao (Mon Oct 15 2012 - 12:12:41 PDT)
- Re: [AMBER] details of energy values for individual frames in MMPBSA.py calculations... Shashidhar Rao (Mon Oct 15 2012 - 12:25:09 PDT)
- Re: [AMBER] details of energy values for individual frames in MMPBSA.py calculations... Jason Swails (Mon Oct 15 2012 - 12:40:53 PDT)
  - Re: [AMBER] details of energy values for individual frames in MMPBSA.py calculations... Jason Swails (Mon Oct 15 2012 - 12:42:00 PDT)
    - Re: [AMBER] details of energy values for individual frames in MMPBSA.py calculations... Shashidhar Rao (Mon Oct 15 2012 - 13:19:59 PDT)
  - Re: [AMBER] details of energy values for individual frames in MMPBSA.py calculations... Shashidhar Rao (Mon Oct 15 2012 - 13:14:13 PDT)
    - Re: [AMBER] details of energy values for individual frames in MMPBSA.py calculations... Jason Swails (Mon Oct 15 2012 - 14:20:44 PDT)
[AMBER] residue split Carlos Romero (Mon Oct 15 2012 - 22:16:42 PDT)
- Re: [AMBER] residue split Carlos Simmerling (Tue Oct 16 2012 - 03:13:57 PDT)
  - Re: [AMBER] residue split Carlos Romero (Tue Oct 16 2012 - 07:20:33 PDT)
    - Re: [AMBER] residue split David A Case (Tue Oct 16 2012 - 18:27:34 PDT)
    - Re: [AMBER] residue split Carlos Romero (Tue Oct 16 2012 - 22:11:04 PDT)
    - Re: [AMBER] residue split David A Case (Wed Oct 17 2012 - 06:19:14 PDT)
    - Re: [AMBER] residue split Carlos Romero (Thu Oct 18 2012 - 00:22:36 PDT)
[AMBER] CHAMBER: error in finding bond type Mike Limb (Tue Oct 16 2012 - 04:28:26 PDT)
- Re: [AMBER] CHAMBER: error in finding bond type Mark Williamson (Tue Oct 16 2012 - 05:24:38 PDT)
  - Re: [AMBER] CHAMBER: error in finding bond type Mark Williamson (Wed Oct 17 2012 - 05:29:17 PDT)
[AMBER] AMBER davide.savy.unina.it (Tue Oct 16 2012 - 06:28:27 PDT)
[AMBER] ACS awards deadline Oct 23 Carlos Simmerling (Tue Oct 16 2012 - 07:05:50 PDT)
[AMBER] genmetalFF.sh Renuka Ganesan (Tue Oct 16 2012 - 07:34:19 PDT)
- Re: [AMBER] genmetalFF.sh David A Case (Tue Oct 16 2012 - 18:33:18 PDT)
[AMBER] ambpdb problems Pyle, Ronald (Tue Oct 16 2012 - 07:59:00 PDT)
- Re: [AMBER] ambpdb problems Jason Swails (Tue Oct 16 2012 - 10:17:24 PDT)
[AMBER] MMPBSA.py Federica Chiappori (Tue Oct 16 2012 - 08:58:16 PDT)
- Re: [AMBER] MMPBSA.py Jason Swails (Tue Oct 16 2012 - 10:01:29 PDT)
  - Re: [AMBER] MMPBSA.py Federica Chiappori (Wed Oct 17 2012 - 02:03:17 PDT)
[AMBER] Incorrect Bond Assignment in AMBERTools 12 LeAP Aron Broom (Tue Oct 16 2012 - 09:59:55 PDT)
- Re: [AMBER] Incorrect Bond Assignment in AMBERTools 12 LeAP Jason Swails (Tue Oct 16 2012 - 10:15:35 PDT)
  - Re: [AMBER] Incorrect Bond Assignment in AMBERTools 12 LeAP Aron Broom (Tue Oct 16 2012 - 11:40:04 PDT)
    - Re: [AMBER] Incorrect Bond Assignment in AMBERTools 12 LeAP Aron Broom (Tue Oct 16 2012 - 16:26:15 PDT)
[AMBER] Request: Tell us your CUDA story Ross Walker (Tue Oct 16 2012 - 10:19:30 PDT)
[AMBER] Vina Docking model is not accepted in Antechamber Chris Chris (Tue Oct 16 2012 - 11:47:09 PDT)
- Re: [AMBER] Vina Docking model is not accepted in Antechamber Aldo Segura (Tue Oct 16 2012 - 13:35:43 PDT)
  - Re: [AMBER] Vina Docking model is not accepted in Antechamber Chris Chris (Tue Oct 16 2012 - 14:55:02 PDT)
    - Re: [AMBER] Vina Docking model is not accepted in Antechamber Aldo Segura (Tue Oct 16 2012 - 15:52:02 PDT)
    - Re: [AMBER] Vina Docking model is not accepted in Antechamber Chris Chris (Tue Oct 16 2012 - 21:09:12 PDT)
    - Re: [AMBER] Vina Docking model is not accepted in Antechamber Aldo Segura (Wed Oct 17 2012 - 07:36:11 PDT)
[AMBER] Temperature in TI run Fabrício Bracht (Tue Oct 16 2012 - 11:49:36 PDT)
- Re: [AMBER] Temperature in TI run Brian Radak (Tue Oct 16 2012 - 12:07:39 PDT)
  - Re: [AMBER] Temperature in TI run steinbrt.rci.rutgers.edu (Wed Oct 17 2012 - 00:48:13 PDT)
[AMBER] Atom-type for aromatic carbon attached by amide nitrogen Yun Shi (Tue Oct 16 2012 - 12:39:15 PDT)
- Re: [AMBER] Atom-type for aromatic carbon attached by amide nitrogen Aron Broom (Tue Oct 16 2012 - 15:21:45 PDT)
  - Re: [AMBER] Atom-type for aromatic carbon attached by amide nitrogen Yun Shi (Tue Oct 16 2012 - 16:07:01 PDT)
- Re: [AMBER] Atom-type for aromatic carbon attached by amide nitrogen Yun Shi (Tue Oct 16 2012 - 20:29:13 PDT)
[AMBER] Pairwise decoposition (MMPBSA) Xioling Chuang (Tue Oct 16 2012 - 19:34:41 PDT)
- Re: [AMBER] Pairwise decoposition (MMPBSA) Bill Miller III (Wed Oct 17 2012 - 08:19:51 PDT)
[AMBER] Accessible surface area Esam Tolba (Wed Oct 17 2012 - 01:47:10 PDT)
- Re: [AMBER] Accessible surface area Jason Swails (Wed Oct 17 2012 - 06:53:36 PDT)
[AMBER] umbrella sampling Elisa Frezza (Wed Oct 17 2012 - 02:32:01 PDT)
- Re: [AMBER] umbrella sampling Ignacio J. General (Wed Oct 17 2012 - 05:13:19 PDT)
  - Re: [AMBER] umbrella sampling Elisa Frezza (Wed Oct 17 2012 - 06:16:56 PDT)
    - Re: [AMBER] umbrella sampling Ignacio J. General (Wed Oct 17 2012 - 07:04:39 PDT)
    - Re: [AMBER] umbrella sampling Elisa Frezza (Wed Oct 17 2012 - 07:06:42 PDT)
    - Re: [AMBER] umbrella sampling Elisa Frezza (Wed Oct 17 2012 - 07:13:55 PDT)
    - Re: [AMBER] umbrella sampling Ignacio J. General (Wed Oct 17 2012 - 07:22:31 PDT)
[AMBER] compilation error on Amber 10 Abderezak-EXT.Mekfouldji.sanofi.com (Wed Oct 17 2012 - 03:41:44 PDT)
- Re: [AMBER] compilation error on Amber 10 David A Case (Wed Oct 17 2012 - 06:39:24 PDT)
[AMBER] distortion of the ligand during MD Mu Xia (Wed Oct 17 2012 - 04:12:45 PDT)
- Re: [AMBER] distortion of the ligand during MD David A Case (Wed Oct 17 2012 - 06:44:06 PDT)
  - Re: [AMBER] distortion of the ligand during MD Mu Xia (Wed Oct 17 2012 - 07:02:42 PDT)
    - Re: [AMBER] distortion of the ligand during MD Jason Swails (Wed Oct 17 2012 - 08:35:52 PDT)
[AMBER] problem umbrella sampling and gpus Elisa Frezza (Wed Oct 17 2012 - 06:08:38 PDT)
- Re: [AMBER] problem umbrella sampling and gpus Jason Swails (Thu Oct 18 2012 - 07:15:08 PDT)
[AMBER] Side chain correction for Asp Steven Neumann (Wed Oct 17 2012 - 07:43:35 PDT)
- Re: [AMBER] Side chain correction for Asp David A Case (Wed Oct 17 2012 - 09:32:16 PDT)
[AMBER] about reproduction of HIS RESP charge Jocelyne Sogotongo (Wed Oct 17 2012 - 08:23:44 PDT)
- Re: [AMBER] about reproduction of HIS RESP charge FyD (Thu Oct 18 2012 - 12:39:39 PDT)
[AMBER] problem with decompostion energy Maryam Hamzehee (Wed Oct 17 2012 - 08:27:14 PDT)
- Re: [AMBER] problem with decompostion energy Bill Miller III (Wed Oct 17 2012 - 08:36:05 PDT)
[AMBER] Side chain correction for ASP Steven Neumann (Wed Oct 17 2012 - 08:35:06 PDT)
[AMBER] Leap ditribution davide.savy.unina.it (Wed Oct 17 2012 - 08:49:01 PDT)
- Re: [AMBER] Leap ditribution Aron Broom (Wed Oct 17 2012 - 09:05:48 PDT)
  - Re: [AMBER] Leap ditribution David A Case (Wed Oct 17 2012 - 09:37:02 PDT)
    - [AMBER] Clustering VS constant rmsd Catein Catherine (Wed Oct 17 2012 - 10:23:50 PDT)
    - Re: [AMBER] Clustering VS constant rmsd vaibhav dixit (Wed Oct 17 2012 - 10:47:02 PDT)
    - Re: [AMBER] Clustering VS constant rmsd David A Case (Wed Oct 17 2012 - 18:09:53 PDT)
    - Re: [AMBER] Clustering VS constant rmsd George Tzotzos (Wed Oct 17 2012 - 18:19:33 PDT)
    - Re: [AMBER] Clustering VS constant rmsd David A Case (Thu Oct 18 2012 - 04:39:06 PDT)
    - Re: [AMBER] Clustering VS constant rmsd George Tzotzos (Thu Oct 18 2012 - 10:33:57 PDT)
    - [AMBER] Should we exclude "equilibri?um state" conformers? Catein Catherine (Wed Oct 17 2012 - 19:48:54 PDT)
    - [AMBER] clustering error message Catein Catherine (Wed Oct 17 2012 - 10:29:13 PDT)
    - Re: [AMBER] clustering error message Daniel Roe (Wed Oct 17 2012 - 13:08:02 PDT)
[AMBER] Random Seed Jordan, Brad (Wed Oct 17 2012 - 10:08:09 PDT)
- Re: [AMBER] Random Seed Brian Radak (Wed Oct 17 2012 - 10:39:14 PDT)
[AMBER] cuda pmemd failed Yubo Fan (Thu Oct 18 2012 - 00:41:11 PDT)
[AMBER] Computer specification for Amber 12 Esam Tolba (Thu Oct 18 2012 - 02:03:32 PDT)
[AMBER] different restraint_wt settings possble? hironori.kokubo.takeda.com (Thu Oct 18 2012 - 02:12:15 PDT)
[AMBER] short bonds in average pdb Mu Xia (Thu Oct 18 2012 - 02:40:34 PDT)
- Re: [AMBER] short bonds in average pdb Jason Swails (Thu Oct 18 2012 - 06:44:31 PDT)
  - Re: [AMBER] short bonds in average pdb steinbrt.rci.rutgers.edu (Thu Oct 18 2012 - 07:09:54 PDT)
    - Re: [AMBER] short bonds in average pdb Carlos Simmerling (Thu Oct 18 2012 - 07:24:47 PDT)
    - Re: [AMBER] short bonds in average pdb vaibhav dixit (Thu Oct 18 2012 - 07:37:44 PDT)
    - Re: [AMBER] short bonds in average pdb Carlos Simmerling (Thu Oct 18 2012 - 07:52:39 PDT)
    - Re: [AMBER] short bonds in average pdb Vaibhav Dixit (Wed Feb 20 2013 - 01:04:37 PST)
    - Re: [AMBER] short bonds in average pdb Vaibhav Dixit (Wed Feb 20 2013 - 01:17:57 PST)
[AMBER] "istrng" option in MMPBSA calculation baogen duan (Thu Oct 18 2012 - 03:57:29 PDT)
- Re: [AMBER] "istrng" option in MMPBSA calculation Jason Swails (Thu Oct 18 2012 - 05:00:50 PDT)
[AMBER] cuda pmemd failed Yubo Fan (Thu Oct 18 2012 - 04:51:52 PDT)
[AMBER] cuda pmemd failed Yubo Fan (Thu Oct 18 2012 - 06:00:05 PDT)
- Re: [AMBER] cuda pmemd failed Jason Swails (Thu Oct 18 2012 - 06:39:17 PDT)
  - Re: [AMBER] cuda pmemd failed Scott Le Grand (Thu Oct 18 2012 - 11:02:15 PDT)
[AMBER] cuda pmemd failed Yubo Fan (Thu Oct 18 2012 - 06:37:55 PDT)
- Re: [AMBER] cuda pmemd failed Ross Walker (Fri Oct 19 2012 - 11:31:05 PDT)
[AMBER] Concerning nonbonded exclusions and MMPBSA Aron Broom (Thu Oct 18 2012 - 08:45:25 PDT)
- Re: [AMBER] Concerning nonbonded exclusions and MMPBSA Jason Swails (Thu Oct 18 2012 - 08:57:58 PDT)
  - Re: [AMBER] Concerning nonbonded exclusions and MMPBSA Aron Broom (Thu Oct 18 2012 - 09:35:24 PDT)
[AMBER] cis form: avoiding atom overlap in all-atom modeling bio lab (Thu Oct 18 2012 - 09:42:13 PDT)
- Re: [AMBER] cis form: avoiding atom overlap in all-atom modeling Aron Broom (Thu Oct 18 2012 - 09:53:40 PDT)
  - Re: [AMBER] cis form: avoiding atom overlap in all-atom modeling bio lab (Thu Oct 18 2012 - 11:10:58 PDT)
    - Re: [AMBER] cis form: avoiding atom overlap in all-atom modeling Aron Broom (Thu Oct 18 2012 - 12:30:30 PDT)
    - Re: [AMBER] cis form: avoiding atom overlap in all-atom modeling bio lab (Thu Oct 18 2012 - 17:05:47 PDT)
    - Re: [AMBER] cis form: avoiding atom overlap in all-atom modeling Aron Broom (Thu Oct 18 2012 - 18:30:02 PDT)
    - Re: [AMBER] cis form: avoiding atom overlap in all-atom modeling Aron Broom (Thu Oct 18 2012 - 21:36:08 PDT)
    - Re: [AMBER] cis form: avoiding atom overlap in all-atom modeling bio lab (Fri Oct 19 2012 - 10:11:16 PDT)
    - Re: [AMBER] cis form: avoiding atom overlap in all-atom modeling Aron Broom (Fri Oct 19 2012 - 11:30:18 PDT)
- Re: [AMBER] cis form: avoiding atom overlap in all-atom modeling Anselm Horn (Tue Oct 23 2012 - 00:50:07 PDT)
  - Re: [AMBER] cis form: avoiding atom overlap in all-atom modeling David A Case (Tue Oct 23 2012 - 05:26:28 PDT)
[AMBER] intdiel / extdiel Gustavo Seabra (Thu Oct 18 2012 - 11:01:02 PDT)
- Re: [AMBER] intdiel / extdiel Jason Swails (Thu Oct 18 2012 - 12:26:22 PDT)
  - Re: [AMBER] intdiel / extdiel Gustavo Seabra (Thu Oct 18 2012 - 15:35:40 PDT)
    - Re: [AMBER] intdiel / extdiel Jason Swails (Thu Oct 18 2012 - 15:59:25 PDT)
    - Re: [AMBER] intdiel / extdiel Daniel Roe (Thu Oct 18 2012 - 16:48:10 PDT)
    - Re: [AMBER] intdiel / extdiel Gustavo Seabra (Thu Oct 18 2012 - 17:12:49 PDT)
[AMBER] Probelms encountered when creating non-standard residue Changqing Yan (Thu Oct 18 2012 - 20:07:59 PDT)
- Re: [AMBER] Probelms encountered when creating non-standard residue Aron Broom (Thu Oct 18 2012 - 21:25:20 PDT)
[AMBER] amber12 (pmemd.cuda) on GeForce GTX 580 ? Tomasz Borowski (Fri Oct 19 2012 - 01:13:38 PDT)
- Re: [AMBER] amber12 (pmemd.cuda) on GeForce GTX 580 ? Robert Crovella (Fri Oct 19 2012 - 06:50:05 PDT)
  - Re: [AMBER] amber12 (pmemd.cuda) on GeForce GTX 580 ? Aron Broom (Fri Oct 19 2012 - 07:45:13 PDT)
- Re: [AMBER] amber12 (pmemd.cuda) on GeForce GTX 580 ? Ross Walker (Fri Oct 19 2012 - 11:09:32 PDT)
  - Re: [AMBER] amber12 (pmemd.cuda) on GeForce GTX 580 ? Tomasz Borowski (Tue Oct 23 2012 - 04:40:02 PDT)
    - Re: [AMBER] amber12 (pmemd.cuda) on GeForce GTX 580 ? peter.stauffert.boehringer-ingelheim.com (Tue Oct 23 2012 - 05:42:10 PDT)
    - Re: [AMBER] amber12 (pmemd.cuda) on GeForce GTX 580 ? Ross Walker (Tue Oct 23 2012 - 09:21:14 PDT)
    - Re: [AMBER] amber12 (pmemd.cuda) on GeForce GTX 580 ? Tomasz Borowski (Mon Oct 29 2012 - 05:25:45 PDT)
- [AMBER] files for RED Urszula Uciechowska (Mon Oct 22 2012 - 01:52:17 PDT)
  - Re: [AMBER] files for RED FyD (Mon Oct 22 2012 - 08:44:09 PDT)
    - Re: [AMBER] files for RED Urszula Uciechowska (Wed Oct 24 2012 - 03:23:44 PDT)
    - Re: [AMBER] files for RED FyD (Wed Oct 24 2012 - 05:13:03 PDT)
    - Re: [AMBER] files for RED Urszula Uciechowska (Thu Oct 25 2012 - 04:10:02 PDT)
    - Re: [AMBER] files for RED FyD (Thu Oct 25 2012 - 05:34:49 PDT)
    - Re: [AMBER] files for RED Urszula Uciechowska (Sat Oct 27 2012 - 07:30:06 PDT)
    - Re: [AMBER] files for RED FyD (Sun Oct 28 2012 - 09:53:44 PDT)
[AMBER] "Bad value during floating point read" of processing dihedral using chamber baogen duan (Fri Oct 19 2012 - 05:56:57 PDT)
[AMBER] NaN question mhclewett.msn.com (Fri Oct 19 2012 - 07:36:49 PDT)
- Re: [AMBER] NaN question Jason Swails (Fri Oct 19 2012 - 07:49:50 PDT)
  - Re: [AMBER] NaN question mhclewett.msn.com (Fri Oct 19 2012 - 09:46:58 PDT)
    - Re: [AMBER] NaN question Jason Swails (Fri Oct 19 2012 - 10:07:32 PDT)
    - [AMBER] How to convert ptraj cluster commands to cpptraj Catein Catherine (Fri Oct 19 2012 - 10:49:28 PDT)
    - [AMBER] How to read the PairwiseDistance file after clustering analysis? Catein Catherine (Fri Oct 19 2012 - 10:54:28 PDT)
- Re: [AMBER] NaN question Aron Broom (Fri Oct 19 2012 - 07:51:35 PDT)
  - Re: [AMBER] NaN question mhclewett.msn.com (Fri Oct 19 2012 - 09:48:09 PDT)
- Re: [AMBER] NaN question Ross Walker (Fri Oct 19 2012 - 11:19:04 PDT)
  - Re: [AMBER] NaN question mhclewett.msn.com (Sat Oct 20 2012 - 08:43:59 PDT)
[AMBER] Cuda test hangs with Amber12 compiled with CUDA5 Jean-Christophe Ducom (Fri Oct 19 2012 - 10:40:27 PDT)
- Re: [AMBER] Cuda test hangs with Amber12 compiled with CUDA5 Ismail, Mohd F. (Fri Oct 19 2012 - 11:12:59 PDT)
  - Re: [AMBER] Cuda test hangs with Amber12 compiled with CUDA5 Jean-Christophe Ducom (Fri Oct 19 2012 - 11:18:46 PDT)
- Re: [AMBER] Cuda test hangs with Amber12 compiled with CUDA5 Ross Walker (Fri Oct 19 2012 - 11:19:59 PDT)
[AMBER] AmberTools12 unset variable in sqm/MNDOChargeSeparation.F90 Ake Sandgren (Fri Oct 19 2012 - 13:11:00 PDT)
- Re: [AMBER] AmberTools12 unset variable in sqm/MNDOChargeSeparation.F90 Andreas Goetz (Mon Oct 22 2012 - 13:11:24 PDT)
  - Re: [AMBER] AmberTools12 unset variable in sqm/MNDOChargeSeparation.F90 Ake Sandgren (Mon Oct 22 2012 - 13:18:47 PDT)
    - Re: [AMBER] AmberTools12 unset variable in sqm/MNDOChargeSeparation.F90 Andreas Goetz (Mon Oct 22 2012 - 15:02:28 PDT)
[AMBER] Amber12 uninitialized variable in sander/nmr.F90 Ake Sandgren (Fri Oct 19 2012 - 14:55:20 PDT)
- Re: [AMBER] Amber12 uninitialized variable in sander/nmr.F90 Jason Swails (Fri Oct 19 2012 - 15:21:51 PDT)
[AMBER] configure problem during installation vaibhav dixit (Sat Oct 20 2012 - 01:40:26 PDT)
- Re: [AMBER] configure problem during installation Jason Swails (Sat Oct 20 2012 - 05:41:26 PDT)
  - Re: [AMBER] configure problem during installation vaibhav dixit (Sat Oct 20 2012 - 07:45:38 PDT)
[AMBER] Bad atom type Osman, Roman (Sat Oct 20 2012 - 17:12:46 PDT)
- Re: [AMBER] Bad atom type Jason Swails (Sat Oct 20 2012 - 19:42:49 PDT)
  - Re: [AMBER] Bad atom type Osman, Roman (Sun Oct 21 2012 - 17:58:56 PDT)
[AMBER] Meaning of the term "pre-equilibrated" waters Sajeewa Pemasinghe (Sun Oct 21 2012 - 09:54:10 PDT)
- Re: [AMBER] Meaning of the term "pre-equilibrated" waters Bill Ross (Sun Oct 21 2012 - 17:31:24 PDT)
  - [AMBER] Hydrophobic cleft is solvent-exposed Mannan (Sun Oct 21 2012 - 19:06:17 PDT)
Re: [AMBER] How Can I modify a amino acid in Amber Changqing Yan (Sun Oct 21 2012 - 19:22:19 PDT)
- Re: [AMBER] How Can I modify a amino acid in Amber FyD (Sun Oct 21 2012 - 22:59:59 PDT)
[AMBER] RNA - build a mismatch and a loop with NAB Amparo Garcia Lopez (Mon Oct 22 2012 - 07:11:13 PDT)
- Re: [AMBER] RNA - build a mismatch and a loop with NAB Jason Swails (Mon Oct 22 2012 - 11:40:34 PDT)
  - Re: [AMBER] RNA - build a mismatch and a loop with NAB Amparo Garcia Lopez (Tue Oct 23 2012 - 01:06:39 PDT)
    - Re: [AMBER] RNA - build a mismatch and a loop with NAB David A Case (Tue Oct 23 2012 - 05:20:17 PDT)
    - Re: [AMBER] RNA - build a mismatch and a loop with NAB Amparo Garcia Lopez (Wed Oct 24 2012 - 02:58:44 PDT)
    - Re: [AMBER] RNA - build a mismatch and a loop with NAB Jason Swails (Wed Oct 24 2012 - 04:30:27 PDT)
    - Re: [AMBER] RNA - build a mismatch and a loop with NAB M. L. Dodson (Tue Oct 23 2012 - 05:31:59 PDT)
[AMBER] MMPBSA.py error in AmberTools 12 fixed Jason Swails (Mon Oct 22 2012 - 08:57:10 PDT)
[AMBER] extract velocities Giulia (Mon Oct 22 2012 - 09:11:48 PDT)
- Re: [AMBER] extract velocities Brian Radak (Mon Oct 22 2012 - 13:47:05 PDT)
[AMBER] [PATCH 0/8] AmberTools cleanups Reinis Danne (Mon Oct 22 2012 - 15:14:53 PDT)
- [AMBER] [PATCH 1/8] AmberTools: Fix buffer overflows in mdgx, nab and ptraj Reinis Danne (Mon Oct 22 2012 - 15:14:54 PDT)
  - Re: [AMBER] [PATCH 1/8] AmberTools: Fix buffer overflows in mdgx, nab and ptraj David A Case (Mon Nov 26 2012 - 05:31:36 PST)
- [AMBER] [PATCH 3/8] nab.c: Don't hardcode CPP path Reinis Danne (Mon Oct 22 2012 - 15:14:56 PDT)
- [AMBER] [PATCH 4/8] sqm: Fix OpenMP build Reinis Danne (Mon Oct 22 2012 - 15:14:57 PDT)
  - Re: [AMBER] [PATCH 4/8] sqm: Fix OpenMP build David A Case (Tue Oct 23 2012 - 06:29:28 PDT)
    - Re: [AMBER] [PATCH 4/8] sqm: Fix OpenMP build Reinis (Tue Oct 23 2012 - 08:37:25 PDT)
    - Re: [AMBER] [PATCH 4/8] sqm: Fix OpenMP build Gustavo Seabra (Tue Oct 23 2012 - 08:50:57 PDT)
    - Re: [AMBER] [PATCH 4/8] sqm: Fix OpenMP build Reinis (Tue Oct 23 2012 - 09:21:05 PDT)
    - Re: [AMBER] [PATCH 4/8] sqm: Fix OpenMP build Gustavo Seabra (Tue Oct 23 2012 - 11:56:42 PDT)
    - Re: [AMBER] [PATCH 4/8] sqm: Fix OpenMP build Reinis (Tue Oct 23 2012 - 12:41:11 PDT)
    - Re: [AMBER] [PATCH 4/8] sqm: Fix OpenMP build Gustavo Seabra (Tue Oct 23 2012 - 12:51:43 PDT)
    - Re: [AMBER] [PATCH 4/8] sqm: Fix OpenMP build Reinis (Tue Oct 23 2012 - 13:55:26 PDT)
    - Re: [AMBER] [PATCH 4/8] sqm: Fix OpenMP build Jason Swails (Tue Oct 23 2012 - 16:20:49 PDT)
    - Re: [AMBER] [PATCH 4/8] sqm: Fix OpenMP build Reinis (Wed Oct 24 2012 - 01:09:25 PDT)
    - Re: [AMBER] [PATCH 4/8] sqm: Fix OpenMP build Ross Walker (Wed Oct 24 2012 - 09:15:18 PDT)
    - Re: [AMBER] [PATCH 4/8] sqm: Fix OpenMP build Reinis (Wed Oct 24 2012 - 11:30:25 PDT)
    - Re: [AMBER] [PATCH 4/8] sqm: Fix OpenMP build Ross Walker (Wed Oct 24 2012 - 12:52:03 PDT)
    - Re: [AMBER] [PATCH 4/8] sqm: Fix OpenMP build Reinis (Wed Oct 24 2012 - 15:55:05 PDT)
    - Re: [AMBER] [PATCH 4/8] sqm: Fix OpenMP build Ross Walker (Tue Oct 23 2012 - 09:26:34 PDT)
    - Re: [AMBER] [PATCH 4/8] sqm: Fix OpenMP build Reinis (Tue Oct 23 2012 - 09:33:54 PDT)
    - Re: [AMBER] [PATCH 4/8] sqm: Fix OpenMP build Ross Walker (Tue Oct 23 2012 - 10:00:36 PDT)
- [AMBER] [PATCH 2/8] dsarpack.f: Move into sff to allow build against arpack-ng Reinis Danne (Mon Oct 22 2012 - 15:14:55 PDT)
- [AMBER] [PATCH 5/8] test/nab: Use paths to scripts Reinis Danne (Mon Oct 22 2012 - 15:14:58 PDT)
  - Re: [AMBER] [PATCH 5/8] test/nab: Use paths to scripts David A Case (Thu Oct 25 2012 - 16:58:56 PDT)
- [AMBER] [PATCH 6/8] AmberTools: Tests should fail when they fail Reinis Danne (Mon Oct 22 2012 - 15:14:59 PDT)
- [AMBER] [PATCH 7/8] AmberTools: Fix parallel tests Reinis Danne (Mon Oct 22 2012 - 15:15:00 PDT)
- [AMBER] [PATCH 8/8] amber_outputs.py: Format floats in csv output Reinis Danne (Mon Oct 22 2012 - 15:15:01 PDT)
- Re: [AMBER] [PATCH 0/8] AmberTools cleanups David A Case (Tue Oct 23 2012 - 05:43:36 PDT)
  - Re: [AMBER] [PATCH 0/8] AmberTools cleanups Reinis (Tue Oct 23 2012 - 08:08:25 PDT)
[AMBER] compilation aborted for ncsu-umbrella.F90 (code 1) hari krishna (Tue Oct 23 2012 - 04:48:44 PDT)
- Re: [AMBER] compilation aborted for ncsu-umbrella.F90 (code 1) Jason Swails (Tue Oct 23 2012 - 06:19:01 PDT)
- Re: [AMBER] compilation aborted for ncsu-umbrella.F90 (code 1) David A Case (Tue Oct 23 2012 - 06:18:41 PDT)
Re: [AMBER] Antechamber Warning Atomtype ashley chen (Tue Oct 23 2012 - 23:37:40 PDT)
- Re: [AMBER] Antechamber Warning Atomtype Jason Swails (Wed Oct 24 2012 - 12:55:43 PDT)
[AMBER] Computational methods to explain the small regioselectivity Mu Xia (Wed Oct 24 2012 - 01:21:55 PDT)
[AMBER] Calculation of single atom radius of gyration Amy Davenport (Wed Oct 24 2012 - 14:50:20 PDT)
- Re: [AMBER] Calculation of single atom radius of gyration Daniel Roe (Wed Oct 24 2012 - 15:51:46 PDT)
- Re: [AMBER] Calculation of single atom radius of gyration Jason Swails (Wed Oct 24 2012 - 15:52:22 PDT)
[AMBER] Possible bug in LEaP with ff12SB Aronica, Pietro (Thu Oct 25 2012 - 04:23:32 PDT)
- Re: [AMBER] Possible bug in LEaP with ff12SB David A Case (Thu Oct 25 2012 - 05:32:43 PDT)
  - Re: [AMBER] Possible bug in LEaP with ff12SB Aronica, Pietro (Thu Oct 25 2012 - 05:36:11 PDT)
  - [AMBER] Misleading leaprc with ff12 Jesper Sørensen (Thu Oct 25 2012 - 10:00:24 PDT)
    - Re: [AMBER] Misleading leaprc with ff12 David A Case (Fri Oct 26 2012 - 04:49:47 PDT)
    - [AMBER] Trajectory Clustering Chiara Pallara (Fri Oct 26 2012 - 05:08:38 PDT)
    - Re: [AMBER] Trajectory Clustering Gustavo Seabra (Fri Oct 26 2012 - 05:39:06 PDT)
    - Re: [AMBER] Trajectory Clustering David Condon (Fri Oct 26 2012 - 05:43:40 PDT)
    - Re: [AMBER] Trajectory Clustering George Tzotzos (Fri Oct 26 2012 - 05:47:16 PDT)
    - Re: [AMBER] Trajectory Clustering Chiara Pallara (Fri Oct 26 2012 - 09:04:24 PDT)
    - Re: [AMBER] Trajectory Clustering Gannett, Peter (Fri Oct 26 2012 - 05:47:03 PDT)
    - Re: [AMBER] Trajectory Clustering Ilyas Yildirim (Fri Oct 26 2012 - 05:47:15 PDT)
    - Re: [AMBER] Trajectory Clustering Daniel Roe (Fri Oct 26 2012 - 07:22:05 PDT)
- Re: [AMBER] Possible bug in LEaP with ff12SB Bill Ross (Thu Oct 25 2012 - 23:47:25 PDT)
[AMBER] Hydrogen bond time series in cpptraj Diego Javier Alonso de Armiño (Thu Oct 25 2012 - 06:23:33 PDT)
- Re: [AMBER] Hydrogen bond time series in cpptraj Daniel Roe (Thu Oct 25 2012 - 08:16:03 PDT)
[AMBER] Calculation of single atom radius of gyration Amy Davenport (Thu Oct 25 2012 - 16:02:50 PDT)
- Re: [AMBER] Calculation of single atom radius of gyration Daniel Sindhikara (Thu Oct 25 2012 - 18:54:15 PDT)
- Re: [AMBER] Calculation of single atom radius of gyration Amy Davenport (Fri Oct 26 2012 - 14:04:04 PDT)
  - Re: [AMBER] Calculation of single atom radius of gyration Daniel Roe (Fri Oct 26 2012 - 14:34:40 PDT)
[AMBER] Error 'Created a new atom named:' Joaquin Barroso Flores (Thu Oct 25 2012 - 18:26:03 PDT)
- Re: [AMBER] Error 'Created a new atom named:' Olguin, Marco A (Thu Oct 25 2012 - 18:43:24 PDT)
[AMBER] can i strip water energy from .out ? 千语千寻 (Thu Oct 25 2012 - 23:22:30 PDT)
- Re: [AMBER] can i strip water energy from .out ? Jason Swails (Fri Oct 26 2012 - 06:32:29 PDT)
- Re: [AMBER] can i strip water energy from .out ? Tong Zhu (Sun Oct 28 2012 - 21:45:19 PDT)
  - Re: [AMBER] can i strip water energy from .out ? Jason Swails (Mon Oct 29 2012 - 06:12:03 PDT)
[AMBER] Problem with CHAMBER (for RNA molecule) Marc van der Kamp (Fri Oct 26 2012 - 01:59:17 PDT)
- Re: [AMBER] Problem with CHAMBER (for RNA molecule) Mark Williamson (Fri Oct 26 2012 - 08:28:04 PDT)
  - Re: [AMBER] Problem with CHAMBER (for RNA molecule) Marc van der Kamp (Tue Oct 30 2012 - 05:09:20 PDT)
[AMBER] Compiling amber parallel Dickson, Callum (Fri Oct 26 2012 - 08:11:18 PDT)
[AMBER] NetCDF and MTK++ configuration issues after applying bugfixes 15-27 Miguel Ortiz Lombardía (Fri Oct 26 2012 - 08:42:51 PDT)
- Re: [AMBER] NetCDF and MTK++ configuration issues after applying bugfixes 15-27 Jason Swails (Fri Oct 26 2012 - 09:19:44 PDT)
  - Re: [AMBER] NetCDF and MTK++ configuration issues after applying bugfixes 15-27 Miguel Ortiz Lombardia (Fri Oct 26 2012 - 14:39:17 PDT)
[AMBER] join amber mailing list Yulin Huang (Fri Oct 26 2012 - 13:44:50 PDT)
[AMBER] Inquiry about how writing out pressure tensor Mo Chen (Fri Oct 26 2012 - 15:57:17 PDT)
- Re: [AMBER] Inquiry about how writing out pressure tensor Ross Walker (Fri Oct 26 2012 - 16:48:16 PDT)
  - Re: [AMBER] Inquiry about how writing out pressure tensor Mo Chen (Fri Oct 26 2012 - 18:57:51 PDT)
    - Re: [AMBER] Inquiry about how writing out pressure tensor Mo Chen (Mon Oct 29 2012 - 00:04:03 PDT)
    - Re: [AMBER] Inquiry about how writing out pressure tensor Mo Chen (Mon Oct 29 2012 - 00:13:12 PDT)
    - Re: [AMBER] Inquiry about how writing out pressure tensor David A Case (Mon Oct 29 2012 - 07:10:30 PDT)
    - Re: [AMBER] Inquiry about how writing out pressure tensor Mo Chen (Mon Oct 29 2012 - 12:29:50 PDT)
[AMBER] Fwd: Re: files for RED FyD (Sun Oct 28 2012 - 09:58:34 PDT)
- Re: [AMBER] Fwd: Re: files for RED Urszula Uciechowska (Tue Oct 30 2012 - 01:54:51 PDT)
  - Re: [AMBER] Fwd: Re: files for RED FyD (Tue Oct 30 2012 - 03:54:57 PDT)
    - Re: [AMBER] Fwd: Re: files for RED Urszula Uciechowska (Wed Oct 31 2012 - 00:55:35 PDT)
    - Re: [AMBER] Fwd: Re: files for RED FyD (Wed Oct 31 2012 - 03:57:55 PDT)
[AMBER] If i strip water from the trajectory files, would it influence the analysis results? 千语千寻 (Sun Oct 28 2012 - 19:17:17 PDT)
- Re: [AMBER] If i strip water from the trajectory files, would it influence the analysis results? Tong Zhu (Sun Oct 28 2012 - 21:43:06 PDT)
- Re: [AMBER] If i strip water from the trajectory files, would it influence the analysis results? Daniel Roe (Mon Oct 29 2012 - 07:28:25 PDT)
[AMBER] Joining two files Marco Malvaldi (Mon Oct 29 2012 - 03:47:35 PDT)
- Re: [AMBER] Joining two files Jacopo Sgrignani (Mon Oct 29 2012 - 05:31:06 PDT)
  - Re: [AMBER] Joining two files Lorenzo Gontrani (Mon Oct 29 2012 - 07:32:47 PDT)
    - Re: [AMBER] Joining two files Marco Malvaldi (Wed Oct 31 2012 - 05:00:03 PDT)
    - Re: [AMBER] Joining two files Lorenzo Gontrani (Wed Oct 31 2012 - 05:45:13 PDT)
[AMBER] Antechamber preparartion Алексей Раевский (Mon Oct 29 2012 - 04:57:10 PDT)
- Re: [AMBER] Antechamber preparartion David A Case (Mon Oct 29 2012 - 07:18:55 PDT)
- Re: [AMBER] Antechamber preparartion FyD (Tue Oct 30 2012 - 01:35:31 PDT)
[AMBER] Nonstandard residue: phosphotyrosine PAUL NEWMAN (Mon Oct 29 2012 - 07:03:47 PDT)
- Re: [AMBER] Nonstandard residue: phosphotyrosine Anselm Horn (Mon Oct 29 2012 - 07:24:02 PDT)
- Re: [AMBER] Nonstandard residue: phosphotyrosine PAUL NEWMAN (Mon Oct 29 2012 - 07:46:41 PDT)
  - Re: [AMBER] Nonstandard residue: phosphotyrosine Jason Swails (Mon Oct 29 2012 - 08:05:43 PDT)
    - Re: [AMBER] Nonstandard residue: phosphotyrosine steinbrt.rci.rutgers.edu (Mon Oct 29 2012 - 11:22:41 PDT)
[AMBER] deprotonated serine Antonija Tomić (Mon Oct 29 2012 - 07:27:06 PDT)
- Re: [AMBER] deprotonated serine BERGY (Fri Nov 02 2012 - 10:19:27 PDT)
[AMBER] questions about thermodynamic integration atom name and order Yulin Huang (Mon Oct 29 2012 - 07:35:55 PDT)
- Re: [AMBER] questions about thermodynamic integration atom name and order 千语千寻 (Mon Oct 29 2012 - 07:59:04 PDT)
- Re: [AMBER] questions about thermodynamic integration atom name and order Jodi Ann Hadden (Tue Oct 30 2012 - 13:48:16 PDT)
  - Re: [AMBER] questions about thermodynamic integration atom name and order Yulin Huang (Wed Oct 31 2012 - 08:27:49 PDT)
- Re: [AMBER] questions about thermodynamic integration atom name and order steinbrt.rci.rutgers.edu (Wed Oct 31 2012 - 01:35:56 PDT)
  - Re: [AMBER] questions about thermodynamic integration atom name and order Yulin Huang (Wed Oct 31 2012 - 08:30:36 PDT)
  - Re: [AMBER] questions about thermodynamic integration atom name and order Daniel Roe (Wed Oct 31 2012 - 08:43:24 PDT)
    - Re: [AMBER] questions about thermodynamic integration atom name and order Yulin Huang (Wed Oct 31 2012 - 09:17:59 PDT)
    - Re: [AMBER] questions about thermodynamic integration atom name and order Yulin Huang (Wed Oct 31 2012 - 19:10:16 PDT)
    - Re: [AMBER] questions about thermodynamic integration atom name and order Yulin Huang (Tue Nov 06 2012 - 07:20:32 PST)
    - Re: [AMBER] questions about thermodynamic integration atom name and order David A Case (Tue Nov 06 2012 - 12:06:20 PST)
    - Re: [AMBER] questions about thermodynamic integration atom name and order Yulin Huang (Tue Nov 06 2012 - 12:30:27 PST)
    - Re: [AMBER] questions about thermodynamic integration atom name and order Jason Swails (Tue Nov 06 2012 - 14:14:31 PST)
    - Re: [AMBER] questions about thermodynamic integration atom name and order David A Case (Wed Nov 07 2012 - 06:36:44 PST)
    - Re: [AMBER] questions about thermodynamic integration atom name and order David A Case (Wed Nov 07 2012 - 06:36:52 PST)
    - Re: [AMBER] questions about thermodynamic integration atom name and order Yulin Huang (Wed Nov 07 2012 - 06:39:18 PST)
[AMBER] radgyr of ptraj or cpptraj Binwu Zhao (Mon Oct 29 2012 - 09:57:45 PDT)
- Re: [AMBER] radgyr of ptraj or cpptraj Daniel Roe (Mon Oct 29 2012 - 11:17:23 PDT)
[AMBER] Updated GLYCAM parameters Lachele Foley (Lists) (Mon Oct 29 2012 - 11:15:04 PDT)
[AMBER] antechamber limitation on molecule size anyiphysics.gmail.com (Mon Oct 29 2012 - 12:37:25 PDT)
- Re: [AMBER] antechamber limitation on molecule size David A Case (Thu Nov 01 2012 - 10:34:59 PDT)
[AMBER] Atom selection for restraints Date, Mihir (Mon Oct 29 2012 - 15:41:10 PDT)
- Re: [AMBER] Atom selection for restraints Daniel Roe (Mon Oct 29 2012 - 16:10:52 PDT)
  - Re: [AMBER] Atom selection for restraints. . Date, Mihir (Tue Oct 30 2012 - 07:18:22 PDT)
    - Re: [AMBER] Atom selection for restraints. .. . Bashford, Donald (Tue Oct 30 2012 - 14:07:50 PDT)
[AMBER] positional restraint to within stipulated distance Eng H Yap (Mon Oct 29 2012 - 20:00:01 PDT)
- [AMBER] Error Message in running MM/GBSA Catein Catherine (Mon Oct 29 2012 - 22:51:59 PDT)
[AMBER] rmsd rmsf Yanyan MENG (Tue Oct 30 2012 - 00:50:10 PDT)
Re: [AMBER] error when Chamber dealing with DNA, RNA and ATP Mark Williamson (Tue Oct 30 2012 - 04:48:27 PDT)
- Re: [AMBER] error when Chamber dealing with DNA, RNA and ATP Ross Walker (Tue Oct 30 2012 - 11:03:56 PDT)
- Re: [AMBER] error when Chamber dealing with DNA, RNA and ATP baogen duan (Wed Oct 31 2012 - 19:40:53 PDT)
[AMBER] Request for MMPBSA files. Anogna (Tue Oct 30 2012 - 04:50:45 PDT)
- Re: [AMBER] Request for MMPBSA files. Jason Swails (Tue Oct 30 2012 - 07:15:25 PDT)
[AMBER] Amber12 installation and testing Rahul Banerjee (Tue Oct 30 2012 - 10:47:09 PDT)
- Re: [AMBER] Amber12 installation and testing Ross Walker (Tue Oct 30 2012 - 10:59:58 PDT)
[AMBER] tleap has error by applying amber ff03ua Yu-Ming Huang (Tue Oct 30 2012 - 17:04:29 PDT)
- [AMBER] tleap has error by applying amber ff03ua Chris Moth (Tue Jun 18 2013 - 15:56:25 PDT)
  - Re: [AMBER] tleap has error by applying amber ff03ua David A Case (Wed Jun 19 2013 - 05:25:11 PDT)
[AMBER] space-time correlation in AMBER 강현아 (Tue Oct 30 2012 - 19:38:58 PDT)
[AMBER] Problem in running parallel hari krishna (Tue Oct 30 2012 - 21:56:22 PDT)
- Re: [AMBER] Problem in running parallel Terry (Tue Oct 30 2012 - 22:33:15 PDT)
- Re: [AMBER] Problem in running parallel David A Case (Wed Oct 31 2012 - 07:46:17 PDT)
- Re: [AMBER] Problem in running parallel hari krishna (Wed Oct 31 2012 - 23:13:52 PDT)
  - Re: [AMBER] Problem in running parallel Terry (Wed Oct 31 2012 - 23:43:25 PDT)
[AMBER] Download problem of amber12 Sanjib Paul (Tue Oct 30 2012 - 23:25:35 PDT)
- Re: [AMBER] Download problem of amber12 David A Case (Wed Oct 31 2012 - 07:49:31 PDT)
  - Re: [AMBER] Download problem of amber12 Sanjib Paul (Thu Nov 01 2012 - 03:59:43 PDT)
[AMBER] Amber12 Parrell Installation Error chenkai_szpku (Wed Oct 31 2012 - 04:52:01 PDT)
- Re: [AMBER] Amber12 Parrell Installation Error BERGY (Fri Nov 02 2012 - 10:15:10 PDT)
[AMBER] Amber and P450 cytochromes Maximilian Ebert (Wed Oct 31 2012 - 07:05:21 PDT)
- Re: [AMBER] Amber and P450 cytochromes David A Case (Wed Oct 31 2012 - 07:55:54 PDT)
  - Re: [AMBER] Amber and P450 cytochromes Maximilian Ebert (Wed Oct 31 2012 - 08:53:56 PDT)
    - Re: [AMBER] Amber and P450 cytochromes Maximilian Ebert (Thu Nov 01 2012 - 08:25:07 PDT)
[AMBER] antechamber limitation on molecule size Yi An (Wed Oct 31 2012 - 12:05:59 PDT)
- Re: [AMBER] antechamber limitation on molecule size Daniel Roe (Wed Oct 31 2012 - 17:06:57 PDT)
  - Re: [AMBER] antechamber limitation on molecule size anyiphysics.gmail.com (Wed Oct 31 2012 - 18:27:50 PDT)
  - Re: [AMBER] antechamber limitation on molecule size FyD (Thu Nov 01 2012 - 01:17:29 PDT)
    - Re: [AMBER] antechamber limitation on molecule size anyiphysics.gmail.com (Wed Nov 07 2012 - 18:21:21 PST)
    - Re: [AMBER] antechamber limitation on molecule size Aron Broom (Wed Nov 07 2012 - 18:34:20 PST)
    - Re: [AMBER] antechamber limitation on molecule size Yi An (Wed Nov 07 2012 - 19:07:40 PST)
    - Re: [AMBER] antechamber limitation on molecule size FyD (Thu Nov 08 2012 - 01:55:44 PST)
    - Re: [AMBER] antechamber limitation on molecule size anyiphysics.gmail.com (Thu Nov 08 2012 - 08:44:36 PST)
[AMBER] solvation free enrgy calculation using PB equation. baogen duan (Thu Nov 01 2012 - 01:56:51 PDT)
- Re: [AMBER] solvation free enrgy calculation using PB equation. Ray Luo, Ph.D. (Thu Nov 01 2012 - 10:31:24 PDT)
- Re: [AMBER] solvation free enrgy calculation using PB equation. David A Case (Thu Nov 01 2012 - 10:37:42 PDT)
[AMBER] metal protein -regarding subramanian boopathi (Thu Nov 01 2012 - 03:49:52 PDT)
[AMBER] Best atom types for N-Oxides compounds like TMAO sa (Thu Nov 01 2012 - 05:39:44 PDT)
- Re: [AMBER] Best atom types for N-Oxides compounds like TMAO Gustavo Seabra (Thu Nov 01 2012 - 06:49:37 PDT)
  - Re: [AMBER] Best atom types for N-Oxides compounds like TMAO sa (Thu Nov 01 2012 - 07:05:40 PDT)
    - Re: [AMBER] Best atom types for N-Oxides compounds like TMAO Gustavo Seabra (Thu Nov 01 2012 - 07:22:00 PDT)
    - Re: [AMBER] Best atom types for N-Oxides compounds like TMAO sa (Thu Nov 01 2012 - 07:30:09 PDT)
[AMBER] force field file problem Changqing Yan (Thu Nov 01 2012 - 06:16:08 PDT)
- Re: [AMBER] force field file problem David A Case (Thu Nov 01 2012 - 11:47:46 PDT)
[AMBER] implementation of string method to find minimum free energy paths in Amber Tan Yaw Sing (Thu Nov 01 2012 - 06:49:34 PDT)
- Re: [AMBER] implementation of string method to find minimum free energy paths in Amber Christina Bergonzo (Thu Nov 01 2012 - 07:28:07 PDT)
[AMBER] references ? JAIME RUBIO MARTINEZ (Thu Nov 01 2012 - 11:27:40 PDT)
- Re: [AMBER] references ? Bill Miller III (Thu Nov 01 2012 - 12:33:24 PDT)
[AMBER] vlimit exceed for step 1- regarding subramanian boopathi (Thu Nov 01 2012 - 21:55:42 PDT)
- Re: [AMBER] vlimit exceed for step 1- regarding Ross Walker (Thu Nov 01 2012 - 22:32:37 PDT)
[AMBER] Amber12 PETASCALE Benchmarking. BERGY (Thu Nov 01 2012 - 22:09:02 PDT)
- Re: [AMBER] Amber12 PETASCALE Benchmarking. Ross Walker (Thu Nov 01 2012 - 22:27:54 PDT)
[AMBER] Cannot setting AMBERHOME on ubuntu 12.04 setyanto md (Fri Nov 02 2012 - 01:14:58 PDT)
- Re: [AMBER] Cannot setting AMBERHOME on ubuntu 12.04 David A Case (Fri Nov 02 2012 - 06:30:37 PDT)
[AMBER] vlimit exceeded error regarding subramanian boopathi (Fri Nov 02 2012 - 08:01:24 PDT)
- Re: [AMBER] vlimit exceeded error regarding Ross Walker (Fri Nov 02 2012 - 09:21:50 PDT)
[AMBER] how to calculate binding energy of one receptor and two ligands? bin wang (Fri Nov 02 2012 - 08:53:14 PDT)
- Re: [AMBER] how to calculate binding energy of one receptor and two ligands? Jason Swails (Fri Nov 02 2012 - 09:37:17 PDT)
  - Re: [AMBER] how to calculate binding energy of one receptor and two ligands? bin wang (Fri Nov 02 2012 - 10:30:22 PDT)
    - Re: [AMBER] how to calculate binding energy of one receptor and two ligands? Jason Swails (Fri Nov 02 2012 - 21:42:05 PDT)
[AMBER] AMBER-Gaussian and Infrared marawan hussain (Fri Nov 02 2012 - 19:07:05 PDT)
- Re: [AMBER] AMBER-Gaussian and Infrared Brian Radak (Sat Nov 03 2012 - 10:05:33 PDT)
  - Re: [AMBER] AMBER-Gaussian and Infrared Andreas Goetz (Sat Nov 03 2012 - 14:33:45 PDT)
    - Re: [AMBER] AMBER-Gaussian and Infrared Brent Krueger (Sun Nov 04 2012 - 03:37:30 PST)
[AMBER] Problem related to the RMSD Sindrila Dutta banik (Sat Nov 03 2012 - 07:25:11 PDT)
- Re: [AMBER] Problem related to the RMSD Jason Swails (Sat Nov 03 2012 - 08:43:20 PDT)
  - [AMBER] Problem related to the RMSD Sindrila Dutta banik (Sat Nov 03 2012 - 22:29:39 PDT)
    - Re: [AMBER] Problem related to the RMSD Niel Henriksen (Sun Nov 04 2012 - 06:52:15 PST)
[AMBER] no leaprc in search path Fabian Glaser (Sun Nov 04 2012 - 06:37:14 PST)
- Re: [AMBER] no leaprc in search path Jason Swails (Sun Nov 04 2012 - 07:14:31 PST)
  - Re: [AMBER] no leaprc in search path Fabian Glaser (Sun Nov 04 2012 - 07:24:16 PST)
    - Re: [AMBER] no leaprc in search path Jason Swails (Sun Nov 04 2012 - 08:40:49 PST)
    - Re: [AMBER] no leaprc in search path Fabian Glaser (Mon Nov 05 2012 - 06:18:55 PST)
[AMBER] Problem related to RMSD Sindrila Dutta banik (Sun Nov 04 2012 - 09:43:08 PST)
- Re: [AMBER] Problem related to RMSD Niel Henriksen (Sun Nov 04 2012 - 09:57:53 PST)
  - Re: [AMBER] Problem related to RMSD Jason Swails (Sun Nov 04 2012 - 17:35:40 PST)
    - [AMBER] Problem related to RMSD Sindrila Dutta banik (Sun Nov 04 2012 - 19:57:44 PST)
    - Re: [AMBER] Problem related to RMSD Niel Henriksen (Sun Nov 04 2012 - 20:20:02 PST)
    - [AMBER] Problem related to RMSD Sindrila Dutta banik (Sun Nov 04 2012 - 20:50:08 PST)
    - Re: [AMBER] Problem related to RMSD Miguel Ortiz Lombardia (Sun Nov 04 2012 - 23:19:21 PST)
[AMBER] MMPBSA.py "timer: need to reset the time before start" Adelene Sim (Sun Nov 04 2012 - 18:51:49 PST)
- Re: [AMBER] MMPBSA.py "timer: need to reset the time before start" Jason Swails (Mon Nov 05 2012 - 10:04:23 PST)
[AMBER] Clarifications in umbrella sampling Sajeewa Pemasinghe (Sun Nov 04 2012 - 20:32:22 PST)
- Re: [AMBER] Clarifications in umbrella sampling Aron Broom (Sun Nov 04 2012 - 22:00:37 PST)
  - Re: [AMBER] Clarifications in umbrella sampling Sajeewa Pemasinghe (Sun Nov 04 2012 - 23:28:03 PST)
    - Re: [AMBER] Clarifications in umbrella sampling steinbrt.rci.rutgers.edu (Mon Nov 05 2012 - 00:20:01 PST)
    - Re: [AMBER] Clarifications in umbrella sampling Sajeewa Pemasinghe (Mon Nov 05 2012 - 06:06:02 PST)
    - Re: [AMBER] Clarifications in umbrella sampling Aron Broom (Mon Nov 05 2012 - 08:45:45 PST)
[AMBER] Problem related to the RMSD Sindrila Dutta banik (Sun Nov 04 2012 - 22:37:27 PST)
[AMBER] How to use q4md-CD? Liu Denis (Mon Nov 05 2012 - 08:07:55 PST)
- Re: [AMBER] How to use q4md-CD? FyD (Mon Nov 05 2012 - 13:29:56 PST)
  - Re: [AMBER] How to use q4md-CD? Liu Denis (Tue Nov 06 2012 - 01:51:18 PST)
    - Re: [AMBER] How to use q4md-CD? FyD (Wed Nov 07 2012 - 00:22:13 PST)
[AMBER] workstation . mirage (Mon Nov 05 2012 - 08:45:39 PST)
- Re: [AMBER] workstation Ross Walker (Mon Nov 05 2012 - 12:39:26 PST)
[AMBER] tleap not recognizing Na+ David Condon (Mon Nov 05 2012 - 10:23:40 PST)
- Re: [AMBER] tleap not recognizing Na+ Aron Broom (Mon Nov 05 2012 - 10:58:37 PST)
- Re: [AMBER] tleap not recognizing Na+ Ilyas Yildirim (Mon Nov 05 2012 - 10:59:25 PST)
- Re: [AMBER] tleap not recognizing Na+ David A Case (Mon Nov 05 2012 - 12:11:17 PST)
Re: [AMBER] [Private q4md] R.E.D. Server: Private assistance FyD (Mon Nov 05 2012 - 12:15:33 PST)
- Re: [AMBER] [Private q4md] R.E.D. Server: Private assistance FyD (Fri Aug 22 2014 - 12:27:23 PDT)
[AMBER] Dipole from a mask Ismail, Mohd F. (Mon Nov 05 2012 - 13:29:34 PST)
- Re: [AMBER] Dipole from a mask Daniel Roe (Tue Nov 06 2012 - 12:31:42 PST)
  - Re: [AMBER] Dipole from a mask Ismail, Mohd F. (Wed Nov 07 2012 - 14:26:56 PST)
    - Re: [AMBER] Dipole from a mask Daniel Roe (Thu Nov 08 2012 - 08:05:29 PST)
    - Re: [AMBER] Dipole from a mask Ismail, Mohd F. (Thu Nov 08 2012 - 21:07:34 PST)
    - Re: [AMBER] Dipole from a mask Daniel Roe (Fri Nov 09 2012 - 07:05:09 PST)
    - Re: [AMBER] Dipole from a mask Ismail, Mohd F. (Fri Nov 09 2012 - 13:16:26 PST)
    - Re: [AMBER] Dipole from a mask Ismail, Mohd F. (Thu Nov 08 2012 - 21:13:15 PST)
[AMBER] pmemd cuda MPI nmropt crashes Scott Brozell (Mon Nov 05 2012 - 22:08:45 PST)
- Re: [AMBER] pmemd cuda MPI nmropt crashes Ross Walker (Mon Nov 05 2012 - 21:29:08 PST)
  - Re: [AMBER] pmemd cuda MPI nmropt crashes Scott Brozell (Mon Nov 05 2012 - 22:36:36 PST)
    - Re: [AMBER] pmemd cuda MPI nmropt crashes Ross Walker (Mon Nov 05 2012 - 21:44:19 PST)
    - Re: [AMBER] pmemd cuda MPI nmropt crashes Ross Walker (Mon Nov 05 2012 - 23:12:55 PST)
    - Re: [AMBER] pmemd cuda MPI nmropt crashes Scott Le Grand (Tue Nov 06 2012 - 05:47:31 PST)
    - Re: [AMBER] pmemd cuda MPI nmropt crashes Scott Le Grand (Tue Nov 06 2012 - 10:04:09 PST)
    - Re: [AMBER] pmemd cuda MPI nmropt crashes Scott Brozell (Wed Nov 07 2012 - 09:44:45 PST)
    - Re: [AMBER] pmemd cuda MPI nmropt crashes Scott Brozell (Wed Nov 07 2012 - 08:55:13 PST)
[AMBER] pmemd cuda MPI and PBS_GPUFILE Scott Brozell (Mon Nov 05 2012 - 22:24:45 PST)
- Re: [AMBER] pmemd cuda MPI and PBS_GPUFILE Ross Walker (Mon Nov 05 2012 - 21:38:58 PST)
  - Re: [AMBER] pmemd cuda MPI and PBS_GPUFILE Jason Swails (Tue Nov 06 2012 - 07:50:52 PST)
    - Re: [AMBER] pmemd cuda MPI and PBS_GPUFILE Scott Brozell (Wed Nov 07 2012 - 09:25:13 PST)
    - Re: [AMBER] pmemd cuda MPI and PBS_GPUFILE Scott Le Grand (Wed Nov 07 2012 - 09:52:20 PST)
- Re: [AMBER] pmemd cuda MPI and PBS_GPUFILE Jodi Ann Hadden (Tue Nov 06 2012 - 08:23:59 PST)
[AMBER] Cannot match namelist object name scee Esam Tolba (Tue Nov 06 2012 - 06:26:47 PST)
- Re: [AMBER] Cannot match namelist object name scee Jason Swails (Tue Nov 06 2012 - 07:10:42 PST)
[AMBER] best tutorials Fabian Glaser (Tue Nov 06 2012 - 06:32:26 PST)
- Re: [AMBER] best tutorials BERGY (Tue Nov 06 2012 - 20:26:33 PST)
- Re: [AMBER] best tutorials Jason Swails (Wed Nov 07 2012 - 15:38:53 PST)
[AMBER] compiler errors Brown, Paul (Tue Nov 06 2012 - 08:06:04 PST)
- Re: [AMBER] compiler errors Jason Swails (Tue Nov 06 2012 - 09:03:51 PST)
  - Re: [AMBER] compiler errors Brown, Paul (Thu Nov 08 2012 - 04:32:20 PST)
    - Re: [AMBER] compiler errors Jason Swails (Thu Nov 08 2012 - 04:57:05 PST)
    - Re: [AMBER] compiler errors Brown, Paul (Fri Nov 09 2012 - 04:07:58 PST)
[AMBER] about angle restraint anyiphysics.gmail.com (Tue Nov 06 2012 - 11:53:22 PST)
- Re: [AMBER] about angle restraint David A Case (Tue Nov 06 2012 - 12:13:06 PST)
  - Re: [AMBER] about angle restraint anyiphysics.gmail.com (Tue Nov 06 2012 - 13:11:40 PST)
- Re: [AMBER] about angle restraint Marek Maly (Tue Nov 06 2012 - 16:21:32 PST)
  - Re: [AMBER] about angle restraint anyiphysics.gmail.com (Tue Nov 06 2012 - 16:48:04 PST)
[AMBER] Image problems with IWRAP=1 Brown, Kyle (Tue Nov 06 2012 - 11:57:05 PST)
- Re: [AMBER] Image problems with IWRAP=1 David A Case (Tue Nov 06 2012 - 12:16:44 PST)
- Re: [AMBER] Image problems with IWRAP=1 Daniel Roe (Tue Nov 06 2012 - 12:36:19 PST)
  - Re: [AMBER] Image problems with IWRAP=1 Brown, Kyle (Tue Nov 06 2012 - 14:52:03 PST)
    - Re: [AMBER] Image problems with IWRAP=1 Daniel Roe (Tue Nov 06 2012 - 15:04:46 PST)
    - Re: [AMBER] Image problems with IWRAP=1 Daniel Roe (Wed Nov 07 2012 - 12:20:37 PST)
[AMBER] questions about AMBER prep files Yulin Huang (Tue Nov 06 2012 - 14:14:43 PST)
- Re: [AMBER] questions about AMBER prep files Jason Swails (Tue Nov 06 2012 - 14:38:47 PST)
  - Re: [AMBER] questions about AMBER prep files Yulin Huang (Tue Nov 06 2012 - 14:43:11 PST)
[AMBER] error of MMPBSA calculation using the prmtop and inpcrd generated by Chamber program baogen duan (Tue Nov 06 2012 - 18:25:19 PST)
- Re: [AMBER] error of MMPBSA calculation using the prmtop and inpcrd generated by Chamber program Bill Miller III (Tue Nov 06 2012 - 18:29:49 PST)
  - Re: [AMBER] error of MMPBSA calculation using the prmtop and inpcrd generated by Chamber program baogen duan (Wed Nov 07 2012 - 01:12:36 PST)
    - Re: [AMBER] error of MMPBSA calculation using the prmtop and inpcrd generated by Chamber program Jason Swails (Wed Nov 07 2012 - 11:16:19 PST)
[AMBER] Energy Analysis from Trajectory Aron Broom (Tue Nov 06 2012 - 22:07:25 PST)
- Re: [AMBER] Energy Analysis from Trajectory Roitberg,Adrian E (Tue Nov 06 2012 - 22:09:14 PST)
  - Re: [AMBER] Energy Analysis from Trajectory Aron Broom (Tue Nov 06 2012 - 22:24:28 PST)
    - Re: [AMBER] Energy Analysis from Trajectory Jason Swails (Wed Nov 07 2012 - 11:10:21 PST)
    - Re: [AMBER] Energy Analysis from Trajectory Kepa K. Burusco (Wed Nov 14 2012 - 13:54:09 PST)
    - Re: [AMBER] Energy Analysis from Trajectory David A Case (Thu Nov 15 2012 - 04:57:51 PST)
    - Re: [AMBER] Energy Analysis from Trajectory Kepa K. Burusco (Thu Nov 15 2012 - 08:21:05 PST)
    - Re: [AMBER] Energy Analysis from Trajectory Jason Swails (Thu Nov 15 2012 - 08:26:02 PST)
[AMBER] Umbrella sampling with pmemd Sajeewa Pemasinghe (Tue Nov 06 2012 - 22:59:17 PST)
- Re: [AMBER] Umbrella sampling with pmemd Roitberg,Adrian E (Tue Nov 06 2012 - 23:03:34 PST)
  - Re: [AMBER] Umbrella sampling with pmemd Sajeewa Pemasinghe (Tue Nov 06 2012 - 23:30:05 PST)
    - Re: [AMBER] Umbrella sampling with pmemd Roitberg,Adrian E (Wed Nov 07 2012 - 07:03:25 PST)
[AMBER] Will Ptraj image the coordinates after rms fitting? Alan (Tue Nov 06 2012 - 23:12:13 PST)
[AMBER] "vlimit exceeded for step ..." during SA protocol Baptiste Legrand (Wed Nov 07 2012 - 01:25:59 PST)
- Re: [AMBER] "vlimit exceeded for step ..." during SA protocol David A Case (Wed Nov 07 2012 - 06:46:22 PST)
  - Re: [AMBER] "vlimit exceeded for step ..." during SA protocol Baptiste Legrand (Thu Nov 08 2012 - 01:28:27 PST)
    - Re: [AMBER] "vlimit exceeded for step ..." during SA protocol Baptiste Legrand (Tue Nov 13 2012 - 07:44:59 PST)
[AMBER] NAMD failed to read Amber parm file Sneha Menon (Wed Nov 07 2012 - 04:25:36 PST)
- Re: [AMBER] NAMD failed to read Amber parm file Aron Broom (Wed Nov 07 2012 - 08:05:37 PST)
- Re: [AMBER] NAMD failed to read Amber parm file Jason Swails (Wed Nov 07 2012 - 11:19:55 PST)
[AMBER] bond missing in phosphate group after antechamber run Krisztina Feher (Wed Nov 07 2012 - 11:00:38 PST)
- Re: [AMBER] bond missing in phosphate group after antechamber run Krisztina Feher (Wed Nov 07 2012 - 13:55:48 PST)
- Re: [AMBER] bond missing in phosphate group after antechamber run Krisztina Feher (Thu Nov 08 2012 - 05:27:04 PST)
- Re: [AMBER] bond missing in phosphate group after antechamber run David A Case (Thu Nov 08 2012 - 06:56:09 PST)
- Re: [AMBER] bond missing in phosphate group after antechamber run Krisztina Feher (Thu Nov 08 2012 - 08:55:45 PST)
[AMBER] problem with Ca2.lib manikanthan bhavaraju (Wed Nov 07 2012 - 11:28:50 PST)
- Re: [AMBER] problem with Ca2.lib Tim Travers (Wed Nov 07 2012 - 11:46:21 PST)
  - Re: [AMBER] problem with Ca2.lib manikanthan bhavaraju (Wed Nov 07 2012 - 12:04:05 PST)
[AMBER] genMetalFF.sh and getCharges.sh not exist Jia Xu (Wed Nov 07 2012 - 23:17:07 PST)
- Re: [AMBER] genMetalFF.sh and getCharges.sh not exist Jason Swails (Thu Nov 08 2012 - 05:27:25 PST)
  - Re: [AMBER] genMetalFF.sh and getCharges.sh not exist Jia Xu (Thu Nov 08 2012 - 09:42:25 PST)
[AMBER] Multi-protein simulation in a box Rajeswari A. (Thu Nov 08 2012 - 01:28:04 PST)
- Re: [AMBER] Multi-protein simulation in a box Aron Broom (Thu Nov 08 2012 - 08:04:43 PST)
- Re: [AMBER] Multi-protein simulation in a box Jason Swails (Thu Nov 08 2012 - 08:30:19 PST)
  - Re: [AMBER] Multi-protein simulation in a box Brian Radak (Thu Nov 08 2012 - 08:50:16 PST)
    - Re: [AMBER] Multi-protein simulation in a box Rajeswari A. (Thu Nov 08 2012 - 23:08:07 PST)
[AMBER] using nudged elastic band method with explicit solvent Tan Yaw Sing (Thu Nov 08 2012 - 02:48:00 PST)
- Re: [AMBER] using nudged elastic band method with explicit solvent Christina Bergonzo (Thu Nov 08 2012 - 08:35:07 PST)
  - Re: [AMBER] using nudged elastic band method with explicit solvent Tan Yaw Sing (Thu Nov 08 2012 - 18:57:18 PST)
[AMBER] Parameters for amide bond isosteres Cecilia Lindgren (Thu Nov 08 2012 - 03:49:38 PST)
[AMBER] Heme iron definition: Atom type missing Maximilian Ebert (Thu Nov 08 2012 - 05:35:28 PST)
- Re: [AMBER] Heme iron definition: Atom type missing Maximilian Ebert (Fri Nov 09 2012 - 11:59:28 PST)
  - Re: [AMBER] Heme iron definition: Atom type missing David A Case (Fri Nov 09 2012 - 17:44:03 PST)
    - Re: [AMBER] Heme iron definition: Atom type missing Maximilian Ebert (Fri Nov 09 2012 - 22:27:18 PST)
[AMBER] different force fields for different molecules in leap Pecher, Josua (Thu Nov 08 2012 - 08:04:04 PST)
- Re: [AMBER] different force fields for different molecules in leap Aron Broom (Thu Nov 08 2012 - 08:10:31 PST)
- Re: [AMBER] different force fields for different molecules in leap Pecher, Josua (Thu Nov 08 2012 - 08:25:29 PST)
[AMBER] Primary structur to 3D structure Sindrila Dutta banik (Thu Nov 08 2012 - 11:18:29 PST)
- Re: [AMBER] Primary structur to 3D structure Aron Broom (Thu Nov 08 2012 - 14:05:30 PST)
[AMBER] AmberTools versions Maxier Acosta Santiago (Thu Nov 08 2012 - 12:05:15 PST)
- Re: [AMBER] AmberTools versions Jason Swails (Thu Nov 08 2012 - 12:36:56 PST)
[AMBER] EHBOND values and RESTRAINT values in mdout file Pyle, Ronald (Thu Nov 08 2012 - 14:55:13 PST)
- Re: [AMBER] EHBOND values and RESTRAINT values in mdout file Jason Swails (Thu Nov 08 2012 - 15:16:33 PST)
- Re: [AMBER] EHBOND values and RESTRAINT values in mdout file tec3.utah.edu (Thu Nov 08 2012 - 15:25:04 PST)
  - Re: [AMBER] EHBOND values and RESTRAINT values in mdout file Pyle, Ronald (Fri Nov 09 2012 - 06:13:27 PST)
    - Re: [AMBER] EHBOND values and RESTRAINT values in mdout file Jason Swails (Fri Nov 09 2012 - 07:02:55 PST)
[AMBER] Obtain trajectory coordinates from LMOD minimization Sangmin Lee (Thu Nov 08 2012 - 22:23:57 PST)
- Re: [AMBER] Obtain trajectory coordinates from LMOD minimization David A Case (Fri Nov 09 2012 - 05:01:39 PST)
[AMBER] No radius found for Mg+ using mm_pbsa.pl script baogen duan (Fri Nov 09 2012 - 01:18:25 PST)
- Re: [AMBER] No radius found for Mg+ using mm_pbsa.pl script Ray Luo, Ph.D. (Fri Nov 09 2012 - 09:48:50 PST)
[AMBER] Error at the end of entropy calculation via MMPBSA.py Miguel Ortiz Lombardía (Fri Nov 09 2012 - 06:31:00 PST)
- Re: [AMBER] Error at the end of entropy calculation via MMPBSA.py Jason Swails (Fri Nov 09 2012 - 07:01:35 PST)
[AMBER] Regarding Quadruplex Formation Souvik Sur (Fri Nov 09 2012 - 09:54:17 PST)
- Re: [AMBER] Regarding Quadruplex Formation David A Case (Fri Nov 09 2012 - 17:53:04 PST)
[AMBER] System blows up after several nanoseconds using Amber 12 Sasha Perkins (Fri Nov 09 2012 - 19:19:40 PST)
- Re: [AMBER] System blows up after several nanoseconds using Amber 12 Jason Swails (Fri Nov 09 2012 - 20:34:26 PST)
  - Re: [AMBER] System blows up after several nanoseconds using Amber 12 Sasha Perkins (Sat Nov 10 2012 - 07:32:45 PST)
    - Re: [AMBER] System blows up after several nanoseconds using Amber 12 Roitberg,Adrian E (Sat Nov 10 2012 - 07:37:48 PST)
    - Re: [AMBER] System blows up after several nanoseconds using Amber 12 Jason Swails (Sat Nov 10 2012 - 08:13:14 PST)
    - Re: [AMBER] System blows up after several nanoseconds using Amber 12 Sasha Perkins (Sat Nov 10 2012 - 09:02:17 PST)
    - Re: [AMBER] System blows up after several nanoseconds using Amber 12 Roitberg,Adrian E (Sat Nov 10 2012 - 09:06:10 PST)
[AMBER] Amber Error : Segmentation fault Sumra Wajid Abbasi 30-FBAS/MSBI/F09 (Sun Nov 11 2012 - 22:15:16 PST)
- Re: [AMBER] Amber Error : Segmentation fault Ross Walker (Sun Nov 11 2012 - 22:33:17 PST)
  - Re: [AMBER] Amber Error : Segmentation fault Sumra Wajid Abbasi 30-FBAS/MSBI/F09 (Sun Nov 11 2012 - 22:51:48 PST)
    - Re: [AMBER] Amber Error : Segmentation fault Sumra Wajid Abbasi 30-FBAS/MSBI/F09 (Mon Nov 12 2012 - 01:05:29 PST)
    - Re: [AMBER] Amber Error : Segmentation fault Jason Swails (Mon Nov 12 2012 - 04:25:09 PST)
    - Re: [AMBER] Amber Error : Segmentation fault Sumra Wajid Abbasi 30-FBAS/MSBI/F09 (Mon Nov 12 2012 - 20:44:16 PST)
    - Re: [AMBER] Amber Error : Segmentation fault Sumra Wajid Abbasi 30-FBAS/MSBI/F09 (Mon Nov 12 2012 - 20:58:50 PST)
    - Re: [AMBER] Amber Error : Segmentation fault Sumra Wajid Abbasi 30-FBAS/MSBI/F09 (Mon Nov 12 2012 - 20:59:46 PST)
    - Re: [AMBER] Amber Error : Segmentation fault David A Case (Tue Nov 13 2012 - 05:10:20 PST)
[AMBER] Urgent Faez Iqbal khan (Sun Nov 11 2012 - 23:14:23 PST)
- Re: [AMBER] Urgent Ross Walker (Sun Nov 11 2012 - 23:26:41 PST)
[AMBER] Generating a solvent Box from organic solvent Mark Zottola (Mon Nov 12 2012 - 16:48:24 PST)
- Re: [AMBER] Generating a solvent Box from organic solvent Bill Ross (Mon Nov 12 2012 - 17:55:46 PST)
[AMBER] Tleap crash while loading frcmod Daniel Sindhikara (Mon Nov 12 2012 - 20:25:59 PST)
- Re: [AMBER] Tleap crash while loading frcmod Bill Ross (Mon Nov 12 2012 - 21:41:36 PST)
  - Re: [AMBER] Tleap crash while loading frcmod Daniel Sindhikara (Mon Nov 12 2012 - 22:00:12 PST)
    - Re: [AMBER] Tleap crash while loading frcmod David A Case (Tue Nov 13 2012 - 05:07:32 PST)
[AMBER] imaging namd-generated dcd trajectories with cpptraj Vlad Cojocaru (Tue Nov 13 2012 - 02:00:47 PST)
- Re: [AMBER] imaging namd-generated dcd trajectories with cpptraj Jason Swails (Tue Nov 13 2012 - 05:36:35 PST)
  - Re: [AMBER] imaging namd-generated dcd trajectories with cpptraj Vlad Cojocaru (Tue Nov 13 2012 - 05:53:48 PST)
    - Re: [AMBER] imaging namd-generated dcd trajectories with cpptraj Jason Swails (Tue Nov 13 2012 - 06:00:20 PST)
    - Re: [AMBER] imaging namd-generated dcd trajectories with cpptraj Vlad Cojocaru (Tue Nov 13 2012 - 06:11:29 PST)
    - Re: [AMBER] imaging namd-generated dcd trajectories with cpptraj Daniel Roe (Tue Nov 13 2012 - 07:20:05 PST)
[AMBER] problem for lipid GAFF Albert (Tue Nov 13 2012 - 02:18:13 PST)
- Re: [AMBER] problem for lipid GAFF Dickson, Callum (Tue Nov 13 2012 - 09:00:00 PST)
- Re: [AMBER] problem for lipid GAFF Ross Walker (Tue Nov 13 2012 - 09:03:32 PST)
  - Re: [AMBER] problem for lipid GAFF Albert (Tue Nov 13 2012 - 09:12:38 PST)
    - Re: [AMBER] problem for lipid GAFF Ross Walker (Tue Nov 13 2012 - 10:23:25 PST)
    - Re: [AMBER] problem for lipid GAFF Albert (Tue Nov 13 2012 - 23:41:30 PST)
    - Re: [AMBER] problem for lipid GAFF Ross Walker (Wed Nov 14 2012 - 09:36:21 PST)
[AMBER] NOE calculation Meli Massimiliano (Tue Nov 13 2012 - 02:26:33 PST)
- Re: [AMBER] NOE calculation David A Case (Tue Nov 13 2012 - 05:18:07 PST)
  - Re: [AMBER] NOE calculation Meli Massimiliano (Tue Nov 13 2012 - 08:14:38 PST)
[AMBER] cppparmstrip command provokes segmentation fault Vlad Cojocaru (Tue Nov 13 2012 - 04:13:55 PST)
- Re: [AMBER] cppparmstrip command provokes segmentation fault Jason Swails (Tue Nov 13 2012 - 05:34:26 PST)
  - Re: [AMBER] cppparmstrip command provokes segmentation fault Vlad Cojocaru (Tue Nov 13 2012 - 05:48:33 PST)
- Re: [AMBER] cppparmstrip command provokes segmentation fault Daniel Roe (Tue Nov 13 2012 - 07:16:26 PST)
Re: [AMBER] Problem with "make install" after "./configure intel" Su, Shiquan (Tue Nov 13 2012 - 13:37:08 PST)
- Re: [AMBER] Problem with "make install" after "./configure intel" Su, Shiquan (Tue Nov 13 2012 - 13:50:18 PST)
[AMBER] MM PBSA error calculating entropy Aron Broom (Tue Nov 13 2012 - 13:52:03 PST)
- Re: [AMBER] MM PBSA error calculating entropy Jason Swails (Tue Nov 13 2012 - 14:55:05 PST)
  - Re: [AMBER] MM PBSA error calculating entropy Aron Broom (Tue Nov 13 2012 - 15:36:54 PST)
[AMBER] Regarding RNA Duplex formation Souvik Sur (Tue Nov 13 2012 - 22:50:26 PST)
- Re: [AMBER] Regarding RNA Duplex formation David A Case (Wed Nov 14 2012 - 09:26:37 PST)
[AMBER] PB Bomb in pb_aaradi(): No radius assigned for atom 8857 FE FE Dmitry Mukha (Wed Nov 14 2012 - 00:52:30 PST)
- Re: [AMBER] PB Bomb in pb_aaradi(): No radius assigned for atom 8857 FE FE Ray Luo, Ph.D. (Wed Nov 14 2012 - 10:08:27 PST)
  - Re: [AMBER] PB Bomb in pb_aaradi(): No radius assigned for atom 8857 FE FE Dmitry Mukha (Wed Nov 14 2012 - 10:21:09 PST)
    - Re: [AMBER] PB Bomb in pb_aaradi(): No radius assigned for atom 8857 FE FE Ray Luo, Ph.D. (Wed Nov 14 2012 - 21:17:44 PST)
    - Re: [AMBER] PB Bomb in pb_aaradi(): No radius assigned for atom 8857 FE FE Ray Luo, Ph.D. (Fri Nov 16 2012 - 15:46:12 PST)
[AMBER] Odp: Re: problem for lipid GAFF klechward.wp.pl (Wed Nov 14 2012 - 01:28:19 PST)
- Re: [AMBER] Odp: Re: problem for lipid GAFF Albert (Wed Nov 14 2012 - 01:57:44 PST)
[AMBER] Problem of atom typing for the LYN residue? FyD (Wed Nov 14 2012 - 01:53:46 PST)
- Re: [AMBER] Problem of atom typing for the LYN residue? David A Case (Mon Nov 26 2012 - 05:18:26 PST)
[AMBER] Explicit 1-4 pairs Joakim Jämbeck (Wed Nov 14 2012 - 02:09:39 PST)
- Re: [AMBER] Explicit 1-4 pairs Jason Swails (Wed Nov 14 2012 - 05:17:35 PST)
[AMBER] Antechamber and GTP Fernando Martín García (Wed Nov 14 2012 - 02:56:42 PST)
- Re: [AMBER] Antechamber and GTP David A Case (Wed Nov 14 2012 - 09:30:27 PST)
  - Re: [AMBER] Antechamber and GTP fmgarcia.cbm.uam.es (Thu Nov 15 2012 - 00:31:52 PST)
    - Re: [AMBER] Antechamber and GTP Alan (Thu Nov 15 2012 - 03:47:02 PST)
    - [AMBER] Kepler II (K20) benchmark results? filip fratev (Thu Nov 15 2012 - 08:59:25 PST)
    - Re: [AMBER] Kepler II (K20) benchmark results? Ross Walker (Thu Nov 15 2012 - 16:42:57 PST)
    - Re: [AMBER] Antechamber and GTP David A Case (Thu Nov 15 2012 - 05:06:59 PST)
    - Re: [AMBER] Antechamber and GTP Fernando Martín García (Fri Nov 16 2012 - 04:09:59 PST)
    - Re: [AMBER] Antechamber and GTP Fernando Martín García (Fri Nov 16 2012 - 08:21:15 PST)
    - Re: [AMBER] Antechamber and GTP FyD (Fri Nov 16 2012 - 08:56:28 PST)
[AMBER] Problem with running QM/MM - MD simulation using AM1/d-PhoT method in AMBER12 vojtech.mlynsky.upol.cz (Wed Nov 14 2012 - 03:05:29 PST)
- Re: [AMBER] Problem with running QM/MM - MD simulation using AM1/d-PhoT method in AMBER12 Gustavo Seabra (Wed Nov 14 2012 - 04:40:30 PST)
- Re: [AMBER] Problem with running QM/MM - MD simulation using AM1/d-PhoT method in AMBER12 vojtech.mlynsky.upol.cz (Wed Nov 14 2012 - 09:15:52 PST)
  - Re: [AMBER] Problem with running QM/MM - MD simulation using AM1/d-PhoT method in AMBER12 Gustavo Seabra (Wed Nov 14 2012 - 10:41:51 PST)
    - Re: [AMBER] Problem with running QM/MM - MD simulation using AM1/d-PhoT method in AMBER12 Brian Radak (Wed Nov 14 2012 - 11:37:55 PST)
    - Re: [AMBER] Problem with running QM/MM - MD simulation using AM1/d-PhoT method in AMBER12 Marc van der Kamp (Wed Nov 14 2012 - 12:46:59 PST)
    - Re: [AMBER] Problem with running QM/MM - MD simulation using AM1/d-PhoT method in AMBER12 Andreas Goetz (Wed Nov 14 2012 - 13:06:40 PST)
- Re: [AMBER] Problem with running QM/MM - MD simulation using AM1/d-PhoT method in AMBER12 vojtech.mlynsky.upol.cz (Thu Nov 15 2012 - 05:08:15 PST)
  - Re: [AMBER] Problem with running QM/MM - MD simulation using AM1/d-PhoT method in AMBER12 Gustavo Seabra (Thu Nov 15 2012 - 06:33:14 PST)
- Re: [AMBER] Problem with running QM/MM - MD simulation using AM1/d-PhoT method in AMBER12 vojtech.mlynsky.upol.cz (Thu Nov 15 2012 - 09:01:06 PST)
  - Re: [AMBER] Problem with running QM/MM - MD simulation using AM1/d-PhoT method in AMBER12 Brian Radak (Thu Nov 15 2012 - 09:30:47 PST)
  - Re: [AMBER] Problem with running QM/MM - MD simulation using AM1/d-PhoT method in AMBER12 Andreas Goetz (Thu Nov 15 2012 - 15:33:50 PST)
[AMBER] mmpbsa restart Giulia (Wed Nov 14 2012 - 04:31:18 PST)
- Re: [AMBER] mmpbsa restart Jason Swails (Wed Nov 14 2012 - 05:18:49 PST)
  - Re: [AMBER] mmpbsa restart Giulia (Wed Nov 14 2012 - 08:14:09 PST)
    - Re: [AMBER] mmpbsa restart Jason Swails (Wed Nov 14 2012 - 08:33:09 PST)
[AMBER] COM removed message and Energy Drift Ismail, Mohd F. (Wed Nov 14 2012 - 12:38:41 PST)
- Re: [AMBER] COM removed message and Energy Drift Ismail, Mohd F. (Wed Nov 14 2012 - 12:50:26 PST)
- Re: [AMBER] COM removed message and Energy Drift Jason Swails (Thu Nov 15 2012 - 04:36:18 PST)
  - Re: [AMBER] COM removed message and Energy Drift Ismail, Mohd F. (Thu Nov 15 2012 - 09:46:16 PST)
[AMBER] residuegen Osman, Roman (Wed Nov 14 2012 - 14:59:52 PST)
[AMBER] AMBER/ORCA marawan hussain (Wed Nov 14 2012 - 19:18:19 PST)
- Re: [AMBER] AMBER/ORCA David A Case (Thu Nov 15 2012 - 05:02:32 PST)
[AMBER] Error in script file while running mm_pbsa.pl Anogna (Wed Nov 14 2012 - 23:32:20 PST)
- Re: [AMBER] Error in script file while running mm_pbsa.pl Jason Swails (Fri Nov 16 2012 - 04:58:55 PST)
[AMBER] AMBER-ORCA marawan hussain (Wed Nov 14 2012 - 23:51:55 PST)
- Re: [AMBER] AMBER-ORCA Andreas Goetz (Thu Nov 15 2012 - 13:38:42 PST)
[AMBER] very large value of "fglen" and "cglen" during MMPBSA.py calculatio using sander.APBS dbaogen (Thu Nov 15 2012 - 05:13:13 PST)
[AMBER] AMBER-ORCA-Freq marawan hussain (Thu Nov 15 2012 - 14:13:25 PST)
- Re: [AMBER] AMBER-ORCA-Freq Brian Radak (Fri Nov 16 2012 - 09:14:25 PST)
[AMBER] Problem with the specification of the bellymask Sajeewa Pemasinghe (Thu Nov 15 2012 - 16:55:38 PST)
- Re: [AMBER] Problem with the specification of the bellymask Jason Swails (Thu Nov 15 2012 - 18:18:40 PST)
  - Re: [AMBER] Problem with the specification of the bellymask Sajeewa Pemasinghe (Thu Nov 15 2012 - 19:39:38 PST)
[AMBER] large value of "fglen" and "cglen"of iAPBS initiation during MMPBSA python script calculation baogen duan (Thu Nov 15 2012 - 17:31:18 PST)
- Re: [AMBER] large value of "fglen" and "cglen"of iAPBS initiation during MMPBSA python script calculation Robert Konecny (Thu Nov 15 2012 - 21:08:27 PST)
[AMBER] WARNING: a parameter is 0.0 for atom Jacopo Sgrignani (Fri Nov 16 2012 - 01:51:09 PST)
- Re: [AMBER] WARNING: a parameter is 0.0 for atom Gustavo Seabra (Fri Nov 16 2012 - 02:51:16 PST)
- Re: [AMBER] WARNING: a parameter is 0.0 for atom Jacopo Sgrignani (Fri Nov 16 2012 - 03:07:31 PST)
  - Re: [AMBER] WARNING: a parameter is 0.0 for atom Gustavo Seabra (Fri Nov 16 2012 - 03:19:46 PST)
[AMBER] Theorical ramachandran map/energy map of modified residues Baptiste Legrand (Fri Nov 16 2012 - 09:25:13 PST)
- Re: [AMBER] Theorical ramachandran map/energy map of modified residues Carlos Simmerling (Fri Nov 16 2012 - 09:45:50 PST)
- Re: [AMBER] Theorical ramachandran map/energy map of modified residues Jason Swails (Fri Nov 16 2012 - 11:11:50 PST)
[AMBER] C-C-N angle parameters for benzonitrile Sharma, Purshotam (Fri Nov 16 2012 - 11:07:48 PST)
[AMBER] QM/MM bugfix for semiempirical NDDO code available, soon Andreas Goetz (Fri Nov 16 2012 - 17:16:04 PST)
[AMBER] Antechamber Maxier Acosta Santiago (Sat Nov 17 2012 - 12:06:32 PST)
- Re: [AMBER] Antechamber Jason Swails (Sat Nov 17 2012 - 12:42:39 PST)
  - Re: [AMBER] Antechamber Maxier Acosta Santiago (Sun Nov 18 2012 - 08:20:37 PST)
[AMBER] Can I mix Glycam and Gaff in a small molecule? Liu Denis (Sun Nov 18 2012 - 23:01:37 PST)
- Re: [AMBER] Can I mix Glycam and Gaff in a small molecule? David A Case (Mon Nov 19 2012 - 04:56:25 PST)
  - Re: [AMBER] Can I mix Glycam and Gaff in a small molecule? Liu Denis (Tue Nov 20 2012 - 16:49:28 PST)
[AMBER] Amber radii of ions Devlina Chakravarty (Sun Nov 18 2012 - 23:24:00 PST)
- Re: [AMBER] Amber radii of ions David A Case (Mon Nov 19 2012 - 04:57:21 PST)
[AMBER] trajout command in ptraj rahul sarma (Sun Nov 18 2012 - 23:52:48 PST)
- Re: [AMBER] trajout command in ptraj Daniel Roe (Mon Nov 19 2012 - 08:33:50 PST)
  - Re: [AMBER] trajout command in ptraj rahul sarma (Mon Nov 19 2012 - 20:14:01 PST)
[AMBER] mixing of scaling factor in amber 12 Subrata Paul (Mon Nov 19 2012 - 00:56:58 PST)
- Re: [AMBER] mixing of scaling factor in amber 12 Jason Swails (Mon Nov 19 2012 - 05:27:44 PST)
  - Re: [AMBER] mixing of scaling factor in amber 12 Subrata Paul (Mon Nov 19 2012 - 11:23:48 PST)
[AMBER] generate rst from mdcrd Yunjie Zhao (Mon Nov 19 2012 - 11:57:04 PST)
- Re: [AMBER] generate rst from mdcrd Jason Swails (Mon Nov 19 2012 - 12:49:08 PST)
[AMBER] unsubscribe Aust, Susanne (Tue Nov 20 2012 - 01:13:01 PST)
[AMBER] cuda-5.0/lib64/libcufft.so: undefined reference to `__isoc99_sscanf@GLIBC_2.7' Thomas Evangelidis (Tue Nov 20 2012 - 01:50:52 PST)
- Re: [AMBER] cuda-5.0/lib64/libcufft.so: undefined reference to `__isoc99_sscanf@GLIBC_2.7' Jason Swails (Tue Nov 20 2012 - 06:38:42 PST)
  - Re: [AMBER] cuda-5.0/lib64/libcufft.so: undefined reference to `__isoc99_sscanf@GLIBC_2.7' Thomas Evangelidis (Tue Nov 20 2012 - 07:53:26 PST)
    - Re: [AMBER] cuda-5.0/lib64/libcufft.so: undefined reference to `__isoc99_sscanf@GLIBC_2.7' Ross Walker (Tue Nov 20 2012 - 08:28:01 PST)
    - Re: [AMBER] cuda-5.0/lib64/libcufft.so: undefined reference to `__isoc99_sscanf@GLIBC_2.7' Thomas Evangelidis (Tue Nov 20 2012 - 12:47:55 PST)
    - Re: [AMBER] cuda-5.0/lib64/libcufft.so: undefined reference to `__isoc99_sscanf@GLIBC_2.7' Su, Shiquan (Tue Nov 20 2012 - 13:04:18 PST)
    - Re: [AMBER] cuda-5.0/lib64/libcufft.so: undefined reference to `__isoc99_sscanf@GLIBC_2.7' Ross Walker (Tue Nov 20 2012 - 13:09:36 PST)
    - Re: [AMBER] cuda-5.0/lib64/libcufft.so: undefined reference to `__isoc99_sscanf@GLIBC_2.7' Thomas Evangelidis (Tue Nov 20 2012 - 13:13:34 PST)
    - Re: [AMBER] cuda-5.0/lib64/libcufft.so: undefined reference to `__isoc99_sscanf@GLIBC_2.7' Ross Walker (Tue Nov 20 2012 - 13:21:23 PST)
    - Re: [AMBER] cuda-5.0/lib64/libcufft.so: undefined reference to `__isoc99_sscanf@GLIBC_2.7' Thomas Evangelidis (Tue Nov 20 2012 - 13:31:44 PST)
    - Re: [AMBER] cuda-5.0/lib64/libcufft.so: undefined reference to `__isoc99_sscanf@GLIBC_2.7' Ross Walker (Tue Nov 20 2012 - 14:14:55 PST)
    - Re: [AMBER] cuda-5.0/lib64/libcufft.so: undefined reference to `__isoc99_sscanf@GLIBC_2.7' Thomas Evangelidis (Tue Nov 20 2012 - 15:01:33 PST)
    - Re: [AMBER] cuda-5.0/lib64/libcufft.so: undefined reference to `__isoc99_sscanf@GLIBC_2.7' Ross Walker (Wed Nov 21 2012 - 10:03:22 PST)
[AMBER] Magnesium ion (Mg2+) simulation dbaogen (Tue Nov 20 2012 - 18:24:21 PST)
[AMBER] is AMBER FF good enough for long time scaled MD? Albert (Tue Nov 20 2012 - 23:17:54 PST)
- Re: [AMBER] is AMBER FF good enough for long time scaled MD? francesco oteri (Wed Nov 21 2012 - 04:03:31 PST)
  - Re: [AMBER] is AMBER FF good enough for long time scaled MD? Albert (Wed Nov 21 2012 - 05:39:51 PST)
- Re: [AMBER] is AMBER FF good enough for long time scaled MD? David A Case (Wed Nov 21 2012 - 04:37:00 PST)
  - Re: [AMBER] is AMBER FF good enough for long time scaled MD? Albert (Wed Nov 21 2012 - 05:37:52 PST)
    - Re: [AMBER] is AMBER FF good enough for long time scaled MD? Vlad Cojocaru (Wed Nov 21 2012 - 05:50:40 PST)
    - Re: [AMBER] is AMBER FF good enough for long time scaled MD? Albert (Wed Nov 21 2012 - 05:56:39 PST)
    - Re: [AMBER] is AMBER FF good enough for long time scaled MD? Vlad Cojocaru (Wed Nov 21 2012 - 06:13:45 PST)
    - Re: [AMBER] is AMBER FF good enough for long time scaled MD? Vlad Cojocaru (Wed Nov 21 2012 - 06:21:38 PST)
    - Re: [AMBER] is AMBER FF good enough for long time scaled MD? Albert (Wed Nov 21 2012 - 06:36:33 PST)
    - Re: [AMBER] is AMBER FF good enough for long time scaled MD? Thomas Evangelidis (Wed Nov 21 2012 - 06:47:43 PST)
    - Re: [AMBER] is AMBER FF good enough for long time scaled MD? Vlad Cojocaru (Wed Nov 21 2012 - 07:35:20 PST)
    - Re: [AMBER] is AMBER FF good enough for long time scaled MD? Thomas Evangelidis (Wed Nov 21 2012 - 07:46:38 PST)
    - Re: [AMBER] is AMBER FF good enough for long time scaled MD? Vlad Cojocaru (Wed Nov 21 2012 - 07:52:13 PST)
    - Re: [AMBER] is AMBER FF good enough for long time scaled MD? Vlad Cojocaru (Wed Nov 21 2012 - 06:51:53 PST)
    - Re: [AMBER] is AMBER FF good enough for long time scaled MD? Albert (Wed Nov 21 2012 - 07:02:17 PST)
[AMBER] Ligand appears broken after minimization Jitesh Doshi (Wed Nov 21 2012 - 01:49:15 PST)
- Re: [AMBER] Ligand appears broken after minimization Kshatresh Dutta Dubey (Wed Nov 21 2012 - 01:56:54 PST)
  - Re: [AMBER] Ligand appears broken after minimization Jitesh Doshi (Tue Nov 27 2012 - 22:04:25 PST)
    - Re: [AMBER] Ligand appears broken after minimization Hirdesh Kumar (Wed Nov 28 2012 - 00:14:07 PST)
[AMBER] selecting a gpu device in multiple gpu system 홍종희 (Wed Nov 21 2012 - 02:42:38 PST)
- Re: [AMBER] selecting a gpu device in multiple gpu system Marc van der Kamp (Wed Nov 21 2012 - 03:02:39 PST)
  - Re: [AMBER] selecting a gpu device in multiple gpu system Jason Swails (Wed Nov 21 2012 - 06:35:54 PST)
- Re: [AMBER] selecting a gpu device in multiple gpu system Ross Walker (Wed Nov 21 2012 - 10:09:35 PST)
[AMBER] strange deprotonation in QM/MM Jacopo Sgrignani (Wed Nov 21 2012 - 07:17:07 PST)
- Re: [AMBER] strange deprotonation in QM/MM Alex Rodriguez (Thu Nov 22 2012 - 02:34:09 PST)
  - Re: [AMBER] strange deprotonation in QM/MM Jacopo Sgrignani (Thu Nov 22 2012 - 02:40:48 PST)
[AMBER] Forcefield Maxier Acosta Santiago (Wed Nov 21 2012 - 12:06:12 PST)
- Re: [AMBER] Forcefield Christina Bergonzo (Wed Nov 21 2012 - 12:34:23 PST)
[AMBER] Problem to run sander with more than 60 atom types Elise Duboué-Dijon (Thu Nov 22 2012 - 00:40:12 PST)
- Re: [AMBER] Problem to run sander with more than 60 atom types Elise Duboué-Dijon (Tue Nov 27 2012 - 03:20:48 PST)
  - Re: [AMBER] Problem to run sander with more than 60 atom types Jason Swails (Tue Nov 27 2012 - 05:29:38 PST)
    - Re: [AMBER] Problem to run sander with more than 60 atom types Elise Duboué-Dijon (Tue Nov 27 2012 - 06:32:34 PST)
    - Re: [AMBER] Problem to run sander with more than 60 atom types Jason Swails (Tue Nov 27 2012 - 06:59:48 PST)
    - Re: [AMBER] Problem to run sander with more than 60 atom types Elise Duboué-Dijon (Thu Feb 28 2013 - 06:24:10 PST)
    - Re: [AMBER] Problem to run sander with more than 60 atom types Jason Swails (Thu Feb 28 2013 - 07:14:17 PST)
    - Re: [AMBER] Problem to run sander with more than 60 atom types Elise Duboué-Dijon (Thu Feb 28 2013 - 08:51:03 PST)
    - Re: [AMBER] Problem to run sander with more than 60 atom types Jason Swails (Thu Feb 28 2013 - 09:02:01 PST)
    - Re: [AMBER] Problem to run sander with more than 60 atom types Elise Duboué-Dijon (Thu Feb 28 2013 - 09:11:57 PST)
[AMBER] Heating process- amber 8 regarding subramanian boopathi (Thu Nov 22 2012 - 23:04:01 PST)
- Re: [AMBER] Heating process- amber 8 regarding David A Case (Mon Nov 26 2012 - 05:10:12 PST)
[AMBER] GPU and ntpr Fernando Martín García (Fri Nov 23 2012 - 03:14:41 PST)
- Re: [AMBER] GPU and ntpr Ross Walker (Fri Nov 23 2012 - 17:27:29 PST)
  - Re: [AMBER] GPU and ntpr Fernando Martín García (Tue Nov 27 2012 - 03:46:02 PST)
    - Re: [AMBER] GPU and ntpr Ross Walker (Tue Nov 27 2012 - 10:48:13 PST)
    - Re: [AMBER] GPU and ntpr Fernando Martín García (Fri Nov 30 2012 - 01:16:38 PST)
[AMBER] INTER-molecular RDF only ? Marek Maly (Fri Nov 23 2012 - 05:22:09 PST)
- Re: [AMBER] INTER-molecular RDF only ? Ismail, Mohd F. (Fri Nov 23 2012 - 12:34:31 PST)
  - Re: [AMBER] INTER-molecular RDF only ? Marek Maly (Fri Nov 23 2012 - 13:13:53 PST)
    - Re: [AMBER] INTER-molecular RDF only ? Ismail, Mohd F. (Fri Nov 23 2012 - 14:09:58 PST)
    - Re: [AMBER] INTER-molecular RDF only ? Marek Maly (Fri Nov 23 2012 - 14:35:59 PST)
Re: [AMBER] Happy Thanksgiving!!!! Eliana Asciutto (Fri Nov 23 2012 - 07:06:34 PST)
[AMBER] Sorry for the previous email Eliana Asciutto (Fri Nov 23 2012 - 07:33:03 PST)
[AMBER] What nonbonded interactions cutoff to use in amber. Itamar Kass (Sun Nov 25 2012 - 18:57:38 PST)
- Re: [AMBER] What nonbonded interactions cutoff to use in amber. Jason Swails (Mon Nov 26 2012 - 05:52:52 PST)
[AMBER] Porcupine_Plots_Script Jia Xu (Mon Nov 26 2012 - 03:17:45 PST)
- Re: [AMBER] Porcupine_Plots_Script monica.imtech.res.in (Mon Nov 26 2012 - 04:11:36 PST)
  - Re: [AMBER] Porcupine_Plots_Script Jia Xu (Mon Nov 26 2012 - 10:18:07 PST)
    - Re: [AMBER] Porcupine_Plots_Script monica.imtech.res.in (Tue Nov 27 2012 - 07:18:38 PST)
    - Re: [AMBER] Porcupine_Plots_Script Jason Swails (Tue Nov 27 2012 - 07:25:29 PST)
    - Re: [AMBER] Porcupine_Plots_Script monica.imtech.res.in (Thu Nov 29 2012 - 04:08:00 PST)
    - Re: [AMBER] Porcupine_Plots_Script Jason Swails (Thu Nov 29 2012 - 04:29:24 PST)
    - Re: [AMBER] Porcupine_Plots_Script monica.imtech.res.in (Fri Nov 30 2012 - 06:19:13 PST)
    - Re: [AMBER] Porcupine_Plots_Script Jason Swails (Fri Nov 30 2012 - 06:33:35 PST)
    - Re: [AMBER] Porcupine_Plots_Script monica.imtech.res.in (Sun Dec 02 2012 - 20:30:13 PST)
[AMBER] definition of receptor_mask and ligand_mask using MMPBSA method dbaogen (Mon Nov 26 2012 - 04:30:09 PST)
- Re: [AMBER] definition of receptor_mask and ligand_mask using MMPBSA method Bill Miller III (Mon Nov 26 2012 - 04:39:31 PST)
[AMBER] ptraj clustering problem (segmentation fault) adarm.nencki.gov.pl (Mon Nov 26 2012 - 05:25:20 PST)
- Re: [AMBER] ptraj clustering problem (segmentation fault) Daniel Roe (Mon Nov 26 2012 - 08:49:43 PST)
  - Re: [AMBER] ptraj clustering problem (segmentation fault) adarm.nencki.gov.pl (Mon Nov 26 2012 - 13:21:33 PST)
[AMBER] ptraj grid by center of mass Daniel Álvarez García (Mon Nov 26 2012 - 05:55:01 PST)
- Re: [AMBER] ptraj grid by center of mass Daniel Roe (Mon Nov 26 2012 - 08:55:15 PST)
  - Re: [AMBER] ptraj grid by center of mass Daniel Álvarez García (Mon Nov 26 2012 - 10:03:08 PST)
[AMBER] LMOD issues in Amber 12 Sarah Edwards (Mon Nov 26 2012 - 11:05:39 PST)
[AMBER] calculation of protein-DNA complex structure 丁鹏飞 (Mon Nov 26 2012 - 23:18:23 PST)
- Re: [AMBER] calculation of protein-DNA complex structure David A Case (Tue Nov 27 2012 - 04:44:54 PST)
  - Re: [AMBER] calculation of protein-DNA complex structure Carlos Simmerling (Tue Nov 27 2012 - 08:43:37 PST)
[AMBER] Xleap rotation in mac OS Hirdesh Kumar (Tue Nov 27 2012 - 00:47:51 PST)
- Re: [AMBER] Xleap rotation in mac OS Jason Swails (Tue Nov 27 2012 - 04:28:22 PST)
  - [AMBER] postdoc RNA/DNA computations Jiri Sponer (Tue Nov 27 2012 - 04:50:23 PST)
[AMBER] complete bond energy list יוכבד (Tue Nov 27 2012 - 01:23:56 PST)
- Re: [AMBER] complete bond energy list Jason Swails (Tue Nov 27 2012 - 05:27:01 PST)
  - Re: [AMBER] complete bond energy list יוכבד (Wed Nov 28 2012 - 00:41:29 PST)
[AMBER] Antechamber-- Creating inputs for Ammonium-Borane Ravi Tripathi (Tue Nov 27 2012 - 02:09:31 PST)
- Re: [AMBER] Antechamber-- Creating inputs for Ammonium-Borane David A Case (Tue Nov 27 2012 - 04:47:15 PST)
  - Re: [AMBER] Antechamber-- Creating inputs for Ammonium-Borane FyD (Tue Nov 27 2012 - 21:48:46 PST)
    - Re: [AMBER] Antechamber-- Creating inputs for Ammonium-Borane Ravi Tripathi (Tue Nov 27 2012 - 21:59:12 PST)
[AMBER] UTP and CTP amber force field parameters dbaogen (Tue Nov 27 2012 - 04:43:54 PST)
- Re: [AMBER] UTP and CTP amber force field parameters FyD (Tue Nov 27 2012 - 21:45:55 PST)
[AMBER] calculate the binding free energy of more than one ligand in MMPBSA Shuyi Cao (Tue Nov 27 2012 - 09:05:28 PST)
- Re: [AMBER] calculate the binding free energy of more than one ligand in MMPBSA Jason Swails (Tue Nov 27 2012 - 09:33:28 PST)
[AMBER] simulation for a protein + ligand system with polarizable force field Jagur Lambix (Tue Nov 27 2012 - 12:44:20 PST)
[AMBER] Reading DESMOND MD trajectory files in CPPTRAJ... Shashidhar Rao (Tue Nov 27 2012 - 13:14:49 PST)
- Re: [AMBER] Reading DESMOND MD trajectory files in CPPTRAJ... Daniel Roe (Tue Nov 27 2012 - 16:42:24 PST)
  - Re: [AMBER] Reading DESMOND MD trajectory files in CPPTRAJ... Shashidhar Rao (Tue Nov 27 2012 - 17:20:44 PST)
[AMBER] Polarizable force field for protein + ligand system Jagur Lambix (Tue Nov 27 2012 - 14:47:01 PST)
Re: [AMBER] MMPBSA.py - problem with complex.prmtop -rdparm: a parameter array overflowed colvin (Tue Nov 27 2012 - 21:46:11 PST)
- Re: [AMBER] MMPBSA.py - problem with complex.prmtop -rdparm: a parameter array overflowed Jason Swails (Wed Nov 28 2012 - 07:23:58 PST)
  - Re: [AMBER] MMPBSA.py - problem with complex.prmtop -rdparm: a parameter array overflowed colvin (Thu Nov 29 2012 - 16:15:35 PST)
[AMBER] error in heating process subramanian boopathi (Tue Nov 27 2012 - 21:47:54 PST)
- Re: [AMBER] error in heating process Bill Ross (Tue Nov 27 2012 - 23:07:25 PST)
- Re: [AMBER] error in heating process David A Case (Wed Nov 28 2012 - 06:16:36 PST)
[AMBER] Antechamber - Problem with protonated oxygen Ravi Tripathi (Tue Nov 27 2012 - 21:58:39 PST)
- Re: [AMBER] Antechamber - Problem with protonated oxygen FyD (Tue Nov 27 2012 - 22:05:58 PST)
  - Re: [AMBER] Antechamber - Problem with protonated oxygen Ravi Tripathi (Tue Nov 27 2012 - 22:20:31 PST)
    - Re: [AMBER] Antechamber - Problem with protonated oxygen FyD (Wed Nov 28 2012 - 01:02:57 PST)
[AMBER] R.E.D calculation cannot be used for CHARMM FF? Albert (Wed Nov 28 2012 - 00:57:19 PST)
- Re: [AMBER] R.E.D calculation cannot be used for CHARMM FF? FyD (Thu Nov 29 2012 - 13:27:21 PST)
[AMBER] Calculating volume of the ligand manikanthan bhavaraju (Wed Nov 28 2012 - 06:30:15 PST)
- Re: [AMBER] Calculating volume of the ligand João Ribeiro (Wed Nov 28 2012 - 07:43:51 PST)
  - Re: [AMBER] Calculating volume of the ligand manikanthan bhavaraju (Wed Nov 28 2012 - 07:51:54 PST)
[AMBER] sander.MPI Fabian Glaser (Wed Nov 28 2012 - 06:30:57 PST)
- Re: [AMBER] sander.MPI David A Case (Wed Nov 28 2012 - 07:29:55 PST)
  - Re: [AMBER] sander.MPI Fabian Glaser (Wed Nov 28 2012 - 22:43:50 PST)
    - Re: [AMBER] sander.MPI Daniel Sindhikara (Wed Nov 28 2012 - 23:56:34 PST)
    - Re: [AMBER] sander.MPI Jason Swails (Thu Nov 29 2012 - 03:40:14 PST)
    - Re: [AMBER] sander.MPI Fabian Glaser (Thu Nov 29 2012 - 05:18:23 PST)
    - Re: [AMBER] sander.MPI Jason Swails (Thu Nov 29 2012 - 05:36:11 PST)
    - Re: [AMBER] sander.MPI Fabian Glaser (Thu Nov 29 2012 - 05:44:05 PST)
    - Re: [AMBER] sander.MPI Jason Swails (Thu Nov 29 2012 - 07:04:34 PST)
    - Re: [AMBER] sander.MPI Fabian Glaser (Sun Dec 02 2012 - 04:59:58 PST)
    - Re: [AMBER] sander.MPI Fabian Glaser (Thu Nov 29 2012 - 05:54:06 PST)
    - Re: [AMBER] sander.MPI Fabian Glaser (Sat Dec 15 2012 - 23:21:35 PST)
    - Re: [AMBER] sander.MPI Jason Swails (Sun Dec 16 2012 - 06:48:36 PST)
    - Re: [AMBER] sander.MPI Fabian Glaser (Sun Dec 16 2012 - 22:38:52 PST)
    - Re: [AMBER] sander.MPI Jason Swails (Mon Dec 17 2012 - 05:44:39 PST)
    - Re: [AMBER] sander.MPI Fabian Glaser (Tue Dec 18 2012 - 01:20:57 PST)
    - Re: [AMBER] sander.MPI Jason Swails (Tue Dec 18 2012 - 03:53:18 PST)
    - Re: [AMBER] sander.MPI Fabian Glaser (Wed Dec 19 2012 - 05:10:54 PST)
    - Re: [AMBER] sander.MPI David A Case (Tue Dec 18 2012 - 06:18:21 PST)
    - Re: [AMBER] sander.MPI Fabian Glaser (Wed Dec 19 2012 - 04:53:33 PST)
    - Re: [AMBER] sander.MPI Jason Swails (Wed Dec 19 2012 - 09:11:13 PST)
    - Re: [AMBER] sander.MPI Fabian Glaser (Tue Dec 18 2012 - 03:21:05 PST)
[AMBER] Doubt about binding dissociation constant manikanthan bhavaraju (Wed Nov 28 2012 - 10:05:59 PST)
- Re: [AMBER] Doubt about binding dissociation constant InSuk Joung (Wed Nov 28 2012 - 10:18:42 PST)
  - Re: [AMBER] Doubt about binding dissociation constant manikanthan bhavaraju (Wed Nov 28 2012 - 10:29:39 PST)
- Re: [AMBER] Doubt about binding dissociation constant Ignacio J. General (Wed Nov 28 2012 - 10:56:57 PST)
[AMBER] Amber 12 and PGI compilers >= 12.5 Ben Roberts (Wed Nov 28 2012 - 15:09:23 PST)
[AMBER] Compiler for Amber12 with GTX680 kurisaki (Thu Nov 29 2012 - 02:46:24 PST)
- Re: [AMBER] Compiler for Amber12 with GTX680 Jason Swails (Thu Nov 29 2012 - 05:37:32 PST)
  - Re: [AMBER] Compiler for Amber12 with GTX680 kurisaki (Thu Nov 29 2012 - 05:58:05 PST)
[AMBER] Solvation in Amber Ravi Tripathi (Thu Nov 29 2012 - 03:46:42 PST)
- Re: [AMBER] Solvation in Amber Jason Swails (Thu Nov 29 2012 - 04:52:37 PST)
  - Re: [AMBER] Solvation in Amber Ravi Tripathi (Fri Nov 30 2012 - 02:02:09 PST)
[AMBER] is there a difference between the GTX 680 GPU's Jonathan Gough (Thu Nov 29 2012 - 14:03:34 PST)
- Re: [AMBER] is there a difference between the GTX 680 GPU's Jason Swails (Thu Nov 29 2012 - 15:19:58 PST)
  - Re: [AMBER] is there a difference between the GTX 680 GPU's Jonathan Gough (Thu Nov 29 2012 - 16:17:07 PST)
  - Re: [AMBER] is there a difference between the GTX 680 GPU's Marek Maly (Thu Nov 29 2012 - 16:13:19 PST)
    - Re: [AMBER] is there a difference between the GTX 680 GPU's Jason Swails (Thu Nov 29 2012 - 16:35:40 PST)
    - Re: [AMBER] is there a difference between the GTX 680 GPU's Marek Maly (Thu Nov 29 2012 - 16:44:58 PST)
    - Re: [AMBER] is there a difference between the GTX 680 GPU's Ross Walker (Thu Nov 29 2012 - 16:58:33 PST)
    - Re: [AMBER] is there a difference between the GTX 680 GPU's Jonathan Gough (Thu Nov 29 2012 - 18:06:37 PST)
    - Re: [AMBER] is there a difference between the GTX 680 GPU's Ross Walker (Thu Nov 29 2012 - 18:31:44 PST)
    - Re: [AMBER] is there a difference between the GTX 680 GPU's Jonathan Gough (Thu Nov 29 2012 - 18:41:34 PST)
    - Re: [AMBER] is there a difference between the GTX 680 GPU's Marek Maly (Thu Nov 29 2012 - 18:16:47 PST)
[AMBER] The differences of MMPBSA calculations between AT1.5 and AT12, especially in PBSA solvation model. 徐见容 (Thu Nov 29 2012 - 18:43:05 PST)
- Re: [AMBER] The differences of MMPBSA calculations between AT1.5 and AT12, especially in PBSA solvation model. Ray Luo (Thu Nov 29 2012 - 19:24:28 PST)
[AMBER] The differences of MMPBSA calculations between AT1.5 andAT12, especially in PBSA solvation model. 徐见容 (Thu Nov 29 2012 - 19:05:52 PST)
[AMBER] GPU compile TEST does not work. kurisaki (Thu Nov 29 2012 - 21:09:33 PST)
- Re: [AMBER] GPU compile TEST does not work. kurisaki (Thu Nov 29 2012 - 23:06:13 PST)
  - Re: [AMBER] GPU compile TEST does not work. Jason Swails (Fri Nov 30 2012 - 05:02:46 PST)
    - Re: [AMBER] GPU compile TEST does not work. kurisaki (Fri Nov 30 2012 - 06:07:25 PST)
[AMBER] 回复: Re: The differences of MMPBSA calculations between AT1.5and AT12, especially in PBSA solvation model. 徐见容 (Thu Nov 29 2012 - 22:51:16 PST)
- Re: [AMBER] 回复: Re: The differences of MMPBSA calculations between AT1.5and AT12, especially in PBSA solvation model. Ray Luo, Ph.D. (Fri Nov 30 2012 - 09:28:55 PST)
[AMBER] imaging issues during RMSF Sangeetha B (Fri Nov 30 2012 - 06:16:52 PST)
- Re: [AMBER] imaging issues during RMSF Daniel Roe (Wed Dec 05 2012 - 13:48:58 PST)
  - Re: [AMBER] imaging issues during RMSF Sangeetha B (Thu Dec 06 2012 - 04:05:03 PST)
    - Re: [AMBER] imaging issues during RMSF Daniel Roe (Wed Dec 12 2012 - 10:56:49 PST)
[AMBER] Atom rename after RESP fitting by antechamber Liu Denis (Fri Nov 30 2012 - 19:17:16 PST)
- Re: [AMBER] Atom rename after RESP fitting by antechamber Ravi Tripathi (Fri Nov 30 2012 - 20:15:08 PST)
[AMBER] problem in loading pdb in xleap Shubhadip Das (Fri Nov 30 2012 - 23:12:53 PST)
- Re: [AMBER] problem in loading pdb in xleap Jason Swails (Sat Dec 01 2012 - 06:35:14 PST)
[AMBER] forcefield for PLP Bala Subramani (Sat Dec 01 2012 - 01:07:49 PST)
[AMBER] problem with cpptraj hbond action Marek Maly (Sat Dec 01 2012 - 17:12:22 PST)
- Re: [AMBER] problem with cpptraj hbond action Daniel Roe (Sat Dec 01 2012 - 21:12:02 PST)
  - Re: [AMBER] problem with cpptraj hbond action Marek Maly (Sun Dec 02 2012 - 04:05:04 PST)
[AMBER] using D-amino acids Thomas Evangelidis (Sun Dec 02 2012 - 14:59:25 PST)
- Re: [AMBER] using D-amino acids case (Sun Dec 02 2012 - 18:16:06 PST)
  - Re: [AMBER] using D-amino acids Thomas Evangelidis (Fri Dec 07 2012 - 08:01:29 PST)
[AMBER] Density in QM/MM marawan hussain (Mon Dec 03 2012 - 01:02:48 PST)
- Re: [AMBER] Density in QM/MM Marc van der Kamp (Mon Dec 03 2012 - 01:10:38 PST)
  - Re: [AMBER] Density in QM/MM Marc van der Kamp (Mon Dec 03 2012 - 01:14:22 PST)
- Re: [AMBER] Density in QM/MM marawan hussain (Mon Dec 03 2012 - 04:19:43 PST)
  - Re: [AMBER] Density in QM/MM case (Mon Dec 03 2012 - 04:40:42 PST)
[AMBER] rmsd of trajectories with different no. of residues in same protein? Vaibhav Dixit (Mon Dec 03 2012 - 03:16:28 PST)
- Re: [AMBER] rmsd of trajectories with different no. of residues in same protein? monica.imtech.res.in (Mon Dec 03 2012 - 04:32:17 PST)
  - Re: [AMBER] rmsd of trajectories with different no. of residues in same protein? Vaibhav Dixit (Mon Dec 03 2012 - 06:25:35 PST)
    - Re: [AMBER] rmsd of trajectories with different no. of residues in same protein? Jason Swails (Mon Dec 03 2012 - 06:53:05 PST)
    - Re: [AMBER] rmsd of trajectories with different no. of residues in same protein? Vaibhav Dixit (Mon Dec 03 2012 - 08:56:14 PST)
    - Re: [AMBER] rmsd of trajectories with different no. of residues in same protein? Daniel Roe (Tue Dec 04 2012 - 09:12:11 PST)
    - Re: [AMBER] rmsd of trajectories with different no. of residues in same protein? Vaibhav Dixit (Tue Dec 04 2012 - 09:17:23 PST)
    - Re: [AMBER] rmsd of trajectories with different no. of residues in same protein? Vaibhav Dixit (Tue Dec 04 2012 - 09:30:52 PST)
    - Re: [AMBER] rmsd of trajectories with different no. of residues in same protein? Daniel Roe (Tue Dec 04 2012 - 14:08:47 PST)
    - Re: [AMBER] rmsd of trajectories with different no. of residues in same protein? Vaibhav Dixit (Tue Dec 04 2012 - 19:15:46 PST)
[AMBER] need assistance to generate forcefield for Pyridoxal phosphate BALA SUBRAMANI G L (Mon Dec 03 2012 - 04:03:31 PST)
- Re: [AMBER] need assistance to generate forcefield for Pyridoxal phosphate case (Mon Dec 03 2012 - 04:44:07 PST)
  - [AMBER] PostDoc molecular modeling of enzymes Jan Brezovsky (Mon Dec 03 2012 - 05:17:17 PST)
[AMBER] pbsa forces printout from sander (amber12) Dr. Holger Kruse (Mon Dec 03 2012 - 07:08:34 PST)
- [AMBER] Fwd: pbsa forces printout from sander (amber12) Ray Luo, Ph.D. (Mon Dec 03 2012 - 09:53:31 PST)
  - Re: [AMBER] pbsa forces printout from sander (amber12) Qin Cai (Mon Dec 03 2012 - 15:01:13 PST)
- Re: [AMBER] pbsa forces printout from sander (amber12) Dr. Holger Kruse (Fri Dec 07 2012 - 01:07:27 PST)
[AMBER] What are Inner Sp2 carbons and non-pure aromatic systems? Yun Shi (Mon Dec 03 2012 - 10:53:17 PST)
[AMBER] PB Bomb in pb_aaradi(): No radius assigned for atom 14 CB 2C Rahul Banerjee (Mon Dec 03 2012 - 11:40:52 PST)
- Re: [AMBER] PB Bomb in pb_aaradi(): No radius assigned for atom 14 CB 2C Jason Swails (Mon Dec 03 2012 - 11:55:06 PST)
  - Re: [AMBER] PB Bomb in pb_aaradi(): No radius assigned for atom 14 CB 2C BERGY (Thu Dec 27 2012 - 03:55:00 PST)
[AMBER] Questions regarding mmpbsa... Jonathan Gough (Mon Dec 03 2012 - 12:29:15 PST)
- Re: [AMBER] Questions regarding mmpbsa... Jason Swails (Mon Dec 03 2012 - 13:08:25 PST)
  - Re: [AMBER] Questions regarding mmpbsa... Jonathan Gough (Mon Dec 03 2012 - 13:45:17 PST)
Re: [AMBER] The differences of MMPBSA calculations between AT1.5and AT12, especially in PBSA solvation model. Ray Luo, Ph.D. (Mon Dec 03 2012 - 12:34:43 PST)
[AMBER] Problem while running MMPBSA - stuck Jonathan Gough (Mon Dec 03 2012 - 15:13:08 PST)
- Re: [AMBER] Problem while running MMPBSA - stuck Ray Luo, Ph.D. (Mon Dec 03 2012 - 15:18:28 PST)
[AMBER] Lys-bound retinal parameters? Scarlett Dong (Mon Dec 03 2012 - 15:31:07 PST)
- Re: [AMBER] Lys-bound retinal parameters? FyD (Mon Dec 03 2012 - 21:17:54 PST)
  - Re: [AMBER] Lys-bound retinal parameters? Scarlett Dong (Mon Dec 10 2012 - 03:59:25 PST)
    - Re: [AMBER] Lys-bound retinal parameters? FyD (Wed Dec 12 2012 - 22:08:19 PST)
[AMBER] iapbs installation Miguel Ortiz Lombardía (Tue Dec 04 2012 - 01:52:17 PST)
- Re: [AMBER] [apbs-users] iapbs installation Robert Konecny (Tue Dec 04 2012 - 10:59:52 PST)
  - Re: [AMBER] [apbs-users] iapbs installation Miguel Ortiz Lombardia (Tue Dec 04 2012 - 23:13:41 PST)
    - Re: [AMBER] [apbs-users] iapbs installation Miguel Ortiz Lombardía (Thu Dec 06 2012 - 08:23:30 PST)
  - Re: [AMBER] [apbs-users] iapbs installation Jason Swails (Fri Dec 07 2012 - 10:49:32 PST)
- Re: [AMBER] iapbs installation Miguel Ortiz Lombardía (Fri Dec 07 2012 - 01:39:12 PST)
  - [AMBER] MMPBSA.py fails with sander.APBS Miguel Ortiz Lombardía (Fri Dec 07 2012 - 05:24:52 PST)
  - Re: [AMBER] [apbs-users] iapbs installation Robert Konecny (Sat Dec 08 2012 - 17:41:45 PST)
    - Re: [AMBER] [apbs-users] iapbs installation Miguel Ortiz Lombardia (Sat Dec 08 2012 - 23:10:43 PST)
    - Re: [AMBER] [apbs-users] iapbs installation Jason Swails (Sun Dec 09 2012 - 07:39:56 PST)
[AMBER] ptraj centering problem Fabian Glaser (Tue Dec 04 2012 - 07:56:59 PST)
- Re: [AMBER] ptraj centering problem Daniel Roe (Tue Dec 04 2012 - 09:00:05 PST)
  - Re: [AMBER] ptraj centering problem Fabian Glaser (Tue Dec 04 2012 - 23:27:48 PST)
    - Re: [AMBER] ptraj centering problem Daniel Roe (Wed Dec 05 2012 - 07:01:57 PST)
  - Re: [AMBER] ptraj centering problem Hirdesh Kumar (Wed Dec 05 2012 - 05:53:45 PST)
    - Re: [AMBER] ptraj centering problem Jason Swails (Wed Dec 05 2012 - 06:49:59 PST)
[AMBER] EGB discrepancy between sander and pmemd Eng H Yap (Tue Dec 04 2012 - 08:02:18 PST)
- Re: [AMBER] EGB discrepancy between sander and pmemd David A Case (Tue Dec 04 2012 - 10:15:30 PST)
- Re: [AMBER] EGB discrepancy between sander and pmemd Jason Swails (Tue Dec 04 2012 - 12:35:42 PST)
- Re: [AMBER] EGB discrepancy between sander and pmemd Eng H Yap (Tue Dec 04 2012 - 13:59:47 PST)
  - Re: [AMBER] EGB discrepancy between sander and pmemd case (Tue Dec 04 2012 - 15:02:47 PST)
    - Re: [AMBER] EGB discrepancy between sander and pmemd Jason Swails (Tue Dec 04 2012 - 15:29:22 PST)
    - Re: [AMBER] EGB discrepancy between sander and pmemd Jason Swails (Tue Dec 04 2012 - 15:40:36 PST)
[AMBER] problem in solvation of binding pocket Zhenquan Hu (Tue Dec 04 2012 - 08:42:31 PST)
- Re: [AMBER] problem in solvation of binding pocket Chris Chris (Tue Dec 04 2012 - 09:00:34 PST)
  - Re: [AMBER] problem in solvation of binding pocket Daniel Sindhikara (Tue Dec 04 2012 - 14:25:49 PST)
[AMBER] amber on intel Xeon 5680 Marcela Madrid (Tue Dec 04 2012 - 15:48:48 PST)
- Re: [AMBER] amber on intel Xeon 5680 Jason Swails (Tue Dec 04 2012 - 16:02:37 PST)
[AMBER] 回复： Re: problem in solvation of binding pocket zhenquan hu (Tue Dec 04 2012 - 15:58:35 PST)
[AMBER] Patching Error occurred while Bugfixing Anogna (Tue Dec 04 2012 - 23:23:14 PST)
- Re: [AMBER] Patching Error occurred while Bugfixing Jason Swails (Wed Dec 05 2012 - 06:49:19 PST)
  - Re: [AMBER] Patching Error occurred while Bugfixing Anogna (Wed Dec 05 2012 - 07:50:32 PST)
[AMBER] Fatal Error: File 'netcdf.mod' opened at (1) is not a GFORTRAN module file Thomas Evangelidis (Wed Dec 05 2012 - 03:52:03 PST)
- Re: [AMBER] Fatal Error: File 'netcdf.mod' opened at (1) is not a GFORTRAN module file case (Wed Dec 05 2012 - 05:41:10 PST)
  - Re: [AMBER] Fatal Error: File 'netcdf.mod' opened at (1) is not a GFORTRAN module file Thomas Evangelidis (Wed Dec 05 2012 - 07:42:21 PST)
    - Re: [AMBER] Fatal Error: File 'netcdf.mod' opened at (1) is not a GFORTRAN module file Jason Swails (Wed Dec 05 2012 - 14:54:30 PST)
    - Re: [AMBER] Fatal Error: File 'netcdf.mod' opened at (1) is not a GFORTRAN module file Thomas Evangelidis (Wed Dec 05 2012 - 15:18:20 PST)
    - Re: [AMBER] Fatal Error: File 'netcdf.mod' opened at (1) is not a GFORTRAN module file Jason Swails (Wed Dec 05 2012 - 16:30:57 PST)
    - Re: [AMBER] Fatal Error: File 'netcdf.mod' opened at (1) is not a GFORTRAN module file Thomas Evangelidis (Thu Dec 06 2012 - 07:37:55 PST)
    - Re: [AMBER] Fatal Error: File 'netcdf.mod' opened at (1) is not a GFORTRAN module file Jason Swails (Thu Dec 06 2012 - 08:53:12 PST)
    - Re: [AMBER] Fatal Error: File 'netcdf.mod' opened at (1) is not a GFORTRAN module file Ismail, Mohd F. (Thu Dec 06 2012 - 10:14:22 PST)
- Re: [AMBER] Fatal Error: File 'netcdf.mod' opened at (1) is not a GFORTRAN module file Mark Williamson (Wed Dec 05 2012 - 10:36:33 PST)
  - Re: [AMBER] Fatal Error: File 'netcdf.mod' opened at (1) is not a GFORTRAN module file Jason Swails (Wed Dec 05 2012 - 11:00:07 PST)
    - Re: [AMBER] Fatal Error: File 'netcdf.mod' opened at (1) is not a GFORTRAN module file Thomas Evangelidis (Wed Dec 05 2012 - 13:57:16 PST)
- [AMBER] glycam_06h atom types Urszula Uciechowska (Fri Dec 14 2012 - 09:03:58 PST)
  - Re: [AMBER] glycam_06h atom types Lachele Foley (Lists) (Fri Dec 14 2012 - 09:35:59 PST)
    - Re: [AMBER] glycam_06h atom types Urszula Uciechowska (Fri Dec 14 2012 - 09:54:11 PST)
    - Re: [AMBER] glycam_06h atom types Lachele Foley (Lists) (Fri Dec 14 2012 - 11:09:49 PST)
    - Re: [AMBER] glycam_06h atom types Urszula Uciechowska (Fri Dec 14 2012 - 12:18:23 PST)
    - Re: [AMBER] glycam_06h atom types Lachele Foley (Lists) (Fri Dec 14 2012 - 12:58:53 PST)
[AMBER] NMR Order Parameter Restraints Brown, Kyle (Wed Dec 05 2012 - 08:52:22 PST)
- Re: [AMBER] NMR Order Parameter Restraints case (Thu Dec 20 2012 - 06:39:58 PST)
  - Re: [AMBER] NMR Order Parameter Restraints Brown, Kyle (Thu Dec 20 2012 - 13:38:50 PST)
[AMBER] FW: EGB discrepancy between sander and pmemd Eng H Yap (Wed Dec 05 2012 - 08:56:30 PST)
- Re: [AMBER] FW: EGB discrepancy between sander and pmemd Jason Swails (Wed Dec 05 2012 - 10:12:33 PST)
  - Re: [AMBER] FW: EGB discrepancy between sander and pmemd Eng H Yap (Wed Dec 05 2012 - 12:41:24 PST)
- Re: [AMBER] FW: EGB discrepancy between sander and pmemd Duke, Robert E Jr (Wed Dec 05 2012 - 12:22:58 PST)
Re: [AMBER] problem with closest in cpptraj: trajout still writes all solvent molecules Marc van der Kamp (Wed Dec 05 2012 - 12:22:16 PST)
- Re: [AMBER] problem with closest in cpptraj: trajout still writes all solvent molecules Daniel Roe (Wed Dec 05 2012 - 12:52:52 PST)
  - Re: [AMBER] problem with closest in cpptraj: trajout still writes all solvent molecules Marc van der Kamp (Wed Dec 05 2012 - 13:48:41 PST)
[AMBER] How to Run MD of Glycol Nucleic Acid (GNA) Mu Xia (Thu Dec 06 2012 - 01:02:07 PST)
- Re: [AMBER] How to Run MD of Glycol Nucleic Acid (GNA) FyD (Thu Dec 06 2012 - 09:37:16 PST)
  - Re: [AMBER] How to Run MD of Glycol Nucleic Acid (GNA) Mu Xia (Thu Dec 06 2012 - 17:01:04 PST)
    - Re: [AMBER] How to Run MD of Glycol Nucleic Acid (GNA) ros (Fri Dec 07 2012 - 08:37:36 PST)
    - Re: [AMBER] How to Run MD of Glycol Nucleic Acid (GNA) FyD (Wed Dec 12 2012 - 22:19:23 PST)
    - Re: [AMBER] How to Run MD of Glycol Nucleic Acid (GNA) FyD (Wed Dec 12 2012 - 21:47:54 PST)
[AMBER] ERROR: Regenerate prmtop file with bondi radii Thomas Evangelidis (Thu Dec 06 2012 - 07:55:31 PST)
- Re: [AMBER] ERROR: Regenerate prmtop file with bondi radii Jason Swails (Thu Dec 06 2012 - 09:05:16 PST)
  - Re: [AMBER] ERROR: Regenerate prmtop file with bondi radii Thomas Evangelidis (Thu Dec 06 2012 - 13:51:46 PST)
    - Re: [AMBER] ERROR: Regenerate prmtop file with bondi radii Jason Swails (Thu Dec 06 2012 - 14:59:14 PST)
    - Re: [AMBER] ERROR: Regenerate prmtop file with bondi radii Jason Swails (Thu Dec 06 2012 - 15:00:39 PST)
[AMBER] Call for paper Siavoush Dastmalchi (Thu Dec 06 2012 - 12:53:21 PST)
[AMBER] nvidia driver installation problem Sanjib Paul (Thu Dec 06 2012 - 22:30:54 PST)
- Re: [AMBER] nvidia driver installation problem Jason Swails (Fri Dec 07 2012 - 04:26:48 PST)
  - Re: [AMBER] nvidia driver installation problem Andreas Goetz (Fri Dec 07 2012 - 12:14:15 PST)
    - Re: [AMBER] nvidia driver installation problem Fenley, Andrew (Fri Dec 07 2012 - 15:30:28 PST)
[AMBER] Error in MM-PBSA execution Anogna (Thu Dec 06 2012 - 22:32:14 PST)
- Re: [AMBER] Error in MM-PBSA execution Ray Luo, Ph.D. (Fri Dec 07 2012 - 10:58:21 PST)
  - [AMBER] Amber force field formula Shaandar Nyamtulga (Sat Dec 08 2012 - 04:41:36 PST)
    - Re: [AMBER] Amber force field formula case (Sat Dec 08 2012 - 05:20:23 PST)
[AMBER] developing parameters for HID-CU osalo.abo.fi (Fri Dec 07 2012 - 00:05:03 PST)
- Re: [AMBER] developing parameters for HID-CU francesco oteri (Fri Dec 07 2012 - 03:53:05 PST)
  - Re: [AMBER] developing parameters for HID-CU Tomasz Borowski (Sat Dec 08 2012 - 22:07:53 PST)
- Re: [AMBER] developing parameters for HID-CU FyD (Wed Dec 12 2012 - 21:59:32 PST)
[AMBER] Error of restraint of atom using "pmemd" program in Amber 11 dbaogen (Fri Dec 07 2012 - 02:42:35 PST)
- Re: [AMBER] Error of restraint of atom using "pmemd" program in Amber 11 Jason Swails (Fri Dec 07 2012 - 04:30:23 PST)
- Re: [AMBER] Error of restraint of atom using "pmemd" program in Amber 11 dbaogen (Fri Dec 07 2012 - 17:53:03 PST)
  - Re: [AMBER] Error of restraint of atom using "pmemd" program in Amber 11 case (Sat Dec 08 2012 - 05:12:45 PST)
[AMBER] Getting error messages during testing the installation. Sanjib Paul (Fri Dec 07 2012 - 05:00:08 PST)
- Re: [AMBER] Getting error messages during testing the installation. Jason Swails (Fri Dec 07 2012 - 05:58:49 PST)
  - Re: [AMBER] Getting error messages during testing the installation. Sanjib Paul (Sat Dec 08 2012 - 03:14:43 PST)
    - Re: [AMBER] Getting error messages during testing the installation. case (Sat Dec 08 2012 - 05:17:35 PST)
    - Re: [AMBER] Getting error messages during testing the installation. Sanjib Paul (Sun Dec 09 2012 - 21:13:29 PST)
    - Re: [AMBER] Getting error messages during testing the installation. David A Case (Mon Dec 10 2012 - 05:39:55 PST)
[AMBER] problem with imposing planarity to a N3P3 ring Giovanni Pavan (Fri Dec 07 2012 - 10:36:08 PST)
[AMBER] FATAL: Atom does not have a type. Jonathan Gough (Fri Dec 07 2012 - 12:47:36 PST)
- Re: [AMBER] FATAL: Atom does not have a type. David A Case (Fri Dec 07 2012 - 13:18:51 PST)
  - Re: [AMBER] FATAL: Atom does not have a type. Jonathan Gough (Fri Dec 07 2012 - 13:39:28 PST)
[AMBER] how to speed up implicit solvent simulation with infinite cutoff Thomas Evangelidis (Sat Dec 08 2012 - 08:17:40 PST)
- Re: [AMBER] how to speed up implicit solvent simulation with infinite cutoff Jason Swails (Sat Dec 08 2012 - 14:50:57 PST)
  - Re: [AMBER] how to speed up implicit solvent simulation with infinite cutoff case (Sat Dec 08 2012 - 18:59:45 PST)
- Re: [AMBER] how to speed up implicit solvent simulation with infinite cutoff Hai Nguyen (Mon Dec 10 2012 - 14:01:59 PST)
[AMBER] compare Delphi result using MMPBSA.py.MPI psu4.uic.edu (Sat Dec 08 2012 - 11:02:22 PST)
- Re: [AMBER] compare Delphi result using MMPBSA.py.MPI Ray Luo, Ph.D. (Sat Dec 08 2012 - 15:45:45 PST)
[AMBER] For TI do corresponding same atoms in ligand pairs need to have the same charge Yulin Huang (Sat Dec 08 2012 - 12:15:34 PST)
- Re: [AMBER] For TI do corresponding same atoms in ligand pairs need to have the same charge case (Sat Dec 08 2012 - 19:03:10 PST)
  - Re: [AMBER] For TI do corresponding same atoms in ligand pairs need to have the same charge Yulin Huang (Sat Dec 08 2012 - 19:13:04 PST)
    - Re: [AMBER] For TI do corresponding same atoms in ligand pairs need to have the same charge Yulin Huang (Mon Dec 10 2012 - 09:51:48 PST)
    - Re: [AMBER] For TI do corresponding same atoms in ligand pairs need to have the same charge steinbrt.rci.rutgers.edu (Mon Dec 10 2012 - 11:26:08 PST)
    - Re: [AMBER] For TI do corresponding same atoms in ligand pairs need to have the same charge Yulin Huang (Mon Dec 10 2012 - 11:28:37 PST)
    - Re: [AMBER] For TI do corresponding same atoms in ligand pairs need to have the same charge David A Case (Mon Dec 10 2012 - 11:45:30 PST)
    - Re: [AMBER] For TI do corresponding same atoms in ligand pairs need to have the same charge Yulin Huang (Mon Dec 10 2012 - 11:56:58 PST)
[AMBER] DNA planarity constraints in AMBER 丁鹏飞 (Sat Dec 08 2012 - 19:14:10 PST)
- Re: [AMBER] DNA planarity constraints in AMBER case (Thu Dec 20 2012 - 06:37:12 PST)
[AMBER] Pairwise interaction energy between resiudes using MMPBSA.py in Amber 11 dbaogen (Sat Dec 08 2012 - 22:08:39 PST)
- Re: [AMBER] Pairwise interaction energy between resiudes using MMPBSA.py in Amber 11 Aron Broom (Sat Dec 08 2012 - 23:51:14 PST)
[AMBER] where is .in file for AMBER GAFF lipids? Albert (Sun Dec 09 2012 - 06:18:06 PST)
[AMBER] solvent accessible volume vs Nihal Korkmaz (Sun Dec 09 2012 - 20:08:14 PST)
- Re: [AMBER] solvent accessible volume vs Daniel Roe (Wed Dec 12 2012 - 10:50:44 PST)
  - Re: [AMBER] solvent accessible volume vs Nihal Korkmaz (Tue Dec 25 2012 - 01:56:54 PST)
    - Re: [AMBER] solvent accessible volume vs Daniel Roe (Mon Jan 21 2013 - 09:41:36 PST)
[AMBER] Any possibility of scripting in tleap? Sajeewa Pemasinghe (Sun Dec 09 2012 - 23:03:08 PST)
- Re: [AMBER] Any possibility of scripting in tleap? Aron Broom (Sun Dec 09 2012 - 23:19:50 PST)
  - Re: [AMBER] Any possibility of scripting in tleap? Sajeewa Pemasinghe (Sun Dec 09 2012 - 23:28:07 PST)
- Re: [AMBER] Any possibility of scripting in tleap? David A Case (Mon Dec 10 2012 - 05:49:44 PST)
  - Re: [AMBER] Any possibility of scripting in tleap? Sajeewa Pemasinghe (Mon Dec 10 2012 - 06:35:57 PST)
[AMBER] enthalpy and sum of per residue energy decomposition not euqal Sangita Kachhap (Mon Dec 10 2012 - 01:09:21 PST)
- Re: [AMBER] enthalpy and sum of per residue energy decomposition not euqal Jason Swails (Mon Dec 10 2012 - 07:44:19 PST)
  - Re: [AMBER] enthalpy and sum of per residue energy decomposition not euqal Sangita Kachhap (Mon Dec 10 2012 - 10:34:08 PST)
[AMBER] Should I optimize the structure before obtaining the RESP charges? Mu Xia (Mon Dec 10 2012 - 01:13:43 PST)
- Re: [AMBER] Should I optimize the structure before obtaining the RESP charges? FyD (Wed Dec 12 2012 - 22:01:15 PST)
[AMBER] Force calculation during SMD (jar=1): I'm looking for insights Jan-Philip Gehrcke (Mon Dec 10 2012 - 02:31:13 PST)
- Re: [AMBER] Force calculation during SMD (jar=1): I'm looking for insights Jason Swails (Mon Dec 10 2012 - 08:29:57 PST)
  - Re: [AMBER] Force calculation during SMD (jar=1): I'm looking for insights Jan-Philip Gehrcke (Tue Dec 11 2012 - 03:01:28 PST)
    - Re: [AMBER] Force calculation during SMD (jar=1): I'm looking for insights Jason Swails (Tue Dec 11 2012 - 05:21:27 PST)
    - Re: [AMBER] Force calculation during SMD (jar=1): I'm looking for insights Jan-Philip Gehrcke (Tue Dec 11 2012 - 05:34:20 PST)
[AMBER] Amber12 with Plumed Rajeswari A. (Mon Dec 10 2012 - 02:32:00 PST)
- Re: [AMBER] Amber12 with Plumed davide branduardi (Mon Dec 10 2012 - 06:14:33 PST)
  - Re: [AMBER] Amber12 with Plumed Rajeswari A. (Mon Dec 10 2012 - 06:40:40 PST)
    - Re: [AMBER] Amber12 with Plumed Rajeswari A. (Thu Dec 13 2012 - 01:26:35 PST)
    - Re: [AMBER] Amber12 with Plumed davide branduardi (Thu Dec 13 2012 - 01:50:48 PST)
[AMBER] Problem with molecule containing sulfonic acid substitution Bernhard Poll (Mon Dec 10 2012 - 02:32:27 PST)
- Re: [AMBER] Problem with molecule containing sulfonic acid substitution David A Case (Mon Dec 10 2012 - 05:56:02 PST)
[AMBER] prmtop file Chandrasekaran, Suryanarayanan (Mon Dec 10 2012 - 04:04:46 PST)
- Re: [AMBER] prmtop file Bill Miller III (Mon Dec 10 2012 - 04:26:46 PST)
[AMBER] Problem in Nmode entropy calculation Mu Xia (Mon Dec 10 2012 - 08:02:52 PST)
- Re: [AMBER] Problem in Nmode entropy calculation Jason Swails (Mon Dec 10 2012 - 08:33:41 PST)
[AMBER] GAFF atom types for the headgroup of the LDAO surfactant ABEL Stephane 175950 (Mon Dec 10 2012 - 08:43:17 PST)
- Re: [AMBER] GAFF atom types for the headgroup of the LDAO surfactant FyD (Wed Dec 12 2012 - 21:35:57 PST)
[AMBER] NAB nmode memory requirements Ryan Pavlovicz (Mon Dec 10 2012 - 09:43:19 PST)
- Re: [AMBER] NAB nmode memory requirements David A Case (Mon Dec 10 2012 - 11:14:15 PST)
- Re: [AMBER] NAB nmode memory requirements Jason Swails (Mon Dec 10 2012 - 11:51:13 PST)
[AMBER] Antechamber with jaguar outputs eneas.usal.es (Mon Dec 10 2012 - 14:53:26 PST)
[AMBER] ptraj vs cpptraj: optimal clusters number choice adarm.nencki.gov.pl (Mon Dec 10 2012 - 16:03:48 PST)
[AMBER] amber workshop question psu4.uic.edu (Mon Dec 10 2012 - 16:57:19 PST)
- Re: [AMBER] amber workshop question Ross Walker (Mon Dec 10 2012 - 17:05:52 PST)
  - Re: [AMBER] amber workshop question Jonathan Gough (Mon Dec 10 2012 - 17:15:19 PST)
    - Re: [AMBER] amber workshop question psu4.uic.edu (Tue Dec 11 2012 - 16:20:22 PST)
[AMBER] prmtop file Chandrasekaran, Suryanarayanan (Mon Dec 10 2012 - 16:35:56 PST)
- Re: [AMBER] prmtop file Jason Swails (Tue Dec 11 2012 - 05:13:26 PST)
[AMBER] conditional restraints Thomas Evangelidis (Tue Dec 11 2012 - 00:31:18 PST)
- Re: [AMBER] conditional restraints Carlos Simmerling (Tue Dec 11 2012 - 03:11:27 PST)
[AMBER] MMGBSA result difference from whether use &decomp or not Liu Denis (Tue Dec 11 2012 - 00:49:06 PST)
- Re: [AMBER] MMGBSA result difference from whether use &decomp or not Jason Swails (Tue Dec 11 2012 - 05:03:08 PST)
  - Re: [AMBER] MMGBSA result difference from whether use &decomp or not Liu Denis (Tue Dec 11 2012 - 16:54:36 PST)
[AMBER] prmtop file Chandrasekaran, Suryanarayanan (Tue Dec 11 2012 - 02:01:51 PST)
[AMBER] calculating single side-chain RMSF with ptraj / cpptraj Marc van der Kamp (Tue Dec 11 2012 - 07:00:57 PST)
- Re: [AMBER] calculating single side-chain RMSF with ptraj / cpptraj Daniel Roe (Wed Dec 12 2012 - 10:38:05 PST)
  - Re: [AMBER] calculating single side-chain RMSF with ptraj / cpptraj Marc van der Kamp (Thu Dec 13 2012 - 02:09:45 PST)
    - Re: [AMBER] calculating single side-chain RMSF with ptraj / cpptraj Daniel Roe (Thu Dec 13 2012 - 08:00:11 PST)
Re: [AMBER] RMSD reported in lmod output Wong, Sergio E. (Tue Dec 11 2012 - 11:37:43 PST)
- Re: [AMBER] RMSD reported in lmod output Daniel Roe (Wed Dec 12 2012 - 10:30:08 PST)
[AMBER] Starting Coordinates Switched? Ismail, Mohd F. (Tue Dec 11 2012 - 14:42:05 PST)
- Re: [AMBER] Starting Coordinates Switched? Aron Broom (Tue Dec 11 2012 - 19:38:50 PST)
[AMBER] MMPBSA.py.MPI import error marawan hussain (Wed Dec 12 2012 - 00:14:23 PST)
- Re: [AMBER] MMPBSA.py.MPI import error Jason Swails (Wed Dec 12 2012 - 04:49:36 PST)
[AMBER] About restraint on GPU 王军 (Wed Dec 12 2012 - 00:37:35 PST)
- Re: [AMBER] About restraint on GPU David A Case (Wed Dec 12 2012 - 04:59:04 PST)
[AMBER] If scee is no longer in Amber11, can I simply remove it? Amparo Garcia Lopez (Wed Dec 12 2012 - 03:19:38 PST)
- Re: [AMBER] If scee is no longer in Amber11, can I simply remove it? Jason Swails (Wed Dec 12 2012 - 04:52:26 PST)
- Re: [AMBER] If scee is no longer in Amber11, can I simply remove it? David A Case (Wed Dec 12 2012 - 05:00:54 PST)
  - Re: [AMBER] If scee is no longer in Amber11, can I simply remove it? Amparo Garcia Lopez (Wed Dec 12 2012 - 05:12:20 PST)
[AMBER] Brookhaven National Labs Jonathan Gough (Wed Dec 12 2012 - 04:53:45 PST)
[AMBER] Antechamber with jaguar outputs eneas.usal.es (Wed Dec 12 2012 - 06:35:49 PST)
[AMBER] MMPBSA.py.MPI: multiple trajectory mmPBSA question psu4.uic.edu (Wed Dec 12 2012 - 10:00:14 PST)
- Re: [AMBER] MMPBSA.py.MPI: multiple trajectory mmPBSA question Aron Broom (Wed Dec 12 2012 - 11:24:02 PST)
[AMBER] cpptraj rmsd, 'perrescenter' clarification Marcus Arieno (Wed Dec 12 2012 - 12:22:09 PST)
- Re: [AMBER] cpptraj rmsd, 'perrescenter' clarification Daniel Roe (Thu Dec 13 2012 - 07:54:35 PST)
[AMBER] MMPBSA.py.MPI import error marawan hussain (Wed Dec 12 2012 - 18:08:42 PST)
- Re: [AMBER] MMPBSA.py.MPI import error Jason Swails (Thu Dec 13 2012 - 05:02:25 PST)
[AMBER] QM/MM AMBER-ORCA repulsion marawan hussain (Wed Dec 12 2012 - 22:07:31 PST)
- Re: [AMBER] QM/MM AMBER-ORCA repulsion Andreas Goetz (Thu Dec 13 2012 - 11:28:47 PST)
[AMBER] extract velocity from traj files Vijay Manickam Achari (Thu Dec 13 2012 - 01:08:20 PST)
- Re: [AMBER] extract velocity from traj files Jason Swails (Thu Dec 13 2012 - 04:54:43 PST)
  - Re: [AMBER] extract velocity from traj files Vijay Manickam Achari (Thu Dec 13 2012 - 21:03:06 PST)
    - Re: [AMBER] extract velocity from traj files Vijay Manickam Achari (Fri Dec 14 2012 - 03:46:03 PST)
    - Re: [AMBER] extract velocity from traj files Jason Swails (Fri Dec 14 2012 - 05:24:19 PST)
    - Re: [AMBER] extract velocity from traj files Vijay Manickam Achari (Fri Dec 14 2012 - 06:27:50 PST)
    - [AMBER] glycam_06h atom types Urszula Uciechowska (Fri Dec 14 2012 - 08:14:54 PST)
[AMBER] Steered Molecular Dynamics: Question George Tzotzos (Thu Dec 13 2012 - 03:35:31 PST)
- Re: [AMBER] Steered Molecular Dynamics: Question Dr. Vitaly Chaban (Thu Dec 13 2012 - 04:20:27 PST)
  - Re: [AMBER] Steered Molecular Dynamics: Question George Tzotzos (Thu Dec 13 2012 - 04:49:56 PST)
    - Re: [AMBER] Steered Molecular Dynamics: Question Jason Swails (Thu Dec 13 2012 - 05:01:08 PST)
    - Re: [AMBER] Steered Molecular Dynamics: Question George Tzotzos (Thu Dec 13 2012 - 05:54:59 PST)
    - Re: [AMBER] Steered Molecular Dynamics: Question Jason Swails (Thu Dec 13 2012 - 06:41:37 PST)
    - Re: [AMBER] Steered Molecular Dynamics: Question Adrian Roitberg (Thu Dec 13 2012 - 06:45:37 PST)
    - Re: [AMBER] Steered Molecular Dynamics: Question George Tzotzos (Thu Dec 13 2012 - 07:17:46 PST)
    - Re: [AMBER] Steered Molecular Dynamics: Question Jan-Philip Gehrcke (Fri Dec 14 2012 - 09:16:37 PST)
    - Re: [AMBER] Steered Molecular Dynamics: Question George Tzotzos (Fri Dec 14 2012 - 11:11:15 PST)
    - Re: [AMBER] Steered Molecular Dynamics: Question Dr. Vitaly Chaban (Thu Dec 13 2012 - 05:59:22 PST)
[AMBER] Ligand parameterization in AMOEBA to use in AMBER Jagur Lambix (Thu Dec 13 2012 - 14:29:04 PST)
- Re: [AMBER] Ligand parameterization in AMOEBA to use in AMBER case (Thu Dec 13 2012 - 18:35:32 PST)
  - Re: [AMBER] Ligand parameterization in AMOEBA to use in AMBER Jagur Lambix (Fri Dec 14 2012 - 08:32:24 PST)
[AMBER] QM/MM AMBER-ORCA repulsion marawan hussain (Thu Dec 13 2012 - 19:47:45 PST)
- Re: [AMBER] QM/MM AMBER-ORCA repulsion Andreas Goetz (Fri Dec 14 2012 - 01:29:39 PST)
[AMBER] FF99CHI and Modified nucleoside parameter combination Indrajit Deb (Thu Dec 13 2012 - 23:38:11 PST)
- Re: [AMBER] FF99CHI and Modified nucleoside parameter combination Jason Swails (Fri Dec 14 2012 - 04:55:25 PST)
  - Re: [AMBER] FF99CHI and Modified nucleoside parameter combination Indrajit Deb (Fri Dec 14 2012 - 11:16:41 PST)
    - Re: [AMBER] FF99CHI and Modified nucleoside parameter combination Ilyas Yildirim (Fri Dec 14 2012 - 11:54:27 PST)
    - Re: [AMBER] FF99CHI and Modified nucleoside parameter combination Indrajit Deb (Mon Dec 17 2012 - 02:25:41 PST)
    - Re: [AMBER] FF99CHI and Modified nucleoside parameter combination Ilyas Yildirim (Mon Dec 17 2012 - 03:52:52 PST)
[AMBER] Building peptides in a random conformation in AMBER.... Shashidhar Rao (Fri Dec 14 2012 - 11:20:56 PST)
- Re: [AMBER] Building peptides in a random conformation in AMBER.... Jason Swails (Fri Dec 14 2012 - 11:58:07 PST)
  - Re: [AMBER] Building peptides in a random conformation in AMBER.... Shashidhar Rao (Fri Dec 14 2012 - 12:02:58 PST)
    - Re: [AMBER] Building peptides in a random conformation in AMBER.... Ilyas Yildirim (Fri Dec 14 2012 - 12:10:03 PST)
    - Re: [AMBER] Building peptides in a random conformation in AMBER.... Shashidhar Rao (Fri Dec 14 2012 - 13:26:34 PST)
    - Re: [AMBER] Building peptides in a random conformation in AMBER.... Baldoni Hector Armando (Fri Dec 14 2012 - 15:41:53 PST)
- Re: [AMBER] Building peptides in a random conformation in AMBER.... Carlos Simmerling (Fri Dec 14 2012 - 12:06:14 PST)
  - Re: [AMBER] Building peptides in a random conformation in AMBER.... Bill Ross (Sat Dec 15 2012 - 10:29:19 PST)
[AMBER] how to define solvated box dimensions Thomas Evangelidis (Fri Dec 14 2012 - 15:02:00 PST)
- Re: [AMBER] how to define solvated box dimensions Thomas Evangelidis (Mon Dec 17 2012 - 02:46:34 PST)
  - Re: [AMBER] how to define solvated box dimensions David A Case (Mon Dec 17 2012 - 05:33:14 PST)
    - Re: [AMBER] how to define solvated box dimensions Thomas Evangelidis (Mon Dec 17 2012 - 06:54:26 PST)
[AMBER] Extraction of Box dimensions from MD Trajectories Jagur Lambix (Fri Dec 14 2012 - 15:20:10 PST)
[AMBER] Higher values for polar contribution RANAJIT SHINDE (Sat Dec 15 2012 - 04:23:01 PST)
- Re: [AMBER] Higher values for polar contribution Jason Swails (Sat Dec 15 2012 - 05:12:58 PST)
[AMBER] branched disaccharide in leap Krisztina Feher (Sat Dec 15 2012 - 12:25:15 PST)
- Re: [AMBER] branched disaccharide in leap Aron Broom (Sat Dec 15 2012 - 14:16:46 PST)
  - Re: [AMBER] branched disaccharide in leap Lachele Foley (Lists) (Sat Dec 15 2012 - 19:01:34 PST)
    - Re: [AMBER] branched disaccharide in leap Aron Broom (Sat Dec 15 2012 - 22:54:54 PST)
    - Re: [AMBER] branched disaccharide in leap Lachele Foley (Lists) (Sun Dec 16 2012 - 10:19:12 PST)
    - Re: [AMBER] branched disaccharide in leap Krisztina Feher (Mon Dec 17 2012 - 03:27:17 PST)
    - Re: [AMBER] branched disaccharide in leap Lachele Foley (Lists) (Mon Dec 17 2012 - 12:14:18 PST)
    - Re: [AMBER] branched disaccharide in leap FyD (Tue Dec 18 2012 - 22:40:50 PST)
- Re: [AMBER] branched disaccharide in leap FyD (Sun Dec 16 2012 - 00:22:28 PST)
[AMBER] Theoretical question about mmpbsa/docking energy values Chris Chris (Sat Dec 15 2012 - 13:21:44 PST)
- Re: [AMBER] Theoretical question about mmpbsa/docking energy values Aron Broom (Sat Dec 15 2012 - 14:22:23 PST)
[AMBER] H-REMD, pmemd fails to calculate potential energy of neighbor coordinates Jiri Wiesner (Sat Dec 15 2012 - 20:26:41 PST)
- Re: [AMBER] H-REMD, pmemd fails to calculate potential energy of neighbor coordinates Jason Swails (Sun Dec 16 2012 - 07:20:39 PST)
  - Re: [AMBER] H-REMD, pmemd fails to calculate potential energy of neighbor coordinates Jiri Wiesner (Sun Dec 16 2012 - 15:06:27 PST)
[AMBER] QM/MM AMBER-ORCA repulsion marawan hussain (Sat Dec 15 2012 - 21:16:14 PST)
- Re: [AMBER] QM/MM AMBER-ORCA repulsion Andreas Goetz (Tue Dec 18 2012 - 12:11:04 PST)
  - Re: [AMBER] QM/MM AMBER-ORCA repulsion marawan hussain (Tue Dec 18 2012 - 14:39:11 PST)
[AMBER] cannot use more than one node Fabian Glaser (Sun Dec 16 2012 - 00:26:13 PST)
- Re: [AMBER] cannot use more than one node Jiri Wiesner (Sun Dec 16 2012 - 05:24:38 PST)
[AMBER] Problems with restart file - coordinates values are too high tommaso.casalini.mail.polimi.it (Sun Dec 16 2012 - 04:53:51 PST)
- Re: [AMBER] Problems with restart file - coordinates values are too high Jason Swails (Sun Dec 16 2012 - 06:53:39 PST)
[AMBER] Ethanol as solvent Chinthaka Ratnaweera (Sun Dec 16 2012 - 21:14:01 PST)
- Re: [AMBER] Ethanol as solvent Aron Broom (Sun Dec 16 2012 - 21:58:25 PST)
  - Re: [AMBER] Ethanol as solvent Chinthaka Ratnaweera (Sun Dec 16 2012 - 22:07:41 PST)
    - Re: [AMBER] Ethanol as solvent Aron Broom (Sun Dec 16 2012 - 22:14:44 PST)
    - Re: [AMBER] Ethanol as solvent Chinthaka Ratnaweera (Sun Dec 16 2012 - 22:33:51 PST)
    - Re: [AMBER] Ethanol as solvent amin.imtech.res.in (Mon Dec 17 2012 - 03:16:25 PST)
    - Re: [AMBER] Ethanol as solvent Jason Swails (Mon Dec 17 2012 - 05:53:17 PST)
    - Re: [AMBER] Ethanol as solvent Chinthaka Ratnaweera (Mon Dec 17 2012 - 15:12:10 PST)
    - Re: [AMBER] Ethanol as solvent Bill Ross (Mon Dec 17 2012 - 16:57:05 PST)
    - Re: [AMBER] Ethanol as solvent David A Case (Tue Dec 18 2012 - 05:15:22 PST)
- Re: [AMBER] Ethanol as solvent FyD (Tue Dec 18 2012 - 22:32:42 PST)
[AMBER] why removal of terminal phosphate group is required? Asmita Gupta (Sun Dec 16 2012 - 22:22:39 PST)
- Re: [AMBER] why removal of terminal phosphate group is required? David A Case (Mon Dec 17 2012 - 05:13:42 PST)
- Re: [AMBER] why removal of terminal phosphate group is required? FyD (Tue Dec 18 2012 - 22:43:59 PST)
[AMBER] some problems in getting the parameters of GLYCAM in Leap deathsnake1991 (Sun Dec 16 2012 - 22:48:21 PST)
- Re: [AMBER] some problems in getting the parameters of GLYCAM in Leap David A Case (Mon Dec 17 2012 - 05:16:35 PST)
- Re: [AMBER] some problems in getting the parameters of GLYCAM in Leap Lachele Foley (Lists) (Mon Dec 17 2012 - 09:54:44 PST)
- Re: [AMBER] some problems in getting the parameters of GLYCAM in Leap 曾晓骏 (Wed Dec 19 2012 - 02:20:33 PST)
  - Re: [AMBER] some problems in getting the parameters of GLYCAM in Leap FyD (Wed Dec 19 2012 - 08:10:16 PST)
    - Re: [AMBER] some problems in getting the parameters of GLYCAM in Leap Lachele Foley (Lists) (Wed Dec 19 2012 - 11:00:51 PST)
[AMBER] AMBER to TINKER style trajectory Indrajit Deb (Mon Dec 17 2012 - 01:58:34 PST)
[AMBER] problem to install amber9 in a cluster. Sindrila Dutta banik (Mon Dec 17 2012 - 03:39:35 PST)
- Re: [AMBER] problem to install amber9 in a cluster. Jason Swails (Mon Dec 17 2012 - 06:01:29 PST)
[AMBER] problem related to the amber9 installation Sindrila Dutta banik (Mon Dec 17 2012 - 04:06:57 PST)
- Re: [AMBER] problem related to the amber9 installation David A Case (Mon Dec 17 2012 - 05:37:57 PST)
  - Re: [AMBER] problem related to the amber9 installation Sindrila Dutta banik (Mon Dec 17 2012 - 21:21:48 PST)
[AMBER] problem related to the amber9 installation Sindrila Dutta banik (Mon Dec 17 2012 - 04:11:11 PST)
- Re: [AMBER] problem related to the amber9 installation Vijay Manickam Achari (Mon Dec 17 2012 - 05:04:14 PST)
  - Re: [AMBER] problem related to the amber9 installation Sindrila Dutta banik (Mon Dec 17 2012 - 05:23:37 PST)
[AMBER] calculating velocity auto-correlation function Vijay Manickam Achari (Mon Dec 17 2012 - 04:27:25 PST)
- Re: [AMBER] calculating velocity auto-correlation function Jason Swails (Mon Dec 17 2012 - 06:08:24 PST)
- Re: [AMBER] calculating velocity auto-correlation function Jason Swails (Mon Dec 17 2012 - 06:45:29 PST)
Re: [AMBER] Fwd: FF99CHI and Modified nucleoside parameter combination Indrajit Deb (Mon Dec 17 2012 - 12:32:21 PST)
- Re: [AMBER] Fwd: FF99CHI and Modified nucleoside parameter combination Indrajit Deb (Mon Dec 17 2012 - 12:45:45 PST)
  - Re: [AMBER] Fwd: FF99CHI and Modified nucleoside parameter combination Indrajit Deb (Mon Dec 17 2012 - 12:58:52 PST)
    - Re: [AMBER] Fwd: FF99CHI and Modified nucleoside parameter combination Ilyas Yildirim (Mon Dec 17 2012 - 13:04:21 PST)
    - Re: [AMBER] Fwd: FF99CHI and Modified nucleoside parameter combination Indrajit Deb (Mon Dec 17 2012 - 13:27:12 PST)
    - Re: [AMBER] Fwd: FF99CHI and Modified nucleoside parameter combination Indrajit Deb (Mon Dec 17 2012 - 13:40:12 PST)
    - Re: [AMBER] Fwd: FF99CHI and Modified nucleoside parameter combination Indrajit Deb (Mon Dec 17 2012 - 14:57:36 PST)
    - Re: [AMBER] Fwd: FF99CHI and Modified nucleoside parameter combination Ilyas Yildirim (Mon Dec 17 2012 - 15:18:33 PST)
    - Re: [AMBER] Fwd: FF99CHI and Modified nucleoside parameter combination Indrajit Deb (Mon Dec 17 2012 - 23:48:53 PST)
    - [AMBER] Fwd: Fwd: FF99CHI and Modified nucleoside parameter combination Indrajit Deb (Tue Dec 18 2012 - 04:49:27 PST)
    - Re: [AMBER] Fwd: Fwd: FF99CHI and Modified nucleoside parameter combination Ilyas Yildirim (Tue Dec 18 2012 - 05:37:41 PST)
    - Re: [AMBER] Fwd: Fwd: FF99CHI and Modified nucleoside parameter combination Indrajit Deb (Thu Dec 20 2012 - 12:04:24 PST)
  - Re: [AMBER] Fwd: FF99CHI and Modified nucleoside parameter combination Ilyas Yildirim (Mon Dec 17 2012 - 13:00:31 PST)
- Re: [AMBER] Fwd: FF99CHI and Modified nucleoside parameter combination Ilyas Yildirim (Mon Dec 17 2012 - 12:57:59 PST)
[AMBER] alanine scanning Jonathan Gough (Mon Dec 17 2012 - 14:01:52 PST)
- Re: [AMBER] alanine scanning Jason Swails (Mon Dec 17 2012 - 17:10:45 PST)
  - Re: [AMBER] alanine scanning Jonathan Gough (Mon Dec 17 2012 - 17:17:41 PST)
Re: [AMBER] lmod error with large number of degrees of freedom Wong, Sergio E. (Mon Dec 17 2012 - 16:04:17 PST)
- Re: [AMBER] lmod error with large number of degrees of freedom David A Case (Tue Dec 18 2012 - 05:19:50 PST)
[AMBER] Antechamber with jaguar outputs eneas.usal.es (Tue Dec 18 2012 - 02:24:41 PST)
- Re: [AMBER] Antechamber with jaguar outputs David A Case (Tue Dec 18 2012 - 06:22:28 PST)
[AMBER] How to disable Coulomb interactions between two group of atoms Shenglong Wang (Tue Dec 18 2012 - 06:43:04 PST)
- Re: [AMBER] How to disable Coulomb interactions between two group of atoms David A Case (Tue Dec 18 2012 - 11:13:41 PST)
  - Re: [AMBER] How to disable Coulomb interactions between two group of atoms Shenglong Wang (Tue Dec 18 2012 - 11:24:46 PST)
    - Re: [AMBER] How to disable Coulomb interactions between two group of atoms David A Case (Wed Dec 19 2012 - 04:56:05 PST)
    - Re: [AMBER] How to disable Coulomb interactions between two group of atoms Shenglong Wang (Wed Dec 19 2012 - 06:13:59 PST)
[AMBER] getting warning when loading PDB created in amber9 in amber12 .. Vijay Manickam Achari (Tue Dec 18 2012 - 08:47:23 PST)
[AMBER] deprotonation with SHAKE Antonija Tomić (Wed Dec 19 2012 - 05:32:11 PST)
- Re: [AMBER] deprotonation with SHAKE Brian Radak (Wed Dec 19 2012 - 05:42:34 PST)
  - Re: [AMBER] deprotonation with SHAKE Antonija Tomić (Wed Dec 19 2012 - 05:48:50 PST)
[AMBER] MMPBSA - GB is negative, but PB is positive? what am I missing? Jonathan Gough (Wed Dec 19 2012 - 08:20:32 PST)
- Re: [AMBER] MMPBSA - GB is negative, but PB is positive? what am I missing? Jason Swails (Wed Dec 19 2012 - 09:40:28 PST)
- Re: [AMBER] MMPBSA - GB is negative, but PB is positive? what am I missing? Jonathan Gough (Thu Dec 20 2012 - 10:58:42 PST)
  - Re: [AMBER] MMPBSA - GB is negative, but PB is positive? what am I missing? Ray Luo, Ph.D. (Thu Dec 20 2012 - 11:05:52 PST)
    - Re: [AMBER] MMPBSA - GB is negative, but PB is positive? what am I missing? Jonathan Gough (Thu Dec 20 2012 - 11:54:12 PST)
    - Re: [AMBER] MMPBSA - GB is negative, but PB is positive? what am I missing? Ray Luo, Ph.D. (Thu Dec 20 2012 - 12:10:05 PST)
    - Re: [AMBER] MMPBSA - GB is negative, but PB is positive? what am I missing? Jonathan Gough (Thu Dec 20 2012 - 12:18:25 PST)
[AMBER] water box of specific dimensions Manikanthan Bhavaraju (Wed Dec 19 2012 - 18:58:01 PST)
[AMBER] cluster analysis groups conformers without doing alignment Sun (Thu Dec 20 2012 - 00:38:33 PST)
- Re: [AMBER] cluster analysis groups conformers without doing alignment Daniel Roe (Thu Dec 20 2012 - 07:22:27 PST)
  - Re: [AMBER] cluster analysis groups conformers without doing alignment Sun (Thu Dec 20 2012 - 19:39:22 PST)
    - Re: [AMBER] cluster analysis groups conformers without doing alignment Daniel Roe (Thu Dec 20 2012 - 19:54:26 PST)
    - Re: [AMBER] cluster analysis groups conformers without doing alignment Sun (Thu Dec 20 2012 - 20:07:44 PST)
[AMBER] how to define head and tail for several residues? osalo.abo.fi (Thu Dec 20 2012 - 01:58:36 PST)
- Re: [AMBER] how to define head and tail for several residues? FyD (Thu Dec 20 2012 - 02:31:34 PST)
[AMBER] problem in applying patches in AMBER12 and AMBERTools12 Prabu Manoharan (Thu Dec 20 2012 - 03:02:06 PST)
- Re: [AMBER] problem in applying patches in AMBER12 and AMBERTools12 case (Thu Dec 20 2012 - 06:24:43 PST)
  - Re: [AMBER] problem in applying patches in AMBER12 and AMBERTools12 Prabu Manoharan (Sun Dec 23 2012 - 23:56:12 PST)
[AMBER] how to use cpptraj in AMBER10 or 11 to generate new topology file HM (Thu Dec 20 2012 - 06:36:07 PST)
- Re: [AMBER] how to use cpptraj in AMBER10 or 11 to generate new topology file Daniel Roe (Thu Dec 20 2012 - 06:49:11 PST)
  - Re: [AMBER] how to use cpptraj in AMBER10 or 11 to generate new topology file HM (Fri Dec 21 2012 - 02:06:09 PST)
    - Re: [AMBER] how to use cpptraj in AMBER10 or 11 to generate new topology file Daniel Roe (Fri Dec 21 2012 - 05:24:28 PST)
    - Re: [AMBER] how to use cpptraj in AMBER10 or 11 to generate new topology file HM (Mon Dec 24 2012 - 13:52:53 PST)
[AMBER] analyzing DESMOND MD trajectories in cpptraj... Shashidhar Rao (Thu Dec 20 2012 - 11:01:44 PST)
- Re: [AMBER] analyzing DESMOND MD trajectories in cpptraj... Jason Swails (Thu Dec 20 2012 - 13:11:04 PST)
  - Re: [AMBER] analyzing DESMOND MD trajectories in cpptraj... Shashidhar Rao (Thu Dec 20 2012 - 13:36:18 PST)
[AMBER] stripping water molecules except few ones (384-408) HM (Fri Dec 21 2012 - 02:19:37 PST)
- Re: [AMBER] stripping water molecules except few ones (384-408) Daniel Roe (Fri Dec 21 2012 - 05:27:21 PST)
  - Re: [AMBER] stripping water molecules except few ones (384-408) HM (Mon Dec 24 2012 - 13:51:04 PST)
[AMBER] MD Average pdb edu troche (Fri Dec 21 2012 - 04:26:11 PST)
- Re: [AMBER] MD Average pdb Aron Broom (Fri Dec 21 2012 - 07:48:23 PST)
  - Re: [AMBER] MD Average pdb Jason Swails (Fri Dec 21 2012 - 10:24:32 PST)
    - Re: [AMBER] MD Average pdb Jonathan Gough (Fri Dec 21 2012 - 11:46:24 PST)
[AMBER] voltage for membrane? Albert (Sun Dec 23 2012 - 01:30:46 PST)
[AMBER] atom type john Kerk (Sun Dec 23 2012 - 01:47:49 PST)
- Re: [AMBER] atom type David A Case (Sun Dec 23 2012 - 05:54:46 PST)
[AMBER] PBC value become small at Z direction Vijay Manickam Achari (Sun Dec 23 2012 - 21:29:02 PST)
[AMBER] ERROR: max pairlist cutoff must be less than unit cell max sphere radius! Vijay Manickam Achari (Sun Dec 23 2012 - 22:23:42 PST)
- Re: [AMBER] ERROR: max pairlist cutoff must be less than unit cell max sphere radius! David A Case (Mon Dec 24 2012 - 06:21:54 PST)
  - Re: [AMBER] ERROR: max pairlist cutoff must be less than unit cell max sphere radius! Vijay Manickam Achari (Tue Dec 25 2012 - 19:10:44 PST)
    - Re: [AMBER] ERROR: max pairlist cutoff must be less than unit cell max sphere radius! David A Case (Wed Dec 26 2012 - 18:15:29 PST)
[AMBER] problem with parallel installation of amber12 - MPI_COMM_WORLD Amparo Garcia Lopez (Mon Dec 24 2012 - 05:50:32 PST)
- Re: [AMBER] problem with parallel installation of amber12 - MPI_COMM_WORLD David A Case (Mon Dec 24 2012 - 06:28:12 PST)
  - Re: [AMBER] problem with parallel installation of amber12 - MPI_COMM_WORLD Amparo Garcia Lopez (Mon Dec 24 2012 - 08:58:01 PST)
    - Re: [AMBER] problem with parallel installation of amber12 - MPI_COMM_WORLD David A Case (Mon Dec 24 2012 - 21:37:47 PST)
    - Re: [AMBER] problem with parallel installation of amber12 - MPI_COMM_WORLD Amparo Garcia Lopez (Tue Dec 25 2012 - 14:41:55 PST)
    - Re: [AMBER] problem with parallel installation of amber12 - MPI_COMM_WORLD Jason Swails (Tue Dec 25 2012 - 17:58:04 PST)
[AMBER] query regarding two different restrain on protein residues HM (Mon Dec 24 2012 - 13:57:14 PST)
[AMBER] restart file ERROR: I could not understand line 71821 Thomas Evangelidis (Tue Dec 25 2012 - 03:00:04 PST)
[AMBER] calcium ion in AMBER HM (Tue Dec 25 2012 - 12:04:32 PST)
- Re: [AMBER] calcium ion in AMBER deeptinayar.gmail.com (Tue Dec 25 2012 - 10:25:47 PST)
[AMBER] movement of PBC Vijay Manickam Achari (Tue Dec 25 2012 - 22:12:02 PST)
- Re: [AMBER] movement of PBC Jason Swails (Wed Dec 26 2012 - 04:58:31 PST)
[AMBER] N-Methylacetamide-molecule-force field Subrata Paul (Wed Dec 26 2012 - 04:51:01 PST)
- Re: [AMBER] N-Methylacetamide-molecule-force field David A Case (Wed Dec 26 2012 - 05:42:59 PST)
- Re: [AMBER] N-Methylacetamide-molecule-force field FyD (Wed Dec 26 2012 - 07:40:37 PST)
[AMBER] Fwd: difference between GLYCAM_06 and GLYCAM_06h Subrata Paul (Wed Dec 26 2012 - 05:01:15 PST)
[AMBER] Amber LES.MPI crash Kirill Nuzhdin (Wed Dec 26 2012 - 10:25:09 PST)
- Re: [AMBER] Amber LES.MPI crash Carlos Simmerling (Wed Dec 26 2012 - 10:39:32 PST)
  - Re: [AMBER] Amber LES.MPI crash Kirill Nuzhdin (Wed Dec 26 2012 - 11:03:21 PST)
  - Re: [AMBER] Amber LES.MPI crash Kirill Nuzhdin (Wed Jan 02 2013 - 08:08:16 PST)
    - Re: [AMBER] Amber LES.MPI crash Carlos Simmerling (Wed Jan 02 2013 - 09:04:07 PST)
    - Re: [AMBER] Amber LES.MPI crash Kirill Nuzhdin (Wed Jan 02 2013 - 11:54:37 PST)
    - Re: [AMBER] Amber LES.MPI crash David A Case (Wed Jan 02 2013 - 12:50:44 PST)
    - Re: [AMBER] Amber LES.MPI crash David A Case (Wed Jan 02 2013 - 09:40:29 PST)
    - Re: [AMBER] Amber LES.MPI crash Kirill Nuzhdin (Wed Jan 02 2013 - 11:54:34 PST)
    - Re: [AMBER] Amber LES.MPI crash David A Case (Wed Jan 02 2013 - 12:52:44 PST)
    - Re: [AMBER] Amber LES.MPI crash Kirill Nuzhdin (Wed Jan 02 2013 - 14:57:47 PST)
[AMBER] GLYCAM_06 & GLYCAM_06h Subrata Paul (Wed Dec 26 2012 - 22:10:41 PST)
- Re: [AMBER] GLYCAM_06 & GLYCAM_06h Lachele Foley (Lists) (Wed Dec 26 2012 - 23:23:33 PST)
  - Re: [AMBER] GLYCAM_06 & GLYCAM_06h Subrata Paul (Thu Dec 27 2012 - 03:03:22 PST)
    - Re: [AMBER] GLYCAM_06 & GLYCAM_06h Lachele Foley (Lists) (Thu Dec 27 2012 - 08:48:37 PST)
[AMBER] MMPBSA Alanine Scanning AttrubuteError BERGY (Thu Dec 27 2012 - 04:12:31 PST)
- Re: [AMBER] MMPBSA Alanine Scanning AttrubuteError Jason Swails (Thu Dec 27 2012 - 16:24:17 PST)
  - Re: [AMBER] MMPBSA Alanine Scanning AttrubuteError BERGY (Thu Dec 27 2012 - 21:26:42 PST)
    - Re: [AMBER] MMPBSA Alanine Scanning AttrubuteError Jason Swails (Fri Dec 28 2012 - 08:51:41 PST)
    - Re: [AMBER] MMPBSA Alanine Scanning AttrubuteError BERGY (Sat Dec 29 2012 - 00:18:26 PST)
    - Re: [AMBER] MMPBSA Alanine Scanning AttrubuteError Jason Swails (Sat Dec 29 2012 - 11:56:54 PST)
[AMBER] Is GTX580/GTX680 compatible with the sever motherboards? Mu Xia (Thu Dec 27 2012 - 22:54:11 PST)
- Re: [AMBER] Is GTX580/GTX680 compatible with the sever motherboards? Jason Swails (Fri Dec 28 2012 - 09:03:28 PST)
  - Re: [AMBER] Is GTX580/GTX680 compatible with the sever motherboards? Mu Xia (Sat Dec 29 2012 - 05:04:05 PST)
    - Re: [AMBER] Is GTX580/GTX680 compatible with the sever motherboards? Ross Walker (Sat Dec 29 2012 - 11:39:36 PST)
- Re: [AMBER] Is GTX580/GTX680 compatible with the sever motherboards? Scott Le Grand (Fri Dec 28 2012 - 12:21:01 PST)
[AMBER] Question in umbrella sampling Sajeewa Pemasinghe (Fri Dec 28 2012 - 06:08:39 PST)
- Re: [AMBER] Question in umbrella sampling Daniel Sindhikara (Fri Dec 28 2012 - 06:37:37 PST)
  - Re: [AMBER] Question in umbrella sampling Sajeewa Pemasinghe (Fri Dec 28 2012 - 07:16:14 PST)
    - Re: [AMBER] Question in umbrella sampling Aron Broom (Sat Dec 29 2012 - 14:36:35 PST)
    - Re: [AMBER] Question in umbrella sampling Sajeewa Pemasinghe (Sat Dec 29 2012 - 17:53:51 PST)
    - Re: [AMBER] Question in umbrella sampling Aron Broom (Mon Dec 31 2012 - 14:53:30 PST)
    - Re: [AMBER] Question in umbrella sampling Aron Broom (Mon Dec 31 2012 - 14:54:46 PST)
[AMBER] MD simulation Jeremy AHHH (Fri Dec 28 2012 - 10:28:10 PST)
- Re: [AMBER] MD simulation Kshatresh Dutta Dubey (Fri Dec 28 2012 - 11:25:11 PST)
[AMBER] NPT and NVE Energy Ismail, Mohd F. (Fri Dec 28 2012 - 13:06:43 PST)
- Re: [AMBER] NPT and NVE Energy Dr. Vitaly Chaban (Fri Dec 28 2012 - 13:50:37 PST)
  - Re: [AMBER] NPT and NVE Energy Andreas Goetz (Fri Dec 28 2012 - 16:28:33 PST)
    - Re: [AMBER] NPT and NVE Energy Ismail, Mohd F. (Sun Dec 30 2012 - 01:19:40 PST)
  - Re: [AMBER] NPT and NVE Energy Ismail, Mohd F. (Sun Dec 30 2012 - 01:28:00 PST)
    - Re: [AMBER] NPT and NVE Energy David A Case (Sun Dec 30 2012 - 06:19:24 PST)
    - Re: [AMBER] NPT and NVE Energy Jason Swails (Sun Dec 30 2012 - 08:34:08 PST)
    - Re: [AMBER] NPT and NVE Energy Ismail, Mohd F. (Tue Jan 01 2013 - 20:58:16 PST)
[AMBER] TI-charge removal step Nihal Korkmaz (Fri Dec 28 2012 - 15:46:46 PST)
- Re: [AMBER] TI-charge removal step steinbrt.rci.rutgers.edu (Sat Dec 29 2012 - 04:59:19 PST)
  - Re: [AMBER] TI-charge removal step Nihal Korkmaz (Sat Dec 29 2012 - 21:18:14 PST)
    - Re: [AMBER] TI-charge removal step steinbrt.rci.rutgers.edu (Sun Dec 30 2012 - 05:34:05 PST)
[AMBER] question about adaptive QM/MM yeqing2.ustc.edu.cn (Sat Dec 29 2012 - 00:29:47 PST)
- Re: [AMBER] question about adaptive QM/MM Andreas Goetz (Sat Dec 29 2012 - 22:26:33 PST)
[AMBER] not getting dipole moment values in pmemd.cuda Sanjib Paul (Tue Jan 01 2013 - 03:36:05 PST)
[AMBER] Need assistance to generate forcefield for PYRIDOXAL-5'-PHOSPHATE BALA SUBRAMANI G L (Wed Jan 02 2013 - 05:27:21 PST)
[AMBER] MMPBSA error marawan hussain (Wed Jan 02 2013 - 21:11:59 PST)
- Re: [AMBER] MMPBSA error Jason Swails (Thu Jan 03 2013 - 04:43:58 PST)
  - Re: [AMBER] MMPBSA error marawan hussain (Thu Jan 03 2013 - 15:10:48 PST)
    - Re: [AMBER] MMPBSA error Jason Swails (Thu Jan 03 2013 - 16:47:04 PST)
    - Re: [AMBER] MMPBSA error marawan hussain (Thu Jan 03 2013 - 18:04:21 PST)
    - Re: [AMBER] MMPBSA error Jason Swails (Fri Jan 04 2013 - 08:19:55 PST)
    - Re: [AMBER] MMPBSA error marawan hussain (Sun Jan 06 2013 - 15:28:32 PST)
    - Re: [AMBER] MMPBSA error Jason Swails (Sun Jan 06 2013 - 16:11:40 PST)
    - Re: [AMBER] MMPBSA error marawan hussain (Mon Jan 07 2013 - 02:44:19 PST)
    - Re: [AMBER] MMPBSA error Jason Swails (Mon Jan 07 2013 - 03:35:19 PST)
    - Re: [AMBER] MMPBSA error marawan hussain (Mon Jan 07 2013 - 18:48:19 PST)
[AMBER] Thermodynamic integration with iwrap=1 in SANDER Miroslav Krepl (Thu Jan 03 2013 - 04:39:30 PST)
[AMBER] Problems creating topology file for Dfrom Giri tomp (Thu Jan 03 2013 - 16:31:41 PST)
[AMBER] Issue with creating topology file due to atom type not being recognised in frcmod Giri tomp (Thu Jan 03 2013 - 16:34:52 PST)
- Re: [AMBER] [q4md-fft] Issue with creating topology file due to atom type not being recognised in frcmod FyD (Fri Jan 04 2013 - 06:06:51 PST)
  - Re: [AMBER] [q4md-fft] Issue with creating topology file due to atom type not being recognised in frcmod David A Case (Fri Jan 04 2013 - 10:50:15 PST)
    - Re: [AMBER] [q4md-fft] Issue with creating topology file due to atom type not being recognised in frcmod Giri tomp (Sat Jan 05 2013 - 11:18:18 PST)
    - [AMBER] frcmod file dihedrals -phase shift question osalo.abo.fi (Tue Jan 08 2013 - 04:28:18 PST)
    - Re: [AMBER] frcmod file dihedrals -phase shift question Carlos Simmerling (Tue Jan 08 2013 - 04:37:08 PST)
[AMBER] bad atom type: f Date, Mihir (Fri Jan 04 2013 - 10:42:21 PST)
- Re: [AMBER] bad atom type: f Vaibhav Dixit (Fri Jan 04 2013 - 20:16:58 PST)
  - Re: [AMBER] bad atom type: f Date, Mihir (Thu Jan 10 2013 - 13:06:03 PST)
    - Re: [AMBER] bad atom type: f Vaibhav Dixit (Thu Jan 10 2013 - 21:08:39 PST)
    - Re: [AMBER] bad atom type: f Jason Swails (Fri Jan 11 2013 - 05:03:58 PST)
[AMBER] Announcement: Release of DOCK 6.6 Scott Brozell (Fri Jan 04 2013 - 20:02:33 PST)
[AMBER] REMD restart gargi borgohai (Fri Jan 04 2013 - 22:46:50 PST)
[AMBER] positive DeltaEel and negative DeltaGsolv in MMPBSA Emilio Angelina (Sat Jan 05 2013 - 11:44:23 PST)
- Re: [AMBER] positive DeltaEel and negative DeltaGsolv in MMPBSA Ray Luo, Ph.D. (Sat Jan 05 2013 - 16:57:09 PST)
  - Re: [AMBER] positive DeltaEel and negative DeltaGsolv in MMPBSA Emilio Angelina (Sat Jan 05 2013 - 20:00:00 PST)
[AMBER] rfree parsing error in group specification Joel Dockray (Sat Jan 05 2013 - 16:51:47 PST)
- [AMBER] Group specification for energy decomposition in thermodynamic integration Joel Dockray (Mon Jan 07 2013 - 10:24:57 PST)
[AMBER] GPUs and PBSPro Vijay Manickam Achari (Sun Jan 06 2013 - 20:05:45 PST)
- Re: [AMBER] GPUs and PBSPro Ross Walker (Sun Jan 06 2013 - 20:50:47 PST)
[AMBER] how to assign atom types. Salma Zahir (Mon Jan 07 2013 - 02:43:12 PST)
- Re: [AMBER] how to assign atom types. Jason Swails (Mon Jan 07 2013 - 03:27:28 PST)
- Re: [AMBER] how to assign atom types. FyD (Tue Jan 08 2013 - 00:03:34 PST)
[AMBER] AMBER parameter problem osalo.abo.fi (Mon Jan 07 2013 - 06:25:08 PST)
- Re: [AMBER] AMBER parameter problem David A Case (Mon Jan 07 2013 - 07:52:58 PST)
[AMBER] Group specification for energy decomposition in thermodynamic integration (Corrected spacing) Joel Dockray (Mon Jan 07 2013 - 10:35:00 PST)
[AMBER] bugfix.31 Norah Schlacter (Mon Jan 07 2013 - 12:50:11 PST)
- Re: [AMBER] bugfix.31 Jason Swails (Mon Jan 07 2013 - 13:24:16 PST)
[AMBER] AMBER12 Installation failed Udaysankar Midya (Mon Jan 07 2013 - 22:39:31 PST)
- Re: [AMBER] AMBER12 Installation failed Jason Swails (Tue Jan 08 2013 - 04:50:27 PST)
  - Re: [AMBER] AMBER12 Installation failed Tru Huynh (Thu Jan 10 2013 - 13:23:36 PST)
[AMBER] Error with TIP4P Chandrasekaran, Suryanarayanan (Tue Jan 08 2013 - 06:18:25 PST)
- Re: [AMBER] Error with TIP4P case (Wed Jan 09 2013 - 06:07:57 PST)
- Re: [AMBER] Error with TIP4P George M Giambasu (Thu Jan 10 2013 - 08:57:44 PST)
[AMBER] Query regarding GB calculation on a protein with FE using MMPBSA.py Prajwal Nandekar (Tue Jan 08 2013 - 06:22:48 PST)
- Re: [AMBER] Query regarding GB calculation on a protein with FE using MMPBSA.py Jason Swails (Tue Jan 08 2013 - 07:24:51 PST)
  - Re: [AMBER] Query regarding GB calculation on a protein with FE using MMPBSA.py Prajwal Nandekar (Wed Jan 09 2013 - 06:04:25 PST)
[AMBER] GAFFlipid FF concern jfloresc.andrew.cmu.edu (Tue Jan 08 2013 - 13:54:28 PST)
- Re: [AMBER] GAFFlipid FF concern Dickson, Callum (Wed Jan 09 2013 - 06:08:24 PST)
  - Re: [AMBER] GAFFlipid FF concern David A Case (Wed Jan 09 2013 - 10:38:54 PST)
    - Re: [AMBER] GAFFlipid FF concern Ganesh Kamath (Wed Jan 09 2013 - 10:46:11 PST)
[AMBER] Is AM1-BCC charges ok for ligands with idodine atoms Shulin Zhuang (Tue Jan 08 2013 - 17:54:10 PST)
- Re: [AMBER] Is AM1-BCC charges ok for ligands with idodine atoms FyD (Wed Jan 09 2013 - 00:56:50 PST)
- Re: [AMBER] Is AM1-BCC charges ok for ligands with idodine atoms FyD (Wed Jan 09 2013 - 04:15:38 PST)
[AMBER] hybrid imlicit/explicit system Алексей Раевский (Wed Jan 09 2013 - 02:44:16 PST)
- Re: [AMBER] hybrid imlicit/explicit system case (Wed Jan 09 2013 - 05:57:25 PST)
[AMBER] problem with identifying Zn ion in Amber11 Agnieszka Dybala-Defratyka (Wed Jan 09 2013 - 13:55:21 PST)
- Re: [AMBER] problem with identifying Zn ion in Amber11 Jason Swails (Thu Jan 10 2013 - 06:01:46 PST)
[AMBER] cudaMemcpyToSymbol: SetSim copy to Sim failed for K20x using JAC and Cellulose benchmarks Mohammad Ashraf Bhuiyan (Wed Jan 09 2013 - 14:02:41 PST)
- Re: [AMBER] cudaMemcpyToSymbol: SetSim copy to Sim failed for K20x using JAC and Cellulose benchmarks Ross Walker (Wed Jan 09 2013 - 14:23:00 PST)
  - Re: [AMBER] cudaMemcpyToSymbol: SetSim copy to Sim failed for K20x using JAC and Cellulose benchmarks Chinh Su Tran To (Thu Apr 25 2013 - 21:00:30 PDT)
    - Re: [AMBER] cudaMemcpyToSymbol: SetSim copy to Sim failed for K20x using JAC and Cellulose benchmarks Ross Walker (Thu Apr 25 2013 - 21:10:22 PDT)
    - Re: [AMBER] cudaMemcpyToSymbol: SetSim copy to Sim failed for K20x using JAC and Cellulose benchmarks Chinh Su Tran To (Thu Apr 25 2013 - 22:46:46 PDT)
[AMBER] bug in sander nmr.F90, amber12? Fabian Zeller (Thu Jan 10 2013 - 06:27:09 PST)
- Re: [AMBER] bug in sander nmr.F90, amber12? David A Case (Fri Jan 11 2013 - 07:17:00 PST)
[AMBER] Problems using NAB and GCC Roberto Vera (Thu Jan 10 2013 - 08:13:58 PST)
- Re: [AMBER] Problems using NAB and GCC David A Case (Thu Jan 10 2013 - 11:22:06 PST)
[AMBER] AMBER bonded parameters Dr. Vitaly Chaban (Thu Jan 10 2013 - 14:50:34 PST)
- Re: [AMBER] AMBER bonded parameters David A Case (Fri Jan 11 2013 - 06:44:29 PST)
[AMBER] antechamber problem Changqing Yan (Thu Jan 10 2013 - 19:15:45 PST)
- Re: [AMBER] antechamber problem Ravi Tripathi (Thu Jan 10 2013 - 20:58:09 PST)
- Re: [AMBER] antechamber problem Jason Swails (Fri Jan 11 2013 - 05:01:33 PST)
  - Re: [AMBER] antechamber problem M. L. Dodson (Fri Jan 11 2013 - 05:30:50 PST)
[AMBER] amber12 Bio Learner (Thu Jan 10 2013 - 22:41:30 PST)
- Re: [AMBER] amber12 Daniel Sindhikara (Thu Jan 10 2013 - 23:05:23 PST)
[AMBER] Simulating Folic Acid JD John (Thu Jan 10 2013 - 22:53:10 PST)
- Re: [AMBER] Simulating Folic Acid M. L. Dodson (Fri Jan 11 2013 - 05:43:01 PST)
[AMBER] how to construct new molecule Bio Learner (Fri Jan 11 2013 - 00:00:50 PST)
- Re: [AMBER] how to construct new molecule Maxier Acosta Santiago (Fri Jan 11 2013 - 00:09:18 PST)
[AMBER] Glycam_06 in amber12 Subrata Paul (Fri Jan 11 2013 - 02:03:53 PST)
- Re: [AMBER] Glycam_06 in amber12 Urszula Uciechowska (Fri Jan 11 2013 - 02:27:35 PST)
  - Re: [AMBER] Glycam_06 in amber12 Lachele Foley (Lists) (Fri Jan 11 2013 - 07:08:44 PST)
    - Re: [AMBER] Glycam_06 in amber12 Subrata Paul (Fri Jan 11 2013 - 20:32:00 PST)
    - Re: [AMBER] Glycam_06 in amber12 Lachele Foley (Lists) (Sat Jan 12 2013 - 10:48:58 PST)
    - Re: [AMBER] Glycam_06 in amber12 Subrata Paul (Sun Jan 13 2013 - 23:54:14 PST)
    - Re: [AMBER] Glycam_06 in amber12 Lachele Foley (Lists) (Mon Jan 14 2013 - 08:23:10 PST)
    - [AMBER] disulfide bonds Urszula Uciechowska (Fri Mar 08 2013 - 06:03:42 PST)
    - Re: [AMBER] disulfide bonds Anselm Horn (Fri Mar 08 2013 - 06:17:00 PST)
[AMBER] AMD pooja chahal (Fri Jan 11 2013 - 02:28:31 PST)
- Re: [AMBER] AMD Jason Swails (Fri Jan 11 2013 - 05:27:14 PST)
  - Re: [AMBER] AMD pooja chahal (Fri Jan 11 2013 - 20:30:44 PST)
    - Re: [AMBER] AMD Daniel Sindhikara (Fri Jan 11 2013 - 20:58:40 PST)
    - Re: [AMBER] AMD Ganesh Kamath (Fri Jan 11 2013 - 21:04:32 PST)
    - Re: [AMBER] AMD Hirdesh Kumar (Sat Jan 12 2013 - 00:31:39 PST)
    - Re: [AMBER] AMD Jason Swails (Sat Jan 12 2013 - 06:52:51 PST)
    - Re: [AMBER] AMD Bill Ross (Fri Jan 11 2013 - 21:01:29 PST)
    - Re: [AMBER] AMD pooja chahal (Tue Jan 15 2013 - 03:18:15 PST)
    - Re: [AMBER] AMD Jason Swails (Tue Jan 15 2013 - 03:27:04 PST)
    - Re: [AMBER] AMD pooja chahal (Tue Jan 15 2013 - 03:32:58 PST)
    - Re: [AMBER] AMD Ross Walker (Tue Jan 15 2013 - 07:46:33 PST)
    - Re: [AMBER] AMD Bill Ross (Tue Jan 15 2013 - 15:08:32 PST)
[AMBER] installation problem Tanmoy Paul (Fri Jan 11 2013 - 03:09:30 PST)
- Re: [AMBER] installation problem Jason Swails (Fri Jan 11 2013 - 05:30:43 PST)
- Re: [AMBER] installation problem JD John (Fri Jan 11 2013 - 09:38:37 PST)
[AMBER] dnaiontracker command in cpptraj Le,Huy Tuan (Fri Jan 11 2013 - 11:50:41 PST)
- Re: [AMBER] dnaiontracker command in cpptraj Daniel Roe (Fri Jan 11 2013 - 12:19:24 PST)
[AMBER] question about force fields and external QM program Kirill Nuzhdin (Fri Jan 11 2013 - 11:59:53 PST)
- Re: [AMBER] question about force fields and external QM program Jason Swails (Fri Jan 11 2013 - 13:27:27 PST)
[AMBER] RMS2D Syed Tarique Moin (Sat Jan 12 2013 - 03:49:22 PST)
- Re: [AMBER] RMS2D Daniel Roe (Sat Jan 12 2013 - 10:26:17 PST)
  - Re: [AMBER] RMS2D Syed Tarique Moin (Mon Jan 14 2013 - 02:05:12 PST)
[AMBER] Fwd: Query regarding umbrella sampling minhazul arfeen (Sat Jan 12 2013 - 08:07:30 PST)
- Re: [AMBER] Fwd: Query regarding umbrella sampling Brian Radak (Sun Jan 13 2013 - 09:31:23 PST)
[AMBER] Software announcement: Release of PUPIL 2.0 Joan Torras (Sun Jan 13 2013 - 15:44:03 PST)
[AMBER] command used to upload pdb Bio Learner (Mon Jan 14 2013 - 00:51:40 PST)
- Re: [AMBER] command used to upload pdb Prajwal Nandekar (Mon Jan 14 2013 - 01:42:37 PST)
[AMBER] installation error Bio Learner (Mon Jan 14 2013 - 01:58:27 PST)
- Re: [AMBER] installation error Daniel Roe (Mon Jan 14 2013 - 07:30:01 PST)
- Re: [AMBER] installation error Jason Swails (Mon Jan 14 2013 - 07:56:46 PST)
  - Re: [AMBER] installation error Bio Learner (Mon Jan 14 2013 - 22:19:48 PST)
    - Re: [AMBER] installation error Jason Swails (Tue Jan 15 2013 - 03:20:42 PST)
[AMBER] amber organic box 纪晓峰 (Mon Jan 14 2013 - 02:16:59 PST)
- Re: [AMBER] amber organic box David A Case (Mon Jan 14 2013 - 05:10:01 PST)
  - Re: [AMBER] amber organic box Bill Ross (Mon Jan 14 2013 - 10:41:32 PST)
[AMBER] Citrate ion (-3) parameters moitrayee.mbu.iisc.ernet.in (Mon Jan 14 2013 - 03:34:13 PST)
- Re: [AMBER] Citrate ion (-3) parameters FyD (Tue Jan 15 2013 - 22:31:29 PST)
  - Re: [AMBER] Citrate ion (-3) parameters moitrayee.mbu.iisc.ernet.in (Wed Jan 16 2013 - 01:28:08 PST)
    - Re: [AMBER] Citrate ion (-3) parameters FyD (Thu Jan 17 2013 - 00:05:38 PST)
    - Re: [AMBER] Citrate ion (-3) parameters moitrayee.mbu.iisc.ernet.in (Sat Jan 19 2013 - 05:27:17 PST)
    - Re: [AMBER] Citrate ion (-3) parameters FyD (Mon Jan 21 2013 - 00:46:32 PST)
    - Re: [AMBER] Citrate ion (-3) parameters moitrayee.mbu.iisc.ernet.in (Mon Jan 21 2013 - 09:39:00 PST)
    - Re: [AMBER] Citrate ion (-3) parameters FyD (Mon Jan 21 2013 - 23:58:41 PST)
    - Re: [AMBER] Modified amino acid parameter generation moitrayee.mbu.iisc.ernet.in (Thu Feb 28 2013 - 09:59:28 PST)
    - Re: [AMBER] Modified amino acid parameter generation FyD (Thu Feb 28 2013 - 22:13:51 PST)
[AMBER] Problem with Identification of bonds Volker Lesch (Mon Jan 14 2013 - 06:33:07 PST)
[AMBER] density for PBC system; addles error Kirill Nuzhdin (Mon Jan 14 2013 - 14:17:53 PST)
- Re: [AMBER] density for PBC system; addles error David A Case (Tue Jan 15 2013 - 04:58:57 PST)
  - Re: [AMBER] density for PBC system; addles error Kirill Nuzhdin (Tue Jan 15 2013 - 15:03:56 PST)
    - Re: [AMBER] density for PBC system; addles error case (Tue Jan 15 2013 - 17:00:25 PST)
    - Re: [AMBER] density for PBC system; addles error Kirill Nuzhdin (Wed Jan 16 2013 - 08:41:42 PST)
    - Re: [AMBER] density for PBC system; addles error Kirill Nuzhdin (Wed Jan 16 2013 - 11:41:47 PST)
    - Re: [AMBER] density for PBC system; addles error David A Case (Wed Jan 16 2013 - 13:35:10 PST)
    - Re: [AMBER] density for PBC system; addles error Kirill Nuzhdin (Wed Jan 16 2013 - 15:24:11 PST)
    - Re: [AMBER] density for PBC system; addles error Kirill Nuzhdin (Wed Jan 16 2013 - 15:33:52 PST)
    - Re: [AMBER] density for PBC system; addles error David A Case (Thu Jan 17 2013 - 06:01:17 PST)
[AMBER] Getting AmberTools12 to work in Ubuntu 12.04? David Dubins (Mon Jan 14 2013 - 14:39:21 PST)
- Re: [AMBER] Getting AmberTools12 to work in Ubuntu 12.04? Jason Swails (Mon Jan 14 2013 - 16:26:39 PST)
[AMBER] vlimit exceeded and distorted bonds Chris Chris (Mon Jan 14 2013 - 15:02:33 PST)
[AMBER] Membrane-protein simulation using amber12 Manikanthan Bhavaraju (Mon Jan 14 2013 - 20:38:11 PST)
- Re: [AMBER] Membrane-protein simulation using amber12 Benjamin D Madej (Tue Jan 15 2013 - 09:08:05 PST)
  - Re: [AMBER] Membrane-protein simulation using amber12 manikanthan bhavaraju (Tue Jan 15 2013 - 09:36:27 PST)
    - Re: [AMBER] Membrane-protein simulation using amber12 Benjamin D Madej (Tue Jan 15 2013 - 10:25:07 PST)
    - Re: [AMBER] Membrane-protein simulation using amber12 manikanthan bhavaraju (Tue Jan 15 2013 - 10:36:44 PST)
[AMBER] xlead aentrena (Tue Jan 15 2013 - 04:03:43 PST)
- Re: [AMBER] xlead David A Case (Tue Jan 15 2013 - 05:05:35 PST)
  - Re: [AMBER] xlead Antonio Entrena Guadix (Wed Jan 16 2013 - 02:40:02 PST)
    - Re: [AMBER] xlead Jan-Philip Gehrcke (Wed Jan 16 2013 - 03:24:34 PST)
    - Re: [AMBER] xlead Jason Swails (Wed Jan 16 2013 - 03:57:03 PST)
    - Re: [AMBER] xlead Daniel Roe (Wed Jan 16 2013 - 07:50:02 PST)
    - Re: [AMBER] xlead Antonio Entrena Guadix (Wed Jan 16 2013 - 23:09:17 PST)
[AMBER] Atom reordering for TI Thomas Exner (Tue Jan 15 2013 - 04:25:01 PST)
- Re: [AMBER] Atom reordering for TI David A Case (Tue Jan 15 2013 - 05:07:32 PST)
  - Re: [AMBER] Atom reordering for TI Thomas Exner (Tue Jan 15 2013 - 07:43:36 PST)
[AMBER] umbrella sampling Elisa Frezza (Tue Jan 15 2013 - 06:12:16 PST)
- Re: [AMBER] umbrella sampling Adrian Roitberg (Tue Jan 15 2013 - 06:19:14 PST)
  - Re: [AMBER] umbrella sampling Elisa Frezza (Tue Jan 15 2013 - 06:25:33 PST)
    - Re: [AMBER] umbrella sampling Elisa Frezza (Tue Jan 15 2013 - 07:11:36 PST)
    - Re: [AMBER] umbrella sampling Aron Broom (Tue Jan 15 2013 - 07:16:48 PST)
    - Re: [AMBER] umbrella sampling Elisa Frezza (Tue Jan 15 2013 - 07:23:24 PST)
    - Re: [AMBER] umbrella sampling Aron Broom (Tue Jan 15 2013 - 07:26:57 PST)
    - Re: [AMBER] umbrella sampling Elisa Frezza (Tue Jan 15 2013 - 07:32:07 PST)
    - Re: [AMBER] umbrella sampling Ross Walker (Tue Jan 15 2013 - 07:40:21 PST)
    - Re: [AMBER] umbrella sampling Elisa Frezza (Tue Jan 15 2013 - 08:05:21 PST)
    - Re: [AMBER] umbrella sampling ros (Tue Jan 15 2013 - 08:36:29 PST)
    - Re: [AMBER] umbrella sampling Elisa Frezza (Tue Jan 15 2013 - 08:56:02 PST)
    - Re: [AMBER] umbrella sampling Adrian Roitberg (Tue Jan 15 2013 - 11:09:03 PST)
    - Re: [AMBER] umbrella sampling Elisa Frezza (Tue Jan 15 2013 - 12:50:04 PST)
    - Re: [AMBER] umbrella sampling Adrian Roitberg (Tue Jan 15 2013 - 12:52:40 PST)
    - Re: [AMBER] umbrella sampling Elisa Frezza (Tue Jan 15 2013 - 13:00:04 PST)
    - Re: [AMBER] umbrella sampling Aron Broom (Tue Jan 15 2013 - 13:21:03 PST)
    - Re: [AMBER] umbrella sampling Elisa Frezza (Wed Jan 16 2013 - 01:57:06 PST)
[AMBER] Getting total dipole moment of molecules in periodic box. 강현아 (Tue Jan 15 2013 - 06:47:00 PST)
- Re: [AMBER] Getting total dipole moment of molecules in periodic box. Jason Swails (Tue Jan 15 2013 - 07:00:02 PST)
[AMBER] Is it possible to do TI calculations with pmemd? Anna Bauß (Tue Jan 15 2013 - 07:10:07 PST)
- Re: [AMBER] Is it possible to do TI calculations with pmemd? steinbrt.rci.rutgers.edu (Tue Jan 15 2013 - 07:40:44 PST)
- Re: [AMBER] Is it possible to do TI calculations with pmemd? Ross Walker (Tue Jan 15 2013 - 07:41:48 PST)
  - Re: [AMBER] Is it possible to do TI calculations with pmemd? Anna Bauß (Wed Jan 16 2013 - 00:23:47 PST)
[AMBER] atom type definition mm_pbsa Andrew Anighoro (Tue Jan 15 2013 - 08:01:13 PST)
- Re: [AMBER] atom type definition mm_pbsa Jason Swails (Tue Jan 15 2013 - 08:38:57 PST)
[AMBER] Membrane-Peptide Simulation ( peptide going away from membrane) HM (Tue Jan 15 2013 - 09:18:16 PST)
- Re: [AMBER] Membrane-Peptide Simulation ( peptide going away from membrane) Benjamin D Madej (Tue Jan 15 2013 - 09:49:00 PST)
  - Re: [AMBER] Membrane-Peptide Simulation ( peptide going away from membrane) manikanthan bhavaraju (Tue Jan 15 2013 - 10:10:35 PST)
    - Re: [AMBER] Membrane-Peptide Simulation ( peptide going away from membrane) Benjamin D Madej (Tue Jan 15 2013 - 10:38:41 PST)
  - Re: [AMBER] Membrane-Peptide Simulation ( peptide going away from membrane) HM (Thu Jan 17 2013 - 02:28:17 PST)
    - Re: [AMBER] Membrane-Peptide Simulation ( peptide going away from membrane) Benjamin D Madej (Thu Jan 17 2013 - 15:07:18 PST)
    - Re: [AMBER] Membrane-Peptide Simulation ( peptide going away from membrane) HM (Thu Jan 17 2013 - 23:29:11 PST)
    - Re: [AMBER] Membrane-Peptide Simulation ( peptide going away from membrane) Thomas Evangelidis (Thu Jan 17 2013 - 23:52:46 PST)
    - Re: [AMBER] Membrane-Peptide Simulation ( peptide going away from membrane) HM (Fri Jan 18 2013 - 00:10:49 PST)
    - Re: [AMBER] Membrane-Peptide Simulation ( peptide going away from membrane) Thomas Evangelidis (Fri Jan 18 2013 - 00:22:34 PST)
    - Re: [AMBER] Membrane-Peptide Simulation ( peptide going away from membrane) HM (Fri Jan 18 2013 - 00:28:41 PST)
    - Re: [AMBER] Membrane-Peptide Simulation ( peptide going away from membrane) Ross Walker (Fri Jan 18 2013 - 00:38:48 PST)
    - Re: [AMBER] Membrane-Peptide Simulation ( peptide going away from membrane) HM (Fri Jan 18 2013 - 01:07:11 PST)
    - Re: [AMBER] Membrane-Peptide Simulation ( peptide going away from membrane) Aldo Segura (Fri Jan 18 2013 - 05:21:00 PST)
    - [AMBER] PMEMD and cutoff Urszula Uciechowska (Fri Jan 18 2013 - 06:02:35 PST)
    - Re: [AMBER] PMEMD and cutoff Ross Walker (Fri Jan 18 2013 - 06:34:25 PST)
    - Re: [AMBER] Membrane-Peptide Simulation ( peptide going away from membrane) Thomas Evangelidis (Fri Jan 18 2013 - 07:09:10 PST)
    - Re: [AMBER] Membrane-Peptide Simulation ( peptide going away from membrane) Benjamin D Madej (Fri Jan 18 2013 - 12:21:36 PST)
    - Re: [AMBER] Membrane-Peptide Simulation ( peptide going away from membrane) HM (Mon Jan 21 2013 - 05:25:30 PST)
    - Re: [AMBER] Membrane-Peptide Simulation ( peptide going away from membrane) Ross Walker (Mon Jan 21 2013 - 15:47:58 PST)
    - Re: [AMBER] Membrane-Peptide Simulation ( peptide going away from membrane) HM (Tue Jan 22 2013 - 00:35:47 PST)
    - Re: [AMBER] Membrane-Peptide Simulation ( peptide going away from membrane) Ross Walker (Sun Jan 27 2013 - 16:53:21 PST)
[AMBER] using image command in cpptraj... Shashidhar Rao (Tue Jan 15 2013 - 10:34:52 PST)
- Re: [AMBER] using image command in cpptraj... Daniel Roe (Tue Jan 15 2013 - 10:52:50 PST)
  - Re: [AMBER] using image command in cpptraj... Shashidhar Rao (Tue Jan 15 2013 - 11:04:04 PST)
[AMBER] MMPBSA/Disulfide bond error Divi (Tue Jan 15 2013 - 11:22:34 PST)
- Re: [AMBER] MMPBSA/Disulfide bond error Jason Swails (Tue Jan 15 2013 - 13:28:08 PST)
- Re: [AMBER] MMPBSA/Disulfide bond error Jason Swails (Tue Jan 15 2013 - 14:37:19 PST)
[AMBER] parameters for deoxyADP Jorgen Simonsen (Tue Jan 15 2013 - 11:30:04 PST)
- Re: [AMBER] parameters for deoxyADP FyD (Tue Jan 15 2013 - 22:22:28 PST)
[AMBER] How to choose the boost for aMD when using restraints Thomas Evangelidis (Tue Jan 15 2013 - 12:32:35 PST)
[AMBER] A link atoms between protein and sugar! john Kerk (Wed Jan 16 2013 - 00:33:52 PST)
- Re: [AMBER] A link atoms between protein and sugar! FyD (Wed Jan 16 2013 - 23:57:27 PST)
  - Re: [AMBER] A link atoms between protein and sugar! john Kerk (Thu Jan 17 2013 - 00:40:13 PST)
    - Re: [AMBER] A link atoms between protein and sugar! FyD (Thu Jan 17 2013 - 01:09:35 PST)
[AMBER] LJ parameters for Ho in GLYCAM06 changes ABEL Stephane 175950 (Wed Jan 16 2013 - 05:05:26 PST)
- Re: [AMBER] LJ parameters for Ho in GLYCAM06 changes Jason Swails (Wed Jan 16 2013 - 09:06:11 PST)
  - [AMBER] RE : LJ parameters for Ho in GLYCAM06 changes ABEL Stephane 175950 (Wed Jan 16 2013 - 11:03:10 PST)
    - Re: [AMBER] RE : LJ parameters for Ho in GLYCAM06 changes Lachele Foley (Lists) (Wed Jan 16 2013 - 14:56:41 PST)
[AMBER] Structure refinement protocol on the AMPS-NMR portal Baptiste Legrand (Wed Jan 16 2013 - 05:40:38 PST)
[AMBER] xtc to mdcrd box coords Federica Chiappori (Wed Jan 16 2013 - 06:04:02 PST)
- Re: [AMBER] xtc to mdcrd box coords Daniel Roe (Wed Jan 16 2013 - 07:45:38 PST)
  - Re: [AMBER] xtc to mdcrd box coords Federica Chiappori (Wed Jan 16 2013 - 09:52:43 PST)
    - Re: [AMBER] xtc to mdcrd box coords Daniel Roe (Wed Jan 16 2013 - 10:11:11 PST)
    - Re: [AMBER] xtc to mdcrd box coords Bill Ross (Wed Jan 16 2013 - 15:16:31 PST)
[AMBER] Errors while reading a MOL2 file with "parm" in cpptraj... Shashidhar Rao (Wed Jan 16 2013 - 15:04:58 PST)
- Re: [AMBER] Errors while reading a MOL2 file with "parm" in cpptraj... Daniel Roe (Wed Jan 16 2013 - 16:04:47 PST)
[AMBER] generating restart file with velocity information Vijay Manickam Achari (Wed Jan 16 2013 - 22:53:31 PST)
- Re: [AMBER] generating restart file with velocity information Jason Swails (Thu Jan 17 2013 - 06:30:11 PST)
[AMBER] Simulating one molecule in the gas phase Volker Lesch (Wed Jan 16 2013 - 23:09:12 PST)
[AMBER] H-bond analysis of backbone atoms HM (Thu Jan 17 2013 - 02:30:53 PST)
[AMBER] SHAKE error with dt=0.002 DEBOSTUTI GHOSHDASTIDAR (Thu Jan 17 2013 - 02:52:22 PST)
- Re: [AMBER] SHAKE error with dt=0.002 David A Case (Thu Jan 17 2013 - 06:09:10 PST)
  - Re: [AMBER] SHAKE error with dt=0.002 DEBOSTUTI GHOSHDASTIDAR (Thu Jan 17 2013 - 09:01:13 PST)
    - Re: [AMBER] SHAKE error with dt=0.002 David A Case (Thu Jan 17 2013 - 10:36:51 PST)
    - Re: [AMBER] SHAKE error with dt=0.002 Jason Swails (Thu Jan 17 2013 - 11:52:02 PST)
[AMBER] velocity information lost in traj files when select frames Vijay Manickam Achari (Thu Jan 17 2013 - 05:43:19 PST)
- Re: [AMBER] velocity information lost in traj files when select frames Jason Swails (Thu Jan 17 2013 - 06:31:13 PST)
[AMBER] Amoeba water model parameters Kirill Nuzhdin (Thu Jan 17 2013 - 08:25:01 PST)
[AMBER] difficulty with basic tutorial 1 mhclewett.msn.com (Thu Jan 17 2013 - 10:50:22 PST)
- Re: [AMBER] difficulty with basic tutorial 1 Daniel Roe (Thu Jan 17 2013 - 11:15:51 PST)
  - Re: [AMBER] difficulty with basic tutorial 1 Brian Radak (Thu Jan 17 2013 - 12:32:33 PST)
    - Re: [AMBER] difficulty with basic tutorial 1 mhclewett.msn.com (Fri Jan 18 2013 - 07:20:25 PST)
[AMBER] pmemd.amoeba.MPI run error 旭东肖 (Thu Jan 17 2013 - 18:12:13 PST)
[AMBER] Query regarding Amber atom type Shubhadip Das (Thu Jan 17 2013 - 23:13:21 PST)
- Re: [AMBER] Query regarding Amber atom type FyD (Fri Jan 18 2013 - 00:43:11 PST)
[AMBER] problem starting amber Ayesha Fatima (Fri Jan 18 2013 - 06:34:51 PST)
- Re: [AMBER] problem starting amber Ross Walker (Fri Jan 18 2013 - 06:40:12 PST)
  - Re: [AMBER] problem starting amber Ayesha Fatima (Fri Jan 18 2013 - 06:53:54 PST)
[AMBER] Using multiple CPU cores with pmemd.cuda Filippo Pullara (Fri Jan 18 2013 - 09:02:15 PST)
- Re: [AMBER] Using multiple CPU cores with pmemd.cuda Ross Walker (Fri Jan 18 2013 - 09:19:45 PST)
[AMBER] RRES and LRES card not recognized when using idecomp with sander WenJuan Huang (Fri Jan 18 2013 - 12:48:48 PST)
Re: [AMBER] [AMBER: gauche effect in OS-CT-CT-F Steven M. Graham (Sat Jan 19 2013 - 15:00:44 PST)
- Re: [AMBER] [AMBER: gauche effect in OS-CT-CT-F Karl N. Kirschner (Mon Jan 21 2013 - 02:20:49 PST)
  - Re: [AMBER] [AMBER: gauche effect in OS-CT-CT-F Steven M. Graham (Mon Jan 21 2013 - 12:46:58 PST)
    - Re: [AMBER] [AMBER: gauche effect in OS-CT-CT-F Jason Swails (Mon Jan 21 2013 - 13:25:31 PST)
  - Re: [AMBER] [AMBER: gauche effect in OS-CT-CT-F Steven M. Graham (Sat Mar 09 2013 - 13:42:14 PST)
[AMBER] Minimum distance between the protein and membrane Manikanthan Bhavaraju (Sun Jan 20 2013 - 16:59:32 PST)
- Re: [AMBER] Minimum distance between the protein and membrane Aron Broom (Sun Jan 20 2013 - 18:54:30 PST)
  - Re: [AMBER] Minimum distance between the protein and membrane Manikanthan Bhavaraju (Sun Jan 20 2013 - 20:21:26 PST)
[AMBER] amber11 installation test files Mary Varughese (Mon Jan 21 2013 - 02:28:40 PST)
- Re: [AMBER] amber11 installation test files Jason Swails (Mon Jan 21 2013 - 09:14:10 PST)
  - Re: [AMBER] amber11 installation test files Daniel Roe (Mon Jan 21 2013 - 09:25:43 PST)
    - Re: [AMBER] amber11 installation test files Mary Varughese (Wed Jan 30 2013 - 10:19:00 PST)
    - [AMBER] amber11 installation test files Mary Varughese (Sun Feb 03 2013 - 21:11:30 PST)
    - Re: [AMBER] amber11 installation test files David A Case (Mon Feb 04 2013 - 05:32:12 PST)
    - Re: [AMBER] amber11 installation test files Mary Varughese (Mon Feb 04 2013 - 19:56:55 PST)
    - Re: [AMBER] amber11 installation test files Mary Varughese (Wed Feb 06 2013 - 20:05:19 PST)
[AMBER] Bug in amber12, pmemd ch2int function Ake Sandgren (Mon Jan 21 2013 - 03:50:35 PST)
- Re: [AMBER] Bug in amber12, pmemd ch2int function Jason Swails (Mon Jan 21 2013 - 05:53:13 PST)
[AMBER] Defining a dihedral torsional energy for non-serial atoms. Negar Ashari Astani (Mon Jan 21 2013 - 06:27:12 PST)
- Re: [AMBER] Defining a dihedral torsional energy for non-serial atoms. Carlos Simmerling (Mon Jan 21 2013 - 06:30:29 PST)
[AMBER] Dihedral energy for non-serial atoms Negar Ashari Astani (Mon Jan 21 2013 - 07:32:25 PST)
- Re: [AMBER] Dihedral energy for non-serial atoms Jason Swails (Mon Jan 21 2013 - 09:09:24 PST)
  - Re: [AMBER] Dihedral energy for non-serial atoms Negar Ashari Astani (Mon Jan 21 2013 - 10:13:21 PST)
[AMBER] Query regarding rms2d with cpptraj HM (Mon Jan 21 2013 - 08:41:17 PST)
- Re: [AMBER] Query regarding rms2d with cpptraj Daniel Roe (Mon Jan 21 2013 - 08:51:19 PST)
  - Re: [AMBER] Query regarding rms2d with cpptraj HM (Mon Jan 21 2013 - 09:04:10 PST)
[AMBER] Charge relocation CHAMI F. (Mon Jan 21 2013 - 08:52:48 PST)
- Re: [AMBER] Charge relocation CHAMI F. (Wed Jan 23 2013 - 05:56:33 PST)
[AMBER] question on the latest manifestation of AMBER force field... Shashidhar Rao (Mon Jan 21 2013 - 20:48:21 PST)
[AMBER] Amber ff03w/tip4p2005 Neha Gandhi (Tue Jan 22 2013 - 00:10:20 PST)
- Re: [AMBER] Amber ff03w/tip4p2005 David A Case (Tue Jan 22 2013 - 04:47:10 PST)
[AMBER] mmpbsa-with and without entropy colvin (Tue Jan 22 2013 - 00:20:18 PST)
- Re: [AMBER] mmpbsa-with and without entropy Kshatresh Dutta Dubey (Tue Jan 22 2013 - 02:02:03 PST)
- Re: [AMBER] mmpbsa-with and without entropy David A Case (Tue Jan 22 2013 - 04:56:15 PST)
  - Re: [AMBER] mmpbsa-with and without entropy colvin (Wed Jun 26 2013 - 03:19:22 PDT)
[AMBER] Minimization failure of a ligand Sun (Tue Jan 22 2013 - 00:58:27 PST)
- Re: [AMBER] Minimization failure of a ligand Hirdesh Kumar (Tue Jan 22 2013 - 01:04:07 PST)
  - Re: [AMBER] Minimization failure of a ligand Sun (Tue Jan 22 2013 - 01:25:43 PST)
- Re: [AMBER] Minimization failure of a ligand David A Case (Tue Jan 22 2013 - 05:01:07 PST)
- Re: [AMBER] Minimization failure of a ligand Bill Ross (Tue Jan 22 2013 - 10:57:01 PST)
[AMBER] multi pmemd and REMD Neha Gandhi (Tue Jan 22 2013 - 01:20:58 PST)
- Re: [AMBER] multi pmemd and REMD Neha Gandhi (Tue Jan 22 2013 - 02:21:06 PST)
  - Re: [AMBER] multi pmemd and REMD Jason Swails (Tue Jan 22 2013 - 04:49:05 PST)
    - [AMBER] Error running sander.MPI "rfree: End of file on unit 5 " Urszula Uciechowska (Thu Jan 24 2013 - 08:25:03 PST)
    - Re: [AMBER] Error running sander.MPI "rfree: End of file on unit 5 " Daniel Roe (Thu Jan 24 2013 - 08:29:42 PST)
    - Re: [AMBER] Error running sander.MPI "rfree: End of file on unit 5 " Jason Swails (Thu Jan 24 2013 - 09:11:59 PST)
  - Re: [AMBER] multi pmemd and REMD David A Case (Tue Jan 22 2013 - 05:03:18 PST)
[AMBER] 27th Molecular Modelling Workshop 2013 Feb., 25th-27th in Erlangen, Germany Harald Lanig (Tue Jan 22 2013 - 02:52:51 PST)
[AMBER] Steered MD in Specific Direction Kyle Roberts (Tue Jan 22 2013 - 07:55:34 PST)
- Re: [AMBER] Steered MD in Specific Direction Jason Swails (Tue Jan 22 2013 - 08:36:28 PST)
[AMBER] Building a new structure! Ibrahim Said (Tue Jan 22 2013 - 08:39:33 PST)
- Re: [AMBER] Building a new structure! David A Case (Wed Jan 23 2013 - 05:21:56 PST)
  - Re: [AMBER] Building a new structure! Ibrahim Said (Wed Jan 23 2013 - 09:25:18 PST)
    - Re: [AMBER] Building a new structure! David A Case (Wed Jan 23 2013 - 10:58:13 PST)
    - Re: [AMBER] Building a new structure! Lachele Foley (Fri Feb 15 2013 - 07:11:41 PST)
    - Re: [AMBER] Building a new structure! FyD (Wed Jan 23 2013 - 23:51:33 PST)
    - Re: [AMBER] Building a new structure! Ibrahim Said (Wed Feb 13 2013 - 00:37:50 PST)
    - Re: [AMBER] Building a new structure! FyD (Wed Feb 13 2013 - 23:00:33 PST)
    - Re: [AMBER] Building a new structure! Ibrahim Said (Thu Feb 14 2013 - 10:20:06 PST)
    - Re: [AMBER] Building a new structure! FyD (Fri Feb 15 2013 - 01:57:06 PST)
    - Re: [AMBER] Building a new structure! FyD (Fri Feb 15 2013 - 08:09:56 PST)
    - Re: [AMBER] Building a new structure! Ibrahim Said (Sun Feb 17 2013 - 01:08:48 PST)
    - Re: [AMBER] Building a new structure! FyD (Sun Feb 17 2013 - 04:38:42 PST)
    - Re: [AMBER] Building a new structure! Ibrahim Said (Thu Feb 21 2013 - 08:56:46 PST)
    - Re: [AMBER] Building a new structure! FyD (Thu Feb 21 2013 - 23:17:26 PST)
    - Re: [AMBER] Building a new structure! Ibrahim Said (Tue Feb 26 2013 - 10:45:20 PST)
    - Re: [AMBER] Building a new structure! FyD (Wed Feb 27 2013 - 01:35:01 PST)
[AMBER] Amber12 Cuda installation issues Vivek Shankar Bharadwaj (Tue Jan 22 2013 - 10:05:43 PST)
- Re: [AMBER] Amber12 Cuda installation issues Ross Walker (Wed Jan 23 2013 - 00:58:54 PST)
[AMBER] Theoretical explanation of adding ions to make the system neutral Mahendra B Thapa (Tue Jan 22 2013 - 14:41:57 PST)
- Re: [AMBER] Theoretical explanation of adding ions to make the system neutral Aron Broom (Tue Jan 22 2013 - 15:41:24 PST)
- Re: [AMBER] Theoretical explanation of adding ions to make the system neutral Brian Radak (Wed Jan 23 2013 - 05:58:57 PST)
[AMBER] glibc detected in ptraj Jagur Lambix (Tue Jan 22 2013 - 15:55:50 PST)
- Re: [AMBER] glibc detected in ptraj Daniel Roe (Tue Jan 22 2013 - 16:53:31 PST)
  - Re: [AMBER] glibc detected in ptraj Jagur Lambix (Wed Jan 23 2013 - 07:56:47 PST)
    - Re: [AMBER] glibc detected in ptraj Jason Swails (Wed Jan 23 2013 - 10:20:02 PST)
[AMBER] Analyzing AMBER10 trajectories using AmberTools1.4 Kamali Sripathi (Wed Jan 23 2013 - 04:52:18 PST)
- Re: [AMBER] Analyzing AMBER10 trajectories using AmberTools1.4 Jason Swails (Wed Jan 23 2013 - 05:19:06 PST)
- Re: [AMBER] Analyzing AMBER10 trajectories using AmberTools1.4 Daniel Roe (Wed Jan 23 2013 - 07:31:12 PST)
  - Re: [AMBER] Analyzing AMBER10 trajectories using AmberTools1.4 Kamali Sripathi (Wed Jan 23 2013 - 14:53:44 PST)
    - Re: [AMBER] Analyzing AMBER10 trajectories using AmberTools1.4 Daniel Roe (Wed Jan 23 2013 - 15:03:06 PST)
    - Re: [AMBER] Analyzing AMBER10 trajectories using AmberTools1.4 Jason Swails (Wed Jan 23 2013 - 15:18:03 PST)
    - Re: [AMBER] Analyzing AMBER10 trajectories using AmberTools1.4 Kamali Sripathi (Sat Jan 26 2013 - 06:55:14 PST)
[AMBER] Problem compatibility pdb in tleap Stefan Knippenberg (Wed Jan 23 2013 - 10:22:35 PST)
- Re: [AMBER] Problem compatibility pdb in tleap Daniel Roe (Wed Jan 23 2013 - 10:29:19 PST)
- Re: [AMBER] Problem compatibility pdb in tleap David A Case (Wed Jan 23 2013 - 10:55:49 PST)
- Re: [AMBER] Problem compatibility pdb in tleap Stefan Knippenberg (Wed Jan 23 2013 - 13:32:43 PST)
  - Re: [AMBER] Problem compatibility pdb in tleap Daniel Roe (Wed Jan 23 2013 - 13:41:30 PST)
- Re: [AMBER] Problem compatibility pdb in tleap Stefan Knippenberg (Thu Jan 24 2013 - 02:33:51 PST)
  - Re: [AMBER] Problem compatibility pdb in tleap David A Case (Thu Jan 24 2013 - 06:41:46 PST)
- Re: [AMBER] Problem compatibility pdb in tleap Stefan Knippenberg (Thu Jan 24 2013 - 10:09:33 PST)
  - [AMBER] RMSD of globular proteins Anselm Horn (Thu Jan 24 2013 - 15:05:13 PST)
    - Re: [AMBER] RMSD of globular proteins Aron Broom (Thu Jan 24 2013 - 16:02:32 PST)
    - Re: [AMBER] RMSD of globular proteins Julio Dominguez (Fri Jan 25 2013 - 12:55:38 PST)
    - Re: [AMBER] RMSD of globular proteins Anselm Horn (Wed Jan 30 2013 - 00:50:33 PST)
[AMBER] KCl crystals with Dang parameters ? Vlad Cojocaru (Wed Jan 23 2013 - 11:23:34 PST)
- Re: [AMBER] KCl crystals with Dang parameters ? Daniel Roe (Wed Jan 23 2013 - 12:03:42 PST)
  - Re: [AMBER] KCl crystals with Dang parameters ? Vlad Cojocaru (Wed Jan 23 2013 - 12:24:39 PST)
    - Re: [AMBER] KCl crystals with Dang parameters ? InSuk Joung (Wed Jan 23 2013 - 15:25:29 PST)
- Re: [AMBER] KCl crystals with Dang parameters ? Thomas Cheatham (Wed Jan 23 2013 - 16:41:00 PST)
  - Re: [AMBER] KCl crystals with Dang parameters ? Vlad Cojocaru (Thu Jan 24 2013 - 00:43:59 PST)
    - Re: [AMBER] KCl crystals with Dang parameters ? Vlad Cojocaru (Fri Jan 25 2013 - 04:49:18 PST)
    - Re: [AMBER] KCl crystals with Dang parameters ? Jason Swails (Fri Jan 25 2013 - 05:00:23 PST)
    - Re: [AMBER] KCl crystals with Dang parameters ? Vlad Cojocaru (Fri Jan 25 2013 - 05:08:49 PST)
    - Re: [AMBER] KCl crystals with Dang parameters ? Jason Swails (Fri Jan 25 2013 - 05:53:32 PST)
    - Re: [AMBER] KCl crystals with Dang parameters ? Vlad Cojocaru (Fri Jan 25 2013 - 06:10:13 PST)
[AMBER] error in running a minimization job.... Shashidhar Rao (Wed Jan 23 2013 - 12:16:32 PST)
- Re: [AMBER] error in running a minimization job.... case (Wed Jan 23 2013 - 14:43:41 PST)
  - Re: [AMBER] error in running a minimization job.... Shashidhar Rao (Thu Jan 24 2013 - 08:12:37 PST)
[AMBER] how to keep the previous restart file when saving the current one Thomas Evangelidis (Wed Jan 23 2013 - 14:17:35 PST)
- Re: [AMBER] how to keep the previous restart file when saving the current one Aron Broom (Wed Jan 23 2013 - 14:33:14 PST)
- Re: [AMBER] how to keep the previous restart file when saving the current one Jason Swails (Wed Jan 23 2013 - 15:26:19 PST)
  - Re: [AMBER] how to keep the previous restart file when saving the current one Thomas Evangelidis (Thu Jan 24 2013 - 05:11:23 PST)
    - Re: [AMBER] how to keep the previous restart file when saving the current one Jason Swails (Thu Jan 24 2013 - 06:45:34 PST)
- Re: [AMBER] how to keep the previous restart file when saving the current one case (Wed Jan 23 2013 - 16:36:08 PST)
[AMBER] minimization problem Sanjib Paul (Wed Jan 23 2013 - 22:27:04 PST)
- Re: [AMBER] minimization problem Sanjib Paul (Thu Jan 24 2013 - 03:52:39 PST)
  - Re: [AMBER] minimization problem Daniel Roe (Thu Jan 24 2013 - 08:17:56 PST)
[AMBER] Cpptraj: distance does not work with center of mass Vlastimil Zíma (Thu Jan 24 2013 - 00:47:05 PST)
- Re: [AMBER] Cpptraj: distance does not work with center of mass Daniel Roe (Thu Jan 24 2013 - 07:52:19 PST)
[AMBER] Dihedral angle PCA Sergey Samsonov (Thu Jan 24 2013 - 08:27:48 PST)
- Re: [AMBER] Dihedral angle PCA Daniel Roe (Thu Jan 24 2013 - 08:31:09 PST)
- Re: [AMBER] Dihedral angle PCA Jian Yin (Thu Jan 24 2013 - 09:40:58 PST)
[AMBER] TI alpha-beta glucose Glycam06h Kepa K. Burusco (Fri Jan 25 2013 - 05:42:45 PST)
- Re: [AMBER] TI alpha-beta glucose Glycam06h steinbrt.rci.rutgers.edu (Fri Jan 25 2013 - 08:30:40 PST)
  - Re: [AMBER] TI alpha-beta glucose Glycam06h Kepa K. Burusco (Mon Jan 28 2013 - 03:32:35 PST)
    - Re: [AMBER] TI alpha-beta glucose Glycam06h steinbrt.rci.rutgers.edu (Mon Jan 28 2013 - 05:10:51 PST)
    - Re: [AMBER] TI alpha-beta glucose Glycam06h Kepa K. Burusco (Mon Jan 28 2013 - 10:03:56 PST)
[AMBER] Mixing Small Organic + Water Ismail, Mohd F. (Sat Jan 26 2013 - 01:27:41 PST)
- Re: [AMBER] Mixing Small Organic + Water case (Sat Jan 26 2013 - 11:31:40 PST)
  - Re: [AMBER] Mixing Small Organic + Water Ismail, Mohd F. (Sat Jan 26 2013 - 20:17:08 PST)
[AMBER] Generating Electrostatic Potential Maps Kamali Sripathi (Sat Jan 26 2013 - 07:00:50 PST)
- Re: [AMBER] Generating Electrostatic Potential Maps Ray Luo, Ph.D. (Sat Jan 26 2013 - 08:14:56 PST)
[AMBER] Generating ".prmtop" and ".inpcrd" from a .pdb file Jonathan Saboury (Sun Jan 27 2013 - 00:42:59 PST)
- Re: [AMBER] Generating ".prmtop" and ".inpcrd" from a .pdb file Jason Swails (Sun Jan 27 2013 - 06:16:14 PST)
- Re: [AMBER] Generating ".prmtop" and ".inpcrd" from a .pdb file Jonathan Saboury (Sun Jan 27 2013 - 11:53:29 PST)
  - Re: [AMBER] Generating ".prmtop" and ".inpcrd" from a .pdb file Jason Swails (Sun Jan 27 2013 - 12:08:08 PST)
- Re: [AMBER] Generating ".prmtop" and ".inpcrd" from a .pdb file Jonathan Saboury (Sun Jan 27 2013 - 12:33:34 PST)
  - Re: [AMBER] Generating ".prmtop" and ".inpcrd" from a .pdb file Jonathan Saboury (Sun Jan 27 2013 - 12:42:45 PST)
  - Re: [AMBER] Generating ".prmtop" and ".inpcrd" from a .pdb file case (Sun Jan 27 2013 - 14:38:24 PST)
- Re: [AMBER] Generating ".prmtop" and ".inpcrd" from a .pdb file FyD (Mon Jan 28 2013 - 02:59:32 PST)
[AMBER] about iwrap=1 and ntxo=2 Thomas Evangelidis (Sun Jan 27 2013 - 03:57:33 PST)
- Re: [AMBER] about iwrap=1 and ntxo=2 Jason Swails (Sun Jan 27 2013 - 06:23:17 PST)
  - Re: [AMBER] about iwrap=1 and ntxo=2 Thomas Evangelidis (Sat Feb 02 2013 - 12:08:40 PST)
    - Re: [AMBER] about iwrap=1 and ntxo=2 Thomas Evangelidis (Tue Feb 05 2013 - 11:20:43 PST)
    - Re: [AMBER] about iwrap=1 and ntxo=2 Jason Swails (Tue Feb 05 2013 - 12:27:48 PST)
[AMBER] distance restraints between the primary molecule and its periodic image Thomas Evangelidis (Sun Jan 27 2013 - 10:22:50 PST)
- Re: [AMBER] distance restraints between the primary molecule and its periodic image Daniel Roe (Sun Jan 27 2013 - 14:34:19 PST)
- Re: [AMBER] distance restraints between the primary molecule and its periodic image Ross Walker (Sun Jan 27 2013 - 17:07:50 PST)
  - Re: [AMBER] distance restraints between the primary molecule and its periodic image Thomas Evangelidis (Mon Jan 28 2013 - 02:56:54 PST)
    - Re: [AMBER] distance restraints between the primary molecule and its periodic image Thomas Evangelidis (Wed Jan 30 2013 - 08:40:51 PST)
    - Re: [AMBER] distance restraints between the primary molecule and its periodic image Jason Swails (Wed Jan 30 2013 - 09:37:22 PST)
    - Re: [AMBER] distance restraints between the primary molecule and its periodic image Scott Le Grand (Sat Feb 09 2013 - 10:17:30 PST)
[AMBER] cudaMemcpyToSymbol Lars Skjærven (Sun Jan 27 2013 - 13:01:02 PST)
- Re: [AMBER] cudaMemcpyToSymbol Ross Walker (Sun Jan 27 2013 - 17:12:12 PST)
  - Re: [AMBER] cudaMemcpyToSymbol Lars Skjærven (Mon Jan 28 2013 - 03:09:09 PST)
[AMBER] Generating ".prmtop" and ".inpcrd" from a .pdb file (2) Jonathan Saboury (Sun Jan 27 2013 - 13:49:17 PST)
[AMBER] installation of amber10 in cluster fails Jorgen Simonsen (Sun Jan 27 2013 - 23:16:44 PST)
- Re: [AMBER] installation of amber10 in cluster fails Jason Swails (Mon Jan 28 2013 - 04:34:21 PST)
[AMBER] amber 12 patch for cuda-5.0 Asmita Gupta (Mon Jan 28 2013 - 00:50:55 PST)
- Re: [AMBER] amber 12 patch for cuda-5.0 Jason Swails (Mon Jan 28 2013 - 04:35:51 PST)
[AMBER] Explicit ions in GB solvent Debayan Chakraborty (Mon Jan 28 2013 - 06:04:31 PST)
- Re: [AMBER] Explicit ions in GB solvent Aron Broom (Mon Jan 28 2013 - 07:09:27 PST)
  - Re: [AMBER] Explicit ions in GB solvent Bill Ross (Tue Jan 29 2013 - 15:34:19 PST)
- Re: [AMBER] Explicit ions in GB solvent Jason Swails (Mon Jan 28 2013 - 07:38:31 PST)
  - Re: [AMBER] Explicit ions in GB solvent manikanthan bhavaraju (Mon Jan 28 2013 - 07:46:29 PST)
[AMBER] Sigmoidal dielectric functions in AMBER Debayan Chakraborty (Mon Jan 28 2013 - 15:50:15 PST)
- Re: [AMBER] Sigmoidal dielectric functions in AMBER case (Mon Jan 28 2013 - 18:12:47 PST)
Re: [AMBER] Generating ".prmtop" and ".inpcrd" from a .pdb file(case) Jonathan Saboury (Mon Jan 28 2013 - 18:38:13 PST)
- Re: [AMBER] Generating ".prmtop" and ".inpcrd" from a .pdb file(case) David A Case (Tue Jan 29 2013 - 07:03:10 PST)
Re: [AMBER] Generating ".prmtop" and ".inpcrd" from a .pdb file(jason) Jonathan Saboury (Mon Jan 28 2013 - 18:43:47 PST)
[AMBER] patching problem amber12 Vaibhav Dixit (Mon Jan 28 2013 - 20:19:26 PST)
- Re: [AMBER] patching problem amber12 Vaibhav Dixit (Tue Jan 29 2013 - 20:03:56 PST)
  - Re: [AMBER] patching problem amber12 Daniel Sindhikara (Tue Jan 29 2013 - 20:31:10 PST)
    - Re: [AMBER] patching problem amber12 Vaibhav Dixit (Tue Jan 29 2013 - 20:55:21 PST)
    - Re: [AMBER] patching problem amber12 Daniel Sindhikara (Tue Jan 29 2013 - 21:17:06 PST)
    - Re: [AMBER] patching problem amber12 Vaibhav Dixit (Tue Jan 29 2013 - 21:27:54 PST)
    - Re: [AMBER] patching problem amber12 Jason Swails (Wed Jan 30 2013 - 04:27:21 PST)
    - Re: [AMBER] patching problem amber12 Daniel Sindhikara (Wed Jan 30 2013 - 04:54:11 PST)
    - Re: [AMBER] patching problem amber12 Vaibhav Dixit (Wed Jan 30 2013 - 05:11:11 PST)
    - Re: [AMBER] patching problem amber12 Jason Swails (Wed Jan 30 2013 - 05:28:41 PST)
    - Re: [AMBER] patching problem amber12 Vaibhav Dixit (Wed Jan 30 2013 - 21:53:55 PST)
    - Re: [AMBER] patching problem amber12 Daniel Sindhikara (Wed Jan 30 2013 - 22:01:29 PST)
    - Re: [AMBER] patching problem amber12 Vaibhav Dixit (Wed Jan 30 2013 - 22:05:07 PST)
    - Re: [AMBER] patching problem amber12 Vaibhav Dixit (Wed Jan 30 2013 - 22:11:42 PST)
    - Re: [AMBER] patching problem amber12 Jason Swails (Wed Jan 30 2013 - 05:24:01 PST)
    - Re: [AMBER] patching problem amber12 Vaibhav Dixit (Wed Jan 30 2013 - 05:28:31 PST)
[AMBER] How to calculate PMF using Jarzynski’s equality? Cuiyl (Tue Jan 29 2013 - 00:34:27 PST)
- Re: [AMBER] How to calculate PMF using Jarzynski’s equality? Brian Radak (Tue Jan 29 2013 - 08:36:33 PST)
  - Re: [AMBER] How to calculate PMF using Jarzynski’s equality? Adrian Roitberg (Tue Jan 29 2013 - 08:39:03 PST)
    - [AMBER] AMBER 4.1 Manual Romelia Salomon (Tue Jan 29 2013 - 09:49:09 PST)
    - Re: [AMBER] AMBER 4.1 Manual Gerald Monard (Tue Jan 29 2013 - 13:03:50 PST)
    - Re: [AMBER] AMBER 4.1 Manual Romelia Salomon (Wed Jan 30 2013 - 08:57:38 PST)
    - Re: [AMBER] AMBER 4.1 Manual David A Case (Wed Jan 30 2013 - 15:02:52 PST)
    - Re: [AMBER] AMBER 4.1 Manual Romelia Salomon (Thu Jan 31 2013 - 10:03:41 PST)
[AMBER] Exiting due to the presence of inconsistent SHAKEH hydrogen clusters Sanjib Paul (Tue Jan 29 2013 - 04:22:28 PST)
- Re: [AMBER] Exiting due to the presence of inconsistent SHAKEH hydrogen clusters David A Case (Tue Jan 29 2013 - 07:12:50 PST)
  - Re: [AMBER] Exiting due to the presence of inconsistent SHAKEH hydrogen clusters Sanjib Paul (Wed Jan 30 2013 - 20:38:40 PST)
[AMBER] Fwd: Regarding the problem with ligand conformation aneesh cna (Tue Jan 29 2013 - 05:12:38 PST)
- Re: [AMBER] Fwd: Regarding the problem with ligand conformation Karl N. Kirschner (Tue Jan 29 2013 - 07:59:56 PST)
  - Re: [AMBER] Fwd: Regarding the problem with ligand conformation aneesh cna (Tue Jan 29 2013 - 21:38:55 PST)
    - Re: [AMBER] Fwd: Regarding the problem with ligand conformation Bill Ross (Tue Jan 29 2013 - 22:01:33 PST)
    - Re: [AMBER] Fwd: Regarding the problem with ligand conformation aneesh cna (Tue Jan 29 2013 - 23:22:33 PST)
    - Re: [AMBER] Fwd: Regarding the problem with ligand conformation Bill Ross (Wed Jan 30 2013 - 07:53:52 PST)
    - Re: [AMBER] Fwd: Regarding the problem with ligand conformation Karl N. Kirschner (Thu Jan 31 2013 - 01:10:05 PST)
    - Re: [AMBER] Fwd: Regarding the problem with ligand conformation aneesh cna (Thu Jan 31 2013 - 03:35:56 PST)
    - Re: [AMBER] Fwd: Regarding the problem with ligand conformation Karl N. Kirschner (Thu Jan 31 2013 - 08:42:42 PST)
    - Re: [AMBER] Fwd: Regarding the problem with ligand conformation aneesh cna (Fri Feb 01 2013 - 01:05:58 PST)
    - [AMBER] average structure Urszula Uciechowska (Fri Feb 01 2013 - 02:31:55 PST)
    - Re: [AMBER] average structure Jason Swails (Fri Feb 01 2013 - 05:15:28 PST)
[AMBER] Pocket Volume Calculation Soumya Lipsa Rath (Tue Jan 29 2013 - 06:29:40 PST)
- Re: [AMBER] Pocket Volume Calculation João Ribeiro (Tue Jan 29 2013 - 07:29:12 PST)
  - Re: [AMBER] Pocket Volume Calculation Soumya Lipsa Rath (Tue Jan 29 2013 - 20:21:47 PST)
[AMBER] CPPTRAJ Parmstrip error HM (Tue Jan 29 2013 - 08:20:00 PST)
- Re: [AMBER] CPPTRAJ Parmstrip error Jason Swails (Tue Jan 29 2013 - 08:59:58 PST)
  - Re: [AMBER] CPPTRAJ Parmstrip error HM (Wed Jan 30 2013 - 06:09:20 PST)
[AMBER] coexisting nab and nab openmp Scott Brozell (Tue Jan 29 2013 - 15:19:14 PST)
- Re: [AMBER] coexisting nab and nab openmp Jason Swails (Tue Jan 29 2013 - 15:24:36 PST)
- Re: [AMBER] coexisting nab and nab openmp David A Case (Tue Jan 29 2013 - 18:09:51 PST)
  - Re: [AMBER] coexisting nab and nab openmp Scott Brozell (Tue Jan 29 2013 - 22:58:51 PST)
[AMBER] saving PDB with chain ID in leap aneesh cna (Wed Jan 30 2013 - 02:59:59 PST)
- Re: [AMBER] saving PDB with chain ID in leap Jason Swails (Wed Jan 30 2013 - 04:32:37 PST)
[AMBER] error while running mmpbsa.py in amber12 Alessandro Contini (Wed Jan 30 2013 - 03:47:41 PST)
- Re: [AMBER] error while running mmpbsa.py in amber12 Jason Swails (Wed Jan 30 2013 - 04:29:43 PST)
  - Re: [AMBER] error while running mmpbsa.py in amber12 Alessandro Contini (Wed Jan 30 2013 - 04:54:55 PST)
    - Re: [AMBER] error while running mmpbsa.py in amber12 Jason Swails (Wed Jan 30 2013 - 05:35:38 PST)
    - Re: [AMBER] error while running mmpbsa.py in amber12 Alessandro Contini (Wed Jan 30 2013 - 06:51:43 PST)
    - Re: [AMBER] error while running mmpbsa.py in amber12 Alessandro Contini (Wed Jan 30 2013 - 07:18:12 PST)
    - Re: [AMBER] error while running mmpbsa.py in amber12 Jason Swails (Wed Jan 30 2013 - 07:23:28 PST)
    - Re: [AMBER] error while running mmpbsa.py in amber12 Alessandro Contini (Wed Jan 30 2013 - 07:27:02 PST)
    - Re: [AMBER] error while running mmpbsa.py in amber12 Jason Swails (Wed Jan 30 2013 - 07:34:37 PST)
    - Re: [AMBER] error while running mmpbsa.py in amber12 Ismail, Mohd F. (Fri Feb 01 2013 - 14:22:19 PST)
    - Re: [AMBER] error while running mmpbsa.py in amber12 Jason Swails (Fri Feb 01 2013 - 14:28:25 PST)
    - Re: [AMBER] error while running mmpbsa.py in amber12 Ismail, Mohd F. (Fri Feb 01 2013 - 14:39:03 PST)
[AMBER] How to save secondary structure gnuplot as image HM (Wed Jan 30 2013 - 06:13:27 PST)
- Re: [AMBER] How to save secondary structure gnuplot as image steinbrt.rci.rutgers.edu (Wed Jan 30 2013 - 06:40:43 PST)
- Re: [AMBER] How to save secondary structure gnuplot as image Daniel Roe (Wed Jan 30 2013 - 10:03:25 PST)
  - Re: [AMBER] How to save secondary structure gnuplot as image HM (Thu Jan 31 2013 - 09:32:17 PST)
    - Re: [AMBER] How to save secondary structure gnuplot as image HM (Thu Jan 31 2013 - 09:36:48 PST)
    - Re: [AMBER] How to save secondary structure gnuplot as image ros (Thu Jan 31 2013 - 09:56:37 PST)
    - Re: [AMBER] How to save secondary structure gnuplot as image HM (Fri Feb 01 2013 - 07:06:58 PST)
[AMBER] AMBER pmemd and pmemd.cuda, not restart files after minimization - fort.16 file instead Marko Wehle (Wed Jan 30 2013 - 07:29:20 PST)
- Re: [AMBER] AMBER pmemd and pmemd.cuda, not restart files after minimization - fort.16 file instead Jason Swails (Wed Jan 30 2013 - 07:43:34 PST)
- Re: [AMBER] AMBER pmemd and pmemd.cuda, not restart files after minimization - fort.16 file instead Marko Wehle (Wed Jan 30 2013 - 12:14:46 PST)
  - Re: [AMBER] AMBER pmemd and pmemd.cuda, not restart files after minimization - fort.16 file instead Marko Wehle (Mon Feb 04 2013 - 04:31:21 PST)
    - Re: [AMBER] AMBER pmemd and pmemd.cuda, not restart files after minimization - fort.16 file instead Daniel Roe (Mon Feb 04 2013 - 07:30:11 PST)
    - Re: [AMBER] AMBER pmemd and pmemd.cuda, not restart files after minimization - fort.16 file instead Ross Walker (Mon Feb 04 2013 - 08:55:01 PST)
- Re: [AMBER] AMBER pmemd and pmemd.cuda, not restart files after minimization - fort.16 file instead Marko Wehle (Tue Feb 05 2013 - 03:07:47 PST)
  - Re: [AMBER] AMBER pmemd and pmemd.cuda, not restart files after minimization - fort.16 file instead Daniel Roe (Tue Feb 05 2013 - 08:20:50 PST)
- Re: [AMBER] AMBER pmemd and pmemd.cuda, not restart files after minimization - fort.16 file instead Marko Wehle (Wed Feb 06 2013 - 03:47:40 PST)
  - Re: [AMBER] AMBER pmemd and pmemd.cuda, not restart files after minimization - fort.16 file instead David A Case (Wed Feb 06 2013 - 05:14:54 PST)
[AMBER] mmPBSA.py: mmGBSA and solute dielectric constant psu4.uic.edu (Wed Jan 30 2013 - 18:01:26 PST)
- Re: [AMBER] mmPBSA.py: mmGBSA and solute dielectric constant Jason Swails (Wed Jan 30 2013 - 19:00:06 PST)
- Re: [AMBER] mmPBSA.py: mmGBSA and solute dielectric constant Changqing Yan (Thu Jul 04 2013 - 08:19:11 PDT)
  - Re: [AMBER] mmPBSA.py: mmGBSA and solute dielectric constant Jason Swails (Thu Jul 04 2013 - 14:09:44 PDT)
[AMBER] two fold difference between MMPBSA.py and NAMDenergy plugin in vmd 1.9.1 dbaogen (Wed Jan 30 2013 - 22:10:55 PST)
- Re: [AMBER] two fold difference between MMPBSA.py and NAMDenergy plugin in vmd 1.9.1 Jason Swails (Thu Jan 31 2013 - 04:23:10 PST)
[AMBER] does iwrap=1 work with dodecahedra ? Thomas Evangelidis (Thu Jan 31 2013 - 04:24:13 PST)
- Re: [AMBER] does iwrap=1 work with dodecahedra ? David A Case (Thu Jan 31 2013 - 04:54:12 PST)
  - Re: [AMBER] does iwrap=1 work with dodecahedra ? Thomas Evangelidis (Thu Jan 31 2013 - 12:21:22 PST)
    - Re: [AMBER] does iwrap=1 work with dodecahedra ? Brian Radak (Thu Jan 31 2013 - 12:58:51 PST)
    - Re: [AMBER] does iwrap=1 work with dodecahedra ? Thomas Evangelidis (Thu Jan 31 2013 - 13:16:52 PST)
    - Re: [AMBER] does iwrap=1 work with dodecahedra ? Jason Swails (Thu Jan 31 2013 - 13:25:28 PST)
    - Re: [AMBER] does iwrap=1 work with dodecahedra ? Daniel Roe (Thu Jan 31 2013 - 13:26:38 PST)
    - Re: [AMBER] does iwrap=1 work with dodecahedra ? Thomas Evangelidis (Thu Jan 31 2013 - 13:49:57 PST)
[AMBER] Sampling of a point by a molecule while keeping the relative position of the molecule unchanged in TMD Sajeewa Pemasinghe (Thu Jan 31 2013 - 10:03:37 PST)
- [AMBER] Fwd: Sampling of a point by a molecule while keeping the relative position of the molecule unchanged in TMD Sajeewa Pemasinghe (Thu Jan 31 2013 - 13:02:05 PST)
- [AMBER] Fwd: Sampling of a point by a molecule while keeping the relative position of the molecule unchanged in TMD Sajeewa Pemasinghe (Fri Feb 01 2013 - 14:59:54 PST)
  - Re: [AMBER] Fwd: Sampling of a point by a molecule while keeping the relative position of the molecule unchanged in TMD Jason Swails (Fri Feb 01 2013 - 19:11:20 PST)
    - Re: [AMBER] Fwd: Sampling of a point by a molecule while keeping the relative position of the molecule unchanged in TMD Sajeewa Pemasinghe (Fri Feb 01 2013 - 21:18:47 PST)
[AMBER] pmemd.cuda compilation with amber12 Vivek Shankar Bharadwaj (Thu Jan 31 2013 - 14:41:34 PST)
[AMBER] mmPBSA and restraint energy decreasing psu4.uic.edu (Thu Jan 31 2013 - 15:37:29 PST)
[AMBER] scaling problem in RADIAL of CPPTRAJ Marek Maly (Thu Jan 31 2013 - 15:47:13 PST)
- Re: [AMBER] scaling problem in RADIAL of CPPTRAJ Daniel Roe (Thu Jan 31 2013 - 20:37:30 PST)
  - Re: [AMBER] scaling problem in RADIAL of CPPTRAJ Marek Maly (Thu Jan 31 2013 - 21:27:54 PST)
    - Re: [AMBER] scaling problem in RADIAL of CPPTRAJ Daniel Roe (Fri Feb 01 2013 - 08:02:56 PST)
    - Re: [AMBER] scaling problem in RADIAL of CPPTRAJ Marek Maly (Fri Feb 01 2013 - 08:51:35 PST)
    - Re: [AMBER] scaling problem in RADIAL of CPPTRAJ Daniel Roe (Fri Feb 01 2013 - 09:41:03 PST)
    - Re: [AMBER] scaling problem in RADIAL of CPPTRAJ Marek Maly (Fri Feb 01 2013 - 10:00:24 PST)
    - Re: [AMBER] scaling problem in RADIAL of CPPTRAJ Thomas Cheatham (Fri Feb 01 2013 - 10:30:48 PST)
    - Re: [AMBER] scaling problem in RADIAL of CPPTRAJ Marek Maly (Fri Feb 01 2013 - 12:40:07 PST)
    - Re: [AMBER] scaling problem in RADIAL of CPPTRAJ Marek Maly (Fri Feb 01 2013 - 12:54:50 PST)
[AMBER] AMBER 10 install issue Joel Tyndall (Thu Jan 31 2013 - 17:27:50 PST)
- Re: [AMBER] AMBER 10 install issue David A Case (Sun Feb 03 2013 - 14:36:17 PST)
- Re: [AMBER] AMBER 10 install issue Joel Tyndall (Mon Feb 04 2013 - 12:28:21 PST)
[AMBER] Problem using solvatebox for large, linear peptide Joe Passman (Thu Jan 31 2013 - 18:16:09 PST)
- Re: [AMBER] Problem using solvatebox for large, linear peptide David A Case (Thu Jan 31 2013 - 18:44:38 PST)
- Re: [AMBER] Problem using solvatebox for large, linear peptide Jason Swails (Fri Feb 01 2013 - 05:00:01 PST)
  - Re: [AMBER] Problem using solvatebox for large, linear peptide David A Case (Fri Feb 01 2013 - 13:14:27 PST)
    - Re: [AMBER] Problem using solvatebox for large, linear peptide Joe Passman (Fri Feb 01 2013 - 15:32:49 PST)
    - Re: [AMBER] Problem using solvatebox for large, linear peptide Ismail, Mohd F. (Fri Feb 01 2013 - 15:34:54 PST)
    - Re: [AMBER] Problem using solvatebox for large, linear peptide David A Case (Fri Feb 01 2013 - 18:36:20 PST)
    - Re: [AMBER] Problem using solvatebox for large, linear peptide Jason Swails (Fri Feb 01 2013 - 19:22:54 PST)
    - Re: [AMBER] Problem using solvatebox for large, linear peptide Joe Passman (Tue Feb 05 2013 - 12:47:00 PST)
[AMBER] Can we model the solvent implicitly outside a solvent shell (irregular shape) Debayan Chakraborty (Thu Jan 31 2013 - 19:29:49 PST)
- Re: [AMBER] Can we model the solvent implicitly outside a solvent shell (irregular shape) David A Case (Fri Feb 01 2013 - 05:03:19 PST)
[AMBER] Query regarding cpptraj multiple input in a single file HM (Fri Feb 01 2013 - 07:11:59 PST)
- Re: [AMBER] Query regarding cpptraj multiple input in a single file Daniel Roe (Fri Feb 01 2013 - 07:29:48 PST)
[AMBER] protein-protein binding free energy Date, Mihir (Fri Feb 01 2013 - 15:14:33 PST)
- Re: [AMBER] protein-protein binding free energy David A Case (Fri Feb 01 2013 - 18:40:43 PST)
  - Re: [AMBER] protein-protein binding free energy Vaibhav Dixit (Sat Feb 02 2013 - 21:03:09 PST)
[AMBER] Error initiating H-REMD Brian Radak (Fri Feb 01 2013 - 15:52:32 PST)
[AMBER] A doubt about averaging time in dynamic cross-correlation analysis aneesh cna (Sat Feb 02 2013 - 02:17:42 PST)
[AMBER] Problems with ti using DFTB for zinc bound hydroxyl Fabrício Bracht (Sat Feb 02 2013 - 11:35:04 PST)
- Re: [AMBER] Problems with ti using DFTB for zinc bound hydroxyl Brian Radak (Sat Feb 02 2013 - 13:03:35 PST)
  - Re: [AMBER] Problems with ti using DFTB for zinc bound hydroxyl Fabrício Bracht (Sat Feb 02 2013 - 17:33:53 PST)
    - Re: [AMBER] Problems with ti using DFTB for zinc bound hydroxyl Brian Radak (Sun Feb 03 2013 - 09:19:00 PST)
    - Re: [AMBER] Problems with ti using DFTB for zinc bound hydroxyl Fabrício Bracht (Mon Feb 04 2013 - 10:31:16 PST)
    - Re: [AMBER] Problems with ti using DFTB for zinc bound hydroxyl Brian Radak (Mon Feb 04 2013 - 10:52:26 PST)
    - Re: [AMBER] Problems with ti using DFTB for zinc bound hydroxyl Fabrício Bracht (Mon Feb 04 2013 - 11:21:10 PST)
    - Re: [AMBER] Problems with ti using DFTB for zinc bound hydroxyl Brian Radak (Mon Feb 04 2013 - 11:51:45 PST)
    - Re: [AMBER] Problems with ti using DFTB for zinc bound hydroxyl Fabrício Bracht (Mon Feb 04 2013 - 12:00:32 PST)
[AMBER] Setting up a Periodic Box Size Jonathan Saboury (Sat Feb 02 2013 - 11:36:15 PST)
- Re: [AMBER] Setting up a Periodic Box Size Jason Swails (Sat Feb 02 2013 - 12:36:04 PST)
[AMBER] igb=7 & 8 CalcError: "pathway" failed with prmtop "protein".prmtop psu4.uic.edu (Sat Feb 02 2013 - 15:48:00 PST)
- Re: [AMBER] igb=7 & 8 CalcError: "pathway" failed with prmtop "protein".prmtop Carlos Simmerling (Sat Feb 02 2013 - 19:08:22 PST)
  - Re: [AMBER] igb=7 & 8 CalcError: "pathway" failed with prmtop "protein".prmtop psu4.uic.edu (Sun Feb 03 2013 - 13:55:38 PST)
    - Re: [AMBER] igb=7 & 8 CalcError: "pathway" failed with prmtop "protein".prmtop Daniel Roe (Mon Feb 04 2013 - 07:46:52 PST)
    - Re: [AMBER] igb=7 & 8 CalcError: "pathway" failed with prmtop "protein".prmtop psu4.uic.edu (Mon Feb 04 2013 - 13:47:52 PST)
    - Re: [AMBER] igb=7 & 8 CalcError: "pathway" failed with prmtop "protein".prmtop Jason Swails (Mon Feb 04 2013 - 14:16:26 PST)
    - Re: [AMBER] igb=7 & 8 CalcError: "pathway" failed with prmtop "protein".prmtop Hai Nguyen (Mon Feb 04 2013 - 14:55:29 PST)
    - Re: [AMBER] igb=7 & 8 CalcError: "pathway" failed with prmtop "protein".prmtop psu4.uic.edu (Thu Feb 07 2013 - 17:23:39 PST)
    - Re: [AMBER] igb=7 & 8 CalcError: "pathway" failed with prmtop "protein".prmtop Jason Swails (Thu Feb 07 2013 - 19:24:55 PST)
    - Re: [AMBER] igb=7 & 8 CalcError: "pathway" failed with prmtop "protein".prmtop psu4.uic.edu (Mon Feb 11 2013 - 22:23:42 PST)
    - Re: [AMBER] igb=7 & 8 CalcError: "pathway" failed with prmtop "protein".prmtop Jason Swails (Tue Feb 12 2013 - 05:01:51 PST)
    - Re: [AMBER] igb=7 & 8 CalcError: "pathway" failed with prmtop "protein".prmtop psu4.uic.edu (Wed Feb 20 2013 - 11:03:57 PST)
[AMBER] ERROR: the best APS is not zero, bonds involved by this atom are frozen Jonathan Saboury (Sun Feb 03 2013 - 20:44:08 PST)
- Re: [AMBER] ERROR: the best APS is not zero, bonds involved by this atom are frozen David A Case (Mon Feb 04 2013 - 08:45:30 PST)
- Re: [AMBER] ERROR: the best APS is not zero, bonds involved by this atom are frozen Jonathan Saboury (Mon Feb 04 2013 - 21:32:46 PST)
  - [AMBER] topology file issue with entropy calculation Rejwan (Mon Feb 04 2013 - 22:58:01 PST)
    - Re: [AMBER] topology file issue with entropy calculation David A Case (Tue Feb 05 2013 - 04:46:28 PST)
    - Re: [AMBER] topology file issue with entropy calculation Rejwan (Wed Feb 06 2013 - 17:14:29 PST)
    - Re: [AMBER] topology file issue with entropy calculation Jason Swails (Wed Feb 06 2013 - 18:24:23 PST)
    - Re: [AMBER] topology file issue with entropy calculation Rejwan (Thu Feb 07 2013 - 11:48:22 PST)
  - Re: [AMBER] ERROR: the best APS is not zero, bonds involved by this atom are frozen David A Case (Tue Feb 05 2013 - 04:44:39 PST)
[AMBER] density calculation in radial cpptraj Asmita Gupta (Mon Feb 04 2013 - 02:08:24 PST)
- Re: [AMBER] density calculation in radial cpptraj Daniel Roe (Mon Feb 04 2013 - 07:36:28 PST)
  - Re: [AMBER] density calculation in radial cpptraj Asmita Gupta (Mon Feb 04 2013 - 08:17:20 PST)
    - Re: [AMBER] density calculation in radial cpptraj David A Case (Mon Feb 04 2013 - 08:37:28 PST)
    - Re: [AMBER] density calculation in radial cpptraj Asmita Gupta (Tue Feb 05 2013 - 09:01:53 PST)
    - Re: [AMBER] density calculation in radial cpptraj Daniel Roe (Tue Feb 05 2013 - 10:08:14 PST)
    - Re: [AMBER] density calculation in radial cpptraj Asmita Gupta (Wed Feb 06 2013 - 00:21:23 PST)
    - Re: [AMBER] density calculation in radial cpptraj Daniel Roe (Wed Feb 06 2013 - 08:43:50 PST)
[AMBER] espgen cannot deal with Gaussian 09 log file HIMANSHU JOSHI (Mon Feb 04 2013 - 03:51:52 PST)
- Re: [AMBER] espgen cannot deal with Gaussian 09 log file Tomasz Borowski (Mon Feb 04 2013 - 03:59:35 PST)
  - Re: [AMBER] espgen cannot deal with Gaussian 09 log file Sören Wacker (Mon Feb 04 2013 - 04:04:41 PST)
    - Re: [AMBER] espgen cannot deal with Gaussian 09 log file HIMANSHU JOSHI (Mon Feb 04 2013 - 21:42:28 PST)
    - Re: [AMBER] espgen cannot deal with Gaussian 09 log file Sören Wacker (Wed Feb 06 2013 - 02:32:16 PST)
    - Re: [AMBER] espgen cannot deal with Gaussian 09 log file David A Case (Wed Feb 06 2013 - 04:53:55 PST)
    - Re: [AMBER] espgen cannot deal with Gaussian 09 log file Sören Wacker (Wed Feb 06 2013 - 05:22:59 PST)
[AMBER] use of parmbsc0 for protein-DNA complex along with ff99SB Sangita Kachhap (Mon Feb 04 2013 - 04:39:14 PST)
- Re: [AMBER] use of parmbsc0 for protein-DNA complex along with ff99SB Jiri Sponer (Mon Feb 04 2013 - 05:01:24 PST)
  - Re: [AMBER] use of parmbsc0 for protein-DNA complex along with ff99SB Sangita Kachhap (Mon Feb 04 2013 - 07:21:58 PST)
    - Re: [AMBER] use of parmbsc0 for protein-DNA complex along with ff99SB Jiri Sponer (Mon Feb 04 2013 - 07:37:12 PST)
    - Re: [AMBER] use of parmbsc0 for protein-DNA complex along with ff99SB Sangita Kachhap (Mon Feb 04 2013 - 08:21:03 PST)
[AMBER] silhouette.pl Tamer Ibrahim (Mon Feb 04 2013 - 07:35:45 PST)
[AMBER] AMBER-Tools cpptraj residue numbering incorrect Marko Wehle (Mon Feb 04 2013 - 07:52:55 PST)
- Re: [AMBER] AMBER-Tools cpptraj residue numbering incorrect Daniel Roe (Mon Feb 04 2013 - 10:52:03 PST)
- Re: [AMBER] AMBER-Tools cpptraj residue numbering incorrect Marko Wehle (Mon Feb 04 2013 - 11:03:22 PST)
  - Re: [AMBER] AMBER-Tools cpptraj residue numbering incorrect Daniel Roe (Mon Feb 04 2013 - 12:18:14 PST)
- Re: [AMBER] AMBER-Tools cpptraj residue numbering incorrect Marko Wehle (Tue Feb 05 2013 - 13:27:53 PST)
  - Re: [AMBER] AMBER-Tools cpptraj residue numbering incorrect Jason Swails (Tue Feb 05 2013 - 17:43:57 PST)
[AMBER] phosporylated residue connectivity problem BALA SUBRAMANI G L (Tue Feb 05 2013 - 01:15:14 PST)
[AMBER] Hbond analysis in ptraj DEBOSTUTI GHOSHDASTIDAR (Tue Feb 05 2013 - 05:07:17 PST)
- Re: [AMBER] Hbond analysis in ptraj Daniel Roe (Tue Feb 05 2013 - 07:27:02 PST)
  - Re: [AMBER] Hbond analysis in ptraj DEBOSTUTI GHOSHDASTIDAR (Tue Feb 05 2013 - 22:00:54 PST)
    - Re: [AMBER] Hbond analysis in ptraj Daniel Roe (Wed Feb 06 2013 - 09:30:31 PST)
    - [AMBER] Details about FF12SB Anselm Horn (Fri Feb 08 2013 - 10:54:21 PST)
[AMBER] active site rmsd (residue 5A around bound ligand) ??? HM (Tue Feb 05 2013 - 05:40:45 PST)
- Re: [AMBER] active site rmsd (residue 5A around bound ligand) ??? Daniel Roe (Tue Feb 05 2013 - 07:37:15 PST)
  - Re: [AMBER] active site rmsd (residue 5A around bound ligand) ??? Daniel Roe (Tue Feb 05 2013 - 09:20:19 PST)
    - Re: [AMBER] active site rmsd (residue 5A around bound ligand) ??? HM (Tue Feb 05 2013 - 11:07:30 PST)
    - Re: [AMBER] active site rmsd (residue 5A around bound ligand) ??? HM (Tue Feb 05 2013 - 11:28:16 PST)
    - Re: [AMBER] active site rmsd (residue 5A around bound ligand) ??? Daniel Roe (Tue Feb 05 2013 - 13:58:47 PST)
[AMBER] iAPBS George Tzotzos (Tue Feb 05 2013 - 05:57:31 PST)
- Re: [AMBER] iAPBS Robert Konecny (Tue Feb 05 2013 - 10:42:48 PST)
[AMBER] Fwd: BERGY (Tue Feb 05 2013 - 07:07:04 PST)
- Re: [AMBER] Fwd: Jason Swails (Tue Feb 05 2013 - 07:23:08 PST)
[AMBER] rmsd of Ethanol Chinthaka Ratnaweera (Tue Feb 05 2013 - 08:37:37 PST)
- Re: [AMBER] rmsd of Ethanol Daniel Roe (Tue Feb 05 2013 - 10:13:58 PST)
  - Re: [AMBER] rmsd of Ethanol Chinthaka Ratnaweera (Tue Feb 05 2013 - 10:52:38 PST)
    - Re: [AMBER] rmsd of Ethanol Daniel Roe (Tue Feb 05 2013 - 14:03:56 PST)
[AMBER] Could you please remove me from AMBER mailing list Yulin Huang (Tue Feb 05 2013 - 09:32:48 PST)
- Re: [AMBER] Could you please remove me from AMBER mailing list Jason Swails (Tue Feb 05 2013 - 09:43:44 PST)
[AMBER] 3D-RISM input file error WenJuan Huang (Tue Feb 05 2013 - 11:05:43 PST)
- Re: [AMBER] 3D-RISM input file error Jason Swails (Tue Feb 05 2013 - 11:16:01 PST)
  - Re: [AMBER] 3D-RISM input file error Tyler Luchko (Tue Feb 05 2013 - 11:36:58 PST)
[AMBER] OPLS to AMBER vdw parameters conversion Prabal Maiti (Tue Feb 05 2013 - 12:07:01 PST)
- Re: [AMBER] OPLS to AMBER vdw parameters conversion Prabal Maiti (Tue Feb 05 2013 - 13:34:55 PST)
[AMBER] setting certain atoms as static Jonathan Saboury (Tue Feb 05 2013 - 23:14:11 PST)
- Re: [AMBER] setting certain atoms as static David A Case (Wed Feb 06 2013 - 04:51:18 PST)
[AMBER] Query about checking of convergence in REMD gargi borgohai (Wed Feb 06 2013 - 04:21:24 PST)
- Re: [AMBER] Query about checking of convergence in REMD Carlos Simmerling (Wed Feb 06 2013 - 04:32:35 PST)
- Re: [AMBER] Query about checking of convergence in REMD gargi borgohai (Fri Apr 26 2013 - 06:14:58 PDT)
  - Re: [AMBER] Query about checking of convergence in REMD Carlos Simmerling (Fri Apr 26 2013 - 06:20:01 PDT)
  - Re: [AMBER] Query about checking of convergence in REMD Daniel Roe (Fri Apr 26 2013 - 09:47:38 PDT)
[AMBER] charge for NMA molecule Subrata Paul (Wed Feb 06 2013 - 04:58:57 PST)
- [AMBER] Fwd: charge for NMA molecule Subrata Paul (Wed Feb 06 2013 - 22:05:52 PST)
[AMBER] hbond analysis acceptor atoms DEBOSTUTI GHOSHDASTIDAR (Wed Feb 06 2013 - 09:08:50 PST)
- Re: [AMBER] hbond analysis acceptor atoms Daniel Roe (Wed Feb 06 2013 - 09:32:39 PST)
  - Re: [AMBER] hbond analysis acceptor atoms DEBOSTUTI GHOSHDASTIDAR (Wed Feb 06 2013 - 21:51:26 PST)
[AMBER] ptraj RMSD- spikes in RMSD and co-ordinates at 0.000 Cassandra Churchill (Wed Feb 06 2013 - 09:58:18 PST)
- Re: [AMBER] ptraj RMSD- spikes in RMSD and co-ordinates at 0.000 Daniel Roe (Wed Feb 06 2013 - 10:34:20 PST)
  - Re: [AMBER] ptraj RMSD- spikes in RMSD and co-ordinates at 0.000 Cassandra Churchill (Thu Feb 07 2013 - 09:46:09 PST)
[AMBER] problems with NAB uday spike (Wed Feb 06 2013 - 23:49:37 PST)
- Re: [AMBER] problems with NAB Daniel Sindhikara (Thu Feb 07 2013 - 00:03:15 PST)
  - Re: [AMBER] problems with NAB uday spike (Sat Feb 16 2013 - 01:34:51 PST)
    - Re: [AMBER] problems with NAB Jason Swails (Sat Feb 16 2013 - 05:47:30 PST)
  - Re: [AMBER] problems with NAB uday spike (Tue Feb 19 2013 - 00:25:55 PST)
[AMBER] Adding buffer and salt Indrajit Deb (Thu Feb 07 2013 - 00:23:55 PST)
- Re: [AMBER] Adding buffer and salt Indrajit Deb (Thu Feb 07 2013 - 02:46:00 PST)
- Re: [AMBER] Adding buffer and salt Jason Swails (Thu Feb 07 2013 - 06:30:47 PST)
  - Re: [AMBER] Adding buffer and salt Indrajit Deb (Thu Feb 07 2013 - 09:18:36 PST)
    - Re: [AMBER] Adding buffer and salt Indrajit Deb (Thu Feb 07 2013 - 09:23:04 PST)
    - Re: [AMBER] Adding buffer and salt Yun Shi (Thu Feb 07 2013 - 10:32:33 PST)
[AMBER] simulation MD - basic questions Anne Kichler (Thu Feb 07 2013 - 02:54:17 PST)
- Re: [AMBER] simulation MD - basic questions Jian Yin (Fri Feb 08 2013 - 13:29:11 PST)
[AMBER] issues with PDB file and tleap Massimiliano Porrini (Thu Feb 07 2013 - 03:45:58 PST)
- Re: [AMBER] issues with PDB file and tleap Jerome.GOLEBIOWSKI.unice.fr (Thu Feb 07 2013 - 05:00:40 PST)
  - Re: [AMBER] issues with PDB file and tleap Massimiliano Porrini (Thu Feb 07 2013 - 06:56:44 PST)
[AMBER] parmed.py error IndexError: list index out of range Jio M (Thu Feb 07 2013 - 07:52:49 PST)
- Re: [AMBER] parmed.py error IndexError: list index out of range Jason Swails (Thu Feb 07 2013 - 08:13:30 PST)
  - Re: [AMBER] parmed.py error IndexError: list index out of range Jason Swails (Thu Feb 07 2013 - 12:40:51 PST)
[AMBER] problem with strip water some distance away from peptide Do Yong Kim (Thu Feb 07 2013 - 16:03:16 PST)
- Re: [AMBER] problem with strip water some distance away from peptide Daniel Roe (Thu Feb 07 2013 - 17:24:02 PST)
  - Re: [AMBER] problem with strip water some distance away from peptide Do Yong Kim (Fri Feb 08 2013 - 15:06:39 PST)
    - Re: [AMBER] problem with strip water some distance away from peptide Daniel Roe (Fri Feb 08 2013 - 15:08:59 PST)
[AMBER] missing parameter of B in .frcmod 纪晓峰 (Thu Feb 07 2013 - 19:19:54 PST)
- Re: [AMBER] missing parameter of B in .frcmod David A Case (Fri Feb 08 2013 - 05:15:33 PST)
[AMBER] restart file with *********** problem Dr. M. Venkata Satish Kumar (Fri Feb 08 2013 - 00:18:19 PST)
- Re: [AMBER] restart file with *********** problem Daniel Roe (Fri Feb 08 2013 - 07:36:36 PST)
[AMBER] change starting time of simulation Thomas Evangelidis (Fri Feb 08 2013 - 01:38:19 PST)
- Re: [AMBER] change starting time of simulation David A Case (Fri Feb 08 2013 - 05:19:01 PST)
  - Re: [AMBER] change starting time of simulation Thomas Evangelidis (Fri Feb 08 2013 - 07:07:32 PST)
    - Re: [AMBER] change starting time of simulation Daniel Roe (Fri Feb 08 2013 - 07:40:59 PST)
    - Re: [AMBER] change starting time of simulation Daniel Roe (Fri Feb 08 2013 - 07:43:08 PST)
[AMBER] NMA(n-methylacetamide) Subrata Paul (Fri Feb 08 2013 - 02:12:31 PST)
- Re: [AMBER] NMA(n-methylacetamide) David A Case (Fri Feb 08 2013 - 05:21:59 PST)
- Re: [AMBER] NMA(n-methylacetamide) FyD (Sun Feb 10 2013 - 08:40:31 PST)
  - Re: [AMBER] NMA(n-methylacetamide) Subrata Paul (Mon Feb 11 2013 - 02:31:33 PST)
    - Re: [AMBER] NMA(n-methylacetamide) Jason Swails (Mon Feb 11 2013 - 03:01:19 PST)
    - Re: [AMBER] NMA(n-methylacetamide) Subrata Paul (Mon Feb 11 2013 - 07:35:17 PST)
    - Re: [AMBER] NMA(n-methylacetamide) FyD (Tue Feb 12 2013 - 01:16:45 PST)
[AMBER] NaN error in restart file Shobana, G . (Fri Feb 08 2013 - 02:26:46 PST)
- Re: [AMBER] NaN error in restart file Anselm Horn (Fri Feb 08 2013 - 04:05:24 PST)
  - [AMBER] Steered Molecular Dynamics Mannan (Fri Feb 08 2013 - 06:05:32 PST)
    - [AMBER] Steered Molecular Dynamics Mannan (Sat Feb 09 2013 - 17:28:56 PST)
    - [AMBER] Steered Molecular Dynamics Mannan (Sat Feb 09 2013 - 17:29:11 PST)
    - Re: [AMBER] Steered Molecular Dynamics case (Sun Feb 10 2013 - 09:41:12 PST)
[AMBER] Problem related with umbrella sampling Sindrila Dutta banik (Fri Feb 08 2013 - 03:20:13 PST)
- Re: [AMBER] Problem related with umbrella sampling Brian Radak (Fri Feb 08 2013 - 06:13:54 PST)
[AMBER] problem with 3-ring system in antechamber Leandro Bortot (Fri Feb 08 2013 - 07:59:49 PST)
- Re: [AMBER] problem with 3-ring system in antechamber David A Case (Fri Feb 08 2013 - 08:41:19 PST)
  - Re: [AMBER] problem with 3-ring system in antechamber Leandro Bortot (Fri Feb 08 2013 - 10:18:27 PST)
    - Re: [AMBER] problem with 3-ring system in antechamber David A Case (Fri Feb 08 2013 - 10:53:32 PST)
    - Re: [AMBER] problem with 3-ring system in antechamber Leandro Bortot (Fri Feb 08 2013 - 11:14:48 PST)
    - Re: [AMBER] problem with 3-ring system in antechamber David A Case (Fri Feb 08 2013 - 12:20:40 PST)
    - Re: [AMBER] problem with 3-ring system in antechamber Leandro Bortot (Fri Feb 08 2013 - 12:55:28 PST)
[AMBER] Problem related to the umbrella sampling Sindrila Dutta banik (Fri Feb 08 2013 - 09:30:03 PST)
- Re: [AMBER] Problem related to the umbrella sampling Brian Radak (Fri Feb 08 2013 - 10:07:02 PST)
  - Re: [AMBER] Problem related to the umbrella sampling Sindrila Dutta banik (Fri Feb 08 2013 - 11:44:02 PST)
- Re: [AMBER] Problem related to the umbrella sampling Sindrila Dutta banik (Fri Feb 08 2013 - 21:34:13 PST)
- Re: [AMBER] Problem related to the umbrella sampling Sindrila Dutta banik (Thu Jul 11 2013 - 21:23:22 PDT)
  - Re: [AMBER] Problem related to the umbrella sampling Jason Swails (Thu Jul 11 2013 - 21:37:29 PDT)
[AMBER] problem with umbrella sampling Sindrila Dutta banik (Fri Feb 08 2013 - 09:33:13 PST)
[AMBER] Problem in running TREMD in AMBER10 Sajeewa Pemasinghe (Fri Feb 08 2013 - 12:37:45 PST)
- Re: [AMBER] Problem in running TREMD in AMBER10 Ross Walker (Fri Feb 08 2013 - 12:46:09 PST)
  - Re: [AMBER] Problem in running TREMD in AMBER10 Sajeewa Pemasinghe (Fri Feb 08 2013 - 13:04:01 PST)
    - Re: [AMBER] Problem in running TREMD in AMBER10 Ross Walker (Fri Feb 08 2013 - 13:12:12 PST)
- Re: [AMBER] Problem in running TREMD in AMBER10 Jason Swails (Fri Feb 08 2013 - 12:53:49 PST)
  - Re: [AMBER] Problem in running TREMD in AMBER10 Sajeewa Pemasinghe (Fri Feb 08 2013 - 13:11:06 PST)
    - Re: [AMBER] Problem in running TREMD in AMBER10 Ross Walker (Fri Feb 08 2013 - 13:17:28 PST)
    - Re: [AMBER] Problem in running TREMD in AMBER10 Sajeewa Pemasinghe (Fri Feb 08 2013 - 13:37:19 PST)
    - Re: [AMBER] Problem in running TREMD in AMBER10 Sajeewa Pemasinghe (Fri Feb 08 2013 - 21:30:42 PST)
    - Re: [AMBER] Problem in running TREMD in AMBER10 Jason Swails (Sat Feb 09 2013 - 08:45:53 PST)
    - Re: [AMBER] Problem in running TREMD in AMBER10 Sajeewa Pemasinghe (Sat Feb 09 2013 - 09:06:18 PST)
    - Re: [AMBER] Problem in running TREMD in AMBER10 Jason Swails (Sat Feb 09 2013 - 09:27:16 PST)
    - Re: [AMBER] Problem in running TREMD in AMBER10 Sajeewa Pemasinghe (Sat Feb 09 2013 - 09:44:21 PST)
[AMBER] Amber 12 and CUDA 5.0 K20 vs GTX 680: GTX 680 is two time faster than K20 Filippo Pullara (Fri Feb 08 2013 - 13:05:21 PST)
- Re: [AMBER] Amber 12 and CUDA 5.0 K20 vs GTX 680: GTX 680 is two time faster than K20 Ross Walker (Fri Feb 08 2013 - 13:15:37 PST)
[AMBER] PMEMD amd mmpbsa.py mpi Chris Chris (Fri Feb 08 2013 - 16:08:44 PST)
- Re: [AMBER] PMEMD amd mmpbsa.py mpi Jason Swails (Fri Feb 08 2013 - 16:41:43 PST)
  - Re: [AMBER] PMEMD amd mmpbsa.py mpi Chris Chris (Fri Feb 08 2013 - 17:09:26 PST)
    - Re: [AMBER] PMEMD amd mmpbsa.py mpi Chris Chris (Sat Feb 09 2013 - 22:42:54 PST)
[AMBER] problem using autoimage from cpptraj Jonathan Saboury (Fri Feb 08 2013 - 20:35:23 PST)
- Re: [AMBER] problem using autoimage from cpptraj Daniel Roe (Fri Feb 08 2013 - 20:57:17 PST)
- Re: [AMBER] problem using autoimage from cpptraj Jonathan Saboury (Sat Feb 09 2013 - 17:13:26 PST)
  - Re: [AMBER] problem using autoimage from cpptraj Daniel Roe (Sat Feb 09 2013 - 18:01:37 PST)
- Re: [AMBER] problem using autoimage from cpptraj Jonathan Saboury (Sun Feb 10 2013 - 13:19:45 PST)
  - Re: [AMBER] problem using autoimage from cpptraj Jason Swails (Sun Feb 10 2013 - 14:33:56 PST)
[AMBER] Query regarding PNA-DNA duplex parameterization in AMBER Souvik Sur (Fri Feb 08 2013 - 23:26:19 PST)
[AMBER] xleap could not find the type Cl- Sanjib Paul (Sat Feb 09 2013 - 04:26:32 PST)
- Re: [AMBER] xleap could not find the type Cl- David A Case (Sat Feb 09 2013 - 06:49:20 PST)
  - Re: [AMBER] xleap could not find the type Cl- Sanjib Paul (Sat Feb 09 2013 - 09:54:03 PST)
[AMBER] Problems with MMPBSA.py for running pbsa calculations manikanthan bhavaraju (Sat Feb 09 2013 - 12:36:19 PST)
- Re: [AMBER] Problems with MMPBSA.py for running pbsa calculations Ray Luo, Ph.D. (Sat Feb 09 2013 - 13:17:00 PST)
- Re: [AMBER] Problems with MMPBSA.py for running pbsa calculations WenJuan Huang (Sun Feb 10 2013 - 21:04:05 PST)
  - Re: [AMBER] Problems with MMPBSA.py for running pbsa calculations Jason Swails (Mon Feb 11 2013 - 03:18:20 PST)
    - Re: [AMBER] Problems with MMPBSA.py for running pbsa calculations manikanthan bhavaraju (Mon Feb 11 2013 - 12:48:28 PST)
    - Re: [AMBER] Problems with MMPBSA.py for running pbsa calculations Ray Luo, Ph.D. (Mon Feb 11 2013 - 13:08:01 PST)
    - Re: [AMBER] Problems with MMPBSA.py for running pbsa calculations Jason Swails (Mon Feb 11 2013 - 14:06:56 PST)
    - Re: [AMBER] Problems with MMPBSA.py for running pbsa calculations manikanthan bhavaraju (Mon Feb 11 2013 - 14:58:17 PST)
    - Re: [AMBER] Problems with MMPBSA.py for running pbsa calculations Ray Luo, Ph.D. (Mon Feb 11 2013 - 15:24:02 PST)
    - Re: [AMBER] Problems with MMPBSA.py for running pbsa calculations Ray Luo, Ph.D. (Tue Feb 12 2013 - 16:06:35 PST)
[AMBER] Issues with idecomp Adam Mepham (Sat Feb 09 2013 - 20:55:19 PST)
- Re: [AMBER] Issues with idecomp Daniel Roe (Sun Feb 10 2013 - 10:11:21 PST)
[AMBER] Wrong Annotation of PREPIN generated by RESIDUEGEN kurisaki (Sun Feb 10 2013 - 01:20:26 PST)
- Re: [AMBER] Wrong Annotation of PREPIN generated by RESIDUEGEN case (Sun Feb 10 2013 - 09:43:54 PST)
  - Re: [AMBER] Wrong Annotation of PREPIN generated by RESIDUEGEN kurisaki (Sun Feb 10 2013 - 19:47:06 PST)
    - Re: [AMBER] Wrong Annotation of PREPIN generated by RESIDUEGEN David A Case (Mon Feb 11 2013 - 05:12:28 PST)
    - Re: [AMBER] Wrong Annotation of PREPIN generated by RESIDUEGEN kurisaki (Tue Mar 05 2013 - 01:42:02 PST)
[AMBER] Using cpptraj to trim a range of water residues while maintaining a periodic box Joe Passman (Sun Feb 10 2013 - 17:15:21 PST)
- Re: [AMBER] Using cpptraj to trim a range of water residues while maintaining a periodic box Jason Swails (Sun Feb 10 2013 - 18:32:30 PST)
- Re: [AMBER] Using cpptraj to trim a range of water residues while maintaining a periodic box Daniel Roe (Sun Feb 10 2013 - 18:58:03 PST)
  - Re: [AMBER] Using cpptraj to trim a range of water residues while maintaining a periodic box Joe Passman (Mon Feb 11 2013 - 20:51:44 PST)
[AMBER] Inquiry from beginner rajith bhaskar (Sun Feb 10 2013 - 20:55:15 PST)
- Re: [AMBER] Inquiry from beginner David A Case (Mon Feb 11 2013 - 05:16:13 PST)
[AMBER] Application of mmpbsa DEBOSTUTI GHOSHDASTIDAR (Sun Feb 10 2013 - 21:46:31 PST)
[AMBER] Warnings when saving prmtop and inpcrd files. Sanjib Paul (Sun Feb 10 2013 - 23:39:51 PST)
- Re: [AMBER] Warnings when saving prmtop and inpcrd files. Jason Swails (Mon Feb 11 2013 - 03:06:05 PST)
[AMBER] Hydrogens AMBER 1H6 and 2H6 vs. Glycam H61 and H62 for Glucose Kepa K. Burusco (Mon Feb 11 2013 - 05:48:07 PST)
- Re: [AMBER] Hydrogens AMBER 1H6 and 2H6 vs. Glycam H61 and H62 for Glucose Lachele Foley (Lists) (Mon Feb 11 2013 - 06:47:45 PST)
  - Re: [AMBER] Hydrogens AMBER 1H6 and 2H6 vs. Glycam H61 and H62 for Glucose Lachele Foley (Lists) (Mon Feb 11 2013 - 12:01:42 PST)
    - Re: [AMBER] Hydrogens AMBER 1H6 and 2H6 vs. Glycam H61 and H62 for Glucose Kepa K. Burusco (Mon Feb 11 2013 - 12:49:19 PST)
[AMBER] Error running large number of trajectories with multisander Brian Radak (Mon Feb 11 2013 - 07:42:21 PST)
- Re: [AMBER] Error running large number of trajectories with multisander Daniel Roe (Mon Feb 11 2013 - 10:30:42 PST)
  - Re: [AMBER] Error running large number of trajectories with multisander Brian Radak (Mon Feb 11 2013 - 10:48:07 PST)
    - Re: [AMBER] Error running large number of trajectories with multisander Daniel Roe (Mon Feb 11 2013 - 11:35:09 PST)
[AMBER] PSF file, atom radii and chamber Massimiliano Porrini (Mon Feb 11 2013 - 10:05:48 PST)
- [AMBER] Fwd: PSF file, atom radii and chamber Massimiliano Porrini (Mon Feb 18 2013 - 01:04:46 PST)
  - Re: [AMBER] Fwd: PSF file, atom radii and chamber Jason Swails (Mon Feb 18 2013 - 05:25:16 PST)
[AMBER] Issues with idecomp Adam Mepham (Mon Feb 11 2013 - 14:17:30 PST)
- Re: [AMBER] Issues with idecomp Jason Swails (Mon Feb 11 2013 - 14:32:46 PST)
[AMBER] Compilation problems for parallel build after applying patches Miguel Ortiz Lombardía (Tue Feb 12 2013 - 06:55:18 PST)
- Re: [AMBER] Compilation problems for parallel build after applying patches Jason Swails (Tue Feb 12 2013 - 07:43:09 PST)
  - Re: [AMBER] Compilation problems for parallel build after applying patches Miguel Ortiz Lombardía (Tue Feb 12 2013 - 08:04:37 PST)
    - Re: [AMBER] Compilation problems for parallel build after applying patches Jason Swails (Tue Feb 12 2013 - 08:29:11 PST)
    - Re: [AMBER] Compilation problems for parallel build after applying patches Miguel Ortiz Lombardía (Tue Feb 12 2013 - 08:38:46 PST)
    - Re: [AMBER] Compilation problems for parallel build after applying patches Jason Swails (Tue Feb 12 2013 - 09:20:14 PST)
    - Re: [AMBER] Compilation problems for parallel build after applying patches Miguel Ortiz Lombardia (Tue Feb 12 2013 - 11:50:28 PST)
[AMBER] A general question about umbrella sampling Sajeewa Pemasinghe (Tue Feb 12 2013 - 12:51:47 PST)
- Re: [AMBER] A general question about umbrella sampling Aron Broom (Tue Feb 12 2013 - 13:16:01 PST)
  - Re: [AMBER] A general question about umbrella sampling Sajeewa Pemasinghe (Tue Feb 12 2013 - 14:48:10 PST)
[AMBER] Anomalous Termination of PMEMD.CUDA jobs kurisaki (Wed Feb 13 2013 - 02:02:23 PST)
- Re: [AMBER] Anomalous Termination of PMEMD.CUDA jobs kurisaki (Wed Feb 13 2013 - 02:17:05 PST)
  - Re: [AMBER] Anomalous Termination of PMEMD.CUDA jobs Ross Walker (Wed Feb 13 2013 - 09:16:41 PST)
    - Re: [AMBER] Anomalous Termination of PMEMD.CUDA jobs kurisaki (Wed Feb 13 2013 - 17:39:29 PST)
    - Re: [AMBER] Anomalous Termination of PMEMD.CUDA jobs kurisaki (Fri Feb 15 2013 - 01:27:38 PST)
    - Re: [AMBER] Anomalous Termination of PMEMD.CUDA jobs Ross Walker (Fri Feb 15 2013 - 10:36:14 PST)
    - Re: [AMBER] Anomalous Termination of PMEMD.CUDA jobs kurisaki (Fri Feb 15 2013 - 21:09:40 PST)
[AMBER] VIBRATIONAL FREQUANCY USING NMODE Rasha Alqus (Wed Feb 13 2013 - 05:32:43 PST)
- Re: [AMBER] VIBRATIONAL FREQUANCY USING NMODE Daniel Roe (Wed Feb 13 2013 - 13:24:18 PST)
[AMBER] MMPBSA.py: about sasopt value with inp=1 Miguel Ortiz Lombardía (Wed Feb 13 2013 - 05:55:45 PST)
- Re: [AMBER] MMPBSA.py: about sasopt value with inp=1 Miguel Ortiz Lombardía (Wed Feb 13 2013 - 06:15:22 PST)
[AMBER] Cannot open the input file: XYZ.pdb in rpdb(), exit Matthias Leeder (Wed Feb 13 2013 - 10:42:02 PST)
- Re: [AMBER] Cannot open the input file: XYZ.pdb in rpdb(), exit Daniel Roe (Wed Feb 13 2013 - 11:04:30 PST)
  - Re: [AMBER] Cannot open the input file: XYZ.pdb in rpdb(), exit Matthias Leeder (Thu Feb 14 2013 - 01:43:20 PST)
    - Re: [AMBER] Cannot open the input file: XYZ.pdb in rpdb(), exit David A Case (Thu Feb 14 2013 - 05:38:45 PST)
- Re: [AMBER] Cannot open the input file: XYZ.pdb in rpdb(), exit David A Case (Wed Feb 13 2013 - 11:44:59 PST)
[AMBER] simulation of a nucleic acid linked on a gold surface Barbault Florent (Wed Feb 13 2013 - 11:54:18 PST)
- Re: [AMBER] simulation of a nucleic acid linked on a gold surface Ilyas Yildirim (Wed Feb 13 2013 - 17:17:58 PST)
- Re: [AMBER] simulation of a nucleic acid linked on a gold surface FyD (Wed Feb 13 2013 - 23:06:47 PST)
[AMBER] idecomp output frequency Adam Mepham (Wed Feb 13 2013 - 17:56:20 PST)
- Re: [AMBER] idecomp output frequency Jason Swails (Wed Feb 13 2013 - 18:30:16 PST)
[AMBER] problems starting amber Ayesha Fatima (Wed Feb 13 2013 - 19:00:02 PST)
- Re: [AMBER] problems starting amber Daniel Sindhikara (Wed Feb 13 2013 - 19:22:34 PST)
  - Re: [AMBER] problems starting amber Ayesha Fatima (Wed Feb 13 2013 - 19:51:31 PST)
[AMBER] What algorithm does ptraj use for solvation of eigen-value problem. kurisaki (Fri Feb 15 2013 - 01:08:46 PST)
- Re: [AMBER] What algorithm does ptraj use for solvation of eigen-value problem. Daniel Roe (Fri Feb 15 2013 - 07:43:18 PST)
  - Re: [AMBER] What algorithm does ptraj use for solvation of eigen-value problem. kurisaki (Fri Feb 15 2013 - 21:40:50 PST)
    - Re: [AMBER] What algorithm does ptraj use for solvation of eigen-value problem. Daniel Roe (Fri Feb 15 2013 - 23:55:10 PST)
    - Re: [AMBER] What algorithm does ptraj use for solvation of eigen-value problem. kurisaki (Sat Feb 16 2013 - 00:14:35 PST)
    - Re: [AMBER] What algorithm does ptraj use for solvation of eigen-value problem. case (Sat Feb 16 2013 - 07:03:54 PST)
    - Re: [AMBER] What algorithm does ptraj use for solvation of eigen-value problem. kurisaki (Sat Feb 16 2013 - 22:35:30 PST)
[AMBER] test David A Case (Fri Feb 15 2013 - 08:13:33 PST)
[AMBER] Sander error - Segmentation fault (core dumped) Symon Gathiaka (Fri Feb 15 2013 - 11:28:51 PST)
- Re: [AMBER] Sander error - Segmentation fault (core dumped) David A Case (Fri Feb 15 2013 - 11:51:49 PST)
[AMBER] Small bug in MMPBSA.py tutorial George A. Khoury (Sat Feb 16 2013 - 09:47:03 PST)
- Re: [AMBER] Small bug in MMPBSA.py tutorial Jason Swails (Sat Feb 16 2013 - 12:24:51 PST)
  - Re: [AMBER] Small bug in MMPBSA.py tutorial Vaibhav Dixit (Sat Feb 16 2013 - 21:21:37 PST)
    - Re: [AMBER] Small bug in MMPBSA.py tutorial Jason Swails (Sun Feb 17 2013 - 06:58:18 PST)
[AMBER] MM PBSA and entropy decomposition Aron Broom (Sat Feb 16 2013 - 10:06:30 PST)
- Re: [AMBER] MM PBSA and entropy decomposition Jason Swails (Sat Feb 16 2013 - 12:24:14 PST)
  - Re: [AMBER] MM PBSA and entropy decomposition Aron Broom (Sat Feb 16 2013 - 13:05:12 PST)
- Re: [AMBER] MM PBSA and entropy decomposition Holger Gohlke (Sun Feb 17 2013 - 04:01:48 PST)
  - Re: [AMBER] MM PBSA and entropy decomposition Aron Broom (Sun Feb 17 2013 - 04:09:47 PST)
[AMBER] pka calculation energy by residue Adam Mepham (Sat Feb 16 2013 - 15:46:28 PST)
[AMBER] the position of counterion Sun (Sun Feb 17 2013 - 10:54:00 PST)
- Re: [AMBER] the position of counterion Daniel Roe (Sun Feb 17 2013 - 11:42:28 PST)
[AMBER] atomic pair correlation function through PCA Date, Mihir (Sun Feb 17 2013 - 20:35:26 PST)
- Re: [AMBER] atomic pair correlation function through PCA Daniel Roe (Mon Feb 18 2013 - 08:19:49 PST)
[AMBER] PCA analysis query Vaibhav Dixit (Sun Feb 17 2013 - 23:34:23 PST)
- Re: [AMBER] PCA analysis query Daniel Roe (Mon Feb 18 2013 - 08:29:03 PST)
[AMBER] Error with MMPBSA calculation aneesh cna (Mon Feb 18 2013 - 01:21:56 PST)
- Re: [AMBER] Error with MMPBSA calculation Jason Swails (Mon Feb 18 2013 - 04:31:49 PST)
  - Re: [AMBER] Error with MMPBSA calculation aneesh cna (Mon Feb 18 2013 - 21:11:16 PST)
    - Re: [AMBER] Error with MMPBSA calculation Jason Swails (Tue Feb 19 2013 - 04:50:47 PST)
[AMBER] xleap problem using savemol2 Charles Do (Mon Feb 18 2013 - 10:44:38 PST)
- Re: [AMBER] xleap problem using savemol2 Jason Swails (Mon Feb 18 2013 - 10:51:50 PST)
  - Re: [AMBER] xleap problem using savemol2 Charles Do (Tue Feb 19 2013 - 06:54:32 PST)
    - Re: [AMBER] xleap problem using savemol2 Jason Swails (Tue Feb 19 2013 - 07:07:41 PST)
[AMBER] Defining parameters for and undefined element. Solid Surface gabrielg.uvic.ca (Mon Feb 18 2013 - 14:10:14 PST)
[AMBER] PROBLEMS IN SETTING UP PHOSPHORYLATED SIMULATION MODELS Theodosia Teo (Mon Feb 18 2013 - 19:46:53 PST)
- Re: [AMBER] PROBLEMS IN SETTING UP PHOSPHORYLATED SIMULATION MODELS David A Case (Tue Feb 19 2013 - 04:45:09 PST)
  - Re: [AMBER] PROBLEMS IN SETTING UP PHOSPHORYLATED SIMULATION MODELS Theodosia Teo (Tue Feb 19 2013 - 13:35:48 PST)
    - Re: [AMBER] PROBLEMS IN SETTING UP PHOSPHORYLATED SIMULATION MODELS case (Tue Feb 19 2013 - 16:51:24 PST)
    - Re: [AMBER] PROBLEMS IN SETTING UP PHOSPHORYLATED SIMULATION MODELS Theodosia Teo (Tue Feb 19 2013 - 22:11:07 PST)
    - Re: [AMBER] PROBLEMS IN SETTING UP PHOSPHORYLATED SIMULATION MODELS Jason Swails (Wed Feb 20 2013 - 04:31:03 PST)
    - Re: [AMBER] PROBLEMS IN SETTING UP PHOSPHORYLATED SIMULATION MODELS David A Case (Wed Feb 20 2013 - 04:39:46 PST)
[AMBER] Analysis in ptraj gargi borgohai (Tue Feb 19 2013 - 01:38:29 PST)
- Re: [AMBER] Analysis in ptraj Hirdesh Kumar (Tue Feb 19 2013 - 03:06:06 PST)
[AMBER] Dumping of center of mass coordinates of protein domain HM (Tue Feb 19 2013 - 04:11:18 PST)
- Re: [AMBER] Dumping of center of mass coordinates of protein domain Jason Swails (Tue Feb 19 2013 - 07:06:22 PST)
- Re: [AMBER] Dumping of center of mass coordinates of protein domain Daniel Roe (Tue Feb 19 2013 - 10:25:33 PST)
  - Re: [AMBER] Dumping of center of mass coordinates of protein domain HM (Thu Feb 28 2013 - 03:54:15 PST)
[AMBER] problem in running MMPBSA Saugata Hazra (Tue Feb 19 2013 - 05:02:45 PST)
- Re: [AMBER] problem in running MMPBSA Jason Swails (Tue Feb 19 2013 - 06:00:37 PST)
  - [AMBER] problem in running MMPBSA Saugata Hazra (Tue Feb 19 2013 - 06:31:43 PST)
    - Re: [AMBER] problem in running MMPBSA Jason Swails (Tue Feb 19 2013 - 06:43:34 PST)
    - Re: [AMBER] problem in running MMPBSA Saugata Hazra (Wed Feb 20 2013 - 00:08:04 PST)
    - Re: [AMBER] problem in running MMPBSA Alessandro Contini (Wed Feb 20 2013 - 00:50:17 PST)
    - Re: [AMBER] problem in running MMPBSA Saugata Hazra (Sat Feb 23 2013 - 16:51:20 PST)
    - Re: [AMBER] problem in running MMPBSA Alessandro Contini (Sun Feb 24 2013 - 00:29:28 PST)
    - Re: [AMBER] problem in running MMPBSA Jason Swails (Sun Feb 24 2013 - 06:43:13 PST)
    - Re: [AMBER] problem in running MMPBSA Saugata Hazra (Mon Feb 25 2013 - 10:33:33 PST)
    - Re: [AMBER] problem in running MMPBSA Jason Swails (Mon Feb 25 2013 - 11:29:16 PST)
    - Re: [AMBER] problem in running MMPBSA Saugata Hazra (Mon Feb 25 2013 - 15:20:51 PST)
[AMBER] Missing comma in input file Sasha Perkins (Tue Feb 19 2013 - 08:18:03 PST)
- Re: [AMBER] Missing comma in input file Jason Swails (Tue Feb 19 2013 - 08:29:01 PST)
- [AMBER] GTX Titan was finally released filip fratev (Tue Feb 19 2013 - 08:40:12 PST)
  - Re: [AMBER] GTX Titan was finally released Marek Maly (Tue Feb 19 2013 - 08:55:24 PST)
    - Re: [AMBER] GTX Titan was finally released Ross Walker (Tue Feb 19 2013 - 09:58:54 PST)
    - Re: [AMBER] GTX Titan was finally released Marek Maly (Tue Feb 19 2013 - 10:14:01 PST)
    - Re: [AMBER] GTX Titan was finally released Ilyas Yildirim (Tue Feb 19 2013 - 10:37:41 PST)
    - Re: [AMBER] GTX Titan was finally released Ross Walker (Tue Feb 19 2013 - 10:43:28 PST)
    - Re: [AMBER] GTX Titan was finally released Scott Le Grand (Tue Feb 19 2013 - 11:08:36 PST)
    - Re: [AMBER] GTX Titan was finally released Ross Walker (Tue Feb 19 2013 - 11:24:54 PST)
    - Re: [AMBER] GTX Titan was finally released filip fratev (Tue Feb 19 2013 - 11:59:39 PST)
    - Re: [AMBER] GTX Titan was finally released Scott Le Grand (Tue Feb 19 2013 - 13:27:38 PST)
    - Re: [AMBER] GTX Titan was finally released filip fratev (Fri Feb 22 2013 - 17:28:18 PST)
    - Re: [AMBER] GTX Titan was finally released Aron Broom (Fri Feb 22 2013 - 20:03:16 PST)
    - Re: [AMBER] GTX Titan was finally released Ross Walker (Fri Feb 22 2013 - 20:45:06 PST)
    - Re: [AMBER] GTX Titan was finally released filip fratev (Sat Feb 23 2013 - 11:33:34 PST)
    - Re: [AMBER] GTX Titan was finally released Aron Broom (Sat Feb 23 2013 - 12:12:49 PST)
    - Re: [AMBER] GTX Titan was finally released filip fratev (Mon Feb 25 2013 - 14:39:04 PST)
    - Re: [AMBER] GTX Titan was finally released Ross Walker (Mon Feb 25 2013 - 17:46:23 PST)
    - Re: [AMBER] GTX Titan was finally released Scott Le Grand (Tue Feb 26 2013 - 08:14:01 PST)
    - Re: [AMBER] GTX Titan was finally released Marek Maly (Wed Feb 27 2013 - 10:23:20 PST)
    - Re: [AMBER] GTX Titan was finally released filip fratev (Wed Feb 27 2013 - 11:21:17 PST)
    - Re: [AMBER] GTX Titan was finally released filip fratev (Thu Mar 14 2013 - 09:33:40 PDT)
    - Re: [AMBER] GTX Titan was finally released Gustavo Seabra (Thu Mar 14 2013 - 10:31:43 PDT)
    - Re: [AMBER] GTX Titan was finally released Aron Broom (Thu Mar 14 2013 - 10:42:22 PDT)
    - Re: [AMBER] GTX Titan was finally released Gustavo Seabra (Thu Mar 14 2013 - 10:49:07 PDT)
    - Re: [AMBER] GTX Titan was finally released Ross Walker (Thu Mar 14 2013 - 11:54:28 PDT)
    - Re: [AMBER] GTX Titan was finally released Scott Le Grand (Thu Mar 14 2013 - 12:14:57 PDT)
    - Re: [AMBER] GTX Titan was finally released filip fratev (Thu Mar 14 2013 - 12:48:45 PDT)
    - Re: [AMBER] GTX Titan was finally released Ross Walker (Sat Mar 16 2013 - 18:08:47 PDT)
    - Re: [AMBER] GTX Titan was finally released Marek Maly (Wed Feb 20 2013 - 05:22:55 PST)
    - Re: [AMBER] GTX Titan was finally released Ross Walker (Wed Feb 20 2013 - 13:03:28 PST)
  - Re: [AMBER] GTX Titan was finally released Ross Walker (Tue Feb 19 2013 - 09:46:42 PST)
    - Re: [AMBER] GTX Titan was finally released David A Case (Tue Feb 19 2013 - 13:39:12 PST)
    - Re: [AMBER] GTX Titan was finally released Ross Walker (Tue Feb 19 2013 - 14:18:01 PST)
    - Re: [AMBER] GTX Titan was finally released Aron Broom (Tue Feb 19 2013 - 15:01:20 PST)
  - Re: [AMBER] GTX Titan was finally released filip fratev (Sun Mar 17 2013 - 06:53:32 PDT)
  - Re: [AMBER] GTX Titan was finally released filip fratev (Mon Mar 18 2013 - 10:58:13 PDT)
    - Re: [AMBER] GTX Titan was finally released Albert (Mon Mar 18 2013 - 11:29:09 PDT)
    - Re: [AMBER] GTX Titan was finally released Ross Walker (Mon Mar 18 2013 - 15:53:11 PDT)
[AMBER] How to calculate the vibrational frequancy Rasha Alqus (Tue Feb 19 2013 - 08:47:11 PST)
- Re: [AMBER] How to calculate the vibrational frequancy David A Case (Tue Feb 19 2013 - 09:50:54 PST)
[AMBER] problem reading CHARMM lipid parameters into chamber Sally Pias (Tue Feb 19 2013 - 13:07:56 PST)
- Re: [AMBER] problem reading CHARMM lipid parameters into chamber Jason Swails (Wed Feb 20 2013 - 05:06:43 PST)
  - Re: [AMBER] problem reading CHARMM lipid parameters into chamber BERGY (Wed Feb 20 2013 - 20:49:22 PST)
    - Re: [AMBER] problem reading CHARMM lipid parameters into chamber Jason Swails (Thu Feb 21 2013 - 04:25:47 PST)
    - Re: [AMBER] problem reading CHARMM lipid parameters into chamber Sally Pias (Thu Feb 21 2013 - 08:32:30 PST)
[AMBER] qmshake=1 did not prevent bonds from being broken Fabrício Bracht (Tue Feb 19 2013 - 14:32:49 PST)
- Re: [AMBER] qmshake=1 did not prevent bonds from being broken Brian Radak (Wed Feb 20 2013 - 06:08:08 PST)
  - Re: [AMBER] qmshake=1 did not prevent bonds from being broken Fabrício Bracht (Wed Feb 20 2013 - 10:56:33 PST)
    - Re: [AMBER] qmshake=1 did not prevent bonds from being broken Brian Radak (Wed Feb 20 2013 - 11:08:07 PST)
    - Re: [AMBER] qmshake=1 did not prevent bonds from being broken Fabrício Bracht (Wed Feb 20 2013 - 13:30:03 PST)
[AMBER] Kepler GTX680 MD Workstation Charles Do (Tue Feb 19 2013 - 19:12:31 PST)
- Re: [AMBER] Kepler GTX680 MD Workstation Ross Walker (Tue Feb 19 2013 - 19:29:07 PST)
  - Re: [AMBER] Kepler GTX680 MD Workstation Charles Do (Tue Feb 19 2013 - 19:38:15 PST)
[AMBER] Problem related to different version of amber Changqing Yan (Tue Feb 19 2013 - 23:42:18 PST)
- Re: [AMBER] Problem related to different version of amber Jian Yin (Wed Feb 20 2013 - 11:39:33 PST)
[AMBER] randomizeions with cpptraj Asmita Gupta (Wed Feb 20 2013 - 02:56:43 PST)
- Re: [AMBER] randomizeions with cpptraj David A Case (Wed Feb 20 2013 - 04:44:45 PST)
[AMBER] problem in nmode Rasha Alqus (Wed Feb 20 2013 - 06:39:39 PST)
- Re: [AMBER] problem in nmode Jason Swails (Wed Feb 20 2013 - 06:50:25 PST)
- Re: [AMBER] problem in nmode Rasha Alqus (Wed Feb 20 2013 - 09:11:37 PST)
[AMBER] mmpbsa_py_nabnmode for single macromolecule Rasha Alqus (Wed Feb 20 2013 - 07:27:16 PST)
- Re: [AMBER] mmpbsa_py_nabnmode for single macromolecule Dwight McGee (Wed Feb 20 2013 - 08:17:54 PST)
[AMBER] glucose marta wisniewska. (Wed Feb 20 2013 - 07:58:25 PST)
- Re: [AMBER] glucose David A Case (Wed Feb 20 2013 - 08:41:37 PST)
[AMBER] ODP: Re: glucose m.wisniewska.aol.pl (Wed Feb 20 2013 - 09:11:09 PST)
[AMBER] Problem with xleap/tleap Ibrahim Moustafa (Wed Feb 20 2013 - 10:14:07 PST)
- Re: [AMBER] Problem with xleap/tleap Jason Swails (Wed Feb 20 2013 - 10:20:02 PST)
- Re: [AMBER] Problem with xleap/tleap Daniel Roe (Wed Feb 20 2013 - 10:22:18 PST)
[AMBER] About EPTOT Mo Chen (Wed Feb 20 2013 - 15:50:01 PST)
- Re: [AMBER] About EPTOT Jason Swails (Wed Feb 20 2013 - 16:47:08 PST)
[AMBER] Amber 11 Installment problem Changqing Yan (Wed Feb 20 2013 - 19:14:31 PST)
- Re: [AMBER] Amber 11 Installment problem Bill Ross (Wed Feb 20 2013 - 19:36:17 PST)
- Re: [AMBER] Amber 11 Installment problem Jian Yin (Thu Feb 21 2013 - 17:44:34 PST)
- Re: [AMBER] Amber 11 Installment problem Jian Yin (Thu Feb 21 2013 - 18:34:48 PST)
- Re: [AMBER] Amber 11 Installment problem Changqing Yan (Thu Feb 21 2013 - 19:12:45 PST)
  - Re: [AMBER] Amber 11 Installment problem Bill Ross (Sat Feb 23 2013 - 11:54:15 PST)
[AMBER] Using OPLS force field parameters in Amber MD run DEBOSTUTI GHOSHDASTIDAR (Wed Feb 20 2013 - 23:13:56 PST)
- Re: [AMBER] Using OPLS force field parameters in Amber MD run Jason Swails (Thu Feb 21 2013 - 05:22:24 PST)
  - Re: [AMBER] Using OPLS force field parameters in Amber MD run DEBOSTUTI GHOSHDASTIDAR (Thu Feb 21 2013 - 05:39:48 PST)
[AMBER] radial distribution function between atoms of the two masks Massimiliano Porrini (Thu Feb 21 2013 - 06:12:24 PST)
- [AMBER] Fwd: radial distribution function between atoms of the two masks Massimiliano Porrini (Mon Feb 25 2013 - 12:54:20 PST)
[AMBER] crgmask and qmmm region compatibility Fabrício Bracht (Thu Feb 21 2013 - 06:44:02 PST)
- Re: [AMBER] crgmask and qmmm region compatibility David A Case (Thu Feb 21 2013 - 09:39:18 PST)
[AMBER] constant pH for transmemrane proteins Thomas Evangelidis (Thu Feb 21 2013 - 07:19:13 PST)
- Re: [AMBER] constant pH for transmemrane proteins Jason Swails (Thu Feb 21 2013 - 07:31:43 PST)
[AMBER] leap insert missing atoms in aminoacids according to ... Marta Perez (Thu Feb 21 2013 - 07:59:20 PST)
- Re: [AMBER] leap insert missing atoms in aminoacids according to ... Jason Swails (Thu Feb 21 2013 - 08:55:50 PST)
  - Re: [AMBER] leap insert missing atoms in aminoacids according to ... Marta Perez (Tue Mar 19 2013 - 03:25:51 PDT)
    - Re: [AMBER] leap insert missing atoms in aminoacids according to ... David A Case (Tue Mar 19 2013 - 05:06:54 PDT)
    - Re: [AMBER] leap insert missing atoms in aminoacids according to ... Marta Perez (Tue Mar 19 2013 - 05:34:18 PDT)
    - Re: [AMBER] leap insert missing atoms in aminoacids according to ... David A Case (Tue Mar 19 2013 - 07:36:52 PDT)
[AMBER] Linear peptide using non standard amino acids moitrayee.mbu.iisc.ernet.in (Thu Feb 21 2013 - 13:12:03 PST)
- Re: [AMBER] Linear peptide using non standard amino acids Jason Swails (Thu Feb 21 2013 - 14:01:38 PST)
[AMBER] amber error about protein containing heme tianchuan1015 (Thu Feb 21 2013 - 23:58:31 PST)
- Re: [AMBER] amber error about protein containing heme Prajwal Nandekar (Fri Feb 22 2013 - 01:42:17 PST)
- Re: [AMBER] amber error about protein containing heme tianchuan1015 (Fri Feb 22 2013 - 06:31:08 PST)
  - Re: [AMBER] amber error about protein containing heme Prajwal Nandekar (Fri Feb 22 2013 - 08:33:30 PST)
    - Re: [AMBER] amber error about protein containing heme Bill Ross (Sat Feb 23 2013 - 12:04:49 PST)
[AMBER] regarding frcmod preparation Aparna P (Fri Feb 22 2013 - 03:07:46 PST)
- Re: [AMBER] regarding frcmod preparation Prajwal Nandekar (Fri Feb 22 2013 - 03:11:57 PST)
  - Re: [AMBER] regarding frcmod preparation Aparna P (Fri Feb 22 2013 - 06:16:13 PST)
[AMBER] ligand moving out of protein incorrect imaging of trajectory using image and center commands with amber 10 ET (Fri Feb 22 2013 - 10:10:20 PST)
- Re: [AMBER] ligand moving out of protein incorrect imaging of trajectory using image and center commands with amber 10 Daniel Roe (Fri Feb 22 2013 - 12:19:08 PST)
  - Re: [AMBER] ligand moving out of protein incorrect imaging of trajectory using image and center commands with amber 10 ET (Fri Feb 22 2013 - 13:45:20 PST)
    - Re: [AMBER] ligand moving out of protein incorrect imaging of trajectory using image and center commands with amber 10 Daniel Roe (Fri Feb 22 2013 - 14:17:14 PST)
    - Re: [AMBER] ligand moving out of protein incorrect imaging of trajectory using image and center commands with amber 10 ET (Fri Feb 22 2013 - 14:38:29 PST)
[AMBER] unspecified launch failure launching kernel kRecalculateVelocities Symon Gathiaka (Fri Feb 22 2013 - 10:58:04 PST)
- Re: [AMBER] unspecified launch failure launching kernel kRecalculateVelocities Ross Walker (Fri Feb 22 2013 - 15:04:41 PST)
[AMBER] Calculating Hydrogen bond energy Ahmed Ayoub (Fri Feb 22 2013 - 23:55:01 PST)
- Re: [AMBER] Calculating Hydrogen bond energy David A Case (Sat Feb 23 2013 - 06:05:26 PST)
- Re: [AMBER] Calculating Hydrogen bond energy Joseph Maxwell (Sun Feb 24 2013 - 06:39:20 PST)
[AMBER] possibility to increase max . num. of bonded atoms ? Marek Maly (Sat Feb 23 2013 - 19:43:18 PST)
- Re: [AMBER] possibility to increase max . num. of bonded atoms ? David A Case (Sun Feb 24 2013 - 07:22:22 PST)
  - Re: [AMBER] possibility to increase max . num. of bonded atoms ? Marek Maly (Mon Feb 25 2013 - 16:31:22 PST)
    - Re: [AMBER] possibility to increase max . num. of bonded atoms ? Jason Swails (Mon Feb 25 2013 - 17:19:17 PST)
    - Re: [AMBER] possibility to increase max . num. of bonded atoms ? Bill Ross (Mon Feb 25 2013 - 17:44:46 PST)
    - Re: [AMBER] possibility to increase max . num. of bonded atoms ? Marek Maly (Wed Feb 27 2013 - 10:03:52 PST)
    - Re: [AMBER] possibility to increase max . num. of bonded atoms ? Jason Swails (Wed Feb 27 2013 - 11:12:43 PST)
    - Re: [AMBER] possibility to increase max . num. of bonded atoms ? Marek Maly (Wed Feb 27 2013 - 11:40:32 PST)
    - Re: [AMBER] possibility to increase max . num. of bonded atoms ? Bill Ross (Wed Feb 27 2013 - 11:18:19 PST)
    - Re: [AMBER] possibility to increase max . num. of bonded atoms ? David A Case (Wed Feb 27 2013 - 12:25:27 PST)
    - Re: [AMBER] possibility to increase max . num. of bonded atoms ? Marek Maly (Wed Feb 27 2013 - 12:27:07 PST)
[AMBER] spectrum simulation francesco oteri (Sun Feb 24 2013 - 12:56:18 PST)
[AMBER] dihedral distribution plot colvin (Sun Feb 24 2013 - 21:33:06 PST)
- Re: [AMBER] dihedral distribution plot Jason Swails (Mon Feb 25 2013 - 05:41:03 PST)
  - Re: [AMBER] dihedral distribution plot colvin (Tue Feb 26 2013 - 17:32:02 PST)
[AMBER] Fwd: Installing Amber in parallel whit Lion javier alejandro rendon carrillo (Sun Feb 24 2013 - 22:17:12 PST)
- Re: [AMBER] Fwd: Installing Amber in parallel whit Lion Jason Swails (Mon Feb 25 2013 - 03:01:25 PST)
[AMBER] PBSA vs MMPBSA.py eneas.usal.es (Sun Feb 24 2013 - 23:57:12 PST)
- Re: [AMBER] PBSA vs MMPBSA.py Jason Swails (Mon Feb 25 2013 - 04:44:14 PST)
- Re: [AMBER] PBSA vs MMPBSA.py Daniel Roe (Mon Feb 25 2013 - 07:18:25 PST)
[AMBER] pseudoatom Anne Kichler (Mon Feb 25 2013 - 03:32:41 PST)
- Re: [AMBER] pseudoatom Jason Swails (Mon Feb 25 2013 - 04:55:57 PST)
- Re: [AMBER] pseudoatom FyD (Mon Feb 25 2013 - 12:48:08 PST)
[AMBER] amber phosphorylated parameters Neha Gandhi (Mon Feb 25 2013 - 04:01:07 PST)
[AMBER] Error in RNA simulation esmaeel azadian (Mon Feb 25 2013 - 04:25:14 PST)
- Re: [AMBER] Error in RNA simulation Jason Swails (Mon Feb 25 2013 - 05:00:51 PST)
[AMBER] mmgbsa minimisation failing with error in trajene() ET (Mon Feb 25 2013 - 04:42:14 PST)
- Re: [AMBER] mmgbsa minimisation failing with error in trajene() ET (Mon Feb 25 2013 - 14:45:13 PST)
[AMBER] heme parameters Giulia (Mon Feb 25 2013 - 05:58:15 PST)
[AMBER] amber 11 installation on server Mary Varughese (Mon Feb 25 2013 - 10:24:31 PST)
[AMBER] Question regarding wham and umbrella sampling Fabrício Bracht (Mon Feb 25 2013 - 12:09:23 PST)
- Re: [AMBER] Question regarding wham and umbrella sampling Aron Broom (Mon Feb 25 2013 - 13:06:59 PST)
  - Re: [AMBER] Question regarding wham and umbrella sampling Fabrício Bracht (Mon Feb 25 2013 - 13:29:13 PST)
- Re: [AMBER] Question regarding wham and umbrella sampling Brian Radak (Mon Feb 25 2013 - 13:07:00 PST)
  - Re: [AMBER] Question regarding wham and umbrella sampling Aron Broom (Mon Feb 25 2013 - 14:52:37 PST)
[AMBER] converting AMBER minimized file to PDB/MOL2 Shashidhar Rao (Mon Feb 25 2013 - 12:17:26 PST)
- Re: [AMBER] converting AMBER minimized file to PDB/MOL2 Kasam, Vinod (Mon Feb 25 2013 - 12:21:38 PST)
  - Re: [AMBER] converting AMBER minimized file to PDB/MOL2 Jason Swails (Mon Feb 25 2013 - 12:27:54 PST)
    - Re: [AMBER] converting AMBER minimized file to PDB/MOL2 Shashidhar Rao (Mon Feb 25 2013 - 12:43:37 PST)
[AMBER] question on input for MMPBSA.py Shashidhar Rao (Mon Feb 25 2013 - 13:08:32 PST)
- Re: [AMBER] question on input for MMPBSA.py Jason Swails (Mon Feb 25 2013 - 17:20:37 PST)
  - Re: [AMBER] question on input for MMPBSA.py Shashidhar Rao (Tue Feb 26 2013 - 06:56:15 PST)
    - Re: [AMBER] question on input for MMPBSA.py Jason Swails (Tue Feb 26 2013 - 07:27:35 PST)
    - Re: [AMBER] question on input for MMPBSA.py Shashidhar Rao (Tue Feb 26 2013 - 08:03:53 PST)
[AMBER] MMPBSA problem Tommy Yap (Mon Feb 25 2013 - 18:15:05 PST)
- Re: [AMBER] MMPBSA problem Jason Swails (Tue Feb 26 2013 - 05:40:17 PST)
- Re: [AMBER] MMPBSA problem David A Case (Tue Feb 26 2013 - 05:48:04 PST)
[AMBER] Problem related to the bfactor calculation Sindrila Dutta banik (Mon Feb 25 2013 - 21:03:39 PST)
- Re: [AMBER] Problem related to the bfactor calculation Aron Broom (Mon Feb 25 2013 - 23:08:29 PST)
  - Re: [AMBER] Problem related to the bfactor calculation Sindrila Dutta banik (Mon Feb 25 2013 - 23:24:20 PST)
    - Re: [AMBER] Problem related to the bfactor calculation Daniel Roe (Tue Feb 26 2013 - 13:30:22 PST)
[AMBER] force field file 徐立平 (Mon Feb 25 2013 - 23:53:29 PST)
- Re: [AMBER] force field file David A Case (Tue Feb 26 2013 - 05:51:10 PST)
- Re: [AMBER] force field file FyD (Thu Feb 28 2013 - 22:32:25 PST)
[AMBER] MMPBSA free energy Soumya Lipsa Rath (Tue Feb 26 2013 - 03:50:13 PST)
- Re: [AMBER] MMPBSA free energy Jason Swails (Tue Feb 26 2013 - 04:50:35 PST)
  - Re: [AMBER] MMPBSA free energy Soumya Lipsa Rath (Tue Feb 26 2013 - 06:04:07 PST)
[AMBER] adding rings using sequence command Jio M (Tue Feb 26 2013 - 06:55:50 PST)
- Re: [AMBER] adding rings using sequence command Jason Swails (Tue Feb 26 2013 - 07:53:57 PST)
  - Re: [AMBER] adding rings using sequence command Jio M (Tue Feb 26 2013 - 11:49:59 PST)
    - Re: [AMBER] adding rings using sequence command Lachele Foley (Tue Feb 26 2013 - 12:02:11 PST)
    - Re: [AMBER] adding rings using sequence command Jio M (Tue Feb 26 2013 - 12:19:49 PST)
    - Re: [AMBER] adding rings using sequence command Jason Swails (Tue Feb 26 2013 - 12:25:43 PST)
    - Re: [AMBER] adding rings using sequence command Jio M (Tue Feb 26 2013 - 12:37:29 PST)
    - Re: [AMBER] adding rings using sequence command Lachele Foley (Tue Feb 26 2013 - 12:49:47 PST)
    - Re: [AMBER] adding rings using sequence command Jio M (Tue Feb 26 2013 - 12:58:53 PST)
    - Re: [AMBER] adding rings using sequence command Bill Ross (Tue Feb 26 2013 - 23:00:26 PST)
    - Re: [AMBER] adding rings using sequence command Jio M (Wed Feb 27 2013 - 01:52:49 PST)
    - Re: [AMBER] adding rings using sequence command Lachele Foley (Wed Feb 27 2013 - 12:29:19 PST)
- Re: [AMBER] adding rings using sequence command FyD (Wed Feb 27 2013 - 01:06:21 PST)
[AMBER] error in nmode Rasha Alqus (Tue Feb 26 2013 - 08:46:16 PST)
- Re: [AMBER] error in nmode Jason Swails (Tue Feb 26 2013 - 09:01:42 PST)
- Re: [AMBER] error in nmode Jason Swails (Wed Feb 27 2013 - 07:05:02 PST)
[AMBER] bond angle fitting CHAMI F. (Tue Feb 26 2013 - 11:17:09 PST)
- Re: [AMBER] bond angle fitting Jason Swails (Tue Feb 26 2013 - 11:29:50 PST)
- Re: [AMBER] bond angle fitting Ross Walker (Tue Feb 26 2013 - 11:38:18 PST)
  - Re: [AMBER] bond angle fitting CHAMI F. (Wed Feb 27 2013 - 04:30:42 PST)
[AMBER] TI without ifsc = 1 crashes Fabrício Bracht (Tue Feb 26 2013 - 15:02:32 PST)
- Re: [AMBER] TI without ifsc = 1 crashes Jason Swails (Tue Feb 26 2013 - 15:31:55 PST)
  - Re: [AMBER] TI without ifsc = 1 crashes Fabrício Bracht (Tue Feb 26 2013 - 16:02:59 PST)
    - Re: [AMBER] TI without ifsc = 1 crashes steinbrt.rci.rutgers.edu (Wed Feb 27 2013 - 00:36:31 PST)
[AMBER] NPT with pmemd.amoeba.MPI Density alway decreasing Cheng Wang (Tue Feb 26 2013 - 15:30:56 PST)
- Re: [AMBER] NPT with pmemd.amoeba.MPI Density alway decreasing Jason Swails (Wed Feb 27 2013 - 03:58:38 PST)
  - Re: [AMBER] NPT with pmemd.amoeba.MPI Density alway decreasing Cheng Wang (Wed Feb 27 2013 - 11:16:51 PST)
    - Re: [AMBER] NPT with pmemd.amoeba.MPI Density alway decreasing Jason Swails (Wed Feb 27 2013 - 11:23:56 PST)
[AMBER] Install amber in Mac Lion javier alejandro rendon carrillo (Tue Feb 26 2013 - 16:57:16 PST)
- Re: [AMBER] Install amber in Mac Lion Jason Swails (Tue Feb 26 2013 - 17:51:58 PST)
[AMBER] periodic image of octahedron box in VMD 吴云剑 (Tue Feb 26 2013 - 18:10:08 PST)
- Re: [AMBER] periodic image of octahedron box in VMD Jason Swails (Tue Feb 26 2013 - 18:37:06 PST)
  - Re: [AMBER] periodic image of octahedron box in VMD Ilyas Yildirim (Tue Feb 26 2013 - 19:04:56 PST)
[AMBER] error in nmode Rasha Alqus (Wed Feb 27 2013 - 07:03:03 PST)
- Re: [AMBER] error in nmode Jason Swails (Wed Feb 27 2013 - 07:07:13 PST)
[AMBER] Error analysing an RNA trajectory with anal Amparo Garcia Lopez (Wed Feb 27 2013 - 10:44:50 PST)
- Re: [AMBER] Error analysing an RNA trajectory with anal Daniel Roe (Wed Feb 27 2013 - 12:08:59 PST)
  - Re: [AMBER] Error analysing an RNA trajectory with anal Amparo Garcia Lopez (Thu Feb 28 2013 - 02:42:04 PST)
    - Re: [AMBER] Error analysing an RNA trajectory with anal Jason Swails (Thu Feb 28 2013 - 05:23:43 PST)
    - Re: [AMBER] Error analysing an RNA trajectory with anal Amparo Garcia Lopez (Thu Feb 28 2013 - 07:55:42 PST)
[AMBER] MMGBSA/MMPBSA Decomposition Analysis Vivek Shankar Bharadwaj (Wed Feb 27 2013 - 16:28:38 PST)
- Re: [AMBER] MMGBSA/MMPBSA Decomposition Analysis Aron Broom (Wed Feb 27 2013 - 16:44:51 PST)
  - Re: [AMBER] MMGBSA/MMPBSA Decomposition Analysis Jason Swails (Wed Feb 27 2013 - 18:02:36 PST)
- Re: [AMBER] MMGBSA/MMPBSA Decomposition Analysis Jason Swails (Wed Feb 27 2013 - 17:53:50 PST)
  - Re: [AMBER] MMGBSA/MMPBSA Decomposition Analysis Vivek Shankar Bharadwaj (Thu Feb 28 2013 - 10:00:00 PST)
    - Re: [AMBER] MMGBSA/MMPBSA Decomposition Analysis Jason Swails (Thu Feb 28 2013 - 10:21:10 PST)
Re: [AMBER] 0 meandme_meandme2003.yahoo.com (Wed Feb 27 2013 - 19:54:29 PST)
[AMBER] remd exchange acceptance Kim Hyunsik (Wed Feb 27 2013 - 22:08:24 PST)
- Re: [AMBER] remd exchange acceptance Daniel Sindhikara (Thu Feb 28 2013 - 02:02:36 PST)
- Re: [AMBER] remd exchange acceptance Adrian Roitberg (Thu Feb 28 2013 - 04:37:40 PST)
[AMBER] GTX 680 vs GTX Titan Gonzalo Jimenez (Wed Feb 27 2013 - 23:22:33 PST)
- Re: [AMBER] GTX 680 vs GTX Titan Ross Walker (Thu Feb 28 2013 - 00:10:43 PST)
  - Re: [AMBER] GTX 680 vs GTX Titan Gonzalo Jimenez (Thu Feb 28 2013 - 00:41:21 PST)
    - Re: [AMBER] GTX 680 vs GTX Titan Gould, Ian R (Thu Feb 28 2013 - 02:49:38 PST)
    - Re: [AMBER] GTX 680 vs GTX Titan Jason Swails (Thu Feb 28 2013 - 05:29:30 PST)
    - Re: [AMBER] GTX 680 vs GTX Titan Gould, Ian R (Thu Feb 28 2013 - 05:40:59 PST)
    - Re: [AMBER] GTX 680 vs GTX Titan Gould, Ian R (Thu Feb 28 2013 - 05:52:06 PST)
    - Re: [AMBER] GTX 680 vs GTX Titan filip fratev (Thu Feb 28 2013 - 08:09:51 PST)
    - Re: [AMBER] GTX 680 vs GTX Titan Aron Broom (Thu Feb 28 2013 - 08:24:00 PST)
[AMBER] generate MDCRD file for two points HM (Thu Feb 28 2013 - 04:00:32 PST)
- Re: [AMBER] generate MDCRD file for two points Jason Swails (Thu Feb 28 2013 - 05:33:28 PST)
  - Re: [AMBER] generate MDCRD file for two points HM (Thu Feb 28 2013 - 06:29:04 PST)
    - Re: [AMBER] generate MDCRD file for two points Jason Swails (Thu Feb 28 2013 - 07:17:21 PST)
[AMBER] aMD Beale, John (Thu Feb 28 2013 - 05:27:17 PST)
- Re: [AMBER] aMD Romelia Salomon (Thu Feb 28 2013 - 07:59:18 PST)
- Re: [AMBER] aMD Moth, Chris (Thu Feb 28 2013 - 08:16:39 PST)
- Re: [AMBER] aMD Romelia Salomon (Thu Feb 28 2013 - 08:22:09 PST)
[AMBER] Amber MD using NAMD Ilyas Yildirim (Thu Feb 28 2013 - 15:32:32 PST)
- Re: [AMBER] Amber MD using NAMD Massimiliano Porrini (Fri Mar 01 2013 - 01:58:01 PST)
[AMBER] PCI-E 2.0 vs 3.0 (AMD vs INTEL?) Jonathan Gough (Thu Feb 28 2013 - 18:53:41 PST)
- Re: [AMBER] PCI-E 2.0 vs 3.0 (AMD vs INTEL?) Aron Broom (Thu Feb 28 2013 - 21:24:10 PST)
- Re: [AMBER] PCI-E 2.0 vs 3.0 (AMD vs INTEL?) Benjamin D Madej (Thu Feb 28 2013 - 22:00:21 PST)
  - Re: [AMBER] PCI-E 2.0 vs 3.0 (AMD vs INTEL?) Benjamin D Madej (Thu Feb 28 2013 - 22:05:38 PST)
    - Re: [AMBER] PCI-E 2.0 vs 3.0 (AMD vs INTEL?) Jonathan Gough (Fri Mar 01 2013 - 04:24:14 PST)
[AMBER] Softcore selection Fabrício Bracht (Thu Feb 28 2013 - 20:19:24 PST)
- Re: [AMBER] Softcore selection steinbrt.rci.rutgers.edu (Fri Mar 01 2013 - 00:41:48 PST)
[AMBER] March 5, 2013 Webinar: AMBER and Kepler GPUs mark94025.comcast.net (Thu Feb 28 2013 - 21:00:11 PST)
[AMBER] amber12 configure error Asmita Gupta (Fri Mar 01 2013 - 00:09:27 PST)
- Re: [AMBER] amber12 configure error Jason Swails (Fri Mar 01 2013 - 06:15:58 PST)
[AMBER] Kepler and Amber11? Ismail, Mohd F. (Fri Mar 01 2013 - 00:16:16 PST)
- Re: [AMBER] Kepler and Amber11? Jason Swails (Fri Mar 01 2013 - 06:16:54 PST)
  - Re: [AMBER] Kepler and Amber11? Ismail, Mohd F. (Sat Mar 02 2013 - 12:14:35 PST)
[AMBER] Build DNA structure based on squence Tong ZHU (Fri Mar 01 2013 - 01:48:25 PST)
- Re: [AMBER] Build DNA structure based on squence Terry (Fri Mar 01 2013 - 01:51:52 PST)
[AMBER] Problem in Arsenite parameterisation Kshatresh Dutta Dubey (Fri Mar 01 2013 - 05:28:00 PST)
- [AMBER] GPU overload Baldoni Hector Armando (Fri Mar 01 2013 - 05:42:04 PST)
  - Re: [AMBER] GPU overload Daniel Roe (Fri Mar 01 2013 - 06:43:08 PST)
    - Re: [AMBER] GPU overload Fenley, Andrew (Fri Mar 01 2013 - 06:54:04 PST)
    - Re: [AMBER] GPU overload Hector A. Baldoni (Fri Mar 01 2013 - 11:57:10 PST)
    - Re: [AMBER] GPU overload Scott Le Grand (Mon Mar 04 2013 - 16:43:11 PST)
- Re: [AMBER] Problem in Arsenite parameterisation Daniel Roe (Fri Mar 01 2013 - 06:44:16 PST)
  - Re: [AMBER] Problem in Arsenite parameterisation Kshatresh Dutta Dubey (Sat Mar 02 2013 - 01:03:09 PST)
    - Re: [AMBER] Problem in Arsenite parameterisation Jason Swails (Sat Mar 02 2013 - 10:22:42 PST)
    - Re: [AMBER] Problem in Arsenite parameterisation Kshatresh Dutta Dubey (Sat Mar 02 2013 - 10:28:31 PST)
    - Re: [AMBER] Problem in Arsenite parameterisation Kshatresh Dutta Dubey (Sat Mar 02 2013 - 10:39:05 PST)
    - Re: [AMBER] Problem in Arsenite parameterisation Daniel Roe (Sat Mar 02 2013 - 12:47:22 PST)
[AMBER] restraint domains zhenquan hu (Fri Mar 01 2013 - 08:42:15 PST)
[AMBER] Implicit membrane models Gustavo Seabra (Fri Mar 01 2013 - 10:32:02 PST)
- Re: [AMBER] Implicit membrane models Ray Luo, Ph.D. (Fri Mar 01 2013 - 12:07:11 PST)
  - Re: [AMBER] Implicit membrane models Gustavo Seabra (Fri Mar 01 2013 - 12:34:04 PST)
[AMBER] ptraj action command Sun (Sun Mar 03 2013 - 18:57:49 PST)
- Re: [AMBER] ptraj action command Daniel Roe (Sun Mar 03 2013 - 20:46:03 PST)
[AMBER] problem in calculating electrostatic potential using PBSA N Nandi (Sun Mar 03 2013 - 21:52:11 PST)
- [AMBER] Fw: problem in calculating electrostatic potential using PBSA N Nandi (Thu Mar 07 2013 - 20:56:53 PST)
[AMBER] Problem parsing PB output using MMPBSA.py in AMBER11 and AmberTools 1.5 dbaogen (Mon Mar 04 2013 - 04:27:08 PST)
- Re: [AMBER] Problem parsing PB output using MMPBSA.py in AMBER11 and AmberTools 1.5 Jason Swails (Mon Mar 04 2013 - 04:37:14 PST)
- Re: [AMBER] Problem parsing PB output using MMPBSA.py in AMBER11 and AmberTools 1.5 dbaogen (Mon Mar 04 2013 - 19:10:55 PST)
  - Re: [AMBER] Problem parsing PB output using MMPBSA.py in AMBER11 and AmberTools 1.5 Jason Swails (Tue Mar 05 2013 - 04:36:38 PST)
[AMBER] temperature fluctuation amber ntp ensemble Neha Gandhi (Mon Mar 04 2013 - 06:50:53 PST)
- Re: [AMBER] temperature fluctuation amber ntp ensemble Brian Radak (Mon Mar 04 2013 - 08:35:50 PST)
  - Re: [AMBER] temperature fluctuation amber ntp ensemble Ross Walker (Thu Mar 07 2013 - 20:09:46 PST)
[AMBER] Segmentation fault with EVB calculations on multiple cores for a system with more than 60 atom types Elise Duboué-Dijon (Mon Mar 04 2013 - 15:19:05 PST)
[AMBER] bug report: tinker_to_amber failed for systems containing counter ions Ye MEI (Mon Mar 04 2013 - 20:54:51 PST)
[AMBER] Annomalous "TER" is inserted in a peptide including non-standard AA kurisaki (Tue Mar 05 2013 - 01:38:00 PST)
- Re: [AMBER] Annomalous "TER" is inserted in a peptide including non-standard AA David A Case (Tue Mar 05 2013 - 04:36:05 PST)
  - Re: [AMBER] Annomalous "TER" is inserted in a peptide including non-standard AA Vishal Maingi (Tue Mar 05 2013 - 04:54:21 PST)
    - Re: [AMBER] Annomalous "TER" is inserted in a peptide including non-standard AA Vishal Maingi (Tue Mar 05 2013 - 05:10:21 PST)
    - Re: [AMBER] Annomalous "TER" is inserted in a peptide including non-standard AA Jason Swails (Tue Mar 05 2013 - 05:38:10 PST)
- Re: [AMBER] Annomalous "TER" is inserted in a peptide including non-standard AA kurisaki (Tue Mar 05 2013 - 05:24:40 PST)
  - Re: [AMBER] Annomalous "TER" is inserted in a peptide including non-standard AA David A Case (Tue Mar 05 2013 - 07:55:58 PST)
    - Re: [AMBER] Annomalous "TER" is inserted in a peptide including non-standard AA kurisaki (Tue Mar 05 2013 - 16:37:19 PST)
[AMBER] Query On Steered Molecular Dynamics siddharth kesharwani (Tue Mar 05 2013 - 05:01:34 PST)
- Re: [AMBER] Query On Steered Molecular Dynamics Dmitry Nilov (Tue Mar 05 2013 - 05:24:02 PST)
[AMBER] Charge relocation Amber 12 CHAMI F. (Tue Mar 05 2013 - 05:54:03 PST)
[AMBER] how to restart a molecular dynamics simulation Emilio Angelina (Tue Mar 05 2013 - 11:46:52 PST)
- Re: [AMBER] how to restart a molecular dynamics simulation Jason Swails (Tue Mar 05 2013 - 11:59:33 PST)
- Re: [AMBER] how to restart a molecular dynamics simulation Hector A. Baldoni (Tue Mar 05 2013 - 12:22:49 PST)
[AMBER] bug report: tinker_to_amber failed for systems containing counter ions Amber Amoeba (Tue Mar 05 2013 - 12:33:21 PST)
[AMBER] test Amber Amoeba (Tue Mar 05 2013 - 14:27:01 PST)
[AMBER] RMSD Fluctuation Theodosia Teo (Tue Mar 05 2013 - 19:28:40 PST)
- Re: [AMBER] RMSD Fluctuation Daniel Roe (Tue Mar 05 2013 - 21:01:46 PST)
- Re: [AMBER] RMSD Fluctuation Carlos Simmerling (Thu Mar 07 2013 - 03:24:01 PST)
Re: [AMBER] bug report: tinker_to_amber failed for systems containingcounter ions Ye MEI (Wed Mar 06 2013 - 00:19:25 PST)
- Re: [AMBER] bug report: tinker_to_amber failed for systems containingcounter ions Amber Amoeba (Wed Mar 06 2013 - 10:27:27 PST)
- Re: [AMBER] bug report: tinker_to_amber failed for systemscontainingcounter ions Ye MEI (Wed Mar 06 2013 - 18:23:58 PST)
  - Re: [AMBER] bug report: tinker_to_amber failed for systemscontainingcounter ions Amber Amoeba (Wed Mar 06 2013 - 22:53:46 PST)
[AMBER] Cross correlation calculation Indrajit Deb (Wed Mar 06 2013 - 01:33:12 PST)
[AMBER] TIP5P water simulation 강현아 (Wed Mar 06 2013 - 03:31:48 PST)
- Re: [AMBER] TIP5P water simulation Brian Radak (Wed Mar 06 2013 - 06:34:41 PST)
- Re: [AMBER] TIP5P water simulation 강현아 (Wed Mar 06 2013 - 07:32:59 PST)
  - Re: [AMBER] TIP5P water simulation Brian Radak (Wed Mar 06 2013 - 10:29:32 PST)
    - Re: [AMBER] TIP5P water simulation David A Case (Wed Mar 06 2013 - 17:49:09 PST)
[AMBER] Amber 2013 workshop psu4.uic.edu (Wed Mar 06 2013 - 09:31:50 PST)
- Re: [AMBER] Amber 2013 workshop Ross Walker (Wed Mar 06 2013 - 10:31:28 PST)
  - Re: [AMBER] Amber 2013 workshop psu4.uic.edu (Fri Mar 08 2013 - 09:30:28 PST)
[AMBER] xleap_the hydrogen atom in C-terminus of peptides Nan Li (Wed Mar 06 2013 - 11:02:14 PST)
- Re: [AMBER] xleap_the hydrogen atom in C-terminus of peptides David A Case (Wed Mar 06 2013 - 17:53:46 PST)
- Re: [AMBER] xleap_the hydrogen atom in C-terminus of peptides FyD (Wed Mar 06 2013 - 22:54:45 PST)
[AMBER] MMPBSA jobs on a cluster Calcerror: Vivek Shankar Bharadwaj (Wed Mar 06 2013 - 12:05:01 PST)
- Re: [AMBER] MMPBSA jobs on a cluster Calcerror: Jason Swails (Wed Mar 06 2013 - 12:25:39 PST)
  - Re: [AMBER] MMPBSA jobs on a cluster Calcerror: Vivek Shankar Bharadwaj (Wed Mar 06 2013 - 12:36:30 PST)
    - Re: [AMBER] MMPBSA jobs on a cluster Calcerror: Jason Swails (Wed Mar 06 2013 - 13:47:18 PST)
    - Re: [AMBER] MMPBSA jobs on a cluster Calcerror: Vivek Shankar Bharadwaj (Wed Mar 06 2013 - 14:00:14 PST)
    - Re: [AMBER] MMPBSA jobs on a cluster Calcerror: Jason Swails (Wed Mar 06 2013 - 14:13:29 PST)
    - Re: [AMBER] MMPBSA jobs on a cluster Calcerror: Vivek Shankar Bharadwaj (Wed Mar 06 2013 - 14:26:53 PST)
    - Re: [AMBER] MMPBSA jobs on a cluster Calcerror: Jason Swails (Wed Mar 06 2013 - 15:16:59 PST)
    - Re: [AMBER] MMPBSA jobs on a cluster Calcerror: Jason Swails (Wed Mar 06 2013 - 15:19:04 PST)
[AMBER] Error in MMPBSA Saugata Hazra (Wed Mar 06 2013 - 12:30:00 PST)
- Re: [AMBER] Error in MMPBSA Ray Luo, Ph.D. (Wed Mar 06 2013 - 12:41:56 PST)
  - Re: [AMBER] Error in MMPBSA Saugata Hazra (Wed Mar 06 2013 - 12:50:15 PST)
    - Re: [AMBER] Error in MMPBSA Jason Swails (Wed Mar 06 2013 - 14:12:43 PST)
    - Re: [AMBER] Error in MMPBSA Saugata Hazra (Wed Mar 06 2013 - 14:52:22 PST)
    - Re: [AMBER] Error in MMPBSA Jason Swails (Wed Mar 06 2013 - 15:15:33 PST)
    - Re: [AMBER] Error in MMPBSA Saugata Hazra (Wed Mar 06 2013 - 15:30:12 PST)
[AMBER] antechamber dCTP YZ Qin (Wed Mar 06 2013 - 17:56:44 PST)
- Re: [AMBER] antechamber dCTP FyD (Wed Mar 06 2013 - 22:30:52 PST)
  - Re: [AMBER] antechamber dCTP YZ Qin (Thu Mar 07 2013 - 01:13:16 PST)
    - Re: [AMBER] antechamber dCTP YZ Qin (Thu Mar 07 2013 - 01:17:47 PST)
    - Re: [AMBER] antechamber dCTP FyD (Thu Mar 07 2013 - 02:55:59 PST)
    - Re: [AMBER] antechamber dCTP YZ Qin (Thu Mar 07 2013 - 06:35:02 PST)
    - Re: [AMBER] antechamber dCTP FyD (Thu Mar 07 2013 - 12:45:38 PST)
    - Re: [AMBER] antechamber dCTP YZ Qin (Fri Mar 08 2013 - 08:01:32 PST)
    - Re: [AMBER] antechamber dCTP FyD (Fri Mar 08 2013 - 23:09:19 PST)
[AMBER] VLIMIT problem with Folic acid (gaff parm) HIMANSHU JOSHI (Wed Mar 06 2013 - 21:19:07 PST)
Re: [AMBER] bug report: tinker_to_amber failed forsystemscontainingcounter ions Ye MEI (Thu Mar 07 2013 - 02:31:24 PST)
- Re: [AMBER] bug report: tinker_to_amber failed forsystemscontainingcounter ions Amber Amoeba (Thu Mar 07 2013 - 08:03:28 PST)
[AMBER] Is there a way to keep ions fixed in a amber MD? Changqing Yan (Thu Mar 07 2013 - 05:39:51 PST)
- Re: [AMBER] Is there a way to keep ions fixed in a amber MD? Jason Swails (Thu Mar 07 2013 - 05:48:42 PST)
[AMBER] Number Excluded Atoms List Generation Browning, Nicholas (Thu Mar 07 2013 - 08:53:40 PST)
- Re: [AMBER] Number Excluded Atoms List Generation cieplak.cgl.ucsf.edu (Thu Mar 07 2013 - 09:04:56 PST)
- Re: [AMBER] Number Excluded Atoms List Generation Jason Swails (Thu Mar 07 2013 - 10:52:41 PST)
[AMBER] tleap output of mol2 format with incorrect bond order Marko Wehle (Thu Mar 07 2013 - 09:08:23 PST)
- [AMBER] WG: tleap output of mol2 format with incorrect bond order Marko Wehle (Thu Mar 07 2013 - 10:44:28 PST)
  - Re: [AMBER] WG: tleap output of mol2 format with incorrect bond order Jason Swails (Thu Mar 07 2013 - 12:01:16 PST)
  - Re: [AMBER] WG: tleap output of mol2 format with incorrect bond order David A Case (Thu Mar 07 2013 - 12:04:44 PST)
    - Re: [AMBER] WG: tleap output of mol2 format with incorrect bond order Bill Ross (Thu Mar 07 2013 - 15:36:22 PST)
  - Re: [AMBER] WG: tleap output of mol2 format with incorrect bond order Marko Wehle (Fri Mar 08 2013 - 08:51:45 PST)
    - Re: [AMBER] WG: tleap output of mol2 format with incorrect bond order David A Case (Fri Mar 08 2013 - 14:57:25 PST)
- Re: [AMBER] tleap output of mol2 format with incorrect bond order FyD (Thu Mar 07 2013 - 12:50:57 PST)
[AMBER] Fwd: failed to run sander .... Shashidhar Rao (Thu Mar 07 2013 - 11:13:58 PST)
- Re: [AMBER] Fwd: failed to run sander .... Brian Radak (Thu Mar 07 2013 - 12:03:28 PST)
- Re: [AMBER] Fwd: failed to run sander .... David A Case (Thu Mar 07 2013 - 12:15:36 PST)
[AMBER] cudaMemcpy GpuBuffer::Download failed unspecified launch failure Tu Zhiping (Thu Mar 07 2013 - 19:12:38 PST)
- Re: [AMBER] cudaMemcpy GpuBuffer::Download failed unspecified launch failure Ross Walker (Thu Mar 07 2013 - 19:53:33 PST)
  - Re: [AMBER] cudaMemcpy GpuBuffer::Download failed unspecified launch failure 涂志萍 (Thu Mar 07 2013 - 20:51:01 PST)
    - Re: [AMBER] cudaMemcpy GpuBuffer::Download failed unspecified launch failure Ross Walker (Thu Mar 07 2013 - 21:02:19 PST)
    - Re: [AMBER] cudaMemcpy GpuBuffer::Download failed unspecified launch failure Jason Swails (Fri Mar 08 2013 - 05:20:12 PST)
    - Re: [AMBER] cudaMemcpy GpuBuffer::Download failed unspecified launch failure 涂志萍 (Sun Mar 10 2013 - 07:20:16 PDT)
    - Re: [AMBER] cudaMemcpy GpuBuffer::Download failed unspecified launch failure Jason Swails (Sun Mar 10 2013 - 08:17:41 PDT)
    - Re: [AMBER] cudaMemcpy GpuBuffer::Download failed unspecified launch failure 涂志萍 (Sat Mar 16 2013 - 02:49:57 PDT)
    - Re: [AMBER] cudaMemcpy GpuBuffer::Download failed unspecified launch failure Jason Swails (Sat Mar 16 2013 - 08:46:56 PDT)
    - Re: [AMBER] cudaMemcpy GpuBuffer::Download failed unspecified launch failure Gerald Monard (Sun Mar 17 2013 - 14:12:47 PDT)
    - Re: [AMBER] cudaMemcpy GpuBuffer::Download failed unspecified launch failure 涂志萍 (Sun Mar 17 2013 - 20:14:58 PDT)
[AMBER] Can IMPOSE apply to improper angle? kurisaki (Thu Mar 07 2013 - 21:05:04 PST)
- Re: [AMBER] Can IMPOSE apply to improper angle? FyD (Thu Mar 07 2013 - 23:11:25 PST)
[AMBER] problem to generate pbsa.phi file using PBSA N Nandi (Thu Mar 07 2013 - 23:38:13 PST)
Re: [AMBER] impose for improper torsion: from I. Kurisaki FyD (Fri Mar 08 2013 - 03:36:35 PST)
- Re: [AMBER] impose for improper torsion: from I. Kurisaki kurisaki (Fri Mar 08 2013 - 03:46:14 PST)
  - Re: [AMBER] impose for improper torsion: from I. Kurisaki Jason Swails (Fri Mar 08 2013 - 05:08:23 PST)
    - Re: [AMBER] impose for improper torsion: from I. Kurisaki kurisaki (Fri Mar 08 2013 - 05:37:20 PST)
[AMBER] Regarding centering a tetrameric molecule dilrajl.bii.a-star.edu.sg (Fri Mar 08 2013 - 04:51:00 PST)
- Re: [AMBER] Regarding centering a tetrameric molecule Jason Swails (Fri Mar 08 2013 - 05:15:20 PST)
- Re: [AMBER] Regarding centering a tetrameric molecule dilrajl.bii.a-star.edu.sg (Sun Mar 10 2013 - 23:50:16 PDT)
  - Re: [AMBER] Regarding centering a tetrameric molecule Daniel Roe (Mon Mar 11 2013 - 05:12:08 PDT)
Re: [AMBER] bug report: tinker_to_amber failedforsystemscontainingcounter ions Ye MEI (Fri Mar 08 2013 - 07:35:35 PST)
- Re: [AMBER] bug report: tinker_to_amber failedforsystemscontainingcounter ions Amber Amoeba (Mon Mar 11 2013 - 11:18:08 PDT)
[AMBER] March 15 deadline for ACS COMP division awards for Fall 2013 Indianapolis national meeting Carlos Simmerling (Sat Mar 02 2013 - 05:04:05 PST)
[AMBER] N-Carboxymethionine charges and parameters for AMBER ABEL Stephane 175950 (Sat Mar 09 2013 - 02:46:58 PST)
- Re: [AMBER] N-Carboxymethionine charges and parameters for AMBER FyD (Sat Mar 09 2013 - 23:23:10 PST)
[AMBER] Imaging issues with ptraj Kira Armacost (Sat Mar 09 2013 - 17:55:06 PST)
- Re: [AMBER] Imaging issues with ptraj Daniel Roe (Sat Mar 09 2013 - 19:50:46 PST)
  - Re: [AMBER] Imaging issues with ptraj Kira Armacost (Mon Mar 11 2013 - 07:05:06 PDT)
[AMBER] generate prepin from mol2 which has charges/atom types for Heme Vaibhav Dixit (Sun Mar 10 2013 - 03:23:17 PDT)
- Re: [AMBER] generate prepin from mol2 which has charges/atom types for Heme Jason Swails (Sun Mar 10 2013 - 08:25:28 PDT)
- Re: [AMBER] generate prepin from mol2 which has charges/atom types for Heme David A Case (Sun Mar 10 2013 - 09:24:03 PDT)
  - Re: [AMBER] generate prepin from mol2 which has charges/atom types for Heme Vaibhav Dixit (Sun Mar 10 2013 - 21:37:45 PDT)
    - Re: [AMBER] generate prepin from mol2 which has charges/atom types for Heme Jason Swails (Mon Mar 11 2013 - 06:09:29 PDT)
    - Re: [AMBER] generate prepin from mol2 which has charges/atom types for Heme Vaibhav Dixit (Mon Mar 11 2013 - 08:24:57 PDT)
[AMBER] Does MMPBSA.py actually make a file called _MMPBSA_nmode.in? Joel Dockray (Sun Mar 10 2013 - 05:33:20 PDT)
- Re: [AMBER] Does MMPBSA.py actually make a file called _MMPBSA_nmode.in? Jason Swails (Sun Mar 10 2013 - 08:20:51 PDT)
  - Re: [AMBER] Does MMPBSA.py actually make a file called _MMPBSA_nmode.in? Joel Dockray (Sun Mar 10 2013 - 09:31:15 PDT)
[AMBER] ligand molecule problem tianchuan881 (Sun Mar 10 2013 - 20:08:09 PDT)
- Re: [AMBER] ligand molecule problem Jason Swails (Mon Mar 11 2013 - 06:18:14 PDT)
[AMBER] GTX 460 ? John Gehman (Sun Mar 10 2013 - 23:54:31 PDT)
- Re: [AMBER] GTX 460 ? Jason Swails (Mon Mar 11 2013 - 06:13:47 PDT)
- Re: [AMBER] GTX 460 ? Baldoni Hector Armando (Mon Mar 11 2013 - 06:59:26 PDT)
- Re: [AMBER] GTX 460 ? Ross Walker (Mon Mar 11 2013 - 08:20:22 PDT)
  - Re: [AMBER] GTX 460 ? John Gehman (Mon Mar 11 2013 - 18:56:30 PDT)
    - Re: [AMBER] GTX 460 ? Scott Le Grand (Tue Mar 12 2013 - 10:39:58 PDT)
    - Re: [AMBER] GTX 460 ? Hector A. Baldoni (Tue Mar 12 2013 - 12:20:57 PDT)
    - Re: [AMBER] GTX 460 ? Aron Broom (Tue Mar 12 2013 - 13:39:24 PDT)
    - Re: [AMBER] GTX 460 ? John Gehman (Wed Mar 13 2013 - 06:40:47 PDT)
    - Re: [AMBER] GTX 460 ? Aron Broom (Wed Mar 13 2013 - 07:35:28 PDT)
[AMBER] RESP charges for iron-sulfur cluster safwat abdel-azeim (Mon Mar 11 2013 - 02:42:45 PDT)
- Re: [AMBER] RESP charges for iron-sulfur cluster francesco oteri (Mon Mar 11 2013 - 03:29:50 PDT)
  - Re: [AMBER] RESP charges for iron-sulfur cluster safwat abdel-azeim (Mon Mar 11 2013 - 04:57:59 PDT)
- Re: [AMBER] RESP charges for iron-sulfur cluster David A Case (Fri Mar 15 2013 - 05:13:31 PDT)
  - Re: [AMBER] RESP charges for iron-sulfur cluster safwat abdel-azeim (Fri Mar 15 2013 - 05:33:28 PDT)
    - Re: [AMBER] RESP charges for iron-sulfur cluster David A Case (Fri Mar 15 2013 - 08:24:03 PDT)
    - Re: [AMBER] RESP charges for iron-sulfur cluster safwat abdel-azeim (Fri Mar 15 2013 - 10:51:21 PDT)
[AMBER] Cyclic peptide Itamar Kass (Med) (Mon Mar 11 2013 - 03:34:59 PDT)
- Re: [AMBER] Cyclic peptide Jason Swails (Mon Mar 11 2013 - 06:21:35 PDT)
  - Re: [AMBER] Cyclic peptide Itamar Kass (Med) (Sun Mar 24 2013 - 03:47:17 PDT)
[AMBER] mapping problem with makeDIST_RST Bayse, Craig A. (Mon Mar 11 2013 - 11:14:05 PDT)
- Re: [AMBER] mapping problem with makeDIST_RST David A Case (Fri Mar 15 2013 - 05:02:04 PDT)
  - Re: [AMBER] mapping problem with makeDIST_RST David A Case (Fri Mar 15 2013 - 08:20:35 PDT)
[AMBER] Amber 11 and Amber 12 David Winogradoff (Mon Mar 11 2013 - 15:34:31 PDT)
- Re: [AMBER] Amber 11 and Amber 12 Jason Swails (Mon Mar 11 2013 - 15:56:58 PDT)
  - Re: [AMBER] Amber 11 and Amber 12 David Winogradoff (Wed Mar 13 2013 - 10:25:40 PDT)
    - Re: [AMBER] Amber 11 and Amber 12 Daniel Roe (Wed Mar 13 2013 - 11:57:57 PDT)
    - Re: [AMBER] Amber 11 and Amber 12 David Winogradoff (Wed Mar 13 2013 - 16:30:36 PDT)
    - Re: [AMBER] Amber 11 and Amber 12 Daniel Roe (Fri Mar 15 2013 - 08:42:30 PDT)
    - Re: [AMBER] Amber 11 and Amber 12 Jason Swails (Fri Mar 15 2013 - 10:11:12 PDT)
[AMBER] Thermodynamic Integration Shruti Koulgi (Tue Mar 12 2013 - 05:25:47 PDT)
- Re: [AMBER] Thermodynamic Integration David A Case (Tue Mar 12 2013 - 05:48:01 PDT)
[AMBER] frcmod file problem tianchuan881 (Tue Mar 12 2013 - 06:09:22 PDT)
- [AMBER] NVIDIA GTX-675 Cenk $Jenk$ Andac (Tue Mar 12 2013 - 07:49:54 PDT)
  - Re: [AMBER] NVIDIA GTX-675 Ross Walker (Tue Mar 12 2013 - 07:57:48 PDT)
- Re: [AMBER] frcmod file problem Jason Swails (Tue Mar 12 2013 - 13:41:49 PDT)
[AMBER] frcmod problem tianchuan881 (Tue Mar 12 2013 - 06:50:03 PDT)
- Re: [AMBER] frcmod problem Daniel Roe (Tue Mar 12 2013 - 06:59:21 PDT)
[AMBER] trajin: command not found uday spike (Tue Mar 12 2013 - 07:31:45 PDT)
- Re: [AMBER] trajin: command not found Daniel Roe (Tue Mar 12 2013 - 07:41:25 PDT)
- Re: [AMBER] trajin: command not found uday spike (Thu Mar 14 2013 - 05:22:41 PDT)
[AMBER] Restart SMD simulation Attilio Vittorio Vargiu (Tue Mar 12 2013 - 08:35:59 PDT)
- Re: [AMBER] Restart SMD simulation Jason Swails (Tue Mar 12 2013 - 15:23:49 PDT)
[AMBER] Problem in parallel installation of Amber 12 Kshatresh Dutta Dubey (Tue Mar 12 2013 - 08:41:49 PDT)
- Re: [AMBER] Problem in parallel installation of Amber 12 Ross Walker (Tue Mar 12 2013 - 08:53:56 PDT)
  - Re: [AMBER] Problem in parallel installation of Amber 12 Kshatresh Dutta Dubey (Tue Mar 12 2013 - 08:59:03 PDT)
    - Re: [AMBER] Problem in parallel installation of Amber 12 Ross Walker (Tue Mar 12 2013 - 09:55:51 PDT)
    - Re: [AMBER] Problem in parallel installation of Amber 12 Jason Swails (Tue Mar 12 2013 - 12:17:28 PDT)
    - Re: [AMBER] Problem in parallel installation of Amber 12 Kshatresh Dutta Dubey (Wed Mar 13 2013 - 04:21:37 PDT)
[AMBER] Amber12 MPI OK on one node but not across nodes Jan Fredin (Tue Mar 12 2013 - 09:38:46 PDT)
- Re: [AMBER] Amber12 MPI OK on one node but not across nodes Ross Walker (Tue Mar 12 2013 - 09:50:58 PDT)
  - Re: [AMBER] Amber12 MPI OK on one node but not across nodes David A Case (Tue Mar 12 2013 - 17:29:26 PDT)
[AMBER] charge problem tianchuan881 (Wed Mar 13 2013 - 04:13:18 PDT)
- Re: [AMBER] charge problem David A Case (Wed Mar 13 2013 - 06:34:45 PDT)
[AMBER] Query on Steered Molecular Dynamics siddharth kesharwani (Wed Mar 13 2013 - 04:29:51 PDT)
- Re: [AMBER] Query on Steered Molecular Dynamics Jason Swails (Wed Mar 13 2013 - 06:44:12 PDT)
- [AMBER] Query on Alanine scanning Mannan (Wed Sep 11 2013 - 02:29:55 PDT)
  - Re: [AMBER] Query on Alanine scanning Jason Swails (Wed Sep 11 2013 - 05:05:00 PDT)
Re: [AMBER] bug report: tinker_to_amberfailedforsystemscontainingcounter ions Ye MEI (Wed Mar 13 2013 - 07:48:07 PDT)
- Re: [AMBER] bug report: tinker_to_amberfailedforsystemscontainingcounter ions Ye MEI (Thu Mar 14 2013 - 09:43:58 PDT)
  - Re: [AMBER] bug report: tinker_to_amberfailedforsystemscontainingcounter ions Amber Amoeba (Wed Apr 10 2013 - 13:52:47 PDT)
[AMBER] The err Install of Amber12 and AmberTools on opensuse 12.3 javacfish (Wed Mar 13 2013 - 10:54:21 PDT)
- Re: [AMBER] The err Install of Amber12 and AmberTools on opensuse 12.3 Jason Swails (Wed Mar 13 2013 - 14:19:14 PDT)
  - Re: [AMBER] The err Install of Amber12 and AmberTools on opensuse 12.3 filip fratev (Wed Mar 13 2013 - 14:55:58 PDT)
    - Re: [AMBER] The err Install of Amber12 and AmberTools on opensuse 12.3 filip fratev (Wed Mar 13 2013 - 15:44:46 PDT)
    - Re: [AMBER] The err Install of Amber12 and AmberTools on opensuse 12.3 javacfish (Thu Mar 14 2013 - 02:05:54 PDT)
  - Re: [AMBER] The err Install of Amber12 and AmberTools on opensuse 12.3 javacfish (Thu Mar 14 2013 - 08:51:21 PDT)
    - Re: [AMBER] The err Install of Amber12 and AmberTools on opensuse 12.3 Jason Swails (Thu Mar 14 2013 - 09:56:37 PDT)
[AMBER] MMPBSA ATP-Mg Chiara Pallara (Wed Mar 13 2013 - 10:54:38 PDT)
- Re: [AMBER] MMPBSA ATP-Mg Jason Swails (Wed Mar 13 2013 - 14:13:24 PDT)
[AMBER] Bad atom type: fe in MMPBSA calculations Cuiyl (Wed Mar 13 2013 - 22:03:59 PDT)
- Re: [AMBER] Bad atom type: fe in MMPBSA calculations siddharth kesharwani (Wed Mar 13 2013 - 22:57:26 PDT)
  - Re: [AMBER] Bad atom type: fe in MMPBSA calculations Cuiyl (Thu Mar 14 2013 - 00:38:10 PDT)
  - Re: [AMBER] Bad atom type: fe in MMPBSA calculations Cuiyl (Thu Mar 14 2013 - 01:57:55 PDT)
    - Re: [AMBER] Bad atom type: fe in MMPBSA calculations siddharth kesharwani (Thu Mar 14 2013 - 02:18:30 PDT)
    - Re: [AMBER] Bad atom type: fe in MMPBSA calculations Cuiyl (Mon Mar 18 2013 - 01:50:13 PDT)
    - Re: [AMBER] Bad atom type: fe in MMPBSA calculations Paul Mortenson (Thu Mar 14 2013 - 03:02:58 PDT)
[AMBER] problem tianchuan881 (Thu Mar 14 2013 - 00:13:54 PDT)
[AMBER] Question about AM1BCC Ismail, Mohd F. (Thu Mar 14 2013 - 00:15:59 PDT)
- Re: [AMBER] Question about AM1BCC steinbrt.rci.rutgers.edu (Thu Mar 14 2013 - 09:40:49 PDT)
[AMBER] angle between two plan . mirage (Thu Mar 14 2013 - 02:10:50 PDT)
- Re: [AMBER] angle between two plan . mirage (Thu Mar 14 2013 - 10:34:34 PDT)
  - Re: [AMBER] angle between two plan Jason Swails (Thu Mar 14 2013 - 11:03:17 PDT)
    - Re: [AMBER] angle between two plan M. L. Dodson (Thu Mar 14 2013 - 11:26:21 PDT)
    - Re: [AMBER] angle between two plan steinbrt.rci.rutgers.edu (Fri Mar 15 2013 - 17:17:52 PDT)
    - Re: [AMBER] angle between two plan M. L. Dodson (Fri Mar 15 2013 - 17:42:47 PDT)
    - Re: [AMBER] angle between two plan . mirage (Sat Mar 16 2013 - 04:04:11 PDT)
    - Re: [AMBER] angle between two plan Jason Swails (Sat Mar 16 2013 - 05:34:19 PDT)
    - Re: [AMBER] angle between two plan Vlad Cojocaru (Sat Mar 16 2013 - 05:59:11 PDT)
    - Re: [AMBER] angle between two plan M. L. Dodson (Sat Mar 16 2013 - 06:37:57 PDT)
    - Re: [AMBER] angle between two plan Bill Ross (Sat Mar 16 2013 - 11:14:49 PDT)
[AMBER] QM/MM restart problem R. Xiong (Thu Mar 14 2013 - 07:42:56 PDT)
- Re: [AMBER] QM/MM restart problem Brian Radak (Thu Mar 14 2013 - 09:26:29 PDT)
  - Re: [AMBER] QM/MM restart problem R. Xiong (Thu Mar 14 2013 - 10:53:09 PDT)
- Re: [AMBER] QM/MM restart problem Gustavo Seabra (Thu Mar 14 2013 - 10:29:55 PDT)
  - Re: [AMBER] QM/MM restart problem R. Xiong (Thu Mar 14 2013 - 11:14:09 PDT)
    - Re: [AMBER] QM/MM restart problem Matthew Zwier (Thu Mar 14 2013 - 11:54:59 PDT)
    - Re: [AMBER] QM/MM restart problem R. Xiong (Thu Mar 14 2013 - 12:23:00 PDT)
    - Re: [AMBER] QM/MM restart problem M. L. Dodson (Thu Mar 14 2013 - 12:49:54 PDT)
    - Re: [AMBER] QM/MM restart problem R. Xiong (Thu Mar 14 2013 - 13:13:57 PDT)
    - Re: [AMBER] QM/MM restart problem Gustavo Seabra (Thu Mar 14 2013 - 13:45:30 PDT)
    - Re: [AMBER] QM/MM restart problem R. Xiong (Thu Mar 14 2013 - 14:01:18 PDT)
[AMBER] PMEMD in amber12 Mary Varughese (Thu Mar 14 2013 - 08:04:05 PDT)
- [AMBER] RE : PMEMD in amber12 ABEL Stephane 175950 (Thu Mar 14 2013 - 08:34:16 PDT)
- Re: [AMBER] PMEMD in amber12 Ross Walker (Thu Mar 14 2013 - 08:46:16 PDT)
  - Re: [AMBER] PMEMD in amber12 Mary Varughese (Thu Mar 14 2013 - 20:20:54 PDT)
    - Re: [AMBER] PMEMD in amber12 Jason Swails (Fri Mar 15 2013 - 06:49:11 PDT)
    - Re: [AMBER] PMEMD in amber12 Ross Walker (Fri Mar 15 2013 - 08:27:42 PDT)
    - Re: [AMBER] PMEMD in amber12 Mary Varughese (Fri Mar 15 2013 - 09:23:53 PDT)
    - Re: [AMBER] PMEMD in amber12 Ross Walker (Fri Mar 15 2013 - 09:27:31 PDT)
    - Re: [AMBER] PMEMD in amber12 Mary Varughese (Fri Mar 15 2013 - 10:01:20 PDT)
    - Re: [AMBER] PMEMD in amber12 Mary Varughese (Mon Mar 18 2013 - 10:58:36 PDT)
    - Re: [AMBER] PMEMD in amber12 Ross Walker (Mon Mar 18 2013 - 16:34:09 PDT)
    - Re: [AMBER] PMEMD in amber12 Mary Varughese (Mon Mar 18 2013 - 22:31:27 PDT)
[AMBER] ptraj skipping frames depending on the computer OS? Miguel Ortiz Lombardía (Thu Mar 14 2013 - 08:31:59 PDT)
- Re: [AMBER] ptraj skipping frames depending on the computer OS? Miguel Ortiz Lombardía (Fri Mar 15 2013 - 03:08:35 PDT)
  - Re: [AMBER] ptraj skipping frames depending on the computer OS? Daniel Roe (Fri Mar 15 2013 - 08:49:55 PDT)
[AMBER] REMD simulation sudipta (Thu Mar 14 2013 - 10:06:51 PDT)
- Re: [AMBER] REMD simulation Niel Henriksen (Thu Mar 14 2013 - 15:51:42 PDT)
  - Re: [AMBER] REMD simulation sudipta (Thu Mar 14 2013 - 16:07:41 PDT)
    - Re: [AMBER] REMD simulation Bill Ross (Thu Mar 14 2013 - 16:12:20 PDT)
    - Re: [AMBER] REMD simulation sudipta (Thu Mar 14 2013 - 16:28:52 PDT)
    - Re: [AMBER] REMD simulation Bill Ross (Thu Mar 14 2013 - 16:47:55 PDT)
    - Re: [AMBER] REMD simulation sudipta (Fri Mar 15 2013 - 09:24:35 PDT)
    - Re: [AMBER] REMD simulation Jason Swails (Thu Mar 14 2013 - 16:43:06 PDT)
    - Re: [AMBER] REMD simulation sudipta (Thu Mar 14 2013 - 16:51:42 PDT)
    - Re: [AMBER] REMD simulation Niel Henriksen (Thu Mar 14 2013 - 18:39:13 PDT)
    - Re: [AMBER] REMD simulation sudipta (Fri Mar 15 2013 - 09:25:31 PDT)
    - Re: [AMBER] REMD simulation Carlos Simmerling (Fri Mar 15 2013 - 09:03:05 PDT)
[AMBER] Cofactor GDP Atom Types Ahmed Ayoub (Thu Mar 14 2013 - 12:22:40 PDT)
- Re: [AMBER] Cofactor GDP Atom Types Daniel Roe (Fri Mar 15 2013 - 08:07:40 PDT)
[AMBER] organic 纪晓峰 (Fri Mar 15 2013 - 00:37:47 PDT)
[AMBER] the protein was crashed 纪晓峰 (Fri Mar 15 2013 - 00:44:55 PDT)
- Re: [AMBER] the protein was crashed David A Case (Fri Mar 15 2013 - 04:52:37 PDT)
- Re: [AMBER] the protein was crashed 纪晓峰 (Mon Mar 25 2013 - 19:23:24 PDT)
- Re: [AMBER] the protein was crashed 纪晓峰 (Mon Mar 25 2013 - 19:24:25 PDT)
[AMBER] modified dna Mary Varughese (Fri Mar 15 2013 - 02:45:49 PDT)
- Re: [AMBER] modified dna Jason Swails (Fri Mar 15 2013 - 06:50:18 PDT)
[AMBER] Regarding MSD calculations in ptraj DEBOSTUTI GHOSHDASTIDAR (Fri Mar 15 2013 - 03:32:32 PDT)
- Re: [AMBER] Regarding MSD calculations in ptraj Daniel Roe (Fri Mar 15 2013 - 08:16:17 PDT)
  - Re: [AMBER] Regarding MSD calculations in ptraj DEBOSTUTI GHOSHDASTIDAR (Fri Mar 15 2013 - 22:56:15 PDT)
[AMBER] Hydration Free Enery by TI Kepa K. Burusco (Fri Mar 15 2013 - 10:06:25 PDT)
- Re: [AMBER] Hydration Free Enery by TI steinbrt.rci.rutgers.edu (Fri Mar 15 2013 - 17:28:29 PDT)
  - Re: [AMBER] Hydration Free Enery by TI Kepa K. Burusco (Mon Mar 18 2013 - 09:11:32 PDT)
  - Re: [AMBER] Hydration Free Enery by TI Kepa K. Burusco (Mon Mar 18 2013 - 09:28:18 PDT)
    - Re: [AMBER] Hydration Free Enery by TI steinbrt.rci.rutgers.edu (Tue Mar 19 2013 - 04:00:39 PDT)
  - Re: [AMBER] Hydration Free Enery by TI Ignacio J. General (Mon Mar 18 2013 - 10:07:36 PDT)
    - Re: [AMBER] Hydration Free Enery by TI steinbrt.rci.rutgers.edu (Tue Mar 19 2013 - 04:07:27 PDT)
    - Re: [AMBER] Hydration Free Enery by TI Kepa K. Burusco (Tue Mar 19 2013 - 12:27:18 PDT)
    - Re: [AMBER] Hydration Free Enery by TI steinbrt.rci.rutgers.edu (Wed Mar 20 2013 - 02:36:19 PDT)
    - Re: [AMBER] Hydration Free Enery by TI Kepa K. Burusco (Wed Mar 20 2013 - 04:50:32 PDT)
[AMBER] Amber 9 pooja chahal (Fri Mar 15 2013 - 20:54:22 PDT)
- Re: [AMBER] Amber 9 Jason Swails (Sat Mar 16 2013 - 07:25:04 PDT)
[AMBER] problem in generating pbsa.phi file using PBSA N Nandi (Sun Mar 17 2013 - 22:15:37 PDT)
- Re: [AMBER] problem in generating pbsa.phi file using PBSA Ray Luo, Ph.D. (Mon Mar 18 2013 - 14:38:31 PDT)
- Re: [AMBER] problem in generating pbsa.phi file using PBSA Ray Luo, Ph.D. (Tue Mar 19 2013 - 15:10:19 PDT)
[AMBER] GPU job scheduling: looking for recommendations and experiences Jan-Philip Gehrcke (Mon Mar 18 2013 - 06:35:07 PDT)
- Re: [AMBER] GPU job scheduling: looking for recommendations and experiences Ross Walker (Mon Mar 18 2013 - 08:04:03 PDT)
  - Re: [AMBER] GPU job scheduling: looking for recommendations and experiences Jonathan Gough (Mon Mar 18 2013 - 09:10:16 PDT)
    - Re: [AMBER] GPU job scheduling: looking for recommendations and experiences Jan-Philip Gehrcke (Fri Apr 05 2013 - 07:35:41 PDT)
[AMBER] no restrains? Albert (Mon Mar 18 2013 - 06:43:30 PDT)
- Re: [AMBER] no restrains? David A Case (Mon Mar 18 2013 - 07:40:21 PDT)
  - Re: [AMBER] no restrains? Albert (Mon Mar 18 2013 - 07:44:10 PDT)
[AMBER] ions (salt concentration) and deep energetics problem Neha Gandhi (Mon Mar 18 2013 - 07:04:24 PDT)
- Re: [AMBER] ions (salt concentration) and deep energetics problem kurisaki (Mon Mar 18 2013 - 17:40:59 PDT)
- Re: [AMBER] ions (salt concentration) and deep energetics problem David A Case (Tue Mar 19 2013 - 05:11:05 PDT)
[AMBER] NVT stacked at GPU running Albert (Mon Mar 18 2013 - 08:51:44 PDT)
- Re: [AMBER] NVT stacked at GPU running Ross Walker (Mon Mar 18 2013 - 09:17:51 PDT)
  - Re: [AMBER] NVT stacked at GPU running Scott Le Grand (Mon Mar 18 2013 - 09:22:34 PDT)
    - Re: [AMBER] NVT stacked at GPU running Albert (Mon Mar 18 2013 - 11:09:05 PDT)
  - Re: [AMBER] NVT stacked at GPU running Albert (Mon Mar 18 2013 - 11:10:24 PDT)
    - Re: [AMBER] NVT stacked at GPU running Albert (Mon Mar 18 2013 - 13:17:42 PDT)
    - Re: [AMBER] NVT stacked at GPU running Ross Walker (Mon Mar 18 2013 - 15:49:24 PDT)
    - Re: [AMBER] NVT stacked at GPU running Albert (Sat Mar 23 2013 - 01:45:30 PDT)
    - Re: [AMBER] NVT stacked at GPU running Ross Walker (Sat Mar 23 2013 - 10:18:01 PDT)
[AMBER] COM support with GPU Fabrício Bracht (Mon Mar 18 2013 - 12:04:27 PDT)
- Re: [AMBER] COM support with GPU Adrian Roitberg (Mon Mar 18 2013 - 12:17:15 PDT)
[AMBER] can we specify mpi path in ./configure? Albert (Mon Mar 18 2013 - 13:30:28 PDT)
- Re: [AMBER] can we specify mpi path in ./configure? Daniel Roe (Mon Mar 18 2013 - 14:39:30 PDT)
- Re: [AMBER] can we specify mpi path in ./configure? David A Case (Mon Mar 18 2013 - 18:09:11 PDT)
  - Re: [AMBER] can we specify mpi path in ./configure? Albert (Tue Mar 19 2013 - 00:38:52 PDT)
    - Re: [AMBER] can we specify mpi path in ./configure? Jan-Philip Gehrcke (Tue Mar 19 2013 - 03:28:51 PDT)
    - Re: [AMBER] can we specify mpi path in ./configure? Albert (Tue Mar 19 2013 - 03:40:17 PDT)
[AMBER] Problem with Alanine Scanning using MMPBSA.py with Terminal Residues Yew Mun Yip (Mon Mar 18 2013 - 20:54:52 PDT)
- Re: [AMBER] Problem with Alanine Scanning using MMPBSA.py with Terminal Residues Jason Swails (Tue Mar 19 2013 - 07:31:28 PDT)
[AMBER] how to save a snapshot from the trajectory Sindrila Dutta banik (Mon Mar 18 2013 - 23:25:07 PDT)
- Re: [AMBER] how to save a snapshot from the trajectory Benjamin D Madej (Tue Mar 19 2013 - 10:46:48 PDT)
- Re: [AMBER] how to save a snapshot from the trajectory Daniel Roe (Tue Mar 19 2013 - 13:00:58 PDT)
[AMBER] urea frcmod file gargi borgohai (Tue Mar 19 2013 - 00:17:29 PDT)
- Re: [AMBER] urea frcmod file FyD (Tue Mar 19 2013 - 05:50:56 PDT)
[AMBER] problem combining trajectories with diff. number of residues Vaibhav Dixit (Tue Mar 19 2013 - 00:28:12 PDT)
- Re: [AMBER] problem combining trajectories with diff. number of residues David A Case (Tue Mar 19 2013 - 04:56:21 PDT)
  - Re: [AMBER] problem combining trajectories with diff. number of residues Vaibhav Dixit (Tue Mar 19 2013 - 21:33:36 PDT)
- Re: [AMBER] problem combining trajectories with diff. number of residues Daniel Roe (Wed Mar 20 2013 - 07:59:59 PDT)
  - Re: [AMBER] problem combining trajectories with diff. number of residues Vaibhav Dixit (Wed Mar 20 2013 - 22:07:03 PDT)
    - Re: [AMBER] problem combining trajectories with diff. number of residues Daniel Roe (Thu Mar 21 2013 - 07:35:12 PDT)
    - Re: [AMBER] problem combining trajectories with diff. number of residues Vaibhav Dixit (Tue Mar 26 2013 - 04:11:28 PDT)
    - Re: [AMBER] problem combining trajectories with diff. number of residues Daniel Roe (Tue Mar 26 2013 - 07:55:08 PDT)
    - Re: [AMBER] problem combining trajectories with diff. number of residues Vaibhav Dixit (Tue Mar 26 2013 - 20:20:01 PDT)
[AMBER] Antechamber: AM1-BCC charges from MOPAC output Miro Moman (Tue Mar 19 2013 - 02:05:03 PDT)
- Re: [AMBER] Antechamber: AM1-BCC charges from MOPAC output David A Case (Tue Mar 19 2013 - 05:01:59 PDT)
[AMBER] Error while generating B factor Graph Sumra Wajid Abbasi 30-FBAS/MSBI/F09 (Tue Mar 19 2013 - 02:55:10 PDT)
- Re: [AMBER] Error while generating B factor Graph Daniel Roe (Tue Mar 19 2013 - 13:16:44 PDT)
[AMBER] tutorial on thermodynamic integration Shruti Koulgi (Tue Mar 19 2013 - 04:44:53 PDT)
[AMBER] IED web link to essential dynamics is broken Vaibhav Dixit (Tue Mar 19 2013 - 05:20:49 PDT)
- Re: [AMBER] IED web link to essential dynamics is broken Vlad Cojocaru (Tue Mar 19 2013 - 06:40:49 PDT)
- Re: [AMBER] IED web link to essential dynamics is broken David A Case (Sat Mar 23 2013 - 07:11:11 PDT)
  - Re: [AMBER] IED web link to essential dynamics is broken Vaibhav Dixit (Sat Mar 23 2013 - 21:34:50 PDT)
    - Re: [AMBER] IED web link to essential dynamics is broken David A Case (Mon Mar 25 2013 - 04:55:14 PDT)
[AMBER] Problem to save a particular snapshot from the trajectory Sindrila Dutta banik (Tue Mar 19 2013 - 05:56:01 PDT)
- Re: [AMBER] Problem to save a particular snapshot from the trajectory David A Case (Tue Mar 19 2013 - 07:39:32 PDT)
[AMBER] why no periodic information? Albert (Tue Mar 19 2013 - 07:00:52 PDT)
- Re: [AMBER] why no periodic information? Kshatresh Dutta Dubey (Tue Mar 19 2013 - 07:21:10 PDT)
  - Re: [AMBER] why no periodic information? Albert (Tue Mar 19 2013 - 07:48:29 PDT)
    - Re: [AMBER] why no periodic information? Brian Radak (Tue Mar 19 2013 - 10:11:13 PDT)
[AMBER] Meaning of electrostatic pairwise interaction in GB/PBSA Josep Maria Campanera Alsina (Tue Mar 19 2013 - 08:00:55 PDT)
- Re: [AMBER] Meaning of electrostatic pairwise interaction in GB/PBSA Jason Swails (Wed Mar 20 2013 - 07:03:35 PDT)
  - Re: [AMBER] Meaning of electrostatic pairwise interaction in GB/PBSA Jason Swails (Wed Mar 20 2013 - 07:05:05 PDT)
    - Re: [AMBER] Meaning of electrostatic pairwise interaction in GB/PBSA steinbrt.rci.rutgers.edu (Wed Mar 20 2013 - 07:20:35 PDT)
[AMBER] Ante-mmpbsa.py error Vivek Shankar Bharadwaj (Tue Mar 19 2013 - 10:22:57 PDT)
- Re: [AMBER] Ante-mmpbsa.py error Jason Swails (Tue Mar 19 2013 - 13:01:14 PDT)
[AMBER] Trouble with MM-PBSA calculations in large complex Amy Davenport (Tue Mar 19 2013 - 17:27:19 PDT)
- Re: [AMBER] Trouble with MM-PBSA calculations in large complex Jason Swails (Wed Mar 20 2013 - 06:04:41 PDT)
[AMBER] How protein-water electrostatic interaction can be turned off keeping protein-protein vdw, protein-protein (vdw+elect) and water-water (vdw+elect) intact somedatta pal (Wed Mar 20 2013 - 03:28:42 PDT)
- Re: [AMBER] How protein-water electrostatic interaction can be turned off keeping protein-protein vdw, protein-protein (vdw+elect) and water-water (vdw+elect) intact steinbrt.rci.rutgers.edu (Wed Mar 20 2013 - 03:34:02 PDT)
[AMBER] solvating and neutralizing a lipid bilayer John Gehman (Wed Mar 20 2013 - 07:16:11 PDT)
- Re: [AMBER] solvating and neutralizing a lipid bilayer Daniel Roe (Wed Mar 20 2013 - 07:40:35 PDT)
  - Re: [AMBER] solvating and neutralizing a lipid bilayer John Gehman (Wed Mar 20 2013 - 08:28:00 PDT)
[AMBER] mmpbsa calculations on a PROTEIN/DNA/LIGAND ternary complex Giulia Palermo (Wed Mar 20 2013 - 10:33:11 PDT)
- Re: [AMBER] mmpbsa calculations on a PROTEIN/DNA/LIGAND ternary complex Miguel Ortiz Lombardia (Wed Mar 20 2013 - 10:52:29 PDT)
  - Re: [AMBER] mmpbsa calculations on a PROTEIN/DNA/LIGAND ternary complex Giulia (Thu Mar 21 2013 - 02:14:13 PDT)
    - Re: [AMBER] mmpbsa calculations on a PROTEIN/DNA/LIGAND ternary complex Miguel Ortiz Lombardía (Thu Mar 21 2013 - 03:18:57 PDT)
    - [AMBER] R: mmpbsa calculations on a PROTEIN/DNA/LIGAND ternary complex Giulia Palermo (Thu Mar 21 2013 - 07:08:02 PDT)
    - Re: [AMBER] R: mmpbsa calculations on a PROTEIN/DNA/LIGAND ternary complex Miguel Ortiz Lombardía (Thu Mar 21 2013 - 07:44:20 PDT)
[AMBER] pmemd.cuda compilation problems on Ubuntu 12.4 Weinzierl, Robert O J (Wed Mar 20 2013 - 10:56:51 PDT)
- Re: [AMBER] pmemd.cuda compilation problems on Ubuntu 12.4 Jan-Philip Gehrcke (Wed Mar 20 2013 - 11:38:40 PDT)
- Re: [AMBER] pmemd.cuda compilation problems on Ubuntu 12.4 Daniel Roe (Wed Mar 20 2013 - 12:15:31 PDT)
Re: [AMBER] AMBER Digest, Vol 457, Issue 1 Amy Davenport (Wed Mar 20 2013 - 12:48:36 PDT)
[AMBER] How to use AMBER parameters for modified amino acids Symon Gathiaka (Wed Mar 20 2013 - 14:27:37 PDT)
- Re: [AMBER] How to use AMBER parameters for modified amino acids David A Case (Thu Mar 21 2013 - 05:29:14 PDT)
  - Re: [AMBER] How to use AMBER parameters for modified amino acids Symon Gathiaka (Sat Mar 23 2013 - 10:38:43 PDT)
[AMBER] how can we plot energy profile for REMD? Albert (Thu Mar 21 2013 - 01:51:11 PDT)
[AMBER] aMD simulations in AMBER 12 (GPU version) Neha Gandhi (Thu Mar 21 2013 - 03:26:44 PDT)
- Re: [AMBER] aMD simulations in AMBER 12 (GPU version) Daniel Roe (Thu Mar 21 2013 - 09:42:27 PDT)
[AMBER] GLYCAM-Web server disruptions Lachele Foley (Thu Mar 21 2013 - 07:17:38 PDT)
[AMBER] mmpbsa calculations for a ternary protein/dna/ligand complex in presence of cocrystalized Mg ions Giulia (Thu Mar 21 2013 - 08:26:00 PDT)
- Re: [AMBER] mmpbsa calculations for a ternary protein/dna/ligand complex in presence of cocrystalized Mg ions Jason Swails (Thu Mar 21 2013 - 08:36:19 PDT)
  - Re: [AMBER] mmpbsa calculations for a ternary protein/dna/ligand complex in presence of cocrystalized Mg ions Miguel Ortiz Lombardía (Thu Mar 21 2013 - 08:52:58 PDT)
    - Re: [AMBER] mmpbsa calculations for a ternary protein/dna/ligand complex in presence of cocrystalized Mg ions Jason Swails (Thu Mar 21 2013 - 15:37:54 PDT)
    - [AMBER] R: mmpbsa calculations for a ternary protein/dna/ligand complex Giulia (Fri Mar 22 2013 - 02:18:26 PDT)
    - Re: [AMBER] R: mmpbsa calculations for a ternary protein/dna/ligand complex Miguel Ortiz Lombardía (Fri Mar 22 2013 - 03:32:02 PDT)
Re: [AMBER] Trouble with MM-PBSA calculations in large complex Amy Davenport (Thu Mar 21 2013 - 12:05:12 PDT)
- Re: [AMBER] Trouble with MM-PBSA calculations in large complex Jason Swails (Thu Mar 21 2013 - 15:34:45 PDT)
[AMBER] RXSGLD Simulation Error Mark Healey (Thu Mar 21 2013 - 12:53:27 PDT)
- [AMBER] RXSGLD Simulation Error Mark Healey (Fri Mar 22 2013 - 13:05:49 PDT)
  - Re: [AMBER] RXSGLD Simulation Error Jason Swails (Fri Mar 22 2013 - 15:51:14 PDT)
Re: [AMBER] aMD simulations in AMBER 12 (GPU version) update Neha Gandhi (Thu Mar 21 2013 - 17:20:26 PDT)
- Re: [AMBER] aMD simulations in AMBER 12 (GPU version) update Jason Swails (Thu Mar 21 2013 - 17:55:56 PDT)
[AMBER] Which memory of GTX580 should I choose in 30, 000-50, 000 atoms system Mu Xia (Thu Mar 21 2013 - 20:24:55 PDT)
- Re: [AMBER] Which memory of GTX580 should I choose in 30, 000-50, 000 atoms system Aron Broom (Thu Mar 21 2013 - 20:32:40 PDT)
- Re: [AMBER] Which memory of GTX580 should I choose in 30, 000-50, 000 atoms system Ross Walker (Fri Mar 22 2013 - 11:14:35 PDT)
[AMBER] amber12 remd problem and solution recompiling sander.MPI with AMBERBUILDFLAGS -DVERBOSE_REM Guillermo Mulliert Carlín (Fri Mar 22 2013 - 00:21:01 PDT)
[AMBER] problem in generating pbsa.phi file using PBSA N Nandi (Fri Mar 22 2013 - 01:57:55 PDT)
[AMBER] can we calculate them together? Albert (Fri Mar 22 2013 - 07:44:32 PDT)
[AMBER] leap - removing terminals problem Ignacio J. General (Fri Mar 22 2013 - 08:59:32 PDT)
- Re: [AMBER] leap - removing terminals problem Daniel Roe (Fri Mar 22 2013 - 09:15:45 PDT)
  - Re: [AMBER] leap - removing terminals problem Ignacio J. General (Fri Mar 22 2013 - 09:59:08 PDT)
- Re: [AMBER] leap - removing terminals problem Jason Swails (Fri Mar 22 2013 - 10:05:09 PDT)
[AMBER] Langevin Dynamics George Tzotzos (Fri Mar 22 2013 - 12:00:27 PDT)
- Re: [AMBER] Langevin Dynamics David A Case (Fri Mar 22 2013 - 13:06:51 PDT)
  - Re: [AMBER] Langevin Dynamics George Tzotzos (Fri Mar 22 2013 - 13:56:54 PDT)
[AMBER] SMD centre of the restraint George Tzotzos (Sat Mar 23 2013 - 14:51:21 PDT)
- Re: [AMBER] SMD centre of the restraint Jason Swails (Sat Mar 23 2013 - 19:24:37 PDT)
[AMBER] one sided connection warning HEM P450 MD input files Vaibhav Dixit (Sat Mar 23 2013 - 22:53:15 PDT)
- Re: [AMBER] one sided connection warning HEM P450 MD input files Vaibhav Dixit (Thu Mar 28 2013 - 22:17:19 PDT)
[AMBER] how can we calculate average dihedral for aMD? Albert (Sun Mar 24 2013 - 04:41:17 PDT)
- Re: [AMBER] how can we calculate average dihedral for aMD? David A Case (Sun Mar 24 2013 - 08:17:11 PDT)
  - Re: [AMBER] how can we calculate average dihedral for aMD? Albert (Sun Mar 24 2013 - 09:30:52 PDT)
  - Re: [AMBER] how can we calculate average dihedral for aMD? Albert (Sun Mar 24 2013 - 09:45:57 PDT)
[AMBER] how to plot CA matrix? Albert (Sun Mar 24 2013 - 05:14:00 PDT)
[AMBER] patching unsuccessful even after modifying patch_amber.py Vaibhav Dixit (Sun Mar 24 2013 - 05:17:50 PDT)
- Re: [AMBER] patching unsuccessful even after modifying patch_amber.py Jason Swails (Sun Mar 24 2013 - 17:12:25 PDT)
- Re: [AMBER] patching unsuccessful even after modifying patch_amber.py Jason Swails (Sun Mar 24 2013 - 17:19:17 PDT)
  - Re: [AMBER] patching unsuccessful even after modifying patch_amber.py Vaibhav Dixit (Sun Mar 24 2013 - 22:43:41 PDT)
    - Re: [AMBER] patching unsuccessful even after modifying patch_amber.py Vaibhav Dixit (Sun Mar 24 2013 - 23:04:02 PDT)
    - Re: [AMBER] patching unsuccessful even after modifying patch_amber.py Jason Swails (Mon Mar 25 2013 - 03:03:44 PDT)
    - Re: [AMBER] patching unsuccessful even after modifying patch_amber.py Vaibhav Dixit (Mon Mar 25 2013 - 03:17:05 PDT)
    - Re: [AMBER] patching unsuccessful even after modifying patch_amber.py Jan-Philip Gehrcke (Mon Mar 25 2013 - 03:32:06 PDT)
    - Re: [AMBER] patching unsuccessful even after modifying patch_amber.py Vaibhav Dixit (Mon Mar 25 2013 - 03:49:36 PDT)
    - Re: [AMBER] patching unsuccessful even after modifying patch_amber.py Jan-Philip Gehrcke (Mon Mar 25 2013 - 04:05:20 PDT)
    - Re: [AMBER] patching unsuccessful even after modifying patch_amber.py Jason Swails (Mon Mar 25 2013 - 04:21:00 PDT)
    - Re: [AMBER] patching unsuccessful even after modifying patch_amber.py Vaibhav Dixit (Mon Mar 25 2013 - 06:16:53 PDT)
    - Re: [AMBER] patching unsuccessful even after modifying patch_amber.py Jason Swails (Mon Mar 25 2013 - 06:24:16 PDT)
    - Re: [AMBER] patching unsuccessful even after modifying patch_amber.py Vaibhav Dixit (Mon Mar 25 2013 - 06:26:41 PDT)
    - Re: [AMBER] patching unsuccessful even after modifying patch_amber.py Jan-Philip Gehrcke (Mon Mar 25 2013 - 06:31:46 PDT)
[AMBER] Amber release time table Jonathan Gough (Sun Mar 24 2013 - 12:11:01 PDT)
- Re: [AMBER] Amber release time table David A Case (Sun Mar 24 2013 - 13:10:17 PDT)
[AMBER] '.' follows exponent in NUMBER-like thing Yun Shi (Sun Mar 24 2013 - 12:15:15 PDT)
- Re: [AMBER] '.' follows exponent in NUMBER-like thing David A Case (Mon Mar 25 2013 - 04:48:49 PDT)
[AMBER] membrane protein modeling Kong, Ren (Sun Mar 24 2013 - 16:55:38 PDT)
- Re: [AMBER] membrane protein modeling Benjamin D Madej (Sun Mar 24 2013 - 22:15:34 PDT)
[AMBER] the prpblem in constructing the close circular DNA llduan (Sun Mar 24 2013 - 18:02:42 PDT)
- Re: [AMBER] the prpblem in constructing the close circular DNA David A Case (Mon Mar 25 2013 - 04:47:29 PDT)
Re: [AMBER] Amber Digest, Vol. 458, Issue 1, Topic 1 pmemd.cuda compilation problems on Ubuntu 12.4 (Daniel Roe) Weinzierl, Robert O J (Mon Mar 25 2013 - 04:01:10 PDT)
[AMBER] Fwd: cudaMemcpy GpuBuffer::Download failed Alessandro Orro (Mon Mar 25 2013 - 05:06:13 PDT)
- Re: [AMBER] Fwd: cudaMemcpy GpuBuffer::Download failed Ross Walker (Mon Mar 25 2013 - 10:22:05 PDT)
  - Re: [AMBER] Fwd: cudaMemcpy GpuBuffer::Download failed Scott Le Grand (Mon Mar 25 2013 - 10:32:07 PDT)
    - Re: [AMBER] Fwd: cudaMemcpy GpuBuffer::Download failed Ross Walker (Mon Mar 25 2013 - 10:35:11 PDT)
[AMBER] problems in parameters calculated with AMBER Anna MARABOTTI (Mon Mar 25 2013 - 05:12:09 PDT)
- Re: [AMBER] problems in parameters calculated with AMBER Jason Swails (Mon Mar 25 2013 - 05:27:59 PDT)
- [AMBER] RE : problems in parameters calculated with AMBER ABEL Stephane 175950 (Mon Mar 25 2013 - 05:30:35 PDT)
- Re: [AMBER] problems in parameters calculated with AMBER Anna Marabotti (Tue Mar 26 2013 - 02:41:00 PDT)
  - Re: [AMBER] problems in parameters calculated with AMBER Brian Radak (Tue Mar 26 2013 - 09:14:09 PDT)
[AMBER] problem in running antechamber Anshuman Dixit (Tue Mar 26 2013 - 00:39:08 PDT)
- Re: [AMBER] problem in running antechamber M. L. Dodson (Tue Mar 26 2013 - 02:22:14 PDT)
[AMBER] residue-wise SASA calculation in CPPTRAJ aneesh cna (Tue Mar 26 2013 - 03:08:48 PDT)
- Re: [AMBER] residue-wise SASA calculation in CPPTRAJ Jason Swails (Tue Mar 26 2013 - 04:54:31 PDT)
  - Re: [AMBER] residue-wise SASA calculation in CPPTRAJ Daniel Roe (Tue Mar 26 2013 - 07:40:20 PDT)
[AMBER] cpptraj Ignacio J. General (Tue Mar 26 2013 - 07:25:58 PDT)
- Re: [AMBER] cpptraj Daniel Roe (Tue Mar 26 2013 - 07:34:29 PDT)
  - Re: [AMBER] cpptraj Ignacio J. General (Tue Mar 26 2013 - 07:38:39 PDT)
    - Re: [AMBER] cpptraj Daniel Roe (Tue Mar 26 2013 - 07:48:00 PDT)
    - Re: [AMBER] cpptraj Jason Swails (Tue Mar 26 2013 - 07:50:39 PDT)
    - Re: [AMBER] cpptraj Vaibhav Dixit (Tue Mar 26 2013 - 20:33:11 PDT)
[AMBER] Question about 'sequence' command Ismail, Mohd F. (Tue Mar 26 2013 - 22:47:34 PDT)
- Re: [AMBER] Question about 'sequence' command Ismail, Mohd F. (Tue Mar 26 2013 - 22:57:16 PDT)
[AMBER] aMD job failed Albert (Wed Mar 27 2013 - 00:21:05 PDT)
- Re: [AMBER] aMD job failed Jason Swails (Wed Mar 27 2013 - 07:32:56 PDT)
  - Re: [AMBER] aMD job failed Albert (Wed Mar 27 2013 - 08:37:21 PDT)
[AMBER] minor development note: make symbolic link to pmemd.cuda relative instead of absolute Jan-Philip Gehrcke (Wed Mar 27 2013 - 05:26:40 PDT)
- Re: [AMBER] minor development note: make symbolic link to pmemd.cuda relative instead of absolute Ross Walker (Wed Mar 27 2013 - 11:07:10 PDT)
[AMBER] MMPBSA calculations Chinthaka Ratnaweera (Wed Mar 27 2013 - 09:08:20 PDT)
- Re: [AMBER] MMPBSA calculations Jason Swails (Wed Mar 27 2013 - 09:48:43 PDT)
  - Re: [AMBER] MMPBSA calculations Chinthaka Ratnaweera (Wed Mar 27 2013 - 10:46:39 PDT)
    - Re: [AMBER] MMPBSA calculations Ray Luo, Ph.D. (Wed Mar 27 2013 - 11:02:45 PDT)
    - Re: [AMBER] MMPBSA calculations Chinthaka Ratnaweera (Wed Mar 27 2013 - 14:01:10 PDT)
    - Re: [AMBER] MMPBSA calculations Ray Luo, Ph.D. (Wed Mar 27 2013 - 14:11:30 PDT)
    - Re: [AMBER] MMPBSA calculations Jason Swails (Wed Mar 27 2013 - 11:31:50 PDT)
[AMBER] RMSD with ptraj fit vs unfit HIMANSHU JOSHI (Wed Mar 27 2013 - 10:17:38 PDT)
- Re: [AMBER] RMSD with ptraj fit vs unfit Daniel Roe (Wed Mar 27 2013 - 10:22:11 PDT)
- Re: [AMBER] RMSD with ptraj fit vs unfit Aron Broom (Wed Mar 27 2013 - 10:22:35 PDT)
  - Re: [AMBER] RMSD with ptraj fit vs unfit HIMANSHU JOSHI (Wed Mar 27 2013 - 23:07:31 PDT)
[AMBER] Histidine problem Changqing Yan (Wed Mar 27 2013 - 20:18:15 PDT)
- Re: [AMBER] Histidine problem Aron Broom (Wed Mar 27 2013 - 20:41:57 PDT)
[AMBER] Generating PDB files with atom radii information aneesh cna (Wed Mar 27 2013 - 22:01:18 PDT)
- Re: [AMBER] Generating PDB files with atom radii information Bill Ross (Wed Mar 27 2013 - 22:32:23 PDT)
  - Re: [AMBER] Generating PDB files with atom radii information aneesh cna (Thu Mar 28 2013 - 02:25:50 PDT)
    - Re: [AMBER] Generating PDB files with atom radii information Jason Swails (Thu Mar 28 2013 - 05:46:51 PDT)
    - Re: [AMBER] Generating PDB files with atom radii information Daniel Roe (Thu Mar 28 2013 - 07:12:32 PDT)
    - Re: [AMBER] Generating PDB files with atom radii information aneesh cna (Thu Mar 28 2013 - 22:20:40 PDT)
    - Re: [AMBER] Generating PDB files with atom radii information Bill Ross (Fri Mar 29 2013 - 16:07:45 PDT)
    - Re: [AMBER] Generating PDB files with atom radii information Bill Ross (Fri Mar 29 2013 - 16:03:13 PDT)
    - Re: [AMBER] Generating PDB files with atom radii information David A Case (Sat Mar 30 2013 - 07:52:51 PDT)
[AMBER] How to implement QM/MM-PBSA method in Amber 11 with AmberTools 12 dbaogen (Wed Mar 27 2013 - 23:36:58 PDT)
- Re: [AMBER] How to implement QM/MM-PBSA method in Amber 11 with AmberTools 12 Jason Swails (Thu Mar 28 2013 - 05:32:01 PDT)
[AMBER] strange output information Albert (Thu Mar 28 2013 - 03:02:53 PDT)
- Re: [AMBER] strange output information Daniel Roe (Thu Mar 28 2013 - 06:02:19 PDT)
[AMBER] ff10 with ILDN + Best&Hummer modifications Vlad Cojocaru (Thu Mar 28 2013 - 03:56:59 PDT)
- Re: [AMBER] ff10 with ILDN + Best&Hummer modifications Jason Swails (Thu Mar 28 2013 - 05:20:02 PDT)
  - Re: [AMBER] ff10 with ILDN + Best&Hummer modifications Vlad Cojocaru (Thu Mar 28 2013 - 07:17:39 PDT)
[AMBER] MM PBSA tutorial rajith bhaskaran (Thu Mar 28 2013 - 05:42:42 PDT)
- Re: [AMBER] MM PBSA tutorial steinbrt.rci.rutgers.edu (Thu Mar 28 2013 - 05:46:31 PDT)
- Re: [AMBER] MM PBSA tutorial Jason Swails (Thu Mar 28 2013 - 05:54:14 PDT)
- Re: [AMBER] MM PBSA tutorial rajith bhaskaran (Thu Mar 28 2013 - 05:55:43 PDT)
- Re: [AMBER] MM PBSA tutorial rajith bhaskaran (Thu Mar 28 2013 - 06:03:12 PDT)
- Re: [AMBER] MM PBSA tutorial steinbrt.rci.rutgers.edu (Thu Mar 28 2013 - 06:16:56 PDT)
  - Re: [AMBER] MM PBSA tutorial Jason Swails (Thu Mar 28 2013 - 06:37:04 PDT)
- Re: [AMBER] MM PBSA tutorial rajith bhaskaran (Thu Mar 28 2013 - 06:26:16 PDT)
- Re: [AMBER] MM PBSA tutorial steinbrt.rci.rutgers.edu (Thu Mar 28 2013 - 08:05:40 PDT)
[AMBER] PB Bomb in pb_aaradi(): No radius assigned for atom 530 C5' CI Xioling Chuang (Thu Mar 28 2013 - 08:25:51 PDT)
- Re: [AMBER] PB Bomb in pb_aaradi(): No radius assigned for atom 530 C5' CI Jason Swails (Thu Mar 28 2013 - 08:37:30 PDT)
  - Re: [AMBER] PB Bomb in pb_aaradi(): No radius assigned for atom 530 C5' CI Xioling Chuang (Thu Mar 28 2013 - 08:56:21 PDT)
    - Re: [AMBER] PB Bomb in pb_aaradi(): No radius assigned for atom 530 C5' CI Jason Swails (Thu Mar 28 2013 - 10:01:58 PDT)
[AMBER] problem in generating pbsa.phi file using PBSA N Nandi (Thu Mar 28 2013 - 22:06:09 PDT)
- Re: [AMBER] problem in generating pbsa.phi file using PBSA Ray Luo, Ph.D. (Fri Mar 29 2013 - 16:39:24 PDT)
[AMBER] rotational diffusion via cpptraj Vijay Manickam Achari (Fri Mar 29 2013 - 04:11:12 PDT)
- Re: [AMBER] rotational diffusion via cpptraj George M Giambasu (Fri Mar 29 2013 - 06:14:03 PDT)
[AMBER] Problem reading a psf file in cpptraj Ganesh Kamath (Fri Mar 29 2013 - 11:43:15 PDT)
- Re: [AMBER] Problem reading a psf file in cpptraj Daniel Roe (Fri Mar 29 2013 - 12:57:41 PDT)
  - Re: [AMBER] Problem reading a psf file in cpptraj Ganesh Kamath (Fri Mar 29 2013 - 13:35:50 PDT)
    - Re: [AMBER] Problem reading a psf file in cpptraj Daniel Roe (Fri Mar 29 2013 - 13:44:17 PDT)
[AMBER] conformational sampling in non helical RNA structures Asmita Gupta (Sat Mar 30 2013 - 08:44:39 PDT)
- Re: [AMBER] conformational sampling in non helical RNA structures Jiri Sponer (Sat Mar 30 2013 - 09:11:07 PDT)
  - Re: [AMBER] conformational sampling in non helical RNA structures Asmita Gupta (Sat Mar 30 2013 - 11:27:27 PDT)
    - Re: [AMBER] conformational sampling in non helical RNA structures Jiri Sponer (Sat Mar 30 2013 - 12:16:57 PDT)
[AMBER] Problems with MMPBSA: mmphsa_py_energy could not be found Tommy Yap (Mon Apr 01 2013 - 00:18:54 PDT)
- Re: [AMBER] Problems with MMPBSA: mmphsa_py_energy could not be found Jason Swails (Mon Apr 01 2013 - 05:07:22 PDT)
[AMBER] clustering based on side-chain conformations anu chandra (Mon Apr 01 2013 - 00:40:07 PDT)
- Re: [AMBER] clustering based on side-chain conformations Daniel Roe (Tue Apr 02 2013 - 07:28:19 PDT)
[AMBER] Is SHAKE necessary in running an MD?V Alan (Mon Apr 01 2013 - 01:29:36 PDT)
- Re: [AMBER] Is SHAKE necessary in running an MD?V Gerald Monard (Mon Apr 01 2013 - 03:08:06 PDT)
  - Re: [AMBER] Is SHAKE necessary in running an MD?V Alan (Mon Apr 01 2013 - 23:12:42 PDT)
    - Re: [AMBER] Is SHAKE necessary in running an MD?V Gerald Monard (Tue Apr 02 2013 - 00:30:34 PDT)
    - Re: [AMBER] Is SHAKE necessary in running an MD?V Alan (Tue Apr 02 2013 - 05:23:27 PDT)
    - Re: [AMBER] Is SHAKE necessary in running an MD?V Adrian Roitberg (Tue Apr 02 2013 - 05:48:48 PDT)
[AMBER] calculating diffusion constants - multiplying factor (10/6)? Vijay Manickam Achari (Mon Apr 01 2013 - 02:21:09 PDT)
- Re: [AMBER] calculating diffusion constants - multiplying factor (10/6)? George M Giambasu (Mon Apr 01 2013 - 07:19:15 PDT)
[AMBER] error in perl script (mm_pbsa.pl) for binding energy kureeckal ramesh (Mon Apr 01 2013 - 02:42:09 PDT)
- Re: [AMBER] error in perl script (mm_pbsa.pl) for binding energy Jason Swails (Mon Apr 01 2013 - 05:09:25 PDT)
[AMBER] Different binding energy order between ATP (GTP) and protein in Amber ff10 FF and CHARMM27 FF using MMPBSA.py script dbaogen (Mon Apr 01 2013 - 19:05:30 PDT)
- Re: [AMBER] Different binding energy order between ATP (GTP) and protein in Amber ff10 FF and CHARMM27 FF using MMPBSA.py script David A Case (Tue Apr 02 2013 - 04:46:36 PDT)
[AMBER] Help with GB-OBC calculations Kamakshi (Tue Apr 02 2013 - 04:34:06 PDT)
- Re: [AMBER] Help with GB-OBC calculations Carlos Simmerling (Tue Apr 02 2013 - 04:38:56 PDT)
[AMBER] need a box Adrian Roitberg (Tue Apr 02 2013 - 08:09:27 PDT)
[AMBER] ante-MMPBSA.py failed Albert (Tue Apr 02 2013 - 11:18:14 PDT)
- Re: [AMBER] ante-MMPBSA.py failed Bill Miller III (Tue Apr 02 2013 - 11:45:27 PDT)
[AMBER] Time step of 5 fs?? HM (Tue Apr 02 2013 - 23:59:55 PDT)
- Re: [AMBER] Time step of 5 fs?? steinbrt.rci.rutgers.edu (Wed Apr 03 2013 - 00:43:17 PDT)
  - Re: [AMBER] Time step of 5 fs?? Gerald Monard (Wed Apr 03 2013 - 01:07:18 PDT)
[AMBER] MMPBSA failed Albert (Wed Apr 03 2013 - 00:12:10 PDT)
- Re: [AMBER] MMPBSA failed Jan-Philip Gehrcke (Wed Apr 03 2013 - 01:30:59 PDT)
  - Re: [AMBER] MMPBSA failed Albert (Wed Apr 03 2013 - 02:05:47 PDT)
  - Re: [AMBER] MMPBSA failed Jason Swails (Wed Apr 03 2013 - 04:53:18 PDT)
    - Re: [AMBER] MMPBSA failed Jan-Philip Gehrcke (Wed Apr 03 2013 - 05:22:53 PDT)
    - Re: [AMBER] MMPBSA failed Albert (Wed Apr 03 2013 - 06:50:15 PDT)
    - Re: [AMBER] MMPBSA failed Bill Miller III (Wed Apr 03 2013 - 07:00:28 PDT)
    - Re: [AMBER] MMPBSA failed Albert (Wed Apr 03 2013 - 07:08:49 PDT)
    - Re: [AMBER] MMPBSA failed Bill Miller III (Wed Apr 03 2013 - 07:26:20 PDT)
    - Re: [AMBER] MMPBSA failed Jason Swails (Wed Apr 03 2013 - 07:30:19 PDT)
    - Re: [AMBER] MMPBSA failed Albert (Wed Apr 03 2013 - 07:40:25 PDT)
    - Re: [AMBER] MMPBSA failed Albert (Wed Apr 03 2013 - 07:56:53 PDT)
[AMBER] Regarding MD run in vacuum Gaurao Dhoke (Wed Apr 03 2013 - 01:56:21 PDT)
- Re: [AMBER] Regarding MD run in vacuum steinbrt.rci.rutgers.edu (Wed Apr 03 2013 - 03:17:13 PDT)
  - Re: [AMBER] Regarding MD run in vacuum Gaurao Dhoke (Wed Apr 03 2013 - 03:26:57 PDT)
    - Re: [AMBER] Regarding MD run in vacuum Aron Broom (Wed Apr 03 2013 - 06:36:33 PDT)
    - Re: [AMBER] Regarding MD run in vacuum Jason Swails (Wed Apr 03 2013 - 06:53:28 PDT)
    - Re: [AMBER] Regarding MD run in vacuum Massimiliano Porrini (Wed Apr 03 2013 - 09:54:50 PDT)
[AMBER] vecs file Rasha Alqus (Wed Apr 03 2013 - 05:26:12 PDT)
- Re: [AMBER] vecs file Deák Robert (Wed Apr 03 2013 - 05:44:43 PDT)
  - Re: [AMBER] vecs file Rasha Alqus (Wed Apr 03 2013 - 05:58:22 PDT)
    - Re: [AMBER] vecs file Deák Robert (Wed Apr 03 2013 - 06:11:25 PDT)
    - Re: [AMBER] vecs file Rasha Alqus (Wed Apr 03 2013 - 07:51:22 PDT)
    - Re: [AMBER] vecs file Deák Robert (Thu Apr 04 2013 - 05:38:30 PDT)
  - Re: [AMBER] vecs file David A Case (Wed Apr 03 2013 - 08:20:05 PDT)
[AMBER] FW: No subject Wholly Peach (Wed Apr 03 2013 - 06:39:22 PDT)
[AMBER] parameter problem for NVE/NPE or NPV ensemble nguyentb.bii.a-star.edu.sg (Thu Apr 04 2013 - 01:36:14 PDT)
- Re: [AMBER] parameter problem for NVE/NPE or NPV ensemble Jason Swails (Thu Apr 04 2013 - 04:34:50 PDT)
- Re: [AMBER] parameter problem for NVE/NPE or NPV ensemble David A Case (Thu Apr 04 2013 - 04:49:38 PDT)
  - Re: [AMBER] parameter problem for NVE/NPE or NPV ensemble nguyentb.bii.a-star.edu.sg (Thu Apr 04 2013 - 05:51:51 PDT)
    - Re: [AMBER] parameter problem for NVE/NPE or NPV ensemble David A Case (Thu Apr 04 2013 - 07:00:27 PDT)
[AMBER] MD Simulation of Heavy Metal(Bi or Sb) compound molecule Yasuo Kurita (Thu Apr 04 2013 - 02:12:34 PDT)
- Re: [AMBER] MD Simulation of Heavy Metal(Bi or Sb) compound molecule FyD (Thu Apr 04 2013 - 02:36:15 PDT)
[AMBER] Analysis of side-chain conformational changes anu chandra (Thu Apr 04 2013 - 03:10:55 PDT)
- [AMBER] Fwd: Analysis of side-chain conformational changes anu chandra (Thu Apr 04 2013 - 05:04:53 PDT)
- Re: [AMBER] Analysis of side-chain conformational changes Daniel Roe (Fri Apr 05 2013 - 09:27:38 PDT)
  - Re: [AMBER] Analysis of side-chain conformational changes anu chandra (Fri Apr 05 2013 - 22:59:44 PDT)
[AMBER] meaning of values for dihedrals of a chromophore Anna Marabotti (Thu Apr 04 2013 - 03:20:15 PDT)
[AMBER] chromium in leap marta wisniewska. (Thu Apr 04 2013 - 15:02:44 PDT)
- Re: [AMBER] chromium in leap FyD (Thu Apr 04 2013 - 23:25:55 PDT)
- [AMBER] Out of Box in PMEMD journal.update (Thu Apr 04 2013 - 23:38:41 PDT)
  - Re: [AMBER] Out of Box in PMEMD Daniel Roe (Fri Apr 05 2013 - 09:15:07 PDT)
  - Re: [AMBER] Out of Box in PMEMD journal.update (Fri Apr 05 2013 - 22:03:21 PDT)
    - Re: [AMBER] Out of Box in PMEMD David A Case (Sat Apr 06 2013 - 06:10:20 PDT)
[AMBER] CalcError: sander.APBS failed with prmtop using MMPBSA.py by Amber 11 and AmberTools 12 dbaogen (Thu Apr 04 2013 - 19:14:43 PDT)
[AMBER] Problem with order parameter calculation in PTRAJ anu chandra (Fri Apr 05 2013 - 00:16:00 PDT)
- Re: [AMBER] Problem with order parameter calculation in PTRAJ Daniel Roe (Fri Apr 05 2013 - 08:38:36 PDT)
  - Re: [AMBER] Problem with order parameter calculation in PTRAJ anu chandra (Fri Apr 05 2013 - 22:48:33 PDT)
    - Re: [AMBER] Problem with order parameter calculation in PTRAJ Daniel Roe (Mon Apr 08 2013 - 10:25:45 PDT)
    - Re: [AMBER] Problem with order parameter calculation in PTRAJ anu chandra (Mon Apr 08 2013 - 23:40:45 PDT)
    - Re: [AMBER] Problem with order parameter calculation in PTRAJ Daniel Roe (Tue Apr 09 2013 - 07:58:45 PDT)
    - Re: [AMBER] Problem with order parameter calculation in PTRAJ anu chandra (Tue Apr 09 2013 - 22:04:27 PDT)
    - Re: [AMBER] Problem with order parameter calculation in PTRAJ anu chandra (Tue Apr 09 2013 - 22:41:50 PDT)
    - Re: [AMBER] Problem with order parameter calculation in PTRAJ anu chandra (Tue Apr 09 2013 - 22:55:55 PDT)
[AMBER] Regarding Accelerated Molecular Dynamics Adam Zalewski (Fri Apr 05 2013 - 04:33:16 PDT)
[AMBER] Accelerated Molecular Dynamics Diego Javier Alonso de Armiño (Fri Apr 05 2013 - 08:44:33 PDT)
- [AMBER] Fwd: Accelerated Molecular Dynamics Diego Javier Alonso de Armiño (Sat Apr 06 2013 - 13:40:18 PDT)
[AMBER] problem in loading 5'terminal phosphate group of tRNA N Nandi (Fri Apr 05 2013 - 09:49:22 PDT)
- Re: [AMBER] problem in loading 5'terminal phosphate group of tRNA FyD (Sat Apr 06 2013 - 05:51:08 PDT)
[AMBER] How to modifie "runmd.f" to calculate force from obtained MD trajectory? kurisaki (Fri Apr 05 2013 - 18:50:40 PDT)
- Re: [AMBER] How to modifie "runmd.f" to calculate force from obtained MD trajectory? Jason Swails (Fri Apr 05 2013 - 20:33:54 PDT)
  - Re: [AMBER] How to modifie "runmd.f" to calculate force from obtained MD trajectory? kurisaki (Sat Apr 06 2013 - 20:46:01 PDT)
- Re: [AMBER] How to modifie "runmd.f" to calculate force from obtained MD trajectory? kurisaki (Sun Apr 07 2013 - 01:22:59 PDT)
- Re: [AMBER] How to modifie "runmd.f" to calculate force from obtained MD trajectory? kurisaki (Sun Apr 07 2013 - 03:39:03 PDT)
[AMBER] Error in lmod minimization parallel test Miguel Ortiz Lombardía (Sat Apr 06 2013 - 06:31:21 PDT)
- Re: [AMBER] Error in lmod minimization parallel test case (Sun Apr 07 2013 - 05:57:41 PDT)
  - Re: [AMBER] Error in lmod minimization parallel test Miguel Ortiz Lombardía (Mon Apr 08 2013 - 01:10:12 PDT)
[AMBER] Measure (and print to file) distances on the fly in pmemd.cuda Diego Javier Alonso de Armiño (Sat Apr 06 2013 - 13:38:11 PDT)
- Re: [AMBER] Measure (and print to file) distances on the fly in pmemd.cuda Jason Swails (Sun Apr 07 2013 - 05:56:39 PDT)
  - Re: [AMBER] Measure (and print to file) distances on the fly in pmemd.cuda Diego Javier Alonso de Armiño (Sun Apr 07 2013 - 09:33:11 PDT)
[AMBER] minimize problem 涂志萍 (Sat Apr 06 2013 - 20:12:45 PDT)
- Re: [AMBER] minimize problem case (Sun Apr 07 2013 - 06:02:00 PDT)
[AMBER] AMBER12 GPU performance Neha Gandhi (Sat Apr 06 2013 - 21:17:09 PDT)
- Re: [AMBER] AMBER12 GPU performance Aron Broom (Sat Apr 06 2013 - 21:55:47 PDT)
[AMBER] where does sander open the output files? kurisaki (Sun Apr 07 2013 - 01:20:48 PDT)
- Re: [AMBER] where does sander open the output files? Jason Swails (Sun Apr 07 2013 - 05:43:29 PDT)
  - Re: [AMBER] where does sander open the output files? kurisaki (Sun Apr 07 2013 - 05:59:23 PDT)
- Re: [AMBER] where does sander open the output files? kurisaki (Sun Apr 07 2013 - 06:00:49 PDT)
[AMBER] =4/7/2013 3:34:47 PM= Acoot Brett (Sun Apr 07 2013 - 07:35:00 PDT)
[AMBER] Anyone (else) at the ACS meeting in NOLA? Jonathan Gough (Sun Apr 07 2013 - 19:26:03 PDT)
[AMBER] GAFFlipid forcefield marawan hussain (Sun Apr 07 2013 - 20:49:44 PDT)
- Re: [AMBER] GAFFlipid forcefield Dickson, Callum (Mon Apr 08 2013 - 05:02:30 PDT)
[AMBER] problem in loading 5'terminal phosphate group of tRNA N Nandi (Sun Apr 07 2013 - 22:18:29 PDT)
- Re: [AMBER] problem in loading 5'terminal phosphate group of tRNA FyD (Mon Apr 08 2013 - 00:48:41 PDT)
[AMBER] Fwd: xleap problem suresh satpati (Sun Apr 07 2013 - 22:52:40 PDT)
[AMBER] LINMIN FAILURE in amber12 Soumya Lipsa Rath (Sun Apr 07 2013 - 23:00:57 PDT)
- Re: [AMBER] LINMIN FAILURE in amber12 David A Case (Mon Apr 08 2013 - 04:48:50 PDT)
  - Re: [AMBER] LINMIN FAILURE in amber12 Soumya Lipsa Rath (Mon Apr 08 2013 - 05:16:30 PDT)
[AMBER] Analysis of side-chain conformational changes anu chandra (Mon Apr 08 2013 - 01:55:18 PDT)
[AMBER] Problem with order parameter calculation in PTRAJ anu chandra (Mon Apr 08 2013 - 01:56:36 PDT)
[AMBER] Problem with the amber12 compilation James Starlight (Mon Apr 08 2013 - 02:36:23 PDT)
- Re: [AMBER] Problem with the amber12 compilation Jan-Philip Gehrcke (Mon Apr 08 2013 - 03:34:05 PDT)
  - Re: [AMBER] Problem with the amber12 compilation James Starlight (Mon Apr 08 2013 - 03:50:04 PDT)
[AMBER] problem in loading 5'terminal phosphate group of tRNA N Nandi (Mon Apr 08 2013 - 04:14:58 PDT)
- Re: [AMBER] problem in loading 5'terminal phosphate group of tRNA FyD (Mon Apr 08 2013 - 05:33:23 PDT)
[AMBER] on the usage of Antechamber for the ligand parametrisation James Starlight (Mon Apr 08 2013 - 04:48:40 PDT)
- Re: [AMBER] on the usage of Antechamber for the ligand parametrisation James Starlight (Mon Apr 08 2013 - 04:52:31 PDT)
  - Re: [AMBER] on the usage of Antechamber for the ligand parametrisation FyD (Tue Apr 09 2013 - 03:12:23 PDT)
    - Re: [AMBER] on the usage of Antechamber for the ligand parametrisation James Starlight (Tue Apr 09 2013 - 22:33:39 PDT)
    - Re: [AMBER] on the usage of Antechamber for the ligand parametrisation FyD (Tue Apr 09 2013 - 23:13:42 PDT)
    - Re: [AMBER] on the usage of Antechamber for the ligand parametrisation Astrid Maaß (Wed Apr 10 2013 - 00:06:45 PDT)
    - Re: [AMBER] on the usage of Antechamber for the ligand parametrisation James Starlight (Wed Apr 10 2013 - 00:18:26 PDT)
[AMBER] tleap problem Odin Zeus (Mon Apr 08 2013 - 07:54:46 PDT)
- Re: [AMBER] tleap problem steinbrt.rci.rutgers.edu (Mon Apr 08 2013 - 08:07:06 PDT)
[AMBER] implicit solvation with periodic boundary Syed Tarique Moin (Mon Apr 08 2013 - 08:39:37 PDT)
- Re: [AMBER] implicit solvation with periodic boundary Nhai (Mon Apr 08 2013 - 08:50:42 PDT)
  - Re: [AMBER] implicit solvation with periodic boundary Syed Tarique Moin (Mon Apr 08 2013 - 09:17:32 PDT)
    - Re: [AMBER] implicit solvation with periodic boundary Ray Luo (Mon Apr 08 2013 - 09:57:43 PDT)
- Re: [AMBER] implicit solvation with periodic boundary Jason Swails (Mon Apr 08 2013 - 13:10:55 PDT)
  - Re: [AMBER] implicit solvation with periodic boundary Carlos Simmerling (Mon Apr 08 2013 - 13:28:20 PDT)
- Re: [AMBER] implicit solvation with periodic boundary Syed Tarique Moin (Mon Apr 08 2013 - 14:27:35 PDT)
  - Re: [AMBER] implicit solvation with periodic boundary Carlos Simmerling (Mon Apr 08 2013 - 14:39:17 PDT)
- Re: [AMBER] implicit solvation with periodic boundary Syed Tarique Moin (Mon Apr 08 2013 - 16:32:59 PDT)
[AMBER] Ligand-Receptor complex MD - ligand doesn't appear? Sebastian Petrik (Mon Apr 08 2013 - 18:26:30 PDT)
- Re: [AMBER] Ligand-Receptor complex MD - ligand doesn't appear? steinbrt.rci.rutgers.edu (Tue Apr 09 2013 - 00:45:38 PDT)
- Re: [AMBER] Ligand-Receptor complex MD - ligand doesn't appear? Julio Dominguez (Tue Apr 09 2013 - 13:13:58 PDT)
  - Re: [AMBER] Ligand-Receptor complex MD - ligand doesn't appear? Sebastian Petrik (Tue Apr 09 2013 - 16:43:24 PDT)
    - Re: [AMBER] Ligand-Receptor complex MD - ligand doesn't appear? steinbrt.rci.rutgers.edu (Wed Apr 10 2013 - 00:53:34 PDT)
    - Re: [AMBER] Ligand-Receptor complex MD - ligand doesn't appear? Sebastian Petrik (Wed Apr 10 2013 - 18:39:20 PDT)
[AMBER] About modelling the separation of the "DNA" strands Mu Xia (Mon Apr 08 2013 - 19:09:33 PDT)
- Re: [AMBER] About modelling the separation of the "DNA" strands Jason Swails (Tue Apr 23 2013 - 19:02:21 PDT)
[AMBER] large difference of nonpolar solvation free energy using MMPBSA.py in AmberTools1.5 or AmberTools12 dbaogen (Tue Apr 09 2013 - 00:24:58 PDT)
- Re: [AMBER] large difference of nonpolar solvation free energy using MMPBSA.py in AmberTools1.5 or AmberTools12 Jason Swails (Tue Apr 09 2013 - 14:56:17 PDT)
- Re: [AMBER] large difference of nonpolar solvation free energy using MMPBSA.py in AmberTools1.5 or AmberTools12 dbaogen (Tue Apr 09 2013 - 18:29:23 PDT)
  - Re: [AMBER] large difference of nonpolar solvation free energy using MMPBSA.py in AmberTools1.5 or AmberTools12 Jason Swails (Tue Apr 09 2013 - 18:45:45 PDT)
[AMBER] xleap error - Created a new atom named: P within residue: .R<DG5 478> suresh satpati (Tue Apr 09 2013 - 01:37:39 PDT)
- Re: [AMBER] xleap error - Created a new atom named: P within residue: .R<DG5 478> Daniel Roe (Tue Apr 09 2013 - 08:00:42 PDT)
[AMBER] The latest topology file format. Takeshi Baba (Tue Apr 09 2013 - 05:56:58 PDT)
- Re: [AMBER] The latest topology file format. Daniel Roe (Tue Apr 09 2013 - 07:54:25 PDT)
  - Re: [AMBER] The latest topology file format. Takeshi Baba (Wed Apr 10 2013 - 16:38:49 PDT)
- [AMBER] Constant pH calculation: calcpka Anselm Horn (Wed Apr 10 2013 - 23:47:18 PDT)
  - Re: [AMBER] Constant pH calculation: calcpka Jason Swails (Thu Apr 11 2013 - 07:36:39 PDT)
    - Re: [AMBER] Constant pH calculation: calcpka Anselm Horn (Thu Apr 11 2013 - 09:17:27 PDT)
[AMBER] Problem with folding simulation moitrayee.mbu.iisc.ernet.in (Tue Apr 09 2013 - 19:07:43 PDT)
- Re: [AMBER] Problem with folding simulation Carlos Simmerling (Tue Apr 09 2013 - 19:41:46 PDT)
- Re: [AMBER] Problem with folding simulation Jason Swails (Tue Apr 09 2013 - 19:51:28 PDT)
[AMBER] Extra Points support in pmemd.cuda.MPI Thomas Evangelidis (Wed Apr 10 2013 - 03:10:51 PDT)
- Re: [AMBER] Extra Points support in pmemd.cuda.MPI Jason Swails (Wed Apr 10 2013 - 05:30:18 PDT)
  - Re: [AMBER] Extra Points support in pmemd.cuda.MPI Thomas Evangelidis (Wed Apr 10 2013 - 06:09:56 PDT)
    - Re: [AMBER] Extra Points support in pmemd.cuda.MPI Jason Swails (Wed Apr 10 2013 - 06:27:41 PDT)
- Re: [AMBER] Extra Points support in pmemd.cuda.MPI Ross Walker (Wed Apr 10 2013 - 06:39:58 PDT)
  - Re: [AMBER] Extra Points support in pmemd.cuda.MPI Thomas Evangelidis (Wed Apr 10 2013 - 13:47:52 PDT)
[AMBER] Amber installation problems Donato Pera (Wed Apr 10 2013 - 06:48:39 PDT)
- Re: [AMBER] Amber installation problems Daniel Roe (Wed Apr 10 2013 - 07:04:11 PDT)
  - Re: [AMBER] Amber installation problems Donato Pera (Wed Apr 10 2013 - 07:32:19 PDT)
    - Re: [AMBER] Amber installation problems Jason Swails (Wed Apr 10 2013 - 07:55:36 PDT)
    - Re: [AMBER] Amber installation problems Donato Pera (Thu Apr 11 2013 - 23:57:20 PDT)
    - Re: [AMBER] Amber installation problems Donato Pera (Fri Apr 12 2013 - 01:49:01 PDT)
    - Re: [AMBER] Amber installation problems David A Case (Fri Apr 12 2013 - 04:44:47 PDT)
    - Re: [AMBER] Amber installation problems Ross Walker (Fri Apr 12 2013 - 08:05:58 PDT)
    - Re: [AMBER] Amber installation problems Igor Marques (Fri Apr 12 2013 - 10:40:34 PDT)
    - Re: [AMBER] Amber installation problems David A Case (Fri Apr 12 2013 - 17:37:54 PDT)
    - Re: [AMBER] Amber installation problems Igor Marques (Sat Apr 13 2013 - 03:31:28 PDT)
    - Re: [AMBER] Amber installation problems Tru Huynh (Mon Apr 15 2013 - 07:40:00 PDT)
    - Re: [AMBER] Amber installation problems Igor Marques (Mon Apr 15 2013 - 08:58:01 PDT)
    - Re: [AMBER] Amber installation problems Donato Pera (Mon Apr 15 2013 - 03:16:31 PDT)
    - Re: [AMBER] Amber installation problems Jason Swails (Mon Apr 15 2013 - 04:29:10 PDT)
[AMBER] RRe: Ligand-Receptor complex MD - ligand doesn't > appear? Julio Dominguez (Wed Apr 10 2013 - 13:39:18 PDT)
- Re: [AMBER] RRe: Ligand-Receptor complex MD - ligand doesn't > appear? Sebastian Petrik (Wed Apr 10 2013 - 20:14:24 PDT)
  - Re: [AMBER] RRe: Ligand-Receptor complex MD - ligand doesn't > appear? steinbrt.rci.rutgers.edu (Thu Apr 11 2013 - 02:01:52 PDT)
[AMBER] Zero vdW parametes for HO in Amber Morteza Chehel Amirani (Wed Apr 10 2013 - 15:55:40 PDT)
- Re: [AMBER] Zero vdW parametes for HO in Amber Bill Ross (Wed Apr 10 2013 - 16:41:27 PDT)
  - Re: [AMBER] Zero vdW parametes for HO in Amber Lachele Foley (Wed Apr 10 2013 - 17:22:03 PDT)
    - Re: [AMBER] Zero vdW parametes for HO in Amber Yong Duan (Wed Apr 10 2013 - 19:27:19 PDT)
    - Re: [AMBER] Zero vdW parametes for HO in Amber Jason Swails (Wed Apr 10 2013 - 21:12:24 PDT)
[AMBER] Error: A residue defined as a "fast 3-point water" is not defined by a triangle of three bonds using CHARMM 27 FF converted by CHAMBER program dbaogen (Wed Apr 10 2013 - 20:37:00 PDT)
- Re: [AMBER] Error: A residue defined as a "fast 3-point water" is not defined by a triangle of three bonds using CHARMM 27 FF converted by CHAMBER program Jason Swails (Thu Apr 11 2013 - 23:07:52 PDT)
- Re: [AMBER] Error: A residue defined as a "fast 3-point water" is not defined by a triangle of three bonds using CHARMM 27 FF converted by CHAMBER program dbaogen (Fri Apr 12 2013 - 03:23:44 PDT)
  - Re: [AMBER] Error: A residue defined as a "fast 3-point water" is not defined by a triangle of three bonds using CHARMM 27 FF converted by CHAMBER program David A Case (Fri Apr 12 2013 - 04:49:01 PDT)
- Re: [AMBER] Error: A residue defined as a "fast 3-point water" is not defined by a triangle of three bonds using CHARMM 27 FF converted by CHAMBER program dbaogen (Sat Apr 13 2013 - 23:17:09 PDT)
[AMBER] About modelling the separation of the "DNA" strands Mu Xia (Thu Apr 11 2013 - 01:36:50 PDT)
[AMBER] Problem compiling AMBER12 sander.MPI with gnu Marc van der Kamp (Thu Apr 11 2013 - 03:19:44 PDT)
- Re: [AMBER] Problem compiling AMBER12 sander.MPI with gnu Jason Swails (Thu Apr 11 2013 - 07:15:15 PDT)
  - Re: [AMBER] Problem compiling AMBER12 sander.MPI with gnu Marc van der Kamp (Thu Apr 11 2013 - 13:39:14 PDT)
[AMBER] large Standard Deviation of binding free energy using QM/MM-GBSA method in Amber 11 with AmberTools 12 dbaogen (Thu Apr 11 2013 - 05:15:31 PDT)
- Re: [AMBER] large Standard Deviation of binding free energy using QM/MM-GBSA method in Amber 11 with AmberTools 12 Jason Swails (Thu Apr 11 2013 - 07:28:11 PDT)
[AMBER] Tool to parameterize the ligand molecules Jagur Lambix (Thu Apr 11 2013 - 16:18:14 PDT)
- Re: [AMBER] Tool to parameterize the ligand molecules Jason Swails (Thu Apr 11 2013 - 16:45:52 PDT)
  - Re: [AMBER] Tool to parameterize the ligand molecules Jagur Lambix (Fri Apr 12 2013 - 08:05:53 PDT)
[AMBER] mopac.sh file missing in amber12/bin directory parul sharma (Thu Apr 11 2013 - 22:20:12 PDT)
- Re: [AMBER] mopac.sh file missing in amber12/bin directory Jason Swails (Thu Apr 11 2013 - 22:59:44 PDT)
[AMBER] problem in loading 5'terminal phosphate group of tRNA N Nandi (Thu Apr 11 2013 - 22:57:07 PDT)
- Re: [AMBER] problem in loading 5'terminal phosphate group of tRNA FyD (Fri Apr 12 2013 - 07:03:34 PDT)
[AMBER] correlation matrix of side-chain dihedral angle in PTRAJ anu chandra (Fri Apr 12 2013 - 04:25:42 PDT)
- Re: [AMBER] correlation matrix of side-chain dihedral angle in PTRAJ Daniel Roe (Mon Apr 15 2013 - 07:12:09 PDT)
[AMBER] aMD simulations in amber12 Neha Gandhi (Fri Apr 12 2013 - 05:59:07 PDT)
- Re: [AMBER] aMD simulations in amber12 Carlos Simmerling (Fri Apr 12 2013 - 06:12:35 PDT)
- [AMBER] ff atom types Urszula Uciechowska (Fri Apr 12 2013 - 06:12:36 PDT)
  - Re: [AMBER] ff atom types FyD (Fri Apr 12 2013 - 06:46:00 PDT)
    - [AMBER] MMPBSA.py Urszula Uciechowska (Sun May 12 2013 - 23:24:35 PDT)
    - Re: [AMBER] MMPBSA.py Jason Swails (Mon May 13 2013 - 05:03:38 PDT)
- Re: [AMBER] aMD simulations in amber12 Ross Walker (Fri Apr 12 2013 - 08:10:43 PDT)
  - Re: [AMBER] aMD simulations in amber12 Neha Gandhi (Fri Apr 12 2013 - 09:20:08 PDT)
    - Re: [AMBER] aMD simulations in amber12 Jian Yin (Fri Apr 12 2013 - 10:21:20 PDT)
  - Re: [AMBER] aMD simulations in amber12 Soumya Lipsa Rath (Fri Apr 12 2013 - 09:28:18 PDT)
[AMBER] NPT ensemble hydrogen bond calculation Binwu Zhao (Fri Apr 12 2013 - 21:20:54 PDT)
- Re: [AMBER] NPT ensemble hydrogen bond calculation Daniel Roe (Mon Apr 15 2013 - 07:21:25 PDT)
[AMBER] on the ussage of mopac with Antechamber James Starlight (Fri Apr 12 2013 - 22:58:56 PDT)
- Re: [AMBER] on the ussage of mopac with Antechamber David A Case (Mon Apr 15 2013 - 10:29:59 PDT)
  - Re: [AMBER] on the ussage of mopac with Antechamber James Starlight (Mon Apr 15 2013 - 21:44:20 PDT)
    - Re: [AMBER] on the ussage of mopac with Antechamber David A Case (Tue Apr 16 2013 - 04:51:32 PDT)
    - Re: [AMBER] on the ussage of mopac with Antechamber Jason Swails (Tue Apr 16 2013 - 04:51:59 PDT)
    - Re: [AMBER] on the ussage of mopac with Antechamber James Starlight (Tue Apr 16 2013 - 08:00:53 PDT)
[AMBER] # of snapshots for force does not match that of mdcrd kurisaki (Sat Apr 13 2013 - 23:20:21 PDT)
- Re: [AMBER] # of snapshots for force does not match that of mdcrd kurisaki (Sun Apr 14 2013 - 01:58:13 PDT)
[AMBER] sander not installed Jonathan Saboury (Mon Apr 15 2013 - 00:50:04 PDT)
- Re: [AMBER] sander not installed Anna Bauß (Mon Apr 15 2013 - 01:34:48 PDT)
[AMBER] clustering places all frames in one cluster Amparo Garcia Lopez (Mon Apr 15 2013 - 01:26:00 PDT)
- [AMBER] clustering places all frames in one cluster Amparo Garcia Lopez (Mon Apr 15 2013 - 05:44:15 PDT)
- Re: [AMBER] clustering places all frames in one cluster Daniel Roe (Mon Apr 15 2013 - 07:09:51 PDT)
  - Re: [AMBER] clustering places all frames in one cluster Amparo Garcia Lopez (Fri Apr 19 2013 - 01:14:55 PDT)
    - Re: [AMBER] clustering places all frames in one cluster Vaibhav Dixit (Sun Apr 21 2013 - 22:20:38 PDT)
    - Re: [AMBER] clustering places all frames in one cluster Miguel Ortiz Lombardía (Mon Apr 22 2013 - 06:11:46 PDT)
    - Re: [AMBER] clustering places all frames in one cluster Amparo Garcia Lopez (Thu Apr 25 2013 - 02:20:04 PDT)
    - Re: [AMBER] clustering places all frames in one cluster Daniel Roe (Thu Apr 25 2013 - 07:32:52 PDT)
[AMBER] problem in creating circular DNA using NAB arnab bhattacharya (Mon Apr 15 2013 - 04:10:33 PDT)
- Re: [AMBER] problem in creating circular DNA using NAB David A Case (Mon Apr 15 2013 - 10:58:48 PDT)
  - Re: [AMBER] problem in creating circular DNA using NAB arnab bhattacharya (Tue Apr 16 2013 - 05:30:53 PDT)
    - Re: [AMBER] problem in creating circular DNA using NAB David A Case (Wed Apr 17 2013 - 00:19:30 PDT)
[AMBER] problem in creating circular DNA with NAB arnab bhattacharya (Mon Apr 15 2013 - 05:00:18 PDT)
[AMBER] Hydration Free Energy by TI Kepa K. Burusco (Mon Apr 15 2013 - 05:09:45 PDT)
- Re: [AMBER] Hydration Free Energy by TI steinbrt.rci.rutgers.edu (Tue Apr 23 2013 - 04:45:40 PDT)
  - Re: [AMBER] Hydration Free Energy by TI Kepa K. Burusco (Tue Apr 23 2013 - 09:33:54 PDT)
[AMBER] GAFFlipid using custom lipids Covington, Cody Lance (Mon Apr 15 2013 - 11:23:27 PDT)
- Re: [AMBER] GAFFlipid using custom lipids Ganesh Kamath (Mon Apr 15 2013 - 11:32:21 PDT)
  - Re: [AMBER] GAFFlipid using custom lipids Benjamin D Madej (Mon Apr 15 2013 - 12:15:30 PDT)
    - Re: [AMBER] GAFFlipid using custom lipids Covington, Cody Lance (Mon Apr 15 2013 - 12:52:03 PDT)
    - [AMBER] RE : GAFFlipid using custom lipids ABEL Stephane 175950 (Mon Apr 15 2013 - 13:29:28 PDT)
    - Re: [AMBER] GAFFlipid using custom lipids Benjamin D Madej (Mon Apr 15 2013 - 15:00:00 PDT)
    - Re: [AMBER] GAFFlipid using custom lipids Covington, Cody Lance (Mon Apr 15 2013 - 18:02:12 PDT)
    - Re: [AMBER] GAFFlipid using custom lipids Benjamin D Madej (Tue Apr 16 2013 - 12:11:30 PDT)
- [AMBER] PBSA focusing Jesper Sørensen (Mon Apr 15 2013 - 14:06:09 PDT)
  - Re: [AMBER] PBSA focusing Ray Luo, Ph.D. (Mon Apr 15 2013 - 14:38:48 PDT)
    - Re: [AMBER] PBSA focusing Jesper Sørensen (Mon Apr 15 2013 - 16:03:50 PDT)
    - Re: [AMBER] PBSA focusing Ray Luo, Ph.D. (Mon Apr 15 2013 - 16:54:43 PDT)
  - Re: [AMBER] PBSA focusing Jesper Sørensen (Tue Apr 16 2013 - 10:33:13 PDT)
    - Re: [AMBER] PBSA focusing Ray Luo, Ph.D. (Tue Apr 16 2013 - 11:27:51 PDT)
[AMBER] Solute concentration waleed zalloum (Mon Apr 15 2013 - 12:45:33 PDT)
- Re: [AMBER] Solute concentration Covington, Cody Lance (Mon Apr 15 2013 - 17:10:39 PDT)
[AMBER] tleap cannot create topology and coordinate files javier alejandro rendon carrillo (Mon Apr 15 2013 - 14:22:52 PDT)
- Re: [AMBER] tleap cannot create topology and coordinate files David A Case (Wed Apr 17 2013 - 06:44:11 PDT)
[AMBER] Whirling ssDNA like a helicopter (Movie attached) Hoshin Kim (Mon Apr 15 2013 - 15:23:05 PDT)
- Re: [AMBER] Whirling ssDNA like a helicopter (Movie attached) David A Case (Tue Apr 16 2013 - 04:47:35 PDT)
[AMBER] Plotting heat maps in AMBER aMD simualtions Neha Gandhi (Tue Apr 16 2013 - 00:19:22 PDT)
- Re: [AMBER] Plotting heat maps in AMBER aMD simualtions Jason Swails (Tue Apr 16 2013 - 08:10:05 PDT)
  - Re: [AMBER] Plotting heat maps in AMBER aMD simualtions Daniel Roe (Tue Apr 16 2013 - 08:38:34 PDT)
    - Re: [AMBER] Plotting heat maps in AMBER aMD simualtions Neha Gandhi (Tue Apr 16 2013 - 22:28:43 PDT)
    - Re: [AMBER] Plotting heat maps in AMBER aMD simualtions Levi Pierce (Wed Apr 17 2013 - 07:52:38 PDT)
    - Re: [AMBER] Plotting heat maps in AMBER aMD simualtions Jason Swails (Thu Apr 18 2013 - 05:04:15 PDT)
    - Re: [AMBER] Plotting heat maps in AMBER aMD simualtions Levi Pierce (Thu Apr 18 2013 - 07:36:12 PDT)
    - [AMBER] MMPBSA result interpretation helppppp Catein Catherine (Thu Apr 18 2013 - 23:07:25 PDT)
    - Re: [AMBER] MMPBSA result interpretation helppppp Jason Swails (Tue Apr 23 2013 - 05:12:43 PDT)
[AMBER] Wolf2Pack Parameterization Tool Karl N. Kirschner (Tue Apr 16 2013 - 02:27:11 PDT)
Re: [AMBER] NPT ensemble hydrogen bond calculation (Binwu Zhao) Binwu Zhao (Tue Apr 16 2013 - 10:46:00 PDT)
- Re: [AMBER] NPT ensemble hydrogen bond calculation (Binwu Zhao) Daniel Roe (Tue Apr 16 2013 - 10:52:46 PDT)
[AMBER] Newbie solvent question Jonathan Gough (Tue Apr 16 2013 - 10:57:55 PDT)
- Re: [AMBER] Newbie solvent question Brian Radak (Tue Apr 16 2013 - 12:19:13 PDT)
- Re: [AMBER] Newbie solvent question Jason Swails (Tue Apr 16 2013 - 12:31:09 PDT)
  - Re: [AMBER] Newbie solvent question Jonathan Gough (Tue Apr 16 2013 - 12:34:48 PDT)
[AMBER] Clarification on sander George Tzotzos (Tue Apr 16 2013 - 11:24:08 PDT)
- Re: [AMBER] Clarification on sander Jason Swails (Tue Apr 16 2013 - 12:07:03 PDT)
  - Re: [AMBER] Clarification on sander George Tzotzos (Tue Apr 16 2013 - 13:02:31 PDT)
    - Re: [AMBER] Clarification on sander Ross Walker (Tue Apr 16 2013 - 13:13:08 PDT)
[AMBER] Problems with tleap and popc membrane with protein Fabrício Bracht (Tue Apr 16 2013 - 14:17:14 PDT)
- Re: [AMBER] Problems with tleap and popc membrane with protein manikanthan bhavaraju (Tue Apr 16 2013 - 14:35:39 PDT)
[AMBER] AmberTools12 re-installation test log file Saugata Hazra (Tue Apr 16 2013 - 14:46:11 PDT)
- Re: [AMBER] AmberTools12 re-installation test log file Jason Swails (Tue Apr 16 2013 - 18:27:50 PDT)
  - Re: [AMBER] AmberTools12 re-installation test log file Saugata Hazra (Tue Apr 16 2013 - 20:23:30 PDT)
[AMBER] aMD question: How to read the amd.log file Diego Javier Alonso de Armiño (Tue Apr 16 2013 - 14:56:54 PDT)
- Re: [AMBER] aMD question: How to read the amd.log file diego alonso (Tue Apr 16 2013 - 16:00:12 PDT)
  - Re: [AMBER] aMD question: How to read the amd.log file filip fratev (Tue Apr 16 2013 - 18:15:50 PDT)
[AMBER] aMD reweighting and amd.log file. Diego Javier Alonso de Armiño (Tue Apr 16 2013 - 16:05:56 PDT)
- Re: [AMBER] aMD reweighting and amd.log file. Diego Javier Alonso de Armiño (Wed Apr 17 2013 - 07:54:04 PDT)
[AMBER] Fwd: Problems with tleap and popc membrane with protein Fabrício Bracht (Tue Apr 16 2013 - 19:16:01 PDT)
- Re: [AMBER] Fwd: Problems with tleap and popc membrane with protein manikanthan bhavaraju (Tue Apr 16 2013 - 20:26:32 PDT)
  - Re: [AMBER] Fwd: Problems with tleap and popc membrane with protein Fabrício Bracht (Wed Apr 17 2013 - 10:40:54 PDT)
    - Re: [AMBER] Fwd: Problems with tleap and popc membrane with protein Benjamin D Madej (Wed Apr 17 2013 - 16:48:09 PDT)
    - Re: [AMBER] Fwd: Problems with tleap and popc membrane with protein Igor Marques (Thu Apr 18 2013 - 06:36:43 PDT)
    - Re: [AMBER] Fwd: Problems with tleap and popc membrane with protein Fabrício Bracht (Thu Apr 18 2013 - 11:19:56 PDT)
[AMBER] Fortran error while runnig javier alejandro rendon carrillo (Tue Apr 16 2013 - 22:00:03 PDT)
- Re: [AMBER] Fortran error while runnig David A Case (Wed Apr 17 2013 - 00:34:14 PDT)
[AMBER] pmemd.cuda.MPI with npt HIMANSHU JOSHI (Wed Apr 17 2013 - 11:03:07 PDT)
- Re: [AMBER] pmemd.cuda.MPI with npt Gustavo Seabra (Wed Apr 17 2013 - 11:10:43 PDT)
  - Re: [AMBER] pmemd.cuda.MPI with npt HIMANSHU JOSHI (Wed Apr 17 2013 - 11:24:37 PDT)
    - Re: [AMBER] pmemd.cuda.MPI with npt Adrian Roitberg (Wed Apr 17 2013 - 11:26:00 PDT)
    - Re: [AMBER] pmemd.cuda.MPI with npt HIMANSHU JOSHI (Wed Apr 17 2013 - 22:24:07 PDT)
    - Re: [AMBER] pmemd.cuda.MPI with npt HIMANSHU JOSHI (Thu Apr 18 2013 - 23:01:05 PDT)
    - Re: [AMBER] pmemd.cuda.MPI with npt Ross Walker (Thu Apr 18 2013 - 23:35:00 PDT)
    - Re: [AMBER] pmemd.cuda.MPI with npt Gustavo Seabra (Wed Apr 17 2013 - 11:30:40 PDT)
- Re: [AMBER] pmemd.cuda.MPI with npt Scott Le Grand (Wed Apr 17 2013 - 17:56:42 PDT)
  - Re: [AMBER] pmemd.cuda.MPI with npt HIMANSHU JOSHI (Wed Apr 17 2013 - 22:33:11 PDT)
[AMBER] GAFFLipid parameters Covington, Cody Lance (Wed Apr 17 2013 - 11:45:14 PDT)
[AMBER] Print pressure tensor components of NVT ensemble by running pmemd.cuda.MPI Wei Lin (Wed Apr 17 2013 - 16:31:02 PDT)
[AMBER] Print pressure tensor components of NVT ensemble by running pmemd.cuda.MPI Wei Lin (Wed Apr 17 2013 - 16:42:18 PDT)
- Re: [AMBER] Print pressure tensor components of NVT ensemble by running pmemd.cuda.MPI Ross Walker (Wed Apr 17 2013 - 16:48:57 PDT)
[AMBER] gaff support for iron? Jonathan Saboury (Thu Apr 18 2013 - 00:51:17 PDT)
- Re: [AMBER] gaff support for iron? David A Case (Thu Apr 18 2013 - 06:14:25 PDT)
[AMBER] paramfit questions Covington, Cody Lance (Thu Apr 18 2013 - 10:42:24 PDT)
- Re: [AMBER] paramfit questions Robin Betz (Thu Apr 18 2013 - 16:53:02 PDT)
- Re: [AMBER] paramfit questions Karl N. Kirschner (Fri Apr 19 2013 - 00:26:09 PDT)
[AMBER] problems with explicit solvent MD Niels Geudens (Fri Apr 19 2013 - 01:09:45 PDT)
- Re: [AMBER] problems with explicit solvent MD Jason Swails (Fri Apr 19 2013 - 03:50:11 PDT)
[AMBER] ante-MMPBSA.py problem Chris Chris (Fri Apr 19 2013 - 09:56:37 PDT)
- Re: [AMBER] ante-MMPBSA.py problem Jason Swails (Fri Apr 19 2013 - 11:07:25 PDT)
  - Re: [AMBER] ante-MMPBSA.py problem Chris Chris (Fri Apr 19 2013 - 23:18:59 PDT)
[AMBER] About halogen in MMPBSA calculation in AMBER9 Wang Bo (Fri Apr 19 2013 - 12:17:11 PDT)
[AMBER] Using 3D-RISM to compute solvation free energy Abhishek Mukhopadhyay (Fri Apr 19 2013 - 13:36:05 PDT)
- Re: [AMBER] Using 3D-RISM to compute solvation free energy tluchko (Fri Apr 19 2013 - 14:02:06 PDT)
  - Re: [AMBER] Using 3D-RISM to compute solvation free energy Abhishek Mukhopadhyay (Fri Apr 19 2013 - 15:10:14 PDT)
    - Re: [AMBER] Using 3D-RISM to compute solvation free energy tluchko (Fri Apr 19 2013 - 15:34:19 PDT)
    - Re: [AMBER] Using 3D-RISM to compute solvation free energy Abhishek Mukhopadhyay (Sat Apr 20 2013 - 15:00:37 PDT)
    - Re: [AMBER] Using 3D-RISM to compute solvation free energy Tyler Luchko (Sat Apr 20 2013 - 15:23:57 PDT)
    - [AMBER] Leap: Setting the bounding box manually Anselm Horn (Sun Apr 21 2013 - 09:04:06 PDT)
    - Re: [AMBER] Leap: Setting the bounding box manually Jason Swails (Sun Apr 21 2013 - 20:05:19 PDT)
[AMBER] Using MTKPP to turn a nonstandard organometallic compound in pdb format into AMBER inpcrd and prmtop files Jonathan Saboury (Fri Apr 19 2013 - 13:50:37 PDT)
- Re: [AMBER] Using MTKPP to turn a nonstandard organometallic compound in pdb format into AMBER inpcrd and prmtop files David A Case (Sat Apr 20 2013 - 05:43:39 PDT)
- Re: [AMBER] Using MTKPP to turn a nonstandard organometallic compound in pdb format into AMBER inpcrd and prmtop files FyD (Sun Apr 21 2013 - 07:42:29 PDT)
[AMBER] About halogen in MMPBSA calculation in AMBER9 Wang Bo (Fri Apr 19 2013 - 14:43:50 PDT)
- Re: [AMBER] About halogen in MMPBSA calculation in AMBER9 Ray Luo, Ph.D. (Fri Apr 19 2013 - 14:52:09 PDT)
[AMBER] Changing vdW parameters for HO-type atom Morteza Chehel Amirani (Fri Apr 19 2013 - 15:17:25 PDT)
- Re: [AMBER] Changing vdW parameters for HO-type atom Brian Radak (Mon Apr 22 2013 - 06:09:59 PDT)
[AMBER] protein-ligand docking James Starlight (Fri Apr 19 2013 - 23:57:37 PDT)
- Re: [AMBER] protein-ligand docking David A Case (Sat Apr 20 2013 - 05:48:27 PDT)
[AMBER] segmentation fault in tleap Jonathan Gough (Sun Apr 21 2013 - 20:09:37 PDT)
- Re: [AMBER] segmentation fault in tleap Robin Betz (Sun Apr 21 2013 - 21:05:33 PDT)
  - Re: [AMBER] segmentation fault in tleap Jonathan Gough (Sun Apr 21 2013 - 21:39:32 PDT)
[AMBER] Input file for NVT simulation Vaibhav Dixit (Mon Apr 22 2013 - 00:43:16 PDT)
- [AMBER] Fwd: Input file for NVT simulation Vaibhav Dixit (Mon Apr 22 2013 - 00:46:53 PDT)
  - Re: [AMBER] Fwd: Input file for NVT simulation kurisaki (Mon Apr 22 2013 - 00:59:49 PDT)
- Re: [AMBER] Input file for NVT simulation Brian Radak (Mon Apr 22 2013 - 05:51:22 PDT)
[AMBER] Amber MPI CPU number problem Donato Pera (Mon Apr 22 2013 - 02:34:43 PDT)
- Re: [AMBER] Amber MPI CPU number problem Jason Swails (Mon Apr 22 2013 - 19:15:37 PDT)
[AMBER] amber tutorial13 :constructing and simulating crystals with amber12 Yongxiu Li (Mon Apr 22 2013 - 05:16:14 PDT)
- Re: [AMBER] amber tutorial13 :constructing and simulating crystals with amber12 David A Case (Thu Apr 25 2013 - 16:48:03 PDT)
[AMBER] parameters for single amino acid MD Rilei Yu (Mon Apr 22 2013 - 05:49:47 PDT)
- Re: [AMBER] parameters for single amino acid MD David A Case (Mon Apr 22 2013 - 08:03:04 PDT)
[AMBER] dihedral term for furan and thiophene molecules Chang Woon Jang (Mon Apr 22 2013 - 07:17:00 PDT)
- Re: [AMBER] dihedral term for furan and thiophene molecules David A Case (Mon Apr 22 2013 - 08:04:18 PDT)
  - Re: [AMBER] dihedral term for furan and thiophene molecules Chang Woon Jang (Mon Apr 22 2013 - 08:21:29 PDT)
- Re: [AMBER] dihedral term for furan and thiophene molecules Karl N. Kirschner (Tue Apr 23 2013 - 04:31:29 PDT)
[AMBER] VMD shows an atom stretched waaaay out Jonathan Gough (Mon Apr 22 2013 - 08:50:10 PDT)
- Re: [AMBER] VMD shows an atom stretched waaaay out Hai Nguyen (Mon Apr 22 2013 - 12:15:02 PDT)
  - Re: [AMBER] VMD shows an atom stretched waaaay out Jonathan Gough (Mon Apr 22 2013 - 12:50:05 PDT)
    - Re: [AMBER] VMD shows an atom stretched waaaay out Daniel Roe (Mon Apr 22 2013 - 14:20:24 PDT)
    - Re: [AMBER] VMD shows an atom stretched waaaay out Jonathan Gough (Mon Apr 22 2013 - 14:27:57 PDT)
[AMBER] carbohydrate-GLYCAM 06-cellulose Iβ Rasha Alqus (Mon Apr 22 2013 - 09:14:49 PDT)
- Re: [AMBER] carbohydrate-GLYCAM 06-cellulose Iβ Lachele Foley (Mon Apr 22 2013 - 09:59:58 PDT)
  - Re: [AMBER] carbohydrate-GLYCAM 06-cellulose Iβ David A Case (Mon Apr 22 2013 - 17:56:33 PDT)
    - Re: [AMBER] carbohydrate-GLYCAM 06-cellulose Iβ Rasha Alqus (Fri Apr 26 2013 - 06:19:53 PDT)
[AMBER] Reducing positional restraint gradually Rahul Banerjee (Mon Apr 22 2013 - 12:11:44 PDT)
- Re: [AMBER] Reducing positional restraint gradually Brian Radak (Mon Apr 22 2013 - 13:12:56 PDT)
- Re: [AMBER] Reducing positional restraint gradually Jan-Philip Gehrcke (Mon Apr 22 2013 - 14:11:07 PDT)
  - Re: [AMBER] Reducing positional restraint gradually Rahul Banerjee (Tue Apr 23 2013 - 06:32:14 PDT)
    - Re: [AMBER] Reducing positional restraint gradually Jason Swails (Tue Apr 23 2013 - 07:05:06 PDT)
    - Re: [AMBER] Reducing positional restraint gradually Jan-Philip Gehrcke (Tue Apr 23 2013 - 07:17:44 PDT)
    - Re: [AMBER] Reducing positional restraint gradually David A Case (Tue Apr 23 2013 - 09:02:30 PDT)
    - Re: [AMBER] Reducing positional restraint gradually Jan-Philip Gehrcke (Wed Apr 24 2013 - 01:46:24 PDT)
[AMBER] AMBER Training Workshop - Recife, Brazil - Save the Date Ross Walker (Mon Apr 22 2013 - 12:53:01 PDT)
[AMBER] Release of AmberTools13 David A Case (Mon Apr 22 2013 - 13:33:11 PDT)
[AMBER] ambertools13 fails to update Jonathan Gough (Mon Apr 22 2013 - 15:32:22 PDT)
- Re: [AMBER] ambertools13 fails to update Jason Swails (Mon Apr 22 2013 - 15:39:04 PDT)
  - Re: [AMBER] ambertools13 fails to update Jonathan Gough (Mon Apr 22 2013 - 15:45:18 PDT)
    - Re: [AMBER] ambertools13 fails to update Jason Swails (Mon Apr 22 2013 - 15:59:40 PDT)
    - Re: [AMBER] ambertools13 fails to update Jonathan Gough (Mon Apr 22 2013 - 17:09:08 PDT)
    - Re: [AMBER] ambertools13 fails to update M. L. Dodson (Mon Apr 22 2013 - 17:25:21 PDT)
[AMBER] Problem with cluster analysis in ptraj nicolai petelski (Mon Apr 22 2013 - 18:12:41 PDT)
- Re: [AMBER] Problem with cluster analysis in ptraj Daniel Roe (Tue Apr 23 2013 - 07:18:22 PDT)
[AMBER] Is there a trick to fix a poor structural feature? Jonathan Gough (Tue Apr 23 2013 - 11:47:19 PDT)
- Re: [AMBER] Is there a trick to fix a poor structural feature? Jason Swails (Tue Apr 23 2013 - 18:01:54 PDT)
  - Re: [AMBER] Is there a trick to fix a poor structural feature? Bill Ross (Tue Apr 23 2013 - 21:26:26 PDT)
    - Re: [AMBER] Is there a trick to fix a poor structural feature? Jonathan Gough (Wed Apr 24 2013 - 10:54:18 PDT)
    - Re: [AMBER] Is there a trick to fix a poor structural feature? David A Case (Wed Apr 24 2013 - 11:20:21 PDT)
    - Re: [AMBER] Is there a trick to fix a poor structural feature? Jonathan Gough (Wed Apr 24 2013 - 13:32:21 PDT)
    - Re: [AMBER] Is there a trick to fix a poor structural feature? Jonathan Gough (Wed Apr 24 2013 - 14:13:00 PDT)
    - Re: [AMBER] Is there a trick to fix a poor structural feature? tec3.utah.edu (Wed Apr 24 2013 - 19:51:23 PDT)
    - Re: [AMBER] Is there a trick to fix a poor structural feature? Bill Ross (Wed Apr 24 2013 - 21:40:14 PDT)
- Re: [AMBER] Is there a trick to fix a poor structural feature? Thomas Evangelidis (Wed Apr 24 2013 - 23:02:23 PDT)
- Re: [AMBER] Is there a trick to fix a poor structural feature? Symon Gathiaka (Thu Apr 25 2013 - 08:04:22 PDT)
  - Re: [AMBER] Is there a trick to fix a poor structural feature? Jonathan Gough (Sat Apr 27 2013 - 17:39:08 PDT)
[AMBER] ig=-1 in NVE simulation Subrata Paul (Tue Apr 23 2013 - 23:02:11 PDT)
- Re: [AMBER] ig=-1 in NVE simulation Ross Walker (Tue Apr 23 2013 - 23:33:10 PDT)
[AMBER] Cyclic peptide problem Changqing Yan (Wed Apr 24 2013 - 07:20:59 PDT)
- Re: [AMBER] Cyclic peptide problem Jason Swails (Wed Apr 24 2013 - 08:34:50 PDT)
- Re: [AMBER] Cyclic peptide problem Changqing Yan (Thu Apr 25 2013 - 00:55:18 PDT)
  - Re: [AMBER] Cyclic peptide problem David A Case (Thu Apr 25 2013 - 04:30:23 PDT)
- Re: [AMBER] Cyclic peptide problem Changqing Yan (Thu Apr 25 2013 - 00:56:02 PDT)
[AMBER] Question for AMBER input files 陶晓芳 (Wed Apr 24 2013 - 18:19:01 PDT)
- Re: [AMBER] Question for AMBER input files Daniel Roe (Thu Apr 25 2013 - 07:33:55 PDT)
[AMBER] Question for AMBER input files (inpcrd file) 陶晓芳 (Wed Apr 24 2013 - 19:00:07 PDT)
[AMBER] pmemd: time-dependent distance restraint (as with jar=1) + torsional restraints Jan-Philip Gehrcke (Thu Apr 25 2013 - 05:08:06 PDT)
- Re: [AMBER] pmemd: time-dependent distance restraint (as with jar=1) + torsional restraints Jan-Philip Gehrcke (Thu Apr 25 2013 - 05:22:58 PDT)
- Re: [AMBER] pmemd: time-dependent distance restraint (as with jar=1) + torsional restraints Jan-Philip Gehrcke (Thu Apr 25 2013 - 07:35:12 PDT)
[AMBER] Compilation errors for AmberTools 13 with OpenMP Eugene Yedvabny (Thu Apr 25 2013 - 18:32:34 PDT)
- Re: [AMBER] Compilation errors for AmberTools 13 with OpenMP Jason Swails (Sat Apr 27 2013 - 06:53:51 PDT)
  - Re: [AMBER] Compilation errors for AmberTools 13 with OpenMP M. L. Dodson (Sat Apr 27 2013 - 07:21:34 PDT)
    - Re: [AMBER] Compilation errors for AmberTools 13 with OpenMP Jason Swails (Sat Apr 27 2013 - 14:43:14 PDT)
    - Re: [AMBER] Compilation errors for AmberTools 13 with OpenMP Eugene Yedvabny (Sat Apr 27 2013 - 15:26:15 PDT)
    - Re: [AMBER] Compilation errors for AmberTools 13 with OpenMP M. L. Dodson (Sat Apr 27 2013 - 17:05:15 PDT)
    - Re: [AMBER-Developers] [AMBER] Compilation errors for AmberTools 13 with OpenMP David A Case (Sun Apr 28 2013 - 04:10:11 PDT)
    - Re: [AMBER] Compilation errors for AmberTools 13 with OpenMP M. L. Dodson (Sun Apr 28 2013 - 05:55:56 PDT)
    - Re: [AMBER] Compilation errors for AmberTools 13 with OpenMP David A Case (Sun Apr 28 2013 - 13:34:08 PDT)
    - Re: [AMBER-Developers] [AMBER] Compilation errors for AmberTools 13 with OpenMP Scott Brozell (Sun Apr 28 2013 - 15:29:57 PDT)
    - Re: [AMBER] Compilation errors for AmberTools 13 with OpenMP M. L. Dodson (Sun Apr 28 2013 - 15:38:45 PDT)
    - Re: [AMBER-Developers] [AMBER] Compilation errors for AmberTools 13 with OpenMP Ross Walker (Sun Apr 28 2013 - 13:18:21 PDT)
    - Re: [AMBER] [AMBER-Developers] Compilation errors for AmberTools 13 with OpenMP M. L. Dodson (Sun Apr 28 2013 - 14:07:32 PDT)
[AMBER] Gradually reduce the restraint within one step crazylyf (Thu Apr 25 2013 - 20:28:45 PDT)
- Re: [AMBER] Gradually reduce the restraint within one step David A Case (Fri Apr 26 2013 - 12:08:33 PDT)
  - Re: [AMBER] Gradually reduce the restraint within one step crazylyf.126.com (Fri Apr 26 2013 - 17:51:32 PDT)
    - [AMBER] Gradually reduce the restraint within one step Jian Yin (Fri Apr 26 2013 - 20:24:56 PDT)
    - Re: [AMBER] Gradually reduce the restraint within one step crazylyf.126.com (Fri Apr 26 2013 - 20:40:51 PDT)
    - Re: [AMBER] Gradually reduce the restraint within one step Jian Yin (Fri Apr 26 2013 - 21:08:50 PDT)
    - Re: [AMBER] Gradually reduce the restraint within one step crazylyf.126.com (Fri Apr 26 2013 - 21:29:53 PDT)
    - Re: [AMBER] Gradually reduce the restraint within one step David A Case (Sat Apr 27 2013 - 03:57:13 PDT)
    - Re: [AMBER] Gradually reduce the restraint within one step crazylyf.126.com (Sat Apr 27 2013 - 17:27:07 PDT)
[AMBER] the role of surface charge Sun (Fri Apr 26 2013 - 01:13:53 PDT)
- Re: [AMBER] the role of surface charge David A Case (Fri Apr 26 2013 - 17:28:28 PDT)
[AMBER] RMD with selected NMR restraints Krisztina Feher (Fri Apr 26 2013 - 06:32:40 PDT)
- Re: [AMBER] RMD with selected NMR restraints David A Case (Fri Apr 26 2013 - 17:24:49 PDT)
[AMBER] list of (dihedral and angle) parameters (GAFF) Vedat Durmaz (Fri Apr 26 2013 - 09:14:24 PDT)
- Re: [AMBER] list of (dihedral and angle) parameters (GAFF) Ilyas Yildirim (Fri Apr 26 2013 - 09:41:48 PDT)
- Re: [AMBER] list of (dihedral and angle) parameters (GAFF) Daniel Roe (Fri Apr 26 2013 - 09:42:30 PDT)
[AMBER] distance restraint Sangita Kachhap (Fri Apr 26 2013 - 10:54:38 PDT)
- Re: [AMBER] distance restraint David A Case (Fri Apr 26 2013 - 17:22:29 PDT)
[AMBER] Compiling problems with -openmp David A Case (Fri Apr 26 2013 - 12:51:28 PDT)
- Re: [AMBER] Compiling problems with -openmp Eugene Yedvabny (Fri Apr 26 2013 - 17:22:00 PDT)
  - Re: [AMBER] Compiling problems with -openmp David A Case (Sun Apr 28 2013 - 03:57:37 PDT)
[AMBER] paramfit question Covington, Cody Lance (Fri Apr 26 2013 - 15:20:08 PDT)
- Re: [AMBER] paramfit question Robin Betz (Fri Apr 26 2013 - 17:16:29 PDT)
[AMBER] how to get force information through MD run kurisaki (Sat Apr 27 2013 - 01:06:54 PDT)
- Re: [AMBER] how to get force information through MD run David A Case (Sat Apr 27 2013 - 04:02:38 PDT)
[AMBER] hbond print option equivalent in cpptraj from AmberTools13? miguel (Sat Apr 27 2013 - 08:01:54 PDT)
- Re: [AMBER] hbond print option equivalent in cpptraj from AmberTools13? Daniel Roe (Sat Apr 27 2013 - 10:01:42 PDT)
  - Re: [AMBER] hbond print option equivalent in cpptraj from AmberTools13? miguel (Sun Apr 28 2013 - 00:48:07 PDT)
[AMBER] Problem in parameter file generation Kshatresh Dutta Dubey (Sat Apr 27 2013 - 13:41:34 PDT)
- Re: [AMBER] Problem in parameter file generation Bill Ross (Sat Apr 27 2013 - 14:03:09 PDT)
  - Re: [AMBER] Problem in parameter file generation Kshatresh Dutta Dubey (Sat Apr 27 2013 - 14:28:23 PDT)
    - Re: [AMBER] Problem in parameter file generation Jason Swails (Sat Apr 27 2013 - 21:58:54 PDT)
    - Re: [AMBER] Problem in parameter file generation Kshatresh Dutta Dubey (Sun Apr 28 2013 - 00:23:31 PDT)
[AMBER] Sander/PMEMD doesn't understand line - corrupted RST output? Sebastian Petrik (Sun Apr 28 2013 - 17:17:26 PDT)
- Re: [AMBER] Sander/PMEMD doesn't understand line - corrupted RST output? Jason Swails (Sun Apr 28 2013 - 17:59:48 PDT)
  - Re: [AMBER] Sander/PMEMD doesn't understand line - corrupted RST output? Sebastian Petrik (Sun Apr 28 2013 - 18:49:56 PDT)
[AMBER] Prepare PRMTOP file for off-SHAKE simulation kurisaki (Sun Apr 28 2013 - 20:18:56 PDT)
- Re: [AMBER] Prepare PRMTOP file for off-SHAKE simulation kurisaki (Sun Apr 28 2013 - 21:14:20 PDT)
[AMBER] Palladium complex parametrization in antechamber Alexey Zeifman (Sun Apr 28 2013 - 23:43:14 PDT)
- Re: [AMBER] Palladium complex parametrization in antechamber David A Case (Mon Apr 29 2013 - 04:53:16 PDT)
  - Re: [AMBER] Palladium complex parametrization in antechamber Alexey Zeifman (Mon Apr 29 2013 - 04:58:02 PDT)
[AMBER] Paper detailing GPU Simulations Compared to CPU code ET (Mon Apr 29 2013 - 08:15:02 PDT)
- Re: [AMBER] Paper detailing GPU Simulations Compared to CPU code Ross Walker (Mon Apr 29 2013 - 09:19:46 PDT)
  - Re: [AMBER] Paper detailing GPU Simulations Compared to CPU code ET (Wed May 08 2013 - 17:12:19 PDT)
[AMBER] bug in impose command in amber tleap sandeep singh (Mon Apr 29 2013 - 11:21:19 PDT)
- Re: [AMBER] bug in impose command in amber tleap David A Case (Mon Apr 29 2013 - 11:42:11 PDT)
[AMBER] antechamber espgen error for molybdenum complex:fitting values are missing Sergio R Aragon (Mon Apr 29 2013 - 17:57:49 PDT)
- Re: [AMBER] antechamber espgen error for molybdenum complex:fitting values are missing Sergio R Aragon (Mon Apr 29 2013 - 19:52:56 PDT)
[AMBER] MMPBSA.py: ECAVITY / ENPOLAR discrepancy Jan-Philip Gehrcke (Tue Apr 30 2013 - 03:06:56 PDT)
- Re: [AMBER] MMPBSA.py: ECAVITY / ENPOLAR discrepancy Jan-Philip Gehrcke (Tue Apr 30 2013 - 03:51:27 PDT)
  - Re: [AMBER] MMPBSA.py: ECAVITY / ENPOLAR discrepancy Jason Swails (Tue Apr 30 2013 - 05:07:27 PDT)
    - Re: [AMBER] MMPBSA.py: ECAVITY / ENPOLAR discrepancy Jan-Philip Gehrcke (Tue Apr 30 2013 - 06:05:09 PDT)
    - Re: [AMBER] MMPBSA.py: ECAVITY / ENPOLAR discrepancy Jason Swails (Tue Apr 30 2013 - 06:32:20 PDT)
    - Re: [AMBER] MMPBSA.py: ECAVITY / ENPOLAR discrepancy Jan-Philip Gehrcke (Tue Apr 30 2013 - 06:37:27 PDT)
    - Re: [AMBER] MMPBSA.py: ECAVITY / ENPOLAR discrepancy Jan-Philip Gehrcke (Fri May 03 2013 - 02:53:36 PDT)
    - Re: [AMBER] MMPBSA.py: ECAVITY / ENPOLAR discrepancy Jason Swails (Fri May 03 2013 - 07:12:15 PDT)
    - Re: [AMBER] MMPBSA.py: ECAVITY / ENPOLAR discrepancy Jan-Philip Gehrcke (Fri May 03 2013 - 08:28:53 PDT)
[AMBER] DNA basestep stacking energy/interaction energy BERGY (Tue Apr 30 2013 - 03:27:03 PDT)
- Re: [AMBER] DNA basestep stacking energy/interaction energy David A Case (Tue Apr 30 2013 - 06:20:49 PDT)
  - Re: [AMBER] DNA basestep stacking energy/interaction energy BERGY (Wed May 01 2013 - 14:56:34 PDT)
[AMBER] pb_read.F90: minor issue // AmberTools . GitHub? Jan-Philip Gehrcke (Tue Apr 30 2013 - 06:27:51 PDT)
[AMBER] AMBER CUDA Installation Kanin Wichapong (Tue Apr 30 2013 - 09:17:59 PDT)
- Re: [AMBER] AMBER CUDA Installation Scott Le Grand (Tue Apr 30 2013 - 11:13:26 PDT)
- Re: [AMBER] AMBER CUDA Installation Massimiliano Porrini (Fri Nov 22 2013 - 03:38:44 PST)
  - Re: [AMBER] AMBER CUDA Installation Jason Swails (Fri Nov 22 2013 - 04:32:18 PST)
[AMBER] improper Dihedral Specification Covington, Cody Lance (Tue Apr 30 2013 - 13:06:35 PDT)
- Re: [AMBER] improper Dihedral Specification David A Case (Wed May 01 2013 - 04:52:51 PDT)
- Re: [AMBER] improper Dihedral Specification Bill Ross (Wed May 01 2013 - 15:51:21 PDT)
[AMBER] psf files from cellulose builder Rasha Alqus (Wed May 01 2013 - 08:59:05 PDT)
[AMBER] restart a md simulation 纪晓峰 (Wed May 01 2013 - 18:42:34 PDT)
[AMBER] restart a md simulation 纪晓峰 (Wed May 01 2013 - 18:53:03 PDT)
- Re: [AMBER] restart a md simulation Anselm Horn (Thu May 02 2013 - 02:04:40 PDT)
[AMBER] occasional distortion of solute molecule crazylyf (Wed May 01 2013 - 21:23:15 PDT)
[AMBER] Amber 12 installation on GPU Shozeb Haider (Wed May 01 2013 - 23:51:46 PDT)
- Re: [AMBER] Amber 12 installation on GPU hannes.loeffler.stfc.ac.uk (Thu May 02 2013 - 00:04:00 PDT)
- Re: [AMBER] Amber 12 installation on GPU David A Case (Thu May 02 2013 - 06:29:48 PDT)
- Re: [AMBER] Amber 12 installation on GPU Ross Walker (Thu May 02 2013 - 07:24:01 PDT)
[AMBER] cpptraj hbond: how to efficiently gather receptor-ligand hydrogen bonding statistics? Jan-Philip Gehrcke (Thu May 02 2013 - 05:30:36 PDT)
- Re: [AMBER] cpptraj hbond: how to efficiently gather receptor-ligand hydrogen bonding statistics? Daniel Roe (Thu May 02 2013 - 07:22:02 PDT)
  - Re: [AMBER] cpptraj hbond: how to efficiently gather receptor-ligand hydrogen bonding statistics? Jan-Philip Gehrcke (Thu May 02 2013 - 08:02:56 PDT)
[AMBER] PM6 fails for DMSO system me, Nancy (Thu May 02 2013 - 14:48:59 PDT)
- Re: [AMBER] PM6 fails for DMSO system Jason Swails (Thu May 02 2013 - 15:25:46 PDT)
  - Re: [AMBER] PM6 fails for DMSO system me, Nancy (Thu May 02 2013 - 16:34:05 PDT)
    - Re: [AMBER] PM6 fails for DMSO system me, Nancy (Fri May 03 2013 - 18:14:52 PDT)
    - Re: [AMBER] PM6 fails for DMSO system Andreas Goetz (Sat May 04 2013 - 18:43:36 PDT)
[AMBER] vlimit exceed followed by SHAKE failure seçkin Boz (Fri May 03 2013 - 03:43:24 PDT)
- Re: [AMBER] vlimit exceed followed by SHAKE failure David A Case (Fri May 03 2013 - 04:59:20 PDT)
  - Re: [AMBER] vlimit exceed followed by SHAKE failure seçkin Boz (Fri May 03 2013 - 05:47:52 PDT)
    - Re: [AMBER] vlimit exceed followed by SHAKE failure David A Case (Fri May 03 2013 - 11:59:33 PDT)
    - Re: [AMBER] vlimit exceed followed by SHAKE failure seçkin Boz (Tue May 07 2013 - 01:48:18 PDT)
    - Re: [AMBER] vlimit exceed followed by SHAKE failure David A Case (Tue May 07 2013 - 05:49:28 PDT)
    - Re: [AMBER] vlimit exceed followed by SHAKE failure seçkin Boz (Thu May 09 2013 - 04:06:22 PDT)
[AMBER] Advice on length of production simulation Chris Chris (Fri May 03 2013 - 09:01:49 PDT)
- Re: [AMBER] Advice on length of production simulation Marc van der Kamp (Sat May 04 2013 - 04:08:34 PDT)
[AMBER] Need your help Poornima Iyer (Fri May 03 2013 - 10:43:22 PDT)
- Re: [AMBER] Need your help David A Case (Fri May 03 2013 - 11:56:51 PDT)
[AMBER] MMPBSA Error: gb>0 is incompatible with periodic boundary conditions. Angelica Parente (Sat May 04 2013 - 02:08:02 PDT)
- Re: [AMBER] MMPBSA Error: gb>0 is incompatible with periodic boundary conditions. Jan-Philip Gehrcke (Sat May 04 2013 - 08:59:59 PDT)
- Re: [AMBER] MMPBSA Error: gb>0 is incompatible with periodic boundary conditions. David A Case (Sat May 04 2013 - 09:56:37 PDT)
- Re: [AMBER] MMPBSA Error: gb>0 is incompatible with periodic boundary conditions. Jason Swails (Sat May 04 2013 - 17:06:02 PDT)
[AMBER] radial distribution function problem Jio M (Sat May 04 2013 - 02:35:28 PDT)
- Re: [AMBER] radial distribution function problem Daniel Roe (Sat May 04 2013 - 09:10:52 PDT)
[AMBER] Ambertools13 installation issue Chinthaka Ratnaweera (Sat May 04 2013 - 13:21:17 PDT)
- Re: [AMBER] Ambertools13 installation issue Daniel Roe (Sat May 04 2013 - 16:13:33 PDT)
  - Re: [AMBER] Ambertools13 installation issue Chinthaka Ratnaweera (Sat May 04 2013 - 17:16:20 PDT)
    - Re: [AMBER] Ambertools13 installation issue Jason Swails (Sat May 04 2013 - 20:07:59 PDT)
    - Re: [AMBER] Ambertools13 installation issue Chinthaka Ratnaweera (Sat May 04 2013 - 20:48:17 PDT)
    - Re: [AMBER] Ambertools13 installation issue Jason Swails (Sun May 05 2013 - 05:15:47 PDT)
    - Re: [AMBER] Ambertools13 installation issue Chinthaka Ratnaweera (Sun May 05 2013 - 06:46:40 PDT)
    - Re: [AMBER] Ambertools13 installation issue Jason Swails (Sun May 05 2013 - 08:26:44 PDT)
- Re: [AMBER] Ambertools13 installation issue Jason Swails (Sat May 04 2013 - 17:14:46 PDT)
- Re: [AMBER] Ambertools13 installation issue Hector A. Baldoni (Sat May 04 2013 - 17:25:14 PDT)
[AMBER] about halogen atom radius in MMPBSA calculation Wang Bo (Sat May 04 2013 - 21:05:00 PDT)
- Re: [AMBER] about halogen atom radius in MMPBSA calculation Nadine Homeyer (Sun May 05 2013 - 23:00:16 PDT)
[AMBER] FW: Busco informacion sobre AMBER Patricia Castro Gutierrez (Sat May 04 2013 - 22:32:22 PDT)
- Re: [AMBER] FW: Busco informacion sobre AMBER ros (Sat May 04 2013 - 23:09:29 PDT)
- Re: [AMBER] FW: Busco informacion sobre AMBER Sergio R Aragon (Sat May 04 2013 - 23:11:18 PDT)
[AMBER] I can't visualize (in vmd) the output from an Accelerated MD (aMD) run Jonathan Gough (Sun May 05 2013 - 05:46:24 PDT)
- Re: [AMBER] I can't visualize (in vmd) the output from an Accelerated MD (aMD) run Daniel Roe (Sun May 05 2013 - 09:05:58 PDT)
  - Re: [AMBER] I can't visualize (in vmd) the output from an Accelerated MD (aMD) run Jonathan Gough (Sun May 05 2013 - 09:20:37 PDT)
[AMBER] problem in cpptraj installation Kshatresh Dutta Dubey (Sun May 05 2013 - 07:56:57 PDT)
- Re: [AMBER] problem in cpptraj installation Daniel Roe (Sun May 05 2013 - 08:59:03 PDT)
  - Re: [AMBER] problem in cpptraj installation Kshatresh Dutta Dubey (Sun May 05 2013 - 09:07:54 PDT)
    - Re: [AMBER] problem in cpptraj installation Daniel Roe (Sun May 05 2013 - 09:26:19 PDT)
    - Re: [AMBER] problem in cpptraj installation Kshatresh Dutta Dubey (Sun May 05 2013 - 10:58:09 PDT)
    - Re: [AMBER] problem in cpptraj installation Daniel Roe (Mon May 06 2013 - 07:54:20 PDT)
    - Re: [AMBER] problem in cpptraj installation Kshatresh Dutta Dubey (Mon May 06 2013 - 08:15:09 PDT)
    - Re: [AMBER] problem in cpptraj installation Daniel Roe (Mon May 06 2013 - 08:45:35 PDT)
[AMBER] Fwd: Robin Jain (Sun May 05 2013 - 22:33:23 PDT)
[AMBER] Bug in cpptraj (AmberTools 13) Ake Sandgren (Sun May 05 2013 - 23:07:12 PDT)
- Re: [AMBER] Bug in cpptraj (AmberTools 13) Daniel Roe (Mon May 06 2013 - 07:15:12 PDT)
[AMBER] Ptraj_segmentation fault KAMAKSHI SHARMA (Mon May 06 2013 - 00:26:22 PDT)
- Re: [AMBER] Ptraj_segmentation fault Jason Swails (Mon May 06 2013 - 05:36:30 PDT)
[AMBER] Protein-ligand docking kanika sharma (Mon May 06 2013 - 04:27:45 PDT)
- Re: [AMBER] Protein-ligand docking David A Case (Mon May 06 2013 - 05:25:33 PDT)
[AMBER] Test for NTP, ntt=3 Deák Robert (Mon May 06 2013 - 06:23:46 PDT)
- Re: [AMBER] Test for NTP, ntt=3 Deák Robert (Mon May 06 2013 - 06:25:38 PDT)
  - Re: [AMBER] Test for NTP, ntt=3 Jason Swails (Mon May 06 2013 - 07:00:15 PDT)
    - Re: [AMBER] Test for NTP, ntt=3 Deák Robert (Tue May 07 2013 - 02:47:41 PDT)
    - Re: [AMBER] Test for NTP, ntt=3 Deák Robert (Tue May 07 2013 - 02:52:22 PDT)
    - Re: [AMBER] Test for NTP, ntt=3 Jason Swails (Tue May 07 2013 - 05:54:27 PDT)
    - Re: [AMBER] Test for NTP, ntt=3 David A Case (Tue May 07 2013 - 15:44:25 PDT)
[AMBER] MMPBSA.py error Le,Huy Tuan (Mon May 06 2013 - 06:39:25 PDT)
- Re: [AMBER] MMPBSA.py error Jason Swails (Mon May 06 2013 - 06:50:45 PDT)
  - Re: [AMBER] MMPBSA.py error Le,Huy Tuan (Mon May 06 2013 - 07:10:54 PDT)
[AMBER] MMPBSA.py error Kshatresh Dutta Dubey (Mon May 06 2013 - 07:16:27 PDT)
- Re: [AMBER] MMPBSA.py error Chris Chris (Mon May 06 2013 - 08:18:28 PDT)
  - Re: [AMBER] MMPBSA.py error Kshatresh Dutta Dubey (Mon May 06 2013 - 08:21:11 PDT)
    - Re: [AMBER] MMPBSA.py error Jason Swails (Mon May 06 2013 - 11:40:48 PDT)
    - Re: [AMBER] MMPBSA.py error Kshatresh Dutta Dubey (Mon May 06 2013 - 12:09:36 PDT)
    - Re: [AMBER] MMPBSA.py error Jason Swails (Mon May 06 2013 - 12:52:41 PDT)
    - Re: [AMBER] MMPBSA.py error Kshatresh Dutta Dubey (Mon May 06 2013 - 13:01:57 PDT)
    - Re: [AMBER] MMPBSA.py error Jason Swails (Mon May 06 2013 - 13:04:42 PDT)
[AMBER] mmpbsa error msg Chinthaka Ratnaweera (Mon May 06 2013 - 07:23:34 PDT)
- Re: [AMBER] mmpbsa error msg Chinthaka Ratnaweera (Mon May 06 2013 - 07:26:05 PDT)
  - Re: [AMBER] mmpbsa error msg Jason Swails (Mon May 06 2013 - 11:41:57 PDT)
    - Re: [AMBER] mmpbsa error msg Chinthaka Ratnaweera (Mon May 06 2013 - 11:53:23 PDT)
    - Re: [AMBER] mmpbsa error msg Jason Swails (Mon May 06 2013 - 12:58:21 PDT)
[AMBER] the best APS is not zero, bonds involved by this atom are frozen Ashutosh Shandilya (Mon May 06 2013 - 08:15:43 PDT)
- Re: [AMBER] the best APS is not zero, bonds involved by this atom are frozen Ashutosh Shandilya (Mon May 06 2013 - 08:24:40 PDT)
[AMBER] Open MPI failure David Winogradoff (Mon May 06 2013 - 09:18:43 PDT)
- Re: [AMBER] Open MPI failure Daniel Roe (Mon May 06 2013 - 09:30:52 PDT)
  - Re: [AMBER] Open MPI failure David Winogradoff (Mon May 06 2013 - 10:25:29 PDT)
- Re: [AMBER] Open MPI failure Ross Walker (Mon May 06 2013 - 10:30:03 PDT)
- Re: [AMBER] Open MPI failure David A Case (Mon May 06 2013 - 12:49:25 PDT)
  - Re: [AMBER] Open MPI failure David Winogradoff (Tue May 07 2013 - 09:17:50 PDT)
    - Re: [AMBER] Open MPI failure Daniel Roe (Tue May 07 2013 - 10:38:44 PDT)
    - Re: [AMBER] Open MPI failure David Winogradoff (Tue May 07 2013 - 11:27:10 PDT)
    - Re: [AMBER] Open MPI failure Daniel Roe (Tue May 07 2013 - 13:41:46 PDT)
[AMBER] Leap adding salt No solvent overlap Johannes Zuegg (Mon May 06 2013 - 18:35:03 PDT)
- Re: [AMBER] Leap adding salt No solvent overlap Jason Swails (Mon May 06 2013 - 20:19:25 PDT)
  - Re: [AMBER] Leap adding salt No solvent overlap Daniel Roe (Tue May 07 2013 - 07:52:01 PDT)
- Re: [AMBER] Leap adding salt No solvent overlap Johannes Zuegg (Tue May 07 2013 - 16:51:44 PDT)
[AMBER] Atom does not have a type. javier alejandro rendon carrillo (Tue May 07 2013 - 00:48:42 PDT)
- Re: [AMBER] Atom does not have a type. David A Case (Tue May 07 2013 - 05:32:22 PDT)
  - Re: [AMBER] Atom does not have a type. Javier Alejandro Rendon Carrillo (Thu Feb 20 2014 - 07:09:52 PST)
    - Re: [AMBER] Atom does not have a type. Jason Swails (Thu Feb 20 2014 - 07:26:08 PST)
    - Re: [AMBER] Atom does not have a type. Javier Alejandro Rendon Carrillo (Thu Feb 20 2014 - 08:12:00 PST)
    - Re: [AMBER] Atom does not have a type. Aldo Segura (Thu Feb 20 2014 - 07:35:35 PST)
    - Re: [AMBER] Atom does not have a type. Javier Alejandro Rendon Carrillo (Thu Feb 20 2014 - 08:23:44 PST)
    - Re: [AMBER] Atom does not have a type. Aldo Segura (Thu Feb 20 2014 - 08:38:47 PST)
    - Re: [AMBER] Atom does not have a type. Aldo Segura (Thu Feb 20 2014 - 08:47:10 PST)
[AMBER] error while restart run Subrata Paul (Tue May 07 2013 - 04:22:41 PDT)
- Re: [AMBER] error while restart run David A Case (Tue May 07 2013 - 05:45:21 PDT)
  - Re: [AMBER] error while restart run Daniel Roe (Tue May 07 2013 - 07:19:44 PDT)
[AMBER] problems solvating Jonathan Gough (Tue May 07 2013 - 05:58:05 PDT)
- Re: [AMBER] problems solvating Daniel Roe (Tue May 07 2013 - 07:16:14 PDT)
[AMBER] Improper atom order Reinis Danne (Tue May 07 2013 - 05:26:53 PDT)
- Re: [AMBER] Improper atom order Karl N. Kirschner (Wed May 08 2013 - 01:16:20 PDT)
  - Re: [AMBER] Improper atom order Reinis Danne (Wed May 08 2013 - 01:19:40 PDT)
- Re: [AMBER] Improper atom order Bill Ross (Wed May 08 2013 - 17:34:52 PDT)
  - Re: [AMBER] Improper atom order Reinis Danne (Thu May 09 2013 - 00:21:05 PDT)
    - Re: [AMBER] Improper atom order Bill Ross (Sat May 11 2013 - 11:51:40 PDT)
[AMBER] PME and vdW cutoffs George Tzotzos (Tue May 07 2013 - 09:37:59 PDT)
- Re: [AMBER] PME and vdW cutoffs Andreas Goetz (Tue May 07 2013 - 13:22:38 PDT)
[AMBER] Error in Membrane protein Simulation Dipankar Roy (Tue May 07 2013 - 09:39:40 PDT)
- Re: [AMBER] Error in Membrane protein Simulation David A Case (Tue May 07 2013 - 15:44:54 PDT)
  - Re: [AMBER] Error in Membrane protein Simulation Ross Walker (Tue May 07 2013 - 16:42:53 PDT)
[AMBER] Optimal APBS parameters - Amber OR APBS defaults ? Marek Maly (Tue May 07 2013 - 11:27:06 PDT)
- Re: [AMBER] Optimal APBS parameters - Amber OR APBS defaults ? Ray Luo, Ph.D. (Tue May 07 2013 - 14:52:26 PDT)
  - Re: [AMBER] Optimal APBS parameters - Amber OR APBS defaults ? Marek Maly (Tue May 07 2013 - 20:20:00 PDT)
[AMBER] when doing accelerated MD... Jonathan Gough (Tue May 07 2013 - 14:01:20 PDT)
- Re: [AMBER] when doing accelerated MD... Jesper Sørensen (Tue May 07 2013 - 15:09:22 PDT)
  - Re: [AMBER] when doing accelerated MD... Jonathan Gough (Tue May 07 2013 - 15:16:57 PDT)
[AMBER] How to average rst ? 赵媛 (Tue May 07 2013 - 20:58:15 PDT)
- Re: [AMBER] How to average rst ? Daniel Roe (Wed May 08 2013 - 08:02:01 PDT)
[AMBER] Kind of RESTYPE setyanto md (Tue May 07 2013 - 22:12:27 PDT)
- Re: [AMBER] Kind of RESTYPE David A Case (Wed May 08 2013 - 05:14:32 PDT)
[AMBER] ATTN: need revision seçkin Boz (Wed May 08 2013 - 02:17:35 PDT)
- Re: [AMBER] ATTN: need revision Karl N. Kirschner (Wed May 08 2013 - 03:00:03 PDT)
  - Re: [AMBER] ATTN: need revision seçkin Boz (Thu May 09 2013 - 04:45:46 PDT)
    - Re: [AMBER] ATTN: need revision Karl N. Kirschner (Mon May 13 2013 - 00:32:00 PDT)
    - Re: [AMBER] ATTN: need revision Karl N. Kirschner (Mon May 13 2013 - 04:07:44 PDT)
[AMBER] unstable sytem-help Mary Varughese (Wed May 08 2013 - 04:01:52 PDT)
- [AMBER] Fwd: unstable sytem-help Mary Varughese (Thu May 09 2013 - 02:05:19 PDT)
  - Re: [AMBER] Fwd: unstable sytem-help David A Case (Thu May 09 2013 - 06:03:28 PDT)
    - Re: [AMBER] Fwd: unstable sytem-help Mary Varughese (Thu May 09 2013 - 06:50:32 PDT)
    - Re: [AMBER] Fwd: unstable sytem-help David A Case (Fri May 10 2013 - 03:48:11 PDT)
    - Re: [AMBER] Fwd: unstable sytem-help Mary Varughese (Fri May 10 2013 - 16:44:16 PDT)
[AMBER] Assistance required for MCPB program BALA SUBRAMANI G L (Wed May 08 2013 - 05:19:51 PDT)
[AMBER] fw: hey Wholly Peach (Wed May 08 2013 - 06:32:28 PDT)
[AMBER] normal modes and intensity for raman spectrum Rasha Alqus (Wed May 08 2013 - 08:51:56 PDT)
- Re: [AMBER] normal modes and intensity for raman spectrum Adrian Roitberg (Wed May 08 2013 - 10:54:46 PDT)
[AMBER] pmemd performance on AMD 16cores x 4 (total 64 CPU cores) + 1 GPU sun (Wed May 08 2013 - 09:40:23 PDT)
- Re: [AMBER] pmemd performance on AMD 16cores x 4 (total 64 CPU cores) + 1 GPU Sergio R Aragon (Wed May 08 2013 - 12:19:20 PDT)
  - Re: [AMBER] pmemd performance on AMD 16cores x 4 (total 64 CPU cores) + 1 GPU Scott Le Grand (Wed May 08 2013 - 12:51:30 PDT)
    - Re: [AMBER] pmemd performance on AMD 16cores x 4 (total 64 CPU cores) + 1 GPU Ross Walker (Wed May 08 2013 - 13:15:31 PDT)
[AMBER] error running pmemd cuda tests Blake Mertz (Wed May 08 2013 - 11:32:46 PDT)
- Re: [AMBER] error running pmemd cuda tests Jason Swails (Wed May 08 2013 - 12:19:55 PDT)
  - Re: [AMBER] error running pmemd cuda tests Blake Mertz (Wed May 08 2013 - 18:53:53 PDT)
    - Re: [AMBER] error running pmemd cuda tests ET (Thu May 09 2013 - 00:57:17 PDT)
    - Re: [AMBER] error running pmemd cuda tests Blake Mertz (Thu May 09 2013 - 06:15:57 PDT)
    - Re: [AMBER] error running pmemd cuda tests Jason Swails (Thu May 09 2013 - 07:28:54 PDT)
    - Re: [AMBER] error running pmemd cuda tests ET (Fri May 10 2013 - 09:33:19 PDT)
[AMBER] About free energy decomposition 赵媛 (Wed May 08 2013 - 20:23:32 PDT)
- Re: [AMBER] About free energy decomposition Bill Miller III (Fri May 10 2013 - 21:02:10 PDT)
[AMBER] DNA ligand system broke up- help please Mary Varughese (Thu May 09 2013 - 03:45:09 PDT)
[AMBER] AMBER GPU Cooling/usage Question ET (Thu May 09 2013 - 05:44:08 PDT)
- Re: [AMBER] AMBER GPU Cooling/usage Question Ross Walker (Thu May 09 2013 - 06:27:54 PDT)
  - Re: [AMBER] AMBER GPU Cooling/usage Question ET (Fri May 10 2013 - 08:49:23 PDT)
[AMBER] how to create parameter file for Zn BALA SUBRAMANI G L (Thu May 09 2013 - 06:13:16 PDT)
[AMBER] best way to get rmsd data between trajectory and DIFFERENT reference structure Andre C. Stiel (Thu May 09 2013 - 10:02:48 PDT)
- Re: [AMBER] best way to get rmsd data between trajectory and DIFFERENT reference structure Daniel Roe (Thu May 09 2013 - 12:41:08 PDT)
  - Re: [AMBER] best way to get rmsd data between trajectory and DIFFERENT reference structure Andre C. Stiel (Fri May 10 2013 - 05:03:18 PDT)
  - Re: [AMBER] best way to get rmsd data between trajectory and DIFFERENT reference structure Andre C. Stiel (Fri May 10 2013 - 05:31:38 PDT)
    - Re: [AMBER] best way to get rmsd data between trajectory and DIFFERENT reference structure Daniel Roe (Fri May 10 2013 - 05:40:01 PDT)
  - Re: [AMBER] best way to get rmsd data between trajectory and DIFFERENT reference structure Andre C. Stiel (Fri May 10 2013 - 05:41:21 PDT)
    - Re: [AMBER] best way to get rmsd data between trajectory and DIFFERENT reference structure Daniel Roe (Fri May 10 2013 - 05:57:11 PDT)
- [AMBER] Convergence criterion Anselm Horn (Fri May 17 2013 - 12:46:16 PDT)
  - Re: [AMBER] Convergence criterion David A Case (Fri May 17 2013 - 17:21:40 PDT)
    - Re: [AMBER] Convergence criterion Anselm Horn (Sat May 18 2013 - 04:14:13 PDT)
    - Re: [AMBER] Convergence criterion Andreas Goetz (Sat May 18 2013 - 13:00:28 PDT)
    - Re: [AMBER] Convergence criterion Anselm Horn (Sat May 18 2013 - 18:06:07 PDT)
[AMBER] Glass Transition Temperature Hector A. Baldoni (Thu May 09 2013 - 12:18:39 PDT)
- Re: [AMBER] Glass Transition Temperature David A Case (Fri May 10 2013 - 08:42:23 PDT)
[AMBER] apbsgrid error during sander.APBS calculation Marek Maly (Thu May 09 2013 - 17:18:54 PDT)
- Re: [AMBER] apbsgrid error during sander.APBS calculation Robert Konecny (Thu May 09 2013 - 18:53:16 PDT)
  - Re: [AMBER] apbsgrid error during sander.APBS calculation Marek Maly (Fri May 10 2013 - 04:48:06 PDT)
[AMBER] Problem with the SMD aplication to proton transfer Santi Tolosa (Fri May 10 2013 - 04:05:56 PDT)
- Re: [AMBER] Problem with the SMD aplication to proton transfer Brian Radak (Fri May 10 2013 - 05:55:58 PDT)
[AMBER] drmsd Chris Chris (Fri May 10 2013 - 22:23:22 PDT)
- Re: [AMBER] drmsd Daniel Roe (Sat May 11 2013 - 08:17:38 PDT)
[AMBER] NaN from Mg2+ near ASP while running aMD Jonathan Gough (Sun May 12 2013 - 12:34:31 PDT)
- Re: [AMBER] NaN from Mg2+ near ASP while running aMD Jonathan Gough (Sun May 12 2013 - 12:38:51 PDT)
[AMBER] sander.MPI is extremely slow Kshatresh Dutta Dubey (Sun May 12 2013 - 21:48:15 PDT)
- Re: [AMBER] sander.MPI is extremely slow Ross Walker (Mon May 13 2013 - 03:23:14 PDT)
[AMBER] The force constants of bond and angle items are zero when the MCPB program reads the internal force constant matrix JiYuan Liu (Mon May 13 2013 - 00:43:43 PDT)
[AMBER] Assistance required for capActivesite program Bala Subramani (Mon May 13 2013 - 06:09:05 PDT)
[AMBER] Inconsistent results for TI calculations Thomas Exner (Mon May 13 2013 - 07:47:36 PDT)
- Re: [AMBER] Inconsistent results for TI calculations steinbrt.rci.rutgers.edu (Mon May 13 2013 - 09:31:50 PDT)
- Re: [AMBER] Inconsistent results for TI calculations Antonios Kolocouris (Mon May 13 2013 - 09:48:58 PDT)
[AMBER] (nessun oggetto) Maurizio CELENTANO (Mon May 13 2013 - 07:52:58 PDT)
- Re: [AMBER] (nessun oggetto) David A Case (Mon May 13 2013 - 09:08:29 PDT)
  - Re: [AMBER] (nessun oggetto) Maurizio CELENTANO (Mon May 13 2013 - 11:00:31 PDT)
    - Re: [AMBER] (nessun oggetto) David A Case (Mon May 13 2013 - 13:08:58 PDT)
[AMBER] cpptraj strange warning with cluster command Miguel Ortiz Lombardía (Mon May 13 2013 - 08:26:03 PDT)
- Re: [AMBER] cpptraj strange warning with cluster command Daniel Roe (Mon May 13 2013 - 08:35:59 PDT)
  - Re: [AMBER] cpptraj strange warning with cluster command Miguel Ortiz Lombardía (Mon May 13 2013 - 09:08:40 PDT)
[AMBER] mpi4py installation error Kshatresh Dutta Dubey (Mon May 13 2013 - 11:18:50 PDT)
- Re: [AMBER] mpi4py installation error Daniel Roe (Mon May 13 2013 - 12:15:39 PDT)
  - Re: [AMBER] mpi4py installation error Kshatresh Dutta Dubey (Mon May 13 2013 - 12:24:21 PDT)
[AMBER] amber tutorial A15 yanyuna (Mon May 13 2013 - 18:16:19 PDT)
- Re: [AMBER] amber tutorial A15 David A Case (Mon May 13 2013 - 18:59:00 PDT)
  - Re: [AMBER] amber tutorial A15 yanyuna (Mon May 13 2013 - 19:04:04 PDT)
    - Re: [AMBER] amber tutorial A15 David A Case (Tue May 14 2013 - 03:35:12 PDT)
  - Re: [AMBER] amber tutorial A15 yanyuna (Mon May 13 2013 - 19:30:21 PDT)
[AMBER] assistance required for MTK++ BALA SUBRAMANI G L (Tue May 14 2013 - 00:20:27 PDT)
[AMBER] error while using tleap with protein more than 248 residues sandeep singh (Sun May 12 2013 - 22:05:11 PDT)
- Re: [AMBER] error while using tleap with protein more than 248 residues David A Case (Tue May 14 2013 - 03:32:20 PDT)
- Re: [AMBER] error while using tleap with protein more than 248 residues Daniel Roe (Tue May 14 2013 - 07:48:39 PDT)
[AMBER] Random Acceleration Molecular Dynamics (RAMD) Lars Skjærven (Tue May 14 2013 - 03:16:50 PDT)
- Re: [AMBER] Random Acceleration Molecular Dynamics (RAMD) Vlad Cojocaru (Tue May 14 2013 - 03:55:48 PDT)
[AMBER] Nonpolar contribution in MMPBSA is very large Kshatresh Dutta Dubey (Tue May 14 2013 - 03:34:19 PDT)
- Re: [AMBER] Nonpolar contribution in MMPBSA is very large Jason Swails (Tue May 14 2013 - 05:04:22 PDT)
  - Re: [AMBER] Nonpolar contribution in MMPBSA is very large Kshatresh Dutta Dubey (Tue May 14 2013 - 05:32:33 PDT)
    - Re: [AMBER] Nonpolar contribution in MMPBSA is very large Jan-Philip Gehrcke (Tue May 14 2013 - 05:39:16 PDT)
    - Re: [AMBER] Nonpolar contribution in MMPBSA is very large Kshatresh Dutta Dubey (Tue May 14 2013 - 05:48:14 PDT)
    - Re: [AMBER] Nonpolar contribution in MMPBSA is very large Jason Swails (Tue May 14 2013 - 07:21:02 PDT)
    - Re: [AMBER] Nonpolar contribution in MMPBSA is very large Kshatresh Dutta Dubey (Tue May 14 2013 - 07:38:19 PDT)
[AMBER] Assistance required for capActivesite program BALA SUBRAMANI G L (Mon May 13 2013 - 06:08:23 PDT)
- Re: [AMBER] Assistance required for capActivesite program steinbrt.rci.rutgers.edu (Tue May 14 2013 - 04:54:03 PDT)
[AMBER] random seed not in output file -> run not reproducible Jan-Philip Gehrcke (Tue May 14 2013 - 04:02:30 PDT)
- Re: [AMBER] random seed not in output file -> run not reproducible Ross Walker (Tue May 14 2013 - 04:35:08 PDT)
  - Re: [AMBER] random seed not in output file -> run not reproducible Jason Swails (Tue May 14 2013 - 05:02:20 PDT)
    - Re: [AMBER] random seed not in output file -> run not reproducible Ross Walker (Tue May 14 2013 - 05:04:20 PDT)
    - Re: [AMBER] random seed not in output file -> run not reproducible Jason Swails (Tue May 14 2013 - 05:20:43 PDT)
  - Re: [AMBER] random seed not in output file -> run not reproducible Jan-Philip Gehrcke (Tue May 14 2013 - 05:15:51 PDT)
[AMBER] Free Energy for the G Quadruplex DNA including channel potassium ions Debayan Chakraborty (Tue May 14 2013 - 05:03:26 PDT)
[AMBER] assistance required for bcl scripts BALA SUBRAMANI G L (Tue May 14 2013 - 05:24:41 PDT)
[AMBER] SMD for proton transfer Santi Tolosa (Tue May 14 2013 - 06:19:54 PDT)
- Re: [AMBER] SMD for proton transfer M. L. Dodson (Tue May 14 2013 - 06:47:30 PDT)
[AMBER] Problem with cpptraj vs ptraj imarcos (Tue May 14 2013 - 06:33:50 PDT)
- Re: [AMBER] Problem with cpptraj vs ptraj Daniel Roe (Tue May 14 2013 - 07:12:12 PDT)
- Re: [AMBER] Problem with cpptraj vs ptraj imarcos (Thu May 16 2013 - 03:55:15 PDT)
[AMBER] preferred nucleic acids pbsa model Le,Huy Tuan (Tue May 14 2013 - 06:55:40 PDT)
[AMBER] memory failure Jonathan Gough (Tue May 14 2013 - 10:39:27 PDT)
- Re: [AMBER] memory failure Jonathan Gough (Tue May 14 2013 - 10:41:56 PDT)
  - Re: [AMBER] memory failure David A Case (Tue May 14 2013 - 11:15:08 PDT)
    - Re: [AMBER] memory failure Jonathan Gough (Tue May 14 2013 - 12:45:05 PDT)
[AMBER] assistance required for prep & frcmod file preparation BALA SUBRAMANI G L (Wed May 15 2013 - 00:00:24 PDT)
[AMBER] NAMD TO AMBER Rasha Alqus (Wed May 15 2013 - 03:37:32 PDT)
- [AMBER] pmemd.CUDA installation problem Cenk $Jenk$ Andac (Wed May 15 2013 - 09:38:14 PDT)
  - Re: [AMBER] pmemd.CUDA installation problem Jason Swails (Wed May 15 2013 - 10:03:29 PDT)
    - Re: [AMBER] pmemd.CUDA installation problem Cenk $Jenk$ Andac (Wed May 15 2013 - 23:11:12 PDT)
    - Re: [AMBER] pmemd.CUDA installation problem Cenk $Jenk$ Andac (Thu May 16 2013 - 00:24:56 PDT)
[AMBER] Interpreting .prmtop files David Winogradoff (Wed May 15 2013 - 14:13:54 PDT)
- Re: [AMBER] Interpreting .prmtop files Hai Nguyen (Wed May 15 2013 - 14:18:33 PDT)
- Re: [AMBER] Interpreting .prmtop files Jason Swails (Wed May 15 2013 - 16:18:14 PDT)
  - Re: [AMBER] Interpreting .prmtop files David Winogradoff (Thu May 16 2013 - 06:07:14 PDT)
    - Re: [AMBER] Interpreting .prmtop files David Winogradoff (Thu May 16 2013 - 08:49:12 PDT)
    - Re: [AMBER] Interpreting .prmtop files Jason Swails (Thu May 16 2013 - 09:15:16 PDT)
    - Re: [AMBER] Interpreting .prmtop files David Winogradoff (Tue May 28 2013 - 08:45:27 PDT)
[AMBER] SMD pulling GPU José Guilherme Vilhena Albuquerque d'Orey (Thu May 16 2013 - 01:44:07 PDT)
- Re: [AMBER] SMD pulling GPU James Murdock (Thu May 16 2013 - 03:42:30 PDT)
- Re: [AMBER] SMD pulling GPU Ross Walker (Thu May 16 2013 - 07:58:09 PDT)
  - Re: [AMBER] SMD pulling GPU José Guilherme Vilhena Albuquerque d'Orey (Thu May 16 2013 - 08:29:39 PDT)
    - Re: [AMBER] SMD pulling GPU Ross Walker (Thu May 16 2013 - 09:59:41 PDT)
[AMBER] References abou FF12SB Alan (Thu May 16 2013 - 05:35:56 PDT)
- [AMBER] cluster Mannan (Tue May 21 2013 - 03:48:43 PDT)
  - Re: [AMBER] cluster Daniel Roe (Tue May 21 2013 - 07:28:47 PDT)
- Re: [AMBER] References abou FF12SB Carlos Simmerling (Tue May 21 2013 - 04:52:44 PDT)
[AMBER] ff10 from amber11 maybe not using OL3?? Amparo Garcia Lopez (Thu May 16 2013 - 09:31:16 PDT)
- Re: [AMBER] ff10 from amber11 maybe not using OL3?? Niel Henriksen (Thu May 16 2013 - 11:57:32 PDT)
- Re: [AMBER] ff10 from amber11 maybe not using OL3?? pavel.banas.upol.cz (Thu May 16 2013 - 13:16:00 PDT)
  - Re: [AMBER] ff10 from amber11 maybe not using OL3?? Amparo Garcia Lopez (Thu May 16 2013 - 14:16:09 PDT)
    - Re: [AMBER] ff10 from amber11 maybe not using OL3?? Amparo Garcia Lopez (Thu May 16 2013 - 14:44:00 PDT)
    - Re: [AMBER] ff10 from amber11 maybe not using OL3?? Ilyas Yildirim (Thu May 16 2013 - 15:18:31 PDT)
- Re: [AMBER] ff10 from amber11 maybe not using OL3?? pavel.banas.upol.cz (Thu May 16 2013 - 16:05:04 PDT)
  - Re: [AMBER] ff10 from amber11 maybe not using OL3?? Amparo Garcia Lopez (Fri May 17 2013 - 00:58:45 PDT)
    - Re: [AMBER] ff10 from amber11 maybe not using OL3?? David A Case (Fri May 17 2013 - 05:35:07 PDT)
[AMBER] How to dump distance information in the form of a vector file? Sajeewa Pemasinghe (Thu May 16 2013 - 14:19:53 PDT)
- Re: [AMBER] How to dump distance information in the form of a vector file? Daniel Roe (Thu May 16 2013 - 14:53:19 PDT)
  - Re: [AMBER] How to dump distance information in the form of a vector file? Sajeewa Pemasinghe (Thu May 16 2013 - 15:38:27 PDT)
    - Re: [AMBER] How to dump distance information in the form of a vector file? Daniel Roe (Thu May 16 2013 - 15:48:18 PDT)
[AMBER] Parameters for Aluminum Ion Sun (Thu May 16 2013 - 21:00:48 PDT)
- Re: [AMBER] Parameters for Aluminum Ion Jason Swails (Fri Jun 14 2013 - 08:42:25 PDT)
[AMBER] How to specify a vector to keep track of the velocities of all residues during a simulation? Sajeewa Pemasinghe (Fri May 17 2013 - 10:05:13 PDT)
- Re: [AMBER] How to specify a vector to keep track of the velocities of all residues during a simulation? Daniel Roe (Fri May 17 2013 - 10:34:40 PDT)
  - Re: [AMBER] How to specify a vector to keep track of the velocities of all residues during a simulation? Sajeewa Pemasinghe (Fri May 17 2013 - 10:58:14 PDT)
  - Re: [AMBER] How to specify a vector to keep track of the velocities of all residues during a simulation? David A Case (Fri May 17 2013 - 11:11:51 PDT)
[AMBER] force field parameters for acetylated lysine Senthil Natesan (Fri May 17 2013 - 11:03:52 PDT)
- Re: [AMBER] force field parameters for acetylated lysine Karl N. Kirschner (Tue May 21 2013 - 00:17:27 PDT)
  - Re: [AMBER] force field parameters for acetylated lysine Senthil Natesan (Tue May 21 2013 - 06:28:15 PDT)
[AMBER] repeat MD simulations Kanin Wichapong (Sat May 18 2013 - 03:19:55 PDT)
- Re: [AMBER] repeat MD simulations Vlad Cojocaru (Sat May 18 2013 - 04:34:24 PDT)
[AMBER] MMPBSA for stability analysis Debayan Chakraborty (Sat May 18 2013 - 10:43:21 PDT)
- Re: [AMBER] MMPBSA for stability analysis Jason Swails (Sat May 18 2013 - 18:12:07 PDT)
[AMBER] Grid command for water density BERGY (Sun May 19 2013 - 02:08:08 PDT)
- [AMBER] antechamber and sqm problem Cenk $Jenk$ Andac (Sun May 19 2013 - 11:07:40 PDT)
  - Re: [AMBER] antechamber and sqm problem Jason Swails (Sun May 19 2013 - 12:26:31 PDT)
- Re: [AMBER] Grid command for water density Jason Swails (Tue May 21 2013 - 04:49:55 PDT)
[AMBER] Molecular Shape Searching on GPUs MARK (Mon May 20 2013 - 11:05:45 PDT)
- Re: [AMBER] Molecular Shape Searching on GPUs MARK (Mon May 20 2013 - 11:09:06 PDT)
  - [AMBER] cpptraj and avgcoord Anselm Horn (Tue May 21 2013 - 14:37:35 PDT)
    - Re: [AMBER] cpptraj and avgcoord Daniel Roe (Tue May 21 2013 - 16:03:01 PDT)
    - Re: [AMBER] cpptraj and avgcoord Anselm Horn (Wed May 22 2013 - 07:10:16 PDT)
[AMBER] JAC benchmark tests on K20X Shan-ho Tsai (Mon May 20 2013 - 12:00:16 PDT)
- Re: [AMBER] JAC benchmark tests on K20X Ross Walker (Mon May 20 2013 - 12:21:49 PDT)
  - Re: [AMBER] JAC benchmark tests on K20X Shan-ho Tsai (Mon May 20 2013 - 13:11:13 PDT)
    - Re: [AMBER] JAC benchmark tests on K20X Jason Swails (Tue May 21 2013 - 04:32:31 PDT)
    - Re: [AMBER] JAC benchmark tests on K20X Shan-ho Tsai (Tue May 21 2013 - 07:05:05 PDT)
[AMBER] Qm/mm gaussian template=1 jcgt (Tue May 21 2013 - 03:32:36 PDT)
- Re: [AMBER] Qm/mm gaussian template=1 Andreas Goetz (Tue May 21 2013 - 16:48:51 PDT)
  - Re: [AMBER] Qm/mm gaussian template=1 jcgt (Wed May 22 2013 - 00:39:00 PDT)
  - Re: [AMBER] Qm/mm gaussian template=1 jcgt (Thu May 23 2013 - 02:13:57 PDT)
    - Re: [AMBER] Qm/mm gaussian template=1 Andreas Goetz (Thu May 23 2013 - 07:21:17 PDT)
[AMBER] how to remove the overlap between molecules Rasha Alqus (Tue May 21 2013 - 03:56:30 PDT)
- Re: [AMBER] how to remove the overlap between molecules Jason Swails (Tue May 21 2013 - 04:44:38 PDT)
[AMBER] Energy and gradient inconsistent between AMBER and NAB Chris Whittleston (Tue May 21 2013 - 08:39:06 PDT)
- Re: [AMBER] Energy and gradient inconsistent between AMBER and NAB Jason Swails (Tue May 21 2013 - 10:26:58 PDT)
[AMBER] How to construct a mol2 file from a PDB and RESP output files ? ABEL Stephane 175950 (Wed May 22 2013 - 04:08:06 PDT)
- Re: [AMBER] How to construct a mol2 file from a PDB and RESP output files ? Ayesha Fatima (Wed May 22 2013 - 05:25:41 PDT)
  - [AMBER] RE : How to construct a mol2 file from a PDB and RESP output files ? ABEL Stephane 175950 (Wed May 22 2013 - 05:52:54 PDT)
    - Re: [AMBER] RE : How to construct a mol2 file from a PDB and RESP output files ? Ayesha Fatima (Wed May 22 2013 - 08:32:03 PDT)
    - Re: [AMBER] RE : How to construct a mol2 file from a PDB and RESP output files ? FyD (Thu May 23 2013 - 04:53:21 PDT)
    - Re: [AMBER] RE : How to construct a mol2 file from a PDB and RESP output files ? Ayesha Fatima (Thu May 23 2013 - 21:26:57 PDT)
- Re: [AMBER] How to construct a mol2 file from a PDB and RESP output files ? David A Case (Wed May 22 2013 - 06:08:22 PDT)
  - [AMBER] RE : How to construct a mol2 file from a PDB and RESP output files ? ABEL Stephane 175950 (Wed May 22 2013 - 06:26:51 PDT)
- Re: [AMBER] How to construct a mol2 file from a PDB and RESP output files ? FyD (Thu May 23 2013 - 03:49:05 PDT)
  - [AMBER] RE : How to construct a mol2 file from a PDB and RESP output files ? ABEL Stephane 175950 (Thu May 23 2013 - 03:55:16 PDT)
[AMBER] Energy and force blow up when I previously performe rmsd-fit for MD trajectory. kurisaki (Wed May 22 2013 - 05:04:14 PDT)
- Re: [AMBER] Energy and force blow up when I previously performe rmsd-fit for MD trajectory. Daniel Roe (Wed May 22 2013 - 05:54:51 PDT)
  - Re: [AMBER] Energy and force blow up when I previously performe rmsd-fit for MD trajectory. kurisaki (Wed May 22 2013 - 06:11:15 PDT)
[AMBER] AMBERTOOLS: sqm fails to read input with more than 1000 external charges Franz Symalla (Wed May 22 2013 - 05:56:42 PDT)
- Re: [AMBER] AMBERTOOLS: sqm fails to read input with more than 1000 external charges Andreas Goetz (Wed May 22 2013 - 14:28:21 PDT)
  - Re: [AMBER] AMBERTOOLS: sqm fails to read input with more than 1000 external charges Franz Symalla (Thu May 23 2013 - 03:12:22 PDT)
[AMBER] create prmtop strcuture file for sumoylated residues crazylyf (Wed May 22 2013 - 06:18:50 PDT)
[AMBER] TR : [PROVENANCE INTERNET] RE : How to construct a mol2 file from a PDB and RESP outputfiles ? ABEL Stephane 175950 (Wed May 22 2013 - 06:31:43 PDT)
[AMBER] Query regarding mechanical unfolding of protein Manish Paul (Wed May 22 2013 - 11:22:12 PDT)
[AMBER] Relationship of time-autocorrelation plots for two lengths of time Sajeewa Pemasinghe (Wed May 22 2013 - 13:35:16 PDT)
- Re: [AMBER] Relationship of time-autocorrelation plots for two lengths of time George Giambasu (Wed May 22 2013 - 14:20:07 PDT)
  - Re: [AMBER] Relationship of time-autocorrelation plots for two lengths of time Sajeewa Pemasinghe (Wed May 22 2013 - 14:28:27 PDT)
    - Re: [AMBER] Relationship of time-autocorrelation plots for two lengths of time George Giambasu (Thu May 23 2013 - 06:42:08 PDT)
    - Re: [AMBER] Relationship of time-autocorrelation plots for two lengths of time Sajeewa Pemasinghe (Thu May 23 2013 - 14:31:04 PDT)
[AMBER] Question about the normalization of velocity autocorrelation function Sajeewa Pemasinghe (Wed May 22 2013 - 15:15:59 PDT)
- Re: [AMBER] Question about the normalization of velocity autocorrelation function David A Case (Thu May 23 2013 - 04:46:02 PDT)
  - Re: [AMBER] Question about the normalization of velocity autocorrelation function Sajeewa Pemasinghe (Thu May 23 2013 - 05:12:43 PDT)
[AMBER] Problem in updating AmberTools 12 Kshatresh Dutta Dubey (Thu May 23 2013 - 06:33:03 PDT)
- Re: [AMBER] Problem in updating AmberTools 12 Jason Swails (Thu May 23 2013 - 15:32:25 PDT)
[AMBER] example karplus.txt file for cpptraj jcoupling command Duggan, Brendan (Thu May 23 2013 - 10:28:42 PDT)
- Re: [AMBER] example karplus.txt file for cpptraj jcoupling command Daniel Roe (Thu May 23 2013 - 12:35:44 PDT)
- Re: [AMBER] example karplus.txt file for cpptraj jcoupling command Duggan, Brendan (Fri May 24 2013 - 13:06:20 PDT)
  - Re: [AMBER] example karplus.txt file for cpptraj jcoupling command Daniel Roe (Fri May 24 2013 - 13:24:03 PDT)
  - Re: [AMBER] example karplus.txt file for cpptraj jcoupling command Duggan, Brendan (Fri May 31 2013 - 15:03:05 PDT)
    - Re: [AMBER] example karplus.txt file for cpptraj jcoupling command Daniel Roe (Fri May 31 2013 - 15:24:20 PDT)
- Re: [AMBER] example karplus.txt file for cpptraj jcoupling command Duggan, Brendan (Tue Jun 04 2013 - 11:42:49 PDT)
  - Re: [AMBER] example karplus.txt file for cpptraj jcoupling command Daniel Roe (Tue Jun 04 2013 - 12:21:41 PDT)
[AMBER] GPU version availability on Gordon-SDSC and Kraken NICS Senthil Natesan (Thu May 23 2013 - 10:39:28 PDT)
- Re: [AMBER] GPU version availability on Gordon-SDSC and Kraken NICS Ross Walker (Thu May 23 2013 - 10:45:27 PDT)
[AMBER] TI erro - atom coordinate disagreement Kumar Sonu (Thu May 23 2013 - 10:50:30 PDT)
- Re: [AMBER] TI erro - atom coordinate disagreement steinbrt.rci.rutgers.edu (Thu May 23 2013 - 12:05:07 PDT)
[AMBER] SQM: How to extract the charge density of sqm runs? Franz Symalla (Thu May 23 2013 - 14:33:04 PDT)
- Re: [AMBER] SQM: How to extract the charge density of sqm runs? David A Case (Fri May 24 2013 - 05:15:07 PDT)
  - Re: [AMBER] SQM: How to extract the charge density of sqm runs? Andreas Goetz (Fri May 24 2013 - 16:13:26 PDT)
    - Re: [AMBER] SQM: How to extract the charge density of sqm runs? Marc van der Kamp (Tue May 20 2014 - 02:35:26 PDT)
[AMBER] Seg Fault in antechamber while writing ANTECHAMBER_AM1BCC_PRE.AC Jacob Monroe (Thu May 23 2013 - 20:38:13 PDT)
- Re: [AMBER] Seg Fault in antechamber while writing ANTECHAMBER_AM1BCC_PRE.AC FyD (Thu May 23 2013 - 23:56:28 PDT)
- Re: [AMBER] Seg Fault in antechamber while writing ANTECHAMBER_AM1BCC_PRE.AC David A Case (Fri May 24 2013 - 05:11:12 PDT)
  - Re: [AMBER] Seg Fault in antechamber while writing ANTECHAMBER_AM1BCC_PRE.AC Jacob Monroe (Fri May 24 2013 - 13:02:49 PDT)
    - Re: [AMBER] Seg Fault in antechamber while writing ANTECHAMBER_AM1BCC_PRE.AC David A Case (Sat May 25 2013 - 05:30:20 PDT)
    - Re: [AMBER] Seg Fault in antechamber while writing ANTECHAMBER_AM1BCC_PRE.AC Jacob Monroe (Mon May 27 2013 - 09:07:44 PDT)
    - Re: [AMBER] Seg Fault in antechamber while writing ANTECHAMBER_AM1BCC_PRE.AC FyD (Sat May 25 2013 - 09:00:09 PDT)
[AMBER] About addIonsRand Marc van der Kamp (Fri May 24 2013 - 06:03:33 PDT)
[AMBER] Steered Molecular dynamics Santi Tolosa (Fri May 24 2013 - 10:01:42 PDT)
[AMBER] problem on compiling sander me, Nancy (Sat May 25 2013 - 11:41:16 PDT)
- Re: [AMBER] problem on compiling sander David A Case (Sun May 26 2013 - 16:29:48 PDT)
  - Re: [AMBER] problem on compiling sander me, Nancy (Mon May 27 2013 - 09:40:31 PDT)
[AMBER] Chained AMBER jobs crash on Dual GPU compute node. ET (Sun May 26 2013 - 00:52:54 PDT)
- Re: [AMBER] Chained AMBER jobs crash on Dual GPU compute node. Jan-Philip Gehrcke (Sun May 26 2013 - 11:30:10 PDT)
  - Re: [AMBER] Chained AMBER jobs crash on Dual GPU compute node. ET (Mon May 27 2013 - 03:41:40 PDT)
    - Re: [AMBER] Chained AMBER jobs crash on Dual GPU compute node. Jan-Philip Gehrcke (Mon May 27 2013 - 09:04:15 PDT)
    - Re: [AMBER] Chained AMBER jobs crash on Dual GPU compute node. ET (Tue May 28 2013 - 02:51:37 PDT)
    - Re: [AMBER] Chained AMBER jobs crash on Dual GPU compute node. Jason Swails (Wed May 29 2013 - 07:15:33 PDT)
    - Re: [AMBER] Chained AMBER jobs crash on Dual GPU compute node. ET (Wed May 29 2013 - 09:39:56 PDT)
    - Re: [AMBER] Chained AMBER jobs crash on Dual GPU compute node. Jason Swails (Wed May 29 2013 - 11:16:24 PDT)
    - Re: [AMBER] Chained AMBER jobs crash on Dual GPU compute node. ET (Thu May 30 2013 - 01:35:16 PDT)
[AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Marek Maly (Mon May 27 2013 - 10:01:39 PDT)
- Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Scott Le Grand (Mon May 27 2013 - 16:25:24 PDT)
  - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Marek Maly (Mon May 27 2013 - 17:41:58 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Scott Le Grand (Tue May 28 2013 - 07:59:33 PDT)
  - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Robert Konecny (Tue May 28 2013 - 08:11:47 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Gould, Ian R (Tue May 28 2013 - 08:50:53 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Scott Le Grand (Tue May 28 2013 - 08:57:33 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? ET (Tue May 28 2013 - 11:42:32 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Scott Le Grand (Tue May 28 2013 - 12:01:20 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Robert Konecny (Tue May 28 2013 - 13:36:52 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Marek Maly (Tue May 28 2013 - 12:24:36 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Scott Le Grand (Tue May 28 2013 - 13:13:36 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Marek Maly (Tue May 28 2013 - 13:20:45 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Scott Le Grand (Tue May 28 2013 - 13:46:30 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? ET (Tue May 28 2013 - 17:11:27 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Divi/GMAIL (Tue May 28 2013 - 17:12:19 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? ET (Tue May 28 2013 - 17:41:05 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Scott Le Grand (Tue May 28 2013 - 17:49:31 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Ross Walker (Tue May 28 2013 - 18:44:33 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Marek Maly (Wed May 29 2013 - 13:11:12 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Scott Le Grand (Wed May 29 2013 - 13:41:46 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Scott Le Grand (Wed May 29 2013 - 13:46:58 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Marek Maly (Wed May 29 2013 - 14:22:34 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Scott Le Grand (Wed May 29 2013 - 16:05:24 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Marek Maly (Wed May 29 2013 - 16:30:53 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Scott Le Grand (Wed May 29 2013 - 17:46:59 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Marek Maly (Wed May 29 2013 - 18:24:30 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Jason Swails (Wed May 29 2013 - 13:44:18 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Marek Maly (Wed May 29 2013 - 15:00:19 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Jason Swails (Wed May 29 2013 - 19:42:10 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? ET (Thu May 30 2013 - 01:33:13 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? ET (Thu May 30 2013 - 05:08:18 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Marek Maly (Thu May 30 2013 - 05:32:57 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? ET (Thu May 30 2013 - 07:06:17 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Marek Maly (Thu May 30 2013 - 07:49:27 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Scott Le Grand (Thu May 30 2013 - 09:55:44 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? ET (Thu May 30 2013 - 10:27:13 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Marek Maly (Thu May 30 2013 - 05:14:55 PDT)
    - [AMBER] Sample LMOD program (nab section of AmberTools manual) Chris Moth (Thu May 30 2013 - 12:56:25 PDT)
- Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? pavel.banas.upol.cz (Thu May 30 2013 - 10:56:15 PDT)
  - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Scott Le Grand (Thu May 30 2013 - 11:01:58 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? filip fratev (Thu May 30 2013 - 11:46:01 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Jason Swails (Thu May 30 2013 - 12:13:29 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Scott Le Grand (Thu May 30 2013 - 12:24:43 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Scott Le Grand (Thu May 30 2013 - 12:27:17 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Marek Maly (Thu May 30 2013 - 15:00:21 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Scott Le Grand (Thu May 30 2013 - 15:45:49 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Marek Maly (Thu May 30 2013 - 15:41:54 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? ET (Fri May 31 2013 - 03:17:07 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? ET (Fri May 31 2013 - 03:21:21 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Marek Maly (Fri May 31 2013 - 03:29:59 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Marek Maly (Fri May 31 2013 - 05:34:27 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? filip fratev (Fri May 31 2013 - 08:30:57 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Marek Maly (Fri May 31 2013 - 08:30:02 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Marek Maly (Fri May 31 2013 - 08:40:01 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? ET (Fri May 31 2013 - 10:17:03 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Marek Maly (Fri May 31 2013 - 10:55:41 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? ET (Fri May 31 2013 - 13:02:34 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Marek Maly (Fri May 31 2013 - 13:14:47 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? ET (Fri May 31 2013 - 15:45:42 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? ET (Sat Jun 01 2013 - 11:26:16 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Scott Le Grand (Sat Jun 01 2013 - 11:46:29 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Scott Le Grand (Sat Jun 01 2013 - 11:48:12 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Jan-Philip Gehrcke (Sat Jun 01 2013 - 12:04:52 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Scott Le Grand (Sat Jun 01 2013 - 12:16:29 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Scott Le Grand (Sat Jun 01 2013 - 12:20:49 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Marek Maly (Sat Jun 01 2013 - 12:26:42 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Scott Le Grand (Sat Jun 01 2013 - 12:48:06 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Marek Maly (Sat Jun 01 2013 - 12:34:17 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? ET (Sat Jun 01 2013 - 13:18:34 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Marek Maly (Sat Jun 01 2013 - 13:32:15 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? ET (Sat Jun 01 2013 - 14:12:26 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Marek Maly (Sat Jun 01 2013 - 14:13:07 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? ET (Sat Jun 01 2013 - 14:42:34 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Scott Le Grand (Sat Jun 01 2013 - 15:28:45 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Marek Maly (Sat Jun 01 2013 - 15:41:13 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Scott Le Grand (Sat Jun 01 2013 - 16:25:44 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Scott Le Grand (Sat Jun 01 2013 - 16:38:34 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Marek Maly (Sat Jun 01 2013 - 16:35:20 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Marek Maly (Sat Jun 01 2013 - 16:49:47 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? ET (Sat Jun 01 2013 - 18:30:22 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? ET (Sat Jun 01 2013 - 18:45:05 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Scott Le Grand (Sat Jun 01 2013 - 19:36:32 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? ET (Sat Jun 01 2013 - 20:29:35 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Scott Le Grand (Sat Jun 01 2013 - 22:45:53 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? ET (Sun Jun 02 2013 - 06:29:49 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Marek Maly (Sat Jun 01 2013 - 16:30:43 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Marek Maly (Sat Jun 01 2013 - 12:09:46 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Marek Maly (Sun Jun 02 2013 - 07:58:38 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Scott Le Grand (Sun Jun 02 2013 - 09:07:14 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Scott Le Grand (Sun Jun 02 2013 - 09:31:17 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Scott Le Grand (Sun Jun 02 2013 - 09:33:52 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Scott Le Grand (Sun Jun 02 2013 - 09:42:31 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? ET (Sun Jun 02 2013 - 09:49:00 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Scott Le Grand (Sun Jun 02 2013 - 09:57:08 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Marek Maly (Sun Jun 02 2013 - 09:44:23 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Scott Le Grand (Sun Jun 02 2013 - 10:15:23 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Marek Maly (Sun Jun 02 2013 - 10:37:15 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? ET (Sun Jun 02 2013 - 11:02:21 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Scott Le Grand (Sun Jun 02 2013 - 12:49:41 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? ET (Sun Jun 02 2013 - 15:34:57 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? ET (Sun Jun 02 2013 - 16:20:27 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Divi/GMAIL (Sun Jun 02 2013 - 17:38:00 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? ET (Mon Jun 03 2013 - 02:28:39 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? ET (Mon Jun 03 2013 - 02:51:46 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Marek Maly (Mon Jun 03 2013 - 03:34:15 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? ET (Mon Jun 03 2013 - 04:31:09 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Marek Maly (Mon Jun 03 2013 - 09:42:24 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Scott Le Grand (Mon Jun 03 2013 - 11:12:04 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Marek Maly (Mon Jun 03 2013 - 11:47:36 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Ross Walker (Mon Jun 03 2013 - 12:17:23 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Marek Maly (Mon Jun 03 2013 - 12:31:03 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? ET (Mon Jun 03 2013 - 13:18:20 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Scott Le Grand (Mon Jun 03 2013 - 19:51:08 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Marek Maly (Mon Jun 03 2013 - 21:14:28 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Marek Maly (Tue Jun 04 2013 - 04:39:57 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? ET (Tue Jun 04 2013 - 06:23:37 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Scott Le Grand (Tue Jun 04 2013 - 13:36:00 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Marek Maly (Tue Jun 04 2013 - 15:20:35 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? filip fratev (Wed Jun 05 2013 - 02:12:54 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Marek Maly (Wed Jun 05 2013 - 03:33:07 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? filip fratev (Wed Jun 05 2013 - 05:23:41 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? ET (Wed Jun 05 2013 - 06:25:33 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? filip fratev (Wed Jun 05 2013 - 06:29:55 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Marek Maly (Wed Jun 05 2013 - 06:18:00 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Scott Le Grand (Wed Jun 05 2013 - 09:15:48 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Marek Maly (Wed Jun 05 2013 - 10:29:36 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Jonathan Gough (Wed Jun 05 2013 - 15:34:39 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Marek Maly (Wed Jun 05 2013 - 15:45:13 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Jonathan Gough (Thu Jun 06 2013 - 03:01:35 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Marek Maly (Thu Jun 06 2013 - 03:40:55 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Scott Le Grand (Thu Jun 06 2013 - 07:23:30 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Marek Maly (Thu Jun 06 2013 - 07:27:28 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Jonathan Gough (Thu Jun 06 2013 - 07:37:03 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Marek Maly (Thu Jun 06 2013 - 07:29:03 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Jonathan Gough (Fri Jun 07 2013 - 12:48:36 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? filip fratev (Fri Jun 07 2013 - 13:34:26 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Scott Le Grand (Fri Jun 07 2013 - 13:46:42 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Jonathan Gough (Fri Jun 07 2013 - 14:00:23 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Scott Le Grand (Fri Jun 07 2013 - 14:32:57 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Scott Le Grand (Fri Jun 07 2013 - 13:45:50 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Marek Maly (Fri Jun 07 2013 - 14:16:47 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Jonathan Gough (Fri Jun 07 2013 - 14:40:53 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Scott Le Grand (Fri Jun 07 2013 - 15:05:43 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Jonathan Gough (Fri Jun 07 2013 - 15:11:48 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? filip fratev (Fri Jun 07 2013 - 15:41:20 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Scott Le Grand (Fri Jun 07 2013 - 15:50:05 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? ET (Sun Jun 09 2013 - 08:22:58 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Scott Le Grand (Mon Jun 10 2013 - 21:31:37 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Marek Maly (Tue Jun 11 2013 - 03:23:29 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? filip fratev (Tue Jun 11 2013 - 04:38:56 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Scott Le Grand (Wed Jun 12 2013 - 10:07:49 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Marek Maly (Wed Jun 12 2013 - 11:16:46 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Jonathan Gough (Tue Jun 04 2013 - 04:54:09 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Marek Maly (Mon Jun 03 2013 - 03:31:08 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Marek Maly (Mon Jun 03 2013 - 04:21:43 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Marek Maly (Sun Jun 02 2013 - 10:22:54 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Marek Maly (Sun Jun 02 2013 - 16:57:36 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Marek Maly (Wed Jun 19 2013 - 08:20:15 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Scott Le Grand (Wed Jun 19 2013 - 08:50:51 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Jonathan Gough (Wed Jun 19 2013 - 09:34:36 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Scott Le Grand (Wed Jun 19 2013 - 10:03:18 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Marek Maly (Wed Jun 19 2013 - 10:00:59 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Scott Le Grand (Wed Jun 19 2013 - 10:23:31 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Robert Konecny (Wed Jun 19 2013 - 11:12:02 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Marek Maly (Wed Jun 19 2013 - 11:08:08 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Marek Maly (Wed Jun 19 2013 - 09:55:32 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Scott Le Grand (Wed Jun 19 2013 - 10:21:53 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Marek Maly (Wed Jun 19 2013 - 10:17:50 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Daniel Roe (Wed Jun 19 2013 - 10:50:35 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Marek Maly (Wed Jun 19 2013 - 10:55:46 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Ross Walker (Wed Jun 19 2013 - 19:25:07 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Marek Maly (Thu Jun 20 2013 - 06:58:00 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Scott Le Grand (Thu Jun 20 2013 - 08:25:05 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Marek Maly (Thu Jun 20 2013 - 09:03:04 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? ET (Thu Jun 20 2013 - 09:51:27 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Scott Le Grand (Thu Jun 20 2013 - 09:57:18 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Marek Maly (Thu Jun 20 2013 - 09:57:09 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Scott Le Grand (Thu Jun 20 2013 - 10:26:58 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Ross Walker (Thu Jun 20 2013 - 10:36:25 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Marek Maly (Thu Jun 20 2013 - 11:05:00 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Jonathan Gough (Wed Jun 26 2013 - 14:22:38 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Scott Le Grand (Wed Jun 26 2013 - 15:12:54 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Ross Walker (Wed Jun 26 2013 - 16:02:48 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Marek Maly (Mon Jul 01 2013 - 03:44:50 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Ross Walker (Mon Jul 01 2013 - 08:03:54 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Marek Maly (Mon Jul 01 2013 - 07:55:10 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Scott Le Grand (Wed Jun 19 2013 - 11:29:50 PDT)
    - Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? Scott Le Grand (Wed Jun 19 2013 - 11:33:58 PDT)
- Re: [AMBER] experiences with EVGA GTX TITAN Superclocked - memtestG80 - UNDERclocking in Linux ? ET (Sun Jun 02 2013 - 10:53:21 PDT)
[AMBER] atomicfluct George Tzotzos (Mon May 27 2013 - 10:34:10 PDT)
- Re: [AMBER] atomicfluct Daniel Roe (Mon May 27 2013 - 12:13:18 PDT)
  - Re: [AMBER] atomicfluct George Tzotzos (Mon May 27 2013 - 12:28:18 PDT)
    - Re: [AMBER] atomicfluct Daniel Roe (Tue May 28 2013 - 08:30:30 PDT)
    - Re: [AMBER] atomicfluct David A Case (Tue May 28 2013 - 09:15:32 PDT)
[AMBER] Free energy calculation of pyridine Bishnu Thapa (Mon May 27 2013 - 14:35:58 PDT)
- Re: [AMBER] Free energy calculation of pyridine David A Case (Mon May 27 2013 - 18:35:56 PDT)
[AMBER] About water flags running parm7 with NAMD Francesco Pietra (Tue May 28 2013 - 00:43:05 PDT)
- Re: [AMBER] About water flags running parm7 with NAMD Daniel Sindhikara (Tue May 28 2013 - 02:08:58 PDT)
  - Re: [AMBER] About water flags running parm7 with NAMD Francesco Pietra (Tue May 28 2013 - 07:33:41 PDT)
    - Re: [AMBER] About water flags running parm7 with NAMD Jason Swails (Tue May 28 2013 - 07:55:19 PDT)
    - Re: [AMBER] About water flags running parm7 with NAMD George Giambasu (Tue May 28 2013 - 08:21:49 PDT)
    - Re: [AMBER] About water flags running parm7 with NAMD Francesco Pietra (Tue May 28 2013 - 08:42:21 PDT)
[AMBER] Cpptraj and hbonds Fernando Martín García (Tue May 28 2013 - 07:06:26 PDT)
- Re: [AMBER] Cpptraj and hbonds Daniel Roe (Tue May 28 2013 - 07:33:43 PDT)
  - Re: [AMBER] Cpptraj and hbonds Fernando Martín García (Tue May 28 2013 - 07:36:56 PDT)
  - Re: [AMBER] Cpptraj and hbonds Miguel Ortiz Lombardía (Tue May 28 2013 - 07:56:42 PDT)
    - Re: [AMBER] Cpptraj and hbonds Daniel Roe (Tue May 28 2013 - 08:19:06 PDT)
    - Re: [AMBER] Cpptraj and hbonds Miguel Ortiz Lombardía (Tue May 28 2013 - 09:14:38 PDT)
[AMBER] GTX780 Fabrício Bracht (Tue May 28 2013 - 10:36:58 PDT)
- Re: [AMBER] GTX780 Scott Le Grand (Tue May 28 2013 - 10:48:26 PDT)
  - Re: [AMBER] GTX780 Fabrício Bracht (Wed Jun 26 2013 - 19:33:32 PDT)
    - Re: [AMBER] GTX780 Ross Walker (Wed Jun 26 2013 - 20:19:01 PDT)
    - Re: [AMBER] GTX780 Michael Lerner (Mon Jul 01 2013 - 10:41:21 PDT)
    - Re: [AMBER] GTX780 Ross Walker (Mon Jul 01 2013 - 10:46:00 PDT)
[AMBER] Steered MD | Pulling Distance (between r2 and r2a in dist.RST file) is limitted to 100A | Offending restraint Emmanuel (Tue May 28 2013 - 12:29:54 PDT)
- Re: [AMBER] Steered MD | Pulling Distance (between r2 and r2a in dist.RST file) is limitted to 100A | Offending restraint Adrian Roitberg (Tue May 28 2013 - 12:32:19 PDT)
- Re: [AMBER] Steered MD | Pulling Distance (between r2 and r2a in dist.RST file) is limitted to 100A | Offending restraint David A Case (Tue May 28 2013 - 17:55:33 PDT)
[AMBER] Error message when using mpirun on amber12_parallel 肖立 (Thu May 30 2013 - 16:31:33 PDT)
- Re: [AMBER] Error message when using mpirun on amber12_parallel Jason Swails (Thu May 30 2013 - 16:37:17 PDT)
  - Re: [AMBER] Error message when using mpirun on amber12_parallel 肖立 (Thu May 30 2013 - 16:47:04 PDT)
    - Re: [AMBER] Error message when using mpirun on amber12_parallel Jason Swails (Thu May 30 2013 - 19:33:28 PDT)
    - Re: [AMBER] Error message when using mpirun on amber12_parallel 肖立 (Thu May 30 2013 - 19:54:52 PDT)
  - Re: [AMBER] Error message when using mpirun on amber12_parallel Mandal, Sanat (Thu May 30 2013 - 16:52:40 PDT)
    - Re: [AMBER] AmberTools vs Amber David A Case (Fri May 31 2013 - 05:02:27 PDT)
    - Re: [AMBER] AmberTools vs Amber Mandal, Sanat (Fri May 31 2013 - 06:20:44 PDT)
[AMBER] FW: Trouble generating topology files Teo, Theodosia Hua Swan - teohy004 (Thu May 30 2013 - 17:58:04 PDT)
- Re: [AMBER] FW: Trouble generating topology files David A Case (Fri May 31 2013 - 05:08:24 PDT)
[AMBER] SMD calculation Santi Tolosa (Fri May 31 2013 - 03:00:40 PDT)
- Re: [AMBER] SMD calculation Jason Swails (Fri May 31 2013 - 07:24:57 PDT)
[AMBER] reference group and pulled group in umbrella sampling Jio M (Fri May 31 2013 - 03:38:17 PDT)
- Re: [AMBER] reference group and pulled group in umbrella sampling Jason Swails (Sat Jun 01 2013 - 21:29:21 PDT)
  - Re: [AMBER] reference group and pulled group in umbrella sampling Jio M (Sun Jun 02 2013 - 01:42:54 PDT)
    - Re: [AMBER] reference group and pulled group in umbrella sampling Jio M (Wed Jun 05 2013 - 12:51:25 PDT)
    - Re: [AMBER] reference group and pulled group in umbrella sampling Jason Swails (Wed Jun 05 2013 - 18:57:32 PDT)
[AMBER] by pmemd.cuda runs Cenk $Jenk$ Andac (Fri May 31 2013 - 05:32:37 PDT)
- Re: [AMBER] by pmemd.cuda runs Marc van der Kamp (Fri May 31 2013 - 06:12:46 PDT)
  - Re: [AMBER] by pmemd.cuda runs Daniel Roe (Fri May 31 2013 - 07:27:55 PDT)
    - Re: [AMBER] by pmemd.cuda runs Moth, Chris (Fri May 31 2013 - 09:09:03 PDT)
    - Re: [AMBER] by pmemd.cuda runs Jason Swails (Fri May 31 2013 - 11:11:01 PDT)
    - Re: [AMBER] by pmemd.cuda runs Cenk $Jenk$ Andac (Sat Jun 01 2013 - 03:08:42 PDT)
    - Re: [AMBER] by pmemd.cuda runs Cenk $Jenk$ Andac (Sat Jun 01 2013 - 03:09:38 PDT)
  - Re: [AMBER] by pmemd.cuda runs Cenk $Jenk$ Andac (Sat Jun 01 2013 - 03:05:31 PDT)
[AMBER] hbond in ptraj and cpptraj pmaj.nencki.gov.pl (Fri May 31 2013 - 06:14:21 PDT)
- Re: [AMBER] hbond in ptraj and cpptraj Daniel Roe (Fri May 31 2013 - 07:24:00 PDT)
  - Re: [AMBER] hbond in ptraj and cpptraj pmaj.nencki.gov.pl (Mon Jun 03 2013 - 03:12:06 PDT)
    - Re: [AMBER] hbond in ptraj and cpptraj pmaj.nencki.gov.pl (Mon Jun 03 2013 - 05:19:39 PDT)
    - Re: [AMBER] hbond in ptraj and cpptraj Daniel Roe (Mon Jun 03 2013 - 06:43:51 PDT)
[AMBER] Unfolding a protein using Accelerated Molecular Dynamics sunita gupta (Sat Jun 01 2013 - 04:11:51 PDT)
[AMBER] search for a method name: 'targeted molecular dynamics'? Jan-Philip Gehrcke (Sat Jun 01 2013 - 07:08:36 PDT)
- Re: [AMBER] search for a method name: 'targeted molecular dynamics'? Jan-Philip Gehrcke (Wed Jun 05 2013 - 00:16:32 PDT)
  - Re: [AMBER] search for a method name: 'targeted molecular dynamics'? Daniel Sindhikara (Wed Jun 05 2013 - 00:59:38 PDT)
    - Re: [AMBER] search for a method name: 'targeted molecular dynamics'? Jan-Philip Gehrcke (Wed Jun 05 2013 - 03:19:20 PDT)
[AMBER] Amber 12 bugfix 18 ? Marek Maly (Sat Jun 01 2013 - 11:22:53 PDT)
- Re: [AMBER] Amber 12 bugfix 18 ? ET (Sat Jun 01 2013 - 13:27:18 PDT)
  - Re: [AMBER] Amber 12 bugfix 18 ? Marek Maly (Sat Jun 01 2013 - 13:26:32 PDT)
- Re: [AMBER] Amber 12 bugfix 18 ? Jason Swails (Sat Jun 01 2013 - 14:23:26 PDT)
  - Re: [AMBER] Amber 12 bugfix 18 ? Jason Swails (Sat Jun 01 2013 - 14:24:33 PDT)
    - Re: [AMBER] Amber 12 bugfix 18 ? Marek Maly (Sat Jun 01 2013 - 14:19:47 PDT)
[AMBER] To all K20 - K20x "positive" Amber users Marek Maly (Sat Jun 01 2013 - 13:22:21 PDT)
[AMBER] Which is the best compiler to use with AMBER 12 ET (Sat Jun 01 2013 - 20:47:05 PDT)
- Re: [AMBER] Which is the best compiler to use with AMBER 12 Jason Swails (Sat Jun 01 2013 - 21:21:50 PDT)
  - Re: [AMBER] Which is the best compiler to use with AMBER 12 ET (Sat Jun 01 2013 - 21:28:51 PDT)
  - Re: [AMBER] Which is the best compiler to use with AMBER 12 Ross Walker (Sat Jun 01 2013 - 22:05:51 PDT)
- Re: [AMBER] Which is the best compiler to use with AMBER 12 Jan-Philip Gehrcke (Sun Jun 02 2013 - 02:58:26 PDT)
  - Re: [AMBER] Which is the best compiler to use with AMBER 12 ET (Sun Jun 02 2013 - 03:23:32 PDT)
[AMBER] tleap and ff02pol.r1 live (Sun Jun 02 2013 - 09:59:21 PDT)
- Re: [AMBER] tleap and ff02pol.r1 Jason Swails (Sun Jun 02 2013 - 14:35:42 PDT)
  - Re: [AMBER] tleap and ff02pol.r1 live (Mon Jun 03 2013 - 05:15:21 PDT)
[AMBER] ptraj error parul sharma (Mon Jun 03 2013 - 04:14:13 PDT)
- Re: [AMBER] ptraj error Sushil Mishra (Mon Jun 03 2013 - 05:39:36 PDT)
- Re: [AMBER] ptraj error Daniel Roe (Mon Jun 03 2013 - 06:50:41 PDT)
[AMBER] Cu+2 problem Fabian Glaser (Mon Jun 03 2013 - 04:40:21 PDT)
- Re: [AMBER] Cu+2 problem ros (Mon Jun 03 2013 - 07:51:06 PDT)
  - Re: [AMBER] Cu+2 problem Francesco Pietra (Mon Jun 03 2013 - 08:22:49 PDT)
    - [AMBER] Fwd: Cu+2 problem Francesco Pietra (Mon Jun 03 2013 - 08:25:17 PDT)
    - Re: [AMBER] Cu+2 problem FyD (Mon Jun 03 2013 - 23:24:27 PDT)
[AMBER] prmtop for stripped down coordinates Paul Driscoll (Mon Jun 03 2013 - 05:38:17 PDT)
- Re: [AMBER] prmtop for stripped down coordinates Marc van der Kamp (Mon Jun 03 2013 - 05:45:57 PDT)
- Re: [AMBER] prmtop for stripped down coordinates Jason Swails (Mon Jun 03 2013 - 06:18:16 PDT)
  - Re: [AMBER] prmtop for stripped down coordinates Paul Driscoll (Mon Jun 03 2013 - 06:34:36 PDT)
[AMBER] Methylated histidine lib and frcomd files George Patargias (Mon Jun 03 2013 - 06:33:46 PDT)
- Re: [AMBER] Methylated histidine lib and frcomd files FyD (Mon Jun 03 2013 - 06:52:43 PDT)
- Re: [AMBER] Methylated histidine lib and frcomd files George Patargias (Tue Jun 04 2013 - 04:26:04 PDT)
  - Re: [AMBER] Methylated histidine lib and frcomd files FyD (Tue Jun 04 2013 - 05:03:49 PDT)
    - [AMBER] LEaP & improper parameters FyD (Wed Jun 05 2013 - 00:05:37 PDT)
    - Re: [AMBER] LEaP & improper parameters Jason Swails (Wed Jun 05 2013 - 07:16:10 PDT)
    - Re: [AMBER] LEaP & improper parameters FyD (Wed Jun 05 2013 - 23:52:01 PDT)
- Re: [AMBER] Methylated histidine lib and frcomd files FyD (Thu Jun 06 2013 - 00:17:04 PDT)
- Re: [AMBER] Methylated histidine lib and frcomd files FyD (Sun Jul 07 2013 - 08:50:28 PDT)
  - Re: [AMBER] Methylated histidine lib and frcomd files George Patargias (Wed Jul 10 2013 - 00:21:52 PDT)
    - Re: [AMBER] Methylated histidine lib and frcomd files FyD (Wed Jul 10 2013 - 07:53:34 PDT)
    - Re: [AMBER] Methylated histidine lib and frcomd files George Patargias (Wed Jul 10 2013 - 09:00:42 PDT)
    - Re: [AMBER] Methylated histidine lib and frcomd files FyD (Thu Jul 11 2013 - 01:29:39 PDT)
    - Re: [AMBER] Methylated histidine lib and frcomd files George Patargias (Thu Jul 11 2013 - 03:59:26 PDT)
    - Re: [AMBER] Methylated histidine lib and frcomd files FyD (Thu Jul 11 2013 - 06:12:42 PDT)
    - Re: [AMBER] Methylated histidine lib and frcomd files FyD (Tue Jul 16 2013 - 08:05:11 PDT)
- Re: [AMBER] Methylated histidine lib and frcomd files FyD (Tue Jul 09 2013 - 06:09:16 PDT)
  - Re: [AMBER] Methylated histidine lib and frcomd files George Patargias (Tue Jul 09 2013 - 06:38:17 PDT)
    - Re: [AMBER] Methylated histidine lib and frcomd files FyD (Tue Jul 09 2013 - 06:57:53 PDT)
    - Re: [AMBER] Methylated histidine lib and frcomd files George Patargias (Tue Jul 09 2013 - 07:07:10 PDT)
- Re: [AMBER] Methylated histidine lib and frcomd files FyD (Tue Jul 09 2013 - 07:22:08 PDT)
[AMBER] mmGBSA bondi/mbondi2 and force field questions psu4.uic.edu (Mon Jun 03 2013 - 09:42:26 PDT)
- Re: [AMBER] mmGBSA bondi/mbondi2 and force field questions Hai Nguyen (Mon Jun 03 2013 - 15:23:56 PDT)
[AMBER] new AmberTools13 update has error in configure2 - needs changing ET (Mon Jun 03 2013 - 11:02:23 PDT)
- Re: [AMBER] new AmberTools13 update has error in configure2 - needs changing Jason Swails (Mon Jun 03 2013 - 11:57:39 PDT)
  - Re: [AMBER] new AmberTools13 update has error in configure2 - needs changing ET (Mon Jun 03 2013 - 13:13:25 PDT)
    - Re: [AMBER] new AmberTools13 update has error in configure2 - needs changing Jason Swails (Mon Jun 03 2013 - 19:40:58 PDT)
[AMBER] CUDA install fails on ubuntu 12.04 using GNU compiler ET (Mon Jun 03 2013 - 13:49:03 PDT)
- Re: [AMBER] CUDA install fails on ubuntu 12.04 using GNU compiler ET (Mon Jun 03 2013 - 14:06:18 PDT)
  - Re: [AMBER] CUDA install fails on ubuntu 12.04 using GNU compiler ET (Mon Jun 03 2013 - 14:26:42 PDT)
    - Re: [AMBER] CUDA install fails on ubuntu 12.04 using GNU compiler Ayesha Fatima (Mon Jun 03 2013 - 18:02:03 PDT)
    - Re: [AMBER] CUDA install fails on ubuntu 12.04 using GNU compiler ET (Mon Jun 03 2013 - 18:17:52 PDT)
[AMBER] enegy minimization with restrain Rasha Alqus (Tue Jun 04 2013 - 03:01:32 PDT)
[AMBER] surf in cpptraj doesn't support 'stripped' trajectories? Marc van der Kamp (Tue Jun 04 2013 - 09:32:18 PDT)
- Re: [AMBER] surf in cpptraj doesn't support 'stripped' trajectories? Daniel Roe (Tue Jun 04 2013 - 11:02:34 PDT)
  - Re: [AMBER] surf in cpptraj doesn't support 'stripped' trajectories? Marc van der Kamp (Tue Jun 04 2013 - 11:38:30 PDT)
    - Re: [AMBER] surf in cpptraj doesn't support 'stripped' trajectories? Marc van der Kamp (Tue Jun 04 2013 - 13:10:55 PDT)
    - Re: [AMBER] surf in cpptraj doesn't support 'stripped' trajectories? Daniel Roe (Tue Jun 04 2013 - 13:12:14 PDT)
    - Re: [AMBER] surf in cpptraj doesn't support 'stripped' trajectories? Daniel Roe (Tue Jun 04 2013 - 14:01:40 PDT)
    - Re: [AMBER] surf in cpptraj doesn't support 'stripped' trajectories? Marc van der Kamp (Wed Jun 05 2013 - 14:19:40 PDT)
[AMBER] Potential smoothing George Tzotzos (Tue Jun 04 2013 - 09:48:21 PDT)
[AMBER] AmberTools 13 igb=8 CalcError: $AMBERHOME/bin/mmpbsa_py_energy failed with prmtop complex.top! psu4.uic.edu (Tue Jun 04 2013 - 14:44:48 PDT)
- Re: [AMBER] AmberTools 13 igb=8 CalcError: $AMBERHOME/bin/mmpbsa_py_energy failed with prmtop complex.top! Hai Nguyen (Tue Jun 04 2013 - 17:26:49 PDT)
- Re: [AMBER] AmberTools 13 igb=8 CalcError: $AMBERHOME/bin/mmpbsa_py_energy failed with prmtop complex.top! Jason Swails (Tue Jun 04 2013 - 17:34:26 PDT)
  - Re: [AMBER] AmberTools 13 igb=8 CalcError: $AMBERHOME/bin/mmpbsa_py_energy failed with prmtop complex.top! psu4.uic.edu (Wed Jun 05 2013 - 11:03:04 PDT)
    - Re: [AMBER] AmberTools 13 igb=8 CalcError: $AMBERHOME/bin/mmpbsa_py_energy failed with prmtop complex.top! Jason Swails (Wed Jun 05 2013 - 11:26:55 PDT)
    - Re: [AMBER] AmberTools 13 igb=8 CalcError: $AMBERHOME/bin/mmpbsa_py_energy failed with prmtop complex.top! psu4.uic.edu (Fri Jun 07 2013 - 17:14:13 PDT)
[AMBER] Any tips on setting up a cluster to run amber? Josh Berryman (Wed Jun 05 2013 - 02:38:00 PDT)
- Re: [AMBER] Any tips on setting up a cluster to run amber? Daniel Sindhikara (Wed Jun 05 2013 - 02:52:17 PDT)
- Re: [AMBER] Any tips on setting up a cluster to run amber? Jan-Philip Gehrcke (Wed Jun 05 2013 - 02:55:00 PDT)
  - Re: [AMBER] Any tips on setting up a cluster to run amber? ET (Wed Jun 05 2013 - 14:32:53 PDT)
[AMBER] errors compiling Jonathan Gough (Wed Jun 05 2013 - 11:23:54 PDT)
- Re: [AMBER] errors compiling Daniel Roe (Wed Jun 05 2013 - 11:47:25 PDT)
  - Re: [AMBER] errors compiling Jonathan Gough (Wed Jun 05 2013 - 12:03:28 PDT)
    - Re: [AMBER] errors compiling Jason Swails (Wed Jun 05 2013 - 12:11:13 PDT)
    - Re: [AMBER] errors compiling Jonathan Gough (Wed Jun 05 2013 - 12:30:10 PDT)
[AMBER] iron-sulfur parameterization venkatesh s (Wed Jun 05 2013 - 11:52:59 PDT)
- Re: [AMBER] iron-sulfur parameterization case (Wed Jun 05 2013 - 12:40:40 PDT)
  - Re: [AMBER] iron-sulfur parameterization Sergio R Aragon (Wed Jun 05 2013 - 13:16:17 PDT)
    - Re: [AMBER] iron-sulfur parameterization francesco oteri (Wed Jun 05 2013 - 14:18:01 PDT)
    - Re: [AMBER] iron-sulfur parameterization Sergio R Aragon (Wed Jun 05 2013 - 15:08:48 PDT)
    - Re: [AMBER] iron-sulfur parameterization francesco oteri (Thu Jun 06 2013 - 00:19:46 PDT)
[AMBER] error energy minimization with restrain Rasha Alqus (Wed Jun 05 2013 - 11:59:22 PDT)
- Re: [AMBER] error energy minimization with restrain Jason Swails (Wed Jun 05 2013 - 12:23:19 PDT)
[AMBER] Karplus.txt file for nucleic acid residues Indrajit Deb (Thu Jun 06 2013 - 02:02:30 PDT)
- Re: [AMBER] Karplus.txt file for nucleic acid residues case (Thu Jun 06 2013 - 06:09:39 PDT)
[AMBER] solvatebox membrane Kanin Wichapong (Thu Jun 06 2013 - 02:53:40 PDT)
- Re: [AMBER] solvatebox membrane Igor Marques (Thu Jun 06 2013 - 02:56:06 PDT)
[AMBER] result of molsurf calculation setyanto md (Thu Jun 06 2013 - 07:36:10 PDT)
- Re: [AMBER] result of molsurf calculation Marcus Arieno (Thu Jun 06 2013 - 08:05:05 PDT)
- Re: [AMBER] result of molsurf calculation Daniel Roe (Thu Jun 06 2013 - 08:08:44 PDT)
[AMBER] Lipid11 DMPC Kanin Wichapong (Thu Jun 06 2013 - 07:56:54 PDT)
- Re: [AMBER] Lipid11 DMPC Dickson, Callum (Fri Jun 07 2013 - 02:21:49 PDT)
[AMBER] CUDA install fails due to undefined netcdf definitions Matthew Wampole (Thu Jun 06 2013 - 08:28:29 PDT)
- Re: [AMBER] CUDA install fails due to undefined netcdf definitions Jason Swails (Thu Jun 06 2013 - 08:51:06 PDT)
- Re: [AMBER] CUDA install fails due to undefined netcdf definitions Matthew Wampole (Thu Jun 06 2013 - 14:12:10 PDT)
- Re: [AMBER] CUDA install fails due to undefined netcdf definitions Daniel Roe (Thu Jun 06 2013 - 14:26:45 PDT)
- Re: [AMBER] CUDA install fails due to undefined netcdf definitions Matthew Wampole (Tue Jun 11 2013 - 13:25:17 PDT)
  - Re: [AMBER] CUDA install fails due to undefined netcdf definitions Jason Swails (Tue Jun 11 2013 - 13:38:42 PDT)
- Re: [AMBER] CUDA install fails due to undefined netcdf definitions Matthew Wampole (Fri Jun 14 2013 - 07:39:32 PDT)
[AMBER] using ntt=2 on gpu Sarah Graham (Thu Jun 06 2013 - 08:43:29 PDT)
[AMBER] MMPBSA.py Error Senthil Natesan (Thu Jun 06 2013 - 08:46:12 PDT)
- Re: [AMBER] MMPBSA.py Error Jason Swails (Thu Jun 06 2013 - 08:56:40 PDT)
  - Re: [AMBER] MMPBSA.py Error Senthil Natesan (Fri Jun 07 2013 - 06:06:04 PDT)
    - Re: [AMBER] MMPBSA.py Error Daniel Roe (Fri Jun 07 2013 - 07:22:24 PDT)
    - Re: [AMBER] MMPBSA.py Error Senthil Natesan (Mon Jun 10 2013 - 06:18:01 PDT)
    - Re: [AMBER] MMPBSA.py Error Daniel Roe (Mon Jun 10 2013 - 08:43:24 PDT)
[AMBER] PM6 and PM3 me, Nancy (Thu Jun 06 2013 - 11:11:01 PDT)
- Re: [AMBER] PM6 and PM3 Brian Radak (Thu Jun 06 2013 - 11:34:11 PDT)
  - Re: [AMBER] PM6 and PM3 me, Nancy (Thu Jun 06 2013 - 11:55:25 PDT)
    - Re: [AMBER] PM6 and PM3 Brian Radak (Thu Jun 06 2013 - 12:22:31 PDT)
    - Re: [AMBER] PM6 and PM3 me, Nancy (Thu Jun 06 2013 - 14:23:42 PDT)
[AMBER] unable to run minimizations after new installation of amber11 Amparo Garcia Lopez (Thu Jun 06 2013 - 11:59:25 PDT)
- Re: [AMBER] unable to run minimizations after new installation of amber11 David A Case (Fri Jun 07 2013 - 09:01:05 PDT)
  - Re: [AMBER] unable to run minimizations after new installation of amber11 Amparo Garcia Lopez (Fri Jun 07 2013 - 09:58:21 PDT)
    - Re: [AMBER] unable to run minimizations after new installation of amber11 David A Case (Fri Jun 07 2013 - 12:01:05 PDT)
    - Re: [AMBER] unable to run minimizations after new installation of amber11 Amparo Garcia Lopez (Sat Jun 08 2013 - 09:09:22 PDT)
    - Re: [AMBER] unable to run minimizations after new installation of amber11 Jason Swails (Mon Jun 10 2013 - 21:00:37 PDT)
    - Re: [AMBER] unable to run minimizations after new installation of amber11 Amparo Garcia Lopez (Tue Jun 11 2013 - 05:54:08 PDT)
[AMBER] ntt=2 on gpu Sarah Graham (Thu Jun 06 2013 - 12:36:34 PDT)
[AMBER] cpptraj diffusion ambertool13 Asmita Gupta (Fri Jun 07 2013 - 05:04:49 PDT)
- Re: [AMBER] cpptraj diffusion ambertool13 Daniel Roe (Fri Jun 07 2013 - 07:42:25 PDT)
[AMBER] Help regarding Mn parameters Mallipeddi, Premalatha (Fri Jun 07 2013 - 11:07:30 PDT)
- Re: [AMBER] Help regarding Mn parameters Daniel Roe (Fri Jun 07 2013 - 14:02:29 PDT)
[AMBER] MMPBSA Alanine scan terminal residues BERGY (Sat Jun 08 2013 - 23:23:48 PDT)
- Re: [AMBER] MMPBSA Alanine scan terminal residues Jason Swails (Mon Jun 10 2013 - 20:16:51 PDT)
- Re: [AMBER] MMPBSA Alanine scan terminal residues Jason Swails (Tue Jun 11 2013 - 05:34:53 PDT)
  - Re: [AMBER] MMPBSA Alanine scan terminal residues BERGY (Tue Jul 23 2013 - 00:38:29 PDT)
    - Re: [AMBER] MMPBSA Alanine scan terminal residues Jason Swails (Tue Jul 23 2013 - 05:23:25 PDT)
[AMBER] Problem with SMD moitrayee.mbu.iisc.ernet.in (Sun Jun 09 2013 - 02:06:55 PDT)
- Re: [AMBER] Problem with SMD Jason Swails (Mon Jun 10 2013 - 21:08:16 PDT)
[AMBER] What is minimum GPU bandwidth to get AMBER to run properly? ET (Sun Jun 09 2013 - 07:46:31 PDT)
- Re: [AMBER] What is minimum GPU bandwidth to get AMBER to run properly? Ross Walker (Sun Jun 09 2013 - 10:02:12 PDT)
  - Re: [AMBER] What is minimum GPU bandwidth to get AMBER to run properly? ET (Mon Jun 10 2013 - 06:32:26 PDT)
    - Re: [AMBER] What is minimum GPU bandwidth to get AMBER to run properly? Ross Walker (Mon Jun 10 2013 - 07:10:31 PDT)
    - Re: [AMBER] What is minimum GPU bandwidth to get AMBER to run properly? ET (Mon Jun 10 2013 - 07:59:48 PDT)
    - Re: [AMBER] What is minimum GPU bandwidth to get AMBER to run properly? Jan-Philip Gehrcke (Mon Jun 10 2013 - 08:18:05 PDT)
[AMBER] How to make a specific non-bonded interaction off kurisaki (Mon Jun 10 2013 - 03:22:53 PDT)
- Re: [AMBER] How to make a specific non-bonded interaction off Jason Swails (Mon Jun 10 2013 - 06:00:46 PDT)
  - Re: [AMBER] How to make a specific non-bonded interaction off kurisaki (Mon Jun 10 2013 - 06:33:01 PDT)
  - Re: [AMBER] How to make a specific non-bonded interaction off kurisaki (Thu Jun 13 2013 - 20:21:12 PDT)
    - Re: [AMBER] How to make a specific non-bonded interaction off Jason Swails (Thu Jun 13 2013 - 20:56:40 PDT)
    - Re: [AMBER] How to make a specific non-bonded interaction off kurisaki (Thu Jun 13 2013 - 22:01:51 PDT)
[AMBER] How to avoid tleap error *** Error: tl_getline(): not interactive, use stdio. kurisaki (Mon Jun 10 2013 - 05:15:04 PDT)
- Re: [AMBER] How to avoid tleap error *** Error: tl_getline(): not interactive, use stdio. Jason Swails (Mon Jun 10 2013 - 06:06:19 PDT)
  - Re: [AMBER] How to avoid tleap error *** Error: tl_getline(): not interactive, use stdio. ET (Mon Jun 10 2013 - 06:12:24 PDT)
    - Re: [AMBER] How to avoid tleap error *** Error: tl_getline(): not interactive, use stdio. David A Case (Mon Jun 10 2013 - 11:53:37 PDT)
    - Re: [AMBER] How to avoid tleap error *** Error: tl_getline(): not interactive, use stdio. Niel Henriksen (Mon Jun 10 2013 - 12:13:22 PDT)
  - Re: [AMBER] How to avoid tleap error *** Error: tl_getline(): not interactive, use stdio. kurisaki (Mon Jun 10 2013 - 06:20:20 PDT)
[AMBER] ntt=2 on gpu Sarah Graham (Mon Jun 10 2013 - 05:26:21 PDT)
- Re: [AMBER] ntt=2 on gpu Ross Walker (Mon Jun 10 2013 - 07:12:36 PDT)
  - Re: [AMBER] ntt=2 on gpu Sarah Graham (Mon Jun 10 2013 - 11:34:53 PDT)
    - Re: [AMBER] ntt=2 on gpu Ross Walker (Wed Jun 12 2013 - 11:01:21 PDT)
[AMBER] Calculating harmonic potential in umbrella sampling Sajeewa Pemasinghe (Mon Jun 10 2013 - 11:25:31 PDT)
- Re: [AMBER] Calculating harmonic potential in umbrella sampling Jason Swails (Mon Jun 10 2013 - 20:14:59 PDT)
  - Re: [AMBER] Calculating harmonic potential in umbrella sampling Sajeewa Pemasinghe (Mon Jun 10 2013 - 21:11:15 PDT)
[AMBER] counterions in md simulation Mary Varughese (Tue Jun 11 2013 - 01:27:45 PDT)
- Re: [AMBER] counterions in md simulation Dr. Vitaly Chaban (Tue Jun 11 2013 - 01:40:27 PDT)
- Re: [AMBER] counterions in md simulation Marc van der Kamp (Tue Jun 11 2013 - 01:42:44 PDT)
  - Re: [AMBER] counterions in md simulation Mary Varughese (Tue Jun 11 2013 - 02:03:13 PDT)
[AMBER] parameters of ions for TIP5P water box Xioling Chuang (Tue Jun 11 2013 - 03:54:57 PDT)
- Re: [AMBER] parameters of ions for TIP5P water box tec3.utah.edu (Tue Jun 11 2013 - 14:29:42 PDT)
  - Re: [AMBER] parameters of ions for TIP5P water box Xioling Chuang (Tue Jun 11 2013 - 20:21:58 PDT)
    - Re: [AMBER] parameters of ions for TIP5P water box David A Case (Wed Jun 12 2013 - 04:58:32 PDT)
    - Re: [AMBER] parameters of ions for TIP5P water box Xioling Chuang (Wed Jun 12 2013 - 18:49:33 PDT)
[AMBER] how does leap-prmtop calculate residues in water Jonathan Gough (Tue Jun 11 2013 - 13:13:05 PDT)
- Re: [AMBER] how does leap-prmtop calculate residues in water Jason Swails (Tue Jun 11 2013 - 13:22:28 PDT)
  - Re: [AMBER] how does leap-prmtop calculate residues in water Jonathan Gough (Tue Jun 11 2013 - 13:45:29 PDT)
[AMBER] nab in AmberTools13: documentation of newton() and getpdb_prm() sample Chris Moth (Tue Jun 11 2013 - 13:49:13 PDT)
- Re: [AMBER] nab in AmberTools13: documentation of newton() and getpdb_prm() sample David A Case (Tue Jun 11 2013 - 18:42:38 PDT)
[AMBER] prmtop Bailey, Steven (Wed Jun 12 2013 - 06:42:46 PDT)
- Re: [AMBER] prmtop Karl N. Kirschner (Wed Jun 12 2013 - 07:02:44 PDT)
  - Re: [AMBER] prmtop cieplak.cgl.ucsf.edu (Wed Jun 12 2013 - 08:33:15 PDT)
    - Re: [AMBER] prmtop Bailey, Steven (Wed Jun 12 2013 - 08:49:22 PDT)
    - Re: [AMBER] prmtop Sarah Graham (Wed Jun 12 2013 - 09:04:06 PDT)
    - Re: [AMBER] prmtop Jason Swails (Wed Jun 12 2013 - 09:17:31 PDT)
    - Re: [AMBER] prmtop David A Case (Wed Jun 12 2013 - 09:53:32 PDT)
[AMBER] csh problem Albert (Wed Jun 12 2013 - 10:44:08 PDT)
- Re: [AMBER] csh problem David A Case (Wed Jun 12 2013 - 18:43:14 PDT)
[AMBER] Protein leaving periodic box Hailin Huang (Wed Jun 12 2013 - 13:56:58 PDT)
- Re: [AMBER] Protein leaving periodic box Daniel Roe (Wed Jun 12 2013 - 14:33:36 PDT)
  - Re: [AMBER] Protein leaving periodic box Hailin Huang (Wed Jun 19 2013 - 11:28:44 PDT)
    - Re: [AMBER] Protein leaving periodic box Daniel Roe (Wed Jun 19 2013 - 12:30:17 PDT)
[AMBER] Running MD NPT Ensemble Error Benjamin Grant (Wed Jun 12 2013 - 14:07:58 PDT)
- Re: [AMBER] Running MD NPT Ensemble Error ET (Wed Jun 12 2013 - 20:11:08 PDT)
  - Re: [AMBER] Running MD NPT Ensemble Error ET (Wed Jun 12 2013 - 20:24:13 PDT)
[AMBER] bad atom type: N3 (In MMGBSA decomp calculations) Jason Slingsby (Wed Jun 12 2013 - 15:38:29 PDT)
- Re: [AMBER] bad atom type: N3 (In MMGBSA decomp calculations) Jason Swails (Thu Jun 13 2013 - 10:43:07 PDT)
[AMBER] Step by step tutorial to using Ptraj in generating DCCM #YIP YEW MUN# (Wed Jun 12 2013 - 18:22:20 PDT)
- Re: [AMBER] Step by step tutorial to using Ptraj in generating DCCM Daniel Roe (Thu Jun 13 2013 - 08:17:27 PDT)
  - Re: [AMBER] Step by step tutorial to using Ptraj in generating DCCM Yip Yew Mun (Sat Jun 15 2013 - 06:27:13 PDT)
[AMBER] Unknown redidue when using tleap Dongshan Wei (Wed Jun 12 2013 - 18:40:42 PDT)
- Re: [AMBER] Unknown redidue when using tleap ET (Wed Jun 12 2013 - 19:56:29 PDT)
- Re: [AMBER] Unknown redidue when using tleap FyD (Thu Jun 13 2013 - 00:37:22 PDT)
  - Re: [AMBER] Unknown redidue when using tleap Dongshan Wei (Thu Jun 13 2013 - 06:49:46 PDT)
    - Re: [AMBER] Unknown redidue when using tleap Dongshan Wei (Fri Jun 21 2013 - 02:12:08 PDT)
    - Re: [AMBER] Unknown redidue when using tleap FyD (Fri Jun 21 2013 - 04:31:34 PDT)
    - Re: [AMBER] Unknown redidue when using tleap David A Case (Fri Jun 21 2013 - 05:33:34 PDT)
[AMBER] MPI Compilation problems Amber 12 on CentOS 6.2 Frank Thommen (Thu Jun 13 2013 - 01:36:43 PDT)
- Re: [AMBER] MPI Compilation problems Amber 12 on CentOS 6.2 David A Case (Thu Jun 13 2013 - 04:47:37 PDT)
  - Re: [AMBER] MPI Compilation problems Amber 12 on CentOS 6.2 Frank Thommen (Thu Jun 13 2013 - 05:03:03 PDT)
    - Re: [AMBER] MPI Compilation problems Amber 12 on CentOS 6.2 David A Case (Thu Jun 13 2013 - 05:35:37 PDT)
    - Re: [AMBER] MPI Compilation problems Amber 12 on CentOS 6.2 Frank Thommen (Thu Jun 13 2013 - 06:27:21 PDT)
[AMBER] glycame06_carbohydrate_hydrogen bond pattern Rasha Alqus (Thu Jun 13 2013 - 02:26:22 PDT)
- Re: [AMBER] glycame06_carbohydrate_hydrogen bond pattern Karl N. Kirschner (Thu Jun 13 2013 - 03:57:55 PDT)
[AMBER] amber2accent perl script Manikanthan Bhavaraju (Thu Jun 13 2013 - 10:59:09 PDT)
- Re: [AMBER] amber2accent perl script Jason Swails (Thu Jun 13 2013 - 13:56:18 PDT)
  - Re: [AMBER] amber2accent perl script Manikanthan Bhavaraju (Thu Jun 13 2013 - 14:03:38 PDT)
[AMBER] How to modify/add velocity entries in .inpcrd file? Yan Duan (Thu Jun 13 2013 - 15:56:52 PDT)
- Re: [AMBER] How to modify/add velocity entries in .inpcrd file? Jason Swails (Thu Jun 13 2013 - 16:18:32 PDT)
[AMBER] problem with restart file in amber 11 Edward Pate (Thu Jun 13 2013 - 17:10:33 PDT)
- Re: [AMBER] problem with restart file in amber 11 Jason Swails (Thu Jun 13 2013 - 18:19:26 PDT)
[AMBER] Amber to Charmm Manikanthan Bhavaraju (Thu Jun 13 2013 - 17:42:53 PDT)
- Re: [AMBER] Amber to Charmm Jason Swails (Thu Jun 13 2013 - 18:23:00 PDT)
[AMBER] Questions about installing Amber 11 Changqing Yan (Fri Jun 14 2013 - 00:03:54 PDT)
- Re: [AMBER] Questions about installing Amber 11 David A Case (Fri Jun 14 2013 - 04:38:17 PDT)
[AMBER] Questions about installation of Amber11 Changqing Yan (Fri Jun 14 2013 - 01:16:44 PDT)
- Re: [AMBER] Questions about installation of Amber11 David A Case (Fri Jun 14 2013 - 04:41:20 PDT)
  - [AMBER] Alanine Scanning MMPBSA Aronica, Pietro (Thu May 08 2014 - 08:56:28 PDT)
    - Re: [AMBER] Alanine Scanning MMPBSA Bill Miller III (Thu May 08 2014 - 09:12:22 PDT)
    - Re: [AMBER] Alanine Scanning MMPBSA Aronica, Pietro (Thu May 08 2014 - 09:45:12 PDT)
    - Re: [AMBER] Alanine Scanning MMPBSA Bill Miller III (Thu May 08 2014 - 09:50:33 PDT)
    - Re: [AMBER] Alanine Scanning MMPBSA Aronica, Pietro (Thu May 08 2014 - 10:08:13 PDT)
    - Re: [AMBER] Alanine Scanning MMPBSA Jason Swails (Thu May 08 2014 - 10:19:36 PDT)
    - Re: [AMBER] Alanine Scanning MMPBSA Aronica, Pietro (Fri May 09 2014 - 03:27:46 PDT)
    - Re: [AMBER] Alanine Scanning MMPBSA Jason Swails (Fri May 09 2014 - 04:43:19 PDT)
    - Re: [AMBER] Alanine Scanning MMPBSA Aronica, Pietro (Fri May 09 2014 - 06:01:57 PDT)
    - Re: [AMBER] Alanine Scanning MMPBSA Aronica, Pietro (Tue May 13 2014 - 04:06:08 PDT)
    - Re: [AMBER] Alanine Scanning MMPBSA Jason Swails (Tue May 13 2014 - 04:27:13 PDT)
    - Re: [AMBER] Alanine Scanning MMPBSA Aronica, Pietro (Tue May 13 2014 - 05:01:54 PDT)
    - Re: [AMBER] Alanine Scanning MMPBSA Aronica, Pietro (Tue May 20 2014 - 06:21:54 PDT)
    - Re: [AMBER] Alanine Scanning MMPBSA Jason Swails (Tue May 20 2014 - 06:33:04 PDT)
    - Re: [AMBER] Alanine Scanning MMPBSA Aronica, Pietro (Wed May 28 2014 - 06:36:07 PDT)
    - Re: [AMBER] Alanine Scanning MMPBSA Jason Swails (Wed May 28 2014 - 06:52:26 PDT)
    - Re: [AMBER] Alanine Scanning MMPBSA Jason Swails (Fri May 30 2014 - 08:11:17 PDT)
    - Re: [AMBER] Alanine Scanning MMPBSA Jason Swails (Fri May 30 2014 - 08:16:22 PDT)
- Re: [AMBER] Questions about installation of Amber11 Changqing Yan (Fri Jun 14 2013 - 19:57:08 PDT)
  - Re: [AMBER] Questions about installation of Amber11 Jason Swails (Fri Jun 14 2013 - 20:24:15 PDT)
[AMBER] Building CUDA-enabled Amber11 (pmemd.cuda) * (Amber 11 only) Changqing Yan (Fri Jun 14 2013 - 02:29:18 PDT)
- Re: [AMBER] Building CUDA-enabled Amber11 (pmemd.cuda) * (Amber 11 only) David A Case (Fri Jun 14 2013 - 04:42:19 PDT)
[AMBER] Cannot find Sander in Amber13 Michelle Mukonyora (Fri Jun 14 2013 - 03:06:15 PDT)
- Re: [AMBER] Cannot find Sander in Amber13 steinbrt.rci.rutgers.edu (Fri Jun 14 2013 - 04:06:32 PDT)
  - Re: [AMBER] Cannot find Sander in Amber13 Michelle Mukonyora (Fri Jun 14 2013 - 04:47:33 PDT)
- Re: [AMBER] Cannot find Sander in Amber13 David A Case (Fri Jun 14 2013 - 04:44:49 PDT)
[AMBER] help 徐俊 (Fri Jun 14 2013 - 03:56:57 PDT)
[AMBER] print forces experienced by molecule during simulation ET (Fri Jun 14 2013 - 05:22:53 PDT)
- Re: [AMBER] print forces experienced by molecule during simulation Jason Swails (Fri Jun 14 2013 - 06:30:12 PDT)
  - Re: [AMBER] print forces experienced by molecule during simulation ET (Fri Jun 14 2013 - 07:02:54 PDT)
  - Re: [AMBER] print forces experienced by molecule during simulation Jason Swails (Fri Jun 14 2013 - 13:18:25 PDT)
[AMBER] Can RMSF be at least 2 times larger than RMSD? Yip Yew Mun (Fri Jun 14 2013 - 08:57:07 PDT)
- Re: [AMBER] Can RMSF be at least 2 times larger than RMSD? Carlos Simmerling (Fri Jun 14 2013 - 09:10:32 PDT)
  - Re: [AMBER] Can RMSF be at least 2 times larger than RMSD? Yip Yew Mun (Sat Jun 15 2013 - 06:26:02 PDT)
- Re: [AMBER] Can RMSF be at least 2 times larger than RMSD? Daniel Roe (Fri Jun 14 2013 - 09:34:19 PDT)
[AMBER] Difficulty compiling amber12/ambertools13 Hunter Brown (Fri Jun 14 2013 - 15:41:11 PDT)
- Re: [AMBER] Difficulty compiling amber12/ambertools13 Bill Ross (Fri Jun 14 2013 - 16:10:57 PDT)
- Re: [AMBER] Difficulty compiling amber12/ambertools13 Jason Swails (Fri Jun 14 2013 - 17:49:36 PDT)
- Re: [AMBER] Difficulty compiling amber12/ambertools13 Hunter Brown (Mon Jun 17 2013 - 07:33:19 PDT)
  - Re: [AMBER] Difficulty compiling amber12/ambertools13 Jan-Philip Gehrcke (Mon Jun 17 2013 - 08:45:04 PDT)
- Re: [AMBER] Difficulty compiling amber12/ambertools13 Daniel Roe (Mon Jun 17 2013 - 09:10:44 PDT)
  - Re: [AMBER] Difficulty compiling amber12/ambertools13 Jason Swails (Mon Jun 17 2013 - 10:42:02 PDT)
- Re: [AMBER] Difficulty compiling amber12/ambertools13 Hunter Brown (Mon Jun 17 2013 - 09:44:16 PDT)
  - Re: [AMBER] Difficulty compiling amber12/ambertools13 Daniel Roe (Mon Jun 17 2013 - 09:46:00 PDT)
    - Re: [AMBER] Difficulty compiling amber12/ambertools13 Jason Swails (Mon Jun 17 2013 - 09:48:45 PDT)
  - Re: [AMBER] Difficulty compiling amber12/ambertools13 Jason Swails (Mon Jun 17 2013 - 09:48:09 PDT)
[AMBER] In regards to my previous question Hunter Brown (Fri Jun 14 2013 - 15:45:22 PDT)
[AMBER] Experience with terachem and amber12 Fabrício Bracht (Fri Jun 14 2013 - 23:36:14 PDT)
- Re: [AMBER] Experience with terachem and amber12 Jason Swails (Sat Jun 15 2013 - 13:59:05 PDT)
  - Re: [AMBER] Experience with terachem and amber12 Fabrício Bracht (Sat Jun 15 2013 - 21:49:50 PDT)
[AMBER] Is that a way to generate free energy landscapes with ptraj? Yip Yew Mun (Sat Jun 15 2013 - 06:29:38 PDT)
- Re: [AMBER] Is that a way to generate free energy landscapes with ptraj? Jason Swails (Sat Jun 15 2013 - 11:47:36 PDT)
[AMBER] Antechamber atom types and all_nuc94.in atom descriptions Kamali Sripathi (Sat Jun 15 2013 - 20:26:12 PDT)
- Re: [AMBER] Antechamber atom types and all_nuc94.in atom descriptions FyD (Tue Jun 18 2013 - 00:31:30 PDT)
  - Re: [AMBER] Antechamber atom types and all_nuc94.in atom descriptions Kamali Sripathi (Tue Jun 18 2013 - 13:06:44 PDT)
    - Re: [AMBER] Antechamber atom types and all_nuc94.in atom descriptions FyD (Wed Jun 19 2013 - 01:13:12 PDT)
    - Re: [AMBER] Antechamber atom types and all_nuc94.in atom descriptions Kamali Sripathi (Sun Jun 23 2013 - 05:06:29 PDT)
    - Re: [AMBER] Antechamber atom types and all_nuc94.in atom descriptions Kamali Sripathi (Sun Jun 23 2013 - 16:10:40 PDT)
    - Re: [AMBER] Antechamber atom types and all_nuc94.in atom descriptions Kamali Sripathi (Mon Jun 24 2013 - 19:01:46 PDT)
    - Re: [AMBER] Antechamber atom types and all_nuc94.in atom descriptions Kamali Sripathi (Mon Jun 24 2013 - 20:26:34 PDT)
    - Re: [AMBER] Antechamber atom types and all_nuc94.in atom descriptions FyD (Tue Jun 25 2013 - 00:55:08 PDT)
    - Re: [AMBER] Antechamber atom types and all_nuc94.in atom descriptions Kamali Sripathi (Tue Jun 25 2013 - 05:53:25 PDT)
    - Re: [AMBER] Antechamber atom types and all_nuc94.in atom descriptions FyD (Wed Jun 26 2013 - 01:43:06 PDT)
    - Re: [AMBER] Antechamber atom types and all_nuc94.in atom descriptions Kamali Sripathi (Wed Jun 26 2013 - 20:07:46 PDT)
    - Re: [AMBER] Antechamber atom types and all_nuc94.in atom descriptions FyD (Thu Jun 27 2013 - 06:48:19 PDT)
    - Re: [AMBER] Antechamber atom types and all_nuc94.in atom descriptions Kamali Sripathi (Thu Jun 27 2013 - 08:00:04 PDT)
    - Re: [AMBER] Antechamber atom types and all_nuc94.in atom descriptions Kamali Sripathi (Wed Jul 03 2013 - 11:22:07 PDT)
    - Re: [AMBER] Antechamber atom types and all_nuc94.in atom descriptions FyD (Thu Jul 04 2013 - 07:51:16 PDT)
    - Re: [AMBER] Antechamber atom types and all_nuc94.in atom descriptions Kamali Sripathi (Sat Jul 06 2013 - 06:03:51 PDT)
    - Re: [AMBER] Antechamber atom types and all_nuc94.in atom descriptions FyD (Sun Jul 07 2013 - 09:03:25 PDT)
    - Re: [AMBER] Antechamber atom types and all_nuc94.in atom descriptions Kamali Sripathi (Tue Jul 09 2013 - 12:21:47 PDT)
    - Re: [AMBER] Antechamber atom types and all_nuc94.in atom descriptions FyD (Wed Jul 10 2013 - 01:16:45 PDT)
    - Re: [AMBER] Antechamber atom types and all_nuc94.in atom descriptions Kamali Sripathi (Sat Jul 13 2013 - 11:14:09 PDT)
    - Re: [AMBER] Antechamber atom types and all_nuc94.in atom descriptions Kamali Sripathi (Fri Jul 19 2013 - 12:20:44 PDT)
  - Re: [AMBER] Antechamber atom types and all_nuc94.in atom descriptions FyD (Sat Jul 20 2013 - 03:14:25 PDT)
    - Re: [AMBER] Antechamber atom types and all_nuc94.in atom descriptions Kamali Sripathi (Sat Jul 20 2013 - 05:57:41 PDT)
    - Re: [AMBER] Antechamber atom types and all_nuc94.in atom descriptions FyD (Sat Jul 20 2013 - 09:54:40 PDT)
    - Re: [AMBER] Antechamber atom types and all_nuc94.in atom descriptions Kamali Sripathi (Sun Jul 21 2013 - 20:01:44 PDT)
    - Re: [AMBER] Antechamber atom types and all_nuc94.in atom descriptions Kamali Sripathi (Thu Jul 25 2013 - 08:29:52 PDT)
    - Re: [AMBER] Antechamber atom types and all_nuc94.in atom descriptions FyD (Fri Jul 26 2013 - 01:36:58 PDT)
    - Re: [AMBER] Antechamber atom types and all_nuc94.in atom descriptions Kamali Sripathi (Fri Jul 26 2013 - 04:36:13 PDT)
[AMBER] cpptraj grid water density Asmita Gupta (Sun Jun 16 2013 - 06:01:26 PDT)
[AMBER] selective aMD Thomas Evangelidis (Sun Jun 16 2013 - 09:43:30 PDT)
- Re: [AMBER] selective aMD Daniel Roe (Sun Jun 16 2013 - 19:13:15 PDT)
  - [AMBER] MMPBSA results for DNA-ligand system Sorensen, Jesper (Sun Jun 16 2013 - 22:33:48 PDT)
    - Re: [AMBER] MMPBSA results for DNA-ligand system deeptinayar.gmail.com (Mon Jun 17 2013 - 12:21:59 PDT)
    - Re: [AMBER] MMPBSA results for DNA-ligand system Josh Berryman (Mon Jun 17 2013 - 01:14:47 PDT)
    - Re: [AMBER] MMPBSA results for DNA-ligand system Sorensen, Jesper (Mon Jun 17 2013 - 07:32:38 PDT)
- Re: [AMBER] selective aMD Chris Moth (Mon Jun 17 2013 - 08:16:50 PDT)
  - Re: [AMBER] selective aMD Romelia Salomon (Tue Jun 18 2013 - 11:07:40 PDT)
[AMBER] How can I calculate the individual PBSA energies of a large set Changqing Yan (Sun Jun 16 2013 - 17:41:01 PDT)
[AMBER] What bugfix.18 actually does to correct the problem in NPT simulations on GPU? Takato Sato (Mon Jun 17 2013 - 01:54:00 PDT)
[AMBER] Assessing Antechamber temporary files Kamali Sripathi (Mon Jun 17 2013 - 05:03:11 PDT)
[AMBER] Graphene topology from GAFF dpiraner.caltech.edu (Mon Jun 17 2013 - 11:48:48 PDT)
- Re: [AMBER] Graphene topology from GAFF David A Case (Mon Jun 17 2013 - 17:33:00 PDT)
- Re: [AMBER] Graphene topology from GAFF FyD (Tue Jun 18 2013 - 00:20:52 PDT)
  - Re: [AMBER] Graphene topology from GAFF Karl N. Kirschner (Tue Jun 18 2013 - 01:17:45 PDT)
    - Re: [AMBER] Graphene topology from GAFF Dan Piraner (Tue Jun 18 2013 - 02:47:06 PDT)
    - Re: [AMBER] Graphene topology from GAFF Hector A. Baldoni (Tue Jun 18 2013 - 14:40:11 PDT)
    - Re: [AMBER] Graphene topology from GAFF Dan Piraner (Tue Jun 18 2013 - 17:05:27 PDT)
[AMBER] Need a higher value for SKINNB Hailin Huang (Mon Jun 17 2013 - 15:20:57 PDT)
- Re: [AMBER] Need a higher value for SKINNB Jason Swails (Mon Jun 17 2013 - 16:31:37 PDT)
  - Re: [AMBER] Need a higher value for SKINNB Hailin Huang (Wed Jun 19 2013 - 05:33:55 PDT)
    - Re: [AMBER] Need a higher value for SKINNB Scott Le Grand (Wed Jun 19 2013 - 10:16:02 PDT)
    - Re: [AMBER] Need a higher value for SKINNB Hailin Huang (Wed Jun 19 2013 - 10:43:47 PDT)
    - Re: [AMBER] Need a higher value for SKINNB Scott Le Grand (Wed Jun 19 2013 - 11:59:02 PDT)
    - Re: [AMBER] Need a higher value for SKINNB Hailin Huang (Wed Jun 19 2013 - 12:14:29 PDT)
    - Re: [AMBER] Need a higher value for SKINNB Scott Le Grand (Wed Jun 19 2013 - 13:03:39 PDT)
    - Re: [AMBER] Need a higher value for SKINNB Hailin Huang (Wed Jun 19 2013 - 13:34:43 PDT)
    - Re: [AMBER] Need a higher value for SKINNB Scott Le Grand (Wed Jun 19 2013 - 14:23:54 PDT)
    - Re: [AMBER] Need a higher value for SKINNB Hailin Huang (Wed Jun 19 2013 - 14:48:42 PDT)
    - Re: [AMBER] Need a higher value for SKINNB Scott Le Grand (Wed Jun 19 2013 - 15:08:36 PDT)
    - Re: [AMBER] Need a higher value for SKINNB Scott Le Grand (Fri Jun 21 2013 - 10:31:41 PDT)
[AMBER] Difficulty in reading .mdcrd file in VMD Yan Duan (Mon Jun 17 2013 - 16:07:31 PDT)
- Re: [AMBER] Difficulty in reading .mdcrd file in VMD Jason Swails (Thu Jun 20 2013 - 04:23:58 PDT)
[AMBER] qmcut in QM/MM simulation with AMBER/GAUSSIAN Tamara Meirelles (Mon Jun 17 2013 - 17:39:00 PDT)
- Re: [AMBER] qmcut in QM/MM simulation with AMBER/GAUSSIAN Eric Berquist (Wed Jun 19 2013 - 07:01:52 PDT)
[AMBER] MMPBSA.py and cpptraj error Sorensen, Jesper (Mon Jun 17 2013 - 20:35:08 PDT)
- Re: [AMBER] MMPBSA.py and cpptraj error David A Case (Tue Jun 18 2013 - 04:54:16 PDT)
  - Re: [AMBER] MMPBSA.py and cpptraj error Sorensen, Jesper (Tue Jun 18 2013 - 19:12:23 PDT)
    - Re: [AMBER] MMPBSA.py and cpptraj error Sorensen, Jesper (Tue Jun 18 2013 - 19:37:46 PDT)
    - Re: [AMBER] MMPBSA.py and cpptraj error Jason Swails (Wed Jun 19 2013 - 03:12:38 PDT)
    - Re: [AMBER] MMPBSA.py and cpptraj error Sorensen, Jesper (Wed Jun 19 2013 - 16:08:33 PDT)
    - Re: [AMBER] MMPBSA.py and cpptraj error Jason Swails (Wed Jun 19 2013 - 18:23:48 PDT)
    - Re: [AMBER] MMPBSA.py and cpptraj error Sorensen, Jesper (Thu Jun 20 2013 - 09:43:59 PDT)
    - Re: [AMBER] MMPBSA.py and cpptraj error Jason Swails (Thu Jun 20 2013 - 10:07:22 PDT)
    - Re: [AMBER] MMPBSA.py and cpptraj error Sorensen, Jesper (Thu Jun 20 2013 - 10:56:48 PDT)
    - Re: [AMBER] MMPBSA.py and cpptraj error Jason Swails (Thu Jun 20 2013 - 11:06:13 PDT)
[AMBER] ERROR: GPU runs fail with nfft Error only when running 2x geforce TITANS in same machine ET (Mon Jun 17 2013 - 22:21:49 PDT)
- Re: [AMBER] ERROR: GPU runs fail with nfft Error only when running 2x geforce TITANS in same machine ET (Mon Jun 17 2013 - 22:24:17 PDT)
  - Re: [AMBER] ERROR: GPU runs fail with nfft Error only when running 2x geforce TITANS in same machine Scott Le Grand (Wed Jun 19 2013 - 10:15:34 PDT)
    - Re: [AMBER] ERROR: GPU runs fail with nfft Error only when running 2x geforce TITANS in same machine ET (Thu Jun 20 2013 - 07:56:37 PDT)
    - Re: [AMBER] ERROR: GPU runs fail with nfft Error only when running 2x geforce TITANS in same machine Ross Walker (Thu Jun 20 2013 - 09:37:06 PDT)
    - Re: [AMBER] ERROR: GPU runs fail with nfft Error only when running 2x geforce TITANS in same machine ET (Thu Jun 20 2013 - 11:42:42 PDT)
    - Re: [AMBER] ERROR: GPU runs fail with nfft Error only when running 2x geforce TITANS in same machine Scott Le Grand (Thu Jun 20 2013 - 12:02:23 PDT)
    - Re: [AMBER] ERROR: GPU runs fail with nfft Error only when running 2x geforce TITANS in same machine ET (Thu Jun 20 2013 - 12:07:12 PDT)
    - Re: [AMBER] ERROR: GPU runs fail with nfft Error only when running 2x geforce TITANS in same machine Ross Walker (Thu Jun 20 2013 - 07:58:28 PDT)
[AMBER] Cellulose NVE with pmemd.cuda.MPI Nakashima, Yoshihisa (Mon Jun 17 2013 - 23:19:50 PDT)
- Re: [AMBER] Cellulose NVE with pmemd.cuda.MPI Ross Walker (Wed Jun 19 2013 - 05:19:12 PDT)
  - Re: [AMBER] Cellulose NVE with pmemd.cuda.MPI Scott Le Grand (Wed Jun 19 2013 - 10:07:31 PDT)
    - Re: [AMBER] Cellulose NVE with pmemd.cuda.MPI Nakashima, Yoshihisa (Wed Jun 19 2013 - 19:28:01 PDT)
[AMBER] hydrogen bond pattern Rasha Alqus (Tue Jun 18 2013 - 04:51:31 PDT)
- Re: [AMBER] hydrogen bond pattern David A Case (Tue Jun 18 2013 - 06:52:11 PDT)
[AMBER] PEG Bailey, Steven (Tue Jun 18 2013 - 05:18:24 PDT)
- Re: [AMBER] PEG FyD (Tue Jun 18 2013 - 05:36:28 PDT)
- Re: [AMBER] PEG Anselm Horn (Tue Jun 18 2013 - 05:54:14 PDT)
- Re: [AMBER] PEG David A Case (Tue Jun 18 2013 - 06:56:16 PDT)
  - Re: [AMBER] PEG Bailey, Steven (Tue Jun 18 2013 - 07:24:48 PDT)
    - Re: [AMBER] PEG David A Case (Tue Jun 18 2013 - 08:15:32 PDT)
    - Re: [AMBER] PEG Bailey, Steven (Tue Jun 18 2013 - 08:25:07 PDT)
[AMBER] A and Z-DNA arnab bhattacharya (Tue Jun 18 2013 - 06:34:31 PDT)
- Re: [AMBER] A and Z-DNA David A Case (Tue Jun 18 2013 - 08:08:21 PDT)
- Re: [AMBER] A and Z-DNA Collins Nganou (Wed Jun 19 2013 - 05:51:48 PDT)
  - Re: [AMBER] A and Z-DNA arnab bhattacharya (Wed Jun 19 2013 - 05:55:40 PDT)
    - Re: [AMBER] A and Z-DNA Collins Nganou (Wed Jun 19 2013 - 06:10:04 PDT)
    - Re: [AMBER] A and Z-DNA Vlad Cojocaru (Wed Jun 19 2013 - 15:49:54 PDT)
    - Re: [AMBER] A and Z-DNA Collins Nganou (Thu Jun 20 2013 - 05:10:46 PDT)
[AMBER] cpptraj: can we retrieve the minimal distance between two sets of residues? Jan-Philip Gehrcke (Tue Jun 18 2013 - 06:56:46 PDT)
- Re: [AMBER] cpptraj: can we retrieve the minimal distance between two sets of residues? Daniel Roe (Tue Jun 18 2013 - 08:22:14 PDT)
[AMBER] D amino acids Krisztina Feher (Tue Jun 18 2013 - 07:11:47 PDT)
- Re: [AMBER] D amino acids FyD (Tue Jun 18 2013 - 07:33:18 PDT)
  - Re: [AMBER] D amino acids Krisztina Feher (Tue Jun 18 2013 - 08:12:47 PDT)
  - Re: [AMBER] D amino acids David A Case (Tue Jun 18 2013 - 08:19:58 PDT)
    - Re: [AMBER] D amino acids Krisztina Feher (Tue Jun 18 2013 - 08:48:58 PDT)
[AMBER] Job stops due to INFO: Old style inpcrd file read Aditya Padhi (Tue Jun 18 2013 - 08:32:28 PDT)
- Re: [AMBER] Job stops due to INFO: Old style inpcrd file read Jason Swails (Tue Jun 18 2013 - 09:14:14 PDT)
  - Re: [AMBER] Job stops due to INFO: Old style inpcrd file read Aditya Padhi (Tue Jun 18 2013 - 11:23:38 PDT)
    - Re: [AMBER] Job stops due to INFO: Old style inpcrd file read Jason Swails (Tue Jun 18 2013 - 12:03:29 PDT)
[AMBER] RADIAL ptraj vs cpptraj Domenico Marson (Tue Jun 18 2013 - 09:42:08 PDT)
- Re: [AMBER] RADIAL ptraj vs cpptraj Daniel Roe (Tue Jun 18 2013 - 10:50:10 PDT)
[AMBER] Amber compile, number of files Hunter Brown (Tue Jun 18 2013 - 10:15:25 PDT)
- Re: [AMBER] Amber compile, number of files Jason Swails (Tue Jun 18 2013 - 11:14:38 PDT)
- [AMBER] problem with tleap Rejwan (Tue Jun 18 2013 - 13:06:45 PDT)
  - Re: [AMBER] problem with tleap Jason Swails (Tue Jun 18 2013 - 14:09:21 PDT)
    - Re: [AMBER] problem with tleap Rejwan (Tue Jun 18 2013 - 18:46:29 PDT)
    - Re: [AMBER] problem with tleap Rejwan (Wed Jun 19 2013 - 08:06:05 PDT)
    - Re: [AMBER] problem with tleap FyD (Fri Jun 21 2013 - 00:11:17 PDT)
    - [AMBER] membrane-protein simulation with AMBER lipid11 FF Rejwan (Fri Jun 21 2013 - 09:30:24 PDT)
  - Re: [AMBER] problem with tleap Bill Ross (Wed Jun 19 2013 - 13:31:03 PDT)
[AMBER] gaff atom type inhee park (Tue Jun 18 2013 - 12:39:26 PDT)
[AMBER] Nonbond cells need to be recalculated, restart simulation from previous checkpoint with a higher value for skinnb. 涂志萍 (Wed Jun 19 2013 - 02:35:01 PDT)
- Re: [AMBER] Nonbond cells need to be recalculated, restart simulation from previous checkpoint with a higher value for skinnb. Jason Swails (Wed Jun 19 2013 - 03:20:53 PDT)
[AMBER] Thanks Hunter Brown (Wed Jun 19 2013 - 09:07:07 PDT)
[AMBER] Curious behavior of cpptraj in ambertools 13.1 Fabrício Bracht (Wed Jun 19 2013 - 09:49:28 PDT)
- Re: [AMBER] Curious behavior of cpptraj in ambertools 13.1 Daniel Roe (Wed Jun 19 2013 - 10:10:56 PDT)
  - Re: [AMBER] Curious behavior of cpptraj in ambertools 13.1 Jason Swails (Wed Jun 19 2013 - 10:39:55 PDT)
    - Re: [AMBER] Curious behavior of cpptraj in ambertools 13.1 Fabrício Bracht (Wed Jun 19 2013 - 19:18:39 PDT)
    - Re: [AMBER] Curious behavior of cpptraj in ambertools 13.1 Jason Swails (Wed Jun 19 2013 - 19:45:18 PDT)
[AMBER] Update 10 for AmberTools 13: CPPTRAJ Daniel Roe (Wed Jun 19 2013 - 10:03:01 PDT)
- Re: [AMBER] Update 10 for AmberTools 13: CPPTRAJ Jan-Philip Gehrcke (Wed Jun 19 2013 - 11:06:07 PDT)
[AMBER] Experiences with GTX 780 in the framework of Amber calculations ? Marek Maly (Wed Jun 19 2013 - 10:35:58 PDT)
- Re: [AMBER] Experiences with GTX 780 in the framework of Amber calculations ? Gould, Ian R (Wed Jun 19 2013 - 11:34:15 PDT)
  - Re: [AMBER] Experiences with GTX 780 in the framework of Amber calculations ? Scott Le Grand (Wed Jun 19 2013 - 11:39:09 PDT)
    - Re: [AMBER] Experiences with GTX 780 in the framework of Amber calculations ? filip fratev (Wed Jun 19 2013 - 12:58:45 PDT)
    - Re: [AMBER] Experiences with GTX 780 in the framework of Amber calculations ? ET (Thu Jun 20 2013 - 06:33:40 PDT)
    - Re: [AMBER] Experiences with GTX 780 in the framework of Amber calculations ? Gould, Ian R (Thu Jun 20 2013 - 07:05:55 PDT)
  - Re: [AMBER] Experiences with GTX 780 in the framework of Amber calculations ? Marek Maly (Wed Jun 19 2013 - 12:14:29 PDT)
- Re: [AMBER] Experiences with GTX 780 in the framework of Amber calculations ? Gould, Ian R (Wed Jun 19 2013 - 11:35:31 PDT)
[AMBER] Difficulty running sander Hunter Brown (Wed Jun 19 2013 - 11:10:35 PDT)
- Re: [AMBER] Difficulty running sander Jason Swails (Wed Jun 19 2013 - 12:34:00 PDT)
[AMBER] NAB extract residue from molecule Le,Huy Tuan (Wed Jun 19 2013 - 11:31:12 PDT)
- Re: [AMBER] NAB extract residue from molecule David A Case (Thu Jun 20 2013 - 08:21:45 PDT)
[AMBER] Access to Quanta or CHARMM software Manikanthan Bhavaraju (Wed Jun 19 2013 - 12:33:13 PDT)
[AMBER] receiving amber digest not separate subject wise as earlier Vaibhav Dixit (Thu Jun 20 2013 - 01:15:07 PDT)
- Re: [AMBER] receiving amber digest not separate subject wise as earlier Ross Walker (Thu Jun 20 2013 - 09:32:41 PDT)
  - Re: [AMBER] receiving amber digest not separate subject wise as earlier Vaibhav Dixit (Fri Jun 21 2013 - 00:33:50 PDT)
[AMBER] Is per atome decomposition in MM-PBSA possible? Haralambos Tzoupis (Thu Jun 20 2013 - 02:37:11 PDT)
- Re: [AMBER] Is per atome decomposition in MM-PBSA possible? Jason Swails (Thu Jun 20 2013 - 03:11:55 PDT)
  - Re: [AMBER] Is per atome decomposition in MM-PBSA possible? Alexander Metz (Thu Jun 20 2013 - 03:37:06 PDT)
[AMBER] Fwd: Re: Graphene topology from GAFF FyD (Thu Jun 20 2013 - 07:02:04 PDT)
- Re: [AMBER] Fwd: Re: Graphene topology from GAFF FyD (Wed Jun 26 2013 - 02:02:29 PDT)
[AMBER] GAFF atom type for CO Krisztina Feher (Thu Jun 20 2013 - 11:16:17 PDT)
- Re: [AMBER] GAFF atom type for CO David A Case (Thu Jun 20 2013 - 13:55:19 PDT)
- Re: [AMBER] GAFF atom type for CO FyD (Thu Jun 20 2013 - 23:49:44 PDT)
- Re: [AMBER] GAFF atom type for CO Krisztina Feher (Fri Jun 21 2013 - 01:59:41 PDT)
  - Re: [AMBER] GAFF atom type for CO Karl N. Kirschner (Fri Jun 21 2013 - 03:02:33 PDT)
  - Re: [AMBER] GAFF atom type for CO David A Case (Sat Jun 22 2013 - 05:48:39 PDT)
- Re: [AMBER] GAFF atom type for CO Krisztina Feher (Fri Jun 21 2013 - 02:51:56 PDT)
  - Re: [AMBER] GAFF atom type for CO FyD (Fri Jun 21 2013 - 09:18:16 PDT)
- Re: [AMBER] GAFF atom type for CO Krisztina Feher (Sat Jun 22 2013 - 07:03:42 PDT)
  - Re: [AMBER] GAFF atom type for CO David A Case (Sat Jun 22 2013 - 09:59:22 PDT)
    - Re: [AMBER] GAFF atom type for CO Krisztina Feher (Sat Jun 22 2013 - 11:22:50 PDT)
    - Re: [AMBER] GAFF atom type for CO David A Case (Sun Jun 23 2013 - 18:28:10 PDT)
[AMBER] adding Mg2+ as Counter ion for MD simulations Pranjal Mahanta (Thu Jun 20 2013 - 11:34:30 PDT)
- Re: [AMBER] adding Mg2+ as Counter ion for MD simulations FyD (Fri Jun 21 2013 - 00:02:50 PDT)
[AMBER] Anyone running machines with Quad GPU setups ET (Thu Jun 20 2013 - 17:18:59 PDT)
- Re: [AMBER] Anyone running machines with Quad GPU setups ET (Fri Jun 21 2013 - 14:04:21 PDT)
- Re: [AMBER] Anyone running machines with Quad GPU setups Divi/GMAIL (Fri Jun 21 2013 - 16:07:44 PDT)
  - Re: [AMBER] Anyone running machines with Quad GPU setups Scott Le Grand (Sat Jun 22 2013 - 08:15:08 PDT)
    - Re: [AMBER] Anyone running machines with Quad GPU setups Jan-Philip Gehrcke (Sat Jun 22 2013 - 08:32:39 PDT)
    - Re: [AMBER] Anyone running machines with Quad GPU setups Divi/GMAIL (Sat Jun 22 2013 - 11:30:28 PDT)
    - Re: [AMBER] Anyone running machines with Quad GPU setups ET (Sat Jun 22 2013 - 10:10:18 PDT)
    - Re: [AMBER] Anyone running machines with Quad GPU setups Jan-Philip Gehrcke (Sat Jun 22 2013 - 10:29:18 PDT)
    - Re: [AMBER] Anyone running machines with Quad GPU setups Jan-Philip Gehrcke (Sat Jun 22 2013 - 10:36:25 PDT)
    - Re: [AMBER] Anyone running machines with Quad GPU setups ET (Sat Jun 22 2013 - 10:40:25 PDT)
    - Re: [AMBER] Anyone running machines with Quad GPU setups Scott Le Grand (Sat Jun 22 2013 - 11:31:27 PDT)
    - Re: [AMBER] Anyone running machines with Quad GPU setups ET (Sat Jun 22 2013 - 12:45:20 PDT)
    - Re: [AMBER] Anyone running machines with Quad GPU setups Ross Walker (Sat Jun 22 2013 - 13:12:26 PDT)
    - Re: [AMBER] Anyone running machines with Quad GPU setups ET (Sat Jun 22 2013 - 13:26:04 PDT)
    - Re: [AMBER] Anyone running machines with Quad GPU setups Scott Le Grand (Sat Jun 22 2013 - 13:31:48 PDT)
    - Re: [AMBER] Anyone running machines with Quad GPU setups ET (Sat Jun 22 2013 - 22:36:41 PDT)
    - Re: [AMBER] Anyone running machines with Quad GPU setups Ross Walker (Sun Jun 23 2013 - 17:21:25 PDT)
    - Re: [AMBER] Anyone running machines with Quad GPU setups deeptinayar.gmail.com (Mon Jun 24 2013 - 19:44:54 PDT)
    - Re: [AMBER] Anyone running machines with Quad GPU setups ET (Mon Jun 24 2013 - 11:48:16 PDT)
    - Re: [AMBER] Anyone running machines with Quad GPU setups Kevin Hauser (Mon Jun 24 2013 - 16:40:03 PDT)
    - Re: [AMBER] Anyone running machines with Quad GPU setups Ross Walker (Mon Jun 24 2013 - 16:58:57 PDT)
    - Re: [AMBER] Anyone running machines with Quad GPU setups ET (Mon Jun 24 2013 - 20:06:40 PDT)
    - Re: [AMBER] Anyone running machines with Quad GPU setups ET (Mon Jun 24 2013 - 22:19:56 PDT)
    - Re: [AMBER] Anyone running machines with Quad GPU setups ET (Mon Jun 24 2013 - 22:29:20 PDT)
    - Re: [AMBER] Anyone running machines with Quad GPU setups Ross Walker (Mon Jun 24 2013 - 22:36:19 PDT)
    - Re: [AMBER] Anyone running machines with Quad GPU setups ET (Mon Jun 24 2013 - 22:56:41 PDT)
    - Re: [AMBER] Anyone running machines with Quad GPU setups ET (Mon Jun 24 2013 - 23:09:40 PDT)
[AMBER] "vlimit exceeded for step" for constant surface tension simulation Wei Lin (Thu Jun 20 2013 - 18:09:32 PDT)
[AMBER] How to define restraint for Umbrella sampling Sindrila Dutta banik (Fri Jun 21 2013 - 00:46:17 PDT)
- Re: [AMBER] How to define restraint for Umbrella sampling Brian Radak (Fri Jun 21 2013 - 06:45:56 PDT)
  - Re: [AMBER] How to define restraint for Umbrella sampling Marc van der Kamp (Fri Jun 21 2013 - 08:28:54 PDT)
[AMBER] Calculating Hydrophobic Interaction Ravi Tripathi (Fri Jun 21 2013 - 05:31:24 PDT)
- Re: [AMBER] Calculating Hydrophobic Interaction ET (Mon Jun 24 2013 - 11:51:02 PDT)
[AMBER] post-clustering calculation of DBI and pSF Amparo Garcia Lopez (Fri Jun 21 2013 - 06:34:26 PDT)
- Re: [AMBER] post-clustering calculation of DBI and pSF Daniel Roe (Fri Jun 21 2013 - 07:30:55 PDT)
  - Re: [AMBER] post-clustering calculation of DBI and pSF Amparo Garcia Lopez (Fri Jun 21 2013 - 08:18:23 PDT)
    - Re: [AMBER] post-clustering calculation of DBI and pSF Daniel Roe (Fri Jun 21 2013 - 09:03:13 PDT)
- Re: [AMBER] post-clustering calculation of DBI and pSF Thomas Cheatham (Fri Jun 21 2013 - 09:25:49 PDT)
  - Re: [AMBER] post-clustering calculation of DBI and pSF Amparo Garcia Lopez (Sat Jun 22 2013 - 10:46:08 PDT)
[AMBER] Troubles running LEaP Hunter Brown (Fri Jun 21 2013 - 11:57:39 PDT)
- Re: [AMBER] Troubles running LEaP Daniel Roe (Fri Jun 21 2013 - 12:08:55 PDT)
[AMBER] Fluctuation of density during equilibration phase Ibrahim Said (Fri Jun 21 2013 - 13:23:54 PDT)
- Re: [AMBER] Fluctuation of density during equilibration phase Jason Swails (Fri Jun 21 2013 - 20:16:27 PDT)
[AMBER] inhomogeneous solvent mixture Chinthaka Ratnaweera (Fri Jun 21 2013 - 21:36:01 PDT)
- Re: [AMBER] inhomogeneous solvent mixture Chinthaka Ratnaweera (Fri Jun 21 2013 - 22:52:56 PDT)
  - Re: [AMBER] inhomogeneous solvent mixture David A Case (Sat Jun 22 2013 - 05:48:03 PDT)
    - Re: [AMBER] inhomogeneous solvent mixture Chinthaka Ratnaweera (Sat Jun 22 2013 - 08:09:38 PDT)
    - Re: [AMBER] inhomogeneous solvent mixture Daniel Roe (Sat Jun 22 2013 - 09:38:44 PDT)
[AMBER] MMPBSA per-residue stuck forever without output even for 3 frames only M Elkot (Sat Jun 22 2013 - 07:36:53 PDT)
- Re: [AMBER] MMPBSA per-residue stuck forever without output even for 3 frames only Jason Swails (Sat Jun 22 2013 - 08:06:25 PDT)
  - Re: [AMBER] MMPBSA per-residue stuck forever without output even for 3 frames only Vaibhav Dixit (Mon Jun 24 2013 - 05:46:47 PDT)
    - Re: [AMBER] MMPBSA per-residue stuck forever without output even for 3 frames only Jason Swails (Mon Jun 24 2013 - 06:34:09 PDT)
    - Re: [AMBER] MMPBSA per-residue stuck forever without output even for 3 frames only Jason Swails (Mon Jun 24 2013 - 07:31:00 PDT)
    - Re: [AMBER] MMPBSA per-residue stuck forever without output even for 3 frames only M Elkot (Mon Jun 24 2013 - 07:48:28 PDT)
  - [AMBER] Per-residue decomposition output file format looks unfriendly Mahmoud Soliman (Tue Jun 25 2013 - 01:53:51 PDT)
    - Re: [AMBER] Per-residue decomposition output file format looks unfriendly Kshatresh Dutta Dubey (Tue Jun 25 2013 - 04:03:52 PDT)
    - Re: [AMBER] Per-residue decomposition output file format looks unfriendly Jan-Philip Gehrcke (Tue Jun 25 2013 - 04:22:13 PDT)
    - Re: [AMBER] Per-residue decomposition output file format looks unfriendly Jason Swails (Tue Jun 25 2013 - 04:52:03 PDT)
    - Re: [AMBER] Per-residue decomposition output file format looks unfriendly Mahmoud Soliman (Tue Jun 25 2013 - 05:00:10 PDT)
[AMBER] Actual Intel Compiler Version Used Ismail, Mohd F. (Sun Jun 23 2013 - 18:47:33 PDT)
- Re: [AMBER] Actual Intel Compiler Version Used Daniel Roe (Sun Jun 23 2013 - 20:10:56 PDT)
  - Re: [AMBER] Actual Intel Compiler Version Used Jan-Philip Gehrcke (Mon Jun 24 2013 - 02:43:03 PDT)
    - Re: [AMBER] Actual Intel Compiler Version Used Ismail, Mohd F. (Mon Jun 24 2013 - 20:30:40 PDT)
- Re: [AMBER] Actual Intel Compiler Version Used Ismail, Mohd F. (Mon Jun 24 2013 - 17:28:35 PDT)
  - Re: [AMBER] Actual Intel Compiler Version Used ET (Mon Jun 24 2013 - 20:18:07 PDT)
    - Re: [AMBER] Actual Intel Compiler Version Used Ismail, Mohd F. (Mon Jun 24 2013 - 20:32:10 PDT)
  - Re: [AMBER] Actual Intel Compiler Version Used Daniel Roe (Mon Jun 24 2013 - 20:35:23 PDT)
    - Re: [AMBER] Actual Intel Compiler Version Used Ismail, Mohd F. (Fri Jun 28 2013 - 00:34:23 PDT)
  - Re: [AMBER] Actual Intel Compiler Version Used David A Case (Tue Jun 25 2013 - 04:39:17 PDT)
    - Re: [AMBER] Actual Intel Compiler Version Used Ismail, Mohd F. (Fri Jun 28 2013 - 00:37:23 PDT)
[AMBER] error of PBSA calculation Changqing Yan (Mon Jun 24 2013 - 01:03:45 PDT)
- Re: [AMBER] error of PBSA calculation Bill Miller III (Mon Jun 24 2013 - 05:11:34 PDT)
[AMBER] Provisional GTX780 Numbers Ross Walker (Mon Jun 24 2013 - 14:23:02 PDT)
- Re: [AMBER] Provisional GTX780 Numbers ET (Tue Jun 25 2013 - 00:28:06 PDT)
  - Re: [AMBER] Provisional GTX780 Numbers Ross Walker (Tue Jun 25 2013 - 09:26:14 PDT)
    - Re: [AMBER] Provisional GTX780 Numbers ET (Tue Jun 25 2013 - 10:56:06 PDT)
    - Re: [AMBER] Provisional GTX780 Numbers Michael Lerner (Wed Jun 26 2013 - 12:38:05 PDT)
    - Re: [AMBER] Provisional GTX780 Numbers Ross Walker (Wed Jun 26 2013 - 12:56:28 PDT)
    - Re: [AMBER] Provisional GTX780 Numbers Michael Lerner (Wed Jun 26 2013 - 13:04:45 PDT)
    - Re: [AMBER] Provisional GTX780 Numbers ET (Wed Jun 26 2013 - 15:47:24 PDT)
[AMBER] issue in tleap Rejwan (Mon Jun 24 2013 - 14:25:27 PDT)
- Re: [AMBER] issue in tleap Jason Swails (Mon Jun 24 2013 - 14:32:06 PDT)
[AMBER] What are the controls parameters for the nmode command line tool Jose Borreguero (Mon Jun 24 2013 - 16:39:21 PDT)
- Re: [AMBER] What are the controls parameters for the nmode command line tool Jason Swails (Tue Jun 25 2013 - 04:28:33 PDT)
  - Re: [AMBER] What are the controls parameters for the nmode command line tool Jose Borreguero (Tue Jun 25 2013 - 07:18:58 PDT)
- Re: [AMBER] What are the controls parameters for the nmode command line tool David A Case (Tue Jun 25 2013 - 04:30:03 PDT)
[AMBER] Questions about ncsu_smd in Amber12 moitrayee.mbu.iisc.ernet.in (Mon Jun 24 2013 - 20:51:34 PDT)
[AMBER] MMPBSA.py problem Asmita Gupta (Tue Jun 25 2013 - 00:07:05 PDT)
- Re: [AMBER] MMPBSA.py problem Jason Swails (Tue Jun 25 2013 - 04:48:45 PDT)
  - Re: [AMBER] MMPBSA.py problem Hai Nguyen (Tue Jun 25 2013 - 13:28:36 PDT)
    - Re: [AMBER] MMPBSA.py problem Asmita Gupta (Wed Jun 26 2013 - 01:43:51 PDT)
    - Re: [AMBER] MMPBSA.py problem David A Case (Wed Jun 26 2013 - 04:40:50 PDT)
[AMBER] Fwd: Fwd: Re: Is it a bug? Compilation Error in Ambertools Matthias Bohner (Tue Jun 25 2013 - 00:40:37 PDT)
- Re: [AMBER] Fwd: Fwd: Re: Is it a bug? Compilation Error in Ambertools David A Case (Tue Jun 25 2013 - 04:49:48 PDT)
  - Re: [AMBER] Fwd: Fwd: Re: Is it a bug? Compilation Error in Ambertools Jason Swails (Tue Jun 25 2013 - 04:55:43 PDT)
    - Re: [AMBER] Fwd: Fwd: Re: Is it a bug? Compilation Error in Ambertools Matthias Bohner (Tue Jun 25 2013 - 05:56:53 PDT)
    - Re: [AMBER] Fwd: Fwd: Re: Is it a bug? Compilation Error in Ambertools David A Case (Tue Jun 25 2013 - 07:44:09 PDT)
  - Re: [AMBER] Fwd: Fwd: Re: Is it a bug? Compilation Error in Ambertools Matthias Bohner (Tue Jun 25 2013 - 05:54:08 PDT)
[AMBER] PB Bomb in pb_aaradi() - missing ff12SB atom types Hannes Loeffler (Tue Jun 25 2013 - 03:05:39 PDT)
- Re: [AMBER] PB Bomb in pb_aaradi() - missing ff12SB atom types Jason Swails (Tue Jun 25 2013 - 04:59:08 PDT)
  - Re: [AMBER] PB Bomb in pb_aaradi() - missing ff12SB atom types Hannes Loeffler (Tue Jun 25 2013 - 05:28:09 PDT)
    - Re: [AMBER] PB Bomb in pb_aaradi() - missing ff12SB atom types Jason Swails (Tue Jun 25 2013 - 05:39:37 PDT)
    - Re: [AMBER] PB Bomb in pb_aaradi() - missing ff12SB atom types Hannes Loeffler (Tue Jun 25 2013 - 08:29:16 PDT)
    - Re: [AMBER] PB Bomb in pb_aaradi() - missing ff12SB atom types Jason Swails (Tue Jun 25 2013 - 08:55:22 PDT)
[AMBER] Amber updater issues eneas.usal.es (Tue Jun 25 2013 - 09:04:22 PDT)
- Re: [AMBER] Amber updater issues Jason Swails (Tue Jun 25 2013 - 09:21:37 PDT)
- Re: [AMBER] Amber updater issues David A Case (Tue Jun 25 2013 - 09:29:01 PDT)
[AMBER] Cutoff smoothing George Tzotzos (Tue Jun 25 2013 - 09:17:24 PDT)
- Re: [AMBER] Cutoff smoothing tec3.utah.edu (Tue Jun 25 2013 - 09:31:21 PDT)
  - Re: [AMBER] Cutoff smoothing George Tzotzos (Tue Jun 25 2013 - 09:41:41 PDT)
[AMBER] [Re:] Amber updater issues eneas.usal.es (Tue Jun 25 2013 - 09:28:09 PDT)
- Re: [AMBER] [Re:] Amber updater issues Jason Swails (Tue Jun 25 2013 - 09:34:35 PDT)
[AMBER] MMPBSA.py error eneas.usal.es (Tue Jun 25 2013 - 09:37:33 PDT)
- Re: [AMBER] MMPBSA.py error Jason Swails (Tue Jun 25 2013 - 09:45:18 PDT)
- Re: [AMBER] MMPBSA.py error Jason Swails (Tue Jun 25 2013 - 10:45:48 PDT)
[AMBER] Amber updater issues eneas.usal.es (Tue Jun 25 2013 - 09:58:26 PDT)
- Re: [AMBER] Amber updater issues Jason Swails (Tue Jun 25 2013 - 10:18:40 PDT)
  - Re: [AMBER] Amber updater issues David A Case (Wed Jun 26 2013 - 04:20:05 PDT)
[AMBER] Amber updater issues eneas.usal.es (Tue Jun 25 2013 - 10:25:52 PDT)
[AMBER] entropy calculation starts from where it stops psu4.uic.edu (Tue Jun 25 2013 - 10:34:15 PDT)
- Re: [AMBER] entropy calculation starts from where it stops Jason Swails (Tue Jun 25 2013 - 10:47:16 PDT)
  - Re: [AMBER] entropy calculation starts from where it stops psu4.uic.edu (Tue Jun 25 2013 - 11:09:57 PDT)
    - Re: [AMBER] entropy calculation starts from where it stops Jason Swails (Tue Jun 25 2013 - 11:59:34 PDT)
    - Re: [AMBER] entropy calculation starts from where it stops psu4.uic.edu (Tue Jun 25 2013 - 13:00:23 PDT)
[AMBER] Questions about SMD using jar=1 moitrayee.mbu.iisc.ernet.in (Tue Jun 25 2013 - 12:23:24 PDT)
- Re: [AMBER] Questions about SMD using jar=1 Jason Swails (Tue Jun 25 2013 - 14:28:05 PDT)
  - Re: [AMBER] Questions about SMD using jar=1 moitrayee.mbu.iisc.ernet.in (Tue Jun 25 2013 - 18:11:33 PDT)
[AMBER] unable to compile amberTools12 Christopher Neale (Tue Jun 25 2013 - 12:38:44 PDT)
- Re: [AMBER] unable to compile amberTools12 David A Case (Wed Jun 26 2013 - 04:37:40 PDT)
  - Re: [AMBER] unable to compile amberTools12 Jason Swails (Wed Jun 26 2013 - 05:03:57 PDT)
    - Re: [AMBER] unable to compile amberTools12 Christopher Neale (Wed Jun 26 2013 - 18:40:05 PDT)
[AMBER] Custom topology parameter usage Parker de Waal (Tue Jun 25 2013 - 21:18:39 PDT)
- Re: [AMBER] Custom topology parameter usage Daniel Roe (Tue Jun 25 2013 - 21:37:48 PDT)
- Re: [AMBER] Custom topology parameter usage FyD (Wed Jun 26 2013 - 01:48:20 PDT)
[AMBER] Force-field for non-native peptide containing fluoride Cheng-I Lee (Wed Jun 26 2013 - 02:14:43 PDT)
- Re: [AMBER] Force-field for non-native peptide containing fluoride Karl N. Kirschner (Wed Jun 26 2013 - 02:41:42 PDT)
  - Re: [AMBER] Force-field for non-native peptide containing fluoride Cheng-I Lee (Wed Jun 26 2013 - 08:19:20 PDT)
    - Re: [AMBER] Force-field for non-native peptide containing fluoride Alessandro Contini (Wed Jun 26 2013 - 08:56:39 PDT)
[AMBER] GTX780 News Ross Walker (Wed Jun 26 2013 - 16:31:26 PDT)
- Re: [AMBER] GTX780 News Scott Le Grand (Wed Jun 26 2013 - 17:47:32 PDT)
  - Re: [AMBER] GTX780 News ET (Wed Jun 26 2013 - 19:13:41 PDT)
    - Re: [AMBER] GTX780 News Scott Le Grand (Thu Jun 27 2013 - 10:50:02 PDT)
    - Re: [AMBER] GTX780 News ET (Thu Jun 27 2013 - 11:20:22 PDT)
    - Re: [AMBER] GTX780 News Scott Le Grand (Thu Jun 27 2013 - 11:36:33 PDT)
    - Re: [AMBER] GTX780 News ET (Thu Jun 27 2013 - 12:15:45 PDT)
    - Re: [AMBER] GTX780 News Ross Walker (Thu Jun 27 2013 - 11:43:34 PDT)
    - Re: [AMBER] GTX780 News ET (Thu Jun 27 2013 - 13:43:59 PDT)
    - Re: [AMBER] GTX780 News ET (Wed Jul 03 2013 - 04:58:40 PDT)
    - Re: [AMBER] GTX780 News ET (Mon Jul 08 2013 - 00:29:23 PDT)
    - Re: [AMBER] GTX780 News ET (Thu Jul 11 2013 - 09:23:22 PDT)
    - Re: [AMBER] GTX780 News Scott Le Grand (Thu Jul 11 2013 - 09:47:54 PDT)
    - Re: [AMBER] GTX780 News ET (Thu Jul 11 2013 - 11:46:33 PDT)
    - Re: [AMBER] GTX780 News ET (Thu Jul 11 2013 - 18:58:32 PDT)
    - Re: [AMBER] GTX780 News Ross Walker (Thu Jul 11 2013 - 20:24:56 PDT)
    - Re: [AMBER] GTX780 News Jason Swails (Thu Jul 11 2013 - 20:48:18 PDT)
    - Re: [AMBER] GTX780 News Fenley, Andrew (Thu Jul 11 2013 - 20:56:50 PDT)
    - Re: [AMBER] GTX780 News Ross Walker (Thu Jul 11 2013 - 21:01:15 PDT)
    - Re: [AMBER] GTX780 News Fenley, Andrew (Thu Jul 11 2013 - 21:11:57 PDT)
    - Re: [AMBER] GTX780 News Ross Walker (Thu Jul 11 2013 - 20:57:27 PDT)
[AMBER] Cupper cluster parametrization with MCPB mmaestre.gate.sinica.edu.tw (Wed Jun 26 2013 - 18:42:25 PDT)
- Re: [AMBER] Cupper cluster parametrization with MCPB mmaestre.gate.sinica.edu.tw (Wed Jun 26 2013 - 19:41:11 PDT)
[AMBER] Binding energy eneas.usal.es (Thu Jun 27 2013 - 01:26:37 PDT)
- Re: [AMBER] Binding energy steinbrt.rci.rutgers.edu (Thu Jun 27 2013 - 02:34:27 PDT)
[AMBER] TI calculations and autocorrelation time Kepa K. Burusco (Thu Jun 27 2013 - 07:56:48 PDT)
- Re: [AMBER] TI calculations and autocorrelation time steinbrt.rci.rutgers.edu (Thu Jun 27 2013 - 10:18:14 PDT)
[AMBER] Warnings in leap about lipid11 eneas.usal.es (Thu Jun 27 2013 - 08:01:54 PDT)
- Re: [AMBER] Warnings in leap about lipid11 Åge Aleksander Skjevik (Thu Jun 27 2013 - 14:55:03 PDT)
[AMBER] Is there any major change of MMPBSA.py in AmberTools 13? psu4.uic.edu (Thu Jun 27 2013 - 09:02:42 PDT)
- Re: [AMBER] Is there any major change of MMPBSA.py in AmberTools 13? Jason Swails (Thu Jun 27 2013 - 09:44:21 PDT)
  - Re: [AMBER] Is there any major change of MMPBSA.py in AmberTools 13? Hannes Loeffler (Fri Jun 28 2013 - 01:22:29 PDT)
    - Re: [AMBER] Is there any major change of MMPBSA.py in AmberTools 13? Jason Swails (Fri Jun 28 2013 - 07:16:25 PDT)
    - Re: [AMBER] Is there any major change of MMPBSA.py in AmberTools 13? Hannes Loeffler (Fri Jun 28 2013 - 08:13:45 PDT)
    - Re: [AMBER] Is there any major change of MMPBSA.py in AmberTools 13? Ray Luo, Ph.D. (Fri Jun 28 2013 - 10:47:53 PDT)
    - Re: [AMBER] Is there any major change of MMPBSA.py in AmberTools 13? hannes.loeffler.stfc.ac.uk (Sun Jun 30 2013 - 01:35:57 PDT)
[AMBER] FATAL: Atom XXX does not have a type sunyeping.aliyun.com (Thu Jun 27 2013 - 11:58:16 PDT)
- Re: [AMBER] FATAL: Atom XXX does not have a type Karl N. Kirschner (Thu Jun 27 2013 - 23:28:02 PDT)
- Re: [AMBER] FATAL: Atom XXX does not have a type FyD (Fri Jun 28 2013 - 00:04:37 PDT)
[AMBER] mmpbsa not included in Amber11? Changqing Yan (Thu Jun 27 2013 - 19:55:27 PDT)
- Re: [AMBER] mmpbsa not included in Amber11? Bill Miller III (Thu Jun 27 2013 - 20:03:48 PDT)
- Re: [AMBER] mmpbsa not included in Amber11? Jason Swails (Thu Jun 27 2013 - 20:00:40 PDT)
- Re: [AMBER] mmpbsa not included in Amber11? Changqing Yan (Thu Jun 27 2013 - 20:10:20 PDT)
[AMBER] energy analysis in amber Asmita Gupta (Thu Jun 27 2013 - 23:11:08 PDT)
- Re: [AMBER] energy analysis in amber Jason Swails (Fri Jun 28 2013 - 07:34:29 PDT)
[AMBER] How to define reaction coordinate in Umbrella sampeling Sindrila Dutta banik (Fri Jun 28 2013 - 00:42:08 PDT)
- Re: [AMBER] How to define reaction coordinate in Umbrella sampeling Jason Swails (Fri Jun 28 2013 - 06:06:13 PDT)
  - Re: [AMBER] How to define reaction coordinate in Umbrella sampeling Sindrila Dutta banik (Fri Jun 28 2013 - 12:35:46 PDT)
    - Re: [AMBER] How to define reaction coordinate in Umbrella sampeling Jason Swails (Fri Jun 28 2013 - 13:24:42 PDT)
    - [AMBER] How to define reaction coordinate in Umbrella sampeling Sindrila Dutta banik (Fri Jun 28 2013 - 19:19:44 PDT)
    - Re: [AMBER] How to define reaction coordinate in Umbrella sampeling Jason Swails (Fri Jun 28 2013 - 20:41:22 PDT)
    - Re: [AMBER] How to define reaction coordinate in Umbrella sampeling Sindrila Dutta banik (Fri Jun 28 2013 - 22:52:09 PDT)
    - Re: [AMBER] How to define reaction coordinate in Umbrella sampeling David A Case (Sat Jun 29 2013 - 06:08:53 PDT)
    - Re: [AMBER] How to define reaction coordinate in Umbrella sampeling Sindrila Dutta banik (Sat Jun 29 2013 - 19:32:19 PDT)
    - Re: [AMBER] How to define reaction coordinate in Umbrella sampeling Jason Swails (Sat Jun 29 2013 - 06:13:07 PDT)
    - [AMBER] How to define reaction coordinate in Umbrella sampeling Sindrila Dutta banik (Mon Jul 01 2013 - 04:42:59 PDT)
[AMBER] Problem with PDB files in LEaP Hunter Brown (Fri Jun 28 2013 - 08:09:58 PDT)
- Re: [AMBER] Problem with PDB files in LEaP Daniel Roe (Fri Jun 28 2013 - 09:43:31 PDT)
- Re: [AMBER] Problem with PDB files in LEaP David A Case (Fri Jun 28 2013 - 10:19:53 PDT)
[AMBER] 回复：Re: FATAL: Atom XXX does not have a type sunyeping.aliyun.com (Fri Jun 28 2013 - 09:05:16 PDT)
- Re: [AMBER] ???Re: FATAL: Atom XXX does not have a type FyD (Sat Jun 29 2013 - 02:35:59 PDT)
  - Re: [AMBER] ???Re: FATAL: Atom XXX does not have a type FyD (Tue Jul 02 2013 - 06:00:01 PDT)
Re: [AMBER] Problematic PDB files Daniel Roe (Fri Jun 28 2013 - 12:35:43 PDT)
- Re: [AMBER] Problematic PDB files Daniel Roe (Fri Jun 28 2013 - 13:22:39 PDT)
[AMBER] avgcoord in AT13 Hongyi WU (Fri Jun 28 2013 - 12:51:19 PDT)
- Re: [AMBER] avgcoord in AT13 Jason Swails (Fri Jun 28 2013 - 13:30:56 PDT)
  - [AMBER] 答复: avgcoord in AT13 Hongyi WU (Fri Jun 28 2013 - 18:50:12 PDT)
    - Re: [AMBER] 答复: avgcoord in AT13 Jason Swails (Sat Jun 29 2013 - 07:34:36 PDT)
- Re: [AMBER] avgcoord in AT13 Daniel Roe (Fri Jun 28 2013 - 13:31:17 PDT)
  - [AMBER] 答复: avgcoord in AT13 Hongyi WU (Fri Jun 28 2013 - 18:43:23 PDT)
[AMBER] How to get correlation matrix of center of mass of partial atoms for residues? Baogen Duan (Fri Jun 28 2013 - 23:44:28 PDT)
- Re: [AMBER] How to get correlation matrix of center of mass of partial atoms for residues? Daniel Roe (Sat Jun 29 2013 - 15:42:32 PDT)
[AMBER] problem with MM-PBSA Maryam Hamzehee (Sat Jun 29 2013 - 08:27:49 PDT)
- Re: [AMBER] problem with MM-PBSA Bill Ross (Wed May 27 2009 - 17:52:19 PDT)
- Re: [AMBER] problem with MM-PBSA Maryam Hamzehee (Sat Jan 02 2010 - 22:15:32 PST)
  - Re: [AMBER] problem with MM-PBSA Ray Luo, Ph.D. (Sat Jan 02 2010 - 22:56:22 PST)
    - Re: [AMBER] problem with MM-PBSA Maryam Hamzehee (Sat Jan 02 2010 - 23:24:48 PST)
    - Re: [AMBER] problem with MM-PBSA Ray Luo, Ph.D. (Sun Jan 03 2010 - 16:51:07 PST)
- Re: [AMBER] problem with MM-PBSA Maryam Hamzehee (Wed Sep 07 2011 - 10:45:20 PDT)
  - Re: [AMBER] problem with MM-PBSA Bill Miller III (Wed Sep 07 2011 - 10:56:31 PDT)
- Re: [AMBER] problem with MM-PBSA Jason Swails (Sat Jun 29 2013 - 10:32:05 PDT)
[AMBER] error in running MMPBSA.MPI onetwo (Sun Jun 30 2013 - 07:50:28 PDT)
[AMBER] error in running MMPBSA.MPI , mmpbsa_py_energy could not be found onetwo (Sun Jun 30 2013 - 23:17:49 PDT)
- Re: [AMBER] error in running MMPBSA.MPI , mmpbsa_py_energy could not be found Jason Swails (Mon Jul 01 2013 - 03:19:44 PDT)
  - Re: [AMBER] error in running MMPBSA.MPI , mmpbsa_py_energy could not be found onetwo (Mon Jul 01 2013 - 04:54:33 PDT)
- Re: [AMBER] error in running MMPBSA.MPI , mmpbsa_py_energy could not be found Bill Miller III (Mon Jul 01 2013 - 06:11:12 PDT)
  - Re: [AMBER] error in running MMPBSA.MPI , mmpbsa_py_energy could not be found onetwo (Mon Jul 01 2013 - 06:38:37 PDT)
  - Re: [AMBER] error in running MMPBSA.MPI , mmpbsa_py_energy could not be found Jason Swails (Mon Jul 01 2013 - 08:15:14 PDT)
    - Re: [AMBER] error in running MMPBSA.MPI , mmpbsa_py_energy could not be found onetwo (Tue Jul 02 2013 - 00:38:02 PDT)
[AMBER] ANN: mdtraj 0.3 released Robert McGibbon (Mon Jul 01 2013 - 00:42:50 PDT)
[AMBER] Anomalous peak of RDF of water when using ptraj of AmberTools12 kurisaki (Mon Jul 01 2013 - 02:51:20 PDT)
- Re: [AMBER] Anomalous peak of RDF of water when using ptraj of AmberTools12 Daniel Roe (Mon Jul 01 2013 - 09:30:56 PDT)
  - Re: [AMBER] Anomalous peak of RDF of water when using ptraj of AmberTools12 kurisaki (Mon Jul 01 2013 - 18:26:12 PDT)
[AMBER] MMPBSA.py.MPI run issues Asmita Gupta (Mon Jul 01 2013 - 06:01:11 PDT)
- Re: [AMBER] MMPBSA.py.MPI run issues Jason Swails (Mon Jul 01 2013 - 15:30:04 PDT)
  - Re: [AMBER] MMPBSA.py.MPI run issues Asmita Gupta (Mon Jul 01 2013 - 23:13:20 PDT)
    - Re: [AMBER] MMPBSA.py.MPI run issues Jason Swails (Tue Jul 02 2013 - 03:52:42 PDT)
[AMBER] The recommended way to create periodic box around lipid bilayer system ? Marek Maly (Mon Jul 01 2013 - 07:20:54 PDT)
- Re: [AMBER] The recommended way to create periodic box around lipid bilayer system ? David A Case (Mon Jul 01 2013 - 09:12:54 PDT)
  - Re: [AMBER] The recommended way to create periodic box around lipid bilayer system ? Marek Maly (Mon Jul 01 2013 - 11:26:11 PDT)
    - Re: [AMBER] The recommended way to create periodic box around lipid bilayer system ? Daniel Roe (Mon Jul 01 2013 - 12:30:27 PDT)
    - Re: [AMBER] The recommended way to create periodic box around lipid bilayer system ? Marek Maly (Mon Jul 01 2013 - 15:48:37 PDT)
    - [AMBER] viewing PREPIN/PREPC files Rejwan (Mon Jul 01 2013 - 12:38:37 PDT)
    - Re: [AMBER] viewing PREPIN/PREPC files David A Case (Mon Jul 01 2013 - 18:21:42 PDT)
    - Re: [AMBER] viewing PREPIN/PREPC files FyD (Tue Jul 02 2013 - 00:24:53 PDT)
[AMBER] AMBER atom types in parm10.dat don't match antechamber Brian Radak (Mon Jul 01 2013 - 07:50:13 PDT)
- Re: [AMBER] AMBER atom types in parm10.dat don't match antechamber David A Case (Mon Jul 01 2013 - 18:54:19 PDT)
  - Re: [AMBER] AMBER atom types in parm10.dat don't match antechamber FyD (Tue Jul 02 2013 - 00:45:47 PDT)
    - Re: [AMBER] AMBER atom types in parm10.dat don't match antechamber Brian Radak (Tue Jul 02 2013 - 06:34:40 PDT)
    - Re: [AMBER] AMBER atom types in parm10.dat don't match antechamber Brian Radak (Tue Jul 02 2013 - 07:04:48 PDT)
    - Re: [AMBER] AMBER atom types in parm10.dat don't match antechamber Jason Swails (Wed Jul 03 2013 - 02:43:19 PDT)
    - Re: [AMBER] AMBER atom types in parm10.dat don't match antechamber Daniel Roe (Wed Jul 03 2013 - 05:40:49 PDT)
[AMBER] MD simulation parameters: urgent please Mary Varughese (Mon Jul 01 2013 - 09:57:29 PDT)
- Re: [AMBER] MD simulation parameters: urgent please David A Case (Mon Jul 01 2013 - 18:38:11 PDT)
  - Re: [AMBER] MD simulation parameters: urgent please Mary Varughese (Mon Jul 01 2013 - 19:01:49 PDT)
    - [AMBER] MD simulation parameters: urgent please Daniel Roe (Mon Jul 01 2013 - 21:32:22 PDT)
    - Re: [AMBER] MD simulation parameters: urgent please Mary Varughese (Mon Jul 01 2013 - 21:47:08 PDT)
    - Re: [AMBER] MD simulation parameters: urgent please Mary Varughese (Mon Jul 01 2013 - 21:56:22 PDT)
[AMBER] Fixing pdb files prepared in VMD, minor errors Hunter Brown (Mon Jul 01 2013 - 10:43:13 PDT)
- Re: [AMBER] Fixing pdb files prepared in VMD, minor errors David A Case (Mon Jul 01 2013 - 18:44:57 PDT)
  - Re: [AMBER] Fixing pdb files prepared in VMD, minor errors David A Case (Tue Jul 02 2013 - 05:03:01 PDT)
- Re: [AMBER] Fixing pdb files prepared in VMD, minor errors Hunter Brown (Tue Jul 02 2013 - 08:50:46 PDT)
  - Re: [AMBER] Fixing pdb files prepared in VMD, minor errors David A Case (Tue Jul 02 2013 - 10:37:29 PDT)
[AMBER] VMD prepared errors (precise error messages) Hunter Brown (Mon Jul 01 2013 - 12:55:33 PDT)
- Re: [AMBER] VMD prepared errors (precise error messages) Daniel Roe (Mon Jul 01 2013 - 13:12:12 PDT)
[AMBER] &ewald skinnb=2.0d0 / 涂志萍 (Mon Jul 01 2013 - 19:47:32 PDT)
- Re: [AMBER] &ewald skinnb=2.0d0 / Scott Le Grand (Mon Jul 01 2013 - 20:16:22 PDT)
  - Re: [AMBER] &ewald skinnb=2.0d0 / 涂志萍 (Mon Jul 01 2013 - 20:25:35 PDT)
- Re: [AMBER] &ewald skinnb=2.0d0 / Ross Walker (Mon Jul 01 2013 - 21:40:07 PDT)
[AMBER] NVE Energy/Temperature Drift Issue James W. Snyder, Jr. (Mon Jul 01 2013 - 20:35:42 PDT)
- Re: [AMBER] NVE Energy/Temperature Drift Issue Ross Walker (Mon Jul 01 2013 - 21:10:48 PDT)
- Re: [AMBER] NVE Energy/Temperature Drift Issue Daniel Roe (Mon Jul 01 2013 - 21:17:59 PDT)
  - Re: [AMBER] NVE Energy/Temperature Drift Issue James W. Snyder, Jr. (Mon Jul 01 2013 - 21:40:05 PDT)
    - Re: [AMBER] NVE Energy/Temperature Drift Issue Ross Walker (Mon Jul 01 2013 - 21:43:06 PDT)
    - Re: [AMBER] NVE Energy/Temperature Drift Issue James W. Snyder, Jr. (Mon Jul 01 2013 - 21:51:20 PDT)
    - Re: [AMBER] NVE Energy/Temperature Drift Issue Ross Walker (Mon Jul 01 2013 - 21:58:50 PDT)
    - Re: [AMBER] NVE Energy/Temperature Drift Issue David A Case (Tue Jul 02 2013 - 05:13:16 PDT)
    - Re: [AMBER] NVE Energy/Temperature Drift Issue Andreas Goetz (Tue Jul 02 2013 - 13:59:24 PDT)
[AMBER] About cntrl error...please help.. 전선희 (Mon Jul 01 2013 - 22:08:25 PDT)
- Re: [AMBER] About cntrl error...please help.. Ross Walker (Mon Jul 01 2013 - 22:20:33 PDT)
- Re: [AMBER] About cntrl error...please help.. Jason Swails (Tue Jul 02 2013 - 03:55:35 PDT)
[AMBER] How to define NO SHAKE Sindrila Dutta banik (Tue Jul 02 2013 - 05:28:58 PDT)
- Re: [AMBER] How to define NO SHAKE Daniel Roe (Tue Jul 02 2013 - 07:18:00 PDT)
[AMBER] stopping simulation in between onetwo (Tue Jul 02 2013 - 06:22:29 PDT)
- Re: [AMBER] stopping simulation in between Daniel Roe (Tue Jul 02 2013 - 07:24:19 PDT)
  - Re: [AMBER] stopping simulation in between onetwo (Tue Jul 02 2013 - 08:27:09 PDT)
[AMBER] Re：Re: ???Re: FATAL: Atom XXX does not have a type sunyeping.aliyun.com (Tue Jul 02 2013 - 06:37:53 PDT)
- Re: [AMBER] FATAL: Atom XXX does not have a type FyD (Tue Jul 02 2013 - 08:00:58 PDT)
[AMBER] ambertools update 10 problem Asmita Gupta (Tue Jul 02 2013 - 07:29:26 PDT)
- Re: [AMBER] ambertools update 10 problem Daniel Roe (Tue Jul 02 2013 - 07:45:22 PDT)
  - Re: [AMBER] ambertools update 10 problem Asmita Gupta (Tue Jul 02 2013 - 07:51:00 PDT)
    - Re: [AMBER] ambertools update 10 problem Daniel Roe (Tue Jul 02 2013 - 07:59:29 PDT)
[AMBER] Amber11 AmberTools1.5 installation problem Sangeetha B (Tue Jul 02 2013 - 08:33:06 PDT)
[AMBER] Exclude H-atom from bfactor calculation Mahendra B Thapa (Tue Jul 02 2013 - 13:02:30 PDT)
- Re: [AMBER] Exclude H-atom from bfactor calculation Daniel Roe (Tue Jul 02 2013 - 14:02:59 PDT)
[AMBER] re sunyeping.aliyun.com (Tue Jul 02 2013 - 18:26:14 PDT)
- Re: [AMBER] re FyD (Wed Jul 03 2013 - 02:26:27 PDT)
[AMBER] Custom Heme Parameters Parker de Waal (Tue Jul 02 2013 - 19:58:12 PDT)
- Re: [AMBER] Custom Heme Parameters Parker de Waal (Wed Jul 03 2013 - 11:10:10 PDT)
  - Re: [AMBER] Custom Heme Parameters Jason Swails (Thu Jul 04 2013 - 07:37:21 PDT)
[AMBER] Line minimizer aborted: step at lower bound Sangita Kachhap (Tue Jul 02 2013 - 22:48:37 PDT)
- Re: [AMBER] Line minimizer aborted: step at lower bound David A Case (Wed Jul 03 2013 - 05:02:41 PDT)
[AMBER] MMPBSA.MPI:IndexError: list index out of range Asmita Gupta (Wed Jul 03 2013 - 03:56:08 PDT)
- Re: [AMBER] MMPBSA.MPI:IndexError: list index out of range Asmita Gupta (Wed Jul 03 2013 - 03:58:39 PDT)
  - Re: [AMBER] MMPBSA.MPI:IndexError: list index out of range Jason Swails (Wed Jul 03 2013 - 06:26:38 PDT)
    - Re: [AMBER] MMPBSA.MPI:IndexError: list index out of range Jason Swails (Wed Jul 03 2013 - 06:27:34 PDT)
[AMBER] Problem related to the WHAM analysis Sindrila Dutta banik (Wed Jul 03 2013 - 03:58:58 PDT)
- Re: [AMBER] Problem related to the WHAM analysis Daniel Roe (Wed Jul 03 2013 - 06:53:46 PDT)
[AMBER] 4x Asus Titan boards :) GB/nucleosome passed Tru Huynh (Wed Jul 03 2013 - 09:00:49 PDT)
- Re: [AMBER] 4x Asus Titan boards :) GB/nucleosome passed Marek Maly (Wed Jul 03 2013 - 08:55:51 PDT)
  - Re: [AMBER] 4x Asus Titan boards :) GB/nucleosome passed Ross Walker (Wed Jul 03 2013 - 10:00:44 PDT)
    - Re: [AMBER] 4x Asus Titan boards :) GB/nucleosome passed Tru Huynh (Wed Jul 03 2013 - 10:35:56 PDT)
    - Re: [AMBER] 4x Asus Titan boards :) GB/nucleosome passed Tru Huynh (Wed Jul 03 2013 - 12:32:46 PDT)
    - Re: [AMBER] 4x Asus Titan boards :) GB/nucleosome passed Tru Huynh (Thu Jul 04 2013 - 01:30:03 PDT)
  - Re: [AMBER] 4x Asus Titan boards :) GB/nucleosome passed Tru Huynh (Wed Jul 03 2013 - 10:34:34 PDT)
- Re: [AMBER] 4x Asus Titan boards :) GB/nucleosome passed Scott Le Grand (Wed Jul 03 2013 - 10:13:45 PDT)
  - Re: [AMBER] 4x Asus Titan boards :) GB/nucleosome passed Tru Huynh (Wed Jul 03 2013 - 10:38:08 PDT)
    - Re: [AMBER] 4x Asus Titan boards :) GB/nucleosome passed Ross Walker (Wed Jul 03 2013 - 10:42:52 PDT)
    - Re: [AMBER] 4x Asus Titan boards :) GB/nucleosome passed Marek Maly (Wed Jul 03 2013 - 10:39:56 PDT)
    - Re: [AMBER] 4x Asus Titan boards :) GB/nucleosome passed Tru Huynh (Wed Jul 03 2013 - 11:28:35 PDT)
    - Re: [AMBER] 4x Asus Titan boards :) GB/nucleosome passed Marek Maly (Wed Jul 03 2013 - 11:18:03 PDT)
    - Re: [AMBER] 4x Asus Titan boards :) GB/nucleosome passed Scott Le Grand (Wed Jul 03 2013 - 12:33:09 PDT)
    - Re: [AMBER] 4x Asus Titan boards :) GB/nucleosome passed Marek Maly (Thu Jul 04 2013 - 02:42:39 PDT)
    - Re: [AMBER] 4x Asus Titan boards :) GB/nucleosome passed Tru Huynh (Thu Jul 04 2013 - 16:05:39 PDT)
    - Re: [AMBER] 4x Asus Titan boards :) GB/nucleosome passed Tru Huynh (Mon Jul 08 2013 - 04:12:18 PDT)
    - Re: [AMBER] 4x Asus Titan boards :) GB/nucleosome passed Marek Maly (Mon Jul 08 2013 - 05:43:57 PDT)
    - Re: [AMBER] 4x Asus Titan boards :) GB/nucleosome passed Tru Huynh (Mon Jul 08 2013 - 07:08:29 PDT)
    - Re: [AMBER] 4x Asus Titan boards :) GB/nucleosome passed Marek Maly (Mon Jul 08 2013 - 08:01:24 PDT)
[AMBER] GTX780 Update Ross Walker (Wed Jul 03 2013 - 10:57:55 PDT)
[AMBER] DihedralSearch.cpp:53: error: unknown escape sequence '\*' Tru Huynh (Wed Jul 03 2013 - 11:05:45 PDT)
- Re: [AMBER] DihedralSearch.cpp:53: error: unknown escape sequence '\*' Marek Maly (Wed Jul 03 2013 - 11:24:56 PDT)
  - Re: [AMBER] DihedralSearch.cpp:53: error: unknown escape sequence '\*' Tru Huynh (Wed Jul 03 2013 - 12:22:44 PDT)
    - Re: [AMBER] DihedralSearch.cpp:53: error: unknown escape sequence '\*' Marek Maly (Wed Jul 03 2013 - 12:18:41 PDT)
    - Re: [AMBER] DihedralSearch.cpp:53: error: unknown escape sequence '\*' Daniel Roe (Wed Jul 03 2013 - 12:51:17 PDT)
    - Re: [AMBER] DihedralSearch.cpp:53: error: unknown escape sequence '\*' David A Case (Thu Jul 04 2013 - 06:09:09 PDT)
    - Re: [AMBER] DihedralSearch.cpp:53: error: unknown escape sequence '\*' Jason Swails (Thu Jul 04 2013 - 06:54:00 PDT)
    - Re: [AMBER] DihedralSearch.cpp:53: error: unknown escape sequence '\*' Marek Maly (Thu Jul 04 2013 - 06:56:27 PDT)
    - Re: [AMBER] DihedralSearch.cpp:53: error: unknown escape sequence '\*' Jason Swails (Thu Jul 04 2013 - 07:34:44 PDT)
    - Re: [AMBER] DihedralSearch.cpp:53: error: unknown escape sequence '\*' Marek Maly (Thu Jul 04 2013 - 07:47:03 PDT)
    - [AMBER] OT? several gcc/CentOS-6 (Re: DihedralSearch.cpp:53: error: unknown escape sequence) '\*' Tru Huynh (Thu Jul 04 2013 - 16:19:07 PDT)
    - Re: [AMBER] OT? several gcc/CentOS-6 (Re: DihedralSearch.cpp:53: error: unknown escape sequence) '\*' Marek Maly (Fri Jul 05 2013 - 09:43:41 PDT)
    - Re: [AMBER] DihedralSearch.cpp:53: error: unknown escape sequence '\*' Jan-Philip Gehrcke (Thu Jul 04 2013 - 07:40:13 PDT)
[AMBER] about run REMD(replica exchange molecular dynamic) Biao Ma (Wed Jul 03 2013 - 17:47:32 PDT)
- Re: [AMBER] about run REMD(replica exchange molecular dynamic) Jason Swails (Thu Jul 04 2013 - 07:20:00 PDT)
  - Re: [AMBER] about run REMD(replica exchange molecular dynamic) Biao Ma (Fri Jul 05 2013 - 00:47:48 PDT)
  - Re: [AMBER] about run REMD(replica exchange molecular dynamic) David A Case (Fri Jul 05 2013 - 05:40:47 PDT)
    - Re: [AMBER] about run REMD(replica exchange molecular dynamic) Jason Swails (Fri Jul 05 2013 - 11:20:22 PDT)
[AMBER] 回复：Re: ???Re: FATAL: Atom XXX does not have a type sunyeping.aliyun.com (Wed Jul 03 2013 - 20:03:37 PDT)
- Re: [AMBER] 回复：Re: ???Re: FATAL: Atom XXX does not have a type Biao Ma (Wed Jul 03 2013 - 20:12:09 PDT)
- Re: [AMBER] ???Re: ???Re: FATAL: Atom XXX does not have a type FyD (Thu Jul 04 2013 - 08:14:33 PDT)
[AMBER] Abnormal simulation in the sulfonic acid group. Xiaoquan Sun (Wed Jul 03 2013 - 21:28:38 PDT)
- Re: [AMBER] Abnormal simulation in the sulfonic acid group. Karl N. Kirschner (Thu Jul 04 2013 - 02:41:23 PDT)
  - Re: [AMBER] Abnormal simulation in the sulfonic acid group. David A Case (Thu Jul 04 2013 - 06:08:01 PDT)
    - Re: [AMBER] Abnormal simulation in the sulfonic acid group. Jason Swails (Thu Jul 04 2013 - 07:42:09 PDT)
    - Re: [AMBER] Abnormal simulation in the sulfonic acid group. Karl N. Kirschner (Thu Jul 04 2013 - 07:58:43 PDT)
    - Re: [AMBER] Abnormal simulation in the sulfonic acid group. David A Case (Fri Jul 05 2013 - 05:40:40 PDT)
[AMBER] Copper parametrization for a laccase center mmaestre.gate.sinica.edu.tw (Wed Jul 03 2013 - 21:57:47 PDT)
- Re: [AMBER] Copper parametrization for a laccase center Eric Berquist (Fri Jul 05 2013 - 17:14:08 PDT)
  - Re: [AMBER] Copper parametrization for a laccase center mmaestre.gate.sinica.edu.tw (Sat Jul 06 2013 - 09:26:47 PDT)
[AMBER] Ligand show error in Dock complex amenshamim.bs.qau.edu.pk (Thu Jul 04 2013 - 01:40:58 PDT)
- Re: [AMBER] Ligand show error in Dock complex David A Case (Thu Jul 04 2013 - 05:58:04 PDT)
[AMBER] 2013 Symposium on Theoretical Chemistry in Erlangen, Germany, September 22nd to 26th Harald Lanig (Thu Jul 04 2013 - 01:45:30 PDT)
[AMBER] question of Radius of Gyration Chinh Su Tran To (Thu Jul 04 2013 - 04:55:38 PDT)
- Re: [AMBER] question of Radius of Gyration Daniel Roe (Thu Jul 04 2013 - 10:36:11 PDT)
  - Re: [AMBER] question of Radius of Gyration Chinh Su Tran To (Thu Jul 04 2013 - 22:00:48 PDT)
    - Re: [AMBER] question of Radius of Gyration Daniel Roe (Fri Jul 05 2013 - 07:51:38 PDT)
    - Re: [AMBER] question of Radius of Gyration Chinh Su Tran To (Sun Jul 07 2013 - 21:15:05 PDT)
    - Re: [AMBER] question of Radius of Gyration Bill Ross (Tue Jul 09 2013 - 22:24:33 PDT)
    - Re: [AMBER] question of Radius of Gyration Chinh Su Tran To (Mon Jul 15 2013 - 23:58:46 PDT)
[AMBER] Re：Re: FATAL: Atom XXX does not have a type sunyeping.aliyun.com (Thu Jul 04 2013 - 05:20:03 PDT)
- Re: [AMBER] Re?Re: FATAL: Atom XXX does not have a type FyD (Thu Jul 04 2013 - 08:22:40 PDT)
[AMBER] simulating complexes Ayesha Fatima (Thu Jul 04 2013 - 09:00:53 PDT)
- Re: [AMBER] simulating complexes Marek Maly (Thu Jul 04 2013 - 08:52:42 PDT)
[AMBER] TI solvated ligand simulation "vlimit exceeded for step" psu4.uic.edu (Thu Jul 04 2013 - 15:59:49 PDT)
[AMBER] Is it possible to run accelerated MD with amber10? Yip Yew Mun (Thu Jul 04 2013 - 20:16:59 PDT)
- Re: [AMBER] Is it possible to run accelerated MD with amber10? Jason Swails (Fri Jul 05 2013 - 18:12:13 PDT)
[AMBER] atom type for N bond to conjugated chain using antechamber zhonghe xu (Thu Jul 04 2013 - 20:32:11 PDT)
- Re: [AMBER] atom type for N bond to conjugated chain using antechamber Karl N. Kirschner (Fri Jul 05 2013 - 00:34:28 PDT)
[AMBER] installing Amber 11 and Amber tools 1.5 Muthukumaran R (Thu Jul 04 2013 - 21:06:25 PDT)
- Re: [AMBER] installing Amber 11 and Amber tools 1.5 Jason Swails (Fri Jul 05 2013 - 18:14:38 PDT)
[AMBER] constant pressure simulation kirtana S (Thu Jul 04 2013 - 23:31:06 PDT)
- Re: [AMBER] constant pressure simulation David A Case (Fri Jul 05 2013 - 05:35:58 PDT)
  - Re: [AMBER] constant pressure simulation kirtana S (Fri Jul 05 2013 - 11:05:00 PDT)
    - [AMBER] compilation error: /usr/bin/ld: cannot find -lStatistics Su, Shiquan (Fri Jul 05 2013 - 14:42:00 PDT)
    - Re: [AMBER] compilation error: /usr/bin/ld: cannot find -lStatistics Jason Swails (Fri Jul 05 2013 - 14:52:41 PDT)
    - Re: [AMBER] compilation error: /usr/bin/ld: cannot find -lStatistics Su, Shiquan (Fri Jul 05 2013 - 17:12:38 PDT)
    - Re: [AMBER] compilation error: /usr/bin/ld: cannot find -lStatistics David A Case (Fri Jul 05 2013 - 19:14:34 PDT)
    - Re: [AMBER] constant pressure simulation David A Case (Fri Jul 05 2013 - 19:05:48 PDT)
    - Re: [AMBER] constant pressure simulation kirtana S (Fri Jul 05 2013 - 19:21:39 PDT)
    - Re: [AMBER] constant pressure simulation David A Case (Fri Jul 05 2013 - 19:44:25 PDT)
    - Re: [AMBER] constant pressure simulation kirtana S (Fri Jul 05 2013 - 19:57:52 PDT)
    - Re: [AMBER] constant pressure simulation David A Case (Sat Jul 06 2013 - 05:39:43 PDT)
    - Re: [AMBER] constant pressure simulation Jason Swails (Fri Jul 05 2013 - 21:07:13 PDT)
[AMBER] AMBER COMPATIBILITIES GESTION DE ACTIVOS DE TI (Fri Jul 05 2013 - 00:11:43 PDT)
- Re: [AMBER] AMBER COMPATIBILITIES Daniel Sindhikara (Fri Jul 05 2013 - 00:38:34 PDT)
  - Re: [AMBER] AMBER COMPATIBILITIES David A Case (Fri Jul 05 2013 - 05:38:01 PDT)
[AMBER] unsubscribe GESTION DE ACTIVOS DE TI (Fri Jul 05 2013 - 00:57:51 PDT)
- Re: [AMBER] unsubscribe David A Case (Fri Jul 05 2013 - 05:39:27 PDT)
[AMBER] A General Question with regards to the NVT & NPT ensembles in MD Simulations Yip Yew Mun (Fri Jul 05 2013 - 01:12:36 PDT)
- Re: [AMBER] A General Question with regards to the NVT & NPT ensembles in MD Simulations David A Case (Fri Jul 05 2013 - 06:01:28 PDT)
  - Re: [AMBER] A General Question with regards to the NVT & NPT ensembles in MD Simulations Yip Yew Mun (Fri Jul 05 2013 - 06:16:34 PDT)
    - Re: [AMBER] A General Question with regards to the NVT & NPT ensembles in MD Simulations Jason Swails (Fri Jul 05 2013 - 18:23:58 PDT)
[AMBER] Is it possible to merge static PDB files of the same PDB ID to become a mdcrd file? Yip Yew Mun (Fri Jul 05 2013 - 01:31:04 PDT)
- Re: [AMBER] Is it possible to merge static PDB files of the same PDB ID to become a mdcrd file? David A Case (Fri Jul 05 2013 - 05:43:11 PDT)
  - Re: [AMBER] Is it possible to merge static PDB files of the same PDB ID to become a mdcrd file? Yip Yew Mun (Fri Jul 05 2013 - 06:19:26 PDT)
  - Re: [AMBER] Is it possible to merge static PDB files of the same PDB ID to become a mdcrd file? Yip Yew Mun (Fri Jul 05 2013 - 08:47:17 PDT)
    - Re: [AMBER] Is it possible to merge static PDB files of the same PDB ID to become a mdcrd file? Daniel Roe (Fri Jul 05 2013 - 08:50:17 PDT)
[AMBER] 'undefined reference to MPI::...' error messages when compiling Amber 12 on CentOS 6 for "-mpi -cuda" Frank Thommen (Fri Jul 05 2013 - 02:45:07 PDT)
- Re: [AMBER] 'undefined reference to MPI::...' error messages when compiling Amber 12 on CentOS 6 for "-mpi -cuda" Tru Huynh (Fri Jul 05 2013 - 05:31:45 PDT)
  - Re: [AMBER] 'undefined reference to MPI::...' error messages when compiling Amber 12 on CentOS 6 for "-mpi -cuda" Frank Thommen (Fri Jul 05 2013 - 08:57:05 PDT)
[AMBER] RE：Re: Re?Re: FATAL: Atom XXX does not have a type sunyeping.aliyun.com (Fri Jul 05 2013 - 11:05:56 PDT)
- Re: [AMBER] FATAL: Atom XXX does not have a type FyD (Sun Jul 07 2013 - 08:59:04 PDT)
[AMBER] Amber 12 installation on OSX George Tzotzos (Fri Jul 05 2013 - 11:42:37 PDT)
- Re: [AMBER] Amber 12 installation on OSX George Tzotzos (Fri Jul 05 2013 - 12:13:18 PDT)
  - Re: [AMBER] Amber 12 installation on OSX Jason Swails (Fri Jul 05 2013 - 14:17:36 PDT)
[AMBER] Error: Atom type amber99_42 (residue HOH) not found in atomtype database Collins Nganou (Fri Jul 05 2013 - 13:26:58 PDT)
- Re: [AMBER] Error: Atom type amber99_42 (residue HOH) not found in atomtype database Thomas Cheatham (Fri Jul 05 2013 - 14:02:47 PDT)
  - Re: [AMBER] Error: Atom type amber99_42 (residue HOH) not found in atomtype database Collins Nganou (Sun Jul 07 2013 - 11:19:30 PDT)
[AMBER] repeat amber run on cuda Kanin Wichapong (Fri Jul 05 2013 - 13:35:23 PDT)
- Re: [AMBER] repeat amber run on cuda Daniel Roe (Fri Jul 05 2013 - 13:45:44 PDT)
- Re: [AMBER] repeat amber run on cuda Ross Walker (Fri Jul 05 2013 - 13:58:07 PDT)
[AMBER] quality membrane protein Kanin Wichapong (Fri Jul 05 2013 - 13:57:28 PDT)
[AMBER] Crystallization of K+ Cl- ions during the protein+lipid bilayer simulation Manikanthan Bhavaraju (Fri Jul 05 2013 - 17:20:06 PDT)
- Re: [AMBER] Crystallization of K+ Cl- ions during the protein+lipid bilayer simulation Jason Swails (Fri Jul 05 2013 - 18:42:54 PDT)
  - Re: [AMBER] Crystallization of K+ Cl- ions during the protein+lipid bilayer simulation Manikanthan Bhavaraju (Fri Jul 05 2013 - 19:26:29 PDT)
    - Re: [AMBER] Crystallization of K+ Cl- ions during the protein+lipid bilayer simulation Jason Swails (Fri Jul 05 2013 - 21:10:22 PDT)
[AMBER] cyclic-di-nucleotid Hector A. Baldoni (Fri Jul 05 2013 - 17:28:40 PDT)
- Re: [AMBER] cyclic-di-nucleotid FyD (Sun Jul 07 2013 - 09:09:23 PDT)
  - Re: [AMBER] cyclic-di-nucleotid Baldoni Hector Armando (Mon Jul 08 2013 - 07:13:15 PDT)
[AMBER] Active site focusing in using "pbsa" kurisaki (Fri Jul 05 2013 - 22:21:03 PDT)
- [AMBER] Active site focusing in using "pbsa" kurisaki (Mon Jul 08 2013 - 06:26:38 PDT)
[AMBER] xlf Command not found mina madah (Sat Jul 06 2013 - 03:50:05 PDT)
- Re: [AMBER] xlf Command not found David A Case (Sat Jul 06 2013 - 05:47:57 PDT)
[AMBER] update Ambertools 12 to 13 fails Robert Wohlhueter (Sat Jul 06 2013 - 14:08:46 PDT)
- Re: [AMBER] update Ambertools 12 to 13 fails Jason Swails (Sat Jul 06 2013 - 14:28:45 PDT)
  - Re: [AMBER] update Ambertools 12 to 13 fails Robert Wohlhueter (Mon Jul 08 2013 - 08:46:44 PDT)
    - Re: [AMBER] update Ambertools 12 to 13 fails David A Case (Mon Jul 08 2013 - 10:05:14 PDT)
    - Re: [AMBER] update Ambertools 12 to 13 fails Jason Swails (Tue Jul 09 2013 - 11:11:56 PDT)
[AMBER] pmemd.cuda Energy Minimization Slow Parker de Waal (Sat Jul 06 2013 - 22:04:49 PDT)
- Re: [AMBER] pmemd.cuda Energy Minimization Slow Ross Walker (Sat Jul 06 2013 - 23:17:52 PDT)
  - Re: [AMBER] pmemd.cuda Energy Minimization Slow Parker de Waal (Sun Jul 07 2013 - 08:08:42 PDT)
[AMBER] SA Bomb in sa_arc()3 error crazylyf (Mon Jul 08 2013 - 01:34:34 PDT)
- Re: [AMBER] SA Bomb in sa_arc()3 error Ray Luo, Ph.D. (Mon Jul 08 2013 - 10:23:29 PDT)
  - Re: [AMBER] SA Bomb in sa_arc()3 error crazylyf.126.com (Mon Jul 08 2013 - 17:59:05 PDT)
    - Re: [AMBER] SA Bomb in sa_arc()3 error Ray Luo, Ph.D. (Mon Jul 08 2013 - 19:05:43 PDT)
    - Re: [AMBER] SA Bomb in sa_arc()3 error crazylyf.126.com (Mon Jul 08 2013 - 20:00:52 PDT)
[AMBER] differences between amber ff10 and ff12SB Neha Gandhi (Mon Jul 08 2013 - 05:15:13 PDT)
- Re: [AMBER] differences between amber ff10 and ff12SB David A Case (Mon Jul 08 2013 - 13:09:00 PDT)
[AMBER] fix_traj_parm.py problems Fabrício Bracht (Mon Jul 08 2013 - 11:32:49 PDT)
- Re: [AMBER] fix_traj_parm.py problems Jason Swails (Mon Jul 08 2013 - 13:21:06 PDT)
  - Re: [AMBER] fix_traj_parm.py problems Fabrício Bracht (Thu Jul 11 2013 - 09:43:23 PDT)
    - Re: [AMBER] fix_traj_parm.py problems Jason Swails (Thu Jul 11 2013 - 09:52:57 PDT)
    - Re: [AMBER] fix_traj_parm.py problems Fabrício Bracht (Thu Jul 11 2013 - 10:30:51 PDT)
    - Re: [AMBER] fix_traj_parm.py problems Jason Swails (Thu Jul 11 2013 - 11:51:36 PDT)
    - Re: [AMBER] fix_traj_parm.py problems Fabrício Bracht (Thu Jul 11 2013 - 16:04:14 PDT)
    - Re: [AMBER] fix_traj_parm.py problems Jason Swails (Thu Jul 11 2013 - 18:15:02 PDT)
    - Re: [AMBER] fix_traj_parm.py problems Fabrício Bracht (Thu Jul 11 2013 - 20:18:14 PDT)
    - Re: [AMBER] fix_traj_parm.py problems Jason Swails (Thu Jul 11 2013 - 20:33:24 PDT)
    - Re: [AMBER] fix_traj_parm.py problems Fabrício Bracht (Thu Jul 11 2013 - 20:55:24 PDT)
    - Re: [AMBER] fix_traj_parm.py problems Daniel Roe (Thu Jul 11 2013 - 21:04:39 PDT)
    - Re: [AMBER] fix_traj_parm.py problems Fabrício Bracht (Thu Jul 11 2013 - 21:12:24 PDT)
    - Re: [AMBER] fix_traj_parm.py problems Daniel Roe (Fri Jul 12 2013 - 09:19:13 PDT)
    - Re: [AMBER] fix_traj_parm.py problems Jason Swails (Thu Jul 11 2013 - 21:26:03 PDT)
[AMBER] question about hydroxyproline and new atom type'OO' Tianchi Chen (Mon Jul 08 2013 - 12:47:51 PDT)
- Re: [AMBER] question about hydroxyproline and new atom type'OO' David A Case (Mon Jul 08 2013 - 13:24:41 PDT)
  - Re: [AMBER] question about hydroxyproline and new atom type'OO' Tianchi Chen (Tue Jul 09 2013 - 09:46:20 PDT)
    - Re: [AMBER] question about hydroxyproline and new atom type'OO' David A Case (Tue Jul 09 2013 - 11:01:09 PDT)
    - Re: [AMBER] question about hydroxyproline and new atom type'OO' Tianchi Chen (Tue Jul 09 2013 - 11:05:06 PDT)
- Re: [AMBER] question about hydroxyproline and new atom type'OO' Karl N. Kirschner (Tue Jul 09 2013 - 00:18:29 PDT)
  - Re: [AMBER] question about hydroxyproline and new atom type'OO' Tianchi Chen (Tue Jul 09 2013 - 09:42:40 PDT)
[AMBER] TIME(ps) value WuYunjian (Mon Jul 08 2013 - 13:06:43 PDT)
- Re: [AMBER] TIME(ps) value David A Case (Mon Jul 08 2013 - 18:09:59 PDT)
[AMBER] Bridging waters Fabrício Bracht (Mon Jul 08 2013 - 14:54:19 PDT)
- Re: [AMBER] Bridging waters Daniel Roe (Mon Jul 08 2013 - 15:14:11 PDT)
[AMBER] Units of summary files produced by process_mdout.perl Hunter Brown (Mon Jul 08 2013 - 15:13:39 PDT)
- Re: [AMBER] Units of summary files produced by process_mdout.perl Ross Walker (Mon Jul 08 2013 - 15:21:27 PDT)
- Re: [AMBER] Units of summary files produced by process_mdout.perl Jason Swails (Mon Jul 08 2013 - 15:36:36 PDT)
[AMBER] Update 12 for AmberTools 13: CPPTRAJ Daniel Roe (Mon Jul 08 2013 - 15:32:28 PDT)
[AMBER] How to run aMD with amber? Yip Yew Mun (Mon Jul 08 2013 - 16:36:16 PDT)
- Re: [AMBER] How to run aMD with amber? Romelia Salomon (Mon Jul 08 2013 - 16:55:59 PDT)
  - Re: [AMBER] How to run aMD with amber? #YIP YEW MUN# (Tue Jul 09 2013 - 01:07:14 PDT)
    - Re: [AMBER] How to run aMD with amber? Ross Walker (Tue Jul 09 2013 - 01:09:47 PDT)
[AMBER] Negative Pressure During Equilibrium Parker de Waal (Mon Jul 08 2013 - 17:25:28 PDT)
- Re: [AMBER] Negative Pressure During Equilibrium Parker de Waal (Tue Jul 09 2013 - 04:38:53 PDT)
- Re: [AMBER] Negative Pressure During Equilibrium David A Case (Tue Jul 09 2013 - 04:58:11 PDT)
- Re: [AMBER] Negative Pressure During Equilibrium Jason Swails (Tue Jul 09 2013 - 05:20:47 PDT)
  - Re: [AMBER] Negative Pressure During Equilibrium Parker de Waal (Tue Jul 09 2013 - 12:53:35 PDT)
[AMBER] Ambertools compilation without Netcdf Collins Nganou (Mon Jul 08 2013 - 17:56:51 PDT)
- Re: [AMBER] Ambertools compilation without Netcdf Daniel Roe (Mon Jul 08 2013 - 20:00:03 PDT)
  - Re: [AMBER] Ambertools compilation without Netcdf Collins Nganou (Mon Jul 08 2013 - 23:48:24 PDT)
[AMBER] different results by sander and sander.MPI John Travers (Mon Jul 08 2013 - 21:06:04 PDT)
- Re: [AMBER] different results by sander and sander.MPI Ross Walker (Mon Jul 08 2013 - 22:51:18 PDT)
  - Re: [AMBER] different results by sander and sander.MPI Jason Swails (Tue Jul 09 2013 - 05:38:40 PDT)
    - Re: [AMBER] different results by sander and sander.MPI David A Case (Tue Jul 09 2013 - 09:59:23 PDT)
[AMBER] timecorr Hongyi WU (Mon Jul 08 2013 - 22:19:35 PDT)
- Re: [AMBER] timecorr David A Case (Tue Jul 09 2013 - 05:03:21 PDT)
  - [AMBER] 答复: timecorr Hongyi WU (Tue Jul 09 2013 - 05:34:45 PDT)
    - Re: [AMBER] 答复: timecorr Daniel Roe (Tue Jul 09 2013 - 07:08:04 PDT)
    - [AMBER] 答复: 答复: timecorr Hongyi WU (Sat Jul 20 2013 - 19:51:19 PDT)
    - Re: [AMBER] 答复: 答复: timecorr Daniel Roe (Sun Jul 21 2013 - 09:02:32 PDT)
    - [AMBER] 答复: 答复: 答复: timecorr Hongyi WU (Fri Jul 26 2013 - 07:53:41 PDT)
    - Re: [AMBER] 答复: 答复: 答复: timecorr Daniel Roe (Sat Jul 27 2013 - 09:29:56 PDT)
    - [AMBER] 答复: 答复: 答复: 答复: timecorr Hongyi WU (Sun Jul 28 2013 - 01:42:59 PDT)
    - Re: [AMBER] 答复: 答复: 答复: 答复: timecorr Daniel Roe (Tue Jul 30 2013 - 20:29:59 PDT)
    - [AMBER] 答复: 答复: 答复: 答复: 答复: timecorr Hongyi WU (Tue Jul 30 2013 - 20:44:23 PDT)
    - Re: [AMBER] 答复: timecorr David A Case (Tue Jul 09 2013 - 09:33:45 PDT)
    - [AMBER] 答复: 答复: timecorr Hongyi WU (Sat Jul 20 2013 - 19:54:35 PDT)
[AMBER] TESTING RELATIVE ERROR over r ranging from 0.0 to cutoff 전선희 (Mon Jul 08 2013 - 23:12:57 PDT)
- Re: [AMBER] TESTING RELATIVE ERROR over r ranging from 0.0 to cutoff Ross Walker (Mon Jul 08 2013 - 23:21:15 PDT)
[AMBER] Fwd: Re: Copper parametrization for a laccase center mmaestre.gate.sinica.edu.tw (Tue Jul 09 2013 - 00:30:54 PDT)
[AMBER] Residue chirality tdo.chem.ucsb.edu (Tue Jul 09 2013 - 02:07:58 PDT)
- Re: [AMBER] Residue chirality Karl N. Kirschner (Tue Jul 09 2013 - 02:21:58 PDT)
  - Re: [AMBER] Residue chirality Carlos Simmerling (Tue Jul 09 2013 - 05:06:05 PDT)
    - Re: [AMBER] Residue chirality Karl N. Kirschner (Tue Jul 09 2013 - 08:27:48 PDT)
    - Re: [AMBER] Residue chirality Carlos Simmerling (Tue Jul 09 2013 - 09:42:02 PDT)
    - Re: [AMBER] Residue chirality Karl N. Kirschner (Thu Jul 11 2013 - 08:51:33 PDT)
    - Re: [AMBER] Residue chirality Carlos Simmerling (Thu Jul 11 2013 - 09:03:35 PDT)
    - Re: [AMBER] Residue chirality Krisztina Feher (Sun Jul 14 2013 - 00:50:17 PDT)
    - Re: [AMBER] Residue chirality Karl N. Kirschner (Mon Jul 15 2013 - 02:12:03 PDT)
    - Re: [AMBER] Residue chirality Krisztina Feher (Tue Jul 16 2013 - 13:20:33 PDT)
  - Re: [AMBER] Residue chirality Jason Swails (Tue Jul 09 2013 - 05:45:06 PDT)
    - Re: [AMBER] Residue chirality Carlos Simmerling (Tue Jul 09 2013 - 05:53:28 PDT)
    - Re: [AMBER] Residue chirality Jason Swails (Tue Jul 09 2013 - 07:06:06 PDT)
    - Re: [AMBER] Residue chirality tdo.chem.ucsb.edu (Tue Jul 09 2013 - 08:25:54 PDT)
[AMBER] AMBER GPU Job Write Fails Mona Minkara (Tue Jul 09 2013 - 09:42:13 PDT)
- Re: [AMBER] AMBER GPU Job Write Fails Jan-Philip Gehrcke (Tue Jul 09 2013 - 10:31:05 PDT)
  - Re: [AMBER] AMBER GPU Job Write Fails Ross Walker (Tue Jul 09 2013 - 12:57:34 PDT)
    - Re: [AMBER] AMBER GPU Job Write Fails ET (Wed Jul 10 2013 - 06:26:48 PDT)
    - Re: [AMBER] AMBER GPU Job Write Fails Jan-Philip Gehrcke (Wed Jul 10 2013 - 06:58:38 PDT)
    - Re: [AMBER] AMBER GPU Job Write Fails Mona Minkara (Wed Jul 10 2013 - 08:57:51 PDT)
- Re: [AMBER] AMBER GPU Job Write Fails Ross Walker (Tue Jul 09 2013 - 11:48:55 PDT)
[AMBER] Assigning protonation o residues for parallel tempering Francesco Pietra (Tue Jul 09 2013 - 10:04:58 PDT)
- Re: [AMBER] Assigning protonation o residues for parallel tempering Daniel Sindhikara (Tue Jul 09 2013 - 16:31:20 PDT)
[AMBER] Troubles with making a movie in VMD, Hunter Brown (Tue Jul 09 2013 - 12:23:37 PDT)
- Re: [AMBER] Troubles with making a movie in VMD, Daniel Roe (Tue Jul 09 2013 - 12:31:07 PDT)
- Re: [AMBER] Troubles with making a movie in VMD, Hunter Brown (Tue Jul 09 2013 - 12:34:53 PDT)
  - Re: [AMBER] Troubles with making a movie in VMD, Daniel Roe (Tue Jul 09 2013 - 12:43:05 PDT)
[AMBER] instablity of ligand during minimization Ibrahim Said (Tue Jul 09 2013 - 13:09:15 PDT)
[AMBER] Re-Imaging Trajectories Parker de Waal (Tue Jul 09 2013 - 19:07:51 PDT)
- Re: [AMBER] Re-Imaging Trajectories Daniel Roe (Tue Jul 09 2013 - 19:47:15 PDT)
  - Re: [AMBER] Re-Imaging Trajectories Jason Swails (Tue Jul 09 2013 - 20:06:07 PDT)
    - Re: [AMBER] Re-Imaging Trajectories ET (Wed Jul 10 2013 - 13:26:11 PDT)
    - Re: [AMBER] Re-Imaging Trajectories Parker de Waal (Wed Jul 10 2013 - 16:36:22 PDT)
[AMBER] aMD tutorial Jerome EBERHARDT (Wed Jul 10 2013 - 02:14:03 PDT)
- Re: [AMBER] aMD tutorial Jason Swails (Sun Jul 14 2013 - 20:50:04 PDT)
[AMBER] "Incomplete Improper Torsion line" error Jose Borreguero (Wed Jul 10 2013 - 14:51:37 PDT)
- Re: [AMBER] "Incomplete Improper Torsion line" error David A Case (Thu Jul 11 2013 - 05:26:07 PDT)
[AMBER] Amber 12 on OSX 10.8.4 Wang Chern Hoe (Dr) (Wed Jul 10 2013 - 16:17:59 PDT)
- Re: [AMBER] Amber 12 on OSX 10.8.4 Jason Swails (Wed Jul 10 2013 - 16:41:12 PDT)
  - Re: [AMBER] Amber 12 on OSX 10.8.4 Wang Chern Hoe (Dr) (Wed Jul 10 2013 - 19:09:00 PDT)
    - Re: [AMBER] Amber 12 on OSX 10.8.4 Jason Swails (Wed Jul 10 2013 - 21:44:22 PDT)
    - Re: [AMBER] Amber 12 on OSX 10.8.4 Wang Chern Hoe (Dr) (Wed Jul 10 2013 - 23:01:34 PDT)
    - Re: [AMBER] Amber 12 on OSX 10.8.4 Jason Swails (Thu Jul 11 2013 - 05:53:16 PDT)
    - Re: [AMBER] Amber 12 on OSX 10.8.4 Wang Chern Hoe (Dr) (Thu Jul 11 2013 - 08:26:52 PDT)
[AMBER] First to Second Frame Position Jump Parker de Waal (Wed Jul 10 2013 - 16:45:15 PDT)
- Re: [AMBER] First to Second Frame Position Jump Carlos Simmerling (Wed Jul 10 2013 - 16:51:31 PDT)
  - Re: [AMBER] First to Second Frame Position Jump Parker de Waal (Wed Jul 10 2013 - 17:54:26 PDT)
    - Re: [AMBER] First to Second Frame Position Jump Carlos Simmerling (Wed Jul 10 2013 - 18:05:36 PDT)
    - Re: [AMBER] First to Second Frame Position Jump Parker de Waal (Wed Jul 10 2013 - 18:22:21 PDT)
    - Re: [AMBER] First to Second Frame Position Jump Carlos Simmerling (Thu Jul 11 2013 - 05:45:03 PDT)
    - Re: [AMBER] First to Second Frame Position Jump Parker de Waal (Thu Jul 11 2013 - 06:36:57 PDT)
    - Re: [AMBER] First to Second Frame Position Jump Daniel Roe (Thu Jul 11 2013 - 07:44:40 PDT)
    - Re: [AMBER] First to Second Frame Position Jump Parker de Waal (Thu Jul 11 2013 - 08:31:55 PDT)
    - Re: [AMBER] First to Second Frame Position Jump Daniel Roe (Thu Jul 11 2013 - 08:41:43 PDT)
    - Re: [AMBER] First to Second Frame Position Jump Parker de Waal (Thu Jul 11 2013 - 09:04:09 PDT)
    - Re: [AMBER] First to Second Frame Position Jump Parker de Waal (Thu Jul 11 2013 - 19:43:21 PDT)
    - Re: [AMBER] First to Second Frame Position Jump Parker de Waal (Fri Jul 12 2013 - 10:02:50 PDT)
- Re: [AMBER] First to Second Frame Position Jump Daniel Roe (Wed Jul 10 2013 - 20:31:27 PDT)
[AMBER] Problem related to the umbrella sampling Sindrila Dutta banik (Wed Jul 10 2013 - 21:44:35 PDT)
- Re: [AMBER] Problem related to the umbrella sampling Jason Swails (Thu Jul 11 2013 - 10:22:03 PDT)
  - Re: [AMBER] Problem related to the umbrella sampling Sindrila Dutta banik (Thu Jul 11 2013 - 11:27:27 PDT)
    - Re: [AMBER] Problem related to the umbrella sampling Adrian Roitberg (Thu Jul 11 2013 - 11:49:17 PDT)
[AMBER] Wrong results in GTX TITAN, correct results on GTX580 iqtcub (Thu Jul 11 2013 - 00:35:47 PDT)
- Re: [AMBER] Wrong results in GTX TITAN, correct results on GTX580 ET (Thu Jul 11 2013 - 05:05:21 PDT)
  - Re: [AMBER] Wrong results in GTX TITAN, correct results on GTX580 Scott Le Grand (Thu Jul 11 2013 - 06:56:12 PDT)
    - Re: [AMBER] Wrong results in GTX TITAN, correct results on GTX580 ET (Thu Jul 11 2013 - 07:52:04 PDT)
    - Re: [AMBER] Wrong results in GTX TITAN, correct results on GTX580 Ross Walker (Thu Jul 11 2013 - 11:47:34 PDT)
    - Re: [AMBER] Wrong results in GTX TITAN, correct results on GTX580 Marek Maly (Thu Jul 11 2013 - 09:16:49 PDT)
    - Re: [AMBER] Wrong results in GTX TITAN, correct results on GTX580 Scott Le Grand (Thu Jul 11 2013 - 09:49:39 PDT)
    - Re: [AMBER] Wrong results in GTX TITAN, correct results on GTX580 Marek Maly (Thu Jul 11 2013 - 09:53:25 PDT)
- Re: [AMBER] Wrong results in GTX TITAN, correct results on GTX580 Ross Walker (Thu Jul 11 2013 - 19:48:53 PDT)
  - Re: [AMBER] Wrong results in GTX TITAN, correct results on GTX580 iqtcub (Mon Jul 15 2013 - 00:08:59 PDT)
[AMBER] Is it possible to do constant pH simulations by titrating the basic residues as well? #YIP YEW MUN# (Thu Jul 11 2013 - 00:58:41 PDT)
- Re: [AMBER] Is it possible to do constant pH simulations by titrating the basic residues as well? Jason Swails (Thu Jul 11 2013 - 05:46:57 PDT)
  - Re: [AMBER] Is it possible to do constant pH simulations by titrating the basic residues as well? Yip Yew Mun (Thu Jul 11 2013 - 07:46:41 PDT)
    - Re: [AMBER] Is it possible to do constant pH simulations by titrating the basic residues as well? Christina Bergonzo (Thu Jul 11 2013 - 08:03:19 PDT)
[AMBER] espgen and G09 Hannes Loeffler (Thu Jul 11 2013 - 07:28:32 PDT)
- Re: [AMBER] espgen and G09 Sergio R Aragon (Thu Jul 11 2013 - 08:19:06 PDT)
  - Re: [AMBER] espgen and G09 Hannes Loeffler (Thu Jul 11 2013 - 09:17:15 PDT)
    - Re: [AMBER] espgen and G09 Sergio R Aragon (Thu Jul 11 2013 - 09:20:43 PDT)
[AMBER] Amber12 installation on SGI cluster George Tzotzos (Thu Jul 11 2013 - 07:51:25 PDT)
- Re: [AMBER] Amber12 installation on SGI cluster David A Case (Thu Jul 11 2013 - 08:28:53 PDT)
[AMBER] MCPB Jinqiang (Thu Jul 11 2013 - 08:54:06 PDT)
- Re: [AMBER] MCPB Ben Roberts (Mon Jul 29 2013 - 01:44:59 PDT)
Re: [AMBER] Problem with visualization in VMD after using AUTOIMAGE Daniel Roe (Thu Jul 11 2013 - 10:38:23 PDT)
[AMBER] hbond analysis - bridgeout Fabrício Bracht (Thu Jul 11 2013 - 11:04:01 PDT)
- Re: [AMBER] hbond analysis - bridgeout Daniel Roe (Thu Jul 11 2013 - 12:00:05 PDT)
  - Re: [AMBER] hbond analysis - bridgeout Fabrício Bracht (Thu Jul 11 2013 - 16:09:32 PDT)
    - Re: [AMBER] hbond analysis - bridgeout Daniel Roe (Thu Jul 11 2013 - 16:18:01 PDT)
    - Re: [AMBER] hbond analysis - bridgeout Fabrício Bracht (Thu Jul 11 2013 - 16:31:43 PDT)
[AMBER] compilation of amber12 on cray system Jorgen Simonsen (Thu Jul 11 2013 - 12:07:00 PDT)
- Re: [AMBER] compilation of amber12 on cray system Jason Swails (Thu Jul 11 2013 - 12:27:51 PDT)
  - Re: [AMBER] compilation of amber12 on cray system Jorgen Simonsen (Thu Jul 11 2013 - 14:05:43 PDT)
    - Re: [AMBER] compilation of amber12 on cray system Jason Swails (Thu Jul 11 2013 - 14:32:34 PDT)
    - Re: [AMBER] compilation of amber12 on cray system Jorgen Simonsen (Thu Jul 11 2013 - 14:41:01 PDT)
    - Re: [AMBER] compilation of amber12 on cray system Jason Swails (Thu Jul 11 2013 - 17:46:07 PDT)
    - Re: [AMBER] compilation of amber12 on cray system Jorgen Simonsen (Thu Jul 11 2013 - 18:00:57 PDT)
    - Re: [AMBER] compilation of amber12 on cray system Jason Swails (Thu Jul 11 2013 - 18:06:00 PDT)
    - Re: [AMBER] compilation of amber12 on cray system Jorgen Simonsen (Thu Jul 11 2013 - 18:17:16 PDT)
    - Re: [AMBER] compilation of amber12 on cray system Jason Swails (Thu Jul 11 2013 - 20:04:32 PDT)
    - [AMBER] CUDA MPI compilation issue Wang Chern Hoe (Dr) (Thu Jul 11 2013 - 20:06:16 PDT)
    - Re: [AMBER] CUDA MPI compilation issue Jason Swails (Thu Jul 11 2013 - 20:26:12 PDT)
    - Re: [AMBER] compilation of amber12 on cray system Jorgen Simonsen (Fri Jul 12 2013 - 09:03:04 PDT)
    - Re: [AMBER] compilation of amber12 on cray system Jason Swails (Fri Jul 12 2013 - 09:45:05 PDT)
[AMBER] Problems with generating histograms in AMBER tutorial 18 Yip Yew Mun (Thu Jul 11 2013 - 18:44:39 PDT)
- Re: [AMBER] Problems with generating histograms in AMBER tutorial 18 Daniel Roe (Thu Jul 11 2013 - 19:48:59 PDT)
  - Re: [AMBER] Problems with generating histograms in AMBER tutorial 18 Yip Yew Mun (Thu Jul 11 2013 - 19:59:05 PDT)
    - Re: [AMBER] Problems with generating histograms in AMBER tutorial 18 Daniel Roe (Thu Jul 11 2013 - 20:20:04 PDT)
[AMBER] Reference for TI derivation Manikanthan Bhavaraju (Thu Jul 11 2013 - 19:04:36 PDT)
- Re: [AMBER] Reference for TI derivation Jason Swails (Thu Jul 11 2013 - 20:19:25 PDT)
  - Re: [AMBER] Reference for TI derivation David A Case (Fri Jul 12 2013 - 05:27:59 PDT)
[AMBER] problem (re)compiling pmemd.cuda_SPFP: Reading module netcdf at line 23 column 34: Expected integer Marc van der Kamp (Fri Jul 12 2013 - 05:37:52 PDT)
- Re: [AMBER] problem (re)compiling pmemd.cuda_SPFP: Reading module netcdf at line 23 column 34: Expected integer David A Case (Fri Jul 12 2013 - 06:02:35 PDT)
  - Re: [AMBER] problem (re)compiling pmemd.cuda_SPFP: Reading module netcdf at line 23 column 34: Expected integer Wang Chern Hoe (Dr) (Fri Jul 12 2013 - 06:05:14 PDT)
  - Re: [AMBER] problem (re)compiling pmemd.cuda_SPFP: Reading module netcdf at line 23 column 34: Expected integer Jason Swails (Fri Jul 12 2013 - 06:45:53 PDT)
  - Re: [AMBER] problem (re)compiling pmemd.cuda_SPFP: Reading module netcdf at line 23 column 34: Expected integer Marc van der Kamp (Fri Jul 12 2013 - 06:53:47 PDT)
    - Re: [AMBER] problem (re)compiling pmemd.cuda_SPFP: Reading module netcdf at line 23 column 34: Expected integer Jason Swails (Fri Jul 12 2013 - 07:21:14 PDT)
    - Re: [AMBER] problem (re)compiling pmemd.cuda_SPFP: Reading module netcdf at line 23 column 34: Expected integer Marc van der Kamp (Fri Jul 12 2013 - 07:35:17 PDT)
[AMBER] GTX780s Ross Walker (Fri Jul 12 2013 - 08:53:56 PDT)
- Re: [AMBER] GTX780s Marek Maly (Fri Jul 12 2013 - 13:17:22 PDT)
  - Re: [AMBER] GTX780s tec3.utah.edu (Fri Jul 12 2013 - 13:50:55 PDT)
    - Re: [AMBER] GTX780s Marek Maly (Fri Jul 12 2013 - 15:18:16 PDT)
    - Re: [AMBER] GTX780s ET (Fri Jul 12 2013 - 20:45:29 PDT)
    - Re: [AMBER] GTX780s ET (Fri Jul 12 2013 - 22:14:42 PDT)
    - Re: [AMBER] GTX780s Ross Walker (Fri Jul 12 2013 - 22:28:33 PDT)
    - Re: [AMBER] GTX780s ET (Fri Jul 12 2013 - 22:35:10 PDT)
[AMBER] solvent accessible surface area (SASA) rajeevy.iitk.ac.in (Fri Jul 12 2013 - 23:25:28 PDT)
- Re: [AMBER] solvent accessible surface area (SASA) Vaibhav Dixit (Sat Jul 13 2013 - 04:48:26 PDT)
  - Re: [AMBER] solvent accessible surface area (SASA) rajeevy.iitk.ac.in (Sat Jul 13 2013 - 08:31:43 PDT)
    - Re: [AMBER] solvent accessible surface area (SASA) Daniel Roe (Sat Jul 13 2013 - 09:56:56 PDT)
- Re: [AMBER] solvent accessible surface area (SASA) Daniel Roe (Sat Jul 13 2013 - 08:04:28 PDT)
[AMBER] GTX-770 Ross Walker (Sat Jul 13 2013 - 17:54:05 PDT)
[AMBER] speed of amber12 Jorgen Simonsen (Sun Jul 14 2013 - 15:54:08 PDT)
- Re: [AMBER] speed of amber12 Ross Walker (Sun Jul 14 2013 - 17:21:22 PDT)
- Re: [AMBER] speed of amber12 David A Case (Sun Jul 14 2013 - 19:33:20 PDT)
- Re: [AMBER] speed of amber12 Jason Swails (Sun Jul 14 2013 - 20:47:05 PDT)
  - Re: [AMBER] speed of amber12 Jorgen Simonsen (Mon Jul 15 2013 - 11:40:31 PDT)
    - Re: [AMBER] speed of amber12 Jason Swails (Mon Jul 15 2013 - 13:19:35 PDT)
[AMBER] unsupported GNU version! gcc 4.7 and up are not supported Kanin Wichapong (Mon Jul 15 2013 - 04:50:34 PDT)
- Re: [AMBER] unsupported GNU version! gcc 4.7 and up are not supported Jason Swails (Mon Jul 15 2013 - 06:45:57 PDT)
[AMBER] Ptraj B Factor PDB Parker de Waal (Mon Jul 15 2013 - 08:52:47 PDT)
- Re: [AMBER] Ptraj B Factor PDB Jason Swails (Mon Jul 15 2013 - 11:06:42 PDT)
  - Re: [AMBER] Ptraj B Factor PDB Parker de Waal (Mon Jul 15 2013 - 11:23:07 PDT)
    - Re: [AMBER] Ptraj B Factor PDB Jason Swails (Mon Jul 15 2013 - 13:45:58 PDT)
    - Re: [AMBER] Ptraj B Factor PDB Thomas Cheatham (Mon Jul 15 2013 - 14:08:38 PDT)
    - Re: [AMBER] Ptraj B Factor PDB Parker de Waal (Mon Jul 15 2013 - 15:59:49 PDT)
[AMBER] Antechamber problem with sqm Hunter Brown (Mon Jul 15 2013 - 09:59:35 PDT)
- Re: [AMBER] Antechamber problem with sqm David A. Case (Mon Jul 15 2013 - 10:58:51 PDT)
[AMBER] Resp charges for large number of atoms in an ONIOM calculation Morteza Chehel Amirani (Mon Jul 15 2013 - 15:52:22 PDT)
- Re: [AMBER] Resp charges for large number of atoms in an ONIOM calculation FyD (Tue Jul 16 2013 - 06:13:26 PDT)
  - Re: [AMBER] Resp charges for large number of atoms in an ONIOM calculation Hamed S. Hayatshahi (Tue Jul 16 2013 - 09:48:27 PDT)
[AMBER] read trajectory using ambertools me, Nancy (Mon Jul 15 2013 - 20:40:17 PDT)
- Re: [AMBER] read trajectory using ambertools Daniel Roe (Mon Jul 15 2013 - 22:35:53 PDT)
[AMBER] What's the difference between NetCDF files and .crd files? #YIP YEW MUN# (Tue Jul 16 2013 - 02:24:19 PDT)
- Re: [AMBER] What's the difference between NetCDF files and .crd files? Daniel Sindhikara (Tue Jul 16 2013 - 02:41:12 PDT)
  - Re: [AMBER] What's the difference between NetCDF files and .crd files? Yip Yew Mun (Tue Jul 16 2013 - 02:46:13 PDT)
    - Re: [AMBER] What's the difference between NetCDF files and .crd files? Jan-Philip Gehrcke (Tue Jul 16 2013 - 03:09:43 PDT)
    - Re: [AMBER] What's the difference between NetCDF files and .crd files? Yip Yew Mun (Tue Jul 16 2013 - 03:19:07 PDT)
    - Re: [AMBER] What's the difference between NetCDF files and .crd files? Marc van der Kamp (Tue Jul 16 2013 - 03:25:46 PDT)
    - Re: [AMBER] What's the difference between NetCDF files and .crd files? Yip Yew Mun (Tue Jul 16 2013 - 03:41:58 PDT)
[AMBER] Resp fiiting method and theory eneas.usal.es (Tue Jul 16 2013 - 07:22:56 PDT)
- Re: [AMBER] Resp fiiting method and theory FyD (Tue Jul 16 2013 - 09:11:26 PDT)
  - Re: [AMBER] Resp fiiting method and theory Karl N. Kirschner (Wed Jul 17 2013 - 01:18:29 PDT)
    - Re: [AMBER] Resp fiiting method and theory Brent Krueger (Wed Jul 17 2013 - 05:45:06 PDT)
[AMBER] cpptraj hbond bridgeout problems with V13.0 Cassandra Churchill (Tue Jul 16 2013 - 09:54:40 PDT)
- Re: [AMBER] cpptraj hbond bridgeout problems with V13.0 Daniel Roe (Tue Jul 16 2013 - 10:46:16 PDT)
[AMBER] Message to AMBER GeForce GPU Users MARK (Tue Jul 16 2013 - 13:04:45 PDT)
- Re: [AMBER] Message to AMBER GeForce GPU Users Jan-Philip Gehrcke (Tue Jul 16 2013 - 14:52:19 PDT)
  - Re: [AMBER] Message to AMBER GeForce GPU Users ET (Wed Jul 17 2013 - 01:07:07 PDT)
[AMBER] Processing of output files using process_mdout.perl #YIP YEW MUN# (Tue Jul 16 2013 - 21:49:18 PDT)
- Re: [AMBER] Processing of output files using process_mdout.perl Jason Swails (Wed Jul 17 2013 - 05:20:30 PDT)
[AMBER] Problems running NAB scripts in the manual Alexander Button (Wed Jul 17 2013 - 00:08:09 PDT)
- Re: [AMBER] Problems running NAB scripts in the manual David A Case (Fri Aug 09 2013 - 10:22:53 PDT)
[AMBER] xleap, unit connectivity and atom name Rasha Alqus (Wed Jul 17 2013 - 01:26:15 PDT)
- Re: [AMBER] xleap, unit connectivity and atom name David A. Case (Wed Jul 17 2013 - 07:39:28 PDT)
[AMBER] antechamber issues Hannes Loeffler (Wed Jul 17 2013 - 02:02:47 PDT)
- Re: [AMBER] antechamber issues Junmei Wang (Thu Jul 18 2013 - 09:55:24 PDT)
  - Re: [AMBER] antechamber issues hannes.loeffler.stfc.ac.uk (Thu Jul 18 2013 - 10:09:49 PDT)
    - Re: [AMBER] antechamber issues Junmei Wang (Tue Jul 23 2013 - 11:59:01 PDT)
[AMBER] MMPBSA.py problem Fernando Martín García (Wed Jul 17 2013 - 02:44:18 PDT)
- Re: [AMBER] MMPBSA.py problem Jason Swails (Wed Jul 17 2013 - 05:28:09 PDT)
  - Re: [AMBER] MMPBSA.py problem Fernando Martín García (Wed Jul 17 2013 - 05:54:57 PDT)
[AMBER] How to add metal ions? 赵媛 (Wed Jul 17 2013 - 04:43:11 PDT)
- Re: [AMBER] How to add metal ions? Jason Swails (Wed Jul 17 2013 - 06:49:17 PDT)
  - Re: [AMBER] How to add metal ions? FyD (Wed Jul 17 2013 - 07:09:30 PDT)
[AMBER] pmemd.cuda.MPI NPT Issues Parker de Waal (Wed Jul 17 2013 - 10:45:23 PDT)
- Re: [AMBER] pmemd.cuda.MPI NPT Issues Ross Walker (Wed Jul 17 2013 - 11:29:44 PDT)
  - Re: [AMBER] pmemd.cuda.MPI NPT Issues Parker de Waal (Wed Jul 17 2013 - 12:28:36 PDT)
- Re: [AMBER] pmemd.cuda.MPI NPT Issues Ross Walker (Wed Jul 17 2013 - 13:12:32 PDT)
  - Re: [AMBER] pmemd.cuda.MPI NPT Issues Parker de Waal (Thu Jul 18 2013 - 10:23:28 PDT)
[AMBER] cudaMemcpy GpuBuffer::Download failed unspecified launch failure Hailin Huang (Wed Jul 17 2013 - 14:23:24 PDT)
- Re: [AMBER] cudaMemcpy GpuBuffer::Download failed unspecified launch failure Ross Walker (Wed Jul 17 2013 - 14:53:46 PDT)
  - Re: [AMBER] cudaMemcpy GpuBuffer::Download failed unspecified launch failure Hailin Huang (Wed Jul 17 2013 - 16:01:18 PDT)
    - Re: [AMBER] cudaMemcpy GpuBuffer::Download failed unspecified launch failure Scott Le Grand (Wed Jul 17 2013 - 16:19:42 PDT)
    - Re: [AMBER] cudaMemcpy GpuBuffer::Download failed unspecified launch failure Hailin Huang (Wed Jul 17 2013 - 16:22:31 PDT)
    - Re: [AMBER] cudaMemcpy GpuBuffer::Download failed unspecified launch failure Scott Le Grand (Wed Jul 17 2013 - 16:28:03 PDT)
    - Re: [AMBER] cudaMemcpy GpuBuffer::Download failed unspecified launch failure Hailin Huang (Wed Jul 17 2013 - 16:37:35 PDT)
    - Re: [AMBER] cudaMemcpy GpuBuffer::Download failed unspecified launch failure Jason Swails (Wed Jul 17 2013 - 21:23:28 PDT)
[AMBER] NAB atom manipulation Daniel Leclerc (Wed Jul 17 2013 - 16:09:48 PDT)
- Re: [AMBER] NAB atom manipulation David A. Case (Thu Jul 18 2013 - 08:43:09 PDT)
[AMBER] improper dihedral with gaff Jio M (Thu Jul 18 2013 - 03:18:04 PDT)
- Re: [AMBER] improper dihedral with gaff David A. Case (Thu Jul 18 2013 - 08:43:19 PDT)
[AMBER-Developers] Amber Workshop in Brazil Gustavo Seabra (Thu Jul 18 2013 - 05:22:45 PDT)
- Re: [AMBER-Developers] Amber Workshop in Brazil Ross Walker (Thu Jul 18 2013 - 06:17:15 PDT)
[AMBER] amber12's performance on AMD wl2290.columbia.edu (Thu Jul 18 2013 - 12:36:20 PDT)
- Re: [AMBER] amber12's performance on AMD Ross Walker (Thu Jul 18 2013 - 14:48:22 PDT)
  - Re: [AMBER] amber12's performance on AMD Jan-Philip Gehrcke (Thu Jul 18 2013 - 15:13:26 PDT)
[AMBER] online server of amber K. Suzie Byun (Thu Jul 18 2013 - 15:37:02 PDT)
- Re: [AMBER] online server of amber Jason Swails (Thu Jul 18 2013 - 16:32:12 PDT)
  - Re: [AMBER] online server of amber Jan-Philip Gehrcke (Fri Jul 19 2013 - 02:02:07 PDT)
    - Re: [AMBER] online server of amber Hannes Loeffler (Fri Jul 19 2013 - 02:15:32 PDT)
    - Re: [AMBER] online server of amber Ross Walker (Fri Jul 19 2013 - 05:46:20 PDT)
[AMBER] amber on-line server K. Suzie Byun (Thu Jul 18 2013 - 15:48:27 PDT)
[AMBER] Multiple Trajectory MMPBSA Yi An (Fri Jul 19 2013 - 12:58:51 PDT)
- Re: [AMBER] Multiple Trajectory MMPBSA Bill Miller III (Fri Jul 19 2013 - 13:03:04 PDT)
  - Re: [AMBER] Multiple Trajectory MMPBSA Jason Swails (Fri Jul 19 2013 - 14:46:34 PDT)
    - Re: [AMBER] Multiple Trajectory MMPBSA Yi An (Fri Jul 19 2013 - 15:33:14 PDT)
[AMBER] Asking suggestion Tanmoy Paul (Fri Jul 19 2013 - 22:02:05 PDT)
- Re: [AMBER] Asking suggestion Carlos Simmerling (Fri Jul 19 2013 - 22:07:26 PDT)
  - Re: [AMBER] Asking suggestion Tanmoy Paul (Mon Jul 22 2013 - 21:24:44 PDT)
    - Re: [AMBER] Asking suggestion Daniel Roe (Tue Jul 23 2013 - 06:27:56 PDT)
[AMBER] problem on heating with restraints on the solute John Travers (Sat Jul 20 2013 - 13:21:58 PDT)
- Re: [AMBER] problem on heating with restraints on the solute Daniel Roe (Sat Jul 20 2013 - 15:17:42 PDT)
- Re: [AMBER] problem on heating with restraints on the solute Daniel Roe (Sun Jul 21 2013 - 11:57:23 PDT)
  - Re: [AMBER] problem on heating with restraints on the solute John Travers (Sun Jul 21 2013 - 16:27:01 PDT)
    - Re: [AMBER] problem on heating with restraints on the solute Daniel Roe (Sun Jul 21 2013 - 17:47:03 PDT)
  - Re: [AMBER] problem on heating with restraints on the solute David A. Case (Sun Jul 21 2013 - 20:49:10 PDT)
- Re: [AMBER] problem on heating with restraints on the solute Daniel Roe (Sun Jul 21 2013 - 22:06:25 PDT)
  - Re: [AMBER] problem on heating with restraints on the solute John Travers (Mon Jul 22 2013 - 06:47:49 PDT)
    - Re: [AMBER] problem on heating with restraints on the solute Daniel Roe (Mon Jul 22 2013 - 11:39:42 PDT)
    - Re: [AMBER] problem on heating with restraints on the solute John Travers (Mon Jul 22 2013 - 11:53:25 PDT)
[AMBER] using acpype with AMBER13 Error: /bin/sh: 1: -i: not found Jonathan Saboury (Sat Jul 20 2013 - 17:42:04 PDT)
- Re: [AMBER] using acpype with AMBER13 Error: /bin/sh: 1: -i: not found Alan (Sun Jul 21 2013 - 01:27:50 PDT)
[AMBER] Problem regarding the cuda installation using NetCFD. ANDREI LEITaO (Sun Jul 21 2013 - 15:29:38 PDT)
- Re: [AMBER] Problem regarding the cuda installation using NetCFD. David A. Case (Sun Jul 21 2013 - 20:58:39 PDT)
- Re: [AMBER] Problem regarding the cuda installation using NetCFD. ANDREI LEITaO (Fri Jul 26 2013 - 13:22:28 PDT)
  - Re: [AMBER] Problem regarding the cuda installation using NetCFD. Jason Swails (Fri Jul 26 2013 - 17:36:34 PDT)
[AMBER] Problem with increasing values in limits.h for resp Hamed S. Hayatshahi (Sun Jul 21 2013 - 18:32:33 PDT)
- Re: [AMBER] Problem with increasing values in limits.h for resp Jean-Paul Becker (Mon Jul 22 2013 - 00:38:23 PDT)
  - Re: [AMBER] Problem with increasing values in limits.h for resp Hamed S. Hayatshahi (Mon Jul 22 2013 - 10:44:50 PDT)
    - Re: [AMBER] Problem with increasing values in limits.h for resp Jean-Paul Becker (Tue Jul 23 2013 - 01:46:40 PDT)
    - Re: [AMBER] Problem with increasing values in limits.h for resp Hamed S. Hayatshahi (Tue Jul 23 2013 - 09:08:27 PDT)
    - Re: [AMBER] Problem with increasing values in limits.h for resp FyD (Tue Jul 23 2013 - 22:57:56 PDT)
    - Re: [AMBER] Problem with increasing values in limits.h for resp Hamed S. Hayatshahi (Tue Jul 23 2013 - 18:52:51 PDT)
    - Re: [AMBER] Problem with increasing values in limits.h for resp FyD (Tue Jul 23 2013 - 23:06:30 PDT)
    - Re: [AMBER] Problem with increasing values in limits.h for resp Hamed S. Hayatshahi (Wed Jul 24 2013 - 10:53:40 PDT)
    - Re: [AMBER] Problem with increasing values in limits.h for resp FyD (Wed Jul 24 2013 - 23:58:19 PDT)
    - Re: [AMBER] Problem with increasing values in limits.h for resp FyD (Thu Jul 25 2013 - 00:14:25 PDT)
- Re: [AMBER] Problem with increasing values in limits.h for resp FyD (Mon Jul 22 2013 - 03:17:49 PDT)
[AMBER] minimization codes Wang Chern Hoe (Dr) (Mon Jul 22 2013 - 00:00:51 PDT)
- Re: [AMBER] minimization codes Karl N. Kirschner (Mon Jul 22 2013 - 01:20:53 PDT)
[AMBER] the question about the atom type of my molecule lujing8556 (Mon Jul 22 2013 - 01:12:33 PDT)
- Re: [AMBER] the question about the atom type of my molecule Karl N. Kirschner (Mon Jul 22 2013 - 02:03:42 PDT)
  - Re: [AMBER] the question about the atom type of my molecule lujing8556 (Mon Jul 22 2013 - 04:05:27 PDT)
[AMBER] Parmed.py deletedihedral Aronica, Pietro (Mon Jul 22 2013 - 09:28:28 PDT)
- Re: [AMBER] Parmed.py deletedihedral Jason Swails (Mon Jul 22 2013 - 11:33:43 PDT)
  - Re: [AMBER] Parmed.py deletedihedral Aronica, Pietro (Tue Jul 23 2013 - 03:37:23 PDT)
    - Re: [AMBER] Parmed.py deletedihedral Jason Swails (Tue Jul 23 2013 - 04:12:09 PDT)
    - Re: [AMBER] Parmed.py deletedihedral Aronica, Pietro (Tue Jul 23 2013 - 04:43:23 PDT)
    - Re: [AMBER] Parmed.py deletedihedral Jason Swails (Tue Jul 23 2013 - 07:30:17 PDT)
    - Re: [AMBER] Parmed.py deletedihedral Aronica, Pietro (Tue Jul 23 2013 - 07:52:56 PDT)
    - Re: [AMBER] Parmed.py deletedihedral Jason Swails (Tue Jul 23 2013 - 10:03:44 PDT)
    - Re: [AMBER] Parmed.py deletedihedral Jason Swails (Wed Jul 24 2013 - 05:16:25 PDT)
    - Re: [AMBER] Parmed.py deletedihedral Aronica, Pietro (Wed Jul 24 2013 - 06:09:45 PDT)
[AMBER] How to modify the formula for non-bonded interactions Pengzhi Zhang (Mon Jul 22 2013 - 11:17:51 PDT)
- Re: [AMBER] How to modify the formula for non-bonded interactions Jason Swails (Mon Jul 22 2013 - 11:55:08 PDT)
[AMBER] plane-plane angle restraint Josep Maria Campanera Alsina (Mon Jul 22 2013 - 11:55:35 PDT)
- Re: [AMBER] plane-plane angle restraint Daniel Roe (Mon Jul 22 2013 - 16:33:40 PDT)
  - Re: [AMBER] plane-plane angle restraint Jason Swails (Mon Jul 22 2013 - 16:37:24 PDT)
[AMBER] Creating a new Solvatebox Chinthaka Ratnaweera (Mon Jul 22 2013 - 14:41:54 PDT)
- Re: [AMBER] Creating a new Solvatebox David A. Case (Mon Jul 22 2013 - 15:49:17 PDT)
  - Re: [AMBER] Creating a new Solvatebox Chinthaka Ratnaweera (Mon Jul 22 2013 - 17:52:45 PDT)
    - Re: [AMBER] Creating a new Solvatebox David A. Case (Tue Jul 23 2013 - 08:02:01 PDT)
    - Re: [AMBER] Creating a new Solvatebox Chinthaka Ratnaweera (Tue Jul 23 2013 - 12:19:01 PDT)
    - Re: [AMBER] Creating a new Solvatebox M. L. Dodson (Tue Jul 23 2013 - 12:45:18 PDT)
    - Re: [AMBER] Creating a new Solvatebox M. L. Dodson (Tue Jul 23 2013 - 12:52:16 PDT)
    - Re: [AMBER] Creating a new Solvatebox Chinthaka Ratnaweera (Tue Jul 23 2013 - 13:10:03 PDT)
    - Re: [AMBER] Creating a new Solvatebox M. L. Dodson (Tue Jul 23 2013 - 13:26:58 PDT)
    - Re: [AMBER] Creating a new Solvatebox Chinthaka Ratnaweera (Tue Jul 23 2013 - 13:49:37 PDT)
    - Re: [AMBER] Creating a new Solvatebox M. L. Dodson (Tue Jul 23 2013 - 14:37:48 PDT)
    - Re: [AMBER] Creating a new Solvatebox Chinthaka Ratnaweera (Tue Jul 23 2013 - 15:43:48 PDT)
    - Re: [AMBER] Creating a new Solvatebox Chinthaka Ratnaweera (Tue Jul 23 2013 - 15:44:57 PDT)
    - Re: [AMBER] Creating a new Solvatebox M. L. Dodson (Tue Jul 23 2013 - 16:36:29 PDT)
[AMBER] mmpbsa input parameters Mary Varughese (Tue Jul 23 2013 - 00:21:59 PDT)
- Re: [AMBER] mmpbsa input parameters Jason Swails (Tue Jul 23 2013 - 07:49:13 PDT)
  - Re: [AMBER] mmpbsa input parameters Ray Luo, Ph.D. (Tue Jul 23 2013 - 18:59:26 PDT)
    - Re: [AMBER] mmpbsa input parameters Mary Varughese (Tue Jul 23 2013 - 21:50:32 PDT)
    - Re: [AMBER] mmpbsa input parameters Ray Luo (Wed Jul 24 2013 - 00:31:53 PDT)
[AMBER] setting up non-standard amino acid residues for MD simulation Suri Moonsamy (Tue Jul 23 2013 - 03:17:36 PDT)
- Re: [AMBER] setting up non-standard amino acid residues for MD simulation David A. Case (Tue Jul 23 2013 - 07:04:26 PDT)
  - Re: [AMBER] setting up non-standard amino acid residues for MD simulation Suri Moonsamy (Mon Aug 05 2013 - 02:22:43 PDT)
[AMBER] Entropy calculation error Changqing Yan (Tue Jul 23 2013 - 05:58:43 PDT)
- Re: [AMBER] Entropy calculation error Jason Swails (Tue Jul 23 2013 - 07:38:31 PDT)
[AMBER] Modified Nucleic Acid Mark Zottola (Tue Jul 23 2013 - 08:18:01 PDT)
- Re: [AMBER] Modified Nucleic Acid David A. Case (Thu Jul 25 2013 - 07:52:28 PDT)
[AMBER] MMPBSA.py decomposition CSV output -- proposal for improvement Jan-Philip Gehrcke (Tue Jul 23 2013 - 08:31:51 PDT)
- Re: [AMBER] MMPBSA.py decomposition CSV output -- proposal for improvement Jason Swails (Tue Jul 23 2013 - 09:51:59 PDT)
[AMBER] ptraj, outprefix not giving a stripped prmtop Hunter Brown (Tue Jul 23 2013 - 13:40:28 PDT)
- Re: [AMBER] ptraj, outprefix not giving a stripped prmtop Jason Swails (Tue Jul 23 2013 - 13:58:12 PDT)
- Re: [AMBER] ptraj, outprefix not giving a stripped prmtop Hunter Brown (Tue Jul 23 2013 - 14:04:15 PDT)
[AMBER] MMPBSA.py problem on G gas Yi An (Tue Jul 23 2013 - 14:53:34 PDT)
- Re: [AMBER] MMPBSA.py problem on G gas Jason Swails (Tue Jul 23 2013 - 17:08:17 PDT)
  - Re: [AMBER] MMPBSA.py problem on G gas Yi An (Tue Jul 23 2013 - 17:42:54 PDT)
[AMBER] simulating Modified residue of Cysteine attached to mercury Manish Paul (Tue Jul 23 2013 - 19:48:21 PDT)
- Re: [AMBER] simulating Modified residue of Cysteine attached to mercury FyD (Wed Jul 24 2013 - 00:58:12 PDT)
[AMBER] extraction of specific region of the trajectory file using ptraj Puspita Halder (Tue Jul 23 2013 - 23:38:21 PDT)
- Re: [AMBER] extraction of specific region of the trajectory file using ptraj Jason Swails (Wed Jul 24 2013 - 05:13:19 PDT)
  - Re: [AMBER] extraction of specific region of the trajectory file using ptraj Daniel Roe (Wed Jul 24 2013 - 08:17:57 PDT)
[AMBER] Problems with NAB Alexander Button (Wed Jul 24 2013 - 00:42:51 PDT)
- Re: [AMBER] Problems with NAB svrci (Wed Jul 24 2013 - 01:19:24 PDT)
- Re: [AMBER] Problems with NAB David A. Case (Wed Jul 24 2013 - 07:07:51 PDT)
  - Re: [AMBER] Problems with NAB Alexander Button (Wed Jul 31 2013 - 19:03:54 PDT)
    - Re: [AMBER] Problems with NAB Jason Swails (Wed Jul 31 2013 - 20:13:33 PDT)
    - Re: [AMBER] Problems with NAB Alexander Button (Wed Jul 31 2013 - 20:27:56 PDT)
[AMBER] Problem in running antechamber.Unable to achieve self consistency to the tolerances specified devawati dutta (Wed Jul 24 2013 - 01:25:36 PDT)
- Re: [AMBER] Problem in running antechamber.Unable to achieve self consistency to the tolerances specified David A. Case (Wed Jul 24 2013 - 07:11:01 PDT)
[AMBER] QM/MM using Gaussian03 as External Alfredo Quevedo (Wed Jul 24 2013 - 08:07:41 PDT)
- Re: [AMBER] QM/MM using Gaussian03 as External Andreas Goetz (Wed Jul 24 2013 - 13:58:19 PDT)
  - Re: [AMBER] QM/MM using Gaussian03 as External Alfredo Quevedo (Thu Jul 25 2013 - 10:41:56 PDT)
    - Re: [AMBER] QM/MM using Gaussian03 as External Andreas Goetz (Thu Jul 25 2013 - 16:11:37 PDT)
[AMBER] bad atom type: cl MMPBSA.py sribone.fcq.unc.edu.ar (Wed Jul 24 2013 - 08:57:26 PDT)
- Re: [AMBER] bad atom type: cl MMPBSA.py siddharth kesharwani (Wed Jul 24 2013 - 09:01:15 PDT)
  - Re: [AMBER] bad atom type: cl MMPBSA.py sribone.fcq.unc.edu.ar (Wed Jul 24 2013 - 10:28:34 PDT)
[AMBER] residue selection Wang Chern Hoe (Dr) (Thu Jul 25 2013 - 01:28:51 PDT)
- Re: [AMBER] residue selection David A. Case (Thu Jul 25 2013 - 06:28:06 PDT)
- Re: [AMBER] residue selection Daniel Roe (Thu Jul 25 2013 - 07:43:34 PDT)
[AMBER] Calculating diffusion Constant D Vijay Manickam Achari (Thu Jul 25 2013 - 03:07:19 PDT)
- Re: [AMBER] Calculating diffusion Constant D Dickson, Callum (Thu Jul 25 2013 - 03:32:39 PDT)
- Re: [AMBER] Calculating diffusion Constant D Dickson, Callum (Thu Jul 25 2013 - 03:39:30 PDT)
  - Re: [AMBER] Calculating diffusion Constant D Vijay Manickam Achari (Thu Jul 25 2013 - 19:42:48 PDT)
    - Re: [AMBER] Calculating diffusion Constant D Dickson, Callum (Fri Jul 26 2013 - 03:14:43 PDT)
[AMBER] Explicit vs Implicit solvent for REMD Parker de Waal (Thu Jul 25 2013 - 06:03:14 PDT)
- Re: [AMBER] Explicit vs Implicit solvent for REMD Jason Swails (Thu Jul 25 2013 - 09:17:36 PDT)
  - Re: [AMBER] Explicit vs Implicit solvent for REMD Parker de Waal (Fri Jul 26 2013 - 07:30:56 PDT)
[AMBER] Amber11 bugfixes 19, 20 and 22 failed Massimiliano Porrini (Thu Jul 25 2013 - 07:55:25 PDT)
- Re: [AMBER] Amber11 bugfixes 19, 20 and 22 failed Ross Walker (Tue Jul 30 2013 - 19:58:50 PDT)
  - Re: [AMBER] Amber11 bugfixes 19, 20 and 22 failed Massimiliano Porrini (Wed Jul 31 2013 - 00:54:16 PDT)
[AMBER] TI with ifsc==2 Kepa K. Burusco (Thu Jul 25 2013 - 09:24:32 PDT)
[AMBER] Amber force field for Benzene sulfonamide. loue chen (Thu Jul 25 2013 - 10:04:59 PDT)
- Re: [AMBER] Amber force field for Benzene sulfonamide. David A. Case (Thu Jul 25 2013 - 10:48:13 PDT)
- Re: [AMBER] Amber force field for Benzene sulfonamide. FyD (Fri Jul 26 2013 - 01:40:30 PDT)
- Re: [AMBER] Amber force field for Benzene sulfonamide. Karl N. Kirschner (Fri Jul 26 2013 - 04:22:36 PDT)
[AMBER] Error while umbrella sampling with distance restraint Meekyum Olivia Kim (Thu Jul 25 2013 - 11:45:56 PDT)
- Re: [AMBER] Error while umbrella sampling with distance restraint Jason Swails (Fri Jul 26 2013 - 05:15:20 PDT)
  - Re: [AMBER] Error while umbrella sampling with distance restraint Meekyum Olivia Kim (Fri Jul 26 2013 - 09:36:35 PDT)
    - Re: [AMBER] Error while umbrella sampling with distance restraint Jason Swails (Fri Jul 26 2013 - 12:13:00 PDT)
[AMBER] PCA Contributions Pavan G (Thu Jul 25 2013 - 13:20:55 PDT)
- Re: [AMBER] PCA Contributions Daniel Roe (Thu Jul 25 2013 - 15:09:58 PDT)
  - Re: [AMBER] PCA Contributions Pavan G (Thu Jul 25 2013 - 15:49:46 PDT)
    - Re: [AMBER] PCA Contributions Daniel Roe (Thu Jul 25 2013 - 22:00:46 PDT)
    - Re: [AMBER] PCA Contributions Pavan G (Fri Jul 26 2013 - 05:16:10 PDT)
[AMBER] Error while umbrella sampling with distance restraint Meekyum Olivia Kim (Thu Jul 25 2013 - 14:08:11 PDT)
- Re: [AMBER] Error while umbrella sampling with distance restraint Levi Pierce (Thu Jul 25 2013 - 20:19:19 PDT)
[AMBER] MMPBSA.py Shashidhar Rao (Thu Jul 25 2013 - 19:49:05 PDT)
- Re: [AMBER] MMPBSA.py Dwight McGee (Thu Jul 25 2013 - 20:05:36 PDT)
  - Re: [AMBER] MMPBSA.py Shashidhar Rao (Sun Jul 28 2013 - 06:17:16 PDT)
    - Re: [AMBER] MMPBSA.py Jason Swails (Sun Jul 28 2013 - 09:00:42 PDT)
    - Re: [AMBER] MMPBSA.py Shashidhar Rao (Sun Jul 28 2013 - 12:56:05 PDT)
    - Re: [AMBER] MMPBSA.py Jason Swails (Sun Jul 28 2013 - 13:34:19 PDT)
    - Re: [AMBER] MMPBSA.py Shashidhar Rao (Sun Jul 28 2013 - 14:50:08 PDT)
    - Re: [AMBER] MMPBSA.py Jason Swails (Sun Jul 28 2013 - 16:38:32 PDT)
- Re: [AMBER] MMPBSA.py siddharth kesharwani (Fri Jul 26 2013 - 07:41:09 PDT)
  - Re: [AMBER] MMPBSA.py Gannett, Peter (Fri Jul 26 2013 - 07:45:05 PDT)
[AMBER] Segmentation Error Sumra Wajid Abbasi 30-FBAS/MSBI/F09 (Thu Jul 25 2013 - 23:01:16 PDT)
- Re: [AMBER] Segmentation Error Daniel Roe (Fri Jul 26 2013 - 05:41:08 PDT)
  - Re: [AMBER] Segmentation Error Sumra Wajid Abbasi 30-FBAS/MSBI/F09 (Fri Jul 26 2013 - 08:44:58 PDT)
    - Re: [AMBER] Segmentation Error Daniel Roe (Sat Jul 27 2013 - 09:10:28 PDT)
    - Re: [AMBER] Segmentation Error Sumra Wajid Abbasi 30-FBAS/MSBI/F09 (Tue Jul 30 2013 - 08:35:49 PDT)
[AMBER] MMPBSA.py decomp, -deo, PB only problem Ryan Pavlovicz (Fri Jul 26 2013 - 08:29:34 PDT)
- Re: [AMBER] MMPBSA.py decomp, -deo, PB only problem Jason Swails (Fri Jul 26 2013 - 12:34:58 PDT)
  - Re: [AMBER] MMPBSA.py decomp, -deo, PB only problem Ryan Pavlovicz (Sat Jul 27 2013 - 08:26:59 PDT)
    - Re: [AMBER] MMPBSA.py decomp, -deo, PB only problem Daniel Roe (Sat Jul 27 2013 - 09:31:40 PDT)
    - Re: [AMBER] MMPBSA.py decomp, -deo, PB only problem Ryan Pavlovicz (Sat Jul 27 2013 - 15:19:09 PDT)
    - Re: [AMBER] MMPBSA.py decomp, -deo, PB only problem Jason Swails (Sun Jul 28 2013 - 06:15:23 PDT)
    - Re: [AMBER] MMPBSA.py decomp, -deo, PB only problem Jason Swails (Sun Jul 28 2013 - 06:16:56 PDT)
    - Re: [AMBER] MMPBSA.py decomp, -deo, PB only problem Ryan Pavlovicz (Mon Jul 29 2013 - 20:46:05 PDT)
[AMBER] validation of MMPBSA results Asmita Gupta (Fri Jul 26 2013 - 08:52:11 PDT)
- Re: [AMBER] validation of MMPBSA results Jason Swails (Fri Jul 26 2013 - 12:29:07 PDT)
[AMBER] DNA Phosphate error mohit mazumder (Fri Jul 26 2013 - 23:36:17 PDT)
- Re: [AMBER] DNA Phosphate error Daniel Roe (Sat Jul 27 2013 - 09:58:42 PDT)
- Re: [AMBER] DNA Phosphate error David A Case (Sat Aug 10 2013 - 06:40:26 PDT)
[AMBER] can thermodynamics integration be used for calculating binding free energy of peptides and proteins? sunyeping.aliyun.com (Sat Jul 27 2013 - 09:24:35 PDT)
- Re: [AMBER] can thermodynamics integration be used for calculating binding free energy of peptides and proteins? David A Case (Mon Jul 29 2013 - 04:32:50 PDT)
[AMBER] bond command sunyeping.aliyun.com (Sat Jul 27 2013 - 21:12:14 PDT)
- Re: [AMBER] bond command David A Case (Mon Jul 29 2013 - 06:29:01 PDT)
[AMBER] Methods for RESP charge generation Kamali Sripathi (Sun Jul 28 2013 - 09:05:02 PDT)
- Re: [AMBER] Methods for RESP charge generation FyD (Mon Jul 29 2013 - 00:23:05 PDT)
  - Re: [AMBER] Methods for RESP charge generation Kamali Sripathi (Mon Jul 29 2013 - 10:33:32 PDT)
[AMBER] isothermal compressibility kirtana S (Sun Jul 28 2013 - 13:29:38 PDT)
- Re: [AMBER] isothermal compressibility Jason Swails (Sun Jul 28 2013 - 21:02:38 PDT)
  - Re: [AMBER] isothermal compressibility kirtana S (Fri Aug 02 2013 - 15:42:19 PDT)
    - Re: [AMBER] isothermal compressibility David A Case (Fri Aug 02 2013 - 18:27:47 PDT)
[AMBER] antechamber yanyuna (Sun Jul 28 2013 - 19:44:12 PDT)
- Re: [AMBER] antechamber David A Case (Mon Jul 29 2013 - 04:40:29 PDT)
[AMBER] about adding counter ions B. Bowie (Sun Jul 28 2013 - 21:44:15 PDT)
- Re: [AMBER] about adding counter ions David A Case (Mon Jul 29 2013 - 04:48:47 PDT)
[AMBER] Interaction energy-based residue-residue correlation matrix anu chandra (Sun Jul 28 2013 - 22:54:17 PDT)
- Re: [AMBER] Interaction energy-based residue-residue correlation matrix Kshatresh Dutta Dubey (Sun Jul 28 2013 - 23:22:43 PDT)
  - Re: [AMBER] Interaction energy-based residue-residue correlation matrix anu chandra (Sun Jul 28 2013 - 23:36:13 PDT)
    - Re: [AMBER] Interaction energy-based residue-residue correlation matrix Jason Swails (Mon Jul 29 2013 - 09:35:09 PDT)
    - Re: [AMBER] Interaction energy-based residue-residue correlation matrix Daniel Roe (Mon Jul 29 2013 - 09:48:01 PDT)
[AMBER] antechamber yanyuna (Sun Jul 28 2013 - 23:16:55 PDT)
[AMBER] mmpbsa nonpolar contribution using stability calculations George Green (Mon Jul 29 2013 - 16:08:18 PDT)
- Re: [AMBER] mmpbsa nonpolar contribution using stability calculations Ray Luo (Mon Jul 29 2013 - 19:18:45 PDT)
  - Re: [AMBER] mmpbsa nonpolar contribution using stability calculations George Green (Wed Jul 31 2013 - 01:08:06 PDT)
    - Re: [AMBER] mmpbsa nonpolar contribution using stability calculations Ray Luo, Ph.D. (Wed Jul 31 2013 - 02:49:24 PDT)
    - Re: [AMBER] mmpbsa nonpolar contribution using stability calculations Jason Swails (Wed Jul 31 2013 - 05:21:06 PDT)
    - Re: [AMBER] mmpbsa nonpolar contribution using stability calculations George Green (Thu Aug 01 2013 - 08:53:37 PDT)
    - Re: [AMBER] mmpbsa nonpolar contribution using stability calculations George Green (Thu Aug 01 2013 - 13:44:14 PDT)
    - Re: [AMBER] mmpbsa nonpolar contribution using stability calculations Jason Swails (Thu Aug 01 2013 - 14:20:41 PDT)
    - Re: [AMBER] mmpbsa nonpolar contribution using stability calculations George Green (Mon Aug 19 2013 - 03:07:51 PDT)
    - Re: [AMBER] mmpbsa nonpolar contribution using stability calculations Jason Swails (Mon Aug 19 2013 - 04:30:53 PDT)
    - Re: [AMBER] mmpbsa nonpolar contribution using stability calculations George Green (Wed Aug 21 2013 - 01:31:24 PDT)
[AMBER] MMPBSA tianchuan1015 (Tue Jul 30 2013 - 03:17:35 PDT)
[AMBER] mdread MMPBSA tianchuan1015 (Tue Jul 30 2013 - 03:19:27 PDT)
- Re: [AMBER] mdread MMPBSA Jason Swails (Tue Jul 30 2013 - 04:43:09 PDT)
  - [AMBER] Force Field for DNA-Protein complex Catein Catherine (Tue Jul 30 2013 - 05:05:12 PDT)
    - Re: [AMBER] Force Field for DNA-Protein complex David A Case (Tue Jul 30 2013 - 07:15:50 PDT)
    - [AMBER] Request Force Fields References Catein Catherine (Tue Jul 30 2013 - 08:24:11 PDT)
    - Re: [AMBER] Request Force Fields References David A Case (Tue Jul 30 2013 - 10:42:22 PDT)
    - [AMBER] MM-GBSA igb=2 or igb=5? [Ref: Exploring Protein Native States and Large-Scale Conformational Changes With a Modified Generalized Born Model] Catein Catherine (Wed Jul 31 2013 - 00:16:46 PDT)
    - Re: [AMBER] MM-GBSA igb=2 or igb=5? [Ref: Exploring Protein Native States and Large-Scale Conformational Changes With a Modified Generalized Born Model] David A Case (Wed Jul 31 2013 - 04:43:13 PDT)
    - Re: [AMBER] MM-GBSA igb=2 or igb=5? [Ref: Exploring Protein Native States and Large-Scale Conformational Changes With a Modified Generalized Born Model] Carlos Simmerling (Wed Jul 31 2013 - 04:47:38 PDT)
    - Re: [AMBER] MM-GBSA igb=2 or igb=5? [Ref: Exploring Protein Native States and Large-Scale Conformational Changes With a Modified Generalized Born Model] Catein Catherine (Wed Jul 31 2013 - 21:09:00 PDT)
    - Re: [AMBER] MM-GBSA igb=2 or igb=5? [Ref: Exploring Protein Native States and Large-Scale Conformational Changes With a Modified Generalized Born Model] Jason Swails (Thu Aug 01 2013 - 06:19:57 PDT)
[AMBER] mdread 372133720 (Tue Jul 30 2013 - 03:36:25 PDT)
[AMBER] sander option "-radii" Soonmin Jang (Tue Jul 30 2013 - 06:14:08 PDT)
- Re: [AMBER] sander option "-radii" Jason Swails (Tue Jul 30 2013 - 20:26:52 PDT)
  - Re: [AMBER] sander option "-radii" Soonmin Jang (Tue Aug 06 2013 - 05:48:49 PDT)
[AMBER] Distance based mask for qmmask Fabrício Bracht (Tue Jul 30 2013 - 12:27:49 PDT)
- Re: [AMBER] Distance based mask for qmmask Jason Swails (Tue Jul 30 2013 - 20:15:05 PDT)
  - Re: [AMBER] Distance based mask for qmmask Ross Walker (Tue Jul 30 2013 - 20:22:42 PDT)
    - Re: [AMBER] Distance based mask for qmmask Jason Swails (Tue Jul 30 2013 - 20:30:01 PDT)
    - Re: [AMBER] Distance based mask for qmmask Ross Walker (Tue Jul 30 2013 - 20:42:13 PDT)
    - Re: [AMBER] Distance based mask for qmmask Ross Walker (Tue Jul 30 2013 - 20:53:45 PDT)
    - Re: [AMBER] Distance based mask for qmmask Fabrício Bracht (Wed Jul 31 2013 - 12:05:00 PDT)
    - Re: [AMBER] Distance based mask for qmmask Jason Swails (Wed Jul 31 2013 - 20:21:41 PDT)
    - Re: [AMBER] Distance based mask for qmmask Andreas Goetz (Thu Aug 01 2013 - 20:34:15 PDT)
    - Re: [AMBER] Distance based mask for qmmask Fabrício Bracht (Thu Aug 01 2013 - 21:26:22 PDT)
    - Re: [AMBER] Distance based mask for qmmask Andreas Goetz (Fri Aug 02 2013 - 10:43:32 PDT)
    - Re: [AMBER] Distance based mask for qmmask Fabrício Bracht (Fri Aug 02 2013 - 17:21:01 PDT)
    - Re: [AMBER] Distance based mask for qmmask Fabrício Bracht (Tue Jul 30 2013 - 20:39:32 PDT)
[AMBER] How to assign initial velocities (directly not by increasing temeperature) to water molecules Yan Duan (Tue Jul 30 2013 - 14:42:33 PDT)
- Re: [AMBER] How to assign initial velocities (directly not by increasing temeperature) to water molecules Adrian Roitberg (Tue Jul 30 2013 - 14:45:21 PDT)
[AMBER] Checking Sander energy values FyD (Wed Jul 31 2013 - 00:15:15 PDT)
- Re: [AMBER] Checking Sander energy values Jason Swails (Wed Jul 31 2013 - 05:41:53 PDT)
[AMBER] igb8 SURFTEN SURFOFF berin karaman (Wed Jul 31 2013 - 01:33:21 PDT)
- Re: [AMBER] igb8 SURFTEN SURFOFF Hai Nguyen (Wed Jul 31 2013 - 13:03:57 PDT)
  - Re: [AMBER] igb8 SURFTEN SURFOFF berin karaman (Thu Aug 01 2013 - 00:47:28 PDT)
    - Re: [AMBER] igb8 SURFTEN SURFOFF David A Case (Thu Aug 01 2013 - 04:50:16 PDT)
[AMBER] how to add the pseudopotential via the Amber-Gaussian interface cwt (Wed Jul 31 2013 - 03:56:11 PDT)
[AMBER] constructing single nucleotides in leap Brian Radak (Wed Jul 31 2013 - 06:21:23 PDT)
[AMBER] Estimate error for TI calculations Kumar Sonu (Wed Jul 31 2013 - 10:07:47 PDT)
- Re: [AMBER] Estimate error for TI calculations Jason Swails (Wed Jul 31 2013 - 10:21:34 PDT)
  - Re: [AMBER] Estimate error for TI calculations Kumar Sonu (Wed Jul 31 2013 - 14:43:11 PDT)
    - Re: [AMBER] Estimate error for TI calculations Jason Swails (Wed Jul 31 2013 - 20:12:33 PDT)
[AMBER] Fw: Re: MMPBSA problem 372133720 (Wed Jul 31 2013 - 19:01:51 PDT)
- Re: [AMBER] Fw: Re: MMPBSA problem Jason Swails (Wed Jul 31 2013 - 20:20:50 PDT)
Re: [AMBER] error when running binding energy in amber nguyentb.bii.a-star.edu.sg (Thu Aug 01 2013 - 00:11:15 PDT)
- [AMBER] error when running binding energy in amber nguyentb.bii.a-star.edu.sg (Thu Aug 01 2013 - 19:29:40 PDT)
  - Re: [AMBER] error when running binding energy in amber Dwight McGee (Thu Aug 01 2013 - 20:03:28 PDT)
    - Re: [AMBER] error when running binding energy in amber nguyentb.bii.a-star.edu.sg (Thu Aug 01 2013 - 20:18:17 PDT)
[AMBER] SASA / AmberTools1.5 fatahiya (Thu Aug 01 2013 - 02:44:52 PDT)
- Re: [AMBER] SASA / AmberTools1.5 David A Case (Thu Aug 01 2013 - 04:52:09 PDT)
  - Re: [AMBER] SASA / AmberTools1.5 fatahiya (Thu Aug 01 2013 - 19:23:13 PDT)
    - Re: [AMBER] SASA / AmberTools1.5 Daniel Roe (Thu Aug 01 2013 - 21:38:10 PDT)
[AMBER] Jobs resubmitted when calculating entropy Changqing Yan (Thu Aug 01 2013 - 03:02:50 PDT)
- Re: [AMBER] Jobs resubmitted when calculating entropy Jason Swails (Thu Aug 01 2013 - 06:54:00 PDT)
[AMBER] Generating snapshots in amber trajectory format aneesh cna (Thu Aug 01 2013 - 03:48:03 PDT)
- Re: [AMBER] Generating snapshots in amber trajectory format Jason Swails (Thu Aug 01 2013 - 06:42:32 PDT)
[AMBER] MMPBSA problem 372133720 (Thu Aug 01 2013 - 03:54:37 PDT)
[AMBER] can't neutralize CH NIMILITHA Nimilitha (Thu Aug 01 2013 - 04:06:27 PDT)
- Re: [AMBER] can't neutralize David A Case (Thu Aug 01 2013 - 04:56:15 PDT)
[AMBER] Fw: Re: MMPBSA problem 372133720 (Thu Aug 01 2013 - 05:57:41 PDT)
- Re: [AMBER] Fw: Re: MMPBSA problem Jason Swails (Thu Aug 01 2013 - 06:22:33 PDT)
- Re: [AMBER] Fw: Re: MMPBSA problem Gannett, Peter (Thu Aug 01 2013 - 06:21:30 PDT)
[AMBER] Charmmgui pdb file error Giorgos Lamprinidis (Thu Aug 01 2013 - 06:17:38 PDT)
- Re: [AMBER] Charmmgui pdb file error David A Case (Thu Aug 01 2013 - 06:44:55 PDT)
- Re: [AMBER] Charmmgui pdb file error Giorgos Lamprinidis (Thu Aug 01 2013 - 07:49:38 PDT)
  - Re: [AMBER] Charmmgui pdb file error David A Case (Thu Aug 01 2013 - 13:40:48 PDT)
    - Re: [AMBER] Charmmgui pdb file error Giorgos Lamprinidis (Fri Aug 02 2013 - 00:22:13 PDT)
[AMBER] radii effect on PB_cavity surften_cavity offset berin karaman (Thu Aug 01 2013 - 06:54:15 PDT)
- Re: [AMBER] radii effect on PB_cavity surften_cavity offset Ray Luo, Ph.D. (Thu Aug 01 2013 - 20:36:09 PDT)
  - Re: [AMBER] radii effect on PB_cavity surften_cavity offset berin karaman (Fri Aug 02 2013 - 00:24:37 PDT)
[AMBER] Using ante-mmpbsa.py to create prmtops Hunter Brown (Thu Aug 01 2013 - 10:07:36 PDT)
- Re: [AMBER] Using ante-mmpbsa.py to create prmtops Jason Swails (Thu Aug 01 2013 - 11:14:00 PDT)
- Re: [AMBER] Using ante-mmpbsa.py to create prmtops Hunter Brown (Thu Aug 01 2013 - 14:05:09 PDT)
  - Re: [AMBER] Using ante-mmpbsa.py to create prmtops Jason Swails (Thu Aug 01 2013 - 14:16:21 PDT)
- Re: [AMBER] Using ante-mmpbsa.py to create prmtops Hunter Brown (Fri Aug 02 2013 - 10:17:34 PDT)
  - Re: [AMBER] Using ante-mmpbsa.py to create prmtops Daniel Roe (Fri Aug 02 2013 - 10:20:52 PDT)
- Re: [AMBER] Using ante-mmpbsa.py to create prmtops Hunter Brown (Fri Aug 02 2013 - 10:39:47 PDT)
  - Re: [AMBER] Using ante-mmpbsa.py to create prmtops Daniel Roe (Fri Aug 02 2013 - 11:00:33 PDT)
    - Re: [AMBER] Using ante-mmpbsa.py to create prmtops Jason Swails (Sat Aug 03 2013 - 06:47:17 PDT)
[AMBER] Updating AmberTools1.5 fatahiya (Thu Aug 01 2013 - 19:49:36 PDT)
- Re: [AMBER] Updating AmberTools1.5 Daniel Roe (Thu Aug 01 2013 - 21:40:39 PDT)
[AMBER] Terminal pair fraying in nucleic acids Asmita Gupta (Thu Aug 01 2013 - 22:46:03 PDT)
- Re: [AMBER] Terminal pair fraying in nucleic acids David A Case (Fri Aug 02 2013 - 05:24:31 PDT)
  - Re: [AMBER] Terminal pair fraying in nucleic acids Asmita Gupta (Fri Aug 02 2013 - 05:45:42 PDT)
    - Re: [AMBER] Terminal pair fraying in nucleic acids David A Case (Fri Aug 02 2013 - 10:10:48 PDT)
[AMBER] 10 ns explicit water NPT Wang Chern Hoe (Dr) (Fri Aug 02 2013 - 02:22:23 PDT)
- Re: [AMBER] 10 ns explicit water NPT David A Case (Fri Aug 02 2013 - 05:26:37 PDT)
  - Re: [AMBER] 10 ns explicit water NPT Wang Chern Hoe (Dr) (Fri Aug 02 2013 - 07:54:22 PDT)
    - Re: [AMBER] 10 ns explicit water NPT Daniel Roe (Fri Aug 02 2013 - 08:07:11 PDT)
    - Re: [AMBER] 10 ns explicit water NPT Wang Chern Hoe (Dr) (Fri Aug 02 2013 - 08:32:47 PDT)
    - Re: [AMBER] 10 ns explicit water NPT Daniel Roe (Fri Aug 02 2013 - 10:32:30 PDT)
    - Re: [AMBER] 10 ns explicit water NPT Wang Chern Hoe (Dr) (Fri Aug 02 2013 - 16:24:31 PDT)
[AMBER] Is there any problem with this input file? Changqing Yan (Fri Aug 02 2013 - 07:34:03 PDT)
- Re: [AMBER] Is there any problem with this input file? Bill Miller III (Mon Aug 05 2013 - 07:47:27 PDT)
[AMBER] How to Calculate Energy Indrajit Deb (Fri Aug 02 2013 - 12:18:24 PDT)
- Re: [AMBER] How to Calculate Energy Brian Radak (Fri Aug 02 2013 - 13:12:41 PDT)
  - Re: [AMBER] How to Calculate Energy Indrajit Deb (Fri Aug 02 2013 - 14:21:47 PDT)
[AMBER] ambpdb -ext ... but how? John Gehman (Sun Aug 04 2013 - 15:13:38 PDT)
- Re: [AMBER] ambpdb -ext ... but how? David A Case (Sun Aug 04 2013 - 18:01:05 PDT)
[AMBER] change coordinate Vijay Manickam Achari (Sun Aug 04 2013 - 20:28:22 PDT)
- Re: [AMBER] change coordinate Daniel Roe (Sun Aug 04 2013 - 20:54:12 PDT)
[AMBER] setbox command Vijay Manickam Achari (Sun Aug 04 2013 - 21:10:53 PDT)
[AMBER] Nmode question Changqing Yan (Mon Aug 05 2013 - 01:57:25 PDT)
- Re: [AMBER] Nmode question David A Case (Mon Aug 05 2013 - 08:49:02 PDT)
  - Re: [AMBER] Nmode question David A Case (Mon Aug 05 2013 - 11:08:08 PDT)
[AMBER] Parameter file is not saved - AMBER! Krati Sharma (Mon Aug 05 2013 - 08:54:03 PDT)
- Re: [AMBER] Parameter file is not saved - AMBER! Daniel Roe (Mon Aug 05 2013 - 09:16:47 PDT)
- Re: [AMBER] Parameter file is not saved - AMBER! David A Case (Mon Aug 05 2013 - 11:11:25 PDT)
[AMBER] output nuclear force and hessian John Travers (Mon Aug 05 2013 - 11:51:53 PDT)
- Re: [AMBER] output nuclear force and hessian Brian Radak (Mon Aug 05 2013 - 12:20:19 PDT)
  - Re: [AMBER] output nuclear force and hessian John Travers (Mon Aug 05 2013 - 15:26:41 PDT)
    - Re: [AMBER] output nuclear force and hessian Jason Swails (Mon Aug 05 2013 - 22:41:56 PDT)
    - Re: [AMBER] output nuclear force and hessian Brian Radak (Tue Aug 06 2013 - 07:25:43 PDT)
    - Re: [AMBER] output nuclear force and hessian John Travers (Tue Aug 06 2013 - 08:26:33 PDT)
    - Re: [AMBER] output nuclear force and hessian David A Case (Tue Aug 06 2013 - 13:04:04 PDT)
    - Re: [AMBER] output nuclear force and hessian John Travers (Tue Aug 06 2013 - 08:47:03 PDT)
    - Re: [AMBER] output nuclear force and hessian Jason Swails (Tue Aug 06 2013 - 11:45:09 PDT)
- Re: [AMBER] output nuclear force and hessian Jason Swails (Wed Aug 07 2013 - 11:41:41 PDT)
  - Re: [AMBER] output nuclear force and hessian John Travers (Wed Aug 07 2013 - 12:29:09 PDT)
  - Re: [AMBER] output nuclear force and hessian John Travers (Fri Aug 09 2013 - 20:01:38 PDT)
    - Re: [AMBER] output nuclear force and hessian David A Case (Sat Aug 10 2013 - 06:30:54 PDT)
    - Re: [AMBER] output nuclear force and hessian John Travers (Sat Aug 10 2013 - 15:38:05 PDT)
[AMBER] Resp charges Morteza Chehel Amirani (Mon Aug 05 2013 - 12:03:07 PDT)
- Re: [AMBER] Resp charges ymei (Mon Aug 05 2013 - 12:11:38 PDT)
- Re: [AMBER] Resp charges Hamed S. Hayatshahi (Mon Aug 05 2013 - 13:55:43 PDT)
  - Re: [AMBER] Resp charges FyD (Thu Aug 08 2013 - 02:47:42 PDT)
[AMBER] Amber12 with CUDA5.0 test results Soonmin Jang (Mon Aug 05 2013 - 12:06:24 PDT)
- Re: [AMBER] Amber12 with CUDA5.0 test results Ross Walker (Mon Aug 05 2013 - 12:35:02 PDT)
  - Re: [AMBER] Amber12 with CUDA5.0 test results Soonmin Jang (Tue Aug 06 2013 - 05:44:37 PDT)
[AMBER] Auto-image "Could not determine atomic number from mass" Hailin Huang (Mon Aug 05 2013 - 12:41:33 PDT)
- [AMBER] Auto-image "Could not determine atomic number from mass" Daniel Roe (Mon Aug 05 2013 - 13:33:15 PDT)
  - Re: [AMBER] Auto-image "Could not determine atomic number from mass" Hailin Huang (Mon Aug 05 2013 - 14:09:40 PDT)
    - Re: [AMBER] Auto-image "Could not determine atomic number from mass" David A Case (Tue Aug 06 2013 - 04:49:25 PDT)
- Re: [AMBER] Auto-image "Could not determine atomic number from mass" Daniel Roe (Mon Aug 05 2013 - 16:35:05 PDT)
- Re: [AMBER] Auto-image "Could not determine atomic number from mass" Daniel Roe (Wed Aug 07 2013 - 09:11:31 PDT)
  - Re: [AMBER] Auto-image "Could not determine atomic number from mass" Hailin Huang (Wed Aug 07 2013 - 12:43:28 PDT)
[AMBER] Error when loading the opls dihedral information. egeh00 (Mon Aug 05 2013 - 16:16:35 PDT)
- Re: [AMBER] Error when loading the opls dihedral information. David A Case (Tue Aug 06 2013 - 04:51:33 PDT)
[AMBER-Developers] GTX-Titan / GTX780 Fix Ross Walker (Mon Aug 05 2013 - 17:01:26 PDT)
- [AMBER] MMPBSA_decomp 372133720 (Mon Aug 05 2013 - 18:30:02 PDT)
  - Re: [AMBER] MMPBSA_decomp Jason Swails (Mon Aug 05 2013 - 22:44:29 PDT)
- Re: [AMBER] GTX-Titan / GTX780 Fix filip fratev (Wed Aug 07 2013 - 10:30:35 PDT)
  - Re: [AMBER] GTX-Titan / GTX780 Fix Scott Le Grand (Wed Aug 07 2013 - 10:46:57 PDT)
  - Re: [AMBER] GTX-Titan / GTX780 Fix Ross Walker (Wed Aug 07 2013 - 10:52:51 PDT)
    - Re: [AMBER] GTX-Titan / GTX780 Fix ET (Wed Aug 14 2013 - 08:07:12 PDT)
- Re: [AMBER] GTX-Titan / GTX780 Fix Marek Maly (Wed Aug 14 2013 - 15:23:17 PDT)
- Re: [AMBER] GTX-Titan / GTX780 Fix iqtcub (Wed Aug 21 2013 - 01:14:06 PDT)
  - Re: [AMBER] GTX-Titan / GTX780 Fix Ross Walker (Wed Aug 21 2013 - 10:33:20 PDT)
[AMBER] Segmentation Fault Souvik Sur (Mon Aug 05 2013 - 22:41:08 PDT)
- Re: [AMBER] Segmentation Fault David A Case (Tue Aug 06 2013 - 04:53:31 PDT)
  - Re: [AMBER] Segmentation Fault Souvik Sur (Tue Aug 06 2013 - 05:59:28 PDT)
    - Re: [AMBER] Segmentation Fault David A Case (Tue Aug 06 2013 - 06:39:21 PDT)
[AMBER] parmed.py with closest command from ptraj Andre C. Stiel (Tue Aug 06 2013 - 03:39:39 PDT)
- Re: [AMBER] parmed.py with closest command from ptraj Daniel Roe (Tue Aug 06 2013 - 05:50:33 PDT)
  - Re: [AMBER] parmed.py with closest command from ptraj Daniel Roe (Tue Aug 06 2013 - 05:51:54 PDT)
- Re: [AMBER] parmed.py with closest command from ptraj Jason Swails (Tue Aug 06 2013 - 11:47:21 PDT)
[AMBER] AmberTools update 15 for CPPTRAJ Daniel Roe (Tue Aug 06 2013 - 09:14:42 PDT)
[AMBER] GTX-Titan / GTX780 Fix Ross Walker (Tue Aug 06 2013 - 10:41:04 PDT)
- Re: [AMBER] GTX-Titan / GTX780 Fix Divi/GMAIL (Wed Aug 07 2013 - 17:53:09 PDT)
  - Re: [AMBER] GTX-Titan / GTX780 Fix Ross Walker (Wed Aug 07 2013 - 18:21:47 PDT)
[AMBER] Trajectory post-processing VanDyne_Aaron (Tue Aug 06 2013 - 13:50:55 PDT)
- Re: [AMBER] Trajectory post-processing Brian Radak (Tue Aug 06 2013 - 14:06:38 PDT)
  - Re: [AMBER] Trajectory post-processing VanDyne_Aaron (Tue Aug 06 2013 - 14:57:27 PDT)
- Re: [AMBER] Trajectory post-processing Daniel Roe (Tue Aug 06 2013 - 14:08:02 PDT)
  - Re: [AMBER] Trajectory post-processing VanDyne_Aaron (Tue Aug 06 2013 - 14:59:21 PDT)
    - Re: [AMBER] Trajectory post-processing Jason Swails (Tue Aug 06 2013 - 17:13:09 PDT)
    - Re: [AMBER] Trajectory post-processing VanDyne_Aaron (Thu Aug 08 2013 - 07:39:01 PDT)
    - Re: [AMBER] Trajectory post-processing Daniel Roe (Thu Aug 08 2013 - 08:27:08 PDT)
    - Re: [AMBER] Trajectory post-processing VanDyne_Aaron (Thu Aug 08 2013 - 09:48:09 PDT)
    - Re: [AMBER] Trajectory post-processing Daniel Roe (Fri Aug 09 2013 - 08:28:32 PDT)
    - Re: [AMBER] Trajectory post-processing Daniel Roe (Sat Aug 10 2013 - 14:09:38 PDT)
    - Re: [AMBER] Trajectory post-processing VanDyne_Aaron (Sat Aug 10 2013 - 17:52:44 PDT)
[AMBER] Questions about improper dihedral scan? egeh00 (Tue Aug 06 2013 - 15:44:21 PDT)
- Re: [AMBER] Questions about improper dihedral scan? Steven M. Graham (Tue Aug 06 2013 - 18:27:53 PDT)
[AMBER] R.E.D server output files Ayesha Fatima (Tue Aug 06 2013 - 19:16:09 PDT)
- Re: [AMBER] R.E.D server output files FyD (Thu Aug 08 2013 - 03:18:43 PDT)
  - Re: [AMBER] R.E.D server output files Ayesha Fatima (Sat Aug 10 2013 - 19:33:56 PDT)
[AMBER] Diffusion constant's unit Vijay Manickam Achari (Tue Aug 06 2013 - 20:33:24 PDT)
- Re: [AMBER] Diffusion constant's unit Ismail, Mohd F. (Tue Aug 06 2013 - 22:26:32 PDT)
  - Re: [AMBER] Diffusion constant's unit Vijay Manickam Achari (Wed Aug 07 2013 - 00:47:15 PDT)
[AMBER] mask command issue Massimiliano Porrini (Wed Aug 07 2013 - 07:05:49 PDT)
- Re: [AMBER] mask command issue Daniel Roe (Wed Aug 07 2013 - 08:26:33 PDT)
  - Re: [AMBER] mask command issue Massimiliano Porrini (Wed Aug 07 2013 - 09:30:11 PDT)
    - Re: [AMBER] mask command issue Daniel Roe (Wed Aug 07 2013 - 10:59:43 PDT)
    - Re: [AMBER] mask command issue Massimiliano Porrini (Wed Aug 07 2013 - 13:18:08 PDT)
    - Re: [AMBER] mask command issue Daniel Roe (Wed Aug 07 2013 - 14:00:29 PDT)
[AMBER] reax forcefield erik.laurini.di3.units.it (Wed Aug 07 2013 - 08:42:14 PDT)
- Re: [AMBER] reax forcefield Yeng-Tseng Wang (Wed Aug 07 2013 - 09:45:23 PDT)
- Re: [AMBER] reax forcefield Ross Walker (Wed Aug 07 2013 - 10:35:28 PDT)
[AMBER] Secondary Structure analysis Chinthaka Ratnaweera (Wed Aug 07 2013 - 09:56:09 PDT)
- Re: [AMBER] Secondary Structure analysis Daniel Roe (Wed Aug 07 2013 - 10:16:50 PDT)
[AMBER] pmemd.cuda.MPI problem Victor Ma (Wed Aug 07 2013 - 09:59:24 PDT)
- Re: [AMBER] pmemd.cuda.MPI problem Jason Swails (Wed Aug 07 2013 - 11:38:26 PDT)
- Re: [AMBER] pmemd.cuda.MPI problem David A Case (Wed Aug 07 2013 - 11:50:02 PDT)
  - Re: [AMBER] pmemd.cuda.MPI problem Victor Ma (Wed Aug 07 2013 - 12:37:50 PDT)
    - Re: [AMBER] pmemd.cuda.MPI problem Jason Swails (Wed Aug 07 2013 - 12:44:52 PDT)
    - Re: [AMBER] pmemd.cuda.MPI problem Victor Ma (Wed Aug 07 2013 - 12:51:45 PDT)
    - Re: [AMBER] pmemd.cuda.MPI problem Ross Walker (Wed Aug 07 2013 - 13:02:50 PDT)
[AMBER] NMR restraints not working with pmemd.cuda.parallel Kyle Sutherland-Cash (Wed Aug 07 2013 - 10:07:17 PDT)
- Re: [AMBER] NMR restraints not working with pmemd.cuda.parallel Ross Walker (Wed Aug 07 2013 - 10:38:31 PDT)
[AMBER] GpuBuffer::Download failed for kNLBuildNeighborListOrthogonal16_kernel Kyle Sutherland-Cash (Wed Aug 07 2013 - 10:12:59 PDT)
- Re: [AMBER] GpuBuffer::Download failed for kNLBuildNeighborListOrthogonal16_kernel Scott Le Grand (Wed Aug 07 2013 - 10:28:58 PDT)
- Re: [AMBER] GpuBuffer::Download failed for kNLBuildNeighborListOrthogonal16_kernel Scott Le Grand (Thu Aug 08 2013 - 17:31:21 PDT)
  - Re: [AMBER] GpuBuffer::Download failed for kNLBuildNeighborListOrthogonal16_kernel Scott Le Grand (Thu Aug 08 2013 - 20:10:14 PDT)
    - Re: [AMBER] GpuBuffer::Download failed for kNLBuildNeighborListOrthogonal16_kernel Scott Le Grand (Fri Aug 09 2013 - 09:46:24 PDT)
[AMBER] multiple heat baths in a single simulation James W. Snyder, Jr. (Wed Aug 07 2013 - 11:38:14 PDT)
- Re: [AMBER] multiple heat baths in a single simulation James W. Snyder, Jr. (Wed Aug 07 2013 - 14:03:21 PDT)
[AMBER] dftb3 me, Nancy (Wed Aug 07 2013 - 15:26:50 PDT)
- Re: [AMBER] dftb3 Andreas Goetz (Wed Aug 07 2013 - 16:10:04 PDT)
[AMBER] Distance between group of atoms using Ptraj HIMANSHU JOSHI (Thu Aug 08 2013 - 03:24:28 PDT)
- Re: [AMBER] Distance between group of atoms using Ptraj Daniel Roe (Thu Aug 08 2013 - 08:34:43 PDT)
  - Re: [AMBER] Distance between group of atoms using Ptraj David A Case (Thu Aug 08 2013 - 09:57:10 PDT)
  - Re: [AMBER] Distance between group of atoms using Ptraj HIMANSHU JOSHI (Thu Aug 08 2013 - 23:28:16 PDT)
[AMBER] Abnormal md output Hailin Huang (Thu Aug 08 2013 - 11:38:47 PDT)
- Re: [AMBER] Abnormal md output Ross Walker (Thu Aug 08 2013 - 12:02:59 PDT)
  - Re: [AMBER] Abnormal md output Hailin Huang (Thu Aug 08 2013 - 14:37:59 PDT)
[AMBER] BOND, ANGLE and TORSION energies discrepancy between amber and gromacs Golshan Hejazi (Thu Aug 08 2013 - 12:26:53 PDT)
- Re: [AMBER] BOND, ANGLE and TORSION energies discrepancy between amber and gromacs Ross Walker (Thu Aug 08 2013 - 12:48:19 PDT)
  - Re: [AMBER] BOND, ANGLE and TORSION energies discrepancy between amber and gromacs Scott Le Grand (Thu Aug 08 2013 - 16:36:27 PDT)
    - Re: [AMBER] BOND, ANGLE and TORSION energies discrepancy between amber and gromacs Golshan Hejazi (Fri Aug 09 2013 - 06:35:55 PDT)
    - Re: [AMBER] BOND, ANGLE and TORSION energies discrepancy between amber and gromacs David A Case (Fri Aug 09 2013 - 06:46:51 PDT)
    - Re: [AMBER] BOND, ANGLE and TORSION energies discrepancy between amber and gromacs Golshan Hejazi (Fri Aug 09 2013 - 07:53:40 PDT)
    - Re: [AMBER] BOND, ANGLE and TORSION energies discrepancy between amber and gromacs Adrian Roitberg (Fri Aug 09 2013 - 08:05:05 PDT)
    - Re: [AMBER] BOND, ANGLE and TORSION energies discrepancy between amber and gromacs Golshan Hejazi (Fri Aug 09 2013 - 10:02:18 PDT)
    - Re: [AMBER] BOND, ANGLE and TORSION energies discrepancy between amber and gromacs Jason Swails (Fri Aug 09 2013 - 14:23:03 PDT)
    - Re: [AMBER] BOND, ANGLE and TORSION energies discrepancy between amber and gromacs Golshan Hejazi (Fri Aug 09 2013 - 15:01:29 PDT)
    - Re: [AMBER] BOND, ANGLE and TORSION energies discrepancy between amber and gromacs Ross Walker (Fri Aug 09 2013 - 14:54:37 PDT)
    - Re: [AMBER] BOND, ANGLE and TORSION energies discrepancy between amber and gromacs Golshan Hejazi (Fri Aug 09 2013 - 15:32:40 PDT)
    - Re: [AMBER] BOND, ANGLE and TORSION energies discrepancy between amber and gromacs Ross Walker (Fri Aug 09 2013 - 15:42:41 PDT)
    - Re: [AMBER] BOND, ANGLE and TORSION energies discrepancy between amber and gromacs Oliver Grant (Sat Aug 10 2013 - 02:26:18 PDT)
    - Re: [AMBER] BOND, ANGLE and TORSION energies discrepancy between amber and gromacs Golshan Hejazi (Mon Aug 12 2013 - 06:32:20 PDT)
    - Re: [AMBER] BOND, ANGLE and TORSION energies discrepancy between amber and gromacs Oliver Grant (Sat Aug 17 2013 - 05:57:04 PDT)
[AMBER] Why are sigma values of OPLS so big? egeh00 (Thu Aug 08 2013 - 14:10:36 PDT)
- Re: [AMBER] Why are sigma values of OPLS so big? David A Case (Thu Aug 08 2013 - 18:33:07 PDT)
[AMBER] Suggestions for using "distance" in cpptraj Hunter Brown (Thu Aug 08 2013 - 13:44:57 PDT)
- Re: [AMBER] Suggestions for using "distance" in cpptraj Daniel Roe (Thu Aug 08 2013 - 14:29:24 PDT)
[AMBER] Chi torsions Steven M. Graham (Thu Aug 08 2013 - 13:57:43 PDT)
- Re: [AMBER] Chi torsions Ilyas Yildirim (Thu Aug 08 2013 - 14:11:50 PDT)
- Re: [AMBER] Chi torsions Jiri Sponer (Fri Aug 09 2013 - 02:06:43 PDT)
  - Re: [AMBER] Chi torsions Petr Jurecka (Fri Aug 09 2013 - 07:20:25 PDT)
    - Re: [AMBER] Chi torsions Steven M. Graham (Fri Aug 09 2013 - 12:49:02 PDT)
[AMBER] Magnesium charges using leaprc.ff99SB - metals move away Mallipeddi, Premalatha (Thu Aug 08 2013 - 14:06:42 PDT)
- Re: [AMBER] Magnesium charges using leaprc.ff99SB - metals move away David A Case (Thu Aug 08 2013 - 18:20:54 PDT)
- Re: [AMBER] Magnesium charges using leaprc.ff99SB - metals move away Mallipeddi, Premalatha (Fri Aug 09 2013 - 08:40:52 PDT)
  - Re: [AMBER] Magnesium charges using leaprc.ff99SB - metals move away David A Case (Fri Aug 09 2013 - 09:36:06 PDT)
- Re: [AMBER] Magnesium charges using leaprc.ff99SB - metals move away Mallipeddi, Premalatha (Mon Aug 12 2013 - 08:40:41 PDT)
  - Re: [AMBER] Magnesium charges using leaprc.ff99SB - metals move away David A Case (Mon Aug 12 2013 - 09:10:56 PDT)
    - Re: [AMBER] Magnesium charges using leaprc.ff99SB - metals move away Sorensen, Jesper (Mon Aug 12 2013 - 14:50:28 PDT)
- Re: [AMBER] Magnesium charges using leaprc.ff99SB - metals move away Mallipeddi, Premalatha (Wed Aug 14 2013 - 08:38:18 PDT)
Re: [AMBER] Suggestions for using Hunter Brown (Thu Aug 08 2013 - 14:44:30 PDT)
[AMBER] cpptraj: noxcol example, order of cmdline args Jan-Philip Gehrcke (Fri Aug 09 2013 - 03:05:56 PDT)
- Re: [AMBER] cpptraj: noxcol example, order of cmdline args Jan-Philip Gehrcke (Fri Aug 09 2013 - 03:44:30 PDT)
  - Re: [AMBER] cpptraj: noxcol example, order of cmdline args Daniel Roe (Fri Aug 09 2013 - 08:01:17 PDT)
    - Re: [AMBER] cpptraj: noxcol example, order of cmdline args Jan-Philip Gehrcke (Fri Aug 09 2013 - 08:16:17 PDT)
    - Re: [AMBER] cpptraj: noxcol example, order of cmdline args Daniel Roe (Fri Aug 09 2013 - 08:26:46 PDT)
- Re: [AMBER] cpptraj: noxcol example, order of cmdline args Daniel Roe (Fri Aug 09 2013 - 07:44:19 PDT)
[AMBER] Energy terms in mdout (Etot, EKtot, ...) José Guilherme Vilhena Albuquerque d'Orey (Fri Aug 09 2013 - 03:23:00 PDT)
- Re: [AMBER] Energy terms in mdout (Etot, EKtot, ...) Brian Radak (Fri Aug 09 2013 - 07:20:15 PDT)
  - Re: [AMBER] Energy terms in mdout (Etot, EKtot, ...) Jason Swails (Fri Aug 09 2013 - 14:15:15 PDT)
    - Re: [AMBER] Energy terms in mdout (Etot, EKtot, ...) José Guilherme Vilhena Albuquerque d'Orey (Sat Aug 10 2013 - 06:46:40 PDT)
[AMBER] ERROR in rms: KRMS_ reported Number of atoms less than 2 Sanjib Paul (Fri Aug 09 2013 - 04:39:58 PDT)
- Re: [AMBER] ERROR in rms: KRMS_ reported Number of atoms less than 2 David A Case (Fri Aug 09 2013 - 06:44:00 PDT)
[AMBER] TI with ifsc==2 (reposted) Kepa K. Burusco (Fri Aug 09 2013 - 08:01:06 PDT)
- Re: [AMBER] TI with ifsc==2 (reposted) David A Case (Fri Aug 09 2013 - 08:30:57 PDT)
  - Re: [AMBER] TI with ifsc==2 (reposted) steinbrt.rci.rutgers.edu (Fri Aug 09 2013 - 08:46:44 PDT)
    - Re: [AMBER] TI with ifsc==2 (reposted) Kepa K. Burusco (Fri Aug 09 2013 - 11:45:24 PDT)
[AMBER] MMPBSA selection error Hunter Brown (Fri Aug 09 2013 - 09:29:13 PDT)
- Re: [AMBER] MMPBSA selection error Bill Miller III (Fri Aug 09 2013 - 11:56:14 PDT)
  - Re: [AMBER] MMPBSA selection error Roitberg,Adrian E (Fri Aug 09 2013 - 12:02:21 PDT)
- Re: [AMBER] MMPBSA selection error Hunter Brown (Fri Aug 09 2013 - 12:33:05 PDT)
  - Re: [AMBER] MMPBSA selection error Jason Swails (Fri Aug 09 2013 - 14:26:12 PDT)
[AMBER] Puzzles about SCEE and SCNB? egeh00 (Fri Aug 09 2013 - 14:54:33 PDT)
- Re: [AMBER] Puzzles about SCEE and SCNB? Jason Swails (Fri Aug 09 2013 - 15:35:46 PDT)
[AMBER] Residue decomposition: not possible with PB ? Jagur Lambix (Fri Aug 09 2013 - 16:04:06 PDT)
[AMBER] ptraj is not splitting LES trajectory James W. Snyder, Jr. (Fri Aug 09 2013 - 17:02:21 PDT)
- Re: [AMBER] ptraj is not splitting LES trajectory Daniel Roe (Fri Aug 09 2013 - 17:59:12 PDT)
  - Re: [AMBER] ptraj is not splitting LES trajectory James W. Snyder, Jr. (Fri Aug 09 2013 - 18:09:17 PDT)
    - Re: [AMBER] ptraj is not splitting LES trajectory Daniel Roe (Sun Aug 11 2013 - 11:20:19 PDT)
    - Re: [AMBER] ptraj is not splitting LES trajectory James W. Snyder, Jr. (Sun Aug 11 2013 - 12:43:47 PDT)
[AMBER] Reading velocity trajectories Ganesh Kamath (Fri Aug 09 2013 - 18:05:53 PDT)
- Re: [AMBER] Reading velocity trajectories Daniel Roe (Sat Aug 10 2013 - 22:19:37 PDT)
[AMBER] Fw: output nuclear force and hessian John Travers (Sat Aug 10 2013 - 15:02:26 PDT)
- Re: [AMBER] Fw: output nuclear force and hessian David A Case (Sat Aug 10 2013 - 18:55:07 PDT)
[AMBER] 2nd Announcement AMBER workshop in Brazil (Oct 7-11 2013) pre-registration open Ross Walker (Sun Aug 11 2013 - 15:35:49 PDT)
- Re: [AMBER] 2nd Announcement AMBER workshop in Brazil (Oct 7-11 2013) pre-registration open Angelica Parente (Sun Aug 11 2013 - 22:23:27 PDT)
  - Re: [AMBER] 2nd Announcement AMBER workshop in Brazil (Oct 7-11 2013) pre-registration open Ross Walker (Sun Aug 11 2013 - 23:01:01 PDT)
- Re: [AMBER] 2nd Announcement AMBER workshop in Brazil (Oct 7-11 2013) pre-registration open psu4.uic.edu (Wed Aug 21 2013 - 19:38:08 PDT)
  - Re: [AMBER] 2nd Announcement AMBER workshop in Brazil (Oct 7-11 2013) pre-registration open Ross Walker (Wed Aug 21 2013 - 19:46:51 PDT)
[AMBER] antechamber returns different results from same molecule structures Hiromasa WATANABE (Sun Aug 11 2013 - 19:36:06 PDT)
- Re: [AMBER] antechamber returns different results from same molecule structures David A Case (Mon Aug 12 2013 - 04:51:17 PDT)
  - Re: [AMBER] antechamber returns different results from same molecule structures Hiromasa WATANABE (Mon Aug 12 2013 - 22:33:16 PDT)
- Re: [AMBER] antechamber returns different results from same molecule structures Hiromasa WATANABE (Sun Aug 18 2013 - 17:45:04 PDT)
  - Re: [AMBER] antechamber returns different results from same molecule structures Hiromasa WATANABE (Mon Aug 26 2013 - 20:14:46 PDT)
    - Re: [AMBER] antechamber returns different results from same molecule structures David A Case (Tue Aug 27 2013 - 06:00:04 PDT)
    - Re: [AMBER] antechamber returns different results from same molecule structures Hiromasa WATANABE (Tue Aug 27 2013 - 17:53:54 PDT)
- Re: [AMBER] antechamber returns different results from same molecule structures Hiromasa WATANABE (Tue Aug 27 2013 - 17:57:28 PDT)
[AMBER] Difference between lower case and upper case in atomtype? egeh00 (Sun Aug 11 2013 - 21:36:43 PDT)
- Re: [AMBER] Difference between lower case and upper case in atomtype? Ross Walker (Sun Aug 11 2013 - 21:33:27 PDT)
[AMBER] Problem with Amber tutorial A.15 Moacyr Comar (Mon Aug 12 2013 - 06:32:46 PDT)
- Re: [AMBER] Problem with Amber tutorial A.15 David A Case (Mon Aug 12 2013 - 07:04:13 PDT)
  - Re: [AMBER] Problem with Amber tutorial A.15 Moacyr Comar (Wed Aug 14 2013 - 08:59:31 PDT)
    - Re: [AMBER] Problem with Amber tutorial A.15 Daniel Roe (Wed Aug 14 2013 - 09:05:58 PDT)
    - Re: [AMBER] Problem with Amber tutorial A.15 Jason Swails (Wed Aug 14 2013 - 09:17:33 PDT)
    - Re: [AMBER] Problem with Amber tutorial A.15 Moacyr Comar (Wed Aug 14 2013 - 11:08:36 PDT)
    - Re: [AMBER] Problem with Amber tutorial A.15 Daniel Roe (Wed Aug 14 2013 - 15:25:23 PDT)
[AMBER] Possibility of mixing OPLS and Glycam? egeh00 (Mon Aug 12 2013 - 21:15:38 PDT)
- Re: [AMBER] Possibility of mixing OPLS and Glycam? Lachele Foley (Tue Aug 13 2013 - 09:04:23 PDT)
[AMBER] which energy terms are included in TI DV/DL and why it fluctuate so wildly? psu4.uic.edu (Mon Aug 12 2013 - 21:26:23 PDT)
- Re: [AMBER] which energy terms are included in TI DV/DL and why it fluctuate so wildly? steinbrt.rci.rutgers.edu (Tue Aug 13 2013 - 01:35:50 PDT)
[AMBER] Question regarding H-bond calculation anu chandra (Mon Aug 12 2013 - 23:37:54 PDT)
- Re: [AMBER] Question regarding H-bond calculation Kshatresh Dutta Dubey (Tue Aug 13 2013 - 01:05:01 PDT)
- Re: [AMBER] Question regarding H-bond calculation Daniel Roe (Tue Aug 13 2013 - 07:24:24 PDT)
  - Re: [AMBER] Question regarding H-bond calculation anu chandra (Tue Aug 13 2013 - 23:21:48 PDT)
[AMBER] Modelling the folding of the c-terminus of a protein Aylin Sahin (Mon Aug 12 2013 - 23:47:33 PDT)
- Re: [AMBER] Modelling the folding of the c-terminus of a protein David A Case (Wed Aug 14 2013 - 04:39:55 PDT)
[AMBER] Forcefield for lipopeptides Prasanna Venkatesh D (Tue Aug 13 2013 - 00:24:04 PDT)
[AMBER] Problem in energy decomposition Kshatresh Dutta Dubey (Tue Aug 13 2013 - 07:45:31 PDT)
- Re: [AMBER] Problem in energy decomposition Bill Miller III (Tue Aug 13 2013 - 20:57:54 PDT)
[AMBER] simulation of single strand DNA Collins Nganou (Tue Aug 13 2013 - 09:19:19 PDT)
- Re: [AMBER] simulation of single strand DNA David A Case (Tue Aug 13 2013 - 11:59:31 PDT)
[AMBER] Add potential energy term William Cantara (Tue Aug 13 2013 - 09:24:45 PDT)
- Re: [AMBER] Add potential energy term David A Case (Wed Aug 14 2013 - 04:38:04 PDT)
[AMBER] Problem with xLeap : Segmentation fault (core dumped) HIMANSHU JOSHI (Wed Aug 14 2013 - 00:55:54 PDT)
- Re: [AMBER] Problem with xLeap : Segmentation fault (core dumped) Hailin Huang (Wed Aug 14 2013 - 01:21:42 PDT)
- Re: [AMBER] Problem with xLeap : Segmentation fault (core dumped) David A Case (Wed Aug 14 2013 - 06:06:57 PDT)
  - Re: [AMBER] Problem with xLeap : Segmentation fault (core dumped) HIMANSHU JOSHI (Wed Aug 14 2013 - 09:28:15 PDT)
[AMBER] MMPBSA doubt Mary Varughese (Wed Aug 14 2013 - 03:20:47 PDT)
- Re: [AMBER] MMPBSA doubt Jason Swails (Wed Aug 14 2013 - 09:11:23 PDT)
  - Re: [AMBER] MMPBSA doubt Mary Varughese (Thu Aug 15 2013 - 21:09:43 PDT)
    - Re: [AMBER] MMPBSA doubt Jason Swails (Fri Aug 16 2013 - 15:33:26 PDT)
    - Re: [AMBER] MMPBSA doubt Mary Varughese (Fri Aug 16 2013 - 20:34:24 PDT)
[AMBER] MTKPP/MCPB charge is not integer Jia Xu (Wed Aug 14 2013 - 11:25:58 PDT)
[AMBER] Thank you - Re: Magnesium charges using leaprc.ff99SB - metals move away Mallipeddi, Premalatha (Wed Aug 14 2013 - 15:41:45 PDT)
[AMBER] RMSD calculation followed by superimposition moitrayee.mbu.iisc.ernet.in (Wed Aug 14 2013 - 19:34:39 PDT)
- Re: [AMBER] RMSD calculation followed by superimposition Jan-Philip Gehrcke (Thu Aug 15 2013 - 01:27:07 PDT)
  - Re: [AMBER] RMSD calculation followed by superimposition moitrayee.mbu.iisc.ernet.in (Wed Aug 21 2013 - 18:25:19 PDT)
    - Re: [AMBER] RMSD calculation followed by superimposition Daniel Roe (Wed Aug 21 2013 - 21:22:05 PDT)
    - Re: [AMBER] RMSD calculation followed by superimposition moitrayee.mbu.iisc.ernet.in (Wed Aug 21 2013 - 21:53:15 PDT)
    - Re: [AMBER] RMSD calculation followed by superimposition Daniel Roe (Wed Aug 21 2013 - 21:59:09 PDT)
    - Re: [AMBER] RMSD calculation followed by superimposition Daniel Roe (Wed Aug 21 2013 - 22:02:37 PDT)
    - Re: [AMBER] RMSD calculation followed by superimposition moitrayee.mbu.iisc.ernet.in (Wed Aug 21 2013 - 23:42:09 PDT)
    - Re: [AMBER] RMSD calculation followed by superimposition moitrayee.mbu.iisc.ernet.in (Thu Aug 22 2013 - 19:25:52 PDT)
    - Re: [AMBER] RMSD calculation followed by superimposition Daniel Roe (Fri Aug 23 2013 - 08:30:51 PDT)
    - Re: [AMBER] RMSD calculation followed by superimposition moitrayee.mbu.iisc.ernet.in (Wed Aug 21 2013 - 22:01:43 PDT)
- Re: [AMBER] RMSD calculation followed by superimposition Bill Ross (Wed Aug 21 2013 - 22:04:00 PDT)
  - Re: [AMBER] RMSD calculation followed by superimposition moitrayee.mbu.iisc.ernet.in (Wed Aug 21 2013 - 23:42:35 PDT)
[AMBER] Cterm and Nterm caps moitrayee.mbu.iisc.ernet.in (Wed Aug 14 2013 - 23:17:12 PDT)
- Re: [AMBER] Cterm and Nterm caps David A Case (Thu Aug 15 2013 - 06:16:14 PDT)
[AMBER] Hbond alaysis in CPPTRAJ anu chandra (Thu Aug 15 2013 - 00:10:18 PDT)
- Re: [AMBER] Hbond alaysis in CPPTRAJ Daniel Roe (Thu Aug 15 2013 - 07:37:52 PDT)
[AMBER] CUDA_VISIBLE_DEVICES and real instance IDs Meij, Henk (Thu Aug 15 2013 - 11:47:39 PDT)
- Re: [AMBER] CUDA_VISIBLE_DEVICES and real instance IDs Jan-Philip Gehrcke (Thu Aug 15 2013 - 12:21:09 PDT)
  - Re: [AMBER] CUDA_VISIBLE_DEVICES and real instance IDs Ross Walker (Thu Aug 15 2013 - 13:50:48 PDT)
[AMBER] Box info not found Rejwan (Thu Aug 15 2013 - 13:17:22 PDT)
- Re: [AMBER] Box info not found David A Case (Thu Aug 15 2013 - 18:03:48 PDT)
[AMBER] PARALLEL PERFORMANCE OF AMBER12 Uday Midya (Thu Aug 15 2013 - 21:53:16 PDT)
- Re: [AMBER] PARALLEL PERFORMANCE OF AMBER12 Ross Walker (Thu Aug 15 2013 - 22:33:05 PDT)
- Re: [AMBER] PARALLEL PERFORMANCE OF AMBER12 Uday Midya (Fri Aug 16 2013 - 05:40:25 PDT)
  - Re: [AMBER] PARALLEL PERFORMANCE OF AMBER12 Ross Walker (Fri Aug 16 2013 - 09:52:53 PDT)
[AMBER] Often, Amber BMT doesn't finish properly with Malti-GPGPU. (pmemd.cuda.MPI problem) Nakashima, Yoshihisa (Fri Aug 16 2013 - 01:16:24 PDT)
[AMBER] no CMAP information written out by chamber ymei (Fri Aug 16 2013 - 10:47:53 PDT)
- Re: [AMBER] no CMAP information written out by chamber ymei (Fri Aug 16 2013 - 16:31:27 PDT)
[AMBER] Tutorial for specified SCEE and SCNB for different atom pairs? egeh00 (Fri Aug 16 2013 - 21:31:58 PDT)
- Re: [AMBER] Tutorial for specified SCEE and SCNB for different atom pairs? Ross Walker (Fri Aug 16 2013 - 21:12:39 PDT)
  - Re: [AMBER] Tutorial for specified SCEE and SCNB for different atom pairs? Ross Walker (Fri Aug 16 2013 - 21:25:15 PDT)
[AMBER] Partial Charges in AMBE force field BERGY (Fri Aug 16 2013 - 23:07:53 PDT)
- Re: [AMBER] Partial Charges in AMBE force field FyD (Sun Aug 18 2013 - 08:29:35 PDT)
[AMBER] problem with ambertools test Majid Taghdir (Sat Aug 17 2013 - 05:22:01 PDT)
- Re: [AMBER] problem with ambertools test Jason Swails (Sun Aug 18 2013 - 18:07:31 PDT)
- Re: [AMBER] problem with ambertools test David A. Case (Thu Aug 22 2013 - 19:06:54 PDT)
[AMBER] Error using Antechamber onetwo (Sat Aug 17 2013 - 07:33:26 PDT)
- Re: [AMBER] Error using Antechamber David A Case (Mon Aug 19 2013 - 06:12:09 PDT)
  - Re: [AMBER] Error using Antechamber onetwo (Mon Aug 19 2013 - 21:06:24 PDT)
[AMBER] Error: Bad topology file. Sum of ATOMS_PER_MOLECULE does not equal NATOM. Thomas Evangelidis (Sun Aug 18 2013 - 16:17:50 PDT)
- Re: [AMBER] Error: Bad topology file. Sum of ATOMS_PER_MOLECULE does not equal NATOM. Jason Swails (Sun Aug 18 2013 - 18:03:58 PDT)
  - Re: [AMBER] Error: Bad topology file. Sum of ATOMS_PER_MOLECULE does not equal NATOM. Thomas Evangelidis (Mon Aug 19 2013 - 05:35:36 PDT)
    - Re: [AMBER] Error: Bad topology file. Sum of ATOMS_PER_MOLECULE does not equal NATOM. Jason Swails (Mon Aug 19 2013 - 10:02:28 PDT)
    - Re: [AMBER] Error: Bad topology file. Sum of ATOMS_PER_MOLECULE does not equal NATOM. Daniel Roe (Mon Aug 19 2013 - 12:00:09 PDT)
[AMBER] Two questions in one... Julio Dominguez (Sun Aug 18 2013 - 20:43:52 PDT)
- Re: [AMBER] Two questions in one... Karl N. Kirschner (Mon Aug 19 2013 - 00:27:40 PDT)
- Re: [AMBER] Two questions in one... Daniel Roe (Mon Aug 19 2013 - 13:13:02 PDT)
[AMBER] Query regarding membrane-peptide simulation Aditya Padhi (Mon Aug 19 2013 - 03:28:16 PDT)
- Re: [AMBER] Query regarding membrane-peptide simulation Ross Walker (Mon Aug 19 2013 - 08:41:59 PDT)
[AMBER] problems with calculation continuing Карлов Дмитрий (Mon Aug 19 2013 - 09:11:52 PDT)
- Re: [AMBER] problems with calculation continuing Brian Radak (Mon Aug 19 2013 - 09:47:31 PDT)
[AMBER] AMBER minimization job Rejwan (Mon Aug 19 2013 - 12:06:17 PDT)
- Re: [AMBER] AMBER minimization job David A Case (Mon Aug 19 2013 - 12:31:42 PDT)
  - Re: [AMBER] AMBER minimization job Rejwan (Mon Aug 19 2013 - 13:00:39 PDT)
    - Re: [AMBER] AMBER minimization job Ross Walker (Mon Aug 19 2013 - 13:18:55 PDT)
    - Re: [AMBER] AMBER minimization job Rejwan (Mon Aug 19 2013 - 13:58:41 PDT)
    - Re: [AMBER] AMBER minimization job Ross Walker (Mon Aug 19 2013 - 14:05:55 PDT)
- Re: [AMBER] AMBER minimization job Ross Walker (Mon Aug 19 2013 - 12:32:13 PDT)
[AMBER] Question about different SCEE&SCNB to specified atom pairs. egeh00 (Mon Aug 19 2013 - 21:45:21 PDT)
- Re: [AMBER] Question about different SCEE&SCNB to specified atom pairs. Ross Walker (Mon Aug 19 2013 - 21:19:25 PDT)
  - Re: [AMBER] Question about different SCEE&SCNB to specified atom pairs. egeh00 (Tue Aug 20 2013 - 09:16:39 PDT)
    - Re: [AMBER] Question about different SCEE&SCNB to specified atom pairs. Jason Swails (Tue Aug 20 2013 - 08:34:41 PDT)
[AMBER] SASA fatahiya (Tue Aug 20 2013 - 01:27:57 PDT)
- Re: [AMBER] SASA Jason Swails (Tue Aug 20 2013 - 06:12:30 PDT)
[AMBER] PLP-L Histidinal Phosphate parameters madhu malar (Tue Aug 20 2013 - 02:20:35 PDT)
- Re: [AMBER] PLP-L Histidinal Phosphate parameters monica.imtech.res.in (Tue Aug 20 2013 - 20:53:41 PDT)
- Re: [AMBER] PLP-L Histidinal Phosphate parameters FyD (Wed Aug 21 2013 - 03:50:15 PDT)
[AMBER] ERROR: max pairlist cutoff must be less than unit cell max sphere radius WuYunjian (Tue Aug 20 2013 - 09:13:56 PDT)
- Re: [AMBER] ERROR: max pairlist cutoff must be less than unit cell max sphere radius Moacyr Comar (Tue Aug 20 2013 - 10:35:23 PDT)
- Re: [AMBER] ERROR: max pairlist cutoff must be less than unit cell max sphere radius Ross Walker (Tue Aug 20 2013 - 11:30:51 PDT)
  - Re: [AMBER] ERROR: max pairlist cutoff must be less than unit cell max sphere radius WuYunjian (Wed Aug 21 2013 - 07:33:06 PDT)
Re: [AMBER] mmpbsa nonpolar contribution using stability wmsmith.uci.edu (Tue Aug 20 2013 - 09:19:47 PDT)
[AMBER] Huge improper dihedral fitting coefficient. X Sun (Tue Aug 20 2013 - 12:47:29 PDT)
- Re: [AMBER] Huge improper dihedral fitting coefficient. Karl N. Kirschner (Wed Aug 21 2013 - 00:48:15 PDT)
[AMBER] Geometricmean sigma in AMBER? X Sun (Tue Aug 20 2013 - 12:51:02 PDT)
[AMBER] Cpu busy looping? Jake Smith (Tue Aug 20 2013 - 12:32:01 PDT)
- Re: [AMBER] Cpu busy looping? Jason Swails (Tue Aug 20 2013 - 13:00:56 PDT)
- Re: [AMBER] Cpu busy looping? Ross Walker (Tue Aug 20 2013 - 13:07:45 PDT)
- Re: [AMBER] Cpu busy looping? Jake Smith (Tue Aug 20 2013 - 15:19:13 PDT)
  - Re: [AMBER] Cpu busy looping? Ross Walker (Tue Aug 20 2013 - 15:35:13 PDT)
    - Re: [AMBER] Cpu busy looping? Jake Smith (Tue Aug 20 2013 - 17:38:37 PDT)
    - Re: [AMBER] Cpu busy looping? Jan-Philip Gehrcke (Wed Aug 21 2013 - 04:56:34 PDT)
[AMBER] Input files for Targeted MD using Amber Sunny Chun (Tue Aug 20 2013 - 14:39:09 PDT)
- Re: [AMBER] Input files for Targeted MD using Amber David A Case (Tue Aug 20 2013 - 18:59:29 PDT)
[AMBER] how to check for errors in a topology library file created with saveOff Jose Borreguero (Tue Aug 20 2013 - 16:05:19 PDT)
- Re: [AMBER] how to check for errors in a topology library file created with saveOff Daniel Roe (Tue Aug 20 2013 - 20:22:50 PDT)
  - Re: [AMBER] how to check for errors in a topology library file created with saveOff Jose Borreguero (Wed Aug 21 2013 - 07:33:07 PDT)
- Re: [AMBER] how to check for errors in a topology library file created with saveOff FyD (Wed Aug 21 2013 - 03:54:15 PDT)
  - Re: [AMBER] how to check for errors in a topology library file created with saveOff Jose Borreguero (Wed Aug 21 2013 - 08:03:03 PDT)
    - Re: [AMBER] how to check for errors in a topology library file created with saveOff Jason Swails (Wed Aug 21 2013 - 08:29:43 PDT)
    - Re: [AMBER] how to check for errors in a topology library file created with saveOff Jose Borreguero (Wed Aug 21 2013 - 10:34:39 PDT)
    - Re: [AMBER] how to check for errors in a topology library file created with saveOff Daniel Roe (Wed Aug 21 2013 - 12:01:45 PDT)
    - Re: [AMBER] how to check for errors in a topology library file created with saveOff FyD (Thu Aug 22 2013 - 05:09:01 PDT)
Re: [AMBER] AMBER Digest, Vol 587, Issue 1 Julio Dominguez (Tue Aug 20 2013 - 19:12:18 PDT)
- Re: [AMBER] AMBER Digest, Vol 587, Issue 1 Karl N. Kirschner (Wed Aug 21 2013 - 00:49:49 PDT)
- Re: [AMBER] AMBER Digest, Vol 587, Issue 1 Julio Dominguez (Thu Aug 22 2013 - 19:43:17 PDT)
  - [AMBER] Phosphate (-1 and -2) parameterization and Wolf2Pack Karl N. Kirschner (Fri Aug 23 2013 - 06:32:23 PDT)
    - Re: [AMBER] Phosphate (-1 and -2) parameterization and Wolf2Pack Karl N. Kirschner (Fri Aug 23 2013 - 06:39:23 PDT)
[AMBER] nmr upper_bond criteria sangita.imtech.res.in (Tue Aug 20 2013 - 22:27:53 PDT)
- Re: [AMBER] nmr upper_bond criteria Jason Swails (Wed Aug 21 2013 - 05:03:48 PDT)
  - Re: [AMBER] nmr upper_bond criteria sangita.imtech.res.in (Thu Aug 22 2013 - 04:57:35 PDT)
    - Re: [AMBER] nmr upper_bond criteria David A. Case (Thu Aug 22 2013 - 19:12:52 PDT)
[AMBER] PMEMD Performance issue on AMD cluster Sangeetha B (Tue Aug 20 2013 - 22:29:58 PDT)
- Re: [AMBER] PMEMD Performance issue on AMD cluster Jason Swails (Wed Aug 21 2013 - 05:20:14 PDT)
- Re: [AMBER] PMEMD Performance issue on AMD cluster Jan-Philip Gehrcke (Wed Aug 21 2013 - 05:40:41 PDT)
[AMBER] PLP- L Histidinal Phosphate parameters madhu malar (Tue Aug 20 2013 - 23:50:30 PDT)
- Re: [AMBER] PLP- L Histidinal Phosphate parameters David A Case (Wed Aug 21 2013 - 06:14:00 PDT)
[AMBER] How to insert a drug near center of lipids in the membrane? Atila Petrosian (Wed Aug 21 2013 - 01:45:04 PDT)
[AMBER] SLipids force field with AMBER12 Thomas Evangelidis (Wed Aug 21 2013 - 06:41:24 PDT)
[AMBER] DMPC GAFF lipid membrane is freezing at 303 K. Subbarao Kanchi (Wed Aug 21 2013 - 06:55:27 PDT)
- Re: [AMBER] DMPC GAFF lipid membrane is freezing at 303 K. Ross Walker (Wed Aug 21 2013 - 10:42:25 PDT)
  - Re: [AMBER] DMPC GAFF lipid membrane is freezing at 303 K. Dickson, Callum (Thu Aug 22 2013 - 11:13:07 PDT)
- Re: [AMBER] DMPC GAFF lipid membrane is freezing at 303 K. Subbarao Kanchi (Sat Sep 21 2013 - 00:16:02 PDT)
[AMBER] rk2 and rk3 values in NMR restraints Bharatham, Nagakumar (Wed Aug 21 2013 - 14:31:17 PDT)
[AMBER] Gaussian charges in xleap HIMANSHU JOSHI (Wed Aug 21 2013 - 22:14:43 PDT)
- Re: [AMBER] Gaussian charges in xleap FyD (Thu Aug 22 2013 - 05:19:58 PDT)
  - Re: [AMBER] Gaussian charges in xleap HIMANSHU JOSHI (Fri Aug 23 2013 - 04:20:00 PDT)
    - Re: [AMBER] Gaussian charges in xleap David Case (Fri Aug 23 2013 - 07:22:45 PDT)
    - Re: [AMBER] Gaussian charges in xleap FyD (Fri Aug 23 2013 - 08:47:51 PDT)
    - Re: [AMBER] Gaussian charges in xleap HIMANSHU JOSHI (Mon Aug 26 2013 - 22:04:34 PDT)
    - Re: [AMBER] Gaussian charges in xleap HIMANSHU JOSHI (Tue Aug 27 2013 - 05:57:49 PDT)
    - Re: [AMBER] Gaussian charges in xleap David A Case (Tue Aug 27 2013 - 06:24:06 PDT)
    - Re: [AMBER] Gaussian charges in xleap FyD (Thu Aug 29 2013 - 01:51:43 PDT)
[AMBER] Density saturates at 0.97 after NPT Sourav Purohit (Thu Aug 22 2013 - 10:59:58 PDT)
- Re: [AMBER] Density saturates at 0.97 after NPT Ross Walker (Thu Aug 22 2013 - 11:35:38 PDT)
  - Re: [AMBER] Density saturates at 0.97 after NPT Sourav Purohit (Thu Aug 22 2013 - 11:50:50 PDT)
[AMBER] not able to build prmtop and inpcrd with glycam lara lara (Thu Aug 22 2013 - 11:29:23 PDT)
- Re: [AMBER] not able to build prmtop and inpcrd with glycam Lachele Foley (Thu Aug 22 2013 - 11:56:24 PDT)
[AMBER] not able to build prmtop and inpcrd with glycam lara lara (Thu Aug 22 2013 - 11:58:09 PDT)
- Re: [AMBER] not able to build prmtop and inpcrd with glycam Lachele Foley (Thu Aug 22 2013 - 12:03:42 PDT)
  - Re: [AMBER] not able to build prmtop and inpcrd with glycam lara lara (Thu Aug 22 2013 - 12:07:56 PDT)
    - Re: [AMBER] not able to build prmtop and inpcrd with glycam Lachele Foley (Thu Aug 22 2013 - 12:10:41 PDT)
[AMBER] mdout2pymbar.pl Use of uninitialized value in array element psu4.uic.edu (Thu Aug 22 2013 - 15:45:09 PDT)
[AMBER] σ in Amber and OPLS-AA? X Sun (Thu Aug 22 2013 - 16:53:27 PDT)
- Re: [AMBER] σ in Amber and OPLS-AA? Jason Swails (Thu Aug 22 2013 - 19:16:52 PDT)
[AMBER] Number of contacts anu chandra (Fri Aug 23 2013 - 05:44:09 PDT)
- Re: [AMBER] Number of contacts Daniel Roe (Fri Aug 23 2013 - 08:35:30 PDT)
  - Re: [AMBER] Number of contacts anu chandra (Sun Aug 25 2013 - 23:20:34 PDT)
    - Re: [AMBER] Number of contacts Daniel Roe (Tue Aug 27 2013 - 09:57:24 PDT)
[AMBER] RED: charge equivalencing with intramolecular charge constraints? Brian Radak (Fri Aug 23 2013 - 08:08:21 PDT)
- Re: [AMBER] RED: charge equivalencing with intramolecular charge constraints? FyD (Fri Aug 23 2013 - 09:16:05 PDT)
  - Re: [AMBER] RED: charge equivalencing with intramolecular charge constraints? Brian Radak (Fri Aug 23 2013 - 09:21:29 PDT)
    - Re: [AMBER] RED: charge equivalencing with intramolecular charge constraints? FyD (Sat Aug 24 2013 - 08:45:24 PDT)
[AMBER] Confused about Hydrogen bond and non-bond interaction. X Sun (Fri Aug 23 2013 - 16:50:14 PDT)
[AMBER] total charge of the ligand Mary Varughese (Fri Aug 23 2013 - 23:20:53 PDT)
[AMBER] "All hydrogens" in antechamber Barnett, James W. (Sat Aug 24 2013 - 08:44:18 PDT)
- Re: [AMBER] "All hydrogens" in antechamber David Case (Sat Aug 24 2013 - 16:17:50 PDT)
  - Re: [AMBER] "All hydrogens" in antechamber Barnett, James W. (Mon Aug 26 2013 - 06:42:55 PDT)
[AMBER] leap question Wang Chern Hoe (Dr) (Sun Aug 25 2013 - 00:56:49 PDT)
- Re: [AMBER] leap question Raman Parkesh (Sun Aug 25 2013 - 02:40:10 PDT)
[AMBER] MMPBSA: AttributeError: 'list' object has no attribute 'stdev' Xioling Chuang (Sun Aug 25 2013 - 19:23:51 PDT)
- Re: [AMBER] MMPBSA: AttributeError: 'list' object has no attribute 'stdev' Jason Swails (Sun Aug 25 2013 - 20:32:24 PDT)
  - Re: [AMBER] MMPBSA: AttributeError: 'list' object has no attribute 'stdev' Xioling Chuang (Mon Aug 26 2013 - 00:37:49 PDT)
[AMBER] Large difference in GB and PB values of binding free energy anu chandra (Sun Aug 25 2013 - 23:04:01 PDT)
- Re: [AMBER] Large difference in GB and PB values of binding free energy Kshatresh Dutta Dubey (Sun Aug 25 2013 - 23:43:31 PDT)
[AMBER] Problematic structure after minimization on GPU Jan-Philip Gehrcke (Mon Aug 26 2013 - 04:52:27 PDT)
- Re: [AMBER] Problematic structure after minimization on GPU Ross Walker (Mon Aug 26 2013 - 07:18:59 PDT)
  - Re: [AMBER] Problematic structure after minimization on GPU Jan-Philip Gehrcke (Mon Aug 26 2013 - 07:48:52 PDT)
    - Re: [AMBER] Problematic structure after minimization on GPU Daniel Roe (Mon Aug 26 2013 - 08:15:31 PDT)
    - Re: [AMBER] Problematic structure after minimization on GPU Ross Walker (Mon Aug 26 2013 - 08:15:02 PDT)
    - Re: [AMBER] Problematic structure after minimization on GPU Scott Le Grand (Mon Aug 26 2013 - 10:05:01 PDT)
    - Re: [AMBER] Problematic structure after minimization on GPU Jan-Philip Gehrcke (Tue Aug 27 2013 - 02:13:11 PDT)
[AMBER] Problematic structure after minimization on GPU Jan-Philip Gehrcke (Mon Aug 26 2013 - 07:25:00 PDT)
[AMBER] About SNB range in statistics command in cpptraj arundhati dutta (Mon Aug 26 2013 - 07:58:22 PDT)
- Re: [AMBER] About SNB range in statistics command in cpptraj Daniel Roe (Mon Aug 26 2013 - 08:51:09 PDT)
  - Re: [AMBER] About SNB range in statistics command in cpptraj arundhati dutta (Mon Aug 26 2013 - 09:20:23 PDT)
[AMBER] Pucker Command In Cpptraj arundhati dutta (Mon Aug 26 2013 - 09:31:29 PDT)
- Re: [AMBER] Pucker Command In Cpptraj Hamed S. Hayatshahi (Mon Aug 26 2013 - 11:55:54 PDT)
- Re: [AMBER] Pucker Command In Cpptraj Daniel Roe (Mon Aug 26 2013 - 12:42:36 PDT)
  - Re: [AMBER] Pucker Command In Cpptraj arundhati dutta (Mon Aug 26 2013 - 12:46:30 PDT)
    - Re: [AMBER] Pucker Command In Cpptraj mish (Mon Aug 26 2013 - 13:14:15 PDT)
    - Re: [AMBER] Pucker Command In Cpptraj Daniel Roe (Mon Aug 26 2013 - 14:06:59 PDT)
[AMBER] glycam_in Xleap lara lara (Mon Aug 26 2013 - 10:22:40 PDT)
- Re: [AMBER] glycam_in Xleap Lachele Foley (Mon Aug 26 2013 - 12:17:58 PDT)
[AMBER] HW-HW for TIP3P? X Sun (Mon Aug 26 2013 - 14:37:10 PDT)
- Re: [AMBER] HW-HW for TIP3P? Brian Radak (Mon Aug 26 2013 - 13:55:18 PDT)
[AMBER] NAB transformation matrix conventions (rotation about x-axis is left handed?) Chaitanya Murthy (Mon Aug 26 2013 - 19:15:52 PDT)
[AMBER] AmberTools13 test: possible FAILURE Xioling Chuang (Mon Aug 26 2013 - 19:29:59 PDT)
- Re: [AMBER] AmberTools13 test: possible FAILURE Xioling Chuang (Mon Aug 26 2013 - 21:15:27 PDT)
[AMBER] Phosphate (-1 and -2) parameterization and Wolf2Pack Julio Dominguez (Mon Aug 26 2013 - 20:06:40 PDT)
[AMBER] Different SASA values in MM/PBSA and MM/GBSA? Mu Xia (Mon Aug 26 2013 - 20:46:29 PDT)
- Re: [AMBER] Different SASA values in MM/PBSA and MM/GBSA? Jason Swails (Tue Aug 27 2013 - 05:38:40 PDT)
  - Re: [AMBER] Different SASA values in MM/PBSA and MM/GBSA? Mu Xia (Tue Aug 27 2013 - 06:32:46 PDT)
[AMBER] mpi4py building error during AmberTools 13 install sunyeping (Tue Aug 27 2013 - 02:56:58 PDT)
- Re: [AMBER] mpi4py building error during AmberTools 13 install Jason Swails (Wed Aug 28 2013 - 07:56:41 PDT)
- Re: [AMBER] mpi4py building error during AmberTools 13 install sunyeping (Sat Sep 14 2013 - 10:18:23 PDT)
Re: [AMBER] AMBER: antechamber error : Cannot open CONNECT.TPL, exit glbala87.imtech.res.in (Tue Aug 27 2013 - 04:10:45 PDT)
- Re: [AMBER] AMBER: antechamber error : Cannot open CONNECT.TPL, exit David A Case (Tue Aug 27 2013 - 06:26:37 PDT)
[AMBER] antechamber bond type error glbala87.imtech.res.in (Tue Aug 27 2013 - 05:10:06 PDT)
- Re: [AMBER] antechamber bond type error David A Case (Tue Aug 27 2013 - 06:29:34 PDT)
[AMBER] Hydroxylysine Parameters Chris Forman (Tue Aug 27 2013 - 08:23:24 PDT)
- Re: [AMBER] Hydroxylysine Parameters David A Case (Tue Aug 27 2013 - 09:11:12 PDT)
  - Re: [AMBER] Hydroxylysine Parameters Chris Forman (Thu Aug 29 2013 - 05:33:45 PDT)
- Re: [AMBER] Hydroxylysine Parameters FyD (Thu Aug 29 2013 - 01:47:49 PDT)
  - Re: [AMBER] Hydroxylysine Parameters Chris Forman (Thu Aug 29 2013 - 05:36:19 PDT)
[AMBER] mmP(G)BSA correlation time psu4.uic.edu (Tue Aug 27 2013 - 16:57:16 PDT)
- Re: [AMBER] mmP(G)BSA correlation time Jason Swails (Wed Aug 28 2013 - 04:59:54 PDT)
  - Re: [AMBER] mmP(G)BSA correlation time psu4.uic.edu (Thu Aug 29 2013 - 20:19:56 PDT)
    - Re: [AMBER] mmP(G)BSA correlation time Jan-Philip Gehrcke (Fri Aug 30 2013 - 00:56:49 PDT)
    - Re: [AMBER] mmP(G)BSA correlation time psu4.uic.edu (Fri Aug 30 2013 - 08:30:58 PDT)
    - Re: [AMBER] mmP(G)BSA correlation time Jason Swails (Fri Aug 30 2013 - 10:29:17 PDT)
    - Re: [AMBER] mmP(G)BSA correlation time psu4.uic.edu (Thu Sep 05 2013 - 12:13:16 PDT)
    - Re: [AMBER] mmP(G)BSA correlation time Adrian Roitberg (Thu Sep 05 2013 - 12:38:12 PDT)
[AMBER] problems with disulfide bond creation sunyeping (Tue Aug 27 2013 - 18:42:43 PDT)
- Re: [AMBER] problems with disulfide bond creation kurisaki (Tue Aug 27 2013 - 18:51:00 PDT)
- Re: [AMBER] problems with disulfide bond creation case (Tue Aug 27 2013 - 19:03:27 PDT)
[AMBER] setting up a covalently bonded ligand to enzyme with tleap Mahmoud Soliman (Wed Aug 28 2013 - 00:46:30 PDT)
- Re: [AMBER] setting up a covalently bonded ligand to enzyme with tleap David A Case (Wed Aug 28 2013 - 05:33:18 PDT)
[AMBER] Fwd: gargi borgohai (Wed Aug 28 2013 - 05:55:21 PDT)
- Re: [AMBER] Fwd: Jason Swails (Wed Aug 28 2013 - 06:00:27 PDT)
[AMBER] 答复: problems with disulfide bond creation sunyeping (Wed Aug 28 2013 - 17:09:07 PDT)
[AMBER] Simmetry problem Rodrigo Salazar (Wed Aug 28 2013 - 18:51:20 PDT)
- Re: [AMBER] Simmetry problem Jason Swails (Thu Aug 29 2013 - 04:54:44 PDT)
[AMBER] problem with making a movie Aylin Sahin (Wed Aug 28 2013 - 23:04:27 PDT)
- Re: [AMBER] problem with making a movie MOHD HOMAIDUR RAHMAN (Thu Aug 29 2013 - 00:18:14 PDT)
[AMBER] Question regarding principal component analysis Puspita Halder (Wed Aug 28 2013 - 23:26:00 PDT)
[AMBER] Simulating two hosts together marawan hussain (Thu Aug 29 2013 - 03:30:35 PDT)
[AMBER] frcmod.ionsjc_*** file and water model Seongeun Yang (Thu Aug 29 2013 - 04:52:08 PDT)
- Re: [AMBER] frcmod.ionsjc_*** file and water model Brian Radak (Thu Aug 29 2013 - 06:48:36 PDT)
[AMBER] ARG as a titratable residue for constant pH simulations Nicole Ippolito (Thu Aug 29 2013 - 07:31:23 PDT)
- Re: [AMBER] ARG as a titratable residue for constant pH simulations Adrian Roitberg (Thu Aug 29 2013 - 07:35:50 PDT)
[AMBER] xLeap : Undo option HIMANSHU JOSHI (Thu Aug 29 2013 - 11:10:22 PDT)
[AMBER] amber11 installation error Carlos Romero (Thu Aug 29 2013 - 11:59:23 PDT)
- Re: [AMBER] amber11 installation error Jason Swails (Thu Aug 29 2013 - 12:29:44 PDT)
  - Re: [AMBER] amber11 installation error Carlos Romero (Thu Aug 29 2013 - 12:42:20 PDT)
    - Re: [AMBER] amber11 installation error Carlos Romero (Thu Aug 29 2013 - 12:47:58 PDT)
[AMBER] Constant ph with replica exchange Fabrício Bracht (Thu Aug 29 2013 - 14:00:39 PDT)
- Re: [AMBER] Constant ph with replica exchange Jason Swails (Thu Aug 29 2013 - 14:37:03 PDT)
[AMBER] question about amber installation Atila Petrosian (Fri Aug 30 2013 - 05:22:17 PDT)
- Re: [AMBER] question about amber installation Jason Swails (Fri Aug 30 2013 - 05:35:59 PDT)
[AMBER] TI input files in A9 tutorial and Amber12 manual Hamed S. Hayatshahi (Fri Aug 30 2013 - 11:14:17 PDT)
- Re: [AMBER] TI input files in A9 tutorial and Amber12 manual David A Case (Fri Aug 30 2013 - 12:45:01 PDT)
  - Re: [AMBER] TI input files in A9 tutorial and Amber12 manual Hamed S. Hayatshahi (Wed Sep 04 2013 - 15:02:32 PDT)
    - Re: [AMBER] TI input files in A9 tutorial and Amber12 manual case (Wed Sep 04 2013 - 18:05:53 PDT)
    - Re: [AMBER] TI input files in A9 tutorial and Amber12 manual steinbrt.rci.rutgers.edu (Thu Sep 05 2013 - 00:27:48 PDT)
    - Re: [AMBER] TI input files in A9 tutorial and Amber12 manual Hamed S. Hayatshahi (Fri Sep 06 2013 - 10:52:32 PDT)
    - Re: [AMBER] TI input files in A9 tutorial and Amber12 manual steinbrt.rci.rutgers.edu (Sun Sep 08 2013 - 09:56:16 PDT)
    - Re: [AMBER] TI input files in A9 tutorial and Amber12 manual Hamed S. Hayatshahi (Tue Sep 10 2013 - 12:35:54 PDT)
    - Re: [AMBER] TI input files in A9 tutorial and Amber12 manual Hamed S. Hayatshahi (Tue Sep 10 2013 - 16:52:56 PDT)
[AMBER] Cannot download Amber12, bugfix.18.bz2 peter.stauffert.boehringer-ingelheim.com (Fri Aug 30 2013 - 12:15:02 PDT)
- Re: [AMBER] Cannot download Amber12, bugfix.18.bz2 Jason Swails (Fri Aug 30 2013 - 20:03:40 PDT)
[AMBER] cpptraj removes velocities upon imaging Eric Berquist (Fri Aug 30 2013 - 12:47:03 PDT)
- Re: [AMBER] cpptraj removes velocities upon imaging Daniel Roe (Sat Aug 31 2013 - 04:14:32 PDT)
  - Re: [AMBER] cpptraj removes velocities upon imaging Eric Berquist (Sat Aug 31 2013 - 07:34:38 PDT)
    - Re: [AMBER] cpptraj removes velocities upon imaging Daniel Roe (Sat Aug 31 2013 - 14:44:51 PDT)
    - Re: [AMBER] cpptraj removes velocities upon imaging Daniel Roe (Thu Sep 05 2013 - 10:45:23 PDT)
[AMBER] CHAMBER: dihe energy in c36 vs c22 Jun Feng (Fri Aug 30 2013 - 14:15:49 PDT)
- Re: [AMBER] CHAMBER: dihe energy in c36 vs c22 Ross Walker (Fri Aug 30 2013 - 15:03:47 PDT)
  - Re: [AMBER] CHAMBER: dihe energy in c36 vs c22 Jun Feng (Tue Sep 03 2013 - 14:32:19 PDT)
[AMBER] CHAMBER VDW energy in PBC Jun Feng (Fri Aug 30 2013 - 14:55:30 PDT)
- Re: [AMBER] CHAMBER VDW energy in PBC Ross Walker (Fri Aug 30 2013 - 15:10:18 PDT)
  - Re: [AMBER] CHAMBER VDW energy in PBC Jun Feng (Tue Sep 03 2013 - 10:54:03 PDT)
    - Re: [AMBER] CHAMBER VDW energy in PBC Ross Walker (Tue Sep 03 2013 - 11:05:41 PDT)
[AMBER] problem installin amber9 in ubuntu 12.04 Rodrigo Salazar (Sat Aug 31 2013 - 20:00:32 PDT)
- Re: [AMBER] problem installin amber9 in ubuntu 12.04 Jason Swails (Sat Aug 31 2013 - 22:01:54 PDT)
[AMBER] Constraint failure in RATTLE algorithm occurs during NAMD simulation with amber force field sunyeping (Sun Sep 01 2013 - 07:31:07 PDT)
- Re: [AMBER] Constraint failure in RATTLE algorithm occurs during NAMD simulation with amber force field case (Sun Sep 01 2013 - 09:35:43 PDT)
[AMBER] compile ambertools with -nofftw3 sunyeping (Sun Sep 01 2013 - 20:37:44 PDT)
- Re: [AMBER] compile ambertools with -nofftw3 case (Mon Sep 02 2013 - 06:27:16 PDT)
[AMBER] deltaG binding obtained from AmberTools 12 and 13 are different Xioling Chuang (Mon Sep 02 2013 - 06:18:58 PDT)
- Re: [AMBER] deltaG binding obtained from AmberTools 12 and 13 are different Jason Swails (Mon Sep 02 2013 - 09:12:23 PDT)
  - Re: [AMBER] deltaG binding obtained from AmberTools 12 and 13 are different Xioling Chuang (Tue Sep 03 2013 - 02:04:50 PDT)
    - Re: [AMBER] deltaG binding obtained from AmberTools 12 and 13 are different Jason Swails (Tue Sep 03 2013 - 05:05:26 PDT)
    - Re: [AMBER] deltaG binding obtained from AmberTools 12 and 13 are different Xioling Chuang (Tue Sep 03 2013 - 06:44:35 PDT)
    - Re: [AMBER] deltaG binding obtained from AmberTools 12 and 13 are different Jason Swails (Tue Sep 03 2013 - 08:06:20 PDT)
    - Re: [AMBER] deltaG binding obtained from AmberTools 12 and 13 are different Xioling Chuang (Tue Sep 03 2013 - 19:06:50 PDT)
    - Re: [AMBER] deltaG binding obtained from AmberTools 12 and 13 are different Adrian Roitberg (Tue Sep 03 2013 - 19:09:13 PDT)
[AMBER] Problem passing cuda tests. Szymon Murawski (Mon Sep 02 2013 - 06:36:06 PDT)
- Re: [AMBER] Problem passing cuda tests. Ross Walker (Mon Sep 02 2013 - 10:25:59 PDT)
[AMBER] Distance restraint using com keyword Sun (Mon Sep 02 2013 - 07:27:50 PDT)
[AMBER] issues with MMPBSA and explicit waters Alfredo Quevedo (Mon Sep 02 2013 - 07:39:19 PDT)
- Re: [AMBER] issues with MMPBSA and explicit waters Jason Swails (Mon Sep 02 2013 - 09:08:57 PDT)
  - Re: [AMBER] issues with MMPBSA and explicit waters Alfredo Quevedo (Tue Sep 03 2013 - 07:09:05 PDT)
    - Re: [AMBER] issues with MMPBSA and explicit waters Jason Swails (Tue Sep 03 2013 - 07:59:44 PDT)
    - Re: [AMBER] issues with MMPBSA and explicit waters Jason Swails (Tue Sep 03 2013 - 11:12:15 PDT)
    - Re: [AMBER] issues with MMPBSA and explicit waters Alfredo Quevedo (Tue Sep 03 2013 - 11:17:28 PDT)
[AMBER] best Generalized Born solvation model for intrinsically disordered peptides Thomas Evangelidis (Mon Sep 02 2013 - 13:48:12 PDT)
- Re: [AMBER] best Generalized Born solvation model for intrinsically disordered peptides Carlos Simmerling (Tue Sep 03 2013 - 04:56:09 PDT)
  - Re: [AMBER] best Generalized Born solvation model for intrinsically disordered peptides Thomas Evangelidis (Tue Sep 03 2013 - 05:03:19 PDT)
    - Re: [AMBER] best Generalized Born solvation model for intrinsically disordered peptides Hai Nguyen (Tue Sep 03 2013 - 12:48:04 PDT)
    - Re: [AMBER] best Generalized Born solvation model for intrinsically disordered peptides Hai Nguyen (Tue Sep 03 2013 - 12:49:58 PDT)
    - Re: [AMBER] best Generalized Born solvation model for intrinsically disordered peptides Thomas Evangelidis (Tue Sep 03 2013 - 13:35:24 PDT)
    - Re: [AMBER] best Generalized Born solvation model for intrinsically disordered peptides Hai Nguyen (Tue Sep 03 2013 - 13:55:21 PDT)
    - Re: [AMBER] best Generalized Born solvation model for intrinsically disordered peptides Daniel Roe (Thu Sep 05 2013 - 07:48:46 PDT)
    - Re: [AMBER] best Generalized Born solvation model for intrinsically disordered peptides Thomas Evangelidis (Thu Sep 05 2013 - 08:36:58 PDT)
    - Re: [AMBER] best Generalized Born solvation model for intrinsically disordered peptides Carlos Simmerling (Thu Sep 05 2013 - 09:01:49 PDT)
[AMBER] Minimization terminates with unknown reason Xiaoquan Sun (Mon Sep 02 2013 - 13:59:18 PDT)
- Re: [AMBER] Minimization terminates with unknown reason Jason Swails (Mon Sep 02 2013 - 14:44:58 PDT)
[AMBER] RED-vIII.52 problems Julio Dominguez (Mon Sep 02 2013 - 18:58:41 PDT)
- Re: [AMBER] RED-vIII.52 problems FyD (Tue Sep 03 2013 - 00:41:47 PDT)
[AMBER] some questions about PCA qiao xue (Mon Sep 02 2013 - 19:55:35 PDT)
- Re: [AMBER] some questions about PCA Daniel Roe (Thu Sep 05 2013 - 09:25:46 PDT)
[AMBER] Sander aborted during the minimization of the whole system. X Sun (Mon Sep 02 2013 - 21:42:17 PDT)
- Re: [AMBER] Sander aborted during the minimization of the whole system. David A Case (Tue Sep 03 2013 - 04:38:40 PDT)
[AMBER] problem in installing AmberTools13 Vijay Manickam Achari (Mon Sep 02 2013 - 23:36:50 PDT)
- Re: [AMBER] problem in installing AmberTools13 Jan-Philip Gehrcke (Tue Sep 03 2013 - 01:12:07 PDT)
  - Re: [AMBER] problem in installing AmberTools13 Vijay Manickam Achari (Tue Sep 03 2013 - 01:21:09 PDT)
    - Re: [AMBER] problem in installing AmberTools13 Jason Swails (Tue Sep 03 2013 - 05:11:17 PDT)
    - Re: [AMBER] problem in installing AmberTools13 Vijay Manickam Achari (Tue Sep 03 2013 - 08:11:23 PDT)
[AMBER] NaN problem with GTX680 JAVAD MAHMOUDZADEH (Tue Sep 03 2013 - 00:12:05 PDT)
- Re: [AMBER] NaN problem with GTX680 David A Case (Tue Sep 03 2013 - 04:43:14 PDT)
  - Re: [AMBER] NaN problem with GTX680 Jason Swails (Tue Sep 03 2013 - 04:50:49 PDT)
[AMBER] updates for amber12 bugfix18 & 19 fail Vijay Manickam Achari (Tue Sep 03 2013 - 01:08:15 PDT)
- Re: [AMBER] updates for amber12 bugfix18 & 19 fail Jason Swails (Tue Sep 03 2013 - 05:18:57 PDT)
- Re: [AMBER] updates for amber12 bugfix18 & 19 fail peter.stauffert.boehringer-ingelheim.com (Tue Sep 03 2013 - 05:48:18 PDT)
  - Re: [AMBER] updates for amber12 bugfix18 & 19 fail Jason Swails (Tue Sep 03 2013 - 06:04:32 PDT)
[AMBER] NaN problem with GTX680 JAVAD MAHMOUDZADEH (Tue Sep 03 2013 - 05:18:20 PDT)
- Re: [AMBER] NaN problem with GTX680 Jason Swails (Tue Sep 03 2013 - 05:21:35 PDT)
[AMBER] missing loop Fabian Glaser (Tue Sep 03 2013 - 07:05:53 PDT)
- Re: [AMBER] missing loop Sergio R Aragon (Tue Sep 03 2013 - 14:58:16 PDT)
- Re: [AMBER] missing loop Wong, Sergio E. (Wed Sep 04 2013 - 09:08:38 PDT)
  - Re: [AMBER] missing loop Vlad Cojocaru (Wed Sep 04 2013 - 09:31:21 PDT)
    - Re: [AMBER] missing loop Bill Ross (Mon Sep 09 2013 - 20:54:17 PDT)
[AMBER] problem in running AMBER12 in GPU Sanjib Paul (Tue Sep 03 2013 - 08:01:24 PDT)
- Re: [AMBER] problem in running AMBER12 in GPU Jason Swails (Tue Sep 03 2013 - 09:08:44 PDT)
  - Re: [AMBER] problem in running AMBER12 in GPU Sanjib Paul (Wed Sep 04 2013 - 07:21:56 PDT)
    - Re: [AMBER] problem in running AMBER12 in GPU Jason Swails (Wed Sep 04 2013 - 07:56:20 PDT)
    - Re: [AMBER] problem in running AMBER12 in GPU Sanjib Paul (Wed Sep 11 2013 - 06:28:26 PDT)
    - Re: [AMBER] problem in running AMBER12 in GPU Jan-Philip Gehrcke (Wed Sep 11 2013 - 06:38:26 PDT)
    - Re: [AMBER] problem in running AMBER12 in GPU Sanjib Paul (Wed Sep 11 2013 - 07:04:22 PDT)
    - Re: [AMBER] problem in running AMBER12 in GPU Jan-Philip Gehrcke (Wed Sep 11 2013 - 07:13:07 PDT)
    - Re: [AMBER] problem in running AMBER12 in GPU Sanjib Paul (Wed Sep 11 2013 - 07:14:01 PDT)
    - Re: [AMBER] problem in running AMBER12 in GPU Jan-Philip Gehrcke (Wed Sep 11 2013 - 07:32:06 PDT)
    - Re: [AMBER] problem in running AMBER12 in GPU David A Case (Wed Sep 11 2013 - 07:31:28 PDT)
[AMBER] problem with antechamber in ambertools 13 Rodrigo Salazar (Tue Sep 03 2013 - 18:01:44 PDT)
- Re: [AMBER] problem with antechamber in ambertools 13 FyD (Wed Sep 04 2013 - 05:35:41 PDT)
  - Re: [AMBER] problem with antechamber in ambertools 13 Rodrigo Salazar (Wed Sep 04 2013 - 07:59:22 PDT)
    - Re: [AMBER] problem with antechamber in ambertools 13 FyD (Wed Sep 04 2013 - 08:33:55 PDT)
- Re: [AMBER] problem with antechamber in ambertools 13 David A Case (Wed Sep 04 2013 - 05:41:51 PDT)
Re: [AMBER] RED-vIII52 problems... Julio Dominguez (Wed Sep 04 2013 - 07:06:22 PDT)
- Re: [AMBER] RED-vIII52 problems... FyD (Wed Sep 04 2013 - 07:47:46 PDT)
[AMBER] Amber Install Lindsay Morrison (Wed Sep 04 2013 - 10:45:27 PDT)
- Re: [AMBER] Amber Install Jason Swails (Wed Sep 04 2013 - 12:04:36 PDT)
[AMBER] Force constant in umbrella sampling Fabrício Bracht (Wed Sep 04 2013 - 13:02:59 PDT)
- Re: [AMBER] Force constant in umbrella sampling Adrian Roitberg (Wed Sep 04 2013 - 13:08:47 PDT)
[AMBER] Convert DCD to MDCRD, lose PBC. X Sun (Wed Sep 04 2013 - 14:54:18 PDT)
- Re: [AMBER] Convert DCD to MDCRD, lose PBC. Thomas Cheatham (Wed Sep 04 2013 - 13:57:56 PDT)
  - Re: [AMBER] Convert DCD to MDCRD, lose PBC. X Sun (Wed Sep 04 2013 - 17:22:21 PDT)
    - Re: [AMBER] Convert DCD to MDCRD, lose PBC. Jason Swails (Wed Sep 04 2013 - 16:33:15 PDT)
- Re: [AMBER] Convert DCD to MDCRD, lose PBC. Bill Ross (Wed Sep 04 2013 - 17:57:44 PDT)
[AMBER] Questions about TI calculation yuandandan05 (Wed Sep 04 2013 - 18:24:30 PDT)
- Re: [AMBER] Questions about TI calculation steinbrt.rci.rutgers.edu (Thu Sep 05 2013 - 00:16:51 PDT)
[AMBER] make error in installing sander.APBS Asmita Gupta (Wed Sep 04 2013 - 23:35:34 PDT)
- Re: [AMBER] make error in installing sander.APBS Daniel Roe (Thu Sep 05 2013 - 07:21:47 PDT)
  - Re: [AMBER] make error in installing sander.APBS Asmita Gupta (Thu Sep 05 2013 - 08:27:47 PDT)
    - Re: [AMBER] make error in installing sander.APBS Jason Swails (Thu Sep 05 2013 - 08:57:23 PDT)
    - Re: [AMBER] make error in installing sander.APBS Asmita Gupta (Thu Sep 05 2013 - 10:25:29 PDT)
    - Re: [AMBER] make error in installing sander.APBS Daniel Roe (Thu Sep 05 2013 - 10:33:26 PDT)
    - Re: [AMBER] make error in installing sander.APBS Asmita Gupta (Thu Sep 05 2013 - 10:40:34 PDT)
    - Re: [AMBER] make error in installing sander.APBS Robert Konecny (Thu Sep 05 2013 - 10:48:22 PDT)
    - Re: [AMBER] make error in installing sander.APBS Daniel Roe (Thu Sep 05 2013 - 10:50:46 PDT)
    - Re: [AMBER] make error in installing sander.APBS Asmita Gupta (Thu Sep 05 2013 - 11:22:42 PDT)
    - Re: [AMBER] make error in installing sander.APBS Robert Konecny (Thu Sep 05 2013 - 11:33:11 PDT)
[AMBER] hbond in Ambertools Neha Gandhi (Thu Sep 05 2013 - 00:31:47 PDT)
- Re: [AMBER] hbond in Ambertools Shesh Nath (Thu Sep 05 2013 - 02:09:36 PDT)
- Re: [AMBER] hbond in Ambertools Daniel Roe (Thu Sep 05 2013 - 07:20:21 PDT)
[AMBER] Average Conformations from trajectory Covington, Cody Lance (Thu Sep 05 2013 - 06:33:39 PDT)
- Re: [AMBER] Average Conformations from trajectory Daniel Roe (Thu Sep 05 2013 - 07:11:06 PDT)
[AMBER] Question about MMPBSA.py rohitarora10.gmail.com (Thu Sep 05 2013 - 08:16:51 PDT)
[AMBER] update_amber script confuses Amber versions Robyn Ayscue (Thu Sep 05 2013 - 12:30:40 PDT)
- Re: [AMBER] update_amber script confuses Amber versions Jason Swails (Thu Sep 05 2013 - 12:58:07 PDT)
  - Re: [AMBER] update_amber script confuses Amber versions David A Case (Thu Sep 05 2013 - 13:25:15 PDT)
- Re: [AMBER] update_amber script confuses Amber versions Robyn Ayscue (Fri Sep 06 2013 - 14:12:09 PDT)
[AMBER] MMPBSA.py EPB problem with idecomp=3 Ryan Pavlovicz (Thu Sep 05 2013 - 16:17:02 PDT)
- Re: [AMBER] MMPBSA.py EPB problem with idecomp=3 Ray Luo, Ph.D. (Fri Sep 06 2013 - 11:14:37 PDT)
[AMBER] For format correction after generating solvent file. Krati Sharma (Thu Sep 05 2013 - 20:25:19 PDT)
- Re: [AMBER] For format correction after generating solvent file. Daniel Roe (Thu Sep 05 2013 - 20:34:58 PDT)
  - Re: [AMBER] For format correction after generating solvent file. Krati Sharma (Fri Sep 06 2013 - 03:35:04 PDT)
- Re: [AMBER] For format correction after generating solvent file. David A Case (Fri Sep 06 2013 - 05:23:34 PDT)
  - Re: [AMBER] For format correction after generating solvent file. Krati Sharma (Fri Sep 06 2013 - 07:33:05 PDT)
    - Re: [AMBER] For format correction after generating solvent file. Daniel Roe (Fri Sep 06 2013 - 07:59:30 PDT)
    - Re: [AMBER] For format correction after generating solvent file. David A Case (Fri Sep 06 2013 - 08:17:14 PDT)
[AMBER] How to get the prmtop and inpcrd files of melamine in Amber? 张明焜 (Thu Sep 05 2013 - 20:52:05 PDT)
- Re: [AMBER] How to get the prmtop and inpcrd files of melamine in Amber? Jason Swails (Fri Sep 06 2013 - 04:58:06 PDT)
- Re: [AMBER] How to get the prmtop and inpcrd files of melamine in Amber? David A Case (Fri Sep 06 2013 - 05:31:05 PDT)
  - Re: [AMBER] How to get the prmtop and inpcrd files of melamine in Amber? 张明焜 (Mon Sep 09 2013 - 00:20:08 PDT)
    - Re: [AMBER] How to get the prmtop and inpcrd files of melamine in Amber? Jason Swails (Mon Sep 09 2013 - 06:22:29 PDT)
[AMBER] to generate a Glycine(NH2-CH2-COOH) complete prmtop file? 张明焜 (Fri Sep 06 2013 - 02:23:27 PDT)
- Re: [AMBER] to generate a Glycine(NH2-CH2-COOH) complete prmtop file? FyD (Fri Sep 06 2013 - 02:51:20 PDT)
  - Re: [AMBER] to generate a Glycine(NH2-CH2-COOH) complete prmtop file? 张明焜 (Sun Sep 08 2013 - 23:54:38 PDT)
    - Re: [AMBER] to generate a Glycine(NH2-CH2-COOH) complete prmtop file? Sangita Kachhap (Mon Sep 09 2013 - 00:17:34 PDT)
    - Re: [AMBER] to generate a Glycine(NH2-CH2-COOH) complete prmtop file? FyD (Mon Sep 09 2013 - 03:05:19 PDT)
[AMBER] REMD jobs crashing repeatedly on GPUs Joe Passman (Fri Sep 06 2013 - 10:57:42 PDT)
- Re: [AMBER] REMD jobs crashing repeatedly on GPUs Christina Bergonzo (Fri Sep 06 2013 - 11:07:59 PDT)
  - Re: [AMBER] REMD jobs crashing repeatedly on GPUs Scott Le Grand (Fri Sep 06 2013 - 11:13:27 PDT)
    - Re: [AMBER] REMD jobs crashing repeatedly on GPUs Scott Brozell (Fri Feb 27 2015 - 09:33:03 PST)
    - Re: [AMBER] REMD jobs crashing repeatedly on GPUs Christina Bergonzo (Wed Mar 04 2015 - 10:19:35 PST)
[AMBER] Xleap Lindsay Morrison (Fri Sep 06 2013 - 11:37:05 PDT)
- Re: [AMBER] Xleap sribone.fcq.unc.edu.ar (Fri Sep 06 2013 - 12:07:58 PDT)
- Re: [AMBER] Xleap arundhati dutta (Fri Sep 06 2013 - 12:09:33 PDT)
[AMBER] Are Amber able to analyze the feature of certain bond? X Sun (Fri Sep 06 2013 - 20:09:24 PDT)
[AMBER] hbond analysis Mary Varughese (Sat Sep 07 2013 - 00:19:29 PDT)
- Re: [AMBER] hbond analysis Daniel Roe (Sat Sep 07 2013 - 09:16:29 PDT)
  - Re: [AMBER] hbond analysis Mary Varughese (Sun Sep 08 2013 - 19:22:56 PDT)
    - Re: [AMBER] hbond analysis Jason Swails (Mon Sep 09 2013 - 05:15:21 PDT)
    - Re: [AMBER] hbond analysis Mary Varughese (Mon Sep 09 2013 - 07:26:32 PDT)
[AMBER] Unable to run decomposition analysis using mmpbsa.py of amber12 Manikanthan Bhavaraju (Sat Sep 07 2013 - 16:21:48 PDT)
- Re: [AMBER] Unable to run decomposition analysis using mmpbsa.py of amber12 Jason Swails (Sat Sep 07 2013 - 20:32:40 PDT)
[AMBER] GTX 600/700 benchmarks Parker de Waal (Sun Sep 08 2013 - 17:03:35 PDT)
[AMBER] Question about QM/MM? X Sun (Sun Sep 08 2013 - 22:39:26 PDT)
- Re: [AMBER] Question about QM/MM? Jason Swails (Mon Sep 09 2013 - 05:23:01 PDT)
[AMBER] Issue with intramolecular pairwise-residue energy decomposition rohitarora10.gmail.com (Mon Sep 09 2013 - 00:33:23 PDT)
- Re: [AMBER] Issue with intramolecular pairwise-residue energy decomposition Jason Swails (Mon Sep 09 2013 - 06:32:45 PDT)
[AMBER] Forcefield for lipopeptides Prasanna Venkatesh D (Mon Sep 09 2013 - 01:28:00 PDT)
- Re: [AMBER] Forcefield for lipopeptides Jason Swails (Mon Sep 09 2013 - 07:24:39 PDT)
  - Re: [AMBER] Forcefield for lipopeptides Prasanna Venkatesh D (Mon Sep 09 2013 - 20:10:59 PDT)
[AMBER] rmsd and hbond Mary Varughese (Mon Sep 09 2013 - 02:20:39 PDT)
- Re: [AMBER] rmsd and hbond Daniel Roe (Mon Sep 09 2013 - 09:54:21 PDT)
  - Re: [AMBER] rmsd and hbond Mary Varughese (Mon Sep 09 2013 - 17:48:00 PDT)
[AMBER] Different MMPBSA results in the use of sander and pmemd 千语千寻 (Mon Sep 09 2013 - 02:49:35 PDT)
- Re: [AMBER] Different MMPBSA results in the use of sander and pmemd Jason Swails (Mon Sep 09 2013 - 09:39:36 PDT)
  - Re: [AMBER] Different MMPBSA results in the use of sander and pmemd wmsmith.uci.edu (Mon Sep 09 2013 - 10:13:26 PDT)
    - Re: [AMBER] Different MMPBSA results in the use of sander and pmemd 千语千寻 (Mon Sep 09 2013 - 20:44:58 PDT)
    - Re: [AMBER] Different MMPBSA results in the use of sander and pmemd Jason Swails (Tue Sep 10 2013 - 04:06:06 PDT)
    - Re: [AMBER] Different MMPBSA results in the use of sander and pmemd 千语千寻 (Wed Sep 11 2013 - 06:16:23 PDT)
    - Re: [AMBER] Different MMPBSA results in the use of sander and pmemd Jason Swails (Wed Sep 11 2013 - 06:34:21 PDT)
[AMBER] question of analyze matrix command of ptraj 张明焜 (Mon Sep 09 2013 - 03:52:12 PDT)
- Re: [AMBER] question of analyze matrix command of ptraj Daniel Roe (Mon Sep 09 2013 - 09:41:53 PDT)
[AMBER] Amber Tools cpptraj woes Geoffrey Gray (Mon Sep 09 2013 - 11:42:54 PDT)
- Re: [AMBER] Amber Tools cpptraj woes Daniel Roe (Mon Sep 09 2013 - 12:27:21 PDT)
  - Re: [AMBER] Amber Tools cpptraj woes Geoffrey Gray (Mon Sep 09 2013 - 12:59:21 PDT)
    - Re: [AMBER] Amber Tools cpptraj woes Jason Swails (Mon Sep 09 2013 - 14:17:44 PDT)
    - Re: [AMBER] Amber Tools cpptraj woes Geoffrey Gray (Mon Sep 09 2013 - 20:32:21 PDT)
[AMBER] Unable to run decomposition analysis using mmpbsa.py of amber12 Manikanthan Bhavaraju (Mon Sep 09 2013 - 12:27:12 PDT)
- Re: [AMBER] Unable to run decomposition analysis using mmpbsa.py of amber12 Jason Swails (Mon Sep 09 2013 - 12:49:42 PDT)
[AMBER] Error with NVT and NPT Simulations Kyler L Cook (Mon Sep 09 2013 - 13:28:29 PDT)
- Re: [AMBER] Error with NVT and NPT Simulations Daniel Roe (Mon Sep 09 2013 - 14:42:24 PDT)
  - Re: [AMBER] Error with NVT and NPT Simulations Brian Radak (Tue Sep 10 2013 - 10:25:33 PDT)
    - Re: [AMBER] Error with NVT and NPT Simulations Ross Walker (Tue Sep 10 2013 - 10:41:44 PDT)
    - Re: [AMBER] Error with NVT and NPT Simulations Jason Swails (Tue Sep 10 2013 - 10:46:46 PDT)
[AMBER] atomic fluctuation and average structure Mary Varughese (Mon Sep 09 2013 - 17:55:54 PDT)
- Re: [AMBER] atomic fluctuation and average structure Daniel Roe (Mon Sep 09 2013 - 19:48:43 PDT)
  - Re: [AMBER] atomic fluctuation and average structure Mary Varughese (Mon Sep 09 2013 - 21:03:28 PDT)
[AMBER] Difference between atomtype s6 and sy? X Sun (Mon Sep 09 2013 - 21:16:08 PDT)
- Re: [AMBER] Difference between atomtype s6 and sy? David A Case (Fri Sep 13 2013 - 06:06:05 PDT)
[AMBER] REMD exchange Francesco Pietra (Tue Sep 10 2013 - 00:38:25 PDT)
- Re: [AMBER] REMD exchange Jason Swails (Tue Sep 10 2013 - 04:12:36 PDT)
  - Re: [AMBER] REMD exchange Francesco Pietra (Tue Sep 10 2013 - 06:45:20 PDT)
    - Re: [AMBER] REMD exchange Niel Henriksen (Tue Sep 10 2013 - 07:01:10 PDT)
    - Re: [AMBER] REMD exchange Carlos Simmerling (Tue Sep 10 2013 - 07:13:58 PDT)
    - Re: [AMBER] REMD exchange Francesco Pietra (Tue Sep 10 2013 - 08:22:53 PDT)
    - Re: [AMBER] REMD exchange Hai Nguyen (Tue Sep 10 2013 - 14:59:58 PDT)
    - Re: [AMBER] REMD exchange Francesco Pietra (Tue Sep 10 2013 - 23:03:16 PDT)
    - Re: [AMBER] REMD exchange Hai Nguyen (Wed Sep 11 2013 - 01:34:27 PDT)
    - Re: [AMBER] REMD exchange Jason Swails (Wed Sep 11 2013 - 04:58:01 PDT)
    - Re: [AMBER] REMD exchange Francesco Pietra (Wed Sep 11 2013 - 06:40:53 PDT)
    - Re: [AMBER] REMD exchange Carlos Simmerling (Wed Sep 11 2013 - 03:55:39 PDT)
    - Re: [AMBER] REMD exchange Ross Walker (Wed Sep 11 2013 - 06:42:59 PDT)
    - Re: [AMBER] REMD exchange Francesco Pietra (Wed Sep 11 2013 - 07:09:22 PDT)
[AMBER] error in leap -- Glycam residue building lara lara (Tue Sep 10 2013 - 12:29:47 PDT)
- Re: [AMBER] error in leap -- Glycam residue building Lachele Foley (Tue Sep 10 2013 - 12:55:17 PDT)
[AMBER] Question: MM/PBSA and MM/GBSA Hiromasa WATANABE (Tue Sep 10 2013 - 22:56:06 PDT)
- Re: [AMBER] Question: MM/PBSA and MM/GBSA Wang Baifan (Wed Sep 11 2013 - 00:12:00 PDT)
- Re: [AMBER] Question: MM/PBSA and MM/GBSA Ray Luo, Ph.D. (Wed Sep 11 2013 - 06:00:46 PDT)
  - Re: [AMBER] Question: MM/PBSA and MM/GBSA Hiromasa WATANABE (Wed Sep 11 2013 - 18:06:42 PDT)
    - Re: [AMBER] Question: MM/PBSA and MM/GBSA Ray Luo, Ph.D. (Wed Sep 11 2013 - 22:06:43 PDT)
    - Re: [AMBER] Question: MM/PBSA and MM/GBSA Hiromasa WATANABE (Thu Sep 12 2013 - 19:06:36 PDT)
    - Re: [AMBER] Question: MM/PBSA and MM/GBSA Ray Luo, Ph.D. (Fri Sep 13 2013 - 11:40:35 PDT)
[AMBER] error in installing ambertools 1.5 Kumud Agarwal (Wed Sep 11 2013 - 00:08:08 PDT)
- Re: [AMBER] error in installing ambertools 1.5 David A Case (Wed Sep 11 2013 - 04:58:02 PDT)
[AMBER] Fwd: DMPC GAFF lipid membrane is freezing at 303 K. Subbarao Kanchi (Wed Sep 11 2013 - 03:23:14 PDT)
[AMBER] Path Setting arundhati dutta (Wed Sep 11 2013 - 12:27:47 PDT)
- Re: [AMBER] Path Setting Aldo Segura (Wed Sep 11 2013 - 13:07:41 PDT)
[AMBER] query reg ptraj RMSD calculation Asmita Gupta (Thu Sep 12 2013 - 06:45:18 PDT)
- Re: [AMBER] query reg ptraj RMSD calculation Daniel Roe (Thu Sep 12 2013 - 08:32:58 PDT)
  - Re: [AMBER] query reg ptraj RMSD calculation Asmita Gupta (Thu Sep 12 2013 - 08:50:56 PDT)
    - Re: [AMBER] query reg ptraj RMSD calculation Daniel Roe (Thu Sep 12 2013 - 09:12:33 PDT)
[AMBER] glycam - leap error lara lara (Thu Sep 12 2013 - 10:31:16 PDT)
- Re: [AMBER] glycam - leap error Lachele Foley (Thu Sep 12 2013 - 11:10:11 PDT)
  - Re: [AMBER] glycam - leap error Lachele Foley (Thu Sep 12 2013 - 14:44:50 PDT)
    - Re: [AMBER] glycam - leap error Karl N. Kirschner (Fri Sep 13 2013 - 07:09:45 PDT)
    - Re: [AMBER] glycam - leap error lara lara (Mon Sep 16 2013 - 07:57:58 PDT)
[AMBER] antechamber no convergence Jianhui Tian (Thu Sep 12 2013 - 12:05:18 PDT)
- Re: [AMBER] antechamber no convergence David A Case (Fri Sep 13 2013 - 06:02:45 PDT)
  - Re: [AMBER] antechamber no convergence Jianhui Tian (Fri Sep 13 2013 - 07:18:51 PDT)
    - Re: [AMBER] antechamber no convergence Jianhui Tian (Mon Sep 16 2013 - 07:06:09 PDT)
    - Re: [AMBER] antechamber no convergence case (Mon Sep 16 2013 - 07:13:55 PDT)
    - Re: [AMBER] antechamber no convergence Jianhui Tian (Mon Sep 16 2013 - 11:49:20 PDT)
    - Re: [AMBER] antechamber no convergence Jianhui Tian (Mon Sep 16 2013 - 12:47:28 PDT)
    - Re: [AMBER] antechamber no convergence FyD (Tue Sep 17 2013 - 00:11:25 PDT)
    - Re: [AMBER] antechamber no convergence Jianhui Tian (Tue Sep 17 2013 - 06:53:07 PDT)
    - Re: [AMBER] antechamber no convergence FyD (Tue Sep 17 2013 - 22:49:12 PDT)
    - Re: [AMBER] antechamber no convergence David A Case (Wed Sep 18 2013 - 04:47:07 PDT)
    - Re: [AMBER] antechamber no convergence FyD (Wed Sep 18 2013 - 22:29:47 PDT)
[AMBER] Antechamber Jasim, Mahmood (Student) (Fri Sep 13 2013 - 06:15:48 PDT)
- Re: [AMBER] Antechamber David A Case (Fri Sep 13 2013 - 07:30:10 PDT)
  - Re: [AMBER] Antechamber Jasim, Mahmood (Student) (Fri Sep 13 2013 - 07:50:42 PDT)
    - Re: [AMBER] Antechamber David A Case (Fri Sep 13 2013 - 09:17:24 PDT)
    - Re: [AMBER] Antechamber Jasim, Mahmood (Student) (Mon Sep 16 2013 - 02:34:50 PDT)
    - Re: [AMBER] Antechamber case (Mon Sep 16 2013 - 04:45:33 PDT)
    - Re: [AMBER] Antechamber Jasim, Mahmood (Student) (Tue Sep 17 2013 - 03:58:56 PDT)
    - Re: [AMBER] Antechamber David A Case (Tue Sep 17 2013 - 04:36:33 PDT)
    - Re: [AMBER] Antechamber Jasim, Mahmood (Student) (Tue Sep 17 2013 - 05:09:21 PDT)
    - Re: [AMBER] Antechamber David A Case (Tue Sep 17 2013 - 05:59:43 PDT)
    - Re: [AMBER] Antechamber Jasim, Mahmood (Student) (Tue Sep 17 2013 - 06:44:02 PDT)
    - Re: [AMBER] Antechamber FyD (Tue Sep 17 2013 - 07:20:58 PDT)
    - Re: [AMBER] Antechamber Jasim, Mahmood (Student) (Mon Sep 16 2013 - 04:12:23 PDT)
    - Re: [AMBER] Antechamber case (Mon Sep 16 2013 - 04:47:48 PDT)
[AMBER] Setting forcefield parameters Tanmoy Paul (Fri Sep 13 2013 - 06:44:28 PDT)
- Re: [AMBER] Setting forcefield parameters Jason Swails (Fri Sep 13 2013 - 07:03:21 PDT)
[AMBER] Assigning atom type. Sanjib Paul (Fri Sep 13 2013 - 06:52:35 PDT)
- Re: [AMBER] Assigning atom type. Jason Swails (Sat Sep 14 2013 - 21:09:22 PDT)
[AMBER] How do I use MMPBSA.py for namd .dcd file? sudipta (Fri Sep 13 2013 - 07:45:50 PDT)
- Re: [AMBER] How do I use MMPBSA.py for namd .dcd file? Daniel Roe (Fri Sep 13 2013 - 08:14:37 PDT)
  - Re: [AMBER] How do I use MMPBSA.py for namd .dcd file? sudipta (Fri Sep 13 2013 - 08:28:43 PDT)
    - Re: [AMBER] How do I use MMPBSA.py for namd .dcd file? Daniel Roe (Fri Sep 13 2013 - 08:35:37 PDT)
    - Re: [AMBER] How do I use MMPBSA.py for namd .dcd file? Jason Swails (Fri Sep 13 2013 - 08:53:55 PDT)
    - Re: [AMBER] How do I use MMPBSA.py for namd .dcd file? sudipta (Fri Sep 13 2013 - 10:20:11 PDT)
    - Re: [AMBER] How do I use MMPBSA.py for namd .dcd file? Ross Walker (Fri Sep 13 2013 - 10:31:18 PDT)
    - Re: [AMBER] How do I use MMPBSA.py for namd .dcd file? sudipta (Fri Sep 13 2013 - 20:51:29 PDT)
    - Re: [AMBER] How do I use MMPBSA.py for namd .dcd file? sudipta (Sat Sep 14 2013 - 11:55:36 PDT)
    - Re: [AMBER] How do I use MMPBSA.py for namd .dcd file? Jason Swails (Sat Sep 14 2013 - 16:18:25 PDT)
    - Re: [AMBER] How do I use MMPBSA.py for namd .dcd file? sudipta (Sat Sep 14 2013 - 19:28:10 PDT)
    - Re: [AMBER] How do I use MMPBSA.py for namd .dcd file? sudipta (Sun Sep 15 2013 - 21:45:01 PDT)
    - Re: [AMBER] How do I use MMPBSA.py for namd .dcd file? Sarah Witzke (Mon Sep 16 2013 - 00:10:56 PDT)
    - Re: [AMBER] How do I use MMPBSA.py for namd .dcd file? Jason Swails (Mon Sep 16 2013 - 02:51:22 PDT)
    - Re: [AMBER] How do I use MMPBSA.py for namd .dcd file? sudipta (Mon Sep 16 2013 - 05:39:25 PDT)
    - Re: [AMBER] How do I use MMPBSA.py for namd .dcd file? Jason Swails (Mon Sep 16 2013 - 06:59:24 PDT)
    - Re: [AMBER] How do I use MMPBSA.py for namd .dcd file? sudipta (Mon Sep 16 2013 - 08:25:20 PDT)
    - Re: [AMBER] How do I use MMPBSA.py for namd .dcd file? Jason Swails (Mon Sep 16 2013 - 09:20:39 PDT)
    - Re: [AMBER] How do I use MMPBSA.py for namd .dcd file? sudipta (Mon Sep 16 2013 - 10:05:28 PDT)
    - Re: [AMBER] How do I use MMPBSA.py for namd .dcd file? Jason Swails (Mon Sep 16 2013 - 10:24:30 PDT)
    - Re: [AMBER] How do I use MMPBSA.py for namd .dcd file? sudipta (Sun Sep 22 2013 - 07:46:44 PDT)
    - Re: [AMBER] How do I use MMPBSA.py for namd .dcd file? sudipta (Sun Sep 22 2013 - 16:13:56 PDT)
    - Re: [AMBER] How do I use MMPBSA.py for namd .dcd file? Daniel Roe (Sun Sep 22 2013 - 19:53:56 PDT)
    - Re: [AMBER] How do I use MMPBSA.py for namd .dcd file? sudipta (Sun Sep 22 2013 - 20:26:18 PDT)
    - Re: [AMBER] How do I use MMPBSA.py for namd .dcd file? Jason Swails (Mon Sep 23 2013 - 03:59:04 PDT)
    - Re: [AMBER] How do I use MMPBSA.py for namd .dcd file? Jason Swails (Mon Sep 23 2013 - 04:04:30 PDT)
    - Re: [AMBER] How do I use MMPBSA.py for namd .dcd file? sudipta (Mon Sep 23 2013 - 08:59:29 PDT)
    - Re: [AMBER] How do I use MMPBSA.py for namd .dcd file? Jason Swails (Mon Sep 23 2013 - 11:31:44 PDT)
    - Re: [AMBER] How do I use MMPBSA.py for namd .dcd file? sudipta (Mon Sep 23 2013 - 16:36:08 PDT)
    - Re: [AMBER] How do I use MMPBSA.py for namd .dcd file? sudipta (Mon Sep 23 2013 - 16:53:09 PDT)
    - Re: [AMBER] How do I use MMPBSA.py for namd .dcd file? Jason Swails (Mon Sep 23 2013 - 16:56:23 PDT)
    - Re: [AMBER] How do I use MMPBSA.py for namd .dcd file? sudipta (Mon Sep 23 2013 - 17:11:02 PDT)
    - Re: [AMBER] How do I use MMPBSA.py for namd .dcd file? Jason Swails (Mon Sep 23 2013 - 19:16:06 PDT)
    - Re: [AMBER] How do I use MMPBSA.py for namd .dcd file? sudipta (Sat Oct 12 2013 - 10:31:35 PDT)
    - Re: [AMBER] How do I use MMPBSA.py for namd .dcd file? Jason Swails (Sat Oct 12 2013 - 17:06:05 PDT)
    - Re: [AMBER] How do I use MMPBSA.py for namd .dcd file? sudipta (Mon Oct 14 2013 - 06:08:01 PDT)
    - Re: [AMBER] How do I use MMPBSA.py for namd .dcd file? Jason Swails (Mon Oct 14 2013 - 06:16:30 PDT)
[AMBER] Three body potential MOHD HOMAIDUR RAHMAN (Fri Sep 13 2013 - 11:47:50 PDT)
- Re: [AMBER] Three body potential David A Case (Fri Sep 13 2013 - 12:15:21 PDT)
- Re: [AMBER] Three body potential Jason Swails (Fri Sep 13 2013 - 12:15:39 PDT)
[AMBER] running simulation using increased number of cores onetwo (Fri Sep 13 2013 - 21:13:50 PDT)
- Re: [AMBER] running simulation using increased number of cores Jason Swails (Sat Sep 14 2013 - 06:53:47 PDT)
  - Re: [AMBER] running simulation using increased number of cores onetwo (Sat Sep 14 2013 - 22:21:18 PDT)
[AMBER] mmpbsa number of atoms issues Ayesha Fatima (Sat Sep 14 2013 - 03:44:31 PDT)
- Re: [AMBER] mmpbsa number of atoms issues Jason Swails (Sat Sep 14 2013 - 21:05:31 PDT)
  - Re: [AMBER] mmpbsa number of atoms issues Ayesha Fatima (Sat Sep 14 2013 - 22:42:35 PDT)
[AMBER] How to choose ntc value? X Sun (Sat Sep 14 2013 - 10:55:08 PDT)
- Re: [AMBER] How to choose ntc value? Jason Swails (Sat Sep 14 2013 - 20:53:55 PDT)
[AMBER] compile ambertools 13 with -nofftw3 sunyeping (Sat Sep 14 2013 - 10:23:21 PDT)
[AMBER] significance of 3-10 helixes in Secstruct Chinthaka Ratnaweera (Sat Sep 14 2013 - 14:51:30 PDT)
- Re: [AMBER] significance of 3-10 helixes in Secstruct Daniel Roe (Sun Sep 15 2013 - 10:28:11 PDT)
Re: [AMBER] namd-l: MMPBSA calculation using NAMD sunyeping (Sun Sep 15 2013 - 21:56:31 PDT)
- Re: [AMBER] namd-l: MMPBSA calculation using NAMD Aron Broom (Sun Sep 15 2013 - 22:52:39 PDT)
- Re: [AMBER] namd-l: MMPBSA calculation using NAMD sunyeping (Sun Sep 15 2013 - 23:35:03 PDT)
[AMBER] Cpptraj bug - low priority Sorensen, Jesper (Mon Sep 16 2013 - 00:23:07 PDT)
- Re: [AMBER] Cpptraj bug - low priority Daniel Roe (Mon Sep 16 2013 - 07:31:01 PDT)
  - Re: [AMBER] Cpptraj bug - low priority Sorensen, Jesper (Mon Sep 16 2013 - 08:41:52 PDT)
[AMBER] MMPBSA.py: energy decomposition Kshatresh Dutta Dubey (Mon Sep 16 2013 - 01:01:11 PDT)
[AMBER] About T-REMD convergence Francesco Pietra (Mon Sep 16 2013 - 02:17:24 PDT)
- Re: [AMBER] About T-REMD convergence Jason Swails (Mon Sep 16 2013 - 03:31:59 PDT)
  - Re: [AMBER] About T-REMD convergence Carlos Simmerling (Mon Sep 16 2013 - 05:50:07 PDT)
  - Re: [AMBER] About T-REMD convergence Francesco Pietra (Mon Sep 16 2013 - 07:57:48 PDT)
    - Re: [AMBER] About T-REMD convergence Jason Swails (Mon Sep 16 2013 - 09:19:36 PDT)
  - Re: [AMBER] About T-REMD convergence Francesco Pietra (Mon Sep 16 2013 - 08:00:48 PDT)
[AMBER] radial distribution function results Vijay Manickam Achari (Mon Sep 16 2013 - 02:25:15 PDT)
- Re: [AMBER] radial distribution function results Daniel Roe (Mon Sep 16 2013 - 08:41:15 PDT)
[AMBER] rem.log file generated in REMD simulation Gargi Borgohai (Mon Sep 16 2013 - 06:00:46 PDT)
- Re: [AMBER] rem.log file generated in REMD simulation Jason Swails (Mon Sep 16 2013 - 07:02:26 PDT)
[AMBER] issue running AMBER on double sockets hexa cores Pascal Bonnet (Mon Sep 16 2013 - 11:42:12 PDT)
- Re: [AMBER] issue running AMBER on double sockets hexa cores case (Mon Sep 16 2013 - 14:32:55 PDT)
- Re: [AMBER] issue running AMBER on double sockets hexa cores Ross Walker (Mon Sep 16 2013 - 15:54:25 PDT)
  - Re: [AMBER] issue running AMBER on double sockets hexa cores Pascal Bonnet (Wed Sep 18 2013 - 08:00:23 PDT)
    - Re: [AMBER] issue running AMBER on double sockets hexa cores Jan-Philip Gehrcke (Wed Sep 18 2013 - 08:15:02 PDT)
[AMBER] How to do clustering analysis by ptraj? Biao Ma (Tue Sep 17 2013 - 00:43:33 PDT)
- Re: [AMBER] How to do clustering analysis by ptraj? Thomas Cheatham (Tue Sep 17 2013 - 09:50:49 PDT)
  - Re: [AMBER] How to do clustering analysis by ptraj? Biao Ma (Thu Sep 19 2013 - 23:56:34 PDT)
    - Re: [AMBER] How to do clustering analysis by ptraj? Thomas Cheatham (Fri Sep 20 2013 - 10:42:07 PDT)
    - Re: [AMBER] How to do clustering analysis by ptraj? Biao Ma (Tue Sep 24 2013 - 01:30:51 PDT)
    - Re: [AMBER] How to do clustering analysis by ptraj? Daniel Roe (Tue Sep 24 2013 - 09:18:38 PDT)
    - Re: [AMBER] How to do clustering analysis by ptraj? Biao Ma (Tue Sep 24 2013 - 22:04:55 PDT)
    - Re: [AMBER] How to do clustering analysis by ptraj? Daniel Roe (Wed Sep 25 2013 - 07:36:02 PDT)
    - Re: [AMBER] How to do clustering analysis by ptraj? Jason Swails (Wed Sep 25 2013 - 10:22:56 PDT)
    - Re: [AMBER] How to do clustering analysis by ptraj? Biao Ma (Wed Sep 25 2013 - 19:18:29 PDT)
[AMBER] Calculate average property Gargi Borgohai (Tue Sep 17 2013 - 04:03:42 PDT)
- Re: [AMBER] Calculate average property Gargi Borgohai (Tue Sep 17 2013 - 04:05:39 PDT)
  - Re: [AMBER] Calculate average property Jason Swails (Tue Sep 17 2013 - 07:24:16 PDT)
    - Re: [AMBER] Calculate average property Daniel Roe (Tue Sep 17 2013 - 08:08:48 PDT)
  - Re: [AMBER] Calculate average property Bill Ross (Fri Sep 20 2013 - 21:37:16 PDT)
[AMBER] Trajectory determination and directionality in TI with softcore potentials Ryan Muraglia (Tue Sep 17 2013 - 12:39:22 PDT)
- Re: [AMBER] Trajectory determination and directionality in TI with softcore potentials David A Case (Tue Sep 17 2013 - 13:05:52 PDT)
- Re: [AMBER] Trajectory determination and directionality in TI with softcore potentials Ying-Chieh Sun (Wed Oct 30 2013 - 01:43:06 PDT)
[AMBER] MMPBSA/GBSA error Sumra Wajid Abbasi 30-FBAS/MSBI/F09 (Wed Sep 18 2013 - 00:27:47 PDT)
- Re: [AMBER] MMPBSA/GBSA error Jason Swails (Wed Sep 18 2013 - 04:08:36 PDT)
- Re: [AMBER] MMPBSA/GBSA error Sumra Wajid Abbasi 30-FBAS/MSBI/F09 (Thu Sep 19 2013 - 01:15:28 PDT)
  - Re: [AMBER] MMPBSA/GBSA error Jason Swails (Thu Sep 19 2013 - 03:41:25 PDT)
    - Re: [AMBER] MMPBSA/GBSA error Sumra Wajid Abbasi 30-FBAS/MSBI/F09 (Thu Sep 19 2013 - 06:56:11 PDT)
    - Re: [AMBER] MMPBSA/GBSA error Jason Swails (Thu Sep 19 2013 - 07:49:17 PDT)
    - Re: [AMBER] MMPBSA/GBSA error Sumra Wajid Abbasi 30-FBAS/MSBI/F09 (Thu Sep 19 2013 - 07:54:07 PDT)
    - Re: [AMBER] MMPBSA/GBSA error Jason Swails (Thu Sep 19 2013 - 08:07:00 PDT)
    - Re: [AMBER] MMPBSA/GBSA error Sumra Wajid Abbasi 30-FBAS/MSBI/F09 (Thu Sep 19 2013 - 08:18:35 PDT)
    - Re: [AMBER] MMPBSA/GBSA error Jason Swails (Thu Sep 19 2013 - 12:08:17 PDT)
    - Re: [AMBER] MMPBSA/GBSA error Ray Luo, Ph.D. (Thu Sep 19 2013 - 09:14:22 PDT)
    - Re: [AMBER] MMPBSA/GBSA error Jason Swails (Thu Sep 19 2013 - 11:16:57 PDT)
    - Re: [AMBER] MMPBSA/GBSA error Ray Luo, Ph.D. (Thu Sep 19 2013 - 11:49:00 PDT)
    - Re: [AMBER] MMPBSA/GBSA error Jason Swails (Thu Sep 19 2013 - 12:06:44 PDT)
    - Re: [AMBER] MMPBSA/GBSA error wmsmith.uci.edu (Thu Sep 19 2013 - 18:05:08 PDT)
    - Re: [AMBER] MMPBSA/GBSA error Sumra Wajid Abbasi 30-FBAS/MSBI/F09 (Thu Sep 19 2013 - 22:25:41 PDT)
    - Re: [AMBER] MMPBSA/GBSA error Jason Swails (Fri Sep 20 2013 - 03:41:46 PDT)
    - Re: [AMBER] MMPBSA/GBSA error Jason Swails (Fri Sep 20 2013 - 11:22:57 PDT)
    - Re: [AMBER] MMPBSA/GBSA error Ray Luo, Ph.D. (Fri Sep 20 2013 - 12:05:53 PDT)
    - Re: [AMBER] MMPBSA/GBSA error Ray Luo, Ph.D. (Wed Sep 25 2013 - 14:45:35 PDT)
    - Re: [AMBER] MMPBSA/GBSA error Sumra Wajid Abbasi 30-FBAS/MSBI/F09 (Wed Sep 25 2013 - 18:41:35 PDT)
    - Re: [AMBER] MMPBSA/GBSA error Ray Luo, Ph.D. (Wed Sep 25 2013 - 20:25:41 PDT)
[AMBER] problems with reimage cmd Chiara Pallara (Wed Sep 18 2013 - 01:11:50 PDT)
- Re: [AMBER] problems with reimage cmd Jason Swails (Wed Sep 18 2013 - 04:00:06 PDT)
[AMBER] Hydrogen bond analysis problem Sumra Wajid Abbasi 30-FBAS/MSBI/F09 (Wed Sep 18 2013 - 02:50:06 PDT)
- Re: [AMBER] Hydrogen bond analysis problem Daniel Roe (Wed Sep 18 2013 - 08:16:51 PDT)
  - Re: [AMBER] Hydrogen bond analysis problem Sumra Wajid Abbasi 30-FBAS/MSBI/F09 (Wed Sep 18 2013 - 23:22:05 PDT)
    - Re: [AMBER] Hydrogen bond analysis problem Daniel Roe (Thu Sep 19 2013 - 07:15:56 PDT)
    - Re: [AMBER] Hydrogen bond analysis problem Sumra Wajid Abbasi 30-FBAS/MSBI/F09 (Thu Sep 19 2013 - 07:28:51 PDT)
    - Re: [AMBER] Hydrogen bond analysis problem Daniel Roe (Thu Sep 19 2013 - 07:42:50 PDT)
    - Re: [AMBER] Hydrogen bond analysis problem Sumra Wajid Abbasi 30-FBAS/MSBI/F09 (Thu Sep 19 2013 - 07:46:47 PDT)
    - Re: [AMBER] Hydrogen bond analysis problem Sumra Wajid Abbasi 30-FBAS/MSBI/F09 (Fri Sep 20 2013 - 02:04:45 PDT)
    - Re: [AMBER] Hydrogen bond analysis problem Daniel Roe (Fri Sep 20 2013 - 08:50:09 PDT)
[AMBER] CPPtraj not producing outputs Neha Sikka (Wed Sep 18 2013 - 08:51:29 PDT)
- Re: [AMBER] CPPtraj not producing outputs Jason Swails (Wed Sep 18 2013 - 09:09:02 PDT)
[AMBER] Ti problem - system must be very inhomogeneous Fabrício Bracht (Wed Sep 18 2013 - 13:02:25 PDT)
- Re: [AMBER] Ti problem - system must be very inhomogeneous David A Case (Wed Sep 18 2013 - 13:24:18 PDT)
  - Re: [AMBER] Ti problem - system must be very inhomogeneous Fabrício Bracht (Wed Sep 18 2013 - 13:39:28 PDT)
[AMBER] RESP_ A1-charge failed Shomesankar Bhunia (Wed Sep 18 2013 - 23:16:30 PDT)
- Re: [AMBER] RESP_ A1-charge failed FyD (Thu Sep 19 2013 - 02:42:40 PDT)
- Re: [AMBER] RESP_ A1-charge failed FyD (Thu Sep 19 2013 - 05:12:34 PDT)
  - Re: [AMBER] RESP_ A1-charge failed Shomesankar Bhunia (Thu Sep 19 2013 - 05:24:10 PDT)
    - Re: [AMBER] RESP_ A1-charge failed FyD (Thu Sep 19 2013 - 05:36:06 PDT)
    - Re: [AMBER] RESP_ A1-charge failed Shomesankar Bhunia (Thu Sep 19 2013 - 05:43:37 PDT)
    - Re: [AMBER] RESP_ A1-charge failed Shomesankar Bhunia (Thu Sep 19 2013 - 05:47:06 PDT)
    - Re: [AMBER] RESP_ A1-charge failed Shomesankar Bhunia (Thu Sep 19 2013 - 08:34:34 PDT)
    - Re: [AMBER] RESP_ A1-charge failed Shomesankar Bhunia (Thu Sep 19 2013 - 05:36:47 PDT)
[AMBER] PCA analysis and porcupine plots Soma Ghosh (Thu Sep 19 2013 - 22:58:54 PDT)
- Re: [AMBER] PCA analysis and porcupine plots monica.imtech.res.in (Thu Sep 19 2013 - 23:22:07 PDT)
  - Re: [AMBER] PCA analysis and porcupine plots Soma Ghosh (Thu Sep 19 2013 - 23:56:01 PDT)
- Re: [AMBER] PCA analysis and porcupine plots wmsmith.uci.edu (Fri Sep 20 2013 - 09:15:13 PDT)
  - Re: [AMBER] PCA analysis and porcupine plots Soma Ghosh (Sat Sep 21 2013 - 05:39:10 PDT)
[AMBER] Adding an extra non-bonded pair list jfloresc.andrew.cmu.edu (Fri Sep 20 2013 - 11:40:11 PDT)
- Re: [AMBER] Adding an extra non-bonded pair list Jason Swails (Fri Sep 20 2013 - 15:27:12 PDT)
  - Re: [AMBER] Adding an extra non-bonded pair list (solved) jfloresc.andrew.cmu.edu (Wed Sep 25 2013 - 18:17:42 PDT)
[AMBER] Word of caution for Xcode 5, Mac OS X Julio Dominguez (Fri Sep 20 2013 - 18:58:27 PDT)
- Re: [AMBER] Word of caution for Xcode 5, Mac OS X M. L. Dodson (Fri Sep 20 2013 - 20:05:24 PDT)
  - Re: [AMBER] Word of caution for Xcode 5, Mac OS X case (Sat Sep 21 2013 - 06:01:26 PDT)
    - Re: [AMBER] Word of caution for Xcode 5, Mac OS X M. L. Dodson (Sat Sep 21 2013 - 06:14:30 PDT)
- Re: [AMBER] Word of caution for Xcode 5, Mac OS X Julio Dominguez (Mon Sep 23 2013 - 06:13:51 PDT)
  - Re: [AMBER] Word of caution for Xcode 5, Mac OS X Jason Swails (Mon Sep 23 2013 - 06:26:09 PDT)
    - Re: [AMBER] Word of caution for Xcode 5, Mac OS X M. L. Dodson (Mon Sep 23 2013 - 07:00:19 PDT)
    - Re: [AMBER] Word of caution for Xcode 5, Mac OS X Jason Swails (Mon Sep 23 2013 - 11:06:07 PDT)
    - Re: [AMBER] Word of caution for Xcode 5, Mac OS X M. L. Dodson (Mon Sep 23 2013 - 11:33:41 PDT)
    - Re: [AMBER] Word of caution for Xcode 5, Mac OS X Jason Swails (Tue Sep 24 2013 - 05:24:29 PDT)
  - Re: [AMBER] Word of caution for Xcode 5, Mac OS X M. L. Dodson (Mon Sep 23 2013 - 06:27:22 PDT)
[AMBER] problem in installation esther nehu (Sat Sep 21 2013 - 02:58:42 PDT)
- Re: [AMBER] problem in installation case (Sat Sep 21 2013 - 06:07:52 PDT)
[AMBER] AMBER: the units of the physical quantities hustgt08 (Sat Sep 21 2013 - 05:08:34 PDT)
- Re: [AMBER] AMBER: the units of the physical quantities case (Sat Sep 21 2013 - 06:12:55 PDT)
[AMBER] DMPC GAFF lipid membrane is freezing at 303 K. Subbarao Kanchi (Sun Sep 22 2013 - 02:48:28 PDT)
- Re: [AMBER] DMPC GAFF lipid membrane is freezing at 303 K. Subbarao Kanchi (Tue Sep 24 2013 - 01:56:16 PDT)
  - Re: [AMBER] DMPC GAFF lipid membrane is freezing at 303 K. Ross Walker (Tue Sep 24 2013 - 09:35:40 PDT)
    - Re: [AMBER] DMPC GAFF lipid membrane is freezing at 303 K. Subbarao Kanchi (Tue Sep 24 2013 - 10:19:06 PDT)
    - Re: [AMBER] DMPC GAFF lipid membrane is freezing at 303 K. jojartb.jgypk.u-szeged.hu (Tue Sep 24 2013 - 11:02:48 PDT)
    - Re: [AMBER] DMPC GAFF lipid membrane is freezing at 303 K. Subbarao Kanchi (Tue Sep 24 2013 - 12:30:09 PDT)
    - Re: [AMBER] DMPC GAFF lipid membrane is freezing at 303 K. Subbarao Kanchi (Fri Sep 27 2013 - 11:22:02 PDT)
    - [AMBER] Fwd: DMPC GAFF lipid membrane is freezing at 303 K. Subbarao Kanchi (Mon Sep 30 2013 - 11:14:01 PDT)
    - Re: [AMBER] Fwd: DMPC GAFF lipid membrane is freezing at 303 K. Ross Walker (Tue Oct 01 2013 - 09:04:27 PDT)
    - Re: [AMBER] Fwd: DMPC GAFF lipid membrane is freezing at 303 K. Subbarao Kanchi (Tue Oct 01 2013 - 19:25:11 PDT)
    - Re: [AMBER] Fwd: DMPC GAFF lipid membrane is freezing at 303 K. Subbarao Kanchi (Sun Oct 06 2013 - 22:05:57 PDT)
    - Re: [AMBER] Fwd: DMPC GAFF lipid membrane is freezing at 303 K. Dickson, Callum (Wed Oct 09 2013 - 01:07:35 PDT)
    - Re: [AMBER] Fwd: DMPC GAFF lipid membrane is freezing at 303 K. Subbarao Kanchi (Wed Oct 09 2013 - 01:44:46 PDT)
    - Re: [AMBER] Fwd: DMPC GAFF lipid membrane is freezing at 303 K. Ross Walker (Wed Oct 09 2013 - 05:19:35 PDT)
    - Re: [AMBER] Fwd: DMPC GAFF lipid membrane is freezing at 303 K. Dickson, Callum (Wed Oct 09 2013 - 05:44:06 PDT)
[AMBER] water cluster analysis Subrata Paul (Sun Sep 22 2013 - 06:46:45 PDT)
- Re: [AMBER] water cluster analysis Jason Swails (Mon Sep 23 2013 - 04:38:44 PDT)
  - Re: [AMBER] water cluster analysis George Green (Mon Sep 23 2013 - 13:48:05 PDT)
    - Re: [AMBER] water cluster analysis Jason Swails (Mon Sep 23 2013 - 14:51:04 PDT)
    - Re: [AMBER] water cluster analysis George Green (Mon Sep 23 2013 - 16:57:41 PDT)
  - Re: [AMBER] water cluster analysis Subrata Paul (Mon Sep 23 2013 - 21:30:44 PDT)
    - Re: [AMBER] water cluster analysis Karl N. Kirschner (Tue Sep 24 2013 - 01:23:33 PDT)
    - Re: [AMBER] water cluster analysis Subrata Paul (Tue Sep 24 2013 - 01:41:58 PDT)
[AMBER] help with RESP tutorial using antechamber and gaussian Fengxue Li (Sun Sep 22 2013 - 19:29:59 PDT)
- Re: [AMBER] help with RESP tutorial using antechamber and gaussian FyD (Sun Sep 22 2013 - 23:29:30 PDT)
[AMBER] AMBER version Mary Varughese (Mon Sep 23 2013 - 01:27:28 PDT)
- Re: [AMBER] AMBER version Jason Swails (Mon Sep 23 2013 - 04:27:08 PDT)
- Re: [AMBER] AMBER version David A Case (Mon Sep 23 2013 - 04:47:58 PDT)
  - Re: [AMBER] AMBER version Mary Varughese (Mon Sep 23 2013 - 16:14:59 PDT)
[AMBER] Jobs hanging on parallel CUDA without producing output Nils Oberhauser (Mon Sep 23 2013 - 03:12:59 PDT)
- Re: [AMBER] Jobs hanging on parallel CUDA without producing output Jason Swails (Mon Sep 23 2013 - 04:36:38 PDT)
  - Re: [AMBER] Jobs hanging on parallel CUDA without producing output Nils Oberhauser (Wed Sep 25 2013 - 23:58:49 PDT)
    - Re: [AMBER] Jobs hanging on parallel CUDA without producing output Jason Swails (Thu Sep 26 2013 - 02:40:07 PDT)
    - Re: [AMBER] Jobs hanging on parallel CUDA without producing output Nils Oberhauser (Thu Sep 26 2013 - 08:26:30 PDT)
- Re: [AMBER] Jobs hanging on parallel CUDA without producing output Ross Walker (Mon Sep 23 2013 - 09:35:32 PDT)
[AMBER] AmberTools update 17 for CPPTRAJ Daniel Roe (Mon Sep 23 2013 - 08:03:06 PDT)
[AMBER] How to use makeDIST_RST without MAPping? Jan-Philip Gehrcke (Mon Sep 23 2013 - 08:43:36 PDT)
- Re: [AMBER] How to use makeDIST_RST without MAPping? David A Case (Mon Sep 23 2013 - 09:15:34 PDT)
[AMBER] Coordinate of excess charge (proton) Fabrício Bracht (Mon Sep 23 2013 - 14:48:04 PDT)
- Re: [AMBER] Coordinate of excess charge (proton) Adrian Roitberg (Mon Sep 23 2013 - 14:51:41 PDT)
[AMBER] REGARDING UMBRELLA SAMPLING TUTORIAL Sourav Purohit (Mon Sep 23 2013 - 20:03:26 PDT)
- Re: [AMBER] REGARDING UMBRELLA SAMPLING TUTORIAL Ross Walker (Mon Sep 23 2013 - 20:36:31 PDT)
  - Re: [AMBER] REGARDING UMBRELLA SAMPLING TUTORIAL Sourav Purohit (Mon Sep 23 2013 - 20:49:56 PDT)
    - Re: [AMBER] REGARDING UMBRELLA SAMPLING TUTORIAL Ross Walker (Mon Sep 23 2013 - 21:23:56 PDT)
    - Re: [AMBER] REGARDING UMBRELLA SAMPLING TUTORIAL Sourav Purohit (Tue Sep 24 2013 - 08:24:54 PDT)
[AMBER] energetics of displacing water molecules from protein binding sites Changqing Yan (Mon Sep 23 2013 - 21:09:51 PDT)
[AMBER] how to use commands “sequence”, “set”, “add”, “bond”, “ impose” or someothers necessary to add a –H and a –OH to the GLY 张明焜 (Mon Sep 23 2013 - 23:53:36 PDT)
- Re: [AMBER] how to use commands “sequence”, “set”, “add”, “bond”, “ impose” or someothers necessary to add a –H and a –OH to the GLY Jason Swails (Tue Sep 24 2013 - 04:04:52 PDT)
[AMBER] help with RESP tutorial using antechambe Fengxue Li (Tue Sep 24 2013 - 00:44:19 PDT)
- Re: [AMBER] help with RESP tutorial using antechambe Anselm Horn (Tue Sep 24 2013 - 01:30:58 PDT)
[AMBER] Temperature based trajectory in REMD Gargi Borgohai (Tue Sep 24 2013 - 05:44:43 PDT)
- Re: [AMBER] Temperature based trajectory in REMD Daniel Roe (Tue Sep 24 2013 - 07:56:54 PDT)
  - Re: [AMBER] Temperature based trajectory in REMD Carlos Simmerling (Tue Sep 24 2013 - 08:11:44 PDT)
- Re: [AMBER] Temperature based trajectory in REMD Gargi Borgohai (Wed Oct 02 2013 - 02:05:13 PDT)
  - Re: [AMBER] Temperature based trajectory in REMD Daniel Roe (Wed Oct 02 2013 - 10:22:15 PDT)
[AMBER] Help on MMPBSA script R R S Pissurlenkar (Tue Sep 24 2013 - 05:59:21 PDT)
- Re: [AMBER] Help on MMPBSA script Jason Swails (Tue Sep 24 2013 - 07:35:53 PDT)
[AMBER] Protonated Histidine (HIP) charges in Amber03 (AMBERFF03) Adam (Tue Sep 24 2013 - 12:07:25 PDT)
- Re: [AMBER] Protonated Histidine (HIP) charges in Amber03 (AMBERFF03) case (Tue Sep 24 2013 - 18:33:54 PDT)
- Re: [AMBER] Protonated Histidine (HIP) charges in Amber03 (AMBERFF03) FyD (Wed Sep 25 2013 - 01:32:01 PDT)
[AMBER] Norleucine Parameters Adam (Tue Sep 24 2013 - 12:16:46 PDT)
[AMBER] AmberTools 1.5.2 compilation Error: Return type mismatch of function 'cgalf' at (1) (REAL(8)/REAL(4)) harry mangalam (Tue Sep 24 2013 - 12:19:37 PDT)
- Re: [AMBER] AmberTools 1.5.2 compilation Error: Return type mismatch of function 'cgalf' at (1) (REAL(8)/REAL(4)) Jason Swails (Tue Sep 24 2013 - 16:31:39 PDT)
  - Re: [AMBER] AmberTools 1.5.2 compilation Error: Return type mismatch of function 'cgalf' at (1) (REAL(8)/REAL(4)) harry mangalam (Tue Sep 24 2013 - 19:11:26 PDT)
- Re: [AMBER] AmberTools 1.5.2 compilation Error: Return type mismatch of function 'cgalf' at (1) (REAL(8)/REAL(4)) case (Tue Sep 24 2013 - 18:56:32 PDT)
[AMBER] HEATING run using SANDER Sourav Purohit (Tue Sep 24 2013 - 12:30:12 PDT)
- Re: [AMBER] HEATING run using SANDER case (Tue Sep 24 2013 - 18:59:20 PDT)
[AMBER] Running Amber on a SGI cluster George Tzotzos (Tue Sep 24 2013 - 12:32:25 PDT)
- Re: [AMBER] Running Amber on a SGI cluster Jason Swails (Wed Sep 25 2013 - 04:52:42 PDT)
  - Re: [AMBER] Running Amber on a SGI cluster George Tzotzos (Wed Sep 25 2013 - 08:26:20 PDT)
    - Re: [AMBER] Running Amber on a SGI cluster Ross Walker (Wed Sep 25 2013 - 08:53:24 PDT)
    - Re: [AMBER] Running Amber on a SGI cluster George Tzotzos (Wed Sep 25 2013 - 09:20:25 PDT)
    - Re: [AMBER] Running Amber on a SGI cluster Ross Walker (Wed Sep 25 2013 - 09:30:38 PDT)
    - Re: [AMBER] Running Amber on a SGI cluster George Tzotzos (Wed Sep 25 2013 - 11:35:43 PDT)
    - Re: [AMBER] Running Amber on a SGI cluster Jason Swails (Wed Sep 25 2013 - 08:54:52 PDT)
[AMBER] Superposition of 3D structures for wid type and mutants with VMD Yanyan ZHU (Tue Sep 24 2013 - 18:46:57 PDT)
- Re: [AMBER] Superposition of 3D structures for wid type and mutants with VMD Daniel Roe (Wed Sep 25 2013 - 07:32:20 PDT)
[AMBER] Probelm with antechamber for resp charge derivation Fengxue Li (Tue Sep 24 2013 - 20:23:37 PDT)
- Re: [AMBER] Probelm with antechamber for resp charge derivation FyD (Wed Sep 25 2013 - 02:27:42 PDT)
- Re: [AMBER] Probelm with antechamber for resp charge derivation David A Case (Wed Sep 25 2013 - 04:33:08 PDT)
[AMBER] Sodium Ion Citation Lars Holte (Tue Sep 24 2013 - 21:27:07 PDT)
- Re: [AMBER] Sodium Ion Citation Brian Radak (Wed Sep 25 2013 - 06:08:34 PDT)
  - Re: [AMBER] Sodium Ion Citation Lars Holte (Wed Sep 25 2013 - 10:26:04 PDT)
    - Re: [AMBER] Sodium Ion Citation Brian Radak (Wed Sep 25 2013 - 12:28:42 PDT)
[AMBER] Problem in antechamber execution Tanmoy Paul (Tue Sep 24 2013 - 22:55:34 PDT)
- Re: [AMBER] Problem in antechamber execution FyD (Wed Sep 25 2013 - 02:36:52 PDT)
- Re: [AMBER] Problem in antechamber execution David A Case (Wed Sep 25 2013 - 04:37:48 PDT)
[AMBER] problem running antechamber - amber Version 10 Concha, Monica (Wed Sep 25 2013 - 07:17:03 PDT)
- Re: [AMBER] problem running antechamber - amber Version 10 Daniel Roe (Wed Sep 25 2013 - 07:43:21 PDT)
- Re: [AMBER] problem running antechamber - amber Version 10 FyD (Wed Sep 25 2013 - 08:02:51 PDT)
[AMBER] the difference between proper torsion and improper torsion Ming Huang (Wed Sep 25 2013 - 08:43:02 PDT)
- Re: [AMBER] the difference between proper torsion and improper torsion James Maier (Wed Sep 25 2013 - 08:58:36 PDT)
[AMBER] Problems with sander.MPI Moacyr Comar (Wed Sep 25 2013 - 10:12:35 PDT)
- Re: [AMBER] Problems with sander.MPI Jason Swails (Wed Sep 25 2013 - 10:18:52 PDT)
  - Re: [AMBER] Problems with sander.MPI Moacyr Comar (Wed Sep 25 2013 - 11:24:54 PDT)
[AMBER] R.E.D. double bond revisit psu4.uic.edu (Wed Sep 25 2013 - 10:51:09 PDT)
- Re: [AMBER] R.E.D. double bond revisit FyD (Wed Sep 25 2013 - 13:40:33 PDT)
[AMBER] November 11 deadline for ACS COMP Division Awards for Spring 2014 meeting Carlos Simmerling (Wed Sep 25 2013 - 10:17:35 PDT)
[AMBER] openmp on 64core/AMD vs MPI over IB on multiple nodes harry mangalam (Wed Sep 25 2013 - 12:42:06 PDT)
- Re: [AMBER] openmp on 64core/AMD vs MPI over IB on multiple nodes Jason Swails (Wed Sep 25 2013 - 13:19:07 PDT)
  - Re: [AMBER] openmp on 64core/AMD vs MPI over IB on multiple nodes harry mangalam (Wed Sep 25 2013 - 14:04:17 PDT)
  - Re: [AMBER] openmp on 64core/AMD vs MPI over IB on multiple nodes harry mangalam (Wed Sep 25 2013 - 14:51:03 PDT)
[AMBER] CORRECTION: Oct 22 deadline for ACS COMP Division Awards for Spring 2014 meeting Carlos Simmerling (Wed Sep 25 2013 - 12:34:32 PDT)
[AMBER] AMBER on AWS - Beta testers wanted. Ross Walker (Wed Sep 25 2013 - 13:14:11 PDT)
[AMBER] protein in popc bilayer simulation Wang Chern Hoe (Dr) (Wed Sep 25 2013 - 19:46:43 PDT)
- Re: [AMBER] protein in popc bilayer simulation Ross Walker (Wed Sep 25 2013 - 20:19:40 PDT)
  - Re: [AMBER] protein in popc bilayer simulation Wang Chern Hoe (Dr) (Wed Sep 25 2013 - 23:58:38 PDT)
    - Re: [AMBER] protein in popc bilayer simulation David A Case (Thu Sep 26 2013 - 04:46:01 PDT)
    - Re: [AMBER] protein in popc bilayer simulation Wang Chern Hoe (Dr) (Thu Sep 26 2013 - 23:23:06 PDT)
    - Re: [AMBER] protein in popc bilayer simulation David A Case (Fri Sep 27 2013 - 04:39:12 PDT)
[AMBER] Generating periodic box parameters for a pdb file already solvated Sajeewa Pemasinghe (Wed Sep 25 2013 - 22:54:22 PDT)
- Re: [AMBER] Generating periodic box parameters for a pdb file already solvated Jason Swails (Thu Sep 26 2013 - 03:45:33 PDT)
  - Re: [AMBER] Generating periodic box parameters for a pdb file already solvated Sajeewa Pemasinghe (Thu Sep 26 2013 - 04:38:52 PDT)
[AMBER] No torsion terms for N-Cg-Cg-Ng sunita gupta (Thu Sep 26 2013 - 00:08:32 PDT)
- Re: [AMBER] No torsion terms for N-Cg-Cg-Ng Lachele Foley (Thu Sep 26 2013 - 07:10:57 PDT)
[AMBER] Fwd: Re: R.E.D. double bond revisit FyD (Thu Sep 26 2013 - 00:10:02 PDT)
[AMBER] How do I read a trail file in the format of NetCDF with VMD ? Yanyan ZHU (Thu Sep 26 2013 - 02:00:40 PDT)
- Re: [AMBER] How do I read a trail file in the format of NetCDF with VMD ? Jason Swails (Thu Sep 26 2013 - 03:43:44 PDT)
[AMBER] Number of residues in a solvent box Chinthaka Ratnaweera (Thu Sep 26 2013 - 09:53:27 PDT)
- Re: [AMBER] Number of residues in a solvent box Brian Radak (Thu Sep 26 2013 - 10:35:29 PDT)
[AMBER] cytidine triphosphate Hallel Freedman (Thu Sep 26 2013 - 11:46:32 PDT)
- Re: [AMBER] cytidine triphosphate FyD (Thu Sep 26 2013 - 13:24:04 PDT)
  - Re: [AMBER] cytidine triphosphate Hallel Freedman (Thu Sep 26 2013 - 13:39:17 PDT)
    - Re: [AMBER] cytidine triphosphate FyD (Thu Sep 26 2013 - 23:17:58 PDT)
    - Re: [AMBER] cytidine triphosphate Hallel Freedman (Thu Sep 26 2013 - 23:24:00 PDT)
[AMBER] Using NMODE with NAMD trajectories Valeria Marquez (Thu Sep 26 2013 - 11:50:38 PDT)
[AMBER] shortest distance Norah Schlacter (Thu Sep 26 2013 - 14:19:20 PDT)
- Re: [AMBER] shortest distance Daniel Roe (Thu Sep 26 2013 - 15:58:09 PDT)
  - Re: [AMBER] shortest distance Norah Schlacter (Thu Sep 26 2013 - 16:39:32 PDT)
    - Re: [AMBER] shortest distance Jason Swails (Thu Sep 26 2013 - 17:01:29 PDT)
[AMBER] Error in QM/MM calculations Cuiyl (Thu Sep 26 2013 - 19:00:00 PDT)
- Re: [AMBER] Error in QM/MM calculations Cuiyl (Thu Sep 26 2013 - 20:05:14 PDT)
  - Re: [AMBER] Error in QM/MM calculations Jason Swails (Fri Sep 27 2013 - 04:03:53 PDT)
    - Re: [AMBER] Error in QM/MM calculations Cuiyl (Fri Sep 27 2013 - 04:45:58 PDT)
[AMBER] Superposition of 3D structures for wid type and mutants with VMD Yanyan ZHU (Thu Sep 26 2013 - 19:16:36 PDT)
- Re: [AMBER] Superposition of 3D structures for wid type and mutants with VMD Nhai (Fri Sep 27 2013 - 01:57:33 PDT)
- Re: [AMBER] Superposition of 3D structures for wid type and mutants with VMD Daniel Roe (Fri Sep 27 2013 - 07:40:57 PDT)
[AMBER] histidine_residue Shomesankar Bhunia (Fri Sep 27 2013 - 02:24:07 PDT)
- Re: [AMBER] histidine_residue Shomesankar Bhunia (Fri Sep 27 2013 - 03:10:28 PDT)
  - Re: [AMBER] histidine_residue Concha, Monica (Fri Sep 27 2013 - 06:10:51 PDT)
    - Re: [AMBER] histidine_residue Shomesankar Bhunia (Fri Sep 27 2013 - 08:38:51 PDT)
    - Re: [AMBER] histidine_residue Jason Swails (Fri Sep 27 2013 - 09:09:22 PDT)
[AMBER] Oct 22nd deadline for ACS COMP division awards for Spring national meeting Carlos Simmerling (Fri Sep 27 2013 - 06:41:27 PDT)
[AMBER] problem with addIons in tleap Fengxue Li (Fri Sep 27 2013 - 06:50:22 PDT)
- Re: [AMBER] problem with addIons in tleap Bill Ross (Fri Jul 22 2011 - 13:51:10 PDT)
  - Re: [AMBER] problem with addIons in tleap Wei Chen (Fri Jul 22 2011 - 13:55:58 PDT)
- Re: [AMBER] problem with addIons in tleap Bill Ross (Sat Jul 23 2011 - 13:45:40 PDT)
  - Re: [AMBER] problem with addIons in tleap Wei Chen (Sat Jul 23 2011 - 14:12:56 PDT)
- Re: [AMBER] problem with addIons in tleap David A Case (Tue Oct 01 2013 - 04:44:03 PDT)
[AMBER] NAMD_AMBER_MD Shomesankar Bhunia (Fri Sep 27 2013 - 08:42:49 PDT)
- Re: [AMBER] NAMD_AMBER_MD Jason Swails (Fri Sep 27 2013 - 08:55:51 PDT)
  - Re: [AMBER] NAMD_AMBER_MD Shomesankar Bhunia (Fri Sep 27 2013 - 20:14:53 PDT)
[AMBER] Changing the Lennard Jones potential Pengzhi Zhang (Sat Sep 28 2013 - 15:44:25 PDT)
- Re: [AMBER] Changing the Lennard Jones potential Jason Swails (Sun Sep 29 2013 - 04:58:23 PDT)
[AMBER] Generating topology files for two proteins in a single input pdb George Green (Sun Sep 29 2013 - 14:26:37 PDT)
- Re: [AMBER] Generating topology files for two proteins in a single input pdb David A Case (Mon Sep 30 2013 - 04:53:43 PDT)
  - Re: [AMBER] Generating topology files for two proteins in a single input pdb George Green (Mon Sep 30 2013 - 08:01:04 PDT)
    - Re: [AMBER] Generating topology files for two proteins in a single input pdb David A Case (Tue Oct 01 2013 - 04:43:07 PDT)
    - Re: [AMBER] Generating topology files for two proteins in a single input pdb George Green (Tue Oct 01 2013 - 04:48:42 PDT)
    - Re: [AMBER] Generating topology files for two proteins in a single input pdb George Green (Tue Oct 01 2013 - 04:49:59 PDT)
    - Re: [AMBER] Generating topology files for two proteins in a single input pdb George Green (Tue Oct 01 2013 - 04:52:54 PDT)
    - Re: [AMBER] Generating topology files for two proteins in a single input pdb George Green (Tue Oct 01 2013 - 04:55:11 PDT)
    - Re: [AMBER] Generating topology files for two proteins in a single input pdb Jason Swails (Tue Oct 01 2013 - 04:54:21 PDT)
    - Re: [AMBER] Generating topology files for two proteins in a single input pdb George Green (Tue Oct 01 2013 - 11:13:49 PDT)
[AMBER] entropy kirtana S (Sun Sep 29 2013 - 17:17:07 PDT)
- Re: [AMBER] entropy Daniel Roe (Mon Sep 30 2013 - 08:59:26 PDT)
  - Re: [AMBER] entropy kirtana S (Mon Sep 30 2013 - 10:58:52 PDT)
    - Re: [AMBER] entropy Daniel Roe (Mon Sep 30 2013 - 11:58:03 PDT)
    - Re: [AMBER] entropy kirtana S (Mon Sep 30 2013 - 12:52:08 PDT)
[AMBER] Erro in the Thermodynamic Intergration using soft core potentials" 冉挺 (Sun Sep 29 2013 - 19:02:28 PDT)
- Re: [AMBER] Erro in the Thermodynamic Intergration using soft core potentials" David A Case (Mon Sep 30 2013 - 05:01:34 PDT)
  - Re: [AMBER] Erro in the Thermodynamic Intergration using soft core potentials" 冉挺 (Mon Sep 30 2013 - 06:18:07 PDT)
    - Re: [AMBER] Erro in the Thermodynamic Intergration using soft core potentials" Daniel Roe (Mon Sep 30 2013 - 09:07:20 PDT)
    - Re: [AMBER] Erro in the Thermodynamic Intergration using soft core potentials" 冉挺 (Tue Oct 01 2013 - 02:17:00 PDT)
    - Re: [AMBER] Erro in the Thermodynamic Intergration using soft core potentials" David A Case (Tue Oct 01 2013 - 04:37:25 PDT)
    - Re: [AMBER] Erro in the Thermodynamic Intergration using soft core potentials" 冉挺 (Tue Oct 01 2013 - 05:35:32 PDT)
    - Re: [AMBER] Erro in the Thermodynamic Intergration using soft core potentials" 冉挺 (Wed Oct 02 2013 - 03:52:36 PDT)
    - Re: [AMBER] Erro in the Thermodynamic Intergration using soft core potentials" David A Case (Wed Oct 02 2013 - 04:39:31 PDT)
    - Re: [AMBER] Erro in the Thermodynamic Intergration using soft core potentials" 冉挺 (Thu Oct 03 2013 - 06:07:40 PDT)
    - Re: [AMBER] Erro in the Thermodynamic Intergration using soft core potentials" David A Case (Thu Oct 03 2013 - 09:08:47 PDT)
    - Re: [AMBER] Erro in the Thermodynamic Intergration using soft core potentials" 冉挺 (Fri Nov 08 2013 - 09:10:10 PST)
    - Re: [AMBER] Erro in the Thermodynamic Intergration using soft core potentials" case (Sat Nov 09 2013 - 07:30:32 PST)
    - Re: [AMBER] Erro in the Thermodynamic Intergration using soft core potentials" 冉挺 (Sun Nov 10 2013 - 20:20:16 PST)
    - Re: [AMBER] Erro in the Thermodynamic Intergration using soft core potentials" David A Case (Mon Nov 11 2013 - 06:18:23 PST)
    - Re: [AMBER] Erro in the Thermodynamic Intergration using soft core potentials" Ying-Chieh Sun (Sat Nov 09 2013 - 23:50:07 PST)
    - Re: [AMBER] Erro in the Thermodynamic Intergration using soft core potentials" David A Case (Mon Sep 30 2013 - 09:15:01 PDT)
[AMBER] Predicting druggable hotspots anu chandra (Sun Sep 29 2013 - 22:54:36 PDT)
[AMBER] rotational diffusion error Vijay Manickam Achari (Mon Sep 30 2013 - 00:15:46 PDT)
- Re: [AMBER] rotational diffusion error David A Case (Mon Sep 30 2013 - 05:08:28 PDT)
- Re: [AMBER] rotational diffusion error Daniel Roe (Mon Sep 30 2013 - 14:49:58 PDT)
  - Re: [AMBER] rotational diffusion error Vijay Manickam Achari (Tue Oct 01 2013 - 19:49:18 PDT)
    - Re: [AMBER] rotational diffusion error David A Case (Wed Oct 02 2013 - 04:34:36 PDT)
    - Re: [AMBER] rotational diffusion error Vijay Manickam Achari (Wed Oct 02 2013 - 19:06:38 PDT)
    - Re: [AMBER] rotational diffusion error Daniel Roe (Fri Oct 04 2013 - 07:11:19 PDT)
  - Re: [AMBER] rotational diffusion error Vijay Manickam Achari (Tue Oct 01 2013 - 21:09:34 PDT)
[AMBER] help to run restricted MD Fengxue Li (Mon Sep 30 2013 - 07:17:23 PDT)
- Re: [AMBER] help to run restricted MD Brian Radak (Mon Sep 30 2013 - 08:32:15 PDT)
[AMBER] MMPBSA.py PB error Aronica, Pietro (Mon Sep 30 2013 - 07:27:38 PDT)
- Re: [AMBER] MMPBSA.py PB error Jason Swails (Mon Sep 30 2013 - 07:44:34 PDT)
- Re: [AMBER] MMPBSA.py PB error Aronica, Pietro (Mon Sep 30 2013 - 07:44:52 PDT)
[AMBER] passing a new argument to sander on command line Kepa K. Burusco (Mon Sep 30 2013 - 08:56:10 PDT)
- Re: [AMBER] passing a new argument to sander on command line Jason Swails (Mon Sep 30 2013 - 09:28:18 PDT)
  - Re: [AMBER] passing a new argument to sander on command line Kepa K. Burusco (Mon Sep 30 2013 - 10:07:32 PDT)
    - Re: [AMBER] passing a new argument to sander on command line Jason Swails (Mon Sep 30 2013 - 10:49:05 PDT)
[AMBER] RED-VIII.52 Problem--cannot find scratch file and punch file Dongshan Wei (Mon Sep 30 2013 - 10:56:42 PDT)
- Re: [AMBER] RED-VIII.52 Problem--cannot find scratch file and punch file FyD (Mon Sep 30 2013 - 13:07:01 PDT)
  - Re: [AMBER] RED-VIII.52 Problem--cannot find scratch file and punch file Dongshan Wei (Mon Sep 30 2013 - 19:05:43 PDT)
    - Re: [AMBER] RED-VIII.52 Problem--cannot find scratch file and punch file FyD (Mon Sep 30 2013 - 22:35:43 PDT)
    - Re: [AMBER] RED-VIII.52 Problem--cannot find scratch file and punch file Dongshan Wei (Tue Oct 08 2013 - 08:37:10 PDT)
    - Re: [AMBER] RED-VIII.52 Problem--cannot find scratch file and punch file Dongshan Wei (Tue Oct 08 2013 - 20:35:42 PDT)
    - Re: [AMBER] RED-VIII.52 Problem--cannot find scratch file and punch file FyD (Wed Oct 09 2013 - 00:03:20 PDT)
    - Re: [AMBER] RED-VIII.52 Problem--cannot find scratch file and punch file Dongshan Wei (Wed Oct 09 2013 - 05:50:33 PDT)
    - Re: [AMBER] RED-VIII.52 Problem--cannot find scratch file and punch file FyD (Thu Oct 10 2013 - 01:04:30 PDT)
    - Re: [AMBER] RED-VIII.52 Problem--cannot find scratch file and punch file FyD (Thu Oct 10 2013 - 02:01:25 PDT)
    - Re: [AMBER] RED-VIII.52 Problem--cannot find scratch file and punch file FyD (Wed Oct 09 2013 - 00:09:44 PDT)
[AMBER] MMPBSA.py MPI problem on TACC Stampede Sorensen, Jesper (Mon Sep 30 2013 - 17:55:49 PDT)
- Re: [AMBER] MMPBSA.py MPI problem on TACC Stampede Jason Swails (Tue Oct 01 2013 - 04:36:10 PDT)
  - Re: [AMBER] MMPBSA.py MPI problem on TACC Stampede Sorensen, Jesper (Tue Oct 01 2013 - 10:19:11 PDT)
    - Re: [AMBER] MMPBSA.py MPI problem on TACC Stampede Sorensen, Jesper (Tue Nov 05 2013 - 05:04:52 PST)
    - Re: [AMBER] MMPBSA.py MPI problem on TACC Stampede Jason Swails (Tue Nov 05 2013 - 05:14:13 PST)
[AMBER] Use of Langevin Thermostat with Amoeba force field Karl Debiec (Mon Sep 30 2013 - 19:40:13 PDT)
- Re: [AMBER] Use of Langevin Thermostat with Amoeba force field David A Case (Tue Oct 01 2013 - 04:34:24 PDT)
[AMBER] Ambiguity in PMF calculated from umbrella sampling of a dihedral angle Mohan Pradhan (Tue Oct 01 2013 - 04:11:32 PDT)
- Re: [AMBER] Ambiguity in PMF calculated from umbrella sampling of a dihedral angle Jason Swails (Tue Oct 01 2013 - 04:50:01 PDT)
  - Re: [AMBER] Ambiguity in PMF calculated from umbrella sampling of a dihedral angle Mohan Pradhan (Tue Oct 01 2013 - 06:11:22 PDT)
    - Re: [AMBER] Ambiguity in PMF calculated from umbrella sampling of a dihedral angle Jason Swails (Tue Oct 01 2013 - 09:20:29 PDT)
[AMBER] Modified Cysteine Devlina Chakravarty (Tue Oct 01 2013 - 04:36:09 PDT)
- Re: [AMBER] Modified Cysteine FyD (Tue Oct 01 2013 - 08:17:42 PDT)
[AMBER] Problem in antechamber execution Problem in antechamber execution problem in antechamber execution Tanmoy Paul (Tue Oct 01 2013 - 08:15:21 PDT)
- Re: [AMBER] Problem in antechamber execution Problem in antechamber execution problem in antechamber execution Daniel Roe (Tue Oct 01 2013 - 09:08:48 PDT)
[AMBER] about error with "Must have more residues than processors!" Biao Ma (Tue Oct 01 2013 - 09:00:20 PDT)
- Re: [AMBER] about error with "Must have more residues than processors!" Jason Swails (Tue Oct 01 2013 - 09:26:01 PDT)
  - Re: [AMBER] about error with "Must have more residues than processors!" Biao Ma (Wed Oct 02 2013 - 20:47:49 PDT)
[AMBER] Predicting druggable hotspots anu chandra (Wed Oct 02 2013 - 03:36:15 PDT)
[AMBER] PROBLEM USING ANTECHAMBER Tanmoy Paul (Wed Oct 02 2013 - 05:36:47 PDT)
- Re: [AMBER] PROBLEM USING ANTECHAMBER Daniel Roe (Wed Oct 02 2013 - 08:50:26 PDT)
[AMBER] About INP in case of MS=1 Hiromasa WATANABE (Wed Oct 02 2013 - 22:55:00 PDT)
- Re: [AMBER] About INP in case of MS=1 Ray Luo, Ph.D. (Thu Oct 03 2013 - 10:00:53 PDT)
  - Re: [AMBER] About INP in case of MS=1 Hiromasa WATANABE (Tue Oct 08 2013 - 23:03:58 PDT)
    - Re: [AMBER] About INP in case of MS=1 Ray Luo, Ph.D. (Wed Oct 09 2013 - 09:53:43 PDT)
[AMBER] The Error when I run MdoutAnalysizer.py Biao Ma (Wed Oct 02 2013 - 23:41:37 PDT)
- Re: [AMBER] The Error when I run MdoutAnalysizer.py Jason Swails (Thu Oct 03 2013 - 04:33:41 PDT)
- Re: [AMBER] The Error when I run MdoutAnalysizer.py Jason Swails (Thu Oct 03 2013 - 07:36:21 PDT)
  - Re: [AMBER] The Error when I run MdoutAnalysizer.py Biao Ma (Thu Oct 03 2013 - 22:36:48 PDT)
[AMBER] Questions about VDW process of thermodynamic integration method 袁丹丹 (Thu Oct 03 2013 - 05:57:43 PDT)
[AMBER] Questions about VDW process of thermodynamic integration method‏ 袁丹丹 (Thu Oct 03 2013 - 06:06:54 PDT)
[AMBER] Replica exchange umbrella sampling Fabrício Bracht (Fri Oct 04 2013 - 00:00:52 PDT)
- Re: [AMBER] Replica exchange umbrella sampling Jason Swails (Fri Oct 04 2013 - 04:17:12 PDT)
  - Re: [AMBER] Replica exchange umbrella sampling Fabrício Bracht (Sat Oct 05 2013 - 00:29:29 PDT)
[AMBER] QM/MM MMPBSA Jacopo Sgrignani (Fri Oct 04 2013 - 01:18:10 PDT)
- Re: [AMBER] QM/MM MMPBSA Jason Swails (Fri Oct 04 2013 - 04:07:07 PDT)
  - Re: [AMBER] QM/MM MMPBSA Jacopo Sgrignani (Fri Oct 04 2013 - 05:15:39 PDT)
    - Re: [AMBER] QM/MM MMPBSA Jason Swails (Fri Oct 04 2013 - 05:34:34 PDT)
    - Re: [AMBER] QM/MM MMPBSA Jacopo Sgrignani (Fri Oct 04 2013 - 06:33:58 PDT)
    - Re: [AMBER] QM/MM MMPBSA Jason Swails (Fri Oct 04 2013 - 06:53:58 PDT)
    - Re: [AMBER] QM/MM MMPBSA Jason Swails (Fri Oct 04 2013 - 06:59:18 PDT)
[AMBER] ITN Marie Curie positions available for early-stage researchers Paolo Ruggerone (Fri Oct 04 2013 - 02:25:08 PDT)
[AMBER] About the Mg charge in AMBER FF George Patargias (Fri Oct 04 2013 - 02:28:36 PDT)
- Re: [AMBER] About the Mg charge in AMBER FF Jacopo Sgrignani (Fri Oct 04 2013 - 03:01:43 PDT)
  - Re: [AMBER] About the Mg charge in AMBER FF George Patargias (Fri Oct 04 2013 - 05:36:32 PDT)
  - Re: [AMBER] About the Mg charge in AMBER FF George Patargias (Wed Nov 27 2013 - 03:07:33 PST)
- Re: [AMBER] About the Mg charge in AMBER FF FyD (Fri Oct 04 2013 - 05:07:43 PDT)
  - Re: [AMBER] About the Mg charge in AMBER FF Jason Swails (Fri Oct 04 2013 - 05:38:02 PDT)
    - Re: [AMBER] About the Mg charge in AMBER FF Andreas Goetz (Fri Oct 04 2013 - 19:20:35 PDT)
[AMBER] changeLJ14Pair CHAMI F. (Fri Oct 04 2013 - 04:52:24 PDT)
- Re: [AMBER] changeLJ14Pair Jason Swails (Fri Oct 04 2013 - 07:04:45 PDT)
[AMBER] Regarding addition of DL_Poly Inversion potential in Amber MOHD HOMAIDUR RAHMAN (Fri Oct 04 2013 - 05:17:33 PDT)
- Re: [AMBER] Regarding addition of DL_Poly Inversion potential in Amber Jason Swails (Sat Oct 05 2013 - 17:52:17 PDT)
[AMBER] Reading NetCDF file Uday Midya (Fri Oct 04 2013 - 05:46:46 PDT)
- Re: [AMBER] Reading NetCDF file Jason Swails (Fri Oct 04 2013 - 06:18:12 PDT)
- Re: [AMBER] Reading NetCDF file Daniel Roe (Fri Oct 04 2013 - 07:05:46 PDT)
  - Re: [AMBER] Reading NetCDF file Uday Midya (Fri Oct 04 2013 - 22:33:12 PDT)
    - Re: [AMBER] Reading NetCDF file Daniel Roe (Mon Oct 07 2013 - 13:25:15 PDT)
[AMBER] Regarding addition of DL_Poly Inversion and three body potential in Amber MOHD HOMAIDUR RAHMAN (Fri Oct 04 2013 - 10:09:02 PDT)
[AMBER] A problem with a specific input in pmemd.cuda.MPI. 4 GPU fails, 2 GPU works fine. Jeremy Hallum (Fri Oct 04 2013 - 11:26:52 PDT)
- Re: [AMBER] A problem with a specific input in pmemd.cuda.MPI. 4 GPU fails, 2 GPU works fine. Ross Walker (Fri Oct 04 2013 - 11:41:17 PDT)
[AMBER] NAB : Orienting a molecule HIMANSHU JOSHI (Fri Oct 04 2013 - 11:33:48 PDT)
- Re: [AMBER] NAB : Orienting a molecule Aldo Segura (Fri Oct 04 2013 - 12:53:09 PDT)
  - Re: [AMBER] NAB : Orienting a molecule Daniel Roe (Fri Oct 04 2013 - 13:38:00 PDT)
- Re: [AMBER] NAB : Orienting a molecule case (Sat Oct 05 2013 - 06:19:57 PDT)
[AMBER] Generating reservoirs for non-Boltzmann T-RREMD Eugene Yedvabny (Fri Oct 04 2013 - 12:50:42 PDT)
- Re: [AMBER] Generating reservoirs for non-Boltzmann T-RREMD Niel Henriksen (Fri Oct 04 2013 - 13:25:18 PDT)
  - Re: [AMBER] Generating reservoirs for non-Boltzmann T-RREMD Eugene Yedvabny (Fri Oct 04 2013 - 17:34:32 PDT)
    - Re: [AMBER] Generating reservoirs for non-Boltzmann T-RREMD Niel Henriksen (Sun Oct 06 2013 - 21:18:00 PDT)
    - Re: [AMBER] Generating reservoirs for non-Boltzmann T-RREMD Eugene Yedvabny (Sun Oct 06 2013 - 21:58:04 PDT)
    - Re: [AMBER] Generating reservoirs for non-Boltzmann T-RREMD Niel Henriksen (Mon Oct 07 2013 - 11:27:56 PDT)
    - Re: [AMBER] Generating reservoirs for non-Boltzmann T-RREMD Jason Swails (Tue Oct 08 2013 - 05:01:24 PDT)
[AMBER] MPI install with openmpi Makoto Chikira (Sat Oct 05 2013 - 00:33:21 PDT)
- Re: [AMBER] MPI install with openmpi case (Sat Oct 05 2013 - 06:28:20 PDT)
  - Re: [AMBER] MPI install with openmpi Makoto Chikira (Sat Oct 05 2013 - 08:37:08 PDT)
    - Re: [AMBER] MPI install with openmpi case (Sat Oct 05 2013 - 09:50:18 PDT)
    - Re: [AMBER] MPI install with openmpi Makoto Chikira (Sat Oct 05 2013 - 18:23:43 PDT)
    - Re: [AMBER] MPI install with openmpi Makoto Chikira (Sun Oct 06 2013 - 06:36:27 PDT)
    - Re: [AMBER] MPI install with openmpi Jason Swails (Sun Oct 06 2013 - 07:17:30 PDT)
    - Re: [AMBER] MPI install with openmpi David A Case (Mon Oct 07 2013 - 05:14:12 PDT)
[AMBER] sumit.saurav.jain.gmail.com has indicated you're a friend. Accept? sumit.saurav.jain.gmail.com (Sat Oct 05 2013 - 16:31:25 PDT)
[AMBER] Error in antechamber Installation Vijayalaxmi Sahoo (Sat Oct 05 2013 - 22:27:27 PDT)
- Re: [AMBER] Error in antechamber Installation Jason Swails (Sun Oct 06 2013 - 05:04:47 PDT)
[AMBER] Hydrogen Bond Term in Amber ff99SB forcefield Asmit Bhowmick (Sun Oct 06 2013 - 18:48:52 PDT)
- Re: [AMBER] Hydrogen Bond Term in Amber ff99SB forcefield David A Case (Mon Oct 07 2013 - 05:16:28 PDT)
[AMBER] Phenyl-boronic acid derivatives lacking of parameter in Mol2 file 陈发生 (Sun Oct 06 2013 - 20:48:07 PDT)
[AMBER] Generation of melting curves Gargi Borgohai (Sun Oct 06 2013 - 20:59:11 PDT)
- Re: [AMBER] Generation of melting curves Brian Radak (Mon Oct 07 2013 - 06:39:08 PDT)
- Re: [AMBER] Generation of melting curves Daniel Roe (Mon Oct 07 2013 - 07:39:04 PDT)
  - Re: [AMBER] Generation of melting curves Carlos Simmerling (Mon Oct 07 2013 - 07:49:43 PDT)
[AMBER] Soft-core questions for TI method yuandandan (Mon Oct 07 2013 - 00:26:16 PDT)
- [AMBER] Soft-core questions for TI method yuandandan (Mon Oct 07 2013 - 00:43:29 PDT)
  - Re: [AMBER] Soft-core questions for TI method Ying-Chieh Sun (Wed Oct 30 2013 - 01:31:57 PDT)
- Re: [AMBER] Soft-core questions for TI method David A Case (Mon Oct 07 2013 - 05:21:19 PDT)
- Re: [AMBER] Soft-core questions for TI method yuandandan (Mon Oct 07 2013 - 19:58:35 PDT)
[AMBER] problem in creating .mol2 and .frcmod files Vijayalaxmi Sahoo (Mon Oct 07 2013 - 06:48:50 PDT)
- Re: [AMBER] problem in creating .mol2 and .frcmod files Jason Swails (Mon Oct 07 2013 - 07:40:27 PDT)
- Re: [AMBER] problem in creating .mol2 and .frcmod files Vijayalaxmi Sahoo (Mon Oct 07 2013 - 08:33:16 PDT)
[AMBER] ambertools patch 19 fails Matthew Wampole (Mon Oct 07 2013 - 07:57:46 PDT)
- Re: [AMBER] ambertools patch 19 fails Jason Swails (Mon Oct 07 2013 - 08:58:53 PDT)
[AMBER] Parameter Discrepancy in Walker Tutorial B1? Robert Molt (Mon Oct 07 2013 - 18:58:12 PDT)
- Re: [AMBER] Parameter Discrepancy in Walker Tutorial B1? Jason Swails (Tue Oct 08 2013 - 04:50:06 PDT)
[AMBER] Block Averaging of Trajectory Mathias Gruber (Tue Oct 08 2013 - 06:03:23 PDT)
[AMBER] GAFF angle term constants with phosphor or sulphur Igor Marques (Tue Oct 08 2013 - 06:30:49 PDT)
- Re: [AMBER] GAFF angle term constants with phosphor or sulphur James Murdock (Mon Oct 14 2013 - 06:13:16 PDT)
[AMBER] ERROR in DISTANCE RESTRAINT Sourav Purohit (Tue Oct 08 2013 - 10:21:26 PDT)
- Re: [AMBER] ERROR in DISTANCE RESTRAINT Brian Radak (Tue Oct 08 2013 - 10:30:38 PDT)
  - Re: [AMBER] ERROR in DISTANCE RESTRAINT Ross Walker (Tue Oct 08 2013 - 10:45:13 PDT)
- Re: [AMBER] ERROR in DISTANCE RESTRAINT David A Case (Tue Oct 08 2013 - 12:29:50 PDT)
[AMBER] Scaling of multi GPU runs peter.stauffert.boehringer-ingelheim.com (Tue Oct 08 2013 - 10:55:29 PDT)
- Re: [AMBER] Scaling of multi GPU runs Ross Walker (Tue Oct 08 2013 - 11:02:45 PDT)
  - Re: [AMBER] Scaling of multi GPU runs Ross Walker (Tue Oct 08 2013 - 11:13:40 PDT)
    - Re: [AMBER] Scaling of multi GPU runs Scott Le Grand (Tue Oct 08 2013 - 11:20:07 PDT)
- Re: [AMBER] Scaling of multi GPU runs Scott Le Grand (Tue Oct 08 2013 - 11:13:14 PDT)
[AMBER] Amber99SB force field Shomesankar Bhunia (Tue Oct 08 2013 - 11:13:52 PDT)
- Re: [AMBER] Amber99SB force field Carlos Simmerling (Tue Oct 08 2013 - 11:18:07 PDT)
  - Re: [AMBER] Amber99SB force field Shomesankar Bhunia (Tue Oct 08 2013 - 12:01:35 PDT)
    - Re: [AMBER] Amber99SB force field Shomesankar Bhunia (Tue Oct 08 2013 - 18:46:55 PDT)
Re: [AMBER] Problem in creating .mol2 and .frcmod files Vijayalaxmi Sahoo (Wed Oct 09 2013 - 06:38:28 PDT)
- Re: [AMBER] Problem in creating .mol2 and .frcmod files David A Case (Wed Oct 09 2013 - 07:22:02 PDT)
[AMBER] AMBER ff99Sbildn Shomesankar Bhunia (Wed Oct 09 2013 - 07:20:48 PDT)
- Re: [AMBER] AMBER ff99Sbildn Jason Swails (Wed Oct 09 2013 - 08:20:26 PDT)
  - Re: [AMBER] AMBER ff99Sbildn Shomesankar Bhunia (Wed Oct 09 2013 - 08:34:38 PDT)
    - Re: [AMBER] AMBER ff99Sbildn Jason Swails (Wed Oct 09 2013 - 08:45:01 PDT)
    - Re: [AMBER] AMBER ff99Sbildn Shomesankar Bhunia (Wed Oct 09 2013 - 08:59:56 PDT)
[AMBER] Shifting molecules by a box length Heribert Reis (Wed Oct 09 2013 - 07:53:29 PDT)
- Re: [AMBER] Shifting molecules by a box length Jason Swails (Wed Oct 09 2013 - 08:06:46 PDT)
[AMBER] Distributions of the phi and psi torsion angles during MD simulations Baptiste Legrand (Thu Oct 10 2013 - 00:51:54 PDT)
- Re: [AMBER] Distributions of the phi and psi torsion angles during MD simulations Jason Swails (Thu Oct 10 2013 - 06:45:17 PDT)
  - Re: [AMBER] Distributions of the phi and psi torsion angles during MD simulations Baptiste Legrand (Thu Oct 10 2013 - 14:50:31 PDT)
[AMBER] Questions about softcore part yuandandan (Thu Oct 10 2013 - 02:22:14 PDT)
- Re: [AMBER] Questions about softcore part David A Case (Thu Oct 10 2013 - 04:43:30 PDT)
[AMBER] High energy in per-residue MMPBSA calculation anu chandra (Thu Oct 10 2013 - 05:22:50 PDT)
[AMBER] How to run npt simulation if IFBOX=0 in .prmtop file? Dongshan Wei (Thu Oct 10 2013 - 05:43:30 PDT)
- Re: [AMBER] How to run npt simulation if IFBOX=0 in .prmtop file? Jason Swails (Thu Oct 10 2013 - 05:56:41 PDT)
  - Re: [AMBER] How to run npt simulation if IFBOX=0 in .prmtop file? Dongshan Wei (Thu Oct 10 2013 - 06:58:37 PDT)
[AMBER] Fwd: Shifting molecules by a box length Heribert Reis (Thu Oct 10 2013 - 07:41:11 PDT)
- Re: [AMBER] Fwd: Shifting molecules by a box length Daniel Roe (Thu Oct 10 2013 - 08:17:44 PDT)
[AMBER] solvate box Rasha Alqus (Thu Oct 10 2013 - 08:35:50 PDT)
- Re: [AMBER] solvate box Jason Swails (Thu Oct 10 2013 - 09:08:55 PDT)
[AMBER] SHAKE flucatuation Zhiye Tang (Thu Oct 10 2013 - 11:54:30 PDT)
- Re: [AMBER] SHAKE flucatuation Thomas Cheatham (Thu Oct 10 2013 - 12:19:09 PDT)
- Re: [AMBER] SHAKE flucatuation Jason Swails (Thu Oct 10 2013 - 12:23:05 PDT)
  - Re: [AMBER] SHAKE flucatuation Zhiye Tang (Thu Oct 10 2013 - 13:33:21 PDT)
  - Re: [AMBER] SHAKE flucatuation Thomas Cheatham (Thu Oct 10 2013 - 13:37:40 PDT)
[AMBER] MMPBSA error Symon Gathiaka (Thu Oct 10 2013 - 12:36:02 PDT)
- Re: [AMBER] MMPBSA error Ray Luo, Ph.D. (Thu Oct 10 2013 - 14:30:35 PDT)
[AMBER] Stuck on AmberTools bugfix.23 Terry M. Gray (Thu Oct 10 2013 - 14:52:14 PDT)
[AMBER] I/O errors while using CHARMM psf with CHAMBER Debayan Chakraborty (Thu Oct 10 2013 - 16:23:01 PDT)
[AMBER] Segmentation fault in tleap mmalett.nmt.edu (Thu Oct 10 2013 - 16:53:58 PDT)
- Re: [AMBER] Segmentation fault in tleap Jason Swails (Thu Oct 10 2013 - 17:19:34 PDT)
  - Re: [AMBER] Segmentation fault in tleap mmalett.nmt.edu (Thu Oct 10 2013 - 17:26:00 PDT)
- Re: [AMBER] Segmentation fault in tleap David A Case (Fri Oct 11 2013 - 07:21:59 PDT)
  - Re: [AMBER] Segmentation fault in tleap mmalett.nmt.edu (Fri Oct 11 2013 - 09:15:15 PDT)
    - Re: [AMBER] Segmentation fault in tleap David A Case (Fri Oct 11 2013 - 10:27:12 PDT)
    - Re: [AMBER] Segmentation fault in tleap mmalett.nmt.edu (Fri Oct 11 2013 - 13:19:17 PDT)
    - Re: [AMBER] Segmentation fault in tleap case (Fri Oct 11 2013 - 17:57:04 PDT)
[AMBER] Protein-DNA covalent bond John Gehman (Thu Oct 10 2013 - 17:51:55 PDT)
- Re: [AMBER] Protein-DNA covalent bond David A Case (Fri Oct 11 2013 - 07:39:12 PDT)
  - Re: [AMBER] Protein-DNA covalent bond John Gehman (Sat Oct 12 2013 - 00:53:12 PDT)
[AMBER] Stuck on AmberTools12 bug fix.23 Terry M. Gray (Thu Oct 10 2013 - 20:25:48 PDT)
- Re: [AMBER] Stuck on AmberTools12 bug fix.23 Jason Swails (Fri Oct 11 2013 - 04:20:11 PDT)
[AMBER] How to calculate the free energy change of a chemical reaction by the thermodynamic integration approach? cwt (Thu Oct 10 2013 - 23:18:00 PDT)
- Re: [AMBER] How to calculate the free energy change of a chemical reaction by the thermodynamic integration approach? Brian Radak (Fri Oct 11 2013 - 06:30:45 PDT)
Re: [AMBER] [Amber]Question about softcore yuandandan (Fri Oct 11 2013 - 06:48:50 PDT)
[AMBER] AmberTools13 and Amber11 Alan (Fri Oct 11 2013 - 08:07:10 PDT)
- Re: [AMBER] AmberTools13 and Amber11 Jason Swails (Fri Oct 11 2013 - 08:45:26 PDT)
  - Re: [AMBER] AmberTools13 and Amber11 Alan (Fri Oct 11 2013 - 09:16:23 PDT)
[AMBER] tleap cannot handle dummies in the middle? Hannes Loeffler (Fri Oct 11 2013 - 09:18:43 PDT)
- Re: [AMBER] tleap cannot handle dummies in the middle? Hannes Loeffler (Mon Mar 24 2014 - 05:10:11 PDT)
  - Re: [AMBER] tleap cannot handle dummies in the middle? David A Case (Tue Mar 25 2014 - 06:48:53 PDT)
    - Re: [AMBER] tleap cannot handle dummies in the middle? Hannes Loeffler (Tue Mar 25 2014 - 07:32:27 PDT)
    - Re: [AMBER] tleap cannot handle dummies in the middle? Jason Swails (Tue Mar 25 2014 - 07:54:44 PDT)
    - Re: [AMBER] tleap cannot handle dummies in the middle? hannes.loeffler.stfc.ac.uk (Wed Mar 26 2014 - 01:36:47 PDT)
[AMBER] running MMPBSA.py on an NMR ensemble Thomas Evangelidis (Sat Oct 12 2013 - 06:50:54 PDT)
- Re: [AMBER] running MMPBSA.py on an NMR ensemble Jason Swails (Sat Oct 12 2013 - 07:51:25 PDT)
[AMBER] Questions regarding AMBER Kamali Sripathi (Sat Oct 12 2013 - 07:22:10 PDT)
- Re: [AMBER] Questions regarding AMBER Jiri Sponer (Sat Oct 12 2013 - 07:39:15 PDT)
- Re: [AMBER] Questions regarding AMBER David Case (Sat Oct 12 2013 - 08:39:09 PDT)
  - Re: [AMBER] Questions regarding AMBER Kamali Sripathi (Sun Oct 13 2013 - 06:01:20 PDT)
    - Re: [AMBER] Questions regarding AMBER FyD (Sun Oct 13 2013 - 07:05:20 PDT)
    - Re: [AMBER] Questions regarding AMBER Kamali Sripathi (Sun Oct 13 2013 - 07:31:04 PDT)
    - Re: [AMBER] Questions regarding AMBER FyD (Sun Oct 13 2013 - 09:44:11 PDT)
    - Re: [AMBER] Questions regarding AMBER Kamali Sripathi (Sun Oct 13 2013 - 15:04:04 PDT)
[AMBER] Iron(III)Hydroxide complexing with Enterobactin (quantum chemistry calculations?) Jonathan Saboury (Sat Oct 12 2013 - 21:43:07 PDT)
- Re: [AMBER] Iron(III)Hydroxide complexing with Enterobactin (quantum chemistry calculations?) FyD (Sun Oct 13 2013 - 01:45:33 PDT)
[AMBER] Problem in deriving RESP charges with RED-3.52 tools Sajeewa Pemasinghe (Sat Oct 12 2013 - 23:12:39 PDT)
- Re: [AMBER] Problem in deriving RESP charges with RED-3.52 tools FyD (Sun Oct 13 2013 - 00:45:40 PDT)
  - Re: [AMBER] Problem in deriving RESP charges with RED-3.52 tools Sajeewa Pemasinghe (Sun Oct 13 2013 - 05:41:00 PDT)
    - Re: [AMBER] Problem in deriving RESP charges with RED-3.52 tools FyD (Sun Oct 13 2013 - 07:02:23 PDT)
    - Re: [AMBER] Problem in deriving RESP charges with RED-3.52 tools Sajeewa Pemasinghe (Tue Oct 15 2013 - 14:19:12 PDT)
    - Re: [AMBER] Problem in deriving RESP charges with RED-3.52 tools Sajeewa Pemasinghe (Tue Oct 15 2013 - 16:47:16 PDT)
    - Re: [AMBER] Problem in deriving RESP charges with RED-3.52 tools FyD (Tue Oct 15 2013 - 22:21:40 PDT)
    - Re: [AMBER] Problem in deriving RESP charges with RED-3.52 tools Sajeewa Pemasinghe (Sun Oct 20 2013 - 08:35:31 PDT)
[AMBER] Problem about water Cap with igb=10 Tong ZHU (Sun Oct 13 2013 - 07:11:39 PDT)
- Re: [AMBER] Problem about water Cap with igb=10 case (Thu Oct 24 2013 - 16:52:16 PDT)
[AMBER] DNA with NAB Jio M (Sun Oct 13 2013 - 15:47:52 PDT)
- Re: [AMBER] DNA with NAB David A Case (Mon Oct 14 2013 - 04:46:57 PDT)
  - Re: [AMBER] DNA with NAB Jio M (Tue Oct 22 2013 - 08:42:21 PDT)
    - Re: [AMBER] DNA with NAB Jio M (Thu Oct 24 2013 - 12:23:39 PDT)
    - Re: [AMBER] DNA with NAB case (Thu Oct 24 2013 - 16:50:25 PDT)
    - Re: [AMBER] DNA with NAB Jio M (Fri Oct 25 2013 - 07:14:34 PDT)
    - Re: [AMBER] DNA with NAB case (Sat Oct 26 2013 - 06:07:45 PDT)
[AMBER] PMEMD trajectory and MMPBSA Sangita Kachhap (Sun Oct 13 2013 - 22:46:51 PDT)
- Re: [AMBER] PMEMD trajectory and MMPBSA Bill Miller III (Mon Oct 14 2013 - 05:33:07 PDT)
  - Re: [AMBER] PMEMD trajectory and MMPBSA Sangita Kachhap (Mon Oct 14 2013 - 08:20:07 PDT)
Re: [AMBER] inquiry Vaibhav Dixit (Mon Oct 14 2013 - 02:43:03 PDT)
[AMBER] about rms atomic fluctuation for protein crystal .thank you very much! Yongxiu Li (Mon Oct 14 2013 - 04:36:06 PDT)
- Re: [AMBER] about rms atomic fluctuation for protein crystal .thank you very much! Pawel (Mon Oct 14 2013 - 09:04:40 PDT)
  - Re: [AMBER] about rms atomic fluctuation for protein crystal .thank you very much! Yongxiu Li (Tue Oct 15 2013 - 06:09:33 PDT)
    - Re: [AMBER] about rms atomic fluctuation for protein crystal .thank you very much! Pawel (Tue Oct 15 2013 - 16:26:42 PDT)
    - Re: [AMBER] about rms atomic fluctuation for protein crystal .thank you very much! Yongxiu Li (Tue Oct 29 2013 - 01:03:39 PDT)
    - Re: [AMBER] about rms atomic fluctuation for protein crystal .thank you very much! Pawel (Wed Oct 30 2013 - 06:12:50 PDT)
    - Re: [AMBER] about rms atomic fluctuation for protein crystal .thank you very much! Yongxiu Li (Fri Nov 08 2013 - 01:19:40 PST)
    - Re: [AMBER] about rms atomic fluctuation for protein crystal .thank you very much! Pawel (Fri Nov 08 2013 - 06:11:27 PST)
[AMBER] Exceed character limit in bellyrestraint mask selection Mike Limb (Tue Oct 15 2013 - 08:29:18 PDT)
- Re: [AMBER] Exceed character limit in bellyrestraint mask selection Jason Swails (Tue Oct 15 2013 - 09:34:01 PDT)
  - Re: [AMBER] Exceed character limit in bellyrestraint mask selection Mike Limb (Fri Oct 18 2013 - 10:35:44 PDT)
    - Re: [AMBER] Exceed character limit in bellyrestraint mask selection Jason Swails (Fri Oct 18 2013 - 11:05:47 PDT)
    - Re: [AMBER] Exceed character limit in bellyrestraint mask selection Mike Limb (Tue Oct 22 2013 - 03:39:32 PDT)
    - Re: [AMBER] Exceed character limit in bellyrestraint mask selection Jason Swails (Tue Oct 22 2013 - 04:52:24 PDT)
[AMBER] Constant pH with ligand Nicole Ippolito (Tue Oct 15 2013 - 14:55:52 PDT)
- Re: [AMBER] Constant pH with ligand Jason Swails (Tue Oct 15 2013 - 17:33:04 PDT)
- Re: [AMBER] Constant pH with ligand FyD (Tue Oct 15 2013 - 22:25:53 PDT)
  - Re: [AMBER] Constant pH with ligand Nicole Ippolito (Wed Oct 16 2013 - 04:37:49 PDT)
[AMBER] PMF for 2 Arginines Nihal Korkmaz (Tue Oct 15 2013 - 20:44:52 PDT)
- Re: [AMBER] PMF for 2 Arginines Brian Radak (Wed Oct 16 2013 - 07:30:21 PDT)
  - Re: [AMBER] PMF for 2 Arginines Nihal Korkmaz (Wed Oct 16 2013 - 09:38:32 PDT)
    - Re: [AMBER] PMF for 2 Arginines Brian Radak (Wed Oct 16 2013 - 10:23:21 PDT)
    - Re: [AMBER] PMF for 2 Arginines Carlos Simmerling (Wed Oct 16 2013 - 10:50:25 PDT)
[AMBER] PTRAJ - Problem with inserting TER card anu chandra (Wed Oct 16 2013 - 00:56:09 PDT)
- Re: [AMBER] PTRAJ - Problem with inserting TER card Daniel Roe (Wed Oct 16 2013 - 08:10:02 PDT)
  - Re: [AMBER] PTRAJ - Problem with inserting TER card anu chandra (Wed Oct 16 2013 - 22:19:16 PDT)
    - Re: [AMBER] PTRAJ - Problem with inserting TER card Daniel Roe (Thu Oct 17 2013 - 11:04:33 PDT)
    - Re: [AMBER] PTRAJ - Problem with inserting TER card anu chandra (Thu Oct 17 2013 - 21:19:32 PDT)
    - Re: [AMBER] PTRAJ - Problem with inserting TER card Daniel Roe (Fri Oct 18 2013 - 06:54:10 PDT)
[AMBER] RESP charge calculation problem for SO4 -2 group Bajarang Kumbhar (Wed Oct 16 2013 - 05:00:00 PDT)
- Re: [AMBER] RESP charge calculation problem for SO4 -2 group FyD (Wed Oct 16 2013 - 07:58:37 PDT)
[AMBER] strange behavior of MCPB houcemeddine (Wed Oct 16 2013 - 08:50:03 PDT)
- Re: [AMBER] strange behavior of MCPB Jia Xu (Wed Oct 16 2013 - 09:51:36 PDT)
[AMBER] Error message from pmemd.cuda Brian Radak (Wed Oct 16 2013 - 13:30:00 PDT)
- Re: [AMBER] Error message from pmemd.cuda Niel Henriksen (Wed Oct 16 2013 - 13:44:43 PDT)
  - Re: [AMBER] Error message from pmemd.cuda Niel Henriksen (Wed Oct 16 2013 - 13:46:33 PDT)
[AMBER] ratio between frames for MM/PBSA and frames for normal mode calculations Thomas Evangelidis (Wed Oct 16 2013 - 16:10:54 PDT)
[AMBER] Python script to reweight aMD simulations filip fratev (Wed Oct 16 2013 - 21:02:59 PDT)
[AMBER] unique atoms in TI softcore Hannes Loeffler (Thu Oct 17 2013 - 03:01:11 PDT)
- Re: [AMBER] unique atoms in TI softcore David Case (Thu Oct 17 2013 - 04:45:04 PDT)
  - Re: [AMBER] unique atoms in TI softcore Hannes Loeffler (Thu Oct 17 2013 - 07:42:58 PDT)
    - Re: [AMBER] unique atoms in TI softcore case (Fri Oct 18 2013 - 08:07:47 PDT)
[AMBER] Doubt regarding the metadynamics simulation Ravi Tripathi (Thu Oct 17 2013 - 07:59:31 PDT)
- Re: [AMBER] Doubt regarding the metadynamics simulation Adrian Roitberg (Thu Oct 17 2013 - 08:01:42 PDT)
  - Re: [AMBER] Doubt regarding the metadynamics simulation Ravi Tripathi (Thu Oct 17 2013 - 09:08:18 PDT)
    - Re: [AMBER] Doubt regarding the metadynamics simulation Adrian Roitberg (Thu Oct 17 2013 - 09:10:55 PDT)
    - Re: [AMBER] Doubt regarding the metadynamics simulation Robert Molt (Thu Oct 17 2013 - 09:14:17 PDT)
    - Re: [AMBER] Doubt regarding the metadynamics simulation Jason Swails (Thu Oct 17 2013 - 09:21:20 PDT)
[AMBER] CYM residue problem(MCPB) houcemeddine (Thu Oct 17 2013 - 08:29:17 PDT)
- Re: [AMBER] CYM residue problem(MCPB) Jason Swails (Thu Oct 17 2013 - 08:49:08 PDT)
  - Re: [AMBER] CYM residue problem(MCPB) FyD (Thu Oct 17 2013 - 11:53:19 PDT)
    - Re: [AMBER] CYM residue problem(MCPB) houcemeddine (Fri Oct 18 2013 - 06:11:14 PDT)
    - Re: [AMBER] CYM residue problem(MCPB) Jason Swails (Fri Oct 18 2013 - 07:11:00 PDT)
    - Re: [AMBER] CYM residue problem(MCPB) FyD (Fri Oct 18 2013 - 12:16:31 PDT)
[AMBER] problem for prmtop and inpcrd file generation Bajarang Kumbhar (Thu Oct 17 2013 - 22:44:42 PDT)
[AMBER] How to deal with duplicate frames during MD? rohitarora10.gmail.com (Fri Oct 18 2013 - 01:34:38 PDT)
- Re: [AMBER] How to deal with duplicate frames during MD? Daniel Roe (Fri Oct 18 2013 - 06:59:42 PDT)
  - Re: [AMBER] How to deal with duplicate frames during MD? rohitarora10.gmail.com (Fri Oct 18 2013 - 07:20:10 PDT)
    - Re: [AMBER] How to deal with duplicate frames during MD? rohitarora10.gmail.com (Fri Oct 18 2013 - 16:23:21 PDT)
    - Re: [AMBER] How to deal with duplicate frames during MD? Jason Swails (Sat Oct 19 2013 - 06:13:56 PDT)
[AMBER] problem with heme parameters bound to HIS moitrayee.mbu.iisc.ernet.in (Fri Oct 18 2013 - 02:05:48 PDT)
- Re: [AMBER] problem with heme parameters bound to HIS case (Fri Oct 18 2013 - 08:10:42 PDT)
  - Re: [AMBER] problem with heme parameters bound to HIS moitrayee.mbu.iisc.ernet.in (Fri Oct 18 2013 - 09:37:15 PDT)
    - Re: [AMBER] problem with heme parameters bound to HIS case (Thu Oct 24 2013 - 13:17:54 PDT)
[AMBER] Running simultaneously AMBER jobs in CPU and GPU Muthukumaran R (Fri Oct 18 2013 - 04:24:54 PDT)
- Re: [AMBER] Running simultaneously AMBER jobs in CPU and GPU Jan-Philip Gehrcke (Fri Oct 18 2013 - 06:29:24 PDT)
[AMBER] parmchk doesn't recognize the changes made in leaprc.ff99SB and parm.99 Sajeewa Pemasinghe (Fri Oct 18 2013 - 06:06:36 PDT)
- Re: [AMBER] parmchk doesn't recognize the changes made in leaprc.ff99SB and parm.99 Jason Swails (Fri Oct 18 2013 - 06:55:07 PDT)
  - Re: [AMBER] parmchk doesn't recognize the changes made in leaprc.ff99SB and parm.99 Sajeewa Pemasinghe (Sat Oct 19 2013 - 12:50:50 PDT)
[AMBER] Fwd: FW: Fwd: DMPC GAFF lipid membrane is freezing at 303 K. Subbarao Kanchi (Fri Oct 18 2013 - 07:21:36 PDT)
[AMBER] PROBLEM IN QM/MM RUN Tanmoy Paul (Sat Oct 19 2013 - 00:17:48 PDT)
- Re: [AMBER] PROBLEM IN QM/MM RUN Gustavo Seabra (Sat Oct 19 2013 - 08:49:11 PDT)
[AMBER] output of diffusion data doesn't show two columns for big number values Vijay Manickam Achari (Sat Oct 19 2013 - 04:01:58 PDT)
- Re: [AMBER] output of diffusion data doesn't show two columns for big number values Daniel Roe (Sat Oct 19 2013 - 09:32:09 PDT)
[AMBER] problem using the R.E.D server output Bajarang Kumbhar (Mon Oct 21 2013 - 01:58:30 PDT)
- Re: [AMBER] problem using the R.E.D server output Jason Swails (Mon Oct 21 2013 - 04:46:02 PDT)
[AMBER] optimization using gaussian and RESP using antechamber Bajarang Kumbhar (Mon Oct 21 2013 - 04:29:16 PDT)
- Re: [AMBER] optimization using gaussian and RESP using antechamber Tanmoy Paul (Wed Oct 30 2013 - 06:15:32 PDT)
[AMBER] example of MTKpp on Ambertools 13 setyanto md (Mon Oct 21 2013 - 07:18:30 PDT)
- Re: [AMBER] example of MTKpp on Ambertools 13 Daniel Roe (Mon Oct 21 2013 - 07:58:43 PDT)
  - Re: [AMBER] example of MTKpp on Ambertools 13 Jason Swails (Mon Oct 21 2013 - 08:03:23 PDT)
    - Re: [AMBER] example of MTKpp on Ambertools 13 setyanto md (Mon Oct 21 2013 - 23:31:25 PDT)
[AMBER] MMPBSA problem with CHAMBER generated topology file Uday Midya (Mon Oct 21 2013 - 20:15:06 PDT)
- Re: [AMBER] MMPBSA problem with CHAMBER generated topology file Bill Miller III (Mon Oct 21 2013 - 20:22:53 PDT)
- Re: [AMBER] MMPBSA problem with CHAMBER generated topology file Jason Swails (Tue Oct 22 2013 - 04:56:44 PDT)
[AMBER] Fwd: requesting in executing CHAMBER Soumya Lipsa Rath (Mon Oct 21 2013 - 22:57:30 PDT)
[AMBER] PCA analysis and amber prmtop file Neha Gandhi (Tue Oct 22 2013 - 01:29:37 PDT)
- Re: [AMBER] PCA analysis and amber prmtop file Jason Swails (Tue Oct 22 2013 - 04:58:07 PDT)
[AMBER] namelist input > 80 columns thomas.fox.boehringer-ingelheim.com (Tue Oct 22 2013 - 02:41:32 PDT)
- Re: [AMBER] namelist input > 80 columns thomas.fox.boehringer-ingelheim.com (Tue Oct 22 2013 - 04:43:07 PDT)
  - Re: [AMBER] namelist input > 80 columns case (Wed Oct 23 2013 - 11:18:34 PDT)
[AMBER] High Temperature at NSTEP = 0 Alessandra Lacetera (Tue Oct 22 2013 - 08:41:12 PDT)
- Re: [AMBER] High Temperature at NSTEP = 0 Brian Radak (Tue Oct 22 2013 - 08:57:03 PDT)
  - Re: [AMBER] High Temperature at NSTEP = 0 Carlos Simmerling (Tue Oct 22 2013 - 10:27:11 PDT)
[AMBER] Script? Beale, John (Tue Oct 22 2013 - 10:30:30 PDT)
- Re: [AMBER] Script? Daniel Roe (Tue Oct 22 2013 - 12:25:03 PDT)
[AMBER] Update 21 for Amber 12: EXTERN QM/MM interface Andreas Goetz (Tue Oct 22 2013 - 15:44:03 PDT)
[AMBER] MMPBSA calculation Mary Varughese (Tue Oct 22 2013 - 15:57:59 PDT)
[AMBER] Terachem tests with trial version Fabrício Bracht (Wed Oct 23 2013 - 00:21:47 PDT)
- Re: [AMBER] Terachem tests with trial version Andreas Goetz (Wed Oct 23 2013 - 10:38:40 PDT)
  - Re: [AMBER] Terachem tests with trial version Fabrício Bracht (Wed Oct 23 2013 - 13:24:41 PDT)
    - Re: [AMBER] Terachem tests with trial version Ross Walker (Wed Oct 23 2013 - 16:38:03 PDT)
    - Re: [AMBER] Terachem tests with trial version Fabrício Bracht (Thu Oct 24 2013 - 00:12:26 PDT)
[AMBER] MMPBSA.py error Rasha Alqus (Wed Oct 23 2013 - 03:11:53 PDT)
- Re: [AMBER] MMPBSA.py error Rasha Alqus (Wed Oct 23 2013 - 03:18:54 PDT)
- Re: [AMBER] MMPBSA.py error Jason Swails (Wed Oct 23 2013 - 04:40:09 PDT)
  - Re: [AMBER] MMPBSA.py error Rasha Alqus (Thu Oct 24 2013 - 06:02:32 PDT)
    - Re: [AMBER] MMPBSA.py error Jason Swails (Thu Oct 24 2013 - 07:08:57 PDT)
    - Re: [AMBER] MMPBSA.py error Rasha Alqus (Thu Oct 24 2013 - 07:31:44 PDT)
    - Re: [AMBER] MMPBSA.py error Jason Swails (Thu Oct 24 2013 - 07:40:23 PDT)
[AMBER] Leap ff10 and Sodium ion Johannes Zuegg (Wed Oct 23 2013 - 17:05:56 PDT)
- Re: [AMBER] Leap ff10 and Sodium ion case (Thu Oct 24 2013 - 04:25:08 PDT)
[AMBER] AMBERTOOLS13 test error: 01_Generalized_Born and 03_Alanine_Scanning marco.molinari (Thu Oct 24 2013 - 03:55:11 PDT)
- Re: [AMBER] AMBERTOOLS13 test error: 01_Generalized_Born and 03_Alanine_Scanning Jason Swails (Thu Oct 24 2013 - 05:21:53 PDT)
[AMBER] Regarding radial distribution function MOHD HOMAIDUR RAHMAN (Thu Oct 24 2013 - 04:46:48 PDT)
- Re: [AMBER] Regarding radial distribution function Daniel Roe (Thu Oct 24 2013 - 06:43:44 PDT)
[AMBER] MMPBSA.py problem Indrajit Deb (Thu Oct 24 2013 - 05:31:01 PDT)
- Re: [AMBER] MMPBSA.py problem Jason Swails (Thu Oct 24 2013 - 07:22:03 PDT)
[AMBER] MMGBSA, Generalized Born, protein-nucleic acid complex Vlad Cojocaru (Thu Oct 24 2013 - 05:53:45 PDT)
- Re: [AMBER] MMGBSA, Generalized Born, protein-nucleic acid complex Hai Nguyen (Thu Oct 24 2013 - 11:37:21 PDT)
[AMBER] parmed.py bug when using the "parmout" command ? Vlad Cojocaru (Thu Oct 24 2013 - 07:55:12 PDT)
- Re: [AMBER] parmed.py bug when using the "parmout" command ? Brian Radak (Thu Oct 24 2013 - 08:06:28 PDT)
  - Re: [AMBER] parmed.py bug when using the "parmout" command ? Vlad Cojocaru (Thu Oct 24 2013 - 08:14:02 PDT)
  - Re: [AMBER] parmed.py bug when using the "parmout" command ? Jason Swails (Thu Oct 24 2013 - 08:42:54 PDT)
    - Re: [AMBER] parmed.py bug when using the "parmout" command ? Vlad Cojocaru (Thu Oct 24 2013 - 09:16:04 PDT)
    - Re: [AMBER] parmed.py bug when using the "parmout" command ? Vlad Cojocaru (Thu Oct 24 2013 - 09:31:41 PDT)
    - Re: [AMBER] parmed.py bug when using the "parmout" command ? Jason Swails (Thu Oct 24 2013 - 10:09:27 PDT)
    - Re: [AMBER] parmed.py bug when using the "parmout" command ? Vlad Cojocaru (Thu Oct 24 2013 - 10:15:31 PDT)
    - Re: [AMBER] parmed.py bug when using the "parmout" command ? Vlad Cojocaru (Thu Oct 24 2013 - 10:20:35 PDT)
    - Re: [AMBER] parmed.py bug when using the "parmout" command ? Jan-Philip Gehrcke (Thu Oct 24 2013 - 10:30:22 PDT)
    - Re: [AMBER] parmed.py bug when using the "parmout" command ? Vlad Cojocaru (Thu Oct 24 2013 - 10:36:33 PDT)
    - Re: [AMBER] parmed.py bug when using the "parmout" command ? Jason Swails (Thu Oct 24 2013 - 10:43:54 PDT)
    - Re: [AMBER] parmed.py bug when using the "parmout" command ? Vlad Cojocaru (Thu Oct 24 2013 - 12:46:11 PDT)
    - Re: [AMBER] parmed.py bug when using the "parmout" command ? Jason Swails (Thu Oct 24 2013 - 10:35:42 PDT)
[AMBER] MMPBSA, ligand sequence maghtar (Fri Oct 25 2013 - 03:29:28 PDT)
- Re: [AMBER] MMPBSA, ligand sequence Jason Swails (Fri Oct 25 2013 - 04:22:32 PDT)
  - Re: [AMBER] MMPBSA, ligand sequence maghtar (Fri Oct 25 2013 - 07:17:32 PDT)
Re: [AMBER] AMBERTOOLS13 test error: 01_Generalized_Born and, 03_Alanine_Scanning (Jason Swails) marco.molinari (Fri Oct 25 2013 - 05:42:27 PDT)
[AMBER] ionic strength conversion between MMPBSA.py and PBSA Vlad Cojocaru (Fri Oct 25 2013 - 07:21:12 PDT)
- Re: [AMBER] ionic strength conversion between MMPBSA.py and PBSA Jason Swails (Fri Oct 25 2013 - 08:08:13 PDT)
  - Re: [AMBER] ionic strength conversion between MMPBSA.py and PBSA Vlad Cojocaru (Fri Oct 25 2013 - 08:44:53 PDT)
    - Re: [AMBER] ionic strength conversion between MMPBSA.py and PBSA Jason Swails (Fri Oct 25 2013 - 08:59:31 PDT)
[AMBER] About foundations of T-REMD Francesco Pietra (Fri Oct 25 2013 - 07:28:51 PDT)
- Re: [AMBER] About foundations of T-REMD Adrian Roitberg (Fri Oct 25 2013 - 07:39:28 PDT)
- Re: [AMBER] About foundations of T-REMD Brian Radak (Fri Oct 25 2013 - 07:42:28 PDT)
[AMBER] Making Au surface using xleap Hoshin Kim (Fri Oct 25 2013 - 08:39:30 PDT)
- Re: [AMBER] Making Au surface using xleap Brian Radak (Fri Oct 25 2013 - 11:23:25 PDT)
[AMBER] why are pres_X, pres_Y, and pres_Z different? Jose Borreguero (Fri Oct 25 2013 - 08:42:02 PDT)
- Re: [AMBER] why are pres_X, pres_Y, and pres_Z different? case (Fri Oct 25 2013 - 15:23:17 PDT)
  - Re: [AMBER] why are pres_X, pres_Y, and pres_Z different? Jose Borreguero (Mon Oct 28 2013 - 08:07:57 PDT)
    - Re: [AMBER] why are pres_X, pres_Y, and pres_Z different? David A Case (Mon Oct 28 2013 - 08:40:00 PDT)
    - Re: [AMBER] why are pres_X, pres_Y, and pres_Z different? Jose Borreguero (Mon Oct 28 2013 - 08:53:01 PDT)
[AMBER] mmpbsa_py_energy and PBSA options Vlad Cojocaru (Fri Oct 25 2013 - 09:02:39 PDT)
- Re: [AMBER] mmpbsa_py_energy and PBSA options Ray Luo, Ph.D. (Fri Oct 25 2013 - 09:56:01 PDT)
  - Re: [AMBER] mmpbsa_py_energy and PBSA options Vlad Cojocaru (Fri Oct 25 2013 - 10:08:52 PDT)
    - Re: [AMBER] mmpbsa_py_energy and PBSA options Ray Luo, Ph.D. (Fri Oct 25 2013 - 10:52:56 PDT)
    - Re: [AMBER] mmpbsa_py_energy and PBSA options Vlad Cojocaru (Fri Oct 25 2013 - 11:18:02 PDT)
    - Re: [AMBER] mmpbsa_py_energy and PBSA options Ray Luo, Ph.D. (Fri Oct 25 2013 - 11:54:27 PDT)
    - [AMBER] AmberTools13 Concha, Monica (Fri Oct 25 2013 - 13:42:29 PDT)
    - Re: [AMBER] AmberTools13 Jason Swails (Fri Oct 25 2013 - 14:05:06 PDT)
    - Re: [AMBER] AmberTools13 Daniel Roe (Fri Oct 25 2013 - 14:05:11 PDT)
    - Re: [AMBER] AmberTools13 Concha, Monica (Fri Oct 25 2013 - 14:37:43 PDT)
[AMBER] Constant pH with enzyme and substrate Nicole Ippolito (Fri Oct 25 2013 - 11:00:28 PDT)
- Re: [AMBER] Constant pH with enzyme and substrate Daniel Roe (Fri Oct 25 2013 - 13:06:23 PDT)
  - Re: [AMBER] Constant pH with enzyme and substrate Nicole Ippolito (Fri Oct 25 2013 - 14:51:58 PDT)
[AMBER] Single quotes in AMBER manual Jonathan Sheehan (Fri Oct 25 2013 - 12:40:34 PDT)
- Re: [AMBER] Single quotes in AMBER manual case (Sat Oct 26 2013 - 06:02:27 PDT)
[AMBER] How to use TIP4P/2005 water model Deborah Howe (Fri Oct 25 2013 - 19:57:22 PDT)
- Re: [AMBER] How to use TIP4P/2005 water model case (Sat Oct 26 2013 - 05:54:23 PDT)
  - Re: [AMBER] How to use TIP4P/2005 water model Deborah Howe (Sat Oct 26 2013 - 08:20:01 PDT)
    - Re: [AMBER] How to use TIP4P/2005 water model James Maier (Sat Oct 26 2013 - 08:56:02 PDT)
[AMBER] Difference between the .crd file format in AMBER-7 and AMBER-12 anu chandra (Sat Oct 26 2013 - 00:40:19 PDT)
- Re: [AMBER] Difference between the .crd file format in AMBER-7 and AMBER-12 case (Sat Oct 26 2013 - 05:58:46 PDT)
  - Re: [AMBER] Difference between the .crd file format in AMBER-7 and AMBER-12 anu chandra (Sun Oct 27 2013 - 21:50:49 PDT)
[AMBER] QM/MM interfacing Gaussian Ahmed Ayoub (Sat Oct 26 2013 - 04:21:45 PDT)
- Re: [AMBER] QM/MM interfacing Gaussian case (Sat Oct 26 2013 - 06:01:05 PDT)
[AMBER] ptraj - loading list of frames Mark Healey (Sat Oct 26 2013 - 13:24:06 PDT)
- Re: [AMBER] ptraj - loading list of frames Daniel Roe (Sat Oct 26 2013 - 13:48:57 PDT)
[AMBER] idecomp does not work for canonical-residues kurisaki (Sat Oct 26 2013 - 23:43:00 PDT)
- Re: [AMBER] idecomp does not work for canonical-residues Jason Swails (Sun Oct 27 2013 - 05:23:58 PDT)
  - Re: [AMBER] idecomp does not work for canonical-residues kurisaki (Sun Oct 27 2013 - 06:01:56 PDT)
    - Re: [AMBER] idecomp does not work for canonical-residues Jason Swails (Sun Oct 27 2013 - 09:05:54 PDT)
    - Re: [AMBER] idecomp does not work for canonical-residues kurisaki (Sun Oct 27 2013 - 18:26:49 PDT)
    - Re: [AMBER] idecomp does not work for canonical-residues Jason Swails (Mon Oct 28 2013 - 03:22:13 PDT)
    - Re: [AMBER] idecomp does not work for canonical-residues kurisaki (Mon Oct 28 2013 - 04:00:53 PDT)
Re: [AMBER] FW: Fwd: DMPC GAFF lipid membrane is freezing at 303 K. Subbarao Kanchi (Sun Oct 27 2013 - 17:39:15 PDT)
- Re: [AMBER] FW: Fwd: DMPC GAFF lipid membrane is freezing at 303 K. Dickson, Callum (Mon Oct 28 2013 - 05:33:20 PDT)
[AMBER] problem after minimization of pure DMF Sohag Biswas (Sun Oct 27 2013 - 21:09:31 PDT)
- Re: [AMBER] problem after minimization of pure DMF David A Case (Mon Oct 28 2013 - 04:44:36 PDT)
- Re: [AMBER] problem after minimization of pure DMF FyD (Wed Oct 30 2013 - 04:59:20 PDT)
[AMBER] Error - PMEMD.MPI cannot understand line in rst file rohitarora10.gmail.com (Mon Oct 28 2013 - 04:34:22 PDT)
- Re: [AMBER] Error - PMEMD.MPI cannot understand line in rst file Daniel Roe (Mon Oct 28 2013 - 06:57:39 PDT)
[AMBER] problem in saving prmtop file in ff12SB force field Subrata Paul (Mon Oct 28 2013 - 06:58:09 PDT)
- Re: [AMBER] problem in saving prmtop file in ff12SB force field Daniel Roe (Mon Oct 28 2013 - 07:04:09 PDT)
  - Re: [AMBER] problem in saving prmtop file in ff12SB force field Subrata Paul (Mon Oct 28 2013 - 07:37:55 PDT)
[AMBER] huge values for the vibrational entropy from ptraj Vlad Cojocaru (Tue Oct 29 2013 - 01:56:31 PDT)
- Re: [AMBER] huge values for the vibrational entropy from ptraj David A Case (Tue Oct 29 2013 - 04:45:24 PDT)
  - Re: [AMBER] huge values for the vibrational entropy from ptraj Vlad Cojocaru (Tue Oct 29 2013 - 05:37:52 PDT)
    - Re: [AMBER] huge values for the vibrational entropy from ptraj David A Case (Tue Oct 29 2013 - 06:21:25 PDT)
    - Re: [AMBER] huge values for the vibrational entropy from ptraj Vlad Cojocaru (Tue Oct 29 2013 - 06:50:53 PDT)
    - Re: [AMBER] huge values for the vibrational entropy from ptraj Jason Swails (Tue Oct 29 2013 - 08:05:29 PDT)
    - Re: [AMBER] huge values for the vibrational entropy from ptraj Vlad Cojocaru (Tue Oct 29 2013 - 08:53:11 PDT)
    - [AMBER] Sander error Concha, Monica (Tue Oct 29 2013 - 13:09:24 PDT)
    - Re: [AMBER] Sander error Jason Swails (Tue Oct 29 2013 - 13:19:41 PDT)
    - Re: [AMBER] Sander error Concha, Monica (Tue Oct 29 2013 - 13:39:09 PDT)
    - Re: [AMBER] Sander error Jason Swails (Tue Oct 29 2013 - 13:55:36 PDT)
    - Re: [AMBER] huge values for the vibrational entropy from ptraj Vlad Cojocaru (Thu Oct 31 2013 - 02:21:15 PDT)
    - Re: [AMBER] huge values for the vibrational entropy from ptraj David A Case (Thu Oct 31 2013 - 04:44:22 PDT)
    - Re: [AMBER] huge values for the vibrational entropy from ptraj Vlad Cojocaru (Thu Oct 31 2013 - 06:03:40 PDT)
    - Re: [AMBER] huge values for the vibrational entropy from ptraj Daniel Roe (Tue Oct 29 2013 - 08:12:40 PDT)
- Re: [AMBER] huge values for the vibrational entropy from ptraj Jason Swails (Tue Oct 29 2013 - 08:00:50 PDT)
[AMBER] acclerated molecular dynamics alphaP Nicole Ippolito (Tue Oct 29 2013 - 07:59:22 PDT)
- Re: [AMBER] acclerated molecular dynamics alphaP Daniel Roe (Tue Oct 29 2013 - 08:19:58 PDT)
[AMBER] calculatie the energy between two groups of atoms from an MD trajectory, is it possible? Jose Borreguero (Tue Oct 29 2013 - 13:37:07 PDT)
- Re: [AMBER] calculatie the energy between two groups of atoms from an MD trajectory, is it possible? Brian Radak (Tue Oct 29 2013 - 14:24:52 PDT)
  - Re: [AMBER] calculatie the energy between two groups of atoms from an MD trajectory, is it possible? Jose Borreguero (Wed Oct 30 2013 - 05:56:27 PDT)
  - Re: [AMBER] calculatie the energy between two groups of atoms from an MD trajectory, is it possible? Jose Borreguero (Thu Oct 31 2013 - 08:45:43 PDT)
    - Re: [AMBER] calculatie the energy between two groups of atoms from an MD trajectory, is it possible? Daniel Roe (Thu Oct 31 2013 - 08:59:24 PDT)
[AMBER] Installation error Dhananjay (Wed Oct 30 2013 - 01:41:49 PDT)
- Re: [AMBER] Installation error Jason Swails (Wed Oct 30 2013 - 04:43:58 PDT)
- Re: [AMBER] Installation error David A Case (Wed Oct 30 2013 - 04:52:45 PDT)
  - Re: [AMBER] Installation error Dhananjay (Thu Oct 31 2013 - 04:07:43 PDT)
    - Re: [AMBER] Installation error Jason Swails (Thu Oct 31 2013 - 04:22:25 PDT)
    - Re: [AMBER] Installation error Dhananjay (Thu Oct 31 2013 - 04:33:37 PDT)
    - Re: [AMBER] Installation error Jason Swails (Thu Oct 31 2013 - 04:36:13 PDT)
    - Re: [AMBER] Installation error Dhananjay (Thu Oct 31 2013 - 04:41:38 PDT)
    - Re: [AMBER] Installation error Jason Swails (Thu Oct 31 2013 - 06:27:25 PDT)
    - Re: [AMBER] Installation error David A Case (Thu Oct 31 2013 - 06:45:06 PDT)
    - Re: [AMBER] Installation error Jason Swails (Thu Oct 31 2013 - 11:36:14 PDT)
    - Re: [AMBER] Installation error Dhananjay (Thu Oct 31 2013 - 20:54:38 PDT)
    - Re: [AMBER] Installation error David A Case (Fri Nov 01 2013 - 05:11:43 PDT)
    - Re: [AMBER] Installation error Dhananjay (Mon Nov 04 2013 - 05:24:46 PST)
    - Re: [AMBER] Installation error Jason Swails (Mon Nov 04 2013 - 06:14:06 PST)
    - Re: [AMBER] Installation error Dhananjay (Tue Nov 05 2013 - 20:57:11 PST)
[AMBER] Free binding energy calculations for Zinc dependent ligands Tivani Mashamba (Wed Oct 30 2013 - 02:09:05 PDT)
- Re: [AMBER] Free binding energy calculations for Zinc dependent ligands Jason Swails (Wed Oct 30 2013 - 05:52:10 PDT)
[AMBER] Amber 12 Updater error on Arch linux M. Reza Ganjalikhany (Wed Oct 30 2013 - 02:52:16 PDT)
- Re: [AMBER] Amber 12 Updater error on Arch linux Jason Swails (Wed Oct 30 2013 - 04:20:18 PDT)
  - Re: [AMBER] Amber 12 Updater error on Arch linux M. Reza Ganjalikhany (Sat Nov 02 2013 - 05:52:23 PDT)
[AMBER] Hbond analysis Fabrício Bracht (Wed Oct 30 2013 - 11:34:26 PDT)
- Re: [AMBER] Hbond analysis Daniel Roe (Wed Oct 30 2013 - 12:01:25 PDT)
  - Re: [AMBER] Hbond analysis Fabrício Bracht (Wed Oct 30 2013 - 13:02:10 PDT)
    - Re: [AMBER] Hbond analysis Daniel Roe (Wed Oct 30 2013 - 13:12:25 PDT)
    - Re: [AMBER] Hbond analysis Fabrício Bracht (Wed Oct 30 2013 - 13:28:36 PDT)
    - Re: [AMBER] Hbond analysis Fabrício Bracht (Wed Oct 30 2013 - 13:31:25 PDT)
    - Re: [AMBER] Hbond analysis Daniel Roe (Wed Oct 30 2013 - 13:36:51 PDT)
Re: [AMBER] AMBER Digest, Vol 659, Issue 1 Sohag Biswas (Wed Oct 30 2013 - 23:23:10 PDT)
[AMBER] Monte Carlo Method/Simulation in AMBER 12 Emmanuel Oluwatobi SALAWU (Thu Oct 31 2013 - 03:38:15 PDT)
- Re: [AMBER] Monte Carlo Method/Simulation in AMBER 12 Jason Swails (Thu Oct 31 2013 - 04:24:59 PDT)
  - [AMBER] Sander error (AmberTools 13 & Amber10) Concha, Monica (Thu Oct 31 2013 - 08:24:39 PDT)
    - Re: [AMBER] Sander error (AmberTools 13 & Amber10) Daniel Roe (Thu Oct 31 2013 - 08:38:57 PDT)
    - Re: [AMBER] Sander error (AmberTools 13 & Amber10) Concha, Monica (Thu Oct 31 2013 - 09:51:12 PDT)
    - Re: [AMBER] Sander error (AmberTools 13 & Amber10) Daniel Roe (Thu Oct 31 2013 - 12:23:43 PDT)
    - Re: [AMBER] Sander error (AmberTools 13 & Amber10) Concha, Monica (Thu Oct 31 2013 - 14:40:54 PDT)
    - Re: [AMBER] Sander error (AmberTools 13 & Amber10) Daniel Roe (Thu Oct 31 2013 - 14:56:44 PDT)
    - Re: [AMBER] Sander error (AmberTools 13 & Amber10) David A Case (Fri Nov 01 2013 - 05:06:17 PDT)
- Re: [AMBER] Monte Carlo Method/Simulation in AMBER 12 David A Case (Thu Oct 31 2013 - 04:44:53 PDT)
[AMBER] About calculating entropy Olayide Arodola (Thu Oct 31 2013 - 04:26:52 PDT)
- Re: [AMBER] About calculating entropy Jason Swails (Thu Oct 31 2013 - 06:14:59 PDT)
  - Re: [AMBER] About calculating entropy Tivani Mashamba (Thu Oct 31 2013 - 06:47:21 PDT)
    - Re: [AMBER] About calculating entropy Hannes Loeffler (Thu Oct 31 2013 - 07:03:28 PDT)
    - Re: [AMBER] About calculating entropy Tivani Mashamba (Thu Oct 31 2013 - 08:39:54 PDT)
[AMBER] mdcrd to dcd 石坪江梨花 (Thu Oct 31 2013 - 04:36:18 PDT)
- Re: [AMBER] mdcrd to dcd kurisaki (Thu Oct 31 2013 - 04:49:45 PDT)
- Re: [AMBER] mdcrd to dcd Daniel Roe (Thu Oct 31 2013 - 06:42:45 PDT)
  - Re: [AMBER] mdcrd to dcd 石坪江梨花 (Thu Oct 31 2013 - 22:54:14 PDT)
[AMBER] TI soft-core parameters Hamed S. Hayatshahi (Thu Oct 31 2013 - 13:13:54 PDT)
- Re: [AMBER] TI soft-core parameters David A Case (Fri Nov 01 2013 - 05:12:15 PDT)
[AMBER] Multidihedral and histogram analysis Fabrício Bracht (Fri Nov 01 2013 - 08:48:14 PDT)
- Re: [AMBER] Multidihedral and histogram analysis Daniel Roe (Fri Nov 01 2013 - 09:20:37 PDT)
  - Re: [AMBER] Multidihedral and histogram analysis Fabrício Bracht (Fri Nov 01 2013 - 12:21:21 PDT)
[AMBER] Hybrid QM/MM Convergence Ahmed Ayoub (Sat Nov 02 2013 - 21:25:51 PDT)
- Re: [AMBER] Hybrid QM/MM Convergence Brian Radak (Sun Nov 03 2013 - 10:53:38 PST)
- Re: [AMBER] Hybrid QM/MM Convergence Tanmoy Paul (Fri Nov 08 2013 - 05:28:17 PST)
[AMBER] Sulfonamide parameters, loue chen (Sat Nov 02 2013 - 23:16:55 PDT)
- Re: [AMBER] Sulfonamide parameters, Karl N. Kirschner (Mon Nov 04 2013 - 06:12:06 PST)
- Re: [AMBER] Sulfonamide parameters, Hector A. Baldoni (Mon Nov 04 2013 - 14:00:49 PST)
  - Re: [AMBER] Sulfonamide parameters, Karl N. Kirschner (Tue Nov 05 2013 - 02:31:54 PST)
[AMBER] Temperature raises abnormally during accelerated MD O Z (Sun Nov 03 2013 - 23:41:07 PST)
- Re: [AMBER] Temperature raises abnormally during accelerated MD Daniel Roe (Mon Nov 04 2013 - 10:22:57 PST)
- Re: [AMBER] Temperature raises abnormally during accelerated MD Daniel Roe (Tue Nov 05 2013 - 07:19:26 PST)
  - Re: [AMBER] Temperature raises abnormally during accelerated MD O Z (Wed Nov 13 2013 - 22:24:25 PST)
- Re: [AMBER] Temperature raises abnormally during accelerated MD O Z (Thu Nov 21 2013 - 17:29:42 PST)
  - Re: [AMBER] Temperature raises abnormally during accelerated MD Ross Walker (Thu Nov 21 2013 - 18:05:08 PST)
    - Re: [AMBER] Temperature raises abnormally during accelerated MD O Z (Wed Dec 04 2013 - 17:02:19 PST)
[AMBER] PBC-connectivity Rasha Alqus (Mon Nov 04 2013 - 09:16:49 PST)
- Re: [AMBER] PBC-connectivity Jason Swails (Mon Nov 04 2013 - 09:28:28 PST)
[AMBER] Running Amber in GPU cluster Soumendranath Bhakat (Tue Nov 05 2013 - 00:25:46 PST)
- Re: [AMBER] Running Amber in GPU cluster Jason Swails (Tue Nov 05 2013 - 04:24:58 PST)
- Re: [AMBER] Running Amber in GPU cluster David A Case (Tue Nov 05 2013 - 04:26:37 PST)
- Re: [AMBER] Running Amber in GPU cluster Ross Walker (Tue Nov 05 2013 - 10:36:54 PST)
[AMBER] nmode and newton optimization divergence maghtar (Tue Nov 05 2013 - 00:35:09 PST)
- Re: [AMBER] nmode and newton optimization divergence David A Case (Tue Nov 05 2013 - 04:34:56 PST)
  - Re: [AMBER] nmode and newton optimization divergence maghtar (Tue Nov 05 2013 - 06:16:12 PST)
[AMBER] nmode and newton optimization divergence maghtar (Tue Nov 05 2013 - 02:05:24 PST)
[AMBER] Location of MMPBSA temporary files rohitarora10.gmail.com (Tue Nov 05 2013 - 05:18:42 PST)
- Re: [AMBER] Location of MMPBSA temporary files Jason Swails (Tue Nov 05 2013 - 05:49:50 PST)
  - Re: [AMBER] Location of MMPBSA temporary files rohitarora10.gmail.com (Tue Nov 05 2013 - 06:47:01 PST)
[AMBER] Ligand has no type kanika sharma (Tue Nov 05 2013 - 09:57:00 PST)
- Re: [AMBER] Ligand has no type David A Case (Tue Nov 05 2013 - 12:15:13 PST)
- Re: [AMBER] Ligand has no type Jason Swails (Tue Nov 05 2013 - 12:22:41 PST)
- [AMBER] Fwd: Ligand has no type kanika sharma (Wed Nov 06 2013 - 05:19:36 PST)
  - Re: [AMBER] Fwd: Ligand has no type Karl N. Kirschner (Wed Nov 06 2013 - 05:25:31 PST)
    - Re: [AMBER] Fwd: Ligand has no type kanika sharma (Wed Nov 06 2013 - 06:13:05 PST)
    - Re: [AMBER] Fwd: Ligand has no type Karl N. Kirschner (Wed Nov 06 2013 - 06:34:20 PST)
[AMBER] Parmed.py script generates additional dihedral terms Meekyum Olivia Kim (Tue Nov 05 2013 - 10:10:53 PST)
- Re: [AMBER] Parmed.py script generates additional dihedral terms Jason Swails (Tue Nov 05 2013 - 12:21:00 PST)
[AMBER] normal mode analysis, AmberTools13, vecs maghtar (Wed Nov 06 2013 - 03:20:38 PST)
- Re: [AMBER] normal mode analysis, AmberTools13, vecs David A Case (Wed Nov 06 2013 - 04:35:50 PST)
  - Re: [AMBER] normal mode analysis, AmberTools13, vecs maghtar (Thu Nov 07 2013 - 02:17:13 PST)
    - Re: [AMBER] normal mode analysis, AmberTools13, vecs case (Thu Nov 07 2013 - 04:54:20 PST)
[AMBER] help!!! I got a error when I used mmpbsa calculate the binding freeenergy David Chen (Wed Nov 06 2013 - 05:18:27 PST)
- Re: [AMBER] help!!! I got a error when I used mmpbsa calculate the binding freeenergy Jason Swails (Wed Nov 06 2013 - 05:41:31 PST)
  - Re: [AMBER] help!!! I got a error when I used mmpbsa calculate the binding freeenergy Hannes Loeffler (Wed Nov 06 2013 - 05:51:00 PST)
    - Re: [AMBER] help!!! I got a error when I used mmpbsa calculate the binding freeenergy Jason Swails (Wed Nov 06 2013 - 06:17:52 PST)
    - Re: [AMBER] help!!! I got a error when I used mmpbsa calculate the binding freeenergy David Chen (Fri Nov 08 2013 - 23:11:58 PST)
    - Re: [AMBER] help!!! I got a error when I used mmpbsa calculate the binding freeenergy hannes.loeffler.stfc.ac.uk (Sat Nov 09 2013 - 02:33:05 PST)
    - Re: [AMBER] help!!! I got a error when I used mmpbsa calculate the binding freeenergy David Chen (Sat Nov 09 2013 - 03:32:24 PST)
[AMBER] Building AMBER/MMPBSA.py.MPI with intel MPI Vlad Cojocaru (Thu Nov 07 2013 - 02:45:39 PST)
- Re: [AMBER] Building AMBER/MMPBSA.py.MPI with intel MPI Jason Swails (Thu Nov 07 2013 - 04:34:08 PST)
  - Re: [AMBER] Building AMBER/MMPBSA.py.MPI with intel MPI Vlad Cojocaru (Thu Nov 07 2013 - 04:42:41 PST)
[AMBER] error while executing sander.MPI sunita.tifrh.res.in (Thu Nov 07 2013 - 04:52:36 PST)
- Re: [AMBER] error while executing sander.MPI Daniel Roe (Thu Nov 07 2013 - 07:30:55 PST)
  - Re: [AMBER] error while executing sander.MPI sunita.tifrh.res.in (Fri Nov 08 2013 - 22:10:55 PST)
[AMBER] MMPBSA.py.MPI: mpi4py not imported via LSF Vlad Cojocaru (Thu Nov 07 2013 - 10:34:44 PST)
- Re: [AMBER] MMPBSA.py.MPI: mpi4py not imported via LSF Vlad Cojocaru (Fri Nov 08 2013 - 01:28:53 PST)
[AMBER] hexagonal unit cell for membrane simulation with NAMD Thomas Evangelidis (Thu Nov 07 2013 - 16:37:19 PST)
- Re: [AMBER] hexagonal unit cell for membrane simulation with NAMD Brian Radak (Fri Nov 08 2013 - 06:32:14 PST)
  - Re: [AMBER] hexagonal unit cell for membrane simulation with NAMD Pawel (Fri Nov 08 2013 - 14:03:40 PST)
    - Re: [AMBER] hexagonal unit cell for membrane simulation with NAMD Thomas Evangelidis (Tue Nov 12 2013 - 04:11:47 PST)
    - Re: [AMBER] hexagonal unit cell for membrane simulation with NAMD Thomas Evangelidis (Tue Nov 12 2013 - 04:28:57 PST)
    - Re: [AMBER] hexagonal unit cell for membrane simulation with NAMD Pawel (Tue Nov 12 2013 - 07:41:59 PST)
    - Re: [AMBER] hexagonal unit cell for membrane simulation with NAMD Thomas Evangelidis (Tue Nov 12 2013 - 09:31:20 PST)
    - Re: [AMBER] hexagonal unit cell for membrane simulation with NAMD Thomas Evangelidis (Tue Nov 12 2013 - 13:11:22 PST)
    - Re: [AMBER] hexagonal unit cell for membrane simulation with NAMD Jason Swails (Tue Nov 12 2013 - 14:06:30 PST)
    - Re: [AMBER] hexagonal unit cell for membrane simulation with NAMD Daniel Roe (Tue Nov 12 2013 - 14:27:32 PST)
    - Re: [AMBER] hexagonal unit cell for membrane simulation with NAMD Thomas Evangelidis (Tue Nov 12 2013 - 15:02:04 PST)
    - Re: [AMBER] hexagonal unit cell for membrane simulation with NAMD Jason Swails (Tue Nov 12 2013 - 16:51:16 PST)
    - Re: [AMBER] hexagonal unit cell for membrane simulation with NAMD Pawel (Wed Nov 13 2013 - 05:07:43 PST)
    - Re: [AMBER] hexagonal unit cell for membrane simulation with NAMD Thomas Evangelidis (Wed Nov 13 2013 - 07:27:15 PST)
    - Re: [AMBER] hexagonal unit cell for membrane simulation with NAMD Pawel Janowski (Wed Nov 13 2013 - 07:34:57 PST)
[AMBER] TI tutorial Terry M. Gray (Thu Nov 07 2013 - 20:53:15 PST)
- Re: [AMBER] TI tutorial David A Case (Fri Nov 08 2013 - 04:09:10 PST)
  - Re: [AMBER] TI tutorial Terry M. Gray (Fri Nov 08 2013 - 15:16:31 PST)
[AMBER] Nonbond cells Problem How to restart? Soumendranath Bhakat (Thu Nov 07 2013 - 23:27:23 PST)
- Re: [AMBER] Nonbond cells Problem How to restart? Daniel Roe (Fri Nov 08 2013 - 06:54:22 PST)
[AMBER] parameters for F- Mannan (Thu Nov 07 2013 - 23:46:59 PST)
- Re: [AMBER] parameters for F- David A Case (Fri Nov 08 2013 - 04:13:03 PST)
[AMBER] writing out atom radii optimized for PBSA (radiopt=1) Vlad Cojocaru (Fri Nov 08 2013 - 00:50:19 PST)
- Re: [AMBER] writing out atom radii optimized for PBSA (radiopt=1) Jason Swails (Fri Nov 08 2013 - 04:11:53 PST)
[AMBER] QMMM with Gaussian 09 not writing structures in mdcrd Claire Coderch Boué (Fri Nov 08 2013 - 01:55:03 PST)
- Re: [AMBER] QMMM with Gaussian 09 not writing structures in mdcrd David A Case (Fri Nov 08 2013 - 04:16:58 PST)
[AMBER] ph md simulation Necmettin Pirinccioglu (Fri Nov 08 2013 - 02:00:27 PST)
- Re: [AMBER] ph md simulation Jason Swails (Fri Nov 08 2013 - 04:22:17 PST)
[AMBER] creation of disulfide bonds Beale, John (Fri Nov 08 2013 - 02:18:57 PST)
- Re: [AMBER] creation of disulfide bonds Hannes Loeffler (Fri Nov 08 2013 - 02:46:51 PST)
[AMBER] MMPBSA.py.MPI Anthony Cruz Balberdi (Fri Nov 08 2013 - 08:01:37 PST)
- Re: [AMBER] MMPBSA.py.MPI David A Case (Fri Nov 08 2013 - 09:16:53 PST)
[AMBER] Input file (_MMPBSA_gb.mdin) doesn't exist Mu Xia (Fri Nov 08 2013 - 18:19:35 PST)
- Re: [AMBER] Input file (_MMPBSA_gb.mdin) doesn't exist Jason Swails (Sat Nov 09 2013 - 06:45:27 PST)
[AMBER] Problem of calculating the Van der Waals energy between two proteins Tan-MIng Chi (Fri Nov 08 2013 - 19:33:14 PST)
[AMBER] Temperature and TI with qm/mm Fabrício Bracht (Fri Nov 08 2013 - 23:33:09 PST)
- Re: [AMBER] Temperature and TI with qm/mm case (Sat Nov 09 2013 - 07:25:45 PST)
  - Re: [AMBER] Temperature and TI with qm/mm Fabrício Bracht (Sat Nov 09 2013 - 10:01:18 PST)
    - Re: [AMBER] Temperature and TI with qm/mm case (Sun Nov 10 2013 - 13:20:39 PST)
[AMBER] dna with different base pairs/turn Jio M (Sun Nov 10 2013 - 09:09:40 PST)
- Re: [AMBER] dna with different base pairs/turn ros (Sun Nov 10 2013 - 10:01:50 PST)
- Re: [AMBER] dna with different base pairs/turn David A Case (Mon Nov 11 2013 - 06:23:36 PST)
  - Re: [AMBER] dna with different base pairs/turn Jio M (Mon Nov 11 2013 - 10:01:33 PST)
    - Re: [AMBER] dna with different base pairs/turn David A Case (Mon Nov 11 2013 - 12:22:55 PST)
Re: [AMBER] update error Raman Parkesh (Sun Nov 10 2013 - 22:25:42 PST)
- Re: [AMBER] update error Raman Parkesh (Mon Nov 11 2013 - 01:44:58 PST)
  - Re: [AMBER] update error Jason Swails (Mon Nov 11 2013 - 04:12:10 PST)
    - Re: [AMBER] update error Raman Parkesh (Mon Nov 11 2013 - 05:12:52 PST)
    - Re: [AMBER] update error Raman Parkesh (Mon Nov 11 2013 - 06:24:12 PST)
    - Re: [AMBER] update error Jason Swails (Mon Nov 11 2013 - 06:37:26 PST)
- Re: [AMBER] update error Jason Swails (Mon Nov 11 2013 - 04:16:38 PST)
[AMBER] estimate memory requirements for MMPBSA.py.MPI Vlad Cojocaru (Mon Nov 11 2013 - 06:52:24 PST)
- Re: [AMBER] estimate memory requirements for MMPBSA.py.MPI Jason Swails (Mon Nov 11 2013 - 08:50:10 PST)
  - Re: [AMBER] estimate memory requirements for MMPBSA.py.MPI Vlad Cojocaru (Tue Nov 12 2013 - 00:17:44 PST)
[AMBER] R.E.D. server updating psu4.uic.edu (Mon Nov 11 2013 - 13:24:33 PST)
- Re: [AMBER] R.E.D. server updating FyD (Mon Nov 11 2013 - 14:51:47 PST)
  - Re: [AMBER] R.E.D. server updating psu4.uic.edu (Tue Nov 12 2013 - 12:20:39 PST)
[AMBER] MMPBSA errors: "failed with prmtop" and "failed when querying netcdf trajectory" Vlad Cojocaru (Tue Nov 12 2013 - 02:53:24 PST)
- Re: [AMBER] MMPBSA errors: "failed with prmtop" and "failed when querying netcdf trajectory" Jason Swails (Tue Nov 12 2013 - 05:17:09 PST)
  - Re: [AMBER] MMPBSA errors: "failed with prmtop" and "failed when querying netcdf trajectory" Vlad Cojocaru (Tue Nov 12 2013 - 05:36:23 PST)
    - Re: [AMBER] MMPBSA errors: "failed with prmtop" and "failed when querying netcdf trajectory" Vlad Cojocaru (Tue Nov 12 2013 - 06:22:50 PST)
    - Re: [AMBER] MMPBSA errors: "failed with prmtop" and "failed when querying netcdf trajectory" Jason Swails (Tue Nov 12 2013 - 07:22:40 PST)
    - Re: [AMBER] MMPBSA errors: "failed with prmtop" and "failed when querying netcdf trajectory" Vlad Cojocaru (Tue Nov 12 2013 - 07:41:41 PST)
    - Re: [AMBER] MMPBSA errors: "failed with prmtop" and "failed when querying netcdf trajectory" Jason Swails (Tue Nov 12 2013 - 08:17:54 PST)
    - Re: [AMBER] MMPBSA errors: "failed with prmtop" and "failed when querying netcdf trajectory" Vlad Cojocaru (Thu Nov 14 2013 - 06:35:48 PST)
    - Re: [AMBER] MMPBSA errors: "failed with prmtop" and "failed when querying netcdf trajectory" Jason Swails (Thu Nov 14 2013 - 07:53:26 PST)
    - Re: [AMBER] MMPBSA errors: "failed with prmtop" and "failed when querying netcdf trajectory" Vlad Cojocaru (Thu Nov 14 2013 - 08:49:48 PST)
[AMBER] Questions about pmemd.cuda and prmtop file with modified A COEF. X Sun (Tue Nov 12 2013 - 00:13:01 PST)
- Re: [AMBER] Questions about pmemd.cuda and prmtop file with modified A COEF. Jason Swails (Tue Nov 12 2013 - 17:04:13 PST)
  - Re: [AMBER] Questions about pmemd.cuda and prmtop file with modified A COEF. X Sun (Tue Nov 12 2013 - 05:03:15 PST)
    - Re: [AMBER] Questions about pmemd.cuda and prmtop file with modified A COEF. case (Wed Nov 13 2013 - 00:40:45 PST)
    - Re: [AMBER] Questions about pmemd.cuda and prmtop file with modified A COEF. Scott Le Grand (Wed Nov 13 2013 - 13:14:38 PST)
- Re: [AMBER] Questions about pmemd.cuda and prmtop file with modified A COEF. Ross Walker (Wed Nov 13 2013 - 13:53:13 PST)
[AMBER] Currently only GPU version 1.3 and 2.x are supported Ashutosh Shandilya (Tue Nov 12 2013 - 23:02:42 PST)
- Re: [AMBER] Currently only GPU version 1.3 and 2.x are supported Ashutosh Shandilya (Wed Nov 13 2013 - 02:35:02 PST)
- Re: [AMBER] Currently only GPU version 1.3 and 2.x are supported Jason Swails (Wed Nov 13 2013 - 02:41:15 PST)
  - Re: [AMBER] Currently only GPU version 1.3 and 2.x are supported Ashutosh Shandilya (Wed Nov 13 2013 - 02:49:57 PST)
    - Re: [AMBER] Currently only GPU version 1.3 and 2.x are supported Jason Swails (Wed Nov 13 2013 - 03:17:16 PST)
    - Re: [AMBER] Currently only GPU version 1.3 and 2.x are supported Ashutosh Shandilya (Wed Nov 13 2013 - 05:01:53 PST)
    - Re: [AMBER] Currently only GPU version 1.3 and 2.x are supported Jason Swails (Wed Nov 13 2013 - 07:18:00 PST)
    - Re: [AMBER] Currently only GPU version 1.3 and 2.x are supported Ashutosh Shandilya (Thu Nov 14 2013 - 23:33:20 PST)
[AMBER] How to calculate charges for a beta peptide Lalita Shaki (Wed Nov 13 2013 - 05:05:58 PST)
[AMBER] ambpdb problem with binary restart file Date, Mihir (Wed Nov 13 2013 - 10:43:02 PST)
- Re: [AMBER] ambpdb problem with binary restart file Daniel Roe (Wed Nov 13 2013 - 11:14:55 PST)
  - Re: [AMBER] ambpdb problem with binary restart file. . Date, Mihir (Wed Nov 13 2013 - 11:38:39 PST)
    - Re: [AMBER] ambpdb problem with binary restart file. . Daniel Roe (Wed Nov 13 2013 - 11:45:46 PST)
    - Re: [AMBER] ambpdb problem with binary restart file. . Jason Swails (Wed Nov 13 2013 - 11:57:47 PST)
- Re: [AMBER] ambpdb problem with binary restart file Jason Swails (Wed Nov 13 2013 - 11:16:45 PST)
[AMBER] Positional restraints George Tzotzos (Wed Nov 13 2013 - 12:41:50 PST)
- Re: [AMBER] Positional restraints Jason Swails (Wed Nov 13 2013 - 13:18:59 PST)
  - Re: [AMBER] Positional restraints George Tzotzos (Wed Nov 13 2013 - 16:10:22 PST)
    - Re: [AMBER] Positional restraints Jason Swails (Thu Nov 14 2013 - 04:26:02 PST)
[AMBER] saquinavir.prep andrea (Thu Nov 14 2013 - 03:26:01 PST)
[AMBER] minimization/equilibration amber 12 - wont generate .mdcrd and .ene files Amparo Garcia Lopez (Thu Nov 14 2013 - 04:16:19 PST)
- Re: [AMBER] minimization/equilibration amber 12 - wont generate .mdcrd and .ene files Jason Swails (Thu Nov 14 2013 - 04:38:35 PST)
  - Re: [AMBER] minimization/equilibration amber 12 - wont generate .mdcrd and .ene files Amparo Garcia Lopez (Thu Nov 14 2013 - 04:54:20 PST)
[AMBER] MMPBSA.py calculation Fernando Martín García (Thu Nov 14 2013 - 05:32:32 PST)
[AMBER] protonation of protein-ligand complex Thomas Evangelidis (Thu Nov 14 2013 - 11:30:45 PST)
- Re: [AMBER] protonation of protein-ligand complex Dwight McGee (Thu Nov 14 2013 - 11:50:42 PST)
  - Re: [AMBER] protonation of protein-ligand complex Thomas Evangelidis (Thu Nov 14 2013 - 12:14:24 PST)
    - Re: [AMBER] protonation of protein-ligand complex Brian Radak (Thu Nov 14 2013 - 12:21:59 PST)
    - Re: [AMBER] protonation of protein-ligand complex Thomas Evangelidis (Thu Nov 14 2013 - 12:52:41 PST)
    - Re: [AMBER] protonation of protein-ligand complex Jason Swails (Thu Nov 14 2013 - 13:33:58 PST)
- Re: [AMBER] protonation of protein-ligand complex Adrian Roitberg (Thu Nov 14 2013 - 13:22:51 PST)
- Re: [AMBER] protonation of protein-ligand complex Jason Swails (Thu Nov 14 2013 - 13:29:27 PST)
[AMBER] Mac OS X Mavericks Julio Dominguez (Thu Nov 14 2013 - 20:29:18 PST)
[AMBER] Inquiring abt the use of NOE pairs in analysis of MD simulations Yew Mun Yip (Fri Nov 15 2013 - 00:32:07 PST)
- Re: [AMBER] Inquiring abt the use of NOE pairs in analysis of MD simulations case (Fri Nov 15 2013 - 02:05:12 PST)
[AMBER] Qns abt REMD simulations Yew Mun Yip (Fri Nov 15 2013 - 02:51:49 PST)
[AMBER] ff12 references Jacopo Sgrignani (Fri Nov 15 2013 - 04:47:30 PST)
[AMBER] QMMM of Ca containing protein Thomas Exner (Fri Nov 15 2013 - 08:10:23 PST)
- Re: [AMBER] QMMM of Ca containing protein Thomas Exner (Fri Nov 15 2013 - 08:30:49 PST)
  - Re: [AMBER] QMMM of Ca containing protein Brian Radak (Fri Nov 15 2013 - 09:12:59 PST)
[AMBER] charmmlipid2amber.x: Permission denied Yuan Lyu (Fri Nov 15 2013 - 13:41:46 PST)
- Re: [AMBER] charmmlipid2amber.x: Permission denied Ross Walker (Fri Nov 15 2013 - 13:48:42 PST)
  - Re: [AMBER] charmmlipid2amber.x: Permission denied Yuan Lyu (Fri Nov 15 2013 - 14:08:50 PST)
    - Re: [AMBER] charmmlipid2amber.x: Permission denied Ross Walker (Fri Nov 15 2013 - 14:27:35 PST)
    - Re: [AMBER] charmmlipid2amber.x: Permission denied Yuan Lyu (Fri Nov 15 2013 - 14:45:31 PST)
[AMBER] Does anyone know how to use nab to generate a single RNA chain 肖立 (Fri Nov 15 2013 - 14:00:32 PST)
- Re: [AMBER] Does anyone know how to use nab to generate a single RNA chain Brian Radak (Fri Nov 15 2013 - 14:09:52 PST)
  - Re: [AMBER] Does anyone know how to use nab to generate a single RNA chain 肖立 (Fri Nov 15 2013 - 14:13:45 PST)
    - Re: [AMBER] Does anyone know how to use nab to generate a single RNA chain Brian Radak (Fri Nov 15 2013 - 14:25:30 PST)
[AMBER] Problem with penta coordinated HEME-HIS moitrayee.mbu.iisc.ernet.in (Fri Nov 15 2013 - 15:59:56 PST)
- Re: [AMBER] Problem with penta coordinated HEME-HIS case (Sat Nov 16 2013 - 01:13:06 PST)
  - Re: [AMBER] Problem with penta coordinated HEME-HIS moitrayee.mbu.iisc.ernet.in (Sat Nov 16 2013 - 13:06:14 PST)
- Re: [AMBER] Problem with penta coordinated HEME-HIS Jason Swails (Sun Nov 17 2013 - 08:38:44 PST)
  - Re: [AMBER] Problem with penta coordinated HEME-HIS moitrayee.mbu.iisc.ernet.in (Wed Nov 20 2013 - 18:48:37 PST)
    - Re: [AMBER] Problem with penta coordinated HEME-HIS Jason Swails (Thu Nov 21 2013 - 04:52:03 PST)
[AMBER] Dump vector problem Indrajit Deb (Fri Nov 15 2013 - 20:50:20 PST)
- Re: [AMBER] Dump vector problem Daniel Roe (Sun Nov 17 2013 - 09:26:27 PST)
[AMBER] Enquiries about running a simulation in vacuum Yip Yew Mun (Sat Nov 16 2013 - 06:57:49 PST)
- Re: [AMBER] Enquiries about running a simulation in vacuum Jason Swails (Sat Nov 16 2013 - 09:25:53 PST)
[AMBER] Amber 12 pmemd.MPI doesn't produce distance output Sajeewa Pemasinghe (Sat Nov 16 2013 - 08:26:07 PST)
- Re: [AMBER] Amber 12 pmemd.MPI doesn't produce distance output Jason Swails (Sat Nov 16 2013 - 09:19:52 PST)
  - Re: [AMBER] Amber 12 pmemd.MPI doesn't produce distance output Sajeewa Pemasinghe (Sat Nov 16 2013 - 10:01:37 PST)
[AMBER] atom does not have a type Helen Lvy (Sat Nov 16 2013 - 13:17:45 PST)
- Re: [AMBER] atom does not have a type Daniel Roe (Mon Nov 18 2013 - 09:18:53 PST)
[AMBER] Query about MM-PBSA free energy calculation for multiple ligand binding Vaibhav Jain (Sat Nov 16 2013 - 21:03:27 PST)
- Re: [AMBER] Query about MM-PBSA free energy calculation for multiple ligand binding Jason Swails (Sun Nov 17 2013 - 08:33:43 PST)
  - Re: [AMBER] Query about MM-PBSA free energy calculation for multiple ligand binding Vaibhav Jain (Mon Nov 18 2013 - 03:04:38 PST)
    - Re: [AMBER] Query about MM-PBSA free energy calculation for multiple ligand binding Jason Swails (Mon Nov 18 2013 - 04:49:08 PST)
    - Re: [AMBER] Query about MM-PBSA free energy calculation for multiple ligand binding Vaibhav Dixit (Tue Nov 19 2013 - 13:50:05 PST)
[AMBER] RMS2D maybe? Fabrício Bracht (Sun Nov 17 2013 - 11:06:33 PST)
- Re: [AMBER] RMS2D maybe? Daniel Roe (Mon Nov 18 2013 - 07:33:58 PST)
[AMBER] making a box with restraints so ligand does not float away ranjit pillai (Sun Nov 17 2013 - 11:55:08 PST)
- Re: [AMBER] making a box with restraints so ligand does not float away case (Sun Nov 17 2013 - 14:35:14 PST)
  - Re: [AMBER] making a box with restraints so ligand does not float away ranjit pillai (Mon Nov 18 2013 - 09:30:59 PST)
[AMBER] Cannot turn on column_fft? yunshi11 . (Sun Nov 17 2013 - 15:17:40 PST)
- Re: [AMBER] Cannot turn on column_fft? Adrian Roitberg (Sun Nov 17 2013 - 15:23:51 PST)
[AMBER] gpu_download_partial_forces: download failed unspecified launch failure Ashutosh Shandilya (Sun Nov 17 2013 - 21:41:19 PST)
- Re: [AMBER] gpu_download_partial_forces: download failed unspecified launch failure Daniel Roe (Mon Nov 18 2013 - 09:32:26 PST)
  - Re: [AMBER] gpu_download_partial_forces: download failed unspecified launch failure Ashutosh Shandilya (Tue Nov 19 2013 - 07:47:48 PST)
    - Re: [AMBER] gpu_download_partial_forces: download failed unspecified launch failure Niel Henriksen (Tue Nov 19 2013 - 08:17:59 PST)
    - Re: [AMBER] gpu_download_partial_forces: download failed unspecified launch failure Jason Swails (Tue Nov 19 2013 - 08:18:46 PST)
    - Re: [AMBER] gpu_download_partial_forces: download failed unspecified launch failure Ross Walker (Tue Nov 19 2013 - 08:14:33 PST)
[AMBER] which PBRadii is best when we use PBSA method to calculate the bonding affinity fjliu (Sun Nov 17 2013 - 23:32:41 PST)
- [AMBER] CL vs Cl & more... FyD (Mon Nov 18 2013 - 02:45:34 PST)
  - Re: [AMBER] CL vs Cl & more... case (Mon Nov 18 2013 - 04:10:05 PST)
    - Re: [AMBER] CL vs Cl & more... FyD (Mon Nov 18 2013 - 04:37:47 PST)
- Re: [AMBER] which PBRadii is best when we use PBSA method to calculate the bonding affinity Jason Swails (Mon Nov 18 2013 - 04:47:39 PST)
[AMBER] Freezing the angle during the simulation anu chandra (Mon Nov 18 2013 - 04:57:54 PST)
- Re: [AMBER] Freezing the angle during the simulation Jason Swails (Mon Nov 18 2013 - 05:19:36 PST)
[AMBER] Substructure potential energy Toomas Kaevand (Mon Nov 18 2013 - 08:32:47 PST)
- Re: [AMBER] Substructure potential energy Carlos Simmerling (Mon Nov 18 2013 - 08:38:54 PST)
  - Re: [AMBER] Substructure potential energy Toomas Kaevand (Mon Nov 18 2013 - 08:44:27 PST)
[AMBER] Bug in ptraj (Ambertools 13 patch 20) Åke Sandgren (Mon Nov 18 2013 - 09:08:23 PST)
[AMBER] PME Direct Force takes up 40% CPU time? yunshi11 . (Mon Nov 18 2013 - 09:46:35 PST)
- Re: [AMBER] PME Direct Force takes up 40% CPU time? Jason Swails (Mon Nov 18 2013 - 10:10:56 PST)
- Re: [AMBER] PME Direct Force takes up 40% CPU time? yunshi11 . (Tue Nov 19 2013 - 08:35:51 PST)
  - Re: [AMBER] PME Direct Force takes up 40% CPU time? Jason Swails (Tue Nov 19 2013 - 09:17:51 PST)
[AMBER] Wham tolerance Fabrício Bracht (Mon Nov 18 2013 - 13:38:53 PST)
- Re: [AMBER] Wham tolerance Adrian Roitberg (Mon Nov 18 2013 - 13:41:16 PST)
  - Re: [AMBER] Wham tolerance Fabrício Bracht (Mon Nov 18 2013 - 14:17:34 PST)
    - Re: [AMBER] Wham tolerance Jason Swails (Mon Nov 18 2013 - 14:41:21 PST)
    - Re: [AMBER] Wham tolerance Brian Radak (Tue Nov 19 2013 - 07:21:05 PST)
[AMBER] CUDA driver insufficient wei zhang (Mon Nov 18 2013 - 14:08:30 PST)
- Re: [AMBER] CUDA driver insufficient Jason Swails (Mon Nov 18 2013 - 14:32:59 PST)
  - Re: [AMBER] CUDA driver insufficient wei zhang (Mon Nov 18 2013 - 15:35:30 PST)
    - Re: [AMBER] CUDA driver insufficient Ross Walker (Mon Nov 18 2013 - 20:26:17 PST)
    - Re: [AMBER] CUDA driver insufficient Scott Le Grand (Mon Nov 18 2013 - 21:13:54 PST)
    - Re: [AMBER] CUDA driver insufficient wei zhang (Tue Nov 19 2013 - 07:19:16 PST)
    - Re: [AMBER] CUDA driver insufficient wei zhang (Wed Nov 20 2013 - 07:09:27 PST)
    - Re: [AMBER] CUDA driver insufficient wei zhang (Tue Nov 26 2013 - 15:35:55 PST)
    - Re: [AMBER] CUDA driver insufficient Ross Walker (Tue Nov 26 2013 - 16:31:22 PST)
    - Re: [AMBER] CUDA driver insufficient wei zhang (Wed Nov 27 2013 - 11:45:24 PST)
[AMBER] PARSE radii and effective radii IN MM/PBSA & MM/GBSA psu4.uic.edu (Mon Nov 18 2013 - 15:50:56 PST)
- Re: [AMBER] PARSE radii and effective radii IN MM/PBSA & MM/GBSA Ray Luo, Ph.D. (Mon Nov 18 2013 - 16:09:12 PST)
  - Re: [AMBER] PARSE radii and effective radii IN MM/PBSA & MM/GBSA psu4.uic.edu (Mon Dec 02 2013 - 15:52:40 PST)
    - Re: [AMBER] PARSE radii and effective radii IN MM/PBSA & MM/GBSA Ray Luo, Ph.D. (Mon Dec 02 2013 - 16:35:17 PST)
[AMBER] Res-Res energy shows different value with or without explicit solvent kurisaki (Tue Nov 19 2013 - 04:06:05 PST)
- Re: [AMBER] Res-Res energy shows different value with or without explicit solvent Jason Swails (Tue Nov 19 2013 - 04:53:48 PST)
  - Re: [AMBER] Res-Res energy shows different value with or without explicit solvent kurisaki (Tue Nov 19 2013 - 05:06:22 PST)
    - Re: [AMBER] Res-Res energy shows different value with or without explicit solvent Carlos Simmerling (Tue Nov 19 2013 - 05:13:58 PST)
    - Re: [AMBER] Res-Res energy shows different value with or without explicit solvent kurisaki (Tue Nov 19 2013 - 16:45:24 PST)
    - Re: [AMBER] Res-Res energy shows different value with or without explicit solvent Carlos Simmerling (Tue Nov 19 2013 - 17:00:17 PST)
    - Re: [AMBER] Res-Res energy shows different value with or without explicit solvent kurisaki (Tue Nov 19 2013 - 18:12:09 PST)
    - Re: [AMBER] Res-Res energy shows different value with or without explicit solvent Jason Swails (Tue Nov 19 2013 - 18:43:20 PST)
    - Re: [AMBER] Res-Res energy shows different value with or without explicit solvent Jason Swails (Tue Nov 19 2013 - 17:10:18 PST)
Re: [AMBER] Fwd: which PBRadii is best when we use PBSA method to calculate the bonding affinity Jason Swails (Tue Nov 19 2013 - 05:15:01 PST)
[AMBER] how to calculate electron density and order parameters of lipid11 membrane Thomas Evangelidis (Tue Nov 19 2013 - 05:33:01 PST)
- Re: [AMBER] how to calculate electron density and order parameters of lipid11 membrane Thomas Evangelidis (Tue Nov 19 2013 - 13:43:22 PST)
  - Re: [AMBER] how to calculate electron density and order parameters of lipid11 membrane Jason Swails (Tue Nov 19 2013 - 17:16:01 PST)
[AMBER] README under pmemd/src? yunshi11 . (Tue Nov 19 2013 - 08:45:45 PST)
- Re: [AMBER] README under pmemd/src? Ross Walker (Tue Nov 19 2013 - 10:35:28 PST)
  - Re: [AMBER] README under pmemd/src? yunshi11 . (Wed Nov 20 2013 - 09:21:41 PST)
    - Re: [AMBER] README under pmemd/src? Jason Swails (Wed Nov 20 2013 - 10:14:21 PST)
[AMBER] Hill coef in constant ph calculation fit Fabrício Bracht (Tue Nov 19 2013 - 09:23:15 PST)
- Re: [AMBER] Hill coef in constant ph calculation fit Jason Swails (Tue Nov 19 2013 - 10:16:52 PST)
[AMBER] van der Waals energy component calculation Dennis Stauffer (Tue Nov 19 2013 - 14:36:52 PST)
- Re: [AMBER] van der Waals energy component calculation David A Case (Wed Nov 20 2013 - 05:16:02 PST)
[AMBER] About turning off energy terms between selected atoms Mo Chen (Tue Nov 19 2013 - 15:27:26 PST)
- Re: [AMBER] About turning off energy terms between selected atoms David A Case (Thu Nov 21 2013 - 04:33:49 PST)
  - Re: [AMBER] About turning off energy terms between selected atoms Jason Swails (Thu Nov 21 2013 - 04:44:31 PST)
[AMBER] the dielectric constant for mixed solvent in mmpbsa Fengxue Li (Tue Nov 19 2013 - 16:39:48 PST)
- Re: [AMBER] the dielectric constant for mixed solvent in mmpbsa Jason Swails (Tue Nov 19 2013 - 17:02:32 PST)
[AMBER] Analysis of REMD trajectories (YM) Yip Yew Mun (Tue Nov 19 2013 - 23:45:34 PST)
- Re: [AMBER] Analysis of REMD trajectories (YM) Jason Swails (Wed Nov 20 2013 - 14:28:57 PST)
[AMBER] Error with angle restrain in CUDA PMEMD anu chandra (Wed Nov 20 2013 - 03:26:46 PST)
- Re: [AMBER] Error with angle restrain in CUDA PMEMD Jason Swails (Wed Nov 20 2013 - 04:35:13 PST)
  - Re: [AMBER] Error with angle restrain in CUDA PMEMD anu chandra (Thu Nov 21 2013 - 23:06:32 PST)
    - Re: [AMBER] Error with angle restrain in CUDA PMEMD Jason Swails (Fri Nov 22 2013 - 06:27:11 PST)
- Re: [AMBER] Error with angle restrain in CUDA PMEMD David A Case (Wed Nov 20 2013 - 05:26:36 PST)
  - Re: [AMBER] Error with angle restrain in CUDA PMEMD anu chandra (Thu Nov 21 2013 - 23:18:38 PST)
[AMBER] RTIL simulation Saeed Nasiri (Wed Nov 20 2013 - 05:09:35 PST)
- Re: [AMBER] RTIL simulation David A Case (Thu Nov 21 2013 - 04:52:47 PST)
[AMBER] ante-MMPBSA Milo Westler (Wed Nov 20 2013 - 08:34:23 PST)
- Re: [AMBER] ante-MMPBSA Milo Westler (Wed Nov 20 2013 - 08:38:12 PST)
  - Re: [AMBER] ante-MMPBSA Milo Westler (Wed Nov 20 2013 - 08:43:33 PST)
- Re: [AMBER] ante-MMPBSA Jason Swails (Wed Nov 20 2013 - 08:54:03 PST)
  - Re: [AMBER] ante-MMPBSA Milo Westler (Wed Nov 20 2013 - 09:10:55 PST)
[AMBER] Fwd: gpu_download_partial_forces: download failed unspecified launch failure Ashutosh Shandilya (Wed Nov 20 2013 - 09:19:10 PST)
- Re: [AMBER] Fwd: gpu_download_partial_forces: download failed unspecified launch failure Jason Swails (Wed Nov 20 2013 - 10:17:01 PST)
- Re: [AMBER] Fwd: gpu_download_partial_forces: download failed unspecified launch failure Niel Henriksen (Wed Nov 20 2013 - 10:17:53 PST)
[AMBER] C2H2 zinc finger stability Michael Garton (Wed Nov 20 2013 - 10:42:12 PST)
[AMBER] Nudged Elastic Band with Explicit Solvent for a Larger Protein James W. Snyder, Jr. (Wed Nov 20 2013 - 12:40:11 PST)
- Re: [AMBER] Nudged Elastic Band with Explicit Solvent for a Larger Protein Daniel Roe (Wed Nov 20 2013 - 12:57:44 PST)
  - Re: [AMBER] Nudged Elastic Band with Explicit Solvent for a Larger Protein James W. Snyder, Jr. (Wed Nov 20 2013 - 13:34:32 PST)
    - Re: [AMBER] Nudged Elastic Band with Explicit Solvent for a Larger Protein Daniel Roe (Wed Nov 20 2013 - 14:35:27 PST)
    - Re: [AMBER] Nudged Elastic Band with Explicit Solvent for a Larger Protein James W. Snyder, Jr. (Wed Nov 20 2013 - 16:33:46 PST)
[AMBER] How do I know if QM is working in sander.MPI? yunshi11 . (Wed Nov 20 2013 - 19:23:11 PST)
- Re: [AMBER] How do I know if QM is working in sander.MPI? Ross Walker (Wed Nov 20 2013 - 19:33:14 PST)
  - Re: [AMBER] How do I know if QM is working in sander.MPI? Brian Radak (Thu Nov 21 2013 - 06:00:32 PST)
    - Re: [AMBER] How do I know if QM is working in sander.MPI? Jason Swails (Thu Nov 21 2013 - 06:53:05 PST)
    - Re: [AMBER] How do I know if QM is working in sander.MPI? Brian Radak (Thu Nov 21 2013 - 07:07:23 PST)
    - Re: [AMBER] How do I know if QM is working in sander.MPI? Gustavo Seabra (Thu Nov 21 2013 - 07:24:33 PST)
    - Re: [AMBER] How do I know if QM is working in sander.MPI? Jason Swails (Thu Nov 21 2013 - 07:46:09 PST)
    - Re: [AMBER] How do I know if QM is working in sander.MPI? Jan-Philip Gehrcke (Fri Nov 22 2013 - 04:02:13 PST)
    - Re: [AMBER] How do I know if QM is working in sander.MPI? yunshi11 . (Fri Nov 22 2013 - 10:04:34 PST)
[AMBER] maximum simulated annealing temperature in explicit solvent Thomas Evangelidis (Thu Nov 21 2013 - 02:23:25 PST)
- Re: [AMBER] maximum simulated annealing temperature in explicit solvent Carlos Simmerling (Thu Nov 21 2013 - 03:33:50 PST)
[AMBER] GTX 780 Ti filip fratev (Fri Nov 22 2013 - 00:03:44 PST)
- Re: [AMBER] GTX 780 Ti Scott Le Grand (Fri Nov 22 2013 - 09:46:23 PST)
- Re: [AMBER] GTX 780 Ti Ross Walker (Fri Nov 22 2013 - 09:54:37 PST)
  - Re: [AMBER] GTX 780 Ti filip fratev (Fri Nov 22 2013 - 20:50:44 PST)
    - Re: [AMBER] GTX 780 Ti Ross Walker (Sat Nov 23 2013 - 14:14:54 PST)
    - Re: [AMBER] GTX 780 Ti filip fratev (Sun Nov 24 2013 - 00:15:40 PST)
- Re: [AMBER] GTX 780 Ti Bill Ross (Mon Nov 25 2013 - 20:39:20 PST)
[AMBER] New empirical force field tools: Release of R.E.D. Server Dev./R.E.D. Python FyD (Fri Nov 22 2013 - 02:22:40 PST)
[AMBER] Query about residue decomposition energy Kshatresh Dutta Dubey (Fri Nov 22 2013 - 02:58:41 PST)
- Re: [AMBER] Query about residue decomposition energy Jason Swails (Fri Nov 22 2013 - 04:51:30 PST)
  - Re: [AMBER] Query about residue decomposition energy Kshatresh Dutta Dubey (Fri Nov 22 2013 - 06:41:13 PST)
    - Re: [AMBER] Query about residue decomposition energy Jason Swails (Fri Nov 22 2013 - 07:17:32 PST)
[AMBER] REMD mdout file in AMBER12 do not show REMD EXCHANGE CALCULATION section sunita.tifrh.res.in (Fri Nov 22 2013 - 06:07:01 PST)
- Re: [AMBER] REMD mdout file in AMBER12 do not show REMD EXCHANGE CALCULATION section Jason Swails (Fri Nov 22 2013 - 06:40:43 PST)
  - Re: [AMBER] REMD mdout file in AMBER12 do not show REMD EXCHANGE CALCULATION section sunita.tifrh.res.in (Fri Nov 22 2013 - 08:36:12 PST)
- Re: [AMBER] REMD mdout file in AMBER12 do not show REMD EXCHANGE CALCULATION section Jason Swails (Fri Nov 22 2013 - 06:42:15 PST)
[AMBER] Fwd: Amber 11 with AM1/d and PM6 Jianzhuang Yao (Fri Nov 22 2013 - 09:33:27 PST)
- Re: [AMBER] Fwd: Amber 11 with AM1/d and PM6 Jason Swails (Fri Nov 22 2013 - 09:40:35 PST)
  - Re: [AMBER] Fwd: Amber 11 with AM1/d and PM6 Jianzhuang Yao (Fri Nov 22 2013 - 09:46:52 PST)
[AMBER] Wanna run nanoseconds of QM/MM MD? yunshi11 . (Fri Nov 22 2013 - 10:19:34 PST)
- Re: [AMBER] Wanna run nanoseconds of QM/MM MD? Jason Swails (Fri Nov 22 2013 - 10:32:54 PST)
  - Re: [AMBER] Wanna run nanoseconds of QM/MM MD? Ross Walker (Fri Nov 22 2013 - 10:59:30 PST)
    - Re: [AMBER] Wanna run nanoseconds of QM/MM MD? yunshi11 . (Fri Nov 22 2013 - 11:47:04 PST)
    - Re: [AMBER] Wanna run nanoseconds of QM/MM MD? Jason Swails (Fri Nov 22 2013 - 12:04:43 PST)
    - Re: [AMBER] Wanna run nanoseconds of QM/MM MD? Brian Radak (Fri Nov 22 2013 - 11:48:46 PST)
[AMBER] SQM file format Geoffrey Gray (Fri Nov 22 2013 - 10:48:38 PST)
- Re: [AMBER] SQM file format Brian Radak (Fri Nov 22 2013 - 11:41:48 PST)
  - Re: [AMBER] SQM file format Brian Radak (Fri Nov 22 2013 - 11:54:23 PST)
    - Re: [AMBER] SQM file format Geoffrey Gray (Sat Nov 23 2013 - 07:10:10 PST)
[AMBER] tleap command Saeed Nasiri (Sat Nov 23 2013 - 02:46:34 PST)
- Re: [AMBER] tleap command case (Sat Nov 23 2013 - 13:32:32 PST)
[AMBER] query about atom nomenclature in NOE restraints Thomas Evangelidis (Sat Nov 23 2013 - 04:26:28 PST)
- Re: [AMBER] query about atom nomenclature in NOE restraints Thomas Evangelidis (Sat Nov 23 2013 - 08:12:31 PST)
  - Re: [AMBER] query about atom nomenclature in NOE restraints case (Sat Nov 23 2013 - 13:35:40 PST)
[AMBER] Fix a atom?? X Sun (Fri Nov 22 2013 - 18:11:16 PST)
- Re: [AMBER] Fix a atom?? case (Sat Nov 23 2013 - 13:28:43 PST)
  - [AMBER] Detailed. Fix a atom?? X Sun (Fri Nov 22 2013 - 23:50:00 PST)
    - Re: [AMBER] Detailed. Fix a atom?? case (Sat Nov 23 2013 - 17:08:42 PST)
[AMBER] About Cv in _MMPBSA_complex_nm.out.0 赵媛 (Mon Nov 25 2013 - 08:52:23 PST)
- Re: [AMBER] About Cv in _MMPBSA_complex_nm.out.0 Ray Luo, Ph.D. (Mon Nov 25 2013 - 09:03:25 PST)
- Re: [AMBER] About Cv in _MMPBSA_complex_nm.out.0 赵媛 (Mon Nov 25 2013 - 18:57:38 PST)
[AMBER] pbsa: solvation radius from topology file not used when radiopt=0 Jan-Philip Gehrcke (Mon Nov 25 2013 - 09:38:43 PST)
- Re: [AMBER] pbsa: solvation radius from topology file not used when radiopt=0 Jan-Philip Gehrcke (Mon Nov 25 2013 - 10:04:08 PST)
  - Re: [AMBER] pbsa: solvation radius from topology file not used when radiopt=0 Ray Luo, Ph.D. (Mon Nov 25 2013 - 10:13:18 PST)
    - Re: [AMBER] pbsa: solvation radius from topology file not used when radiopt=0 Jan-Philip Gehrcke (Mon Nov 25 2013 - 10:52:26 PST)
    - Re: [AMBER] pbsa: solvation radius from topology file not used when radiopt=0 Ray Luo, Ph.D. (Mon Nov 25 2013 - 11:16:11 PST)
    - Re: [AMBER] pbsa: solvation radius from topology file not used when radiopt=0 wmsmith.uci.edu (Mon Nov 25 2013 - 12:00:00 PST)
    - Re: [AMBER] pbsa: solvation radius from topology file not used when radiopt=0 Ray Luo, Ph.D. (Tue Nov 26 2013 - 10:49:17 PST)
    - Re: [AMBER] pbsa: solvation radius from topology file not used when radiopt=0 Jan-Philip Gehrcke (Tue Dec 03 2013 - 04:54:29 PST)
    - Re: [AMBER] pbsa: solvation radius from topology file not used when radiopt=0 Ray Luo, Ph.D. (Tue Dec 03 2013 - 10:38:47 PST)
    - Re: [AMBER] pbsa: solvation radius from topology file not used when radiopt=0 wmsmith.uci.edu (Tue Dec 03 2013 - 12:21:15 PST)
    - Re: [AMBER] pbsa: solvation radius from topology file not used when radiopt=0 Jan-Philip Gehrcke (Sat May 24 2014 - 10:37:25 PDT)
    - Re: [AMBER] pbsa: solvation radius from topology file not used when radiopt=0 Ray Luo, Ph.D. (Sat May 24 2014 - 11:52:15 PDT)
- Re: [AMBER] pbsa: solvation radius from topology file not used when radiopt=0 Jason Swails (Mon Nov 25 2013 - 10:38:05 PST)
[AMBER] error while loading shared libraries: libgfortran.so.3 Jio M (Mon Nov 25 2013 - 11:43:19 PST)
- Re: [AMBER] error while loading shared libraries: libgfortran.so.3 Jason Swails (Mon Nov 25 2013 - 12:10:38 PST)
  - Re: [AMBER] error while loading shared libraries: libgfortran.so.3 Jio M (Mon Nov 25 2013 - 13:21:51 PST)
[AMBER] MMPBSA.py strip_mask issue psu4.uic.edu (Mon Nov 25 2013 - 12:24:22 PST)
- Re: [AMBER] MMPBSA.py strip_mask issue Jason Swails (Mon Nov 25 2013 - 15:08:35 PST)
  - Re: [AMBER] MMPBSA.py strip_mask issue psu4.uic.edu (Sun Dec 15 2013 - 20:52:43 PST)
    - Re: [AMBER] MMPBSA.py strip_mask issue Jason Swails (Mon Dec 16 2013 - 05:29:37 PST)
[AMBER] Multiple restraint masks Michael Garton (Tue Nov 26 2013 - 07:34:47 PST)
- Re: [AMBER] Multiple restraint masks Jason Swails (Tue Nov 26 2013 - 08:29:42 PST)
  - Re: [AMBER] Multiple restraint masks case (Tue Nov 26 2013 - 14:52:54 PST)
    - Re: [AMBER] Multiple restraint masks Jio M (Tue Nov 26 2013 - 20:19:00 PST)
    - Re: [AMBER] Multiple restraint masks case (Wed Nov 27 2013 - 18:23:44 PST)
[AMBER] internal geometry restraint Jio M (Tue Nov 26 2013 - 08:06:20 PST)
- Re: [AMBER] internal geometry restraint Jason Swails (Tue Nov 26 2013 - 08:31:35 PST)
- Re: [AMBER] internal geometry restraint case (Tue Nov 26 2013 - 14:56:11 PST)
  - Re: [AMBER] internal geometry restraint Jio M (Tue Nov 26 2013 - 19:09:18 PST)
    - Re: [AMBER] internal geometry restraint Jio M (Thu Nov 28 2013 - 07:40:28 PST)
    - Re: [AMBER] internal geometry restraint Jio M (Sun Dec 01 2013 - 16:41:12 PST)
    - Re: [AMBER] internal geometry restraint David A Case (Mon Dec 02 2013 - 05:04:10 PST)
    - Re: [AMBER] internal geometry restraint Jio M (Mon Dec 02 2013 - 09:50:42 PST)
    - Re: [AMBER] internal geometry restraint David A Case (Mon Dec 02 2013 - 12:06:53 PST)
[AMBER] AMBER 2 LAMMPS Arjun Sharma (Wed Nov 27 2013 - 08:40:48 PST)
- Re: [AMBER] AMBER 2 LAMMPS Brian Radak (Wed Nov 27 2013 - 12:20:18 PST)
[AMBER] ff99SB with nmr and ildn corrections Norah Schlacter (Wed Nov 27 2013 - 13:10:33 PST)
- Re: [AMBER] ff99SB with nmr and ildn corrections case (Wed Nov 27 2013 - 18:31:07 PST)
[AMBER] Atom types for "alkene carbons", R.E.D. Cecilia Lindgren (Thu Nov 28 2013 - 06:40:34 PST)
- Re: [AMBER] Atom types for "alkene carbons", R.E.D. FyD (Thu Nov 28 2013 - 08:06:34 PST)
- Re: [AMBER] Atom types for "alkene carbons", R.E.D. case (Fri Nov 29 2013 - 06:30:34 PST)
  - Re: [AMBER] Atom types for "alkene carbons", R.E.D. FyD (Fri Nov 29 2013 - 08:50:54 PST)
    - Re: [AMBER] Atom types for "alkene carbons", R.E.D. FyD (Sat Nov 30 2013 - 01:04:49 PST)
[AMBER] Trying to relax selected residues in tleap gives a null list error Sajeewa Pemasinghe (Thu Nov 28 2013 - 20:50:05 PST)
- Re: [AMBER] Trying to relax selected residues in tleap gives a null list error FyD (Thu Nov 28 2013 - 21:41:59 PST)
  - Re: [AMBER] Trying to relax selected residues in tleap gives a null list error Sajeewa Pemasinghe (Fri Nov 29 2013 - 12:35:58 PST)
[AMBER] Error "glibc detected" sander Souvik Sur (Fri Nov 29 2013 - 01:18:11 PST)
- Re: [AMBER] Error "glibc detected" sander Jan-Philip Gehrcke (Fri Nov 29 2013 - 02:09:22 PST)
[AMBER] Volume calculation Sanjib Paul (Fri Nov 29 2013 - 04:47:05 PST)
- [AMBER] RE : Volume calculation ABEL Stephane 175950 (Fri Nov 29 2013 - 05:05:08 PST)
[AMBER] TR : [PROVENANCE INTERNET] RE : Volume calculation ABEL Stephane 175950 (Fri Nov 29 2013 - 05:09:36 PST)
- Re: [AMBER] TR : [PROVENANCE INTERNET] RE : Volume calculation Sanjib Paul (Fri Nov 29 2013 - 06:35:53 PST)
[AMBER] Topology files of homodimer-ligand complex George Tzotzos (Fri Nov 29 2013 - 11:02:18 PST)
- Re: [AMBER] Topology files of homodimer-ligand complex Jason Swails (Thu Dec 05 2013 - 07:20:20 PST)
[AMBER] planarity of Trp side chain and improper torsion term Jorge Iulek (Fri Nov 29 2013 - 14:15:31 PST)
- Re: [AMBER] planarity of Trp side chain and improper torsion term case (Sat Nov 30 2013 - 06:13:41 PST)
  - Re: [AMBER] planarity of Trp side chain and improper torsion term Jorge Iulek (Sun Dec 01 2013 - 03:30:21 PST)
    - Re: [AMBER] planarity of Trp side chain and improper torsion term case (Sun Dec 01 2013 - 14:23:28 PST)
[AMBER] Does pmemd or pmemd.mpi support center of mass restraint? zhongqiao hu (Sat Nov 30 2013 - 08:01:36 PST)
- Re: [AMBER] Does pmemd or pmemd.mpi support center of mass restraint? case (Sat Nov 30 2013 - 08:39:44 PST)
- Re: [AMBER] Does pmemd or pmemd.mpi support center of mass restraint? Jason Swails (Sat Nov 30 2013 - 08:42:56 PST)
  - Re: [AMBER] Does pmemd or pmemd.mpi support center of mass restraint? Igor Marques (Fri Dec 13 2013 - 12:17:57 PST)
    - Re: [AMBER] Does pmemd or pmemd.mpi support center of mass restraint? Ross Walker (Fri Dec 13 2013 - 12:25:18 PST)
- Re: [AMBER] Does pmemd or pmemd.mpi support center of mass restraint? zhongqiao hu (Sun Dec 01 2013 - 06:52:35 PST)
[AMBER] SETTING QM ZONE Tanmoy Paul (Mon Dec 02 2013 - 02:52:46 PST)
[AMBER] saveamberparameters problem Saeed Nasiri (Mon Dec 02 2013 - 08:25:22 PST)
- Re: [AMBER] saveamberparameters problem David A Case (Mon Dec 02 2013 - 11:59:56 PST)
[AMBER] Compare the result between pmemd.cuda and pmemd.mpi? X Sun (Mon Dec 02 2013 - 10:11:42 PST)
- Re: [AMBER] Compare the result between pmemd.cuda and pmemd.mpi? Ross Walker (Mon Dec 02 2013 - 10:42:49 PST)
- Re: [AMBER] Compare the result between pmemd.cuda and pmemd.mpi? Jason Swails (Mon Dec 02 2013 - 10:49:42 PST)
[AMBER] Calculation of NMR relaxation rates Mahendra B Thapa (Mon Dec 02 2013 - 16:43:10 PST)
- Re: [AMBER] Calculation of NMR relaxation rates case (Tue Dec 03 2013 - 18:39:33 PST)
- Re: [AMBER] Calculation of NMR relaxation rates Daniel Roe (Wed Dec 04 2013 - 08:17:00 PST)
[AMBER] zinc parameters Hallel Freedman (Mon Dec 02 2013 - 16:46:50 PST)
- Re: [AMBER] zinc parameters Hallel Freedman (Tue Dec 03 2013 - 10:13:43 PST)
  - Re: [AMBER] zinc parameters Bill Ross (Tue Dec 03 2013 - 10:26:07 PST)
    - Re: [AMBER] zinc parameters Hallel Freedman (Tue Dec 03 2013 - 10:30:47 PST)
    - Re: [AMBER] zinc parameters Bill Ross (Wed Dec 04 2013 - 23:46:13 PST)
    - Re: [AMBER] zinc parameters Hallel Freedman (Thu Dec 05 2013 - 06:30:56 PST)
[AMBER] AMBER12 test discrepancy Guanglei Cui (Tue Dec 03 2013 - 07:55:44 PST)
- [AMBER] parmed.py setBond Aronica, Pietro (Tue Dec 03 2013 - 09:44:27 PST)
  - Re: [AMBER] parmed.py setBond Brian Radak (Tue Dec 03 2013 - 09:59:47 PST)
    - Re: [AMBER] parmed.py setBond Aronica, Pietro (Tue Dec 03 2013 - 10:03:14 PST)
    - Re: [AMBER] parmed.py setBond Brian Radak (Tue Dec 03 2013 - 10:07:30 PST)
    - Re: [AMBER] parmed.py setBond Aronica, Pietro (Tue Dec 03 2013 - 10:25:21 PST)
    - Re: [AMBER] parmed.py setBond Jason Swails (Tue Dec 03 2013 - 11:04:36 PST)
    - Re: [AMBER] parmed.py setBond Jason Swails (Tue Dec 03 2013 - 11:22:48 PST)
    - Re: [AMBER] parmed.py setBond Aronica, Pietro (Tue Dec 03 2013 - 11:43:17 PST)
    - Re: [AMBER] parmed.py setBond Jason Swails (Tue Dec 03 2013 - 14:51:20 PST)
  - Re: [AMBER] parmed.py setBond Jason Swails (Tue Dec 03 2013 - 10:45:49 PST)
[AMBER] How to compile amber12 in AIX UNIX? Mengyuan Zhu (Tue Dec 03 2013 - 11:19:32 PST)
- Re: [AMBER] How to compile amber12 in AIX UNIX? case (Tue Dec 03 2013 - 18:22:31 PST)
  - Re: [AMBER] How to compile amber12 in AIX UNIX? Mengyuan Zhu (Tue Dec 03 2013 - 18:55:37 PST)
  - Re: [AMBER] How to compile amber12 in AIX UNIX? Mengyuan Zhu (Tue Dec 03 2013 - 19:05:40 PST)
    - Re: [AMBER] How to compile amber12 in AIX UNIX? Daniel Roe (Tue Dec 03 2013 - 20:26:50 PST)
    - Re: [AMBER] How to compile amber12 in AIX UNIX? Mengyuan Zhu (Thu Dec 05 2013 - 21:17:46 PST)
[AMBER] Restrained MD with COM restraint with PMEMD Mike Limb (Tue Dec 03 2013 - 14:16:59 PST)
- Re: [AMBER] Restrained MD with COM restraint with PMEMD case (Tue Dec 03 2013 - 18:33:17 PST)
  - Re: [AMBER] Restrained MD with COM restraint with PMEMD Mike Limb (Wed Dec 04 2013 - 03:41:03 PST)
    - Re: [AMBER] Restrained MD with COM restraint with PMEMD Jason Swails (Wed Dec 04 2013 - 04:51:15 PST)
[AMBER] nasiri Saeed Nasiri (Wed Dec 04 2013 - 07:00:02 PST)
- Re: [AMBER] nasiri Jason Swails (Wed Dec 04 2013 - 07:15:04 PST)
[AMBER] Keeping an hexamer whole. Julio Dominguez (Wed Dec 04 2013 - 16:38:16 PST)
- Re: [AMBER] Keeping an hexamer whole. Jason Swails (Wed Dec 04 2013 - 17:56:13 PST)
  - Re: [AMBER] Keeping an hexamer whole. Daniel Roe (Wed Dec 04 2013 - 20:27:42 PST)
- Re: [AMBER] Keeping an hexamer whole. Julio Dominguez (Thu Dec 05 2013 - 21:06:33 PST)
[AMBER] Constant pH anurag.dobhal (Thu Dec 05 2013 - 04:32:04 PST)
[AMBER] RMSF John Smith (Thu Dec 05 2013 - 04:41:14 PST)
- Re: [AMBER] RMSF David A Case (Thu Dec 05 2013 - 05:02:58 PST)
  - Re: [AMBER] RMSF John Smith (Thu Dec 05 2013 - 05:32:12 PST)
    - Re: [AMBER] RMSF Jason Swails (Thu Dec 05 2013 - 05:54:39 PST)
    - Re: [AMBER] RMSF John Smith (Thu Dec 05 2013 - 07:03:30 PST)
    - Re: [AMBER] RMSF John Smith (Thu Dec 05 2013 - 07:22:39 PST)
    - Re: [AMBER] RMSF Jason Swails (Thu Dec 05 2013 - 07:41:26 PST)
- Re: [AMBER] RMSF Jason Swails (Thu Dec 05 2013 - 05:04:22 PST)
[AMBER] constant pH anurag.dobhal (Thu Dec 05 2013 - 04:36:08 PST)
- Re: [AMBER] constant pH Kshatresh Dutta Dubey (Thu Dec 05 2013 - 04:53:03 PST)
- Re: [AMBER] constant pH David A Case (Thu Dec 05 2013 - 05:01:03 PST)
[AMBER] question Zahra Khatti (Thu Dec 05 2013 - 09:13:37 PST)
- Re: [AMBER] question Jason Swails (Thu Dec 05 2013 - 09:35:57 PST)
- Re: [AMBER] question Hamed S. Hayatshahi (Thu Dec 05 2013 - 09:38:43 PST)
[AMBER] Error in amber12 serial installation in file alltasks_setup.F90:352 Sajeewa Pemasinghe (Thu Dec 05 2013 - 19:46:38 PST)
- Re: [AMBER] Error in amber12 serial installation in file alltasks_setup.F90:352 David A Case (Fri Dec 06 2013 - 05:14:14 PST)
  - Re: [AMBER] Error in amber12 serial installation in file alltasks_setup.F90:352 Jason Swails (Fri Dec 06 2013 - 14:04:58 PST)
[AMBER] Converting Amoeba .xyz for use with Amber Eugene Yedvabny (Thu Dec 05 2013 - 20:05:09 PST)
- Re: [AMBER] Converting Amoeba .xyz for use with Amber David A Case (Fri Dec 06 2013 - 05:27:10 PST)
  - Re: [AMBER] Converting Amoeba .xyz for use with Amber Jason Swails (Fri Dec 06 2013 - 14:11:08 PST)
- Re: [AMBER] Converting Amoeba .xyz for use with Amber Eugene Yedvabny (Mon Dec 09 2013 - 14:27:38 PST)
- Re: [AMBER] Converting Amoeba .xyz for use with Amber Eugene Yedvabny (Fri Dec 13 2013 - 14:08:40 PST)
  - Re: [AMBER] Converting Amoeba .xyz for use with Amber case (Sat Dec 14 2013 - 08:09:50 PST)
    - Re: [AMBER] Converting Amoeba .xyz for use with Amber Eugene Yedvabny (Sat Dec 14 2013 - 16:01:27 PST)
    - Re: [AMBER] Converting Amoeba .xyz for use with Amber Jason Swails (Fri Feb 07 2014 - 11:57:57 PST)
[AMBER] When to use semi-anisotropic pressure couplings Vijay Manickam Achari (Thu Dec 05 2013 - 22:34:33 PST)
[AMBER] Plotting a Dynamic Cross Correlation Map Yip Yew Mun (Fri Dec 06 2013 - 00:28:25 PST)
[AMBER] anisotropic & semi-anisotropic pressure coupling. Vijay Manickam Achari (Fri Dec 06 2013 - 01:24:29 PST)
[AMBER] ptraj hbond output format Andre C. Stiel (Fri Dec 06 2013 - 05:39:47 PST)
- Re: [AMBER] ptraj hbond output format Daniel Roe (Fri Dec 06 2013 - 16:05:38 PST)
  - Re: [AMBER] ptraj hbond output format André C. Stiel (Sun Dec 08 2013 - 03:39:54 PST)
    - Re: [AMBER] ptraj hbond output format Jan-Philip Gehrcke (Sun Dec 08 2013 - 07:26:40 PST)
[AMBER] compile parallel mpi Zahra Khatti (Fri Dec 06 2013 - 06:55:03 PST)
- Re: [AMBER] compile parallel mpi Jason Swails (Fri Dec 06 2013 - 08:50:40 PST)
[AMBER] Should vdW cutoff distance be system-dependent? yunshi11 . (Fri Dec 06 2013 - 09:38:28 PST)
- Re: [AMBER] Should vdW cutoff distance be system-dependent? David A Case (Fri Dec 06 2013 - 11:22:27 PST)
  - Re: [AMBER] Should vdW cutoff distance be system-dependent? Brian Radak (Fri Dec 06 2013 - 12:03:53 PST)
[AMBER] Using the RED Server Dev. to parameterize a model transition state Kamali Sripathi (Fri Dec 06 2013 - 13:19:46 PST)
- Re: [AMBER] Using the RED Server Dev. to parameterize a model transition state FyD (Sat Dec 07 2013 - 13:30:00 PST)
  - Re: [AMBER] Using the RED Server Dev. to parameterize a model transition state Kamali Sripathi (Mon Dec 09 2013 - 08:30:10 PST)
    - Re: [AMBER] Using the RED Server Dev. to parameterize a model transition state FyD (Mon Dec 09 2013 - 11:56:21 PST)
    - Re: [AMBER] Using the RED Server Dev. to parameterize a model transition state Kamali Sripathi (Mon Dec 09 2013 - 15:26:00 PST)
    - Re: [AMBER] Using the RED Server Dev. to parameterize a model transition state FyD (Mon Dec 09 2013 - 23:52:41 PST)
    - Re: [AMBER] Using the RED Server Dev. to parameterize a model transition state Kamali Sripathi (Tue Dec 10 2013 - 05:12:58 PST)
    - Re: [AMBER] Using the RED Server Dev. to parameterize a model transition state Kamali Sripathi (Wed Dec 11 2013 - 12:56:35 PST)
    - Re: [AMBER] Using the RED Server Dev. to parameterize a model transition state FyD (Wed Dec 11 2013 - 21:21:51 PST)
    - Re: [AMBER] Using the RED Server Dev. to parameterize a model transition state FyD (Wed Dec 11 2013 - 22:36:42 PST)
    - Re: [AMBER] Using the RED Server Dev. to parameterize a model transition state FyD (Fri Dec 13 2013 - 01:24:35 PST)
    - Re: [AMBER] Using the RED Server Dev. to parameterize a model transition state Kamali Sripathi (Fri Dec 13 2013 - 06:56:26 PST)
    - Re: [AMBER] Using the RED Server Dev. to parameterize a model transition state FyD (Fri Dec 13 2013 - 07:30:51 PST)
    - Re: [AMBER] Using the RED Server Dev. to parameterize a model transition state Kamali Sripathi (Sun Dec 15 2013 - 15:43:19 PST)
    - Re: [AMBER] Using the RED Server Dev. to parameterize a model transition state FyD (Mon Dec 16 2013 - 01:49:30 PST)
[AMBER] Anisotropic & semi-anisotropic Vijay Manickam Achari (Sat Dec 07 2013 - 00:46:54 PST)
- Re: [AMBER] Anisotropic & semi-anisotropic Jason Swails (Sat Dec 07 2013 - 07:32:09 PST)
  - Re: [AMBER] Anisotropic & semi-anisotropic Vijay Manickam Achari (Mon Dec 09 2013 - 19:35:11 PST)
[AMBER] not getting correct density for N,N-dimethylformamide Sohag Biswas (Sat Dec 07 2013 - 08:39:58 PST)
- Re: [AMBER] not getting correct density for N,N-dimethylformamide FyD (Sat Dec 07 2013 - 13:12:23 PST)
- Re: [AMBER] not getting correct density for N,N-dimethylformamide David A Case (Mon Dec 09 2013 - 13:16:33 PST)
[AMBER] Atom Expression in NAB sunita gupta (Sun Dec 08 2013 - 07:59:58 PST)
- Re: [AMBER] Atom Expression in NAB case (Sun Dec 08 2013 - 08:29:57 PST)
  - Re: [AMBER] Atom Expression in NAB sunita gupta (Sun Dec 08 2013 - 21:11:49 PST)
    - Re: [AMBER] Atom Expression in NAB sunita gupta (Sun Dec 08 2013 - 21:21:09 PST)
    - Re: [AMBER] Atom Expression in NAB Jason Swails (Mon Dec 09 2013 - 04:08:20 PST)
[AMBER] Brookhaven pdb format 闫玉娜 (Sun Dec 08 2013 - 19:22:40 PST)
- Re: [AMBER] Brookhaven pdb format Daniel Roe (Sun Dec 08 2013 - 19:53:07 PST)
  - Re: [AMBER] Brookhaven pdb format 闫玉娜 (Sun Dec 08 2013 - 21:04:44 PST)
[AMBER] accelerated Molecular dynamics Ibrahim Said (Mon Dec 09 2013 - 00:17:33 PST)
- Re: [AMBER] accelerated Molecular dynamics Jason Swails (Mon Dec 09 2013 - 04:12:03 PST)
[AMBER] MMPBSA errors ：setting grid spacing larger than solvent probe Fengxue Li (Mon Dec 09 2013 - 05:25:09 PST)
- Re: [AMBER] MMPBSA errors ：setting grid spacing larger than solvent probe Jason Swails (Mon Dec 09 2013 - 07:53:55 PST)
  - Re: [AMBER] MMPBSA errors ：setting grid spacing larger than solvent probe Ray Luo, Ph.D. (Mon Dec 09 2013 - 10:03:18 PST)
[AMBER] math operations in cpptraj Andre C. Stiel (Mon Dec 09 2013 - 08:26:14 PST)
- Re: [AMBER] math operations in cpptraj Daniel Roe (Mon Dec 09 2013 - 08:43:09 PST)
[AMBER] please tell me why this error is coming while doing the constant pH MD anurag.dobhal (Mon Dec 09 2013 - 10:37:47 PST)
- Re: [AMBER] please tell me why this error is coming while doing the constant pH MD Jason Swails (Mon Dec 09 2013 - 11:30:09 PST)
[AMBER] Fwd: Re: Using the RED Server Dev. to parameterize a model transition state FyD (Mon Dec 09 2013 - 12:00:15 PST)
[AMBER] Amber Tools v.13 Silvestre (Mon Dec 09 2013 - 13:18:48 PST)
- Re: [AMBER] Amber Tools v.13 Jason Swails (Mon Dec 09 2013 - 14:00:44 PST)
  - Re: [AMBER] Amber Tools v.13 Silvestre (Mon Dec 09 2013 - 14:25:48 PST)
    - Re: [AMBER] Amber Tools v.13 Silvestre (Wed Dec 11 2013 - 12:57:45 PST)
    - Re: [AMBER] Amber Tools v.13 Daniel Roe (Wed Dec 11 2013 - 14:25:12 PST)
    - Re: [AMBER] Amber Tools v.13 Jason Swails (Wed Dec 11 2013 - 17:15:47 PST)
[AMBER] Converting Amoeba .xyz for use with Amber Eugene Yedvabny (Mon Dec 09 2013 - 14:24:31 PST)
[AMBER] netcdf compilation error in Amber12 serial installation: Couldn't compile conftest.c Sajeewa Pemasinghe (Mon Dec 09 2013 - 16:25:59 PST)
- Re: [AMBER] netcdf compilation error in Amber12 serial installation: Couldn't compile conftest.c Aldo Segura (Mon Dec 09 2013 - 17:13:18 PST)
- Re: [AMBER] netcdf compilation error in Amber12 serial installation: Couldn't compile conftest.c Jason Swails (Mon Dec 09 2013 - 17:40:59 PST)
  - Re: [AMBER] netcdf compilation error in Amber12 serial installation: Couldn't compile conftest.c Sajeewa Pemasinghe (Tue Dec 10 2013 - 10:14:24 PST)
    - Re: [AMBER] netcdf compilation error in Amber12 serial installation: Couldn't compile conftest.c Daniel Roe (Tue Dec 10 2013 - 10:18:42 PST)
[AMBER] Does anyone know which parameter controls the wavenumber related to the Helmholtz equation 肖立 (Mon Dec 09 2013 - 20:47:04 PST)
- Re: [AMBER] Does anyone know which parameter controls the wavenumber related to the Helmholtz equation wmsmith.uci.edu (Tue Dec 10 2013 - 08:11:45 PST)
  - Re: [AMBER] Does anyone know which parameter controls the wavenumber related to the Helmholtz equation 肖立 (Tue Dec 10 2013 - 09:03:15 PST)
    - Re: [AMBER] Does anyone know which parameter controls the wavenumber related to the Helmholtz equation wmsmith.uci.edu (Tue Dec 10 2013 - 10:08:12 PST)
[AMBER] sander command Saeed Nasiri (Tue Dec 10 2013 - 00:07:37 PST)
- Re: [AMBER] sander command Jason Swails (Wed Dec 11 2013 - 04:22:10 PST)
[AMBER] MMPBSA errors :failed with prmtop Fengxue Li (Tue Dec 10 2013 - 01:49:53 PST)
- Re: [AMBER] MMPBSA errors :failed with prmtop Ray Luo, Ph.D. (Tue Dec 10 2013 - 10:04:22 PST)
  - Re: [AMBER] MMPBSA errors :failed with prmtop Ray Luo, Ph.D. (Mon Dec 16 2013 - 15:13:44 PST)
[AMBER] capturing free energy landscape anu chandra (Tue Dec 10 2013 - 02:23:46 PST)
- Re: [AMBER] capturing free energy landscape Jason Swails (Tue Dec 10 2013 - 12:45:46 PST)
  - Re: [AMBER] capturing free energy landscape Thomas Evangelidis (Tue Dec 10 2013 - 12:59:46 PST)
    - Re: [AMBER] capturing free energy landscape Adrian Roitberg (Tue Dec 10 2013 - 13:26:58 PST)
    - Re: [AMBER] capturing free energy landscape anu chandra (Wed Dec 11 2013 - 03:09:46 PST)
    - Re: [AMBER] capturing free energy landscape anu chandra (Fri Dec 20 2013 - 00:55:50 PST)
    - Re: [AMBER] capturing free energy landscape Jason Swails (Fri Dec 20 2013 - 04:03:37 PST)
    - Re: [AMBER] capturing free energy landscape Thomas Evangelidis (Fri Dec 20 2013 - 05:35:31 PST)
    - Re: [AMBER] capturing free energy landscape anu chandra (Thu Dec 26 2013 - 03:59:03 PST)
    - Re: [AMBER] capturing free energy landscape Daniel Roe (Thu Dec 26 2013 - 06:35:45 PST)
    - Re: [AMBER] capturing free energy landscape anu chandra (Mon Dec 30 2013 - 03:04:13 PST)
    - Re: [AMBER] capturing free energy landscape Daniel Roe (Tue Dec 31 2013 - 08:04:46 PST)
[AMBER] AMBER GPU performance issue Neha Gandhi (Tue Dec 10 2013 - 03:04:37 PST)
- Re: [AMBER] AMBER GPU performance issue Jason Swails (Tue Dec 10 2013 - 12:42:53 PST)
[AMBER] cpptraj output and hbond André C. Stiel (Wed Dec 11 2013 - 01:40:12 PST)
[AMBER] Is there any way I can complete a production run which has been interrupted by a sudden power cut ? Roza M (Wed Dec 11 2013 - 05:44:14 PST)
- Re: [AMBER] Is there any way I can complete a production run which has been interrupted by a sudden power cut ? Gustavo Seabra (Wed Dec 11 2013 - 06:58:16 PST)
  - Re: [AMBER] Is there any way I can complete a production run which has been interrupted by a sudden power cut ? Roza M (Wed Dec 11 2013 - 08:29:42 PST)
[AMBER] Amber QM/MM Fengxue Li (Wed Dec 11 2013 - 05:54:27 PST)
- Re: [AMBER] Amber QM/MM Brian Radak (Wed Dec 11 2013 - 06:55:31 PST)
- Re: [AMBER] Amber QM/MM Gustavo Seabra (Wed Dec 11 2013 - 06:57:02 PST)
  - Re: [AMBER] Amber QM/MM Ross Walker (Thu Dec 12 2013 - 07:38:32 PST)
[AMBER] runing sander Saeed Nasiri (Wed Dec 11 2013 - 07:38:50 PST)
- Re: [AMBER] runing sander Jason Swails (Wed Dec 11 2013 - 09:53:27 PST)
[AMBER] Plotting heat maps in AMBER aMD simualtions filip fratev (Wed Dec 11 2013 - 07:56:58 PST)
- Re: [AMBER] Plotting heat maps in AMBER aMD simualtions Brian Radak (Wed Dec 11 2013 - 08:10:32 PST)
- Re: [AMBER] Plotting heat maps in AMBER aMD simualtions Jason Swails (Wed Dec 11 2013 - 09:52:19 PST)
  - Re: [AMBER] Plotting heat maps in AMBER aMD simualtions filip fratev (Wed Dec 11 2013 - 10:18:20 PST)
    - Re: [AMBER] Plotting heat maps in AMBER aMD simualtions Daniel Roe (Wed Dec 11 2013 - 10:38:40 PST)
[AMBER] cpptraj output and hbond André C. Stiel (Wed Dec 11 2013 - 11:10:55 PST)
[AMBER] Regarding generating parameters for protein with NAD+ Prema Mallipeddi (Wed Dec 11 2013 - 14:49:55 PST)
- Re: [AMBER] Regarding generating parameters for protein with NAD+ case (Wed Dec 11 2013 - 18:19:34 PST)
[AMBER] Does anyone knows how to generate an ired vector 肖立 (Wed Dec 11 2013 - 14:51:47 PST)
- Re: [AMBER] Does anyone knows how to generate an ired vector Daniel Roe (Wed Dec 11 2013 - 15:10:24 PST)
  - Re: [AMBER] Does anyone knows how to generate an ired vector 肖立 (Wed Dec 11 2013 - 15:49:47 PST)
    - Re: [AMBER] Does anyone knows how to generate an ired vector wmsmith.uci.edu (Wed Dec 11 2013 - 16:45:28 PST)
    - Re: [AMBER] Does anyone knows how to generate an ired vector Daniel Roe (Wed Dec 11 2013 - 19:57:49 PST)
    - Re: [AMBER] Does anyone knows how to generate an ired vector Daniel Roe (Wed Dec 11 2013 - 20:07:42 PST)
    - Re: [AMBER] Does anyone knows how to generate an ired vector 肖立 (Wed Dec 11 2013 - 21:36:37 PST)
[AMBER] The use of ansiotropic & semi-anisotropic pressure couplings in bilayer simulation. Vijay Manickam Achari (Wed Dec 11 2013 - 20:20:00 PST)
- Re: [AMBER] The use of ansiotropic & semi-anisotropic pressure couplings in bilayer simulation. Dickson, Callum J (Tue Dec 17 2013 - 09:37:23 PST)
[AMBER] atom-atom contact analysis in PTRAj Pranjal Mahanta (Wed Dec 11 2013 - 23:51:09 PST)
[AMBER] I got a error David Chen (Thu Dec 12 2013 - 04:22:58 PST)
[AMBER] Puzzles about calculating the binding energy of residues Yanyan ZHU (Thu Dec 12 2013 - 06:10:40 PST)
[AMBER] Simulation time help Nicole Ippolito (Thu Dec 12 2013 - 08:28:31 PST)
- Re: [AMBER] Simulation time help Adrian Roitberg (Thu Dec 12 2013 - 08:30:49 PST)
  - Re: [AMBER] Simulation time help Nicole Ippolito (Thu Dec 12 2013 - 08:44:45 PST)
    - Re: [AMBER] Simulation time help Adrian Roitberg (Thu Dec 12 2013 - 08:48:20 PST)
    - Re: [AMBER] Simulation time help Nicole Ippolito (Thu Dec 12 2013 - 08:56:56 PST)
[AMBER] changeLJSingleType problem in parmed.py Hamed S. Hayatshahi (Thu Dec 12 2013 - 14:26:29 PST)
- Re: [AMBER] changeLJSingleType problem in parmed.py Jason Swails (Thu Dec 12 2013 - 14:45:30 PST)
[AMBER] how to remove the rotational center-of-mass motion ? 张明焜 (Thu Dec 12 2013 - 22:30:26 PST)
- Re: [AMBER] how to remove the rotational center-of-mass motion ? David A Case (Fri Dec 13 2013 - 04:44:41 PST)
[AMBER] MGMS-DS: Molecular Modelling Workshop 2014 in Erlangen, Germany Harald Lanig (Fri Dec 13 2013 - 01:29:25 PST)
[AMBER] I got a error David Chen (Fri Dec 13 2013 - 02:42:35 PST)
- Re: [AMBER] I got a error Jason Swails (Fri Dec 13 2013 - 09:10:14 PST)
[AMBER] 3D projection of pairwise-RMSD Sangeetha B (Fri Dec 13 2013 - 06:11:57 PST)
- Re: [AMBER] 3D projection of pairwise-RMSD Daniel Roe (Fri Dec 13 2013 - 08:41:05 PST)
  - Re: [AMBER] 3D projection of pairwise-RMSD Sangeetha B (Fri Dec 13 2013 - 09:28:52 PST)
    - Re: [AMBER] 3D projection of pairwise-RMSD Adrian Roitberg (Fri Dec 13 2013 - 09:42:42 PST)
    - Re: [AMBER] 3D projection of pairwise-RMSD Sangeetha B (Fri Dec 13 2013 - 10:00:18 PST)
    - Re: [AMBER] 3D projection of pairwise-RMSD Adrian Roitberg (Fri Dec 13 2013 - 09:42:50 PST)
    - Re: [AMBER] 3D projection of pairwise-RMSD David A Case (Fri Dec 13 2013 - 10:08:40 PST)
[AMBER] AmberTools update 22 for CPPTRAJ Daniel Roe (Fri Dec 13 2013 - 09:04:37 PST)
[AMBER] error in installing ambertools 1.2 anurag.dobhal (Fri Dec 13 2013 - 10:31:31 PST)
- Re: [AMBER] error in installing ambertools 1.2 case (Sat Dec 14 2013 - 08:18:33 PST)
[AMBER] issues with MMPBSA tutorial/MMPBSA.py Bennion, Brian (Fri Dec 13 2013 - 11:03:42 PST)
[AMBER] Puzzles about calculating binding energy using MMGBSA Yanyan ZHU (Sat Dec 14 2013 - 04:05:41 PST)
- Re: [AMBER] Puzzles about calculating binding energy using MMGBSA Jason Swails (Sat Dec 14 2013 - 06:44:07 PST)
- Re: [AMBER] Puzzles about calculating binding energy using MMGBSA Jason Swails (Thu Dec 19 2013 - 14:18:42 PST)
[AMBER] Proper Algorithm for GPU? X Sun (Sat Dec 14 2013 - 15:31:10 PST)
- Re: [AMBER] Proper Algorithm for GPU? case (Sun Dec 15 2013 - 10:06:26 PST)
[AMBER] Help: Producing a Prmtop file for a Truncated-Protein Trajectory #YIP YEW MUN# (Sun Dec 15 2013 - 21:22:37 PST)
- Re: [AMBER] Help: Producing a Prmtop file for a Truncated-Protein Trajectory Jason Swails (Mon Dec 16 2013 - 05:11:05 PST)
[AMBER] Manually extending the size of the virtual box Eugene Yedvabny (Mon Dec 16 2013 - 01:19:44 PST)
- Re: [AMBER] Manually extending the size of the virtual box David A Case (Mon Dec 16 2013 - 04:30:00 PST)
  - Re: [AMBER] Manually extending the size of the virtual box Eugene Yedvabny (Mon Dec 16 2013 - 11:03:54 PST)
    - Re: [AMBER] Manually extending the size of the virtual box Carlos Simmerling (Mon Dec 16 2013 - 11:18:42 PST)
    - Re: [AMBER] Manually extending the size of the virtual box Jason Swails (Mon Dec 16 2013 - 12:12:54 PST)
    - Re: [AMBER] Manually extending the size of the virtual box Eugene Yedvabny (Mon Dec 16 2013 - 17:58:33 PST)
    - Re: [AMBER] Manually extending the size of the virtual box case (Thu Dec 26 2013 - 07:08:41 PST)
Re: [AMBER] Need some advice on calculating diffusion constant Brian Radak (Mon Dec 16 2013 - 06:05:15 PST)
[AMBER] amber QM/MM :vlimit exceeded for step 1; vmax = 71.9072 Fengxue Li (Mon Dec 16 2013 - 06:06:30 PST)
- Re: [AMBER] amber QM/MM :vlimit exceeded for step 1; vmax = 71.9072 Brian Radak (Mon Dec 16 2013 - 06:18:13 PST)
- Re: [AMBER] amber QM/MM :vlimit exceeded for step 1; vmax = 71.9072 Ross Walker (Mon Dec 16 2013 - 09:26:23 PST)
[AMBER] MMPBSA: eneopt=1 versus eneopt=3 Vlad Cojocaru (Mon Dec 16 2013 - 08:06:51 PST)
[AMBER] Improper terms in Amber Meng (Mon Dec 16 2013 - 13:26:11 PST)
- Re: [AMBER] Improper terms in Amber case (Mon Dec 16 2013 - 17:48:30 PST)
[AMBER] MMPBSA of protein_DNA complex Aditya sarkar (Tue Dec 17 2013 - 02:18:21 PST)
- Re: [AMBER] MMPBSA of protein_DNA complex Vlad Cojocaru (Tue Dec 17 2013 - 02:49:06 PST)
[AMBER] CpptrajPairDist JAIME RUBIO MARTINEZ (Tue Dec 17 2013 - 11:37:28 PST)
- Re: [AMBER] CpptrajPairDist Daniel Roe (Tue Dec 17 2013 - 13:44:32 PST)
  - Re: [AMBER] CpptrajPairDist Daniel Roe (Tue Dec 17 2013 - 13:52:15 PST)
    - Re: [AMBER] CpptrajPairDist JAIME RUBIO MARTINEZ (Sat Dec 28 2013 - 11:58:49 PST)
    - Re: [AMBER] CpptrajPairDist bharat lakhani (Tue Jul 21 2015 - 19:50:08 PDT)
    - Re: [AMBER] CpptrajPairDist Daniel Roe (Thu Jul 23 2015 - 08:56:55 PDT)
[AMBER] MMGBSA Entropy Error: Trajectory _MMPBSA_complex.mdcrd.1 has 0 frames! Cuiyl (Tue Dec 17 2013 - 18:13:22 PST)
[AMBER] Is restart file size different between minimization and heating MD? Biao Ma (Tue Dec 17 2013 - 22:08:13 PST)
- Re: [AMBER] Is restart file size different between minimization and heating MD? David A Case (Wed Dec 18 2013 - 04:57:01 PST)
  - Re: [AMBER] Is restart file size different between minimization and heating MD? Biao Ma (Thu Dec 19 2013 - 08:36:22 PST)
[AMBER] Error while visualizing radius of gyration graph Sumra Wajid Abbasi 30-FBAS/MSBI/F09 (Tue Dec 17 2013 - 22:56:03 PST)
- Re: [AMBER] Error while visualizing radius of gyration graph David A Case (Wed Dec 18 2013 - 04:58:21 PST)
- Re: [AMBER] Error while visualizing radius of gyration graph Jonathan Sheehan (Wed Dec 18 2013 - 07:15:35 PST)
[AMBER] AMD simulation Mele N. (Wed Dec 18 2013 - 03:47:00 PST)
- Re: [AMBER] AMD simulation Mele N. (Wed Dec 18 2013 - 03:57:07 PST)
[AMBER] Bad atom type error during MMGBSA decomposition calsulations 王衍 (Thu Dec 19 2013 - 00:47:06 PST)
- Re: [AMBER] Bad atom type error during MMGBSA decomposition calsulations Jason Swails (Thu Dec 19 2013 - 07:47:36 PST)
[AMBER] How to decompose PMF into electrostatic and van der Waals contributions. zhongqiao hu (Thu Dec 19 2013 - 01:44:00 PST)
- Re: [AMBER] How to decompose PMF into electrostatic and van der Waals contributions. Brian Radak (Thu Dec 19 2013 - 06:39:58 PST)
[AMBER] MMPBSA with inp=1 Vlad Cojocaru (Thu Dec 19 2013 - 02:38:25 PST)
- Re: [AMBER] MMPBSA with inp=1 Ray Luo, Ph.D. (Thu Dec 19 2013 - 09:40:05 PST)
  - Re: [AMBER] MMPBSA with inp=1 Vlad Cojocaru (Thu Dec 19 2013 - 10:28:07 PST)
    - Re: [AMBER] MMPBSA with inp=1 Ray Luo, Ph.D. (Thu Dec 19 2013 - 10:34:21 PST)
    - Re: [AMBER] MMPBSA with inp=1 wmsmith.uci.edu (Thu Dec 19 2013 - 11:47:06 PST)
    - Re: [AMBER] MMPBSA with inp=1 wmsmith.uci.edu (Thu Dec 19 2013 - 11:49:41 PST)
- Re: [AMBER] MMPBSA with inp=1 Ray Luo, Ph.D. (Mon Dec 23 2013 - 11:31:30 PST)
[AMBER] Regarding distance between residue masks (ptraj) agarai.physics.iisc.ernet.in (Thu Dec 19 2013 - 04:47:13 PST)
- Re: [AMBER] Regarding distance between residue masks (ptraj) Daniel Roe (Thu Dec 19 2013 - 07:37:58 PST)
- Re: [AMBER] Regarding distance between residue masks (ptraj) Jason Swails (Thu Dec 19 2013 - 07:45:53 PST)
  - Re: [AMBER] Regarding distance between residue masks (ptraj) agarai.physics.iisc.ernet.in (Sun Dec 22 2013 - 00:12:04 PST)
[AMBER] status of the Amber lipid framework? Sally Pias (Thu Dec 19 2013 - 11:54:59 PST)
- Re: [AMBER] status of the Amber lipid framework? Ross Walker (Thu Dec 19 2013 - 12:01:21 PST)
  - Re: [AMBER] status of the Amber lipid framework? Igor Marques (Fri Jan 24 2014 - 09:12:33 PST)
    - Re: [AMBER] status of the Amber lipid framework? Ross Walker (Thu Jan 30 2014 - 11:27:49 PST)
    - Re: [AMBER] status of the Amber lipid framework? Jio M (Fri Jan 31 2014 - 06:00:24 PST)
    - Re: [AMBER] status of the Amber lipid framework? Jason Swails (Fri Jan 31 2014 - 06:26:53 PST)
    - Re: [AMBER] status of the Amber lipid framework? Jio M (Fri Jan 31 2014 - 06:43:39 PST)
    - Re: [AMBER] status of the Amber lipid framework? Jason Swails (Fri Jan 31 2014 - 06:57:13 PST)
    - Re: [AMBER] status of the Amber lipid framework? Jio M (Fri Jan 31 2014 - 07:11:09 PST)
    - Re: [AMBER] status of the Amber lipid framework? Ross Walker (Fri Jan 31 2014 - 09:04:14 PST)
    - Re: [AMBER] status of the Amber lipid framework? Dickson, Callum J (Fri Jan 31 2014 - 09:12:40 PST)
    - Re: [AMBER] status of the Amber lipid framework? Jio M (Fri Jan 31 2014 - 09:40:14 PST)
Re: [AMBER] How to decompose PMF into electrostatic and van der Waals contributions zhongqiao hu (Thu Dec 19 2013 - 18:35:41 PST)
- Re: [AMBER] How to decompose PMF into electrostatic and van der Waals contributions David A Case (Fri Dec 20 2013 - 06:37:41 PST)
- Re: [AMBER] How to decompose PMF into electrostatic and van der Waals contributions zhongqiao hu (Sat Dec 21 2013 - 05:48:42 PST)
  - Re: [AMBER] How to decompose PMF into electrostatic and van der Waals contributions Brian Radak (Tue Dec 24 2013 - 14:34:12 PST)
- Re: [AMBER] How to decompose PMF into electrostatic and van der Waals contributions zhongqiao hu (Thu Dec 26 2013 - 06:10:34 PST)
  - Re: [AMBER] How to decompose PMF into electrostatic and van der Waals contributions Jason Swails (Thu Dec 26 2013 - 13:48:16 PST)
[AMBER] RE： Bad atom type error during MMGBSA decompositioncalsulations wangyanforward.gmail.com (Thu Dec 19 2013 - 18:47:33 PST)
[AMBER] RMSD-based clustering in CPPTRAJ/PTRAJ anu chandra (Thu Dec 19 2013 - 21:53:36 PST)
- Re: [AMBER] RMSD-based clustering in CPPTRAJ/PTRAJ Daniel Roe (Fri Dec 20 2013 - 07:39:18 PST)
[AMBER] FINAL_RESULTS_MMPBSA error filip fratev (Thu Dec 19 2013 - 23:23:41 PST)
- Re: [AMBER] FINAL_RESULTS_MMPBSA error Jason Swails (Fri Dec 20 2013 - 03:58:03 PST)
[AMBER] Problems of invoking the Amber 12 Yanyan ZHU (Thu Dec 19 2013 - 23:53:41 PST)
- Re: [AMBER] Problems of invoking the Amber 12 Jason Swails (Fri Dec 20 2013 - 04:02:35 PST)
[AMBER] ANTECHAMBER PROBLEM Arjun Sharma (Fri Dec 20 2013 - 08:50:08 PST)
- Re: [AMBER] ANTECHAMBER PROBLEM David A Case (Fri Dec 20 2013 - 10:41:17 PST)
[AMBER] cpptraj can not pass empty trajectory entry which is ok for ptraj Asaminew Haile (Fri Dec 20 2013 - 08:52:56 PST)
- Re: [AMBER] cpptraj can not pass empty trajectory entry which is ok for ptraj ros (Fri Dec 20 2013 - 09:00:37 PST)
- Re: [AMBER] cpptraj can not pass empty trajectory entry which is ok for ptraj Daniel Roe (Fri Dec 20 2013 - 09:39:51 PST)
  - Re: [AMBER] cpptraj can not pass empty trajectory entry which is ok for ptraj Asaminew Haile (Fri Dec 20 2013 - 09:43:07 PST)
[AMBER] cudaMemcpy GpuBuffer::Download failed unspecified launch failure filip fratev (Sat Dec 21 2013 - 11:08:39 PST)
- Re: [AMBER] cudaMemcpy GpuBuffer::Download failed unspecified launch failure Ross Walker (Sat Dec 21 2013 - 11:23:20 PST)
[AMBER] Problems of invoking the Amber 12 and calculating the energy of each residue using the MMPBSA Yanyan ZHU (Sat Dec 21 2013 - 20:13:29 PST)
[AMBER] doubt in alanine scanning of phosphorylated residue suma jayakrishnan (Mon Dec 23 2013 - 02:39:08 PST)
- Re: [AMBER] doubt in alanine scanning of phosphorylated residue Jason Swails (Mon Dec 23 2013 - 05:44:55 PST)
- Re: [AMBER] doubt in alanine scanning of phosphorylated residue Jason Swails (Tue Dec 24 2013 - 10:57:55 PST)
  - [AMBER] Fwd: doubt in alanine scanning of phosphorylated residue suma jayakrishnan (Tue Dec 24 2013 - 18:45:17 PST)
[AMBER] MMPBSA for single re-minimised coordinate sunita gupta (Mon Dec 23 2013 - 04:23:31 PST)
- Re: [AMBER] MMPBSA for single re-minimised coordinate Jason Swails (Mon Dec 23 2013 - 05:50:47 PST)
[AMBER] ErrorWithLeap JAIME RUBIO MARTINEZ (Mon Dec 23 2013 - 16:17:20 PST)
- Re: [AMBER] ErrorWithLeap case (Mon Dec 23 2013 - 19:21:16 PST)
- Re: [AMBER] ErrorWithLeap case (Mon Dec 23 2013 - 19:24:48 PST)
  - Re: [AMBER] ErrorWithLeap Jason Swails (Mon Dec 23 2013 - 19:29:43 PST)
  - Re: [AMBER] ErrorWithLeap JAIME RUBIO MARTINEZ (Tue Dec 24 2013 - 09:14:55 PST)
    - Re: [AMBER] ErrorWithLeap Jason Swails (Tue Dec 24 2013 - 10:18:39 PST)
[AMBER] amber parameter for S2P (phosphoserine) sunita.tifrh.res.in (Mon Dec 23 2013 - 22:47:54 PST)
- Re: [AMBER] amber parameter for S2P (phosphoserine) sunita.tifrh.res.in (Tue Dec 24 2013 - 00:32:15 PST)
  - Re: [AMBER] amber parameter for S2P (phosphoserine) Jonathan Sheehan (Tue Dec 24 2013 - 11:20:35 PST)
[AMBER] problems in nmode and -use-mdins option (MMPBSA.py) houcemeddine (Tue Dec 24 2013 - 07:55:12 PST)
- Re: [AMBER] problems in nmode and -use-mdins option (MMPBSA.py) Jason Swails (Tue Dec 24 2013 - 10:31:07 PST)
  - Re: [AMBER] problems in nmode and -use-mdins option (MMPBSA.py) houcemeddine (Tue Dec 24 2013 - 11:09:15 PST)
[AMBER] Polarizing solute in non-polarizing solvent Hemant Gangwar (Tue Dec 24 2013 - 12:02:19 PST)
- Re: [AMBER] Polarizing solute in non-polarizing solvent case (Thu Dec 26 2013 - 07:00:18 PST)
[AMBER] Simulating protein with Fe atom onetwo (Tue Dec 24 2013 - 20:45:50 PST)
- Re: [AMBER] Simulating protein with Fe atom case (Thu Dec 26 2013 - 06:55:59 PST)
[AMBER] input file with leap or antechamber? Zahra Khatti (Wed Dec 25 2013 - 00:02:19 PST)
- Re: [AMBER] input file with leap or antechamber? Ye MEI (Wed Dec 25 2013 - 00:18:01 PST)
[AMBER] Errors about the values of PBSUR when calculating binding energy using MMPBSA Yanyan ZHU (Wed Dec 25 2013 - 01:35:57 PST)
- Re: [AMBER] Errors about the values of PBSUR when calculating binding energy using MMPBSA Jason Swails (Wed Dec 25 2013 - 06:55:08 PST)
[AMBER] Fwd: Asfa Ali (Wed Dec 25 2013 - 04:01:04 PST)
- Re: [AMBER] Fwd: Jason Swails (Wed Dec 25 2013 - 11:42:52 PST)
  - Re: [AMBER] Fwd: Asfa Ali (Thu Dec 26 2013 - 05:37:55 PST)
    - Re: [AMBER] Fwd: Jason Swails (Thu Dec 26 2013 - 18:33:01 PST)
    - Re: [AMBER] Fwd: Asfa Ali (Sat Dec 28 2013 - 01:40:31 PST)
    - Re: [AMBER] Fwd: Jason Swails (Sat Dec 28 2013 - 10:17:37 PST)
    - Re: [AMBER] Fwd: Asfa Ali (Mon Dec 30 2013 - 13:44:13 PST)
[AMBER] Amber Asfa Ali (Wed Dec 25 2013 - 04:03:41 PST)
[AMBER] modified the amber parameter Saeed Nasiri (Wed Dec 25 2013 - 08:12:13 PST)
- Re: [AMBER] modified the amber parameter Jason Swails (Wed Dec 25 2013 - 12:10:24 PST)
[AMBER] unable to recognize Chlorine atom even after defining in lib and frcmod file onetwo (Wed Dec 25 2013 - 21:57:20 PST)
- Re: [AMBER] unable to recognize Chlorine atom even after defining in lib and frcmod file case (Thu Dec 26 2013 - 06:48:49 PST)
  - Re: [AMBER] unable to recognize Chlorine atom even after defining in lib and frcmod file onetwo (Thu Dec 26 2013 - 22:42:40 PST)
- Re: [AMBER] unable to recognize Chlorine atom even after defining in lib and frcmod file case (Fri Dec 27 2013 - 06:09:30 PST)
[AMBER] cpptraj clustering Neha Gandhi (Thu Dec 26 2013 - 03:03:39 PST)
- Re: [AMBER] cpptraj clustering Daniel Roe (Thu Dec 26 2013 - 06:44:17 PST)
[AMBER] RMSD vs RMSF vs nofit-RMSD Nitin Sharma (Thu Dec 26 2013 - 09:40:05 PST)
- Re: [AMBER] RMSD vs RMSF vs nofit-RMSD vadiraj kurdekar (Fri Dec 27 2013 - 02:34:33 PST)
- Re: [AMBER] RMSD vs RMSF vs nofit-RMSD Daniel Roe (Fri Dec 27 2013 - 06:01:12 PST)
  - Re: [AMBER] RMSD vs RMSF vs nofit-RMSD Nitin Sharma (Fri Dec 27 2013 - 09:29:06 PST)
    - Re: [AMBER] RMSD vs RMSF vs nofit-RMSD Daniel Roe (Tue Dec 31 2013 - 08:47:46 PST)
    - Re: [AMBER] RMSD vs RMSF vs nofit-RMSD Nitin Sharma (Wed Jan 01 2014 - 02:51:27 PST)
[AMBER] Problems about invoking AMBER12 in calculating binding energy Yanyan ZHU (Thu Dec 26 2013 - 18:19:00 PST)
- Re: [AMBER] Problems about invoking AMBER12 in calculating binding energy Jason Swails (Thu Dec 26 2013 - 18:36:45 PST)
[AMBER] Problem when calculating MMPBSA dongying0512 (Thu Dec 26 2013 - 22:50:34 PST)
- Re: [AMBER] Problem when calculating MMPBSA Jason Swails (Thu Dec 26 2013 - 23:03:35 PST)
- Re: [AMBER] Problem when calculating MMPBSA dongying0512 (Tue Jan 21 2014 - 18:31:54 PST)
  - Re: [AMBER] Problem when calculating MMPBSA Jason Swails (Tue Jan 21 2014 - 20:04:35 PST)
[AMBER] Problem when calculating MMPBSA dongying0512 (Thu Dec 26 2013 - 22:53:49 PST)
[AMBER] xLeap Himanshu Joshi (Fri Dec 27 2013 - 04:08:07 PST)
- Re: [AMBER] xLeap case (Fri Dec 27 2013 - 06:23:07 PST)
  - Re: [AMBER] xLeap Jio M (Fri Dec 27 2013 - 17:45:57 PST)
[AMBER] binding free energy and pose analysis Nitin Sharma (Fri Dec 27 2013 - 09:52:50 PST)
- Re: [AMBER] binding free energy and pose analysis case (Fri Dec 27 2013 - 18:58:49 PST)
  - Re: [AMBER] binding free energy and pose analysis Nitin Sharma (Sat Dec 28 2013 - 02:42:59 PST)
    - Re: [AMBER] binding free energy and pose analysis case (Sat Dec 28 2013 - 05:38:04 PST)
    - Re: [AMBER] binding free energy and pose analysis Nitin Sharma (Sun Dec 29 2013 - 07:44:24 PST)
    - Re: [AMBER] binding free energy and pose analysis Jason Swails (Sun Dec 29 2013 - 09:10:31 PST)
    - Re: [AMBER] binding free energy and pose analysis Nitin Sharma (Sun Dec 29 2013 - 09:23:58 PST)
[AMBER] AMDTutorial Ibrahim Said (Fri Dec 27 2013 - 10:08:38 PST)
[AMBER] sander's Segmentation fault Saeed Nasiri (Sat Dec 28 2013 - 03:36:13 PST)
- Re: [AMBER] sander's Segmentation fault case (Sat Dec 28 2013 - 05:40:58 PST)
[AMBER] Finding difficulty during calculation of diffusion coefficient from MSD plot Sohag Biswas (Sat Dec 28 2013 - 21:40:33 PST)
Re: [AMBER] Problem when calculating MMPBSA (Jason Swails) dongying0512 (Sun Dec 29 2013 - 17:21:37 PST)
- Re: [AMBER] Problem when calculating MMPBSA (Jason Swails) Jason Swails (Thu Jan 09 2014 - 11:47:28 PST)
[AMBER] request for help in water shell and closest command Robin Jain (Sun Dec 29 2013 - 22:43:57 PST)
- Re: [AMBER] request for help in water shell and closest command Daniel Roe (Tue Dec 31 2013 - 08:27:29 PST)
[AMBER] Tleap Problem - Unable to bond atoms in amide linkages #YIP YEW MUN# (Mon Dec 30 2013 - 00:43:15 PST)
- Re: [AMBER] Tleap Problem - Unable to bond atoms in amide linkages Mohammed Khaled Tumbi (Mon Dec 30 2013 - 00:54:23 PST)
  - Re: [AMBER] Tleap Problem - Unable to bond atoms in amide linkages Yip Yew Mun (Mon Dec 30 2013 - 01:27:02 PST)
    - Re: [AMBER] Tleap Problem - Unable to bond atoms in amide linkages David A Case (Mon Dec 30 2013 - 04:41:41 PST)
[AMBER] angle restraint with atom groups Sourav Purohit (Mon Dec 30 2013 - 10:49:08 PST)
- Re: [AMBER] angle restraint with atom groups David A Case (Mon Dec 30 2013 - 10:58:39 PST)
  - Re: [AMBER] angle restraint with atom groups Sourav Purohit (Mon Dec 30 2013 - 13:30:54 PST)
[AMBER] SQM seems to run out of memory? Jonathan Saboury (Mon Dec 30 2013 - 11:20:37 PST)
- Re: [AMBER] SQM seems to run out of memory? David A Case (Tue Dec 31 2013 - 05:10:40 PST)
- Re: [AMBER] SQM seems to run out of memory? Jonathan Saboury (Wed Jan 01 2014 - 12:51:57 PST)
  - Re: [AMBER] SQM seems to run out of memory? Alan (Wed Jan 01 2014 - 13:21:15 PST)
  - Re: [AMBER] SQM seems to run out of memory? FyD (Thu Jan 02 2014 - 00:22:21 PST)
  - Re: [AMBER] SQM seems to run out of memory? case (Thu Jan 02 2014 - 05:17:54 PST)
[AMBER] how to minimize with full electrostatics and no boundary conditions? Jose Borreguero (Mon Dec 30 2013 - 11:36:15 PST)
- Re: [AMBER] how to minimize with full electrostatics and no boundary conditions? Jason Swails (Mon Dec 30 2013 - 12:32:21 PST)
  - Re: [AMBER] how to minimize with full electrostatics and no boundary conditions? Jose Borreguero (Mon Dec 30 2013 - 12:59:33 PST)
- Re: [AMBER] how to minimize with full electrostatics and no boundary conditions? David A Case (Tue Dec 31 2013 - 05:14:24 PST)
  - Re: [AMBER] how to minimize with full electrostatics and no boundary conditions? Jose Borreguero (Tue Dec 31 2013 - 11:26:06 PST)
[AMBER] AMBER Asfa Ali (Mon Dec 30 2013 - 13:43:52 PST)
- Re: [AMBER] AMBER Daniel Roe (Tue Dec 31 2013 - 07:58:39 PST)
  - Re: [AMBER] AMBER Asfa Ali (Wed Jan 01 2014 - 06:23:35 PST)
    - Re: [AMBER] AMBER Jason Swails (Wed Jan 01 2014 - 06:35:52 PST)
[AMBER] C12 from OL Rejwan (Tue Dec 31 2013 - 10:32:08 PST)
[AMBER] how to calculate diffusion coefficient ? Sohag Biswas (Tue Dec 31 2013 - 19:31:06 PST)
- Re: [AMBER] how to calculate diffusion coefficient ? Daniel Roe (Wed Jan 22 2014 - 13:46:31 PST)
[AMBER] request for help in radial command Robin Jain (Thu Jan 02 2014 - 00:42:29 PST)
- Re: [AMBER] request for help in radial command Jason Swails (Thu Jan 02 2014 - 06:04:06 PST)
[AMBER] binding free energy analysis Nitin Sharma (Thu Jan 02 2014 - 02:48:49 PST)
- Re: [AMBER] binding free energy analysis Jason Swails (Thu Jan 02 2014 - 05:23:38 PST)
  - Re: [AMBER] binding free energy analysis Nitin Sharma (Wed Jan 08 2014 - 08:55:36 PST)
    - Re: [AMBER] binding free energy analysis Jason Swails (Wed Jan 08 2014 - 09:43:34 PST)
    - Re: [AMBER] binding free energy analysis Nitin Sharma (Wed Jan 08 2014 - 09:46:40 PST)
[AMBER] Binding free energy for two small polymers? X Sun (Thu Jan 02 2014 - 11:21:05 PST)
[AMBER] Langevin Dynamics on selected atoms? Jose Borreguero (Thu Jan 02 2014 - 12:21:41 PST)
- Re: [AMBER] Langevin Dynamics on selected atoms? Jason Swails (Thu Jan 02 2014 - 21:34:14 PST)
  - Re: [AMBER] Langevin Dynamics on selected atoms? Jose Borreguero (Fri Jan 03 2014 - 07:46:07 PST)
    - Re: [AMBER] Langevin Dynamics on selected atoms? Adrian Roitberg (Fri Jan 03 2014 - 07:52:29 PST)
    - Re: [AMBER] Langevin Dynamics on selected atoms? Jose Borreguero (Fri Jan 03 2014 - 08:08:03 PST)
[AMBER] OSX Mavericks: Failure in parallel installation of Amber12 George Tzotzos (Fri Jan 03 2014 - 03:13:18 PST)
- Re: [AMBER] OSX Mavericks: Failure in parallel installation of Amber12 case (Fri Jan 03 2014 - 11:03:03 PST)
  - Re: [AMBER] OSX Mavericks: Failure in parallel installation of Amber12 George Tzotzos (Sat Jan 04 2014 - 10:40:42 PST)
    - Re: [AMBER] OSX Mavericks: Failure in parallel installation of Amber12 David A Case (Sat Jan 04 2014 - 14:57:01 PST)
- Re: [AMBER] OSX Mavericks: Failure in parallel installation of Amber12 Julio Dominguez (Mon Jan 06 2014 - 18:46:05 PST)
  - Re: [AMBER] OSX Mavericks: Failure in parallel installation of Amber12 David Case (Mon Jan 06 2014 - 19:41:07 PST)
- Re: [AMBER] OSX Mavericks: Failure in parallel installation of Amber12 Robyn Ayscue (Tue Jan 28 2014 - 10:53:43 PST)
  - Re: [AMBER] OSX Mavericks: Failure in parallel installation of Amber12 Jason Swails (Tue Jan 28 2014 - 12:06:52 PST)
  - Re: [AMBER] OSX Mavericks: Failure in parallel installation of Amber12 David A Case (Tue Jan 28 2014 - 18:39:25 PST)
[AMBER] atoms with non-standard hybridization Ivanov, Maxim (Fri Jan 03 2014 - 11:30:25 PST)
[AMBER] cuda job not working Jio M (Fri Jan 03 2014 - 15:26:46 PST)
- Re: [AMBER] cuda job not working Jio M (Fri Jan 03 2014 - 16:16:00 PST)
  - Re: [AMBER] cuda job not working Daniel Roe (Fri Jan 03 2014 - 20:37:41 PST)
    - Re: [AMBER] cuda job not working Jio M (Sat Jan 04 2014 - 07:00:07 PST)
    - Re: [AMBER] cuda job not working Jio M (Sat Jan 04 2014 - 07:59:41 PST)
    - Re: [AMBER] cuda job not working Daniel Roe (Sat Jan 04 2014 - 10:14:47 PST)
[AMBER] antechamber charge method Zahra Khatti (Fri Jan 03 2014 - 22:44:52 PST)
- Re: [AMBER] antechamber charge method David A Case (Sat Jan 04 2014 - 06:40:02 PST)
[AMBER] ANN: MDTraj 0.5.0 Release Robert (Fri Jan 03 2014 - 23:19:59 PST)
[AMBER] antechamber charge method? Zahra Khatti (Sat Jan 04 2014 - 06:47:28 PST)
[AMBER] antechamber charge method Zahra Khatti (Sat Jan 04 2014 - 06:53:53 PST)
- Re: [AMBER] antechamber charge method David A Case (Sat Jan 04 2014 - 07:27:45 PST)
[AMBER] standard for atomic fluctioantion Nitin Sharma (Sat Jan 04 2014 - 09:09:42 PST)
- Re: [AMBER] standard for atomic fluctioantion Daniel Roe (Sat Jan 04 2014 - 10:34:53 PST)
  - Re: [AMBER] standard for atomic fluctioantion Nitin Sharma (Sun Jan 05 2014 - 04:47:17 PST)
    - Re: [AMBER] standard for atomic fluctioantion Daniel Roe (Sun Jan 05 2014 - 10:28:00 PST)
    - Re: [AMBER] standard for atomic fluctioantion Nitin Sharma (Sun Jan 05 2014 - 10:39:35 PST)
[AMBER] Dynamics with R_OF_GYRATION Nihal Korkmaz (Sat Jan 04 2014 - 20:42:09 PST)
- Re: [AMBER] Dynamics with R_OF_GYRATION David A Case (Wed Jan 08 2014 - 15:09:21 PST)
[AMBER] not reading a second dihedral term in frcmod Allen, Scott Edward (Sun Jan 05 2014 - 16:52:45 PST)
- Re: [AMBER] not reading a second dihedral term in frcmod Jason Swails (Mon Jan 06 2014 - 09:32:59 PST)
  - Re: [AMBER] not reading a second dihedral term in frcmod Allen, Scott Edward (Mon Jan 06 2014 - 10:05:05 PST)
  - Re: [AMBER] not reading a second dihedral term in frcmod Allen, Scott Edward (Mon Jan 06 2014 - 12:14:56 PST)
[AMBER] Calculating the bending angle of a DNA sequence Yip Yew Mun (Mon Jan 06 2014 - 01:55:32 PST)
- Re: [AMBER] Calculating the bending angle of a DNA sequence ros (Mon Jan 06 2014 - 06:46:29 PST)
  - Re: [AMBER] Calculating the bending angle of a DNA sequence #YIP YEW MUN# (Tue Jan 07 2014 - 00:16:02 PST)
[AMBER] bondbydistance Sourav Purohit (Mon Jan 06 2014 - 09:27:00 PST)
- [AMBER] Fwd: bondbydistance Sourav Purohit (Mon Jan 06 2014 - 09:28:59 PST)
[AMBER] bondbydiatance Sourav Purohit (Mon Jan 06 2014 - 09:42:57 PST)
- Re: [AMBER] bondbydiatance Jason Swails (Mon Jan 06 2014 - 13:38:07 PST)
  - Re: [AMBER] bondbydiatance Sourav Purohit (Mon Jan 06 2014 - 13:56:58 PST)
[AMBER] Error with cpptraj strip and MMGBSA.py Brian Radak (Mon Jan 06 2014 - 12:28:57 PST)
- Re: [AMBER] Error with cpptraj strip and MMGBSA.py Jason Swails (Mon Jan 06 2014 - 12:45:38 PST)
- Re: [AMBER] Error with cpptraj strip and MMGBSA.py Daniel Roe (Mon Jan 06 2014 - 12:46:14 PST)
  - Re: [AMBER] Error with cpptraj strip and MMGBSA.py Jason Swails (Mon Jan 06 2014 - 17:50:10 PST)
[AMBER] PCA/ essential dynamics Andre C. Stiel (Tue Jan 07 2014 - 06:53:55 PST)
- Re: [AMBER] PCA/ essential dynamics George Tzotzos (Tue Jan 07 2014 - 08:14:33 PST)
  - Re: [AMBER] PCA/ essential dynamics wmsmith.uci.edu (Tue Jan 07 2014 - 10:50:46 PST)
[AMBER] parameters from frcmod not overwriting gaff.dat Allen, Scott Edward (Tue Jan 07 2014 - 09:11:24 PST)
- Re: [AMBER] parameters from frcmod not overwriting gaff.dat David A Case (Thu Jan 09 2014 - 04:56:21 PST)
[AMBER] calculating MSD by correcting the center-of-mass-motion Vijay Manickam Achari (Tue Jan 07 2014 - 23:45:07 PST)
- Re: [AMBER] calculating MSD by correcting the center-of-mass-motion Daniel Roe (Wed Jan 08 2014 - 08:23:08 PST)
  - Re: [AMBER] calculating MSD by correcting the center-of-mass-motion Vijay Manickam Achari (Fri Jan 10 2014 - 03:27:51 PST)
    - Re: [AMBER] calculating MSD by correcting the center-of-mass-motion Hannes Loeffler (Fri Jan 10 2014 - 04:02:00 PST)
    - Re: [AMBER] calculating MSD by correcting the center-of-mass-motion Daniel Roe (Fri Jan 10 2014 - 10:42:31 PST)
    - Re: [AMBER] calculating MSD by correcting the center-of-mass-motion Vijay Manickam Achari (Mon Jan 13 2014 - 01:00:01 PST)
    - Re: [AMBER] calculating MSD by correcting the center-of-mass-motion Vijay Manickam Achari (Mon Jan 13 2014 - 00:59:33 PST)
- Re: [AMBER] calculating MSD by correcting the center-of-mass-motion Vijay Manickam Achari (Wed Jan 08 2014 - 19:37:22 PST)
[AMBER] Charge calculation methods for RED server Yip Yew Mun (Wed Jan 08 2014 - 01:56:04 PST)
- Re: [AMBER] Charge calculation methods for RED server Ken Merz (Wed Jan 08 2014 - 10:08:32 PST)
  - Re: [AMBER] Charge calculation methods for RED server FyD (Thu Jan 09 2014 - 12:12:55 PST)
    - Re: [AMBER] Charge calculation methods for RED server Ken Merz (Thu Jan 09 2014 - 12:18:36 PST)
    - Re: [AMBER] Charge calculation methods for RED server FyD (Fri Jan 10 2014 - 00:04:11 PST)
- Re: [AMBER] Charge calculation methods for RED server FyD (Thu Jan 09 2014 - 12:05:58 PST)
  - Re: [AMBER] Charge calculation methods for RED server FyD (Thu Jan 09 2014 - 23:55:37 PST)
[AMBER] am1bcc method charge Zahra Khatti (Wed Jan 08 2014 - 02:44:33 PST)
- Re: [AMBER] am1bcc method charge David A Case (Wed Jan 08 2014 - 05:07:07 PST)
[AMBER] Visualisation of metal ions ligand after tleap Mahendra B Thapa (Wed Jan 08 2014 - 12:42:02 PST)
- Re: [AMBER] Visualisation of metal ions ligand after tleap David A Case (Thu Jan 09 2014 - 04:48:39 PST)
- Re: [AMBER] Visualisation of metal ions ligand after tleap FyD (Thu Jan 09 2014 - 12:23:00 PST)
[AMBER] Applying nmr restraints: Radius of gyration or COM distance for large groups of atoms Nihal Korkmaz (Wed Jan 08 2014 - 13:15:33 PST)
- Re: [AMBER] Applying nmr restraints: Radius of gyration or COM distance for large groups of atoms Jason Swails (Thu Jan 09 2014 - 07:33:34 PST)
[AMBER] Modelling stereochemical molecule with "R" and "S" type. Vijay Manickam Achari (Wed Jan 08 2014 - 19:48:28 PST)
- Re: [AMBER] Modelling stereochemical molecule with "R" and "S" type. Daniel Roe (Thu Jan 09 2014 - 08:57:22 PST)
  - Re: [AMBER] Modelling stereochemical molecule with "R" and "S" type. Vijay Manickam Achari (Thu Jan 09 2014 - 21:44:06 PST)
- Re: [AMBER] Modelling stereochemical molecule with "R" and "S" type. FyD (Thu Jan 09 2014 - 12:28:41 PST)
  - Re: [AMBER] Modelling stereochemical molecule with "R" and "S" type. Vijay Manickam Achari (Thu Jan 09 2014 - 21:43:08 PST)
[AMBER] Is the RMSD using ptraj normalized with respect to residues ?? Himanshu Joshi (Wed Jan 08 2014 - 20:25:14 PST)
- Re: [AMBER] Is the RMSD using ptraj normalized with respect to residues ?? David A Case (Thu Jan 09 2014 - 04:42:19 PST)
[AMBER] Error Nmode entropy calculation Nitin Sharma (Wed Jan 08 2014 - 22:39:33 PST)
- Re: [AMBER] Error Nmode entropy calculation Jason Swails (Thu Jan 09 2014 - 07:37:47 PST)
  - Re: [AMBER] Error Nmode entropy calculation Nitin Sharma (Thu Jan 09 2014 - 07:58:01 PST)
    - Re: [AMBER] Error Nmode entropy calculation Jason Swails (Thu Jan 09 2014 - 08:10:22 PST)
    - Re: [AMBER] Error Nmode entropy calculation Nitin Sharma (Sun Jan 12 2014 - 20:02:56 PST)
[AMBER] "image" command with "familiar" option kurisaki (Thu Jan 09 2014 - 01:03:13 PST)
- Re: [AMBER] "image" command with "familiar" option Jason Swails (Thu Jan 09 2014 - 07:45:02 PST)
  - Re: [AMBER] "image" command with "familiar" option kurisaki (Thu Jan 09 2014 - 16:40:56 PST)
[AMBER] R.E.D, alkene isostere, Gly-Pro, P9501 Cecilia Lindgren (Thu Jan 09 2014 - 02:28:40 PST)
- Re: [AMBER] R.E.D, alkene isostere, Gly-Pro, P9501 FyD (Thu Jan 09 2014 - 23:38:04 PST)
  - Re: [AMBER] R.E.D, alkene isostere, Gly-Pro, P9501 FyD (Fri Jan 10 2014 - 05:36:34 PST)
  - Re: [AMBER] R.E.D, alkene isostere, Gly-Pro, P9501 Cecilia Lindgren (Sun Jan 12 2014 - 23:57:36 PST)
- Re: [AMBER] R.E.D, alkene isostere, Gly-Pro, P9501 Fan Wang (Fri Jan 10 2014 - 07:25:44 PST)
[AMBER] Utility to compute the auto-correlation function for a dihedral angle? Jose Borreguero (Thu Jan 09 2014 - 12:02:19 PST)
- Re: [AMBER] Utility to compute the auto-correlation function for a dihedral angle? Daniel Roe (Thu Jan 09 2014 - 14:55:41 PST)
  - Re: [AMBER] Utility to compute the auto-correlation function for a dihedral angle? Jose Borreguero (Thu Jan 09 2014 - 16:58:50 PST)
[AMBER] How to generate boron atom paramaters? Mengyuan Zhu (Fri Jan 10 2014 - 08:15:32 PST)
- Re: [AMBER] How to generate boron atom paramaters? David A Case (Fri Jan 10 2014 - 12:09:49 PST)
  - Re: [AMBER] How to generate boron atom paramaters? Mengyuan Zhu (Fri Jan 10 2014 - 12:32:44 PST)
    - Re: [AMBER] How to generate boron atom paramaters? Ken Merz (Fri Jan 10 2014 - 12:57:59 PST)
    - Re: [AMBER] How to generate boron atom paramaters? Mengyuan Zhu (Fri Jan 10 2014 - 13:40:40 PST)
    - Re: [AMBER] How to generate boron atom paramaters? Ken Merz (Fri Jan 10 2014 - 13:52:34 PST)
- Re: [AMBER] How to generate boron atom paramaters? FyD (Sat Jan 11 2014 - 00:12:42 PST)
  - Re: [AMBER] How to generate boron atom paramaters? Vaibhav Dixit (Sat Jan 11 2014 - 22:54:13 PST)
    - Re: [AMBER] How to generate boron atom paramaters? FyD (Sun Jan 12 2014 - 00:57:42 PST)
    - Re: [AMBER] How to generate boron atom paramaters? Vaibhav Dixit (Sun Jan 12 2014 - 02:44:24 PST)
[AMBER] restart for second time Saeed Nasiri (Fri Jan 10 2014 - 11:07:43 PST)
- Re: [AMBER] restart for second time David A Case (Fri Jan 10 2014 - 12:26:59 PST)
[AMBER] request for help Robin Jain (Sat Jan 11 2014 - 00:54:36 PST)
- Re: [AMBER] request for help Daniel Roe (Sat Jan 11 2014 - 16:14:33 PST)
[AMBER] Building parameter files for a zinc finger Yip Yew Mun (Sat Jan 11 2014 - 02:47:41 PST)
- Re: [AMBER] Building parameter files for a zinc finger Tong (Sat Jan 11 2014 - 04:03:03 PST)
  - Re: [AMBER] Building parameter files for a zinc finger Ken Merz (Sat Jan 11 2014 - 04:54:52 PST)
- Re: [AMBER] Building parameter files for a zinc finger FyD (Sat Jan 11 2014 - 05:01:13 PST)
[AMBER] Creating an frcmod file for zinc finger Yip Yew Mun (Sat Jan 11 2014 - 04:08:26 PST)
[AMBER] restart for second time Saeed Nasiri (Sat Jan 11 2014 - 21:26:46 PST)
- Re: [AMBER] restart for second time Jason Swails (Sat Jan 11 2014 - 21:38:59 PST)
[AMBER] Problems on IRED analyses for order parameter Ye Wei (Sun Jan 12 2014 - 06:37:33 PST)
- Re: [AMBER] Problems on IRED analyses for order parameter David A Case (Sun Jan 12 2014 - 10:52:24 PST)
  - Re: [AMBER] Problems on IRED analyses for order parameter Ye Wei (Sun Jan 12 2014 - 20:29:30 PST)
    - Re: [AMBER] Problems on IRED analyses for order parameter David A Case (Mon Jan 13 2014 - 05:02:56 PST)
    - Re: [AMBER] Problems on IRED analyses for order parameter Ye Wei (Mon Jan 13 2014 - 05:14:42 PST)
[AMBER] ionic liquid simulation Saeed Nasiri (Sun Jan 12 2014 - 09:24:16 PST)
- Re: [AMBER] ionic liquid simulation David A Case (Sun Jan 12 2014 - 10:57:50 PST)
[AMBER] restarting the MD Saeed Nasiri (Sun Jan 12 2014 - 22:54:07 PST)
- Re: [AMBER] restarting the MD David A Case (Mon Jan 13 2014 - 05:06:40 PST)
[AMBER] Antechamber Segmentation fault (core dumped) Arun Kumar Somavarapu (Sun Jan 12 2014 - 23:27:38 PST)
- Re: [AMBER] Antechamber Segmentation fault (core dumped) David A Case (Mon Jan 13 2014 - 05:10:25 PST)
  - Re: [AMBER] Antechamber Segmentation fault (core dumped) Arun Kumar Somavarapu (Mon Jan 13 2014 - 10:58:30 PST)
    - Re: [AMBER] Antechamber Segmentation fault (core dumped) David A Case (Mon Jan 13 2014 - 12:16:47 PST)
    - Re: [AMBER] Antechamber Segmentation fault (core dumped) Arun Kumar Somavarapu (Wed Jan 15 2014 - 08:13:50 PST)
    - Re: [AMBER] Antechamber Segmentation fault (core dumped) David A Case (Wed Jan 15 2014 - 08:45:10 PST)
    - Re: [AMBER] Antechamber Segmentation fault (core dumped) Arun Kumar Somavarapu (Wed Jan 15 2014 - 23:03:26 PST)
    - Re: [AMBER] Antechamber Segmentation fault (core dumped) FyD (Thu Jan 16 2014 - 00:23:31 PST)
    - Re: [AMBER] Antechamber Segmentation fault (core dumped) Arun Kumar Somavarapu (Thu Jan 16 2014 - 08:42:36 PST)
    - Re: [AMBER] Antechamber Segmentation fault (core dumped) FyD (Fri Jan 17 2014 - 00:03:21 PST)
    - [AMBER] RE : Antechamber Segmentation fault (core dumped) ABEL Stephane 175950 (Mon Jan 13 2014 - 12:20:45 PST)
[AMBER] request for help me in hydrogen bond analysis Robin Jain (Mon Jan 13 2014 - 00:28:37 PST)
- Re: [AMBER] request for help me in hydrogen bond analysis Jason Swails (Mon Jan 13 2014 - 04:42:42 PST)
[AMBER] polymers interaction Zhuang, Yu (Mon Jan 13 2014 - 04:58:32 PST)
- Re: [AMBER] polymers interaction David A Case (Mon Jan 13 2014 - 05:28:26 PST)
Re: [AMBER] makeDIST command disfuntion Jan Zalesak (Mon Jan 13 2014 - 12:10:26 PST)
- Re: [AMBER] makeDIST command disfuntion David A Case (Mon Jan 13 2014 - 18:16:24 PST)
  - Re: [AMBER] makeDIST command disfuntion Jan Zalesak (Tue Jan 14 2014 - 03:06:01 PST)
[AMBER] Converting DL_POLY OPLS dihedral ff function to AMBER format Parker, Qamreen (Tue Jan 14 2014 - 02:06:37 PST)
- Re: [AMBER] Converting DL_POLY OPLS dihedral ff function to AMBER format David A Case (Tue Jan 14 2014 - 05:39:18 PST)
[AMBER] iwrap=1 or netcdf Jio M (Tue Jan 14 2014 - 05:10:13 PST)
- Re: [AMBER] iwrap=1 or netcdf Daniel Roe (Tue Jan 14 2014 - 07:31:02 PST)
  - Re: [AMBER] iwrap=1 or netcdf Jio M (Tue Jan 14 2014 - 07:41:21 PST)
    - Re: [AMBER] iwrap=1 or netcdf Daniel Roe (Tue Jan 14 2014 - 07:55:02 PST)
    - Re: [AMBER] iwrap=1 or netcdf Marek Maly (Tue Jan 14 2014 - 08:35:22 PST)
    - Re: [AMBER] iwrap=1 or netcdf Jason Swails (Wed Jan 15 2014 - 08:12:35 PST)
    - Re: [AMBER] iwrap=1 or netcdf Jio M (Wed Jan 15 2014 - 08:28:49 PST)
    - Re: [AMBER] iwrap=1 or netcdf Marek Maly (Wed Jan 15 2014 - 09:17:35 PST)
    - Re: [AMBER] iwrap=1 or netcdf Jio M (Thu Jan 16 2014 - 01:46:20 PST)
    - Re: [AMBER] iwrap=1 or netcdf Marek Maly (Thu Jan 16 2014 - 08:52:06 PST)
    - Re: [AMBER] iwrap=1 or netcdf Jio M (Thu Jan 16 2014 - 09:01:23 PST)
    - Re: [AMBER] iwrap=1 or netcdf Marek Maly (Thu Jan 16 2014 - 09:43:46 PST)
    - Re: [AMBER] iwrap=1 or netcdf Jio M (Thu Jan 16 2014 - 09:55:20 PST)
    - Re: [AMBER] iwrap=1 or netcdf Marek Maly (Thu Jan 16 2014 - 09:59:55 PST)
    - Re: [AMBER] iwrap=1 or netcdf Marek Maly (Wed Jan 15 2014 - 09:00:38 PST)
[AMBER] QMMM SCC-DFTB: ERROR ON EWEVGE (Eigenvalue solver) Kanin Wichapong (Tue Jan 14 2014 - 06:24:47 PST)
- Re: [AMBER] QMMM SCC-DFTB: ERROR ON EWEVGE (Eigenvalue solver) Brian Radak (Tue Jan 14 2014 - 06:41:28 PST)
[AMBER] Query about next amber release Kshatresh Dutta Dubey (Wed Jan 15 2014 - 03:20:47 PST)
- Re: [AMBER] Query about next amber release David A Case (Wed Jan 15 2014 - 05:23:45 PST)
  - Re: [AMBER] Query about next amber release Kshatresh Dutta Dubey (Wed Jan 15 2014 - 05:42:40 PST)
    - Re: [AMBER] Query about next amber release David A Case (Wed Jan 15 2014 - 07:35:37 PST)
[AMBER] question for pre-treat protein model Zhuang, Yu (Wed Jan 15 2014 - 06:17:27 PST)
- Re: [AMBER] question for pre-treat protein model Ye Wei (Wed Jan 15 2014 - 06:25:12 PST)
  - Re: [AMBER] question for pre-treat protein model Zhuang, Yu (Wed Jan 15 2014 - 06:42:41 PST)
    - Re: [AMBER] question for pre-treat protein model 126 (Wed Jan 15 2014 - 06:51:19 PST)
    - Re: [AMBER] question for pre-treat protein model Zhuang, Yu (Wed Jan 15 2014 - 07:07:19 PST)
- Re: [AMBER] question for pre-treat protein model Jason Swails (Wed Jan 15 2014 - 08:04:22 PST)
[AMBER] cpptraj density routine Dickson, Callum J (Wed Jan 15 2014 - 07:01:14 PST)
- Re: [AMBER] cpptraj density routine Daniel Roe (Wed Jan 22 2014 - 13:17:23 PST)
[AMBER] question on how to keep the protein coordinate when adding solvateoct in xleap 肖立 (Wed Jan 15 2014 - 11:24:36 PST)
- Re: [AMBER] question on how to keep the protein coordinate when adding solvateoct in xleap James Maier (Wed Jan 15 2014 - 11:29:55 PST)
  - Re: [AMBER] question on how to keep the protein coordinate when adding solvateoct in xleap 肖立 (Wed Jan 15 2014 - 11:51:14 PST)
    - Re: [AMBER] question on how to keep the protein coordinate when adding solvateoct in xleap Kevin Hauser (Wed Jan 15 2014 - 12:21:55 PST)
    - Re: [AMBER] question on how to keep the protein coordinate when adding solvateoct in xleap 肖立 (Wed Jan 15 2014 - 13:30:52 PST)
    - Re: [AMBER] question on how to keep the protein coordinate when adding solvateoct in xleap David A Case (Wed Jan 15 2014 - 14:04:22 PST)
    - Re: [AMBER] question on how to keep the protein coordinate when adding solvateoct in xleap 肖立 (Wed Jan 15 2014 - 14:06:50 PST)
    - Re: [AMBER] question on how to keep the protein coordinate when adding solvateoct in xleap 肖立 (Wed Jan 15 2014 - 14:53:22 PST)
    - Re: [AMBER] question on how to keep the protein coordinate when adding solvateoct in xleap Jio M (Wed Jan 15 2014 - 15:17:27 PST)
    - Re: [AMBER] question on how to keep the protein coordinate when adding solvateoct in xleap 肖立 (Wed Jan 15 2014 - 15:24:36 PST)
    - Re: [AMBER] question on how to keep the protein coordinate when adding solvateoct in xleap Kevin Hauser (Wed Jan 15 2014 - 19:07:52 PST)
    - Re: [AMBER] question on how to keep the protein coordinate when adding solvateoct in xleap 肖立 (Wed Jan 15 2014 - 21:56:18 PST)
    - Re: [AMBER] question on how to keep the protein coordinate when adding solvateoct in xleap Kevin Hauser (Sun Jan 19 2014 - 22:11:08 PST)
    - Re: [AMBER] question on how to keep the protein coordinate when adding solvateoct in xleap 肖立 (Mon Jan 20 2014 - 15:37:24 PST)
    - Re: [AMBER] question on how to keep the protein coordinate when adding solvateoct in xleap James Maier (Mon Jan 20 2014 - 12:37:48 PST)
    - Re: [AMBER] question on how to keep the protein coordinate when adding solvateoct in xleap 肖立 (Mon Jan 20 2014 - 15:37:56 PST)
[AMBER] stfcdiffusion error Diego de paula (Wed Jan 15 2014 - 18:43:46 PST)
- Re: [AMBER] stfcdiffusion error Daniel Roe (Wed Jan 22 2014 - 13:32:36 PST)
[AMBER] IGB doubt Sushi Shilpa (Wed Jan 15 2014 - 20:06:00 PST)
- Re: [AMBER] IGB doubt James Maier (Wed Jan 15 2014 - 20:14:59 PST)
[AMBER] How to make a nonequilibrium molecular dynamics on an external force field like electromagnetic or microwave? 张明焜 (Thu Jan 16 2014 - 18:06:07 PST)
[AMBER] order params Jio M (Fri Jan 17 2014 - 08:16:34 PST)
[AMBER] Free energy workshop in May, 2014 David A Case (Fri Jan 17 2014 - 15:21:07 PST)
[AMBER] error in naming list problem Sushi Shilpa (Sun Jan 19 2014 - 20:21:22 PST)
- Re: [AMBER] error in naming list problem Ross Walker (Sun Jan 19 2014 - 21:44:25 PST)
- Re: [AMBER] error in naming list problem Jason Swails (Mon Jan 20 2014 - 04:29:08 PST)
- Re: [AMBER] error in naming list problem David A Case (Mon Jan 20 2014 - 04:36:59 PST)
[AMBER] output of radius of gyration Zhuang, Yu (Mon Jan 20 2014 - 03:13:00 PST)
- Re: [AMBER] output of radius of gyration Jason Swails (Mon Jan 20 2014 - 04:31:19 PST)
  - Re: [AMBER] output of radius of gyration Zhuang, Yu (Mon Jan 20 2014 - 06:01:48 PST)
    - Re: [AMBER] output of radius of gyration Daniel Roe (Mon Jan 20 2014 - 08:56:55 PST)
    - Re: [AMBER] output of radius of gyration Zhuang, Yu (Mon Jan 20 2014 - 23:58:27 PST)
[AMBER] append more nucleotides to solution structure Asaminew Haile (Mon Jan 20 2014 - 09:09:09 PST)
- Re: [AMBER] append more nucleotides to solution structure Vlad Cojocaru (Mon Jan 20 2014 - 09:25:34 PST)
  - Re: [AMBER] append more nucleotides to solution structure Asaminew Haile (Mon Jan 20 2014 - 10:14:12 PST)
    - Re: [AMBER] append more nucleotides to solution structure Vlad Cojocaru (Mon Jan 20 2014 - 10:53:38 PST)
    - Re: [AMBER] append more nucleotides to solution structure Asaminew Haile (Mon Jan 20 2014 - 11:17:00 PST)
    - Re: [AMBER] append more nucleotides to solution structure Vlad Cojocaru (Mon Jan 20 2014 - 11:30:39 PST)
[AMBER] restart MD Saeed Nasiri (Mon Jan 20 2014 - 12:42:30 PST)
- Re: [AMBER] restart MD Daniel Roe (Mon Jan 20 2014 - 17:05:17 PST)
[AMBER] rmsd with fit Jio M (Mon Jan 20 2014 - 15:46:46 PST)
- Re: [AMBER] rmsd with fit 126 (Mon Jan 20 2014 - 15:57:06 PST)
- Re: [AMBER] rmsd with fit Daniel Roe (Mon Jan 20 2014 - 16:49:22 PST)
  - Re: [AMBER] rmsd with fit Jio M (Mon Jan 20 2014 - 17:34:23 PST)
    - Re: [AMBER] rmsd with fit Daniel Roe (Mon Jan 20 2014 - 19:08:33 PST)
[AMBER] Creating a restart file from a trajectory file Ahmed Ayoub (Tue Jan 21 2014 - 00:45:49 PST)
- Re: [AMBER] Creating a restart file from a trajectory file David A Case (Tue Jan 21 2014 - 04:42:12 PST)
[AMBER] AMBER-cis-trans conversion Gözde YALÇIN (Tue Jan 21 2014 - 07:19:31 PST)
- Re: [AMBER] AMBER-cis-trans conversion Jason Swails (Tue Jan 21 2014 - 08:13:24 PST)
[AMBER] Current system recommendations Jonathan Sheehan (Tue Jan 21 2014 - 14:06:23 PST)
- Re: [AMBER] Current system recommendations Jason Swails (Tue Jan 21 2014 - 15:21:37 PST)
  - Re: [AMBER] Current system recommendations Jonathan Sheehan (Wed Jan 22 2014 - 04:48:31 PST)
    - Re: [AMBER] Current system recommendations Ase (Wed Jan 22 2014 - 15:10:18 PST)
[AMBER] Question Eric Smoll (Tue Jan 21 2014 - 15:26:39 PST)
- Re: [AMBER] Question Ben Roberts (Tue Jan 21 2014 - 18:03:50 PST)
- Re: [AMBER] Question Ross Walker (Tue Jan 21 2014 - 19:01:28 PST)
[AMBER] Compiling Amber 12 using IBM XL compilers - fixed versus free format Fortran Ben Roberts (Tue Jan 21 2014 - 17:49:10 PST)
- Re: [AMBER] Compiling Amber 12 using IBM XL compilers - fixed versus free format Fortran Jason Swails (Tue Jan 21 2014 - 19:56:34 PST)
  - Re: [AMBER] Compiling Amber 12 using IBM XL compilers - fixed versus free format Fortran Ben Roberts (Mon Jan 27 2014 - 19:32:35 PST)
[AMBER] fluctuation of pressure during MD Zhuang, Yu (Wed Jan 22 2014 - 00:53:45 PST)
- Re: [AMBER] fluctuation of pressure during MD Jason Swails (Wed Jan 22 2014 - 06:58:14 PST)
  - Re: [AMBER] fluctuation of pressure during MD Zhuang, Yu (Thu Jan 23 2014 - 00:11:58 PST)
[AMBER] Oscillating electric fields Bernhard Reuter (Wed Jan 22 2014 - 04:10:32 PST)
- Re: [AMBER] Oscillating electric fields Jason Swails (Wed Jan 22 2014 - 07:15:18 PST)
  - Re: [AMBER] Oscillating electric fields Brian Radak (Wed Jan 22 2014 - 08:05:02 PST)
[AMBER] AmberTools vs. Amber: Installation practice subject to different licenses Sternberg, Michael G. (Wed Jan 22 2014 - 15:46:30 PST)
- Re: [AMBER] AmberTools vs. Amber: Installation practice subject to different licenses Jason Swails (Thu Jan 23 2014 - 03:46:41 PST)
  - Re: [AMBER] AmberTools vs. Amber: Installation practice subject to different licenses - Solved. Sternberg, Michael G. (Wed Jan 29 2014 - 11:36:54 PST)
[AMBER] simulation output Saeed Nasiri (Wed Jan 22 2014 - 22:56:06 PST)
- Re: [AMBER] simulation output Jason Swails (Thu Jan 23 2014 - 03:52:57 PST)
[AMBER] PIMD_pure_QM_EXTERN Jheng Wei Li (Wed Jan 22 2014 - 23:54:35 PST)
- Re: [AMBER] PIMD_pure_QM_EXTERN Jason Swails (Thu Jan 23 2014 - 05:21:40 PST)
  - Re: [AMBER] PIMD_pure_QM_EXTERN David A Case (Thu Jan 23 2014 - 12:22:08 PST)
  - Re: [AMBER] PIMD_pure_QM_EXTERN Andreas Goetz (Fri Jan 24 2014 - 10:27:14 PST)
    - Re: [AMBER] PIMD_pure_QM_EXTERN Jason Swails (Fri Jan 24 2014 - 13:02:35 PST)
    - Re: [AMBER] PIMD_pure_QM_EXTERN Andreas Goetz (Fri Jan 24 2014 - 17:15:24 PST)
[AMBER] Release of FESetup 1.0 Hannes Loeffler (Thu Jan 23 2014 - 03:03:17 PST)
[AMBER] restart MD Saeed Nasiri (Thu Jan 23 2014 - 03:33:47 PST)
[AMBER] input preparation esther nehu (Thu Jan 23 2014 - 04:49:13 PST)
- Re: [AMBER] input preparation Jason Swails (Thu Jan 23 2014 - 05:08:53 PST)
  - Re: [AMBER] input preparation esther nehu (Sat Jan 25 2014 - 03:56:43 PST)
    - Re: [AMBER] input preparation David A Case (Sat Jan 25 2014 - 06:31:44 PST)
    - Re: [AMBER] input preparation esther nehu (Tue Jan 28 2014 - 04:00:41 PST)
    - Re: [AMBER] input preparation David A Case (Tue Jan 28 2014 - 04:50:50 PST)
[AMBER] checkpoint on Amber within batch job Zhuang, Yu (Thu Jan 23 2014 - 05:33:53 PST)
- Re: [AMBER] checkpoint on Amber within batch job Jason Swails (Thu Jan 23 2014 - 05:43:58 PST)
  - Re: [AMBER] checkpoint on Amber within batch job Zhuang, Yu (Thu Jan 23 2014 - 05:57:44 PST)
    - Re: [AMBER] checkpoint on Amber within batch job Jason Swails (Thu Jan 23 2014 - 06:54:55 PST)
    - Re: [AMBER] checkpoint on Amber within batch job James Maier (Thu Jan 23 2014 - 06:54:47 PST)
    - Re: [AMBER] checkpoint on Amber within batch job Ross Walker (Thu Jan 23 2014 - 09:38:04 PST)
    - Re: [AMBER] checkpoint on Amber within batch job David A Case (Thu Jan 23 2014 - 12:22:16 PST)
    - Re: [AMBER] checkpoint on Amber within batch job Daniel Roe (Thu Jan 23 2014 - 07:11:33 PST)
    - Re: [AMBER] checkpoint on Amber within batch job Zhuang, Yu (Thu Jan 23 2014 - 07:54:25 PST)
[AMBER] SPAM: A Simple Approach for Profiling Bound Water Molecules Sergey Samsonov (Thu Jan 23 2014 - 05:57:18 PST)
- Re: [AMBER] SPAM: A Simple Approach for Profiling Bound Water Molecules Jason Swails (Thu Jan 23 2014 - 10:04:34 PST)
  - Re: [AMBER] SPAM: A Simple Approach for Profiling Bound Water Molecules Sergey Samsonov (Fri Jan 24 2014 - 02:06:42 PST)
    - Re: [AMBER] SPAM: A Simple Approach for Profiling Bound Water Molecules Jason Swails (Fri Jan 24 2014 - 05:47:17 PST)
    - Re: [AMBER] SPAM: A Simple Approach for Profiling Bound Water Molecules Sergey Samsonov (Fri Jan 24 2014 - 06:54:48 PST)
    - Re: [AMBER] SPAM: A Simple Approach for Profiling Bound Water Molecules Guanglei Cui (Fri Jan 24 2014 - 07:27:53 PST)
[AMBER] correct way of imaging for rdf Jio M (Thu Jan 23 2014 - 08:06:19 PST)
- Re: [AMBER] correct way of imaging for rdf Daniel Roe (Thu Jan 23 2014 - 08:28:22 PST)
  - Re: [AMBER] correct way of imaging for rdf Jio M (Thu Jan 23 2014 - 08:52:33 PST)
    - Re: [AMBER] correct way of imaging for rdf Daniel Roe (Thu Jan 23 2014 - 09:27:11 PST)
    - Re: [AMBER] correct way of imaging for rdf Jio M (Thu Jan 23 2014 - 10:05:26 PST)
    - Re: [AMBER] correct way of imaging for rdf Daniel Roe (Thu Jan 23 2014 - 10:44:04 PST)
    - Re: [AMBER] correct way of imaging for rdf Jio M (Thu Jan 23 2014 - 12:22:31 PST)
[AMBER] Can we solvate the box with ligand Ayesha Fatima (Thu Jan 23 2014 - 23:42:26 PST)
- Re: [AMBER] Can we solvate the box with ligand David A Case (Fri Jan 24 2014 - 07:57:48 PST)
[AMBER] mpi-pmemd Saeed Nasiri (Fri Jan 24 2014 - 01:00:07 PST)
- Re: [AMBER] mpi-pmemd Daniel Roe (Fri Jan 24 2014 - 07:02:38 PST)
[AMBER] MMPBSA bharat lakhani (Fri Jan 24 2014 - 11:24:29 PST)
- Re: [AMBER] MMPBSA Carlos Simmerling (Fri Jan 24 2014 - 12:03:22 PST)
- Re: [AMBER] MMPBSA Jason Swails (Fri Jan 24 2014 - 13:05:05 PST)
[AMBER] effect of born radii on the binding energies of a protein-ligand system Manikanthan Bhavaraju (Fri Jan 24 2014 - 12:58:06 PST)
[AMBER] REMD on one GPU Milo Westler (Fri Jan 24 2014 - 13:28:17 PST)
- Re: [AMBER] REMD on one GPU Ross Walker (Fri Jan 24 2014 - 13:51:19 PST)
  - Re: [AMBER] REMD on one GPU Milo Westler (Fri Jan 24 2014 - 13:55:35 PST)
    - Re: [AMBER] REMD on one GPU Ross Walker (Fri Jan 24 2014 - 14:02:22 PST)
[AMBER] Error generating prmtop file for protein with NAD+ Prema Mallipeddi (Fri Jan 24 2014 - 13:43:16 PST)
- [AMBER] request to unsubscribe from the amber mailing list Su, Shiquan (Fri Jan 24 2014 - 17:43:22 PST)
  - Re: [AMBER] request to unsubscribe from the amber mailing list Jason Swails (Fri Jan 24 2014 - 20:37:00 PST)
[AMBER] Ptraj's "NO ATOMS DETECTED" problem Yip Yew Mun (Fri Jan 24 2014 - 17:36:17 PST)
- Re: [AMBER] Ptraj's "NO ATOMS DETECTED" problem David A Case (Fri Jan 24 2014 - 18:08:33 PST)
  - Re: [AMBER] Ptraj's "NO ATOMS DETECTED" problem #YIP YEW MUN# (Fri Jan 24 2014 - 23:14:12 PST)
    - Re: [AMBER] Ptraj's "NO ATOMS DETECTED" problem David A Case (Sat Jan 25 2014 - 06:28:31 PST)
- Re: [AMBER] Ptraj's "NO ATOMS DETECTED" problem Vijay Singh (Sat Mar 15 2014 - 20:33:05 PDT)
[AMBER] enquiry regarding latest Amber Ved Prakash (Sat Jan 25 2014 - 08:14:48 PST)
- Re: [AMBER] enquiry regarding latest Amber Divi/GMAIL (Sat Jan 25 2014 - 10:14:55 PST)
  - Re: [AMBER] enquiry regarding latest Amber Ved Prakash (Mon Feb 10 2014 - 03:36:12 PST)
    - Re: [AMBER] enquiry regarding latest Amber Jason Swails (Mon Feb 10 2014 - 04:43:19 PST)
    - Re: [AMBER] enquiry regarding latest Amber Ross Walker (Mon Feb 10 2014 - 10:10:10 PST)
    - Re: [AMBER] enquiry regarding latest Amber Ved Prakash (Tue Feb 11 2014 - 04:35:02 PST)
    - Re: [AMBER] enquiry regarding latest Amber Francesco Pietra (Tue Feb 11 2014 - 06:42:29 PST)
    - Re: [AMBER] enquiry regarding latest Amber Ross Walker (Tue Feb 11 2014 - 12:11:52 PST)
    - Re: [AMBER] enquiry regarding latest Amber Francesco Pietra (Wed Feb 12 2014 - 00:36:36 PST)
    - Re: [AMBER] enquiry regarding latest Amber Ross Walker (Wed Feb 12 2014 - 09:37:23 PST)
[AMBER] no output file when running espgen Kim TaeHwan (Sun Jan 26 2014 - 00:47:00 PST)
- Re: [AMBER] no output file when running espgen FyD (Sun Jan 26 2014 - 07:00:42 PST)
[AMBER] How to make a nonequilibrium molecular dynamics on an external force field like electromagnetic or microwave? 张明焜 (Sun Jan 26 2014 - 01:18:18 PST)
- Re: [AMBER] How to make a nonequilibrium molecular dynamics on an external force field like electromagnetic or microwave? Jason Swails (Sun Jan 26 2014 - 07:03:44 PST)
[AMBER] Unable to read coords from rst Yip Yew Mun (Sun Jan 26 2014 - 19:04:39 PST)
- Re: [AMBER] Unable to read coords from rst Jason Swails (Mon Jan 27 2014 - 01:47:59 PST)
[AMBER] Creating Non-canonical Structures in NAB Robyn Ayscue (Sun Jan 26 2014 - 20:07:24 PST)
- Re: [AMBER] Creating Non-canonical Structures in NAB David A Case (Tue Jan 28 2014 - 05:11:51 PST)
[AMBER] question . mirage (Mon Jan 27 2014 - 05:04:23 PST)
- Re: [AMBER] question . mirage (Wed Jan 29 2014 - 04:53:28 PST)
- Re: [AMBER] question Jason Swails (Wed Jan 29 2014 - 05:37:08 PST)
  - Re: [AMBER] question . mirage (Wed Jan 29 2014 - 06:39:13 PST)
[AMBER] tracking ions in protein channel Jio M (Mon Jan 27 2014 - 06:15:38 PST)
- Re: [AMBER] tracking ions in protein channel Jio M (Wed Feb 05 2014 - 03:22:24 PST)
  - Re: [AMBER] tracking ions in protein channel Daniel Roe (Wed Feb 05 2014 - 12:41:01 PST)
[AMBER] internal energy in TI decomposition Schackert Nico (Mon Jan 27 2014 - 07:13:28 PST)
[AMBER] Explicit solvent constant pH simulation Logan Ahlstrom (Mon Jan 27 2014 - 08:40:04 PST)
- Re: [AMBER] Explicit solvent constant pH simulation Adrian Roitberg (Mon Jan 27 2014 - 08:42:12 PST)
  - Re: [AMBER] Explicit solvent constant pH simulation Logan Ahlstrom (Mon Jan 27 2014 - 08:44:10 PST)
  - Re: [AMBER] Explicit solvent constant pH simulation Thomas Evangelidis (Fri Jan 31 2014 - 03:58:21 PST)
    - Re: [AMBER] Explicit solvent constant pH simulation Jason Swails (Fri Jan 31 2014 - 05:10:37 PST)
[AMBER] Indentified the cause - Error generating prmtop file for protein with NAD+ Prema Mallipeddi (Mon Jan 27 2014 - 11:10:10 PST)
[AMBER] internal energy in TI decomposition Schackert Nico (Tue Jan 28 2014 - 01:18:51 PST)
- Re: [AMBER] internal energy in TI decomposition Jason Swails (Tue Jan 28 2014 - 04:01:24 PST)
  - Re: [AMBER] internal energy in TI decomposition Schackert Nico (Mon Feb 03 2014 - 03:55:11 PST)
    - Re: [AMBER] internal energy in TI decomposition Jason Swails (Mon Feb 03 2014 - 04:21:29 PST)
    - Re: [AMBER] internal energy in TI decomposition Schackert Nico (Wed Feb 05 2014 - 05:22:14 PST)
    - Re: [AMBER] internal energy in TI decomposition Jason Swails (Wed Feb 05 2014 - 05:54:32 PST)
[AMBER] Number of cores for a parallel job FyD (Tue Jan 28 2014 - 04:29:01 PST)
- Re: [AMBER] Number of cores for a parallel job David A Case (Tue Jan 28 2014 - 04:55:18 PST)
- Re: [AMBER] Number of cores for a parallel job Hannes Loeffler (Tue Jan 28 2014 - 05:03:38 PST)
[AMBER] fun with units? Brian Radak (Tue Jan 28 2014 - 06:43:19 PST)
- Re: [AMBER] fun with units? Jason Swails (Tue Jan 28 2014 - 07:57:54 PST)
  - Re: [AMBER] fun with units? Brian Radak (Tue Jan 28 2014 - 08:02:52 PST)
[AMBER] amber12 GPU performance degrades? Guanglei Cui (Tue Jan 28 2014 - 08:37:07 PST)
- Re: [AMBER] amber12 GPU performance degrades? Jan-Philip Gehrcke (Tue Jan 28 2014 - 08:53:24 PST)
- Re: [AMBER] amber12 GPU performance degrades? Ross Walker (Tue Jan 28 2014 - 09:03:56 PST)
  - Re: [AMBER] amber12 GPU performance degrades? Guanglei Cui (Tue Jan 28 2014 - 11:21:33 PST)
    - Re: [AMBER] amber12 GPU performance degrades? Jason Swails (Tue Jan 28 2014 - 11:56:10 PST)
    - Re: [AMBER] amber12 GPU performance degrades? Guanglei Cui (Tue Jan 28 2014 - 12:27:32 PST)
[AMBER] optimise ligand geomatry before MD Nitin Sharma (Tue Jan 28 2014 - 10:44:53 PST)
- Re: [AMBER] optimise ligand geomatry before MD Karl Kirschner (Wed Jan 29 2014 - 01:13:53 PST)
  - Re: [AMBER] optimise ligand geomatry before MD Nitin Sharma (Wed Feb 05 2014 - 09:14:42 PST)
[AMBER] Prep file is empty DEBOSTUTI GHOSHDASTIDAR (Wed Jan 29 2014 - 06:07:14 PST)
- Re: [AMBER] Prep file is empty David A Case (Wed Jan 29 2014 - 07:27:40 PST)
  - Re: [AMBER] Prep file is empty DEBOSTUTI GHOSHDASTIDAR (Wed Jan 29 2014 - 20:50:13 PST)
    - Re: [AMBER] Prep file is empty David A Case (Thu Jan 30 2014 - 04:59:08 PST)
    - Re: [AMBER] Prep file is empty DEBOSTUTI GHOSHDASTIDAR (Thu Jan 30 2014 - 19:47:22 PST)
- Re: [AMBER] Prep file is empty FyD (Wed Jan 29 2014 - 23:21:22 PST)
[AMBER] Has anyone tested to newer nvidia drivers for linux? Matthew Wampole (Wed Jan 29 2014 - 07:43:12 PST)
- Re: [AMBER] Has anyone tested to newer nvidia drivers for linux? Ross Walker (Wed Jan 29 2014 - 08:28:33 PST)
  - Re: [AMBER] Has anyone tested to newer nvidia drivers for linux? Jan-Philip Gehrcke (Wed Jan 29 2014 - 08:45:14 PST)
- Re: [AMBER] Has anyone tested to newer nvidia drivers for linux? Julio Dominguez (Wed Jan 29 2014 - 12:09:52 PST)
[AMBER] Fwd: Re: Prep file is empty FyD (Wed Jan 29 2014 - 23:25:21 PST)
[AMBER] GTX 780: 8 file comparisons failed de Waal, Parker (Thu Jan 30 2014 - 15:36:47 PST)
- Re: [AMBER] GTX 780: 8 file comparisons failed Ross Walker (Thu Jan 30 2014 - 15:53:27 PST)
  - Re: [AMBER] GTX 780: 8 file comparisons failed de Waal, Parker (Thu Jan 30 2014 - 16:16:23 PST)
[AMBER] Accuracy of solvation free energy calculated by 3D-RISM n.ricky0204.gmail.com (Fri Jan 31 2014 - 03:07:02 PST)
- Re: [AMBER] Accuracy of solvation free energy calculated by 3D-RISM David A Case (Fri Jan 31 2014 - 05:09:10 PST)
  - Re: [AMBER] Accuracy of solvation free energy calculated by 3D-RISM Kayo (Sat Feb 01 2014 - 03:38:56 PST)
[AMBER] Problems with MM_GBSA Joachim Stump (Fri Jan 31 2014 - 05:18:31 PST)
- Re: [AMBER] Problems with MM_GBSA Daniel Roe (Fri Jan 31 2014 - 08:12:23 PST)
  - Re: [AMBER] Problems with MM_GBSA Jason Swails (Fri Jan 31 2014 - 09:09:55 PST)
[AMBER] continuing runs with latest patched AMBER Jio M (Fri Jan 31 2014 - 09:24:26 PST)
- Re: [AMBER] continuing runs with latest patched AMBER Ross Walker (Fri Jan 31 2014 - 09:46:05 PST)
[AMBER] ATOMIC NUMBER section in prmtop file - Sustiva example rohitarora10.gmail.com (Fri Jan 31 2014 - 10:29:01 PST)
- Re: [AMBER] ATOMIC NUMBER section in prmtop file - Sustiva example James Maier (Fri Jan 31 2014 - 11:33:18 PST)
  - Re: [AMBER] ATOMIC NUMBER section in prmtop file - Sustiva example David A Case (Fri Jan 31 2014 - 13:27:22 PST)
- Re: [AMBER] ATOMIC NUMBER section in prmtop file - Sustiva example ye renlo (Sat Apr 05 2014 - 07:39:38 PDT)
[AMBER] VMD lipid in AMBER Rejwan (Fri Jan 31 2014 - 11:40:21 PST)
- Re: [AMBER] VMD lipid in AMBER Benjamin Madej (Fri Jan 31 2014 - 12:27:44 PST)
[AMBER] Fwd: amber Jorgen Simonsen (Fri Jan 31 2014 - 21:25:38 PST)
- Re: [AMBER] Fwd: amber Daniel Roe (Sat Feb 01 2014 - 07:42:46 PST)
  - Re: [AMBER] Fwd: amber Daniel Roe (Sat Feb 01 2014 - 07:54:25 PST)
    - Re: [AMBER] Fwd: amber David A Case (Sat Feb 01 2014 - 08:33:28 PST)
    - Re: [AMBER] Fwd: amber Daniel Roe (Sat Feb 01 2014 - 08:47:49 PST)
[AMBER] MMPBSA on Protein/DNA complex Yip Yew Mun (Fri Jan 31 2014 - 23:12:34 PST)
- Re: [AMBER] MMPBSA on Protein/DNA complex Ray Luo, Ph.D. (Sun Feb 02 2014 - 09:07:09 PST)
[AMBER] combine results Saeed Nasiri (Sun Feb 02 2014 - 00:57:05 PST)
[AMBER] Parallel running problem of MMPBSA zhongqiao hu (Mon Feb 03 2014 - 00:47:45 PST)
- Re: [AMBER] Parallel running problem of MMPBSA zhongqiao hu (Mon Feb 03 2014 - 01:35:47 PST)
  - Re: [AMBER] Parallel running problem of MMPBSA Jason Swails (Mon Feb 03 2014 - 04:29:24 PST)
- Re: [AMBER] Parallel running problem of MMPBSA zhongqiao hu (Tue Feb 04 2014 - 00:12:07 PST)
[AMBER] Protein insertion into a membrane Stéphane Azoulay (Mon Feb 03 2014 - 05:50:52 PST)
- Re: [AMBER] Protein insertion into a membrane Stéphane Azoulay (Tue Feb 11 2014 - 00:51:33 PST)
  - [AMBER] RE : Protein insertion into a membrane ABEL Stephane 175950 (Tue Feb 11 2014 - 02:51:16 PST)
    - Re: [AMBER] Protein insertion into a membrane Stéphane Azoulay (Tue Feb 11 2014 - 03:05:51 PST)
    - [AMBER] RE : Protein insertion into a membrane ABEL Stephane 175950 (Tue Feb 11 2014 - 03:41:40 PST)
    - Re: [AMBER] RE : Protein insertion into a membrane Stéphane Azoulay (Tue Feb 11 2014 - 05:44:23 PST)
    - [AMBER] RE : RE : Protein insertion into a membrane ABEL Stephane 175950 (Tue Feb 11 2014 - 06:00:54 PST)
    - Re: [AMBER] RE : RE : Protein insertion into a membrane Stéphane Azoulay (Tue Feb 11 2014 - 07:43:42 PST)
    - Re: [AMBER] RE : RE : Protein insertion into a membrane Benjamin Madej (Tue Feb 11 2014 - 14:41:50 PST)
[AMBER] error in extending simulation from .rst file Nitin Sharma (Mon Feb 03 2014 - 21:18:54 PST)
- Re: [AMBER] error in extending simulation from .rst file David A Case (Tue Feb 04 2014 - 05:00:56 PST)
- Re: [AMBER] error in extending simulation from .rst file Jason Swails (Tue Feb 04 2014 - 05:02:07 PST)
  - Re: [AMBER] error in extending simulation from .rst file Nitin Sharma (Tue Feb 04 2014 - 10:07:11 PST)
    - Re: [AMBER] error in extending simulation from .rst file Jason Swails (Tue Feb 04 2014 - 10:20:57 PST)
[AMBER] cpptraj: linear interaction energy - lie Anselm Horn (Tue Feb 04 2014 - 05:01:19 PST)
- Re: [AMBER] cpptraj: linear interaction energy - lie Jason Swails (Tue Feb 04 2014 - 05:45:53 PST)
  - Re: [AMBER] cpptraj: linear interaction energy - lie Anselm Horn (Wed Feb 05 2014 - 01:09:37 PST)
    - Re: [AMBER] cpptraj: linear interaction energy - lie Jason Swails (Wed Feb 05 2014 - 05:45:38 PST)
[AMBER] Query on introducing a protein Aditya Padhi (Tue Feb 04 2014 - 21:12:10 PST)
- Re: [AMBER] Query on introducing a protein David A Case (Wed Feb 05 2014 - 04:31:17 PST)
  - Re: [AMBER] Query on introducing a protein Aditya Padhi (Wed Feb 05 2014 - 05:01:02 PST)
[AMBER] Generating RST file using Cpptraj Yip Yew Mun (Tue Feb 04 2014 - 21:12:52 PST)
- Re: [AMBER] Generating RST file using Cpptraj Nitin Sharma (Tue Feb 04 2014 - 23:24:51 PST)
[AMBER] Convergence failure Tanmoy Paul (Tue Feb 04 2014 - 23:30:22 PST)
- Re: [AMBER] Convergence failure Gustavo Seabra (Wed Feb 05 2014 - 06:18:13 PST)
[AMBER] calculating rotational diffusion for a portion in a lipid Vijay Manickam Achari (Wed Feb 05 2014 - 01:52:30 PST)
- Re: [AMBER] calculating rotational diffusion for a portion in a lipid David A Case (Wed Feb 05 2014 - 04:45:29 PST)
[AMBER] LEAP-CHARMM Gözde YALÇIN (Wed Feb 05 2014 - 06:14:10 PST)
- Re: [AMBER] LEAP-CHARMM Hannes Loeffler (Wed Feb 05 2014 - 07:15:06 PST)
- Re: [AMBER] LEAP-CHARMM Jason Swails (Wed Feb 05 2014 - 08:05:43 PST)
[AMBER] Specifying the number of water molecules for solvateBox Yip Yew Mun (Wed Feb 05 2014 - 19:01:24 PST)
- Re: [AMBER] Specifying the number of water molecules for solvateBox Jason Swails (Wed Feb 05 2014 - 19:29:02 PST)
  - Re: [AMBER] Specifying the number of water molecules for solvateBox Pawel (Wed Feb 05 2014 - 19:47:03 PST)
    - Re: [AMBER] Specifying the number of water molecules for solvateBox Yip Yew Mun (Wed Feb 05 2014 - 20:23:03 PST)
    - Re: [AMBER] Specifying the number of water molecules for solvateBox Pawel (Wed Feb 05 2014 - 20:40:33 PST)
[AMBER] MMGBSA problem Maryam Azimzadeh Irani (Thu Feb 06 2014 - 00:11:41 PST)
- Re: [AMBER] MMGBSA problem Jason Swails (Tue Feb 25 2014 - 09:32:12 PST)
[AMBER] protein amide conjugate parameters Nahoum Anthony (Thu Feb 06 2014 - 01:41:58 PST)
- Re: [AMBER] protein amide conjugate parameters Jason Swails (Thu Feb 06 2014 - 04:54:50 PST)
- Re: [AMBER] protein amide conjugate parameters FyD (Thu Feb 06 2014 - 22:31:22 PST)
[AMBER] optimization of the ligand Mary Varughese (Thu Feb 06 2014 - 02:04:41 PST)
- Re: [AMBER] optimization of the ligand Jason Swails (Thu Feb 06 2014 - 04:49:16 PST)
- Re: [AMBER] optimization of the ligand David A Case (Thu Feb 06 2014 - 05:07:27 PST)
  - Re: [AMBER] optimization of the ligand Mary Varughese (Thu Feb 06 2014 - 07:08:34 PST)
[AMBER] problem with installing amber Hanna Thamleena (Thu Feb 06 2014 - 02:49:19 PST)
- Re: [AMBER] problem with installing amber Jason Swails (Thu Feb 06 2014 - 05:01:28 PST)
- Re: [AMBER] problem with installing amber David A Case (Thu Feb 06 2014 - 05:11:21 PST)
[AMBER] mopac.sh error sammia khatak (Thu Feb 06 2014 - 04:43:23 PST)
- Re: [AMBER] mopac.sh error Jason Swails (Thu Feb 06 2014 - 05:46:15 PST)
[AMBER] protein amide conjugate parameters Nahoum Anthony (Thu Feb 06 2014 - 04:55:33 PST)
[AMBER] Modifying Gaussian input files for the RED Server Kamali Sripathi (Fri Feb 07 2014 - 05:55:14 PST)
- Re: [AMBER] Modifying Gaussian input files for the RED Server FyD (Fri Feb 07 2014 - 22:42:11 PST)
[AMBER] sander minimization issue Arjun Sharma (Fri Feb 07 2014 - 13:38:45 PST)
- Re: [AMBER] sander minimization issue David A Case (Fri Feb 07 2014 - 18:06:21 PST)
[AMBER] Could not find target 281.850000 in any of the replica trajectories sunita.tifrh.res.in (Sat Feb 08 2014 - 03:39:30 PST)
- Re: [AMBER] Could not find target 281.850000 in any of the replica trajectories Daniel Roe (Sat Feb 08 2014 - 09:34:09 PST)
  - Re: [AMBER] Could not find target 281.850000 in any of the replica trajectories sunita.tifrh.res.in (Mon Feb 10 2014 - 04:01:33 PST)
[AMBER] XLeap in Cygwin - Does it work? Ilyas Yildirim (Sat Feb 08 2014 - 06:16:30 PST)
- Re: [AMBER] XLeap in Cygwin - Does it work? Daniel Roe (Sat Feb 08 2014 - 13:30:19 PST)
  - Re: [AMBER] XLeap in Cygwin - Does it work? Ilyas Yildirim (Sat Feb 08 2014 - 13:34:48 PST)
- Re: [AMBER] XLeap in Cygwin - Does it work? Bill Ross (Tue Feb 11 2014 - 21:05:43 PST)
Re: [AMBER] AMBER Digest, Vol 759, Issue 1 Arjun Sharma (Sat Feb 08 2014 - 15:15:02 PST)
- Re: [AMBER] AMBER Digest, Vol 759, Issue 1 David A Case (Sat Feb 08 2014 - 19:08:33 PST)
Re: [AMBER] AMBER Digest, Vol 760, Issue 1 Arjun Sharma (Sun Feb 09 2014 - 12:40:16 PST)
- Re: [AMBER] AMBER Digest, Vol 760, Issue 1 David A Case (Sun Feb 09 2014 - 14:08:51 PST)
[AMBER] Illegal CONECT record in pdb file after mutations Xu Zhou (Mon Feb 10 2014 - 09:07:09 PST)
- Re: [AMBER] Illegal CONECT record in pdb file after mutations Jason Swails (Mon Feb 10 2014 - 09:22:31 PST)
[AMBER] Does chain type matter? David Winogradoff (Mon Feb 10 2014 - 14:33:30 PST)
- Re: [AMBER] Does chain type matter? David A Case (Mon Feb 10 2014 - 19:00:28 PST)
  - Re: [AMBER] Does chain type matter? David Winogradoff (Mon Feb 10 2014 - 19:44:55 PST)
    - Re: [AMBER] Does chain type matter? David A Case (Tue Feb 11 2014 - 03:34:30 PST)
- Re: [AMBER] Does chain type matter? Bill Ross (Tue Feb 11 2014 - 21:42:26 PST)
[AMBER] PDB to prmtop inpcrd using tleap Jheng Wei Li (Tue Feb 11 2014 - 02:58:20 PST)
- Re: [AMBER] PDB to prmtop inpcrd using tleap David A Case (Tue Feb 11 2014 - 03:41:20 PST)
[AMBER] about protonation state check. setyanto md (Tue Feb 11 2014 - 04:15:55 PST)
- Re: [AMBER] about protonation state check. Brian Radak (Wed Feb 12 2014 - 05:37:48 PST)
[AMBER] FapydG parameters Norbert GARNIER (Tue Feb 11 2014 - 05:34:42 PST)
- Re: [AMBER] FapydG parameters Christina Bergonzo (Tue Feb 11 2014 - 06:56:43 PST)
[AMBER] Total charge not zero George Patargias (Wed Feb 12 2014 - 02:42:10 PST)
- Re: [AMBER] Total charge not zero Jason Swails (Wed Feb 12 2014 - 05:11:34 PST)
  - Re: [AMBER] Total charge not zero George Patargias (Wed Feb 12 2014 - 06:13:05 PST)
    - Re: [AMBER] Total charge not zero Ross Walker (Wed Feb 12 2014 - 09:39:15 PST)
    - Re: [AMBER] Total charge not zero George Patargias (Wed Feb 12 2014 - 09:46:44 PST)
    - Re: [AMBER] Total charge not zero Ross Walker (Wed Feb 12 2014 - 10:05:39 PST)
- Re: [AMBER] Total charge not zero FyD (Wed Feb 12 2014 - 05:19:17 PST)
  - Re: [AMBER] Total charge not zero George Patargias (Wed Feb 12 2014 - 06:33:00 PST)
- Re: [AMBER] Total charge not zero George Patargias (Wed Feb 12 2014 - 09:33:26 PST)
- Re: [AMBER] Total charge not zero FyD (Wed Feb 12 2014 - 22:08:55 PST)
[AMBER] To post to amber list richa anand (Wed Feb 12 2014 - 03:17:26 PST)
- Re: [AMBER] To post to amber list Jason Swails (Wed Feb 12 2014 - 05:05:53 PST)
[AMBER] Falling apart of membrane Gözde YALÇIN (Wed Feb 12 2014 - 05:24:57 PST)
- Re: [AMBER] Falling apart of membrane Dickson, Callum J (Wed Feb 12 2014 - 06:14:00 PST)
- Re: [AMBER] Falling apart of membrane Ross Walker (Wed Feb 12 2014 - 09:42:07 PST)
  - Re: [AMBER] Falling apart of membrane Gözde YALÇIN (Thu Feb 13 2014 - 02:51:10 PST)
  - Re: [AMBER] Falling apart of membrane Gözde YALÇIN (Tue Feb 25 2014 - 09:43:10 PST)
    - Re: [AMBER] Falling apart of membrane Gözde YALÇIN (Tue Feb 25 2014 - 09:45:11 PST)
    - Re: [AMBER] Falling apart of membrane Ross Walker (Tue Feb 25 2014 - 09:48:58 PST)
- Re: [AMBER] Falling apart of membrane Gözde YALÇIN (Mon Jun 30 2014 - 07:07:26 PDT)
  - Re: [AMBER] Falling apart of membrane Benjamin D Madej (Mon Jun 30 2014 - 13:58:14 PDT)
[AMBER] membrane Gözde YALÇIN (Wed Feb 12 2014 - 06:21:30 PST)
Re: [AMBER] nastruct Daniel Roe (Wed Feb 12 2014 - 07:58:01 PST)
[AMBER] Tesla K40 Chinthaka Ratnaweera (Wed Feb 12 2014 - 13:58:46 PST)
- Re: [AMBER] Tesla K40 Shaw, Sharon (Wed Feb 12 2014 - 14:42:56 PST)
  - Re: [AMBER] Tesla K40 Scott Le Grand (Wed Feb 12 2014 - 14:47:36 PST)
    - Re: [AMBER] Tesla K40 Chinthaka Ratnaweera (Wed Feb 12 2014 - 15:39:27 PST)
    - Re: [AMBER] Tesla K40 Scott Le Grand (Wed Feb 12 2014 - 15:48:04 PST)
    - Re: [AMBER] Tesla K40 Ross Walker (Thu Feb 13 2014 - 09:39:35 PST)
    - Re: [AMBER] Tesla K40 Ross Walker (Thu Feb 13 2014 - 09:52:10 PST)
    - Re: [AMBER] Tesla K40 Gustavo Seabra (Wed Feb 12 2014 - 17:02:11 PST)
    - Re: [AMBER] Tesla K40 Scott Le Grand (Wed Feb 12 2014 - 18:26:56 PST)
Re: [AMBER] Regarding MD simulation input files richa anand (Wed Feb 12 2014 - 20:12:39 PST)
[AMBER] rewriting trajectory Hector A. Baldoni (Thu Feb 13 2014 - 04:51:36 PST)
- Re: [AMBER] rewriting trajectory Christina Bergonzo (Thu Feb 13 2014 - 07:31:58 PST)
[AMBER] MMGBSA decomposition for a ligand molecule Rajeswari A. (Thu Feb 13 2014 - 05:27:19 PST)
- Re: [AMBER] MMGBSA decomposition for a ligand molecule Jason Swails (Thu Feb 13 2014 - 07:33:33 PST)
[AMBER] Calculating second rank Legendre polynomial C_2(t) autocorrelation function Vijay Manickam Achari (Thu Feb 13 2014 - 06:15:12 PST)
- Re: [AMBER] Calculating second rank Legendre polynomial C_2(t) autocorrelation function George M Giambasu (Thu Feb 13 2014 - 06:50:30 PST)
[AMBER] TACC Stampede AMBER David Cowburn (Thu Feb 13 2014 - 08:40:40 PST)
- Re: [AMBER] TACC Stampede AMBER de Waal, Parker (Thu Feb 13 2014 - 08:55:30 PST)
- Re: [AMBER] TACC Stampede AMBER de Waal, Parker (Thu Feb 13 2014 - 09:57:01 PST)
- Re: [AMBER] TACC Stampede AMBER Ross Walker (Thu Feb 13 2014 - 09:59:14 PST)
- Re: [AMBER] TACC Stampede AMBER Ross Walker (Thu Feb 13 2014 - 10:06:47 PST)
[AMBER] The unperturbed charge of the unit Nitin Sharma (Thu Feb 13 2014 - 09:18:51 PST)
- Re: [AMBER] The unperturbed charge of the unit Jason Swails (Thu Feb 13 2014 - 10:23:52 PST)
  - Re: [AMBER] The unperturbed charge of the unit Nitin Sharma (Thu Feb 13 2014 - 10:46:31 PST)
[AMBER] reg: the charges for methylated cytosine atoms satyanarayan rao (Thu Feb 13 2014 - 16:40:18 PST)
- Re: [AMBER] reg: the charges for methylated cytosine atoms Jason Swails (Fri Feb 14 2014 - 03:04:43 PST)
  - Re: [AMBER] reg: the charges for methylated cytosine atoms Filip Lankas (Thu Feb 20 2014 - 04:34:47 PST)
    - Re: [AMBER] reg: the charges for methylated cytosine atoms Jason Swails (Thu Feb 20 2014 - 05:25:48 PST)
    - Re: [AMBER] reg: the charges for methylated cytosine atoms Sidney Elmer (Wed Mar 12 2014 - 11:46:08 PDT)
    - Re: [AMBER] reg: the charges for methylated cytosine atoms David A Case (Wed Mar 12 2014 - 12:33:59 PDT)
    - Re: [AMBER] reg: the charges for methylated cytosine atoms Sidney Elmer (Wed Mar 12 2014 - 17:01:58 PDT)
    - Re: [AMBER] reg: the charges for methylated cytosine atoms Sidney Elmer (Fri Mar 28 2014 - 12:21:26 PDT)
    - Re: [AMBER] reg: the charges for methylated cytosine atoms David A Case (Fri Mar 28 2014 - 13:44:38 PDT)
    - Re: [AMBER] reg: the charges for methylated cytosine atoms Sidney Elmer (Fri Mar 28 2014 - 15:03:34 PDT)
    - Re: [AMBER] reg: the charges for methylated cytosine atoms David A Case (Sat Mar 29 2014 - 12:23:52 PDT)
    - Re: [AMBER] reg: the charges for methylated cytosine atoms Filip Lankas (Mon Mar 31 2014 - 01:53:31 PDT)
    - Re: [AMBER] reg: the charges for methylated cytosine atoms Sidney Elmer (Mon Mar 31 2014 - 13:45:01 PDT)
    - Re: [AMBER] reg: the charges for methylated cytosine atoms Filip Lankas (Wed Apr 02 2014 - 02:25:24 PDT)
[AMBER] R.E.D. server seems to be down? psu4.uic.edu (Thu Feb 13 2014 - 21:31:33 PST)
- Re: [AMBER] R.E.D. server seems to be down? FyD (Fri Feb 14 2014 - 09:32:41 PST)
  - Re: [AMBER] R.E.D. server seems to be down? psu4.uic.edu (Fri Feb 14 2014 - 09:40:14 PST)
[AMBER] MMPBSA/MMGBSA issues Soumendranath Bhakat (Thu Feb 13 2014 - 22:07:49 PST)
- Re: [AMBER] MMPBSA/MMGBSA issues Jason Swails (Fri Feb 14 2014 - 05:13:39 PST)
  - Re: [AMBER] MMPBSA/MMGBSA issues Soumendranath Bhakat (Fri Feb 14 2014 - 05:22:12 PST)
    - Re: [AMBER] MMPBSA/MMGBSA issues Jason Swails (Fri Feb 14 2014 - 05:36:05 PST)
[AMBER] Amntechamber MOPAC and SQM Nitin Sharma (Thu Feb 13 2014 - 23:36:49 PST)
- Re: [AMBER] Amntechamber MOPAC and SQM hannes.loeffler.stfc.ac.uk (Fri Feb 14 2014 - 00:22:03 PST)
- Re: [AMBER] Amntechamber MOPAC and SQM David A Case (Fri Feb 14 2014 - 05:43:29 PST)
  - Re: [AMBER] Amntechamber MOPAC and SQM Nitin Sharma (Fri Feb 14 2014 - 10:58:53 PST)
  - Re: [AMBER] Amntechamber MOPAC and SQM Nitin Sharma (Fri Feb 14 2014 - 18:04:44 PST)
    - Re: [AMBER] Amntechamber MOPAC and SQM David A Case (Sat Feb 15 2014 - 07:33:56 PST)
    - Re: [AMBER] Amntechamber MOPAC and SQM Nitin Sharma (Sat Feb 15 2014 - 08:13:04 PST)
Re: [AMBER] using chamber to convert psf generated by VMD Yi Shang (Fri Feb 14 2014 - 08:15:53 PST)
- Re: [AMBER] using chamber to convert psf generated by VMD Jason Swails (Fri Feb 14 2014 - 08:24:30 PST)
  - Re: [AMBER] using chamber to convert psf generated by VMD Ross Walker (Fri Feb 14 2014 - 10:29:01 PST)
    - Re: [AMBER] using chamber to convert psf generated by VMD Yi Shang (Fri Feb 14 2014 - 10:51:27 PST)
    - Re: [AMBER] differences in PBSA energies (INP=1 verses INP=2) Divi/GMAIL (Sat Feb 15 2014 - 09:29:21 PST)
    - Re: [AMBER] differences in PBSA energies (INP=1 verses INP=2) Ray Luo, Ph.D. (Sat Feb 15 2014 - 10:47:48 PST)
    - Re: [AMBER] using chamber to convert psf generated by VMD Jason Swails (Fri Feb 14 2014 - 11:09:36 PST)
    - Re: [AMBER] using chamber to convert psf generated by VMD Ross Walker (Fri Feb 14 2014 - 11:23:52 PST)
    - [AMBER] MM-PBSA problem almarques (Fri Feb 14 2014 - 11:26:10 PST)
    - Re: [AMBER] MM-PBSA problem almarques (Fri Feb 14 2014 - 11:28:18 PST)
    - Re: [AMBER] MM-PBSA problem Ray Luo, Ph.D. (Fri Feb 14 2014 - 12:05:18 PST)
    - Re: [AMBER] MM-PBSA problem almarques (Sat Feb 15 2014 - 01:45:38 PST)
    - Re: [AMBER] MM-PBSA problem almarques (Sat Feb 15 2014 - 03:37:36 PST)
  - Re: [AMBER] using chamber to convert psf generated by VMD Yi Shang (Sun Feb 23 2014 - 21:32:44 PST)
[AMBER] PDDG-PM3/MMGBSA calculation Giovanni Grazioso (Fri Feb 14 2014 - 08:26:49 PST)
- Re: [AMBER] PDDG-PM3/MMGBSA calculation Jason Swails (Sat Feb 15 2014 - 08:13:13 PST)
  - Re: [AMBER] PDDG-PM3/MMGBSA calculation Jason Swails (Sat Feb 15 2014 - 09:08:16 PST)
[AMBER] distance and angle rst to zinc atoms Jorgen Simonsen (Fri Feb 14 2014 - 12:10:21 PST)
- Re: [AMBER] distance and angle rst to zinc atoms David A Case (Fri Feb 14 2014 - 12:45:17 PST)
  - Re: [AMBER] distance and angle rst to zinc atoms Jorgen Simonsen (Fri Feb 14 2014 - 14:17:40 PST)
    - Re: [AMBER] distance and angle rst to zinc atoms David A Case (Sat Feb 15 2014 - 07:31:24 PST)
[AMBER] MMGBSA/BSA electrostatic energy values very high Rajesh Kumar (Sat Feb 15 2014 - 04:01:35 PST)
- Re: [AMBER] MMGBSA/BSA electrostatic energy values very high Jason Swails (Sat Feb 15 2014 - 08:10:41 PST)
[AMBER] Ris:Re: PDDG-PM3/MMGBSA calculation Giovanni Grazioso (Sat Feb 15 2014 - 11:49:44 PST)
- Re: [AMBER] Ris:Re: PDDG-PM3/MMGBSA calculation Jason Swails (Sat Feb 15 2014 - 18:13:13 PST)
  - Re: [AMBER] Ris:Re: PDDG-PM3/MMGBSA calculation Giovanni Grazioso (Tue Feb 18 2014 - 08:05:37 PST)
[AMBER] Charge on zinc ion bound to residues. nalini chauhan (Sat Feb 15 2014 - 22:56:49 PST)
- Re: [AMBER] Charge on zinc ion bound to residues. tongzhu9110 (Sat Feb 15 2014 - 23:08:17 PST)
- Re: [AMBER] Charge on zinc ion bound to residues. FyD (Sun Feb 16 2014 - 03:30:13 PST)
[AMBER] error with md simulation Zahra Khatti (Sun Feb 16 2014 - 13:22:40 PST)
- Re: [AMBER] error with md simulation David A Case (Sun Feb 16 2014 - 14:46:47 PST)
  - [AMBER] Fw: error with md simulation Zahra Khatti (Mon Feb 17 2014 - 09:00:37 PST)
    - Re: [AMBER] Fw: error with md simulation David A Case (Mon Feb 17 2014 - 17:23:47 PST)
[AMBER] Correlation times Mutangana Dieudonne (Mon Feb 17 2014 - 00:45:29 PST)
- Re: [AMBER] Correlation times psu4.uic.edu (Mon Feb 17 2014 - 10:44:10 PST)
[AMBER] GLYCAM parameters for cis double conformation ABEL Stephane 175950 (Mon Feb 17 2014 - 05:35:54 PST)
- Re: [AMBER] GLYCAM parameters for cis double conformation Lachele Foley (Mon Feb 17 2014 - 07:08:52 PST)
- Re: [AMBER] GLYCAM parameters for cis double conformation Karl Kirschner (Mon Feb 17 2014 - 07:26:34 PST)
  - Re: [AMBER] GLYCAM parameters for cis double conformation Lachele Foley (Mon Feb 17 2014 - 07:33:59 PST)
    - Re: [AMBER] GLYCAM parameters for cis double conformation ABEL Stephane 175950 (Mon Feb 17 2014 - 08:00:20 PST)
    - Re: [AMBER] GLYCAM parameters for cis double conformation Karl Kirschner (Fri Feb 21 2014 - 01:22:22 PST)
    - Re: [AMBER] GLYCAM parameters for cis double conformation ABEL Stephane 175950 (Fri Feb 21 2014 - 02:34:12 PST)
[AMBER] amber 14 release psu4.uic.edu (Mon Feb 17 2014 - 10:58:59 PST)
- Re: [AMBER] amber 14 release Ross Walker (Mon Feb 17 2014 - 11:18:25 PST)
- Re: [AMBER] amber 14 release Jason Swails (Mon Feb 17 2014 - 12:34:07 PST)
  - Re: [AMBER] amber 14 release psu4.uic.edu (Sun Feb 23 2014 - 12:46:38 PST)
    - Re: [AMBER] amber 14 release Ross Walker (Sun Feb 23 2014 - 16:34:51 PST)
[AMBER] Compiling amber12 with openmp Quentin Kaas (Mon Feb 17 2014 - 21:09:34 PST)
- Re: [AMBER] Compiling amber12 with openmp Eugene Yedvabny (Mon Feb 17 2014 - 22:12:04 PST)
[AMBER] CUDA 4 support in future Amber Eugene Yedvabny (Mon Feb 17 2014 - 22:44:23 PST)
- Re: [AMBER] CUDA 4 support in future Amber Ross Walker (Mon Feb 17 2014 - 23:04:41 PST)
[AMBER] Question about force field parameters for RDX and PETN Ganesh Kamath (Tue Feb 18 2014 - 06:23:16 PST)
- Re: [AMBER] Question about force field parameters for RDX and PETN ABEL Stephane 175950 (Tue Feb 18 2014 - 06:30:20 PST)
  - Re: [AMBER] Question about force field parameters for RDX and PETN Ganesh Kamath (Tue Feb 18 2014 - 06:51:56 PST)
    - Re: [AMBER] Question about force field parameters for RDX and PETN Ilyas Yildirim (Tue Feb 18 2014 - 07:05:22 PST)
    - Re: [AMBER] Question about force field parameters for RDX and PETN ABEL Stephane 175950 (Tue Feb 18 2014 - 07:24:16 PST)
    - Re: [AMBER] Question about force field parameters for RDX and PETN FyD (Tue Feb 18 2014 - 12:19:21 PST)
    - Re: [AMBER] Question about force field parameters for RDX and PETN Ganesh Kamath (Tue Feb 18 2014 - 13:38:23 PST)
    - Re: [AMBER] Question about force field parameters for RDX and PETN FyD (Tue Feb 18 2014 - 22:40:19 PST)
[AMBER] Postdoctoral position Fernando Martín García (Tue Feb 18 2014 - 08:30:00 PST)
[AMBER] ACS COMP Division student and junior faculty awards for Fall 2014 meeting in San Francisco Carlos Simmerling (Tue Feb 18 2014 - 13:30:45 PST)
[AMBER] Bond continues to break in simulation even after the bond command was used. Yip Yew Mun (Tue Feb 18 2014 - 20:04:33 PST)
- Re: [AMBER] Bond continues to break in simulation even after the bond command was used. Daniel Roe (Tue Feb 18 2014 - 21:44:26 PST)
[AMBER] Print Pressure value by using PMEMD kurisaki (Tue Feb 18 2014 - 21:42:33 PST)
- Re: [AMBER] Print Pressure value by using PMEMD Ross Walker (Tue Feb 18 2014 - 21:52:05 PST)
- Re: [AMBER] Print Pressure value by using PMEMD Daniel Roe (Tue Feb 18 2014 - 21:53:41 PST)
  - Re: [AMBER] Print Pressure value by using PMEMD kurisaki (Tue Feb 18 2014 - 22:22:32 PST)
[AMBER] AmberTools13-conformational search in MTK++ Sun (Wed Feb 19 2014 - 05:14:09 PST)
- Re: [AMBER] AmberTools13-conformational search in MTK++ Jason Swails (Wed Feb 19 2014 - 05:36:57 PST)
  - Re: [AMBER] AmberTools13-conformational search in MTK++ Sun (Wed Feb 19 2014 - 05:51:22 PST)
[AMBER] Bad topology file. Sum of ATOMS_PER_MOLECULE does not equal NATOM Saeed Nasiri (Wed Feb 19 2014 - 06:17:00 PST)
- Re: [AMBER] Bad topology file. Sum of ATOMS_PER_MOLECULE does not equal NATOM Daniel Roe (Wed Feb 19 2014 - 07:12:37 PST)
- Re: [AMBER] Bad topology file. Sum of ATOMS_PER_MOLECULE does not equal NATOM David A Case (Wed Feb 19 2014 - 07:13:13 PST)
[AMBER] Fwd: Contact angle simulation of brine drop onto halite NaCl surface -different results between Amber11 and Amber12 Vu Truong (Wed Feb 19 2014 - 12:52:12 PST)
- Re: [AMBER] Fwd: Contact angle simulation of brine drop onto halite NaCl surface -different results between Amber11 and Amber12 David A Case (Wed Feb 19 2014 - 18:09:58 PST)
[AMBER] What does "Bond types are assigned for valence state 1 with penalty of 1" mean? Yew Mun Yip (Wed Feb 19 2014 - 20:37:13 PST)
- Re: [AMBER] What does "Bond types are assigned for valence state 1 with penalty of 1" mean? David A Case (Thu Feb 20 2014 - 09:22:46 PST)
[AMBER] MMPBSA binding energy for all frames Arun Kumar Somavarapu (Thu Feb 20 2014 - 03:12:56 PST)
- Re: [AMBER] MMPBSA binding energy for all frames Vlad Cojocaru (Thu Feb 20 2014 - 03:18:29 PST)
  - Re: [AMBER] MMPBSA binding energy for all frames Arun Kumar Somavarapu (Thu Feb 20 2014 - 03:45:19 PST)
    - Re: [AMBER] MMPBSA binding energy for all frames Vlad Cojocaru (Thu Feb 20 2014 - 04:39:13 PST)
    - Re: [AMBER] MMPBSA binding energy for all frames Arun Kumar Somavarapu (Thu Feb 20 2014 - 08:55:25 PST)
    - Re: [AMBER] MMPBSA binding energy for all frames Jason Swails (Thu Feb 20 2014 - 09:29:44 PST)
    - Re: [AMBER] MMPBSA binding energy for all frames Vlad Cojocaru (Thu Feb 20 2014 - 09:51:52 PST)
    - Re: [AMBER] MMPBSA binding energy for all frames Vlad Cojocaru (Thu Feb 20 2014 - 10:42:44 PST)
    - Re: [AMBER] MMPBSA binding energy for all frames Arun Kumar Somavarapu (Fri Feb 21 2014 - 03:56:52 PST)
    - Re: [AMBER] MMPBSA binding energy for all frames Vlad Cojocaru (Fri Feb 21 2014 - 04:41:34 PST)
    - Re: [AMBER] MMPBSA binding energy for all frames Arun Kumar Somavarapu (Mon Feb 24 2014 - 05:21:27 PST)
    - Re: [AMBER] MMPBSA binding energy for all frames Vlad Cojocaru (Mon Feb 24 2014 - 05:34:25 PST)
[AMBER] defects in modified parameter with parmed.py Saeed Nasiri (Fri Feb 21 2014 - 01:49:39 PST)
- Re: [AMBER] defects in modified parameter with parmed.py Daniel Roe (Fri Feb 21 2014 - 05:34:54 PST)
  - Re: [AMBER] defects in modified parameter with parmed.py Jason Swails (Fri Feb 21 2014 - 06:04:49 PST)
[AMBER] MMPBSA.py and entropy Fernando Martín García (Fri Feb 21 2014 - 07:38:55 PST)
- Re: [AMBER] MMPBSA.py and entropy Hannes Loeffler (Fri Feb 21 2014 - 08:04:55 PST)
  - [AMBER] MMPBSA.py error almarques (Mon Feb 24 2014 - 03:31:18 PST)
    - Re: [AMBER] MMPBSA.py error Jason Swails (Mon Feb 24 2014 - 05:13:31 PST)
    - Re: [AMBER] MMPBSA.py error almarques (Mon Feb 24 2014 - 06:28:09 PST)
    - Re: [AMBER] MMPBSA.py error Jason Swails (Mon Feb 24 2014 - 06:57:57 PST)
    - Re: [AMBER] MMPBSA.py error almarques (Wed Feb 26 2014 - 14:13:38 PST)
    - Re: [AMBER] MMPBSA.py error Jason Swails (Thu Feb 27 2014 - 09:37:21 PST)
    - Re: [AMBER] MMPBSA.py error almarques (Fri Feb 28 2014 - 07:35:22 PST)
    - Re: [AMBER] MMPBSA.py error Jason Swails (Fri Feb 28 2014 - 08:02:53 PST)
    - Re: [AMBER] MMPBSA.py error almarques (Mon Mar 03 2014 - 03:06:13 PST)
    - Re: [AMBER] MMPBSA.py error Jason Swails (Mon Mar 03 2014 - 05:14:02 PST)
  - Re: [AMBER] MMPBSA.py and entropy Javier Alejandro Rendon Carrillo (Wed Feb 26 2014 - 22:05:46 PST)
    - Re: [AMBER] MMPBSA.py and entropy hannes.loeffler.stfc.ac.uk (Wed Feb 26 2014 - 23:05:02 PST)
    - Re: [AMBER] MMPBSA.py and entropy Aldo Segura (Thu Feb 27 2014 - 06:03:54 PST)
[AMBER] GTX-Titan Black Edition Timings Ross Walker (Fri Feb 21 2014 - 13:17:26 PST)
- Re: [AMBER] GTX-Titan Black Edition Timings filip fratev (Fri Feb 21 2014 - 14:19:41 PST)
[AMBER] Unable to apply patches on AmberTools 13 George Tzotzos (Fri Feb 21 2014 - 16:17:56 PST)
- Re: [AMBER] Unable to apply patches on AmberTools 13 Jason Swails (Fri Feb 21 2014 - 19:37:30 PST)
[AMBER] broken bond in minimization Zahra Khatti (Sat Feb 22 2014 - 21:35:34 PST)
- Re: [AMBER] broken bond in minimization Dr. Vitaly Chaban (Sun Feb 23 2014 - 05:26:59 PST)
  - Re: [AMBER] broken bond in minimization Zahra Khatti (Sun Feb 23 2014 - 07:04:57 PST)
    - Re: [AMBER] broken bond in minimization Jason Swails (Sun Feb 23 2014 - 07:38:08 PST)
[AMBER] Amber12 CUDA input file richa anand (Sat Feb 22 2014 - 21:45:13 PST)
- Re: [AMBER] Amber12 CUDA input file Jason Swails (Sun Feb 23 2014 - 07:30:37 PST)
[AMBER] SMD Problem: r4 and r4a values are not read from the restraint file Ali M. Naserian-Nik (Sun Feb 23 2014 - 00:16:10 PST)
- Re: [AMBER] SMD Problem: r4 and r4a values are not read from the restraint file Jason Swails (Sun Feb 23 2014 - 07:42:17 PST)
  - [AMBER] PME with cutoff = 0 FyD (Sun Feb 23 2014 - 09:19:23 PST)
    - Re: [AMBER] PME with cutoff = 0 Ross Walker (Sun Feb 23 2014 - 09:38:49 PST)
    - Re: [AMBER] PME with cutoff = 0 Duke, Robert E Jr (Sun Feb 23 2014 - 11:06:33 PST)
    - Re: [AMBER] PME with cutoff = 0 FyD (Mon Feb 24 2014 - 01:31:26 PST)
    - Re: [AMBER] PME with cutoff = 0 Jason Swails (Mon Feb 24 2014 - 05:45:57 PST)
    - Re: [AMBER] PME with cutoff = 0 Ross Walker (Mon Feb 24 2014 - 09:54:00 PST)
    - Re: [AMBER] PME with cutoff = 0 FyD (Tue Feb 25 2014 - 22:34:17 PST)
    - Re: [AMBER] PME with cutoff = 0 Jason Swails (Wed Feb 26 2014 - 05:03:33 PST)
    - Re: [AMBER] PME with cutoff = 0 Duke, Robert E Jr (Mon Feb 24 2014 - 09:44:49 PST)
    - Re: [AMBER] PME with cutoff = 0 FyD (Tue Feb 25 2014 - 22:19:35 PST)
    - Re: [AMBER] PME with cutoff = 0 FyD (Mon Feb 24 2014 - 04:52:45 PST)
  - Re: [AMBER] SMD Problem: r4 and r4a values are not read from the restraint file Ali M. Naserian-Nik (Sun Feb 23 2014 - 09:48:51 PST)
    - Re: [AMBER] SMD Problem: r4 and r4a values are not read from the restraint file Adrian Roitberg (Sun Feb 23 2014 - 09:53:02 PST)
    - Re: [AMBER] SMD Problem: r4 and r4a values are not read from the restraint file Ali M. Naserian-Nik (Sun Feb 23 2014 - 11:45:57 PST)
    - Re: [AMBER] SMD Problem: r4 and r4a values are not read from the restraint file Jason Swails (Sun Feb 23 2014 - 10:12:05 PST)
    - Re: [AMBER] SMD Problem: r4 and r4a values are not read from the restraint file Ali M. Naserian-Nik (Sun Feb 23 2014 - 11:33:33 PST)
    - Re: [AMBER] SMD Problem: r4 and r4a values are not read from the restraint file Jason Swails (Sun Feb 23 2014 - 17:52:09 PST)
[AMBER] How to prepare the leap files for protein residues covalently bonded to ligand? Yip Yew Mun (Sun Feb 23 2014 - 04:53:10 PST)
- Re: [AMBER] How to prepare the leap files for protein residues covalently bonded to ligand? Jason Swails (Sun Feb 23 2014 - 07:39:57 PST)
- Re: [AMBER] How to prepare the leap files for protein residues covalently bonded to ligand? Nitin Sharma (Sun Feb 23 2014 - 10:31:54 PST)
  - Re: [AMBER] How to prepare the leap files for protein residues covalently bonded to ligand? #YIP YEW MUN# (Sun Feb 23 2014 - 17:40:51 PST)
[AMBER] New bonds in PyMol? de Waal, Parker (Sun Feb 23 2014 - 20:37:02 PST)
- Re: [AMBER] New bonds in PyMol? David A Case (Mon Feb 24 2014 - 04:43:51 PST)
  - Re: [AMBER] New bonds in PyMol? de Waal, Parker (Mon Feb 24 2014 - 05:11:09 PST)
[AMBER] pmemd.CUDA.mpi micro-second long simulation psu4.uic.edu (Sun Feb 23 2014 - 22:58:42 PST)
- Re: [AMBER] pmemd.CUDA.mpi micro-second long simulation Ross Walker (Mon Feb 24 2014 - 07:26:46 PST)
  - Re: [AMBER] pmemd.CUDA.mpi micro-second long simulation Carlos Simmerling (Mon Feb 24 2014 - 07:33:23 PST)
  - Re: [AMBER] pmemd.CUDA.mpi micro-second long simulation psu4.uic.edu (Tue Mar 04 2014 - 10:40:14 PST)
    - Re: [AMBER] pmemd.CUDA.mpi micro-second long simulation Ross Walker (Tue Mar 04 2014 - 10:49:14 PST)
[AMBER] pbsa calculation using sander Sun (Mon Feb 24 2014 - 00:01:20 PST)
- Re: [AMBER] pbsa calculation using sander David A Case (Mon Feb 24 2014 - 04:47:09 PST)
  - Re: [AMBER] pbsa calculation using sander Sun (Mon Feb 24 2014 - 04:58:43 PST)
    - Re: [AMBER] pbsa calculation using sander Jason Swails (Mon Feb 24 2014 - 05:11:13 PST)
    - Re: [AMBER] pbsa calculation using sander Sun (Mon Feb 24 2014 - 05:29:48 PST)
[AMBER] asking about pmemd and GTX 660 Ti compatibility setyanto md (Mon Feb 24 2014 - 00:31:46 PST)
- Re: [AMBER] asking about pmemd and GTX 660 Ti compatibility Jason Swails (Mon Feb 24 2014 - 05:07:49 PST)
  - Re: [AMBER] asking about pmemd and GTX 660 Ti compatibility Setyanto Md (Mon Feb 24 2014 - 23:28:24 PST)
[AMBER] request for help in analysis Robin Jain (Mon Feb 24 2014 - 01:11:49 PST)
- Re: [AMBER] request for help in analysis Daniel Roe (Wed Feb 26 2014 - 07:17:06 PST)
[AMBER] using ff99SB forcefiled to a complex where ligand charge is from Glycam_04 Arun Kumar Somavarapu (Mon Feb 24 2014 - 01:12:04 PST)
- Re: [AMBER] using ff99SB forcefiled to a complex where ligand charge is from Glycam_04 Karl Kirschner (Mon Feb 24 2014 - 01:57:18 PST)
  - Re: [AMBER] using ff99SB forcefiled to a complex where ligand charge is from Glycam_04 Arun Kumar Somavarapu (Mon Feb 24 2014 - 02:20:09 PST)
  - Re: [AMBER] using ff99SB forcefiled to a complex where ligand charge is from Glycam_04 David A Case (Mon Feb 24 2014 - 04:50:53 PST)
    - Re: [AMBER] using ff99SB forcefiled to a complex where ligand charge is from Glycam_04 Arun Kumar Somavarapu (Mon Feb 24 2014 - 05:08:28 PST)
    - Re: [AMBER] using ff99SB forcefiled to a complex where ligand charge is from Glycam_04 Karl Kirschner (Mon Feb 24 2014 - 06:50:43 PST)
    - Re: [AMBER] using ff99SB forcefiled to a complex where ligand charge is from Glycam_04 Arun Kumar Somavarapu (Mon Feb 24 2014 - 08:47:54 PST)
- Re: [AMBER] using ff99SB forcefiled to a complex where ligand charge is from Glycam_04 FyD (Mon Feb 24 2014 - 02:49:54 PST)
[AMBER] Shake problem: Coordinate resetting (SHAKE) cannot be accomplished Mele N. (Mon Feb 24 2014 - 01:45:58 PST)
- Re: [AMBER] Shake problem: Coordinate resetting (SHAKE) cannot be accomplished David A Case (Mon Feb 24 2014 - 04:54:50 PST)
  - Re: [AMBER] Shake problem: Coordinate resetting (SHAKE) cannot be accomplished Mele N. (Mon Feb 24 2014 - 08:56:44 PST)
    - Re: [AMBER] Shake problem: Coordinate resetting (SHAKE) cannot be accomplished Jason Swails (Mon Feb 24 2014 - 09:10:04 PST)
    - Re: [AMBER] Shake problem: Coordinate resetting (SHAKE) cannot be accomplished Mele N. (Mon Feb 24 2014 - 09:22:06 PST)
    - Re: [AMBER] Shake problem: Coordinate resetting (SHAKE) cannot be accomplished Jason Swails (Mon Feb 24 2014 - 09:55:47 PST)
    - Re: [AMBER] Shake problem: Coordinate resetting (SHAKE) cannot be accomplished Mele N. (Tue Feb 25 2014 - 01:58:35 PST)
    - Re: [AMBER] Shake problem: Coordinate resetting (SHAKE) cannot be accomplished Jason Swails (Tue Feb 25 2014 - 04:56:24 PST)
    - Re: [AMBER] Shake problem: Coordinate resetting (SHAKE) cannot be accomplished Mele N. (Tue Feb 25 2014 - 08:18:22 PST)
    - Re: [AMBER] Shake problem: Coordinate resetting (SHAKE) cannot be accomplished ABEL Stephane 175950 (Tue Feb 25 2014 - 08:59:00 PST)
    - Re: [AMBER] Shake problem: Coordinate resetting (SHAKE) cannot be accomplished Jason Swails (Tue Feb 25 2014 - 09:28:58 PST)
    - Re: [AMBER] Shake problem: Coordinate resetting (SHAKE) cannot be accomplished Mele N. (Tue Feb 25 2014 - 09:42:24 PST)
    - Re: [AMBER] Shake problem: Coordinate resetting (SHAKE) cannot be accomplished Thomas Cheatham (Tue Feb 25 2014 - 09:54:05 PST)
    - Re: [AMBER] Shake problem: Coordinate resetting (SHAKE) cannot be accomplished Jason Swails (Tue Feb 25 2014 - 10:04:46 PST)
    - Re: [AMBER] Shake problem: Coordinate resetting (SHAKE) cannot be accomplished David A Case (Mon Feb 24 2014 - 10:32:28 PST)
    - Re: [AMBER] Shake problem: Coordinate resetting (SHAKE) cannot be accomplished Mele N. (Tue Feb 25 2014 - 02:47:24 PST)
[AMBER] GTX670 Deák Robert (Mon Feb 24 2014 - 03:01:26 PST)
- Re: [AMBER] GTX670 Scott Le Grand (Mon Feb 24 2014 - 08:03:08 PST)
- Re: [AMBER] GTX670 Ross Walker (Mon Feb 24 2014 - 08:12:43 PST)
  - Re: [AMBER] GTX670 Deák Robert (Mon Feb 24 2014 - 08:30:15 PST)
    - Re: [AMBER] GTX670 Ross Walker (Mon Feb 24 2014 - 09:26:52 PST)
    - Re: [AMBER] GTX670 Deák Robert (Thu Feb 27 2014 - 02:22:57 PST)
  - Re: [AMBER] GTX670 Gould, Ian R (Mon Feb 24 2014 - 08:33:59 PST)
    - Re: [AMBER] GTX670 Deák Robert (Mon Feb 24 2014 - 08:48:52 PST)
    - Re: [AMBER] GTX670 Carlos Simmerling (Mon Feb 24 2014 - 09:03:48 PST)
[AMBER] Error In Amber installation Arunima Shilpi (Mon Feb 24 2014 - 21:03:27 PST)
- Re: [AMBER] Error In Amber installation Ross Walker (Mon Feb 24 2014 - 21:10:58 PST)
[AMBER] about MCPB : addFragment terminal/CH3 Setyanto Md (Tue Feb 25 2014 - 04:48:17 PST)
- Re: [AMBER] about MCPB : addFragment terminal/CH3 Jason Swails (Tue Feb 25 2014 - 05:17:57 PST)
[AMBER] MMPBSA.py.MPI hangs George Tzotzos (Tue Feb 25 2014 - 08:52:51 PST)
- Re: [AMBER] MMPBSA.py.MPI hangs Bill Miller III (Tue Feb 25 2014 - 12:10:39 PST)
- Re: [AMBER] MMPBSA.py.MPI hangs Jason Swails (Tue Feb 25 2014 - 12:21:31 PST)
  - Re: [AMBER] MMPBSA.py.MPI hangs George Tzotzos (Tue Feb 25 2014 - 14:16:30 PST)
    - Re: [AMBER] MMPBSA.py.MPI hangs Jason Swails (Tue Feb 25 2014 - 15:58:37 PST)
    - Re: [AMBER] MMPBSA.py.MPI hangs George Tzotzos (Tue Feb 25 2014 - 16:56:48 PST)
    - Re: [AMBER] MMPBSA.py.MPI hangs George Tzotzos (Wed Feb 26 2014 - 12:18:38 PST)
    - Re: [AMBER] MMPBSA.py.MPI hangs Jason Swails (Wed Feb 26 2014 - 14:13:44 PST)
    - Re: [AMBER] MMPBSA.py.MPI hangs George Tzotzos (Wed Feb 26 2014 - 14:37:53 PST)
    - Re: [AMBER] MMPBSA.py.MPI hangs George Tzotzos (Wed Feb 26 2014 - 16:31:27 PST)
    - Re: [AMBER] MMPBSA.py.MPI hangs George Tzotzos (Thu Feb 27 2014 - 09:16:25 PST)
    - Re: [AMBER] MMPBSA.py.MPI hangs Jason Swails (Thu Feb 27 2014 - 09:27:51 PST)
    - Re: [AMBER] MMPBSA.py.MPI hangs George Tzotzos (Thu Feb 27 2014 - 09:49:51 PST)
    - Re: [AMBER] MMPBSA.py.MPI hangs Jason Swails (Thu Feb 27 2014 - 11:08:36 PST)
    - Re: [AMBER] MMPBSA.py.MPI hangs George Tzotzos (Thu Feb 27 2014 - 11:27:18 PST)
    - Re: [AMBER] MMPBSA.py.MPI hangs Jason Swails (Thu Feb 27 2014 - 11:44:17 PST)
    - Re: [AMBER] MMPBSA.py.MPI hangs George Tzotzos (Thu Feb 27 2014 - 12:08:18 PST)
    - Re: [AMBER] MMPBSA.py.MPI hangs Jason Swails (Thu Feb 27 2014 - 12:19:41 PST)
- Re: [AMBER] MMPBSA.py.MPI hangs Jason Swails (Tue Feb 25 2014 - 12:23:37 PST)
[AMBER] Calculating parameters for glycosides R R S Pissurlenkar (Tue Feb 25 2014 - 09:20:49 PST)
- Re: [AMBER] Calculating parameters for glycosides Lachele Foley (Tue Feb 25 2014 - 10:51:03 PST)
- Re: [AMBER] Calculating parameters for glycosides FyD (Tue Feb 25 2014 - 22:42:58 PST)
[AMBER] Adaptive Biasing calculations Geoffrey Gray (Tue Feb 25 2014 - 13:21:06 PST)
- Re: [AMBER] Adaptive Biasing calculations de Waal, Parker (Tue Feb 25 2014 - 14:14:03 PST)
  - Re: [AMBER] Adaptive Biasing calculations Geoffrey Gray (Tue Feb 25 2014 - 16:46:17 PST)
[AMBER] error in amber installation Arunima Shilpi (Tue Feb 25 2014 - 22:07:26 PST)
- Re: [AMBER] error in amber installation Kshatresh Dutta Dubey (Tue Feb 25 2014 - 22:25:45 PST)
[AMBER] no pdb file after running nab /AMBER11 Urszula Uciechowska (Wed Feb 26 2014 - 00:57:04 PST)
- Re: [AMBER] no pdb file after running nab /AMBER11 David A Case (Wed Feb 26 2014 - 04:54:19 PST)
[AMBER] Change email address Fernando Martín García (Wed Feb 26 2014 - 02:55:12 PST)
- Re: [AMBER] Change email address David A Case (Wed Feb 26 2014 - 04:55:20 PST)
[AMBER] Pmf ....restrain Rasha Alqus (Wed Feb 26 2014 - 03:29:02 PST)
- Re: [AMBER] Pmf ....restrain David A Case (Wed Feb 26 2014 - 04:58:05 PST)
[AMBER] aligning Jio M (Wed Feb 26 2014 - 06:09:40 PST)
- Re: [AMBER] aligning Daniel Roe (Wed Feb 26 2014 - 07:12:36 PST)
  - Re: [AMBER] aligning Jio M (Wed Feb 26 2014 - 07:27:29 PST)
    - Re: [AMBER] aligning Daniel Roe (Wed Feb 26 2014 - 07:38:23 PST)
    - Re: [AMBER] aligning Jio M (Wed Feb 26 2014 - 08:22:27 PST)
    - Re: [AMBER] aligning Daniel Roe (Wed Feb 26 2014 - 17:23:49 PST)
    - Re: [AMBER] aligning Jio M (Thu Feb 27 2014 - 05:14:29 PST)
    - Re: [AMBER] aligning Daniel Roe (Thu Feb 27 2014 - 07:37:36 PST)
    - Re: [AMBER] aligning Jio M (Thu Feb 27 2014 - 08:14:59 PST)
[AMBER] Including amino acid backbone into QM part during QM/MM Dmitry Nilov (Wed Feb 26 2014 - 06:17:34 PST)
- Re: [AMBER] Including amino acid backbone into QM part during QM/MM Andreas Goetz (Wed Feb 26 2014 - 14:44:16 PST)
  - Re: [AMBER] Including amino acid backbone into QM part during QM/MM Dmitry Nilov (Wed Feb 26 2014 - 23:59:50 PST)
    - Re: [AMBER] Including amino acid backbone into QM part during QM/MM Andreas Goetz (Thu Mar 06 2014 - 11:50:31 PST)
[AMBER] LIPID 14 Ghulam Mustafa (Wed Feb 26 2014 - 10:12:04 PST)
- Re: [AMBER] LIPID 14 Jason Swails (Wed Feb 26 2014 - 10:16:43 PST)
  - Re: [AMBER] LIPID 14 Jason Swails (Wed Feb 26 2014 - 10:17:04 PST)
[AMBER] Forcefield for transition metals Kshatresh Dutta Dubey (Wed Feb 26 2014 - 13:39:46 PST)
- Re: [AMBER] Forcefield for transition metals de Waal, Parker (Wed Feb 26 2014 - 14:05:09 PST)
  - Re: [AMBER] Forcefield for transition metals Kshatresh Dutta Dubey (Wed Feb 26 2014 - 14:17:57 PST)
    - Re: [AMBER] Forcefield for transition metals de Waal, Parker (Wed Feb 26 2014 - 14:50:33 PST)
- Re: [AMBER] Forcefield for transition metals Thomas Cheatham (Wed Feb 26 2014 - 19:57:39 PST)
  - Re: [AMBER] Forcefield for transition metals Kshatresh Dutta Dubey (Wed Feb 26 2014 - 21:32:30 PST)
[AMBER] Charged Ions Sticking Together Alexander Chiu (Wed Feb 26 2014 - 17:11:16 PST)
- Re: [AMBER] Charged Ions Sticking Together Thomas Cheatham (Wed Feb 26 2014 - 19:28:47 PST)
  - Re: [AMBER] Charged Ions Sticking Together Jio M (Thu Feb 27 2014 - 06:57:33 PST)
[AMBER] Problem running amber on some gpu's Jagga Soorma (Wed Feb 26 2014 - 21:31:01 PST)
- Re: [AMBER] Problem running amber on some gpu's Ross Walker (Wed Feb 26 2014 - 21:43:49 PST)
- Re: [AMBER] Problem running amber on some gpu's David A Case (Thu Feb 27 2014 - 04:55:32 PST)
[AMBER] Force field generation Gargi Borgohai (Wed Feb 26 2014 - 22:13:14 PST)
- Re: [AMBER] Force field generation hannes.loeffler.stfc.ac.uk (Thu Feb 27 2014 - 00:30:39 PST)
- Re: [AMBER] Force field generation David A Case (Thu Feb 27 2014 - 04:59:24 PST)
[AMBER] Amber 12 bugfix 22 ahmed.sajid.stfc.ac.uk (Thu Feb 27 2014 - 01:26:43 PST)
- Re: [AMBER] Amber 12 bugfix 22 Jason Swails (Thu Feb 27 2014 - 05:22:57 PST)
  - Re: [AMBER] Amber 12 bugfix 22 ahmed.sajid.stfc.ac.uk (Thu Feb 27 2014 - 05:23:26 PST)
[AMBER] Desmond vs Amber vs Analysis vs VMD Soumendranath Bhakat (Thu Feb 27 2014 - 06:05:51 PST)
- Re: [AMBER] Desmond vs Amber vs Analysis vs VMD Jason Swails (Thu Feb 27 2014 - 06:28:54 PST)
  - Re: [AMBER] Desmond vs Amber vs Analysis vs VMD filip fratev (Thu Feb 27 2014 - 07:10:44 PST)
[AMBER] Unable to read coords from XXX.rst - How can I resolve this once and for all? Yew Mun Yip (Thu Feb 27 2014 - 07:11:00 PST)
- Re: [AMBER] Unable to read coords from XXX.rst - How can I resolve this once and for all? Daniel Roe (Thu Feb 27 2014 - 07:55:45 PST)
- Re: [AMBER] Unable to read coords from XXX.rst - How can I resolve this once and for all? Nitin Sharma (Thu Feb 27 2014 - 07:58:21 PST)
  - Re: [AMBER] Unable to read coords from XXX.rst - How can I resolve this once and for all? Yip Yew Mun (Thu Feb 27 2014 - 08:05:31 PST)
    - Re: [AMBER] Unable to read coords from XXX.rst - How can I resolve this once and for all? Nitin Sharma (Thu Feb 27 2014 - 08:11:35 PST)
    - Re: [AMBER] Unable to read coords from XXX.rst - How can I resolve this once and for all? Daniel Roe (Thu Feb 27 2014 - 08:21:29 PST)
[AMBER] alanine scanning and free energy decomposition Nitin Sharma (Thu Feb 27 2014 - 07:40:36 PST)
- Re: [AMBER] alanine scanning and free energy decomposition Bill Miller III (Thu Feb 27 2014 - 12:21:30 PST)
- Re: [AMBER] alanine scanning and free energy decomposition Nitin Sharma (Thu Feb 27 2014 - 19:33:51 PST)
[AMBER] Cpptraj bridge Alessandra Lacetera (Thu Feb 27 2014 - 09:33:03 PST)
- Re: [AMBER] Cpptraj bridge Daniel Roe (Thu Feb 27 2014 - 09:48:16 PST)
- Re: [AMBER] Cpptraj bridge Alessandra Lacetera (Fri Feb 28 2014 - 07:05:01 PST)
  - Re: [AMBER] Cpptraj bridge Daniel Roe (Mon Mar 03 2014 - 07:42:48 PST)
[AMBER] corrplane in cpptraj and ptraj Michael F. Bruist (Thu Feb 27 2014 - 11:52:26 PST)
- Re: [AMBER] corrplane in cpptraj and ptraj Daniel Roe (Thu Feb 27 2014 - 15:18:26 PST)
  - Re: [AMBER] corrplane in cpptraj and ptraj Michael F. Bruist (Fri Feb 28 2014 - 11:59:57 PST)
[AMBER] Fwd: James Luginsland (Thu Feb 27 2014 - 17:49:25 PST)
- [AMBER] Fwd: James Luginsland (Thu Feb 27 2014 - 18:15:21 PST)
  - [AMBER] CDC20 / temperature David A Case (Thu Feb 27 2014 - 19:09:08 PST)
[AMBER] MMPBSA.py positive delta G? de Waal, Parker (Thu Feb 27 2014 - 21:11:22 PST)
- Re: [AMBER] MMPBSA.py positive delta G? de Waal, Parker (Thu Feb 27 2014 - 21:49:02 PST)
  - Re: [AMBER] MMPBSA.py positive delta G? Jason Swails (Fri Feb 28 2014 - 05:00:06 PST)
[AMBER] error in creating topology file Arunima Shilpi (Thu Feb 27 2014 - 23:19:16 PST)
- Re: [AMBER] error in creating topology file Jason Swails (Fri Feb 28 2014 - 05:07:36 PST)
[AMBER] TI calculation Fatal error in PMPI_Bcast Changqing Yan (Thu Feb 27 2014 - 23:40:33 PST)
- Re: [AMBER] TI calculation Fatal error in PMPI_Bcast Ying-Chieh Sun (Fri Feb 28 2014 - 00:29:03 PST)
  - Re: [AMBER] TI calculation Fatal error in PMPI_Bcast Jason Swails (Fri Feb 28 2014 - 05:12:43 PST)
- Re: [AMBER] TI calculation Fatal error in PMPI_Bcast David A Case (Fri Feb 28 2014 - 05:04:44 PST)
- Re: [AMBER] TI calculation Fatal error in PMPI_Bcast Jason Swails (Fri Feb 28 2014 - 05:11:54 PST)
[AMBER] error in editing Ligand file Arunima Shilpi (Fri Feb 28 2014 - 07:13:29 PST)
- Re: [AMBER] error in editing Ligand file Jason Swails (Fri Feb 28 2014 - 07:36:29 PST)
[AMBER] error in running antechamber Arunima Shilpi (Sat Mar 01 2014 - 03:11:59 PST)
- Re: [AMBER] error in running antechamber hannes.loeffler.stfc.ac.uk (Sat Mar 01 2014 - 06:40:41 PST)
- Re: [AMBER] error in running antechamber David A Case (Sat Mar 01 2014 - 06:46:35 PST)
[AMBER] amber trajectory to gromacs trajectory conversion Sohag Biswas (Sat Mar 01 2014 - 22:55:23 PST)
- Re: [AMBER] amber trajectory to gromacs trajectory conversion Daniel Roe (Mon Mar 03 2014 - 15:28:14 PST)
[AMBER] extracting selected lipids from bilayer Vijay Manickam Achari (Mon Mar 03 2014 - 00:57:07 PST)
- Re: [AMBER] extracting selected lipids from bilayer Dickson, Callum J (Mon Mar 03 2014 - 02:02:14 PST)
- Re: [AMBER] extracting selected lipids from bilayer Daniel Roe (Mon Mar 03 2014 - 07:16:16 PST)
[AMBER] PairwiseDistance file after clustering analysis Elisa Frezza (Mon Mar 03 2014 - 04:15:16 PST)
- Re: [AMBER] PairwiseDistance file after clustering analysis Daniel Roe (Mon Mar 03 2014 - 07:34:03 PST)
[AMBER] mass Zahra Khatti (Mon Mar 03 2014 - 06:13:13 PST)
- Re: [AMBER] mass Jason Swails (Mon Mar 03 2014 - 06:45:28 PST)
[AMBER] pmemd.cuda segfaults pavel.banas.upol.cz (Mon Mar 03 2014 - 08:09:38 PST)
- Re: [AMBER] pmemd.cuda segfaults Ross Walker (Mon Mar 03 2014 - 08:43:12 PST)
- Re: [AMBER] pmemd.cuda segfaults Jan-Philip Gehrcke (Mon Mar 03 2014 - 08:44:29 PST)
  - Re: [AMBER] pmemd.cuda segfaults Ross Walker (Mon Mar 03 2014 - 08:49:31 PST)
  - Re: [AMBER] pmemd.cuda segfaults Jason Swails (Mon Mar 03 2014 - 09:01:04 PST)
    - Re: [AMBER] pmemd.cuda segfaults Ross Walker (Mon Mar 03 2014 - 09:03:02 PST)
- Re: [AMBER] pmemd.cuda segfaults pavel.banas.upol.cz (Mon Mar 03 2014 - 12:44:24 PST)
  - Re: [AMBER] pmemd.cuda segfaults Ross Walker (Mon Mar 03 2014 - 13:43:45 PST)
- Re: [AMBER] pmemd.cuda segfaults pavel.banas.upol.cz (Tue Mar 04 2014 - 00:10:51 PST)
- Re: [AMBER] pmemd.cuda segfaults pavel.banas.upol.cz (Wed Mar 05 2014 - 12:09:15 PST)
  - Re: [AMBER] pmemd.cuda segfaults Jason Swails (Wed Mar 05 2014 - 12:20:55 PST)
  - Re: [AMBER] pmemd.cuda segfaults Ross Walker (Wed Mar 05 2014 - 12:49:26 PST)
  - Re: [AMBER] pmemd.cuda segfaults Tru Huynh (Thu Mar 06 2014 - 11:25:01 PST)
- Re: [AMBER] pmemd.cuda segfaults pavel.banas.upol.cz (Sat Mar 08 2014 - 00:39:13 PST)
  - Re: [AMBER] pmemd.cuda segfaults Ross Walker (Sat Mar 08 2014 - 10:00:00 PST)
    - Re: [AMBER] pmemd.cuda segfaults Jason Swails (Sat Mar 08 2014 - 11:09:25 PST)
- Re: [AMBER] pmemd.cuda segfaults pavel.banas.upol.cz (Tue Mar 11 2014 - 07:50:51 PDT)
- Re: [AMBER] pmemd.cuda segfaults pavel.banas.upol.cz (Tue Mar 11 2014 - 07:54:23 PDT)
[AMBER] format of FINAL_DECOMP_MMPBSA.dat Nitin Sharma (Mon Mar 03 2014 - 08:29:00 PST)
- Re: [AMBER] format of FINAL_DECOMP_MMPBSA.dat Jason Swails (Mon Mar 03 2014 - 09:24:08 PST)
[AMBER] MMPBSA TrajError Ahmed Ayoub (Mon Mar 03 2014 - 15:08:31 PST)
- Re: [AMBER] MMPBSA TrajError Daniel Roe (Mon Mar 03 2014 - 15:16:02 PST)
- Re: [AMBER] MMPBSA TrajError Ahmed Ayoub (Tue Mar 04 2014 - 12:58:58 PST)
- Re: [AMBER] MMPBSA TrajError Jason Swails (Tue Mar 04 2014 - 13:41:31 PST)
- Re: [AMBER] MMPBSA TrajError Ahmed Ayoub (Wed Mar 05 2014 - 20:46:59 PST)
  - Re: [AMBER] MMPBSA TrajError Jason Swails (Thu Mar 06 2014 - 04:58:53 PST)
- Re: [AMBER] MMPBSA TrajError Ahmed Ayoub (Fri Mar 07 2014 - 11:32:16 PST)
  - Re: [AMBER] MMPBSA TrajError Daniel Roe (Fri Mar 07 2014 - 12:02:04 PST)
- Re: [AMBER] MMPBSA TrajError Ahmed Ayoub (Tue Mar 11 2014 - 13:14:30 PDT)
  - Re: [AMBER] MMPBSA TrajError Daniel Roe (Tue Mar 11 2014 - 21:07:47 PDT)
    - Re: [AMBER] MMPBSA TrajError Daniel Roe (Tue Mar 11 2014 - 21:41:19 PDT)
    - Re: [AMBER] MMPBSA TrajError Daniel Roe (Thu Mar 13 2014 - 07:37:30 PDT)
- Re: [AMBER] MMPBSA TrajError Ahmed Ayoub (Thu Mar 13 2014 - 13:27:30 PDT)
[AMBER] mass Zahra Khatti (Sun Feb 23 2014 - 12:47:18 PST)
[AMBER] question about mmpbsa result . mirage (Mon Mar 03 2014 - 22:47:55 PST)
- Re: [AMBER] question about mmpbsa result Jason Swails (Tue Mar 04 2014 - 05:10:30 PST)
[AMBER] deprotonated histidine parameters Ahmet yıldırım (Tue Mar 04 2014 - 01:12:11 PST)
- Re: [AMBER] deprotonated histidine parameters Jason Swails (Tue Mar 04 2014 - 05:17:39 PST)
  - Re: [AMBER] deprotonated histidine parameters Gmail2 (Tue Mar 04 2014 - 08:42:02 PST)
    - Re: [AMBER] deprotonated histidine parameters Jason Swails (Tue Mar 04 2014 - 08:51:05 PST)
    - Re: [AMBER] deprotonated histidine parameters Gmail2 (Tue Mar 04 2014 - 09:11:18 PST)
    - Re: [AMBER] deprotonated histidine parameters David A Case (Tue Mar 04 2014 - 10:58:19 PST)
    - Re: [AMBER] deprotonated histidine parameters Ken Merz (Tue Mar 04 2014 - 13:25:25 PST)
[AMBER] calculate charge and spin multiplicity Arunima Shilpi (Tue Mar 04 2014 - 03:17:43 PST)
- Re: [AMBER] calculate charge and spin multiplicity David A Case (Tue Mar 04 2014 - 04:59:01 PST)
[AMBER] Pmf-plane to plane restrain Rasha Alqus (Tue Mar 04 2014 - 09:03:19 PST)
[AMBER] non-bonded parameters for ferric iron and ferrous iron Jean-Paul Becker (Tue Mar 04 2014 - 09:08:48 PST)
- Re: [AMBER] non-bonded parameters for ferric iron and ferrous iron Ken Merz (Tue Mar 04 2014 - 13:45:57 PST)
- Re: [AMBER] non-bonded parameters for ferric iron and ferrous iron Jean-Paul Becker (Wed Mar 05 2014 - 13:11:51 PST)
  - Re: [AMBER] non-bonded parameters for ferric iron and ferrous iron Pengfei Li (Wed Mar 05 2014 - 13:38:47 PST)
    - Re: [AMBER] non-bonded parameters for ferric iron and ferrous iron Jean-Paul Becker (Thu Mar 06 2014 - 06:47:14 PST)
    - Re: [AMBER] non-bonded parameters for ferric iron and ferrous iron Pengfei Li (Thu Mar 06 2014 - 14:22:14 PST)
    - Re: [AMBER] non-bonded parameters for ferric iron and ferrous iron JPB (Fri Mar 07 2014 - 08:07:49 PST)
    - Re: [AMBER] non-bonded parameters for ferric iron and ferrous iron Ken Merz (Fri Mar 07 2014 - 08:19:11 PST)
    - Re: [AMBER] non-bonded parameters for ferric iron and ferrous iron Jason Swails (Fri Mar 07 2014 - 08:26:54 PST)
    - Re: [AMBER] non-bonded parameters for ferric iron and ferrous iron Ken Merz (Fri Mar 07 2014 - 08:27:05 PST)
    - Re: [AMBER] non-bonded parameters for ferric iron and ferrous iron FyD (Fri Mar 07 2014 - 09:30:12 PST)
    - Re: [AMBER] non-bonded parameters for ferric iron and ferrous iron David A Case (Fri Mar 07 2014 - 10:33:00 PST)
    - Re: [AMBER] non-bonded parameters for ferric iron and ferrous iron Jason Swails (Fri Mar 07 2014 - 10:34:24 PST)
    - Re: [AMBER] non-bonded parameters for ferric iron and ferrous iron JPB (Mon Mar 10 2014 - 01:03:05 PDT)
    - Re: [AMBER] non-bonded parameters for ferric iron and ferrous iron Pengfei Li (Thu Mar 13 2014 - 08:31:44 PDT)
[AMBER] MMPBSA alanine scanning Maryam Azimzadeh Irani (Tue Mar 04 2014 - 17:56:40 PST)
- Re: [AMBER] MMPBSA alanine scanning Jason Swails (Tue Mar 04 2014 - 18:08:54 PST)
  - Re: [AMBER] MMPBSA alanine scanning Maryam Azimzadeh Irani (Thu Mar 06 2014 - 23:35:50 PST)
[AMBER] Amber settings in pymol Entomology Research Institute (Tue Mar 04 2014 - 22:54:40 PST)
[AMBER] sander command Arunima Shilpi (Tue Mar 04 2014 - 23:09:54 PST)
- Re: [AMBER] sander command David A Case (Wed Mar 05 2014 - 05:07:05 PST)
[AMBER] pmf-plane to plane restrain Rasha Alqus (Wed Mar 05 2014 - 00:02:13 PST)
- Re: [AMBER] pmf-plane to plane restrain Jason Swails (Wed Mar 05 2014 - 05:12:29 PST)
[AMBER] how to produce the prmtop of 'ch3cn' 闫玉娜 (Wed Mar 05 2014 - 00:16:25 PST)
- Re: [AMBER] how to produce the prmtop of 'ch3cn' Jason Swails (Wed Mar 05 2014 - 04:56:33 PST)
- Re: [AMBER] how to produce the prmtop of 'ch3cn' David A Case (Wed Mar 05 2014 - 05:11:02 PST)
- Re: [AMBER] how to produce the prmtop of 'ch3cn' FyD (Wed Mar 05 2014 - 22:29:52 PST)
[AMBER] Unable to restrain A-DNA conformation DEBOSTUTI GHOSHDASTIDAR (Wed Mar 05 2014 - 02:23:56 PST)
- Re: [AMBER] Unable to restrain A-DNA conformation Jason Swails (Wed Mar 05 2014 - 04:53:02 PST)
- Re: [AMBER] Unable to restrain A-DNA conformation David A Case (Wed Mar 05 2014 - 05:17:39 PST)
  - Re: [AMBER] Unable to restrain A-DNA conformation DEBOSTUTI GHOSHDASTIDAR (Wed Mar 05 2014 - 05:48:48 PST)
    - Re: [AMBER] Unable to restrain A-DNA conformation Brian Radak (Wed Mar 05 2014 - 06:46:31 PST)
    - Re: [AMBER] Unable to restrain A-DNA conformation Carlos Simmerling (Wed Mar 05 2014 - 06:52:35 PST)
[AMBER] print molecular orbitals Florent Barbault (Wed Mar 05 2014 - 05:01:48 PST)
- Re: [AMBER] print molecular orbitals Brian Radak (Wed Mar 05 2014 - 06:28:51 PST)
[AMBER] Multiple vs Continuous MD opinion Soumendranath Bhakat (Wed Mar 05 2014 - 06:33:50 PST)
- Re: [AMBER] Multiple vs Continuous MD opinion Carlos Simmerling (Wed Mar 05 2014 - 06:46:10 PST)
  - Re: [AMBER] Multiple vs Continuous MD opinion Brian Radak (Wed Mar 05 2014 - 07:00:10 PST)
    - Re: [AMBER] Multiple vs Continuous MD opinion Soumendranath Bhakat (Wed Mar 05 2014 - 07:58:58 PST)
    - Re: [AMBER] Multiple vs Continuous MD opinion Robert Molt (Wed Mar 05 2014 - 08:09:02 PST)
    - Re: [AMBER] Multiple vs Continuous MD opinion filip fratev (Wed Mar 05 2014 - 08:21:53 PST)
    - Re: [AMBER] Multiple vs Continuous MD opinion Ross Walker (Wed Mar 05 2014 - 09:08:35 PST)
    - Re: [AMBER] Multiple vs Continuous MD opinion Bill Ross (Fri Mar 14 2014 - 19:23:48 PDT)
    - Re: [AMBER] Multiple vs Continuous MD opinion Soumendranath Bhakat (Sun Mar 16 2014 - 23:40:23 PDT)
    - Re: [AMBER] Multiple vs Continuous MD opinion filip fratev (Mon Mar 17 2014 - 03:55:14 PDT)
    - Re: [AMBER] Multiple vs Continuous MD opinion filip fratev (Mon Mar 17 2014 - 03:56:15 PDT)
    - Re: [AMBER] Multiple vs Continuous MD opinion filip fratev (Mon Mar 17 2014 - 03:57:38 PDT)
    - Re: [AMBER] Multiple vs Continuous MD opinion Soumendranath Bhakat (Mon Mar 17 2014 - 04:25:51 PDT)
    - Re: [AMBER] Multiple vs Continuous MD opinion Hai Nguyen (Mon Mar 17 2014 - 15:38:34 PDT)
    - Re: [AMBER] Multiple vs Continuous MD opinion Soumendranath Bhakat (Wed Mar 19 2014 - 00:30:34 PDT)
    - Re: [AMBER] Multiple vs Continuous MD opinion nhai.wn (Wed Mar 19 2014 - 01:00:37 PDT)
    - Re: [AMBER] Multiple vs Continuous MD opinion Carlos Simmerling (Wed Mar 19 2014 - 07:50:58 PDT)
    - Re: [AMBER] Multiple vs Continuous MD opinion Robert Molt (Wed Mar 19 2014 - 08:32:30 PDT)
    - Re: [AMBER] Multiple vs Continuous MD opinion Carlos Simmerling (Mon Mar 17 2014 - 04:31:25 PDT)
    - Re: [AMBER] Multiple vs Continuous MD opinion Soumendranath Bhakat (Mon Mar 17 2014 - 04:45:46 PDT)
    - Re: [AMBER] Multiple vs Continuous MD opinion Jason Swails (Mon Mar 17 2014 - 05:28:53 PDT)
    - Re: [AMBER] Multiple vs Continuous MD opinion Bill Ross (Wed Mar 19 2014 - 19:01:12 PDT)
    - Re: [AMBER] Multiple vs Continuous MD opinion Jason Swails (Wed Mar 19 2014 - 19:13:39 PDT)
    - Re: [AMBER] Multiple vs Continuous MD opinion Bill Ross (Wed Mar 19 2014 - 19:43:04 PDT)
- Re: [AMBER] Multiple vs Continuous MD opinion Massimiliano Porrini (Wed Mar 19 2014 - 10:10:17 PDT)
  - Re: [AMBER] Multiple vs Continuous MD opinion Robert Molt (Wed Mar 19 2014 - 10:16:37 PDT)
    - Re: [AMBER] Multiple vs Continuous MD opinion Massimiliano Porrini (Wed Mar 19 2014 - 10:40:12 PDT)
    - Re: [AMBER] Multiple vs Continuous MD opinion Jason Swails (Wed Mar 19 2014 - 12:53:56 PDT)
  - Re: [AMBER] Multiple vs Continuous MD opinion Ross Walker (Wed Mar 19 2014 - 10:25:44 PDT)
[AMBER] Trouble obtaining force field parameters via Antechamber Hyun-seok Kim (Wed Mar 05 2014 - 10:43:49 PST)
- Re: [AMBER] Trouble obtaining force field parameters via Antechamber David A Case (Wed Mar 05 2014 - 10:58:56 PST)
- Re: [AMBER] Trouble obtaining force field parameters via Antechamber FyD (Wed Mar 05 2014 - 22:50:12 PST)
[AMBER] Error : while running force field modification files nalini chauhan (Wed Mar 05 2014 - 23:23:26 PST)
[AMBER] ERROR in sidechain.bcl file in MCPB nalini chauhan (Thu Mar 06 2014 - 00:29:32 PST)
- Re: [AMBER] ERROR in sidechain.bcl file in MCPB nalini chauhan (Mon Feb 24 2014 - 09:23:47 PST)
  - Re: [AMBER] ERROR in sidechain.bcl file in MCPB Jason Swails (Mon Feb 24 2014 - 18:09:44 PST)
  - [AMBER] Fwd: RE: ERROR in sidechain.bcl file in MCPB nalini chauhan (Mon Feb 24 2014 - 22:43:44 PST)
[AMBER] Problem in using xleap 肖立 (Thu Mar 06 2014 - 21:07:53 PST)
- Re: [AMBER] Problem in using xleap Baifan Wang (Thu Mar 06 2014 - 22:50:41 PST)
  - Re: [AMBER] Problem in using xleap David A Case (Fri Mar 07 2014 - 05:48:27 PST)
Re: [AMBER] PgP protein and amber14 lipid FF filip fratev (Thu Mar 06 2014 - 21:14:27 PST)
- Re: [AMBER] PgP protein and amber14 lipid FF filip fratev (Mon Mar 17 2014 - 04:10:49 PDT)
- Re: [AMBER] PgP protein and amber14 lipid FF filip fratev (Thu Mar 20 2014 - 16:04:04 PDT)
  - Re: [AMBER] PgP protein and amber14 lipid FF Dickson, Callum J (Thu Mar 20 2014 - 16:07:49 PDT)
[AMBER] Request for help in using Amberlite Robin Jain (Thu Mar 06 2014 - 23:02:33 PST)
- Re: [AMBER] Request for help in using Amberlite David A Case (Fri Mar 07 2014 - 05:51:32 PST)
- Re: [AMBER] Request for help in using Amberlite Jason Swails (Fri Mar 07 2014 - 05:58:03 PST)
[AMBER] problem when performing the ired anaysis 肖立 (Fri Mar 07 2014 - 15:18:46 PST)
- Re: [AMBER] problem when performing the ired anaysis Daniel Roe (Fri Mar 07 2014 - 16:26:48 PST)
  - Re: [AMBER] problem when performing the ired anaysis 肖立 (Fri Mar 07 2014 - 16:31:51 PST)
    - Re: [AMBER] problem when performing the ired anaysis Daniel Roe (Sat Mar 08 2014 - 08:04:36 PST)
[AMBER] FF10 Error Sorensen, Jesper (Fri Mar 07 2014 - 16:47:59 PST)
- Re: [AMBER] FF10 Error David A Case (Sat Mar 08 2014 - 06:17:10 PST)
- Re: [AMBER] FF10 Error Sorensen, Jesper (Sat Mar 08 2014 - 10:30:12 PST)
[AMBER] Modified RNA frcmod error Sorensen, Jesper (Fri Mar 07 2014 - 16:51:49 PST)
- Re: [AMBER] Modified RNA frcmod error David A Case (Sat Mar 08 2014 - 09:56:15 PST)
[AMBER] Mutating residues in an RNA Raviprasad Aduri (Fri Mar 07 2014 - 23:14:36 PST)
- Re: [AMBER] Mutating residues in an RNA Jason Swails (Sat Mar 08 2014 - 07:20:26 PST)
  - Re: [AMBER] Mutating residues in an RNA Debayan Chakraborty (Sat Mar 08 2014 - 08:02:18 PST)
    - Re: [AMBER] Mutating residues in an RNA Brian Radak (Sun Mar 09 2014 - 12:56:00 PDT)
[AMBER] Fwd: cpptraj -fixatomorder Saeed Nasiri (Sat Mar 08 2014 - 01:42:59 PST)
- Re: [AMBER] Fwd: cpptraj -fixatomorder Daniel Roe (Sat Mar 08 2014 - 08:02:17 PST)
[AMBER] modeling glucoside Vijay Manickam Achari (Sat Mar 08 2014 - 02:29:36 PST)
- Re: [AMBER] modeling glucoside ABEL Stephane 175950 (Sat Mar 08 2014 - 04:44:35 PST)
  - Re: [AMBER] modeling glucoside Vijay Manickam Achari (Sun Mar 09 2014 - 01:37:48 PST)
    - Re: [AMBER] modeling glucoside Lachele Foley (Fri Mar 14 2014 - 08:33:32 PDT)
[AMBER] Antechamber add new parameter Mengyuan Zhu (Sat Mar 08 2014 - 09:40:54 PST)
- Re: [AMBER] Antechamber add new parameter David A Case (Sat Mar 08 2014 - 10:00:48 PST)
  - Re: [AMBER] Antechamber add new parameter Mengyuan Zhu (Sat Mar 08 2014 - 10:09:25 PST)
[AMBER] how to get around "cudaDeviceEnablePeerAccess all CUDA-capable devices are busy or unavailable" Chris McClendon (Sat Mar 08 2014 - 17:52:45 PST)
- Re: [AMBER] how to get around "cudaDeviceEnablePeerAccess all CUDA-capable devices are busy or unavailable" filip fratev (Sat Mar 08 2014 - 18:21:35 PST)
  - Re: [AMBER] how to get around "cudaDeviceEnablePeerAccess all CUDA-capable devices are busy or unavailable" Ross Walker (Sat Mar 08 2014 - 18:39:14 PST)
[AMBER] How can I create input for two molecule? Zahra Khatti (Sun Mar 09 2014 - 06:18:48 PDT)
- Re: [AMBER] How can I create input for two molecule? Jason Swails (Sun Mar 09 2014 - 06:39:57 PDT)
  - Re: [AMBER] How can I create input for two molecule? Zahra Khatti (Sun Mar 09 2014 - 08:58:16 PDT)
    - Re: [AMBER] How can I create input for two molecule? Jason Swails (Sun Mar 09 2014 - 09:19:42 PDT)
[AMBER] error in running Antechamber Arunima Shilpi (Sun Mar 09 2014 - 08:27:28 PDT)
- Re: [AMBER] error in running Antechamber Jason Swails (Sun Mar 09 2014 - 09:21:30 PDT)
[AMBER] cpptraj -fixatomorder Saeed Nasiri (Mon Mar 10 2014 - 00:01:00 PDT)
- Re: [AMBER] cpptraj -fixatomorder Jason Swails (Mon Mar 10 2014 - 05:01:36 PDT)
[AMBER] rism3d.snglpnt output in dx format Brian Radak (Mon Mar 10 2014 - 07:09:55 PDT)
- Re: [AMBER] rism3d.snglpnt output in dx format Jason Swails (Mon Mar 10 2014 - 07:34:34 PDT)
  - Re: [AMBER] rism3d.snglpnt output in dx format T Luchko (Lists) (Mon Mar 10 2014 - 09:33:54 PDT)
[AMBER] problem in "re-image" and "unwarp" Vijay Manickam Achari (Mon Mar 10 2014 - 07:18:49 PDT)
- Re: [AMBER] problem in "re-image" and "unwarp" Daniel Roe (Mon Mar 10 2014 - 07:43:15 PDT)
  - Re: [AMBER] problem in "re-image" and "unwarp" Thomas Cheatham (Mon Mar 10 2014 - 08:27:02 PDT)
    - Re: [AMBER] problem in "re-image" and "unwarp" David A Case (Mon Mar 10 2014 - 08:52:26 PDT)
    - Re: [AMBER] problem in "re-image" and "unwarp" Thomas Cheatham (Mon Mar 10 2014 - 08:57:45 PDT)
    - Re: [AMBER] problem in "re-image" and "unwarp" Jason Swails (Mon Mar 10 2014 - 09:45:09 PDT)
- Re: [AMBER] problem in "re-image" and "unwarp" Jason Swails (Mon Mar 10 2014 - 08:00:28 PDT)
  - Re: [AMBER] problem in "re-image" and "unwarp" Jason Swails (Mon Mar 10 2014 - 08:04:36 PDT)
- Re: [AMBER] problem in "re-image" and "unwarp" Vijay Manickam Achari (Mon Mar 10 2014 - 23:37:38 PDT)
  - Re: [AMBER] problem in "re-image" and "unwarp" Jason Swails (Tue Mar 11 2014 - 04:45:55 PDT)
    - Re: [AMBER] problem in "re-image" and "unwarp" Him Shweta (Wed Jul 16 2014 - 04:13:42 PDT)
[AMBER] Updater problems George Tzotzos (Mon Mar 10 2014 - 08:32:48 PDT)
- Re: [AMBER] Updater problems Jason Swails (Mon Mar 10 2014 - 09:59:02 PDT)
[AMBER] Call for participation: ISQBP Meeting, Telluride 15-19.06.2014 Thomas Cheatham (Mon Mar 10 2014 - 09:27:42 PDT)
[AMBER] MMPBSA.py.MPI - Runtime error George Tzotzos (Mon Mar 10 2014 - 14:02:18 PDT)
[AMBER] MMPBSA.py.MPI - Runtime error cont.d George Tzotzos (Mon Mar 10 2014 - 14:16:56 PDT)
[AMBER] error in executing pmemd Arunima Shilpi (Mon Mar 10 2014 - 21:33:29 PDT)
[AMBER] cpptraj -fixatomorder Saeed Nasiri (Tue Mar 11 2014 - 02:15:30 PDT)
- Re: [AMBER] cpptraj -fixatomorder Jason Swails (Tue Mar 11 2014 - 04:59:22 PDT)
  - Re: [AMBER] cpptraj -fixatomorder Daniel Roe (Tue Mar 11 2014 - 05:54:55 PDT)
    - Re: [AMBER] cpptraj -fixatomorder Jason Swails (Tue Mar 11 2014 - 06:33:20 PDT)
[AMBER] PM6-DH+ QM/MM-GBSA Kanin Wichapong (Tue Mar 11 2014 - 02:38:56 PDT)
- Re: [AMBER] PM6-DH+ QM/MM-GBSA Jason Swails (Tue Mar 11 2014 - 05:28:57 PDT)
[AMBER] charges for QM/MM simulations Asaminew Haile (Tue Mar 11 2014 - 07:10:57 PDT)
[AMBER] Help for system configuration Kshatresh Dutta Dubey (Tue Mar 11 2014 - 09:46:10 PDT)
- Re: [AMBER] Help for system configuration Jan-Philip Gehrcke (Tue Mar 11 2014 - 10:02:57 PDT)
- Re: [AMBER] Help for system configuration Ross Walker (Tue Mar 11 2014 - 12:32:09 PDT)
- Re: [AMBER] Help for system configuration Ross Walker (Tue Mar 11 2014 - 12:31:26 PDT)
  - Re: [AMBER] Help for system configuration Kshatresh Dutta Dubey (Tue Mar 11 2014 - 14:35:24 PDT)
    - Re: [AMBER] Help for system configuration Ross Walker (Tue Mar 11 2014 - 15:22:22 PDT)
    - Re: [AMBER] Help for system configuration filip fratev (Tue Mar 11 2014 - 15:31:44 PDT)
    - Re: [AMBER] Help for system configuration Ross Walker (Tue Mar 11 2014 - 16:57:32 PDT)
    - Re: [AMBER] Help for system configuration Kshatresh Dutta Dubey (Tue Mar 11 2014 - 21:39:24 PDT)
    - Re: [AMBER] Help for system configuration Ross Walker (Thu Mar 13 2014 - 16:22:12 PDT)
    - Re: [AMBER] Help for system configuration Kshatresh Dutta Dubey (Fri Mar 14 2014 - 00:24:28 PDT)
    - Re: [AMBER] Help for system configuration Gustavo Seabra (Wed Mar 12 2014 - 06:50:19 PDT)
    - Re: [AMBER] Help for system configuration Ross Walker (Thu Mar 13 2014 - 08:50:09 PDT)
[AMBER] scale molecular dynamic / GPU available in Amber 12? psu4.uic.edu (Tue Mar 11 2014 - 12:57:18 PDT)
- Re: [AMBER] scale molecular dynamic / GPU available in Amber 12? Ross Walker (Tue Mar 11 2014 - 13:10:31 PDT)
[AMBER] MutateError: Mismatch in atom lnubbs2014 (Wed Mar 12 2014 - 01:43:11 PDT)
- Re: [AMBER] MutateError: Mismatch in atom Jason Swails (Wed Mar 12 2014 - 03:28:03 PDT)
[AMBER] MutateError: Mismatch in atom lnubbs2014 (Wed Mar 12 2014 - 03:07:27 PDT)
[AMBER] MutateError: Mismatch in atom lnubbs2014 (Wed Mar 12 2014 - 04:06:27 PDT)
[AMBER] MutateError: Mismatch in atom # in residue VAL lnubbs2014 (Wed Mar 12 2014 - 04:49:28 PDT)
- Re: [AMBER] MutateError: Mismatch in atom # in residue VAL Jason Swails (Wed Mar 12 2014 - 05:07:58 PDT)
  - Re: [AMBER] MutateError: Mismatch in atom # in residue VAL lnubbs2014.163.com (Wed Mar 12 2014 - 05:17:37 PDT)
[AMBER] 3DRISM and orientationally averaged 3D pair distribution functions Brian Radak (Wed Mar 12 2014 - 11:34:46 PDT)
- Re: [AMBER] 3DRISM and orientationally averaged 3D pair distribution functions T Luchko (Lists) (Wed Mar 12 2014 - 13:07:12 PDT)
[AMBER] problem with -make-mdins mode in entropy MMPBSA.py.MPI calculations Marek Maly (Wed Mar 12 2014 - 17:40:12 PDT)
- Re: [AMBER] problem with -make-mdins mode in entropy MMPBSA.py.MPI calculations Jason Swails (Wed Mar 12 2014 - 18:24:35 PDT)
  - Re: [AMBER] problem with -make-mdins mode in entropy MMPBSA.py.MPI calculations Marek Maly (Thu Mar 13 2014 - 06:58:05 PDT)
    - Re: [AMBER] problem with -make-mdins mode in entropy MMPBSA.py.MPI calculations Jason Swails (Thu Mar 13 2014 - 10:44:15 PDT)
    - Re: [AMBER] problem with -make-mdins mode in entropy MMPBSA.py.MPI calculations Marek Maly (Fri Mar 14 2014 - 03:53:09 PDT)
[AMBER] AmberTools update 24 for CPPTRAJ Daniel Roe (Thu Mar 13 2014 - 07:35:58 PDT)
- Re: [AMBER] AmberTools update 24 for CPPTRAJ Jio M (Thu Mar 13 2014 - 16:21:40 PDT)
  - Re: [AMBER] AmberTools update 24 for CPPTRAJ Daniel Roe (Fri Mar 14 2014 - 06:56:18 PDT)
[AMBER] Specifying a particular angle in ptraj when there is more than one residue with the same residue number Sajeewa Pemasinghe (Thu Mar 13 2014 - 18:00:42 PDT)
- Re: [AMBER] Specifying a particular angle in ptraj when there is more than one residue with the same residue number Sajeewa Pemasinghe (Thu Mar 13 2014 - 18:03:46 PDT)
- Re: [AMBER] Specifying a particular angle in ptraj when there is more than one residue with the same residue number David A Case (Thu Mar 13 2014 - 19:08:58 PDT)
- Re: [AMBER] Specifying a particular angle in ptraj when there is more than one residue with the same residue number Daniel Roe (Fri Mar 14 2014 - 07:07:22 PDT)
[AMBER] Arsenic co-ordinates Sushi Shilpa (Thu Mar 13 2014 - 23:17:05 PDT)
- Re: [AMBER] Arsenic co-ordinates David A Case (Fri Mar 14 2014 - 06:14:09 PDT)
[AMBER] Problem in rst file Sushi Shilpa (Thu Mar 13 2014 - 23:33:35 PDT)
- Re: [AMBER] Problem in rst file Jason Swails (Fri Mar 14 2014 - 04:54:37 PDT)
[AMBER] unsubscribe mailing list John Chuang莊曜遠 (Fri Mar 14 2014 - 02:09:38 PDT)
- Re: [AMBER] unsubscribe mailing list Jason Swails (Fri Mar 14 2014 - 04:45:58 PDT)
[AMBER] electric field Neha Gandhi (Fri Mar 14 2014 - 03:50:52 PDT)
- Re: [AMBER] electric field Jason Swails (Fri Mar 14 2014 - 04:43:41 PDT)
  - Re: [AMBER] electric field Neha Gandhi (Fri Mar 14 2014 - 04:48:47 PDT)
    - Re: [AMBER] electric field Jason Swails (Fri Mar 14 2014 - 05:51:34 PDT)
    - Re: [AMBER] electric field Neha Gandhi (Sat Mar 15 2014 - 04:32:52 PDT)
    - Re: [AMBER] electric field Robert McGibbon (Sat Mar 15 2014 - 13:46:21 PDT)
[AMBER] Parameters for a residue R R S Pissurlenkar (Fri Mar 14 2014 - 05:55:08 PDT)
- Re: [AMBER] Parameters for a residue Lachele Foley (Fri Mar 14 2014 - 08:39:25 PDT)
[AMBER] Water cap without MM-PBSA Antoine Marion (Fri Mar 14 2014 - 06:29:06 PDT)
- Re: [AMBER] Water cap without MM-PBSA Daniel Roe (Fri Mar 14 2014 - 07:00:52 PDT)
  - Re: [AMBER] Water cap without MM-PBSA Antoine Marion (Fri Mar 14 2014 - 07:22:20 PDT)
    - Re: [AMBER] Water cap without MM-PBSA Daniel Roe (Fri Mar 14 2014 - 08:39:46 PDT)
    - Re: [AMBER] Water cap without MM-PBSA Antoine Marion (Fri Mar 14 2014 - 08:46:59 PDT)
    - Re: [AMBER] Water cap without MM-PBSA Antoine Marion (Fri Mar 14 2014 - 10:09:32 PDT)
[AMBER] Compilation of amber12 on GRAY XE6 Stefan Richter (Fri Mar 14 2014 - 07:29:56 PDT)
- Re: [AMBER] Compilation of amber12 on GRAY XE6 Daniel Roe (Fri Mar 14 2014 - 08:08:42 PDT)
[AMBER] Question about Ambertools 1.5 installation Wook Lee (Fri Mar 14 2014 - 09:53:04 PDT)
- Re: [AMBER] Question about Ambertools 1.5 installation Jason Swails (Fri Mar 14 2014 - 10:14:47 PDT)
  - Re: [AMBER] Question about Ambertools 1.5 installation Wook Lee (Fri Mar 14 2014 - 10:37:30 PDT)
    - Re: [AMBER] Question about Ambertools 1.5 installation David A Case (Fri Mar 14 2014 - 11:44:12 PDT)
    - Re: [AMBER] Question about Ambertools 1.5 installation Jason Swails (Fri Mar 14 2014 - 12:25:38 PDT)
    - Re: [AMBER] Question about Ambertools 1.5 installation Wook Lee (Fri Mar 14 2014 - 12:53:56 PDT)
Re: [AMBER] AMBER Digest, Vol 793, Issue 1 R R S Pissurlenkar (Fri Mar 14 2014 - 20:40:09 PDT)
[AMBER] linker error Ayesha Fatima (Fri Mar 14 2014 - 23:30:15 PDT)
- Re: [AMBER] linker error Daniel Roe (Sat Mar 15 2014 - 00:43:27 PDT)
  - Re: [AMBER] linker error Ayesha Fatima (Sat Mar 15 2014 - 01:14:25 PDT)
  - Re: [AMBER] linker error Ayesha Fatima (Sat Mar 15 2014 - 01:23:25 PDT)
[AMBER] iRED: relaxation rates and NOEs with ptraj Ignacio Faustino (Sat Mar 15 2014 - 03:43:52 PDT)
- Re: [AMBER] iRED: relaxation rates and NOEs with ptraj David A Case (Sat Mar 15 2014 - 05:25:48 PDT)
  - Re: [AMBER] iRED: relaxation rates and NOEs with ptraj Daniel Roe (Sat Mar 15 2014 - 09:34:14 PDT)
[AMBER] MMPBSA.py not generating specified frames for analysis manikanthan bhavaraju (Sat Mar 15 2014 - 19:34:44 PDT)
- Re: [AMBER] MMPBSA.py not generating specified frames for analysis Daniel Roe (Sat Mar 15 2014 - 21:08:18 PDT)
  - Re: [AMBER] MMPBSA.py not generating specified frames for analysis manikanthan bhavaraju (Sat Mar 15 2014 - 21:50:30 PDT)
[AMBER] tleap lipid residue splitting warnings de Waal, Parker (Sun Mar 16 2014 - 09:35:19 PDT)
- Re: [AMBER] tleap lipid residue splitting warnings Jason Swails (Sun Mar 16 2014 - 11:32:27 PDT)
- Re: [AMBER] tleap lipid residue splitting warnings Ross Walker (Sun Mar 16 2014 - 20:29:21 PDT)
  - Re: [AMBER] tleap lipid residue splitting warnings de Waal, Parker (Mon Mar 17 2014 - 07:52:38 PDT)
    - Re: [AMBER] tleap lipid residue splitting warnings Ross Walker (Mon Mar 17 2014 - 08:45:09 PDT)
[AMBER] qm/mm Jacopo Sgrignani (Sun Mar 16 2014 - 10:57:54 PDT)
- Re: [AMBER] qm/mm Jason Swails (Sun Mar 16 2014 - 11:22:42 PDT)
[AMBER] MMPBSA Mary Varughese (Mon Mar 17 2014 - 03:51:51 PDT)
- Re: [AMBER] MMPBSA Marcus Arieno (Mon Mar 17 2014 - 04:08:06 PDT)
  - Re: [AMBER] MMPBSA Mary Varughese (Mon Mar 17 2014 - 11:10:06 PDT)
[AMBER] pmf -Equilibration termination Rasha Alqus (Mon Mar 17 2014 - 05:25:04 PDT)
- Re: [AMBER] pmf -Equilibration termination Jason Swails (Mon Mar 17 2014 - 05:56:00 PDT)
[AMBER] calculating binding free energy using MM-GBSA FOR ZIF268-DNA complex Roza M (Mon Mar 17 2014 - 07:58:00 PDT)
- Re: [AMBER] calculating binding free energy using MM-GBSA FOR ZIF268-DNA complex Jason Swails (Mon Mar 17 2014 - 09:28:37 PDT)
  - Re: [AMBER] calculating binding free energy using MM-GBSA FOR ZIF268-DNA complex Roza M (Mon Mar 17 2014 - 09:52:35 PDT)
    - Re: [AMBER] calculating binding free energy using MM-GBSA FOR ZIF268-DNA complex Jason Swails (Mon Mar 17 2014 - 10:04:01 PDT)
[AMBER] rdf around atom Jio M (Mon Mar 17 2014 - 12:18:24 PDT)
- Re: [AMBER] rdf around atom Daniel Roe (Mon Mar 17 2014 - 12:46:39 PDT)
  - Re: [AMBER] rdf around atom Jio M (Mon Mar 17 2014 - 16:16:17 PDT)
    - Re: [AMBER] rdf around atom Daniel Roe (Mon Mar 17 2014 - 16:47:23 PDT)
[AMBER] error in running MMPBSA.py Arunima Shilpi (Mon Mar 17 2014 - 19:55:55 PDT)
- Re: [AMBER] error in running MMPBSA.py Jason Swails (Tue Mar 18 2014 - 02:46:01 PDT)
[AMBER] Energy unit in sqm Jacopo Sgrignani (Tue Mar 18 2014 - 02:12:33 PDT)
- Re: [AMBER] Energy unit in sqm Brian Radak (Tue Mar 18 2014 - 07:03:12 PDT)
  - Re: [AMBER] Energy unit in sqm David A Case (Tue Mar 18 2014 - 08:16:37 PDT)
[AMBER] Percentage of secondary structure determination Tanmoy Paul (Tue Mar 18 2014 - 04:23:19 PDT)
- Re: [AMBER] Percentage of secondary structure determination Daniel Roe (Tue Mar 18 2014 - 07:23:07 PDT)
[AMBER] tleap output of mol2 format incorrect bond order/atom types Browning, Nicholas (Tue Mar 18 2014 - 07:59:47 PDT)
- Re: [AMBER] tleap output of mol2 format incorrect bond order/atom types Hannes Loeffler (Tue Mar 18 2014 - 08:23:15 PDT)
  - Re: [AMBER] tleap output of mol2 format incorrect bond order/atom types Browning, Nicholas (Tue Mar 18 2014 - 09:25:09 PDT)
    - Re: [AMBER] tleap output of mol2 format incorrect bond order/atom types Jason Swails (Tue Mar 18 2014 - 09:49:57 PDT)
    - Re: [AMBER] tleap output of mol2 format incorrect bond order/atom types Hannes Loeffler (Tue Mar 18 2014 - 09:57:22 PDT)
    - Re: [AMBER] tleap output of mol2 format incorrect bond order/atom types Browning, Nicholas (Wed Mar 19 2014 - 11:11:50 PDT)
    - Re: [AMBER] tleap output of mol2 format incorrect bond order/atom types David A Case (Wed Mar 19 2014 - 18:44:12 PDT)
    - Re: [AMBER] tleap output of mol2 format incorrect bond order/atom types Browning, Nicholas (Thu Mar 20 2014 - 02:47:04 PDT)
    - Re: [AMBER] tleap output of mol2 format incorrect bond order/atom types Hannes Loeffler (Thu Mar 20 2014 - 03:07:08 PDT)
    - Re: [AMBER] tleap output of mol2 format incorrect bond order/atom types Browning, Nicholas (Thu Mar 20 2014 - 03:52:04 PDT)
- Re: [AMBER] tleap output of mol2 format incorrect bond order/atom types David A Case (Tue Mar 18 2014 - 09:45:40 PDT)
- Re: [AMBER] tleap output of mol2 format incorrect bond order/atom types FyD (Thu Mar 20 2014 - 00:36:07 PDT)
[AMBER] bugzilla searches Scott Brozell (Tue Mar 18 2014 - 08:52:47 PDT)
[AMBER] Hbond Nitin Sharma (Tue Mar 18 2014 - 12:47:37 PDT)
- Re: [AMBER] Hbond David A Case (Tue Mar 18 2014 - 13:16:09 PDT)
  - Re: [AMBER] Hbond Nitin Sharma (Tue Mar 18 2014 - 21:42:20 PDT)
[AMBER] error in MMPBSA.py Arunima Shilpi (Tue Mar 18 2014 - 21:06:10 PDT)
- Re: [AMBER] error in MMPBSA.py Manikanthan Bhavaraju (Tue Mar 18 2014 - 21:42:25 PDT)
- Re: [AMBER] error in MMPBSA.py Jason Swails (Wed Mar 19 2014 - 06:05:15 PDT)
[AMBER] How to get the ESP on the grid point Kim TaeHwan (Wed Mar 19 2014 - 00:19:13 PDT)
- Re: [AMBER] How to get the ESP on the grid point Ivanov, Maxim (Wed Mar 19 2014 - 07:00:13 PDT)
  - Re: [AMBER] How to get the ESP on the grid point Kim TaeHwan (Wed Mar 19 2014 - 07:24:55 PDT)
- Re: [AMBER] How to get the ESP on the grid point Ray Luo, Ph.D. (Wed Mar 19 2014 - 10:19:32 PDT)
[AMBER] generating topology Vijay Manickam Achari (Wed Mar 19 2014 - 06:47:05 PDT)
- Re: [AMBER] generating topology David A Case (Wed Mar 19 2014 - 07:01:34 PDT)
  - Re: [AMBER] generating topology Bill Ross (Wed Mar 19 2014 - 19:22:47 PDT)
- Re: [AMBER] generating topology Jason Swails (Wed Mar 19 2014 - 09:01:58 PDT)
[AMBER] Error: Prmtop appears to contain modified off-diagonal elements for VDW A coef BERGY (Wed Mar 19 2014 - 08:55:06 PDT)
- Re: [AMBER] Error: Prmtop appears to contain modified off-diagonal elements for VDW A coef Jason Swails (Wed Mar 19 2014 - 09:05:17 PDT)
  - Re: [AMBER] Error: Prmtop appears to contain modified off-diagonal elements for VDW A coef BERGY (Thu Mar 20 2014 - 02:37:05 PDT)
    - Re: [AMBER] Error: Prmtop appears to contain modified off-diagonal elements for VDW A coef Jason Swails (Thu Mar 20 2014 - 04:40:17 PDT)
    - Re: [AMBER] Error: Prmtop appears to contain modified off-diagonal elements for VDW A coef BERGY (Fri Mar 21 2014 - 04:44:39 PDT)
[AMBER] strain/energy of backbone atoms Jio M (Wed Mar 19 2014 - 09:14:21 PDT)
- Re: [AMBER] strain/energy of backbone atoms Carlos Simmerling (Wed Mar 19 2014 - 09:42:47 PDT)
  - Re: [AMBER] strain/energy of backbone atoms Jio M (Wed Mar 19 2014 - 10:14:05 PDT)
    - Re: [AMBER] strain/energy of backbone atoms Carlos Simmerling (Wed Mar 19 2014 - 11:43:57 PDT)
    - Re: [AMBER] strain/energy of backbone atoms Jio M (Fri Mar 21 2014 - 12:03:23 PDT)
[AMBER] RESTRAINT FILE Sourav Purohit (Wed Mar 19 2014 - 16:16:32 PDT)
- Re: [AMBER] RESTRAINT FILE Jason Swails (Wed Mar 19 2014 - 16:20:33 PDT)
  - Re: [AMBER] RESTRAINT FILE Sourav Purohit (Wed Mar 19 2014 - 16:28:09 PDT)
    - Re: [AMBER] RESTRAINT FILE Jason Swails (Wed Mar 19 2014 - 18:40:33 PDT)
    - Re: [AMBER] RESTRAINT FILE David A Case (Wed Mar 19 2014 - 18:54:03 PDT)
    - Re: [AMBER] RESTRAINT FILE Sourav Purohit (Thu Mar 20 2014 - 08:20:54 PDT)
[AMBER] problem in generating .prmtop and .inpcrd file using amber9 Vijayalaxmi Sahoo (Wed Mar 19 2014 - 20:08:47 PDT)
- Re: [AMBER] problem in generating .prmtop and .inpcrd file using amber9 Jason Swails (Thu Mar 20 2014 - 04:37:49 PDT)
- Re: [AMBER] problem in generating .prmtop and .inpcrd file using amber9 David A Case (Thu Mar 20 2014 - 04:45:59 PDT)
[AMBER] Compilation error on Ubuntu 13.10 Weinzierl, Robert O J (Thu Mar 20 2014 - 00:57:50 PDT)
- Re: [AMBER] Compilation error on Ubuntu 13.10 Ayesha Fatima (Thu Mar 20 2014 - 03:21:48 PDT)
- Re: [AMBER] Compilation error on Ubuntu 13.10 Jason Swails (Thu Mar 20 2014 - 04:47:39 PDT)
[AMBER] trajectory concatenation using cpptraj Neha Gandhi (Thu Mar 20 2014 - 01:32:12 PDT)
- Re: [AMBER] trajectory concatenation using cpptraj Jason Swails (Thu Mar 20 2014 - 04:52:48 PDT)
[AMBER] problem in generating .prmtop and .inpcrd file using amber9 Vijayalaxmi Sahoo (Thu Mar 20 2014 - 03:47:32 PDT)
[AMBER] protein-ligand tutorial Arunima Shilpi (Thu Mar 20 2014 - 04:15:18 PDT)
- Re: [AMBER] protein-ligand tutorial Jason Swails (Thu Mar 20 2014 - 04:44:50 PDT)
[AMBER] the combination ntb != 0, ntp != 0, ifbox == 0 is not supported! Saeed Nasiri (Thu Mar 20 2014 - 08:31:10 PDT)
- Re: [AMBER] the combination ntb != 0, ntp != 0, ifbox == 0 is not supported! Daniel Roe (Thu Mar 20 2014 - 08:43:55 PDT)
[AMBER] Lipid14 falling apart Ghulam Mustafa (Thu Mar 20 2014 - 08:50:28 PDT)
- Re: [AMBER] Lipid14 falling apart Benjamin Madej (Thu Mar 20 2014 - 11:13:05 PDT)
  - Re: [AMBER] Lipid14 falling apart filip fratev (Thu Mar 20 2014 - 11:38:46 PDT)
    - Re: [AMBER] Lipid14 falling apart Benjamin Madej (Thu Mar 20 2014 - 14:19:42 PDT)
    - Re: [AMBER] Lipid14 falling apart Dickson, Callum J (Thu Mar 20 2014 - 14:56:56 PDT)
    - Re: [AMBER] Lipid14 falling apart Ross Walker (Thu Mar 20 2014 - 15:02:20 PDT)
    - Re: [AMBER] Lipid14 falling apart filip fratev (Thu Mar 20 2014 - 15:29:24 PDT)
  - Re: [AMBER] Lipid14 falling apart Ghulam Mustafa (Fri Mar 21 2014 - 09:28:41 PDT)
[AMBER] Antechamber not converting HyperChem .hin files correctly CHRISTOPHER PATRICK MCNARY (Thu Mar 20 2014 - 10:50:56 PDT)
- Re: [AMBER] Antechamber not converting HyperChem .hin files correctly David A Case (Thu Mar 20 2014 - 11:25:40 PDT)
[AMBER] AMOEBA force field in amber Geoffrey Gray (Thu Mar 20 2014 - 11:50:21 PDT)
- Re: [AMBER] AMOEBA force field in amber Jason Swails (Thu Mar 20 2014 - 12:26:18 PDT)
  - Re: [AMBER] AMOEBA force field in amber Geoffrey Gray (Thu Mar 20 2014 - 14:52:20 PDT)
[AMBER] Cpptraj hbond bridgeout segmentation fault Juan.Aranda.uv.es (Thu Mar 20 2014 - 14:01:12 PDT)
- Re: [AMBER] Cpptraj hbond bridgeout segmentation fault Daniel Roe (Thu Mar 20 2014 - 15:30:36 PDT)
[AMBER] rescue amd.log psu4.uic.edu (Thu Mar 20 2014 - 16:49:41 PDT)
[AMBER] strip_mask syntax error George Tzotzos (Fri Mar 21 2014 - 07:35:05 PDT)
- Re: [AMBER] strip_mask syntax error Daniel Roe (Fri Mar 21 2014 - 07:56:58 PDT)
[AMBER] Cuda compilation problems with Ubuntu 13.10 Weinzierl, Robert O J (Fri Mar 21 2014 - 07:55:06 PDT)
- Re: [AMBER] Cuda compilation problems with Ubuntu 13.10 Daniel Roe (Fri Mar 21 2014 - 07:58:05 PDT)
[AMBER] Incomplete frcmod from parmchk Prema Mallipeddi (Fri Mar 21 2014 - 11:11:43 PDT)
- Re: [AMBER] Incomplete frcmod from parmchk David A Case (Fri Mar 21 2014 - 11:48:55 PDT)
[AMBER] Error: EOF when searching for tprmtop Nelson Max (Fri Mar 21 2014 - 17:32:04 PDT)
- Re: [AMBER] Error: EOF when searching for tprmtop Jason Swails (Fri Mar 21 2014 - 18:35:33 PDT)
  - Re: [AMBER] Error: EOF when searching for tprmtop Nelson Max (Fri Mar 21 2014 - 20:57:16 PDT)
    - Re: [AMBER] Error: EOF when searching for tprmtop Jason Swails (Fri Mar 21 2014 - 21:10:00 PDT)
[AMBER] cpptraj grid function Jio M (Sat Mar 22 2014 - 11:43:02 PDT)
- Re: [AMBER] cpptraj grid function Daniel Roe (Sat Mar 22 2014 - 15:01:12 PDT)
  - Re: [AMBER] cpptraj grid function Jio M (Sat Mar 22 2014 - 19:35:11 PDT)
    - Re: [AMBER] cpptraj grid function Daniel Roe (Mon Mar 24 2014 - 07:22:18 PDT)
    - Re: [AMBER] cpptraj grid function Jio M (Mon Mar 24 2014 - 14:06:11 PDT)
    - Re: [AMBER] cpptraj grid function Jio M (Tue Mar 25 2014 - 12:02:18 PDT)
    - Re: [AMBER] cpptraj grid function Daniel Roe (Tue Mar 25 2014 - 12:11:55 PDT)
    - Re: [AMBER] cpptraj grid function Jio M (Tue Mar 25 2014 - 13:11:11 PDT)
    - Re: [AMBER] cpptraj grid function Jio M (Wed Mar 26 2014 - 15:21:13 PDT)
    - Re: [AMBER] cpptraj grid function Jio M (Wed Mar 26 2014 - 19:04:43 PDT)
[AMBER] cpptraj h-bond: error George Tzotzos (Sat Mar 22 2014 - 13:13:00 PDT)
- [AMBER] ΑΠ: cpptraj h-bond: error Antonios Kolocouris (Sat Mar 22 2014 - 14:35:01 PDT)
- Re: [AMBER] cpptraj h-bond: error Daniel Roe (Sat Mar 22 2014 - 14:54:54 PDT)
[AMBER] delta G calculation in MMPBSA Arunima Shilpi (Sat Mar 22 2014 - 23:01:26 PDT)
- Re: [AMBER] delta G calculation in MMPBSA Sushil Mishra (Sun Mar 23 2014 - 00:52:50 PDT)
[AMBER] MMPBSA.py: decomposition error Kshatresh Dutta Dubey (Sun Mar 23 2014 - 10:57:46 PDT)
- Re: [AMBER] MMPBSA.py: decomposition error Kshatresh Dutta Dubey (Sun Mar 23 2014 - 13:43:36 PDT)
[AMBER] aMD error for the coordinates file maryam azimzadehirani (Sun Mar 23 2014 - 19:24:23 PDT)
- Re: [AMBER] aMD error for the coordinates file Jason Swails (Sun Mar 23 2014 - 19:34:52 PDT)
[AMBER] Problem with Decomposition of Binding Free Energy loue chen (Sun Mar 23 2014 - 20:31:25 PDT)
- Re: [AMBER] Problem with Decomposition of Binding Free Energy Jason Swails (Mon Mar 24 2014 - 04:59:13 PDT)
  - [AMBER] error during installation of AMBERtools13 Urszula Uciechowska (Mon Mar 24 2014 - 06:35:31 PDT)
    - Re: [AMBER] error during installation of AMBERtools13 Jason Swails (Mon Mar 24 2014 - 06:43:51 PDT)
    - [AMBER] igb=1 Urszula Uciechowska (Tue Mar 25 2014 - 03:11:42 PDT)
    - Re: [AMBER] igb=1 David A Case (Tue Mar 25 2014 - 04:56:09 PDT)
    - [AMBER] ibelly Urszula Uciechowska (Tue Mar 25 2014 - 06:13:06 PDT)
    - Re: [AMBER] ibelly Gerald Monard (Tue Mar 25 2014 - 06:27:20 PDT)
    - Re: [AMBER] ibelly Urszula Uciechowska (Tue Mar 25 2014 - 06:39:14 PDT)
    - Re: [AMBER] ibelly Jason Swails (Tue Mar 25 2014 - 06:54:37 PDT)
    - Re: [AMBER] ibelly David A Case (Tue Mar 25 2014 - 06:41:46 PDT)
    - Re: [AMBER] ibelly Urszula Uciechowska (Tue Mar 25 2014 - 07:16:15 PDT)
    - Re: [AMBER] ibelly Gerald Monard (Tue Mar 25 2014 - 08:17:33 PDT)
    - Re: [AMBER] ibelly David A Case (Tue Mar 25 2014 - 08:19:04 PDT)
    - Re: [AMBER] ibelly Jason Swails (Tue Mar 25 2014 - 07:36:45 PDT)
    - Re: [AMBER] ibelly Daniel Roe (Tue Mar 25 2014 - 07:31:18 PDT)
    - [AMBER] error in input file /nmropt=1 Urszula Uciechowska (Wed Apr 09 2014 - 01:22:57 PDT)
    - Re: [AMBER] error in input file /nmropt=1 Asaminew Haile (Wed Apr 09 2014 - 03:46:27 PDT)
[AMBER] Positive value of delta G Arunima Shilpi (Sun Mar 23 2014 - 20:58:51 PDT)
- Re: [AMBER] Positive value of delta G Jason Swails (Mon Mar 24 2014 - 05:15:14 PDT)
  - Re: [AMBER] Positive value of delta G George Tzotzos (Mon Mar 24 2014 - 08:24:52 PDT)
    - Re: [AMBER] Positive value of delta G Jason Swails (Mon Mar 24 2014 - 08:41:53 PDT)
    - Re: [AMBER] Positive value of delta G Vlad Cojocaru (Mon Mar 24 2014 - 08:52:02 PDT)
    - Re: [AMBER] Positive value of delta G Ray Luo, Ph.D. (Mon Mar 24 2014 - 12:31:08 PDT)
[AMBER] Open Source Drug Design and In Silico Molecules Pledge to AMBER developers Soumendranath Bhakat (Mon Mar 24 2014 - 06:35:19 PDT)
- Re: [AMBER] Open Source Drug Design and In Silico Molecules Pledge to AMBER developers Carlos Simmerling (Mon Mar 24 2014 - 06:53:19 PDT)
- Re: [AMBER] Open Source Drug Design and In Silico Molecules Pledge to AMBER developers David A Case (Mon Mar 24 2014 - 13:23:30 PDT)
[AMBER] Generalized Born subroutines Debayan Chakraborty (Mon Mar 24 2014 - 06:41:19 PDT)
- Re: [AMBER] Generalized Born subroutines Jason Swails (Mon Mar 24 2014 - 06:56:15 PDT)
  - Re: [AMBER] Generalized Born subroutines Debayan Chakraborty (Mon Mar 24 2014 - 07:15:02 PDT)
    - Re: [AMBER] Generalized Born subroutines Robert McGibbon (Tue Mar 25 2014 - 04:12:24 PDT)
[AMBER] Adenine parameters and topology files Valentina Romano (Mon Mar 24 2014 - 08:20:29 PDT)
- Re: [AMBER] Adenine parameters and topology files FyD (Mon Mar 24 2014 - 13:19:51 PDT)
  - Re: [AMBER] Adenine parameters and topology files Valentina Romano (Tue Mar 25 2014 - 03:09:05 PDT)
[AMBER] QM/MM John Smith (Mon Mar 24 2014 - 09:17:32 PDT)
- RE: [AMBER] QM/MM Syed Tarique Moin (Mon May 04 2009 - 15:13:22 PDT)
  - RE: [AMBER] QM/MM Ross Walker (Tue May 05 2009 - 15:16:26 PDT)
    - RE: [AMBER] QM/MM Catein Catherine (Tue May 05 2009 - 19:48:44 PDT)
    - [AMBER] Error message in "make test.sander" Catein Catherine (Tue May 05 2009 - 19:52:26 PDT)
    - RE: [AMBER] Error message in "make test.sander" Ross Walker (Tue May 05 2009 - 20:37:28 PDT)
    - RE: [AMBER] Error message in "make test.sander" Catein Catherine (Tue May 05 2009 - 22:40:54 PDT)
    - RE: [AMBER] Error message in "make test.sander" Ross Walker (Tue May 05 2009 - 23:28:01 PDT)
    - RE: [AMBER] Error message in "make test.sander" Catein Catherine (Tue May 05 2009 - 23:58:04 PDT)
    - [AMBER] Error message in "make test.sander" Is amber compatible with dual processors? Catein Catherine (Wed May 06 2009 - 06:08:49 PDT)
- RE: [AMBER] QM/MM Syed Tarique Moin (Wed May 06 2009 - 00:11:54 PDT)
- RE: [AMBER] QM/MM Syed Tarique Moin (Wed May 06 2009 - 00:12:17 PDT)
- Re: [AMBER] QM/MM Yeng-Tseng Wang (Mon Mar 24 2014 - 09:19:47 PDT)
- Re: [AMBER] QM/MM Asaminew Haile (Mon Mar 24 2014 - 09:25:01 PDT)
- Re: [AMBER] QM/MM Jason Swails (Mon Mar 24 2014 - 09:35:58 PDT)
  - Re: [AMBER] QM/MM Brian Radak (Mon Mar 24 2014 - 09:46:33 PDT)
    - Re: [AMBER] QM/MM John Smith (Mon Mar 24 2014 - 10:18:27 PDT)
[AMBER] Adenine without ribose ring and/or phosphate groups Valentina Romano (Mon Mar 24 2014 - 09:46:20 PDT)
[AMBER] using chamber with vmd-generated psf (after reformatting to extended format) Pete Kekenes-Huskey (Mon Mar 24 2014 - 11:42:18 PDT)
[AMBER] libgfortran.2.dylib Fabian Glaser (Tue Mar 25 2014 - 00:54:05 PDT)
- Re: [AMBER] libgfortran.2.dylib Jason Swails (Tue Mar 25 2014 - 05:16:51 PDT)
[AMBER] Generating frc and prep files DEBOSTUTI GHOSHDASTIDAR (Tue Mar 25 2014 - 07:38:52 PDT)
- Re: [AMBER] Generating frc and prep files Yeng-Tseng Wang (Tue Mar 25 2014 - 09:27:15 PDT)
- Re: [AMBER] Generating frc and prep files Jason Swails (Tue Mar 25 2014 - 10:22:50 PDT)
- Re: [AMBER] Generating frc and prep files FyD (Wed Mar 26 2014 - 00:24:56 PDT)
  - Re: [AMBER] Generating frc and prep files Jason Swails (Wed Mar 26 2014 - 03:00:44 PDT)
    - Re: [AMBER] Generating frc and prep files FyD (Wed Mar 26 2014 - 05:16:44 PDT)
    - Re: [AMBER] Generating frc and prep files DEBOSTUTI GHOSHDASTIDAR (Mon Mar 31 2014 - 06:56:52 PDT)
    - Re: [AMBER] Generating frc and prep files Jason Swails (Mon Mar 31 2014 - 07:20:42 PDT)
[AMBER] Problem in configuring the amber Akashdeep Biswas (Tue Mar 25 2014 - 23:55:59 PDT)
- Re: [AMBER] Problem in configuring the amber Jason Swails (Wed Mar 26 2014 - 02:55:21 PDT)
[AMBER] How to update cpptraj and setting donor/acceptormask Setyanto Md (Wed Mar 26 2014 - 01:34:38 PDT)
- Re: [AMBER] How to update cpptraj and setting donor/acceptormask Daniel Roe (Wed Mar 26 2014 - 07:40:58 PDT)
  - Re: [AMBER] How to update cpptraj and setting donor/acceptormask Setyanto Md (Tue Apr 01 2014 - 20:03:00 PDT)
[AMBER] Fwd: MMGBSA of protein DNA complex Aditya Sarkar (Wed Mar 26 2014 - 03:40:01 PDT)
- Re: [AMBER] Fwd: MMGBSA of protein DNA complex Carlos Simmerling (Wed Mar 26 2014 - 05:32:12 PDT)
- [AMBER] Distance constraints Urszula Uciechowska (Wed Apr 02 2014 - 06:33:23 PDT)
  - Re: [AMBER] Distance constraints Jason Swails (Wed Apr 02 2014 - 06:45:17 PDT)
  - Re: [AMBER] Distance constraints Sajeewa Pemasinghe (Wed Apr 02 2014 - 06:53:53 PDT)
    - Re: [AMBER] Distance constraints Sajeewa Pemasinghe (Wed Apr 02 2014 - 07:40:01 PDT)
    - [AMBER] igb=1 Urszula Uciechowska (Fri Apr 04 2014 - 03:47:39 PDT)
    - Re: [AMBER] igb=1 Jason Swails (Fri Apr 04 2014 - 04:30:08 PDT)
    - Re: [AMBER] igb=1 Carlos Simmerling (Fri Apr 04 2014 - 04:40:38 PDT)
    - [AMBER] error in input file /nmropt=1 Urszula Uciechowska (Tue Apr 08 2014 - 05:57:58 PDT)
    - Re: [AMBER] error in input file /nmropt=1 Asaminew Haile (Tue Apr 08 2014 - 06:03:31 PDT)
    - Re: [AMBER] error in input file /nmropt=1 with dist.RST Urszula Uciechowska (Tue Apr 08 2014 - 06:12:56 PDT)
    - Re: [AMBER] error in input file /nmropt=1 with dist.RST Urszula Uciechowska (Tue Apr 08 2014 - 06:31:41 PDT)
    - Re: [AMBER] error in input file /nmropt=1 Brian Radak (Tue Apr 08 2014 - 06:49:49 PDT)
    - Re: [AMBER] error in input file /nmropt=1 David A Case (Tue Apr 08 2014 - 09:02:30 PDT)
    - Re: [AMBER] error in input file /nmropt=1 Urszula Uciechowska (Wed Apr 09 2014 - 00:22:03 PDT)
[AMBER] combining trajectories with diff. number of residues for same protein Nitin Sharma (Wed Mar 26 2014 - 06:29:37 PDT)
- Re: [AMBER] combining trajectories with diff. number of residues for same protein Jason Swails (Wed Mar 26 2014 - 07:27:01 PDT)
  - Re: [AMBER] combining trajectories with diff. number of residues for same protein Nitin Sharma (Wed Mar 26 2014 - 10:42:35 PDT)
    - Re: [AMBER] combining trajectories with diff. number of residues for same protein Jason Swails (Wed Mar 26 2014 - 11:18:10 PDT)
    - Re: [AMBER] combining trajectories with diff. number of residues for same protein Nitin Sharma (Wed Mar 26 2014 - 12:38:38 PDT)
    - Re: [AMBER] combining trajectories with diff. number of residues for same protein Daniel Roe (Wed Mar 26 2014 - 13:15:31 PDT)
    - Re: [AMBER] combining trajectories with diff. number of residues for same protein Nitin Sharma (Thu Mar 27 2014 - 00:57:11 PDT)
    - Re: [AMBER] combining trajectories with diff. number of residues for same protein Nitin Sharma (Thu Mar 27 2014 - 20:13:57 PDT)
[AMBER] running amber on multigpu Neha Gandhi (Wed Mar 26 2014 - 07:17:52 PDT)
[AMBER] setangle in parmed API hannes.loeffler.stfc.ac.uk (Wed Mar 26 2014 - 08:01:11 PDT)
- Re: [AMBER] setangle in parmed API Jason Swails (Wed Mar 26 2014 - 09:00:34 PDT)
  - Re: [AMBER] setangle in parmed API hannes.loeffler.stfc.ac.uk (Wed Mar 26 2014 - 09:24:47 PDT)
    - Re: [AMBER] setangle in parmed API Jason Swails (Wed Mar 26 2014 - 10:19:23 PDT)
[AMBER] Possible bug in xleap Ilias Patmanidis (Wed Mar 26 2014 - 08:10:11 PDT)
- Re: [AMBER] Possible bug in xleap Daniel Roe (Wed Mar 26 2014 - 08:16:07 PDT)
  - Re: [AMBER] Possible bug in xleap Ilias Patmanidis (Wed Mar 26 2014 - 08:49:36 PDT)
- Re: [AMBER] Possible bug in xleap David A Case (Wed Mar 26 2014 - 10:33:18 PDT)
  - Re: [AMBER] Possible bug in xleap Ilias Patmanidis (Thu Mar 27 2014 - 03:54:25 PDT)
- Re: [AMBER] Possible bug in xleap Bill Ross (Tue Apr 01 2014 - 16:44:23 PDT)
[AMBER] Regarding SPC/E water model MOHD HOMAIDUR RAHMAN (Wed Mar 26 2014 - 11:07:01 PDT)
- Re: [AMBER] Regarding SPC/E water model David A Case (Wed Mar 26 2014 - 12:46:25 PDT)
  - Re: [AMBER] Regarding SPC/E water model MOHD HOMAIDUR RAHMAN (Wed Mar 26 2014 - 22:27:31 PDT)
    - Re: [AMBER] Regarding SPC/E water model David A Case (Thu Mar 27 2014 - 06:16:13 PDT)
    - Re: [AMBER] Regarding SPC/E water model MOHD HOMAIDUR RAHMAN (Thu Mar 27 2014 - 11:35:45 PDT)
[AMBER] why the 1-4 electric and vdw scaling factor are 0.0 in my .prmtop file? Dongshan Wei (Wed Mar 26 2014 - 20:04:58 PDT)
- Re: [AMBER] why the 1-4 electric and vdw scaling factor are 0.0 in my .prmtop file? Dongshan Wei (Thu Mar 27 2014 - 02:06:35 PDT)
  - Re: [AMBER] why the 1-4 electric and vdw scaling factor are 0.0 in my .prmtop file? Hannes Loeffler (Thu Mar 27 2014 - 02:24:49 PDT)
    - Re: [AMBER] why the 1-4 electric and vdw scaling factor are 0.0 in my .prmtop file? Dongshan Wei (Thu Mar 27 2014 - 03:01:07 PDT)
    - Re: [AMBER] why the 1-4 electric and vdw scaling factor are 0.0 in my .prmtop file? Dongshan Wei (Thu Mar 27 2014 - 03:05:56 PDT)
    - Re: [AMBER] why the 1-4 electric and vdw scaling factor are 0.0 in my .prmtop file? Hannes Loeffler (Thu Mar 27 2014 - 03:29:57 PDT)
    - Re: [AMBER] why the 1-4 electric and vdw scaling factor are 0.0 in my .prmtop file? Jason Swails (Thu Mar 27 2014 - 03:04:34 PDT)
- Re: [AMBER] why the 1-4 electric and vdw scaling factor are 0.0 in my .prmtop file? Jason Swails (Thu Mar 27 2014 - 03:12:03 PDT)
[AMBER] error in running density coomand Arunima Shilpi (Wed Mar 26 2014 - 23:33:11 PDT)
- Re: [AMBER] error in running density coomand Daniel Roe (Thu Mar 27 2014 - 07:57:07 PDT)
[AMBER] antechamber for two ligands Fabian Glaser (Thu Mar 27 2014 - 05:40:15 PDT)
- Re: [AMBER] antechamber for two ligands David A Case (Thu Mar 27 2014 - 06:19:28 PDT)
  - Re: [AMBER] antechamber for two ligands Fabian Glaser (Thu Mar 27 2014 - 06:22:31 PDT)
    - Re: [AMBER] antechamber for two ligands David A Case (Thu Mar 27 2014 - 06:35:39 PDT)
    - Re: [AMBER] antechamber for two ligands Jason Swails (Thu Mar 27 2014 - 06:37:40 PDT)
    - Re: [AMBER] antechamber for two ligands Aldo Segura (Thu Mar 27 2014 - 06:40:23 PDT)
    - Re: [AMBER] antechamber for two ligands Fabian Glaser (Thu Mar 27 2014 - 07:50:12 PDT)
    - Re: [AMBER] antechamber for two ligands Jason Swails (Thu Mar 27 2014 - 08:22:26 PDT)
    - Re: [AMBER] antechamber for two ligands Fabian Glaser (Sun Mar 30 2014 - 03:49:37 PDT)
    - Re: [AMBER] antechamber for two ligands Jonathan Sheehan (Sun Mar 30 2014 - 07:03:06 PDT)
- Re: [AMBER] antechamber for two ligands FyD (Sun Mar 30 2014 - 10:11:59 PDT)
[AMBER] Problem with REMD simulation Gargi Borgohai (Thu Mar 27 2014 - 08:03:15 PDT)
- Re: [AMBER] Problem with REMD simulation Jason Swails (Thu Mar 27 2014 - 08:14:43 PDT)
  - Re: [AMBER] Problem with REMD simulation Carlos Simmerling (Thu Mar 27 2014 - 09:08:23 PDT)
[AMBER] repulsive restraints Thomas Evangelidis (Thu Mar 27 2014 - 08:34:12 PDT)
- Re: [AMBER] repulsive restraints Carlos Simmerling (Thu Mar 27 2014 - 09:03:34 PDT)
  - Re: [AMBER] repulsive restraints Brian Radak (Thu Mar 27 2014 - 09:43:53 PDT)
[AMBER] How is ZN treated in AMBER14 R R S Pissurlenkar (Thu Mar 27 2014 - 08:46:17 PDT)
- Re: [AMBER] How is ZN treated in AMBER14 Jason Swails (Thu Mar 27 2014 - 09:16:55 PDT)
  - Re: [AMBER] How is ZN treated in AMBER14 Pengfei Li (Thu Mar 27 2014 - 15:43:41 PDT)
[AMBER] non-protonated and protonated phosphate Thomas Exner (Thu Mar 27 2014 - 08:47:14 PDT)
- Re: [AMBER] non-protonated and protonated phosphate David A Case (Thu Mar 27 2014 - 09:26:25 PDT)
- Re: [AMBER] non-protonated and protonated phosphate FyD (Sat Mar 29 2014 - 00:20:38 PDT)
[AMBER] data overflow in dx output from rism3d Brian Radak (Thu Mar 27 2014 - 14:02:03 PDT)
- Re: [AMBER] data overflow in dx output from rism3d wmsmith.uci.edu (Thu Mar 27 2014 - 23:31:39 PDT)
  - Re: [AMBER] data overflow in dx output from rism3d wmsmith.uci.edu (Thu Mar 27 2014 - 23:40:30 PDT)
[AMBER] small box changes still fail with 'Nonbond cells need to be recalculated' Pete Kekenes-Huskey (Thu Mar 27 2014 - 21:46:34 PDT)
[AMBER] MMPBSA calculation with entropy Arun Kumar Somavarapu (Thu Mar 27 2014 - 22:02:02 PDT)
- Re: [AMBER] MMPBSA calculation with entropy Jason Swails (Fri Mar 28 2014 - 04:14:19 PDT)
  - Re: [AMBER] MMPBSA calculation with entropy Arun Kumar Somavarapu (Wed Apr 02 2014 - 02:11:07 PDT)
    - Re: [AMBER] MMPBSA calculation with entropy Jason Swails (Wed Apr 02 2014 - 04:44:43 PDT)
[AMBER] Replica exchange restart file Mele N. (Fri Mar 28 2014 - 05:15:17 PDT)
- Re: [AMBER] Replica exchange restart file Jason Swails (Fri Mar 28 2014 - 05:48:14 PDT)
  - Re: [AMBER] Replica exchange restart file Mele N. (Fri Mar 28 2014 - 06:20:05 PDT)
    - Re: [AMBER] Replica exchange restart file Daniel Roe (Fri Mar 28 2014 - 07:48:21 PDT)
    - Re: [AMBER] Replica exchange restart file Jason Swails (Fri Mar 28 2014 - 07:53:02 PDT)
[AMBER] anybody knows how Langevin dynamics affects time-correlation functions? Jose Borreguero (Fri Mar 28 2014 - 12:27:41 PDT)
[AMBER] cpptraj hbond analysis cutoff angle DEBOSTUTI GHOSHDASTIDAR (Fri Mar 28 2014 - 22:37:22 PDT)
- Re: [AMBER] cpptraj hbond analysis cutoff angle Daniel Roe (Sat Mar 29 2014 - 12:06:18 PDT)
[AMBER] Problem regarding running job in AMBER 12 Souvik Sur (Sat Mar 29 2014 - 04:16:29 PDT)
- Re: [AMBER] Problem regarding running job in AMBER 12 Jason Swails (Sat Mar 29 2014 - 10:23:26 PDT)
[AMBER] restart MD from arbitrary snapshot Milo Westler (Sun Mar 30 2014 - 13:29:35 PDT)
- Re: [AMBER] restart MD from arbitrary snapshot Daniel Roe (Sun Mar 30 2014 - 13:42:17 PDT)
  - Re: [AMBER] restart MD from arbitrary snapshot Milo Westler (Sun Mar 30 2014 - 16:27:14 PDT)
    - Re: [AMBER] restart MD from arbitrary snapshot Daniel Roe (Sun Mar 30 2014 - 19:30:25 PDT)
    - Re: [AMBER] restart MD from arbitrary snapshot Milo Westler (Mon Mar 31 2014 - 05:59:56 PDT)
[AMBER] GPU not being recognised Ayesha Fatima (Mon Mar 31 2014 - 03:38:58 PDT)
- Re: [AMBER] GPU not being recognised David A Case (Mon Mar 31 2014 - 04:39:15 PDT)
  - Re: [AMBER] GPU not being recognised Tru Huynh (Mon Mar 31 2014 - 09:26:32 PDT)
- Re: [AMBER] GPU not being recognised Ross Walker (Mon Mar 31 2014 - 09:37:16 PDT)
  - Re: [AMBER] GPU not being recognised Ayesha Fatima (Mon Mar 31 2014 - 09:52:05 PDT)
- Re: [AMBER] GPU not being recognised Jan-Philip Gehrcke (Mon Mar 31 2014 - 12:11:25 PDT)
[AMBER] central atom always 3rd in improper Hannes Loeffler (Mon Mar 31 2014 - 07:45:21 PDT)
- Re: [AMBER] central atom always 3rd in improper Jason Swails (Mon Mar 31 2014 - 08:40:06 PDT)
[AMBER] AMBER on GTX-Titan Black Ross Walker (Mon Mar 31 2014 - 09:51:09 PDT)
[AMBER] SHAWKTRAJ, a new trajectory analysis tool Jason Swails (Tue Apr 01 2014 - 04:03:25 PDT)
- Re: [AMBER] SHAWKTRAJ, a new trajectory analysis tool Fabian Glaser (Tue Apr 01 2014 - 04:20:10 PDT)
- Re: [AMBER] SHAWKTRAJ, a new trajectory analysis tool Adrian Roitberg (Tue Apr 01 2014 - 07:02:55 PDT)
  - Re: [AMBER] SHAWKTRAJ, a new trajectory analysis tool Marcus Arieno (Tue Apr 01 2014 - 08:52:54 PDT)
    - Re: [AMBER] SHAWKTRAJ, a new trajectory analysis tool MOHD HOMAIDUR RAHMAN (Tue Apr 01 2014 - 10:04:29 PDT)
    - Re: [AMBER] SHAWKTRAJ, a new trajectory analysis tool Jason Swails (Tue Apr 01 2014 - 10:30:23 PDT)
    - Re: [AMBER] SHAWKTRAJ, a new trajectory analysis tool Bill Ross (Tue Apr 01 2014 - 18:04:43 PDT)
    - Re: [AMBER] SHAWKTRAJ, a new trajectory analysis tool Pengfei Li (Tue Apr 01 2014 - 20:13:53 PDT)
[AMBER] WHAM Analysis Histograms amr hamed (Tue Apr 01 2014 - 21:33:50 PDT)
- Re: [AMBER] WHAM Analysis Histograms Hamed S. Hayatshahi (Wed Apr 02 2014 - 21:28:41 PDT)
[AMBER] loading multiple prepin file in xleap - gives warning Vijay Manickam Achari (Wed Apr 02 2014 - 02:57:31 PDT)
- Re: [AMBER] loading multiple prepin file in xleap - gives warning Jason Swails (Wed Apr 02 2014 - 04:50:56 PDT)
- [AMBER] Fw: loading multiple prepin file in xleap - gives warning Vijay Manickam Achari (Wed Apr 02 2014 - 23:20:16 PDT)
  - Re: [AMBER] Fw: loading multiple prepin file in xleap - gives warning Jason Swails (Thu Apr 03 2014 - 04:29:14 PDT)
    - Re: [AMBER] Fw: loading multiple prepin file in xleap - gives warning Vijay Manickam Achari (Thu Apr 03 2014 - 21:16:11 PDT)
  - Re: [AMBER] Fw: loading multiple prepin file in xleap - gives warning David A Case (Thu Apr 03 2014 - 04:45:20 PDT)
[AMBER] truncatiing water molecules Nitin Sharma (Wed Apr 02 2014 - 04:36:27 PDT)
- Re: [AMBER] truncatiing water molecules Jason Swails (Wed Apr 02 2014 - 04:54:15 PDT)
  - Re: [AMBER] truncatiing water molecules Nitin Sharma (Wed Apr 02 2014 - 06:03:13 PDT)
    - Re: [AMBER] truncatiing water molecules Jason Swails (Wed Apr 02 2014 - 06:52:13 PDT)
    - Re: [AMBER] truncatiing water molecules Nitin Sharma (Wed Apr 02 2014 - 07:57:12 PDT)
    - Re: [AMBER] truncatiing water molecules Jason Swails (Wed Apr 02 2014 - 08:21:39 PDT)
    - Re: [AMBER] truncatiing water molecules Nitin Sharma (Wed Apr 02 2014 - 08:38:48 PDT)
    - Re: [AMBER] truncatiing water molecules Bill Ross (Mon Apr 21 2014 - 21:13:08 PDT)
[AMBER] Normal mode for truncated system Ahmed Ayoub (Wed Apr 02 2014 - 11:45:19 PDT)
[AMBER] coordinates for replicating truncated octahedron Jio M (Wed Apr 02 2014 - 13:51:45 PDT)
[AMBER] Asking about using Vector Analysis: Thermo Setyanto Md (Wed Apr 02 2014 - 20:10:26 PDT)
- Re: [AMBER] Asking about using Vector Analysis: Thermo David A Case (Thu Apr 03 2014 - 04:41:13 PDT)
- Re: [AMBER] Asking about using Vector Analysis: Thermo Daniel Roe (Thu Apr 03 2014 - 07:31:21 PDT)
  - Re: [AMBER] Asking about using Vector Analysis: Thermo Setyanto Md (Tue Apr 08 2014 - 07:38:49 PDT)
    - Re: [AMBER] Asking about using Vector Analysis: Thermo David A Case (Tue Apr 08 2014 - 09:08:44 PDT)
    - Re: [AMBER] Asking about using Vector Analysis: Thermo Setyanto Md (Fri Apr 11 2014 - 02:13:14 PDT)
[AMBER] Asking about using Vector Analysis: Thermo Setyanto Md (Wed Apr 02 2014 - 22:35:44 PDT)
[AMBER] antechamber Lara rajam (Thu Apr 03 2014 - 08:29:13 PDT)
- Re: [AMBER] antechamber David A Case (Thu Apr 03 2014 - 09:26:56 PDT)
  - Re: [AMBER] antechamber Lara rajam (Mon Apr 07 2014 - 10:08:13 PDT)
    - Re: [AMBER] antechamber David A Case (Mon Apr 07 2014 - 12:12:13 PDT)
    - Re: [AMBER] antechamber Lara rajam (Mon Apr 07 2014 - 13:24:34 PDT)
    - Re: [AMBER] antechamber Jason Swails (Mon Apr 07 2014 - 15:00:15 PDT)
    - Re: [AMBER] antechamber Lara rajam (Tue Apr 08 2014 - 07:57:40 PDT)
[AMBER] antechamber_error Lara rajam (Thu Apr 03 2014 - 08:38:19 PDT)
[AMBER] leap error sammia khatak (Thu Apr 03 2014 - 08:49:09 PDT)
- Re: [AMBER] leap error Jason Swails (Thu Apr 03 2014 - 08:57:22 PDT)
  - Re: [AMBER] leap error sammia khatak (Thu Apr 03 2014 - 09:02:29 PDT)
    - Re: [AMBER] leap error Daniel Roe (Thu Apr 03 2014 - 09:06:06 PDT)
    - Re: [AMBER] leap error sammia khatak (Thu Apr 03 2014 - 10:18:17 PDT)
    - Re: [AMBER] leap error sammia khatak (Thu Apr 03 2014 - 21:40:39 PDT)
    - Re: [AMBER] leap error Jason Swails (Fri Apr 04 2014 - 04:59:08 PDT)
- Re: [AMBER] leap error Daniel Roe (Thu Apr 03 2014 - 08:58:42 PDT)
[AMBER] pmemd.cuda.mpi installation Cenk $Jenk$ Andac (Thu Apr 03 2014 - 09:03:27 PDT)
[AMBER] pmemd.cuda.mpi installation Cenk $Jenk$ Andac (Thu Apr 03 2014 - 09:29:01 PDT)
- [AMBER] pmemd.cuda.mpi installation Cenk $Jenk$ Andac (Thu Apr 03 2014 - 10:28:34 PDT)
  - Re: [AMBER] pmemd.cuda.mpi installation Jason Swails (Thu Apr 03 2014 - 11:05:24 PDT)
    - Re: [AMBER] pmemd.cuda.mpi installation Cenk $Jenk$ Andac (Thu Apr 03 2014 - 11:47:33 PDT)
    - Re: [AMBER] pmemd.cuda.mpi installation Jason Swails (Thu Apr 03 2014 - 12:03:50 PDT)
    - Re: [AMBER] pmemd.cuda.mpi installation Cenk $Jenk$ Andac (Sun Apr 06 2014 - 10:47:04 PDT)
    - Re: [AMBER] pmemd.cuda.mpi installation David A Case (Sun Apr 06 2014 - 10:55:19 PDT)
[AMBER] Parameters for Ca+2 ion for the decomposition analysis Manikanthan Bhavaraju (Thu Apr 03 2014 - 12:22:01 PDT)
- [AMBER] Fwd: Parameters for Ca+2 ion for the decomposition analysis Manikanthan Bhavaraju (Thu Apr 03 2014 - 12:55:46 PDT)
[AMBER] distance in one plane Jio M (Thu Apr 03 2014 - 12:35:37 PDT)
- Re: [AMBER] distance in one plane Daniel Roe (Thu Apr 03 2014 - 13:08:51 PDT)
  - Re: [AMBER] distance in one plane Jio M (Thu Apr 03 2014 - 13:33:36 PDT)
[AMBER] Error: Could not parse mask [(:1]: radial calculation Jio M (Thu Apr 03 2014 - 14:57:31 PDT)
- Re: [AMBER] Error: Could not parse mask [(:1]: radial calculation Jason Swails (Thu Apr 03 2014 - 15:27:42 PDT)
  - Re: [AMBER] Error: Could not parse mask [(:1]: radial calculation Daniel Roe (Thu Apr 03 2014 - 15:48:11 PDT)
    - Re: [AMBER] Error: Could not parse mask [(:1]: radial calculation Jio M (Thu Apr 03 2014 - 17:44:15 PDT)
[AMBER] query regarding simulation! Pallavi Mohanty (Thu Apr 03 2014 - 23:40:49 PDT)
[AMBER] Query regrading simulation Pallavi Mohanty (Fri Apr 04 2014 - 00:00:27 PDT)
[AMBER] Regarding Interaction energy calculation MOHD HOMAIDUR RAHMAN (Fri Apr 04 2014 - 01:57:49 PDT)
- Re: [AMBER] Regarding Interaction energy calculation Jason Swails (Thu Apr 17 2014 - 07:14:12 PDT)
[AMBER] Query regrading simulation Pallavi Mohanty (Fri Apr 04 2014 - 02:02:20 PDT)
[AMBER] Error using MMPBSA.py Souvik Sur (Fri Apr 04 2014 - 03:00:04 PDT)
- Re: [AMBER] Error using MMPBSA.py Jason Swails (Fri Apr 04 2014 - 04:35:01 PDT)
[AMBER] new error sammia khatak (Fri Apr 04 2014 - 05:21:33 PDT)
- Re: [AMBER] new error Jason Swails (Fri Apr 04 2014 - 05:53:45 PDT)
  - Re: [AMBER] new error sammia khatak (Fri Apr 04 2014 - 06:26:17 PDT)
    - Re: [AMBER] new error de Waal, Parker (Fri Apr 04 2014 - 06:28:41 PDT)
- Re: [AMBER] new error de Waal, Parker (Fri Apr 04 2014 - 05:58:39 PDT)
[AMBER] Bad atom type: C0 Manikanthan Bhavaraju (Fri Apr 04 2014 - 07:32:21 PDT)
- [AMBER] Fwd: Bad atom type: C0 manikanthan bhavaraju (Fri Apr 04 2014 - 07:52:23 PDT)
- [AMBER] Fwd: Bad atom type: C0 Manikanthan Bhavaraju (Fri Apr 04 2014 - 08:27:43 PDT)
[AMBER] Inconsistent results of MMPBSA.py with option inp=1 and inp=2 tong (Fri Apr 04 2014 - 07:57:04 PDT)
- Re: [AMBER] Inconsistent results of MMPBSA.py with option inp=1 and inp=2 Ray Luo, Ph.D. (Fri Apr 04 2014 - 09:29:49 PDT)
[AMBER] Bad atom type: C0 Mani Bhavaraju (Fri Apr 04 2014 - 09:04:54 PDT)
- Re: [AMBER] Bad atom type: C0 Jason Swails (Fri Apr 04 2014 - 10:25:59 PDT)
- Re: [AMBER] Bad atom type: C0 Bill Ross (Fri Apr 04 2014 - 12:00:29 PDT)
  - Re: [AMBER] Bad atom type: C0 Manikanthan Bhavaraju (Fri Apr 04 2014 - 14:55:45 PDT)
    - Re: [AMBER] Bad atom type: C0 Jason Swails (Fri Apr 04 2014 - 16:25:54 PDT)
    - Re: [AMBER] Bad atom type: C0 Jason Swails (Fri Apr 04 2014 - 16:26:31 PDT)
[AMBER] Why do I get an error in antechamber when a metal is involved? CHRISTOPHER PATRICK MCNARY (Fri Apr 04 2014 - 12:01:43 PDT)
- Re: [AMBER] Why do I get an error in antechamber when a metal is involved? David A Case (Fri Apr 04 2014 - 12:56:00 PDT)
[AMBER] Why do I get an error in antechamber when a metal is involved? CHRISTOPHER PATRICK MCNARY (Fri Apr 04 2014 - 12:24:10 PDT)
[AMBER] Principal component analysis Ibrahim Said (Fri Apr 04 2014 - 13:19:45 PDT)
- Re: [AMBER] Principal component analysis Soumendranath Bhakat (Sat Apr 05 2014 - 03:30:40 PDT)
  - Re: [AMBER] Principal component analysis Daniel Roe (Sat Apr 05 2014 - 08:02:07 PDT)
[AMBER] Regarding Interaction energy calculation MOHD HOMAIDUR RAHMAN (Fri Apr 04 2014 - 21:05:35 PDT)
- Re: [AMBER] Regarding Interaction energy calculation Jason Swails (Sun Apr 06 2014 - 06:38:36 PDT)
  - Re: [AMBER] Regarding Interaction energy calculation MOHD HOMAIDUR RAHMAN (Wed Apr 16 2014 - 05:16:20 PDT)
    - Re: [AMBER] Regarding Interaction energy calculation Jason Swails (Wed Apr 16 2014 - 05:42:31 PDT)
[AMBER] Ligand-residue interaction plot Arunima Shilpi (Sat Apr 05 2014 - 00:08:37 PDT)
- Re: [AMBER] Ligand-residue interaction plot Soumendranath Bhakat (Sat Apr 05 2014 - 03:27:53 PDT)
[AMBER] Ligand-residue interaction plot Arunima Shilpi (Sat Apr 05 2014 - 04:39:54 PDT)
- Re: [AMBER] Ligand-residue interaction plot Jason Swails (Sat Apr 05 2014 - 05:39:31 PDT)
  - Re: [AMBER] Ligand-residue interaction plot Soumendranath Bhakat (Sat Apr 05 2014 - 08:59:45 PDT)
Re: [AMBER] ATOMIC NUMBER section in prmtop file - Sustiva example:potential bug ye renlo (Sat Apr 05 2014 - 08:56:32 PDT)
- Re: [AMBER] ATOMIC NUMBER section in prmtop file - Sustiva example:potential bug David A Case (Sat Apr 05 2014 - 10:59:34 PDT)
[AMBER] ligand residue interaction Arunima Shilpi (Sat Apr 05 2014 - 20:00:39 PDT)
[AMBER] ligand residue interaction Arunima Shilpi (Sat Apr 05 2014 - 20:37:53 PDT)
[AMBER] protein-ligand interaction Arunima Shilpi (Sat Apr 05 2014 - 21:07:04 PDT)
- Re: [AMBER] protein-ligand interaction Soumendranath Bhakat (Sun Apr 06 2014 - 04:54:33 PDT)
[AMBER] Protein-ligand interaction Arunima Shilpi (Sun Apr 06 2014 - 09:05:28 PDT)
- Re: [AMBER] Protein-ligand interaction Soumendranath Bhakat (Sun Apr 06 2014 - 09:09:50 PDT)
[AMBER] averaged NMR distance Neha Gandhi (Sun Apr 06 2014 - 20:00:01 PDT)
- Re: [AMBER] averaged NMR distance David A Case (Mon Apr 07 2014 - 04:52:05 PDT)
  - Re: [AMBER] averaged NMR distance Daniel Roe (Mon Apr 07 2014 - 07:49:45 PDT)
[AMBER] US+QM/MM enzyme + substrate - howto Tamara Meirelles (Mon Apr 07 2014 - 00:26:05 PDT)
[AMBER] entropy calculation mmpbsa_nm Arunima Shilpi (Mon Apr 07 2014 - 04:35:15 PDT)
- Re: [AMBER] entropy calculation mmpbsa_nm Jason Swails (Mon Apr 07 2014 - 05:07:51 PDT)
[AMBER] simulating small molecules systems Fabian Glaser (Mon Apr 07 2014 - 05:10:59 PDT)
[AMBER] small molecules Fabian Glaser (Mon Apr 07 2014 - 05:14:14 PDT)
[AMBER] Really Weird Problem with Replica Exchange Christopher A Thiebaut (Mon Apr 07 2014 - 11:58:26 PDT)
- Re: [AMBER] Really Weird Problem with Replica Exchange Carlos Simmerling (Mon Apr 07 2014 - 12:48:18 PDT)
  - Re: [AMBER] Really Weird Problem with Replica Exchange Christopher A Thiebaut (Mon Apr 07 2014 - 13:02:28 PDT)
    - Re: [AMBER] Really Weird Problem with Replica Exchange Christina Bergonzo (Mon Apr 07 2014 - 13:08:28 PDT)
    - Re: [AMBER] Really Weird Problem with Replica Exchange Christopher A Thiebaut (Mon Apr 07 2014 - 13:21:54 PDT)
    - Re: [AMBER] Really Weird Problem with Replica Exchange Christina Bergonzo (Tue Apr 08 2014 - 07:46:33 PDT)
    - Re: [AMBER] Really Weird Problem with Replica Exchange Christopher A Thiebaut (Wed Apr 09 2014 - 10:05:06 PDT)
    - Re: [AMBER] Really Weird Problem with Replica Exchange Jason Swails (Wed Apr 09 2014 - 10:20:34 PDT)
    - Re: [AMBER] Really Weird Problem with Replica Exchange Christopher A Thiebaut (Wed Apr 09 2014 - 10:20:32 PDT)
    - Re: [AMBER] Really Weird Problem with Replica Exchange Christopher A Thiebaut (Wed Apr 09 2014 - 10:32:46 PDT)
    - Re: [AMBER] Really Weird Problem with Replica Exchange Jason Swails (Wed Apr 09 2014 - 10:42:35 PDT)
    - Re: [AMBER] Really Weird Problem with Replica Exchange Carlos Simmerling (Wed Apr 09 2014 - 10:47:23 PDT)
    - Re: [AMBER] Really Weird Problem with Replica Exchange Jason Swails (Wed Apr 09 2014 - 11:05:40 PDT)
    - Re: [AMBER] Really Weird Problem with Replica Exchange Jason Swails (Wed Apr 09 2014 - 10:37:11 PDT)
    - Re: [AMBER] Really Weird Problem with Replica Exchange Daniel Roe (Wed Apr 09 2014 - 10:27:10 PDT)
    - Re: [AMBER] Really Weird Problem with Replica Exchange Christopher A Thiebaut (Wed Apr 09 2014 - 11:19:32 PDT)
    - Re: [AMBER] Really Weird Problem with Replica Exchange Jason Swails (Wed Apr 09 2014 - 11:26:59 PDT)
    - Re: [AMBER] Really Weird Problem with Replica Exchange Brian Radak (Wed Apr 09 2014 - 10:29:48 PDT)
    - Re: [AMBER] Really Weird Problem with Replica Exchange Christopher A Thiebaut (Wed Apr 09 2014 - 10:36:23 PDT)
    - Re: [AMBER] Really Weird Problem with Replica Exchange Jason Swails (Wed Apr 09 2014 - 10:50:32 PDT)
[AMBER] REMD with pmemd.cuda Milo Westler (Mon Apr 07 2014 - 18:04:52 PDT)
- Re: [AMBER] REMD with pmemd.cuda Nhai (Tue Apr 08 2014 - 00:37:29 PDT)
  - Re: [AMBER] REMD with pmemd.cuda Jason Swails (Tue Apr 08 2014 - 04:45:18 PDT)
    - Re: [AMBER] REMD with pmemd.cuda Ashutosh Shandilya (Tue Apr 08 2014 - 04:54:23 PDT)
    - Re: [AMBER] REMD with pmemd.cuda Jason Swails (Tue Apr 08 2014 - 05:40:55 PDT)
    - Re: [AMBER] REMD with pmemd.cuda Ashutosh Shandilya (Tue Apr 08 2014 - 05:45:09 PDT)
    - Re: [AMBER] REMD with pmemd.cuda Milo Westler (Tue Apr 08 2014 - 07:36:20 PDT)
    - Re: [AMBER] REMD with pmemd.cuda Milo Westler (Tue Apr 08 2014 - 07:46:45 PDT)
    - Re: [AMBER] REMD with pmemd.cuda Jason Swails (Tue Apr 08 2014 - 07:59:20 PDT)
    - Re: [AMBER] REMD with pmemd.cuda Milo Westler (Tue Apr 08 2014 - 09:49:08 PDT)
[AMBER] number of ions (integral) too much in RDF plot Jio M (Mon Apr 07 2014 - 19:33:01 PDT)
- [AMBER] number of ions (integral) too much in RDF plot Jio M (Tue Apr 08 2014 - 05:44:35 PDT)
- Re: [AMBER] number of ions (integral) too much in RDF plot Daniel Roe (Wed Apr 09 2014 - 07:28:19 PDT)
  - Re: [AMBER] number of ions (integral) too much in RDF plot newamber list (Wed Apr 09 2014 - 10:17:36 PDT)
    - Re: [AMBER] number of ions (integral) too much in RDF plot newamber list (Wed Apr 09 2014 - 10:52:40 PDT)
[AMBER] About the error "Unable to correctly identify element CU" in QMMM simulation Yeng-Tseng Wang (Mon Apr 07 2014 - 20:43:54 PDT)
- Re: [AMBER] About the error "Unable to correctly identify element CU" in QMMM simulation Jason Swails (Tue Apr 08 2014 - 04:29:14 PDT)
[AMBER] When I run the pmemd.cuda, sometimes computer will be rebooted. KangMooseok (Mon Apr 07 2014 - 22:34:26 PDT)
- Re: [AMBER] When I run the pmemd.cuda, sometimes computer will be rebooted. Jason Swails (Tue Apr 08 2014 - 04:35:45 PDT)
[AMBER] error in reading protein file Arunima Shilpi (Mon Apr 07 2014 - 22:58:18 PDT)
- Re: [AMBER] error in reading protein file Jason Swails (Tue Apr 08 2014 - 04:42:09 PDT)
[AMBER] When I run the pmemd.cuda, sometimes computer will be rebooted.‏‏ KangMooseok (Mon Apr 07 2014 - 23:01:45 PDT)
[AMBER] error in loading protein Arunima Shilpi (Mon Apr 07 2014 - 23:05:11 PDT)
- Re: [AMBER] error in loading protein Soumendranath Bhakat (Tue Apr 08 2014 - 00:20:18 PDT)
[AMBER] Karplus J-coupling Neha Gandhi (Tue Apr 08 2014 - 02:32:39 PDT)
- Re: [AMBER] Karplus J-coupling David A Case (Tue Apr 08 2014 - 05:24:27 PDT)
[AMBER] Questions about the energy of H3O+ jinfenghuang (Tue Apr 08 2014 - 07:26:22 PDT)
- Re: [AMBER] Questions about the energy of H3O+ Jason Swails (Tue Apr 08 2014 - 08:52:12 PDT)
[AMBER] comparing RDF plots Jio M (Tue Apr 08 2014 - 19:12:17 PDT)
- Re: [AMBER] comparing RDF plots Jio M (Tue Apr 08 2014 - 19:38:33 PDT)
- Re: [AMBER] comparing RDF plots Daniel Roe (Wed Apr 09 2014 - 07:22:01 PDT)
  - Re: [AMBER] comparing RDF plots newamber list (Wed Apr 09 2014 - 10:15:07 PDT)
    - Re: [AMBER] comparing RDF plots Daniel Roe (Wed Apr 09 2014 - 12:20:15 PDT)
    - Re: [AMBER] comparing RDF plots newamber list (Wed Apr 09 2014 - 13:34:28 PDT)
[AMBER] Fwd: MMPBSA.py PrmtopError: Complex natom != receptor natom + ligand natom Javier Alejandro Rendon Carrillo (Tue Apr 08 2014 - 20:47:14 PDT)
- Re: [AMBER] Fwd: MMPBSA.py PrmtopError: Complex natom != receptor natom + ligand natom Jason Swails (Wed Apr 09 2014 - 03:23:59 PDT)
[AMBER] MMPBSA.py PrmtopError: Complex natom != receptor natom + ligand natom Javier Alejandro Rendon Carrillo (Tue Apr 08 2014 - 21:54:12 PDT)
[AMBER] I make box with solvatebox complex TIP3PBOX 15.0 and unfilled gap remains near wall Vytautas Rakeviius (Wed Apr 09 2014 - 05:39:12 PDT)
- Re: [AMBER] I make box with solvatebox complex TIP3PBOX 15.0 and unfilled gap remains near wall David A Case (Wed Apr 09 2014 - 05:59:57 PDT)
- Re: [AMBER] I make box with solvatebox complex TIP3PBOX 15.0 and unfilled gap remains near wall Christopher A Thiebaut (Wed Apr 09 2014 - 10:13:00 PDT)
  - Re: [AMBER] I make box with solvatebox complex TIP3PBOX 15.0 and unfilled gap remains near wall Jason Swails (Wed Apr 09 2014 - 10:29:52 PDT)
[AMBER] KShake problem with GPU Lorenzo Gontrani (Wed Apr 09 2014 - 07:05:33 PDT)
- Re: [AMBER] KShake problem with GPU Daniel Roe (Wed Apr 09 2014 - 07:11:15 PDT)
  - Re: [AMBER] KShake problem with GPU Lorenzo Gontrani (Wed Apr 09 2014 - 08:00:31 PDT)
  - Re: [AMBER] KShake problem with GPU Scott Le Grand (Wed Apr 09 2014 - 08:01:54 PDT)
[AMBER] antechamber Lara rajam (Thu Apr 10 2014 - 06:39:41 PDT)
- Re: [AMBER] antechamber David A Case (Thu Apr 10 2014 - 09:34:38 PDT)
  - Re: [AMBER] antechamber Lara rajam (Thu Apr 10 2014 - 11:07:31 PDT)
[AMBER] rdf averaging problem newamber list (Thu Apr 10 2014 - 15:08:49 PDT)
- Re: [AMBER] rdf averaging problem Daniel Roe (Fri Apr 11 2014 - 11:33:49 PDT)
  - Re: [AMBER] rdf averaging problem newamber list (Fri Apr 11 2014 - 12:13:29 PDT)
    - Re: [AMBER] rdf averaging problem Daniel Roe (Fri Apr 11 2014 - 12:57:42 PDT)
    - Re: [AMBER] rdf averaging problem newamber list (Fri Apr 11 2014 - 16:32:27 PDT)
    - Re: [AMBER] rdf averaging problem newamber list (Mon Apr 14 2014 - 09:58:11 PDT)
    - Re: [AMBER] rdf averaging problem Daniel Roe (Mon Apr 14 2014 - 12:12:26 PDT)
    - Re: [AMBER] rdf averaging problem newamber list (Mon Apr 14 2014 - 20:35:22 PDT)
    - Re: [AMBER] rdf averaging problem Daniel Roe (Tue Apr 15 2014 - 13:43:13 PDT)
Re: [AMBER] AMBER Digest, Vol 818, Issue 1 jinfenghuang (Thu Apr 10 2014 - 19:18:48 PDT)
[AMBER] Fw:Problems with the gas energy of H3O+ and H2O jinfenghuang (Thu Apr 10 2014 - 20:06:53 PDT)
[AMBER] Error when runing sietraj for AMBER trajectory Shulin Zhuang (Thu Apr 10 2014 - 22:34:14 PDT)
- Re: [AMBER] Error when runing sietraj for AMBER trajectory Shulin Zhuang (Thu Apr 10 2014 - 22:41:49 PDT)
[AMBER] Problems with the gas energy of H3O+ and H2O 黄 (Fri Apr 11 2014 - 07:46:09 PDT)
[AMBER] Mailing list problems David A Case (Fri Apr 11 2014 - 08:02:26 PDT)
[AMBER] rism1d error Brian Radak (Fri Apr 11 2014 - 17:19:08 PDT)
- Re: [AMBER] rism1d error Lists (Sun Apr 13 2014 - 14:52:23 PDT)
- Re: [AMBER] rism1d error Lists (Mon Apr 14 2014 - 09:37:10 PDT)
[AMBER] MMPBSA Sourav Purohit (Sun Apr 13 2014 - 02:39:17 PDT)
- [AMBER] Fwd: MMPBSA Sourav Purohit (Sun Apr 13 2014 - 03:20:21 PDT)
- Re: [AMBER] MMPBSA Jason Swails (Sun Apr 13 2014 - 08:20:52 PDT)
[AMBER] MMPBSA Sourav Purohit (Sun Apr 13 2014 - 07:09:44 PDT)
[AMBER] MMPBSA Sourav Purohit (Sun Apr 13 2014 - 12:04:53 PDT)
- [AMBER] Fwd: MMPBSA Sourav Purohit (Sun Apr 13 2014 - 12:15:32 PDT)
- Re: [AMBER] MMPBSA Jason Swails (Mon Apr 14 2014 - 04:56:57 PDT)
[AMBER] Generate a pdb with unique atom names Jean-Patrick Francoia (Sun Apr 13 2014 - 12:38:37 PDT)
[AMBER] Generate a pdb with unique atom names Jean-Patrick Francoia (Sun Apr 13 2014 - 12:40:18 PDT)
- Re: [AMBER] Generate a pdb with unique atom names Bill Ross (Sun Apr 13 2014 - 13:30:24 PDT)
  - Re: [AMBER] Generate a pdb with unique atom names Jean-Patrick Francoia (Sun Apr 13 2014 - 15:06:00 PDT)
- Re: [AMBER] Generate a pdb with unique atom names FyD (Sun Apr 13 2014 - 22:08:46 PDT)
  - Re: [AMBER] Generate a pdb with unique atom names Jean-Patrick Francoia (Mon Apr 14 2014 - 00:18:54 PDT)
    - Re: [AMBER] Generate a pdb with unique atom names FyD (Mon Apr 14 2014 - 12:20:12 PDT)
- Re: [AMBER] Generate a pdb with unique atom names Jason Swails (Mon Apr 14 2014 - 05:10:25 PDT)
  - Re: [AMBER] Generate a pdb with unique atom names Jean-Patrick Francoia (Mon Apr 14 2014 - 05:50:35 PDT)
    - Re: [AMBER] Generate a pdb with unique atom names Jason Swails (Mon Apr 14 2014 - 06:01:44 PDT)
    - Re: [AMBER] Generate a pdb with unique atom names Jean-Patrick Francoia (Mon Apr 14 2014 - 11:57:44 PDT)
    - Re: [AMBER] Generate a pdb with unique atom names Jason Swails (Mon Apr 14 2014 - 12:24:13 PDT)
    - Re: [AMBER] Generate a pdb with unique atom names FyD (Mon Apr 14 2014 - 22:31:31 PDT)
    - Re: [AMBER] Generate a pdb with unique atom names Jean-Patrick Francoia (Tue Apr 15 2014 - 00:52:37 PDT)
    - Re: [AMBER] Generate a pdb with unique atom names FyD (Tue Apr 15 2014 - 05:51:15 PDT)
    - Re: [AMBER] Generate a pdb with unique atom names Jean-Patrick Francoia (Tue Apr 15 2014 - 06:35:49 PDT)
    - Re: [AMBER] Generate a pdb with unique atom names FyD (Tue Apr 15 2014 - 07:06:39 PDT)
[AMBER] MMPBSA Sourav Purohit (Sun Apr 13 2014 - 23:35:29 PDT)
- [AMBER] distance restraint Urszula Uciechowska (Mon Apr 14 2014 - 00:51:42 PDT)
  - Re: [AMBER] distance restraint Jason Swails (Mon Apr 14 2014 - 05:04:06 PDT)
  - Re: [AMBER] distance restraint David A Case (Mon Apr 14 2014 - 05:05:46 PDT)
[AMBER] PCA analysis and histogram Neha Gandhi (Mon Apr 14 2014 - 04:45:42 PDT)
- Re: [AMBER] PCA analysis and histogram Daniel Roe (Mon Apr 14 2014 - 08:20:46 PDT)
  - Re: [AMBER] PCA analysis and histogram Setyanto Md (Mon Apr 21 2014 - 01:19:51 PDT)
    - Re: [AMBER] PCA analysis and histogram Daniel Roe (Mon Apr 21 2014 - 07:30:14 PDT)
[AMBER] Nonbond Energy for Single Water Molecule ? 黄 (Mon Apr 14 2014 - 07:59:20 PDT)
- Re: [AMBER] Nonbond Energy for Single Water Molecule ? Brian Radak (Mon Apr 14 2014 - 08:08:41 PDT)
- Re: [AMBER] Nonbond Energy for Single Water Molecule ? Jason Swails (Mon Apr 14 2014 - 08:37:58 PDT)
  - Re: [AMBER] Nonbond Energy for Single Water Molecule ? Jinfeng Huang (Tue Apr 15 2014 - 21:11:25 PDT)
    - Re: [AMBER] Nonbond Energy for Single Water Molecule ? Jason Swails (Wed Apr 16 2014 - 08:10:18 PDT)
[AMBER] SDS parameters in AMBER ABEL Stephane 175950 (Tue Apr 15 2014 - 05:39:10 PDT)
[AMBER] Announcement: Release of Amber14 and AmberTools14 David A Case (Tue Apr 15 2014 - 13:35:18 PDT)
[AMBER] GTX780Ti consistent error "cudaMemcpy GpuBuffer::Download failed unspecified launch failure." Keiran Rowell (Tue Apr 15 2014 - 23:14:58 PDT)
- Re: [AMBER] GTX780Ti consistent error "cudaMemcpy GpuBuffer::Download failed unspecified launch failure." Ross Walker (Wed Apr 16 2014 - 10:27:45 PDT)
  - Re: [AMBER] GTX780Ti consistent error "cudaMemcpy GpuBuffer::Download failed unspecified launch failure." filip fratev (Thu Apr 17 2014 - 09:14:31 PDT)
    - Re: [AMBER] GTX780Ti consistent error "cudaMemcpy GpuBuffer::Download failed unspecified launch failure." Keiran Rowell (Thu May 29 2014 - 22:43:53 PDT)
    - Re: [AMBER] GTX780Ti consistent error "cudaMemcpy GpuBuffer::Download failed unspecified launch failure." Ross Walker (Fri May 30 2014 - 08:42:42 PDT)
    - Re: [AMBER] GTX780Ti consistent error "cudaMemcpy GpuBuffer::Download failed unspecified launch failure." Keiran Rowell (Mon Jun 02 2014 - 16:54:55 PDT)
    - Re: [AMBER] GTX780Ti consistent error "cudaMemcpy GpuBuffer::Download failed unspecified launch failure." Scott Le Grand (Mon Jun 02 2014 - 17:05:22 PDT)
    - Re: [AMBER] GTX780Ti consistent error "cudaMemcpy GpuBuffer::Download failed unspecified launch failure." Keiran Rowell (Mon Jun 02 2014 - 18:34:17 PDT)
    - Re: [AMBER] GTX780Ti consistent error "cudaMemcpy GpuBuffer::Download failed unspecified launch failure." Scott Le Grand (Mon Jun 02 2014 - 22:45:38 PDT)
    - Re: [AMBER] GTX780Ti consistent error "cudaMemcpy GpuBuffer::Download failed unspecified launch failure." Keiran Rowell (Thu Jun 12 2014 - 18:40:14 PDT)
    - Re: [AMBER] GTX780Ti consistent error "cudaMemcpy GpuBuffer::Download failed unspecified launch failure." Ross Walker (Thu Jun 12 2014 - 19:10:20 PDT)
[AMBER] making test not successful in ambertool14 Mahendra B Thapa (Thu Apr 17 2014 - 05:55:05 PDT)
- Re: [AMBER] making test not successful in ambertool14 Brian Radak (Thu Apr 17 2014 - 06:24:42 PDT)
- Re: [AMBER] making test not successful in ambertool14 David A Case (Thu Apr 17 2014 - 09:44:27 PDT)
[AMBER-Developers] AMBER Workshop Announcement Ross Walker (Thu Apr 17 2014 - 08:47:35 PDT)
- Re: [AMBER] AMBER Workshop Announcement Ved Prakash (Fri Apr 18 2014 - 21:34:50 PDT)
  - Re: [AMBER] AMBER Workshop Announcement Ross Walker (Sat Apr 19 2014 - 10:51:41 PDT)
    - Re: [AMBER] AMBER Workshop Announcement Setyanto Md (Mon Apr 21 2014 - 01:15:54 PDT)
    - Re: [AMBER] AMBER Workshop Announcement Ross Walker (Mon Apr 21 2014 - 08:03:07 PDT)
    - Re: [AMBER] AMBER Workshop Announcement Setyanto Md (Mon Apr 28 2014 - 20:02:23 PDT)
[AMBER] AMBER Workshop Announcement Ross Walker (Thu Apr 17 2014 - 09:26:43 PDT)
Re: [AMBER] FW: making test not successful in ambertool14 Mahendra B Thapa (Fri Apr 18 2014 - 05:59:15 PDT)
[AMBER] How to use "divergence" command Mahendra B Thapa (Fri Apr 18 2014 - 09:53:08 PDT)
- Re: [AMBER] How to use "divergence" command Jason Swails (Fri Apr 18 2014 - 11:02:44 PDT)
- Re: [AMBER] How to use "divergence" command Daniel Roe (Fri Apr 18 2014 - 13:05:56 PDT)
[AMBER] 【AMBER12】Including water when using General Amber Force Field leaprc.gaff 石坪江梨花 (Sat Apr 19 2014 - 03:22:48 PDT)
- Re: [AMBER] 【AMBER12】Including water when using General Amber Force Field leaprc.gaff ABEL Stephane 175950 (Sat Apr 19 2014 - 03:47:50 PDT)
- Re: [AMBER] 【AMBER12】Including water when using General Amber Force Field leaprc.gaff Jason Swails (Sat Apr 19 2014 - 04:44:10 PDT)
[AMBER] Running parallel simulations on different no of cores Muthukumaran R (Sat Apr 19 2014 - 10:31:48 PDT)
- Re: [AMBER] Running parallel simulations on different no of cores Jason Swails (Sat Apr 19 2014 - 14:48:12 PDT)
[AMBER] Combining trajectories with velocities Eugene Yedvabny (Sat Apr 19 2014 - 11:01:29 PDT)
- Re: [AMBER] Combining trajectories with velocities Daniel Roe (Sat Apr 19 2014 - 14:59:01 PDT)
  - Re: [AMBER] Combining trajectories with velocities Eugene Yedvabny (Sat Apr 19 2014 - 15:43:02 PDT)
    - Re: [AMBER] Combining trajectories with velocities Daniel Roe (Sat Apr 19 2014 - 15:57:44 PDT)
[AMBER] Can I do PCA on simply a particular domain of the whole protein? Yip Yew Mun (Sat Apr 19 2014 - 21:38:11 PDT)
- Re: [AMBER] Can I do PCA on simply a particular domain of the whole protein? Daniel Roe (Mon Apr 21 2014 - 07:34:15 PDT)
[AMBER] error in running entropy Arunima Shilpi (Sat Apr 19 2014 - 21:55:36 PDT)
- Re: [AMBER] error in running entropy Jason Swails (Sat Apr 19 2014 - 23:19:11 PDT)
[AMBER] simulated annelaing condtions and requiremnets Nitin Sharma (Sun Apr 20 2014 - 06:47:42 PDT)
- Re: [AMBER] simulated annelaing condtions and requiremnets Jason Swails (Sun Apr 20 2014 - 08:06:24 PDT)
[AMBER] Accelerated MD Sourav Purohit (Mon Apr 21 2014 - 02:34:29 PDT)
[AMBER] Problems during installation of amber-14 with cuda-5 on GTX 670 James Starlight (Mon Apr 21 2014 - 02:43:15 PDT)
- Re: [AMBER] Problems during installation of amber-14 with cuda-5 on GTX 670 James Starlight (Mon Apr 21 2014 - 03:37:39 PDT)
  - Re: [AMBER] Problems during installation of amber-14 with cuda-5 on GTX 670 Jason Swails (Mon Apr 21 2014 - 04:47:33 PDT)
    - Re: [AMBER] Problems during installation of amber-14 with cuda-5 on GTX 670 James Starlight (Mon Apr 21 2014 - 07:32:12 PDT)
    - Re: [AMBER] Problems during installation of amber-14 with cuda-5 on GTX 670 Jason Swails (Mon Apr 21 2014 - 07:36:54 PDT)
    - Re: [AMBER] Problems during installation of amber-14 with cuda-5 on GTX 670 James Starlight (Tue Apr 22 2014 - 01:54:20 PDT)
- Re: [AMBER] Problems during installation of amber-14 with cuda-5 on GTX 670 Jason Swails (Mon Apr 21 2014 - 04:44:24 PDT)
- Re: [AMBER] Problems during installation of amber-14 with cuda-5 on GTX 670 James Starlight (Tue Apr 22 2014 - 02:49:40 PDT)
  - Re: [AMBER] Problems during installation of amber-14 with cuda-5 on GTX 670 James Starlight (Tue Apr 22 2014 - 03:43:26 PDT)
    - Re: [AMBER] Problems during installation of amber-14 with cuda-5 on GTX 670 Jason Swails (Tue Apr 22 2014 - 04:16:47 PDT)
    - Re: [AMBER] Problems during installation of amber-14 with cuda-5 on GTX 670 Daniel Roe (Tue Apr 22 2014 - 07:31:11 PDT)
    - Re: [AMBER] Problems during installation of amber-14 with cuda-5 on GTX 670 James Starlight (Wed Apr 23 2014 - 00:57:13 PDT)
    - Re: [AMBER] Problems during installation of amber-14 with cuda-5 on GTX 670 James Starlight (Wed Apr 23 2014 - 03:14:20 PDT)
    - Re: [AMBER] Problems during installation of amber-14 with cuda-5 on GTX 670 Jason Swails (Wed Apr 23 2014 - 04:18:49 PDT)
    - Re: [AMBER] Problems during installation of amber-14 with cuda-5 on GTX 670 James Starlight (Fri Apr 25 2014 - 00:27:47 PDT)
    - Re: [AMBER] Problems during installation of amber-14 with cuda-5 on GTX 670 James Starlight (Fri Apr 25 2014 - 00:55:19 PDT)
    - Re: [AMBER] Problems during installation of amber-14 with cuda-5 on GTX 670 Jason Swails (Fri Apr 25 2014 - 04:10:38 PDT)
    - Re: [AMBER] Problems during installation of amber-14 with cuda-5 on GTX 670 James Starlight (Fri Apr 25 2014 - 07:17:19 PDT)
    - Re: [AMBER] Problems during installation of amber-14 with cuda-5 on GTX 670 Jason Swails (Fri Apr 25 2014 - 08:10:25 PDT)
    - Re: [AMBER] Problems during installation of amber-14 with cuda-5 on GTX 670 James Starlight (Sat Apr 26 2014 - 05:12:41 PDT)
    - Re: [AMBER] Problems during installation of amber-14 with cuda-5 on GTX 670 Jason Swails (Sat Apr 26 2014 - 05:26:08 PDT)
    - Re: [AMBER] Problems during installation of amber-14 with cuda-5 on GTX 670 James Starlight (Sat Apr 26 2014 - 05:35:28 PDT)
    - Re: [AMBER] Problems during installation of amber-14 with cuda-5 on GTX 670 Jason Swails (Sat Apr 26 2014 - 05:48:25 PDT)
    - Re: [AMBER] Problems during installation of amber-14 with cuda-5 on GTX 670 James Starlight (Sat Apr 26 2014 - 07:12:03 PDT)
    - Re: [AMBER] Problems during installation of amber-14 with cuda-5 on GTX 670 Jason Swails (Sat Apr 26 2014 - 07:24:44 PDT)
    - Re: [AMBER] Problems during installation of amber-14 with cuda-5 on GTX 670 James Starlight (Sun Apr 27 2014 - 23:58:58 PDT)
    - Re: [AMBER] Problems during installation of amber-14 with cuda-5 on GTX 670 James Starlight (Mon Apr 28 2014 - 00:17:45 PDT)
    - Re: [AMBER] Problems during installation of amber-14 with cuda-5 on GTX 670 David A Case (Mon Apr 28 2014 - 04:36:50 PDT)
    - Re: [AMBER] Problems during installation of amber-14 with cuda-5 on GTX 670 Jason Swails (Mon Apr 28 2014 - 04:44:45 PDT)
    - Re: [AMBER] Problems during installation of amber-14 with cuda-5 on GTX 670 Jason Swails (Mon Apr 28 2014 - 04:54:41 PDT)
    - Re: [AMBER] Problems during installation of amber-14 with cuda-5 on GTX 670 James Starlight (Mon Apr 28 2014 - 23:20:34 PDT)
    - Re: [AMBER] Problems during installation of amber-14 with cuda-5 on GTX 670 James Starlight (Tue Apr 29 2014 - 22:58:12 PDT)
    - Re: [AMBER] Problems during installation of amber-14 with cuda-5 on GTX 670 Jason Swails (Wed Apr 30 2014 - 04:22:46 PDT)
    - Re: [AMBER] Problems during installation of amber-14 with cuda-5 on GTX 670 James Starlight (Thu May 01 2014 - 02:05:27 PDT)
    - Re: [AMBER] Problems during installation of amber-14 with cuda-5 on GTX 670 Jason Swails (Thu May 01 2014 - 06:15:49 PDT)
    - Re: [AMBER] Problems during installation of amber-14 with cuda-5 on GTX 670 Josh Berryman (Thu May 01 2014 - 23:43:39 PDT)
    - Re: [AMBER] Problems during installation of amber-14 with cuda-5 on GTX 670 Josh Berryman (Thu May 01 2014 - 23:45:19 PDT)
[AMBER] updates for amber12 bugfix18 Ahmet yıldırım (Mon Apr 21 2014 - 03:43:14 PDT)
- Re: [AMBER] updates for amber12 bugfix18 Jason Swails (Mon Apr 21 2014 - 04:38:06 PDT)
  - Re: [AMBER] updates for amber12 bugfix18 Ahmet yıldırım (Mon Apr 21 2014 - 04:49:29 PDT)
    - Re: [AMBER] updates for amber12 bugfix18 Ahmet yıldırım (Mon Apr 21 2014 - 05:43:04 PDT)
    - Re: [AMBER] updates for amber12 bugfix18 Jason Swails (Mon Apr 21 2014 - 05:52:48 PDT)
[AMBER] Umbrella Slice module Geoffrey Gray (Mon Apr 21 2014 - 06:29:16 PDT)
- Re: [AMBER] Umbrella Slice module Jason Swails (Mon Apr 21 2014 - 09:58:19 PDT)
  - Re: [AMBER] Umbrella Slice module Geoffrey Gray (Mon Apr 21 2014 - 10:42:29 PDT)
    - Re: [AMBER] Umbrella Slice module Jason Swails (Mon Apr 21 2014 - 10:50:51 PDT)
Re: [AMBER] FW: How to use "divergence" command Mahendra B Thapa (Mon Apr 21 2014 - 07:15:43 PDT)
- Re: [AMBER] FW: How to use "divergence" command Daniel Roe (Mon Apr 21 2014 - 07:24:06 PDT)
[AMBER] RESP procedure Ahmet Yıldırım (Mon Apr 21 2014 - 08:51:47 PDT)
- Re: [AMBER] RESP procedure Ved Prakash (Mon Apr 21 2014 - 12:05:31 PDT)
  - Re: [AMBER] RESP procedure Ahmet Yıldırım (Mon Apr 21 2014 - 21:13:30 PDT)
    - Re: [AMBER] RESP procedure Pengfei Li (Thu Apr 24 2014 - 10:36:35 PDT)
- Re: [AMBER] RESP procedure FyD (Tue Apr 22 2014 - 23:41:20 PDT)
[AMBER] antechamber problem Carlos Romero (Mon Apr 21 2014 - 21:51:02 PDT)
- Re: [AMBER] antechamber problem JAIME RUBIO MARTINEZ (Tue Apr 22 2014 - 01:33:21 PDT)
  - Re: [AMBER] antechamber problem Carlos Romero (Tue Apr 22 2014 - 10:17:52 PDT)
    - Re: [AMBER] antechamber problem JAIME RUBIO MARTINEZ (Tue Apr 22 2014 - 11:18:15 PDT)
- Re: [AMBER] antechamber problem David A Case (Tue Apr 22 2014 - 11:05:34 PDT)
  - Re: [AMBER] antechamber problem Carlos Romero (Tue Apr 22 2014 - 11:23:22 PDT)
- Re: [AMBER] antechamber problem FyD (Tue Apr 22 2014 - 23:37:58 PDT)
  - Re: [AMBER] antechamber problem Carlos Romero (Wed Apr 23 2014 - 09:23:36 PDT)
[AMBER] MMPBSA Mary Varughese (Mon Apr 21 2014 - 22:00:53 PDT)
[AMBER] Native Contact Help kara tuong vi (Mon Apr 21 2014 - 22:59:38 PDT)
- Re: [AMBER] Native Contact Help Daniel Roe (Tue Apr 22 2014 - 08:18:12 PDT)
  - Re: [AMBER] Native Contact Help kara tuong vi ngo (Thu Apr 24 2014 - 16:48:31 PDT)
    - Re: [AMBER] Native Contact Help Daniel Roe (Sat Apr 26 2014 - 09:44:45 PDT)
    - Re: [AMBER] Native Contact Help Daniel Roe (Mon Apr 28 2014 - 12:22:56 PDT)
    - Re: [AMBER] Native Contact Help Daniel Roe (Mon Apr 28 2014 - 12:28:18 PDT)
[AMBER] strip some atoms to compute RMSD Marlet Martinez (Tue Apr 22 2014 - 04:56:40 PDT)
- Re: [AMBER] strip some atoms to compute RMSD Asaminew Haile (Tue Apr 22 2014 - 05:12:19 PDT)
  - Re: [AMBER] strip some atoms to compute RMSD Daniel Roe (Tue Apr 22 2014 - 07:10:32 PDT)
    - Re: [AMBER] strip some atoms to compute RMSD Marlet Martinez (Tue Apr 22 2014 - 08:43:23 PDT)
    - Re: [AMBER] strip some atoms to compute RMSD Nitin Sharma (Tue Apr 22 2014 - 08:47:26 PDT)
    - Re: [AMBER] strip some atoms to compute RMSD Asaminew Haile (Tue Apr 22 2014 - 08:50:47 PDT)
    - Re: [AMBER] strip some atoms to compute RMSD Marlet Martinez (Thu Apr 24 2014 - 01:57:15 PDT)
    - Re: [AMBER] strip some atoms to compute RMSD Jason Swails (Thu Apr 24 2014 - 04:23:32 PDT)
    - Re: [AMBER] strip some atoms to compute RMSD Marlet Martinez (Thu Apr 24 2014 - 08:41:23 PDT)
[AMBER] diferent results zahra khatti (Tue Apr 22 2014 - 07:55:25 PDT)
- Re: [AMBER] diferent results Christopher A Thiebaut (Tue Apr 22 2014 - 08:03:43 PDT)
  - Re: [AMBER] diferent results Marc van der Kamp (Tue Apr 22 2014 - 08:10:49 PDT)
[AMBER] Error with quasi-harmonic MMPBSA.py calculations Kipp Johnson (Tue Apr 22 2014 - 16:21:42 PDT)
- Re: [AMBER] Error with quasi-harmonic MMPBSA.py calculations Daniel Roe (Tue Apr 22 2014 - 17:10:49 PDT)
- Re: [AMBER] Error with quasi-harmonic MMPBSA.py calculations Abhishek TYAGI (Fri Apr 17 2015 - 08:30:04 PDT)
  - Re: [AMBER] Error with quasi-harmonic MMPBSA.py calculations Jason Swails (Fri Apr 17 2015 - 08:43:03 PDT)
[AMBER] xmin Fabiana Caporuscio (Wed Apr 23 2014 - 03:15:18 PDT)
- Re: [AMBER] xmin David A Case (Wed Apr 23 2014 - 04:44:40 PDT)
- Re: [AMBER] xmin Jason Swails (Wed Apr 23 2014 - 04:27:03 PDT)
  - Re: [AMBER] xmin Fabiana Caporuscio (Wed Apr 23 2014 - 08:23:23 PDT)
[AMBER] AMBER minimization problem Valentina Romano (Wed Apr 23 2014 - 09:11:54 PDT)
- Re: [AMBER] AMBER minimization problem David A Case (Wed Apr 23 2014 - 10:27:07 PDT)
  - Re: [AMBER] AMBER minimization problem Valentina Romano (Thu Apr 24 2014 - 01:22:29 PDT)
    - Re: [AMBER] AMBER minimization problem David A Case (Thu Apr 24 2014 - 05:00:56 PDT)
    - Re: [AMBER] AMBER minimization problem Valentina Romano (Thu Apr 24 2014 - 06:52:03 PDT)
    - Re: [AMBER] AMBER minimization problem Jason Swails (Thu Apr 24 2014 - 07:47:14 PDT)
    - Re: [AMBER] AMBER minimization problem Valentina Romano (Thu Apr 24 2014 - 07:58:12 PDT)
    - Re: [AMBER] AMBER minimization problem Nitin Sharma (Thu Apr 24 2014 - 08:38:57 PDT)
[AMBER] FFTW3 related error when compiling AmberTools13 on Fedora20 Soren Wacker (Wed Apr 23 2014 - 13:51:31 PDT)
- Re: [AMBER] FFTW3 related error when compiling AmberTools13 on Fedora20 Jason Swails (Wed Apr 23 2014 - 14:27:50 PDT)
  - Re: [AMBER] FFTW3 related error when compiling AmberTools13 on Fedora20 Soren Wacker (Wed Apr 23 2014 - 16:24:17 PDT)
    - Re: [AMBER] FFTW3 related error when compiling AmberTools13 on Fedora20 Jason Swails (Wed Apr 23 2014 - 19:02:27 PDT)
    - Re: [AMBER] FFTW3 related error when compiling AmberTools13 on Fedora20 Soren Wacker (Thu Apr 24 2014 - 10:37:02 PDT)
[AMBER] OpenMP and MKL Eugene Yedvabny (Wed Apr 23 2014 - 16:21:23 PDT)
- Re: [AMBER] OpenMP and MKL Jason Swails (Wed Apr 23 2014 - 19:29:34 PDT)
  - Re: [AMBER] OpenMP and MKL Daniel Roe (Thu Apr 24 2014 - 07:15:35 PDT)
[AMBER] temperature increments newamber list (Wed Apr 23 2014 - 19:30:54 PDT)
- Re: [AMBER] temperature increments David A Case (Thu Apr 24 2014 - 04:50:09 PDT)
[AMBER] positive value of delta G in MMPBSA calculation Arunima Shilpi (Wed Apr 23 2014 - 20:08:09 PDT)
- Re: [AMBER] positive value of delta G in MMPBSA calculation Jason Swails (Thu Apr 24 2014 - 04:19:25 PDT)
  - Re: [AMBER] positive value of delta G in MMPBSA calculation Vlad Cojocaru (Thu Apr 24 2014 - 04:36:24 PDT)
[AMBER] modified residues Lara rajam (Wed Apr 23 2014 - 20:32:45 PDT)
- Re: [AMBER] modified residues FyD (Wed Apr 23 2014 - 21:38:26 PDT)
  - Re: [AMBER] modified residues Lara rajam (Wed Apr 23 2014 - 22:16:10 PDT)
    - Re: [AMBER] modified residues FyD (Wed Apr 23 2014 - 22:45:57 PDT)
    - Re: [AMBER] modified residues Lara rajam (Wed Apr 23 2014 - 23:03:43 PDT)
    - Re: [AMBER] modified residues FyD (Wed Apr 23 2014 - 23:27:48 PDT)
    - Re: [AMBER] modified residues David A Case (Thu Apr 24 2014 - 04:56:05 PDT)
- Re: [AMBER] modified residues Ilyas Yildirim (Thu Apr 24 2014 - 06:00:06 PDT)
[AMBER] Error: invalid argument launching kernel kNLGenerateSpatialHash ASFARINA AMIR HASSAN (Thu Apr 24 2014 - 02:01:44 PDT)
- Re: [AMBER] Error: invalid argument launching kernel kNLGenerateSpatialHash Jason Swails (Thu Apr 24 2014 - 04:26:33 PDT)
  - Re: [AMBER] Error: invalid argument launching kernel kNLGenerateSpatialHash ASFARINA AMIR HASSAN (Sun Apr 27 2014 - 22:51:54 PDT)
[AMBER] distance restraints Neha Gandhi (Thu Apr 24 2014 - 03:04:32 PDT)
- Re: [AMBER] distance restraints Bill Ross (Wed Jun 02 2010 - 10:24:55 PDT)
  - Re: [AMBER] distance restraints Jason Swails (Wed Jun 02 2010 - 10:56:38 PDT)
- Re: [AMBER] distance restraints Jason Swails (Thu Apr 24 2014 - 04:29:08 PDT)
[AMBER] Corresponding dry trajectory and PDB Soumendranath Bhakat (Thu Apr 24 2014 - 03:45:21 PDT)
- Re: [AMBER] Corresponding dry trajectory and PDB Jason Swails (Thu Apr 24 2014 - 04:32:01 PDT)
  - Re: [AMBER] Corresponding dry trajectory and PDB Soumendranath Bhakat (Thu Apr 24 2014 - 05:22:23 PDT)
[AMBER] MM-PBSA for two drug molecules Fabian Glaser (Thu Apr 24 2014 - 03:46:58 PDT)
- Re: [AMBER] MM-PBSA for two drug molecules Jason Swails (Thu Apr 24 2014 - 04:38:45 PDT)
  - Re: [AMBER] MM-PBSA for two drug molecules Fabian Glaser (Thu Apr 24 2014 - 04:48:05 PDT)
    - Re: [AMBER] MM-PBSA for two drug molecules Gustavo Seabra (Fri Apr 25 2014 - 13:27:27 PDT)
    - Re: [AMBER] MM-PBSA for two drug molecules wmsmith.uci.edu (Fri Apr 25 2014 - 18:09:38 PDT)
- Re: [AMBER] MM-PBSA for two drug molecules David A Case (Thu Apr 24 2014 - 05:07:49 PDT)
  - Re: [AMBER] MM-PBSA for two drug molecules Ayesha Fatima (Thu Apr 24 2014 - 05:18:18 PDT)
  - Re: [AMBER] MM-PBSA for two drug molecules Fabian Glaser (Thu Apr 24 2014 - 05:34:24 PDT)
    - Re: [AMBER] MM-PBSA for two drug molecules Ilyas Yildirim (Thu Apr 24 2014 - 06:12:35 PDT)
    - Re: [AMBER] MM-PBSA for two drug molecules Fabian Glaser (Sun Apr 27 2014 - 21:38:11 PDT)
    - Re: [AMBER] MM-PBSA for two drug molecules Fabian Glaser (Tue Apr 29 2014 - 23:41:28 PDT)
    - Re: [AMBER] MM-PBSA for two drug molecules David A Case (Thu Apr 24 2014 - 06:29:54 PDT)
[AMBER] could not extend the MD simulation sunita.tifrh.res.in (Thu Apr 24 2014 - 05:18:59 PDT)
- Re: [AMBER] could not extend the MD simulation Jason Swails (Thu Apr 24 2014 - 05:44:01 PDT)
[AMBER] MMPBSA error Nitin Sharma (Thu Apr 24 2014 - 07:05:47 PDT)
- Re: [AMBER] MMPBSA error Jason Swails (Thu Apr 24 2014 - 07:30:40 PDT)
  - Re: [AMBER] MMPBSA error Nitin Sharma (Thu Apr 24 2014 - 07:52:15 PDT)
[AMBER] installation error zahra khatti (Thu Apr 24 2014 - 08:50:04 PDT)
- Re: [AMBER] installation error David A Case (Thu Apr 24 2014 - 11:37:20 PDT)
  - Re: [AMBER] installation error zahra khatti (Fri Apr 25 2014 - 00:38:17 PDT)
[AMBER] Question about volume when switching from NPT to NVE ensemble Quynh Vo (Thu Apr 24 2014 - 11:08:08 PDT)
- Re: [AMBER] Question about volume when switching from NPT to NVE ensemble David A Case (Thu Apr 24 2014 - 12:31:35 PDT)
  - Re: [AMBER] Question about volume when switching from NPT to NVE ensemble Quynh Vo (Thu Apr 24 2014 - 12:58:15 PDT)
[AMBER] Reminder: AMBER Molecular Dynamics Workshop Barcelona Jun 2-6. Pre-Registration closes Apr 28th. Ross Walker (Thu Apr 24 2014 - 11:32:55 PDT)
[AMBER] About Clustering arundhati dutta (Thu Apr 24 2014 - 15:05:10 PDT)
[AMBER] average problem........ 전선희 (Thu Apr 24 2014 - 21:11:01 PDT)
- Re: [AMBER] average problem........ Daniel Roe (Fri Apr 25 2014 - 06:53:11 PDT)
[AMBER] MMPBSA query Arunima Shilpi (Thu Apr 24 2014 - 23:07:32 PDT)
- Re: [AMBER] MMPBSA query Soumendranath Bhakat (Thu Apr 24 2014 - 23:53:12 PDT)
  - [AMBER] Fwd: MMPBSA query Soumendranath Bhakat (Fri Apr 25 2014 - 00:04:29 PDT)
  - Re: [AMBER] MMPBSA query Jason Swails (Fri Apr 25 2014 - 04:25:41 PDT)
- Re: [AMBER] MMPBSA query Jason Swails (Fri Apr 25 2014 - 04:18:38 PDT)
[AMBER] LIPID14 force field for DPPC gel phase simulation Him Shweta (Fri Apr 25 2014 - 00:52:14 PDT)
[AMBER] Calculation of charges, force constanst, bonds, angles of a ligand using antechamber and gaussian Ahmet yıldırım (Fri Apr 25 2014 - 01:07:26 PDT)
- Re: [AMBER] Calculation of charges, force constanst, bonds, angles of a ligand using antechamber and gaussian Karl Kirschner (Fri Apr 25 2014 - 01:26:08 PDT)
  - Re: [AMBER] Calculation of charges, force constanst, bonds, angles of a ligand using antechamber and gaussian Ahmet yıldırım (Fri Apr 25 2014 - 23:57:41 PDT)
    - Re: [AMBER] Calculation of charges, force constanst, bonds, angles of a ligand using antechamber and gaussian FyD (Sat Apr 26 2014 - 04:31:12 PDT)
    - Re: [AMBER] Calculation of charges, force constanst, bonds, angles of a ligand using antechamber and gaussian Ahmet Yıldırım (Sat Apr 26 2014 - 05:22:51 PDT)
    - Re: [AMBER] Calculation of charges, force constanst, bonds, angles of a ligand using antechamber and gaussian FyD (Sat Apr 26 2014 - 06:46:33 PDT)
[AMBER] MD run Lara rajam (Fri Apr 25 2014 - 07:32:58 PDT)
- Re: [AMBER] MD run Jason Swails (Fri Apr 25 2014 - 08:11:44 PDT)
  - Re: [AMBER] MD run Lara rajam (Fri Apr 25 2014 - 08:23:33 PDT)
[AMBER] How to use Divalent ion parameters in tleap mish (Fri Apr 25 2014 - 07:40:23 PDT)
- Re: [AMBER] How to use Divalent ion parameters in tleap Pengfei Li (Fri Apr 25 2014 - 08:08:56 PDT)
  - Re: [AMBER] How to use Divalent ion parameters in tleap Pengfei Li (Fri Apr 25 2014 - 08:12:32 PDT)
- Re: [AMBER] How to use Divalent ion parameters in tleap Jason Swails (Fri Apr 25 2014 - 08:15:26 PDT)
  - Re: [AMBER] How to use Divalent ion parameters in tleap mish (Mon Apr 28 2014 - 00:27:27 PDT)
[AMBER] Hofmeister Effects Brown, Kyle (Fri Apr 25 2014 - 09:47:38 PDT)
[AMBER] problem with installation amber12 and ambertools13 in ubuntu zahra khatti (Fri Apr 25 2014 - 11:21:42 PDT)
- Re: [AMBER] problem with installation amber12 and ambertools13 in ubuntu zahra khatti (Fri Apr 25 2014 - 21:18:31 PDT)
  - Re: [AMBER] problem with installation amber12 and ambertools13 in ubuntu David A Case (Sat Apr 26 2014 - 06:13:48 PDT)
    - Re: [AMBER] problem with installation amber12 and ambertools13 in ubuntu Daniel Roe (Sat Apr 26 2014 - 09:28:50 PDT)
    - Re: [AMBER] problem with installation amber12 and ambertools13 in ubuntu zahra khatti (Sat Apr 26 2014 - 12:04:46 PDT)
[AMBER] simulated annelaing of protein ligand complex Nitin Sharma (Fri Apr 25 2014 - 11:46:17 PDT)
- Re: [AMBER] simulated annelaing of protein ligand complex David A Case (Fri Apr 25 2014 - 12:18:18 PDT)
[AMBER] problems with Amber12 installation - cuda and mpi zottisad (Fri Apr 25 2014 - 20:24:52 PDT)
- Re: [AMBER] problems with Amber12 installation - cuda and mpi Daniel Roe (Fri Apr 25 2014 - 21:03:45 PDT)
[AMBER] Accelerated MD Sourav Purohit (Sat Apr 26 2014 - 04:18:19 PDT)
[AMBER] Accelerated MD Sourav Purohit (Sun Apr 27 2014 - 04:01:08 PDT)
- Re: [AMBER] Accelerated MD Jason Swails (Sun Apr 27 2014 - 07:01:31 PDT)
  - Re: [AMBER] Accelerated MD Vlad Cojocaru (Sun Apr 27 2014 - 07:26:39 PDT)
[AMBER] Corresponding PDB and snapshot PDB Soumendranath Bhakat (Sun Apr 27 2014 - 05:00:50 PDT)
- Re: [AMBER] Corresponding PDB and snapshot PDB David A Case (Sun Apr 27 2014 - 05:33:50 PDT)
- Re: [AMBER] Corresponding PDB and snapshot PDB Jason Swails (Sun Apr 27 2014 - 06:50:37 PDT)
  - Re: [AMBER] Corresponding PDB and snapshot PDB Daniel Roe (Sun Apr 27 2014 - 12:59:49 PDT)
[AMBER] negative dihedral energy with ff14ipq Thomas Evangelidis (Sun Apr 27 2014 - 12:42:50 PDT)
- Re: [AMBER] negative dihedral energy with ff14ipq Jason Swails (Sun Apr 27 2014 - 14:34:46 PDT)
  - Re: [AMBER] negative dihedral energy with ff14ipq Thomas Evangelidis (Mon Apr 28 2014 - 02:17:12 PDT)
    - Re: [AMBER] negative dihedral energy with ff14ipq David A Case (Mon Apr 28 2014 - 04:39:01 PDT)
    - Re: [AMBER] negative dihedral energy with ff14ipq Thomas Evangelidis (Mon Apr 28 2014 - 05:05:08 PDT)
    - Re: [AMBER] negative dihedral energy with ff14ipq Jason Swails (Mon Apr 28 2014 - 05:13:13 PDT)
[AMBER] velocity information in restart file HM (Mon Apr 28 2014 - 04:54:29 PDT)
- Re: [AMBER] velocity information in restart file Jason Swails (Mon Apr 28 2014 - 05:16:36 PDT)
[AMBER] Simulation of protein- cyclic nucleotide complex James Starlight (Mon Apr 28 2014 - 05:02:21 PDT)
- Re: [AMBER] Simulation of protein- cyclic nucleotide complex de Waal, Parker (Mon Apr 28 2014 - 05:19:55 PDT)
  - Re: [AMBER] Simulation of protein- cyclic nucleotide complex James Starlight (Tue Apr 29 2014 - 02:48:49 PDT)
    - Re: [AMBER] Simulation of protein- cyclic nucleotide complex David A Case (Tue Apr 29 2014 - 04:54:12 PDT)
    - Re: [AMBER] Simulation of protein- cyclic nucleotide complex James Starlight (Tue Apr 29 2014 - 08:34:53 PDT)
    - Re: [AMBER] Simulation of protein- cyclic nucleotide complex James Starlight (Tue Apr 29 2014 - 09:54:26 PDT)
    - Re: [AMBER] Simulation of protein- cyclic nucleotide complex David A Case (Tue Apr 29 2014 - 10:12:38 PDT)
    - Re: [AMBER] Simulation of protein- cyclic nucleotide complex James Starlight (Tue Apr 29 2014 - 11:48:11 PDT)
    - Re: [AMBER] Simulation of protein- cyclic nucleotide complex Jason Swails (Tue Apr 29 2014 - 12:38:50 PDT)
    - Re: [AMBER] Simulation of protein- cyclic nucleotide complex James Starlight (Tue Apr 29 2014 - 23:33:49 PDT)
    - Re: [AMBER] Simulation of protein- cyclic nucleotide complex James Starlight (Tue Apr 29 2014 - 23:52:23 PDT)
    - Re: [AMBER] Simulation of protein- cyclic nucleotide complex James Starlight (Tue Apr 29 2014 - 23:53:19 PDT)
    - Re: [AMBER] Simulation of protein- cyclic nucleotide complex James Starlight (Wed Apr 30 2014 - 03:27:55 PDT)
    - Re: [AMBER] Simulation of protein- cyclic nucleotide complex Jason Swails (Wed Apr 30 2014 - 04:43:10 PDT)
    - Re: [AMBER] Simulation of protein- cyclic nucleotide complex James Starlight (Wed Apr 30 2014 - 06:59:00 PDT)
[AMBER] pmemd.cuda error amber14 Pierpaolo Cacciotto (Mon Apr 28 2014 - 09:05:09 PDT)
- Re: [AMBER] pmemd.cuda error amber14 Jason Swails (Mon Apr 28 2014 - 09:34:43 PDT)
[AMBER] Regarding simulation of alanine molecules in water box MOHD HOMAIDUR RAHMAN (Tue Apr 29 2014 - 03:47:33 PDT)
- Re: [AMBER] Regarding simulation of alanine molecules in water box Jason Swails (Tue Apr 29 2014 - 04:21:33 PDT)
[AMBER] Quantification of alpha helix Suchetana Gupta (Tue Apr 29 2014 - 08:06:56 PDT)
- Re: [AMBER] Quantification of alpha helix Carlos Simmerling (Tue Apr 29 2014 - 08:34:46 PDT)
  - Re: [AMBER] Quantification of alpha helix Suchetana Gupta (Tue Apr 29 2014 - 11:06:02 PDT)
[AMBER] Minimization with (0, 0, 0) coordinates Jean-Patrick Francoia (Tue Apr 29 2014 - 08:19:45 PDT)
- Re: [AMBER] Minimization with (0, 0, 0) coordinates Robert Molt (Tue Apr 29 2014 - 08:24:10 PDT)
- Re: [AMBER] Minimization with (0, 0, 0) coordinates Daniel Roe (Tue Apr 29 2014 - 08:30:08 PDT)
  - Re: [AMBER] Minimization with (0, 0, 0) coordinates Jean-Patrick Francoia (Tue Apr 29 2014 - 08:44:09 PDT)
[AMBER] PCA analysis Ibrahim Said (Tue Apr 29 2014 - 08:40:05 PDT)
- Re: [AMBER] PCA analysis Andre C. Stiel (Tue Apr 29 2014 - 08:55:22 PDT)
  - Re: [AMBER] PCA analysis Daniel Roe (Tue Apr 29 2014 - 09:05:39 PDT)
[AMBER] Extract velocity from the restart file Yin, Guowei (Tue Apr 29 2014 - 14:03:42 PDT)
- Re: [AMBER] Extract velocity from the restart file David A Case (Tue Apr 29 2014 - 17:54:30 PDT)
- Re: [AMBER] Extract velocity from the restart file Yin, Guowei (Wed Apr 30 2014 - 08:14:28 PDT)
  - Re: [AMBER] Extract velocity from the restart file Jason Swails (Wed Apr 30 2014 - 08:32:54 PDT)
    - Re: [AMBER] Extract velocity from the restart file Yin, Guowei (Mon May 05 2014 - 06:39:17 PDT)
    - Re: [AMBER] Extract velocity from the restart file Jason Swails (Mon May 05 2014 - 07:13:10 PDT)
    - Re: [AMBER] Extract velocity from the restart file Yin, Guowei (Mon May 05 2014 - 07:16:27 PDT)
[AMBER] Minimization with restraints Valentina Romano (Wed Apr 30 2014 - 02:42:02 PDT)
- Re: [AMBER] Minimization with restraints Jason Swails (Wed Apr 30 2014 - 04:51:44 PDT)
  - Re: [AMBER] Minimization with restraints Valentina Romano (Wed Apr 30 2014 - 05:45:24 PDT)
[AMBER] How to extract each frame of a trajectory as individual .mdcrd files? Yip Yew Mun (Wed Apr 30 2014 - 06:28:48 PDT)
- Re: [AMBER] How to extract each frame of a trajectory as individual .mdcrd files? Brian Radak (Wed Apr 30 2014 - 06:43:51 PDT)
  - Re: [AMBER] How to extract each frame of a trajectory as individual .mdcrd files? Yip Yew Mun (Wed Apr 30 2014 - 08:45:30 PDT)
    - Re: [AMBER] How to extract each frame of a trajectory as individual .mdcrd files? Jason Swails (Wed Apr 30 2014 - 08:55:26 PDT)
  - Re: [AMBER] How to extract each frame of a trajectory as individual .mdcrd files? Yew Mun Yip (Wed Apr 30 2014 - 09:05:39 PDT)
[AMBER] ptraj in parallel zahra khatti (Wed Apr 30 2014 - 08:56:49 PDT)
- Re: [AMBER] ptraj in parallel Jason Swails (Wed Apr 30 2014 - 10:43:18 PDT)
[AMBER] how to protonate phosphate groups of nucleotides Valentina D'Atri (Wed Apr 30 2014 - 10:13:32 PDT)
- Re: [AMBER] how to protonate phosphate groups of nucleotides FyD (Sun May 04 2014 - 22:19:14 PDT)
  - Re: [AMBER] how to protonate phosphate groups of nucleotides Valentina D'Atri (Wed May 28 2014 - 08:59:37 PDT)
    - Re: [AMBER] how to protonate phosphate groups of nucleotides FyD (Thu May 29 2014 - 00:08:35 PDT)
[AMBER] Problems with the Amber-14 compilation with CUDA-5.5 James Starlight (Thu May 01 2014 - 00:03:22 PDT)
- Re: [AMBER] Problems with the Amber-14 compilation with CUDA-5.5 David A Case (Thu May 01 2014 - 05:52:15 PDT)
  - Re: [AMBER] Problems with the Amber-14 compilation with CUDA-5.5 James Starlight (Thu May 01 2014 - 06:47:32 PDT)
    - Re: [AMBER] Problems with the Amber-14 compilation with CUDA-5.5 David A Case (Thu May 01 2014 - 06:54:42 PDT)
    - Re: [AMBER] Problems with the Amber-14 compilation with CUDA-5.5 James Starlight (Thu May 01 2014 - 07:06:05 PDT)
    - Re: [AMBER] Problems with the Amber-14 compilation with CUDA-5.5 Daniel Roe (Thu May 01 2014 - 07:15:39 PDT)
    - Re: [AMBER] Problems with the Amber-14 compilation with CUDA-5.5 James Starlight (Thu May 01 2014 - 07:17:15 PDT)
    - Re: [AMBER] Problems with the Amber-14 compilation with CUDA-5.5 James Starlight (Thu May 01 2014 - 07:19:30 PDT)
    - Re: [AMBER] Problems with the Amber-14 compilation with CUDA-5.5 Jason Swails (Thu May 01 2014 - 07:25:57 PDT)
    - Re: [AMBER] Problems with the Amber-14 compilation with CUDA-5.5 James Starlight (Sat May 03 2014 - 00:10:44 PDT)
[AMBER] Parameters for FAD amin.imtech.res.in (Thu May 01 2014 - 06:26:59 PDT)
- Re: [AMBER] Parameters for FAD ABEL Stephane 175950 (Thu May 01 2014 - 06:37:41 PDT)
  - Re: [AMBER] Parameters for FAD amin.imtech.res.in (Thu May 01 2014 - 12:05:44 PDT)
    - Re: [AMBER] Parameters for FAD Jason Swails (Thu May 01 2014 - 12:20:38 PDT)
    - Re: [AMBER] Parameters for FAD amin.imtech.res.in (Thu May 01 2014 - 22:19:09 PDT)
    - Re: [AMBER] Parameters for FAD Jason Swails (Fri May 02 2014 - 04:40:01 PDT)
[AMBER] solvating molecule kirtana S (Thu May 01 2014 - 18:26:36 PDT)
[AMBER] Prepareing branched residue kurisaki (Thu May 01 2014 - 22:57:23 PDT)
- Re: [AMBER] Prepareing branched residue FyD (Sun May 04 2014 - 23:47:14 PDT)
  - Re: [AMBER] Prepareing branched residue kurisaki (Tue May 06 2014 - 19:19:04 PDT)
    - Re: [AMBER] Prepareing branched residue FyD (Wed May 07 2014 - 12:05:34 PDT)
[AMBER] Intermittent error during T-REMD on 8 GPU computer Milo Westler (Fri May 02 2014 - 07:33:48 PDT)
- Re: [AMBER] Intermittent error during T-REMD on 8 GPU computer Jason Swails (Fri May 02 2014 - 08:16:20 PDT)
  - Re: [AMBER] Intermittent error during T-REMD on 8 GPU computer Milo Westler (Fri May 02 2014 - 08:33:05 PDT)
[AMBER] Percent Occupancey with PCA Nicole Ippolito (Fri May 02 2014 - 08:17:34 PDT)
- Re: [AMBER] Percent Occupancey with PCA Daniel Roe (Sat May 03 2014 - 00:11:50 PDT)
  - Re: [AMBER] Percent Occupancey with PCA Nicole Ippolito (Mon May 05 2014 - 08:28:27 PDT)
[AMBER] alanine scanning Nitin Sharma (Sat May 03 2014 - 06:47:35 PDT)
- Re: [AMBER] alanine scanning Bill Miller III (Sat May 03 2014 - 12:03:45 PDT)
  - Re: [AMBER] alanine scanning Nitin Sharma (Sun May 04 2014 - 08:29:30 PDT)
[AMBER] vlimit exceeded error when switch from NPT to NVE Quynh Vo (Sat May 03 2014 - 22:39:22 PDT)
- Re: [AMBER] vlimit exceeded error when switch from NPT to NVE David A Case (Sun May 04 2014 - 04:46:46 PDT)
  - Re: [AMBER] vlimit exceeded error when switch from NPT to NVE Quynh Vo (Sun May 04 2014 - 11:06:42 PDT)
[AMBER] sander? sammia khatak (Sat May 03 2014 - 23:37:16 PDT)
- Re: [AMBER] sander? David A Case (Sun May 04 2014 - 08:27:33 PDT)
[AMBER] Questions about nmode Command 张明焜 (Sun May 04 2014 - 00:59:01 PDT)
- Re: [AMBER] Questions about nmode Command David A Case (Sun May 04 2014 - 08:25:22 PDT)
[AMBER] Fwd: Re: [q4md-fft] FAD parameters from F-90 FyD (Sun May 04 2014 - 22:02:54 PDT)
[AMBER] acpype on ambertools13 Ahmet yıldırım (Mon May 05 2014 - 01:08:22 PDT)
- Re: [AMBER] acpype on ambertools13 Jason Swails (Mon May 05 2014 - 03:08:31 PDT)
  - Re: [AMBER] acpype on ambertools13 Ahmet yıldırım (Mon May 05 2014 - 03:14:20 PDT)
    - Re: [AMBER] acpype on ambertools13 Jason Swails (Mon May 05 2014 - 04:18:57 PDT)
- Re: [AMBER] acpype on ambertools13 Alan (Mon May 05 2014 - 08:16:36 PDT)
[AMBER] psf generation sammia khatak (Mon May 05 2014 - 01:44:42 PDT)
- Re: [AMBER] psf generation Soumendranath Bhakat (Mon May 05 2014 - 01:58:27 PDT)
- Re: [AMBER] psf generation Jason Swails (Mon May 05 2014 - 03:06:13 PDT)
[AMBER] Empirical force fields: release new version of RED Server Dev/PyRED FyD (Mon May 05 2014 - 04:00:11 PDT)
- Re: [AMBER] Empirical force fields: release new version of RED Server Dev/PyRED Marek Maly (Mon May 05 2014 - 06:22:56 PDT)
  - Re: [AMBER] Empirical force fields: release new version of RED Server Dev/PyRED FyD (Mon May 05 2014 - 23:22:33 PDT)
    - Re: [AMBER] Empirical force fields: release new version of RED Server Dev/PyRED Marek Maly (Tue May 06 2014 - 15:06:49 PDT)
    - Re: [AMBER] Empirical force fields: release new version of RED Server Dev/PyRED FyD (Wed May 07 2014 - 08:05:26 PDT)
    - Re: [AMBER] Empirical force fields: release new version of RED Server Dev/PyRED Marek Maly (Wed May 07 2014 - 09:22:40 PDT)
    - Re: [AMBER] Empirical force fields: release new version of RED Server Dev/PyRED FyD (Wed May 07 2014 - 11:38:09 PDT)
    - Re: [AMBER] Empirical force fields: release new version of RED Server Dev/PyRED Marek Maly (Wed May 07 2014 - 12:13:45 PDT)
[AMBER] Extract MD co-ordinates Soumendranath Bhakat (Mon May 05 2014 - 07:19:14 PDT)
- Re: [AMBER] Extract MD co-ordinates Daniel Roe (Mon May 05 2014 - 09:27:24 PDT)
  - Re: [AMBER] Extract MD co-ordinates Soumendranath Bhakat (Mon May 05 2014 - 10:28:42 PDT)
    - Re: [AMBER] Extract MD co-ordinates Jason Swails (Mon May 05 2014 - 10:56:45 PDT)
[AMBER] Installation of AmberTools13 fabien.ibanez.modis.fr.netgrs.com (Mon May 05 2014 - 08:11:56 PDT)
- Re: [AMBER] Installation of AmberTools13 Jason Swails (Mon May 05 2014 - 08:47:58 PDT)
[AMBER] Percent Occupancy with PCA Nicole Ippolito (Mon May 05 2014 - 08:25:26 PDT)
- Re: [AMBER] Percent Occupancy with PCA Jason Swails (Mon May 05 2014 - 08:50:50 PDT)
[AMBER] PMF as a function of Q, fraction of native contacts Nihal Korkmaz (Mon May 05 2014 - 15:47:13 PDT)
- Re: [AMBER] PMF as a function of Q, fraction of native contacts Carlos Simmerling (Mon May 05 2014 - 16:25:58 PDT)
  - Re: [AMBER] PMF as a function of Q, fraction of native contacts Brian Radak (Tue May 06 2014 - 06:51:02 PDT)
  - Re: [AMBER] PMF as a function of Q, fraction of native contacts Adrian Roitberg (Tue May 06 2014 - 06:59:29 PDT)
[AMBER] handling long trajs for PCA and components plot newamber list (Mon May 05 2014 - 16:23:26 PDT)
- Re: [AMBER] handling long trajs for PCA and components plot David A Case (Mon May 05 2014 - 18:26:09 PDT)
- Re: [AMBER] handling long trajs for PCA and components plot Daniel Roe (Tue May 06 2014 - 10:24:53 PDT)
  - Re: [AMBER] handling long trajs for PCA and components plot newamber list (Tue May 06 2014 - 19:13:37 PDT)
    - Re: [AMBER] handling long trajs for PCA and components plot Daniel Roe (Tue May 06 2014 - 20:27:07 PDT)
    - Re: [AMBER] handling long trajs for PCA and components plot newamber list (Tue May 06 2014 - 21:21:41 PDT)
    - Re: [AMBER] handling long trajs for PCA and components plot Daniel Roe (Wed May 07 2014 - 07:52:12 PDT)
    - Re: [AMBER] handling long trajs for PCA and components plot newamber list (Wed May 07 2014 - 15:27:25 PDT)
    - Re: [AMBER] handling long trajs for PCA and components plot Daniel Roe (Thu May 08 2014 - 08:04:14 PDT)
    - Re: [AMBER] handling long trajs for PCA and components plot newamber list (Sun May 11 2014 - 12:10:13 PDT)
    - Re: [AMBER] handling long trajs for PCA and components plot Daniel Roe (Mon May 12 2014 - 10:28:25 PDT)
    - Re: [AMBER] handling long trajs for PCA and components plot Daniel Roe (Mon May 19 2014 - 09:33:03 PDT)
    - Re: [AMBER] handling long trajs for PCA and components plot newamber list (Wed May 21 2014 - 14:07:02 PDT)
[AMBER] Regarding Calculation of Hydrogen Bond Energy MOHD HOMAIDUR RAHMAN (Mon May 05 2014 - 23:30:05 PDT)
[AMBER] Problem with the amber-14 compilation on Debian James Starlight (Tue May 06 2014 - 00:09:37 PDT)
- Re: [AMBER] Problem with the amber-14 compilation on Debian Jason Swails (Tue May 06 2014 - 05:05:15 PDT)
  - Re: [AMBER] Problem with the amber-14 compilation on Debian James Starlight (Tue May 06 2014 - 07:04:22 PDT)
    - Re: [AMBER] Problem with the amber-14 compilation on Debian Jason Swails (Tue May 06 2014 - 07:55:47 PDT)
[AMBER] Pairwise interaction energy between each residue MOHD HOMAIDUR RAHMAN (Tue May 06 2014 - 00:28:04 PDT)
- Re: [AMBER] Pairwise interaction energy between each residue Jason Swails (Tue May 06 2014 - 07:26:24 PDT)
[AMBER] Membrane protein simulation James Starlight (Tue May 06 2014 - 03:15:29 PDT)
- Re: [AMBER] Membrane protein simulation Jason Swails (Tue May 06 2014 - 04:57:52 PDT)
  - Re: [AMBER] Membrane protein simulation James Starlight (Wed May 07 2014 - 23:50:22 PDT)
    - Re: [AMBER] Membrane protein simulation Ross Walker (Thu May 08 2014 - 00:04:46 PDT)
[AMBER] number of frames in MMPBGBSA Nitin Sharma (Tue May 06 2014 - 05:15:24 PDT)
- Re: [AMBER] number of frames in MMPBGBSA Bill Miller III (Tue May 06 2014 - 07:29:07 PDT)
- Re: [AMBER] number of frames in MMPBGBSA Soumendranath Bhakat (Tue May 06 2014 - 08:22:44 PDT)
  - Re: [AMBER] number of frames in MMPBGBSA Nitin Sharma (Tue May 06 2014 - 08:38:06 PDT)
    - Re: [AMBER] number of frames in MMPBGBSA Soumendranath Bhakat (Tue May 06 2014 - 11:17:02 PDT)
[AMBER] dihedrals in CYT residue Sidney Elmer (Tue May 06 2014 - 10:04:16 PDT)
- Re: [AMBER] dihedrals in CYT residue Sidney Elmer (Tue May 06 2014 - 10:30:14 PDT)
- Re: [AMBER] dihedrals in CYT residue Jason Swails (Tue May 06 2014 - 10:33:28 PDT)
  - Re: [AMBER] dihedrals in CYT residue Sidney Elmer (Tue May 06 2014 - 11:04:48 PDT)
[AMBER] Fwd: Re: Amber webminar Adrian Roitberg (Tue May 06 2014 - 11:55:07 PDT)
[AMBER] Processing a subset of mdcrd frames Eugene Yedvabny (Tue May 06 2014 - 13:34:19 PDT)
- Re: [AMBER] Processing a subset of mdcrd frames Daniel Roe (Tue May 06 2014 - 13:54:15 PDT)
  - Re: [AMBER] Processing a subset of mdcrd frames Eugene Yedvabny (Tue May 06 2014 - 15:19:21 PDT)
    - Re: [AMBER] Processing a subset of mdcrd frames Daniel Roe (Tue May 06 2014 - 20:29:20 PDT)
[AMBER] MMPBSA & mmpbsa_py_nabnmode frequent crashes Amir Shahmoradi (Tue May 06 2014 - 17:07:45 PDT)
- Re: [AMBER] MMPBSA & mmpbsa_py_nabnmode frequent crashes Jason Swails (Tue May 06 2014 - 18:53:01 PDT)
[AMBER] how to generate a complete amino acid in suitable for the vacuum simulation 张明焜 (Tue May 06 2014 - 20:38:49 PDT)
- Re: [AMBER] how to generate a complete amino acid in suitable for the vacuum simulation David A Case (Wed May 07 2014 - 05:13:18 PDT)
- Re: [AMBER] how to generate a complete amino acid in suitable for the vacuum simulation FyD (Wed May 07 2014 - 08:10:38 PDT)
[AMBER] PDB for 1-octanol molecules Mari Mak (Tue May 06 2014 - 23:13:18 PDT)
- Re: [AMBER] PDB for 1-octanol molecules Jason Swails (Wed May 07 2014 - 04:55:04 PDT)
- Re: [AMBER] PDB for 1-octanol molecules David A Case (Wed May 07 2014 - 05:17:09 PDT)
- Re: [AMBER] PDB for 1-octanol molecules FyD (Wed May 07 2014 - 08:13:05 PDT)
- [AMBER] please let me unsubscribe of this adm (Wed May 07 2014 - 23:31:28 PDT)
  - Re: [AMBER] please let me unsubscribe of this Jason Swails (Thu May 08 2014 - 04:12:46 PDT)
[AMBER] Amber12 parallel installation error with MPICH2 UBUNTU 14.04 M. Reza Ganjalikhany (Wed May 07 2014 - 01:32:52 PDT)
- Re: [AMBER] Amber12 parallel installation error with MPICH2 UBUNTU 14.04 Jason Swails (Wed May 07 2014 - 05:04:37 PDT)
- Re: [AMBER] Amber12 parallel installation error with MPICH2 UBUNTU 14.04 David A Case (Wed May 07 2014 - 05:32:25 PDT)
  - Re: [AMBER] Amber12 parallel installation error with MPICH2 UBUNTU 14.04 M. Reza Ganjalikhany (Fri May 09 2014 - 23:09:08 PDT)
    - Re: [AMBER] Amber12 parallel installation error with MPICH2 UBUNTU 14.04 David A Case (Sat May 10 2014 - 05:30:40 PDT)
    - Re: [AMBER] Amber12 parallel installation error with MPICH2 UBUNTU 14.04 M. Reza Ganjalikhany (Sat May 10 2014 - 12:09:08 PDT)
    - Re: [AMBER] Amber12 parallel installation error with MPICH2 UBUNTU 14.04 David A Case (Sat May 10 2014 - 14:58:43 PDT)
[AMBER] Simulations using pmemd.cuda James Starlight (Wed May 07 2014 - 02:31:53 PDT)
- Re: [AMBER] Simulations using pmemd.cuda Marc van der Kamp (Wed May 07 2014 - 03:10:34 PDT)
  - Re: [AMBER] Simulations using pmemd.cuda James Starlight (Wed May 07 2014 - 03:18:00 PDT)
    - Re: [AMBER] Simulations using pmemd.cuda James Starlight (Wed May 07 2014 - 03:39:12 PDT)
    - Re: [AMBER] Simulations using pmemd.cuda Jason Swails (Wed May 07 2014 - 04:34:15 PDT)
    - Re: [AMBER] Simulations using pmemd.cuda Ross Walker (Wed May 07 2014 - 08:44:36 PDT)
    - Re: [AMBER] Simulations using pmemd.cuda James Starlight (Wed May 07 2014 - 23:36:06 PDT)
[AMBER] "cudaDeviceEnablePeerAccess all CUDA-capable devices are busy or unavailable" ahmed.sajid.stfc.ac.uk (Wed May 07 2014 - 02:46:13 PDT)
- Re: [AMBER] "cudaDeviceEnablePeerAccess all CUDA-capable devices are busy or unavailable" Jason Swails (Wed May 07 2014 - 04:37:55 PDT)
- Re: [AMBER] "cudaDeviceEnablePeerAccess all CUDA-capable devices are busy or unavailable" Ross Walker (Wed May 07 2014 - 08:41:02 PDT)
  - Re: [AMBER] "cudaDeviceEnablePeerAccess all CUDA-capable devices are busy or unavailable" Scott Le Grand (Wed May 07 2014 - 10:31:16 PDT)
    - Re: [AMBER] "cudaDeviceEnablePeerAccess all CUDA-capable devices are busy or unavailable" ahmed.sajid.stfc.ac.uk (Wed May 07 2014 - 23:28:05 PDT)
    - Re: [AMBER] "cudaDeviceEnablePeerAccess all CUDA-capable devices are busy or unavailable" Ross Walker (Thu May 08 2014 - 00:00:46 PDT)
    - Re: [AMBER] "cudaDeviceEnablePeerAccess all CUDA-capable devices are busy or unavailable" ahmed.sajid.stfc.ac.uk (Thu May 08 2014 - 01:28:40 PDT)
    - Re: [AMBER] "cudaDeviceEnablePeerAccess all CUDA-capable devices are busy or unavailable" ahmed.sajid.stfc.ac.uk (Thu May 08 2014 - 01:31:07 PDT)
    - Re: [AMBER] "cudaDeviceEnablePeerAccess all CUDA-capable devices are busy or unavailable" Ross Walker (Thu May 08 2014 - 01:59:05 PDT)
    - Re: [AMBER] "cudaDeviceEnablePeerAccess all CUDA-capable devices are busy or unavailable" Gustavo Seabra (Thu May 08 2014 - 06:10:58 PDT)
[AMBER] re-imaging bilayer Vijay Manickam Achari (Wed May 07 2014 - 05:00:14 PDT)
- Re: [AMBER] re-imaging bilayer Jason Swails (Wed May 07 2014 - 05:36:41 PDT)
- Re: [AMBER] re-imaging bilayer Daniel Roe (Wed May 07 2014 - 07:45:45 PDT)
- Re: [AMBER] re-imaging bilayer Sally Pias (Thu Jul 07 2016 - 06:41:17 PDT)
  - Re: [AMBER] re-imaging bilayer Daniel Roe (Thu Jul 07 2016 - 07:37:57 PDT)
    - Re: [AMBER] re-imaging bilayer Dickson, Callum J (Thu Jul 07 2016 - 08:43:37 PDT)
    - Re: [AMBER] re-imaging bilayer Amy Rice (Thu Jul 07 2016 - 09:12:48 PDT)
    - Re: [AMBER] re-imaging bilayer Sally Pias (Tue Jul 19 2016 - 19:49:20 PDT)
[AMBER] FapydG parameters Norbert GARNIER (Wed May 07 2014 - 05:30:27 PDT)
- Re: [AMBER] FapydG parameters Christina Bergonzo (Wed May 07 2014 - 06:51:25 PDT)
- Re: [AMBER] FapydG parameters Carlos Simmerling (Wed May 07 2014 - 06:54:04 PDT)
  - Re: [AMBER] FapydG parameters Norbert GARNIER (Wed May 07 2014 - 07:02:58 PDT)
[AMBER] error in equilibration Lara rajam (Wed May 07 2014 - 07:03:23 PDT)
- Re: [AMBER] error in equilibration Jason Swails (Wed May 07 2014 - 07:21:29 PDT)
[AMBER] Fwd: Re: PDB for 1-octanol molecules FyD (Wed May 07 2014 - 08:16:17 PDT)
[AMBER] Question about structure factor? Xiaoquan Sun (Wed May 07 2014 - 13:33:53 PDT)
- Re: [AMBER] Question about structure factor? David A Case (Wed May 07 2014 - 15:18:20 PDT)
[AMBER] Modeling systems with non-standard residues James Starlight (Wed May 07 2014 - 23:43:15 PDT)
- Re: [AMBER] Modeling systems with non-standard residues FyD (Thu May 08 2014 - 04:08:52 PDT)
- Re: [AMBER] Modeling systems with non-standard residues Jason Swails (Thu May 08 2014 - 04:17:18 PDT)
  - Re: [AMBER] Modeling systems with non-standard residues James Starlight (Sun May 11 2014 - 03:24:39 PDT)
    - Re: [AMBER] Modeling systems with non-standard residues Brent Krueger (Sun May 11 2014 - 05:35:29 PDT)
    - Re: [AMBER] Modeling systems with non-standard residues James Starlight (Mon May 12 2014 - 00:05:54 PDT)
    - Re: [AMBER] Modeling systems with non-standard residues Parker de Waal (Mon May 12 2014 - 04:31:30 PDT)
    - Re: [AMBER] Modeling systems with non-standard residues Jason Swails (Mon May 12 2014 - 04:41:33 PDT)
    - Re: [AMBER] Modeling systems with non-standard residues James Starlight (Tue May 13 2014 - 04:41:03 PDT)
[AMBER] Error: invalid argument launching kernel kNLGenerateSpatialHash ASFARINA AMIR HASSAN (Thu May 08 2014 - 01:31:27 PDT)
- Re: [AMBER] Error: invalid argument launching kernel kNLGenerateSpatialHash Ross Walker (Thu May 08 2014 - 02:00:50 PDT)
[AMBER] syntax error and nab2c failed when using NAB Dongshan Wei (Thu May 08 2014 - 02:23:18 PDT)
- Re: [AMBER] syntax error and nab2c failed when using NAB Jason Swails (Thu May 08 2014 - 04:56:49 PDT)
  - Re: [AMBER] syntax error and nab2c failed when using NAB Dongshan Wei (Thu May 08 2014 - 05:14:00 PDT)
    - Re: [AMBER] syntax error and nab2c failed when using NAB Jason Swails (Thu May 08 2014 - 05:23:40 PDT)
    - Re: [AMBER] syntax error and nab2c failed when using NAB Dongshan Wei (Thu May 08 2014 - 05:36:37 PDT)
    - Re: [AMBER] syntax error and nab2c failed when using NAB Jason Swails (Thu May 08 2014 - 05:54:43 PDT)
    - Re: [AMBER] syntax error and nab2c failed when using NAB Dongshan Wei (Thu May 08 2014 - 06:05:30 PDT)
    - Re: [AMBER] syntax error and nab2c failed when using NAB Jason Swails (Thu May 08 2014 - 06:41:20 PDT)
    - Re: [AMBER] syntax error and nab2c failed when using NAB David A Case (Thu May 08 2014 - 05:59:21 PDT)
    - Re: [AMBER] syntax error and nab2c failed when using NAB Dongshan Wei (Thu May 08 2014 - 06:27:15 PDT)
[AMBER] Defining memory for QM/MM calculations Kshatresh Dutta Dubey (Thu May 08 2014 - 02:40:48 PDT)
- Re: [AMBER] Defining memory for QM/MM calculations Jason Swails (Thu May 08 2014 - 04:29:23 PDT)
  - Re: [AMBER] Defining memory for QM/MM calculations Kshatresh Dutta Dubey (Thu May 08 2014 - 05:02:30 PDT)
[AMBER] sqm convergence failure Hannes Loeffler (Thu May 08 2014 - 03:16:06 PDT)
- Re: [AMBER] sqm convergence failure FyD (Thu May 08 2014 - 04:23:27 PDT)
  - Re: [AMBER] sqm convergence failure Hannes Loeffler (Thu May 08 2014 - 05:03:56 PDT)
- Re: [AMBER] sqm convergence failure Jason Swails (Thu May 08 2014 - 05:22:41 PDT)
  - Re: [AMBER] sqm convergence failure Hannes Loeffler (Thu May 08 2014 - 05:49:09 PDT)
    - Re: [AMBER] sqm convergence failure Jason Swails (Thu May 08 2014 - 06:25:02 PDT)
    - Re: [AMBER] sqm convergence failure hannes.loeffler.stfc.ac.uk (Thu May 08 2014 - 10:44:41 PDT)
    - Re: [AMBER] sqm convergence failure David A Case (Fri May 09 2014 - 12:49:27 PDT)
    - Re: [AMBER] sqm convergence failure Hannes Loeffler (Mon May 12 2014 - 02:54:48 PDT)
    - Re: [AMBER] sqm convergence failure Jason Swails (Mon May 12 2014 - 04:10:35 PDT)
    - Re: [AMBER] sqm convergence failure David A Case (Mon May 12 2014 - 05:01:22 PDT)
- Re: [AMBER] sqm convergence failure Gerald Monard (Tue May 20 2014 - 07:57:04 PDT)
  - Re: [AMBER] sqm convergence failure David A Case (Tue May 20 2014 - 08:30:20 PDT)
    - Re: [AMBER] sqm convergence failure Jason Swails (Tue May 20 2014 - 09:00:02 PDT)
    - Re: [AMBER] sqm convergence failure FyD (Tue May 20 2014 - 13:30:38 PDT)
[AMBER] SolvateBox command George Patargias (Thu May 08 2014 - 03:50:34 PDT)
- Re: [AMBER] SolvateBox command Jason Swails (Thu May 08 2014 - 04:25:42 PDT)
  - Re: [AMBER] SolvateBox command George Patargias (Thu May 08 2014 - 08:13:35 PDT)
  - Re: [AMBER] SolvateBox command Bill Ross (Mon Jun 02 2014 - 17:18:41 PDT)
- Re: [AMBER] SolvateBox command Bill Ross (Thu May 15 2014 - 16:30:00 PDT)
[AMBER] valve of VDW too high David Chen (Thu May 08 2014 - 04:28:25 PDT)
- Re: [AMBER] valve of VDW too high Jason Swails (Thu May 08 2014 - 04:41:34 PDT)
[AMBER] creating quadruplex structure with NAB Ander (Thu May 08 2014 - 05:12:41 PDT)
[AMBER] mmpbsa: the nmode calculation Fengxue Li (Thu May 08 2014 - 06:41:53 PDT)
[AMBER] softcore potential flag Asaminew Haile (Thu May 08 2014 - 07:37:23 PDT)
- Re: [AMBER] softcore potential flag David A Case (Thu May 08 2014 - 09:32:33 PDT)
  - Re: [AMBER] softcore potential flag Asaminew Haile (Thu May 08 2014 - 09:44:04 PDT)
    - Re: [AMBER] softcore potential flag Brian Radak (Thu May 08 2014 - 10:17:58 PDT)
[AMBER] Analysis of minimization stage Valentina Romano (Thu May 08 2014 - 09:04:41 PDT)
- Re: [AMBER] Analysis of minimization stage Asaminew Haile (Thu May 08 2014 - 09:13:57 PDT)
- Re: [AMBER] Analysis of minimization stage Daniel Roe (Thu May 08 2014 - 09:21:40 PDT)
  - Re: [AMBER] Analysis of minimization stage Valentina Romano (Thu May 08 2014 - 09:32:02 PDT)
    - Re: [AMBER] Analysis of minimization stage Daniel Roe (Thu May 08 2014 - 10:10:02 PDT)
    - Re: [AMBER] Analysis of minimization stage Valentina Romano (Fri May 09 2014 - 01:52:04 PDT)
    - Re: [AMBER] Analysis of minimization stage Daniel Roe (Fri May 09 2014 - 07:04:58 PDT)
    - Re: [AMBER] Analysis of minimization stage Valentina Romano (Fri May 09 2014 - 09:39:04 PDT)
    - Re: [AMBER] Analysis of minimization stage Valentina Romano (Mon May 12 2014 - 01:47:42 PDT)
    - Re: [AMBER] Analysis of minimization stage Jason Swails (Mon May 12 2014 - 04:39:03 PDT)
    - Re: [AMBER] Analysis of minimization stage David A Case (Mon May 12 2014 - 04:47:04 PDT)
    - Re: [AMBER] Analysis of minimization stage Valentina Romano (Mon May 12 2014 - 04:53:26 PDT)
    - Re: [AMBER] Analysis of minimization stage Jason Swails (Mon May 12 2014 - 06:22:05 PDT)
    - Re: [AMBER] Analysis of minimization stage David A Case (Mon May 12 2014 - 06:59:47 PDT)
    - Re: [AMBER] Analysis of minimization stage Valentina Romano (Mon May 12 2014 - 07:15:13 PDT)
    - Re: [AMBER] Analysis of minimization stage Jason Swails (Mon May 12 2014 - 07:18:47 PDT)
    - Re: [AMBER] Analysis of minimization stage Valentina Romano (Mon May 12 2014 - 09:26:44 PDT)
    - Re: [AMBER] Analysis of minimization stage Daniel Roe (Mon May 12 2014 - 11:00:40 PDT)
    - Re: [AMBER] Analysis of minimization stage Valentina Romano (Tue May 13 2014 - 07:02:11 PDT)
    - Re: [AMBER] Analysis of minimization stage Valentina Romano (Tue May 13 2014 - 07:30:41 PDT)
    - Re: [AMBER] Analysis of minimization stage Daniel Roe (Tue May 13 2014 - 08:58:07 PDT)
    - Re: [AMBER] Analysis of minimization stage Valentina Romano (Wed May 14 2014 - 06:58:08 PDT)
    - Re: [AMBER] Analysis of minimization stage David A Case (Wed May 14 2014 - 08:01:13 PDT)
    - Re: [AMBER] Analysis of minimization stage Valentina Romano (Thu May 15 2014 - 06:07:43 PDT)
    - Re: [AMBER] Analysis of minimization stage Daniel Roe (Thu May 15 2014 - 08:35:17 PDT)
    - Re: [AMBER] Analysis of minimization stage Jason Swails (Thu May 15 2014 - 08:46:54 PDT)
    - Re: [AMBER] Analysis of minimization stage Valentina Romano (Fri May 16 2014 - 04:39:19 PDT)
    - Re: [AMBER] Analysis of minimization stage David A Case (Fri May 16 2014 - 05:26:34 PDT)
    - Re: [AMBER] Analysis of minimization stage Valentina Romano (Fri May 16 2014 - 05:58:33 PDT)
    - Re: [AMBER] Analysis of minimization stage Jason Swails (Fri May 16 2014 - 06:43:49 PDT)
    - Re: [AMBER] Analysis of minimization stage Valentina Romano (Fri May 16 2014 - 06:50:49 PDT)
    - Re: [AMBER] Analysis of minimization stage David A Case (Fri May 16 2014 - 17:46:14 PDT)
    - Re: [AMBER] Analysis of minimization stage Valentina Romano (Tue May 20 2014 - 06:46:03 PDT)
    - Re: [AMBER] Analysis of minimization stage Brian Radak (Tue May 20 2014 - 06:51:37 PDT)
[AMBER] Regarding Calculation of Hydrogen Bond Energy MOHD HOMAIDUR RAHMAN (Thu May 08 2014 - 11:00:50 PDT)
- Re: [AMBER] Regarding Calculation of Hydrogen Bond Energy Jason Swails (Thu May 08 2014 - 11:42:20 PDT)
[AMBER] mmpbsa: the nmode calculation Fengxue Li (Thu May 08 2014 - 23:11:07 PDT)
[AMBER] multinode NPT runs on GPU Sourav Purohit (Fri May 09 2014 - 05:50:19 PDT)
- Re: [AMBER] multinode NPT runs on GPU Jason Swails (Fri May 09 2014 - 06:34:56 PDT)
- Re: [AMBER] multinode NPT runs on GPU Sourav Purohit (Fri May 09 2014 - 06:43:59 PDT)
  - Re: [AMBER] multinode NPT runs on GPU Jason Swails (Fri May 09 2014 - 07:00:29 PDT)
- Re: [AMBER] multinode NPT runs on GPU Sourav Purohit (Fri May 09 2014 - 07:19:06 PDT)
  - Re: [AMBER] multinode NPT runs on GPU Jason Swails (Fri May 09 2014 - 08:32:56 PDT)
    - Re: [AMBER] multinode NPT runs on GPU Brian Radak (Fri May 09 2014 - 09:04:14 PDT)
[AMBER] Siginificance of delta G Arunima Shilpi (Fri May 09 2014 - 06:09:27 PDT)
- Re: [AMBER] Siginificance of delta G Jason Swails (Fri May 09 2014 - 06:36:52 PDT)
[AMBER] delta Ggas and Delta Gsolv Arunima Shilpi (Fri May 09 2014 - 06:31:29 PDT)
- Re: [AMBER] delta Ggas and Delta Gsolv Jason Swails (Fri May 09 2014 - 06:40:53 PDT)
[AMBER] Analysis of evecs.dat file Ibrahim Said (Fri May 09 2014 - 09:58:22 PDT)
- Re: [AMBER] Analysis of evecs.dat file newamber list (Fri May 09 2014 - 10:52:11 PDT)
[AMBER] pmemd.MPI failure George Tzotzos (Fri May 09 2014 - 10:59:53 PDT)
- Re: [AMBER] pmemd.MPI failure James Maier (Fri May 09 2014 - 11:18:28 PDT)
[AMBER] Error when using PB implicit solvent in XMIN in NAB(PB Bomb in pb_init(): Allocation aborted) Guqin Shi (Fri May 09 2014 - 11:44:03 PDT)
- Re: [AMBER] Error when using PB implicit solvent in XMIN in NAB(PB Bomb in pb_init(): Allocation aborted) Ray Luo, Ph.D. (Fri May 09 2014 - 12:19:28 PDT)
  - Re: [AMBER] Error when using PB implicit solvent in XMIN in NAB(PB Bomb in pb_init(): Allocation aborted) Guqin Shi (Fri May 09 2014 - 13:35:50 PDT)
- Re: [AMBER] Error when using PB implicit solvent in XMIN in NAB(PB Bomb in pb_init(): Allocation aborted) David A Case (Fri May 09 2014 - 12:47:10 PDT)
  - Re: [AMBER] Error when using PB implicit solvent in XMIN in NAB(PB Bomb in pb_init(): Allocation aborted) Guqin Shi (Fri May 09 2014 - 13:42:58 PDT)
[AMBER] AMBER : mmpbsa rms in nmode Fengxue Li (Sat May 10 2014 - 05:54:29 PDT)
[AMBER] Additional random motion of com for unwrapped trajectory Sourav Purohit (Sat May 10 2014 - 16:23:18 PDT)
- Re: [AMBER] Additional random motion of com for unwrapped trajectory David A Case (Sun May 11 2014 - 06:00:34 PDT)
- Re: [AMBER] Additional random motion of com for unwrapped trajectory Sourav Purohit (Tue May 20 2014 - 04:29:58 PDT)
[AMBER] Analysis of the mmpbsa output James Starlight (Sun May 11 2014 - 00:43:44 PDT)
- Re: [AMBER] Analysis of the mmpbsa output Jason Swails (Mon May 12 2014 - 04:52:22 PDT)
  - Re: [AMBER] Analysis of the mmpbsa output James Starlight (Wed May 14 2014 - 02:42:08 PDT)
    - Re: [AMBER] Analysis of the mmpbsa output Jason Swails (Wed May 14 2014 - 04:40:37 PDT)
[AMBER] Inputs QM/MM MD and MMGBSA Soumendranath Bhakat (Sun May 11 2014 - 12:57:16 PDT)
[AMBER] Amber workshops coming soon ? Saba Sulaiman (Sun May 11 2014 - 22:51:22 PDT)
[AMBER] problem with nmode Fengxue Li (Mon May 12 2014 - 01:54:07 PDT)
- Re: [AMBER] problem with nmode David A Case (Mon May 12 2014 - 04:49:44 PDT)
[AMBER] Force field of antechamber , parm94 ? parm99? Jinfeng Huang (Mon May 12 2014 - 02:22:57 PDT)
- Re: [AMBER] Force field of antechamber , parm94 ? parm99? Jason Swails (Mon May 12 2014 - 04:32:58 PDT)
  - Re: [AMBER] Force field of antechamber , parm94 ? parm99? Jinfeng Huang (Mon May 12 2014 - 07:24:58 PDT)
    - Re: [AMBER] Force field of antechamber , parm94 ? parm99? Jason Swails (Mon May 12 2014 - 07:56:35 PDT)
    - Re: [AMBER] Force field of antechamber , parm94 ? parm99? Jinfeng Huang (Tue May 13 2014 - 03:14:48 PDT)
    - Re: [AMBER] Force field of antechamber , parm94 ? parm99? Jason Swails (Tue May 13 2014 - 04:40:07 PDT)
- Re: [AMBER] Force field of antechamber , parm94 ? parm99? David A Case (Mon May 12 2014 - 04:52:04 PDT)
[AMBER] QM/MM tutorial James Starlight (Mon May 12 2014 - 02:32:14 PDT)
- Re: [AMBER] QM/MM tutorial Jason Swails (Mon May 12 2014 - 04:13:33 PDT)
  - Re: [AMBER] QM/MM tutorial James Starlight (Tue May 13 2014 - 04:34:54 PDT)
    - Re: [AMBER] QM/MM tutorial Marc van der Kamp (Tue May 13 2014 - 04:39:28 PDT)
    - Re: [AMBER] QM/MM tutorial James Starlight (Tue May 13 2014 - 05:02:46 PDT)
    - Re: [AMBER] QM/MM tutorial Marc van der Kamp (Tue May 13 2014 - 05:42:52 PDT)
    - Re: [AMBER] QM/MM tutorial James Starlight (Tue May 13 2014 - 06:09:04 PDT)
    - Re: [AMBER] QM/MM tutorial Marc van der Kamp (Tue May 13 2014 - 07:06:03 PDT)
    - Re: [AMBER] QM/MM tutorial James Starlight (Wed May 14 2014 - 01:44:08 PDT)
    - Re: [AMBER] QM/MM tutorial Mark Williamson (Wed May 14 2014 - 02:12:43 PDT)
    - Re: [AMBER] QM/MM tutorial James Starlight (Wed May 14 2014 - 03:15:10 PDT)
    - Re: [AMBER] QM/MM tutorial James Starlight (Wed May 14 2014 - 04:00:12 PDT)
    - Re: [AMBER] QM/MM tutorial Jason Swails (Wed May 14 2014 - 04:29:32 PDT)
    - Re: [AMBER] QM/MM tutorial Marc van der Kamp (Wed May 14 2014 - 05:00:00 PDT)
    - Re: [AMBER] QM/MM tutorial Jason Swails (Wed May 14 2014 - 05:12:17 PDT)
    - Re: [AMBER] QM/MM tutorial James Starlight (Wed May 14 2014 - 08:20:44 PDT)
    - Re: [AMBER] QM/MM tutorial James Starlight (Wed May 14 2014 - 08:55:33 PDT)
    - Re: [AMBER] QM/MM tutorial Daniel Roe (Wed May 14 2014 - 09:42:56 PDT)
    - Re: [AMBER] QM/MM tutorial James Starlight (Thu May 15 2014 - 02:33:28 PDT)
    - Re: [AMBER] QM/MM tutorial Jason Swails (Thu May 15 2014 - 04:00:11 PDT)
    - Re: [AMBER] QM/MM tutorial James Starlight (Thu May 15 2014 - 04:06:36 PDT)
    - Re: [AMBER] QM/MM tutorial James Starlight (Fri May 16 2014 - 00:26:15 PDT)
    - Re: [AMBER] QM/MM tutorial James Starlight (Fri May 16 2014 - 03:05:30 PDT)
    - Re: [AMBER] QM/MM tutorial Marc van der Kamp (Fri May 16 2014 - 03:33:28 PDT)
    - Re: [AMBER] QM/MM tutorial James Starlight (Fri May 16 2014 - 03:39:50 PDT)
    - Re: [AMBER] QM/MM tutorial James Starlight (Fri May 16 2014 - 03:45:20 PDT)
    - Re: [AMBER] QM/MM tutorial Marc van der Kamp (Fri May 16 2014 - 04:18:03 PDT)
    - Re: [AMBER] QM/MM tutorial James Starlight (Sun May 18 2014 - 03:49:47 PDT)
    - Re: [AMBER] QM/MM tutorial Marc van der Kamp (Mon May 19 2014 - 05:06:56 PDT)
    - Re: [AMBER] QM/MM tutorial James Starlight (Thu May 22 2014 - 03:27:02 PDT)
    - Re: [AMBER] QM/MM tutorial Jason Swails (Thu May 22 2014 - 04:29:19 PDT)
    - Re: [AMBER] QM/MM tutorial James Starlight (Thu May 22 2014 - 05:10:59 PDT)
    - Re: [AMBER] QM/MM tutorial Jason Swails (Thu May 22 2014 - 05:34:35 PDT)
    - Re: [AMBER] QM/MM tutorial James Starlight (Thu May 22 2014 - 05:42:28 PDT)
    - Re: [AMBER] QM/MM tutorial Soumendranath Bhakat (Thu May 22 2014 - 05:49:38 PDT)
    - Re: [AMBER] QM/MM tutorial Jason Swails (Thu May 22 2014 - 06:50:24 PDT)
    - Re: [AMBER] QM/MM tutorial Ross Walker (Thu May 22 2014 - 06:49:52 PDT)
    - Re: [AMBER] QM/MM tutorial Soumendranath Bhakat (Thu May 22 2014 - 07:09:32 PDT)
[AMBER] about GPU memory requirements Thomas Evangelidis (Mon May 12 2014 - 11:58:29 PDT)
- Re: [AMBER] about GPU memory requirements Jason Swails (Mon May 12 2014 - 12:14:32 PDT)
- Re: [AMBER] about GPU memory requirements Ross Walker (Mon May 12 2014 - 12:20:59 PDT)
  - Re: [AMBER] about GPU memory requirements Thomas Evangelidis (Tue May 13 2014 - 14:12:13 PDT)
    - Re: [AMBER] about GPU memory requirements Ross Walker (Tue May 13 2014 - 14:21:37 PDT)
    - Re: [AMBER] about GPU memory requirements Thomas Evangelidis (Wed May 14 2014 - 02:41:15 PDT)
    - Re: [AMBER] about GPU memory requirements Daniel Roe (Wed May 14 2014 - 10:21:01 PDT)
    - Re: [AMBER] about GPU memory requirements Ross Walker (Wed May 14 2014 - 10:46:18 PDT)
[AMBER] Recompile amber12 whit cuda 6.0 Hector A. Baldoni (Mon May 12 2014 - 12:00:36 PDT)
- Re: [AMBER] Recompile amber12 whit cuda 6.0 Jason Swails (Mon May 12 2014 - 12:18:17 PDT)
- Re: [AMBER] Recompile amber12 whit cuda 6.0 Ross Walker (Mon May 12 2014 - 12:17:24 PDT)
  - Re: [AMBER] Recompile amber12 whit cuda 6.0 Hector A. Baldoni (Mon May 12 2014 - 12:46:15 PDT)
[AMBER] get sqm Error when run antechamber Biao Ma (Mon May 12 2014 - 23:44:04 PDT)
- Re: [AMBER] get sqm Error when run antechamber liu junjun (Tue May 13 2014 - 03:32:46 PDT)
- Re: [AMBER] get sqm Error when run antechamber Daniel Roe (Tue May 13 2014 - 10:36:37 PDT)
  - Re: [AMBER] get sqm Error when run antechamber Biao Ma (Wed May 14 2014 - 07:24:41 PDT)
    - Re: [AMBER] get sqm Error when run antechamber Jason Swails (Wed May 14 2014 - 07:48:34 PDT)
    - Re: [AMBER] get sqm Error when run antechamber Biao Ma (Wed May 14 2014 - 19:36:16 PDT)
    - Re: [AMBER] get sqm Error when run antechamber David A Case (Thu May 15 2014 - 04:52:00 PDT)
    - Re: [AMBER] get sqm Error when run antechamber Biao Ma (Fri May 16 2014 - 00:38:46 PDT)
[AMBER] Urgent: unable to generate files Faez Iqbal khan (Tue May 13 2014 - 01:20:43 PDT)
- Re: [AMBER] Urgent: unable to generate files liu junjun (Tue May 13 2014 - 03:49:36 PDT)
- Re: [AMBER] Urgent: unable to generate files Jason Swails (Tue May 13 2014 - 04:37:30 PDT)
[AMBER] REMD velocity information Saikat Dutta Chowdhury (Tue May 13 2014 - 05:05:08 PDT)
- Re: [AMBER] REMD velocity information Jason Swails (Tue May 13 2014 - 06:06:24 PDT)
[AMBER] exctracting indivdual frames into seperate files Nitin Sharma (Tue May 13 2014 - 05:54:09 PDT)
- Re: [AMBER] exctracting indivdual frames into seperate files Jason Swails (Tue May 13 2014 - 06:01:19 PDT)
  - Re: [AMBER] exctracting indivdual frames into seperate files Nitin Sharma (Tue May 13 2014 - 06:40:56 PDT)
    - Re: [AMBER] exctracting indivdual frames into seperate files Jason Swails (Tue May 13 2014 - 07:00:54 PDT)
    - Re: [AMBER] exctracting indivdual frames into seperate files Nitin Sharma (Tue May 13 2014 - 07:01:39 PDT)
[AMBER] Installation AmberTools13 fabien.ibanez.modis.fr.netgrs.com (Tue May 13 2014 - 07:30:53 PDT)
- Re: [AMBER] Installation AmberTools13 fabien.ibanez.modis.fr.netgrs.com (Thu May 15 2014 - 01:24:13 PDT)
  - Re: [AMBER] Installation AmberTools13 Jason Swails (Thu May 15 2014 - 04:07:04 PDT)
[AMBER] Scaling of atomic mass of water molecules Manikanthan Bhavaraju (Tue May 13 2014 - 07:51:44 PDT)
- Re: [AMBER] Scaling of atomic mass of water molecules Brian Radak (Tue May 13 2014 - 07:59:59 PDT)
  - Re: [AMBER] Scaling of atomic mass of water molecules Manikanthan Bhavaraju (Tue May 13 2014 - 08:16:41 PDT)
    - Re: [AMBER] Scaling of atomic mass of water molecules Brian Radak (Tue May 13 2014 - 08:21:58 PDT)
    - Re: [AMBER] Scaling of atomic mass of water molecules Manikanthan Bhavaraju (Tue May 13 2014 - 08:26:26 PDT)
    - Re: [AMBER] Scaling of atomic mass of water molecules Carlos Simmerling (Tue May 13 2014 - 08:31:26 PDT)
    - Re: [AMBER] Scaling of atomic mass of water molecules Manikanthan Bhavaraju (Tue May 13 2014 - 08:37:55 PDT)
  - Re: [AMBER] Scaling of atomic mass of water molecules Adrian Roitberg (Tue May 13 2014 - 09:50:20 PDT)
    - Re: [AMBER] Scaling of atomic mass of water molecules Manikanthan Bhavaraju (Tue May 13 2014 - 10:05:22 PDT)
    - Re: [AMBER] Scaling of atomic mass of water molecules Sergio R Aragon (Tue May 13 2014 - 10:35:18 PDT)
    - Re: [AMBER] Scaling of atomic mass of water molecules Manikanthan Bhavaraju (Tue May 13 2014 - 10:45:47 PDT)
[AMBER] Need help as a beginner MURAT OZTURK (Tue May 13 2014 - 12:31:59 PDT)
- Re: [AMBER] Need help as a beginner Ilyas Yildirim (Tue May 13 2014 - 12:46:24 PDT)
  - Re: [AMBER] Need help as a beginner MURAT OZTURK (Tue May 13 2014 - 13:17:49 PDT)
    - Re: [AMBER] Need help as a beginner Ilyas Yildirim (Tue May 13 2014 - 13:48:59 PDT)
- Re: [AMBER] Need help as a beginner David A Case (Tue May 13 2014 - 13:28:33 PDT)
  - Re: [AMBER] Need help as a beginner MURAT OZTURK (Tue May 13 2014 - 13:47:35 PDT)
    - Re: [AMBER] Need help as a beginner Jason Swails (Tue May 13 2014 - 15:16:57 PDT)
    - Re: [AMBER] Need help as a beginner MURAT OZTURK (Tue May 13 2014 - 16:02:53 PDT)
    - Re: [AMBER] Need help as a beginner Jason Swails (Wed May 14 2014 - 05:25:09 PDT)
    - Re: [AMBER] Need help as a beginner MURAT OZTURK (Wed May 14 2014 - 05:42:54 PDT)
    - Re: [AMBER] Need help as a beginner MURAT OZTURK (Wed May 14 2014 - 05:44:08 PDT)
    - Re: [AMBER] Need help as a beginner Jason Swails (Wed May 14 2014 - 05:52:21 PDT)
[AMBER] Installation Problem of AmberTools14 ujihara.ryuuta.47u.st.kyoto-u.ac.jp (Tue May 13 2014 - 21:54:10 PDT)
- Re: [AMBER] Installation Problem of AmberTools14 Jason Swails (Wed May 14 2014 - 04:45:29 PDT)
  - Re: [AMBER] Installation Problem of AmberTools14 ujihara.ryuuta.47u.st.kyoto-u.ac.jp (Wed May 14 2014 - 06:09:41 PDT)
    - Re: [AMBER] Installation Problem of AmberTools14 Jason Swails (Wed May 14 2014 - 07:42:28 PDT)
[AMBER] AmberTools 14 compilation on OSX fails Fabian Glaser (Wed May 14 2014 - 01:48:08 PDT)
- Re: [AMBER] AmberTools 14 compilation on OSX fails Jason Swails (Wed May 14 2014 - 04:47:24 PDT)
  - Re: [AMBER] AmberTools 14 compilation on OSX fails Fabian Glaser (Wed May 14 2014 - 06:44:44 PDT)
    - Re: [AMBER] AmberTools 14 compilation on OSX fails Jason Swails (Wed May 14 2014 - 07:34:54 PDT)
    - Re: [AMBER] AmberTools 14 compilation on OSX fails Fabian Glaser (Wed May 14 2014 - 22:42:11 PDT)
    - Re: [AMBER] AmberTools 14 compilation on OSX fails Jason Swails (Thu May 15 2014 - 04:18:20 PDT)
    - Re: [AMBER] AmberTools 14 compilation on OSX fails Fabian Glaser (Thu May 15 2014 - 05:44:34 PDT)
    - Re: [AMBER] AmberTools 14 compilation on OSX fails Fabian Glaser (Thu May 15 2014 - 05:50:01 PDT)
    - Re: [AMBER] AmberTools 14 compilation on OSX fails Jason Swails (Thu May 15 2014 - 06:23:35 PDT)
    - Re: [AMBER] AmberTools 14 compilation on OSX fails Fabian Glaser (Thu May 15 2014 - 06:58:04 PDT)
[AMBER] thermodynamic integration (TI) simulation: pmemd of amber14 vs sander of amber11- vdw transformation Ying-Chieh Sun (Wed May 14 2014 - 03:21:17 PDT)
- Re: [AMBER] thermodynamic integration (TI) simulation: pmemd of amber14 vs sander of amber11- vdw transformation Jason Swails (Wed May 14 2014 - 04:37:01 PDT)
  - Re: [AMBER] thermodynamic integration (TI) simulation: pmemd of amber14 vs sander of amber11- vdw transformation Ross Walker (Wed May 14 2014 - 08:05:39 PDT)
[AMBER] Protocol for multiple CPU+ single GPU run on a single node, MURAT OZTURK (Wed May 14 2014 - 07:49:16 PDT)
- Re: [AMBER] Protocol for multiple CPU+ single GPU run on a single node, Jason Swails (Wed May 14 2014 - 08:17:32 PDT)
  - Re: [AMBER] Protocol for multiple CPU+ single GPU run on a single node, Ross Walker (Wed May 14 2014 - 08:57:33 PDT)
    - Re: [AMBER] Protocol for multiple CPU+ single GPU run on a single node, MURAT OZTURK (Wed May 14 2014 - 10:13:25 PDT)
    - Re: [AMBER] Protocol for multiple CPU+ single GPU run on a single node, Jason Swails (Wed May 14 2014 - 10:34:53 PDT)
    - Re: [AMBER] Protocol for multiple CPU+ single GPU run on a single node, Ross Walker (Wed May 14 2014 - 10:39:22 PDT)
    - Re: [AMBER] Protocol for multiple CPU+ single GPU run on a single node, Scott Le Grand (Wed May 14 2014 - 11:10:13 PDT)
    - Re: [AMBER] Protocol for multiple CPU+ single GPU run on a single node, MURAT OZTURK (Wed May 14 2014 - 11:35:26 PDT)
    - Re: [AMBER] Protocol for multiple CPU+ single GPU run on a single node, Ross Walker (Wed May 14 2014 - 11:49:41 PDT)
    - Re: [AMBER] Protocol for multiple CPU+ single GPU run on a single node, MURAT OZTURK (Wed May 14 2014 - 12:22:24 PDT)
    - Re: [AMBER] Protocol for multiple CPU+ single GPU run on a single node, James Maier (Wed May 14 2014 - 12:30:08 PDT)
    - Re: [AMBER] Protocol for multiple CPU+ single GPU run on a single node, Jason Swails (Wed May 14 2014 - 12:33:13 PDT)
    - Re: [AMBER] Protocol for multiple CPU+ single GPU run on a single node, MURAT OZTURK (Wed May 14 2014 - 12:41:37 PDT)
    - Re: [AMBER] Protocol for multiple CPU+ single GPU run on a single node, Ross Walker (Wed May 14 2014 - 12:49:10 PDT)
    - Re: [AMBER] Protocol for multiple CPU+ single GPU run on a single node, David A Case (Wed May 14 2014 - 13:13:19 PDT)
    - Re: [AMBER] Protocol for multiple CPU+ single GPU run on a single node, Ross Walker (Wed May 14 2014 - 12:36:11 PDT)
[AMBER] TI(amber14's pmemd.cuda) on GPUs RE: thermodynamic integration (TI) simulation: pmemd of amber14 vs sander of amber11- vdw transformation Ying-Chieh Sun (Wed May 14 2014 - 20:42:24 PDT)
- Re: [AMBER] TI(amber14's pmemd.cuda) on GPUs RE: thermodynamic integration (TI) simulation: pmemd of amber14 vs sander of amber11- vdw transformation Ross Walker (Wed May 14 2014 - 21:16:29 PDT)
[AMBER] Error: Could not compile with NetCDF Fortran interface gfortran-4.7 and amber14 Ben.Cossins.ucb.com (Thu May 15 2014 - 04:22:44 PDT)
- Re: [AMBER] Error: Could not compile with NetCDF Fortran interface gfortran-4.7 and amber14 Daniel Roe (Thu May 15 2014 - 08:19:30 PDT)
[AMBER] ALA and NALA charges in Amber03 and Amber99 Rossen Apostolov (Thu May 15 2014 - 07:05:22 PDT)
- Re: [AMBER] ALA and NALA charges in Amber03 and Amber99 Jason Swails (Thu May 15 2014 - 08:30:10 PDT)
  - Re: [AMBER] ALA and NALA charges in Amber03 and Amber99 Rossen Apostolov (Thu May 15 2014 - 08:44:19 PDT)
  - Re: [AMBER] ALA and NALA charges in Amber03 and Amber99 Rossen Apostolov (Wed May 21 2014 - 07:14:26 PDT)
    - Re: [AMBER] ALA and NALA charges in Amber03 and Amber99 Jason Swails (Wed May 21 2014 - 07:38:34 PDT)
- Re: [AMBER] ALA and NALA charges in Amber03 and Amber99 Jason Swails (Thu May 15 2014 - 09:00:47 PDT)
[AMBER] sander and processor sammia khatak (Thu May 15 2014 - 07:09:14 PDT)
- Re: [AMBER] sander and processor Daniel Roe (Thu May 15 2014 - 08:27:14 PDT)
- Re: [AMBER] sander and processor Jason Swails (Thu May 15 2014 - 08:38:05 PDT)
[AMBER] when nastruct does NOT print the basepair information newamber list (Thu May 15 2014 - 07:52:04 PDT)
- Re: [AMBER] when nastruct does NOT print the basepair information Daniel Roe (Thu May 15 2014 - 08:25:38 PDT)
[AMBER] pairwise option in cpptraj newamber list (Thu May 15 2014 - 10:25:28 PDT)
- Re: [AMBER] pairwise option in cpptraj Daniel Roe (Thu May 15 2014 - 11:15:09 PDT)
  - Re: [AMBER] pairwise option in cpptraj newamber list (Thu May 15 2014 - 12:14:40 PDT)
    - Re: [AMBER] pairwise option in cpptraj Daniel Roe (Thu May 15 2014 - 14:06:58 PDT)
[AMBER] torsion restraints not defined properly? Duggan, Brendan (Thu May 15 2014 - 10:55:29 PDT)
- Re: [AMBER] torsion restraints not defined properly? Daniel Roe (Thu May 15 2014 - 11:05:53 PDT)
- Re: [AMBER] torsion restraints not defined properly? David A Case (Thu May 15 2014 - 12:12:52 PDT)
- Re: [AMBER] torsion restraints not defined properly? Daniel Roe (Thu May 15 2014 - 13:43:40 PDT)
- Re: [AMBER] torsion restraints not defined properly? Duggan, Brendan (Tue May 20 2014 - 11:55:30 PDT)
[AMBER] AMBER Workshop Jun 2nd to 6th - Barcelona - Small number of additional places available. Ross Walker (Thu May 15 2014 - 12:03:04 PDT)
Re: [AMBER] AMBER Digest, Vol 855, Issue 1 Duggan, Brendan (Thu May 15 2014 - 12:18:17 PDT)
[AMBER] acetylated lysine - OXT berin karaman (Fri May 16 2014 - 01:00:48 PDT)
- Re: [AMBER] acetylated lysine - OXT David A Case (Fri May 16 2014 - 05:19:49 PDT)
  - Re: [AMBER] acetylated lysine - OXT berin karaman (Fri May 16 2014 - 05:39:00 PDT)
    - Re: [AMBER] acetylated lysine - OXT Jason Swails (Fri May 16 2014 - 06:46:03 PDT)
    - Re: [AMBER] acetylated lysine - OXT berin karaman (Fri May 16 2014 - 07:07:11 PDT)
[AMBER] parmchk2 segfaults Hannes Loeffler (Fri May 16 2014 - 06:50:54 PDT)
- Re: [AMBER] parmchk2 segfaults Sushil Mishra (Fri Jul 11 2014 - 01:41:28 PDT)
  - Re: [AMBER] parmchk2 segfaults Jason Swails (Fri Jul 11 2014 - 08:16:55 PDT)
    - Re: [AMBER] parmchk2 segfaults Hannes Loeffler (Thu Jul 24 2014 - 07:47:27 PDT)
    - Re: [AMBER] parmchk2 segfaults Jason Swails (Thu Jul 24 2014 - 14:36:24 PDT)
    - Re: [AMBER] parmchk2 segfaults Hannes Loeffler (Fri Jul 25 2014 - 02:48:01 PDT)
Re: [AMBER] Help with ptraj RDF/ion coordination shells/number of ions within regions Ben Ahmady (Fri May 16 2014 - 07:29:42 PDT)
- Re: [AMBER] Help with ptraj RDF/ion coordination shells/number of ions within regions Brian Radak (Fri May 16 2014 - 07:45:58 PDT)
  - Re: [AMBER] Help with ptraj RDF/ion coordination shells/number of ions within regions Ben Ahmady (Fri May 16 2014 - 09:40:04 PDT)
    - Re: [AMBER] Help with ptraj RDF/ion coordination shells/number of ions within regions Brian Radak (Fri May 16 2014 - 10:53:56 PDT)
    - Re: [AMBER] Help with ptraj RDF/ion coordination shells/number of ions within regions Jason Swails (Fri May 16 2014 - 20:50:53 PDT)
    - Re: [AMBER] Help with ptraj RDF/ion coordination shells/number of ions within regions Jason Swails (Fri May 16 2014 - 20:56:16 PDT)
    - Re: [AMBER] Help with ptraj RDF/ion coordination shells/number of ions within regions Ben Ahmady (Sun May 18 2014 - 13:43:45 PDT)
    - Re: [AMBER] Help with ptraj RDF/ion coordination shells/number of ions within regions Ben Ahmady (Mon May 19 2014 - 02:04:01 PDT)
[AMBER] Problem with Decomposition of Binding Free Energy loue chen (Fri May 16 2014 - 12:08:46 PDT)
- Re: [AMBER] Problem with Decomposition of Binding Free Energy Jason Swails (Fri May 16 2014 - 21:06:05 PDT)
Re: [AMBER] Saturday Bill Ross (Fri May 16 2014 - 13:08:11 PDT)
[AMBER] How to plot Eigenvectors against % Positional Fluctuations Yip Yew Mun (Fri May 16 2014 - 21:09:18 PDT)
- Re: [AMBER] How to plot Eigenvectors against % Positional Fluctuations Daniel Roe (Mon May 19 2014 - 07:24:14 PDT)
[AMBER] Problem in generating xml param files Sushi Shilpa (Fri May 16 2014 - 23:06:18 PDT)
[AMBER] error in minimization Sajda Ashraf (Fri May 16 2014 - 23:48:21 PDT)
- Re: [AMBER] error in minimization David A Case (Sat May 17 2014 - 12:50:32 PDT)
  - Re: [AMBER] error in minimization Sajda Ashraf (Sun May 18 2014 - 22:21:02 PDT)
    - Re: [AMBER] error in minimization David A Case (Mon May 19 2014 - 04:48:54 PDT)
[AMBER] MMPBSA Soumya Lipsa Rath (Sat May 17 2014 - 03:04:38 PDT)
- Re: [AMBER] MMPBSA Bill Miller III (Sat May 17 2014 - 04:11:43 PDT)
  - Re: [AMBER] MMPBSA Soumendranath Bhakat (Sat May 17 2014 - 05:48:50 PDT)
[AMBER] Extending MMPBSA Arun Kumar Somavarapu (Sat May 17 2014 - 04:50:44 PDT)
- Re: [AMBER] Extending MMPBSA Bill Miller III (Sat May 17 2014 - 05:01:18 PDT)
[AMBER] Script for Calculating RMSIP Yip Yew Mun (Sat May 17 2014 - 08:54:30 PDT)
- Re: [AMBER] Script for Calculating RMSIP Hector A. Baldoni (Sat May 17 2014 - 16:31:52 PDT)
  - Re: [AMBER] Script for Calculating RMSIP Yip Yew Mun (Tue May 20 2014 - 19:33:20 PDT)
- Re: [AMBER] Script for Calculating RMSIP Daniel Roe (Mon May 19 2014 - 07:10:35 PDT)
[AMBER] Bad prmtop during density run Kshatresh Dutta Dubey (Sat May 17 2014 - 09:17:03 PDT)
- Re: [AMBER] Bad prmtop during density run Jason Swails (Sat May 17 2014 - 10:46:22 PDT)
[AMBER] Unit cell vectors are NOT rotated; imaging will not be possible newamber list (Sat May 17 2014 - 09:41:38 PDT)
- Re: [AMBER] Unit cell vectors are NOT rotated; imaging will not be possible Jason Swails (Sat May 17 2014 - 10:49:45 PDT)
  - Re: [AMBER] Unit cell vectors are NOT rotated; imaging will not be possible newamber list (Sat May 17 2014 - 11:09:56 PDT)
[AMBER] QM/MM based binding free energy analysis AMBER Soumendranath Bhakat (Sun May 18 2014 - 12:29:58 PDT)
- Re: [AMBER] QM/MM based binding free energy analysis AMBER Nitin Sharma (Sun May 18 2014 - 12:38:26 PDT)
  - Re: [AMBER] QM/MM based binding free energy analysis AMBER Soumendranath Bhakat (Sun May 18 2014 - 12:48:28 PDT)
    - Re: [AMBER] QM/MM based binding free energy analysis AMBER Nitin Sharma (Sun May 18 2014 - 13:00:26 PDT)
    - Re: [AMBER] QM/MM based binding free energy analysis AMBER Soumendranath Bhakat (Sun May 18 2014 - 13:28:46 PDT)
    - Re: [AMBER] QM/MM based binding free energy analysis AMBER Nitin Sharma (Mon May 19 2014 - 02:53:24 PDT)
    - Re: [AMBER] QM/MM based binding free energy analysis AMBER Soumendranath Bhakat (Mon May 19 2014 - 03:23:09 PDT)
[AMBER] Abdullahi Abubakar invited you to check out Dropbox Dropbox (Sun May 18 2014 - 18:58:02 PDT)
[AMBER] Fwd: MMPBSA Soumya Lipsa Rath (Sun May 18 2014 - 22:19:18 PDT)
- Re: [AMBER] Fwd: MMPBSA Jason Swails (Mon May 19 2014 - 05:55:18 PDT)
  - Re: [AMBER] Fwd: MMPBSA Soumya Lipsa Rath (Mon May 19 2014 - 21:31:29 PDT)
    - Re: [AMBER] Fwd: MMPBSA Jason Swails (Tue May 20 2014 - 04:28:21 PDT)
    - Re: [AMBER] Fwd: MMPBSA Soumya Lipsa Rath (Tue May 20 2014 - 04:49:27 PDT)
    - Re: [AMBER] Fwd: MMPBSA Jason Swails (Tue May 20 2014 - 05:45:04 PDT)
    - Re: [AMBER] Fwd: MMPBSA Soumya Lipsa Rath (Tue May 20 2014 - 06:36:39 PDT)
[AMBER] sander restart sammia khatak (Sun May 18 2014 - 23:57:15 PDT)
- Re: [AMBER] sander restart Soumendranath Bhakat (Mon May 19 2014 - 00:28:58 PDT)
  - Re: [AMBER] sander restart sammia khatak (Mon May 19 2014 - 02:25:09 PDT)
    - Re: [AMBER] sander restart Soumendranath Bhakat (Mon May 19 2014 - 02:35:10 PDT)
    - Re: [AMBER] sander restart sammia khatak (Mon May 19 2014 - 02:55:22 PDT)
    - Re: [AMBER] sander restart Soumendranath Bhakat (Mon May 19 2014 - 03:18:41 PDT)
[AMBER] antechamber with Au atom giulia palermo (Mon May 19 2014 - 00:24:50 PDT)
- Re: [AMBER] antechamber with Au atom David A Case (Mon May 19 2014 - 04:50:41 PDT)
- Re: [AMBER] antechamber with Au atom FyD (Mon May 19 2014 - 10:02:53 PDT)
[AMBER] can “NAB: Molecular mechanics and dynamics” do qmmm caculation? 张明焜 (Mon May 19 2014 - 01:59:42 PDT)
- Re: [AMBER] can “NAB: Molecular mechanics and dynamics” do qmmm caculation? David A Case (Mon May 19 2014 - 04:51:22 PDT)
[AMBER] About the reproducibility of pmemd Val Yu (Mon May 19 2014 - 05:01:48 PDT)
- Re: [AMBER] About the reproducibility of pmemd Jason Swails (Mon May 19 2014 - 05:48:38 PDT)
  - [AMBER] 答复: About the reproducibility of pmemd Val Yu (Tue May 20 2014 - 05:56:53 PDT)
    - Re: [AMBER] 答复: About the reproducibility of pmemd Jason Swails (Tue May 20 2014 - 06:30:29 PDT)
- Re: [AMBER] About the reproducibility of pmemd David A Case (Mon May 19 2014 - 05:50:13 PDT)
- Re: [AMBER] About the reproducibility of pmemd Ross Walker (Mon May 19 2014 - 11:23:46 PDT)
[AMBER] NH4+ Thomas Exner (Mon May 19 2014 - 05:31:56 PDT)
- Re: [AMBER] NH4+ Alessandro Contini (Mon May 19 2014 - 05:54:24 PDT)
  - Re: [AMBER] NH4+ Thomas Exner (Mon May 19 2014 - 06:00:21 PDT)
    - Re: [AMBER] NH4+ Alessandro Contini (Mon May 19 2014 - 06:29:00 PDT)
- Re: [AMBER] NH4+ FyD (Mon May 19 2014 - 09:59:40 PDT)
  - Re: [AMBER] NH4+ Thomas Exner (Wed May 21 2014 - 01:15:26 PDT)
    - Re: [AMBER] NH4+ Alessandro Contini (Wed May 21 2014 - 01:19:19 PDT)
[AMBER] Antechamber CHRISTOPHER PATRICK MCNARY (Mon May 19 2014 - 08:18:03 PDT)
[AMBER] Problem in parallel version of pmemd.cuda Sanjib Paul (Mon May 19 2014 - 11:16:41 PDT)
- Re: [AMBER] Problem in parallel version of pmemd.cuda Ross Walker (Mon May 19 2014 - 11:25:59 PDT)
- Re: [AMBER] Problem in parallel version of pmemd.cuda David A Case (Mon May 19 2014 - 13:58:45 PDT)
  - Re: [AMBER] Problem in parallel version of pmemd.cuda Sanjib Paul (Tue May 20 2014 - 06:26:59 PDT)
    - Re: [AMBER] Problem in parallel version of pmemd.cuda Jason Swails (Tue May 20 2014 - 06:40:37 PDT)
    - Re: [AMBER] Problem in parallel version of pmemd.cuda Daniel Roe (Tue May 20 2014 - 07:23:47 PDT)
    - Re: [AMBER] Problem in parallel version of pmemd.cuda Sanjib Paul (Tue May 20 2014 - 08:23:29 PDT)
    - Re: [AMBER] Problem in parallel version of pmemd.cuda Jason Swails (Tue May 20 2014 - 08:31:41 PDT)
    - Re: [AMBER] Problem in parallel version of pmemd.cuda Sanjib Paul (Tue May 20 2014 - 09:32:09 PDT)
    - Re: [AMBER] Problem in parallel version of pmemd.cuda Jason Swails (Tue May 20 2014 - 10:04:39 PDT)
[AMBER] conversion force constant giulia palermo (Mon May 19 2014 - 12:26:04 PDT)
- Re: [AMBER] conversion force constant James Maier (Mon May 19 2014 - 12:44:22 PDT)
  - Re: [AMBER] conversion force constant giulia palermo (Wed May 21 2014 - 01:32:15 PDT)
    - Re: [AMBER] conversion force constant Jason Swails (Wed May 21 2014 - 05:25:42 PDT)
[AMBER] Announcement: New GLYCAM-Web Lachele Foley (Mon May 19 2014 - 14:40:55 PDT)
[AMBER] Constant protein diffusion across PB boundaties James Starlight (Tue May 20 2014 - 01:59:22 PDT)
- Re: [AMBER] Constant protein diffusion across PB boundaties Jason Swails (Tue May 20 2014 - 04:30:41 PDT)
  - Re: [AMBER] Constant protein diffusion across PB boundaties Jason Swails (Tue May 20 2014 - 04:32:30 PDT)
[AMBER] Trajectory analysis using pptraj James Starlight (Tue May 20 2014 - 08:05:38 PDT)
- Re: [AMBER] Trajectory analysis using pptraj Daniel Roe (Tue May 20 2014 - 08:57:29 PDT)
  - Re: [AMBER] Trajectory analysis using pptraj James Starlight (Wed May 21 2014 - 08:19:42 PDT)
    - Re: [AMBER] Trajectory analysis using pptraj Vlad Cojocaru (Wed May 21 2014 - 08:24:17 PDT)
    - Re: [AMBER] Trajectory analysis using pptraj Jason Swails (Wed May 21 2014 - 08:38:27 PDT)
    - Re: [AMBER] Trajectory analysis using pptraj James Starlight (Thu May 22 2014 - 05:52:19 PDT)
    - Re: [AMBER] Trajectory analysis using pptraj Jason Swails (Thu May 22 2014 - 06:22:44 PDT)
    - Re: [AMBER] Trajectory analysis using pptraj James Starlight (Sun May 25 2014 - 03:50:01 PDT)
    - Re: [AMBER] Trajectory analysis using pptraj Daniel Roe (Tue May 27 2014 - 06:37:18 PDT)
[AMBER] Error in setting irest=1 Valentina Romano (Tue May 20 2014 - 09:14:07 PDT)
- Re: [AMBER] Error in setting irest=1 Daniel Roe (Tue May 20 2014 - 09:39:29 PDT)
  - Re: [AMBER] Error in setting irest=1 Soumendranath Bhakat (Wed May 21 2014 - 00:19:58 PDT)
[AMBER] csurften requirement for semiisotropic coupling Eric Hill (Tue May 20 2014 - 09:34:42 PDT)
[AMBER] cant run ntp=3 without csurften Eric Hill (Tue May 20 2014 - 09:48:46 PDT)
- Re: [AMBER] cant run ntp=3 without csurften Jason Swails (Tue May 20 2014 - 10:11:40 PDT)
  - Re: [AMBER] cant run ntp=3 without csurften Benjamin D Madej (Tue May 20 2014 - 11:15:21 PDT)
    - Re: [AMBER] cant run ntp=3 without csurften Benjamin D Madej (Tue May 20 2014 - 11:22:34 PDT)
    - Re: [AMBER] cant run ntp=3 without csurften Eric Hill (Tue May 20 2014 - 11:40:25 PDT)
    - Re: [AMBER] cant run ntp=3 without csurften Ross Walker (Tue May 20 2014 - 12:24:49 PDT)
    - Re: [AMBER] cant run ntp=3 without csurften Eric Hill (Tue May 20 2014 - 12:56:29 PDT)
    - Re: [AMBER] cant run ntp=3 without csurften Ross Walker (Tue May 20 2014 - 13:27:33 PDT)
[AMBER] secondary structure calculation using Cpptraj Marlet Martinez (Tue May 20 2014 - 13:00:20 PDT)
- Re: [AMBER] secondary structure calculation using Cpptraj Daniel Roe (Tue May 20 2014 - 13:45:41 PDT)
  - Re: [AMBER] secondary structure calculation using Cpptraj Marlet Martinez (Wed May 21 2014 - 00:30:54 PDT)
[AMBER] Attempting to modify Amber Nelson Max (Tue May 20 2014 - 17:47:39 PDT)
- Re: [AMBER] Attempting to modify Amber David A Case (Thu May 22 2014 - 07:24:00 PDT)
[AMBER] error in mdcrd file Sajda Ashraf (Tue May 20 2014 - 22:48:42 PDT)
[AMBER] Simulation of the protein with internal water James Starlight (Wed May 21 2014 - 05:39:02 PDT)
- Re: [AMBER] Simulation of the protein with internal water Bill Ross (Thu Jun 05 2014 - 19:04:21 PDT)
[AMBER] Low energy path Hector A. Baldoni (Wed May 21 2014 - 05:40:27 PDT)
- Re: [AMBER] Low energy path James Maier (Wed May 21 2014 - 07:07:22 PDT)
  - Re: [AMBER] Low energy path Hector A. Baldoni (Wed May 21 2014 - 15:22:10 PDT)
[AMBER] Peptides moving out of the water box Ilias Patmanidis (Wed May 21 2014 - 06:47:39 PDT)
- Re: [AMBER] Peptides moving out of the water box Daniel Roe (Wed May 21 2014 - 07:01:20 PDT)
[AMBER] Temperature rises to 4000K during NVT equilibration Indrajit Deb (Wed May 21 2014 - 06:55:46 PDT)
- Re: [AMBER] Temperature rises to 4000K during NVT equilibration Daniel Roe (Wed May 21 2014 - 07:03:19 PDT)
  - Re: [AMBER] Temperature rises to 4000K during NVT equilibration Indrajit Deb (Wed May 21 2014 - 07:07:51 PDT)
    - Re: [AMBER] Temperature rises to 4000K during NVT equilibration Daniel Roe (Wed May 21 2014 - 07:14:07 PDT)
    - Re: [AMBER] Temperature rises to 4000K during NVT equilibration Indrajit Deb (Wed May 21 2014 - 07:56:35 PDT)
    - Re: [AMBER] Temperature rises to 4000K during NVT equilibration Jason Swails (Wed May 21 2014 - 08:40:51 PDT)
    - Re: [AMBER] Temperature rises to 4000K during NVT equilibration Indrajit Deb (Wed May 21 2014 - 11:14:20 PDT)
    - Re: [AMBER] Temperature rises to 4000K during NVT equilibration Daniel Roe (Wed May 21 2014 - 11:51:13 PDT)
- Re: [AMBER] Temperature rises to 4000K during NVT equilibration David A Case (Wed May 21 2014 - 07:29:57 PDT)
[AMBER] Interactions across the periodic box boundaries Eugene Yedvabny (Wed May 21 2014 - 12:19:40 PDT)
- Re: [AMBER] Interactions across the periodic box boundaries Daniel Roe (Wed May 21 2014 - 14:00:48 PDT)
- Re: [AMBER] Interactions across the periodic box boundaries Jason Swails (Wed May 21 2014 - 14:45:52 PDT)
[AMBER] About the chamber in Ambertools 14 Yeng-Tseng Wang (Wed May 21 2014 - 18:23:14 PDT)
- Re: [AMBER] About the chamber in Ambertools 14 Ross Walker (Wed May 21 2014 - 20:31:09 PDT)
  - Re: [AMBER] About the chamber in Ambertools 14 Yeng-Tseng Wang (Thu May 22 2014 - 02:19:33 PDT)
    - Re: [AMBER] About the chamber in Ambertools 14 Yeng-Tseng Wang (Thu May 22 2014 - 21:34:04 PDT)
[AMBER] antechamber error Sajda Ashraf (Thu May 22 2014 - 03:53:39 PDT)
- Re: [AMBER] antechamber error Jason Swails (Thu May 22 2014 - 04:36:23 PDT)
[AMBER] z-axis restraints Pierpaolo Cacciotto (Thu May 22 2014 - 06:49:37 PDT)
[AMBER] mmpbsa zahra khatti (Thu May 22 2014 - 07:59:23 PDT)
- Re: [AMBER] mmpbsa Jason Swails (Thu May 22 2014 - 08:31:53 PDT)
[AMBER] mmpbsa Lara rajam (Thu May 22 2014 - 11:41:16 PDT)
[AMBER] prmtop error Lara rajam (Thu May 22 2014 - 12:08:41 PDT)
- Re: [AMBER] prmtop error Soumendranath Bhakat (Thu May 22 2014 - 12:42:25 PDT)
- Re: [AMBER] prmtop error Jason Swails (Thu May 22 2014 - 14:45:39 PDT)
  - Re: [AMBER] prmtop error Thomas Cheatham (Thu May 22 2014 - 15:07:07 PDT)
    - Re: [AMBER] prmtop error Jason Swails (Thu May 22 2014 - 19:15:38 PDT)
[AMBER] in vacuo dynamics Massimiliano Porrini (Thu May 22 2014 - 12:52:26 PDT)
- Re: [AMBER] in vacuo dynamics Jason Swails (Thu May 22 2014 - 14:42:36 PDT)
  - Re: [AMBER] in vacuo dynamics Massimiliano Porrini (Fri May 23 2014 - 03:18:44 PDT)
    - Re: [AMBER] in vacuo dynamics Massimiliano Porrini (Fri May 23 2014 - 03:30:37 PDT)
    - Re: [AMBER] in vacuo dynamics Jason Swails (Fri May 23 2014 - 05:11:58 PDT)
    - Re: [AMBER] in vacuo dynamics Massimiliano Porrini (Fri May 23 2014 - 07:06:00 PDT)
    - Re: [AMBER] in vacuo dynamics Jason Swails (Fri May 23 2014 - 07:41:01 PDT)
    - Re: [AMBER] in vacuo dynamics Massimiliano Porrini (Sun May 25 2014 - 06:42:50 PDT)
    - Re: [AMBER] in vacuo dynamics Robert McGibbon (Sun May 25 2014 - 12:30:49 PDT)
    - Re: [AMBER] in vacuo dynamics Massimiliano Porrini (Mon May 26 2014 - 03:34:20 PDT)
    - Re: [AMBER] in vacuo dynamics Jason Swails (Mon May 26 2014 - 12:21:59 PDT)
    - Re: [AMBER] in vacuo dynamics Massimiliano Porrini (Tue May 27 2014 - 06:04:49 PDT)
    - Re: [AMBER] in vacuo dynamics Jason Swails (Tue May 27 2014 - 06:19:37 PDT)
    - Re: [AMBER] in vacuo dynamics Massimiliano Porrini (Tue May 27 2014 - 06:40:46 PDT)
    - Re: [AMBER] in vacuo dynamics Jason Swails (Mon May 26 2014 - 12:30:48 PDT)
    - Re: [AMBER] in vacuo dynamics Robert McGibbon (Mon May 26 2014 - 14:09:13 PDT)
[AMBER] Problem in loading leaprc.zinc amin.imtech.res.in (Thu May 22 2014 - 23:05:06 PDT)
- Re: [AMBER] Problem in loading leaprc.zinc Jason Swails (Fri May 23 2014 - 05:23:57 PDT)
  - Re: [AMBER] Problem in loading leaprc.zinc amin.imtech.res.in (Fri May 23 2014 - 06:55:55 PDT)
[AMBER] Secondary Structure Script Soumendranath Bhakat (Fri May 23 2014 - 03:45:42 PDT)
[AMBER] SASA calculation Soumendranath Bhakat (Fri May 23 2014 - 05:07:53 PDT)
- Re: [AMBER] SASA calculation Jason Swails (Fri May 23 2014 - 05:16:42 PDT)
  - Re: [AMBER] SASA calculation Soumendranath Bhakat (Fri May 23 2014 - 05:29:38 PDT)
    - Re: [AMBER] SASA calculation Soumendranath Bhakat (Fri May 23 2014 - 06:14:07 PDT)
  - Re: [AMBER] SASA calculation Asaminew Haile (Fri May 23 2014 - 06:18:42 PDT)
[AMBER] SASA error Soumendranath Bhakat (Fri May 23 2014 - 06:31:13 PDT)
- Re: [AMBER] SASA error Asaminew Haile (Fri May 23 2014 - 08:19:03 PDT)
  - Re: [AMBER] SASA error Soumendranath Bhakat (Fri May 23 2014 - 08:29:07 PDT)
[AMBER] compiling iAPBS and sander.APBS? Brian Radak (Fri May 23 2014 - 13:54:06 PDT)
- Re: [AMBER] compiling iAPBS and sander.APBS? Robert Konecny (Sat May 24 2014 - 19:54:28 PDT)
  - Re: [AMBER] compiling iAPBS and sander.APBS? Brian Radak (Sun May 25 2014 - 08:17:43 PDT)
    - Re: [AMBER] compiling iAPBS and sander.APBS? Robert Konecny (Sun May 25 2014 - 19:44:05 PDT)
    - Re: [AMBER] compiling iAPBS and sander.APBS? Brian Radak (Tue May 27 2014 - 05:40:10 PDT)
[AMBER] I want to know about formula of RESP Charge in the Amber Kim TaeHwan (Sat May 24 2014 - 08:43:39 PDT)
[AMBER] Topology and Corresponding PDB Amber Soumendranath Bhakat (Sat May 24 2014 - 12:39:49 PDT)
- Re: [AMBER] Topology and Corresponding PDB Amber Jason Swails (Sat May 24 2014 - 13:37:47 PDT)
[AMBER] Accelerated MD in Amber James Starlight (Sun May 25 2014 - 06:28:33 PDT)
- Re: [AMBER] Accelerated MD in Amber Daniel Roe (Tue May 27 2014 - 06:39:32 PDT)
  - Re: [AMBER] Accelerated MD in Amber James Starlight (Wed May 28 2014 - 00:18:09 PDT)
    - Re: [AMBER] Accelerated MD in Amber Daniel Roe (Wed May 28 2014 - 06:57:56 PDT)
    - Re: [AMBER] Accelerated MD in Amber James Starlight (Wed May 28 2014 - 10:37:38 PDT)
    - Re: [AMBER] Accelerated MD in Amber Christina Bergonzo (Wed May 28 2014 - 11:48:06 PDT)
[AMBER] MD at constant pH and high temperature Sangita Kachhap (Sun May 25 2014 - 06:48:41 PDT)
- Re: [AMBER] MD at constant pH and high temperature David A Case (Mon May 26 2014 - 06:58:36 PDT)
  - Re: [AMBER] MD at constant pH and high temperature Sangita Kachhap (Mon May 26 2014 - 07:47:52 PDT)
    - Re: [AMBER] MD at constant pH and high temperature. . Bharatham, Nagakumar (Mon May 26 2014 - 08:48:21 PDT)
    - Re: [AMBER] MD at constant pH and high temperature. . Sangita Kachhap (Mon May 26 2014 - 09:09:05 PDT)
    - Re: [AMBER] MD at constant pH and high temperature Jason Swails (Mon May 26 2014 - 12:10:07 PDT)
    - Re: [AMBER] MD at constant pH and high temperature Sangita Kachhap (Tue May 27 2014 - 09:13:12 PDT)
- Re: [AMBER] MD at constant pH and high temperature Adrian Roitberg (Mon May 26 2014 - 07:18:31 PDT)
  - Re: [AMBER] MD at constant pH and high temperature Sangita Kachhap (Mon May 26 2014 - 10:42:49 PDT)
[AMBER] How to define the direction of the force in SMD method? Cuiyl (Sun May 25 2014 - 19:14:08 PDT)
- Re: [AMBER] How to define the direction of the force in SMD method? Jason Swails (Mon May 26 2014 - 12:36:08 PDT)
  - Re: [AMBER] How to define the direction of the force in SMD method? Cuiyl (Mon May 26 2014 - 23:10:08 PDT)
[AMBER] MD at pH5 and 50-55 degree celcius Sangita Kachhap (Sun May 25 2014 - 23:47:28 PDT)
- Re: [AMBER] MD at pH5 and 50-55 degree celcius Daniel Roe (Tue May 27 2014 - 06:42:11 PDT)
  - Re: [AMBER] MD at pH5 and 50-55 degree celcius Sangita Kachhap (Tue May 27 2014 - 09:12:11 PDT)
[AMBER] Loop refirement James Starlight (Mon May 26 2014 - 03:06:13 PDT)
- Re: [AMBER] Loop refirement James Starlight (Wed May 28 2014 - 00:29:44 PDT)
  - Re: [AMBER] Loop refirement Vlad Cojocaru (Wed May 28 2014 - 00:53:40 PDT)
    - Re: [AMBER] Loop refirement James Starlight (Fri Jun 13 2014 - 12:50:36 PDT)
    - Re: [AMBER] Loop refirement James Starlight (Sat Jun 14 2014 - 13:21:02 PDT)
    - Re: [AMBER] Loop refirement James Starlight (Wed Jul 09 2014 - 03:01:15 PDT)
    - Re: [AMBER] Loop refirement James Starlight (Thu Jul 10 2014 - 02:44:21 PDT)
    - Re: [AMBER] Loop refirement Carlos Simmerling (Wed Jul 16 2014 - 08:37:04 PDT)
    - Re: [AMBER] Loop refirement James Starlight (Thu Jul 17 2014 - 00:27:46 PDT)
    - Re: [AMBER] Loop refirement James Starlight (Thu Jul 17 2014 - 04:47:53 PDT)
    - Re: [AMBER] Loop refirement Carlos Simmerling (Thu Jul 17 2014 - 05:00:04 PDT)
    - Re: [AMBER] Loop refirement James Starlight (Thu Jul 17 2014 - 09:01:59 PDT)
    - Re: [AMBER] Loop refirement James Starlight (Thu Jul 17 2014 - 09:32:19 PDT)
    - Re: [AMBER] Loop refirement Carlos Simmerling (Thu Jul 17 2014 - 10:06:50 PDT)
    - Re: [AMBER] Loop refirement James Starlight (Thu Jul 17 2014 - 10:31:19 PDT)
    - Re: [AMBER] Loop refirement Carlos Simmerling (Thu Jul 17 2014 - 10:05:47 PDT)
[AMBER] PCA and the corresponding pdb Ibrahim Said (Mon May 26 2014 - 11:54:38 PDT)
- Re: [AMBER] PCA and the corresponding pdb Daniel Roe (Tue May 27 2014 - 06:49:39 PDT)
  - Re: [AMBER] PCA and the corresponding pdb Ibrahim Said (Tue May 27 2014 - 13:32:12 PDT)
    - Re: [AMBER] PCA and the corresponding pdb Daniel Roe (Tue May 27 2014 - 13:39:36 PDT)
    - Re: [AMBER] PCA and the corresponding pdb Soumendranath Bhakat (Wed May 28 2014 - 01:08:31 PDT)
    - Re: [AMBER] PCA and the corresponding pdb Daniel Roe (Wed May 28 2014 - 06:37:39 PDT)
[AMBER] OpenMM Performance (was Re: in vacuo dynamics) Jason Swails (Mon May 26 2014 - 15:35:44 PDT)
- Re: [AMBER] OpenMM Performance (was Re: in vacuo dynamics) Scott Le Grand (Tue May 27 2014 - 12:21:18 PDT)
  - Re: [AMBER] OpenMM Performance (was Re: in vacuo dynamics) Robert McGibbon (Tue May 27 2014 - 14:11:41 PDT)
    - Re: [AMBER] OpenMM Performance (was Re: in vacuo dynamics) Jason Swails (Tue May 27 2014 - 19:14:38 PDT)
    - Re: [AMBER] OpenMM Performance (was Re: in vacuo dynamics) Scott Le Grand (Tue May 27 2014 - 20:57:03 PDT)
[AMBER] MMPBSA: Per Residue vs Pairwise decomposition Calculation Rodriguez, Yoel (Mon May 26 2014 - 18:01:44 PDT)
[AMBER] Residue Pairing ih MMPBSA calculation Arunima Shilpi (Mon May 26 2014 - 20:52:57 PDT)
- Re: [AMBER] Residue Pairing ih MMPBSA calculation Jason Swails (Tue May 27 2014 - 03:21:57 PDT)
  - Re: [AMBER] Residue Pairing ih MMPBSA calculation Soumendranath Bhakat (Tue May 27 2014 - 04:13:43 PDT)
    - Re: [AMBER] Residue Pairing ih MMPBSA calculation Soumendranath Bhakat (Tue May 27 2014 - 04:15:53 PDT)
[AMBER] 3NKB5 王珍 (Tue May 27 2014 - 00:08:27 PDT)
- Re: [AMBER] 3NKB5 Jason Swails (Tue May 27 2014 - 03:20:14 PDT)
  - Re: [AMBER] 3NKB5 王珍 (Wed May 28 2014 - 06:00:20 PDT)
    - Re: [AMBER] 3NKB5 王珍 (Wed May 28 2014 - 07:19:11 PDT)
    - Re: [AMBER] 3NKB5 Jason Swails (Wed May 28 2014 - 07:29:13 PDT)
    - Re: [AMBER] 3NKB5 王珍 (Wed May 28 2014 - 07:56:49 PDT)
    - Re: [AMBER] 3NKB5 Jason Swails (Wed May 28 2014 - 08:12:39 PDT)
    - Re: [AMBER] 3NKB5 王珍 (Wed May 28 2014 - 18:17:00 PDT)
[AMBER] rmsd of multiple trajectories with different topologies and sizes but same reference Brian Radak (Tue May 27 2014 - 07:43:08 PDT)
- Re: [AMBER] rmsd of multiple trajectories with different topologies and sizes but same reference Daniel Roe (Tue May 27 2014 - 08:20:55 PDT)
  - Re: [AMBER] rmsd of multiple trajectories with different topologies and sizes but same reference Brian Radak (Tue May 27 2014 - 08:41:24 PDT)
[AMBER] Disulfide Bond Info and XMIN Stuck Problems Guqin Shi (Tue May 27 2014 - 09:14:29 PDT)
- Re: [AMBER] Disulfide Bond Info and XMIN Stuck Problems David A Case (Tue May 27 2014 - 17:25:07 PDT)
  - Re: [AMBER] Disulfide Bond Info and XMIN Stuck Problems Guqin Shi (Tue May 27 2014 - 19:34:59 PDT)
    - Re: [AMBER] Disulfide Bond Info and XMIN Stuck Problems David A Case (Wed May 28 2014 - 06:39:00 PDT)
    - Re: [AMBER] Disulfide Bond Info and XMIN Stuck Problems Guqin Shi (Wed May 28 2014 - 14:05:21 PDT)
    - Re: [AMBER] Disulfide Bond Info and XMIN Stuck Problems David A Case (Wed May 28 2014 - 16:55:31 PDT)
    - Re: [AMBER] Disulfide Bond Info and XMIN Stuck Problems Guqin Shi (Thu May 29 2014 - 07:25:08 PDT)
    - Re: [AMBER] Disulfide Bond Info and XMIN Stuck Problems David A Case (Thu Jun 12 2014 - 13:39:40 PDT)
    - Re: [AMBER] Disulfide Bond Info and XMIN Stuck Problems Daniel Roe (Sat Jun 14 2014 - 10:49:48 PDT)
    - Re: [AMBER] Disulfide Bond Info and XMIN Stuck Problems Guqin Shi (Tue Jun 17 2014 - 14:15:49 PDT)
    - Re: [AMBER] Disulfide Bond Info and XMIN Stuck Problems Daniel Roe (Thu Jun 19 2014 - 14:17:33 PDT)
    - Re: [AMBER] Disulfide Bond Info and XMIN Stuck Problems Guqin Shi (Tue Jun 17 2014 - 14:11:23 PDT)
[AMBER] MMPBSA: Per Residue vs Pairwise decomposition Calculation(idecomp= 2 o idecomp=4) Rodriguez, Yoel (Tue May 27 2014 - 10:22:06 PDT)
[AMBER] MMPBSA Hallel Freedman (Tue May 27 2014 - 11:05:32 PDT)
- Re: [AMBER] MMPBSA Ray Luo, Ph.D. (Tue May 27 2014 - 12:41:24 PDT)
  - Re: [AMBER] MMPBSA Hallel Freedman (Wed May 28 2014 - 11:13:17 PDT)
    - Re: [AMBER] MMPBSA Hallel Freedman (Wed May 28 2014 - 11:54:19 PDT)
    - Re: [AMBER] MMPBSA Ray Luo, Ph.D. (Wed May 28 2014 - 16:22:04 PDT)
    - Re: [AMBER] MMPBSA Hallel Freedman (Wed May 28 2014 - 16:23:25 PDT)
    - Re: [AMBER] MMPBSA Hallel Freedman (Wed May 28 2014 - 19:33:00 PDT)
[AMBER] print residue Arunima Shilpi (Tue May 27 2014 - 22:07:04 PDT)
- Re: [AMBER] print residue Jason Swails (Wed May 28 2014 - 05:03:20 PDT)
  - Re: [AMBER] print residue Soumendranath Bhakat (Wed May 28 2014 - 05:15:18 PDT)
[AMBER] zinc partial charges Nash, Anthony (Tue May 27 2014 - 23:30:38 PDT)
- Re: [AMBER] zinc partial charges FyD (Wed May 28 2014 - 23:57:42 PDT)
[AMBER] command to check non bonded interactions like vander waal's interactions Nitin Sharma (Wed May 28 2014 - 06:27:12 PDT)
- Re: [AMBER] command to check non bonded interactions like vander waal's interactions Jason Swails (Wed May 28 2014 - 06:37:26 PDT)
  - Re: [AMBER] command to check non bonded interactions like vander waal's interactions Soumendranath Bhakat (Wed May 28 2014 - 06:40:18 PDT)
[AMBER] amber in namd Lara rajam (Wed May 28 2014 - 08:21:53 PDT)
- Re: [AMBER] amber in namd Jason Swails (Wed May 28 2014 - 08:41:54 PDT)
[AMBER] Contributing new water models Lee-Ping Wang (Wed May 28 2014 - 11:35:30 PDT)
- Re: [AMBER] Contributing new water models Jason Swails (Wed May 28 2014 - 12:22:15 PDT)
  - Re: [AMBER] Contributing new water models Lee-Ping Wang (Wed May 28 2014 - 12:26:43 PDT)
- Re: [AMBER] Contributing new water models David A Case (Wed May 28 2014 - 18:28:41 PDT)
- Re: [AMBER] Contributing new water models adm (Mon Jun 02 2014 - 00:35:57 PDT)
  - Re: [AMBER] Contributing new water models Jason Swails (Mon Jun 02 2014 - 04:18:52 PDT)
[AMBER] print residue Arunima Shilpi (Wed May 28 2014 - 22:07:29 PDT)
- Re: [AMBER] print residue Soumendranath Bhakat (Wed May 28 2014 - 23:40:33 PDT)
[AMBER] Query regarding Amber Advance Tutorial 17 Kshatresh Dutta Dubey (Thu May 29 2014 - 01:54:51 PDT)
- Re: [AMBER] Query regarding Amber Advance Tutorial 17 Jason Swails (Thu May 29 2014 - 05:01:17 PDT)
  - Re: [AMBER] Query regarding Amber Advance Tutorial 17 Kshatresh Dutta Dubey (Thu May 29 2014 - 06:54:23 PDT)
[AMBER] MMPBSA_complex.mdcrd.0 error mahnam karim (Thu May 29 2014 - 07:03:58 PDT)
- Re: [AMBER] MMPBSA_complex.mdcrd.0 error Ray Luo, Ph.D. (Thu May 29 2014 - 10:01:30 PDT)
[AMBER] protonate question 王珍 (Thu May 29 2014 - 17:45:24 PDT)
- Re: [AMBER] protonate question Jason Swails (Fri May 30 2014 - 06:30:13 PDT)
  - Re: [AMBER] protonate question 王珍 (Sat May 31 2014 - 00:52:15 PDT)
[AMBER] sudden and rapid configuration change in NVT simulation yjlee (Fri May 30 2014 - 01:44:46 PDT)
- Re: [AMBER] sudden and rapid configuration change in NVT simulation Soumendranath Bhakat (Fri May 30 2014 - 02:17:51 PDT)
- Re: [AMBER] sudden and rapid configuration change in NVT simulation yjlee (Sun Jun 01 2014 - 23:47:17 PDT)
  - Re: [AMBER] sudden and rapid configuration change in NVT simulation Jason Swails (Mon Jun 02 2014 - 04:20:43 PDT)
- Re: [AMBER] sudden and rapid configuration change in NVT simulation yjlee (Mon Jun 02 2014 - 23:43:02 PDT)
  - Re: [AMBER] sudden and rapid configuration change in NVT simulation Jason Swails (Tue Jun 03 2014 - 06:23:09 PDT)
    - Re: [AMBER] sudden and rapid configuration change in NVT simulation Soumendranath Bhakat (Tue Jun 03 2014 - 06:46:30 PDT)
    - Re: [AMBER] sudden and rapid configuration change in NVT simulation Daniel Roe (Tue Jun 03 2014 - 07:12:07 PDT)
- Re: [AMBER] sudden and rapid configuration change in NVT simulation yjlee (Thu Jun 05 2014 - 04:47:02 PDT)
  - Re: [AMBER] sudden and rapid configuration change in NVT simulation Jason Swails (Thu Jun 05 2014 - 05:40:17 PDT)
- Re: [AMBER] sudden and rapid configuration change in NVT simulation yjlee (Fri Jun 06 2014 - 05:46:03 PDT)
[AMBER] Problem in restarting simulation from restart file Kshatresh Dutta Dubey (Fri May 30 2014 - 05:04:59 PDT)
- Re: [AMBER] Problem in restarting simulation from restart file Jason Swails (Fri May 30 2014 - 05:44:50 PDT)
[AMBER] periodic box buffer zone Paulsen, Janet (Fri May 30 2014 - 08:35:34 PDT)
- Re: [AMBER] periodic box buffer zone Brian Radak (Fri May 30 2014 - 08:52:19 PDT)
[AMBER] amber in namd Lara rajam (Fri May 30 2014 - 08:46:40 PDT)
- Re: [AMBER] amber in namd Jason Swails (Fri May 30 2014 - 08:58:12 PDT)
  - Re: [AMBER] amber in namd amin.imtech.res.in (Fri May 30 2014 - 09:52:04 PDT)
[AMBER] Parametrization of non-standart residues James Starlight (Fri May 30 2014 - 11:12:33 PDT)
- Re: [AMBER] Parametrization of non-standart residues Jason Swails (Fri May 30 2014 - 11:25:47 PDT)
  - Re: [AMBER] Parametrization of non-standart residues James Starlight (Fri May 30 2014 - 12:00:14 PDT)
    - Re: [AMBER] Parametrization of non-standart residues James Starlight (Fri May 30 2014 - 12:04:01 PDT)
    - Re: [AMBER] Parametrization of non-standart residues Parker de Waal (Fri May 30 2014 - 12:43:16 PDT)
    - Re: [AMBER] Parametrization of non-standart residues James Starlight (Fri May 30 2014 - 23:07:39 PDT)
    - Re: [AMBER] Parametrization of non-standart residues FyD (Sat May 31 2014 - 01:11:00 PDT)
    - Re: [AMBER] Parametrization of non-standart residues James Starlight (Sat May 31 2014 - 04:50:56 PDT)
    - Re: [AMBER] Parametrization of non-standart residues Parker de Waal (Sat May 31 2014 - 05:50:12 PDT)
    - Re: [AMBER] Parametrization of non-standart residues James Starlight (Sat May 31 2014 - 06:21:30 PDT)
    - Re: [AMBER] Parametrization of non-standart residues FyD (Sat May 31 2014 - 06:54:48 PDT)
    - Re: [AMBER] Parametrization of non-standart residues Jason Swails (Sat May 31 2014 - 07:53:51 PDT)
    - Re: [AMBER] Parametrization of non-standart residues James Starlight (Tue Jun 03 2014 - 05:57:57 PDT)
    - Re: [AMBER] Parametrization of non-standart residues Parker de Waal (Tue Jun 03 2014 - 06:15:30 PDT)
    - Re: [AMBER] Parametrization of non-standart residues James Starlight (Tue Jun 03 2014 - 08:15:55 PDT)
[AMBER] request for help in plotting distance matrix plot Robin Jain (Fri May 30 2014 - 23:10:22 PDT)
- Re: [AMBER] request for help in plotting distance matrix plot Soumendranath Bhakat (Fri May 30 2014 - 23:29:24 PDT)
- Re: [AMBER] request for help in plotting distance matrix plot Jason Swails (Sat May 31 2014 - 08:00:17 PDT)
- Re: [AMBER] request for help in plotting distance matrix plot Daniel Roe (Sun Jun 01 2014 - 09:35:30 PDT)
  - Re: [AMBER] request for help in plotting distance matrix plot Soumendranath Bhakat (Sun Jun 01 2014 - 09:53:55 PDT)
[AMBER] error in plot of interaction energy in xmgrace Arunima Shilpi (Sat May 31 2014 - 06:03:22 PDT)
- Re: [AMBER] error in plot of interaction energy in xmgrace Soumendranath Bhakat (Sat May 31 2014 - 06:54:53 PDT)
[AMBER] problem using pmemd.cuda with barostat=2 option Asaminew Haile (Sat May 31 2014 - 08:10:50 PDT)
- Re: [AMBER] problem using pmemd.cuda with barostat=2 option Jason Swails (Sat May 31 2014 - 08:51:25 PDT)
  - Re: [AMBER] problem using pmemd.cuda with barostat=2 option Asaminew Haile (Sat May 31 2014 - 09:01:30 PDT)
  - Re: [AMBER] problem using pmemd.cuda with barostat=2 option Sorensen, Jesper (Wed Nov 05 2014 - 10:18:57 PST)
    - Re: [AMBER] problem using pmemd.cuda with barostat=2 option Scott Le Grand (Wed Nov 05 2014 - 10:23:44 PST)
    - Re: [AMBER] problem using pmemd.cuda with barostat=2 option Ross Walker (Wed Nov 05 2014 - 09:41:58 PST)
    - Re: [AMBER] problem using pmemd.cuda with barostat=2 option Jason Swails (Wed Nov 05 2014 - 10:47:20 PST)
    - Re: [AMBER] problem using pmemd.cuda with barostat=2 option Sorensen, Jesper (Wed Nov 05 2014 - 12:27:36 PST)
[AMBER] sander QM/MM with terachem using MPI Daniel Hollas (Sat May 31 2014 - 08:21:42 PDT)
- Re: [AMBER] sander QM/MM with terachem using MPI Andreas Goetz (Thu Sep 18 2014 - 22:52:20 PDT)
[AMBER] ff99SB-ildn-nmr Nihal Korkmaz (Sat May 31 2014 - 11:44:23 PDT)
- Re: [AMBER] ff99SB-ildn-nmr Jason Swails (Sat May 31 2014 - 11:59:30 PDT)
[AMBER] calculation diffusion coefficient Sohag Biswas (Sun Jun 01 2014 - 02:28:21 PDT)
- Re: [AMBER] calculation diffusion coefficient David A Case (Sun Jun 01 2014 - 04:37:50 PDT)
[AMBER] FF12SB (and FF14?) - any benchmarks/evidence of its quality? Marc van der Kamp (Sun Jun 01 2014 - 07:39:27 PDT)
- Re: [AMBER] FF12SB (and FF14?) - any benchmarks/evidence of its quality? Hai Nguyen (Sun Jun 01 2014 - 12:09:44 PDT)
- Re: [AMBER] FF12SB (and FF14?) - any benchmarks/evidence of its quality? Carlos Simmerling (Sun Jun 01 2014 - 12:59:19 PDT)
[AMBER] error in plot of interaction energy in xmgrace Arunima Shilpi (Sun Jun 01 2014 - 09:05:15 PDT)
- Re: [AMBER] error in plot of interaction energy in xmgrace Asaminew Haile (Sun Jun 01 2014 - 09:30:24 PDT)
  - Re: [AMBER] error in plot of interaction energy in xmgrace Soumendranath Bhakat (Sun Jun 01 2014 - 13:24:11 PDT)
[AMBER] defining reaction coordinate for umbrella sampling Jorgen Simonsen (Sun Jun 01 2014 - 18:12:32 PDT)
- Re: [AMBER] defining reaction coordinate for umbrella sampling Jason Swails (Sun Jun 01 2014 - 19:09:50 PDT)
[AMBER] Ligand movement in protein cavatiy Jurgens de Bruin (Sun Jun 01 2014 - 19:20:10 PDT)
- Re: [AMBER] Ligand movement in protein cavatiy Aldo Segura (Sun Jun 01 2014 - 20:34:56 PDT)
  - Re: [AMBER] Ligand movement in protein cavatiy Jurgens de Bruin (Sun Jun 01 2014 - 22:22:41 PDT)
- Re: [AMBER] Ligand movement in protein cavatiy Jason Swails (Mon Jun 02 2014 - 04:25:24 PDT)
  - Re: [AMBER] Ligand movement in protein cavatiy Jurgens de Bruin (Mon Jun 02 2014 - 04:31:09 PDT)
    - Re: [AMBER] Ligand movement in protein cavatiy Jason Swails (Mon Jun 02 2014 - 04:47:37 PDT)
    - Re: [AMBER] Ligand movement in protein cavatiy Soumendranath Bhakat (Mon Jun 02 2014 - 04:59:04 PDT)
    - Re: [AMBER] Ligand movement in protein cavatiy Jurgens de Bruin (Mon Jun 02 2014 - 05:22:59 PDT)
    - Re: [AMBER] Ligand movement in protein cavatiy Aldo Segura (Mon Jun 02 2014 - 06:12:26 PDT)
    - Re: [AMBER] Ligand movement in protein cavatiy Jurgens de Bruin (Mon Jun 02 2014 - 23:09:41 PDT)
    - Re: [AMBER] Ligand movement in protein cavatiy Jurgens de Bruin (Wed Jun 04 2014 - 05:14:19 PDT)
    - Re: [AMBER] Ligand movement in protein cavatiy Jason Swails (Wed Jun 04 2014 - 05:55:59 PDT)
    - Re: [AMBER] Ligand movement in protein cavatiy Jurgens de Bruin (Wed Jun 04 2014 - 05:56:18 PDT)
[AMBER] plot in xmgrace (interaction energy per residues) Arunima Shilpi (Sun Jun 01 2014 - 23:45:18 PDT)
- Re: [AMBER] plot in xmgrace (interaction energy per residues) David A Case (Mon Jun 02 2014 - 04:07:10 PDT)
[AMBER] Pressure fluctuation problem during NPT simulation Saikat Dutta chowdhury (Mon Jun 02 2014 - 03:53:30 PDT)
- Re: [AMBER] Pressure fluctuation problem during NPT simulation Jason Swails (Mon Jun 02 2014 - 04:35:00 PDT)
  - Re: [AMBER] Pressure fluctuation problem during NPT simulation Saikat Dutta chowdhury (Mon Jun 02 2014 - 04:41:19 PDT)
[AMBER] Using MM-PBSA to find binding free energy for Zif 268-DNA complex Roza M (Mon Jun 02 2014 - 04:04:28 PDT)
- Re: [AMBER] Using MM-PBSA to find binding free energy for Zif 268-DNA complex Jason Swails (Mon Jun 02 2014 - 04:27:13 PDT)
  - Re: [AMBER] Using MM-PBSA to find binding free energy for Zif 268-DNA complex Roza M (Mon Jun 02 2014 - 05:02:15 PDT)
    - Re: [AMBER] Using MM-PBSA to find binding free energy for Zif 268-DNA complex Jason Swails (Mon Jun 02 2014 - 05:15:48 PDT)
  - Re: [AMBER] Using MM-PBSA to find binding free energy for Zif 268-DNA complex Soumendranath Bhakat (Mon Jun 02 2014 - 05:10:57 PDT)
[AMBER] Regarding molecule's breaking during simulation. richa anand (Mon Jun 02 2014 - 04:52:09 PDT)
- Re: [AMBER] Regarding molecule's breaking during simulation. Jason Swails (Mon Jun 02 2014 - 05:12:38 PDT)
[AMBER] Using MM-PBSA to find binding free energy for Zif268-DNA complex Roza M (Mon Jun 02 2014 - 06:20:04 PDT)
[AMBER] image distances newamber list (Mon Jun 02 2014 - 07:46:38 PDT)
- Re: [AMBER] image distances Daniel Roe (Mon Jun 02 2014 - 07:50:22 PDT)
  - Re: [AMBER] image distances newamber list (Mon Jun 02 2014 - 08:36:34 PDT)
    - Re: [AMBER] image distances newamber list (Wed Jun 04 2014 - 07:06:05 PDT)
    - Re: [AMBER] image distances Daniel Roe (Wed Jun 04 2014 - 11:06:55 PDT)
[AMBER] mmpbsa.py zahra khatti (Mon Jun 02 2014 - 07:54:40 PDT)
[AMBER] error in MMPBSA Lara rajam (Mon Jun 02 2014 - 13:48:47 PDT)
- Re: [AMBER] error in MMPBSA Ray Luo, Ph.D. (Mon Jun 02 2014 - 15:39:54 PDT)
[AMBER] WaterBox Dimensions Ahmed Ayoub (Mon Jun 02 2014 - 14:53:00 PDT)
- Re: [AMBER] WaterBox Dimensions David A Case (Tue Jun 03 2014 - 05:10:35 PDT)
[AMBER] Distance matrix time series Eugene Yedvabny (Mon Jun 02 2014 - 15:19:35 PDT)
- Re: [AMBER] Distance matrix time series Daniel Roe (Tue Jun 03 2014 - 07:22:47 PDT)
[AMBER] Mistake in water density Vu Truong (Mon Jun 02 2014 - 15:50:08 PDT)
- Re: [AMBER] Mistake in water density David A Case (Tue Jun 03 2014 - 05:14:20 PDT)
[AMBER] Error in cpptraj remlog command Eugene Yedvabny (Mon Jun 02 2014 - 17:25:04 PDT)
- Re: [AMBER] Error in cpptraj remlog command Daniel Roe (Mon Jun 02 2014 - 19:54:21 PDT)
  - Re: [AMBER] Error in cpptraj remlog command Daniel Roe (Tue Jun 03 2014 - 12:20:05 PDT)
[AMBER] help in grid command Robin Jain (Mon Jun 02 2014 - 23:17:08 PDT)
- Re: [AMBER] help in grid command Jason Swails (Tue Jun 03 2014 - 05:52:56 PDT)
[AMBER] help in calculating Angular distribution function Robin Jain (Tue Jun 03 2014 - 00:12:16 PDT)
[AMBER] active site water cluster analysis Ahmet yıldırım (Tue Jun 03 2014 - 02:41:47 PDT)
[AMBER] Could not find angle parameter: S - S - S Sangita Kachhap (Tue Jun 03 2014 - 02:49:52 PDT)
- Re: [AMBER] Could not find angle parameter: S - S - S Hector A. Baldoni (Tue Jun 03 2014 - 03:47:48 PDT)
  - Re: [AMBER] Could not find angle parameter: S - S - S Sangita Kachhap (Tue Jun 03 2014 - 03:55:30 PDT)
[AMBER] sander14 MPI produces different results depending on number of used cores David Abia (Tue Jun 03 2014 - 05:00:53 PDT)
- Re: [AMBER] sander14 MPI produces different results depending on number of used cores David A Case (Tue Jun 03 2014 - 06:10:59 PDT)
[AMBER] MMPBSA error zahra khatti (Tue Jun 03 2014 - 07:15:45 PDT)
- Re: [AMBER] MMPBSA error Jason Swails (Tue Jun 03 2014 - 08:11:32 PDT)
  - Re: [AMBER] MMPBSA error zahra khatti (Tue Jun 03 2014 - 13:17:48 PDT)
    - Re: [AMBER] MMPBSA error zahra khatti (Wed Jun 04 2014 - 05:46:48 PDT)
    - Re: [AMBER] MMPBSA error Jason Swails (Wed Jun 04 2014 - 06:02:14 PDT)
    - Re: [AMBER] MMPBSA error Ray Luo, Ph.D. (Wed Jun 04 2014 - 10:52:40 PDT)
    - Re: [AMBER] MMPBSA error zahra khatti (Wed Jun 04 2014 - 11:43:38 PDT)
    - Re: [AMBER] MMPBSA error zahra khatti (Thu Jun 05 2014 - 00:28:06 PDT)
    - Re: [AMBER] MMPBSA error Ray Luo, Ph.D. (Thu Jun 05 2014 - 16:25:43 PDT)
    - Re: [AMBER] MMPBSA error zahra khatti (Fri Jun 06 2014 - 05:57:41 PDT)
    - Re: [AMBER] MMPBSA error Ray Luo, Ph.D. (Tue Jun 10 2014 - 12:58:53 PDT)
    - Re: [AMBER] MMPBSA error zahra khatti (Fri Jun 20 2014 - 08:03:32 PDT)
[AMBER] QM/MM and spin parameter Jinfeng Huang (Tue Jun 03 2014 - 07:39:10 PDT)
- Re: [AMBER] QM/MM and spin parameter Brian Radak (Tue Jun 03 2014 - 08:16:36 PDT)
- Re: [AMBER] QM/MM and spin parameter Jason Swails (Tue Jun 03 2014 - 08:18:47 PDT)
[AMBER] (probably) benign error when writing iapbs-pot.dx files with sander.APBS Brian Radak (Tue Jun 03 2014 - 10:03:21 PDT)
[AMBER] Parametrization of the protein with the assigned protonation states James Starlight (Tue Jun 03 2014 - 10:44:07 PDT)
- Re: [AMBER] Parametrization of the protein with the assigned protonation states Jason Swails (Tue Jun 03 2014 - 10:59:34 PDT)
  - Re: [AMBER] Parametrization of the protein with the assigned protonation states James Starlight (Wed Jun 04 2014 - 06:43:53 PDT)
    - Re: [AMBER] Parametrization of the protein with the assigned protonation states Jason Swails (Wed Jun 04 2014 - 07:35:02 PDT)
[AMBER] MTKPP installation error Kshatresh Dutta Dubey (Tue Jun 03 2014 - 12:47:12 PDT)
- Re: [AMBER] MTKPP installation error Jason Swails (Tue Jun 03 2014 - 12:52:03 PDT)
  - Re: [AMBER] MTKPP installation error Kshatresh Dutta Dubey (Tue Jun 03 2014 - 13:04:09 PDT)
    - Re: [AMBER] MTKPP installation error Kshatresh Dutta Dubey (Tue Jun 03 2014 - 22:07:44 PDT)
    - Re: [AMBER] MTKPP installation error Jason Swails (Wed Jun 04 2014 - 04:39:45 PDT)
    - Re: [AMBER] MTKPP installation error Kshatresh Dutta Dubey (Wed Jun 04 2014 - 04:46:23 PDT)
[AMBER] compatibility of lipid14 with AMBER12 and lipid11/14 with NAMD v.2.10 Thomas Evangelidis (Tue Jun 03 2014 - 14:30:21 PDT)
- Re: [AMBER] compatibility of lipid14 with AMBER12 and lipid11/14 with NAMD v.2.10 Jason Swails (Tue Jun 03 2014 - 14:58:11 PDT)
  - Re: [AMBER] compatibility of lipid14 with AMBER12 and lipid11/14 with NAMD v.2.10 Hannes Loeffler (Wed Jun 04 2014 - 03:07:33 PDT)
    - Re: [AMBER] compatibility of lipid14 with AMBER12 and lipid11/14 with NAMD v.2.10 Thomas Evangelidis (Wed Jun 04 2014 - 04:03:04 PDT)
    - Re: [AMBER] compatibility of lipid14 with AMBER12 and lipid11/14 with NAMD v.2.10 Benjamin D Madej (Wed Jun 04 2014 - 13:43:33 PDT)
[AMBER] donor and acceptor group in hbond Arunima Shilpi (Tue Jun 03 2014 - 21:59:17 PDT)
- Re: [AMBER] donor and acceptor group in hbond Daniel Roe (Wed Jun 04 2014 - 06:47:16 PDT)
[AMBER] set up for the ScaledMD zhou gong (Tue Jun 03 2014 - 23:55:06 PDT)
- Re: [AMBER] set up for the ScaledMD Neha Gandhi (Wed Jun 04 2014 - 00:10:49 PDT)
[AMBER] Calculating absolute binding free energy menwer momo (Wed Jun 04 2014 - 00:04:41 PDT)
[AMBER] GAFFlipid parameters Антипина Александра (Wed Jun 04 2014 - 02:01:16 PDT)
- Re: [AMBER] GAFFlipid parameters Dickson, Callum J (Wed Jun 04 2014 - 04:37:42 PDT)
  - Re: [AMBER] GAFFlipid parameters Антипина Александра (Wed Jun 04 2014 - 05:24:17 PDT)
    - Re: [AMBER] GAFFlipid parameters Dickson, Callum J (Wed Jun 04 2014 - 05:52:44 PDT)
    - Re: [AMBER] GAFFlipid parameters Alexandra Antipina (Wed Jun 11 2014 - 02:35:02 PDT)
    - Re: [AMBER] GAFFlipid parameters Dickson, Callum J (Wed Jun 11 2014 - 04:25:31 PDT)
    - Re: [AMBER] GAFFlipid parameters Aldo Segura (Wed Jun 04 2014 - 05:56:48 PDT)
    - Re: [AMBER] GAFFlipid parameters Benjamin D Madej (Wed Jun 04 2014 - 14:13:51 PDT)
[AMBER] calculating absolute binding free energy using MMPBSA menwer momo (Wed Jun 04 2014 - 02:17:49 PDT)
- Re: [AMBER] calculating absolute binding free energy using MMPBSA Jason Swails (Wed Jun 04 2014 - 04:55:57 PDT)
  - [AMBER] Isopeptide bond Asp-Lys - parameters? Anselm Horn (Wed Jun 04 2014 - 05:08:17 PDT)
    - Re: [AMBER] Isopeptide bond Asp-Lys - parameters? FyD (Wed Jun 04 2014 - 22:56:03 PDT)
  - Re: [AMBER] calculating absolute binding free energy using MMPBSA David A Case (Wed Jun 04 2014 - 12:24:46 PDT)
[AMBER] principal axes error using cpptraj Asmita Gupta (Wed Jun 04 2014 - 03:16:43 PDT)
- Re: [AMBER] principal axes error using cpptraj Daniel Roe (Wed Jun 04 2014 - 06:05:24 PDT)
[AMBER] RDF Plot zahra khatti (Wed Jun 04 2014 - 08:04:57 PDT)
- [AMBER] Fw: RDF Plot zahra khatti (Wed Jun 04 2014 - 08:13:45 PDT)
- Re: [AMBER] RDF Plot Jason Swails (Wed Jun 04 2014 - 09:08:42 PDT)
[AMBER] CPPTRAJ autoimage corresponds to 2 mols, should only be 1. mish (Wed Jun 04 2014 - 08:11:47 PDT)
- Re: [AMBER] CPPTRAJ autoimage corresponds to 2 mols, should only be 1. Daniel Roe (Wed Jun 04 2014 - 08:26:12 PDT)
  - Re: [AMBER] CPPTRAJ autoimage corresponds to 2 mols, should only be 1. mish (Wed Jun 04 2014 - 08:43:48 PDT)
    - Re: [AMBER] CPPTRAJ autoimage corresponds to 2 mols, should only be 1. Daniel Roe (Wed Jun 04 2014 - 10:15:58 PDT)
    - Re: [AMBER] CPPTRAJ autoimage corresponds to 2 mols, should only be 1. Daniel Roe (Wed Jun 04 2014 - 10:54:02 PDT)
    - Re: [AMBER] CPPTRAJ autoimage corresponds to 2 mols, should only be 1. mish (Thu Jun 05 2014 - 07:49:33 PDT)
[AMBER] Analysis of CHARMM DNA trajectory using nastruct Geoffrey Gray (Wed Jun 04 2014 - 08:38:07 PDT)
- Re: [AMBER] Analysis of CHARMM DNA trajectory using nastruct Daniel Roe (Wed Jun 04 2014 - 12:06:06 PDT)
  - Re: [AMBER] Analysis of CHARMM DNA trajectory using nastruct Geoffrey Gray (Wed Jun 04 2014 - 12:11:48 PDT)
    - Re: [AMBER] Analysis of CHARMM DNA trajectory using nastruct Jason Swails (Wed Jun 04 2014 - 12:40:11 PDT)
[AMBER] VMD and binary trajectories James Starlight (Thu Jun 05 2014 - 01:00:45 PDT)
- Re: [AMBER] VMD and binary trajectories Jason Swails (Thu Jun 05 2014 - 04:39:54 PDT)
  - Re: [AMBER] VMD and binary trajectories James Starlight (Thu Jun 05 2014 - 07:19:08 PDT)
[AMBER] On the choosing of coordinate for the umbrella sampling James Starlight (Thu Jun 05 2014 - 04:03:46 PDT)
- Re: [AMBER] On the choosing of coordinate for the umbrella sampling Jason Swails (Thu Jun 05 2014 - 04:45:56 PDT)
  - Re: [AMBER] On the choosing of coordinate for the umbrella sampling Brian Radak (Thu Jun 05 2014 - 06:37:29 PDT)
- Re: [AMBER] On the choosing of coordinate for the umbrella sampling Carlos Simmerling (Thu Jun 05 2014 - 12:28:32 PDT)
[AMBER] error in hbond analysis Arunima Shilpi (Thu Jun 05 2014 - 23:51:22 PDT)
- Re: [AMBER] error in hbond analysis Jason Swails (Fri Jun 06 2014 - 05:15:25 PDT)
[AMBER] 【amber】center of mass&umbrella sampling whb (Fri Jun 06 2014 - 00:11:40 PDT)
- Re: [AMBER] 【amber】center of mass&umbrella sampling Jason Swails (Fri Jun 06 2014 - 05:20:20 PDT)
  - Re: [AMBER] 【amber】center of mass&umbrella sampling Daniel Roe (Fri Jun 06 2014 - 06:57:16 PDT)
[AMBER] Constant surface tension on the membrane James Starlight (Fri Jun 06 2014 - 01:28:27 PDT)
- Re: [AMBER] Constant surface tension on the membrane Jason Swails (Fri Jun 06 2014 - 05:27:01 PDT)
  - Re: [AMBER] Constant surface tension on the membrane Benjamin D Madej (Mon Jun 09 2014 - 11:53:29 PDT)
    - Re: [AMBER] Constant surface tension on the membrane James Starlight (Mon Jun 09 2014 - 12:24:08 PDT)
    - Re: [AMBER] Constant surface tension on the membrane Benjamin D Madej (Mon Jun 09 2014 - 16:19:53 PDT)
[AMBER] Density Plot Jurgens de Bruin (Fri Jun 06 2014 - 00:58:32 PDT)
- Re: [AMBER] Density Plot Jason Swails (Fri Jun 06 2014 - 05:21:43 PDT)
[AMBER] cpptraj error : not parsing mdvel file Himanshu Joshi (Fri Jun 06 2014 - 04:00:17 PDT)
- Re: [AMBER] cpptraj error : not parsing mdvel file Daniel Roe (Fri Jun 06 2014 - 06:53:53 PDT)
  - Re: [AMBER] cpptraj error : not parsing mdvel file Himanshu Joshi (Sat Jun 07 2014 - 05:17:41 PDT)
[AMBER] charmmlipid2amber.py James Starlight (Fri Jun 06 2014 - 07:40:45 PDT)
- Re: [AMBER] charmmlipid2amber.py James Starlight (Fri Jun 06 2014 - 09:26:53 PDT)
  - Re: [AMBER] charmmlipid2amber.py Benjamin D Madej (Mon Jun 09 2014 - 12:02:09 PDT)
    - Re: [AMBER] charmmlipid2amber.py James Starlight (Mon Jun 09 2014 - 12:18:47 PDT)
    - Re: [AMBER] charmmlipid2amber.py Benjamin D Madej (Mon Jun 09 2014 - 15:48:20 PDT)
    - Re: [AMBER] charmmlipid2amber.py James Starlight (Mon Jun 09 2014 - 22:36:06 PDT)
    - Re: [AMBER] charmmlipid2amber.py James Starlight (Mon Jun 09 2014 - 22:47:52 PDT)
    - Re: [AMBER] charmmlipid2amber.py James Starlight (Tue Jun 10 2014 - 09:06:49 PDT)
    - Re: [AMBER] charmmlipid2amber.py Benjamin D Madej (Tue Jun 10 2014 - 11:51:40 PDT)
    - Re: [AMBER] charmmlipid2amber.py James Starlight (Tue Jun 10 2014 - 12:04:30 PDT)
    - Re: [AMBER] charmmlipid2amber.py Benjamin D Madej (Tue Jun 10 2014 - 12:16:41 PDT)
    - Re: [AMBER] charmmlipid2amber.py James Starlight (Tue Jun 10 2014 - 12:39:24 PDT)
    - Re: [AMBER] charmmlipid2amber.py Benjamin D Madej (Tue Jun 10 2014 - 13:38:54 PDT)
    - Re: [AMBER] charmmlipid2amber.py James Starlight (Tue Jun 10 2014 - 22:15:49 PDT)
    - Re: [AMBER] charmmlipid2amber.py James Starlight (Tue Jun 10 2014 - 23:54:48 PDT)
    - Re: [AMBER] charmmlipid2amber.py James Starlight (Wed Jun 11 2014 - 00:16:33 PDT)
    - Re: [AMBER] charmmlipid2amber.py Benjamin D Madej (Wed Jun 11 2014 - 13:47:58 PDT)
    - Re: [AMBER] charmmlipid2amber.py James Starlight (Wed Jun 11 2014 - 22:45:00 PDT)
    - Re: [AMBER] charmmlipid2amber.py Benjamin D Madej (Thu Jun 12 2014 - 11:27:54 PDT)
    - Re: [AMBER] charmmlipid2amber.py James Starlight (Thu Jun 12 2014 - 12:49:23 PDT)
[AMBER] Problem using charmmlipid2amber.py with VMD wmsmith.uci.edu (Fri Jun 06 2014 - 09:27:59 PDT)
- Re: [AMBER] Problem using charmmlipid2amber.py with VMD James Starlight (Sun Jun 08 2014 - 00:52:22 PDT)
  - Re: [AMBER] Problem using charmmlipid2amber.py with VMD Benjamin D Madej (Mon Jun 09 2014 - 12:03:13 PDT)
  - Re: [AMBER] Problem using charmmlipid2amber.py with VMD Benjamin D Madej (Mon Jun 09 2014 - 12:18:57 PDT)
    - Re: [AMBER] Problem using charmmlipid2amber.py with VMD Thomas Evangelidis (Mon Jun 09 2014 - 12:48:40 PDT)
    - Re: [AMBER] Problem using charmmlipid2amber.py with VMD Benjamin D Madej (Mon Jun 09 2014 - 17:10:36 PDT)
[AMBER] error in hydrogen bond Arunima Shilpi (Fri Jun 06 2014 - 21:48:04 PDT)
- Re: [AMBER] error in hydrogen bond Jason Swails (Sat Jun 07 2014 - 04:24:26 PDT)
  - Re: [AMBER] error in hydrogen bond Soumendranath Bhakat (Sat Jun 07 2014 - 06:43:18 PDT)
[AMBER] Question about how a charged system can be simulated using PBC? yuandandan05.gmail.com (Sat Jun 07 2014 - 21:12:27 PDT)
- Re: [AMBER] Question about how a charged system can be simulated using PBC? Dr. Vitaly Chaban (Sun Jun 08 2014 - 03:27:05 PDT)
  - Re: [AMBER] Question about how a charged system can be simulated using PBC? Jason Swails (Sun Jun 08 2014 - 18:26:37 PDT)
- Re: [AMBER] Question about how a charged system can be simulated using PBC? yuandandan05.gmail.com (Sun Jun 08 2014 - 18:13:31 PDT)
[AMBER] hbond analysis Arunima Shilpi (Sun Jun 08 2014 - 06:05:47 PDT)
[AMBER] Hbond analysi Arunima Shilpi (Sun Jun 08 2014 - 16:41:45 PDT)
- Re: [AMBER] Hbond analysi Daniel Roe (Sun Jun 08 2014 - 19:23:24 PDT)
[AMBER] NVT equilibration crash using CUDA James Starlight (Mon Jun 09 2014 - 01:17:04 PDT)
- Re: [AMBER] NVT equilibration crash using CUDA James Starlight (Mon Jun 09 2014 - 01:34:29 PDT)
  - Re: [AMBER] NVT equilibration crash using CUDA Soumendranath Bhakat (Mon Jun 09 2014 - 02:15:27 PDT)
    - Re: [AMBER] NVT equilibration crash using CUDA James Starlight (Mon Jun 09 2014 - 03:26:08 PDT)
- Re: [AMBER] NVT equilibration crash using CUDA Jason Swails (Mon Jun 09 2014 - 05:21:06 PDT)
  - Re: [AMBER] NVT equilibration crash using CUDA James Starlight (Mon Jun 09 2014 - 07:59:44 PDT)
    - Re: [AMBER] NVT equilibration crash using CUDA Jason Swails (Mon Jun 09 2014 - 08:39:34 PDT)
    - Re: [AMBER] NVT equilibration crash using CUDA James Starlight (Mon Jun 09 2014 - 11:13:26 PDT)
    - Re: [AMBER] NVT equilibration crash using CUDA James Starlight (Tue Jun 10 2014 - 02:36:04 PDT)
    - Re: [AMBER] NVT equilibration crash using CUDA Jason Swails (Tue Jun 10 2014 - 05:10:03 PDT)
    - Re: [AMBER] NVT equilibration crash using CUDA Daniel Roe (Tue Jun 10 2014 - 07:39:26 PDT)
[AMBER] problem during add ions Sohag Biswas (Mon Jun 09 2014 - 03:21:02 PDT)
- Re: [AMBER] problem during add ions David A Case (Mon Jun 09 2014 - 05:02:49 PDT)
- Re: [AMBER] problem during add ions Parvesh Singh (Mon Jun 09 2014 - 07:08:50 PDT)
[AMBER] Fwd: Substrate moving out of the box during MD simulation-- reg Rajeswari A. (Mon Jun 09 2014 - 04:10:35 PDT)
- Re: [AMBER] Fwd: Substrate moving out of the box during MD simulation-- reg Jason Swails (Mon Jun 09 2014 - 05:24:05 PDT)
[AMBER] [Amber 14] multi-GPU calculation error occers when specify eight GPUs with Tesla K20Xm Keisuke Aono (Mon Jun 09 2014 - 04:17:52 PDT)
- Re: [AMBER] [Amber 14] multi-GPU calculation error occers when specify eight GPUs with Tesla K20Xm Ross Walker (Mon Jun 09 2014 - 05:42:42 PDT)
  - Re: [AMBER] [Amber 14] multi-GPU calculation error occers when specify eight GPUs with Tesla K20Xm Scott Le Grand (Mon Jun 09 2014 - 09:50:56 PDT)
[AMBER] Is it possible to tleap a protein molecule without adding terminal atoms? #YIP YEW MUN# (Mon Jun 09 2014 - 05:12:30 PDT)
- Re: [AMBER] Is it possible to tleap a protein molecule without adding terminal atoms? Jason Swails (Mon Jun 09 2014 - 05:33:49 PDT)
- Re: [AMBER] Is it possible to tleap a protein molecule without adding terminal atoms? Ray Luo, Ph.D. (Mon Jun 09 2014 - 10:13:40 PDT)
[AMBER] zlib issues during compilation. Harris, Danni (Mon Jun 09 2014 - 12:46:51 PDT)
- Re: [AMBER] zlib issues during compilation. Daniel Roe (Mon Jun 09 2014 - 14:44:56 PDT)
  - Re: [AMBER] zlib issues during compilation. Harris, Danni (Mon Jun 09 2014 - 16:29:24 PDT)
    - Re: [AMBER] zlib issues during compilation. Daniel Roe (Mon Jun 09 2014 - 20:17:41 PDT)
    - Re: [AMBER] zlib issues during compilation. Harris, Danni (Tue Jun 10 2014 - 04:56:02 PDT)
[AMBER] Equilibration of membrane protein James Starlight (Tue Jun 10 2014 - 00:05:13 PDT)
- Re: [AMBER] Equilibration of membrane protein Benjamin D Madej (Tue Jun 10 2014 - 12:04:41 PDT)
  - Re: [AMBER] Equilibration of membrane protein James Starlight (Tue Jun 10 2014 - 22:13:36 PDT)
[AMBER] Query about GPU model Indrajit Deb (Tue Jun 10 2014 - 01:19:19 PDT)
- Re: [AMBER] Query about GPU model Ross Walker (Tue Jun 10 2014 - 09:27:10 PDT)
  - Re: [AMBER] Query about GPU model Scott Le Grand (Tue Jun 10 2014 - 10:28:21 PDT)
    - Re: [AMBER] Query about GPU model Indrajit Deb (Tue Jun 10 2014 - 12:25:16 PDT)
[AMBER] error in using pmemd Valentina Romano (Tue Jun 10 2014 - 08:13:26 PDT)
- Re: [AMBER] error in using pmemd Jason Swails (Tue Jun 10 2014 - 08:22:20 PDT)
[AMBER] Free Energy Calculation of Zn-containing protein-peptides using MMPBSA.py Senthil Natesan (Tue Jun 10 2014 - 08:22:38 PDT)
- Re: [AMBER] Free Energy Calculation of Zn-containing protein-peptides using MMPBSA.py Jason Swails (Tue Jun 10 2014 - 08:39:03 PDT)
  - Re: [AMBER] Free Energy Calculation of Zn-containing protein-peptides using MMPBSA.py Senthil Natesan (Tue Jun 10 2014 - 08:57:51 PDT)
    - Re: [AMBER] Free Energy Calculation of Zn-containing protein-peptides using MMPBSA.py Jason Swails (Tue Jun 10 2014 - 09:26:48 PDT)
- Re: [AMBER] Free Energy Calculation of Zn-containing protein-peptides using MMPBSA.py Jason Swails (Tue Jun 10 2014 - 10:06:17 PDT)
  - Re: [AMBER] Free Energy Calculation of Zn-containing protein-peptides using MMPBSA.py Senthil Natesan (Tue Jun 10 2014 - 11:08:01 PDT)
[AMBER] Membrane protein tutorial James Starlight (Tue Jun 10 2014 - 08:58:13 PDT)
- Re: [AMBER] Membrane protein tutorial Brian Radak (Tue Jun 10 2014 - 09:19:08 PDT)
  - Re: [AMBER] Membrane protein tutorial Jason Swails (Tue Jun 10 2014 - 09:35:56 PDT)
    - Re: [AMBER] Membrane protein tutorial Brian Radak (Tue Jun 10 2014 - 10:03:45 PDT)
    - Re: [AMBER] Membrane protein tutorial Jason Swails (Tue Jun 10 2014 - 10:48:31 PDT)
    - Re: [AMBER] Membrane protein tutorial James Starlight (Tue Jun 10 2014 - 11:36:59 PDT)
[AMBER] Side chain and backbone-specific parameters. Lee-Ping Wang (Tue Jun 10 2014 - 10:25:24 PDT)
- Re: [AMBER] Side chain and backbone-specific parameters. Jason Swails (Tue Jun 10 2014 - 10:46:32 PDT)
  - Re: [AMBER] Side chain and backbone-specific parameters. Lee-Ping Wang (Tue Jun 10 2014 - 10:50:35 PDT)
    - Re: [AMBER] Side chain and backbone-specific parameters. Jason Swails (Tue Jun 10 2014 - 11:30:03 PDT)
    - Re: [AMBER] Side chain and backbone-specific parameters. Lee-Ping Wang (Tue Jun 10 2014 - 11:50:40 PDT)
    - Re: [AMBER] Side chain and backbone-specific parameters. Jason Swails (Tue Jun 10 2014 - 12:07:35 PDT)
[AMBER] restarting MDs generated in Amber10 with Amber12 Silvia Bonomo (Wed Jun 11 2014 - 01:52:29 PDT)
- Re: [AMBER] restarting MDs generated in Amber10 with Amber12 David A Case (Wed Jun 11 2014 - 04:29:24 PDT)
[AMBER] QM/MMPBSA John Smith (Wed Jun 11 2014 - 04:31:29 PDT)
- Re: [AMBER] QM/MMPBSA Jason Swails (Wed Jun 11 2014 - 05:35:07 PDT)
  - Re: [AMBER] QM/MMPBSA John Smith (Wed Jun 11 2014 - 09:01:42 PDT)
    - Re: [AMBER] QM/MMPBSA Brian Radak (Wed Jun 11 2014 - 09:24:26 PDT)
    - Re: [AMBER] QM/MMPBSA Jason Swails (Wed Jun 11 2014 - 09:32:02 PDT)
    - Re: [AMBER] QM/MMPBSA John Smith (Wed Jun 11 2014 - 09:53:15 PDT)
    - Re: [AMBER] QM/MMPBSA Jason Swails (Wed Jun 11 2014 - 10:14:06 PDT)
[AMBER] Metal Center Parameter Builder (MCPB) manual Senthil Natesan (Wed Jun 11 2014 - 10:19:27 PDT)
- [AMBER] Metal Center Parameter Builder (MCPB) manual Senthil Natesan (Wed Jun 11 2014 - 14:49:41 PDT)
  - Re: [AMBER] Metal Center Parameter Builder (MCPB) manual Jason Swails (Thu Jun 12 2014 - 10:32:53 PDT)
    - Re: [AMBER] Metal Center Parameter Builder (MCPB) manual Senthil Natesan (Thu Jun 12 2014 - 10:47:07 PDT)
    - Re: [AMBER] Metal Center Parameter Builder (MCPB) manual Senthil Natesan (Thu Jun 12 2014 - 11:24:00 PDT)
[AMBER] GLYCAM parameter ATOM TYPE Soumendranath Bhakat (Wed Jun 11 2014 - 11:54:15 PDT)
- Re: [AMBER] GLYCAM parameter ATOM TYPE Lachele Foley (Wed Jun 11 2014 - 12:34:17 PDT)
  - Re: [AMBER] GLYCAM parameter ATOM TYPE Soumendranath Bhakat (Thu Jun 12 2014 - 01:42:07 PDT)
[AMBER] MMPBSA huge VDW values maryam azimzadehirani (Thu Jun 12 2014 - 00:28:36 PDT)
- Re: [AMBER] MMPBSA huge VDW values Jason Swails (Thu Jun 12 2014 - 04:11:39 PDT)
  - Re: [AMBER] MMPBSA huge VDW values maryam azimzadehirani (Thu Jun 12 2014 - 04:44:16 PDT)
[AMBER] Magnesium FATAL error Soumendranath Bhakat (Thu Jun 12 2014 - 01:46:00 PDT)
- Re: [AMBER] Magnesium FATAL error David A Case (Thu Jun 12 2014 - 04:10:36 PDT)
[AMBER] Adding residue in two end of DNA mehdi bagherpoor (Thu Jun 12 2014 - 09:59:50 PDT)
- Re: [AMBER] Adding residue in two end of DNA FyD (Sat Jun 14 2014 - 10:08:01 PDT)
[AMBER] "Invalid start to time: 28..." error Vu Truong (Thu Jun 12 2014 - 11:43:21 PDT)
- Re: [AMBER] "Invalid start to time: 28..." error Daniel Roe (Thu Jun 12 2014 - 13:09:06 PDT)
- Re: [AMBER] "Invalid start to time: 28..." error David A Case (Thu Jun 12 2014 - 13:37:13 PDT)
- Re: [AMBER] "Invalid start to time: 28..." error Bill Ross (Thu Jun 12 2014 - 17:20:10 PDT)
- Re: [AMBER] "Invalid start to time: 28..." error Vu Truong (Fri Jun 13 2014 - 14:35:42 PDT)
  - Re: [AMBER] "Invalid start to time: 28..." error Jason Swails (Fri Jun 13 2014 - 16:05:22 PDT)
  - Re: [AMBER] "Invalid start to time: 28..." error Daniel Roe (Sat Jun 14 2014 - 11:41:58 PDT)
- Re: [AMBER] "Invalid start to time: 28..." error Bill Ross (Fri Jun 13 2014 - 18:21:38 PDT)
[AMBER] Query about QM/MM calculation using Amber/Gaussian interface Kshatresh Dutta Dubey (Fri Jun 13 2014 - 02:16:03 PDT)
- Re: [AMBER] Query about QM/MM calculation using Amber/Gaussian interface Gerald Monard (Fri Jun 13 2014 - 02:31:17 PDT)
  - Re: [AMBER] Query about QM/MM calculation using Amber/Gaussian interface Kshatresh Dutta Dubey (Fri Jun 13 2014 - 02:50:31 PDT)
    - Re: [AMBER] Query about QM/MM calculation using Amber/Gaussian interface Jason Swails (Fri Jun 13 2014 - 03:54:41 PDT)
    - Re: [AMBER] Query about QM/MM calculation using Amber/Gaussian interface Soumendranath Bhakat (Fri Jun 13 2014 - 04:01:44 PDT)
    - Re: [AMBER] Query about QM/MM calculation using Amber/Gaussian interface Kshatresh Dutta Dubey (Fri Jun 13 2014 - 04:26:48 PDT)
    - Re: [AMBER] Query about QM/MM calculation using Amber/Gaussian interface Kshatresh Dutta Dubey (Fri Jun 13 2014 - 04:31:51 PDT)
    - Re: [AMBER] Query about QM/MM calculation using Amber/Gaussian interface Soumendranath Bhakat (Fri Jun 13 2014 - 04:34:47 PDT)
    - Re: [AMBER] Query about QM/MM calculation using Amber/Gaussian interface Soumendranath Bhakat (Fri Jun 13 2014 - 04:36:26 PDT)
    - Re: [AMBER] Query about QM/MM calculation using Amber/Gaussian interface Kshatresh Dutta Dubey (Fri Jun 13 2014 - 04:44:39 PDT)
    - Re: [AMBER] Query about QM/MM calculation using Amber/Gaussian interface Soumendranath Bhakat (Fri Jun 13 2014 - 04:42:31 PDT)
    - Re: [AMBER] Query about QM/MM calculation using Amber/Gaussian interface Kshatresh Dutta Dubey (Fri Jun 13 2014 - 06:01:00 PDT)
    - Re: [AMBER] Query about QM/MM calculation using Amber/Gaussian interface Gerald Monard (Fri Jun 13 2014 - 06:48:11 PDT)
    - Re: [AMBER] Query about QM/MM calculation using Amber/Gaussian interface Kshatresh Dutta Dubey (Fri Jun 13 2014 - 07:58:59 PDT)
    - Re: [AMBER] Query about QM/MM calculation using Amber/Gaussian interface David A Case (Fri Jun 13 2014 - 12:08:35 PDT)
    - Re: [AMBER] Query about QM/MM calculation using Amber/Gaussian interface Gerald Monard (Fri Jun 13 2014 - 12:39:14 PDT)
    - Re: [AMBER] Query about QM/MM calculation using Amber/Gaussian interface Kshatresh Dutta Dubey (Fri Jun 13 2014 - 14:24:54 PDT)
[AMBER] different number of waters newamber list (Fri Jun 13 2014 - 06:04:22 PDT)
- Re: [AMBER] different number of waters MURAT OZTURK (Sat Jun 14 2014 - 16:07:34 PDT)
- Re: [AMBER] different number of waters Jason Swails (Sat Jun 14 2014 - 22:07:41 PDT)
  - Re: [AMBER] different number of waters newamber list (Sun Jun 15 2014 - 07:18:48 PDT)
    - Re: [AMBER] different number of waters newamber list (Sun Jun 15 2014 - 08:06:10 PDT)
    - Re: [AMBER] different number of waters David A Case (Sun Jun 15 2014 - 08:52:48 PDT)
    - Re: [AMBER] different number of waters newamber list (Wed Jun 18 2014 - 06:43:34 PDT)
    - Re: [AMBER] different number of waters Brian Radak (Wed Jun 18 2014 - 07:09:48 PDT)
    - Re: [AMBER] different number of waters newamber list (Wed Jun 18 2014 - 07:30:05 PDT)
    - Re: [AMBER] different number of waters David A Case (Wed Jun 18 2014 - 07:49:05 PDT)
    - Re: [AMBER] different number of waters Brian Radak (Wed Jun 18 2014 - 08:01:27 PDT)
[AMBER] Rmsd with reference structure having different number of total atoms Rajeswari A. (Fri Jun 13 2014 - 07:13:05 PDT)
- Re: [AMBER] Rmsd with reference structure having different number of total atoms Rajeswari A. (Fri Jun 13 2014 - 07:26:25 PDT)
[AMBER] Integration scheme used in Amber 9 and 11 ? Ravi Tripathi (Fri Jun 13 2014 - 23:30:57 PDT)
- Re: [AMBER] Integration scheme used in Amber 9 and 11 ? Kshatresh Dutta Dubey (Sat Jun 14 2014 - 02:03:56 PDT)
  - Re: [AMBER] Integration scheme used in Amber 9 and 11 ? Jason Swails (Sat Jun 14 2014 - 06:07:45 PDT)
    - Re: [AMBER] Integration scheme used in Amber 9 and 11 ? Kshatresh Dutta Dubey (Sat Jun 14 2014 - 06:28:40 PDT)
    - Re: [AMBER] Integration scheme used in Amber 9 and 11 ? Ravi Tripathi (Sun Jun 15 2014 - 21:14:00 PDT)
[AMBER] The linkage of Amber and Gaussian in Amber 14. Jinfeng Huang (Sat Jun 14 2014 - 01:41:41 PDT)
- Re: [AMBER] The linkage of Amber and Gaussian in Amber 14. Jason Swails (Sat Jun 14 2014 - 06:05:39 PDT)
[AMBER] Deleting Box info from trajectory Kshatresh Dutta Dubey (Sat Jun 14 2014 - 13:09:26 PDT)
- Re: [AMBER] Deleting Box info from trajectory David A Case (Sat Jun 14 2014 - 13:51:36 PDT)
  - Re: [AMBER] Deleting Box info from trajectory Kshatresh Dutta Dubey (Sat Jun 14 2014 - 14:40:35 PDT)
    - Re: [AMBER] Deleting Box info from trajectory David A Case (Sat Jun 14 2014 - 20:32:31 PDT)
    - Re: [AMBER] Deleting Box info from trajectory Kshatresh Dutta Dubey (Sat Jun 14 2014 - 20:53:05 PDT)
    - Re: [AMBER] Deleting Box info from trajectory Jason Swails (Sat Jun 14 2014 - 22:03:19 PDT)
    - Re: [AMBER] Deleting Box info from trajectory Kshatresh Dutta Dubey (Sun Jun 15 2014 - 00:47:00 PDT)
- Re: [AMBER] Deleting Box info from trajectory Daniel Roe (Sat Jun 14 2014 - 14:27:11 PDT)
[AMBER] sebomd and qmmm2 test failing in serial/parallel for Amber14 余青芬 (Sat Jun 14 2014 - 23:26:54 PDT)
- Re: [AMBER] sebomd and qmmm2 test failing in serial/parallel for Amber14 Gerald Monard (Sun Jun 15 2014 - 00:27:25 PDT)
- Re: [AMBER] sebomd and qmmm2 test failing in serial/parallel for Amber14 余青芬 (Mon Jun 16 2014 - 02:26:38 PDT)
  - Re: [AMBER] sebomd and qmmm2 test failing in serial/parallel for Amber14 Gerald Monard (Mon Jun 16 2014 - 06:04:37 PDT)
- Re: [AMBER] sebomd and qmmm2 test failing in serial/parallel for Amber14 余青芬 (Wed Jun 18 2014 - 03:03:55 PDT)
  - Re: [AMBER] sebomd and qmmm2 test failing in serial/parallel for Amber14 David A Case (Wed Jun 18 2014 - 06:02:45 PDT)
  - Re: [AMBER] sebomd and qmmm2 test failing in serial/parallel for Amber14 Gerald Monard (Wed Jun 18 2014 - 12:44:13 PDT)
    - Re: [AMBER] sebomd and qmmm2 test failing in serial/parallel for Amber14 Gerald Monard (Thu Jun 19 2014 - 03:09:55 PDT)
- Re: [AMBER] sebomd and qmmm2 test failing in serial/parallel for Amber14 余青芬 (Thu Jun 19 2014 - 02:27:21 PDT)
[AMBER] Topology issue with MMPBSA.py JPB (Mon Jun 16 2014 - 03:29:39 PDT)
- Re: [AMBER] Topology issue with MMPBSA.py Jason Swails (Mon Jun 16 2014 - 05:27:52 PDT)
  - Re: [AMBER] Topology issue with MMPBSA.py JPB (Mon Jun 16 2014 - 06:37:06 PDT)
    - Re: [AMBER] Topology issue with MMPBSA.py Jason Swails (Mon Jun 16 2014 - 07:03:43 PDT)
    - Re: [AMBER] Topology issue with MMPBSA.py Daniel Roe (Thu Jun 19 2014 - 14:24:40 PDT)
[AMBER] fitting of atomic structures to cryo-em maps Asmita Gupta (Mon Jun 16 2014 - 06:12:02 PDT)
- Re: [AMBER] fitting of atomic structures to cryo-em maps Jason Swails (Mon Jun 16 2014 - 06:17:41 PDT)
  - Re: [AMBER] fitting of atomic structures to cryo-em maps Asmita Gupta (Mon Jun 16 2014 - 06:36:41 PDT)
    - Re: [AMBER] fitting of atomic structures to cryo-em maps Jason Swails (Mon Jun 16 2014 - 07:07:03 PDT)
[AMBER] bash scripting for MD tasks James Starlight (Mon Jun 16 2014 - 12:59:08 PDT)
- Re: [AMBER] bash scripting for MD tasks Daniel Roe (Mon Jun 16 2014 - 14:11:03 PDT)
  - Re: [AMBER] bash scripting for MD tasks James Starlight (Tue Jun 17 2014 - 11:16:31 PDT)
    - Re: [AMBER] bash scripting for MD tasks Lachele Foley (Tue Jun 17 2014 - 11:38:30 PDT)
    - Re: [AMBER] bash scripting for MD tasks Jason Swails (Tue Jun 17 2014 - 12:25:49 PDT)
    - Re: [AMBER] bash scripting for MD tasks James Starlight (Thu Jun 19 2014 - 06:52:51 PDT)
    - Re: [AMBER] bash scripting for MD tasks James Starlight (Fri Jun 20 2014 - 07:25:06 PDT)
    - Re: [AMBER] bash scripting for MD tasks Daniel Roe (Fri Jun 20 2014 - 07:47:22 PDT)
    - Re: [AMBER] bash scripting for MD tasks James Starlight (Sun Jun 22 2014 - 06:24:34 PDT)
    - Re: [AMBER] bash scripting for MD tasks Parker de Waal (Sun Jun 22 2014 - 07:04:13 PDT)
- Re: [AMBER] bash scripting for MD tasks Parker de Waal (Sun Jun 22 2014 - 07:07:17 PDT)
  - Re: [AMBER] bash scripting for MD tasks James Starlight (Mon Jun 23 2014 - 04:48:29 PDT)
    - Re: [AMBER] bash scripting for MD tasks Parker de Waal (Mon Jun 23 2014 - 07:30:54 PDT)
    - Re: [AMBER] bash scripting for MD tasks James Starlight (Mon Jul 21 2014 - 04:54:00 PDT)
    - Re: [AMBER] bash scripting for MD tasks Parker de Waal (Mon Jul 21 2014 - 06:32:19 PDT)
    - Re: [AMBER] bash scripting for MD tasks James Starlight (Mon Sep 08 2014 - 12:24:42 PDT)
    - Re: [AMBER] bash scripting for MD tasks James Maier (Wed Sep 10 2014 - 07:48:36 PDT)
    - Re: [AMBER] bash scripting for MD tasks James Starlight (Thu Sep 11 2014 - 02:15:54 PDT)
    - Re: [AMBER] bash scripting for MD tasks James Starlight (Wed Sep 24 2014 - 01:59:04 PDT)
    - Re: [AMBER] bash scripting for MD tasks Hannes Loeffler (Wed Sep 24 2014 - 02:14:55 PDT)
    - Re: [AMBER] bash scripting for MD tasks James Starlight (Wed Sep 24 2014 - 02:21:40 PDT)
    - Re: [AMBER] bash scripting for MD tasks Hannes Loeffler (Wed Sep 24 2014 - 02:46:40 PDT)
- Re: [AMBER] bash scripting for MD tasks Anselm Horn (Wed Sep 24 2014 - 03:43:17 PDT)
  - Re: [AMBER] bash scripting for MD tasks Hannes Loeffler (Wed Sep 24 2014 - 05:18:00 PDT)
    - Re: [AMBER] bash scripting for MD tasks James Starlight (Wed Sep 24 2014 - 05:35:35 PDT)
- Re: [AMBER] bash scripting for MD tasks Anselm Horn (Wed Sep 24 2014 - 05:45:11 PDT)
  - Re: [AMBER] bash scripting for MD tasks Hannes Loeffler (Wed Sep 24 2014 - 06:27:50 PDT)
    - Re: [AMBER] bash scripting for MD tasks James Starlight (Wed Sep 24 2014 - 07:41:05 PDT)
    - Re: [AMBER] bash scripting for MD tasks James Starlight (Fri Sep 26 2014 - 02:43:22 PDT)
    - Re: [AMBER] bash scripting for MD tasks James Starlight (Fri Sep 26 2014 - 04:14:05 PDT)
    - Re: [AMBER] bash scripting for MD tasks Ross Walker (Fri Sep 26 2014 - 08:57:15 PDT)
- Re: [AMBER] bash scripting for MD tasks James Starlight (Mon Sep 29 2014 - 00:06:17 PDT)
  - Re: [AMBER] bash scripting for MD tasks James Starlight (Mon Sep 29 2014 - 02:22:35 PDT)
    - Re: [AMBER] bash scripting for MD tasks James Starlight (Thu Feb 05 2015 - 06:10:34 PST)
[AMBER] GLYCAM_06 reference Chinthaka Ratnaweera (Tue Jun 17 2014 - 00:18:35 PDT)
- Re: [AMBER] GLYCAM_06 reference Lachele Foley (Tue Jun 17 2014 - 07:55:59 PDT)
[AMBER] Glycophosphate parametrization using GLYCAM Raj Schneider (Tue Jun 17 2014 - 09:26:51 PDT)
- Re: [AMBER] Glycophosphate parametrization using GLYCAM Lachele Foley (Tue Jun 17 2014 - 09:57:47 PDT)
- Re: [AMBER] Glycophosphate parametrization using GLYCAM FyD (Tue Jun 17 2014 - 23:34:08 PDT)
- Re: [AMBER] Glycophosphate parametrization using GLYCAM Jochen Heil (Wed Jun 18 2014 - 02:23:33 PDT)
  - Re: [AMBER] Glycophosphate parametrization using GLYCAM Lachele Foley (Wed Jun 18 2014 - 10:48:44 PDT)
    - Re: [AMBER] Glycophosphate parametrization using GLYCAM Thomas Pochapsky (Wed Jun 18 2014 - 11:13:31 PDT)
    - Re: [AMBER] Glycophosphate parametrization using GLYCAM Thomas Pochapsky (Wed Jun 18 2014 - 11:15:10 PDT)
  - Re: [AMBER] Glycophosphate parametrization using GLYCAM FyD (Thu Jun 19 2014 - 01:53:30 PDT)
    - Re: [AMBER] Glycophosphate parametrization using GLYCAM Jochen Heil (Thu Jun 19 2014 - 04:57:00 PDT)
    - Re: [AMBER] Glycophosphate parametrization using GLYCAM Lachele Foley (Thu Jun 19 2014 - 08:46:31 PDT)
    - Re: [AMBER] Glycophosphate parametrization using GLYCAM FyD (Fri Jun 20 2014 - 01:46:35 PDT)
[AMBER] cpptraj hbond - warning message Mahendra B Thapa (Tue Jun 17 2014 - 16:16:16 PDT)
- Re: [AMBER] cpptraj hbond - warning message Jason Swails (Wed Jun 18 2014 - 08:13:00 PDT)
[AMBER] Queries about QM/MM Tanmoy Paul (Tue Jun 17 2014 - 23:36:51 PDT)
- Re: [AMBER] Queries about QM/MM Jason Swails (Wed Jun 18 2014 - 05:41:31 PDT)
- Re: [AMBER] Queries about QM/MM David A Case (Wed Jun 18 2014 - 05:54:51 PDT)
  - Re: [AMBER] Queries about QM/MM Brian Radak (Wed Jun 18 2014 - 07:03:36 PDT)
[AMBER] Setting up z-constraint Ylenia Cau (Wed Jun 18 2014 - 08:47:03 PDT)
- Re: [AMBER] Setting up z-constraint Brian Radak (Wed Jun 18 2014 - 09:11:22 PDT)
- Re: [AMBER] Setting up z-constraint Pierpaolo Cacciotto (Wed Jun 18 2014 - 10:03:31 PDT)
  - Re: [AMBER] Setting up z-constraint Benjamin D Madej (Thu Jun 19 2014 - 19:40:27 PDT)
    - Re: [AMBER] Setting up z-constraint Pierpaolo Cacciotto (Fri Jun 20 2014 - 03:26:48 PDT)
    - Re: [AMBER] Setting up z-constraint Ross Walker (Fri Jun 20 2014 - 08:57:56 PDT)
    - Re: [AMBER] Setting up z-constraint Scott Le Grand (Fri Jun 20 2014 - 09:13:01 PDT)
    - Re: [AMBER] Setting up z-constraint Scott Le Grand (Fri Jun 20 2014 - 09:16:37 PDT)
    - Re: [AMBER] Setting up z-constraint Pierpaolo Cacciotto (Mon Jun 23 2014 - 03:20:29 PDT)
    - Re: [AMBER] Setting up z-constraint Ross Walker (Mon Jun 23 2014 - 08:04:56 PDT)
    - Re: [AMBER] Setting up z-constraint Pierpaolo Cacciotto (Tue Jul 01 2014 - 03:22:17 PDT)
[AMBER] Leapfrog algorithm zahra khatti (Wed Jun 18 2014 - 10:20:48 PDT)
- Re: [AMBER] Leapfrog algorithm Jason Swails (Wed Jun 18 2014 - 11:12:35 PDT)
  - Re: [AMBER] Leapfrog algorithm David A Case (Wed Jun 18 2014 - 13:34:09 PDT)
[AMBER] MPI and parallel installation Simone Fulle (Wed Jun 18 2014 - 10:44:26 PDT)
- Re: [AMBER] MPI and parallel installation Gerald Monard (Wed Jun 18 2014 - 12:06:49 PDT)
- Re: [AMBER] MPI and parallel installation Jason Swails (Wed Jun 18 2014 - 12:09:36 PDT)
[AMBER] EAMBER (non-restraint) in sander output Duggan, Brendan (Wed Jun 18 2014 - 11:26:37 PDT)
- Re: [AMBER] EAMBER (non-restraint) in sander output David A Case (Wed Jun 18 2014 - 20:25:07 PDT)
- Re: [AMBER] EAMBER (non-restraint) in sander output Duggan, Brendan (Thu Jun 19 2014 - 14:55:12 PDT)
[AMBER] torsion restraint violation reporting Duggan, Brendan (Wed Jun 18 2014 - 11:36:08 PDT)
[AMBER] MMPBSA - calculating energy decomposition by residue in a trajectory without a ligand Andrew.Warden.csiro.au (Wed Jun 18 2014 - 14:53:57 PDT)
- Re: [AMBER] MMPBSA - calculating energy decomposition by residue in a trajectory without a ligand Bill Miller III (Wed Jun 18 2014 - 15:40:42 PDT)
- Re: [AMBER] MMPBSA - calculating energy decomposition by residue in a trajectory without a ligand Andrew.Warden.csiro.au (Mon Jun 23 2014 - 14:11:40 PDT)
[AMBER] remd whb (Wed Jun 18 2014 - 17:35:19 PDT)
- Re: [AMBER] remd Daniel Roe (Thu Jun 19 2014 - 13:57:09 PDT)
[AMBER] Se atom type Krisztina Feher (Thu Jun 19 2014 - 08:32:24 PDT)
[AMBER] Se atom type Krisztina Feher (Thu Jun 19 2014 - 11:29:18 PDT)
[AMBER] Derive charge of multiple molecules sunita gupta (Thu Jun 19 2014 - 11:38:45 PDT)
- Re: [AMBER] Derive charge of multiple molecules Jason Swails (Thu Jun 19 2014 - 12:02:16 PDT)
  - Re: [AMBER] Derive charge of multiple molecules sunita gupta (Fri Jun 20 2014 - 22:29:14 PDT)
    - Re: [AMBER] Derive charge of multiple molecules Daniel Roe (Sat Jun 21 2014 - 08:45:29 PDT)
    - Re: [AMBER] Derive charge of multiple molecules Soumendranath Bhakat (Sun Jun 22 2014 - 06:34:13 PDT)
    - Re: [AMBER] Derive charge of multiple molecules Soumendranath Bhakat (Sun Jun 22 2014 - 06:44:31 PDT)
[AMBER] Hi Him Shweta (Thu Jun 19 2014 - 12:30:32 PDT)
- Re: [AMBER] Hi Daniel Roe (Thu Jun 19 2014 - 13:58:44 PDT)
[AMBER] AmberTools14 installation zahra khatti (Fri Jun 20 2014 - 01:30:18 PDT)
- Re: [AMBER] AmberTools14 installation Gerald Monard (Fri Jun 20 2014 - 02:12:56 PDT)
[AMBER] On the usage of the position restrains during equilibration James Starlight (Fri Jun 20 2014 - 07:30:50 PDT)
- Re: [AMBER] On the usage of the position restrains during equilibration Bill Ross (Fri Jun 20 2014 - 08:36:06 PDT)
  - Re: [AMBER] On the usage of the position restrains during equilibration James Starlight (Fri Jun 20 2014 - 11:31:33 PDT)
- Re: [AMBER] On the usage of the position restrains during equilibration Bill Ross (Fri Jun 20 2014 - 18:48:33 PDT)
  - Re: [AMBER] On the usage of the position restrains during equilibration Jason Swails (Sun Jun 22 2014 - 12:34:06 PDT)
- Re: [AMBER] On the usage of the position restrains during equilibration Bill Ross (Fri Jun 20 2014 - 18:57:36 PDT)
  - Re: [AMBER] On the usage of the position restrains during equilibration James Starlight (Fri Jun 20 2014 - 22:23:38 PDT)
[AMBER] metal ion parameterisation problem Kshatresh Dutta Dubey (Fri Jun 20 2014 - 14:29:30 PDT)
- Re: [AMBER] metal ion parameterisation problem Ben Roberts (Sun Jun 22 2014 - 14:57:11 PDT)
  - Re: [AMBER] metal ion parameterisation problem Ken Merz (Mon Jun 23 2014 - 07:10:40 PDT)
    - Re: [AMBER] metal ion parameterisation problem Kshatresh Dutta Dubey (Mon Jun 23 2014 - 08:02:06 PDT)
    - Re: [AMBER] metal ion parameterisation problem Pengfei Li (Mon Jun 23 2014 - 11:53:46 PDT)
    - Re: [AMBER] metal ion parameterisation problem Kshatresh Dutta Dubey (Mon Jun 23 2014 - 12:52:07 PDT)
    - Re: [AMBER] metal ion parameterisation problem Pengfei Li (Wed Jun 25 2014 - 13:25:54 PDT)
[AMBER] Se atom type Krisztina Feher (Sat Jun 21 2014 - 05:37:34 PDT)
- Re: [AMBER] Se atom type Jason Swails (Sat Jun 21 2014 - 20:16:18 PDT)
  - Re: [AMBER] Se atom type Krisztina Feher (Mon Jun 23 2014 - 04:43:35 PDT)
    - Re: [AMBER] Se atom type David A Case (Mon Jun 23 2014 - 05:04:42 PDT)
[AMBER] segmentation_fault_loading_pdb in tleap Shomesankar Bhunia (Sat Jun 21 2014 - 05:56:11 PDT)
- Re: [AMBER] segmentation_fault_loading_pdb in tleap Soumendranath Bhakat (Sat Jun 21 2014 - 06:34:50 PDT)
  - Re: [AMBER] segmentation_fault_loading_pdb in tleap Shomesankar Bhunia (Sat Jun 21 2014 - 06:45:30 PDT)
[AMBER] filter trajectory with modes same number of frames newamber list (Sat Jun 21 2014 - 10:07:53 PDT)
- Re: [AMBER] filter trajectory with modes same number of frames Daniel Roe (Sat Jun 21 2014 - 13:48:33 PDT)
  - Re: [AMBER] filter trajectory with modes same number of frames newamber list (Sat Jun 21 2014 - 18:34:01 PDT)
    - Re: [AMBER] filter trajectory with modes same number of frames Daniel Roe (Tue Jun 24 2014 - 08:42:55 PDT)
    - Re: [AMBER] filter trajectory with modes same number of frames newamber list (Tue Jun 24 2014 - 17:28:08 PDT)
[AMBER] MTK++ Error Kshatresh Dutta Dubey (Sat Jun 21 2014 - 13:43:44 PDT)
- Re: [AMBER] MTK++ Error Kshatresh Dutta Dubey (Sat Jun 21 2014 - 16:00:46 PDT)
[AMBER] AMBER 12 Nucleic Acid Builder (NAB) language loue chen (Sun Jun 22 2014 - 08:50:09 PDT)
[AMBER] MM/PBSA calculation. Him Shweta (Mon Jun 23 2014 - 03:09:47 PDT)
- Re: [AMBER] MM/PBSA calculation. Jason Swails (Mon Jun 23 2014 - 05:51:47 PDT)
  - Re: [AMBER] MM/PBSA calculation. Him Shweta (Mon Jun 23 2014 - 10:21:17 PDT)
    - Re: [AMBER] MM/PBSA calculation. Jason Swails (Mon Jun 23 2014 - 12:01:27 PDT)
    - Re: [AMBER] MM/PBSA calculation. Him Shweta (Mon Jun 23 2014 - 23:02:51 PDT)
[AMBER] Low performance in multi-pmemd.mpi James Starlight (Mon Jun 23 2014 - 04:38:32 PDT)
- Re: [AMBER] Low performance in multi-pmemd.mpi Daniel Roe (Mon Jun 23 2014 - 06:52:58 PDT)
[AMBER] tleap using GLYCAM force field Shreeramesh (Mon Jun 23 2014 - 05:00:49 PDT)
- Re: [AMBER] tleap using GLYCAM force field Lachele Foley (Mon Jun 23 2014 - 08:32:51 PDT)
[AMBER] Condensed Glycam notation for gammacyclodextrin Shreeramesh (Mon Jun 23 2014 - 05:08:09 PDT)
- Re: [AMBER] Condensed Glycam notation for gammacyclodextrin Lachele Foley (Mon Jun 23 2014 - 10:49:16 PDT)
[AMBER] Clustering using CPPTRAJ Soumendranath Bhakat (Mon Jun 23 2014 - 06:51:15 PDT)
- Re: [AMBER] Clustering using CPPTRAJ Daniel Roe (Mon Jun 23 2014 - 06:58:50 PDT)
  - Re: [AMBER] Clustering using CPPTRAJ Soumendranath Bhakat (Mon Jun 23 2014 - 07:07:47 PDT)
    - Re: [AMBER] Clustering using CPPTRAJ Soumendranath Bhakat (Mon Jun 23 2014 - 07:45:54 PDT)
    - Re: [AMBER] Clustering using CPPTRAJ Jason Swails (Mon Jun 23 2014 - 08:19:04 PDT)
    - Re: [AMBER] Clustering using CPPTRAJ Soumendranath Bhakat (Mon Jun 23 2014 - 12:08:50 PDT)
    - Re: [AMBER] Clustering using CPPTRAJ Jason Swails (Mon Jun 23 2014 - 12:35:25 PDT)
[AMBER] Some error in output file and restart kirtana S (Mon Jun 23 2014 - 08:40:35 PDT)
- Re: [AMBER] Some error in output file and restart Jason Swails (Mon Jun 23 2014 - 09:54:08 PDT)
- Re: [AMBER] Some error in output file and restart Ross Walker (Mon Jun 23 2014 - 13:11:59 PDT)
  - Re: [AMBER] Some error in output file and restart kirtana S (Mon Jun 23 2014 - 21:42:24 PDT)
    - Re: [AMBER] Some error in output file and restart Ross Walker (Tue Jun 24 2014 - 09:59:27 PDT)
[AMBER] Query about parallel GPU multijob Kshatresh Dutta Dubey (Mon Jun 23 2014 - 12:43:59 PDT)
- Re: [AMBER] Query about parallel GPU multijob Ross Walker (Mon Jun 23 2014 - 13:04:44 PDT)
  - Re: [AMBER] Query about parallel GPU multijob Kshatresh Dutta Dubey (Mon Jun 23 2014 - 13:25:18 PDT)
    - Re: [AMBER] Query about parallel GPU multijob Kshatresh Dutta Dubey (Mon Jun 23 2014 - 13:36:45 PDT)
    - Re: [AMBER] Query about parallel GPU multijob Ross Walker (Mon Jun 23 2014 - 13:45:57 PDT)
    - Re: [AMBER] Query about parallel GPU multijob Kshatresh Dutta Dubey (Mon Jun 23 2014 - 13:54:22 PDT)
    - Re: [AMBER] Query about parallel GPU multijob Ross Walker (Mon Jun 23 2014 - 14:15:11 PDT)
    - Re: [AMBER] Query about parallel GPU multijob Kshatresh Dutta Dubey (Mon Jun 23 2014 - 14:27:35 PDT)
    - Re: [AMBER] Query about parallel GPU multijob Ross Walker (Mon Jun 23 2014 - 13:37:43 PDT)
    - Re: [AMBER] Query about parallel GPU multijob Kshatresh Dutta Dubey (Mon Jun 23 2014 - 13:44:14 PDT)
[AMBER] Force field for carbohydrates-Reg. Shreeramesh (Tue Jun 24 2014 - 01:56:11 PDT)
- Re: [AMBER] Force field for carbohydrates-Reg. FyD (Tue Jun 24 2014 - 23:14:23 PDT)
  - Re: [AMBER] Force field for carbohydrates-Reg. Lachele Foley (Wed Jun 25 2014 - 07:46:20 PDT)
    - Re: [AMBER] Force field for carbohydrates-Reg. Lachele Foley (Wed Jun 25 2014 - 07:46:57 PDT)
[AMBER] Sirius executable not available anymore? Felix Terwesten (Tue Jun 24 2014 - 04:19:57 PDT)
- Re: [AMBER] Sirius executable not available anymore? David A Case (Tue Jun 24 2014 - 04:53:18 PDT)
- Re: [AMBER] Sirius executable not available anymore? Ross Walker (Tue Jun 24 2014 - 11:09:49 PDT)
  - Re: [AMBER] Sirius executable not available anymore? Felix Terwesten (Thu Jun 26 2014 - 04:05:23 PDT)
    - Re: [AMBER] Sirius executable not available anymore? David A Case (Thu Jun 26 2014 - 04:30:55 PDT)
[AMBER] about setting iwrap kirtana S (Tue Jun 24 2014 - 08:04:15 PDT)
- Re: [AMBER] about setting iwrap Daniel Roe (Tue Jun 24 2014 - 08:27:59 PDT)
[AMBER] tleap for gammacyclodextrin-Reg. Shreeramesh (Tue Jun 24 2014 - 08:18:25 PDT)
- Re: [AMBER] tleap for gammacyclodextrin-Reg. Lachele Foley (Tue Jun 24 2014 - 10:32:00 PDT)
  - Re: [AMBER] tleap for gammacyclodextrin-Reg. Lachele Foley (Tue Jun 24 2014 - 10:54:54 PDT)
[AMBER] Amber scaling on culster George Tzotzos (Tue Jun 24 2014 - 13:19:24 PDT)
- Re: [AMBER] Amber scaling on culster Roitberg,Adrian E (Tue Jun 24 2014 - 13:39:18 PDT)
  - Re: [AMBER] Amber scaling on culster Ross Walker (Tue Jun 24 2014 - 13:48:46 PDT)
    - Re: [AMBER] Amber scaling on culster Ross Walker (Tue Jun 24 2014 - 14:11:49 PDT)
    - Re: [AMBER] Amber scaling on culster George Tzotzos (Wed Jun 25 2014 - 06:29:56 PDT)
[AMBER] Problem in creating prmtop inpcrd file in leap 肖立 (Tue Jun 24 2014 - 17:31:37 PDT)
- Re: [AMBER] Problem in creating prmtop inpcrd file in leap Bill Ross (Tue Jun 24 2014 - 18:06:02 PDT)
- Re: [AMBER] Problem in creating prmtop inpcrd file in leap David A Case (Tue Jun 24 2014 - 18:20:52 PDT)
  - Re: [AMBER] Problem in creating prmtop inpcrd file in leap 肖立 (Wed Jun 25 2014 - 10:25:42 PDT)
[AMBER] Issues in .out trying to simulat a polymer in AMBER Andrew.Warden.csiro.au (Tue Jun 24 2014 - 22:23:34 PDT)
- Re: [AMBER] Issues in .out trying to simulat a polymer in AMBER David A Case (Wed Jun 25 2014 - 04:42:05 PDT)
[AMBER] Issues in .out trying to simulat a polymer in AMBER Andrew.Warden.csiro.au (Wed Jun 25 2014 - 13:28:30 PDT)
[AMBER] simulation differences in pmemd.MPI and pmemd.cuda Manikanthan Bhavaraju (Wed Jun 25 2014 - 14:56:45 PDT)
- Re: [AMBER] simulation differences in pmemd.MPI and pmemd.cuda Soumendranath Bhakat (Wed Jun 25 2014 - 15:13:53 PDT)
- Re: [AMBER] simulation differences in pmemd.MPI and pmemd.cuda Ross Walker (Wed Jun 25 2014 - 17:57:26 PDT)
  - Re: [AMBER] simulation differences in pmemd.MPI and pmemd.cuda Manikanthan Bhavaraju (Wed Jun 25 2014 - 18:33:00 PDT)
[AMBER] Fwd: problem while USING GLYCAM for Gammacyclodextrin-Reg. Shreeramesh (Thu Jun 26 2014 - 05:46:31 PDT)
- Re: [AMBER] Fwd: problem while USING GLYCAM for Gammacyclodextrin-Reg. Lachele Foley (Thu Jun 26 2014 - 11:13:14 PDT)
[AMBER] Torsional profile of butane Yingjie Wang (Thu Jun 26 2014 - 10:57:32 PDT)
- Re: [AMBER] Torsional profile of butane Jason Swails (Thu Jun 26 2014 - 11:54:25 PDT)
  - Re: [AMBER] Torsional profile of butane Yingjie Wang (Thu Jun 26 2014 - 13:08:32 PDT)
    - Re: [AMBER] Torsional profile of butane Jason Swails (Thu Jun 26 2014 - 15:14:00 PDT)
- Re: [AMBER] Torsional profile of butane FyD (Thu Jun 26 2014 - 22:55:02 PDT)
  - Re: [AMBER] Torsional profile of butane Yingjie Wang (Fri Jun 27 2014 - 07:38:41 PDT)
[AMBER] 3D-RISM: charge density, charge distribution, and electrostatic potential Brian Radak (Thu Jun 26 2014 - 14:06:16 PDT)
- Re: [AMBER] 3D-RISM: charge density, charge distribution, and electrostatic potential T Luchko (Lists) (Fri Jun 27 2014 - 11:53:33 PDT)
[AMBER] periodic box drifted during NVE run Quynh Vo (Thu Jun 26 2014 - 15:56:25 PDT)
- Re: [AMBER] periodic box drifted during NVE run David A Case (Sat Jun 28 2014 - 08:45:39 PDT)
  - Re: [AMBER] periodic box drifted during NVE run Quynh Vo (Tue Jul 01 2014 - 13:11:10 PDT)
    - Re: [AMBER] periodic box drifted during NVE run David A Case (Wed Jul 02 2014 - 04:40:16 PDT)
    - Re: [AMBER] periodic box drifted during NVE run Quynh Vo (Thu Jul 03 2014 - 13:19:34 PDT)
[AMBER] formal charge of the ligand Mary Varughese (Fri Jun 27 2014 - 02:35:55 PDT)
- Re: [AMBER] formal charge of the ligand Jason Swails (Fri Jun 27 2014 - 05:05:29 PDT)
  - Re: [AMBER] formal charge of the ligand Soumendranath Bhakat (Fri Jun 27 2014 - 05:33:59 PDT)
    - Re: [AMBER] formal charge of the ligand Jason Swails (Fri Jun 27 2014 - 06:52:36 PDT)
    - Re: [AMBER] formal charge of the ligand Soumendranath Bhakat (Fri Jun 27 2014 - 09:40:19 PDT)
    - Re: [AMBER] formal charge of the ligand Mary Varughese (Fri Jun 27 2014 - 23:13:21 PDT)
[AMBER] Analyze properties of in parallel MD Valentina Romano (Fri Jun 27 2014 - 07:37:34 PDT)
- Re: [AMBER] Analyze properties of in parallel MD Brian Radak (Fri Jun 27 2014 - 08:09:00 PDT)
  - Re: [AMBER] Analyze properties of in parallel MD Jason Swails (Fri Jun 27 2014 - 08:41:38 PDT)
[AMBER] No VDWAALS EEL in PB MMPBSA.py job JPB (Fri Jun 27 2014 - 08:27:25 PDT)
- Re: [AMBER] No VDWAALS EEL in PB MMPBSA.py job Ray Luo, Ph.D. (Fri Jun 27 2014 - 09:57:28 PDT)
[AMBER] Per residue rmsd Chinthaka Ratnaweera (Fri Jun 27 2014 - 13:59:49 PDT)
- Re: [AMBER] Per residue rmsd Soumendranath Bhakat (Fri Jun 27 2014 - 14:19:40 PDT)
  - Re: [AMBER] Per residue rmsd Chinthaka Ratnaweera (Fri Jun 27 2014 - 14:46:58 PDT)
    - Re: [AMBER] Per residue rmsd Jason Swails (Fri Jun 27 2014 - 15:50:54 PDT)
    - Re: [AMBER] Per residue rmsd Daniel Roe (Fri Jun 27 2014 - 16:07:53 PDT)
    - Re: [AMBER] Per residue rmsd bharat lakhani (Mon Jun 22 2015 - 09:59:05 PDT)
    - Re: [AMBER] Per residue rmsd Daniel Roe (Tue Jun 23 2015 - 07:55:01 PDT)
    - Re: [AMBER] Per residue rmsd Soumendranath Bhakat (Fri Jun 27 2014 - 15:56:31 PDT)
[AMBER] Printing out matrix labels Eugene Yedvabny (Fri Jun 27 2014 - 18:09:12 PDT)
- Re: [AMBER] Printing out matrix labels Daniel Roe (Fri Jun 27 2014 - 21:13:10 PDT)
  - Re: [AMBER] Printing out matrix labels Eugene Yedvabny (Sun Jun 29 2014 - 21:44:08 PDT)
    - Re: [AMBER] Printing out matrix labels Eugene Yedvabny (Sun Jun 29 2014 - 21:51:09 PDT)
    - Re: [AMBER] Printing out matrix labels Hai Nguyen (Fri Jan 30 2015 - 19:20:42 PST)
    - Re: [AMBER] Printing out matrix labels Jason Swails (Mon Jun 30 2014 - 06:37:50 PDT)
    - Re: [AMBER] Printing out matrix labels Daniel Roe (Mon Jun 30 2014 - 06:41:12 PDT)
[AMBER] QMMM NEB reaction pathway calculation with AMBER Teerapong Pirojsirikul (Sat Jun 28 2014 - 17:50:17 PDT)
- Re: [AMBER] QMMM NEB reaction pathway calculation with AMBER Jason Swails (Sun Jun 29 2014 - 17:52:49 PDT)
  - Re: [AMBER] QMMM NEB reaction pathway calculation with AMBER Teerapong Pirojsirikul (Mon Jun 30 2014 - 11:17:51 PDT)
[AMBER] Early termination of parallel MD Valentina Romano (Mon Jun 30 2014 - 00:52:24 PDT)
- Re: [AMBER] Early termination of parallel MD Anna Bauß (Mon Jun 30 2014 - 01:32:04 PDT)
  - Re: [AMBER] Early termination of parallel MD Valentina Romano (Mon Jun 30 2014 - 01:49:07 PDT)
- Re: [AMBER] Early termination of parallel MD Anselm Horn (Mon Jun 30 2014 - 03:20:17 PDT)
- Re: [AMBER] Early termination of parallel MD Jason Swails (Mon Jun 30 2014 - 06:30:44 PDT)
[AMBER] Efficient, accurate estimation of relative binding free energies Guo, Zhuyan (Mon Jun 30 2014 - 05:13:50 PDT)
- Re: [AMBER] Efficient, accurate estimation of relative binding free energies Jason Swails (Mon Jun 30 2014 - 06:17:01 PDT)
[AMBER] cpptraj: arithmetic on data sets? Brian Radak (Mon Jun 30 2014 - 07:24:47 PDT)
- Re: [AMBER] cpptraj: arithmetic on data sets? Daniel Roe (Tue Jul 01 2014 - 09:24:47 PDT)
[AMBER] AmberTools parallel test experienced errors sunita.tifrh.res.in (Mon Jun 30 2014 - 21:01:27 PDT)
- Re: [AMBER] AmberTools parallel test experienced errors David A Case (Tue Jul 01 2014 - 04:22:22 PDT)
[AMBER] RDF zahra khatti (Tue Jul 01 2014 - 03:04:24 PDT)
- Re: [AMBER] RDF Brian Radak (Tue Jul 01 2014 - 09:13:43 PDT)
[AMBER] support of "center of mass restraint" Takeshi Baba (Tue Jul 01 2014 - 05:53:02 PDT)
- Re: [AMBER] support of "center of mass restraint" Jason Swails (Tue Jul 01 2014 - 08:29:11 PDT)
  - Re: [AMBER] support of "center of mass restraint" Takeshi Baba (Wed Jul 02 2014 - 08:52:30 PDT)
    - Re: [AMBER] support of "center of mass restraint" Ross Walker (Wed Jul 02 2014 - 09:18:33 PDT)
    - Re: [AMBER] support of "center of mass restraint" Takeshi Baba (Wed Jul 02 2014 - 09:42:25 PDT)
    - Re: [AMBER] support of "center of mass restraint" Gustavo Seabra (Wed Jul 02 2014 - 10:11:10 PDT)
[AMBER] sander error "Could not find cntrl namelist" Asmita Gupta (Tue Jul 01 2014 - 08:31:36 PDT)
- Re: [AMBER] sander error "Could not find cntrl namelist" Jason Swails (Tue Jul 01 2014 - 08:40:20 PDT)
  - Re: [AMBER] sander error "Could not find cntrl namelist" Asmita Gupta (Tue Jul 01 2014 - 09:22:06 PDT)
    - Re: [AMBER] sander error "Could not find cntrl namelist" David A Case (Tue Jul 01 2014 - 12:10:54 PDT)
    - Re: [AMBER] sander error "Could not find cntrl namelist" Asmita Gupta (Wed Jul 02 2014 - 07:20:21 PDT)
[AMBER] Cuda tests failure on GeForce GTX 780 Serzhan Sakipov (Tue Jul 01 2014 - 09:17:10 PDT)
- Re: [AMBER] Cuda tests failure on GeForce GTX 780 Jason Swails (Tue Jul 01 2014 - 09:50:51 PDT)
[AMBER] about setting nscm kirtana S (Tue Jul 01 2014 - 09:27:58 PDT)
- Re: [AMBER] about setting nscm Jason Swails (Tue Jul 01 2014 - 17:28:51 PDT)
[AMBER] ZAFF-CCCH Histidine charge problem Christy Lee (Tue Jul 01 2014 - 14:00:09 PDT)
- Re: [AMBER] ZAFF-CCCH Histidine charge problem Pengfei Li (Tue Jul 01 2014 - 14:10:36 PDT)
  - Re: [AMBER] ZAFF-CCCH Histidine charge problem Christy Lee (Wed Jul 02 2014 - 14:07:43 PDT)
    - Re: [AMBER] ZAFF-CCCH Histidine charge problem Pengfei Li (Wed Jul 02 2014 - 14:12:03 PDT)
    - Re: [AMBER] ZAFF-CCCH Histidine charge problem Christy Lee (Thu Jul 03 2014 - 16:11:30 PDT)
    - Re: [AMBER] ZAFF-CCCH Histidine charge problem Pengfei Li (Sun Jul 06 2014 - 09:37:26 PDT)
    - Re: [AMBER] ZAFF-CCCH Histidine charge problem Christy Lee (Mon Jul 07 2014 - 10:18:35 PDT)
    - Re: [AMBER] ZAFF-CCCH Histidine charge problem Pengfei Li (Mon Jul 07 2014 - 14:03:24 PDT)
    - Re: [AMBER] ZAFF-CCCH Histidine charge problem Christy Lee (Mon Jul 07 2014 - 14:54:24 PDT)
    - Re: [AMBER] ZAFF-CCCH Histidine charge problem Pengfei Li (Tue Jul 08 2014 - 08:12:51 PDT)
    - Re: [AMBER] ZAFF-CCCH Histidine charge problem Christy Lee (Thu Jul 10 2014 - 11:39:50 PDT)
    - Re: [AMBER] ZAFF-CCCH Histidine charge problem Pengfei Li (Thu Jul 10 2014 - 14:46:16 PDT)
    - Re: [AMBER] ZAFF-CCCH Histidine charge problem Yue (Thu Jul 10 2014 - 15:01:15 PDT)
[AMBER] Visualizing average solvent-oxygen density/occupancy from an MD trajectory Abhishek Mukhopadhyay (Tue Jul 01 2014 - 17:34:10 PDT)
- Re: [AMBER] Visualizing average solvent-oxygen density/occupancy from an MD trajectory Daniel Roe (Wed Jul 02 2014 - 06:52:28 PDT)
- Re: [AMBER] Visualizing average solvent-oxygen density/occupancy from an MD trajectory Eric Pettersen (Thu Jul 03 2014 - 12:37:29 PDT)
[AMBER] Understand the AMBER coordinate files Wujie Wang (Tue Jul 01 2014 - 18:52:13 PDT)
- Re: [AMBER] Understand the AMBER coordinate files Ross Walker (Tue Jul 01 2014 - 19:33:36 PDT)
  - Re: [AMBER] Understand the AMBER coordinate files Wujie Wang (Wed Jul 02 2014 - 06:32:42 PDT)
  - Re: [AMBER] Understand the AMBER coordinate files Daniel Roe (Wed Jul 02 2014 - 07:23:13 PDT)
[AMBER] grid analysis Mary Varughese (Tue Jul 01 2014 - 19:04:44 PDT)
- Re: [AMBER] grid analysis Daniel Roe (Wed Jul 02 2014 - 07:03:25 PDT)
  - Re: [AMBER] grid analysis Mary Varughese (Wed Jul 02 2014 - 11:19:12 PDT)
    - Re: [AMBER] grid analysis Daniel Roe (Wed Jul 02 2014 - 12:11:54 PDT)
    - Re: [AMBER] grid analysis Mary Varughese (Wed Jul 02 2014 - 21:48:29 PDT)
[AMBER] Fwd: error: unable to generate parameter file Harmeet Kaur (Wed Jul 02 2014 - 00:07:45 PDT)
- Re: [AMBER] Fwd: error: unable to generate parameter file Soumendranath Bhakat (Wed Jul 02 2014 - 00:19:00 PDT)
[AMBER] Extracting total energy and other enegy componenets of ligand Soumendranath Bhakat (Wed Jul 02 2014 - 02:51:27 PDT)
- Re: [AMBER] Extracting total energy and other enegy componenets of ligand Daniel Roe (Wed Jul 02 2014 - 07:20:21 PDT)
[AMBER] How to Extract Energy Contribution of Ligand Only Soumendranath Bhakat (Wed Jul 02 2014 - 02:57:38 PDT)
[AMBER] MM-PBSA Zeinab Tavasoli (Wed Jul 02 2014 - 03:08:44 PDT)
- Re: [AMBER] MM-PBSA David A Case (Wed Jul 02 2014 - 04:55:18 PDT)
  - Re: [AMBER] MM-PBSA Soumendranath Bhakat (Wed Jul 02 2014 - 05:05:15 PDT)
- Re: [AMBER] MM-PBSA Jason Swails (Wed Jul 02 2014 - 07:13:37 PDT)
  - Re: [AMBER] MM-PBSA Soumendranath Bhakat (Wed Jul 02 2014 - 07:32:03 PDT)
    - Re: [AMBER] MM-PBSA Jason Swails (Wed Jul 02 2014 - 09:19:10 PDT)
[AMBER] No parameters for PGR in lipid14 Niels Geudens (Wed Jul 02 2014 - 03:41:19 PDT)
- Re: [AMBER] No parameters for PGR in lipid14 Dickson, Callum J (Wed Jul 02 2014 - 03:52:50 PDT)
  - Re: [AMBER] No parameters for PGR in lipid14 Niels Geudens (Wed Jul 02 2014 - 05:12:33 PDT)
    - Re: [AMBER] No parameters for PGR in lipid14 Jason Swails (Wed Jul 02 2014 - 07:00:59 PDT)
[AMBER] NMR distance restrains Valentina Romano (Wed Jul 02 2014 - 06:28:55 PDT)
- Re: [AMBER] NMR distance restrains David A Case (Wed Jul 02 2014 - 07:14:29 PDT)
  - Re: [AMBER] QM on Adenosine Steven M. Graham (Wed Jul 02 2014 - 07:25:51 PDT)
    - Re: [AMBER] QM on Adenosine Christina Bergonzo (Wed Jul 02 2014 - 07:50:33 PDT)
  - Re: [AMBER] NMR distance restrains Valentina Romano (Wed Jul 02 2014 - 07:50:16 PDT)
    - Re: [AMBER] NMR distance restrains David A Case (Wed Jul 02 2014 - 08:04:32 PDT)
    - Re: [AMBER] NMR distance restrains Valentina Romano (Thu Jul 03 2014 - 00:39:14 PDT)
[AMBER] Attempting to compile fresh version of Amber 11, bugfixes > 17 won't apply cleanly Bob Healey (Wed Jul 02 2014 - 08:22:11 PDT)
- Re: [AMBER] Attempting to compile fresh version of Amber 11, bugfixes > 17 won't apply cleanly Jason Swails (Wed Jul 02 2014 - 09:47:50 PDT)
[AMBER] high energy output kirtana S (Wed Jul 02 2014 - 11:52:58 PDT)
- Re: [AMBER] high energy output Ross Walker (Wed Jul 02 2014 - 12:06:13 PDT)
[AMBER] Issues Compiling AmberTools13 Malachi Phillips (Wed Jul 02 2014 - 12:20:15 PDT)
- Re: [AMBER] Issues Compiling AmberTools13 Jason Swails (Wed Jul 02 2014 - 12:54:20 PDT)
[AMBER] Debug amber energy parameters Ramuntcho Moretti (Thu Jul 03 2014 - 02:17:08 PDT)
- Re: [AMBER] Debug amber energy parameters Daniel Roe (Thu Jul 03 2014 - 08:46:10 PDT)
[AMBER] Wrong number of restrained atoms Valentina Romano (Thu Jul 03 2014 - 02:45:01 PDT)
- Re: [AMBER] Wrong number of restrained atoms David A Case (Thu Jul 03 2014 - 05:22:47 PDT)
[AMBER] Failed to generate parameter file Vishal Nemaysh (Thu Jul 03 2014 - 02:45:46 PDT)
- Re: [AMBER] Failed to generate parameter file Soumendranath Bhakat (Thu Jul 03 2014 - 04:45:38 PDT)
- Re: [AMBER] Failed to generate parameter file David A Case (Thu Jul 03 2014 - 05:19:33 PDT)
[AMBER] ncsu_smd support in pmemd amber12 Asmita Gupta (Thu Jul 03 2014 - 06:31:56 PDT)
- Re: [AMBER] ncsu_smd support in pmemd amber12 Jason Swails (Thu Jul 03 2014 - 07:38:34 PDT)
[AMBER] neighbours around an atom Krisztina Feher (Thu Jul 03 2014 - 07:16:14 PDT)
- Re: [AMBER] neighbours around an atom Jason Swails (Thu Jul 03 2014 - 09:21:57 PDT)
  - Re: [AMBER] neighbours around an atom Daniel Roe (Thu Jul 03 2014 - 09:46:43 PDT)
[AMBER] Time information lost. Domenico Marson (Thu Jul 03 2014 - 08:52:34 PDT)
- Re: [AMBER] Time information lost. Daniel Roe (Thu Jul 03 2014 - 09:52:14 PDT)
[AMBER] amoeba into ambertools Jorgen Simonsen (Thu Jul 03 2014 - 11:35:18 PDT)
- Re: [AMBER] amoeba into ambertools Jason Swails (Thu Jul 03 2014 - 12:48:54 PDT)
[AMBER] PMEMD running on Intel Xeon Phi Hai Long (Thu Jul 03 2014 - 12:22:29 PDT)
- Re: [AMBER] PMEMD running on Intel Xeon Phi Scott Le Grand (Thu Jul 03 2014 - 19:17:57 PDT)
- Re: [AMBER] PMEMD running on Intel Xeon Phi Ross Walker (Thu Jul 03 2014 - 20:22:02 PDT)
  - Re: [AMBER] PMEMD running on Intel Xeon Phi Hai Long (Mon Jul 07 2014 - 09:52:18 PDT)
[AMBER] MMPBSA Energy between system and its image Ahmed Ayoub (Thu Jul 03 2014 - 12:41:17 PDT)
- Re: [AMBER] MMPBSA Energy between system and its image Jason Swails (Thu Jul 03 2014 - 13:02:20 PDT)
- Re: [AMBER] MMPBSA Energy between system and its image Ahmed Ayoub (Fri Jul 04 2014 - 14:15:44 PDT)
  - Re: [AMBER] MMPBSA Energy between system and its image Jason Swails (Fri Jul 04 2014 - 15:29:16 PDT)
[AMBER] How to strip water from .mdcrd file? Wujie Wang (Thu Jul 03 2014 - 18:36:13 PDT)
- Re: [AMBER] How to strip water from .mdcrd file? Soumendranath Bhakat (Fri Jul 04 2014 - 00:06:25 PDT)
  - [AMBER] errors in compiling AmberTools14 Alessandro Contini (Fri Jul 04 2014 - 00:26:19 PDT)
  - Re: [AMBER] How to strip water from .mdcrd file? Wujie Wang (Fri Jul 04 2014 - 09:48:06 PDT)
    - Re: [AMBER] How to strip water from .mdcrd file? Wujie Wang (Fri Jul 04 2014 - 09:56:07 PDT)
[AMBER] MMPBSA Sourav Purohit (Fri Jul 04 2014 - 02:10:46 PDT)
- Re: [AMBER] MMPBSA Jason Swails (Fri Jul 04 2014 - 12:04:41 PDT)
[AMBER] Fwd: neighbours around an atom Krisztina Fehér (Fri Jul 04 2014 - 02:48:08 PDT)
- Re: [AMBER] Fwd: neighbours around an atom Daniel Roe (Fri Jul 04 2014 - 10:59:31 PDT)
  - Re: [AMBER] Fwd: neighbours around an atom Krisztina Fehér (Sat Jul 05 2014 - 07:18:55 PDT)
    - Re: [AMBER] Fwd: neighbours around an atom Jason Swails (Sat Jul 05 2014 - 07:31:39 PDT)
    - Re: [AMBER] Fwd: neighbours around an atom Krisztina Fehér (Sat Jul 05 2014 - 08:15:07 PDT)
    - Re: [AMBER] Fwd: neighbours around an atom Daniel Roe (Sat Jul 05 2014 - 07:49:40 PDT)
    - Re: [AMBER] Fwd: neighbours around an atom Krisztina Fehér (Sat Jul 05 2014 - 08:10:02 PDT)
[AMBER] Fwd: neighbours around an atom Krisztina Fehér (Fri Jul 04 2014 - 04:49:44 PDT)
- Re: [AMBER] Fwd: neighbours around an atom Krisztina Feher (Fri Jul 04 2014 - 05:20:09 PDT)
[AMBER] ptraj: Could not find target 302.280000 in any of the replica trajectories Mele N. (Fri Jul 04 2014 - 06:19:41 PDT)
- Re: [AMBER] ptraj: Could not find target 302.280000 in any of the replica trajectories Daniel Roe (Fri Jul 04 2014 - 11:05:53 PDT)
  - Re: [AMBER] ptraj: Could not find target 302.280000 in any of the replica trajectories Mele N. (Fri Jul 04 2014 - 12:23:56 PDT)
    - Re: [AMBER] ptraj: Could not find target 302.280000 in any of the replica trajectories Jason Swails (Fri Jul 04 2014 - 12:58:02 PDT)
    - Re: [AMBER] ptraj: Could not find target 302.280000 in any of the replica trajectories Mele N. (Fri Jul 04 2014 - 13:22:05 PDT)
    - Re: [AMBER] ptraj: Could not find target 302.280000 in any of the replica trajectories Mele N. (Sat Jul 05 2014 - 02:48:42 PDT)
    - Re: [AMBER] ptraj: Could not find target 302.280000 in any of the replica trajectories Daniel Roe (Sat Jul 05 2014 - 07:57:04 PDT)
    - Re: [AMBER] ptraj: Could not find target 302.280000 in any of the replica trajectories Mele N. (Sun Jul 06 2014 - 02:20:00 PDT)
    - Re: [AMBER] ptraj: Could not find target 302.280000 in any of the replica trajectories Daniel Roe (Tue Jul 08 2014 - 19:42:03 PDT)
    - Re: [AMBER] ptraj: Could not find target 302.280000 in any of the replica trajectories Jason Swails (Tue Jul 08 2014 - 21:01:01 PDT)
[AMBER] imaging problem Jonathan Gough (Sun Jul 06 2014 - 14:41:48 PDT)
- Re: [AMBER] imaging problem Daniel Roe (Mon Jul 07 2014 - 07:16:24 PDT)
  - Re: [AMBER] imaging problem Jonathan Gough (Tue Jul 08 2014 - 07:12:06 PDT)
    - Re: [AMBER] imaging problem Daniel Roe (Tue Jul 08 2014 - 10:52:03 PDT)
    - Re: [AMBER] imaging problem Jonathan Gough (Tue Jul 08 2014 - 11:17:18 PDT)
    - Re: [AMBER] imaging problem Daniel Roe (Tue Jul 08 2014 - 12:21:16 PDT)
[AMBER] Build Xleap Baptiste Legrand (Mon Jul 07 2014 - 01:24:32 PDT)
- Re: [AMBER] Build Xleap David A Case (Mon Jul 07 2014 - 04:43:39 PDT)
  - Re: [AMBER] Build Xleap Baptiste Legrand (Mon Jul 07 2014 - 06:15:14 PDT)
    - Re: [AMBER] Build Xleap David A Case (Mon Jul 07 2014 - 07:20:22 PDT)
    - Re: [AMBER] Build Xleap Baptiste Legrand (Mon Jul 07 2014 - 08:35:51 PDT)
[AMBER] errors in compiling AmberTools14 Alessandro Contini (Mon Jul 07 2014 - 02:21:40 PDT)
- Re: [AMBER] errors in compiling AmberTools14 Jason Swails (Mon Jul 07 2014 - 07:35:22 PDT)
  - Re: [AMBER] errors in compiling AmberTools14 Alessandro Contini (Mon Jul 07 2014 - 07:42:51 PDT)
[AMBER] Imaging issue Michael Criddle (Mon Jul 07 2014 - 02:24:49 PDT)
- Re: [AMBER] Imaging issue David A Case (Mon Jul 07 2014 - 04:47:12 PDT)
[AMBER] questions on output files of hbond analysis zhangmk (Mon Jul 07 2014 - 03:01:23 PDT)
- Re: [AMBER] questions on output files of hbond analysis Daniel Roe (Mon Jul 07 2014 - 07:10:37 PDT)
  - Re: [AMBER] questions on output files of hbond analysis zhangmk (Mon Jul 07 2014 - 21:00:12 PDT)
    - Re: [AMBER] questions on output files of hbond analysis David A Case (Tue Jul 08 2014 - 04:46:32 PDT)
[AMBER] inositol hexakisphosphate Hector A. Baldoni (Mon Jul 07 2014 - 14:12:39 PDT)
- Re: [AMBER] inositol hexakisphosphate FyD (Tue Jul 08 2014 - 08:18:24 PDT)
[AMBER] cpptraj hbond Neha Gandhi (Mon Jul 07 2014 - 23:55:34 PDT)
- Re: [AMBER] cpptraj hbond Daniel Roe (Tue Jul 08 2014 - 12:31:28 PDT)
  - Re: [AMBER] cpptraj hbond Neha Gandhi (Wed Jul 09 2014 - 07:34:47 PDT)
[AMBER] ATP and Mg2+ parameters Valentina Romano (Tue Jul 08 2014 - 03:41:26 PDT)
- Re: [AMBER] ATP and Mg2+ parameters Soumendranath Bhakat (Tue Jul 08 2014 - 03:48:49 PDT)
- Re: [AMBER] ATP and Mg2+ parameters Hector A. Baldoni (Tue Jul 08 2014 - 03:50:37 PDT)
- Re: [AMBER] ATP and Mg2+ parameters Alessandro Contini (Tue Jul 08 2014 - 03:50:50 PDT)
  - Re: [AMBER] ATP and Mg2+ parameters Valentina Romano (Tue Jul 08 2014 - 07:54:33 PDT)
    - Re: [AMBER] ATP and Mg2+ parameters Jason Swails (Tue Jul 08 2014 - 08:38:13 PDT)
- Re: [AMBER] ATP and Mg2+ parameters FyD (Tue Jul 08 2014 - 08:20:01 PDT)
  - Re: [AMBER] ATP and Mg2+ parameters Valentina Romano (Tue Jul 15 2014 - 03:27:55 PDT)
    - Re: [AMBER] ATP and Mg2+ parameters FyD (Tue Jul 15 2014 - 04:05:20 PDT)
[AMBER] RESP fitting with group restraint Niels Geudens (Tue Jul 08 2014 - 06:08:17 PDT)
- Re: [AMBER] RESP fitting with group restraint FyD (Tue Jul 08 2014 - 08:24:04 PDT)
  - Re: [AMBER] RESP fitting with group restraint niels.geudens.ugent.be (Mon Jul 07 2014 - 11:09:34 PDT)
[AMBER] imin=5, maxcyc>1 stalls Allen, Scott Edward (Tue Jul 08 2014 - 06:59:59 PDT)
- Re: [AMBER] imin=5, maxcyc>1 stalls Jason Swails (Tue Jul 08 2014 - 08:21:26 PDT)
  - Re: [AMBER] imin=5, maxcyc>1 stalls Allen, Scott Edward (Tue Jul 08 2014 - 08:56:08 PDT)
[AMBER] Problem with MMPBSA.py Rajeswari A. (Tue Jul 08 2014 - 07:07:03 PDT)
- Re: [AMBER] Problem with MMPBSA.py Jason Swails (Tue Jul 08 2014 - 08:44:03 PDT)
  - Re: [AMBER] Problem with MMPBSA.py Rajeswari A. (Tue Jul 08 2014 - 22:32:09 PDT)
    - Re: [AMBER] Problem with MMPBSA.py Jason Swails (Tue Jul 08 2014 - 22:50:50 PDT)
[AMBER] R: Re: ATP and Mg2+ parameters Alessandro Contini (Tue Jul 08 2014 - 08:21:14 PDT)
[AMBER] Issues running RED ESP software Malachi Phillips (Tue Jul 08 2014 - 10:25:40 PDT)
[AMBER] pmemdTI test failure Blake Mertz (Tue Jul 08 2014 - 10:32:49 PDT)
- Re: [AMBER] pmemdTI test failure David A Case (Tue Jul 08 2014 - 11:55:01 PDT)
- Re: [AMBER] pmemdTI test failure Huang (Tue Aug 19 2014 - 05:15:46 PDT)
  - Re: [AMBER] pmemdTI test failure Jason Swails (Tue Aug 19 2014 - 05:41:30 PDT)
  - Re: [AMBER] pmemdTI test failure Huang (Mon Aug 25 2014 - 02:37:24 PDT)
    - Re: [AMBER] pmemdTI test failure David A Case (Mon Aug 25 2014 - 18:00:01 PDT)
[AMBER] Parameter file for polyethyleglycol PEG Iqbal, Muhammad Sajid (Tue Jul 08 2014 - 11:03:04 PDT)
- Re: [AMBER] Parameter file for polyethyleglycol PEG Jason Swails (Tue Jul 08 2014 - 11:16:04 PDT)
- Re: [AMBER] Parameter file for polyethyleglycol PEG FyD (Thu Jul 10 2014 - 02:53:39 PDT)
[AMBER] atomiccorr: glibc detected *** cpptraj: malloc(): memory corruption: Krisztina Feher (Tue Jul 08 2014 - 14:26:53 PDT)
- Re: [AMBER] atomiccorr: glibc detected *** cpptraj: malloc(): memory corruption: Jason Swails (Tue Jul 08 2014 - 15:05:14 PDT)
- Re: [AMBER] atomiccorr: glibc detected *** cpptraj: malloc(): memory corruption: Jason Swails (Tue Jul 08 2014 - 16:06:14 PDT)
  - Re: [AMBER] atomiccorr: glibc detected *** cpptraj: malloc(): memory corruption: Daniel Roe (Tue Jul 08 2014 - 19:46:20 PDT)
[AMBER] Orbital Hessian Not Positive Definite Error Malachi Phillips (Tue Jul 08 2014 - 14:49:17 PDT)
[AMBER] how to quantify and visualize the flow of water into a protein Thomas Evangelidis (Tue Jul 08 2014 - 16:20:14 PDT)
[AMBER] entropy Calculation Him Shweta (Tue Jul 08 2014 - 22:12:06 PDT)
- Re: [AMBER] entropy Calculation Jason Swails (Tue Jul 08 2014 - 22:38:40 PDT)
  - Re: [AMBER] entropy Calculation Him Shweta (Thu Jul 10 2014 - 05:52:06 PDT)
    - Re: [AMBER] entropy Calculation Him Shweta (Thu Jul 10 2014 - 09:30:56 PDT)
    - Re: [AMBER] entropy Calculation Jason Swails (Thu Jul 10 2014 - 11:11:17 PDT)
    - Re: [AMBER] entropy Calculation Him Shweta (Thu Jul 10 2014 - 20:50:31 PDT)
[AMBER] Question Brittany Boykin (Wed Jul 09 2014 - 09:51:19 PDT)
- Re: [AMBER] Question Daniel Roe (Wed Jul 09 2014 - 09:58:10 PDT)
[AMBER] Finding a good REMD temperature ladder Eugene Yedvabny (Wed Jul 09 2014 - 11:01:39 PDT)
- Re: [AMBER] Finding a good REMD temperature ladder Daniel Roe (Wed Jul 09 2014 - 12:47:16 PDT)
  - Re: [AMBER] Finding a good REMD temperature ladder Carlos Simmerling (Wed Jul 09 2014 - 13:13:51 PDT)
[AMBER] autoimage doesn't work 肖立 (Wed Jul 09 2014 - 12:03:25 PDT)
- Re: [AMBER] autoimage doesn't work Daniel Roe (Wed Jul 09 2014 - 12:09:18 PDT)
  - Re: [AMBER] autoimage doesn't work 肖立 (Wed Jul 09 2014 - 12:36:19 PDT)
    - Re: [AMBER] autoimage doesn't work 肖立 (Wed Jul 09 2014 - 12:38:56 PDT)
[AMBER] tinker to amber format Jorgen Simonsen (Wed Jul 09 2014 - 21:44:14 PDT)
- Re: [AMBER] tinker to amber format Jason Swails (Thu Jul 10 2014 - 03:11:50 PDT)
[AMBER] Switch function in Amber Ramuntcho Moretti (Thu Jul 10 2014 - 01:04:43 PDT)
- Re: [AMBER] Switch function in Amber David A Case (Thu Jul 10 2014 - 04:46:45 PDT)
[AMBER] Ag+ ion parameters Rebeca García Fandiño (Thu Jul 10 2014 - 01:35:03 PDT)
- Re: [AMBER] Ag+ ion parameters Pengfei Li (Fri Jul 11 2014 - 07:41:43 PDT)
[AMBER] DCCP analysis Soumendranath Bhakat (Thu Jul 10 2014 - 02:04:18 PDT)
- Re: [AMBER] DCCP analysis Daniel Roe (Thu Jul 10 2014 - 06:57:43 PDT)
[AMBER] Fwd: Re: [q4md-fft] Issues Running, missing Ante_RED 2 FyD (Thu Jul 10 2014 - 02:43:55 PDT)
[AMBER] Fwd: Re: [q4md-fft] URGENT:Orbital Hessian Not Positive Definite FyD (Thu Jul 10 2014 - 02:57:12 PDT)
[AMBER] Free Binding Energy Calculation Him Shweta (Thu Jul 10 2014 - 05:58:01 PDT)
- Re: [AMBER] Free Binding Energy Calculation Bill Miller III (Thu Jul 10 2014 - 06:11:28 PDT)
  - Re: [AMBER] Free Binding Energy Calculation Him Shweta (Thu Jul 10 2014 - 06:20:39 PDT)
[AMBER] Sander of Amber11, Amber12 and AmberTools14 Massimiliano Porrini (Thu Jul 10 2014 - 10:59:30 PDT)
- Re: [AMBER] Sander of Amber11, Amber12 and AmberTools14 Jason Swails (Thu Jul 10 2014 - 11:13:46 PDT)
  - Re: [AMBER] Sander of Amber11, Amber12 and AmberTools14 Massimiliano Porrini (Fri Jul 11 2014 - 03:30:43 PDT)
[AMBER] cpptraj rotdif parameters Alegrete, Matthew (Thu Jul 10 2014 - 12:34:29 PDT)
- Re: [AMBER] cpptraj rotdif parameters David A Case (Thu Jul 10 2014 - 17:17:44 PDT)
[AMBER] How is temperature in Amber MD simulations calculated? Arthur Roberts (Thu Jul 10 2014 - 13:04:20 PDT)
- Re: [AMBER] How is temperature in Amber MD simulations calculated? Brian Radak (Thu Jul 10 2014 - 13:40:11 PDT)
  - Re: [AMBER] How is temperature in Amber MD simulations calculated? Jason Swails (Thu Jul 10 2014 - 13:53:30 PDT)
[AMBER] Question Brittany Boykin (Thu Jul 10 2014 - 14:01:53 PDT)
- Re: [AMBER] Question Jason Swails (Thu Jul 10 2014 - 14:11:50 PDT)
[AMBER] evaluating hydrogen bond using ptraj Vijay Manickam Achari (Thu Jul 10 2014 - 23:31:05 PDT)
[AMBER] cholesterol with lipid14 Thomas Evangelidis (Fri Jul 11 2014 - 00:44:33 PDT)
[AMBER] Thermodynamic Integration by using pmemd Sun (Fri Jul 11 2014 - 02:33:21 PDT)
- Re: [AMBER] Thermodynamic Integration by using pmemd Hannes Loeffler (Fri Jul 11 2014 - 03:01:57 PDT)
  - Re: [AMBER] Thermodynamic Integration by using pmemd Ying-Chieh Sun (Fri Jul 11 2014 - 05:54:19 PDT)
[AMBER] graph energy check after minimization amor san juan (Fri Jul 11 2014 - 11:59:47 PDT)
- Re: [AMBER] graph energy check after minimization Jason Swails (Fri Jul 11 2014 - 12:19:44 PDT)
  - Re: [AMBER] graph energy check after minimization amor san juan (Sat Jul 12 2014 - 03:03:44 PDT)
[AMBER] diffusion path length newamber list (Fri Jul 11 2014 - 12:11:03 PDT)
- Re: [AMBER] diffusion path length Daniel Roe (Fri Jul 11 2014 - 12:57:34 PDT)
  - Re: [AMBER] diffusion path length newamber list (Fri Jul 11 2014 - 13:41:00 PDT)
    - Re: [AMBER] diffusion path length newamber list (Sat Jul 12 2014 - 09:01:27 PDT)
    - Re: [AMBER] diffusion path length Daniel Roe (Sat Jul 12 2014 - 11:02:19 PDT)
    - Re: [AMBER] diffusion path length newamber list (Sat Jul 12 2014 - 13:54:31 PDT)
    - Re: [AMBER] diffusion path length Daniel Roe (Mon Jul 14 2014 - 08:51:13 PDT)
    - Re: [AMBER] diffusion path length newamber list (Mon Jul 14 2014 - 09:52:48 PDT)
[AMBER] cuda.test errors Jonathan Gough (Fri Jul 11 2014 - 14:53:28 PDT)
- Re: [AMBER] cuda.test errors Ross Walker (Fri Jul 11 2014 - 15:03:54 PDT)
  - Re: [AMBER] cuda.test errors Jonathan Gough (Sat Jul 12 2014 - 06:10:45 PDT)
[AMBER] pressure tensor kirtana S (Sat Jul 12 2014 - 10:45:23 PDT)
- Re: [AMBER] pressure tensor Jason Swails (Tue Jul 15 2014 - 10:36:47 PDT)
[AMBER] Query about QM/MM scanning using amber Kshatresh Dutta Dubey (Sun Jul 13 2014 - 04:24:50 PDT)
- Re: [AMBER] Query about QM/MM scanning using amber Jason Swails (Sun Jul 13 2014 - 09:15:58 PDT)
[AMBER] hydrogen bond evaluation Vijay Manickam Achari (Mon Jul 14 2014 - 02:28:26 PDT)
- Re: [AMBER] hydrogen bond evaluation Jason Swails (Mon Jul 14 2014 - 08:49:28 PDT)
  - Re: [AMBER] hydrogen bond evaluation Daniel Roe (Mon Jul 14 2014 - 09:05:51 PDT)
- Re: [AMBER] hydrogen bond evaluation Jason Swails (Tue Jul 15 2014 - 08:35:16 PDT)
[AMBER] cpptraj help Saikat Dutta chowdhury (Mon Jul 14 2014 - 04:40:16 PDT)
- Re: [AMBER] cpptraj help Daniel Roe (Mon Jul 14 2014 - 05:38:20 PDT)
  - Re: [AMBER] cpptraj help Saikat Dutta chowdhury (Mon Jul 14 2014 - 06:21:38 PDT)
[AMBER] update amber12 zahra khatti (Mon Jul 14 2014 - 14:05:56 PDT)
- Re: [AMBER] update amber12 Jason Swails (Mon Jul 14 2014 - 14:35:07 PDT)
[AMBER] coordinate and topology files using tleap from RED server output files Iqbal, Muhammad Sajid (Mon Jul 14 2014 - 14:17:40 PDT)
- Re: [AMBER] coordinate and topology files using tleap from RED server output files FyD (Tue Jul 15 2014 - 04:01:41 PDT)
[AMBER] Downloading old versions of AMBERTools Marawan Hussien (Mon Jul 14 2014 - 14:55:19 PDT)
- Re: [AMBER] Downloading old versions of AMBERTools Jason Swails (Mon Jul 14 2014 - 16:10:50 PDT)
  - Re: [AMBER] Downloading old versions of AMBERTools Marawan Hussien (Tue Jul 15 2014 - 09:09:30 PDT)
    - Re: [AMBER] Downloading old versions of AMBERTools Jason Swails (Tue Jul 15 2014 - 10:09:06 PDT)
[AMBER] gpu and cpu runs Mary Varughese (Tue Jul 15 2014 - 00:23:24 PDT)
- Re: [AMBER] gpu and cpu runs Jason Swails (Tue Jul 15 2014 - 08:43:55 PDT)
  - Re: [AMBER] gpu and cpu runs Mary Varughese (Tue Jul 15 2014 - 18:57:47 PDT)
    - Re: [AMBER] gpu and cpu runs Jason Swails (Tue Jul 15 2014 - 19:08:14 PDT)
    - Re: [AMBER] gpu and cpu runs Mary Varughese (Tue Jul 15 2014 - 20:29:02 PDT)
    - Re: [AMBER] gpu and cpu runs Ross Walker (Wed Jul 16 2014 - 10:03:59 PDT)
    - Re: [AMBER] gpu and cpu runs Scott Le Grand (Wed Jul 16 2014 - 10:21:52 PDT)
    - Re: [AMBER] gpu and cpu runs Mary Varughese (Wed Jul 16 2014 - 21:31:14 PDT)
[AMBER] Error output file Faez Iqbal khan (Tue Jul 15 2014 - 01:17:49 PDT)
- Re: [AMBER] Error output file Soumendranath Bhakat (Tue Jul 15 2014 - 01:51:27 PDT)
  - Re: [AMBER] Error output file Soumendranath Bhakat (Tue Jul 15 2014 - 01:59:07 PDT)
- Re: [AMBER] Error output file Jason Swails (Tue Jul 15 2014 - 08:47:21 PDT)
[AMBER] Error while running tleap Suchetana Gupta (Tue Jul 15 2014 - 02:13:20 PDT)
- Re: [AMBER] Error while running tleap Jason Swails (Tue Jul 15 2014 - 08:55:24 PDT)
  - Re: [AMBER] Error while running tleap Suchetana Gupta (Tue Jul 15 2014 - 09:00:09 PDT)
[AMBER] nativecontacts by amber14 cpptraj Rajeswari A. (Tue Jul 15 2014 - 04:36:00 PDT)
- Re: [AMBER] nativecontacts by amber14 cpptraj Daniel Roe (Tue Jul 15 2014 - 09:47:33 PDT)
  - Re: [AMBER] nativecontacts by amber14 cpptraj Rajeswari A. (Tue Jul 15 2014 - 21:52:43 PDT)
[AMBER] Could not find cntrl namelist Fengxue Li (Tue Jul 15 2014 - 06:19:27 PDT)
- Re: [AMBER] Could not find cntrl namelist Pengfei Li (Tue Jul 15 2014 - 07:41:55 PDT)
[AMBER] To get resp charges of a modified central residue (not an integer). Baptiste Legrand (Tue Jul 15 2014 - 08:24:52 PDT)
- Re: [AMBER] To get resp charges of a modified central residue (not an integer). Jason Swails (Tue Jul 15 2014 - 09:02:00 PDT)
- Re: [AMBER] To get resp charges of a modified central residue (not an integer). FyD (Tue Jul 15 2014 - 23:20:58 PDT)
  - Re: [AMBER] To get resp charges of a modified central residue (not an integer). Baptiste Legrand (Thu Jul 17 2014 - 00:47:04 PDT)
    - Re: [AMBER] To get resp charges of a modified central residue (not an integer). FyD (Thu Jul 17 2014 - 09:03:29 PDT)
[AMBER] installation of AMBER 12 in MAC 10.7 lion Vishal Nemaysh (Wed Jul 16 2014 - 00:14:42 PDT)
- Re: [AMBER] installation of AMBER 12 in MAC 10.7 lion David A Case (Wed Jul 16 2014 - 05:23:11 PDT)
[AMBER] RNA covalent bond angles Blatter Markus (Wed Jul 16 2014 - 02:33:35 PDT)
- Re: [AMBER] RNA covalent bond angles Christina Bergonzo (Wed Jul 16 2014 - 07:44:06 PDT)
  - Re: [AMBER] RNA covalent bond angles Blatter Markus (Wed Jul 16 2014 - 08:11:37 PDT)
    - Re: [AMBER] RNA covalent bond angles Niel Henriksen (Wed Jul 16 2014 - 08:19:38 PDT)
    - Re: [AMBER] RNA covalent bond angles Blatter Markus (Wed Jul 16 2014 - 08:38:07 PDT)
[AMBER] Tool in PTRAJ/CPPTRAJ to analyse residue movement anu chandra (Wed Jul 16 2014 - 05:00:25 PDT)
- Re: [AMBER] Tool in PTRAJ/CPPTRAJ to analyse residue movement Soumendranath Bhakat (Wed Jul 16 2014 - 05:10:22 PDT)
[AMBER] Problem with atommap in cpptraj Rajeswari A. (Wed Jul 16 2014 - 07:04:15 PDT)
- Re: [AMBER] Problem with atommap in cpptraj Daniel Roe (Wed Jul 16 2014 - 21:47:52 PDT)
- Re: [AMBER] Problem with atommap in cpptraj Daniel Roe (Thu Jul 31 2014 - 13:31:15 PDT)
  - Re: [AMBER] Problem with atommap in cpptraj Rajeswari A. (Fri Aug 01 2014 - 22:03:23 PDT)
[AMBER] ATP parameters: tleap error Valentina Romano (Wed Jul 16 2014 - 09:41:55 PDT)
- Re: [AMBER] ATP parameters: tleap error Jason Swails (Wed Jul 16 2014 - 09:51:37 PDT)
- Re: [AMBER] ATP parameters: tleap error George Patargias (Wed Jul 16 2014 - 23:21:19 PDT)
[AMBER] How do I apply cpptraj.timecorr to the output dataset of cpptraj.dihedral? Jose Borreguero (Wed Jul 16 2014 - 16:40:48 PDT)
- Re: [AMBER] How do I apply cpptraj.timecorr to the output dataset of cpptraj.dihedral? Daniel Roe (Wed Jul 16 2014 - 21:56:39 PDT)
  - Re: [AMBER] How do I apply cpptraj.timecorr to the output dataset of cpptraj.dihedral? Jose Borreguero (Thu Jul 17 2014 - 06:50:44 PDT)
- Re: [AMBER] How do I apply cpptraj.timecorr to the output dataset of cpptraj.dihedral? Jose Borreguero (Thu Jul 17 2014 - 11:36:54 PDT)
[AMBER] Implicit solvent and membrane protein James Starlight (Thu Jul 17 2014 - 00:21:29 PDT)
- Re: [AMBER] Implicit solvent and membrane protein Ray Luo, Ph.D. (Thu Jul 17 2014 - 11:27:50 PDT)
  - Re: [AMBER] Implicit solvent and membrane protein James Starlight (Thu Jul 17 2014 - 12:51:15 PDT)
    - Re: [AMBER] Implicit solvent and membrane protein Carlos Simmerling (Thu Jul 17 2014 - 12:55:41 PDT)
    - Re: [AMBER] Implicit solvent and membrane protein James Starlight (Fri Jul 18 2014 - 02:06:33 PDT)
    - Re: [AMBER] Implicit solvent and membrane protein Thomas Evangelidis (Fri Jul 18 2014 - 02:18:59 PDT)
    - Re: [AMBER] Implicit solvent and membrane protein James Starlight (Fri Jul 18 2014 - 03:05:20 PDT)
    - Re: [AMBER] Implicit solvent and membrane protein Thomas Evangelidis (Fri Jul 18 2014 - 03:22:00 PDT)
    - Re: [AMBER] Implicit solvent and membrane protein James Starlight (Fri Jul 18 2014 - 03:31:26 PDT)
[AMBER] Error installing Ambertools on Centos 6.3 and open suse 12.3 Charu Suri (Thu Jul 17 2014 - 05:45:58 PDT)
- Re: [AMBER] Error installing Ambertools on Centos 6.3 and open suse 12.3 Jason Swails (Thu Jul 17 2014 - 08:11:46 PDT)
[AMBER] imin=5 Lara rajam (Thu Jul 17 2014 - 08:12:13 PDT)
- Re: [AMBER] imin=5 Carlos Simmerling (Thu Jul 17 2014 - 08:24:44 PDT)
- Re: [AMBER] imin=5 Brian Radak (Thu Jul 17 2014 - 08:31:44 PDT)
  - Re: [AMBER] imin=5 Lara rajam (Thu Jul 17 2014 - 09:19:57 PDT)
[AMBER] iwrap Sourav Purohit (Thu Jul 17 2014 - 10:03:43 PDT)
- Re: [AMBER] iwrap Teerapong Pirojsirikul (Thu Jul 17 2014 - 10:33:51 PDT)
[AMBER] parameterizing a connected moiety Mohammad Salem (Thu Jul 17 2014 - 14:31:15 PDT)
- Re: [AMBER] parameterizing a connected moiety Jason Swails (Thu Jul 17 2014 - 14:51:14 PDT)
- Re: [AMBER] parameterizing a connected moiety FyD (Fri Jul 18 2014 - 06:38:11 PDT)
[AMBER] ScaledMD for proline dipeptide Niels Geudens (Thu Jul 17 2014 - 23:02:37 PDT)
- Re: [AMBER] ScaledMD for proline dipeptide Jason Swails (Thu Jul 17 2014 - 23:35:03 PDT)
  - Re: [AMBER] ScaledMD for proline dipeptide Niels Geudens (Fri Jul 18 2014 - 00:55:36 PDT)
    - Re: [AMBER] ScaledMD for proline dipeptide Jason Swails (Fri Jul 18 2014 - 02:05:08 PDT)
    - Re: [AMBER] ScaledMD for proline dipeptide Niels Geudens (Mon Aug 04 2014 - 05:20:59 PDT)
[AMBER] Fwd: problem in installation of ambertools14 Vidushi Sharma (Fri Jul 18 2014 - 04:13:12 PDT)
- Re: [AMBER] Fwd: problem in installation of ambertools14 Raman Parkesh (Fri Jul 18 2014 - 04:25:17 PDT)
- Re: [AMBER] Fwd: problem in installation of ambertools14 David A Case (Fri Jul 18 2014 - 04:50:21 PDT)
  - Re: [AMBER] Fwd: problem in installation of ambertools14 Hirdesh Kumar (Sat Jul 19 2014 - 04:38:29 PDT)
    - Re: [AMBER] Fwd: problem in installation of ambertools14 David A Case (Sat Jul 19 2014 - 05:36:59 PDT)
[AMBER] Electrostatic energy calculated by MD in MM/GBSA menwer momo (Fri Jul 18 2014 - 13:06:08 PDT)
- Re: [AMBER] Electrostatic energy calculated by MD in MM/GBSA Jason Swails (Fri Jul 18 2014 - 13:18:46 PDT)
  - Re: [AMBER] Electrostatic energy calculated by MD in MM/GBSA menwer momo (Fri Jul 18 2014 - 13:38:42 PDT)
    - Re: [AMBER] Electrostatic energy calculated by MD in MM/GBSA Jason Swails (Fri Jul 18 2014 - 13:45:00 PDT)
  - Re: [AMBER] Electrostatic energy calculated by MD in MM/GBSA Jason Swails (Fri Jul 18 2014 - 14:17:38 PDT)
  - Re: [AMBER] Electrostatic energy calculated by MD in MM/GBSA Jason Swails (Fri Jul 18 2014 - 14:48:16 PDT)
    - Re: [AMBER] Electrostatic energy calculated by MD in MM/GBSA menwer momo (Fri Jul 18 2014 - 14:53:04 PDT)
[AMBER] memory allocation error for *bond Vishal Nemaysh (Sat Jul 19 2014 - 03:18:57 PDT)
- Re: [AMBER] memory allocation error for *bond David A Case (Sat Jul 19 2014 - 05:34:05 PDT)
  - Re: [AMBER] memory allocation error for *bond Vishal Nemaysh (Sat Jul 19 2014 - 09:36:00 PDT)
[AMBER] Hydrogen bond analysis menwer momo (Sat Jul 19 2014 - 03:56:41 PDT)
- Re: [AMBER] Hydrogen bond analysis Daniel Roe (Tue Jul 22 2014 - 08:13:35 PDT)
[AMBER] mailing list problem Vidushi Sharma (Sat Jul 19 2014 - 04:04:34 PDT)
[AMBER] X11 error Vidushi Sharma (Sat Jul 19 2014 - 07:00:53 PDT)
- Re: [AMBER] X11 error David A Case (Sat Jul 19 2014 - 09:04:31 PDT)
[AMBER] memory allocation error for *bond Vishal Nemaysh (Sun Jul 20 2014 - 02:38:17 PDT)
- Re: [AMBER] memory allocation error for *bond David A Case (Sun Jul 20 2014 - 05:05:57 PDT)
[AMBER] Lipid and protein - error reading group during heat Jonathan Gough (Sun Jul 20 2014 - 20:50:39 PDT)
- Re: [AMBER] Lipid and protein - error reading group during heat David A Case (Mon Jul 21 2014 - 03:46:17 PDT)
[AMBER] NVT and NPT ensemble Sangita Kachhap (Mon Jul 21 2014 - 01:17:41 PDT)
- Re: [AMBER] NVT and NPT ensemble Soumendranath Bhakat (Mon Jul 21 2014 - 01:55:47 PDT)
  - Re: [AMBER] NVT and NPT ensemble Raman Parkesh (Tue Jul 22 2014 - 19:54:46 PDT)
    - Re: [AMBER] NVT and NPT ensemble Sangita Kachhap (Tue Jul 22 2014 - 21:20:00 PDT)
    - Re: [AMBER] NVT and NPT ensemble Sangita Kachhap (Sun Nov 02 2014 - 21:07:05 PST)
    - Re: [AMBER] NVT and NPT ensemble Jason Swails (Mon Nov 03 2014 - 04:53:42 PST)
    - Re: [AMBER] NVT and NPT ensemble Sangita Kachhap (Mon Nov 03 2014 - 05:56:21 PST)
    - Re: [AMBER] NVT and NPT ensemble Jason Swails (Mon Nov 03 2014 - 06:23:17 PST)
    - Re: [AMBER] NVT and NPT ensemble Sangita Kachhap (Mon Nov 03 2014 - 06:20:37 PST)
[AMBER] Amber12 CUDA problems Lorenzo Gontrani (Mon Jul 21 2014 - 03:45:05 PDT)
- Re: [AMBER] Amber12 CUDA problems Ross Walker (Mon Jul 21 2014 - 06:39:04 PDT)
  - Re: [AMBER] Amber12 CUDA problems Lorenzo Gontrani (Mon Jul 21 2014 - 07:18:36 PDT)
    - Re: [AMBER] Amber12 CUDA problems Lorenzo Gontrani (Mon Jul 21 2014 - 07:20:25 PDT)
[AMBER] error in md simulation in pmemd.cuda.MPI Subrata Paul (Mon Jul 21 2014 - 07:07:05 PDT)
- [AMBER] Fwd: error in md simulation in pmemd.cuda.MPI Subrata Paul (Mon Jul 21 2014 - 07:10:16 PDT)
- Re: [AMBER] error in md simulation in pmemd.cuda.MPI Ross Walker (Mon Jul 21 2014 - 08:32:16 PDT)
[AMBER] Regarding LIE in cpptraj Kshatresh Dutta Dubey (Tue Jul 22 2014 - 00:23:50 PDT)
- Re: [AMBER] Regarding LIE in cpptraj Daniel Roe (Tue Jul 22 2014 - 07:43:25 PDT)
[AMBER] AMP Parameters cye927.mail.ustc.edu.cn (Tue Jul 22 2014 - 01:40:26 PDT)
- Re: [AMBER] AMP Parameters FyD (Wed Jul 23 2014 - 01:52:52 PDT)
[AMBER] sander.APBS: automatic grid adjustments in output? Brian Radak (Tue Jul 22 2014 - 09:55:47 PDT)
- Re: [AMBER] sander.APBS: automatic grid adjustments in output? Robert Konecny (Tue Jul 22 2014 - 20:47:46 PDT)
  - Re: [AMBER] sander.APBS: automatic grid adjustments in output? Brian Radak (Wed Jul 23 2014 - 05:35:21 PDT)
[AMBER] Unable to compile cuda version of amber14 Manikanthan Bhavaraju (Tue Jul 22 2014 - 12:45:48 PDT)
- Re: [AMBER] Unable to compile cuda version of amber14 Jason Swails (Tue Jul 22 2014 - 12:57:56 PDT)
[AMBER] help Zeynep Topdemir (Tue Jul 22 2014 - 16:01:20 PDT)
- Re: [AMBER] help Jason Swails (Tue Jul 22 2014 - 16:17:53 PDT)
- Re: [AMBER] help David A Case (Tue Jul 22 2014 - 16:28:16 PDT)
[AMBER] atom number same as line number for cpptraj newamber list (Tue Jul 22 2014 - 17:02:54 PDT)
- Re: [AMBER] atom number same as line number for cpptraj Jason Swails (Tue Jul 22 2014 - 19:12:03 PDT)
- Re: [AMBER] atom number same as line number for cpptraj Daniel Roe (Tue Jul 22 2014 - 19:12:25 PDT)
  - Re: [AMBER] atom number same as line number for cpptraj newamber list (Wed Jul 23 2014 - 08:23:42 PDT)
    - Re: [AMBER] atom number same as line number for cpptraj Jason Swails (Wed Jul 23 2014 - 09:03:02 PDT)
    - Re: [AMBER] atom number same as line number for cpptraj newamber list (Wed Jul 23 2014 - 09:30:55 PDT)
[AMBER] Hello SaeeD PourasaD (Tue Jul 22 2014 - 19:34:13 PDT)
- Re: [AMBER] Hello Pengfei Li (Tue Jul 22 2014 - 19:59:08 PDT)
- Re: [AMBER] Hello David A Case (Wed Jul 23 2014 - 04:51:12 PDT)
[AMBER] GIST - unusually high water-water energies Waldner, Birgit (Tue Jul 22 2014 - 23:13:33 PDT)
[AMBER] On the values of boost potential for aMD based on amd.log James Starlight (Wed Jul 23 2014 - 02:08:40 PDT)
- Re: [AMBER] On the values of boost potential for aMD based on amd.log Daniel Roe (Wed Jul 23 2014 - 07:02:03 PDT)
  - Re: [AMBER] On the values of boost potential for aMD based on amd.log James Starlight (Wed Jul 23 2014 - 07:54:56 PDT)
    - Re: [AMBER] On the values of boost potential for aMD based on amd.log Thomas Evangelidis (Wed Jul 23 2014 - 08:26:56 PDT)
    - Re: [AMBER] On the values of boost potential for aMD based on amd.log Brian Radak (Wed Jul 23 2014 - 08:28:35 PDT)
    - Re: [AMBER] On the values of boost potential for aMD based on amd.log James Starlight (Wed Jul 23 2014 - 12:20:45 PDT)
[AMBER] Z-axis coordinates Him Shweta (Wed Jul 23 2014 - 02:34:25 PDT)
- Re: [AMBER] Z-axis coordinates Daniel Roe (Wed Jul 23 2014 - 06:57:57 PDT)
  - Re: [AMBER] Z-axis coordinates Him Shweta (Wed Jul 23 2014 - 07:44:00 PDT)
[AMBER] Bug in tleap savemol2? David Minh (Wed Jul 23 2014 - 09:41:59 PDT)
- Re: [AMBER] Bug in tleap savemol2? Jason Swails (Wed Jul 23 2014 - 10:39:24 PDT)
- Re: [AMBER] Bug in tleap savemol2? David Minh (Wed Jul 23 2014 - 13:05:22 PDT)
[AMBER] ptraj binary missing from AmberTools 13 install? Raik Grünberg (Wed Jul 23 2014 - 13:14:41 PDT)
- Re: [AMBER] ptraj binary missing from AmberTools 13 install? Raik Grünberg (Wed Jul 23 2014 - 13:23:08 PDT)
- Re: [AMBER] ptraj binary missing from AmberTools 13 install? Daniel Roe (Wed Jul 23 2014 - 13:42:48 PDT)
  - Re: [AMBER] ptraj binary missing from AmberTools 13 install? Raik Grünberg (Wed Jul 23 2014 - 17:59:21 PDT)
    - Re: [AMBER] ptraj binary missing from AmberTools 13 install? Jason Swails (Wed Jul 23 2014 - 18:58:30 PDT)
[AMBER] renumber all residues in prmtop Thomas Evangelidis (Wed Jul 23 2014 - 16:33:01 PDT)
- Re: [AMBER] renumber all residues in prmtop Jason Swails (Wed Jul 23 2014 - 19:04:41 PDT)
  - Re: [AMBER] renumber all residues in prmtop Thomas Evangelidis (Thu Jul 24 2014 - 00:09:06 PDT)
- Re: [AMBER] renumber all residues in prmtop David A Case (Thu Jul 24 2014 - 05:02:33 PDT)
[AMBER] Hi SaeeD PourasaD (Thu Jul 24 2014 - 00:14:15 PDT)
- Re: [AMBER] Hi Marc van der Kamp (Thu Jul 24 2014 - 01:23:28 PDT)
[AMBER] CYM charges in amino14ipq.lib wrong? Marc van der Kamp (Thu Jul 24 2014 - 05:27:11 PDT)
- Re: [AMBER] CYM charges in amino14ipq.lib wrong? David A Case (Thu Jul 24 2014 - 06:00:11 PDT)
Re: [AMBER] GPU error Attempting MC barostat change: Failed Raman Parkesh (Thu Jul 24 2014 - 07:10:07 PDT)
- Re: [AMBER] GPU error Attempting MC barostat change: Failed Jason Swails (Thu Jul 24 2014 - 11:03:58 PDT)
  - Re: [AMBER] GPU error Attempting MC barostat change: Failed Raman Parkesh (Thu Jul 24 2014 - 17:35:49 PDT)
    - Re: [AMBER] GPU error Attempting MC barostat change: Failed Jason Swails (Thu Jul 24 2014 - 22:01:04 PDT)
[AMBER] Cpptraj clustering James Starlight (Thu Jul 24 2014 - 08:13:19 PDT)
[AMBER] pbc problem Niloofar Nayebi (Thu Jul 24 2014 - 09:21:24 PDT)
- Re: [AMBER] pbc problem David A Case (Thu Jul 24 2014 - 13:38:53 PDT)
[AMBER] Not integer charge for glycoprotein Tommaso Casalini (Thu Jul 24 2014 - 09:28:52 PDT)
- Re: [AMBER] Not integer charge for glycoprotein Lachele Foley (Thu Jul 24 2014 - 10:27:46 PDT)
[AMBER] cpptraj not processing all mdcrd files Kshatresh Dutta Dubey (Thu Jul 24 2014 - 14:50:24 PDT)
- Re: [AMBER] cpptraj not processing all mdcrd files Daniel Roe (Fri Jul 25 2014 - 09:25:50 PDT)
[AMBER] problems with paramfit Marek Maly (Thu Jul 24 2014 - 14:56:00 PDT)
- Re: [AMBER] problems with paramfit Robin Betz (Fri Jul 25 2014 - 08:33:37 PDT)
  - Re: [AMBER] problems with paramfit Marek Maly (Fri Jul 25 2014 - 08:52:48 PDT)
  - Re: [AMBER] problems with paramfit Marek Maly (Sun Jul 27 2014 - 09:12:35 PDT)
    - Re: [AMBER] problems with paramfit Robin Betz (Mon Jul 28 2014 - 13:12:58 PDT)
    - Re: [AMBER] problems with paramfit Marek Maly (Mon Jul 28 2014 - 13:51:11 PDT)
    - Re: [AMBER] problems with paramfit Robin Betz (Mon Jul 28 2014 - 17:52:14 PDT)
    - Re: [AMBER] problems with paramfit Marek Maly (Mon Jul 28 2014 - 18:25:16 PDT)
    - Re: [AMBER] problems with paramfit Marek Maly (Wed Jul 30 2014 - 13:29:56 PDT)
[AMBER] Berendsen vs. Monte Carlo Parker de Waal (Thu Jul 24 2014 - 19:14:06 PDT)
- Re: [AMBER] Berendsen vs. Monte Carlo Jason Swails (Thu Jul 24 2014 - 22:20:29 PDT)
  - Re: [AMBER] Berendsen vs. Monte Carlo Parker de Waal (Fri Jul 25 2014 - 05:23:21 PDT)
    - Re: [AMBER] Berendsen vs. Monte Carlo Brian Radak (Fri Jul 25 2014 - 07:49:06 PDT)
[AMBER] values of λ in Thermodynamic Integration Sun (Thu Jul 24 2014 - 19:25:16 PDT)
- Re: [AMBER] values of λ in Thermodynamic Integration Ying-Chieh Sun (Thu Jul 24 2014 - 19:50:01 PDT)
- Re: [AMBER] values of λ in Thermodynamic Integration David A Case (Fri Jul 25 2014 - 04:17:04 PDT)
[AMBER] element symbol error in tleap cq y (Fri Jul 25 2014 - 01:35:03 PDT)
[AMBER] element symbol error in tleap Changqing Yan (Fri Jul 25 2014 - 01:52:40 PDT)
- Re: [AMBER] element symbol error in tleap Changqing Yan (Fri Jul 25 2014 - 02:19:16 PDT)
- Re: [AMBER] element symbol error in tleap David A Case (Fri Jul 25 2014 - 04:23:54 PDT)
[AMBER] Hi Him Shweta (Fri Jul 25 2014 - 02:19:46 PDT)
[AMBER] Running PCA Nicole Ippolito (Fri Jul 25 2014 - 10:56:31 PDT)
- [AMBER] Fwd: Running PCA Nicole Ippolito (Tue Jul 29 2014 - 06:24:45 PDT)
- Re: [AMBER] Running PCA Daniel Roe (Tue Jul 29 2014 - 07:16:28 PDT)
  - Re: [AMBER] Running PCA Daniel Roe (Tue Jul 29 2014 - 07:31:20 PDT)
    - Re: [AMBER] Running PCA Nicole Ippolito (Tue Jul 29 2014 - 08:07:55 PDT)
    - Re: [AMBER] Running PCA Nicole Ippolito (Wed Jul 30 2014 - 06:46:55 PDT)
    - Re: [AMBER] Running PCA Daniel Roe (Wed Jul 30 2014 - 07:05:04 PDT)
  - [AMBER] ambpdb error Urszula Uciechowska (Tue Aug 19 2014 - 04:01:13 PDT)
    - Re: [AMBER] ambpdb error Jason Swails (Tue Aug 19 2014 - 04:13:56 PDT)
    - Re: [AMBER] ambpdb error Urszula Uciechowska (Tue Aug 19 2014 - 04:12:58 PDT)
    - Re: [AMBER] ambpdb error Jason Swails (Tue Aug 19 2014 - 05:04:03 PDT)
    - [AMBER] error ambpdb - Old style inpcrd file read Urszula Uciechowska (Wed Aug 20 2014 - 01:20:23 PDT)
    - Re: [AMBER] error ambpdb - Old style inpcrd file read Urszula Uciechowska (Wed Aug 20 2014 - 03:55:11 PDT)
    - Re: [AMBER] error ambpdb - Old style inpcrd file read Valentina Romano (Wed Aug 20 2014 - 04:09:25 PDT)
    - Re: [AMBER] error ambpdb - Old style inpcrd file read Urszula Uciechowska (Wed Aug 20 2014 - 04:22:51 PDT)
    - Re: [AMBER] error ambpdb - Old style inpcrd file read Jason Swails (Wed Aug 20 2014 - 04:30:55 PDT)
    - Re: [AMBER] error ambpdb - Old style inpcrd file read Jason Swails (Wed Aug 20 2014 - 04:34:24 PDT)
    - Re: [AMBER] error ambpdb - Old style inpcrd file read Urszula Uciechowska (Wed Aug 20 2014 - 04:38:46 PDT)
    - Re: [AMBER] error ambpdb - Old style inpcrd file read Jason Swails (Wed Aug 20 2014 - 05:09:52 PDT)
    - Re: [AMBER] error ambpdb - Old style inpcrd file read Urszula Uciechowska (Wed Aug 20 2014 - 05:15:08 PDT)
    - Re: [AMBER] error ambpdb - Old style inpcrd file read Jason Swails (Wed Aug 20 2014 - 05:33:22 PDT)
    - Re: [AMBER] error ambpdb - Old style inpcrd file read Urszula Uciechowska (Wed Aug 20 2014 - 07:20:42 PDT)
    - Re: [AMBER] error ambpdb - Old style inpcrd file read Jason Swails (Wed Aug 20 2014 - 07:48:21 PDT)
    - Re: [AMBER] ambpdb error David A Case (Tue Aug 19 2014 - 05:01:16 PDT)
[AMBER] Fwd: AMBER Digest, Vol 926, Issue 1 Changqing Yan (Fri Jul 25 2014 - 19:22:45 PDT)
- Re: [AMBER] Fwd: AMBER Digest, Vol 926, Issue 1 David A Case (Sat Jul 26 2014 - 06:21:12 PDT)
[AMBER] On the ussage of the langevens thermostat with the gb models James Starlight (Sat Jul 26 2014 - 00:03:20 PDT)
- Re: [AMBER] On the ussage of the langevens thermostat with the gb models Carlos Simmerling (Sat Jul 26 2014 - 04:50:10 PDT)
  - Re: [AMBER] On the ussage of the langevens thermostat with the gb models James Starlight (Mon Jul 28 2014 - 04:22:05 PDT)
[AMBER] problem to apply AmberTools patch 7 and induced crash of the whole Amber14 installation process Marek Maly (Sun Jul 27 2014 - 09:35:39 PDT)
- Re: [AMBER] problem to apply AmberTools patch 7 and induced crash of the whole Amber14 installation process Marc van der Kamp (Mon Jul 28 2014 - 04:49:23 PDT)
  - Re: [AMBER] problem to apply AmberTools patch 7 and induced crash of the whole Amber14 installation process David A Case (Mon Jul 28 2014 - 05:58:15 PDT)
    - Re: [AMBER] problem to apply AmberTools patch 7 and induced crash of the whole Amber14 installation process Marek Maly (Mon Jul 28 2014 - 05:56:07 PDT)
  - Re: [AMBER] problem to apply AmberTools patch 7 and induced crash of the whole Amber14 installation process Jason Swails (Mon Jul 28 2014 - 06:58:21 PDT)
    - Re: [AMBER] problem to apply AmberTools patch 7 and induced crash of the whole Amber14 installation process Marek Maly (Mon Jul 28 2014 - 07:17:18 PDT)
[AMBER] Problem on making inpcrd file 肖立 (Sun Jul 27 2014 - 13:06:34 PDT)
- Re: [AMBER] Problem on making inpcrd file David A Case (Sun Jul 27 2014 - 20:52:27 PDT)
- Re: [AMBER] Problem on making inpcrd file Jason Swails (Mon Jul 28 2014 - 06:36:55 PDT)
  - Re: [AMBER] Problem on making inpcrd file 肖立 (Mon Jul 28 2014 - 16:13:26 PDT)
    - Re: [AMBER] Problem on making inpcrd file Jason Swails (Mon Jul 28 2014 - 16:24:02 PDT)
[AMBER] Error: invalid configuration argument launching kernel kPMEFillChargeGridBuffer Pablo Ródenas (Mon Jul 28 2014 - 06:04:14 PDT)
- Re: [AMBER] Error: invalid configuration argument launching kernel kPMEFillChargeGridBuffer Jason Swails (Mon Jul 28 2014 - 06:42:09 PDT)
  - Re: [AMBER] Error: invalid configuration argument launching kernel kPMEFillChargeGridBuffer Pablo Ródenas (Thu Aug 07 2014 - 07:54:05 PDT)
    - Re: [AMBER] Error: invalid configuration argument launching kernel kPMEFillChargeGridBuffer Pablo Ródenas (Mon Aug 11 2014 - 23:00:26 PDT)
    - Re: [AMBER] Error: invalid configuration argument launching kernel kPMEFillChargeGridBuffer Daniel Roe (Tue Aug 12 2014 - 10:34:34 PDT)
    - Re: [AMBER] Error: invalid configuration argument launching kernel kPMEFillChargeGridBuffer Pablo Ródenas (Tue Aug 12 2014 - 23:59:17 PDT)
    - Re: [AMBER] Error: invalid configuration argument launching kernel kPMEFillChargeGridBuffer Pablo Ródenas (Wed Aug 13 2014 - 04:11:39 PDT)
    - Re: [AMBER] Error: invalid configuration argument launching kernel kPMEFillChargeGridBuffer Jason Swails (Wed Aug 13 2014 - 04:56:51 PDT)
    - Re: [AMBER] Error: invalid configuration argument launching kernel kPMEFillChargeGridBuffer Pablo Ródenas (Wed Aug 13 2014 - 06:31:58 PDT)
    - Re: [AMBER] Error: invalid configuration argument launching kernel kPMEFillChargeGridBuffer Pablo Ródenas (Wed Sep 03 2014 - 23:17:05 PDT)
    - Re: [AMBER] Error: invalid configuration argument launching kernel kPMEFillChargeGridBuffer Jason Swails (Thu Sep 04 2014 - 06:48:04 PDT)
    - Re: [AMBER] Error: invalid configuration argument launching kernel kPMEFillChargeGridBuffer Pablo Ródenas (Fri Sep 12 2014 - 04:24:05 PDT)
    - Re: [AMBER] Error: invalid configuration argument launching kernel kPMEFillChargeGridBuffer Pablo Ródenas (Thu Oct 09 2014 - 07:22:37 PDT)
    - Re: [AMBER] Error: invalid configuration argument launching kernel kPMEFillChargeGridBuffer Scott Le Grand (Thu Oct 09 2014 - 07:58:26 PDT)
    - Re: [AMBER] Error: invalid configuration argument launching kernel kPMEFillChargeGridBuffer Scott Le Grand (Thu Oct 09 2014 - 08:06:14 PDT)
    - Re: [AMBER] Error: invalid configuration argument launching kernel kPMEFillChargeGridBuffer Scott Le Grand (Thu Oct 09 2014 - 08:09:46 PDT)
    - Re: [AMBER] Error: invalid configuration argument launching kernel kPMEFillChargeGridBuffer Pablo Ródenas (Thu Oct 09 2014 - 08:20:38 PDT)
    - Re: [AMBER] Error: invalid configuration argument launching kernel kPMEFillChargeGridBuffer Scott Le Grand (Thu Oct 09 2014 - 08:23:37 PDT)
    - Re: [AMBER] Error: invalid configuration argument launching kernel kPMEFillChargeGridBuffer Scott Le Grand (Thu Oct 09 2014 - 08:25:28 PDT)
    - Re: [AMBER] Error: invalid configuration argument launching kernel kPMEFillChargeGridBuffer Pablo Ródenas (Thu Oct 09 2014 - 08:44:42 PDT)
    - Re: [AMBER] Error: invalid configuration argument launching kernel kPMEFillChargeGridBuffer Pablo Ródenas (Thu Oct 09 2014 - 08:54:37 PDT)
    - Re: [AMBER] Error: invalid configuration argument launching kernel kPMEFillChargeGridBuffer Scott Le Grand (Thu Oct 09 2014 - 09:06:43 PDT)
    - Re: [AMBER] Error: invalid configuration argument launching kernel kPMEFillChargeGridBuffer Pablo Ródenas (Thu Oct 09 2014 - 23:36:43 PDT)
    - Re: [AMBER] Error: invalid configuration argument launching kernel kPMEFillChargeGridBuffer Scott Le Grand (Fri Oct 10 2014 - 12:16:41 PDT)
    - Re: [AMBER] Error: invalid configuration argument launching kernel kPMEFillChargeGridBuffer Pablo Ródenas (Sun Oct 12 2014 - 23:45:34 PDT)
    - Re: [AMBER] Error: invalid configuration argument launching kernel kPMEFillChargeGridBuffer Pablo Ródenas (Tue Oct 14 2014 - 00:44:23 PDT)
    - Re: [AMBER] Error: invalid configuration argument launching kernel kPMEFillChargeGridBuffer Scott Le Grand (Tue Oct 14 2014 - 06:54:15 PDT)
    - Re: [AMBER] Error: invalid configuration argument launching kernel kPMEFillChargeGridBuffer Pablo Ródenas (Tue Oct 14 2014 - 07:03:02 PDT)
    - Re: [AMBER] Error: invalid configuration argument launching kernel kPMEFillChargeGridBuffer Scott Le Grand (Tue Oct 14 2014 - 09:11:37 PDT)
    - Re: [AMBER] Error: invalid configuration argument launching kernel kPMEFillChargeGridBuffer Pablo Ródenas (Tue Oct 28 2014 - 01:39:25 PDT)
    - Re: [AMBER] Error: invalid configuration argument launching kernel kPMEFillChargeGridBuffer Scott Le Grand (Thu Oct 09 2014 - 08:54:42 PDT)
[AMBER] PMF by WHAM Marta Wisniewska (Mon Jul 28 2014 - 06:22:46 PDT)
- Re: [AMBER] PMF by WHAM Brian Radak (Mon Jul 28 2014 - 06:53:57 PDT)
[AMBER] Solvating the system with polyethylene glycol PEG Iqbal, Muhammad Sajid (Mon Jul 28 2014 - 10:07:35 PDT)
- Re: [AMBER] Solvating the system with polyethylene glycol PEG ABEL Stephane 175950 (Mon Jul 28 2014 - 11:01:04 PDT)
- Re: [AMBER] Solvating the system with polyethylene glycol PEG Hector A. Baldoni (Mon Jul 28 2014 - 11:08:00 PDT)
- Re: [AMBER] Solvating the system with polyethylene glycol PEG FyD (Wed Jul 30 2014 - 02:16:30 PDT)
[AMBER] NONBONDED_PARM_INDEX Him Shweta (Tue Jul 29 2014 - 00:37:39 PDT)
- Re: [AMBER] NONBONDED_PARM_INDEX David A Case (Tue Jul 29 2014 - 05:09:09 PDT)
- Re: [AMBER] NONBONDED_PARM_INDEX Shweta (Wed Jul 30 2014 - 05:31:28 PDT)
[AMBER] !Help!: Normal Mode Analysis xy21hb (Tue Jul 29 2014 - 07:56:24 PDT)
- Re: [AMBER] !Help!: Normal Mode Analysis Jason Swails (Tue Jul 29 2014 - 08:22:03 PDT)
[AMBER] HELP Needed: AMBER12 cuda compilation ERROR Saikat Dutta chowdhury (Wed Jul 30 2014 - 04:18:19 PDT)
- Re: [AMBER] HELP Needed: AMBER12 cuda compilation ERROR Jason Swails (Wed Jul 30 2014 - 05:26:08 PDT)
  - Re: [AMBER] HELP Needed: AMBER12 cuda compilation ERROR Saikat Dutta chowdhury (Thu Jul 31 2014 - 23:03:38 PDT)
[AMBER] Parameters for SulfoTyrosine Stephane Azoulay (Wed Jul 30 2014 - 07:52:19 PDT)
- Re: [AMBER] Parameters for SulfoTyrosine Brian Radak (Wed Jul 30 2014 - 08:08:31 PDT)
[AMBER] AMBER renatoac.ufpa.br (Wed Jul 30 2014 - 12:15:24 PDT)
[AMBER] erro na criação do complexo renatoac.ufpa.br (Wed Jul 30 2014 - 12:43:10 PDT)
- Re: [AMBER] erro na criação do complexo Daniel Roe (Wed Jul 30 2014 - 12:53:50 PDT)
  - Re: [AMBER] erro na criação do complexo renatoac.ufpa.br (Wed Jul 30 2014 - 13:00:15 PDT)
[AMBER] erro na criação do complexo renatoac.ufpa.br (Wed Jul 30 2014 - 12:50:07 PDT)
[AMBER] Could not find vdW (or other) parameters for type Pedro Swagger (Wed Jul 30 2014 - 16:38:35 PDT)
[AMBER] this a very green neophyte's question. J.W. Halley (Wed Jul 30 2014 - 17:56:49 PDT)
- Re: [AMBER] this a very green neophyte's question. David A Case (Wed Jul 30 2014 - 18:18:55 PDT)
- Re: [AMBER] this a very green neophyte's question. Parker de Waal (Wed Jul 30 2014 - 18:26:32 PDT)
  - Re: [AMBER] this a very green neophyte's question. J.W. Halley (Thu Jul 31 2014 - 14:47:08 PDT)
    - Re: [AMBER] this a very green neophyte's question. Parker de Waal (Thu Jul 31 2014 - 14:52:34 PDT)
    - Re: [AMBER] this a very green neophyte's question. Jason Swails (Thu Jul 31 2014 - 14:52:28 PDT)
    - Re: [AMBER] this a very green neophyte's question. J.W. Halley (Thu Jul 31 2014 - 17:29:53 PDT)
    - Re: [AMBER] this a very green neophyte's question. Jason Swails (Thu Jul 31 2014 - 19:49:52 PDT)
    - Re: [AMBER] this a very green neophyte's question. Parker de Waal (Thu Jul 31 2014 - 20:13:57 PDT)
    - Re: [AMBER] this a very green neophyte's question. J.W. Halley (Fri Aug 01 2014 - 18:02:27 PDT)
    - Re: [AMBER] this a very green neophyte's question. David A Case (Sat Aug 02 2014 - 05:27:46 PDT)
    - Re: [AMBER] this a very green neophyte's question. David A Case (Fri Aug 01 2014 - 06:40:31 PDT)
    - Re: [AMBER] this a very green neophyte's question. Daniel Roe (Thu Jul 31 2014 - 15:05:03 PDT)
    - Re: [AMBER] this a very green neophyte's question. J.W. Halley (Thu Jul 31 2014 - 15:31:23 PDT)
    - Re: [AMBER] this a very green neophyte's question. Jason Swails (Thu Jul 31 2014 - 16:31:26 PDT)
[AMBER] How to calculate the parameters of metal ions? Jinfeng Huang (Thu Jul 31 2014 - 06:58:50 PDT)
- Re: [AMBER] How to calculate the parameters of metal ions? Christina Bergonzo (Thu Jul 31 2014 - 07:07:58 PDT)
  - Re: [AMBER] How to calculate the parameters of metal ions? Brian Radak (Thu Jul 31 2014 - 07:17:05 PDT)
- Re: [AMBER] How to calculate the parameters of metal ions? FyD (Thu Jul 31 2014 - 07:20:03 PDT)
- Re: [AMBER] How to calculate the parameters of metal ions? Ken Merz (Thu Jul 31 2014 - 07:36:39 PDT)
[AMBER] Zinc parameterization Nadia Li (Thu Jul 31 2014 - 09:55:01 PDT)
- Re: [AMBER] Zinc parameterization Pengfei Li (Thu Jul 31 2014 - 14:34:40 PDT)
  - Re: [AMBER] Zinc parameterization Nadia Li (Thu Jul 31 2014 - 15:37:37 PDT)
    - Re: [AMBER] Zinc parameterization Pengfei Li (Thu Jul 31 2014 - 18:28:59 PDT)
    - Re: [AMBER] Zinc parameterization Nadia Li (Fri Aug 01 2014 - 10:34:41 PDT)
    - Re: [AMBER] Zinc parameterization Pengfei Li (Fri Aug 01 2014 - 14:54:40 PDT)
    - Re: [AMBER] Zinc parameterization Nadia Li (Fri Aug 01 2014 - 15:11:18 PDT)
    - Re: [AMBER] Zinc parameterization Jason Swails (Fri Aug 01 2014 - 15:15:03 PDT)
    - Re: [AMBER] Zinc parameterization Nadia Li (Fri Aug 01 2014 - 15:20:44 PDT)
[AMBER] Equilibirum/System convergence Parker de Waal (Thu Jul 31 2014 - 10:15:37 PDT)
- Re: [AMBER] Equilibirum/System convergence Carlos Simmerling (Thu Jul 31 2014 - 10:33:38 PDT)
[AMBER] question about lipid tutorial Jonathan Gough (Thu Jul 31 2014 - 13:15:57 PDT)
- Re: [AMBER] question about lipid tutorial Dickson, Callum J (Fri Aug 01 2014 - 04:49:09 PDT)
  - Re: [AMBER] question about lipid tutorial Jonathan Gough (Fri Aug 01 2014 - 07:24:15 PDT)
[AMBER] MMPBSA: calcerror Failed with prmtop complex.prmtop Vivek Shankar Bharadwaj (Thu Jul 31 2014 - 18:23:43 PDT)
- Re: [AMBER] MMPBSA: calcerror Failed with prmtop complex.prmtop Jason Swails (Thu Jul 31 2014 - 19:51:54 PDT)
  - Re: [AMBER] MMPBSA: calcerror Failed with prmtop complex.prmtop Vivek Shankar Bharadwaj (Thu Jul 31 2014 - 19:59:29 PDT)
    - Re: [AMBER] MMPBSA: calcerror Failed with prmtop complex.prmtop Vivek Shankar Bharadwaj (Thu Jul 31 2014 - 20:07:35 PDT)
    - Re: [AMBER] MMPBSA: calcerror Failed with prmtop complex.prmtop Jason Swails (Thu Jul 31 2014 - 20:33:05 PDT)
    - Re: [AMBER] MMPBSA: calcerror Failed with prmtop complex.prmtop Vivek Shankar Bharadwaj (Thu Jul 31 2014 - 20:46:39 PDT)
    - Re: [AMBER] MMPBSA: calcerror Failed with prmtop complex.prmtop Vivek Shankar Bharadwaj (Thu Jul 31 2014 - 20:55:52 PDT)
[AMBER] what's the difference between imin=1 and imin=5 when performing minimizations on structures from MD trajectory ye renlo (Fri Aug 01 2014 - 01:18:56 PDT)
- Re: [AMBER] what's the difference between imin=1 and imin=5 when performing minimizations on structures from MD trajectory Brian Radak (Fri Aug 01 2014 - 06:16:41 PDT)
[AMBER] parameters for Mutant HP35 NelNel (PDB code 2F4K) Subrata Paul (Fri Aug 01 2014 - 05:42:08 PDT)
[AMBER] AMBER14 Tutorial: Lipid14 Edition Shekter, Lee R (Fri Aug 01 2014 - 11:03:58 PDT)
- Re: [AMBER] AMBER14 Tutorial: Lipid14 Edition Daniel Roe (Sat Aug 02 2014 - 09:46:22 PDT)
[AMBER] Metal parametrization problem!! Pedro A. Baldera Aguayo (Fri Aug 01 2014 - 11:17:24 PDT)
- Re: [AMBER] Metal parametrization problem!! Jason Swails (Fri Aug 01 2014 - 11:29:48 PDT)
  - Re: [AMBER] Metal parametrization problem!! Pedro A. Baldera Aguayo (Fri Aug 01 2014 - 11:38:29 PDT)
    - Re: [AMBER] Metal parametrization problem!! Jason Swails (Fri Aug 01 2014 - 12:27:07 PDT)
    - Re: [AMBER] Metal parametrization problem!! Pedro A. Baldera Aguayo (Fri Aug 01 2014 - 13:13:27 PDT)
    - Re: [AMBER] Metal parametrization problem!! Pengfei Li (Fri Aug 01 2014 - 14:42:57 PDT)
    - Re: [AMBER] Metal parametrization problem!! Pedro A. Baldera Aguayo (Mon Aug 04 2014 - 18:39:06 PDT)
    - Re: [AMBER] Metal parametrization problem!! Pengfei Li (Mon Aug 04 2014 - 18:51:30 PDT)
    - Re: [AMBER] Metal parametrization problem!! Pengfei Li (Mon Aug 04 2014 - 18:58:40 PDT)
    - Re: [AMBER] Metal parametrization problem!! Pedro A. Baldera Aguayo (Mon Aug 04 2014 - 19:46:58 PDT)
    - Re: [AMBER] Metal parametrization problem!! Pedro A. Baldera Aguayo (Tue Aug 05 2014 - 10:56:10 PDT)
    - Re: [AMBER] Metal parametrization problem!! Pengfei Li (Tue Aug 05 2014 - 13:33:05 PDT)
- Re: [AMBER] Metal parametrization problem!! Pedro A. Baldera Aguayo (Tue Aug 05 2014 - 14:01:25 PDT)
[AMBER] MM-PBSA ALA scanning module bharat lakhani (Fri Aug 01 2014 - 14:17:36 PDT)
- Re: [AMBER] MM-PBSA ALA scanning module Jason Swails (Fri Aug 01 2014 - 14:41:53 PDT)
[AMBER] MMPBSA prmtop problem Nadia Li (Fri Aug 01 2014 - 23:40:59 PDT)
- Re: [AMBER] MMPBSA prmtop problem Jason Swails (Sat Aug 02 2014 - 05:00:51 PDT)
- Re: [AMBER] MMPBSA prmtop problem David A Case (Sat Aug 02 2014 - 05:27:38 PDT)
  - Re: [AMBER] MMPBSA prmtop problem Nadia Li (Sat Aug 02 2014 - 08:47:06 PDT)
    - Re: [AMBER] MMPBSA prmtop problem Jason Swails (Sat Aug 02 2014 - 15:16:00 PDT)
[AMBER] Script error in Umbrella tutorial Kshatresh Dutta Dubey (Sun Aug 03 2014 - 11:56:46 PDT)
- Re: [AMBER] Script error in Umbrella tutorial Asaminew Haile (Sun Aug 03 2014 - 12:35:45 PDT)
  - Re: [AMBER] Script error in Umbrella tutorial Kshatresh Dutta Dubey (Sun Aug 03 2014 - 12:42:58 PDT)
- Re: [AMBER] Script error in Umbrella tutorial Jason Swails (Sun Aug 03 2014 - 13:03:34 PDT)
  - Re: [AMBER] Script error in Umbrella tutorial Kshatresh Dutta Dubey (Sun Aug 03 2014 - 13:10:15 PDT)
[AMBER] glycated residue parameter Sangita Kachhap (Sun Aug 03 2014 - 22:10:39 PDT)
- Re: [AMBER] glycated residue parameter mmaestre.gate.sinica.edu.tw (Sun Aug 03 2014 - 23:45:49 PDT)
  - Re: [AMBER] glycated residue parameter Sangita Kachhap (Sun Aug 03 2014 - 23:57:47 PDT)
    - Re: [AMBER] glycated residue parameter mmaestre.gate.sinica.edu.tw (Mon Aug 04 2014 - 00:35:39 PDT)
    - Re: [AMBER] glycated residue parameter Sangita Kachhap (Mon Aug 04 2014 - 02:24:51 PDT)
    - Re: [AMBER] glycated residue parameter mmaestre.gate.sinica.edu.tw (Mon Aug 04 2014 - 02:45:56 PDT)
    - Re: [AMBER] glycated residue parameter Sangita Kachhap (Mon Aug 04 2014 - 02:49:16 PDT)
[AMBER] MMPBSA.py -make-mdins does not work with nmode Hiromasa WATANABE (Mon Aug 04 2014 - 03:57:36 PDT)
- Re: [AMBER] MMPBSA.py -make-mdins does not work with nmode Jason Swails (Mon Aug 04 2014 - 04:32:09 PDT)
  - Re: [AMBER] MMPBSA.py -make-mdins does not work with nmode Hiromasa WATANABE (Mon Aug 04 2014 - 18:55:23 PDT)
    - Re: [AMBER] MMPBSA.py -make-mdins does not work with nmode Jason Swails (Tue Aug 05 2014 - 07:10:37 PDT)
    - Re: [AMBER] MMPBSA.py -make-mdins does not work with nmode Hiromasa WATANABE (Tue Aug 05 2014 - 17:13:48 PDT)
[AMBER] Potential Energy is positve for a normal ligand Sun (Mon Aug 04 2014 - 07:49:06 PDT)
- Re: [AMBER] Potential Energy is positve for a normal ligand Carlos Simmerling (Mon Aug 04 2014 - 07:53:34 PDT)
[AMBER] Ptraj cluster error Valentina Romano (Mon Aug 04 2014 - 07:58:42 PDT)
- Re: [AMBER] Ptraj cluster error Thomas Cheatham (Mon Aug 04 2014 - 08:21:28 PDT)
[AMBER] pmemd.MPI of amber14: run MD twice with the same input but got different output (within statistical error) sun (Mon Aug 04 2014 - 08:39:02 PDT)
- Re: [AMBER] pmemd.MPI of amber14: run MD twice with the same input but got different output (within statistical error) Ross Walker (Mon Aug 04 2014 - 09:23:06 PDT)
  - Re: [AMBER] pmemd.MPI of amber14: run MD twice with the same input but got different output (within statistical error) sun (Mon Aug 04 2014 - 10:06:14 PDT)
    - Re: [AMBER] pmemd.MPI of amber14: run MD twice with the same input but got different output (within statistical error) Brian Radak (Mon Aug 04 2014 - 11:27:30 PDT)
    - Re: [AMBER] pmemd.MPI of amber14: run MD twice with the same input but got different output (within statistical error) Ying-Chieh Sun (Mon Aug 04 2014 - 19:45:27 PDT)
    - Re: [AMBER] pmemd.MPI of amber14: run MD twice with the same input but got different output (within statistical error) Jason Swails (Tue Aug 05 2014 - 07:03:25 PDT)
    - Re: [AMBER] pmemd.MPI of amber14: run MD twice with the same input but got different output (within statistical error) Ying-Chieh Sun (Tue Aug 05 2014 - 22:28:03 PDT)
[AMBER] NaN and asterisks error in md.out, and mdinfo files Hoshin Kim (Mon Aug 04 2014 - 12:04:34 PDT)
- Re: [AMBER] NaN and asterisks error in md.out, and mdinfo files Ross Walker (Mon Aug 04 2014 - 12:14:14 PDT)
  - Re: [AMBER] NaN and asterisks error in md.out, and mdinfo files Hoshin Kim (Tue Aug 05 2014 - 10:49:39 PDT)
    - Re: [AMBER] NaN and asterisks error in md.out, and mdinfo files Ross Walker (Tue Aug 05 2014 - 10:55:44 PDT)
    - Re: [AMBER] NaN and asterisks error in md.out, and mdinfo files Hoshin Kim (Tue Aug 05 2014 - 11:08:27 PDT)
    - Re: [AMBER] NaN and asterisks error in md.out, and mdinfo files Ross Walker (Wed Aug 06 2014 - 11:38:15 PDT)
    - Re: [AMBER] NaN and asterisks error in md.out, and mdinfo files Scott Le Grand (Wed Aug 06 2014 - 12:24:15 PDT)
    - Re: [AMBER] NaN and asterisks error in md.out, and mdinfo files Hoshin Kim (Fri Aug 08 2014 - 10:54:30 PDT)
    - Re: [AMBER] NaN and asterisks error in md.out, and mdinfo files Scott Le Grand (Sat Aug 09 2014 - 08:23:49 PDT)
    - Re: [AMBER] NaN and asterisks error in md.out, and mdinfo files Hoshin Kim (Mon Aug 11 2014 - 09:52:46 PDT)
[AMBER] mmpbsa on charged sytem Mary Varughese (Tue Aug 05 2014 - 00:19:26 PDT)
- Re: [AMBER] mmpbsa on charged sytem Brian Radak (Tue Aug 05 2014 - 07:42:00 PDT)
- Re: [AMBER] mmpbsa on charged sytem Thomas Cheatham (Tue Aug 05 2014 - 08:24:41 PDT)
  - Re: [AMBER] mmpbsa on charged sytem Alessandro Contini (Tue Aug 05 2014 - 09:04:49 PDT)
[AMBER] Visualyze avg structure in VMD Valentina Romano (Tue Aug 05 2014 - 03:23:16 PDT)
- Re: [AMBER] Visualyze avg structure in VMD Marc van der Kamp (Tue Aug 05 2014 - 03:39:44 PDT)
- Re: [AMBER] Visualyze avg structure in VMD Daniel Roe (Tue Aug 05 2014 - 05:33:58 PDT)
[AMBER] Hydrogen bond analysis menwer momo (Tue Aug 05 2014 - 04:45:35 PDT)
- Re: [AMBER] Hydrogen bond analysis David A Case (Tue Aug 05 2014 - 08:50:30 PDT)
[AMBER] SCF convergence failed during QMMM Muthukumaran R (Tue Aug 05 2014 - 09:23:55 PDT)
- Re: [AMBER] SCF convergence failed during QMMM Brian Radak (Tue Aug 05 2014 - 11:12:00 PDT)
  - Re: [AMBER] SCF convergence failed during QMMM Muthukumaran R (Tue Aug 05 2014 - 21:55:39 PDT)
    - Re: [AMBER] SCF convergence failed during QMMM Brian Radak (Wed Aug 06 2014 - 06:32:58 PDT)
[AMBER] problem with chamber & vmd generated psf (line 2349 of file psfprm.F90) Marc van der Kamp (Tue Aug 05 2014 - 09:27:19 PDT)
- Re: [AMBER] problem with chamber & vmd generated psf (line 2349 of file psfprm.F90) Jason Swails (Tue Aug 05 2014 - 12:30:45 PDT)
  - Re: [AMBER] problem with chamber & vmd generated psf (line 2349 of file psfprm.F90) Marc van der Kamp (Wed Aug 06 2014 - 00:39:39 PDT)
    - Re: [AMBER] problem with chamber & vmd generated psf (line 2349 of file psfprm.F90) Marc van der Kamp (Wed Aug 06 2014 - 00:55:07 PDT)
    - Re: [AMBER] problem with chamber & vmd generated psf (line 2349 of file psfprm.F90) Sarah Witzke (Wed Aug 06 2014 - 04:50:14 PDT)
    - Re: [AMBER] problem with chamber & vmd generated psf (line 2349 of file psfprm.F90) Marc van der Kamp (Wed Aug 06 2014 - 05:01:25 PDT)
    - Re: [AMBER] problem with chamber & vmd generated psf (line 2349 of file psfprm.F90) Sarah Witzke (Wed Aug 06 2014 - 08:27:08 PDT)
    - Re: [AMBER] problem with chamber & vmd generated psf (line 2349 of file psfprm.F90) Robin Betz (Wed Aug 06 2014 - 08:50:34 PDT)
    - Re: [AMBER] problem with chamber & vmd generated psf (line 2349 of file psfprm.F90) Marc van der Kamp (Wed Aug 06 2014 - 09:06:34 PDT)
    - Re: [AMBER] problem with chamber & vmd generated psf (line 2349 of file psfprm.F90) Jason Swails (Wed Aug 06 2014 - 09:18:46 PDT)
    - Re: [AMBER] problem with chamber & vmd generated psf (line 2349 of file psfprm.F90) Marc van der Kamp (Thu Aug 07 2014 - 04:53:23 PDT)
    - Re: [AMBER] problem with chamber & vmd generated psf (line 2349 of file psfprm.F90) Jason Swails (Thu Aug 07 2014 - 08:27:07 PDT)
    - Re: [AMBER] problem with chamber & vmd generated psf (line 2349 of file psfprm.F90) Marc van der Kamp (Thu Aug 07 2014 - 08:58:12 PDT)
    - Re: [AMBER] problem with chamber & vmd generated psf (line 2349 of file psfprm.F90) Jason Swails (Sat Aug 09 2014 - 14:16:29 PDT)
    - Re: [AMBER] problem with chamber & vmd generated psf (line 2349 of file psfprm.F90) Marc van der Kamp (Sun Aug 10 2014 - 14:05:36 PDT)
    - Re: [AMBER] problem with chamber & vmd generated psf (line 2349 of file psfprm.F90) Jason Swails (Sun Aug 10 2014 - 14:44:19 PDT)
    - Re: [AMBER] problem with chamber & vmd generated psf (line 2349 of file psfprm.F90) Marc van der Kamp (Mon Aug 11 2014 - 06:40:53 PDT)
    - Re: [AMBER] problem with chamber & vmd generated psf (line 2349 of file psfprm.F90) Jason Swails (Mon Aug 11 2014 - 10:37:48 PDT)
    - Re: [AMBER] problem with chamber & vmd generated psf (line 2349 of file psfprm.F90) Marc van der Kamp (Mon Aug 11 2014 - 13:14:04 PDT)
    - Re: [AMBER] problem with chamber & vmd generated psf (line 2349 of file psfprm.F90) Jason Swails (Mon Aug 11 2014 - 19:37:48 PDT)
    - Re: [AMBER] problem with chamber & vmd generated psf (line 2349 of file psfprm.F90) Marc van der Kamp (Mon Aug 11 2014 - 22:50:03 PDT)
    - Re: [AMBER] problem with chamber & vmd generated psf (line 2349 of file psfprm.F90) Jason Swails (Tue Aug 12 2014 - 04:52:09 PDT)
    - Re: [AMBER] problem with chamber & vmd generated psf (line 2349 of file psfprm.F90) Marc van der Kamp (Tue Aug 12 2014 - 05:43:11 PDT)
    - Re: [AMBER] problem with chamber & vmd generated psf (line 2349 of file psfprm.F90) Jason Swails (Tue Aug 12 2014 - 07:16:06 PDT)
    - Re: [AMBER] problem with chamber & vmd generated psf (line 2349 of file psfprm.F90) Marc van der Kamp (Tue Aug 12 2014 - 09:20:13 PDT)
    - [AMBER] problem with chamber & vmd generated psf (line 2349 of file psfprm.F90) Jason Swails (Tue Aug 12 2014 - 13:36:59 PDT)
    - [AMBER] Fwd: problem with chamber & vmd generated psf (line 2349 of file psfprm.F90) Sarah Witzke (Thu Aug 14 2014 - 09:31:16 PDT)
    - Re: [AMBER] Fwd: problem with chamber & vmd generated psf (line 2349 of file psfprm.F90) Jason Swails (Thu Aug 14 2014 - 09:48:09 PDT)
    - Re: [AMBER] problem with chamber & vmd generated psf (line 2349 of file psfprm.F90) Sarah Witzke (Thu Aug 14 2014 - 10:09:14 PDT)
    - Re: [AMBER] problem with chamber & vmd generated psf (line 2349 of file psfprm.F90) Jason Swails (Thu Aug 14 2014 - 10:37:46 PDT)
    - Re: [AMBER] problem with chamber & vmd generated psf (line 2349 of file psfprm.F90) Jason Swails (Wed Aug 06 2014 - 09:17:47 PDT)
    - Re: [AMBER] problem with chamber & vmd generated psf (line 2349 of file psfprm.F90) Jason Swails (Wed Aug 06 2014 - 08:44:59 PDT)
- Re: [AMBER] problem with chamber & vmd generated psf (line 2349 of file psfprm.F90) Sarah Witzke (Wed Aug 06 2014 - 11:30:09 PDT)
  - Re: [AMBER] problem with chamber & vmd generated psf (line 2349 of file psfprm.F90) Jason Swails (Wed Aug 06 2014 - 11:54:34 PDT)
    - Re: [AMBER] problem with chamber & vmd generated psf (line 2349 of file psfprm.F90) Sarah Witzke (Wed Aug 06 2014 - 13:56:24 PDT)
[AMBER] Converting (rst) file to PDB using ambpdb menwer momo (Tue Aug 05 2014 - 13:40:11 PDT)
- Re: [AMBER] Converting (rst) file to PDB using ambpdb Jason Swails (Tue Aug 05 2014 - 14:57:48 PDT)
  - Re: [AMBER] Converting (rst) file to PDB using ambpdb menwer momo (Tue Aug 05 2014 - 15:23:33 PDT)
- Re: [AMBER] Converting (rst) file to PDB using ambpdb Bill Ross (Tue Aug 05 2014 - 15:18:52 PDT)
  - Re: [AMBER] Converting (rst) file to PDB using ambpdb menwer momo (Tue Aug 05 2014 - 15:24:44 PDT)
  - Re: [AMBER] Converting (rst) file to PDB using ambpdb Soumendranath Bhakat (Wed Aug 06 2014 - 01:48:25 PDT)
[AMBER] Memory keyword for QM/MM using ORCA Kshatresh Dutta Dubey (Wed Aug 06 2014 - 00:43:53 PDT)
[AMBER] help in analysis Robin Jain (Wed Aug 06 2014 - 02:44:16 PDT)
- Re: [AMBER] help in analysis Daniel Roe (Wed Aug 06 2014 - 07:55:05 PDT)
[AMBER] help in analysis Robin Jain (Wed Aug 06 2014 - 02:44:16 PDT)
[AMBER] Cluster results Valentina Romano (Wed Aug 06 2014 - 05:22:41 PDT)
- Re: [AMBER] Cluster results Brian Radak (Wed Aug 06 2014 - 06:37:44 PDT)
  - Re: [AMBER] Cluster results Valentina Romano (Wed Aug 06 2014 - 07:27:40 PDT)
    - Re: [AMBER] Cluster results Daniel Roe (Wed Aug 06 2014 - 08:09:23 PDT)
    - Re: [AMBER] Cluster results Valentina Romano (Thu Aug 07 2014 - 01:34:00 PDT)
    - Re: [AMBER] Cluster results Daniel Roe (Thu Aug 07 2014 - 07:18:09 PDT)
    - Re: [AMBER] Cluster results Valentina Romano (Fri Aug 08 2014 - 04:42:49 PDT)
    - Re: [AMBER] Cluster results Daniel Roe (Fri Aug 08 2014 - 06:56:34 PDT)
    - Re: [AMBER] Cluster results Valentina Romano (Fri Aug 08 2014 - 07:10:02 PDT)
    - Re: [AMBER] Cluster results Daniel Roe (Fri Aug 08 2014 - 07:25:36 PDT)
    - Re: [AMBER] Cluster results Valentina Romano (Fri Aug 08 2014 - 07:30:39 PDT)
    - Re: [AMBER] Cluster results Daniel Roe (Fri Aug 08 2014 - 07:35:53 PDT)
    - Re: [AMBER] Cluster results Jason Swails (Fri Aug 08 2014 - 07:40:15 PDT)
    - Re: [AMBER] Cluster results Daniel Roe (Fri Aug 08 2014 - 08:00:52 PDT)
    - Re: [AMBER] Cluster results Valentina Romano (Mon Aug 11 2014 - 03:13:24 PDT)
    - Re: [AMBER] Cluster results Daniel Roe (Mon Aug 11 2014 - 09:02:22 PDT)
    - Re: [AMBER] Cluster results Valentina Romano (Wed Aug 13 2014 - 05:59:34 PDT)
    - Re: [AMBER] Cluster results Marc van der Kamp (Wed Aug 13 2014 - 06:22:03 PDT)
    - Re: [AMBER] Cluster results Valentina Romano (Wed Aug 13 2014 - 07:25:31 PDT)
    - Re: [AMBER] Cluster results Daniel Roe (Fri Aug 15 2014 - 13:06:39 PDT)
    - Re: [AMBER] Cluster results Thomas Cheatham (Wed Aug 06 2014 - 11:28:34 PDT)
[AMBER] Adding new Bondi radii for mmpbsa Sergey Samsonov (Wed Aug 06 2014 - 07:18:39 PDT)
- Re: [AMBER] Adding new Bondi radii for mmpbsa Jason Swails (Wed Aug 06 2014 - 09:35:12 PDT)
  - Re: [AMBER] Adding new Bondi radii for mmpbsa Sergey Samsonov (Wed Aug 06 2014 - 23:46:43 PDT)
[AMBER] Fwd: Unable to generate RESP charges for a charged ligand Manikanthan Bhavaraju (Wed Aug 06 2014 - 07:36:44 PDT)
[AMBER] SQM error while preparing ATP with antechamber Hirdesh Kumar (Wed Aug 06 2014 - 07:47:54 PDT)
- Re: [AMBER] SQM error while preparing ATP with antechamber David A Case (Wed Aug 06 2014 - 09:04:30 PDT)
[AMBER] Questions for pH-REMD by Jason Swails M Olivia Kim (Wed Aug 06 2014 - 10:43:35 PDT)
- Re: [AMBER] Questions for pH-REMD by Jason Swails Brian Radak (Wed Aug 06 2014 - 11:40:17 PDT)
[AMBER] Question concerning a torsion parameter Mohammad Salem (Wed Aug 06 2014 - 17:26:29 PDT)
- Re: [AMBER] Question concerning a torsion parameter Mohammad Salem (Wed Aug 06 2014 - 17:35:47 PDT)
  - Re: [AMBER] Question concerning a torsion parameter Ross Walker (Wed Aug 06 2014 - 18:42:58 PDT)
    - Re: [AMBER] Question concerning a torsion parameter Mohammad Salem (Wed Aug 06 2014 - 21:47:53 PDT)
    - Re: [AMBER] Question concerning a torsion parameter Ross Walker (Thu Aug 07 2014 - 10:23:09 PDT)
    - Re: [AMBER] Question concerning a torsion parameter Mohammad Salem (Thu Aug 07 2014 - 12:14:58 PDT)
- Re: [AMBER] Question concerning a torsion parameter David A Case (Wed Aug 06 2014 - 20:55:52 PDT)
[AMBER] Percent occupancy of a hydrogen bond menwer momo (Thu Aug 07 2014 - 05:00:46 PDT)
- Re: [AMBER] Percent occupancy of a hydrogen bond Jason Swails (Thu Aug 07 2014 - 08:32:05 PDT)
  - Re: [AMBER] Percent occupancy of a hydrogen bond menwer momo (Thu Aug 07 2014 - 08:40:44 PDT)
[AMBER] Fwd: problem with chamber & vmd generated psf (line 2349 of file psfprm.F90) Sarah Witzke (Thu Aug 07 2014 - 09:11:48 PDT)
[AMBER] significance of attaching a dummy atom in smd Asmita Gupta (Thu Aug 07 2014 - 10:32:12 PDT)
- Re: [AMBER] significance of attaching a dummy atom in smd Jason Swails (Thu Aug 07 2014 - 10:52:20 PDT)
[AMBER] unfolding molecule after heating Annika Wittenbecher (Thu Aug 07 2014 - 21:14:51 PDT)
[AMBER] unfolding molecule after heating Annika Wittenbecher (Thu Aug 07 2014 - 22:16:03 PDT)
- Re: [AMBER] unfolding molecule after heating Ross Walker (Thu Aug 07 2014 - 22:33:47 PDT)
  - Re: [AMBER] unfolding molecule after heating Ross Walker (Thu Aug 07 2014 - 22:35:15 PDT)
[AMBER] chamber prmtop with changed LJ parameters not accepted by pmemd.cuda? Marc van der Kamp (Fri Aug 08 2014 - 04:12:44 PDT)
- Re: [AMBER] chamber prmtop with changed LJ parameters not accepted by pmemd.cuda? Jason Swails (Fri Aug 08 2014 - 06:25:48 PDT)
- Re: [AMBER] chamber prmtop with changed LJ parameters not accepted by pmemd.cuda? Ross Walker (Fri Aug 08 2014 - 08:49:31 PDT)
[AMBER] Principal Component/Kullback-Leibler Analysis Jonathan Gough (Fri Aug 08 2014 - 09:17:26 PDT)
- Re: [AMBER] Principal Component/Kullback-Leibler Analysis Daniel Roe (Fri Aug 08 2014 - 09:41:55 PDT)
  - Re: [AMBER] Principal Component/Kullback-Leibler Analysis Jonathan Gough (Tue Aug 12 2014 - 10:47:19 PDT)
    - Re: [AMBER] Principal Component/Kullback-Leibler Analysis Daniel Roe (Tue Aug 12 2014 - 12:06:30 PDT)
    - Re: [AMBER] Principal Component/Kullback-Leibler Analysis Jonathan Gough (Tue Aug 12 2014 - 12:17:11 PDT)
    - Re: [AMBER] Principal Component/Kullback-Leibler Analysis Daniel Roe (Tue Aug 12 2014 - 12:33:12 PDT)
    - Re: [AMBER] Principal Component/Kullback-Leibler Analysis Jonathan Gough (Tue Aug 12 2014 - 12:47:50 PDT)
[AMBER] New CPPTRAJ Tutorials Daniel Roe (Fri Aug 08 2014 - 12:49:19 PDT)
[AMBER] cpptraj.MPI running in 'ensemble' mode. Jonathan Gough (Sat Aug 09 2014 - 11:28:41 PDT)
- Re: [AMBER] cpptraj.MPI running in 'ensemble' mode. Jonathan Gough (Sat Aug 09 2014 - 11:31:47 PDT)
- Re: [AMBER] cpptraj.MPI running in 'ensemble' mode. Jason Swails (Sat Aug 09 2014 - 11:55:14 PDT)
  - Re: [AMBER] cpptraj.MPI running in 'ensemble' mode. Jonathan Gough (Sat Aug 09 2014 - 12:53:24 PDT)
  - Re: [AMBER] cpptraj.MPI running in 'ensemble' mode. Daniel Roe (Sat Aug 09 2014 - 15:54:26 PDT)
[AMBER] Performance of RuBisCo (74, 916) atoms on NVIDIA Tesla K40 GPU Amit Harode (Mon Aug 11 2014 - 05:34:30 PDT)
- Re: [AMBER] Performance of RuBisCo (74, 916) atoms on NVIDIA Tesla K40 GPU Ross Walker (Mon Aug 11 2014 - 10:08:16 PDT)
  - Re: [AMBER] Performance of RuBisCo (74, 916) atoms on NVIDIA Tesla K40 GPU Amit Harode (Tue Aug 12 2014 - 00:03:04 PDT)
    - Re: [AMBER] Performance of RuBisCo (74, 916) atoms on NVIDIA Tesla K40 GPU David A Case (Tue Aug 12 2014 - 07:37:30 PDT)
    - Re: [AMBER] Performance of RuBisCo (74, 916) atoms on NVIDIA Tesla K40 GPU Gerald Monard (Wed Aug 13 2014 - 12:36:08 PDT)
[AMBER] Antechamber Error: Cannot open file CORR_NAME_TYPE.DAT, exit Andy Tsai (Mon Aug 11 2014 - 16:41:42 PDT)
- Re: [AMBER] Antechamber Error: Cannot open file CORR_NAME_TYPE.DAT, exit David A Case (Mon Aug 11 2014 - 17:43:19 PDT)
[AMBER] Minimization and equilibration with SANDER.MPI and production with PMEMD.cuda ?? Hirdesh Kumar (Tue Aug 12 2014 - 07:09:58 PDT)
- Re: [AMBER] Minimization and equilibration with SANDER.MPI and production with PMEMD.cuda ?? Jason Swails (Tue Aug 12 2014 - 07:17:48 PDT)
  - Re: [AMBER] Minimization and equilibration with SANDER.MPI and production with PMEMD.cuda ?? Hirdesh Kumar (Tue Aug 12 2014 - 07:30:30 PDT)
    - Re: [AMBER] Minimization and equilibration with SANDER.MPI and production with PMEMD.cuda ?? Hirdesh Kumar (Tue Aug 12 2014 - 07:45:57 PDT)
    - Re: [AMBER] Minimization and equilibration with SANDER.MPI and production with PMEMD.cuda ?? Jason Swails (Tue Aug 12 2014 - 09:15:24 PDT)
[AMBER] build branched polymer in leap? Sally Pias (Tue Aug 12 2014 - 16:32:59 PDT)
- Re: [AMBER] build branched polymer in leap? Jason Swails (Tue Aug 12 2014 - 19:51:35 PDT)
[AMBER] error: "STOP PMEMD terminated abnormally" Chinh Su Tran To (Wed Aug 13 2014 - 00:06:48 PDT)
- Re: [AMBER] error: "STOP PMEMD terminated abnormally" David A Case (Wed Aug 13 2014 - 07:51:32 PDT)
  - Re: [AMBER] error: "STOP PMEMD terminated abnormally" Hirdesh Kumar (Wed Aug 13 2014 - 08:57:00 PDT)
    - Re: [AMBER] error: "STOP PMEMD terminated abnormally" Jason Swails (Wed Aug 13 2014 - 09:15:50 PDT)
    - Re: [AMBER] error: "STOP PMEMD terminated abnormally" Hirdesh Kumar (Wed Aug 13 2014 - 13:15:40 PDT)
    - Re: [AMBER] error: "STOP PMEMD terminated abnormally" Hirdesh Kumar (Wed Aug 13 2014 - 13:18:26 PDT)
[AMBER] amber/gaussian find the transition state 王珍 (Wed Aug 13 2014 - 02:03:19 PDT)
- Re: [AMBER] amber/gaussian find the transition state Jason Swails (Wed Aug 13 2014 - 05:07:08 PDT)
[AMBER] Parameters for ATP and MG2+ Valentina Romano (Wed Aug 13 2014 - 07:56:32 PDT)
- Re: [AMBER] Parameters for ATP and MG2+ Jason Swails (Wed Aug 13 2014 - 09:24:23 PDT)
[AMBER] ATP and MG2+prep and frcmod files Valentina Romano (Wed Aug 13 2014 - 08:28:27 PDT)
- Re: [AMBER] ATP and MG2+prep and frcmod files Jason Swails (Wed Aug 13 2014 - 09:21:34 PDT)
  - Re: [AMBER] ATP and MG2+prep and frcmod files Valentina Romano (Thu Aug 14 2014 - 00:59:39 PDT)
    - Re: [AMBER] ATP and MG2+prep and frcmod files Jason Swails (Thu Aug 14 2014 - 05:15:31 PDT)
[AMBER] Very high values of Diffusion coefficient of water DEBOSTUTI GHOSHDASTIDAR (Wed Aug 13 2014 - 22:09:52 PDT)
- Re: [AMBER] Very high values of Diffusion coefficient of water Daniel Roe (Fri Aug 15 2014 - 08:07:05 PDT)
  - Re: [AMBER] Very high values of Diffusion coefficient of water DEBOSTUTI GHOSHDASTIDAR (Fri Aug 15 2014 - 09:46:13 PDT)
    - Re: [AMBER] Very high values of Diffusion coefficient of water Jason Swails (Fri Aug 15 2014 - 12:27:41 PDT)
    - Re: [AMBER] Very high values of Diffusion coefficient of water DEBOSTUTI GHOSHDASTIDAR (Sat Aug 16 2014 - 02:52:13 PDT)
[AMBER] Using polarized force field lead to large RMS in the second step of minimization 张冬冬 (Thu Aug 14 2014 - 02:23:13 PDT)
- Re: [AMBER] Using polarized force field lead to large RMS in the second step of minimization David A Case (Thu Aug 14 2014 - 08:44:38 PDT)
  - Re: [AMBER] Using polarized force field lead to large RMS in the second step of minimization 张冬冬 (Fri Aug 15 2014 - 02:26:33 PDT)
    - Re: [AMBER] Using polarized force field lead to large RMS in the second step of minimization David A Case (Fri Aug 15 2014 - 07:17:16 PDT)
    - Re: [AMBER] Using polarized force field lead to large RMS in the second step of minimization 张冬冬 (Fri Aug 22 2014 - 07:56:01 PDT)
    - Re: [AMBER] Using polarized force field lead to large RMS in the second step of minimization Jason Swails (Fri Aug 22 2014 - 09:10:56 PDT)
[AMBER] Antechamber error Valentina Romano (Thu Aug 14 2014 - 02:38:24 PDT)
- Re: [AMBER] Antechamber error David A Case (Thu Aug 14 2014 - 08:47:09 PDT)
[AMBER] Help on Normal Mode Analysis xy21hb (Thu Aug 14 2014 - 07:55:12 PDT)
- Re: [AMBER] Help on Normal Mode Analysis Jason Swails (Thu Aug 14 2014 - 08:19:10 PDT)
[AMBER] Kinase and ATP MD simulation Valentina Romano (Thu Aug 14 2014 - 08:49:45 PDT)
- Re: [AMBER] Kinase and ATP MD simulation Jason Swails (Thu Aug 14 2014 - 09:18:49 PDT)
[AMBER] Dynamic selection of donor and acceptor mask for hbond analysis DEBOSTUTI GHOSHDASTIDAR (Fri Aug 15 2014 - 03:11:22 PDT)
- Re: [AMBER] Dynamic selection of donor and acceptor mask for hbond analysis Daniel Roe (Fri Aug 15 2014 - 12:52:50 PDT)
[AMBER] errors for surf command in cpptraj Wei Chen (Fri Aug 15 2014 - 09:50:07 PDT)
- Re: [AMBER] errors for surf command in cpptraj Daniel Roe (Fri Aug 15 2014 - 10:47:39 PDT)
  - Re: [AMBER] errors for surf command in cpptraj Wei Chen (Fri Aug 15 2014 - 12:58:49 PDT)
    - Re: [AMBER] errors for surf command in cpptraj Daniel Roe (Fri Aug 15 2014 - 13:15:32 PDT)
[AMBER] restraints with natural language Hugo Azurmendi (Fri Aug 15 2014 - 12:11:21 PDT)
- Re: [AMBER] restraints with natural language Jason Swails (Fri Aug 15 2014 - 12:33:22 PDT)
  - Re: [AMBER] restraints with natural language Hugo Azurmendi (Fri Aug 15 2014 - 13:06:53 PDT)
    - Re: [AMBER] restraints with natural language Jason Swails (Fri Aug 15 2014 - 15:49:46 PDT)
[AMBER] Calculating electrostatic potential in cpptraj Covington, Cody Lance (Fri Aug 15 2014 - 13:21:41 PDT)
- Re: [AMBER] Calculating electrostatic potential in cpptraj Jason Swails (Fri Aug 15 2014 - 17:00:46 PDT)
  - Re: [AMBER] Calculating electrostatic potential in cpptraj Covington, Cody Lance (Sat Aug 16 2014 - 13:11:24 PDT)
  - Re: [AMBER] Calculating electrostatic potential in cpptraj Covington, Cody Lance (Sat Aug 16 2014 - 13:20:42 PDT)
    - Re: [AMBER] Calculating electrostatic potential in cpptraj Jason Swails (Sat Aug 16 2014 - 18:05:24 PDT)
[AMBER] bad atom type o Hallel Freedman (Sun Aug 17 2014 - 15:42:38 PDT)
- Re: [AMBER] bad atom type o Jason Swails (Mon Aug 18 2014 - 04:14:45 PDT)
  - Re: [AMBER] bad atom type o Hallel Freedman (Mon Aug 18 2014 - 09:58:58 PDT)
    - Re: [AMBER] bad atom type o Hallel Freedman (Wed Aug 20 2014 - 09:44:45 PDT)
    - Re: [AMBER] bad atom type o Jason Swails (Wed Aug 20 2014 - 09:56:15 PDT)
    - Re: [AMBER] bad atom type o Hallel Freedman (Wed Aug 20 2014 - 10:24:05 PDT)
    - Re: [AMBER] bad atom type o Jason Swails (Wed Aug 20 2014 - 10:31:53 PDT)
    - Re: [AMBER] bad atom type o Hallel Freedman (Wed Aug 20 2014 - 10:37:57 PDT)
    - Re: [AMBER] bad atom type o Jason Swails (Wed Aug 20 2014 - 10:41:31 PDT)
    - Re: [AMBER] bad atom type o Hallel Freedman (Wed Aug 20 2014 - 10:56:47 PDT)
    - Re: [AMBER] bad atom type o Hallel Freedman (Wed Aug 20 2014 - 12:17:40 PDT)
    - Re: [AMBER] bad atom type o Jason Swails (Wed Aug 20 2014 - 14:08:56 PDT)
    - Re: [AMBER] bad atom type o Hallel Freedman (Wed Aug 20 2014 - 14:11:11 PDT)
    - Re: [AMBER] bad atom type o Jason Swails (Wed Aug 20 2014 - 14:26:42 PDT)
    - Re: [AMBER] bad atom type o Hallel Freedman (Wed Aug 20 2014 - 14:36:51 PDT)
    - Re: [AMBER] bad atom type o Jason Swails (Wed Aug 20 2014 - 15:34:43 PDT)
[AMBER] nmode for chamber prmtop Wei Chen (Mon Aug 18 2014 - 07:01:01 PDT)
- Re: [AMBER] nmode for chamber prmtop David A Case (Mon Aug 18 2014 - 07:26:57 PDT)
[AMBER] QM/MM in Amber Muthukumaran R (Mon Aug 18 2014 - 10:12:00 PDT)
- Re: [AMBER] QM/MM in Amber Brian Radak (Mon Aug 18 2014 - 11:13:21 PDT)
- Re: [AMBER] QM/MM in Amber Dr. Vitaly Chaban (Mon Aug 18 2014 - 12:47:46 PDT)
[AMBER] perl script to convert GIST output to .dx file DEBOSTUTI GHOSHDASTIDAR (Mon Aug 18 2014 - 11:11:13 PDT)
- Re: [AMBER] perl script to convert GIST output to .dx file Nguyen, Crystal (Mon Aug 18 2014 - 11:23:04 PDT)
  - Re: [AMBER] perl script to convert GIST output to .dx file DEBOSTUTI GHOSHDASTIDAR (Mon Aug 18 2014 - 21:45:29 PDT)
[AMBER] How to visualize PCA Tamara Meirelles (Mon Aug 18 2014 - 18:08:39 PDT)
- Re: [AMBER] How to visualize PCA Daniel Roe (Mon Aug 18 2014 - 20:11:24 PDT)
[AMBER] 10 Error on OPEN: ANTECHAMBER.ESP 전선희 (Mon Aug 18 2014 - 23:17:38 PDT)
- Re: [AMBER] 10 Error on OPEN: ANTECHAMBER.ESP FyD (Tue Aug 19 2014 - 04:43:04 PDT)
- Re: [AMBER] 10 Error on OPEN: ANTECHAMBER.ESP Jason Swails (Tue Aug 19 2014 - 04:56:51 PDT)
- Re: [AMBER] 10 Error on OPEN: ANTECHAMBER.ESP David A Case (Tue Aug 19 2014 - 04:55:08 PDT)
[AMBER] Calculating lipid diffusion using mass weighted feature Vijay Manickam Achari (Tue Aug 19 2014 - 00:02:09 PDT)
[AMBER] principal axes calculation in ptraj Asmita Gupta (Tue Aug 19 2014 - 02:12:48 PDT)
- Re: [AMBER] principal axes calculation in ptraj Daniel Roe (Tue Aug 19 2014 - 07:50:28 PDT)
  - Re: [AMBER] principal axes calculation in ptraj Asmita Gupta (Wed Aug 20 2014 - 00:45:37 PDT)
    - Re: [AMBER] principal axes calculation in ptraj Daniel Roe (Wed Aug 20 2014 - 07:11:37 PDT)
[AMBER] PCA projection de Manzanos Guinot, Angela (Tue Aug 19 2014 - 02:52:42 PDT)
- Re: [AMBER] PCA projection Daniel Roe (Tue Aug 19 2014 - 07:32:32 PDT)
[AMBER] Question on Updating AMBER Gulsevin,Alican (Tue Aug 19 2014 - 05:18:58 PDT)
- Re: [AMBER] Question on Updating AMBER Jason Swails (Tue Aug 19 2014 - 05:51:45 PDT)
  - Re: [AMBER] Question on Updating AMBER Gulsevin,Alican (Tue Aug 19 2014 - 08:42:34 PDT)
    - Re: [AMBER] Question on Updating AMBER Jason Swails (Tue Aug 19 2014 - 09:16:24 PDT)
[AMBER] puckering of 6 member ring Lara rajam (Tue Aug 19 2014 - 06:06:31 PDT)
- Re: [AMBER] puckering of 6 member ring Jason Swails (Tue Aug 19 2014 - 07:11:17 PDT)
[AMBER] Calculating lipid diffusion Vijyan Achari (Tue Aug 19 2014 - 19:07:36 PDT)
- Re: [AMBER] Calculating lipid diffusion Daniel Roe (Wed Aug 20 2014 - 07:57:14 PDT)
[AMBER] antechamber 闫玉娜 (Tue Aug 19 2014 - 19:31:10 PDT)
- Re: [AMBER] antechamber Ying-Chieh Sun (Tue Aug 19 2014 - 21:06:29 PDT)
- Re: [AMBER] antechamber Jason Swails (Wed Aug 20 2014 - 04:41:36 PDT)
  - Re: [AMBER] antechamber Mark Williamson (Wed Aug 20 2014 - 05:04:48 PDT)
  - Re: [AMBER] antechamber 闫玉娜 (Wed Aug 20 2014 - 05:21:26 PDT)
    - Re: [AMBER] antechamber 闫玉娜 (Thu Aug 21 2014 - 06:52:51 PDT)
    - Re: [AMBER] antechamber Jason Swails (Thu Aug 21 2014 - 07:18:02 PDT)
    - Re: [AMBER] antechamber David A Case (Thu Aug 21 2014 - 07:42:54 PDT)
[AMBER] Problem with Firefly optimisation in R.E.D server George Patargias (Wed Aug 20 2014 - 02:06:44 PDT)
[AMBER] Contacts Sourav Purohit (Wed Aug 20 2014 - 05:22:07 PDT)
- Re: [AMBER] Contacts Jason Swails (Wed Aug 20 2014 - 05:34:54 PDT)
  - Re: [AMBER] Contacts Sourav Purohit (Wed Aug 20 2014 - 06:14:30 PDT)
    - Re: [AMBER] Contacts Jason Swails (Wed Aug 20 2014 - 06:58:32 PDT)
    - Re: [AMBER] Contacts Sourav Purohit (Wed Aug 20 2014 - 07:26:04 PDT)
    - Re: [AMBER] Contacts Daniel Roe (Wed Aug 20 2014 - 08:23:06 PDT)
    - Re: [AMBER] Contacts Sourav Purohit (Wed Aug 20 2014 - 09:56:12 PDT)
[AMBER] ATTN NEED REVISION error - reg Radhika Swathi (Wed Aug 20 2014 - 10:49:45 PDT)
- Re: [AMBER] ATTN NEED REVISION error - reg Jason Swails (Wed Aug 20 2014 - 11:07:35 PDT)
[AMBER] Parametrization of glycerol and desoxycorticosterone BATUHAN KAV (Wed Aug 20 2014 - 10:54:56 PDT)
[AMBER] Parametrization of glycerol and desoxycorticosterone BATUHAN KAV (Wed Aug 20 2014 - 10:59:16 PDT)
- Re: [AMBER] Parametrization of glycerol and desoxycorticosterone Jason Swails (Wed Aug 20 2014 - 11:21:51 PDT)
- Re: [AMBER] Parametrization of glycerol and desoxycorticosterone David A Case (Wed Aug 20 2014 - 11:32:57 PDT)
[AMBER] positive free energy zahra khatti (Wed Aug 20 2014 - 11:11:29 PDT)
- Re: [AMBER] positive free energy Jason Swails (Wed Aug 20 2014 - 11:34:17 PDT)
  - Re: [AMBER] positive free energy Ray Luo, Ph.D. (Wed Aug 20 2014 - 11:59:23 PDT)
  - Re: [AMBER] positive free energy Ray Luo, Ph.D. (Wed Aug 20 2014 - 12:21:13 PDT)
    - Re: [AMBER] positive free energy Vlad Cojocaru (Wed Aug 20 2014 - 13:29:06 PDT)
    - Re: [AMBER] positive free energy Vlad Cojocaru (Wed Aug 20 2014 - 13:32:03 PDT)
    - Re: [AMBER] positive free energy Jason Swails (Wed Aug 20 2014 - 14:36:44 PDT)
    - Re: [AMBER] positive free energy Vlad Cojocaru (Wed Aug 20 2014 - 14:45:26 PDT)
    - Re: [AMBER] positive free energy Jason Swails (Wed Aug 20 2014 - 15:29:46 PDT)
    - Re: [AMBER] positive free energy Ray Luo, Ph.D. (Wed Aug 20 2014 - 17:03:02 PDT)
- Re: [AMBER] positive free energy David A Case (Wed Aug 20 2014 - 11:48:37 PDT)
[AMBER] antechamber parametrization of desoxycorticosterone BATUHAN KAV (Thu Aug 21 2014 - 05:59:39 PDT)
- Re: [AMBER] antechamber parametrization of desoxycorticosterone Jason Swails (Thu Aug 21 2014 - 06:26:13 PDT)
- Re: [AMBER] antechamber parametrization of desoxycorticosterone David A Case (Thu Aug 21 2014 - 06:30:08 PDT)
- Re: [AMBER] antechamber parametrization of desoxycorticosterone Jason Swails (Fri Aug 22 2014 - 04:20:00 PDT)
[AMBER] antechamber parametrization of desoxycorticosterone BATUHAN KAV (Thu Aug 21 2014 - 06:14:41 PDT)
- Re: [AMBER] antechamber parametrization of desoxycorticosterone Jason Swails (Thu Aug 21 2014 - 06:26:58 PDT)
[AMBER] Using iwrap with a dimer Caitlin Scott (Thu Aug 21 2014 - 06:45:28 PDT)
- Re: [AMBER] Using iwrap with a dimer Daniel Roe (Thu Aug 21 2014 - 06:52:02 PDT)
[AMBER] clustering Lara rajam (Thu Aug 21 2014 - 10:27:07 PDT)
- Re: [AMBER] clustering David A Case (Thu Aug 21 2014 - 11:14:47 PDT)
[AMBER] Using setbox command to prepare files for Umbrella Sampling George Green (Thu Aug 21 2014 - 12:28:45 PDT)
- Re: [AMBER] Using setbox command to prepare files for Umbrella Sampling David A Case (Thu Aug 21 2014 - 13:08:57 PDT)
  - Re: [AMBER] Using setbox command to prepare files for Umbrella Sampling George Green (Fri Aug 22 2014 - 10:25:21 PDT)
    - Re: [AMBER] Using setbox command to prepare files for Umbrella Sampling David A Case (Fri Aug 22 2014 - 10:54:32 PDT)
    - Re: [AMBER] Using setbox command to prepare files for Umbrella Sampling George Green (Tue Aug 26 2014 - 10:58:46 PDT)
    - Re: [AMBER] Using setbox command to prepare files for Umbrella Sampling Daniel Roe (Tue Aug 26 2014 - 11:35:28 PDT)
    - Re: [AMBER] Using setbox command to prepare files for Umbrella Sampling Brian Radak (Tue Aug 26 2014 - 11:41:26 PDT)
    - Re: [AMBER] Using setbox command to prepare files for Umbrella Sampling Jason Swails (Tue Aug 26 2014 - 12:09:24 PDT)
    - Re: [AMBER] Using setbox command to prepare files for Umbrella Sampling George Green (Wed Aug 27 2014 - 13:16:18 PDT)
[AMBER] MCPB and sidechain.bcl problem 高彧辉 (Fri Aug 22 2014 - 05:55:30 PDT)
- Re: [AMBER] MCPB and sidechain.bcl problem Pengfei Li (Sat Aug 23 2014 - 05:34:24 PDT)
  - Re: [AMBER] MCPB and sidechain.bcl problem Chris Gao (Sun Aug 24 2014 - 04:21:10 PDT)
    - Re: [AMBER] MCPB and sidechain.bcl problem Pengfei Li (Mon Aug 25 2014 - 06:26:37 PDT)
    - Re: [AMBER] MCPB and sidechain.bcl problem Chris Gao (Mon Aug 25 2014 - 20:32:23 PDT)
    - Re: [AMBER] MCPB and sidechain.bcl problem Pengfei Li (Tue Aug 26 2014 - 12:05:58 PDT)
    - Re: [AMBER] MCPB and sidechain.bcl problem 高彧辉 (Tue Aug 26 2014 - 22:33:23 PDT)
    - Re: [AMBER] MCPB and sidechain.bcl problem Pengfei Li (Wed Aug 27 2014 - 07:47:14 PDT)
[AMBER] Testing of the convergence by means of PCA James Starlight (Fri Aug 22 2014 - 10:00:13 PDT)
[AMBER] Implicit solvent simulation study Bajarang Kumbhar (Sat Aug 23 2014 - 22:42:54 PDT)
- Re: [AMBER] Implicit solvent simulation study Jason Swails (Sun Aug 24 2014 - 07:12:27 PDT)
- Re: [AMBER] Implicit solvent simulation study Carlos Simmerling (Sun Aug 24 2014 - 08:06:47 PDT)
Re: [AMBER] AMBER Digest, Vol 956, Issue 1 Bajarang Kumbhar (Sun Aug 24 2014 - 23:32:02 PDT)
[AMBER] Error in making and running xleap ammarah.ghaffar.comsats.edu.pk (Mon Aug 25 2014 - 02:25:46 PDT)
- Re: [AMBER] Error in making and running xleap David A Case (Mon Aug 25 2014 - 05:01:04 PDT)
  - Re: [AMBER] Error in making and running xleap ammarah.ghaffar.comsats.edu.pk (Tue Aug 26 2014 - 01:16:09 PDT)
    - Re: [AMBER] Error in making and running xleap Jason Swails (Tue Aug 26 2014 - 04:30:45 PDT)
[AMBER] Implicit solvation method: problem with the rst file M.Venkata Satish Kumar (Mon Aug 25 2014 - 04:08:51 PDT)
- Re: [AMBER] Implicit solvation method: problem with the rst file Jason Swails (Mon Aug 25 2014 - 04:33:41 PDT)
  - Re: [AMBER] Implicit solvation method: problem with the rst file M.Venkata Satish Kumar (Mon Aug 25 2014 - 04:54:52 PDT)
    - Re: [AMBER] Implicit solvation method: problem with the rst file Jason Swails (Mon Aug 25 2014 - 05:10:17 PDT)
[AMBER] MMPBSA.py -nan values. Dhananjay (Mon Aug 25 2014 - 09:36:58 PDT)
- Re: [AMBER] MMPBSA.py -nan values. Jason Swails (Mon Aug 25 2014 - 10:27:02 PDT)
[AMBER] Undocumented DSSP commands and torsional analysis Eugene Yedvabny (Tue Aug 26 2014 - 00:48:53 PDT)
- Re: [AMBER] Undocumented DSSP commands and torsional analysis Daniel Roe (Tue Aug 26 2014 - 10:33:01 PDT)
[AMBER] Distance command zahra khatti (Tue Aug 26 2014 - 05:30:38 PDT)
- Re: [AMBER] Distance command zahra khatti (Tue Aug 26 2014 - 12:10:15 PDT)
- Re: [AMBER] Distance command Daniel Roe (Wed Sep 03 2014 - 08:39:09 PDT)
[AMBER] problem in understanding the K+ parameter Indrajit Deb (Tue Aug 26 2014 - 05:34:54 PDT)
- Re: [AMBER] problem in understanding the K+ parameter Jason Swails (Tue Aug 26 2014 - 06:25:33 PDT)
  - Re: [AMBER] problem in understanding the K+ parameter Indrajit Deb (Tue Aug 26 2014 - 06:28:04 PDT)
[AMBER] Triply bonded oxygen Gulsevin,Alican (Tue Aug 26 2014 - 15:21:05 PDT)
- Re: [AMBER] Triply bonded oxygen David A Case (Wed Aug 27 2014 - 05:02:51 PDT)
[AMBER] Prediction of the protonation state for the ensemble of pdb structures James Starlight (Wed Aug 27 2014 - 00:40:51 PDT)
- Re: [AMBER] Prediction of the protonation state for the ensemble of pdb structures Chris Gao (Wed Aug 27 2014 - 02:33:54 PDT)
  - Re: [AMBER] Prediction of the protonation state for the ensemble of pdb structures James Starlight (Wed Aug 27 2014 - 02:39:39 PDT)
    - Re: [AMBER] Prediction of the protonation state for the ensemble of pdb structures James Starlight (Wed Aug 27 2014 - 03:27:47 PDT)
    - Re: [AMBER] Prediction of the protonation state for the ensemble of pdb structures Chris Gao (Wed Aug 27 2014 - 05:00:57 PDT)
[AMBER] Question for residues.py to parameterize a nonstandard residue for constant pH MD M Olivia Kim (Wed Aug 27 2014 - 12:30:20 PDT)
- Re: [AMBER] Question for residues.py to parameterize a nonstandard residue for constant pH MD Jason Swails (Wed Aug 27 2014 - 14:26:55 PDT)
  - Re: [AMBER] Question for residues.py to parameterize a nonstandard residue for constant pH MD M Olivia Kim (Wed Sep 17 2014 - 11:11:32 PDT)
    - Re: [AMBER] Question for residues.py to parameterize a nonstandard residue for constant pH MD Jason Swails (Wed Sep 17 2014 - 11:40:00 PDT)
    - Re: [AMBER] Question for residues.py to parameterize a nonstandard residue for constant pH MD M Olivia Kim (Wed Sep 17 2014 - 13:00:42 PDT)
    - Re: [AMBER] Question for residues.py to parameterize a nonstandard residue for constant pH MD Levi Pierce (Sun Sep 28 2014 - 11:46:06 PDT)
    - Re: [AMBER] Question for residues.py to parameterize a nonstandard residue for constant pH MD Jason Swails (Mon Sep 29 2014 - 04:47:42 PDT)
[AMBER] harmonic restraint Nadia Li (Wed Aug 27 2014 - 17:00:42 PDT)
- Re: [AMBER] harmonic restraint David A Case (Wed Aug 27 2014 - 19:10:19 PDT)
  - Re: [AMBER] harmonic restraint Nadia Li (Wed Aug 27 2014 - 21:09:15 PDT)
[AMBER] antechamber error message 전선희 (Wed Aug 27 2014 - 20:02:13 PDT)
- Re: [AMBER] antechamber error message Daniel Roe (Wed Aug 27 2014 - 22:16:25 PDT)
  - Re: [AMBER] antechamber error message 전선희 (Mon Sep 01 2014 - 23:17:25 PDT)
[AMBER] Error in making and running xleap ammarah.ghaffar.comsats.edu.pk (Thu Aug 28 2014 - 02:52:23 PDT)
- Re: [AMBER] Error in making and running xleap Jason Swails (Thu Aug 28 2014 - 04:34:59 PDT)
[AMBER] amber 14 tests errors Jordi Bujons (Thu Aug 28 2014 - 11:23:27 PDT)
- Re: [AMBER] amber 14 tests errors Jason Swails (Thu Aug 28 2014 - 12:15:47 PDT)
[AMBER] system size more than 1000 residues Pengzhi Zhang (Thu Aug 28 2014 - 12:36:12 PDT)
- Re: [AMBER] system size more than 1000 residues Jason Swails (Thu Aug 28 2014 - 13:53:14 PDT)
- Re: [AMBER] system size more than 1000 residues Pengzhi Zhang (Tue Sep 02 2014 - 14:32:59 PDT)
  - Re: [AMBER] system size more than 1000 residues Jason Swails (Tue Sep 02 2014 - 14:39:51 PDT)
- Re: [AMBER] system size more than 1000 residues Pengzhi Zhang (Wed Sep 03 2014 - 12:23:53 PDT)
[AMBER] Mg 12-6-4 potential using parmed Brian Radak (Thu Aug 28 2014 - 12:45:19 PDT)
- Re: [AMBER] Mg 12-6-4 potential using parmed Pengfei Li (Thu Aug 28 2014 - 15:23:17 PDT)
  - Re: [AMBER] Mg 12-6-4 potential using parmed Brian Radak (Thu Aug 28 2014 - 16:47:35 PDT)
    - Re: [AMBER] Mg 12-6-4 potential using parmed Brian Radak (Fri Aug 29 2014 - 06:39:19 PDT)
    - Re: [AMBER] Mg 12-6-4 potential using parmed Pengfei Li (Fri Aug 29 2014 - 07:51:35 PDT)
[AMBER] On combining different force-fields and charge-derivation methods Mohammad Salem (Thu Aug 28 2014 - 16:27:29 PDT)
- Re: [AMBER] On combining different force-fields and charge-derivation methods Jason Swails (Thu Aug 28 2014 - 18:03:47 PDT)
  - Re: [AMBER] On combining different force-fields and charge-derivation methods Mohammad Salem (Thu Aug 28 2014 - 21:13:35 PDT)
- Re: [AMBER] On combining different force-fields and charge-derivation methods FyD (Sat Aug 30 2014 - 04:08:48 PDT)
  - Re: [AMBER] On combining different force-fields and charge-derivation methods Mohammad Salem (Wed Sep 03 2014 - 15:26:27 PDT)
[AMBER] nab Mary Varughese (Fri Aug 29 2014 - 01:56:39 PDT)
- Re: [AMBER] nab svrci (Fri Aug 29 2014 - 03:37:36 PDT)
  - Re: [AMBER] nab Mary Varughese (Fri Aug 29 2014 - 22:16:26 PDT)
    - Re: [AMBER] nab David A Case (Sat Aug 30 2014 - 05:28:58 PDT)
    - Re: [AMBER] nab Mary Varughese (Sun Aug 31 2014 - 00:26:21 PDT)
[AMBER] Obtaining representative structures from clustering Jonathan Gough (Fri Aug 29 2014 - 07:56:06 PDT)
- Re: [AMBER] Obtaining representative structures from clustering Daniel Roe (Fri Aug 29 2014 - 08:22:51 PDT)
  - Re: [AMBER] Obtaining representative structures from clustering Jonathan Gough (Fri Aug 29 2014 - 08:40:10 PDT)
    - Re: [AMBER] Obtaining representative structures from clustering Jonathan Gough (Fri Aug 29 2014 - 09:01:04 PDT)
    - Re: [AMBER] Obtaining representative structures from clustering Daniel Roe (Fri Aug 29 2014 - 09:21:33 PDT)
    - Re: [AMBER] Obtaining representative structures from clustering Jonathan Gough (Fri Aug 29 2014 - 09:22:39 PDT)
[AMBER] updates about ACPYPE Alan (Sat Aug 30 2014 - 03:41:24 PDT)
[AMBER] the force constant in umberlla simpling Sun (Sun Aug 31 2014 - 01:35:42 PDT)
[AMBER] Do the Charmm FF parameters apply to Amber? 张冬冬 (Sun Aug 31 2014 - 08:09:42 PDT)
- Re: [AMBER] Do the Charmm FF parameters apply to Amber? David A Case (Sun Aug 31 2014 - 10:56:24 PDT)
[AMBER] mmpbsa amber error while running decomp Sucharita Dey (Sun Aug 31 2014 - 22:52:26 PDT)
- Re: [AMBER] mmpbsa amber error while running decomp Jason Swails (Mon Sep 01 2014 - 07:51:16 PDT)
  - Re: [AMBER] mmpbsa amber error while running decomp Sucharita Dey (Tue Sep 02 2014 - 00:31:55 PDT)
[AMBER] Reading Error Soumendranath Bhakat (Mon Sep 01 2014 - 02:39:14 PDT)
- Re: [AMBER] Reading Error David A Case (Mon Sep 01 2014 - 05:18:48 PDT)
- Re: [AMBER] Reading Error Jason Swails (Mon Sep 01 2014 - 07:46:19 PDT)
[AMBER] Bridging Sodium ions using hbond DEBOSTUTI GHOSHDASTIDAR (Mon Sep 01 2014 - 03:36:28 PDT)
- Re: [AMBER] Bridging Sodium ions using hbond Daniel Roe (Mon Sep 01 2014 - 08:11:54 PDT)
  - Re: [AMBER] Bridging Sodium ions using hbond DEBOSTUTI GHOSHDASTIDAR (Tue Sep 02 2014 - 09:19:07 PDT)
[AMBER] time scales for running MD Asmita Gupta (Mon Sep 01 2014 - 03:42:21 PDT)
- Re: [AMBER] time scales for running MD David A Case (Mon Sep 01 2014 - 05:24:05 PDT)
  - Re: [AMBER] time scales for running MD Asmita Gupta (Mon Sep 01 2014 - 06:38:17 PDT)
    - Re: [AMBER] time scales for running MD Daniel Roe (Mon Sep 01 2014 - 07:34:47 PDT)
    - Re: [AMBER] time scales for running MD Carlos Simmerling (Mon Sep 01 2014 - 08:50:23 PDT)
    - Re: [AMBER] time scales for running MD Asmita Gupta (Mon Sep 01 2014 - 10:15:41 PDT)
    - Re: [AMBER] time scales for running MD Carlos Simmerling (Mon Sep 01 2014 - 11:36:20 PDT)
[AMBER] Reaction profile calculation in Amber by QM/MM method MOHD HOMAIDUR RAHMAN (Tue Sep 02 2014 - 00:24:31 PDT)
- Re: [AMBER] Reaction profile calculation in Amber by QM/MM method Jason Swails (Tue Sep 02 2014 - 06:00:27 PDT)
[AMBER] atom types for QM region in QM/MM Spelnikov Dmitriy (Tue Sep 02 2014 - 00:29:00 PDT)
- Re: [AMBER] atom types for QM region in QM/MM Marc van der Kamp (Tue Sep 02 2014 - 01:35:49 PDT)
[AMBER] meeting a problem when using ptraj to extract the replica exchanging self-guided MD trajectory wliu (Tue Sep 02 2014 - 06:05:15 PDT)
- Re: [AMBER] meeting a problem when using ptraj to extract the replica exchanging self-guided MD trajectory Jason Swails (Tue Sep 02 2014 - 06:27:44 PDT)
  - Re: [AMBER] meeting a problem when using ptraj to extract the replica exchanging self-guided MD trajectory wliu (Tue Sep 02 2014 - 06:40:19 PDT)
    - Re: [AMBER] meeting a problem when using ptraj to extract the replica exchanging self-guided MD trajectory Daniel Roe (Tue Sep 02 2014 - 06:59:33 PDT)
    - Re: [AMBER] meeting a problem when using ptraj to extract the replica exchanging self-guided MD trajectory wliu (Tue Sep 02 2014 - 07:08:44 PDT)
    - Re: [AMBER] meeting a problem when using ptraj to extract the replica exchanging self-guided MD trajectory wliu (Wed Sep 03 2014 - 02:58:57 PDT)
    - Re: [AMBER] meeting a problem when using ptraj to extract the replica exchanging self-guided MD trajectory Jason Swails (Wed Sep 03 2014 - 03:43:57 PDT)
    - Re: [AMBER] meeting a problem when using ptraj to extract the replica exchanging self-guided MD trajectory wliu (Wed Sep 03 2014 - 04:41:26 PDT)
[AMBER] PHI Intel Compilation Jacopo Sgrignani (Tue Sep 02 2014 - 06:40:39 PDT)
- Re: [AMBER] PHI Intel Compilation Ross Walker (Tue Sep 02 2014 - 10:11:35 PDT)
  - Re: [AMBER] PHI Intel Compilation Jacopo Sgrignani (Tue Sep 02 2014 - 10:16:53 PDT)
    - Re: [AMBER] PHI Intel Compilation Ross Walker (Tue Sep 02 2014 - 10:34:15 PDT)
    - Re: [AMBER] PHI Intel Compilation Jacopo Sgrignani (Thu Sep 04 2014 - 04:08:05 PDT)
[AMBER] protein-peptide alanine scaning Renato Freitas (Tue Sep 02 2014 - 10:12:21 PDT)
- Re: [AMBER] protein-peptide alanine scaning Jason Swails (Tue Sep 02 2014 - 12:03:15 PDT)
  - Re: [AMBER] protein-peptide alanine scaning Renato Freitas (Tue Sep 02 2014 - 12:41:16 PDT)
    - Re: [AMBER] protein-peptide alanine scaning Jason Swails (Tue Sep 02 2014 - 14:02:01 PDT)
[AMBER] cuda versions advice Scott Brozell (Tue Sep 02 2014 - 12:50:13 PDT)
- Re: [AMBER] cuda versions advice Scott Le Grand (Tue Sep 02 2014 - 13:26:32 PDT)
  - Re: [AMBER] cuda versions advice Ross Walker (Tue Sep 02 2014 - 14:02:43 PDT)
    - Re: [AMBER] cuda versions advice Scott Brozell (Thu Sep 04 2014 - 09:29:05 PDT)
    - Re: [AMBER] cuda versions advice Scott Le Grand (Thu Sep 04 2014 - 14:10:56 PDT)
[AMBER] ncsu_abmd qm/mm Fekete Attila (Wed Sep 03 2014 - 01:35:58 PDT)
[AMBER] many initial systems for a two molecules system Fabian Glaser (Wed Sep 03 2014 - 04:26:10 PDT)
- Re: [AMBER] many initial systems for a two molecules system Jason Swails (Wed Sep 03 2014 - 08:07:32 PDT)
  - Re: [AMBER] many initial systems for a two molecules system Fabian Glaser (Thu Sep 04 2014 - 00:44:45 PDT)
    - Re: [AMBER] many initial systems for a two molecules system Jason Swails (Thu Sep 04 2014 - 04:29:05 PDT)
    - Re: [AMBER] many initial systems for a two molecules system Fabian Glaser (Thu Sep 04 2014 - 04:37:13 PDT)
    - Re: [AMBER] many initial systems for a two molecules system Jason Swails (Thu Sep 04 2014 - 04:55:13 PDT)
    - Re: [AMBER] many initial systems for a two molecules system Fabian Glaser (Sun Sep 07 2014 - 05:05:23 PDT)
    - Re: [AMBER] many initial systems for a two molecules system Jason Swails (Mon Sep 08 2014 - 07:22:30 PDT)
    - Re: [AMBER] many initial systems for a two molecules system Fabian Glaser (Mon Sep 08 2014 - 07:35:36 PDT)
    - Re: [AMBER] many initial systems for a two molecules system Jason Swails (Mon Sep 08 2014 - 07:58:44 PDT)
    - Re: [AMBER] many initial systems for a two molecules system Fabian Glaser (Mon Sep 08 2014 - 08:01:16 PDT)
    - Re: [AMBER] many initial systems for a two molecules system Fabian Glaser (Mon Sep 08 2014 - 07:51:57 PDT)
    - Re: [AMBER] many initial systems for a two molecules system Fabian Glaser (Mon Sep 08 2014 - 06:44:36 PDT)
[AMBER] amber force field 王珍 (Wed Sep 03 2014 - 06:50:11 PDT)
- Re: [AMBER] amber force field Jason Swails (Wed Sep 03 2014 - 07:40:30 PDT)
- Re: [AMBER] amber force field pavel.banas.upol.cz (Mon Dec 29 2014 - 08:32:13 PST)
  - Re: [AMBER] amber force field Jiri Sponer (Tue Dec 30 2014 - 02:12:52 PST)
[AMBER] Ambertools14 sander_pbsa_decres test failure Shan-ho Tsai (Wed Sep 03 2014 - 12:31:53 PDT)
- Re: [AMBER] Ambertools14 sander_pbsa_decres test failure David A Case (Wed Sep 03 2014 - 18:12:04 PDT)
  - Re: [AMBER] Ambertools14 sander_pbsa_decres test failure Shan-ho Tsai (Wed Sep 03 2014 - 18:38:41 PDT)
    - Re: [AMBER] Ambertools14 sander_pbsa_decres test failure Ray Luo, Ph.D. (Fri Sep 19 2014 - 10:28:00 PDT)
  - Re: [AMBER] Ambertools14 sander_pbsa_decres test failure Ray Luo, Ph.D. (Fri Sep 19 2014 - 10:27:39 PDT)
[AMBER] parallel cuda test errors Gard Nelson (Wed Sep 03 2014 - 12:49:38 PDT)
- Re: [AMBER] parallel cuda test errors Ross Walker (Wed Sep 03 2014 - 13:00:23 PDT)
  - Re: [AMBER] parallel cuda test errors Gard Nelson (Wed Sep 03 2014 - 13:46:43 PDT)
[AMBER] No hybrid REMD for cuda? Hugo Azurmendi (Wed Sep 03 2014 - 12:53:25 PDT)
- Re: [AMBER] No hybrid REMD for cuda? Jason Swails (Wed Sep 03 2014 - 13:30:18 PDT)
  - Re: [AMBER] No hybrid REMD for cuda? Hugo Azurmendi (Wed Sep 03 2014 - 14:07:14 PDT)
[AMBER] iwrap on very long simulation Setyanto Md (Wed Sep 03 2014 - 18:12:31 PDT)
- Re: [AMBER] iwrap on very long simulation David A Case (Thu Sep 04 2014 - 05:01:17 PDT)
  - Re: [AMBER] iwrap on very long simulation Setyanto Md (Sat Sep 06 2014 - 17:33:29 PDT)
    - Re: [AMBER] iwrap on very long simulation Setyanto Md (Sat Sep 06 2014 - 17:34:16 PDT)
    - Re: [AMBER] iwrap on very long simulation sunita.tifrh.res.in (Mon Sep 08 2014 - 05:32:02 PDT)
    - Re: [AMBER] iwrap on very long simulation Jason Swails (Mon Sep 08 2014 - 06:07:11 PDT)
    - Re: [AMBER] iwrap on very long simulation sunita.tifrh.res.in (Mon Sep 08 2014 - 06:23:01 PDT)
    - Re: [AMBER] iwrap on very long simulation Jason Swails (Mon Sep 08 2014 - 06:34:51 PDT)
- Re: [AMBER] iwrap on very long simulation sunita.tifrh.res.in (Mon Sep 08 2014 - 06:52:28 PDT)
  - Re: [AMBER] iwrap on very long simulation Jason Swails (Mon Sep 08 2014 - 07:02:46 PDT)
[AMBER] building AmberTools14 to use with Amber12 i iordanov (Wed Sep 03 2014 - 19:34:53 PDT)
- Re: [AMBER] building AmberTools14 to use with Amber12 Jason Swails (Thu Sep 04 2014 - 04:02:15 PDT)
  - Re: [AMBER] building AmberTools14 to use with Amber12 i iordanov (Thu Sep 04 2014 - 10:12:23 PDT)
[AMBER] decomposition output file Nadia Li (Wed Sep 03 2014 - 21:47:06 PDT)
- Re: [AMBER] decomposition output file Bill Miller III (Wed Sep 03 2014 - 21:51:11 PDT)
  - Re: [AMBER] decomposition output file Jason Swails (Thu Sep 04 2014 - 04:39:18 PDT)
    - Re: [AMBER] decomposition output file Nadia Li (Thu Sep 04 2014 - 07:19:11 PDT)
[AMBER] Which atomtype in Amber99sb FF correspond to the Nitro atomtype of GAFF bipin singh (Thu Sep 04 2014 - 00:28:45 PDT)
- Re: [AMBER] Which atomtype in Amber99sb FF correspond to the Nitro atomtype of GAFF David A Case (Thu Sep 04 2014 - 04:54:49 PDT)
- Re: [AMBER] Which atomtype in Amber99sb FF correspond to the Nitro atomtype of GAFF FyD (Thu Sep 04 2014 - 05:02:24 PDT)
[AMBER] dihedral in parmtop: negative third index vs ICP(H) Hannes Loeffler (Thu Sep 04 2014 - 01:57:53 PDT)
- Re: [AMBER] dihedral in parmtop: negative third index vs ICP(H) Jason Swails (Thu Sep 04 2014 - 04:11:01 PDT)
  - Re: [AMBER] dihedral in parmtop: negative third index vs ICP(H) Hannes Loeffler (Fri Sep 05 2014 - 02:42:44 PDT)
    - Re: [AMBER] dihedral in parmtop: negative third index vs ICP(H) Jason Swails (Fri Sep 05 2014 - 05:39:31 PDT)
[AMBER] DMPG lipid bilayer simulations? Smith, Jarrod A (Thu Sep 04 2014 - 13:28:34 PDT)
- Re: [AMBER] DMPG lipid bilayer simulations? Dickson, Callum J (Thu Sep 11 2014 - 06:23:32 PDT)
[AMBER] extract energies from trajectory Milo Westler (Thu Sep 04 2014 - 15:55:31 PDT)
- Re: [AMBER] extract energies from trajectory Daniel Roe (Thu Sep 04 2014 - 19:19:34 PDT)
[AMBER] Can (cp)ptraj calculate the diffusion of the center of mass? Jose Borreguero (Thu Sep 04 2014 - 15:59:21 PDT)
- Re: [AMBER] Can (cp)ptraj calculate the diffusion of the center of mass? Daniel Roe (Thu Sep 04 2014 - 19:17:34 PDT)
  - Re: [AMBER] Can (cp)ptraj calculate the diffusion of the center of mass? Jose Borreguero (Fri Sep 05 2014 - 10:51:48 PDT)
    - Re: [AMBER] Can (cp)ptraj calculate the diffusion of the center of mass? hannes.loeffler.stfc.ac.uk (Fri Sep 05 2014 - 11:09:20 PDT)
    - Re: [AMBER] Can (cp)ptraj calculate the diffusion of the center of mass? Jose Borreguero (Fri Sep 05 2014 - 11:13:00 PDT)
[AMBER] One third of Amber 14's test.cuda tests are failing for me Jan-Philip Gehrcke (Fri Sep 05 2014 - 03:18:27 PDT)
- Re: [AMBER] One third of Amber 14's test.cuda tests are failing for me Ross Walker (Fri Sep 05 2014 - 04:50:49 PDT)
  - Re: [AMBER] One third of Amber 14's test.cuda tests are failing for me Jan-Philip Gehrcke (Fri Sep 05 2014 - 05:04:32 PDT)
[AMBER] diffusion in octahedron box newamber list (Fri Sep 05 2014 - 04:55:43 PDT)
- Re: [AMBER] diffusion in octahedron box Jason Swails (Fri Sep 05 2014 - 05:09:50 PDT)
  - Re: [AMBER] diffusion in octahedron box newamber list (Fri Sep 05 2014 - 05:12:30 PDT)
    - Re: [AMBER] diffusion in octahedron box Jason Swails (Fri Sep 05 2014 - 05:40:45 PDT)
[AMBER] Equilibration of the membrane protein with the restrains James Starlight (Fri Sep 05 2014 - 05:30:45 PDT)
- Re: [AMBER] Equilibration of the membrane protein with the restrains James Starlight (Tue Sep 09 2014 - 00:33:34 PDT)
[AMBER] Lennard-Jones Parameters for Each Atom Uday Midya (Fri Sep 05 2014 - 06:46:54 PDT)
- Re: [AMBER] Lennard-Jones Parameters for Each Atom Brian Radak (Fri Sep 05 2014 - 06:56:44 PDT)
- Re: [AMBER] Lennard-Jones Parameters for Each Atom Jason Swails (Fri Sep 05 2014 - 06:59:08 PDT)
  - Re: [AMBER] Lennard-Jones Parameters for Each Atom Uday Midya (Fri Sep 05 2014 - 10:02:10 PDT)
    - Re: [AMBER] Lennard-Jones Parameters for Each Atom Jason Swails (Fri Sep 05 2014 - 10:11:09 PDT)
[AMBER] Calculation of Urea_Urea Interaction energy MOHD HOMAIDUR RAHMAN (Fri Sep 05 2014 - 08:06:51 PDT)
- Re: [AMBER] Calculation of Urea_Urea Interaction energy Jason Swails (Fri Sep 05 2014 - 08:17:27 PDT)
  - Re: [AMBER] Calculation of Urea_Urea Interaction energy MOHD HOMAIDUR RAHMAN (Fri Sep 05 2014 - 11:06:27 PDT)
    - Re: [AMBER] Calculation of Urea_Urea Interaction energy Daniel Roe (Fri Sep 05 2014 - 19:41:15 PDT)
    - Re: [AMBER] Calculation of Urea_Urea Interaction energy MOHD HOMAIDUR RAHMAN (Mon Sep 08 2014 - 00:56:30 PDT)
    - Re: [AMBER] Calculation of Urea_Urea Interaction energy Jason Swails (Mon Sep 08 2014 - 04:49:43 PDT)
    - Re: [AMBER] Calculation of Urea_Urea Interaction energy Daniel Roe (Mon Sep 08 2014 - 06:44:56 PDT)
[AMBER] MMGBSA giving to high VDW energies Ahmed Ayoub (Fri Sep 05 2014 - 12:12:00 PDT)
[AMBER] Solvation of the membrane bilayer using tleap James Starlight (Sun Sep 07 2014 - 00:34:14 PDT)
- Re: [AMBER] Solvation of the membrane bilayer using tleap James Starlight (Tue Sep 09 2014 - 07:27:30 PDT)
[AMBER] amber-Gaussian find the transition 王珍 (Sun Sep 07 2014 - 02:04:25 PDT)
- Re: [AMBER] amber-Gaussian find the transition Brian Radak (Sun Sep 07 2014 - 06:23:18 PDT)
[AMBER] QM/MM optimization error 王珍 (Sun Sep 07 2014 - 19:46:32 PDT)
- Re: [AMBER] QM/MM optimization error Jason Swails (Mon Sep 08 2014 - 04:52:25 PDT)
[AMBER] Enquiring about RMSD of small and large proteins Yip Yew Mun (Sun Sep 07 2014 - 19:52:54 PDT)
- Re: [AMBER] Enquiring about RMSD of small and large proteins Daniel Roe (Mon Sep 08 2014 - 06:54:02 PDT)
  - Re: [AMBER] Enquiring about RMSD of small and large proteins newamber list (Wed Sep 17 2014 - 07:56:23 PDT)
    - Re: [AMBER] Enquiring about RMSD of small and large proteins Daniel Roe (Wed Sep 17 2014 - 10:02:48 PDT)
    - Re: [AMBER] Enquiring about RMSD of small and large proteins newamber list (Wed Sep 17 2014 - 10:13:07 PDT)
[AMBER] Trajectory analysis using ptraj James Starlight (Mon Sep 08 2014 - 01:45:44 PDT)
- Re: [AMBER] Trajectory analysis using ptraj Daniel Roe (Mon Sep 08 2014 - 06:59:26 PDT)
  - Re: [AMBER] Trajectory analysis using ptraj James Starlight (Mon Sep 08 2014 - 23:07:35 PDT)
    - Re: [AMBER] Trajectory analysis using ptraj Daniel Roe (Tue Sep 09 2014 - 06:43:41 PDT)
    - Re: [AMBER] Trajectory analysis using ptraj James Starlight (Wed Sep 10 2014 - 00:02:13 PDT)
[AMBER] mismatch pdb files when created using ambpdb and savepdb sunita.tifrh.res.in (Mon Sep 08 2014 - 06:13:05 PDT)
- Re: [AMBER] mismatch pdb files when created using ambpdb and savepdb David A Case (Mon Sep 08 2014 - 07:17:40 PDT)
  - Re: [AMBER] mismatch pdb files when created using ambpdb and savepdb Daniel Roe (Mon Sep 08 2014 - 08:22:53 PDT)
- Re: [AMBER] mismatch pdb files when created using ambpdb and savepdb sunita.tifrh.res.in (Wed Sep 10 2014 - 01:47:21 PDT)
  - Re: [AMBER] mismatch pdb files when created using ambpdb and savepdb sunita.tifrh.res.in (Wed Sep 10 2014 - 02:14:53 PDT)
    - Re: [AMBER] mismatch pdb files when created using ambpdb and savepdb Thomas Cheatham (Wed Sep 10 2014 - 02:22:18 PDT)
    - Re: [AMBER] mismatch pdb files when created using ambpdb and savepdb Daniel Roe (Wed Sep 10 2014 - 06:43:30 PDT)
    - Re: [AMBER] mismatch pdb files when created using ambpdb and savepdb Jason Swails (Wed Sep 10 2014 - 05:08:41 PDT)
    - Re: [AMBER] mismatch pdb files when created using ambpdb and savepdb sunita.tifrh.res.in (Wed Sep 10 2014 - 06:21:50 PDT)
  - Re: [AMBER] mismatch pdb files when created using ambpdb and savepdb David A Case (Wed Sep 10 2014 - 04:49:04 PDT)
[AMBER] HID or HIE which one to consider? sunita.tifrh.res.in (Mon Sep 08 2014 - 06:34:07 PDT)
- Re: [AMBER] HID or HIE which one to consider? Marc van der Kamp (Mon Sep 08 2014 - 06:45:54 PDT)
  - Re: [AMBER] HID or HIE which one to consider? sunita.tifrh.res.in (Tue Sep 09 2014 - 23:49:13 PDT)
    - Re: [AMBER] HID or HIE which one to consider? Marc van der Kamp (Wed Sep 10 2014 - 00:45:04 PDT)
[AMBER] amber course Fabian Glaser (Mon Sep 08 2014 - 06:35:04 PDT)
- Re: [AMBER] amber course Ross Walker (Mon Sep 08 2014 - 07:54:54 PDT)
  - Re: [AMBER] amber course MOHD HOMAIDUR RAHMAN (Mon Sep 08 2014 - 09:25:33 PDT)
[AMBER] PBSA in AT14: invalid test case, estatic potential values are written in wrong units to DX files. Jan-Philip Gehrcke (Mon Sep 08 2014 - 06:57:00 PDT)
- Re: [AMBER] PBSA in AT14: invalid test case, estatic potential values are written in wrong units to DX files. Ray Luo, Ph.D. (Mon Sep 08 2014 - 15:22:12 PDT)
  - Re: [AMBER] PBSA in AT14: invalid test case, estatic potential values are written in wrong units to DX files. Jan-Philip Gehrcke (Tue Sep 09 2014 - 03:28:05 PDT)
    - Re: [AMBER] PBSA in AT14: invalid test case, estatic potential values are written in wrong units to DX files. Ray Luo, Ph.D. (Tue Sep 09 2014 - 12:28:16 PDT)
    - Re: [AMBER] PBSA in AT14: invalid test case, estatic potential values are written in wrong units to DX files. Ray Luo, Ph.D. (Wed Sep 10 2014 - 16:53:11 PDT)
[AMBER] Rewrapping restart file Geoffrey Gray (Mon Sep 08 2014 - 09:08:21 PDT)
- Re: [AMBER] Rewrapping restart file Daniel Roe (Mon Sep 08 2014 - 09:51:09 PDT)
  - Re: [AMBER] Rewrapping restart file Geoffrey Gray (Mon Sep 08 2014 - 11:17:23 PDT)
[AMBER] ligand shift Nadia Li (Mon Sep 08 2014 - 12:03:00 PDT)
- Re: [AMBER] ligand shift Carlos Simmerling (Mon Sep 08 2014 - 12:12:28 PDT)
- Re: [AMBER] ligand shift Daniel Roe (Mon Sep 08 2014 - 12:28:11 PDT)
  - Re: [AMBER] ligand shift George Tzotzos (Mon Sep 08 2014 - 12:35:09 PDT)
    - Re: [AMBER] ligand shift Carlos Simmerling (Mon Sep 08 2014 - 12:47:39 PDT)
  - Re: [AMBER] ligand shift Nadia Li (Wed Sep 10 2014 - 13:10:57 PDT)
[AMBER] Slow dissociation of ligand from binding pocket of protein George Tzotzos (Mon Sep 08 2014 - 13:11:36 PDT)
[AMBER] [ANN] MDTraj 1.0: Trajectory Analysis in Python Robert McGibbon (Mon Sep 08 2014 - 13:17:02 PDT)
[AMBER] Postdoc Position Available Dirar Homouz (Tue Sep 09 2014 - 03:20:51 PDT)
[AMBER] Amber/ Orca problem Aixiao Li (Tue Sep 09 2014 - 04:11:12 PDT)
- Re: [AMBER] Amber/ Orca problem David A Case (Tue Sep 09 2014 - 05:14:18 PDT)
  - Re: [AMBER] Amber/ Orca problem Aixiao Li (Tue Sep 09 2014 - 05:03:27 PDT)
    - Re: [AMBER] Amber/ Orca problem David A Case (Tue Sep 09 2014 - 08:02:12 PDT)
    - Re: [AMBER] Amber/ Orca problem Aixiao Li (Wed Sep 10 2014 - 02:01:41 PDT)
[AMBER] mm_pbsa vertex atom mismatch Fengxue Li (Tue Sep 09 2014 - 05:36:15 PDT)
- Re: [AMBER] mm_pbsa vertex atom mismatch Ray Luo, Ph.D. (Tue Sep 09 2014 - 12:26:40 PDT)
[AMBER] distance restraint Mary Varughese (Tue Sep 09 2014 - 13:08:31 PDT)
- Re: [AMBER] distance restraint David A Case (Tue Sep 09 2014 - 15:09:39 PDT)
  - Re: [AMBER] distance restraint Mary Varughese (Tue Sep 09 2014 - 19:34:01 PDT)
    - Re: [AMBER] distance restraint Thomas Cheatham (Tue Sep 09 2014 - 19:40:15 PDT)
    - Re: [AMBER] distance restraint Mary Varughese (Tue Sep 09 2014 - 20:01:40 PDT)
[AMBER] frcmod format file Maria Osorios (Tue Sep 09 2014 - 18:57:53 PDT)
- Re: [AMBER] frcmod format file David A Case (Wed Sep 10 2014 - 04:43:47 PDT)
  - Re: [AMBER] frcmod format file Maria Osorios (Wed Sep 10 2014 - 13:32:35 PDT)
[AMBER] cudaMemcpyToSymbol: SetSim copy to cSim failed invalid device symbol Scott Brozell (Tue Sep 09 2014 - 23:23:18 PDT)
- Re: [AMBER] cudaMemcpyToSymbol: SetSim copy to cSim failed invalid device symbol Ross Walker (Wed Sep 10 2014 - 09:51:22 PDT)
- Re: [AMBER] cudaMemcpyToSymbol: SetSim copy to cSim failed invalid device symbol Scott Le Grand (Wed Sep 10 2014 - 09:57:49 PDT)
[AMBER] Query for Hbond lifetime analysis with AmberTools14 Indrajit Deb (Wed Sep 10 2014 - 03:00:33 PDT)
- Re: [AMBER] Query for Hbond lifetime analysis with AmberTools14 Daniel Roe (Wed Sep 10 2014 - 06:52:37 PDT)
[AMBER] Not getting solute-solvent hbond by cpptraj (AmberTools14) Indrajit Deb (Wed Sep 10 2014 - 04:27:44 PDT)
- Re: [AMBER] Not getting solute-solvent hbond by cpptraj (AmberTools14) Daniel Roe (Wed Sep 10 2014 - 06:46:25 PDT)
[AMBER] the out file of qm/mm in amber 王珍 (Wed Sep 10 2014 - 05:09:22 PDT)
- Re: [AMBER] the out file of qm/mm in amber Jason Swails (Wed Sep 10 2014 - 05:25:14 PDT)
[AMBER] mm_pbsa vertex atom mismatch Fengxue Li (Wed Sep 10 2014 - 07:03:21 PDT)
[AMBER] FW: about trajectory unwrap Kong, Ren (Wed Sep 10 2014 - 08:06:34 PDT)
- Re: [AMBER] FW: about trajectory unwrap Jason Swails (Wed Sep 10 2014 - 08:34:06 PDT)
- Re: [AMBER] FW: about trajectory unwrap Daniel Roe (Wed Sep 10 2014 - 08:32:50 PDT)
[AMBER] Problem running multiple GPU's jon.maguire.louisville.edu (Wed Sep 10 2014 - 08:53:26 PDT)
- Re: [AMBER] Problem running multiple GPU's Jason Swails (Wed Sep 10 2014 - 09:45:14 PDT)
  - Re: [AMBER] Problem running multiple GPU's jon.maguire.louisville.edu (Wed Sep 10 2014 - 09:46:33 PDT)
    - Re: [AMBER] Problem running multiple GPU's Ross Walker (Wed Sep 10 2014 - 10:03:10 PDT)
    - Re: [AMBER] Problem running multiple GPU's - FIXED jon.maguire.louisville.edu (Wed Sep 10 2014 - 10:56:20 PDT)
    - Re: [AMBER] Problem running multiple GPU's - FIXED Ross Walker (Wed Sep 10 2014 - 11:06:10 PDT)
[AMBER] Problem running pmemd.cuda.mpi REMD with different number of replicas Thiago Lipinski Paes (Wed Sep 10 2014 - 09:21:40 PDT)
- Re: [AMBER] Problem running pmemd.cuda.mpi REMD with different number of replicas Christina Bergonzo (Wed Sep 10 2014 - 09:29:27 PDT)
  - Re: [AMBER] Problem running pmemd.cuda.mpi REMD with different number of replicas Thiago Lipinski Paes (Wed Sep 10 2014 - 12:13:36 PDT)
[AMBER] Total vs per-residue MMGBSA energies Ahmed Ayoub (Wed Sep 10 2014 - 11:54:20 PDT)
- Re: [AMBER] Total vs per-residue MMGBSA energies Jason Swails (Wed Sep 10 2014 - 12:07:47 PDT)
[AMBER] hbond lifetime George Tzotzos (Wed Sep 10 2014 - 13:13:13 PDT)
- Re: [AMBER] hbond lifetime Daniel Roe (Wed Sep 10 2014 - 13:27:08 PDT)
  - Re: [AMBER] hbond lifetime George Tzotzos (Wed Sep 10 2014 - 13:52:46 PDT)
    - Re: [AMBER] hbond lifetime Daniel Roe (Wed Sep 10 2014 - 19:51:06 PDT)
[AMBER] Equilibration phase and RMSD Ibrahim Said (Wed Sep 10 2014 - 13:22:17 PDT)
- Re: [AMBER] Equilibration phase and RMSD David A Case (Thu Sep 11 2014 - 05:18:20 PDT)
- Re: [AMBER] Equilibration phase and RMSD Carlos Simmerling (Thu Sep 11 2014 - 05:43:59 PDT)
- Re: [AMBER] Equilibration phase and RMSD Ibrahim Said (Thu Sep 11 2014 - 07:56:30 PDT)
  - Re: [AMBER] Equilibration phase and RMSD Carlos Simmerling (Thu Sep 11 2014 - 08:05:56 PDT)
    - Re: [AMBER] Equilibration phase and RMSD Ibrahim Said (Thu Sep 11 2014 - 12:18:17 PDT)
    - Re: [AMBER] Equilibration phase and RMSD Carlos Simmerling (Thu Sep 11 2014 - 12:23:52 PDT)
    - Re: [AMBER] Equilibration phase and RMSD David A Case (Thu Sep 11 2014 - 12:30:31 PDT)
[AMBER] mmpbsa: PB Bomb in pb_aaradi() Wei Chen (Wed Sep 10 2014 - 14:18:53 PDT)
- Re: [AMBER] mmpbsa: PB Bomb in pb_aaradi() Ray Luo, Ph.D. (Wed Sep 10 2014 - 14:57:56 PDT)
  - Re: [AMBER] mmpbsa: PB Bomb in pb_aaradi() Wei Chen (Wed Sep 10 2014 - 15:03:57 PDT)
[AMBER] Problems to minimize with Sander Maria Osorios (Wed Sep 10 2014 - 14:54:18 PDT)
- Re: [AMBER] Problems to minimize with Sander Jason Swails (Wed Sep 10 2014 - 18:39:17 PDT)
[AMBER] cuda version not working Fabian Glaser (Thu Sep 11 2014 - 02:39:07 PDT)
- Re: [AMBER] cuda version not working Jason Swails (Thu Sep 11 2014 - 04:48:51 PDT)
  - Re: [AMBER] cuda version not working Fabian Glaser (Sat Sep 13 2014 - 21:55:19 PDT)
    - Re: [AMBER] cuda version not working Fabian Glaser (Sat Sep 13 2014 - 21:55:35 PDT)
    - Re: [AMBER] cuda version not working David A Case (Sun Sep 14 2014 - 07:02:21 PDT)
    - Re: [AMBER] cuda version not working Fabian Glaser (Sun Sep 14 2014 - 07:07:49 PDT)
- Re: [AMBER] cuda version not working David A Case (Thu Sep 11 2014 - 05:22:32 PDT)
[AMBER] setting up topology file using GLYCAM Vijyan Achari (Thu Sep 11 2014 - 06:59:53 PDT)
- Re: [AMBER] setting up topology file using GLYCAM Lachele Foley (Thu Sep 11 2014 - 07:18:36 PDT)
[AMBER] Solvation and processing of lipid bilayers using tleap James Starlight (Thu Sep 11 2014 - 14:02:08 PDT)
- Re: [AMBER] Solvation and processing of lipid bilayers using tleap Dickson, Callum J (Fri Sep 12 2014 - 03:47:49 PDT)
  - Re: [AMBER] Solvation and processing of lipid bilayers using tleap James Starlight (Fri Sep 12 2014 - 04:07:51 PDT)
[AMBER] Compiling Amber14 using --with-netcdf Lawrenz, Morgan (Thu Sep 11 2014 - 16:20:48 PDT)
- Re: [AMBER] Compiling Amber14 using --with-netcdf Jason Swails (Thu Sep 11 2014 - 17:27:47 PDT)
  - Re: [AMBER] Compiling Amber14 using --with-netcdf Lawrenz, Morgan (Thu Sep 11 2014 - 17:46:35 PDT)
[AMBER] Force field ff99SB*-ILDN request sunita.tifrh.res.in (Fri Sep 12 2014 - 06:18:22 PDT)
- Re: [AMBER] Force field ff99SB*-ILDN request Jason Swails (Fri Sep 12 2014 - 06:43:56 PDT)
  - Re: [AMBER] Force field ff99SB*-ILDN request Thomas Evangelidis (Fri Sep 12 2014 - 17:40:05 PDT)
    - Re: [AMBER] Force field ff99SB*-ILDN request Carlos Simmerling (Fri Sep 12 2014 - 18:17:28 PDT)
    - Re: [AMBER] Force field ff99SB*-ILDN request David A Case (Sun Sep 14 2014 - 16:46:57 PDT)
    - Re: [AMBER] Force field ff99SB*-ILDN request Carlos Simmerling (Tue Sep 16 2014 - 09:06:44 PDT)
    - Re: [AMBER] Force field ff99SB*-ILDN request Vlad Cojocaru (Tue Sep 16 2014 - 09:34:32 PDT)
    - Re: [AMBER] Force field ff99SB*-ILDN request Jason Swails (Tue Sep 16 2014 - 10:30:21 PDT)
    - Re: [AMBER] Force field ff99SB*-ILDN request David A Case (Tue Sep 16 2014 - 13:11:07 PDT)
    - Re: [AMBER] Force field ff99SB*-ILDN request Jason Swails (Tue Sep 16 2014 - 14:42:45 PDT)
    - Re: [AMBER] Force field ff99SB*-ILDN request sunita.tifrh.res.in (Tue Sep 16 2014 - 20:58:30 PDT)
    - Re: [AMBER] Force field ff99SB*-ILDN request Jason Swails (Wed Sep 17 2014 - 05:53:07 PDT)
    - Re: [AMBER] Force field ff99SB*-ILDN request sunita.tifrh.res.in (Wed Sep 17 2014 - 09:03:07 PDT)
    - Re: [AMBER] Force field ff99SB*-ILDN request Carlos Simmerling (Wed Sep 17 2014 - 04:31:10 PDT)
    - Re: [AMBER] Force field ff99SB*-ILDN request Vlad Cojocaru (Wed Sep 17 2014 - 05:07:23 PDT)
- Re: [AMBER] Force field ff99SB*-ILDN request David A Case (Fri Sep 12 2014 - 08:16:55 PDT)
  - Re: [AMBER] Force field ff99SB*-ILDN request Hannes Loeffler (Fri Sep 12 2014 - 08:35:12 PDT)
    - Re: [AMBER] Force field ff99SB*-ILDN request Carlos Simmerling (Fri Sep 12 2014 - 13:31:35 PDT)
[AMBER] ACS COMP Division travel awards for Spring 2015 National Meeting in Denver Carlos Simmerling (Fri Sep 12 2014 - 07:41:21 PDT)
[AMBER] Building Amber14 with -nofftw3 Lawrenz, Morgan (Fri Sep 12 2014 - 09:45:26 PDT)
- Re: [AMBER] Building Amber14 with -nofftw3 Jason Swails (Fri Sep 12 2014 - 10:23:20 PDT)
  - Re: [AMBER] Building Amber14 with -nofftw3 Lawrenz, Morgan (Fri Sep 19 2014 - 11:11:11 PDT)
    - Re: [AMBER] Building Amber14 with -nofftw3 Jason Swails (Fri Sep 19 2014 - 11:26:26 PDT)
- Re: [AMBER] Building Amber14 with -nofftw3 David A Case (Fri Sep 12 2014 - 10:35:22 PDT)
[AMBER] Amber12 serial test failure Samaneh Ghassabi Kondalaji (Fri Sep 12 2014 - 11:01:07 PDT)
- Re: [AMBER] Amber12 serial test failure Jason Swails (Fri Sep 12 2014 - 11:27:06 PDT)
[AMBER] generate amoeba parameters for amber Jorgen Simonsen (Sat Sep 13 2014 - 21:34:19 PDT)
- Re: [AMBER] generate amoeba parameters for amber Lorenzo Gontrani (Mon Sep 15 2014 - 00:38:25 PDT)
[AMBER] tleap neutralization bug? Gulsevin,Alican (Sun Sep 14 2014 - 11:28:53 PDT)
- Re: [AMBER] tleap neutralization bug? Niel Henriksen (Sun Sep 14 2014 - 13:29:41 PDT)
  - Re: [AMBER] tleap neutralization bug? Marcus Arieno (Mon Sep 15 2014 - 08:45:06 PDT)
    - Re: [AMBER] tleap neutralization bug? Jason Swails (Mon Sep 15 2014 - 09:23:17 PDT)
    - Re: [AMBER] tleap neutralization bug? Gulsevin,Alican (Tue Sep 16 2014 - 08:54:11 PDT)
    - Re: [AMBER] tleap neutralization bug? Jason Swails (Tue Sep 16 2014 - 10:25:21 PDT)
    - Re: [AMBER] tleap neutralization bug? Jason Swails (Thu Sep 18 2014 - 09:44:25 PDT)
    - Re: [AMBER] tleap neutralization bug? Gulsevin,Alican (Thu Sep 18 2014 - 17:00:21 PDT)
    - Re: [AMBER] tleap neutralization bug? David A Case (Fri Sep 19 2014 - 08:45:06 PDT)
[AMBER] about dihedral type Arun Srikanth (Sun Sep 14 2014 - 11:47:20 PDT)
- Re: [AMBER] about dihedral type Jason Swails (Sun Sep 14 2014 - 12:34:07 PDT)
  - Re: [AMBER] about dihedral type Arun Srikanth (Sun Sep 14 2014 - 14:03:39 PDT)
    - Re: [AMBER] about dihedral type Arun Srikanth (Sun Sep 14 2014 - 15:22:13 PDT)
[AMBER] ESP fitting centers exist, but the fitting values are missing 张冬冬 (Mon Sep 15 2014 - 05:29:08 PDT)
- Re: [AMBER] ESP fitting centers exist, but the fitting values are missing David A Case (Mon Sep 15 2014 - 06:17:42 PDT)
  - Re: [AMBER] ESP fitting centers exist, but the fitting values are missing 张冬冬 (Tue Sep 16 2014 - 07:43:42 PDT)
- Re: [AMBER] ESP fitting centers exist, but the fitting values are missing FyD (Wed Sep 17 2014 - 02:48:54 PDT)
[AMBER] cpptraj - atomicfluct George Tzotzos (Mon Sep 15 2014 - 11:57:57 PDT)
- Re: [AMBER] cpptraj - atomicfluct David A Case (Mon Sep 15 2014 - 12:28:18 PDT)
- Re: [AMBER] cpptraj - atomicfluct Thomas Cheatham (Mon Sep 15 2014 - 18:47:37 PDT)
  - Re: [AMBER] cpptraj - atomicfluct Daniel Roe (Tue Sep 16 2014 - 07:30:36 PDT)
[AMBER] CHAMBER: problem with water and swissparam generated ligand Eric Lang (Mon Sep 15 2014 - 13:59:53 PDT)
- Re: [AMBER] CHAMBER: problem with water and swissparam generated ligand Sarah Witzke (Mon Sep 15 2014 - 15:47:32 PDT)
  - Re: [AMBER] CHAMBER: problem with water and swissparam generated ligand Jason Swails (Mon Sep 15 2014 - 18:05:48 PDT)
- Re: [AMBER] CHAMBER: problem with water and swissparam generated ligand Eric Lang (Tue Sep 16 2014 - 06:52:40 PDT)
  - Re: [AMBER] CHAMBER: problem with water and swissparam generated ligand Sarah Witzke (Tue Sep 16 2014 - 07:20:25 PDT)
- Re: [AMBER] CHAMBER: problem with water and swissparam generated ligand Eric Lang (Tue Sep 16 2014 - 11:33:50 PDT)
  - Re: [AMBER] CHAMBER: problem with water and swissparam generated ligand Jason Swails (Tue Sep 16 2014 - 12:20:12 PDT)
- Re: [AMBER] CHAMBER: problem with water and swissparam generated ligand Eric Lang (Wed Sep 17 2014 - 05:19:58 PDT)
  - Re: [AMBER] CHAMBER: problem with water and swissparam generated ligand Jason Swails (Wed Sep 17 2014 - 07:31:57 PDT)
  - Re: [AMBER] CHAMBER: problem with water and swissparam generated ligand Jason Swails (Wed Sep 17 2014 - 11:53:21 PDT)
- Re: [AMBER] CHAMBER: problem with water and swissparam generated ligand Eric Lang (Wed Sep 17 2014 - 07:48:04 PDT)
- Re: [AMBER] CHAMBER: problem with water and swissparam generated ligand Eric Lang (Thu Sep 18 2014 - 02:52:43 PDT)
  - Re: [AMBER] CHAMBER: problem with water and swissparam generated ligand Jason Swails (Thu Sep 18 2014 - 05:52:30 PDT)
- Re: [AMBER] CHAMBER: problem with water and swissparam generated ligand Eric Lang (Thu Sep 18 2014 - 06:24:35 PDT)
[AMBER] Replica Exchange Jacopo Sgrignani (Tue Sep 16 2014 - 01:39:34 PDT)
- Re: [AMBER] Replica Exchange Jason Swails (Tue Sep 16 2014 - 05:31:47 PDT)
[AMBER] Antechamber ligand parametrization James Starlight (Tue Sep 16 2014 - 04:14:59 PDT)
- Re: [AMBER] Antechamber ligand parametrization Hannes Loeffler (Tue Sep 16 2014 - 04:55:55 PDT)
  - Re: [AMBER] Antechamber ligand parametrization James Starlight (Tue Sep 16 2014 - 07:46:15 PDT)
    - Re: [AMBER] Antechamber ligand parametrization David A Case (Tue Sep 16 2014 - 12:53:36 PDT)
    - Re: [AMBER] Antechamber ligand parametrization James Starlight (Wed Sep 17 2014 - 02:45:14 PDT)
    - Re: [AMBER] Antechamber ligand parametrization David A Case (Wed Sep 17 2014 - 04:40:15 PDT)
    - Re: [AMBER] Antechamber ligand parametrization James Starlight (Wed Sep 17 2014 - 06:02:52 PDT)
    - Re: [AMBER] Antechamber ligand parametrization David A Case (Wed Sep 17 2014 - 12:41:28 PDT)
    - Re: [AMBER] Antechamber ligand parametrization James Starlight (Thu Sep 18 2014 - 00:38:54 PDT)
    - Re: [AMBER] Antechamber ligand parametrization David A Case (Thu Sep 18 2014 - 05:10:52 PDT)
    - Re: [AMBER] Antechamber ligand parametrization James Starlight (Thu Sep 18 2014 - 06:33:29 PDT)
    - Re: [AMBER] Antechamber ligand parametrization Parker de Waal (Thu Sep 18 2014 - 04:21:04 PDT)
    - Re: [AMBER] Antechamber ligand parametrization James Starlight (Thu Sep 18 2014 - 04:39:12 PDT)
[AMBER] MMPBSA.py: PrmtopError: Residue mismatch while mapping. Incompatible topology files or bad mask definitions Thomas Evangelidis (Tue Sep 16 2014 - 07:05:34 PDT)
- Re: [AMBER] MMPBSA.py: PrmtopError: Residue mismatch while mapping. Incompatible topology files or bad mask definitions Jason Swails (Tue Sep 16 2014 - 09:13:44 PDT)
  - Re: [AMBER] MMPBSA.py: PrmtopError: Residue mismatch while mapping. Incompatible topology files or bad mask definitions Thomas Evangelidis (Wed Sep 17 2014 - 08:33:44 PDT)
    - Re: [AMBER] MMPBSA.py: PrmtopError: Residue mismatch while mapping. Incompatible topology files or bad mask definitions Jason Swails (Wed Sep 17 2014 - 08:42:17 PDT)
    - Re: [AMBER] MMPBSA.py: PrmtopError: Residue mismatch while mapping. Incompatible topology files or bad mask definitions Thomas Evangelidis (Thu Sep 18 2014 - 02:39:05 PDT)
    - Re: [AMBER] MMPBSA.py: PrmtopError: Residue mismatch while mapping. Incompatible topology files or bad mask definitions Jason Swails (Thu Sep 18 2014 - 04:55:46 PDT)
    - Re: [AMBER] MMPBSA.py: PrmtopError: Residue mismatch while mapping. Incompatible topology files or bad mask definitions Thomas Evangelidis (Thu Sep 18 2014 - 05:15:42 PDT)
    - Re: [AMBER] MMPBSA.py: PrmtopError: Residue mismatch while mapping. Incompatible topology files or bad mask definitions Jason Swails (Thu Sep 18 2014 - 05:59:09 PDT)
    - Re: [AMBER] MMPBSA.py: PrmtopError: Residue mismatch while mapping. Incompatible topology files or bad mask definitions Thomas Evangelidis (Thu Sep 18 2014 - 06:07:41 PDT)
    - Re: [AMBER] MMPBSA.py: PrmtopError: Residue mismatch while mapping. Incompatible topology files or bad mask definitions Jason Swails (Thu Sep 18 2014 - 06:23:48 PDT)
[AMBER] how to simulate a polyester? 张冬冬 (Tue Sep 16 2014 - 07:52:19 PDT)
- Re: [AMBER] how to simulate a polyester? Jason Swails (Tue Sep 16 2014 - 08:18:58 PDT)
  - Re: [AMBER] how to simulate a polyester? FyD (Wed Sep 17 2014 - 03:12:35 PDT)
- Re: [AMBER] how to simulate a polyester? David A Case (Tue Sep 16 2014 - 12:58:11 PDT)
[AMBER] Tetrazole: parameters Esra Bozkurt (Tue Sep 16 2014 - 08:23:11 PDT)
[AMBER] For Amber14 TI, how to perform only the discharge/recharge steps? Lawrenz, Morgan (Tue Sep 16 2014 - 18:01:04 PDT)
- Re: [AMBER] For Amber14 TI, how to perform only the discharge/recharge steps? Ying-Chieh Sun (Tue Sep 16 2014 - 18:41:42 PDT)
  - Re: [AMBER] For Amber14 TI, how to perform only the discharge/recharge steps? Lawrenz, Morgan (Fri Sep 19 2014 - 11:08:49 PDT)
[AMBER] Simulating Silver Salt Soumendranath Bhakat (Wed Sep 17 2014 - 03:56:31 PDT)
- Re: [AMBER] Simulating Silver Salt Jason Swails (Wed Sep 17 2014 - 05:03:38 PDT)
[AMBER] h-bond erik.laurini.di3.units.it (Wed Sep 17 2014 - 04:38:33 PDT)
- Re: [AMBER] h-bond Soumendranath Bhakat (Wed Sep 17 2014 - 04:48:02 PDT)
- Re: [AMBER] h-bond Jason Swails (Wed Sep 17 2014 - 05:07:26 PDT)
  - Re: [AMBER] h-bond erik.laurini.di3.units.it (Wed Sep 17 2014 - 05:20:28 PDT)
[AMBER] Clustering problem Alessandro Mariani (Wed Sep 17 2014 - 04:43:00 PDT)
- Re: [AMBER] Clustering problem Lorenzo Gontrani (Wed Sep 17 2014 - 05:56:15 PDT)
  - Re: [AMBER] Clustering problem Lorenzo Gontrani (Wed Sep 17 2014 - 05:57:46 PDT)
[AMBER] Aligning a trajectory Jonathan Gough (Wed Sep 17 2014 - 05:20:27 PDT)
- Re: [AMBER] Aligning a trajectory Jason Swails (Wed Sep 17 2014 - 05:39:41 PDT)
[AMBER] average structure with RMSF or RMSD? newamber list (Wed Sep 17 2014 - 07:17:29 PDT)
- Re: [AMBER] average structure with RMSF or RMSD? Matt Alegrete (Wed Sep 17 2014 - 09:27:01 PDT)
- Re: [AMBER] average structure with RMSF or RMSD? Daniel Roe (Wed Sep 17 2014 - 09:51:36 PDT)
  - Re: [AMBER] average structure with RMSF or RMSD? newamber list (Wed Sep 17 2014 - 10:07:04 PDT)
[AMBER] Cpptraj hbond function - solvent bridge Miroslav Krepl (Wed Sep 17 2014 - 08:36:49 PDT)
- Re: [AMBER] Cpptraj hbond function - solvent bridge Daniel Roe (Wed Sep 17 2014 - 09:42:21 PDT)
[AMBER] MMPBSA: Default inp warnings George Tzotzos (Wed Sep 17 2014 - 10:39:25 PDT)
- Re: [AMBER] MMPBSA: Default inp warnings Jason Swails (Wed Sep 17 2014 - 10:57:24 PDT)
  - Re: [AMBER] MMPBSA: Default inp warnings George Tzotzos (Wed Sep 17 2014 - 11:00:05 PDT)
    - Re: [AMBER] MMPBSA: Default inp warnings Jason Swails (Wed Sep 17 2014 - 11:40:57 PDT)
[AMBER] Problems to minimize with Sander Investigador Química (Wed Sep 17 2014 - 11:19:58 PDT)
- Re: [AMBER] Problems to minimize with Sander Jason Swails (Wed Sep 17 2014 - 11:45:28 PDT)
  - Re: [AMBER] Problems to minimize with Sander Hector A. Baldoni (Wed Sep 17 2014 - 17:45:38 PDT)
[AMBER] MMPBSA Sourav Purohit (Wed Sep 17 2014 - 15:46:32 PDT)
- Re: [AMBER] MMPBSA Jason Swails (Wed Sep 17 2014 - 16:08:35 PDT)
  - Re: [AMBER] MMPBSA Sourav Purohit (Wed Sep 17 2014 - 16:18:37 PDT)
    - Re: [AMBER] MMPBSA Jason Swails (Wed Sep 17 2014 - 16:23:45 PDT)
    - Re: [AMBER] MMPBSA Sourav Purohit (Wed Sep 17 2014 - 16:29:03 PDT)
    - Re: [AMBER] MMPBSA Sourav Purohit (Wed Sep 17 2014 - 17:04:12 PDT)
[AMBER] Two questions about Net charge and write frcmod in parmed.py Arun Srikanth (Wed Sep 17 2014 - 18:36:39 PDT)
- Re: [AMBER] Two questions about Net charge and write frcmod in parmed.py Jason Swails (Thu Sep 18 2014 - 04:29:31 PDT)
  - Re: [AMBER] Two questions about Net charge and write frcmod in parmed.py Arun Srikanth (Thu Sep 18 2014 - 11:32:16 PDT)
    - Re: [AMBER] Two questions about Net charge and write frcmod in parmed.py Jason Swails (Thu Sep 18 2014 - 12:26:58 PDT)
    - Re: [AMBER] Two questions about Net charge and write frcmod in parmed.py Arun Srikanth (Thu Sep 18 2014 - 13:36:34 PDT)
    - Re: [AMBER] Two questions about Net charge and write frcmod in parmed.py Arun Srikanth (Thu Sep 18 2014 - 18:43:17 PDT)
    - Re: [AMBER] Two questions about Net charge and write frcmod in parmed.py Jason Swails (Thu Sep 18 2014 - 19:27:04 PDT)
    - Re: [AMBER] Two questions about Net charge and write frcmod in parmed.py Arun Srikanth (Thu Sep 18 2014 - 20:41:49 PDT)
    - Re: [AMBER] Two questions about Net charge and write frcmod in parmed.py Arun Srikanth (Thu Sep 18 2014 - 20:50:41 PDT)
    - Re: [AMBER] Two questions about Net charge and write frcmod in parmed.py Jason Swails (Fri Sep 19 2014 - 05:12:45 PDT)
[AMBER] Preparing a system of 7.4 PH ammarah.ghaffar.comsats.edu.pk (Wed Sep 17 2014 - 23:12:02 PDT)
- Re: [AMBER] Preparing a system of 7.4 PH Jason Swails (Thu Sep 18 2014 - 04:34:14 PDT)
[AMBER] MMPBSA Sourav Purohit (Thu Sep 18 2014 - 01:00:51 PDT)
- Re: [AMBER] MMPBSA Jason Swails (Thu Sep 18 2014 - 04:37:07 PDT)
[AMBER] CUDA version still not working Fabian Glaser (Thu Sep 18 2014 - 01:39:32 PDT)
- Re: [AMBER] CUDA version still not working Jason Swails (Thu Sep 18 2014 - 04:40:48 PDT)
  - Re: [AMBER] CUDA version still not working Fabian Glaser (Thu Sep 18 2014 - 05:50:20 PDT)
    - Re: [AMBER] CUDA version still not working Ross Walker (Thu Sep 18 2014 - 10:30:39 PDT)
  - Re: [AMBER] CUDA version still not working Fabian Glaser (Thu Sep 18 2014 - 06:04:38 PDT)
    - Re: [AMBER] CUDA version still not working Jason Swails (Thu Sep 18 2014 - 06:26:18 PDT)
    - Re: [AMBER] CUDA version still not working Ross Walker (Thu Sep 18 2014 - 10:31:34 PDT)
    - Re: [AMBER] CUDA version still not working Fabian Glaser (Sun Sep 21 2014 - 05:51:21 PDT)
    - Re: [AMBER] CUDA version still not working Jason Swails (Sun Sep 21 2014 - 06:44:35 PDT)
    - Re: [AMBER] CUDA version still not working Fabian Glaser (Sun Sep 21 2014 - 06:57:09 PDT)
    - Re: [AMBER] CUDA version still not working Daniel Roe (Sun Sep 21 2014 - 09:30:04 PDT)
- Re: [AMBER] CUDA version still not working Ross Walker (Thu Sep 18 2014 - 10:20:52 PDT)
- Re: [AMBER] CUDA version still not working Ross Walker (Sun Sep 21 2014 - 10:02:48 PDT)
[AMBER] GTX 780SC error "cudaMempcpy GpuBuffer :: Download failed unspecified launch failure" Dieter Buyst (Thu Sep 18 2014 - 01:51:19 PDT)
- Re: [AMBER] GTX 780SC error "cudaMempcpy GpuBuffer :: Download failed unspecified launch failure" Jason Swails (Thu Sep 18 2014 - 04:52:26 PDT)
- Re: [AMBER] GTX 780SC error "cudaMempcpy GpuBuffer :: Download failed unspecified launch failure" Ross Walker (Thu Sep 18 2014 - 10:23:27 PDT)
  - Re: [AMBER] GTX 780SC error "cudaMempcpy GpuBuffer :: Download failed unspecified launch failure" Dieter Buyst (Tue Sep 23 2014 - 02:46:22 PDT)
[AMBER] Error: cannot run Vishal Nemaysh (Thu Sep 18 2014 - 02:50:12 PDT)
- Re: [AMBER] Error: cannot run Jason Swails (Thu Sep 18 2014 - 04:57:55 PDT)
  - Re: [AMBER] Error: cannot run Vishal Nemaysh (Thu Sep 18 2014 - 07:37:34 PDT)
    - Re: [AMBER] Error: cannot run Daniel Roe (Thu Sep 18 2014 - 07:54:26 PDT)
    - Re: [AMBER] Error: cannot run David A Case (Thu Sep 18 2014 - 08:00:50 PDT)
[AMBER] pmemd cuda error Kshatresh Dutta Dubey (Thu Sep 18 2014 - 04:47:41 PDT)
- Re: [AMBER] pmemd cuda error Scott Le Grand (Thu Sep 18 2014 - 09:57:36 PDT)
- Re: [AMBER] pmemd cuda error Ross Walker (Thu Sep 18 2014 - 10:28:24 PDT)
  - Re: [AMBER] pmemd cuda error Kshatresh Dutta Dubey (Mon Sep 22 2014 - 05:51:33 PDT)
[AMBER] Distance restraint John Smith (Thu Sep 18 2014 - 04:50:04 PDT)
- Re: [AMBER] Distance restraint Ilyas Yildirim (Thu Sep 18 2014 - 04:59:52 PDT)
- Re: [AMBER] Distance restraint David A Case (Thu Sep 18 2014 - 05:19:55 PDT)
  - Re: [AMBER] Distance restraint John Smith (Thu Sep 18 2014 - 06:33:21 PDT)
    - Re: [AMBER] Distance restraint Marc van der Kamp (Thu Sep 18 2014 - 07:09:34 PDT)
    - Re: [AMBER] Distance restraint John Smith (Thu Sep 18 2014 - 07:24:21 PDT)
    - Re: [AMBER] Distance restraint Marc van der Kamp (Thu Sep 18 2014 - 08:15:09 PDT)
    - Re: [AMBER] Distance restraint David A Case (Thu Sep 18 2014 - 07:51:12 PDT)
[AMBER] MMPBSA Asfa Ali (Thu Sep 18 2014 - 07:10:13 PDT)
- Re: [AMBER] MMPBSA Jason Swails (Thu Sep 18 2014 - 07:42:22 PDT)
  - Re: [AMBER] MMPBSA Asfa Ali (Thu Sep 18 2014 - 11:26:09 PDT)
    - Re: [AMBER] MMPBSA Ray Luo, Ph.D. (Thu Sep 18 2014 - 11:32:32 PDT)
    - Re: [AMBER] MMPBSA Asfa Ali (Thu Sep 18 2014 - 11:39:54 PDT)
    - Re: [AMBER] MMPBSA Ray Luo, Ph.D. (Thu Sep 18 2014 - 11:41:42 PDT)
    - Re: [AMBER] MMPBSA Daniel Roe (Thu Sep 18 2014 - 12:19:23 PDT)
[AMBER] GTX780 versus K40? Carlos Sosa (Thu Sep 18 2014 - 10:33:11 PDT)
- Re: [AMBER] GTX780 versus K40? Ross Walker (Thu Sep 18 2014 - 10:46:15 PDT)
  - Re: [AMBER] GTX780 versus K40? Carlos Sosa (Thu Sep 18 2014 - 14:04:50 PDT)
[AMBER] ask for help m13654940810 (Thu Sep 18 2014 - 18:18:52 PDT)
- Re: [AMBER] ask for help Jason Swails (Thu Sep 18 2014 - 19:06:48 PDT)
  - Re: [AMBER] ask for help m13654940810 (Thu Sep 18 2014 - 19:39:58 PDT)
    - Re: [AMBER] ask for help David A Case (Fri Sep 19 2014 - 07:16:40 PDT)
    - Re: [AMBER] ask for help m13654940810 (Fri Sep 19 2014 - 18:01:28 PDT)
[AMBER] Any other way ? Arun Srikanth (Thu Sep 18 2014 - 19:13:16 PDT)
- Re: [AMBER] Any other way ? Jason Swails (Thu Sep 18 2014 - 19:27:45 PDT)
[AMBER] lipids14 pdb format Sergio Decherchi (Fri Sep 19 2014 - 04:31:45 PDT)
[AMBER] CUDA 5.0 versus 5.5/6.0 Carlos Sosa (Fri Sep 19 2014 - 05:31:40 PDT)
- Re: [AMBER] CUDA 5.0 versus 5.5/6.0 Marc van der Kamp (Fri Sep 19 2014 - 05:34:04 PDT)
  - Re: [AMBER] CUDA 5.0 versus 5.5/6.0 Marc van der Kamp (Fri Sep 19 2014 - 05:37:00 PDT)
    - Re: [AMBER] CUDA 5.0 versus 5.5/6.0 Carlos Sosa (Fri Sep 19 2014 - 05:42:58 PDT)
  - Re: [AMBER] CUDA 5.0 versus 5.5/6.0 Carlos Sosa (Fri Sep 19 2014 - 05:41:55 PDT)
[AMBER] cpptraj Error: Atom was assigned a lower molecule # than previous atom Oliver Grant (Fri Sep 19 2014 - 06:12:20 PDT)
- Re: [AMBER] cpptraj Error: Atom was assigned a lower molecule # than previous atom Jason Swails (Fri Sep 19 2014 - 06:29:55 PDT)
  - Re: [AMBER] cpptraj Error: Atom was assigned a lower molecule # than previous atom Daniel Roe (Fri Sep 19 2014 - 06:47:16 PDT)
[AMBER] PMEMD Distance Restraints Parker de Waal (Sat Sep 20 2014 - 13:55:44 PDT)
- Re: [AMBER] PMEMD Distance Restraints David A Case (Sun Sep 21 2014 - 07:20:59 PDT)
[AMBER] Suitability of MMPBSA to intercalator binding. 3-trajectory no improvement over 1-trajectory? Keiran Rowell (Sun Sep 21 2014 - 02:51:16 PDT)
- Re: [AMBER] Suitability of MMPBSA to intercalator binding. 3-trajectory no improvement over 1-trajectory? Vlad Cojocaru (Sun Sep 21 2014 - 03:36:06 PDT)
- Re: [AMBER] Suitability of MMPBSA to intercalator binding. 3-trajectory no improvement over 1-trajectory? Jason Swails (Sun Sep 21 2014 - 06:42:09 PDT)
  - Re: [AMBER] Suitability of MMPBSA to intercalator binding. 3-trajectory no improvement over 1-trajectory? Keiran Rowell (Mon Sep 22 2014 - 03:49:15 PDT)
    - Re: [AMBER] Suitability of MMPBSA to intercalator binding. 3-trajectory no improvement over 1-trajectory? Vlad Cojocaru (Mon Sep 22 2014 - 04:25:16 PDT)
[AMBER] Hbond Difference For Ambertools 12 and 14, or bug leexa.intern.bii.a-star.edu.sg (Sun Sep 21 2014 - 23:37:41 PDT)
- Re: [AMBER] Hbond Difference For Ambertools 12 and 14, or bug Daniel Roe (Mon Sep 22 2014 - 07:24:06 PDT)
  - Re: [AMBER] Hbond Difference For Ambertools 12 and 14, or bug Mary Varughese (Mon Sep 22 2014 - 10:05:38 PDT)
- Re: [AMBER] Hbond Difference For Ambertools 12 and 14, or bug leexa.intern.bii.a-star.edu.sg (Mon Sep 22 2014 - 17:56:55 PDT)
  - Re: [AMBER] Hbond Difference For Ambertools 12 and 14, or bug David A Case (Mon Sep 22 2014 - 18:30:29 PDT)
  - Re: [AMBER] Hbond Difference For Ambertools 12 and 14, or bug Daniel Roe (Mon Sep 22 2014 - 19:59:33 PDT)
- Re: [AMBER] Hbond Difference For Ambertools 12 and 14, or bug leexa.intern.bii.a-star.edu.sg (Tue Sep 23 2014 - 19:54:27 PDT)
[AMBER] RMSD on two slightly different structures Guillaume Roellinger (Mon Sep 22 2014 - 00:18:47 PDT)
- Re: [AMBER] RMSD on two slightly different structures Jason Swails (Mon Sep 22 2014 - 05:23:46 PDT)
  - Re: [AMBER] RMSD on two slightly different structures Guillaume Roellinger (Thu Sep 25 2014 - 01:39:49 PDT)
    - Re: [AMBER] RMSD on two slightly different structures Daniel Roe (Thu Sep 25 2014 - 08:14:08 PDT)
    - Re: [AMBER] RMSD on two slightly different structures Guillaume Roellinger (Fri Sep 26 2014 - 03:56:30 PDT)
- Re: [AMBER] RMSD on two slightly different structures Daniel Roe (Mon Sep 22 2014 - 07:03:16 PDT)
[AMBER] restart file Jacopo Sgrignani (Mon Sep 22 2014 - 02:26:31 PDT)
- Re: [AMBER] restart file Sourav Purohit (Mon Sep 22 2014 - 02:44:47 PDT)
- Re: [AMBER] restart file David A Case (Mon Sep 22 2014 - 04:27:02 PDT)
[AMBER] Sudden change of energies in min.out files maryam azimzadehirani (Mon Sep 22 2014 - 03:15:40 PDT)
- Re: [AMBER] Sudden change of energies in min.out files Jason Swails (Mon Sep 22 2014 - 07:10:14 PDT)
[AMBER] questions about Amber to run MD of Amoeba m13654940810 (Mon Sep 22 2014 - 05:12:40 PDT)
- Re: [AMBER] questions about Amber to run MD of Amoeba Jason Swails (Mon Sep 22 2014 - 05:36:29 PDT)
  - Re: [AMBER] questions about Amber to run MD of Amoeba m13654940810 (Mon Sep 22 2014 - 05:45:19 PDT)
    - Re: [AMBER] questions about Amber to run MD of Amoeba m13654940810 (Mon Sep 22 2014 - 06:28:08 PDT)
    - Re: [AMBER] questions about Amber to run MD of Amoeba Jason Swails (Mon Sep 22 2014 - 07:05:55 PDT)
    - Re: [AMBER] questions about Amber to run MD of Amoeba Daniel Roe (Mon Sep 22 2014 - 07:06:12 PDT)
    - Re: [AMBER] questions about Amber to run MD of Amoeba m13654940810 (Mon Sep 22 2014 - 07:45:30 PDT)
[AMBER] How can I run Production MD for lipid in Amber12 using Lipid11-ff? Bikash Ranjan Sahoo (Tue Sep 23 2014 - 01:06:31 PDT)
- Re: [AMBER] How can I run Production MD for lipid in Amber12 using Lipid11-ff? Hannes Loeffler (Tue Sep 23 2014 - 01:21:00 PDT)
  - Re: [AMBER] How can I run Production MD for lipid in Amber12 using Lipid11-ff? Bikash Ranjan Sahoo (Tue Sep 23 2014 - 01:43:10 PDT)
- Re: [AMBER] How can I run Production MD for lipid in Amber12 using Lipid11-ff? David A Case (Tue Sep 23 2014 - 04:01:32 PDT)
  - Re: [AMBER] How can I run Production MD for lipid in Amber12 using Lipid11-ff? Bikash Ranjan Sahoo (Tue Sep 23 2014 - 04:44:12 PDT)
    - Re: [AMBER] How can I run Production MD for lipid in Amber12 using Lipid11-ff? Jason Swails (Tue Sep 23 2014 - 05:04:53 PDT)
[AMBER] metalloproteins modeling Spelnikov Dmitriy (Tue Sep 23 2014 - 02:22:58 PDT)
[AMBER] trajout frames that statisfy hbond criteria George Green (Tue Sep 23 2014 - 04:57:01 PDT)
- Re: [AMBER] trajout frames that statisfy hbond criteria Daniel Roe (Tue Sep 23 2014 - 07:01:25 PDT)
  - Re: [AMBER] trajout frames that statisfy hbond criteria George Green (Tue Sep 23 2014 - 07:06:44 PDT)
[AMBER] file contains 2 atoms not in residue templates Vishal Nemaysh (Tue Sep 23 2014 - 06:22:57 PDT)
- [AMBER] Fwd: file contains 2 atoms not in residue templates Vishal Nemaysh (Tue Sep 23 2014 - 06:24:57 PDT)
- Re: [AMBER] file contains 2 atoms not in residue templates Jason Swails (Tue Sep 23 2014 - 06:46:33 PDT)
[AMBER] restrainr problem with PMEMD: using nmropt=1 and NTR=1 simultaneously George Green (Tue Sep 23 2014 - 06:39:58 PDT)
- Re: [AMBER] restrainr problem with PMEMD: using nmropt=1 and NTR=1 simultaneously Jason Swails (Tue Sep 23 2014 - 08:30:46 PDT)
  - Re: [AMBER] restrainr problem with PMEMD: using nmropt=1 and NTR=1 simultaneously George Green (Tue Sep 23 2014 - 12:20:42 PDT)
    - Re: [AMBER] restrainr problem with PMEMD: using nmropt=1 and NTR=1 simultaneously Gerald Monard (Tue Sep 23 2014 - 13:18:30 PDT)
    - Re: [AMBER] restrainr problem with PMEMD: using nmropt=1 and NTR=1 simultaneously Jason Swails (Tue Sep 23 2014 - 13:27:20 PDT)
    - Re: [AMBER] restrainr problem with PMEMD: using nmropt=1 and NTR=1 simultaneously George Green (Tue Sep 23 2014 - 14:28:39 PDT)
[AMBER] why the same structure and same topology have different energies using CHARMM and AMBER ? wliu (Tue Sep 23 2014 - 07:52:11 PDT)
[AMBER] negative values for the dihedral height barrier in GLYCAM ABEL Stephane 175950 (Tue Sep 23 2014 - 08:09:30 PDT)
- Re: [AMBER] negative values for the dihedral height barrier in GLYCAM Jason Swails (Tue Sep 23 2014 - 09:01:21 PDT)
  - Re: [AMBER] negative values for the dihedral height barrier in GLYCAM Lachele Foley (Tue Sep 23 2014 - 15:24:30 PDT)
[AMBER] Charmmlipid2amber.py failure Julio Dominguez (Tue Sep 23 2014 - 13:20:05 PDT)
[AMBER] Minimizing Size of Membrane Simulation Box Parker de Waal (Tue Sep 23 2014 - 18:05:57 PDT)
[AMBER] Zn CCCH Fonti Giulia (Wed Sep 24 2014 - 00:49:55 PDT)
- Re: [AMBER] Zn CCCH Esra Bozkurt (Wed Sep 24 2014 - 06:44:56 PDT)
- Re: [AMBER] Zn CCCH Pengfei Li (Wed Sep 24 2014 - 12:30:35 PDT)
[AMBER] Patches Installation Failure 张后今 (Wed Sep 24 2014 - 01:42:12 PDT)
- Re: [AMBER] Patches Installation Failure Jason Swails (Wed Sep 24 2014 - 04:52:28 PDT)
[AMBER] Using nvt production run after npt equilibration James Starlight (Wed Sep 24 2014 - 03:28:01 PDT)
[AMBER] problem on minimization ZHAO Ruisheng (Wed Sep 24 2014 - 05:18:48 PDT)
- Re: [AMBER] problem on minimization David A Case (Wed Sep 24 2014 - 06:43:48 PDT)
  - Re: [AMBER] problem on minimization ZHAO Ruisheng (Thu Sep 25 2014 - 01:09:46 PDT)
[AMBER] Parameter bond and angle file could not find Vishal Nemaysh (Wed Sep 24 2014 - 06:39:27 PDT)
- Re: [AMBER] Parameter bond and angle file could not find Jason Swails (Wed Sep 24 2014 - 07:26:39 PDT)
[AMBER] Xparmed.py Arun Srikanth (Wed Sep 24 2014 - 06:43:42 PDT)
- Re: [AMBER] Xparmed.py David A Case (Wed Sep 24 2014 - 07:49:23 PDT)
  - Re: [AMBER] Xparmed.py Arun Srikanth (Wed Sep 24 2014 - 08:22:23 PDT)
- Re: [AMBER] Xparmed.py Jason Swails (Wed Sep 24 2014 - 08:04:42 PDT)
  - Re: [AMBER] Xparmed.py Arun Srikanth (Wed Sep 24 2014 - 08:58:32 PDT)
    - Re: [AMBER] Xparmed.py Daniel Roe (Wed Sep 24 2014 - 09:05:15 PDT)
    - Re: [AMBER] Xparmed.py Arun Srikanth (Wed Sep 24 2014 - 09:25:18 PDT)
    - Re: [AMBER] Xparmed.py Jason Swails (Wed Sep 24 2014 - 11:57:51 PDT)
    - Re: [AMBER] Xparmed.py Arun Srikanth (Wed Sep 24 2014 - 12:07:26 PDT)
    - Re: [AMBER] Xparmed.py Jason Swails (Wed Sep 24 2014 - 13:28:54 PDT)
[AMBER] Removing periodicity from the restart file James Starlight (Wed Sep 24 2014 - 07:38:07 PDT)
- Re: [AMBER] Removing periodicity from the restart file Daniel Roe (Wed Sep 24 2014 - 07:42:59 PDT)
  - Re: [AMBER] Removing periodicity from the restart file James Starlight (Thu Sep 25 2014 - 00:52:23 PDT)
    - Re: [AMBER] Removing periodicity from the restart file Daniel Roe (Thu Sep 25 2014 - 08:03:01 PDT)
[AMBER] failure to run MMPBSA job... Shashidhar Rao (Wed Sep 24 2014 - 08:13:17 PDT)
- Re: [AMBER] failure to run MMPBSA job... Ray Luo, Ph.D. (Wed Sep 24 2014 - 10:40:52 PDT)
  - Re: [AMBER] failure to run MMPBSA job... Shashidhar Rao (Wed Sep 24 2014 - 11:00:37 PDT)
[AMBER] neutralizing systems for AMBER TI Lawrenz, Morgan (Wed Sep 24 2014 - 16:02:09 PDT)
- Re: [AMBER] neutralizing systems for AMBER TI Ying-Chieh Sun (Wed Sep 24 2014 - 20:05:01 PDT)
- Re: [AMBER] neutralizing systems for AMBER TI Jason Swails (Thu Sep 25 2014 - 07:20:41 PDT)
  - Re: [AMBER] neutralizing systems for AMBER TI Lawrenz, Morgan (Thu Sep 25 2014 - 09:23:19 PDT)
[AMBER] entropy Asfa Ali (Thu Sep 25 2014 - 00:31:48 PDT)
- Re: [AMBER] entropy David A Case (Thu Sep 25 2014 - 04:29:16 PDT)
[AMBER] Strip pdb from the hydrogens James Starlight (Thu Sep 25 2014 - 01:25:05 PDT)
- Re: [AMBER] Strip pdb from the hydrogens David A Case (Thu Sep 25 2014 - 04:34:54 PDT)
  - Re: [AMBER] Strip pdb from the hydrogens James Starlight (Thu Sep 25 2014 - 05:20:47 PDT)
[AMBER] Combined cartesian and NMR restraints Parker de Waal (Thu Sep 25 2014 - 18:43:54 PDT)
- Re: [AMBER] Combined cartesian and NMR restraints Parker de Waal (Thu Sep 25 2014 - 19:37:44 PDT)
- Re: [AMBER] Combined cartesian and NMR restraints David A Case (Thu Sep 25 2014 - 19:56:31 PDT)
  - Re: [AMBER] Combined cartesian and NMR restraints Parker de Waal (Thu Sep 25 2014 - 20:26:14 PDT)
    - Re: [AMBER] Combined cartesian and NMR restraints Parker de Waal (Fri Sep 26 2014 - 05:31:26 PDT)
    - Re: [AMBER] Combined cartesian and NMR restraints Jason Swails (Fri Sep 26 2014 - 07:05:01 PDT)
- Re: [AMBER] Combined cartesian and NMR restraints Peter Podbevšek (Fri Nov 13 2015 - 05:32:46 PST)
[AMBER] US AMBER Workshop - Save the date Ross Walker (Thu Sep 25 2014 - 21:27:26 PDT)
- [AMBER] single strand DNA Urszula Uciechowska (Mon Dec 08 2014 - 05:45:34 PST)
  - Re: [AMBER] single strand DNA Carlos Simmerling (Mon Dec 08 2014 - 06:09:57 PST)
[AMBER] cpptraj/parmbox amirhossein taghavi (Fri Sep 26 2014 - 00:13:59 PDT)
- Re: [AMBER] cpptraj/parmbox Jason Swails (Fri Sep 26 2014 - 06:47:45 PDT)
- Re: [AMBER] cpptraj/parmbox Daniel Roe (Fri Sep 26 2014 - 06:59:59 PDT)
- Re: [AMBER] cpptraj/parmbox Daniel Roe (Fri Sep 26 2014 - 10:21:42 PDT)
[AMBER] Fw: Welcome to Beijing for the 15th International Congress of Quantum Chemistry 石文 (Fri Sep 26 2014 - 05:49:17 PDT)
[AMBER] FATAL: Atom .R<NLEU -1>.A<H 22> does not have a type Soumendranath Bhakat (Fri Sep 26 2014 - 08:21:04 PDT)
- Re: [AMBER] FATAL: Atom .R<NLEU -1>.A<H 22> does not have a type Carlos Simmerling (Fri Sep 26 2014 - 08:26:22 PDT)
- Re: [AMBER] FATAL: Atom .R<NLEU -1>.A<H 22> does not have a type David A Case (Fri Sep 26 2014 - 08:54:02 PDT)
[AMBER] about MD m13654940810 (Fri Sep 26 2014 - 19:47:18 PDT)
- Re: [AMBER] about MD Jason Swails (Fri Sep 26 2014 - 20:51:03 PDT)
- Re: [AMBER] about MD David A Case (Sun Sep 28 2014 - 11:36:29 PDT)
[AMBER] Wrong atom type in the JCTC paper of lipid 14 ? ABEL Stephane 175950 (Sat Sep 27 2014 - 11:45:16 PDT)
[AMBER] Wrong atom type in the JCTC paper of lipid 14 ? - update ABEL Stephane 175950 (Sat Sep 27 2014 - 12:09:50 PDT)
[AMBER] MD simulation at 1M or 2M salt concentration 张后今 (Sat Sep 27 2014 - 18:59:03 PDT)
- Re: [AMBER] MD simulation at 1M or 2M salt concentration Jason Swails (Mon Sep 29 2014 - 05:23:05 PDT)
  - Re: [AMBER] MD simulation at 1M or 2M salt concentration 张后今 (Mon Sep 29 2014 - 05:48:24 PDT)
    - Re: [AMBER] MD simulation at 1M or 2M salt concentration Jason Swails (Mon Sep 29 2014 - 05:43:24 PDT)
    - Re: [AMBER] MD simulation at 1M or 2M salt concentration Jason Swails (Mon Sep 29 2014 - 06:01:11 PDT)
    - Re: [AMBER] MD simulation at 1M or 2M salt concentration Carlos Simmerling (Mon Sep 29 2014 - 05:47:28 PDT)
[AMBER] Entropy calculation using nmode fails Neha Rana (Sun Sep 28 2014 - 07:35:27 PDT)
Re: [AMBER] AMBER Digest, Vol 989, Issue 1 amirhossein taghavi (Mon Sep 29 2014 - 00:42:41 PDT)
- Re: [AMBER] AMBER Digest, Vol 989, Issue 1 Jason Swails (Mon Sep 29 2014 - 05:06:25 PDT)
[AMBER] some problems when using pmemd.cuda xueqiaoup.gmail.com (Mon Sep 29 2014 - 01:05:22 PDT)
- Re: [AMBER] some problems when using pmemd.cuda Jason Swails (Mon Sep 29 2014 - 05:15:29 PDT)
- Re: [AMBER] some problems when using pmemd.cuda xueqiaoup.gmail.com (Mon Sep 29 2014 - 19:33:39 PDT)
  - Re: [AMBER] some problems when using pmemd.cuda Jason Swails (Tue Sep 30 2014 - 04:11:32 PDT)
[AMBER] Parameter file was not saved. Vishal Nemaysh (Mon Sep 29 2014 - 06:38:05 PDT)
- Re: [AMBER] Parameter file was not saved. Jason Swails (Mon Sep 29 2014 - 07:13:50 PDT)
- Re: [AMBER] Parameter file was not saved. ros (Mon Sep 29 2014 - 07:58:45 PDT)
[AMBER] key word to pull out eigenvalues Nicole Ippolito (Mon Sep 29 2014 - 21:37:15 PDT)
- Re: [AMBER] key word to pull out eigenvalues Daniel Roe (Tue Sep 30 2014 - 07:14:48 PDT)
  - Re: [AMBER] key word to pull out eigenvalues newamber list (Tue Sep 30 2014 - 16:30:11 PDT)
[AMBER] about amoeba m13654940810 (Tue Sep 30 2014 - 01:04:40 PDT)
- Re: [AMBER] about amoeba Jason Swails (Tue Sep 30 2014 - 04:28:23 PDT)
[AMBER] learn more about cpptraj amirhossein taghavi (Tue Sep 30 2014 - 02:53:48 PDT)
- Re: [AMBER] learn more about cpptraj Jason Swails (Tue Sep 30 2014 - 04:20:25 PDT)
- Re: [AMBER] learn more about cpptraj Daniel Roe (Tue Sep 30 2014 - 07:17:25 PDT)
[AMBER] writing trr trajectory newamber list (Tue Sep 30 2014 - 15:50:43 PDT)
- Re: [AMBER] writing trr trajectory newamber list (Tue Sep 30 2014 - 16:16:50 PDT)
  - Re: [AMBER] writing trr trajectory Daniel Roe (Wed Oct 01 2014 - 07:11:50 PDT)
[AMBER] LIE FUNCTION Loïc Etheve (Wed Oct 01 2014 - 02:21:48 PDT)
- Re: [AMBER] LIE FUNCTION Jason Swails (Wed Oct 01 2014 - 04:20:17 PDT)
- Re: [AMBER] LIE FUNCTION Jason Swails (Wed Oct 01 2014 - 08:17:30 PDT)
[AMBER] switch from digest amirhossein taghavi (Wed Oct 01 2014 - 23:55:45 PDT)
- Re: [AMBER] switch from digest Jason Swails (Thu Oct 02 2014 - 19:49:40 PDT)
[AMBER] RAM error during multiple MMGBSA runs James Starlight (Thu Oct 02 2014 - 00:36:05 PDT)
- Re: [AMBER] RAM error during multiple MMGBSA runs Ray Luo, Ph.D. (Thu Oct 02 2014 - 13:24:05 PDT)
  - Re: [AMBER] RAM error during multiple MMGBSA runs James Starlight (Fri Oct 03 2014 - 01:45:17 PDT)
[AMBER] help: MD on DNA pradeep pant (Thu Oct 02 2014 - 03:33:58 PDT)
- Re: [AMBER] help: MD on DNA David A Case (Thu Oct 02 2014 - 05:17:00 PDT)
- [AMBER] help: MD on DNA pradeep pant (Fri Oct 03 2014 - 07:15:58 PDT)
  - Re: [AMBER] help: MD on DNA Jason Swails (Fri Oct 03 2014 - 09:23:37 PDT)
[AMBER] Problems with MMPBSA.py.MPI James Starlight (Fri Oct 03 2014 - 00:30:23 PDT)
[AMBER] carbon and nitrogen chemical shift restraints Alexandra Balaceanu (Fri Oct 03 2014 - 01:54:45 PDT)
- Re: [AMBER] carbon and nitrogen chemical shift restraints David A Case (Fri Oct 03 2014 - 06:32:15 PDT)
  - Re: [AMBER] carbon and nitrogen chemical shift restraints Alexandra Balaceanu (Fri Oct 03 2014 - 12:03:59 PDT)
[AMBER] Cluster RMSD Soumendranath Bhakat (Fri Oct 03 2014 - 02:48:54 PDT)
- Re: [AMBER] Cluster RMSD Daniel Roe (Fri Oct 03 2014 - 07:15:58 PDT)
[AMBER] Processing of the trajectories using ptraj James Starlight (Fri Oct 03 2014 - 05:13:18 PDT)
- Re: [AMBER] Processing of the trajectories using ptraj Daniel Roe (Fri Oct 03 2014 - 07:09:22 PDT)
  - Re: [AMBER] Processing of the trajectories using ptraj James Starlight (Mon Oct 06 2014 - 00:15:41 PDT)
    - Re: [AMBER] Processing of the trajectories using ptraj Daniel Roe (Mon Oct 06 2014 - 07:59:34 PDT)
[AMBER] QM/MM in amber, PME when qm_theory='extern' Aixiao Li (Fri Oct 03 2014 - 06:57:28 PDT)
- Re: [AMBER] QM/MM in amber, PME when qm_theory='extern' Brian Radak (Mon Oct 06 2014 - 14:27:59 PDT)
  - Re: [AMBER] QM/MM in amber, PME when qm_theory='extern' Andreas Goetz (Tue Oct 14 2014 - 22:00:19 PDT)
[AMBER] cpptraj Tutorial C1 George Tzotzos (Fri Oct 03 2014 - 11:25:11 PDT)
- Re: [AMBER] cpptraj Tutorial C1 George Tzotzos (Fri Oct 03 2014 - 11:36:40 PDT)
  - Re: [AMBER] cpptraj Tutorial C1 Jason Swails (Fri Oct 03 2014 - 11:50:06 PDT)
  - Re: [AMBER] cpptraj Tutorial C1 Daniel Roe (Fri Oct 03 2014 - 11:57:56 PDT)
[AMBER] Tethering water molecules in the receptor George Tzotzos (Sat Oct 04 2014 - 12:37:01 PDT)
- Re: [AMBER] Tethering water molecules in the receptor Jason Swails (Sat Oct 04 2014 - 14:09:00 PDT)
  - Re: [AMBER] Tethering water molecules in the receptor George Tzotzos (Sat Oct 04 2014 - 16:14:06 PDT)
    - Re: [AMBER] Tethering water molecules in the receptor Jason Swails (Sat Oct 04 2014 - 20:50:54 PDT)
[AMBER] Langevin thermostat in vacuu simulation o ..High RMSF of TEMP CHAMI F. (Sun Oct 05 2014 - 10:21:34 PDT)
- Re: [AMBER] Langevin thermostat in vacuu simulation o ..High RMSF of TEMP Jason Swails (Sun Oct 05 2014 - 19:24:56 PDT)
[AMBER] Dummy atom and PMEMD Miroslav Krepl (Sun Oct 05 2014 - 13:11:58 PDT)
- Re: [AMBER] Dummy atom and PMEMD Jason Swails (Sun Oct 05 2014 - 18:02:01 PDT)
  - Re: [AMBER] Dummy atom and PMEMD Miroslav Krepl (Mon Oct 06 2014 - 01:13:10 PDT)
    - Re: [AMBER] Dummy atom and PMEMD Jason Swails (Mon Oct 06 2014 - 04:26:38 PDT)
[AMBER] Trouble making frcmod file (ultimately to create prmtop file) Evans, Shalton (Mon Oct 06 2014 - 13:34:12 PDT)
- Re: [AMBER] Trouble making frcmod file (ultimately to create prmtop file) Jason Swails (Mon Oct 06 2014 - 13:42:53 PDT)
  - Re: [AMBER] Trouble making frcmod file (ultimately to create prmtop file) Brian Radak (Mon Oct 06 2014 - 14:35:01 PDT)
[AMBER] On the enthropy estimation in MMPBSA James Starlight (Tue Oct 07 2014 - 00:39:51 PDT)
- Re: [AMBER] On the enthropy estimation in MMPBSA James Starlight (Wed Oct 08 2014 - 01:30:55 PDT)
[AMBER] Chloroform box Neha Gandhi (Tue Oct 07 2014 - 00:49:12 PDT)
- Re: [AMBER] Chloroform box David A Case (Tue Oct 07 2014 - 04:30:20 PDT)
- Re: [AMBER] Chloroform box Jason Swails (Tue Oct 07 2014 - 04:52:18 PDT)
[AMBER] Need help for retrained MD Sudhanshu Shanker (Tue Oct 07 2014 - 03:37:59 PDT)
- Re: [AMBER] Need help for retrained MD Jason Swails (Tue Oct 07 2014 - 04:55:58 PDT)
  - Re: [AMBER] Need help for retrained MD Daniel Roe (Tue Oct 07 2014 - 07:36:41 PDT)
[AMBER] Fwd: parallel amber installation failed Fabian (Tue Oct 07 2014 - 06:45:39 PDT)
- Re: [AMBER] Fwd: parallel amber installation failed Daniel Roe (Tue Oct 07 2014 - 07:29:17 PDT)
  - Re: [AMBER] Fwd: parallel amber installation failed Fabian Glaser (Tue Oct 07 2014 - 09:42:58 PDT)
    - Re: [AMBER] Fwd: parallel amber installation failed David A Case (Tue Oct 07 2014 - 10:53:30 PDT)
    - Re: [AMBER] Fwd: parallel amber installation failed Jason Swails (Tue Oct 07 2014 - 10:58:59 PDT)
    - Re: [AMBER] Fwd: parallel amber installation failed Fabian Gmail (Tue Oct 07 2014 - 11:14:39 PDT)
    - Re: [AMBER] Fwd: parallel amber installation failed Jason Swails (Tue Oct 07 2014 - 10:55:49 PDT)
[AMBER] amber12 Installation Error MAC OS X BERGY (Tue Oct 07 2014 - 12:14:34 PDT)
- Re: [AMBER] amber12 Installation Error MAC OS X David A Case (Tue Oct 07 2014 - 13:27:14 PDT)
  - Re: [AMBER] amber12 Installation Error MAC OS X BERGY (Tue Oct 07 2014 - 14:46:12 PDT)
    - Re: [AMBER] amber12 Installation Error MAC OS X BERGY (Tue Oct 07 2014 - 15:12:11 PDT)
[AMBER] RNA with Malachite Green simulation Kasprzak, Wojciech (NIH/NCI) [C] (Tue Oct 07 2014 - 13:15:31 PDT)
[AMBER] Lambda Exchange Jeff Wereszczynski (Tue Oct 07 2014 - 19:19:29 PDT)
- Re: [AMBER] Lambda Exchange Jason Swails (Wed Oct 08 2014 - 05:18:38 PDT)
- Re: [AMBER] Lambda Exchange Jeff Wereszczynski (Wed Oct 08 2014 - 10:23:22 PDT)
  - Re: [AMBER] Lambda Exchange Jason Swails (Wed Oct 08 2014 - 11:30:40 PDT)
    - Re: [AMBER] Lambda Exchange Jeff Wereszczynski (Wed Oct 08 2014 - 11:50:31 PDT)
    - Re: [AMBER] Lambda Exchange Jason Swails (Wed Oct 08 2014 - 12:29:53 PDT)
[AMBER] No AMBERHOME/dat/mtkpp folder mmaestre.gate.sinica.edu.tw (Tue Oct 07 2014 - 20:15:54 PDT)
- Re: [AMBER] No AMBERHOME/dat/mtkpp folder Jason Swails (Wed Oct 08 2014 - 04:56:03 PDT)
- Re: [AMBER] No AMBERHOME/dat/mtkpp folder David A Case (Wed Oct 08 2014 - 05:03:26 PDT)
  - Re: [AMBER] No AMBERHOME/dat/mtkpp folder mmaestre.gate.sinica.edu.tw (Wed Oct 08 2014 - 16:35:44 PDT)
    - Re: [AMBER] No AMBERHOME/dat/mtkpp folder Jason Swails (Wed Oct 08 2014 - 16:56:08 PDT)
[AMBER] Regarding dihedrals in GAFF need clarification Arun Srikanth (Wed Oct 08 2014 - 07:09:37 PDT)
- Re: [AMBER] Regarding dihedrals in GAFF need clarification Jason Swails (Wed Oct 08 2014 - 07:19:58 PDT)
  - Re: [AMBER] Regarding dihedrals in GAFF need clarification Arun Srikanth (Wed Oct 08 2014 - 07:32:45 PDT)
    - Re: [AMBER] Regarding dihedrals in GAFF need clarification Jason Swails (Wed Oct 08 2014 - 07:35:22 PDT)
[AMBER] problems with "Could not find vdW" Investigador Química (Wed Oct 08 2014 - 07:40:50 PDT)
- Re: [AMBER] problems with "Could not find vdW" Jason Swails (Wed Oct 08 2014 - 07:51:00 PDT)
  - Re: [AMBER] problems with "Could not find vdW" Investigador Química (Wed Oct 08 2014 - 08:07:36 PDT)
    - Re: [AMBER] problems with "Could not find vdW" Jason Swails (Wed Oct 08 2014 - 08:13:59 PDT)
    - Re: [AMBER] problems with "Could not find vdW" Daniel Roe (Wed Oct 08 2014 - 08:15:45 PDT)
    - Re: [AMBER] problems with "Could not find vdW" Investigador Química (Thu Oct 09 2014 - 06:59:17 PDT)
    - Re: [AMBER] problems with "Could not find vdW" Daniel Roe (Thu Oct 09 2014 - 07:08:02 PDT)
    - Re: [AMBER] problems with "Could not find vdW" Investigador Química (Thu Oct 09 2014 - 07:18:20 PDT)
[AMBER] Is there a way to maintain pdb coordinates into leap? Jonathan Gough (Wed Oct 08 2014 - 11:14:22 PDT)
- Re: [AMBER] Is there a way to maintain pdb coordinates into leap? Bill Ross (Wed Oct 08 2014 - 11:48:12 PDT)
- Re: [AMBER] Is there a way to maintain pdb coordinates into leap? David A Case (Wed Oct 08 2014 - 14:19:56 PDT)
  - Re: [AMBER] Is there a way to maintain pdb coordinates into leap? Jonathan Gough (Wed Oct 08 2014 - 18:10:21 PDT)
[AMBER] Problem on generating topology file of lithium based electrolyte using GAFF Debashis Kundu (Wed Oct 08 2014 - 16:56:47 PDT)
[AMBER] Torsion Scan Zachary Davis (Wed Oct 08 2014 - 20:31:24 PDT)
- Re: [AMBER] Torsion Scan Dwight McGee (Wed Oct 08 2014 - 23:24:11 PDT)
[AMBER] Error: FFTW configure returned 77 during AMBER 12 installation sunita.tifrh.res.in (Thu Oct 09 2014 - 00:11:14 PDT)
- Re: [AMBER] Error: FFTW configure returned 77 during AMBER 12 installation Jason Swails (Thu Oct 09 2014 - 05:30:53 PDT)
  - Re: [AMBER] Error: FFTW configure returned 77 during AMBER 12 installation sunita.tifrh.res.in (Thu Oct 09 2014 - 06:02:20 PDT)
[AMBER] Zinc Paramitarization Patrick Appiah-Kubi (Thu Oct 09 2014 - 01:02:28 PDT)
- Re: [AMBER] Zinc Paramitarization Pengfei Li (Thu Oct 09 2014 - 08:25:50 PDT)
[AMBER] atom coordinate disagreement with sander TI Hannes Loeffler (Thu Oct 09 2014 - 04:15:27 PDT)
- Re: [AMBER] atom coordinate disagreement with sander TI David A Case (Thu Oct 09 2014 - 05:25:52 PDT)
  - Re: [AMBER] atom coordinate disagreement with sander TI Hannes Loeffler (Thu Oct 09 2014 - 08:15:30 PDT)
[AMBER] Zinc Parameterization Patrick Appiah-Kubi (Thu Oct 09 2014 - 08:26:14 PDT)
[AMBER] cpptraj hbond: query on output George Tzotzos (Thu Oct 09 2014 - 13:33:25 PDT)
- Re: [AMBER] cpptraj hbond: query on output Daniel Roe (Thu Oct 09 2014 - 15:24:35 PDT)
  - Re: [AMBER] cpptraj hbond: query on output George Tzotzos (Thu Oct 09 2014 - 17:00:58 PDT)
    - Re: [AMBER] cpptraj hbond: query on output Daniel Roe (Thu Oct 09 2014 - 18:14:53 PDT)
[AMBER] force field for lithium ion Evans, Shalton (Thu Oct 09 2014 - 16:11:11 PDT)
- Re: [AMBER] force field for lithium ion Mohd Farid Ismail (Thu Oct 09 2014 - 16:38:58 PDT)
[AMBER] Questions about restarting REMD simulations 王漠野 (Thu Oct 09 2014 - 23:25:58 PDT)
- Re: [AMBER] Questions about restarting REMD simulations Daniel Roe (Fri Oct 10 2014 - 06:48:16 PDT)
  - Re: [AMBER] Questions about restarting REMD simulations 王漠野 (Fri Oct 10 2014 - 19:01:00 PDT)
- Re: [AMBER] Questions about restarting REMD simulations Jason Swails (Fri Oct 10 2014 - 12:41:17 PDT)
  - Re: [AMBER] Questions about restarting REMD simulations 王漠野 (Fri Oct 10 2014 - 18:54:26 PDT)
    - Re: [AMBER] Questions about restarting REMD simulations Jason Swails (Fri Oct 10 2014 - 19:01:49 PDT)
[AMBER] CUDA test failed Niels Geudens (Fri Oct 10 2014 - 03:42:56 PDT)
- Re: [AMBER] CUDA test failed Jason Swails (Fri Oct 10 2014 - 09:25:21 PDT)
[AMBER] crashing multisander with TI/dummy Hannes Loeffler (Fri Oct 10 2014 - 04:11:21 PDT)
[AMBER] Restarting MD production run Soumendranath Bhakat (Sat Oct 11 2014 - 05:21:41 PDT)
- Re: [AMBER] Restarting MD production run Daniel Roe (Sat Oct 11 2014 - 10:07:07 PDT)
[AMBER] Forcefield_PTM Sourav Purohit (Sat Oct 11 2014 - 11:22:12 PDT)
- Re: [AMBER] Forcefield_PTM Adrian Roitberg (Sat Oct 11 2014 - 15:54:09 PDT)
- Re: [AMBER] Forcefield_PTM Ying-Chieh Sun (Sun Oct 12 2014 - 20:04:21 PDT)
- Re: [AMBER] Forcefield_PTM Sourav Purohit (Mon Oct 13 2014 - 02:35:31 PDT)
[AMBER] solvation free energy kirtana S (Sat Oct 11 2014 - 22:15:17 PDT)
- Re: [AMBER] solvation free energy David A Case (Sun Oct 12 2014 - 05:38:04 PDT)
  - Re: [AMBER] solvation free energy kirtana S (Sun Oct 12 2014 - 12:58:06 PDT)
    - Re: [AMBER] solvation free energy David A Case (Sun Oct 12 2014 - 13:44:03 PDT)
    - [AMBER] Calcium possibly replaced by carbon with MCPB mmaestre.gate.sinica.edu.tw (Sun Oct 12 2014 - 17:00:12 PDT)
    - Re: [AMBER] Calcium possibly replaced by carbon with MCPB Ken Merz (Mon Oct 13 2014 - 05:06:03 PDT)
    - Re: [AMBER] Calcium possibly replaced by carbon with MCPB mmaestre.gate.sinica.edu.tw (Mon Oct 13 2014 - 07:22:03 PDT)
    - Re: [AMBER] Calcium possibly replaced by carbon with MCPB Ken Merz (Mon Oct 13 2014 - 07:39:03 PDT)
    - Re: [AMBER] Calcium possibly replaced by carbon with MCPB Pengfei Li (Mon Oct 13 2014 - 07:45:43 PDT)
    - Re: [AMBER] Calcium possibly replaced by carbon with MCPB mmaestre.gate.sinica.edu.tw (Mon Oct 13 2014 - 16:22:45 PDT)
    - Re: [AMBER] Calcium possibly replaced by carbon with MCPB mmaestre.gate.sinica.edu.tw (Mon Oct 13 2014 - 16:19:41 PDT)
    - Re: [AMBER] Calcium possibly replaced by carbon with MCPB FyD (Mon Oct 13 2014 - 12:40:29 PDT)
    - Re: [AMBER] Calcium possibly replaced by carbon with MCPB mmaestre.gate.sinica.edu.tw (Mon Oct 13 2014 - 16:28:38 PDT)
    - Re: [AMBER] Calcium possibly replaced by carbon with MCPB Pengfei Li (Tue Oct 14 2014 - 08:26:44 PDT)
    - Re: [AMBER] Calcium possibly replaced by carbon with MCPB Pengfei Li (Tue Oct 14 2014 - 08:30:12 PDT)
    - Re: [AMBER] Calcium possibly replaced by carbon with MCPB mmaestre.gate.sinica.edu.tw (Tue Oct 14 2014 - 15:11:34 PDT)
    - Re: [AMBER] Calcium possibly replaced by carbon with MCPB mmaestre.gate.sinica.edu.tw (Tue Oct 14 2014 - 18:25:07 PDT)
    - Re: [AMBER] Calcium possibly replaced by carbon with MCPB Pengfei Li (Tue Oct 14 2014 - 21:17:05 PDT)
    - Re: [AMBER] solvation free energy kirtana S (Mon Oct 13 2014 - 21:53:58 PDT)
    - Re: [AMBER] solvation free energy kirtana S (Mon Oct 13 2014 - 22:07:27 PDT)
    - Re: [AMBER] solvation free energy David A Case (Tue Oct 14 2014 - 05:27:23 PDT)
[AMBER] About error of the Pmemd.cuda (14)/ aMD Yeng-Tseng Wang (Sun Oct 12 2014 - 07:15:07 PDT)
- Re: [AMBER] About error of the Pmemd.cuda (14)/ aMD Daniel Roe (Sun Oct 12 2014 - 09:34:59 PDT)
[AMBER] dendrimer-query Martiniano Bello Ramirez (Sun Oct 12 2014 - 09:59:42 PDT)
- Re: [AMBER] dendrimer-query Daniel Roe (Sun Oct 12 2014 - 10:14:57 PDT)
  - Re: [AMBER] dendrimer-query Vishal Maingi (Mon Oct 13 2014 - 08:33:34 PDT)
    - Re: [AMBER] dendrimer-query Daniel Roe (Tue Oct 14 2014 - 13:49:24 PDT)
    - Re: [AMBER] dendrimer-query Vishal Maingi (Thu Oct 16 2014 - 08:03:09 PDT)
[AMBER] why total energy of the system is on the rise in NVE ensemble zhangmk (Sun Oct 12 2014 - 19:43:03 PDT)
- Re: [AMBER] why total energy of the system is on the rise in NVE ensemble James Maier (Sun Oct 12 2014 - 19:52:58 PDT)
- Re: [AMBER] why total energy of the system is on the rise in NVE ensemble Hector A. Baldoni (Tue Oct 14 2014 - 16:34:16 PDT)
  - Re: [AMBER] why total energy of the system is on the rise in NVE ensemble David A Case (Wed Oct 15 2014 - 05:58:12 PDT)
[AMBER] DFTB3 in Amber Eric Lang (Sun Oct 12 2014 - 20:26:02 PDT)
- Re: [AMBER] DFTB3 in Amber Gustavo Seabra (Mon Oct 13 2014 - 05:50:07 PDT)
[AMBER] Setting exclusions correctly Arun Srikanth (Mon Oct 13 2014 - 00:12:15 PDT)
- Re: [AMBER] Setting exclusions correctly Jason Swails (Tue Oct 14 2014 - 14:12:28 PDT)
- Re: [AMBER] Setting exclusions correctly Daniel Roe (Tue Oct 14 2014 - 14:13:38 PDT)
  - Re: [AMBER] Setting exclusions correctly Arun Srikanth (Tue Oct 14 2014 - 15:38:33 PDT)
    - Re: [AMBER] Setting exclusions correctly Jason Swails (Wed Oct 15 2014 - 20:42:33 PDT)
[AMBER] Problem with lone pair Giachetti Andrea - CERM (Mon Oct 13 2014 - 01:23:03 PDT)
- Re: [AMBER] Problem with lone pair Jason Swails (Tue Oct 14 2014 - 14:37:17 PDT)
[AMBER] Building Amber 14 for Intel PHIs Baker D.J. (Mon Oct 13 2014 - 02:10:31 PDT)
- Re: [AMBER] Building Amber 14 for Intel PHIs Ross Walker (Mon Oct 13 2014 - 11:31:09 PDT)
  - Re: [AMBER] Building Amber 14 for Intel PHIs Baker D.J. (Tue Oct 14 2014 - 01:44:18 PDT)
[AMBER] Problem installing amber14 肖立 (Mon Oct 13 2014 - 11:08:44 PDT)
[AMBER] ATOMS DO NOT MATCH BETWEEN PARM AND MIN FILES 46946 0 Hirdesh Kumar (Mon Oct 13 2014 - 13:19:50 PDT)
- Re: [AMBER] ATOMS DO NOT MATCH BETWEEN PARM AND MIN FILES 46946 0 David A Case (Mon Oct 13 2014 - 13:28:37 PDT)
  - Re: [AMBER] ATOMS DO NOT MATCH BETWEEN PARM AND MIN FILES 46946 0 Hirdesh Kumar (Mon Oct 13 2014 - 13:41:58 PDT)
    - Re: [AMBER] ATOMS DO NOT MATCH BETWEEN PARM AND MIN FILES 46946 0 David A Case (Mon Oct 13 2014 - 18:02:29 PDT)
[AMBER] How to install sander.MPI? Zhong, Roger (Mon Oct 13 2014 - 13:50:11 PDT)
- Re: [AMBER] How to install sander.MPI? David A Case (Mon Oct 13 2014 - 18:05:55 PDT)
[AMBER] Amber 14 compile error 汪盛 (Mon Oct 13 2014 - 15:12:26 PDT)
- Re: [AMBER] Amber 14 compile error David A Case (Mon Oct 13 2014 - 18:10:12 PDT)
[AMBER] principal axes cpptraj Asmita Gupta (Tue Oct 14 2014 - 04:25:59 PDT)
- Re: [AMBER] principal axes cpptraj Daniel Roe (Tue Oct 14 2014 - 13:44:30 PDT)
[AMBER] Errors while attempting .prmtop file production Evans, Shalton (Tue Oct 14 2014 - 09:09:02 PDT)
- Re: [AMBER] Errors while attempting .prmtop file production David A Case (Tue Oct 14 2014 - 12:12:15 PDT)
[AMBER] GIST dx files Gard Nelson (Tue Oct 14 2014 - 11:42:35 PDT)
- Re: [AMBER] GIST dx files Jonathan Gough (Tue Oct 14 2014 - 12:34:28 PDT)
- Re: [AMBER] GIST dx files Nguyen, Crystal (Tue Oct 14 2014 - 12:31:59 PDT)
  - Re: [AMBER] GIST dx files Gard Nelson (Tue Oct 14 2014 - 15:23:51 PDT)
[AMBER] Loss of secondary structure in GB simulations Nihal Korkmaz (Tue Oct 14 2014 - 13:50:13 PDT)
- Re: [AMBER] Loss of secondary structure in GB simulations Carlos Simmerling (Tue Oct 14 2014 - 17:19:14 PDT)
  - Re: [AMBER] Loss of secondary structure in GB simulations Nihal Korkmaz (Tue Oct 14 2014 - 18:32:32 PDT)
- Re: [AMBER] Loss of secondary structure in GB simulations Hai Nguyen (Tue Oct 14 2014 - 22:00:49 PDT)
  - Re: [AMBER] Loss of secondary structure in GB simulations Nihal Korkmaz (Wed Oct 15 2014 - 14:29:51 PDT)
    - Re: [AMBER] Loss of secondary structure in GB simulations Nhai (Wed Oct 15 2014 - 15:49:34 PDT)
[AMBER] Amber for beginner Suraya Abdul Sani (Tue Oct 14 2014 - 17:21:29 PDT)
- Re: [AMBER] Amber for beginner Jonathan Gough (Tue Oct 14 2014 - 18:01:40 PDT)
- Re: [AMBER] Amber for beginner Raman Parkesh (Tue Oct 14 2014 - 20:01:55 PDT)
[AMBER] How can I do MD simulation of a protein-ligand complex where the ligand is covalently attached to the protein Bikash Ranjan Sahoo (Tue Oct 14 2014 - 21:04:54 PDT)
- [AMBER] How can I do MD simulation of a protein-ligand complex where the ligand is covalently attached to the protein Bikash Ranjan Sahoo (Wed Oct 15 2014 - 06:01:49 PDT)
[AMBER] TI and FEW sabine.ruppel.boehringer-ingelheim.com (Wed Oct 15 2014 - 13:11:22 PDT)
- Re: [AMBER] TI and FEW David A Case (Wed Oct 15 2014 - 17:57:07 PDT)
  - Re: [AMBER] TI and FEW sabine.ruppel.boehringer-ingelheim.com (Thu Oct 16 2014 - 06:03:57 PDT)
    - Re: [AMBER] TI and FEW David A Case (Thu Oct 16 2014 - 06:32:42 PDT)
    - Re: [AMBER] TI and FEW Nadine Homeyer (Mon Oct 20 2014 - 06:38:12 PDT)
    - Re: [AMBER] TI and FEW Nadine Homeyer (Mon Dec 01 2014 - 23:34:40 PST)
[AMBER] Setting exclusions - am i overcounting ? Arun Srikanth (Wed Oct 15 2014 - 14:56:12 PDT)
- Re: [AMBER] Setting exclusions - am i overcounting ? Daniel Roe (Wed Oct 15 2014 - 15:57:55 PDT)
  - Re: [AMBER] Setting exclusions - am i overcounting ? Arun Srikanth (Wed Oct 15 2014 - 17:05:23 PDT)
    - Re: [AMBER] Setting exclusions - am i overcounting ? Jason Swails (Wed Oct 15 2014 - 17:51:12 PDT)
[AMBER] How can I do MD simulation of a protein-ligand complex where the ligand is covalently attached to the protein Bikash Ranjan Sahoo (Wed Oct 15 2014 - 17:50:03 PDT)
Re: [AMBER] Setting exclusions - am i overcounting ?-Last question Arun Srikanth (Wed Oct 15 2014 - 19:54:42 PDT)
- Re: [AMBER] Setting exclusions - am i overcounting ?-Last question Jason Swails (Wed Oct 15 2014 - 21:24:38 PDT)
  - Re: [AMBER] Setting exclusions - am i overcounting ?-Last question Arun Srikanth (Wed Oct 15 2014 - 22:35:59 PDT)
[AMBER] Small NAB program: Not getting desired output Himanshu Joshi (Wed Oct 15 2014 - 22:41:28 PDT)
- Re: [AMBER] Small NAB program: Not getting desired output Himanshu Joshi (Wed Oct 15 2014 - 23:23:00 PDT)
  - Re: [AMBER] Small NAB program: Not getting desired output David A Case (Thu Oct 16 2014 - 05:11:07 PDT)
    - Re: [AMBER] Small NAB program: Not getting desired output Himanshu Joshi (Fri Oct 17 2014 - 00:45:39 PDT)
    - Re: [AMBER] Small NAB program: Not getting desired output David A Case (Fri Oct 17 2014 - 05:30:41 PDT)
[AMBER] amber-Gaussian 王珍 (Thu Oct 16 2014 - 05:41:43 PDT)
[AMBER] Plotting Issue Soumendranath Bhakat (Thu Oct 16 2014 - 07:26:49 PDT)
- Re: [AMBER] Plotting Issue Jason Swails (Thu Oct 16 2014 - 07:55:18 PDT)
[AMBER] Problem with input coordinates file Francesco Gentile (Thu Oct 16 2014 - 10:55:19 PDT)
- Re: [AMBER] Problem with input coordinates file Daniel Roe (Thu Oct 16 2014 - 12:52:36 PDT)
  - Re: [AMBER] Problem with input coordinates file Francesco Gentile (Thu Oct 16 2014 - 14:06:54 PDT)
    - Re: [AMBER] Problem with input coordinates file Daniel Roe (Thu Oct 16 2014 - 14:36:01 PDT)
    - Re: [AMBER] Problem with input coordinates file Daniel Roe (Fri Oct 17 2014 - 12:23:17 PDT)
    - Re: [AMBER] Problem with input coordinates file Francesco Gentile (Fri Oct 17 2014 - 13:01:13 PDT)
    - Re: [AMBER] Problem with input coordinates file Francesco Gentile (Tue Oct 21 2014 - 13:05:00 PDT)
[AMBER] Loadpdb in Tleap takes forever Ahmed Ayoub (Thu Oct 16 2014 - 11:16:44 PDT)
- Re: [AMBER] Loadpdb in Tleap takes forever Daniel Roe (Thu Oct 16 2014 - 12:55:26 PDT)
[AMBER] install error after updates Nihal Korkmaz (Thu Oct 16 2014 - 11:22:42 PDT)
- Re: [AMBER] install error after updates Daniel Roe (Thu Oct 16 2014 - 12:24:57 PDT)
[AMBER] source leaprc.constph error jinfeng liu (Thu Oct 16 2014 - 15:07:24 PDT)
- Re: [AMBER] source leaprc.constph error Jason Swails (Thu Oct 16 2014 - 16:11:24 PDT)
  - Re: [AMBER] source leaprc.constph error jinfeng liu (Thu Oct 16 2014 - 17:29:35 PDT)
    - Re: [AMBER] source leaprc.constph error Jason Swails (Thu Oct 16 2014 - 17:51:37 PDT)
    - Re: [AMBER] source leaprc.constph error jinfeng liu (Thu Oct 16 2014 - 18:12:49 PDT)
[AMBER] Which GPU is recommended? xueqiaoup.gmail.com (Thu Oct 16 2014 - 22:29:52 PDT)
- Re: [AMBER] Which GPU is recommended? Ross Walker (Fri Oct 17 2014 - 12:16:04 PDT)
- Re: [AMBER] Which GPU is recommended? Alexander Metz (Wed Oct 22 2014 - 03:54:31 PDT)
  - Re: [AMBER] Which GPU is recommended? Jason Swails (Wed Oct 22 2014 - 05:37:00 PDT)
Re: [AMBER] Need help for retrained MD (Daniel Roe) Sudhanshu Shanker (Fri Oct 17 2014 - 00:20:40 PDT)
- Re: [AMBER] Need help for retrained MD (Daniel Roe) Daniel Roe (Fri Oct 17 2014 - 06:54:54 PDT)
[AMBER] Jarzynski SMD George Tzotzos (Fri Oct 17 2014 - 12:39:19 PDT)
- Re: [AMBER] Jarzynski SMD Jason Swails (Fri Oct 17 2014 - 14:38:47 PDT)
[AMBER] thanks zayan alhalabi (Sat Oct 18 2014 - 07:45:10 PDT)
[AMBER] Regarding impropers from parmed.py and guessing from bond topology Arun Srikanth (Sat Oct 18 2014 - 14:38:36 PDT)
- Re: [AMBER] Regarding impropers from parmed.py and guessing from bond topology Daniel Roe (Sat Oct 18 2014 - 16:24:23 PDT)
  - Re: [AMBER] Regarding impropers from parmed.py and guessing from bond topology Arun Srikanth (Sat Oct 18 2014 - 20:20:41 PDT)
    - Re: [AMBER] Regarding impropers from parmed.py and guessing from bond topology Jason Swails (Sat Oct 18 2014 - 21:52:51 PDT)
    - Re: [AMBER] Regarding impropers from parmed.py and guessing from bond topology Arun Srikanth (Sun Oct 19 2014 - 21:16:10 PDT)
    - Re: [AMBER] Regarding impropers from parmed.py and guessing from bond topology Jason Swails (Sun Oct 19 2014 - 21:27:52 PDT)
    - Re: [AMBER] Regarding impropers from parmed.py and guessing from bond topology Arun Srikanth (Sun Oct 19 2014 - 21:45:08 PDT)
    - Re: [AMBER] Regarding impropers from parmed.py and guessing from bond topology Jason Swails (Sun Oct 19 2014 - 23:08:30 PDT)
    - Re: [AMBER] Regarding impropers from parmed.py and guessing from bond topology Arun Srikanth (Sun Oct 19 2014 - 23:24:39 PDT)
- Re: [AMBER] Regarding impropers from parmed.py and guessing from bond topology Jason Swails (Sat Oct 18 2014 - 16:27:12 PDT)
- Re: [AMBER] Regarding impropers from parmed.py and guessing from bond topology David A Case (Sat Oct 18 2014 - 18:13:59 PDT)
[AMBER] solvation of a pdb file Robin Jain (Sun Oct 19 2014 - 08:19:37 PDT)
- Re: [AMBER] solvation of a pdb file David A Case (Sun Oct 19 2014 - 10:47:46 PDT)
[AMBER] Fwd: Desmond trajectory use with AMBER D.A. Ragland (Sun Oct 19 2014 - 11:26:28 PDT)
- Re: [AMBER] Fwd: Desmond trajectory use with AMBER Daniel Roe (Sun Oct 19 2014 - 11:49:37 PDT)
  - Re: [AMBER] Desmond trajectory use with AMBER D.A. Ragland (Sun Oct 19 2014 - 11:53:11 PDT)
    - Re: [AMBER] Desmond trajectory use with AMBER Daniel Roe (Sun Oct 19 2014 - 12:06:49 PDT)
    - Re: [AMBER] Desmond trajectory use with AMBER D.A. Ragland (Sun Oct 19 2014 - 12:09:36 PDT)
    - Re: [AMBER] Desmond trajectory use with AMBER Daniel Roe (Sun Oct 19 2014 - 12:20:01 PDT)
- Re: [AMBER] Fwd: Desmond trajectory use with AMBER jojartb.jgypk.u-szeged.hu (Sun Oct 19 2014 - 21:15:39 PDT)
[AMBER] Heating Problem jinfeng liu (Sun Oct 19 2014 - 11:49:21 PDT)
- Re: [AMBER] Heating Problem Daniel Roe (Sun Oct 19 2014 - 12:01:39 PDT)
[AMBER] Parameters for Boron atom 王璇 (Sun Oct 19 2014 - 18:26:39 PDT)
- Re: [AMBER] Parameters for Boron atom David A Case (Mon Oct 20 2014 - 05:06:08 PDT)
[AMBER] Complex MD with protein ligand covalent bond Bikash Ranjan Sahoo (Mon Oct 20 2014 - 00:01:36 PDT)
- Re: [AMBER] Complex MD with protein ligand covalent bond David A Case (Mon Oct 20 2014 - 05:10:28 PDT)
[AMBER] MMGBSA & igb 8 jojartb.jgypk.u-szeged.hu (Mon Oct 20 2014 - 03:01:27 PDT)
- Re: [AMBER] MMGBSA & igb 8 Jason Swails (Mon Oct 20 2014 - 07:34:01 PDT)
  - Re: [AMBER] MMGBSA & igb 8 Carlos Simmerling (Mon Oct 20 2014 - 07:43:06 PDT)
[AMBER] Problem regarding Chamber Shubhadip Das (Mon Oct 20 2014 - 04:28:43 PDT)
- Re: [AMBER] Problem regarding Chamber Jason Swails (Mon Oct 20 2014 - 07:32:12 PDT)
- Re: [AMBER] Problem regarding Chamber Jason Swails (Thu Oct 23 2014 - 00:45:33 PDT)
- Re: [AMBER] Problem regarding Chamber Jason Swails (Fri Oct 24 2014 - 08:14:56 PDT)
[AMBER] Carboxyl and Carboxylate groups with GLYCAM sa (Mon Oct 20 2014 - 08:52:47 PDT)
- Re: [AMBER] Carboxyl and Carboxylate groups with GLYCAM Lachele Foley (Tue Oct 21 2014 - 10:44:32 PDT)
  - Re: [AMBER] Carboxyl and Carboxylate groups with GLYCAM sa (Tue Oct 21 2014 - 11:33:36 PDT)
    - Re: [AMBER] Carboxyl and Carboxylate groups with GLYCAM Lachele Foley (Tue Oct 21 2014 - 13:06:12 PDT)
    - Re: [AMBER] Carboxyl and Carboxylate groups with GLYCAM sa (Tue Oct 21 2014 - 13:32:59 PDT)
    - Re: [AMBER] Carboxyl and Carboxylate groups with GLYCAM Lachele Foley (Tue Oct 21 2014 - 13:57:27 PDT)
    - Re: [AMBER] Carboxyl and Carboxylate groups with GLYCAM sa (Tue Oct 21 2014 - 14:24:21 PDT)
[AMBER] How can I get amber know calcium jinfeng liu (Mon Oct 20 2014 - 09:35:44 PDT)
- Re: [AMBER] How can I get amber know calcium Sajeewa Pemasinghe (Mon Oct 20 2014 - 10:41:44 PDT)
- Re: [AMBER] How can I get amber know calcium Jason Swails (Mon Oct 20 2014 - 10:44:23 PDT)
  - Re: [AMBER] How can I get amber know calcium jinfeng liu (Mon Oct 20 2014 - 10:57:29 PDT)
    - Re: [AMBER] How can I get amber know calcium Chinthaka Ratnaweera (Mon Oct 20 2014 - 11:28:01 PDT)
    - Re: [AMBER] How can I get amber know calcium Pengfei Li (Mon Oct 20 2014 - 11:38:20 PDT)
    - Re: [AMBER] How can I get amber know calcium Chinthaka Ratnaweera (Mon Oct 20 2014 - 11:47:19 PDT)
    - Re: [AMBER] How can I get amber know calcium Pengfei Li (Mon Oct 20 2014 - 11:50:18 PDT)
    - Re: [AMBER] How can I get amber know calcium Ken Merz (Mon Oct 20 2014 - 11:50:47 PDT)
    - Re: [AMBER] How can I get amber know calcium Chinthaka Ratnaweera (Mon Oct 20 2014 - 12:09:44 PDT)
    - Re: [AMBER] How can I get amber know calcium Pengfei Li (Mon Oct 20 2014 - 14:08:33 PDT)
    - Re: [AMBER] How can I get amber know calcium mmaestre.gate.sinica.edu.tw (Mon Oct 20 2014 - 16:15:09 PDT)
[AMBER] Chains missing during the simulation Harshavardhan Khare (Tue Oct 21 2014 - 00:56:58 PDT)
- Re: [AMBER] Chains missing during the simulation Jason Swails (Tue Oct 21 2014 - 04:39:46 PDT)
  - Re: [AMBER] Chains missing during the simulation Harshavardhan Khare (Wed Oct 22 2014 - 04:23:31 PDT)
[AMBER] Forcefield_PTM Sourav Purohit (Tue Oct 21 2014 - 05:25:40 PDT)
- Re: [AMBER] Forcefield_PTM Jason Swails (Tue Oct 21 2014 - 06:02:30 PDT)
  - Re: [AMBER] Forcefield_PTM David A Case (Tue Oct 21 2014 - 07:47:22 PDT)
    - Re: [AMBER] Forcefield_PTM Sourav Purohit (Tue Oct 21 2014 - 08:35:00 PDT)
[AMBER] Cpptraj: Move origin to specific coordinates Waldner, Birgit (Tue Oct 21 2014 - 06:09:31 PDT)
- Re: [AMBER] Cpptraj: Move origin to specific coordinates Daniel Roe (Tue Oct 21 2014 - 08:06:58 PDT)
  - Re: [AMBER] Cpptraj: Move origin to specific coordinates Waldner, Birgit (Tue Oct 21 2014 - 08:37:15 PDT)
    - Re: [AMBER] Cpptraj: Move origin to specific coordinates Daniel Roe (Tue Oct 21 2014 - 09:07:31 PDT)
[AMBER] BSUB on LSF cluster D.A. Ragland (Tue Oct 21 2014 - 14:54:55 PDT)
- Re: [AMBER] BSUB on LSF cluster Jason Swails (Tue Oct 21 2014 - 17:10:02 PDT)
  - Re: [AMBER] BSUB on LSF cluster D.A. Ragland (Tue Oct 21 2014 - 17:12:02 PDT)
    - Re: [AMBER] BSUB on LSF cluster Jason Swails (Tue Oct 21 2014 - 17:56:05 PDT)
  - Re: [AMBER] BSUB on LSF cluster D.A. Ragland (Tue Oct 21 2014 - 17:18:47 PDT)
[AMBER] Info About GPU and PMEMD versions Lorenzo Gontrani (Wed Oct 22 2014 - 01:55:50 PDT)
- Re: [AMBER] Info About GPU and PMEMD versions Jason Swails (Wed Oct 22 2014 - 05:55:33 PDT)
- Re: [AMBER] Info About GPU and PMEMD versions Ross Walker (Wed Oct 22 2014 - 07:56:30 PDT)
[AMBER] ANTECHAMBER tutorial Sourav Purohit (Wed Oct 22 2014 - 03:35:04 PDT)
- Re: [AMBER] ANTECHAMBER tutorial Jason Swails (Wed Oct 22 2014 - 05:41:57 PDT)
  - Re: [AMBER] ANTECHAMBER tutorial Sourav Purohit (Wed Oct 22 2014 - 05:43:29 PDT)
[AMBER] Forcefield for RNA Asfa Ali (Wed Oct 22 2014 - 22:52:47 PDT)
- Re: [AMBER] Forcefield for RNA Jiri Sponer (Thu Oct 23 2014 - 00:57:06 PDT)
- Re: [AMBER] Forcefield for RNA Jiri Sponer (Thu Oct 23 2014 - 01:12:50 PDT)
- Re: [AMBER] Forcefield for RNA Ilyas Yildirim (Thu Oct 23 2014 - 02:26:01 PDT)
- Re: [AMBER] Forcefield for RNA Jason Swails (Thu Oct 23 2014 - 04:07:19 PDT)
  - Re: [AMBER] Forcefield for RNA Asfa Ali (Thu Oct 23 2014 - 04:26:48 PDT)
    - Re: [AMBER] Forcefield for RNA David A Case (Thu Oct 23 2014 - 04:54:12 PDT)
    - Re: [AMBER] Forcefield for RNA Jiri Sponer (Thu Oct 23 2014 - 13:58:58 PDT)
    - Re: [AMBER] Forcefield for RNA koushik (Thu Oct 23 2014 - 14:03:54 PDT)
    - Re: [AMBER] Forcefield for RNA koushik (Thu Oct 23 2014 - 14:06:58 PDT)
- Re: [AMBER] Forcefield for RNA pavel.banas.upol.cz (Thu Oct 23 2014 - 13:54:28 PDT)
  - Re: [AMBER] Forcefield for RNA Jiri Sponer (Thu Oct 23 2014 - 14:15:20 PDT)
    - Re: [AMBER] Forcefield for RNA Asfa Ali (Fri Oct 24 2014 - 05:46:02 PDT)
    - Re: [AMBER] Forcefield for RNA Jason Swails (Fri Oct 24 2014 - 06:19:43 PDT)
    - Re: [AMBER] Forcefield for RNA Asfa Ali (Sat Oct 25 2014 - 04:19:22 PDT)
    - [AMBER] loading force field ff14SB Vlad Cojocaru (Tue Oct 28 2014 - 08:12:18 PDT)
    - Re: [AMBER] loading force field ff14SB Jason Swails (Tue Oct 28 2014 - 08:36:05 PDT)
    - Re: [AMBER] loading force field ff14SB Vlad Cojocaru (Tue Oct 28 2014 - 08:56:57 PDT)
    - Re: [AMBER] loading force field ff14SB Jiri Sponer (Tue Oct 28 2014 - 09:17:05 PDT)
    - Re: [AMBER] loading force field ff14SB Christina Bergonzo (Tue Oct 28 2014 - 08:31:19 PDT)
[AMBER] peptideligandParameters zayan alhalabi (Thu Oct 23 2014 - 01:58:08 PDT)
- Re: [AMBER] peptideligandParameters Jason Swails (Fri Oct 24 2014 - 05:48:15 PDT)
- Re: [AMBER] peptideligandParameters FyD (Fri Oct 24 2014 - 22:17:11 PDT)
[AMBER] Number of water hits and density Suhaib Shekfeh (Thu Oct 23 2014 - 08:01:05 PDT)
- Re: [AMBER] Number of water hits and density Carlos Simmerling (Thu Oct 23 2014 - 10:18:00 PDT)
- Re: [AMBER] Number of water hits and density Thomas Cheatham (Thu Oct 23 2014 - 10:19:06 PDT)
- Re: [AMBER] Number of water hits and density Suhaib Shekfeh (Sun Oct 26 2014 - 06:50:42 PDT)
[AMBER] MMGBSA doesn't finish Bernhard Poll (Thu Oct 23 2014 - 23:22:40 PDT)
- Re: [AMBER] MMGBSA doesn't finish Jason Swails (Fri Oct 24 2014 - 04:53:10 PDT)
[AMBER] AMBER GAUSSIAN QM/MM Ayesha Fatima (Fri Oct 24 2014 - 00:23:29 PDT)
- Re: [AMBER] AMBER GAUSSIAN QM/MM Marc van der Kamp (Fri Oct 24 2014 - 01:07:50 PDT)
  - Re: [AMBER] AMBER GAUSSIAN QM/MM Ayesha Fatima (Fri Oct 24 2014 - 01:52:46 PDT)
[AMBER] Heme Parameters 杨川 (Fri Oct 24 2014 - 01:08:42 PDT)
- Re: [AMBER] Heme Parameters Jason Swails (Fri Oct 24 2014 - 04:44:57 PDT)
- Re: [AMBER] Heme Parameters David A Case (Fri Oct 24 2014 - 05:29:17 PDT)
[AMBER] PDB to P2N conversion Sylvester Tumusiime (Sat Oct 25 2014 - 09:14:53 PDT)
- Re: [AMBER] PDB to P2N conversion ABEL Stephane 175950 (Sat Oct 25 2014 - 12:09:28 PDT)
[AMBER] problem with extra-point Emilio Angelina (Sat Oct 25 2014 - 09:38:55 PDT)
- Re: [AMBER] problem with extra-point David A Case (Sat Oct 25 2014 - 13:05:01 PDT)
[AMBER] Temperature not correctly maintained using AMBER14 Gonzalo Jimenez (Sat Oct 25 2014 - 18:07:38 PDT)
- Re: [AMBER] Temperature not correctly maintained using AMBER14 Ross Walker (Sat Oct 25 2014 - 18:44:59 PDT)
  - Re: [AMBER] Temperature not correctly maintained using AMBER14 Gonzalo Jimenez (Sat Oct 25 2014 - 19:41:52 PDT)
    - Re: [AMBER] Temperature not correctly maintained using AMBER14 Ross Walker (Sun Oct 26 2014 - 13:22:33 PDT)
    - Re: [AMBER] Temperature not correctly maintained using AMBER14 Gonzalo Jimenez (Sun Oct 26 2014 - 14:15:46 PDT)
    - Re: [AMBER] Temperature not correctly maintained using AMBER14 Ross Walker (Sun Oct 26 2014 - 18:57:13 PDT)
[AMBER] Problem regarding Chamber Shubhadip Das (Sun Oct 26 2014 - 21:28:54 PDT)
- Re: [AMBER] Problem regarding Chamber Jason Swails (Mon Oct 27 2014 - 09:04:26 PDT)
[AMBER] MMPBSA Error: PB Bomb in pb_atmlist(): maxnba too short MOHD HOMAIDUR RAHMAN (Mon Oct 27 2014 - 00:27:34 PDT)
- Re: [AMBER] MMPBSA Error: PB Bomb in pb_atmlist(): maxnba too short Jason Swails (Mon Oct 27 2014 - 05:19:41 PDT)
[AMBER] Problem regarding Chamber and psf file Caitlin Scott (Mon Oct 27 2014 - 06:25:45 PDT)
- Re: [AMBER] Problem regarding Chamber and psf file Jason Swails (Mon Oct 27 2014 - 06:52:50 PDT)
  - Re: [AMBER] Problem regarding Chamber and psf file Caitlin Scott (Fri Oct 31 2014 - 07:20:04 PDT)
    - Re: [AMBER] Problem regarding Chamber and psf file Jason Swails (Fri Oct 31 2014 - 08:51:40 PDT)
    - Re: [AMBER] Problem regarding Chamber and psf file Pete Kekenes-Huskey (Fri Oct 31 2014 - 13:36:06 PDT)
    - Re: [AMBER] Problem regarding Chamber and psf file Jason Swails (Sat Nov 01 2014 - 15:35:39 PDT)
    - Re: [AMBER] Problem regarding Chamber and psf file Pete Kekenes-Huskey (Sun Nov 02 2014 - 17:18:23 PST)
- Re: [AMBER] Problem regarding Chamber and psf file David Sáez (Thu Sep 21 2017 - 13:45:09 PDT)
  - Re: [AMBER] Problem regarding Chamber and psf file Jason Swails (Thu Sep 21 2017 - 20:16:41 PDT)
    - Re: [AMBER] Problem regarding Chamber and psf file David Sáez (Thu Sep 21 2017 - 21:30:22 PDT)
[AMBER] Running G03 Brittany Boykin (Mon Oct 27 2014 - 12:14:43 PDT)
- Re: [AMBER] Running G03 Kshatresh Dutta Dubey (Mon Oct 27 2014 - 13:19:53 PDT)
- Re: [AMBER] Running G03 FyD (Mon Oct 27 2014 - 23:50:10 PDT)
[AMBER] GPU enabled Hardware specification M. Reza Ganjalikhany (Mon Oct 27 2014 - 13:39:41 PDT)
- Re: [AMBER] GPU enabled Hardware specification Scott Le Grand (Mon Oct 27 2014 - 14:19:45 PDT)
  - Re: [AMBER] GPU enabled Hardware specification M. Reza Ganjalikhany (Tue Oct 28 2014 - 02:41:10 PDT)
    - Re: [AMBER] GPU enabled Hardware specification Jonathan Gough (Tue Oct 28 2014 - 06:35:20 PDT)
    - Re: [AMBER] GPU enabled Hardware specification Jonathan Gough (Tue Oct 28 2014 - 07:42:41 PDT)
    - Re: [AMBER] GPU enabled Hardware specification Ross Walker (Tue Oct 28 2014 - 07:53:31 PDT)
    - Re: [AMBER] GPU enabled Hardware specification M. Reza Ganjalikhany (Tue Oct 28 2014 - 12:50:36 PDT)
    - Re: [AMBER] GPU enabled Hardware specification Scott Le Grand (Tue Oct 28 2014 - 12:59:37 PDT)
    - Re: [AMBER] GPU enabled Hardware specification Ross Walker (Tue Oct 28 2014 - 14:02:49 PDT)
    - Re: [AMBER] GPU enabled Hardware specification M. Reza Ganjalikhany (Sat Nov 15 2014 - 02:41:01 PST)
    - Re: [AMBER] GPU enabled Hardware specification Ross Walker (Sat Nov 15 2014 - 12:49:49 PST)
    - Re: [AMBER] GPU enabled Hardware specification M. Reza Ganjalikhany (Sat Nov 15 2014 - 23:49:46 PST)
    - Re: [AMBER] GPU enabled Hardware specification Ross Walker (Sun Nov 16 2014 - 12:22:46 PST)
    - Re: [AMBER] GPU enabled Hardware specification M. Reza Ganjalikhany (Mon Nov 17 2014 - 01:17:18 PST)
    - Re: [AMBER] GPU enabled Hardware specification Ross Walker (Mon Nov 17 2014 - 11:35:24 PST)
    - Re: [AMBER] GPU enabled Hardware specification M. Reza Ganjalikhany (Mon Nov 17 2014 - 12:28:15 PST)
[AMBER] Regarding Protein-ligand MD Bikash Ranjan Sahoo (Mon Oct 27 2014 - 19:58:33 PDT)
- Re: [AMBER] Regarding Protein-ligand MD Robin Betz (Mon Oct 27 2014 - 20:02:48 PDT)
  - Re: [AMBER] Regarding Protein-ligand MD Bikash Ranjan Sahoo (Mon Oct 27 2014 - 20:17:02 PDT)
- Re: [AMBER] Regarding Protein-ligand MD FyD (Tue Oct 28 2014 - 02:02:22 PDT)
[AMBER] Problem about "Too many dipole_dipole interactions for allocated" when heat Ya Gao (Tue Oct 28 2014 - 19:30:34 PDT)
- Re: [AMBER] Problem about "Too many dipole_dipole interactions for allocated" when heat David A Case (Wed Oct 29 2014 - 04:38:52 PDT)
  - Re: [AMBER] Problem about "Too many dipole_dipole interactions for allocated" when heat Lorenzo Gontrani (Wed Oct 29 2014 - 04:58:33 PDT)
  - Re: [AMBER] Problem about "Too many dipole_dipole interactions for allocated" when heat Ya Gao (Wed Oct 29 2014 - 05:31:16 PDT)
[AMBER] Entropy calculation asdda asa (Tue Oct 28 2014 - 19:38:13 PDT)
- Re: [AMBER] Entropy calculation Jason Swails (Wed Oct 29 2014 - 10:44:29 PDT)
  - Re: [AMBER] Entropy calculation asdda asa (Wed Oct 29 2014 - 20:31:58 PDT)
Re: [AMBER] How do MCPB make sidechain.bcl? Saeed Nasiri (Tue Oct 28 2014 - 21:31:30 PDT)
- Re: [AMBER] How do MCPB make sidechain.bcl? Pengfei Li (Wed Oct 29 2014 - 12:50:22 PDT)
[AMBER] Problem about "Too many dipole_dipole interactions for allocated" in heat simulation Tong Zhu (Tue Oct 28 2014 - 22:23:48 PDT)
[AMBER] problem in DNA-ligand trajectory Mina Madah (Wed Oct 29 2014 - 03:54:31 PDT)
- Re: [AMBER] problem in DNA-ligand trajectory Jason Swails (Wed Oct 29 2014 - 10:22:57 PDT)
[AMBER] Imaging Sylvester Tumusiime (Wed Oct 29 2014 - 08:10:36 PDT)
- Re: [AMBER] Imaging Daniel Roe (Wed Oct 29 2014 - 08:20:16 PDT)
  - Re: [AMBER] Imaging Sylvester Tumusiime (Wed Oct 29 2014 - 08:38:36 PDT)
    - Re: [AMBER] Imaging Daniel Roe (Wed Oct 29 2014 - 08:53:42 PDT)
    - Re: [AMBER] Imaging Sylvester Tumusiime (Wed Oct 29 2014 - 09:11:05 PDT)
    - Re: [AMBER] Imaging Sylvester Tumusiime (Wed Oct 29 2014 - 09:22:13 PDT)
    - Re: [AMBER] Imaging Daniel Roe (Wed Oct 29 2014 - 13:31:17 PDT)
    - Re: [AMBER] Imaging Sylvester Tumusiime (Wed Oct 29 2014 - 14:29:24 PDT)
    - Re: [AMBER] Imaging Sylvester Tumusiime (Thu Oct 30 2014 - 12:23:55 PDT)
    - Re: [AMBER] Imaging Thomas Cheatham (Thu Oct 30 2014 - 13:27:37 PDT)
    - Re: [AMBER] Imaging Daniel Roe (Thu Oct 30 2014 - 13:33:06 PDT)
    - Re: [AMBER] Imaging Sylvester Tumusiime (Thu Oct 30 2014 - 14:51:19 PDT)
    - Re: [AMBER] Imaging Daniel Roe (Mon Nov 03 2014 - 10:45:09 PST)
[AMBER] restart file position Fabian Glaser (Wed Oct 29 2014 - 08:31:42 PDT)
- Re: [AMBER] restart file position Jason Swails (Wed Oct 29 2014 - 10:17:22 PDT)
  - Re: [AMBER] restart file position Fabian Glaser (Sun Nov 02 2014 - 05:57:19 PST)
    - Re: [AMBER] restart file position Jason Swails (Sun Nov 02 2014 - 06:15:49 PST)
[AMBER] Implementing parameterized heme? Kevin Murphy (Wed Oct 29 2014 - 10:21:21 PDT)
- Re: [AMBER] Implementing parameterized heme? Pengfei Li (Wed Oct 29 2014 - 12:35:07 PDT)
  - Re: [AMBER] Implementing parameterized heme? Pengfei Li (Wed Oct 29 2014 - 12:44:02 PDT)
    - Re: [AMBER] Implementing parameterized heme? Yarrow Madrona (Wed Oct 29 2014 - 17:34:21 PDT)
    - Re: [AMBER] Implementing parameterized heme? Yarrow Madrona (Wed Oct 29 2014 - 17:46:23 PDT)
    - Re: [AMBER] Implementing parameterized heme? Pengfei Li (Thu Oct 30 2014 - 12:18:20 PDT)
    - Re: [AMBER] Implementing parameterized heme? Pengfei Li (Thu Oct 30 2014 - 12:15:27 PDT)
[AMBER] using multiple force fields in a simulation Bhushan (Thu Oct 30 2014 - 00:45:40 PDT)
- Re: [AMBER] using multiple force fields in a simulation Hannes Loeffler (Thu Oct 30 2014 - 02:26:37 PDT)
  - Re: [AMBER] using multiple force fields in a simulation Carlos Simmerling (Thu Oct 30 2014 - 08:00:06 PDT)
[AMBER] visualize CPPTRAJ clculated modes Vlad Cojocaru (Thu Oct 30 2014 - 02:35:20 PDT)
- Re: [AMBER] visualize CPPTRAJ clculated modes Jason Swails (Thu Oct 30 2014 - 04:33:21 PDT)
  - Re: [AMBER] visualize CPPTRAJ clculated modes Vlad Cojocaru (Thu Oct 30 2014 - 07:15:50 PDT)
    - Re: [AMBER] visualize CPPTRAJ clculated modes Daniel Roe (Thu Oct 30 2014 - 07:34:28 PDT)
[AMBER] Multiple timecorr commands in one cpptraj script Eugene Yedvabny (Thu Oct 30 2014 - 09:54:51 PDT)
- Re: [AMBER] Multiple timecorr commands in one cpptraj script George M Giambasu (Thu Oct 30 2014 - 11:29:36 PDT)
[AMBER] 3D Histogram in cpptraj CHAMI F. (Thu Oct 30 2014 - 10:18:44 PDT)
- Re: [AMBER] 3D Histogram in cpptraj Asaminew Haile (Thu Oct 30 2014 - 10:25:55 PDT)
  - Re: [AMBER] 3D Histogram in cpptraj CHAMI F. (Thu Oct 30 2014 - 10:31:17 PDT)
- Re: [AMBER] 3D Histogram in cpptraj Daniel Roe (Fri Oct 31 2014 - 09:53:42 PDT)
[AMBER] pyroglutamic acid or 5-oxoproline Yves Boulard (Fri Oct 31 2014 - 04:08:52 PDT)
[AMBER] About geometry of FAD in the F-90 project of http://q4md-forcefieldtools.org/ Emilio Lence (Fri Oct 31 2014 - 05:47:31 PDT)
[AMBER] Looking force field for beta-peptide MOHD HOMAIDUR RAHMAN (Fri Oct 31 2014 - 06:25:54 PDT)
- Re: [AMBER] Looking force field for beta-peptide David A Case (Fri Oct 31 2014 - 10:26:51 PDT)
[AMBER] Calculating Normalised electron density for DOPC. Him Shweta (Sat Nov 01 2014 - 06:10:58 PDT)
Re: [AMBER] [q4md-fft] FAD wrong geometry in F-90 project FyD (Sat Nov 01 2014 - 13:50:17 PDT)
[AMBER] Fwd: Re: [q4md-fft] FAD wrong geometry in F-90 project FyD (Sat Nov 01 2014 - 22:39:35 PDT)
[AMBER] Fully random MPI error after updating CentOS from release 6.5 to 6.6 Massimiliano Porrini (Mon Nov 03 2014 - 02:54:20 PST)
- Re: [AMBER] Fully random MPI error after updating CentOS from release 6.5 to 6.6 Jason Swails (Mon Nov 03 2014 - 04:36:57 PST)
  - Re: [AMBER] Fully random MPI error after updating CentOS from release 6.5 to 6.6 Massimiliano Porrini (Mon Nov 03 2014 - 08:25:52 PST)
[AMBER] The question about REMD exchange ratio 王漠野 (Mon Nov 03 2014 - 05:12:50 PST)
- Re: [AMBER] The question about REMD exchange ratio Jason Swails (Mon Nov 03 2014 - 06:03:25 PST)
[AMBER] Strange behavior AMBER12 IBRAHIM M ABDELRADY (Mon Nov 03 2014 - 07:52:59 PST)
- Re: [AMBER] Strange behavior AMBER12 Adrian Roitberg (Mon Nov 03 2014 - 07:55:22 PST)
- Re: [AMBER] Strange behavior AMBER12 Jason Swails (Mon Nov 03 2014 - 07:56:40 PST)
- Re: [AMBER] Strange behavior AMBER12 IBRAHIM M ABDELRADY (Mon Nov 03 2014 - 07:57:51 PST)
- Re: [AMBER] Strange behavior AMBER12 IBRAHIM M ABDELRADY (Mon Nov 03 2014 - 08:15:12 PST)
[AMBER] error message of addLJType of parmed: Action addLJType failed. UnhandledArgumentWarning: 0.0 0.0 sun (Mon Nov 03 2014 - 08:11:57 PST)
- Re: [AMBER] error message of addLJType of parmed: Action addLJType failed. UnhandledArgumentWarning: 0.0 0.0 Jason Swails (Mon Nov 03 2014 - 09:09:25 PST)
  - Re: [AMBER] error message of addLJType of parmed: Action addLJType failed. UnhandledArgumentWarning: 0.0 0.0 Ying-Chieh Sun (Mon Nov 03 2014 - 18:40:24 PST)
    - Re: [AMBER] error message of addLJType of parmed: Action addLJType failed. UnhandledArgumentWarning: 0.0 0.0 Jason Swails (Tue Nov 04 2014 - 04:33:54 PST)
[AMBER] single dimension PMF calculation joan.montesdeoca.uns.edu.ar (Mon Nov 03 2014 - 16:32:59 PST)
[AMBER] aMD error maryam azimzadehirani (Mon Nov 03 2014 - 23:23:10 PST)
- Re: [AMBER] aMD error Jason Swails (Tue Nov 04 2014 - 04:35:55 PST)
  - Re: [AMBER] aMD error maryam azimzadehirani (Wed Nov 05 2014 - 00:37:43 PST)
[AMBER] Error logs James Starlight (Tue Nov 04 2014 - 00:24:15 PST)
[AMBER] bug in pmemd softcore TI with SHAKE Hannes Loeffler (Tue Nov 04 2014 - 02:07:39 PST)
[AMBER] AMBER Question: Setting box angle in tleap 曲薇 (Wed Nov 05 2014 - 01:22:48 PST)
- Re: [AMBER] AMBER Question: Setting box angle in tleap David A Case (Wed Nov 05 2014 - 04:00:44 PST)
[AMBER] AM1-BCC dipole moment CHAMI F. (Wed Nov 05 2014 - 04:20:04 PST)
- Re: [AMBER] AM1-BCC dipole moment David A Case (Wed Nov 05 2014 - 07:10:11 PST)
  - Re: [AMBER] AM1-BCC dipole moment Jason Swails (Wed Nov 05 2014 - 07:21:05 PST)
    - Re: [AMBER] AM1-BCC dipole moment CHAMI F. (Mon Nov 10 2014 - 05:51:33 PST)
    - Re: [AMBER] AM1-BCC dipole moment Jason Swails (Mon Nov 10 2014 - 06:01:52 PST)
    - Re: [AMBER] AM1-BCC dipole moment CHAMI F. (Mon Nov 10 2014 - 07:10:10 PST)
    - Re: [AMBER] AM1-BCC dipole moment Hannes Loeffler (Mon Nov 10 2014 - 07:59:09 PST)
[AMBER] H-REMD Mele N. (Wed Nov 05 2014 - 08:20:33 PST)
- Re: [AMBER] H-REMD Carlos Simmerling (Wed Nov 05 2014 - 08:52:48 PST)
- Re: [AMBER] H-REMD Jason Swails (Wed Nov 05 2014 - 09:05:07 PST)
[AMBER] NBCR AMBER Workshop - UCSD - Mon Dec 15th to Thur Dec 18th 2014 - Registration open. Ross Walker (Wed Nov 05 2014 - 12:40:05 PST)
[AMBER] cpptraj hist 3D CHAMI F. (Thu Nov 06 2014 - 04:54:58 PST)
- Re: [AMBER] cpptraj hist 3D Jason Swails (Thu Nov 06 2014 - 06:29:21 PST)
  - Re: [AMBER] cpptraj hist 3D andrea spitaleri (Thu Nov 06 2014 - 06:38:23 PST)
    - Re: [AMBER] cpptraj hist 3D Jason Swails (Thu Nov 06 2014 - 11:36:39 PST)
    - Re: [AMBER] cpptraj hist 3D andrea spitaleri (Thu Nov 06 2014 - 11:54:52 PST)
- Re: [AMBER] cpptraj hist 3D Daniel Roe (Thu Nov 06 2014 - 09:35:46 PST)
  - Re: [AMBER] cpptraj hist 3D andrea spitaleri (Thu Nov 06 2014 - 10:39:55 PST)
[AMBER] Binding energy using mm_pbsa.pl Wong, Sook (NIH/NCATS) [V] (Thu Nov 06 2014 - 08:28:57 PST)
- Re: [AMBER] Binding energy using mm_pbsa.pl Aron Broom (Thu Nov 06 2014 - 11:51:30 PST)
  - Re: [AMBER] Binding energy using mm_pbsa.pl Wong, Sook (NIH/NCATS) [V] (Thu Nov 06 2014 - 12:05:34 PST)
    - Re: [AMBER] Binding energy using mm_pbsa.pl Aron Broom (Thu Nov 06 2014 - 12:14:04 PST)
    - Re: [AMBER] Binding energy using mm_pbsa.pl Jason Swails (Thu Nov 06 2014 - 12:18:46 PST)
    - Re: [AMBER] Binding energy using mm_pbsa.pl Wong, Sook (NIH/NCATS) [V] (Thu Nov 06 2014 - 12:24:03 PST)
    - Re: [AMBER] Binding energy using mm_pbsa.pl Jason Swails (Thu Nov 06 2014 - 12:34:39 PST)
    - Re: [AMBER] Binding energy using mm_pbsa.pl Wong, Sook (NIH/NCATS) [V] (Thu Nov 06 2014 - 12:54:14 PST)
    - Re: [AMBER] Binding energy using mm_pbsa.pl Aron Broom (Thu Nov 06 2014 - 13:50:38 PST)
    - Re: [AMBER] Binding energy using mm_pbsa.pl Jason Swails (Thu Nov 06 2014 - 13:55:10 PST)
    - Re: [AMBER] Binding energy using mm_pbsa.pl Wong, Sook (NIH/NCATS) [V] (Fri Nov 07 2014 - 13:15:03 PST)
[AMBER] determine free available space in simulation box Iqbal, Muhammad Sajid (Thu Nov 06 2014 - 11:04:12 PST)
[AMBER] Problems on PRMTOP file generation under ff02pol.r1 Wei Ye (Thu Nov 06 2014 - 20:09:02 PST)
- Re: [AMBER] Problems on PRMTOP file generation under ff02pol.r1 David A Case (Fri Nov 07 2014 - 05:53:09 PST)
  - Re: [AMBER] Problems on PRMTOP file generation under ff02pol.r1 Wei Ye (Fri Nov 07 2014 - 06:01:54 PST)
[AMBER] DRUG_PROTEIN INTERACTIOM Ruchika Bhat (Thu Nov 06 2014 - 22:53:11 PST)
- Re: [AMBER] DRUG_PROTEIN INTERACTIOM Wei Ye (Thu Nov 06 2014 - 23:57:40 PST)
  - Re: [AMBER] DRUG_PROTEIN INTERACTIOM Ruchika Bhat (Fri Nov 07 2014 - 01:00:58 PST)
    - Re: [AMBER] DRUG_PROTEIN INTERACTIOM Wei Ye (Fri Nov 07 2014 - 04:28:06 PST)
    - Re: [AMBER] DRUG_PROTEIN INTERACTIOM Jason Swails (Fri Nov 07 2014 - 04:31:14 PST)
[AMBER] bond distances in amber Mary Varughese (Fri Nov 07 2014 - 01:47:53 PST)
- Re: [AMBER] bond distances in amber Jason Swails (Fri Nov 07 2014 - 04:55:38 PST)
  - Re: [AMBER] bond distances in amber Mary Varughese (Sat Nov 08 2014 - 09:15:21 PST)
    - Re: [AMBER] bond distances in amber Niel Henriksen (Sat Nov 08 2014 - 15:31:08 PST)
    - Re: [AMBER] bond distances in amber David A Case (Sat Nov 08 2014 - 17:10:50 PST)
    - Re: [AMBER] bond distances in amber Mary Varughese (Sun Nov 09 2014 - 01:59:20 PST)
[AMBER] hbonds Mary Varughese (Fri Nov 07 2014 - 02:27:10 PST)
- Re: [AMBER] hbonds Jason Swails (Fri Nov 07 2014 - 05:02:11 PST)
  - Re: [AMBER] hbonds Mary Varughese (Sat Nov 08 2014 - 09:23:36 PST)
[AMBER] Help needed regarding Ligand Protein MD studies Ruchika Bhat (Fri Nov 07 2014 - 05:39:07 PST)
- Re: [AMBER] Help needed regarding Ligand Protein MD studies Jason Swails (Fri Nov 07 2014 - 06:12:48 PST)
- Re: [AMBER] Help needed regarding Ligand Protein MD studies Wei Ye (Fri Nov 07 2014 - 06:17:02 PST)
- Re: [AMBER] Help needed regarding Ligand Protein MD studies Gulsevin,Alican (Fri Nov 07 2014 - 06:38:48 PST)
  - Re: [AMBER] Help needed regarding Ligand Protein MD studies Ruchika Bhat (Fri Nov 07 2014 - 06:47:01 PST)
    - Re: [AMBER] Help needed regarding Ligand Protein MD studies Wei Ye (Fri Nov 07 2014 - 06:52:31 PST)
    - Re: [AMBER] Help needed regarding Ligand Protein MD studies Ruchika Bhat (Fri Nov 07 2014 - 10:11:11 PST)
    - Re: [AMBER] Help needed regarding Ligand Protein MD studies Ruchika Bhat (Fri Nov 07 2014 - 10:16:27 PST)
    - Re: [AMBER] Help needed regarding Ligand Protein MD studies David A Case (Sat Nov 08 2014 - 07:14:42 PST)
    - Re: [AMBER] Help needed regarding Ligand Protein MD studies Ruchika Bhat (Sat Nov 08 2014 - 07:47:27 PST)
[AMBER] writing out restart files in netcdf format Sylvester Tumusiime (Fri Nov 07 2014 - 08:24:41 PST)
- Re: [AMBER] writing out restart files in netcdf format Christina Bergonzo (Fri Nov 07 2014 - 08:30:36 PST)
  - Re: [AMBER] writing out restart files in netcdf format Sylvester Tumusiime (Fri Nov 07 2014 - 08:33:13 PST)
    - Re: [AMBER] writing out restart files in netcdf format Christina Bergonzo (Fri Nov 07 2014 - 08:39:24 PST)
[AMBER] HEAT and PROD files for 10 ns run Ruchika Bhat (Sat Nov 08 2014 - 08:45:44 PST)
- Re: [AMBER] HEAT and PROD files for 10 ns run Jason Swails (Sat Nov 08 2014 - 09:11:34 PST)
[AMBER] simulation of peptide in alkane slab samarprit chakraborty (Sat Nov 08 2014 - 09:43:30 PST)
- Re: [AMBER] simulation of peptide in alkane slab nabil bennenni (Sat Nov 08 2014 - 11:15:49 PST)
  - Re: [AMBER] simulation of peptide in alkane slab samarprit chakraborty (Sun Nov 09 2014 - 02:38:23 PST)
Re: [AMBER] Implicit simulation and MMPBSA/GBSA caculations Bajarang Kumbhar (Sat Nov 08 2014 - 22:26:51 PST)
- Re: [AMBER] Implicit simulation and MMPBSA/GBSA caculations Jason Swails (Sun Nov 09 2014 - 06:10:58 PST)
  - Re: [AMBER] Implicit simulation and MMPBSA/GBSA caculations Aron Broom (Sun Nov 09 2014 - 11:53:58 PST)
[AMBER] Which force field is "the best" Gonzalo Jimenez (Sun Nov 09 2014 - 11:10:41 PST)
- Re: [AMBER] Which force field is "the best" David A Case (Sun Nov 09 2014 - 14:29:46 PST)
  - Re: [AMBER] Which force field is "the best" Gonzalo Jimenez (Mon Nov 10 2014 - 04:20:55 PST)
[AMBER] MMPBSA.py Sourav Purohit (Sun Nov 09 2014 - 11:20:22 PST)
- Re: [AMBER] MMPBSA.py Jason Swails (Sun Nov 09 2014 - 14:49:26 PST)
[AMBER] Issue with DFTB-MD trajectory Perry, Jamin W. (Sun Nov 09 2014 - 14:02:08 PST)
- Re: [AMBER] Issue with DFTB-MD trajectory David A Case (Tue Nov 11 2014 - 03:56:44 PST)
  - Re: [AMBER] Issue with DFTB-MD trajectory Perry, Jamin W. (Sun Nov 16 2014 - 22:19:05 PST)
[AMBER] Problems of pdb file convertion by pdb4amber and mmtsb LI An-Bang (Sun Nov 09 2014 - 18:31:43 PST)
- Re: [AMBER] Problems of pdb file convertion by pdb4amber and mmtsb David A Case (Mon Nov 10 2014 - 04:12:02 PST)
- Re: [AMBER] Problems of pdb file convertion by pdb4amber and mmtsb Jason Swails (Mon Nov 10 2014 - 04:42:29 PST)
[AMBER] a problem on heating the system ZHAO Ruisheng (Mon Nov 10 2014 - 05:25:56 PST)
- Re: [AMBER] a problem on heating the system Jason Swails (Mon Nov 10 2014 - 05:30:06 PST)
- Re: [AMBER] a problem on heating the system David A Case (Mon Nov 10 2014 - 06:01:54 PST)
  - Re: [AMBER] a problem on heating the system ZHAO Ruisheng (Tue Nov 11 2014 - 00:32:16 PST)
    - Re: [AMBER] a problem on heating the system David A Case (Tue Nov 11 2014 - 03:54:32 PST)
    - Re: [AMBER] a problem on heating the system ZHAO Ruisheng (Tue Nov 11 2014 - 04:53:02 PST)
    - Re: [AMBER] a problem on heating the system David A Case (Wed Nov 12 2014 - 04:15:11 PST)
    - Re: [AMBER] a problem on heating the system Jason Swails (Wed Nov 12 2014 - 04:34:10 PST)
[AMBER] Transition state John Smith (Mon Nov 10 2014 - 10:13:36 PST)
[AMBER] Constant pH MD with CUDA not working BATUHAN KAV (Mon Nov 10 2014 - 12:05:55 PST)
[AMBER] small molecules Lara rajam (Mon Nov 10 2014 - 12:46:02 PST)
- Re: [AMBER] small molecules David A Case (Mon Nov 10 2014 - 14:11:34 PST)
[AMBER] Representing Sphere and Its parameterization in Amber. ATUL KUMAR (Mon Nov 10 2014 - 22:42:50 PST)
- Re: [AMBER] Representing Sphere and Its parameterization in Amber. David A Case (Tue Nov 11 2014 - 03:47:48 PST)
  - Re: [AMBER] Representing Sphere and Its parameterization in Amber. ATUL KUMAR (Tue Nov 11 2014 - 22:30:38 PST)
    - Re: [AMBER] Representing Sphere and Its parameterization in Amber. ATUL KUMAR (Thu Nov 13 2014 - 04:21:35 PST)
[AMBER] problem reimaging after strip WAT Pablo D. Dans Puiggròs (Tue Nov 11 2014 - 07:24:34 PST)
- Re: [AMBER] problem reimaging after strip WAT Jason Swails (Tue Nov 11 2014 - 07:28:09 PST)
  - Re: [AMBER] problem reimaging after strip WAT Pablo D. Dans Puiggròs (Tue Nov 11 2014 - 07:59:36 PST)
    - Re: [AMBER] problem reimaging after strip WAT Daniel Roe (Tue Nov 11 2014 - 08:05:15 PST)
    - Re: [AMBER] problem reimaging after strip WAT Pablo D. Dans Puiggròs (Tue Nov 11 2014 - 08:24:03 PST)
    - Re: [AMBER] problem reimaging after strip WAT nabil bennenni (Tue Nov 11 2014 - 09:16:06 PST)
[AMBER] nativecontacts in ambertools14 Asmita Gupta (Tue Nov 11 2014 - 09:03:31 PST)
- Re: [AMBER] nativecontacts in ambertools14 Daniel Roe (Tue Nov 11 2014 - 11:55:40 PST)
[AMBER] cpptraj Sylvester Tumusiime (Tue Nov 11 2014 - 11:30:23 PST)
- Re: [AMBER] cpptraj Daniel Roe (Tue Nov 11 2014 - 11:46:03 PST)
  - Re: [AMBER] cpptraj nabil bennenni (Tue Nov 11 2014 - 11:55:42 PST)
  - Re: [AMBER] cpptraj Sylvester Tumusiime (Tue Nov 11 2014 - 11:58:39 PST)
    - Re: [AMBER] cpptraj Daniel Roe (Tue Nov 11 2014 - 12:04:38 PST)
[AMBER] options "-ext" and "-pqr" of ambpdb are exlusive LI An-Bang (Tue Nov 11 2014 - 19:48:52 PST)
- Re: [AMBER] options "-ext" and "-pqr" of ambpdb are exlusive Daniel Roe (Wed Nov 12 2014 - 07:27:02 PST)
- Re: [AMBER] options "-ext" and "-pqr" of ambpdb are exlusive David A Case (Fri Nov 14 2014 - 05:19:36 PST)
  - Re: [AMBER] options "-ext" and "-pqr" of ambpdb are exlusive LI An-Bang (Sun Nov 16 2014 - 16:21:34 PST)
[AMBER] [Amber] Amber14 does not find parameters for Mg2+, please help Genin, Nicolas J (Wed Nov 12 2014 - 07:35:49 PST)
- Re: [AMBER] [Amber] Amber14 does not find parameters for Mg2+, please help Jason Swails (Wed Nov 12 2014 - 08:34:58 PST)
  - Re: [AMBER] [Amber] Amber14 does not find parameters for Mg2+, please help Genin, Nicolas J (Wed Nov 12 2014 - 11:29:09 PST)
[AMBER] time correlation function giulia palermo (Wed Nov 12 2014 - 10:04:00 PST)
- Re: [AMBER] time correlation function Daniel Roe (Wed Nov 12 2014 - 10:37:44 PST)
  - Re: [AMBER] time correlation function giulia palermo (Thu Nov 13 2014 - 03:44:52 PST)
    - Re: [AMBER] time correlation function Daniel Roe (Thu Nov 13 2014 - 07:09:54 PST)
[AMBER] Running explicit solvent CpHMD on GPUs Garrido Ruiz, Diego (Wed Nov 12 2014 - 11:40:52 PST)
[AMBER] help Robin Jain (Wed Nov 12 2014 - 21:59:24 PST)
- Re: [AMBER] help David A Case (Thu Nov 13 2014 - 03:57:42 PST)
- Re: [AMBER] help Robin Jain (Mon Nov 17 2014 - 09:30:41 PST)
  - Re: [AMBER] help Jason Swails (Mon Nov 17 2014 - 10:48:24 PST)
[AMBER] The question about REMD exchange ratio 王漠野 (Wed Nov 12 2014 - 22:43:55 PST)
- Re: [AMBER] The question about REMD exchange ratio Carlos Simmerling (Thu Nov 13 2014 - 03:35:05 PST)
  - Re: [AMBER] The question about REMD exchange ratio 王漠野 (Thu Nov 13 2014 - 17:34:09 PST)
- Re: [AMBER] The question about REMD exchange ratio Jason Swails (Thu Nov 13 2014 - 05:17:18 PST)
[AMBER] help in MD Robin Jain (Wed Nov 12 2014 - 23:48:20 PST)
- Re: [AMBER] help in MD Ayesha Fatima (Thu Nov 13 2014 - 03:09:10 PST)
[AMBER] Transition state Mahmood Jasim (Thu Nov 13 2014 - 01:43:51 PST)
- Re: [AMBER] Transition state Jason Swails (Thu Nov 13 2014 - 05:24:30 PST)
[AMBER] Calcium parameters in calmodulin bharat lakhani (Thu Nov 13 2014 - 08:16:59 PST)
- Re: [AMBER] Calcium parameters in calmodulin Jason Swails (Thu Nov 13 2014 - 08:58:19 PST)
[AMBER] error in mmpbsa calculation Abdul wadood (Thu Nov 13 2014 - 08:30:40 PST)
- Re: [AMBER] error in mmpbsa calculation Jason Swails (Thu Nov 13 2014 - 09:02:51 PST)
  - Re: [AMBER] error in mmpbsa calculation Abdul wadood (Fri Nov 14 2014 - 08:37:42 PST)
[AMBER] minimization problem Emilio Angelina (Thu Nov 13 2014 - 12:52:28 PST)
- Re: [AMBER] minimization problem David A Case (Fri Nov 14 2014 - 04:59:56 PST)
  - Re: [AMBER] minimization problem Emilio Angelina (Fri Nov 14 2014 - 06:49:18 PST)
[AMBER] Amber 14 installation problems 汪小涧 (Thu Nov 13 2014 - 19:07:29 PST)
- Re: [AMBER] Amber 14 installation problems David A Case (Fri Nov 14 2014 - 04:55:33 PST)
[AMBER] Entropy using Nmode Wong, Sook (NIH/NCATS) [V] (Fri Nov 14 2014 - 10:57:38 PST)
- Re: [AMBER] Entropy using Nmode Jason Swails (Fri Nov 14 2014 - 20:14:46 PST)
[AMBER] Postdoctoral Position at the U.S. Army Research Laboratory in Coarse-Grain Modeling and Simulation Izvyekov, Sergiy (Sergey) CIV USARMY ARL (US) (Fri Nov 14 2014 - 13:11:51 PST)
[AMBER] pmemd.MPI thermodynamic integration (TI) relative binding free energy set up psu4.uic.edu (Fri Nov 14 2014 - 14:32:49 PST)
- Re: [AMBER] pmemd.MPI thermodynamic integration (TI) relative binding free energy set up hannes.loeffler.stfc.ac.uk (Sat Nov 15 2014 - 00:40:15 PST)
[AMBER] Is there a tool to calculate electron density maps averaged over a trajectory? Jose Borreguero (Fri Nov 14 2014 - 15:16:10 PST)
- Re: [AMBER] Is there a tool to calculate electron density maps averaged over a trajectory? David A Case (Fri Nov 14 2014 - 18:31:54 PST)
  - Re: [AMBER] Is there a tool to calculate electron density maps averaged over a trajectory? Jose Borreguero (Sat Nov 15 2014 - 06:58:23 PST)
    - Re: [AMBER] Is there a tool to calculate electron density maps averaged over a trajectory? Pawel Janowski (Mon Nov 24 2014 - 14:43:57 PST)
[AMBER] heme amber parameter Fatemeh Sadat Alavi (Sat Nov 15 2014 - 07:56:27 PST)
- Re: [AMBER] heme amber parameter David A Case (Sat Nov 15 2014 - 17:58:46 PST)
[AMBER] Prmtop Sylvester Tumusiime (Sat Nov 15 2014 - 08:55:40 PST)
- Re: [AMBER] Prmtop Jason Swails (Sat Nov 15 2014 - 09:51:34 PST)
[AMBER] Failure of antechamber with c -1 m 2 Francesco Pietra (Sun Nov 16 2014 - 09:35:45 PST)
- Re: [AMBER] Failure of antechamber with c -1 m 2 David A Case (Sun Nov 16 2014 - 13:20:04 PST)
  - Re: [AMBER] Failure of antechamber with c -1 m 2 Francesco Pietra (Sun Nov 16 2014 - 13:57:15 PST)
    - Re: [AMBER] Failure of antechamber with c -1 m 2 David A Case (Mon Nov 17 2014 - 08:01:25 PST)
    - Re: [AMBER] Failure of antechamber with c -1 m 2 Francesco Pietra (Mon Nov 17 2014 - 08:55:07 PST)
[AMBER] MMPBSA.py nmode Sourav Purohit (Sun Nov 16 2014 - 18:13:37 PST)
- Re: [AMBER] MMPBSA.py nmode Jason Swails (Mon Nov 17 2014 - 06:02:28 PST)
[AMBER] 4x GTX 980 Parker de Waal (Sun Nov 16 2014 - 18:28:07 PST)
- Re: [AMBER] 4x GTX 980 James Maier (Sun Nov 16 2014 - 20:13:24 PST)
  - Re: [AMBER] 4x GTX 980 James Maier (Sun Nov 16 2014 - 20:16:18 PST)
    - Re: [AMBER] 4x GTX 980 Scott Le Grand (Mon Nov 17 2014 - 14:42:53 PST)
    - [AMBER] aMD on Amber 12 Aldo Segura (Mon Nov 17 2014 - 21:53:21 PST)
    - Re: [AMBER] aMD on Amber 12 Daniel Roe (Tue Nov 18 2014 - 07:01:20 PST)
    - Re: [AMBER] aMD on Amber 12 Aldo Segura (Tue Nov 18 2014 - 08:49:14 PST)
    - Re: [AMBER] aMD on Amber 12 Daniel Roe (Tue Nov 18 2014 - 09:47:25 PST)
    - Re: [AMBER] 4x GTX 980 Parker de Waal (Sun Nov 23 2014 - 16:22:22 PST)
    - Re: [AMBER] 4x GTX 980 Scott Le Grand (Sun Nov 23 2014 - 16:31:34 PST)
    - Re: [AMBER] 4x GTX 980 Scott Le Grand (Sun Nov 23 2014 - 16:32:38 PST)
    - Re: [AMBER] 4x GTX 980 Parker de Waal (Sun Nov 23 2014 - 16:51:16 PST)
    - Re: [AMBER] 4x GTX 980 Scott Le Grand (Sun Nov 23 2014 - 17:26:41 PST)
    - Re: [AMBER] 4x GTX 980 Parker de Waal (Sun Nov 23 2014 - 17:32:46 PST)
    - Re: [AMBER] 4x GTX 980 Scott Le Grand (Sun Nov 23 2014 - 17:34:40 PST)
    - Re: [AMBER] 4x GTX 980 Ross Walker (Sun Nov 23 2014 - 18:02:57 PST)
    - Re: [AMBER] 4x GTX 980 Ross Walker (Sun Nov 23 2014 - 18:01:29 PST)
    - Re: [AMBER] 4x GTX 980 Ross Walker (Sun Nov 23 2014 - 18:03:50 PST)
[AMBER] MMPBSA warning : No skew or curtosis when zero variance in moment Mina Madah (Mon Nov 17 2014 - 00:23:22 PST)
- Re: [AMBER] MMPBSA warning : No skew or curtosis when zero variance in moment Jason Swails (Mon Nov 17 2014 - 05:57:32 PST)
[AMBER] Regarding pairdist function in cpptraj DEBOSTUTI GHOSHDASTIDAR (Mon Nov 17 2014 - 06:49:06 PST)
- Re: [AMBER] Regarding pairdist function in cpptraj Daniel Roe (Mon Nov 17 2014 - 07:17:31 PST)
  - Re: [AMBER] Regarding pairdist function in cpptraj DEBOSTUTI GHOSHDASTIDAR (Mon Nov 17 2014 - 21:56:15 PST)
[AMBER] MMPBSA.py normal mode analysis Sourav Purohit (Mon Nov 17 2014 - 12:00:19 PST)
- Re: [AMBER] MMPBSA.py normal mode analysis Jason Swails (Mon Nov 17 2014 - 12:08:39 PST)
  - Re: [AMBER] MMPBSA.py normal mode analysis Sourav Purohit (Mon Nov 17 2014 - 12:08:53 PST)
[AMBER] ERROR DURING "TESTING" OF AMBER INSTALLATION ROOPALI VERMA (Mon Nov 17 2014 - 23:47:31 PST)
- Re: [AMBER] ERROR DURING "TESTING" OF AMBER INSTALLATION David A Case (Tue Nov 18 2014 - 04:34:10 PST)
  - Re: [AMBER] ERROR DURING "TESTING" OF AMBER INSTALLATION ROOPALI VERMA (Tue Nov 18 2014 - 22:43:38 PST)
    - Re: [AMBER] ERROR DURING "TESTING" OF AMBER INSTALLATION David A Case (Wed Nov 19 2014 - 04:08:00 PST)
    - Re: [AMBER] ERROR DURING "TESTING" OF AMBER INSTALLATION Amihai (Wed Nov 19 2014 - 04:21:25 PST)
    - Re: [AMBER] ERROR DURING "TESTING" OF AMBER INSTALLATION ROOPALI VERMA (Wed Nov 19 2014 - 22:55:27 PST)
[AMBER] amber error about protein containing heme Fatemeh Sadat Alavi (Tue Nov 18 2014 - 02:31:57 PST)
- Re: [AMBER] amber error about protein containing heme Jason Swails (Tue Nov 18 2014 - 06:56:15 PST)
[AMBER] amber error about protein containing heme Fatemeh Sadat Alavi (Tue Nov 18 2014 - 02:37:16 PST)
- Re: [AMBER] amber error about protein containing heme David A Case (Tue Nov 18 2014 - 04:38:56 PST)
  - Re: [AMBER] amber error about protein containing heme Fatemeh Sadat Alavi (Sat Nov 22 2014 - 00:04:33 PST)
    - Re: [AMBER] amber error about protein containing heme David A Case (Sat Nov 22 2014 - 04:35:03 PST)
[AMBER] citation for mdout_analyser.py Krisztina Feher (Tue Nov 18 2014 - 05:14:33 PST)
- Re: [AMBER] citation for mdout_analyser.py Jason Swails (Tue Nov 18 2014 - 06:49:03 PST)
[AMBER] tleap not found in parallel amber14 Amihai (Tue Nov 18 2014 - 06:12:45 PST)
- Re: [AMBER] tleap not found in parallel amber14 Jason Swails (Tue Nov 18 2014 - 06:53:47 PST)
Re: [AMBER] AMBER Digest, Vol 1041, Issue 1 Robin Jain (Tue Nov 18 2014 - 07:34:02 PST)
- Re: [AMBER] AMBER Digest, Vol 1041, Issue 1 Jason Swails (Tue Nov 18 2014 - 08:32:04 PST)
[AMBER] nmr restraints and periodic boundary conditions Chris Moth (Tue Nov 18 2014 - 14:20:06 PST)
- Re: [AMBER] nmr restraints and periodic boundary conditions Jason Swails (Tue Nov 18 2014 - 14:57:54 PST)
- Re: [AMBER] nmr restraints and periodic boundary conditions Niel Henriksen (Tue Nov 18 2014 - 15:02:07 PST)
- Re: [AMBER] nmr restraints and periodic boundary conditions David A Case (Tue Nov 18 2014 - 17:50:37 PST)
[AMBER] InputError when running MMBPSA.py HERBERT MAX VENTHUR PE¥A (Tue Nov 18 2014 - 18:16:54 PST)
- Re: [AMBER] InputError when running MMBPSA.py Jason Swails (Tue Nov 18 2014 - 22:52:46 PST)
- [AMBER] Fwd: InputError when running MMBPSA.py HERBERT MAX VENTHUR PE¥A (Fri Nov 21 2014 - 19:28:58 PST)
  - Re: [AMBER] Fwd: InputError when running MMBPSA.py Jason Swails (Fri Nov 21 2014 - 21:49:30 PST)
[AMBER] Is it possible to extract atomic charge information from the trajectory? Yip Yew Mun (Tue Nov 18 2014 - 18:53:20 PST)
- Re: [AMBER] Is it possible to extract atomic charge information from the trajectory? Jason Swails (Tue Nov 18 2014 - 22:47:21 PST)
[AMBER] Help generating Heme parameters 杨川 (Tue Nov 18 2014 - 23:20:29 PST)
- Re: [AMBER] Help generating Heme parameters Pengfei Li (Fri Nov 21 2014 - 07:18:00 PST)
[AMBER] box size changing during equilibration Robin Jain (Wed Nov 19 2014 - 07:20:29 PST)
- Re: [AMBER] box size changing during equilibration Daniel Roe (Wed Nov 19 2014 - 07:26:45 PST)
[AMBER] Pairwise vs Sander with imin=5 kurisaki (Wed Nov 19 2014 - 18:01:08 PST)
- Re: [AMBER] Pairwise vs Sander with imin=5 Daniel Roe (Wed Nov 19 2014 - 21:14:27 PST)
  - Re: [AMBER] Pairwise vs Sander with imin=5 kurisaki (Wed Nov 19 2014 - 22:02:00 PST)
    - Re: [AMBER] Pairwise vs Sander with imin=5 Daniel Roe (Thu Nov 20 2014 - 10:01:58 PST)
[AMBER] ERROR atom with mass 1 has type alreadydesignated as non-hydrogen type Abhishek TYAGI (Wed Nov 19 2014 - 19:01:08 PST)
[AMBER] Error in CHAMBER output Abhishek TYAGI (Wed Nov 19 2014 - 22:18:25 PST)
- Re: [AMBER] Error in CHAMBER output Robin Betz (Wed Nov 19 2014 - 22:23:33 PST)
[AMBER] Reminder: NBCR AMBER Workshop - UCSD - Mon Dec 15th to Thur Dec 18th 2014 - Registration open. Ross Walker (Wed Nov 19 2014 - 21:39:51 PST)
- [AMBER] adQM/MM vlimit exceeded problem Aixiao Li (Thu Nov 20 2014 - 02:32:49 PST)
  - Re: [AMBER] adQM/MM vlimit exceeded problem Andreas Goetz (Sun Nov 23 2014 - 21:30:49 PST)
    - Re: [AMBER] adQM/MM vlimit exceeded problem Andreas Goetz (Mon Nov 24 2014 - 13:44:25 PST)
[AMBER] Problems with AmberTools test suite David A Case (Thu Nov 20 2014 - 08:15:31 PST)
[AMBER] Errors compiling Amber 14 after applying update 7 Bob Healey (Thu Nov 20 2014 - 09:45:08 PST)
- Re: [AMBER] Errors compiling Amber 14 after applying update 7 Jason Swails (Thu Nov 20 2014 - 12:17:51 PST)
- Re: [AMBER] Errors compiling Amber 14 after applying update 7 David A Case (Thu Nov 20 2014 - 12:33:32 PST)
  - Re: [AMBER] Errors compiling Amber 14 after applying update 7 Ross Walker (Thu Nov 20 2014 - 12:38:46 PST)
[AMBER] PBSA error Kshatresh Dutta Dubey (Thu Nov 20 2014 - 10:10:08 PST)
- Re: [AMBER] PBSA error Jason Swails (Thu Nov 20 2014 - 12:21:23 PST)
- Re: [AMBER] PBSA error David A Case (Thu Nov 20 2014 - 12:32:45 PST)
  - Re: [AMBER] PBSA error David A Case (Thu Nov 20 2014 - 12:42:25 PST)
    - Re: [AMBER] PBSA error Kshatresh Dutta Dubey (Thu Nov 20 2014 - 12:45:49 PST)
    - Re: [AMBER] PBSA error Kshatresh Dutta Dubey (Thu Nov 20 2014 - 12:52:22 PST)
    - Re: [AMBER] PBSA error Ray Luo, Ph.D. (Thu Nov 20 2014 - 14:49:07 PST)
[AMBER] Can you use cholesterol lipid 11 parameters and lipid 14 lipid parameters? Jonathan Gough (Thu Nov 20 2014 - 12:06:19 PST)
[AMBER] MMPBSA.py bug with amber mask for stability/QH calculations Lawrenz, Morgan (Thu Nov 20 2014 - 15:34:06 PST)
- Re: [AMBER] MMPBSA.py bug with amber mask for stability/QH calculations Jason Swails (Thu Nov 20 2014 - 15:47:42 PST)
[AMBER] The error when install amber12+AmberTools13 on Ubuntucd Biao Ma (Thu Nov 20 2014 - 18:31:18 PST)
- Re: [AMBER] The error when install amber12+AmberTools13 on Ubuntucd Jason Swails (Thu Nov 20 2014 - 19:06:29 PST)
  - Re: [AMBER] The error when install amber12+AmberTools13 on Ubuntucd Biao Ma (Mon Nov 24 2014 - 18:26:25 PST)
[AMBER] cut value in minimisation Robin Jain (Thu Nov 20 2014 - 23:17:49 PST)
- Re: [AMBER] cut value in minimisation Jason Swails (Fri Nov 21 2014 - 02:18:44 PST)
- Re: [AMBER] cut value in minimisation David A Case (Fri Nov 21 2014 - 04:26:26 PST)
[AMBER] Bug Report Liu, Hui (Thu Nov 20 2014 - 23:38:52 PST)
- Re: [AMBER] Bug Report Jason Swails (Fri Nov 21 2014 - 02:30:30 PST)
[AMBER] cyclic peptide side chains Maria Diaz (Fri Nov 21 2014 - 02:43:50 PST)
- Re: [AMBER] cyclic peptide side chains David A Case (Fri Nov 21 2014 - 04:29:02 PST)
[AMBER] about nab m13654940810 (Fri Nov 21 2014 - 03:12:07 PST)
- Re: [AMBER] about nab David A Case (Fri Nov 21 2014 - 04:36:23 PST)
[AMBER] Issues with Cholesterol lipid11, lipid14 and lipid14_supp.lib Jonathan Gough (Fri Nov 21 2014 - 10:15:02 PST)
[AMBER] Questions regarding GB simulations in Amber14 - ff14SBonlysc vs ff14SB - igb1 vs igb8 - hydrphobic force Marek Maly (Fri Nov 21 2014 - 17:58:14 PST)
- Re: [AMBER] Questions regarding GB simulations in Amber14 - ff14SBonlysc vs ff14SB - igb1 vs igb8 - hydrphobic force Carlos Simmerling (Fri Nov 21 2014 - 18:35:02 PST)
  - Re: [AMBER] Questions regarding GB simulations in Amber14 - ff14SBonlysc vs ff14SB - igb1 vs igb8 - hydrphobic force Marek Maly (Sun Nov 23 2014 - 18:40:49 PST)
Re: [AMBER] AMBER Digest, Vol 1045, Issue 1 Robin Jain (Sat Nov 22 2014 - 00:25:58 PST)
- Re: [AMBER] AMBER Digest, Vol 1045, Issue 1 David A Case (Sat Nov 22 2014 - 04:39:51 PST)
[AMBER] AMBER error: peek_ewald_inpcrd: SHOULD NOT BE HERE Hadeer ELHabashy (Sat Nov 22 2014 - 07:43:24 PST)
- Re: [AMBER] AMBER error: peek_ewald_inpcrd: SHOULD NOT BE HERE David A Case (Sat Nov 22 2014 - 11:35:45 PST)
[AMBER] Installation error: recipe for target 'pupildata.o' failed Parker de Waal (Sat Nov 22 2014 - 14:37:30 PST)
- Re: [AMBER] Installation error: recipe for target 'pupildata.o' failed Parker de Waal (Sat Nov 22 2014 - 17:03:29 PST)
  - Re: [AMBER] Installation error: recipe for target 'pupildata.o' failed David A Case (Sat Nov 22 2014 - 18:09:49 PST)
    - Re: [AMBER] Installation error: recipe for target 'pupildata.o' failed Parker de Waal (Sat Nov 22 2014 - 19:47:44 PST)
- Re: [AMBER] Installation error: recipe for target 'pupildata.o' failed Jason Swails (Sat Nov 22 2014 - 20:58:01 PST)
  - Re: [AMBER] Installation error: recipe for target 'pupildata.o' failed Parker de Waal (Sun Nov 23 2014 - 08:24:25 PST)
    - Re: [AMBER] Installation error: recipe for target 'pupildata.o' failed Jason Swails (Sun Nov 23 2014 - 09:55:57 PST)
    - Re: [AMBER] Installation error: recipe for target 'pupildata.o' failed Parker de Waal (Sun Nov 23 2014 - 13:59:02 PST)
    - Re: [AMBER] Installation error: recipe for target 'pupildata.o' failed Jason Swails (Sun Nov 23 2014 - 17:36:22 PST)
    - Re: [AMBER] Installation error: recipe for target 'pupildata.o' failed Parker de Waal (Sun Nov 23 2014 - 18:18:10 PST)
[AMBER] AMBER Unique atom types Brittany Boykin (Sat Nov 22 2014 - 14:45:39 PST)
- Re: [AMBER] AMBER Unique atom types David A Case (Sat Nov 22 2014 - 18:28:26 PST)
- Re: [AMBER] AMBER Unique atom types FyD (Sat Nov 22 2014 - 23:45:25 PST)
[AMBER] How to seperate a protein-protein complex in PRMTOP and INPCRD files? LI An-Bang (Sun Nov 23 2014 - 16:27:56 PST)
- Re: [AMBER] How to seperate a protein-protein complex in PRMTOP and INPCRD files? Jason Swails (Sun Nov 23 2014 - 17:42:54 PST)
  - Re: [AMBER] How to seperate a protein-protein complex in PRMTOP and INPCRD files? Daniel Roe (Mon Nov 24 2014 - 07:26:46 PST)
Re: [AMBER] AMBER Digest, Vol 1044, Issue 1 Abhishek TYAGI (Sun Nov 23 2014 - 22:08:48 PST)
- Re: [AMBER] AMBER Digest, Vol 1044, Issue 1 Jason Swails (Mon Nov 24 2014 - 02:44:31 PST)
[AMBER] errors in qm/mm Ayesha Fatima (Sun Nov 23 2014 - 22:10:57 PST)
- Re: [AMBER] errors in qm/mm Andreas Goetz (Sun Nov 23 2014 - 22:27:33 PST)
  - Re: [AMBER] errors in qm/mm Ayesha Fatima (Sun Nov 23 2014 - 22:39:49 PST)
  - Re: [AMBER] errors in qm/mm Ayesha Fatima (Sun Nov 23 2014 - 23:02:47 PST)
    - Re: [AMBER] errors in qm/mm Marc van der Kamp (Mon Nov 24 2014 - 00:03:32 PST)
    - Re: [AMBER] errors in qm/mm Ayesha Fatima (Mon Nov 24 2014 - 01:22:47 PST)
- Re: [AMBER] errors in qm/mm Gustavo Seabra (Mon Nov 24 2014 - 04:43:18 PST)
  - Re: [AMBER] errors in qm/mm Ayesha Fatima (Mon Nov 24 2014 - 05:27:50 PST)
    - Re: [AMBER] errors in qm/mm Gustavo Seabra (Mon Nov 24 2014 - 05:53:42 PST)
    - Re: [AMBER] errors in qm/mm Ayesha Fatima (Mon Nov 24 2014 - 05:56:29 PST)
[AMBER] Counseling about the GPU series supporting PMEMD geyushu.ustc.edu.cn (Sun Nov 23 2014 - 23:06:03 PST)
- Re: [AMBER] Counseling about the GPU series supporting PMEMD Ross Walker (Sun Nov 23 2014 - 23:11:56 PST)
[AMBER] Glycan bond error leap maryam azimzadehirani (Mon Nov 24 2014 - 00:11:31 PST)
- Re: [AMBER] Glycan bond error leap Jason Swails (Mon Nov 24 2014 - 08:20:03 PST)
  - Re: [AMBER] Glycan bond error leap Lachele Foley (Mon Nov 24 2014 - 10:18:56 PST)
    - Re: [AMBER] Glycan bond error leap maryam azimzadehirani (Mon Nov 24 2014 - 20:51:35 PST)
[AMBER] Forcefield for DNA Baifan Wang (Mon Nov 24 2014 - 06:55:15 PST)
- Re: [AMBER] Forcefield for DNA Petr Jurecka (Tue Nov 25 2014 - 01:52:22 PST)
  - Re: [AMBER] Forcefield for DNA Baifan Wang (Tue Nov 25 2014 - 04:29:09 PST)
    - Re: [AMBER] Forcefield for DNA Nihal Korkmaz (Sun Feb 01 2015 - 11:25:18 PST)
    - Re: [AMBER] Forcefield for DNA Petr Jurecka (Wed Feb 04 2015 - 06:34:55 PST)
  - Re: [AMBER] Forcefield for DNA Nihal Korkmaz (Wed Dec 24 2014 - 19:44:59 PST)
[AMBER] Thermodynamic integration: Delta G of less soft core atoms is different from the one with more soft core atoms sun (Mon Nov 24 2014 - 08:10:22 PST)
- Re: [AMBER] Thermodynamic integration: Delta G of less soft core atoms is different from the one with more soft core atoms Hannes Loeffler (Mon Nov 24 2014 - 08:21:51 PST)
[AMBER] confirm b31b76c2dc0c4f0c33e4cac638252d6c6723f46d Zgarbova Marie (Mon Nov 24 2014 - 12:56:57 PST)
- Re: [AMBER] confirm b31b76c2dc0c4f0c33e4cac638252d6c6723f46d vojtech.mlynsky.upol.cz (Wed Nov 26 2014 - 01:43:56 PST)
[AMBER] CHAMBER error Abhishek TYAGI (Mon Nov 24 2014 - 20:37:46 PST)
- Re: [AMBER] CHAMBER error Jason Swails (Wed Nov 26 2014 - 18:56:39 PST)
- Re: [AMBER] CHAMBER error Abhishek TYAGI (Thu Dec 04 2014 - 19:25:06 PST)
[AMBER] doubt in RMD Mary Varughese (Mon Nov 24 2014 - 23:57:32 PST)
- Re: [AMBER] doubt in RMD Jason Swails (Wed Nov 26 2014 - 14:58:27 PST)
  - Re: [AMBER] doubt in RMD Mary Varughese (Wed Nov 26 2014 - 21:58:04 PST)
    - Re: [AMBER] doubt in RMD Jason Swails (Thu Nov 27 2014 - 03:48:15 PST)
    - Re: [AMBER] doubt in RMD Mary Varughese (Thu Nov 27 2014 - 09:40:22 PST)
    - Re: [AMBER] doubt in RMD Jason Swails (Fri Nov 28 2014 - 19:17:02 PST)
    - Re: [AMBER] doubt in RMD Mary Varughese (Sat Nov 29 2014 - 04:40:02 PST)
[AMBER] hydophobicity Mary Varughese (Mon Nov 24 2014 - 23:59:24 PST)
- Re: [AMBER] hydophobicity Jason Swails (Wed Nov 26 2014 - 15:28:04 PST)
  - Re: [AMBER] hydophobicity Mary Varughese (Wed Nov 26 2014 - 22:00:03 PST)
    - Re: [AMBER] hydophobicity Jason Swails (Thu Nov 27 2014 - 03:34:51 PST)
    - Re: [AMBER] hydophobicity Mary Varughese (Thu Nov 27 2014 - 09:43:11 PST)
    - Re: [AMBER] hydophobicity Daniel Roe (Sun Nov 30 2014 - 10:42:13 PST)
    - Re: [AMBER] hydophobicity Mary Varughese (Sun Nov 30 2014 - 17:38:19 PST)
[AMBER] Different PCA results when loading trajectories in a different order Guillaume Roellinger (Tue Nov 25 2014 - 09:49:05 PST)
- Re: [AMBER] Different PCA results when loading trajectories in a different order Daniel Roe (Tue Nov 25 2014 - 10:03:42 PST)
  - Re: [AMBER] Different PCA results when loading trajectories in a different order Daniel Roe (Tue Nov 25 2014 - 10:08:33 PST)
    - Re: [AMBER] Different PCA results when loading trajectories in a different order Guillaume Roellinger (Wed Nov 26 2014 - 01:58:43 PST)
    - Re: [AMBER] Different PCA results when loading trajectories in a different order Daniel Roe (Wed Nov 26 2014 - 07:36:50 PST)
    - Re: [AMBER] Different PCA results when loading trajectories in a different order Daniel Roe (Wed Nov 26 2014 - 09:52:04 PST)
[AMBER] How to restrain atoms Akihiro Yamane (Tue Nov 25 2014 - 22:03:13 PST)
- Re: [AMBER] How to restrain atoms David A Case (Wed Nov 26 2014 - 05:11:30 PST)
- Re: [AMBER] How to restrain atoms Akihiro Yamane (Fri Nov 28 2014 - 04:57:26 PST)
[AMBER] Free energy landscape anu chandra (Wed Nov 26 2014 - 03:07:19 PST)
- Re: [AMBER] Free energy landscape Daniel Roe (Wed Nov 26 2014 - 09:01:33 PST)
- Re: [AMBER] Free energy landscape Carlos Simmerling (Wed Nov 26 2014 - 09:12:53 PST)
  - Re: [AMBER] Free energy landscape anu chandra (Thu Nov 27 2014 - 03:44:44 PST)
    - Re: [AMBER] Free energy landscape Carlos Simmerling (Thu Dec 11 2014 - 06:08:55 PST)
[AMBER] AmberTools13 Ibrahim Said (Wed Nov 26 2014 - 09:32:44 PST)
- Re: [AMBER] AmberTools13 Daniel Roe (Wed Nov 26 2014 - 09:54:27 PST)
  - Re: [AMBER] AmberTools13 Ibrahim Said (Thu Nov 27 2014 - 02:01:57 PST)
    - Re: [AMBER] AmberTools13 Jason Swails (Thu Nov 27 2014 - 03:58:55 PST)
- Re: [AMBER] AmberTools13 Jason Swails (Wed Nov 26 2014 - 10:28:26 PST)
- Re: [AMBER] AmberTools13 David A Case (Wed Nov 26 2014 - 10:31:59 PST)
[AMBER] GTX 780 Ti & GTX 980 Jordi Bujons (Wed Nov 26 2014 - 09:35:06 PST)
- Re: [AMBER] GTX 780 Ti & GTX 980 Ross Walker (Wed Nov 26 2014 - 13:18:39 PST)
[AMBER] Fw: Elham tazikeh (Thu Nov 27 2014 - 00:57:29 PST)
- Re: [AMBER] (no subject) Jason Swails (Thu Nov 27 2014 - 03:49:52 PST)
[AMBER] Amber 14 and NetCDF installation issue Fernando Ezequiel Chain (Thu Nov 27 2014 - 01:14:37 PST)
- Re: [AMBER] Amber 14 and NetCDF installation issue Jason Swails (Thu Nov 27 2014 - 03:55:11 PST)
[AMBER] xLEaP Na+ Cl- Weinzierl, Robert O J (Thu Nov 27 2014 - 04:01:03 PST)
- Re: [AMBER] xLEaP Na+ Cl- Asaminew Haile (Thu Nov 27 2014 - 04:05:42 PST)
[AMBER] Interaction energy between two dimer unit Soumendranath Bhakat (Thu Nov 27 2014 - 21:26:21 PST)
- Re: [AMBER] Interaction energy between two dimer unit Jason Swails (Fri Nov 28 2014 - 16:03:44 PST)
[AMBER] installing amber12 in GPU Vijay Achari (Fri Nov 28 2014 - 05:49:35 PST)
- Re: [AMBER] installing amber12 in GPU Jason Swails (Fri Nov 28 2014 - 15:31:46 PST)
  - Re: [AMBER] installing amber12 in GPU Vijay Achari (Sun Nov 30 2014 - 23:30:21 PST)
    - Re: [AMBER] installing amber12 in GPU Ross Walker (Mon Dec 01 2014 - 06:31:54 PST)
[AMBER] minimization question Carlos Romero (Fri Nov 28 2014 - 07:03:37 PST)
- Re: [AMBER] minimization question David A Case (Fri Nov 28 2014 - 07:32:41 PST)
  - Re: [AMBER] minimization question Carlos Romero (Fri Nov 28 2014 - 07:38:53 PST)
[AMBER] Correct script for B-factor Soumendranath Bhakat (Fri Nov 28 2014 - 07:38:19 PST)
- Re: [AMBER] Correct script for B-factor Marcus Arieno (Fri Nov 28 2014 - 08:06:43 PST)
- Re: [AMBER] Correct script for B-factor David A Case (Fri Nov 28 2014 - 09:22:10 PST)
  - Re: [AMBER] Correct script for B-factor Soumendranath Bhakat (Fri Nov 28 2014 - 19:37:22 PST)
    - Re: [AMBER] Correct script for B-factor Daniel Roe (Sun Nov 30 2014 - 10:33:05 PST)
[AMBER] QM/MM adaptive biased MD_ABMD Aixiao Li (Fri Nov 28 2014 - 08:36:12 PST)
- Re: [AMBER] QM/MM adaptive biased MD_ABMD David A Case (Fri Nov 28 2014 - 09:28:25 PST)
  - Re: [AMBER] QM/MM adaptive biased MD_ABMD Aixiao Li (Fri Nov 28 2014 - 12:32:36 PST)
[AMBER] generate topology file and parameter file for complex with dummy atoms Jorgen Simonsen (Fri Nov 28 2014 - 15:45:21 PST)
- Re: [AMBER] generate topology file and parameter file for complex with dummy atoms Jason Swails (Fri Nov 28 2014 - 15:53:21 PST)
  - Re: [AMBER] generate topology file and parameter file for complex with dummy atoms Jorgen Simonsen (Sat Nov 29 2014 - 16:08:00 PST)
[AMBER] Calcium vdW parameters Caitlin Scott (Fri Nov 28 2014 - 16:14:40 PST)
- Re: [AMBER] Calcium vdW parameters mmaestre.gate.sinica.edu.tw (Fri Nov 28 2014 - 19:15:03 PST)
- Re: [AMBER] Calcium vdW parameters Ken Merz (Sat Nov 29 2014 - 05:07:38 PST)
[AMBER] Metal parameterization sailu (Fri Nov 28 2014 - 20:50:46 PST)
- Re: [AMBER] Metal parameterization Ken Merz (Sat Nov 29 2014 - 05:11:56 PST)
[AMBER] Monitoring pi-cationic interaction asdda asa (Fri Nov 28 2014 - 23:12:14 PST)
- Re: [AMBER] Monitoring pi-cationic interaction Daniel Roe (Sun Nov 30 2014 - 11:01:11 PST)
  - Re: [AMBER] Monitoring pi-cationic interaction asdda asa (Sun Nov 30 2014 - 19:37:03 PST)
[AMBER] PARALLEL INSTALLATION ERROR Nalini Chauhan (Sun Nov 30 2014 - 03:47:23 PST)
- Re: [AMBER] PARALLEL INSTALLATION ERROR Jason Swails (Sun Nov 30 2014 - 04:46:59 PST)
[AMBER] 100ps long minimization script pradeep pant (Sun Nov 30 2014 - 05:38:01 PST)
- Re: [AMBER] 100ps long minimization script Carlos Simmerling (Sun Nov 30 2014 - 05:53:13 PST)
- Re: [AMBER] 100ps long minimization script David A Case (Sun Nov 30 2014 - 12:38:21 PST)
[AMBER] Problem with triangular point in parameter file Jorgen Simonsen (Sun Nov 30 2014 - 09:52:56 PST)
- Re: [AMBER] Problem with triangular point in parameter file David A Case (Sun Nov 30 2014 - 12:43:36 PST)
  - Re: [AMBER] Problem with triangular point in parameter file Jorgen Simonsen (Sun Nov 30 2014 - 14:53:42 PST)
    - Re: [AMBER] Problem with triangular point in parameter file David A Case (Mon Dec 01 2014 - 04:24:52 PST)
    - Re: [AMBER] Problem with triangular point in parameter file Jorgen Simonsen (Mon Dec 01 2014 - 15:20:59 PST)
    - Re: [AMBER] Problem with triangular point in parameter file David A Case (Tue Dec 02 2014 - 05:06:13 PST)
[AMBER] LEaP Error Aronica, Pietro (Mon Dec 01 2014 - 03:23:28 PST)
- Re: [AMBER] LEaP Error David A Case (Mon Dec 01 2014 - 04:36:23 PST)
  - Re: [AMBER] LEaP Error Aronica, Pietro (Mon Dec 01 2014 - 14:00:17 PST)
    - Re: [AMBER] LEaP Error Aronica, Pietro (Mon Dec 01 2014 - 14:21:12 PST)
    - Re: [AMBER] LEaP Error Daniel Roe (Mon Dec 01 2014 - 15:01:12 PST)
    - Re: [AMBER] LEaP Error Daniel Roe (Mon Dec 01 2014 - 14:24:43 PST)
[AMBER] tleap segmentation fault George Tzotzos (Mon Dec 01 2014 - 11:44:32 PST)
- Re: [AMBER] tleap segmentation fault Bill Ross (Tue May 11 2010 - 10:39:06 PDT)
  - Re: [AMBER] tleap segmentation fault Omair A. Khan (Tue May 11 2010 - 12:55:26 PDT)
    - Re: [AMBER] tleap segmentation fault Jason Swails (Tue May 11 2010 - 14:28:36 PDT)
- Re: [AMBER] tleap segmentation fault Bill Ross (Tue May 11 2010 - 13:03:54 PDT)
  - Re: [AMBER] tleap segmentation fault Omair A. Khan (Tue May 11 2010 - 14:27:41 PDT)
    - Re: [AMBER] tleap segmentation fault case (Tue May 11 2010 - 14:57:20 PDT)
    - Re: [AMBER] tleap segmentation fault Omair A. Khan (Wed May 12 2010 - 14:57:17 PDT)
    - Re: [AMBER] tleap segmentation fault Jason Swails (Wed May 12 2010 - 15:15:01 PDT)
    - Re: [AMBER] tleap segmentation fault case (Wed May 12 2010 - 17:58:54 PDT)
- Re: [AMBER] tleap segmentation fault Bill Ross (Tue May 11 2010 - 14:39:34 PDT)
- Re: [AMBER] tleap segmentation fault Daniel Roe (Mon Dec 01 2014 - 12:00:40 PST)
  - Re: [AMBER] tleap segmentation fault George Tzotzos (Mon Dec 01 2014 - 12:06:01 PST)
    - Re: [AMBER] tleap segmentation fault Jason Swails (Mon Dec 01 2014 - 12:15:45 PST)
    - Re: [AMBER] tleap segmentation fault George Tzotzos (Mon Dec 01 2014 - 12:17:20 PST)
    - Re: [AMBER] tleap segmentation fault Daniel Roe (Mon Dec 01 2014 - 12:32:07 PST)
[AMBER] Problems with amber14 intallation in parallel Dailin Li (Mon Dec 01 2014 - 17:39:58 PST)
- Re: [AMBER] Problems with amber14 intallation in parallel Daniel Roe (Mon Dec 01 2014 - 19:54:21 PST)
- Re: [AMBER] Problems with amber14 intallation in parallel Jason Swails (Mon Dec 08 2014 - 06:47:26 PST)
[AMBER] Ambertools14 Installation Appears to Reset Edward Kalkreuter (Mon Dec 01 2014 - 18:16:12 PST)
- Re: [AMBER] Ambertools14 Installation Appears to Reset Jason Swails (Mon Dec 01 2014 - 18:37:15 PST)
[AMBER] bug in "natural language" system to define nmropt restraints: generalized distance coordinate Marc van der Kamp (Tue Dec 02 2014 - 01:29:50 PST)
[AMBER] accelerated MD set up Asmita Gupta (Tue Dec 02 2014 - 03:15:27 PST)
- Re: [AMBER] accelerated MD set up Vlad Cojocaru (Tue Dec 02 2014 - 04:32:16 PST)
  - Re: [AMBER] accelerated MD set up Asmita Gupta (Tue Dec 02 2014 - 07:43:19 PST)
[AMBER] how to retain the MG++ coordination geometry during simulation BERGY (Tue Dec 02 2014 - 11:59:57 PST)
- Re: [AMBER] how to retain the MG++ coordination geometry during simulation Ken Merz (Tue Dec 02 2014 - 12:31:55 PST)
- Re: [AMBER] how to retain the MG++ coordination geometry during simulation Marc van der Kamp (Tue Dec 02 2014 - 12:33:51 PST)
  - Re: [AMBER] how to retain the MG++ coordination geometry during simulation BERGY (Tue Dec 02 2014 - 13:42:17 PST)
[AMBER] On the significant dG error in the MMGBSA results.dat James Starlight (Tue Dec 02 2014 - 13:29:27 PST)
- Re: [AMBER] On the significant dG error in the MMGBSA results.dat Aron Broom (Tue Dec 02 2014 - 15:35:47 PST)
  - Re: [AMBER] On the significant dG error in the MMGBSA results.dat James Starlight (Wed Dec 03 2014 - 00:15:18 PST)
    - Re: [AMBER] On the significant dG error in the MMGBSA results.dat Aron Broom (Wed Dec 03 2014 - 06:50:20 PST)
    - Re: [AMBER] On the significant dG error in the MMGBSA results.dat James Starlight (Fri Dec 05 2014 - 03:33:58 PST)
    - Re: [AMBER] On the significant dG error in the MMGBSA results.dat Jason Swails (Fri Dec 05 2014 - 05:59:56 PST)
    - Re: [AMBER] On the significant dG error in the MMGBSA results.dat Aron Broom (Fri Dec 05 2014 - 07:19:34 PST)
    - Re: [AMBER] On the significant dG error in the MMGBSA results.dat James Starlight (Mon Dec 08 2014 - 00:35:06 PST)
    - Re: [AMBER] On the significant dG error in the MMGBSA results.dat James Starlight (Mon Dec 08 2014 - 23:36:35 PST)
[AMBER] Linker Attached to DNA Brittany Boykin (Tue Dec 02 2014 - 13:58:41 PST)
- Re: [AMBER] Linker Attached to DNA chandan patel (Tue Dec 02 2014 - 16:24:58 PST)
- Re: [AMBER] Linker Attached to DNA FyD (Tue Dec 02 2014 - 23:13:30 PST)
[AMBER] DMPC lipids are slightly charged in lipid14? Matthew Harrigan (Tue Dec 02 2014 - 22:00:41 PST)
- Re: [AMBER] DMPC lipids are slightly charged in lipid14? Gould, Ian R (Tue Dec 02 2014 - 22:37:43 PST)
[AMBER] MMGBSA.py cpptraj - autoimaging issue de Manzanos Guinot, Angela (Wed Dec 03 2014 - 02:54:09 PST)
- Re: [AMBER] MMGBSA.py cpptraj - autoimaging issue de Manzanos Guinot, Angela (Wed Dec 03 2014 - 03:22:46 PST)
  - Re: [AMBER] MMGBSA.py cpptraj - autoimaging issue Jason Swails (Wed Dec 03 2014 - 04:19:58 PST)
- Re: [AMBER] MMGBSA.py cpptraj - autoimaging issue Daniel Roe (Wed Dec 03 2014 - 06:57:56 PST)
[AMBER] B-factor values George Tzotzos (Wed Dec 03 2014 - 10:49:28 PST)
- Re: [AMBER] B-factor values Jason Swails (Wed Dec 03 2014 - 11:18:35 PST)
[AMBER] Help regarding error in top n crd generation Ruchika Bhat (Wed Dec 03 2014 - 23:14:29 PST)
- Re: [AMBER] Help regarding error in top n crd generation Ayesha Fatima (Thu Dec 04 2014 - 03:37:05 PST)
  - Re: [AMBER] Help regarding error in top n crd generation Ruchika Bhat (Thu Dec 04 2014 - 04:32:17 PST)
- Re: [AMBER] Help regarding error in top n crd generation David A Case (Thu Dec 04 2014 - 04:38:30 PST)
[AMBER] How to calculate energy change between two conformations Kshatresh Dutta Dubey (Thu Dec 04 2014 - 07:28:57 PST)
- Re: [AMBER] How to calculate energy change between two conformations Jason Swails (Thu Dec 04 2014 - 12:20:03 PST)
  - Re: [AMBER] How to calculate energy change between two conformations Kshatresh Dutta Dubey (Thu Dec 04 2014 - 13:18:16 PST)
    - Re: [AMBER] How to calculate energy change between two conformations Jason Swails (Thu Dec 04 2014 - 13:33:38 PST)
    - Re: [AMBER] How to calculate energy change between two conformations Kshatresh Dutta Dubey (Thu Dec 04 2014 - 13:43:58 PST)
[AMBER] Docking with Dock6 Wong, Sook (NIH/NCATS) [V] (Thu Dec 04 2014 - 09:28:28 PST)
- Re: [AMBER] Docking with Dock6 Aldo Segura (Thu Dec 04 2014 - 10:14:22 PST)
- Re: [AMBER] Docking with Dock6 David A Case (Thu Dec 04 2014 - 10:53:54 PST)
  - Re: [AMBER] Docking with Dock6 Wong, Sook (NIH/NCATS) [V] (Thu Dec 04 2014 - 12:00:12 PST)
[AMBER] Monitoring GPU voltage Kenneth Lam (Thu Dec 04 2014 - 12:08:32 PST)
- Re: [AMBER] Monitoring GPU voltage Tru Huynh (Thu Dec 04 2014 - 12:30:26 PST)
  - Re: [AMBER] Monitoring GPU voltage Kenneth Lam (Thu Dec 04 2014 - 13:02:41 PST)
- Re: [AMBER] Monitoring GPU voltage Jason Swails (Thu Dec 04 2014 - 13:14:59 PST)
  - Re: [AMBER] Monitoring GPU voltage Kenneth Lam (Thu Dec 04 2014 - 13:24:17 PST)
    - Re: [AMBER] Monitoring GPU voltage Ross Walker (Thu Dec 04 2014 - 14:16:32 PST)
    - Re: [AMBER] Monitoring GPU voltage Kenneth Lam (Thu Dec 04 2014 - 15:00:52 PST)
    - Re: [AMBER] Monitoring GPU voltage Ross Walker (Thu Dec 04 2014 - 19:06:31 PST)
    - Re: [AMBER] Monitoring GPU voltage Kenneth Lam (Fri Dec 05 2014 - 13:08:16 PST)
    - Re: [AMBER] Monitoring GPU voltage Tru Huynh (Tue Dec 09 2014 - 15:46:43 PST)
    - Re: [AMBER] Monitoring GPU voltage Tru Huynh (Wed Jul 22 2015 - 12:52:30 PDT)
    - Re: [AMBER] Monitoring GPU voltage Tru Huynh (Wed Jul 22 2015 - 13:01:49 PDT)
    - Re: [AMBER] Monitoring GPU voltage Ross Walker (Wed Jul 22 2015 - 17:57:43 PDT)
[AMBER] xleap segmentation fault when removing residues Mickey Richards (Thu Dec 04 2014 - 15:03:42 PST)
[AMBER] TINKER and SANDER minimization (AMOEBA force field) 양지현 (Thu Dec 04 2014 - 18:17:11 PST)
- Re: [AMBER] TINKER and SANDER minimization (AMOEBA force field) David A Case (Thu Dec 04 2014 - 18:55:45 PST)
[AMBER] closeness Sylvester Tumusiime (Thu Dec 04 2014 - 21:12:36 PST)
- Re: [AMBER] closeness Daniel Roe (Thu Dec 04 2014 - 21:32:26 PST)
  - Re: [AMBER] closeness Sylvester Tumusiime (Fri Dec 05 2014 - 03:49:35 PST)
    - Re: [AMBER] closeness David A Case (Fri Dec 05 2014 - 05:41:33 PST)
    - Re: [AMBER] closeness Daniel Roe (Fri Dec 05 2014 - 08:07:51 PST)
    - Re: [AMBER] closeness Sylvester Tumusiime (Fri Dec 05 2014 - 10:05:37 PST)
    - Re: [AMBER] closeness Sylvester Tumusiime (Fri Dec 05 2014 - 10:44:38 PST)
    - Re: [AMBER] closeness Daniel Roe (Fri Dec 05 2014 - 10:58:15 PST)
    - Re: [AMBER] closeness Sylvester Tumusiime (Fri Dec 05 2014 - 18:32:55 PST)
    - Re: [AMBER] closeness David A Case (Sat Dec 06 2014 - 06:05:33 PST)
[AMBER] MMGBSA.py - issues with molsurf de Manzanos Guinot, Angela (Fri Dec 05 2014 - 02:29:41 PST)
- Re: [AMBER] MMGBSA.py - issues with molsurf Daniel Roe (Fri Dec 05 2014 - 07:58:48 PST)
- Re: [AMBER] MMGBSA.py - issues with molsurf Marcus Arieno (Fri Dec 05 2014 - 08:50:31 PST)
[AMBER] Problems with implicit solvent Carlo Guardiani (Fri Dec 05 2014 - 03:11:56 PST)
- Re: [AMBER] Problems with implicit solvent Carlos Simmerling (Fri Dec 05 2014 - 03:53:08 PST)
Re: [AMBER] problem with unknown compiler: gnu Narendar Kolimi (Fri Dec 05 2014 - 04:20:40 PST)
- Re: [AMBER] problem with unknown compiler: gnu David A Case (Fri Dec 05 2014 - 05:48:52 PST)
  - Re: [AMBER] problem with unknown compiler: gnu Narendar Kolimi (Fri Dec 05 2014 - 08:20:56 PST)
    - Re: [AMBER] problem with unknown compiler: gnu Jason Swails (Fri Dec 05 2014 - 08:22:32 PST)
    - Re: [AMBER] problem with unknown compiler: gnu Narendar Kolimi (Fri Dec 05 2014 - 08:29:50 PST)
[AMBER] Alignment before calculation? Soumendranath Bhakat (Fri Dec 05 2014 - 07:12:38 PST)
- Re: [AMBER] Alignment before calculation? Daniel Roe (Fri Dec 05 2014 - 08:11:39 PST)
[AMBER] error creating mol2 files Anupam Goel (Fri Dec 05 2014 - 08:26:13 PST)
- Re: [AMBER] error creating mol2 files Aldo Segura (Fri Dec 05 2014 - 08:54:04 PST)
  - Re: [AMBER] error creating mol2 files Anupam Goel (Fri Dec 05 2014 - 09:16:58 PST)
    - Re: [AMBER] error creating mol2 files Aldo Segura (Fri Dec 05 2014 - 10:05:38 PST)
    - Re: [AMBER] error creating mol2 files Anupam Goel (Fri Dec 05 2014 - 10:34:32 PST)
    - Re: [AMBER] error creating mol2 files Anupam Goel (Fri Dec 05 2014 - 10:35:13 PST)
    - Re: [AMBER] error creating mol2 files Aldo Segura (Fri Dec 05 2014 - 11:59:01 PST)
    - Re: [AMBER] error creating mol2 files Anupam Goel (Fri Dec 05 2014 - 12:41:10 PST)
    - Re: [AMBER] error creating mol2 files Aldo Segura (Fri Dec 05 2014 - 12:49:45 PST)
    - Re: [AMBER] error creating mol2 files Anupam Goel (Fri Dec 05 2014 - 12:51:31 PST)
- Re: [AMBER] error creating mol2 files hannes.loeffler.stfc.ac.uk (Fri Dec 05 2014 - 10:36:29 PST)
  - Re: [AMBER] error creating mol2 files David A Case (Fri Dec 05 2014 - 12:08:36 PST)
- Re: [AMBER] error creating mol2 files FyD (Sat Dec 06 2014 - 05:27:16 PST)
[AMBER] Can i combine the result given by sander and pmemd together wangmt (Sat Dec 06 2014 - 01:21:54 PST)
- Re: [AMBER] Can i combine the result given by sander and pmemd together YC Sun (Sat Dec 06 2014 - 02:22:23 PST)
- Re: [AMBER] Can i combine the result given by sander and pmemd together David A Case (Sat Dec 06 2014 - 06:14:30 PST)
[AMBER] Use of special characters * and ? in ambermask Emilio Lence (Sat Dec 06 2014 - 11:31:27 PST)
[AMBER] Problems with amber14 intallation in parallel Dailin Li (Sat Dec 06 2014 - 17:42:10 PST)
- Re: [AMBER] Problems with amber14 intallation in parallel Jason Swails (Sun Dec 07 2014 - 19:17:34 PST)
[AMBER] acetate params for mtkpp Francesco Pietra (Sun Dec 07 2014 - 09:41:32 PST)
- Re: [AMBER] acetate params for mtkpp Francesco Pietra (Sun Dec 07 2014 - 13:47:08 PST)
  - Re: [AMBER] acetate params for mtkpp Jason Swails (Sun Dec 07 2014 - 19:18:27 PST)
    - Re: [AMBER] acetate params for mtkpp Francesco Pietra (Mon Dec 08 2014 - 08:19:36 PST)
[AMBER] ERROR USING tleap ROOPALI VERMA (Mon Dec 08 2014 - 03:08:15 PST)
- Re: [AMBER] ERROR USING tleap David A Case (Mon Dec 08 2014 - 04:39:09 PST)
  - Re: [AMBER] ERROR USING tleap Hai Nguyen (Mon Dec 08 2014 - 20:12:06 PST)
    - Re: [AMBER] ERROR USING tleap ROOPALI VERMA (Tue Dec 09 2014 - 00:25:07 PST)
    - Re: [AMBER] ERROR USING tleap Jason Swails (Tue Dec 09 2014 - 04:16:16 PST)
    - Re: [AMBER] ERROR USING tleap David A Case (Tue Dec 09 2014 - 04:24:01 PST)
[AMBER] Calculating of charge MOHD HOMAIDUR RAHMAN (Mon Dec 08 2014 - 03:57:47 PST)
- Re: [AMBER] Calculating of charge David A Case (Mon Dec 08 2014 - 04:43:18 PST)
[AMBER] Problem with AMBER mail list wangmt (Mon Dec 08 2014 - 06:26:47 PST)
- Re: [AMBER] Problem with AMBER mail list David A Case (Mon Dec 08 2014 - 06:57:03 PST)
- Re: [AMBER] Problem with AMBER mail list Jason Swails (Mon Dec 08 2014 - 07:56:31 PST)
[AMBER] help in calculating diffusion coefficient Robin Jain (Mon Dec 08 2014 - 06:40:52 PST)
- Re: [AMBER] help in calculating diffusion coefficient David A Case (Mon Dec 08 2014 - 07:00:58 PST)
Re: [AMBER] MMPBSA.py bad atom type Jason Swails (Mon Dec 08 2014 - 07:10:22 PST)
[AMBER] Wrong bond types in Antechamber MOL2 Denis Schmidt (Mon Dec 08 2014 - 07:21:11 PST)
- Re: [AMBER] Wrong bond types in Antechamber MOL2 Hannes Loeffler (Tue Dec 09 2014 - 01:30:11 PST)
  - Re: [AMBER] Wrong bond types in Antechamber MOL2 Denis Schmidt (Tue Dec 09 2014 - 02:08:22 PST)
    - Re: [AMBER] Wrong bond types in Antechamber MOL2 Hannes Loeffler (Tue Dec 09 2014 - 02:43:07 PST)
Re: [AMBER] Instructions on How to install Amber on Suse Linux Jin Zhang (Mon Dec 08 2014 - 07:55:55 PST)
- Re: [AMBER] Instructions on How to install Amber on Suse Linux Daniel Roe (Mon Dec 08 2014 - 09:56:51 PST)
- Re: [AMBER] Instructions on How to install Amber on Suse Linux Aldo Segura (Mon Dec 08 2014 - 12:54:39 PST)
[AMBER] analyze.x error when dealing with the system containing ions in tinker Ya Gao (Mon Dec 08 2014 - 08:47:05 PST)
- Re: [AMBER] analyze.x error when dealing with the system containing ions in tinker Jason Swails (Mon Dec 08 2014 - 10:00:51 PST)
  - Re: [AMBER] analyze.x error when dealing with the system containing ions in tinker Ya Gao (Mon Dec 08 2014 - 21:40:12 PST)
- Re: [AMBER] analyze.x error when dealing with the system containing ions in tinker David A Case (Mon Dec 08 2014 - 17:30:50 PST)
  - Re: [AMBER] analyze.x error when dealing with the system containing ions in tinker Ya Gao (Mon Dec 08 2014 - 21:41:19 PST)
[AMBER] Lipid 14 PDB format Romero, Raquel (Mon Dec 08 2014 - 10:56:58 PST)
[AMBER] selecting the best docking pose with MM/PBSA Thomas Evangelidis (Mon Dec 08 2014 - 15:22:39 PST)
- Re: [AMBER] selecting the best docking pose with MM/PBSA Ray Luo, Ph.D. (Tue Dec 09 2014 - 10:54:53 PST)
  - Re: [AMBER] selecting the best docking pose with MM/PBSA Thomas Evangelidis (Tue Dec 09 2014 - 13:32:15 PST)
    - Re: [AMBER] selecting the best docking pose with MM/PBSA Ray Luo, Ph.D. (Tue Dec 09 2014 - 15:55:14 PST)
[AMBER] Software announcement: Release of PUPIL 3.0 Joan Torras (Mon Dec 08 2014 - 15:36:14 PST)
- Re: [AMBER] Software announcement: Release of PUPIL 3.0 hannes.loeffler.stfc.ac.uk (Mon Dec 08 2014 - 23:42:56 PST)
  - Re: [AMBER] Software announcement: Release of PUPIL 3.0 Torras, Joan (Tue Dec 09 2014 - 00:50:15 PST)
  - Re: [AMBER] Software announcement: Release of PUPIL 3.0 Marc van der Kamp (Tue Dec 09 2014 - 00:52:04 PST)
    - Re: [AMBER] Software announcement: Release of PUPIL 3.0 Torras, Joan (Tue Dec 09 2014 - 01:17:12 PST)
[AMBER] sander.PUPIL compile error 汪盛 (Mon Dec 08 2014 - 19:12:49 PST)
[AMBER] questions about bcc charge 徐晓庶 (Mon Dec 08 2014 - 22:07:11 PST)
- Re: [AMBER] questions about bcc charge hannes.loeffler.stfc.ac.uk (Mon Dec 08 2014 - 23:53:26 PST)
[AMBER] Antechamber problem Atila Petrosian (Mon Dec 08 2014 - 22:49:45 PST)
- Re: [AMBER] Antechamber problem hannes.loeffler.stfc.ac.uk (Mon Dec 08 2014 - 23:28:38 PST)
  - Re: [AMBER] Antechamber problem Jason Swails (Tue Dec 09 2014 - 04:11:38 PST)
[AMBER] Empirical force fields: release of R.E.D. Server Dev./PyRED Nov. 2014 FyD (Tue Dec 09 2014 - 00:30:32 PST)
[AMBER] Query about MMPBSA.py de Manzanos Guinot, Angela (Tue Dec 09 2014 - 08:49:04 PST)
- Re: [AMBER] Query about MMPBSA.py Jason Swails (Tue Dec 09 2014 - 09:12:07 PST)
  - Re: [AMBER] Query about MMPBSA.py de Manzanos Guinot, Angela (Wed Dec 10 2014 - 02:28:37 PST)
    - Re: [AMBER] Query about MMPBSA.py Jason Swails (Wed Dec 10 2014 - 04:04:28 PST)
[AMBER] getting the input files for antechamber Ahmet yıldırım (Tue Dec 09 2014 - 11:49:05 PST)
[AMBER] AmberTools suppose program Yu Chen (Tue Dec 09 2014 - 12:27:28 PST)
- Re: [AMBER] AmberTools suppose program Chris Moth (Tue Dec 09 2014 - 13:50:14 PST)
- Re: [AMBER] AmberTools suppose program David A Case (Tue Dec 09 2014 - 18:56:18 PST)
  - Re: [AMBER] AmberTools suppose program Yu Chen (Tue Dec 09 2014 - 19:30:44 PST)
[AMBER] Add MgCl2 salts Haining Liu (Tue Dec 09 2014 - 13:13:58 PST)
- Re: [AMBER] Add MgCl2 salts Jason Swails (Tue Dec 09 2014 - 18:07:33 PST)
- Re: [AMBER] Add MgCl2 salts David A Case (Tue Dec 09 2014 - 18:58:50 PST)
[AMBER] TLEAP issues Wong, Sook (NIH/NCATS) [V] (Tue Dec 09 2014 - 13:59:01 PST)
- Re: [AMBER] TLEAP issues Jason Swails (Tue Dec 09 2014 - 18:06:38 PST)
- Re: [AMBER] TLEAP issues David A Case (Tue Dec 09 2014 - 19:03:17 PST)
- Re: [AMBER] TLEAP issues Aldo Segura (Wed Dec 10 2014 - 07:23:52 PST)
[AMBER] switch digest model to normal fjliu (Tue Dec 09 2014 - 19:17:07 PST)
[AMBER] Failure to restart H-REMD Carlo Guardiani (Wed Dec 10 2014 - 01:57:03 PST)
- Re: [AMBER] Failure to restart H-REMD Jason Swails (Wed Dec 10 2014 - 04:11:09 PST)
  - Re: [AMBER] Failure to restart H-REMD Carlo Guardiani (Wed Dec 10 2014 - 07:27:41 PST)
[AMBER] another segfault with sander14 and TI/softcore Hannes Loeffler (Wed Dec 10 2014 - 02:04:48 PST)
- Re: [AMBER] another segfault with sander14 and TI/softcore David A Case (Wed Dec 17 2014 - 05:41:32 PST)
  - Re: [AMBER] another segfault with sander14 and TI/softcore Hannes Loeffler (Wed Dec 17 2014 - 06:46:19 PST)
[AMBER] Amber12 parallel installation error Kanin Wichapong (Wed Dec 10 2014 - 06:43:05 PST)
- Re: [AMBER] Amber12 parallel installation error Jason Swails (Wed Dec 10 2014 - 07:22:50 PST)
  - Re: [AMBER] Amber12 parallel installation error David A Case (Thu Dec 11 2014 - 04:30:51 PST)
[AMBER] PM6-DH+ simulation problem Marcos Serrou do Amaral (Wed Dec 10 2014 - 09:05:57 PST)
- Re: [AMBER] PM6-DH+ simulation problem Andreas Goetz (Thu Dec 11 2014 - 15:51:14 PST)
  - Re: [AMBER] PM6-DH+ simulation problem Marcos Serrou do Amaral (Fri Dec 12 2014 - 06:16:27 PST)
[AMBER] Information on ff12polA and ff12polL Manikanthan Bhavaraju (Wed Dec 10 2014 - 10:55:18 PST)
- Re: [AMBER] Information on ff12polA and ff12polL David A Case (Thu Dec 11 2014 - 04:22:14 PST)
[AMBER] MMPBSA-ERROR for firstmolecule-dna Abhishek TYAGI (Wed Dec 10 2014 - 19:05:46 PST)
- Re: [AMBER] MMPBSA-ERROR for firstmolecule-dna Jason Swails (Thu Dec 11 2014 - 05:50:10 PST)
- Re: [AMBER] MMPBSA-ERROR for firstmolecule-dna Abhishek TYAGI (Fri Dec 12 2014 - 23:48:14 PST)
  - Re: [AMBER] MMPBSA-ERROR for firstmolecule-dna Abhishek TYAGI (Mon Dec 15 2014 - 03:03:41 PST)
    - Re: [AMBER] MMPBSA-ERROR for firstmolecule-dna Abhishek TYAGI (Tue Dec 16 2014 - 19:56:30 PST)
    - Re: [AMBER] MMPBSA-ERROR for firstmolecule-dna Jason Swails (Tue Dec 16 2014 - 20:44:04 PST)
    - Re: [AMBER] MMPBSA-ERROR for firstmolecule-dna Ray Luo, Ph.D. (Wed Dec 17 2014 - 09:53:58 PST)
- Re: [AMBER] MMPBSA-ERROR for firstmolecule-dna Abhishek TYAGI (Fri Dec 19 2014 - 01:14:49 PST)
  - Re: [AMBER] MMPBSA-ERROR for firstmolecule-dna Ray Luo, Ph.D. (Fri Dec 19 2014 - 09:47:39 PST)
    - Re: [AMBER] MMPBSA-ERROR for firstmolecule-dna Jason Swails (Fri Dec 19 2014 - 10:15:35 PST)
    - Re: [AMBER] MMPBSA-ERROR for firstmolecule-dna Ray Luo, Ph.D. (Fri Dec 19 2014 - 10:25:23 PST)
    - Re: [AMBER] MMPBSA-ERROR for firstmolecule-dna Daniel Roe (Fri Dec 19 2014 - 11:00:01 PST)
    - Re: [AMBER] MMPBSA-ERROR for firstmolecule-dna Ray Luo, Ph.D. (Fri Dec 19 2014 - 15:48:03 PST)
- Re: [AMBER] MMPBSA-ERROR for firstmolecule-dna Abhishek TYAGI (Sat Dec 20 2014 - 22:57:52 PST)
[AMBER] Is BUG in cpptraj of version 14?? Chris Gao (Wed Dec 10 2014 - 22:51:43 PST)
- Re: [AMBER] Is BUG in cpptraj of version 14?? Daniel Roe (Thu Dec 11 2014 - 07:01:25 PST)
[AMBER] steered MD based on PCA Guillaume Roellinger (Thu Dec 11 2014 - 00:34:12 PST)
[AMBER] Generate pmf of small molecule membrane insertion wmsmith (Thu Dec 11 2014 - 14:34:02 PST)
[AMBER] Problem with simulation of protein-DNA complex Aditya Sarkar (Fri Dec 12 2014 - 00:49:20 PST)
- Re: [AMBER] Problem with simulation of protein-DNA complex Daniel Roe (Fri Dec 12 2014 - 06:50:39 PST)
- Re: [AMBER] Problem with simulation of protein-DNA complex Aditya Sarkar (Fri Dec 12 2014 - 22:12:52 PST)
  - Re: [AMBER] Problem with simulation of protein-DNA complex Jason Swails (Sat Dec 13 2014 - 07:10:04 PST)
- Re: [AMBER] Problem with simulation of protein-DNA complex Aditya Sarkar (Mon Dec 15 2014 - 03:10:59 PST)
  - Re: [AMBER] Problem with simulation of protein-DNA complex Daniel Roe (Mon Dec 15 2014 - 07:22:05 PST)
[AMBER] script to convert the Gromacs topology to Amber topology? Ravi Tripathi (Fri Dec 12 2014 - 01:19:47 PST)
- Re: [AMBER] script to convert the Gromacs topology to Amber topology? Jason Swails (Fri Dec 12 2014 - 05:00:41 PST)
- Re: [AMBER] script to convert the Gromacs topology to Amber topology? Josep Maria Campanera Alsina (Tue Mar 17 2015 - 02:57:59 PDT)
  - Re: [AMBER] script to convert the Gromacs topology to Amber topology? Jason Swails (Tue Mar 17 2015 - 05:39:36 PDT)
[AMBER] MM-PBSA (addions) Atila Petrosian (Fri Dec 12 2014 - 03:20:02 PST)
- Re: [AMBER] MM-PBSA (addions) Jason Swails (Fri Dec 12 2014 - 04:45:16 PST)
[AMBER] AmberTools14/Amber10 Francesco Pietra (Fri Dec 12 2014 - 03:40:56 PST)
- Re: [AMBER] AmberTools14/Amber10 aksbmbg_s.caluniv.ac.in (Fri Dec 12 2014 - 03:54:12 PST)
- Re: [AMBER] AmberTools14/Amber10 aksbmbg_s.caluniv.ac.in (Fri Dec 12 2014 - 03:56:49 PST)
  - Re: [AMBER] AmberTools14/Amber10 Francesco Pietra (Fri Dec 12 2014 - 06:59:03 PST)
- Re: [AMBER] AmberTools14/Amber10 Jason Swails (Fri Dec 12 2014 - 04:43:36 PST)
  - Re: [AMBER] AmberTools14/Amber10 Francesco Pietra (Fri Dec 12 2014 - 07:10:44 PST)
[AMBER] change the mode of my AMBER mail list from digest to normal fjliu (Fri Dec 12 2014 - 03:56:56 PST)
- Re: [AMBER] change the mode of my AMBER mail list from digest to normal aksbmbg_s.caluniv.ac.in (Fri Dec 12 2014 - 04:02:51 PST)
- Re: [AMBER] change the mode of my AMBER mail list from digest to normal Ross Walker (Fri Dec 12 2014 - 08:39:22 PST)
  - Re: [AMBER] change the mode of my AMBER mail list from digest to normal fjliu (Fri Dec 12 2014 - 17:51:47 PST)
[AMBER] MM-PBSA (addions) Atila Petrosian (Fri Dec 12 2014 - 04:54:15 PST)
[AMBER] conversion of AMBER trajectory to Gromacs trajectory Robin Jain (Fri Dec 12 2014 - 23:14:24 PST)
- Re: [AMBER] conversion of AMBER trajectory to Gromacs trajectory aksbmbg_s.caluniv.ac.in (Fri Dec 12 2014 - 23:25:45 PST)
- Re: [AMBER] conversion of AMBER trajectory to Gromacs trajectory Jason Swails (Sat Dec 13 2014 - 07:11:19 PST)
- Re: [AMBER] conversion of AMBER trajectory to Gromacs trajectory Daniel Roe (Sat Dec 13 2014 - 08:27:20 PST)
[AMBER] Generation of 3D structure of polypeptides with modified amino acids Suman Chakrabarty (Sat Dec 13 2014 - 02:01:47 PST)
- Re: [AMBER] Generation of 3D structure of polypeptides with modified amino acids Jason Swails (Sat Dec 13 2014 - 07:24:56 PST)
[AMBER] 8Mureabox URE residue unknown CHAMI F. (Sat Dec 13 2014 - 06:13:21 PST)
- Re: [AMBER] 8Mureabox URE residue unknown Jason Swails (Sat Dec 13 2014 - 07:31:17 PST)
[AMBER] PCA 2dprojection with xtal data and energy information BERGY (Sat Dec 13 2014 - 14:39:58 PST)
- Re: [AMBER] PCA 2dprojection with xtal data and energy information Daniel Roe (Sat Dec 13 2014 - 15:48:58 PST)
  - Re: [AMBER] PCA 2dprojection with xtal data and energy information BERGY (Sat Dec 13 2014 - 18:45:17 PST)
    - Re: [AMBER] PCA 2dprojection with xtal data and energy information Daniel Roe (Sat Dec 13 2014 - 20:26:54 PST)
    - Re: [AMBER] PCA 2dprojection with xtal data and energy information BERGY (Tue Dec 16 2014 - 13:23:52 PST)
    - Re: [AMBER] PCA 2dprojection with xtal data and energy information Daniel Roe (Tue Dec 16 2014 - 14:53:44 PST)
    - Re: [AMBER] PCA 2dprojection with xtal data and energy information BERGY (Tue Dec 16 2014 - 21:47:42 PST)
[AMBER] "Unit 18 Error on OPEN: logfile" kurisaki (Sat Dec 13 2014 - 16:57:28 PST)
- Re: [AMBER] "Unit 18 Error on OPEN: logfile" kurisaki (Sat Dec 13 2014 - 17:04:24 PST)
- Re: [AMBER] "Unit 18 Error on OPEN: logfile" kurisaki (Sat Dec 13 2014 - 17:20:34 PST)
[AMBER] production run for diffusion constant Robin Jain (Sun Dec 14 2014 - 07:39:17 PST)
- Re: [AMBER] production run for diffusion constant Daniel Roe (Sun Dec 14 2014 - 08:45:51 PST)
[AMBER] Looking for AMBER FF12SB for CHARMM Zhang, Sixue (Sun Dec 14 2014 - 14:52:03 PST)
[AMBER] Glycan-protein h-bond ptraj maryam azimzadehirani (Sun Dec 14 2014 - 19:40:05 PST)
- Re: [AMBER] Glycan-protein h-bond ptraj Daniel Roe (Sun Dec 14 2014 - 20:23:15 PST)
  - Re: [AMBER] Glycan-protein h-bond ptraj maryam azimzadehirani (Sun Dec 14 2014 - 23:05:57 PST)
    - Re: [AMBER] Glycan-protein h-bond ptraj Daniel Roe (Mon Dec 15 2014 - 00:37:14 PST)
[AMBER] Error in Box Dimension 杨川 (Sun Dec 14 2014 - 20:13:13 PST)
- Re: [AMBER] Error in Box Dimension Daniel Roe (Sun Dec 14 2014 - 20:27:17 PST)
- Re: [AMBER] Error in Box Dimension 杨川 (Mon Dec 15 2014 - 21:15:43 PST)
  - Re: [AMBER] Error in Box Dimension David A Case (Tue Dec 16 2014 - 05:01:19 PST)
[AMBER] Optimization under restraint atoms using ibelly option Akihiro Yamane (Mon Dec 15 2014 - 04:12:08 PST)
- Re: [AMBER] Optimization under restraint atoms using ibelly option David A Case (Mon Dec 15 2014 - 17:33:59 PST)
- Re: [AMBER] Optimization under restraint atoms using ibelly option Akihiro Yamane (Thu Dec 18 2014 - 04:09:11 PST)
[AMBER] gas phase, nonperiodic system with AMOEBA ff in AMBER Lawrenz, Morgan (Mon Dec 15 2014 - 12:17:51 PST)
- Re: [AMBER] gas phase, nonperiodic system with AMOEBA ff in AMBER Jason Swails (Mon Dec 15 2014 - 14:42:06 PST)
  - Re: [AMBER] gas phase, nonperiodic system with AMOEBA ff in AMBER Lawrenz, Morgan (Mon Dec 15 2014 - 14:52:13 PST)
[AMBER] Missing psi dihedral at cationic N-terminus of protein/peptide? nealec (Mon Dec 15 2014 - 13:32:42 PST)
- Re: [AMBER] Missing psi dihedral at cationic N-terminus of protein/peptide? David A Case (Mon Dec 22 2014 - 05:36:27 PST)
  - Re: [AMBER] Missing psi dihedral at cationic N-terminus of protein/peptide? Carlos Simmerling (Mon Dec 22 2014 - 15:38:48 PST)
[AMBER] error while saving prmtop and inpcrd Anupam Goel (Mon Dec 15 2014 - 14:38:07 PST)
- Re: [AMBER] error while saving prmtop and inpcrd David A Case (Mon Dec 15 2014 - 17:30:04 PST)
[AMBER] Analyzing multiple trajectories in cpptraj Gard Nelson (Mon Dec 15 2014 - 17:37:32 PST)
- Re: [AMBER] Analyzing multiple trajectories in cpptraj Daniel Roe (Mon Dec 15 2014 - 19:21:26 PST)
  - Re: [AMBER] Analyzing multiple trajectories in cpptraj Gard Nelson (Tue Dec 16 2014 - 09:50:11 PST)
    - Re: [AMBER] Analyzing multiple trajectories in cpptraj Daniel Roe (Tue Dec 16 2014 - 09:52:46 PST)
[AMBER] Different convergence in pmemd.cuda against CPU Hiromasa WATANABE (Mon Dec 15 2014 - 20:42:18 PST)
- Re: [AMBER] Different convergence in pmemd.cuda against CPU Ross Walker (Mon Dec 15 2014 - 21:43:42 PST)
  - Re: [AMBER] Different convergence in pmemd.cuda against CPU Hiromasa WATANABE (Mon Dec 15 2014 - 22:26:37 PST)
- Re: [AMBER] Different convergence in pmemd.cuda against CPU Ross Walker (Tue Dec 16 2014 - 10:19:02 PST)
  - Re: [AMBER] Different convergence in pmemd.cuda against CPU Hiromasa WATANABE (Sun Dec 21 2014 - 22:18:02 PST)
[AMBER] How to analyze REMD results Wang Moye (Mon Dec 15 2014 - 22:42:04 PST)
[AMBER] Fwd: RED-III.52-Tools stopped to work suddenly. Zeinab Emami (Tue Dec 16 2014 - 03:05:19 PST)
- Re: [AMBER] Fwd: RED-III.52-Tools stopped to work suddenly. FyD (Tue Dec 16 2014 - 10:15:07 PST)
  - Re: [AMBER] Fwd: RED-III.52-Tools stopped to work suddenly. Zeinab Emami (Wed Dec 17 2014 - 02:45:59 PST)
[AMBER] Amber 12 on K20 GPUs -- how am I doing? Baker D.J. (Tue Dec 16 2014 - 04:22:22 PST)
- Re: [AMBER] Amber 12 on K20 GPUs -- how am I doing? Ross Walker (Tue Dec 16 2014 - 10:15:36 PST)
[AMBER] phosphoserine parameters Jacopo Sgrignani (Tue Dec 16 2014 - 07:17:06 PST)
- Re: [AMBER] phosphoserine parameters Christina Bergonzo (Tue Dec 16 2014 - 07:24:36 PST)
  - Re: [AMBER] phosphoserine parameters David A Case (Tue Dec 16 2014 - 08:27:34 PST)
[AMBER] clustering problem in ambertool14 Mahendra B Thapa (Tue Dec 16 2014 - 10:28:13 PST)
- Re: [AMBER] clustering problem in ambertool14 Daniel Roe (Tue Dec 16 2014 - 12:19:51 PST)
[AMBER] excluding atom sets from MMPB/GB-SA calculations Hallel Freedman (Tue Dec 16 2014 - 16:49:18 PST)
- Re: [AMBER] excluding atom sets from MMPB/GB-SA calculations Hallel Freedman (Tue Dec 16 2014 - 16:50:34 PST)
  - Re: [AMBER] excluding atom sets from MMPB/GB-SA calculations Ray Luo, Ph.D. (Wed Dec 17 2014 - 09:58:28 PST)
    - Re: [AMBER] excluding atom sets from MMPB/GB-SA calculations Hallel Freedman (Wed Dec 17 2014 - 10:06:40 PST)
    - Re: [AMBER] excluding atom sets from MMPB/GB-SA calculations Jason Swails (Wed Dec 17 2014 - 11:06:31 PST)
    - Re: [AMBER] excluding atom sets from MMPB/GB-SA calculations Hallel Freedman (Wed Dec 17 2014 - 11:20:52 PST)
    - Re: [AMBER] excluding atom sets from MMPB/GB-SA calculations Jason Swails (Wed Dec 17 2014 - 11:30:08 PST)
    - Re: [AMBER] excluding atom sets from MMPB/GB-SA calculations Hallel Freedman (Wed Dec 17 2014 - 12:33:50 PST)
    - Re: [AMBER] excluding atom sets from MMPB/GB-SA calculations Jason Swails (Wed Dec 17 2014 - 19:35:48 PST)
    - Re: [AMBER] excluding atom sets from MMPB/GB-SA calculations Hallel Freedman (Wed Dec 17 2014 - 21:04:36 PST)
[AMBER] TiMergeError fjliu (Tue Dec 16 2014 - 22:18:15 PST)
- Re: [AMBER] TiMergeError hannes.loeffler.stfc.ac.uk (Tue Dec 16 2014 - 23:20:29 PST)
  - Re: [AMBER] TiMergeError fjliu (Tue Dec 16 2014 - 23:51:54 PST)
    - Re: [AMBER] TiMergeError hannes.loeffler.stfc.ac.uk (Wed Dec 17 2014 - 00:27:25 PST)
    - Re: [AMBER] TiMergeError Hannes Loeffler (Wed Dec 17 2014 - 01:24:20 PST)
    - Re: [AMBER] TiMergeError fjliu (Wed Dec 17 2014 - 03:09:53 PST)
    - Re: [AMBER] TiMergeError Hannes Loeffler (Wed Dec 17 2014 - 03:34:47 PST)
Re: [AMBER] subscribe amber wliu (Tue Dec 16 2014 - 23:53:07 PST)
- Re: [AMBER] subscribe amber Jason Swails (Wed Dec 17 2014 - 07:29:00 PST)
[AMBER] error in parallel installation of Amber 12 with AmberTools13 Robin Jain (Wed Dec 17 2014 - 01:47:07 PST)
- Re: [AMBER] error in parallel installation of Amber 12 with AmberTools13 aksbmbg_s.caluniv.ac.in (Wed Dec 17 2014 - 02:53:33 PST)
- Re: [AMBER] error in parallel installation of Amber 12 with AmberTools13 David A Case (Wed Dec 17 2014 - 04:32:24 PST)
[AMBER] error running equilibration (wall clock called) Anupam Goel (Wed Dec 17 2014 - 11:41:00 PST)
- Re: [AMBER] error running equilibration (wall clock called) David A Case (Wed Dec 17 2014 - 12:17:43 PST)
  - Re: [AMBER] error running equilibration (wall clock called) Anupam Goel (Wed Dec 17 2014 - 13:50:42 PST)
[AMBER] leap crashes and set: Improper number of arguments! Francesco Pietra (Wed Dec 17 2014 - 13:52:57 PST)
- [AMBER] Fwd: leap crashes and set: Improper number of arguments! Francesco Pietra (Wed Dec 17 2014 - 14:15:49 PST)
  - Re: [AMBER] Fwd: leap crashes and set: Improper number of arguments! Bill Ross (Wed Dec 17 2014 - 18:16:03 PST)
[AMBER] help in calculation of diffusion coefficient Robin Jain (Thu Dec 18 2014 - 07:28:33 PST)
- Re: [AMBER] help in calculation of diffusion coefficient Daniel Roe (Thu Dec 18 2014 - 08:01:39 PST)
[AMBER] installing error Amber 12 Error Houcemeddine Othman (Thu Dec 18 2014 - 07:37:54 PST)
- Re: [AMBER] installing error Amber 12 Error Daniel Roe (Thu Dec 18 2014 - 07:56:43 PST)
[AMBER] help on the AMBER Tutorial B0 Dabing Chen (Thu Dec 18 2014 - 08:37:52 PST)
- Re: [AMBER] help on the AMBER Tutorial B0 Daniel Roe (Thu Dec 18 2014 - 08:40:14 PST)
Re: [AMBER] how can i use acpype yaser (Thu Dec 18 2014 - 08:55:18 PST)
- Re: [AMBER] how can i use acpype David A Case (Thu Dec 18 2014 - 09:50:27 PST)
  - Re: [AMBER] how can i use acpype Yaser Hosseini (Thu Dec 18 2014 - 10:39:06 PST)
    - Re: [AMBER] how can i use acpype Jason Swails (Thu Dec 18 2014 - 11:13:53 PST)
    - Re: [AMBER] how can i use acpype Yaser Hosseini (Fri Dec 19 2014 - 00:04:11 PST)
    - Re: [AMBER] how can i use acpype Jason Swails (Fri Dec 19 2014 - 06:03:59 PST)
[AMBER] unclear leap crashing Francesco Pietra (Thu Dec 18 2014 - 10:53:21 PST)
- Re: [AMBER] unclear leap crashing FyD (Fri Dec 19 2014 - 02:33:31 PST)
- Re: [AMBER] unclear leap crashing David A Case (Fri Dec 19 2014 - 05:05:43 PST)
  - Re: [AMBER] unclear leap crashing Francesco Pietra (Fri Dec 19 2014 - 12:55:51 PST)
    - [AMBER] Fwd: unclear leap crashing Francesco Pietra (Sat Dec 20 2014 - 08:23:22 PST)
    - Re: [AMBER] unclear leap crashing Francesco Pietra (Sat Dec 20 2014 - 11:40:40 PST)
    - Re: [AMBER] Fwd: unclear leap crashing David A Case (Mon Dec 22 2014 - 05:30:56 PST)
[AMBER] Improper torsions in NMA Ganesh Kamath (Thu Dec 18 2014 - 14:13:17 PST)
- Re: [AMBER] Improper torsions in NMA David A Case (Fri Dec 19 2014 - 05:07:10 PST)
  - Re: [AMBER] Improper torsions in NMA Ganesh Kamath (Fri Dec 19 2014 - 12:08:57 PST)
    - Re: [AMBER] Improper torsions in NMA David A Case (Sat Dec 20 2014 - 06:43:45 PST)
- Re: [AMBER] Improper torsions in NMA FyD (Fri Mar 06 2015 - 00:02:49 PST)
[AMBER] pseudo F-statistic (pSF) Jonathan Gough (Thu Dec 18 2014 - 14:54:39 PST)
- Re: [AMBER] pseudo F-statistic (pSF) Daniel Roe (Fri Dec 19 2014 - 08:52:55 PST)
  - Re: [AMBER] pseudo F-statistic (pSF) Jonathan Gough (Mon Dec 22 2014 - 16:36:09 PST)
    - Re: [AMBER] pseudo F-statistic (pSF) Daniel Roe (Mon Dec 22 2014 - 18:30:55 PST)
    - Re: [AMBER] pseudo F-statistic (pSF) Jonathan Gough (Mon Dec 22 2014 - 18:59:12 PST)
    - Re: [AMBER] pseudo F-statistic (pSF) Jonathan Gough (Sun Jan 04 2015 - 10:05:00 PST)
    - Re: [AMBER] pseudo F-statistic (pSF) Jonathan Gough (Thu Jan 08 2015 - 08:20:32 PST)
    - Re: [AMBER] pseudo F-statistic (pSF) Daniel Roe (Thu Jan 08 2015 - 08:57:39 PST)
    - Re: [AMBER] pseudo F-statistic (pSF) Thomas Cheatham (Thu Jan 08 2015 - 09:05:58 PST)
    - Re: [AMBER] pseudo F-statistic (pSF) Jonathan Gough (Thu Jan 08 2015 - 09:20:33 PST)
    - Re: [AMBER] pseudo F-statistic (pSF) Daniel Roe (Thu Jan 08 2015 - 08:56:02 PST)
    - Re: [AMBER] pseudo F-statistic (pSF) Jonathan Gough (Thu Jan 08 2015 - 09:00:36 PST)
[AMBER] error in install amber Yaser Hosseini (Fri Dec 19 2014 - 02:05:24 PST)
- Re: [AMBER] error in install amber David A Case (Fri Dec 19 2014 - 05:10:51 PST)
  - Re: [AMBER] error in install amber Yaser Hosseini (Sun Dec 21 2014 - 08:36:49 PST)
    - Re: [AMBER] error in install amber Jason Swails (Sun Dec 21 2014 - 11:14:47 PST)
    - Re: [AMBER] error in install amber Alan (Sun Dec 21 2014 - 13:55:02 PST)
[AMBER] Free Energy Workshop, Münster, March 9-11, 2015 Vlad Cojocaru (Fri Dec 19 2014 - 04:58:42 PST)
[AMBER] Hydrogen charge site and Oxygen V-site displacement Sylvester Tumusiime (Sun Dec 21 2014 - 04:29:18 PST)
- Re: [AMBER] Hydrogen charge site and Oxygen V-site displacement David A Case (Mon Dec 22 2014 - 05:29:07 PST)
  - Re: [AMBER] Hydrogen charge site and Oxygen V-site displacement Sylvester Tumusiime (Mon Dec 22 2014 - 19:12:19 PST)
[AMBER] Error in pmemd.amoeba.MPI run Ya Gao (Sun Dec 21 2014 - 05:17:01 PST)
- Re: [AMBER] Error in pmemd.amoeba.MPI run Jason Swails (Sun Dec 21 2014 - 07:35:54 PST)
[AMBER] pmemd.MPI fails to run Fabian Glaser (Sun Dec 21 2014 - 06:02:10 PST)
- Re: [AMBER] pmemd.MPI fails to run Jason Swails (Sun Dec 21 2014 - 07:39:21 PST)
  - Re: [AMBER] pmemd.MPI fails to run Fabian Glaser (Sun Dec 28 2014 - 08:31:25 PST)
    - Re: [AMBER] pmemd.MPI fails to run Ross Walker (Sun Dec 28 2014 - 09:35:59 PST)
    - Re: [AMBER] pmemd.MPI fails to run Fabian (Sun Dec 28 2014 - 10:42:25 PST)
    - Re: [AMBER] pmemd.MPI fails to run Thomas Cheatham (Sun Dec 28 2014 - 11:07:56 PST)
    - Re: [AMBER] pmemd.MPI fails to run Fabian Gmail (Sun Dec 28 2014 - 11:20:03 PST)
    - Re: [AMBER] pmemd.MPI fails to run Bill Ross (Sun Dec 28 2014 - 20:19:14 PST)
    - Re: [AMBER] pmemd.MPI fails to run Fabian Glaser (Mon Dec 29 2014 - 02:33:18 PST)
    - Re: [AMBER] pmemd.MPI fails to run Jason Swails (Mon Dec 29 2014 - 03:53:18 PST)
- Re: [AMBER] pmemd.MPI fails to run Ryan Novosielski (Sun Dec 28 2014 - 09:06:48 PST)
[AMBER] pmemd.MPI fails Fabian Glaser (Sun Dec 21 2014 - 07:39:31 PST)
[AMBER] error in acpype Yaser Hosseini (Sun Dec 21 2014 - 08:34:13 PST)
[AMBER] Singe point QM/MM energy using Gaussian interface Bence Hégely (Sun Dec 21 2014 - 10:37:43 PST)
- Re: [AMBER] Singe point QM/MM energy using Gaussian interface Jason Swails (Sun Dec 21 2014 - 11:19:08 PST)
[AMBER] How to analyze REMD results Wang Moye (Sun Dec 21 2014 - 16:13:15 PST)
- Re: [AMBER] How to analyze REMD results Carlos Simmerling (Sun Dec 21 2014 - 19:10:59 PST)
[AMBER] NVE simulation Robin Jain (Sun Dec 21 2014 - 21:48:07 PST)
- Re: [AMBER] NVE simulation Daniel Roe (Sun Dec 21 2014 - 22:04:13 PST)
  - Re: [AMBER] NVE simulation George M Giambasu (Mon Dec 22 2014 - 08:30:37 PST)
[AMBER] Laccase studies of 2013 mmaestre.gate.sinica.edu.tw (Sun Dec 21 2014 - 22:24:12 PST)
[AMBER] target dynamics problem antonio.coluccia.uniroma1.it (Mon Dec 22 2014 - 05:31:20 PST)
- Re: [AMBER] target dynamics problem Carlos Simmerling (Mon Dec 22 2014 - 05:42:09 PST)
  - Re: [AMBER] target dynamics problem antonio.coluccia.uniroma1.it (Mon Dec 22 2014 - 05:52:57 PST)
    - Re: [AMBER] target dynamics problem Carlos Simmerling (Mon Dec 22 2014 - 06:05:49 PST)
    - Re: [AMBER] target dynamics problem antonio.coluccia.uniroma1.it (Mon Dec 22 2014 - 06:37:44 PST)
    - Re: [AMBER] target dynamics problem Jason Swails (Mon Dec 22 2014 - 09:43:33 PST)
    - Re: [AMBER] target dynamics problem Carlos Simmerling (Mon Dec 22 2014 - 09:51:41 PST)
[AMBER] antechamber script Ahmet yıldırım (Mon Dec 22 2014 - 07:05:48 PST)
- Re: [AMBER] antechamber script Bill Ross (Mon Dec 22 2014 - 08:39:18 PST)
- Re: [AMBER] antechamber script Marc van der Kamp (Mon Dec 22 2014 - 08:45:50 PST)
  - Re: [AMBER] antechamber script Ahmet yıldırım (Mon Dec 22 2014 - 10:10:11 PST)
    - Re: [AMBER] antechamber script hannes.loeffler.stfc.ac.uk (Mon Dec 22 2014 - 10:17:59 PST)
- Re: [AMBER] antechamber script Nhai (Mon Dec 22 2014 - 13:19:33 PST)
  - Re: [AMBER] antechamber script David A Case (Mon Dec 22 2014 - 14:13:52 PST)
    - Re: [AMBER] antechamber script Ahmet yıldırım (Mon Dec 22 2014 - 15:10:10 PST)
[AMBER] Umbrella sampling for molecules moving Helen Lvy (Mon Dec 22 2014 - 13:22:38 PST)
- Re: [AMBER] Umbrella sampling for molecules moving Carlos Simmerling (Mon Dec 22 2014 - 15:36:42 PST)
[AMBER] Parameter could not be saved Harmeet Kaur (Tue Dec 23 2014 - 03:00:25 PST)
- Re: [AMBER] Parameter could not be saved Soumendranath Bhakat (Tue Dec 23 2014 - 03:11:04 PST)
- Re: [AMBER] Parameter could not be saved Jason Swails (Tue Dec 23 2014 - 06:06:40 PST)
  - Re: [AMBER] Parameter could not be saved Kshatresh Dutta Dubey (Tue Dec 23 2014 - 06:39:30 PST)
[AMBER] a problem in MM-GBSA calculation 朱亚莉 (Tue Dec 23 2014 - 05:22:11 PST)
- Re: [AMBER] a problem in MM-GBSA calculation Carlos Simmerling (Tue Dec 23 2014 - 05:31:45 PST)
  - Re: [AMBER] a problem in MM-GBSA calculation Jinfeng Huang (Tue Dec 23 2014 - 18:33:24 PST)
    - Re: [AMBER] a problem in MM-GBSA calculation Jason Swails (Tue Dec 23 2014 - 19:53:22 PST)
[AMBER] ifqnt chemjxn (Tue Dec 23 2014 - 18:24:56 PST)
- Re: [AMBER] ifqnt Jason Swails (Tue Dec 23 2014 - 19:57:23 PST)
  - Re: [AMBER] ifqnt chemjxn.126.com (Tue Dec 23 2014 - 20:12:54 PST)
    - Re: [AMBER] ifqnt Jason Swails (Tue Dec 23 2014 - 21:26:18 PST)
    - Re: [AMBER] ifqnt chemjxn.126.com (Tue Dec 23 2014 - 22:06:20 PST)
    - Re: [AMBER] ifqnt Kshatresh Dutta Dubey (Wed Dec 24 2014 - 03:06:45 PST)
    - Re: [AMBER] ifqnt Jason Swails (Wed Dec 24 2014 - 08:00:51 PST)
    - Re: [AMBER] ifqnt Jason Swails (Wed Dec 24 2014 - 07:59:09 PST)
[AMBER] Errors during Adding hydrogen atoms to the PDB file（MCPB program） wjli (Tue Dec 23 2014 - 20:42:50 PST)
- [AMBER] 回复： Errors during Adding hydrogen atoms to the PDB file（MCPB program） wjli (Tue Dec 23 2014 - 21:01:27 PST)
  - Re: [AMBER] 回复： Errors during Adding hydrogen atoms to the PDB file（MCPB program） Pengfei Li (Thu Jan 08 2015 - 08:55:12 PST)
[AMBER] WHAM tolerance Sun (Thu Dec 25 2014 - 19:46:20 PST)
- Re: [AMBER] WHAM tolerance Jason Swails (Tue Dec 30 2014 - 15:11:08 PST)
[AMBER] conversion of amber outputs to gromacs shahab shariati (Thu Dec 25 2014 - 23:48:35 PST)
[AMBER] conversion of amber outputs to gromacs shahab shariati (Thu Dec 25 2014 - 23:55:43 PST)
- Re: [AMBER] conversion of amber outputs to gromacs Kshatresh Dutta Dubey (Fri Dec 26 2014 - 04:17:25 PST)
[AMBER] conversion of amber outputs to gromacs shahab shariati (Fri Dec 26 2014 - 05:16:41 PST)
- Re: [AMBER] conversion of amber outputs to gromacs Jason Swails (Fri Dec 26 2014 - 07:07:25 PST)
  - Re: [AMBER] conversion of amber outputs to gromacs Sarah Witzke (Fri Dec 26 2014 - 16:24:27 PST)
[AMBER] charmmlipid2amber.py Jacopo Sgrignani (Fri Dec 26 2014 - 06:21:24 PST)
[AMBER] Amber 14 Performance and Other Questions Novosielski, Ryan (Fri Dec 26 2014 - 13:16:05 PST)
- Re: [AMBER] Amber 14 Performance and Other Questions Ross Walker (Fri Dec 26 2014 - 14:13:25 PST)
  - Re: [AMBER] Amber 14 Performance and Other Questions Novosielski, Ryan (Mon Jan 12 2015 - 11:11:38 PST)
    - Re: [AMBER] Amber 14 Performance and Other Questions Jason Swails (Mon Jan 12 2015 - 11:26:03 PST)
    - Re: [AMBER] Amber 14 Performance and Other Questions Novosielski, Ryan (Mon Jan 12 2015 - 11:43:07 PST)
    - Re: [AMBER] Amber 14 Performance and Other Questions Ross Walker (Mon Jan 12 2015 - 11:53:46 PST)
[AMBER] lipid conversion Jacopo Sgrignani (Sat Dec 27 2014 - 08:17:37 PST)
- Re: [AMBER] lipid conversion Sarah Witzke (Sat Dec 27 2014 - 10:00:01 PST)
  - Re: [AMBER] lipid conversion Jacopo Sgrignani (Sat Dec 27 2014 - 10:07:12 PST)
    - Re: [AMBER] lipid conversion Jonathan Gough (Sat Dec 27 2014 - 16:57:07 PST)
[AMBER] Error during Adding Fragment（about MCPB ） wjli (Sat Dec 27 2014 - 20:26:35 PST)
- Re: [AMBER] Error during Adding Fragment（about MCPB ） Pengfei Li (Thu Jan 08 2015 - 08:45:28 PST)
[AMBER] Enthalpy calculation of protein. Abhilash J (Sat Dec 27 2014 - 23:42:46 PST)
- Re: [AMBER] Enthalpy calculation of protein. David A Case (Sun Dec 28 2014 - 06:16:05 PST)
  - Re: [AMBER] Enthalpy calculation of protein. Abhilash J (Sun Dec 28 2014 - 07:30:17 PST)
    - Re: [AMBER] Enthalpy calculation of protein. David A Case (Sun Dec 28 2014 - 19:27:04 PST)
    - Re: [AMBER] Enthalpy calculation of protein. aneesh cna (Sun Dec 28 2014 - 21:05:10 PST)
    - Re: [AMBER] Enthalpy calculation of protein. Abhilash J (Sun Dec 28 2014 - 21:09:32 PST)
[AMBER] amber force field 王珍 (Sun Dec 28 2014 - 03:51:25 PST)
[AMBER] Total energy of system is positive MOHD HOMAIDUR RAHMAN (Sun Dec 28 2014 - 21:40:26 PST)
- Re: [AMBER] Total energy of system is positive Jason Swails (Mon Dec 29 2014 - 08:31:53 PST)
  - Re: [AMBER] Total energy of system is positive MOHD HOMAIDUR RAHMAN (Mon Dec 29 2014 - 11:51:53 PST)
    - Re: [AMBER] Total energy of system is positive Adrian Roitberg (Mon Dec 29 2014 - 14:29:33 PST)
    - Re: [AMBER] Total energy of system is positive Jason Swails (Mon Dec 29 2014 - 15:23:49 PST)
    - Re: [AMBER] Total energy of system is positive MOHD HOMAIDUR RAHMAN (Mon Dec 29 2014 - 21:46:26 PST)
    - Re: [AMBER] Total energy of system is positive Jason Swails (Mon Dec 29 2014 - 22:05:01 PST)
[AMBER] convergence problem in antechamber with Ambertools14 Rebeca García Fandiño (Mon Dec 29 2014 - 05:05:12 PST)
- Re: [AMBER] convergence problem in antechamber with Ambertools14 David A Case (Mon Dec 29 2014 - 18:11:39 PST)
  - Re: [AMBER] convergence problem in antechamber with Ambertools14 Rebeca García Fandiño (Tue Dec 30 2014 - 00:58:22 PST)
[AMBER] Fwd: pmemd.MPI fails to run Fabian Glaser (Mon Dec 29 2014 - 05:28:09 PST)
- Re: [AMBER] Fwd: pmemd.MPI fails to run Ross Walker (Mon Dec 29 2014 - 08:05:21 PST)
[AMBER] TI calculation using pmemd wangmt (Mon Dec 29 2014 - 06:21:51 PST)
- Re: [AMBER] TI calculation using pmemd hannes.loeffler.stfc.ac.uk (Mon Dec 29 2014 - 09:22:57 PST)
[AMBER] rms fit Sylvester Tumusiime (Mon Dec 29 2014 - 12:47:16 PST)
- Re: [AMBER] rms fit David A Case (Mon Dec 29 2014 - 18:22:51 PST)
  - Re: [AMBER] rms fit Sylvester Tumusiime (Tue Dec 30 2014 - 12:33:44 PST)
[AMBER] Peter Kollman lectureship, Jan 8 David A Case (Mon Dec 29 2014 - 14:11:49 PST)
- Re: [AMBER] Peter Kollman lectureship, Jan 8 Gustavo Seabra (Tue Dec 30 2014 - 06:04:01 PST)
  - Re: [AMBER] Peter Kollman lectureship, Jan 8 David A Case (Tue Dec 30 2014 - 14:29:33 PST)
[AMBER] Imaging membrane proteins Parker de Waal (Mon Dec 29 2014 - 16:37:26 PST)
- Re: [AMBER] Imaging membrane proteins David A Case (Mon Dec 29 2014 - 18:29:58 PST)
[AMBER] Need help in SMD Kshatresh Dutta Dubey (Tue Dec 30 2014 - 09:32:34 PST)
- Re: [AMBER] Need help in SMD Jason Swails (Tue Dec 30 2014 - 15:03:53 PST)
  - Re: [AMBER] Need help in SMD Kshatresh Dutta Dubey (Wed Dec 31 2014 - 04:20:37 PST)
[AMBER] amber14 CUDA GPU for workstation? Michael Shokhen (Tue Dec 30 2014 - 11:31:33 PST)
- Re: [AMBER] amber14 CUDA GPU for workstation? Ross Walker (Tue Dec 30 2014 - 12:11:42 PST)
  - Re: [AMBER] amber14 CUDA GPU for workstation? Michael Shokhen (Tue Dec 30 2014 - 12:51:48 PST)
    - Re: [AMBER] amber14 CUDA GPU for workstation? Adrian Roitberg (Tue Dec 30 2014 - 12:56:31 PST)
    - Re: [AMBER] amber14 CUDA GPU for workstation? Michael Shokhen (Tue Dec 30 2014 - 13:49:24 PST)
    - Re: [AMBER] amber14 CUDA GPU for workstation? Ross Walker (Tue Dec 30 2014 - 14:03:19 PST)
    - Re: [AMBER] amber14 CUDA GPU for workstation? Jason Swails (Tue Dec 30 2014 - 14:55:33 PST)
[AMBER] Need help in Targeted MD Pallavi Mohanty (Wed Dec 31 2014 - 03:57:14 PST)
- Re: [AMBER] Need help in Targeted MD David A Case (Wed Dec 31 2014 - 06:35:08 PST)
  - Re: [AMBER] Need help in Targeted MD Carlos Simmerling (Wed Dec 31 2014 - 06:55:15 PST)
    - Re: [AMBER] Need help in Targeted MD Pallavi Mohanty (Thu Jan 01 2015 - 22:14:03 PST)
    - Re: [AMBER] Need help in Targeted MD David A Case (Fri Jan 02 2015 - 05:06:39 PST)
    - Re: [AMBER] Need help in Targeted MD Pallavi Mohanty (Mon Jan 05 2015 - 04:01:47 PST)
    - Re: [AMBER] Need help in Targeted MD David A Case (Mon Jan 05 2015 - 04:34:52 PST)
    - Re: [AMBER] Need help in Targeted MD Pallavi Mohanty (Mon Jan 05 2015 - 05:04:02 PST)
    - Re: [AMBER] Need help in Targeted MD Jason Swails (Mon Jan 05 2015 - 05:22:56 PST)
[AMBER] Solvation free energy using soft core potential Teerapong Pirojsirikul (Wed Dec 31 2014 - 17:08:02 PST)
- Re: [AMBER] Solvation free energy using soft core potential hannes.loeffler.stfc.ac.uk (Thu Jan 01 2015 - 07:26:13 PST)
[AMBER] diffusion time step newamber list (Wed Dec 31 2014 - 18:14:59 PST)
- Re: [AMBER] diffusion time step David A Case (Fri Jan 02 2015 - 05:10:01 PST)
  - Re: [AMBER] diffusion time step newamber list (Fri Jan 02 2015 - 08:12:07 PST)
    - Re: [AMBER] diffusion time step Daniel Roe (Fri Jan 02 2015 - 11:24:50 PST)
    - Re: [AMBER] diffusion time step newamber list (Fri Jan 02 2015 - 13:24:11 PST)
[AMBER] chamber : psf to amber parmtop Himanshu Joshi (Thu Jan 01 2015 - 04:33:47 PST)
- Re: [AMBER] chamber : psf to amber parmtop Jason Swails (Thu Jan 01 2015 - 13:25:48 PST)
  - Re: [AMBER] chamber : psf to amber parmtop Himanshu Joshi (Thu Jan 01 2015 - 20:00:43 PST)
[AMBER] ZN metal parametrization using MCPB -reg sailu (Thu Jan 01 2015 - 05:43:40 PST)
- Re: [AMBER] ZN metal parametrization using MCPB -reg Pengfei Li (Thu Jan 08 2015 - 08:37:24 PST)
[AMBER] aMD plot 汪盛 (Thu Jan 01 2015 - 14:46:49 PST)
- Re: [AMBER] aMD plot Daniel Roe (Fri Jan 02 2015 - 10:26:01 PST)
  - Re: [AMBER] aMD plot Thomas Evangelidis (Sat Jan 03 2015 - 02:38:31 PST)
- Re: [AMBER] aMD plot 汪盛 (Sat Jan 03 2015 - 15:22:55 PST)
- Re: [AMBER] aMD plot 汪盛 (Tue Jan 06 2015 - 16:48:48 PST)
  - Re: [AMBER] aMD plot Daniel Roe (Tue Jan 06 2015 - 20:34:59 PST)
[AMBER] Matrix correlation Sylvester Tumusiime (Thu Jan 01 2015 - 16:19:25 PST)
- Re: [AMBER] Matrix correlation Daniel Roe (Fri Jan 02 2015 - 10:46:00 PST)
  - Re: [AMBER] Matrix correlation Sylvester Tumusiime (Sun Jan 04 2015 - 15:58:12 PST)
[AMBER] Matrix correl Sylvester Tumusiime (Thu Jan 01 2015 - 19:18:34 PST)
[AMBER] contacts with water Chinthaka Ratnaweera (Thu Jan 01 2015 - 20:51:31 PST)
- Re: [AMBER] contacts with water Daniel Roe (Fri Jan 02 2015 - 10:54:23 PST)
Re: [AMBER] FW: clustering problem in ambertool14 Mahendra B Thapa (Fri Jan 02 2015 - 08:08:40 PST)
- Re: [AMBER] FW: clustering problem in ambertool14 Daniel Roe (Fri Jan 02 2015 - 11:00:45 PST)
- Re: [AMBER] FW: clustering problem in ambertool14 Mahendra B Thapa (Tue Jan 06 2015 - 14:47:36 PST)
  - Re: [AMBER] FW: clustering problem in ambertool14 Daniel Roe (Tue Jan 06 2015 - 15:24:28 PST)
Re: [AMBER] FW: FW: clustering problem in ambertool14 Mahendra B Thapa (Fri Jan 02 2015 - 12:48:39 PST)
- Re: [AMBER] FW: FW: clustering problem in ambertool14 Chris Moth (Fri Jan 02 2015 - 13:03:50 PST)
- Re: [AMBER] clustering problem in ambertool14 Daniel Roe (Fri Jan 02 2015 - 13:35:17 PST)
- Re: [AMBER] FW: FW: clustering problem in ambertool14 Mahendra B Thapa (Sat Jan 17 2015 - 08:01:24 PST)
  - Re: [AMBER] FW: FW: clustering problem in ambertool14 Daniel Roe (Sat Jan 17 2015 - 15:58:55 PST)
[AMBER] About amber parameters for free dioxygen in water solution Francesco Pietra (Sat Jan 03 2015 - 01:27:15 PST)
- Re: [AMBER] About amber parameters for free dioxygen in water solution Jason Swails (Sat Jan 03 2015 - 04:51:06 PST)
[AMBER] Checking bonds commanded with leap Francesco Pietra (Sat Jan 03 2015 - 10:25:29 PST)
- Re: [AMBER] Checking bonds commanded with leap Gerald Monard (Sun Jan 04 2015 - 08:35:52 PST)
  - Re: [AMBER] Checking bonds commanded with leap Francesco Pietra (Mon Jan 05 2015 - 00:37:57 PST)
    - [AMBER] Fwd: Checking bonds commanded with leap Francesco Pietra (Mon Jan 05 2015 - 00:45:47 PST)
    - Re: [AMBER] Fwd: Checking bonds commanded with leap David A Case (Mon Jan 05 2015 - 04:31:40 PST)
    - Re: [AMBER] Fwd: Checking bonds commanded with leap Francesco Pietra (Mon Jan 05 2015 - 07:07:18 PST)
    - Re: [AMBER] Fwd: Checking bonds commanded with leap David A Case (Mon Jan 05 2015 - 08:19:36 PST)
    - Re: [AMBER] Fwd: Checking bonds commanded with leap FyD (Mon Jan 05 2015 - 23:01:27 PST)
    - Re: [AMBER] Fwd: Checking bonds commanded with leap Francesco Pietra (Mon Jan 05 2015 - 23:12:59 PST)
[AMBER] RMSD calculation of a homodimer Ibrahim Said (Sun Jan 04 2015 - 08:21:23 PST)
- Re: [AMBER] RMSD calculation of a homodimer Daniel Roe (Sun Jan 04 2015 - 16:32:12 PST)
[AMBER] ESP Charge for Fe Fatemeh Sadat Alavi (Mon Jan 05 2015 - 00:47:20 PST)
- Re: [AMBER] ESP Charge for Fe FyD (Tue Jan 06 2015 - 01:18:59 PST)
[AMBER] nocut MD SHAKE error Anupam Goel (Mon Jan 05 2015 - 13:14:20 PST)
- Re: [AMBER] nocut MD SHAKE error Daniel Roe (Mon Jan 05 2015 - 14:31:08 PST)
  - Re: [AMBER] nocut MD SHAKE error Anupam Goel (Tue Jan 06 2015 - 13:19:00 PST)
- Re: [AMBER] nocut MD SHAKE error David A Case (Mon Jan 05 2015 - 14:39:35 PST)
[AMBER] confusion about effect of number of solvent molecules on density Vipin Ruhela (Tue Jan 06 2015 - 05:08:14 PST)
- Re: [AMBER] confusion about effect of number of solvent molecules on density Carlos Simmerling (Tue Jan 06 2015 - 05:15:00 PST)
  - Re: [AMBER] confusion about effect of number of solvent molecules on density Carlos Simmerling (Tue Jan 06 2015 - 05:16:38 PST)
[AMBER] Missing psi dihedral at cationic N-terminus of protein/peptide? nealec (Tue Jan 06 2015 - 16:54:01 PST)
[AMBER] Equilibration problem large system in explicit solvent Waldner, Birgit (Wed Jan 07 2015 - 05:12:20 PST)
- Re: [AMBER] Equilibration problem large system in explicit solvent Jason Swails (Wed Jan 07 2015 - 06:20:24 PST)
- Re: [AMBER] Equilibration problem large system in explicit solvent David A Case (Wed Jan 07 2015 - 08:29:24 PST)
  - Re: [AMBER] Equilibration problem large system in explicit solvent Waldner, Birgit (Thu Jan 08 2015 - 00:30:30 PST)
[AMBER] CpptrajFile: error Ibrahim Said (Wed Jan 07 2015 - 09:04:08 PST)
- Re: [AMBER] CpptrajFile: error Daniel Roe (Wed Jan 07 2015 - 09:26:49 PST)
  - Re: [AMBER] CpptrajFile: error Ibrahim Said (Wed Jan 07 2015 - 09:42:24 PST)
    - Re: [AMBER] CpptrajFile: error Daniel Roe (Wed Jan 07 2015 - 10:05:35 PST)
    - Re: [AMBER] CpptrajFile: error Ibrahim Said (Wed Jan 07 2015 - 11:08:49 PST)
    - Re: [AMBER] CpptrajFile: error David A Case (Wed Jan 07 2015 - 11:33:08 PST)
    - Re: [AMBER] CpptrajFile: error Ibrahim Said (Wed Jan 07 2015 - 11:39:52 PST)
    - Re: [AMBER] CpptrajFile: error Daniel Roe (Wed Jan 07 2015 - 11:47:41 PST)
    - Re: [AMBER] CpptrajFile: error Ibrahim Said (Wed Jan 07 2015 - 12:12:00 PST)
    - Re: [AMBER] CpptrajFile: error Daniel Roe (Wed Jan 07 2015 - 12:26:00 PST)
    - Re: [AMBER] CpptrajFile: error Ibrahim Said (Wed Jan 07 2015 - 12:33:50 PST)
    - Re: [AMBER] CpptrajFile: error Daniel Roe (Wed Jan 07 2015 - 13:53:49 PST)
    - Re: [AMBER] CpptrajFile: error Ibrahim Said (Thu Jan 08 2015 - 04:03:56 PST)
    - Re: [AMBER] CpptrajFile: error Daniel Roe (Thu Jan 08 2015 - 08:12:09 PST)
Re: [AMBER] aMD plot (Daniel Roe) 汪盛 (Wed Jan 07 2015 - 16:14:47 PST)
- Re: [AMBER] aMD plot (Daniel Roe) Daniel Roe (Thu Jan 08 2015 - 07:29:24 PST)
[AMBER] The protein unfolded through the simulation Hadeer ELHabashy (Wed Jan 07 2015 - 17:06:36 PST)
- Re: [AMBER] The protein unfolded through the simulation Thomas Cheatham (Wed Jan 07 2015 - 20:13:34 PST)
  - Re: [AMBER] The protein unfolded through the simulation Carlos Simmerling (Wed Jan 07 2015 - 20:21:39 PST)
[AMBER] ABOUT NPT and PMEMD.CUDA Yeng-Tseng Wang (Wed Jan 07 2015 - 22:49:34 PST)
- Re: [AMBER] ABOUT NPT and PMEMD.CUDA Jason Swails (Thu Jan 08 2015 - 05:16:37 PST)
[AMBER] extract torsion angle data Anupam Goel (Wed Jan 07 2015 - 23:34:17 PST)
- Re: [AMBER] extract torsion angle data Jason Swails (Thu Jan 08 2015 - 05:28:12 PST)
  - Re: [AMBER] extract torsion angle data Daniel Roe (Thu Jan 08 2015 - 08:07:09 PST)
    - Re: [AMBER] extract torsion angle data Anupam Goel (Thu Jan 08 2015 - 14:43:04 PST)
[AMBER] Using restraints to get a complex mmaestre.gate.sinica.edu.tw (Thu Jan 08 2015 - 00:32:14 PST)
- Re: [AMBER] Using restraints to get a complex mmaestre.gate.sinica.edu.tw (Thu Jan 08 2015 - 16:40:09 PST)
- Re: [AMBER] Using restraints to get a complex David A Case (Thu Jan 08 2015 - 19:06:35 PST)
  - Re: [AMBER] Using restraints to get a complex mmaestre.gate.sinica.edu.tw (Thu Jan 08 2015 - 21:56:14 PST)
    - Re: [AMBER] Using restraints to get a complex David A Case (Fri Jan 09 2015 - 05:06:56 PST)
    - Re: [AMBER] Using restraints to get a complex mmaestre.gate.sinica.edu.tw (Sun Jan 11 2015 - 16:48:51 PST)
    - Re: [AMBER] Using restraints to get a complex Ross Walker (Sun Jan 11 2015 - 18:37:44 PST)
    - Re: [AMBER] Using restraints to get a complex mmaestre.gate.sinica.edu.tw (Sun Jan 11 2015 - 18:44:03 PST)
[AMBER] Vector command CPPTRAJ Sourav Purohit (Fri Jan 09 2015 - 00:44:35 PST)
- Re: [AMBER] Vector command CPPTRAJ Daniel Roe (Fri Jan 09 2015 - 07:21:48 PST)
[AMBER] Free Energy Workshop, Münster, March 9-11, 2015 Vlad Cojocaru (Fri Jan 09 2015 - 01:20:48 PST)
[AMBER] Constant values in prmtop Mohd Farid Ismail (Fri Jan 09 2015 - 01:45:59 PST)
- Re: [AMBER] Constant values in prmtop Jason Swails (Fri Jan 09 2015 - 04:03:25 PST)
[AMBER] How to defined a steered direction in SMD? Chris (Fri Jan 09 2015 - 05:59:37 PST)
- Re: [AMBER] How to defined a steered direction in SMD? Emilio Lence (Sun Jan 11 2015 - 04:50:23 PST)
  - Re: [AMBER] How to defined a steered direction in SMD? Jason Swails (Sun Jan 11 2015 - 07:05:16 PST)
[AMBER] cpptraj.MPI Jonathan Gough (Fri Jan 09 2015 - 10:30:54 PST)
- Re: [AMBER] cpptraj.MPI Daniel Roe (Fri Jan 09 2015 - 10:40:17 PST)
  - Re: [AMBER] cpptraj.MPI Jonathan Gough (Fri Jan 09 2015 - 11:10:24 PST)
    - Re: [AMBER] cpptraj.MPI Jonathan Gough (Fri Jan 09 2015 - 11:39:34 PST)
    - Re: [AMBER] cpptraj.MPI Daniel Roe (Fri Jan 09 2015 - 12:45:05 PST)
[AMBER] problem with rdparm in amb2gmx.pl Rebeca García Fandiño (Sat Jan 10 2015 - 02:47:35 PST)
- Re: [AMBER] problem with rdparm in amb2gmx.pl hannes.loeffler.stfc.ac.uk (Sat Jan 10 2015 - 03:51:32 PST)
- Re: [AMBER] problem with rdparm in amb2gmx.pl David A Case (Sat Jan 10 2015 - 06:38:40 PST)
[AMBER] Significantly different results between MMPBSA and MMGBSA asdda asa (Sat Jan 10 2015 - 19:55:04 PST)
- Re: [AMBER] Significantly different results between MMPBSA and MMGBSA Jason Swails (Sat Jan 10 2015 - 20:04:21 PST)
  - Re: [AMBER] Significantly different results between MMPBSA and MMGBSA asdda asa (Sun Jan 11 2015 - 01:26:07 PST)
    - Re: [AMBER] Significantly different results between MMPBSA and MMGBSA Ray Luo, Ph.D. (Sun Jan 11 2015 - 16:08:59 PST)
[AMBER] accelerated MD on 2 GPU cards Asmita Gupta (Sun Jan 11 2015 - 04:43:26 PST)
- Re: [AMBER] accelerated MD on 2 GPU cards Ryan Novosielski (Sun Jan 11 2015 - 06:39:31 PST)
  - Re: [AMBER] accelerated MD on 2 GPU cards Asmita Gupta (Sun Jan 11 2015 - 07:41:41 PST)
    - Re: [AMBER] accelerated MD on 2 GPU cards Novosielski, Ryan (Sun Jan 11 2015 - 07:45:03 PST)
    - Re: [AMBER] accelerated MD on 2 GPU cards Ross Walker (Sun Jan 11 2015 - 11:31:55 PST)
    - Re: [AMBER] accelerated MD on 2 GPU cards Thomas Cheatham (Sun Jan 11 2015 - 11:38:13 PST)
[AMBER] Calculating density during Radial distribution analysis Sylvester Tumusiime (Sun Jan 11 2015 - 12:45:22 PST)
- Re: [AMBER] Calculating density during Radial distribution analysis Jason Swails (Mon Jan 12 2015 - 05:18:11 PST)
- Re: [AMBER] Calculating density during Radial distribution analysis Daniel Roe (Mon Jan 12 2015 - 07:40:49 PST)
[AMBER] Error in Simulation of MN2+ containing complex 杨川 (Mon Jan 12 2015 - 00:19:32 PST)
- Re: [AMBER] Error in Simulation of MN2+ containing complex David A Case (Mon Jan 12 2015 - 05:07:44 PST)
[AMBER] Problem in creating prepin file Jasmine (Mon Jan 12 2015 - 00:42:04 PST)
- Re: [AMBER] Problem in creating prepin file Hannes Loeffler (Mon Jan 12 2015 - 01:19:02 PST)
[AMBER] Help in AMBER Robin Jain (Mon Jan 12 2015 - 00:45:11 PST)
- Re: [AMBER] Help in AMBER Hannes Loeffler (Mon Jan 12 2015 - 01:24:36 PST)
[AMBER] pbsa question zahra khatti (Mon Jan 12 2015 - 01:23:41 PST)
- Re: [AMBER] pbsa question Jason Swails (Mon Jan 12 2015 - 05:20:11 PST)
  - Re: [AMBER] pbsa question zahra khatti (Mon Jan 12 2015 - 08:25:33 PST)
    - Re: [AMBER] pbsa question Jason Swails (Mon Jan 12 2015 - 08:41:44 PST)
[AMBER] diffusion coeficient zahra khatti (Mon Jan 12 2015 - 01:32:45 PST)
- Re: [AMBER] diffusion coeficient Hannes Loeffler (Mon Jan 12 2015 - 01:51:26 PST)
[AMBER] could not find vdW (Na+) type IP Francesco Pietra (Mon Jan 12 2015 - 01:57:26 PST)
- Re: [AMBER] could not find vdW (Na+) type IP David A Case (Mon Jan 12 2015 - 05:09:59 PST)
  - Re: [AMBER] could not find vdW (Na+) type IP Francesco Pietra (Mon Jan 12 2015 - 07:52:54 PST)
    - Re: [AMBER] could not find vdW (Na+) type IP Jason Swails (Mon Jan 12 2015 - 08:31:50 PST)
    - Re: [AMBER] could not find vdW (Na+) type IP Francesco Pietra (Mon Jan 12 2015 - 09:09:53 PST)
    - Re: [AMBER] could not find vdW (Na+) type IP Jason Swails (Mon Jan 12 2015 - 09:16:46 PST)
- Re: [AMBER] could not find vdW (Na+) type IP pradeep pant (Tue Jan 13 2015 - 00:33:17 PST)
- Re: [AMBER] could not find vdW (Na+) type IP Bill Ross (Tue Jan 13 2015 - 08:46:42 PST)
[AMBER] Free energy decomposing calculation time with MMPBSA.py Houcemeddine Othman (Mon Jan 12 2015 - 02:12:17 PST)
- Re: [AMBER] Free energy decomposing calculation time with MMPBSA.py Jason Swails (Mon Jan 12 2015 - 05:28:07 PST)
[AMBER] AmberTools14 MMPBSA CalcError with complex.prmtop and SA Bomb in use_sander=1 Kenneth Huang (Mon Jan 12 2015 - 11:45:52 PST)
- Re: [AMBER] AmberTools14 MMPBSA CalcError with complex.prmtop and SA Bomb in use_sander=1 Jason Swails (Mon Jan 12 2015 - 12:10:00 PST)
  - Re: [AMBER] AmberTools14 MMPBSA CalcError with complex.prmtop and SA Bomb in use_sander=1 Ray Luo, Ph.D. (Mon Jan 12 2015 - 15:26:01 PST)
    - Re: [AMBER] AmberTools14 MMPBSA CalcError with complex.prmtop and SA Bomb in use_sander=1 Kenneth Huang (Mon Jan 12 2015 - 22:28:03 PST)
    - Re: [AMBER] AmberTools14 MMPBSA CalcError with complex.prmtop and SA Bomb in use_sander=1 Ray Luo, Ph.D. (Tue Jan 13 2015 - 10:08:41 PST)
    - Re: [AMBER] AmberTools14 MMPBSA CalcError with complex.prmtop and SA Bomb in use_sander=1 Kenneth Huang (Tue Jan 13 2015 - 20:46:23 PST)
    - Re: [AMBER] AmberTools14 MMPBSA CalcError with complex.prmtop and SA Bomb in use_sander=1 Ray Luo, Ph.D. (Wed Jan 14 2015 - 09:51:28 PST)
    - Re: [AMBER] AmberTools14 MMPBSA CalcError with complex.prmtop and SA Bomb in use_sander=1 Jason Swails (Wed Jan 14 2015 - 11:24:22 PST)
    - Re: [AMBER] AmberTools14 MMPBSA CalcError with complex.prmtop and SA Bomb in use_sander=1 Kenneth Huang (Wed Jan 14 2015 - 14:30:37 PST)
[AMBER] Intel Compilers, SSE_TYPES, and auto CPU dispatch Novosielski, Ryan (Mon Jan 12 2015 - 14:47:06 PST)
- Re: [AMBER] Intel Compilers, SSE_TYPES, and auto CPU dispatch Daniel Roe (Mon Jan 12 2015 - 17:44:32 PST)
  - Re: [AMBER] Intel Compilers, SSE_TYPES, and auto CPU dispatch Novosielski, Ryan (Tue Jan 13 2015 - 09:20:39 PST)
    - Re: [AMBER] Intel Compilers, SSE_TYPES, and auto CPU dispatch Jason Swails (Tue Jan 13 2015 - 09:38:38 PST)
    - Re: [AMBER] Intel Compilers, SSE_TYPES, and auto CPU dispatch Novosielski, Ryan (Tue Jan 13 2015 - 09:46:29 PST)
    - Re: [AMBER] Intel Compilers, SSE_TYPES, and auto CPU dispatch Jason Swails (Tue Jan 13 2015 - 10:18:57 PST)
    - Re: [AMBER] Intel Compilers, SSE_TYPES, and auto CPU dispatch Novosielski, Ryan (Tue Jan 13 2015 - 10:53:55 PST)
    - Re: [AMBER] Intel Compilers, SSE_TYPES, and auto CPU dispatch Brent Krueger (Tue Jan 13 2015 - 11:10:22 PST)
    - Re: [AMBER] Intel Compilers, SSE_TYPES, and auto CPU dispatch Novosielski, Ryan (Tue Jan 13 2015 - 11:23:40 PST)
    - Re: [AMBER] Intel Compilers, SSE_TYPES, and auto CPU dispatch Jan-Philip Gehrcke (Wed Jan 14 2015 - 04:26:33 PST)
    - Re: [AMBER] Intel Compilers, SSE_TYPES, and auto CPU dispatch Hannes Loeffler (Wed Jan 14 2015 - 05:26:50 PST)
    - Re: [AMBER] Intel Compilers, SSE_TYPES, and auto CPU dispatch Novosielski, Ryan (Wed Jan 14 2015 - 07:33:39 PST)
    - Re: [AMBER] Intel Compilers, SSE_TYPES, and auto CPU dispatch Brent Krueger (Wed Jan 14 2015 - 07:57:19 PST)
    - Re: [AMBER] Intel Compilers, SSE_TYPES, and auto CPU dispatch Novosielski, Ryan (Wed Jan 14 2015 - 08:05:29 PST)
    - Re: [AMBER] Intel Compilers, SSE_TYPES, and auto CPU dispatch Scott Brozell (Wed Jan 14 2015 - 09:52:58 PST)
[AMBER] Using DFTB parameters (Halorg) in Amber12 柳成文 (Mon Jan 12 2015 - 18:15:57 PST)
- Re: [AMBER] Using DFTB parameters (Halorg) in Amber12 Gustavo Seabra (Tue Jan 13 2015 - 03:58:07 PST)
[AMBER] Fe(III)-OH2 vs Fe(II)-OH2 force constant Francesco Pietra (Tue Jan 13 2015 - 00:09:52 PST)
[AMBER] Torsion restrain Lara rajam (Tue Jan 13 2015 - 14:31:16 PST)
- Re: [AMBER] Torsion restrain mmaestre.gate.sinica.edu.tw (Tue Jan 13 2015 - 15:20:26 PST)
- Re: [AMBER] Torsion restrain David A Case (Tue Jan 13 2015 - 16:25:38 PST)
[AMBER] Amber11: CUDA-enabled version does not work Khuong Truong Gia (Tue Jan 13 2015 - 22:02:50 PST)
- Re: [AMBER] Amber11: CUDA-enabled version does not work David A Case (Wed Jan 14 2015 - 04:31:46 PST)
  - Re: [AMBER] Amber11: CUDA-enabled version does not work Khuong Truong Gia (Thu Jan 15 2015 - 00:24:51 PST)
    - Re: [AMBER] Amber11: CUDA-enabled version does not work Jason Swails (Thu Jan 15 2015 - 04:11:49 PST)
    - Re: [AMBER] Amber11: CUDA-enabled version does not work Khuong Truong Gia (Thu Jan 15 2015 - 18:23:09 PST)
    - Re: [AMBER] Amber11: CUDA-enabled version does not work Mohd Farid Ismail (Thu Jan 15 2015 - 18:53:24 PST)
    - Re: [AMBER] Amber11: CUDA-enabled version does not work Novosielski, Ryan (Thu Jan 15 2015 - 20:48:10 PST)
    - Re: [AMBER] Amber11: CUDA-enabled version does not work Khuong Truong Gia (Fri Jan 16 2015 - 18:27:13 PST)
    - Re: [AMBER] Amber11: CUDA-enabled version does not work Mohd Farid Ismail (Fri Jan 16 2015 - 23:17:13 PST)
[AMBER] FEP Federica Chiappori (Wed Jan 14 2015 - 03:24:37 PST)
- Re: [AMBER] FEP Hannes Loeffler (Wed Jan 14 2015 - 03:48:37 PST)
- Re: [AMBER] FEP Jason Swails (Wed Jan 14 2015 - 16:10:18 PST)
  - Re: [AMBER] FEP Federica Chiappori (Wed Jan 28 2015 - 02:10:45 PST)
    - Re: [AMBER] FEP Hannes Loeffler (Wed Jan 28 2015 - 02:34:47 PST)
    - Re: [AMBER] FEP filip fratev (Wed Jan 28 2015 - 10:12:09 PST)
    - Re: [AMBER] FEP hannes.loeffler.stfc.ac.uk (Wed Jan 28 2015 - 10:56:17 PST)
    - Re: [AMBER] FEP Brian Radak (Wed Jan 28 2015 - 11:15:24 PST)
    - Re: [AMBER] FEP hannes.loeffler.stfc.ac.uk (Wed Jan 28 2015 - 11:44:14 PST)
    - Re: [AMBER] FEP Jason Swails (Wed Jan 28 2015 - 12:04:21 PST)
    - Re: [AMBER] FEP hannes.loeffler.stfc.ac.uk (Wed Jan 28 2015 - 12:52:10 PST)
    - Re: [AMBER] FEP Jason Swails (Wed Jan 28 2015 - 14:25:02 PST)
    - Re: [AMBER] FEP Hannes Loeffler (Thu Jan 29 2015 - 03:05:46 PST)
    - Re: [AMBER] FEP David A Case (Wed Jan 28 2015 - 18:31:59 PST)
[AMBER] [MGMS-DS]: Molecular Modelling Workshop March 9-11, 2015 in Erlangen, Germany Harald Lanig (Wed Jan 14 2015 - 03:39:07 PST)
[AMBER] cpptraj: structures not aligned anymore after 'run' keyword Guillaume Roellinger (Wed Jan 14 2015 - 05:06:23 PST)
- Re: [AMBER] cpptraj: structures not aligned anymore after 'run' keyword Jason Swails (Wed Jan 14 2015 - 19:03:50 PST)
  - Re: [AMBER] cpptraj: structures not aligned anymore after 'run' keyword Daniel Roe (Thu Jan 15 2015 - 08:24:30 PST)
[AMBER] help in force field Robin Jain (Wed Jan 14 2015 - 06:43:47 PST)
- Re: [AMBER] help in force field David A Case (Wed Jan 14 2015 - 08:03:59 PST)
[AMBER] Fwd: MMPBSA problem when using idecomp Lucia Alvarez (Wed Jan 14 2015 - 09:18:44 PST)
[AMBER] Errors during Building Sidechain Model（MCPB program） wjli (Wed Jan 14 2015 - 20:18:51 PST)
- Re: [AMBER] Errors during Building Sidechain Model（MCPB program） Pengfei Li (Sat Jan 17 2015 - 07:37:44 PST)
  - [AMBER] 回复： Errors during Building Sidechain Model（MCPB program） wjli (Sun Jan 18 2015 - 03:04:46 PST)
[AMBER] Reading chemical bonds from par7 files Francesco Pietra (Thu Jan 15 2015 - 00:18:22 PST)
- Re: [AMBER] Reading chemical bonds from par7 files Jason Swails (Thu Jan 15 2015 - 05:10:33 PST)
  - Re: [AMBER] Reading chemical bonds from par7 files Francesco Pietra (Fri Jan 16 2015 - 09:04:57 PST)
    - Re: [AMBER] Reading chemical bonds from par7 files David A Case (Sat Jan 17 2015 - 06:55:48 PST)
    - Re: [AMBER] Reading chemical bonds from par7 files Francesco Pietra (Sat Jan 17 2015 - 07:33:13 PST)
[AMBER] unusual structure after heating. why? Atila Petrosian (Thu Jan 15 2015 - 00:49:33 PST)
- Re: [AMBER] unusual structure after heating. why? Jason Swails (Thu Jan 15 2015 - 04:42:29 PST)
[AMBER] Error while running tleap in AMBER Shreeramesh (Thu Jan 15 2015 - 05:08:05 PST)
- Re: [AMBER] Error while running tleap in AMBER Jason Swails (Thu Jan 15 2015 - 06:23:33 PST)
- Re: [AMBER] Error while running tleap in AMBER David A Case (Thu Jan 15 2015 - 06:29:49 PST)
[AMBER] Problem with idecomp in MMPBSA lalvarez.qi.fcen.uba.ar (Thu Jan 15 2015 - 07:01:03 PST)
- Re: [AMBER] Problem with idecomp in MMPBSA Jason Swails (Thu Jan 15 2015 - 07:52:28 PST)
[AMBER] How to fix 1-4 ELE error Kshatresh Dutta Dubey (Thu Jan 15 2015 - 07:17:18 PST)
- Re: [AMBER] How to fix 1-4 ELE error Daniel Roe (Thu Jan 15 2015 - 08:35:26 PST)
  - Re: [AMBER] How to fix 1-4 ELE error Kshatresh Dutta Dubey (Thu Jan 15 2015 - 08:59:54 PST)
[AMBER] Which papers should be cited for ff14SB Jonathan Gough (Thu Jan 15 2015 - 09:56:13 PST)
- Re: [AMBER] Which papers should be cited for ff14SB Carlos Simmerling (Fri Jan 16 2015 - 08:24:41 PST)
[AMBER] unusual structure after heating. why? Atila Petrosian (Thu Jan 15 2015 - 10:31:04 PST)
- Re: [AMBER] unusual structure after heating. why? Daniel Roe (Thu Jan 15 2015 - 10:39:25 PST)
[AMBER] hydrogen bond charmm vs amber newamber list (Thu Jan 15 2015 - 11:20:20 PST)
- Re: [AMBER] hydrogen bond charmm vs amber Jason Swails (Thu Jan 15 2015 - 11:32:51 PST)
  - Re: [AMBER] hydrogen bond charmm vs amber newamber list (Thu Jan 15 2015 - 12:06:10 PST)
    - Re: [AMBER] hydrogen bond charmm vs amber Daniel Roe (Thu Jan 15 2015 - 12:42:20 PST)
    - Re: [AMBER] hydrogen bond charmm vs amber newamber list (Thu Jan 15 2015 - 13:00:09 PST)
    - Re: [AMBER] hydrogen bond charmm vs amber Daniel Roe (Thu Jan 15 2015 - 13:14:57 PST)
[AMBER] unusual structure after heating. why? Atila Petrosian (Thu Jan 15 2015 - 11:38:36 PST)
- Re: [AMBER] unusual structure after heating. why? Daniel Roe (Thu Jan 15 2015 - 11:58:18 PST)
[AMBER] Extracting multiple frames by cpptraj Mahendra B Thapa (Thu Jan 15 2015 - 11:45:06 PST)
- Re: [AMBER] Extracting multiple frames by cpptraj Daniel Roe (Thu Jan 15 2015 - 11:56:20 PST)
[AMBER] unusual structure after heating. why? Atila Petrosian (Thu Jan 15 2015 - 12:08:13 PST)
- Re: [AMBER] unusual structure after heating. why? Daniel Roe (Thu Jan 15 2015 - 12:50:00 PST)
  - Re: [AMBER] unusual structure after heating. why? Atila Petrosian (Sat Jan 24 2015 - 11:14:06 PST)
    - Re: [AMBER] unusual structure after heating. why? Jason Swails (Sat Jan 24 2015 - 12:26:51 PST)
    - Re: [AMBER] unusual structure after heating. why? Daniel Roe (Sat Jan 24 2015 - 15:52:49 PST)
[AMBER] Purchase second GPU for AMBER? orion shih (Thu Jan 15 2015 - 21:34:05 PST)
- Re: [AMBER] Purchase second GPU for AMBER? Ross Walker (Fri Jan 16 2015 - 12:09:59 PST)
  - Re: [AMBER] Purchase second GPU for AMBER? Scott Le Grand (Fri Jan 16 2015 - 12:16:08 PST)
[AMBER] Principal Axis Karl Kirschner (Fri Jan 16 2015 - 02:01:15 PST)
- Re: [AMBER] Principal Axis Daniel Roe (Fri Jan 16 2015 - 10:09:10 PST)
  - Re: [AMBER] Principal Axis Daniel Roe (Tue Jan 20 2015 - 09:43:25 PST)
    - Re: [AMBER] Principal Axis Karl Kirschner (Wed Jan 21 2015 - 00:49:35 PST)
Re: [AMBER] energies too high David A Case (Fri Jan 16 2015 - 04:45:31 PST)
- Re: [AMBER] energies too high Anupam Goel (Fri Jan 16 2015 - 06:47:16 PST)
[AMBER] cuda version 5 using gnu V 4.9.1 issues CHAMI F. (Fri Jan 16 2015 - 07:25:00 PST)
- Re: [AMBER] cuda version 5 using gnu V 4.9.1 issues Ross Walker (Fri Jan 16 2015 - 12:16:43 PST)
[AMBER] Why there is a conflict between ibelly and igb in REMD? Jinfeng Huang (Sat Jan 17 2015 - 05:59:52 PST)
- Re: [AMBER] Why there is a conflict between ibelly and igb in REMD? David A Case (Sat Jan 17 2015 - 07:23:42 PST)
[AMBER] AMBER 14 installation in cray machine : Problem related to parallel building Himanshu Joshi (Sat Jan 17 2015 - 09:53:47 PST)
- Re: [AMBER] AMBER 14 installation in cray machine : Problem related to parallel building Jason Swails (Sat Jan 17 2015 - 10:13:53 PST)
  - Re: [AMBER] AMBER 14 installation in cray machine : Problem related to parallel building Himanshu Joshi (Mon Jan 19 2015 - 02:03:42 PST)
    - Re: [AMBER] AMBER 14 installation in cray machine : Problem related to parallel building Jason Swails (Mon Jan 19 2015 - 05:32:04 PST)
Re: [AMBER] FW: FW: FW: clustering problem in ambertool14 Mahendra B Thapa (Sun Jan 18 2015 - 08:01:46 PST)
- Re: [AMBER] FW: FW: FW: clustering problem in ambertool14 Daniel Roe (Tue Jan 20 2015 - 09:59:42 PST)
[AMBER] installation of AmberTools14 Atila Petrosian (Sun Jan 18 2015 - 10:22:16 PST)
- Re: [AMBER] installation of AmberTools14 Daniel Roe (Sun Jan 18 2015 - 10:38:18 PST)
  - Re: [AMBER] installation of AmberTools14 Atila Petrosian (Sun Jan 18 2015 - 11:01:13 PST)
    - Re: [AMBER] installation of AmberTools14 David A Case (Sun Jan 18 2015 - 13:09:54 PST)
    - Re: [AMBER] installation of AmberTools14 Atila Petrosian (Mon Jan 19 2015 - 11:21:36 PST)
    - Re: [AMBER] installation of AmberTools14 David A Case (Mon Jan 19 2015 - 12:09:58 PST)
    - Re: [AMBER] installation of AmberTools14 Atila Petrosian (Mon Jan 19 2015 - 14:02:19 PST)
    - Re: [AMBER] installation of AmberTools14 David A Case (Tue Jan 20 2015 - 04:47:22 PST)
[AMBER] Periodic image of iwrapped structure Hadeer ELHabashy (Sun Jan 18 2015 - 15:05:13 PST)
- Re: [AMBER] Periodic image of iwrapped structure David A Case (Sun Jan 18 2015 - 17:04:55 PST)
  - Re: [AMBER] Periodic image of iwrapped structure Hadeer ELHabashy (Thu Jan 22 2015 - 14:46:12 PST)
    - Re: [AMBER] Periodic image of iwrapped structure Jason Swails (Thu Jan 22 2015 - 14:57:05 PST)
[AMBER] About: AMBER Advanced Tutorial 22 Hadeer ELHabashy (Sun Jan 18 2015 - 15:34:50 PST)
- Re: [AMBER] About: AMBER Advanced Tutorial 22 David A Case (Sun Jan 18 2015 - 17:07:11 PST)
[AMBER] HBond ANALYSIS Sylvester Tumusiime (Sun Jan 18 2015 - 21:44:01 PST)
- Re: [AMBER] HBond ANALYSIS Daniel Roe (Tue Jan 20 2015 - 10:04:52 PST)
  - Re: [AMBER] HBond ANALYSIS Sylvester Tumusiime (Tue Jan 20 2015 - 11:36:38 PST)
    - Re: [AMBER] HBond ANALYSIS Daniel Roe (Tue Jan 20 2015 - 11:49:24 PST)
    - Re: [AMBER] HBond ANALYSIS Sylvester Tumusiime (Tue Jan 20 2015 - 12:25:00 PST)
[AMBER] bad atom type: OA Houcemeddine Othman (Tue Jan 20 2015 - 02:59:01 PST)
- Re: [AMBER] bad atom type: OA Jason Swails (Tue Jan 20 2015 - 05:19:59 PST)
  - Re: [AMBER] bad atom type: OA Brent Krueger (Tue Jan 20 2015 - 06:55:12 PST)
    - Re: [AMBER] bad atom type: OA Jason Swails (Tue Jan 20 2015 - 09:21:29 PST)
    - Re: [AMBER] bad atom type: OA Houcemeddine Othman (Wed Feb 04 2015 - 04:26:09 PST)
    - [AMBER] MMPBSA Molsurf vs LCPO Aronica, Pietro (Tue Jan 20 2015 - 10:43:29 PST)
    - Re: [AMBER] MMPBSA Molsurf vs LCPO Ray Luo, Ph.D. (Tue Jan 20 2015 - 11:01:31 PST)
    - Re: [AMBER] MMPBSA Molsurf vs LCPO Aronica, Pietro (Tue Jan 20 2015 - 11:39:02 PST)
    - Re: [AMBER] MMPBSA Molsurf vs LCPO Jason Swails (Tue Jan 20 2015 - 11:52:10 PST)
    - Re: [AMBER] MMPBSA Molsurf vs LCPO Ray Luo, Ph.D. (Tue Jan 20 2015 - 12:06:11 PST)
[AMBER] Proper output form of DCCM Analysis using ptraj Suchetana Gupta bt13d072 (Tue Jan 20 2015 - 05:40:09 PST)
- Re: [AMBER] Proper output form of DCCM Analysis using ptraj Daniel Roe (Tue Jan 20 2015 - 10:19:44 PST)
  - Re: [AMBER] Proper output form of DCCM Analysis using ptraj Suchetana Gupta (Tue Jan 20 2015 - 20:01:16 PST)
    - Re: [AMBER] Proper output form of DCCM Analysis using ptraj Suchetana Gupta (Tue Jan 20 2015 - 20:45:44 PST)
    - Re: [AMBER] Proper output form of DCCM Analysis using ptraj Jason Swails (Wed Jan 21 2015 - 04:41:19 PST)
    - Re: [AMBER] Proper output form of DCCM Analysis using ptraj Suchetana Gupta (Wed Jan 21 2015 - 21:16:30 PST)
[AMBER] Trajectory processing using ptraj James Starlight (Tue Jan 20 2015 - 09:53:41 PST)
- Re: [AMBER] Trajectory processing using ptraj Daniel Roe (Tue Jan 20 2015 - 10:27:55 PST)
  - Re: [AMBER] Trajectory processing using ptraj James Starlight (Wed Jan 21 2015 - 05:45:00 PST)
    - Re: [AMBER] Trajectory processing using ptraj Daniel Roe (Wed Jan 21 2015 - 07:36:35 PST)
[AMBER] Question of AM1-BCC asdda asa (Tue Jan 20 2015 - 19:46:36 PST)
- Re: [AMBER] Question of AM1-BCC Gerald Monard (Wed Jan 21 2015 - 00:18:17 PST)
- Re: [AMBER] Question of AM1-BCC Jason Swails (Wed Jan 21 2015 - 04:26:22 PST)
  - Re: [AMBER] Question of AM1-BCC Dean Cuebas (Wed Jan 21 2015 - 13:19:06 PST)
    - Re: [AMBER] Question of AM1-BCC asdda asa (Wed Jan 21 2015 - 16:03:23 PST)
[AMBER] Querry about puckering Aparna P (Tue Jan 20 2015 - 22:36:29 PST)
[AMBER] About statistical report of 'RMS deviation from ideal bonds/angles' Yi Zhang (Wed Jan 21 2015 - 00:13:09 PST)
- Re: [AMBER] About statistical report of 'RMS deviation from ideal bonds/angles' David A Case (Wed Jan 21 2015 - 05:06:28 PST)
[AMBER] help in analysis Robin Jain (Wed Jan 21 2015 - 02:38:41 PST)
- Re: [AMBER] help in analysis Jason Swails (Wed Jan 21 2015 - 04:12:30 PST)
  - Re: [AMBER] help in analysis Paul Mortenson (Wed Jan 21 2015 - 05:34:41 PST)
    - Re: [AMBER] help in analysis Jason Swails (Wed Jan 21 2015 - 06:08:49 PST)
[AMBER] Group defining heavy atoms Thomas Exner (Wed Jan 21 2015 - 09:20:15 PST)
- Re: [AMBER] Group defining heavy atoms David A Case (Wed Jan 21 2015 - 16:56:24 PST)
  - Re: [AMBER] Group defining heavy atoms Thomas Exner (Thu Jan 22 2015 - 00:47:31 PST)
    - Re: [AMBER] Group defining heavy atoms Alessandro Contini (Thu Jan 22 2015 - 01:11:58 PST)
    - Re: [AMBER] Group defining heavy atoms Jason Swails (Thu Jan 22 2015 - 04:09:00 PST)
    - Re: [AMBER] Group defining heavy atoms David A Case (Thu Jan 22 2015 - 04:58:52 PST)
[AMBER] GPU error GTX card. BERGY (Wed Jan 21 2015 - 09:27:58 PST)
- Re: [AMBER] GPU error GTX card. David A Case (Wed Jan 21 2015 - 16:58:31 PST)
- Re: [AMBER] GPU error GTX card. Ross Walker (Thu Jan 22 2015 - 09:34:32 PST)
  - Re: [AMBER] GPU error GTX card. BERGY (Thu Jan 22 2015 - 09:43:26 PST)
[AMBER] R: Group defining heavy atoms Alessandro Contini (Wed Jan 21 2015 - 09:43:16 PST)
- Re: [AMBER] R: Group defining heavy atoms Thomas Exner (Wed Jan 21 2015 - 11:01:16 PST)
[AMBER] Question in Amber atom types asdda asa (Wed Jan 21 2015 - 16:26:13 PST)
- Re: [AMBER] Question in Amber atom types David A Case (Wed Jan 21 2015 - 18:13:10 PST)
  - Re: [AMBER] Question in Amber atom types asdda asa (Thu Jan 22 2015 - 22:18:16 PST)
[AMBER] PMEMD Error Sourav Purohit (Wed Jan 21 2015 - 23:20:07 PST)
- Re: [AMBER] PMEMD Error Jason Swails (Thu Jan 22 2015 - 03:38:57 PST)
[AMBER] help in diffusion coefficient Robin Jain (Thu Jan 22 2015 - 01:22:03 PST)
- Re: [AMBER] help in diffusion coefficient Daniel Roe (Thu Jan 22 2015 - 06:50:21 PST)
[AMBER] Protein Drug explicit MD simulation pradeep pant (Thu Jan 22 2015 - 05:03:30 PST)
- Re: [AMBER] Protein Drug explicit MD simulation Carlos Simmerling (Thu Jan 22 2015 - 05:07:07 PST)
Re: [AMBER] NVE GPU question Ross Walker (Thu Jan 22 2015 - 10:48:28 PST)
- Re: [AMBER] NVE GPU question Gerald Monard (Thu Jan 22 2015 - 11:13:17 PST)
[AMBER] Fwd: NVE GPU question Joseph Baker (Thu Jan 22 2015 - 11:20:58 PST)
- Re: [AMBER] Fwd: NVE GPU question Jason Swails (Thu Jan 22 2015 - 12:05:52 PST)
  - Re: [AMBER] Fwd: NVE GPU question Joseph Baker (Thu Jan 22 2015 - 12:37:21 PST)
    - Re: [AMBER] Fwd: NVE GPU question Jason Swails (Thu Jan 22 2015 - 13:28:41 PST)
    - Re: [AMBER] Fwd: NVE GPU question Joseph Baker (Thu Jan 22 2015 - 14:22:59 PST)
    - Re: [AMBER] Fwd: NVE GPU question Jason Swails (Thu Jan 22 2015 - 14:50:31 PST)
    - Re: [AMBER] Fwd: NVE GPU question Thomas Cheatham (Thu Jan 22 2015 - 14:58:06 PST)
    - Re: [AMBER] Fwd: NVE GPU question Joseph Baker (Thu Jan 22 2015 - 15:24:04 PST)
    - Re: [AMBER] Fwd: NVE GPU question Joseph Baker (Thu Jan 22 2015 - 16:26:24 PST)
    - Re: [AMBER] Fwd: NVE GPU question Hector A. Baldoni (Thu Jan 22 2015 - 16:58:56 PST)
    - Re: [AMBER] NVE GPU question Ross Walker (Fri Jan 23 2015 - 06:04:59 PST)
    - Re: [AMBER] NVE GPU question Joseph Baker (Fri Jan 23 2015 - 07:03:30 PST)
    - Re: [AMBER] NVE GPU question Jason Swails (Fri Jan 23 2015 - 07:37:55 PST)
    - Re: [AMBER] NVE GPU question Joseph Baker (Fri Jan 23 2015 - 08:10:54 PST)
    - Re: [AMBER] NVE GPU question Jason Swails (Fri Jan 23 2015 - 08:18:54 PST)
    - Re: [AMBER] Fwd: NVE GPU question Gerald Monard (Thu Jan 22 2015 - 14:56:14 PST)
[AMBER] How to write the Amber code(s) to calculate pi-pi stacking interactions, polar contacts Jiapu Zhang (Thu Jan 22 2015 - 22:36:32 PST)
- Re: [AMBER] How to write the Amber code(s) to calculate pi-pi stacking interactions, polar contacts Jason Swails (Fri Jan 23 2015 - 01:30:55 PST)
[AMBER] help in diffusion coefficient analysis Robin Jain (Fri Jan 23 2015 - 00:02:40 PST)
- Re: [AMBER] help in diffusion coefficient analysis Jason Swails (Fri Jan 23 2015 - 01:36:55 PST)
- Re: [AMBER] help in diffusion coefficient analysis Daniel Roe (Fri Jan 23 2015 - 09:57:40 PST)
[AMBER] How to save structure at every minimisation/optimization cycle Kshatresh Dutta Dubey (Fri Jan 23 2015 - 02:09:26 PST)
- Re: [AMBER] How to save structure at every minimisation/optimization cycle David A Case (Fri Jan 23 2015 - 05:24:59 PST)
  - Re: [AMBER] How to save structure at every minimisation/optimization cycle Kshatresh Dutta Dubey (Fri Jan 23 2015 - 10:02:14 PST)
    - Re: [AMBER] How to save structure at every minimisation/optimization cycle David A Case (Sat Jan 24 2015 - 09:16:48 PST)
Re: [AMBER] FW: FW: FW: FW: clustering problem in ambertool14 Mahendra B Thapa (Fri Jan 23 2015 - 06:24:53 PST)
- Re: [AMBER] FW: FW: FW: FW: clustering problem in ambertool14 Daniel Roe (Fri Jan 23 2015 - 09:02:31 PST)
[AMBER] Force ramp pulling agarai.physics.iisc.ernet.in (Fri Jan 23 2015 - 09:14:07 PST)
- Re: [AMBER] Force ramp pulling Jason Swails (Sat Jan 24 2015 - 12:06:02 PST)
[AMBER] bcl script side chain optimization using Gaussian-Reg sailu (Sat Jan 24 2015 - 03:14:51 PST)
- Re: [AMBER] bcl script side chain optimization using Gaussian-Reg Pengfei Li (Sat Jan 24 2015 - 04:53:19 PST)
Re: [AMBER] AMBER Digest, Vol 1109, Issue 1 sailu (Sat Jan 24 2015 - 21:09:33 PST)
[AMBER] MMGBSA of several MD trajectories James Starlight (Sun Jan 25 2015 - 06:31:31 PST)
- Re: [AMBER] MMGBSA of several MD trajectories Carlos Simmerling (Sun Jan 25 2015 - 06:49:52 PST)
[AMBER] PCA variance using Freq = 108.587 * sqrt( 0.6 / Eigenvalue ) Muthukumaran R (Sun Jan 25 2015 - 07:42:40 PST)
- Re: [AMBER] PCA variance using Freq = 108.587 * sqrt( 0.6 / Eigenvalue ) Daniel Roe (Sun Jan 25 2015 - 08:23:35 PST)
  - Re: [AMBER] PCA variance using Freq = 108.587 * sqrt( 0.6 / Eigenvalue ) Muthukumaran R (Sun Jan 25 2015 - 21:40:25 PST)
    - Re: [AMBER] PCA variance using Freq = 108.587 * sqrt( 0.6 / Eigenvalue ) Daniel Roe (Wed Jan 28 2015 - 07:26:03 PST)
[AMBER] Atom type parameterization and prmtop file asdda asa (Sun Jan 25 2015 - 16:57:41 PST)
- Re: [AMBER] Atom type parameterization and prmtop file David A Case (Sun Jan 25 2015 - 18:34:47 PST)
  - Re: [AMBER] Atom type parameterization and prmtop file asdda asa (Mon Jan 26 2015 - 18:15:55 PST)
    - Re: [AMBER] Atom type parameterization and prmtop file David A Case (Tue Jan 27 2015 - 08:19:33 PST)
    - Re: [AMBER] Atom type parameterization and prmtop file asdda asa (Tue Jan 27 2015 - 19:32:00 PST)
[AMBER] how to choose the final binding mode 徐晓庶 (Mon Jan 26 2015 - 03:23:41 PST)
- Re: [AMBER] how to choose the final binding mode Jason Swails (Mon Jan 26 2015 - 07:27:20 PST)
[AMBER] Lipid 14 format problem Romero, Raquel (Mon Jan 26 2015 - 04:44:48 PST)
- Re: [AMBER] Lipid 14 format problem Ross Walker (Mon Jan 26 2015 - 07:18:09 PST)
  - Re: [AMBER] Lipid 14 format problem Romero, Raquel (Mon Jan 26 2015 - 08:56:06 PST)
    - Re: [AMBER] Lipid 14 format problem Benjamin D Madej (Mon Jan 26 2015 - 11:45:16 PST)
    - Re: [AMBER] Lipid 14 format problem Daniel Roe (Mon Jan 26 2015 - 11:53:00 PST)
    - Re: [AMBER] Lipid 14 format problem Romero, Raquel (Mon Jan 26 2015 - 14:07:22 PST)
    - Re: [AMBER] Lipid 14 format problem Sarah Witzke (Mon Jan 26 2015 - 16:26:59 PST)
    - Re: [AMBER] Lipid 14 format problem Benjamin D Madej (Mon Jan 26 2015 - 16:50:23 PST)
    - Re: [AMBER] Lipid 14 format problem Romero, Raquel (Tue Jan 27 2015 - 05:38:46 PST)
    - Re: [AMBER] Lipid 14 format problem Jason Swails (Tue Jan 27 2015 - 07:59:05 PST)
[AMBER] AMBER 14 DPFP single energy calculations inconsistent R.G. Mantell (Mon Jan 26 2015 - 06:42:55 PST)
- Re: [AMBER] AMBER 14 DPFP single energy calculations inconsistent David A Case (Mon Jan 26 2015 - 07:09:27 PST)
  - Re: [AMBER] AMBER 14 DPFP single energy calculations inconsistent R.G. Mantell (Mon Jan 26 2015 - 07:34:13 PST)
    - Re: [AMBER] AMBER 14 DPFP single energy calculations inconsistent Jason Swails (Mon Jan 26 2015 - 07:48:22 PST)
    - Re: [AMBER] AMBER 14 DPFP single energy calculations inconsistent Rosemary Mantell (Tue Jan 27 2015 - 10:14:24 PST)
    - Re: [AMBER] AMBER 14 DPFP single energy calculations inconsistent Ross Walker (Mon Jan 26 2015 - 07:48:27 PST)
    - Re: [AMBER] AMBER 14 DPFP single energy calculations inconsistent Rosemary Mantell (Tue Jan 27 2015 - 10:13:05 PST)
    - Re: [AMBER] AMBER 14 DPFP single energy calculations inconsistent Ross Walker (Tue Jan 27 2015 - 10:54:32 PST)
    - Re: [AMBER] AMBER 14 DPFP single energy calculations inconsistent R.G. Mantell (Wed Jan 28 2015 - 10:27:41 PST)
    - Re: [AMBER] AMBER 14 DPFP single energy calculations inconsistent Scott Le Grand (Wed Jan 28 2015 - 12:22:10 PST)
    - Re: [AMBER] AMBER 14 DPFP single energy calculations inconsistent Scott Le Grand (Wed Jan 28 2015 - 19:52:59 PST)
    - Re: [AMBER] AMBER 14 DPFP single energy calculations inconsistent Scott Le Grand (Thu Jan 29 2015 - 08:51:22 PST)
    - Re: [AMBER] AMBER 14 DPFP single energy calculations inconsistent Jason Swails (Thu Jan 29 2015 - 09:42:32 PST)
    - Re: [AMBER] AMBER 14 DPFP single energy calculations inconsistent Scott Le Grand (Thu Jan 29 2015 - 18:14:44 PST)
    - Re: [AMBER] AMBER 14 DPFP single energy calculations inconsistent Jason Swails (Thu Jan 29 2015 - 18:26:05 PST)
    - Re: [AMBER] AMBER 14 DPFP single energy calculations inconsistent Ilyas Yildirim (Fri Jan 30 2015 - 02:13:58 PST)
    - Re: [AMBER] AMBER 14 DPFP single energy calculations inconsistent David A Case (Tue Jan 27 2015 - 12:06:03 PST)
    - Re: [AMBER] AMBER 14 DPFP single energy calculations inconsistent Scott Le Grand (Tue Jan 27 2015 - 15:31:19 PST)
    - Re: [AMBER] AMBER 14 DPFP single energy calculations inconsistent Scott Le Grand (Wed Jan 28 2015 - 10:00:11 PST)
    - Re: [AMBER] AMBER 14 DPFP single energy calculations inconsistent R.G. Mantell (Wed Jan 28 2015 - 10:20:29 PST)
- Re: [AMBER] AMBER 14 DPFP single energy calculations inconsistent Ilyas Yildirim (Fri Jan 30 2015 - 07:11:03 PST)
  - Re: [AMBER] AMBER 14 DPFP single energy calculations inconsistent Carlos Simmerling (Fri Jan 30 2015 - 07:34:16 PST)
  - Re: [AMBER] AMBER 14 DPFP single energy calculations inconsistent Ross Walker (Fri Jan 30 2015 - 09:24:02 PST)
    - Re: [AMBER] AMBER 14 DPFP single energy calculations inconsistent Scott Le Grand (Fri Jan 30 2015 - 09:38:54 PST)
  - Re: [AMBER] AMBER 14 DPFP single energy calculations inconsistent Jason Swails (Fri Jan 30 2015 - 10:07:39 PST)
- Re: [AMBER] AMBER 14 DPFP single energy calculations inconsistent Ilyas Yildirim (Fri Jan 30 2015 - 11:22:39 PST)
  - Re: [AMBER] AMBER 14 DPFP single energy calculations inconsistent Adrian Roitberg (Fri Jan 30 2015 - 11:27:20 PST)
  - Re: [AMBER] AMBER 14 DPFP single energy calculations inconsistent Hai Nguyen (Fri Jan 30 2015 - 11:35:16 PST)
    - Re: [AMBER] AMBER 14 DPFP single energy calculations inconsistent Ross Walker (Fri Jan 30 2015 - 12:00:35 PST)
  - Re: [AMBER] AMBER 14 DPFP single energy calculations inconsistent Jason Swails (Fri Jan 30 2015 - 11:57:07 PST)
    - Re: [AMBER] AMBER 14 DPFP single energy calculations inconsistent Ross Walker (Fri Jan 30 2015 - 12:03:36 PST)
Re: [AMBER] FW: FW: FW: FW: FW: clustering problem in ambertool14 Mahendra B Thapa (Mon Jan 26 2015 - 07:42:41 PST)
- Re: [AMBER] FW: FW: FW: FW: FW: clustering problem in ambertool14 Jason Swails (Mon Jan 26 2015 - 08:21:30 PST)
- Re: [AMBER] FW: FW: FW: FW: FW: clustering problem in ambertool14 Daniel Roe (Mon Jan 26 2015 - 12:18:53 PST)
[AMBER] cbrange in gnuplot Sylvester Tumusiime (Mon Jan 26 2015 - 12:26:42 PST)
- Re: [AMBER] cbrange in gnuplot Daniel Roe (Wed Jan 28 2015 - 08:23:13 PST)
  - Re: [AMBER] cbrange in gnuplot Sylvester Tumusiime (Wed Jan 28 2015 - 12:00:22 PST)
[AMBER] xleap does not known when compiling with mpi Saeed Nasiri (Mon Jan 26 2015 - 23:50:59 PST)
- Re: [AMBER] xleap does not known when compiling with mpi David A Case (Tue Jan 27 2015 - 07:41:23 PST)
[AMBER] max GPU cards per run Harmeet Kaur (Tue Jan 27 2015 - 01:03:49 PST)
- Re: [AMBER] max GPU cards per run David A Case (Tue Jan 27 2015 - 05:38:00 PST)
  - Re: [AMBER] max GPU cards per run Scott Le Grand (Thu Jan 29 2015 - 18:15:59 PST)
[AMBER] ambertools14 fresh installation fails Fabian Glaser (Tue Jan 27 2015 - 05:52:45 PST)
- Re: [AMBER] ambertools14 fresh installation fails Fabian Glaser (Tue Jan 27 2015 - 05:55:13 PST)
- Re: [AMBER] ambertools14 fresh installation fails David A Case (Tue Jan 27 2015 - 07:47:32 PST)
  - Re: [AMBER] ambertools14 fresh installation fails Jason Swails (Tue Jan 27 2015 - 08:33:54 PST)
    - Re: [AMBER] ambertools14 fresh installation fails Fabian Gmail (Tue Jan 27 2015 - 12:35:42 PST)
    - Re: [AMBER] ambertools14 fresh installation fails Jason Swails (Tue Jan 27 2015 - 14:12:25 PST)
    - Re: [AMBER] ambertools14 fresh installation fails Fabian Glaser (Wed Jan 28 2015 - 05:01:24 PST)
[AMBER] help in minimization Robin Jain (Tue Jan 27 2015 - 07:29:34 PST)
- Re: [AMBER] help in minimization Jason Swails (Tue Jan 27 2015 - 08:17:30 PST)
[AMBER] GBSA speeds for big molecules Asmit Bhowmick (Tue Jan 27 2015 - 13:18:16 PST)
- Re: [AMBER] GBSA speeds for big molecules Jason Swails (Tue Jan 27 2015 - 14:18:35 PST)
  - Re: [AMBER] GBSA speeds for big molecules Carlos Simmerling (Wed Jan 28 2015 - 07:08:15 PST)
    - Re: [AMBER] GBSA speeds for big molecules Daniel Roe (Wed Jan 28 2015 - 07:15:40 PST)
[AMBER] AMBER Workshop Announcement - Haifa Israel, Sun Apr 26th to 30th. Ross Walker (Tue Jan 27 2015 - 16:55:10 PST)
[AMBER] Targeted MD error Pallavi Mohanty (Tue Jan 27 2015 - 22:11:21 PST)
- Re: [AMBER] Targeted MD error David A Case (Wed Jan 28 2015 - 04:56:50 PST)
- Re: [AMBER] Targeted MD error Jason Swails (Wed Jan 28 2015 - 05:00:44 PST)
[AMBER] problem with antechamber Maryam Hamzehee (Tue Jan 27 2015 - 22:27:46 PST)
- Re: [AMBER] problem with antechamber hannes.loeffler.stfc.ac.uk (Wed Jan 28 2015 - 00:10:20 PST)
  - Re: [AMBER] problem with antechamber Maryam Hamzehee (Wed Jan 28 2015 - 01:40:58 PST)
    - Re: [AMBER] problem with antechamber Hannes Loeffler (Wed Jan 28 2015 - 01:58:16 PST)
    - Re: [AMBER] problem with antechamber Hannes Loeffler (Wed Jan 28 2015 - 02:04:43 PST)
    - Re: [AMBER] problem with antechamber Maryam Hamzehee (Wed Jan 28 2015 - 03:45:46 PST)
    - Re: [AMBER] problem with antechamber Hannes Loeffler (Wed Jan 28 2015 - 03:52:48 PST)
    - Re: [AMBER] problem with antechamber Maryam Hamzehee (Wed Jan 28 2015 - 05:22:22 PST)
[AMBER] Help in AMBER+PLUMED interface Giovanni Bussi (Tue Jan 27 2015 - 23:37:44 PST)
- Re: [AMBER] Help in AMBER+PLUMED interface Jason Swails (Wed Jan 28 2015 - 06:02:41 PST)
  - Re: [AMBER] Help in AMBER+PLUMED interface Giovanni Bussi (Wed Jan 28 2015 - 23:41:27 PST)
[AMBER] shell scripting within cpptraj input files James Starlight (Wed Jan 28 2015 - 01:21:28 PST)
- Re: [AMBER] shell scripting within cpptraj input files Marc van der Kamp (Wed Jan 28 2015 - 01:35:06 PST)
  - Re: [AMBER] shell scripting within cpptraj input files James Starlight (Wed Jan 28 2015 - 01:38:56 PST)
- Re: [AMBER] shell scripting within cpptraj input files Daniel Roe (Wed Jan 28 2015 - 08:18:41 PST)
[AMBER] [cpptraj] Problem with nativecontacts Juan Eiros Zamora (Wed Jan 28 2015 - 05:02:10 PST)
- Re: [AMBER] [cpptraj] Problem with nativecontacts Daniel Roe (Wed Jan 28 2015 - 07:56:12 PST)
  - Re: [AMBER] [cpptraj] Problem with nativecontacts Eiros Zamora, Juan (Thu Jan 29 2015 - 08:46:47 PST)
[AMBER] How to run an antechamber for ligands containing silver [Ag] atom? Shreeramesh (Wed Jan 28 2015 - 05:44:00 PST)
- Re: [AMBER] How to run an antechamber for ligands containing silver [Ag] atom? David A Case (Wed Jan 28 2015 - 06:08:29 PST)
[AMBER] POPC membrane separation. William Hester (Wed Jan 28 2015 - 08:13:10 PST)
- Re: [AMBER] POPC membrane separation. Ross Walker (Wed Jan 28 2015 - 19:13:07 PST)
  - Re: [AMBER] POPC membrane separation. William Hester (Thu Jan 29 2015 - 04:32:26 PST)
    - Re: [AMBER] POPC membrane separation. Jason Swails (Thu Jan 29 2015 - 05:49:42 PST)
    - Re: [AMBER] POPC membrane separation. William Hester (Fri Jan 30 2015 - 03:55:12 PST)
[AMBER] harmonic restraint file abdennour braka (Wed Jan 28 2015 - 08:21:56 PST)
- Re: [AMBER] harmonic restraint file David A Case (Wed Jan 28 2015 - 10:17:24 PST)
  - Re: [AMBER] harmonic restraint file abdennour braka (Tue Feb 03 2015 - 02:47:58 PST)
    - Re: [AMBER] harmonic restraint file David A Case (Tue Feb 03 2015 - 05:14:52 PST)
    - Re: [AMBER] harmonic restraint file abdennour braka (Tue Feb 03 2015 - 05:26:29 PST)
    - [AMBER] restraintmask error Urszula Uciechowska (Tue Feb 03 2015 - 06:45:53 PST)
    - Re: [AMBER] restraintmask error Jason Swails (Tue Feb 03 2015 - 06:51:34 PST)
[AMBER] FATAL: Atom .R<RU5 13>.A does not have a type. Mahad Gatti Iou (Wed Jan 28 2015 - 09:01:52 PST)
- Re: [AMBER] FATAL: Atom .R<RU5 13>.A does not have a type. Jason Swails (Wed Jan 28 2015 - 09:54:08 PST)
 - Re: [AMBER] FATAL: Atom .R<RU5 13>.A does not have a type. Mahad Gatti Iou (Thu Jan 29 2015 - 01:50:41 PST)
 - Re: [AMBER] FATAL: Atom .R<RU5 13>.A does not have a type. Hannes Loeffler (Thu Jan 29 2015 - 02:43:35 PST)
 - Re: [AMBER] FATAL: Atom .R<RU5 13>.A does not have a type. David A Case (Thu Jan 29 2015 - 04:50:32 PST)
 - Re: [AMBER] FATAL: Atom .R<RU5 13>.A does not have a type. Mahad Gatti Iou (Thu Jan 29 2015 - 05:10:32 PST)
 - Re: [AMBER] FATAL: Atom .R<RU5 13>.A does not have a type. David A Case (Thu Jan 29 2015 - 08:24:21 PST)
 - Re: [AMBER] FATAL: Atom .R<RU5 13>.A does not have a type. Mahad Gatti Iou (Fri Jan 30 2015 - 07:33:03 PST)
 - Re: [AMBER] FATAL: Atom .R<RU5 13>.A does not have a type. Jason Swails (Fri Jan 30 2015 - 07:48:07 PST)
 - Re: [AMBER] FATAL: Atom .R<RU5 13>.A does not have a type. Mahad Gatti Iou (Thu Feb 05 2015 - 08:58:31 PST)
[AMBER] wrap warning Fabian Glaser (Thu Jan 29 2015 - 00:33:17 PST)
- Re: [AMBER] wrap warning David A Case (Thu Jan 29 2015 - 04:42:47 PST)
  - Re: [AMBER] wrap warning Fabian Glaser (Thu Jan 29 2015 - 04:54:28 PST)
    - Re: [AMBER] wrap warning Jason Swails (Thu Jan 29 2015 - 05:45:26 PST)
    - Re: [AMBER] wrap warning Daniel Roe (Thu Jan 29 2015 - 08:14:31 PST)
[AMBER] Regarding MCPB Pragya Priyadarshini (Thu Jan 29 2015 - 03:53:29 PST)
- Re: [AMBER] Regarding MCPB Jason Swails (Thu Jan 29 2015 - 06:27:06 PST)
[AMBER] big cavity in the trajectory Tong Zhu (Fri Jan 30 2015 - 00:29:01 PST)
- Re: [AMBER] big cavity in the trajectory Jason Swails (Fri Jan 30 2015 - 01:04:25 PST)
[AMBER] Regarding MCPB Pragya Priyadarshini (Fri Jan 30 2015 - 01:01:26 PST)
- Re: [AMBER] Regarding MCPB Jason Swails (Fri Jan 30 2015 - 03:15:27 PST)
[AMBER] clustering in PC subspace Asmita Gupta (Fri Jan 30 2015 - 03:09:31 PST)
- Re: [AMBER] clustering in PC subspace Daniel Roe (Fri Jan 30 2015 - 13:24:59 PST)
- Re: [AMBER] clustering in PC subspace filip fratev (Mon Sep 28 2015 - 15:41:59 PDT)
- Re: [AMBER] clustering in PC subspace filip fratev (Mon Sep 28 2015 - 16:10:18 PDT)
  - Re: [AMBER] clustering in PC subspace filip fratev (Mon Sep 28 2015 - 16:17:14 PDT)
    - Re: [AMBER] clustering in PC subspace Daniel Roe (Mon Sep 28 2015 - 20:00:48 PDT)
[AMBER] Clustering molecule between copies (not between frames) 浅井賢 (Fri Jan 30 2015 - 04:06:20 PST)
- Re: [AMBER] Clustering molecule between copies (not between frames) Marc van der Kamp (Fri Jan 30 2015 - 04:41:20 PST)
  - Re: [AMBER] Clustering molecule between copies (not between frames) 浅井賢 (Fri Jan 30 2015 - 06:45:10 PST)
    - Re: [AMBER] Clustering molecule between copies (not between frames) Marc van der Kamp (Fri Jan 30 2015 - 06:50:42 PST)
    - Re: [AMBER] Clustering molecule between copies (not between frames) 浅井賢 (Fri Jan 30 2015 - 06:56:54 PST)
    - Re: [AMBER] Clustering molecule between copies (not between frames) Marc van der Kamp (Fri Jan 30 2015 - 07:04:18 PST)
    - Re: [AMBER] Clustering molecule between copies (not between frames) 浅井賢 (Fri Jan 30 2015 - 07:19:47 PST)
    - Re: [AMBER] Clustering molecule between copies (not between frames) Thomas Cheatham (Fri Jan 30 2015 - 07:36:49 PST)
    - Re: [AMBER] Clustering molecule between copies (not between frames) 浅井賢 (Fri Jan 30 2015 - 07:54:14 PST)
    - Re: [AMBER] Clustering molecule between copies (not between frames) Thomas Cheatham (Fri Jan 30 2015 - 08:40:25 PST)
    - Re: [AMBER] Clustering molecule between copies (not between frames) Daniel Roe (Fri Jan 30 2015 - 13:43:55 PST)
[AMBER] parameterization using antechember Debasish Mandal (Fri Jan 30 2015 - 04:07:39 PST)
- Re: [AMBER] parameterization using antechember Hannes Loeffler (Fri Jan 30 2015 - 04:16:12 PST)
Re: [AMBER] Printer Bill Ross (Fri Jan 30 2015 - 14:06:59 PST)
[AMBER] Problem with Ambertools14 Fugui (Sat Jan 31 2015 - 10:27:12 PST)
- Re: [AMBER] Problem with Ambertools14 David A Case (Sat Jan 31 2015 - 13:03:30 PST)
[AMBER] Help regarding potential surface scan using external interface Kshatresh Dutta Dubey (Sat Jan 31 2015 - 12:02:57 PST)
[AMBER] AmberTools 14 Dhiraj Srivastava (Sat Jan 31 2015 - 19:31:38 PST)
- Re: [AMBER] AmberTools 14 Daniel Roe (Sat Jan 31 2015 - 19:40:41 PST)
[AMBER] Constructing a single Zwitterion in xleap Robert Molt (Sat Jan 31 2015 - 21:36:16 PST)
- Re: [AMBER] Constructing a single Zwitterion in xleap Jason Swails (Sun Feb 01 2015 - 04:55:02 PST)
  - Re: [AMBER] Constructing a single Zwitterion in xleap Karl Kirschner (Sun Feb 01 2015 - 07:13:04 PST)
    - Re: [AMBER] Constructing a single Zwitterion in xleap hannes.loeffler.stfc.ac.uk (Sun Feb 01 2015 - 07:37:00 PST)
[AMBER] missing atom of heme Fatemeh Sadat Alavi (Sun Feb 01 2015 - 00:14:31 PST)
- Re: [AMBER] missing atom of heme David A Case (Sun Feb 01 2015 - 05:48:41 PST)
[AMBER] Create one larger averaged trajectory file ! Hadeer ELHabashy (Sun Feb 01 2015 - 02:36:25 PST)
- Re: [AMBER] Create one larger averaged trajectory file ! Jason Swails (Sun Feb 01 2015 - 03:35:03 PST)
[AMBER] AMD stuck with v-limit exceeded error Hadeer ELHabashy (Sun Feb 01 2015 - 02:56:00 PST)
- Re: [AMBER] AMD stuck with v-limit exceeded error Daniel Roe (Sun Feb 01 2015 - 11:38:20 PST)
[AMBER] reparametrize water molecule near metal site Jorgen Simonsen (Sun Feb 01 2015 - 11:21:58 PST)
- Re: [AMBER] reparametrize water molecule near metal site David A Case (Mon Feb 02 2015 - 05:05:22 PST)
[AMBER] Error: Unable to run flex; this is required for NAB and antechamber Please check your PATH, or install the program vijay kumar narsapuram (Sun Feb 01 2015 - 12:59:16 PST)
- Re: [AMBER] Error: Unable to run flex; this is required for NAB and antechamber Please check your PATH, or install the program Daniel Roe (Sun Feb 01 2015 - 15:27:36 PST)
  - Re: [AMBER] Error: Unable to run flex; this is required for NAB and antechamber Please check your PATH, or install the program vijay kumar narsapuram (Sun Feb 01 2015 - 22:15:41 PST)
    - Re: [AMBER] Error: Unable to run flex; this is required for NAB and antechamber Please check your PATH, or install the program Jason Swails (Mon Feb 02 2015 - 05:16:52 PST)
    - Re: [AMBER] Error: Unable to run flex; this is required for NAB and antechamber Please check your PATH, or install the program vijay kumar narsapuram (Mon Feb 02 2015 - 05:48:46 PST)
- Re: [AMBER] Error: Unable to run flex; this is required for NAB and antechamber Please check your PATH, or install the program David A Case (Mon Feb 02 2015 - 05:15:12 PST)
  - Re: [AMBER] Error: Unable to run flex; this is required for NAB and antechamber Please check your PATH, or install the program vijay kumar narsapuram (Mon Feb 02 2015 - 05:47:12 PST)
    - Re: [AMBER] Error: Unable to run flex; this is required for NAB and antechamber Please check your PATH, or install the program Jason Swails (Mon Feb 02 2015 - 06:07:51 PST)
    - Re: [AMBER] Error: Unable to run flex; this is required for NAB and antechamber Please check your PATH, or install the program vijay kumar narsapuram (Mon Feb 23 2015 - 04:49:54 PST)
    - Re: [AMBER] Error: Unable to run flex; this is required for NAB and antechamber Please check your PATH, or install the program Jason Swails (Mon Feb 23 2015 - 05:26:40 PST)
    - Re: [AMBER] Error: Unable to run flex; this is required for NAB and antechamber Please check your PATH, or install the program vijay kumar narsapuram (Mon Feb 23 2015 - 06:45:40 PST)
    - Re: [AMBER] Error: Unable to run flex; this is required for NAB and antechamber Please check your PATH, or install the program Jason Swails (Mon Feb 23 2015 - 07:56:04 PST)
    - Re: [AMBER] Error: Unable to run flex; this is required for NAB and antechamber Please check your PATH, or install the program vijay kumar narsapuram (Fri Feb 27 2015 - 05:11:21 PST)
    - Re: [AMBER] Error: Unable to run flex; this is required for NAB and antechamber Please check your PATH, or install the program Jason Swails (Fri Feb 27 2015 - 05:15:02 PST)
    - Re: [AMBER] Error: Unable to run flex; this is required for NAB and antechamber Please check your PATH, or install the program vijay kumar narsapuram (Fri Feb 27 2015 - 05:25:45 PST)
    - Re: [AMBER] Error: Unable to run flex; this is required for NAB and antechamber Please check your PATH, or install the program Jason Swails (Fri Feb 27 2015 - 05:27:36 PST)
    - Re: [AMBER] Error: Unable to run flex; this is required for NAB and antechamber Please check your PATH, or install the program vijay kumar narsapuram (Fri Mar 06 2015 - 07:22:58 PST)
    - Re: [AMBER] Error: Unable to run flex; this is required for NAB and antechamber Please check your PATH, or install the program Jason Swails (Fri Mar 06 2015 - 07:28:14 PST)
    - Re: [AMBER] Error: Unable to run flex; this is required for NAB and antechamber Please check your PATH, or install the program vijay kumar narsapuram (Fri Mar 06 2015 - 08:56:46 PST)
    - Re: [AMBER] Error: Unable to run flex; this is required for NAB and antechamber Please check your PATH, or install the program vijay kumar narsapuram (Fri Mar 13 2015 - 02:12:01 PDT)
    - Re: [AMBER] Error: Unable to run flex; this is required for NAB and antechamber Please check your PATH, or install the program David A Case (Fri Mar 13 2015 - 04:06:53 PDT)
    - Re: [AMBER] Error: Unable to run flex; this is required for NAB and antechamber Please check your PATH, or install the program vijay kumar narsapuram (Sat Mar 28 2015 - 04:47:48 PDT)
    - Re: [AMBER] Error: Unable to run flex; this is required for NAB and antechamber Please check your PATH, or install the program Jason Swails (Sat Mar 28 2015 - 11:51:53 PDT)
    - Re: [AMBER] Error: Unable to run flex; this is required for NAB and antechamber Please check your PATH, or install the program David A Case (Sat Mar 28 2015 - 15:10:25 PDT)
    - Re: [AMBER] Error: Unable to run flex; this is required for NAB and antechamber Please check your PATH, or install the program vijay kumar narsapuram (Thu Apr 23 2015 - 03:15:09 PDT)
    - Re: [AMBER] Error: Unable to run flex; this is required for NAB and antechamber Please check your PATH, or install the program Jason Swails (Thu Apr 23 2015 - 03:59:32 PDT)
    - Re: [AMBER] Error: Unable to run flex; this is required for NAB and antechamber Please check your PATH, or install the program vijay kumar narsapuram (Thu Apr 23 2015 - 04:02:01 PDT)
    - Re: [AMBER] Error: Unable to run flex; this is required for NAB and antechamber Please check your PATH, or install the program vijay kumar narsapuram (Thu Apr 23 2015 - 04:48:19 PDT)
    - Re: [AMBER] Error: Unable to run flex; this is required for NAB and antechamber Please check your PATH, or install the program Jason Swails (Thu Apr 23 2015 - 05:06:05 PDT)
    - Re: [AMBER] Error: Unable to run flex; this is required for NAB and antechamber Please check your PATH, or install the program Jason Swails (Thu Apr 23 2015 - 12:19:45 PDT)
    - Re: [AMBER] Error: Unable to run flex; this is required for NAB and antechamber Please check your PATH, or install the program vijay kumar narsapuram (Thu Apr 23 2015 - 12:56:43 PDT)
    - Re: [AMBER] Error: Unable to run flex; this is required for NAB and antechamber Please check your PATH, or install the program Jason Swails (Fri Apr 24 2015 - 04:59:14 PDT)
    - Re: [AMBER] Error: Unable to run flex; this is required for NAB and antechamber Please check your PATH, or install the program vijay kumar narsapuram (Fri Apr 24 2015 - 07:52:10 PDT)
- Re: [AMBER] Error: Unable to run flex; this is required for NAB and antechamber Please check your PATH, or install the program vijay kumar narsapuram (Thu Apr 23 2015 - 09:50:14 PDT)
  - Re: [AMBER] Error: Unable to run flex; this is required for NAB and antechamber Please check your PATH, or install the program Jason Swails (Thu Apr 23 2015 - 11:26:29 PDT)
[AMBER] can not be a parameter fitting Takuya Uto (Sun Feb 01 2015 - 21:54:36 PST)
- Re: [AMBER] can not be a parameter fitting Jason Swails (Mon Feb 02 2015 - 05:28:22 PST)
[AMBER] (无主题) chemjxn.126.com (Sun Feb 01 2015 - 22:58:20 PST)
[AMBER] parameterization chemjxn.126.com (Sun Feb 01 2015 - 23:22:40 PST)
- Re: [AMBER] parameterization Jason Swails (Mon Feb 02 2015 - 05:22:29 PST)
  - Re: [AMBER] parameterization David A Case (Mon Feb 02 2015 - 06:52:18 PST)
[AMBER] Issue during mmgbsa decomposition James Starlight (Mon Feb 02 2015 - 04:26:49 PST)
- Re: [AMBER] Issue during mmgbsa decomposition James Starlight (Tue Feb 03 2015 - 00:09:11 PST)
  - Re: [AMBER] Issue during mmgbsa decomposition Kenneth Huang (Tue Feb 03 2015 - 07:22:31 PST)
    - Re: [AMBER] Issue during mmgbsa decomposition James Starlight (Tue Feb 03 2015 - 07:38:36 PST)
    - Re: [AMBER] Issue during mmgbsa decomposition Kenneth Huang (Tue Feb 03 2015 - 11:24:09 PST)
    - Re: [AMBER] Issue during mmgbsa decomposition James Starlight (Tue Feb 03 2015 - 12:38:31 PST)
[AMBER] error in equil.rst steps of AMBER Shreeramesh (Mon Feb 02 2015 - 06:32:51 PST)
- Re: [AMBER] error in equil.rst steps of AMBER Daniel Roe (Mon Feb 02 2015 - 06:52:04 PST)
- Re: [AMBER] error in equil.rst steps of AMBER David A Case (Mon Feb 02 2015 - 06:59:21 PST)
[AMBER] AmberTools14 installation Dhiraj Srivastava (Mon Feb 02 2015 - 11:25:25 PST)
- Re: [AMBER] AmberTools14 installation Novosielski, Ryan (Mon Feb 02 2015 - 11:30:09 PST)
  - Re: [AMBER] AmberTools14 installation Dhiraj Srivastava (Mon Feb 02 2015 - 11:37:36 PST)
    - Re: [AMBER] AmberTools14 installation Dhiraj Srivastava (Mon Feb 02 2015 - 11:38:48 PST)
    - Re: [AMBER] AmberTools14 installation Jason Swails (Mon Feb 02 2015 - 11:44:36 PST)
[AMBER] ante-MMPBSA IndexError: list index out of range Kenneth Huang (Mon Feb 02 2015 - 11:57:15 PST)
- Re: [AMBER] ante-MMPBSA IndexError: list index out of range Jason Swails (Mon Feb 02 2015 - 17:16:21 PST)
  - Re: [AMBER] ante-MMPBSA IndexError: list index out of range Kenneth Huang (Tue Feb 03 2015 - 10:30:55 PST)
    - Re: [AMBER] ante-MMPBSA IndexError: list index out of range Jason Swails (Tue Feb 03 2015 - 12:23:53 PST)
[AMBER] Create a 2M urea box Ibrahim Said (Mon Feb 02 2015 - 12:33:06 PST)
- Re: [AMBER] Create a 2M urea box mmaestre.gate.sinica.edu.tw (Mon Feb 02 2015 - 15:36:05 PST)
  - Re: [AMBER] Create a 2M urea box Jason Swails (Mon Feb 02 2015 - 17:01:33 PST)
    - Re: [AMBER] Create a 2M urea box mmaestre.gate.sinica.edu.tw (Mon Feb 02 2015 - 23:41:20 PST)
[AMBER] pmemd.cuda.MPI interruption error! 汪盛 (Mon Feb 02 2015 - 16:13:45 PST)
- Re: [AMBER] pmemd.cuda.MPI interruption error! Ross Walker (Mon Feb 02 2015 - 16:31:49 PST)
[AMBER] Analysis of the MMGBSA decomposition output James Starlight (Tue Feb 03 2015 - 06:34:44 PST)
- Re: [AMBER] Analysis of the MMGBSA decomposition output Kenneth Huang (Thu Feb 05 2015 - 10:52:52 PST)
  - Re: [AMBER] Analysis of the MMGBSA decomposition output James Starlight (Fri Feb 06 2015 - 01:07:44 PST)
    - Re: [AMBER] Analysis of the MMGBSA decomposition output James Starlight (Fri Feb 06 2015 - 10:14:39 PST)
    - Re: [AMBER] Analysis of the MMGBSA decomposition output Kenneth Huang (Fri Feb 06 2015 - 14:49:22 PST)
    - Re: [AMBER] Analysis of the MMGBSA decomposition output Jason Swails (Fri Feb 06 2015 - 17:28:31 PST)
[AMBER] REGARDING GAUSSIAN BASED SIDE CHAIN MODEL OPTIMIZATION Swithin Hanosh (Tue Feb 03 2015 - 07:06:12 PST)
- Re: [AMBER] REGARDING GAUSSIAN BASED SIDE CHAIN MODEL OPTIMIZATION Pengfei Li (Tue Feb 03 2015 - 07:57:13 PST)
[AMBER] Calculation of the number of internal waters during md simulation James Starlight (Tue Feb 03 2015 - 07:54:03 PST)
- Re: [AMBER] Calculation of the number of internal waters during md simulation Daniel Roe (Tue Feb 03 2015 - 08:12:39 PST)
  - Re: [AMBER] Calculation of the number of internal waters during md simulation James Starlight (Tue Feb 03 2015 - 08:38:02 PST)
    - Re: [AMBER] Calculation of the number of internal waters during md simulation James Starlight (Wed Feb 04 2015 - 01:30:51 PST)
    - Re: [AMBER] Calculation of the number of internal waters during md simulation James Starlight (Thu Feb 05 2015 - 01:24:22 PST)
    - Re: [AMBER] Calculation of the number of internal waters during md simulation Daniel Roe (Thu Feb 05 2015 - 08:06:29 PST)
    - Re: [AMBER] Calculation of the number of internal waters during md simulation James Starlight (Fri Feb 06 2015 - 00:23:39 PST)
    - Re: [AMBER] Calculation of the number of internal waters during md simulation James Starlight (Fri Feb 06 2015 - 01:05:28 PST)
    - Re: [AMBER] Calculation of the number of internal waters during md simulation Daniel Roe (Fri Feb 06 2015 - 09:52:11 PST)
    - Re: [AMBER] Calculation of the number of internal waters during md simulation James Starlight (Tue Feb 10 2015 - 04:58:19 PST)
    - Re: [AMBER] Calculation of the number of internal waters during md simulation Daniel Roe (Tue Feb 10 2015 - 06:43:25 PST)
    - Re: [AMBER] Calculation of the number of internal waters during md simulation James Starlight (Tue Feb 10 2015 - 09:23:24 PST)
    - Re: [AMBER] Calculation of the number of internal waters during md simulation James Starlight (Tue Feb 10 2015 - 10:36:06 PST)
    - Re: [AMBER] Calculation of the number of internal waters during md simulation Daniel Roe (Thu Feb 12 2015 - 07:59:45 PST)
    - Re: [AMBER] Calculation of the number of internal waters during md simulation James Starlight (Fri Feb 13 2015 - 01:50:54 PST)
    - Re: [AMBER] Calculation of the number of internal waters during md simulation James Starlight (Wed Feb 25 2015 - 07:00:31 PST)
    - [AMBER] Calculation of the number of internal waters during md simulation Daniel Roe (Wed Feb 25 2015 - 07:12:33 PST)
    - Re: [AMBER] Calculation of the number of internal waters during md simulation James Starlight (Thu Feb 26 2015 - 07:12:17 PST)
    - Re: [AMBER] Calculation of the number of internal waters during md simulation Daniel Roe (Thu Feb 05 2015 - 08:02:55 PST)
[AMBER] LAST CALL: Free Energy Workshop, Münster, March 9-11, 2015 Vlad Cojocaru (Tue Feb 03 2015 - 12:35:33 PST)
[AMBER] Second announcement: AMBER Workshop - Haifa Israel, Sun Apr 26th to 30th. Ross Walker (Tue Feb 03 2015 - 13:44:39 PST)
[AMBER] have not atom type Fatemeh Sadat Alavi (Tue Feb 03 2015 - 22:20:36 PST)
- Re: [AMBER] have not atom type David A Case (Wed Feb 04 2015 - 04:58:42 PST)
[AMBER] confusion in md run Robin Jain (Wed Feb 04 2015 - 00:12:43 PST)
- Re: [AMBER] confusion in md run Jason Swails (Wed Feb 04 2015 - 02:00:49 PST)
[AMBER] REGARDING GAUSSIAN BASED SIDE CHAIN MODEL OPTIMIZATION Swithin Hanosh (Wed Feb 04 2015 - 01:30:08 PST)
- Re: [AMBER] REGARDING GAUSSIAN BASED SIDE CHAIN MODEL OPTIMIZATION Jason Swails (Wed Feb 04 2015 - 02:28:35 PST)
[AMBER] no parameter for nicotine Harmeet Kaur (Wed Feb 04 2015 - 02:07:40 PST)
- Re: [AMBER] no parameter for nicotine Ashutosh Shandilya (Wed Feb 04 2015 - 02:11:27 PST)
- Re: [AMBER] no parameter for nicotine Jason Swails (Wed Feb 04 2015 - 02:12:23 PST)
[AMBER] Error while running antechamber and tleap for silver salt of carboxylic acid Shreeramesh (Wed Feb 04 2015 - 03:06:06 PST)
- Re: [AMBER] Error while running antechamber and tleap for silver salt of carboxylic acid Hannes Loeffler (Wed Feb 04 2015 - 03:52:03 PST)
  - Re: [AMBER] Error while running antechamber and tleap for silver salt of carboxylic acid Shreeramesh (Wed Feb 04 2015 - 04:25:24 PST)
    - Re: [AMBER] Error while running antechamber and tleap for silver salt of carboxylic acid Hannes Loeffler (Wed Feb 04 2015 - 05:38:53 PST)
- [AMBER] problem with nab Urszula Uciechowska (Wed Feb 11 2015 - 05:53:12 PST)
  - Re: [AMBER] problem with nab Jason Swails (Wed Feb 11 2015 - 06:06:49 PST)
  - [AMBER] single strand DNA in hairpin conformation Urszula Uciechowska (Thu Feb 12 2015 - 01:13:02 PST)
    - Re: [AMBER] single strand DNA in hairpin conformation David A Case (Thu Feb 12 2015 - 04:24:56 PST)
    - Re: [AMBER] single strand DNA in hairpin conformation Urszula Uciechowska (Wed Feb 18 2015 - 08:55:42 PST)
    - Re: [AMBER] single strand DNA in hairpin conformation David A Case (Wed Feb 18 2015 - 12:27:24 PST)
    - Re: [AMBER] single strand DNA in hairpin conformation Urszula Uciechowska (Fri Feb 20 2015 - 05:46:52 PST)
    - Re: [AMBER] single strand DNA in hairpin conformation Christina Bergonzo (Fri Feb 20 2015 - 06:47:08 PST)
    - Re: [AMBER] single strand DNA in hairpin conformation David A Case (Fri Feb 20 2015 - 08:57:34 PST)
[AMBER] seek help 新生大侠 (Wed Feb 04 2015 - 03:42:57 PST)
- Re: [AMBER] seek help David A Case (Wed Feb 04 2015 - 05:11:38 PST)
  - [AMBER] 回复： seek help 新生大侠 (Wed Feb 04 2015 - 06:55:13 PST)
    - Re: [AMBER] 回复： seek help Jason Swails (Wed Feb 04 2015 - 08:01:25 PST)
    - [AMBER] 回复：回复： seek help 新生大侠 (Wed Feb 04 2015 - 19:02:31 PST)
    - Re: [AMBER] 回复：回复： seek help Jason Swails (Wed Feb 04 2015 - 20:23:34 PST)
    - [AMBER] 回复：回复：回复： seek help 新生大侠 (Wed Feb 04 2015 - 22:38:16 PST)
    - Re: [AMBER] 回复：回复： seek help Jason Swails (Thu Feb 05 2015 - 04:25:11 PST)
    - [AMBER] 回复：回复：回复： seek help 新生大侠 (Thu Feb 05 2015 - 06:09:07 PST)
[AMBER] Amber14 hardware setup Sofia Vasilakaki (Wed Feb 04 2015 - 04:59:49 PST)
- Re: [AMBER] Amber14 hardware setup Jason Swails (Wed Feb 04 2015 - 05:30:00 PST)
[AMBER] MD cis-azobenzene error Anya Leach (Wed Feb 04 2015 - 13:38:43 PST)
- Re: [AMBER] MD cis-azobenzene error Jason Swails (Wed Feb 04 2015 - 15:43:35 PST)
[AMBER] Xeon Phi Novosielski, Ryan (Wed Feb 04 2015 - 15:48:21 PST)
- Re: [AMBER] Xeon Phi Ross Walker (Wed Feb 04 2015 - 16:42:23 PST)
- Re: [AMBER] Xeon Phi Ryan Novosielski (Thu Feb 05 2015 - 12:45:40 PST)
  - Re: [AMBER] Xeon Phi Ross Walker (Thu Feb 05 2015 - 12:57:40 PST)
    - Re: [AMBER] Xeon Phi Novosielski, Ryan (Thu Feb 05 2015 - 13:07:07 PST)
    - Re: [AMBER] Xeon Phi Ross Walker (Thu Feb 05 2015 - 13:27:24 PST)
[AMBER] ERRORS AND FATAL ERRORS (Apparently died to faulty connections) Evans, Shalton (Wed Feb 04 2015 - 22:22:39 PST)
- Re: [AMBER] ERRORS AND FATAL ERRORS (Apparently died to faulty connections) Jason Swails (Thu Feb 05 2015 - 04:28:49 PST)
  - Re: [AMBER] ERRORS AND FATAL ERRORS (Apparently died to faulty connections) Evans, Shalton (Fri Feb 13 2015 - 13:30:13 PST)
    - Re: [AMBER] ERRORS AND FATAL ERRORS (Apparently died to faulty connections) Jason Swails (Fri Feb 13 2015 - 13:58:18 PST)
[AMBER] Error while running tleap for carboxylate anion Shreeramesh (Thu Feb 05 2015 - 01:18:37 PST)
- Re: [AMBER] Error while running tleap for carboxylate anion Marc van der Kamp (Thu Feb 05 2015 - 01:23:27 PST)
[AMBER] Real time event with amber mds with shake Hadeer ELHabashy (Thu Feb 05 2015 - 03:49:28 PST)
- Re: [AMBER] Real time event with amber mds with shake Jason Swails (Thu Feb 05 2015 - 04:55:13 PST)
  - Re: [AMBER] Real time event with amber mds with shake Hadeer ELHabashy (Thu Feb 05 2015 - 10:44:16 PST)
    - Re: [AMBER] Real time event with amber mds with shake Jason Swails (Thu Feb 05 2015 - 11:33:26 PST)
    - Re: [AMBER] Real time event with amber mds with shake Hadeer ELHabashy (Fri Feb 06 2015 - 04:46:27 PST)
[AMBER] ACS COMP Division awards for Fall 2015 National Meeting in Boston Carlos Simmerling (Thu Feb 05 2015 - 08:55:09 PST)
[AMBER] xleap syntax error Ahmet yıldırım (Thu Feb 05 2015 - 09:26:53 PST)
- Re: [AMBER] xleap syntax error Daniel Roe (Thu Feb 05 2015 - 10:25:55 PST)
- Re: [AMBER] xleap syntax error David A Case (Thu Feb 05 2015 - 10:40:51 PST)
  - Re: [AMBER] xleap syntax error Ahmet yıldırım (Thu Feb 05 2015 - 11:47:19 PST)
    - Re: [AMBER] xleap syntax error Jason Swails (Thu Feb 05 2015 - 12:46:40 PST)
    - Re: [AMBER] xleap syntax error Ahmet yıldırım (Thu Feb 05 2015 - 12:59:18 PST)
[AMBER] CUDA 5.0 vs 6.5 Ryan Novosielski (Thu Feb 05 2015 - 12:48:03 PST)
- Re: [AMBER] CUDA 5.0 vs 6.5 Ross Walker (Thu Feb 05 2015 - 12:54:30 PST)
  - Re: [AMBER] CUDA 5.0 vs 6.5 Novosielski, Ryan (Thu Feb 05 2015 - 12:59:46 PST)
[AMBER] charmmlipid2amber.x Chris Chris (Thu Feb 05 2015 - 19:28:15 PST)
- Re: [AMBER] charmmlipid2amber.x Jason Swails (Fri Feb 06 2015 - 03:21:48 PST)
[AMBER] Restraint bugs after most recent patch Niel Henriksen (Thu Feb 05 2015 - 22:41:26 PST)
- Re: [AMBER] Restraint bugs after most recent patch Ross Walker (Fri Feb 06 2015 - 12:53:42 PST)
[AMBER] MCPB chemjxn.126.com (Fri Feb 06 2015 - 00:21:14 PST)
- [AMBER] 回复： MCPB wjli (Fri Feb 06 2015 - 02:01:10 PST)
Re: [AMBER] Error while running MD for carboxylate anion Shreeramesh (Fri Feb 06 2015 - 01:25:44 PST)
- Re: [AMBER] Error while running MD for carboxylate anion Jason Swails (Fri Feb 06 2015 - 03:25:34 PST)
[AMBER] MD JOB was terminated before achieving the No. of steps Shreeramesh (Fri Feb 06 2015 - 01:28:53 PST)
- Re: [AMBER] MD JOB was terminated before achieving the No. of steps Ross Walker (Fri Feb 06 2015 - 12:56:30 PST)
[AMBER] Query regarding Dynamics Studies Ruchika Bhat (Fri Feb 06 2015 - 05:03:26 PST)
- Re: [AMBER] Query regarding Dynamics Studies Jason Swails (Fri Feb 06 2015 - 06:53:11 PST)
  - Re: [AMBER] Query regarding Dynamics Studies Ruchika Bhat (Fri Feb 06 2015 - 11:04:14 PST)
- Re: [AMBER] Query regarding Dynamics Studies Chris Chris (Fri Feb 06 2015 - 07:22:06 PST)
[AMBER] Assignment of charges for Guanidine Ibrahim Said (Fri Feb 06 2015 - 07:54:14 PST)
- Re: [AMBER] Assignment of charges for Guanidine Daniel Roe (Fri Feb 06 2015 - 08:23:57 PST)
  - Re: [AMBER] Assignment of charges for Guanidine Ibrahim Said (Fri Feb 06 2015 - 11:02:24 PST)
    - Re: [AMBER] Assignment of charges for Guanidine Jason Swails (Fri Feb 06 2015 - 11:19:06 PST)
    - Re: [AMBER] Assignment of charges for Guanidine Ibrahim Said (Sat Feb 07 2015 - 00:16:39 PST)
    - Re: [AMBER] Assignment of charges for Guanidine Jason Swails (Sat Feb 07 2015 - 05:23:20 PST)
    - Re: [AMBER] Assignment of charges for Guanidine Ibrahim Said (Sat Feb 07 2015 - 14:19:32 PST)
    - Re: [AMBER] Assignment of charges for Guanidine Jason Swails (Sat Feb 07 2015 - 16:03:16 PST)
    - Re: [AMBER] Assignment of charges for Guanidine David Case (Sat Feb 07 2015 - 18:03:46 PST)
    - Re: [AMBER] Assignment of charges for Guanidine Ibrahim Said (Sun Feb 08 2015 - 10:01:28 PST)
    - Re: [AMBER] Assignment of charges for Guanidine Jason Swails (Sun Feb 08 2015 - 13:15:08 PST)
    - Re: [AMBER] Assignment of charges for Guanidine Daniel Roe (Sun Feb 08 2015 - 15:42:54 PST)
[AMBER] cis peptide bond Dhiraj Srivastava (Fri Feb 06 2015 - 08:40:34 PST)
- Re: [AMBER] cis peptide bond Carlos Simmerling (Fri Feb 06 2015 - 09:32:53 PST)
  - Re: [AMBER] cis peptide bond Dhiraj Srivastava (Fri Feb 06 2015 - 09:45:17 PST)
    - Re: [AMBER] cis peptide bond Carlos Simmerling (Fri Feb 06 2015 - 10:07:14 PST)
[AMBER] protein falls apart on explicit solvation md Anupam Goel (Fri Feb 06 2015 - 12:04:36 PST)
- Re: [AMBER] protein falls apart on explicit solvation md Daniel Roe (Fri Feb 06 2015 - 12:10:02 PST)
  - Re: [AMBER] protein falls apart on explicit solvation md Anupam Goel (Fri Feb 06 2015 - 12:28:56 PST)
[AMBER] vmd_box_dims.sh Chris Chris (Fri Feb 06 2015 - 20:18:22 PST)
- Re: [AMBER] vmd_box_dims.sh hannes.loeffler.stfc.ac.uk (Sat Feb 07 2015 - 01:12:50 PST)
  - Re: [AMBER] vmd_box_dims.sh Chris Chris (Sat Feb 07 2015 - 08:27:03 PST)
    - Re: [AMBER] vmd_box_dims.sh David Case (Sat Feb 07 2015 - 17:54:09 PST)
  - Re: [AMBER] vmd_box_dims.sh Chris Chris (Sat Feb 07 2015 - 09:57:27 PST)
[AMBER] Strange md and RMSD behavior Hadeer ELHabashy (Sat Feb 07 2015 - 13:22:43 PST)
- Re: [AMBER] Strange md and RMSD behavior Daniel Roe (Sun Feb 08 2015 - 15:39:10 PST)
[AMBER] New web server for setup of membrane simulation systems Jochen Hub (Sun Feb 08 2015 - 03:32:28 PST)
- Re: [AMBER] New web server for setup of membrane simulation systems Jochen Hub (Wed Feb 18 2015 - 02:22:22 PST)
[AMBER] Output Forces Acting of Each Atom During MD Simulation using Amber14 Emmanuel (Sun Feb 08 2015 - 16:05:23 PST)
- Re: [AMBER] Output Forces Acting of Each Atom During MD Simulation using Amber14 Jason Swails (Sun Feb 08 2015 - 18:00:41 PST)
[AMBER] Inexperienced User Trying to Solve Simulation Blowup Robert Molt (Sun Feb 08 2015 - 20:02:03 PST)
- Re: [AMBER] Inexperienced User Trying to Solve Simulation Blowup Jason Swails (Sun Feb 08 2015 - 20:16:24 PST)
[AMBER] Test Andreas Goetz (Mon Feb 09 2015 - 07:41:57 PST)
[AMBER] unexpected behaviour with antechamber Hannes Loeffler (Mon Feb 09 2015 - 08:31:07 PST)
- Re: [AMBER] unexpected behaviour with antechamber David A Case (Mon Feb 09 2015 - 17:46:58 PST)
  - [AMBER] Disentangling domains mmaestre (Tue Feb 10 2015 - 01:17:04 PST)
  - Re: [AMBER] unexpected behaviour with antechamber Hannes Loeffler (Tue Feb 10 2015 - 01:24:30 PST)
  - Re: [AMBER] unexpected behaviour with antechamber Hannes Loeffler (Wed Feb 11 2015 - 02:18:34 PST)
    - Re: [AMBER] unexpected behaviour with antechamber David A Case (Wed Feb 11 2015 - 04:54:25 PST)
[AMBER] Average Internal Coordinates in cpptraj Dr. Robert Molt Jr. (Mon Feb 09 2015 - 08:37:52 PST)
- Re: [AMBER] Average Internal Coordinates in cpptraj Carlos Simmerling (Mon Feb 09 2015 - 08:49:17 PST)
  - Re: [AMBER] Average Internal Coordinates in cpptraj Dr. Robert Molt Jr. (Mon Feb 09 2015 - 08:50:17 PST)
[AMBER] How to find out buried waters? Jose Borreguero (Mon Feb 09 2015 - 12:40:35 PST)
- Re: [AMBER] How to find out buried waters? Jason Swails (Mon Feb 09 2015 - 13:25:08 PST)
  - Re: [AMBER] How to find out buried waters? Jose Borreguero (Mon Feb 09 2015 - 14:45:52 PST)
[AMBER] memory issue in mmpbsa_py_nabnmode Marek Maly (Mon Feb 09 2015 - 15:54:20 PST)
- Re: [AMBER] memory issue in mmpbsa_py_nabnmode David A Case (Mon Feb 09 2015 - 17:28:37 PST)
  - Re: [AMBER] memory issue in mmpbsa_py_nabnmode Jason Swails (Mon Feb 09 2015 - 19:51:23 PST)
    - Re: [AMBER] memory issue in mmpbsa_py_nabnmode Marek Maly (Tue Feb 10 2015 - 07:49:44 PST)
    - Re: [AMBER] memory issue in mmpbsa_py_nabnmode Jason Swails (Thu Feb 12 2015 - 05:48:49 PST)
    - Re: [AMBER] memory issue in mmpbsa_py_nabnmode Marek Maly (Thu Feb 12 2015 - 14:14:51 PST)
    - Re: [AMBER] memory issue in mmpbsa_py_nabnmode Jason Swails (Thu Feb 12 2015 - 14:44:14 PST)
    - Re: [AMBER] memory issue in mmpbsa_py_nabnmode Marek Maly (Thu Feb 12 2015 - 15:00:29 PST)
- Re: [AMBER] memory issue in mmpbsa_py_nabnmode Marek Maly (Tue Feb 17 2015 - 07:30:02 PST)
  - Re: [AMBER] memory issue in mmpbsa_py_nabnmode Jason Swails (Tue Feb 17 2015 - 10:17:35 PST)
    - Re: [AMBER] memory issue in mmpbsa_py_nabnmode Jason Swails (Tue Feb 17 2015 - 10:18:56 PST)
    - Re: [AMBER] memory issue in mmpbsa_py_nabnmode Marek Maly (Tue Feb 17 2015 - 12:09:52 PST)
    - Re: [AMBER] memory issue in mmpbsa_py_nabnmode Jason Swails (Tue Feb 17 2015 - 13:21:43 PST)
    - Re: [AMBER] memory issue in mmpbsa_py_nabnmode Marek Maly (Tue Feb 17 2015 - 13:42:17 PST)
    - Re: [AMBER] memory issue in mmpbsa_py_nabnmode Jason Swails (Tue Feb 17 2015 - 16:15:37 PST)
    - Re: [AMBER] memory issue in mmpbsa_py_nabnmode Marek Maly (Tue Feb 17 2015 - 18:18:22 PST)
    - Re: [AMBER] memory issue in mmpbsa_py_nabnmode Jason Swails (Tue Feb 17 2015 - 18:58:18 PST)
    - Re: [AMBER] memory issue in mmpbsa_py_nabnmode Marek Maly (Fri Feb 20 2015 - 06:48:51 PST)
[AMBER] On the crushing of the membrane protein simulation James Starlight (Tue Feb 10 2015 - 07:44:01 PST)
- Re: [AMBER] On the crushing of the membrane protein simulation Ross Walker (Tue Feb 10 2015 - 09:06:38 PST)
  - Re: [AMBER] On the crushing of the membrane protein simulation James Starlight (Tue Feb 10 2015 - 09:31:00 PST)
[AMBER] antechamber error Harmeet Kaur (Tue Feb 10 2015 - 23:07:13 PST)
- Re: [AMBER] antechamber error hannes.loeffler.stfc.ac.uk (Wed Feb 11 2015 - 00:14:56 PST)
[AMBER] Fwd: MMPBSA a.mohseni (Wed Feb 11 2015 - 00:59:55 PST)
- Re: [AMBER] Fwd: MMPBSA Jason Swails (Wed Feb 11 2015 - 04:03:22 PST)
  - Re: [AMBER] Fwd: MMPBSA Ray Luo, Ph.D. (Wed Feb 11 2015 - 13:32:14 PST)
[AMBER] calculating HB lifetime Vijay Achari (Wed Feb 11 2015 - 02:18:08 PST)
- Re: [AMBER] calculating HB lifetime Daniel Roe (Wed Feb 11 2015 - 08:44:05 PST)
  - Re: [AMBER] calculating HB lifetime Vijay Achari (Wed Feb 11 2015 - 09:35:50 PST)
    - Re: [AMBER] calculating HB lifetime Daniel Roe (Wed Feb 11 2015 - 10:21:56 PST)
    - Re: [AMBER] calculating HB lifetime Vijay Achari (Wed Feb 11 2015 - 17:32:23 PST)
    - Re: [AMBER] calculating HB lifetime Daniel Roe (Wed Feb 11 2015 - 21:46:16 PST)
    - Re: [AMBER] calculating HB lifetime Vijay Achari (Thu Feb 12 2015 - 00:09:58 PST)
    - Re: [AMBER] calculating HB lifetime Vijay Achari (Thu Feb 12 2015 - 01:19:13 PST)
    - Re: [AMBER] calculating HB lifetime Daniel Roe (Thu Feb 12 2015 - 06:51:52 PST)
    - Re: [AMBER] calculating HB lifetime Daniel Roe (Thu Feb 12 2015 - 07:06:44 PST)
    - Re: [AMBER] calculating HB lifetime Vijay Achari (Thu Feb 12 2015 - 07:28:08 PST)
    - Re: [AMBER] calculating HB lifetime Vijay Achari (Thu Feb 12 2015 - 07:37:13 PST)
    - Re: [AMBER] calculating HB lifetime Daniel Roe (Thu Feb 12 2015 - 07:40:24 PST)
    - Re: [AMBER] calculating HB lifetime Vijay Achari (Mon Mar 09 2015 - 23:52:03 PDT)
    - Re: [AMBER] calculating HB lifetime Vijay Achari (Thu Feb 12 2015 - 07:19:12 PST)
    - Re: [AMBER] calculating HB lifetime Daniel Roe (Thu Feb 12 2015 - 07:22:42 PST)
    - Re: [AMBER] calculating HB lifetime Vijay Achari (Thu Feb 12 2015 - 07:39:18 PST)
[AMBER] Density equilibration crash in cuda Kshatresh Dutta Dubey (Wed Feb 11 2015 - 03:36:33 PST)
- Re: [AMBER] Density equilibration crash in cuda Jason Swails (Wed Feb 11 2015 - 04:05:55 PST)
  - Re: [AMBER] Density equilibration crash in cuda Kshatresh Dutta Dubey (Wed Feb 11 2015 - 04:09:57 PST)
    - Re: [AMBER] Density equilibration crash in cuda Jason Swails (Wed Feb 11 2015 - 04:41:16 PST)
[AMBER] Number of molecules for md calculations Ibrahim Said (Wed Feb 11 2015 - 08:57:30 PST)
[AMBER] list of atomic coordinates involved in solvent accessible area Iqbal, Muhammad Sajid (Wed Feb 11 2015 - 14:26:51 PST)
- Re: [AMBER] list of atomic coordinates involved in solvent accessible area David A Case (Wed Feb 11 2015 - 19:36:26 PST)
[AMBER] alkynes in GAFF Rebeca García Fandiño (Thu Feb 12 2015 - 01:42:06 PST)
- Re: [AMBER] alkynes in GAFF David A Case (Thu Feb 12 2015 - 04:27:32 PST)
  - Re: [AMBER] alkynes in GAFF Rebeca García Fandiño (Thu Feb 12 2015 - 04:56:46 PST)
  - Re: [AMBER] alkynes in GAFF Rebeca García Fandiño (Thu Feb 12 2015 - 13:51:40 PST)
[AMBER] aMD and scaled MD in amber 14 Neha Gandhi (Thu Feb 12 2015 - 04:59:24 PST)
[AMBER] MMPBSA - standard deviation (again) George Tzotzos (Thu Feb 12 2015 - 06:29:04 PST)
- Re: [AMBER] MMPBSA - standard deviation (again) Jason Swails (Thu Feb 12 2015 - 06:49:15 PST)
  - Re: [AMBER] MMPBSA - standard deviation (again) George Tzotzos (Thu Feb 12 2015 - 07:29:31 PST)
    - Re: [AMBER] MMPBSA - standard deviation (again) Jason Swails (Thu Feb 12 2015 - 08:56:18 PST)
[AMBER] Announcement: Release of DOCK 6.7 Scott Brozell (Thu Feb 12 2015 - 16:27:51 PST)
[AMBER] Water diffusion - in 2D and 3D Vijay Achari (Thu Feb 12 2015 - 22:11:24 PST)
- Re: [AMBER] Water diffusion - in 2D and 3D hannes.loeffler.stfc.ac.uk (Fri Feb 13 2015 - 00:28:28 PST)
  - Re: [AMBER] Water diffusion - in 2D and 3D Vijay Achari (Fri Feb 13 2015 - 02:04:02 PST)
    - Re: [AMBER] Water diffusion - in 2D and 3D Hannes Loeffler (Fri Feb 13 2015 - 02:20:55 PST)
    - Re: [AMBER] Water diffusion - in 2D and 3D Vijay Achari (Fri Feb 13 2015 - 02:42:07 PST)
[AMBER] hbond analysis Ayesha Fatima (Thu Feb 12 2015 - 23:48:42 PST)
- Re: [AMBER] hbond analysis Jason Swails (Fri Feb 13 2015 - 02:04:55 PST)
  - Re: [AMBER] hbond analysis Ayesha Fatima (Fri Feb 13 2015 - 06:40:21 PST)
    - Re: [AMBER] hbond analysis Ayesha Fatima (Sat Feb 14 2015 - 04:28:05 PST)
[AMBER] rotational diffusion Vijay Achari (Fri Feb 13 2015 - 03:00:08 PST)
- Re: [AMBER] rotational diffusion Daniel Roe (Sun Feb 15 2015 - 08:51:51 PST)
[AMBER] assignment of Water molecules Ibrahim Said (Fri Feb 13 2015 - 04:13:47 PST)
- Re: [AMBER] assignment of Water molecules David A Case (Fri Feb 13 2015 - 09:25:36 PST)
[AMBER] Umbrella Sampling Mahmood Jasim (Fri Feb 13 2015 - 04:36:08 PST)
[AMBER] d 김준기 (Fri Feb 13 2015 - 07:26:27 PST)
- Re: [AMBER] d Jason Swails (Fri Feb 13 2015 - 13:46:37 PST)
  - Re: [AMBER] d Lachele Foley (Fri Feb 13 2015 - 22:51:08 PST)
[AMBER] Error: Restart File Corrupted Edward Kalkreuter (Fri Feb 13 2015 - 10:03:10 PST)
- Re: [AMBER] Error: Restart File Corrupted Daniel Roe (Fri Feb 13 2015 - 12:32:35 PST)
[AMBER] angles values in GAFF for alkynes Rebeca García Fandiño (Fri Feb 13 2015 - 10:19:12 PST)
- Re: [AMBER] angles values in GAFF for alkynes hannes.loeffler.stfc.ac.uk (Fri Feb 13 2015 - 10:40:35 PST)
  - Re: [AMBER] angles values in GAFF for alkynes Rebeca García Fandiño (Fri Feb 13 2015 - 10:47:39 PST)
    - Re: [AMBER] angles values in GAFF for alkynes hannes.loeffler.stfc.ac.uk (Fri Feb 13 2015 - 11:28:49 PST)
[AMBER] csv file for DPC Sylvester Tumusiime (Fri Feb 13 2015 - 12:41:39 PST)
[AMBER] pmemd.cuda error cudaMemcpy GpuBuffer:: BERGY (Fri Feb 13 2015 - 22:38:35 PST)
- Re: [AMBER] pmemd.cuda error cudaMemcpy GpuBuffer:: Ross Walker (Sat Feb 14 2015 - 05:49:46 PST)
  - Re: [AMBER] pmemd.cuda error cudaMemcpy GpuBuffer:: BERGY (Sat Feb 14 2015 - 09:43:50 PST)
    - Re: [AMBER] pmemd.cuda error cudaMemcpy GpuBuffer:: Ross Walker (Sat Feb 14 2015 - 10:38:53 PST)
    - Re: [AMBER] pmemd.cuda error cudaMemcpy GpuBuffer:: BERGY (Tue Feb 17 2015 - 10:56:44 PST)
    - Re: [AMBER] pmemd.cuda error cudaMemcpy GpuBuffer:: David A Case (Thu Feb 19 2015 - 05:03:06 PST)
[AMBER] pbsa zahra khatti (Sat Feb 14 2015 - 21:31:46 PST)
- Re: [AMBER] pbsa Jason Swails (Sun Feb 15 2015 - 05:37:39 PST)
  - Re: [AMBER] pbsa zahra khatti (Sun Feb 15 2015 - 06:48:24 PST)
    - Re: [AMBER] pbsa zahra khatti (Sun Feb 15 2015 - 09:44:13 PST)
[AMBER] Question about hbond analysis 徐晓庶 (Sat Feb 14 2015 - 23:06:51 PST)
- Re: [AMBER] Question about hbond analysis Daniel Roe (Sun Feb 15 2015 - 08:36:16 PST)
[AMBER] pressure fluctuation problem Aditya Sarkar (Sun Feb 15 2015 - 00:05:10 PST)
- Re: [AMBER] pressure fluctuation problem Jason Swails (Sun Feb 15 2015 - 05:35:20 PST)
- Re: [AMBER] pressure fluctuation problem Aditya Sarkar (Mon Feb 16 2015 - 04:25:16 PST)
  - Re: [AMBER] pressure fluctuation problem Jason Swails (Mon Feb 16 2015 - 05:25:57 PST)
[AMBER] pbsa zahra khatti (Sun Feb 15 2015 - 10:53:34 PST)
- Re: [AMBER] pbsa David A Case (Sun Feb 15 2015 - 14:40:17 PST)
[AMBER] amber14 hangs on Python datetime module Robert Wohlhueter (Sun Feb 15 2015 - 11:06:55 PST)
- Re: [AMBER] amber14 hangs on Python datetime module Novosielski, Ryan (Sun Feb 15 2015 - 11:53:24 PST)
  - Re: [AMBER] amber14 hangs on Python datetime module Robert Wohlhueter (Sun Feb 15 2015 - 12:13:12 PST)
  - Re: [AMBER] amber14 hangs on Python datetime module Robert Wohlhueter (Sun Feb 15 2015 - 12:34:05 PST)
  - Re: [AMBER] amber14 hangs on Python datetime module Robert Wohlhueter (Sun Feb 15 2015 - 12:36:53 PST)
    - Re: [AMBER] amber14 hangs on Python datetime module Jason Swails (Sun Feb 15 2015 - 13:28:50 PST)
[AMBER] Could not find vdW (or other) parameters for type: Fe2+ Pragya Priyadarshini (Sun Feb 15 2015 - 19:45:46 PST)
- Re: [AMBER] Could not find vdW (or other) parameters for type: Fe2+(Problem Solved) Pragya Priyadarshini (Sun Feb 15 2015 - 23:18:42 PST)
[AMBER] dont have atom type Fatemeh Sadat Alavi (Mon Feb 16 2015 - 04:44:10 PST)
- Re: [AMBER] dont have atom type Jason Swails (Mon Feb 16 2015 - 05:32:49 PST)
[AMBER] AMBER: MPI run issue Bajarang Kumbhar (Mon Feb 16 2015 - 05:38:31 PST)
- Re: [AMBER] AMBER: MPI run issue Jason Swails (Mon Feb 16 2015 - 06:15:05 PST)
[AMBER] combining trajectories Ayesha Fatima (Mon Feb 16 2015 - 06:29:05 PST)
- Re: [AMBER] combining trajectories Daniel Roe (Mon Feb 16 2015 - 08:25:02 PST)
- Re: [AMBER] combining trajectories Mahmood Jasim (Mon Feb 16 2015 - 08:39:28 PST)
  - Re: [AMBER] combining trajectories Daniel Roe (Mon Feb 16 2015 - 09:00:14 PST)
    - Re: [AMBER] combining trajectories Ayesha Fatima (Mon Feb 16 2015 - 09:58:33 PST)
    - Re: [AMBER] combining trajectories Daniel Roe (Mon Feb 16 2015 - 10:53:20 PST)
    - Re: [AMBER] combining trajectories Vijay Achari (Mon Feb 16 2015 - 21:12:58 PST)
    - Re: [AMBER] combining trajectories Ayesha Fatima (Mon Feb 16 2015 - 22:19:31 PST)
    - Re: [AMBER] combining trajectories Daniel Roe (Tue Feb 17 2015 - 00:35:02 PST)
    - [AMBER] Problems with COM distance restraints plus positional restraints using pmemd.cuda mmaestre (Tue Feb 17 2015 - 01:27:08 PST)
[AMBER] torsion restrain Lara rajam (Mon Feb 16 2015 - 07:16:20 PST)
[AMBER] reweighing aMD trajectory Asmita Gupta (Mon Feb 16 2015 - 07:46:43 PST)
- Re: [AMBER] reweighing aMD trajectory Jason Swails (Mon Feb 16 2015 - 10:03:37 PST)
[AMBER] MMGBSA question George Tzotzos (Mon Feb 16 2015 - 11:11:28 PST)
- Re: [AMBER] MMGBSA question Jason Swails (Mon Feb 16 2015 - 13:51:57 PST)
[AMBER] MMGBSA question George Tzotzos (Mon Feb 16 2015 - 11:53:26 PST)
[AMBER] Announcement: "Hands-On" Workshop on Computational Biophysics in Urbana, IL (April 6-10, 2015) Jodi Ann Hadden (Mon Feb 16 2015 - 13:41:55 PST)
[AMBER] solute-solvent hbond fraction value is more than 1.0 Vijay Achari (Mon Feb 16 2015 - 23:14:55 PST)
- Re: [AMBER] solute-solvent hbond fraction value is more than 1.0 Daniel Roe (Tue Feb 17 2015 - 09:20:35 PST)
  - Re: [AMBER] solute-solvent hbond fraction value is more than 1.0 Vijay Achari (Tue Feb 17 2015 - 20:37:34 PST)
[AMBER] Regarding AmberTool 14 installation MOHD HOMAIDUR RAHMAN (Tue Feb 17 2015 - 00:08:40 PST)
- Re: [AMBER] Regarding AmberTool 14 installation Jason Swails (Tue Feb 17 2015 - 06:54:53 PST)
- Re: [AMBER] Regarding AmberTool 14 installation David A Case (Tue Feb 17 2015 - 07:00:25 PST)
  - Re: [AMBER] Regarding AmberTool 14 installation Setyanto Md (Mon Sep 07 2015 - 22:03:50 PDT)
    - Re: [AMBER] Regarding AmberTool 14 installation MOHD HOMAIDUR RAHMAN (Mon Sep 07 2015 - 22:32:16 PDT)
    - Re: [AMBER] Regarding AmberTool 14 installation Setyanto Md (Mon Sep 07 2015 - 22:44:40 PDT)
    - Re: [AMBER] Regarding AmberTool 14 installation MOHD HOMAIDUR RAHMAN (Tue Sep 08 2015 - 00:37:10 PDT)
    - Re: [AMBER] Regarding AmberTool 14 installation Setyanto Md (Tue Sep 08 2015 - 01:42:55 PDT)
[AMBER] [MGMS-DS]: Molecular Modelling Workshop March 9-11, 2015 in Erlangen, Germany Harald Lanig (Tue Feb 17 2015 - 06:10:03 PST)
[AMBER] Question regarding the calculation of binding constants Kornelius Zeth (Tue Feb 17 2015 - 07:17:06 PST)
- Re: [AMBER] Question regarding the calculation of binding constants David A Case (Wed Feb 18 2015 - 07:41:18 PST)
[AMBER] Can cpptraj-hbond report the lifetimes of H-bonds between protein and water? Jose Borreguero (Tue Feb 17 2015 - 07:57:46 PST)
- Re: [AMBER] Can cpptraj-hbond report the lifetimes of H-bonds between protein and water? Daniel Roe (Tue Feb 17 2015 - 09:45:27 PST)
  - Re: [AMBER] Can cpptraj-hbond report the lifetimes of H-bonds between protein and water? Jose Borreguero (Tue Feb 17 2015 - 12:36:41 PST)
[AMBER] Invitation to Attend Computational Chemical Biology Conference (Aug 6th to 9th 2015), Cairns, Australia (http://tinyurl.com/nyblv7o) Ross Walker (Tue Feb 17 2015 - 08:26:26 PST)
[AMBER] MMPBSA pairwise decomposition error George Tzotzos (Tue Feb 17 2015 - 12:00:34 PST)
[AMBER] Simulations in CCl4 pradeep pant (Tue Feb 17 2015 - 23:14:38 PST)
- [AMBER] Fwd: Simulations in CCl4 pradeep pant (Wed Feb 18 2015 - 04:25:21 PST)
- Re: [AMBER] Simulations in CCl4 David A Case (Wed Feb 18 2015 - 06:13:54 PST)
[AMBER] Distance/Angle distribution along the trajectory using cpptraj James Starlight (Wed Feb 18 2015 - 01:51:28 PST)
- Re: [AMBER] Distance/Angle distribution along the trajectory using cpptraj Nhai (Wed Feb 18 2015 - 02:50:50 PST)
  - Re: [AMBER] Distance/Angle distribution along the trajectory using cpptraj James Starlight (Wed Feb 18 2015 - 02:53:15 PST)
    - Re: [AMBER] Distance/Angle distribution along the trajectory using cpptraj Parker de Waal (Wed Feb 18 2015 - 05:08:44 PST)
- Re: [AMBER] Distance/Angle distribution along the trajectory using cpptraj Daniel Roe (Wed Feb 18 2015 - 05:31:18 PST)
[AMBER] restraining the torsion Lara rajam (Wed Feb 18 2015 - 07:03:09 PST)
- Re: [AMBER] restraining the torsion David A Case (Wed Feb 18 2015 - 07:35:10 PST)
[AMBER] cpptraj hbond analysis Ayesha Fatima (Wed Feb 18 2015 - 07:42:28 PST)
- Re: [AMBER] cpptraj hbond analysis Daniel Roe (Wed Feb 18 2015 - 08:24:35 PST)
[AMBER] Forces from Potential Ahmed Ayoub (Wed Feb 18 2015 - 08:39:13 PST)
- Re: [AMBER] Forces from Potential Jason Swails (Wed Feb 18 2015 - 09:39:34 PST)
[AMBER] Help creating custom monosaccharide unit in Glycam Gustavo Seabra (Wed Feb 18 2015 - 10:54:40 PST)
- Re: [AMBER] Help creating custom monosaccharide unit in Glycam Lachele Foley (Wed Feb 18 2015 - 19:16:23 PST)
  - Re: [AMBER] Help creating custom monosaccharide unit in Glycam Gustavo Seabra (Thu Feb 19 2015 - 03:42:38 PST)
    - Re: [AMBER] Help creating custom monosaccharide unit in Glycam Lachele Foley (Fri Feb 20 2015 - 10:39:34 PST)
    - Re: [AMBER] Help creating custom monosaccharide unit in Glycam Gustavo Seabra (Fri Feb 20 2015 - 11:23:30 PST)
[AMBER] Bad atom type error in MMPBSA Kenneth Huang (Wed Feb 18 2015 - 13:02:48 PST)
- Re: [AMBER] Bad atom type error in MMPBSA Jason Swails (Wed Feb 18 2015 - 14:09:11 PST)
  - Re: [AMBER] Bad atom type error in MMPBSA Kenneth Huang (Thu Feb 19 2015 - 09:51:55 PST)
[AMBER] problem with RMSD for small molecule Maryam Hamzehee (Thu Feb 19 2015 - 01:45:06 PST)
- Re: [AMBER] problem with RMSD for small molecule David A Case (Thu Feb 19 2015 - 04:58:40 PST)
- Re: [AMBER] problem with RMSD for small molecule Daniel Roe (Thu Feb 19 2015 - 08:12:50 PST)
[AMBER] cpptraj hbond analysis Ayesha Fatima (Thu Feb 19 2015 - 01:59:46 PST)
[AMBER] rmsavgcorr Jacopo Sgrignani (Thu Feb 19 2015 - 07:46:17 PST)
- Re: [AMBER] rmsavgcorr Daniel Roe (Thu Feb 19 2015 - 08:11:34 PST)
[AMBER] Help calculating RMSD between two proteins Nicole Ippolito (Thu Feb 19 2015 - 10:09:29 PST)
- Re: [AMBER] Help calculating RMSD between two proteins Kenneth Huang (Thu Feb 19 2015 - 11:00:03 PST)
- Re: [AMBER] Help calculating RMSD between two proteins Hai Nguyen (Thu Feb 19 2015 - 11:55:20 PST)
- Re: [AMBER] Help calculating RMSD between two proteins Daniel Roe (Thu Feb 19 2015 - 12:00:43 PST)
  - Re: [AMBER] Help calculating RMSD between two proteins Nicole Ippolito (Thu Feb 19 2015 - 13:20:33 PST)
    - Re: [AMBER] Help calculating RMSD between two proteins Hai Nguyen (Thu Feb 19 2015 - 13:28:09 PST)
    - Re: [AMBER] Help calculating RMSD between two proteins Jason Swails (Thu Feb 19 2015 - 13:38:59 PST)
    - Re: [AMBER] Help calculating RMSD between two proteins Daniel Roe (Thu Feb 19 2015 - 13:43:34 PST)
[AMBER] ired t1 relaxation time Khanna, Tarun (Thu Feb 19 2015 - 10:56:57 PST)
[AMBER] ANTECHAMBER: error in mol2 file Valentina Romano (Fri Feb 20 2015 - 01:59:45 PST)
- Re: [AMBER] ANTECHAMBER: error in mol2 file hannes.loeffler.stfc.ac.uk (Fri Feb 20 2015 - 03:05:29 PST)
  - Re: [AMBER] ANTECHAMBER: error in mol2 file Valentina Romano (Fri Feb 20 2015 - 03:56:49 PST)
    - Re: [AMBER] ANTECHAMBER: error in mol2 file hannes.loeffler.stfc.ac.uk (Fri Feb 20 2015 - 04:12:13 PST)
[AMBER] Error while running tleap for the ligand containing two chlorine atoms Shreeramesh (Fri Feb 20 2015 - 02:58:03 PST)
- Re: [AMBER] Error while running tleap for the ligand containing two chlorine atoms hannes.loeffler.stfc.ac.uk (Fri Feb 20 2015 - 03:13:31 PST)
  - Re: [AMBER] Error while running tleap for the ligand containing two chlorine atoms Shreeramesh (Fri Feb 20 2015 - 03:23:44 PST)
    - Re: [AMBER] Error while running tleap for the ligand containing two chlorine atoms hannes.loeffler.stfc.ac.uk (Fri Feb 20 2015 - 03:39:04 PST)
    - Re: [AMBER] Error while running tleap for the ligand containing two chlorine atoms Shreeramesh (Fri Feb 20 2015 - 04:33:05 PST)
    - Re: [AMBER] Error while running tleap for the ligand containing two chlorine atoms hannes.loeffler.stfc.ac.uk (Fri Feb 20 2015 - 05:07:26 PST)
    - Re: [AMBER] Error while running tleap for the ligand containing two chlorine atoms Jason Swails (Fri Feb 20 2015 - 05:08:12 PST)
    - Re: [AMBER] Error while running tleap for the ligand containing two chlorine atoms David A Case (Fri Feb 20 2015 - 05:24:50 PST)
    - Re: [AMBER] Error while running tleap for the ligand containing two chlorine atoms Jason Swails (Fri Feb 20 2015 - 05:34:06 PST)
    - Re: [AMBER] Error while running tleap for the ligand containing two chlorine atoms David A Case (Fri Feb 20 2015 - 07:38:47 PST)
    - Re: [AMBER] Error while running tleap for the ligand containing two chlorine atoms David A Case (Fri Feb 20 2015 - 07:40:16 PST)
    - Re: [AMBER] Error while running tleap for the ligand containing two chlorine atoms Jason Swails (Fri Feb 20 2015 - 07:48:24 PST)
    - Re: [AMBER] Error while running tleap for the ligand containing two chlorine atoms Shreeramesh (Sat Feb 21 2015 - 07:29:47 PST)
    - Re: [AMBER] Error while running tleap for the ligand containing two chlorine atoms Shreeramesh (Sat Feb 21 2015 - 07:41:08 PST)
    - Re: [AMBER] Error while running tleap for the ligand containing two chlorine atoms Jason Swails (Sat Feb 21 2015 - 09:32:29 PST)
[AMBER] Lipid14 POPE lipids Joseph Baker (Fri Feb 20 2015 - 04:42:09 PST)
- Re: [AMBER] Lipid14 POPE lipids Gould, Ian R (Fri Feb 20 2015 - 06:31:26 PST)
- Re: [AMBER] Lipid14 POPE lipids Ross Walker (Fri Feb 20 2015 - 12:58:21 PST)
  - Re: [AMBER] Lipid14 POPE lipids Joseph Baker (Fri Feb 27 2015 - 08:29:45 PST)
    - Re: [AMBER] Lipid14 POPE lipids Ross Walker (Fri Feb 27 2015 - 08:58:09 PST)
    - Re: [AMBER] Lipid14 POPE lipids Joseph Baker (Tue Mar 10 2015 - 10:08:57 PDT)
    - Re: [AMBER] Lipid14 POPE lipids Jason Swails (Tue Mar 10 2015 - 11:06:49 PDT)
[AMBER] Sander in background Valentina Romano (Fri Feb 20 2015 - 05:36:28 PST)
- Re: [AMBER] Sander in background Jason Swails (Fri Feb 20 2015 - 05:42:52 PST)
[AMBER] hbond analysis Ayesha Fatima (Fri Feb 20 2015 - 05:37:40 PST)
- Re: [AMBER] hbond analysis Daniel Roe (Fri Feb 20 2015 - 12:59:29 PST)
  - Re: [AMBER] hbond analysis Ayesha Fatima (Sat Feb 21 2015 - 08:39:13 PST)
[AMBER] LIPID14 and ff15SB Ghulam Mustafa (Fri Feb 20 2015 - 09:06:35 PST)
[AMBER] Solvent Box Wrapping Issue Zhang, Sixue (Fri Feb 20 2015 - 13:04:43 PST)
- Re: [AMBER] Solvent Box Wrapping Issue Daniel Roe (Fri Feb 20 2015 - 13:11:57 PST)
- Re: [AMBER] Solvent Box Wrapping Issue Bill Ross (Fri Feb 20 2015 - 14:02:00 PST)
  - Re: [AMBER] Solvent Box Wrapping Issue Zhang, Sixue (Sat Feb 21 2015 - 09:21:32 PST)
    - Re: [AMBER] Solvent Box Wrapping Issue Jonathan Sheehan (Sat Feb 21 2015 - 14:03:39 PST)
    - Re: [AMBER] Solvent Box Wrapping Issue David A Case (Sun Feb 22 2015 - 13:12:35 PST)
[AMBER] vlimit exceeded for step Fatemeh Sadat Alavi (Sat Feb 21 2015 - 03:51:15 PST)
- Re: [AMBER] vlimit exceeded for step Jason Swails (Sat Feb 21 2015 - 12:30:30 PST)
[AMBER] Error: Expected DCD block size of 48, got -1029941464 Thomas Evangelidis (Sat Feb 21 2015 - 13:06:03 PST)
- Re: [AMBER] Error: Expected DCD block size of 48, got -1029941464 Thomas Evangelidis (Sat Feb 21 2015 - 13:21:06 PST)
  - Re: [AMBER] Error: Expected DCD block size of 48, got -1029941464 Daniel Roe (Sat Feb 21 2015 - 13:50:10 PST)
    - Re: [AMBER] Error: Expected DCD block size of 48, got -1029941464 Thomas Evangelidis (Sat Feb 21 2015 - 16:04:48 PST)
    - Re: [AMBER] Error: Expected DCD block size of 48, got -1029941464 Daniel Roe (Mon Feb 23 2015 - 07:38:53 PST)
    - Re: [AMBER] Error: Expected DCD block size of 48, got -1029941464 Thomas Evangelidis (Mon Feb 23 2015 - 09:16:24 PST)
[AMBER] rms: Warning: [rms] Not all arguments handled: [ rmsd.agr ] George Tzotzos (Sat Feb 21 2015 - 13:14:45 PST)
- Re: [AMBER] rms: Warning: [rms] Not all arguments handled: [ rmsd.agr ] Daniel Roe (Sat Feb 21 2015 - 13:39:48 PST)
  - Re: [AMBER] rms: Warning: [rms] Not all arguments handled: [ rmsd.agr ] George Tzotzos (Sat Feb 21 2015 - 13:57:18 PST)
    - Re: [AMBER] rms: Warning: [rms] Not all arguments handled: [ rmsd.agr ] George Tzotzos (Sat Feb 21 2015 - 16:05:21 PST)
[AMBER] cpptraj hbond lifetime problem Ayesha Fatima (Sun Feb 22 2015 - 01:59:56 PST)
- Re: [AMBER] cpptraj hbond lifetime problem Daniel Roe (Sun Feb 22 2015 - 07:58:12 PST)
[AMBER] A tool to analyze amberesults Valentina Romano (Sun Feb 22 2015 - 06:56:15 PST)
- Re: [AMBER] A tool to analyze amberesults Jason Swails (Sun Feb 22 2015 - 06:58:39 PST)
[AMBER] Problem in generating CCL4 solvent Box pradeep pant (Sun Feb 22 2015 - 10:02:44 PST)
- Re: [AMBER] Problem in generating CCL4 solvent Box David A Case (Sun Feb 22 2015 - 13:16:54 PST)
  - Re: [AMBER] Problem in generating CCL4 solvent Box pradeep pant (Sun Feb 22 2015 - 23:05:52 PST)
    - Re: [AMBER] Problem in generating CCL4 solvent Box Jason Swails (Mon Feb 23 2015 - 03:21:40 PST)
[AMBER] Fwd: Amber tleap error Garisekurthi Satheesh (Sun Feb 22 2015 - 19:30:09 PST)
- Re: [AMBER] Fwd: Amber tleap error David A Case (Mon Feb 23 2015 - 05:47:30 PST)
  - Re: [AMBER] Fwd: Amber tleap error Garisekurthi Satheesh (Mon Feb 23 2015 - 21:01:41 PST)
[AMBER] RV: segmentation fault when running parmchk belen nieto (Mon Feb 23 2015 - 02:45:43 PST)
- Re: [AMBER] RV: segmentation fault when running parmchk Hannes Loeffler (Mon Feb 23 2015 - 02:59:33 PST)
[AMBER] Help in choosing right MD tool anu chandra (Mon Feb 23 2015 - 04:09:04 PST)
- Re: [AMBER] Help in choosing right MD tool David A Case (Mon Feb 23 2015 - 07:29:35 PST)
  - Re: [AMBER] Help in choosing right MD tool anu chandra (Tue Feb 24 2015 - 04:22:24 PST)
    - Re: [AMBER] Help in choosing right MD tool David A Case (Tue Feb 24 2015 - 14:37:55 PST)
[AMBER] atomicfluct issue George Tzotzos (Mon Feb 23 2015 - 05:30:04 PST)
- Re: [AMBER] atomicfluct issue Vlad Cojocaru (Mon Feb 23 2015 - 05:56:42 PST)
- Re: [AMBER] atomicfluct issue Daniel Roe (Mon Feb 23 2015 - 07:31:38 PST)
[AMBER] Regarding ff02 force field and RESP method documentation Martin Olsson (Mon Feb 23 2015 - 07:50:13 PST)
- Re: [AMBER] Regarding ff02 force field and RESP method documentation David A Case (Mon Feb 23 2015 - 08:31:18 PST)
[AMBER] how to find out if a prmtop file was created with ff12 or ff14 Thomas Evangelidis (Mon Feb 23 2015 - 08:27:37 PST)
- Re: [AMBER] how to find out if a prmtop file was created with ff12 or ff14 Jason Swails (Mon Feb 23 2015 - 09:41:47 PST)
- Re: [AMBER] how to find out if a prmtop file was created with ff12 or ff14 David A Case (Mon Feb 23 2015 - 10:01:36 PST)
[AMBER] cpptraj: H-bond clarification sought George Tzotzos (Mon Feb 23 2015 - 10:12:33 PST)
- Re: [AMBER] cpptraj: H-bond clarification sought Daniel Roe (Mon Feb 23 2015 - 10:30:33 PST)
  - Re: [AMBER] cpptraj: H-bond clarification sought George Tzotzos (Mon Feb 23 2015 - 10:40:16 PST)
[AMBER] Create a unit of mixture Ibrahim Said (Mon Feb 23 2015 - 10:56:59 PST)
- Re: [AMBER] Create a unit of mixture David A Case (Tue Feb 24 2015 - 14:42:38 PST)
[AMBER] Steered MD using the jar=1 option Joseph Baker (Mon Feb 23 2015 - 14:07:08 PST)
- Re: [AMBER] Steered MD using the jar=1 option Adrian Roitberg (Mon Feb 23 2015 - 14:13:31 PST)
  - Re: [AMBER] Steered MD using the jar=1 option Joseph Baker (Mon Feb 23 2015 - 14:32:46 PST)
    - Re: [AMBER] Steered MD using the jar=1 option Adrian Roitberg (Mon Feb 23 2015 - 14:35:56 PST)
    - Re: [AMBER] Steered MD using the jar=1 option Joseph Baker (Mon Feb 23 2015 - 15:20:52 PST)
    - Re: [AMBER] Steered MD using the jar=1 option Jason Swails (Tue Feb 24 2015 - 04:40:19 PST)
    - Re: [AMBER] Steered MD using the jar=1 option Joseph Baker (Thu Feb 26 2015 - 15:13:44 PST)
    - Re: [AMBER] Steered MD using the jar=1 option Adrian Roitberg (Fri Feb 27 2015 - 08:13:04 PST)
    - Re: [AMBER] Steered MD using the jar=1 option Joseph Baker (Fri Feb 27 2015 - 08:59:52 PST)
[AMBER] Invitation for proposing a book chapter Maryam Hamzehee (Mon Feb 23 2015 - 23:20:20 PST)
[AMBER] On the collective dynamics in terms of NMA and PCA James Starlight (Tue Feb 24 2015 - 02:23:55 PST)
- Re: [AMBER] On the collective dynamics in terms of NMA and PCA David A Case (Tue Feb 24 2015 - 14:39:54 PST)
  - Re: [AMBER] On the collective dynamics in terms of NMA and PCA Jason Swails (Tue Feb 24 2015 - 18:02:32 PST)
    - Re: [AMBER] On the collective dynamics in terms of NMA and PCA James Starlight (Thu Feb 26 2015 - 03:04:34 PST)
[AMBER] Announcement: release of FESetup 1.1 Hannes Loeffler (Tue Feb 24 2015 - 07:48:25 PST)
[AMBER] Can I use the presence of a particular hydrogen bond as a condition to filter out frames? Jose Borreguero (Tue Feb 24 2015 - 10:16:18 PST)
- Re: [AMBER] Can I use the presence of a particular hydrogen bond as a condition to filter out frames? Daniel Roe (Tue Feb 24 2015 - 10:51:40 PST)
  - Re: [AMBER] Can I use the presence of a particular hydrogen bond as a condition to filter out frames? Jose Borreguero (Tue Feb 24 2015 - 11:09:05 PST)
    - Re: [AMBER] Can I use the presence of a particular hydrogen bond as a condition to filter out frames? Daniel Roe (Tue Feb 24 2015 - 11:20:39 PST)
    - Re: [AMBER] Can I use the presence of a particular hydrogen bond as a condition to filter out frames? Jose Borreguero (Tue Feb 24 2015 - 11:34:10 PST)
    - Re: [AMBER] Can I use the presence of a particular hydrogen bond as a condition to filter out frames? Daniel Roe (Tue Feb 24 2015 - 13:57:00 PST)
[AMBER] REGARDING WARNINGS RETURNED DURING FORCE FIELD GENERATION Swithin Hanosh (Tue Feb 24 2015 - 11:19:27 PST)
- Re: [AMBER] REGARDING WARNINGS RETURNED DURING FORCE FIELD GENERATION David A Case (Tue Feb 24 2015 - 14:33:27 PST)
[AMBER] Bond Energy Term for a TIP3P Water Zhang, Sixue (Tue Feb 24 2015 - 11:30:55 PST)
- Re: [AMBER] Bond Energy Term for a TIP3P Water Zhang, Sixue (Tue Feb 24 2015 - 11:37:18 PST)
  - Re: [AMBER] Bond Energy Term for a TIP3P Water Jason Swails (Tue Feb 24 2015 - 11:58:12 PST)
    - Re: [AMBER] Bond Energy Term for a TIP3P Water Zhang, Sixue (Tue Feb 24 2015 - 13:08:17 PST)
  - Re: [AMBER] Bond Energy Term for a TIP3P Water Zhang, Sixue (Tue Feb 24 2015 - 16:51:16 PST)
    - Re: [AMBER] Bond Energy Term for a TIP3P Water David A Case (Wed Feb 25 2015 - 05:30:42 PST)
[AMBER] Closest residues to an atom in ptraj Alessandra Lacetera (Tue Feb 24 2015 - 11:42:06 PST)
- Re: [AMBER] Closest residues to an atom in ptraj Daniel Roe (Tue Feb 24 2015 - 11:59:35 PST)
- Re: [AMBER] Closest residues to an atom in ptraj Alessandra Lacetera (Wed Feb 25 2015 - 04:36:32 PST)
  - Re: [AMBER] Closest residues to an atom in ptraj Jason Swails (Wed Feb 25 2015 - 05:17:01 PST)
    - Re: [AMBER] Closest residues to an atom in ptraj Daniel Roe (Wed Feb 25 2015 - 06:54:59 PST)
[AMBER] Unexpected behavior of trajout after invoking filter: Bug? Jose Borreguero (Tue Feb 24 2015 - 14:57:59 PST)
- Re: [AMBER] Unexpected behavior of trajout after invoking filter: Bug? Daniel Roe (Tue Feb 24 2015 - 17:02:11 PST)
[AMBER] Chamber problem Shukla, Saurabh (Tue Feb 24 2015 - 17:24:05 PST)
- Re: [AMBER] Chamber problem Jason Swails (Tue Feb 24 2015 - 17:56:07 PST)
  - Re: [AMBER] Chamber problem Shukla, Saurabh (Mon Mar 02 2015 - 11:50:29 PST)
    - Re: [AMBER] Chamber problem Jason Swails (Mon Mar 02 2015 - 12:07:38 PST)
[AMBER] H-REMD failure on GPU Carlo Guardiani (Wed Feb 25 2015 - 08:57:43 PST)
- Re: [AMBER] H-REMD failure on GPU Jason Swails (Thu Feb 26 2015 - 05:51:49 PST)
[AMBER] An Amber Lipid Force Field Tutorial: problem with shell script Chris Gaughan (Wed Feb 25 2015 - 20:02:58 PST)
- Re: [AMBER] An Amber Lipid Force Field Tutorial: problem with shell script David A Case (Thu Feb 26 2015 - 05:02:13 PST)
[AMBER] Center of mass restraints work on pmemd.MPI, but not on the GPU mmaestre (Wed Feb 25 2015 - 20:19:51 PST)
- Re: [AMBER] Center of mass restraints work on pmemd.MPI, but not on the GPU Ross Walker (Wed Feb 25 2015 - 20:29:53 PST)
  - Re: [AMBER] Center of mass restraints work on pmemd.MPI, but not on the GPU Needham, Perri (Fri Feb 27 2015 - 11:44:43 PST)
    - Re: [AMBER] Center of mass restraints work on pmemd.MPI, but not on the GPU Jason Swails (Fri Feb 27 2015 - 12:06:51 PST)
    - Re: [AMBER] Center of mass restraints work on pmemd.MPI, but not on the GPU Needham, Perri (Fri Feb 27 2015 - 13:19:23 PST)
    - Re: [AMBER] Center of mass restraints work on pmemd.MPI, but not on the GPU Jason Swails (Fri Feb 27 2015 - 14:00:06 PST)
[AMBER] Cofactor parametrization Francesca Tessaro (Thu Feb 26 2015 - 06:45:59 PST)
- Re: [AMBER] Cofactor parametrization Jason Swails (Thu Feb 26 2015 - 08:22:08 PST)
  - Re: [AMBER] Cofactor parametrization Francesca Tessaro (Mon Mar 02 2015 - 03:08:08 PST)
    - Re: [AMBER] Cofactor parametrization Hannes Loeffler (Mon Mar 02 2015 - 03:29:31 PST)
- Re: [AMBER] Cofactor parametrization FyD (Tue Mar 03 2015 - 01:18:13 PST)
  - Re: [AMBER] Cofactor parametrization Dr. M. Shahid (Tue Mar 03 2015 - 03:18:01 PST)
    - Re: [AMBER] Cofactor parametrization FyD (Tue Mar 03 2015 - 04:47:26 PST)
    - Re: [AMBER] Cofactor parametrization Francesca Tessaro (Thu Mar 05 2015 - 04:55:06 PST)
    - Re: [AMBER] Cofactor parametrization Hannes Loeffler (Thu Mar 05 2015 - 05:34:00 PST)
    - Re: [AMBER] Cofactor parametrization FyD (Thu Mar 05 2015 - 07:43:44 PST)
    - Re: [AMBER] Cofactor parametrization Carlos Simmerling (Thu Mar 05 2015 - 05:04:09 PST)
[AMBER] MMGBSA: calculation of deltaG of ligand binding at dimer interface George Tzotzos (Thu Feb 26 2015 - 07:46:45 PST)
- Re: [AMBER] MMGBSA: calculation of deltaG of ligand binding at dimer interface Jason Swails (Thu Feb 26 2015 - 08:11:12 PST)
  - Re: [AMBER] MMGBSA: calculation of deltaG of ligand binding at dimer interface George Tzotzos (Thu Feb 26 2015 - 09:16:50 PST)
    - Re: [AMBER] MMGBSA: calculation of deltaG of ligand binding at dimer interface Jason Swails (Thu Feb 26 2015 - 09:21:34 PST)
    - Re: [AMBER] MMGBSA: calculation of deltaG of ligand binding at dimer interface George Tzotzos (Thu Feb 26 2015 - 10:08:57 PST)
    - Re: [AMBER] MMGBSA: calculation of deltaG of ligand binding at dimer interface Jason Swails (Thu Feb 26 2015 - 11:32:49 PST)
[AMBER] Can't get shell script to work with Lipid tutorial Chris Chris (Thu Feb 26 2015 - 09:52:14 PST)
[AMBER] CUDA- Error pmemd Lipid Membrane Romero, Raquel (Thu Feb 26 2015 - 18:02:11 PST)
- Re: [AMBER] CUDA- Error pmemd Lipid Membrane Parker de Waal (Thu Feb 26 2015 - 19:27:07 PST)
- Re: [AMBER] CUDA- Error pmemd Lipid Membrane Ross Walker (Thu Feb 26 2015 - 19:36:26 PST)
[AMBER] FATAL: Atom .R<GRA 1>.A<H31 197> does not have a type. Evans, Shalton (Thu Feb 26 2015 - 22:51:43 PST)
- Re: [AMBER] FATAL: Atom .R<GRA 1>.A<H31 197> does not have a type. Wei Ye (Thu Feb 26 2015 - 22:59:18 PST)
[AMBER] Parallel GPU calculation Stefano Motta (Fri Feb 27 2015 - 03:46:42 PST)
- Re: [AMBER] Parallel GPU calculation Jason Swails (Fri Feb 27 2015 - 05:06:09 PST)
  - Re: [AMBER] Parallel GPU calculation Stefano Motta (Fri Feb 27 2015 - 06:14:12 PST)
    - Re: [AMBER] Parallel GPU calculation Jason Swails (Fri Feb 27 2015 - 06:59:02 PST)
    - Re: [AMBER] Parallel GPU calculation Novosielski, Ryan (Fri Feb 27 2015 - 06:59:00 PST)
[AMBER] GTX980 PERFORMANCE carmendigiovanni75.alice.it (Fri Feb 27 2015 - 05:31:01 PST)
- Re: [AMBER] GTX980 PERFORMANCE Ross Walker (Fri Feb 27 2015 - 09:05:53 PST)
[AMBER] SDPC and SAPC lipid bilayer Hector A. Baldoni (Fri Feb 27 2015 - 06:21:14 PST)
[AMBER] Inability to use antechamber on Anion Robert Molt (Fri Feb 27 2015 - 18:04:32 PST)
- Re: [AMBER] Inability to use antechamber on Anion hannes.loeffler.stfc.ac.uk (Sat Feb 28 2015 - 00:19:57 PST)
  - Re: [AMBER] Inability to use antechamber on Anion Robert Molt (Fri Mar 06 2015 - 17:43:23 PST)
    - Re: [AMBER] Inability to use antechamber on Anion David A Case (Fri Mar 06 2015 - 18:06:11 PST)
    - Re: [AMBER] Inability to use antechamber on Anion hannes.loeffler.stfc.ac.uk (Fri Mar 06 2015 - 23:50:52 PST)
[AMBER] problem with running tutorial C1 Maryam Hamzehee (Fri Feb 27 2015 - 23:14:21 PST)
- Re: [AMBER] problem with running tutorial C1 Jason Swails (Sat Feb 28 2015 - 03:13:08 PST)
  - Re: [AMBER] problem with running tutorial C1 Maryam Hamzehee (Sat Feb 28 2015 - 04:27:14 PST)
    - Re: [AMBER] problem with running tutorial C1 Jason Swails (Sat Feb 28 2015 - 04:46:39 PST)
    - Re: [AMBER] problem with running tutorial C1 Daniel Roe (Sat Feb 28 2015 - 06:38:25 PST)
[AMBER] help in sdf Robin Jain (Sat Feb 28 2015 - 08:39:58 PST)
- Re: [AMBER] help in sdf Jason Swails (Sat Feb 28 2015 - 13:15:18 PST)
- [AMBER] Fwd: help in sdf Robin Jain (Sun Mar 01 2015 - 06:40:44 PST)
  - Re: [AMBER] Fwd: help in sdf Jason Swails (Sun Mar 01 2015 - 07:47:50 PST)
[AMBER] Param PROC does not exist (MM-PBSA) Atila Petrosian (Sun Mar 01 2015 - 06:49:33 PST)
[AMBER] tleap box neutralization Sergio Decherchi (Mon Mar 02 2015 - 01:13:58 PST)
- Re: [AMBER] tleap box neutralization Jason Swails (Mon Mar 02 2015 - 05:55:57 PST)
  - Re: [AMBER] tleap box neutralization Sergio Decherchi (Mon Mar 02 2015 - 06:01:28 PST)
[AMBER] R: Re: GTX980 PERFORMANCE carmendigiovanni75.alice.it (Mon Mar 02 2015 - 01:22:28 PST)
[AMBER] Error while creating force field Swithin Hanosh (Mon Mar 02 2015 - 02:21:07 PST)
- Re: [AMBER] Error while creating force field Hannes Loeffler (Mon Mar 02 2015 - 02:28:57 PST)
- Re: [AMBER] Error while creating force field FyD (Tue Mar 03 2015 - 01:15:25 PST)
[AMBER] COM restrain support in Amber14 Srinivasaraghavan Kannan (Mon Mar 02 2015 - 02:29:42 PST)
- Re: [AMBER] COM restrain support in Amber14 Jason Swails (Mon Mar 02 2015 - 05:36:05 PST)
[AMBER] ERROR no map function for FE2 FE2 :data= 91 CYS SG 170 FE2 FE2 2.4 Pragya Priyadarshini (Mon Mar 02 2015 - 03:37:48 PST)
[AMBER] using internal geometry newamber list (Mon Mar 02 2015 - 10:07:47 PST)
- Re: [AMBER] using internal geometry Jason Swails (Mon Mar 02 2015 - 10:35:10 PST)
  - Re: [AMBER] using internal geometry newamber list (Mon Mar 02 2015 - 11:34:11 PST)
[AMBER] Replacing water with oxygen molecules Shukla, Saurabh (Mon Mar 02 2015 - 10:19:51 PST)
- Re: [AMBER] Replacing water with oxygen molecules David A Case (Mon Mar 02 2015 - 17:29:57 PST)
[AMBER] ATP and ADP-Pi simulations Joseph Baker (Mon Mar 02 2015 - 13:04:45 PST)
- Re: [AMBER] ATP and ADP-Pi simulations David A Case (Mon Mar 02 2015 - 17:38:22 PST)
  - Re: [AMBER] ATP and ADP-Pi simulations Joseph Baker (Mon Mar 02 2015 - 20:05:25 PST)
    - Re: [AMBER] ATP and ADP-Pi simulations David A Case (Tue Mar 03 2015 - 06:05:19 PST)
- Re: [AMBER] ATP and ADP-Pi simulations FyD (Tue Mar 03 2015 - 01:28:50 PST)
  - Re: [AMBER] ATP and ADP-Pi simulations Joseph Baker (Tue Mar 03 2015 - 21:36:07 PST)
    - Re: [AMBER] ATP and ADP-Pi simulations FyD (Wed Mar 04 2015 - 00:56:52 PST)
    - Re: [AMBER] ATP and ADP-Pi simulations Joseph Baker (Wed Mar 04 2015 - 21:38:33 PST)
    - Re: [AMBER] ATP and ADP-Pi simulations FyD (Wed Mar 04 2015 - 23:33:12 PST)
[AMBER] ERROR: max pairlist cutoff must be less than unit cell max sphere radius! Jordan Graziadei (Mon Mar 02 2015 - 14:01:41 PST)
- Re: [AMBER] ERROR: max pairlist cutoff must be less than unit cell max sphere radius! Gabriel Jara (Fri Aug 31 2012 - 13:50:14 PDT)
  - Re: [AMBER] ERROR: max pairlist cutoff must be less than unit cell max sphere radius! case (Fri Aug 31 2012 - 15:38:57 PDT)
- Re: [AMBER] ERROR: max pairlist cutoff must be less than unit cell max sphere radius! Jordan Graziadei (Fri Mar 06 2015 - 11:11:54 PST)
  - Re: [AMBER] ERROR: max pairlist cutoff must be less than unit cell max sphere radius! Jason Swails (Fri Mar 06 2015 - 11:22:16 PST)
    - Re: [AMBER] ERROR: max pairlist cutoff must be less than unit cell max sphere radius! Jordan Graziadei (Thu Mar 12 2015 - 09:33:19 PDT)
[AMBER] Problem with Creating Unit for Non-standard N-Cap Residue Huang Tao (Mon Mar 02 2015 - 17:33:51 PST)
- Re: [AMBER] Problem with Creating Unit for Non-standard N-Cap Residue FyD (Tue Mar 03 2015 - 01:31:34 PST)
  - Re: [AMBER] Problem with Creating Unit for Non-standard N-Cap Residue Huang Tao (Fri Mar 06 2015 - 00:26:24 PST)
    - Re: [AMBER] Problem with Creating Unit for Non-standard N-Cap Residue FyD (Fri Mar 06 2015 - 08:20:06 PST)
    - Re: [AMBER] Problem with Creating Unit for Non-standard N-Cap Residue Huang Tao (Sun Mar 08 2015 - 00:59:24 PST)
    - Re: [AMBER] Problem with Creating Unit for Non-standard N-Cap Residue FyD (Sun Mar 08 2015 - 09:56:43 PDT)
[AMBER] Problem in capping ACE and NME. Harshala Haldankar (Mon Mar 02 2015 - 22:13:19 PST)
- Re: [AMBER] Problem in capping ACE and NME. Jason Swails (Tue Mar 03 2015 - 05:27:54 PST)
[AMBER] Problem in calculation per residue free energy decomposition maryam azimzadehirani (Tue Mar 03 2015 - 02:04:42 PST)
- Re: [AMBER] Problem in calculation per residue free energy decomposition Jason Swails (Tue Mar 03 2015 - 05:53:42 PST)
[AMBER] Error while creating force field Swithin Hanosh (Tue Mar 03 2015 - 03:35:37 PST)
- Re: [AMBER] Error while creating force field Akash Deep Biswas (Tue Mar 03 2015 - 03:50:12 PST)
  - Re: [AMBER] Error while creating force field Hannes Loeffler (Tue Mar 03 2015 - 03:59:39 PST)
- Re: [AMBER] Error while creating force field Hannes Loeffler (Tue Mar 03 2015 - 03:55:24 PST)
[AMBER] Decomposition of the MMGBSA based on multi trajectory input James Starlight (Tue Mar 03 2015 - 03:58:44 PST)
- Re: [AMBER] Decomposition of the MMGBSA based on multi trajectory input Bill Miller III (Tue Mar 03 2015 - 07:23:56 PST)
  - Re: [AMBER] Decomposition of the MMGBSA based on multi trajectory input James Starlight (Wed Mar 04 2015 - 06:10:46 PST)
    - Re: [AMBER] Decomposition of the MMGBSA based on multi trajectory input James Starlight (Wed Mar 04 2015 - 06:48:34 PST)
    - Re: [AMBER] Decomposition of the MMGBSA based on multi trajectory input Bill Miller III (Wed Mar 04 2015 - 07:38:10 PST)
    - Re: [AMBER] Decomposition of the MMGBSA based on multi trajectory input James Starlight (Thu Mar 05 2015 - 02:45:02 PST)
    - Re: [AMBER] Decomposition of the MMGBSA based on multi trajectory input James Starlight (Thu Mar 05 2015 - 03:39:16 PST)
    - Re: [AMBER] Decomposition of the MMGBSA based on multi trajectory input Bill Miller III (Thu Mar 05 2015 - 04:44:26 PST)
    - Re: [AMBER] Decomposition of the MMGBSA based on multi trajectory input James Starlight (Mon Mar 16 2015 - 06:00:19 PDT)
    - Re: [AMBER] Decomposition of the MMGBSA based on multi trajectory input James Starlight (Mon Mar 16 2015 - 06:42:16 PDT)
[AMBER] SMD average work Mahmood Jasim (Tue Mar 03 2015 - 07:58:09 PST)
- Re: [AMBER] SMD average work Adrian Roitberg (Tue Mar 03 2015 - 09:04:06 PST)
[AMBER] matrix newtransform command Sylvester Tumusiime (Tue Mar 03 2015 - 12:03:24 PST)
- Re: [AMBER] matrix newtransform command David A Case (Tue Mar 03 2015 - 14:35:19 PST)
  - Re: [AMBER] matrix newtransform command Sylvester Tumusiime (Wed Mar 04 2015 - 14:51:46 PST)
[AMBER] Tutorial B0 Sanmeet Chahal (Tue Mar 03 2015 - 15:05:57 PST)
- Re: [AMBER] Tutorial B0 Jason Swails (Wed Mar 04 2015 - 04:58:59 PST)
- Re: [AMBER] Tutorial B0 David A Case (Wed Mar 04 2015 - 05:10:17 PST)
  - Re: [AMBER] Tutorial B0 Sanmeet Chahal (Wed Mar 04 2015 - 08:34:51 PST)
    - Re: [AMBER] Tutorial B0 Sanmeet Chahal (Wed Mar 04 2015 - 08:44:43 PST)
    - Re: [AMBER] Tutorial B0 Sanmeet Chahal (Wed Mar 04 2015 - 08:47:02 PST)
    - Re: [AMBER] Tutorial B0 Sanmeet Chahal (Wed Mar 04 2015 - 08:49:48 PST)
  - Re: [AMBER] Tutorial B0 Sanmeet Chahal (Wed Mar 04 2015 - 13:29:24 PST)
    - Re: [AMBER] Tutorial B0 Sanmeet Chahal (Wed Mar 04 2015 - 13:32:28 PST)
    - Re: [AMBER] Tutorial B0 Jason Swails (Wed Mar 04 2015 - 13:33:11 PST)
    - Re: [AMBER] Tutorial B0 Sanmeet Chahal (Fri Mar 06 2015 - 13:25:27 PST)
    - Re: [AMBER] Tutorial B0 Sanmeet Chahal (Fri Mar 06 2015 - 16:06:18 PST)
    - Re: [AMBER] Tutorial B0 Sanmeet Chahal (Mon Mar 09 2015 - 14:11:17 PDT)
    - Re: [AMBER] Tutorial B0 David A Case (Mon Mar 09 2015 - 14:57:31 PDT)
    - Re: [AMBER] Tutorial B0 Jason Swails (Mon Mar 09 2015 - 19:10:12 PDT)
    - Re: [AMBER] Tutorial B0 Jason Swails (Wed Mar 04 2015 - 13:32:49 PST)
[AMBER] How to calculate interaction energy between any two residues of one protein danieldefoe (Tue Mar 03 2015 - 21:04:40 PST)
- Re: [AMBER] How to calculate interaction energy between any two residues of one protein Biao Ma (Tue Mar 03 2015 - 21:24:28 PST)
- Re: [AMBER] How to calculate interaction energy between any two residues of one protein Jason Swails (Wed Mar 04 2015 - 04:45:32 PST)
[AMBER] Param PROC does not exist --- MM-PBSA problem Atila Petrosian (Tue Mar 03 2015 - 23:49:18 PST)
- Re: [AMBER] Param PROC does not exist --- MM-PBSA problem Jason Swails (Wed Mar 04 2015 - 04:43:11 PST)
  - Re: [AMBER] Param PROC does not exist --- MM-PBSA problem Atila Petrosian (Thu Mar 05 2015 - 08:39:33 PST)
[AMBER] Targeted MD shows blank output file! Pallavi Mohanty (Wed Mar 04 2015 - 02:44:22 PST)
- Re: [AMBER] Targeted MD shows blank output file! Carlos Simmerling (Wed Mar 04 2015 - 04:13:07 PST)
  - Re: [AMBER] Targeted MD shows blank output file! Pallavi Mohanty (Wed Mar 04 2015 - 04:21:32 PST)
    - Re: [AMBER] Targeted MD shows blank output file! Jason Swails (Wed Mar 04 2015 - 04:53:05 PST)
    - Re: [AMBER] Targeted MD shows blank output file! Pallavi Mohanty (Wed Mar 04 2015 - 05:05:07 PST)
    - Re: [AMBER] Targeted MD shows blank output file! Jason Swails (Wed Mar 04 2015 - 05:12:47 PST)
    - Re: [AMBER] Targeted MD shows blank output file! Carlos Simmerling (Wed Mar 04 2015 - 05:37:23 PST)
    - Re: [AMBER] Targeted MD shows blank output file! Pallavi Mohanty (Wed Mar 04 2015 - 22:10:50 PST)
[AMBER] GTX TITAN X was introduced filip fratev (Wed Mar 04 2015 - 13:38:54 PST)
- Re: [AMBER] GTX TITAN X was introduced Ross Walker (Wed Mar 04 2015 - 18:19:18 PST)
  - Re: [AMBER] GTX TITAN X was introduced filip fratev (Thu Mar 05 2015 - 00:16:34 PST)
[AMBER] Solvent Box Issue When Running AMBER Dynamics Zhang, Sixue (Wed Mar 04 2015 - 14:46:37 PST)
- Re: [AMBER] Solvent Box Issue When Running AMBER Dynamics David Case (Wed Mar 04 2015 - 17:02:12 PST)
  - Re: [AMBER] Solvent Box Issue When Running AMBER Dynamics Zhang, Sixue (Wed Mar 04 2015 - 18:44:51 PST)
    - Re: [AMBER] Solvent Box Issue When Running AMBER Dynamics David A Case (Thu Mar 05 2015 - 05:12:44 PST)
- Re: [AMBER] Solvent Box Issue When Running AMBER Dynamics Daniel Roe (Mon Mar 09 2015 - 07:58:42 PDT)
  - Re: [AMBER] Solvent Box Issue When Running AMBER Dynamics Zhang, Sixue (Mon Mar 09 2015 - 13:58:53 PDT)
[AMBER] error in MMPBSA.py Emilio Angelina (Thu Mar 05 2015 - 03:26:43 PST)
- Re: [AMBER] error in MMPBSA.py Bill Miller III (Thu Mar 05 2015 - 07:04:45 PST)
[AMBER] mm-pbsa & extra-point Emilio Angelina (Thu Mar 05 2015 - 13:42:19 PST)
- Re: [AMBER] mm-pbsa & extra-point Jason Swails (Thu Mar 05 2015 - 14:38:29 PST)
  - Re: [AMBER] mm-pbsa & extra-point Emilio Angelina (Thu Mar 05 2015 - 16:21:21 PST)
    - Re: [AMBER] mm-pbsa & extra-point Jason Swails (Thu Mar 05 2015 - 17:36:04 PST)
    - Re: [AMBER] mm-pbsa & extra-point Emilio Angelina (Thu Mar 05 2015 - 19:43:23 PST)
[AMBER] a question on molecular dynamics simulation Brett (Fri Mar 06 2015 - 05:14:35 PST)
- Re: [AMBER] a question on molecular dynamics simulation Jason Swails (Fri Mar 06 2015 - 07:03:48 PST)
- Re: [AMBER] a question on molecular dynamics simulation David A Case (Fri Mar 06 2015 - 07:09:44 PST)
[AMBER] cpptraj H-bond: clarification sought George Tzotzos (Fri Mar 06 2015 - 09:44:55 PST)
- Re: [AMBER] cpptraj H-bond: clarification sought Daniel Roe (Sat Mar 07 2015 - 14:38:03 PST)
  - Re: [AMBER] cpptraj H-bond: clarification sought George Tzotzos (Sat Mar 07 2015 - 15:12:12 PST)
    - Re: [AMBER] cpptraj H-bond: clarification sought Daniel Roe (Mon Mar 09 2015 - 07:29:22 PDT)
[AMBER] Reading two units from same .mol2 file Sanmeet Chahal (Fri Mar 06 2015 - 17:16:10 PST)
- Re: [AMBER] Reading two units from same .mol2 file David A Case (Sat Mar 07 2015 - 17:45:36 PST)
  - Re: [AMBER] Reading two units from same .mol2 file Daniel Roe (Mon Mar 09 2015 - 07:17:36 PDT)
  - Re: [AMBER] Reading two units from same .mol2 file Sanmeet Chahal (Mon Mar 09 2015 - 07:44:36 PDT)
[AMBER] General question about MM-PB(GB)SA Atila Petrosian (Fri Mar 06 2015 - 21:56:14 PST)
- Re: [AMBER] General question about MM-PB(GB)SA Jason Swails (Sat Mar 07 2015 - 04:25:14 PST)
  - Re: [AMBER] General question about MM-PB(GB)SA Atila Petrosian (Sun Mar 08 2015 - 05:22:16 PDT)
    - Re: [AMBER] General question about MM-PB(GB)SA Jason Swails (Sun Mar 08 2015 - 18:40:24 PDT)
[AMBER] ideal range values for distance restraint b/w 2 non-bonded atoms. GG Smith (Sat Mar 07 2015 - 03:22:59 PST)
- Re: [AMBER] ideal range values for distance restraint b/w 2 non-bonded atoms. Jason Swails (Sat Mar 07 2015 - 04:30:39 PST)
  - Re: [AMBER] ideal range values for distance restraint b/w 2 non-bonded atoms. GG Smith (Sat Mar 07 2015 - 05:56:18 PST)
  - Re: [AMBER] ideal range values for distance restraint b/w 2 non-bonded atoms. GG Smith (Sun Mar 08 2015 - 23:02:01 PDT)
[AMBER] acetyl lysine Dhiraj Srivastava (Sat Mar 07 2015 - 14:15:29 PST)
- Re: [AMBER] acetyl lysine David A Case (Sat Mar 07 2015 - 17:43:48 PST)
  - Re: [AMBER] acetyl lysine achim.sandmann.chemie.stud.uni-erlangen.de (Mon Mar 09 2015 - 02:04:34 PDT)
[AMBER] on the force field Brett (Sat Mar 07 2015 - 19:04:55 PST)
- Re: [AMBER] on the force field Nhai (Sat Mar 07 2015 - 20:57:52 PST)
- Re: [AMBER] on the force field David A Case (Sun Mar 08 2015 - 06:18:30 PDT)
[AMBER] free energy plot zahra khatti (Sat Mar 07 2015 - 22:09:59 PST)
[AMBER] force field parameter for fructose 1 6 bisphosphate Dhiraj Srivastava (Sat Mar 07 2015 - 22:13:55 PST)
- Re: [AMBER] force field parameter for fructose 1 6 bisphosphate Lachele Foley (Sat Mar 07 2015 - 22:23:35 PST)
[AMBER] free energy plot zahra khatti (Sat Mar 07 2015 - 22:12:53 PST)
[AMBER] free energy plot zahra khatti (Sun Mar 08 2015 - 08:18:25 PDT)
- Re: [AMBER] free energy plot David A Case (Sun Mar 08 2015 - 10:50:18 PDT)
- Re: [AMBER] free energy plot Jason Swails (Sun Mar 08 2015 - 18:44:13 PDT)
[AMBER] Syntax Confusion on Radial Command Robert Molt (Sun Mar 08 2015 - 14:55:59 PDT)
- Re: [AMBER] Syntax Confusion on Radial Command Thomas Cheatham (Sun Mar 08 2015 - 15:29:37 PDT)
[AMBER] Invitation to Computational Chemical Biology Conference (Aug 6th to 9th 2015), Cairns, Australia (http://tinyurl.com/nyblv7o) Ross Walker (Sun Mar 08 2015 - 18:14:45 PDT)
[AMBER] clustering in ptraj Mary Varughese (Sun Mar 08 2015 - 23:48:43 PDT)
- Re: [AMBER] clustering in ptraj Daniel Roe (Mon Mar 09 2015 - 07:12:25 PDT)
  - Re: [AMBER] clustering in ptraj Mary Varughese (Mon Mar 09 2015 - 10:39:33 PDT)
    - Re: [AMBER] clustering in ptraj Daniel Roe (Tue Mar 10 2015 - 07:08:14 PDT)
    - Re: [AMBER] clustering in ptraj Mary Varughese (Tue Mar 10 2015 - 08:12:32 PDT)
[AMBER] PCA_representation_in_Cpptraj abdennour braka (Mon Mar 09 2015 - 02:14:51 PDT)
- Re: [AMBER] PCA_representation_in_Cpptraj Jason Swails (Mon Mar 09 2015 - 05:52:07 PDT)
- Re: [AMBER] PCA_representation_in_Cpptraj Daniel Roe (Mon Mar 09 2015 - 07:07:17 PDT)
  - Re: [AMBER] PCA_representation_in_Cpptraj Juan Eiros Zamora (Tue Mar 10 2015 - 04:37:50 PDT)
    - Re: [AMBER] PCA_representation_in_Cpptraj Jason Swails (Tue Mar 10 2015 - 07:15:20 PDT)
    - Re: [AMBER] PCA_representation_in_Cpptraj Daniel Roe (Tue Mar 10 2015 - 07:46:46 PDT)
    - Re: [AMBER] PCA_representation_in_Cpptraj Juan Eiros Zamora (Wed Mar 11 2015 - 05:52:48 PDT)
    - Re: [AMBER] PCA_representation_in_Cpptraj Daniel Roe (Wed Mar 11 2015 - 07:25:57 PDT)
    - Re: [AMBER] PCA_representation_in_Cpptraj Jason Swails (Wed Mar 11 2015 - 07:30:22 PDT)
[AMBER] Evaluating hydrogen boding lifetime Vijay Achari (Tue Mar 10 2015 - 01:53:39 PDT)
- Re: [AMBER] Evaluating hydrogen boding lifetime Daniel Roe (Tue Mar 10 2015 - 07:15:29 PDT)
  - Re: [AMBER] Evaluating hydrogen boding lifetime Vijay Achari (Tue Mar 10 2015 - 20:24:34 PDT)
    - Re: [AMBER] Evaluating hydrogen boding lifetime Daniel Roe (Tue Mar 10 2015 - 20:50:13 PDT)
    - Re: [AMBER] Evaluating hydrogen boding lifetime Vijay Achari (Tue Mar 10 2015 - 23:57:17 PDT)
    - Re: [AMBER] Evaluating hydrogen boding lifetime Daniel Roe (Wed Mar 11 2015 - 08:11:50 PDT)
    - Re: [AMBER] Evaluating hydrogen boding lifetime Vijay Achari (Thu Mar 12 2015 - 01:53:20 PDT)
    - Re: [AMBER] Evaluating hydrogen boding lifetime Daniel Roe (Thu Mar 12 2015 - 08:33:36 PDT)
    - Re: [AMBER] Evaluating hydrogen boding lifetime Vijay Achari (Mon Mar 16 2015 - 09:50:20 PDT)
    - Re: [AMBER] Evaluating hydrogen boding lifetime Daniel Roe (Sat Mar 21 2015 - 09:06:20 PDT)
    - Re: [AMBER] Evaluating hydrogen boding lifetime Vijay Achari (Sat Mar 21 2015 - 22:23:50 PDT)
    - Re: [AMBER] Evaluating hydrogen boding lifetime Vijay Achari (Mon Mar 23 2015 - 20:42:32 PDT)
    - Re: [AMBER] Evaluating hydrogen boding lifetime Vijay Achari (Wed Apr 15 2015 - 23:41:54 PDT)
    - Re: [AMBER] Evaluating hydrogen boding lifetime Daniel Roe (Thu Apr 16 2015 - 07:41:21 PDT)
    - Re: [AMBER] Evaluating hydrogen boding lifetime Vijay Achari (Thu Apr 16 2015 - 22:47:05 PDT)
    - Re: [AMBER] Evaluating hydrogen boding lifetime Daniel Roe (Fri Apr 17 2015 - 07:12:07 PDT)
    - Re: [AMBER] Evaluating hydrogen boding lifetime Vijay Achari (Fri Apr 17 2015 - 20:40:52 PDT)
[AMBER] Sudden RMSD blow-up in trajectory analysis Anasuya Dighe (Tue Mar 10 2015 - 02:54:17 PDT)
- Re: [AMBER] Sudden RMSD blow-up in trajectory analysis Carlos Simmerling (Tue Mar 10 2015 - 03:25:03 PDT)
- Re: [AMBER] Sudden RMSD blow-up in trajectory analysis Himanshu Joshi (Tue Mar 10 2015 - 03:27:56 PDT)
- Re: [AMBER] Sudden RMSD blow-up in trajectory analysis Daniel Roe (Tue Mar 10 2015 - 07:23:49 PDT)
[AMBER] MMPBSA tutorial: MMPBSA.py camm-kansai (Tue Mar 10 2015 - 04:32:06 PDT)
- Re: [AMBER] MMPBSA tutorial: MMPBSA.py David A Case (Tue Mar 10 2015 - 04:51:45 PDT)
  - Re: [AMBER] MMPBSA tutorial: MMPBSA.py camm-kansai (Fri Mar 13 2015 - 06:18:22 PDT)
[AMBER] Reg: Query on distance restrain and its effect on conformation GG Smith (Tue Mar 10 2015 - 21:41:18 PDT)
- Re: [AMBER] Reg: Query on distance restrain and its effect on conformation Jason Swails (Wed Mar 11 2015 - 08:41:12 PDT)
  - Re: [AMBER] Reg: Query on distance restrain and its effect on conformation GG Smith (Wed Mar 11 2015 - 22:20:30 PDT)
[AMBER] calculating angle between to vectors Vijay Achari (Wed Mar 11 2015 - 01:01:28 PDT)
- Re: [AMBER] calculating angle between to vectors Daniel Roe (Wed Mar 11 2015 - 07:39:54 PDT)
  - Re: [AMBER] calculating angle between to vectors Vijay Achari (Wed Mar 11 2015 - 22:22:45 PDT)
  - Re: [AMBER] calculating angle between to vectors Vijay Achari (Thu Mar 12 2015 - 03:14:19 PDT)
[AMBER] help in getting 3D isodensity surface Robin Jain (Wed Mar 11 2015 - 01:09:48 PDT)
- Re: [AMBER] help in getting 3D isodensity surface Jason Swails (Wed Mar 11 2015 - 07:15:52 PDT)
- Re: [AMBER] help in getting 3D isodensity surface Daniel Roe (Wed Mar 11 2015 - 07:35:58 PDT)
[AMBER] D- amino acids in ff10 Neha Gandhi (Wed Mar 11 2015 - 06:45:07 PDT)
- Re: [AMBER] D- amino acids in ff10 Carlos Simmerling (Wed Mar 11 2015 - 06:55:01 PDT)
  - Re: [AMBER] D- amino acids in ff10 FyD (Fri Mar 13 2015 - 09:21:03 PDT)
[AMBER] mmpbsa conflict with Ca2+ ? Jinfeng Huang (Wed Mar 11 2015 - 07:52:10 PDT)
- Re: [AMBER] mmpbsa conflict with Ca2+ ? Bill Ross (Wed Mar 11 2015 - 08:40:00 PDT)
- Re: [AMBER] mmpbsa conflict with Ca2+ ? Jason Swails (Wed Mar 11 2015 - 09:21:45 PDT)
  - Re: [AMBER] mmpbsa conflict with Ca2+ ? Jinfeng Huang (Wed Mar 11 2015 - 19:35:09 PDT)
    - Re: [AMBER] mmpbsa conflict with Ca2+ ? Jinfeng Huang (Thu Mar 12 2015 - 01:31:01 PDT)
    - Re: [AMBER] mmpbsa conflict with Ca2+ ? Jason Swails (Thu Mar 12 2015 - 05:32:59 PDT)
[AMBER] Truncated octahedron Arjun Sharma (Wed Mar 11 2015 - 08:24:31 PDT)
- Re: [AMBER] Truncated octahedron Bill Ross (Wed Mar 11 2015 - 08:35:36 PDT)
- Re: [AMBER] Truncated octahedron Crowley, Michael (Wed Mar 11 2015 - 08:39:03 PDT)
  - Re: [AMBER] Truncated octahedron Jason Swails (Wed Mar 11 2015 - 09:19:03 PDT)
- Re: [AMBER] Truncated octahedron Jason Swails (Wed Mar 11 2015 - 09:06:19 PDT)
[AMBER] : Dimer Imaging Problem Waldner, Birgit (Wed Mar 11 2015 - 09:28:35 PDT)
- Re: [AMBER] : Dimer Imaging Problem Daniel Roe (Wed Mar 11 2015 - 09:31:23 PDT)
  - Re: [AMBER] : Dimer Imaging Problem Waldner, Birgit (Wed Mar 11 2015 - 09:41:00 PDT)
[AMBER] Putting oxygen molecules around protein structure Shukla, Saurabh (Wed Mar 11 2015 - 20:38:24 PDT)
- Re: [AMBER] Putting oxygen molecules around protein structure David A Case (Thu Mar 12 2015 - 14:19:25 PDT)
[AMBER] Fitting velocity autocorrelation data DEBOSTUTI GHOSHDASTIDAR (Thu Mar 12 2015 - 03:27:00 PDT)
[AMBER] finding angles Vijay Achari (Thu Mar 12 2015 - 07:00:31 PDT)
- Re: [AMBER] finding angles Daniel Roe (Thu Mar 12 2015 - 08:20:19 PDT)
  - Re: [AMBER] finding angles Vijay Achari (Thu Mar 12 2015 - 18:24:05 PDT)
    - Re: [AMBER] finding angles Daniel Roe (Thu Mar 12 2015 - 20:15:39 PDT)
    - Re: [AMBER] finding angles Vijay Achari (Thu Mar 12 2015 - 20:40:49 PDT)
    - Re: [AMBER] finding angles Vijay Achari (Mon Mar 16 2015 - 03:18:03 PDT)
    - Re: [AMBER] finding angles Daniel Roe (Mon Mar 16 2015 - 06:58:33 PDT)
    - Re: [AMBER] finding angles Vijay Achari (Mon Mar 16 2015 - 10:49:31 PDT)
    - Re: [AMBER] finding angles Jason Swails (Mon Mar 16 2015 - 10:53:12 PDT)
    - Re: [AMBER] finding angles Vijay Achari (Mon Mar 16 2015 - 15:36:03 PDT)
    - Re: [AMBER] finding angles Jason Swails (Mon Mar 16 2015 - 17:23:18 PDT)
    - Re: [AMBER] finding angles Vijay Achari (Mon Mar 16 2015 - 19:22:09 PDT)
    - Re: [AMBER] finding angles Daniel Roe (Tue Mar 17 2015 - 07:12:39 PDT)
    - Re: [AMBER] finding angles Jason Swails (Tue Mar 17 2015 - 07:23:33 PDT)
[AMBER] RNA Simulation jacob wick (Thu Mar 12 2015 - 11:28:59 PDT)
- Re: [AMBER] RNA Simulation Jiri Sponer (Thu Mar 12 2015 - 12:16:10 PDT)
- Re: [AMBER] RNA Simulation Jiri Sponer (Thu Mar 12 2015 - 12:28:48 PDT)
- Re: [AMBER] RNA Simulation Bill Ross (Thu Mar 12 2015 - 14:15:29 PDT)
  - Re: [AMBER] RNA Simulation jacob wick (Thu Mar 12 2015 - 22:17:12 PDT)
[AMBER] Predefined number of water molecules in waterbox jacob wick (Thu Mar 12 2015 - 22:17:44 PDT)
- Re: [AMBER] Predefined number of water molecules in waterbox Michele Bonus (Thu Mar 12 2015 - 23:12:20 PDT)
  - Re: [AMBER] Predefined number of water molecules in waterbox jacob wick (Fri Mar 13 2015 - 22:20:38 PDT)
[AMBER] error in antechamber: Bond types are assigned for valence state 1 with penalty of 1 Rebeca García Fandiño (Fri Mar 13 2015 - 02:24:20 PDT)
- Re: [AMBER] error in antechamber: Bond types are assigned for valence state 1 with penalty of 1 Hannes Loeffler (Fri Mar 13 2015 - 02:59:40 PDT)
[AMBER] Problem in protonating. Harshala Haldankar (Fri Mar 13 2015 - 04:16:02 PDT)
- Re: [AMBER] Problem in protonating. Jason Swails (Fri Mar 13 2015 - 05:14:42 PDT)
[AMBER] Force field for Inositol triphosphate anu chandra (Fri Mar 13 2015 - 05:35:00 PDT)
[AMBER] leap and centering Hannes Loeffler (Fri Mar 13 2015 - 08:20:35 PDT)
- Re: [AMBER] leap and centering David A Case (Fri Mar 13 2015 - 08:32:09 PDT)
  - Re: [AMBER] leap and centering Hannes Loeffler (Fri Mar 13 2015 - 09:04:45 PDT)
    - Re: [AMBER] leap and centering David A Case (Sat Mar 14 2015 - 06:31:56 PDT)
    - Re: [AMBER] leap and centering hannes.loeffler.stfc.ac.uk (Sun Mar 15 2015 - 01:52:02 PDT)
Re: [AMBER] [q4md-fft] Fwd: D- amino acids in ff10 FyD (Fri Mar 13 2015 - 09:51:04 PDT)
- Re: [AMBER] [q4md-fft] Fwd: D- amino acids in ff10 Carlos Simmerling (Fri Mar 13 2015 - 10:01:04 PDT)
  - Re: [AMBER] [q4md-fft] Fwd: D- amino acids in ff10 FyD (Fri Mar 13 2015 - 10:51:42 PDT)
    - Re: [AMBER] [q4md-fft] Fwd: D- amino acids in ff10 Carlos Simmerling (Fri Mar 13 2015 - 11:28:17 PDT)
[AMBER] Errors in AmberTools14 Jonathan Gough (Fri Mar 13 2015 - 10:52:33 PDT)
- Re: [AMBER] Errors in AmberTools14 Jonathan Gough (Fri Mar 13 2015 - 10:54:38 PDT)
  - Re: [AMBER] Errors in AmberTools14 Jason Swails (Fri Mar 13 2015 - 12:27:36 PDT)
    - Re: [AMBER] Errors in AmberTools14 Jonathan Gough (Fri Mar 13 2015 - 12:28:53 PDT)
    - Re: [AMBER] Errors in AmberTools14 Jason Swails (Fri Mar 13 2015 - 13:32:13 PDT)
- Re: [AMBER] Errors in AmberTools14 Jason Swails (Fri Mar 13 2015 - 11:14:58 PDT)
  - Re: [AMBER] Errors in AmberTools14 Jonathan Gough (Fri Mar 13 2015 - 11:31:49 PDT)
    - Re: [AMBER] Errors in AmberTools14 Jason Swails (Fri Mar 13 2015 - 12:21:24 PDT)
    - Re: [AMBER] Errors in AmberTools14 Jonathan Gough (Fri Mar 13 2015 - 12:27:23 PDT)
[AMBER] Unable to load OLS OLT NLN in tleap (AmberTools14) Pedro Swagger (Fri Mar 13 2015 - 17:28:43 PDT)
- Re: [AMBER] Unable to load OLS OLT NLN in tleap (AmberTools14) Lachele Foley (Fri Mar 13 2015 - 17:40:33 PDT)
  - Re: [AMBER] Unable to load OLS OLT NLN in tleap (AmberTools14) Pedro Swagger (Sat Mar 14 2015 - 08:04:09 PDT)
    - Re: [AMBER] Unable to load OLS OLT NLN in tleap (AmberTools14) Jason Swails (Sat Mar 14 2015 - 08:56:22 PDT)
    - Re: [AMBER] Unable to load OLS OLT NLN in tleap (AmberTools14) Lachele Foley (Sat Mar 14 2015 - 12:36:06 PDT)
[AMBER] 10-12 Potentials, HBOND David Poole (Fri Mar 13 2015 - 20:37:13 PDT)
- Re: [AMBER] 10-12 Potentials, HBOND Jason Swails (Sat Mar 14 2015 - 16:12:10 PDT)
[AMBER] Fwd: [Fwd: Purchase of Amber-14] N.R. Jena (Sat Mar 14 2015 - 12:14:23 PDT)
[AMBER] set command and VMD Arjun Sharma (Sat Mar 14 2015 - 15:44:23 PDT)
- Re: [AMBER] set command and VMD Jason Swails (Sat Mar 14 2015 - 18:16:02 PDT)
- Re: [AMBER] set command and VMD David A Case (Sun Mar 15 2015 - 17:45:43 PDT)
[AMBER] RNA's sugar modification jacob wick (Sun Mar 15 2015 - 11:05:20 PDT)
- Re: [AMBER] RNA's sugar modification Bill Ross (Sun Mar 15 2015 - 13:13:20 PDT)
- Re: [AMBER] RNA's sugar modification Bill Ross (Sun Mar 15 2015 - 13:17:57 PDT)
[AMBER] Nuclicacid forcefield in AMBER mish (Sun Mar 15 2015 - 12:12:49 PDT)
- Re: [AMBER] Nuclicacid forcefield in AMBER David A Case (Sun Mar 15 2015 - 17:33:34 PDT)
  - Re: [AMBER] Nuclicacid forcefield in AMBER mish (Tue Mar 17 2015 - 09:27:54 PDT)
    - Re: [AMBER] Nuclicacid forcefield in AMBER Jason Swails (Wed Mar 18 2015 - 04:54:59 PDT)
    - Re: [AMBER] Nuclicacid forcefield in AMBER Carlos Simmerling (Wed Mar 18 2015 - 05:01:29 PDT)
    - Re: [AMBER] Nuclicacid forcefield in AMBER Nhai (Wed Mar 18 2015 - 08:20:35 PDT)
[AMBER] ** No torsion terms Evans, Shalton (Sun Mar 15 2015 - 17:57:30 PDT)
Re: [AMBER] [q4md-fft] Modify RNA's sugar and adding partial charges FyD (Mon Mar 16 2015 - 00:15:03 PDT)
[AMBER] Using WHAM to get 3D free energy surface in AMBER12 Wang Moye (Mon Mar 16 2015 - 00:30:40 PDT)
- Re: [AMBER] Using WHAM to get 3D free energy surface in AMBER12 Jason Swails (Mon Mar 16 2015 - 05:19:18 PDT)
  - Re: [AMBER] Using WHAM to get 3D free energy surface in AMBER12 Wang Moye (Mon Mar 16 2015 - 18:06:56 PDT)
    - Re: [AMBER] Using WHAM to get 3D free energy surface in AMBER12 Jason Swails (Mon Mar 16 2015 - 18:44:53 PDT)
    - Re: [AMBER] Using WHAM to get 3D free energy surface in AMBER12 Wang Moye (Wed Mar 18 2015 - 18:21:21 PDT)
[AMBER] facing problem to create a prmtop file for oxonium cation Sohag Biswas (Mon Mar 16 2015 - 02:59:06 PDT)
- Re: [AMBER] facing problem to create a prmtop file for oxonium cation Hannes Loeffler (Mon Mar 16 2015 - 03:32:25 PDT)
- Re: [AMBER] facing problem to create a prmtop file for oxonium cation David A Case (Mon Mar 16 2015 - 04:47:41 PDT)
- Re: [AMBER] facing problem to create a prmtop file for oxonium cation FyD (Mon Mar 16 2015 - 05:31:01 PDT)
[AMBER] diisopropylethylene parameter Jennifer Vo (Mon Mar 16 2015 - 03:06:47 PDT)
- Re: [AMBER] diisopropylethylene parameter Hannes Loeffler (Mon Mar 16 2015 - 03:37:41 PDT)
[AMBER] organic molecule Lara rajam (Mon Mar 16 2015 - 06:45:47 PDT)
- Re: [AMBER] organic molecule Jason Swails (Mon Mar 16 2015 - 07:15:59 PDT)
[AMBER] Per-residue decomposition energy MMGBSA.py maryam azimzadehirani (Mon Mar 16 2015 - 06:49:12 PDT)
- Re: [AMBER] Per-residue decomposition energy MMGBSA.py Jason Swails (Mon Mar 16 2015 - 07:26:57 PDT)
  - Re: [AMBER] Per-residue decomposition energy MMGBSA.py maryam azimzadehirani (Mon Mar 16 2015 - 20:52:58 PDT)
    - Re: [AMBER] Per-residue decomposition energy MMGBSA.py Jason Swails (Tue Mar 17 2015 - 05:45:47 PDT)
[AMBER] ante-mmpbsa.py: problem with the mask syntax George Tzotzos (Mon Mar 16 2015 - 10:26:16 PDT)
- Re: [AMBER] ante-mmpbsa.py: problem with the mask syntax Kenneth Huang (Mon Mar 16 2015 - 11:21:13 PDT)
- Re: [AMBER] ante-mmpbsa.py: problem with the mask syntax Jason Swails (Mon Mar 16 2015 - 11:37:47 PDT)
  - Re: [AMBER] ante-mmpbsa.py: problem with the mask syntax George Tzotzos (Mon Mar 16 2015 - 12:12:44 PDT)
    - Re: [AMBER] ante-mmpbsa.py: problem with the mask syntax Jason Swails (Mon Mar 16 2015 - 12:18:13 PDT)
    - Re: [AMBER] ante-mmpbsa.py: problem with the mask syntax George Tzotzos (Mon Mar 16 2015 - 12:59:49 PDT)
[AMBER] pmemd.MPI error George Tzotzos (Mon Mar 16 2015 - 13:07:55 PDT)
- Re: [AMBER] pmemd.MPI error David A Case (Mon Mar 16 2015 - 14:48:39 PDT)
[AMBER] HMR Adrian Roitberg (Mon Mar 16 2015 - 14:40:23 PDT)
- Re: [AMBER] HMR Parker de Waal (Mon Mar 16 2015 - 15:28:05 PDT)
- Re: [AMBER] HMR Hai Nguyen (Mon Mar 16 2015 - 17:27:31 PDT)
[AMBER] Format of solventhb.dat file in hydrogen bonding calculation Vijay Achari (Mon Mar 16 2015 - 19:10:40 PDT)
- Re: [AMBER] Format of solventhb.dat file in hydrogen bonding calculation Daniel Roe (Fri Mar 20 2015 - 07:23:26 PDT)
  - Re: [AMBER] Format of solventhb.dat file in hydrogen bonding calculation Vijay Achari (Tue Mar 24 2015 - 01:14:54 PDT)
Re: [AMBER] AMBER Digest, Vol 1160, Issue 1 Sohag Biswas (Tue Mar 17 2015 - 01:39:53 PDT)
[AMBER] unfolding protein and solvent density Ibrahim Said (Tue Mar 17 2015 - 02:32:03 PDT)
- Re: [AMBER] unfolding protein and solvent density Carlos Simmerling (Tue Mar 17 2015 - 03:30:29 PDT)
  - Re: [AMBER] unfolding protein and solvent density Ibrahim Said (Tue Mar 17 2015 - 03:54:10 PDT)
    - Re: [AMBER] unfolding protein and solvent density Jason Swails (Tue Mar 17 2015 - 06:05:21 PDT)
[AMBER] Differences in AMBER force fields Thomas Exner (Tue Mar 17 2015 - 02:46:24 PDT)
- Re: [AMBER] Differences in AMBER force fields David A Case (Tue Mar 17 2015 - 04:49:08 PDT)
  - Re: [AMBER] Differences in AMBER force fields Petr Jurecka (Tue Mar 17 2015 - 10:47:57 PDT)
- Re: [AMBER] Differences in AMBER force fields Jiri Sponer (Fri Mar 20 2015 - 09:03:07 PDT)
[AMBER] Backbone Rmsd jacob wick (Tue Mar 17 2015 - 03:17:46 PDT)
- Re: [AMBER] Backbone Rmsd David A Case (Tue Mar 17 2015 - 04:52:50 PDT)
  - Re: [AMBER] Backbone Rmsd jacob wick (Fri Mar 20 2015 - 03:03:43 PDT)
    - Re: [AMBER] Backbone Rmsd Jason Swails (Fri Mar 20 2015 - 18:26:32 PDT)
    - Re: [AMBER] Backbone Rmsd Daniel Roe (Sat Mar 21 2015 - 08:44:56 PDT)
[AMBER] About TIP4-Ew water model usage Saikat Dutta chowdhury (Tue Mar 17 2015 - 03:31:56 PDT)
- Re: [AMBER] About TIP4-Ew water model usage Jason Swails (Tue Mar 17 2015 - 05:53:54 PDT)
  - Re: [AMBER] About TIP4-Ew water model usage Saikat Dutta chowdhury (Tue Mar 17 2015 - 23:47:16 PDT)
    - Re: [AMBER] About TIP4-Ew water model usage Carlos Simmerling (Wed Mar 18 2015 - 03:16:36 PDT)
    - Re: [AMBER] About TIP4-Ew water model usage Saikat Dutta chowdhury (Thu Mar 19 2015 - 01:25:35 PDT)
[AMBER] Dielectric constant for dna-ligand in TIP3P system Him Shweta (Tue Mar 17 2015 - 07:45:13 PDT)
- Re: [AMBER] Dielectric constant for dna-ligand in TIP3P system Jason Swails (Tue Mar 17 2015 - 08:15:01 PDT)
[AMBER] Dielectric constant for dna-ligand in TIP3P system Him Shweta (Tue Mar 17 2015 - 07:49:59 PDT)
- Re: [AMBER] Dielectric constant for dna-ligand in TIP3P system Thomas Cheatham (Tue Mar 17 2015 - 08:40:36 PDT)
  - Re: [AMBER] Dielectric constant for dna-ligand in TIP3P system Him Shweta (Wed Mar 18 2015 - 03:09:10 PDT)
[AMBER] **No Torsion terms Evans, Shalton (Tue Mar 17 2015 - 09:28:47 PDT)
- Re: [AMBER] **No Torsion terms David A Case (Wed Mar 18 2015 - 06:35:28 PDT)
  - Re: [AMBER] **No Torsion terms David A Case (Wed Mar 18 2015 - 10:39:51 PDT)
[AMBER] Starting antechamber for preparing ligand molecule Anasuya Dighe (Tue Mar 17 2015 - 10:23:51 PDT)
- Re: [AMBER] Starting antechamber for preparing ligand molecule Hannes Loeffler (Wed Mar 18 2015 - 02:15:38 PDT)
  - Re: [AMBER] Starting antechamber for preparing ligand molecule FyD (Wed Mar 18 2015 - 06:09:04 PDT)
- Re: [AMBER] Starting antechamber for preparing ligand molecule David A Case (Wed Mar 18 2015 - 06:37:27 PDT)
Re: [AMBER] Amber on Red Hat? Agnieszka Szarecka (Tue Mar 17 2015 - 12:23:04 PDT)
- Re: [AMBER] Amber on Red Hat? Jason Swails (Tue Mar 17 2015 - 12:36:37 PDT)
  - Re: [AMBER] Amber on Red Hat? Agnieszka Szarecka (Tue Mar 17 2015 - 13:29:19 PDT)
[AMBER] topology file, segment id and the pathways plugin Shoresh Shafei (Tue Mar 17 2015 - 13:33:32 PDT)
- Re: [AMBER] topology file, segment id and the pathways plugin Jason Swails (Tue Mar 17 2015 - 13:54:18 PDT)
[AMBER] Non-Standard Residue / Non-Integer Charge Maral Aminpour (Tue Mar 17 2015 - 14:09:50 PDT)
- Re: [AMBER] Non-Standard Residue / Non-Integer Charge FyD (Wed Mar 18 2015 - 02:07:46 PDT)
  - Re: [AMBER] Non-Standard Residue / Non-Integer Charge Maral Aminpour (Thu Mar 19 2015 - 12:35:39 PDT)
    - Re: [AMBER] Non-Standard Residue / Non-Integer Charge FyD (Thu Mar 19 2015 - 23:58:31 PDT)
    - Re: [AMBER] Non-Standard Residue / Non-Integer Charge Maral Aminpour (Fri Mar 20 2015 - 10:51:14 PDT)
- Re: [AMBER] Non-Standard Residue / Non-Integer Charge David A Case (Wed Mar 18 2015 - 17:32:35 PDT)
- Re: [AMBER] Non-Standard Residue / Non-Integer Charge Bill Ross (Fri Mar 20 2015 - 11:03:14 PDT)
  - Re: [AMBER] Non-Standard Residue / Non-Integer Charge Maral Aminpour (Fri Mar 20 2015 - 19:27:15 PDT)
    - Re: [AMBER] Non-Standard Residue / Non-Integer Charge FyD (Mon Mar 23 2015 - 09:27:28 PDT)
[AMBER] PMF for dimer dissociation Sanmeet Chahal (Tue Mar 17 2015 - 14:18:33 PDT)
- Re: [AMBER] PMF for dimer dissociation Carlos Simmerling (Tue Mar 17 2015 - 16:25:07 PDT)
  - Re: [AMBER] PMF for dimer dissociation Sanmeet Chahal (Tue Mar 17 2015 - 19:04:53 PDT)
    - Re: [AMBER] PMF for dimer dissociation Jason Swails (Tue Mar 17 2015 - 19:33:44 PDT)
[AMBER] MMGBSA pairwise decomposition - differences in Non-Polar Solv. & TOTAL for same residue pairs Cassandra Churchill (Tue Mar 17 2015 - 14:53:43 PDT)
- Re: [AMBER] MMGBSA pairwise decomposition - differences in Non-Polar Solv. & TOTAL for same residue pairs Jason Swails (Tue Mar 17 2015 - 19:25:47 PDT)
[AMBER] help in hbond analysis Robin Jain (Tue Mar 17 2015 - 23:26:35 PDT)
- Re: [AMBER] help in hbond analysis Daniel Roe (Thu Mar 26 2015 - 10:33:46 PDT)
[AMBER] CHAMBER and CMAP difficulty Brian Radak (Wed Mar 18 2015 - 08:03:53 PDT)
- Re: [AMBER] CHAMBER and CMAP difficulty Jason Swails (Wed Mar 18 2015 - 08:14:29 PDT)
  - Re: [AMBER] CHAMBER and CMAP difficulty Brian Radak (Wed Mar 18 2015 - 08:27:29 PDT)
    - Re: [AMBER] CHAMBER and CMAP difficulty Jason Swails (Wed Mar 18 2015 - 08:36:33 PDT)
    - Re: [AMBER] CHAMBER and CMAP difficulty Brian Radak (Wed Mar 18 2015 - 08:54:10 PDT)
    - Re: [AMBER] CHAMBER and CMAP difficulty Jason Swails (Wed Mar 18 2015 - 09:03:47 PDT)
    - Re: [AMBER] CHAMBER and CMAP difficulty Brian Radak (Wed Mar 18 2015 - 09:13:28 PDT)
    - Re: [AMBER] CHAMBER and CMAP difficulty Brian Radak (Wed Mar 18 2015 - 09:31:55 PDT)
    - Re: [AMBER] CHAMBER and CMAP difficulty Jason Swails (Wed Mar 18 2015 - 09:50:17 PDT)
    - Re: [AMBER] CHAMBER and CMAP difficulty Brian Radak (Wed Mar 18 2015 - 09:59:33 PDT)
[AMBER] how to use cpptraj for pdb files generated from external software Mahendra B Thapa (Wed Mar 18 2015 - 09:34:29 PDT)
- Re: [AMBER] how to use cpptraj for pdb files generated from external software Hai Nguyen (Wed Mar 18 2015 - 09:37:58 PDT)
[AMBER] trajectory of minimization using generalized Born Edwin Helbert Aponte Angarita (Wed Mar 18 2015 - 09:41:43 PDT)
- Re: [AMBER] trajectory of minimization using generalized Born Edwin Helbert Aponte Angarita (Wed Mar 18 2015 - 13:27:44 PDT)
  - Re: [AMBER] trajectory of minimization using generalized Born David A Case (Wed Mar 18 2015 - 15:03:54 PDT)
- Re: [AMBER] trajectory of minimization using generalized Born Jason Swails (Wed Mar 18 2015 - 14:03:42 PDT)
- Re: [AMBER] trajectory of minimization using generalized Born Daniel Roe (Wed Mar 18 2015 - 19:50:25 PDT)
  - Re: [AMBER] trajectory of minimization using generalized Born Edwin Helbert Aponte Angarita (Thu Mar 19 2015 - 12:30:23 PDT)
    - Re: [AMBER] trajectory of minimization using generalized Born Edwin Helbert Aponte Angarita (Thu Mar 19 2015 - 13:21:55 PDT)
    - Re: [AMBER] trajectory of minimization using generalized Born Carlos Simmerling (Thu Mar 19 2015 - 13:35:48 PDT)
    - Re: [AMBER] trajectory of minimization using generalized Born Edwin Helbert Aponte Angarita (Thu Mar 19 2015 - 15:05:25 PDT)
    - Re: [AMBER] trajectory of minimization using generalized Born Carlos Simmerling (Thu Mar 19 2015 - 15:26:50 PDT)
    - Re: [AMBER] trajectory of minimization using generalized Born Edwin Helbert Aponte Angarita (Thu Mar 19 2015 - 16:00:42 PDT)
    - Re: [AMBER] trajectory of minimization using generalized Born Carlos Simmerling (Fri Mar 20 2015 - 08:26:05 PDT)
    - Re: [AMBER] trajectory of minimization using generalized Born Edwin Helbert Aponte Angarita (Fri Mar 20 2015 - 12:03:27 PDT)
    - Re: [AMBER] trajectory of minimization using generalized Born Jason Swails (Fri Mar 20 2015 - 12:49:50 PDT)
    - Re: [AMBER] trajectory of minimization using generalized Born Carlos Simmerling (Fri Mar 20 2015 - 13:00:08 PDT)
    - Re: [AMBER] trajectory of minimization using generalized Born Edwin Helbert Aponte Angarita (Fri Mar 20 2015 - 13:47:16 PDT)
    - Re: [AMBER] trajectory of minimization using generalized Born Carlos Simmerling (Fri Mar 20 2015 - 14:08:47 PDT)
    - Re: [AMBER] trajectory of minimization using generalized Born Edwin Helbert Aponte Angarita (Sat Mar 21 2015 - 04:48:56 PDT)
    - Re: [AMBER] trajectory of minimization using generalized Born Edwin Helbert Aponte Angarita (Mon Mar 23 2015 - 04:47:37 PDT)
    - Re: [AMBER] trajectory of minimization using generalized Born Jason Swails (Mon Mar 23 2015 - 11:36:20 PDT)
    - Re: [AMBER] trajectory of minimization using generalized Born Jason Swails (Fri Mar 20 2015 - 05:29:03 PDT)
    - Re: [AMBER] trajectory of minimization using generalized Born Edwin Helbert Aponte Angarita (Fri Mar 20 2015 - 06:13:25 PDT)
    - Re: [AMBER] trajectory of minimization using generalized Born Jason Swails (Fri Mar 20 2015 - 06:23:50 PDT)
    - Re: [AMBER] trajectory of minimization using generalized Born Carlos Simmerling (Fri Mar 20 2015 - 06:25:47 PDT)
Re: [AMBER] FW: how to use cpptraj for pdb files generated from external software Mahendra B Thapa (Wed Mar 18 2015 - 09:57:18 PDT)
[AMBER] Amber 14 tests errors Gustavo Avelar Molina (Wed Mar 18 2015 - 16:34:26 PDT)
- Re: [AMBER] Amber 14 tests errors David A Case (Wed Mar 18 2015 - 17:41:34 PDT)
[AMBER] Fwd: CPPTRAJ trajout results "weird" pdb Chinh Su Tran To (Wed Mar 18 2015 - 20:40:59 PDT)
- Re: [AMBER] Fwd: CPPTRAJ trajout results "weird" pdb David A Case (Thu Mar 19 2015 - 05:03:07 PDT)
- Re: [AMBER] Fwd: CPPTRAJ trajout results "weird" pdb Daniel Roe (Thu Mar 19 2015 - 21:17:55 PDT)
[AMBER] Error during Adding Fragment（about MCPB ） wjli (Thu Mar 19 2015 - 03:33:23 PDT)
- Re: [AMBER] Error during Adding Fragment（about MCPB ） David A Case (Thu Mar 19 2015 - 05:11:34 PDT)
[AMBER] Amber standard residue name wjli (Thu Mar 19 2015 - 03:45:34 PDT)
[AMBER] NetCDF AMBER file corrupted Jacopo Sgrignani (Thu Mar 19 2015 - 07:20:09 PDT)
- Re: [AMBER] NetCDF AMBER file corrupted Jason Swails (Thu Mar 19 2015 - 08:26:55 PDT)
  - Re: [AMBER] NetCDF AMBER file corrupted Jacopo Sgrignani (Thu Mar 19 2015 - 08:46:36 PDT)
    - Re: [AMBER] NetCDF AMBER file corrupted Daniel Roe (Thu Mar 19 2015 - 21:21:24 PDT)
[AMBER] On the clustering of the ligand position within the cavity James Starlight (Thu Mar 19 2015 - 08:50:12 PDT)
- Re: [AMBER] On the clustering of the ligand position within the cavity James Starlight (Thu Mar 19 2015 - 09:30:57 PDT)
  - Re: [AMBER] On the clustering of the ligand position within the cavity Kenneth Huang (Thu Mar 19 2015 - 10:23:21 PDT)
- Re: [AMBER] On the clustering of the ligand position within the cavity Daniel Roe (Fri Mar 20 2015 - 07:14:48 PDT)
[AMBER] sander.MPI error George Tzotzos (Thu Mar 19 2015 - 11:02:40 PDT)
- Re: [AMBER] sander.MPI error Bill Ross (Sun Oct 03 2010 - 12:35:52 PDT)
- Re: [AMBER] sander.MPI error George Tzotzos (Thu Mar 19 2015 - 11:06:41 PDT)
- Re: [AMBER] sander.MPI error Jason Swails (Thu Mar 19 2015 - 11:13:52 PDT)
[AMBER] | ERROR: PMEMD does not support intermolecular PRFs! Jorgen Simonsen (Thu Mar 19 2015 - 11:15:30 PDT)
- Re: [AMBER] | ERROR: PMEMD does not support intermolecular PRFs! Jason Swails (Thu Mar 19 2015 - 11:34:33 PDT)
  - Re: [AMBER] | ERROR: PMEMD does not support intermolecular PRFs! Jorgen Simonsen (Thu Mar 19 2015 - 12:31:19 PDT)
    - Re: [AMBER] | ERROR: PMEMD does not support intermolecular PRFs! Jorgen Simonsen (Thu Mar 19 2015 - 12:51:16 PDT)
    - Re: [AMBER] | ERROR: PMEMD does not support intermolecular PRFs! Jorgen Simonsen (Thu Mar 19 2015 - 15:12:50 PDT)
    - Re: [AMBER] | ERROR: PMEMD does not support intermolecular PRFs! Jason Swails (Fri Mar 20 2015 - 05:06:49 PDT)
[AMBER] post processing temperature replica exchange trajectories Sandeep Somani (Thu Mar 19 2015 - 13:00:49 PDT)
- Re: [AMBER] post processing temperature replica exchange trajectories Daniel Roe (Thu Mar 19 2015 - 19:57:03 PDT)
  - Re: [AMBER] post processing temperature replica exchange trajectories Sandeep Somani (Fri Mar 20 2015 - 04:42:42 PDT)
- Re: [AMBER] post processing temperature replica exchange trajectories Jason Swails (Fri Mar 20 2015 - 05:24:02 PDT)
[AMBER] Problem with heating lipid bilayer in amber 12 Chris Gaughan (Thu Mar 19 2015 - 14:31:26 PDT)
- Re: [AMBER] Problem with heating lipid bilayer in amber 12 Ross Walker (Thu Mar 19 2015 - 14:49:30 PDT)
[AMBER] Drifting molecules despite strong restraints Sanmeet Chahal (Thu Mar 19 2015 - 15:32:42 PDT)
- Re: [AMBER] Drifting molecules despite strong restraints Jason Swails (Fri Mar 20 2015 - 05:22:03 PDT)
  - Re: [AMBER] Drifting molecules despite strong restraints Sanmeet Chahal (Fri Mar 20 2015 - 07:18:19 PDT)
    - Re: [AMBER] Drifting molecules despite strong restraints Jason Swails (Fri Mar 20 2015 - 08:23:15 PDT)
[AMBER] Reduce not working properly Francesco Gentile (Thu Mar 19 2015 - 21:47:14 PDT)
- Re: [AMBER] Reduce not working properly David A Case (Fri Mar 20 2015 - 05:44:45 PDT)
  - [AMBER] Citation from the apostrophe police David A Case (Fri Mar 20 2015 - 06:13:07 PDT)
[AMBER] loading molecule in xleap and saving it in mol2 format jacob wick (Fri Mar 20 2015 - 00:17:05 PDT)
- Re: [AMBER] loading molecule in xleap and saving it in mol2 format hannes.loeffler.stfc.ac.uk (Fri Mar 20 2015 - 01:01:48 PDT)
- Re: [AMBER] loading molecule in xleap and saving it in mol2 format FyD (Fri Mar 20 2015 - 03:14:19 PDT)
  - Re: [AMBER] loading molecule in xleap and saving it in mol2 format Hannes Loeffler (Fri Mar 20 2015 - 03:37:29 PDT)
    - Re: [AMBER] loading molecule in xleap and saving it in mol2 format jacob wick (Fri Mar 20 2015 - 04:01:49 PDT)
    - Re: [AMBER] loading molecule in xleap and saving it in mol2 formatDear Hannes Loeffler (Fri Mar 20 2015 - 07:14:23 PDT)
    - Re: [AMBER] loading molecule in xleap and saving it in mol2 formatDear jacob wick (Fri Mar 20 2015 - 07:27:21 PDT)
- Re: [AMBER] loading molecule in xleap and saving it in mol2 format Bill Ross (Fri Mar 20 2015 - 07:45:23 PDT)
  - Re: [AMBER] loading molecule in xleap and saving it in mol2 format jacob wick (Fri Mar 20 2015 - 08:09:50 PDT)
    - Re: [AMBER] loading molecule in xleap and saving it in mol2 format Hannes Loeffler (Fri Mar 20 2015 - 08:15:32 PDT)
- Re: [AMBER] loading molecule in xleap and saving it in mol2 format Bill Ross (Fri Mar 20 2015 - 08:19:59 PDT)
- Re: [AMBER] loading molecule in xleap and saving it in mol2 format Bill Ross (Fri Mar 20 2015 - 08:31:38 PDT)
[AMBER] Bond distance and Box shape Arjun Sharma (Fri Mar 20 2015 - 07:21:58 PDT)
- Re: [AMBER] Bond distance and Box shape Daniel Roe (Fri Mar 20 2015 - 07:34:53 PDT)
[AMBER] error with mmpbsa.py Norbert GARNIER (Fri Mar 20 2015 - 08:32:24 PDT)
- Re: [AMBER] error with mmpbsa.py Kenneth Huang (Fri Mar 20 2015 - 09:21:05 PDT)
  - Re: [AMBER] error with mmpbsa.py Norbert GARNIER (Fri Mar 20 2015 - 10:08:52 PDT)
- Re: [AMBER] error with mmpbsa.py Jason Swails (Fri Mar 20 2015 - 09:23:29 PDT)
[AMBER] Leap warning George Tzotzos (Fri Mar 20 2015 - 10:55:18 PDT)
- Re: [AMBER] Leap warning Bill Ross (Wed Sep 09 2009 - 09:49:05 PDT)
- Re: [AMBER] Leap warning Bill Ross (Fri Mar 20 2015 - 11:07:47 PDT)
[AMBER] heat capacity Ahmet yıldırım (Fri Mar 20 2015 - 13:07:34 PDT)
- Re: [AMBER] heat capacity David A Case (Sat Mar 21 2015 - 06:17:25 PDT)
[AMBER] [Fwd: ] vladimir.palivec.marge.uochb.cas.cz (Sat Mar 21 2015 - 04:46:19 PDT)
[AMBER] Error message from FEW in Amber14 tutorial A24 Michael Shokhen (Sun Mar 22 2015 - 06:44:30 PDT)
- Re: [AMBER] Error message from FEW in Amber14 tutorial A24 Michele Bonus (Sun Mar 22 2015 - 11:19:28 PDT)
  - Re: [AMBER] Error message from FEW in Amber14 tutorial A24 Jason Swails (Sun Mar 22 2015 - 13:22:37 PDT)
    - Re: [AMBER] Error message from FEW in Amber14 tutorial A24 Michael Shokhen (Mon Mar 23 2015 - 04:57:50 PDT)
    - Re: [AMBER] Error message from FEW in Amber14 tutorial A24 Jason Swails (Mon Mar 23 2015 - 07:41:10 PDT)
    - Re: [AMBER] Error message from FEW in Amber14 tutorial A24 Hannes Loeffler (Mon Mar 23 2015 - 07:52:14 PDT)
    - Re: [AMBER] Error message from FEW in Amber14 tutorial A24 Jason Swails (Mon Mar 23 2015 - 08:17:31 PDT)
    - Re: [AMBER] Error message from FEW in Amber14 tutorial A24 Hannes Loeffler (Mon Mar 23 2015 - 08:51:59 PDT)
    - Re: [AMBER] Error message from FEW in Amber14 tutorial A24 David A Case (Mon Mar 23 2015 - 11:50:59 PDT)
    - Re: [AMBER] Error message from FEW in Amber14 tutorial A24 hannes.loeffler.stfc.ac.uk (Mon Mar 23 2015 - 12:05:52 PDT)
    - Re: [AMBER] Error message from FEW in Amber14 tutorial A24 Jason Swails (Mon Mar 23 2015 - 13:24:57 PDT)
[AMBER] Immediate Postdoctoral Position Opening In Dr. Khaled Barakat’s Lab, Faculty Of Pharmacy, University Of Alberta Marawan Hussien (Sun Mar 22 2015 - 14:01:11 PDT)
- Re: [AMBER] Immediate Postdoctoral Position Opening In Dr. Khaled Barakat’s Lab, Faculty Of Pharmacy, University Of Alberta Ayesha Fatima (Tue Jul 21 2015 - 00:26:02 PDT)
[AMBER] error when doing lifetime calculation Vijay Achari (Sun Mar 22 2015 - 23:32:36 PDT)
- Re: [AMBER] error when doing lifetime calculation Daniel Roe (Mon Mar 23 2015 - 07:32:08 PDT)
  - Re: [AMBER] error when doing lifetime calculation Vijay Achari (Mon Mar 23 2015 - 09:06:44 PDT)
    - Re: [AMBER] error when doing lifetime calculation Daniel Roe (Mon Mar 23 2015 - 12:34:00 PDT)
[AMBER] "Error opening unit 30: File "inpcrd" is missing or unreadable" on Tutorial A15 christian.yongky.ui.ac.id (Sun Mar 22 2015 - 23:47:08 PDT)
- Re: [AMBER] "Error opening unit 30: File "inpcrd" is missing or unreadable" on Tutorial A15 Jason Swails (Mon Mar 23 2015 - 02:33:58 PDT)
  - Re: [AMBER] "Error opening unit 30: File "inpcrd" is missing or unreadable" on Tutorial A15 christian.yongky.ui.ac.id (Mon Mar 23 2015 - 03:24:20 PDT)
[AMBER] Fwd: Regarding the MCPB tutorial Garisekurthi Satheesh (Mon Mar 23 2015 - 02:41:35 PDT)
[AMBER] CUDA problems Beale, John (Mon Mar 23 2015 - 07:41:30 PDT)
- Re: [AMBER] CUDA problems Ross Walker (Mon Mar 23 2015 - 09:52:29 PDT)
[AMBER] Replica Exchange on a single Titan-X GPU amr hamed (Mon Mar 23 2015 - 08:19:09 PDT)
- Re: [AMBER] Replica Exchange on a single Titan-X GPU filip fratev (Mon Mar 23 2015 - 08:35:13 PDT)
  - Re: [AMBER] Replica Exchange on a single Titan-X GPU Ross Walker (Mon Mar 23 2015 - 11:28:30 PDT)
    - Re: [AMBER] Replica Exchange on a single Titan-X GPU filip fratev (Mon Mar 23 2015 - 12:19:56 PDT)
- Re: [AMBER] Replica Exchange on a single Titan-X GPU Ross Walker (Mon Mar 23 2015 - 10:01:04 PDT)
[AMBER] RMSF & changes of the secondary structure of protein shahab shariati (Mon Mar 23 2015 - 11:45:41 PDT)
- Re: [AMBER] RMSF & changes of the secondary structure of protein Daniel Roe (Mon Mar 23 2015 - 11:50:55 PDT)
[AMBER] vdw energy and electrostatic energy calculation for osmolyte Subrata Paul (Tue Mar 24 2015 - 00:31:49 PDT)
- Re: [AMBER] vdw energy and electrostatic energy calculation for osmolyte Jason Swails (Tue Mar 24 2015 - 06:55:54 PDT)
  - Re: [AMBER] vdw energy and electrostatic energy calculation for osmolyte Subrata Paul (Tue Mar 24 2015 - 22:30:26 PDT)
    - Re: [AMBER] vdw energy and electrostatic energy calculation for osmolyte Jason Swails (Wed Mar 25 2015 - 05:14:00 PDT)
    - Re: [AMBER] vdw energy and electrostatic energy calculation for osmolyte Subrata Paul (Wed Mar 25 2015 - 11:40:58 PDT)
    - Re: [AMBER] vdw energy and electrostatic energy calculation for osmolyte Jason Swails (Wed Mar 25 2015 - 11:47:02 PDT)
    - Re: [AMBER] vdw energy and electrostatic energy calculation for osmolyte Daniel Roe (Wed Mar 25 2015 - 12:18:47 PDT)
[AMBER] About generalized restraints in AMBER14 with GPU support Attilio Vittorio Vargiu (Tue Mar 24 2015 - 07:29:28 PDT)
- Re: [AMBER] About generalized restraints in AMBER14 with GPU support Jason Swails (Tue Mar 24 2015 - 07:48:46 PDT)
[AMBER] EGB and ESCF might not be converged if the net charge not equal to 0 in the QM/MM-GBSA psu4.uic.edu (Tue Mar 24 2015 - 10:06:49 PDT)
- Re: [AMBER] EGB and ESCF might not be converged if the net charge not equal to 0 in the QM/MM-GBSA Gerald Monard (Fri Mar 27 2015 - 01:27:39 PDT)
  - Re: [AMBER] EGB and ESCF might not be converged if the net charge not equal to 0 in the QM/MM-GBSA psu4.uic.edu (Thu Apr 02 2015 - 00:27:31 PDT)
    - Re: [AMBER] EGB and ESCF might not be converged if the net charge not equal to 0 in the QM/MM-GBSA Gerald Monard (Thu Apr 02 2015 - 01:42:11 PDT)
    - Re: [AMBER] EGB and ESCF might not be converged if the net charge not equal to 0 in the QM/MM-GBSA psu4.uic.edu (Fri Apr 03 2015 - 15:48:37 PDT)
    - Re: [AMBER] EGB and ESCF might not be converged if the net charge not equal to 0 in the QM/MM-GBSA Ross Walker (Fri Apr 03 2015 - 15:57:23 PDT)
    - Re: [AMBER] EGB and ESCF might not be converged if the net charge not equal to 0 in the QM/MM-GBSA psu4.uic.edu (Sun Apr 05 2015 - 17:35:39 PDT)
    - Re: [AMBER] EGB and ESCF might not be converged if the net charge not equal to 0 in the QM/MM-GBSA Ross Walker (Mon Apr 06 2015 - 09:21:03 PDT)
[AMBER] CpHMD-pHREX AMBER14 Arjun Sharma (Tue Mar 24 2015 - 10:37:29 PDT)
- Re: [AMBER] CpHMD-pHREX AMBER14 Jason Swails (Tue Mar 24 2015 - 18:36:02 PDT)
[AMBER] concave edge on torus has mismatched atoms Sylvester Tumusiime (Tue Mar 24 2015 - 12:28:12 PDT)
- Re: [AMBER] concave edge on torus has mismatched atoms Daniel Roe (Tue Mar 24 2015 - 13:02:16 PDT)
  - Re: [AMBER] concave edge on torus has mismatched atoms Sylvester Tumusiime (Tue Mar 24 2015 - 13:06:15 PDT)
[AMBER] The unperturbed charge of the unit: -2.980000 is not integral 王华 (Tue Mar 24 2015 - 18:40:20 PDT)
- Re: [AMBER] The unperturbed charge of the unit: -2.980000 is not integral Jason Swails (Tue Mar 24 2015 - 19:06:34 PDT)
- Re: [AMBER] The unperturbed charge of the unit: -2.980000 is not integral George Tzotzos (Tue Mar 24 2015 - 19:48:08 PDT)
[AMBER] iterative calculation in CPPTRAJ using "for... do... done" Vijay Achari (Wed Mar 25 2015 - 04:42:16 PDT)
- Re: [AMBER] iterative calculation in CPPTRAJ using "for... do... done" Daniel Roe (Wed Mar 25 2015 - 06:50:26 PDT)
  - Re: [AMBER] iterative calculation in CPPTRAJ using "for... do... done" Vijay Achari (Wed Mar 25 2015 - 09:51:56 PDT)
- Re: [AMBER] iterative calculation in CPPTRAJ using "for... do... done" Jason Swails (Wed Mar 25 2015 - 06:52:06 PDT)
  - Re: [AMBER] iterative calculation in CPPTRAJ using "for... do... done" Vijay Achari (Wed Mar 25 2015 - 09:53:56 PDT)
[AMBER] trouble running pmemd.cuda Brian Radak (Wed Mar 25 2015 - 10:30:23 PDT)
- Re: [AMBER] trouble running pmemd.cuda Ross Walker (Wed Mar 25 2015 - 10:41:27 PDT)
  - Re: [AMBER] trouble running pmemd.cuda Brian Radak (Wed Mar 25 2015 - 11:46:24 PDT)
    - Re: [AMBER] trouble running pmemd.cuda Jason Swails (Wed Mar 25 2015 - 11:49:52 PDT)
    - Re: [AMBER] trouble running pmemd.cuda Brian Radak (Thu Mar 26 2015 - 07:41:38 PDT)
    - Re: [AMBER] trouble running pmemd.cuda Jason Swails (Thu Mar 26 2015 - 08:07:05 PDT)
    - Re: [AMBER] trouble running pmemd.cuda Ross Walker (Thu Mar 26 2015 - 08:49:53 PDT)
    - Re: [AMBER] trouble running pmemd.cuda Jason Swails (Thu Mar 26 2015 - 09:46:51 PDT)
    - Re: [AMBER] trouble running pmemd.cuda Brian Radak (Thu Mar 26 2015 - 10:08:54 PDT)
    - Re: [AMBER] trouble running pmemd.cuda Jason Swails (Thu Mar 26 2015 - 10:17:07 PDT)
    - Re: [AMBER] trouble running pmemd.cuda Ross Walker (Thu Mar 26 2015 - 10:17:54 PDT)
    - Re: [AMBER] trouble running pmemd.cuda Brian Radak (Thu Mar 26 2015 - 11:08:24 PDT)
    - Re: [AMBER] trouble running pmemd.cuda Jason Swails (Thu Mar 26 2015 - 11:14:57 PDT)
[AMBER] Free energy calculation: Thermodynamic integration with use of restraints vladimir.palivec.marge.uochb.cas.cz (Wed Mar 25 2015 - 10:55:45 PDT)
- Re: [AMBER] Free energy calculation: Thermodynamic integration with use of restraints hannes.loeffler.stfc.ac.uk (Wed Mar 25 2015 - 12:12:34 PDT)
  - Re: [AMBER] Free energy calculation: Thermodynamic integration with use of restraints hannes.loeffler.stfc.ac.uk (Thu Mar 26 2015 - 00:32:07 PDT)
    - Re: [AMBER] Free energy calculation: Thermodynamic integration with use of restraints vladimir.palivec.marge.uochb.cas.cz (Thu Mar 26 2015 - 01:34:47 PDT)
    - Re: [AMBER] Free energy calculation: Thermodynamic integration with use of restraints hannes.loeffler.stfc.ac.uk (Thu Mar 26 2015 - 02:20:25 PDT)
    - Re: [AMBER] Free energy calculation: Thermodynamic integration with use of restraints vladimir.palivec.marge.uochb.cas.cz (Thu Mar 26 2015 - 08:22:03 PDT)
    - Re: [AMBER] Free energy calculation: Thermodynamic integration with use of restraints hannes.loeffler.stfc.ac.uk (Thu Mar 26 2015 - 09:02:58 PDT)
    - Re: [AMBER] Free energy calculation: Thermodynamic integration with use of restraints vladimir.palivec.marge.uochb.cas.cz (Fri Mar 27 2015 - 08:46:47 PDT)
    - Re: [AMBER] Free energy calculation: Thermodynamic integration with use of restraints hannes.loeffler.stfc.ac.uk (Fri Mar 27 2015 - 09:30:57 PDT)
Re: [AMBER] AMBER Digest, Vol 1169, Issue 1 Arjun Sharma (Wed Mar 25 2015 - 14:54:31 PDT)
[AMBER] Implicit solvent simulation with Andersen thermostat Glenn Carrington [bs10g3c] (Wed Mar 25 2015 - 16:41:38 PDT)
- Re: [AMBER] Implicit solvent simulation with Andersen thermostat Jason Swails (Wed Mar 25 2015 - 19:06:18 PDT)
- Re: [AMBER] Implicit solvent simulation with Andersen thermostat Hai Nguyen (Wed Mar 25 2015 - 22:56:16 PDT)
  - Re: [AMBER] Implicit solvent simulation with Andersen thermostat Glenn Carrington [bs10g3c] (Thu Mar 26 2015 - 04:59:42 PDT)
    - Re: [AMBER] Implicit solvent simulation with Andersen thermostat Jason Swails (Thu Mar 26 2015 - 07:25:55 PDT)
    - Re: [AMBER] Implicit solvent simulation with Andersen thermostat Ross Walker (Thu Mar 26 2015 - 08:54:14 PDT)
    - Re: [AMBER] Implicit solvent simulation with Andersen thermostat Ross Walker (Thu Mar 26 2015 - 08:57:17 PDT)
    - Re: [AMBER] Implicit solvent simulation with Andersen thermostat David A Case (Thu Mar 26 2015 - 09:33:31 PDT)
    - Re: [AMBER] Implicit solvent simulation with Andersen thermostat Glenn Carrington [bs10g3c] (Fri Mar 27 2015 - 04:31:17 PDT)
    - Re: [AMBER] Implicit solvent simulation with Andersen thermostat Jason Swails (Fri Mar 27 2015 - 04:43:16 PDT)
[AMBER] vdw energy and electrostatic energy calculation for osmolyte MOHD HOMAIDUR RAHMAN (Wed Mar 25 2015 - 22:59:40 PDT)
- Re: [AMBER] vdw energy and electrostatic energy calculation for osmolyte Jason Swails (Thu Mar 26 2015 - 07:29:28 PDT)
[AMBER] MMGBSA error Abhishek TYAGI (Wed Mar 25 2015 - 23:06:44 PDT)
- [AMBER] MMGBSA error Kenneth Huang (Thu Mar 26 2015 - 05:55:35 PDT)
[AMBER] Antechamber - TURBOMOLE Sanja Zivanovic (Thu Mar 26 2015 - 04:48:26 PDT)
- Re: [AMBER] Antechamber - TURBOMOLE hannes.loeffler.stfc.ac.uk (Thu Mar 26 2015 - 05:03:54 PDT)
[AMBER] Water sigma parameters Paolo Tosco (Thu Mar 26 2015 - 13:16:44 PDT)
- Re: [AMBER] Water sigma parameters David A Case (Thu Mar 26 2015 - 14:38:43 PDT)
[AMBER] combinatorial library Hector A. Baldoni (Thu Mar 26 2015 - 17:22:05 PDT)
[AMBER] problem regarding different pmf graph Shubhadip Das (Thu Mar 26 2015 - 21:21:52 PDT)
[AMBER] Histogram analysis of the dihedral distributions using cpptraj James Starlight (Fri Mar 27 2015 - 08:13:10 PDT)
- Re: [AMBER] Histogram analysis of the dihedral distributions using cpptraj Daniel Roe (Fri Mar 27 2015 - 08:39:26 PDT)
  - Re: [AMBER] Histogram analysis of the dihedral distributions using cpptraj James Starlight (Fri Mar 27 2015 - 09:28:07 PDT)
    - Re: [AMBER] Histogram analysis of the dihedral distributions using cpptraj Daniel Roe (Fri Mar 27 2015 - 09:33:10 PDT)
    - Re: [AMBER] Histogram analysis of the dihedral distributions using cpptraj James Starlight (Mon Mar 30 2015 - 03:52:48 PDT)
    - Re: [AMBER] Histogram analysis of the dihedral distributions using cpptraj James Starlight (Mon Mar 30 2015 - 06:02:18 PDT)
    - Re: [AMBER] Histogram analysis of the dihedral distributions using cpptraj Daniel Roe (Mon Mar 30 2015 - 07:04:50 PDT)
[AMBER] aMD boost parameters for CHARMM force field? Brian Radak (Fri Mar 27 2015 - 08:39:13 PDT)
- Re: [AMBER] aMD boost parameters for CHARMM force field? Daniel Roe (Fri Mar 27 2015 - 08:43:13 PDT)
[AMBER] Intel Compiler and MKL Novosielski, Ryan (Fri Mar 27 2015 - 11:03:32 PDT)
- Re: [AMBER] Intel Compiler and MKL Scott Brozell (Fri Mar 27 2015 - 13:04:44 PDT)
  - Re: [AMBER] Intel Compiler and MKL Novosielski, Ryan (Fri Mar 27 2015 - 13:39:16 PDT)
    - Re: [AMBER] Intel Compiler and MKL Scott Brozell (Fri Mar 27 2015 - 14:14:22 PDT)
[AMBER] REGARDING ATOM TYPE ERROR Swithin Hanosh (Sat Mar 28 2015 - 05:01:43 PDT)
- Re: [AMBER] REGARDING ATOM TYPE ERROR hannes.loeffler.stfc.ac.uk (Sat Mar 28 2015 - 05:51:45 PDT)
[AMBER] Gromacs towards Amber conversion Simone Fulle (Sat Mar 28 2015 - 07:25:27 PDT)
- Re: [AMBER] Gromacs towards Amber conversion Carlos Simmerling (Sat Mar 28 2015 - 07:30:07 PDT)
- Re: [AMBER] Gromacs towards Amber conversion Karl Kirschner (Sun Mar 29 2015 - 03:12:51 PDT)
[AMBER] Projection on modes calculated by distcovar matrix Vishal Kumar Jaiswal (Sun Mar 29 2015 - 02:53:00 PDT)
- Re: [AMBER] Projection on modes calculated by distcovar matrix Daniel Roe (Sun Mar 29 2015 - 08:43:27 PDT)
[AMBER] Restrained MD James Starlight (Sun Mar 29 2015 - 03:50:31 PDT)
- Re: [AMBER] Restrained MD David A Case (Sun Mar 29 2015 - 07:42:50 PDT)
  - Re: [AMBER] Restrained MD James Starlight (Mon Mar 30 2015 - 05:38:46 PDT)
    - Re: [AMBER] Restrained MD David A Case (Mon Mar 30 2015 - 08:19:30 PDT)
    - Re: [AMBER] Restrained MD James Starlight (Tue Mar 31 2015 - 04:58:59 PDT)
    - Re: [AMBER] Restrained MD James Starlight (Tue Mar 31 2015 - 05:09:02 PDT)
    - Re: [AMBER] Restrained MD David A Case (Tue Mar 31 2015 - 05:32:04 PDT)
    - Re: [AMBER] Restrained MD James Starlight (Tue Mar 31 2015 - 07:03:34 PDT)
    - Re: [AMBER] Restrained MD David A Case (Tue Mar 31 2015 - 09:01:29 PDT)
    - Re: [AMBER] Restrained MD James Starlight (Thu Apr 02 2015 - 05:38:02 PDT)
    - Re: [AMBER] Restrained MD James Starlight (Tue Apr 07 2015 - 05:16:39 PDT)
    - Re: [AMBER] Restrained MD Daniel Roe (Tue Apr 07 2015 - 07:23:25 PDT)
    - Re: [AMBER] Restrained MD James Starlight (Tue Apr 07 2015 - 07:44:45 PDT)
[AMBER] flag for fast water FyD (Sun Mar 29 2015 - 07:54:06 PDT)
- Re: [AMBER] flag for fast water David A Case (Mon Mar 30 2015 - 05:20:27 PDT)
  - Re: [AMBER] flag for fast water Jason Swails (Mon Mar 30 2015 - 05:27:04 PDT)
[AMBER] Problem Regarding Different PMF Graph Shubhadip Das (Sun Mar 29 2015 - 22:02:34 PDT)
- Re: [AMBER] Problem Regarding Different PMF Graph Jason Swails (Mon Mar 30 2015 - 05:41:21 PDT)
[AMBER] Problem Regarding Different PMF Graphs Shubhadip Das (Sun Mar 29 2015 - 22:04:22 PDT)
[AMBER] How to obtain potential energy using mdcrd trajectories in AMBER12 Wang Moye (Mon Mar 30 2015 - 05:39:03 PDT)
- Re: [AMBER] How to obtain potential energy using mdcrd trajectories in AMBER12 Christina Bergonzo (Mon Mar 30 2015 - 07:08:17 PDT)
- Re: [AMBER] How to obtain potential energy using mdcrd trajectories in AMBER12 Jason Swails (Mon Mar 30 2015 - 08:34:08 PDT)
  - Re: [AMBER] How to obtain potential energy using mdcrd trajectories in AMBER12 Brian Radak (Thu Apr 02 2015 - 12:06:23 PDT)
    - Re: [AMBER] How to obtain potential energy using mdcrd trajectories in AMBER12 Jason Swails (Thu Apr 02 2015 - 13:12:09 PDT)
    - Re: [AMBER] How to obtain potential energy using mdcrd trajectories in AMBER12 Brian Radak (Thu Apr 02 2015 - 13:49:14 PDT)
    - Re: [AMBER] How to obtain potential energy using mdcrd trajectories in AMBER12 Jason Swails (Fri Apr 03 2015 - 07:07:47 PDT)
    - Re: [AMBER] How to obtain potential energy using mdcrd trajectories in AMBER12 Gerald Monard (Fri Apr 03 2015 - 08:44:24 PDT)
[AMBER] Projection on distance covariance modes Vishal Kumar Jaiswal (Mon Mar 30 2015 - 06:11:55 PDT)
- Re: [AMBER] Projection on distance covariance modes Christina Bergonzo (Mon Mar 30 2015 - 06:49:08 PDT)
[AMBER] Manual still ambiguous about igb=8 and pmemd Edwin Helbert Aponte Angarita (Mon Mar 30 2015 - 09:32:44 PDT)
- Re: [AMBER] Manual still ambiguous about igb=8 and pmemd Jason Swails (Mon Mar 30 2015 - 09:39:55 PDT)
[AMBER] Help regarding appropriate analysis for correlated motion using cpptraj Kshatresh Dutta Dubey (Mon Mar 30 2015 - 12:44:39 PDT)
- Re: [AMBER] Help regarding appropriate analysis for correlated motion using cpptraj Jason Swails (Wed Apr 01 2015 - 06:04:26 PDT)
  - Re: [AMBER] Help regarding appropriate analysis for correlated motion using cpptraj Kshatresh Dutta Dubey (Wed Apr 01 2015 - 07:42:50 PDT)
    - Re: [AMBER] Help regarding appropriate analysis for correlated motion using cpptraj Jason Swails (Wed Apr 01 2015 - 07:49:17 PDT)
    - Re: [AMBER] Help regarding appropriate analysis for correlated motion using cpptraj Kshatresh Dutta Dubey (Wed Apr 01 2015 - 07:59:14 PDT)
[AMBER] issue with LRT calculation in sander Emilio Angelina (Mon Mar 30 2015 - 13:01:18 PDT)
[AMBER] temp ramping in tutorial A5 Robert Wohlhueter (Mon Mar 30 2015 - 15:33:31 PDT)
- Re: [AMBER] temp ramping in tutorial A5 Jason Swails (Tue Mar 31 2015 - 05:11:41 PDT)
- Re: [AMBER] temp ramping in tutorial A5 Robert Wohlhueter (Tue Mar 31 2015 - 06:52:12 PDT)
  - Re: [AMBER] temp ramping in tutorial A5 Jason Swails (Tue Mar 31 2015 - 07:38:38 PDT)
    - Re: [AMBER] temp ramping in tutorial A5 Robert Wohlhueter (Tue Mar 31 2015 - 13:22:30 PDT)
[AMBER] Stability MMPBSA Parker de Waal (Mon Mar 30 2015 - 18:44:20 PDT)
- Re: [AMBER] Stability MMPBSA Parker de Waal (Mon Mar 30 2015 - 19:47:00 PDT)
  - Re: [AMBER] Stability MMPBSA Jason Swails (Tue Mar 31 2015 - 05:05:52 PDT)
- Re: [AMBER] Stability MMPBSA Kenneth Huang (Mon Mar 30 2015 - 19:47:59 PDT)
[AMBER] Multiple MEPs option in R.E.D tools Yip Yew Mun (Mon Mar 30 2015 - 19:26:05 PDT)
- Re: [AMBER] Multiple MEPs option in R.E.D tools Brent Krueger (Tue Mar 31 2015 - 04:40:40 PDT)
  - Re: [AMBER] Multiple MEPs option in R.E.D tools FyD (Tue Mar 31 2015 - 12:07:43 PDT)
    - Re: [AMBER] Multiple MEPs option in R.E.D tools Jason Swails (Tue Mar 31 2015 - 13:53:52 PDT)
    - Re: [AMBER] Multiple MEPs option in R.E.D tools Hannes Loeffler (Wed Apr 01 2015 - 01:58:34 PDT)
    - Re: [AMBER] Multiple MEPs option in R.E.D tools FyD (Thu Apr 02 2015 - 00:46:58 PDT)
    - Re: [AMBER] Multiple MEPs option in R.E.D tools FyD (Thu Apr 02 2015 - 00:30:47 PDT)
    - Re: [AMBER] Multiple MEPs option in R.E.D tools Yip Yew Mun (Tue Mar 31 2015 - 20:08:17 PDT)
- Re: [AMBER] Multiple MEPs option in R.E.D tools Jason Swails (Tue Mar 31 2015 - 05:07:41 PDT)
- Re: [AMBER] Multiple MEPs option in R.E.D tools FyD (Tue Mar 31 2015 - 11:44:52 PDT)
[AMBER] Problems with Amber installation Pinchas Aped (Tue Mar 31 2015 - 06:45:53 PDT)
- Re: [AMBER] Problems with Amber installation Gerald Monard (Tue Mar 31 2015 - 07:28:18 PDT)
  - Re: [AMBER] Problems with Amber installation Pinchas Aped (Tue Mar 31 2015 - 08:07:09 PDT)
    - Re: [AMBER] Problems with Amber installation Jason Swails (Tue Mar 31 2015 - 08:40:14 PDT)
[AMBER] Pressure units in 1D-RISM Maksim Mišin (Tue Mar 31 2015 - 07:27:00 PDT)
- Re: [AMBER] Pressure units in 1D-RISM David A Case (Tue Mar 31 2015 - 09:09:08 PDT)
  - Re: [AMBER] Pressure units in 1D-RISM Maksim Mišin (Tue Mar 31 2015 - 10:25:28 PDT)
- Re: [AMBER] Pressure units in 1D-RISM Tyler Luchko (Tue Mar 31 2015 - 22:00:08 PDT)
[AMBER] AMBER14 pmemd.cuda.MPI : *** in mdout files Himanshu Joshi (Tue Mar 31 2015 - 10:58:51 PDT)
- Re: [AMBER] AMBER14 pmemd.cuda.MPI : *** in mdout files Ross Walker (Tue Mar 31 2015 - 11:06:19 PDT)
  - Re: [AMBER] AMBER14 pmemd.cuda.MPI : *** in mdout files Himanshu Joshi (Tue Mar 31 2015 - 20:32:38 PDT)
    - Re: [AMBER] AMBER14 pmemd.cuda.MPI : *** in mdout files Ross Walker (Tue Mar 31 2015 - 20:39:06 PDT)
    - Re: [AMBER] AMBER14 pmemd.cuda.MPI : *** in mdout files Himanshu Joshi (Tue Mar 31 2015 - 21:13:02 PDT)
    - Re: [AMBER] AMBER14 pmemd.cuda.MPI : *** in mdout files Ross Walker (Tue Mar 31 2015 - 23:33:34 PDT)
    - Re: [AMBER] AMBER14 pmemd.cuda.MPI : *** in mdout files Ross Walker (Fri Apr 03 2015 - 22:18:58 PDT)
- Re: [AMBER] AMBER14 pmemd.cuda.MPI : *** in mdout files Bill Ross (Tue Mar 31 2015 - 18:00:34 PDT)
[AMBER] 发送给你的文件 chemjxn (Tue Mar 31 2015 - 23:29:00 PDT)
[AMBER] MCPB subprogram problem chemjxn (Tue Mar 31 2015 - 23:41:50 PDT)
- Re: [AMBER] MCPB subprogram problem Pengfei Li (Wed Apr 01 2015 - 12:43:11 PDT)
- [AMBER] Free energy calculation of ligand binding energy: Thermodynamic integration - long range dispersion correction - recalculate trajectory with different potential vladimir.palivec.marge.uochb.cas.cz (Thu Apr 02 2015 - 03:57:35 PDT)
  - Re: [AMBER] Free energy calculation of ligand binding energy: Thermodynamic integration - long range dispersion correction - recalculate trajectory with different potential Hannes Loeffler (Thu Apr 02 2015 - 04:31:11 PDT)
[AMBER] New Force Field Jason Swails (Wed Apr 01 2015 - 04:12:07 PDT)
- Re: [AMBER] New Force Field Adrian Roitberg (Wed Apr 01 2015 - 05:25:31 PDT)
  - Re: [AMBER] New Force Field Jason Swails (Wed Apr 01 2015 - 05:36:25 PDT)
    - Re: [AMBER] New Force Field Jiri Sponer (Wed Apr 01 2015 - 05:58:18 PDT)
    - Re: [AMBER] New Force Field Alessandro Contini (Wed Apr 01 2015 - 06:18:58 PDT)
    - Re: [AMBER] New Force Field Carlos Simmerling (Wed Apr 01 2015 - 06:41:26 PDT)
    - Re: [AMBER] New Force Field abdennour braka (Wed Apr 01 2015 - 07:06:42 PDT)
    - Re: [AMBER] New Force Field sribone.fcq.unc.edu.ar (Wed Apr 01 2015 - 07:47:38 PDT)
    - Re: [AMBER] New Force Field Alessandro Contini (Wed Apr 01 2015 - 07:08:13 PDT)
    - Re: [AMBER] New Force Field Peter Kekenes-Huskey (Wed Apr 01 2015 - 06:20:00 PDT)
- Re: [AMBER] New Force Field Daniel Roe (Wed Apr 01 2015 - 07:10:22 PDT)
  - Re: [AMBER] New Force Field Carlos Simmerling (Wed Apr 01 2015 - 07:36:35 PDT)
    - Re: [AMBER] New Force Field James Maier (Wed Apr 01 2015 - 07:43:55 PDT)
[AMBER] error **** in output file with wrapping first molecule on GPU Quynh Vo (Wed Apr 01 2015 - 23:00:08 PDT)
- Re: [AMBER] error **** in output file with wrapping first molecule on GPU Gerald Monard (Thu Apr 02 2015 - 00:13:44 PDT)
  - Re: [AMBER] error **** in output file with wrapping first molecule on GPU Quynh Vo (Thu Apr 02 2015 - 09:41:23 PDT)
    - Re: [AMBER] error **** in output file with wrapping first molecule on GPU Jason Swails (Thu Apr 02 2015 - 10:27:21 PDT)
    - Re: [AMBER] error **** in output file with wrapping first molecule on GPU Gerald Monard (Fri Apr 03 2015 - 05:15:53 PDT)
- Re: [AMBER] error **** in output file with wrapping first molecule on GPU Jason Swails (Thu Apr 02 2015 - 11:35:14 PDT)
- Re: [AMBER] error **** in output file with wrapping first molecule on GPU Gerald Monard (Fri Apr 03 2015 - 14:50:15 PDT)
[AMBER] Error while running MMPBSA Shreeramesh (Thu Apr 02 2015 - 00:00:59 PDT)
- Re: [AMBER] Error while running MMPBSA Jason Swails (Thu Apr 02 2015 - 05:40:32 PDT)
  - Re: [AMBER] Error while running MMPBSA Shreeramesh (Thu Apr 02 2015 - 07:47:42 PDT)
    - Re: [AMBER] Error while running MMPBSA Kenneth Huang (Thu Apr 02 2015 - 07:57:33 PDT)
    - Re: [AMBER] Error while running MMPBSA Shreeramesh (Thu Apr 02 2015 - 08:15:21 PDT)
    - Re: [AMBER] Error while running MMPBSA Kenneth Huang (Thu Apr 02 2015 - 08:25:34 PDT)
    - Re: [AMBER] Error while running MMPBSA Shreeramesh (Fri Apr 03 2015 - 02:24:10 PDT)
    - Re: [AMBER] Error while running MMPBSA Kenneth Huang (Fri Apr 03 2015 - 08:01:26 PDT)
- Re: [AMBER] Error while running MMPBSA Bill Ross (Thu Apr 02 2015 - 08:31:25 PDT)
[AMBER] Build long polymer from the monomer using Xleap James Starlight (Thu Apr 02 2015 - 05:41:24 PDT)
- Re: [AMBER] Build long polymer from the monomer using Xleap Karl Kirschner (Thu Apr 02 2015 - 06:23:42 PDT)
  - Re: [AMBER] Build long polymer from the monomer using Xleap James Starlight (Thu Apr 02 2015 - 07:08:54 PDT)
    - Re: [AMBER] Build long polymer from the monomer using Xleap Karl Kirschner (Thu Apr 02 2015 - 07:39:46 PDT)
- Re: [AMBER] Build long polymer from the monomer using Xleap FyD (Mon Apr 06 2015 - 22:52:51 PDT)
  - Re: [AMBER] Build long polymer from the monomer using Xleap James Starlight (Fri Apr 10 2015 - 04:40:12 PDT)
[AMBER] mmbsa.py issue with the complex.parmtop James Starlight (Thu Apr 02 2015 - 06:17:05 PDT)
- [AMBER] mmbsa.py issue with the complex.parmtop Kenneth Huang (Thu Apr 02 2015 - 07:50:54 PDT)
  - Re: [AMBER] mmbsa.py issue with the complex.parmtop James Starlight (Thu Apr 02 2015 - 08:08:27 PDT)
    - Re: [AMBER] mmbsa.py issue with the complex.parmtop James Starlight (Thu Apr 02 2015 - 08:27:39 PDT)
    - Re: [AMBER] mmbsa.py issue with the complex.parmtop Kenneth Huang (Thu Apr 02 2015 - 08:38:20 PDT)
    - Re: [AMBER] mmbsa.py issue with the complex.parmtop James Starlight (Fri Apr 03 2015 - 04:53:46 PDT)
    - Re: [AMBER] mmbsa.py issue with the complex.parmtop James Starlight (Fri Apr 03 2015 - 05:28:48 PDT)
    - Re: [AMBER] mmbsa.py issue with the complex.parmtop Kenneth Huang (Fri Apr 03 2015 - 08:22:25 PDT)
    - Re: [AMBER] mmbsa.py issue with the complex.parmtop James Starlight (Mon Apr 06 2015 - 06:12:17 PDT)
    - Re: [AMBER] mmbsa.py issue with the complex.parmtop James Starlight (Mon Apr 06 2015 - 07:13:47 PDT)
    - Re: [AMBER] mmbsa.py issue with the complex.parmtop Kenneth Huang (Mon Apr 06 2015 - 07:23:25 PDT)
    - Re: [AMBER] mmbsa.py issue with the complex.parmtop James Starlight (Mon Apr 06 2015 - 07:58:23 PDT)
    - Re: [AMBER] mmbsa.py issue with the complex.parmtop Kenneth Huang (Mon Apr 06 2015 - 08:25:55 PDT)
    - Re: [AMBER] mmbsa.py issue with the complex.parmtop James Starlight (Tue Apr 07 2015 - 05:19:17 PDT)
    - Re: [AMBER] mmbsa.py issue with the complex.parmtop Kenneth Huang (Mon Apr 06 2015 - 07:19:00 PDT)
[AMBER] Sander QMMM Bomb Problem Gulsevin,Alican (Thu Apr 02 2015 - 08:52:30 PDT)
[AMBER] FW: amber14 errors IBRAHIM M ABDELRADY (Thu Apr 02 2015 - 11:16:28 PDT)
- Re: [AMBER] FW: amber14 errors Jason Swails (Thu Apr 02 2015 - 11:59:19 PDT)
  - Re: [AMBER] amber14 errors Novosielski, Ryan (Thu Apr 02 2015 - 12:10:29 PDT)
- Re: [AMBER] FW: amber14 errors IBRAHIM M ABDELRADY (Thu Apr 02 2015 - 12:42:22 PDT)
- Re: [AMBER] FW: amber14 errors Jason Swails (Thu Apr 02 2015 - 13:08:49 PDT)
[AMBER] Lipid Conversion from Charmm PDB to Lipid14 PDB Wong, Sook (NIH/NCATS) [V] (Thu Apr 02 2015 - 12:35:27 PDT)
- Re: [AMBER] Lipid Conversion from Charmm PDB to Lipid14 PDB Daniel Roe (Thu Apr 02 2015 - 12:39:35 PDT)
  - Re: [AMBER] Lipid Conversion from Charmm PDB to Lipid14 PDB Wong, Sook (NIH/NCATS) [V] (Thu Apr 02 2015 - 12:51:33 PDT)
    - Re: [AMBER] Lipid Conversion from Charmm PDB to Lipid14 PDB Wong, Sook (NIH/NCATS) [V] (Thu Apr 02 2015 - 12:59:40 PDT)
[AMBER] MMPBSA issues with ff12SB Neha Gandhi (Fri Apr 03 2015 - 08:34:21 PDT)
- Re: [AMBER] MMPBSA issues with ff12SB Ray Luo, Ph.D. (Fri Apr 03 2015 - 10:28:20 PDT)
  - Re: [AMBER] MMPBSA issues with ff12SB Neha Gandhi (Fri Apr 03 2015 - 19:43:50 PDT)
    - Re: [AMBER] MMPBSA issues with ff12SB Ray Luo, Ph.D. (Fri Apr 03 2015 - 22:00:53 PDT)
[AMBER] Trouble recomputing aMD boost from amdlog/mdout Brian Radak (Fri Apr 03 2015 - 12:42:02 PDT)
[AMBER] MMPBSA.py.MPI Installation Failure Laura Tociu (Sat Apr 04 2015 - 11:34:04 PDT)
- Re: [AMBER] MMPBSA.py.MPI Installation Failure Jason Swails (Tue Apr 07 2015 - 08:36:40 PDT)
  - Re: [AMBER] MMPBSA.py.MPI Installation Failure Laura Tociu (Wed Apr 08 2015 - 22:22:52 PDT)
[AMBER] Question Regarding reduce function of Antechamber Ziheng Wang (Sat Apr 04 2015 - 12:34:22 PDT)
- Re: [AMBER] Question Regarding reduce function of Antechamber David A Case (Sun Apr 05 2015 - 04:22:40 PDT)
- Re: [AMBER] Question Regarding reduce function of Antechamber Ziheng Wang (Sun Apr 05 2015 - 12:07:47 PDT)
  - Re: [AMBER] Question Regarding reduce function of Antechamber David A Case (Sun Apr 05 2015 - 18:13:14 PDT)
[AMBER] The Meaning of Some Parameters wjli (Sun Apr 05 2015 - 05:14:27 PDT)
- Re: [AMBER] The Meaning of Some Parameters Carlos Simmerling (Sun Apr 05 2015 - 05:19:17 PDT)
[AMBER] barosts command in amber 12 Chris Gaughan (Sun Apr 05 2015 - 11:04:52 PDT)
- Re: [AMBER] barosts command in amber 12 Jason Swails (Sun Apr 05 2015 - 17:33:52 PDT)
[AMBER] query sanjaykumar.imtech.res.in (Mon Apr 06 2015 - 01:46:29 PDT)
- Re: [AMBER] query FyD (Mon Apr 06 2015 - 23:09:21 PDT)
  - Re: [AMBER] query sanjaykumar.imtech.res.in (Tue Apr 07 2015 - 03:31:16 PDT)
[AMBER] Radial distribution function (RDF) for sugars in disaccharides Vijay Achari (Mon Apr 06 2015 - 19:51:19 PDT)
- Re: [AMBER] Radial distribution function (RDF) for sugars in disaccharides Daniel Roe (Tue Apr 07 2015 - 07:19:08 PDT)
[AMBER] REGARDING ATOM TYPE ERROR Swithin Hanosh (Mon Apr 06 2015 - 22:17:24 PDT)
- Re: [AMBER] REGARDING ATOM TYPE ERROR Jason Swails (Tue Apr 07 2015 - 05:01:56 PDT)
[AMBER] The force field used in MCPB wjli (Mon Apr 06 2015 - 23:28:41 PDT)
- Re: [AMBER] The force field used in MCPB Pengfei Li (Tue Apr 07 2015 - 08:14:20 PDT)
  - Re: [AMBER] The force field used in MCPB Carlos Simmerling (Tue Apr 07 2015 - 09:01:08 PDT)
    - Re: [AMBER] The force field used in MCPB Pengfei Li (Tue Apr 07 2015 - 09:42:45 PDT)
[AMBER] typo error in the amber14 manual Vijay Achari (Tue Apr 07 2015 - 00:41:04 PDT)
- Re: [AMBER] typo error in the amber14 manual David A Case (Tue Apr 07 2015 - 04:56:14 PDT)
[AMBER] The Stand Model in MCPB wjli (Tue Apr 07 2015 - 02:00:29 PDT)
- Re: [AMBER] The Stand Model in MCPB Pengfei Li (Tue Apr 07 2015 - 08:24:26 PDT)
[AMBER] error generating P450 prmtop incrd file Vaibhav Dixit (Tue Apr 07 2015 - 04:54:14 PDT)
- Re: [AMBER] error generating P450 prmtop incrd file David A Case (Tue Apr 07 2015 - 05:10:39 PDT)
  - Re: [AMBER] error generating P450 prmtop incrd file Vaibhav Dixit (Tue Apr 07 2015 - 05:54:02 PDT)
    - Re: [AMBER] error generating P450 prmtop incrd file Jason Swails (Tue Apr 07 2015 - 06:01:29 PDT)
    - Re: [AMBER] error generating P450 prmtop incrd file Daniel Roe (Tue Apr 07 2015 - 07:27:11 PDT)
- Re: [AMBER] error generating P450 prmtop incrd file Mark Williamson (Tue Apr 07 2015 - 07:29:00 PDT)
  - Re: [AMBER] error generating P450 prmtop incrd file Vaibhav Dixit (Wed Apr 08 2015 - 08:33:48 PDT)
    - Re: [AMBER] error generating P450 prmtop incrd file Jason Swails (Wed Apr 08 2015 - 10:06:43 PDT)
    - Re: [AMBER] error generating P450 prmtop incrd file Jason Swails (Wed Apr 08 2015 - 10:08:58 PDT)
    - Re: [AMBER] error generating P450 prmtop incrd file Vaibhav Dixit (Thu Apr 09 2015 - 02:22:29 PDT)
[AMBER] potential issue with energy drift Steven Ramsey (Tue Apr 07 2015 - 06:30:25 PDT)
[AMBER] Calculating protein center of mass (COM) using vector command George Green (Tue Apr 07 2015 - 07:51:11 PDT)
- Re: [AMBER] Calculating protein center of mass (COM) using vector command Daniel Roe (Tue Apr 07 2015 - 08:30:53 PDT)
  - Re: [AMBER] Calculating protein center of mass (COM) using vector command George Green (Tue Apr 07 2015 - 08:39:38 PDT)
[AMBER] FW: TLEAP Fatal Error Wong, Sook (NIH/NCATS) [V] (Tue Apr 07 2015 - 08:15:15 PDT)
- Re: [AMBER] FW: TLEAP Fatal Error Jason Swails (Tue Apr 07 2015 - 08:40:44 PDT)
  - Re: [AMBER] FW: TLEAP Fatal Error Wong, Sook (NIH/NCATS) [V] (Tue Apr 07 2015 - 09:23:51 PDT)
- Re: [AMBER] FW: TLEAP Fatal Error FyD (Thu Apr 09 2015 - 00:00:32 PDT)
[AMBER] COM distance restraints and pmemd.cuda Ilyas Yildirim (Tue Apr 07 2015 - 10:12:51 PDT)
- Re: [AMBER] COM distance restraints and pmemd.cuda David A Case (Tue Apr 07 2015 - 10:39:24 PDT)
  - Re: [AMBER] COM distance restraints and pmemd.cuda Ilyas Yildirim (Tue Apr 07 2015 - 15:30:26 PDT)
[AMBER] Possible bug in nativecontacts command of cpptraj (v14)? Samuel Bowerman (Tue Apr 07 2015 - 10:52:57 PDT)
- Re: [AMBER] Possible bug in nativecontacts command of cpptraj (v14)? Daniel Roe (Tue Apr 07 2015 - 11:52:45 PDT)
  - Re: [AMBER] Possible bug in nativecontacts command of cpptraj (v14)? Samuel Bowerman (Tue Apr 07 2015 - 13:28:37 PDT)
[AMBER] Boltzman Weights from MD trajectory Emilio Angelina (Tue Apr 07 2015 - 11:33:33 PDT)
- Re: [AMBER] Boltzman Weights from MD trajectory Jason Swails (Tue Apr 07 2015 - 11:41:36 PDT)
  - Re: [AMBER] Boltzman Weights from MD trajectory Emilio Angelina (Tue Apr 07 2015 - 13:22:24 PDT)
[AMBER] Energy drift issue Steven Ramsey (Tue Apr 07 2015 - 12:52:55 PDT)
- Re: [AMBER] Energy drift issue Jason Swails (Tue Apr 07 2015 - 13:09:14 PDT)
[AMBER] Error message in Amber14 tutorial A16 Michael Shokhen (Tue Apr 07 2015 - 12:57:12 PDT)
[AMBER] Error in tutorial A16, Amber 14 Michael Shokhen (Tue Apr 07 2015 - 23:16:48 PDT)
- Re: [AMBER] Error in tutorial A16, Amber 14 Benjamin D Madej (Wed Apr 08 2015 - 20:15:08 PDT)
  - Re: [AMBER] Error in tutorial A16, Amber 14 Michael Shokhen (Thu Apr 09 2015 - 03:14:54 PDT)
    - Re: [AMBER] Error in tutorial A16, Amber 14 Benjamin D Madej (Thu Apr 09 2015 - 13:28:19 PDT)
[AMBER] AHTECHAMBER - G09 Sanja Zivanovic (Wed Apr 08 2015 - 06:33:10 PDT)
- Re: [AMBER] AHTECHAMBER - G09 Ayesha Fatima (Wed Apr 08 2015 - 07:33:47 PDT)
[AMBER] defining residues in steered molecular dynamics Ayesha Fatima (Wed Apr 08 2015 - 07:57:53 PDT)
- Re: [AMBER] defining residues in steered molecular dynamics Sourav Purohit (Wed Apr 08 2015 - 09:08:25 PDT)
[AMBER] Visualization of the MMGBSA per-residue decomposition James Starlight (Wed Apr 08 2015 - 09:43:02 PDT)
[AMBER] xleap Menu bar problems Pierre Bertin (Wed Apr 08 2015 - 18:21:20 PDT)
- Re: [AMBER] xleap Menu bar problems Jason Swails (Thu Apr 09 2015 - 04:18:33 PDT)
  - Re: [AMBER] xleap Menu bar problems Pierre Bertin (Thu Apr 09 2015 - 09:16:08 PDT)
[AMBER] MMBP(GB)SA free energy decomposition error: sander failed with prmtop maryam azimzadehirani (Wed Apr 08 2015 - 20:40:05 PDT)
- Re: [AMBER] MMBP(GB)SA free energy decomposition error: sander failed with prmtop Kenneth Huang (Wed Apr 08 2015 - 21:59:13 PDT)
- Re: [AMBER] MMBP(GB)SA free energy decomposition error: sander failed with prmtop maryam azimzadehirani (Thu Apr 23 2015 - 00:22:27 PDT)
  - Re: [AMBER] MMBP(GB)SA free energy decomposition error: sander failed with prmtop Jason Swails (Thu Apr 23 2015 - 03:58:09 PDT)
[AMBER] larger bonds between protein atoms Vaibhav Dixit (Thu Apr 09 2015 - 04:15:09 PDT)
- Re: [AMBER] larger bonds between protein atoms Jason Swails (Thu Apr 09 2015 - 04:24:30 PDT)
- Re: [AMBER] larger bonds between protein atoms David A Case (Thu Apr 09 2015 - 05:00:56 PDT)
  - Re: [AMBER] larger bonds between protein atoms Vaibhav Dixit (Thu Apr 09 2015 - 07:19:25 PDT)
[AMBER] Problem with MMPBSA.py.MPI for nmode Sofia Vasilakaki (Thu Apr 09 2015 - 07:39:15 PDT)
- Re: [AMBER] Problem with MMPBSA.py.MPI for nmode Kenneth Huang (Thu Apr 09 2015 - 08:19:19 PDT)
  - Re: [AMBER] Problem with MMPBSA.py.MPI for nmode Sofia Vasilakaki (Thu Apr 09 2015 - 09:07:56 PDT)
    - [AMBER] Problem with MMPBSA.py.MPI for nmode Kenneth Huang (Fri Apr 10 2015 - 09:36:04 PDT)
    - Re: [AMBER] Problem with MMPBSA.py.MPI for nmode Sofia Vasilakaki (Fri Apr 10 2015 - 15:23:03 PDT)
    - Re: [AMBER] Problem with MMPBSA.py.MPI for nmode Kenneth Huang (Sat Apr 11 2015 - 15:35:04 PDT)
    - Re: [AMBER] Problem with MMPBSA.py.MPI for nmode Jason Swails (Sat Apr 11 2015 - 20:59:12 PDT)
[AMBER] a question for hydrocarbons simulation using amber FF Nahid Khiabani (Thu Apr 09 2015 - 13:33:43 PDT)
[AMBER] Organic solvent from imported molecule (e.g. : nitric acid) Pierre Bertin (Thu Apr 09 2015 - 18:51:52 PDT)
- Re: [AMBER] Organic solvent from imported molecule (e.g. : nitric acid) Karl Kirschner (Fri Apr 10 2015 - 00:13:02 PDT)
[AMBER] How to use the mmpbsa.py to calcualte the free energy of a modified protein ? windy (Thu Apr 09 2015 - 19:29:59 PDT)
- Re: [AMBER] How to use the mmpbsa.py to calcualte the free energy of a modified protein ? Jason Swails (Fri Apr 10 2015 - 03:09:31 PDT)
  - Re: [AMBER] How to use the mmpbsa.py to calcualte the free energy of a modified protein ? windy (Fri Apr 10 2015 - 21:35:39 PDT)
    - Re: [AMBER] How to use the mmpbsa.py to calcualte the free energy of a modified protein ? Jason Swails (Tue Apr 14 2015 - 07:31:28 PDT)
[AMBER] Diffusion constant calculation pooja chahal (Thu Apr 09 2015 - 23:20:24 PDT)
- Re: [AMBER] Diffusion constant calculation Daniel Roe (Mon Apr 13 2015 - 08:42:35 PDT)
  - Re: [AMBER] Diffusion constant calculation pooja chahal (Mon Apr 13 2015 - 21:42:24 PDT)
    - Re: [AMBER] Diffusion constant calculation Daniel Roe (Tue Apr 14 2015 - 07:06:05 PDT)
    - Re: [AMBER] Diffusion constant calculation pooja chahal (Wed Apr 15 2015 - 05:25:58 PDT)
    - Re: [AMBER] Diffusion constant calculation Daniel Roe (Wed Apr 15 2015 - 10:13:01 PDT)
    - Re: [AMBER] Diffusion constant calculation pooja chahal (Wed Apr 15 2015 - 20:42:21 PDT)
    - Re: [AMBER] Diffusion constant calculation Daniel Roe (Thu Apr 16 2015 - 07:44:41 PDT)
[AMBER] Force Field Parameters for Monoamino Acids at acidic and basic conditions? Alain Chaumont (Fri Apr 10 2015 - 00:08:21 PDT)
- Re: [AMBER] Force Field Parameters for Monoamino Acids at acidic and basic conditions? Gerald Monard (Fri Apr 10 2015 - 00:25:31 PDT)
- Re: [AMBER] Force Field Parameters for Monoamino Acids at acidic and basic conditions? Jason Swails (Fri Apr 10 2015 - 03:12:25 PDT)
[AMBER] MMPBSA on NAMD DCD Trajectories Ahmed Ezat (Fri Apr 10 2015 - 03:55:25 PDT)
- Re: [AMBER] MMPBSA on NAMD DCD Trajectories Jason Swails (Fri Apr 10 2015 - 04:42:35 PDT)
  - Re: [AMBER] MMPBSA on NAMD DCD Trajectories Ahmed Ezat (Fri Apr 10 2015 - 05:37:36 PDT)
[AMBER] cpptraj write data from runanalysis Gard Nelson (Fri Apr 10 2015 - 11:29:45 PDT)
- Re: [AMBER] cpptraj write data from runanalysis Daniel Roe (Fri Apr 10 2015 - 13:29:14 PDT)
  - Re: [AMBER] cpptraj write data from runanalysis Gard Nelson (Fri Apr 10 2015 - 15:25:08 PDT)
[AMBER] Unsupported CUDA version 7.0 detected. Emilio Angelina (Fri Apr 10 2015 - 13:38:09 PDT)
- Re: [AMBER] Unsupported CUDA version 7.0 detected. Jason Swails (Fri Apr 10 2015 - 14:29:54 PDT)
  - Re: [AMBER] Unsupported CUDA version 7.0 detected. Emilio Angelina (Fri Apr 10 2015 - 14:33:44 PDT)
  - Re: [AMBER] Unsupported CUDA version 7.0 detected. Ross Walker (Fri Apr 10 2015 - 14:39:09 PDT)
[AMBER] Invitation to Computational Chemical Biology Conference (Aug 6th to 9th 2015), Cairns, Australia (http://tinyurl.com/nyblv7o) Ross Walker (Fri Apr 10 2015 - 15:25:23 PDT)
[AMBER] Does atomicflut byres report the fluctuations of the residue CM? Jose Borreguero (Fri Apr 10 2015 - 15:44:38 PDT)
- Re: [AMBER] Does atomicflut byres report the fluctuations of the residue CM? Daniel Roe (Mon Apr 13 2015 - 08:49:11 PDT)
  - Re: [AMBER] Does atomicflut byres report the fluctuations of the residue CM? Jose Borreguero (Mon Apr 13 2015 - 09:01:59 PDT)
[AMBER] intercalations Arjun Sharma (Fri Apr 10 2015 - 16:36:30 PDT)
- Re: [AMBER] intercalations David A Case (Sun Apr 12 2015 - 05:57:54 PDT)
- Re: [AMBER] intercalations Bill Ross (Sun Apr 12 2015 - 09:50:02 PDT)
[AMBER] Bad atom Type in MMPBSA.py wjli (Fri Apr 10 2015 - 19:35:15 PDT)
- Re: [AMBER] Bad atom Type in MMPBSA.py Kenneth Huang (Sat Apr 11 2015 - 11:17:42 PDT)
  - [AMBER] 回复：Re: Bad atom Type in MMPBSA.py wjli (Sat Apr 11 2015 - 23:09:04 PDT)
    - Re: [AMBER] Bad atom Type in MMPBSA.py wjli (Sun Apr 12 2015 - 00:19:24 PDT)
    - Re: [AMBER] Bad atom Type in MMPBSA.py Kenneth Huang (Sun Apr 12 2015 - 12:15:48 PDT)
    - [AMBER] re： Bad atom Type in MMPBSA.py wjli (Mon Apr 13 2015 - 05:42:10 PDT)
    - Re: [AMBER] re： Bad atom Type in MMPBSA.py Kenneth Huang (Mon Apr 13 2015 - 10:40:01 PDT)
    - [AMBER] MMPBSA.py error:length mismatch in energy vectors wjli (Tue Apr 14 2015 - 01:38:26 PDT)
    - Re: [AMBER] MMPBSA.py error:length mismatch in energy vectors Jason Swails (Tue Apr 14 2015 - 07:10:32 PDT)
[AMBER] Quasi-harmonic Entropy Calculated using MMPBSA.py Laura Tociu (Fri Apr 10 2015 - 19:56:48 PDT)
- Re: [AMBER] Quasi-harmonic Entropy Calculated using MMPBSA.py Jason Swails (Sat Apr 11 2015 - 21:10:22 PDT)
[AMBER] a question for hydrocarbons simulation using amber FF Nahid Khiabani (Sat Apr 11 2015 - 00:09:14 PDT)
- Re: [AMBER] a question for hydrocarbons simulation using amber FF David A Case (Sun Apr 12 2015 - 06:04:14 PDT)
[AMBER] error in minimization Carlos Romero (Sat Apr 11 2015 - 13:55:32 PDT)
- Re: [AMBER] error in minimization Bill Ross (Sat Apr 11 2015 - 21:03:58 PDT)
  - Re: [AMBER] error in minimization Carlos Romero (Sat Apr 11 2015 - 22:25:53 PDT)
    - Re: [AMBER] error in minimization David A Case (Sun Apr 12 2015 - 06:06:58 PDT)
    - Re: [AMBER] error in minimization Carlos Romero (Sun Apr 12 2015 - 08:37:00 PDT)
- Re: [AMBER] error in minimization Bill Ross (Sun Apr 12 2015 - 09:53:30 PDT)
  - Re: [AMBER] error in minimization Carlos Romero (Sun Apr 12 2015 - 12:05:08 PDT)
    - Re: [AMBER] error in minimization David A Case (Sun Apr 12 2015 - 19:52:55 PDT)
    - Re: [AMBER] error in minimization Carlos Romero (Sun Apr 12 2015 - 20:18:37 PDT)
    - Re: [AMBER] error in minimization David A Case (Mon Apr 13 2015 - 04:25:04 PDT)
    - Re: [AMBER] error in minimization Carlos Romero (Mon Apr 13 2015 - 06:30:20 PDT)
    - Re: [AMBER] error in minimization Jason Swails (Mon Apr 13 2015 - 06:43:21 PDT)
- Re: [AMBER] error in minimization Bill Ross (Sun Apr 12 2015 - 16:06:22 PDT)
  - Re: [AMBER] error in minimization Carlos Romero (Sun Apr 12 2015 - 16:45:38 PDT)
- Re: [AMBER] error in minimization Bill Ross (Sun Apr 12 2015 - 21:20:41 PDT)
  - Re: [AMBER] error in minimization Vaibhav Dixit (Mon Apr 13 2015 - 03:18:02 PDT)
    - Re: [AMBER] error in minimization Carlos Romero (Mon Apr 13 2015 - 10:00:28 PDT)
    - Re: [AMBER] error in minimization Jason Swails (Mon Apr 13 2015 - 10:11:01 PDT)
    - Re: [AMBER] error in minimization Carlos Romero (Mon Apr 13 2015 - 10:23:07 PDT)
    - Re: [AMBER] error in minimization Jason Swails (Mon Apr 13 2015 - 10:26:09 PDT)
    - Re: [AMBER] error in minimization Carlos Romero (Mon Apr 13 2015 - 10:29:09 PDT)
    - Re: [AMBER] error in minimization Carlos Romero (Tue Apr 14 2015 - 08:55:38 PDT)
    - Re: [AMBER] error in minimization Jason Swails (Tue Apr 14 2015 - 09:01:14 PDT)
    - Re: [AMBER] error in minimization Carlos Romero (Tue Apr 14 2015 - 09:52:28 PDT)
    - Re: [AMBER] error in minimization Jason Swails (Tue Apr 14 2015 - 10:03:01 PDT)
[AMBER] Error Adnan Gulzar (Sat Apr 11 2015 - 15:18:53 PDT)
- Re: [AMBER] Error David A Case (Sun Apr 12 2015 - 06:14:12 PDT)
[AMBER] Amino acid as ligand Dhiraj Srivastava (Sat Apr 11 2015 - 20:06:20 PDT)
- Re: [AMBER] Amino acid as ligand Jason Swails (Sat Apr 11 2015 - 21:01:58 PDT)
[AMBER] a question for hydrocarbons simulation using amber FF Nahid Khiabani (Sun Apr 12 2015 - 03:33:15 PDT)
- Re: [AMBER] a question for hydrocarbons simulation using amber FF hannes.loeffler.stfc.ac.uk (Sun Apr 12 2015 - 03:50:24 PDT)
  - Re: [AMBER] a question for hydrocarbons simulation using amber FF Nahid Khiabani (Sun Apr 12 2015 - 03:53:54 PDT)
    - Re: [AMBER] a question for hydrocarbons simulation using amber FF Marc van der Kamp (Sun Apr 12 2015 - 04:12:14 PDT)
    - Re: [AMBER] a question for hydrocarbons simulation using amber FF Nahid Khiabani (Sun Apr 12 2015 - 04:50:51 PDT)
    - Re: [AMBER] a question for hydrocarbons simulation using amber FF David A Case (Sun Apr 12 2015 - 06:18:19 PDT)
    - Re: [AMBER] a question for hydrocarbons simulation using amber FF Nahid Khiabani (Sun Apr 12 2015 - 06:22:16 PDT)
[AMBER] Arrangement of molecules in 3D packed state jacob wick (Sun Apr 12 2015 - 11:30:25 PDT)
- Re: [AMBER] Arrangement of molecules in 3D packed state Bill Ross (Sun Apr 12 2015 - 17:04:50 PDT)
- Re: [AMBER] Arrangement of molecules in 3D packed state David A Case (Sun Apr 12 2015 - 19:50:34 PDT)
  - Re: [AMBER] Arrangement of molecules in 3D packed state jacob wick (Tue Apr 21 2015 - 01:16:25 PDT)
    - Re: [AMBER] Arrangement of molecules in 3D packed state David A Case (Wed Apr 22 2015 - 08:13:29 PDT)
    - Re: [AMBER] Arrangement of molecules in 3D packed state jacob wick (Thu Apr 23 2015 - 01:59:59 PDT)
    - Re: [AMBER] Arrangement of molecules in 3D packed state David A Case (Thu Apr 23 2015 - 07:31:08 PDT)
    - Re: [AMBER] Arrangement of molecules in 3D packed state Pawel Janowski (Thu Apr 23 2015 - 07:57:12 PDT)
    - Re: [AMBER] Arrangement of molecules in 3D packed state jacob wick (Thu Apr 23 2015 - 10:46:39 PDT)
    - Re: [AMBER] Arrangement of molecules in 3D packed state jacob wick (Thu Apr 23 2015 - 10:43:11 PDT)
[AMBER] Mmgbsa decomposition James Starlight (Mon Apr 13 2015 - 01:19:01 PDT)
[AMBER] AMBER parametrization questions Jeffrey Teillet (Mon Apr 13 2015 - 06:20:11 PDT)
- Re: [AMBER] AMBER parametrization questions Carlos Simmerling (Mon Apr 13 2015 - 06:36:12 PDT)
[AMBER] Charmm force field parameters in Amber anu chandra (Mon Apr 13 2015 - 06:33:30 PDT)
- Re: [AMBER] Charmm force field parameters in Amber Jason Swails (Mon Apr 13 2015 - 06:47:47 PDT)
[AMBER] is it possible to output the trajectory of the center of mass of the residues? Jose Borreguero (Mon Apr 13 2015 - 07:05:51 PDT)
- Re: [AMBER] is it possible to output the trajectory of the center of mass of the residues? Daniel Roe (Mon Apr 13 2015 - 09:22:58 PDT)
  - Re: [AMBER] is it possible to output the trajectory of the center of mass of the residues? Jose Borreguero (Mon Apr 13 2015 - 10:22:29 PDT)
[AMBER] hydrogen bond analysis using cpptraj in amber tools 14 Atila Petrosian (Tue Apr 14 2015 - 01:25:27 PDT)
- Re: [AMBER] hydrogen bond analysis using cpptraj in amber tools 14 Daniel Roe (Tue Apr 14 2015 - 06:56:04 PDT)
[AMBER] Restart file with velocity loic etheve (Tue Apr 14 2015 - 03:40:34 PDT)
- Re: [AMBER] Restart file with velocity David A Case (Tue Apr 14 2015 - 04:13:29 PDT)
[AMBER] REGARDING ENERGY MINIMISATION Swithin Hanosh (Tue Apr 14 2015 - 04:42:26 PDT)
- Re: [AMBER] REGARDING ENERGY MINIMISATION Jason Swails (Tue Apr 14 2015 - 07:16:10 PDT)
[AMBER] Community network analysis for the Amber trajectories James Starlight (Tue Apr 14 2015 - 07:25:27 PDT)
- Re: [AMBER] Community network analysis for the Amber trajectories Daniel Roe (Tue Apr 14 2015 - 08:59:51 PDT)
  - Re: [AMBER] Community network analysis for the Amber trajectories James Starlight (Tue Apr 14 2015 - 11:32:04 PDT)
    - Re: [AMBER] Community network analysis for the Amber trajectories Vlad Cojocaru (Tue Apr 14 2015 - 12:11:56 PDT)
    - Re: [AMBER] Community network analysis for the Amber trajectories Vlad Cojocaru (Tue Apr 14 2015 - 12:19:13 PDT)
    - Re: [AMBER] Community network analysis for the Amber trajectories James Starlight (Wed Apr 15 2015 - 05:39:03 PDT)
[AMBER] Calculating Cp values from NPT simulations using ptraj Vivek Shankar Bharadwaj (Tue Apr 14 2015 - 14:42:13 PDT)
- Re: [AMBER] Calculating Cp values from NPT simulations using ptraj Daniel Roe (Tue Apr 21 2015 - 11:01:18 PDT)
[AMBER] Deletion of H atoms from pdb file used for MD simulations muhammad tahir ayub (Tue Apr 14 2015 - 23:35:51 PDT)
- Re: [AMBER] Deletion of H atoms from pdb file used for MD simulations Ashutosh Shandilya (Wed Apr 15 2015 - 02:19:03 PDT)
  - Re: [AMBER] Deletion of H atoms from pdb file used for MD simulations suma jayakrishnan (Wed Apr 15 2015 - 03:21:20 PDT)
- Re: [AMBER] Deletion of H atoms from pdb file used for MD simulations Hannes Loeffler (Wed Apr 15 2015 - 03:49:09 PDT)
  - Re: [AMBER] Deletion of H atoms from pdb file used for MD simulations Sofia Vasilakaki (Wed Apr 15 2015 - 05:46:22 PDT)
- Re: [AMBER] Deletion of H atoms from pdb file used for MD simulations Jason Swails (Wed Apr 15 2015 - 06:05:11 PDT)
- Re: [AMBER] Deletion of H atoms from pdb file used for MD simulations Daniel Roe (Wed Apr 15 2015 - 08:02:22 PDT)
[AMBER] REGARDING ENERGY MINIMISATION Swithin Hanosh (Wed Apr 15 2015 - 05:32:32 PDT)
- Re: [AMBER] REGARDING ENERGY MINIMISATION Jason Swails (Wed Apr 15 2015 - 06:03:49 PDT)
- Re: [AMBER] REGARDING ENERGY MINIMISATION David A Case (Wed Apr 15 2015 - 06:15:54 PDT)
[AMBER] The influence of parameters in md.in when restart a MD (from rst file) windy (Wed Apr 15 2015 - 07:05:31 PDT)
- Re: [AMBER] The influence of parameters in md.in when restart a MD (from rst file) Daniel Roe (Wed Apr 15 2015 - 07:30:46 PDT)
  - Re: [AMBER] The influence of parameters in md.in when restart a MD (from rst file) windy (Fri Apr 17 2015 - 02:51:53 PDT)
[AMBER] Error with quasi-harmonic MMPBSA.py calculations Abhishek TYAGI (Wed Apr 15 2015 - 21:26:20 PDT)
- Re: [AMBER] Error with quasi-harmonic MMPBSA.py calculations Jason Swails (Thu Apr 16 2015 - 06:40:26 PDT)
- Re: [AMBER] Error with quasi-harmonic MMPBSA.py calculations Abhishek TYAGI (Thu Apr 23 2015 - 00:56:00 PDT)
  - Re: [AMBER] Error with quasi-harmonic MMPBSA.py calculations Jason Swails (Thu Apr 23 2015 - 03:55:19 PDT)
[AMBER] Alanin scanning MMGBSA.py error: TypeError: not all arguments converted during string formatting maryam azimzadehirani (Thu Apr 16 2015 - 00:06:05 PDT)
- Re: [AMBER] Alanin scanning MMGBSA.py error: TypeError: not all arguments converted during string formatting Jason Swails (Thu Apr 16 2015 - 06:33:00 PDT)
  - Re: [AMBER] Alanin scanning MMGBSA.py error: TypeError: not all arguments converted during string formatting maryam azimzadehirani (Fri Apr 17 2015 - 01:38:21 PDT)
    - Re: [AMBER] Alanin scanning MMGBSA.py error: TypeError: not all arguments converted during string formatting Jason Swails (Fri Apr 17 2015 - 04:56:36 PDT)
[AMBER] Writing out restart files gepaula.web.de (Thu Apr 16 2015 - 07:14:21 PDT)
- Re: [AMBER] Writing out restart files Christina Bergonzo (Thu Apr 16 2015 - 07:27:33 PDT)
  - Re: [AMBER] Writing out restart files Daniel Roe (Thu Apr 16 2015 - 07:30:47 PDT)
- Re: [AMBER] Writing out restart files Jason Swails (Thu Apr 16 2015 - 07:20:43 PDT)
[AMBER] all in one pc for MD simulation calculations Atila Petrosian (Thu Apr 16 2015 - 07:50:45 PDT)
- Re: [AMBER] all in one pc for MD simulation calculations Jason Swails (Thu Apr 16 2015 - 07:57:55 PDT)
[AMBER] NMode Analysis Using Truncated Trajectory Laura Tociu (Thu Apr 16 2015 - 11:53:19 PDT)
- Re: [AMBER] NMode Analysis Using Truncated Trajectory Jason Swails (Thu Apr 16 2015 - 13:10:07 PDT)
  - Re: [AMBER] NMode Analysis Using Truncated Trajectory Laura Tociu (Thu Apr 16 2015 - 20:52:06 PDT)
    - Re: [AMBER] NMode Analysis Using Truncated Trajectory Jason Swails (Fri Apr 17 2015 - 05:00:39 PDT)
    - Re: [AMBER] NMode Analysis Using Truncated Trajectory Laura Tociu (Fri Apr 17 2015 - 05:47:40 PDT)
Re: [AMBER] deletion of H atoms for pdb file hannes.loeffler.stfc.ac.uk (Thu Apr 16 2015 - 12:16:34 PDT)
- Re: [AMBER] deletion of H atoms for pdb file Daniel Roe (Thu Apr 16 2015 - 12:38:54 PDT)
[AMBER] Could anyone tell me how to run targeted MD correctly 肖立 (Thu Apr 16 2015 - 23:45:08 PDT)
- Re: [AMBER] Could anyone tell me how to run targeted MD correctly Carlos Simmerling (Fri Apr 17 2015 - 05:24:37 PDT)
  - Re: [AMBER] Could anyone tell me how to run targeted MD correctly 肖立 (Fri Apr 17 2015 - 10:10:10 PDT)
    - Re: [AMBER] Could anyone tell me how to run targeted MD correctly Carlos Simmerling (Fri Apr 17 2015 - 10:17:19 PDT)
    - Re: [AMBER] Could anyone tell me how to run targeted MD correctly 肖立 (Fri Apr 17 2015 - 11:03:23 PDT)
    - Re: [AMBER] Could anyone tell me how to run targeted MD correctly 肖立 (Fri Apr 17 2015 - 11:04:29 PDT)
[AMBER] Carbon nanotube simulation Pierre Bertin (Thu Apr 16 2015 - 23:51:08 PDT)
- Re: [AMBER] Carbon nanotube simulation Karl Kirschner (Fri Apr 17 2015 - 00:32:56 PDT)
  - Re: [AMBER] Carbon nanotube simulation Daniel Roe (Fri Apr 17 2015 - 07:00:46 PDT)
    - Re: [AMBER] Carbon nanotube simulation Pierre Bertin (Fri Apr 17 2015 - 08:32:06 PDT)
[AMBER] ligand-solvent interaction energy Hannes Loeffler (Fri Apr 17 2015 - 02:23:41 PDT)
- Re: [AMBER] ligand-solvent interaction energy Jason Swails (Fri Apr 17 2015 - 05:34:15 PDT)
[AMBER] Batch leap error! Pallavi Mohanty (Fri Apr 17 2015 - 04:02:00 PDT)
- Re: [AMBER] Batch leap error! Hannes Loeffler (Fri Apr 17 2015 - 04:17:59 PDT)
  - Re: [AMBER] Batch leap error! Pallavi Mohanty (Fri Apr 17 2015 - 04:59:43 PDT)
    - Re: [AMBER] Batch leap error! Jason Swails (Fri Apr 17 2015 - 05:12:29 PDT)
    - Re: [AMBER] Batch leap error! hannes.loeffler.stfc.ac.uk (Fri Apr 17 2015 - 05:07:47 PDT)
  - Re: [AMBER] Batch leap error! Jason Swails (Fri Apr 17 2015 - 05:07:17 PDT)
    - Re: [AMBER] Batch leap error! Hannes Loeffler (Fri Apr 17 2015 - 06:31:29 PDT)
    - Re: [AMBER] Batch leap error! Jason Swails (Fri Apr 17 2015 - 06:42:29 PDT)
    - Re: [AMBER] Batch leap error! Pallavi Mohanty (Fri Apr 17 2015 - 08:45:57 PDT)
    - Re: [AMBER] Batch leap error! Hannes Loeffler (Fri Apr 17 2015 - 08:52:22 PDT)
    - Re: [AMBER] Batch leap error! Hector A. Baldoni (Fri Apr 17 2015 - 09:16:25 PDT)
[AMBER] How to resolve the problem when amber14 configured with cuda 6.5 金毅 (Fri Apr 17 2015 - 23:28:41 PDT)
- Re: [AMBER] How to resolve the problem when amber14 configured with cuda 6.5 Ross Walker (Sat Apr 18 2015 - 01:53:07 PDT)
  - Re: [AMBER] How to resolve the problem when amber14 configured with cuda 6.5 金毅 (Sat Apr 18 2015 - 06:35:29 PDT)
    - Re: [AMBER] How to resolve the problem when amber14 configured with cuda 6.5 Jason Swails (Sun Apr 19 2015 - 12:29:51 PDT)
- Re: [AMBER] How to resolve the problem when amber14 configured with cuda 6.5 Jason Swails (Sat Apr 18 2015 - 04:48:50 PDT)
  - Re: [AMBER] How to resolve the problem when amber14 configured with cuda 6.5 金毅 (Sat Apr 18 2015 - 04:50:02 PDT)
[AMBER] Problem regarding PMF curve Shubhadip Das (Sun Apr 19 2015 - 08:49:15 PDT)
- Re: [AMBER] Problem regarding PMF curve Brian Radak (Thu Apr 23 2015 - 06:12:19 PDT)
[AMBER] One chain of protein going out of box Shukla, Saurabh (Sun Apr 19 2015 - 18:27:55 PDT)
- Re: [AMBER] One chain of protein going out of box Jason Swails (Mon Apr 20 2015 - 05:37:02 PDT)
[AMBER] Problem in running with steered MD 肖立 (Sun Apr 19 2015 - 18:29:42 PDT)
- Re: [AMBER] Problem in running with steered MD Jason Swails (Mon Apr 20 2015 - 05:34:13 PDT)
[AMBER] In MMPBSY.py , how to set interval value when large conformation change ? windy (Mon Apr 20 2015 - 01:41:27 PDT)
- Re: [AMBER] In MMPBSY.py , how to set interval value when large conformation change ? Jason Swails (Mon Apr 20 2015 - 06:09:45 PDT)
  - Re: [AMBER] In MMPBSY.py , how to set interval value when large conformation change ? George Tzotzos (Mon Apr 20 2015 - 11:20:36 PDT)
    - Re: [AMBER] In MMPBSY.py , how to set interval value when large conformation change ? Jason Swails (Mon Apr 20 2015 - 11:47:27 PDT)
    - Re: [AMBER] In MMPBSY.py , how to set interval value when large conformation change ? windy (Tue Apr 21 2015 - 18:58:22 PDT)
    - Re: [AMBER] In MMPBSY.py , how to set interval value when large conformation change ? Jason Swails (Wed Apr 22 2015 - 03:59:58 PDT)
    - Re: [AMBER] In MMPBSY.py , how to set interval value when large conformation change ? windy (Wed Apr 22 2015 - 21:05:50 PDT)
[AMBER] regarding .prmtop file generation neha chaudhary (Mon Apr 20 2015 - 03:58:06 PDT)
- Re: [AMBER] regarding .prmtop file generation Jason Swails (Mon Apr 20 2015 - 06:01:06 PDT)
  - Re: [AMBER] regarding .prmtop file generation neha chaudhary (Sat Apr 25 2015 - 01:46:32 PDT)
    - Re: [AMBER] regarding .prmtop file generation Jason Swails (Sat Apr 25 2015 - 13:33:10 PDT)
    - Re: [AMBER] regarding .prmtop file generation neha chaudhary (Sun Apr 26 2015 - 21:46:10 PDT)
    - Re: [AMBER] regarding .prmtop file generation David A Case (Mon Apr 27 2015 - 04:58:54 PDT)
[AMBER] PCA analysis Muthukumaran R (Mon Apr 20 2015 - 04:44:46 PDT)
- Re: [AMBER] PCA analysis Jason Swails (Mon Apr 20 2015 - 05:54:29 PDT)
  - Re: [AMBER] PCA analysis Muthukumaran R (Mon Apr 20 2015 - 06:24:01 PDT)
[AMBER] cpptraj writting box coordinates issue CHAMI F. (Mon Apr 20 2015 - 08:00:09 PDT)
- Re: [AMBER] cpptraj writting box coordinates issue Daniel Roe (Mon Apr 20 2015 - 08:04:46 PDT)
  - Re: [AMBER] cpptraj writting box coordinates issue CHAMI F. (Mon Apr 20 2015 - 08:24:43 PDT)
[AMBER] sander error "peek_ewald_inpcrd: SHOULD NOT BE HERE" Vaibhav Dixit (Tue Apr 21 2015 - 02:29:07 PDT)
- Re: [AMBER] sander error "peek_ewald_inpcrd: SHOULD NOT BE HERE" Kenneth Huang (Tue Apr 21 2015 - 05:57:32 PDT)
  - Re: [AMBER] sander error "peek_ewald_inpcrd: SHOULD NOT BE HERE" Vaibhav Dixit (Tue Apr 21 2015 - 06:12:13 PDT)
- Re: [AMBER] sander error "peek_ewald_inpcrd: SHOULD NOT BE HERE" Daniel Roe (Tue Apr 21 2015 - 06:54:19 PDT)
  - Re: [AMBER] sander error "peek_ewald_inpcrd: SHOULD NOT BE HERE" Vaibhav Dixit (Tue Apr 21 2015 - 07:04:32 PDT)
    - Re: [AMBER] sander error "peek_ewald_inpcrd: SHOULD NOT BE HERE" Vaibhav Dixit (Tue Apr 21 2015 - 07:05:28 PDT)
    - Re: [AMBER] sander error "peek_ewald_inpcrd: SHOULD NOT BE HERE" Sajeewa Pemasinghe (Tue Apr 21 2015 - 07:39:48 PDT)
    - Re: [AMBER] sander error "peek_ewald_inpcrd: SHOULD NOT BE HERE" Vaibhav Dixit (Tue Apr 21 2015 - 07:45:02 PDT)
    - Re: [AMBER] sander error "peek_ewald_inpcrd: SHOULD NOT BE HERE" Sajeewa Pemasinghe (Tue Apr 21 2015 - 07:55:29 PDT)
    - Re: [AMBER] sander error "peek_ewald_inpcrd: SHOULD NOT BE HERE" Jason Swails (Tue Apr 21 2015 - 08:04:10 PDT)
    - Re: [AMBER] sander error "peek_ewald_inpcrd: SHOULD NOT BE HERE" David A Case (Tue Apr 21 2015 - 08:07:02 PDT)
    - Re: [AMBER] sander error "peek_ewald_inpcrd: SHOULD NOT BE HERE" Vaibhav Dixit (Tue Apr 21 2015 - 09:16:19 PDT)
    - Re: [AMBER] sander error "peek_ewald_inpcrd: SHOULD NOT BE HERE" Kenneth Huang (Tue Apr 21 2015 - 09:54:03 PDT)
    - Re: [AMBER] sander error "peek_ewald_inpcrd: SHOULD NOT BE HERE" Vaibhav Dixit (Tue Apr 21 2015 - 10:04:35 PDT)
    - Re: [AMBER] sander error "peek_ewald_inpcrd: SHOULD NOT BE HERE" Jason Swails (Tue Apr 21 2015 - 10:33:21 PDT)
    - Re: [AMBER] sander error "peek_ewald_inpcrd: SHOULD NOT BE HERE" Vaibhav Dixit (Thu Apr 23 2015 - 12:29:14 PDT)
- Re: [AMBER] sander error "peek_ewald_inpcrd: SHOULD NOT BE HERE" Hector A. Baldoni (Tue Apr 21 2015 - 07:24:10 PDT)
[AMBER] ATTN needs revision Sanja Zivanovic (Tue Apr 21 2015 - 08:13:35 PDT)
- Re: [AMBER] ATTN needs revision David A Case (Wed Apr 22 2015 - 08:08:52 PDT)
[AMBER] The error occurs when I set radiopt =1 in MMPBSA.py wliu (Tue Apr 21 2015 - 08:28:07 PDT)
- Re: [AMBER] The error occurs when I set radiopt =1 in MMPBSA.py Kenneth Huang (Tue Apr 21 2015 - 10:22:25 PDT)
- Re: [AMBER] The error occurs when I set radiopt =1 in MMPBSA.py Jason Swails (Tue Apr 21 2015 - 10:39:17 PDT)
  - Re: [AMBER] The error occurs when I set radiopt =1 in MMPBSA.py wliu (Thu Apr 23 2015 - 05:38:28 PDT)
[AMBER] install Amber 11 and AmberTools 1.5 on CentoS 6.3 Atila Petrosian (Tue Apr 21 2015 - 12:02:46 PDT)
- Re: [AMBER] install Amber 11 and AmberTools 1.5 on CentoS 6.3 Jason Swails (Tue Apr 21 2015 - 12:23:12 PDT)
[AMBER] Amber GPU Segmentation fault AJ Venkatakrishnan (Tue Apr 21 2015 - 15:29:31 PDT)
- Re: [AMBER] Amber GPU Segmentation fault Ross Walker (Tue Apr 21 2015 - 16:06:21 PDT)
  - Re: [AMBER] Amber GPU Segmentation fault AJ Venkatakrishnan (Fri Apr 24 2015 - 19:02:05 PDT)
[AMBER] install Amber 11 and AmberTools 1.5 on CentoS 6.3 Atila Petrosian (Tue Apr 21 2015 - 21:18:05 PDT)
- Re: [AMBER] install Amber 11 and AmberTools 1.5 on CentoS 6.3 Jason Swails (Wed Apr 22 2015 - 04:05:50 PDT)
  - Re: [AMBER] install Amber 11 and AmberTools 1.5 on CentoS 6.3 Atila Petrosian (Wed Apr 22 2015 - 10:47:31 PDT)
    - Re: [AMBER] install Amber 11 and AmberTools 1.5 on CentoS 6.3 Hai Nguyen (Wed Apr 22 2015 - 10:49:57 PDT)
    - Re: [AMBER] install Amber 11 and AmberTools 1.5 on CentoS 6.3 Jason Swails (Wed Apr 22 2015 - 11:08:15 PDT)
[AMBER] Any timeline for TI on GPU's? Ucisik, Melek Nihan (Wed Apr 22 2015 - 09:39:56 PDT)
- Re: [AMBER] Any timeline for TI on GPU's? filip fratev (Wed Apr 22 2015 - 11:01:45 PDT)
- Re: [AMBER] Any timeline for TI on GPU's? Ross Walker (Wed Apr 22 2015 - 23:10:42 PDT)
[AMBER] CENTOS 6.6 :ERROR - INSTALLATION OF AMBERTOOLS14/AMBER14 vitonoja.yahoo.com (Wed Apr 22 2015 - 20:06:11 PDT)
- Re: [AMBER] CENTOS 6.6 :ERROR - INSTALLATION OF AMBERTOOLS14/AMBER14 Jason Swails (Thu Apr 23 2015 - 03:42:56 PDT)
[AMBER] mcpb problem chemjxn (Wed Apr 22 2015 - 21:12:08 PDT)
- Re: [AMBER] mcpb problem Pengfei Li (Thu Apr 23 2015 - 07:28:01 PDT)
[AMBER] AMBER 14 installation problem Sanjib Paul (Wed Apr 22 2015 - 22:49:14 PDT)
- Re: [AMBER] AMBER 14 installation problem Jason Swails (Thu Apr 23 2015 - 03:50:59 PDT)
  - Re: [AMBER] AMBER 14 installation problem Sanjib Paul (Thu Apr 23 2015 - 06:27:33 PDT)
[AMBER] Free energy calculation of ligand binding energy: Thermodynamic integration - pmemd - single topology - vdw vladimir.palivec.marge.uochb.cas.cz (Thu Apr 23 2015 - 08:26:11 PDT)
- Re: [AMBER] Free energy calculation of ligand binding energy: Thermodynamic integration - pmemd - single topology - vdw hannes.loeffler.stfc.ac.uk (Thu Apr 23 2015 - 09:04:34 PDT)
  - Re: [AMBER] Free energy calculation of ligand binding energy: Thermodynamic integration - pmemd - single topology - vdw vladimir.palivec.marge.uochb.cas.cz (Sat Apr 25 2015 - 04:58:53 PDT)
    - Re: [AMBER] Free energy calculation of ligand binding energy: Thermodynamic integration - pmemd - single topology - vdw hannes.loeffler.stfc.ac.uk (Sat Apr 25 2015 - 07:46:20 PDT)
[AMBER] water box for steered md amber14 Asmita Gupta (Thu Apr 23 2015 - 10:50:54 PDT)
[AMBER] DNA partial charges in Amber library jacob wick (Thu Apr 23 2015 - 22:23:08 PDT)
- Re: [AMBER] DNA partial charges in Amber library Thomas Cheatham (Thu Apr 23 2015 - 22:54:28 PDT)
[AMBER] Simulations at High temperature (425K) Biswa Ranjan Meher (Fri Apr 24 2015 - 07:17:17 PDT)
- Re: [AMBER] Simulations at High temperature (425K) Carlos Simmerling (Fri Apr 24 2015 - 07:21:50 PDT)
- Re: [AMBER] Simulations at High temperature (425K) David A Case (Fri Apr 24 2015 - 08:14:42 PDT)
[AMBER] mcpb problem chemjxn (Sat Apr 25 2015 - 01:17:20 PDT)
- Re: [AMBER] mcpb problem Jia Xu (Sat Apr 25 2015 - 08:40:30 PDT)
[AMBER] Regarding running to independent simulations Soumendranath Bhakat (Sat Apr 25 2015 - 03:10:36 PDT)
- [AMBER] Regarding running to independent simulations Kenneth Huang (Sat Apr 25 2015 - 05:12:27 PDT)
- Re: [AMBER] Regarding running to independent simulations David A Case (Sat Apr 25 2015 - 07:05:30 PDT)
  - Re: [AMBER] Regarding running to independent simulations Soumendranath Bhakat (Sun Apr 26 2015 - 07:51:23 PDT)
[AMBER] charmmlipid2amber2.py error Gözde YALÇIN (Sat Apr 25 2015 - 04:35:51 PDT)
- Re: [AMBER] charmmlipid2amber2.py error Michele Bonus (Sat Apr 25 2015 - 06:10:25 PDT)
[AMBER] segmentation fault in AmberTool 14.25 MOHD HOMAIDUR RAHMAN (Sat Apr 25 2015 - 07:56:44 PDT)
- Re: [AMBER] segmentation fault in AmberTool 14.25 Jason Swails (Sat Apr 25 2015 - 13:36:10 PDT)
  - Re: [AMBER] segmentation fault in AmberTool 14.25 Bill Ross (Sat Apr 25 2015 - 13:49:16 PDT)
[AMBER] close contacts in equilibrated structure Asmita Gupta (Sat Apr 25 2015 - 08:37:25 PDT)
- Re: [AMBER] close contacts in equilibrated structure Jason Swails (Sat Apr 25 2015 - 13:40:35 PDT)
  - Re: [AMBER] close contacts in equilibrated structure Asmita Gupta (Sat Apr 25 2015 - 14:59:35 PDT)
[AMBER] the vectors of the moment of inertia protein CHAMI F. (Sat Apr 25 2015 - 09:07:07 PDT)
[AMBER] problem with CHAMBER sudipta (Sat Apr 25 2015 - 11:21:19 PDT)
- Re: [AMBER] problem with CHAMBER Jason Swails (Sat Apr 25 2015 - 13:52:48 PDT)
[AMBER] charmmlipid2amber.py error Gözde YALÇIN (Sat Apr 25 2015 - 11:39:33 PDT)
- Re: [AMBER] charmmlipid2amber.py error Jason Swails (Sat Apr 25 2015 - 13:48:03 PDT)
  - Re: [AMBER] charmmlipid2amber.py error Gözde YALÇIN (Wed Apr 29 2015 - 00:03:40 PDT)
[AMBER] mpirun error shahab shariati (Sun Apr 26 2015 - 09:23:40 PDT)
- Re: [AMBER] mpirun error Jason Swails (Sun Apr 26 2015 - 16:19:05 PDT)
[AMBER] Quasi-harmonic Approximation Using a Trajectory Stripped of Hydrogens Laura Tociu (Sun Apr 26 2015 - 20:35:08 PDT)
- Re: [AMBER] Quasi-harmonic Approximation Using a Trajectory Stripped of Hydrogens Josh Berryman (Tue Apr 28 2015 - 03:51:46 PDT)
  - Re: [AMBER] Quasi-harmonic Approximation Using a Trajectory Stripped of Hydrogens Hannes Loeffler (Tue Apr 28 2015 - 04:19:54 PDT)
    - Re: [AMBER] Quasi-harmonic Approximation Using a Trajectory Stripped of Hydrogens Laura Tociu (Tue Apr 28 2015 - 12:40:06 PDT)
    - Re: [AMBER] Quasi-harmonic Approximation Using a Trajectory Stripped of Hydrogens Jason Swails (Tue Apr 28 2015 - 18:40:03 PDT)
    - Re: [AMBER] Quasi-harmonic Approximation Using a Trajectory Stripped of Hydrogens Laura Tociu (Tue Apr 28 2015 - 21:44:57 PDT)
    - Re: [AMBER] Quasi-harmonic Approximation Using a Trajectory Stripped of Hydrogens Hannes Loeffler (Thu Apr 30 2015 - 03:15:19 PDT)
[AMBER] Segmentation fault in AmberTool 14.25 MOHD HOMAIDUR RAHMAN (Sun Apr 26 2015 - 23:20:15 PDT)
- Re: [AMBER] Segmentation fault in AmberTool 14.25 David A Case (Mon Apr 27 2015 - 05:11:33 PDT)
  - Re: [AMBER] Segmentation fault in AmberTool 14.25 MOHD HOMAIDUR RAHMAN (Mon Apr 27 2015 - 23:28:59 PDT)
    - Re: [AMBER] Segmentation fault in AmberTool 14.25 David A Case (Tue Apr 28 2015 - 05:05:30 PDT)
[AMBER] parameterization Zn2+ with MCPB chemjxn (Mon Apr 27 2015 - 00:42:48 PDT)
- Re: [AMBER] parameterization Zn2+ with MCPB Pengfei Li (Mon Apr 27 2015 - 06:54:21 PDT)
[AMBER] Questions about T-REMD lipengfei (Mon Apr 27 2015 - 05:30:45 PDT)
- Re: [AMBER] Questions about T-REMD Jason Swails (Mon Apr 27 2015 - 06:38:52 PDT)
[AMBER] cpptraj V14.25 issues with old Amber topology files (Amber 11) CHAMI F. (Mon Apr 27 2015 - 07:11:32 PDT)
- Re: [AMBER] cpptraj V14.25 issues with old Amber topology files (Amber 11) Jason Swails (Mon Apr 27 2015 - 08:22:29 PDT)
- Re: [AMBER] cpptraj V14.25 issues with old Amber topology files (Amber 11) Daniel Roe (Mon Apr 27 2015 - 08:36:43 PDT)
  - Re: [AMBER] cpptraj V14.25 issues with old Amber topology files (Amber 11) CHAMI F. (Mon Apr 27 2015 - 10:31:53 PDT)
    - Re: [AMBER] cpptraj V14.25 issues with old Amber topology files (Amber 11) Daniel Roe (Mon Apr 27 2015 - 10:35:54 PDT)
[AMBER] how to run non standard simulation muhammad tahir ayub (Mon Apr 27 2015 - 11:39:46 PDT)
- Re: [AMBER] how to run non standard simulation David A Case (Mon Apr 27 2015 - 14:51:35 PDT)
[AMBER] Antechamber Algorithm for Atom Type Robert Molt (Mon Apr 27 2015 - 18:19:57 PDT)
- Re: [AMBER] Antechamber Algorithm for Atom Type hannes.loeffler.stfc.ac.uk (Mon Apr 27 2015 - 23:21:32 PDT)
  - Re: [AMBER] Antechamber Algorithm for Atom Type Robert Molt (Tue Apr 28 2015 - 06:03:24 PDT)
    - Re: [AMBER] Antechamber Algorithm for Atom Type Hannes Loeffler (Tue Apr 28 2015 - 06:29:57 PDT)
    - Re: [AMBER] Antechamber Algorithm for Atom Type Robert Molt (Tue Apr 28 2015 - 06:51:08 PDT)
    - Re: [AMBER] Antechamber Algorithm for Atom Type Jason Swails (Tue Apr 28 2015 - 06:56:02 PDT)
    - Re: [AMBER] Antechamber Algorithm for Atom Type Hannes Loeffler (Tue Apr 28 2015 - 07:08:23 PDT)
    - Re: [AMBER] Antechamber Algorithm for Atom Type Jason Swails (Tue Apr 28 2015 - 07:14:41 PDT)
    - Re: [AMBER] Antechamber Algorithm for Atom Type Robert Molt (Tue Apr 28 2015 - 17:42:08 PDT)
    - Re: [AMBER] Antechamber Algorithm for Atom Type Hannes Loeffler (Tue Apr 28 2015 - 07:06:14 PDT)
[AMBER] Is there NHE cap in the ff02 library files? Yip Yew Mun (Mon Apr 27 2015 - 21:06:06 PDT)
- Re: [AMBER] Is there NHE cap in the ff02 library files? David A Case (Tue Apr 28 2015 - 04:56:20 PDT)
[AMBER] Fwd: Tleap atom type - template not found Balaji Selvam (Mon Apr 27 2015 - 23:02:29 PDT)
- Re: [AMBER] Fwd: Tleap atom type - template not found David A Case (Tue Apr 28 2015 - 04:59:24 PDT)
[AMBER] Nmode analysis calculation problem for Implicit simulation. Bajarang Kumbhar (Tue Apr 28 2015 - 04:06:53 PDT)
- Re: [AMBER] Nmode analysis calculation problem for Implicit simulation. David A Case (Tue Apr 28 2015 - 05:09:51 PDT)
- Re: [AMBER] Nmode analysis calculation problem for Implicit simulation. Bajarang Kumbhar (Wed May 06 2015 - 07:25:38 PDT)
  - Re: [AMBER] Nmode analysis calculation problem for Implicit simulation. David A Case (Wed May 06 2015 - 08:25:52 PDT)
[AMBER] error in amber installation Atila Petrosian (Tue Apr 28 2015 - 04:14:55 PDT)
- Re: [AMBER] error in amber installation David A Case (Tue Apr 28 2015 - 05:14:30 PDT)
  - Re: [AMBER] error in amber installation Atila Petrosian (Sun May 03 2015 - 04:23:27 PDT)
    - Re: [AMBER] error in amber installation David A Case (Sun May 03 2015 - 04:52:04 PDT)
    - Re: [AMBER] error in amber installation Atila Petrosian (Sun May 03 2015 - 07:21:30 PDT)
    - Re: [AMBER] error in amber installation David A Case (Sun May 03 2015 - 09:10:28 PDT)
    - Re: [AMBER] error in amber installation Jason Swails (Sun May 03 2015 - 17:26:59 PDT)
    - Re: [AMBER] error in amber installation Atila Petrosian (Mon May 04 2015 - 10:51:14 PDT)
    - Re: [AMBER] error in amber installation Jason Swails (Mon May 04 2015 - 11:03:05 PDT)
    - Re: [AMBER] error in amber installation Atila Petrosian (Mon May 04 2015 - 23:08:11 PDT)
    - Re: [AMBER] error in amber installation David A Case (Tue May 05 2015 - 04:41:49 PDT)
[AMBER] pdbamb gives wrong resnumber Miguel Ángel Mompeán García (Tue Apr 28 2015 - 10:32:59 PDT)
- Re: [AMBER] pdbamb gives wrong resnumber Jason Swails (Tue Apr 28 2015 - 10:39:46 PDT)
  - Re: [AMBER] pdbamb gives wrong resnumber David A Case (Tue Apr 28 2015 - 11:49:16 PDT)
[AMBER] EGB and EEL Values in MM-GBSA -reg Muthukumaran R (Tue Apr 28 2015 - 11:03:58 PDT)
- Re: [AMBER] EGB and EEL Values in MM-GBSA -reg Jason Swails (Tue Apr 28 2015 - 11:54:37 PDT)
[AMBER] dispersion for QM/MM missing parameters Jorgen Simonsen (Wed Apr 29 2015 - 00:17:16 PDT)
[AMBER] The question about how to restart REMD simulation in AMBER12 and Langavin dynamics Wang Moye (Wed Apr 29 2015 - 00:46:23 PDT)
- Re: [AMBER] The question about how to restart REMD simulation in AMBER12 and Langavin dynamics Jason Swails (Wed Apr 29 2015 - 05:28:06 PDT)
[AMBER] Query about microsecond long simulation anu chandra (Wed Apr 29 2015 - 06:20:22 PDT)
- Re: [AMBER] Query about microsecond long simulation Ross Walker (Wed Apr 29 2015 - 06:37:04 PDT)
  - Re: [AMBER] Query about microsecond long simulation Ahmed Ezat (Wed Apr 29 2015 - 06:53:15 PDT)
    - Re: [AMBER] Query about microsecond long simulation Jason Swails (Wed Apr 29 2015 - 06:57:16 PDT)
    - Re: [AMBER] Query about microsecond long simulation Ahmed Ezat (Wed Apr 29 2015 - 07:00:50 PDT)
    - Re: [AMBER] Query about microsecond long simulation anu chandra (Wed Apr 29 2015 - 07:34:04 PDT)
    - Re: [AMBER] Query about microsecond long simulation Jason Swails (Wed Apr 29 2015 - 07:48:31 PDT)
    - Re: [AMBER] Query about microsecond long simulation David A Case (Wed Apr 29 2015 - 08:31:23 PDT)
    - Re: [AMBER] Query about microsecond long simulation anu chandra (Wed Apr 29 2015 - 08:46:01 PDT)
    - Re: [AMBER] Query about microsecond long simulation David A Case (Thu Apr 30 2015 - 04:48:00 PDT)
    - Re: [AMBER] Query about microsecond long simulation anu chandra (Thu Apr 30 2015 - 05:06:54 PDT)
  - Re: [AMBER] Query about microsecond long simulation Robert Molt (Wed Apr 29 2015 - 09:13:15 PDT)
    - Re: [AMBER] Query about microsecond long simulation Bill Ross (Wed Apr 29 2015 - 10:47:15 PDT)
    - Re: [AMBER] Query about microsecond long simulation David A Case (Wed Apr 29 2015 - 12:55:18 PDT)
    - Re: [AMBER] Query about microsecond long simulation Thomas C. Bishop (Wed Apr 29 2015 - 13:03:17 PDT)
    - Re: [AMBER] Query about microsecond long simulation Dr. Robert Molt Jr. (Wed Apr 29 2015 - 15:05:41 PDT)
    - Re: [AMBER] Query about microsecond long simulation Andrew Schaub (Wed Apr 29 2015 - 15:30:33 PDT)
    - Re: [AMBER] Query about microsecond long simulation David A Case (Thu Apr 30 2015 - 05:04:13 PDT)
    - Re: [AMBER] Query about microsecond long simulation Jason Swails (Thu Apr 30 2015 - 10:45:04 PDT)
    - Re: [AMBER] Query about microsecond long simulation Jonathan Gough (Thu Apr 30 2015 - 10:55:38 PDT)
    - Re: [AMBER] Query about microsecond long simulation Jason Swails (Thu Apr 30 2015 - 11:00:00 PDT)
    - Re: [AMBER] Query about microsecond long simulation Jonathan Gough (Thu Apr 30 2015 - 11:05:03 PDT)
    - Re: [AMBER] Query about microsecond long simulation Jason Swails (Thu Apr 30 2015 - 11:19:07 PDT)
    - Re: [AMBER] Query about microsecond long simulation Gustavo Seabra (Thu Apr 30 2015 - 03:51:00 PDT)
    - Re: [AMBER] Query about microsecond long simulation Ross Walker (Thu Apr 30 2015 - 04:21:42 PDT)
    - Re: [AMBER] Query about microsecond long simulation Jason Swails (Thu Apr 30 2015 - 10:40:15 PDT)
[AMBER] lipid simulation queries Bala subramanian (Wed Apr 29 2015 - 10:03:33 PDT)
[AMBER] MMPBSA problem with calcium Francesco Gentile (Wed Apr 29 2015 - 11:15:36 PDT)
- Re: [AMBER] MMPBSA problem with calcium Jason Swails (Thu Apr 30 2015 - 09:38:47 PDT)
- Re: [AMBER] MMPBSA problem with calcium Francesco Gentile (Thu Apr 30 2015 - 14:56:18 PDT)
  - Re: [AMBER] MMPBSA problem with calcium Jason Swails (Thu Apr 30 2015 - 15:38:29 PDT)
- Re: [AMBER] MMPBSA problem with calcium Francesco Gentile (Thu May 07 2015 - 14:02:44 PDT)
[AMBER] restraining in xz coordinates only Samaneh Mesbahi (Wed Apr 29 2015 - 20:33:25 PDT)
[AMBER] STRUCTURAL CHANGE AFTER HEATING Swithin Hanosh (Thu Apr 30 2015 - 05:06:44 PDT)
- Re: [AMBER] STRUCTURAL CHANGE AFTER HEATING David A Case (Thu Apr 30 2015 - 07:32:10 PDT)
[AMBER] restraining in xz coordinates only Samaneh Mesbahi (Thu Apr 30 2015 - 06:33:32 PDT)
- Re: [AMBER] restraining in xz coordinates only Jason Swails (Thu Apr 30 2015 - 11:12:51 PDT)
[AMBER] Bursary deadline, May 15, 2015: Drug Discovery Workshops Milan Thomas Exner (Thu Apr 30 2015 - 12:59:52 PDT)
[AMBER] Bursary deadline, May 15, 2015: Drug Discovery Workshops Canada Thomas Exner (Thu Apr 30 2015 - 13:01:24 PDT)
[AMBER] Implicit water for MD studies Shreeramesh (Fri May 01 2015 - 06:17:10 PDT)
- Re: [AMBER] Implicit water for MD studies Jason Swails (Fri May 01 2015 - 07:20:52 PDT)
  - Re: [AMBER] Implicit water for MD studies Carlos Simmerling (Fri May 01 2015 - 09:13:38 PDT)
    - Re: [AMBER] Implicit water for MD studies Shreeramesh (Mon May 04 2015 - 01:44:21 PDT)
    - Re: [AMBER] Implicit water for MD studies Debayan Chakraborty (Mon May 04 2015 - 02:58:08 PDT)
    - Re: [AMBER] Implicit water for MD studies Jason Swails (Mon May 04 2015 - 05:41:59 PDT)
    - Re: [AMBER] Implicit water for MD studies Shreeramesh (Thu May 07 2015 - 03:45:58 PDT)
[AMBER] CPPTRAJ V12.1 principal axis different to V13.22 and V14.25 CHAMI F. (Fri May 01 2015 - 07:34:43 PDT)
- Re: [AMBER] CPPTRAJ V12.1 principal axis different to V13.22 and V14.25 Daniel Roe (Fri May 01 2015 - 09:06:13 PDT)
  - Re: [AMBER] CPPTRAJ V12.1 principal axis different to V13.22 and V14.25 CHAMI F. (Fri May 01 2015 - 09:29:39 PDT)
[AMBER] Solvation of a long protein Steven Ramsey (Fri May 01 2015 - 07:39:38 PDT)
- Re: [AMBER] Solvation of a long protein amin.imtech.res.in (Fri May 01 2015 - 08:00:08 PDT)
- Re: [AMBER] Solvation of a long protein Jason Swails (Fri May 01 2015 - 08:48:03 PDT)
- Re: [AMBER] Solvation of a long protein Daniel Roe (Fri May 01 2015 - 09:09:27 PDT)
  - Re: [AMBER] Solvation of a long protein Steven Ramsey (Fri May 01 2015 - 09:31:20 PDT)
[AMBER] cpptraj: Per residue rmsd George Tzotzos (Sat May 02 2015 - 11:37:51 PDT)
- Re: [AMBER] cpptraj: Per residue rmsd Daniel Roe (Sat May 02 2015 - 15:32:24 PDT)
  - Re: [AMBER] cpptraj: Per residue rmsd George Tzotzos (Sun May 03 2015 - 02:27:44 PDT)
[AMBER] Problem Regarding PMF Graph Shubhadip Das (Mon May 04 2015 - 04:27:27 PDT)
- [AMBER] Fw: Problem Regarding PMF Graph Shubhadip Das (Mon May 04 2015 - 04:34:01 PDT)
  - Re: [AMBER] Fw: Problem Regarding PMF Graph Adrian Roitberg (Mon May 04 2015 - 06:34:52 PDT)
    - Re: [AMBER] Fw: Problem Regarding PMF Graph Shubhadip Das (Thu May 14 2015 - 21:47:22 PDT)
    - Re: [AMBER] Fw: Problem Regarding PMF Graph Jason Swails (Fri May 15 2015 - 02:27:19 PDT)
[AMBER] Problem regarding PMF curve Shubhadip Das (Mon May 04 2015 - 04:35:51 PDT)
[AMBER] Announcement: Release of AmberTools15 David A Case (Mon May 04 2015 - 06:28:43 PDT)
[AMBER] amber tools 15 upgrade problem Michael Shokhen (Mon May 04 2015 - 07:54:32 PDT)
- Re: [AMBER] amber tools 15 upgrade problem Daniel Roe (Mon May 04 2015 - 08:10:37 PDT)
- Re: [AMBER] amber tools 15 upgrade problem Kenneth Huang (Mon May 04 2015 - 08:12:41 PDT)
  - Re: [AMBER] amber tools 15 upgrade problem Michael Shokhen (Mon May 04 2015 - 08:53:48 PDT)
    - Re: [AMBER] amber tools 15 upgrade problem Jason Swails (Mon May 04 2015 - 08:59:16 PDT)
    - Re: [AMBER] amber tools 15 upgrade problem Kenneth Huang (Mon May 04 2015 - 09:09:44 PDT)
    - Re: [AMBER] amber tools 15 upgrade problem David A Case (Mon May 04 2015 - 09:04:54 PDT)
    - Re: [AMBER] amber tools 15 upgrade problem David A Case (Mon May 04 2015 - 09:57:30 PDT)
    - Re: [AMBER] amber tools 15 upgrade problem Michael Shokhen (Thu May 07 2015 - 03:57:24 PDT)
[AMBER] representing structure from equilibrium newamber list (Mon May 04 2015 - 09:35:25 PDT)
- Re: [AMBER] representing structure from equilibrium Daniel Roe (Mon May 11 2015 - 13:09:46 PDT)
  - Re: [AMBER] representing structure from equilibrium newamber list (Mon May 11 2015 - 13:45:55 PDT)
[AMBER] MM_PBSA analysis Ramin Ekhteiari (Mon May 04 2015 - 11:06:47 PDT)
- Re: [AMBER] MM_PBSA analysis Jason Swails (Mon May 04 2015 - 17:38:55 PDT)
- Re: [AMBER] MM_PBSA analysis Hai Nguyen (Fri May 08 2015 - 19:16:48 PDT)
  - Re: [AMBER] MM_PBSA analysis Ramin Ekhteiari (Sat May 09 2015 - 03:09:47 PDT)
    - Re: [AMBER] MM_PBSA analysis Vlad Cojocaru (Sat May 09 2015 - 03:23:17 PDT)
    - Re: [AMBER] MM_PBSA analysis Ramin Ekhteiari (Sat May 09 2015 - 04:18:10 PDT)
    - Re: [AMBER] MM_PBSA analysis Vlad Cojocaru (Sat May 09 2015 - 04:42:36 PDT)
[AMBER] Difference between EXTDIEL and EPSOUT? Chinh Su Tran To (Mon May 04 2015 - 23:54:53 PDT)
- Re: [AMBER] Difference between EXTDIEL and EPSOUT? Jason Swails (Tue May 05 2015 - 05:21:50 PDT)
[AMBER] Is it necessary to cap the N and C terminal using ACE and NHE in tleap? Wang Moye (Tue May 05 2015 - 00:09:28 PDT)
- Re: [AMBER] Is it necessary to cap the N and C terminal using ACE and NHE in tleap? Carlos Simmerling (Tue May 05 2015 - 03:19:01 PDT)
  - Re: [AMBER] Is it necessary to cap the N and C terminal using ACE and NHE in tleap? Wang Moye (Tue May 05 2015 - 18:15:46 PDT)
[AMBER] forcefield for DNA 王珍 (Tue May 05 2015 - 01:52:23 PDT)
- Re: [AMBER] forcefield for DNA David A Case (Tue May 05 2015 - 04:44:09 PDT)
  - Re: [AMBER] forcefield for DNA 王珍 (Tue May 05 2015 - 06:22:54 PDT)
  - Re: [AMBER] forcefield for DNA Thomas C. Bishop (Tue May 05 2015 - 06:37:48 PDT)
    - Re: [AMBER] forcefield for DNA Christina Bergonzo (Tue May 05 2015 - 06:53:40 PDT)
[AMBER] IRED Sylvester Tumusiime (Tue May 05 2015 - 08:40:05 PDT)
- Re: [AMBER] IRED Christina Bergonzo (Tue May 05 2015 - 08:52:06 PDT)
  - Re: [AMBER] IRED Sylvester Tumusiime (Tue May 05 2015 - 09:12:36 PDT)
    - Re: [AMBER] IRED Christina Bergonzo (Tue May 05 2015 - 09:22:52 PDT)
    - Re: [AMBER] IRED Sylvester Tumusiime (Tue May 05 2015 - 09:49:44 PDT)
[AMBER] Computational Chemical Biology Conference - Abstract Deadline May 15th Ross Walker (Tue May 05 2015 - 10:32:34 PDT)
[AMBER] GPCR-MM_PBSA Ramin Ekhteiari (Tue May 05 2015 - 10:56:23 PDT)
[AMBER] GPCR-MM_PBSA Ramin Ekhteiari (Tue May 05 2015 - 10:59:41 PDT)
[AMBER] GPCR-MM_PBSA Ramin Ekhteiari (Tue May 05 2015 - 11:02:10 PDT)
- Re: [AMBER] GPCR-MM_PBSA Holger Gohlke (Tue May 05 2015 - 11:55:15 PDT)
[AMBER] Atome type fatal error Pierre Bertin (Wed May 06 2015 - 01:20:34 PDT)
- Re: [AMBER] Atome type fatal error Hannes Loeffler (Wed May 06 2015 - 01:28:18 PDT)
- Re: [AMBER] Atome type fatal error David A Case (Wed May 06 2015 - 06:12:53 PDT)
  - Re: [AMBER] Atome type fatal error Pierre Bertin (Thu May 07 2015 - 12:52:19 PDT)
[AMBER] Query on how to simulate bulk no.of molecules in AMBER srilaxmi reddy (Wed May 06 2015 - 02:39:12 PDT)
- Re: [AMBER] Query on how to simulate bulk no.of molecules in AMBER Ashutosh Shandilya (Wed May 06 2015 - 03:37:30 PDT)
- Re: [AMBER] Query on how to simulate bulk no.of molecules in AMBER Jason Swails (Wed May 06 2015 - 06:15:07 PDT)
[AMBER] Error when compile ambertools15 amber amber (Wed May 06 2015 - 04:32:24 PDT)
- Re: [AMBER] Error when compile ambertools15 Jason Swails (Wed May 06 2015 - 06:11:57 PDT)
[AMBER] CUDA compiling of Amber tools 14 anu chandra (Wed May 06 2015 - 04:49:35 PDT)
- Re: [AMBER] CUDA compiling of Amber tools 14 Jason Swails (Wed May 06 2015 - 06:08:46 PDT)
[AMBER] MMPBSA.py Ramin Ekhteiari (Wed May 06 2015 - 07:18:49 PDT)
- Re: [AMBER] MMPBSA.py Hunter Brown (Fri Jul 26 2013 - 07:39:18 PDT)
  - Re: [AMBER] MMPBSA.py Jason Swails (Fri Jul 26 2013 - 12:36:30 PDT)
    - Re: [AMBER] MMPBSA.py Shashidhar Rao (Sun Jul 28 2013 - 06:19:04 PDT)
- Re: [AMBER] MMPBSA.py David A Case (Wed May 06 2015 - 08:16:45 PDT)
  - Re: [AMBER] MMPBSA.py Ramin Ekhteiari (Wed May 06 2015 - 11:14:02 PDT)
    - Re: [AMBER] MMPBSA.py David A Case (Wed May 06 2015 - 12:45:45 PDT)
    - Re: [AMBER] MMPBSA.py Ramin Ekhteiari (Wed May 06 2015 - 14:06:58 PDT)
    - Re: [AMBER] MMPBSA.py Jason Swails (Wed May 06 2015 - 18:46:52 PDT)
    - Re: [AMBER] MMPBSA.py Ramin Ekhteiari (Wed May 06 2015 - 23:32:34 PDT)
    - Re: [AMBER] MMPBSA.py Jason Swails (Thu May 07 2015 - 05:41:31 PDT)
    - [AMBER] MMPBSA.py error Urszula Uciechowska (Thu Aug 13 2015 - 03:59:19 PDT)
    - Re: [AMBER] MMPBSA.py Jason Swails (Thu May 07 2015 - 06:12:52 PDT)
    - Re: [AMBER] MMPBSA.py Ramin Ekhteiari (Thu May 07 2015 - 10:02:14 PDT)
    - [AMBER] MCPB error Takeshi Baba (Fri May 08 2015 - 03:33:46 PDT)
    - Re: [AMBER] MCPB error Pengfei Li (Fri May 08 2015 - 07:32:51 PDT)
    - [AMBER] cpptraj checkoverlap Aronica, Pietro (Fri May 08 2015 - 09:12:36 PDT)
    - Re: [AMBER] cpptraj checkoverlap Jason Swails (Fri May 08 2015 - 09:28:26 PDT)
    - Re: [AMBER] cpptraj checkoverlap Aronica, Pietro (Fri May 08 2015 - 09:39:42 PDT)
    - Re: [AMBER] cpptraj checkoverlap Daniel Roe (Fri May 08 2015 - 09:51:00 PDT)
    - Re: [AMBER] cpptraj checkoverlap Daniel Roe (Fri May 08 2015 - 09:44:26 PDT)
    - Re: [AMBER] cpptraj checkoverlap Daniel Roe (Wed May 13 2015 - 14:51:51 PDT)
    - Re: [AMBER] MCPB error Takeshi Baba (Fri May 08 2015 - 23:54:26 PDT)
[AMBER] Trouble understanding DBSCAN clustering algorithm Juan Eiros Zamora (Wed May 06 2015 - 09:22:04 PDT)
- Re: [AMBER] Trouble understanding DBSCAN clustering algorithm Christina Bergonzo (Wed May 06 2015 - 09:47:01 PDT)
- Re: [AMBER] Trouble understanding DBSCAN clustering algorithm Daniel Roe (Wed May 06 2015 - 09:49:29 PDT)
  - Re: [AMBER] Trouble understanding DBSCAN clustering algorithm Juan Eiros Zamora (Thu May 07 2015 - 02:29:34 PDT)
    - Re: [AMBER] Trouble understanding DBSCAN clustering algorithm Daniel Roe (Thu May 07 2015 - 09:12:11 PDT)
    - Re: [AMBER] Trouble understanding DBSCAN clustering algorithm Juan Eiros Zamora (Fri May 08 2015 - 07:06:30 PDT)
    - Re: [AMBER] Trouble understanding DBSCAN clustering algorithm Daniel Roe (Fri May 08 2015 - 07:24:49 PDT)
[AMBER] Error with running ParmEd Yinglong Miao (Wed May 06 2015 - 09:42:31 PDT)
- Re: [AMBER] Error with running ParmEd Jason Swails (Wed May 06 2015 - 18:59:27 PDT)
  - Re: [AMBER] Error with running ParmEd Yinglong Miao (Thu May 07 2015 - 09:58:25 PDT)
    - Re: [AMBER] Error with running ParmEd Jason Swails (Thu May 07 2015 - 12:16:44 PDT)
[AMBER] Replica-exchange molecular dynamics 新生大侠 (Wed May 06 2015 - 23:15:09 PDT)
- Re: [AMBER] Replica-exchange molecular dynamics Carlos Simmerling (Thu May 07 2015 - 03:24:13 PDT)
[AMBER] leap: adding a residue to a unit Hannes Loeffler (Thu May 07 2015 - 02:24:41 PDT)
- Re: [AMBER] leap: adding a residue to a unit David A Case (Fri May 08 2015 - 05:19:37 PDT)
[AMBER] CpHMD for Ser residue? Michael Shokhen (Thu May 07 2015 - 03:39:18 PDT)
- Re: [AMBER] CpHMD for Ser residue? Jason Swails (Thu May 07 2015 - 04:17:29 PDT)
- Re: [AMBER] CpHMD for Ser residue? Carlos Simmerling (Thu May 07 2015 - 04:19:48 PDT)
[AMBER] bad atom type: Ng (*.prmtop files from tleap) Carlos Modenutti (Thu May 07 2015 - 05:04:20 PDT)
- Re: [AMBER] bad atom type: Ng (*.prmtop files from tleap) Jason Swails (Thu May 07 2015 - 06:49:24 PDT)
  - Re: [AMBER] bad atom type: Ng (*.prmtop files from tleap) Daniel Roe (Thu May 07 2015 - 09:17:31 PDT)
- Re: [AMBER] bad atom type: Ng (*.prmtop files from tleap) Carlos Modenutti (Thu May 07 2015 - 09:55:37 PDT)
[AMBER] Error when compile ambertools15 amber amber (Thu May 07 2015 - 05:11:43 PDT)
- Re: [AMBER] Error when compile ambertools15 Jason Swails (Thu May 07 2015 - 06:43:15 PDT)
  - Re: [AMBER] Error when compile ambertools15 Yu Chen (Thu May 07 2015 - 14:14:03 PDT)
    - Re: [AMBER] Error when compile ambertools15 Jason Swails (Thu May 07 2015 - 14:20:08 PDT)
    - Re: [AMBER] Error when compile ambertools15 Yu Chen (Thu May 07 2015 - 18:21:46 PDT)
    - Re: [AMBER] Error when compile ambertools15 Jason Swails (Fri May 08 2015 - 04:30:45 PDT)
[AMBER] query parameter files for mercuric ions Ya Gao (Thu May 07 2015 - 06:18:01 PDT)
- Re: [AMBER] query parameter files for mercuric ions Pengfei Li (Thu May 07 2015 - 06:52:21 PDT)
[AMBER] box's information Fatemeh Sadat Alavi (Thu May 07 2015 - 06:45:44 PDT)
- Re: [AMBER] box's information Jason Swails (Thu May 07 2015 - 07:23:27 PDT)
- Re: [AMBER] box's information Fatemeh Sadat Alavi (Fri May 08 2015 - 00:42:57 PDT)
  - Re: [AMBER] box's information Jason Swails (Fri May 08 2015 - 04:34:20 PDT)
  - Re: [AMBER] box's information David A Case (Fri May 08 2015 - 05:07:49 PDT)
[AMBER] problem with prepgen in an organic molecule parameterization Rebeca García Fandiño (Thu May 07 2015 - 07:37:14 PDT)
- Re: [AMBER] problem with prepgen in an organic molecule parameterization Daniel Roe (Thu May 07 2015 - 07:51:09 PDT)
  - Re: [AMBER] problem with prepgen in an organic molecule parameterization Rebeca García Fandiño (Thu May 07 2015 - 08:12:31 PDT)
    - Re: [AMBER] problem with prepgen in an organic molecule parameterization Daniel Roe (Thu May 07 2015 - 09:31:01 PDT)
    - Re: [AMBER] problem with prepgen in an organic molecule parameterization Rebeca García Fandiño (Thu May 07 2015 - 10:05:32 PDT)
    - Re: [AMBER] problem with prepgen in an organic molecule parameterization Daniel Roe (Thu May 07 2015 - 10:54:20 PDT)
    - Re: [AMBER] problem with prepgen in an organic molecule parameterization Rebeca García Fandiño (Fri May 08 2015 - 02:11:00 PDT)
[AMBER] Assistance required installing amber in cuda Bala Subramani (Thu May 07 2015 - 09:14:29 PDT)
- Re: [AMBER] Assistance required installing amber in cuda Daniel Roe (Thu May 07 2015 - 09:33:05 PDT)
  - Re: [AMBER] Assistance required installing amber in cuda Bala Subramani (Thu May 07 2015 - 10:52:08 PDT)
  - Re: [AMBER] Assistance required installing amber in cuda Bala Subramani (Thu May 07 2015 - 10:54:14 PDT)
- Re: [AMBER] Assistance required installing amber in cuda Jason Swails (Thu May 07 2015 - 12:15:02 PDT)
[AMBER] Error when compile ambertools15 amber amber (Fri May 08 2015 - 01:37:29 PDT)
[AMBER] Faulty_atom_connection error nibedita jana (Fri May 08 2015 - 03:06:02 PDT)
- Re: [AMBER] Faulty_atom_connection error David A Case (Fri May 08 2015 - 05:03:38 PDT)
[AMBER] MMPBSA.py.MPI George Tzotzos (Fri May 08 2015 - 12:24:20 PDT)
- Re: [AMBER] MMPBSA.py.MPI Anthony Cruz-Balberdy (Sat Nov 09 2013 - 15:57:25 PST)
- Re: [AMBER] MMPBSA.py.MPI Jason Swails (Sat May 09 2015 - 05:02:31 PDT)
  - Re: [AMBER] MMPBSA.py.MPI George Tzotzos (Fri May 15 2015 - 13:22:18 PDT)
    - Re: [AMBER] MMPBSA.py.MPI Jason Swails (Fri May 15 2015 - 17:47:42 PDT)
    - Re: [AMBER] MMPBSA.py.MPI George Tzotzos (Sat May 16 2015 - 06:05:26 PDT)
    - Re: [AMBER] MMPBSA.py.MPI Jason Swails (Sat May 16 2015 - 09:30:17 PDT)
    - Re: [AMBER] MMPBSA.py.MPI George Tzotzos (Sat May 16 2015 - 11:31:56 PDT)
[AMBER] The output file about SMD wjli (Sat May 09 2015 - 06:24:05 PDT)
- Re: [AMBER] The output file about SMD Jason Swails (Sat May 09 2015 - 08:37:57 PDT)
[AMBER] Problem with Configuring NetCDF Alaa Mohye El-din Soliman (Sat May 09 2015 - 06:42:18 PDT)
- Re: [AMBER] Problem with Configuring NetCDF Jason Swails (Sat May 09 2015 - 07:25:08 PDT)
  - Re: [AMBER] Problem with Configuring NetCDF Alaa Mohye El-din Soliman (Sat May 09 2015 - 12:19:29 PDT)
    - Re: [AMBER] Problem with Configuring NetCDF Jason Swails (Sat May 09 2015 - 12:43:58 PDT)
    - Re: [AMBER] Problem with Configuring NetCDF Alaa Mohye El-din Soliman (Sun May 10 2015 - 16:05:22 PDT)
    - Re: [AMBER] Problem with Configuring NetCDF Jason Swails (Sun May 10 2015 - 17:18:44 PDT)
[AMBER] question regarding SMD simulation Asmita Gupta (Sat May 09 2015 - 07:38:39 PDT)
[AMBER] Selection of chain muhammad tahir ayub (Sat May 09 2015 - 11:54:01 PDT)
- Re: [AMBER] Selection of chain David A Case (Sat May 09 2015 - 19:37:29 PDT)
- [AMBER] Fwd: Selection of chain muhammad tahir ayub (Sun May 10 2015 - 07:57:03 PDT)
  - Re: [AMBER] Fwd: Selection of chain Kenneth Huang (Sun May 10 2015 - 08:47:58 PDT)
[AMBER] QM/MM Protein-Ligand interaction w/cofactor William Martin (Sat May 09 2015 - 12:35:30 PDT)
- Re: [AMBER] QM/MM Protein-Ligand interaction w/cofactor Gustavo Seabra (Sat May 09 2015 - 13:04:03 PDT)
- Re: [AMBER] QM/MM Protein-Ligand interaction w/cofactor David A Case (Sat May 09 2015 - 19:43:01 PDT)
  - Re: [AMBER] QM/MM Protein-Ligand interaction w/cofactor William Martin (Sat May 09 2015 - 22:27:30 PDT)
[AMBER] parameters for type: Cl- Michael Shokhen (Sun May 10 2015 - 11:08:20 PDT)
- Re: [AMBER] parameters for type: Cl- Kenneth Huang (Sun May 10 2015 - 11:35:59 PDT)
  - Re: [AMBER] parameters for type: Cl- Michael Shokhen (Sun May 10 2015 - 11:57:49 PDT)
    - Re: [AMBER] parameters for type: Cl- Marc van der Kamp (Sun May 10 2015 - 12:28:04 PDT)
- Re: [AMBER] parameters for type: Cl- David A Case (Sun May 10 2015 - 14:08:53 PDT)
[AMBER] Algorithms for integrating the equations of motion gepaula.web.de (Sun May 10 2015 - 16:15:40 PDT)
- Re: [AMBER] Algorithms for integrating the equations of motion Hai Nguyen (Sun May 10 2015 - 16:37:10 PDT)
[AMBER] qmcut in Amber14 Manual Robert Molt (Sun May 10 2015 - 23:13:18 PDT)
- Re: [AMBER] qmcut in Amber14 Manual Marc van der Kamp (Mon May 11 2015 - 01:43:32 PDT)
  - Re: [AMBER] qmcut in Amber14 Manual Jason Swails (Mon May 11 2015 - 05:05:52 PDT)
[AMBER] restart an SMD run Asmita Gupta (Sun May 10 2015 - 23:31:21 PDT)
- Re: [AMBER] restart an SMD run Jason Swails (Mon May 11 2015 - 05:44:35 PDT)
  - Re: [AMBER] restart an SMD run Asmita Gupta (Tue May 12 2015 - 04:42:08 PDT)
    - Re: [AMBER] restart an SMD run Jason Swails (Tue May 12 2015 - 04:51:26 PDT)
    - Re: [AMBER] restart an SMD run Asmita Gupta (Tue May 12 2015 - 05:07:39 PDT)
    - Re: [AMBER] restart an SMD run Jason Swails (Tue May 12 2015 - 05:15:29 PDT)
[AMBER] Error while running tleap for protein-RNA complex Shreeramesh (Mon May 11 2015 - 01:59:30 PDT)
- Re: [AMBER] Error while running tleap for protein-RNA complex Hector A. Baldoni (Mon May 11 2015 - 04:10:37 PDT)
- Re: [AMBER] Error while running tleap for protein-RNA complex David A Case (Mon May 11 2015 - 04:55:17 PDT)
  - Re: [AMBER] Error while running tleap for protein-RNA complex Shreeramesh (Tue May 12 2015 - 02:48:47 PDT)
    - Re: [AMBER] Error while running tleap for protein-RNA complex Jason Swails (Tue May 12 2015 - 05:12:39 PDT)
[AMBER] principal component analysis abdennour braka (Mon May 11 2015 - 02:27:13 PDT)
- Re: [AMBER] principal component analysis Daniel Roe (Mon May 11 2015 - 12:55:38 PDT)
[AMBER] AMD with restrained molecule. Binwu Zhao (Mon May 11 2015 - 11:09:21 PDT)
[AMBER] mmpbsa.py error George Tzotzos (Mon May 11 2015 - 11:52:04 PDT)
- Re: [AMBER] mmpbsa.py error Jason Swails (Mon May 11 2015 - 12:00:11 PDT)
  - Re: [AMBER] mmpbsa.py error George Tzotzos (Mon May 11 2015 - 12:11:23 PDT)
[AMBER] parallel installation of ambertools14 on centOS-rocks system Andrew Bostick (Mon May 11 2015 - 12:17:29 PDT)
- Re: [AMBER] parallel installation of ambertools14 on centOS-rocks system Jason Swails (Mon May 11 2015 - 12:31:52 PDT)
[AMBER] experimental coulomb and van der Waals cutoffs Ahmet yıldırım (Tue May 12 2015 - 01:52:16 PDT)
- Re: [AMBER] experimental coulomb and van der Waals cutoffs Carlos Simmerling (Tue May 12 2015 - 03:28:06 PDT)
  - Re: [AMBER] experimental coulomb and van der Waals cutoffs Ahmet yıldırım (Tue May 12 2015 - 04:03:29 PDT)
    - Re: [AMBER] experimental coulomb and van der Waals cutoffs Jason Swails (Tue May 12 2015 - 05:03:13 PDT)
[AMBER] How to fix missing residues Shreeramesh (Tue May 12 2015 - 03:48:18 PDT)
- Re: [AMBER] How to fix missing residues Sajeewa Pemasinghe (Tue May 12 2015 - 04:21:03 PDT)
[AMBER] mmpbsa.py: new error message George Tzotzos (Tue May 12 2015 - 07:15:46 PDT)
- [AMBER] mmpbsa.py: new error message Kenneth Huang (Tue May 12 2015 - 07:27:38 PDT)
- Re: [AMBER] mmpbsa.py: new error message Jason Swails (Tue May 12 2015 - 10:03:03 PDT)
  - Re: [AMBER] mmpbsa.py: new error message George Tzotzos (Tue May 12 2015 - 10:40:24 PDT)
    - Re: [AMBER] mmpbsa.py: new error message Jason Swails (Tue May 12 2015 - 10:58:13 PDT)
[AMBER] pmemd performance on GTX Titan Z Kenneth Huang (Tue May 12 2015 - 09:22:13 PDT)
- Re: [AMBER] pmemd performance on GTX Titan Z Ross Walker (Tue May 12 2015 - 20:42:17 PDT)
  - [AMBER] pmemd performance on GTX Titan Z Kenneth Huang (Wed May 13 2015 - 18:05:29 PDT)
[AMBER] Atoms overlapped in vacuum minimization anu chandra (Wed May 13 2015 - 04:08:54 PDT)
- Re: [AMBER] Atoms overlapped in vacuum minimization Carlos Simmerling (Wed May 13 2015 - 04:58:34 PDT)
  - Re: [AMBER] Atoms overlapped in vacuum minimization David A Case (Wed May 13 2015 - 05:53:35 PDT)
    - Re: [AMBER] Atoms overlapped in vacuum minimization anu chandra (Wed May 13 2015 - 06:21:31 PDT)
    - Re: [AMBER] Atoms overlapped in vacuum minimization Carlos Simmerling (Wed May 13 2015 - 07:08:50 PDT)
[AMBER] "Free energy fluctiontions over trajectory in MMGBSA.py" James Starlight (Wed May 13 2015 - 06:55:04 PDT)
- Re: [AMBER] "Free energy fluctiontions over trajectory in MMGBSA.py" Vlad Cojocaru (Wed May 13 2015 - 07:04:36 PDT)
  - Re: [AMBER] "Free energy fluctiontions over trajectory in MMGBSA.py" James Starlight (Wed May 13 2015 - 08:26:24 PDT)
    - Re: [AMBER] "Free energy fluctiontions over trajectory in MMGBSA.py" Vlad Cojocaru (Wed May 13 2015 - 08:47:28 PDT)
    - Re: [AMBER] "Free energy fluctiontions over trajectory in MMGBSA.py" James Starlight (Fri May 15 2015 - 04:30:32 PDT)
    - Re: [AMBER] "Free energy fluctiontions over trajectory in MMGBSA.py" James Starlight (Mon May 18 2015 - 04:38:00 PDT)
    - Re: [AMBER] "Free energy fluctiontions over trajectory in MMGBSA.py" Vlad Cojocaru (Mon May 18 2015 - 05:37:58 PDT)
    - Re: [AMBER] "Free energy fluctiontions over trajectory in MMGBSA.py" James Starlight (Mon May 18 2015 - 06:15:03 PDT)
    - Re: [AMBER] "Free energy fluctiontions over trajectory in MMGBSA.py" Vlad Cojocaru (Mon May 18 2015 - 06:53:51 PDT)
    - Re: [AMBER] "Free energy fluctiontions over trajectory in MMGBSA.py" James Starlight (Mon May 18 2015 - 07:16:21 PDT)
    - Re: [AMBER] "Free energy fluctiontions over trajectory in MMGBSA.py" James Starlight (Mon May 18 2015 - 07:23:53 PDT)
    - Re: [AMBER] "Free energy fluctiontions over trajectory in MMGBSA.py" Vlad Cojocaru (Mon May 18 2015 - 07:31:54 PDT)
    - Re: [AMBER] "Free energy fluctiontions over trajectory in MMGBSA.py" Vlad Cojocaru (Mon May 18 2015 - 07:57:12 PDT)
    - Re: [AMBER] "Free energy fluctiontions over trajectory in MMGBSA.py" James Starlight (Mon May 18 2015 - 08:37:31 PDT)
    - Re: [AMBER] "Free energy fluctiontions over trajectory in MMGBSA.py" Vlad Cojocaru (Mon May 18 2015 - 10:27:00 PDT)
    - Re: [AMBER] "Free energy fluctiontions over trajectory in MMGBSA.py" James Starlight (Tue May 19 2015 - 05:23:11 PDT)
    - Re: [AMBER] "Free energy fluctiontions over trajectory in MMGBSA.py" James Starlight (Tue May 19 2015 - 05:32:42 PDT)
    - Re: [AMBER] "Free energy fluctiontions over trajectory in MMGBSA.py" Vlad Cojocaru (Tue May 19 2015 - 06:04:03 PDT)
    - Re: [AMBER] "Free energy fluctiontions over trajectory in MMGBSA.py" Vlad Cojocaru (Mon May 18 2015 - 07:25:55 PDT)
[AMBER] Principal moments of inertia Sylvester Tumusiime (Wed May 13 2015 - 07:18:31 PDT)
- Re: [AMBER] Principal moments of inertia Daniel Roe (Thu May 14 2015 - 06:49:38 PDT)
[AMBER] site down? Gerald Monard (Wed May 13 2015 - 08:00:58 PDT)
- Re: [AMBER] site down? Akash Deep Biswas (Wed May 13 2015 - 08:10:36 PDT)
  - Re: [AMBER] site down? Marc van der Kamp (Wed May 13 2015 - 08:13:35 PDT)
    - Re: [AMBER] site down? Gerald Monard (Wed May 13 2015 - 08:19:39 PDT)
    - Re: [AMBER] site down? Ross Walker (Wed May 13 2015 - 08:23:43 PDT)
    - Re: [AMBER] site down? Gerald Monard (Wed May 13 2015 - 08:31:15 PDT)
    - Re: [AMBER] site down? Jason Swails (Wed May 13 2015 - 09:23:24 PDT)
    - Re: [AMBER] site down? Jonathan Gough (Wed May 13 2015 - 08:19:54 PDT)
    - Re: [AMBER] site down? Ross Walker (Wed May 13 2015 - 08:21:35 PDT)
- Re: [AMBER] site down? Wang Moye (Wed May 13 2015 - 18:26:25 PDT)
  - Re: [AMBER] site down? Gerald Monard (Thu May 14 2015 - 05:11:28 PDT)
  - Re: [AMBER] site down? David A Case (Thu May 14 2015 - 04:57:38 PDT)
[AMBER] adp amber parameters Carlos Romero (Wed May 13 2015 - 08:36:44 PDT)
- Re: [AMBER] adp amber parameters David A Case (Wed May 13 2015 - 10:09:14 PDT)
  - Re: [AMBER] adp amber parameters Carlos Romero (Wed May 13 2015 - 10:14:39 PDT)
[AMBER] error using the lipidorder command Sylvester Tumusiime (Wed May 13 2015 - 08:49:34 PDT)
- Re: [AMBER] error using the lipidorder command Daniel Roe (Thu May 14 2015 - 06:51:46 PDT)
[AMBER] Amber website down Crystal VanderZanden (Wed May 13 2015 - 09:04:14 PDT)
- Re: [AMBER] Amber website down James Maier (Wed May 13 2015 - 09:07:54 PDT)
- Re: [AMBER] Amber website down Wang Moye (Wed May 13 2015 - 19:02:00 PDT)
[AMBER] DOPC lipid bilayer in Amber using lipid14 force field. Him Shweta (Wed May 13 2015 - 10:26:26 PDT)
- Re: [AMBER] DOPC lipid bilayer in Amber using lipid14 force field. Ross Walker (Wed May 13 2015 - 11:03:23 PDT)
[AMBER] Question about lipid simulation Victor Ma (Wed May 13 2015 - 10:51:48 PDT)
- Re: [AMBER] Question about lipid simulation Ross Walker (Wed May 13 2015 - 10:59:52 PDT)
[AMBER] ante-mmpbsa.py: troubleshooting George Tzotzos (Wed May 13 2015 - 11:26:36 PDT)
- Re: [AMBER] ante-mmpbsa.py: troubleshooting Jason Swails (Wed May 13 2015 - 12:19:10 PDT)
  - Re: [AMBER] ante-mmpbsa.py: troubleshooting George Tzotzos (Wed May 13 2015 - 12:28:37 PDT)
    - Re: [AMBER] ante-mmpbsa.py: troubleshooting Jason Swails (Wed May 13 2015 - 12:41:26 PDT)
    - Re: [AMBER] ante-mmpbsa.py: troubleshooting George Tzotzos (Wed May 13 2015 - 13:33:15 PDT)
[AMBER] Error selecting compatible GPU all CUDA-capable devices are busy or unavailable Jagga Soorma (Wed May 13 2015 - 15:02:10 PDT)
- Re: [AMBER] Error selecting compatible GPU all CUDA-capable devices are busy or unavailable Jason Swails (Thu May 14 2015 - 07:14:08 PDT)
[AMBER] Praise Dr. Robert Molt Jr. (Wed May 13 2015 - 15:10:11 PDT)
[AMBER] minimization error Carlos Romero (Thu May 14 2015 - 07:26:36 PDT)
- Re: [AMBER] minimization error Jason Swails (Thu May 14 2015 - 10:16:44 PDT)
  - Re: [AMBER] minimization error Carlos Romero (Thu May 14 2015 - 11:32:20 PDT)
[AMBER] Warning when trying to get RMS Mohammad Salem (Thu May 14 2015 - 11:56:15 PDT)
- Re: [AMBER] Warning when trying to get RMS Daniel Roe (Thu May 14 2015 - 12:14:49 PDT)
[AMBER] Announcement: GLYCAM/GLYCAM-Web mailing list Lachele Foley (Thu May 14 2015 - 15:25:33 PDT)
[AMBER] How to run GBSA in MD and binding energy calculation (MMPBSA.py)? Huang (Thu May 14 2015 - 20:46:35 PDT)
- Re: [AMBER] How to run GBSA in MD and binding energy calculation (MMPBSA.py)? Jason Swails (Fri May 15 2015 - 02:07:51 PDT)
  - Re: [AMBER] How to run GBSA in MD and binding energy calculation (MMPBSA.py)? Carlos Simmerling (Fri May 15 2015 - 03:15:10 PDT)
[AMBER] Arsenic force field parametrization Sushi Shilpa (Fri May 15 2015 - 00:03:56 PDT)
- Re: [AMBER] Arsenic force field parametrization Andrew Schaub (Sat May 16 2015 - 22:55:13 PDT)
  - Re: [AMBER] Arsenic force field parametrization Pengfei Li (Mon May 18 2015 - 14:18:14 PDT)
    - Re: [AMBER] Arsenic force field parametrization Pengfei Li (Wed May 27 2015 - 08:28:07 PDT)
    - Re: [AMBER] Arsenic force field parametrization Jason Swails (Wed May 27 2015 - 08:47:08 PDT)
    - Re: [AMBER] Arsenic force field parametrization Pengfei Li (Fri May 29 2015 - 12:31:38 PDT)
    - Re: [AMBER] Arsenic force field parametrization Pengfei Li (Mon Jun 01 2015 - 15:56:59 PDT)
    - Re: [AMBER] Arsenic force field parametrization Sushi Shilpa (Tue Jun 02 2015 - 23:17:32 PDT)
    - Re: [AMBER] Arsenic force field parametrization Pengfei Li (Fri Jun 26 2015 - 12:36:18 PDT)
[AMBER] ESURF in MMPBSA.py results Huang (Fri May 15 2015 - 01:26:22 PDT)
- Re: [AMBER] ESURF in MMPBSA.py results Jason Swails (Fri May 15 2015 - 02:15:40 PDT)
[AMBER] the energy between two ligand molecules chemjxn (Fri May 15 2015 - 02:10:02 PDT)
- Re: [AMBER] the energy between two ligand molecules Jason Swails (Fri May 15 2015 - 02:18:54 PDT)
[AMBER] Biligand, trimetal subtrate simulation Julio Dominguez (Fri May 15 2015 - 12:47:23 PDT)
[AMBER] disable minimization in nmode MMPBSA.py Carlos Modenutti (Fri May 15 2015 - 14:02:22 PDT)
- Re: [AMBER] disable minimization in nmode MMPBSA.py Jason Swails (Fri May 15 2015 - 15:07:03 PDT)
[AMBER] Help needed on MMPBSA for a system with different protonation states in free & bound forms, using multiple trajectory protocol Shailesh Pandey (Sat May 16 2015 - 04:18:42 PDT)
- Re: [AMBER] Help needed on MMPBSA for a system with different protonation states in free & bound forms, using multiple trajectory protocol Jason Swails (Sat May 16 2015 - 09:59:21 PDT)
[AMBER] Regarding - "Help needed on MMPBSA for a system with different protonation states in free & bound forms" Shailesh Pandey (Sun May 17 2015 - 03:05:28 PDT)
- Re: [AMBER] Regarding - "Help needed on MMPBSA for a system with different protonation states in free & bound forms" Jason Swails (Mon May 18 2015 - 06:06:59 PDT)
  - Re: [AMBER] Regarding - "Help needed on MMPBSA for a system with different protonation states in free & bound forms" Shailesh Pandey (Mon May 18 2015 - 08:54:22 PDT)
[AMBER] Polymorphism study using Amber jacob wick (Sun May 17 2015 - 23:53:29 PDT)
- Re: [AMBER] Polymorphism study using Amber David A Case (Mon May 18 2015 - 05:10:03 PDT)
[AMBER] Changing two conditions simultaneously in pmemd Juan Eiros Zamora (Mon May 18 2015 - 05:06:56 PDT)
- Re: [AMBER] Changing two conditions simultaneously in pmemd Hannes Loeffler (Mon May 18 2015 - 05:13:10 PDT)
  - Re: [AMBER] Changing two conditions simultaneously in pmemd Juan Eiros Zamora (Mon May 18 2015 - 06:37:13 PDT)
    - Re: [AMBER] Changing two conditions simultaneously in pmemd Hannes Loeffler (Mon May 18 2015 - 06:55:01 PDT)
    - Re: [AMBER] Changing two conditions simultaneously in pmemd Vlad Cojocaru (Mon May 18 2015 - 06:56:11 PDT)
    - Re: [AMBER] Changing two conditions simultaneously in pmemd Vlad Cojocaru (Mon May 18 2015 - 07:00:48 PDT)
    - Re: [AMBER] Changing two conditions simultaneously in pmemd Juan Eiros Zamora (Mon May 18 2015 - 07:13:14 PDT)
    - Re: [AMBER] Changing two conditions simultaneously in pmemd Hannes Loeffler (Mon May 18 2015 - 07:18:38 PDT)
    - Re: [AMBER] Changing two conditions simultaneously in pmemd Jason Swails (Mon May 18 2015 - 07:29:16 PDT)
    - Re: [AMBER] Changing two conditions simultaneously in pmemd Vlad Cojocaru (Mon May 18 2015 - 07:39:24 PDT)
    - Re: [AMBER] Changing two conditions simultaneously in pmemd Ross Walker (Mon May 18 2015 - 09:07:07 PDT)
    - Re: [AMBER] Changing two conditions simultaneously in pmemd Vlad Cojocaru (Mon May 18 2015 - 10:30:00 PDT)
- Re: [AMBER] Changing two conditions simultaneously in pmemd Christina Bergonzo (Mon May 18 2015 - 08:05:09 PDT)
  - Re: [AMBER] Changing two conditions simultaneously in pmemd Hannes Loeffler (Mon May 18 2015 - 08:44:28 PDT)
[AMBER] WEBSITE not opening Elvis Martis (Mon May 18 2015 - 05:57:30 PDT)
- Re: [AMBER] WEBSITE not opening Jason Swails (Mon May 18 2015 - 06:00:03 PDT)
- Re: [AMBER] WEBSITE not opening Elvis Martis (Mon May 18 2015 - 20:06:08 PDT)
  - Re: [AMBER] WEBSITE not opening Ross Walker (Mon May 18 2015 - 20:18:05 PDT)
    - Re: [AMBER] DNS manipulations David A Case (Tue May 19 2015 - 05:06:00 PDT)
    - Re: [AMBER] DNS manipulations Ross Walker (Tue May 19 2015 - 10:10:31 PDT)
    - Re: [AMBER] DNS manipulations Bill Ross (Tue May 19 2015 - 17:19:21 PDT)
  - Re: [AMBER] WEBSITE not opening Ye Mei (Mon May 18 2015 - 20:46:08 PDT)
- Re: [AMBER] WEBSITE not opening Elvis Martis (Tue May 19 2015 - 20:12:05 PDT)
[AMBER] Problem with amb2gmx in AmberTools 15 Soumendranath Bhakat (Tue May 19 2015 - 04:01:50 PDT)
- Re: [AMBER] Problem with amb2gmx in AmberTools 15 David A Case (Tue May 19 2015 - 05:03:30 PDT)
  - Re: [AMBER] Problem with amb2gmx in AmberTools 15 Soumendranath Bhakat (Wed May 20 2015 - 02:52:02 PDT)
    - Re: [AMBER] Problem with amb2gmx in AmberTools 15 Hannes Loeffler (Wed May 20 2015 - 03:04:46 PDT)
    - Re: [AMBER] Problem with amb2gmx in AmberTools 15 Soumendranath Bhakat (Wed May 20 2015 - 03:13:11 PDT)
    - Re: [AMBER] Problem with amb2gmx in AmberTools 15 Soumendranath Bhakat (Wed May 20 2015 - 03:15:18 PDT)
    - Re: [AMBER] Problem with amb2gmx in AmberTools 15 Hannes Loeffler (Wed May 20 2015 - 03:25:25 PDT)
    - Re: [AMBER] Problem with amb2gmx in AmberTools 15 David A Case (Wed May 20 2015 - 04:33:46 PDT)
    - Re: [AMBER] Problem with amb2gmx in AmberTools 15 Soumendranath Bhakat (Wed May 20 2015 - 05:14:10 PDT)
    - Re: [AMBER] Problem with amb2gmx in AmberTools 15 Soumendranath Bhakat (Wed May 20 2015 - 09:45:13 PDT)
[AMBER] Sander QMMM Bomb Problem Gulsevin,Alican (Thu May 14 2015 - 12:56:59 PDT)
- Re: [AMBER] Sander QMMM Bomb Problem Gustavo Seabra (Tue May 19 2015 - 10:13:42 PDT)
[AMBER] Computational Chemical Biology Conference - TALK DEADLINE EXTENDED Ross Walker (Tue May 19 2015 - 09:46:43 PDT)
[AMBER] MCPB.py issues David Poole (Tue May 19 2015 - 10:46:15 PDT)
- Re: [AMBER] MCPB.py issues David A Case (Wed May 20 2015 - 04:48:18 PDT)
  - Re: [AMBER] MCPB.py issues Pengfei Li (Wed May 20 2015 - 07:24:02 PDT)
- Re: [AMBER] MCPB.py issues David Poole (Fri May 22 2015 - 17:11:08 PDT)
- Re: [AMBER] MCPB.py issues Pengfei Li (Tue May 26 2015 - 09:30:06 PDT)
[AMBER] Computational Chemical Biology Conference - Abstract Deadline Extended to June 1st Ross Walker (Tue May 19 2015 - 13:00:14 PDT)
[AMBER] problems with "explicit solvent" Investigador Química (Tue May 19 2015 - 17:20:16 PDT)
- Re: [AMBER] problems with "explicit solvent" David A Case (Tue May 19 2015 - 18:19:17 PDT)
[AMBER] MC-simulation-MM-PBSA Ramin Ekhteiari (Tue May 19 2015 - 23:51:30 PDT)
[AMBER] MMGBSA: interpretation of results George Tzotzos (Wed May 20 2015 - 05:09:19 PDT)
- Re: [AMBER] MMGBSA: interpretation of results George Tzotzos (Wed May 20 2015 - 11:37:02 PDT)
  - Re: [AMBER] MMGBSA: interpretation of results Kenneth Huang (Wed May 20 2015 - 12:13:13 PDT)
[AMBER] Amber12 + GTX 980 Robinson, Roger (Wed May 20 2015 - 06:09:54 PDT)
[AMBER] Amber 12 + GTX 980 Robinson, Roger (Wed May 20 2015 - 06:14:03 PDT)
- Re: [AMBER] Amber 12 + GTX 980 Ross Walker (Wed May 20 2015 - 09:13:18 PDT)
  - Re: [AMBER] Amber 12 + GTX 980 Robinson, Roger (Wed May 20 2015 - 23:31:44 PDT)
    - Re: [AMBER] Amber 12 + GTX 980 Scott Le Grand (Thu May 21 2015 - 15:29:45 PDT)
[AMBER] AMBERHOME environment variable setting problem Gustavo Avelar Molina (Wed May 20 2015 - 08:15:16 PDT)
- Re: [AMBER] AMBERHOME environment variable setting problem Jason Swails (Wed May 20 2015 - 08:20:37 PDT)
  - Re: [AMBER] AMBERHOME environment variable setting problem MOHD HOMAIDUR RAHMAN (Wed May 20 2015 - 10:25:24 PDT)
[AMBER] Bad Contact from lack of QM/MM Heating? Dr. Robert Molt Jr. (Wed May 20 2015 - 20:43:07 PDT)
[AMBER] MC-MM-PBSA Ramin Ekhteiari (Wed May 20 2015 - 22:46:09 PDT)
- Re: [AMBER] MC-MM-PBSA Jason Swails (Thu May 21 2015 - 05:37:53 PDT)
[AMBER] Question about Extra Point zhouhaibin2008.ok (Fri May 22 2015 - 00:14:07 PDT)
- Re: [AMBER] Question about Extra Point David A Case (Fri May 22 2015 - 04:47:16 PDT)
[AMBER] Regarding AMD simulation Aditya Sarkar (Fri May 22 2015 - 04:08:44 PDT)
- Re: [AMBER] Regarding AMD simulation Daniel Roe (Fri May 22 2015 - 07:27:24 PDT)
[AMBER] Does GLYCAM only can deal with Oligosaccharides or Polysaccharides BUT NOT Monosaccharide？？？ Chris (Fri May 22 2015 - 07:02:18 PDT)
- Re: [AMBER] Does GLYCAM only can deal with Oligosaccharides or Polysaccharides BUT NOT Monosaccharide？？？ Lachele Foley (Fri May 22 2015 - 09:55:14 PDT)
[AMBER] Developing Parameters using tleap Brittany Boykin (Fri May 22 2015 - 12:44:55 PDT)
- Re: [AMBER] Developing Parameters using tleap David A Case (Sat May 23 2015 - 09:29:33 PDT)
[AMBER] Determining number of molecules from a point by integration using xmgrace Sylvester Tumusiime (Fri May 22 2015 - 12:48:26 PDT)
- Re: [AMBER] Determining number of molecules from a point by integration using xmgrace hannes.loeffler.stfc.ac.uk (Fri May 22 2015 - 12:59:56 PDT)
[AMBER] Regarding high temp simulation of DNA and amber MD module MOHD HOMAIDUR RAHMAN (Fri May 22 2015 - 14:23:29 PDT)
- Re: [AMBER] Regarding high temp simulation of DNA and amber MD module Carlos Simmerling (Sat May 23 2015 - 02:33:58 PDT)
- Re: [AMBER] Regarding high temp simulation of DNA and amber MD module David A Case (Sat May 23 2015 - 09:38:54 PDT)
[AMBER] Problem with covalently bonded ligand parametrization Gustavo Avelar Molina (Fri May 22 2015 - 19:07:43 PDT)
- Re: [AMBER] Problem with covalently bonded ligand parametrization David A Case (Sat May 23 2015 - 09:45:27 PDT)
  - Re: [AMBER] Problem with covalently bonded ligand parametrization Gustavo Avelar Molina (Sat May 23 2015 - 16:59:03 PDT)
[AMBER] tleap maintainer Matt Harvey (Sat May 23 2015 - 05:13:29 PDT)
- Re: [AMBER] tleap maintainer David A Case (Sat May 23 2015 - 09:48:44 PDT)
[AMBER] Doubt about ligand binding in proteins Gustavo Avelar Molina (Sat May 23 2015 - 18:05:28 PDT)
- Re: [AMBER] Doubt about ligand binding in proteins Kenneth Huang (Sun May 24 2015 - 10:51:22 PDT)
[AMBER] cpptraj: lie George Tzotzos (Sun May 24 2015 - 04:18:49 PDT)
- Re: [AMBER] cpptraj: lie Jason Swails (Sun May 24 2015 - 08:31:46 PDT)
- Re: [AMBER] cpptraj: lie Daniel Roe (Sun May 24 2015 - 10:30:53 PDT)
[AMBER] NTX Keyword Robert Molt (Sun May 24 2015 - 10:10:23 PDT)
- Re: [AMBER] NTX Keyword Kenneth Huang (Sun May 24 2015 - 11:13:35 PDT)
- Re: [AMBER] NTX Keyword Jason Swails (Sun May 24 2015 - 15:38:01 PDT)
[AMBER] help me to understand using GLYCAM!!! Chris (Mon May 25 2015 - 06:52:37 PDT)
- Re: [AMBER] help me to understand using GLYCAM!!! Lachele Foley (Mon May 25 2015 - 18:02:55 PDT)
  - Re: [AMBER] help me to understand using GLYCAM!!! Chris (Mon May 25 2015 - 19:22:39 PDT)
    - Re: [AMBER] help me to understand using GLYCAM!!! David A Case (Tue May 26 2015 - 04:35:48 PDT)
    - Re: [AMBER] help me to understand using GLYCAM!!! Lachele Foley (Tue May 26 2015 - 10:25:28 PDT)
[AMBER] Extracting temperature-based potential energies from REMD Lee-Ping Wang (Mon May 25 2015 - 09:44:10 PDT)
- Re: [AMBER] Extracting temperature-based potential energies from REMD Jason Swails (Mon May 25 2015 - 12:12:03 PDT)
  - Re: [AMBER] Extracting temperature-based potential energies from REMD Lee-Ping Wang (Mon May 25 2015 - 13:43:32 PDT)
    - Re: [AMBER] Extracting temperature-based potential energies from REMD Hai Nguyen (Mon May 25 2015 - 18:29:07 PDT)
    - Re: [AMBER] Extracting temperature-based potential energies from REMD Lee-Ping Wang (Mon May 25 2015 - 20:04:55 PDT)
    - Re: [AMBER] Extracting temperature-based potential energies from REMD Lee-Ping Wang (Sun May 31 2015 - 05:09:00 PDT)
    - Re: [AMBER] Extracting temperature-based potential energies from REMD Hai Nguyen (Sun May 31 2015 - 06:02:35 PDT)
[AMBER] Protein-Membrane assembly Ofir Tal (Tue May 26 2015 - 00:44:01 PDT)
[AMBER] partition error in shake Evgenia Dueva (Tue May 26 2015 - 06:37:44 PDT)
- Re: [AMBER] partition error in shake David A Case (Tue May 26 2015 - 08:11:50 PDT)
[AMBER] MMGBSA: pairwise decomposition George Tzotzos (Tue May 26 2015 - 10:53:39 PDT)
- Re: [AMBER] MMGBSA: pairwise decomposition Jason Swails (Tue May 26 2015 - 12:19:58 PDT)
[AMBER] membrane protein simulation Victor Ma (Tue May 26 2015 - 14:13:48 PDT)
- Re: [AMBER] membrane protein simulation Ross Walker (Tue May 26 2015 - 18:16:22 PDT)
  - Re: [AMBER] membrane protein simulation Victor Ma (Wed May 27 2015 - 08:35:53 PDT)
    - Re: [AMBER] membrane protein simulation Ross Walker (Wed May 27 2015 - 08:43:34 PDT)
    - Re: [AMBER] membrane protein simulation Victor Ma (Wed May 27 2015 - 09:55:06 PDT)
[AMBER] Next AMBER release? Mohd Farid Ismail (Tue May 26 2015 - 17:20:35 PDT)
- Re: [AMBER] Next AMBER release? Ross Walker (Tue May 26 2015 - 18:18:26 PDT)
[AMBER] RNA unfolding studies.. Asmita Gupta (Wed May 27 2015 - 03:54:40 PDT)
- Re: [AMBER] RNA unfolding studies.. David A Case (Wed May 27 2015 - 05:14:49 PDT)
[AMBER] loading molecule in leap jacob wick (Wed May 27 2015 - 04:23:46 PDT)
- Re: [AMBER] loading molecule in leap David A Case (Wed May 27 2015 - 05:30:15 PDT)
[AMBER] WARNING: SGFT, instead of TEMPSG, should be set for SGMDfp/SGLDfp! barbara rossi (Wed May 27 2015 - 06:22:22 PDT)
[AMBER] Fwd: Using the CHARMM force field to run simulations with AMBER Shalini Gupta (Wed May 27 2015 - 12:22:13 PDT)
- Re: [AMBER] Fwd: Using the CHARMM force field to run simulations with AMBER Jason Swails (Wed May 27 2015 - 13:50:46 PDT)
  - Re: [AMBER] Fwd: Using the CHARMM force field to run simulations with AMBER Brian Radak (Wed May 27 2015 - 14:27:58 PDT)
    - Re: [AMBER] Fwd: Using the CHARMM force field to run simulations with AMBER hannes.loeffler.stfc.ac.uk (Wed May 27 2015 - 23:36:39 PDT)
[AMBER] Bug in LIE action command of cpptraj? Samuel Bowerman (Wed May 27 2015 - 12:25:27 PDT)
- Re: [AMBER] Bug in LIE action command of cpptraj? Jason Swails (Wed May 27 2015 - 12:34:20 PDT)
  - Re: [AMBER] Bug in LIE action command of cpptraj? Samuel Bowerman (Wed May 27 2015 - 13:07:21 PDT)
    - Re: [AMBER] Bug in LIE action command of cpptraj? Jason Swails (Wed May 27 2015 - 13:44:30 PDT)
    - Re: [AMBER] Bug in LIE action command of cpptraj? Samuel Bowerman (Wed May 27 2015 - 14:49:54 PDT)
[AMBER] AMBER 15 ERROR 汪盛 (Wed May 27 2015 - 20:45:23 PDT)
- Re: [AMBER] AMBER 15 ERROR Hai Nguyen (Wed May 27 2015 - 21:24:29 PDT)
- Re: [AMBER] AMBER 15 ERROR Ye Mei (Wed May 27 2015 - 22:04:56 PDT)
[AMBER] Torsion restraints with pmemd.amoeba Karl Debiec (Thu May 28 2015 - 09:17:07 PDT)
- Re: [AMBER] Torsion restraints with pmemd.amoeba David A Case (Thu May 28 2015 - 09:44:35 PDT)
- Re: [AMBER] Torsion restraints with pmemd.amoeba Karl Debiec (Thu Jun 04 2015 - 08:41:41 PDT)
  - Re: [AMBER] Torsion restraints with pmemd.amoeba David A Case (Thu Jun 04 2015 - 09:12:53 PDT)
[AMBER] mmpbsa.py.MPI: patching George Tzotzos (Thu May 28 2015 - 11:33:11 PDT)
- Re: [AMBER] mmpbsa.py.MPI: patching Kenneth Huang (Thu May 28 2015 - 11:55:09 PDT)
[AMBER] MMPBSA.py API AttributeError: 'MMPBSA_App' object has no attribute ‘using_chamber' D.J. Pattinson (Fri May 29 2015 - 03:46:44 PDT)
- Re: [AMBER] MMPBSA.py API AttributeError: 'MMPBSA_App' object has no attribute ‘using_chamber' Jason Swails (Fri May 29 2015 - 06:28:27 PDT)
  - Re: [AMBER] MMPBSA.py API AttributeError: 'MMPBSA_App' object has no attribute ‘using_chamber' D.J. Pattinson (Fri May 29 2015 - 06:58:08 PDT)
[AMBER] Ambertools 12 Download xy21hb (Fri May 29 2015 - 06:43:06 PDT)
- Re: [AMBER] Ambertools 12 Download Jason Swails (Fri May 29 2015 - 06:45:47 PDT)
  - Re: [AMBER] Ambertools 12 Download Jason Swails (Fri May 29 2015 - 06:46:34 PDT)
  - Re: [AMBER] Ambertools 12 Download xy21hb (Fri May 29 2015 - 06:53:57 PDT)
    - Re: [AMBER] Ambertools 12 Download Jason Swails (Fri May 29 2015 - 07:13:15 PDT)
[AMBER] Umbrella Sampling and wham MOHD HOMAIDUR RAHMAN (Fri May 29 2015 - 07:46:58 PDT)
- Re: [AMBER] Umbrella Sampling and wham Brian Radak (Sat May 30 2015 - 11:13:37 PDT)
[AMBER] Fwd: MPI Runtime Error Kusum Mehla (Fri May 29 2015 - 21:38:42 PDT)
- Re: [AMBER] Fwd: MPI Runtime Error David A Case (Sat May 30 2015 - 09:18:40 PDT)
[AMBER] water bridges Hector A. Baldoni (Sat May 30 2015 - 09:43:48 PDT)
- Re: [AMBER] water bridges Sylvester Tumusiime (Sat May 30 2015 - 14:44:31 PDT)
[AMBER] Entropy Ramin Ekhteiari (Sun May 31 2015 - 23:25:36 PDT)
- Re: [AMBER] Entropy Vlad Cojocaru (Mon Jun 01 2015 - 00:07:11 PDT)
[AMBER] How to Simulate Monoclinic crystal packing arrangement. srilaxmi reddy (Mon Jun 01 2015 - 02:55:20 PDT)
- Re: [AMBER] How to Simulate Monoclinic crystal packing arrangement. David A Case (Mon Jun 01 2015 - 04:54:20 PDT)
  - Re: [AMBER] How to Simulate Monoclinic crystal packing arrangement. srilaxmi reddy (Mon Jun 01 2015 - 05:17:32 PDT)
[AMBER] How to generate Phi_Psi by cpptraj ? Michael Shokhen (Mon Jun 01 2015 - 12:27:19 PDT)
- Re: [AMBER] How to generate Phi_Psi by cpptraj ? James Maier (Mon Jun 01 2015 - 12:44:35 PDT)
  - Re: [AMBER] How to generate Phi_Psi by cpptraj ? Soumendranath Bhakat (Mon Jun 01 2015 - 13:41:11 PDT)
- Re: [AMBER] How to generate Phi_Psi by cpptraj ? Hai Nguyen (Mon Jun 01 2015 - 14:03:28 PDT)
  - Re: [AMBER] How to generate Phi_Psi by cpptraj ? Jason Swails (Mon Jun 01 2015 - 14:33:02 PDT)
    - Re: [AMBER] How to generate Phi_Psi by cpptraj ? Daniel Roe (Mon Jun 01 2015 - 16:40:40 PDT)
[AMBER] Bug or feature of tleap Julio Dominguez (Mon Jun 01 2015 - 16:01:27 PDT)
- Re: [AMBER] Bug or feature of tleap David A Case (Mon Jun 01 2015 - 18:00:39 PDT)
- Re: [AMBER] Bug or feature of tleap Jason Swails (Mon Jun 01 2015 - 18:06:27 PDT)
- Re: [AMBER] Bug or feature of tleap Julio Dominguez (Tue Jun 02 2015 - 13:48:13 PDT)
  - Re: [AMBER] Bug or feature of tleap Pengfei Li (Tue Jun 02 2015 - 19:19:31 PDT)
[AMBER] torsions in parm10.dat Jeffrey Teillet (Tue Jun 02 2015 - 01:28:58 PDT)
- Re: [AMBER] torsions in parm10.dat Jason Swails (Tue Jun 02 2015 - 08:05:04 PDT)
[AMBER] How can I do a thermodynamic integration using Simpson's rules ? Jinfeng Huang (Tue Jun 02 2015 - 02:20:25 PDT)
- Re: [AMBER] How can I do a thermodynamic integration using Simpson's rules ? Hannes Loeffler (Tue Jun 02 2015 - 02:43:52 PDT)
  - Re: [AMBER] How can I do a thermodynamic integration using Simpson's rules ? Jinfeng Huang (Tue Jun 02 2015 - 06:03:27 PDT)
    - Re: [AMBER] How can I do a thermodynamic integration using Simpson's rules ? Hannes Loeffler (Tue Jun 02 2015 - 06:18:43 PDT)
    - Re: [AMBER] How can I do a thermodynamic integration using Simpson's rules ? Jinfeng Huang (Tue Jun 02 2015 - 07:04:07 PDT)
[AMBER] Density for a protein ligand complex run Mrinda Jones (Tue Jun 02 2015 - 05:16:03 PDT)
- Re: [AMBER] Density for a protein ligand complex run Hector A. Baldoni (Tue Jun 02 2015 - 07:14:37 PDT)
- Re: [AMBER] Density for a protein ligand complex run David A Case (Tue Jun 02 2015 - 12:41:53 PDT)
  - Re: [AMBER] Density for a protein ligand complex run Mrinda Jones (Tue Jun 02 2015 - 23:26:00 PDT)
    - Re: [AMBER] Density for a protein ligand complex run Hector A. Baldoni (Wed Jun 03 2015 - 05:58:49 PDT)
    - Re: [AMBER] Density for a protein ligand complex run Jason Swails (Wed Jun 03 2015 - 06:01:23 PDT)
    - Re: [AMBER] Density for a protein ligand complex run David A Case (Wed Jun 03 2015 - 06:14:39 PDT)
    - Re: [AMBER] Density for a protein ligand complex run Mrinda Jones (Fri Jun 05 2015 - 11:12:40 PDT)
    - Re: [AMBER] Density for a protein ligand complex run Jason Swails (Fri Jun 05 2015 - 11:31:59 PDT)
    - Re: [AMBER] Density for a protein ligand complex run Hector A. Baldoni (Sun Jun 07 2015 - 16:37:59 PDT)
[AMBER] GPU machines in the UK. Peter Winn (Tue Jun 02 2015 - 06:49:33 PDT)
- Re: [AMBER] GPU machines in the UK. Ross Walker (Tue Jun 02 2015 - 08:53:15 PDT)
  - Re: [AMBER] GPU machines in the UK. Gould, Ian R (Tue Jun 02 2015 - 09:05:31 PDT)
  - Re: [AMBER] GPU machines in the UK. George Tzotzos (Tue Jun 02 2015 - 10:01:19 PDT)
[AMBER] Only -mpi option creates the python modules. Is this right? Eduardo Almeida Costa (Tue Jun 02 2015 - 07:26:47 PDT)
- Re: [AMBER] Only -mpi option creates the python modules. Is this right? Jason Swails (Tue Jun 02 2015 - 07:58:42 PDT)
  - Re: [AMBER] Only -mpi option creates the python modules. Is this right? Eduardo Almeida Costa (Tue Jun 02 2015 - 08:06:21 PDT)
[AMBER] Imaging & centering Angela de Manzanos (Tue Jun 02 2015 - 09:33:58 PDT)
- Re: [AMBER] Imaging & centering Jason Swails (Tue Jun 02 2015 - 09:49:42 PDT)
- Re: [AMBER] Imaging & centering Daniel Roe (Tue Jun 02 2015 - 10:05:27 PDT)
  - Re: [AMBER] Imaging & centering de Manzanos Guinot, Angela (Tue Jun 02 2015 - 10:11:44 PDT)
[AMBER] ERROR WHILE RUNNING ANTECHAMBER ROOPALI VERMA (Wed Jun 03 2015 - 01:08:00 PDT)
- Re: [AMBER] ERROR WHILE RUNNING ANTECHAMBER Hannes Loeffler (Wed Jun 03 2015 - 01:40:39 PDT)
- Re: [AMBER] ERROR WHILE RUNNING ANTECHAMBER Marc van der Kamp (Wed Jun 03 2015 - 01:41:57 PDT)
  - Re: [AMBER] ERROR WHILE RUNNING ANTECHAMBER Aleksandra Skoric (Wed Jun 03 2015 - 02:36:02 PDT)
    - Re: [AMBER] ERROR WHILE RUNNING ANTECHAMBER ROOPALI VERMA (Wed Jun 03 2015 - 21:51:08 PDT)
    - Re: [AMBER] ERROR WHILE RUNNING ANTECHAMBER ROOPALI VERMA (Wed Jun 03 2015 - 21:58:18 PDT)
    - Re: [AMBER] ERROR WHILE RUNNING ANTECHAMBER ROOPALI VERMA (Thu Jun 04 2015 - 02:04:24 PDT)
    - Re: [AMBER] ERROR WHILE RUNNING ANTECHAMBER Marc van der Kamp (Thu Jun 04 2015 - 02:20:35 PDT)
    - Re: [AMBER] ERROR WHILE RUNNING ANTECHAMBER Aleksandra Skoric (Thu Jun 04 2015 - 03:47:14 PDT)
[AMBER] force-momentum based SGLD algorithm barbara rossi (Wed Jun 03 2015 - 02:22:16 PDT)
- Re: [AMBER] force-momentum based SGLD algorithm Wu, Xiongwu (NIH/NHLBI) [E] (Thu Jun 04 2015 - 08:14:51 PDT)
[AMBER] circle of correlation - PCA - AMBERtools Jose Manuel Gally (Wed Jun 03 2015 - 07:33:36 PDT)
[AMBER] pmemd.cuda.MPI vs openmpi Victor Ma (Wed Jun 03 2015 - 10:54:44 PDT)
- Re: [AMBER] pmemd.cuda.MPI vs openmpi Ross Walker (Wed Jun 03 2015 - 11:31:48 PDT)
  - Re: [AMBER] pmemd.cuda.MPI vs openmpi Victor Ma (Wed Jun 03 2015 - 11:58:01 PDT)
    - Re: [AMBER] pmemd.cuda.MPI vs openmpi Ross Walker (Wed Jun 03 2015 - 12:29:00 PDT)
    - Re: [AMBER] pmemd.cuda.MPI vs openmpi Victor Ma (Wed Jun 03 2015 - 13:29:13 PDT)
    - Re: [AMBER] pmemd.cuda.MPI vs openmpi Ross Walker (Wed Jun 03 2015 - 13:42:43 PDT)
[AMBER] Bad Frames in Corrupted Trajectories Amanda Li (Wed Jun 03 2015 - 12:22:55 PDT)
- Re: [AMBER] Bad Frames in Corrupted Trajectories Daniel Roe (Wed Jun 03 2015 - 12:40:59 PDT)
[AMBER] cpptraj crosscorr command Gard Nelson (Wed Jun 03 2015 - 16:53:25 PDT)
- Re: [AMBER] cpptraj crosscorr command Daniel Roe (Thu Jun 04 2015 - 09:00:39 PDT)
  - Re: [AMBER] cpptraj crosscorr command Gard Nelson (Thu Jun 04 2015 - 10:44:38 PDT)
    - Re: [AMBER] cpptraj crosscorr command Daniel Roe (Thu Jun 04 2015 - 11:00:56 PDT)
    - Re: [AMBER] cpptraj crosscorr command Gard Nelson (Thu Jun 04 2015 - 11:22:05 PDT)
[AMBER] Fwd: GPU pmemd.cuda runs very slow (3ns/day)??? Chinh Su Tran To (Thu Jun 04 2015 - 01:13:55 PDT)
- Re: [AMBER] Fwd: GPU pmemd.cuda runs very slow (3ns/day)??? Gerald Monard (Thu Jun 04 2015 - 02:52:32 PDT)
  - Re: [AMBER] Fwd: GPU pmemd.cuda runs very slow (3ns/day)??? Chinh Su Tran To (Thu Jun 04 2015 - 03:58:08 PDT)
    - Re: [AMBER] Fwd: GPU pmemd.cuda runs very slow (3ns/day)??? Gerald Monard (Thu Jun 04 2015 - 05:04:59 PDT)
    - Re: [AMBER] Fwd: GPU pmemd.cuda runs very slow (3ns/day)??? Jason Swails (Thu Jun 04 2015 - 05:15:12 PDT)
    - Re: [AMBER] Fwd: GPU pmemd.cuda runs very slow (3ns/day)??? Patrick McGrath (Thu Jun 04 2015 - 05:35:51 PDT)
    - Re: [AMBER] Fwd: GPU pmemd.cuda runs very slow (3ns/day)??? Jason Swails (Thu Jun 04 2015 - 05:51:11 PDT)
    - Re: [AMBER] Fwd: GPU pmemd.cuda runs very slow (3ns/day)??? Chinh Su Tran To (Thu Jun 04 2015 - 18:59:16 PDT)
    - Re: [AMBER] Fwd: GPU pmemd.cuda runs very slow (3ns/day)??? Jason Swails (Thu Jun 04 2015 - 20:32:16 PDT)
    - Re: [AMBER] Fwd: GPU pmemd.cuda runs very slow (3ns/day)??? Chinh Su Tran To (Thu Jun 04 2015 - 22:43:57 PDT)
[AMBER] Regarding dihedral scanning Soumendranath Bhakat (Thu Jun 04 2015 - 01:36:21 PDT)
- Re: [AMBER] Regarding dihedral scanning Daniel Roe (Thu Jun 04 2015 - 08:30:26 PDT)
  - Re: [AMBER] Regarding dihedral scanning Soumendranath Bhakat (Thu Jun 04 2015 - 08:49:40 PDT)
    - Re: [AMBER] Regarding dihedral scanning Soumendranath Bhakat (Fri Jun 05 2015 - 02:45:12 PDT)
    - [AMBER] ΑΠ: Regarding dihedral scanning Antonios Kolocouris (Fri Jun 05 2015 - 02:51:35 PDT)
    - Re: [AMBER] ΑΠ: Regarding dihedral scanning Jason Swails (Fri Jun 05 2015 - 04:39:03 PDT)
    - Re: [AMBER] Regarding dihedral scanning Daniel Roe (Fri Jun 05 2015 - 13:03:16 PDT)
    - Re: [AMBER] Regarding dihedral scanning Soumendranath Bhakat (Mon Jun 08 2015 - 02:48:09 PDT)
    - Re: [AMBER] Regarding dihedral scanning Daniel Roe (Fri Jun 12 2015 - 12:48:31 PDT)
[AMBER] proxy configuration abdennour braka (Thu Jun 04 2015 - 02:48:45 PDT)
- Re: [AMBER] proxy configuration Jason Swails (Thu Jun 04 2015 - 05:09:12 PDT)
[AMBER] Converting Gromacs topology files to Amber format Jason Swails (Thu Jun 04 2015 - 06:33:09 PDT)
- Re: [AMBER] Converting Gromacs topology files to Amber format MOHD HOMAIDUR RAHMAN (Sat Jun 06 2015 - 10:48:38 PDT)
  - Re: [AMBER] Converting Gromacs topology files to Amber format Vishal Nemaysh (Sun Jun 07 2015 - 02:12:49 PDT)
    - Re: [AMBER] Converting Gromacs topology files to Amber format Jason Swails (Sun Jun 07 2015 - 09:22:02 PDT)
  - Re: [AMBER] Converting Gromacs topology files to Amber format Jason Swails (Sun Jun 07 2015 - 09:25:52 PDT)
    - Re: [AMBER] Converting Gromacs topology files to Amber format Vishal Nemaysh (Mon Jun 08 2015 - 22:30:42 PDT)
- Re: [AMBER] Converting Gromacs topology files to Amber format Sarah Witzke (Mon Jun 15 2015 - 06:46:59 PDT)
  - Re: [AMBER] Converting Gromacs topology files to Amber format Jason Swails (Mon Jun 15 2015 - 07:37:34 PDT)
[AMBER] Abrupt RMSD change during DNA simulation for a short interval of time jacob wick (Thu Jun 04 2015 - 06:38:17 PDT)
- Re: [AMBER] Abrupt RMSD change during DNA simulation for a short interval of time Jason Swails (Thu Jun 04 2015 - 06:51:00 PDT)
  - Re: [AMBER] Abrupt RMSD change during DNA simulation for a short interval of time jacob wick (Thu Jun 04 2015 - 06:59:23 PDT)
    - Re: [AMBER] Abrupt RMSD change during DNA simulation for a short interval of time Daniel Roe (Thu Jun 04 2015 - 08:20:22 PDT)
    - Re: [AMBER] Abrupt RMSD change during DNA simulation for a short interval of time Jason Swails (Thu Jun 04 2015 - 09:17:44 PDT)
    - Re: [AMBER] Abrupt RMSD change during DNA simulation for a short interval of time jacob wick (Fri Jun 05 2015 - 01:08:00 PDT)
[AMBER] write PCA mode trajectory with cpptraj Vlad Cojocaru (Fri Jun 05 2015 - 01:18:35 PDT)
- Re: [AMBER] write PCA mode trajectory with cpptraj Daniel Roe (Fri Jun 05 2015 - 13:10:06 PDT)
[AMBER] how to convert pdb to rst file ? Indrajit Deb (Fri Jun 05 2015 - 08:26:47 PDT)
- Re: [AMBER] how to convert pdb to rst file ? Jason Swails (Fri Jun 05 2015 - 08:49:44 PDT)
- Re: [AMBER] how to convert pdb to rst file ? Kenneth Huang (Fri Jun 05 2015 - 08:49:47 PDT)
  - Re: [AMBER] how to convert pdb to rst file ? Indrajit Deb (Fri Jun 05 2015 - 09:34:01 PDT)
    - Re: [AMBER] how to convert pdb to rst file ? Indrajit Deb (Fri Jun 05 2015 - 09:35:38 PDT)
    - Re: [AMBER] how to convert pdb to rst file ? Jason Swails (Fri Jun 05 2015 - 09:54:24 PDT)
    - Re: [AMBER] how to convert pdb to rst file ? Indrajit Deb (Fri Jun 05 2015 - 10:21:36 PDT)
[AMBER] Error unknown flag: –O Michael Shokhen (Sat Jun 06 2015 - 01:24:19 PDT)
- Re: [AMBER] Error unknown flag: –O hannes.loeffler.stfc.ac.uk (Sat Jun 06 2015 - 02:02:05 PDT)
  - Re: [AMBER] Error unknown flag: –O Michael Shokhen (Sat Jun 06 2015 - 02:40:55 PDT)
[AMBER] During MD simulation protein drifts out of periodic cell Michael Shokhen (Sun Jun 07 2015 - 03:35:23 PDT)
[AMBER] How to avoid protein drift? Michael Shokhen (Sun Jun 07 2015 - 05:08:36 PDT)
- Re: [AMBER] How to avoid protein drift? Jason Swails (Sun Jun 07 2015 - 09:36:51 PDT)
[AMBER] problem with extraction of potential energy for the ligand Maryam Hamzehee (Sun Jun 07 2015 - 10:14:26 PDT)
- Re: [AMBER] problem with extraction of potential energy for the ligand Bill Ross (Sun Jun 07 2015 - 14:20:28 PDT)
[AMBER] Leap : problem with copying and combining DNA items Jérémie Knoops (Sun Jun 07 2015 - 23:58:18 PDT)
- Re: [AMBER] Leap : problem with copying and combining DNA items Jason Swails (Mon Jun 08 2015 - 05:19:12 PDT)
- Re: [AMBER] Leap : problem with copying and combining DNA items Jérémie Knoops (Mon Oct 05 2015 - 05:34:14 PDT)
  - Re: [AMBER] Leap : problem with copying and combining DNA items David A Case (Mon Oct 05 2015 - 14:01:29 PDT)
[AMBER] Regarding creating Mg2+ ions topology and parameter file ROOPALI VERMA (Mon Jun 08 2015 - 03:31:53 PDT)
- Re: [AMBER] Regarding creating Mg2+ ions topology and parameter file David A Case (Mon Jun 08 2015 - 04:49:30 PDT)
  - Re: [AMBER] Regarding creating Mg2+ ions topology and parameter file Kenneth Huang (Mon Jun 08 2015 - 07:12:55 PDT)
[AMBER] Error while running leap for a protein containing Co2+ Suchetana Gupta (Mon Jun 08 2015 - 05:05:38 PDT)
- Re: [AMBER] Error while running leap for a protein containing Co2+ Kenneth Huang (Mon Jun 08 2015 - 07:21:23 PDT)
- Re: [AMBER] Error while running leap for a protein containing Co2+ Jason Swails (Mon Jun 08 2015 - 07:30:36 PDT)
[AMBER] Fwd: Question about building a branched levan oligosaccharide Surasak Chunsrivirot (Mon Jun 08 2015 - 07:26:17 PDT)
- Re: [AMBER] Fwd: Question about building a branched levan oligosaccharide Lachele Foley (Mon Jun 08 2015 - 11:42:19 PDT)
  - Re: [AMBER] Fwd: Question about building a branched levan oligosaccharide Surasak Chunsrivirot (Tue Jun 09 2015 - 04:05:08 PDT)
    - Re: [AMBER] Fwd: Question about building a branched levan oligosaccharide Lachele Foley (Tue Jun 09 2015 - 15:35:11 PDT)
    - Re: [AMBER] Fwd: Question about building a branched levan oligosaccharide Surasak Chunsrivirot (Tue Jun 09 2015 - 19:47:41 PDT)
[AMBER] Few queries about membrane protein simulations anu chandra (Mon Jun 08 2015 - 07:45:18 PDT)
- Re: [AMBER] Few queries about membrane protein simulations Jason Swails (Mon Jun 08 2015 - 09:04:11 PDT)
- Re: [AMBER] Few queries about membrane protein simulations Ross Walker (Mon Jun 08 2015 - 09:17:38 PDT)
  - Re: [AMBER] Few queries about membrane protein simulations anu chandra (Fri Jun 12 2015 - 02:26:51 PDT)
    - Re: [AMBER] Few queries about membrane protein simulations Joseph Baker (Fri Jun 12 2015 - 07:25:47 PDT)
    - Re: [AMBER] Few queries about membrane protein simulations Ross Walker (Fri Jun 12 2015 - 19:46:50 PDT)
    - Re: [AMBER] Few queries about membrane protein simulations Joseph Baker (Fri Jun 12 2015 - 21:07:48 PDT)
    - Re: [AMBER] Few queries about membrane protein simulations Ross Walker (Sat Jun 13 2015 - 10:48:05 PDT)
    - Re: [AMBER] Few queries about membrane protein simulations Joseph Baker (Sat Jun 13 2015 - 17:04:26 PDT)
[AMBER] Centre of Mass or geometry issue Soumendranath Bhakat (Tue Jun 09 2015 - 01:33:49 PDT)
- Re: [AMBER] Centre of Mass or geometry issue Juan Eiros Zamora (Tue Jun 09 2015 - 01:55:58 PDT)
  - Re: [AMBER] Centre of Mass or geometry issue Juan Eiros Zamora (Tue Jun 09 2015 - 01:57:33 PDT)
    - Re: [AMBER] Centre of Mass or geometry issue Soumendranath Bhakat (Tue Jun 09 2015 - 02:02:49 PDT)
    - Re: [AMBER] Centre of Mass or geometry issue Juan Eiros Zamora (Tue Jun 09 2015 - 02:14:20 PDT)
    - Re: [AMBER] Centre of Mass or geometry issue Jason Swails (Tue Jun 09 2015 - 04:36:59 PDT)
[AMBER] HMR Parker de Waal (Tue Jun 09 2015 - 11:09:43 PDT)
- Re: [AMBER] HMR Ross Walker (Tue Jun 09 2015 - 11:34:47 PDT)
[AMBER] problem with extraction of potential energy for the ligand Maryam Hamzehee (Wed Jun 10 2015 - 02:50:14 PDT)
[AMBER] Parmed.py_ImportError: No module named ParmedTools.logos Sheehan, Alice (Wed Jun 10 2015 - 08:54:20 PDT)
- Re: [AMBER] Parmed.py_ImportError: No module named ParmedTools.logos Jason Swails (Wed Jun 10 2015 - 09:22:39 PDT)
  - Re: [AMBER] Parmed.py_ImportError: No module named ParmedTools.logos Sheehan, Alice (Thu Jun 11 2015 - 02:45:29 PDT)
[AMBER] Announcement: AMBER Workshop - London, Mon July 6th to Fri July 10th 2015 - Registration deadline June 15th (this coming Monday!) Ross Walker (Wed Jun 10 2015 - 09:23:17 PDT)
[AMBER] Steered Molecular Dynamics Brittany Boykin (Wed Jun 10 2015 - 09:35:53 PDT)
- Re: [AMBER] Steered Molecular Dynamics Marcos Serrou do Amaral (Wed Jun 10 2015 - 13:35:09 PDT)
[AMBER] Charges for H-atoms in GLYCAM? Chris (Wed Jun 10 2015 - 10:32:57 PDT)
- Re: [AMBER] Charges for H-atoms in GLYCAM? Lachele Foley (Wed Jun 10 2015 - 10:44:33 PDT)
  - Re: [AMBER] Charges for H-atoms in GLYCAM? David A Case (Wed Jun 10 2015 - 11:20:39 PDT)
    - Re: [AMBER] Charges for H-atoms in GLYCAM? Lachele Foley (Wed Jun 10 2015 - 11:37:04 PDT)
[AMBER] problem with extraction of potential energy for the ligand Maryam Hamzehee (Wed Jun 10 2015 - 10:45:29 PDT)
- Re: [AMBER] problem with extraction of potential energy for the ligand Bill Ross (Wed Jun 10 2015 - 07:29:48 PDT)
- Re: [AMBER] problem with extraction of potential energy for the ligand Jason Swails (Wed Jun 10 2015 - 11:16:33 PDT)
  - Re: [AMBER] problem with extraction of potential energy for the ligand Maryam Hamzehee (Wed Jun 10 2015 - 12:03:44 PDT)
- Re: [AMBER] problem with extraction of potential energy for the ligand Bill Ross (Wed Jun 10 2015 - 13:32:50 PDT)
  - Re: [AMBER] problem with extraction of potential energy for the ligand Maryam Hamzehee (Thu Jun 11 2015 - 04:46:39 PDT)
[AMBER] basic question - sanity check Jonathan Gough (Wed Jun 10 2015 - 10:48:32 PDT)
- Re: [AMBER] basic question - sanity check Jason Swails (Wed Jun 10 2015 - 11:07:42 PDT)
- Re: [AMBER] basic question - sanity check Jason Swails (Wed Jun 10 2015 - 11:09:52 PDT)
  - Re: [AMBER] basic question - sanity check Jonathan Gough (Wed Jun 10 2015 - 12:04:21 PDT)
[AMBER] Restraining distance between molecules initially jacob wick (Wed Jun 10 2015 - 23:40:55 PDT)
[AMBER] Regarding the protonation states of Histidine muhammad tahir ayub (Wed Jun 10 2015 - 23:50:10 PDT)
- Re: [AMBER] Regarding the protonation states of Histidine Soumendranath Bhakat (Thu Jun 11 2015 - 01:13:13 PDT)
[AMBER] Help - setting up parallel machine anu chandra (Thu Jun 11 2015 - 03:39:26 PDT)
- Re: [AMBER] Help - setting up parallel machine David A Case (Thu Jun 11 2015 - 05:17:33 PDT)
  - Re: [AMBER] Help - setting up parallel machine David A Case (Thu Jun 11 2015 - 07:00:55 PDT)
    - Re: [AMBER] Help - setting up parallel machine anu chandra (Fri Jun 12 2015 - 02:31:16 PDT)
    - Re: [AMBER] Help - setting up parallel machine Jason Swails (Fri Jun 12 2015 - 02:32:50 PDT)
[AMBER] Antechamber on regular nucleotides Mrinda Jones (Thu Jun 11 2015 - 05:58:14 PDT)
- Re: [AMBER] Antechamber on regular nucleotides David A Case (Thu Jun 11 2015 - 07:08:42 PDT)
  - Re: [AMBER] Antechamber on regular nucleotides Mrinda Jones (Thu Jun 11 2015 - 22:58:14 PDT)
    - Re: [AMBER] Antechamber on regular nucleotides hannes.loeffler.stfc.ac.uk (Thu Jun 11 2015 - 23:38:48 PDT)
[AMBER] tinker_to_amber doesn't like AMOEBA reference frames for chloride Baker, Lewis Robert (Thu Jun 11 2015 - 10:30:02 PDT)
- Re: [AMBER] tinker_to_amber doesn't like AMOEBA reference frames for chloride David A Case (Thu Jun 11 2015 - 11:05:58 PDT)
  - Re: [AMBER] tinker_to_amber doesn't like AMOEBA reference frames for chloride David A Case (Thu Jun 11 2015 - 11:08:18 PDT)
[AMBER] cpptraj matrix dist modifications Gard Nelson (Thu Jun 11 2015 - 11:59:19 PDT)
[AMBER] distance restrain Lara rajam (Thu Jun 11 2015 - 13:11:38 PDT)
- Re: [AMBER] distance restrain Jason Swails (Fri Jun 12 2015 - 02:24:44 PDT)
- Re: [AMBER] distance restrain David A Case (Fri Jun 12 2015 - 05:54:00 PDT)
[AMBER] Problem with stripped combined mdcrd files Soong Jiaxin (Thu Jun 11 2015 - 19:48:06 PDT)
- Re: [AMBER] Problem with stripped combined mdcrd files Hai Nguyen (Thu Jun 11 2015 - 20:14:36 PDT)
  - Re: [AMBER] Problem with stripped combined mdcrd files Soong Jiaxin (Thu Jun 11 2015 - 20:29:50 PDT)
    - Re: [AMBER] Problem with stripped combined mdcrd files Hai Nguyen (Thu Jun 11 2015 - 20:39:02 PDT)
    - Re: [AMBER] Problem with stripped combined mdcrd files Soong Jiaxin (Thu Jun 11 2015 - 20:40:25 PDT)
    - Re: [AMBER] Problem with stripped combined mdcrd files Daniel Roe (Thu Jun 11 2015 - 20:49:21 PDT)
    - Re: [AMBER] Problem with stripped combined mdcrd files Soong Jiaxin (Thu Jun 11 2015 - 21:04:57 PDT)
    - Re: [AMBER] Problem with stripped combined mdcrd files Daniel Roe (Thu Jun 11 2015 - 21:17:43 PDT)
    - Re: [AMBER] Problem with stripped combined mdcrd files Soong Jiaxin (Fri Jun 12 2015 - 00:20:09 PDT)
[AMBER] MMPBSA sasopt problem Debodyuti Dutta (Thu Jun 11 2015 - 23:40:31 PDT)
- Re: [AMBER] MMPBSA sasopt problem Jason Swails (Fri Jun 12 2015 - 02:32:22 PDT)
[AMBER] Pairwise Interaction Energy between two urea pairs MOHD HOMAIDUR RAHMAN (Thu Jun 11 2015 - 23:45:51 PDT)
- Re: [AMBER] Pairwise Interaction Energy between two urea pairs Jason Swails (Fri Jun 12 2015 - 02:20:57 PDT)
  - Re: [AMBER] Pairwise Interaction Energy between two urea pairs MOHD HOMAIDUR RAHMAN (Fri Jun 12 2015 - 05:15:32 PDT)
    - Re: [AMBER] Pairwise Interaction Energy between two urea pairs Jason Swails (Fri Jun 12 2015 - 05:42:12 PDT)
[AMBER] conserved water in MMPBSA Albert (Fri Jun 12 2015 - 06:03:15 PDT)
- Re: [AMBER] conserved water in MMPBSA Alessandro Contini (Fri Jun 12 2015 - 06:15:56 PDT)
- Re: [AMBER] conserved water in MMPBSA George Tzotzos (Fri Jun 12 2015 - 06:31:38 PDT)
  - Re: [AMBER] conserved water in MMPBSA Albert (Fri Jun 12 2015 - 07:16:56 PDT)
[AMBER] modifying cpptraj Gard Nelson (Fri Jun 12 2015 - 10:16:32 PDT)
- Re: [AMBER] modifying cpptraj Daniel Roe (Fri Jun 12 2015 - 13:19:46 PDT)
  - Re: [AMBER] modifying cpptraj Gard Nelson (Fri Jun 12 2015 - 14:16:03 PDT)
[AMBER] Dimer Rotations Brittany Boykin (Fri Jun 12 2015 - 14:56:03 PDT)
- Re: [AMBER] Dimer Rotations Kenneth Huang (Fri Jun 12 2015 - 15:18:33 PDT)
[AMBER] error encountered on extending production simulation on Amber14 Harmeet Kaur (Sat Jun 13 2015 - 01:30:01 PDT)
- Re: [AMBER] error encountered on extending production simulation on Amber14 Jason Swails (Sat Jun 13 2015 - 03:49:20 PDT)
[AMBER] Issue Lennard jones interaction Loic ETHEVE (Sat Jun 13 2015 - 02:01:33 PDT)
- Re: [AMBER] Issue Lennard jones interaction Jason Swails (Sat Jun 13 2015 - 04:02:20 PDT)
[AMBER] Alternative Membrane System Tutorial Parker de Waal (Sat Jun 13 2015 - 18:08:29 PDT)
[AMBER] Python: AttributeError: 'dict' object has no attribute 'property' Jean-Patrick Francoia (Sun Jun 14 2015 - 10:44:43 PDT)
- Re: [AMBER] Python: AttributeError: 'dict' object has no attribute 'property' Gerald Monard (Sun Jun 14 2015 - 13:40:29 PDT)
  - Re: [AMBER] Python: AttributeError: 'dict' object has no attribute 'property' Jean-Patrick Francoia (Mon Jun 15 2015 - 01:45:23 PDT)
    - Re: [AMBER] Python: AttributeError: 'dict' object has no attribute 'property' Hai Nguyen (Mon Jun 15 2015 - 01:55:59 PDT)
    - Re: [AMBER] Python: AttributeError: 'dict' object has no attribute 'property' Hannes Loeffler (Mon Jun 15 2015 - 01:57:04 PDT)
    - Re: [AMBER] Python: AttributeError: 'dict' object has no attribute 'property' Jean-Patrick Francoia (Mon Jun 15 2015 - 02:02:41 PDT)
    - Re: [AMBER] Python: AttributeError: 'dict' object has no attribute 'property' Gerald Monard (Mon Jun 15 2015 - 02:40:23 PDT)
    - Re: [AMBER] Python: AttributeError: 'dict' object has no attribute 'property' Jason Swails (Mon Jun 15 2015 - 06:18:31 PDT)
[AMBER] Population analysis Kshatresh Dutta Dubey (Mon Jun 15 2015 - 00:54:25 PDT)
- Re: [AMBER] Population analysis Jason Swails (Mon Jun 15 2015 - 06:25:08 PDT)
  - Re: [AMBER] Population analysis Parker de Waal (Mon Jun 15 2015 - 06:39:44 PDT)
    - Re: [AMBER] Population analysis Kshatresh Dutta Dubey (Mon Jun 15 2015 - 07:51:11 PDT)
    - Re: [AMBER] Population analysis Daniel Roe (Mon Jun 15 2015 - 08:21:29 PDT)
    - Re: [AMBER] Population analysis Kshatresh Dutta Dubey (Mon Jun 15 2015 - 08:33:46 PDT)
[AMBER] MMPBSA: Generalised Born Warning George Tzotzos (Mon Jun 15 2015 - 06:13:47 PDT)
- Re: [AMBER] MMPBSA: Generalised Born Warning Jason Swails (Mon Jun 15 2015 - 06:22:25 PDT)
[AMBER] QM-MM Equilibration of the System Brittany Boykin (Mon Jun 15 2015 - 09:11:25 PDT)
- Re: [AMBER] QM-MM Equilibration of the System Gustavo Seabra (Mon Jun 15 2015 - 09:26:31 PDT)
[AMBER] A problem in using tLeap Morteza Chehel Amirani (Mon Jun 15 2015 - 11:12:50 PDT)
- Re: [AMBER] A problem in using tLeap David A Case (Mon Jun 15 2015 - 16:19:38 PDT)
[AMBER] tcorr and order parameters Travis Hughes (Mon Jun 15 2015 - 16:08:30 PDT)
- Re: [AMBER] tcorr and order parameters Daniel Roe (Mon Jun 15 2015 - 20:27:00 PDT)
  - Re: [AMBER] tcorr and order parameters Travis Hughes (Tue Jun 16 2015 - 12:49:48 PDT)
Re: [AMBER] AMBER Digest, Vol 1220, Issue 1 Huang (Mon Jun 15 2015 - 21:45:01 PDT)
- Re: [AMBER] AMBER Digest, Vol 1220, Issue 1 Jason Swails (Mon Jun 15 2015 - 22:51:44 PDT)
[AMBER] what's the default radius? Albert (Mon Jun 15 2015 - 23:06:31 PDT)
- Re: [AMBER] what's the default radius? Carlos Simmerling (Tue Jun 16 2015 - 02:23:30 PDT)
  - Re: [AMBER] what's the default radius? Albert (Tue Jun 16 2015 - 02:26:01 PDT)
[AMBER] problem in .pdb after md simulation Vishal Nemaysh (Mon Jun 15 2015 - 23:52:58 PDT)
- Re: [AMBER] problem in .pdb after md simulation Soong Jiaxin (Mon Jun 15 2015 - 23:55:01 PDT)
  - Re: [AMBER] problem in .pdb after md simulation Vishal Nemaysh (Tue Jun 16 2015 - 00:34:28 PDT)
    - Re: [AMBER] problem in .pdb after md simulation Vishal Nemaysh (Tue Jun 16 2015 - 00:34:54 PDT)
    - Re: [AMBER] problem in .pdb after md simulation Soong Jiaxin (Tue Jun 16 2015 - 00:52:22 PDT)
    - Re: [AMBER] problem in .pdb after md simulation Soumendranath Bhakat (Tue Jun 16 2015 - 00:54:25 PDT)
[AMBER] Problem generating peptide Harshala Haldankar (Tue Jun 16 2015 - 04:38:50 PDT)
[AMBER] Freezing atoms in space during a simulation Jonathan Gough (Tue Jun 16 2015 - 11:06:30 PDT)
- Re: [AMBER] Freezing atoms in space during a simulation David A Case (Tue Jun 16 2015 - 13:19:00 PDT)
  - Re: [AMBER] Freezing atoms in space during a simulation Gustavo Seabra (Tue Jun 16 2015 - 13:38:19 PDT)
    - Re: [AMBER] Freezing atoms in space during a simulation Jonathan Gough (Wed Jun 17 2015 - 06:22:54 PDT)
[AMBER] GPI-anchor protein cleavage Aditya Padhi (Tue Jun 16 2015 - 11:49:04 PDT)
- Re: [AMBER] GPI-anchor protein cleavage Jason Swails (Tue Jun 16 2015 - 17:06:20 PDT)
  - Re: [AMBER] GPI-anchor protein cleavage Aditya Padhi (Tue Jun 16 2015 - 17:36:11 PDT)
    - Re: [AMBER] GPI-anchor protein cleavage Jason Swails (Tue Jun 16 2015 - 19:11:34 PDT)
    - Re: [AMBER] GPI-anchor protein cleavage Aditya Padhi (Wed Jun 17 2015 - 07:18:58 PDT)
[AMBER] [cpptraj] Changing frames in a trajectory file Juan Eiros Zamora (Tue Jun 16 2015 - 12:19:08 PDT)
- Re: [AMBER] [cpptraj] Changing frames in a trajectory file Hai Nguyen (Tue Jun 16 2015 - 12:27:44 PDT)
  - Re: [AMBER] [cpptraj] Changing frames in a trajectory file Juan Eiros Zamora (Tue Jun 16 2015 - 12:44:19 PDT)
[AMBER] NMR restraints with pmemd.cuda problem Miroslav Krepl (Tue Jun 16 2015 - 14:25:41 PDT)
- Re: [AMBER] NMR restraints with pmemd.cuda problem David A Case (Wed Jun 17 2015 - 07:23:42 PDT)
  - Re: [AMBER] NMR restraints with pmemd.cuda problem Ross Walker (Wed Jun 17 2015 - 08:00:52 PDT)
    - Re: [AMBER] NMR restraints with pmemd.cuda problem Miroslav Krepl (Wed Jun 17 2015 - 11:50:13 PDT)
    - Re: [AMBER] NMR restraints with pmemd.cuda problem Needham, Perri (Thu Jul 16 2015 - 12:34:18 PDT)
[AMBER] The respective references suggested by the developers of Amber and HADDOCK Zhichao Lou (Tue Jun 16 2015 - 20:01:30 PDT)
- Re: [AMBER] The respective references suggested by the developers of Amber and HADDOCK Hai Nguyen (Tue Jun 16 2015 - 20:15:46 PDT)
  - Re: [AMBER] The respective references suggested by the developers of Amber and HADDOCK Zhichao Lou (Tue Jun 16 2015 - 20:38:19 PDT)
[AMBER] error in ante-MMPBSA.py Chris (Tue Jun 16 2015 - 21:41:25 PDT)
- Re: [AMBER] error in ante-MMPBSA.py Jason Swails (Tue Jun 16 2015 - 22:21:46 PDT)
[AMBER] help in radial command Robin Jain (Wed Jun 17 2015 - 01:32:19 PDT)
- Re: [AMBER] help in radial command Daniel Roe (Wed Jun 17 2015 - 07:34:15 PDT)
[AMBER] binding energy for the frames Maryam Hamzehee (Wed Jun 17 2015 - 04:14:53 PDT)
[AMBER] Error: unspecified launch failure launching kernel kNLSkinTest zayan alhalabi (Wed Jun 17 2015 - 06:18:26 PDT)
- Re: [AMBER] Error: unspecified launch failure launching kernel kNLSkinTest David A Case (Wed Jun 17 2015 - 07:27:33 PDT)
[AMBER] subroutine qm_write_pdb Hector A. Baldoni (Wed Jun 17 2015 - 06:30:25 PDT)
[AMBER] cpptraj : gzip or bzip2 netcdf trajectory files not recognized Marion, Antoine (Wed Jun 17 2015 - 06:37:47 PDT)
- Re: [AMBER] cpptraj : gzip or bzip2 netcdf trajectory files not recognized Nhai (Wed Jun 17 2015 - 07:04:50 PDT)
- Re: [AMBER] cpptraj : gzip or bzip2 netcdf trajectory files not recognized Daniel Roe (Wed Jun 17 2015 - 07:24:35 PDT)
  - Re: [AMBER] cpptraj : gzip or bzip2 netcdf trajectory files not recognized Marion, Antoine (Wed Jun 17 2015 - 09:37:41 PDT)
  - Re: [AMBER] cpptraj : gzip or bzip2 netcdf trajectory files not recognized Gerald Monard (Wed Jun 17 2015 - 11:28:10 PDT)
    - Re: [AMBER] cpptraj : gzip or bzip2 netcdf trajectory files not recognized David A Case (Wed Jun 17 2015 - 12:27:04 PDT)
    - Re: [AMBER] cpptraj : gzip or bzip2 netcdf trajectory files not recognized Marion, Antoine (Wed Jun 17 2015 - 13:03:52 PDT)
    - Re: [AMBER] cpptraj : gzip or bzip2 netcdf trajectory files not recognized Gerald Monard (Wed Jun 17 2015 - 13:20:37 PDT)
    - Re: [AMBER] cpptraj : gzip or bzip2 netcdf trajectory files not recognized Hai Nguyen (Wed Jun 17 2015 - 13:23:26 PDT)
    - Re: [AMBER] cpptraj : gzip or bzip2 netcdf trajectory files not recognized Jason Swails (Wed Jun 17 2015 - 21:18:49 PDT)
[AMBER] 2nd mail: subroutine qm_write_pdb Hector A. Baldoni (Wed Jun 17 2015 - 06:47:41 PDT)
[AMBER] problem zayan alhalabi (Wed Jun 17 2015 - 06:52:01 PDT)
- Re: [AMBER] problem Daniel Roe (Wed Jun 17 2015 - 07:27:10 PDT)
- Re: [AMBER] problem zayan alhalabi (Wed Jun 17 2015 - 07:47:30 PDT)
- Re: [AMBER] problem Bill Ross (Wed Jun 17 2015 - 09:01:25 PDT)
[AMBER] savepdb command not working in xleap muhammad tahir ayub (Wed Jun 17 2015 - 08:20:02 PDT)
- Re: [AMBER] savepdb command not working in xleap David A Case (Wed Jun 17 2015 - 09:27:21 PDT)
[AMBER] Spreading water molecules over the simulation time Morteza Chehel Amirani (Wed Jun 17 2015 - 12:40:34 PDT)
- Re: [AMBER] Spreading water molecules over the simulation time windy (Wed Jun 17 2015 - 18:30:28 PDT)
- Re: [AMBER] Spreading water molecules over the simulation time Jason Swails (Wed Jun 17 2015 - 21:19:57 PDT)
- Re: [AMBER] Spreading water molecules over the simulation time Daniel Roe (Thu Jun 18 2015 - 08:18:17 PDT)
[AMBER] Free Energy Landscape for cMD bharat lakhani (Wed Jun 17 2015 - 12:53:05 PDT)
[AMBER] combine multiple trajectory Yin, Guowei (Wed Jun 17 2015 - 13:33:18 PDT)
- Re: [AMBER] combine multiple trajectory Hai Nguyen (Wed Jun 17 2015 - 13:45:28 PDT)
- Re: [AMBER] combine multiple trajectory Daniel Roe (Thu Jun 18 2015 - 08:25:54 PDT)
[AMBER] Free Energy Landscape for cMD Help bharat lakhani (Wed Jun 17 2015 - 19:17:04 PDT)
- Re: [AMBER] Free Energy Landscape for cMD Help Jason Swails (Wed Jun 17 2015 - 21:26:18 PDT)
- Re: [AMBER] Free Energy Landscape for cMD Help Daniel Roe (Thu Jun 18 2015 - 08:16:07 PDT)
[AMBER] Get energy information loic etheve (Thu Jun 18 2015 - 00:28:09 PDT)
- Re: [AMBER] Get energy information Jason Swails (Thu Jun 18 2015 - 06:42:01 PDT)
[AMBER] To Add or Not To Add - Salt Conc in Explicit Solvent Yip Yew Mun (Thu Jun 18 2015 - 00:32:41 PDT)
- Re: [AMBER] To Add or Not To Add - Salt Conc in Explicit Solvent Marc van der Kamp (Thu Jun 18 2015 - 01:10:20 PDT)
[AMBER] Connect atoms in a pdb created with nab Jean-Patrick Francoia (Thu Jun 18 2015 - 01:31:52 PDT)
- Re: [AMBER] Connect atoms in a pdb created with nab Jason Swails (Thu Jun 18 2015 - 06:47:29 PDT)
  - Re: [AMBER] Connect atoms in a pdb created with nab Jean-Patrick Francoia (Thu Jun 18 2015 - 06:59:15 PDT)
    - Re: [AMBER] Connect atoms in a pdb created with nab Jason Swails (Thu Jun 18 2015 - 07:05:16 PDT)
    - Re: [AMBER] Connect atoms in a pdb created with nab Jean-Patrick Francoia (Thu Jun 18 2015 - 07:09:19 PDT)
[AMBER] energy difference between GBSA and PBSA Chris (Thu Jun 18 2015 - 02:32:58 PDT)
- Re: [AMBER] energy difference between GBSA and PBSA Carlos Simmerling (Thu Jun 18 2015 - 05:05:11 PDT)
  - Re: [AMBER] energy difference between GBSA and PBSA Chris (Thu Jun 18 2015 - 05:30:15 PDT)
    - Re: [AMBER] energy difference between GBSA and PBSA Carlos Simmerling (Thu Jun 18 2015 - 05:36:37 PDT)
[AMBER] problems with relative TI calculations hannes.loeffler.stfc.ac.uk (Thu Jun 18 2015 - 02:35:42 PDT)
- Re: [AMBER] problems with relative TI calculations Brian Radak (Thu Jun 18 2015 - 09:01:48 PDT)
  - Re: [AMBER] problems with relative TI calculations hannes.loeffler.stfc.ac.uk (Thu Jun 18 2015 - 09:18:34 PDT)
[AMBER] Energy contribution of phosphorylated residues Parker de Waal (Thu Jun 18 2015 - 06:57:14 PDT)
- Re: [AMBER] Energy contribution of phosphorylated residues Kenneth Huang (Thu Jun 18 2015 - 09:06:25 PDT)
  - Re: [AMBER] Energy contribution of phosphorylated residues Parker de Waal (Thu Jun 18 2015 - 13:50:54 PDT)
    - [AMBER] Energy contribution of phosphorylated residues Kenneth Huang (Thu Jun 18 2015 - 14:28:40 PDT)
    - Re: [AMBER] Energy contribution of phosphorylated residues Jason Swails (Fri Jun 19 2015 - 09:26:52 PDT)
[AMBER] Recover .lib from .prmtop and .inpcrd Yin, Xing (Thu Jun 18 2015 - 08:35:14 PDT)
- Re: [AMBER] Recover .lib from .prmtop and .inpcrd Jason Swails (Thu Jun 18 2015 - 09:18:59 PDT)
  - Re: [AMBER] Recover .lib from .prmtop and .inpcrd Yin, Xing (Thu Jun 18 2015 - 14:15:29 PDT)
[AMBER] QM-MM Equilibration Step Brittany Boykin (Thu Jun 18 2015 - 10:06:34 PDT)
- Re: [AMBER] QM-MM Equilibration Step Gustavo Seabra (Thu Jun 18 2015 - 11:06:23 PDT)
[AMBER] ERROR while running XLEAP Pierre Bertin (Thu Jun 18 2015 - 11:13:29 PDT)
- Re: [AMBER] ERROR while running XLEAP David A Case (Fri Jun 19 2015 - 06:59:54 PDT)
  - Re: [AMBER] ERROR while running XLEAP Pierre Bertin (Fri Jun 19 2015 - 07:49:47 PDT)
[AMBER] amber 15 compiled with multiple GPUs nam kim (Thu Jun 18 2015 - 22:43:01 PDT)
- Re: [AMBER] amber 15 compiled with multiple GPUs Nhai (Fri Jun 19 2015 - 00:10:10 PDT)
  - Re: [AMBER] amber 15 compiled with multiple GPUs nam kim (Fri Jun 19 2015 - 07:47:04 PDT)
    - Re: [AMBER] amber 15 compiled with multiple GPUs Kenneth Huang (Fri Jun 19 2015 - 07:55:34 PDT)
    - Re: [AMBER] amber 15 compiled with multiple GPUs nam kim (Fri Jun 19 2015 - 08:47:12 PDT)
    - Re: [AMBER] amber 15 compiled with multiple GPUs Ross Walker (Fri Jun 19 2015 - 09:06:55 PDT)
    - Re: [AMBER] amber 15 compiled with multiple GPUs nam kim (Thu Jun 25 2015 - 14:17:27 PDT)
[AMBER] solid surface interacting with organic Azade Yazdan Yar (Fri Jun 19 2015 - 03:12:55 PDT)
- Re: [AMBER] solid surface interacting with organic Jason Swails (Fri Jun 19 2015 - 09:59:38 PDT)
[AMBER] About OH conformation in protonated Asp/Glu (ASH/GLH) Marc van der Kamp (Fri Jun 19 2015 - 04:29:02 PDT)
- Re: [AMBER] About OH conformation in protonated Asp/Glu (ASH/GLH) Jason Swails (Fri Jun 19 2015 - 09:09:36 PDT)
[AMBER] RESP charge derivation Neelanjana Sengupta (Fri Jun 19 2015 - 10:56:08 PDT)
- Re: [AMBER] RESP charge derivation Jason Swails (Fri Jun 19 2015 - 12:31:37 PDT)
  - Re: [AMBER] RESP charge derivation Neelanjana Sengupta (Fri Jun 19 2015 - 14:17:43 PDT)
    - Re: [AMBER] RESP charge derivation Jason Swails (Fri Jun 19 2015 - 19:47:18 PDT)
    - Re: [AMBER] RESP charge derivation Suman Chakrabarty (Sun Jun 21 2015 - 06:25:37 PDT)
[AMBER] accuracy of FEW free energy calculation Albert (Fri Jun 19 2015 - 13:44:15 PDT)
- Re: [AMBER] accuracy of FEW free energy calculation Ross Walker (Fri Jun 19 2015 - 14:31:32 PDT)
  - Re: [AMBER] accuracy of FEW free energy calculation filip fratev (Fri Jun 19 2015 - 15:25:54 PDT)
  - Re: [AMBER] accuracy of FEW free energy calculation Albert (Fri Jun 19 2015 - 22:08:42 PDT)
    - Re: [AMBER] accuracy of FEW free energy calculation Jason Swails (Sat Jun 20 2015 - 09:29:10 PDT)
    - Re: [AMBER] accuracy of FEW free energy calculation Jiri Sponer (Sat Jun 20 2015 - 10:38:09 PDT)
    - Re: [AMBER] accuracy of FEW free energy calculation Ross Walker (Sat Jun 20 2015 - 15:54:36 PDT)
    - Re: [AMBER] accuracy of FEW free energy calculation Jiri Sponer (Sun Jun 21 2015 - 02:16:12 PDT)
    - Re: [AMBER] accuracy of FEW free energy calculation Jason Swails (Sun Jun 21 2015 - 09:30:01 PDT)
    - Re: [AMBER] accuracy of FEW free energy calculation Robert Molt (Sun Jun 21 2015 - 09:43:10 PDT)
    - Re: [AMBER] accuracy of FEW free energy calculation Albert (Sat Jun 20 2015 - 12:07:42 PDT)
    - Re: [AMBER] accuracy of FEW free energy calculation Jason Swails (Sat Jun 20 2015 - 18:56:36 PDT)
    - Re: [AMBER] accuracy of FEW free energy calculation Albert (Sun Jun 21 2015 - 00:10:37 PDT)
    - Re: [AMBER] accuracy of FEW free energy calculation Jason Swails (Sun Jun 21 2015 - 10:00:55 PDT)
[AMBER] Regarding hydrogen bond time correlation function in cpptraj MOHD HOMAIDUR RAHMAN (Sat Jun 20 2015 - 03:27:34 PDT)
- Re: [AMBER] Regarding hydrogen bond time correlation function in cpptraj Daniel Roe (Sat Jun 20 2015 - 09:53:08 PDT)
[AMBER] problem zayan alhalabi (Sat Jun 20 2015 - 06:25:59 PDT)
[AMBER] Quasi harmonic bad eigenvalue error D.J. Pattinson (Sat Jun 20 2015 - 07:28:45 PDT)
- Re: [AMBER] Quasi harmonic bad eigenvalue error Jason Swails (Sat Jun 20 2015 - 09:33:36 PDT)
[AMBER] standard and non-standard residues Ramin Ekhteiari (Sat Jun 20 2015 - 08:09:43 PDT)
- Re: [AMBER] standard and non-standard residues Jason Swails (Sat Jun 20 2015 - 09:39:44 PDT)
- Re: [AMBER] standard and non-standard residues Ramin Ekhteiari (Sun Jun 21 2015 - 01:37:55 PDT)
[AMBER] resp: errors in reading the electrostatic potential Neelanjana Sengupta (Sun Jun 21 2015 - 02:51:03 PDT)
- Re: [AMBER] resp: errors in reading the electrostatic potential David A Case (Sun Jun 21 2015 - 08:40:54 PDT)
[AMBER] Load "library" of custom residues Jean-Patrick Francoia (Sun Jun 21 2015 - 04:57:55 PDT)
- Re: [AMBER] Load "library" of custom residues David A Case (Sun Jun 21 2015 - 08:26:37 PDT)
  - Re: [AMBER] Load "library" of custom residues Jean-Patrick Francoia (Sun Jun 21 2015 - 08:43:50 PDT)
    - Re: [AMBER] Load "library" of custom residues David A Case (Sun Jun 21 2015 - 10:14:20 PDT)
[AMBER] resp: errors in reading the electrostatic potential Neelanjana Sengupta (Sun Jun 21 2015 - 05:29:47 PDT)
[AMBER] using AMBER 14sb force-field in CHARMM program Iceriver Forever (Sun Jun 21 2015 - 09:21:50 PDT)
[AMBER] aMD and scaled MD simulation-NVT production runs Neha Gandhi (Sun Jun 21 2015 - 23:24:25 PDT)
- Re: [AMBER] aMD and scaled MD simulation-NVT production runs Vlad Cojocaru (Mon Jun 22 2015 - 00:43:57 PDT)
[AMBER] how to export pdb in 'cluster' with 'autoimage' windy (Mon Jun 22 2015 - 02:11:32 PDT)
- Re: [AMBER] how to export pdb in 'cluster' with 'autoimage' Daniel Roe (Mon Jun 22 2015 - 09:09:18 PDT)
[AMBER] Recover the water model and periodic box from built parm files Yin, Xing (Mon Jun 22 2015 - 07:01:10 PDT)
- Re: [AMBER] Recover the water model and periodic box from built parm files Jason Swails (Mon Jun 22 2015 - 07:12:59 PDT)
  - Re: [AMBER] Recover the water model and periodic box from built parm files Brian Radak (Mon Jun 22 2015 - 08:44:06 PDT)
    - Re: [AMBER] Recover the water model and periodic box from built parm files David A Case (Mon Jun 22 2015 - 10:17:26 PDT)
    - Re: [AMBER] Recover the water model and periodic box from built parm files Brian Radak (Mon Jun 22 2015 - 13:34:03 PDT)
    - Re: [AMBER] Recover the water model and periodic box from built parm files Jason Swails (Mon Jun 22 2015 - 13:52:46 PDT)
    - Re: [AMBER] Recover the water model and periodic box from built parm files Yin, Xing (Tue Jun 23 2015 - 07:04:17 PDT)
[AMBER] united atom force field anu chandra (Mon Jun 22 2015 - 07:26:54 PDT)
[AMBER] Ligand entry and exit path Debodyuti Dutta (Mon Jun 22 2015 - 08:26:41 PDT)
- Re: [AMBER] Ligand entry and exit path Vlad Cojocaru (Mon Jun 22 2015 - 08:55:34 PDT)
[AMBER] Use of OPLS-AA/M force field in AMBER via CHAMBER Karl Debiec (Mon Jun 22 2015 - 08:54:31 PDT)
- Re: [AMBER] Use of OPLS-AA/M force field in AMBER via CHAMBER Brian Radak (Mon Jun 22 2015 - 13:30:52 PDT)
[AMBER] Is there a way to do simultaneous Cartesian position and distance restraints in amber? Arthur Roberts (Mon Jun 22 2015 - 09:53:42 PDT)
- Re: [AMBER] Is there a way to do simultaneous Cartesian position and distance restraints in amber? David A Case (Mon Jun 22 2015 - 10:29:55 PDT)
[AMBER] Required time for a typical MD run Morteza Chehel Amirani (Mon Jun 22 2015 - 14:10:39 PDT)
- Re: [AMBER] Required time for a typical MD run Kenneth Huang (Mon Jun 22 2015 - 14:23:01 PDT)
- Re: [AMBER] Required time for a typical MD run Daniel Roe (Mon Jun 22 2015 - 14:32:31 PDT)
- Re: [AMBER] Required time for a typical MD run Jason Swails (Mon Jun 22 2015 - 17:22:55 PDT)
- Re: [AMBER] Required time for a typical MD run David A Case (Mon Jun 22 2015 - 17:53:44 PDT)
  - [AMBER] Question About RESP/AmberTools14 ivan.gladich.marge.uochb.cas.cz (Mon Jun 22 2015 - 22:49:54 PDT)
    - Re: [AMBER] Question About RESP/AmberTools14 David A Case (Tue Jun 23 2015 - 05:16:39 PDT)
    - Re: [AMBER] Question About RESP/AmberTools14 ivan.gladich.marge.uochb.cas.cz (Tue Jun 23 2015 - 23:12:39 PDT)
    - Re: [AMBER] Question About RESP/AmberTools14 ivan.gladich.marge.uochb.cas.cz (Wed Jun 24 2015 - 03:05:08 PDT)
[AMBER] MMGBSA on Protein-DNA/RNA complex Muthukumaran R (Tue Jun 23 2015 - 03:32:15 PDT)
- Re: [AMBER] MMGBSA on Protein-DNA/RNA complex Vlad Cojocaru (Tue Jun 23 2015 - 04:32:42 PDT)
  - Re: [AMBER] MMGBSA on Protein-DNA/RNA complex Carlos Simmerling (Tue Jun 23 2015 - 04:49:57 PDT)
    - Re: [AMBER] MMGBSA on Protein-DNA/RNA complex Muthukumaran R (Tue Jun 23 2015 - 09:04:31 PDT)
    - Re: [AMBER] MMGBSA on Protein-DNA/RNA complex Vlad Cojocaru (Tue Jun 23 2015 - 09:16:12 PDT)
    - Re: [AMBER] MMGBSA on Protein-DNA/RNA complex Muthukumaran R (Wed Jun 24 2015 - 01:02:59 PDT)
    - Re: [AMBER] MMGBSA on Protein-DNA/RNA complex Jason Swails (Wed Jun 24 2015 - 05:27:32 PDT)
    - Re: [AMBER] MMGBSA on Protein-DNA/RNA complex Vlad Cojocaru (Wed Jun 24 2015 - 06:21:40 PDT)
    - Re: [AMBER] MMGBSA on Protein-DNA/RNA complex Vlad Cojocaru (Wed Jun 24 2015 - 06:47:39 PDT)
    - Re: [AMBER] MMGBSA on Protein-DNA/RNA complex Jason Swails (Wed Jun 24 2015 - 07:46:02 PDT)
    - Re: [AMBER] MMGBSA on Protein-DNA/RNA complex Muthukumaran R (Wed Jun 24 2015 - 09:58:45 PDT)
[AMBER] parmwrite in cpptraj: AmberTools13 vs. 15 Gerald Monard (Tue Jun 23 2015 - 05:15:21 PDT)
- Re: [AMBER] parmwrite in cpptraj: AmberTools13 vs. 15 Daniel Roe (Tue Jun 23 2015 - 07:42:43 PDT)
  - Re: [AMBER] parmwrite in cpptraj: AmberTools13 vs. 15 Gerald Monard (Tue Jun 23 2015 - 07:59:49 PDT)
    - Re: [AMBER] parmwrite in cpptraj: AmberTools13 vs. 15 Daniel Roe (Tue Jun 23 2015 - 08:47:39 PDT)
    - Re: [AMBER] parmwrite in cpptraj: AmberTools13 vs. 15 Gerald Monard (Tue Jun 23 2015 - 09:00:00 PDT)
[AMBER] MMPBSA on DNA-Protein-Ligand complex Norbert GARNIER (Tue Jun 23 2015 - 05:26:07 PDT)
- Re: [AMBER] MMPBSA on DNA-Protein-Ligand complex Jason Swails (Tue Jun 23 2015 - 05:37:10 PDT)
  - Re: [AMBER] MMPBSA on DNA-Protein-Ligand complex Norbert GARNIER (Tue Jun 23 2015 - 08:00:47 PDT)
    - Re: [AMBER] MMPBSA on DNA-Protein-Ligand complex Ray Luo, Ph.D. (Tue Jun 23 2015 - 10:35:57 PDT)
  - Re: [AMBER] MMPBSA on DNA-Protein-Ligand complex Norbert GARNIER (Wed Jun 24 2015 - 08:32:44 PDT)
    - Re: [AMBER] MMPBSA on DNA-Protein-Ligand complex Ray Luo, Ph.D. (Wed Jun 24 2015 - 10:06:34 PDT)
    - Re: [AMBER] MMPBSA on DNA-Protein-Ligand complex Norbert GARNIER (Mon Jun 29 2015 - 04:31:33 PDT)
    - Re: [AMBER] MMPBSA on DNA-Protein-Ligand complex Vlad Cojocaru (Mon Jun 29 2015 - 04:39:35 PDT)
- Re: [AMBER] MMPBSA on DNA-Protein-Ligand complex Vlad Cojocaru (Tue Jun 23 2015 - 05:53:10 PDT)
[AMBER] MMPBSA_API: AmberTools13 vs. 15 Gerald Monard (Tue Jun 23 2015 - 06:49:27 PDT)
- Re: [AMBER] MMPBSA_API: AmberTools13 vs. 15 Jason Swails (Tue Jun 23 2015 - 07:32:56 PDT)
  - Re: [AMBER] MMPBSA_API: AmberTools13 vs. 15 Gerald Monard (Tue Jun 23 2015 - 07:46:42 PDT)
    - Re: [AMBER] MMPBSA_API: AmberTools13 vs. 15 Jason Swails (Tue Jun 23 2015 - 07:52:07 PDT)
[AMBER] Error during action on loaded multiple trajectory in cpptraj 15 MOHD HOMAIDUR RAHMAN (Wed Jun 24 2015 - 05:52:14 PDT)
- Re: [AMBER] Error during action on loaded multiple trajectory in cpptraj 15 Daniel Roe (Wed Jun 24 2015 - 12:32:43 PDT)
  - Re: [AMBER] Error during action on loaded multiple trajectory in cpptraj 15 MOHD HOMAIDUR RAHMAN (Wed Jun 24 2015 - 14:09:01 PDT)
    - Re: [AMBER] Error during action on loaded multiple trajectory in cpptraj 15 MOHD HOMAIDUR RAHMAN (Mon Jun 29 2015 - 13:46:49 PDT)
    - Re: [AMBER] Error during action on loaded multiple trajectory in cpptraj 15 Daniel Roe (Mon Jun 29 2015 - 14:24:32 PDT)
    - Re: [AMBER] Error during action on loaded multiple trajectory in cpptraj 15 MOHD HOMAIDUR RAHMAN (Mon Jun 29 2015 - 23:19:56 PDT)
[AMBER] Hydrogen bond bridges DEBOSTUTI GHOSHDASTIDAR (Wed Jun 24 2015 - 06:52:23 PDT)
- Re: [AMBER] Hydrogen bond bridges Daniel Roe (Wed Jun 24 2015 - 12:50:48 PDT)
  - Re: [AMBER] Hydrogen bond bridges DEBOSTUTI GHOSHDASTIDAR (Wed Jun 24 2015 - 23:35:01 PDT)
    - Re: [AMBER] Hydrogen bond bridges DEBOSTUTI GHOSHDASTIDAR (Wed Jun 24 2015 - 23:38:43 PDT)
    - Re: [AMBER] Hydrogen bond bridges Daniel Roe (Thu Jun 25 2015 - 07:48:44 PDT)
    - Re: [AMBER] Hydrogen bond bridges DEBOSTUTI GHOSHDASTIDAR (Thu Jun 25 2015 - 21:48:05 PDT)
    - Re: [AMBER] Hydrogen bond bridges Daniel Roe (Fri Jun 26 2015 - 10:25:33 PDT)
    - Re: [AMBER] Hydrogen bond bridges DEBOSTUTI GHOSHDASTIDAR (Fri Jun 26 2015 - 21:45:16 PDT)
    - Re: [AMBER] Hydrogen bond bridges Daniel Roe (Sat Jun 27 2015 - 06:36:10 PDT)
    - Re: [AMBER] Hydrogen bond bridges DEBOSTUTI GHOSHDASTIDAR (Mon Jun 29 2015 - 10:16:48 PDT)
[AMBER] unsaturated sugars Lara rajam (Wed Jun 24 2015 - 07:06:07 PDT)
- Re: [AMBER] unsaturated sugars Lachele Foley (Wed Jun 24 2015 - 10:31:25 PDT)
  - Re: [AMBER] unsaturated sugars Lara rajam (Fri Jun 26 2015 - 09:08:47 PDT)
[AMBER] generating topology without loading Frcmod file Arun Srikanth (Wed Jun 24 2015 - 10:07:08 PDT)
- Re: [AMBER] generating topology without loading Frcmod file Jason Swails (Wed Jun 24 2015 - 10:19:01 PDT)
  - Re: [AMBER] generating topology without loading Frcmod file Arun Srikanth (Wed Jun 24 2015 - 13:45:40 PDT)
    - Re: [AMBER] generating topology without loading Frcmod file Jason Swails (Wed Jun 24 2015 - 14:26:16 PDT)
    - Re: [AMBER] generating topology without loading Frcmod file Arun Srikanth (Wed Jun 24 2015 - 15:13:00 PDT)
    - Re: [AMBER] generating topology without loading Frcmod file Arun Srikanth (Wed Jun 24 2015 - 16:01:50 PDT)
[AMBER] cpptraj Help rmsd between two homologous proteins and their Trajectory bharat lakhani (Wed Jun 24 2015 - 10:56:18 PDT)
- Re: [AMBER] cpptraj Help rmsd between two homologous proteins and their Trajectory Daniel Roe (Wed Jun 24 2015 - 12:56:23 PDT)
  - Re: [AMBER] cpptraj Help rmsd between two homologous proteins and their Trajectory bharat lakhani (Wed Jun 24 2015 - 13:35:03 PDT)
    - Re: [AMBER] cpptraj Help rmsd between two homologous proteins and their Trajectory Daniel Roe (Wed Jun 24 2015 - 14:01:19 PDT)
    - Re: [AMBER] cpptraj Help rmsd between two homologous proteins and their Trajectory bharat lakhani (Wed Jun 24 2015 - 18:38:04 PDT)
    - Re: [AMBER] cpptraj Help rmsd between two homologous proteins and their Trajectory Daniel Roe (Wed Jun 24 2015 - 20:02:32 PDT)
    - Re: [AMBER] cpptraj Help rmsd between two homologous proteins and their Trajectory bharat lakhani (Wed Jun 24 2015 - 20:52:03 PDT)
    - Re: [AMBER] cpptraj Help rmsd between two homologous proteins and their Trajectory Daniel Roe (Thu Jun 25 2015 - 07:28:55 PDT)
    - Re: [AMBER] cpptraj Help rmsd between two homologous proteins and their Trajectory bharat lakhani (Wed Jul 29 2015 - 19:47:32 PDT)
    - Re: [AMBER] cpptraj Help rmsd between two homologous proteins and their Trajectory Daniel Roe (Thu Jul 30 2015 - 08:19:43 PDT)
    - Re: [AMBER] cpptraj Help rmsd between two homologous proteins and their Trajectory bharat lakhani (Wed Jun 24 2015 - 19:58:20 PDT)
[AMBER] hbond lifetime cpptraj Lara rajam (Wed Jun 24 2015 - 11:48:08 PDT)
- Re: [AMBER] hbond lifetime cpptraj Daniel Roe (Wed Jun 24 2015 - 13:17:36 PDT)
- Re: [AMBER] hbond lifetime cpptraj Lara rajam (Wed Jun 24 2015 - 13:32:44 PDT)
  - Re: [AMBER] hbond lifetime cpptraj Daniel Roe (Wed Jun 24 2015 - 14:00:06 PDT)
[AMBER] hbond zahra khatti (Wed Jun 24 2015 - 14:37:12 PDT)
- Re: [AMBER] hbond Daniel Roe (Wed Jun 24 2015 - 14:50:47 PDT)
[AMBER] relaxation in t/xleap newamber list (Wed Jun 24 2015 - 15:33:51 PDT)
- Re: [AMBER] relaxation in t/xleap David A Case (Wed Jun 24 2015 - 18:07:53 PDT)
  - Re: [AMBER] relaxation in t/xleap newamber list (Thu Jun 25 2015 - 03:35:08 PDT)
    - Re: [AMBER] relaxation in t/xleap David A Case (Thu Jun 25 2015 - 05:14:31 PDT)
    - Re: [AMBER] relaxation in t/xleap Bill Ross (Sat Jun 27 2015 - 16:15:14 PDT)
    - Re: [AMBER] relaxation in t/xleap newamber list (Mon Jun 29 2015 - 03:46:04 PDT)
[AMBER] Defining the box dimensions while making the top and crd files Iqbal, Muhammad Sajid (Wed Jun 24 2015 - 17:02:03 PDT)
- Re: [AMBER] Defining the box dimensions while making the top and crd files Jason Swails (Thu Jun 25 2015 - 06:39:03 PDT)
  - Re: [AMBER] Defining the box dimensions while making the top and crd files David A Case (Thu Jun 25 2015 - 07:14:17 PDT)
[AMBER] A possible bug in t leap when creating topology file ? Arun Srikanth (Wed Jun 24 2015 - 20:59:57 PDT)
- Re: [AMBER] A possible bug in t leap when creating topology file ? David A Case (Thu Jun 25 2015 - 05:22:39 PDT)
  - Re: [AMBER] A possible bug in t leap when creating topology file ? Arun Srikanth (Thu Jun 25 2015 - 08:21:30 PDT)
    - Re: [AMBER] A possible bug in t leap when creating topology file ? Arun Srikanth (Thu Jun 25 2015 - 11:22:11 PDT)
    - Re: [AMBER] A possible bug in t leap when creating topology file ? Arun Srikanth (Thu Jun 25 2015 - 11:41:28 PDT)
[AMBER] Problem in Radial command Robin Jain (Wed Jun 24 2015 - 22:43:01 PDT)
- Re: [AMBER] Problem in Radial command Daniel Roe (Thu Jun 25 2015 - 07:46:12 PDT)
[AMBER] error in MD simulation erik.laurini.di3.units.it (Thu Jun 25 2015 - 07:17:56 PDT)
- Re: [AMBER] error in MD simulation Jason Swails (Thu Jun 25 2015 - 07:47:59 PDT)
  - Re: [AMBER] error in MD simulation erik.laurini.di3.units.it (Fri Jun 26 2015 - 05:15:40 PDT)
    - Re: [AMBER] error in MD simulation Jason Swails (Fri Jun 26 2015 - 05:25:40 PDT)
[AMBER] help in radial command Robin Jain (Thu Jun 25 2015 - 22:20:22 PDT)
- Re: [AMBER] help in radial command newamber list (Fri Jun 26 2015 - 04:01:49 PDT)
[AMBER] Align 1000 frames into one .crd file Hadeer ELHabashy (Fri Jun 26 2015 - 04:17:46 PDT)
- Re: [AMBER] Align 1000 frames into one .crd file Jason Swails (Fri Jun 26 2015 - 05:40:35 PDT)
  - Re: [AMBER] Align 1000 frames into one .crd file Hadeer ELHabashy (Fri Jun 26 2015 - 06:48:49 PDT)
[AMBER] Regarding calculation of viscosity of system MOHD HOMAIDUR RAHMAN (Fri Jun 26 2015 - 05:09:56 PDT)
- Re: [AMBER] Regarding calculation of viscosity of system David A Case (Fri Jun 26 2015 - 08:38:25 PDT)
[AMBER] Lipid 14 force field Ning Xiang (Fri Jun 26 2015 - 07:16:24 PDT)
- Re: [AMBER] Lipid 14 force field Benjamin D Madej (Fri Jun 26 2015 - 10:48:26 PDT)
[AMBER] Defining the box dimensions while making the top and crd files Iqbal, Muhammad Sajid (Fri Jun 26 2015 - 11:48:46 PDT)
- Re: [AMBER] Defining the box dimensions while making the top and crd files David A Case (Fri Jun 26 2015 - 18:59:55 PDT)
[AMBER] Halogen at the dftb level Hector A. Baldoni (Fri Jun 26 2015 - 12:42:54 PDT)
[AMBER] Amber14 compatibilty with GTX-760 GPU card Elvis Martis (Fri Jun 26 2015 - 20:46:37 PDT)
- Re: [AMBER] Amber14 compatibilty with GTX-760 GPU card Hector A. Baldoni (Fri Jun 26 2015 - 20:57:51 PDT)
- Re: [AMBER] Amber14 compatibilty with GTX-760 GPU card Ross Walker (Fri Jun 26 2015 - 21:01:50 PDT)
[AMBER] some doubts about simulation analysis Mary Varughese (Sat Jun 27 2015 - 00:53:28 PDT)
- Re: [AMBER] some doubts about simulation analysis Jiri Sponer (Sat Jun 27 2015 - 01:28:59 PDT)
Re: [AMBER] Amber14 compatibility with GTX-760 GPU card Elvis Martis (Sat Jun 27 2015 - 12:35:28 PDT)
[AMBER] lifetime analysis zahra khatti (Sat Jun 27 2015 - 15:12:00 PDT)
[AMBER] Generating RESP Charges For Tightly-Bound Complexes - Charges from the complexes or the fragments? Damian G. Allis, Ph.D. (Sat Jun 27 2015 - 19:08:43 PDT)
- Re: [AMBER] Generating RESP Charges For Tightly-Bound Complexes - Charges from the complexes or the fragments? David A Case (Sun Jun 28 2015 - 05:09:52 PDT)
[AMBER] lifetime analysis zahra khatti (Sun Jun 28 2015 - 14:22:52 PDT)
- Re: [AMBER] lifetime analysis Jason Swails (Mon Jun 29 2015 - 05:08:38 PDT)
[AMBER] lifetime analysis zahra khatti (Sun Jun 28 2015 - 14:34:26 PDT)
[AMBER] lifetime zahra khatti (Sun Jun 28 2015 - 14:53:54 PDT)
[AMBER] lifetime zahra khatti (Sun Jun 28 2015 - 15:06:50 PDT)
- Re: [AMBER] lifetime Daniel Roe (Sun Jun 28 2015 - 15:48:46 PDT)
[AMBER] Experimental values about some orgnaic solvent BOX wangmt (Sun Jun 28 2015 - 23:43:41 PDT)
- Re: [AMBER] Experimental values about some orgnaic solvent BOX David A Case (Mon Jun 29 2015 - 04:41:16 PDT)
  - Re: [AMBER] Experimental values about some orgnaic solvent BOX Karl Kirschner (Mon Jun 29 2015 - 05:04:36 PDT)
[AMBER] Running amber forcefield in NAMD Yogeeshwar Ajjugal (Mon Jun 29 2015 - 05:02:32 PDT)
- Re: [AMBER] Running amber forcefield in NAMD Jason Swails (Mon Jun 29 2015 - 05:12:52 PDT)
[AMBER] built-in scc-dftb method amber15 Hector A. Baldoni (Mon Jun 29 2015 - 05:22:55 PDT)
[AMBER] cuda7 not supported? Albert (Mon Jun 29 2015 - 10:34:15 PDT)
- Re: [AMBER] cuda7 not supported? Daniel Roe (Mon Jun 29 2015 - 14:27:42 PDT)
  - Re: [AMBER] cuda7 not supported? Albert (Tue Jun 30 2015 - 02:30:26 PDT)
    - Re: [AMBER] cuda7 not supported? Jason Swails (Tue Jun 30 2015 - 06:31:05 PDT)
- Re: [AMBER] cuda7 not supported? nam kim (Mon Jun 29 2015 - 14:45:47 PDT)
[AMBER] Quantifying Membrane Contact or insertion Parker de Waal (Mon Jun 29 2015 - 11:39:35 PDT)
[AMBER] acpype fails to run on provided tests Daniel Bork (Mon Jun 29 2015 - 13:27:14 PDT)
- Re: [AMBER] acpype fails to run on provided tests Jason Swails (Mon Jun 29 2015 - 21:16:57 PDT)
[AMBER] Installation Question - Missing file? Jim Wu (Mon Jun 29 2015 - 15:36:19 PDT)
- Re: [AMBER] Installation Question - Missing file? Jason Swails (Mon Jun 29 2015 - 21:01:40 PDT)
- Re: [AMBER] Installation Question - Missing file? David A Case (Tue Jun 30 2015 - 04:43:49 PDT)
[AMBER] Normal mode calculation was failed with MMPBSA.py wliu (Mon Jun 29 2015 - 19:30:00 PDT)
- Re: [AMBER] Normal mode calculation was failed with MMPBSA.py Jason Swails (Mon Jun 29 2015 - 21:05:13 PDT)
[AMBER] PCA Calculations Parker de Waal (Mon Jun 29 2015 - 19:43:43 PDT)
- Re: [AMBER] PCA Calculations Daniel Roe (Tue Jun 30 2015 - 08:44:44 PDT)
[AMBER] svdcmp in sander/ncsu-rmsd.F90 (AmberTools15) is sensitive to higher optimizations, suggest using lapack routine instead Åke Sandgren (Mon Jun 29 2015 - 23:41:35 PDT)
- Re: [AMBER] svdcmp in sander/ncsu-rmsd.F90 (AmberTools15) is sensitive to higher optimizations, suggest using lapack routine instead David A Case (Thu Jul 16 2015 - 09:30:18 PDT)
  - Re: [AMBER] svdcmp in sander/ncsu-rmsd.F90 (AmberTools15) is sensitive to higher optimizations, suggest using lapack routine instead Åke Sandgren (Thu Jul 16 2015 - 10:05:29 PDT)
[AMBER] RESP: charges on equivalent atoms Neelanjana Sengupta (Tue Jun 30 2015 - 01:55:20 PDT)
- Re: [AMBER] RESP: charges on equivalent atoms David A Case (Tue Jun 30 2015 - 04:50:46 PDT)
[AMBER] Post processing of trajectory with sander MOHD HOMAIDUR RAHMAN (Tue Jun 30 2015 - 05:59:02 PDT)
- Re: [AMBER] Post processing of trajectory with sander Jason Swails (Tue Jun 30 2015 - 08:26:01 PDT)
[AMBER] folding RNA using SGLD Asmita Gupta (Tue Jun 30 2015 - 07:11:21 PDT)
- Re: [AMBER] folding RNA using SGLD Wu, Xiongwu (NIH/NHLBI) [E] (Tue Jun 30 2015 - 07:44:37 PDT)
- Re: [AMBER] folding RNA using SGLD Jason Swails (Tue Jun 30 2015 - 08:30:40 PDT)
  - Re: [AMBER] folding RNA using SGLD Asmita Gupta (Thu Jul 02 2015 - 05:49:02 PDT)
[AMBER] simulation phosphorylated complex of protein Ziba Bahadori (Tue Jun 30 2015 - 07:24:36 PDT)
- Re: [AMBER] simulation phosphorylated complex of protein David A Case (Tue Jun 30 2015 - 09:11:52 PDT)
[AMBER] RESP Charge Fit - Intramolecular Hydrogen Bond Yip Yew Mun (Tue Jun 30 2015 - 07:48:36 PDT)
[AMBER] Output format in sander John Dood (Tue Jun 30 2015 - 10:03:01 PDT)
- Re: [AMBER] Output format in sander David A Case (Tue Jun 30 2015 - 11:00:19 PDT)
  - Re: [AMBER] Output format in sander John Dood (Tue Jun 30 2015 - 11:38:17 PDT)
    - Re: [AMBER] Output format in sander Brent Krueger (Tue Jun 30 2015 - 21:38:53 PDT)
    - Re: [AMBER] Output format in sander Jason Swails (Wed Jul 01 2015 - 03:16:15 PDT)
    - Re: [AMBER] Output format in sander Jason Swails (Wed Jul 01 2015 - 08:55:59 PDT)
    - Re: [AMBER] Output format in sander David A Case (Wed Jul 01 2015 - 05:38:05 PDT)
    - Re: [AMBER] Output format in sander Jason Swails (Wed Jul 01 2015 - 09:00:17 PDT)
    - Re: [AMBER] Output format in sander John Dood (Thu Jul 02 2015 - 10:24:19 PDT)
[AMBER] error in parallel run Lara rajam (Tue Jun 30 2015 - 10:20:37 PDT)
- Re: [AMBER] error in parallel run David A Case (Tue Jun 30 2015 - 11:02:39 PDT)
[AMBER] Rms fitting to a reference structure with a differnt number atoms to top file George Green (Tue Jun 30 2015 - 12:42:12 PDT)
- Re: [AMBER] Rms fitting to a reference structure with a differnt number atoms to top file George Green (Tue Jun 30 2015 - 12:54:53 PDT)
- Re: [AMBER] Rms fitting to a reference structure with a differnt number atoms to top file Daniel Roe (Tue Jun 30 2015 - 13:15:56 PDT)
  - Re: [AMBER] Rms fitting to a reference structure with a differnt number atoms to top file George Green (Wed Jul 01 2015 - 02:35:04 PDT)
[AMBER] Explicit Solvent Constant pH MD Rahul Ramesh (Tue Jun 30 2015 - 13:53:13 PDT)
- Re: [AMBER] Explicit Solvent Constant pH MD Jason Swails (Tue Jun 30 2015 - 20:11:43 PDT)
  - Re: [AMBER] Explicit Solvent Constant pH MD Rahul Ramesh (Thu Jul 09 2015 - 09:42:17 PDT)
    - Re: [AMBER] Explicit Solvent Constant pH MD Jason Swails (Thu Jul 09 2015 - 09:49:38 PDT)
    - Re: [AMBER] Explicit Solvent Constant pH MD Alan (Thu Jul 09 2015 - 13:47:05 PDT)
    - Re: [AMBER] Explicit Solvent Constant pH MD Rahul Ramesh (Fri Jul 10 2015 - 14:52:52 PDT)
    - Re: [AMBER] Explicit Solvent Constant pH MD Jason Swails (Sat Jul 11 2015 - 05:50:55 PDT)
[AMBER] Compile Failure Jim Wu (Tue Jun 30 2015 - 15:06:36 PDT)
- Re: [AMBER] Compile Failure Jason Swails (Tue Jun 30 2015 - 19:40:34 PDT)
  - Re: [AMBER] Compile Failure Jim Wu (Tue Jun 30 2015 - 19:44:41 PDT)
- Re: [AMBER] Compile Failure Jason Swails (Tue Jun 30 2015 - 20:20:21 PDT)
  - Re: [AMBER] Compile Failure Jim Wu (Tue Jun 30 2015 - 21:12:54 PDT)
- Re: [AMBER] Compile Failure David A Case (Wed Jul 01 2015 - 05:41:39 PDT)
  - Re: [AMBER] Compile Failure Jim Wu (Wed Jul 01 2015 - 09:38:56 PDT)
    - Re: [AMBER] Compile Failure David A Case (Thu Jul 02 2015 - 06:13:00 PDT)
[AMBER] Cpptraj failure Lin Song (Tue Jun 30 2015 - 19:47:37 PDT)
- Re: [AMBER] Cpptraj failure Daniel Roe (Thu Jul 02 2015 - 09:45:37 PDT)
  - Re: [AMBER] Cpptraj failure Lin Song (Mon Jul 13 2015 - 09:14:42 PDT)
[AMBER] Why the entropy contribution from quasi-harmonic and normal mode methods are so different? wliu (Wed Jul 01 2015 - 02:13:54 PDT)
- Re: [AMBER] Why the entropy contribution from quasi-harmonic and normal mode methods are so different? Hannes Loeffler (Wed Jul 01 2015 - 02:52:11 PDT)
  - Re: [AMBER] Why the entropy contribution from quasi-harmonic and normal mode methods are so different? wliu (Wed Jul 01 2015 - 21:19:47 PDT)
[AMBER] Lipid diffusion in cpptraj Life Sciences Inc (Wed Jul 01 2015 - 07:11:56 PDT)
- Re: [AMBER] Lipid diffusion in cpptraj Daniel Roe (Thu Jul 02 2015 - 09:36:20 PDT)
  - Re: [AMBER] Lipid diffusion in cpptraj Life Sciences Inc (Wed Jul 08 2015 - 15:45:45 PDT)
    - Re: [AMBER] Lipid diffusion in cpptraj Daniel Roe (Thu Jul 09 2015 - 08:15:59 PDT)
    - Re: [AMBER] Lipid diffusion in cpptraj Life Sciences Inc (Mon Jul 13 2015 - 14:50:54 PDT)
    - Re: [AMBER] Lipid diffusion in cpptraj hannes.loeffler.stfc.ac.uk (Mon Jul 13 2015 - 23:42:40 PDT)
    - Re: [AMBER] Lipid diffusion in cpptraj Daniel Roe (Tue Jul 14 2015 - 07:40:45 PDT)
    - Re: [AMBER] Lipid diffusion in cpptraj Life Sciences Inc (Thu Jul 30 2015 - 14:22:16 PDT)
    - Re: [AMBER] Lipid diffusion in cpptraj hannes.loeffler.stfc.ac.uk (Thu Jul 30 2015 - 23:42:35 PDT)
[AMBER] leap changes residue order Ignacio Faustino (Wed Jul 01 2015 - 09:04:37 PDT)
- Re: [AMBER] leap changes residue order Hannes Loeffler (Wed Jul 01 2015 - 09:12:05 PDT)
- Re: [AMBER] leap changes residue order Jason Swails (Wed Jul 01 2015 - 09:14:17 PDT)
  - Re: [AMBER] leap changes residue order Ignacio Faustino (Thu Jul 02 2015 - 09:51:58 PDT)
[AMBER] water networks and bridge option of the hbond command in cpptraj Vlad Cojocaru (Wed Jul 01 2015 - 10:44:49 PDT)
- Re: [AMBER] water networks and bridge option of the hbond command in cpptraj Daniel Roe (Thu Jul 02 2015 - 09:49:45 PDT)
[AMBER] QM/MM Equilibration Troubles Brittany Boykin (Wed Jul 01 2015 - 11:00:11 PDT)
- Re: [AMBER] QM/MM Equilibration Troubles Brian Radak (Wed Jul 01 2015 - 11:31:27 PDT)
[AMBER] anisotropic vs. semi-isotropic membrane simulations Naomi Rose Latorraca (Wed Jul 01 2015 - 15:01:51 PDT)
- Re: [AMBER] anisotropic vs. semi-isotropic membrane simulations Ross Walker (Wed Jul 01 2015 - 15:48:05 PDT)
  - Re: [AMBER] anisotropic vs. semi-isotropic membrane simulations David A Case (Thu Jul 02 2015 - 06:19:27 PDT)
- Re: [AMBER] anisotropic vs. semi-isotropic membrane simulations Jason Swails (Thu Jul 02 2015 - 05:34:25 PDT)
[AMBER] Ambertools15 installation without Amber ANWESHA SARKAR (Thu Jul 02 2015 - 02:16:42 PDT)
- Re: [AMBER] Ambertools15 installation without Amber Gerald Monard (Thu Jul 02 2015 - 02:30:12 PDT)
  - Re: [AMBER] Ambertools15 installation without Amber ANWESHA SARKAR (Thu Jul 02 2015 - 02:45:47 PDT)
    - Re: [AMBER] Ambertools15 installation without Amber Gerald Monard (Thu Jul 02 2015 - 02:54:32 PDT)
    - Re: [AMBER] Ambertools15 installation without Amber ANWESHA SARKAR (Thu Jul 02 2015 - 03:25:37 PDT)
    - Re: [AMBER] Ambertools15 installation without Amber Gerald Monard (Thu Jul 02 2015 - 04:49:46 PDT)
[AMBER] kclust help Harmeet Kaur (Thu Jul 02 2015 - 05:00:37 PDT)
- Re: [AMBER] kclust help Daniel Roe (Thu Jul 02 2015 - 10:08:11 PDT)
[AMBER] another leap inconsistency Hannes Loeffler (Thu Jul 02 2015 - 06:44:03 PDT)
- Re: [AMBER] another leap inconsistency Jason Swails (Thu Jul 02 2015 - 07:53:31 PDT)
  - Re: [AMBER] another leap inconsistency hannes.loeffler.stfc.ac.uk (Fri Jul 03 2015 - 13:02:49 PDT)
[AMBER] Chlorophyll A .mol2 file Ofir Tal (Thu Jul 02 2015 - 06:45:12 PDT)
[AMBER] Cpptraj able to identify coordinates written by VMD? Karl Debiec (Thu Jul 02 2015 - 10:31:48 PDT)
- Re: [AMBER] Cpptraj able to identify coordinates written by VMD? Brian Radak (Thu Jul 02 2015 - 11:58:19 PDT)
- Re: [AMBER] Cpptraj able to identify coordinates written by VMD? Thomas Cheatham (Thu Jul 02 2015 - 12:47:48 PDT)
[AMBER] Regarding melt curve MOHD HOMAIDUR RAHMAN (Thu Jul 02 2015 - 21:16:31 PDT)
- Re: [AMBER] Regarding melt curve nhai.wn (Thu Jul 02 2015 - 21:26:12 PDT)
[AMBER] help in make .prepin file Robin Jain (Fri Jul 03 2015 - 00:06:00 PDT)
- Re: [AMBER] help in make .prepin file David A Case (Fri Jul 03 2015 - 05:22:16 PDT)
[AMBER] How to set interatomic distance restraint? Michael Shokhen (Fri Jul 03 2015 - 00:19:37 PDT)
- Re: [AMBER] How to set interatomic distance restraint? David A Case (Fri Jul 03 2015 - 05:26:56 PDT)
  - Re: [AMBER] How to set interatomic distance restraint? Michael Shokhen (Sun Jul 05 2015 - 05:04:46 PDT)
    - Re: [AMBER] How to set interatomic distance restraint? David A Case (Sun Jul 05 2015 - 06:06:09 PDT)
    - Re: [AMBER] How to set interatomic distance restraint? Michael Shokhen (Mon Jul 06 2015 - 08:43:08 PDT)
    - Re: [AMBER] How to set interatomic distance restraint? Jason Swails (Mon Jul 06 2015 - 09:00:00 PDT)
    - Re: [AMBER] How to set interatomic distance restraint? Michael Shokhen (Thu Jul 09 2015 - 01:18:40 PDT)
[AMBER] Question about AMBER energy decomposition Lee-Ping Wang (Fri Jul 03 2015 - 12:28:53 PDT)
- Re: [AMBER] Question about AMBER energy decomposition Jason Swails (Fri Jul 03 2015 - 14:30:00 PDT)
  - Re: [AMBER] Question about AMBER energy decomposition Lee-Ping Wang (Sat Jul 04 2015 - 06:41:04 PDT)
    - Re: [AMBER] Question about AMBER energy decomposition Jason Swails (Sat Jul 04 2015 - 16:00:18 PDT)
[AMBER] extract coordinates of a specific atom Morteza Chehel Amirani (Fri Jul 03 2015 - 16:43:20 PDT)
- Re: [AMBER] extract coordinates of a specific atom Nhai (Fri Jul 03 2015 - 16:50:42 PDT)
[AMBER] charmmlipid2amber.py Ramin Ekhteiari (Sat Jul 04 2015 - 11:35:49 PDT)
[AMBER] NOESY volumes restraints Eugene Sviridov (Mon Jul 06 2015 - 04:08:30 PDT)
- Re: [AMBER] NOESY volumes restraints David A Case (Mon Jul 06 2015 - 07:42:02 PDT)
  - Re: [AMBER] NOESY volumes restraints Eugene Sviridov (Fri Jul 10 2015 - 03:39:02 PDT)
    - Re: [AMBER] NOESY volumes restraints David A Case (Mon Jul 13 2015 - 04:50:01 PDT)
[AMBER] assigning atom type and charge Sanjib Paul (Mon Jul 06 2015 - 04:41:08 PDT)
- Re: [AMBER] assigning atom type and charge Jason Swails (Mon Jul 06 2015 - 05:50:32 PDT)
- Re: [AMBER] assigning atom type and charge FyD (Thu Jul 09 2015 - 01:51:58 PDT)
[AMBER] PME large NFFT John Dood (Mon Jul 06 2015 - 06:18:47 PDT)
- Re: [AMBER] PME large NFFT Jason Swails (Mon Jul 06 2015 - 08:15:33 PDT)
[AMBER] amber topology file for cytochrome c covalently bond to Heme Shoresh Shafei (Mon Jul 06 2015 - 10:07:58 PDT)
- Re: [AMBER] amber topology file for cytochrome c covalently bond to Heme David A Case (Tue Jul 07 2015 - 10:27:42 PDT)
[AMBER] Reference energies for Explicit solvent CpHMD Arjun Sharma (Mon Jul 06 2015 - 10:33:36 PDT)
- Re: [AMBER] Reference energies for Explicit solvent CpHMD Jason Swails (Mon Jul 06 2015 - 11:09:19 PDT)
[AMBER] cpptraj: bounds command -> grid Thomas Fox (Tue Jul 07 2015 - 00:10:11 PDT)
- Re: [AMBER] cpptraj: bounds command -> grid Daniel Roe (Tue Jul 07 2015 - 03:24:27 PDT)
[AMBER] cpptraj: rmsd problem Thomas Fox (Tue Jul 07 2015 - 02:15:34 PDT)
- Re: [AMBER] cpptraj: rmsd problem Daniel Roe (Tue Jul 07 2015 - 07:20:17 PDT)
[AMBER] Lipid linked to a peptide Arnoult, Eric [JRDUS] (Tue Jul 07 2015 - 09:57:48 PDT)
- Re: [AMBER] Lipid linked to a peptide David A Case (Tue Jul 07 2015 - 10:23:46 PDT)
[AMBER] About python usage in AmberTools Juan Eiros Zamora (Tue Jul 07 2015 - 11:05:23 PDT)
- Re: [AMBER] About python usage in AmberTools Hai Nguyen (Tue Jul 07 2015 - 11:33:42 PDT)
  - Re: [AMBER] About python usage in AmberTools Hai Nguyen (Tue Jul 07 2015 - 14:54:30 PDT)
- Re: [AMBER] About python usage in AmberTools Jason Swails (Tue Jul 07 2015 - 11:55:28 PDT)
  - Re: [AMBER] About python usage in AmberTools Eiros Zamora, Juan (Tue Jul 07 2015 - 12:50:45 PDT)
    - Re: [AMBER] About python usage in AmberTools Jason Swails (Tue Jul 07 2015 - 12:54:19 PDT)
    - Re: [AMBER] About python usage in AmberTools Juan Eiros Zamora (Wed Jul 08 2015 - 06:31:46 PDT)
    - Re: [AMBER] About python usage in AmberTools Jason Swails (Wed Jul 08 2015 - 06:59:11 PDT)
    - Re: [AMBER] About python usage in AmberTools Juan Eiros Zamora (Wed Jul 08 2015 - 07:19:02 PDT)
    - Re: [AMBER] About python usage in AmberTools Jason Swails (Wed Jul 08 2015 - 07:20:13 PDT)
    - Re: [AMBER] About python usage in AmberTools Juan Eiros Zamora (Wed Jul 08 2015 - 07:26:35 PDT)
    - Re: [AMBER] About python usage in AmberTools Hai Nguyen (Wed Jul 08 2015 - 09:42:10 PDT)
    - Re: [AMBER] About python usage in AmberTools Jason Swails (Wed Jul 08 2015 - 12:07:06 PDT)
    - Re: [AMBER] About python usage in AmberTools Hai Nguyen (Wed Jul 08 2015 - 09:37:20 PDT)
[AMBER] NumPy Import Error for MCPB.py on Amber15 Eleftherios A P Lambros (Tue Jul 07 2015 - 16:23:54 PDT)
- Re: [AMBER] NumPy Import Error for MCPB.py on Amber15 Takeshi Baba (Tue Jul 07 2015 - 16:39:25 PDT)
- Re: [AMBER] NumPy Import Error for MCPB.py on Amber15 Hai Nguyen (Tue Jul 07 2015 - 17:10:57 PDT)
[AMBER] issue using CUDA+MPI+OpenMP Éric Germaneau (Tue Jul 07 2015 - 23:12:45 PDT)
- Re: [AMBER] issue using CUDA+MPI+OpenMP Gerald Monard (Wed Jul 08 2015 - 01:10:42 PDT)
  - Re: [AMBER] issue using CUDA+MPI+OpenMP Éric Germaneau (Wed Jul 08 2015 - 17:02:08 PDT)
    - Re: [AMBER] issue using CUDA+MPI+OpenMP David A Case (Wed Jul 08 2015 - 17:26:49 PDT)
    - Re: [AMBER] issue using CUDA+MPI+OpenMP Éric Germaneau (Wed Jul 08 2015 - 17:33:57 PDT)
    - Re: [AMBER] issue using CUDA+MPI+OpenMP Ross Walker (Thu Jul 09 2015 - 04:27:58 PDT)
    - Re: [AMBER] issue using CUDA+MPI+OpenMP Brent Krueger (Thu Jul 09 2015 - 05:40:45 PDT)
    - Re: [AMBER] issue using CUDA+MPI+OpenMP Jason Swails (Thu Jul 09 2015 - 06:06:51 PDT)
    - Re: [AMBER] issue using CUDA+MPI+OpenMP Scott Le Grand (Thu Jul 09 2015 - 07:47:24 PDT)
[AMBER] Paramentrization of a Uracil base with an O3' terminus deprotonated. giulia palermo (Wed Jul 08 2015 - 01:14:39 PDT)
- Re: [AMBER] Paramentrization of a Uracil base with an O3' terminus deprotonated. Jason Swails (Wed Jul 08 2015 - 06:11:02 PDT)
  - Re: [AMBER] Paramentrization of a Uracil base with an O3' terminus deprotonated. giulia palermo (Wed Jul 08 2015 - 07:20:56 PDT)
- Re: [AMBER] Paramentrization of a Uracil base with an O3' terminus deprotonated. FyD (Thu Jul 09 2015 - 01:44:28 PDT)
  - Re: [AMBER] Paramentrization of a Uracil base with an O3' terminus deprotonated. Brent Krueger (Thu Jul 09 2015 - 03:45:21 PDT)
    - Re: [AMBER] Paramentrization of a Uracil base with an O3' terminus deprotonated. giulia palermo (Thu Jul 09 2015 - 08:47:35 PDT)
[AMBER] help in amber Robin Jain (Wed Jul 08 2015 - 02:31:26 PDT)
- Re: [AMBER] help in amber Jason Swails (Wed Jul 08 2015 - 06:13:46 PDT)
[AMBER] problem in amber Robin Jain (Thu Jul 09 2015 - 00:32:05 PDT)
- Re: [AMBER] problem in amber Jason Swails (Thu Jul 09 2015 - 04:52:00 PDT)
[AMBER] Unexpected prochirality change from si to re during MD simulation Michael Shokhen (Thu Jul 09 2015 - 01:28:59 PDT)
- Re: [AMBER] Unexpected prochirality change from si to re during MD simulation David A Case (Mon Jul 13 2015 - 05:13:31 PDT)
[AMBER] Namdenergy problems with non-standard amino acids Clavel (Thu Jul 09 2015 - 02:34:53 PDT)
- Re: [AMBER] Namdenergy problems with non-standard amino acids Jason Swails (Thu Jul 09 2015 - 05:04:08 PDT)
[AMBER] Problem in loading the pdb file Harshala Haldankar (Thu Jul 09 2015 - 03:58:07 PDT)
- Re: [AMBER] Problem in loading the pdb file Jason Swails (Thu Jul 09 2015 - 05:23:54 PDT)
- Re: [AMBER] Problem in loading the pdb file Harshala Haldankar (Thu Jul 09 2015 - 21:39:03 PDT)
  - Re: [AMBER] Problem in loading the pdb file Jason Swails (Fri Jul 10 2015 - 03:49:46 PDT)
[AMBER] parameters dATP Francesca Cardamone (Thu Jul 09 2015 - 06:07:07 PDT)
[AMBER] articles published for ff14SB and GBneck2 Carlos Simmerling (Thu Jul 09 2015 - 07:03:56 PDT)
- Re: [AMBER] articles published for ff14SB and GBneck2 Vlad Cojocaru (Fri Jul 10 2015 - 05:45:35 PDT)
Re: [AMBER] AMBER Digest, Vol 1274, Issue 1 Eleftherios A P Lambros (Thu Jul 09 2015 - 14:16:36 PDT)
- Re: [AMBER] AMBER Digest, Vol 1274, Issue 1 Eleftherios A P Lambros (Thu Jul 09 2015 - 15:12:58 PDT)
- Re: [AMBER] AMBER Digest, Vol 1274, Issue 1 Hai Nguyen (Thu Jul 09 2015 - 15:33:46 PDT)
[AMBER] Magnesium in MMGBSA Ahmed Ayoub (Thu Jul 09 2015 - 19:27:53 PDT)
- Re: [AMBER] Magnesium in MMGBSA Jason Swails (Fri Jul 10 2015 - 04:55:48 PDT)
[AMBER] ESURF term in MMGBSA Ahmed Ayoub (Thu Jul 09 2015 - 19:46:54 PDT)
- Re: [AMBER] ESURF term in MMGBSA Jason Swails (Fri Jul 10 2015 - 04:58:20 PDT)
[AMBER] Order of the atom in prep ourput of antechamber Nicholus Bhattacharjee (Fri Jul 10 2015 - 01:52:24 PDT)
- Re: [AMBER] Order of the atom in prep ourput of antechamber Hannes Loeffler (Fri Jul 10 2015 - 02:01:52 PDT)
  - Re: [AMBER] Order of the atom in prep ourput of antechamber Thomas Fox (Fri Jul 10 2015 - 02:54:38 PDT)
- Re: [AMBER] Order of the atom in prep ourput of antechamber David A Case (Sat Jul 11 2015 - 05:23:44 PDT)
[AMBER] problems on amoeba force filed implemented in amber fjliu (Fri Jul 10 2015 - 01:53:01 PDT)
- Re: [AMBER] problems on amoeba force filed implemented in amber Jason Swails (Fri Jul 10 2015 - 04:54:04 PDT)
  - Re: [AMBER] problems on amoeba force filed implemented in amber fjliu (Tue Jul 14 2015 - 02:35:30 PDT)
    - Re: [AMBER] problems on amoeba force filed implemented in amber Jason Swails (Tue Jul 14 2015 - 05:11:54 PDT)
    - Re: [AMBER] problems on amoeba force filed implemented in amber fjliu (Tue Jul 14 2015 - 19:43:32 PDT)
    - Re: [AMBER] problems on amoeba force filed implemented in amber Brian Radak (Wed Jul 15 2015 - 09:53:17 PDT)
[AMBER] Changing NMR restraint weights Oliver Grant (Fri Jul 10 2015 - 02:02:29 PDT)
- Re: [AMBER] Changing NMR restraint weights David A Case (Mon Jul 13 2015 - 06:52:04 PDT)
- Re: [AMBER] Changing NMR restraint weights Oliver Grant (Tue Jul 14 2015 - 07:02:35 PDT)
  - Re: [AMBER] Changing NMR restraint weights David A Case (Tue Jul 14 2015 - 08:48:29 PDT)
[AMBER] question about advanced tutorial 3 Mohsen Zakeri (Fri Jul 10 2015 - 03:12:03 PDT)
- Re: [AMBER] question about advanced tutorial 3 Juan Eiros Zamora (Fri Jul 10 2015 - 03:30:29 PDT)
[AMBER] FEW tutorial Mohsen Zakeri (Fri Jul 10 2015 - 03:37:43 PDT)
- Re: [AMBER] FEW tutorial Hannes Loeffler (Fri Jul 10 2015 - 03:54:23 PDT)
[AMBER] molecules split apart during MD Lara rajam (Fri Jul 10 2015 - 07:20:43 PDT)
- Re: [AMBER] molecules split apart during MD Jason Swails (Fri Jul 10 2015 - 07:37:29 PDT)
- [AMBER] molecules split apart during MD Kenneth Huang (Fri Jul 10 2015 - 07:39:42 PDT)
[AMBER] atom mapping Gard Nelson (Fri Jul 10 2015 - 11:38:40 PDT)
- Re: [AMBER] atom mapping Daniel Roe (Sun Jul 12 2015 - 08:30:33 PDT)
[AMBER] compare two trajectories Xing (Fri Jul 10 2015 - 12:35:10 PDT)
- Re: [AMBER] compare two trajectories Hai Nguyen (Fri Jul 10 2015 - 12:41:27 PDT)
  - Re: [AMBER] compare two trajectories Xing (Thu Oct 15 2015 - 19:29:08 PDT)
[AMBER] FATAL: Atom () does not have a type???? Evans, Shalton (Fri Jul 10 2015 - 13:36:05 PDT)
- Re: [AMBER] FATAL: Atom () does not have a type???? Kenneth Huang (Fri Jul 10 2015 - 13:55:47 PDT)
  - Re: [AMBER] FATAL: Atom () does not have a type???? Evans, Shalton (Fri Jul 10 2015 - 14:32:49 PDT)
    - [AMBER] FATAL: Atom () does not have a type???? Kenneth Huang (Fri Jul 10 2015 - 15:16:38 PDT)
[AMBER] About charge derivation for enantiomers Tommaso Casalini (Fri Jul 10 2015 - 13:51:40 PDT)
[AMBER] pmemd.cuda.MPI error - integer divide by zero Bill Miller III (Fri Jul 10 2015 - 14:36:38 PDT)
- Re: [AMBER] pmemd.cuda.MPI error - integer divide by zero David A Case (Fri Jul 10 2015 - 17:03:12 PDT)
  - Re: [AMBER] pmemd.cuda.MPI error - integer divide by zero Jason Swails (Sat Jul 11 2015 - 05:27:58 PDT)
    - Re: [AMBER] pmemd.cuda.MPI error - integer divide by zero Bill Miller III (Tue Jul 14 2015 - 18:11:34 PDT)
[AMBER] pmemd.cuda implementation of sgld Asmita Gupta (Sat Jul 11 2015 - 00:50:31 PDT)
- Re: [AMBER] pmemd.cuda implementation of sgld Daniel Roe (Sat Jul 11 2015 - 06:41:53 PDT)
[AMBER] About charge derivation for enantiomeric molecules Tommaso Casalini (Sat Jul 11 2015 - 02:30:39 PDT)
- Re: [AMBER] About charge derivation for enantiomeric molecules case (Sat Jul 11 2015 - 05:41:25 PDT)
  - Re: [AMBER] About charge derivation for enantiomeric molecules Casalini Tommaso (Sat Jul 11 2015 - 05:48:49 PDT)
[AMBER] Query about adding hydrogens anu chandra (Sat Jul 11 2015 - 13:08:54 PDT)
- Re: [AMBER] Query about adding hydrogens Bill Ross (Sat Jul 11 2015 - 15:20:41 PDT)
- Re: [AMBER] Query about adding hydrogens David Case (Sat Oct 24 2015 - 07:31:03 PDT)
[AMBER] Producing Decoys with AmberTools Mohsen Zakeri (Sun Jul 12 2015 - 12:49:25 PDT)
[AMBER] Problem in Using the Average Command in Cpptraj Robert Molt (Mon Jul 13 2015 - 08:38:15 PDT)
- Re: [AMBER] Problem in Using the Average Command in Cpptraj Jason Swails (Mon Jul 13 2015 - 09:04:35 PDT)
  - Re: [AMBER] Problem in Using the Average Command in Cpptraj Robert Molt (Mon Jul 13 2015 - 09:12:38 PDT)
- Re: [AMBER] Problem in Using the Average Command in Cpptraj Daniel Roe (Mon Jul 13 2015 - 09:04:43 PDT)
[AMBER] Relaxing a heme molecule Amber Maharaj (Mon Jul 13 2015 - 13:02:17 PDT)
- Re: [AMBER] Relaxing a heme molecule case (Mon Jul 13 2015 - 17:35:19 PDT)
  - Re: [AMBER] Relaxing a heme molecule Amber Maharaj (Wed Jul 15 2015 - 12:26:49 PDT)
[AMBER] help in making xyz file Robin Jain (Tue Jul 14 2015 - 02:14:01 PDT)
- Re: [AMBER] help in making xyz file Jason Swails (Tue Jul 14 2015 - 05:24:43 PDT)
- Re: [AMBER] help in making xyz file David A Case (Tue Jul 14 2015 - 05:31:40 PDT)
[AMBER] Accelerated md for protein dna complex with modified residue Muthukumaran R (Tue Jul 14 2015 - 11:05:59 PDT)
- Re: [AMBER] Accelerated md for protein dna complex with modified residue Vlad Cojocaru (Wed Jul 15 2015 - 06:11:13 PDT)
[AMBER] ETOT drift and nscm in NVE for calculation of diffusion CHAMI F. (Tue Jul 14 2015 - 11:13:52 PDT)
- Re: [AMBER] ETOT drift and nscm in NVE for calculation of diffusion Jason Swails (Tue Jul 21 2015 - 15:36:12 PDT)
[AMBER] strange output from vacuum minimization Albert (Wed Jul 15 2015 - 01:30:48 PDT)
- Re: [AMBER] strange output from vacuum minimization David A Case (Wed Jul 15 2015 - 04:42:07 PDT)
[AMBER] MMPBSA.py API quasi-harmonic error D.J. Pattinson (Wed Jul 15 2015 - 01:36:03 PDT)
[AMBER] MPI compiling failed Albert (Wed Jul 15 2015 - 02:32:11 PDT)
- Re: [AMBER] MPI compiling failed David A Case (Wed Jul 15 2015 - 04:50:00 PDT)
  - Re: [AMBER] MPI compiling failed Albert (Wed Jul 15 2015 - 05:10:55 PDT)
    - Re: [AMBER] MPI compiling failed Jason Swails (Wed Jul 15 2015 - 10:29:29 PDT)
[AMBER] test failed but still work Albert (Wed Jul 15 2015 - 05:31:47 PDT)
- Re: [AMBER] test failed but still work David A Case (Wed Jul 15 2015 - 08:35:55 PDT)
  - Re: [AMBER] test failed but still work Jason Swails (Wed Jul 15 2015 - 10:32:44 PDT)
    - Re: [AMBER] test failed but still work Albert (Wed Jul 15 2015 - 10:43:22 PDT)
    - Re: [AMBER] test failed but still work Albert (Wed Jul 15 2015 - 10:53:17 PDT)
    - Re: [AMBER] test failed but still work case (Wed Jul 15 2015 - 14:51:22 PDT)
    - Re: [AMBER] test failed but still work Albert (Wed Jul 15 2015 - 23:36:31 PDT)
    - Re: [AMBER] test failed but still work David A Case (Thu Jul 16 2015 - 05:37:46 PDT)
    - Re: [AMBER] test failed but still work Albert (Thu Jul 16 2015 - 06:46:40 PDT)
[AMBER] setting up a MD simulation using AMBER Amber mail (Wed Jul 15 2015 - 06:11:10 PDT)
- Re: [AMBER] setting up a MD simulation using AMBER David A Case (Wed Jul 15 2015 - 08:41:18 PDT)
[AMBER] NetCDF file Marta Wisniewska (Wed Jul 15 2015 - 07:21:16 PDT)
- Re: [AMBER] NetCDF file Hannes Loeffler (Wed Jul 15 2015 - 07:33:46 PDT)
- Re: [AMBER] NetCDF file Hai Nguyen (Wed Jul 15 2015 - 07:34:35 PDT)
- Re: [AMBER] NetCDF file Marcus Arieno (Wed Jul 15 2015 - 07:34:51 PDT)
  - Re: [AMBER] NetCDF file Hannes Loeffler (Wed Jul 15 2015 - 07:47:22 PDT)
[AMBER] Error in writing .lib file Elvis Martis (Wed Jul 15 2015 - 20:13:18 PDT)
- Re: [AMBER] Error in writing .lib file David A Case (Thu Jul 16 2015 - 05:30:21 PDT)
- Re: [AMBER] Error in writing .lib file Elvis Martis (Fri Jul 17 2015 - 01:04:15 PDT)
[AMBER] Coordinate resetting (SHAKE) cannot be accomplished Vahid Kshani (Wed Jul 15 2015 - 22:27:59 PDT)
- Re: [AMBER] Coordinate resetting (SHAKE) cannot be accomplished David A Case (Thu Jul 16 2015 - 05:36:58 PDT)
[AMBER] AMBER error : Coordinate resetting (SHAKE) cannot be accomplish ed MASAOKI FUJII (Thu Jul 16 2015 - 00:37:37 PDT)
- Re: [AMBER] AMBER error : Coordinate resetting (SHAKE) cannot be accomplish ed David A Case (Thu Jul 16 2015 - 05:42:02 PDT)
[AMBER] running sgld in explicit solvent Asmita Gupta (Thu Jul 16 2015 - 04:01:48 PDT)
- Re: [AMBER] running sgld in explicit solvent David A Case (Thu Jul 16 2015 - 05:48:15 PDT)
  - Re: [AMBER] running sgld in explicit solvent Asmita Gupta (Thu Jul 16 2015 - 07:28:23 PDT)
[AMBER] RESP Fit to Atomic Multipoles Yip Yew Mun (Thu Jul 16 2015 - 08:01:46 PDT)
- Re: [AMBER] RESP Fit to Atomic Multipoles ymei (Thu Jul 16 2015 - 08:18:54 PDT)
  - Re: [AMBER] RESP Fit to Atomic Multipoles Yip Yew Mun (Thu Jul 16 2015 - 08:30:53 PDT)
[AMBER] Mutation of a protein residue in TI computation with pmemd.MPI M Olivia Kim (Thu Jul 16 2015 - 15:13:06 PDT)
- Re: [AMBER] Mutation of a protein residue in TI computation with pmemd.MPI Daniel Mermelstein (Thu Jul 16 2015 - 16:42:12 PDT)
- Re: [AMBER] Mutation of a protein residue in TI computation with pmemd.MPI hannes.loeffler.stfc.ac.uk (Thu Jul 16 2015 - 23:30:40 PDT)
  - Re: [AMBER] Mutation of a protein residue in TI computation with pmemd.MPI Olivia Pierce (Fri Jul 17 2015 - 09:52:02 PDT)
    - Re: [AMBER] Mutation of a protein residue in TI computation with pmemd.MPI hannes.loeffler.stfc.ac.uk (Fri Jul 17 2015 - 10:22:22 PDT)
    - Re: [AMBER] Mutation of a protein residue in TI computation with pmemd.MPI Olivia Pierce (Fri Jul 17 2015 - 12:57:13 PDT)
    - Re: [AMBER] Mutation of a protein residue in TI computation with pmemd.MPI hannes.loeffler.stfc.ac.uk (Fri Jul 17 2015 - 13:35:02 PDT)
    - Re: [AMBER] Mutation of a protein residue in TI computation with pmemd.MPI Olivia Pierce (Fri Jul 17 2015 - 16:36:34 PDT)
- Re: [AMBER] Mutation of a protein residue in TI computation with pmemd.MPI hannes.loeffler.stfc.ac.uk (Sat Jul 18 2015 - 02:00:26 PDT)
[AMBER] MCPB.py ValueError Eleftherios A P Lambros (Thu Jul 16 2015 - 18:48:03 PDT)
- Re: [AMBER] MCPB.py ValueError Takeshi Baba (Thu Jul 16 2015 - 19:01:28 PDT)
[AMBER] frames in mmpbsa.py Albert (Fri Jul 17 2015 - 03:12:45 PDT)
- Re: [AMBER] frames in mmpbsa.py Jason Swails (Fri Jul 17 2015 - 12:51:23 PDT)
  - Re: [AMBER] frames in mmpbsa.py Albert (Sun Jul 19 2015 - 23:10:16 PDT)
    - Re: [AMBER] frames in mmpbsa.py Jason Swails (Mon Jul 20 2015 - 07:27:51 PDT)
[AMBER] Deleting multiple atoms in xleap jacob wick (Fri Jul 17 2015 - 05:32:54 PDT)
- Re: [AMBER] Deleting multiple atoms in xleap jacob wick (Fri Jul 17 2015 - 05:58:35 PDT)
- Re: [AMBER] Deleting multiple atoms in xleap Jason Swails (Sat Jul 18 2015 - 07:29:36 PDT)
[AMBER] no FINAL_RESULTS_MMPBSA.dat generated Albert (Fri Jul 17 2015 - 05:46:23 PDT)
- Re: [AMBER] no FINAL_RESULTS_MMPBSA.dat generated Jason Swails (Fri Jul 17 2015 - 12:54:22 PDT)
[AMBER] countless warnning Albert (Fri Jul 17 2015 - 08:17:10 PDT)
- Re: [AMBER] countless warnning Ray Luo, Ph.D. (Fri Jul 17 2015 - 11:34:13 PDT)
[AMBER] illegal memory access in amber GPU simulations Latorraca, Naomi Rose (Fri Jul 17 2015 - 19:48:47 PDT)
- Re: [AMBER] illegal memory access in amber GPU simulations Ross Walker (Fri Jul 17 2015 - 21:22:52 PDT)
[AMBER] Problem in saving parameter/topology and coordinate file. Harshala Haldankar (Fri Jul 17 2015 - 22:44:47 PDT)
- Re: [AMBER] Problem in saving parameter/topology and coordinate file. Bill Ross (Sat Jul 18 2015 - 00:13:46 PDT)
- Re: [AMBER] Problem in saving parameter/topology and coordinate file. Harshala Haldankar (Mon Jul 20 2015 - 04:34:07 PDT)
  - Re: [AMBER] Problem in saving parameter/topology and coordinate file. David A Case (Tue Jul 21 2015 - 05:53:08 PDT)
- Re: [AMBER] Problem in saving parameter/topology and coordinate file. Bill Ross (Mon Jul 20 2015 - 13:11:46 PDT)
[AMBER] help in resp charge Robin Jain (Sat Jul 18 2015 - 00:16:50 PDT)
- Re: [AMBER] help in resp charge hannes.loeffler.stfc.ac.uk (Sat Jul 18 2015 - 01:05:29 PDT)
[AMBER] help in box size detremination Robin Jain (Sun Jul 19 2015 - 02:19:04 PDT)
[AMBER] help in box size determination Robin Jain (Sun Jul 19 2015 - 22:08:33 PDT)
- Re: [AMBER] help in box size determination David A Case (Mon Jul 20 2015 - 07:24:54 PDT)
[AMBER] installation without ambertools Asmita Gupta (Mon Jul 20 2015 - 01:17:03 PDT)
- Re: [AMBER] installation without ambertools Jason Swails (Mon Jul 20 2015 - 07:29:31 PDT)
[AMBER] Distance restraint in AMBER 14 and GPU Lionel Sacconnay (Mon Jul 20 2015 - 02:28:23 PDT)
- Re: [AMBER] Distance restraint in AMBER 14 and GPU David A Case (Mon Jul 20 2015 - 07:28:28 PDT)
[AMBER] incorrect determination of atomic number for atom Cl in tleap Ye Renlo (Mon Jul 20 2015 - 06:32:15 PDT)
- Re: [AMBER] incorrect determination of atomic number for atom Cl in tleap David A Case (Mon Jul 20 2015 - 07:31:16 PDT)
[AMBER] Problem cpptraj Bridging H-Bond analysis Beuerle, Matthias (Mon Jul 20 2015 - 06:52:22 PDT)
- Re: [AMBER] Problem cpptraj Bridging H-Bond analysis Daniel Roe (Mon Jul 20 2015 - 10:32:23 PDT)
[AMBER] CPPTRAJ - Filtering frames based on lowest of the two RMSD values Stevens, David (Mon Jul 20 2015 - 15:30:00 PDT)
- Re: [AMBER] CPPTRAJ - Filtering frames based on lowest of the two RMSD values Hai Nguyen (Mon Jul 20 2015 - 16:00:43 PDT)
- Re: [AMBER] CPPTRAJ - Filtering frames based on lowest of the two RMSD values Daniel Roe (Mon Jul 20 2015 - 16:40:53 PDT)
[AMBER] Gaff Parameters Si Sharapa (Mon Jul 20 2015 - 16:08:47 PDT)
- Re: [AMBER] Gaff Parameters Si David A Case (Tue Jul 21 2015 - 05:58:29 PDT)
  - Re: [AMBER] Gaff Parameters Si Sharapa (Thu Jul 30 2015 - 04:30:51 PDT)
[AMBER] GTX980Ti's now supported for AMBER and Exxact GTX780Tis available at discounted prices Ross Walker (Mon Jul 20 2015 - 17:16:54 PDT)
- Re: [AMBER] GTX980Ti's now supported for AMBER and Exxact GTX780Tis available at discounted prices Albert (Tue Jul 21 2015 - 02:11:12 PDT)
- Re: [AMBER] GTX980Ti's now supported for AMBER and Exxact GTX780Tis available at discounted prices David Abia (Tue Jul 21 2015 - 03:15:34 PDT)
[AMBER] MCPB.py Value / Syntax error Eleftherios A P Lambros (Mon Jul 20 2015 - 18:13:25 PDT)
- Re: [AMBER] MCPB.py Value / Syntax error Pengfei Li (Wed Jul 22 2015 - 14:18:24 PDT)
[AMBER] qm-mmgbsa error Ayesha Fatima (Mon Jul 20 2015 - 21:55:17 PDT)
- Re: [AMBER] qm-mmgbsa error Jason Swails (Tue Jul 21 2015 - 09:23:20 PDT)
  - Re: [AMBER] qm-mmgbsa error Ayesha Fatima (Tue Jul 21 2015 - 18:19:52 PDT)
    - Re: [AMBER] qm-mmgbsa error Jason Swails (Tue Jul 21 2015 - 18:27:16 PDT)
    - Re: [AMBER] qm-mmgbsa error Ayesha Fatima (Tue Jul 21 2015 - 22:59:19 PDT)
[AMBER] Unchanged coordinates in leap mish (Tue Jul 21 2015 - 02:13:07 PDT)
- Re: [AMBER] Unchanged coordinates in leap David A Case (Tue Jul 21 2015 - 06:05:50 PDT)
  - Re: [AMBER] Unchanged coordinates in leap mish (Wed Jul 22 2015 - 07:44:30 PDT)
[AMBER] PCA and motions visualization antonio.coluccia.uniroma1.it (Tue Jul 21 2015 - 02:59:54 PDT)
- Re: [AMBER] PCA and motions visualization Jason Swails (Tue Jul 21 2015 - 09:20:20 PDT)
- Re: [AMBER] PCA and motions visualization Daniel Roe (Tue Jul 21 2015 - 16:04:55 PDT)
[AMBER] "nstlim" is not reflected correctly in REMD with pmemd.MPI kurisaki (Tue Jul 21 2015 - 04:16:30 PDT)
- Re: [AMBER] "nstlim" is not reflected correctly in REMD with pmemd.MPI kurisaki (Tue Jul 21 2015 - 05:33:55 PDT)
- Re: [AMBER] "nstlim" is not reflected correctly in REMD with pmemd.MPI Gerald Monard (Tue Jul 21 2015 - 06:46:20 PDT)
[AMBER] MCPB.py N terminal error Jon Uranga (Tue Jul 21 2015 - 06:21:52 PDT)
- Re: [AMBER] MCPB.py N terminal error Takeshi Baba (Tue Jul 21 2015 - 07:34:19 PDT)
[AMBER] Testing the titratable group definition CpHMD Arjun Sharma (Tue Jul 21 2015 - 08:22:55 PDT)
- Re: [AMBER] Testing the titratable group definition CpHMD Jason Swails (Tue Jul 21 2015 - 09:13:58 PDT)
[AMBER] hbond cpptraj Lara rajam (Tue Jul 21 2015 - 08:26:31 PDT)
- Re: [AMBER] hbond cpptraj Daniel Roe (Tue Jul 21 2015 - 13:34:15 PDT)
[AMBER] Error in loading inpcrd file in sander Mohsen Zakeri (Tue Jul 21 2015 - 14:29:25 PDT)
- Re: [AMBER] Error in loading inpcrd file in sander Hai Nguyen (Tue Jul 21 2015 - 14:41:15 PDT)
  - Re: [AMBER] Error in loading inpcrd file in sander Mohsen Zakeri (Tue Jul 21 2015 - 15:06:14 PDT)
- Re: [AMBER] Error in loading inpcrd file in sander Daniel Roe (Tue Jul 21 2015 - 14:52:50 PDT)
  - Re: [AMBER] Error in loading inpcrd file in sander Mohsen Zakeri (Tue Jul 21 2015 - 15:08:49 PDT)
    - Re: [AMBER] Error in loading inpcrd file in sander Daniel Roe (Tue Jul 21 2015 - 15:24:30 PDT)
    - Re: [AMBER] Error in loading inpcrd file in sander Mohsen Zakeri (Tue Jul 21 2015 - 15:26:08 PDT)
[AMBER] QM/GBSA calculation failed Albert (Wed Jul 22 2015 - 00:25:17 PDT)
- Re: [AMBER] QM/GBSA calculation failed Jason Swails (Wed Jul 22 2015 - 04:38:37 PDT)
  - Re: [AMBER] QM/GBSA calculation failed Albert (Wed Jul 22 2015 - 07:24:57 PDT)
    - Re: [AMBER] QM/GBSA calculation failed Jason Swails (Wed Jul 22 2015 - 07:31:00 PDT)
[AMBER] Periodic Box Size and Charge Determination Aronica, Pietro (Wed Jul 22 2015 - 04:31:11 PDT)
- Re: [AMBER] Periodic Box Size and Charge Determination Jason Swails (Wed Jul 22 2015 - 05:22:39 PDT)
  - Re: [AMBER] Periodic Box Size and Charge Determination Aronica, Pietro (Wed Jul 22 2015 - 05:43:46 PDT)
    - Re: [AMBER] Periodic Box Size and Charge Determination Jason Swails (Wed Jul 22 2015 - 06:06:10 PDT)
    - Re: [AMBER] Periodic Box Size and Charge Determination Aronica, Pietro (Wed Jul 22 2015 - 08:02:23 PDT)
    - Re: [AMBER] Periodic Box Size and Charge Determination David A Case (Wed Jul 22 2015 - 09:51:29 PDT)
[AMBER] Explicit solvent pH-REMD whb (Wed Jul 22 2015 - 07:33:14 PDT)
- Re: [AMBER] Explicit solvent pH-REMD Jason Swails (Wed Jul 22 2015 - 09:47:37 PDT)
[AMBER] [cpptraj] Nativecontacts failing with long trajectory Juan Eiros Zamora (Wed Jul 22 2015 - 12:36:08 PDT)
- Re: [AMBER] [cpptraj] Nativecontacts failing with long trajectory Daniel Roe (Wed Jul 22 2015 - 13:53:18 PDT)
  - Re: [AMBER] [cpptraj] Nativecontacts failing with long trajectory Juan Eiros Zamora (Thu Jul 23 2015 - 00:59:57 PDT)
    - Re: [AMBER] [cpptraj] Nativecontacts failing with long trajectory Daniel Roe (Thu Jul 23 2015 - 08:48:54 PDT)
    - Re: [AMBER] [cpptraj] Nativecontacts failing with long trajectory Juan Eiros Zamora (Fri Jul 24 2015 - 03:21:30 PDT)
[AMBER] Amber for phophorylated residue Ziba Bahadori (Thu Jul 23 2015 - 03:12:19 PDT)
- Re: [AMBER] Amber for phophorylated residue David A Case (Thu Jul 23 2015 - 07:45:29 PDT)
  - Re: [AMBER] Amber for phophorylated residue Ziba Bahadori (Thu Jul 23 2015 - 08:27:39 PDT)
[AMBER] GTX Titan Xs slowing down after 200ns Mohamed Faizan Momin (Thu Jul 23 2015 - 07:12:37 PDT)
- Re: [AMBER] GTX Titan Xs slowing down after 200ns Ross Walker (Thu Jul 23 2015 - 07:41:12 PDT)
  - Re: [AMBER] GTX Titan Xs slowing down after 200ns Mohamed Faizan Momin (Thu Jul 23 2015 - 07:47:34 PDT)
    - Re: [AMBER] GTX Titan Xs slowing down after 200ns Ross Walker (Thu Jul 23 2015 - 07:51:31 PDT)
    - Re: [AMBER] GTX Titan Xs slowing down after 200ns Scott Le Grand (Thu Jul 23 2015 - 08:12:15 PDT)
    - Re: [AMBER] GTX Titan Xs slowing down after 200ns Mohamed Faizan Momin (Thu Jul 23 2015 - 08:26:42 PDT)
    - Re: [AMBER] GTX Titan Xs slowing down after 200ns Scott Le Grand (Thu Jul 23 2015 - 08:39:28 PDT)
    - Re: [AMBER] GTX Titan Xs slowing down after 200ns Mohamed Faizan Momin (Thu Jul 23 2015 - 08:46:11 PDT)
    - Re: [AMBER] GTX Titan Xs slowing down after 200ns Ross Walker (Thu Jul 23 2015 - 09:05:01 PDT)
    - Re: [AMBER] GTX Titan Xs slowing down after 200ns David A Case (Thu Jul 23 2015 - 11:14:17 PDT)
[AMBER] Using TIP4PEW amber FF in NAMD peter.schmidtke.discngine.servier.com (Fri Jul 24 2015 - 01:27:34 PDT)
- Re: [AMBER] Using TIP4PEW amber FF in NAMD peter.schmidtke.discngine.servier.com (Fri Jul 24 2015 - 05:13:18 PDT)
[AMBER] MPI_ABORT error Amber mail (Fri Jul 24 2015 - 05:28:02 PDT)
- Re: [AMBER] MPI_ABORT error Amber mail (Fri Jul 24 2015 - 05:33:12 PDT)
- Re: [AMBER] MPI_ABORT error Jason Swails (Fri Jul 24 2015 - 06:28:11 PDT)
  - Re: [AMBER] MPI_ABORT error Amber mail (Fri Jul 24 2015 - 06:43:52 PDT)
    - Re: [AMBER] MPI_ABORT error Jason Swails (Fri Jul 24 2015 - 12:24:36 PDT)
    - Re: [AMBER] MPI_ABORT error Amber mail (Fri Jul 24 2015 - 12:41:17 PDT)
    - Re: [AMBER] MPI_ABORT error Jason Swails (Fri Jul 24 2015 - 13:56:01 PDT)
[AMBER] impose restraint mask for specific residues Latorraca, Naomi Rose (Fri Jul 24 2015 - 11:09:02 PDT)
- Re: [AMBER] impose restraint mask for specific residues Jason Swails (Fri Jul 24 2015 - 12:30:04 PDT)
[AMBER] Speed of heating MD Amber mail (Sat Jul 25 2015 - 02:32:33 PDT)
- Re: [AMBER] Speed of heating MD Jason Swails (Sat Jul 25 2015 - 17:51:44 PDT)
  - Re: [AMBER] Speed of heating MD Amber mail (Sun Jul 26 2015 - 04:20:33 PDT)
[AMBER] GPU EVGA GTX 980 SC ACX M. Reza Ganjalikhany (Sat Jul 25 2015 - 04:48:36 PDT)
- Re: [AMBER] GPU EVGA GTX 980 SC ACX Ross Walker (Sat Jul 25 2015 - 07:59:16 PDT)
  - Re: [AMBER] GPU EVGA GTX 980 SC ACX M. Reza Ganjalikhany (Sat Jul 25 2015 - 08:50:27 PDT)
    - Re: [AMBER] GPU EVGA GTX 980 SC ACX Ross Walker (Sat Jul 25 2015 - 14:47:32 PDT)
[AMBER] MD simulation: cis isomer of peptide bond Michael Shokhen (Sun Jul 26 2015 - 09:07:07 PDT)
- Re: [AMBER] MD simulation: cis isomer of peptide bond Carlos Simmerling (Sun Jul 26 2015 - 09:43:23 PDT)
  - Re: [AMBER] MD simulation: cis isomer of peptide bond Michael Shokhen (Sun Jul 26 2015 - 10:34:38 PDT)
    - Re: [AMBER] MD simulation: cis isomer of peptide bond Carlos Simmerling (Sun Jul 26 2015 - 10:49:38 PDT)
    - Re: [AMBER] MD simulation: cis isomer of peptide bond Michael Shokhen (Sun Jul 26 2015 - 11:21:13 PDT)
    - Re: [AMBER] MD simulation: cis isomer of peptide bond Carlos Simmerling (Sun Jul 26 2015 - 11:24:33 PDT)
    - Re: [AMBER] MD simulation: cis isomer of peptide bond Michael Shokhen (Sun Jul 26 2015 - 12:00:51 PDT)
[AMBER] strange pbsa results Albert (Mon Jul 27 2015 - 02:54:45 PDT)
- Re: [AMBER] strange pbsa results Jason Swails (Mon Jul 27 2015 - 06:32:55 PDT)
[AMBER] Targeted Molecular dynamics in Amber ROOPALI VERMA (Mon Jul 27 2015 - 03:00:43 PDT)
- Re: [AMBER] Targeted Molecular dynamics in Amber Carlos Simmerling (Wed Jul 29 2015 - 07:12:57 PDT)
[AMBER] detecting and removing corrupted frames Thomas Evangelidis (Mon Jul 27 2015 - 03:32:23 PDT)
- Re: [AMBER] detecting and removing corrupted frames Daniel Roe (Mon Jul 27 2015 - 06:24:35 PDT)
[AMBER] which solvent model to use with solvateCap peter.schmidtke.discngine.servier.com (Mon Jul 27 2015 - 04:12:18 PDT)
- Re: [AMBER] which solvent model to use with solvateCap Jason Swails (Mon Jul 27 2015 - 07:19:10 PDT)
  - Re: [AMBER] which solvent model to use with solvateCap peter.schmidtke.discngine.servier.com (Mon Jul 27 2015 - 07:23:26 PDT)
    - Re: [AMBER] which solvent model to use with solvateCap Jason Swails (Mon Jul 27 2015 - 07:35:25 PDT)
[AMBER] How to combine distance and torsion restraint? Michael Shokhen (Mon Jul 27 2015 - 06:16:30 PDT)
- Re: [AMBER] How to combine distance and torsion restraint? Jason Swails (Mon Jul 27 2015 - 06:54:32 PDT)
[AMBER] Prep file for chiral position Nicholus Bhattacharjee (Mon Jul 27 2015 - 09:51:56 PDT)
- Re: [AMBER] Prep file for chiral position Carlos Simmerling (Mon Jul 27 2015 - 10:07:44 PDT)
  - Re: [AMBER] Prep file for chiral position Nicholus Bhattacharjee (Mon Jul 27 2015 - 10:37:14 PDT)
    - Re: [AMBER] Prep file for chiral position Carlos Simmerling (Mon Jul 27 2015 - 10:54:29 PDT)
[AMBER] MCPB.py mismatch error Eleftherios A P Lambros (Mon Jul 27 2015 - 12:36:35 PDT)
- Re: [AMBER] MCPB.py mismatch error Pengfei Li (Tue Jul 28 2015 - 20:26:56 PDT)
  - Re: [AMBER] MCPB.py mismatch error Pengfei Li (Fri Jul 31 2015 - 13:50:30 PDT)
    - Re: [AMBER] MCPB.py mismatch error Eleftherios A P Lambros (Mon Aug 03 2015 - 13:39:05 PDT)
[AMBER] Cluster restraints Damiano Spadoni (Tue Jul 28 2015 - 09:24:39 PDT)
- Re: [AMBER] Cluster restraints David A Case (Tue Jul 28 2015 - 17:49:47 PDT)
[AMBER] Restart of MMPBSA Osman, Roman (Tue Jul 28 2015 - 11:09:29 PDT)
- Re: [AMBER] Restart of MMPBSA Jason Swails (Tue Jul 28 2015 - 11:11:39 PDT)
[AMBER] Issues with running simulation after ParmEd conversion Rohith Mohan (Tue Jul 28 2015 - 16:30:26 PDT)
- Re: [AMBER] Issues with running simulation after ParmEd conversion Jason Swails (Wed Jul 29 2015 - 06:49:44 PDT)
- Re: [AMBER] Issues with running simulation after ParmEd conversion Rohith Mohan (Wed Jul 29 2015 - 14:06:47 PDT)
  - Re: [AMBER] Issues with running simulation after ParmEd conversion Jason Swails (Wed Jul 29 2015 - 18:30:26 PDT)
    - Re: [AMBER] Issues with running simulation after ParmEd conversion Rohith Mohan (Thu Jul 30 2015 - 13:06:11 PDT)
    - Re: [AMBER] Issues with running simulation after ParmEd conversion Jason Swails (Thu Jul 30 2015 - 13:53:14 PDT)
    - Re: [AMBER] Issues with running simulation after ParmEd conversion Rohith Mohan (Fri Jul 31 2015 - 13:49:14 PDT)
[AMBER] MM-GBSA at different temperature Shruti Koulgi (Tue Jul 28 2015 - 23:02:00 PDT)
- Re: [AMBER] MM-GBSA at different temperature Jason Swails (Wed Jul 29 2015 - 07:05:19 PDT)
[AMBER] Utilization of 3 GPUs suddenly drop to 0% and won't work any more 浅井賢 (Tue Jul 28 2015 - 23:35:38 PDT)
- Re: [AMBER] Utilization of 3 GPUs suddenly drop to 0% and won't work any more Ross Walker (Wed Jul 29 2015 - 07:31:45 PDT)
  - Re: [AMBER] Utilization of 3 GPUs suddenly drop to 0% and won't work any more 浅井賢 (Thu Jul 30 2015 - 23:36:37 PDT)
    - Re: [AMBER] Utilization of 3 GPUs suddenly drop to 0% and won't work any more Ross Walker (Fri Jul 31 2015 - 09:00:41 PDT)
[AMBER] how to center on ligand? Albert (Wed Jul 29 2015 - 07:25:35 PDT)
- Re: [AMBER] how to center on ligand? Jason Swails (Wed Jul 29 2015 - 07:28:30 PDT)
  - Re: [AMBER] how to center on ligand? Daniel Roe (Wed Jul 29 2015 - 07:49:00 PDT)
    - Re: [AMBER] how to center on ligand? Albert (Wed Jul 29 2015 - 08:50:38 PDT)
    - Re: [AMBER] how to center on ligand? Jason Swails (Wed Jul 29 2015 - 09:05:50 PDT)
    - Re: [AMBER] how to center on ligand? Albert (Wed Jul 29 2015 - 23:08:16 PDT)
    - Re: [AMBER] how to center on ligand? Daniel Roe (Thu Jul 30 2015 - 04:16:52 PDT)
[AMBER] Antechamber for boronic acid derivatives? Michael Shokhen (Thu Jul 30 2015 - 00:19:17 PDT)
- Re: [AMBER] Antechamber for boronic acid derivatives? David A Case (Mon Aug 03 2015 - 04:56:36 PDT)
  - Re: [AMBER] Antechamber for boronic acid derivatives? Michael Shokhen (Tue Aug 04 2015 - 04:26:06 PDT)
Re: [AMBER] Fwd: NMR restraints with pmemd.cuda problem Miroslav Krepl (Thu Jul 30 2015 - 02:43:04 PDT)
- Re: [AMBER] NMR restraints with pmemd.cuda problem Ross Walker (Thu Jul 30 2015 - 07:54:56 PDT)
[AMBER] Solvents that are not in a list. Sharapa (Thu Jul 30 2015 - 04:16:55 PDT)
[AMBER] multiple cpus per single gpu job Meij, Henk (Thu Jul 30 2015 - 08:11:13 PDT)
- Re: [AMBER] multiple cpus per single gpu job Ross Walker (Thu Jul 30 2015 - 09:06:37 PDT)
  - Re: [AMBER] multiple cpus per single gpu job Meij, Henk (Thu Jul 30 2015 - 10:04:48 PDT)
[AMBER] Explicit-solvent-pH-REMD whb (Fri Jul 31 2015 - 00:48:28 PDT)
- Re: [AMBER] Explicit-solvent-pH-REMD Jason Swails (Fri Jul 31 2015 - 05:16:56 PDT)
[AMBER] Regarding ADP molecule force fields Yogeeshwar Ajjugal (Fri Jul 31 2015 - 02:41:24 PDT)
- Re: [AMBER] Regarding ADP molecule force fields Jason Swails (Fri Jul 31 2015 - 05:19:26 PDT)
[AMBER] mdfrc units Georgios Gerogiokas (Fri Jul 31 2015 - 06:41:04 PDT)
- Re: [AMBER] mdfrc units Jason Swails (Fri Jul 31 2015 - 06:58:12 PDT)
[AMBER] cudaMemcpy GpuBuffer::Download failed - hardware or software? Eugene Radchenko (Sat Aug 01 2015 - 13:30:14 PDT)
- Re: [AMBER] cudaMemcpy GpuBuffer::Download failed - hardware orsoftware? Eugene Radchenko (Sun Aug 02 2015 - 01:52:04 PDT)
  - Re: [AMBER] cudaMemcpy GpuBuffer::Download failed - hardware orsoftware? Ross Walker (Sun Aug 02 2015 - 20:22:45 PDT)
    - Re: [AMBER] cudaMemcpy GpuBuffer::Download failed - hardwareorsoftware? Eugene Radchenko (Sun Aug 02 2015 - 23:56:46 PDT)
    - Re: [AMBER] cudaMemcpy GpuBuffer::Download failed - hardwareorsoftware? Ross Walker (Mon Aug 03 2015 - 12:54:35 PDT)
[AMBER] algorithm for clustering solvent molecules? Jose Borreguero (Sat Aug 01 2015 - 18:23:42 PDT)
- Re: [AMBER] algorithm for clustering solvent molecules? Jason Swails (Mon Aug 03 2015 - 07:00:18 PDT)
  - Re: [AMBER] algorithm for clustering solvent molecules? Jose Borreguero (Mon Aug 03 2015 - 09:57:08 PDT)
    - Re: [AMBER] algorithm for clustering solvent molecules? Jason Swails (Mon Aug 03 2015 - 10:17:09 PDT)
    - Re: [AMBER] algorithm for clustering solvent molecules? Jose Borreguero (Mon Aug 03 2015 - 12:21:09 PDT)
    - Re: [AMBER] algorithm for clustering solvent molecules? Jason Swails (Mon Aug 03 2015 - 12:31:21 PDT)
    - Re: [AMBER] algorithm for clustering solvent molecules? Hai Nguyen (Mon Aug 03 2015 - 13:48:24 PDT)
    - Re: [AMBER] algorithm for clustering solvent molecules? Jose Borreguero (Mon Aug 03 2015 - 14:35:57 PDT)
    - Re: [AMBER] algorithm for clustering solvent molecules? Hai Nguyen (Mon Aug 03 2015 - 14:43:39 PDT)
    - Re: [AMBER] algorithm for clustering solvent molecules? Jose Borreguero (Mon Aug 03 2015 - 15:07:23 PDT)
[AMBER] Implicit solvent simulation is unexpectedly slow 浅井賢 (Sun Aug 02 2015 - 01:21:43 PDT)
- Re: [AMBER] Implicit solvent simulation is unexpectedly slow David A Case (Sun Aug 02 2015 - 05:30:43 PDT)
  - Re: [AMBER] Implicit solvent simulation is unexpectedly slow 浅井賢 (Sun Aug 02 2015 - 06:59:57 PDT)
[AMBER] Does the "contacts" command of cpptraj implement imaging? Jose Borreguero (Sun Aug 02 2015 - 15:47:19 PDT)
- Re: [AMBER] Does the "contacts" command of cpptraj implement imaging? Jason Swails (Mon Aug 03 2015 - 06:07:30 PDT)
  - Re: [AMBER] Does the "contacts" command of cpptraj implement imaging? Jose Borreguero (Mon Aug 03 2015 - 09:53:04 PDT)
[AMBER] PCA: generate histogram George Tzotzos (Mon Aug 03 2015 - 03:46:55 PDT)
- Re: [AMBER] PCA: generate histogram Daniel Roe (Mon Aug 03 2015 - 06:14:52 PDT)
  - Re: [AMBER] PCA: generate histogram George Tzotzos (Mon Aug 03 2015 - 06:48:32 PDT)
    - Re: [AMBER] PCA: generate histogram Daniel Roe (Mon Aug 03 2015 - 07:01:30 PDT)
    - Re: [AMBER] PCA: generate histogram George Tzotzos (Mon Aug 03 2015 - 07:04:28 PDT)
    - Re: [AMBER] PCA: generate histogram Daniel Roe (Mon Aug 03 2015 - 07:47:48 PDT)
[AMBER] FW: PMEMD: Warning: ieee_inexact is signaling Khabiri, Morteza (Mon Aug 03 2015 - 06:26:01 PDT)
- Re: [AMBER] FW: PMEMD: Warning: ieee_inexact is signaling Jason Swails (Mon Aug 03 2015 - 08:19:11 PDT)
[AMBER] Installation of AmberTools 15. Overriding earlier installation George Tzotzos (Mon Aug 03 2015 - 12:26:25 PDT)
- Re: [AMBER] Installation of AmberTools 15. Overriding earlier installation Jason Swails (Mon Aug 03 2015 - 12:35:50 PDT)
Re: [AMBER] PMEMD: Warning: ieee_inexact is signaling Khabiri, Morteza (Mon Aug 03 2015 - 12:40:14 PDT)
- Re: [AMBER] PMEMD: Warning: ieee_inexact is signaling Daniel Roe (Mon Aug 03 2015 - 12:59:58 PDT)
[AMBER] MM-PBSA free energy calculation with keeping x-ray water bharat lakhani (Mon Aug 03 2015 - 12:45:26 PDT)
- Re: [AMBER] MM-PBSA free energy calculation with keeping x-ray water Kenneth Huang (Mon Aug 03 2015 - 12:57:14 PDT)
[AMBER] MM-PBSA atom types bharat lakhani (Mon Aug 03 2015 - 15:24:53 PDT)
- Re: [AMBER] MM-PBSA atom types Jason Swails (Mon Aug 03 2015 - 15:37:59 PDT)
  - Re: [AMBER] MM-PBSA atom types bharat lakhani (Mon Aug 03 2015 - 15:50:47 PDT)
    - Re: [AMBER] MM-PBSA atom types bharat lakhani (Tue Aug 04 2015 - 08:40:42 PDT)
    - Re: [AMBER] MM-PBSA atom types Kenneth Huang (Tue Aug 04 2015 - 09:09:13 PDT)
    - Re: [AMBER] MM-PBSA atom types Jason Swails (Tue Aug 04 2015 - 09:09:18 PDT)
    - Re: [AMBER] MM-PBSA atom types bharat lakhani (Wed Aug 05 2015 - 11:32:41 PDT)
[AMBER] Bad Atom type during running MMPBSA with cobalt metal ion MOHD HOMAIDUR RAHMAN (Mon Aug 03 2015 - 23:23:36 PDT)
- Re: [AMBER] Bad Atom type during running MMPBSA with cobalt metal ion Jason Swails (Tue Aug 04 2015 - 05:52:14 PDT)
  - Re: [AMBER] Bad Atom type during running MMPBSA with cobalt metal ion MOHD HOMAIDUR RAHMAN (Tue Aug 04 2015 - 22:51:41 PDT)
    - Re: [AMBER] Bad Atom type during running MMPBSA with cobalt metal ion Hai Nguyen (Tue Aug 04 2015 - 22:54:57 PDT)
[AMBER] Trying to perform a heating MD in increments Amber mail (Tue Aug 04 2015 - 01:39:02 PDT)
- Re: [AMBER] Trying to perform a heating MD in increments Abelak, Kavin (Tue Aug 04 2015 - 03:13:19 PDT)
  - Re: [AMBER] Trying to perform a heating MD in increments Jason Swails (Tue Aug 04 2015 - 05:55:30 PDT)
    - Re: [AMBER] Trying to perform a heating MD in increments Amber mail (Tue Aug 04 2015 - 07:02:03 PDT)
[AMBER] MMPBSA.py problem Debodyuti Dutta (Tue Aug 04 2015 - 03:16:45 PDT)
- Re: [AMBER] MMPBSA.py problem s. Bill (Mon Mar 15 2010 - 02:00:23 PDT)
  - Re: [AMBER] MMPBSA.py problem Billy Miller III (Mon Mar 15 2010 - 05:53:57 PDT)
- Re: [AMBER] MMPBSA.py problem Jason Swails (Tue Aug 04 2015 - 06:22:10 PDT)
  - Re: [AMBER] MMPBSA.py problem psu4.uic.edu (Tue Aug 04 2015 - 10:46:09 PDT)
[AMBER] How to construct the Ala3 peptide shown in this picture? lipengfei_mail (Tue Aug 04 2015 - 05:12:38 PDT)
- Re: [AMBER] How to construct the Ala3 peptide shown in this picture? Jason Swails (Tue Aug 04 2015 - 05:50:16 PDT)
- Re: [AMBER] How to construct the Ala3 peptide shown in this picture? David A Case (Tue Aug 04 2015 - 06:06:35 PDT)
[AMBER] ired analysis: No modes data specified Kris Feher (Tue Aug 04 2015 - 05:23:53 PDT)
- Re: [AMBER] ired analysis: No modes data specified David A Case (Tue Aug 04 2015 - 06:44:13 PDT)
  - Re: [AMBER] ired analysis: No modes data specified Kris Feher (Tue Aug 04 2015 - 10:07:04 PDT)
[AMBER] PCA analysis anu chandra (Tue Aug 04 2015 - 15:55:05 PDT)
- Re: [AMBER] PCA analysis Daniel Roe (Tue Aug 04 2015 - 19:10:47 PDT)
[AMBER] NaN with pmemd.cuda Joseph Baker (Tue Aug 04 2015 - 21:43:22 PDT)
- Re: [AMBER] NaN with pmemd.cuda Gould, Ian R (Tue Aug 04 2015 - 22:14:27 PDT)
  - Re: [AMBER] NaN with pmemd.cuda Joseph Baker (Wed Aug 05 2015 - 12:00:58 PDT)
    - Re: [AMBER] NaN with pmemd.cuda Jason Swails (Wed Aug 05 2015 - 17:10:32 PDT)
    - Re: [AMBER] NaN with pmemd.cuda Joseph Baker (Wed Aug 05 2015 - 19:41:55 PDT)
    - Re: [AMBER] NaN with pmemd.cuda koushik kasavajhala (Wed Aug 05 2015 - 20:29:57 PDT)
    - Re: [AMBER] NaN with pmemd.cuda Ross Walker (Thu Aug 06 2015 - 00:46:39 PDT)
    - Re: [AMBER] NaN with pmemd.cuda Joseph Baker (Thu Aug 06 2015 - 11:59:32 PDT)
    - Re: [AMBER] NaN with pmemd.cuda Scott Le Grand (Fri Aug 07 2015 - 01:26:10 PDT)
[AMBER] Regarding DNA forcefield in Amber14 Pragya Priyadarshini (Wed Aug 05 2015 - 00:35:34 PDT)
- Re: [AMBER] Regarding DNA forcefield in Amber14 Vlad Cojocaru (Wed Aug 05 2015 - 01:25:06 PDT)
  - Re: [AMBER] Regarding DNA forcefield in Amber14 Vlad Cojocaru (Wed Aug 05 2015 - 01:40:11 PDT)
    - Re: [AMBER] Regarding DNA forcefield in Amber14 Mahad Gatti Iou (Wed Aug 05 2015 - 05:47:30 PDT)
    - Re: [AMBER] Regarding DNA forcefield in Amber14 Vlad Cojocaru (Wed Aug 05 2015 - 06:03:05 PDT)
    - Re: [AMBER] Regarding DNA forcefield in Amber14 Thomas Cheatham (Thu Aug 06 2015 - 18:31:22 PDT)
    - Re: [AMBER] Regarding DNA forcefield in Amber14 Vlad Cojocaru (Fri Aug 07 2015 - 00:55:30 PDT)
- Re: [AMBER] Regarding DNA forcefield in Amber14 Hai Nguyen (Wed Aug 05 2015 - 05:48:22 PDT)
  - Re: [AMBER] Regarding DNA forcefield in Amber14 Mahad Gatti Iou (Wed Aug 05 2015 - 05:59:51 PDT)
    - Re: [AMBER] Regarding DNA forcefield in Amber14 Nhai (Wed Aug 05 2015 - 06:07:45 PDT)
[AMBER] PCA: comparing PCs from different trajectories George Tzotzos (Wed Aug 05 2015 - 01:24:45 PDT)
- Re: [AMBER] PCA: comparing PCs from different trajectories Daniel Roe (Wed Aug 05 2015 - 10:16:24 PDT)
  - Re: [AMBER] PCA: comparing PCs from different trajectories George Tzotzos (Wed Aug 05 2015 - 10:39:05 PDT)
    - Re: [AMBER] PCA: comparing PCs from different trajectories Daniel Roe (Wed Aug 05 2015 - 11:18:55 PDT)
    - Re: [AMBER] PCA: comparing PCs from different trajectories George Tzotzos (Thu Aug 06 2015 - 07:18:08 PDT)
    - Re: [AMBER] PCA: comparing PCs from different trajectories Eiros Zamora, Juan (Thu Aug 06 2015 - 09:32:48 PDT)
    - Re: [AMBER] PCA: comparing PCs from different trajectories Daniel Roe (Thu Aug 06 2015 - 13:06:45 PDT)
[AMBER] MMPBSA_Ras-Raf complex tutorial Ruchika Bhat (Wed Aug 05 2015 - 06:48:17 PDT)
[AMBER] antechamber error Lara rajam (Wed Aug 05 2015 - 07:27:08 PDT)
- Re: [AMBER] antechamber error David A Case (Wed Aug 05 2015 - 09:19:09 PDT)
[AMBER] .mdcrd to .trr conversion problem Vishal Nemaysh (Wed Aug 05 2015 - 08:41:51 PDT)
- Re: [AMBER] .mdcrd to .trr conversion problem Hai Nguyen (Wed Aug 05 2015 - 08:47:37 PDT)
  - Re: [AMBER] .mdcrd to .trr conversion problem Hai Nguyen (Wed Aug 05 2015 - 08:48:51 PDT)
    - Re: [AMBER] .mdcrd to .trr conversion problem Daniel Roe (Wed Aug 05 2015 - 09:09:13 PDT)
[AMBER] [cpptraj] Kullback Leibler Divergence cutoff choice Eiros Zamora, Juan (Wed Aug 05 2015 - 09:01:18 PDT)
- Re: [AMBER] [cpptraj] Kullback Leibler Divergence cutoff choice Adrian Roitberg (Wed Aug 05 2015 - 09:09:45 PDT)
  - Re: [AMBER] [cpptraj] Kullback Leibler Divergence cutoff choice Eiros Zamora, Juan (Wed Aug 05 2015 - 09:23:44 PDT)
- Re: [AMBER] [cpptraj] Kullback Leibler Divergence cutoff choice Daniel Roe (Wed Aug 05 2015 - 10:31:31 PDT)
[AMBER] issue with 4 fs hydrogen mass repartitioning taking more time than a standard 2 fs simulation in AMBER14 George Green (Wed Aug 05 2015 - 16:28:31 PDT)
- Re: [AMBER] issue with 4 fs hydrogen mass repartitioning taking more time than a standard 2 fs simulation in AMBER14 Adrian Roitberg (Wed Aug 05 2015 - 16:34:10 PDT)
  - Re: [AMBER] issue with 4 fs hydrogen mass repartitioning taking more time than a standard 2 fs simulation in AMBER14 Jason Swails (Wed Aug 05 2015 - 17:03:14 PDT)
    - Re: [AMBER] issue with 4 fs hydrogen mass repartitioning taking more time than a standard 2 fs simulation in AMBER14 George Green (Wed Aug 05 2015 - 17:27:23 PDT)
[AMBER] Thermodynamic integration goes wrong in lambda =0 while lambda = 1 is ok!! Khabiri, Morteza (Wed Aug 05 2015 - 18:34:39 PDT)
- Re: [AMBER] Thermodynamic integration goes wrong in lambda =0 while lambda = 1 is ok!! Ying-Chieh Sun (Wed Aug 05 2015 - 20:29:23 PDT)
- Re: [AMBER] Thermodynamic integration goes wrong in lambda =0 while lambda = 1 is ok!! David A Case (Thu Aug 06 2015 - 05:35:01 PDT)
- [AMBER] Thermodynamic integration goes wrong in lambda =0 while lambda = 1 is ok!! Khabiri, Morteza (Thu Aug 06 2015 - 07:43:17 PDT)
  - Re: [AMBER] Thermodynamic integration goes wrong in lambda =0 while lambda = 1 is ok!! David A Case (Thu Aug 06 2015 - 09:55:44 PDT)
[AMBER] RED Server for Altered Amino Acid Edward Kalkreuter (Wed Aug 05 2015 - 19:56:11 PDT)
[AMBER] large .mdcrd splitting Vishal Nemaysh (Thu Aug 06 2015 - 00:49:02 PDT)
- Re: [AMBER] large .mdcrd splitting Daniel Roe (Thu Aug 06 2015 - 04:39:35 PDT)
  - Re: [AMBER] large .mdcrd splitting Hai Nguyen (Thu Aug 06 2015 - 10:44:54 PDT)
- Re: [AMBER] large .mdcrd splitting David A Case (Thu Aug 06 2015 - 05:38:20 PDT)
[AMBER] could not open mdcrd file Vahid Kshani (Thu Aug 06 2015 - 04:22:21 PDT)
- Re: [AMBER] could not open mdcrd file Daniel Roe (Thu Aug 06 2015 - 04:32:49 PDT)
  - Re: [AMBER] could not open mdcrd file Vahid Kshani (Fri Aug 07 2015 - 00:05:55 PDT)
[AMBER] Problem with cpptraj autoimage command Karolina Markowska (Thu Aug 06 2015 - 04:35:59 PDT)
- Re: [AMBER] Problem with cpptraj autoimage command Jason Swails (Thu Aug 06 2015 - 06:19:53 PDT)
  - Re: [AMBER] Problem with cpptraj autoimage command Daniel Roe (Thu Aug 06 2015 - 07:29:35 PDT)
  - Re: [AMBER] Problem with cpptraj autoimage command Karolina Markowska (Fri Aug 07 2015 - 02:35:48 PDT)
    - Re: [AMBER] Problem with cpptraj autoimage command Daniel Roe (Fri Aug 07 2015 - 06:18:33 PDT)
    - Re: [AMBER] Problem with cpptraj autoimage command Karolina Markowska (Fri Aug 07 2015 - 13:48:25 PDT)
[AMBER] SPAM Sarah Graham (Thu Aug 06 2015 - 11:06:23 PDT)
- Re: [AMBER] SPAM Jason Swails (Tue Aug 11 2015 - 06:39:24 PDT)
[AMBER] "mask" command failure Ucisik, Melek Nihan (Thu Aug 06 2015 - 14:26:40 PDT)
- Re: [AMBER] "mask" command failure Hai Nguyen (Thu Aug 06 2015 - 17:26:45 PDT)
- Re: [AMBER] "mask" command failure Daniel Roe (Thu Aug 06 2015 - 19:42:45 PDT)
  - Re: [AMBER] "mask" command failure Hai Nguyen (Thu Aug 06 2015 - 19:46:59 PDT)
    - Re: [AMBER] "mask" command failure Daniel Roe (Thu Aug 06 2015 - 19:51:49 PDT)
    - Re: [AMBER] "mask" command failure Jason Swails (Thu Aug 06 2015 - 23:21:08 PDT)
    - Re: [AMBER] "mask" command failure Ucisik, Melek Nihan (Fri Aug 07 2015 - 09:20:54 PDT)
    - Re: [AMBER] "mask" command failure Ucisik, Melek Nihan (Sun Aug 09 2015 - 13:37:06 PDT)
    - Re: [AMBER] "mask" command failure Daniel Roe (Mon Aug 10 2015 - 10:16:13 PDT)
    - Re: [AMBER] "mask" command failure Ucisik, Melek Nihan (Tue Aug 11 2015 - 08:20:38 PDT)
    - Re: [AMBER] "mask" command failure Daniel Roe (Tue Aug 11 2015 - 12:25:24 PDT)
[AMBER] parmch2 versus parmchk CHAMI F. (Fri Aug 07 2015 - 06:00:23 PDT)
[AMBER] awards applications open for ACS Division of Computers in Chemistry Carlos Simmerling (Fri Aug 07 2015 - 08:33:37 PDT)
[AMBER] MMPBSA error using pbsa2 shenna shearin (Fri Aug 07 2015 - 17:33:56 PDT)
- Re: [AMBER] MMPBSA error using pbsa2 Ray Luo, Ph.D. (Fri Aug 07 2015 - 20:59:12 PDT)
  - Re: [AMBER] MMPBSA error using pbsa2 shenna shearin (Sun Aug 09 2015 - 04:38:24 PDT)
    - Re: [AMBER] MMPBSA error using pbsa2 Kenneth Huang (Sun Aug 09 2015 - 12:09:17 PDT)
    - Re: [AMBER] MMPBSA error using pbsa2 Ray Luo, Ph.D. (Sun Aug 09 2015 - 22:11:25 PDT)
[AMBER] Automated restart Eugene Radchenko (Sat Aug 08 2015 - 03:40:50 PDT)
- Re: [AMBER] Automated restart David A Case (Sat Aug 08 2015 - 05:42:16 PDT)
  - Re: [AMBER] Automated restart Eugene Radchenko (Sat Aug 08 2015 - 11:25:27 PDT)
    - Re: [AMBER] Automated restart Jason Swails (Sat Aug 08 2015 - 12:03:53 PDT)
[AMBER] cpptraj - RMSD Amber mail (Sat Aug 08 2015 - 23:51:02 PDT)
- Re: [AMBER] cpptraj - RMSD David A Case (Sun Aug 09 2015 - 05:02:44 PDT)
  - Re: [AMBER] cpptraj - RMSD Amber mail (Sun Aug 09 2015 - 13:50:33 PDT)
    - Re: [AMBER] cpptraj - RMSD Hai Nguyen (Sun Aug 09 2015 - 14:15:51 PDT)
    - Re: [AMBER] cpptraj - RMSD Hai Nguyen (Sun Aug 09 2015 - 16:01:51 PDT)
[AMBER] cpptraj gist: Eww energies Thomas Fox (Mon Aug 10 2015 - 02:49:21 PDT)
- Re: [AMBER] cpptraj gist: Eww energies Tom Kurtzman (Mon Aug 10 2015 - 07:59:44 PDT)
  - Re: [AMBER] cpptraj gist: Eww energies Jason Swails (Mon Aug 10 2015 - 08:21:59 PDT)
- Re: [AMBER] cpptraj gist: Eww energies Nguyen, Crystal (Mon Aug 10 2015 - 08:42:30 PDT)
- Re: [AMBER] cpptraj gist: Eww energies Steven Ramsey (Mon Aug 10 2015 - 09:35:00 PDT)
- Re: [AMBER] cpptraj gist: Eww energies Daniel Roe (Mon Aug 10 2015 - 10:12:57 PDT)
  - Re: [AMBER] cpptraj gist: Eww energies Tom Kurtzman (Mon Aug 10 2015 - 10:54:49 PDT)
    - Re: [AMBER] cpptraj gist: Eww energies Thomas Fox (Wed Aug 12 2015 - 08:31:09 PDT)
[AMBER] mmpbsa.py: Error George Tzotzos (Mon Aug 10 2015 - 09:49:29 PDT)
- Re: [AMBER] mmpbsa.py: Error Jason Swails (Mon Aug 10 2015 - 10:22:13 PDT)
  - Re: [AMBER] mmpbsa.py: Error George Tzotzos (Mon Aug 10 2015 - 10:23:09 PDT)
- Re: [AMBER] mmpbsa.py: Error Kenneth Huang (Mon Aug 10 2015 - 10:23:36 PDT)
  - Re: [AMBER] mmpbsa.py: Error George Tzotzos (Mon Aug 10 2015 - 10:37:10 PDT)
    - Re: [AMBER] mmpbsa.py: Error Kenneth Huang (Mon Aug 10 2015 - 11:43:10 PDT)
    - Re: [AMBER] mmpbsa.py: Error George Tzotzos (Mon Aug 10 2015 - 12:00:39 PDT)
    - [AMBER] mmpbsa.py: Error Kenneth Huang (Mon Aug 10 2015 - 12:30:00 PDT)
    - Re: [AMBER] mmpbsa.py: Error George Tzotzos (Mon Aug 10 2015 - 12:56:12 PDT)
    - Re: [AMBER] mmpbsa.py: Error Jason Swails (Mon Aug 10 2015 - 13:11:23 PDT)
[AMBER] FW: Regarding AMBER 14 praSanna kuMar naYak (Tue Aug 11 2015 - 01:47:38 PDT)
- Re: [AMBER] FW: Regarding AMBER 14 David A Case (Tue Aug 11 2015 - 04:41:18 PDT)
  - Re: [AMBER] FW: Regarding AMBER 14 praSanna kuMar naYak (Tue Aug 11 2015 - 04:59:48 PDT)
    - Re: [AMBER] FW: Regarding AMBER 14 Kenneth Huang (Tue Aug 11 2015 - 06:05:07 PDT)
    - Re: [AMBER] FW: Regarding AMBER 14 Jason Swails (Tue Aug 11 2015 - 06:10:54 PDT)
    - Re: [AMBER] FW: Regarding AMBER 14 praSanna kuMar naYak (Tue Aug 11 2015 - 06:23:25 PDT)
    - Re: [AMBER] FW: Regarding AMBER 14 Jason Swails (Tue Aug 11 2015 - 06:31:22 PDT)
    - Re: [AMBER] FW: Regarding AMBER 14 praSanna kuMar naYak (Wed Aug 12 2015 - 00:04:10 PDT)
    - Re: [AMBER] FW: Regarding AMBER 14 Jason Swails (Wed Aug 12 2015 - 04:00:56 PDT)
    - Re: [AMBER] FW: Regarding AMBER 14 praSanna kuMar naYak (Wed Aug 12 2015 - 04:26:51 PDT)
[AMBER] FW: Regarding AMBER14 Error praSanna kuMar naYak (Tue Aug 11 2015 - 01:47:52 PDT)
- Re: [AMBER] FW: Regarding AMBER14 Error David A Case (Tue Aug 11 2015 - 04:42:16 PDT)
[AMBER] PB Bomb in pb_aaradi(): No radius assigned for atom Sangita Kachhap (Tue Aug 11 2015 - 03:05:20 PDT)
- Re: [AMBER] PB Bomb in pb_aaradi(): No radius assigned for atom Jason Swails (Tue Aug 11 2015 - 04:53:13 PDT)
  - Re: [AMBER] PB Bomb in pb_aaradi(): No radius assigned for atom Sangita Kachhap (Tue Aug 11 2015 - 05:09:01 PDT)
    - Re: [AMBER] PB Bomb in pb_aaradi(): No radius assigned for atom Jason Swails (Tue Aug 11 2015 - 06:04:03 PDT)
    - Re: [AMBER] PB Bomb in pb_aaradi(): No radius assigned for atom Sangita Kachhap (Tue Aug 11 2015 - 07:15:08 PDT)
    - Re: [AMBER] PB Bomb in pb_aaradi(): No radius assigned for atom Jason Swails (Tue Aug 11 2015 - 07:43:55 PDT)
    - Re: [AMBER] PB Bomb in pb_aaradi(): No radius assigned for atom Sangita Kachhap (Tue Aug 11 2015 - 08:08:37 PDT)
    - Re: [AMBER] PB Bomb in pb_aaradi(): No radius assigned for atom Jason Swails (Tue Aug 11 2015 - 08:44:55 PDT)
    - Re: [AMBER] PB Bomb in pb_aaradi(): No radius assigned for atom Sangita Kachhap (Tue Aug 11 2015 - 09:13:30 PDT)
[AMBER] AMBER 14 installation Problem Himansu (Tue Aug 11 2015 - 03:23:45 PDT)
[AMBER] Overflow of the Fortran format used to store coordinates in the inpcrd/restart files. Amber mail (Tue Aug 11 2015 - 10:18:16 PDT)
- Re: [AMBER] Overflow of the Fortran format used to store coordinates in the inpcrd/restart files. Jason Swails (Tue Aug 11 2015 - 10:26:27 PDT)
  - Re: [AMBER] Overflow of the Fortran format used to store coordinates in the inpcrd/restart files. Amber mail (Tue Aug 11 2015 - 10:33:45 PDT)
- Re: [AMBER] Overflow of the Fortran format used to store coordinates in the inpcrd/restart files. Adrian Roitberg (Tue Aug 11 2015 - 11:46:44 PDT)
  - Re: [AMBER] Overflow of the Fortran format used to store coordinates in the inpcrd/restart files. Daniel Roe (Tue Aug 11 2015 - 12:03:09 PDT)
    - Re: [AMBER] Overflow of the Fortran format used to store coordinates in the inpcrd/restart files. Amber mail (Tue Aug 11 2015 - 13:53:05 PDT)
    - Re: [AMBER] Overflow of the Fortran format used to store coordinates in the inpcrd/restart files. Jason Swails (Tue Aug 11 2015 - 15:00:03 PDT)
    - Re: [AMBER] Overflow of the Fortran format used to store coordinates in the inpcrd/restart files. Amber mail (Wed Aug 12 2015 - 06:34:40 PDT)
    - Re: [AMBER] Overflow of the Fortran format used to store coordinates in the inpcrd/restart files. Jason Swails (Wed Aug 12 2015 - 06:53:47 PDT)
[AMBER] using chamber to convert psf to prmtop KK R (Tue Aug 11 2015 - 13:08:42 PDT)
- Re: [AMBER] using chamber to convert psf to prmtop Jason Swails (Tue Aug 11 2015 - 15:02:15 PDT)
[AMBER] Macromolecular crowding force-field and parameters richa anand (Tue Aug 11 2015 - 20:55:40 PDT)
- Re: [AMBER] Macromolecular crowding force-field and parameters Lijuan Yu (Wed Aug 12 2015 - 21:15:55 PDT)
[AMBER] acetylate and ammoniate mohammad r (Wed Aug 12 2015 - 05:23:39 PDT)
- Re: [AMBER] acetylate and ammoniate Jason Swails (Wed Aug 12 2015 - 06:10:30 PDT)
  - Re: [AMBER] acetylate and ammoniate mohammad r (Wed Aug 12 2015 - 08:04:20 PDT)
    - Re: [AMBER] acetylate and ammoniate David A Case (Wed Aug 12 2015 - 08:39:54 PDT)
    - Re: [AMBER] acetylate and ammoniate mohammad r (Thu Aug 13 2015 - 00:06:16 PDT)
    - Re: [AMBER] acetylate and ammoniate Jason Swails (Thu Aug 13 2015 - 04:23:38 PDT)
[AMBER] Warning: ieee_inexact is signaling PMEMD Terminated Abnormally! Khabiri, Morteza (Wed Aug 12 2015 - 06:36:57 PDT)
- Re: [AMBER] Warning: ieee_inexact is signaling PMEMD Terminated Abnormally! Daniel Roe (Wed Aug 12 2015 - 08:18:21 PDT)
- Re: [AMBER] Warning: ieee_inexact is signaling PMEMD Terminated Abnormally! Khabiri, Morteza (Wed Aug 12 2015 - 09:43:14 PDT)
  - Re: [AMBER] Warning: ieee_inexact is signaling PMEMD Terminated Abnormally! Daniel Roe (Wed Aug 12 2015 - 09:58:05 PDT)
  - Re: [AMBER] Warning: ieee_inexact is signaling PMEMD Terminated Abnormally! Khabiri, Morteza (Wed Aug 12 2015 - 11:06:34 PDT)
[AMBER] cpptraj frames clustering limit Gaurao Dhoke (Wed Aug 12 2015 - 06:46:07 PDT)
- Re: [AMBER] cpptraj frames clustering limit Amber mail (Wed Aug 12 2015 - 06:55:03 PDT)
- Re: [AMBER] cpptraj frames clustering limit Jason Swails (Wed Aug 12 2015 - 06:59:58 PDT)
  - Re: [AMBER] cpptraj frames clustering limit Daniel Roe (Wed Aug 12 2015 - 08:06:15 PDT)
    - Re: [AMBER] cpptraj frames clustering limit Gaurao Dhoke (Thu Aug 13 2015 - 01:28:01 PDT)
    - Re: [AMBER] cpptraj frames clustering limit Daniel Roe (Thu Aug 13 2015 - 11:43:25 PDT)
[AMBER] GIST vs. 3D-RISM Thomas Fox (Wed Aug 12 2015 - 08:36:45 PDT)
- Re: [AMBER] GIST vs. 3D-RISM Nguyen, Crystal (Wed Aug 12 2015 - 11:01:26 PDT)
  - Re: [AMBER] GIST vs. 3D-RISM Tyler Luchko (Lists) (Wed Aug 12 2015 - 14:30:25 PDT)
[AMBER] cg in GAFF: amb2gmx.pl vs virtualchemistry - LJ well depth Sharapa (Wed Aug 12 2015 - 15:01:40 PDT)
- Re: [AMBER] cg in GAFF: amb2gmx.pl vs virtualchemistry - LJ well depth David A Case (Wed Aug 12 2015 - 18:16:16 PDT)
[AMBER] amber14 gpu webpage lists cuda 7.0 as supported Dow Hurst (Wed Aug 12 2015 - 18:53:11 PDT)
- Re: [AMBER] amber14 gpu webpage lists cuda 7.0 as supported diane lynch (Wed Aug 12 2015 - 19:01:56 PDT)
[AMBER] [Solved] amber14 gpu webpage lists cuda 7.0 as supported Dow Hurst (Wed Aug 12 2015 - 18:59:31 PDT)
- Re: [AMBER] [Solved] amber14 gpu webpage lists cuda 7.0 as supported diane lynch (Wed Aug 12 2015 - 19:02:36 PDT)
[AMBER] Force-field and parameters richa anand (Wed Aug 12 2015 - 21:32:06 PDT)
[AMBER] pH-REMD theory whb (Wed Aug 12 2015 - 23:58:47 PDT)
- Re: [AMBER] pH-REMD theory Jason Swails (Thu Aug 13 2015 - 05:43:41 PDT)
[AMBER] Imaging and connectivity error Harmeet Kaur (Thu Aug 13 2015 - 04:27:24 PDT)
- Re: [AMBER] Imaging and connectivity error Jason Swails (Thu Aug 13 2015 - 07:06:29 PDT)
[AMBER] dynlmb and TI Khabiri, Morteza (Thu Aug 13 2015 - 11:36:11 PDT)
[AMBER] ImportError: No module named mcpb.gene_model_files Marcelo Andrade Chagas (Thu Aug 13 2015 - 12:14:22 PDT)
- Re: [AMBER] ImportError: No module named mcpb.gene_model_files Marcelo Andrade Chagas (Mon Aug 17 2015 - 04:57:53 PDT)
- Re: [AMBER] ImportError: No module named mcpb.gene_model_files Daniel Roe (Mon Aug 17 2015 - 08:24:12 PDT)
  - Re: [AMBER] ImportError: No module named mcpb.gene_model_files Marcelo Andrade Chagas (Mon Aug 17 2015 - 09:05:36 PDT)
    - Re: [AMBER] ImportError: No module named mcpb.gene_model_files Marcelo Andrade Chagas (Fri Aug 21 2015 - 08:15:12 PDT)
    - Re: [AMBER] ImportError: No module named mcpb.gene_model_files Jason Swails (Fri Aug 21 2015 - 08:27:38 PDT)
    - Re: [AMBER] ImportError: No module named mcpb.gene_model_files Marcelo Andrade Chagas (Fri Aug 21 2015 - 08:43:50 PDT)
    - Re: [AMBER] ImportError: No module named mcpb.gene_model_files David A Case (Fri Aug 21 2015 - 10:33:41 PDT)
[AMBER] Job submission script for SGE Himansu (Thu Aug 13 2015 - 16:50:59 PDT)
- Re: [AMBER] Job submission script for SGE Jason Swails (Fri Aug 14 2015 - 04:46:27 PDT)
- Re: [AMBER] Job submission script for SGE Gerald Monard (Fri Aug 14 2015 - 04:46:34 PDT)
[AMBER] The protein is Leaving the water box! Amber mail (Thu Aug 13 2015 - 17:36:59 PDT)
- Re: [AMBER] The protein is Leaving the water box! Jason Swails (Fri Aug 14 2015 - 04:38:36 PDT)
  - Re: [AMBER] The protein is Leaving the water box! Amber mail (Fri Aug 14 2015 - 05:11:25 PDT)
    - Re: [AMBER] The protein is Leaving the water box! Jason Swails (Fri Aug 14 2015 - 06:00:11 PDT)
[AMBER] help in rdf Robin Jain (Fri Aug 14 2015 - 00:59:12 PDT)
- Re: [AMBER] help in rdf Daniel Roe (Fri Aug 14 2015 - 08:47:07 PDT)
[AMBER] the better box size Investigador Química (Fri Aug 14 2015 - 10:45:56 PDT)
- Re: [AMBER] the better box size Jason Swails (Fri Aug 14 2015 - 11:12:20 PDT)
- Re: [AMBER] the better box size Bill Ross (Fri Aug 14 2015 - 12:18:17 PDT)
[AMBER] RMSD and average value of interatomic distance? Michael Shokhen (Sat Aug 15 2015 - 00:30:26 PDT)
- Re: [AMBER] RMSD and average value of interatomic distance? Jason Swails (Sat Aug 15 2015 - 05:45:33 PDT)
  - Re: [AMBER] RMSD and average value of interatomic distance? Michael Shokhen (Sat Aug 15 2015 - 07:12:58 PDT)
    - Re: [AMBER] RMSD and average value of interatomic distance? Adrian Roitberg (Sat Aug 15 2015 - 07:15:34 PDT)
    - Re: [AMBER] RMSD and average value of interatomic distance? Michael Shokhen (Sat Aug 15 2015 - 07:49:14 PDT)
    - Re: [AMBER] RMSD and average value of interatomic distance? Daniel Roe (Sat Aug 15 2015 - 08:13:50 PDT)
    - Re: [AMBER] RMSD and average value of interatomic distance? Michael Shokhen (Sat Aug 15 2015 - 08:31:34 PDT)
Re: [AMBER] AMBER Digest, Vol 1311, Issue 1 Robin Jain (Sat Aug 15 2015 - 01:58:47 PDT)
- Re: [AMBER] AMBER Digest, Vol 1311, Issue 1 Jason Swails (Sat Aug 15 2015 - 06:21:17 PDT)
[AMBER] About the QMMM simulation with LIO software Yeng-Tseng Wang (Sat Aug 15 2015 - 09:58:47 PDT)
- Re: [AMBER] About the QMMM simulation with LIO software Jason Swails (Sat Aug 15 2015 - 10:22:09 PDT)
  - Re: [AMBER] About the QMMM simulation with LIO software Yeng-Tseng Wang (Mon Aug 17 2015 - 09:21:22 PDT)
    - Re: [AMBER] About the QMMM simulation with LIO software Jason Swails (Mon Aug 17 2015 - 09:48:00 PDT)
    - Re: [AMBER] About the QMMM simulation with LIO software Adrian Roitberg (Mon Aug 17 2015 - 11:10:36 PDT)
    - Re: [AMBER] About the QMMM simulation with LIO software Yeng-Tseng Wang (Tue Aug 18 2015 - 00:59:56 PDT)
    - Re: [AMBER] About the QMMM simulation with LIO software Yeng-Tseng Wang (Tue Aug 18 2015 - 01:08:05 PDT)
[AMBER] A query about MMPBSA.py calcualtion anu chandra (Sun Aug 16 2015 - 06:45:50 PDT)
- Re: [AMBER] A query about MMPBSA.py calcualtion Jason Swails (Sun Aug 16 2015 - 17:36:22 PDT)
  - [AMBER] error running mmpbsa.pl Urszula Uciechowska (Mon Aug 17 2015 - 02:12:40 PDT)
    - Re: [AMBER] error running mmpbsa.pl Urszula Uciechowska (Mon Aug 17 2015 - 02:27:03 PDT)
[AMBER] ****** in results? Chinh Su Tran To (Sun Aug 16 2015 - 23:51:48 PDT)
- Re: [AMBER] ****** in results? David A Case (Mon Aug 17 2015 - 04:38:03 PDT)
[AMBER] Help needed regarding simulating Lipopolysaccharide Mrinda Jones (Mon Aug 17 2015 - 03:41:39 PDT)
- Re: [AMBER] Help needed regarding simulating Lipopolysaccharide David A Case (Mon Aug 17 2015 - 04:49:21 PDT)
  - Re: [AMBER] Help needed regarding simulating Lipopolysaccharide Mrinda Jones (Mon Aug 17 2015 - 05:43:25 PDT)
    - Re: [AMBER] Help needed regarding simulating Lipopolysaccharide Lachele Foley (Mon Aug 17 2015 - 08:30:24 PDT)
    - Re: [AMBER] Help needed regarding simulating Lipopolysaccharide Mrinda Jones (Wed Aug 19 2015 - 00:20:11 PDT)
    - Re: [AMBER] Help needed regarding simulating Lipopolysaccharide David A Case (Wed Aug 19 2015 - 07:53:11 PDT)
[AMBER] STOP PMEMD Terminated Abnormally! Pragya Priyadarshini (Mon Aug 17 2015 - 04:14:11 PDT)
- Re: [AMBER] STOP PMEMD Terminated Abnormally! David A Case (Mon Aug 17 2015 - 04:51:55 PDT)
  - Re: [AMBER] STOP PMEMD Terminated Abnormally! Pragya Priyadarshini (Mon Aug 17 2015 - 07:24:53 PDT)
    - Re: [AMBER] STOP PMEMD Terminated Abnormally! Jason Swails (Mon Aug 17 2015 - 09:49:38 PDT)
    - Re: [AMBER] STOP PMEMD Terminated Abnormally! Pragya Priyadarshini (Mon Aug 17 2015 - 21:15:12 PDT)
[AMBER] saveamberparm mohammad r (Mon Aug 17 2015 - 07:14:26 PDT)
- Re: [AMBER] saveamberparm Daniel Roe (Mon Aug 17 2015 - 08:17:23 PDT)
- Re: [AMBER] saveamberparm David A Case (Mon Aug 17 2015 - 08:34:19 PDT)
  - Re: [AMBER] saveamberparm mohammad r (Mon Aug 17 2015 - 13:20:40 PDT)
[AMBER] Big potential difference between conformation in MD simulation and optimized conformation in Gaussian. Eg eh (Mon Aug 17 2015 - 12:08:44 PDT)
- Re: [AMBER] Big potential difference between conformation in MD simulation and optimized conformation in Gaussian. Bill Ross (Mon Aug 17 2015 - 13:09:34 PDT)
- Re: [AMBER] Big potential difference between conformation in MD simulation and optimized conformation in Gaussian. Jason Swails (Mon Aug 17 2015 - 13:18:36 PDT)
[AMBER] calculation of rmsd with cpptraj Krantzman, Kristin D (Mon Aug 17 2015 - 12:53:05 PDT)
- Re: [AMBER] calculation of rmsd with cpptraj Jason Swails (Mon Aug 17 2015 - 13:03:23 PDT)
  - Re: [AMBER] calculation of rmsd with cpptraj Krantzman, Kristin D (Mon Aug 17 2015 - 13:15:08 PDT)
[AMBER] cpptraj cluster in MPI Lara rajam (Mon Aug 17 2015 - 19:43:09 PDT)
- Re: [AMBER] cpptraj cluster in MPI Kenneth Huang (Mon Aug 17 2015 - 19:55:16 PDT)
  - Re: [AMBER] cpptraj cluster in MPI Lara rajam (Mon Aug 17 2015 - 20:03:55 PDT)
- Re: [AMBER] cpptraj cluster in MPI Daniel Roe (Mon Aug 17 2015 - 20:12:01 PDT)
[AMBER] Immediate PhD Opening In Computational Structural Biology Of Membrane Proteins Marawan Hussien (Mon Aug 17 2015 - 20:25:18 PDT)
[AMBER] Immediate Postdoctoral Position Opening In Computational Chemistry And Computer-Aided Drug Design (CADD) Marawan Hussien (Mon Aug 17 2015 - 20:26:39 PDT)
[AMBER] acpype mohammad r (Mon Aug 17 2015 - 23:58:54 PDT)
- Re: [AMBER] acpype David A Case (Tue Aug 18 2015 - 06:28:25 PDT)
  - Re: [AMBER] acpype mohammad r (Tue Aug 18 2015 - 07:04:12 PDT)
    - Re: [AMBER] acpype Suman Chakrabarty (Tue Aug 18 2015 - 07:30:17 PDT)
[AMBER] acpype mohammad r (Tue Aug 18 2015 - 01:17:59 PDT)
[AMBER] ancpype problem mohammad r (Tue Aug 18 2015 - 02:00:36 PDT)
[AMBER] Total interaction energy between monomeric units of a dimer anu chandra (Tue Aug 18 2015 - 04:55:46 PDT)
- Re: [AMBER] Total interaction energy between monomeric units of a dimer Daniel Roe (Tue Aug 18 2015 - 06:05:49 PDT)
- Re: [AMBER] Total interaction energy between monomeric units of a dimer Jason Swails (Tue Aug 18 2015 - 06:08:12 PDT)
  - Re: [AMBER] Total interaction energy between monomeric units of a dimer anu chandra (Tue Aug 18 2015 - 07:17:19 PDT)
  - Re: [AMBER] Total interaction energy between monomeric units of a dimer George Tzotzos (Wed Aug 19 2015 - 08:57:09 PDT)
    - Re: [AMBER] Total interaction energy between monomeric units of a dimer David A Case (Wed Aug 19 2015 - 09:22:16 PDT)
    - Re: [AMBER] Total interaction energy between monomeric units of a dimer anu chandra (Thu Aug 20 2015 - 04:04:10 PDT)
    - Re: [AMBER] Total interaction energy between monomeric units of a dimer David A Case (Thu Aug 20 2015 - 05:00:55 PDT)
    - Re: [AMBER] Total interaction energy between monomeric units of a dimer Hector A. Baldoni (Thu Aug 20 2015 - 05:09:43 PDT)
    - Re: [AMBER] Total interaction energy between monomeric units of a dimer Jason Swails (Thu Aug 20 2015 - 06:12:14 PDT)
    - Re: [AMBER] Total interaction energy between monomeric units of a dimer Hector A. Baldoni (Thu Aug 20 2015 - 06:21:15 PDT)
    - Re: [AMBER] Total interaction energy between monomeric units of a dimer anu chandra (Wed Aug 26 2015 - 10:04:15 PDT)
    - Re: [AMBER] Total interaction energy between monomeric units of a dimer Jason Swails (Wed Aug 26 2015 - 10:21:49 PDT)
[AMBER] converting amber files mohammad r (Tue Aug 18 2015 - 05:12:49 PDT)
- Re: [AMBER] converting amber files George Tzotzos (Tue Aug 18 2015 - 05:23:27 PDT)
  - Re: [AMBER] converting amber files mohammad r (Tue Aug 18 2015 - 06:10:12 PDT)
    - Re: [AMBER] converting amber files Jason Swails (Tue Aug 18 2015 - 06:27:30 PDT)
    - Re: [AMBER] converting amber files mohammad r (Tue Aug 18 2015 - 06:49:37 PDT)
    - Re: [AMBER] converting amber files Kenneth Huang (Tue Aug 18 2015 - 07:22:38 PDT)
    - Re: [AMBER] converting amber files Jason Swails (Tue Aug 18 2015 - 07:42:52 PDT)
    - Re: [AMBER] converting amber files mohammad r (Tue Aug 18 2015 - 08:03:07 PDT)
- Re: [AMBER] converting amber files Jason Swails (Tue Aug 18 2015 - 05:57:11 PDT)
[AMBER] NPT equilibration failed Albert (Tue Aug 18 2015 - 05:58:56 PDT)
- Re: [AMBER] NPT equilibration failed Adrian Roitberg (Tue Aug 18 2015 - 06:02:38 PDT)
  - Re: [AMBER] NPT equilibration failed Albert (Tue Aug 18 2015 - 06:09:08 PDT)
[AMBER] hpc error Damiano Spadoni (Tue Aug 18 2015 - 06:43:23 PDT)
- Re: [AMBER] hpc error David A Case (Tue Aug 18 2015 - 07:12:59 PDT)
  - Re: [AMBER] hpc error Damiano Spadoni (Fri Aug 28 2015 - 04:37:17 PDT)
    - Re: [AMBER] hpc error David A Case (Fri Aug 28 2015 - 05:20:16 PDT)
    - Re: [AMBER] hpc error Damiano Spadoni (Thu Sep 03 2015 - 03:16:19 PDT)
    - Re: [AMBER] hpc error Jason Swails (Thu Sep 03 2015 - 05:25:58 PDT)
  - Re: [AMBER] hpc error Damiano Spadoni (Thu Sep 24 2015 - 03:55:45 PDT)
    - Re: [AMBER] hpc error Jason Swails (Thu Sep 24 2015 - 05:18:50 PDT)
    - Re: [AMBER] hpc error David A Case (Thu Sep 24 2015 - 05:48:22 PDT)
    - Re: [AMBER] hpc error Jason Swails (Thu Sep 24 2015 - 06:23:39 PDT)
    - Re: [AMBER] hpc error Duke, Robert E Jr (Thu Sep 24 2015 - 09:12:33 PDT)
    - Re: [AMBER] hpc error Damiano Spadoni (Sun Sep 27 2015 - 10:23:53 PDT)
    - Re: [AMBER] hpc error Jason Swails (Sun Sep 27 2015 - 12:43:14 PDT)
    - Re: [AMBER] hpc error Duke, Robert E Jr (Sun Sep 27 2015 - 13:24:25 PDT)
    - Re: [AMBER] hpc error Jason Swails (Mon Sep 28 2015 - 14:41:14 PDT)
[AMBER] cpptraj RMSD stats George Tzotzos (Tue Aug 18 2015 - 06:43:52 PDT)
- Re: [AMBER] cpptraj RMSD stats Daniel Roe (Tue Aug 18 2015 - 06:50:20 PDT)
  - Re: [AMBER] cpptraj RMSD stats George Tzotzos (Tue Aug 18 2015 - 08:18:22 PDT)
    - Re: [AMBER] cpptraj RMSD stats Daniel Roe (Tue Aug 18 2015 - 08:34:46 PDT)
[AMBER] cpptraj perress RMSD George Tzotzos (Tue Aug 18 2015 - 07:47:36 PDT)
- Re: [AMBER] cpptraj perress RMSD Daniel Roe (Tue Aug 18 2015 - 07:53:51 PDT)
  - Re: [AMBER] cpptraj perress RMSD George Tzotzos (Tue Aug 18 2015 - 09:57:17 PDT)
[AMBER] upgrading to AT15 (from AT14) Massimiliano Porrini (Tue Aug 18 2015 - 09:47:00 PDT)
- Re: [AMBER] upgrading to AT15 (from AT14) Jason Swails (Tue Aug 18 2015 - 10:25:55 PDT)
  - Re: [AMBER] upgrading to AT15 (from AT14) David A Case (Tue Aug 18 2015 - 10:48:51 PDT)
    - Re: [AMBER] upgrading to AT15 (from AT14) mohammad r (Tue Aug 18 2015 - 23:10:09 PDT)
    - Re: [AMBER] upgrading to AT15 (from AT14) Massimiliano Porrini (Fri Aug 21 2015 - 02:46:05 PDT)
    - Re: [AMBER] upgrading to AT15 (from AT14) David A Case (Fri Aug 21 2015 - 04:58:44 PDT)
    - Re: [AMBER] upgrading to AT15 (from AT14) Massimiliano Porrini (Mon Aug 24 2015 - 03:28:46 PDT)
    - Re: [AMBER] upgrading to AT15 (from AT14) David A Case (Mon Aug 24 2015 - 05:52:05 PDT)
[AMBER] adding NaCl mohammad r (Tue Aug 18 2015 - 21:32:47 PDT)
[AMBER] adding NaCl mohammad r (Tue Aug 18 2015 - 22:44:23 PDT)
[AMBER] CL topology Albert (Wed Aug 19 2015 - 00:04:44 PDT)
- Re: [AMBER] CL topology Jason Swails (Wed Aug 19 2015 - 04:42:02 PDT)
[AMBER] adding NaCl mohammad r (Wed Aug 19 2015 - 00:25:07 PDT)
- Re: [AMBER] adding NaCl Bill Ross (Wed Aug 19 2015 - 01:37:32 PDT)
  - Re: [AMBER] adding NaCl mohammad r (Wed Aug 19 2015 - 01:45:14 PDT)
    - Re: [AMBER] adding NaCl Jason Swails (Wed Aug 19 2015 - 04:16:42 PDT)
[AMBER] RESP fitting Mahmood Jasim (Wed Aug 19 2015 - 05:46:21 PDT)
- Re: [AMBER] RESP fitting David A Case (Wed Aug 19 2015 - 08:03:07 PDT)
- Re: [AMBER] RESP fitting cieplak.cgl.ucsf.edu (Wed Aug 19 2015 - 13:48:16 PDT)
  - Re: [AMBER] RESP fitting Mahmood Jasim (Thu Aug 20 2015 - 08:43:57 PDT)
Re: [AMBER] the better box size for calculating host-guest interaction energies Investigador Química (Wed Aug 19 2015 - 07:43:41 PDT)
- Re: [AMBER] the better box size for calculating host-guest interaction energies Jason Swails (Wed Aug 19 2015 - 08:18:06 PDT)
  - Re: [AMBER] the better box size for calculating host-guest interaction energies Investigador Química (Thu Aug 20 2015 - 07:09:12 PDT)
    - Re: [AMBER] the better box size for calculating host-guest interaction energies Jason Swails (Thu Aug 20 2015 - 07:32:34 PDT)
    - Re: [AMBER] the better box size for calculating host-guest interaction energies Investigador Química (Sat Aug 22 2015 - 13:34:10 PDT)
    - Re: [AMBER] the better box size for calculating host-guest interaction energies David A Case (Thu Aug 20 2015 - 08:51:23 PDT)
    - Re: [AMBER] the better box size for calculating host-guest interaction energies Investigador Química (Sat Aug 22 2015 - 13:35:50 PDT)
    - Re: [AMBER] the better box size for calculating host-guest interaction energies Adrian Roitberg (Thu Aug 20 2015 - 09:41:52 PDT)
    - Re: [AMBER] the better box size for calculating host-guest interaction energies Investigador Química (Sat Aug 22 2015 - 13:38:37 PDT)
[AMBER] xleap numbering in residues Lara rajam (Wed Aug 19 2015 - 18:32:00 PDT)
- Re: [AMBER] xleap numbering in residues David A Case (Thu Aug 20 2015 - 04:54:43 PDT)
[AMBER] Solvent accessible surface area (SASA) calculation in CPPTRJ anu chandra (Thu Aug 20 2015 - 09:35:31 PDT)
- Re: [AMBER] Solvent accessible surface area (SASA) calculation in CPPTRJ Jason Swails (Thu Aug 20 2015 - 11:25:46 PDT)
  - Re: [AMBER] Solvent accessible surface area (SASA) calculation in CPPTRJ anu chandra (Fri Aug 21 2015 - 08:58:51 PDT)
    - Re: [AMBER] Solvent accessible surface area (SASA) calculation in CPPTRJ David A Case (Fri Aug 21 2015 - 10:36:59 PDT)
    - Re: [AMBER] Solvent accessible surface area (SASA) calculation in CPPTRJ George Tzotzos (Mon Aug 24 2015 - 09:29:15 PDT)
    - Re: [AMBER] Solvent accessible surface area (SASA) calculation in CPPTRJ Jason Swails (Mon Aug 24 2015 - 10:02:33 PDT)
    - Re: [AMBER] Solvent accessible surface area (SASA) calculation in CPPTRJ George Tzotzos (Mon Aug 24 2015 - 12:03:56 PDT)
    - Re: [AMBER] Solvent accessible surface area (SASA) calculation in CPPTRJ Jason Swails (Mon Aug 24 2015 - 12:23:21 PDT)
[AMBER] Problem with using the 12-6-4 LJ-Type Nonbonded Model in a an RNA-Mg system Kasprzak, Wojciech (NIH/NCI) [C] (Thu Aug 20 2015 - 13:08:09 PDT)
[AMBER] Using MMPBSA.py with CHARMM force field Ara Abramyan (Thu Aug 20 2015 - 13:43:11 PDT)
- Re: [AMBER] Using MMPBSA.py with CHARMM force field Jason Swails (Fri Aug 21 2015 - 06:40:41 PDT)
  - Re: [AMBER] Using MMPBSA.py with CHARMM force field David A Case (Fri Aug 21 2015 - 08:10:27 PDT)
    - Re: [AMBER] Using MMPBSA.py with CHARMM force field Ara Abramyan (Fri Aug 21 2015 - 08:47:48 PDT)
    - Re: [AMBER] Using MMPBSA.py with CHARMM force field Jason Swails (Fri Aug 21 2015 - 10:42:17 PDT)
[AMBER] hydrogen mass repartitioning visualization in chimera George Green (Thu Aug 20 2015 - 16:49:14 PDT)
- Re: [AMBER] hydrogen mass repartitioning visualization in chimera Adrian Roitberg (Thu Aug 20 2015 - 17:15:04 PDT)
  - Re: [AMBER] hydrogen mass repartitioning visualization in chimera George Green (Thu Aug 20 2015 - 17:18:42 PDT)
    - Re: [AMBER] hydrogen mass repartitioning visualization in chimera George Green (Thu Aug 20 2015 - 17:31:22 PDT)
    - Re: [AMBER] hydrogen mass repartitioning visualization in chimera Nhai (Thu Aug 20 2015 - 17:32:47 PDT)
    - Re: [AMBER] hydrogen mass repartitioning visualization in chimera George Green (Thu Aug 20 2015 - 18:03:12 PDT)
    - Re: [AMBER] hydrogen mass repartitioning visualization in chimera Jason Swails (Fri Aug 21 2015 - 06:36:37 PDT)
    - Re: [AMBER] hydrogen mass repartitioning visualization in chimera George Green (Fri Aug 21 2015 - 06:49:33 PDT)
[AMBER] Autoimage Warning Brittany Boykin (Fri Aug 21 2015 - 08:10:12 PDT)
- Re: [AMBER] Autoimage Warning Jason Swails (Fri Aug 21 2015 - 08:29:38 PDT)
[AMBER] closest command in cpptraj Joseph Baker (Fri Aug 21 2015 - 12:31:26 PDT)
- Re: [AMBER] closest command in cpptraj Daniel Roe (Fri Aug 21 2015 - 14:46:05 PDT)
  - Re: [AMBER] closest command in cpptraj Joseph Baker (Mon Aug 24 2015 - 07:17:22 PDT)
    - Re: [AMBER] closest command in cpptraj Joseph Baker (Mon Aug 24 2015 - 12:34:57 PDT)
    - Re: [AMBER] closest command in cpptraj Joseph Baker (Mon Aug 24 2015 - 14:05:48 PDT)
    - Re: [AMBER] closest command in cpptraj Hai Nguyen (Mon Aug 24 2015 - 14:31:31 PDT)
    - Re: [AMBER] closest command in cpptraj Daniel Roe (Tue Aug 25 2015 - 06:23:48 PDT)
    - Re: [AMBER] closest command in cpptraj Joseph Baker (Tue Aug 25 2015 - 19:21:50 PDT)
    - Re: [AMBER] closest command in cpptraj Daniel Roe (Wed Aug 26 2015 - 07:48:44 PDT)
    - Re: [AMBER] closest command in cpptraj Joseph Baker (Mon Sep 07 2015 - 11:22:57 PDT)
    - Re: [AMBER] closest command in cpptraj Daniel Roe (Tue Sep 08 2015 - 08:48:02 PDT)
[AMBER] help in density equilibration Robin Jain (Fri Aug 21 2015 - 22:30:39 PDT)
[AMBER] Error: an illegal memory access was encountered launching kernel kClearForces Parker de Waal (Sat Aug 22 2015 - 13:58:21 PDT)
- Re: [AMBER] Error: an illegal memory access was encountered launching kernel kClearForces Ross Walker (Mon Aug 24 2015 - 08:53:49 PDT)
[AMBER] adding lipid mohammad r (Sun Aug 23 2015 - 06:41:32 PDT)
[AMBER] how to add lipid mohammad r (Sun Aug 23 2015 - 06:47:36 PDT)
[AMBER] how to add lipid mohammad roostaie (Sun Aug 23 2015 - 07:08:02 PDT)
- Re: [AMBER] how to add lipid Bill Ross (Sun Aug 23 2015 - 14:05:43 PDT)
  - Re: [AMBER] how to add lipid mohammad r (Sun Aug 23 2015 - 21:38:44 PDT)
[AMBER] tleap ask for bond to zinc ion Jorgen Simonsen (Sun Aug 23 2015 - 08:49:01 PDT)
- Re: [AMBER] tleap ask for bond to zinc ion Bill Ross (Sun Aug 23 2015 - 14:15:46 PDT)
- Re: [AMBER] tleap ask for bond to zinc ion David A Case (Mon Aug 24 2015 - 05:34:04 PDT)
- Re: [AMBER] tleap ask for bond to zinc ion Marcelo Andrade Chagas (Mon Aug 24 2015 - 10:33:00 PDT)
[AMBER] help in density equilibration Robin Jain (Sun Aug 23 2015 - 21:00:17 PDT)
- Re: [AMBER] help in density equilibration Bill Ross (Sun Aug 23 2015 - 23:21:39 PDT)
- Re: [AMBER] help in density equilibration David A Case (Mon Aug 24 2015 - 05:47:41 PDT)
[AMBER] Regarding No of Hydrogen bonds (vs) Residue wise Garisekurthi Satheesh (Sun Aug 23 2015 - 21:15:03 PDT)
- Re: [AMBER] Regarding No of Hydrogen bonds (vs) Residue wise Daniel Roe (Mon Aug 24 2015 - 07:40:28 PDT)
  - Re: [AMBER] Regarding No of Hydrogen bonds (vs) Residue wise Hai Nguyen (Mon Aug 24 2015 - 10:26:12 PDT)
    - Re: [AMBER] Regarding No of Hydrogen bonds (vs) Residue wise Garisekurthi Satheesh (Mon Aug 24 2015 - 11:22:15 PDT)
[AMBER] AMBER Autoimage Warning Brittany Boykin (Mon Aug 24 2015 - 09:42:04 PDT)
- Re: [AMBER] AMBER Autoimage Warning Jason Swails (Mon Aug 24 2015 - 10:38:00 PDT)
- Re: [AMBER] AMBER Autoimage Warning Daniel Roe (Mon Aug 24 2015 - 10:42:42 PDT)
[AMBER] ImportError: No module named scipy.optimize Sushi Shilpa (Mon Aug 24 2015 - 21:07:25 PDT)
- Re: [AMBER] ImportError: No module named scipy.optimize Nhai (Mon Aug 24 2015 - 21:23:44 PDT)
[AMBER] how to neutralized my system with Na+ ions Martina Devi (Mon Aug 24 2015 - 23:53:54 PDT)
- Re: [AMBER] how to neutralized my system with Na+ ions David A Case (Tue Aug 25 2015 - 05:15:12 PDT)
  - Re: [AMBER] how to neutralized my system with Na+ ions Kasprzak, Wojciech (NIH/NCI) [C] (Tue Aug 25 2015 - 05:43:08 PDT)
    - Re: [AMBER] how to neutralized my system with Na+ ions Martina Devi (Tue Aug 25 2015 - 06:57:52 PDT)
- Re: [AMBER] how to neutralized my system with Na+ ions Jason Swails (Tue Aug 25 2015 - 07:16:01 PDT)
  - Re: [AMBER] how to neutralized my system with Na+ ions Martina Devi (Tue Aug 25 2015 - 07:33:43 PDT)
    - Re: [AMBER] how to neutralized my system with Na+ ions Martina Devi (Tue Aug 25 2015 - 09:25:44 PDT)
    - Re: [AMBER] how to neutralized my system with Na+ ions Jason Swails (Tue Aug 25 2015 - 10:12:34 PDT)
    - Re: [AMBER] how to neutralized my system with Na+ ions Hai Nguyen (Tue Aug 25 2015 - 10:19:14 PDT)
[AMBER] Regarding printing of trajectory MOHD HOMAIDUR RAHMAN (Tue Aug 25 2015 - 00:11:55 PDT)
- Re: [AMBER] Regarding printing of trajectory David A Case (Tue Aug 25 2015 - 05:20:19 PDT)
  - Re: [AMBER] Regarding printing of trajectory MOHD HOMAIDUR RAHMAN (Tue Aug 25 2015 - 07:22:11 PDT)
    - Re: [AMBER] Regarding printing of trajectory Daniel Roe (Tue Aug 25 2015 - 07:34:16 PDT)
    - Re: [AMBER] Regarding printing of trajectory MOHD HOMAIDUR RAHMAN (Tue Aug 25 2015 - 11:11:30 PDT)
[AMBER] mismatch base pair from nab Martina Devi (Tue Aug 25 2015 - 04:49:01 PDT)
- Re: [AMBER] mismatch base pair from nab Carlos Simmerling (Tue Aug 25 2015 - 04:54:29 PDT)
  - Re: [AMBER] mismatch base pair from nab Martina Devi (Tue Aug 25 2015 - 05:59:38 PDT)
    - Re: [AMBER] mismatch base pair from nab Carlos Simmerling (Tue Aug 25 2015 - 06:20:10 PDT)
    - Re: [AMBER] mismatch base pair from nab David A Case (Tue Aug 25 2015 - 12:57:41 PDT)
    - Re: [AMBER] mismatch base pair from nab Martina Devi (Sat Aug 29 2015 - 05:39:10 PDT)
[AMBER] Problem In Performing MMPBSA Calculation for System Containing Lipids anilkumarsahoo.physics.iisc.ernet.in (Tue Aug 25 2015 - 04:29:38 PDT)
- Re: [AMBER] Problem In Performing MMPBSA Calculation for System Containing Lipids Daniel Roe (Tue Aug 25 2015 - 06:26:16 PDT)
  - Re: [AMBER] Problem In Performing MMPBSA Calculation for System Containing Lipids anilkumarsahoo.physics.iisc.ernet.in (Tue Aug 25 2015 - 17:04:47 PDT)
    - Re: [AMBER] Problem In Performing MMPBSA Calculation for System Containing Lipids David A Case (Wed Aug 26 2015 - 05:33:02 PDT)
    - Re: [AMBER] Problem In Performing MMPBSA Calculation for System Containing Lipids Jason Swails (Wed Aug 26 2015 - 05:41:47 PDT)
[AMBER] Non-equilibrium pulling with plane-point restraints Jacob Monroe (Tue Aug 25 2015 - 10:45:22 PDT)
- Re: [AMBER] Non-equilibrium pulling with plane-point restraints achim.sandmann.chemie.stud.uni-erlangen.de (Thu Aug 27 2015 - 00:46:14 PDT)
  - Re: [AMBER] Non-equilibrium pulling with plane-point restraints Jacob Monroe (Thu Aug 27 2015 - 11:02:29 PDT)
    - Re: [AMBER] Non-equilibrium pulling with plane-point restraints achim.sandmann.chemie.stud.uni-erlangen.de (Fri Aug 28 2015 - 01:20:03 PDT)
    - Re: [AMBER] Non-equilibrium pulling with plane-point restraints Jacob Monroe (Mon Aug 31 2015 - 16:29:59 PDT)
    - Re: [AMBER] Non-equilibrium pulling with plane-point restraints achim.sandmann.chemie.stud.uni-erlangen.de (Tue Sep 01 2015 - 05:42:07 PDT)
[AMBER] What is the best way to study a dynamics route of a molecule to enter a protein Wenyu Qian (Tue Aug 25 2015 - 15:04:08 PDT)
- Re: [AMBER] What is the best way to study a dynamics route of a molecule to enter a protein David A Case (Wed Aug 26 2015 - 05:26:19 PDT)
  - Re: [AMBER] What is the best way to study a dynamics route of a molecule to enter a protein Mohammad Salem (Thu Aug 27 2015 - 15:44:10 PDT)
    - Re: [AMBER] What is the best way to study a dynamics route of a molecule to enter a protein David A Case (Fri Aug 28 2015 - 05:11:22 PDT)
    - Re: [AMBER] What is the best way to study a dynamics route of a molecule to enter a protein Wenyu Qian (Fri Aug 28 2015 - 07:55:45 PDT)
    - Re: [AMBER] What is the best way to study a dynamics route of a molecule to enter a protein David A Case (Fri Aug 28 2015 - 10:23:58 PDT)
- Re: [AMBER] What is the best way to study a dynamics route of a molecule to enter a protein Bill Ross (Thu Aug 27 2015 - 16:47:45 PDT)
[AMBER] cpin error Arjun Sharma (Tue Aug 25 2015 - 16:45:04 PDT)
- Re: [AMBER] cpin error Jason Swails (Wed Aug 26 2015 - 06:43:08 PDT)
[AMBER] Does it mean the card is damaged? Karolina Markowska (Thu Aug 27 2015 - 01:40:19 PDT)
- Re: [AMBER] Does it mean the card is damaged? Ross Walker (Thu Aug 27 2015 - 08:06:09 PDT)
  - Re: [AMBER] Does it mean the card is damaged? Karolina Markowska (Fri Aug 28 2015 - 01:04:13 PDT)
    - Re: [AMBER] Does it mean the card is damaged? Karolina Markowska (Mon Aug 31 2015 - 01:37:44 PDT)
    - Re: [AMBER] Does it mean the card is damaged? Ross Walker (Mon Aug 31 2015 - 08:56:48 PDT)
[AMBER] Charge-dependent exchange-dispersion corrections Lucas A. Defelipe (Thu Aug 27 2015 - 07:46:23 PDT)
[AMBER] Molsurf: some questions on usage George Tzotzos (Thu Aug 27 2015 - 08:05:44 PDT)
- Re: [AMBER] Molsurf: some questions on usage David A Case (Fri Aug 28 2015 - 05:03:18 PDT)
Re: [AMBER] Cpin error Arjun Sharma (Thu Aug 27 2015 - 08:31:18 PDT)
- Re: [AMBER] Cpin error Jason Swails (Thu Aug 27 2015 - 09:16:14 PDT)
[AMBER] Looking for suggestion for analysis Mohd Farid Ismail (Thu Aug 27 2015 - 19:42:17 PDT)
[AMBER] Confusion in running QM/MMGBSA MOHD HOMAIDUR RAHMAN (Fri Aug 28 2015 - 12:08:49 PDT)
- Re: [AMBER] Confusion in running QM/MMGBSA David A Case (Fri Aug 28 2015 - 18:34:08 PDT)
- Re: [AMBER] Confusion in running QM/MMGBSA Jason Swails (Sat Aug 29 2015 - 04:09:28 PDT)
[AMBER] How do I study the dimerisation energy (i.e. energy required to form a dimer from two monomeric units) using AMBER? Suchetana Gupta (Sat Aug 29 2015 - 00:15:11 PDT)
- Re: [AMBER] How do I study the dimerisation energy (i.e. energy required to form a dimer from two monomeric units) using AMBER? David A Case (Sat Aug 29 2015 - 04:38:01 PDT)
[AMBER] Segmentation Fault with pmemd Ziheng Wang (Sat Aug 29 2015 - 01:02:03 PDT)
- Re: [AMBER] Segmentation Fault with pmemd Jason Swails (Sat Aug 29 2015 - 04:22:42 PDT)
- Re: [AMBER] Segmentation Fault with pmemd David A Case (Sat Aug 29 2015 - 04:42:34 PDT)
- Re: [AMBER] Segmentation Fault with pmemd Ziheng Wang (Sun Aug 30 2015 - 07:26:15 PDT)
  - Re: [AMBER] Segmentation Fault with pmemd David A Case (Sun Aug 30 2015 - 12:46:12 PDT)
[AMBER] cyclic peptides Lara rajam (Sun Aug 30 2015 - 17:26:27 PDT)
- Re: [AMBER] cyclic peptides David A Case (Sun Aug 30 2015 - 18:13:33 PDT)
[AMBER] job submission in RED Martina Devi (Mon Aug 31 2015 - 03:34:40 PDT)
- Re: [AMBER] job submission in RED FyD (Thu Sep 03 2015 - 02:12:10 PDT)
[AMBER] Thermodynamic integration and segmentation fault Khabiri, Morteza (Mon Aug 31 2015 - 06:40:15 PDT)
[AMBER] Draw a cube around the molecules Iqbal, Muhammad Sajid (Mon Aug 31 2015 - 11:56:19 PDT)
- Re: [AMBER] Draw a cube around the molecules Lorenzo Gontrani (Mon Aug 31 2015 - 12:02:58 PDT)
- Re: [AMBER] Draw a cube around the molecules Jason Swails (Mon Aug 31 2015 - 12:04:14 PDT)
- Re: [AMBER] Draw a cube around the molecules Repic Matej (Mon Aug 31 2015 - 15:46:32 PDT)
[AMBER] MMPBSA error - start frame (1) > total frames (0) Sangeetha B (Tue Sep 01 2015 - 08:39:44 PDT)
- Re: [AMBER] MMPBSA error - start frame (1) > total frames (0) Daniel Roe (Tue Sep 01 2015 - 10:48:06 PDT)
[AMBER] KeyError: 4018 Sushi Shilpa (Tue Sep 01 2015 - 20:42:09 PDT)
- Re: [AMBER] KeyError: 4018 Pengfei Li (Wed Sep 02 2015 - 18:35:15 PDT)
[AMBER] lifetime analysis loic etheve (Wed Sep 02 2015 - 06:37:45 PDT)
- Re: [AMBER] lifetime analysis Daniel Roe (Wed Sep 02 2015 - 06:43:53 PDT)
  - Re: [AMBER] lifetime analysis loic etheve (Wed Sep 02 2015 - 06:47:39 PDT)
    - Re: [AMBER] lifetime analysis Daniel Roe (Wed Sep 02 2015 - 07:10:26 PDT)
    - Re: [AMBER] lifetime analysis loic etheve (Wed Sep 02 2015 - 07:14:27 PDT)
[AMBER] lifetime analysis loic etheve (Wed Sep 02 2015 - 06:41:46 PDT)
[AMBER] Amber14 Update 13 fails. Oliver Grant (Wed Sep 02 2015 - 07:44:51 PDT)
- Re: [AMBER] Amber14 Update 13 fails. Jason Swails (Wed Sep 02 2015 - 08:22:16 PDT)
[AMBER] error in GPU during equilibration Lara rajam (Wed Sep 02 2015 - 09:30:26 PDT)
- Re: [AMBER] error in GPU during equilibration David A Case (Wed Sep 02 2015 - 11:40:14 PDT)
  - Re: [AMBER] error in GPU during equilibration Lara rajam (Wed Sep 02 2015 - 11:51:41 PDT)
    - Re: [AMBER] error in GPU during equilibration Ross Walker (Wed Sep 02 2015 - 12:04:55 PDT)
    - Re: [AMBER] error in GPU during equilibration Ross Walker (Wed Sep 02 2015 - 12:09:48 PDT)
    - Re: [AMBER] error in GPU during equilibration Lara rajam (Wed Sep 02 2015 - 15:17:51 PDT)
    - Re: [AMBER] error in GPU during equilibration Ross Walker (Wed Sep 02 2015 - 15:30:31 PDT)
    - Re: [AMBER] error in GPU during equilibration Lara rajam (Wed Sep 02 2015 - 15:35:39 PDT)
[AMBER] Different result before and after AUTOIMAGE from CPPTRAJ? Eg eh (Wed Sep 02 2015 - 13:21:50 PDT)
- Re: [AMBER] Different result before and after AUTOIMAGE from CPPTRAJ? Jason Swails (Wed Sep 02 2015 - 13:46:14 PDT)
[AMBER] RESP charge fitting CHAMI F. (Thu Sep 03 2015 - 11:10:49 PDT)
- Re: [AMBER] RESP charge fitting David A Case (Thu Sep 03 2015 - 11:18:39 PDT)
- Re: [AMBER] RESP charge fitting FyD (Thu Sep 03 2015 - 22:57:47 PDT)
  - Re: [AMBER] RESP charge fitting li he (Wed Oct 14 2015 - 10:58:30 PDT)
- Re: [AMBER] RESP charge fitting Xing (Wed Oct 14 2015 - 08:03:40 PDT)
[AMBER] Trouble running Thermodynamic Integration in Amber14 with pmemd. Timothy Christopher Schutt (Thu Sep 03 2015 - 15:04:26 PDT)
- Re: [AMBER] Trouble running Thermodynamic Integration in Amber14 with pmemd. David A Case (Thu Sep 03 2015 - 18:14:27 PDT)
- Re: [AMBER] Trouble running Thermodynamic Integration in Amber14 with pmemd. hannes.loeffler.stfc.ac.uk (Thu Sep 03 2015 - 23:38:07 PDT)
  - Re: [AMBER] Trouble running Thermodynamic Integration in Amber14 with pmemd. Timothy Christopher Schutt (Fri Sep 04 2015 - 10:10:18 PDT)
    - Re: [AMBER] Trouble running Thermodynamic Integration in Amber14 with pmemd. hannes.loeffler.stfc.ac.uk (Fri Sep 04 2015 - 10:17:27 PDT)
    - Re: [AMBER] Trouble running Thermodynamic Integration in Amber14 with pmemd. Timothy Christopher Schutt (Mon Sep 07 2015 - 09:48:49 PDT)
    - Re: [AMBER] Trouble running Thermodynamic Integration in Amber14 with pmemd. Jason Swails (Mon Sep 07 2015 - 10:49:05 PDT)
[AMBER] MMPBSA error sunita gupta (Fri Sep 04 2015 - 00:12:49 PDT)
- Re: [AMBER] MMPBSA error Jason Swails (Fri Sep 04 2015 - 04:24:01 PDT)
  - [AMBER] chirality.c Aronica, Pietro (Fri Sep 04 2015 - 08:20:39 PDT)
    - Re: [AMBER] chirality.c David A Case (Sat Sep 05 2015 - 09:13:47 PDT)
    - Re: [AMBER] chirality.c Aronica, Pietro (Tue Sep 08 2015 - 07:05:53 PDT)
[AMBER] mmpbsa with Iodine problems 21428087.zju.edu.cn (Fri Sep 04 2015 - 21:48:29 PDT)
- Re: [AMBER] mmpbsa with Iodine problems Kenneth Huang (Sat Sep 05 2015 - 17:18:17 PDT)
[AMBER] gpu run Lara rajam (Sat Sep 05 2015 - 16:32:13 PDT)
- Re: [AMBER] gpu run Kenneth Huang (Sat Sep 05 2015 - 18:12:05 PDT)
  - Re: [AMBER] gpu run Jason Swails (Sun Sep 06 2015 - 10:26:03 PDT)
- Re: [AMBER] gpu run Ross Walker (Sun Sep 06 2015 - 09:14:12 PDT)
  - Re: [AMBER] gpu run Lara rajam (Sun Sep 06 2015 - 09:41:55 PDT)
[AMBER] MMPBSA is not performing Asma Abro 28-FBAS/MSBI/F09 (Sun Sep 06 2015 - 22:03:23 PDT)
- Re: [AMBER] MMPBSA is not performing Jason Swails (Mon Sep 07 2015 - 05:31:07 PDT)
  - Re: [AMBER] MMPBSA is not performing Asma Abro 28-FBAS/MSBI/F09 (Tue Sep 08 2015 - 00:21:10 PDT)
    - Re: [AMBER] MMPBSA is not performing Aleksandra Skoric (Tue Sep 08 2015 - 00:59:21 PDT)
    - Re: [AMBER] MMPBSA is not performing asma.msbi28.iiu.edu.pk (Tue Sep 08 2015 - 01:08:33 PDT)
    - Re: [AMBER] MMPBSA is not performing Aleksandra Skoric (Tue Sep 08 2015 - 01:30:12 PDT)
    - Re: [AMBER] MMPBSA is not performing asma.msbi28.iiu.edu.pk (Tue Sep 08 2015 - 01:35:42 PDT)
    - Re: [AMBER] MMPBSA is not performing Asma Abro 28-FBAS/MSBI/F09 (Tue Sep 08 2015 - 02:13:29 PDT)
    - Re: [AMBER] MMPBSA is not performing Aleksandra Skoric (Tue Sep 08 2015 - 02:46:24 PDT)
    - Re: [AMBER] MMPBSA is not performing Asma Abro 28-FBAS/MSBI/F09 (Tue Sep 08 2015 - 03:02:38 PDT)
    - Re: [AMBER] MMPBSA is not performing Aleksandra Skoric (Tue Sep 08 2015 - 03:59:04 PDT)
    - Re: [AMBER] MMPBSA is not performing asma.msbi28.iiu.edu.pk (Tue Sep 08 2015 - 05:07:23 PDT)
    - Re: [AMBER] MMPBSA is not performing Jason Swails (Tue Sep 08 2015 - 06:36:07 PDT)
    - Re: [AMBER] MMPBSA is not performing asma.msbi28.iiu.edu.pk (Tue Sep 08 2015 - 07:25:37 PDT)
[AMBER] Multiplicity in QM/MM calculations Kshatresh Dutta Dubey (Mon Sep 07 2015 - 10:13:38 PDT)
- Re: [AMBER] Multiplicity in QM/MM calculations Jason Swails (Mon Sep 07 2015 - 10:45:38 PDT)
[AMBER] Parameters for benzene sulfonamide Jovanovic, Srdan (Mon Sep 07 2015 - 10:16:55 PDT)
- Re: [AMBER] Parameters for benzene sulfonamide Karl Kirschner (Tue Sep 08 2015 - 01:24:30 PDT)
[AMBER] REMD to sample the conformational space of a defined part of the system Sergey Samsonov (Tue Sep 08 2015 - 00:50:33 PDT)
- Re: [AMBER] REMD to sample the conformational space of a defined part of the system Jason Swails (Tue Sep 08 2015 - 04:29:53 PDT)
  - Re: [AMBER] REMD to sample the conformational space of a defined part of the system Sergey Samsonov (Tue Sep 08 2015 - 07:05:47 PDT)
    - Re: [AMBER] REMD to sample the conformational space of a defined part of the system Jason Swails (Tue Sep 08 2015 - 13:15:02 PDT)
    - Re: [AMBER] REMD to sample the conformational space of a defined part of the system Sergey Samsonov (Fri Sep 11 2015 - 00:11:21 PDT)
    - Re: [AMBER] REMD to sample the conformational space of a defined part of the system Carlos Simmerling (Fri Sep 11 2015 - 04:25:55 PDT)
    - Re: [AMBER] REMD to sample the conformational space of a defined part of the system Sergey Samsonov (Fri Sep 11 2015 - 07:46:47 PDT)
[AMBER] Amber15 compiler error 'undefined reference to `fftw_plan_dft_r2c_3d'' with Cygwin Nigel Palmer (Tue Sep 08 2015 - 06:16:29 PDT)
- Re: [AMBER] Amber15 compiler error 'undefined reference to `fftw_plan_dft_r2c_3d'' with Cygwin Jason Swails (Tue Sep 08 2015 - 06:38:51 PDT)
  - Re: [AMBER] Amber15 compiler error 'undefined reference to `fftw_plan_dft_r2c_3d'' with Cygwin Nigel Palmer (Tue Sep 08 2015 - 06:50:24 PDT)
[AMBER] index and sort order in prmtop Hannes Loeffler (Tue Sep 08 2015 - 07:55:06 PDT)
- Re: [AMBER] index and sort order in prmtop Jason Swails (Tue Sep 08 2015 - 13:19:29 PDT)
[AMBER] watershell cpptraj question Travis Hughes (Tue Sep 08 2015 - 08:08:37 PDT)
- Re: [AMBER] watershell cpptraj question Daniel Roe (Tue Sep 08 2015 - 08:54:01 PDT)
[AMBER] Problem compiling cpptraj with openmp Marc van der Kamp (Tue Sep 08 2015 - 08:32:51 PDT)
- Re: [AMBER] Problem compiling cpptraj with openmp Daniel Roe (Tue Sep 08 2015 - 08:43:50 PDT)
  - Re: [AMBER] Problem compiling cpptraj with openmp Marc van der Kamp (Tue Sep 08 2015 - 09:05:48 PDT)
- Re: [AMBER] Problem compiling cpptraj with openmp Hannes Loeffler (Tue Sep 08 2015 - 08:46:08 PDT)
[AMBER] ParmEd problem: LJ12_6_4Error: Could not find parameters for ATOM_TYPE CX Karolina Markowska (Tue Sep 08 2015 - 14:41:10 PDT)
- Re: [AMBER] ParmEd problem: LJ12_6_4Error: Could not find parameters for ATOM_TYPE CX Jason Swails (Wed Sep 09 2015 - 08:27:54 PDT)
  - Re: [AMBER] ParmEd problem: LJ12_6_4Error: Could not find parameters for ATOM_TYPE CX Karolina Markowska (Wed Sep 09 2015 - 12:21:53 PDT)
[AMBER] Fw: important Do Yong Kim (Wed Sep 09 2015 - 00:06:23 PDT)
[AMBER] Contact map residues Neha Gandhi (Wed Sep 09 2015 - 00:30:30 PDT)
- Re: [AMBER] Contact map residues Daniel Roe (Wed Sep 16 2015 - 07:40:01 PDT)
[AMBER] Cphmd Arjun Sharma (Wed Sep 09 2015 - 08:17:13 PDT)
- Re: [AMBER] Cphmd Jason Swails (Wed Sep 09 2015 - 08:49:50 PDT)
[AMBER] Changing font size with mdout_analyzer.py Krantzman, Kristin D (Wed Sep 09 2015 - 08:19:31 PDT)
- Re: [AMBER] Changing font size with mdout_analyzer.py Jason Swails (Wed Sep 09 2015 - 08:47:21 PDT)
[AMBER] [parmed.py] chemistry.exceptions.AmberParmError loading topology file Eiros Zamora, Juan (Wed Sep 09 2015 - 10:34:50 PDT)
- Re: [AMBER] [parmed.py] chemistry.exceptions.AmberParmError loading topology file Jason Swails (Wed Sep 09 2015 - 18:50:01 PDT)
  - Re: [AMBER] [parmed.py] chemistry.exceptions.AmberParmError loading topology file Eiros Zamora, Juan (Thu Sep 10 2015 - 03:41:52 PDT)
    - Re: [AMBER] [parmed.py] chemistry.exceptions.AmberParmError loading topology file Jason Swails (Thu Sep 10 2015 - 05:36:16 PDT)
    - Re: [AMBER] [parmed.py] chemistry.exceptions.AmberParmError loading topology file Juan Eiros Zamora (Fri Sep 11 2015 - 04:16:26 PDT)
[AMBER] QM/MM Equilibration Errors Brittany Boykin (Wed Sep 09 2015 - 14:41:55 PDT)
- Re: [AMBER] QM/MM Equilibration Errors David A Case (Thu Sep 10 2015 - 06:07:02 PDT)
[AMBER] cpptraj script for average 3D protein structure? Michael Shokhen (Thu Sep 10 2015 - 01:23:13 PDT)
- Re: [AMBER] cpptraj script for average 3D protein structure? Repic Matej (Thu Sep 10 2015 - 02:58:59 PDT)
  - Re: [AMBER] cpptraj script for average 3D protein structure? Michael Shokhen (Thu Sep 10 2015 - 03:11:09 PDT)
    - Re: [AMBER] cpptraj script for average 3D protein structure? Eiros Zamora, Juan (Thu Sep 10 2015 - 03:37:59 PDT)
    - Re: [AMBER] cpptraj script for average 3D protein structure? Michael Shokhen (Thu Sep 10 2015 - 05:53:49 PDT)
[AMBER] several peptides in my input can be identified by cpptraj? Fabian gmail (Thu Sep 10 2015 - 03:05:50 PDT)
- Re: [AMBER] several peptides in my input can be identified by cpptraj? Daniel Roe (Wed Sep 16 2015 - 08:02:07 PDT)
  - Re: [AMBER] several peptides in my input can be identified by cpptraj? Fabian gmail (Wed Sep 16 2015 - 08:20:58 PDT)
[AMBER] xmgrace in microsoft Martina Devi (Thu Sep 10 2015 - 06:03:09 PDT)
- Re: [AMBER] xmgrace in microsoft Jason Swails (Thu Sep 10 2015 - 06:31:26 PDT)
- Re: [AMBER] xmgrace in microsoft David A Case (Thu Sep 10 2015 - 06:37:17 PDT)
  - Re: [AMBER] xmgrace in microsoft Martina Devi (Thu Sep 10 2015 - 06:43:13 PDT)
    - Re: [AMBER] xmgrace in microsoft Luciano Costa (Fri Sep 11 2015 - 19:14:13 PDT)
    - Re: [AMBER] xmgrace in microsoft Martina Devi (Thu Sep 17 2015 - 22:43:50 PDT)
    - Re: [AMBER] xmgrace in microsoft Ye Mei (Thu Sep 17 2015 - 22:55:54 PDT)
[AMBER] pca Lara rajam (Thu Sep 10 2015 - 08:30:44 PDT)
- Re: [AMBER] pca Daniel Roe (Wed Sep 16 2015 - 08:04:23 PDT)
[AMBER] setting a box mohammad r (Thu Sep 10 2015 - 08:35:07 PDT)
- Re: [AMBER] setting a box David A Case (Thu Sep 10 2015 - 09:02:27 PDT)
  - Re: [AMBER] setting a box mohammad r (Thu Sep 10 2015 - 10:45:10 PDT)
[AMBER] HPC Sofia Vasilakaki (Thu Sep 10 2015 - 12:17:43 PDT)
- Re: [AMBER] HPC Ross Walker (Thu Sep 10 2015 - 12:33:48 PDT)
  - Re: [AMBER] HPC Sofia Vasilakaki (Thu Sep 10 2015 - 13:32:38 PDT)
[AMBER] MCPB problem Kshatresh Dutta Dubey (Thu Sep 10 2015 - 13:25:00 PDT)
- Re: [AMBER] MCPB problem Pengfei Li (Fri Sep 11 2015 - 08:56:14 PDT)
  - Re: [AMBER] MCPB problem Kshatresh Dutta Dubey (Fri Sep 11 2015 - 09:15:19 PDT)
    - Re: [AMBER] MCPB problem Pengfei Li (Fri Sep 11 2015 - 09:19:52 PDT)
    - Re: [AMBER] MCPB problem Kshatresh Dutta Dubey (Fri Sep 11 2015 - 09:50:41 PDT)
    - Re: [AMBER] MCPB problem Kshatresh Dutta Dubey (Sat Sep 12 2015 - 07:45:29 PDT)
    - Re: [AMBER] MCPB problem Pengfei Li (Sat Sep 12 2015 - 16:30:02 PDT)
    - Re: [AMBER] MCPB problem Kshatresh Dutta Dubey (Sat Sep 12 2015 - 19:11:10 PDT)
    - Re: [AMBER] MCPB problem Kshatresh Dutta Dubey (Sat Sep 12 2015 - 20:05:24 PDT)
    - Re: [AMBER] MCPB problem Pengfei Li (Mon Sep 14 2015 - 09:15:29 PDT)
    - Re: [AMBER] MCPB problem Kshatresh Dutta Dubey (Mon Sep 14 2015 - 10:42:01 PDT)
    - Re: [AMBER] MCPB problem Pengfei Li (Mon Sep 14 2015 - 14:28:42 PDT)
[AMBER] keep residue numbering? Albert (Fri Sep 11 2015 - 00:12:24 PDT)
- Re: [AMBER] keep residue numbering? David A Case (Fri Sep 11 2015 - 08:06:09 PDT)
[AMBER] limit exceeded and high temperature Ruth Helena Tichauer (Fri Sep 11 2015 - 07:52:05 PDT)
- Re: [AMBER] limit exceeded and high temperature Jason Swails (Fri Sep 11 2015 - 08:26:17 PDT)
  - Re: [AMBER] limit exceeded and high temperature Ruth Helena Tichauer (Fri Sep 11 2015 - 08:40:13 PDT)
  - Re: [AMBER] limit exceeded and high temperature Ross Walker (Fri Sep 11 2015 - 08:48:30 PDT)
    - Re: [AMBER] limit exceeded and high temperature Ruth Helena Tichauer (Fri Sep 11 2015 - 09:06:21 PDT)
    - Re: [AMBER] limit exceeded and high temperature Ruth Helena Tichauer (Mon Sep 14 2015 - 02:56:46 PDT)
[AMBER] Parameterization empirical method Marcelo Andrade Chagas (Fri Sep 11 2015 - 11:40:41 PDT)
[AMBER] Addition of single water molecules Eric Berquist (Fri Sep 11 2015 - 13:21:06 PDT)
- Re: [AMBER] Addition of single water molecules Jason Swails (Fri Sep 11 2015 - 15:40:20 PDT)
[AMBER] CpHMD of Succinic Acid Rahul Ramesh (Fri Sep 11 2015 - 18:02:24 PDT)
- Re: [AMBER] CpHMD of Succinic Acid Jason Swails (Sat Sep 12 2015 - 19:56:59 PDT)
[AMBER] FW: No output Damiano Spadoni (Sat Sep 12 2015 - 13:52:00 PDT)
- Re: [AMBER] No output Ross Walker (Sat Sep 12 2015 - 14:02:09 PDT)
  - Re: [AMBER] No output Jason Swails (Sat Sep 12 2015 - 20:12:29 PDT)
    - Re: [AMBER] No output Damiano Spadoni (Mon Sep 14 2015 - 05:50:12 PDT)
    - Re: [AMBER] No output Jason Swails (Mon Sep 14 2015 - 06:04:19 PDT)
[AMBER] Testing the mail server George Tzotzos (Sun Sep 13 2015 - 14:51:27 PDT)
[AMBER] Proper Insertion of Covalently Bound Unit in Helical Structure Robert Molt (Sun Sep 13 2015 - 17:06:36 PDT)
- Re: [AMBER] Proper Insertion of Covalently Bound Unit in Helical Structure David A Case (Sun Sep 13 2015 - 21:01:02 PDT)
  - Re: [AMBER] Proper Insertion of Covalently Bound Unit in Helical Structure Dr. Robert Molt Jr. (Mon Sep 14 2015 - 11:29:22 PDT)
    - Re: [AMBER] Proper Insertion of Covalently Bound Unit in Helical Structure David A Case (Mon Sep 14 2015 - 15:04:13 PDT)
  - Re: [AMBER] Proper Insertion of Covalently Bound Unit in Helical Structure Robert Molt (Mon Sep 14 2015 - 13:58:22 PDT)
[AMBER] What is wrong with the minimization? Huggins, Esther, C (Sun Sep 13 2015 - 17:30:50 PDT)
- Re: [AMBER] What is wrong with the minimization? David A Case (Sun Sep 13 2015 - 21:08:41 PDT)
  - Re: [AMBER] What is wrong with the minimization? Huggins, Esther, C (Mon Sep 14 2015 - 07:14:42 PDT)
    - Re: [AMBER] What is wrong with the minimization? Jason Swails (Mon Sep 14 2015 - 09:02:20 PDT)
    - Re: [AMBER] What is wrong with the minimization? Huggins, Esther, C (Mon Sep 14 2015 - 09:12:07 PDT)
    - Re: [AMBER] What is wrong with the minimization? Jason Swails (Mon Sep 14 2015 - 09:22:57 PDT)
    - Re: [AMBER] What is wrong with the minimization? David A Case (Mon Sep 14 2015 - 14:40:47 PDT)
[AMBER] Simulation stops without errors Bala subramanian (Mon Sep 14 2015 - 00:46:49 PDT)
- Re: [AMBER] Simulation stops without errors Jason Swails (Mon Sep 14 2015 - 06:08:56 PDT)
  - Re: [AMBER] Simulation stops without errors Bala subramanian (Wed Sep 16 2015 - 02:06:26 PDT)
    - Re: [AMBER] Simulation stops without errors Jason Swails (Wed Sep 16 2015 - 05:28:15 PDT)
    - Re: [AMBER] Simulation stops without errors David A Case (Wed Sep 16 2015 - 05:56:09 PDT)
    - Re: [AMBER] Simulation stops without errors Bala subramanian (Thu Sep 17 2015 - 02:36:22 PDT)
    - Re: [AMBER] Simulation stops without errors Jason Swails (Thu Sep 17 2015 - 04:28:56 PDT)
[AMBER] Paramfit issues David Poole (Mon Sep 14 2015 - 03:31:57 PDT)
- Re: [AMBER] Paramfit issues Robin Betz (Mon Sep 14 2015 - 14:53:44 PDT)
[AMBER] Parmed crash Mykola Dimura (Mon Sep 14 2015 - 08:50:12 PDT)
- Re: [AMBER] Parmed crash Jason Swails (Mon Sep 14 2015 - 09:04:23 PDT)
  - Re: [AMBER] Parmed crash Mykola Dimura (Mon Sep 14 2015 - 09:23:14 PDT)
    - Re: [AMBER] Parmed crash Jason Swails (Mon Sep 14 2015 - 09:44:40 PDT)
[AMBER] mmpbsa error Lara rajam (Mon Sep 14 2015 - 18:40:49 PDT)
- Re: [AMBER] mmpbsa error Jason Swails (Tue Sep 15 2015 - 07:27:42 PDT)
  - Re: [AMBER] mmpbsa error Lara rajam (Tue Sep 15 2015 - 09:50:37 PDT)
    - Re: [AMBER] mmpbsa error Jason Swails (Tue Sep 15 2015 - 10:25:48 PDT)
[AMBER] Regarding Simulations of Ionic Liquids on GPU MOHD HOMAIDUR RAHMAN (Mon Sep 14 2015 - 22:45:41 PDT)
- Re: [AMBER] Regarding Simulations of Ionic Liquids on GPU David A Case (Tue Sep 15 2015 - 05:48:45 PDT)
[AMBER] A question on binding free energy decomposition output wliu (Mon Sep 14 2015 - 23:22:27 PDT)
- Re: [AMBER] A question on binding free energy decomposition output Sofia Vasilakaki (Tue Sep 15 2015 - 01:01:20 PDT)
- Re: [AMBER] A question on binding free energy decomposition output Jason Swails (Tue Sep 15 2015 - 07:30:30 PDT)
  - Re: [AMBER] A question on binding free energy decomposition output wliu (Tue Sep 15 2015 - 18:28:58 PDT)
[AMBER] query ankita mehta (Tue Sep 15 2015 - 06:22:01 PDT)
- [AMBER] query Kenneth Huang (Tue Sep 15 2015 - 06:38:05 PDT)
- Re: [AMBER] query David A Case (Tue Sep 15 2015 - 11:31:34 PDT)
  - Re: [AMBER] query ankita mehta (Wed Sep 16 2015 - 03:27:32 PDT)
    - Re: [AMBER] query Kenneth Huang (Wed Sep 16 2015 - 05:42:20 PDT)
    - Re: [AMBER] query David A Case (Wed Sep 16 2015 - 07:02:35 PDT)
    - Re: [AMBER] query ankita mehta (Wed Sep 16 2015 - 08:06:35 PDT)
    - Re: [AMBER] query Jason Swails (Wed Sep 16 2015 - 08:17:14 PDT)
    - Re: [AMBER] query ankita mehta (Wed Sep 16 2015 - 08:22:04 PDT)
    - Re: [AMBER] query David A Case (Wed Sep 16 2015 - 12:14:22 PDT)
    - Re: [AMBER] query ankita mehta (Fri Sep 18 2015 - 07:35:46 PDT)
    - Re: [AMBER] query Nic Steussy (Wed Sep 16 2015 - 08:47:56 PDT)
[AMBER] sqm Sofia Vasilakaki (Tue Sep 15 2015 - 07:11:40 PDT)
- Re: [AMBER] sqm Hannes Loeffler (Tue Sep 15 2015 - 07:18:09 PDT)
  - Re: [AMBER] sqm Sofia Vasilakaki (Tue Sep 15 2015 - 07:29:45 PDT)
    - Re: [AMBER] sqm Jason Swails (Tue Sep 15 2015 - 07:33:10 PDT)
    - Re: [AMBER] sqm Hannes Loeffler (Tue Sep 15 2015 - 07:34:01 PDT)
- Re: [AMBER] sqm David A Case (Tue Sep 15 2015 - 11:39:57 PDT)
  - Re: [AMBER] sqm Sofia Vasilakaki (Tue Sep 15 2015 - 12:37:41 PDT)
[AMBER] Has anyone tried VMD in the second step of tutorial A1? Xing (Tue Sep 15 2015 - 08:52:33 PDT)
[AMBER] vlimit exceeded and high temperature Ruth Helena Tichauer (Tue Sep 15 2015 - 09:06:34 PDT)
- Re: [AMBER] vlimit exceeded and high temperature David A Case (Tue Sep 15 2015 - 11:52:01 PDT)
  - Re: [AMBER] vlimit exceeded and high temperature Ruth Helena Tichauer (Wed Sep 16 2015 - 06:16:29 PDT)
    - Re: [AMBER] vlimit exceeded and high temperature Jason Swails (Wed Sep 16 2015 - 08:07:41 PDT)
    - Re: [AMBER] vlimit exceeded and high temperature Ruth Helena Tichauer (Fri Sep 18 2015 - 01:52:23 PDT)
    - [AMBER] parmed.py Urszula Uciechowska (Fri Sep 18 2015 - 03:31:15 PDT)
    - Re: [AMBER] parmed.py Jason Swails (Fri Sep 18 2015 - 04:40:43 PDT)
    - Re: [AMBER] vlimit exceeded and high temperature Jason Swails (Fri Sep 18 2015 - 04:29:13 PDT)
    - Re: [AMBER] vlimit exceeded and high temperature Ruth Helena Tichauer (Fri Sep 18 2015 - 05:48:55 PDT)
[AMBER] cyclic peptides and bond command in leap Jonathan Gough (Tue Sep 15 2015 - 10:04:18 PDT)
- Re: [AMBER] cyclic peptides and bond command in leap David A Case (Tue Sep 15 2015 - 12:02:04 PDT)
  - Re: [AMBER] cyclic peptides and bond command in leap Jonathan Gough (Tue Sep 15 2015 - 12:11:29 PDT)
  - Re: [AMBER] cyclic peptides and bond command in leap Jonathan Gough (Tue Sep 15 2015 - 12:55:49 PDT)
    - Re: [AMBER] cyclic peptides and bond command in leap David A Case (Tue Sep 15 2015 - 14:50:59 PDT)
    - Re: [AMBER] cyclic peptides and bond command in leap Anselm Horn (Thu Sep 17 2015 - 00:19:13 PDT)
[AMBER] Antechamber error Kalenkiewicz, Andrew (NIH/NICHD) [F] (Tue Sep 15 2015 - 11:38:43 PDT)
- Re: [AMBER] Antechamber error David A Case (Tue Sep 15 2015 - 14:41:08 PDT)
[AMBER] Fwd: Mail ceased to work in the last 72 hours George Tzotzos (Tue Sep 15 2015 - 19:01:37 PDT)
[AMBER] problem in plotting secondary structure graph Sehrish Naz (Tue Sep 15 2015 - 21:11:19 PDT)
- Re: [AMBER] problem in plotting secondary structure graph Daniel Roe (Wed Sep 16 2015 - 08:09:40 PDT)
[AMBER] Problems with the Amber-14 compilation and using MMPBSA.py with ubuntu ayesha kanwal (Tue Sep 15 2015 - 23:10:16 PDT)
- Re: [AMBER] Problems with the Amber-14 compilation and using MMPBSA.py with ubuntu Jason Swails (Wed Sep 16 2015 - 05:25:34 PDT)
- Re: [AMBER] Problems with the Amber-14 compilation and using MMPBSA.py with ubuntu David A Case (Wed Sep 16 2015 - 05:53:49 PDT)
[AMBER] help in parallel run Robin Jain (Wed Sep 16 2015 - 02:36:36 PDT)
- Re: [AMBER] help in parallel run Jason Swails (Wed Sep 16 2015 - 05:41:05 PDT)
- Re: [AMBER] help in parallel run David A Case (Wed Sep 16 2015 - 05:58:37 PDT)
[AMBER] Test George Tzotzos (Wed Sep 16 2015 - 05:18:31 PDT)
[AMBER] cphmd reference energy Arjun Sharma (Wed Sep 16 2015 - 07:44:10 PDT)
- Re: [AMBER] cphmd reference energy Jason Swails (Wed Sep 16 2015 - 08:16:01 PDT)
[AMBER] Splitting LES trajectory Sergey Samsonov (Wed Sep 16 2015 - 08:29:52 PDT)
- Re: [AMBER] Splitting LES trajectory Daniel Roe (Wed Sep 16 2015 - 08:53:32 PDT)
[AMBER] DISAVE does not work on pmemd.cuda / GPU Mykola Dimura (Wed Sep 16 2015 - 09:57:33 PDT)
- Re: [AMBER] DISAVE does not work on pmemd.cuda / GPU David A Case (Wed Sep 16 2015 - 19:42:13 PDT)
[AMBER] Michaelis complex Hector A. Baldoni (Wed Sep 16 2015 - 13:11:06 PDT)
- Re: [AMBER] Michaelis complex Jason Swails (Thu Sep 17 2015 - 04:25:44 PDT)
  - Re: [AMBER] Michaelis complex Hector A. Baldoni (Thu Sep 17 2015 - 06:44:18 PDT)
    - Re: [AMBER] Michaelis complex Carlos Simmerling (Thu Sep 17 2015 - 06:48:33 PDT)
    - Re: [AMBER] Michaelis complex Jason Swails (Thu Sep 17 2015 - 08:16:59 PDT)
    - Re: [AMBER] Michaelis complex Carlos Simmerling (Thu Sep 17 2015 - 08:34:12 PDT)
    - Re: [AMBER] Michaelis complex Hector A. Baldoni (Thu Sep 17 2015 - 10:35:48 PDT)
    - Re: [AMBER] Michaelis complex Jason Swails (Thu Sep 17 2015 - 10:57:03 PDT)
    - Re: [AMBER] Michaelis complex Carlos Simmerling (Thu Sep 17 2015 - 11:07:49 PDT)
    - Re: [AMBER] Michaelis complex Jason Swails (Thu Sep 17 2015 - 08:20:50 PDT)
[AMBER] Leap Connection of Covalent Unit Continued Robert Molt (Wed Sep 16 2015 - 18:30:45 PDT)
- Re: [AMBER] Leap Connection of Covalent Unit Continued David A Case (Wed Sep 16 2015 - 19:27:48 PDT)
[AMBER] antechamber error Atila Petrosian (Thu Sep 17 2015 - 06:51:03 PDT)
- Re: [AMBER] antechamber error Atila Petrosian (Thu Sep 17 2015 - 06:56:54 PDT)
  - Re: [AMBER] antechamber error David A Case (Thu Sep 17 2015 - 08:29:17 PDT)
    - Re: [AMBER] antechamber error Atila Petrosian (Thu Sep 17 2015 - 08:44:08 PDT)
    - Re: [AMBER] antechamber error hannes.loeffler.stfc.ac.uk (Thu Sep 17 2015 - 10:29:00 PDT)
    - Re: [AMBER] antechamber error Nic Steussy (Thu Sep 17 2015 - 10:35:42 PDT)
    - Re: [AMBER] antechamber error David A Case (Thu Sep 17 2015 - 11:47:15 PDT)
    - Re: [AMBER] antechamber error Atila Petrosian (Thu Sep 17 2015 - 23:21:22 PDT)
    - Re: [AMBER] antechamber error Atila Petrosian (Fri Sep 18 2015 - 04:29:01 PDT)
    - Re: [AMBER] antechamber error Jason Swails (Fri Sep 18 2015 - 04:34:51 PDT)
    - Re: [AMBER] antechamber error David A Case (Fri Sep 18 2015 - 06:02:33 PDT)
    - Re: [AMBER] antechamber error Atila Petrosian (Fri Sep 18 2015 - 10:55:26 PDT)
    - Re: [AMBER] antechamber error Atila Petrosian (Fri Sep 18 2015 - 11:04:08 PDT)
    - Re: [AMBER] antechamber error David A Case (Fri Sep 18 2015 - 11:56:07 PDT)
    - Re: [AMBER] antechamber error Atila Petrosian (Fri Sep 18 2015 - 12:57:54 PDT)
[AMBER] Issues with gaff cd=cc atom type Francesco Pietra (Fri Sep 18 2015 - 00:46:20 PDT)
- Re: [AMBER] Issues with gaff cd=cc atom type Jason Swails (Fri Sep 18 2015 - 04:36:52 PDT)
  - Re: [AMBER] Issues with gaff cd=cc atom type Francesco Pietra (Fri Sep 18 2015 - 09:57:12 PDT)
    - Re: [AMBER] Issues with gaff cd=cc atom type Jason Swails (Fri Sep 18 2015 - 10:47:57 PDT)
    - Re: [AMBER] Issues with gaff cd=cc atom type Francesco Pietra (Fri Sep 18 2015 - 13:39:46 PDT)
    - Re: [AMBER] Issues with gaff cd=cc atom type Robert Molt (Fri Sep 18 2015 - 17:52:24 PDT)
    - Re: [AMBER] Issues with gaff cd=cc atom type Francesco Pietra (Sat Sep 19 2015 - 00:21:33 PDT)
[AMBER] MG ions being misplaced Kalenkiewicz, Andrew (NIH/NICHD) [F] (Fri Sep 18 2015 - 09:44:27 PDT)
- Re: [AMBER] MG ions being misplaced David A Case (Fri Sep 18 2015 - 11:43:27 PDT)
[AMBER] Molecular Dynamics for Porphyrin Amber Maharaj (Fri Sep 18 2015 - 09:45:47 PDT)
- Re: [AMBER] Molecular Dynamics for Porphyrin Jason Swails (Fri Sep 18 2015 - 09:55:28 PDT)
- Re: [AMBER] Molecular Dynamics for Porphyrin David A Case (Fri Sep 18 2015 - 11:48:09 PDT)
[AMBER] per residue decomposition MMPBSA Lara rajam (Fri Sep 18 2015 - 10:03:29 PDT)
- Re: [AMBER] per residue decomposition MMPBSA Jason Swails (Fri Sep 18 2015 - 10:49:43 PDT)
[AMBER] CpHMD for non protein residues Rahul Ramesh (Fri Sep 18 2015 - 13:59:29 PDT)
- Re: [AMBER] CpHMD for non protein residues Jason Swails (Fri Sep 18 2015 - 14:04:09 PDT)
  - Re: [AMBER] CpHMD for non protein residues Rahul Ramesh (Fri Sep 18 2015 - 14:23:02 PDT)
[AMBER] Minimization Marcelo Andrade Chagas (Fri Sep 18 2015 - 14:13:25 PDT)
[AMBER] Calculating energy of solute Krantzman, Kristin D (Fri Sep 18 2015 - 14:33:10 PDT)
- Re: [AMBER] Calculating energy of solute Christina Bergonzo (Fri Sep 18 2015 - 14:44:08 PDT)
[AMBER] Antechamber Flags Robert Molt (Fri Sep 18 2015 - 18:00:04 PDT)
- Re: [AMBER] Antechamber Flags David A Case (Fri Sep 18 2015 - 18:24:45 PDT)
[AMBER] ambertools14 Andrew Bostick (Sat Sep 19 2015 - 04:30:55 PDT)
- Re: [AMBER] ambertools14 Jason Swails (Sat Sep 19 2015 - 06:04:49 PDT)
[AMBER] q4md FF with two "small" molecules Francesco Pietra (Sun Sep 20 2015 - 02:01:08 PDT)
- Re: [AMBER] q4md FF with two "small" molecules David A Case (Sun Sep 20 2015 - 05:40:16 PDT)
  - Re: [AMBER] q4md FF with two "small" molecules Francesco Pietra (Sun Sep 20 2015 - 07:47:22 PDT)
    - [AMBER] Fwd: q4md FF with two "small" molecules Francesco Pietra (Mon Sep 21 2015 - 03:11:00 PDT)
    - Re: [AMBER] Fwd: q4md FF with two "small" molecules Jason Swails (Mon Sep 21 2015 - 04:23:50 PDT)
    - Re: [AMBER] Fwd: q4md FF with two "small" molecules Francesco Pietra (Mon Sep 21 2015 - 09:38:44 PDT)
[AMBER] on MD and Ramachandran outlier Brett (Sun Sep 20 2015 - 04:49:12 PDT)
- Re: [AMBER] on MD and Ramachandran outlier Carlos Simmerling (Sun Sep 20 2015 - 05:04:31 PDT)
[AMBER] Extracting Information for each Frames Considered for Entropy Calculation by Normal Modes anilkumarsahoo.physics.iisc.ernet.in (Sun Sep 20 2015 - 15:09:22 PDT)
- Re: [AMBER] Extracting Information for each Frames Considered for Entropy Calculation by Normal Modes Jason Swails (Sun Sep 20 2015 - 19:09:32 PDT)
  - Re: [AMBER] Extracting Information for each Frames Considered for Entropy Calculation by Normal Modes anilkumarsahoo.physics.iisc.ernet.in (Mon Sep 21 2015 - 05:17:30 PDT)
[AMBER] QM&Lipid14 Sofia Vasilakaki (Sun Sep 20 2015 - 16:58:28 PDT)
- Re: [AMBER] QM&Lipid14 Ross Walker (Mon Sep 21 2015 - 00:19:30 PDT)
[AMBER] SHAKE&Vlimit 罗艳玲 (Sun Sep 20 2015 - 18:56:30 PDT)
- Re: [AMBER] SHAKE&Vlimit Jason Swails (Mon Sep 21 2015 - 04:28:21 PDT)
  - Re: [AMBER] SHAKE&Vlimit 罗艳玲 (Mon Sep 21 2015 - 04:48:51 PDT)
    - Re: [AMBER] SHAKE&Vlimit David A Case (Mon Sep 21 2015 - 08:48:01 PDT)
[AMBER] Problem In Performing MMPBSA Calculation for System containing Ligand and Protein 杨川 (Sun Sep 20 2015 - 21:30:38 PDT)
- Re: [AMBER] Problem In Performing MMPBSA Calculation for System containing Ligand and Protein Jason Swails (Mon Sep 21 2015 - 04:19:50 PDT)
- [AMBER] Problem In Performing MMPBSA Calculation for System containing Ligand and Protein 杨川 (Mon Sep 21 2015 - 19:15:12 PDT)
  - Re: [AMBER] Problem In Performing MMPBSA Calculation for System containing Ligand and Protein Ray Luo, Ph.D. (Tue Sep 22 2015 - 11:28:45 PDT)
[AMBER] glycam parameter file Batuhan Kav (Mon Sep 21 2015 - 03:23:39 PDT)
- Re: [AMBER] glycam parameter file Jason Swails (Mon Sep 21 2015 - 04:18:01 PDT)
  - Re: [AMBER] glycam parameter file Batuhan Kav (Mon Sep 21 2015 - 05:45:09 PDT)
    - Re: [AMBER] glycam parameter file Jason Swails (Mon Sep 21 2015 - 06:35:01 PDT)
    - Re: [AMBER] glycam parameter file Lachele Foley (Mon Sep 21 2015 - 06:55:32 PDT)
    - Re: [AMBER] glycam parameter file Batuhan Kav (Mon Sep 21 2015 - 07:27:50 PDT)
[AMBER] warning when using cpptraj on BB atoms missing Fabian gmail (Mon Sep 21 2015 - 07:16:43 PDT)
- Re: [AMBER] warning when using cpptraj on BB atoms missing Daniel Roe (Mon Sep 21 2015 - 07:54:32 PDT)
  - Re: [AMBER] warning when using cpptraj on BB atoms missing Fabian Glaser (Mon Sep 21 2015 - 09:09:24 PDT)
[AMBER] Prospective research areas of AMBER Sabyasachi Sahoo (Mon Sep 21 2015 - 10:25:23 PDT)
- Re: [AMBER] Prospective research areas of AMBER David A Case (Mon Sep 21 2015 - 11:34:58 PDT)
  - Re: [AMBER] Prospective research areas of AMBER Sabyasachi Sahoo (Tue Sep 22 2015 - 02:40:10 PDT)
[AMBER] Freeze atoms to DM Marcelo Andrade Chagas (Mon Sep 21 2015 - 12:21:27 PDT)
- Re: [AMBER] Freeze atoms to DM Gustavo Seabra (Mon Sep 21 2015 - 12:33:00 PDT)
  - Re: [AMBER] Freeze atoms to DM Marcelo Andrade Chagas (Mon Sep 21 2015 - 12:55:55 PDT)
- Re: [AMBER] Freeze atoms to DM Jason Swails (Mon Sep 21 2015 - 12:33:37 PDT)
  - Re: [AMBER] Freeze atoms to DM Jason Swails (Mon Sep 21 2015 - 12:34:27 PDT)
[AMBER] Prepgen Robert Molt (Mon Sep 21 2015 - 18:36:43 PDT)
- Re: [AMBER] Prepgen David A Case (Tue Sep 22 2015 - 05:10:35 PDT)
[AMBER] Installing AMBER Wong Li Zhe (Mon Sep 21 2015 - 20:19:54 PDT)
- Re: [AMBER] Installing AMBER Hector A. Baldoni (Tue Sep 22 2015 - 04:12:37 PDT)
- Re: [AMBER] Installing AMBER David A Case (Tue Sep 22 2015 - 05:17:06 PDT)
[AMBER] distance based mask problem Chris (Mon Sep 21 2015 - 21:01:19 PDT)
- Re: [AMBER] distance based mask problem Jason Swails (Tue Sep 22 2015 - 05:15:26 PDT)
  - Re: [AMBER] distance based mask problem Chris (Thu Sep 24 2015 - 05:46:10 PDT)
    - Re: [AMBER] distance based mask problem Daniel Roe (Thu Sep 24 2015 - 07:55:32 PDT)
    - Re: [AMBER] distance based mask problem Daniel Roe (Thu Sep 24 2015 - 08:19:47 PDT)
    - Re: [AMBER] distance based mask problem Chris (Mon Sep 28 2015 - 05:57:13 PDT)
    - Re: [AMBER] distance based mask problem Daniel Roe (Mon Sep 28 2015 - 08:00:20 PDT)
[AMBER] Usage of off-diagonal coupling parameters for EVB model bijyalaxmi athokpam (Tue Sep 22 2015 - 00:38:17 PDT)
[AMBER] help in RDF Robin Jain (Tue Sep 22 2015 - 01:18:57 PDT)
- Re: [AMBER] help in RDF Jason Swails (Tue Sep 22 2015 - 05:20:01 PDT)
  - Re: [AMBER] help in RDF Tom Kurtzman (Tue Sep 22 2015 - 07:26:38 PDT)
[AMBER] Protein - RNA modelling Sidhu, Khushwant (Dr.) (Tue Sep 22 2015 - 06:50:01 PDT)
- Re: [AMBER] Protein - RNA modelling Brian Radak (Tue Sep 22 2015 - 11:45:53 PDT)
- Re: [AMBER] Protein - RNA modelling David A Case (Wed Sep 23 2015 - 18:21:52 PDT)
[AMBER] degraded GPU performance Alessandro Contini (alessandro.contini) (Tue Sep 22 2015 - 07:22:00 PDT)
- Re: [AMBER] degraded GPU performance Ross Walker (Tue Sep 22 2015 - 07:41:47 PDT)
[AMBER] R: Re: degraded GPU performance Alessandro Contini (Tue Sep 22 2015 - 07:50:08 PDT)
[AMBER] Addions Na+ Marcelo Andrade Chagas (Tue Sep 22 2015 - 11:52:44 PDT)
- Re: [AMBER] Addions Na+ Bill Ross (Tue Sep 22 2015 - 12:11:10 PDT)
  - Re: [AMBER] Addions Na+ Marcelo Andrade Chagas (Tue Sep 22 2015 - 12:20:08 PDT)
    - Re: [AMBER] Addions Na+ Kenneth Huang (Tue Sep 22 2015 - 12:26:10 PDT)
    - Re: [AMBER] Addions Na+ Jason Swails (Tue Sep 22 2015 - 12:33:44 PDT)
- Re: [AMBER] Addions Na+ Bill Ross (Tue Sep 22 2015 - 13:44:35 PDT)
  - Re: [AMBER] Addions Na+ Marcelo Andrade Chagas (Tue Sep 22 2015 - 14:07:47 PDT)
    - Re: [AMBER] Addions Na+ Jason Swails (Tue Sep 22 2015 - 14:17:02 PDT)
    - Re: [AMBER] Addions Na+ Marcelo Andrade Chagas (Tue Sep 22 2015 - 14:20:26 PDT)
    - Re: [AMBER] Addions Na+ David A Case (Wed Sep 23 2015 - 06:40:11 PDT)
[AMBER] AMBER Tutorial B1 Backbone atoms Aishani Prem (Tue Sep 22 2015 - 13:32:28 PDT)
- Re: [AMBER] AMBER Tutorial B1 Backbone atoms Thomas Cheatham (Tue Sep 22 2015 - 13:46:18 PDT)
  - Re: [AMBER] AMBER Tutorial B1 Backbone atoms Aishani Prem (Wed Sep 23 2015 - 18:51:18 PDT)
[AMBER] Halogen bond force field in AMBER psu4.uic.edu (Tue Sep 22 2015 - 15:49:39 PDT)
- Re: [AMBER] Halogen bond force field in AMBER Thomas Cheatham (Tue Sep 22 2015 - 16:04:56 PDT)
  - Re: [AMBER] Halogen bond force field in AMBER Mahmoud A. A. Ibrahim (Wed Sep 23 2015 - 02:00:00 PDT)
    - Re: [AMBER] Halogen bond force field in AMBER psu4.uic.edu (Wed Oct 28 2015 - 23:03:39 PDT)
[AMBER] OpenMM Sofia Vasilakaki (Tue Sep 22 2015 - 17:26:45 PDT)
- Re: [AMBER] OpenMM Hai Nguyen (Tue Sep 22 2015 - 18:32:39 PDT)
- Re: [AMBER] OpenMM Jason Swails (Wed Sep 23 2015 - 06:23:38 PDT)
[AMBER] Implementation of GBSA in AMBER. Abhilash J (Tue Sep 22 2015 - 22:14:07 PDT)
- Re: [AMBER] Implementation of GBSA in AMBER. Hai Nguyen (Tue Sep 22 2015 - 22:32:11 PDT)
  - Re: [AMBER] Implementation of GBSA in AMBER. Abhilash J (Tue Sep 22 2015 - 23:26:03 PDT)
    - Re: [AMBER] Implementation of GBSA in AMBER. Jason Swails (Wed Sep 23 2015 - 06:31:37 PDT)
[AMBER] Command for hbond analysis Martina Devi (Wed Sep 23 2015 - 00:41:35 PDT)
- [AMBER] Command for hbond analysis Daniel Roe (Wed Sep 23 2015 - 04:11:57 PDT)
  - Re: [AMBER] Command for hbond analysis Martina Devi (Wed Sep 23 2015 - 07:08:51 PDT)
[AMBER] HELP in Emperical Valence bond model (EVB) bijyalaxmi athokpam (Wed Sep 23 2015 - 01:55:54 PDT)
- Re: [AMBER] HELP in Emperical Valence bond model (EVB) David A Case (Wed Sep 23 2015 - 12:16:13 PDT)
  - Re: [AMBER] HELP in Emperical Valence bond model (EVB) bijyalaxmi athokpam (Thu Sep 24 2015 - 08:19:59 PDT)
[AMBER] Hoogsteen-Watson Base pair Martina Devi (Wed Sep 23 2015 - 08:02:01 PDT)
- Re: [AMBER] Hoogsteen-Watson Base pair David A Case (Wed Sep 23 2015 - 12:21:33 PDT)
[AMBER] CpHMD simulation for non protein residues Rahul Ramesh (Wed Sep 23 2015 - 09:05:46 PDT)
- Re: [AMBER] CpHMD simulation for non protein residues Jason Swails (Wed Sep 23 2015 - 10:28:54 PDT)
  - Re: [AMBER] CpHMD simulation for non protein residues Rahul Ramesh (Wed Sep 23 2015 - 10:55:22 PDT)
[AMBER] analysis from mixed amber 12 and amber 14 simulations George Green (Wed Sep 23 2015 - 12:22:24 PDT)
- Re: [AMBER] analysis from mixed amber 12 and amber 14 simulations David A Case (Wed Sep 23 2015 - 18:21:59 PDT)
  - Re: [AMBER] analysis from mixed amber 12 and amber 14 simulations George Green (Wed Sep 23 2015 - 22:27:27 PDT)
[AMBER] free -COOH at the C-terminus Xing (Thu Sep 24 2015 - 12:11:27 PDT)
- Re: [AMBER] free -COOH at the C-terminus Jason Swails (Thu Sep 24 2015 - 12:13:46 PDT)
  - Re: [AMBER] free -COOH at the C-terminus Xing (Thu Sep 24 2015 - 13:01:34 PDT)
[AMBER] Membrane simulation without a membrane, only lipophilic solvent (membranemimetic) Marawan Hussien (Thu Sep 24 2015 - 18:10:50 PDT)
- [AMBER] Membrane simulation without a membrane, only lipophilic solvent (membranemimetic) Marawan Hussien (Thu Sep 24 2015 - 19:11:03 PDT)
[AMBER] Membrane simulation without a membrane, only lipophilic solvent (membranemimetic) sridhar ganesan (Thu Sep 24 2015 - 20:10:43 PDT)
[AMBER] AMBER benchmarks Neha Gandhi (Fri Sep 25 2015 - 03:05:55 PDT)
- Re: [AMBER] AMBER benchmarks Hannes Loeffler (Fri Sep 25 2015 - 03:26:08 PDT)
[AMBER] jfastw=4 and vlimit exceeded Ruth Helena Tichauer (Fri Sep 25 2015 - 06:46:06 PDT)
- Re: [AMBER] jfastw=4 and vlimit exceeded Jason Swails (Fri Sep 25 2015 - 07:27:43 PDT)
  - Re: [AMBER] jfastw=4 and vlimit exceeded Ruth Helena Tichauer (Fri Sep 25 2015 - 08:08:38 PDT)
    - Re: [AMBER] jfastw=4 and vlimit exceeded Jason Swails (Fri Sep 25 2015 - 08:24:32 PDT)
    - Re: [AMBER] jfastw=4 and vlimit exceeded Ruth Helena Tichauer (Fri Sep 25 2015 - 08:45:08 PDT)
[AMBER] adQMMM multiple solvation regions Covington, Cody Lance (Fri Sep 25 2015 - 08:03:31 PDT)
[AMBER] T-REMD Reproducibility - Cluster v.s Desktop Thiago Lipinski Paes (Fri Sep 25 2015 - 09:11:55 PDT)
- Re: [AMBER] T-REMD Reproducibility - Cluster v.s Desktop Carlos Simmerling (Fri Sep 25 2015 - 09:17:12 PDT)
  - Re: [AMBER] T-REMD Reproducibility - Cluster v.s Desktop Thiago Lipinski Paes (Fri Sep 25 2015 - 09:58:49 PDT)
    - Re: [AMBER] T-REMD Reproducibility - Cluster v.s Desktop Carlos Simmerling (Fri Sep 25 2015 - 10:04:13 PDT)
    - Re: [AMBER] T-REMD Reproducibility - Cluster v.s Desktop Jason Swails (Fri Sep 25 2015 - 10:32:58 PDT)
- Re: [AMBER] T-REMD Reproducibility - Cluster v.s Desktop Gustavo Seabra (Fri Sep 25 2015 - 11:18:20 PDT)
  - Re: [AMBER] T-REMD Reproducibility - Cluster v.s Desktop Thiago Lipinski Paes (Fri Sep 25 2015 - 12:04:16 PDT)
[AMBER] Minimization of steps Marcelo Andrade Chagas (Fri Sep 25 2015 - 11:26:39 PDT)
- Re: [AMBER] Minimization of steps David A Case (Fri Sep 25 2015 - 17:53:34 PDT)
[AMBER] Fwd: ISC-2015-3BS-09 Sushi Shilpa (Sat Sep 26 2015 - 03:39:40 PDT)
[AMBER] wrap problem with QM/MM Covington, Cody Lance (Sun Sep 27 2015 - 13:49:38 PDT)
- Re: [AMBER] wrap problem with QM/MM Marc van der Kamp (Mon Sep 28 2015 - 01:01:22 PDT)
  - Re: [AMBER] wrap problem with QM/MM Covington, Cody Lance (Mon Sep 28 2015 - 07:18:49 PDT)
[AMBER] Problem with saving parameters for a complex having Heme group 杨川 (Sun Sep 27 2015 - 21:29:35 PDT)
- Re: [AMBER] Problem with saving parameters for a complex having Heme group Jason Swails (Mon Sep 28 2015 - 05:22:29 PDT)
- Re: [AMBER] Problem with saving parameters for a complex having Heme group David A Case (Mon Sep 28 2015 - 05:28:53 PDT)
- [AMBER] Problem with saving parameters for a complex having Heme group 杨川 (Tue Sep 29 2015 - 20:25:36 PDT)
  - Re: [AMBER] Problem with saving parameters for a complex having Heme group Emilio Lence (Mon Feb 08 2016 - 08:46:43 PST)
[AMBER] Updates for PBSA energy calculations Christina Berti (Mon Sep 28 2015 - 16:17:04 PDT)
- Re: [AMBER] Updates for PBSA energy calculations Jason Swails (Mon Sep 28 2015 - 22:07:47 PDT)
  - Re: [AMBER] Updates for PBSA energy calculations Ray Luo, Ph.D. (Tue Sep 29 2015 - 09:57:05 PDT)
  - Re: [AMBER] Updates for PBSA energy calculations Christina Berti (Wed Sep 30 2015 - 08:50:49 PDT)
    - Re: [AMBER] Updates for PBSA energy calculations David A Case (Wed Sep 30 2015 - 11:41:23 PDT)
    - Re: [AMBER] Updates for PBSA energy calculations Christina Berti (Wed Sep 30 2015 - 13:14:04 PDT)
    - Re: [AMBER] Updates for PBSA energy calculations Jason Swails (Wed Sep 30 2015 - 15:00:18 PDT)
    - Re: [AMBER] Updates for PBSA energy calculations Christina Berti (Thu Oct 01 2015 - 12:29:03 PDT)
    - Re: [AMBER] Updates for PBSA energy calculations Jason Swails (Thu Oct 01 2015 - 13:13:28 PDT)
[AMBER] 12 PhD positions for the Marie Skłodowska-Curie ITN-European MoGglyNet Alessandro Contini (Tue Sep 29 2015 - 02:23:46 PDT)
[AMBER] Error: ptraj is needed for MMPBSA Ayesha Kanwal (Tue Sep 29 2015 - 15:07:43 PDT)
- Re: [AMBER] Error: ptraj is needed for MMPBSA Daniel Roe (Tue Sep 29 2015 - 15:52:16 PDT)
  - Re: [AMBER] Error: ptraj is needed for MMPBSA Ayesha Kanwal (Wed Sep 30 2015 - 07:46:04 PDT)
    - Re: [AMBER] Error: ptraj is needed for MMPBSA Jason Swails (Wed Sep 30 2015 - 08:37:45 PDT)
    - Re: [AMBER] Error: ptraj is needed for MMPBSA Ayesha Kanwal (Sun Oct 11 2015 - 07:23:49 PDT)
    - Re: [AMBER] Error: ptraj is needed for MMPBSA Ayesha Kanwal (Sun Oct 11 2015 - 07:30:18 PDT)
    - Re: [AMBER] Error: ptraj is needed for MMPBSA Jason Swails (Sun Oct 11 2015 - 08:28:47 PDT)
    - Re: [AMBER] Error: ptraj is needed for MMPBSA Ayesha Kanwal (Mon Oct 12 2015 - 06:48:32 PDT)
    - Re: [AMBER] Error: ptraj is needed for MMPBSA Daniel Roe (Mon Oct 12 2015 - 07:34:21 PDT)
    - Re: [AMBER] Error: ptraj is needed for MMPBSA Ayesha Kanwal (Mon Oct 12 2015 - 07:55:35 PDT)
    - Re: [AMBER] Error: ptraj is needed for MMPBSA Kenneth Huang (Mon Oct 12 2015 - 08:08:12 PDT)
    - Re: [AMBER] Error: ptraj is needed for MMPBSA Jason Swails (Mon Oct 12 2015 - 08:12:35 PDT)
    - Re: [AMBER] Error: ptraj is needed for MMPBSA Ayesha Kanwal (Mon Oct 12 2015 - 20:59:56 PDT)
    - Re: [AMBER] Error: ptraj is needed for MMPBSA Jason Swails (Tue Oct 13 2015 - 04:47:53 PDT)
    - Re: [AMBER] Error: ptraj is needed for MMPBSA Ayesha Kanwal (Tue Oct 13 2015 - 13:04:28 PDT)
    - Re: [AMBER] Error: ptraj is needed for MMPBSA Jason Swails (Tue Oct 13 2015 - 14:06:10 PDT)
    - Re: [AMBER] Error: ptraj is needed for MMPBSA Ayesha Kanwal (Wed Oct 14 2015 - 02:12:48 PDT)
    - Re: [AMBER] Error: ptraj is needed for MMPBSA Jason Swails (Wed Oct 14 2015 - 05:44:19 PDT)
    - Re: [AMBER] Error: ptraj is needed for MMPBSA Ayesha Kanwal (Wed Oct 14 2015 - 11:35:47 PDT)
    - Re: [AMBER] Error: ptraj is needed for MMPBSA Ayesha Kanwal (Fri Nov 13 2015 - 04:17:35 PST)
    - Re: [AMBER] Error: ptraj is needed for MMPBSA Jason Swails (Sun Oct 11 2015 - 08:26:18 PDT)
[AMBER] Amber compilation problem Weinzierl, Robert O J (Wed Sep 30 2015 - 04:43:54 PDT)
- Re: [AMBER] Amber compilation problem Theoretical Research (Wed Sep 30 2015 - 05:13:59 PDT)
- Re: [AMBER] Amber compilation problem Jason Swails (Wed Sep 30 2015 - 05:22:06 PDT)
[AMBER] Need help regarding references Saikat Dutta chowdhury (Wed Sep 30 2015 - 05:42:07 PDT)
- Re: [AMBER] Need help regarding references Carlos Simmerling (Wed Sep 30 2015 - 05:50:30 PDT)
  - Re: [AMBER] Need help regarding references Saikat Dutta chowdhury (Wed Sep 30 2015 - 06:28:59 PDT)
    - Re: [AMBER] Need help regarding references Carlos Simmerling (Wed Sep 30 2015 - 06:45:14 PDT)
- Re: [AMBER] Need help regarding references Gustavo Seabra (Wed Sep 30 2015 - 07:20:07 PDT)
[AMBER] Oxygen parameters for AMBER99SB-ILDN Ebert Maximilian (Wed Sep 30 2015 - 10:04:27 PDT)
- Re: [AMBER] Oxygen parameters for AMBER99SB-ILDN Jason Swails (Wed Sep 30 2015 - 10:20:59 PDT)
- Re: [AMBER] Oxygen parameters for AMBER99SB-ILDN Ebert Maximilian (Wed Sep 30 2015 - 10:42:45 PDT)
- Re: [AMBER] Oxygen parameters for AMBER99SB-ILDN Ebert Maximilian (Mon Oct 26 2015 - 07:05:52 PDT)
[AMBER] /share/apps/amber/amber14/bin/sander.MPI: error while loading shared libraries: libmpi_cxx.so.1: cannot open shared object file: No such file or directory Atila Petrosian (Thu Oct 01 2015 - 01:34:23 PDT)
- Re: [AMBER] /share/apps/amber/amber14/bin/sander.MPI: error while loading shared libraries: libmpi_cxx.so.1: cannot open shared object file: No such file or directory Repic Matej (Thu Oct 01 2015 - 02:21:13 PDT)
[AMBER] QMMM SCC-DFTB: ERROR ON EWEVGE in AMBER 12 using the new set 3ob-3-1 Emilio Lence (Thu Oct 01 2015 - 05:47:07 PDT)
- Re: [AMBER] QMMM SCC-DFTB: ERROR ON EWEVGE in AMBER 12 using the new set 3ob-3-1 Gustavo Seabra (Thu Oct 01 2015 - 06:43:22 PDT)
  - Re: [AMBER] QMMM SCC-DFTB: ERROR ON EWEVGE in AMBER 12 using the new set 3ob-3-1 Emilio Lence (Thu Oct 01 2015 - 07:22:46 PDT)
[AMBER] Parameters for trigonal bi-pyramid and square bi-pyramid Fe(II) Francesco Pietra (Thu Oct 01 2015 - 08:17:33 PDT)
[AMBER] Units of the dipole moment? Ucisik, Melek Nihan (Thu Oct 01 2015 - 10:02:23 PDT)
- Re: [AMBER] Units of the dipole moment? Daniel Roe (Thu Oct 01 2015 - 11:51:06 PDT)
[AMBER] Building a structure of levansucrase (1PT2) with a fructosyl residue attached to Asp86 Surasak Chunsrivirot (Thu Oct 01 2015 - 21:28:12 PDT)
- Re: [AMBER] Building a structure of levansucrase (1PT2) with a fructosyl residue attached to Asp86 Lachele Foley (Sat Oct 03 2015 - 21:17:59 PDT)
  - Re: [AMBER] Building a structure of levansucrase (1PT2) with a fructosyl residue attached to Asp86 Surasak Chunsrivirot (Mon Oct 05 2015 - 00:53:49 PDT)
[AMBER] Problem with VDW energy Brent Krueger (Fri Oct 02 2015 - 10:54:07 PDT)
- Re: [AMBER] Problem with VDW energy Ross Walker (Fri Oct 02 2015 - 11:04:45 PDT)
- Re: [AMBER] Problem with VDW energy David A Case (Fri Oct 02 2015 - 11:30:42 PDT)
  - Re: [AMBER] Problem with VDW energy Brent Krueger (Fri Oct 02 2015 - 11:33:14 PDT)
[AMBER] ^.^@ as a new atom type when running DFTB with sander from Ambertools 15 Emilio Lence (Fri Oct 02 2015 - 11:11:03 PDT)
- Re: [AMBER] ^.^@ as a new atom type when running DFTB with sander from Ambertools 15 Gustavo Seabra (Fri Oct 02 2015 - 12:51:29 PDT)
  - Re: [AMBER] ^.^@ as a new atom type when running DFTB with sander from Ambertools 15 Emilio Lence (Mon Oct 05 2015 - 03:26:03 PDT)
    - Re: [AMBER] ^.^@ as a new atom type when running DFTB with sander from Ambertools 15 Gustavo Seabra (Mon Oct 05 2015 - 06:03:04 PDT)
    - Re: [AMBER] ^.^@ as a new atom type when running DFTB with sander from Ambertools 15 Jonathan Sheehan (Mon Oct 05 2015 - 11:28:04 PDT)
    - Re: [AMBER] ^.^@ as a new atom type when running DFTB with sander from Ambertools 15 Jonathan Sheehan (Mon Oct 05 2015 - 12:02:24 PDT)
    - Re: [AMBER] ^.^@ as a new atom type when running DFTB with sander from Ambertools 15 Gustavo Seabra (Mon Oct 05 2015 - 13:17:11 PDT)
    - Re: [AMBER] ^.^@ as a new atom type when running DFTB with sander from Ambertools 15 Emilio Lence (Tue Oct 06 2015 - 04:54:31 PDT)
    - Re: [AMBER] ^.^@ as a new atom type when running DFTB with sander from Ambertools 15 Jonathan Sheehan (Wed Oct 07 2015 - 13:41:46 PDT)
    - Re: [AMBER] ^.^@ as a new atom type when running DFTB with sander from Ambertools 15 Gustavo Seabra (Wed Oct 07 2015 - 19:16:13 PDT)
    - Re: [AMBER] ^.^@ as a new atom type when running DFTB with sander from Ambertools 15 David A Case (Wed Oct 07 2015 - 20:06:33 PDT)
    - Re: [AMBER] ^.^@ as a new atom type when running DFTB with sander from Ambertools 15 Jonathan Sheehan (Wed Oct 07 2015 - 23:28:11 PDT)
    - Re: [AMBER] ^.^@ as a new atom type when running DFTB with sander from Ambertools 15 Emilio Lence (Thu Oct 08 2015 - 01:07:06 PDT)
    - Re: [AMBER] ^.^@ as a new atom type when running DFTB with sander from Ambertools 15 Jason Swails (Thu Oct 08 2015 - 04:48:45 PDT)
    - Re: [AMBER] ^.^@ as a new atom type when running DFTB with sander from Ambertools 15 Daniel Roe (Wed Oct 07 2015 - 20:58:40 PDT)
[AMBER] problem with randomizing velocities Kalenkiewicz, Andrew (NIH/NICHD) [F] (Fri Oct 02 2015 - 13:58:55 PDT)
- Re: [AMBER] problem with randomizing velocities Bill Ross (Fri Oct 02 2015 - 14:05:39 PDT)
  - Re: [AMBER] problem with randomizing velocities Bill Ross (Fri Oct 02 2015 - 14:12:11 PDT)
- Re: [AMBER] problem with randomizing velocities Hector A. Baldoni (Fri Oct 02 2015 - 21:14:09 PDT)
- Re: [AMBER-Developers] [AMBER] problem with randomizing velocities David A Case (Sun Oct 04 2015 - 23:17:15 PDT)
  - Re: [AMBER] problem with randomizing velocities Kalenkiewicz, Andrew (NIH/NICHD) [F] (Thu Oct 15 2015 - 08:41:28 PDT)
    - Re: [AMBER] problem with randomizing velocities David A Case (Thu Oct 15 2015 - 09:30:54 PDT)
    - Re: [AMBER-Developers] [AMBER] problem with randomizing velocities Ross Walker (Thu Oct 15 2015 - 10:00:41 PDT)
[AMBER] TIP3 water not recognized Chitrak Gupta (Fri Oct 02 2015 - 16:03:35 PDT)
- Re: [AMBER] TIP3 water not recognized Bill Ross (Fri Oct 02 2015 - 18:04:57 PDT)
[AMBER] mixing rules for various water models in AMBER conor parks (Sat Oct 03 2015 - 21:14:26 PDT)
- Re: [AMBER] mixing rules for various water models in AMBER Jason Swails (Sat Oct 03 2015 - 22:27:28 PDT)
  - Re: [AMBER] mixing rules for various water models in AMBER conor parks (Sat Oct 03 2015 - 23:32:58 PDT)
    - Re: [AMBER] mixing rules for various water models in AMBER Jason Swails (Sun Oct 04 2015 - 07:31:45 PDT)
    - Re: [AMBER] mixing rules for various water models in AMBER Conor Parks (Sun Oct 04 2015 - 09:30:31 PDT)
    - Re: [AMBER] mixing rules for various water models in AMBER Jason Swails (Sun Oct 04 2015 - 10:38:18 PDT)
[AMBER] QM/MM performance Sofia Vasilakaki (Sun Oct 04 2015 - 04:23:02 PDT)
- Re: [AMBER] QM/MM performance David A Case (Sun Oct 04 2015 - 11:13:28 PDT)
Re: [AMBER] AMBER Digest, Vol 1361, Issue 1 Chitrak Gupta (Sun Oct 04 2015 - 11:00:49 PDT)
- Re: [AMBER] AMBER Digest, Vol 1361, Issue 1 Jason Swails (Sun Oct 04 2015 - 13:33:28 PDT)
[AMBER] CpHMD for non protein residues Rahul Ramesh (Sun Oct 04 2015 - 14:42:42 PDT)
- Re: [AMBER] CpHMD for non protein residues Adrian Roitberg (Sun Oct 04 2015 - 16:34:35 PDT)
  - Re: [AMBER] CpHMD for non protein residues Rahul Ramesh (Sun Oct 04 2015 - 17:30:25 PDT)
- Re: [AMBER] CpHMD for non protein residues Jason Swails (Sun Oct 04 2015 - 19:01:24 PDT)
  - Re: [AMBER] CpHMD for non protein residues Brian Radak (Mon Oct 05 2015 - 06:57:03 PDT)
[AMBER] Question about mask in cpptraj Mohd Farid Ismail (Sun Oct 04 2015 - 20:42:58 PDT)
- Re: [AMBER] Question about mask in cpptraj Daniel Roe (Sun Oct 04 2015 - 20:53:52 PDT)
  - Re: [AMBER] Question about mask in cpptraj Mohd Farid Ismail (Sun Oct 04 2015 - 21:19:05 PDT)
    - Re: [AMBER] Question about mask in cpptraj Daniel Roe (Mon Oct 05 2015 - 06:02:09 PDT)
    - Re: [AMBER] Question about mask in cpptraj Mohd Farid Ismail (Mon Oct 05 2015 - 22:12:19 PDT)
[AMBER] SC15 Call for abstracts - "Producing High-Performance and Sustainable Software for Molecular Simulation" Ross Walker (Mon Oct 05 2015 - 11:10:41 PDT)
[AMBER] Atom 1512 was assigned a lower molecule # than previous atom Osman, Roman (Mon Oct 05 2015 - 11:51:19 PDT)
- Re: [AMBER] Atom 1512 was assigned a lower molecule # than previous atom Daniel Roe (Mon Oct 05 2015 - 12:09:12 PDT)
  - Re: [AMBER] Atom 1512 was assigned a lower molecule # than previous atom Osman, Roman (Mon Oct 05 2015 - 12:15:01 PDT)
    - Re: [AMBER] Atom 1512 was assigned a lower molecule # than previous atom Daniel Roe (Mon Oct 05 2015 - 12:36:32 PDT)
[AMBER] Info: Bond types are assigned for valence state 5 with penalty of 1 Atila Petrosian (Mon Oct 05 2015 - 13:57:53 PDT)
- Re: [AMBER] Info: Bond types are assigned for valence state 5 with penalty of 1 David A Case (Mon Oct 05 2015 - 19:44:39 PDT)
[AMBER] Pairwise energy decomposition Sara Omar (Mon Oct 05 2015 - 22:28:09 PDT)
- Re: [AMBER] Pairwise energy decomposition Carlos Simmerling (Tue Oct 06 2015 - 03:39:08 PDT)
[AMBER] cpin file Arjun Sharma (Tue Oct 06 2015 - 07:16:33 PDT)
- Re: [AMBER] cpin file Jason Swails (Tue Oct 06 2015 - 09:14:09 PDT)
[AMBER] How to do a QMMM calculation with a dynamic QM region 崔克新 (Wed Oct 07 2015 - 02:18:00 PDT)
- Re: [AMBER] How to do a QMMM calculation with a dynamic QM region Emilio Lence (Wed Oct 07 2015 - 02:55:20 PDT)
  - Re: [AMBER] How to do a QMMM calculation with a dynamic QM region Hector A. Baldoni (Wed Oct 07 2015 - 04:05:53 PDT)
[AMBER] SIGSEGV: Segmentation Fault Steven Cole Mercer (Wed Oct 07 2015 - 16:46:12 PDT)
- Re: [AMBER] SIGSEGV: Segmentation Fault Scott Brozell (Wed Oct 07 2015 - 17:53:42 PDT)
[AMBER] hydrogen bond cpptraj Lara rajam (Wed Oct 07 2015 - 18:18:51 PDT)
[AMBER] Dihedral/improper coefficient in AMBER + rmin vs sigma for lennard jones conor parks (Wed Oct 07 2015 - 21:33:05 PDT)
- Re: [AMBER] Dihedral/improper coefficient in AMBER + rmin vs sigma for lennard jones Jason Swails (Thu Oct 08 2015 - 05:14:15 PDT)
[AMBER] Controlling size of the box Nicholus Bhattacharjee (Thu Oct 08 2015 - 08:48:31 PDT)
- Re: [AMBER] Controlling size of the box Jason Swails (Thu Oct 08 2015 - 08:51:57 PDT)
- Re: [AMBER] Controlling size of the box David A Case (Thu Oct 08 2015 - 09:41:00 PDT)
  - Re: [AMBER] Controlling size of the box Jason Swails (Thu Oct 08 2015 - 09:50:01 PDT)
    - Re: [AMBER] Controlling size of the box Nicholus Bhattacharjee (Fri Oct 09 2015 - 01:49:01 PDT)
    - Re: [AMBER] Controlling size of the box Daniel Roe (Fri Oct 09 2015 - 02:51:39 PDT)
[AMBER] "Vlimit exceeded for step..." error Vu Truong (Thu Oct 08 2015 - 13:21:47 PDT)
- Re: [AMBER] "Vlimit exceeded for step..." error David A Case (Thu Oct 08 2015 - 14:37:33 PDT)
- Re: [AMBER] "Vlimit exceeded for step..." error Vu Truong (Fri Oct 09 2015 - 12:16:31 PDT)
  - Re: [AMBER] "Vlimit exceeded for step..." error David A Case (Sat Oct 10 2015 - 06:56:32 PDT)
    - Re: [AMBER] "Vlimit exceeded for step..." error Vishnudatt Pandey (Wed Nov 18 2015 - 01:35:39 PST)
    - Re: [AMBER] "Vlimit exceeded for step..." error Jason Swails (Wed Nov 18 2015 - 08:21:49 PST)
[AMBER] Cytochrome P450 with heme simulation Abelak, Kavin (Fri Oct 09 2015 - 03:47:47 PDT)
- Re: [AMBER] Cytochrome P450 with heme simulation Jason Swails (Fri Oct 09 2015 - 06:18:31 PDT)
[AMBER] AIB parameter Elisa Frezza (Fri Oct 09 2015 - 04:56:06 PDT)
[AMBER] http://q4md-forcefieldtools.org/ unavailable Jérémie Knoops (Fri Oct 09 2015 - 04:59:54 PDT)
- Re: [AMBER] http://q4md-forcefieldtools.org/ unavailable Emilio Lence (Mon Oct 12 2015 - 01:06:07 PDT)
[AMBER] Restraints Wong Li Zhe (Fri Oct 09 2015 - 05:23:53 PDT)
- Re: [AMBER] Restraints Emilio Lence (Fri Oct 09 2015 - 05:41:08 PDT)
  - Re: [AMBER] Restraints Wong Li Zhe (Fri Oct 09 2015 - 05:48:41 PDT)
- Re: [AMBER] Restraints David A Case (Fri Oct 09 2015 - 06:03:49 PDT)
  - [AMBER] Restraints Wong Li Zhe (Fri Oct 09 2015 - 06:20:02 PDT)
    - Re: [AMBER] Restraints Jason Swails (Fri Oct 09 2015 - 06:23:09 PDT)
    - [AMBER] Restraints Wong Li Zhe (Fri Oct 09 2015 - 06:27:28 PDT)
    - [AMBER] Restraints Wong Li Zhe (Fri Oct 09 2015 - 06:31:47 PDT)
    - Re: [AMBER] Restraints Jason Swails (Fri Oct 09 2015 - 06:41:37 PDT)
    - [AMBER] Restraints Wong Li Zhe (Fri Oct 09 2015 - 06:50:03 PDT)
  - Re: [AMBER] Restraints Jason Swails (Fri Oct 09 2015 - 06:20:37 PDT)
Re: [AMBER] AMBER Digest, Vol 1364, Issue 1 Arjun Sharma (Fri Oct 09 2015 - 07:02:14 PDT)
- Re: [AMBER] AMBER Digest, Vol 1364, Issue 1 Jason Swails (Fri Oct 09 2015 - 07:49:12 PDT)
[AMBER] resp input format 16I5 stecue.gmail.com (Fri Oct 09 2015 - 07:30:54 PDT)
- Re: [AMBER] resp input format 16I5 Jason Swails (Fri Oct 09 2015 - 08:22:31 PDT)
  - Re: [AMBER] resp input format 16I5 stecue.gmail.com (Fri Oct 09 2015 - 09:08:58 PDT)
[AMBER] h-bond calculation - tokenise error Sidhu, Khushwant (Dr.) (Fri Oct 09 2015 - 07:57:40 PDT)
- Re: [AMBER] h-bond calculation - tokenise error Daniel Roe (Fri Oct 09 2015 - 08:14:01 PDT)
[AMBER] non-standard residue (DNA-protein crosslink) Jackle, Chasen (Fri Oct 09 2015 - 09:35:14 PDT)
- Re: [AMBER] non-standard residue (DNA-protein crosslink) Carlos Simmerling (Fri Oct 09 2015 - 09:41:17 PDT)
[AMBER] Making Parameter and Topology Files for Protein-Ligand Complex Jim Wu (Fri Oct 09 2015 - 16:14:09 PDT)
- Re: [AMBER] Making Parameter and Topology Files for Protein-Ligand Complex Emilio Lence (Sat Oct 10 2015 - 04:09:04 PDT)
- Re: [AMBER] Making Parameter and Topology Files for Protein-Ligand Complex David A Case (Sat Oct 10 2015 - 07:04:12 PDT)
[AMBER] Prepgen difficulty Robert Molt (Sun Oct 11 2015 - 08:41:48 PDT)
- Re: [AMBER] Prepgen difficulty David A Case (Mon Oct 12 2015 - 05:45:52 PDT)
  - Re: [AMBER] Prepgen difficulty Marion, Antoine (Mon Oct 12 2015 - 07:22:32 PDT)
[AMBER] query about Bromide ion forcefield parameter jagannath mondal (Mon Oct 12 2015 - 04:01:09 PDT)
- Re: [AMBER] query about Bromide ion forcefield parameter David A Case (Mon Oct 12 2015 - 05:47:36 PDT)
  - Re: [AMBER] query about Bromide ion forcefield parameter jagannath mondal (Thu Oct 15 2015 - 21:56:30 PDT)
    - Re: [AMBER] query about Bromide ion forcefield parameter Jason Swails (Fri Oct 16 2015 - 05:12:00 PDT)
    - Re: [AMBER] query about Bromide ion forcefield parameter Brent Krueger (Fri Oct 16 2015 - 05:59:04 PDT)
[AMBER] A question about MMPBSA calculation anu chandra (Mon Oct 12 2015 - 09:14:08 PDT)
- Re: [AMBER] A question about MMPBSA calculation Jason Swails (Mon Oct 12 2015 - 09:59:41 PDT)
[AMBER] How do you place two molecules in one water box? David Eugene Jones (Mon Oct 12 2015 - 11:28:54 PDT)
- Re: [AMBER] How do you place two molecules in one water box? Ben Roberts (Mon Oct 12 2015 - 11:45:22 PDT)
  - Re: [AMBER] How do you place two molecules in one water box? Lachele Foley (Mon Oct 12 2015 - 12:01:39 PDT)
    - Re: [AMBER] How do you place two molecules in one water box? David Eugene Jones (Mon Oct 12 2015 - 12:22:44 PDT)
  - Re: [AMBER] How do you place two molecules in one water box? David Eugene Jones (Mon Oct 12 2015 - 12:02:17 PDT)
    - Re: [AMBER] How do you place two molecules in one water box? Ben Roberts (Mon Oct 12 2015 - 12:13:53 PDT)
[AMBER] Temperature fluctuations in stage heating Anitha Jagadesh (Mon Oct 12 2015 - 22:06:26 PDT)
- Re: [AMBER] Temperature fluctuations in stage heating Repic Matej (Tue Oct 13 2015 - 02:19:49 PDT)
[AMBER] many atoms, same name Hadeer ELHabashy (Tue Oct 13 2015 - 11:08:08 PDT)
- Re: [AMBER] many atoms, same name Jason Swails (Tue Oct 13 2015 - 11:34:17 PDT)
- Re: [AMBER] many atoms, same name case (Tue Oct 13 2015 - 18:29:33 PDT)
[AMBER] cpptraj density Björn Karlsson (Tue Oct 13 2015 - 11:10:54 PDT)
[AMBER] AmberTools14 configuration problem Ivanov, Maxim (Tue Oct 13 2015 - 14:25:14 PDT)
- Re: [AMBER] AmberTools14 configuration problem David A Case (Fri Oct 16 2015 - 11:00:32 PDT)
  - Re: [AMBER] AmberTools14 configuration problem Jason Swails (Sat Oct 17 2015 - 09:09:19 PDT)
[AMBER] Real-time hydrogen bond formation using VMD Abhipriya K (Tue Oct 13 2015 - 23:21:52 PDT)
- Re: [AMBER] Real-time hydrogen bond formation using VMD Repic Matej (Wed Oct 14 2015 - 00:06:37 PDT)
  - Re: [AMBER] Real-time hydrogen bond formation using VMD Abhipriya K (Wed Oct 14 2015 - 00:55:56 PDT)
    - Re: [AMBER] Real-time hydrogen bond formation using VMD amin.imtech.res.in (Wed Oct 14 2015 - 01:47:38 PDT)
[AMBER] EVB related query bijyalaxmi athokpam (Wed Oct 14 2015 - 01:54:26 PDT)
- [AMBER] Fwd: EVB related query bijyalaxmi athokpam (Thu Oct 15 2015 - 04:39:50 PDT)
- Re: [AMBER] EVB related query David A Case (Thu Oct 15 2015 - 05:13:18 PDT)
Re: [AMBER] [SPAM] AMBER Digest, Vol 1365, Issue 1 崔克新 (Wed Oct 14 2015 - 02:10:05 PDT)
[AMBER] Minimization Wong Li Zhe (Wed Oct 14 2015 - 02:17:34 PDT)
- Re: [AMBER] Minimization Bill Ross (Sat Sep 19 2015 - 18:04:36 PDT)
- Re: [AMBER] Minimization Emilio Lence (Wed Oct 14 2015 - 03:38:06 PDT)
[AMBER] difficulties in generate .prmtop and .inpcrd file for complex using Guassian calculated ligand charges Jin Zhang (Wed Oct 14 2015 - 02:20:36 PDT)
- Re: [AMBER] difficulties in generate .prmtop and .inpcrd file for complex using Guassian calculated ligand charges Emilio Lence (Wed Oct 14 2015 - 03:31:53 PDT)
[AMBER] error with line 165 of cpinutil.py Hadeer ELHabashy (Wed Oct 14 2015 - 03:34:04 PDT)
- Re: [AMBER] error with line 165 of cpinutil.py Jason Swails (Wed Oct 14 2015 - 05:47:33 PDT)
  - Re: [AMBER] error with line 165 of cpinutil.py Hadeer ELHabashy (Wed Oct 14 2015 - 06:41:36 PDT)
    - Re: [AMBER] error with line 165 of cpinutil.py Juan Eiros Zamora (Wed Oct 14 2015 - 07:01:23 PDT)
    - Re: [AMBER] error with line 165 of cpinutil.py Jason Swails (Wed Oct 14 2015 - 07:04:22 PDT)
    - Re: [AMBER] error with line 165 of cpinutil.py Hadeer ELHabashy (Wed Oct 14 2015 - 07:07:09 PDT)
[AMBER] Is it possible to simulate a periodic crystal ? Hadeer ELHabashy (Wed Oct 14 2015 - 06:51:37 PDT)
- Re: [AMBER] Is it possible to simulate a periodic crystal ? Jason Swails (Wed Oct 14 2015 - 07:05:45 PDT)
  - Re: [AMBER] Is it possible to simulate a periodic crystal ? Hadeer ELHabashy (Wed Oct 14 2015 - 11:23:29 PDT)
    - Re: [AMBER] Is it possible to simulate a periodic crystal ? Hadeer ELHabashy (Wed Oct 14 2015 - 11:38:17 PDT)
    - Re: [AMBER] Is it possible to simulate a periodic crystal ? David A Case (Thu Oct 15 2015 - 10:20:38 PDT)
[AMBER] RESP charge calculation li he (Wed Oct 14 2015 - 11:17:45 PDT)
- Re: [AMBER] RESP charge calculation li he (Wed Oct 14 2015 - 11:22:37 PDT)
- Re: [AMBER] RESP charge calculation li he (Thu Oct 15 2015 - 09:12:48 PDT)
  - Re: [AMBER] RESP charge calculation David A Case (Thu Oct 15 2015 - 13:10:03 PDT)
    - Re: [AMBER] RESP charge calculation li he (Thu Oct 15 2015 - 18:46:19 PDT)
    - Re: [AMBER] RESP charge calculation Luciano Costa (Fri Oct 16 2015 - 19:47:42 PDT)
[AMBER] Ho Atom Inclusion in PDB from Leap Robert Molt (Wed Oct 14 2015 - 11:31:00 PDT)
- Re: [AMBER] Ho Atom Inclusion in PDB from Leap David A Case (Wed Oct 14 2015 - 13:26:27 PDT)
  - Re: [AMBER] Ho Atom Inclusion in PDB from Leap Robert Molt (Wed Oct 14 2015 - 15:20:09 PDT)
[AMBER] tinker_to_amber does not work Sun (Wed Oct 14 2015 - 14:52:10 PDT)
- Re: [AMBER] tinker_to_amber does not work Jason Swails (Wed Oct 14 2015 - 18:09:23 PDT)
  - Re: [AMBER] tinker_to_amber does not work Sun (Thu Oct 15 2015 - 07:21:26 PDT)
    - Re: [AMBER] tinker_to_amber does not work Jason Swails (Thu Oct 15 2015 - 07:54:04 PDT)
    - Re: [AMBER] tinker_to_amber does not work David A Case (Fri Oct 16 2015 - 08:49:31 PDT)
[AMBER] cutoff problem with a periodic crystal box Hadeer ELHabashy (Thu Oct 15 2015 - 00:26:43 PDT)
- Re: [AMBER] cutoff problem with a periodic crystal box Jason Swails (Thu Oct 15 2015 - 04:59:56 PDT)
  - Re: [AMBER] cutoff problem with a periodic crystal box Hadeer ELHabashy (Thu Oct 15 2015 - 05:08:53 PDT)
- Re: [AMBER] cutoff problem with a periodic crystal box David A Case (Thu Oct 15 2015 - 05:33:22 PDT)
[AMBER] difficulties in generate .prmtop and .inpcrd file for complex using Guassian calculated ligand charges MarcZhang (Thu Oct 15 2015 - 01:23:01 PDT)
- Re: [AMBER] difficulties in generate .prmtop and .inpcrd file for complex using Guassian calculated ligand charges Emilio Lence (Thu Oct 15 2015 - 02:02:20 PDT)
- Re: [AMBER] difficulties in generate .prmtop and .inpcrd file for complex using Guassian calculated ligand charges David A Case (Thu Oct 15 2015 - 05:35:46 PDT)
[AMBER] No Internet Access Shahryar Alavi (Thu Oct 15 2015 - 01:27:00 PDT)
- Re: [AMBER] No Internet Access Ross Walker (Thu Oct 15 2015 - 07:59:22 PDT)
[AMBER] What is the formula for calculating EPtot? Yip Yew Mun (Thu Oct 15 2015 - 02:26:29 PDT)
- Re: [AMBER] What is the formula for calculating EPtot? Jason Swails (Thu Oct 15 2015 - 04:52:58 PDT)
- Re: [AMBER] What is the formula for calculating EPtot? David A Case (Thu Oct 15 2015 - 05:42:08 PDT)
  - Re: [AMBER] What is the formula for calculating EPtot? Conor Parks (Thu Oct 15 2015 - 07:17:30 PDT)
    - Re: [AMBER] What is the formula for calculating EPtot? Daniel Roe (Thu Oct 15 2015 - 07:31:05 PDT)
    - Re: [AMBER] What is the formula for calculating EPtot? Jason Swails (Thu Oct 15 2015 - 07:56:20 PDT)
    - Re: [AMBER] What is the formula for calculating EPtot? conor parks (Thu Oct 15 2015 - 08:15:16 PDT)
    - Re: [AMBER] What is the formula for calculating EPtot? Jason Swails (Thu Oct 15 2015 - 08:58:19 PDT)
    - Re: [AMBER] What is the formula for calculating EPtot? conor parks (Thu Oct 15 2015 - 10:05:53 PDT)
[AMBER] Correctly deriving force constants for Amber Nash, Anthony (Thu Oct 15 2015 - 05:07:22 PDT)
- Re: [AMBER] Correctly deriving force constants for Amber David A Case (Thu Oct 15 2015 - 09:35:33 PDT)
  - Re: [AMBER] Correctly deriving force constants for Amber Nash, Anthony (Thu Oct 15 2015 - 11:47:19 PDT)
    - Re: [AMBER] Correctly deriving force constants for Amber Adrian Roitberg (Thu Oct 15 2015 - 11:53:02 PDT)
    - Re: [AMBER] Correctly deriving force constants for Amber Nash, Anthony (Thu Oct 15 2015 - 11:58:30 PDT)
[AMBER] System gets unwrap while iwrap=1 in ti Khabiri, Morteza (Thu Oct 15 2015 - 06:18:17 PDT)
- Re: [AMBER] System gets unwrap while iwrap=1 in ti Jason Swails (Thu Oct 15 2015 - 06:32:54 PDT)
- Re: [AMBER] System gets unwrap while iwrap=1 in ti Khabiri, Morteza (Thu Oct 15 2015 - 07:02:37 PDT)
  - Re: [AMBER] System gets unwrap while iwrap=1 in ti Jason Swails (Thu Oct 15 2015 - 07:14:58 PDT)
[AMBER] Not atom type for Bromine atom in amber GAFF force field? MarcZhang (Thu Oct 15 2015 - 09:42:08 PDT)
- Re: [AMBER] Not atom type for Bromine atom in amber GAFF force field? Jason Swails (Thu Oct 15 2015 - 10:14:13 PDT)
[AMBER] FW: System gets unwrap while iwrap=1 in ti Khabiri, Morteza (Thu Oct 15 2015 - 11:46:48 PDT)
- Re: [AMBER] FW: System gets unwrap while iwrap=1 in ti case (Thu Oct 15 2015 - 18:55:57 PDT)
- Re: [AMBER] FW: System gets unwrap while iwrap=1 in ti Jason Swails (Fri Oct 16 2015 - 04:54:43 PDT)
- Re: [AMBER] System gets unwrap while iwrap=1 in ti Khabiri, Morteza (Fri Oct 16 2015 - 06:52:41 PDT)
Re: [AMBER] difficulties in generate .prmtop and .inpcrd file MarcZhang (Thu Oct 15 2015 - 13:07:10 PDT)
- Re: [AMBER] difficulties in generate .prmtop and .inpcrd file Emilio Lence (Sat Oct 17 2015 - 07:40:27 PDT)
Re: [AMBER] Not atom type for Bromine atom in amber GAFF MarcZhang (Thu Oct 15 2015 - 13:29:07 PDT)
[AMBER] CpHMD for non protein residues Rahul Ramesh (Thu Oct 15 2015 - 20:43:18 PDT)
- Re: [AMBER] CpHMD for non protein residues Jason Swails (Fri Oct 16 2015 - 04:57:55 PDT)
  - Re: [AMBER] CpHMD for non protein residues Rahul Ramesh (Fri Oct 16 2015 - 10:57:57 PDT)
    - Re: [AMBER] CpHMD for non protein residues Jason Swails (Fri Oct 16 2015 - 12:58:09 PDT)
    - Re: [AMBER] CpHMD for non protein residues Rahul Ramesh (Sun Oct 18 2015 - 15:22:15 PDT)
[AMBER] Documentation on Prepin File Format Robert Molt (Fri Oct 16 2015 - 05:00:19 PDT)
- Re: [AMBER] Documentation on Prepin File Format Jason Swails (Fri Oct 16 2015 - 05:13:55 PDT)
  - Re: [AMBER] Documentation on Prepin File Format Robert Molt (Fri Oct 16 2015 - 05:19:32 PDT)
  - Re: [AMBER] Documentation on Prepin File Format David A Case (Fri Oct 16 2015 - 10:50:53 PDT)
[AMBER] CPPTRAJ : different RMSD calculation in a single run anu chandra (Fri Oct 16 2015 - 05:02:10 PDT)
- Re: [AMBER] CPPTRAJ : different RMSD calculation in a single run Jason Swails (Fri Oct 16 2015 - 05:19:01 PDT)
  - Re: [AMBER] CPPTRAJ : different RMSD calculation in a single run anu chandra (Fri Oct 16 2015 - 06:29:25 PDT)
    - Re: [AMBER] CPPTRAJ : different RMSD calculation in a single run Jason Swails (Fri Oct 16 2015 - 08:49:19 PDT)
[AMBER] Random Number Generator Flag Ig Guqin Shi (Fri Oct 16 2015 - 09:13:35 PDT)
- Re: [AMBER] Random Number Generator Flag Ig Jason Swails (Fri Oct 16 2015 - 09:49:57 PDT)
[AMBER] Random Number Generator Flag Ig Guqin Shi (Fri Oct 16 2015 - 09:17:34 PDT)
- Re: [AMBER] Random Number Generator Flag Ig Ross Walker (Fri Oct 16 2015 - 09:25:03 PDT)
  - Re: [AMBER] Random Number Generator Flag Ig Guqin Shi (Fri Oct 16 2015 - 09:48:37 PDT)
    - Re: [AMBER] Random Number Generator Flag Ig Jason Swails (Fri Oct 16 2015 - 09:55:46 PDT)
    - Re: [AMBER] Random Number Generator Flag Ig Guqin Shi (Fri Oct 16 2015 - 12:34:09 PDT)
[AMBER] sander missing from AmberTools15? Novosielski, Ryan (Fri Oct 16 2015 - 12:44:38 PDT)
- Re: [AMBER] sander missing from AmberTools15? David A Case (Fri Oct 16 2015 - 12:55:03 PDT)
  - Re: [AMBER] sander missing from AmberTools15? Jason Swails (Fri Oct 16 2015 - 12:56:58 PDT)
  - Re: [AMBER] sander missing from AmberTools15? Novosielski, Ryan (Fri Oct 16 2015 - 12:55:59 PDT)
    - Re: [AMBER] sander missing from AmberTools15? Jason Swails (Fri Oct 16 2015 - 13:03:21 PDT)
    - Re: [AMBER] sander missing from AmberTools15? Novosielski, Ryan (Fri Oct 16 2015 - 13:14:56 PDT)
    - Re: [AMBER] sander missing from AmberTools15? Daniel Roe (Fri Oct 16 2015 - 13:34:28 PDT)
    - Re: [AMBER] sander missing from AmberTools15? Novosielski, Ryan (Fri Oct 16 2015 - 13:51:09 PDT)
    - Re: [AMBER] sander missing from AmberTools15? Daniel Roe (Fri Oct 16 2015 - 14:13:46 PDT)
    - Re: [AMBER] sander missing from AmberTools15? Jason Swails (Fri Oct 16 2015 - 14:20:29 PDT)
    - Re: [AMBER] sander missing from AmberTools15? Novosielski, Ryan (Fri Oct 16 2015 - 14:26:52 PDT)
[AMBER] Help Balajee Ramachandran (Fri Oct 16 2015 - 12:55:26 PDT)
- Re: [AMBER] Help Jason Swails (Fri Oct 16 2015 - 13:01:49 PDT)
- Re: [AMBER] Help Carlos Simmerling (Fri Oct 16 2015 - 13:01:53 PDT)
[AMBER] Leap PDB Input Error Robert Molt (Fri Oct 16 2015 - 16:13:31 PDT)
- Re: [AMBER] Leap PDB Input Error case (Fri Oct 16 2015 - 18:18:23 PDT)
[AMBER] donor and acceptor masks Hadeer ELHabashy (Sat Oct 17 2015 - 07:06:27 PDT)
- Re: [AMBER] donor and acceptor masks Emilio Lence (Sat Oct 17 2015 - 07:23:24 PDT)
  - Re: [AMBER] donor and acceptor masks Emilio Lence (Sat Oct 17 2015 - 07:43:57 PDT)
- Re: [AMBER] donor and acceptor masks Daniel Roe (Sat Oct 17 2015 - 07:42:44 PDT)
  - [AMBER] Fwd: donor and acceptor masks Emilio Lence (Sat Oct 17 2015 - 07:51:36 PDT)
  - Re: [AMBER] donor and acceptor masks Hadeer ELHabashy (Sat Oct 17 2015 - 08:05:49 PDT)
    - Re: [AMBER] donor and acceptor masks Jason Swails (Sat Oct 17 2015 - 08:09:30 PDT)
    - Re: [AMBER] donor and acceptor masks Hadeer ELHabashy (Sat Oct 17 2015 - 08:14:27 PDT)
    - Re: [AMBER] donor and acceptor masks Jason Swails (Sat Oct 17 2015 - 08:16:37 PDT)
    - Re: [AMBER] donor and acceptor masks Hadeer ELHabashy (Sat Oct 17 2015 - 08:20:36 PDT)
    - Re: [AMBER] donor and acceptor masks Hadeer ELHabashy (Sat Oct 17 2015 - 08:22:18 PDT)
    - Re: [AMBER] donor and acceptor masks Daniel Roe (Sat Oct 17 2015 - 08:22:57 PDT)
    - Re: [AMBER] donor and acceptor masks Hadeer ELHabashy (Sat Oct 17 2015 - 09:09:43 PDT)
    - Re: [AMBER] donor and acceptor masks Hadeer ELHabashy (Sat Oct 17 2015 - 09:34:54 PDT)
    - Re: [AMBER] donor and acceptor masks Thomas Cheatham (Sat Oct 17 2015 - 09:41:47 PDT)
    - Re: [AMBER] donor and acceptor masks Hadeer ELHabashy (Sat Oct 17 2015 - 09:56:21 PDT)
    - Re: [AMBER] donor and acceptor masks Daniel Roe (Sat Oct 17 2015 - 10:43:58 PDT)
    - Re: [AMBER] donor and acceptor masks Hadeer ELHabashy (Sat Oct 17 2015 - 10:57:16 PDT)
    - Re: [AMBER] donor and acceptor masks Daniel Roe (Sat Oct 17 2015 - 11:39:58 PDT)
[AMBER] Membrane protein imagining problems Romero, Raquel (Sun Oct 18 2015 - 15:33:09 PDT)
- Re: [AMBER] Membrane protein imagining problems Daniel Roe (Mon Oct 19 2015 - 12:43:01 PDT)
- Re: [AMBER] Membrane protein imagining problems Hai Nguyen (Mon Oct 19 2015 - 12:59:07 PDT)
  - Re: [AMBER] Membrane protein imagining problems Romero, Raquel (Tue Oct 20 2015 - 04:51:20 PDT)
[AMBER] R.E.D. server down or out? Tan Yaw Sing (Sun Oct 18 2015 - 19:43:19 PDT)
[AMBER] CPPTRAJ Wong Li Zhe (Sun Oct 18 2015 - 21:06:48 PDT)
- Re: [AMBER] CPPTRAJ Nhai (Sun Oct 18 2015 - 21:16:37 PDT)
- Re: [AMBER] CPPTRAJ Thomas Cheatham (Sun Oct 18 2015 - 21:41:09 PDT)
[AMBER] RED-tools Repic Matej (Mon Oct 19 2015 - 00:21:41 PDT)
- Re: [AMBER] RED-tools Nash, Anthony (Thu Oct 22 2015 - 12:36:40 PDT)
  - Re: [AMBER] RED-tools Jason Swails (Thu Oct 22 2015 - 13:17:14 PDT)
    - Re: [AMBER] RED-tools Nash, Anthony (Thu Oct 22 2015 - 13:27:27 PDT)
    - Re: [AMBER] RED-tools Hector A. Baldoni (Thu Oct 22 2015 - 15:29:09 PDT)
- Re: [AMBER] RED-tools Hector A. Baldoni (Fri Oct 23 2015 - 10:12:20 PDT)
  - Re: [AMBER] RED-tools Steven M. Graham (Sun Oct 25 2015 - 15:33:13 PDT)
- Re: [AMBER] RED-tools Hector A. Baldoni (Sun Oct 25 2015 - 19:33:37 PDT)
[AMBER] Why is water box getting bigger? Karolina Markowska (Mon Oct 19 2015 - 04:57:20 PDT)
- Re: [AMBER] Why is water box getting bigger? David A Case (Mon Oct 19 2015 - 06:16:16 PDT)
  - Re: [AMBER] Why is water box getting bigger? Karolina Markowska (Wed Oct 21 2015 - 02:13:49 PDT)
    - Re: [AMBER] Why is water box getting bigger? Jason Swails (Wed Oct 21 2015 - 05:10:18 PDT)
    - Re: [AMBER] Why is water box getting bigger? Karolina Markowska (Thu Oct 22 2015 - 06:41:53 PDT)
    - Re: [AMBER] Why is water box getting bigger? Jason Swails (Thu Oct 22 2015 - 07:05:38 PDT)
    - Re: [AMBER] Why is water box getting bigger? Karolina Markowska (Fri Oct 23 2015 - 07:26:11 PDT)
    - Re: [AMBER] Why is water box getting bigger? Karolina Markowska (Mon Oct 26 2015 - 05:34:42 PDT)
    - Re: [AMBER] Why is water box getting bigger? Jason Swails (Mon Oct 26 2015 - 05:45:23 PDT)
    - Re: [AMBER] Why is water box getting bigger? Karolina Markowska (Mon Oct 26 2015 - 05:51:00 PDT)
[AMBER] MMPBSA tutorial A3.2 Fabian gmail (Mon Oct 19 2015 - 07:17:02 PDT)
- Re: [AMBER] MMPBSA tutorial A3.2 Fabian gmail (Mon Oct 19 2015 - 07:26:33 PDT)
- Re: [AMBER] MMPBSA tutorial A3.2 Jason Swails (Mon Oct 19 2015 - 08:24:11 PDT)
  - Re: [AMBER] MMPBSA tutorial A3.2 Fabian gmail (Mon Oct 19 2015 - 08:34:35 PDT)
  - Re: [AMBER] MMPBSA tutorial A3.2 Fabian gmail (Tue Oct 20 2015 - 03:19:47 PDT)
    - Re: [AMBER] MMPBSA tutorial A3.2 Vlad Cojocaru (Tue Oct 20 2015 - 04:50:42 PDT)
    - Re: [AMBER] MMPBSA tutorial A3.2 Fabian gmail (Tue Oct 20 2015 - 05:20:00 PDT)
    - Re: [AMBER] MMPBSA tutorial A3.2 Fabian gmail (Tue Oct 20 2015 - 05:41:24 PDT)
    - Re: [AMBER] MMPBSA tutorial A3.2 Jason Swails (Tue Oct 20 2015 - 06:59:06 PDT)
    - Re: [AMBER] MMPBSA tutorial A3.2 Fabian gmail (Tue Oct 20 2015 - 07:08:16 PDT)
    - Re: [AMBER] MMPBSA tutorial A3.2 Jason Swails (Tue Oct 20 2015 - 10:59:05 PDT)
    - Re: [AMBER] MMPBSA tutorial A3.2 Fabian gmail (Thu Oct 22 2015 - 03:11:06 PDT)
    - Re: [AMBER] MMPBSA tutorial A3.2 Jason Swails (Thu Oct 22 2015 - 06:14:20 PDT)
    - Re: [AMBER] MMPBSA tutorial A3.2 Fabian gmail (Thu Oct 22 2015 - 06:17:19 PDT)
    - Re: [AMBER] MMPBSA tutorial A3.2 Fabian gmail (Thu Oct 22 2015 - 03:38:16 PDT)
    - Re: [AMBER] MMPBSA tutorial A3.2 Fabian gmail (Thu Oct 22 2015 - 03:51:06 PDT)
[AMBER] Differences on MMPBSA calculation results MarcZhang (Mon Oct 19 2015 - 07:58:57 PDT)
- Re: [AMBER] Differences on MMPBSA calculation results Jason Swails (Mon Oct 19 2015 - 08:25:46 PDT)
[AMBER] Differences on MMPBSA calculation results MarcZhang (Mon Oct 19 2015 - 08:00:18 PDT)
- Re: [AMBER] Differences on MMPBSA calculation results MarcZhang (Tue Oct 20 2015 - 03:01:03 PDT)
  - Re: [AMBER] Differences on MMPBSA calculation results Jason Swails (Tue Oct 20 2015 - 06:46:28 PDT)
    - Re: [AMBER] Differences on MMPBSA calculation results Ray Luo, Ph.D. (Tue Oct 20 2015 - 12:13:54 PDT)
[AMBER] [cpptraj] Changes in RMSF functionality? Juan Eiros Zamora (Mon Oct 19 2015 - 09:30:48 PDT)
- Re: [AMBER] [cpptraj] Changes in RMSF functionality? Daniel Roe (Mon Oct 19 2015 - 10:10:36 PDT)
[AMBER] 1-4 nonbonded interactions does not cancel in MMPBSA calculation Renato Freitas (Mon Oct 19 2015 - 14:22:51 PDT)
- Re: [AMBER] 1-4 nonbonded interactions does not cancel in MMPBSA calculation Jérémie Knoops (Tue Oct 20 2015 - 00:48:32 PDT)
- Re: [AMBER] 1-4 nonbonded interactions does not cancel in MMPBSA calculation Jason Swails (Tue Oct 20 2015 - 06:42:19 PDT)
[AMBER] Lennard-Jones parameter for Sp, Sp2 and Sp3 Nitrogen Ebert Maximilian (Mon Oct 19 2015 - 14:37:43 PDT)
[AMBER] Problems with the installation of ambertools15. Jinfeng Huang (Mon Oct 19 2015 - 20:33:15 PDT)
- Re: [AMBER] Problems with the installation of ambertools15. David A Case (Tue Oct 20 2015 - 04:51:49 PDT)
[AMBER] The formulas of per-residue and pairwise-residue free energy decomposition in mm_pbsa wliu (Mon Oct 19 2015 - 23:33:20 PDT)
- Re: [AMBER] The formulas of per-residue and pairwise-residue free energy decomposition in mm_pbsa Jason Swails (Tue Oct 20 2015 - 06:40:15 PDT)
  - Re: [AMBER] The formulas of per-residue and pairwise-residue free energy decomposition in mm_pbsa wliu (Tue Oct 27 2015 - 23:14:27 PDT)
[AMBER] Tutorial 3 section 1 Abelak, Kavin (Tue Oct 20 2015 - 04:54:58 PDT)
- Re: [AMBER] Tutorial 3 section 1 Vlad Cojocaru (Tue Oct 20 2015 - 05:03:15 PDT)
[AMBER] gromacs to amber file format neha chaudhary (Tue Oct 20 2015 - 05:07:03 PDT)
- Re: [AMBER] gromacs to amber file format Hai Nguyen (Tue Oct 20 2015 - 06:31:40 PDT)
  - Re: [AMBER] gromacs to amber file format Jason Swails (Tue Oct 20 2015 - 06:52:23 PDT)
[AMBER] Measuring distance between protein and graphene surface Krantzman, Kristin D (Tue Oct 20 2015 - 11:01:37 PDT)
- Re: [AMBER] Measuring distance between protein and graphene surface Hai Nguyen (Tue Oct 20 2015 - 11:09:41 PDT)
Re: [AMBER] Measuring minimum distance between protein and graphene surface Krantzman, Kristin D (Tue Oct 20 2015 - 11:20:15 PDT)
- Re: [AMBER] Measuring minimum distance between protein and graphene surface Christina Bergonzo (Tue Oct 20 2015 - 12:26:54 PDT)
  - Re: [AMBER] Measuring minimum distance between protein and graphene surface Krantzman, Kristin D (Tue Oct 20 2015 - 15:07:38 PDT)
[AMBER] SGLDg Jérémie Knoops (Tue Oct 20 2015 - 22:45:23 PDT)
- Re: [AMBER] SGLDg Wu, Xiongwu (NIH/NHLBI) [E] (Wed Oct 21 2015 - 08:54:18 PDT)
[AMBER] The magnitude and the direction of the electric field Hadeer ELHabashy (Wed Oct 21 2015 - 05:54:48 PDT)
[AMBER] MMPBSA: multiple trajectory approach usage George Tzotzos (Wed Oct 21 2015 - 08:19:44 PDT)
- Re: [AMBER] MMPBSA: multiple trajectory approach usage Dwight McGee (Wed Oct 21 2015 - 08:53:41 PDT)
  - Re: [AMBER] MMPBSA: multiple trajectory approach usage George Tzotzos (Wed Oct 21 2015 - 09:10:54 PDT)
    - Re: [AMBER] MMPBSA: multiple trajectory approach usage Dwight McGee (Wed Oct 21 2015 - 09:31:49 PDT)
    - Re: [AMBER] MMPBSA: multiple trajectory approach usage George Tzotzos (Wed Oct 21 2015 - 09:38:01 PDT)
[AMBER] pmemd.cuda.MPI on Comet- MPI dying Kenneth Huang (Wed Oct 21 2015 - 09:30:41 PDT)
- Re: [AMBER] pmemd.cuda.MPI on Comet- MPI dying Ross Walker (Wed Oct 21 2015 - 14:14:28 PDT)
  - Re: [AMBER] pmemd.cuda.MPI on Comet- MPI dying Kenneth Huang (Thu Oct 22 2015 - 07:08:11 PDT)
    - Re: [AMBER] pmemd.cuda.MPI on Comet- MPI dying Ross Walker (Thu Oct 22 2015 - 09:16:53 PDT)
    - Re: [AMBER] pmemd.cuda.MPI on Comet- MPI dying Kenneth Huang (Thu Oct 22 2015 - 20:39:47 PDT)
    - Re: [AMBER] pmemd.cuda.MPI on Comet- MPI dying Ross Walker (Thu Oct 22 2015 - 21:37:32 PDT)
    - Re: [AMBER] pmemd.cuda.MPI on Comet- MPI dying Kenneth Huang (Tue Oct 27 2015 - 09:56:56 PDT)
    - Re: [AMBER] pmemd.cuda.MPI on Comet- MPI dying Ross Walker (Tue Oct 27 2015 - 10:01:54 PDT)
    - Re: [AMBER] pmemd.cuda.MPI on Comet- MPI dying Kenneth Huang (Wed Oct 28 2015 - 19:48:31 PDT)
[AMBER] Problem configuring amber14 Mochena, Mogus D. (Wed Oct 21 2015 - 11:11:21 PDT)
- Re: [AMBER] Problem configuring amber14 Jason Swails (Wed Oct 21 2015 - 12:38:34 PDT)
  - Re: [AMBER] Problem configuring amber14 Fabian gmail (Thu Oct 22 2015 - 03:18:43 PDT)
  - Re: [AMBER] Problem configuring amber14 Mochena, Mogus D. (Fri Oct 23 2015 - 06:41:48 PDT)
    - Re: [AMBER] Problem configuring amber14 Jason Swails (Fri Oct 23 2015 - 07:08:13 PDT)
- Re: [AMBER] Problem configuring amber14 David A Case (Wed Oct 21 2015 - 12:58:05 PDT)
[AMBER] ff12SB vs ff14SB for protein-ligand MD simulations? yunshi11 . (Wed Oct 21 2015 - 18:10:07 PDT)
- Re: [AMBER] ff12SB vs ff14SB for protein-ligand MD simulations? Carlos Simmerling (Wed Oct 21 2015 - 18:16:48 PDT)
  - Re: [AMBER] ff12SB vs ff14SB for protein-ligand MD simulations? yunshi11 . (Wed Oct 21 2015 - 18:28:34 PDT)
- [AMBER] ff12SB vs ff14SB for protein-ligand MD simulations? koushik kasavajhala (Wed Oct 21 2015 - 18:39:23 PDT)
[AMBER] MMPBSA for peptides interaction Fabian gmail (Thu Oct 22 2015 - 06:16:22 PDT)
[AMBER] How can amber differentiate between terminal Oxygens Hadeer ELHabashy (Thu Oct 22 2015 - 07:00:59 PDT)
- Re: [AMBER] How can amber differentiate between terminal Oxygens David A Case (Thu Oct 22 2015 - 15:21:08 PDT)
  - Re: [AMBER] How can amber differentiate between terminal Oxygens Hadeer ELHabashy (Mon Oct 26 2015 - 04:41:10 PDT)
    - Re: [AMBER] How can amber differentiate between terminal Oxygens Jason Swails (Mon Oct 26 2015 - 05:37:20 PDT)
    - Re: [AMBER] How can amber differentiate between terminal Oxygens Hadeer ELHabashy (Mon Oct 26 2015 - 05:58:23 PDT)
    - Re: [AMBER] How can amber differentiate between terminal Oxygens Jason Swails (Mon Oct 26 2015 - 06:09:50 PDT)
    - Re: [AMBER] How can amber differentiate between terminal Oxygens Hadeer ELHabashy (Mon Oct 26 2015 - 06:37:50 PDT)
    - Re: [AMBER] How can amber differentiate between terminal Oxygens Jason Swails (Mon Oct 26 2015 - 06:59:49 PDT)
    - Re: [AMBER] How can amber differentiate between terminal Oxygens Hadeer ELHabashy (Mon Oct 26 2015 - 07:01:37 PDT)
    - Re: [AMBER] How can amber differentiate between terminal Oxygens Jason Swails (Mon Oct 26 2015 - 07:21:35 PDT)
    - Re: [AMBER] How can amber differentiate between terminal Oxygens Hadeer ELHabashy (Mon Oct 26 2015 - 07:29:04 PDT)
    - Re: [AMBER] How can amber differentiate between terminal Oxygens Jason Swails (Mon Oct 26 2015 - 09:19:20 PDT)
    - Re: [AMBER] How can amber differentiate between terminal Oxygens Hadeer ELHabashy (Tue Oct 27 2015 - 03:58:55 PDT)
[AMBER] 12-6-4 LJ-type nonbonded model Fe(III)-M(II) Marcelo Andrade Chagas (Thu Oct 22 2015 - 07:34:51 PDT)
- Re: [AMBER] 12-6-4 LJ-type nonbonded model Fe(III)-M(II) Pengfei Li (Thu Oct 22 2015 - 07:36:43 PDT)
  - Re: [AMBER] 12-6-4 LJ-type nonbonded model Fe(III)-M(II) Marcelo Andrade Chagas (Thu Oct 22 2015 - 08:37:28 PDT)
  - Re: [AMBER] 12-6-4 LJ-type nonbonded model Fe(III)-M(II) Marcelo Andrade Chagas (Thu Oct 22 2015 - 09:34:02 PDT)
    - Re: [AMBER] 12-6-4 LJ-type nonbonded model Fe(III)-M(II) Marcelo Andrade Chagas (Thu Oct 22 2015 - 09:37:09 PDT)
  - Re: [AMBER] 12-6-4 LJ-type nonbonded model Fe(III)-M(II) Marcelo Andrade Chagas (Thu Oct 22 2015 - 12:24:17 PDT)
    - Re: [AMBER] 12-6-4 LJ-type nonbonded model Fe(III)-M(II) Pengfei Li (Thu Oct 22 2015 - 13:58:17 PDT)
    - Re: [AMBER] 12-6-4 LJ-type nonbonded model Fe(III)-M(II) Marcelo Andrade Chagas (Fri Oct 23 2015 - 15:41:43 PDT)
    - Re: [AMBER] 12-6-4 LJ-type nonbonded model Fe(III)-M(II) Ross Walker (Fri Oct 23 2015 - 15:48:57 PDT)
    - Re: [AMBER] 12-6-4 LJ-type nonbonded model Fe(III)-M(II) Pengfei Li (Sat Oct 24 2015 - 07:23:41 PDT)
[AMBER] Time correlation function of an atom Hadeer ELHabashy (Thu Oct 22 2015 - 08:54:24 PDT)
- Re: [AMBER] Time correlation function of an atom Adrian Roitberg (Thu Oct 22 2015 - 08:56:00 PDT)
  - Re: [AMBER] Time correlation function of an atom Hadeer ELHabashy (Thu Oct 22 2015 - 09:06:07 PDT)
    - Re: [AMBER] Time correlation function of an atom David A Case (Thu Oct 22 2015 - 15:30:19 PDT)
[AMBER] Polardecomp in 3D-RISM fails Josep Maria Campanera Alsina (Thu Oct 22 2015 - 12:33:43 PDT)
- Re: [AMBER] Polardecomp in 3D-RISM fails Tyler Luchko (Lists) (Thu Oct 22 2015 - 12:47:53 PDT)
- Re: [AMBER] Polardecomp in 3D-RISM fails Jason Swails (Thu Oct 22 2015 - 13:20:06 PDT)
- Re: [AMBER] Polardecomp in 3D-RISM fails Josep Maria Campanera Alsina (Tue Oct 27 2015 - 05:29:47 PDT)
  - Re: [AMBER] Polardecomp in 3D-RISM fails Josep Maria Campanera Alsina (Thu Nov 12 2015 - 04:31:54 PST)
    - Re: [AMBER] Polardecomp in 3D-RISM fails Jason Swails (Thu Nov 12 2015 - 05:19:05 PST)
[AMBER] Atom match error in MMPBSA calculation Progress Zhang (Thu Oct 22 2015 - 14:31:52 PDT)
[AMBER] Metal Ion Model Carlos Modenutti (Thu Oct 22 2015 - 15:42:05 PDT)
- Re: [AMBER] Metal Ion Model Pengfei Li (Fri Oct 23 2015 - 12:28:42 PDT)
  - Re: [AMBER] Metal Ion Model Carlos Modenutti (Fri Oct 30 2015 - 12:06:42 PDT)
    - Re: [AMBER] Metal Ion Model Pengfei Li (Fri Oct 30 2015 - 12:57:07 PDT)
[AMBER] If it's possible to add restraint on the steered MD ? 崔克新 (Fri Oct 23 2015 - 02:06:55 PDT)
[AMBER] Steps after: AMBER annealing with restraints in vacuum.? towards improving the quality of structure with out RDC, Dihedrals V. Kumar (Fri Oct 23 2015 - 02:22:05 PDT)
[AMBER] Steps after: AMBER annealing with restraints in vacuum.? towards improving the quality of structure with out RDC, Dihedrals V. Kumar (Fri Oct 23 2015 - 02:41:36 PDT)
[AMBER] QM/MM Umbrella Mahmood Jasim (Fri Oct 23 2015 - 04:56:31 PDT)
- Re: [AMBER] QM/MM Umbrella Adrian Roitberg (Fri Oct 23 2015 - 06:39:38 PDT)
  - Re: [AMBER] QM/MM Umbrella Mahmood Jasim (Tue Oct 27 2015 - 05:05:38 PDT)
    - Re: [AMBER] QM/MM Umbrella Adrian Roitberg (Tue Oct 27 2015 - 05:30:54 PDT)
    - Re: [AMBER] QM/MM Umbrella Brian Radak (Tue Oct 27 2015 - 07:00:58 PDT)
    - Re: [AMBER] QM/MM Umbrella Emilio Lence (Tue Oct 27 2015 - 09:11:39 PDT)
    - Re: [AMBER] QM/MM Umbrella Mahmood Jasim (Mon Nov 09 2015 - 07:05:31 PST)
    - Re: [AMBER] QM/MM Umbrella Adrian Roitberg (Mon Nov 09 2015 - 08:00:32 PST)
[AMBER] Stopping sander in production phase. Why? Atila Petrosian (Fri Oct 23 2015 - 06:40:41 PDT)
- Re: [AMBER] Stopping sander in production phase. Why? Atila Petrosian (Fri Oct 23 2015 - 07:10:24 PDT)
  - Re: [AMBER] Stopping sander in production phase. Why? Adrian Roitberg (Fri Oct 23 2015 - 07:13:24 PDT)
    - Re: [AMBER] Stopping sander in production phase. Why? Atila Petrosian (Fri Oct 23 2015 - 08:12:31 PDT)
    - Re: [AMBER] Stopping sander in production phase. Why? Jason Swails (Fri Oct 23 2015 - 08:24:06 PDT)
    - Re: [AMBER] Stopping sander in production phase. Why? Atila Petrosian (Fri Oct 23 2015 - 08:48:54 PDT)
    - Re: [AMBER] Stopping sander in production phase. Why? Jason Swails (Fri Oct 23 2015 - 09:01:26 PDT)
[AMBER] Best suitable 'igb' value for MMPBSA.py calculation anu chandra (Fri Oct 23 2015 - 07:02:25 PDT)
- Re: [AMBER] Best suitable 'igb' value for MMPBSA.py calculation Jason Swails (Fri Oct 23 2015 - 07:16:29 PDT)
- Re: [AMBER] Best suitable 'igb' value for MMPBSA.py calculation Hai Nguyen (Fri Oct 23 2015 - 08:20:47 PDT)
  - Re: [AMBER] Best suitable 'igb' value for MMPBSA.py calculation Ray Luo, Ph.D. (Fri Oct 23 2015 - 11:23:29 PDT)
- Re: [AMBER] Best suitable 'igb' value for MMPBSA.py calculation Carlos Simmerling (Fri Oct 23 2015 - 12:02:16 PDT)
  - Re: [AMBER] Best suitable 'igb' value for MMPBSA.py calculation psu4.uic.edu (Sat Oct 24 2015 - 13:10:48 PDT)
[AMBER] aMD: Bad data for namelist object ethreshp Claire Coderch Boué (Fri Oct 23 2015 - 09:29:56 PDT)
- Re: [AMBER] aMD: Bad data for namelist object ethreshp David A Case (Sat Oct 24 2015 - 05:28:39 PDT)
[AMBER] compatibility of targeted MD with GPU amber vs. sander Naomi Rose Latorraca (Fri Oct 23 2015 - 15:13:46 PDT)
- Re: [AMBER] compatibility of targeted MD with GPU amber vs. sander Charles Lin (Fri Oct 23 2015 - 15:18:16 PDT)
[AMBER] ALA but must be GLY MM-PBSA bharat lakhani (Sun Oct 25 2015 - 08:46:42 PDT)
- Re: [AMBER] ALA but must be GLY MM-PBSA Aleksandra Skoric (Sun Oct 25 2015 - 11:26:57 PDT)
[AMBER] how to convert mdcrd to NetCDF trajectory file? shahab shariati (Sun Oct 25 2015 - 10:16:42 PDT)
- Re: [AMBER] how to convert mdcrd to NetCDF trajectory file? shahab shariati (Sun Oct 25 2015 - 10:19:19 PDT)
  - Re: [AMBER] how to convert mdcrd to NetCDF trajectory file? shahab shariati (Sun Oct 25 2015 - 10:39:17 PDT)
    - Re: [AMBER] how to convert mdcrd to NetCDF trajectory file? Nhai (Sun Oct 25 2015 - 12:51:56 PDT)
    - Re: [AMBER] how to convert mdcrd to NetCDF trajectory file? Soumendranath Bhakat (Sun Oct 25 2015 - 13:47:58 PDT)
    - Re: [AMBER] how to convert mdcrd to NetCDF trajectory file? V. Kumar (Mon Oct 26 2015 - 02:14:26 PDT)
- Re: [AMBER] how to convert mdcrd to NetCDF trajectory file? Daniel Roe (Thu Oct 29 2015 - 07:52:50 PDT)
[AMBER] Constant pH MD Hadeer ELHabashy (Mon Oct 26 2015 - 01:07:05 PDT)
- Re: [AMBER] Constant pH MD Hadeer ELHabashy (Mon Oct 26 2015 - 01:11:40 PDT)
[AMBER] atomiccorr Hadeer ELHabashy (Mon Oct 26 2015 - 04:43:47 PDT)
- Re: [AMBER] atomiccorr Daniel Roe (Thu Oct 29 2015 - 07:49:16 PDT)
[AMBER] paramfit multiple dihedrals combination CHAMI F. (Mon Oct 26 2015 - 10:53:57 PDT)
[AMBER] paramfit multiple dihedral commbination CHAMI F. (Mon Oct 26 2015 - 11:47:17 PDT)
- Re: [AMBER] paramfit multiple dihedral commbination Adrian Roitberg (Mon Oct 26 2015 - 11:50:02 PDT)
  - Re: [AMBER] paramfit multiple dihedral commbination Carlos Simmerling (Mon Oct 26 2015 - 12:32:35 PDT)
[AMBER] cpptraj - bridging water Lara rajam (Mon Oct 26 2015 - 11:56:39 PDT)
- Re: [AMBER] cpptraj - bridging water Daniel Roe (Tue Oct 27 2015 - 07:25:12 PDT)
  - Re: [AMBER] cpptraj - bridging water Lara rajam (Tue Oct 27 2015 - 08:54:52 PDT)
[AMBER] ante-MMPBSA question Mohammad Salem (Mon Oct 26 2015 - 15:18:25 PDT)
- Re: [AMBER] ante-MMPBSA question Mohammad Salem (Mon Oct 26 2015 - 15:49:23 PDT)
  - Re: [AMBER] ante-MMPBSA question Daniel Roe (Tue Oct 27 2015 - 07:22:53 PDT)
    - Re: [AMBER] ante-MMPBSA question Jason Swails (Tue Oct 27 2015 - 08:41:15 PDT)
[AMBER] AmberTools 15, Mac El Captain and Fink Alan (Mon Oct 26 2015 - 16:03:33 PDT)
- Re: [AMBER] AmberTools 15, Mac El Captain and Fink Ross Walker (Mon Oct 26 2015 - 16:15:22 PDT)
  - Re: [AMBER] AmberTools 15, Mac El Captain and Fink Alan (Mon Oct 26 2015 - 16:24:48 PDT)
    - Re: [AMBER] AmberTools 15, Mac El Captain and Fink Jason Swails (Mon Oct 26 2015 - 18:02:23 PDT)
    - Re: [AMBER] AmberTools 15, Mac El Captain and Fink Alan (Tue Oct 27 2015 - 03:29:15 PDT)
- Re: [AMBER] AmberTools 15, Mac El Captain and Fink Jason Swails (Mon Oct 26 2015 - 18:08:10 PDT)
[AMBER] parameters for Boron jixiaofeng (Tue Oct 27 2015 - 00:36:09 PDT)
[AMBER] (too) high absolute values for charges using resp and gaussian Jérémie Knoops (Tue Oct 27 2015 - 01:38:47 PDT)
- Re: [AMBER] (too) high absolute values for charges using resp and gaussian Karl Kirschner (Tue Oct 27 2015 - 02:36:36 PDT)
- Re: [AMBER] (too) high absolute values for charges using resp and gaussian Ye Mei (Tue Oct 27 2015 - 03:02:40 PDT)
- Re: [AMBER] (too) high absolute values for charges using resp and gaussian Jérémie Knoops (Mon Nov 02 2015 - 01:06:55 PST)
  - Re: [AMBER] (too) high absolute values for charges using resp and gaussian Jérémie Knoops (Mon Nov 02 2015 - 05:20:14 PST)
    - Re: [AMBER] (too) high absolute values for charges using resp and gaussian Karl Kirschner (Mon Nov 02 2015 - 07:53:31 PST)
[AMBER] coordination number Hadeer ELHabashy (Tue Oct 27 2015 - 03:57:02 PDT)
[AMBER] Help - buy the Amber software Adam Winiarski (Tue Oct 27 2015 - 04:01:13 PDT)
[AMBER] unusual structure_after equilibration Andrew Bostick (Tue Oct 27 2015 - 05:44:43 PDT)
- Re: [AMBER] unusual structure_after equilibration Carlos Simmerling (Tue Oct 27 2015 - 06:19:18 PDT)
[AMBER] Resulting cutoff is too small for your lower limit jfliu (Tue Oct 27 2015 - 05:58:22 PDT)
- Re: [AMBER] Resulting cutoff is too small for your lower limit Carlos Simmerling (Tue Oct 27 2015 - 06:18:18 PDT)
- Re: [AMBER] Resulting cutoff is too small for your lower limit case (Tue Oct 27 2015 - 10:27:30 PDT)
[AMBER] N- and C- terminals constant PH simulation Hadeer ELHabashy (Tue Oct 27 2015 - 06:32:56 PDT)
- Re: [AMBER] N- and C- terminals constant PH simulation Jason Swails (Tue Oct 27 2015 - 08:34:02 PDT)
  - Re: [AMBER] N- and C- terminals constant PH simulation Hadeer ELHabashy (Fri Oct 30 2015 - 04:22:02 PDT)
    - Re: [AMBER] N- and C- terminals constant PH simulation Dr. Anselm Horn (Fri Oct 30 2015 - 05:10:46 PDT)
  - Re: [AMBER] N- and C- terminals constant PH simulation Hadeer ELHabashy (Wed Nov 11 2015 - 01:16:56 PST)
    - Re: [AMBER] N- and C- terminals constant PH simulation Carlos Simmerling (Wed Nov 11 2015 - 04:31:19 PST)
    - Re: [AMBER] N- and C- terminals constant PH simulation Jason Swails (Wed Nov 11 2015 - 05:23:58 PST)
[AMBER] small energy jump when restoring a simulation production Fabian gmail (Tue Oct 27 2015 - 06:36:05 PDT)
- Re: [AMBER] small energy jump when restoring a simulation production Carlos Simmerling (Tue Oct 27 2015 - 06:56:44 PDT)
  - Re: [AMBER] small energy jump when restoring a simulation production Fabian gmail (Tue Oct 27 2015 - 07:03:19 PDT)
    - Re: [AMBER] small energy jump when restoring a simulation production Jason Swails (Tue Oct 27 2015 - 08:46:05 PDT)
    - Re: [AMBER] small energy jump when restoring a simulation production Adrian Roitberg (Tue Oct 27 2015 - 09:02:32 PDT)
    - Re: [AMBER] small energy jump when restoring a simulation production Fabian gmail (Tue Oct 27 2015 - 09:10:44 PDT)
    - Re: [AMBER] small energy jump when restoring a simulation production Jason Swails (Tue Oct 27 2015 - 09:39:49 PDT)
    - Re: [AMBER] small energy jump when restoring a simulation production Fabian gmail (Tue Oct 27 2015 - 09:42:13 PDT)
    - Re: [AMBER] small energy jump when restoring a simulation production Fabian gmail (Tue Oct 27 2015 - 10:02:08 PDT)
    - Re: [AMBER] small energy jump when restoring a simulation production Carlos Simmerling (Tue Oct 27 2015 - 10:04:47 PDT)
    - Re: [AMBER] small energy jump when restoring a simulation production Jason Swails (Tue Oct 27 2015 - 10:23:15 PDT)
    - Re: [AMBER] small energy jump when restoring a simulation production Fabian Glaser (Tue Oct 27 2015 - 11:35:53 PDT)
    - Re: [AMBER] small energy jump when restoring a simulation production Jason Swails (Tue Oct 27 2015 - 12:48:29 PDT)
    - Re: [AMBER] small energy jump when restoring a simulation production Jason Swails (Tue Oct 27 2015 - 10:26:25 PDT)
[AMBER] QMMM with inorganic molecules Robert Arbon (Tue Oct 27 2015 - 10:09:42 PDT)
- Re: [AMBER] QMMM with inorganic molecules Brian Radak (Tue Oct 27 2015 - 10:31:45 PDT)
  - Re: [AMBER] QMMM with inorganic molecules Robert Arbon (Thu Oct 29 2015 - 02:27:14 PDT)
[AMBER] missingdisulfide Abelak, Kavin (Tue Oct 27 2015 - 11:51:43 PDT)
- Re: [AMBER] missingdisulfide Jason Swails (Tue Oct 27 2015 - 12:54:56 PDT)
[AMBER] Replica exchange temperature distribution maryam azimzadehirani (Tue Oct 27 2015 - 18:54:33 PDT)
- Re: [AMBER] Replica exchange temperature distribution Jason Swails (Tue Oct 27 2015 - 20:07:53 PDT)
  - Re: [AMBER] Replica exchange temperature distribution maryam azimzadehirani (Tue Oct 27 2015 - 23:49:39 PDT)
[AMBER] Charmm to Amber (where’s chamber?) Alan (Wed Oct 28 2015 - 02:32:32 PDT)
- Re: [AMBER] Charmm to Amber (where’s chamber?) Alan (Wed Oct 28 2015 - 04:27:37 PDT)
  - Re: [AMBER] Charmm to Amber (where’s chamber?) David A Case (Wed Oct 28 2015 - 05:25:16 PDT)
  - Re: [AMBER] Charmm to Amber (where’s chamber?) Jason Swails (Wed Oct 28 2015 - 07:08:05 PDT)
    - Re: [AMBER] Charmm to Amber (where’s chamber?) Alan (Thu Oct 29 2015 - 16:21:51 PDT)
    - Re: [AMBER] Charmm to Amber (where’s chamber?) Jason Swails (Thu Oct 29 2015 - 18:40:39 PDT)
    - Re: [AMBER] Charmm to Amber (where’s chamber?) Alan (Fri Oct 30 2015 - 08:02:46 PDT)
    - Re: [AMBER] Charmm to Amber (where’s chamber?) Jason Swails (Fri Oct 30 2015 - 08:47:37 PDT)
[AMBER] cpptraj uses huge memory space while doing molsurf calculation anu chandra (Wed Oct 28 2015 - 05:48:40 PDT)
- Re: [AMBER] cpptraj uses huge memory space while doing molsurf calculation Daniel Roe (Thu Oct 29 2015 - 11:46:58 PDT)
  - Re: [AMBER] cpptraj uses huge memory space while doing molsurf calculation anu chandra (Wed Nov 11 2015 - 05:16:31 PST)
    - Re: [AMBER] cpptraj uses huge memory space while doing molsurf calculation David A Case (Wed Nov 11 2015 - 07:31:47 PST)
[AMBER] Different Parameters for Nonbonded Interactions Batuhan Kav (Wed Oct 28 2015 - 08:02:08 PDT)
- Re: [AMBER] Different Parameters for Nonbonded Interactions Jason Swails (Wed Oct 28 2015 - 18:49:09 PDT)
[AMBER] Guanine base pair planarity in G-guadruplex V. Kumar (Wed Oct 28 2015 - 09:02:10 PDT)
[AMBER] how to generate a model beta-sheet structure Jagannath Mondal (Wed Oct 28 2015 - 10:13:18 PDT)
- Re: [AMBER] how to generate a model beta-sheet structure Hai Nguyen (Wed Oct 28 2015 - 10:22:14 PDT)
  - Re: [AMBER] how to generate a model beta-sheet structure Daniel Roe (Thu Oct 29 2015 - 07:34:25 PDT)
[AMBER] applying restraints using tinker Christina Berti (Wed Oct 28 2015 - 10:51:16 PDT)
- Re: [AMBER] applying restraints using tinker Jason Swails (Wed Oct 28 2015 - 13:04:01 PDT)
[AMBER] Tutorial 22 - aMD - how long should it last on Titan Black? Karolina Markowska (Thu Oct 29 2015 - 02:35:40 PDT)
- Re: [AMBER] Tutorial 22 - aMD - how long should it last on Titan Black? case (Thu Oct 29 2015 - 04:40:17 PDT)
  - Re: [AMBER] Tutorial 22 - aMD - how long should it last on Titan Black? Ross Walker (Thu Oct 29 2015 - 08:08:31 PDT)
    - Re: [AMBER] Tutorial 22 - aMD - how long should it last on Titan Black? Karolina Markowska (Thu Oct 29 2015 - 08:32:17 PDT)
    - Re: [AMBER] Tutorial 22 - aMD - how long should it last on Titan Black? Karolina Markowska (Mon Nov 02 2015 - 05:23:23 PST)
[AMBER] Guanine base pair planarity in G-guadruplex V. Kumar (Thu Oct 29 2015 - 04:26:47 PDT)
[AMBER] [AMEBR] Amino acid side-chain carbonyl C=O(ASP, GLU) and side-cahin -HN (LYS, ARG) close proximity V. Kumar (Thu Oct 29 2015 - 05:05:20 PDT)
- Re: [AMBER] [AMEBR] Amino acid side-chain carbonyl C=O(ASP, GLU) and side-cahin -HN (LYS, ARG) close proximity Carlos Simmerling (Fri Oct 30 2015 - 04:05:32 PDT)
[AMBER] MMPBSA for multiple mutants Fabian gmail (Thu Oct 29 2015 - 08:27:58 PDT)
- Re: [AMBER] MMPBSA for multiple mutants Jason Swails (Thu Oct 29 2015 - 08:32:24 PDT)
  - Re: [AMBER] MMPBSA for multiple mutants Fabian gmail (Thu Oct 29 2015 - 08:35:18 PDT)
[AMBER] Glycam force field parameters for derivatives? yunshi11 . (Thu Oct 29 2015 - 21:51:36 PDT)
- Re: [AMBER] Glycam force field parameters for derivatives? Lachele Foley (Fri Oct 30 2015 - 18:40:35 PDT)
[AMBER] How to prevent the water molecules entering into the binding pocket during the MD simulation ? fjliu (Thu Oct 29 2015 - 23:20:57 PDT)
- Re: [AMBER] How to prevent the water molecules entering into the binding pocket during the MD simulation ? Vitaly V. Chaban (Fri Oct 30 2015 - 03:48:54 PDT)
[AMBER] Why PBSA decomposition takes so long time? MarcZhang (Fri Oct 30 2015 - 03:52:40 PDT)
- Re: [AMBER] Why PBSA decomposition takes so long time? Jason Swails (Fri Oct 30 2015 - 07:10:01 PDT)
[AMBER] ions cannot be viewed in gaussview Martina Devi (Fri Oct 30 2015 - 07:18:37 PDT)
- Re: [AMBER] ions cannot be viewed in gaussview Jason Swails (Fri Oct 30 2015 - 08:50:02 PDT)
  - Re: [AMBER] ions cannot be viewed in gaussview Martina Devi (Sat Oct 31 2015 - 09:08:25 PDT)
    - Re: [AMBER] ions cannot be viewed in gaussview Jason Swails (Sat Oct 31 2015 - 09:23:58 PDT)
    - Re: [AMBER] ions cannot be viewed in gaussview Gustavo Seabra (Sat Oct 31 2015 - 10:53:32 PDT)
    - Re: [AMBER] ions cannot be viewed in gaussview Martina Devi (Sat Oct 31 2015 - 12:12:20 PDT)
    - Re: [AMBER] ions cannot be viewed in gaussview Martina Devi (Sun Nov 01 2015 - 07:12:43 PST)
    - Re: [AMBER] ions cannot be viewed in gaussview Robert Molt (Sun Nov 01 2015 - 07:28:17 PST)
    - Re: [AMBER] ions cannot be viewed in gaussview Gustavo Seabra (Sun Nov 01 2015 - 09:04:04 PST)
    - Re: [AMBER] ions cannot be viewed in gaussview Martina Devi (Sun Nov 01 2015 - 10:34:26 PST)
    - Re: [AMBER] ions cannot be viewed in gaussview Jason Swails (Sun Nov 01 2015 - 10:43:48 PST)
    - Re: [AMBER] ions cannot be viewed in gaussview Gustavo Seabra (Sun Nov 01 2015 - 14:37:21 PST)
    - Re: [AMBER] ions cannot be viewed in gaussview MOHD HOMAIDUR RAHMAN (Sun Nov 01 2015 - 21:44:06 PST)
    - Re: [AMBER] ions cannot be viewed in gaussview Martina Devi (Mon Nov 02 2015 - 05:20:34 PST)
    - Re: [AMBER] ions cannot be viewed in gaussview David A Case (Mon Nov 02 2015 - 05:54:36 PST)
    - Re: [AMBER] ions cannot be viewed in gaussview Jason Swails (Mon Nov 02 2015 - 05:41:43 PST)
    - Re: [AMBER] ions cannot be viewed in gaussview Aleksandra Skoric (Mon Nov 02 2015 - 05:54:44 PST)
    - Re: [AMBER] ions cannot be viewed in gaussview Daniel Roe (Mon Nov 02 2015 - 07:47:10 PST)
    - Re: [AMBER] ions cannot be viewed in gaussview Martina Devi (Mon Nov 02 2015 - 08:14:30 PST)
    - Re: [AMBER] ions cannot be viewed in gaussview Jason Swails (Mon Nov 02 2015 - 08:16:44 PST)
    - Re: [AMBER] ions cannot be viewed in gaussview Martina Devi (Mon Nov 02 2015 - 09:24:17 PST)
    - Re: [AMBER] ions cannot be viewed in gaussview Jason Swails (Mon Nov 02 2015 - 09:40:13 PST)
[AMBER] AMBER14 testing error Mahmoud A. A. Ibrahim (Fri Oct 30 2015 - 11:40:41 PDT)
- Re: [AMBER] AMBER14 testing error Hai Nguyen (Fri Oct 30 2015 - 11:56:49 PDT)
- Re: [AMBER] AMBER14 testing error Marcelo Andrade Chagas (Fri Oct 30 2015 - 12:06:18 PDT)
  - Re: [AMBER] AMBER14 testing error Mahmoud A. A. Ibrahim (Sat Oct 31 2015 - 00:25:22 PDT)
    - Re: [AMBER] AMBER14 testing error Jason Swails (Sat Oct 31 2015 - 08:47:11 PDT)
[AMBER] Elementary VMD Problem with Amber Trajectory Robert Molt (Fri Oct 30 2015 - 14:24:31 PDT)
- Re: [AMBER] Elementary VMD Problem with Amber Trajectory Jason Swails (Fri Oct 30 2015 - 14:45:54 PDT)
  - Re: [AMBER] Elementary VMD Problem with Amber Trajectory Robert Molt (Fri Oct 30 2015 - 16:25:06 PDT)
[AMBER] mmpbsa.py error Mohammad Salem (Fri Oct 30 2015 - 17:08:21 PDT)
- Re: [AMBER] mmpbsa.py error Jason Swails (Fri Oct 30 2015 - 17:18:33 PDT)
  - Re: [AMBER] mmpbsa.py error Mohammad Salem (Sat Oct 31 2015 - 10:24:24 PDT)
    - Re: [AMBER] mmpbsa.py error Jason Swails (Sat Oct 31 2015 - 11:57:26 PDT)
[AMBER] &rst + distance + coordinate restraint Gerald Monard (Sat Oct 31 2015 - 10:02:00 PDT)
- Re: [AMBER] &rst + distance + coordinate restraint Gerald Monard (Sat Oct 31 2015 - 10:21:50 PDT)
  - Re: [AMBER] &rst + distance + coordinate restraint Jason Swails (Sun Nov 01 2015 - 02:52:20 PST)
    - Re: [AMBER] &rst + distance + coordinate restraint Gerald Monard (Tue Nov 03 2015 - 06:39:32 PST)
    - Re: [AMBER] &rst + distance + coordinate restraint Jason Swails (Tue Nov 03 2015 - 06:56:57 PST)
    - Re: [AMBER] &rst + distance + coordinate restraint Gerald Monard (Tue Nov 03 2015 - 07:27:50 PST)
- Re: [AMBER] &rst + distance + coordinate restraint Daniel Roe (Mon Nov 02 2015 - 09:09:06 PST)
[AMBER] Can't install AMBER14: MissingProgram...Install patch from your package manager Jose Borreguero (Sat Oct 31 2015 - 15:54:06 PDT)
- Re: [AMBER] Can't install AMBER14: MissingProgram...Install patch from your package manager Daniel Roe (Sat Oct 31 2015 - 16:33:31 PDT)
  - Re: [AMBER] Can't install AMBER14: MissingProgram...Install patch from your package manager Jose Borreguero (Sun Nov 01 2015 - 07:54:55 PST)
[AMBER] MM-PBSA quasi harmonic Debodyuti Dutta (Sat Oct 31 2015 - 20:32:33 PDT)
- Re: [AMBER] MM-PBSA quasi harmonic Jason Swails (Sun Nov 01 2015 - 03:04:07 PST)
[AMBER] Tutorial A26: error in reading nameless control Ruth Helena Tichauer (Mon Nov 02 2015 - 01:28:19 PST)
- Re: [AMBER] Tutorial A26: error in reading nameless control David A Case (Mon Nov 02 2015 - 04:37:48 PST)
  - Re: [AMBER] Tutorial A26: error in reading nameless control Ruth Helena Tichauer (Mon Nov 02 2015 - 06:13:05 PST)
    - Re: [AMBER] Tutorial A26: error in reading nameless control Jason Swails (Mon Nov 02 2015 - 06:17:45 PST)
    - Re: [AMBER] Tutorial A26: error in reading nameless control Ruth Helena Tichauer (Mon Nov 02 2015 - 06:22:39 PST)
[AMBER] How comment in mdin sander input file? Alan (Mon Nov 02 2015 - 01:49:12 PST)
- Re: [AMBER] How comment in mdin sander input file? Eiros Zamora, Juan (Mon Nov 02 2015 - 04:22:15 PST)
- Re: [AMBER] How comment in mdin sander input file? David A Case (Mon Nov 02 2015 - 04:39:15 PST)
  - Re: [AMBER] How comment in mdin sander input file? Alan (Mon Nov 02 2015 - 05:07:54 PST)
[AMBER] rMD || Distance-Restrained Molecular Dynamics Refinement in Explicit Solvent (AMBER) -- SCRIPT V. Kumar (Mon Nov 02 2015 - 04:29:08 PST)
- Re: [AMBER] rMD || Distance-Restrained Molecular Dynamics Refinement in Explicit Solvent (AMBER) -- SCRIPT Carlos Simmerling (Mon Nov 02 2015 - 04:38:37 PST)
  - Re: [AMBER] rMD || Distance-Restrained Molecular Dynamics Refinement in Explicit Solvent (AMBER) -- SCRIPT V. Kumar (Mon Nov 02 2015 - 07:12:13 PST)
    - Re: [AMBER] rMD || Distance-Restrained Molecular Dynamics Refinement in Explicit Solvent (AMBER) -- SCRIPT Jason Swails (Mon Nov 02 2015 - 08:49:27 PST)
    - Re: [AMBER] rMD || Distance-Restrained Molecular Dynamics Refinement in Explicit Solvent (AMBER) -- SCRIPT V. Kumar (Mon Nov 02 2015 - 09:28:37 PST)
[AMBER] Fwd: Regarding QM/MM calculation in AMBER14 Sivanandam M (Mon Nov 02 2015 - 04:41:01 PST)
- Re: [AMBER] Fwd: Regarding QM/MM calculation in AMBER14 Adrian Roitberg (Mon Nov 02 2015 - 05:45:10 PST)
- Re: [AMBER] Fwd: Regarding QM/MM calculation in AMBER14 Jason Swails (Mon Nov 02 2015 - 05:46:33 PST)
- Re: [AMBER] Fwd: Regarding QM/MM calculation in AMBER14 David A Case (Mon Nov 02 2015 - 05:51:27 PST)
[AMBER] How to add restraints to a ligand correctly while decoupling it from complex? wliu (Mon Nov 02 2015 - 04:56:29 PST)
- Re: [AMBER] How to add restraints to a ligand correctly while decoupling it from complex? Jason Swails (Tue Nov 03 2015 - 06:14:57 PST)
[AMBER] decomp bad atom type: fe Abelak, Kavin (Mon Nov 02 2015 - 06:44:49 PST)
[AMBER] trajout our mask pdb with connection records windy (Mon Nov 02 2015 - 18:53:29 PST)
[AMBER] trajout or mask pdb with connection records (title is wrong, see this one) windy (Mon Nov 02 2015 - 18:55:53 PST)
- Re: [AMBER] trajout or mask pdb with connection records (title is wrong, see this one) Jason Swails (Tue Nov 03 2015 - 05:06:44 PST)
  - Re: [AMBER] trajout or mask pdb with connection records (title is wrong, see this one) windy (Wed Nov 04 2015 - 22:21:45 PST)
    - Re: [AMBER] trajout or mask pdb with connection records (title is wrong, see this one) Daniel Roe (Thu Nov 05 2015 - 08:00:24 PST)
[AMBER] Entropy can be neglecected under which condition Marc Zhang (Tue Nov 03 2015 - 01:05:57 PST)
- Re: [AMBER] Entropy can be neglecected under which condition sunita gupta (Tue Nov 03 2015 - 01:22:22 PST)
- Re: [AMBER] Entropy can be neglecected under which condition Carlos Simmerling (Tue Nov 03 2015 - 02:50:16 PST)
  - Re: [AMBER] Entropy can be neglecected under which condition Marc Zhang (Tue Nov 03 2015 - 05:35:54 PST)
[AMBER] ff14SB acetylated residues Neha Gandhi (Tue Nov 03 2015 - 01:37:47 PST)
- Re: [AMBER] ff14SB acetylated residues Carlos Simmerling (Tue Nov 03 2015 - 02:43:11 PST)
[AMBER] ncorr in rotdif command seems redundant to me. Please help. Jose Borreguero (Tue Nov 03 2015 - 14:39:41 PST)
- Re: [AMBER] ncorr in rotdif command seems redundant to me. Please help. case (Tue Nov 03 2015 - 17:49:28 PST)
  - Re: [AMBER] ncorr in rotdif command seems redundant to me. Please help. Daniel Roe (Tue Nov 03 2015 - 19:38:15 PST)
    - Re: [AMBER] ncorr in rotdif command seems redundant to me. Please help. Jose Borreguero (Wed Nov 04 2015 - 03:28:43 PST)
    - Re: [AMBER] ncorr in rotdif command seems redundant to me. Please help. David A Case (Wed Nov 04 2015 - 04:16:37 PST)
[AMBER] How to choose between implicit and explicit solvent Jean-Patrick Francoia (Wed Nov 04 2015 - 01:15:29 PST)
- Re: [AMBER] How to choose between implicit and explicit solvent Carlos Simmerling (Wed Nov 04 2015 - 03:12:06 PST)
  - Re: [AMBER] How to choose between implicit and explicit solvent Jean-Patrick Francoia (Wed Nov 04 2015 - 05:18:07 PST)
    - Re: [AMBER] How to choose between implicit and explicit solvent Carlos Simmerling (Wed Nov 04 2015 - 05:27:08 PST)
    - Re: [AMBER] How to choose between implicit and explicit solvent Jean-Patrick Francoia (Wed Nov 04 2015 - 05:47:03 PST)
    - Re: [AMBER] How to choose between implicit and explicit solvent Jason Swails (Wed Nov 04 2015 - 06:07:48 PST)
    - Re: [AMBER] How to choose between implicit and explicit solvent Jean-Patrick Francoia (Thu Nov 05 2015 - 01:39:23 PST)
    - Re: [AMBER] How to choose between implicit and explicit solvent Carlos Simmerling (Wed Nov 04 2015 - 06:15:39 PST)
  - Re: [AMBER] How to choose between implicit and explicit solvent Fabian gmail (Wed Nov 04 2015 - 08:21:40 PST)
    - Re: [AMBER] How to choose between implicit and explicit solvent David A Case (Wed Nov 04 2015 - 10:07:04 PST)
    - Re: [AMBER] How to choose between implicit and explicit solvent Fabian gmail (Thu Nov 05 2015 - 00:51:13 PST)
    - Re: [AMBER] How to choose between implicit and explicit solvent David A Case (Thu Nov 05 2015 - 04:27:28 PST)
    - Re: [AMBER] How to choose between implicit and explicit solvent Fabian gmail (Thu Nov 05 2015 - 04:45:45 PST)
    - Re: [AMBER] How to choose between implicit and explicit solvent Josh Berryman (Mon Nov 09 2015 - 12:43:37 PST)
    - Re: [AMBER] How to choose between implicit and explicit solvent Ross Walker (Mon Nov 09 2015 - 13:09:37 PST)
    - Re: [AMBER] How to choose between implicit and explicit solvent Josh Berryman (Mon Nov 09 2015 - 23:09:09 PST)
[AMBER] What to expect when MD a peptide and a small organic molecule ? Jean-Patrick Francoia (Wed Nov 04 2015 - 05:42:22 PST)
- Re: [AMBER] What to expect when MD a peptide and a small organic molecule ? Jason Swails (Wed Nov 04 2015 - 06:01:04 PST)
  - Re: [AMBER] What to expect when MD a peptide and a small organic molecule ? Jean-Patrick Francoia (Thu Nov 05 2015 - 01:37:59 PST)
    - Re: [AMBER] What to expect when MD a peptide and a small organic molecule ? Carlos Simmerling (Thu Nov 05 2015 - 03:38:06 PST)
    - Re: [AMBER] What to expect when MD a peptide and a small organic molecule ? Jean-Patrick Francoia (Fri Nov 06 2015 - 02:06:35 PST)
[AMBER] Center of mass restraints with pmemd.cuda abdennour braka (Wed Nov 04 2015 - 06:57:12 PST)
- Re: [AMBER] Center of mass restraints with pmemd.cuda Kevin Hauser (Wed Nov 04 2015 - 07:00:24 PST)
  - Re: [AMBER] Center of mass restraints with pmemd.cuda abdennour braka (Wed Nov 04 2015 - 07:26:28 PST)
    - Re: [AMBER] Center of mass restraints with pmemd.cuda Jason Swails (Wed Nov 04 2015 - 07:29:54 PST)
    - [AMBER] REMD tutorial abdennour braka (Thu Feb 04 2016 - 09:51:23 PST)
    - Re: [AMBER] REMD tutorial Daniel Roe (Thu Feb 04 2016 - 10:51:28 PST)
[AMBER] Gaussian Accelerated Molecular Dynamics Filip Fratev (Wed Nov 04 2015 - 10:31:40 PST)
- Re: [AMBER] Gaussian Accelerated Molecular Dynamics Ross Walker (Wed Nov 04 2015 - 10:59:41 PST)
  - Re: [AMBER] Gaussian Accelerated Molecular Dynamics Albert (Wed Nov 04 2015 - 11:03:07 PST)
    - Re: [AMBER] Gaussian Accelerated Molecular Dynamics Jason Swails (Wed Nov 04 2015 - 12:14:11 PST)
  - Re: [AMBER] Gaussian Accelerated Molecular Dynamics Filip Fratev (Wed Nov 04 2015 - 18:28:35 PST)
    - Re: [AMBER] Gaussian Accelerated Molecular Dynamics Ross Walker (Wed Nov 04 2015 - 19:32:32 PST)
[AMBER] AMBER14 cuda installation problem Sanjib Paul (Wed Nov 04 2015 - 22:20:32 PST)
- Re: [AMBER] AMBER14 cuda installation problem Charles Lin (Wed Nov 04 2015 - 22:35:53 PST)
  - Re: [AMBER] AMBER14 cuda installation problem Charles Lin (Wed Nov 04 2015 - 22:38:03 PST)
    - Re: [AMBER] AMBER14 cuda installation problem Sanjib Paul (Thu Nov 05 2015 - 02:27:52 PST)
[AMBER] orientational restraints in MD simulation Naomi Rose Latorraca (Thu Nov 05 2015 - 00:34:12 PST)
[AMBER] ptraj and cpptraj 袁浩亮 (Thu Nov 05 2015 - 08:10:13 PST)
- Re: [AMBER] ptraj and cpptraj Jason Swails (Thu Nov 05 2015 - 08:11:20 PST)
[AMBER] NMR restraints + minimization+Could not find cntrl namelist V. Kumar (Thu Nov 05 2015 - 09:21:42 PST)
- Re: [AMBER] NMR restraints + minimization+Could not find cntrl namelist Carlos Simmerling (Thu Nov 05 2015 - 09:25:14 PST)
  - Re: [AMBER] NMR restraints + minimization+Could not find cntrl namelist V. Kumar (Thu Nov 05 2015 - 09:29:56 PST)
- Re: [AMBER] NMR restraints + minimization+Could not find cntrl namelist David A Case (Thu Nov 05 2015 - 11:49:47 PST)
  - Re: [AMBER] NMR restraints + minimization+Could not find cntrl namelist V. Kumar (Thu Nov 05 2015 - 12:57:17 PST)
[AMBER] MMPBSA.py QM entropy calculation error Nic Steussy (Thu Nov 05 2015 - 11:35:28 PST)
- Re: [AMBER] MMPBSA.py QM entropy calculation error Jason Swails (Thu Nov 05 2015 - 14:44:07 PST)
  - Re: [AMBER] MMPBSA.py QM entropy calculation error Daniel Roe (Thu Nov 05 2015 - 14:58:12 PST)
[AMBER] Cpptraj Tutorial B1 Aishani Prem (Thu Nov 05 2015 - 13:45:35 PST)
- Re: [AMBER] Cpptraj Tutorial B1 V. Kumar (Thu Nov 05 2015 - 14:11:19 PST)
  - Re: [AMBER] Cpptraj Tutorial B1 Aishani Prem (Thu Nov 05 2015 - 14:18:17 PST)
    - Re: [AMBER] Cpptraj Tutorial B1 Aishani Prem (Thu Nov 05 2015 - 14:20:53 PST)
- Re: [AMBER] Cpptraj Tutorial B1 Daniel Roe (Thu Nov 05 2015 - 14:17:03 PST)
[AMBER] power failure + resume shahab shariati (Fri Nov 06 2015 - 05:59:19 PST)
- Re: [AMBER] power failure + resume Daniel Roe (Fri Nov 06 2015 - 07:53:09 PST)
  - Re: [AMBER] power failure + resume shahab shariati (Fri Nov 06 2015 - 08:29:38 PST)
- Re: [AMBER] power failure + resume Jason Swails (Fri Nov 06 2015 - 09:00:00 PST)
  - Re: [AMBER] power failure + resume shahab shariati (Sun Nov 08 2015 - 03:32:29 PST)
    - Re: [AMBER] power failure + resume shahab shariati (Sun Nov 08 2015 - 03:40:49 PST)
    - Re: [AMBER] power failure + resume Bill (Sun Nov 08 2015 - 03:57:00 PST)
    - Re: [AMBER] power failure + resume Bill (Sun Nov 08 2015 - 04:14:37 PST)
    - Re: [AMBER] power failure + resume Jason Swails (Sun Nov 08 2015 - 08:25:31 PST)
[AMBER] Convert namd input file into sander input format? Xing (Fri Nov 06 2015 - 08:33:23 PST)
- Re: [AMBER] Convert namd input file into sander input format? Jason Swails (Fri Nov 06 2015 - 08:50:44 PST)
[AMBER] make complex Fatemeh Sadat Alavi (Sun Nov 08 2015 - 02:24:58 PST)
- Re: [AMBER] make complex case (Sun Nov 08 2015 - 09:50:42 PST)
- Re: [AMBER] make complex Fatemeh Sadat Alavi (Mon Nov 09 2015 - 00:03:47 PST)
  - Re: [AMBER] make complex Jason Swails (Mon Nov 09 2015 - 04:56:23 PST)
  - Re: [AMBER] make complex David A Case (Mon Nov 09 2015 - 05:21:09 PST)
[AMBER] NOE calculation cpptraj Neha Gandhi (Sun Nov 08 2015 - 18:49:22 PST)
- Re: [AMBER] NOE calculation cpptraj Jason Swails (Mon Nov 09 2015 - 05:00:50 PST)
- Re: [AMBER] NOE calculation cpptraj David A Case (Mon Nov 09 2015 - 05:13:25 PST)
  - Re: [AMBER] NOE calculation cpptraj Neha Gandhi (Mon Nov 09 2015 - 20:00:03 PST)
[AMBER] How to solve the unfilled valence problem in antechamber 张敏华 (Sun Nov 08 2015 - 19:12:35 PST)
- Re: [AMBER] How to solve the unfilled valence problem in antechamber David A Case (Mon Nov 09 2015 - 05:15:53 PST)
- Re: [AMBER] How to solve the unfilled valence problem in antechamber Ashish Radadiya (Thu Jun 15 2017 - 06:23:31 PDT)
  - Re: [AMBER] How to solve the unfilled valence problem in antechamber David Case (Thu Jun 15 2017 - 12:29:58 PDT)
    - Re: [AMBER] How to solve the unfilled valence problem in antechamber Ashish Radadiya (Fri Jun 16 2017 - 02:41:58 PDT)
    - Re: [AMBER] How to solve the unfilled valence problem in antechamber David Case (Fri Jun 16 2017 - 07:54:59 PDT)
    - Re: [AMBER] How to solve the unfilled valence problem in antechamber Ashish Radadiya (Fri Jun 16 2017 - 11:17:58 PDT)
    - Re: [AMBER] How to solve the unfilled valence problem in antechamber David Case (Sun Jun 18 2017 - 11:51:09 PDT)
[AMBER] PLUMED patching with AMBER Sanjib Paul (Sun Nov 08 2015 - 21:24:45 PST)
- Re: [AMBER] PLUMED patching with AMBER Giovanni Bussi (Sun Nov 08 2015 - 23:14:35 PST)
  - Re: [AMBER] PLUMED patching with AMBER Sanjib Paul (Thu Nov 12 2015 - 02:40:49 PST)
    - Re: [AMBER] PLUMED patching with AMBER Giovanni Bussi (Thu Nov 12 2015 - 04:09:53 PST)
    - Re: [AMBER] PLUMED patching with AMBER Jason Swails (Thu Nov 12 2015 - 04:55:53 PST)
    - Re: [AMBER] PLUMED patching with AMBER Giovanni Bussi (Thu Nov 12 2015 - 08:35:06 PST)
    - Re: [AMBER] PLUMED patching with AMBER Jason Swails (Thu Nov 12 2015 - 08:45:35 PST)
    - Re: [AMBER] PLUMED patching with AMBER Sanjib Paul (Fri Nov 13 2015 - 04:06:56 PST)
    - Re: [AMBER] PLUMED patching with AMBER Giovanni Bussi (Fri Nov 13 2015 - 07:18:13 PST)
    - Re: [AMBER] PLUMED patching with AMBER Sanjib Paul (Sat Nov 14 2015 - 04:57:51 PST)
    - Re: [AMBER] PLUMED patching with AMBER Giovanni Bussi (Sat Nov 14 2015 - 08:48:59 PST)
    - Re: [AMBER] PLUMED patching with AMBER Sanjib Paul (Sun Nov 15 2015 - 22:02:25 PST)
[AMBER] A query about distance between periodic images anu chandra (Mon Nov 09 2015 - 08:20:03 PST)
[AMBER] can't install MMPBSA.py.MPI 情生太郎 (Mon Nov 09 2015 - 14:31:37 PST)
- Re: [AMBER] can't install MMPBSA.py.MPI Hai Nguyen (Mon Nov 09 2015 - 14:44:19 PST)
- Re: [AMBER] can't install MMPBSA.py.MPI case (Mon Nov 09 2015 - 17:20:23 PST)
[AMBER] Role of VDWAALS and EEL in minimization muhammad tahir ayub (Mon Nov 09 2015 - 22:22:13 PST)
- Re: [AMBER] Role of VDWAALS and EEL in minimization Carlos Simmerling (Tue Nov 10 2015 - 03:18:50 PST)
[AMBER] GIST Yulian Gavrilov (Tue Nov 10 2015 - 00:24:42 PST)
- Re: [AMBER] GIST Steven Ramsey (Tue Nov 10 2015 - 07:04:56 PST)
  - Re: [AMBER] GIST Jonathan Gough (Tue Nov 10 2015 - 07:28:46 PST)
    - Re: [AMBER] GIST Yulian Gavrilov (Wed Nov 11 2015 - 04:21:39 PST)
    - Re: [AMBER] GIST Steven Ramsey (Wed Nov 11 2015 - 08:33:00 PST)
    - Re: [AMBER] GIST Yulian Gavrilov (Thu Nov 12 2015 - 01:00:13 PST)
[AMBER] neighbouring protons Neha Gandhi (Tue Nov 10 2015 - 01:59:41 PST)
- Re: [AMBER] neighbouring protons Jason Swails (Tue Nov 10 2015 - 04:32:34 PST)
[AMBER] Stability calculations from MMGB/PBSA Rajeswari A. (Wed Nov 11 2015 - 00:54:14 PST)
- Re: [AMBER] Stability calculations from MMGB/PBSA Carlos Simmerling (Wed Nov 11 2015 - 04:35:56 PST)
- Re: [AMBER] Stability calculations from MMGB/PBSA David A Case (Wed Nov 11 2015 - 04:59:37 PST)
- Re: [AMBER] Stability calculations from MMGB/PBSA Jason Swails (Wed Nov 11 2015 - 05:33:32 PST)
  - Re: [AMBER] Stability calculations from MMGB/PBSA Rajeswari A. (Wed Nov 11 2015 - 23:55:25 PST)
    - Re: [AMBER] Stability calculations from MMGB/PBSA Andrea Spitaleri (Thu Nov 12 2015 - 01:20:41 PST)
[AMBER] Problem with MMPBSA Soong Jiaxin (Wed Nov 11 2015 - 01:26:30 PST)
- Re: [AMBER] Problem with MMPBSA Bill (Wed Nov 11 2015 - 01:49:26 PST)
  - Re: [AMBER] Problem with MMPBSA Soong Jiaxin (Wed Nov 11 2015 - 02:23:16 PST)
    - Re: [AMBER] Problem with MMPBSA Jason Swails (Wed Nov 11 2015 - 04:59:21 PST)
    - Re: [AMBER] Problem with MMPBSA Soong Jiaxin (Wed Nov 11 2015 - 05:18:06 PST)
    - Re: [AMBER] Problem with MMPBSA Jason Swails (Wed Nov 11 2015 - 05:27:42 PST)
    - Re: [AMBER] Problem with MMPBSA Soong Jiaxin (Wed Nov 11 2015 - 06:12:20 PST)
    - Re: [AMBER] Problem with MMPBSA psu4.uic.edu (Sat Nov 14 2015 - 13:08:16 PST)
[AMBER] High Positive Values of delta G in MMPBSA Hira Jabeen (Wed Nov 11 2015 - 03:11:01 PST)
- Re: [AMBER] High Positive Values of delta G in MMPBSA Jason Swails (Wed Nov 11 2015 - 05:13:33 PST)
[AMBER] Sampling of membrane-protein system Ofir Tal (Wed Nov 11 2015 - 03:13:21 PST)
- Re: [AMBER] Sampling of membrane-protein system Jason Swails (Wed Nov 11 2015 - 05:10:42 PST)
  - Re: [AMBER] Sampling of membrane-protein system Ofir Tal (Wed Nov 11 2015 - 06:02:11 PST)
  - Re: [AMBER] Sampling of membrane-protein system Brian Radak (Wed Nov 11 2015 - 07:43:44 PST)
[AMBER] High Positive Values of delta G in MMPBSA Hira Jabeen (Wed Nov 11 2015 - 03:16:34 PST)
[AMBER] Few queries about simulation of protein - carbohydrate system anu chandra (Wed Nov 11 2015 - 04:59:07 PST)
- Re: [AMBER] Few queries about simulation of protein - carbohydrate system David A Case (Fri Nov 13 2015 - 04:50:14 PST)
  - Re: [AMBER] Few queries about simulation of protein - carbohydrate system aneesh cna (Fri Nov 13 2015 - 05:20:05 PST)
    - Re: [AMBER] Few queries about simulation of protein - carbohydrate system Lachele Foley (Mon Nov 16 2015 - 11:40:12 PST)
    - Re: [AMBER] Few queries about simulation of protein - carbohydrate system anu chandra (Tue Nov 17 2015 - 05:32:12 PST)
[AMBER] MMPBSA Electrostatic energy Asma Abro 28-FBAS/MSBI/F09 (Wed Nov 11 2015 - 08:22:33 PST)
- Re: [AMBER] MMPBSA Electrostatic energy Jason Swails (Wed Nov 11 2015 - 08:33:12 PST)
  - Re: [AMBER] MMPBSA Electrostatic energy Asma Abro 28-FBAS/MSBI/F09 (Wed Nov 11 2015 - 08:49:35 PST)
    - Re: [AMBER] MMPBSA Electrostatic energy Jason Swails (Wed Nov 11 2015 - 08:52:28 PST)
    - Re: [AMBER] MMPBSA Electrostatic energy Asma Abro 28-FBAS/MSBI/F09 (Wed Nov 11 2015 - 08:58:09 PST)
    - Re: [AMBER] MMPBSA Electrostatic energy Jason Swails (Wed Nov 11 2015 - 10:24:53 PST)
    - Re: [AMBER] MMPBSA Electrostatic energy asma.msbi28.iiu.edu.pk (Wed Nov 11 2015 - 17:44:38 PST)
[AMBER] For atom: .R<Na+ 264>.A<Na+ 1> Could not find vdW (or other) parameters for type: IP Sumra Wajid Abbasi 30-FBAS/MSBI/F09 (Thu Nov 12 2015 - 00:44:55 PST)
- Re: [AMBER] For atom: .R<Na+ 264>.A<Na+ 1> Could not find vdW (or other) parameters for type: IP Bill (Thu Nov 12 2015 - 01:57:21 PST)
- Re: [AMBER] For atom: .R<Na+ 264>.A<Na+ 1> Could not find vdW (or other) parameters for type: IP David A Case (Thu Nov 12 2015 - 04:42:49 PST)
 - Re: [AMBER] For atom: .R<Na+ 264>.A<Na+ 1> Could not find vdW (or other) parameters for type: IP Sumra Wajid Abbasi 30-FBAS/MSBI/F09 (Fri Nov 13 2015 - 23:01:31 PST)
[AMBER] Questions about TI lipengfei_mail (Thu Nov 12 2015 - 06:45:41 PST)
- Re: [AMBER] Questions about TI psu4.uic.edu (Wed Nov 18 2015 - 00:17:43 PST)
  - Re: [AMBER] Questions about TI hannes.loeffler.stfc.ac.uk (Wed Nov 18 2015 - 01:35:58 PST)
[AMBER] how to create a 20% or 30% acetone / water equilibrated solvent box Fabian gmail (Thu Nov 12 2015 - 08:43:18 PST)
- Re: [AMBER] how to create a 20% or 30% acetone / water equilibrated solvent box David A Case (Thu Nov 12 2015 - 10:39:41 PST)
  - Re: [AMBER] how to create a 20% or 30% acetone / water equilibrated solvent box Fabian gmail (Sun Nov 15 2015 - 01:51:03 PST)
[AMBER] GPU run fails Fabian gmail (Thu Nov 12 2015 - 08:47:59 PST)
- Re: [AMBER] GPU run fails Jason Swails (Thu Nov 12 2015 - 09:02:31 PST)
  - Re: [AMBER] GPU run fails Fabian gmail (Sun Nov 15 2015 - 01:14:37 PST)
- Re: [AMBER] GPU run fails Ross Walker (Thu Nov 12 2015 - 09:04:47 PST)
[AMBER] Simulating Inifinite DNA molecules Balaji Selvam (Thu Nov 12 2015 - 08:56:31 PST)
- Re: [AMBER] Simulating Inifinite DNA molecules Ilyas Yildirim (Thu Nov 12 2015 - 08:59:34 PST)
- Re: [AMBER] Simulating Inifinite DNA molecules Jason Swails (Thu Nov 12 2015 - 10:28:34 PST)
[AMBER] Gpu info Carlos Romero (Thu Nov 12 2015 - 09:24:02 PST)
- Re: [AMBER] Gpu info Ross Walker (Thu Nov 12 2015 - 09:41:07 PST)
  - Re: [AMBER] Gpu info Carlos Romero (Thu Nov 12 2015 - 10:43:00 PST)
    - Re: [AMBER] Gpu info Scott Le Grand (Thu Nov 12 2015 - 16:15:21 PST)
- Re: [AMBER] Gpu info Carlos Romero (Thu Nov 12 2015 - 16:42:12 PST)
[AMBER] add support 4 file format antechamber Sofia Vasilakaki (Thu Nov 12 2015 - 10:50:14 PST)
- Re: [AMBER] add support 4 file format antechamber David A Case (Fri Nov 13 2015 - 04:54:15 PST)
[AMBER] Lipid14 simulation :MC Barostat vs Berendsen Barostat and NTR=1 Himanshu Joshi (Fri Nov 13 2015 - 03:42:49 PST)
- Re: [AMBER] Lipid14 simulation :MC Barostat vs Berendsen Barostat and NTR=1 Himanshu Joshi (Fri Nov 13 2015 - 03:47:37 PST)
- Re: [AMBER] Lipid14 simulation :MC Barostat vs Berendsen Barostat and NTR=1 Ross Walker (Fri Nov 13 2015 - 09:11:49 PST)
  - Re: [AMBER] Lipid14 simulation :MC Barostat vs Berendsen Barostat and NTR=1 Himanshu Joshi (Fri Nov 13 2015 - 12:03:56 PST)
    - Re: [AMBER] Lipid14 simulation :MC Barostat vs Berendsen Barostat and NTR=1 Jason Swails (Fri Nov 13 2015 - 13:17:32 PST)
[AMBER] Saving trajectories with ntwprt Batuhan Kav (Fri Nov 13 2015 - 05:25:02 PST)
- Re: [AMBER] Saving trajectories with ntwprt Jason Swails (Fri Nov 13 2015 - 05:29:57 PST)
[AMBER] relaxation time CphMD Arjun Sharma (Fri Nov 13 2015 - 07:03:55 PST)
- Re: [AMBER] relaxation time CphMD Brian Radak (Fri Nov 13 2015 - 07:41:20 PST)
- Re: [AMBER] relaxation time CphMD Jason Swails (Fri Nov 13 2015 - 07:59:08 PST)
[AMBER] error with NMA calculation Mohammad Salem (Fri Nov 13 2015 - 15:33:33 PST)
- Re: [AMBER] error with NMA calculation Jason Swails (Fri Nov 13 2015 - 19:05:41 PST)
  - Re: [AMBER] error with NMA calculation Mohammad (Mon Nov 16 2015 - 21:36:34 PST)
    - Re: [AMBER] error with NMA calculation David A Case (Tue Nov 17 2015 - 04:19:03 PST)
    - Re: [AMBER] error with NMA calculation Mohammad Salem (Wed Nov 18 2015 - 15:38:54 PST)
    - Re: [AMBER] error with NMA calculation Jason Swails (Wed Nov 18 2015 - 18:51:45 PST)
    - Re: [AMBER] error with NMA calculation David A Case (Thu Nov 19 2015 - 05:12:46 PST)
[AMBER] how to plot a graph for enthalpy ayesha afzaal (Sat Nov 14 2015 - 02:09:17 PST)
- Re: [AMBER] how to plot a graph for enthalpy Jason Swails (Sat Nov 14 2015 - 03:54:33 PST)
  - Re: [AMBER] how to plot a graph for enthalpy Ayesha Kanwal (Sat Nov 14 2015 - 06:43:46 PST)
    - Re: [AMBER] how to plot a graph for enthalpy Ayesha Kanwal (Sat Nov 14 2015 - 07:33:11 PST)
    - Re: [AMBER] how to plot a graph for enthalpy asma.msbi28.iiu.edu.pk (Sat Nov 14 2015 - 07:37:47 PST)
    - Re: [AMBER] how to plot a graph for enthalpy Jason Swails (Sat Nov 14 2015 - 08:16:41 PST)
    - Re: [AMBER] how to plot a graph for enthalpy Jason Swails (Sat Nov 14 2015 - 09:29:15 PST)
    - Re: [AMBER] how to plot a graph for enthalpy psu4.uic.edu (Sat Nov 14 2015 - 12:55:27 PST)
- Re: [AMBER] how to plot a graph for enthalpy Ayesha Kanwal (Sat Nov 14 2015 - 13:03:58 PST)
[AMBER] query for plotting enthalpy graph Ayesha Kanwal (Sat Nov 14 2015 - 05:53:18 PST)
- Re: [AMBER] query for plotting enthalpy graph Jason Swails (Sat Nov 14 2015 - 05:58:23 PST)
- Re: [AMBER] query for plotting enthalpy graph Ayesha Kanwal (Thu Nov 19 2015 - 23:56:50 PST)
  - Re: [AMBER] query for plotting enthalpy graph David A Case (Fri Nov 20 2015 - 04:46:16 PST)
Re: [AMBER] Positive delta G in MM-PBSA Jason Swails (Sat Nov 14 2015 - 10:14:41 PST)
[AMBER] mono methylated lysine Bala subramanian (Mon Nov 16 2015 - 01:16:36 PST)
- Re: [AMBER] mono methylated lysine Sourav Purohit (Mon Nov 16 2015 - 22:01:50 PST)
[AMBER] temperature control issue during constant pH simulation with explicit solvent model zhonghe xu (Tue Nov 17 2015 - 05:14:13 PST)
- Re: [AMBER] temperature control issue during constant pH simulation with explicit solvent model Carlos Simmerling (Tue Nov 17 2015 - 05:19:25 PST)
- Re: [AMBER] temperature control issue during constant pH simulation with explicit solvent model Jason Swails (Tue Nov 17 2015 - 05:26:05 PST)
[AMBER] free energy of solvation of small molecules Fabian gmail (Tue Nov 17 2015 - 05:51:50 PST)
- Re: [AMBER] free energy of solvation of small molecules Hannes Loeffler (Tue Nov 17 2015 - 06:17:16 PST)
  - Re: [AMBER] free energy of solvation of small molecules Fabian gmail (Tue Nov 17 2015 - 07:35:04 PST)
    - Re: [AMBER] free energy of solvation of small molecules Hannes Loeffler (Tue Nov 17 2015 - 08:06:45 PST)
    - Re: [AMBER] free energy of solvation of small molecules Fabian gmail (Tue Nov 17 2015 - 08:11:33 PST)
    - Re: [AMBER] free energy of solvation of small molecules Fabian gmail (Thu Nov 19 2015 - 08:40:19 PST)
    - Re: [AMBER] free energy of solvation of small molecules Hannes Loeffler (Thu Nov 19 2015 - 08:54:49 PST)
    - Re: [AMBER] free energy of solvation of small molecules Josh Berryman (Sun Nov 22 2015 - 23:24:54 PST)
    - Re: [AMBER] free energy of solvation of small molecules Fabian gmail (Mon Nov 23 2015 - 05:11:44 PST)
    - Re: [AMBER] free energy of solvation of small molecules Fabian gmail (Sun Nov 29 2015 - 02:52:22 PST)
    - Re: [AMBER] free energy of solvation of small molecules Fabian gmail (Wed Nov 25 2015 - 01:43:36 PST)
    - Re: [AMBER] free energy of solvation of small molecules Hannes Loeffler (Wed Nov 25 2015 - 02:16:34 PST)
    - Re: [AMBER] free energy of solvation of small molecules Fabian gmail (Wed Nov 25 2015 - 02:39:59 PST)
    - Re: [AMBER] free energy of solvation of small molecules Hannes Loeffler (Wed Nov 25 2015 - 03:10:41 PST)
    - Re: [AMBER] free energy of solvation of small molecules Fabian gmail (Wed Nov 25 2015 - 04:26:31 PST)
    - Re: [AMBER] free energy of solvation of small molecules hannes.loeffler.stfc.ac.uk (Wed Nov 25 2015 - 05:03:46 PST)
    - Re: [AMBER] free energy of solvation of small molecules Fabian gmail (Wed Nov 25 2015 - 07:15:06 PST)
    - Re: [AMBER] free energy of solvation of small molecules Hannes Loeffler (Wed Nov 25 2015 - 07:38:18 PST)
    - Re: [AMBER] free energy of solvation of small molecules Fabian gmail (Wed Nov 25 2015 - 08:00:35 PST)
    - Re: [AMBER] free energy of solvation of small molecules Fabian gmail (Sun Nov 29 2015 - 08:08:05 PST)
    - Re: [AMBER] free energy of solvation of small molecules hannes.loeffler.stfc.ac.uk (Mon Nov 30 2015 - 00:57:33 PST)
    - Re: [AMBER] free energy of solvation of small molecules Fabian gmail (Mon Nov 30 2015 - 01:12:16 PST)
    - Re: [AMBER] free energy of solvation of small molecules Fabian gmail (Wed Dec 02 2015 - 04:41:31 PST)
    - Re: [AMBER] free energy of solvation of small molecules Jason Swails (Wed Dec 02 2015 - 05:42:10 PST)
    - Re: [AMBER] free energy of solvation of small molecules Fabian gmail (Wed Dec 02 2015 - 06:49:20 PST)
    - Re: [AMBER] free energy of solvation of small molecules Hannes Loeffler (Thu Dec 03 2015 - 03:46:45 PST)
    - Re: [AMBER] free energy of solvation of small molecules Fabian gmail (Thu Dec 03 2015 - 04:15:17 PST)
    - Re: [AMBER] free energy of solvation of small molecules Hannes Loeffler (Fri Dec 04 2015 - 01:44:40 PST)
    - Re: [AMBER] free energy of solvation of small molecules Fabian Glaser (Fri Dec 04 2015 - 04:09:29 PST)
    - Re: [AMBER] free energy of solvation of small molecules Hannes Loeffler (Fri Dec 04 2015 - 06:21:23 PST)
    - Re: [AMBER] free energy of solvation of small molecules Fabian Glaser (Fri Dec 04 2015 - 07:06:22 PST)
    - Re: [AMBER] free energy of solvation of small molecules Fabian gmail (Mon Dec 07 2015 - 06:58:51 PST)
    - Re: [AMBER] free energy of solvation of small molecules David A Case (Mon Dec 07 2015 - 07:06:33 PST)
    - Re: [AMBER] free energy of solvation of small molecules Fabian Glaser (Mon Dec 07 2015 - 13:07:03 PST)
    - Re: [AMBER] free energy of solvation of small molecules Fabian gmail (Sun Dec 13 2015 - 06:10:25 PST)
    - Re: [AMBER] free energy of solvation of small molecules Hannes Loeffler (Mon Dec 14 2015 - 01:35:43 PST)
    - Re: [AMBER] free energy of solvation of small molecules Fabian gmail (Wed Dec 02 2015 - 06:55:43 PST)
    - Re: [AMBER] free energy of solvation of small molecules Hannes Loeffler (Thu Dec 03 2015 - 03:35:12 PST)
[AMBER] Making .mdl files for 1DRISM calculations Ella Gale (Tue Nov 17 2015 - 07:22:53 PST)
- Re: [AMBER] Making .mdl files for 1DRISM calculations Tyler Luchko (Lists) (Tue Nov 17 2015 - 12:56:27 PST)
  - Re: [AMBER] Making .mdl files for 1DRISM calculations Ella Gale (Wed Nov 18 2015 - 04:51:40 PST)
    - Re: [AMBER] Making .mdl files for 1DRISM calculations Tyler Luchko (Lists) (Wed Nov 18 2015 - 09:51:52 PST)
    - Re: [AMBER] Making .mdl files for 1DRISM calculations David A Case (Wed Nov 18 2015 - 12:27:02 PST)
[AMBER] Typo or My Confusion Robert Molt (Tue Nov 17 2015 - 19:56:42 PST)
[AMBER] Typo or My Confusion Robert Molt (Tue Nov 17 2015 - 19:57:02 PST)
- Re: [AMBER] Typo or My Confusion David A Case (Wed Nov 18 2015 - 06:11:31 PST)
  - Re: [AMBER] Typo or My Confusion Robert Molt (Wed Nov 18 2015 - 07:25:10 PST)
    - Re: [AMBER] Typo or My Confusion Jason Swails (Wed Nov 18 2015 - 08:20:49 PST)
    - Re: [AMBER] Typo or My Confusion Ross Walker (Thu Nov 19 2015 - 08:16:45 PST)
[AMBER] net charge issue during constant pH simulation with explicit solvent model zhonghe xu (Tue Nov 17 2015 - 23:19:34 PST)
- Re: [AMBER] net charge issue during constant pH simulation with explicit solvent model Jason Swails (Wed Nov 18 2015 - 08:40:32 PST)
[AMBER] Number of water molecule to solvate 2.5KDa peptide in TIP3PBOX V. Kumar (Wed Nov 18 2015 - 01:32:30 PST)
- Re: [AMBER] Number of water molecule to solvate 2.5KDa peptide in TIP3PBOX David A Case (Wed Nov 18 2015 - 06:22:17 PST)
  - Re: [AMBER] Number of water molecule to solvate 2.5KDa peptide in TIP3PBOX V. Kumar (Wed Nov 18 2015 - 06:39:49 PST)
[AMBER] Backbone mohammad roostaie (Wed Nov 18 2015 - 01:52:09 PST)
- Re: [AMBER] Backbone Karl Kirschner (Wed Nov 18 2015 - 02:09:26 PST)
  - Re: [AMBER] Backbone mohammad r (Wed Nov 18 2015 - 05:15:25 PST)
    - Re: [AMBER] Backbone Jason Swails (Wed Nov 18 2015 - 06:12:57 PST)
    - Re: [AMBER] Backbone Daniel Roe (Wed Nov 18 2015 - 07:15:34 PST)
    - Re: [AMBER] Backbone mohammad r (Wed Nov 18 2015 - 07:36:15 PST)
    - Re: [AMBER] Backbone David A Case (Wed Nov 18 2015 - 12:34:41 PST)
    - Re: [AMBER] Backbone mohammad r (Wed Nov 18 2015 - 12:40:28 PST)
[AMBER] Backbone mohammad r (Wed Nov 18 2015 - 01:49:57 PST)
[AMBER] Backbone mohammad r (Wed Nov 18 2015 - 01:50:30 PST)
[AMBER] urea force field Carlos Romero (Wed Nov 18 2015 - 16:39:34 PST)
- Re: [AMBER] urea force field Karl Kirschner (Wed Nov 18 2015 - 23:24:23 PST)
  - Re: [AMBER] urea force field Carlos Romero (Thu Nov 19 2015 - 06:47:01 PST)
    - Re: [AMBER] urea force field Jason Swails (Thu Nov 19 2015 - 07:29:30 PST)
    - Re: [AMBER] urea force field Carlos Romero (Fri Nov 20 2015 - 13:23:12 PST)
[AMBER] (no subject) Facebook (Wed Nov 18 2015 - 22:30:12 PST)
[AMBER] Distorted and Failed Phosphate Simulations Sigurd Friis Truelsen (Thu Nov 19 2015 - 02:48:32 PST)
- Re: [AMBER] Distorted and Failed Phosphate Simulations Karl Kirschner (Thu Nov 19 2015 - 03:14:22 PST)
- Re: [AMBER] Distorted and Failed Phosphate Simulations pavel.banas.upol.cz (Thu Nov 19 2015 - 05:23:03 PST)
- Re: [AMBER] Distorted and Failed Phosphate Simulations David A Case (Thu Nov 19 2015 - 05:26:20 PST)
  - Re: [AMBER] Distorted and Failed Phosphate Simulations Karl Kirschner (Fri Nov 20 2015 - 01:36:16 PST)
    - Re: [AMBER] Distorted and Failed Phosphate Simulations Sigurd Friis Truelsen (Tue Nov 24 2015 - 02:08:00 PST)
    - Re: [AMBER] Distorted and Failed Phosphate Simulations Jason Swails (Tue Nov 24 2015 - 05:17:54 PST)
[AMBER] cpptraj grid command Thomas Fox (Thu Nov 19 2015 - 04:43:05 PST)
- Re: [AMBER] cpptraj grid command Daniel Roe (Thu Nov 19 2015 - 08:44:30 PST)
  - Re: [AMBER] cpptraj grid command Thomas Fox (Thu Nov 19 2015 - 09:09:56 PST)
    - Re: [AMBER] cpptraj grid command Daniel Roe (Fri Nov 20 2015 - 15:02:10 PST)
    - Re: [AMBER] cpptraj grid command Thomas Fox (Wed Nov 25 2015 - 00:27:48 PST)
    - Re: [AMBER] cpptraj grid command Daniel Roe (Thu Nov 26 2015 - 05:51:08 PST)
    - Re: [AMBER] cpptraj grid command Thomas Fox (Mon Dec 14 2015 - 08:24:46 PST)
[AMBER] Putting a harmonic constraint between atoms Debodyuti Dutta (Thu Nov 19 2015 - 05:52:16 PST)
- Re: [AMBER] Putting a harmonic constraint between atoms Jason Swails (Thu Nov 19 2015 - 06:26:28 PST)
[AMBER] decomposition energy Fabian gmail (Thu Nov 19 2015 - 08:32:29 PST)
- Re: [AMBER] decomposition energy Jason Swails (Thu Nov 19 2015 - 09:16:47 PST)
[AMBER] Error compiling amber14 with CUDA-7.0 (CentOS 7) Elvis Martis (Thu Nov 19 2015 - 23:36:04 PST)
- Re: [AMBER] Error compiling amber14 with CUDA-7.0 (CentOS 7) Jason Swails (Fri Nov 20 2015 - 04:56:40 PST)
- Re: [AMBER] Error compiling amber14 with CUDA-7.0 (CentOS 7) Elvis Martis (Fri Nov 20 2015 - 20:51:24 PST)
  - Re: [AMBER] Error compiling amber14 with CUDA-7.0 (CentOS 7) Sofia Vasilakaki (Sat Nov 21 2015 - 02:39:50 PST)
  - Re: [AMBER] Error compiling amber14 with CUDA-7.0 (CentOS 7) Jason Swails (Sat Nov 21 2015 - 04:25:26 PST)
- Re: [AMBER] Error compiling amber14 with CUDA-7.0 (CentOS 7) Elvis Martis (Sat Nov 21 2015 - 19:29:15 PST)
[AMBER] (no subject) Facebook (Fri Nov 20 2015 - 03:58:07 PST)
[AMBER] units of charge density Ignacio J. General (Fri Nov 20 2015 - 06:24:45 PST)
[AMBER] (no subject) Facebook (Fri Nov 20 2015 - 10:06:55 PST)
[AMBER] (no subject) Facebook (Fri Nov 20 2015 - 11:32:07 PST)
[AMBER] cpptraj density command Ignacio J. General (Sat Nov 21 2015 - 05:10:17 PST)
- Re: [AMBER] cpptraj density command David A Case (Sat Nov 21 2015 - 05:54:39 PST)
  - Re: [AMBER] cpptraj density command Daniel Roe (Sat Nov 21 2015 - 09:59:26 PST)
    - Re: [AMBER] cpptraj density command Ignacio J. General (Sun Nov 22 2015 - 06:09:41 PST)
[AMBER] 10 Lowest energy structures from GB ==>Explicit solvent refinement V. Kumar (Sat Nov 21 2015 - 07:25:37 PST)
- Re: [AMBER] 10 Lowest energy structures from GB ==>Explicit solvent refinement David A Case (Sat Nov 21 2015 - 17:34:08 PST)
  - Re: [AMBER] 10 Lowest energy structures from GB ==>Explicit solvent refinement V. Kumar (Sun Nov 22 2015 - 04:19:37 PST)
[AMBER] Apologize Carlos Romero (Sat Nov 21 2015 - 17:59:14 PST)
[AMBER] QMMM: ERROR! Ayesha Kanwal (Sun Nov 22 2015 - 21:32:02 PST)
- Re: [AMBER] QMMM: ERROR! Ross Walker (Sun Nov 22 2015 - 21:42:20 PST)
  - Re: [AMBER] QMMM: ERROR! Ayesha Kanwal (Mon Nov 23 2015 - 02:36:48 PST)
    - Re: [AMBER] QMMM: ERROR! Ayesha Kanwal (Mon Nov 23 2015 - 04:05:14 PST)
    - Re: [AMBER] QMMM: ERROR! Jason Swails (Mon Nov 23 2015 - 04:12:14 PST)
    - Re: [AMBER] QMMM: ERROR! David A Case (Mon Nov 23 2015 - 05:26:42 PST)
[AMBER] Can LEaP create peptides with D-amino acids? Yip Yew Mun (Mon Nov 23 2015 - 00:19:37 PST)
- Re: [AMBER] Can LEaP create peptides with D-amino acids? Carlos Simmerling (Mon Nov 23 2015 - 03:10:23 PST)
  - Re: [AMBER] Can LEaP create peptides with D-amino acids? Marion, Antoine (Mon Nov 23 2015 - 04:00:38 PST)
    - Re: [AMBER] Can LEaP create peptides with D-amino acids? Carlos Simmerling (Mon Nov 23 2015 - 05:07:57 PST)
Re: [AMBER] How to fix the QM/MM region box size and visualize it Sivanandam M (Mon Nov 23 2015 - 05:15:28 PST)
- Re: [AMBER] How to fix the QM/MM region box size and visualize it Gustavo Seabra (Mon Nov 23 2015 - 06:12:12 PST)
[AMBER] MD simulation for multiple ligands Balajee Ramachandran (Mon Nov 23 2015 - 07:57:47 PST)
- Re: [AMBER] MD simulation for multiple ligands Jason Swails (Mon Nov 23 2015 - 14:28:50 PST)
[AMBER] how to add lipid mohammad r (Mon Nov 23 2015 - 09:01:11 PST)
[AMBER] how to add lipid mohammad r (Mon Nov 23 2015 - 09:01:46 PST)
- Re: [AMBER] how to add lipid Bill Ross (Sun Aug 23 2015 - 23:15:09 PDT)
  - Re: [AMBER] how to add lipid mohammad r (Mon Aug 24 2015 - 00:07:42 PDT)
    - Re: [AMBER] how to add lipid mohammad r (Mon Aug 24 2015 - 09:53:35 PDT)
    - Re: [AMBER] how to add lipid mohammad r (Mon Aug 24 2015 - 10:28:48 PDT)
    - Re: [AMBER] how to add lipid Jason Swails (Mon Aug 24 2015 - 10:41:52 PDT)
    - Re: [AMBER] how to add lipid mohammad r (Mon Aug 24 2015 - 10:44:33 PDT)
    - Re: [AMBER] how to add lipid Jason Swails (Mon Aug 24 2015 - 10:41:06 PDT)
- Re: [AMBER] how to add lipid Bill Ross (Mon Aug 24 2015 - 12:20:41 PDT)
  - Re: [AMBER] how to add lipid mohammad r (Mon Aug 24 2015 - 21:43:28 PDT)
    - Re: [AMBER] how to add lipid mohammad r (Mon Aug 24 2015 - 23:14:45 PDT)
- Re: [AMBER] how to add lipid Bill Ross (Tue Aug 25 2015 - 01:36:57 PDT)
  - Re: [AMBER] how to add lipid mohammad r (Tue Aug 25 2015 - 03:28:23 PDT)
    - Re: [AMBER] how to add lipid mohammad r (Tue Aug 25 2015 - 03:43:31 PDT)
    - Re: [AMBER] how to add lipid Charles Lin (Tue Aug 25 2015 - 10:10:15 PDT)
- Re: [AMBER] how to add lipid Bill Ross (Tue Aug 25 2015 - 13:13:22 PDT)
  - Re: [AMBER] how to add lipid mohammad r (Wed Aug 26 2015 - 07:17:22 PDT)
    - Re: [AMBER] how to add lipid mohammad r (Wed Aug 26 2015 - 07:31:13 PDT)
    - Re: [AMBER] how to add lipid Charles Lin (Thu Aug 27 2015 - 10:22:14 PDT)
    - Re: [AMBER] how to add lipid Repic Matej (Thu Aug 27 2015 - 14:16:18 PDT)
    - Re: [AMBER] how to add lipid mohammad r (Fri Aug 28 2015 - 00:09:54 PDT)
    - Re: [AMBER] how to add lipid Jason Swails (Fri Aug 28 2015 - 06:34:35 PDT)
    - Re: [AMBER] how to add lipid mohammad r (Fri Aug 28 2015 - 07:26:49 PDT)
- Re: [AMBER] how to add lipid Brian Radak (Mon Nov 23 2015 - 09:03:56 PST)
  - Re: [AMBER] how to add lipid mohammad r (Mon Nov 23 2015 - 09:52:41 PST)
    - Re: [AMBER] how to add lipid Brian Radak (Mon Nov 23 2015 - 09:57:25 PST)
    - Re: [AMBER] how to add lipid Parker de Waal (Mon Nov 23 2015 - 10:17:13 PST)
    - Re: [AMBER] how to add lipid mohammad r (Mon Nov 23 2015 - 10:31:15 PST)
    - Re: [AMBER] how to add lipid Parker de Waal (Mon Nov 23 2015 - 10:41:51 PST)
    - Re: [AMBER] how to add lipid mohammad r (Mon Nov 23 2015 - 10:48:28 PST)
[AMBER] Running simulations in a cluster Aishani Prem (Mon Nov 23 2015 - 14:22:47 PST)
- Re: [AMBER] Running simulations in a cluster Jason Swails (Mon Nov 23 2015 - 14:26:20 PST)
[AMBER] query about Br Ayesha Kanwal (Tue Nov 24 2015 - 00:20:00 PST)
- Re: [AMBER] query about Br Ayesha Kanwal (Tue Nov 24 2015 - 05:03:02 PST)
  - Re: [AMBER] query about Br David A Case (Tue Nov 24 2015 - 08:32:00 PST)
[AMBER] Protein-Drug complex MD simulation issues Vahid Kshani (Tue Nov 24 2015 - 03:28:12 PST)
- Re: [AMBER] Protein-Drug complex MD simulation issues Bill (Tue Nov 24 2015 - 03:58:24 PST)
[AMBER] (no subject) Facebook (Tue Nov 24 2015 - 05:13:14 PST)
[AMBER] (no subject) Facebook (Tue Nov 24 2015 - 07:09:44 PST)
[AMBER] MMGBSA Decomp on Heme Systems Vivek Bharadwaj (Tue Nov 24 2015 - 08:46:43 PST)
- Re: [AMBER] MMGBSA Decomp on Heme Systems Jason Swails (Tue Nov 24 2015 - 09:24:38 PST)
  - Re: [AMBER] MMGBSA Decomp on Heme Systems Vivek Bharadwaj (Wed Nov 25 2015 - 09:20:02 PST)
[AMBER] Import error when running MMPBSA.py Cockroft, Nicholas T. (Tue Nov 24 2015 - 14:00:11 PST)
- Re: [AMBER] Import error when running MMPBSA.py Dwight McGee (Tue Nov 24 2015 - 16:30:41 PST)
  - Re: [AMBER] Import error when running MMPBSA.py Cockroft, Nicholas T. (Tue Nov 24 2015 - 16:41:51 PST)
    - Re: [AMBER] Import error when running MMPBSA.py Nhai (Tue Nov 24 2015 - 16:57:53 PST)
    - Re: [AMBER] Import error when running MMPBSA.py Hai Nguyen (Tue Nov 24 2015 - 16:59:55 PST)
    - Re: [AMBER] Import error when running MMPBSA.py Dwight McGee (Tue Nov 24 2015 - 17:16:48 PST)
    - Re: [AMBER] Import error when running MMPBSA.py Cockroft, Nicholas T. (Wed Nov 25 2015 - 10:25:03 PST)
[AMBER] NAB nmode() output Clarification Guqin Shi (Tue Nov 24 2015 - 14:57:19 PST)
- Re: [AMBER] NAB nmode() output Clarification David A Case (Wed Nov 25 2015 - 06:59:56 PST)
- Re: [AMBER] NAB nmode() output Clarification Guqin Shi (Wed Nov 25 2015 - 07:20:39 PST)
[AMBER] iwrap=1 "can mess up diffusion and other calculations" Robert Molt (Tue Nov 24 2015 - 17:45:57 PST)
- Re: [AMBER] iwrap=1 "can mess up diffusion and other calculations" Charles Lin (Tue Nov 24 2015 - 18:56:52 PST)
  - Re: [AMBER] iwrap=1 "can mess up diffusion and other calculations" Jason Swails (Tue Nov 24 2015 - 20:57:26 PST)
- Re: [AMBER] iwrap=1 "can mess up diffusion and other calculations" Jason Swails (Tue Nov 24 2015 - 18:57:12 PST)
  - Re: [AMBER] iwrap=1 "can mess up diffusion and other calculations" Robert Molt (Tue Nov 24 2015 - 19:02:49 PST)
[AMBER] Equilibrium temperature is higher than the target temperature in Langevin dynamics jinfeng liu (Wed Nov 25 2015 - 00:23:40 PST)
- Re: [AMBER] Equilibrium temperature is higher than the target temperature in Langevin dynamics David A Case (Wed Nov 25 2015 - 07:02:50 PST)
  - Re: [AMBER] Equilibrium temperature is higher than the target temperature in Langevin dynamics jinfeng liu (Wed Nov 25 2015 - 07:24:16 PST)
    - Re: [AMBER] Equilibrium temperature is higher than the target temperature in Langevin dynamics Daniel Roe (Wed Nov 25 2015 - 08:38:54 PST)
    - Re: [AMBER] Equilibrium temperature is higher than the target temperature in Langevin dynamics jinfeng liu (Wed Nov 25 2015 - 17:40:16 PST)
    - Re: [AMBER] Equilibrium temperature is higher than the target temperature in Langevin dynamics David A Case (Thu Nov 26 2015 - 10:26:11 PST)
    - Re: [AMBER] Equilibrium temperature is higher than the target temperature in Langevin dynamics jinfeng liu (Thu Nov 26 2015 - 22:16:33 PST)
    - Re: [AMBER] Equilibrium temperature is higher than the target temperature in Langevin dynamics David A Case (Fri Nov 27 2015 - 07:14:43 PST)
    - Re: [AMBER] Equilibrium temperature is higher than the target temperature in Langevin dynamics David A Case (Thu Nov 26 2015 - 10:37:00 PST)
[AMBER] Deformed structures Damiano Spadoni (Wed Nov 25 2015 - 08:23:29 PST)
- Re: [AMBER] Deformed structures David A Case (Wed Nov 25 2015 - 16:27:29 PST)
  - Re: [AMBER] Deformed structures Damiano Spadoni (Thu Nov 26 2015 - 03:44:38 PST)
[AMBER] At line 434 of file make_crd_hg.F (unit = 5, file = 'stdin') Fortran runtime error: Bad value during floating point read. leila karami (Thu Nov 26 2015 - 08:14:12 PST)
- Re: [AMBER] At line 434 of file make_crd_hg.F (unit = 5, file = 'stdin') Fortran runtime error: Bad value during floating point read. leila karami (Thu Nov 26 2015 - 11:50:16 PST)
- Re: [AMBER] At line 434 of file make_crd_hg.F (unit = 5, file = 'stdin') Fortran runtime error: Bad value during floating point read. David A Case (Thu Nov 26 2015 - 14:07:46 PST)
  - Re: [AMBER] At line 434 of file make_crd_hg.F (unit = 5, file = 'stdin') Fortran runtime error: Bad value during floating point read. Bill (Thu Nov 26 2015 - 14:38:32 PST)
[AMBER] Error message while running alanine dipeptide tutorial (minimization) Nikolay N. Kuzmich (Fri Nov 27 2015 - 00:28:39 PST)
- Re: [AMBER] Error message while running alanine dipeptide tutorial (minimization) Bill (Fri Nov 27 2015 - 00:35:33 PST)
- Re: [AMBER] Error message while running alanine dipeptide tutorial (minimization) David A Case (Fri Nov 27 2015 - 07:17:24 PST)
- Re: [AMBER] Error message while running alanine dipeptide tutorial (minimization) Nikolay N. Kuzmich (Mon Nov 30 2015 - 03:39:41 PST)
  - Re: [AMBER] Error message while running alanine dipeptide tutorial (minimization) Carlos Simmerling (Mon Nov 30 2015 - 04:06:15 PST)
  - Re: [AMBER] Error message while running alanine dipeptide tutorial (minimization) Bill (Mon Nov 30 2015 - 14:49:41 PST)
  - Re: [AMBER] Error message while running alanine dipeptide tutorial (minimization) David A Case (Mon Nov 30 2015 - 15:41:52 PST)
  - Re: [AMBER] Error message while running alanine dipeptide tutorial (minimization) Nikolay N. Kuzmich (Tue Dec 01 2015 - 01:08:49 PST)
    - Re: [AMBER] Error message while running alanine dipeptide tutorial (minimization) Nikolay N. Kuzmich (Tue Dec 01 2015 - 01:27:53 PST)
    - Re: [AMBER] Error message while running alanine dipeptide tutorial (minimization) Bill (Tue Dec 01 2015 - 02:13:33 PST)
    - Re: [AMBER] Error message while running alanine dipeptide tutorial (minimization) Nikolay N. Kuzmich (Fri Dec 04 2015 - 00:51:21 PST)
    - Re: [AMBER] Error message while running alanine dipeptide tutorial (minimization) Bill (Fri Dec 04 2015 - 01:02:05 PST)
    - Re: [AMBER] Error message while running alanine dipeptide tutorial (minimization) David A Case (Fri Dec 04 2015 - 05:13:37 PST)
[AMBER] Fwd: Replica exchange problem in visualization and interpretation of the MD out files maryam azimzadehirani (Fri Nov 27 2015 - 02:58:09 PST)
- Re: [AMBER] Fwd: Replica exchange problem in visualization and interpretation of the MD out files Carlos Simmerling (Fri Nov 27 2015 - 06:35:12 PST)
[AMBER] Adding parameters to the force field Timofey Tyugashev (Fri Nov 27 2015 - 04:07:04 PST)
- Re: [AMBER] Adding parameters to the force field David A Case (Sun Nov 29 2015 - 17:34:30 PST)
[AMBER] MMPBSA Balajee Ramachandran (Sun Nov 29 2015 - 11:06:45 PST)
- Re: [AMBER] MMPBSA David A Case (Sun Nov 29 2015 - 17:29:31 PST)
[AMBER] Not matching test AMBER14 with CUDA Mijiddorj Batsaikhan (Sun Nov 29 2015 - 21:22:56 PST)
- Re: [AMBER] Not matching test AMBER14 with CUDA Ross Walker (Sun Nov 29 2015 - 21:52:27 PST)
  - Re: [AMBER] Not matching test AMBER14 with CUDA Mijiddorj Batsaikhan (Mon Nov 30 2015 - 20:20:13 PST)
    - Re: [AMBER] Not matching test AMBER14 with CUDA Jason Swails (Tue Dec 01 2015 - 04:55:29 PST)
[AMBER] How to fix malloc error during MM-PBSA calculation on AMBER14 ... mmpbsa_py_energy: malloc.c:2372: sysmalloc: Mijiddorj Batsaikhan (Mon Nov 30 2015 - 06:15:44 PST)
[AMBER] zinc ordination 2-CYM 2-HID || CYM-CYM covalent bond V. Kumar (Mon Nov 30 2015 - 09:00:21 PST)
- Re: [AMBER] zinc ordination 2-CYM 2-HID || CYM-CYM covalent bond Carlos Simmerling (Mon Nov 30 2015 - 09:02:45 PST)
  - Re: [AMBER] zinc ordination 2-CYM 2-HID || CYM-CYM covalent bond V. Kumar (Mon Nov 30 2015 - 12:38:10 PST)
    - Re: [AMBER] zinc ordination 2-CYM 2-HID || CYM-CYM covalent bond Pengfei Li (Mon Nov 30 2015 - 13:51:13 PST)
    - Re: [AMBER] zinc ordination 2-CYM 2-HID || CYM-CYM covalent bond Carlos Simmerling (Mon Nov 30 2015 - 13:58:51 PST)
    - Re: [AMBER] zinc ordination 2-CYM 2-HID || CYM-CYM covalent bond V. Kumar (Mon Nov 30 2015 - 23:52:56 PST)
    - Re: [AMBER] zinc ordination 2-CYM 2-HID || CYM-CYM covalent bond V. Kumar (Mon Nov 30 2015 - 23:54:06 PST)
    - Re: [AMBER] zinc ordination 2-CYM 2-HID || CYM-CYM covalent bond V. Kumar (Thu Dec 10 2015 - 08:05:43 PST)
    - Re: [AMBER] zinc ordination 2-CYM 2-HID || CYM-CYM covalent bond Carlos Simmerling (Thu Dec 10 2015 - 12:08:08 PST)
    - Re: [AMBER] zinc ordination 2-CYM 2-HID || CYM-CYM covalent bond V. Kumar (Thu Dec 10 2015 - 12:34:16 PST)
    - Re: [AMBER] zinc ordination 2-CYM 2-HID || CYM-CYM covalent bond Pengfei Li (Fri Dec 11 2015 - 19:59:11 PST)
    - Re: [AMBER] zinc ordination 2-CYM 2-HID || CYM-CYM covalent bond V. Kumar (Sat Dec 12 2015 - 05:58:42 PST)
[AMBER] mac hangs when compile ambertools15 on El capitan Yong Yao (Mon Nov 30 2015 - 19:13:31 PST)
- Re: [AMBER] mac hangs when compile ambertools15 on El capitan Hai Nguyen (Mon Nov 30 2015 - 20:38:54 PST)
  - Re: [AMBER] mac hangs when compile ambertools15 on El capitan Yong Yao (Mon Nov 30 2015 - 20:54:28 PST)
    - Re: [AMBER] mac hangs when compile ambertools15 on El capitan Jason Swails (Tue Dec 01 2015 - 05:07:45 PST)
    - Re: [AMBER] mac hangs when compile ambertools15 on El capitan Yong Yao (Tue Dec 01 2015 - 20:10:45 PST)
    - Re: [AMBER] mac hangs when compile ambertools15 on El capitan Jason Swails (Wed Dec 02 2015 - 04:40:26 PST)
[AMBER] How to run two single-card jobs on the node with two GPU cards Stephen Wang (Mon Nov 30 2015 - 22:25:57 PST)
- Re: [AMBER] How to run two single-card jobs on the node with two GPU cards Kenneth Huang (Mon Nov 30 2015 - 22:34:36 PST)
[AMBER] Utilizing two different nodes simultaneously for one job muhammad tahir ayub (Mon Nov 30 2015 - 22:35:26 PST)
- Re: [AMBER] Utilizing two different nodes simultaneously for one job Jason Swails (Tue Dec 01 2015 - 05:11:15 PST)
[AMBER] Docking before MD of scratch ligands OR not muhammad tahir ayub (Mon Nov 30 2015 - 23:49:57 PST)
- Re: [AMBER] Docking before MD of scratch ligands OR not Jason Swails (Tue Dec 01 2015 - 05:13:12 PST)
[AMBER] mmgbsa_CalcError Atila Petrosian (Tue Dec 01 2015 - 04:13:48 PST)
- Re: [AMBER] mmgbsa_CalcError Jason Swails (Tue Dec 01 2015 - 05:19:25 PST)
  - Re: [AMBER] mmgbsa_CalcError Atila Petrosian (Tue Dec 01 2015 - 10:59:15 PST)
    - Re: [AMBER] mmgbsa_CalcError Jason Swails (Tue Dec 01 2015 - 11:08:10 PST)
[AMBER] malloc error during MM-PBSA calculation on AMBER14 ... mmpbsa_py_energy: malloc.c:2372: sysmalloc Mijiddorj Batsaikhan (Tue Dec 01 2015 - 08:44:19 PST)
- Re: [AMBER] malloc error during MM-PBSA calculation on AMBER14 ... mmpbsa_py_energy: malloc.c:2372: sysmalloc Jason Swails (Tue Dec 01 2015 - 08:50:04 PST)
[AMBER] [Amber] nmode() results with imaginary frequencies Guqin Shi (Tue Dec 01 2015 - 15:18:17 PST)
- Re: [AMBER] [Amber] nmode() results with imaginary frequencies Jason Swails (Tue Dec 01 2015 - 19:05:55 PST)
  - Re: [AMBER] [Amber] nmode() results with imaginary frequencies Guqin Shi (Wed Dec 02 2015 - 06:15:58 PST)
  - Re: [AMBER] [Amber] nmode() results with imaginary frequencies Guqin Shi (Sun Dec 06 2015 - 11:13:28 PST)
[AMBER] How does the collision frequency gamma_ln value affect the temperature in Langevin dynamics jfliu (Tue Dec 01 2015 - 18:07:17 PST)
- Re: [AMBER] How does the collision frequency gamma_ln value affect the temperature in Langevin dynamics David A Case (Wed Dec 02 2015 - 06:03:08 PST)
[AMBER] Can I use the Nose-Hoover thermostat in Amber jfliu (Tue Dec 01 2015 - 18:12:54 PST)
- Re: [AMBER] Can I use the Nose-Hoover thermostat in Amber Jason Swails (Tue Dec 01 2015 - 19:02:59 PST)
[AMBER] bug or not bug ???? Min Li (Tue Dec 01 2015 - 19:54:38 PST)
- Re: [AMBER] bug or not bug ???? Åke Sandgren (Sat Dec 19 2015 - 05:24:05 PST)
  - Re: [AMBER] bug or not bug ???? David A Case (Sun Dec 20 2015 - 08:42:40 PST)
[AMBER] Principal Component Analysis Beale, John (Wed Dec 02 2015 - 02:23:57 PST)
- Re: [AMBER] Principal Component Analysis Jason Swails (Wed Dec 02 2015 - 05:50:24 PST)
- Re: [AMBER] Principal Component Analysis Daniel Roe (Wed Dec 02 2015 - 10:00:49 PST)
[AMBER] kinetic Ziba Bahadori (Wed Dec 02 2015 - 04:14:32 PST)
- Re: [AMBER] kinetic Jason Swails (Wed Dec 02 2015 - 05:34:35 PST)
  - Re: [AMBER] kinetic Andrea Spitaleri (Fri Dec 04 2015 - 06:24:20 PST)
- Re: [AMBER] kinetic David A Case (Wed Dec 02 2015 - 06:06:13 PST)
[AMBER] pH-REMD GPU runs Arjun Sharma (Wed Dec 02 2015 - 05:53:22 PST)
- Re: [AMBER] pH-REMD GPU runs Adrian Roitberg (Wed Dec 02 2015 - 06:01:16 PST)
- Re: [AMBER] pH-REMD GPU runs Jason Swails (Wed Dec 02 2015 - 06:23:26 PST)
[AMBER] High PB deltaG values from MMPBSA.py calculation anu chandra (Wed Dec 02 2015 - 05:59:48 PST)
- Re: [AMBER] High PB deltaG values from MMPBSA.py calculation Jason Swails (Wed Dec 02 2015 - 06:25:20 PST)
  - Re: [AMBER] High PB deltaG values from MMPBSA.py calculation anu chandra (Wed Dec 02 2015 - 06:48:05 PST)
    - Re: [AMBER] High PB deltaG values from MMPBSA.py calculation Ray Luo, Ph.D. (Wed Dec 02 2015 - 16:09:14 PST)
    - Re: [AMBER] High PB deltaG values from MMPBSA.py calculation anu chandra (Thu Dec 03 2015 - 02:28:58 PST)
    - Re: [AMBER] High PB deltaG values from MMPBSA.py calculation Ray Luo, Ph.D. (Thu Dec 03 2015 - 10:26:51 PST)
    - Re: [AMBER] High PB deltaG values from MMPBSA.py calculation anu chandra (Sat Dec 05 2015 - 03:46:40 PST)
[AMBER] Amber calculated structure(PDB) visualization in pymol vs chimera V. Kumar (Wed Dec 02 2015 - 11:38:00 PST)
- Re: [AMBER] Amber calculated structure(PDB) visualization in pymol vs chimera Carlos Simmerling (Wed Dec 02 2015 - 11:56:23 PST)
- Re: [AMBER] Amber calculated structure(PDB) visualization in pymol vs chimera Daniel Roe (Wed Dec 02 2015 - 12:06:07 PST)
  - Re: [AMBER] Amber calculated structure(PDB) visualization in pymol vs chimera V. Kumar (Wed Dec 02 2015 - 12:17:32 PST)
  - Re: [AMBER] Amber calculated structure(PDB) visualization in pymol vs chimera V. Kumar (Wed Dec 02 2015 - 12:42:01 PST)
[AMBER] bond connections mohammad r (Wed Dec 02 2015 - 23:02:03 PST)
- Re: [AMBER] bond connections Bill (Wed Dec 02 2015 - 23:51:04 PST)
  - Re: [AMBER] bond connections mohammad r (Thu Dec 03 2015 - 04:26:05 PST)
- Re: [AMBER] bond connections Jason Swails (Thu Dec 03 2015 - 04:41:11 PST)
- Re: [AMBER] bond connections David A Case (Thu Dec 03 2015 - 05:26:15 PST)
- Re: [AMBER] bond connections Jason Swails (Thu Dec 03 2015 - 10:05:15 PST)
  - Re: [AMBER] bond connections Brian Radak (Thu Dec 03 2015 - 10:16:56 PST)
    - Re: [AMBER] bond connections mohammad r (Thu Dec 03 2015 - 11:27:51 PST)
    - Re: [AMBER] bond connections Jason Swails (Thu Dec 03 2015 - 12:59:30 PST)
- Re: [AMBER] bond connections Jason Swails (Thu Dec 03 2015 - 20:39:04 PST)
- Re: [AMBER] bond connections Jason Swails (Sat Dec 05 2015 - 12:05:47 PST)
  - Re: [AMBER] bond connections Jonathan Sheehan (Sun Dec 06 2015 - 00:41:34 PST)
    - Re: [AMBER] bond connections mohammad r (Sun Dec 06 2015 - 00:59:33 PST)
    - Re: [AMBER] bond connections Jason Swails (Sun Dec 06 2015 - 06:07:45 PST)
    - Re: [AMBER] bond connections mohammad r (Sun Dec 06 2015 - 14:53:43 PST)
    - Re: [AMBER] bond connections Jason Swails (Sun Dec 06 2015 - 16:54:45 PST)
    - [AMBER] rmsd as order parameter in umbrella sampling Srinivasaraghavan Kannan (Sun Dec 06 2015 - 19:09:46 PST)
    - Re: [AMBER] rmsd as order parameter in umbrella sampling Carlos Simmerling (Mon Dec 07 2015 - 03:18:25 PST)
    - Re: [AMBER] bond connections mohammad r (Mon Dec 07 2015 - 00:08:15 PST)
    - Re: [AMBER] bond connections Bill (Sun Dec 06 2015 - 01:24:34 PST)
[AMBER] AMBER 12 XLEAP options were disabled V. Kumar (Thu Dec 03 2015 - 03:36:58 PST)
- Re: [AMBER] AMBER 12 XLEAP options were disabled Jason Swails (Thu Dec 03 2015 - 04:36:01 PST)
- Re: [AMBER] AMBER 12 XLEAP options were disabled David A Case (Thu Dec 03 2015 - 05:28:32 PST)
  - Re: [AMBER] AMBER 12 XLEAP options were disabled V. Kumar (Thu Dec 03 2015 - 06:14:02 PST)
[AMBER] Simulation of the docked complex with phosphorylated tyrosine Pallavi Mohanty (Thu Dec 03 2015 - 03:53:38 PST)
- Re: [AMBER] Simulation of the docked complex with phosphorylated tyrosine David A Case (Thu Dec 03 2015 - 05:33:30 PST)
  - Re: [AMBER] Simulation of the docked complex with phosphorylated tyrosine Pallavi Mohanty (Fri Dec 04 2015 - 01:27:35 PST)
[AMBER] xleap terminal terminate Ayesha Kanwal (Thu Dec 03 2015 - 04:33:08 PST)
- Re: [AMBER] xleap terminal terminate Jason Swails (Thu Dec 03 2015 - 04:42:50 PST)
  - Re: [AMBER] xleap terminal terminate Ayesha Kanwal (Fri Dec 04 2015 - 00:36:07 PST)
    - Re: [AMBER] xleap terminal terminate Mary Dutta (Fri Dec 04 2015 - 02:22:17 PST)
    - Re: [AMBER] xleap terminal terminate Jason Swails (Fri Dec 04 2015 - 04:11:48 PST)
[AMBER] pmemd.cuda with CoM restraints 達南杰 (Thu Dec 03 2015 - 06:56:20 PST)
- Re: [AMBER] pmemd.cuda with CoM restraints Charles Lin (Thu Dec 03 2015 - 09:22:33 PST)
  - Re: [AMBER] pmemd.cuda with CoM restraints Marc van der Kamp (Thu Dec 03 2015 - 09:25:00 PST)
    - Re: [AMBER] pmemd.cuda with CoM restraints 達南杰 (Thu Dec 03 2015 - 20:09:24 PST)
    - Re: [AMBER] pmemd.cuda with CoM restraints Charles Lin (Thu Dec 03 2015 - 22:30:04 PST)
[AMBER] QM/MM Implementation Details Jim William Snyder Jr (Thu Dec 03 2015 - 10:38:35 PST)
[AMBER] problem with "closest" waters being wrapped Kalenkiewicz, Andrew (NIH/NICHD) [F] (Thu Dec 03 2015 - 13:17:57 PST)
- Re: [AMBER] problem with "closest" waters being wrapped Daniel Roe (Thu Dec 03 2015 - 13:20:04 PST)
  - Re: [AMBER] problem with "closest" waters being wrapped Kalenkiewicz, Andrew (NIH/NICHD) [F] (Thu Dec 03 2015 - 14:34:59 PST)
    - Re: [AMBER] problem with "closest" waters being wrapped Marc van der Kamp (Thu Dec 03 2015 - 14:45:40 PST)
    - Re: [AMBER] problem with "closest" waters being wrapped Thomas Cheatham (Thu Dec 03 2015 - 14:53:25 PST)
[AMBER] Question Regarding Input File Preparation Ziheng Wang (Thu Dec 03 2015 - 18:35:49 PST)
- Re: [AMBER] Question Regarding Input File Preparation Jason Swails (Fri Dec 04 2015 - 04:29:44 PST)
- Re: [AMBER] Question Regarding Input File Preparation David A Case (Fri Dec 04 2015 - 05:10:24 PST)
[AMBER] Add charges to new molecule with out Gaussian package V. Kumar (Sat Dec 05 2015 - 06:08:41 PST)
- Re: [AMBER] Add charges to new molecule with out Gaussian package Karl Kirschner (Sat Dec 05 2015 - 06:42:07 PST)
  - Re: [AMBER] Add charges to new molecule with out Gaussian package V. Kumar (Sat Dec 05 2015 - 12:01:09 PST)
[AMBER] per-residue or pairwise per-residue basis in decomposing the free energy contributions to the binding free energy Andrew Bostick (Sat Dec 05 2015 - 11:20:19 PST)
- Re: [AMBER] per-residue or pairwise per-residue basis in decomposing the free energy contributions to the binding free energy Jason Swails (Sat Dec 05 2015 - 12:06:57 PST)
[AMBER] standard deviation of Hbond lengths and angles Hadeer ELHabashy (Sun Dec 06 2015 - 07:20:12 PST)
- Re: [AMBER] standard deviation of Hbond lengths and angles Daniel Roe (Mon Dec 07 2015 - 08:04:07 PST)
  - Re: [AMBER] standard deviation of Hbond lengths and angles Hai Nguyen (Mon Dec 07 2015 - 12:24:16 PST)
[AMBER] per-residue or pairwise per-residue basis in decomposing the free energy contributions to the binding free energy Andrew Bostick (Sun Dec 06 2015 - 10:45:18 PST)
- Re: [AMBER] per-residue or pairwise per-residue basis in decomposing the free energy contributions to the binding free energy Jason Swails (Sun Dec 06 2015 - 13:38:32 PST)
[AMBER] cpptraj: grid and gist Thomas Fox (Mon Dec 07 2015 - 02:22:19 PST)
- Re: [AMBER] cpptraj: grid and gist Daniel Roe (Mon Dec 07 2015 - 07:39:02 PST)
  - Re: [AMBER] cpptraj: grid and gist Steven Ramsey (Mon Dec 07 2015 - 08:34:29 PST)
    - Re: [AMBER] cpptraj: grid and gist Thomas Fox (Tue Dec 08 2015 - 05:15:38 PST)
    - Re: [AMBER] cpptraj: grid and gist Jason Swails (Tue Dec 08 2015 - 05:28:50 PST)
    - Re: [AMBER] cpptraj: grid and gist Thomas Fox (Tue Dec 08 2015 - 08:50:15 PST)
[AMBER] weird output of SMD simulation combined with Constant pH zhonghe xu (Mon Dec 07 2015 - 06:25:27 PST)
- Re: [AMBER] weird output of SMD simulation combined with Constant pH Jason Swails (Mon Dec 07 2015 - 06:29:41 PST)
- Re: [AMBER] weird output of SMD simulation combined with Constant pH Gustavo Seabra (Mon Dec 07 2015 - 11:38:49 PST)
  - Re: [AMBER] weird output of SMD simulation combined with Constant pH Jason Swails (Mon Dec 07 2015 - 12:14:30 PST)
    - Re: [AMBER] weird output of SMD simulation combined with Constant pH Gustavo Seabra (Mon Dec 07 2015 - 17:34:47 PST)
    - Re: [AMBER] weird output of SMD simulation combined with Constant pH Jason Swails (Mon Dec 07 2015 - 18:55:31 PST)
[AMBER] External forces Jack Shepherd (Mon Dec 07 2015 - 09:29:07 PST)
- Re: [AMBER] External forces Josh Berryman (Tue Dec 08 2015 - 02:12:00 PST)
  - Re: [AMBER] External forces Christina Bergonzo (Tue Dec 08 2015 - 07:26:42 PST)
[AMBER] MMPBSA bad atom type error persisting Kenneth Huang (Mon Dec 07 2015 - 10:40:13 PST)
Re: [AMBER] xparmed.py Nathalie Willems (Tue Dec 08 2015 - 07:23:19 PST)
- Re: [AMBER] xparmed.py Jason Swails (Tue Dec 08 2015 - 07:55:02 PST)
  - Re: [AMBER] xparmed.py Nathalie Willems (Tue Dec 08 2015 - 08:12:21 PST)
    - Re: [AMBER] xparmed.py Jason Swails (Tue Dec 08 2015 - 12:07:38 PST)
[AMBER] Amber 14, sander.MPI, NaN Starovoytov, Oleg (Tue Dec 08 2015 - 12:38:07 PST)
- Re: [AMBER] Amber 14, sander.MPI, NaN David A Case (Sat Dec 12 2015 - 07:42:14 PST)
[AMBER] problem with hist command in cpptraj in AmberTools15 Osman, Roman (Tue Dec 08 2015 - 12:59:46 PST)
- Re: [AMBER] problem with hist command in cpptraj in AmberTools15 Daniel Roe (Tue Dec 08 2015 - 13:00:53 PST)
  - Re: [AMBER] problem with hist command in cpptraj in AmberTools15 Osman, Roman (Tue Dec 08 2015 - 13:22:19 PST)
    - Re: [AMBER] problem with hist command in cpptraj in AmberTools15 Daniel Roe (Tue Dec 08 2015 - 14:03:47 PST)
    - Re: [AMBER] problem with hist command in cpptraj in AmberTools15 Osman, Roman (Tue Dec 08 2015 - 16:35:56 PST)
[AMBER] [Amber] Imaginary Frequencies from nmode() Guqin Shi (Tue Dec 08 2015 - 13:19:53 PST)
- Re: [AMBER] [Amber] Imaginary Frequencies from nmode() David A Case (Sat Dec 12 2015 - 13:32:03 PST)
  - Re: [AMBER] [Amber] Imaginary Frequencies from nmode() Guqin Shi (Tue Dec 15 2015 - 13:51:27 PST)
[AMBER] Problem with GPU equilibration step [ cudaMalloc GpuBuffer::Allocate failed out of memory] Yogeeshwar Ajjugal (Tue Dec 08 2015 - 21:42:25 PST)
- Re: [AMBER] Problem with GPU equilibration step [ cudaMalloc GpuBuffer::Allocate failed out of memory] Jason Swails (Wed Dec 09 2015 - 04:46:00 PST)
  - Re: [AMBER] Problem with GPU equilibration step [ cudaMalloc GpuBuffer::Allocate failed out of memory] Yogeeshwar Ajjugal (Wed Dec 09 2015 - 22:04:51 PST)
Re: [AMBER] FW: FW: How to use "divergence" command Mahendra B Thapa (Wed Dec 09 2015 - 05:08:30 PST)
- Re: [AMBER] FW: FW: How to use "divergence" command Jason Swails (Wed Dec 09 2015 - 05:28:22 PST)
  - Re: [AMBER] FW: FW: How to use "divergence" command Daniel Roe (Wed Dec 09 2015 - 08:51:15 PST)
[AMBER] Charmm-gui conversion mohammad r (Wed Dec 09 2015 - 08:02:20 PST)
- Re: [AMBER] Charmm-gui conversion Brian Radak (Wed Dec 09 2015 - 08:10:06 PST)
  - Re: [AMBER] Charmm-gui conversion Arnoult, Eric [JRDUS] (Wed Dec 09 2015 - 10:26:54 PST)
    - Re: [AMBER] Charmm-gui conversion mohammad r (Wed Dec 09 2015 - 11:58:29 PST)
    - Re: [AMBER] Charmm-gui conversion Bill Ross (Wed Dec 09 2015 - 12:07:49 PST)
    - Re: [AMBER] Charmm-gui conversion mohammad r (Wed Dec 09 2015 - 12:31:01 PST)
    - Re: [AMBER] Charmm-gui conversion Bill Ross (Wed Dec 09 2015 - 12:48:44 PST)
    - Re: [AMBER] Charmm-gui conversion mohammad r (Thu Dec 10 2015 - 12:25:11 PST)
    - Re: [AMBER] Charmm-gui conversion Bill Ross (Thu Dec 10 2015 - 12:31:36 PST)
    - Re: [AMBER] Charmm-gui conversion mohammad r (Thu Dec 10 2015 - 12:57:17 PST)
    - Re: [AMBER] Charmm-gui conversion Brian Radak (Thu Dec 10 2015 - 13:12:26 PST)
    - Re: [AMBER] Charmm-gui conversion mohammad r (Thu Dec 10 2015 - 13:13:25 PST)
    - Re: [AMBER] Charmm-gui conversion mohammad r (Thu Dec 10 2015 - 13:28:46 PST)
    - Re: [AMBER] Charmm-gui conversion David A Case (Thu Dec 10 2015 - 13:34:08 PST)
    - Re: [AMBER] Charmm-gui conversion mohammad r (Thu Dec 10 2015 - 21:06:04 PST)
    - Re: [AMBER] Charmm-gui conversion Bill Ross (Fri Dec 11 2015 - 00:05:29 PST)
    - Re: [AMBER] Charmm-gui conversion Jason Swails (Fri Dec 11 2015 - 04:07:01 PST)
    - Re: [AMBER] Charmm-gui conversion Arnoult, Eric [JRDUS] (Wed Dec 09 2015 - 12:31:09 PST)
    - Re: [AMBER] Charmm-gui conversion Brian Radak (Wed Dec 09 2015 - 12:55:29 PST)
- Re: [AMBER] Charmm-gui conversion Jason Swails (Fri Dec 11 2015 - 05:40:43 PST)
  - Re: [AMBER] Charmm-gui conversion mohammad r (Fri Dec 11 2015 - 07:30:06 PST)
[AMBER] OSX 10.11.1: Amber installation problem George Tzotzos (Wed Dec 09 2015 - 10:19:47 PST)
- Re: [AMBER] OSX 10.11.1: Amber installation problem Jason Swails (Wed Dec 09 2015 - 12:34:25 PST)
  - Re: [AMBER] OSX 10.11.1: Amber installation problem George Tzotzos (Thu Dec 10 2015 - 02:16:14 PST)
[AMBER] gnu plot of cpptraj Secstruct George Tzotzos (Thu Dec 10 2015 - 13:42:20 PST)
- Re: [AMBER] gnu plot of cpptraj Secstruct Lachele Foley (Thu Dec 10 2015 - 20:55:47 PST)
  - Re: [AMBER] gnu plot of cpptraj Secstruct George Tzotzos (Fri Dec 11 2015 - 04:22:28 PST)
    - Re: [AMBER] gnu plot of cpptraj Secstruct Jason Swails (Fri Dec 11 2015 - 05:43:30 PST)
    - Re: [AMBER] gnu plot of cpptraj Secstruct George Tzotzos (Fri Dec 11 2015 - 06:01:54 PST)
    - Re: [AMBER] gnu plot of cpptraj Secstruct Daniel Roe (Fri Dec 11 2015 - 07:55:28 PST)
    - Re: [AMBER] gnu plot of cpptraj Secstruct George Tzotzos (Fri Dec 11 2015 - 07:58:36 PST)
    - Re: [AMBER] gnu plot of cpptraj Secstruct Lachele Foley (Fri Dec 11 2015 - 11:28:53 PST)
    - Re: [AMBER] gnu plot of cpptraj Secstruct George Tzotzos (Fri Dec 11 2015 - 11:32:42 PST)
[AMBER] ligand is not opening in the binding site of protein muhammad tahir ayub (Fri Dec 11 2015 - 00:22:36 PST)
- Re: [AMBER] ligand is not opening in the binding site of protein Bill Ross (Fri Dec 11 2015 - 00:36:03 PST)
[AMBER] WARNING: There is a bond of 420.000806 angstroms between: ------- .R<LIG 546>.A<O2 28> and .R<LIG 546>.A<H2 31> Andrew Bostick (Fri Dec 11 2015 - 07:30:16 PST)
- Re: [AMBER] WARNING: There is a bond of 420.000806 angstroms between: ------- .R<LIG 546>.A<O2 28> and .R<LIG 546>.A<H2 31> Carlos Simmerling (Fri Dec 11 2015 - 07:48:59 PST)
[AMBER] Problem with initial complex structure for TI Kalenkiewicz, Andrew (NIH/NICHD) [F] (Fri Dec 11 2015 - 15:17:11 PST)
- Re: [AMBER] Problem with initial complex structure for TI Kalenkiewicz, Andrew (NIH/NICHD) [F] (Mon Dec 14 2015 - 13:37:56 PST)
[AMBER] problem in adding ACE and NME to CSX. Saman Yousuf ali (Sun Dec 13 2015 - 04:58:06 PST)
- Re: [AMBER] problem in adding ACE and NME to CSX. Jason Swails (Sun Dec 13 2015 - 08:28:16 PST)
[AMBER] RED vIII for Amber Nash, Anthony (Sun Dec 13 2015 - 13:41:19 PST)
- Re: [AMBER] RED vIII for Amber Karl Kirschner (Sun Dec 13 2015 - 23:42:54 PST)
  - Re: [AMBER] RED vIII for Amber Nash, Anthony (Sun Dec 13 2015 - 23:50:56 PST)
    - Re: [AMBER] RED vIII for Amber Nash, Anthony (Sun Dec 20 2015 - 09:23:28 PST)
    - Re: [AMBER] RED vIII for Amber Steven M. Graham (Sun Dec 20 2015 - 15:40:56 PST)
[AMBER] Time Step Wong Li Zhe (Sun Dec 13 2015 - 23:01:18 PST)
- Re: [AMBER] Time Step Bill Ross (Sun Dec 13 2015 - 23:10:05 PST)
- Re: [AMBER] Time Step Jason Swails (Mon Dec 14 2015 - 09:05:29 PST)
  - [AMBER] Time Step Wong Li Zhe (Mon Dec 14 2015 - 16:21:37 PST)
Re: [AMBER] Problems regarding using ZAFF Bill Ross (Sun Dec 13 2015 - 23:01:56 PST)
[AMBER] restraints on group of atoms Dhananjay (Mon Dec 14 2015 - 01:47:47 PST)
- Re: [AMBER] restraints on group of atoms David A Case (Mon Dec 14 2015 - 05:06:57 PST)
[AMBER] HBOND_water mediated Lara rajam (Mon Dec 14 2015 - 07:16:58 PST)
- Re: [AMBER] HBOND_water mediated Daniel Roe (Tue Dec 15 2015 - 09:01:24 PST)
  - Re: [AMBER] HBOND_water mediated Lara rajam (Thu Dec 17 2015 - 06:49:00 PST)
[AMBER] MMPBSA.py.MPI compling issue Marc Zhang (Mon Dec 14 2015 - 13:22:14 PST)
- Re: [AMBER] MMPBSA.py.MPI compling issue Daniel Roe (Tue Dec 15 2015 - 08:51:57 PST)
[AMBER] charge fitting procedure in amber conor parks (Mon Dec 14 2015 - 13:27:21 PST)
- Re: [AMBER] charge fitting procedure in amber Karl Kirschner (Tue Dec 15 2015 - 00:16:51 PST)
  - Re: [AMBER] charge fitting procedure in amber Karl Kirschner (Tue Dec 15 2015 - 02:16:13 PST)
[AMBER] Irregular ligand positioning in simulations Anasuya Dighe (Mon Dec 14 2015 - 22:58:43 PST)
- Re: [AMBER] Irregular ligand positioning in simulations Carlos Simmerling (Tue Dec 15 2015 - 03:08:32 PST)
- Re: [AMBER] Irregular ligand positioning in simulations Daniel Roe (Tue Dec 15 2015 - 08:38:36 PST)
[AMBER] problem in plotting secondary structure graph Sehrish Naz (Mon Dec 14 2015 - 23:19:32 PST)
- Re: [AMBER] problem in plotting secondary structure graph Daniel Roe (Tue Dec 15 2015 - 08:12:41 PST)
[AMBER] confusion in xleap for ligand and comlex Ayesha Kanwal (Mon Dec 14 2015 - 23:50:07 PST)
- Re: [AMBER] confusion in xleap for ligand and comlex David A Case (Tue Dec 15 2015 - 04:53:20 PST)
[AMBER] mbar Johannes Loeffler (Tue Dec 15 2015 - 05:36:06 PST)
- Re: [AMBER] mbar Hannes Loeffler (Tue Dec 15 2015 - 05:46:51 PST)
  - Re: [AMBER] mbar Johannes Loeffler (Tue Dec 15 2015 - 06:42:18 PST)
    - Re: [AMBER] mbar Hannes Loeffler (Tue Dec 15 2015 - 07:17:05 PST)
    - Re: [AMBER] mbar Johannes Loeffler (Tue Dec 15 2015 - 07:24:02 PST)
    - Re: [AMBER] mbar Brian Radak (Tue Dec 15 2015 - 07:35:36 PST)
    - Re: [AMBER] mbar Hannes Loeffler (Tue Dec 15 2015 - 08:14:07 PST)
    - Re: [AMBER] mbar Johannes Löffler (Tue Dec 15 2015 - 08:42:25 PST)
    - Re: [AMBER] mbar Hannes Loeffler (Tue Dec 15 2015 - 09:02:41 PST)
[AMBER] Warning regarding "triangular bond" Xiong Jiawei (Tue Dec 15 2015 - 23:30:52 PST)
- Re: [AMBER] Warning regarding "triangular bond" David A Case (Wed Dec 16 2015 - 04:57:44 PST)
  - Re: [AMBER] Warning regarding "triangular bond" Bill Ross (Wed Dec 16 2015 - 11:45:48 PST)
[AMBER] Ligand's parameterization Trang Nguyen (Wed Dec 16 2015 - 06:07:55 PST)
- Re: [AMBER] Ligand's parameterization Carlos Simmerling (Wed Dec 16 2015 - 06:20:13 PST)
- Re: [AMBER] Ligand's parameterization Mathy Froeyen (Wed Dec 16 2015 - 06:47:50 PST)
- Re: [AMBER] Ligand's parameterization Karl Kirschner (Thu Dec 17 2015 - 04:02:27 PST)
[AMBER] Minimization after simulated annealing (0° C) ans CSH script need to be combined V. Kumar (Wed Dec 16 2015 - 09:14:26 PST)
[AMBER] cpptraj average structure warning George Tzotzos (Thu Dec 17 2015 - 01:05:26 PST)
- Re: [AMBER] cpptraj average structure warning George Tzotzos (Thu Dec 17 2015 - 02:22:12 PST)
[AMBER] Termodinamic Integration setup error Claire Coderch Boué (Thu Dec 17 2015 - 01:46:17 PST)
- Re: [AMBER] Termodinamic Integration setup error Hannes Loeffler (Thu Dec 17 2015 - 01:59:01 PST)
[AMBER] Water model jfliu (Thu Dec 17 2015 - 05:07:40 PST)
- Re: [AMBER] Water model David A Case (Fri Dec 18 2015 - 08:17:38 PST)
[AMBER] How to have special residues in trajectory file using cpptraj shahab shariati (Thu Dec 17 2015 - 06:14:43 PST)
- Re: [AMBER] How to have special residues in trajectory file using cpptraj Kenneth Huang (Thu Dec 17 2015 - 06:39:14 PST)
  - Re: [AMBER] How to have special residues in trajectory file using cpptraj Daniel Roe (Thu Dec 17 2015 - 07:23:29 PST)
[AMBER] Confusion on "No Pressure" Robert Molt (Thu Dec 17 2015 - 08:38:13 PST)
- Re: [AMBER] Confusion on "No Pressure" Jason Swails (Thu Dec 17 2015 - 09:27:41 PST)
[AMBER] Is triplicate analysis required for pmemd.MPI and ig=-1? Morrow,John Kenneth (Thu Dec 17 2015 - 14:25:51 PST)
- Re: [AMBER] Is triplicate analysis required for pmemd.MPI and ig=-1? Ross Walker (Thu Dec 17 2015 - 14:56:01 PST)
[AMBER] average structure Andrew Bostick (Thu Dec 17 2015 - 14:35:59 PST)
- Re: [AMBER] average structure Hai Nguyen (Thu Dec 17 2015 - 14:43:59 PST)
- Re: [AMBER] average structure Ross Walker (Thu Dec 17 2015 - 14:44:04 PST)
[AMBER] How to calculate the interplanar angle between 2 Trp residues? Yew Mun Yip (Sun Dec 20 2015 - 01:12:00 PST)
- Re: [AMBER] How to calculate the interplanar angle between 2 Trp residues? Daniel Roe (Mon Dec 21 2015 - 08:38:44 PST)
[AMBER] TIP3 simulated annealing, 200ps*50 loops = 10ns ==> Minimization of lower energy structures V. Kumar (Sun Dec 20 2015 - 04:23:27 PST)
- Re: [AMBER] TIP3 simulated annealing, 200ps*50 loops = 10ns ==> Minimization of lower energy structures Carlos Simmerling (Sun Dec 20 2015 - 05:04:31 PST)
  - Re: [AMBER] TIP3 simulated annealing, 200ps*50 loops = 10ns ==> Minimization of lower energy structures V. Kumar (Sun Dec 20 2015 - 05:27:03 PST)
- Re: [AMBER] TIP3 simulated annealing, 200ps*50 loops = 10ns ==> Minimization of lower energy structures Carlos Simmerling (Sun Dec 20 2015 - 06:44:15 PST)
  - Re: [AMBER] TIP3 simulated annealing, 200ps*50 loops = 10ns ==> Minimization of lower energy structures V. Kumar (Sun Dec 20 2015 - 07:23:18 PST)
[AMBER] GPU support Rupak Pal (Sun Dec 20 2015 - 22:51:10 PST)
- Re: [AMBER] GPU support Ross Walker (Mon Dec 21 2015 - 08:31:07 PST)
- Re: [AMBER] GPU support Jason Swails (Mon Dec 21 2015 - 08:53:38 PST)
  - Re: [AMBER] GPU support Rupak Pal (Tue Dec 22 2015 - 01:03:46 PST)
[AMBER] pmemd issue Mahmoud A. A. Ibrahim (Mon Dec 21 2015 - 02:04:08 PST)
- Re: [AMBER] pmemd issue Jason Swails (Mon Dec 21 2015 - 05:03:42 PST)
- Re: [AMBER] pmemd issue David A Case (Mon Dec 21 2015 - 05:18:42 PST)
[AMBER] ig=-1 for multi production runs Fabian gmail (Mon Dec 21 2015 - 04:31:01 PST)
- Re: [AMBER] ig=-1 for multi production runs Jason Swails (Mon Dec 21 2015 - 05:09:40 PST)
- Re: [AMBER] ig=-1 for multi production runs David A Case (Mon Dec 21 2015 - 05:20:50 PST)
  - Re: [AMBER] ig=-1 for multi production runs Fabian gmail (Mon Dec 21 2015 - 05:36:04 PST)
    - Re: [AMBER] ig=-1 for multi production runs Jason Swails (Mon Dec 21 2015 - 06:38:43 PST)
[AMBER] Finding PDF of individual dihedral angles Mahendra B Thapa (Mon Dec 21 2015 - 09:27:37 PST)
[AMBER] TI/MBAR energy re-calculating with imin5 wliu (Wed Dec 23 2015 - 01:16:12 PST)
[AMBER] MMPBSA error Lara rajam (Wed Dec 23 2015 - 10:05:05 PST)
- Re: [AMBER] MMPBSA error Jason Swails (Wed Dec 23 2015 - 10:09:59 PST)
[AMBER] A problem about using AMBER 东不拉 (Sun Dec 27 2015 - 21:34:01 PST)
[AMBER] MD study of transition of protein from one conformation to another Abhilash J (Mon Dec 28 2015 - 09:40:28 PST)
- Re: [AMBER] MD study of transition of protein from one conformation to another David A Case (Mon Dec 28 2015 - 12:42:40 PST)
  - Re: [AMBER] MD study of transition of protein from one conformation to another Abhilash J (Mon Dec 28 2015 - 20:58:55 PST)
[AMBER] Group specification Havva Mehralitabar (Mon Dec 28 2015 - 12:52:51 PST)
- Re: [AMBER] Group specification David A Case (Tue Dec 29 2015 - 17:43:05 PST)
[AMBER] different dielectric constant value for polar non-polar hydrophobic residue in MMGBSA bharat lakhani (Tue Dec 29 2015 - 21:47:05 PST)
- Re: [AMBER] different dielectric constant value for polar non-polar hydrophobic residue in MMGBSA David A Case (Wed Dec 30 2015 - 05:30:30 PST)
[AMBER] which chain to select for MD simulation. Saman Yousuf ali (Wed Dec 30 2015 - 11:58:24 PST)
- Re: [AMBER] which chain to select for MD simulation. Jason Swails (Wed Dec 30 2015 - 17:55:44 PST)
[AMBER] Problem in interpreting snapshot_statistics.out after per-residue decomposition analysis Soong Jiaxin (Wed Dec 30 2015 - 19:36:54 PST)
[AMBER] Error in running AMBER 12 GPU simulations Yogeeshwar Ajjugal (Thu Dec 31 2015 - 05:35:30 PST)
- Re: [AMBER] Error in running AMBER 12 GPU simulations David A Case (Thu Dec 31 2015 - 08:22:59 PST)
[AMBER] Active site conserve water issue. Saman Yousuf ali (Sat Jan 02 2016 - 05:24:31 PST)
- Re: [AMBER] Active site conserve water issue. David A Case (Sat Jan 02 2016 - 07:05:29 PST)
[AMBER] PMF Rasha Alqus (Sat Jan 02 2016 - 22:34:59 PST)
- Re: [AMBER] PMF Bill Ross (Sat Jan 02 2016 - 22:49:56 PST)
  - Re: [AMBER] PMF Barbault Florent (Sun Jan 03 2016 - 01:09:16 PST)
- Re: [AMBER] PMF Carlos Simmerling (Sun Jan 03 2016 - 05:05:23 PST)
[AMBER] Convert gromacs output file to Amber format neha chaudhary (Sun Jan 03 2016 - 00:40:16 PST)
- Re: [AMBER] Convert gromacs output file to Amber format Jason Swails (Sun Jan 03 2016 - 07:01:12 PST)
  - Re: [AMBER] Convert gromacs output file to Amber format neha chaudhary (Sun Jan 03 2016 - 21:13:39 PST)
- Re: [AMBER] Convert gromacs output file to Amber format Lorenzo Gontrani (Sun Jan 03 2016 - 09:15:26 PST)
[AMBER] pH dependent calculation for Oligomers Mijiddorj Batsaikhan (Mon Jan 04 2016 - 02:19:06 PST)
- Re: [AMBER] pH dependent calculation for Oligomers Jason Swails (Mon Jan 04 2016 - 03:02:46 PST)
  - Re: [AMBER] pH dependent calculation for Oligomers Mijiddorj Batsaikhan (Tue Jan 05 2016 - 00:42:25 PST)
    - Re: [AMBER] pH dependent calculation for Oligomers Jason Swails (Tue Jan 05 2016 - 04:29:27 PST)
[AMBER] shape of a peptide array Fabian gmail (Mon Jan 04 2016 - 03:54:34 PST)
- Re: [AMBER] shape of a peptide array Josh Berryman (Wed Jan 13 2016 - 02:34:18 PST)
[AMBER] Fwd: Requesting clarifications about QM/MM minimization Manjula Saravanan (Mon Jan 04 2016 - 21:39:25 PST)
- Re: [AMBER] Fwd: Requesting clarifications about QM/MM minimization Jason Swails (Tue Jan 05 2016 - 04:34:35 PST)
[AMBER] ligand topology genaration neha chaudhary (Tue Jan 05 2016 - 02:24:34 PST)
- Re: [AMBER] ligand topology genaration Jason Swails (Tue Jan 05 2016 - 04:38:52 PST)
- Re: [AMBER] ligand topology genaration David A Case (Tue Jan 05 2016 - 05:20:39 PST)
  - Re: [AMBER] ligand topology genaration neha chaudhary (Wed Jan 06 2016 - 01:25:04 PST)
    - Re: [AMBER] ligand topology genaration Jason Swails (Wed Jan 06 2016 - 04:24:28 PST)
    - Re: [AMBER] ligand topology genaration neha chaudhary (Wed Jan 06 2016 - 21:33:36 PST)
    - Re: [AMBER] ligand topology genaration Jason Swails (Thu Jan 07 2016 - 03:52:05 PST)
    - Re: [AMBER] ligand topology genaration neha chaudhary (Thu Jan 07 2016 - 04:26:38 PST)
    - Re: [AMBER] ligand topology genaration David A Case (Thu Jan 07 2016 - 05:04:12 PST)
    - Re: [AMBER] ligand topology genaration Jason Swails (Thu Jan 07 2016 - 05:21:35 PST)
    - Re: [AMBER] ligand topology genaration neha chaudhary (Tue Jan 12 2016 - 03:35:31 PST)
    - Re: [AMBER] ligand topology genaration Jason Swails (Tue Jan 12 2016 - 04:28:02 PST)
[AMBER] Problems with tleap when generating gib structures Levan Tsereteli (Tue Jan 05 2016 - 03:36:32 PST)
- Re: [AMBER] Problems with tleap when generating gib structures David A Case (Tue Jan 05 2016 - 05:25:52 PST)
  - Re: [AMBER] Problems with tleap when generating gib structures Levan Tsereteli (Tue Jan 05 2016 - 06:26:07 PST)
  - Re: [AMBER] Problems with tleap when generating gib structures Levan Tsereteli (Tue Jan 05 2016 - 08:51:12 PST)
    - Re: [AMBER] Problems with tleap when generating gib structures Jason Swails (Tue Jan 05 2016 - 08:57:39 PST)
    - Re: [AMBER] Problems with tleap when generating gib structures Levan Tsereteli (Tue Jan 05 2016 - 10:11:18 PST)
    - Re: [AMBER] Problems with tleap when generating gib structures Daniel Roe (Tue Jan 05 2016 - 11:05:52 PST)
    - Re: [AMBER] Problems with tleap when generating gib structures Levan Tsereteli (Tue Jan 05 2016 - 11:11:51 PST)
[AMBER] Sander minimization of protein-ligand complex Manjula Saravanan (Tue Jan 05 2016 - 21:21:23 PST)
- [AMBER] q4md-forcefieldtools is back with new features FyD (Tue Jan 05 2016 - 22:09:20 PST)
[AMBER] xleap : adding ions out of box Himanshu Joshi (Tue Jan 05 2016 - 23:45:48 PST)
- Re: [AMBER] xleap : adding ions out of box David A Case (Wed Jan 06 2016 - 04:53:09 PST)
  - Re: [AMBER] xleap : adding ions out of box Himanshu Joshi (Wed Jan 06 2016 - 10:22:10 PST)
    - Re: [AMBER] xleap : adding ions out of box Himanshu Joshi (Fri Jan 08 2016 - 02:50:17 PST)
[AMBER] MMPBSA_Error: Could not find necessary program [mmpbsa_py_energy] Pallavi Mohanty (Tue Jan 05 2016 - 23:48:37 PST)
- Re: [AMBER] MMPBSA_Error: Could not find necessary program [mmpbsa_py_energy] Jason Swails (Wed Jan 06 2016 - 04:25:34 PST)
[AMBER] How to appropriately replace the amber force in the source codes ? jinfeng liu (Wed Jan 06 2016 - 05:37:46 PST)
- Re: [AMBER] How to appropriately replace the amber force in the source codes ? Jason Swails (Wed Jan 06 2016 - 06:02:51 PST)
[AMBER] Fwd: arrêt de travail Elisa Frezza (Wed Jan 06 2016 - 05:40:06 PST)
[AMBER] hbond and image problem in cpptraj Chris (Wed Jan 06 2016 - 19:46:03 PST)
- Re: [AMBER] hbond and image problem in cpptraj Daniel Roe (Thu Jan 07 2016 - 09:50:45 PST)
  - Re: [AMBER] hbond and image problem in cpptraj Chris (Thu Jan 07 2016 - 10:50:18 PST)
[AMBER] Errors during Building Sidechain Model（MCPB program） 王远强 (Wed Jan 06 2016 - 20:38:31 PST)
- Re: [AMBER] Errors during Building Sidechain Model（MCPB program） Bill Ross (Wed Jan 06 2016 - 20:47:49 PST)
  - Re: [AMBER] Errors during Building Sidechain Model（MCPB program） 王远强 (Wed Jan 06 2016 - 20:58:26 PST)
    - Re: [AMBER] Errors during Building Sidechain Model（MCPB program） Bill Ross (Wed Jan 06 2016 - 21:25:22 PST)
- Re: [AMBER] Errors during Building Sidechain Model（MCPB program） wyq (Fri Jan 08 2016 - 03:44:06 PST)
[AMBER] Error in running AMBER 12 GPU simulations[application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0] Yogeeshwar Ajjugal (Wed Jan 06 2016 - 21:43:47 PST)
- Re: [AMBER] Error in running AMBER 12 GPU simulations[application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0] David A Case (Thu Jan 07 2016 - 05:08:52 PST)
[AMBER] Help: parameters of Equilibration and production scripts Sehrish Naz (Wed Jan 06 2016 - 22:05:43 PST)
- Re: [AMBER] Help: parameters of Equilibration and production scripts Jason Swails (Thu Jan 07 2016 - 03:59:45 PST)
[AMBER] how to make active site conserve water unique before loading pdb on xleap? Saman Yousuf ali (Thu Jan 07 2016 - 11:11:36 PST)
- Re: [AMBER] how to make active site conserve water unique before loading pdb on xleap? David A Case (Fri Jan 08 2016 - 06:01:54 PST)
[AMBER] Remove single water molecule using thermodynamic integration Johannes Loeffler (Fri Jan 08 2016 - 00:10:09 PST)
- Re: [AMBER] Remove single water molecule using thermodynamic integration hannes.loeffler.stfc.ac.uk (Fri Jan 08 2016 - 00:39:39 PST)
  - Re: [AMBER] Remove single water molecule using thermodynamic integration Johannes Loeffler (Fri Jan 08 2016 - 00:41:52 PST)
[AMBER] parmed question regarding modifying Lennard-Jones parameters InSuk Joung (Fri Jan 08 2016 - 00:45:03 PST)
- Re: [AMBER] parmed question regarding modifying Lennard-Jones parameters Jason Swails (Fri Jan 08 2016 - 03:50:18 PST)
  - Re: [AMBER] parmed question regarding modifying Lennard-Jones parameters InSuk Joung (Fri Jan 08 2016 - 06:00:01 PST)
    - Re: [AMBER] parmed question regarding modifying Lennard-Jones parameters Jason Swails (Fri Jan 08 2016 - 06:08:43 PST)
[AMBER] High RMSD values due to use of iwrap richa anand (Fri Jan 08 2016 - 03:09:12 PST)
- Re: [AMBER] High RMSD values due to use of iwrap Jason Swails (Fri Jan 08 2016 - 03:44:11 PST)
- Re: [AMBER] High RMSD values due to use of iwrap David A Case (Fri Jan 08 2016 - 06:07:59 PST)
- [AMBER] Fwd: High RMSD values due to use of iwrap richa anand (Tue Jan 19 2016 - 21:42:24 PST)
  - Re: [AMBER] Fwd: High RMSD values due to use of iwrap David A Case (Wed Jan 20 2016 - 05:06:05 PST)
[AMBER] Questions about Steered MD in Amber Vu Truong (Fri Jan 08 2016 - 15:23:36 PST)
[AMBER] Dr Baliram Lone Dr Baliram lone (Sat Jan 09 2016 - 00:31:38 PST)
- Re: [AMBER] Dr Baliram Lone David A Case (Sat Jan 09 2016 - 05:58:55 PST)
[AMBER] exact values corresponding to the grid points in GIST calculations Mohan Pradhan (Sat Jan 09 2016 - 02:36:25 PST)
- Re: [AMBER] exact values corresponding to the grid points in GIST calculations Steven Ramsey (Sat Jan 09 2016 - 15:29:14 PST)
[AMBER] Problem when using lipid14 force filed in Amber 11 Bin Wang (Sat Jan 09 2016 - 14:40:26 PST)
- Re: [AMBER] Problem when using lipid14 force filed in Amber 11 Jean-Marc (Sun Jan 10 2016 - 21:34:18 PST)
  - Re: [AMBER] Problem when using lipid14 force filed in Amber 11 Bin Wang (Mon Jan 11 2016 - 07:40:23 PST)
    - Re: [AMBER] Problem when using lipid14 force filed in Amber 11 Bill Ross (Mon Jan 11 2016 - 12:02:20 PST)
    - Re: [AMBER] Problem when using lipid14 force filed in Amber 11 JEAN MARC BILLOD (Mon Jan 11 2016 - 12:17:47 PST)
    - Re: [AMBER] Problem when using lipid14 force filed in Amber 11 Bin Wang (Mon Jan 11 2016 - 14:50:41 PST)
    - Re: [AMBER] Problem when using lipid14 force filed in Amber 11 Bill Ross (Mon Jan 11 2016 - 15:18:51 PST)
    - Re: [AMBER] Problem when using lipid14 force filed in Amber 11 Jean-Marc (Mon Jan 11 2016 - 21:25:51 PST)
    - Re: [AMBER] Problem when using lipid14 force filed in Amber 11 Bin Wang (Mon Jan 11 2016 - 21:52:16 PST)
    - Re: [AMBER] Problem when using lipid14 force filed in Amber 11 Bin Wang (Mon Jan 18 2016 - 20:11:39 PST)
    - Re: [AMBER] Problem when using lipid14 force filed in Amber 11 Jean-Marc Billod (Mon Jan 18 2016 - 21:46:51 PST)
    - Re: [AMBER] Problem when using lipid14 force filed in Amber 11 Bin Wang (Tue Jan 19 2016 - 06:50:12 PST)
    - Re: [AMBER] Problem when using lipid14 force filed in Amber 11 Ross Walker (Tue Jan 19 2016 - 07:43:40 PST)
    - Re: [AMBER] Problem when using lipid14 force filed in Amber 11 David A Case (Tue Jan 19 2016 - 09:05:21 PST)
    - Re: [AMBER] Problem when using lipid14 force filed in Amber 11 Bin Wang (Tue Jan 19 2016 - 10:40:45 PST)
    - Re: [AMBER] Problem when using lipid14 force filed in Amber 11 Ross Walker (Tue Jan 19 2016 - 11:06:51 PST)
    - Re: [AMBER] Problem when using lipid14 force filed in Amber 11 Bin Wang (Tue Jan 19 2016 - 12:11:43 PST)
    - Re: [AMBER] Problem when using lipid14 force filed in Amber 11 Ross Walker (Tue Jan 19 2016 - 13:05:46 PST)
    - Re: [AMBER] Problem when using lipid14 force filed in Amber 11 Benjamin D Madej (Tue Jan 19 2016 - 13:26:36 PST)
    - Re: [AMBER] Problem when using lipid14 force filed in Amber 11 Bin Wang (Thu Jan 21 2016 - 20:03:16 PST)
    - Re: [AMBER] Problem when using lipid14 force filed in Amber 11 Bill Ross (Thu Jan 21 2016 - 20:09:10 PST)
    - Re: [AMBER] Problem when using lipid14 force filed in Amber 11 Bin Wang (Fri Jan 22 2016 - 17:58:13 PST)
    - Re: [AMBER] Problem when using lipid14 force filed in Amber 11 Bin Wang (Tue Jan 19 2016 - 13:46:35 PST)
  - Re: [AMBER] Problem when using lipid14 force filed in Amber 11 Bin Wang (Mon Jan 11 2016 - 07:41:21 PST)
    - Re: [AMBER] Problem when using lipid14 force filed in Amber 11 David A Case (Mon Jan 11 2016 - 08:59:13 PST)
  - Re: [AMBER] Problem when using lipid14 force filed in Amber 11 Bin Wang (Mon Jan 11 2016 - 07:45:42 PST)
    - Re: [AMBER] Problem when using lipid14 force filed in Amber 11 Ross Walker (Mon Jan 11 2016 - 08:18:16 PST)
    - Re: [AMBER] Problem when using lipid14 force filed in Amber 11 Bin Wang (Mon Jan 11 2016 - 08:26:02 PST)
    - Re: [AMBER] Problem when using lipid14 force filed in Amber 11 JEAN MARC BILLOD (Mon Jan 11 2016 - 08:33:46 PST)
    - Re: [AMBER] Problem when using lipid14 force filed in Amber 11 Bin Wang (Mon Jan 11 2016 - 11:55:43 PST)
    - Re: [AMBER] Problem when using lipid14 force filed in Amber 11 David A Case (Tue Jan 12 2016 - 05:49:06 PST)
    - Re: [AMBER] Problem when using lipid14 force filed in Amber 11 David A Case (Mon Jan 11 2016 - 08:46:32 PST)
[AMBER] Scripting CPPTRAJ Analysis Commands within a PBS Script Robert Molt (Sat Jan 09 2016 - 21:12:53 PST)
- Re: [AMBER] Scripting CPPTRAJ Analysis Commands within a PBS Script Eiros Zamora, Juan (Sun Jan 10 2016 - 03:56:58 PST)
- Re: [AMBER] Scripting CPPTRAJ Analysis Commands within a PBS Script Kenneth Huang (Sun Jan 10 2016 - 09:00:54 PST)
  - Re: [AMBER] Scripting CPPTRAJ Analysis Commands within a PBS Script Robert Molt (Sun Jan 10 2016 - 19:10:12 PST)
[AMBER] premed.MPI warning George Tzotzos (Sun Jan 10 2016 - 02:37:45 PST)
- Re: [AMBER] premed.MPI warning David A Case (Sun Jan 10 2016 - 05:45:10 PST)
  - Re: [AMBER] premed.MPI warning Jason Swails (Sun Jan 10 2016 - 08:43:33 PST)
    - Re: [AMBER] premed.MPI warning Ross Walker (Sun Jan 10 2016 - 10:20:26 PST)
    - Re: [AMBER] premed.MPI warning George Tzotzos (Sun Jan 10 2016 - 12:38:39 PST)
    - Re: [AMBER] premed.MPI warning Jason Swails (Mon Jan 11 2016 - 05:12:47 PST)
    - Re: [AMBER] premed.MPI warning Ross Walker (Mon Jan 11 2016 - 08:14:28 PST)
    - Re: [AMBER] premed.MPI warning George Tzotzos (Mon Jan 11 2016 - 08:23:28 PST)
    - Re: [AMBER] premed.MPI warning George Tzotzos (Mon Jan 11 2016 - 15:26:12 PST)
    - Re: [AMBER] premed.MPI warning Jason Swails (Mon Jan 11 2016 - 16:46:16 PST)
    - Re: [AMBER] premed.MPI warning Ross Walker (Mon Jan 11 2016 - 18:35:11 PST)
    - Re: [AMBER] premed.MPI warning George Tzotzos (Mon Jan 11 2016 - 18:44:27 PST)
    - [AMBER] premed.MPI warning Irfan Alibay (Tue Jan 12 2016 - 07:44:01 PST)
    - Re: [AMBER] premed.MPI warning Jason Swails (Tue Jan 12 2016 - 08:05:47 PST)
    - [AMBER] premed.MPI warning Irfan Alibay (Tue Jan 12 2016 - 08:34:21 PST)
    - Re: [AMBER] premed.MPI warning Jason Swails (Tue Jan 12 2016 - 08:54:58 PST)
[AMBER] problem with pmemd.cuda and PBS Indrajit Deb (Mon Jan 11 2016 - 05:52:32 PST)
- Re: [AMBER] problem with pmemd.cuda and PBS Jason Swails (Mon Jan 11 2016 - 06:01:16 PST)
[AMBER] MMPBSA Job Parallel Running Guqin Shi (Mon Jan 11 2016 - 11:29:39 PST)
- Re: [AMBER] MMPBSA Job Parallel Running Kenneth Huang (Mon Jan 11 2016 - 14:10:35 PST)
  - Re: [AMBER] MMPBSA Job Parallel Running Pallavi Mohanty (Mon Jan 11 2016 - 20:41:59 PST)
    - Re: [AMBER] MMPBSA Job Parallel Running Guqin Shi (Wed Jan 13 2016 - 07:46:55 PST)
    - Re: [AMBER] MMPBSA Job Parallel Running Jason Swails (Wed Jan 13 2016 - 08:40:12 PST)
    - Re: [AMBER] MMPBSA Job Parallel Running Jason Swails (Wed Jan 13 2016 - 08:40:45 PST)
    - Re: [AMBER] MMPBSA Job Parallel Running Guqin Shi (Thu Jan 14 2016 - 08:47:54 PST)
    - Re: [AMBER] MMPBSA Job Parallel Running Jason Swails (Thu Jan 14 2016 - 19:57:39 PST)
    - Re: [AMBER] MMPBSA Job Parallel Running Guqin Shi (Fri Jan 15 2016 - 06:29:36 PST)
  - Re: [AMBER] MMPBSA Job Parallel Running Guqin Shi (Wed Jan 13 2016 - 07:56:45 PST)
[AMBER] MCPB Step 2s help Tavenor, Nathan Albert (Mon Jan 11 2016 - 12:30:42 PST)
- Re: [AMBER] MCPB Step 2s help Pengfei Li (Tue Jan 12 2016 - 09:16:00 PST)
  - Re: [AMBER] MCPB Step 2s help Tavenor, Nathan Albert (Wed Jan 13 2016 - 04:49:47 PST)
[AMBER] Xmgrace Wong Li Zhe (Mon Jan 11 2016 - 18:26:54 PST)
[AMBER] mmpbsa calculation elham sattarinezhad (Tue Jan 12 2016 - 02:53:53 PST)
- Re: [AMBER] mmpbsa calculation Hannes Loeffler (Tue Jan 12 2016 - 03:08:38 PST)
Re: [AMBER] parameters for Mono-methylated Lysine Yin, Guowei (Tue Jan 12 2016 - 11:13:09 PST)
- Re: [AMBER] parameters for Mono-methylated Lysine Karl Kirschner (Wed Jan 13 2016 - 02:20:23 PST)
  - Re: [AMBER] parameters for Mono-methylated Lysine amin.imtech.res.in (Wed Jan 13 2016 - 02:22:45 PST)
    - Re: [AMBER] parameters for Mono-methylated Lysine Hannes Loeffler (Wed Jan 13 2016 - 03:03:58 PST)
[AMBER] RMSD selected residues Vertika Gautam (Tue Jan 12 2016 - 23:02:58 PST)
- Re: [AMBER] RMSD selected residues Daniel Roe (Wed Jan 13 2016 - 08:51:25 PST)
  - Re: [AMBER] RMSD selected residues Vertika Gautam (Fri Jan 15 2016 - 23:52:18 PST)
[AMBER] X-OS-P-X and X-os-p5-X AMBER99SB and GAFF parameters mismatch tarak karmakar (Wed Jan 13 2016 - 05:42:37 PST)
- Re: [AMBER] X-OS-P-X and X-os-p5-X AMBER99SB and GAFF parameters mismatch Hannes Loeffler (Wed Jan 13 2016 - 06:20:27 PST)
  - Re: [AMBER] X-OS-P-X and X-os-p5-X AMBER99SB and GAFF parameters mismatch tarak karmakar (Wed Jan 13 2016 - 06:39:13 PST)
    - Re: [AMBER] X-OS-P-X and X-os-p5-X AMBER99SB and GAFF parameters mismatch Hannes Loeffler (Wed Jan 13 2016 - 07:03:10 PST)
    - Re: [AMBER] X-OS-P-X and X-os-p5-X AMBER99SB and GAFF parameters mismatch Jason Swails (Wed Jan 13 2016 - 08:43:47 PST)
    - Re: [AMBER] X-OS-P-X and X-os-p5-X AMBER99SB and GAFF parameters mismatch Hannes Loeffler (Wed Jan 13 2016 - 09:04:23 PST)
    - Re: [AMBER] X-OS-P-X and X-os-p5-X AMBER99SB and GAFF parameters mismatch tarak karmakar (Wed Jan 13 2016 - 09:42:35 PST)
- Re: [AMBER] X-OS-P-X and X-os-p5-X AMBER99SB and GAFF parameters mismatch Alan (Thu Jan 14 2016 - 01:13:55 PST)
  - Re: [AMBER] X-OS-P-X and X-os-p5-X AMBER99SB and GAFF parameters mismatch tarak karmakar (Fri Jan 15 2016 - 08:44:14 PST)
[AMBER] System becomes unstable upon heating Sudip Das (Wed Jan 13 2016 - 07:19:47 PST)
- Re: [AMBER] System becomes unstable upon heating Jason Swails (Wed Jan 13 2016 - 08:50:24 PST)
  - Re: [AMBER] System becomes unstable upon heating Sudip Das (Wed Jan 13 2016 - 20:31:54 PST)
    - Re: [AMBER] System becomes unstable upon heating David A Case (Thu Jan 14 2016 - 04:38:21 PST)
[AMBER] Contact analysis using cpptraj Kucharski Jr., Amir N (Wed Jan 13 2016 - 07:25:22 PST)
- Re: [AMBER] Contact analysis using cpptraj Daniel Roe (Wed Jan 13 2016 - 09:10:15 PST)
[AMBER] Kinetic Energy Wong Li Zhe (Wed Jan 13 2016 - 15:54:50 PST)
- Re: [AMBER] Kinetic Energy Jason Swails (Wed Jan 13 2016 - 16:42:03 PST)
  - Re: [AMBER] Kinetic Energy Wong Li Zhe (Wed Jan 13 2016 - 17:25:13 PST)
    - Re: [AMBER] Kinetic Energy Hai Nguyen (Wed Jan 13 2016 - 18:03:53 PST)
    - Re: [AMBER] Kinetic Energy Wong Li Zhe (Wed Jan 13 2016 - 18:09:43 PST)
    - Re: [AMBER] Kinetic Energy Hai Nguyen (Wed Jan 13 2016 - 18:31:16 PST)
[AMBER] How to maintain planerity of graphene sheets jagannath mondal (Wed Jan 13 2016 - 23:16:34 PST)
- Re: [AMBER] How to maintain planerity of graphene sheets Bill Ross (Thu Jan 14 2016 - 00:38:18 PST)
[AMBER] Howto cpptraj - multiple trajin-commands in one line Falko Jähnert (Thu Jan 14 2016 - 04:25:22 PST)
- Re: [AMBER] Howto cpptraj - multiple trajin-commands in one line Chris Moth (Thu Jan 14 2016 - 07:40:23 PST)
- Re: [AMBER] Howto cpptraj - multiple trajin-commands in one line Jean-Marc Billod (Thu Jan 14 2016 - 07:40:35 PST)
  - Re: [AMBER] Howto cpptraj - multiple trajin-commands in one line Falko Jähnert (Wed Jan 20 2016 - 07:37:09 PST)
- Re: [AMBER] Howto cpptraj - multiple trajin-commands in one line Daniel Roe (Thu Jan 14 2016 - 08:15:11 PST)
  - Re: [AMBER] Howto cpptraj - multiple trajin-commands in one line Chris Moth (Thu Jan 14 2016 - 08:43:09 PST)
    - Re: [AMBER] Howto cpptraj - multiple trajin-commands in one line Daniel Roe (Thu Jan 14 2016 - 12:49:21 PST)
- Re: [AMBER] Howto cpptraj - multiple trajin-commands in one line Hai Nguyen (Thu Jan 14 2016 - 15:08:25 PST)
[AMBER] Problem with A08 tutorial, solvateBox error Elisa Pieri (Thu Jan 14 2016 - 04:41:12 PST)
- Re: [AMBER] Problem with A08 tutorial, solvateBox error Kenneth Huang (Thu Jan 14 2016 - 06:36:17 PST)
- Re: [AMBER] Problem with A08 tutorial, solvateBox error Jason Swails (Thu Jan 14 2016 - 20:12:04 PST)
[AMBER] Questions about Steered MD in Amber Vu Truong (Thu Jan 14 2016 - 12:10:59 PST)
- Re: [AMBER] Questions about Steered MD in Amber Jason Swails (Thu Jan 14 2016 - 20:04:56 PST)
[AMBER] contact analysis with CPPTRAJ anu chandra (Fri Jan 15 2016 - 03:59:04 PST)
- Re: [AMBER] contact analysis with CPPTRAJ Daniel Roe (Fri Jan 15 2016 - 08:12:24 PST)
  - Re: [AMBER] contact analysis with CPPTRAJ anu chandra (Fri Jan 15 2016 - 09:25:41 PST)
[AMBER] Problem installing AmberTools1.5 on Mac OS X 10.11 EL Capitan Ekaterina Ratkova (Fri Jan 15 2016 - 04:15:05 PST)
- Re: [AMBER] Problem installing AmberTools1.5 on Mac OS X 10.11 EL Capitan Jason Swails (Fri Jan 15 2016 - 07:28:45 PST)
  - Re: [AMBER] Problem installing AmberTools1.5 on Mac OS X 10.11 EL Capitan Ekaterina Ratkova (Fri Jan 15 2016 - 07:39:38 PST)
    - Re: [AMBER] Problem installing AmberTools1.5 on Mac OS X 10.11 EL Capitan David A Case (Fri Jan 15 2016 - 09:02:55 PST)
    - Re: [AMBER] Problem installing AmberTools1.5 on Mac OS X 10.11 EL Capitan Ekaterina Ratkova (Mon Jan 18 2016 - 02:27:21 PST)
[AMBER] Fwd: Problem installing AmberTools1.5 on Mac OS X 10.11 EL Capitan Ekaterina Ratkova (Fri Jan 15 2016 - 04:21:21 PST)
[AMBER] Problem installing AmberTools1.5 on Mac OS X 10.11 EL Capitan Ratkova, Ekaterina, Dr. (Fri Jan 15 2016 - 04:53:42 PST)
[AMBER] Angle calculation between two structures anu chandra (Fri Jan 15 2016 - 04:58:21 PST)
- Re: [AMBER] Angle calculation between two structures Daniel Roe (Fri Jan 15 2016 - 07:59:52 PST)
  - Re: [AMBER] Angle calculation between two structures anu chandra (Fri Jan 15 2016 - 09:24:55 PST)
    - Re: [AMBER] Angle calculation between two structures Daniel Roe (Fri Jan 15 2016 - 10:28:19 PST)
    - Re: [AMBER] Angle calculation between two structures anu chandra (Fri Jan 15 2016 - 12:12:52 PST)
[AMBER] QM/MM/MD simulation zengxitao (Fri Jan 15 2016 - 05:49:17 PST)
[AMBER] cpptraj question Robert Molt (Sat Jan 16 2016 - 08:38:36 PST)
- Re: [AMBER] cpptraj question Jason Swails (Sat Jan 16 2016 - 09:55:00 PST)
[AMBER] Parameter and coordinate files Stefano Sarao S215563 (Sat Jan 16 2016 - 11:12:47 PST)
- Re: [AMBER] Parameter and coordinate files David Case (Sat Jan 16 2016 - 19:17:00 PST)
  - Re: [AMBER] Parameter and coordinate files Stefano Sarao S215563 (Sun Jan 17 2016 - 02:50:05 PST)
    - Re: [AMBER] Parameter and coordinate files David A Case (Mon Jan 18 2016 - 05:02:08 PST)
[AMBER] format of seconday structure calculation by cpptraj Sangita Kachhap (Sun Jan 17 2016 - 05:26:21 PST)
- Re: [AMBER] format of seconday structure calculation by cpptraj Christina Bergonzo (Sun Jan 17 2016 - 06:29:47 PST)
  - Re: [AMBER] format of seconday structure calculation by cpptraj Sangita Kachhap (Sun Jan 17 2016 - 06:28:23 PST)
[AMBER] Fail to start nab Nikolay N. Kuzmich (Mon Jan 18 2016 - 02:32:53 PST)
- Re: [AMBER] Fail to start nab Bill Ross (Mon Jan 18 2016 - 02:44:35 PST)
[AMBER] Need Help regarding Energy Calculation Saikat Dutta chowdhury (Mon Jan 18 2016 - 03:57:46 PST)
- Re: [AMBER] Need Help regarding Energy Calculation Jason Swails (Mon Jan 18 2016 - 07:06:54 PST)
  - Re: [AMBER] Need Help regarding Energy Calculation Saikat Dutta chowdhury (Mon Jan 18 2016 - 19:49:29 PST)
[AMBER] python error when using pdb4amber Elisa Pieri (Mon Jan 18 2016 - 04:34:15 PST)
- Re: [AMBER] python error when using pdb4amber Jason Swails (Mon Jan 18 2016 - 13:24:04 PST)
  - Re: [AMBER] python error when using pdb4amber Elisa Pieri (Tue Jan 19 2016 - 00:38:42 PST)
    - Re: [AMBER] python error when using pdb4amber David A Case (Tue Jan 19 2016 - 05:00:24 PST)
    - Re: [AMBER] python error when using pdb4amber Vasantha Kumar (Tue Jan 19 2016 - 05:29:19 PST)
    - Re: [AMBER] python error when using pdb4amber Jason Swails (Tue Jan 19 2016 - 05:47:50 PST)
- Re: [AMBER] python error when using pdb4amber Jason Swails (Tue Jan 19 2016 - 06:00:46 PST)
  - Re: [AMBER] python error when using pdb4amber Elisa Pieri (Thu Jan 21 2016 - 01:15:03 PST)
[AMBER] Problems when trying to improve angle parameters whith paramfit Jérémie KNOOPS [531802] (Mon Jan 18 2016 - 04:45:29 PST)
- Re: [AMBER] Problems when trying to improve angle parameters whith paramfit Sigurd Friis Truelsen (Mon Mar 14 2016 - 08:28:52 PDT)
  - Re: [AMBER] Problems when trying to improve angle parameters whith paramfit David Cerutti (Mon Mar 14 2016 - 09:42:53 PDT)
[AMBER] Enthalpy of solute+solvent Sergey Samsonov (Mon Jan 18 2016 - 07:12:54 PST)
- Re: [AMBER] Enthalpy of solute+solvent Sergey Samsonov (Tue Jan 19 2016 - 00:42:39 PST)
[AMBER] Completely fixed atoms in MD Simulation (pmemd) Melisa Averina (Mon Jan 18 2016 - 12:03:36 PST)
- Re: [AMBER] Completely fixed atoms in MD Simulation (pmemd) Jason Swails (Mon Jan 18 2016 - 13:12:16 PST)
[AMBER] Improving the quality of the model Sushi Shilpa (Tue Jan 19 2016 - 22:50:23 PST)
- Re: [AMBER] Improving the quality of the model Carlos Simmerling (Wed Jan 20 2016 - 05:31:41 PST)
[AMBER] problem with reduce and energy minimization Maryam Hamzehee (Wed Jan 20 2016 - 23:55:38 PST)
- Re: [AMBER] problem with reduce and energy minimization David A Case (Thu Jan 21 2016 - 04:53:40 PST)
  - Re: [AMBER] problem with reduce and energy minimization Maryam Hamzehee (Sun Jan 24 2016 - 01:59:04 PST)
[AMBER] Amber14 Installation with cuda יוכבד (Thu Jan 21 2016 - 06:30:12 PST)
- Re: [AMBER] Amber14 Installation with cuda Jason Swails (Thu Jan 21 2016 - 06:56:01 PST)
  - Re: [AMBER] Amber14 Installation with cuda יוכבד (Thu Jan 21 2016 - 10:31:13 PST)
[AMBER] Amber 12 GTX-980 Sarah Graham (Thu Jan 21 2016 - 07:07:48 PST)
[AMBER] MMPBSA for apo-proteins Kucharski Jr., Amir N (Thu Jan 21 2016 - 10:56:23 PST)
- Re: [AMBER] MMPBSA for apo-proteins Jason Swails (Thu Jan 21 2016 - 11:50:06 PST)
[AMBER] Problem with Tleap Luis Esteban (Thu Jan 21 2016 - 17:00:47 PST)
- Re: [AMBER] Problem with Tleap Marcelo Andrade Chagas (Thu Jan 21 2016 - 17:20:37 PST)
  - Re: [AMBER] Problem with Tleap Robert Molt (Thu Jan 21 2016 - 17:31:35 PST)
  - Re: [AMBER] Problem with Tleap Marcelo Andrade Chagas (Thu Jan 21 2016 - 17:42:46 PST)
- Re: [AMBER] Problem with Tleap Bill Ross (Thu Jan 21 2016 - 18:41:59 PST)
- Re: [AMBER] Problem with Tleap case (Thu Jan 21 2016 - 19:03:06 PST)
[AMBER] FW: Problem with Tleap Luis Esteban (Thu Jan 21 2016 - 21:07:31 PST)
[AMBER] MCPB.py error chemjxn (Thu Jan 21 2016 - 22:48:51 PST)
- Re: [AMBER] MCPB.py error Pengfei Li (Fri Jan 22 2016 - 08:08:52 PST)
[AMBER] Stability Calculation using MMPBSA.py Saikat Dutta chowdhury (Fri Jan 22 2016 - 02:08:25 PST)
- Re: [AMBER] Stability Calculation using MMPBSA.py Jason Swails (Fri Jan 22 2016 - 04:49:52 PST)
[AMBER] Error: A residue defined as a "fast 3-point water" Saman Yousuf ali (Fri Jan 22 2016 - 03:28:34 PST)
- Re: [AMBER] Error: A residue defined as a "fast 3-point water" Jason Swails (Fri Jan 22 2016 - 04:59:07 PST)
- Re: [AMBER] Error: A residue defined as a "fast 3-point water" David A Case (Fri Jan 22 2016 - 05:13:06 PST)
  - Re: [AMBER] Error: A residue defined as a "fast 3-point water" Saman Yousuf ali (Fri Jan 22 2016 - 06:29:59 PST)
    - Re: [AMBER] Error: A residue defined as a "fast 3-point water" Daniel Roe (Fri Jan 22 2016 - 07:18:06 PST)
[AMBER] use of LIE command richa anand (Fri Jan 22 2016 - 04:08:06 PST)
- Re: [AMBER] use of LIE command Jason Swails (Fri Jan 22 2016 - 05:03:26 PST)
[AMBER] PCA analysis richa anand (Fri Jan 22 2016 - 04:18:53 PST)
- Re: [AMBER] PCA analysis Jason Swails (Fri Jan 22 2016 - 05:09:35 PST)
[AMBER] How to put ACE and NME on the ends of a missing loop Elisa Pieri (Fri Jan 22 2016 - 05:20:39 PST)
- Re: [AMBER] How to put ACE and NME on the ends of a missing loop Vasantha Kumar (Fri Jan 22 2016 - 06:37:36 PST)
  - Re: [AMBER] How to put ACE and NME on the ends of a missing loop Elisa Pieri (Fri Jan 22 2016 - 07:02:46 PST)
[AMBER] KeyError - MCPB.py tutorial David Mayes (Fri Jan 22 2016 - 05:25:07 PST)
- Re: [AMBER] KeyError - MCPB.py tutorial Pengfei Li (Fri Jan 22 2016 - 08:10:15 PST)
  - Re: [AMBER] KeyError - MCPB.py tutorial David Mayes (Mon Jan 25 2016 - 07:04:53 PST)
    - Re: [AMBER] KeyError - MCPB.py tutorial Pengfei Li (Mon Jan 25 2016 - 14:49:49 PST)
    - Re: [AMBER] KeyError - MCPB.py tutorial David Mayes (Tue Jan 26 2016 - 06:01:37 PST)
    - [AMBER] Iron/ligand parameters for AMBER Christian Schafmeister (Tue Jan 26 2016 - 06:55:20 PST)
    - Re: [AMBER] KeyError - MCPB.py tutorial Pengfei Li (Tue Jan 26 2016 - 07:40:49 PST)
    - Re: [AMBER] KeyError - MCPB.py tutorial David Mayes (Tue Jan 26 2016 - 07:43:26 PST)
    - Re: [AMBER] KeyError - MCPB.py tutorial Pengfei Li (Thu Jan 28 2016 - 09:08:43 PST)
    - Re: [AMBER] KeyError - MCPB.py tutorial David Mayes (Fri Jan 29 2016 - 01:20:15 PST)
    - Re: [AMBER] KeyError - MCPB.py tutorial Pengfei Li (Fri Jan 29 2016 - 07:06:54 PST)
[AMBER] What is the most modern AMBER parm/top format? Christian Schafmeister (Fri Jan 22 2016 - 07:58:31 PST)
- Re: [AMBER] What is the most modern AMBER parm/top format? Jason Swails (Fri Jan 22 2016 - 09:19:04 PST)
  - Re: [AMBER] What is the most modern AMBER parm/top format? Thomas Cheatham (Fri Jan 22 2016 - 09:23:30 PST)
[AMBER] Run your Amber simulations in the cloud with Rescale Sidney Elmer (Fri Jan 22 2016 - 08:45:27 PST)
[AMBER] Water diffusion constant obtained in Nose-Hoover thermostat in Amber14+AmberTools15 jinfeng liu (Sat Jan 23 2016 - 03:10:34 PST)
- Re: [AMBER] Water diffusion constant obtained in Nose-Hoover thermostat in Amber14+AmberTools15 hannes.loeffler.stfc.ac.uk (Sat Jan 23 2016 - 03:23:23 PST)
  - Re: [AMBER] Water diffusion constant obtained in Nose-Hoover thermostat in Amber14+AmberTools15 jinfeng liu (Sat Jan 23 2016 - 03:27:41 PST)
    - Re: [AMBER] Water diffusion constant obtained in Nose-Hoover thermostat in Amber14+AmberTools15 hannes.loeffler.stfc.ac.uk (Sat Jan 23 2016 - 03:35:02 PST)
    - Re: [AMBER] Water diffusion constant obtained in Nose-Hoover thermostat in Amber14+AmberTools15 jinfeng liu (Sat Jan 23 2016 - 03:49:38 PST)
    - Re: [AMBER] Water diffusion constant obtained in Nose-Hoover thermostat in Amber14+AmberTools15 hannes.loeffler.stfc.ac.uk (Sat Jan 23 2016 - 03:59:12 PST)
    - Re: [AMBER] Water diffusion constant obtained in Nose-Hoover thermostat in Amber14+AmberTools15 Christina Bergonzo (Sat Jan 23 2016 - 05:33:03 PST)
    - Re: [AMBER] Water diffusion constant obtained in Nose-Hoover thermostat in Amber14+AmberTools15 Tom Kurtzman (Sat Jan 23 2016 - 05:47:09 PST)
    - [AMBER] Water diffusion constant obtained in Nose-Hoover thermostat in Amber14+AmberTools15 Irfan Alibay (Sat Jan 23 2016 - 14:07:18 PST)
- Re: [AMBER] Water diffusion constant obtained in Nose-Hoover thermostat in Amber14+AmberTools15 David A Case (Sat Jan 23 2016 - 07:02:19 PST)
  - Re: [AMBER] Water diffusion constant obtained in Nose-Hoover thermostat in Amber14+AmberTools15 David A Case (Sat Jan 23 2016 - 12:52:56 PST)
[AMBER] Dear All ankita mehta (Sat Jan 23 2016 - 06:49:59 PST)
- Re: [AMBER] Dear All David A Case (Sat Jan 23 2016 - 12:51:21 PST)
  - Re: [AMBER] Dear All Jason Swails (Sat Jan 23 2016 - 17:16:45 PST)
[AMBER] cuda info Carlos Romero (Sat Jan 23 2016 - 22:46:30 PST)
- Re: [AMBER] cuda info Ross Walker (Sat Jan 23 2016 - 23:39:13 PST)
  - Re: [AMBER] cuda info Carlos Romero (Sun Jan 24 2016 - 09:08:17 PST)
[AMBER] troubles in understanding, amber minimization input Saman Yousuf ali (Sun Jan 24 2016 - 01:51:32 PST)
- Re: [AMBER] troubles in understanding, amber minimization input Jason Swails (Sun Jan 24 2016 - 04:54:53 PST)
- Re: [AMBER] troubles in understanding, amber minimization input Jason Swails (Sun Jan 24 2016 - 18:19:06 PST)
  - Re: [AMBER] troubles in understanding, amber minimization input kenfack cyril (Mon Jan 25 2016 - 00:00:27 PST)
[AMBER] g03 error message Damiano Spadoni (Sun Jan 24 2016 - 10:15:49 PST)
- Re: [AMBER] g03 error message hannes.loeffler.stfc.ac.uk (Sun Jan 24 2016 - 11:12:20 PST)
  - Re: [AMBER] g03 error message Damiano Spadoni (Mon Jan 25 2016 - 02:10:08 PST)
    - Re: [AMBER] g03 error message Hannes Loeffler (Mon Jan 25 2016 - 02:38:11 PST)
    - Re: [AMBER] g03 error message Damiano Spadoni (Mon Jan 25 2016 - 02:58:13 PST)
[AMBER] Running simulations in parallel Aishani Prem (Mon Jan 25 2016 - 10:19:13 PST)
- Re: [AMBER] Running simulations in parallel Daniel Roe (Mon Jan 25 2016 - 11:03:59 PST)
- Re: [AMBER] Running simulations in parallel Jason Swails (Mon Jan 25 2016 - 14:32:45 PST)
[AMBER] restraints in simulations Lara rajam (Mon Jan 25 2016 - 10:23:04 PST)
- Re: [AMBER] restraints in simulations Jason Swails (Tue Jan 26 2016 - 04:50:18 PST)
  - Re: [AMBER] restraints in simulations Lara rajam (Tue Jan 26 2016 - 07:27:42 PST)
    - Re: [AMBER] restraints in simulations Jason Swails (Tue Jan 26 2016 - 07:49:26 PST)
    - Re: [AMBER] restraints in simulations Carlos Simmerling (Tue Jan 26 2016 - 08:53:48 PST)
    - Re: [AMBER] restraints in simulations Lara rajam (Tue Jan 26 2016 - 10:08:56 PST)
[AMBER] General question on applying restraints during production MD George Tzotzos (Tue Jan 26 2016 - 02:16:26 PST)
- Re: [AMBER] General question on applying restraints during production MD Jason Swails (Tue Jan 26 2016 - 04:57:58 PST)
[AMBER] Question about LJ_1264 for Eu3+? Chris (Tue Jan 26 2016 - 07:15:24 PST)
- Re: [AMBER] Question about LJ_1264 for Eu3+? Pengfei Li (Tue Jan 26 2016 - 08:45:21 PST)
[AMBER] Right metal ion model anu chandra (Tue Jan 26 2016 - 08:34:26 PST)
- Re: [AMBER] Right metal ion model Pengfei Li (Tue Jan 26 2016 - 08:39:13 PST)
  - Re: [AMBER] Right metal ion model anu chandra (Tue Jan 26 2016 - 11:41:44 PST)
[AMBER] setup for non-periodic system Covington, Cody Lance (Tue Jan 26 2016 - 13:01:00 PST)
- Re: [AMBER] setup for non-periodic system Jason Swails (Tue Jan 26 2016 - 14:26:13 PST)
[AMBER] PCA richa anand (Wed Jan 27 2016 - 01:18:11 PST)
- Re: [AMBER] PCA Hannes Loeffler (Wed Jan 27 2016 - 01:40:26 PST)
[AMBER] RMSD w.r.t reference structure richa anand (Wed Jan 27 2016 - 01:24:02 PST)
- Re: [AMBER] RMSD w.r.t reference structure Vasantha Kumar (Wed Jan 27 2016 - 03:21:53 PST)
- Re: [AMBER] RMSD w.r.t reference structure Daniel Roe (Wed Jan 27 2016 - 06:53:22 PST)
[AMBER] 3DRISM: erratic values for partial molar volume Josh Berryman (Wed Jan 27 2016 - 02:05:15 PST)
- Re: [AMBER] 3DRISM: erratic values for partial molar volume Josh Berryman (Mon Feb 01 2016 - 05:16:01 PST)
  - Re: [AMBER] 3DRISM: erratic values for partial molar volume Tyler Luchko (Lists) (Wed Feb 03 2016 - 11:30:39 PST)
[AMBER] two elongated bonds while visualuizing prmtop and inprcd in vmd Nida Baig (Wed Jan 27 2016 - 03:05:38 PST)
- Re: [AMBER] two elongated bonds while visualuizing prmtop and inprcd in vmd Jason Swails (Wed Jan 27 2016 - 06:03:59 PST)
[AMBER] cpptraj molsurf error anu chandra (Wed Jan 27 2016 - 04:23:06 PST)
- Re: [AMBER] cpptraj molsurf error Daniel Roe (Wed Jan 27 2016 - 10:26:52 PST)
[AMBER] atom clash and close contact after MD simulation in water Vasantha Kumar (Wed Jan 27 2016 - 05:50:41 PST)
- Re: [AMBER] atom clash and close contact after MD simulation in water Jacopo Sgrignani (Wed Jan 27 2016 - 06:03:05 PST)
- Re: [AMBER] atom clash and close contact after MD simulation in water Carlos Simmerling (Wed Jan 27 2016 - 06:33:36 PST)
  - Re: [AMBER] atom clash and close contact after MD simulation in water Vasantha Kumar (Wed Jan 27 2016 - 08:40:14 PST)
    - Re: [AMBER] atom clash and close contact after MD simulation in water Vasantha Kumar (Wed Jan 27 2016 - 08:48:44 PST)
[AMBER] free energy calculation of folding Asmita Gupta (Thu Jan 28 2016 - 04:14:33 PST)
- Re: [AMBER] free energy calculation of folding Jason Swails (Thu Jan 28 2016 - 08:55:17 PST)
  - Re: [AMBER] free energy calculation of folding Asmita Gupta (Fri Jan 29 2016 - 00:50:05 PST)
    - Re: [AMBER] free energy calculation of folding Jason Swails (Fri Jan 29 2016 - 07:02:17 PST)
    - Re: [AMBER] free energy calculation of folding Carlos Simmerling (Fri Jan 29 2016 - 07:15:13 PST)
    - Re: [AMBER] free energy calculation of folding Josh Berryman (Wed Feb 03 2016 - 04:06:21 PST)
[AMBER] Error Message Wong Li Zhe (Thu Jan 28 2016 - 19:07:41 PST)
- Re: [AMBER] Error Message Jason Swails (Fri Jan 29 2016 - 07:05:16 PST)
[AMBER] Help to choose best-fit ion model anu chandra (Fri Jan 29 2016 - 06:26:39 PST)
- [AMBER] Cpptraj Filter of Radius of gyration josephine (Fri Jan 29 2016 - 07:02:19 PST)
  - Re: [AMBER] Cpptraj Filter of Radius of gyration Daniel Roe (Fri Jan 29 2016 - 07:35:14 PST)
- Re: [AMBER] Help to choose best-fit ion model Pengfei Li (Fri Jan 29 2016 - 07:15:26 PST)
  - Re: [AMBER] Help to choose best-fit ion model anu chandra (Fri Jan 29 2016 - 14:56:07 PST)
    - Re: [AMBER] Help to choose best-fit ion model Pengfei Li (Wed Feb 03 2016 - 08:17:48 PST)
    - Re: [AMBER] Help to choose best-fit ion model Pengfei Li (Wed Feb 03 2016 - 08:37:06 PST)
[AMBER] aMD with two component Khabiri, Morteza (Fri Jan 29 2016 - 10:26:47 PST)
[AMBER] Wrong or no center in RdPar. Fatemeh Sadat Alavi (Sun Jan 31 2016 - 22:25:38 PST)
- Re: [AMBER] Wrong or no center in RdPar. Jason Swails (Mon Feb 01 2016 - 06:08:54 PST)
- Re: [AMBER] Wrong or no center in RdPar. Ruixing Wang (Mon Feb 01 2016 - 17:54:51 PST)
[AMBER] Replacement for xmgrace Jean-Patrick Francoia (Mon Feb 01 2016 - 01:48:31 PST)
- Re: [AMBER] Replacement for xmgrace Andrea Spitaleri (Mon Feb 01 2016 - 01:52:01 PST)
  - Re: [AMBER] Replacement for xmgrace Jean-Patrick Francoia (Mon Feb 01 2016 - 02:17:42 PST)
    - Re: [AMBER] Replacement for xmgrace Vasantha Kumar (Mon Feb 01 2016 - 02:51:52 PST)
    - Re: [AMBER] Replacement for xmgrace Bill Ross (Mon Feb 01 2016 - 02:58:55 PST)
- Re: [AMBER] Replacement for xmgrace Hannes Loeffler (Mon Feb 01 2016 - 02:13:11 PST)
- Re: [AMBER] Replacement for xmgrace Lorenzo Gontrani (Mon Feb 01 2016 - 03:26:39 PST)
  - Re: [AMBER] Replacement for xmgrace David A Case (Mon Feb 01 2016 - 05:08:48 PST)
    - Re: [AMBER] Replacement for xmgrace Jean-Patrick Francoia (Mon Feb 01 2016 - 05:57:41 PST)
    - Re: [AMBER] Replacement for xmgrace Jason Swails (Mon Feb 01 2016 - 06:05:48 PST)
    - Re: [AMBER] Replacement for xmgrace Jean-Patrick Francoia (Mon Feb 01 2016 - 06:32:41 PST)
    - Re: [AMBER] Replacement for xmgrace Jason Swails (Mon Feb 01 2016 - 06:36:39 PST)
    - Re: [AMBER] Replacement for xmgrace Jean-Patrick Francoia (Mon Feb 01 2016 - 06:52:42 PST)
    - Re: [AMBER] Replacement for xmgrace Jason Swails (Mon Feb 01 2016 - 08:27:51 PST)
    - Re: [AMBER] Replacement for xmgrace Jean-Patrick Francoia (Mon Feb 01 2016 - 11:27:13 PST)
    - Re: [AMBER] Replacement for xmgrace Hai Nguyen (Mon Feb 01 2016 - 11:32:26 PST)
    - Re: [AMBER] Replacement for xmgrace Jason Swails (Mon Feb 01 2016 - 11:53:43 PST)
    - Re: [AMBER] Replacement for xmgrace Jean-Patrick Francoia (Mon Feb 01 2016 - 12:46:13 PST)
    - Re: [AMBER] Replacement for xmgrace Hai Nguyen (Mon Feb 01 2016 - 09:09:55 PST)
[AMBER] Value of ntrx=7 Krantzman, Kristin D (Mon Feb 01 2016 - 11:50:21 PST)
- Re: [AMBER] Value of ntrx=7 Jason Swails (Mon Feb 01 2016 - 11:55:43 PST)
  - Re: [AMBER] Value of ntrx=7 Krantzman, Kristin D (Mon Feb 01 2016 - 12:02:09 PST)
    - Re: [AMBER] Value of ntrx=7 Jason Swails (Mon Feb 01 2016 - 12:58:35 PST)
[AMBER] Segmentation fault when converting charmm to amber toppar using chamber Gary Zhang (Mon Feb 01 2016 - 13:09:27 PST)
- Re: [AMBER] Segmentation fault when converting charmm to amber toppar using chamber Jason Swails (Mon Feb 01 2016 - 15:08:07 PST)
  - Re: [AMBER] Segmentation fault when converting charmm to amber toppar using chamber Gary Zhang (Tue Feb 02 2016 - 06:53:12 PST)
[AMBER] amber14 update Carlos Romero (Mon Feb 01 2016 - 16:50:14 PST)
[AMBER] SP3 Nitrogen planarity issue with ff14SB Prayagraj Fandilolu (Mon Feb 01 2016 - 20:15:17 PST)
- Re: [AMBER] SP3 Nitrogen planarity issue with ff14SB Jason Swails (Tue Feb 02 2016 - 04:13:22 PST)
  - Re: [AMBER] SP3 Nitrogen planarity issue with ff14SB Prayagraj Fandilolu (Sat Feb 27 2016 - 01:07:48 PST)
    - Re: [AMBER] SP3 Nitrogen planarity issue with ff14SB Lorenzo Gontrani (Sat Feb 27 2016 - 01:14:11 PST)
    - Re: [AMBER] SP3 Nitrogen planarity issue with ff14SB Prayagraj Fandilolu (Sat Feb 27 2016 - 01:40:09 PST)
    - Re: [AMBER] SP3 Nitrogen planarity issue with ff14SB Carlos Simmerling (Sat Feb 27 2016 - 04:34:40 PST)
    - Re: [AMBER] SP3 Nitrogen planarity issue with ff14SB Prayagraj Fandilolu (Sat Feb 27 2016 - 05:00:30 PST)
    - Re: [AMBER] SP3 Nitrogen planarity issue with ff14SB Carlos Simmerling (Sat Feb 27 2016 - 05:17:51 PST)
    - Re: [AMBER] SP3 Nitrogen planarity issue with ff14SB Prayagraj Fandilolu (Sat Feb 27 2016 - 23:53:20 PST)
    - Re: [AMBER] SP3 Nitrogen planarity issue with ff14SB Carlos Simmerling (Sun Feb 28 2016 - 06:20:38 PST)
    - Re: [AMBER] SP3 Nitrogen planarity issue with ff14SB Prayagraj Fandilolu (Mon Feb 29 2016 - 21:37:14 PST)
    - Re: [AMBER] SP3 Nitrogen planarity issue with ff14SB Carlos Simmerling (Tue Mar 01 2016 - 16:49:22 PST)
    - Re: [AMBER] SP3 Nitrogen planarity issue with ff14SB Prayagraj Fandilolu (Wed Mar 02 2016 - 01:48:07 PST)
    - Re: [AMBER] SP3 Nitrogen planarity issue with ff14SB David A Case (Wed Mar 02 2016 - 04:54:58 PST)
    - Re: [AMBER] SP3 Nitrogen planarity issue with ff14SB Prayagraj Fandilolu (Mon Mar 21 2016 - 22:28:16 PDT)
    - Re: [AMBER] SP3 Nitrogen planarity issue with ff14SB Carlos Simmerling (Tue Mar 22 2016 - 04:30:13 PDT)
    - Re: [AMBER] SP3 Nitrogen planarity issue with ff14SB Prayagraj Fandilolu (Wed Mar 30 2016 - 20:13:23 PDT)
    - Re: [AMBER] SP3 Nitrogen planarity issue with ff14SB Carlos Simmerling (Thu Mar 31 2016 - 02:51:51 PDT)
- Re: [AMBER] SP3 Nitrogen planarity issue with ff14SB Carlos Simmerling (Tue Feb 02 2016 - 04:26:46 PST)
[AMBER] Regaridng FIle preparation in AMBERTOOLS14 Sivanandam M (Tue Feb 02 2016 - 01:24:26 PST)
- Re: [AMBER] Regaridng FIle preparation in AMBERTOOLS14 A kS (Tue Feb 02 2016 - 01:32:11 PST)
- Re: [AMBER] Regaridng FIle preparation in AMBERTOOLS14 David A Case (Tue Feb 02 2016 - 04:57:21 PST)
[AMBER] Question about mask command A kS (Tue Feb 02 2016 - 01:28:24 PST)
- Re: [AMBER] Question about mask command Daniel Roe (Tue Feb 02 2016 - 07:27:52 PST)
  - Re: [AMBER] Question about mask command Daniel Roe (Wed Feb 03 2016 - 08:17:53 PST)
[AMBER] Dear All ankita mehta (Tue Feb 02 2016 - 03:18:52 PST)
- Re: [AMBER] Dear All Jason Swails (Tue Feb 02 2016 - 04:20:11 PST)
  - Re: [AMBER] Dear All ankita mehta (Tue Feb 02 2016 - 04:29:56 PST)
    - Re: [AMBER] Dear All Carlos Simmerling (Tue Feb 02 2016 - 04:43:48 PST)
  - Re: [AMBER] Dear All David A Case (Tue Feb 02 2016 - 04:59:43 PST)
[AMBER] Amber/tutorial/advanced/tutorial16/ zoran matovic (Tue Feb 02 2016 - 06:10:42 PST)
- Re: [AMBER] Amber/tutorial/advanced/tutorial16/ JEAN MARC BILLOD (Tue Feb 02 2016 - 06:52:24 PST)
  - Re: [AMBER] Amber/tutorial/advanced/tutorial16/ zoran matovic (Tue Feb 02 2016 - 07:44:56 PST)
- Re: [AMBER] Amber/tutorial/advanced/tutorial16/ zoran matovic (Tue Feb 02 2016 - 09:09:04 PST)
[AMBER] MMPBSA ImportError Joseph Baker (Tue Feb 02 2016 - 18:25:51 PST)
- Re: [AMBER] MMPBSA ImportError Joseph Baker (Tue Feb 02 2016 - 21:02:11 PST)
  - Re: [AMBER] MMPBSA ImportError Jason Swails (Wed Feb 03 2016 - 04:49:51 PST)
    - Re: [AMBER] MMPBSA ImportError Josh Berryman (Wed Feb 03 2016 - 05:33:45 PST)
    - Re: [AMBER] MMPBSA ImportError Jason Swails (Wed Feb 03 2016 - 05:41:21 PST)
    - Re: [AMBER] MMPBSA ImportError David A Case (Wed Feb 03 2016 - 12:16:57 PST)
    - Re: [AMBER] MMPBSA ImportError Joseph Baker (Thu Feb 04 2016 - 13:54:11 PST)
    - Re: [AMBER] MMPBSA ImportError David A Case (Thu Feb 04 2016 - 14:50:28 PST)
    - Re: [AMBER] MMPBSA ImportError Joseph Baker (Thu Feb 04 2016 - 15:06:02 PST)
    - Re: [AMBER] MMPBSA ImportError Jason Swails (Thu Feb 04 2016 - 19:22:55 PST)
    - Re: [AMBER] MMPBSA ImportError Joseph Baker (Fri Feb 05 2016 - 03:51:13 PST)
    - Re: [AMBER] MMPBSA ImportError Jason Swails (Fri Feb 05 2016 - 05:13:47 PST)
    - Re: [AMBER] MMPBSA ImportError Ross Walker (Fri Feb 05 2016 - 16:46:19 PST)
    - Re: [AMBER] MMPBSA ImportError Joseph Baker (Fri Feb 05 2016 - 17:57:00 PST)
    - Re: [AMBER] MMPBSA ImportError Jason Swails (Fri Feb 05 2016 - 18:49:18 PST)
    - Re: [AMBER] MMPBSA ImportError Ross Walker (Sat Feb 06 2016 - 09:31:12 PST)
    - Re: [AMBER] MMPBSA ImportError Jason Swails (Fri Feb 05 2016 - 18:45:13 PST)
    - Re: [AMBER] MMPBSA ImportError Ross Walker (Sat Feb 06 2016 - 09:29:57 PST)
    - Re: [AMBER] MMPBSA ImportError zoran matovic (Sat Feb 06 2016 - 10:10:28 PST)
    - Re: [AMBER] MMPBSA ImportError Jason Swails (Sat Feb 06 2016 - 18:53:24 PST)
    - Re: [AMBER] MMPBSA ImportError Ross Walker (Sun Feb 07 2016 - 09:36:08 PST)
    - Re: [AMBER] MMPBSA ImportError zoran matovic (Sun Feb 07 2016 - 10:40:44 PST)
[AMBER] standard deviation of rmsd values Atila Petrosian (Tue Feb 02 2016 - 23:39:04 PST)
- Re: [AMBER] standard deviation of rmsd values Jason Swails (Wed Feb 03 2016 - 05:49:31 PST)
- Re: [AMBER] standard deviation of rmsd values Daniel Roe (Wed Feb 03 2016 - 05:50:43 PST)
[AMBER] Dihedral angles restraints from x-ray to NMR Vasantha Kumar (Wed Feb 03 2016 - 02:52:59 PST)
- Re: [AMBER] Dihedral angles restraints from x-ray to NMR Carlos Simmerling (Wed Feb 03 2016 - 04:32:51 PST)
- Re: [AMBER] Dihedral angles restraints from x-ray to NMR David A Case (Wed Feb 03 2016 - 04:49:47 PST)
  - Re: [AMBER] Dihedral angles restraints from x-ray to NMR Vasantha Kumar (Wed Feb 03 2016 - 05:00:09 PST)
[AMBER] Size of solvent box Krantzman, Kristin D (Wed Feb 03 2016 - 09:27:20 PST)
- Re: [AMBER] Size of solvent box Jason Swails (Wed Feb 03 2016 - 10:31:23 PST)
  - Re: [AMBER] Size of solvent box Carlos Simmerling (Wed Feb 03 2016 - 10:38:24 PST)
[AMBER] Problems with when using DFTB halorg .skf files in sqm Marc van der Kamp (Thu Feb 04 2016 - 04:37:42 PST)
- Re: [AMBER] Problems with when using DFTB halorg .skf files in sqm Gustavo Seabra (Thu Feb 04 2016 - 05:28:07 PST)
  - Re: [AMBER] Problems with when using DFTB halorg .skf files in sqm Marc van der Kamp (Thu Feb 04 2016 - 06:08:00 PST)
  - Re: [AMBER] Problems with when using DFTB halorg .skf files in sqm David A Case (Thu Feb 04 2016 - 11:01:32 PST)
Re: [AMBER] Size of solvent box, RDF Krantzman, Kristin D (Thu Feb 04 2016 - 10:42:50 PST)
- Re: [AMBER] Size of solvent box, RDF Carlos Simmerling (Fri Feb 05 2016 - 04:10:05 PST)
  - Re: [AMBER] Size of solvent box, RDF Krantzman, Kristin D (Fri Feb 05 2016 - 09:44:27 PST)
    - Re: [AMBER] Size of solvent box, RDF Jason Swails (Fri Feb 05 2016 - 10:36:16 PST)
    - Re: [AMBER] Size of solvent box, RDF Carlos Simmerling (Fri Feb 05 2016 - 10:42:01 PST)
    - Re: [AMBER] Size of solvent box, RDF Krantzman, Kristin D (Fri Feb 05 2016 - 14:31:26 PST)
    - Re: [AMBER] Size of solvent box, RDF Jason Swails (Fri Feb 05 2016 - 18:52:18 PST)
[AMBER] Regarding MMGBSA calculation neha chaudhary (Thu Feb 04 2016 - 23:48:24 PST)
- Re: [AMBER] Regarding MMGBSA calculation Jason Swails (Fri Feb 05 2016 - 04:58:33 PST)
- Re: [AMBER] Regarding MMGBSA calculation David A Case (Fri Feb 05 2016 - 05:05:07 PST)
  - Re: [AMBER] Regarding MMGBSA calculation neha chaudhary (Fri Feb 05 2016 - 23:20:28 PST)
    - Re: [AMBER] Regarding MMGBSA calculation David A Case (Sat Feb 06 2016 - 05:24:34 PST)
    - Re: [AMBER] Regarding MMGBSA calculation neha chaudhary (Thu Feb 11 2016 - 02:45:44 PST)
    - Re: [AMBER] Regarding MMGBSA calculation David A Case (Thu Feb 11 2016 - 04:45:22 PST)
    - Re: [AMBER] Regarding MMGBSA calculation Daniel Roe (Thu Feb 11 2016 - 07:22:49 PST)
[AMBER] Zero pressure with pmemd.cuda Batuhan Kav (Fri Feb 05 2016 - 08:10:57 PST)
- Re: [AMBER] Zero pressure with pmemd.cuda Ross Walker (Fri Feb 05 2016 - 09:03:06 PST)
- Re: [AMBER] Zero pressure with pmemd.cuda Jason Swails (Fri Feb 05 2016 - 10:27:14 PST)
[AMBER] accelerated MD - frequency of conformational change Weinzierl, Robert O J (Fri Feb 05 2016 - 09:54:33 PST)
- Re: [AMBER] accelerated MD - frequency of conformational change Daniel Roe (Fri Feb 05 2016 - 10:00:58 PST)
Re: [AMBER] Wrong or no center in RdPar Fatemeh Sadat Alavi (Sat Feb 06 2016 - 01:05:38 PST)
[AMBER] Z-constraint PMF method zoran matovic (Sat Feb 06 2016 - 05:32:26 PST)
- Re: [AMBER] Z-constraint PMF method zoran matovic (Sun Feb 07 2016 - 10:28:20 PST)
  - Re: [AMBER] Z-constraint PMF method Jason Swails (Sun Feb 07 2016 - 12:50:03 PST)
    - Re: [AMBER] Z-constraint PMF method zoran matovic (Sun Feb 07 2016 - 13:07:50 PST)
    - Re: [AMBER] Z-constraint PMF method Dickson, Callum J (Mon Feb 08 2016 - 06:36:22 PST)
    - Re: [AMBER] Z-constraint PMF method Adrian Roitberg (Mon Feb 08 2016 - 06:38:30 PST)
    - Re: [AMBER] Z-constraint PMF method zoran matovic (Mon Feb 08 2016 - 07:01:47 PST)
[AMBER] aMD Secondary Structure Weinzierl, Robert O J (Sun Feb 07 2016 - 03:12:57 PST)
- Re: [AMBER] aMD Secondary Structure Jason Swails (Sun Feb 07 2016 - 12:54:34 PST)
[AMBER] error in minimization whole system Fatemeh Sadat Alavi (Sun Feb 07 2016 - 04:26:32 PST)
- Re: [AMBER] error in minimization whole system David A Case (Sun Feb 07 2016 - 05:24:44 PST)
[AMBER] Question about AmberTools14/15 installation A kS (Mon Feb 08 2016 - 00:15:28 PST)
- Re: [AMBER] Question about AmberTools14/15 installation Jason Swails (Mon Feb 08 2016 - 05:15:05 PST)
  - Re: [AMBER] Question about AmberTools14/15 installation A kS (Tue Feb 09 2016 - 11:10:03 PST)
    - Re: [AMBER] Question about AmberTools14/15 installation Jason Swails (Tue Feb 09 2016 - 11:18:41 PST)
    - Re: [AMBER] Question about AmberTools14/15 installation A kS (Tue Feb 09 2016 - 21:33:12 PST)
- Re: [AMBER] Question about AmberTools14/15 installation Novosielski, Ryan (Mon Feb 08 2016 - 07:41:10 PST)
[AMBER] Steered MD of membrane proteins Ofir Tal (Mon Feb 08 2016 - 01:14:04 PST)
[AMBER] Error atommask selectElemMask Ruth Helena Tichauer (Mon Feb 08 2016 - 05:36:38 PST)
- Re: [AMBER] Error atommask selectElemMask Jason Swails (Mon Feb 08 2016 - 05:42:07 PST)
  - Re: [AMBER] Error atommask selectElemMask Ruth Helena Tichauer (Mon Feb 08 2016 - 05:44:48 PST)
[AMBER] Getting and keeping ACPYPE updated Alan (Tue Feb 09 2016 - 03:33:03 PST)
- Re: [AMBER] Getting and keeping ACPYPE updated David A Case (Tue Feb 16 2016 - 11:01:46 PST)
[AMBER] Is the Force Constant in the Parm**.dat file derived from a mass-weighted Hessian Thomas Collier (Tue Feb 09 2016 - 03:56:15 PST)
- Re: [AMBER] Is the Force Constant in the Parm**.dat file derived from a mass-weighted Hessian Jason Swails (Tue Feb 09 2016 - 04:39:37 PST)
  - Re: [AMBER] Is the Force Constant in the Parm**.dat file derived from a mass-weighted Hessian Nash, Anthony (Tue Feb 09 2016 - 05:34:52 PST)
[AMBER] Parameter for Aspartic Acid-Lysine Cyclic peptide Mohammed Khaled Tumbi (Tue Feb 09 2016 - 06:44:18 PST)
- Re: [AMBER] Parameter for Aspartic Acid-Lysine Cyclic peptide Carlos Simmerling (Tue Feb 09 2016 - 06:55:11 PST)
- Re: [AMBER] Parameter for Aspartic Acid-Lysine Cyclic peptide Mohammed Khaled Tumbi (Wed Feb 10 2016 - 04:12:04 PST)
  - Re: [AMBER] Parameter for Aspartic Acid-Lysine Cyclic peptide Carlos Simmerling (Wed Feb 10 2016 - 04:52:14 PST)
    - Re: [AMBER] Parameter for Aspartic Acid-Lysine Cyclic peptide Dr. Anselm Horn (Wed Feb 10 2016 - 06:31:13 PST)
[AMBER] Parameter for Aspartic Acid-Lysine Cyclic peptide Mohammed Khaled Tumbi (Tue Feb 09 2016 - 07:05:26 PST)
[AMBER] problem with energy minimization (sander) Maryam Hamzehee (Wed Feb 10 2016 - 04:26:06 PST)
- Re: [AMBER] problem with energy minimization (sander) Jason Swails (Wed Feb 10 2016 - 04:44:28 PST)
  - Re: [AMBER] problem with energy minimization (sander) Maryam Hamzehee (Wed Feb 10 2016 - 05:13:27 PST)
    - Re: [AMBER] problem with energy minimization (sander) Jason Swails (Wed Feb 10 2016 - 05:49:07 PST)
[AMBER] citrulline parameters Marie Brut (Wed Feb 10 2016 - 06:13:46 PST)
- Re: [AMBER] citrulline parameters Karl Kirschner (Wed Feb 10 2016 - 06:36:11 PST)
  - Re: [AMBER] citrulline parameters Marie Brut (Wed Feb 10 2016 - 12:06:11 PST)
[AMBER] MMPB (GB) SA cpptraj failed with prmtop Arati Paudyal (Wed Feb 10 2016 - 06:39:53 PST)
- Re: [AMBER] MMPB (GB) SA cpptraj failed with prmtop Jason Swails (Wed Feb 10 2016 - 07:12:59 PST)
  - Re: [AMBER] MMPB (GB) SA cpptraj failed with prmtop Arati Paudyal (Wed Feb 10 2016 - 07:26:28 PST)
    - Re: [AMBER] MMPB (GB) SA cpptraj failed with prmtop Daniel Roe (Wed Feb 10 2016 - 07:37:15 PST)
    - Re: [AMBER] MMPB (GB) SA cpptraj failed with prmtop Arati Paudyal (Wed Feb 10 2016 - 07:53:40 PST)
    - Re: [AMBER] MMPB (GB) SA cpptraj failed with prmtop Daniel Roe (Wed Feb 10 2016 - 08:00:40 PST)
    - Re: [AMBER] MMPB (GB) SA cpptraj failed with prmtop Jason Swails (Wed Feb 10 2016 - 09:00:58 PST)
    - Re: [AMBER] MMPB (GB) SA cpptraj failed with prmtop Arati Paudyal (Wed Feb 10 2016 - 15:42:47 PST)
    - Re: [AMBER] MMPB (GB) SA cpptraj failed with prmtop Jason Swails (Wed Feb 10 2016 - 18:15:44 PST)
    - Re: [AMBER] MMPB (GB) SA cpptraj failed with prmtop Arati Paudyal (Thu Feb 11 2016 - 04:47:00 PST)
    - Re: [AMBER] MMPB (GB) SA cpptraj failed with prmtop Jason Swails (Thu Feb 11 2016 - 04:50:09 PST)
[AMBER] PDB to distance in AMBER Vasantha Kumar (Wed Feb 10 2016 - 07:39:57 PST)
- Re: [AMBER] PDB to distance in AMBER Hai Nguyen (Wed Feb 10 2016 - 07:51:54 PST)
  - Re: [AMBER] PDB to distance in AMBER Vasantha Kumar (Mon Feb 15 2016 - 02:30:34 PST)
[AMBER] Normalizing histogram with CPPTRAJ anu chandra (Wed Feb 10 2016 - 09:05:25 PST)
- Re: [AMBER] Normalizing histogram with CPPTRAJ Daniel Roe (Wed Feb 10 2016 - 09:25:40 PST)
[AMBER] Gist Installation in Amber12 Mongam Riba (Wed Feb 10 2016 - 22:39:15 PST)
- Re: [AMBER] Gist Installation in Amber12 David A Case (Thu Feb 11 2016 - 04:17:03 PST)
[AMBER] minimization error : segmentation fault Saman Yousuf ali (Wed Feb 10 2016 - 23:34:09 PST)
- Re: [AMBER] minimization error : segmentation fault Bill Ross (Wed Feb 10 2016 - 23:39:50 PST)
[AMBER] Is there a way to compare trajectories? Karolina Markowska (Thu Feb 11 2016 - 01:07:01 PST)
- Re: [AMBER] Is there a way to compare trajectories? Bill Ross (Thu Feb 11 2016 - 01:19:49 PST)
- Re: [AMBER] Is there a way to compare trajectories? Dr. Anselm Horn (Thu Feb 11 2016 - 01:27:03 PST)
  - Re: [AMBER] Is there a way to compare trajectories? Karolina Markowska (Thu Feb 11 2016 - 01:44:52 PST)
    - Re: [AMBER] Is there a way to compare trajectories? Osman, Roman (Thu Feb 11 2016 - 07:40:50 PST)
    - Re: [AMBER] Is there a way to compare trajectories? Karolina Markowska (Fri Feb 12 2016 - 00:25:39 PST)
    - Re: [AMBER] Is there a way to compare trajectories? Marc van der Kamp (Fri Feb 12 2016 - 01:20:51 PST)
    - Re: [AMBER] Is there a way to compare trajectories? Karolina Markowska (Fri Feb 12 2016 - 02:41:05 PST)
    - Re: [AMBER] Is there a way to compare trajectories? Daniel Roe (Fri Feb 12 2016 - 02:48:00 PST)
  - Re: [AMBER] Is there a way to compare trajectories? Carlos Simmerling (Thu Feb 11 2016 - 03:15:39 PST)
    - Re: [AMBER] Is there a way to compare trajectories? Karolina Markowska (Thu Feb 11 2016 - 03:27:46 PST)
    - Re: [AMBER] Is there a way to compare trajectories? Daniel Roe (Thu Feb 11 2016 - 07:20:04 PST)
    - Re: [AMBER] Is there a way to compare trajectories? Mohammed Khaled Tumbi (Thu Feb 11 2016 - 03:30:50 PST)
[AMBER] Restarting a heating simulation Elisa Pieri (Thu Feb 11 2016 - 02:43:50 PST)
- Re: [AMBER] Restarting a heating simulation David A Case (Thu Feb 11 2016 - 04:50:39 PST)
- Re: [AMBER] Restarting a heating simulation Jason Swails (Thu Feb 11 2016 - 05:00:24 PST)
  - Re: [AMBER] Restarting a heating simulation Elisa Pieri (Thu Feb 11 2016 - 05:05:21 PST)
    - Re: [AMBER] Restarting a heating simulation Carlos Simmerling (Thu Feb 11 2016 - 05:14:29 PST)
[AMBER] Amber 14 w/ CUDA - unclear "make test"-errors Falko Jähnert (Thu Feb 11 2016 - 04:36:50 PST)
- Re: [AMBER] Amber 14 w/ CUDA - unclear "make test"-errors Jason Swails (Thu Feb 11 2016 - 05:03:19 PST)
  - Re: [AMBER] Amber 14 w/ CUDA - unclear "make test"-errors Falko Jähnert (Thu Feb 11 2016 - 05:37:32 PST)
  - Re: [AMBER] Amber 14 w/ CUDA - unclear "make test"-errors Ross Walker (Thu Feb 11 2016 - 07:31:54 PST)
    - Re: [AMBER] Amber 14 w/ CUDA - unclear "make test"-errors Jason Swails (Thu Feb 11 2016 - 08:04:12 PST)
    - Re: [AMBER] Amber 14 w/ CUDA - unclear "make test"-errors Falko Jähnert (Thu Feb 11 2016 - 13:40:10 PST)
  - Re: [AMBER] Amber 14 w/ CUDA - unclear "make test"-errors Ross Walker (Thu Feb 11 2016 - 07:29:26 PST)
    - [AMBER] Quasi-harmonic Calculations Aronica, Pietro (Thu Feb 11 2016 - 07:34:56 PST)
    - Re: [AMBER] Quasi-harmonic Calculations Jason Swails (Thu Feb 11 2016 - 08:42:57 PST)
    - Re: [AMBER] Quasi-harmonic Calculations Daniel Roe (Thu Feb 11 2016 - 09:20:48 PST)
[AMBER] Unable to run QM/MM with RNA and sodium ion kaushik chakraborty (Thu Feb 11 2016 - 08:57:39 PST)
- Re: [AMBER] Unable to run QM/MM with RNA and sodium ion David A Case (Thu Feb 11 2016 - 14:33:38 PST)
[AMBER] interpret results Carlos Romero (Thu Feb 11 2016 - 09:27:08 PST)
[AMBER] Error: Bad > topology file. Batuhan Kav (Thu Feb 11 2016 - 11:56:50 PST)
- Re: [AMBER] Error: Bad > topology file. Daniel Roe (Thu Feb 11 2016 - 12:07:50 PST)
  - Re: [AMBER] Error: Bad > topology file. Batuhan Kav (Thu Feb 11 2016 - 12:24:54 PST)
    - Re: [AMBER] Error: Bad > topology file. Jason Swails (Thu Feb 11 2016 - 12:48:51 PST)
[AMBER] cpptraj nativecontacts. George Tzotzos (Thu Feb 11 2016 - 13:49:58 PST)
- Re: [AMBER] cpptraj nativecontacts. Daniel Roe (Thu Feb 11 2016 - 15:10:21 PST)
  - Re: [AMBER] cpptraj nativecontacts. George Tzotzos (Thu Feb 11 2016 - 15:38:34 PST)
    - Re: [AMBER] cpptraj nativecontacts. Daniel Roe (Thu Feb 11 2016 - 15:48:24 PST)
[AMBER] Paramfit, negative bond parameters David Poole (Thu Feb 11 2016 - 15:53:41 PST)
- Re: [AMBER] Paramfit, negative bond parameters Robin Betz (Thu Feb 11 2016 - 16:37:48 PST)
- Re: [AMBER] Paramfit, negative bond parameters David Poole (Fri Feb 12 2016 - 12:25:22 PST)
Re: [AMBER] minimization error : segmentation fault (AMBER Digest, Vol 1483, Issue 1) Saman Yousuf ali (Thu Feb 11 2016 - 21:14:54 PST)
- Re: [AMBER] minimization error : segmentation fault (AMBER Digest, Vol 1483, Issue 1) Bill Ross (Thu Feb 11 2016 - 21:19:43 PST)
  - Re: [AMBER] minimization error : segmentation fault (AMBER Digest, Vol 1483, Issue 1) Saman Yousuf ali (Thu Feb 11 2016 - 21:41:51 PST)
    - Re: [AMBER] minimization error : segmentation fault (AMBER Digest, Vol 1483, Issue 1) Bill Ross (Thu Feb 11 2016 - 22:09:30 PST)
    - Re: [AMBER] minimization error : segmentation fault (AMBER Digest, Vol 1483, Issue 1) Bill Ross (Thu Feb 11 2016 - 22:10:47 PST)
[AMBER] Downloading of Ambertools15 Mongam Riba (Fri Feb 12 2016 - 01:23:22 PST)
- Re: [AMBER] Downloading of Ambertools15 Eiros Zamora, Juan (Fri Feb 12 2016 - 01:40:20 PST)
  - Re: [AMBER] Downloading of Ambertools15 Mongam Riba (Fri Feb 12 2016 - 01:44:33 PST)
    - Re: [AMBER] Downloading of Ambertools15 Marc van der Kamp (Fri Feb 12 2016 - 02:16:07 PST)
[AMBER] Dear all ankita mehta (Fri Feb 12 2016 - 03:03:33 PST)
- Re: [AMBER] Dear all Bill Ross (Fri Feb 12 2016 - 03:36:18 PST)
  - Re: [AMBER] Dear all ankita mehta (Fri Feb 12 2016 - 03:40:22 PST)
    - Re: [AMBER] Dear all Bill Ross (Fri Feb 12 2016 - 03:49:43 PST)
    - Re: [AMBER] Dear all ankita mehta (Fri Feb 12 2016 - 04:10:13 PST)
    - Re: [AMBER] Dear all Bill Ross (Fri Feb 12 2016 - 04:12:50 PST)
    - Re: [AMBER] Dear all ankita mehta (Fri Feb 12 2016 - 04:18:58 PST)
    - Re: [AMBER] Dear all Bill Ross (Fri Feb 12 2016 - 04:40:26 PST)
    - Re: [AMBER] Dear all Jason Swails (Fri Feb 12 2016 - 05:57:48 PST)
- Re: [AMBER] Dear all Gustavo Seabra (Fri Feb 12 2016 - 06:21:49 PST)
  - Re: [AMBER] Dear all ankita mehta (Tue Feb 16 2016 - 02:43:57 PST)
    - Re: [AMBER] Dear all David A Case (Tue Feb 16 2016 - 04:54:27 PST)
    - Re: [AMBER] Dear all ankita mehta (Tue Feb 16 2016 - 21:21:25 PST)
    - Re: [AMBER] Dear all David A Case (Wed Feb 17 2016 - 06:58:56 PST)
[AMBER] Li & Mertz ion parameters Vlad Cojocaru (Fri Feb 12 2016 - 09:51:06 PST)
- Re: [AMBER] Li & Mertz ion parameters Jason Swails (Fri Feb 12 2016 - 14:38:35 PST)
  - Re: [AMBER] Li & Mertz ion parameters Pengfei Li (Sat Feb 13 2016 - 13:29:31 PST)
    - Re: [AMBER] Li & Mertz ion parameters Bill Ross (Sat Feb 13 2016 - 13:34:35 PST)
[AMBER] gpu_allreduce cudaDeviceSynchronize failed an illegal memory access was encountered Sarah Anderson (Fri Feb 12 2016 - 10:42:09 PST)
- Re: [AMBER] gpu_allreduce cudaDeviceSynchronize failed an illegal memory access was encountered Ross Walker (Fri Feb 12 2016 - 11:16:46 PST)
  - Re: [AMBER] gpu_allreduce cudaDeviceSynchronize failed an illegal memory access was encountered Sarah Anderson (Fri Feb 12 2016 - 14:24:10 PST)
    - Re: [AMBER] gpu_allreduce cudaDeviceSynchronize failed an illegal memory access was encountered Ross Walker (Fri Feb 12 2016 - 14:36:23 PST)
    - Re: [AMBER] gpu_allreduce cudaDeviceSynchronize failed an illegal memory access was encountered Sarah Anderson (Fri Feb 12 2016 - 16:58:34 PST)
    - Re: [AMBER] gpu_allreduce cudaDeviceSynchronize failed an illegal memory access was encountered Ross Walker (Fri Feb 12 2016 - 17:03:44 PST)
    - Re: [AMBER] gpu_allreduce cudaDeviceSynchronize failed an illegal memory access was encountered Sarah Anderson (Mon Feb 15 2016 - 09:04:13 PST)
    - Re: [AMBER] gpu_allreduce cudaDeviceSynchronize failed an illegal memory access was encountered Ryan Novosielski (Tue Feb 16 2016 - 06:20:49 PST)
    - Re: [AMBER] gpu_allreduce cudaDeviceSynchronize failed an illegal memory access was encountered Ross Walker (Tue Feb 16 2016 - 06:33:02 PST)
    - Re: [AMBER] gpu_allreduce cudaDeviceSynchronize failed an illegal memory access was encountered Daniel Roe (Sat Feb 13 2016 - 08:18:28 PST)
    - Re: [AMBER] gpu_allreduce cudaDeviceSynchronize failed an illegal memory access was encountered Scott Le Grand (Sat Feb 13 2016 - 08:41:04 PST)
    - Re: [AMBER] gpu_allreduce cudaDeviceSynchronize failed an illegal memory access was encountered Ross Walker (Sat Feb 13 2016 - 10:13:19 PST)
[AMBER] MMPBSA.py.MPI won't recognise mpy4pi Wesley Michael Botello-Smith (Fri Feb 12 2016 - 16:45:14 PST)
- Re: [AMBER] MMPBSA.py.MPI won't recognise mpy4pi Jason Swails (Fri Feb 12 2016 - 17:03:12 PST)
  - Re: [AMBER] MMPBSA.py.MPI won't recognise mpy4pi Wesley Michael Botello-Smith (Sun Feb 14 2016 - 14:58:37 PST)
    - Re: [AMBER] MMPBSA.py.MPI won't recognise mpy4pi Jason Swails (Sun Feb 14 2016 - 16:13:20 PST)
[AMBER] Regarding minimization in AMBER neha chaudhary (Fri Feb 12 2016 - 22:26:18 PST)
- Re: [AMBER] Regarding minimization in AMBER Ross Walker (Fri Feb 12 2016 - 22:47:31 PST)
[AMBER] broken iodine bond problem in NEWPDB.PDB file. Saman Yousuf ali (Fri Feb 12 2016 - 22:30:41 PST)
- Re: [AMBER] broken iodine bond problem in NEWPDB.PDB file. Saman Yousuf ali (Fri Feb 12 2016 - 23:04:20 PST)
  - Re: [AMBER] broken iodine bond problem in NEWPDB.PDB file. Bill Ross (Sat Feb 13 2016 - 11:44:11 PST)
[AMBER] summary.ETOT analysis Michael Shokhen (Sun Feb 14 2016 - 01:47:03 PST)
- Re: [AMBER] summary.ETOT analysis Jason Swails (Sun Feb 14 2016 - 04:14:39 PST)
  - Re: [AMBER] summary.ETOT analysis and MMPBSA.py Michael Shokhen (Sun Feb 14 2016 - 05:10:58 PST)
    - Re: [AMBER] summary.ETOT analysis and MMPBSA.py Jason Swails (Sun Feb 14 2016 - 06:15:24 PST)
    - Re: [AMBER] summary.ETOT analysis and MMPBSA.py George Tzotzos (Sun Feb 14 2016 - 07:09:02 PST)
[AMBER] Fwd: PC square fluctuations Rajeswari A. (Mon Feb 15 2016 - 01:02:24 PST)
- Re: [AMBER] Fwd: PC square fluctuations Daniel Roe (Tue Feb 16 2016 - 07:31:36 PST)
  - Re: [AMBER] Fwd: PC square fluctuations Rajeswari A. (Wed Feb 17 2016 - 03:01:15 PST)
[AMBER] delta G computation (MMPBSA.py) Карлов Дмитрий (Mon Feb 15 2016 - 04:29:11 PST)
[AMBER] average 3D structure with condition Michael Shokhen (Mon Feb 15 2016 - 08:42:05 PST)
- Re: [AMBER] average 3D structure with condition Carlos Simmerling (Mon Feb 15 2016 - 08:54:26 PST)
- Re: [AMBER] average 3D structure with condition Daniel Roe (Mon Feb 15 2016 - 08:59:35 PST)
  - Re: [AMBER] average 3D structure with condition Michael Shokhen (Mon Feb 15 2016 - 10:51:41 PST)
    - Re: [AMBER] average 3D structure with condition Daniel Roe (Mon Feb 15 2016 - 13:22:37 PST)
    - Re: [AMBER] average 3D structure with condition Michael Shokhen (Mon Feb 15 2016 - 14:43:38 PST)
[AMBER] Fw: Hg parameterization nida baig (Mon Feb 15 2016 - 08:43:35 PST)
- Re: [AMBER] Hg parameterization Pengfei Li (Mon Feb 15 2016 - 12:48:33 PST)
[AMBER] want to ask you about PCA plotting Ayesha Kanwal (Tue Feb 16 2016 - 01:58:58 PST)
- Re: [AMBER] want to ask you about PCA plotting Daniel Roe (Tue Feb 16 2016 - 07:26:47 PST)
  - Re: [AMBER] want to ask you about PCA plotting Ayesha Kanwal (Tue Feb 16 2016 - 12:42:08 PST)
[AMBER] Reg: problem in generating prmtop and crd files by using ff12SB of magnesium ions Yogeeshwar Ajjugal (Tue Feb 16 2016 - 04:35:32 PST)
- Re: [AMBER] Reg: problem in generating prmtop and crd files by using ff12SB of magnesium ions David A Case (Tue Feb 16 2016 - 10:22:57 PST)
  - Re: [AMBER] Reg: problem in generating prmtop and crd files by using ff12SB of magnesium ions Yogeeshwar Ajjugal (Tue Feb 16 2016 - 21:10:53 PST)
[AMBER] parmed/chamber problem recognizing atom types Amy Rice (Tue Feb 16 2016 - 10:02:42 PST)
- Re: [AMBER] parmed/chamber problem recognizing atom types Jason Swails (Tue Feb 16 2016 - 18:35:45 PST)
[AMBER] [AMBER} nonpolar term for MMPBSA decomp showing up as 0 Kalenkiewicz, Andrew (NIH/NICHD) [F] (Tue Feb 16 2016 - 11:55:29 PST)
- Re: [AMBER] [AMBER} nonpolar term for MMPBSA decomp showing up as 0 Ray Luo, Ph.D. (Tue Feb 16 2016 - 14:04:45 PST)
[AMBER] how to check protonation state Ayesha Kanwal (Tue Feb 16 2016 - 12:46:13 PST)
- Re: [AMBER] how to check protonation state Carlos Simmerling (Tue Feb 16 2016 - 13:25:01 PST)
[AMBER] unable to generate Mercury parameter file Sehrish Naz Aijaz (Tue Feb 16 2016 - 21:06:51 PST)
- Re: [AMBER] unable to generate Mercury parameter file Bill Ross (Tue Feb 16 2016 - 22:14:09 PST)
- Re: [AMBER] unable to generate Mercury parameter file David A Case (Wed Feb 17 2016 - 06:53:31 PST)
[AMBER] Technical problem running pH-REMD Elisa Pieri (Wed Feb 17 2016 - 06:22:06 PST)
- Re: [AMBER] Technical problem running pH-REMD Adrian Roitberg (Wed Feb 17 2016 - 06:34:26 PST)
  - Re: [AMBER] Technical problem running pH-REMD Elisa Pieri (Wed Feb 17 2016 - 06:53:37 PST)
    - Re: [AMBER] Technical problem running pH-REMD Daniel Roe (Wed Feb 17 2016 - 07:25:10 PST)
    - Re: [AMBER] Technical problem running pH-REMD Elisa Pieri (Wed Feb 17 2016 - 07:35:16 PST)
    - Re: [AMBER] Technical problem running pH-REMD Daniel Roe (Wed Feb 17 2016 - 07:57:09 PST)
- Re: [AMBER] Technical problem running pH-REMD Daniel Roe (Wed Feb 17 2016 - 07:23:50 PST)
[AMBER] cationic-pi interactions Jose luis Borioni (Wed Feb 17 2016 - 19:56:48 PST)
- Re: [AMBER] cationic-pi interactions Jason Swails (Fri Feb 19 2016 - 20:37:02 PST)
[AMBER] A question about cpptraj autoimage 肖立 (Thu Feb 18 2016 - 17:02:17 PST)
- Re: [AMBER] A question about cpptraj autoimage Daniel Roe (Thu Feb 18 2016 - 19:09:23 PST)
[AMBER] membrane potential Balaji Selvam (Thu Feb 18 2016 - 17:22:04 PST)
- Re: [AMBER] membrane potential Dickson, Callum J (Fri Feb 19 2016 - 10:04:06 PST)
[AMBER] antechamber run for FAD 홍종희 (Fri Feb 19 2016 - 02:12:20 PST)
- Re: [AMBER] antechamber run for FAD Hannes Loeffler (Fri Feb 19 2016 - 02:59:02 PST)
[AMBER] Relabeling Atoms after a Run Trajectory Robert Molt (Fri Feb 19 2016 - 06:54:59 PST)
- Re: [AMBER] Relabeling Atoms after a Run Trajectory Thomas Cheatham (Fri Feb 19 2016 - 07:01:02 PST)
  - Re: [AMBER] Relabeling Atoms after a Run Trajectory Robert Molt (Fri Feb 19 2016 - 07:03:20 PST)
- Re: [AMBER] Relabeling Atoms after a Run Trajectory Gustavo Seabra (Fri Feb 19 2016 - 09:57:22 PST)
[AMBER] charge derivation Abelak, Kavin (Fri Feb 19 2016 - 07:48:18 PST)
- Re: [AMBER] charge derivation David A Case (Fri Feb 19 2016 - 09:24:49 PST)
  - Re: [AMBER] charge derivation Abelak, Kavin (Tue Feb 23 2016 - 07:48:51 PST)
    - Re: [AMBER] charge derivation David Cerutti (Tue Feb 23 2016 - 08:04:56 PST)
    - Re: [AMBER] charge derivation Abelak, Kavin (Fri Feb 26 2016 - 02:52:37 PST)
    - Re: [AMBER] charge derivation FyD (Fri Feb 26 2016 - 01:10:17 PST)
    - Re: [AMBER] charge derivation Abelak, Kavin (Fri Feb 26 2016 - 02:41:11 PST)
    - Re: [AMBER] charge derivation FyD (Fri Feb 26 2016 - 02:57:57 PST)
    - Re: [AMBER] charge derivation David Cerutti (Fri Feb 26 2016 - 07:41:10 PST)
[AMBER] Energy decomposition error Renato Freitas (Fri Feb 19 2016 - 13:17:20 PST)
- Re: [AMBER] Energy decomposition error Jason Swails (Fri Feb 19 2016 - 20:34:44 PST)
[AMBER] Covariance Matrix in CPPTRAJ Joel Lapin (Sat Feb 20 2016 - 15:10:46 PST)
- Re: [AMBER] Covariance Matrix in CPPTRAJ Daniel Roe (Sat Feb 20 2016 - 15:40:59 PST)
  - Re: [AMBER] Covariance Matrix in CPPTRAJ Joel Lapin (Sat Feb 20 2016 - 16:29:57 PST)
    - Re: [AMBER] Covariance Matrix in CPPTRAJ Jason Swails (Sat Feb 20 2016 - 17:27:56 PST)
    - Re: [AMBER] Covariance Matrix in CPPTRAJ Joel Lapin (Sat Feb 20 2016 - 17:33:16 PST)
    - Re: [AMBER] Covariance Matrix in CPPTRAJ Joel Lapin (Sat Feb 20 2016 - 19:57:12 PST)
    - Re: [AMBER] Covariance Matrix in CPPTRAJ Daniel Roe (Sun Feb 21 2016 - 06:53:42 PST)
[AMBER] lmod & xmin in sander Jérémie KNOOPS [531802] (Sun Feb 21 2016 - 06:09:47 PST)
- Re: [AMBER] lmod & xmin in sander Daniel Roe (Sun Feb 21 2016 - 06:59:58 PST)
- Re: [AMBER] lmod & xmin in sander David A Case (Mon Feb 22 2016 - 04:47:37 PST)
- Re: [AMBER] lmod & xmin in sander Jérémie KNOOPS [531802] (Tue Feb 23 2016 - 06:11:36 PST)
[AMBER] Defining Units in nastruct Robert Molt (Sun Feb 21 2016 - 15:45:16 PST)
- Re: [AMBER] Defining Units in nastruct Daniel Roe (Tue Feb 23 2016 - 07:49:49 PST)
- [AMBER] Sign of outputs of MMPBSA.py Aronica, Pietro (Thu Mar 03 2016 - 08:02:58 PST)
  - Re: [AMBER] Sign of outputs of MMPBSA.py Jason Swails (Thu Mar 03 2016 - 17:34:31 PST)
[AMBER] KeyError - MCPB.py Taylor, Cooper (Sun Feb 21 2016 - 18:58:44 PST)
- Re: [AMBER] KeyError - MCPB.py Pengfei Li (Mon Feb 22 2016 - 07:10:16 PST)
  - Re: [AMBER] KeyError - MCPB.py Taylor, Cooper (Mon Feb 22 2016 - 07:17:38 PST)
    - Re: [AMBER] KeyError - MCPB.py Pengfei Li (Mon Feb 22 2016 - 07:26:57 PST)
    - Re: [AMBER] KeyError - MCPB.py Pengfei Li (Mon Feb 22 2016 - 07:44:36 PST)
- Re: [AMBER] KeyError - MCPB.py Pengfei Li (Mon Feb 22 2016 - 17:20:06 PST)
[AMBER] velocity auto correlation function Vertika Gautam (Sun Feb 21 2016 - 21:27:16 PST)
- Re: [AMBER] velocity auto correlation function Daniel Roe (Tue Feb 23 2016 - 07:57:52 PST)
  - Re: [AMBER] velocity auto correlation function Vertika Gautam (Wed Mar 09 2016 - 21:25:02 PST)
    - Re: [AMBER] velocity auto correlation function Daniel Roe (Thu Mar 10 2016 - 07:43:03 PST)
[AMBER] Fwd: Error with disulphide bonds in tleap maryam azimzadehirani (Mon Feb 22 2016 - 01:10:54 PST)
- Re: [AMBER] Fwd: Error with disulphide bonds in tleap David A Case (Mon Feb 22 2016 - 04:50:17 PST)
  - Re: [AMBER] Fwd: Error with disulphide bonds in tleap maryam azimzadehirani (Mon Feb 22 2016 - 22:11:52 PST)
[AMBER] parameter file for isoaspartate acid Jesmita Dhar (Mon Feb 22 2016 - 01:15:20 PST)
- Re: [AMBER] parameter file for isoaspartate acid Bill Ross (Mon Feb 22 2016 - 01:18:57 PST)
  - Re: [AMBER] parameter file for isoaspartate acid Jesmita Dhar (Mon Feb 22 2016 - 02:15:23 PST)
    - Re: [AMBER] parameter file for isoaspartate acid Bill Ross (Mon Feb 22 2016 - 02:40:32 PST)
    - Re: [AMBER] parameter file for isoaspartate acid Jesmita Dhar (Mon Feb 22 2016 - 03:15:50 PST)
    - Re: [AMBER] parameter file for isoaspartate acid Jesmita Dhar (Mon Feb 22 2016 - 03:58:13 PST)
- Re: [AMBER] parameter file for isoaspartate acid David A Case (Mon Feb 22 2016 - 04:57:11 PST)
  - Re: [AMBER] parameter file for isoaspartate acid Jesmita Dhar (Tue Feb 23 2016 - 03:36:02 PST)
[AMBER] want script for plotting graph on entropy Ayesha Kanwal (Mon Feb 22 2016 - 03:40:15 PST)
- Re: [AMBER] want script for plotting graph on entropy David A Case (Mon Feb 22 2016 - 05:00:38 PST)
[AMBER] charmmlipid2amber.py Batuhan Kav (Mon Feb 22 2016 - 04:44:57 PST)
- Re: [AMBER] charmmlipid2amber.py Bill Ross (Tue Jun 10 2014 - 13:43:35 PDT)
[AMBER] Paradynamics with Amber Ulf Ryde (Mon Feb 22 2016 - 06:56:43 PST)
- Re: [AMBER] Paradynamics with Amber Gerald Monard (Mon Feb 22 2016 - 07:28:26 PST)
- Re: [AMBER] Paradynamics with Amber David A Case (Mon Feb 22 2016 - 07:30:58 PST)
  - Re: [AMBER] Paradynamics with Amber Gerald Monard (Mon Feb 22 2016 - 07:54:27 PST)
    - Re: [AMBER] Paradynamics with Amber Adrian Roitberg (Mon Feb 22 2016 - 08:24:01 PST)
    - Re: [AMBER] Paradynamics with Amber David A Case (Mon Feb 22 2016 - 08:51:20 PST)
  - Re: [AMBER] Paradynamics with Amber David A Case (Mon Feb 22 2016 - 12:06:26 PST)
  - Re: [AMBER] Paradynamics with Amber Ulf Ryde (Fri Feb 26 2016 - 08:07:06 PST)
[AMBER] calculate ligand RMSD for MD simulations; nofit or not? Marc Zhang (Mon Feb 22 2016 - 07:52:23 PST)
- Re: [AMBER] calculate ligand RMSD for MD simulations; nofit or not? Daniel Roe (Mon Feb 22 2016 - 09:15:47 PST)
- Re: [AMBER] calculate ligand RMSD for MD simulations; nofit or not? David A Case (Mon Feb 22 2016 - 09:21:32 PST)
  - Re: [AMBER] calculate ligand RMSD for MD simulations; nofit or not? Marc Zhang (Mon Feb 22 2016 - 12:03:30 PST)
[AMBER] CPPtraj & ParmEd - delete atoms Balaji Selvam (Mon Feb 22 2016 - 10:41:20 PST)
- Re: [AMBER] CPPtraj & ParmEd - delete atoms Daniel Roe (Mon Feb 22 2016 - 10:53:16 PST)
[AMBER] No exe file in Amberhome Mahdieh Hadi (Mon Feb 22 2016 - 10:53:15 PST)
- Re: [AMBER] No exe file in Amberhome Ebert Maximilian (Mon Feb 22 2016 - 11:11:26 PST)
- Re: [AMBER] No exe file in Amberhome David A Case (Mon Feb 22 2016 - 11:53:02 PST)
  - Re: [AMBER] No exe file in Amberhome Mahdieh Hadi (Mon Feb 22 2016 - 12:37:52 PST)
    - Re: [AMBER] No exe file in Amberhome David A Case (Mon Feb 22 2016 - 13:03:33 PST)
    - Re: [AMBER] No exe file in Amberhome Marcelo Andrade Chagas (Mon Feb 22 2016 - 15:22:59 PST)
    - Re: [AMBER] No exe file in Amberhome Mahdieh Hadi (Mon Feb 22 2016 - 23:51:04 PST)
    - Re: [AMBER] No exe file in Amberhome Hai Nguyen (Mon Feb 22 2016 - 23:54:23 PST)
    - Re: [AMBER] No exe file in Amberhome Mahdieh Hadi (Tue Feb 23 2016 - 01:18:27 PST)
    - Re: [AMBER] No exe file in Amberhome David A Case (Tue Feb 23 2016 - 04:52:50 PST)
    - Re: [AMBER] No exe file in Amberhome Mahdieh Hadi (Tue Feb 23 2016 - 05:25:35 PST)
    - Re: [AMBER] No exe file in Amberhome Daniel Roe (Tue Feb 23 2016 - 08:07:06 PST)
    - Re: [AMBER] No exe file in Amberhome Marcelo Andrade Chagas (Tue Feb 23 2016 - 08:44:08 PST)
    - Re: [AMBER] No exe file in Amberhome David A Case (Tue Feb 23 2016 - 09:03:17 PST)
    - Re: [AMBER] No exe file in Amberhome Daniel Roe (Tue Feb 23 2016 - 09:05:04 PST)
    - Re: [AMBER] No exe file in Amberhome Mahdieh Hadi (Wed Feb 24 2016 - 02:13:18 PST)
    - Re: [AMBER] No exe file in Amberhome Mahdieh Hadi (Wed Feb 24 2016 - 02:27:26 PST)
    - Re: [AMBER] No exe file in Amberhome Gustavo Seabra (Wed Feb 24 2016 - 03:35:06 PST)
    - Re: [AMBER] No exe file in Amberhome Marcelo Andrade Chagas (Wed Feb 24 2016 - 03:33:51 PST)
    - Re: [AMBER] No exe file in Amberhome Jason Swails (Wed Feb 24 2016 - 09:24:54 PST)
[AMBER] Ligand Molecules Being Rejected in SHIFTS 5.0.1 Dan Morris (Mon Feb 22 2016 - 12:01:11 PST)
- Re: [AMBER] Ligand Molecules Being Rejected in SHIFTS 5.0.1 David A Case (Tue Feb 23 2016 - 05:03:58 PST)
[AMBER] cpptraj command for pi-stacking or hydrophobic interactions. Saman Yousuf ali (Mon Feb 22 2016 - 20:34:58 PST)
- Re: [AMBER] cpptraj command for pi-stacking or hydrophobic interactions. Daniel Roe (Tue Feb 23 2016 - 08:05:51 PST)
[AMBER] tMD with ligand Jean-Marc Billod (Tue Feb 23 2016 - 01:45:45 PST)
- Re: [AMBER] tMD with ligand Carlos Simmerling (Tue Feb 23 2016 - 03:14:36 PST)
  - Re: [AMBER] tMD with ligand Jean-Marc Billod (Tue Feb 23 2016 - 03:26:46 PST)
    - Re: [AMBER] tMD with ligand Carlos Simmerling (Tue Feb 23 2016 - 04:19:03 PST)
    - Re: [AMBER] tMD with ligand Jean-Marc Billod (Tue Feb 23 2016 - 05:32:49 PST)
    - Re: [AMBER] tMD with ligand Carlos Simmerling (Tue Feb 23 2016 - 06:14:45 PST)
[AMBER] Post-doctoral position in Computational Physics Andrea Spitaleri (Tue Feb 23 2016 - 02:08:26 PST)
[AMBER] parameter file for graphene oxide Jesmita Dhar (Tue Feb 23 2016 - 03:34:23 PST)
- Re: [AMBER] parameter file for graphene oxide Jesmita Dhar (Thu Feb 25 2016 - 01:36:57 PST)
  - Re: [AMBER] parameter file for graphene oxide Karl Kirschner (Thu Feb 25 2016 - 01:54:23 PST)
- Re: [AMBER] parameter file for graphene oxide FyD (Fri Feb 26 2016 - 01:28:00 PST)
[AMBER] Fwd: cpinutil.py problem Elisa Pieri (Tue Feb 23 2016 - 07:39:38 PST)
- Re: [AMBER] Fwd: cpinutil.py problem Jason Swails (Tue Feb 23 2016 - 18:45:46 PST)
- Re: [AMBER] Fwd: cpinutil.py problem Marcelo Andrade Chagas (Tue Feb 23 2016 - 19:26:41 PST)
  - Re: [AMBER] Fwd: cpinutil.py problem Elisa Pieri (Wed Feb 24 2016 - 05:15:03 PST)
    - Re: [AMBER] Fwd: cpinutil.py problem Marcelo Andrade Chagas (Wed Feb 24 2016 - 07:05:12 PST)
    - Re: [AMBER] Fwd: cpinutil.py problem Elisa Pieri (Wed Feb 24 2016 - 07:14:25 PST)
    - Re: [AMBER] Fwd: cpinutil.py problem Jason Swails (Wed Feb 24 2016 - 09:31:40 PST)
    - [AMBER] R: Fwd: cpinutil.py problem Elisa Pieri (Wed Feb 24 2016 - 10:18:12 PST)
    - Re: [AMBER] R: Fwd: cpinutil.py problem Jason Swails (Wed Feb 24 2016 - 18:28:37 PST)
    - [AMBER] R: R: Fwd: cpinutil.py problem Elisa Pieri (Wed Feb 24 2016 - 22:33:45 PST)
    - Re: [AMBER] R: R: Fwd: cpinutil.py problem Jason Swails (Thu Feb 25 2016 - 15:56:35 PST)
    - Re: [AMBER] R: R: Fwd: cpinutil.py problem Elisa Pieri (Fri Feb 26 2016 - 01:59:02 PST)
    - Re: [AMBER] R: R: Fwd: cpinutil.py problem Elisa Pieri (Fri Mar 11 2016 - 04:03:10 PST)
    - Re: [AMBER] R: R: Fwd: cpinutil.py problem Jason Swails (Fri Mar 11 2016 - 09:00:29 PST)
[AMBER] Dihedral parameters Jungho Yang (Tue Feb 23 2016 - 07:54:36 PST)
- Re: [AMBER] Dihedral parameters David Cerutti (Tue Feb 23 2016 - 08:42:22 PST)
[AMBER] Nucleic acid builder yhzahsc (Tue Feb 23 2016 - 18:04:39 PST)
- Re: [AMBER] Nucleic acid builder nhai.wn (Tue Feb 23 2016 - 18:15:08 PST)
  - [AMBER] 回复：Re: Nucleic acid builder yhzahsc (Tue Feb 23 2016 - 18:40:45 PST)
    - Re: [AMBER] 回复：Re: Nucleic acid builder Robert Molt (Tue Feb 23 2016 - 18:42:27 PST)
    - Re: [AMBER] 回复：Re: Nucleic acid builder yhzahsc (Tue Feb 23 2016 - 19:39:59 PST)
    - Re: [AMBER] 回复：Re: Nucleic acid builder Hai Nguyen (Tue Feb 23 2016 - 19:46:52 PST)
    - Re: [AMBER] 回复：Re: Nucleic acid builder yhzahsc (Tue Feb 23 2016 - 20:08:49 PST)
    - Re: [AMBER] 回复：Re: Nucleic acid builder yhzahsc (Tue Feb 23 2016 - 19:41:27 PST)
    - Re: [AMBER] 回复：Re: Nucleic acid builder Hai Nguyen (Tue Feb 23 2016 - 19:00:18 PST)
[AMBER] manually addition of parameters in frcmod file Mongam Riba (Tue Feb 23 2016 - 22:22:55 PST)
[AMBER] Query regarding extracting protons from coordinate/trajectory file Madhura De (Wed Feb 24 2016 - 00:42:16 PST)
- Re: [AMBER] Query regarding extracting protons from coordinate/trajectory file David A Case (Wed Feb 24 2016 - 04:53:50 PST)
[AMBER] Typing {} in Xleap Mahdieh Hadi (Wed Feb 24 2016 - 01:48:28 PST)
- Re: [AMBER] Typing {} in Xleap Bill Ross (Wed Feb 24 2016 - 02:10:33 PST)
  - Re: [AMBER] Typing {} in Xleap Mahdieh Hadi (Wed Feb 24 2016 - 02:18:16 PST)
    - Re: [AMBER] Typing {} in Xleap Mahdieh Hadi (Wed Feb 24 2016 - 02:32:47 PST)
    - Re: [AMBER] Typing {} in Xleap Bill Ross (Wed Feb 24 2016 - 02:50:00 PST)
Re: [AMBER] How to transfer amino acid sequence to Xleap. Mahdieh Hadi (Wed Feb 24 2016 - 02:54:20 PST)
- Re: [AMBER] How to transfer amino acid sequence to Xleap. Bill Ross (Wed Feb 24 2016 - 03:00:41 PST)
  - Re: [AMBER] How to transfer amino acid sequence to Xleap. Mahdieh Hadi (Wed Feb 24 2016 - 03:07:12 PST)
    - Re: [AMBER] How to transfer amino acid sequence to Xleap. Bill Ross (Wed Feb 24 2016 - 03:13:24 PST)
    - Re: [AMBER] How to transfer amino acid sequence to Xleap. Mahdieh Hadi (Wed Feb 24 2016 - 03:23:10 PST)
    - Re: [AMBER] How to transfer amino acid sequence to Xleap. Mahdieh Hadi (Wed Feb 24 2016 - 03:32:15 PST)
    - Re: [AMBER] How to transfer amino acid sequence to Xleap. David A Case (Wed Feb 24 2016 - 04:56:35 PST)
    - Re: [AMBER] How to transfer amino acid sequence to Xleap. Mahdieh Hadi (Wed Feb 24 2016 - 07:36:20 PST)
    - Re: [AMBER] How to transfer amino acid sequence to Xleap. David A Case (Wed Feb 24 2016 - 10:54:06 PST)
    - Re: [AMBER] How to transfer amino acid sequence to Xleap. Mahdieh Hadi (Wed Feb 24 2016 - 10:59:32 PST)
    - Re: [AMBER] How to transfer amino acid sequence to Xleap. Bill Ross (Wed Feb 24 2016 - 11:28:57 PST)
[AMBER] Query: extracting protons from trajectory/coordinate file Madhura De (Wed Feb 24 2016 - 03:52:00 PST)
- Re: [AMBER] Query: extracting protons from trajectory/coordinate file Daniel Roe (Wed Feb 24 2016 - 07:18:27 PST)
[AMBER] error in running rmsf command cpptraj Saman Yousuf ali (Wed Feb 24 2016 - 06:01:16 PST)
- Re: [AMBER] error in running rmsf command cpptraj Daniel Roe (Wed Feb 24 2016 - 07:19:57 PST)
[AMBER] Thermodynamic Integration Vertika Gautam (Wed Feb 24 2016 - 22:44:05 PST)
- [AMBER] Fwd: Thermodynamic Integration Vertika Gautam (Wed Feb 24 2016 - 22:49:25 PST)
  - Re: [AMBER] Fwd: Thermodynamic Integration Nhai (Wed Feb 24 2016 - 22:58:50 PST)
    - Re: [AMBER] Fwd: Thermodynamic Integration David Cerutti (Wed Feb 24 2016 - 23:45:09 PST)
[AMBER] Ph.D. position, Nancy, France Gerald Monard (Thu Feb 25 2016 - 00:39:31 PST)
[AMBER] problem running MD for diphosphoric acid anion necmettin pirinccioglu (Thu Feb 25 2016 - 00:48:45 PST)
- Re: [AMBER] problem running MD for diphosphoric acid anion Ross Walker (Thu Feb 25 2016 - 01:00:15 PST)
- Re: [AMBER] problem running MD for diphosphoric acid anion necmettin pirinccioglu (Sun Feb 28 2016 - 23:56:44 PST)
  - Re: [AMBER] problem running MD for diphosphoric acid anion David A Case (Mon Feb 29 2016 - 04:43:19 PST)
- Re: [AMBER] problem running MD for diphosphoric acid anion necmettin pirinccioglu (Thu Mar 03 2016 - 00:49:28 PST)
  - Re: [AMBER] problem running MD for diphosphoric acid anion Bill Ross (Thu Mar 03 2016 - 01:22:43 PST)
    - Re: [AMBER] problem running MD for diphosphoric acid anion chandan patel (Thu Mar 03 2016 - 03:07:13 PST)
  - Re: [AMBER] problem running MD for diphosphoric acid anion David A Case (Thu Mar 03 2016 - 06:24:22 PST)
- Re: [AMBER] problem running MD for diphosphoric acid anion necmettin pirinccioglu (Wed Mar 16 2016 - 00:36:52 PDT)
  - Re: [AMBER] problem running MD for diphosphoric acid anion Nhai (Wed Mar 16 2016 - 00:58:32 PDT)
[AMBER] Minimization error using Sander Anna Cebrian Prats (Thu Feb 25 2016 - 02:17:15 PST)
- Re: [AMBER] Minimization error using Sander Bill Ross (Thu Feb 25 2016 - 03:27:55 PST)
- Re: [AMBER] Minimization error using Sander David A Case (Thu Feb 25 2016 - 05:16:49 PST)
  - Re: [AMBER] Minimization error using Sander Anna Cebrian Prats (Thu Feb 25 2016 - 06:24:54 PST)
[AMBER] Maximum input value for the isothermal compressibility in AMBER BLEY Michael (Thu Feb 25 2016 - 05:25:55 PST)
- Re: [AMBER] Maximum input value for the isothermal compressibility in AMBER David A Case (Thu Feb 25 2016 - 06:06:39 PST)
[AMBER] Question regarding protein-Dna binding free energy Mahdieh Hadi (Thu Feb 25 2016 - 06:25:54 PST)
- Re: [AMBER] Question regarding protein-Dna binding free energy Vlad Cojocaru (Thu Feb 25 2016 - 06:52:15 PST)
  - Re: [AMBER] Question regarding protein-Dna binding free energy Mahdieh Hadi (Thu Feb 25 2016 - 06:56:48 PST)
- Re: [AMBER] Question regarding protein-Dna binding free energy Vlad Cojocaru (Thu Feb 25 2016 - 07:15:32 PST)
[AMBER] MMGBSA error Indrajit Deb (Thu Feb 25 2016 - 09:24:38 PST)
- Re: [AMBER] MMGBSA error Indrajit Deb (Thu Feb 25 2016 - 16:27:29 PST)
  - Re: [AMBER] MMGBSA error Jason Swails (Thu Feb 25 2016 - 17:01:38 PST)
    - Re: [AMBER] MMGBSA error Indrajit Deb (Thu Feb 25 2016 - 17:06:42 PST)
[AMBER] the angle between two axis maryam azimzadehirani (Thu Feb 25 2016 - 23:20:57 PST)
- Re: [AMBER] the angle between two axis Hai Nguyen (Thu Feb 25 2016 - 23:27:10 PST)
- Re: [AMBER] the angle between two axis mmaestre (Fri Feb 26 2016 - 00:01:29 PST)
  - Re: [AMBER] the angle between two axis maryam azimzadehirani (Fri Feb 26 2016 - 00:26:48 PST)
[AMBER] error in sqm.out file Jesmita Dhar (Fri Feb 26 2016 - 00:15:31 PST)
- Re: [AMBER] error in sqm.out file David A Case (Fri Feb 26 2016 - 05:26:47 PST)
[AMBER] Problem with HIS/HIE residue and ff14SB force field Casalini Tommaso (Fri Feb 26 2016 - 02:20:02 PST)
- Re: [AMBER] Problem with HIS/HIE residue and ff14SB force field Hannes Loeffler (Fri Feb 26 2016 - 02:34:02 PST)
  - Re: [AMBER] Problem with HIS/HIE residue and ff14SB force field Casalini Tommaso (Fri Feb 26 2016 - 02:38:59 PST)
    - Re: [AMBER] Problem with HIS/HIE residue and ff14SB force field Casalini Tommaso (Fri Feb 26 2016 - 02:45:10 PST)
    - Re: [AMBER] Problem with HIS/HIE residue and ff14SB force field Hannes Loeffler (Fri Feb 26 2016 - 02:53:35 PST)
- Re: [AMBER] Problem with HIS/HIE residue and ff14SB force field David A Case (Fri Feb 26 2016 - 05:31:36 PST)
[AMBER] Regarding trajectory analysis using CPPTRAJ Sivanandam M (Fri Feb 26 2016 - 02:38:17 PST)
- Re: [AMBER] Regarding trajectory analysis using CPPTRAJ Bill Ross (Fri Feb 26 2016 - 02:44:32 PST)
- Re: [AMBER] Regarding trajectory analysis using CPPTRAJ Daniel Roe (Fri Feb 26 2016 - 07:18:20 PST)
[AMBER] Gaussian error with MCPB ion modeling calculation anu chandra (Fri Feb 26 2016 - 03:20:22 PST)
- Re: [AMBER] Gaussian error with MCPB ion modeling calculation Pengfei Li (Fri Feb 26 2016 - 08:56:15 PST)
[AMBER] Regarding caution message in the out file with pmemd.cuda.MPI anu chandra (Fri Feb 26 2016 - 03:28:45 PST)
- Re: [AMBER] Regarding caution message in the out file with pmemd.cuda.MPI Ross Walker (Fri Feb 26 2016 - 14:36:27 PST)
  - Re: [AMBER] Regarding caution message in the out file with pmemd.cuda.MPI anu chandra (Mon Feb 29 2016 - 06:33:09 PST)
[AMBER] Pdb file to Mol2 Mahdieh Hadi (Fri Feb 26 2016 - 04:03:47 PST)
- Re: [AMBER] Pdb file to Mol2 Marcelo Andrade Chagas (Fri Feb 26 2016 - 04:18:35 PST)
  - Re: [AMBER] Pdb file to Mol2 Marcelo Andrade Chagas (Fri Feb 26 2016 - 04:24:22 PST)
- Re: [AMBER] Pdb file to Mol2 Daniel Roe (Fri Feb 26 2016 - 07:20:25 PST)
  - Re: [AMBER] Pdb file to Mol2 Mahdieh Hadi (Fri Feb 26 2016 - 07:30:34 PST)
    - Re: [AMBER] Pdb file to Mol2 Daniel Roe (Fri Feb 26 2016 - 07:47:03 PST)
    - Re: [AMBER] Pdb file to Mol2 Mahdieh Hadi (Fri Feb 26 2016 - 07:56:09 PST)
    - Re: [AMBER] Pdb file to Mol2 Daniel Roe (Fri Feb 26 2016 - 08:08:00 PST)
    - Re: [AMBER] Pdb file to Mol2 Mahdieh Hadi (Mon Feb 29 2016 - 06:31:44 PST)
    - Re: [AMBER] Pdb file to Mol2 Mahdieh Hadi (Mon Feb 29 2016 - 07:19:44 PST)
    - Re: [AMBER] Pdb file to Mol2 Daniel Roe (Mon Feb 29 2016 - 07:34:20 PST)
    - Re: [AMBER] Pdb file to Mol2 Thomas Cheatham (Mon Feb 29 2016 - 09:59:07 PST)
    - Re: [AMBER] Pdb file to Mol2 Mahdieh Hadi (Mon Feb 29 2016 - 05:13:48 PST)
    - Re: [AMBER] Pdb file to Mol2 Carlos Simmerling (Mon Feb 29 2016 - 05:30:32 PST)
[AMBER] Duration parmchk Stefano Sarao S215563 (Fri Feb 26 2016 - 04:41:54 PST)
- Re: [AMBER] Duration parmchk Daniel Roe (Fri Feb 26 2016 - 07:21:30 PST)
[AMBER] External library for leap Anna Cebrian Prats (Fri Feb 26 2016 - 05:14:28 PST)
- Re: [AMBER] External library for leap Daniel Roe (Fri Feb 26 2016 - 07:24:10 PST)
  - Re: [AMBER] External library for leap Anna Cebrian Prats (Mon Feb 29 2016 - 01:39:28 PST)
Re: [AMBER] AMBER Digest, Vol 1497, Issue 1 necmettin pirinccioglu (Fri Feb 26 2016 - 05:21:53 PST)
- Re: [AMBER] AMBER Digest, Vol 1497, Issue 1 Daniel Roe (Fri Feb 26 2016 - 07:26:28 PST)
[AMBER] waters inside cavity Elisa Pieri (Fri Feb 26 2016 - 07:00:54 PST)
- Re: [AMBER] waters inside cavity Niel Henriksen (Fri Feb 26 2016 - 09:59:11 PST)
[AMBER] How to analyze mutational free energy difference? Mijiddorj Batsaikhan (Fri Feb 26 2016 - 23:34:20 PST)
- Re: [AMBER] How to analyze mutational free energy difference? Carlos Simmerling (Sat Feb 27 2016 - 04:39:14 PST)
  - Re: [AMBER] How to analyze mutational free energy difference? Mahdieh Hadi (Sat Feb 27 2016 - 04:46:20 PST)
    - Re: [AMBER] How to analyze mutational free energy difference? Carlos Simmerling (Sat Feb 27 2016 - 04:48:38 PST)
    - Re: [AMBER] How to analyze mutational free energy difference? Mahdieh Hadi (Sat Feb 27 2016 - 05:02:28 PST)
    - Re: [AMBER] How to analyze mutational free energy difference? Carlos Simmerling (Sat Feb 27 2016 - 05:13:31 PST)
    - Re: [AMBER] How to analyze mutational free energy difference? Rajeswari A. (Sat Feb 27 2016 - 09:11:47 PST)
    - Re: [AMBER] How to analyze mutational free energy difference? Carlos Simmerling (Sat Feb 27 2016 - 09:32:00 PST)
    - Re: [AMBER] How to analyze mutational free energy difference? Mijiddorj Batsaikhan (Sat Feb 27 2016 - 10:48:48 PST)
    - Re: [AMBER] How to analyze mutational free energy difference? Carlos Simmerling (Sat Feb 27 2016 - 10:55:21 PST)
    - Re: [AMBER] How to analyze mutational free energy difference? Rajeswari A. (Mon Feb 29 2016 - 04:22:16 PST)
[AMBER] gzip -9 heat.mdcrd Error Mahdieh Hadi (Sat Feb 27 2016 - 06:27:03 PST)
- Re: [AMBER] gzip -9 heat.mdcrd Error Batuhan Kav (Sat Feb 27 2016 - 06:54:50 PST)
[AMBER] draw vector along axis of an alpha helix Emilio Angelina (Sat Feb 27 2016 - 07:50:28 PST)
- Re: [AMBER] draw vector along axis of an alpha helix Joel Lapin (Sat Feb 27 2016 - 12:53:39 PST)
- Re: [AMBER] draw vector along axis of an alpha helix Daniel Roe (Sat Feb 27 2016 - 12:57:38 PST)
  - Re: [AMBER] draw vector along axis of an alpha helix Emilio Angelina (Sat Feb 27 2016 - 13:50:14 PST)
[AMBER] How to separate a protein complex to its components Mahdieh Hadi (Sat Feb 27 2016 - 23:39:00 PST)
- Re: [AMBER] How to separate a protein complex to its components Marcelo Andrade Chagas (Sun Feb 28 2016 - 04:05:03 PST)
- Re: [AMBER] How to separate a protein complex to its components Arati Paudyal (Sun Feb 28 2016 - 04:56:21 PST)
- Re: [AMBER] How to separate a protein complex to its components Daniel Roe (Sun Feb 28 2016 - 05:57:07 PST)
[AMBER] Bounds command with GIst peter.schmidtke.discngine.servier.com (Mon Feb 29 2016 - 02:35:04 PST)
- Re: [AMBER] Bounds command with GIst Daniel Roe (Mon Feb 29 2016 - 07:32:29 PST)
  - Re: [AMBER] Bounds command with GIst peter.schmidtke.discngine.servier.com (Mon Feb 29 2016 - 23:18:28 PST)
[AMBER] Preparing needed input files for TI Mahdieh Hadi (Mon Feb 29 2016 - 03:26:02 PST)
- Re: [AMBER] Preparing needed input files for TI Hannes Loeffler (Mon Feb 29 2016 - 04:00:53 PST)
  - Re: [AMBER] Preparing needed input files for TI mahdie hadi (Mon Feb 29 2016 - 07:11:31 PST)
[AMBER] Need Amber entropy calculated values Ayesha Kanwal (Mon Feb 29 2016 - 06:48:41 PST)
- Re: [AMBER] Need Amber entropy calculated values Jason Swails (Mon Feb 29 2016 - 20:25:25 PST)
- Re: [AMBER] Need Amber entropy calculated values Ayesha Kanwal (Tue Mar 01 2016 - 00:51:38 PST)
  - [AMBER] Doc of Amber to the html version FyD (Tue Mar 01 2016 - 01:25:09 PST)
    - Re: [AMBER] Doc of Amber to the html version David A Case (Wed Mar 02 2016 - 04:58:42 PST)
  - Re: [AMBER] Need Amber entropy calculated values Jason Swails (Tue Mar 01 2016 - 04:56:14 PST)
    - Re: [AMBER] Need Amber entropy calculated values psu4.uic.edu (Sat Mar 12 2016 - 14:12:01 PST)
- Re: [AMBER] Need Amber entropy calculated values Ayesha Kanwal (Sat Mar 12 2016 - 14:29:11 PST)
[AMBER] reading Amber trajectory files with chamber topology file Song-Ho Chong (Mon Feb 29 2016 - 07:31:12 PST)
- Re: [AMBER] reading Amber trajectory files with chamber topology file Daniel Roe (Mon Feb 29 2016 - 07:42:01 PST)
  - Re: [AMBER] reading Amber trajectory files with chamber topology file Song-Ho Chong (Mon Feb 29 2016 - 08:01:36 PST)
    - Re: [AMBER] reading Amber trajectory files with chamber topology file Daniel Roe (Mon Feb 29 2016 - 08:17:35 PST)
    - Re: [AMBER] reading Amber trajectory files with chamber topology file Song-Ho Chong (Mon Feb 29 2016 - 08:24:04 PST)
[AMBER] more extra points needed Ivanov, Maxim (Mon Feb 29 2016 - 09:15:17 PST)
- Re: [AMBER] more extra points needed Jason Swails (Mon Feb 29 2016 - 20:34:44 PST)
  - Re: [AMBER] more extra points needed David Cerutti (Mon Feb 29 2016 - 21:09:38 PST)
- Re: [AMBER] more extra points needed Ivanov, Maxim (Tue Mar 01 2016 - 18:31:49 PST)
[AMBER] EPtot, Angle, Bond, Dihed Starovoytov, Oleg (Mon Feb 29 2016 - 18:02:26 PST)
- Re: [AMBER] EPtot, Angle, Bond, Dihed David Cerutti (Mon Feb 29 2016 - 19:11:19 PST)
- Re: [AMBER] EPtot, Angle, Bond, Dihed Jason Swails (Mon Feb 29 2016 - 20:20:29 PST)
- Re: [AMBER] EPtot, Angle, Bond, Dihed Thomas Cheatham (Mon Feb 29 2016 - 20:34:38 PST)
[AMBER] Inquiry regarding amber installation Sreemol G (Mon Feb 29 2016 - 22:05:14 PST)
- Re: [AMBER] Inquiry regarding amber installation Nhai (Mon Feb 29 2016 - 23:25:04 PST)
- Re: [AMBER] Inquiry regarding amber installation David A Case (Tue Mar 01 2016 - 11:25:04 PST)
[AMBER] adding ion zahra khatti (Mon Feb 29 2016 - 22:45:19 PST)
- Re: [AMBER] adding ion Jason Swails (Tue Mar 01 2016 - 05:07:47 PST)
  - Re: [AMBER] adding ion Carlos Simmerling (Tue Mar 01 2016 - 05:26:46 PST)
[AMBER] Gist calculation on clustered structures peter.schmidtke.discngine.servier.com (Mon Feb 29 2016 - 23:23:01 PST)
- Re: [AMBER] Gist calculation on clustered structures Steven Ramsey (Tue Mar 01 2016 - 06:30:26 PST)
  - Re: [AMBER] Gist calculation on clustered structures peter.schmidtke.discngine.servier.com (Mon Mar 07 2016 - 23:31:40 PST)
[AMBER] I have a problem when installing GPU version of Pmemd(Amber14). yhzahsc (Tue Mar 01 2016 - 00:44:07 PST)
- Re: [AMBER] I have a problem when installing GPU version of Pmemd(Amber14). Ross Walker (Tue Mar 01 2016 - 08:13:04 PST)
[AMBER] Error while creating neutralized topology and coordinates file Sreemol G (Tue Mar 01 2016 - 03:33:44 PST)
- Re: [AMBER] Error while creating neutralized topology and coordinates file Bill Ross (Tue Mar 01 2016 - 03:38:47 PST)
  - Re: [AMBER] Error while creating neutralized topology and coordinates file Mohammed Khaled Tumbi (Tue Mar 01 2016 - 03:41:42 PST)
    - Re: [AMBER] Error while creating neutralized topology and coordinates file Sreemol G (Tue Mar 01 2016 - 22:54:08 PST)
    - Re: [AMBER] Error while creating neutralized topology and coordinates file David A Case (Wed Mar 02 2016 - 05:04:19 PST)
[AMBER] mmpbsa.py question Carlos Romero (Tue Mar 01 2016 - 11:03:44 PST)
[AMBER] LINMEN Arati Paudyal (Tue Mar 01 2016 - 14:48:58 PST)
- Re: [AMBER] LINMEN David A Case (Tue Mar 01 2016 - 17:53:40 PST)
[AMBER] MMPBSA error Hira Jabeen (Tue Mar 01 2016 - 21:56:42 PST)
[AMBER] calculate free energy binding in presence of ions witn mmpbsa Carlos Romero (Tue Mar 01 2016 - 22:48:03 PST)
- Re: [AMBER] calculate free energy binding in presence of ions witn mmpbsa Josh Berryman (Thu Mar 17 2016 - 00:25:33 PDT)
- Re: [AMBER] calculate free energy binding in presence of ions witn mmpbsa Carlos Romero (Sat Mar 26 2016 - 14:51:22 PDT)
[AMBER] Dihedral angle values from .mdcrd file Vasantha Kumar (Wed Mar 02 2016 - 03:47:21 PST)
- Re: [AMBER] Dihedral angle values from .mdcrd file Carlos Simmerling (Wed Mar 02 2016 - 04:10:18 PST)
- Re: [AMBER] Dihedral angle values from .mdcrd file Daniel Roe (Wed Mar 02 2016 - 09:49:16 PST)
  - Re: [AMBER] Dihedral angle values from .mdcrd file Vasantha Kumar (Wed Mar 02 2016 - 11:18:10 PST)
  - Re: [AMBER] Dihedral angle values from .mdcrd file Vasantha Kumar (Wed Mar 02 2016 - 11:18:11 PST)
[AMBER] cpptraj molsurf: query on results George Tzotzos (Wed Mar 02 2016 - 13:58:19 PST)
- Re: [AMBER] cpptraj molsurf: query on results Daniel Roe (Thu Mar 03 2016 - 07:30:45 PST)
  - Re: [AMBER] cpptraj molsurf: query on results George Tzotzos (Thu Mar 03 2016 - 12:16:22 PST)
    - Re: [AMBER] cpptraj molsurf: query on results Daniel Roe (Fri Mar 04 2016 - 14:16:31 PST)
[AMBER] mmgbsa_error chemjxn (Thu Mar 03 2016 - 00:09:42 PST)
[AMBER] mmgbsa_error chemjxn (Thu Mar 03 2016 - 00:10:35 PST)
- Re: [AMBER] mmgbsa_error Jason Swails (Thu Mar 03 2016 - 03:52:59 PST)
  - Re: [AMBER] mmgbsa_error chemjxn (Fri Mar 04 2016 - 01:00:03 PST)
    - Re: [AMBER] mmgbsa_error Jason Swails (Fri Mar 04 2016 - 05:11:02 PST)
    - Re: [AMBER] mmgbsa_error David A Case (Fri Mar 04 2016 - 05:55:16 PST)
[AMBER] pseudo trajectories with 4 center of mass? Hirdesh Kumar (Thu Mar 03 2016 - 11:49:23 PST)
- Re: [AMBER] pseudo trajectories with 4 center of mass? Daniel Roe (Thu Mar 03 2016 - 11:53:53 PST)
[AMBER] GB Parameterization Taylor Harville (Thu Mar 03 2016 - 19:27:13 PST)
- Re: [AMBER] GB Parameterization Carlos Simmerling (Thu Mar 03 2016 - 19:51:48 PST)
  - Re: [AMBER] GB Parameterization Taylor Harville (Fri Mar 04 2016 - 08:28:14 PST)
    - Re: [AMBER] GB Parameterization David A Case (Fri Mar 04 2016 - 09:35:53 PST)
- Re: [AMBER] GB Parameterization David A Case (Fri Mar 04 2016 - 05:42:11 PST)
[AMBER] Error while creating topology file after adding ions Sreemol G (Thu Mar 03 2016 - 20:40:03 PST)
- Re: [AMBER] Error while creating topology file after adding ions Bill Ross (Thu Mar 03 2016 - 20:55:03 PST)
  - Re: [AMBER] Error while creating topology file after adding ions Sreemol G (Thu Mar 03 2016 - 21:04:18 PST)
    - Re: [AMBER] Error while creating topology file after adding ions Hai Nguyen (Thu Mar 03 2016 - 21:08:00 PST)
    - Re: [AMBER] Error while creating topology file after adding ions Sreemol G (Thu Mar 03 2016 - 21:24:45 PST)
    - Re: [AMBER] Error while creating topology file after adding ions Nhai (Thu Mar 03 2016 - 21:30:20 PST)
    - Re: [AMBER] Error while creating topology file after adding ions Sreemol G (Thu Mar 03 2016 - 21:40:26 PST)
    - Re: [AMBER] Error while creating topology file after adding ions Bill Ross (Thu Mar 03 2016 - 22:39:57 PST)
    - Re: [AMBER] Error while creating topology file after adding ions Sreemol G (Fri Mar 04 2016 - 01:14:49 PST)
    - Re: [AMBER] Error while creating topology file after adding ions Marcelo Andrade Chagas (Fri Mar 04 2016 - 01:55:46 PST)
    - Re: [AMBER] Error while creating topology file after adding ions Marcelo Andrade Chagas (Fri Mar 04 2016 - 02:13:55 PST)
    - Re: [AMBER] Error while creating topology file after adding ions David A Case (Fri Mar 04 2016 - 05:49:50 PST)
[AMBER] Query regarding NMR refinement Madhura De (Fri Mar 04 2016 - 02:47:15 PST)
- Re: [AMBER] Query regarding NMR refinement David A Case (Fri Mar 04 2016 - 06:00:50 PST)
[AMBER] long bond lengths after parmed.py setMolecules command in metal-containing system Arjun Narayanan (Fri Mar 04 2016 - 08:26:36 PST)
- Re: [AMBER] long bond lengths after parmed.py setMolecules command in metal-containing system Jason Swails (Fri Mar 04 2016 - 19:00:40 PST)
  - Re: [AMBER] long bond lengths after parmed.py setMolecules command in metal-containing system Arjun Narayanan (Mon Mar 07 2016 - 04:58:28 PST)
    - Re: [AMBER] long bond lengths after parmed.py setMolecules command in metal-containing system Arjun Narayanan (Mon Mar 07 2016 - 05:19:59 PST)
- Re: [AMBER] long bond lengths after parmed.py setMolecules command in metal-containing system Daniel Roe (Mon Mar 07 2016 - 07:44:41 PST)
  - Re: [AMBER] long bond lengths after parmed.py setMolecules command in metal-containing system Arjun Narayanan (Mon Mar 07 2016 - 08:03:34 PST)
    - Re: [AMBER] long bond lengths after parmed.py setMolecules command in metal-containing system David A Case (Mon Mar 07 2016 - 08:51:55 PST)
[AMBER] cpptraj surf George Tzotzos (Fri Mar 04 2016 - 13:35:45 PST)
[AMBER] Analysis of Radius of gyration Iqbal, Muhammad Sajid (Fri Mar 04 2016 - 14:19:26 PST)
- Re: [AMBER] Analysis of Radius of gyration Daniel Roe (Fri Mar 04 2016 - 14:28:28 PST)
[AMBER] for protein- RNA complex simulation Sreemol G (Fri Mar 04 2016 - 19:49:46 PST)
- Re: [AMBER] for protein- RNA complex simulation Thomas Cheatham (Fri Mar 04 2016 - 20:09:30 PST)
- Re: [AMBER] for protein- RNA complex simulation Jiri Sponer (Sat Mar 05 2016 - 00:39:56 PST)
[AMBER] regarding mm-pbsa calculation neha chaudhary (Fri Mar 04 2016 - 20:58:10 PST)
- Re: [AMBER] regarding mm-pbsa calculation Ray Luo (Fri Mar 04 2016 - 21:32:14 PST)
[AMBER] nucleic acid residue representation in leap Sreemol G (Fri Mar 04 2016 - 23:04:00 PST)
- Re: [AMBER] nucleic acid residue representation in leap Hai Nguyen (Fri Mar 04 2016 - 23:13:08 PST)
- Re: [AMBER] nucleic acid residue representation in leap Jason Swails (Fri Mar 04 2016 - 23:14:01 PST)
  - Re: [AMBER] nucleic acid residue representation in leap Sreemol G (Fri Mar 04 2016 - 23:26:03 PST)
    - Re: [AMBER] nucleic acid residue representation in leap Vlad Cojocaru (Sat Mar 05 2016 - 01:28:30 PST)
    - Re: [AMBER] nucleic acid residue representation in leap David A Case (Sat Mar 05 2016 - 06:45:04 PST)
[AMBER] IMPORTANT FOR 12-6-4 USERS Pengfei Li (Sat Mar 05 2016 - 18:30:10 PST)
[AMBER] cpptraj rmsd error (Orthogonal box), unknown #frames, start=0 offset=1 Saman Yousuf ali (Sun Mar 06 2016 - 22:52:23 PST)
- Re: [AMBER] cpptraj rmsd error (Orthogonal box), unknown #frames, start=0 offset=1 Daniel Roe (Mon Mar 07 2016 - 07:41:53 PST)
  - Re: [AMBER] cpptraj rmsd error (Orthogonal box), unknown #frames, start=0 offset=1 David A Case (Mon Mar 07 2016 - 08:55:04 PST)
[AMBER] How to deal with fractional electron unit charges on small molecules?? SHAILESH KUMAR (Mon Mar 07 2016 - 02:30:44 PST)
- Re: [AMBER] How to deal with fractional electron unit charges on small molecules?? Hannes Loeffler (Mon Mar 07 2016 - 02:52:23 PST)
[AMBER] tests dont work for serial, parallel or cuda amber instalation. Wesley Alves (Mon Mar 07 2016 - 12:20:05 PST)
- Re: [AMBER] tests dont work for serial, parallel or cuda amber instalation. Daniel Roe (Mon Mar 07 2016 - 13:23:07 PST)
[AMBER] Chamber tool, error using the prmtop and inpcrd files Anna Cebrian Prats (Tue Mar 08 2016 - 02:36:47 PST)
- Re: [AMBER] Chamber tool, error using the prmtop and inpcrd files Jason Swails (Tue Mar 08 2016 - 05:09:08 PST)
[AMBER] pseudo trajectories for 4 centers of mass? Hirdesh Kumar (Tue Mar 08 2016 - 06:34:48 PST)
- Re: [AMBER] pseudo trajectories for 4 centers of mass? Daniel Roe (Tue Mar 08 2016 - 07:02:38 PST)
- Re: [AMBER] pseudo trajectories for 4 centers of mass? Hirdesh Kumar (Sun Mar 13 2016 - 10:57:46 PDT)
  - Re: [AMBER] pseudo trajectories for 4 centers of mass? Vlad Cojocaru (Sun Mar 13 2016 - 11:11:09 PDT)
  - Re: [AMBER] pseudo trajectories for 4 centers of mass? Hai Nguyen (Sun Mar 13 2016 - 11:53:39 PDT)
  - Re: [AMBER] pseudo trajectories for 4 centers of mass? Daniel Roe (Sun Mar 13 2016 - 13:40:39 PDT)
- Re: [AMBER] pseudo trajectories for 4 centers of mass? Hirdesh Kumar (Tue Mar 15 2016 - 05:54:46 PDT)
  - Re: [AMBER] pseudo trajectories for 4 centers of mass? Daniel Roe (Tue Mar 15 2016 - 07:31:19 PDT)
- Re: [AMBER] pseudo trajectories for 4 centers of mass? Hirdesh Kumar (Wed Mar 16 2016 - 09:58:29 PDT)
  - Re: [AMBER] pseudo trajectories for 4 centers of mass? Daniel Roe (Wed Mar 16 2016 - 10:01:54 PDT)
[AMBER] How to interpret MMGBSA ligand binding free energy decomposition results Zhang Marc (Tue Mar 08 2016 - 09:08:08 PST)
- Re: [AMBER] How to interpret MMGBSA ligand binding free energy decomposition results Jason Swails (Tue Mar 08 2016 - 18:44:13 PST)
  - Re: [AMBER] How to interpret MMGBSA ligand binding free energy decomposition results Zhang Marc (Wed Mar 09 2016 - 00:26:15 PST)
    - Re: [AMBER] How to interpret MMGBSA ligand binding free energy decomposition results Carlos Simmerling (Wed Mar 09 2016 - 03:13:24 PST)
    - Re: [AMBER] How to interpret MMGBSA ligand binding free energy decomposition results Jason Swails (Wed Mar 09 2016 - 04:41:00 PST)
    - Re: [AMBER] How to interpret MMGBSA ligand binding free energy decomposition results Daniel Roe (Wed Mar 09 2016 - 07:55:37 PST)
[AMBER] Production phase for MMPBSA Arati Paudyal (Tue Mar 08 2016 - 11:06:10 PST)
- Re: [AMBER] Production phase for MMPBSA Jason Swails (Tue Mar 08 2016 - 18:39:39 PST)
  - Re: [AMBER] Production phase for MMPBSA Andy Watkins (Wed Mar 09 2016 - 01:06:31 PST)
    - Re: [AMBER] Production phase for MMPBSA Hannes Loeffler (Wed Mar 09 2016 - 01:49:41 PST)
    - Re: [AMBER] Production phase for MMPBSA Andy Watkins (Wed Mar 09 2016 - 02:10:24 PST)
    - Re: [AMBER] Production phase for MMPBSA Hannes Loeffler (Wed Mar 09 2016 - 09:08:21 PST)
  - Re: [AMBER] Production phase for MMPBSA Arati Paudyal (Wed Mar 09 2016 - 05:53:56 PST)
    - Re: [AMBER] Production phase for MMPBSA Hannes Loeffler (Wed Mar 09 2016 - 08:30:21 PST)
[AMBER] Diffusion/msd cpptraj bug? Timothy Christopher Schutt (Tue Mar 08 2016 - 13:11:54 PST)
- Re: [AMBER] Diffusion/msd cpptraj bug? Daniel Roe (Tue Mar 08 2016 - 13:43:39 PST)
  - Re: [AMBER] Diffusion/msd cpptraj bug? Timothy Christopher Schutt (Tue Mar 08 2016 - 14:30:00 PST)
    - Re: [AMBER] Diffusion/msd cpptraj bug? Daniel Roe (Tue Mar 08 2016 - 14:38:22 PST)
    - Re: [AMBER] Diffusion/msd cpptraj bug? Timothy Christopher Schutt (Tue Mar 08 2016 - 14:54:19 PST)
- Re: [AMBER] Diffusion/msd cpptraj bug? David A Case (Tue Mar 08 2016 - 16:34:15 PST)
  - Re: [AMBER] Diffusion/msd cpptraj bug? Timothy Christopher Schutt (Tue Mar 08 2016 - 17:05:07 PST)
    - Re: [AMBER] Diffusion/msd cpptraj bug? Daniel Roe (Tue Mar 08 2016 - 20:43:04 PST)
    - Re: [AMBER] Diffusion/msd cpptraj bug? Timothy Christopher Schutt (Tue Mar 08 2016 - 22:43:56 PST)
    - Re: [AMBER] Diffusion/msd cpptraj bug? Bill Ross (Wed Mar 09 2016 - 00:13:42 PST)
    - Re: [AMBER] Diffusion/msd cpptraj bug? Daniel Roe (Wed Mar 09 2016 - 07:41:14 PST)
    - Re: [AMBER] Diffusion/msd cpptraj bug? Timothy Christopher Schutt (Wed Mar 09 2016 - 10:02:53 PST)
    - Re: [AMBER] Diffusion/msd cpptraj bug? Daniel Roe (Wed Mar 09 2016 - 10:06:23 PST)
    - Re: [AMBER] Diffusion/msd cpptraj bug? Daniel Roe (Wed Mar 09 2016 - 10:07:32 PST)
    - Re: [AMBER] Diffusion/msd cpptraj bug? Timothy Christopher Schutt (Wed Mar 09 2016 - 11:24:03 PST)
    - Re: [AMBER] Diffusion/msd cpptraj bug? Daniel Roe (Wed Mar 09 2016 - 11:54:38 PST)
    - Re: [AMBER] Diffusion/msd cpptraj bug? Timothy Christopher Schutt (Wed Mar 09 2016 - 13:13:54 PST)
    - Re: [AMBER] Diffusion/msd cpptraj bug? Daniel Roe (Thu Mar 10 2016 - 08:18:03 PST)
[AMBER] Does the PBSA Calculation Include the Neutralizing Plasma？姜阳 (Tue Mar 08 2016 - 19:27:01 PST)
- Re: [AMBER] Does the PBSA Calculation Include the Neutralizing Plasma？ Ray Luo (Tue Mar 08 2016 - 20:43:23 PST)
[AMBER] How did GAFF get force constants? Ruixing Wang (Tue Mar 08 2016 - 20:01:13 PST)
- Re: [AMBER] How did GAFF get force constants? Hai Nguyen (Tue Mar 08 2016 - 21:48:25 PST)
  - Re: [AMBER] How did GAFF get force constants? David Cerutti (Tue Mar 08 2016 - 22:13:02 PST)
    - Re: [AMBER] How did GAFF get force constants? Thomas Cheatham (Fri Mar 11 2016 - 19:52:11 PST)
    - Re: [AMBER] How did GAFF get force constants? David Cerutti (Sat Mar 12 2016 - 16:01:50 PST)
- Re: [AMBER] How did GAFF get force constants? Ruixing Wang (Wed Mar 16 2016 - 02:24:18 PDT)
[AMBER] Optimize in Gaussian with RESP Jesmita Dhar (Wed Mar 09 2016 - 00:36:50 PST)
- Re: [AMBER] Optimize in Gaussian with RESP Marcelo Andrade Chagas (Wed Mar 09 2016 - 04:40:12 PST)
  - Re: [AMBER] Optimize in Gaussian with RESP Jesmita Dhar (Thu Mar 10 2016 - 22:47:21 PST)
    - [AMBER] Fwd: Optimize in Gaussian with RESP Jesmita Dhar (Fri Mar 11 2016 - 00:33:38 PST)
    - Re: [AMBER] Optimize in Gaussian with RESP David A Case (Fri Mar 11 2016 - 04:19:43 PST)
    - Re: [AMBER] Optimize in Gaussian with RESP Jesmita Dhar (Fri Mar 11 2016 - 04:40:27 PST)
    - Re: [AMBER] Optimize in Gaussian with RESP FyD (Fri Mar 11 2016 - 04:42:24 PST)
- Re: [AMBER] Optimize in Gaussian with RESP David A Case (Wed Mar 09 2016 - 04:43:49 PST)
- Re: [AMBER] Optimize in Gaussian with RESP FyD (Fri Mar 11 2016 - 04:27:19 PST)
[AMBER] Optimize in Gaussian with RESP Jesmita Dhar (Wed Mar 09 2016 - 00:37:50 PST)
[AMBER] How to using distance based strip action and generate the corresponding prmtop windy (Wed Mar 09 2016 - 07:02:39 PST)
- Re: [AMBER] How to using distance based strip action and generate the corresponding prmtop Daniel Roe (Wed Mar 09 2016 - 07:51:30 PST)
Re: [AMBER] tests dont work for serial, parallel or cuda amber instalation Wesley Alves (Wed Mar 09 2016 - 08:57:24 PST)
- Re: [AMBER] tests dont work for serial, parallel or cuda amber instalation Daniel Roe (Wed Mar 09 2016 - 10:44:21 PST)
[AMBER] geforce 970 versus 780 George Green (Wed Mar 09 2016 - 11:14:04 PST)
- Re: [AMBER] geforce 970 versus 780 Gerald Monard (Mon Mar 28 2016 - 14:12:19 PDT)
[AMBER] ambpdb could not read restart atoms/time. Bin Wang (Wed Mar 09 2016 - 19:07:31 PST)
- Re: [AMBER] ambpdb could not read restart atoms/time. Bill Ross (Wed Mar 09 2016 - 19:25:02 PST)
  - Re: [AMBER] ambpdb could not read restart atoms/time. Bin Wang (Wed Mar 09 2016 - 19:40:09 PST)
  - Re: [AMBER] ambpdb could not read restart atoms/time. Bin Wang (Wed Mar 09 2016 - 19:41:31 PST)
    - Re: [AMBER] ambpdb could not read restart atoms/time. Kshatresh Dutta Dubey (Wed Mar 09 2016 - 20:30:21 PST)
    - Re: [AMBER] ambpdb could not read restart atoms/time. Daniel Roe (Wed Mar 09 2016 - 20:32:02 PST)
    - Re: [AMBER] ambpdb could not read restart atoms/time. David A Case (Thu Mar 10 2016 - 04:14:10 PST)
    - Re: [AMBER] ambpdb could not read restart atoms/time. Daniel Roe (Thu Mar 10 2016 - 07:24:14 PST)
[AMBER] Creating new atom Sreemol G (Wed Mar 09 2016 - 20:25:09 PST)
- Re: [AMBER] Creating new atom Bill Ross (Wed Mar 09 2016 - 21:46:51 PST)
[AMBER] Installation error amber14 Dr. M. K. Yadav (Thu Mar 10 2016 - 00:28:20 PST)
- Re: [AMBER] Installation error amber14 David A Case (Thu Mar 10 2016 - 04:17:28 PST)
[AMBER] problem with ionized residues Michael Shokhen (Thu Mar 10 2016 - 02:30:20 PST)
- Re: [AMBER] problem with ionized residues Carlos Simmerling (Thu Mar 10 2016 - 03:16:15 PST)
  - Re: [AMBER] problem with ionized residues Michael Shokhen (Thu Mar 10 2016 - 03:33:25 PST)
    - Re: [AMBER] problem with ionized residues Carlos Simmerling (Thu Mar 10 2016 - 03:47:31 PST)
[AMBER] energy calculation with cpptraj based on chamber topology file Song-Ho Chong (Thu Mar 10 2016 - 04:30:08 PST)
- Re: [AMBER] energy calculation with cpptraj based on chamber topology file Daniel Roe (Thu Mar 10 2016 - 07:34:00 PST)
  - Re: [AMBER] energy calculation with cpptraj based on chamber topology file Song-Ho Chong (Thu Mar 10 2016 - 07:51:54 PST)
    - Re: [AMBER] energy calculation with cpptraj based on chamber topology file Daniel Roe (Thu Mar 10 2016 - 08:07:48 PST)
    - Re: [AMBER] energy calculation with cpptraj based on chamber topology file Song-Ho Chong (Thu Mar 10 2016 - 08:37:45 PST)
    - Re: [AMBER] energy calculation with cpptraj based on chamber topology file Jason Swails (Thu Mar 10 2016 - 09:35:17 PST)
[AMBER] Failed installation of latest MCPB version anu chandra (Thu Mar 10 2016 - 04:37:18 PST)
- Re: [AMBER] Failed installation of latest MCPB version Marcelo Andrade Chagas (Thu Mar 10 2016 - 04:42:09 PST)
- Re: [AMBER] Failed installation of latest MCPB version Daniel Roe (Thu Mar 10 2016 - 08:16:21 PST)
  - Re: [AMBER] Failed installation of latest MCPB version anu chandra (Thu Mar 10 2016 - 09:41:43 PST)
    - Re: [AMBER] Failed installation of latest MCPB version Marcelo Andrade Chagas (Thu Mar 10 2016 - 10:39:52 PST)
    - Re: [AMBER] Failed installation of latest MCPB version Marcelo Andrade Chagas (Thu Mar 10 2016 - 10:52:54 PST)
  - Re: [AMBER] Failed installation of latest MCPB version Marcelo Andrade Chagas (Thu Mar 10 2016 - 10:38:38 PST)
[AMBER] On Amber to Gromacs Parameter Conversion Robert Molt (Thu Mar 10 2016 - 12:55:19 PST)
- Re: [AMBER] On Amber to Gromacs Parameter Conversion Daniel Roe (Thu Mar 10 2016 - 13:53:15 PST)
[AMBER] On Amber to Gromacs Parameter Conversion Robert Molt (Thu Mar 10 2016 - 12:55:13 PST)
- Re: [AMBER] On Amber to Gromacs Parameter Conversion Hai Nguyen (Thu Mar 10 2016 - 13:13:08 PST)
  - Re: [AMBER] On Amber to Gromacs Parameter Conversion Robert Molt (Thu Mar 10 2016 - 17:45:00 PST)
    - Re: [AMBER] On Amber to Gromacs Parameter Conversion Hai Nguyen (Thu Mar 10 2016 - 19:32:47 PST)
    - Re: [AMBER] On Amber to Gromacs Parameter Conversion Robert Molt (Thu Mar 10 2016 - 20:48:23 PST)
    - Re: [AMBER] On Amber to Gromacs Parameter Conversion Hai Nguyen (Thu Mar 10 2016 - 22:21:25 PST)
    - Re: [AMBER] On Amber to Gromacs Parameter Conversion Sarah Witzke (Fri Mar 11 2016 - 03:57:24 PST)
    - Re: [AMBER] On Amber to Gromacs Parameter Conversion Robert Molt (Fri Mar 11 2016 - 05:32:30 PST)
    - Re: [AMBER] On Amber to Gromacs Parameter Conversion Hai Nguyen (Fri Mar 11 2016 - 08:00:29 PST)
    - Re: [AMBER] On Amber to Gromacs Parameter Conversion Hai Nguyen (Fri Mar 11 2016 - 11:11:52 PST)
    - Re: [AMBER] On Amber to Gromacs Parameter Conversion Robert Molt (Fri Mar 11 2016 - 12:28:42 PST)
    - Re: [AMBER] On Amber to Gromacs Parameter Conversion Jason Swails (Fri Mar 11 2016 - 16:50:09 PST)
    - Re: [AMBER] On Amber to Gromacs Parameter Conversion Robert Molt (Fri Mar 11 2016 - 17:33:03 PST)
    - Re: [AMBER] On Amber to Gromacs Parameter Conversion Jason Swails (Fri Mar 11 2016 - 17:51:49 PST)
    - Re: [AMBER] On Amber to Gromacs Parameter Conversion Robert Molt (Fri Mar 11 2016 - 18:47:35 PST)
[AMBER] Paradynamics simulations with Amber lipengfei_mail (Thu Mar 10 2016 - 23:02:13 PST)
- Re: [AMBER] Paradynamics simulations with Amber David A Case (Fri Mar 11 2016 - 04:26:22 PST)
- Re: [AMBER] Paradynamics simulations with Amber lipengfei_mail (Fri Mar 11 2016 - 22:36:51 PST)
  - Re: [AMBER] Paradynamics simulations with Amber Pengfei Li (Sat Mar 12 2016 - 05:10:13 PST)
[AMBER] Lower energy frame from summary.EPTOT Vasantha Kumar (Fri Mar 11 2016 - 01:06:47 PST)
- Re: [AMBER] Lower energy frame from summary.EPTOT David A Case (Fri Mar 11 2016 - 04:32:03 PST)
  - Re: [AMBER] Lower energy frame from summary.EPTOT Vasantha Kumar (Fri Mar 11 2016 - 08:49:20 PST)
    - Re: [AMBER] Lower energy frame from summary.EPTOT Jason Swails (Fri Mar 11 2016 - 17:53:29 PST)
[AMBER] generate frcmod.user file for missing parameters Jesmita Dhar (Fri Mar 11 2016 - 03:03:04 PST)
- Re: [AMBER] generate frcmod.user file for missing parameters David A Case (Fri Mar 11 2016 - 04:33:41 PST)
- Re: [AMBER] generate frcmod.user file for missing parameters FyD (Fri Mar 11 2016 - 04:48:00 PST)
[AMBER] protein-RNA complex simulation Sreemol G (Fri Mar 11 2016 - 03:57:51 PST)
- Re: [AMBER] protein-RNA complex simulation David A Case (Fri Mar 11 2016 - 04:35:03 PST)
  - Re: [AMBER] protein-RNA complex simulation Sreemol G (Fri Mar 11 2016 - 04:47:18 PST)
    - Re: [AMBER] protein-RNA complex simulation Vlad Cojocaru (Fri Mar 11 2016 - 05:04:33 PST)
    - Re: [AMBER] protein-RNA complex simulation Sreemol G (Fri Mar 11 2016 - 05:26:32 PST)
    - Re: [AMBER] protein-RNA complex simulation Vlad Cojocaru (Fri Mar 11 2016 - 05:33:07 PST)
    - [AMBER] TIP3P Wu Xu (Sat Mar 12 2016 - 14:11:44 PST)
    - Re: [AMBER] TIP3P David Cerutti (Sat Mar 12 2016 - 15:57:31 PST)
    - Re: [AMBER] TIP3P Wu Xu (Sat Mar 12 2016 - 16:51:39 PST)
    - Re: [AMBER] protein-RNA complex simulation Carlos Simmerling (Fri Mar 11 2016 - 05:47:07 PST)
    - Re: [AMBER] protein-RNA complex simulation David A Case (Fri Mar 11 2016 - 05:49:08 PST)
    - Re: [AMBER] protein-RNA complex simulation Sreemol G (Fri Mar 11 2016 - 22:07:45 PST)
    - Re: [AMBER] protein-RNA complex simulation Thomas Cheatham (Fri Mar 11 2016 - 22:19:05 PST)
    - Re: [AMBER] protein-RNA complex simulation Thomas Cheatham (Fri Mar 11 2016 - 22:21:27 PST)
    - Re: [AMBER] protein-RNA complex simulation Vlad Cojocaru (Fri Mar 11 2016 - 22:59:10 PST)
[AMBER] References Hadeer ELHabashy (Fri Mar 11 2016 - 07:55:29 PST)
- Re: [AMBER] References Christina Bergonzo (Fri Mar 11 2016 - 07:57:26 PST)
  - Re: [AMBER] References Hadeer ELHabashy (Fri Mar 11 2016 - 08:04:02 PST)
    - Re: [AMBER] References Christina Bergonzo (Fri Mar 11 2016 - 08:05:28 PST)
    - Re: [AMBER] References Robert Molt (Fri Mar 11 2016 - 08:07:31 PST)
[AMBER] Igb and salt concentration for GBSA Arati Paudyal (Fri Mar 11 2016 - 15:09:02 PST)
- Re: [AMBER] Igb and salt concentration for GBSA Jason Swails (Fri Mar 11 2016 - 16:51:59 PST)
  - Re: [AMBER] Igb and salt concentration for GBSA Nhai (Fri Mar 11 2016 - 17:24:41 PST)
    - Re: [AMBER] Igb and salt concentration for GBSA Carlos Simmerling (Fri Mar 11 2016 - 17:37:41 PST)
    - Re: [AMBER] Igb and salt concentration for GBSA Jason Swails (Fri Mar 11 2016 - 17:50:39 PST)
[AMBER] RMSD too high after simulation Arati Paudyal (Fri Mar 11 2016 - 17:41:36 PST)
- Re: [AMBER] RMSD too high after simulation Carlos Simmerling (Fri Mar 11 2016 - 17:49:13 PST)
  - Re: [AMBER] RMSD too high after simulation Arati Paudyal (Fri Mar 11 2016 - 18:07:23 PST)
    - Re: [AMBER] RMSD too high after simulation Carlos Simmerling (Sat Mar 12 2016 - 03:09:02 PST)
- Re: [AMBER] RMSD too high after simulation conor parks (Fri Mar 11 2016 - 17:50:32 PST)
[AMBER] How is ΔGnonpolar computed in MMPBSA.py in AMBER 14? (inp=2 in &pb namelist) Stefan Ivanov (Fri Mar 11 2016 - 23:28:32 PST)
- Re: [AMBER] How is ΔGnonpolar computed in MMPBSA.py in AMBER 14? (inp=2 in &pb namelist) Ray Luo (Sat Mar 12 2016 - 20:21:58 PST)
  - Re: [AMBER] How is ΔGnonpolar computed in MMPBSA.py in AMBER 14? (inp=2 in &pb namelist) Stefan Ivanov (Sun Mar 13 2016 - 19:11:01 PDT)
    - Re: [AMBER] How is ΔGnonpolar computed in MMPBSA.py in AMBER 14? (inp=2 in &pb namelist) Ray Luo (Sun Mar 13 2016 - 20:52:30 PDT)
    - Re: [AMBER] How is ΔGnonpolar computed in MMPBSA.py in AMBER 14? (inp=2 in &pb namelist) Stefan Ivanov (Sun Mar 13 2016 - 22:11:33 PDT)
[AMBER] Problem with 'hydrogen' having multiple bonds using SHAKEH alexander.zlobin (Sat Mar 12 2016 - 06:47:28 PST)
- Re: [AMBER] Problem with 'hydrogen' having multiple bonds using SHAKEH David A Case (Sat Mar 12 2016 - 09:19:09 PST)
[AMBER] MMPBSA error Arati Paudyal (Sat Mar 12 2016 - 11:07:18 PST)
- Re: [AMBER] MMPBSA error Ray Luo (Sat Mar 12 2016 - 20:00:12 PST)
[AMBER] ISQBP 2016 meeting - registration opened! Thomas Cheatham (Sun Mar 13 2016 - 22:15:46 PDT)
Re: [AMBER] AMBER:neutralisation of non integral charges Shilpa Gupta (Mon Mar 14 2016 - 06:22:42 PDT)
- Re: [AMBER] AMBER:neutralisation of non integral charges Hannes Loeffler (Mon Mar 14 2016 - 06:37:42 PDT)
[AMBER] bad atom type with MMPBSA decomposition? Kenneth Huang (Mon Mar 14 2016 - 06:58:25 PDT)
[AMBER] parmed -setBond command Balaji Selvam (Mon Mar 14 2016 - 11:19:39 PDT)
- Re: [AMBER] parmed -setBond command Daniel Roe (Mon Mar 14 2016 - 11:36:04 PDT)
[AMBER] Lifetime analysis of backbone hydrogen bonds Krantzman, Kristin D (Mon Mar 14 2016 - 12:28:55 PDT)
- Re: [AMBER] Lifetime analysis of backbone hydrogen bonds Daniel Roe (Mon Mar 14 2016 - 12:45:09 PDT)
  - Re: [AMBER] Lifetime analysis of backbone hydrogen bonds Krantzman, Kristin D (Mon Mar 14 2016 - 13:34:30 PDT)
    - Re: [AMBER] Lifetime analysis of backbone hydrogen bonds Krantzman, Kristin D (Mon Mar 14 2016 - 13:37:02 PDT)
    - Re: [AMBER] Lifetime analysis of backbone hydrogen bonds Daniel Roe (Mon Mar 14 2016 - 13:46:32 PDT)
Re: [AMBER] Problems when trying to improve angle parameters whith paramfit Jérémie KNOOPS [531802] (Mon Mar 14 2016 - 14:34:57 PDT)
- Re: [AMBER] Problems when trying to improve angle parameters whith paramfit David Cerutti (Mon Mar 14 2016 - 15:07:10 PDT)
  - Re: [AMBER] Problems when trying to improve angle parameters whith paramfit Robin Betz (Mon Mar 14 2016 - 15:38:56 PDT)
[AMBER] Convergence problem with the SCC-DFTB example. Jinfeng Huang (Tue Mar 15 2016 - 01:29:17 PDT)
- Re: [AMBER] Convergence problem with the SCC-DFTB example. Gustavo Seabra (Tue Mar 15 2016 - 12:09:05 PDT)
  - Re: [AMBER] Convergence problem with the SCC-DFTB example. Jinfeng Huang (Fri Mar 25 2016 - 07:55:26 PDT)
    - Re: [AMBER] Convergence problem with the SCC-DFTB example. Gustavo Seabra (Wed Apr 06 2016 - 07:21:29 PDT)
[AMBER] A query about using random seed generator in simulations anu chandra (Tue Mar 15 2016 - 05:14:45 PDT)
- Re: [AMBER] A query about using random seed generator in simulations David A Case (Tue Mar 15 2016 - 06:58:52 PDT)
[AMBER] Attempting MC barostat change: Failed Michael Shokhen (Tue Mar 15 2016 - 05:51:21 PDT)
- Re: [AMBER] Attempting MC barostat change: Failed Daniel Roe (Tue Mar 15 2016 - 07:42:37 PDT)
- Re: [AMBER] Attempting MC barostat change: Failed Niel Henriksen (Tue Mar 15 2016 - 09:49:32 PDT)
[AMBER] PBSA fails with error message PB Bomb in epsmap(): epsz out of range Bruno Falcone (Tue Mar 15 2016 - 14:55:20 PDT)
- Re: [AMBER] PBSA fails with error message PB Bomb in epsmap(): epsz out of range Ray Luo (Tue Mar 15 2016 - 15:16:48 PDT)
  - Re: [AMBER] PBSA fails with error message PB Bomb in epsmap(): epsz out of range Bruno Falcone (Wed Mar 16 2016 - 07:27:22 PDT)
    - Re: [AMBER] PBSA fails with error message PB Bomb in epsmap(): epsz out of range Ray Luo (Fri Mar 18 2016 - 18:16:12 PDT)
[AMBER] shell script yhzahsc (Tue Mar 15 2016 - 19:27:35 PDT)
- Re: [AMBER] shell script Daniel Roe (Tue Mar 15 2016 - 19:35:53 PDT)
- Re: [AMBER] shell script Marc van der Kamp (Wed Mar 16 2016 - 02:18:34 PDT)
  - [AMBER] 回复：Re: shell script yhzahsc (Wed Mar 16 2016 - 17:54:06 PDT)
[AMBER] MMPBSA doubt Mary Varughese (Wed Mar 16 2016 - 02:20:21 PDT)
- Re: [AMBER] MMPBSA doubt Ray Luo (Fri Mar 18 2016 - 18:13:36 PDT)
  - Re: [AMBER] MMPBSA doubt Mary Varughese (Fri Mar 18 2016 - 21:48:15 PDT)
    - Re: [AMBER] MMPBSA doubt Ray Luo (Mon Mar 21 2016 - 17:39:19 PDT)
    - Re: [AMBER] MMPBSA doubt Mary Varughese (Mon Mar 21 2016 - 19:06:45 PDT)
    - Re: [AMBER] MMPBSA doubt Ray Luo (Mon Mar 21 2016 - 23:11:15 PDT)
    - Re: [AMBER] MMPBSA doubt Mary Varughese (Tue Mar 22 2016 - 02:43:11 PDT)
    - Re: [AMBER] MMPBSA doubt Ray Luo (Tue Mar 22 2016 - 11:08:51 PDT)
    - Re: [AMBER] MMPBSA doubt Mary Varughese (Tue Mar 22 2016 - 16:26:24 PDT)
[AMBER] rmsd y axis value deviation. Saman Yousuf ali (Wed Mar 16 2016 - 02:55:35 PDT)
- Re: [AMBER] rmsd y axis value deviation. Hannes Loeffler (Wed Mar 16 2016 - 03:08:39 PDT)
  - Re: [AMBER] rmsd y axis value deviation. Saman Yousuf ali (Wed Mar 16 2016 - 03:29:58 PDT)
    - Re: [AMBER] rmsd y axis value deviation. Hannes Loeffler (Wed Mar 16 2016 - 04:59:52 PDT)
- Re: [AMBER] rmsd y axis value deviation. Saman Yousuf ali (Wed Mar 16 2016 - 12:04:40 PDT)
  - Re: [AMBER] rmsd y axis value deviation. Daniel Roe (Wed Mar 16 2016 - 12:12:32 PDT)
[AMBER] topology file for a graphene oxide with repetitive pattern Jesmita Dhar (Wed Mar 16 2016 - 03:07:29 PDT)
- Re: [AMBER] topology file for a graphene oxide with repetitive pattern Hannes Loeffler (Wed Mar 16 2016 - 03:27:13 PDT)
- Re: [AMBER] topology file for a graphene oxide with repetitive pattern FyD (Fri Mar 18 2016 - 03:22:00 PDT)
[AMBER] red server error: ddikick.x: Fatal error detected Jesmita Dhar (Wed Mar 16 2016 - 03:44:10 PDT)
- Re: [AMBER] red server error: ddikick.x: Fatal error detected Hannes Loeffler (Wed Mar 16 2016 - 03:56:56 PDT)
- Re: [AMBER] red server error: ddikick.x: Fatal error detected FyD (Fri Mar 18 2016 - 03:18:07 PDT)
[AMBER] Error with make test.parallel in AmberTools 15 installation anu chandra (Wed Mar 16 2016 - 09:28:10 PDT)
- Re: [AMBER] Error with make test.parallel in AmberTools 15 installation Daniel Roe (Wed Mar 16 2016 - 09:32:38 PDT)
  - Re: [AMBER] Error with make test.parallel in AmberTools 15 installation anu chandra (Thu Mar 17 2016 - 06:03:51 PDT)
[AMBER] tests dont work after installation Wesley Alves (Wed Mar 16 2016 - 10:48:02 PDT)
- Re: [AMBER] tests dont work after installation Daniel Roe (Wed Mar 16 2016 - 10:56:25 PDT)
- Re: [AMBER] tests dont work after installation Marcelo Andrade Chagas (Wed Mar 16 2016 - 11:19:10 PDT)
[AMBER] GROMACS File Conversion Subtlety Robert Molt (Wed Mar 16 2016 - 23:03:10 PDT)
- Re: [AMBER] GROMACS File Conversion Subtlety Daniel Roe (Thu Mar 17 2016 - 06:37:19 PDT)
  - Re: [AMBER] GROMACS File Conversion Subtlety Dr. Robert Molt (Thu Mar 17 2016 - 17:00:39 PDT)
    - Re: [AMBER] GROMACS File Conversion Subtlety Daniel Roe (Thu Mar 17 2016 - 17:09:21 PDT)
    - Re: [AMBER] GROMACS File Conversion Subtlety Daniel Roe (Thu Mar 17 2016 - 17:13:43 PDT)
    - Re: [AMBER] GROMACS File Conversion Subtlety Dr. Robert Molt (Thu Mar 17 2016 - 17:18:28 PDT)
    - Re: [AMBER] GROMACS File Conversion Subtlety Daniel Roe (Fri Mar 18 2016 - 16:32:50 PDT)
    - Re: [AMBER] GROMACS File Conversion Subtlety Mark Abraham (Fri Mar 18 2016 - 21:04:24 PDT)
    - Re: [AMBER] GROMACS File Conversion Subtlety Thomas Cheatham (Fri Mar 18 2016 - 22:04:23 PDT)
    - Re: [AMBER] GROMACS File Conversion Subtlety Dr. Robert Molt (Fri Mar 18 2016 - 22:15:11 PDT)
    - Re: [AMBER] GROMACS File Conversion Subtlety hannes.loeffler.stfc.ac.uk (Sat Mar 19 2016 - 00:42:00 PDT)
    - Re: [AMBER] GROMACS File Conversion Subtlety Mark Abraham (Sat Mar 19 2016 - 09:48:06 PDT)
    - Re: [AMBER] GROMACS File Conversion Subtlety Daniel Roe (Sat Mar 19 2016 - 07:20:47 PDT)
    - Re: [AMBER] GROMACS File Conversion Subtlety Jason Swails (Sat Mar 19 2016 - 11:33:30 PDT)
    - Re: [AMBER] GROMACS File Conversion Subtlety Mark Abraham (Sat Mar 19 2016 - 12:32:57 PDT)
    - Re: [AMBER] GROMACS File Conversion Subtlety Jason Swails (Sun Mar 20 2016 - 08:03:03 PDT)
    - Re: [AMBER] GROMACS File Conversion Subtlety Mark Abraham (Sun Mar 20 2016 - 08:26:00 PDT)
    - Re: [AMBER] GROMACS File Conversion Subtlety Daniel Roe (Sun Mar 20 2016 - 08:29:54 PDT)
    - Re: [AMBER] GROMACS File Conversion Subtlety Daniel Roe (Sun Mar 20 2016 - 09:00:33 PDT)
    - Re: [AMBER] GROMACS File Conversion Subtlety Mark Abraham (Mon Sep 05 2016 - 08:19:19 PDT)
[AMBER] errors in plumed and amber14 patch jixiaofeng (Thu Mar 17 2016 - 01:06:04 PDT)
- Re: [AMBER] errors in plumed and amber14 patch hannes.loeffler.stfc.ac.uk (Thu Mar 17 2016 - 01:41:37 PDT)
  - Re: [AMBER] errors in plumed and amber14 patch Jason Swails (Thu Mar 17 2016 - 03:02:26 PDT)
[AMBER] 2016 ISQBP Meeting: early registration / abstract submission deadline approaching Vlad Cojocaru (Thu Mar 17 2016 - 01:50:08 PDT)
[AMBER] Amber 14 - "Error: Unsupported CUDA version 7.5 detected" Enrique Frio (Thu Mar 17 2016 - 04:02:29 PDT)
- Re: [AMBER] Amber 14 - "Error: Unsupported CUDA version 7.5 detected" Ross Walker (Thu Mar 17 2016 - 08:02:24 PDT)
  - Re: [AMBER] Amber 14 - "Error: Unsupported CUDA version 7.5 detected" Enrique Frio (Thu Mar 17 2016 - 15:55:15 PDT)
    - Re: [AMBER] Amber 14 - "Error: Unsupported CUDA version 7.5 detected" Jason Swails (Thu Mar 17 2016 - 16:05:47 PDT)
    - Re: [AMBER] Amber 14 - "Error: Unsupported CUDA version 7.5 detected" Enrique Frio (Thu Mar 17 2016 - 18:25:18 PDT)
    - Re: [AMBER] Amber 14 - "Error: Unsupported CUDA version 7.5 detected" Enrique Frio (Fri Mar 18 2016 - 05:48:08 PDT)
    - Re: [AMBER] Amber 14 - "Error: Unsupported CUDA version 7.5 detected" Enrique Frio (Fri Mar 18 2016 - 05:55:49 PDT)
    - Re: [AMBER] Amber 14 - "Error: Unsupported CUDA version 7.5 detected" Jason Swails (Fri Mar 18 2016 - 10:15:55 PDT)
    - Re: [AMBER] Amber 14 - "Error: Unsupported CUDA version 7.5 detected" Enrique Frio (Fri Mar 18 2016 - 14:45:30 PDT)
    - Re: [AMBER] Amber 14 - "Error: Unsupported CUDA version 7.5 detected" Jason Swails (Fri Mar 18 2016 - 15:07:10 PDT)
    - Re: [AMBER] Amber 14 - "Error: Unsupported CUDA version 7.5 detected" Enrique Frio (Sun Mar 20 2016 - 20:53:10 PDT)
    - Re: [AMBER] Amber 14 - "Error: Unsupported CUDA version 7.5 detected" Jason Swails (Fri Mar 18 2016 - 10:09:55 PDT)
[AMBER] Training and Innovation Course in Drug Design Thomas Exner (Thu Mar 17 2016 - 08:02:56 PDT)
[AMBER] nitro tyrosine Wu Xu (Thu Mar 17 2016 - 19:06:00 PDT)
- Re: [AMBER] nitro tyrosine FyD (Fri Mar 18 2016 - 05:03:12 PDT)
Re: [AMBER] errors in plumed and amber14 patch (Jason Swails) jixiaofeng (Thu Mar 17 2016 - 19:12:38 PDT)
- Re: [AMBER] errors in plumed and amber14 patch (Jason Swails) Jason Swails (Sun Mar 20 2016 - 10:14:40 PDT)
- Re: [AMBER] errors in plumed and amber14 patch (Jason Swails) jixiaofeng (Sun Mar 20 2016 - 20:14:41 PDT)
[AMBER] The basis for selecting step sizes Bin ZOU (Thu Mar 17 2016 - 22:51:41 PDT)
- Re: [AMBER] The basis for selecting step sizes hannes.loeffler.stfc.ac.uk (Fri Mar 18 2016 - 00:19:56 PDT)
[AMBER] restart file error Sidhu, Khushwant (Dr.) (Fri Mar 18 2016 - 03:59:37 PDT)
- Re: [AMBER] restart file error Bill Ross (Fri Mar 18 2016 - 12:47:01 PDT)
- Re: [AMBER] restart file error Jason Swails (Fri Mar 18 2016 - 14:19:30 PDT)
[AMBER] Is there a shift of QM energy in a QM/MM simulation? Pengfei Li (Fri Mar 18 2016 - 05:26:47 PDT)
[AMBER] MPI_ABORT in pH-REMD Elisa Pieri (Fri Mar 18 2016 - 06:05:02 PDT)
- Re: [AMBER] MPI_ABORT in pH-REMD Jason Swails (Fri Mar 18 2016 - 11:46:33 PDT)
  - Re: [AMBER] MPI_ABORT in pH-REMD Elisa Pieri (Mon Mar 21 2016 - 02:08:42 PDT)
    - Re: [AMBER] MPI_ABORT in pH-REMD Bin ZOU (Mon Mar 21 2016 - 02:36:25 PDT)
    - Re: [AMBER] MPI_ABORT in pH-REMD Elisa Pieri (Mon Mar 21 2016 - 02:46:21 PDT)
    - Re: [AMBER] MPI_ABORT in pH-REMD Jason Swails (Mon Mar 21 2016 - 07:59:21 PDT)
    - Re: [AMBER] MPI_ABORT in pH-REMD Elisa Pieri (Mon Mar 21 2016 - 08:13:05 PDT)
    - Re: [AMBER] MPI_ABORT in pH-REMD Daniel Roe (Mon Mar 21 2016 - 08:23:52 PDT)
[AMBER] set up for a binding event MD Arnoult, Eric [JRDUS] (Fri Mar 18 2016 - 11:02:17 PDT)
- Re: [AMBER] set up for a binding event MD Jason Swails (Tue Mar 22 2016 - 18:48:08 PDT)
- Re: [AMBER] set up for a binding event MD Marcos Serrou do Amaral (Tue Mar 22 2016 - 19:41:04 PDT)
  - Re: [AMBER] set up for a binding event MD Arnoult, Eric [JRDUS] (Fri Mar 25 2016 - 07:24:57 PDT)
    - Re: [AMBER] set up for a binding event MD Carlos Simmerling (Fri Mar 25 2016 - 07:30:05 PDT)
    - Re: [AMBER] set up for a binding event MD Arnoult, Eric [JRDUS] (Fri Mar 25 2016 - 13:47:06 PDT)
[AMBER] FW: problem in plotting total energy graph by using perl script Sehrish Naz Aijaz (Sat Mar 19 2016 - 01:20:41 PDT)
- Re: [AMBER] FW: problem in plotting total energy graph by using perl script Hai Nguyen (Sat Mar 19 2016 - 01:23:34 PDT)
[AMBER] problem in plotting total energy graphs by perl script Sehrish Naz Aijaz (Sat Mar 19 2016 - 01:25:27 PDT)
- Re: [AMBER] problem in plotting total energy graphs by perl script Hai Nguyen (Sat Mar 19 2016 - 01:55:51 PDT)
- Re: [AMBER] problem in plotting total energy graphs by perl script Sehrish Naz Aijaz (Sat Mar 19 2016 - 02:26:32 PDT)
  - Re: [AMBER] problem in plotting total energy graphs by perl script Hai Nguyen (Sat Mar 19 2016 - 02:48:35 PDT)
- Re: [AMBER] problem in plotting total energy graphs by perl script Sehrish Naz Aijaz (Sat Mar 19 2016 - 03:16:30 PDT)
  - Re: [AMBER] problem in plotting total energy graphs by perl script Bill Ross (Sat Mar 19 2016 - 13:11:40 PDT)
- Re: [AMBER] problem in plotting total energy graphs by perl script Sehrish Naz Aijaz (Sat Mar 19 2016 - 03:29:52 PDT)
  - Re: [AMBER] problem in plotting total energy graphs by perl script Jason Swails (Sun Mar 20 2016 - 10:12:40 PDT)
- Re: [AMBER] problem in plotting total energy graphs by perl script Sehrish Naz Aijaz (Sun Mar 20 2016 - 21:56:46 PDT)
  - Re: [AMBER] problem in plotting total energy graphs by perl script Bill Ross (Sun Mar 20 2016 - 22:10:36 PDT)
  - Re: [AMBER] problem in plotting total energy graphs by perl script Daniel Roe (Mon Mar 21 2016 - 07:38:16 PDT)
- Re: [AMBER] problem in plotting total energy graphs by perl script Sehrish Naz Aijaz (Sun Mar 20 2016 - 21:58:01 PDT)
- Re: [AMBER] problem in plotting total energy graphs by perl script Sehrish Naz Aijaz (Tue Mar 22 2016 - 08:50:41 PDT)
  - Re: [AMBER] problem in plotting total energy graphs by perl script Daniel Roe (Tue Mar 22 2016 - 09:01:00 PDT)
  - Re: [AMBER] problem in plotting total energy graphs by perl script David A Case (Tue Mar 22 2016 - 09:57:05 PDT)
- Re: [AMBER] problem in plotting total energy graphs by perl script Sehrish Naz Aijaz (Thu Mar 24 2016 - 21:59:13 PDT)
  - Re: [AMBER] problem in plotting total energy graphs by perl script Bill Ross (Thu Mar 24 2016 - 22:39:25 PDT)
    - Re: [AMBER] problem in plotting total energy graphs by perl script Bill Ross (Thu Mar 24 2016 - 22:41:07 PDT)
  - Re: [AMBER] problem in plotting total energy graphs by perl script Daniel Roe (Fri Mar 25 2016 - 07:48:40 PDT)
- Re: [AMBER] problem in plotting total energy graphs by perl script Sehrish Naz Aijaz (Fri Mar 25 2016 - 04:18:01 PDT)
- Re: [AMBER] problem in plotting total energy graphs by perl script Sehrish Naz Aijaz (Mon Mar 28 2016 - 02:54:44 PDT)
  - Re: [AMBER] problem in plotting total energy graphs by perl script Daniel Roe (Mon Mar 28 2016 - 06:37:52 PDT)
- Re: [AMBER] problem in plotting total energy graphs by perl script Sehrish Naz Aijaz (Mon Mar 28 2016 - 21:03:01 PDT)
  - Re: [AMBER] problem in plotting total energy graphs by perl script Jason Swails (Tue Mar 29 2016 - 02:57:25 PDT)
- Re: [AMBER] problem in plotting total energy graphs by perl script Sehrish Naz Aijaz (Wed Mar 30 2016 - 00:49:34 PDT)
  - Re: [AMBER] problem in plotting total energy graphs by perl script Daniel Roe (Wed Mar 30 2016 - 04:46:24 PDT)
- Re: [AMBER] problem in plotting total energy graphs by perl script Sehrish Naz Aijaz (Wed Mar 30 2016 - 21:38:44 PDT)
[AMBER] Normal Mode Job Allocation Failure Cockroft, Nicholas T. (Mon Mar 21 2016 - 08:18:03 PDT)
- Re: [AMBER] Normal Mode Job Allocation Failure Daniel Roe (Wed Mar 23 2016 - 08:54:59 PDT)
  - Re: [AMBER] Normal Mode Job Allocation Failure Cockroft, Nicholas T. (Wed Mar 23 2016 - 11:12:50 PDT)
[AMBER] mmpbsa discrepancies George Tzotzos (Mon Mar 21 2016 - 10:05:36 PDT)
- Re: [AMBER] mmpbsa discrepancies Jason Swails (Tue Mar 22 2016 - 18:45:18 PDT)
  - Re: [AMBER] mmpbsa discrepancies George Tzotzos (Wed Mar 23 2016 - 05:44:02 PDT)
[AMBER] strange output with nativecontacts command Krantzman, Kristin D (Mon Mar 21 2016 - 17:22:06 PDT)
- Re: [AMBER] strange output with nativecontacts command Daniel Roe (Mon Mar 21 2016 - 17:53:30 PDT)
  - Re: [AMBER] strange output with nativecontacts command Krantzman, Kristin D (Mon Mar 21 2016 - 17:57:19 PDT)
    - Re: [AMBER] strange output with nativecontacts command Daniel Roe (Mon Mar 21 2016 - 18:52:21 PDT)
    - Re: [AMBER] strange output with nativecontacts command Krantzman, Kristin D (Tue Mar 22 2016 - 11:58:55 PDT)
    - Re: [AMBER] strange output with nativecontacts command Daniel Roe (Tue Mar 22 2016 - 12:38:30 PDT)
    - Re: [AMBER] strange output with nativecontacts command Krantzman, Kristin D (Thu Mar 24 2016 - 10:32:25 PDT)
[AMBER] Calculating pair-wise interaction energy using MMPBSA for Gromacs files Suchetana Gupta (Mon Mar 21 2016 - 22:01:48 PDT)
- Re: [AMBER] Calculating pair-wise interaction energy using MMPBSA for Gromacs files Daniel Roe (Tue Mar 22 2016 - 07:30:31 PDT)
[AMBER] Combining parameter of Phosphoserine with 99SBILDN+bsc0 A kS (Mon Mar 21 2016 - 23:25:09 PDT)
- Re: [AMBER] Combining parameter of Phosphoserine with 99SBILDN+bsc0 Carlos Simmerling (Tue Mar 22 2016 - 04:29:03 PDT)
  - Re: [AMBER] Combining parameter of Phosphoserine with 99SBILDN+bsc0 A kS (Tue Mar 22 2016 - 05:22:53 PDT)
- Re: [AMBER] Combining parameter of Phosphoserine with 99SBILDN+bsc0 Daniel Roe (Tue Mar 22 2016 - 07:25:15 PDT)
  - Re: [AMBER] Combining parameter of Phosphoserine with 99SBILDN+bsc0 A kS (Tue Mar 22 2016 - 23:09:11 PDT)
    - Re: [AMBER] Combining parameter of Phosphoserine with 99SBILDN+bsc0 David A Case (Thu Mar 31 2016 - 04:52:11 PDT)
[AMBER] GAFF of Amber 'ff..' force field to prepare ligands? alexander.zlobin (Tue Mar 22 2016 - 03:50:29 PDT)
- Re: [AMBER] GAFF of Amber 'ff..' force field to prepare ligands? Karl Kirschner (Tue Mar 22 2016 - 04:43:33 PDT)
[AMBER] Tutorial 18 - CpHMD with pmemd R.G. Mantell (Tue Mar 22 2016 - 05:09:45 PDT)
- Re: [AMBER] Tutorial 18 - CpHMD with pmemd Marcos Serrou do Amaral (Tue Mar 22 2016 - 08:37:15 PDT)
  - Re: [AMBER] Tutorial 18 - CpHMD with pmemd Jason Swails (Tue Mar 22 2016 - 09:36:01 PDT)
- Re: [AMBER] Tutorial 18 - CpHMD with pmemd Jason Swails (Tue Mar 22 2016 - 09:03:25 PDT)
  - Re: [AMBER] Tutorial 18 - CpHMD with pmemd R.G. Mantell (Tue Mar 22 2016 - 10:31:34 PDT)
[AMBER] interview with David Case Nikolai Skrynnikov (Tue Mar 22 2016 - 22:02:17 PDT)
- Re: [AMBER] interview with David Case Nhai (Tue Mar 22 2016 - 22:19:28 PDT)
[AMBER] Problems running MD simulations with pseudocontact shifts as restraints Francisco Corzana López (Wed Mar 23 2016 - 01:44:12 PDT)
- Re: [AMBER] Problems running MD simulations with pseudocontact shifts as restraints Gustavo Seabra (Wed Mar 23 2016 - 06:34:00 PDT)
  - Re: [AMBER] Problems running MD simulations with pseudocontact shifts as restraints Francisco Corzana López (Wed Mar 23 2016 - 09:34:41 PDT)
    - Re: [AMBER] Problems running MD simulations with pseudocontact shifts as restraints Gustavo Seabra (Wed Mar 23 2016 - 13:15:55 PDT)
    - Re: [AMBER] Problems running MD simulations with pseudocontact shifts as restraints Francisco Corzana López (Wed Mar 23 2016 - 13:43:54 PDT)
[AMBER] Fwd: MMPBSA CalceError mmpbsa_py_energy failed with prmtop com.prmtop! Annie Ancy (Wed Mar 23 2016 - 03:49:00 PDT)
- Re: [AMBER] Fwd: MMPBSA CalceError mmpbsa_py_energy failed with prmtop com.prmtop! Jason Swails (Wed Mar 23 2016 - 06:09:38 PDT)
[AMBER] questions about mol2 and pdb file. Hong Sun (Wed Mar 23 2016 - 20:57:22 PDT)
- Re: [AMBER] questions about mol2 and pdb file. hannes.loeffler.stfc.ac.uk (Thu Mar 24 2016 - 00:26:48 PDT)
  - Re: [AMBER] questions about mol2 and pdb file. David A Case (Thu Mar 24 2016 - 04:16:23 PDT)
    - Re: [AMBER] questions about mol2 and pdb file. Hannes Loeffler (Thu Mar 24 2016 - 07:12:57 PDT)
- Re: [AMBER] questions about mol2 and pdb file. FyD (Thu Mar 24 2016 - 02:04:29 PDT)
[AMBER] RMSD of 0 for coordinated ion Francesco Gentile (Wed Mar 23 2016 - 21:25:36 PDT)
- Re: [AMBER] RMSD of 0 for coordinated ion Hai Nguyen (Wed Mar 23 2016 - 21:30:28 PDT)
  - Re: [AMBER] RMSD of 0 for coordinated ion Bill Ross (Wed Mar 23 2016 - 21:40:00 PDT)
- Re: [AMBER] RMSD of 0 for coordinated ion Daniel Roe (Thu Mar 24 2016 - 09:20:00 PDT)
- Re: [AMBER] RMSD of 0 for coordinated ion Francesco Gentile (Thu Mar 24 2016 - 16:19:19 PDT)
  - Re: [AMBER] RMSD of 0 for coordinated ion Daniel Roe (Thu Mar 24 2016 - 18:28:25 PDT)
  - Re: [AMBER] RMSD of 0 for coordinated ion Francesco Gentile (Fri Mar 25 2016 - 12:23:17 PDT)
[AMBER] On alphabetizing impropers David Cerutti (Wed Mar 23 2016 - 22:42:52 PDT)
- Re: [AMBER] On alphabetizing impropers Bill Ross (Wed Mar 23 2016 - 23:01:10 PDT)
  - Re: [AMBER] On alphabetizing impropers David Cerutti (Wed Mar 23 2016 - 23:02:56 PDT)
    - Re: [AMBER] On alphabetizing impropers Christian Schafmeister (Wed Mar 23 2016 - 23:10:18 PDT)
- Re: [AMBER] On alphabetizing impropers David A Case (Thu Mar 24 2016 - 04:23:29 PDT)
  - Re: [AMBER] On alphabetizing impropers Brent Krueger (Thu Mar 24 2016 - 06:53:18 PDT)
    - Re: [AMBER] On alphabetizing impropers David Cerutti (Thu Mar 24 2016 - 07:47:20 PDT)
    - Re: [AMBER] On alphabetizing impropers Jason Swails (Fri Mar 25 2016 - 05:47:20 PDT)
    - Re: [AMBER] On alphabetizing impropers David Cerutti (Fri Mar 25 2016 - 08:07:42 PDT)
    - Re: [AMBER] On alphabetizing impropers Jason Swails (Fri Mar 25 2016 - 09:04:46 PDT)
    - Re: [AMBER] On alphabetizing impropers David Cerutti (Fri Mar 25 2016 - 09:08:09 PDT)
    - Re: [AMBER] On alphabetizing impropers Bill Ross (Fri Mar 25 2016 - 12:03:42 PDT)
    - Re: [AMBER] On alphabetizing impropers Bill Ross (Fri Mar 25 2016 - 12:01:02 PDT)
    - Re: [AMBER] On alphabetizing impropers David A Case (Thu Mar 24 2016 - 09:00:04 PDT)
    - Re: [AMBER] On alphabetizing impropers Brent Krueger (Thu Mar 24 2016 - 09:22:47 PDT)
  - Re: [AMBER] On alphabetizing impropers Bill Ross (Thu Mar 24 2016 - 12:24:30 PDT)
    - Re: [AMBER] On alphabetizing impropers David Cerutti (Thu Mar 24 2016 - 15:40:09 PDT)
    - Re: [AMBER] On alphabetizing impropers Bill Ross (Thu Mar 24 2016 - 18:35:51 PDT)
    - Re: [AMBER] On alphabetizing impropers David Cerutti (Thu Mar 24 2016 - 21:21:12 PDT)
    - Re: [AMBER] On alphabetizing impropers David A Case (Fri Mar 25 2016 - 04:14:33 PDT)
  - Re: [AMBER] On alphabetizing impropers Jason Swails (Fri Mar 25 2016 - 05:43:01 PDT)
[AMBER] [Amber] Polarizable ff for vacuum Edwin Aponte (Thu Mar 24 2016 - 07:48:21 PDT)
- Re: [AMBER] [Amber] Polarizable ff for vacuum Carlos Simmerling (Thu Mar 24 2016 - 09:16:19 PDT)
  - Re: [AMBER] [Amber] Polarizable ff for vacuum Edwin Aponte (Thu Mar 24 2016 - 09:41:52 PDT)
- Re: [AMBER] [Amber] Polarizable ff for vacuum David A Case (Thu Mar 24 2016 - 09:46:42 PDT)
  - Re: [AMBER] [Amber] Polarizable ff for vacuum Carlos Simmerling (Thu Mar 24 2016 - 10:05:22 PDT)
[AMBER] Amber parameters for deprotonated threonine anu chandra (Thu Mar 24 2016 - 09:03:54 PDT)
- Re: [AMBER] Amber parameters for deprotonated threonine Carlos Simmerling (Thu Mar 24 2016 - 09:14:04 PDT)
  - Re: [AMBER] Amber parameters for deprotonated threonine anu chandra (Thu Mar 24 2016 - 14:59:55 PDT)
[AMBER] desc in leap amirhossein taghavi (Thu Mar 24 2016 - 09:05:26 PDT)
- Re: [AMBER] desc in leap Daniel Roe (Thu Mar 24 2016 - 09:29:06 PDT)
- Re: [AMBER] desc in leap Bill Ross (Thu Mar 24 2016 - 17:53:35 PDT)
[AMBER] nonnative contacts Krantzman, Kristin D (Thu Mar 24 2016 - 10:27:09 PDT)
- Re: [AMBER] nonnative contacts Daniel Roe (Fri Mar 25 2016 - 08:08:04 PDT)
  - Re: [AMBER] nonnative contacts Krantzman, Kristin D (Fri Mar 25 2016 - 08:53:55 PDT)
[AMBER] mpirun .... hwloc Marcelo Andrade Chagas (Thu Mar 24 2016 - 11:29:03 PDT)
- Re: [AMBER] mpirun .... hwloc David A Case (Fri Mar 25 2016 - 04:20:15 PDT)
[AMBER] [AmberTools15 & Amber14 Installation] Make Test Possible Failures Can Be Ignored or Not Guqin Shi (Thu Mar 24 2016 - 12:12:11 PDT)
- Re: [AMBER] [AmberTools15 & Amber14 Installation] Make Test Possible Failures Can Be Ignored or Not Charles Lin (Thu Mar 24 2016 - 12:19:58 PDT)
  - Re: [AMBER] [AmberTools15 & Amber14 Installation] Make Test Possible Failures Can Be Ignored or Not Guqin Shi (Thu Mar 24 2016 - 12:24:54 PDT)
    - Re: [AMBER] [AmberTools15 & Amber14 Installation] Make Test Possible Failures Can Be Ignored or Not Charles Lin (Thu Mar 24 2016 - 12:29:04 PDT)
    - Re: [AMBER] [AmberTools15 & Amber14 Installation] Make Test Possible Failures Can Be Ignored or Not Guqin Shi (Thu Mar 24 2016 - 13:48:56 PDT)
    - Re: [AMBER] [AmberTools15 & Amber14 Installation] Make Test Possible Failures Can Be Ignored or Not Hai Nguyen (Thu Mar 24 2016 - 15:02:13 PDT)
- Re: [AMBER] [AmberTools15 & Amber14 Installation] Make Test Possible Failures Can Be Ignored or Not Ross Walker (Thu Mar 24 2016 - 12:22:56 PDT)
  - Re: [AMBER] [AmberTools15 & Amber14 Installation] Make Test Possible Failures Can Be Ignored or Not Guqin Shi (Thu Mar 24 2016 - 12:27:36 PDT)
[AMBER] AT_15 install/osx notes, xleap deselect not working Bill Ross (Thu Mar 24 2016 - 18:27:08 PDT)
- Re: [AMBER] AT_15 install/osx notes, xleap deselect not working Jason Swails (Fri Mar 25 2016 - 09:22:26 PDT)
  - Re: [AMBER] AT_15 install/osx notes, xleap deselect not working Daniel Roe (Fri Mar 25 2016 - 09:35:05 PDT)
[AMBER] Clustering waleed zalloum (Fri Mar 25 2016 - 02:06:13 PDT)
- Re: [AMBER] Clustering Daniel Roe (Fri Mar 25 2016 - 07:53:00 PDT)
[AMBER] MMPBSApy - APBS bug Marek Maly (Sat Mar 26 2016 - 10:09:30 PDT)
[AMBER] membrane protein problem Michael Shokhen (Sat Mar 26 2016 - 11:35:55 PDT)
- Re: [AMBER] membrane protein problem Jason Swails (Sat Mar 26 2016 - 12:18:05 PDT)
  - Re: [AMBER] membrane protein problem Michael Shokhen (Sat Mar 26 2016 - 12:45:42 PDT)
    - Re: [AMBER] membrane protein problem Jason Swails (Sat Mar 26 2016 - 13:08:16 PDT)
    - Re: [AMBER] membrane protein problem Bill Ross (Sat Mar 26 2016 - 13:45:37 PDT)
    - Re: [AMBER] membrane protein problem Chris Moth (Sat Mar 26 2016 - 15:14:51 PDT)
    - Re: [AMBER] membrane protein problem David Cerutti (Sat Mar 26 2016 - 15:51:14 PDT)
[AMBER] charge membrane Fabian gmail (Mon Mar 28 2016 - 02:18:59 PDT)
[AMBER] membrane protein complex preparation Fabian gmail (Mon Mar 28 2016 - 04:15:16 PDT)
- Re: [AMBER] membrane protein complex preparation Dickson, Callum J (Mon Mar 28 2016 - 06:52:38 PDT)
  - Re: [AMBER] membrane protein complex preparation Fabian gmail (Mon Mar 28 2016 - 07:42:19 PDT)
    - Re: [AMBER] membrane protein complex preparation Dickson, Callum J (Mon Mar 28 2016 - 08:01:42 PDT)
    - Re: [AMBER] membrane protein complex preparation Fabian gmail (Mon Mar 28 2016 - 08:14:56 PDT)
    - Re: [AMBER] membrane protein complex preparation Dickson, Callum J (Mon Mar 28 2016 - 09:42:03 PDT)
    - Re: [AMBER] membrane protein complex preparation Fabian gmail (Tue Mar 29 2016 - 03:26:14 PDT)
    - Re: [AMBER] membrane protein complex preparation Fabian gmail (Tue Mar 29 2016 - 08:28:06 PDT)
    - Re: [AMBER] membrane protein complex preparation Dickson, Callum J (Tue Mar 29 2016 - 10:12:00 PDT)
    - Re: [AMBER] membrane protein complex preparation Bill Ross (Wed Mar 30 2016 - 00:46:09 PDT)
    - Re: [AMBER] membrane protein complex preparation Fabian Glaser (Wed Mar 30 2016 - 02:59:11 PDT)
    - Re: [AMBER] membrane protein complex preparation Bill Ross (Wed Mar 30 2016 - 04:23:19 PDT)
[AMBER] problem in nmode calculation by NAB Sanjib Paul (Mon Mar 28 2016 - 07:19:37 PDT)
- Re: [AMBER] problem in nmode calculation by NAB David A Case (Mon Mar 28 2016 - 14:34:01 PDT)
[AMBER] Relation between binding affinity and free enegy Sangita Kachhap (Mon Mar 28 2016 - 11:55:34 PDT)
- Re: [AMBER] Relation between binding affinity and free enegy Carlos Simmerling (Mon Mar 28 2016 - 12:36:09 PDT)
  - Re: [AMBER] Relation between binding affinity and free enegy Sangita Kachhap (Thu Mar 31 2016 - 21:49:55 PDT)
    - Re: [AMBER] Relation between binding affinity and free enegy Carlos Simmerling (Fri Apr 01 2016 - 07:15:45 PDT)
[AMBER] trajin reads box info from a trajectory with no box info. Jose Borreguero (Mon Mar 28 2016 - 13:21:41 PDT)
- Re: [AMBER] trajin reads box info from a trajectory with no box info. Daniel Roe (Mon Mar 28 2016 - 14:07:10 PDT)
  - Re: [AMBER] trajin reads box info from a trajectory with no box info. Jose Borreguero (Mon Mar 28 2016 - 14:14:17 PDT)
[AMBER] How does one derive parameters to modify GAFF? David Cerutti (Mon Mar 28 2016 - 14:34:11 PDT)
- Re: [AMBER] How does one derive parameters to modify GAFF? David A Case (Mon Mar 28 2016 - 18:13:13 PDT)
  - Re: [AMBER] How does one derive parameters to modify GAFF? David Cerutti (Mon Mar 28 2016 - 19:52:02 PDT)
[AMBER] [AmberTools15] “Cluster” with cpptraj: looking for SSR/SST ratio Guqin Shi (Mon Mar 28 2016 - 14:35:15 PDT)
[AMBER] amber14 installation Carlos Romero (Mon Mar 28 2016 - 22:52:38 PDT)
- Re: [AMBER] amber14 installation David A Case (Tue Mar 29 2016 - 04:24:15 PDT)
[AMBER] salt concentration KCl Fabian gmail (Tue Mar 29 2016 - 03:33:35 PDT)
- Re: [AMBER] salt concentration KCl Dickson, Callum J (Tue Mar 29 2016 - 06:25:07 PDT)
  - Re: [AMBER] salt concentration KCl Fabian gmail (Tue Mar 29 2016 - 07:23:23 PDT)
[AMBER] cpptraj mask definition Weinzierl, Robert O J (Tue Mar 29 2016 - 03:51:26 PDT)
- Re: [AMBER] cpptraj mask definition David A Case (Tue Mar 29 2016 - 04:25:40 PDT)
[AMBER] torsion angle rmsd by cpptraj ? Michael Shokhen (Tue Mar 29 2016 - 05:00:49 PDT)
- Re: [AMBER] torsion angle rmsd by cpptraj ? David A Case (Tue Mar 29 2016 - 09:35:23 PDT)
[AMBER] Amber MD simulation - viewing artifacts in VMD? Enrique Frio (Tue Mar 29 2016 - 05:05:05 PDT)
- Re: [AMBER] Amber MD simulation - viewing artifacts in VMD? Carlos Simmerling (Tue Mar 29 2016 - 05:10:29 PDT)
  - Re: [AMBER] Amber MD simulation - viewing artifacts in VMD? Enrique Frio (Tue Mar 29 2016 - 05:34:32 PDT)
[AMBER] General question George Tzotzos (Tue Mar 29 2016 - 09:35:22 PDT)
- Re: [AMBER] General question Ross Walker (Tue Mar 29 2016 - 09:54:52 PDT)
[AMBER] aMD simulation of membrane protein ? Michael Shokhen (Wed Mar 30 2016 - 03:18:51 PDT)
- Re: [AMBER] aMD simulation of membrane protein ? Michael Shokhen (Thu Mar 31 2016 - 03:07:56 PDT)
  - Re: [AMBER] aMD simulation of membrane protein ? Ofir Tal (Thu Mar 31 2016 - 07:10:27 PDT)
    - Re: [AMBER] aMD simulation of membrane protein ? Fabian gmail (Thu Mar 31 2016 - 08:00:27 PDT)
[AMBER] Need python code for the calculation of binding energy Ayesha Kanwal (Wed Mar 30 2016 - 03:21:55 PDT)
- Re: [AMBER] Need python code for the calculation of binding energy Jason Swails (Wed Mar 30 2016 - 05:36:10 PDT)
[AMBER] need help for using Re_fit Jesmita Dhar (Wed Mar 30 2016 - 04:45:37 PDT)
[AMBER] Strange problem of running MD simulation with sander ? Jinfeng Huang (Wed Mar 30 2016 - 08:07:28 PDT)
- Re: [AMBER] Strange problem of running MD simulation with sander ? David A Case (Wed Mar 30 2016 - 08:40:47 PDT)
[AMBER] Align namelist for direct dipolar coupling restraints Francisco Corzana López (Wed Mar 30 2016 - 08:59:39 PDT)
- Re: [AMBER] Align namelist for direct dipolar coupling restraints David A Case (Wed Mar 30 2016 - 10:18:05 PDT)
  - Re: [AMBER] Align namelist for direct dipolar coupling restraints Francisco Corzana López (Thu Mar 31 2016 - 10:13:38 PDT)
[AMBER] Periodicity box Fabian Glaser (Wed Mar 30 2016 - 09:21:02 PDT)
- Re: [AMBER] Periodicity box Eiros Zamora, Juan (Fri Apr 01 2016 - 02:21:15 PDT)
[AMBER] Hydrophobic solution environment ??? Mijiddorj Batsaikhan (Wed Mar 30 2016 - 09:33:17 PDT)
- Re: [AMBER] Hydrophobic solution environment ??? David A Case (Wed Mar 30 2016 - 10:24:00 PDT)
  - Re: [AMBER] Hydrophobic solution environment ??? Mijiddorj Batsaikhan (Thu Mar 31 2016 - 06:53:08 PDT)
    - Re: [AMBER] Hydrophobic solution environment ??? Mijiddorj Batsaikhan (Sat Apr 02 2016 - 01:50:43 PDT)
    - Re: [AMBER] Hydrophobic solution environment ??? David A Case (Sat Apr 02 2016 - 07:59:20 PDT)
[AMBER] Proper nfft* parameters for a very long solvent box? Kasprzak, Wojciech (NIH/NCI) [C] (Wed Mar 30 2016 - 11:14:59 PDT)
- Re: [AMBER] Proper nfft* parameters for a very long solvent box? David Cerutti (Wed Mar 30 2016 - 12:46:42 PDT)
  - Re: [AMBER] Proper nfft* parameters for a very long solvent box? Kasprzak, Wojciech (NIH/NCI) [C] (Wed Mar 30 2016 - 13:08:03 PDT)
    - Re: [AMBER] Proper nfft* parameters for a very long solvent box? Ross Walker (Wed Mar 30 2016 - 13:14:36 PDT)
    - Re: [AMBER] Proper nfft* parameters for a very long solvent box? David Cerutti (Wed Mar 30 2016 - 13:25:21 PDT)
    - Re: [AMBER] Proper nfft* parameters for a very long solvent box? Kasprzak, Wojciech (NIH/NCI) [C] (Wed Mar 30 2016 - 13:28:04 PDT)
[AMBER] Command to display simulation completion time Sreemol G (Wed Mar 30 2016 - 23:58:48 PDT)
- Re: [AMBER] Command to display simulation completion time Bill Ross (Thu Mar 31 2016 - 00:35:34 PDT)
  - Re: [AMBER] Command to display simulation completion time Bill Ross (Thu Mar 31 2016 - 00:41:19 PDT)
    - Re: [AMBER] Command to display simulation completion time Sreemol G (Thu Mar 31 2016 - 07:27:25 PDT)
    - Re: [AMBER] Command to display simulation completion time Charlotte RIEUX (Thu Mar 31 2016 - 07:41:20 PDT)
    - Re: [AMBER] Command to display simulation completion time Ross Walker (Thu Mar 31 2016 - 07:56:38 PDT)
    - Re: [AMBER] Command to display simulation completion time Hannes Loeffler (Thu Mar 31 2016 - 08:06:09 PDT)
[AMBER] mmpbsa_py_energy failed with prmtop lig_tleap.prm sunita gupta (Thu Mar 31 2016 - 23:22:59 PDT)
- Re: [AMBER] mmpbsa_py_energy failed with prmtop lig_tleap.prm Bill Miller III (Fri Apr 01 2016 - 05:22:32 PDT)
  - Re: [AMBER] mmpbsa_py_energy failed with prmtop lig_tleap.prm sunita gupta (Mon Apr 04 2016 - 05:17:32 PDT)
    - Re: [AMBER] mmpbsa_py_energy failed with prmtop lig_tleap.prm Jason Swails (Mon Apr 04 2016 - 06:47:34 PDT)
[AMBER] Problems running MD simulation using residual dipolar couplings as restraints Francisco Corzana López (Thu Mar 31 2016 - 23:31:35 PDT)
- Re: [AMBER] Problems running MD simulation using residual dipolar couplings as restraints David A Case (Fri Apr 01 2016 - 06:20:15 PDT)
  - Re: [AMBER] Problems running MD simulation using residual dipolar couplings as restraints Francisco Corzana López (Fri Apr 01 2016 - 08:13:01 PDT)
[AMBER] aMD ruins membrane structure Michael Shokhen (Fri Apr 01 2016 - 01:03:06 PDT)
- Re: [AMBER] aMD ruins membrane structure Dickson, Callum J (Mon Apr 04 2016 - 07:11:11 PDT)
[AMBER] Introducing the exciting next step in MD software development Jason Swails (Fri Apr 01 2016 - 03:32:51 PDT)
- Re: [AMBER] Introducing the exciting next step in MD software development ABEL Stephane 175950 (Fri Apr 01 2016 - 03:55:00 PDT)
  - Re: [AMBER] Introducing the exciting next step in MD software development Brent Krueger (Fri Apr 01 2016 - 04:05:04 PDT)
- Re: [AMBER] Introducing the exciting next step in MD software development Adrian Roitberg (Fri Apr 01 2016 - 04:31:02 PDT)
  - Re: [AMBER] Introducing the exciting next step in MD software development Thomas Pochapsky (Fri Apr 01 2016 - 05:48:59 PDT)
    - Re: [AMBER] Introducing the exciting next step in MD software development Chris Moth (Fri Apr 01 2016 - 06:20:34 PDT)
    - Re: [AMBER] Introducing the exciting next step in MD software development Adrian Roitberg (Fri Apr 01 2016 - 06:36:36 PDT)
    - [AMBER] A contrarian note about gravity potentials in MD David A Case (Fri Apr 01 2016 - 09:21:01 PDT)
- Re: [AMBER] Introducing the exciting next step in MD software development Bill Ross (Fri Apr 01 2016 - 06:34:19 PDT)
[AMBER] Problems with periodic boundaries Luke Presson (Fri Apr 01 2016 - 06:24:53 PDT)
- Re: [AMBER] Problems with periodic boundaries Daniel Roe (Fri Apr 01 2016 - 10:51:38 PDT)
  - Re: [AMBER] Problems with periodic boundaries Luke Presson (Fri Apr 01 2016 - 12:37:01 PDT)
    - Re: [AMBER] Problems with periodic boundaries Carlos Simmerling (Fri Apr 01 2016 - 12:40:51 PDT)
    - Re: [AMBER] Problems with periodic boundaries Luke Presson (Fri Apr 01 2016 - 13:27:53 PDT)
    - Re: [AMBER] Problems with periodic boundaries Carlos Simmerling (Fri Apr 01 2016 - 13:38:42 PDT)
    - Re: [AMBER] Problems with periodic boundaries David A Case (Sat Apr 02 2016 - 07:53:51 PDT)
[AMBER] hoogsteen base pair Martina Devi (Fri Apr 01 2016 - 08:23:48 PDT)
- Re: [AMBER] hoogsteen base pair Martina Devi (Fri Apr 01 2016 - 08:25:28 PDT)
  - Re: [AMBER] hoogsteen base pair David A Case (Fri Apr 01 2016 - 09:32:47 PDT)
[AMBER] QM calculation mohammad r (Fri Apr 01 2016 - 22:54:34 PDT)
- Re: [AMBER] QM calculation David A Case (Sat Apr 02 2016 - 07:56:39 PDT)
  - Re: [AMBER] QM calculation mohammad r (Sun Apr 03 2016 - 03:48:04 PDT)
    - Re: [AMBER] QM calculation David A Case (Sun Apr 03 2016 - 06:05:25 PDT)
    - Re: [AMBER] QM calculation mohammad r (Sun Apr 03 2016 - 11:20:49 PDT)
    - Re: [AMBER] QM calculation David A Case (Mon Apr 04 2016 - 05:54:03 PDT)
    - Re: [AMBER] QM calculation mohammad r (Mon Apr 04 2016 - 12:06:04 PDT)
    - Re: [AMBER] QM calculation Gustavo Seabra (Tue Apr 05 2016 - 13:06:51 PDT)
    - Re: [AMBER] QM calculation Marc van der Kamp (Tue Apr 05 2016 - 14:31:24 PDT)
    - Re: [AMBER] QM calculation mohammad r (Fri Apr 08 2016 - 02:12:24 PDT)
[AMBER] Run Stage 2 of the RESP fit yhzahsc (Sun Apr 03 2016 - 00:17:13 PDT)
- Re: [AMBER] Run Stage 2 of the RESP fit Brent Krueger (Sun Apr 03 2016 - 06:49:40 PDT)
  - Re: [AMBER] Run Stage 2 of the RESP fit yhzahsc (Sun Apr 03 2016 - 17:35:20 PDT)
    - Re: [AMBER] Run Stage 2 of the RESP fit FyD (Wed Apr 06 2016 - 06:50:27 PDT)
[AMBER] How to use tiMerge properly in pmemd TI calculation jfliu.itcs.ecnu.edu.cn (Sun Apr 03 2016 - 06:29:11 PDT)
- Re: [AMBER] How to use tiMerge properly in pmemd TI calculation hannes.loeffler.stfc.ac.uk (Sun Apr 03 2016 - 06:41:22 PDT)
  - Re: [AMBER] How to use tiMerge properly in pmemd TI calculation jfliu.itcs.ecnu.edu.cn (Sun Apr 03 2016 - 06:55:48 PDT)
    - Re: [AMBER] How to use tiMerge properly in pmemd TI calculation hannes.loeffler.stfc.ac.uk (Sun Apr 03 2016 - 07:03:23 PDT)
    - Re: [AMBER] How to use tiMerge properly in pmemd TI calculation jfliu.itcs.ecnu.edu.cn (Sun Apr 03 2016 - 07:22:50 PDT)
[AMBER] how to prepare a pdb file of a protein being phosphorylated at specific residues 欧阳艳华 (Sun Apr 03 2016 - 20:15:03 PDT)
- Re: [AMBER] how to prepare a pdb file of a protein being phosphorylated at specific residues Mijiddorj Batsaikhan (Sun Apr 03 2016 - 21:53:13 PDT)
  - Re: [AMBER] how to prepare a pdb file of a protein being phosphorylated at specific residues YanhuaOuyang (Mon Apr 04 2016 - 00:06:29 PDT)
[AMBER] how to run a MD of a phosphorylated protein using amber 欧阳艳华 (Sun Apr 03 2016 - 20:21:43 PDT)
- Re: [AMBER] how to run a MD of a phosphorylated protein using amber Mijiddorj Batsaikhan (Sun Apr 03 2016 - 21:30:28 PDT)
  - Re: [AMBER] how to run a MD of a phosphorylated protein using amber YanhuaOuyang (Sun Apr 03 2016 - 23:46:28 PDT)
[AMBER] General question Sreemol G (Sun Apr 03 2016 - 23:04:28 PDT)
- Re: [AMBER] General question David Cerutti (Sun Apr 03 2016 - 23:19:53 PDT)
- Re: [AMBER] General question hannes.loeffler.stfc.ac.uk (Sun Apr 03 2016 - 23:21:12 PDT)
  - Re: [AMBER] General question Sreemol G (Sun Apr 03 2016 - 23:47:58 PDT)
    - Re: [AMBER] General question hannes.loeffler.stfc.ac.uk (Mon Apr 04 2016 - 00:08:57 PDT)
    - Re: [AMBER] General question Sreemol G (Mon Apr 04 2016 - 02:57:41 PDT)
    - Re: [AMBER] General question hannes.loeffler.stfc.ac.uk (Mon Apr 04 2016 - 03:17:38 PDT)
    - Re: [AMBER] General question Sreemol G (Mon Apr 04 2016 - 03:39:24 PDT)
    - Re: [AMBER] General question hannes.loeffler.stfc.ac.uk (Mon Apr 04 2016 - 03:57:40 PDT)
    - Re: [AMBER] General question Sreemol G (Mon Apr 04 2016 - 04:35:01 PDT)
    - Re: [AMBER] General question hannes.loeffler.stfc.ac.uk (Mon Apr 04 2016 - 05:27:05 PDT)
    - Re: [AMBER] General question David A Case (Mon Apr 04 2016 - 06:01:39 PDT)
    - Re: [AMBER] General question Sreemol G (Tue Apr 05 2016 - 21:31:13 PDT)
    - Re: [AMBER] General question Charles Lin (Tue Apr 05 2016 - 21:43:16 PDT)
    - Re: [AMBER] General question Sreemol G (Tue Apr 05 2016 - 22:42:48 PDT)
    - Re: [AMBER] General question Charles Lin (Tue Apr 05 2016 - 22:57:17 PDT)
[AMBER] build a phosphorylated protein structure pdb file YanhuaOuyang (Mon Apr 04 2016 - 00:21:29 PDT)
- Re: [AMBER] build a phosphorylated protein structure pdb file Carlos Simmerling (Mon Apr 04 2016 - 03:10:17 PDT)
  - Re: [AMBER] build a phosphorylated protein structure pdb file YanhuaOuyang (Mon Apr 04 2016 - 18:04:40 PDT)
    - Re: [AMBER] build a phosphorylated protein structure pdb file YanhuaOuyang (Mon Apr 04 2016 - 18:25:46 PDT)
    - Re: [AMBER] build a phosphorylated protein structure pdb file Bill Ross (Mon Apr 04 2016 - 18:34:03 PDT)
    - Re: [AMBER] build a phosphorylated protein structure pdb file David A Case (Mon Apr 04 2016 - 18:50:05 PDT)
    - Re: [AMBER] build a phosphorylated protein structure pdb file YanhuaOuyang (Tue Apr 05 2016 - 04:58:21 PDT)
[AMBER] turning of non-bonded interactions with addExclusions Batuhan Kav (Mon Apr 04 2016 - 02:42:30 PDT)
- Re: [AMBER] turning of non-bonded interactions with addExclusions Jason Swails (Mon Apr 04 2016 - 09:10:09 PDT)
[AMBER] MD simulations of deprotonated tyrosine residue with AMBER ABEL Stephane 175950 (Mon Apr 04 2016 - 06:22:41 PDT)
- Re: [AMBER] MD simulations of deprotonated tyrosine residue with AMBER Adrian Roitberg (Mon Apr 04 2016 - 06:31:22 PDT)
  - Re: [AMBER] MD simulations of deprotonated tyrosine residue with AMBER ABEL Stephane 175950 (Mon Apr 04 2016 - 06:55:55 PDT)
    - Re: [AMBER] MD simulations of deprotonated tyrosine residue with AMBER Jason Swails (Mon Apr 04 2016 - 09:03:17 PDT)
[AMBER] spherical restraint flatwell potentials Kenneth McGuinness (Mon Apr 04 2016 - 11:03:05 PDT)
- Re: [AMBER] spherical restraint flatwell potentials David Cerutti (Mon Apr 04 2016 - 11:32:18 PDT)
  - Re: [AMBER] spherical restraint flatwell potentials Kenneth McGuinness (Mon Apr 04 2016 - 11:52:26 PDT)
    - Re: [AMBER] spherical restraint flatwell potentials David Cerutti (Mon Apr 04 2016 - 12:33:29 PDT)
    - Re: [AMBER] spherical restraint flatwell potentials Kenneth McGuinness (Mon Apr 04 2016 - 14:35:55 PDT)
[AMBER] sander number of atoms limit TERREUX RAPHAEL (Tue Apr 05 2016 - 01:59:59 PDT)
- Re: [AMBER] sander number of atoms limit Gould, Ian R (Tue Apr 05 2016 - 02:12:54 PDT)
  - Re: [AMBER] sander number of atoms limit TERREUX RAPHAEL (Tue Apr 05 2016 - 02:16:04 PDT)
    - Re: [AMBER] sander number of atoms limit Bill Ross (Tue Apr 05 2016 - 02:26:13 PDT)
    - Re: [AMBER] sander number of atoms limit Gould, Ian R (Tue Apr 05 2016 - 02:30:44 PDT)
    - Re: [AMBER] sander number of atoms limit Gould, Ian R (Tue Apr 05 2016 - 02:27:26 PDT)
    - Re: [AMBER] sander number of atoms limit Jason Swails (Tue Apr 05 2016 - 05:07:23 PDT)
    - Re: [AMBER] sander number of atoms limit David A Case (Tue Apr 05 2016 - 09:13:11 PDT)
[AMBER] The question about SMD wjli (Tue Apr 05 2016 - 06:56:05 PDT)
- Re: [AMBER] The question about SMD Adrian Roitberg (Tue Apr 05 2016 - 07:23:47 PDT)
  - [AMBER] 回复： The question about SMD wjli (Tue Apr 05 2016 - 18:01:39 PDT)
[AMBER] cpptraj: reading in previously created covariance matrix Vlad Cojocaru (Tue Apr 05 2016 - 12:52:57 PDT)
- Re: [AMBER] cpptraj: reading in previously created covariance matrix Daniel Roe (Tue Apr 05 2016 - 13:12:42 PDT)
[AMBER] 回复： The question about SMD wjli (Tue Apr 05 2016 - 18:08:36 PDT)
[AMBER] cpptraj: reading in previously created covariance matrix Vlad Cojocaru (Wed Apr 06 2016 - 01:09:16 PDT)
[AMBER] Amber: .rst file not created ABHIJEET CHOWDHURY (Wed Apr 06 2016 - 05:08:56 PDT)
- Re: [AMBER] Amber: .rst file not created Marcelo Andrade Chagas (Wed Apr 06 2016 - 07:42:30 PDT)
  - Re: [AMBER] Amber: .rst file not created ABHIJEET CHOWDHURY (Thu Apr 07 2016 - 04:47:27 PDT)
    - Re: [AMBER] Amber: .rst file not created Jason Swails (Thu Apr 07 2016 - 09:28:33 PDT)
[AMBER] Amber14/AmberTools15 compliation error Kris Feher (Wed Apr 06 2016 - 07:34:04 PDT)
- Re: [AMBER] Amber14/AmberTools15 compliation error Jason Swails (Wed Apr 06 2016 - 07:42:00 PDT)
  - Re: [AMBER] Amber14/AmberTools15 compliation error Kris Feher (Tue Apr 12 2016 - 01:19:19 PDT)
[AMBER] Any issues if I make PMEMD understand bonds span imaging? David Cerutti (Wed Apr 06 2016 - 13:49:28 PDT)
[AMBER] General Type Improper Dihedrals vs. Specifics Robert Molt (Wed Apr 06 2016 - 14:20:15 PDT)
- Re: [AMBER] General Type Improper Dihedrals vs. Specifics David Cerutti (Wed Apr 06 2016 - 14:50:37 PDT)
  - Re: [AMBER] General Type Improper Dihedrals vs. Specifics David A Case (Wed Apr 06 2016 - 17:46:43 PDT)
    - Re: [AMBER] General Type Improper Dihedrals vs. Specifics David Cerutti (Wed Apr 06 2016 - 18:25:15 PDT)
[AMBER] running charmm force field in amber Neha Gandhi (Wed Apr 06 2016 - 17:37:56 PDT)
- Re: [AMBER] running charmm force field in amber Hai Nguyen (Wed Apr 06 2016 - 17:47:55 PDT)
- Re: [AMBER] running charmm force field in amber Ross Walker (Wed Apr 06 2016 - 17:50:23 PDT)
- Re: [AMBER] running charmm force field in amber Jason Swails (Wed Apr 06 2016 - 18:05:18 PDT)
  - Re: [AMBER] running charmm force field in amber Neha Gandhi (Wed Apr 06 2016 - 18:40:52 PDT)
[AMBER] test: not getting emails from the list Vlad Cojocaru (Thu Apr 07 2016 - 01:24:04 PDT)
- Re: [AMBER] test: not getting emails from the list Jason Swails (Thu Apr 07 2016 - 09:31:35 PDT)
[AMBER] Hbond command use with non-hydrogen bonds Krantzman, Kristin D (Thu Apr 07 2016 - 07:49:56 PDT)
- Re: [AMBER] Hbond command use with non-hydrogen bonds Daniel Roe (Thu Apr 07 2016 - 08:39:34 PDT)
[AMBER] PCA Sofia Vasilakaki (Thu Apr 07 2016 - 11:59:38 PDT)
- Re: [AMBER] PCA Daniel Roe (Fri Apr 08 2016 - 09:34:11 PDT)
[AMBER] MMPBSA : Calculation when keeping explicit water molecules 楊承翰 (Thu Apr 07 2016 - 21:14:59 PDT)
- Re: [AMBER] MMPBSA : Calculation when keeping explicit water molecules Jason Swails (Fri Apr 08 2016 - 05:11:17 PDT)
- Re: [AMBER] MMPBSA : Calculation when keeping explicit water molecules Alessandro Contini (Fri Apr 08 2016 - 05:38:24 PDT)
[AMBER] on the MD of protein-ligand Brett (Thu Apr 07 2016 - 22:48:53 PDT)
- Re: [AMBER] on the MD of protein-ligand David Cerutti (Thu Apr 07 2016 - 23:08:13 PDT)
[AMBER] RMSD graph for protein-RNA complex Sreemol G (Fri Apr 08 2016 - 01:15:07 PDT)
- Re: [AMBER] RMSD graph for protein-RNA complex Dr. Anselm Horn (Fri Apr 08 2016 - 02:30:14 PDT)
  - Re: [AMBER] RMSD graph for protein-RNA complex Sreemol G (Fri Apr 08 2016 - 04:04:35 PDT)
    - Re: [AMBER] RMSD graph for protein-RNA complex Daniel Roe (Fri Apr 08 2016 - 09:14:32 PDT)
    - Re: [AMBER] RMSD graph for protein-RNA complex Sreemol G (Mon Apr 11 2016 - 22:07:55 PDT)
    - Re: [AMBER] RMSD graph for protein-RNA complex David A Case (Tue Apr 12 2016 - 04:45:25 PDT)
    - Re: [AMBER] RMSD graph for protein-RNA complex Sreemol G (Tue Apr 12 2016 - 05:13:42 PDT)
    - Re: [AMBER] RMSD graph for protein-RNA complex Daniel Roe (Tue Apr 12 2016 - 12:50:46 PDT)
    - Re: [AMBER] RMSD graph for protein-RNA complex Sreemol G (Tue Apr 12 2016 - 22:06:57 PDT)
    - Re: [AMBER] RMSD graph for protein-RNA complex Andy Watkins (Tue Apr 12 2016 - 22:12:30 PDT)
    - Re: [AMBER] RMSD graph for protein-RNA complex Sreemol G (Tue Apr 12 2016 - 22:16:10 PDT)
    - Re: [AMBER] RMSD graph for protein-RNA complex Daniel Roe (Wed Apr 13 2016 - 05:01:25 PDT)
    - Re: [AMBER] RMSD graph for protein-RNA complex David A Case (Wed Apr 13 2016 - 05:23:55 PDT)
- Re: [AMBER] RMSD graph for protein-RNA complex David A Case (Fri Apr 08 2016 - 04:31:53 PDT)
[AMBER] CpHMD 赵聪 (Fri Apr 08 2016 - 01:17:00 PDT)
- Re: [AMBER] CpHMD Jason Swails (Fri Apr 08 2016 - 05:07:50 PDT)
[AMBER] Regarding MM-PBSA calculation Sivanandam M (Fri Apr 08 2016 - 03:44:33 PDT)
- Re: [AMBER] Regarding MM-PBSA calculation Jason Swails (Fri Apr 08 2016 - 05:12:32 PDT)
[AMBER] Regarding MM-PBSA free energy calculation Sivanandam M (Fri Apr 08 2016 - 03:51:05 PDT)
- Re: [AMBER] Regarding MM-PBSA free energy calculation Jason Swails (Fri Apr 08 2016 - 05:13:57 PDT)
[AMBER] Metal geometry Vasantha Kumar (Fri Apr 08 2016 - 06:13:15 PDT)
- Re: [AMBER] Metal geometry Carlos Simmerling (Fri Apr 08 2016 - 07:32:51 PDT)
  - Re: [AMBER] Metal geometry David Cerutti (Fri Apr 08 2016 - 08:01:26 PDT)
    - Re: [AMBER] Metal geometry Vasantha Kumar (Fri Apr 08 2016 - 16:29:14 PDT)
    - Re: [AMBER] Metal geometry Vasantha Kumar (Fri Apr 08 2016 - 16:42:04 PDT)
    - Re: [AMBER] Metal geometry Pengfei Li (Sat Apr 09 2016 - 07:29:15 PDT)
    - Re: [AMBER] Metal geometry Pengfei Li (Sat Apr 09 2016 - 19:42:44 PDT)
    - Re: [AMBER] Metal geometry Vasantha Kumar (Sun Apr 10 2016 - 06:40:34 PDT)
    - Re: [AMBER] Metal geometry Pengfei Li (Mon Apr 11 2016 - 20:11:44 PDT)
- Re: [AMBER] Metal geometry FyD (Sat Apr 09 2016 - 01:19:01 PDT)
  - Re: [AMBER] Metal geometry Vasantha Kumar (Sat Apr 09 2016 - 04:20:27 PDT)
[AMBER] Problem with MCPB.py Surya Prakash Tiwari (Fri Apr 08 2016 - 11:09:32 PDT)
- Re: [AMBER] Problem with MCPB.py FyD (Sat Apr 09 2016 - 01:28:41 PDT)
  - Re: [AMBER] Problem with MCPB.py Surya Prakash Tiwari (Thu May 05 2016 - 10:37:59 PDT)
[AMBER] Error -per residue Energy Decomposition Arati Paudyal (Fri Apr 08 2016 - 12:12:41 PDT)
- Re: [AMBER] Error -per residue Energy Decomposition Jason Swails (Fri Apr 08 2016 - 18:39:45 PDT)
  - Re: [AMBER] Error -per residue Energy Decomposition Arati Paudyal (Sat Apr 09 2016 - 16:56:24 PDT)
[AMBER] How to prepare files cyclodextrin to use witch glycam04 CRISTIAN ROSSI PERARO (Fri Apr 08 2016 - 19:35:28 PDT)
- Re: [AMBER] How to prepare files cyclodextrin to use witch glycam04 Lachele Foley (Fri Apr 08 2016 - 20:07:24 PDT)
  - Re: [AMBER] How to prepare files cyclodextrin to use witch glycam04 CRISTIAN ROSSI PERARO (Fri Apr 08 2016 - 20:32:49 PDT)
    - Re: [AMBER] How to prepare files cyclodextrin to use witch glycam04 Lachele Foley (Fri Apr 08 2016 - 21:29:02 PDT)
    - Re: [AMBER] How to prepare files cyclodextrin to use witch glycam04 CRISTIAN ROSSI PERARO (Sat Apr 09 2016 - 10:49:56 PDT)
- Re: [AMBER] How to prepare files cyclodextrin to use witch glycam04 FyD (Sat Apr 09 2016 - 01:10:52 PDT)
[AMBER] query regarding dssp plot cpptraj. Saman Yousuf ali (Sat Apr 09 2016 - 08:20:18 PDT)
- Re: [AMBER] query regarding dssp plot cpptraj. Daniel Roe (Sun Apr 10 2016 - 08:04:29 PDT)
[AMBER] Amber script to delete all hydrogen atoms from protein? Michael Shokhen (Sun Apr 10 2016 - 02:11:18 PDT)
- Re: [AMBER] Amber script to delete all hydrogen atoms from protein? Marcelo Andrade Chagas (Sun Apr 10 2016 - 04:05:38 PDT)
- Re: [AMBER] Amber script to delete all hydrogen atoms from protein? Arati Paudyal (Sun Apr 10 2016 - 04:22:31 PDT)
  - Re: [AMBER] Amber script to delete all hydrogen atoms from protein? Michael Shokhen (Sun Apr 10 2016 - 05:25:45 PDT)
[AMBER] PMF calculation via tunnel (SMD) wjli (Sun Apr 10 2016 - 05:03:23 PDT)
[AMBER] mm_pbsa.pl, that I'm doing this right? CRISTIAN ROSSI PERARO (Sun Apr 10 2016 - 11:17:32 PDT)
- Re: [AMBER] mm_pbsa.pl, that I'm doing this right? Ray Luo (Mon Apr 11 2016 - 08:25:21 PDT)
  - Re: [AMBER] mm_pbsa.pl, that I'm doing this right? CRISTIAN ROSSI PERARO (Mon Apr 11 2016 - 12:07:42 PDT)
[AMBER] Is it possible to run TI with pmemd using the AMOEBA force field? Sumsamber Lee (Sun Apr 10 2016 - 15:07:03 PDT)
- Re: [AMBER] Is it possible to run TI with pmemd using the AMOEBA force field? Jason Swails (Sun Apr 10 2016 - 17:13:27 PDT)
  - Re: [AMBER] Is it possible to run TI with pmemd using the AMOEBA force field? David Cerutti (Sun Apr 10 2016 - 19:36:29 PDT)
[AMBER] query regarding -refc ABHIJEET CHOWDHURY (Sun Apr 10 2016 - 21:11:07 PDT)
- Re: [AMBER] query regarding -refc David Cerutti (Sun Apr 10 2016 - 21:29:53 PDT)
  - Re: [AMBER] query regarding -refc ABHIJEET CHOWDHURY (Sun Apr 10 2016 - 23:02:59 PDT)
    - Re: [AMBER] query regarding -refc David Cerutti (Mon Apr 11 2016 - 05:58:12 PDT)
[AMBER] Refinement in explicit solvent Vasantha Kumar (Mon Apr 11 2016 - 01:13:19 PDT)
- Re: [AMBER] Refinement in explicit solvent David A Case (Mon Apr 11 2016 - 05:23:05 PDT)
  - Re: [AMBER] Refinement in explicit solvent Vasantha Kumar (Mon Apr 11 2016 - 16:30:22 PDT)
[AMBER] MD tutorial workflows James Starlight (Mon Apr 11 2016 - 01:36:35 PDT)
[AMBER] Could not find angle parameter Jesmita Dhar (Mon Apr 11 2016 - 02:32:32 PDT)
- Re: [AMBER] Could not find angle parameter Daniel Roe (Mon Apr 11 2016 - 09:35:43 PDT)
  - Re: [AMBER] Could not find angle parameter Jesmita Dhar (Mon Apr 11 2016 - 22:34:13 PDT)
- Re: [AMBER] Could not find angle parameter David A Case (Wed Apr 13 2016 - 05:34:49 PDT)
[AMBER] geometric center with cpptraj Batuhan Kav (Mon Apr 11 2016 - 03:00:52 PDT)
- Re: [AMBER] geometric center with cpptraj Hai Nguyen (Mon Apr 11 2016 - 07:01:05 PDT)
[AMBER] Box dimensions 達南杰 (Mon Apr 11 2016 - 04:28:21 PDT)
- Re: [AMBER] Box dimensions Daniel Roe (Mon Apr 11 2016 - 09:40:29 PDT)
  - Re: [AMBER] Box dimensions 達南杰 (Mon Apr 11 2016 - 19:36:17 PDT)
    - Re: [AMBER] Box dimensions Daniel Roe (Mon Apr 11 2016 - 19:44:09 PDT)
    - Re: [AMBER] Box dimensions 達南杰 (Mon Apr 11 2016 - 20:18:20 PDT)
[AMBER] ff12SB force field wjli (Mon Apr 11 2016 - 06:47:05 PDT)
- Re: [AMBER] ff12SB force field Carlos Simmerling (Mon Apr 11 2016 - 06:50:55 PDT)
  - Re: [AMBER] ff12SB force field wjli (Mon Apr 11 2016 - 07:02:23 PDT)
    - Re: [AMBER] ff12SB force field David Cerutti (Mon Apr 11 2016 - 13:48:59 PDT)
[AMBER] Multiple restraints for minimization Stevens, David Ryan (Mon Apr 11 2016 - 09:03:08 PDT)
- Re: [AMBER] Multiple restraints for minimization Daniel Roe (Mon Apr 11 2016 - 10:08:54 PDT)
  - Re: [AMBER] Multiple restraints for minimization Bill Ross (Mon Apr 11 2016 - 11:53:15 PDT)
  - Re: [AMBER] Multiple restraints for minimization Stevens, David Ryan (Mon Apr 11 2016 - 11:56:29 PDT)
    - Re: [AMBER] Multiple restraints for minimization Daniel Roe (Mon Apr 11 2016 - 12:34:55 PDT)
    - Re: [AMBER] Multiple restraints for minimization Stevens, David Ryan (Mon Apr 11 2016 - 14:25:07 PDT)
[AMBER] CHAMBER and CMAP error using new c36 FF Jun Feng (Mon Apr 11 2016 - 10:18:17 PDT)
- Re: [AMBER] CHAMBER and CMAP error using new c36 FF Jason Swails (Tue Apr 12 2016 - 07:27:38 PDT)
  - Re: [AMBER] CHAMBER and CMAP error using new c36 FF Jun Feng (Tue Apr 12 2016 - 11:35:44 PDT)
    - Re: [AMBER] CHAMBER and CMAP error using new c36 FF Jason Swails (Wed Apr 13 2016 - 03:33:11 PDT)
[AMBER] Implicit Solvent simulation - membrane proteins Balaji Selvam (Mon Apr 11 2016 - 10:51:35 PDT)
- Re: [AMBER] Implicit Solvent simulation - membrane proteins Hai Nguyen (Mon Apr 11 2016 - 10:58:51 PDT)
- Re: [AMBER] Implicit Solvent simulation - membrane proteins Ray Luo (Mon Apr 11 2016 - 11:21:47 PDT)
[AMBER] Alanine Scanning ERROR!!! Jag Silwal (Mon Apr 11 2016 - 19:11:17 PDT)
- Re: [AMBER] Alanine Scanning ERROR!!! Jason Swails (Wed Apr 13 2016 - 09:53:29 PDT)
  - Re: [AMBER] Alanine Scanning ERROR!!! Jag Silwal (Wed Apr 13 2016 - 15:22:39 PDT)
    - Re: [AMBER] Alanine Scanning ERROR!!! Jason Swails (Wed Apr 13 2016 - 19:01:46 PDT)
    - Re: [AMBER] Alanine Scanning ERROR!!! Jag Silwal (Thu Apr 14 2016 - 04:46:49 PDT)
[AMBER] error while running MMPBSA script Harmeet Kaur (Mon Apr 11 2016 - 21:52:12 PDT)
- Re: [AMBER] error while running MMPBSA script Jason Swails (Tue Apr 12 2016 - 07:07:26 PDT)
[AMBER] CHAMBER and CMAP error using new c36 FF Jun Feng (Tue Apr 12 2016 - 07:22:49 PDT)
- Re: [AMBER] CHAMBER and CMAP error using new c36 FF Hai Nguyen (Tue Apr 12 2016 - 07:34:02 PDT)
[AMBER] CHAMBER error for the updated CHARMM36 force fields Chitrak Gupta (Tue Apr 12 2016 - 08:23:46 PDT)
- Re: [AMBER] CHAMBER error for the updated CHARMM36 force fields Hai Nguyen (Tue Apr 12 2016 - 09:23:37 PDT)
[AMBER] Protein-DNA docking Lara rajam (Tue Apr 12 2016 - 13:38:40 PDT)
- Re: [AMBER] Protein-DNA docking Hai Nguyen (Tue Apr 12 2016 - 13:51:07 PDT)
- Re: [AMBER] Protein-DNA docking Carlos Simmerling (Tue Apr 12 2016 - 13:50:46 PDT)
  - Re: [AMBER] Protein-DNA docking Lara rajam (Tue Apr 12 2016 - 13:56:02 PDT)
[AMBER] Antechamber Problem Beale, John (Wed Apr 13 2016 - 00:18:07 PDT)
- Re: [AMBER] Antechamber Problem Bill Ross (Wed Apr 13 2016 - 00:42:09 PDT)
  - Re: [AMBER] Antechamber Problem Beale, John (Wed Apr 13 2016 - 00:47:28 PDT)
    - Re: [AMBER] Antechamber Problem Bill Ross (Wed Apr 13 2016 - 01:15:47 PDT)
[AMBER] Quasi-harmonic calculation Amika Sood (Wed Apr 13 2016 - 06:15:06 PDT)
- Re: [AMBER] Quasi-harmonic calculation David A Case (Mon Apr 18 2016 - 04:35:41 PDT)
[AMBER] Both positional and distance restraints Damiano Spadoni (Wed Apr 13 2016 - 06:59:06 PDT)
- Re: [AMBER] Both positional and distance restraints David A Case (Mon Apr 18 2016 - 04:31:18 PDT)
  - Re: [AMBER] Both positional and distance restraints Damiano Spadoni (Mon Apr 18 2016 - 11:46:39 PDT)
[AMBER] Natural bond orbital analysis Kenneth McGuinness (Wed Apr 13 2016 - 07:31:40 PDT)
- Re: [AMBER] Natural bond orbital analysis David A Case (Wed Apr 13 2016 - 17:59:49 PDT)
  - Re: [AMBER] Natural bond orbital analysis Kenneth McGuinness (Thu Apr 14 2016 - 13:06:53 PDT)
[AMBER] MMGBSA and dielectric constants Cortopassi, Wilian (Wed Apr 13 2016 - 09:37:34 PDT)
- Re: [AMBER] MMGBSA and dielectric constants Jason Swails (Wed Apr 13 2016 - 09:49:58 PDT)
[AMBER] Amber custom hardware setup Leonardo Lazzaro (Wed Apr 13 2016 - 17:39:55 PDT)
- Re: [AMBER] Amber custom hardware setup Jason Swails (Wed Apr 13 2016 - 19:05:44 PDT)
[AMBER] Regarding Input file preparation in AMBER Sivanandam M (Thu Apr 14 2016 - 00:01:41 PDT)
- Re: [AMBER] Regarding Input file preparation in AMBER Bill Ross (Thu Apr 14 2016 - 00:40:20 PDT)
[AMBER] mm_pbsa.pl ERROR yhzahsc (Thu Apr 14 2016 - 00:42:02 PDT)
- Re: [AMBER] mm_pbsa.pl ERROR Bill Ross (Thu Apr 14 2016 - 01:44:49 PDT)
  - Re: [AMBER] mm_pbsa.pl ERROR yhzahsc (Thu Apr 14 2016 - 19:25:59 PDT)
- Re: [AMBER] mm_pbsa.pl ERROR David A Case (Thu Apr 14 2016 - 04:45:32 PDT)
  - Re: [AMBER] mm_pbsa.pl ERROR yhzahsc (Thu Apr 14 2016 - 19:26:46 PDT)
[AMBER] LEAP RUN FAILED Neal Broomhead (Thu Apr 14 2016 - 02:38:06 PDT)
- Re: [AMBER] LEAP RUN FAILED Bill Ross (Thu Apr 14 2016 - 04:10:10 PDT)
[AMBER] how to embed amber14 Ayesha Kanwal (Thu Apr 14 2016 - 03:34:57 PDT)
- Re: [AMBER] how to embed amber14 Jason Swails (Sun Apr 17 2016 - 09:27:03 PDT)
  - Re: [AMBER] how to embed amber14 Ayesha Kanwal (Mon Apr 18 2016 - 03:47:23 PDT)
    - Re: [AMBER] how to embed amber14 Jason Swails (Mon Apr 18 2016 - 03:54:09 PDT)
    - Re: [AMBER] how to embed amber14 David A Case (Mon Apr 18 2016 - 04:26:23 PDT)
[AMBER] Modelling of proteins Aishani Prem (Thu Apr 14 2016 - 14:30:00 PDT)
- Re: [AMBER] Modelling of proteins David Cerutti (Thu Apr 14 2016 - 14:42:52 PDT)
  - Re: [AMBER] Modelling of proteins Aishani Prem (Fri Apr 22 2016 - 11:56:18 PDT)
    - Re: [AMBER] Modelling of proteins Bill Ross (Fri Apr 22 2016 - 12:03:07 PDT)
[AMBER] How can I extract PDB files from a molecular dynamics simulation Luis Esteban (Thu Apr 14 2016 - 19:02:03 PDT)
- Re: [AMBER] How can I extract PDB files from a molecular dynamics simulation Kenneth McGuinness (Thu Apr 14 2016 - 19:10:23 PDT)
  - Re: [AMBER] How can I extract PDB files from a molecular dynamics simulation Luis Esteban (Thu Apr 14 2016 - 19:39:01 PDT)
- Re: [AMBER] How can I extract PDB files from a molecular dynamics simulation Daniel Roe (Fri Apr 15 2016 - 08:42:17 PDT)
  - Re: [AMBER] How can I extract PDB files from a molecular dynamics simulation Luis Esteban (Sat Apr 16 2016 - 17:29:07 PDT)
[AMBER] hbond analysis of phosphotyrosine Wu Xu (Thu Apr 14 2016 - 19:55:56 PDT)
- Re: [AMBER] hbond analysis of phosphotyrosine Hai Nguyen (Thu Apr 14 2016 - 23:48:38 PDT)
  - Re: [AMBER] hbond analysis of phosphotyrosine David A Case (Fri Apr 15 2016 - 04:59:26 PDT)
    - Re: [AMBER] hbond analysis of phosphotyrosine Wu Xu (Fri Apr 15 2016 - 05:13:13 PDT)
- Re: [AMBER] hbond analysis of phosphotyrosine Daniel Roe (Fri Apr 15 2016 - 08:35:34 PDT)
  - Re: [AMBER] hbond analysis of phosphotyrosine Wu Xu (Fri Apr 15 2016 - 10:09:41 PDT)
    - Re: [AMBER] hbond analysis of phosphotyrosine Daniel Roe (Sat Apr 16 2016 - 09:38:45 PDT)
    - Re: [AMBER] hbond analysis of phosphotyrosine Wu Xu (Sat Apr 16 2016 - 09:41:32 PDT)
[AMBER] Fortran Modernisation Workshop - Numerical Algorithms Group NAG CHAMI F. (Fri Apr 15 2016 - 03:23:45 PDT)
[AMBER] To convert the CHARMM-GUI formatted .pdb file into Lipid14 formatted .pdb file Shreeramesh (Fri Apr 15 2016 - 04:27:48 PDT)
- Re: [AMBER] To convert the CHARMM-GUI formatted .pdb file into Lipid14 formatted .pdb file David A Case (Fri Apr 15 2016 - 05:03:10 PDT)
  - Re: [AMBER] To convert the CHARMM-GUI formatted .pdb file into Lipid14 formatted .pdb file Shreeramesh (Fri Apr 15 2016 - 05:16:18 PDT)
    - Re: [AMBER] To convert the CHARMM-GUI formatted .pdb file into Lipid14 formatted .pdb file Batuhan Kav (Fri Apr 15 2016 - 05:28:29 PDT)
    - Re: [AMBER] To convert the CHARMM-GUI formatted .pdb file into Lipid14 formatted .pdb file Jason Swails (Fri Apr 15 2016 - 13:07:54 PDT)
[AMBER] Conversion of CHARMM-GUI generated file into Lipid14 readable file Shreeramesh (Fri Apr 15 2016 - 05:01:04 PDT)
[AMBER] TI Calculation doubt Mary Varughese (Fri Apr 15 2016 - 23:34:02 PDT)
- Re: [AMBER] TI Calculation doubt Hannes Loeffler (Sat Apr 16 2016 - 01:18:23 PDT)
[AMBER] facing problems simulating in implicit solvent Avik Bhattacharjee (Sat Apr 16 2016 - 09:43:42 PDT)
- Re: [AMBER] facing problems simulating in implicit solvent Daniel Roe (Sat Apr 16 2016 - 09:50:43 PDT)
  - Re: [AMBER] facing problems simulating in implicit solvent Avik Bhattacharjee (Sat Apr 16 2016 - 10:20:02 PDT)
    - Re: [AMBER] facing problems simulating in implicit solvent Carlos Simmerling (Sat Apr 16 2016 - 10:42:37 PDT)
[AMBER] Change PBRadii after simulation Jag Silwal (Sat Apr 16 2016 - 20:30:27 PDT)
- Re: [AMBER] Change PBRadii after simulation Carlos Simmerling (Sat Apr 16 2016 - 20:33:43 PDT)
  - Re: [AMBER] Change PBRadii after simulation Jag Silwal (Sat Apr 16 2016 - 21:20:37 PDT)
    - Re: [AMBER] Change PBRadii after simulation Carlos Simmerling (Sun Apr 17 2016 - 04:53:37 PDT)
    - Re: [AMBER] Change PBRadii after simulation Jason Swails (Sun Apr 17 2016 - 08:00:52 PDT)
    - Re: [AMBER] Change PBRadii after simulation Jag Silwal (Mon Apr 18 2016 - 05:50:14 PDT)
    - Re: [AMBER] Change PBRadii after simulation Carlos Simmerling (Mon Apr 18 2016 - 06:04:05 PDT)
    - Re: [AMBER] Change PBRadii after simulation Arati Paudyal (Mon Apr 18 2016 - 06:34:50 PDT)
[AMBER] cpptraj SolventAcc and ligand distance plotting Saman Yousuf ali (Sat Apr 16 2016 - 23:59:11 PDT)
- Re: [AMBER] cpptraj SolventAcc and ligand distance plotting Daniel Roe (Mon Apr 18 2016 - 07:33:23 PDT)
  - Re: [AMBER] cpptraj SolventAcc and ligand distance plotting Daniel Roe (Tue Apr 19 2016 - 09:02:48 PDT)
  - Re: [AMBER] cpptraj SolventAcc and ligand distance plotting Daniel Roe (Wed Apr 20 2016 - 13:21:57 PDT)
  - Re: [AMBER] cpptraj SolventAcc and ligand distance plotting Saman Yousuf ali (Thu Apr 21 2016 - 14:17:40 PDT)
[AMBER] error in MCPB.py 3b jixiaofeng (Sun Apr 17 2016 - 19:43:18 PDT)
[AMBER] was the MCPB.py compiled correctly？ jixiaofeng (Sun Apr 17 2016 - 19:59:35 PDT)
[AMBER] Error in 3DRISM calculation ATUL KUMAR (Sun Apr 17 2016 - 22:46:49 PDT)
- Re: [AMBER] Error in 3DRISM calculation Tyler Luchko (Lists) (Sun Apr 17 2016 - 22:51:08 PDT)
[AMBER] on antechamber Brett (Sun Apr 17 2016 - 23:38:26 PDT)
- Re: [AMBER] on antechamber hannes.loeffler.stfc.ac.uk (Sun Apr 17 2016 - 23:49:59 PDT)
- Re: [AMBER] on antechamber Daniel Roe (Mon Apr 18 2016 - 07:24:29 PDT)
[AMBER] on antechamber Brett (Mon Apr 18 2016 - 02:28:10 PDT)
- Re: [AMBER] on antechamber David A Case (Mon Apr 18 2016 - 04:24:15 PDT)
[AMBER] clustering waleed zalloum (Mon Apr 18 2016 - 11:14:33 PDT)
[AMBER] mpi problems Gard Nelson (Mon Apr 18 2016 - 11:46:06 PDT)
- Re: [AMBER] mpi problems Marcelo Andrade Chagas (Mon Apr 18 2016 - 12:16:22 PDT)
[AMBER] Early bird extended! ISQBP2016 meeting - Bergen Norway Vlad Cojocaru (Mon Apr 18 2016 - 12:34:15 PDT)
[AMBER] amber v16 Arjun Sharma (Mon Apr 18 2016 - 12:38:01 PDT)
- Re: [AMBER] amber v16 Hai Nguyen (Mon Apr 18 2016 - 12:43:04 PDT)
[AMBER] glycam O-glycosylation at Ser Neha Gandhi (Mon Apr 18 2016 - 22:17:43 PDT)
- Re: [AMBER] glycam O-glycosylation at Ser Lachele Foley (Mon Apr 18 2016 - 23:59:06 PDT)
  - Re: [AMBER] glycam O-glycosylation at Ser Neha Gandhi (Tue Apr 19 2016 - 00:16:46 PDT)
[AMBER] want to ask you about MMPBSA.py .mdcrd file Ayesha Kanwal (Tue Apr 19 2016 - 00:55:36 PDT)
- Re: [AMBER] want to ask you about MMPBSA.py .mdcrd file Dr. M. Shahid (Tue Apr 19 2016 - 01:12:40 PDT)
  - Re: [AMBER] want to ask you about MMPBSA.py .mdcrd file Ayesha Kanwal (Tue Apr 19 2016 - 02:21:44 PDT)
    - Re: [AMBER] want to ask you about MMPBSA.py .mdcrd file Dr. M. Shahid (Tue Apr 19 2016 - 02:47:02 PDT)
    - Re: [AMBER] want to ask you about MMPBSA.py .mdcrd file Ayesha Kanwal (Tue Apr 19 2016 - 02:59:01 PDT)
    - Re: [AMBER] want to ask you about MMPBSA.py .mdcrd file Ayesha Kanwal (Tue Apr 19 2016 - 03:01:53 PDT)
    - Re: [AMBER] want to ask you about MMPBSA.py .mdcrd file Dr. M. Shahid (Tue Apr 19 2016 - 03:04:39 PDT)
    - Re: [AMBER] want to ask you about MMPBSA.py .mdcrd file Ayesha Kanwal (Tue Apr 19 2016 - 03:16:13 PDT)
    - Re: [AMBER] want to ask you about MMPBSA.py .mdcrd file Ayesha Kanwal (Tue Apr 19 2016 - 03:32:31 PDT)
    - Re: [AMBER] want to ask you about MMPBSA.py .mdcrd file Ayesha Kanwal (Tue Apr 19 2016 - 03:38:58 PDT)
[AMBER] HEME group in a protein Anna Cebrian Prats (Tue Apr 19 2016 - 04:14:45 PDT)
- Re: [AMBER] HEME group in a protein David A Case (Tue Apr 19 2016 - 04:41:03 PDT)
[AMBER] query about .mdcrd file Ayesha Kanwal (Tue Apr 19 2016 - 04:23:44 PDT)
- Re: [AMBER] query about .mdcrd file Dr. M. Shahid (Tue Apr 19 2016 - 05:48:20 PDT)
  - Re: [AMBER] query about .mdcrd file Ayesha Kanwal (Tue Apr 19 2016 - 10:12:36 PDT)
    - Re: [AMBER] query about .mdcrd file Christina Bergonzo (Tue Apr 19 2016 - 10:27:08 PDT)
    - Re: [AMBER] query about .mdcrd file Ayesha Kanwal (Tue Apr 19 2016 - 23:12:36 PDT)
[AMBER] [cpptraj] Automating pcmin/pcmax selection of modes command Eiros Zamora, Juan (Tue Apr 19 2016 - 04:52:01 PDT)
- Re: [AMBER] [cpptraj] Automating pcmin/pcmax selection of modes command Daniel Roe (Tue Apr 19 2016 - 08:49:31 PDT)
[AMBER] Approach for transmembrane protein Elisa Pieri (Tue Apr 19 2016 - 05:03:53 PDT)
- Re: [AMBER] Approach for transmembrane protein anu chandra (Tue Apr 19 2016 - 08:07:39 PDT)
[AMBER] atom serials instead of residue names and atom names in nativecontacts cpptraj peter.schmidtke.discngine.servier.com (Tue Apr 19 2016 - 05:41:14 PDT)
- Re: [AMBER] atom serials instead of residue names and atom names in nativecontacts cpptraj David A Case (Tue Apr 19 2016 - 06:20:00 PDT)
  - Re: [AMBER] atom serials instead of residue names and atom names in nativecontacts cpptraj peter.schmidtke.discngine.servier.com (Tue Apr 19 2016 - 08:23:13 PDT)
    - Re: [AMBER] atom serials instead of residue names and atom names in nativecontacts cpptraj Daniel Roe (Tue Apr 19 2016 - 09:00:24 PDT)
    - Re: [AMBER] atom serials instead of residue names and atom names in nativecontacts cpptraj David A Case (Tue Apr 19 2016 - 11:20:14 PDT)
    - Re: [AMBER] atom serials instead of residue names and atom names in nativecontacts cpptraj peter.schmidtke.discngine.servier.com (Wed Apr 20 2016 - 01:27:25 PDT)
    - Re: [AMBER] atom serials instead of residue names and atom names in nativecontacts cpptraj David A Case (Wed Apr 20 2016 - 05:09:30 PDT)
    - Re: [AMBER] atom serials instead of residue names and atom names in nativecontacts cpptraj peter.schmidtke.discngine.servier.com (Wed Apr 20 2016 - 05:30:27 PDT)
[AMBER] building DNA with extruded base giulia palermo (Tue Apr 19 2016 - 10:17:46 PDT)
- Re: [AMBER] building DNA with extruded base David A Case (Tue Apr 19 2016 - 11:24:03 PDT)
  - Re: [AMBER] building DNA with extruded base Christina Bergonzo (Tue Apr 19 2016 - 11:56:54 PDT)
    - Re: [AMBER] building DNA with extruded base giulia palermo (Tue Apr 19 2016 - 13:50:12 PDT)
[AMBER] interactive MD applied to AI Bill Ross (Tue Apr 19 2016 - 12:19:05 PDT)
- Re: [AMBER] interactive MD applied to AI Bill Ross (Thu Apr 21 2016 - 17:25:58 PDT)
  - Re: [AMBER] interactive MD applied to AI Hai Nguyen (Thu Apr 21 2016 - 18:17:39 PDT)
    - Re: [AMBER] interactive MD applied to AI Bill Ross (Thu Apr 21 2016 - 18:37:27 PDT)
    - Re: [AMBER] interactive MD applied to AI Hai Nguyen (Thu Apr 21 2016 - 19:59:10 PDT)
    - Re: [AMBER] interactive MD applied to AI Bill Ross (Thu Apr 21 2016 - 20:16:19 PDT)
    - [AMBER] fortran i/o on system shared memory Bill Ross (Thu Apr 28 2016 - 23:20:53 PDT)
    - Re: [AMBER] fortran i/o on system shared memory Bill Ross (Thu Apr 28 2016 - 23:31:13 PDT)
[AMBER] Electrostatic Energies - MMPBSA Cortopassi, Wilian (Tue Apr 19 2016 - 13:55:24 PDT)
- Re: [AMBER] Electrostatic Energies - MMPBSA Jason Swails (Tue Apr 19 2016 - 18:36:24 PDT)
- Re: [AMBER] Electrostatic Energies - MMPBSA Cortopassi, Wilian (Wed Apr 20 2016 - 04:04:24 PDT)
  - Re: [AMBER] Electrostatic Energies - MMPBSA Jason Swails (Wed Apr 20 2016 - 11:30:55 PDT)
[AMBER] Regarding atom types Elvis Martis (Tue Apr 19 2016 - 21:56:47 PDT)
- Re: [AMBER] Regarding atom types Daniel Roe (Thu Apr 21 2016 - 10:16:48 PDT)
- Re: [AMBER] Regarding atom types Elvis Martis (Fri Apr 22 2016 - 07:08:00 PDT)
[AMBER] error while putting the whole path into python script Ayesha Kanwal (Wed Apr 20 2016 - 00:37:51 PDT)
- Re: [AMBER] error while putting the whole path into python script Marc van der Kamp (Wed Apr 20 2016 - 00:51:13 PDT)
- Re: [AMBER] error while putting the whole path into python script Bill Ross (Wed Apr 20 2016 - 01:00:09 PDT)
[AMBER] XLeap didn't save the parameter file Nikolay N. Kuzmich (Wed Apr 20 2016 - 01:27:17 PDT)
- Re: [AMBER] XLeap didn't save the parameter file Bill Ross (Wed Apr 20 2016 - 01:33:09 PDT)
- Re: [AMBER] XLeap didn't save the parameter file David A Case (Wed Apr 20 2016 - 05:04:54 PDT)
- Re: [AMBER] XLeap didn't save the parameter file Nikolay N. Kuzmich (Fri Apr 22 2016 - 05:39:11 PDT)
  - Re: [AMBER] XLeap didn't save the parameter file Bill Ross (Fri Apr 22 2016 - 09:28:56 PDT)
  - Re: [AMBER] XLeap didn't save the parameter file David A Case (Fri Apr 22 2016 - 10:38:45 PDT)
[AMBER] problem in 3DRISM convergence ATUL KUMAR (Wed Apr 20 2016 - 03:29:41 PDT)
- Re: [AMBER] problem in 3DRISM convergence David A Case (Wed Apr 20 2016 - 05:17:23 PDT)
[AMBER] questions about energy terms of amber MD yuandandan (Wed Apr 20 2016 - 06:57:38 PDT)
- Re: [AMBER] questions about energy terms of amber MD David A Case (Thu Apr 21 2016 - 05:05:40 PDT)
[AMBER] warning message for antechamber by acpype Brett (Wed Apr 20 2016 - 07:41:28 PDT)
- Re: [AMBER] warning message for antechamber by acpype David A Case (Thu Apr 21 2016 - 12:26:40 PDT)
[AMBER] Force field parameters for glycerophophate anu chandra (Wed Apr 20 2016 - 15:24:47 PDT)
[AMBER] Error in the conversion of CHARMM-GUI generated file into lipid14 readable format Shreeramesh (Thu Apr 21 2016 - 00:52:48 PDT)
[AMBER] How to read mdinfo file without crashing the simulation? Karolina Markowska (Thu Apr 21 2016 - 02:01:03 PDT)
- Re: [AMBER] How to read mdinfo file without crashing the simulation? Dr. M. Shahid (Thu Apr 21 2016 - 02:29:41 PDT)
  - Re: [AMBER] How to read mdinfo file without crashing the simulation? Karolina Markowska (Thu Apr 21 2016 - 03:11:56 PDT)
- Re: [AMBER] How to read mdinfo file without crashing the simulation? Hannes Loeffler (Thu Apr 21 2016 - 03:13:49 PDT)
  - Re: [AMBER] How to read mdinfo file without crashing the simulation? Karolina Markowska (Thu Apr 21 2016 - 03:43:18 PDT)
    - Re: [AMBER] How to read mdinfo file without crashing the simulation? Bill Ross (Thu Apr 21 2016 - 11:10:07 PDT)
    - Re: [AMBER] How to read mdinfo file without crashing the simulation? Bill Ross (Thu Apr 21 2016 - 11:22:16 PDT)
- Re: [AMBER] How to read mdinfo file without crashing the simulation? David A Case (Thu Apr 21 2016 - 05:14:54 PDT)
  - Re: [AMBER] How to read mdinfo file without crashing the simulation? Hannes Loeffler (Thu Apr 21 2016 - 05:46:24 PDT)
  - Re: [AMBER] How to read mdinfo file without crashing the simulation? Karolina Markowska (Fri Apr 22 2016 - 02:24:26 PDT)
    - Re: [AMBER] How to read mdinfo file without crashing the simulation? Bill Ross (Sat Apr 23 2016 - 11:53:25 PDT)
    - Re: [AMBER] How to read mdinfo file without crashing the simulation? Bill Ross (Sat Apr 23 2016 - 11:55:45 PDT)
    - Re: [AMBER] How to read mdinfo file without crashing the simulation? Karolina Markowska (Sun Apr 24 2016 - 12:16:02 PDT)
    - Re: [AMBER] How to read mdinfo file without crashing the simulation? Bill Ross (Sun Apr 24 2016 - 15:46:55 PDT)
    - Re: [AMBER] How to read mdinfo file without crashing the simulation? Karolina Markowska (Mon Apr 25 2016 - 05:00:08 PDT)
    - Re: [AMBER] How to read mdinfo file without crashing the simulation? Dr. M. Shahid (Mon Apr 25 2016 - 05:31:51 PDT)
[AMBER] qmmm mmpbsa spin multiplicity problem Ayesha Fatima (Thu Apr 21 2016 - 08:32:28 PDT)
- Re: [AMBER] qmmm mmpbsa spin multiplicity problem Jason Swails (Thu Apr 21 2016 - 10:02:04 PDT)
  - Re: [AMBER] qmmm mmpbsa spin multiplicity problem Ayesha Fatima (Thu Apr 21 2016 - 19:18:16 PDT)
[AMBER] GeForce GTX 960 ? Marek Maly (Thu Apr 21 2016 - 08:51:43 PDT)
- Re: [AMBER] GeForce GTX 960 ? Ross Walker (Thu Apr 21 2016 - 10:18:30 PDT)
  - Re: [AMBER] GeForce GTX 960 ? Marek Maly (Thu Apr 21 2016 - 15:36:45 PDT)
    - Re: [AMBER] GeForce GTX 960 ? Ross Walker (Mon Apr 25 2016 - 08:20:44 PDT)
[AMBER] mmpbsa complex McElheny, Dan (Thu Apr 21 2016 - 12:42:52 PDT)
- Re: [AMBER] mmpbsa complex Jason Swails (Thu Apr 21 2016 - 19:12:53 PDT)
  - Re: [AMBER] mmpbsa complex McElheny, Dan (Fri Apr 29 2016 - 13:57:42 PDT)
    - Re: [AMBER] mmpbsa complex Jason Swails (Fri Apr 29 2016 - 18:46:45 PDT)
[AMBER] Building Cyclic Peptide in xleap Maral Aminpour (Thu Apr 21 2016 - 13:55:19 PDT)
- Re: [AMBER] Building Cyclic Peptide in xleap David A Case (Thu Apr 21 2016 - 16:35:06 PDT)
  - Re: [AMBER] Building Cyclic Peptide in xleap Bill Ross (Thu Apr 21 2016 - 16:53:42 PDT)
    - Re: [AMBER] Building Cyclic Peptide in xleap Kenneth McGuinness (Fri Apr 22 2016 - 09:43:36 PDT)
    - Re: [AMBER] Building Cyclic Peptide in xleap David Cerutti (Fri Apr 22 2016 - 09:52:09 PDT)
    - Re: [AMBER] Building Cyclic Peptide in xleap Maral Aminpour (Thu Apr 28 2016 - 08:15:02 PDT)
[AMBER] How to deal with monoatomic ion, such as ILs cation Takuya Uto (Thu Apr 21 2016 - 18:29:56 PDT)
- Re: [AMBER] How to deal with monoatomic ion, such as ILs cation Bill Ross (Thu Apr 21 2016 - 18:39:21 PDT)
[AMBER] How to deal with monoatomic ion, such as ILs anion Takuya Uto (Thu Apr 21 2016 - 18:45:45 PDT)
- Re: [AMBER] How to deal with monoatomic ion, such as ILs anion kurisaki (Thu Apr 21 2016 - 18:57:39 PDT)
- Re: [AMBER] How to deal with monoatomic ion, such as ILs anion Takuya Uto (Sat Apr 23 2016 - 02:49:22 PDT)
  - Re: [AMBER] How to deal with monoatomic ion, such as ILs anion Bill Ross (Sat Apr 23 2016 - 11:30:51 PDT)
    - Re: [AMBER] How to deal with monoatomic ion, such as ILs anion Andrew Schaub (Sat Apr 23 2016 - 11:41:21 PDT)
    - Re: [AMBER] How to deal with monoatomic ion, such as ILs anion Bill Ross (Sat Apr 23 2016 - 11:50:33 PDT)
- Re: [AMBER] How to deal with monoatomic ion, such as ILs anion Takuya Uto (Mon Apr 25 2016 - 03:50:16 PDT)
[AMBER] atom does not have a type jixiaofeng (Thu Apr 21 2016 - 19:23:53 PDT)
- Re: [AMBER] atom does not have a type jixiaofeng (Thu Apr 21 2016 - 19:31:45 PDT)
[AMBER] CUDA and restraint Domenico Marson (Fri Apr 22 2016 - 02:21:43 PDT)
[AMBER] System size limitations for Amber 14 pmemd.cuda? Kasprzak, Wojciech (NIH/NCI) [C] (Fri Apr 22 2016 - 05:48:38 PDT)
[AMBER] Decomposition energy after mutation! Jag Silwal (Fri Apr 22 2016 - 09:52:14 PDT)
- Re: [AMBER] Decomposition energy after mutation! Jason Swails (Sat Apr 23 2016 - 21:58:51 PDT)
[AMBER] Hydroxyproline Mijiddorj Batsaikhan (Sat Apr 23 2016 - 05:00:41 PDT)
- Re: [AMBER] Hydroxyproline Carlos Simmerling (Sat Apr 23 2016 - 05:36:26 PDT)
- Re: [AMBER] Hydroxyproline David A Case (Sat Apr 23 2016 - 05:38:51 PDT)
[AMBER] No torsion terms for CB-N*-CR-H5 Prayagraj Fandilolu (Sun Apr 24 2016 - 00:12:13 PDT)
- Re: [AMBER] No torsion terms for CB-N*-CR-H5 David A Case (Sun Apr 24 2016 - 17:33:16 PDT)
  - Re: [AMBER] No torsion terms for CB-N*-CR-H5 Prayagraj Fandilolu (Wed Apr 27 2016 - 23:29:11 PDT)
    - Re: [AMBER] No torsion terms for CB-N*-CR-H5 Bill Ross (Thu Apr 28 2016 - 01:14:05 PDT)
[AMBER] Read/visualize volmap output (opendx) Jean-Patrick Francoia (Mon Apr 25 2016 - 01:44:54 PDT)
- Re: [AMBER] Read/visualize volmap output (opendx) Jason Swails (Mon Apr 25 2016 - 03:14:01 PDT)
  - Re: [AMBER] Read/visualize volmap output (opendx) Jean-Patrick Francoia (Mon Apr 25 2016 - 03:54:13 PDT)
    - Re: [AMBER] Read/visualize volmap output (opendx) Jason Swails (Mon Apr 25 2016 - 05:53:40 PDT)
    - Re: [AMBER] Read/visualize volmap output (opendx) Jean-Patrick Francoia (Mon Apr 25 2016 - 06:12:45 PDT)
    - Re: [AMBER] Read/visualize volmap output (opendx) Daniel Roe (Mon Apr 25 2016 - 07:41:47 PDT)
    - Re: [AMBER] Read/visualize volmap output (opendx) Jean-Patrick Francoia (Mon Apr 25 2016 - 12:26:08 PDT)
    - Re: [AMBER] Read/visualize volmap output (opendx) Daniel Roe (Mon Apr 25 2016 - 12:41:02 PDT)
    - Re: [AMBER] Read/visualize volmap output (opendx) Jean-Patrick Francoia (Mon Apr 25 2016 - 13:46:47 PDT)
[AMBER] Energies in QM/MM MD 王美婷 (Mon Apr 25 2016 - 01:46:48 PDT)
- Re: [AMBER] Energies in QM/MM MD Brian Radak (Mon Apr 25 2016 - 16:50:45 PDT)
  - Re: [AMBER] Energies in QM/MM MD Dr. Andreas W. Goetz (Tue Apr 26 2016 - 16:02:20 PDT)
[AMBER] How to rebuild pH-based trajectory files from CpHMD restarted simulations Elisa Pieri (Mon Apr 25 2016 - 02:39:46 PDT)
- Re: [AMBER] How to rebuild pH-based trajectory files from CpHMD restarted simulations Jason Swails (Mon Apr 25 2016 - 03:16:18 PDT)
[AMBER] Error while converting CHARMM-GUI generated file Shreeramesh (Mon Apr 25 2016 - 05:17:08 PDT)
- Re: [AMBER] Error while converting CHARMM-GUI generated file Batuhan Kav (Mon Apr 25 2016 - 06:39:47 PDT)
[AMBER] protein complex dissociation during md Brett (Mon Apr 25 2016 - 06:54:34 PDT)
- Re: [AMBER] protein complex dissociation during md Dr. Anselm Horn (Fri Apr 29 2016 - 01:56:27 PDT)
[AMBER] rotation angle around an axes giulia palermo (Mon Apr 25 2016 - 10:55:54 PDT)
- Re: [AMBER] rotation angle around an axes Daniel Roe (Mon Apr 25 2016 - 10:59:24 PDT)
[AMBER] Problem Running MMPBSA.py Martin Floor (Mon Apr 25 2016 - 15:29:23 PDT)
- Re: [AMBER] Problem Running MMPBSA.py Dwight McGee (Mon Apr 25 2016 - 21:41:20 PDT)
- Re: [AMBER] Problem Running MMPBSA.py Jason Swails (Tue Apr 26 2016 - 05:45:06 PDT)
[AMBER] Using PBSA to Calculate Solvation Free Energy Jiaqi Jin (Mon Apr 25 2016 - 15:31:48 PDT)
- Re: [AMBER] Using PBSA to Calculate Solvation Free Energy Ray Luo (Mon Apr 25 2016 - 15:56:49 PDT)
[AMBER] parmed.py Sanjib Paul (Tue Apr 26 2016 - 07:44:15 PDT)
- Re: [AMBER] parmed.py Daniel Roe (Tue Apr 26 2016 - 08:14:35 PDT)
Re: [AMBER] AMBER Project Niharikav Veeresh (Tue Apr 26 2016 - 11:52:30 PDT)
- Re: [AMBER] AMBER Project Daniel Roe (Tue Apr 26 2016 - 11:54:23 PDT)
[AMBER] MD of 1:1 mixture compound Saman Yousuf ali (Tue Apr 26 2016 - 22:10:56 PDT)
[AMBER] debug issue Zhenyu Meng (Tue Apr 26 2016 - 23:53:13 PDT)
- Re: [AMBER] debug issue David A Case (Wed Apr 27 2016 - 05:20:07 PDT)
  - Re: [AMBER] debug issue Zhenyu Meng (Wed Apr 27 2016 - 20:32:44 PDT)
  - Re: [AMBER] debug issue Zhenyu Meng (Thu Apr 28 2016 - 02:46:49 PDT)
[AMBER] tleap parametrization of metalo-binding proteins James Starlight (Wed Apr 27 2016 - 02:25:23 PDT)
- Re: [AMBER] tleap parametrization of metalo-binding proteins Yigal Lahav (Wed Apr 27 2016 - 04:07:26 PDT)
  - Re: [AMBER] tleap parametrization of metalo-binding proteins James Starlight (Wed Apr 27 2016 - 05:54:55 PDT)
    - Re: [AMBER] tleap parametrization of metalo-binding proteins Pengfei Li (Wed Apr 27 2016 - 06:53:03 PDT)
    - Re: [AMBER] tleap parametrization of metalo-binding proteins James Starlight (Wed Apr 27 2016 - 07:01:05 PDT)
    - Re: [AMBER] tleap parametrization of metalo-binding proteins Pengfei Li (Thu Apr 28 2016 - 07:51:29 PDT)
[AMBER] Question about RESP with iodine Lorenzo Gontrani (Wed Apr 27 2016 - 03:55:29 PDT)
- Re: [AMBER] Question about RESP with iodine David A Case (Wed Apr 27 2016 - 05:26:19 PDT)
  - Re: [AMBER] Question about RESP with iodine Pengfei Li (Wed Apr 27 2016 - 06:39:37 PDT)
    - Re: [AMBER] Question about RESP with iodine Lorenzo Gontrani (Wed Apr 27 2016 - 06:50:53 PDT)
[AMBER] Problem in calculating auto time correlation function with ptraj Saheb Dutta (Wed Apr 27 2016 - 08:32:55 PDT)
- Re: [AMBER] Problem in calculating auto time correlation function with ptraj Daniel Roe (Wed Apr 27 2016 - 09:26:16 PDT)
- Re: [AMBER] Problem in calculating auto time correlation function with ptraj David A Case (Wed Apr 27 2016 - 18:20:55 PDT)
[AMBER] How can I use FF14SB in DOCK6 calculation? Mijiddorj Batsaikhan (Thu Apr 28 2016 - 03:20:40 PDT)
- Re: [AMBER] How can I use FF14SB in DOCK6 calculation? Dwight McGee (Thu Apr 28 2016 - 06:53:43 PDT)
  - Re: [AMBER] How can I use FF14SB in DOCK6 calculation? Mijiddorj Batsaikhan (Thu Apr 28 2016 - 22:03:55 PDT)
    - Re: [AMBER] How can I use FF14SB in DOCK6 calculation? Marc van der Kamp (Fri Apr 29 2016 - 01:09:37 PDT)
[AMBER] CUDA and restraint Domenico Marson (Thu Apr 28 2016 - 03:31:34 PDT)
- Re: [AMBER] CUDA and restraint Charles Lin (Thu Apr 28 2016 - 09:27:00 PDT)
  - Re: [AMBER] CUDA and restraint Domenico Marson (Fri Apr 29 2016 - 01:19:41 PDT)
    - Re: [AMBER] CUDA and restraint Bill Ross (Fri Apr 29 2016 - 01:25:32 PDT)
    - Re: [AMBER] CUDA and restraint Bill Ross (Fri Apr 29 2016 - 01:28:22 PDT)
    - Re: [AMBER] CUDA and restraint Domenico Marson (Fri Apr 29 2016 - 02:35:06 PDT)
    - Re: [AMBER] CUDA and restraint Charles Lin (Fri Apr 29 2016 - 04:52:35 PDT)
    - Re: [AMBER] CUDA and restraint Domenico Marson (Fri Apr 29 2016 - 06:37:19 PDT)
    - Re: [AMBER] CUDA and restraint Ross Walker (Fri Apr 29 2016 - 08:28:42 PDT)
[AMBER] tleap - protein + ligand + heme group Anna Cebrian Prats (Thu Apr 28 2016 - 08:52:13 PDT)
- Re: [AMBER] tleap - protein + ligand + heme group David A Case (Thu Apr 28 2016 - 10:28:36 PDT)
- Re: [AMBER] tleap - protein + ligand + heme group Scott Brozell (Thu Apr 28 2016 - 10:35:26 PDT)
  - Re: [AMBER] tleap - protein + ligand + heme group Anna Cebrian Prats (Fri Apr 29 2016 - 08:16:21 PDT)
    - Re: [AMBER] tleap - protein + ligand + heme group David A Case (Fri Apr 29 2016 - 09:27:28 PDT)
    - Re: [AMBER] tleap - protein + ligand + heme group Anna Cebrian Prats (Tue May 03 2016 - 02:47:55 PDT)
    - Re: [AMBER] tleap - protein + ligand + heme group Anna Cebrian Prats (Tue May 03 2016 - 03:16:18 PDT)
    - Re: [AMBER] tleap - protein + ligand + heme group Anna Cebrian Prats (Fri May 06 2016 - 04:23:50 PDT)
    - Re: [AMBER] tleap - protein + ligand + heme group Bill Ross (Fri May 06 2016 - 05:48:39 PDT)
[AMBER] Targeted MD error Shukla, Saurabh (Thu Apr 28 2016 - 09:46:03 PDT)
- Re: [AMBER] Targeted MD error Charles Lin (Thu Apr 28 2016 - 09:56:57 PDT)
- Re: [AMBER] Targeted MD error Carlos Simmerling (Thu Apr 28 2016 - 10:03:03 PDT)
[AMBER] Cpptraj LipidOrder error: mask groups are not the same length Amy Rice (Thu Apr 28 2016 - 11:30:14 PDT)
- Re: [AMBER] Cpptraj LipidOrder error: mask groups are not the same length Chris Moth (Thu Apr 28 2016 - 11:53:45 PDT)
- Re: [AMBER] Cpptraj LipidOrder error: mask groups are not the same length hannes.loeffler.stfc.ac.uk (Thu Apr 28 2016 - 12:06:04 PDT)
- Re: [AMBER] Cpptraj LipidOrder error: mask groups are not the same length hannes.loeffler.stfc.ac.uk (Thu Apr 28 2016 - 12:10:55 PDT)
  - Re: [AMBER] Cpptraj LipidOrder error: mask groups are not the same length Amy Rice (Thu Apr 28 2016 - 12:29:44 PDT)
[AMBER] Calculate Percentage of Hydrogen Occurrence Jag Silwal (Fri Apr 29 2016 - 06:27:54 PDT)
- Re: [AMBER] Calculate Percentage of Hydrogen Occurrence Daniel Roe (Fri Apr 29 2016 - 08:24:33 PDT)
[AMBER] ambpdb error Arati Paudyal (Fri Apr 29 2016 - 06:41:40 PDT)
- Re: [AMBER] ambpdb error Daniel Roe (Fri Apr 29 2016 - 07:21:44 PDT)
  - Re: [AMBER] ambpdb error Arati Paudyal (Fri Apr 29 2016 - 08:25:42 PDT)
    - Re: [AMBER] ambpdb error Daniel Roe (Fri Apr 29 2016 - 08:27:56 PDT)
    - Re: [AMBER] ambpdb error Daniel Roe (Fri Apr 29 2016 - 09:16:03 PDT)
    - Re: [AMBER] ambpdb error Daniel Roe (Fri Apr 29 2016 - 09:17:28 PDT)
    - Re: [AMBER] ambpdb error Arati Paudyal (Fri Apr 29 2016 - 10:01:20 PDT)
    - Re: [AMBER] ambpdb error Daniel Roe (Fri Apr 29 2016 - 10:14:31 PDT)
    - Re: [AMBER] ambpdb error Jason Swails (Fri Apr 29 2016 - 10:22:33 PDT)
    - Re: [AMBER] ambpdb error Jason Swails (Fri Apr 29 2016 - 08:59:13 PDT)
[AMBER] accelerated MD on set of dihedrals Giuseppina La Sala (Fri Apr 29 2016 - 09:56:00 PDT)
- Re: [AMBER] accelerated MD on set of dihedrals Daniel Roe (Fri Apr 29 2016 - 10:18:41 PDT)
  - Re: [AMBER] accelerated MD on set of dihedrals Giuseppina La Sala (Fri Apr 29 2016 - 15:15:52 PDT)
- Re: [AMBER] accelerated MD on set of dihedrals giulia palermo (Fri Apr 29 2016 - 11:47:21 PDT)
  - Re: [AMBER] accelerated MD on set of dihedrals Giuseppina La Sala (Fri Apr 29 2016 - 15:14:06 PDT)
[AMBER] on antechamber Brett (Sat Apr 30 2016 - 02:00:14 PDT)
- Re: [AMBER] on antechamber David A Case (Sat Apr 30 2016 - 05:16:06 PDT)
  - Re: [AMBER] on antechamber Brett (Sat Apr 30 2016 - 20:51:58 PDT)
    - Re: [AMBER] on antechamber David A Case (Mon May 02 2016 - 04:56:57 PDT)
[AMBER] Release of Amber16 and AmberTools16 David A Case (Sat Apr 30 2016 - 09:27:51 PDT)
[AMBER] help identifying dihedral parameters for paracetemol using Antechamber conor parks (Sat Apr 30 2016 - 21:13:49 PDT)
- Re: [AMBER] help identifying dihedral parameters for paracetemol using Antechamber Andrew Schaub (Sat Apr 30 2016 - 22:01:04 PDT)
- Re: [AMBER] help identifying dihedral parameters for paracetemol using Antechamber David A Case (Sun May 01 2016 - 05:42:21 PDT)
  - Re: [AMBER] help identifying dihedral parameters for paracetemol using Antechamber conor parks (Mon May 02 2016 - 09:11:28 PDT)
    - Re: [AMBER] help identifying dihedral parameters for paracetemol using Antechamber David A Case (Tue May 03 2016 - 08:05:31 PDT)
    - Re: [AMBER] help identifying dihedral parameters for paracetemol using Antechamber conor parks (Tue May 03 2016 - 08:51:06 PDT)
    - Re: [AMBER] help identifying dihedral parameters for paracetemol using Antechamber David A Case (Tue May 03 2016 - 12:53:58 PDT)
    - Re: [AMBER] help identifying dihedral parameters for paracetemol using Antechamber conor parks (Tue May 03 2016 - 13:13:05 PDT)
    - Re: [AMBER] help identifying dihedral parameters for paracetemol using Antechamber Karl Kirschner (Wed May 04 2016 - 01:28:34 PDT)
    - Re: [AMBER] help identifying dihedral parameters for paracetemol using Antechamber conor parks (Thu May 05 2016 - 16:13:28 PDT)
    - Re: [AMBER] help identifying dihedral parameters for paracetemol using Antechamber David A Case (Thu May 05 2016 - 17:50:49 PDT)
    - Re: [AMBER] help identifying dihedral parameters for paracetemol using Antechamber Karl Kirschner (Sat May 07 2016 - 12:16:00 PDT)
[AMBER] water residence time calculation maryam azimzadehirani (Sun May 01 2016 - 05:59:57 PDT)
- Re: [AMBER] water residence time calculation Daniel Roe (Sun May 01 2016 - 08:42:20 PDT)
  - Re: [AMBER] water residence time calculation maryam azimzadehirani (Sun May 01 2016 - 20:55:18 PDT)
    - Re: [AMBER] water residence time calculation Daniel Roe (Mon May 02 2016 - 07:44:59 PDT)
[AMBER] Query about amber 16, external electric field support Kshatresh Dutta Dubey (Sun May 01 2016 - 06:54:50 PDT)
- Re: [AMBER] Query about amber 16, external electric field support Charles Lin (Sun May 01 2016 - 07:15:46 PDT)
  - Re: [AMBER] Query about amber 16, external electric field support Kshatresh Dutta Dubey (Sun May 01 2016 - 07:25:03 PDT)
[AMBER] cpptraj mask command Saman Yousuf ali (Sun May 01 2016 - 08:29:43 PDT)
- Re: [AMBER] cpptraj mask command Daniel Roe (Sun May 01 2016 - 08:40:20 PDT)
[AMBER] angle between normals to dna bases? Bill Ross (Sun May 01 2016 - 20:00:50 PDT)
- Re: [AMBER] angle between normals to dna bases? Hai Nguyen (Sun May 01 2016 - 20:46:41 PDT)
  - Re: [AMBER] angle between normals to dna bases? Bill Ross (Sun May 01 2016 - 20:57:56 PDT)
[AMBER] Paramfit trajectory read error David Poole (Sun May 01 2016 - 21:28:56 PDT)
[AMBER] Ewald force using debugf Zhenyu Meng (Mon May 02 2016 - 04:07:17 PDT)
- Re: [AMBER] Ewald force using debugf David A Case (Mon May 02 2016 - 04:52:05 PDT)
  - Re: [AMBER] Ewald force using debugf Zhenyu Meng (Tue May 03 2016 - 04:43:20 PDT)
    - Re: [AMBER] Ewald force using debugf David A Case (Tue May 03 2016 - 07:48:08 PDT)
    - Re: [AMBER] Ewald force using debugf David Cerutti (Tue May 03 2016 - 12:06:56 PDT)
    - Re: [AMBER] Ewald force using debugf Zhenyu Meng (Tue May 03 2016 - 20:28:42 PDT)
[AMBER] iwrap=1 issue Hirdesh Kumar (Mon May 02 2016 - 04:57:07 PDT)
- Re: [AMBER] iwrap=1 issue Carlos Simmerling (Mon May 02 2016 - 05:11:02 PDT)
  - Re: [AMBER] iwrap=1 issue Kenneth McGuinness (Mon May 02 2016 - 06:53:16 PDT)
    - Re: [AMBER] iwrap=1 issue Daniel Roe (Mon May 02 2016 - 07:40:28 PDT)
    - Re: [AMBER] iwrap=1 issue Kenneth McGuinness (Mon May 02 2016 - 08:26:43 PDT)
[AMBER] on antechamber of AMBER Brett (Mon May 02 2016 - 06:02:48 PDT)
- Re: [AMBER] on antechamber of AMBER David A Case (Mon May 02 2016 - 07:25:30 PDT)
  - Re: [AMBER] on antechamber of AMBER Brett (Mon May 02 2016 - 08:01:13 PDT)
[AMBER] Amber 8 on RHEL 6 boyken.divms.uiowa.edu (Mon May 02 2016 - 09:30:41 PDT)
- Re: [AMBER] Amber 8 on RHEL 6 Nhai (Mon May 02 2016 - 09:42:37 PDT)
- Re: [AMBER] Amber 8 on RHEL 6 Jason Swails (Mon May 02 2016 - 18:03:59 PDT)
[AMBER] Rotating the protein along x-axis Aishani Prem (Mon May 02 2016 - 14:53:27 PDT)
- Re: [AMBER] Rotating the protein along x-axis Hai Nguyen (Mon May 02 2016 - 16:02:23 PDT)
  - Re: [AMBER] Rotating the protein along x-axis Aishani Prem (Mon May 02 2016 - 16:04:09 PDT)
    - Re: [AMBER] Rotating the protein along x-axis Hai Nguyen (Mon May 02 2016 - 16:13:18 PDT)
    - Re: [AMBER] Rotating the protein along x-axis Bill Ross (Mon May 02 2016 - 16:55:13 PDT)
[AMBER] rdf cpptraj. Saman Yousuf ali (Tue May 03 2016 - 02:37:48 PDT)
- Re: [AMBER] rdf cpptraj. Daniel Roe (Tue May 03 2016 - 06:41:25 PDT)
[AMBER] Problem interpreting cpptraj hbond output file maryam azimzadehirani (Tue May 03 2016 - 05:00:03 PDT)
- Re: [AMBER] Problem interpreting cpptraj hbond output file Daniel Roe (Tue May 03 2016 - 06:44:08 PDT)
[AMBER] process_mdout.perl script Ruth Helena Tichauer (Tue May 03 2016 - 06:35:47 PDT)
[AMBER] DFTB convergence Jacopo Sgrignani (Tue May 03 2016 - 12:23:17 PDT)
- Re: [AMBER] DFTB convergence Marc van der Kamp (Tue May 03 2016 - 13:35:47 PDT)
[AMBER] Amber 12 and VMware workstation 12 player Ibrahim Said (Tue May 03 2016 - 13:00:42 PDT)
- Re: [AMBER] Amber 12 and VMware workstation 12 player Jason Swails (Tue May 03 2016 - 17:20:56 PDT)
[AMBER] non zero net charge on molecule from AM1-BCC charge parameter fit conor parks (Tue May 03 2016 - 20:25:44 PDT)
- Re: [AMBER] non zero net charge on molecule from AM1-BCC charge parameter fit Thomas Cheatham (Tue May 03 2016 - 22:22:09 PDT)
  - Re: [AMBER] non zero net charge on molecule from AM1-BCC charge parameter fit conor parks (Wed May 04 2016 - 12:54:29 PDT)
    - Re: [AMBER] non zero net charge on molecule from AM1-BCC charge parameter fit Bill Ross (Wed May 04 2016 - 13:06:33 PDT)
    - Re: [AMBER] non zero net charge on molecule from AM1-BCC charge parameter fit Thomas Cheatham (Wed May 04 2016 - 13:49:29 PDT)
    - Re: [AMBER] non zero net charge on molecule from AM1-BCC charge parameter fit Jason Swails (Wed May 04 2016 - 18:01:47 PDT)
[AMBER] cpptraj rms fit to rst file Bill Ross (Tue May 03 2016 - 21:22:04 PDT)
- Re: [AMBER] cpptraj rms fit to rst file Bill Ross (Tue May 03 2016 - 23:23:02 PDT)
[AMBER] Thermodynamic Integration introduce charge Johannes Loeffler (Tue May 03 2016 - 22:36:39 PDT)
- Re: [AMBER] Thermodynamic Integration introduce charge hannes.loeffler.stfc.ac.uk (Tue May 03 2016 - 23:10:23 PDT)
  - Re: [AMBER] Thermodynamic Integration introduce charge Ignacio J. General (Wed May 04 2016 - 04:15:35 PDT)
[AMBER] bad data error in sander run Mary Varughese (Wed May 04 2016 - 04:07:47 PDT)
- Re: [AMBER] bad data error in sander run Carlos Simmerling (Wed May 04 2016 - 04:19:40 PDT)
- Re: [AMBER] bad data error in sander run David A Case (Wed May 04 2016 - 04:46:39 PDT)
  - Re: [AMBER] bad data error in sander run Mary Varughese (Wed May 04 2016 - 05:11:09 PDT)
    - Re: [AMBER] bad data error in sander run Jason Swails (Wed May 04 2016 - 05:22:13 PDT)
- Re: [AMBER] bad data error in sander run Bill Ross (Wed May 04 2016 - 07:57:46 PDT)
  - Re: [AMBER] bad data error in sander run Mary Varughese (Wed May 04 2016 - 09:44:49 PDT)
[AMBER] metal ion models for Zn+2 Fabian gmail (Wed May 04 2016 - 06:10:33 PDT)
[AMBER] DNA Origami Ramkumar B (Wed May 04 2016 - 11:35:27 PDT)
- Re: [AMBER] DNA Origami David A Case (Wed May 04 2016 - 12:36:44 PDT)
[AMBER] MMPBSA: question of pairwise per residue decomposition George Tzotzos (Wed May 04 2016 - 12:27:21 PDT)
- Re: [AMBER] MMPBSA: question of pairwise per residue decomposition Bill Ross (Wed May 04 2016 - 12:36:11 PDT)
  - Re: [AMBER] MMPBSA: question of pairwise per residue decomposition George Tzotzos (Wed May 04 2016 - 12:42:39 PDT)
- Re: [AMBER] MMPBSA: question of pairwise per residue decomposition Jason Swails (Wed May 04 2016 - 18:03:28 PDT)
  - Re: [AMBER] MMPBSA: question of pairwise per residue decomposition George Tzotzos (Thu May 05 2016 - 03:23:12 PDT)
    - Re: [AMBER] MMPBSA: question of pairwise per residue decomposition Jason Swails (Thu May 05 2016 - 06:09:26 PDT)
[AMBER] xLeap Ramkumar B (Thu May 05 2016 - 00:20:55 PDT)
- Re: [AMBER] xLeap Bill Ross (Fri Dec 27 2013 - 18:20:13 PST)
- Re: [AMBER] xLeap hannes.loeffler.stfc.ac.uk (Thu May 05 2016 - 00:46:54 PDT)
  - Re: [AMBER] xLeap Ramkumar B (Thu May 05 2016 - 04:33:29 PDT)
[AMBER] HMR with protein-ligand system Alessio Atzori (Thu May 05 2016 - 00:36:26 PDT)
- Re: [AMBER] HMR with protein-ligand system Niel Henriksen (Thu May 05 2016 - 10:43:03 PDT)
[AMBER] pdb2pqr PDB processing for Amber force field James Starlight (Thu May 05 2016 - 03:39:49 PDT)
- Re: [AMBER] pdb2pqr PDB processing for Amber force field Abelak, Kavin (Thu May 05 2016 - 05:14:16 PDT)
  - Re: [AMBER] pdb2pqr PDB processing for Amber force field James Starlight (Thu May 05 2016 - 06:46:41 PDT)
[AMBER] Regarding RMSF calculation of protein using AMBER Sivanandam M (Thu May 05 2016 - 05:46:34 PDT)
- Re: [AMBER] Regarding RMSF calculation of protein using AMBER David A Case (Thu May 05 2016 - 06:54:53 PDT)
[AMBER] help: what cause Sandar crash Yang, Hui (Thu May 05 2016 - 06:23:23 PDT)
- Re: [AMBER] help: what cause Sandar crash David A Case (Thu May 05 2016 - 07:01:06 PDT)
[AMBER] Calculating LJ parameters in Amber format anu chandra (Thu May 05 2016 - 06:45:58 PDT)
- Re: [AMBER] Calculating LJ parameters in Amber format Jason Swails (Thu May 05 2016 - 07:08:38 PDT)
- Re: [AMBER] Calculating LJ parameters in Amber format David A Case (Thu May 05 2016 - 07:28:20 PDT)
  - Re: [AMBER] Calculating LJ parameters in Amber format anu chandra (Thu May 05 2016 - 08:15:52 PDT)
[AMBER] RESP charges Chi Jin (Thu May 05 2016 - 15:11:16 PDT)
[AMBER] live dCAT simulation Bill Ross (Thu May 05 2016 - 16:52:40 PDT)
- Re: [AMBER] live dCAT simulation Bill Ross (Tue May 10 2016 - 19:42:22 PDT)
  - Re: [AMBER] live dCAT simulation Charles Lin (Tue May 10 2016 - 19:59:28 PDT)
    - Re: [AMBER] live dCAT simulation Bill Ross (Tue May 10 2016 - 20:09:04 PDT)
    - Re: [AMBER] live dCAT simulation Charles Lin (Tue May 10 2016 - 20:55:54 PDT)
    - Re: [AMBER] live dCAT simulation Bill Ross (Tue May 10 2016 - 22:39:49 PDT)
    - Re: [AMBER] live dCAT simulation Bill Ross (Wed May 11 2016 - 03:05:32 PDT)
    - Re: [AMBER] live dCAT simulation Bill Ross (Wed May 11 2016 - 21:25:29 PDT)
    - Re: [AMBER] live dCAT simulation Bill Ross (Wed May 11 2016 - 21:39:27 PDT)
[AMBER] Paramfit'ing forces David Poole (Thu May 05 2016 - 17:53:53 PDT)
- Re: [AMBER] Paramfit'ing forces Robin Betz (Sat May 07 2016 - 10:45:43 PDT)
[AMBER] DNA Origami Ramkumar B (Fri May 06 2016 - 10:26:55 PDT)
[AMBER] Problems with cpinutil.py in CpHMD as adding a new titratable ligand Yong Wang (Fri May 06 2016 - 13:43:20 PDT)
- Re: [AMBER] Problems with cpinutil.py in CpHMD as adding a new titratable ligand Jason Swails (Fri May 06 2016 - 15:27:41 PDT)
[AMBER] Units in dist_vs_t file from SMD simulation Nisler, Collin R. (Fri May 06 2016 - 14:08:34 PDT)
- Re: [AMBER] Units in dist_vs_t file from SMD simulation Adrian Roitberg (Sat May 07 2016 - 16:33:03 PDT)
  - Re: [AMBER] Units in dist_vs_t file from SMD simulation Xing (Mon Aug 14 2017 - 21:08:24 PDT)
    - Re: [AMBER] Units in dist_vs_t file from SMD simulation Adrian Roitberg (Tue Aug 15 2017 - 08:22:52 PDT)
    - Re: [AMBER] Units in dist_vs_t file from SMD simulation Xing (Tue Aug 15 2017 - 17:10:51 PDT)
[AMBER] Hydroxyapatites force field Mijiddorj Batsaikhan (Sat May 07 2016 - 00:00:40 PDT)
[AMBER] Hydroxyapatites force field Mijiddorj Batsaikhan (Sat May 07 2016 - 00:03:57 PDT)
- Re: [AMBER] Hydroxyapatites force field Pengfei Li (Sat May 07 2016 - 19:45:53 PDT)
[AMBER] Fw: Fatemeh Arabi (Sat May 07 2016 - 00:16:15 PDT)
- [AMBER] Fw: Fatemeh Arabi (Sat May 07 2016 - 05:42:09 PDT)
- Re: [AMBER] Fw: David A Case (Sat May 07 2016 - 06:07:00 PDT)
[AMBER] How to modify the LENNARD_JONES_BCOEF in amber topology anu chandra (Sat May 07 2016 - 08:52:25 PDT)
- Re: [AMBER] How to modify the LENNARD_JONES_BCOEF in amber topology Pengfei Li (Sat May 07 2016 - 19:55:58 PDT)
  - Re: [AMBER] How to modify the LENNARD_JONES_BCOEF in amber topology anu chandra (Mon May 09 2016 - 03:51:57 PDT)
    - Re: [AMBER] How to modify the LENNARD_JONES_BCOEF in amber topology Pengfei Li (Mon May 09 2016 - 07:23:33 PDT)
    - Re: [AMBER] How to modify the LENNARD_JONES_BCOEF in amber topology Jason Swails (Mon May 09 2016 - 09:23:10 PDT)
Re: [AMBER] How to modify the LENNARD_JONES_BCOEF in amber topologyer JAIME RUBIO MARTINEZ (Sun May 08 2016 - 06:12:28 PDT)
[AMBER] Analysis of protein-protein interaction James Starlight (Mon May 09 2016 - 03:10:22 PDT)
- Re: [AMBER] Analysis of protein-protein interaction Daniel Roe (Tue May 10 2016 - 07:12:14 PDT)
[AMBER] on GAFF Brett (Mon May 09 2016 - 06:55:45 PDT)
- Re: [AMBER] on GAFF Carlos Simmerling (Mon May 09 2016 - 07:18:41 PDT)
[AMBER] Amber12 install error 유효정 (Mon May 09 2016 - 08:39:11 PDT)
- Re: [AMBER] Amber12 install error Hai Nguyen (Mon May 09 2016 - 09:41:39 PDT)
- Re: [AMBER] Amber12 install error Hai Nguyen (Mon May 09 2016 - 09:48:26 PDT)
[AMBER] Restrain a single atom in the residue during minimization, instead of all the atoms in a residue with RES option Vasantha Kumar (Mon May 09 2016 - 13:32:39 PDT)
- Re: [AMBER] Restrain a single atom in the residue during minimization, instead of all the atoms in a residue with RES option Carlos Simmerling (Mon May 09 2016 - 13:34:31 PDT)
  - Re: [AMBER] Restrain a single atom in the residue during minimization, instead of all the atoms in a residue with RES option Vasantha Kumar (Tue May 10 2016 - 01:32:54 PDT)
    - Re: [AMBER] Restrain a single atom in the residue during minimization, instead of all the atoms in a residue with RES option Vasantha Kumar (Tue May 10 2016 - 02:28:55 PDT)
    - Re: [AMBER] Restrain a single atom in the residue during minimization, instead of all the atoms in a residue with RES option Carlos Simmerling (Tue May 10 2016 - 02:47:02 PDT)
[AMBER] Phosphorylated-RNA yhzahsc (Mon May 09 2016 - 17:48:38 PDT)
- Re: [AMBER] Phosphorylated-RNA Thomas Cheatham (Mon May 09 2016 - 19:11:30 PDT)
[AMBER] acetone as solvent for simulation Shilpa Gupta (Mon May 09 2016 - 22:53:48 PDT)
[AMBER] VMD visualization of netcdf trajectories through the terminal James Starlight (Tue May 10 2016 - 02:24:57 PDT)
- Re: [AMBER] VMD visualization of netcdf trajectories through the terminal Karolina Markowska (Tue May 10 2016 - 02:36:29 PDT)
  - Re: [AMBER] VMD visualization of netcdf trajectories through the terminal James Starlight (Tue May 10 2016 - 04:28:03 PDT)
[AMBER] How adding cluster to a model Damiano Spadoni (Tue May 10 2016 - 04:57:14 PDT)
[AMBER] Constant pH simulation Tanmoy Paul (Tue May 10 2016 - 06:16:18 PDT)
- Re: [AMBER] Constant pH simulation Jason Swails (Tue May 10 2016 - 07:12:33 PDT)
[AMBER] Installing AmberTools16 on OSX 10.11 Adams, John E. (Tue May 10 2016 - 07:48:54 PDT)
- Re: [AMBER] Installing AmberTools16 on OSX 10.11 Jason Swails (Tue May 10 2016 - 08:57:31 PDT)
  - Re: [AMBER] Installing AmberTools16 on OSX 10.11 Hai Nguyen (Tue May 10 2016 - 09:48:31 PDT)
  - Re: [AMBER] Installing AmberTools16 on OSX 10.11 Adams, John E. (Tue May 10 2016 - 10:42:36 PDT)
[AMBER] Visualization of all-in-one mdcrd file in VMD Trang Nguyen (Tue May 10 2016 - 11:26:02 PDT)
- Re: [AMBER] Visualization of all-in-one mdcrd file in VMD Nhai (Tue May 10 2016 - 11:33:25 PDT)
  - Re: [AMBER] Visualization of all-in-one mdcrd file in VMD Trang Nguyen (Tue May 10 2016 - 11:53:08 PDT)
    - Re: [AMBER] Visualization of all-in-one mdcrd file in VMD Hai Nguyen (Tue May 10 2016 - 12:21:57 PDT)
    - Re: [AMBER] Visualization of all-in-one mdcrd file in VMD Hai Nguyen (Tue May 10 2016 - 12:24:11 PDT)
    - Re: [AMBER] Visualization of all-in-one mdcrd file in VMD Trang Nguyen (Tue May 10 2016 - 12:46:54 PDT)
[AMBER] MMPBSA doubt Mary Varughese (Tue May 10 2016 - 21:01:03 PDT)
- Re: [AMBER] MMPBSA doubt Jason Swails (Wed May 11 2016 - 03:25:37 PDT)
  - Re: [AMBER] MMPBSA doubt Mary Varughese (Wed May 11 2016 - 04:28:03 PDT)
    - [AMBER] MMPBSA doubt Kenneth Huang (Wed May 11 2016 - 04:43:38 PDT)
    - Re: [AMBER] MMPBSA doubt Jason Swails (Wed May 11 2016 - 05:25:34 PDT)
    - Re: [AMBER] MMPBSA doubt Mary Varughese (Wed May 11 2016 - 21:26:46 PDT)
    - Re: [AMBER] MMPBSA doubt Jason Swails (Thu May 12 2016 - 10:50:40 PDT)
    - Re: [AMBER] MMPBSA doubt Mary Varughese (Thu May 12 2016 - 21:07:54 PDT)
[AMBER] Regarding joining of two pdb file MOHD HOMAIDUR RAHMAN (Tue May 10 2016 - 22:53:14 PDT)
- Re: [AMBER] Regarding joining of two pdb file Bill Ross (Tue May 10 2016 - 23:14:34 PDT)
- Re: [AMBER] Regarding joining of two pdb file David A Case (Wed May 11 2016 - 05:08:13 PDT)
  - Re: [AMBER] Regarding joining of two pdb file MOHD HOMAIDUR RAHMAN (Wed May 11 2016 - 07:12:12 PDT)
[AMBER] amber error - reg Arthi Venkat (Wed May 11 2016 - 02:35:17 PDT)
- Re: [AMBER] amber error - reg Bill Ross (Wed May 11 2016 - 03:13:16 PDT)
- Re: [AMBER] amber error - reg Jason Swails (Wed May 11 2016 - 03:42:56 PDT)
  - Re: [AMBER] amber error - reg Arthi Venkat (Wed May 11 2016 - 04:50:58 PDT)
    - Re: [AMBER] amber error - reg Jason Swails (Wed May 11 2016 - 05:16:57 PDT)
- Re: [AMBER] amber error - reg David A Case (Wed May 11 2016 - 05:04:43 PDT)
[AMBER] Problem with closest command in cpptraj Indrajit Deb (Wed May 11 2016 - 07:16:14 PDT)
- Re: [AMBER] Problem with closest command in cpptraj Daniel Roe (Wed May 11 2016 - 08:03:40 PDT)
  - Re: [AMBER] Problem with closest command in cpptraj Indrajit Deb (Wed May 11 2016 - 08:38:54 PDT)
    - Re: [AMBER] Problem with closest command in cpptraj Daniel Roe (Wed May 11 2016 - 09:49:30 PDT)
    - Re: [AMBER] Problem with closest command in cpptraj Indrajit Deb (Wed May 11 2016 - 10:17:33 PDT)
[AMBER] Problem in Restarting production run ATUL KUMAR (Thu May 12 2016 - 00:19:04 PDT)
- Re: [AMBER] Problem in Restarting production run Bill Ross (Thu May 12 2016 - 00:23:08 PDT)
- Re: [AMBER] Problem in Restarting production run ATUL KUMAR (Thu May 12 2016 - 00:46:52 PDT)
  - Re: [AMBER] Problem in Restarting production run Bill Ross (Thu May 12 2016 - 01:00:13 PDT)
- Re: [AMBER] Problem in Restarting production run David A Case (Thu May 12 2016 - 03:57:29 PDT)
[AMBER] Error during frames generation from production run Sneha Rai (Thu May 12 2016 - 01:18:34 PDT)
- Re: [AMBER] Error during frames generation from production run Bill Ross (Thu May 12 2016 - 01:21:27 PDT)
  - Re: [AMBER] Error during frames generation from production run Bill Ross (Thu May 12 2016 - 01:33:27 PDT)
    - Re: [AMBER] Error during frames generation from production run Bill Ross (Thu May 12 2016 - 01:37:56 PDT)
    - Re: [AMBER] Error during frames generation from production run Sneha Rai (Thu May 12 2016 - 02:07:25 PDT)
- Re: [AMBER] Error during frames generation from production run Daniel Roe (Thu May 12 2016 - 08:50:23 PDT)
- Re: [AMBER] Error during frames generation from production run Jason Swails (Thu May 12 2016 - 13:10:38 PDT)
[AMBER] error in cluster analysis by cpptraj Michael Shokhen (Thu May 12 2016 - 03:06:39 PDT)
- Re: [AMBER] error in cluster analysis by cpptraj Dr. Anselm Horn (Thu May 12 2016 - 03:28:29 PDT)
  - Re: [AMBER] error in cluster analysis by cpptraj Michael Shokhen (Thu May 12 2016 - 04:12:48 PDT)
    - Re: [AMBER] error in cluster analysis by cpptraj Dr. Anselm Horn (Thu May 12 2016 - 05:05:43 PDT)
- Re: [AMBER] error in cluster analysis by cpptraj Daniel Roe (Thu May 12 2016 - 07:21:48 PDT)
[AMBER] About harmonic restraints on dihedral angle in pmemd.cuda mish (Thu May 12 2016 - 06:58:21 PDT)
- Re: [AMBER] About harmonic restraints on dihedral angle in pmemd.cuda David Cerutti (Thu May 12 2016 - 07:05:24 PDT)
  - Re: [AMBER] About harmonic restraints on dihedral angle in pmemd.cuda mish (Thu May 12 2016 - 16:16:27 PDT)
    - Re: [AMBER] About harmonic restraints on dihedral angle in pmemd.cuda Hector A. Baldoni (Thu May 12 2016 - 16:55:26 PDT)
[AMBER] How to deal with Heme? Morteza Chehel Amirani (Thu May 12 2016 - 10:53:44 PDT)
- Re: [AMBER] How to deal with Heme? David A Case (Fri May 13 2016 - 05:21:04 PDT)
  - [AMBER] Nickel parameters in Amber Rebeca García Fandiño (Fri May 13 2016 - 08:14:44 PDT)
    - Re: [AMBER] Nickel parameters in Amber Marcelo Andrade Chagas (Fri May 13 2016 - 08:40:22 PDT)
    - Re: [AMBER] Nickel parameters in Amber Pengfei Li (Fri May 13 2016 - 13:56:00 PDT)
- Re: [AMBER] How to deal with Heme? Morteza Chehel Amirani (Fri May 13 2016 - 15:44:20 PDT)
  - Re: [AMBER] How to deal with Heme? David A Case (Sat May 14 2016 - 06:16:45 PDT)
    - Re: [AMBER] How to deal with Heme? Abelak, Kavin (Wed May 18 2016 - 05:16:32 PDT)
    - Re: [AMBER] How to deal with Heme? Anna Cebrian Prats (Wed May 18 2016 - 07:32:59 PDT)
    - Re: [AMBER] How to deal with Heme? David A Case (Wed May 18 2016 - 09:06:11 PDT)
    - Re: [AMBER] How to deal with Heme? Anna Cebrian Prats (Wed May 18 2016 - 09:15:14 PDT)
[AMBER] slinky on a hot tin roof Bill Ross (Fri May 13 2016 - 01:25:12 PDT)
[AMBER] Parametrisation of ligand with ions julian.zachmann selvita.home.pl (Fri May 13 2016 - 02:30:27 PDT)
[AMBER] Scripts to gradually remove NMR restraints during MD simulation Vasantha Kumar (Fri May 13 2016 - 02:46:10 PDT)
- Re: [AMBER] Scripts to gradually remove NMR restraints during MD simulation ankita mehta (Fri May 13 2016 - 03:02:48 PDT)
[AMBER] Unable to run Antechamber Shreeramesh (Fri May 13 2016 - 05:12:48 PDT)
- Re: [AMBER] Unable to run Antechamber David A Case (Fri May 13 2016 - 07:55:36 PDT)
[AMBER] Amber compilation fail after plumed patch Fabrício Bracht (Fri May 13 2016 - 13:29:41 PDT)
- Re: [AMBER] Amber compilation fail after plumed patch Fabrício Bracht (Fri May 13 2016 - 13:36:34 PDT)
  - Re: [AMBER] Amber compilation fail after plumed patch Charles Lin (Fri May 13 2016 - 13:39:42 PDT)
[AMBER] Combining .mdvel and .nc(NetCDF) into one file ATUL KUMAR (Sat May 14 2016 - 00:12:55 PDT)
- Re: [AMBER] Combining .mdvel and .nc(NetCDF) into one file Daniel Roe (Sat May 14 2016 - 05:13:16 PDT)
  - Re: [AMBER] Combining .mdvel and .nc(NetCDF) into one file ATUL KUMAR (Sat May 14 2016 - 06:26:59 PDT)
[AMBER] parmed units and version numbers hannes.loeffler.stfc.ac.uk (Sat May 14 2016 - 06:49:24 PDT)
- Re: [AMBER] parmed units and version numbers Hai Nguyen (Sat May 14 2016 - 09:01:56 PDT)
- Re: [AMBER] parmed units and version numbers Jason Swails (Sat May 14 2016 - 19:50:15 PDT)
[AMBER] Fix dimension of the box throughout the MD simulations Iqbal, Muhammad Sajid (Sat May 14 2016 - 12:49:43 PDT)
- Re: [AMBER] Fix dimension of the box throughout the MD simulations Carlos Simmerling (Sat May 14 2016 - 12:56:24 PDT)
- Re: [AMBER] Fix dimension of the box throughout the MD simulations David A Case (Sat May 14 2016 - 14:52:57 PDT)
  - Re: [AMBER] Fix dimension of the box throughout the MD simulations Carlos Simmerling (Sat May 14 2016 - 14:59:18 PDT)
- Re: [AMBER] Fix dimension of the box throughout the MD simulations Iqbal, Muhammad Sajid (Mon May 16 2016 - 08:56:15 PDT)
  - Re: [AMBER] Fix dimension of the box throughout the MD simulations David A Case (Mon May 16 2016 - 11:50:49 PDT)
[AMBER] problem in calculating velocity autocorrelation ATUL KUMAR (Sun May 15 2016 - 06:34:09 PDT)
- Re: [AMBER] problem in calculating velocity autocorrelation Hai Nguyen (Sun May 15 2016 - 09:22:15 PDT)
[AMBER] MMPBSA for homo-dimer system with ligands Kat G (Sun May 15 2016 - 22:03:35 PDT)
[AMBER] problem installing AmberTools16 pytraj on Mac Marc van der Kamp (Mon May 16 2016 - 08:23:11 PDT)
- Re: [AMBER] problem installing AmberTools16 pytraj on Mac Hannes Loeffler (Mon May 16 2016 - 08:37:14 PDT)
  - Re: [AMBER] problem installing AmberTools16 pytraj on Mac Marc van der Kamp (Mon May 16 2016 - 08:39:32 PDT)
[AMBER] No leaprc.ff14SB anymore in AmberTools16 - reason? Marc van der Kamp (Mon May 16 2016 - 08:27:38 PDT)
- Re: [AMBER] No leaprc.ff14SB anymore in AmberTools16 - reason? Nhai (Mon May 16 2016 - 08:30:49 PDT)
- Re: [AMBER] No leaprc.ff14SB anymore in AmberTools16 - reason? Hannes Loeffler (Mon May 16 2016 - 08:33:04 PDT)
  - Re: [AMBER] No leaprc.ff14SB anymore in AmberTools16 - reason? Marc van der Kamp (Mon May 16 2016 - 08:37:11 PDT)
    - Re: [AMBER] No leaprc.ff14SB anymore in AmberTools16 - reason? Hannes Loeffler (Mon May 16 2016 - 08:42:55 PDT)
[AMBER] Working with pytraj MOHD HOMAIDUR RAHMAN (Mon May 16 2016 - 12:05:00 PDT)
- Re: [AMBER] Working with pytraj Hai Nguyen (Mon May 16 2016 - 12:28:05 PDT)
Re: [AMBER] AMBER Digest, Vol 1578, Issue 1 Iqbal, Muhammad Sajid (Mon May 16 2016 - 22:21:12 PDT)
[AMBER] MD Output File Wong Li Zhe (Tue May 17 2016 - 00:56:59 PDT)
[AMBER] problem with new residu in Xleap Muriel Jourdan (Tue May 17 2016 - 07:15:10 PDT)
- Re: [AMBER] problem with new residu in Xleap Muriel Jourdan (Tue May 17 2016 - 08:06:07 PDT)
[AMBER] tleap: opls-ua parm for an arbitrary molecule Ekaterina Ratkova (Tue May 17 2016 - 07:02:33 PDT)
- Re: [AMBER] tleap: opls-ua parm for an arbitrary molecule David A Case (Tue May 17 2016 - 08:47:57 PDT)
  - Re: [AMBER] tleap: opls-ua parm for an arbitrary molecule Nhai (Tue May 17 2016 - 09:05:32 PDT)
[AMBER] issues with NONBOND LIST? Thomas Pochapsky (Tue May 17 2016 - 11:45:32 PDT)
- Re: [AMBER] issues with NONBOND LIST? Carlos Simmerling (Tue May 17 2016 - 12:01:31 PDT)
  - Re: [AMBER] issues with NONBOND LIST? Thomas Pochapsky (Tue May 17 2016 - 12:27:40 PDT)
    - Re: [AMBER] issues with NONBOND LIST? Carlos Simmerling (Tue May 17 2016 - 12:37:51 PDT)
    - Re: [AMBER] issues with NONBOND LIST? Thomas Pochapsky (Tue May 17 2016 - 13:05:20 PDT)
    - Re: [AMBER] issues with NONBOND LIST? David A Case (Wed May 18 2016 - 04:51:02 PDT)
[AMBER] Problems with pairwise command in cpptraj Osman, Roman (Tue May 17 2016 - 13:24:41 PDT)
[AMBER] .nc trajectory format Neha Gandhi (Tue May 17 2016 - 21:35:01 PDT)
- Re: [AMBER] .nc trajectory format David A Case (Wed May 18 2016 - 04:44:19 PDT)
  - Re: [AMBER] .nc trajectory format Neha Gandhi (Wed May 18 2016 - 18:19:30 PDT)
[AMBER] Bug: Gasteiger parameters for S(-1) Mahmoud A. A. Ibrahim (Wed May 18 2016 - 00:42:02 PDT)
[AMBER] Licence Jacopo Sgrignani (Wed May 18 2016 - 08:46:36 PDT)
[AMBER] mmpbsa Ziba Bahadori (Wed May 18 2016 - 10:37:26 PDT)
- Re: [AMBER] mmpbsa Jason Swails (Wed May 18 2016 - 10:53:54 PDT)
[AMBER] Problems with pairwise command in cpptraj Osman, Roman (Wed May 18 2016 - 10:47:13 PDT)
- Re: [AMBER] Problems with pairwise command in cpptraj Daniel Roe (Wed May 18 2016 - 11:01:36 PDT)
  - Re: [AMBER] Problems with pairwise command in cpptraj Osman, Roman (Wed May 18 2016 - 11:14:38 PDT)
    - Re: [AMBER] Problems with pairwise command in cpptraj Daniel Roe (Wed May 18 2016 - 11:43:49 PDT)
    - Re: [AMBER] Problems with pairwise command in cpptraj Osman, Roman (Thu May 19 2016 - 07:17:36 PDT)
[AMBER] GAFF2 setup Hannes Loeffler (Thu May 19 2016 - 02:03:25 PDT)
- Re: [AMBER] GAFF2 setup David A Case (Thu May 19 2016 - 05:06:23 PDT)
  - Re: [AMBER] GAFF2 setup Igor Marques (Fri Jun 03 2016 - 12:40:19 PDT)
    - Re: [AMBER] GAFF2 setup David A Case (Tue Jun 21 2016 - 05:49:11 PDT)
[AMBER] MMPBSA Results asdda asa (Thu May 19 2016 - 02:19:45 PDT)
- Re: [AMBER] MMPBSA Results Jason Swails (Thu May 19 2016 - 05:22:13 PDT)
  - Re: [AMBER] MMPBSA Results asdda asa (Thu May 19 2016 - 15:02:33 PDT)
[AMBER] rms to pdb for a subset of atoms [cpptraj] Eiros Zamora, Juan (Thu May 19 2016 - 06:55:25 PDT)
- Re: [AMBER] rms to pdb for a subset of atoms [cpptraj] Daniel Roe (Thu May 19 2016 - 07:37:31 PDT)
  - Re: [AMBER] rms to pdb for a subset of atoms [cpptraj] Bill Ross (Thu May 19 2016 - 12:13:18 PDT)
[AMBER] Clustering of MD trajectories: ptraj, cpptraj Francesco Gentile (Thu May 19 2016 - 11:41:16 PDT)
- Re: [AMBER] Clustering of MD trajectories: ptraj, cpptraj Daniel Roe (Fri May 27 2016 - 13:31:17 PDT)
  - Re: [AMBER] Clustering of MD trajectories: ptraj, cpptraj Daniel Roe (Mon Jun 06 2016 - 12:57:41 PDT)
[AMBER] clustering with ptraj Francesco Gentile (Thu May 19 2016 - 17:08:37 PDT)
- Re: [AMBER] clustering with ptraj Nhai (Thu May 19 2016 - 17:20:13 PDT)
[AMBER] Protein moving out of the water box Arati Paudyal (Thu May 19 2016 - 19:11:17 PDT)
- Re: [AMBER] Protein moving out of the water box Nhai (Thu May 19 2016 - 19:26:38 PDT)
  - Re: [AMBER] Protein moving out of the water box Arati Paudyal (Fri May 20 2016 - 12:58:31 PDT)
    - Re: [AMBER] Protein moving out of the water box Hai Nguyen (Fri May 20 2016 - 13:37:18 PDT)
    - Re: [AMBER] Protein moving out of the water box Arati Paudyal (Fri May 20 2016 - 17:21:33 PDT)
    - Re: [AMBER] Protein moving out of the water box David A Case (Sat May 21 2016 - 05:21:18 PDT)
    - Re: [AMBER] Protein moving out of the water box Arati Paudyal (Sat May 21 2016 - 06:32:51 PDT)
    - Re: [AMBER] Protein moving out of the water box David A Case (Sat May 21 2016 - 09:58:05 PDT)
[AMBER] obtain or build parameters for non-natural residues ALINE THOMAS (Fri May 20 2016 - 00:45:10 PDT)
- Re: [AMBER] obtain or build parameters for non-natural residues Karl Kirschner (Mon May 23 2016 - 00:31:24 PDT)
  - Re: [AMBER] obtain or build parameters for non-natural residues David Cerutti (Mon May 23 2016 - 07:12:23 PDT)
- Re: [AMBER] obtain or build parameters for non-natural residues FyD (Wed May 25 2016 - 00:09:19 PDT)
[AMBER] choice of lipid type in MD simulation Zhang Marc (Fri May 20 2016 - 00:51:40 PDT)
[AMBER] QM/MM energy minimization Stanislav Simko (Fri May 20 2016 - 03:34:28 PDT)
[AMBER] Best Linux Choice Robert Molt (Fri May 20 2016 - 06:03:27 PDT)
- Re: [AMBER] Best Linux Choice Marcos Serrou do Amaral (Fri May 20 2016 - 06:54:47 PDT)
- Re: [AMBER] Best Linux Choice Kenneth Huang (Fri May 20 2016 - 07:02:36 PDT)
- Re: [AMBER] Best Linux Choice Ross Walker (Fri May 20 2016 - 07:51:17 PDT)
  - Re: [AMBER] Best Linux Choice Vlad Cojocaru (Fri May 20 2016 - 08:38:35 PDT)
- Re: [AMBER] Best Linux Choice Jason Swails (Fri May 20 2016 - 11:04:59 PDT)
  - Re: [AMBER] Best Linux Choice Wesley Michael Botello-Smith (Fri May 20 2016 - 15:42:49 PDT)
- Re: [AMBER] Best Linux Choice Ho Leung Ng (Fri May 20 2016 - 16:13:36 PDT)
  - Re: [AMBER] Best Linux Choice Karl Kirschner (Fri May 20 2016 - 23:55:40 PDT)
    - Re: [AMBER] Best Linux Choice Mark Abraham (Sat May 21 2016 - 10:48:44 PDT)
    - Re: [AMBER] Best Linux Choice Robert Molt (Sat May 21 2016 - 13:28:04 PDT)
    - [AMBER] cpptraj + nastruct Thomas C. Bishop (Wed May 25 2016 - 16:31:23 PDT)
    - Re: [AMBER] cpptraj + nastruct Vlad Cojocaru (Thu May 26 2016 - 00:33:52 PDT)
    - Re: [AMBER] cpptraj + nastruct Thomas C. Bishop (Thu May 26 2016 - 05:49:38 PDT)
    - Re: [AMBER] cpptraj + nastruct Vlad Cojocaru (Thu May 26 2016 - 07:09:51 PDT)
    - Re: [AMBER] cpptraj + nastruct Daniel Roe (Thu May 26 2016 - 07:21:08 PDT)
    - Re: [AMBER] cpptraj + nastruct Thomas C. Bishop (Thu May 26 2016 - 12:27:42 PDT)
    - Re: [AMBER] cpptraj + nastruct Daniel Roe (Fri May 27 2016 - 08:03:17 PDT)
    - Re: [AMBER] cpptraj + nastruct Daniel Roe (Thu May 26 2016 - 06:16:03 PDT)
    - Re: [AMBER] cpptraj + nastruct Hai Nguyen (Thu May 26 2016 - 06:48:14 PDT)
[AMBER] Amber coordinates to chemshell coords file (coords.c) Jenner Bonanata (Fri May 20 2016 - 06:10:25 PDT)
- Re: [AMBER] Amber coordinates to chemshell coords file (coords.c) Jason Swails (Tue May 24 2016 - 08:23:04 PDT)
[AMBER] Opening mol2 file in xleap Nikolay N. Kuzmich (Fri May 20 2016 - 06:36:19 PDT)
- Re: [AMBER] Opening mol2 file in xleap Yves Boulard (Fri May 20 2016 - 06:51:23 PDT)
- Re: [AMBER] Opening mol2 file in xleap FyD (Wed May 25 2016 - 00:04:29 PDT)
[AMBER] MMPBSA.py issue with complex prmtop file Kalenkiewicz, Andrew (NIH/NICHD) [F] (Fri May 20 2016 - 15:23:16 PDT)
- Re: [AMBER] MMPBSA.py issue with complex prmtop file Jason Swails (Mon May 23 2016 - 05:53:50 PDT)
  - Re: [AMBER] MMPBSA.py issue with complex prmtop file Kalenkiewicz, Andrew (NIH/NICHD) [F] (Mon May 23 2016 - 14:33:59 PDT)
    - [AMBER] FW: MMPBSA.py issue with complex prmtop file Kalenkiewicz, Andrew (NIH/NICHD) [F] (Wed Jun 01 2016 - 11:34:44 PDT)
    - Re: [AMBER] FW: MMPBSA.py issue with complex prmtop file Hai Nguyen (Wed Jun 01 2016 - 11:40:57 PDT)
    - Re: [AMBER] FW: MMPBSA.py issue with complex prmtop file Hai Nguyen (Wed Jun 01 2016 - 11:43:37 PDT)
[AMBER] MMPBSA final results of MMPBSA.py different from tutorial LI An-Bang (Fri May 20 2016 - 19:38:17 PDT)
- Re: [AMBER] MMPBSA final results of MMPBSA.py different from tutorial David A Case (Sat May 21 2016 - 05:25:53 PDT)
[AMBER] QM/MM Interface Nisler, Collin R. (Fri May 20 2016 - 22:37:11 PDT)
- Re: [AMBER] QM/MM Interface Stanislav Simko (Sat May 21 2016 - 00:37:58 PDT)
  - Re: [AMBER] QM/MM Interface Nisler, Collin R. (Sat May 21 2016 - 16:00:52 PDT)
    - Re: [AMBER] QM/MM Interface Stanislav Simko (Sat May 21 2016 - 16:44:40 PDT)
    - Re: [AMBER] QM/MM Interface Nisler, Collin R. (Sat May 21 2016 - 17:19:13 PDT)
    - Re: [AMBER] QM/MM Interface Stanislav Simko (Sun May 22 2016 - 02:31:58 PDT)
    - Re: [AMBER] QM/MM Interface Nisler, Collin R. (Sun May 22 2016 - 16:46:39 PDT)
    - Re: [AMBER] QM/MM Interface Nisler, Collin R. (Sun May 22 2016 - 23:27:13 PDT)
  - Re: [AMBER] QM/MM Interface Dr. Andreas W. Goetz (Mon May 23 2016 - 19:44:41 PDT)
[AMBER] Problems with GTX titan-X GPU Elvis Martis (Sat May 21 2016 - 03:19:54 PDT)
- Re: [AMBER] Problems with GTX titan-X GPU Ross Walker (Mon May 23 2016 - 08:35:23 PDT)
- Re: [AMBER] Problems with GTX titan-X GPU Elvis Martis (Mon May 23 2016 - 17:27:08 PDT)
- Re: [AMBER] Problems with GTX titan-X GPU Elvis Martis (Tue May 24 2016 - 05:20:13 PDT)
  - Re: [AMBER] Problems with GTX titan-X GPU Ross Walker (Tue May 24 2016 - 07:40:30 PDT)
Re: [AMBER] MMPBSA final results of MMPBSA.py different fromtutorial LI An-Bang (Sat May 21 2016 - 06:29:04 PDT)
- Re: [AMBER] MMPBSA final results of MMPBSA.py different fromtutorial David A Case (Sat May 21 2016 - 10:01:08 PDT)
  - Re: [AMBER] MMPBSA final results of MMPBSA.py different fromtutorial Ray Luo (Sun May 22 2016 - 08:47:15 PDT)
[AMBER] MMPBSA- topology files preparation Kat G (Sat May 21 2016 - 19:44:56 PDT)
- Re: [AMBER] MMPBSA- topology files preparation Jason Swails (Mon May 23 2016 - 05:57:44 PDT)
[AMBER] optimised corrections to ff03 Neha Gandhi (Sun May 22 2016 - 18:09:04 PDT)
- Re: [AMBER] optimised corrections to ff03 David Cerutti (Sun May 22 2016 - 19:21:07 PDT)
[AMBER] nativecontacts Neha Gandhi (Mon May 23 2016 - 00:25:36 PDT)
- Re: [AMBER] nativecontacts Abelak, Kavin (Mon May 23 2016 - 02:40:02 PDT)
[AMBER] CUDA MPI issues Biplab Ghosh (Mon May 23 2016 - 03:45:08 PDT)
- Re: [AMBER] CUDA MPI issues Bill Ross (Mon May 23 2016 - 04:01:05 PDT)
- Re: [AMBER] CUDA MPI issues Jason Swails (Mon May 23 2016 - 06:22:20 PDT)
- Re: [AMBER] CUDA MPI issues Ross Walker (Mon May 23 2016 - 08:47:36 PDT)
- Re: [AMBER] CUDA MPI issues Biplab Ghosh (Wed May 25 2016 - 23:00:53 PDT)
  - Re: [AMBER] CUDA MPI issues Ross Walker (Thu May 26 2016 - 09:20:10 PDT)
    - Re: [AMBER] CUDA MPI issues Biplab Ghosh (Thu May 26 2016 - 10:40:56 PDT)
    - Re: [AMBER] CUDA MPI issues Ross Walker (Thu May 26 2016 - 10:57:14 PDT)
    - Re: [AMBER] CUDA MPI issues Biplab Ghosh (Thu May 26 2016 - 11:12:18 PDT)
    - Re: [AMBER] CUDA MPI issues David A Case (Fri May 27 2016 - 04:44:24 PDT)
- Re: [AMBER] CUDA MPI issues Biplab Ghosh (Fri May 27 2016 - 00:12:49 PDT)
  - Re: [AMBER] CUDA MPI issues Brent Krueger (Fri May 27 2016 - 04:36:55 PDT)
[AMBER] RE_POSITION Wong Li Zhe (Mon May 23 2016 - 18:07:15 PDT)
- Re: [AMBER] RE_POSITION Nisler, Collin R. (Mon May 23 2016 - 18:15:24 PDT)
[AMBER] Amino Acid Residues in QM/MM Simulation Nisler, Collin R. (Mon May 23 2016 - 19:25:23 PDT)
- Re: [AMBER] Amino Acid Residues in QM/MM Simulation Gustavo Seabra (Tue May 24 2016 - 12:00:44 PDT)
[AMBER] Organic solvent box - Amber do not see the molecule but its atoms Stregone (Tue May 24 2016 - 04:27:40 PDT)
- Re: [AMBER] Organic solvent box - Amber do not see the molecule but its atoms David A Case (Tue May 24 2016 - 06:03:37 PDT)
[AMBER] MMPBSA Lara rajam (Tue May 24 2016 - 06:15:41 PDT)
- Re: [AMBER] MMPBSA Jason Swails (Tue May 24 2016 - 08:57:04 PDT)
[AMBER] autoimage and TI Khabiri, Morteza (Tue May 24 2016 - 07:44:34 PDT)
- Re: [AMBER] autoimage and TI Daniel Roe (Tue May 24 2016 - 08:06:02 PDT)
[AMBER] Regarding parameter file not saved Vishal Nemaysh (Tue May 24 2016 - 09:21:10 PDT)
- Re: [AMBER] Regarding parameter file not saved Hai Nguyen (Tue May 24 2016 - 09:38:36 PDT)
  - Re: [AMBER] Regarding parameter file not saved Vishal Nemaysh (Tue May 24 2016 - 10:02:07 PDT)
    - Re: [AMBER] Regarding parameter file not saved Daniel Roe (Tue May 24 2016 - 10:10:31 PDT)
[AMBER] How to do QHA with outputs after considering every n-frames of trajectory? SHAILESH KUMAR (Tue May 24 2016 - 11:16:56 PDT)
- Re: [AMBER] How to do QHA with outputs after considering every n-frames of trajectory? Daniel Roe (Tue May 24 2016 - 12:18:21 PDT)
[AMBER] mmpbsa Ziba Bahadori (Tue May 24 2016 - 11:14:24 PDT)
[AMBER] Release of FESetup 1.2 Hannes Loeffler (Tue May 24 2016 - 12:55:19 PDT)
[AMBER] MM-PBSA result asdda asa (Tue May 24 2016 - 15:20:43 PDT)
- Re: [AMBER] MM-PBSA result David A Case (Wed May 25 2016 - 04:34:10 PDT)
  - Re: [AMBER] MM-PBSA result asdda asa (Wed May 25 2016 - 04:36:28 PDT)
[AMBER] Solvation free energy in rism1d Jingyi Yan (Tue May 24 2016 - 15:51:39 PDT)
- Re: [AMBER] Solvation free energy in rism1d David A Case (Wed May 25 2016 - 04:38:48 PDT)
[AMBER] query ankita mehta (Tue May 24 2016 - 22:57:07 PDT)
- Re: [AMBER] query Daniel Roe (Wed May 25 2016 - 13:55:36 PDT)
  - Re: [AMBER] query ankita mehta (Wed May 25 2016 - 23:30:28 PDT)
    - Re: [AMBER] query Vasantha Kumar (Thu May 26 2016 - 02:24:33 PDT)
    - Re: [AMBER] query David A Case (Thu May 26 2016 - 04:46:29 PDT)
    - Re: [AMBER] query Vasantha Kumar (Thu May 26 2016 - 05:27:30 PDT)
[AMBER] Can I build parameters of hydroxyapatites? Mijiddorj Batsaikhan (Wed May 25 2016 - 02:34:39 PDT)
- Re: [AMBER] Can I build parameters of hydroxyapatites? FyD (Wed May 25 2016 - 10:45:22 PDT)
[AMBER] Regarding Force Field Inquiry Vishal Nemaysh (Wed May 25 2016 - 04:22:48 PDT)
- Re: [AMBER] Regarding Force Field Inquiry Carlos Simmerling (Wed May 25 2016 - 04:34:20 PDT)
- Re: [AMBER] Regarding Force Field Inquiry David A Case (Wed May 25 2016 - 04:41:40 PDT)
- Re: [AMBER] Regarding Force Field Inquiry Dr. Anselm Horn (Wed May 25 2016 - 04:51:05 PDT)
  - Re: [AMBER] Regarding Force Field Inquiry Vishal Nemaysh (Wed May 25 2016 - 05:41:01 PDT)
    - Re: [AMBER] Regarding Force Field Inquiry Kevin Hauser (Wed May 25 2016 - 06:31:30 PDT)
[AMBER] Modified ARG LYS parameters Vlad Cojocaru (Wed May 25 2016 - 04:51:35 PDT)
[AMBER] adaptive qm/mm NVT not reaching target temperature Stanislav Simko (Wed May 25 2016 - 05:58:39 PDT)
- Re: [AMBER] adaptive qm/mm NVT not reaching target temperature Dr. Andreas W. Goetz (Wed May 25 2016 - 16:45:50 PDT)
[AMBER] standard parameter for sialic acid Bisignano, Paola (Wed May 25 2016 - 16:43:53 PDT)
- Re: [AMBER] standard parameter for sialic acid David A Case (Wed May 25 2016 - 17:02:39 PDT)
  - Re: [AMBER] standard parameter for sialic acid Lachele Foley (Wed May 25 2016 - 22:08:28 PDT)
    - Re: [AMBER] standard parameter for sialic acid Bisignano, Paola (Thu May 26 2016 - 12:02:22 PDT)
[AMBER] acetone as solvent for simulation Shilpa Gupta (Wed May 25 2016 - 22:39:22 PDT)
- Re: [AMBER] acetone as solvent for simulation FyD (Wed May 25 2016 - 23:11:38 PDT)
[AMBER] cpptraj - rmsd/rmsf & reference structure colvin (Thu May 26 2016 - 02:19:16 PDT)
- Re: [AMBER] cpptraj - rmsd/rmsf & reference structure Daniel Roe (Thu May 26 2016 - 06:22:55 PDT)
  - Re: [AMBER] cpptraj - rmsd/rmsf & reference structure colvin chin (Thu May 26 2016 - 06:56:03 PDT)
    - Re: [AMBER] cpptraj - rmsd/rmsf & reference structure Daniel Roe (Thu May 26 2016 - 07:42:04 PDT)
    - Re: [AMBER] cpptraj - rmsd/rmsf & reference structure colvin chin (Thu May 26 2016 - 07:58:34 PDT)
    - Re: [AMBER] cpptraj - rmsd/rmsf & reference structure Daniel Roe (Thu May 26 2016 - 08:07:29 PDT)
[AMBER] Amber16: COM's in GPU version Åsmund Røhr Kjendseth (Thu May 26 2016 - 05:50:52 PDT)
- Re: [AMBER] Amber16: COM's in GPU version Ross Walker (Thu May 26 2016 - 09:06:42 PDT)
  - Re: [AMBER] Amber16: COM's in GPU version Ilyas Yildirim (Thu May 26 2016 - 10:01:27 PDT)
    - Re: [AMBER] Amber16: COM's in GPU version Ross Walker (Thu May 26 2016 - 10:12:55 PDT)
    - Re: [AMBER] Amber16: COM's in GPU version Jason Swails (Thu May 26 2016 - 11:07:16 PDT)
    - Re: [AMBER] Amber16: COM's in GPU version Ilyas Yildirim (Fri May 27 2016 - 06:26:47 PDT)
- Re: [AMBER] Amber16: COM's in GPU version Feng Pan (Fri May 27 2016 - 13:29:51 PDT)
  - Re: [AMBER] Amber16: COM's in GPU version Carlos Simmerling (Tue Sep 20 2016 - 07:53:13 PDT)
    - Re: [AMBER] Amber16: COM's in GPU version Ross Walker (Tue Sep 20 2016 - 08:05:43 PDT)
[AMBER] ante-mmpbsa.py: general question George Tzotzos (Thu May 26 2016 - 11:33:44 PDT)
- Re: [AMBER] ante-mmpbsa.py: general question Jason Swails (Fri May 27 2016 - 05:57:54 PDT)
[AMBER] Replacing water with a H2O2 and restart the simulation Morteza Chehel Amirani (Thu May 26 2016 - 15:21:16 PDT)
- Re: [AMBER] Replacing water with a H2O2 and restart the simulation David A Case (Fri May 27 2016 - 04:51:17 PDT)
- Re: [AMBER] Replacing water with a H2O2 and restart the simulation Morteza Chehel Amirani (Thu Jun 02 2016 - 13:37:09 PDT)
  - Re: [AMBER] Replacing water with a H2O2 and restart the simulation Bill Ross (Thu Jun 02 2016 - 15:02:45 PDT)
[AMBER] calculating binding free energy Carlos Romero (Thu May 26 2016 - 17:18:56 PDT)
[AMBER] Simulation of DNA structure with a three-phosphate at 5' M. Reza Ganjalikhany (Fri May 27 2016 - 01:11:30 PDT)
- Re: [AMBER] Simulation of DNA structure with a three-phosphate at 5' Vlad Cojocaru (Fri May 27 2016 - 01:25:30 PDT)
  - Re: [AMBER] Simulation of DNA structure with a three-phosphate at 5' M. Reza Ganjalikhany (Fri May 27 2016 - 02:32:06 PDT)
    - Re: [AMBER] Simulation of DNA structure with a three-phosphate at 5' M. Reza Ganjalikhany (Sun May 29 2016 - 05:23:50 PDT)
    - Re: [AMBER] Simulation of DNA structure with a three-phosphate at 5' Vlad Cojocaru (Sun May 29 2016 - 05:44:52 PDT)
    - Re: [AMBER] Simulation of DNA structure with a three-phosphate at 5' FyD (Sun May 29 2016 - 23:55:38 PDT)
[AMBER] Constant area simulation Batuhan Kav (Fri May 27 2016 - 02:07:39 PDT)
[AMBER] nativecontacts resout command change with AmberTools16 [cpptraj] Eiros Zamora, Juan (Fri May 27 2016 - 02:25:23 PDT)
- Re: [AMBER] nativecontacts resout command change with AmberTools16 [cpptraj] Daniel Roe (Fri May 27 2016 - 07:54:06 PDT)
  - Re: [AMBER] nativecontacts resout command change with AmberTools16 [cpptraj] Daniel Roe (Fri May 27 2016 - 13:22:22 PDT)
- Re: [AMBER] nativecontacts resout command change with AmberTools16 [cpptraj] Daniel Roe (Tue May 31 2016 - 07:53:33 PDT)
[AMBER] About AMBER Advanced Tutorial 17 on GPUs mish (Fri May 27 2016 - 07:44:08 PDT)
- Re: [AMBER] About AMBER Advanced Tutorial 17 on GPUs Ross Walker (Fri May 27 2016 - 10:50:43 PDT)
[AMBER] Adaptively Biased MD: Problems with executing groupfile Jason Imamoto (Fri May 27 2016 - 10:20:07 PDT)
- Re: [AMBER] Adaptively Biased MD: Problems with executing groupfile Feng Pan (Fri May 27 2016 - 13:09:26 PDT)
[AMBER] mdl file for 1d-rism Jingyi Yan (Fri May 27 2016 - 15:39:41 PDT)
- Re: [AMBER] mdl file for 1d-rism David A Case (Fri May 27 2016 - 18:22:06 PDT)
- Re: [AMBER] mdl file for 1d-rism Jingyi Yan (Thu Jun 02 2016 - 14:51:58 PDT)
  - Re: [AMBER] mdl file for 1d-rism Tyler Luchko (Lists) (Tue Jun 21 2016 - 10:37:31 PDT)
[AMBER] Choline Chloride Christopher Jesudason (Sun May 29 2016 - 13:06:20 PDT)
[AMBER] cpptraj clustering based on ligand cavity Neha Gandhi (Sun May 29 2016 - 18:12:10 PDT)
- Re: [AMBER] cpptraj clustering based on ligand cavity Daniel Roe (Tue May 31 2016 - 08:00:18 PDT)
  - Re: [AMBER] cpptraj clustering based on ligand cavity Neha Gandhi (Tue May 31 2016 - 18:28:22 PDT)
    - Re: [AMBER] cpptraj clustering based on ligand cavity Daniel Roe (Wed Jun 01 2016 - 07:45:51 PDT)
[AMBER] Magnesium ion in AMBER Shreeramesh (Mon May 30 2016 - 05:03:46 PDT)
- Re: [AMBER] Magnesium ion in AMBER David A Case (Mon May 30 2016 - 06:19:36 PDT)
  - Re: [AMBER] Magnesium ion in AMBER Pengfei Li (Tue May 31 2016 - 07:36:15 PDT)
[AMBER] NMR restraints violation limit Vasantha Kumar (Mon May 30 2016 - 07:38:10 PDT)
- Re: [AMBER] NMR restraints violation limit Duggan, Brendan (Tue May 31 2016 - 12:04:56 PDT)
[AMBER] calculated rmsd Ziba Bahadori (Tue May 31 2016 - 00:12:29 PDT)
- Re: [AMBER] calculated rmsd Daniel Roe (Tue May 31 2016 - 07:58:19 PDT)
[AMBER] "sanderf" Odin Zeus (Tue May 31 2016 - 06:37:23 PDT)
- Re: [AMBER] "sanderf" Jason Swails (Tue May 31 2016 - 10:11:36 PDT)
[AMBER] rdf or watershell Neha Gandhi (Tue May 31 2016 - 18:31:54 PDT)
- Re: [AMBER] rdf or watershell Daniel Roe (Wed Jun 01 2016 - 07:47:45 PDT)
[AMBER] QMS-QMMM Odin Zeus (Tue May 31 2016 - 20:51:50 PDT)
- Re: [AMBER] QMS-QMMM Adrian Roitberg (Wed Jun 01 2016 - 06:30:37 PDT)
[AMBER] radial (rdf) computation time Neha Gandhi (Wed Jun 01 2016 - 00:28:03 PDT)
- Re: [AMBER] radial (rdf) computation time Daniel Roe (Wed Jun 01 2016 - 07:42:49 PDT)
  - Re: [AMBER] radial (rdf) computation time Neha Gandhi (Wed Jun 01 2016 - 20:58:19 PDT)
    - Re: [AMBER] radial (rdf) computation time Daniel Roe (Thu Jun 02 2016 - 08:50:27 PDT)
[AMBER] Amber Cpptraj troubleshoot Angelina Malagodi (Wed Jun 01 2016 - 15:55:50 PDT)
- Re: [AMBER] Amber Cpptraj troubleshoot Hai Nguyen (Wed Jun 01 2016 - 16:02:59 PDT)
  - Re: [AMBER] Amber Cpptraj troubleshoot Angelina Malagodi (Wed Jun 01 2016 - 16:34:52 PDT)
    - Re: [AMBER] Amber Cpptraj troubleshoot Angelina Malagodi (Wed Jun 01 2016 - 16:37:08 PDT)
    - Re: [AMBER] Amber Cpptraj troubleshoot Hai Nguyen (Wed Jun 01 2016 - 16:40:45 PDT)
    - Re: [AMBER] Amber Cpptraj troubleshoot David A Case (Wed Jun 01 2016 - 17:04:42 PDT)
    - Re: [AMBER] Amber Cpptraj troubleshoot Hai Nguyen (Wed Jun 01 2016 - 16:38:15 PDT)
- Re: [AMBER] Amber Cpptraj troubleshoot Daniel Roe (Wed Jun 01 2016 - 16:25:37 PDT)
[AMBER] mmgbsa calculation chemjxn (Wed Jun 01 2016 - 17:25:53 PDT)
- Re: [AMBER] mmgbsa calculation Jason Swails (Thu Jun 02 2016 - 06:11:56 PDT)
[AMBER] parmchk and parmchk2 segmentation fault Neha Gandhi (Wed Jun 01 2016 - 18:41:51 PDT)
- Re: [AMBER] parmchk and parmchk2 segmentation fault David A Case (Wed Jun 01 2016 - 20:50:48 PDT)
[AMBER] Unreadable rst7 Elisa Pieri (Thu Jun 02 2016 - 01:51:14 PDT)
- Re: [AMBER] Unreadable rst7 Bill Ross (Thu Jun 02 2016 - 02:17:22 PDT)
  - Re: [AMBER] Unreadable rst7 Elisa Pieri (Thu Jun 02 2016 - 02:23:33 PDT)
    - Re: [AMBER] Unreadable rst7 Bill Ross (Thu Jun 02 2016 - 03:20:16 PDT)
    - Re: [AMBER] Unreadable rst7 Bill Ross (Thu Jun 02 2016 - 03:50:00 PDT)
    - Re: [AMBER] Unreadable rst7 Elisa Pieri (Thu Jun 02 2016 - 04:02:46 PDT)
    - Re: [AMBER] Unreadable rst7 Jason Swails (Thu Jun 02 2016 - 06:13:48 PDT)
- Re: [AMBER] Unreadable rst7 David A Case (Thu Jun 02 2016 - 06:16:34 PDT)
  - Re: [AMBER] Unreadable rst7 Elisa Pieri (Thu Jun 02 2016 - 06:18:35 PDT)
    - Re: [AMBER] Unreadable rst7 Jason Swails (Thu Jun 02 2016 - 06:33:46 PDT)
[AMBER] mmpbsa analys Ziba Bahadori (Thu Jun 02 2016 - 10:05:21 PDT)
- Re: [AMBER] mmpbsa analys Jason Swails (Thu Jun 02 2016 - 10:44:20 PDT)
[AMBER] Some problems about heme 163邮箱 (Fri Jun 03 2016 - 02:25:01 PDT)
- Re: [AMBER] Some problems about heme Vaibhav Dixit (Fri Jun 03 2016 - 04:23:30 PDT)
- Re: [AMBER] Some problems about heme David A Case (Fri Jun 03 2016 - 13:33:57 PDT)
[AMBER] iwrap and mmpbsa Mary Varughese (Fri Jun 03 2016 - 03:16:40 PDT)
- Re: [AMBER] iwrap and mmpbsa Jason Swails (Fri Jun 03 2016 - 12:04:41 PDT)
[AMBER] re imaging doubt Mary Varughese (Fri Jun 03 2016 - 03:58:20 PDT)
- Re: [AMBER] re imaging doubt Hai Nguyen (Fri Jun 03 2016 - 07:36:13 PDT)
[AMBER] Amber16 won't install Gulsevin,Alican (Fri Jun 03 2016 - 04:01:23 PDT)
- Re: [AMBER] Amber16 won't install Hai Nguyen (Fri Jun 03 2016 - 10:11:00 PDT)
  - Re: [AMBER] Amber16 won't install Hai Nguyen (Fri Jun 03 2016 - 10:11:40 PDT)
  - Re: [AMBER] Amber16 won't install Gulsevin,Alican (Fri Jun 03 2016 - 10:22:41 PDT)
    - Re: [AMBER] Amber16 won't install Hai Nguyen (Fri Jun 03 2016 - 10:25:02 PDT)
    - Re: [AMBER] Amber16 won't install Gulsevin,Alican (Fri Jun 03 2016 - 10:58:43 PDT)
    - Re: [AMBER] Amber16 won't install Hai Nguyen (Fri Jun 03 2016 - 11:43:08 PDT)
[AMBER] proper box size to calculate binding enthalpy of host-guest in explicit solvent Budhathoki, Dipesh (Fri Jun 03 2016 - 10:27:42 PDT)
[AMBER] TI calculation with ligand dimer Hu, Yuan (Fri Jun 03 2016 - 15:39:31 PDT)
- Re: [AMBER] TI calculation with ligand dimer Hannes Loeffler (Sat Jun 04 2016 - 03:01:16 PDT)
- Re: [AMBER] TI calculation with ligand dimer Hu, Yuan (Mon Jun 06 2016 - 07:33:59 PDT)
[AMBER] problems compiling cuda enabled amber on ubuntu 16.04 mmaestre (Fri Jun 03 2016 - 22:41:40 PDT)
- Re: [AMBER] problems compiling cuda enabled amber on ubuntu 16.04 Mark Abraham (Sat Jun 04 2016 - 07:31:11 PDT)
- Re: [AMBER] problems compiling cuda enabled amber on ubuntu 16.04 Ross Walker (Sat Jun 04 2016 - 09:36:52 PDT)
  - Re: [AMBER] problems compiling cuda enabled amber on ubuntu 16.04 Mark Abraham (Sat Jun 04 2016 - 10:43:08 PDT)
    - Re: [AMBER] problems compiling cuda enabled amber on ubuntu 16.04 Ross Walker (Sat Jun 04 2016 - 12:18:52 PDT)
    - Re: [AMBER] problems compiling cuda enabled amber on ubuntu 16.04 mmaestre (Sat Jun 04 2016 - 21:08:43 PDT)
[AMBER] Principle Component Analysis (PCA) in cpptraj Himanshu Joshi (Sat Jun 04 2016 - 06:14:43 PDT)
- Re: [AMBER] Principle Component Analysis (PCA) in cpptraj Daniel Roe (Sun Jun 05 2016 - 10:58:08 PDT)
  - Re: [AMBER] Principle Component Analysis (PCA) in cpptraj Himanshu Joshi (Sun Jun 05 2016 - 11:28:48 PDT)
    - Re: [AMBER] Principle Component Analysis (PCA) in cpptraj Himanshu Joshi (Sun Jun 05 2016 - 12:17:54 PDT)
    - Re: [AMBER] Principle Component Analysis (PCA) in cpptraj Daniel Roe (Sun Jun 05 2016 - 12:42:14 PDT)
[AMBER] Some problems about Heme 163邮箱 (Sat Jun 04 2016 - 06:29:09 PDT)
- Re: [AMBER] Some problems about Heme Vaibhav Dixit (Sat Jun 04 2016 - 06:55:12 PDT)
- Re: [AMBER] Some problems about Heme David A Case (Sat Jun 04 2016 - 21:26:51 PDT)
  - Re: [AMBER] Some problems about Heme Lachele Foley (Mon Jun 06 2016 - 06:52:11 PDT)
    - Re: [AMBER] Some problems about Heme Pengfei Li (Tue Jun 07 2016 - 19:54:02 PDT)
[AMBER] mmpbsa problem Ziba Bahadori (Sat Jun 04 2016 - 07:05:50 PDT)
[AMBER] Ambertools16 test failed for leap zoran matovic (Sat Jun 04 2016 - 14:18:22 PDT)
- Re: [AMBER] Ambertools16 test failed for leap David A Case (Sat Jun 04 2016 - 21:46:51 PDT)
  - Re: [AMBER] Ambertools16 test failed for leap zmatovic.kg.ac.rs (Sat Jun 04 2016 - 23:50:31 PDT)
[AMBER] pulling a zn ion with SMD Fabian gmail (Sun Jun 05 2016 - 04:29:05 PDT)
- Re: [AMBER] pulling a zn ion with SMD Himanshu Joshi (Sun Jun 05 2016 - 06:58:57 PDT)
  - Re: [AMBER] pulling a zn ion with SMD Fabian gmail (Tue Jun 07 2016 - 02:04:42 PDT)
[AMBER] [Amber] Build parameters on HEME-Fe-HIS system 163邮箱 (Sun Jun 05 2016 - 08:28:22 PDT)
[AMBER] Protein - ligand tutorials - reg arthivenkat2.gmail.com (Sun Jun 05 2016 - 11:13:59 PDT)
- Re: [AMBER] Protein - ligand tutorials - reg Hai Nguyen (Sun Jun 05 2016 - 12:53:07 PDT)
- Re: [AMBER] Protein - ligand tutorials - reg David A Case (Sun Jun 05 2016 - 13:04:07 PDT)
[AMBER] proper box size to calculate binding enthalpy of host-guest in explicit solvent Budhathoki, Dipesh (Sun Jun 05 2016 - 14:16:12 PDT)
[AMBER] test 4096wat mmaestre (Sun Jun 05 2016 - 22:16:35 PDT)
- Re: [AMBER] test 4096wat Charles Lin (Sun Jun 05 2016 - 22:19:00 PDT)
  - Re: [AMBER] test 4096wat Charles Lin (Sun Jun 05 2016 - 22:20:22 PDT)
[AMBER] Issue of AMBER 2016 with CUDA Huian Li (Mon Jun 06 2016 - 06:24:07 PDT)
- Re: [AMBER] Issue of AMBER 2016 with CUDA David A Case (Mon Jun 06 2016 - 08:05:49 PDT)
  - Re: [AMBER] Issue of AMBER 2016 with CUDA Huian Li (Tue Jun 07 2016 - 08:23:05 PDT)
    - Re: [AMBER] Issue of AMBER 2016 with CUDA Jason Swails (Tue Jun 07 2016 - 20:51:14 PDT)
[AMBER] restarting a run Thomas Pochapsky (Mon Jun 06 2016 - 06:27:54 PDT)
- Re: [AMBER] restarting a run David A Case (Mon Jun 06 2016 - 10:06:33 PDT)
  - Re: [AMBER] restarting a run Thomas Pochapsky (Mon Jun 06 2016 - 10:26:35 PDT)
    - Re: [AMBER] restarting a run David A Case (Tue Jun 07 2016 - 01:04:10 PDT)
    - Re: [AMBER] restarting a run Thomas Pochapsky (Tue Jun 07 2016 - 05:50:35 PDT)
[AMBER] cpinutil.py problem Elisa Pieri (Mon Jun 06 2016 - 06:46:53 PDT)
- Re: [AMBER] cpinutil.py problem Jason Swails (Mon Jun 06 2016 - 07:16:07 PDT)
  - Re: [AMBER] cpinutil.py problem Elisa Pieri (Mon Jun 06 2016 - 07:21:43 PDT)
    - Re: [AMBER] cpinutil.py problem Elisa Pieri (Mon Jun 06 2016 - 07:30:33 PDT)
Re: [AMBER] proper box size to calculate binding enthalpy of host-guest Budhathoki, Dipesh (Mon Jun 06 2016 - 11:06:55 PDT)
- Re: [AMBER] proper box size to calculate binding enthalpy of host-guest Niel Henriksen (Mon Jun 06 2016 - 12:58:04 PDT)
  - Re: [AMBER] proper box size to calculate binding enthalpy of host-guest Budhathoki, Dipesh (Mon Jun 06 2016 - 18:36:40 PDT)
    - Re: [AMBER] proper box size to calculate binding enthalpy of host-guest Niel Henriksen (Mon Jun 06 2016 - 18:56:07 PDT)
    - Re: [AMBER] proper box size to calculate binding enthalpy of host-guest Budhathoki, Dipesh (Mon Jun 06 2016 - 20:32:01 PDT)
[AMBER] setMolecules failed Damiano Spadoni (Mon Jun 06 2016 - 13:01:52 PDT)
- Re: [AMBER] setMolecules failed Daniel Roe (Mon Jun 06 2016 - 13:04:27 PDT)
- Re: [AMBER] setMolecules failed David A Case (Tue Jun 07 2016 - 01:14:34 PDT)
  - Re: [AMBER] setMolecules failed Damiano Spadoni (Tue Jun 07 2016 - 05:00:48 PDT)
    - Re: [AMBER] setMolecules failed Jason Swails (Tue Jun 07 2016 - 07:31:02 PDT)
    - Re: [AMBER] setMolecules failed David A Case (Tue Jun 07 2016 - 10:04:46 PDT)
    - Re: [AMBER] setMolecules failed Jason Swails (Tue Jun 07 2016 - 11:26:36 PDT)
[AMBER] cpptraj reading a reference coordinate for analyses Neha Gandhi (Tue Jun 07 2016 - 01:43:18 PDT)
- Re: [AMBER] cpptraj reading a reference coordinate for analyses Daniel Roe (Tue Jun 07 2016 - 07:56:29 PDT)
[AMBER] Amber14 & Cuda 7.5 Nikolay N. Kuzmich (Tue Jun 07 2016 - 05:03:52 PDT)
- Re: [AMBER] Amber14 & Cuda 7.5 Irfan Alibay (Tue Jun 07 2016 - 07:16:08 PDT)
[AMBER] Umbrella sampling with two degrees of freedom Airy Sanjeev (Tue Jun 07 2016 - 21:16:50 PDT)
- Re: [AMBER] Umbrella sampling with two degrees of freedom Feng Pan (Tue Jun 07 2016 - 21:34:58 PDT)
- Re: [AMBER] Umbrella sampling with two degrees of freedom David Cerutti (Tue Jun 07 2016 - 21:41:11 PDT)
- Re: [AMBER] Umbrella sampling with two degrees of freedom Carlos Simmerling (Wed Jun 08 2016 - 04:27:04 PDT)
[AMBER] Energy decomposition in MM/GBSA mish (Tue Jun 07 2016 - 22:35:21 PDT)
[AMBER] neuraminic acid mmaestre (Wed Jun 08 2016 - 00:44:00 PDT)
- Re: [AMBER] neuraminic acid Lachele Foley (Wed Jun 08 2016 - 00:52:47 PDT)
  - Re: [AMBER] neuraminic acid mmaestre (Wed Jun 08 2016 - 01:01:41 PDT)
[AMBER] Error while trying to upgrade AmberTools 15 Nikolay N. Kuzmich (Wed Jun 08 2016 - 02:48:28 PDT)
- Re: [AMBER] Error while trying to upgrade AmberTools 15 Jason Swails (Wed Jun 08 2016 - 03:31:16 PDT)
[AMBER] MD simulations with jar=1 and more than one nmropt restraint James Murdock (Wed Jun 08 2016 - 03:39:46 PDT)
- Re: [AMBER] MD simulations with jar=1 and more than one nmropt restraint Feng Pan (Wed Jun 08 2016 - 09:01:14 PDT)
[AMBER] How to define COM group of atoms greater than 1024 atoms when nmropt=1 and pmemd.cuda.MPI Shuntaro Chiba (Wed Jun 08 2016 - 08:07:55 PDT)
[AMBER] Umbrella Sampling Airy Sanjeev (Wed Jun 08 2016 - 09:15:58 PDT)
- Re: [AMBER] Umbrella Sampling David Cerutti (Wed Jun 08 2016 - 09:30:19 PDT)
  - Re: [AMBER] Umbrella Sampling Carlos Simmerling (Wed Jun 08 2016 - 09:43:51 PDT)
- Re: [AMBER] Umbrella Sampling bharat gupta (Thu Jun 30 2016 - 22:00:58 PDT)
- Re: [AMBER] Umbrella Sampling bharat gupta (Sat Jul 02 2016 - 06:19:45 PDT)
[AMBER] Dismal QM/MM Efficiency Nisler, Collin R. (Wed Jun 08 2016 - 11:52:45 PDT)
- Re: [AMBER] Dismal QM/MM Efficiency Adrian Roitberg (Wed Jun 08 2016 - 12:14:04 PDT)
  - Re: [AMBER] Dismal QM/MM Efficiency Nisler, Collin R. (Wed Jun 08 2016 - 12:29:29 PDT)
    - Re: [AMBER] Dismal QM/MM Efficiency Jason Swails (Wed Jun 08 2016 - 13:14:11 PDT)
- Re: [AMBER] Dismal QM/MM Efficiency Dr. Andreas W. Goetz (Wed Jun 08 2016 - 12:16:36 PDT)
  - Re: [AMBER] Dismal QM/MM Efficiency Nisler, Collin R. (Wed Jun 08 2016 - 12:31:30 PDT)
    - Re: [AMBER] Dismal QM/MM Efficiency Dr. Andreas W. Goetz (Wed Jun 08 2016 - 13:51:05 PDT)
[AMBER] hanging test mdgx/1p7e for installation to 'long' path Kenneth Hoste (Wed Jun 08 2016 - 13:28:23 PDT)
- Re: [AMBER] hanging test mdgx/1p7e for installation to 'long' path David Cerutti (Wed Jun 08 2016 - 14:53:29 PDT)
  - Re: [AMBER] hanging test mdgx/1p7e for installation to 'long' path Kenneth Hoste (Fri Jun 10 2016 - 04:19:14 PDT)
[AMBER] Principal Component Analysis Kat G (Wed Jun 08 2016 - 18:10:47 PDT)
- Re: [AMBER] Principal Component Analysis Jason Swails (Wed Jun 08 2016 - 19:36:05 PDT)
[AMBER] buffer OR buffer_xyz_list in setBox command mish (Wed Jun 08 2016 - 18:35:35 PDT)
[AMBER] energy decomposition Sanjib Paul (Wed Jun 08 2016 - 23:55:35 PDT)
- Re: [AMBER] energy decomposition David A Case (Thu Jun 09 2016 - 08:13:13 PDT)
  - Re: [AMBER] energy decomposition Sanjib Paul (Fri Jun 17 2016 - 03:22:46 PDT)
[AMBER] INDIGO-DataCloud Newsletter, May 2016 galileo.galile22.yahoo.com (Thu Jun 09 2016 - 02:28:03 PDT)
[AMBER] THF parametrization Norbert GARNIER (Thu Jun 09 2016 - 05:39:54 PDT)
[AMBER] PCA error not Lara rajam (Thu Jun 09 2016 - 11:28:30 PDT)
- Re: [AMBER] PCA error not Daniel Roe (Thu Jun 09 2016 - 11:41:27 PDT)
[AMBER] RMSD for the backbone atoms of residues Aishani Prem (Thu Jun 09 2016 - 12:14:32 PDT)
- Re: [AMBER] RMSD for the backbone atoms of residues Daniel Roe (Thu Jun 09 2016 - 12:17:43 PDT)
  - Re: [AMBER] RMSD for the backbone atoms of residues Aishani Prem (Thu Jun 09 2016 - 12:31:46 PDT)
    - Re: [AMBER] RMSD for the backbone atoms of residues Daniel Roe (Thu Jun 09 2016 - 12:33:14 PDT)
    - Re: [AMBER] RMSD for the backbone atoms of residues Aishani Prem (Thu Jun 09 2016 - 12:40:50 PDT)
    - Re: [AMBER] RMSD for the backbone atoms of residues Hai Nguyen (Thu Jun 09 2016 - 12:47:42 PDT)
    - Re: [AMBER] RMSD for the backbone atoms of residues Dr. Anselm Horn (Fri Jun 10 2016 - 01:21:01 PDT)
    - Re: [AMBER] RMSD for the backbone atoms of residues Daniel Roe (Fri Jun 10 2016 - 07:41:25 PDT)
[AMBER] QM/MM MD problem Debodyuti Dutta (Thu Jun 09 2016 - 21:31:55 PDT)
[AMBER] Issue with with the nocenter in tLeap Sushil Mishra (Thu Jun 09 2016 - 23:39:02 PDT)
- Re: [AMBER] Issue with with the nocenter in tLeap David A Case (Wed Jun 22 2016 - 20:22:04 PDT)
  - Re: [AMBER] Issue with with the nocenter in tLeap Sushil Mishra (Wed Jun 22 2016 - 21:58:23 PDT)
    - Re: [AMBER] Issue with with the nocenter in tLeap Daniel Roe (Thu Jun 23 2016 - 08:09:28 PDT)
    - Re: [AMBER] Issue with with the nocenter in tLeap Sushil Mishra (Thu Jun 23 2016 - 16:49:36 PDT)
    - Re: [AMBER] Issue with with the nocenter in tLeap Daniel Roe (Fri Jun 24 2016 - 10:33:47 PDT)
[AMBER] FF14SB implementation Miroslav Krepl (Fri Jun 10 2016 - 06:37:38 PDT)
- Re: [AMBER] FF14SB implementation David A Case (Tue Jun 14 2016 - 05:04:30 PDT)
  - Re: [AMBER] FF14SB implementation Vlad Cojocaru (Tue Jun 14 2016 - 05:53:25 PDT)
    - Re: [AMBER] FF14SB implementation Carlos Simmerling (Tue Jun 14 2016 - 06:17:33 PDT)
    - Re: [AMBER] FF14SB implementation Vlad Cojocaru (Tue Jun 14 2016 - 06:41:42 PDT)
    - Re: [AMBER] FF14SB implementation Carlos Simmerling (Tue Jun 14 2016 - 06:46:40 PDT)
- Re: [AMBER] FF14SB implementation Miroslav Krepl (Tue Jun 14 2016 - 06:14:23 PDT)
[AMBER] Error in tleap for the atom type of OCT1 and OCT2 of glutamic acid at C-terminal Shreeramesh (Fri Jun 10 2016 - 07:16:49 PDT)
- Re: [AMBER] Error in tleap for the atom type of OCT1 and OCT2 of glutamic acid at C-terminal David A Case (Sat Jun 11 2016 - 09:50:01 PDT)
  - Re: [AMBER] Error in tleap for the atom type of OCT1 and OCT2 of glutamic acid at C-terminal Shreeramesh (Mon Jun 13 2016 - 03:11:57 PDT)
    - Re: [AMBER] Error in tleap for the atom type of OCT1 and OCT2 of glutamic acid at C-terminal Daniel Roe (Mon Jun 13 2016 - 07:36:14 PDT)
[AMBER] addition of hydrogen to unionised the -COO group Martina Devi (Fri Jun 10 2016 - 08:00:42 PDT)
- Re: [AMBER] addition of hydrogen to unionised the -COO group David A Case (Sat Jun 11 2016 - 09:53:04 PDT)
  - Re: [AMBER] addition of hydrogen to unionised the -COO group Martina Devi (Sat Jun 11 2016 - 11:00:32 PDT)
    - Re: [AMBER] addition of hydrogen to unionised the -COO group David A Case (Sat Jun 11 2016 - 18:18:45 PDT)
    - Re: [AMBER] addition of hydrogen to unionised the -COO group Martina Devi (Mon Jun 13 2016 - 23:59:53 PDT)
[AMBER] Regarding error in MMPBSA MOHD HOMAIDUR RAHMAN (Fri Jun 10 2016 - 14:35:26 PDT)
[AMBER] radial distribution function tails for liquids using GAFF conor parks (Fri Jun 10 2016 - 18:51:35 PDT)
- Re: [AMBER] radial distribution function tails for liquids using GAFF David A Case (Sat Jun 11 2016 - 10:26:24 PDT)
  - Re: [AMBER] radial distribution function tails for liquids using GAFF Conor Parks (Sat Jun 11 2016 - 11:41:49 PDT)
[AMBER] Free energy decomposition of QM/MM-GBSA Allen Zou (Sat Jun 11 2016 - 07:48:37 PDT)
- Re: [AMBER] Free energy decomposition of QM/MM-GBSA Jason Swails (Tue Jun 14 2016 - 20:12:07 PDT)
[AMBER] Help me with double ambiguous noe.map files!!! PLEASE tanfei777.sina.cn (Sun Jun 12 2016 - 00:28:05 PDT)
- Re: [AMBER] Help me with double ambiguous noe.map files!!! PLEASE David A Case (Sun Jun 12 2016 - 06:09:52 PDT)
- Re: [AMBER] Help me with double ambiguous noe.map files!!! PLEASE Duggan, Brendan (Mon Jun 13 2016 - 10:26:18 PDT)
[AMBER] Problem in Calculating Rotational diffusion ATUL KUMAR (Sun Jun 12 2016 - 06:22:52 PDT)
- Re: [AMBER] Problem in Calculating Rotational diffusion Daniel Roe (Sun Jun 12 2016 - 08:44:10 PDT)
  - Re: [AMBER] Problem in Calculating Rotational diffusion ATUL KUMAR (Sun Jun 12 2016 - 22:44:47 PDT)
    - Re: [AMBER] Problem in Calculating Rotational diffusion Daniel Roe (Mon Jun 13 2016 - 07:39:18 PDT)
[AMBER] 回复：Re: Help me with double ambiguous noe.map files!!! PLEASE tanfei777.sina.cn (Sun Jun 12 2016 - 21:15:45 PDT)
[AMBER] Can I turn off group coordinate averaging? tanfei777.sina.cn (Sun Jun 12 2016 - 21:59:17 PDT)
- Re: [AMBER] Can I turn off group coordinate averaging? David A Case (Mon Jun 13 2016 - 10:54:50 PDT)
[AMBER] problems with building sulfo sialil-lacnac mmaestre (Mon Jun 13 2016 - 01:00:37 PDT)
[AMBER] umbrella sampling with two degrees of freedom Airy Sanjeev (Mon Jun 13 2016 - 05:06:29 PDT)
[AMBER] Choose reference frame for rmsd Jean-Patrick Francoia (Mon Jun 13 2016 - 05:55:31 PDT)
- Re: [AMBER] Choose reference frame for rmsd Daniel Roe (Mon Jun 13 2016 - 07:18:46 PDT)
  - Re: [AMBER] Choose reference frame for rmsd Jean-Patrick Francoia (Mon Jun 13 2016 - 12:43:42 PDT)
[AMBER] umbrella sampling long axex problem Airy Sanjeev (Mon Jun 13 2016 - 08:50:11 PDT)
[AMBER] Radial Distribution Function Angelina Malagodi (Mon Jun 13 2016 - 10:38:24 PDT)
- Re: [AMBER] Radial Distribution Function Daniel Roe (Mon Jun 13 2016 - 10:44:37 PDT)
  - Re: [AMBER] Radial Distribution Function Angelina Malagodi (Mon Jun 13 2016 - 10:50:39 PDT)
    - Re: [AMBER] Radial Distribution Function Daniel Roe (Mon Jun 13 2016 - 11:02:18 PDT)
    - Re: [AMBER] Radial Distribution Function Angelina Malagodi (Mon Jun 13 2016 - 11:32:38 PDT)
    - Re: [AMBER] Radial Distribution Function Hai Nguyen (Mon Jun 13 2016 - 11:37:12 PDT)
    - Re: [AMBER] Radial Distribution Function Angelina Malagodi (Mon Jun 13 2016 - 11:43:56 PDT)
    - Re: [AMBER] Radial Distribution Function Daniel Roe (Mon Jun 13 2016 - 11:46:23 PDT)
[AMBER] 回复：Re: Help me with double ambiguous noe.map files!!! PLEASE tanfei777.sina.cn (Mon Jun 13 2016 - 20:06:30 PDT)
[AMBER] Fwd: eChemInfo Workshop on Rational Drug Design in Milano Thomas Exner (Mon Jun 13 2016 - 23:01:44 PDT)
[AMBER] antechamber error message Martina Devi (Tue Jun 14 2016 - 00:02:07 PDT)
- Re: [AMBER] antechamber error message David A Case (Tue Jun 14 2016 - 04:55:24 PDT)
- Re: [AMBER] antechamber error message Martina Devi (Tue Jun 14 2016 - 08:04:31 PDT)
  - Re: [AMBER] antechamber error message David A Case (Tue Jun 14 2016 - 09:27:29 PDT)
[AMBER] Errors in my installation Abdul-Rashid Iii Sampaco (Tue Jun 14 2016 - 01:22:56 PDT)
- Re: [AMBER] Errors in my installation Marcelo Andrade Chagas (Tue Jun 14 2016 - 04:47:26 PDT)
- Re: [AMBER] Errors in my installation David A Case (Tue Jun 14 2016 - 05:00:47 PDT)
- Re: [AMBER] Errors in my installation Hai Nguyen (Tue Jun 14 2016 - 07:25:08 PDT)
  - Re: [AMBER] Errors in my installation Abdul-Rashid Iii Sampaco (Tue Jun 14 2016 - 19:06:50 PDT)
    - Re: [AMBER] Errors in my installation Hai Nguyen (Tue Jun 14 2016 - 19:48:28 PDT)
    - Re: [AMBER] Errors in my installation Abdul-Rashid Iii Sampaco (Tue Jun 14 2016 - 19:54:35 PDT)
    - Re: [AMBER] Errors in my installation Hai Nguyen (Tue Jun 14 2016 - 19:59:33 PDT)
    - Re: [AMBER] Errors in my installation Abdul-Rashid Iii Sampaco (Tue Jun 14 2016 - 20:21:57 PDT)
    - Re: [AMBER] Errors in my installation Hai Nguyen (Tue Jun 14 2016 - 20:26:23 PDT)
    - Re: [AMBER] Errors in my installation koushik kasavajhala (Tue Jun 14 2016 - 20:44:48 PDT)
    - Re: [AMBER] Errors in my installation Abdul-Rashid Iii Sampaco (Tue Jun 14 2016 - 20:50:06 PDT)
    - Re: [AMBER] Errors in my installation Abdul-Rashid Iii Sampaco (Tue Jun 14 2016 - 20:52:26 PDT)
[AMBER] Problem: Do not receive mails from Amber list but Amber digest SHAILESH KUMAR (Tue Jun 14 2016 - 02:10:42 PDT)
- Re: [AMBER] Problem: Do not receive mails from Amber list but Amber digest Ross Walker (Tue Jun 14 2016 - 10:44:04 PDT)
  - Re: [AMBER] Problem: Do not receive mails from Amber list but Amber digest SHAILESH KUMAR (Tue Jun 14 2016 - 11:12:05 PDT)
[AMBER] Difference between radius of gyration and max radius of gyration Jean-Patrick Francoia (Tue Jun 14 2016 - 04:42:12 PDT)
- Re: [AMBER] Difference between radius of gyration and max radius of gyration Daniel Roe (Tue Jun 14 2016 - 07:45:13 PDT)
  - Re: [AMBER] Difference between radius of gyration and max radius of gyration Jean-Patrick Francoia (Tue Jun 14 2016 - 08:11:47 PDT)
[AMBER] [ANN] Release of NGLView for interactive trajectory visualization in Jupyter notebooks. Hai Nguyen (Tue Jun 14 2016 - 11:05:11 PDT)
[AMBER] amber16 pmemd cuda rst file Neha Gandhi (Tue Jun 14 2016 - 14:29:43 PDT)
- Re: [AMBER] amber16 pmemd cuda rst file Daniel Roe (Tue Jun 14 2016 - 14:34:56 PDT)
  - Re: [AMBER] amber16 pmemd cuda rst file Neha Gandhi (Tue Jun 14 2016 - 14:49:15 PDT)
    - Re: [AMBER] amber16 pmemd cuda rst file Daniel Roe (Tue Jun 14 2016 - 14:59:10 PDT)
    - Re: [AMBER] amber16 pmemd cuda rst file Daniel Roe (Wed Jun 15 2016 - 08:32:16 PDT)
    - Re: [AMBER] amber16 pmemd cuda rst file Marc van der Kamp (Fri Jun 17 2016 - 03:07:25 PDT)
    - Re: [AMBER] amber16 pmemd cuda rst file Hannes Loeffler (Fri Jun 17 2016 - 03:35:09 PDT)
    - Re: [AMBER] amber16 pmemd cuda rst file David A Case (Fri Jun 17 2016 - 05:01:04 PDT)
    - Re: [AMBER] amber16 pmemd cuda rst file David A Case (Sat Jun 18 2016 - 05:33:16 PDT)
    - Re: [AMBER] amber16 pmemd cuda rst file Hannes Loeffler (Mon Jun 20 2016 - 08:28:10 PDT)
    - Re: [AMBER] amber16 pmemd cuda rst file David A Case (Mon Jun 20 2016 - 11:41:10 PDT)
[AMBER] Visualizing QM/MM Simulations Nisler, Collin R. (Tue Jun 14 2016 - 19:26:07 PDT)
- Re: [AMBER] Visualizing QM/MM Simulations Dr. Andreas W. Goetz (Tue Jun 14 2016 - 19:42:32 PDT)
[AMBER] Density File Wong Li Zhe (Tue Jun 14 2016 - 19:27:36 PDT)
- Re: [AMBER] Density File David A Case (Wed Jun 15 2016 - 04:49:45 PDT)
[AMBER] Reminder: Training and Innovation Course in Drug Design Thomas Exner (Tue Jun 14 2016 - 23:59:22 PDT)
[AMBER] Lipidorder/No output Batuhan Kav (Wed Jun 15 2016 - 02:56:31 PDT)
- Re: [AMBER] Lipidorder/No output Hannes Loeffler (Wed Jun 15 2016 - 03:19:14 PDT)
  - Re: [AMBER] Lipidorder/No output Batuhan Kav (Wed Jun 15 2016 - 03:24:49 PDT)
    - Re: [AMBER] Lipidorder/No output Hannes Loeffler (Wed Jun 15 2016 - 04:13:14 PDT)
    - Re: [AMBER] Lipidorder/No output Batuhan Kav (Wed Jun 15 2016 - 05:23:28 PDT)
    - Re: [AMBER] Lipidorder/No output Hannes Loeffler (Wed Jun 15 2016 - 06:11:39 PDT)
    - Re: [AMBER] Lipidorder/No output Batuhan Kav (Wed Jun 15 2016 - 06:42:40 PDT)
    - Re: [AMBER] Lipidorder/No output Hannes Loeffler (Wed Jun 15 2016 - 07:04:35 PDT)
    - Re: [AMBER] Lipidorder/No output Daniel Roe (Wed Jun 15 2016 - 07:09:29 PDT)
[AMBER] ABOUT the GaMD patch for Amber14 Yeng-Tseng Wang (Wed Jun 15 2016 - 08:50:45 PDT)
- Re: [AMBER] ABOUT the GaMD patch for Amber14 Ross Walker (Wed Jun 15 2016 - 09:05:52 PDT)
  - Re: [AMBER] ABOUT the GaMD patch for Amber14 Yeng-Tseng Wang (Wed Jun 15 2016 - 09:14:05 PDT)
- Re: [AMBER] ABOUT the GaMD patch for Amber14 Neha Gandhi (Wed Jun 15 2016 - 09:36:05 PDT)
[AMBER] Which of charge methods in antechamber are appropriate? Atila Petrosian (Wed Jun 15 2016 - 11:10:54 PDT)
- Re: [AMBER] Which of charge methods in antechamber are appropriate? Gustavo Seabra (Wed Jun 15 2016 - 11:32:55 PDT)
[AMBER] Imaging problem? colvin (Wed Jun 15 2016 - 21:11:39 PDT)
- Re: [AMBER] Imaging problem? Dr. Anselm Horn (Thu Jun 16 2016 - 03:31:06 PDT)
  - Re: [AMBER] Imaging problem? colvin (Fri Jun 17 2016 - 00:02:04 PDT)
- Re: [AMBER] Imaging problem? colvin (Fri Jun 17 2016 - 00:06:52 PDT)
  - Re: [AMBER] Imaging problem? Dr. Anselm Horn (Fri Jun 17 2016 - 03:48:31 PDT)
  - Re: [AMBER] Imaging problem? Carlos Simmerling (Fri Jun 17 2016 - 04:08:21 PDT)
[AMBER] QMMM-MD Odin Zeus (Wed Jun 15 2016 - 22:36:37 PDT)
- Re: [AMBER] QMMM-MD David A Case (Thu Jun 16 2016 - 06:01:41 PDT)
  - Re: [AMBER] QMMM-MD Adrian Roitberg (Thu Jun 16 2016 - 06:05:48 PDT)
- Re: [AMBER] QMMM-MD Gustavo Seabra (Thu Jun 16 2016 - 08:08:28 PDT)
[AMBER] mmpbsa doubt Mary Varughese (Thu Jun 16 2016 - 00:42:36 PDT)
[AMBER] extremely slow cluster analysis with cpptraj Michael Shokhen (Thu Jun 16 2016 - 01:17:18 PDT)
- Re: [AMBER] extremely slow cluster analysis with cpptraj Daniel Roe (Thu Jun 16 2016 - 07:39:56 PDT)
[AMBER] Reading and Writing mdfrc files generated by pmemd SHAILESH KUMAR (Thu Jun 16 2016 - 06:33:21 PDT)
- Re: [AMBER] Reading and Writing mdfrc files generated by pmemd Hai Nguyen (Thu Jun 16 2016 - 07:54:55 PDT)
  - Re: [AMBER] Reading and Writing mdfrc files generated by pmemd SHAILESH KUMAR (Thu Jun 16 2016 - 09:53:28 PDT)
    - Re: [AMBER] Reading and Writing mdfrc files generated by pmemd Hai Nguyen (Thu Jun 16 2016 - 10:07:42 PDT)
    - Re: [AMBER] Reading and Writing mdfrc files generated by pmemd Hai Nguyen (Thu Jun 16 2016 - 10:41:48 PDT)
    - Re: [AMBER] Reading and Writing mdfrc files generated by pmemd SHAILESH KUMAR (Thu Jun 16 2016 - 10:52:50 PDT)
    - Re: [AMBER] Reading and Writing mdfrc files generated by pmemd SHAILESH KUMAR (Thu Jun 16 2016 - 11:56:34 PDT)
    - Re: [AMBER] Reading and Writing mdfrc files generated by pmemd Daniel Roe (Fri Jun 17 2016 - 12:44:43 PDT)
    - Re: [AMBER] Reading and Writing mdfrc files generated by pmemd SHAILESH KUMAR (Sat Jun 18 2016 - 02:44:15 PDT)
    - Re: [AMBER] Reading and Writing mdfrc files generated by pmemd Daniel Roe (Sat Jun 18 2016 - 07:17:09 PDT)
    - Re: [AMBER] Reading and Writing mdfrc files generated by pmemd Daniel Roe (Mon Jun 20 2016 - 11:45:06 PDT)
    - Re: [AMBER] Reading and Writing mdfrc files generated by pmemd SHAILESH KUMAR (Wed Jun 22 2016 - 01:00:06 PDT)
    - Re: [AMBER] Reading and Writing mdfrc files generated by pmemd Daniel Roe (Wed Jun 22 2016 - 04:50:50 PDT)
    - Re: [AMBER] Reading and Writing mdfrc files generated by pmemd Daniel Roe (Thu Jun 23 2016 - 10:30:27 PDT)
    - Re: [AMBER] Reading and Writing mdfrc files generated by pmemd SHAILESH KUMAR (Sat Jun 25 2016 - 02:36:40 PDT)
    - Re: [AMBER] Reading and Writing mdfrc files generated by pmemd Daniel Roe (Sat Jun 25 2016 - 05:42:57 PDT)
    - Re: [AMBER] Reading and Writing mdfrc files generated by pmemd SHAILESH KUMAR (Sat Jun 25 2016 - 09:02:27 PDT)
[AMBER] Entropy normal mode error George Tzotzos (Thu Jun 16 2016 - 08:08:16 PDT)
- Re: [AMBER] Entropy normal mode error SHAILESH KUMAR (Thu Jun 16 2016 - 10:10:23 PDT)
[AMBER] script for calculation of dihedral angle frequency Sehrish Naz Aijaz (Fri Jun 17 2016 - 00:36:14 PDT)
- Re: [AMBER] script for calculation of dihedral angle frequency David A Case (Fri Jun 17 2016 - 04:47:52 PDT)
[AMBER] Une demande d'aide avec GAFF ( 2 ) Chloe Renard (Fri Jun 17 2016 - 01:36:44 PDT)
- Re: [AMBER] Une demande d'aide avec GAFF ( 2 ) David A Case (Fri Jun 17 2016 - 04:50:50 PDT)
  - Re: [AMBER] Une demande d'aide avec GAFF ( 2 ) Chloe Renard (Mon Jun 20 2016 - 08:45:22 PDT)
[AMBER] NMR restraints on GPU (asterisks in output) Miroslav Krepl (Fri Jun 17 2016 - 02:21:15 PDT)
- Re: [AMBER] NMR restraints on GPU (asterisks in output) David A Case (Tue Jun 21 2016 - 05:34:25 PDT)
[AMBER] volmap: densities too low Jean-Patrick Francoia (Sat Jun 18 2016 - 03:38:35 PDT)
- Re: [AMBER] volmap: densities too low Jason Swails (Sat Jun 18 2016 - 04:33:04 PDT)
  - Re: [AMBER] volmap: densities too low Jean-Patrick Francoia (Mon Jun 20 2016 - 05:18:17 PDT)
    - Re: [AMBER] volmap: densities too low Jason Swails (Mon Jun 20 2016 - 08:48:25 PDT)
[AMBER] GIST calculation Sanjib Paul (Sat Jun 18 2016 - 04:46:05 PDT)
[AMBER] Saving the coordinates during a simulation Aishani Prem (Mon Jun 20 2016 - 11:31:12 PDT)
- Re: [AMBER] Saving the coordinates during a simulation Daniel Roe (Mon Jun 20 2016 - 11:34:03 PDT)
- Re: [AMBER] Saving the coordinates during a simulation Cruzeiro,Vinicius Wilian D (Mon Jun 20 2016 - 11:39:41 PDT)
[AMBER] Bad atom type: FE when calculating free energy using mmpbsa 163邮箱 (Tue Jun 21 2016 - 01:08:34 PDT)
- [AMBER] Stripping waters from trajectory on a distance-based criteria Alessandro Contini (Tue Jun 21 2016 - 02:27:25 PDT)
  - Re: [AMBER] Stripping waters from trajectory on a distance-based criteria Daniel Roe (Tue Jun 21 2016 - 07:16:45 PDT)
    - Re: [AMBER] Stripping waters from trajectory on a distance-based criteria Alessandro Contini (Wed Jun 22 2016 - 03:27:07 PDT)
- Re: [AMBER] Bad atom type: FE when calculating free energy using mmpbsa David A Case (Tue Jun 21 2016 - 05:29:02 PDT)
[AMBER] Principle component analysis: percentage contribution of eigenvectors Hirdesh Kumar (Tue Jun 21 2016 - 05:52:11 PDT)
- Re: [AMBER] Principle component analysis: percentage contribution of eigenvectors Daniel Roe (Tue Jun 21 2016 - 07:21:51 PDT)
[AMBER] Amber16+CUDA8.0 pmemd.cuda worked, and then stopped working, saying "cudaMemcpyToSymbol: SetSim copy to cSim failed invalid device symbol" Zack Scholl (Tue Jun 21 2016 - 08:03:19 PDT)
[AMBER] Problem analysing output with process_mdout.perl script Ruth Helena Tichauer (Tue Jun 21 2016 - 08:46:40 PDT)
- Re: [AMBER] Problem analysing output with process_mdout.perl script David A Case (Tue Jun 21 2016 - 10:25:30 PDT)
  - Re: [AMBER] Problem analysing output with process_mdout.perl script Ruth Helena Tichauer (Wed Jun 22 2016 - 06:22:44 PDT)
    - Re: [AMBER] Problem analysing output with process_mdout.perl script Hai Nguyen (Wed Jun 22 2016 - 10:25:05 PDT)
    - Re: [AMBER] Problem analysing output with process_mdout.perl script Ruth Helena Tichauer (Thu Jun 23 2016 - 08:10:22 PDT)
[AMBER] Problem with PCA projection Kat G (Tue Jun 21 2016 - 09:26:01 PDT)
- Re: [AMBER] Problem with PCA projection Daniel Roe (Tue Jun 21 2016 - 10:01:06 PDT)
[AMBER] Amber16 and CUDA8.0 pmemd.cuda worked, and then stopped working, saying "cudaMemcpyToSymbol: SetSim copy to cSim failed invalid device symbol" Zack Scholl (Tue Jun 21 2016 - 09:44:14 PDT)
[AMBER] Problem with PCA projection (cont) Kat G (Tue Jun 21 2016 - 10:41:32 PDT)
- Re: [AMBER] Problem with PCA projection (cont) Daniel Roe (Tue Jun 21 2016 - 10:50:49 PDT)
[AMBER] AMBER support for gtx1080 Anton Perera (Tue Jun 21 2016 - 21:56:06 PDT)
- Re: [AMBER] AMBER support for gtx1080 Charles Lin (Wed Jun 22 2016 - 02:17:40 PDT)
  - Re: [AMBER] AMBER support for gtx1080 Zack Scholl (Thu Jun 23 2016 - 07:35:33 PDT)
[AMBER] Query regarding dihedral angles Sehrish Naz Aijaz (Tue Jun 21 2016 - 22:17:51 PDT)
- Re: [AMBER] Query regarding dihedral angles Hai Nguyen (Tue Jun 21 2016 - 22:29:59 PDT)
- Re: [AMBER] Query regarding dihedral angles Carlos Simmerling (Wed Jun 22 2016 - 03:19:38 PDT)
[AMBER] convergence criteria in enhanced md techniques Neha Gandhi (Wed Jun 22 2016 - 05:43:18 PDT)
- Re: [AMBER] convergence criteria in enhanced md techniques Daniel Roe (Wed Jun 22 2016 - 06:07:42 PDT)
[AMBER] RESP charges amir sadeghi (Wed Jun 22 2016 - 11:53:14 PDT)
- Re: [AMBER] RESP charges FyD (Wed Jun 22 2016 - 23:08:44 PDT)
[AMBER] MMPBSA.PY Error :LengthError: length mismatch in energy vectors 徐明远 (Thu Jun 23 2016 - 04:07:06 PDT)
- Re: [AMBER] MMPBSA.PY Error :LengthError: length mismatch in energy vectors Daniel Roe (Thu Jun 23 2016 - 07:18:46 PDT)
[AMBER] Running pmemd.MPI across the nodes Himanshu Joshi (Thu Jun 23 2016 - 04:30:35 PDT)
- Re: [AMBER] Running pmemd.MPI across the nodes Daniel Roe (Thu Jun 23 2016 - 07:17:42 PDT)
[AMBER] MMPBSA.py nmode output problem Xiao-Lei Wang (Thu Jun 23 2016 - 05:38:00 PDT)
- Re: [AMBER] MMPBSA.py nmode output problem Daniel Roe (Thu Jun 23 2016 - 07:17:09 PDT)
  - Re: [AMBER] MMPBSA.py nmode output problem Xiao-Lei Wang (Thu Jun 23 2016 - 07:56:34 PDT)
[AMBER] measures of data reliability in Steered MD Asmita Gupta (Thu Jun 23 2016 - 07:25:30 PDT)
- Re: [AMBER] measures of data reliability in Steered MD Adrian Roitberg (Thu Jun 23 2016 - 07:27:51 PDT)
[AMBER] Error in MMPBSA Shreeramesh (Thu Jun 23 2016 - 07:50:16 PDT)
- Re: [AMBER] Error in MMPBSA Jason Swails (Thu Jun 23 2016 - 10:00:39 PDT)
[AMBER] Error in MCPB.py Fabrício Bracht (Thu Jun 23 2016 - 09:19:31 PDT)
- Re: [AMBER] Error in MCPB.py Marcelo Andrade Chagas (Thu Jun 23 2016 - 10:27:58 PDT)
  - Re: [AMBER] Error in MCPB.py Fabrício Bracht (Thu Jun 23 2016 - 10:38:27 PDT)
    - Re: [AMBER] Error in MCPB.py Pengfei Li (Thu Jun 23 2016 - 14:51:35 PDT)
[AMBER] Amber16 + GTX1080 - working well Beavil, Andrew (Thu Jun 23 2016 - 13:49:26 PDT)
- Re: [AMBER] Amber16 + GTX1080 - working well Ross Walker (Fri Jun 24 2016 - 06:11:50 PDT)
- Re: [AMBER] Amber16 + GTX1080 - working well Zack Scholl (Wed Jun 29 2016 - 12:02:25 PDT)
[AMBER] cpptraj analysis of water in cavity Michael Shokhen (Fri Jun 24 2016 - 00:58:04 PDT)
- Re: [AMBER] cpptraj analysis of water in cavity Daniel Roe (Fri Jun 24 2016 - 10:31:49 PDT)
Re: [AMBER] SHAKE Error bharat gupta (Fri Jun 24 2016 - 03:42:55 PDT)
- Re: [AMBER] SHAKE Error David A Case (Fri Jun 24 2016 - 06:38:46 PDT)
- Re: [AMBER] SHAKE Error bharat gupta (Mon Jun 27 2016 - 17:41:38 PDT)
  - Re: [AMBER] SHAKE Error David A Case (Mon Jun 27 2016 - 19:15:30 PDT)
[AMBER] HYDROGEN BONDING ANALYSIS chemjxn (Fri Jun 24 2016 - 04:35:19 PDT)
- Re: [AMBER] HYDROGEN BONDING ANALYSIS Hai Nguyen (Fri Jun 24 2016 - 07:41:38 PDT)
[AMBER] How to compare protein dynamics in free and bound-ligands states with cpptraj Kat G (Fri Jun 24 2016 - 11:38:37 PDT)
- Re: [AMBER] How to compare protein dynamics in free and bound-ligands states with cpptraj Adrian Roitberg (Fri Jun 24 2016 - 11:42:54 PDT)
[AMBER] solvent equilibration Shilpa Gupta (Sat Jun 25 2016 - 06:03:57 PDT)
- Re: [AMBER] solvent equilibration Bill Ross (Sat Jun 25 2016 - 06:08:52 PDT)
- Re: [AMBER] solvent equilibration Hector A. Baldoni (Sat Jun 25 2016 - 18:18:29 PDT)
- Re: [AMBER] solvent equilibration David A Case (Sun Jun 26 2016 - 10:38:00 PDT)
[AMBER] Fw: Ziba Bahadori (Sat Jun 25 2016 - 23:00:04 PDT)
[AMBER] Mmpbsa problem Ziba Bahadori (Sat Jun 25 2016 - 23:08:40 PDT)
[AMBER] Regarding run.rst file generation Vishal Nemaysh (Sun Jun 26 2016 - 07:10:59 PDT)
- Re: [AMBER] Regarding run.rst file generation David A Case (Sun Jun 26 2016 - 10:42:50 PDT)
Re: [AMBER] AMBER Digest, Vol 1616, Issue 1 bharat gupta (Sun Jun 26 2016 - 08:09:49 PDT)
- [AMBER] Problem with SHAKE in water molecule David A Case (Sun Jun 26 2016 - 10:53:58 PDT)
[AMBER] can we sample ligand conformation in Amber Albert (Sun Jun 26 2016 - 11:31:43 PDT)
- Re: [AMBER] can we sample ligand conformation in Amber Ilyas Yildirim (Sun Jun 26 2016 - 11:39:33 PDT)
- Re: [AMBER] can we sample ligand conformation in Amber Carlos Simmerling (Sun Jun 26 2016 - 11:45:09 PDT)
  - Re: [AMBER] can we sample ligand conformation in Amber Albert (Sun Jun 26 2016 - 11:45:41 PDT)
  - Re: [AMBER] can we sample ligand conformation in Amber Albert (Mon Jun 27 2016 - 01:13:57 PDT)
Re: [AMBER] AMBER Digest, Vol 1618, Issue 1 bharat gupta (Sun Jun 26 2016 - 18:06:36 PDT)
- Re: [AMBER] AMBER Digest, Vol 1618, Issue 1 bharat gupta (Mon Jun 27 2016 - 06:06:42 PDT)
[AMBER] Thermodynamic Integration with QM/MM Hamiltonian Xiangyu Jia (Mon Jun 27 2016 - 00:07:30 PDT)
- Re: [AMBER] Thermodynamic Integration with QM/MM Hamiltonian David A Case (Mon Jun 27 2016 - 05:07:18 PDT)
  - Re: [AMBER] Thermodynamic Integration with QM/MM Hamiltonian Xiangyu Jia (Mon Jun 27 2016 - 07:07:00 PDT)
  - Re: [AMBER] Thermodynamic Integration with QM/MM Hamiltonian Dr. Andreas W. Goetz (Mon Jun 27 2016 - 14:08:14 PDT)
[AMBER] Distorted and clumped structures after cpptraj average structure calculation Prayagraj Fandilolu (Mon Jun 27 2016 - 03:52:57 PDT)
- Re: [AMBER] Distorted and clumped structures after cpptraj average structure calculation Dr. Anselm Horn (Mon Jun 27 2016 - 04:44:15 PDT)
- Re: [AMBER] Distorted and clumped structures after cpptraj average structure calculation David A Case (Mon Jun 27 2016 - 05:10:49 PDT)
[AMBER] MCPB Fabrício Bracht (Mon Jun 27 2016 - 12:56:17 PDT)
- Re: [AMBER] MCPB Pengfei Li (Tue Jun 28 2016 - 07:33:03 PDT)
  - Re: [AMBER] MCPB Fabrício Bracht (Wed Jun 29 2016 - 09:32:57 PDT)
    - Re: [AMBER] MCPB Fabrício Bracht (Wed Jun 29 2016 - 09:50:15 PDT)
    - Re: [AMBER] MCPB Marcelo Andrade Chagas (Wed Jun 29 2016 - 09:57:35 PDT)
    - Re: [AMBER] MCPB Fabrício Bracht (Wed Jun 29 2016 - 12:00:55 PDT)
    - Re: [AMBER] MCPB Pengfei Li (Thu Jun 30 2016 - 09:42:27 PDT)
    - Re: [AMBER] MCPB Pengfei Li (Thu Jun 30 2016 - 09:51:41 PDT)
    - Re: [AMBER] MCPB Fabrício Bracht (Fri Jul 01 2016 - 16:29:58 PDT)
    - Re: [AMBER] MCPB Fabrício Bracht (Mon Jul 04 2016 - 11:49:16 PDT)
    - Re: [AMBER] MCPB Marcelo Andrade Chagas (Mon Jul 04 2016 - 13:02:54 PDT)
    - Re: [AMBER] MCPB Pengfei Li (Mon Jul 04 2016 - 16:19:57 PDT)
    - Re: [AMBER] MCPB Pengfei Li (Mon Jul 04 2016 - 20:05:39 PDT)
    - Re: [AMBER] MCPB Fabrício Bracht (Tue Jul 05 2016 - 10:16:39 PDT)
    - Re: [AMBER] MCPB Fabrício Bracht (Tue Jul 05 2016 - 10:27:37 PDT)
    - Re: [AMBER] MCPB Pengfei Li (Tue Jul 05 2016 - 18:17:54 PDT)
    - Re: [AMBER] MCPB Fabrício Bracht (Wed Jul 06 2016 - 10:51:27 PDT)
    - Re: [AMBER] MCPB Fabrício Bracht (Wed Jul 06 2016 - 12:51:37 PDT)
    - Re: [AMBER] MCPB Pengfei Li (Thu Jul 07 2016 - 13:46:35 PDT)
    - Re: [AMBER] MCPB Fabrício Bracht (Thu Jul 07 2016 - 13:53:58 PDT)
[AMBER] problem:hydrogen bonding analysis contain water molecular chemjxn (Mon Jun 27 2016 - 21:35:00 PDT)
- Re: [AMBER] problem:hydrogen bonding analysis contain water molecular Daniel Roe (Tue Jun 28 2016 - 05:32:52 PDT)
[AMBER] charge of aminoacids in an special pH Atila Petrosian (Tue Jun 28 2016 - 00:18:01 PDT)
- Re: [AMBER] charge of aminoacids in an special pH Marc van der Kamp (Tue Jun 28 2016 - 01:29:20 PDT)
Re: [AMBER] QM/MM - SCF converge error bharat gupta (Tue Jun 28 2016 - 02:12:06 PDT)
- Re: [AMBER] QM/MM - SCF converge error David A Case (Tue Jun 28 2016 - 04:35:52 PDT)
[AMBER] Hidden parameters for tleap Lea Natalia Toledo Carvajal (Tue Jun 28 2016 - 04:22:01 PDT)
- Re: [AMBER] Hidden parameters for tleap David A Case (Tue Jun 28 2016 - 07:10:19 PDT)
[AMBER] prepin to mol2 Martina Devi (Tue Jun 28 2016 - 09:37:23 PDT)
- Re: [AMBER] prepin to mol2 David A Case (Tue Jun 28 2016 - 10:18:31 PDT)
  - Re: [AMBER] prepin to mol2 FyD (Wed Jun 29 2016 - 07:38:01 PDT)
[AMBER] convert mol2 to prepin Martina Devi (Tue Jun 28 2016 - 09:40:39 PDT)
[AMBER] difference in ptraj for ambertools-12 and 15 Thakur, Abhishek (Tue Jun 28 2016 - 13:54:54 PDT)
[AMBER] Error: [cluster] Not all arguments handled: [ pdb ] Thakur, Abhishek (Tue Jun 28 2016 - 13:59:18 PDT)
- Re: [AMBER] Error: [cluster] Not all arguments handled: [ pdb ] Hai Nguyen (Tue Jun 28 2016 - 14:07:54 PDT)
  - Re: [AMBER] Error: [cluster] Not all arguments handled: [ pdb ] Thakur, Abhishek (Tue Jun 28 2016 - 14:36:32 PDT)
[AMBER] the meaning of NONBON in frcmod Zhenyu Meng (Tue Jun 28 2016 - 21:26:18 PDT)
- Re: [AMBER] the meaning of NONBON in frcmod David Cerutti (Tue Jun 28 2016 - 21:44:15 PDT)
  - Re: [AMBER] the meaning of NONBON in frcmod Zhenyu Meng (Wed Jun 29 2016 - 01:34:36 PDT)
    - Re: [AMBER] the meaning of NONBON in frcmod David Cerutti (Wed Jun 29 2016 - 02:11:06 PDT)
    - Re: [AMBER] the meaning of NONBON in frcmod David Cerutti (Wed Jun 29 2016 - 02:11:53 PDT)
    - Re: [AMBER] the meaning of NONBON in frcmod Zhenyu Meng (Wed Jun 29 2016 - 02:30:55 PDT)
    - Re: [AMBER] the meaning of NONBON in frcmod zoran matovic (Wed Jun 29 2016 - 04:12:08 PDT)
    - Re: [AMBER] the meaning of NONBON in frcmod Zhenyu Meng (Thu Jun 30 2016 - 05:07:26 PDT)
[AMBER] equilibration problem esther nehu (Tue Jun 28 2016 - 22:40:59 PDT)
- [AMBER] Fwd: equilibration problem esther nehu (Tue Jun 28 2016 - 22:41:51 PDT)
- Re: [AMBER] equilibration problem Thakur, Abhishek (Wed Jun 29 2016 - 07:27:51 PDT)
  - Re: [AMBER] equilibration problem esther nehu (Wed Jun 29 2016 - 08:07:01 PDT)
    - Re: [AMBER] equilibration problem Thakur, Abhishek (Wed Jun 29 2016 - 08:17:54 PDT)
    - Re: [AMBER] equilibration problem esther nehu (Wed Jun 29 2016 - 08:39:35 PDT)
    - Re: [AMBER] equilibration problem Thakur, Abhishek (Wed Jun 29 2016 - 09:00:09 PDT)
    - Re: [AMBER] equilibration problem esther nehu (Wed Jun 29 2016 - 09:24:05 PDT)
    - Re: [AMBER] equilibration problem Thakur, Abhishek (Wed Jun 29 2016 - 09:34:19 PDT)
    - Re: [AMBER] equilibration problem esther nehu (Wed Jun 29 2016 - 09:43:48 PDT)
[AMBER] Does Amber14 work with CUDA higher than 6.5? Karolina Markowska (Wed Jun 29 2016 - 00:25:44 PDT)
- Re: [AMBER] Does Amber14 work with CUDA higher than 6.5? Thakur, Abhishek (Wed Jun 29 2016 - 07:16:25 PDT)
  - Re: [AMBER] Does Amber14 work with CUDA higher than 6.5? Ross Walker (Wed Jun 29 2016 - 09:25:33 PDT)
    - Re: [AMBER] Does Amber14 work with CUDA higher than 6.5? Markowska (Wed Jun 29 2016 - 11:13:18 PDT)
Re: [AMBER] Slow performance of Amber12 on cluster bharat gupta (Wed Jun 29 2016 - 01:56:28 PDT)
- Re: [AMBER] Slow performance of Amber12 on cluster Gustavo Seabra (Wed Jun 29 2016 - 06:57:01 PDT)
- Re: [AMBER] Slow performance of Amber12 on cluster bharat gupta (Thu Jun 30 2016 - 22:03:14 PDT)
  - Re: [AMBER] Slow performance of Amber12 on cluster Hai Nguyen (Thu Jun 30 2016 - 22:43:47 PDT)
  - Re: [AMBER] Slow performance of Amber12 on cluster Ross Walker (Fri Jul 01 2016 - 08:03:00 PDT)
[AMBER] RMSD PLot ankita mehta (Wed Jun 29 2016 - 02:22:14 PDT)
- Re: [AMBER] RMSD PLot Gustavo Seabra (Wed Jun 29 2016 - 06:49:35 PDT)
  - Re: [AMBER] RMSD PLot Thiago Lipinski Paes (Wed Jun 29 2016 - 07:05:42 PDT)
    - Re: [AMBER] RMSD PLot ankita mehta (Wed Jun 29 2016 - 21:27:52 PDT)
    - Re: [AMBER] RMSD PLot Hai Nguyen (Wed Jun 29 2016 - 22:55:36 PDT)
[AMBER] Using Gromcas trajectories with CPPTRAJ anu chandra (Wed Jun 29 2016 - 02:57:01 PDT)
- Re: [AMBER] Using Gromcas trajectories with CPPTRAJ Daniel Roe (Wed Jun 29 2016 - 07:12:15 PDT)
  - Re: [AMBER] Using Gromcas trajectories with CPPTRAJ Nhai (Wed Jun 29 2016 - 09:58:56 PDT)
Re: [AMBER] 9. Hidden parameters for tleap Lea Natalia Toledo Carvajal (Wed Jun 29 2016 - 03:09:26 PDT)
- Re: [AMBER] 9. Hidden parameters for tleap David A Case (Thu Jun 30 2016 - 05:29:52 PDT)
[AMBER] TIP3PFBOX: water model Shilpa Gupta (Wed Jun 29 2016 - 05:32:49 PDT)
- Re: [AMBER] TIP3PFBOX: water model Thakur, Abhishek (Wed Jun 29 2016 - 07:12:23 PDT)
- Re: [AMBER] TIP3PFBOX: water model Christina Bergonzo (Wed Jun 29 2016 - 07:21:51 PDT)
[AMBER] Advice for Implicit Solvent MD with Nucleic Acids Kasprzak, Wojciech (NIH/NCI) [C] (Wed Jun 29 2016 - 07:22:16 PDT)
- Re: [AMBER] Advice for Implicit Solvent MD with Nucleic Acids Carlos Simmerling (Wed Jun 29 2016 - 07:33:21 PDT)
  - Re: [AMBER] Advice for Implicit Solvent MD with Nucleic Acids Kasprzak, Wojciech (NIH/NCI) [C] (Wed Jun 29 2016 - 08:04:16 PDT)
    - Re: [AMBER] Advice for Implicit Solvent MD with Nucleic Acids Carlos Simmerling (Wed Jun 29 2016 - 08:29:58 PDT)
    - Re: [AMBER] Advice for Implicit Solvent MD with Nucleic Acids Nhai (Wed Jun 29 2016 - 08:37:18 PDT)
    - Re: [AMBER] Advice for Implicit Solvent MD with Nucleic Acids Kasprzak, Wojciech (NIH/NCI) [C] (Wed Jun 29 2016 - 08:47:45 PDT)
    - Re: [AMBER] Advice for Implicit Solvent MD with Nucleic Acids Nhai (Wed Jun 29 2016 - 09:07:07 PDT)
[AMBER] Structural refinement of the protein complexed with metalo-ions James Starlight (Wed Jun 29 2016 - 07:39:21 PDT)
- Re: [AMBER] Structural refinement of the protein complexed with metalo-ions James Starlight (Thu Jun 30 2016 - 03:44:47 PDT)
  - Re: [AMBER] Structural refinement of the protein complexed withmetalo-ions zoran matovic (Thu Jun 30 2016 - 05:08:33 PDT)
  - Re: [AMBER] Structural refinement of the protein complexed with metalo-ions David A Case (Thu Jun 30 2016 - 05:13:03 PDT)
    - Re: [AMBER] Structural refinement of the protein complexed with metalo-ions James Starlight (Thu Jun 30 2016 - 06:05:03 PDT)
    - Re: [AMBER] Structural refinement of the protein complexed with metalo-ions Pengfei Li (Thu Jun 30 2016 - 09:20:42 PDT)
    - Re: [AMBER] Structural refinement of the protein complexed with metalo-ions James Starlight (Fri Jul 01 2016 - 01:37:14 PDT)
    - Re: [AMBER] Structural refinement of the protein complexed with metalo-ions Pengfei Li (Fri Jul 01 2016 - 08:51:07 PDT)
    - Re: [AMBER] Structural refinement of the protein complexed with metalo-ions James Starlight (Mon Jul 04 2016 - 04:39:50 PDT)
[AMBER] convert mol2 to pdb Martina Devi (Wed Jun 29 2016 - 07:57:36 PDT)
- Re: [AMBER] convert mol2 to pdb Hai Nguyen (Wed Jun 29 2016 - 08:02:46 PDT)
  - Re: [AMBER] convert mol2 to pdb Martina Devi (Wed Jun 29 2016 - 08:04:56 PDT)
    - Re: [AMBER] convert mol2 to pdb Gerald Monard (Wed Jun 29 2016 - 08:08:39 PDT)
    - Re: [AMBER] convert mol2 to pdb Hai Nguyen (Wed Jun 29 2016 - 08:15:12 PDT)
    - Re: [AMBER] convert mol2 to pdb Martina Devi (Wed Jun 29 2016 - 08:24:40 PDT)
    - Re: [AMBER] convert mol2 to pdb FyD (Wed Jun 29 2016 - 23:27:26 PDT)
    - Re: [AMBER] convert mol2 to pdb Hai Nguyen (Wed Jun 29 2016 - 23:56:56 PDT)
- Re: [AMBER] convert mol2 to pdb FyD (Wed Jun 29 2016 - 23:22:27 PDT)
[AMBER] Ambertools16 error compiling Esteban Gabriel Vega Hissi (Wed Jun 29 2016 - 10:43:36 PDT)
- Re: [AMBER] Ambertools16 error compiling Hai Nguyen (Wed Jun 29 2016 - 10:56:48 PDT)
[AMBER] Library errors while using NAB on Amber16 Slava Chushak (Wed Jun 29 2016 - 12:01:04 PDT)
- Re: [AMBER] Library errors while using NAB on Amber16 David A Case (Wed Jun 29 2016 - 18:53:19 PDT)
- Re: [AMBER] Library errors while using NAB on Amber16 Slava Chushak (Fri Jul 08 2016 - 07:15:55 PDT)
  - Re: [AMBER] Library errors while using NAB on Amber16 David A Case (Fri Jul 08 2016 - 13:22:49 PDT)
- Re: [AMBER] Library errors while using NAB on Amber16 Slava Chushak (Mon Jul 11 2016 - 07:22:52 PDT)
[AMBER] cutoff and switching Bisignano, Paola (Wed Jun 29 2016 - 17:24:15 PDT)
- Re: [AMBER] cutoff and switching Ross Walker (Wed Jun 29 2016 - 17:48:20 PDT)
  - Re: [AMBER] cutoff and switching Bisignano, Paola (Wed Jun 29 2016 - 17:59:56 PDT)
  - Re: [AMBER] cutoff and switching Bisignano, Paola (Wed Jun 29 2016 - 18:00:40 PDT)
[AMBER] adding missing ligand records to $AMBERHOME/dat/reduce_wwPDB_het_dict.txt Jose Manuel Gally (Thu Jun 30 2016 - 00:48:14 PDT)
- Re: [AMBER] adding missing ligand records to $AMBERHOME/dat/reduce_wwPDB_het_dict.txt David A Case (Thu Jun 30 2016 - 05:25:49 PDT)
  - Re: [AMBER] adding missing ligand records to $AMBERHOME/dat/reduce_wwPDB_het_dict.txt Jose Manuel (Sat Jul 02 2016 - 01:46:09 PDT)
    - Re: [AMBER] adding missing ligand records to $AMBERHOME/dat/reduce_wwPDB_het_dict.txt David A Case (Sat Jul 02 2016 - 04:58:41 PDT)
[AMBER] compiling reduce with gcc6 David A Case (Thu Jun 30 2016 - 05:45:07 PDT)
[AMBER] one more point about gcc6 David A Case (Thu Jun 30 2016 - 06:06:24 PDT)
[AMBER] addAtomType problem Lea Natalia Toledo Carvajal (Thu Jun 30 2016 - 08:58:49 PDT)
- Re: [AMBER] addAtomType problem zoran matovic (Thu Jun 30 2016 - 10:00:32 PDT)
- Re: [AMBER] addAtomType problem David A Case (Sat Jul 02 2016 - 05:55:16 PDT)
- Re: [AMBER] addAtomType problem Lea Natalia Toledo Carvajal (Fri Jul 08 2016 - 15:18:25 PDT)
[AMBER] how to calculate the correlation function for first water shell? Parviz Seifpanahi Shabane (Thu Jun 30 2016 - 09:20:10 PDT)
- Re: [AMBER] how to calculate the correlation function for first water shell? Hai Nguyen (Thu Jun 30 2016 - 19:29:19 PDT)
[AMBER] Regarding ho parameter in gaff MOHD HOMAIDUR RAHMAN (Thu Jun 30 2016 - 11:01:35 PDT)
- Re: [AMBER] Regarding ho parameter in gaff David A Case (Sat Jul 02 2016 - 05:51:11 PDT)
[AMBER] GB-neck2 MD with nucleic acids Kasprzak, Wojciech (NIH/NCI) [C] (Thu Jun 30 2016 - 11:29:48 PDT)
- Re: [AMBER] GB-neck2 MD with nucleic acids Hai Nguyen (Thu Jun 30 2016 - 11:48:00 PDT)
  - Re: [AMBER] GB-neck2 MD with nucleic acids Kasprzak, Wojciech (NIH/NCI) [C] (Thu Jun 30 2016 - 12:09:59 PDT)
    - Re: [AMBER] GB-neck2 MD with nucleic acids Hai Nguyen (Thu Jun 30 2016 - 12:23:39 PDT)
- Re: [AMBER] GB-neck2 MD with nucleic acids Carlos Simmerling (Thu Jun 30 2016 - 12:02:46 PDT)
[AMBER] bad atom type decomp Bruno Falcone (Thu Jun 30 2016 - 11:33:39 PDT)
- Re: [AMBER] bad atom type decomp Hai Nguyen (Thu Jun 30 2016 - 19:12:33 PDT)
  - Re: [AMBER] bad atom type decomp Bruno Falcone (Thu Jun 30 2016 - 20:45:48 PDT)
    - Re: [AMBER] bad atom type decomp Bruno Falcone (Tue Jul 05 2016 - 07:04:21 PDT)
    - Re: [AMBER] bad atom type decomp Jason Swails (Tue Jul 05 2016 - 11:27:55 PDT)
Re: [AMBER] Progress with testing GB-neck2 MD with nucleic acids Kasprzak, Wojciech (NIH/NCI) [C] (Thu Jun 30 2016 - 13:16:19 PDT)
- Re: [AMBER] Progress with testing GB-neck2 MD with nucleic acids Hai Nguyen (Thu Jun 30 2016 - 13:48:16 PDT)
  - Re: [AMBER] Progress with testing GB-neck2 MD with nucleic acids Carlos Simmerling (Thu Jun 30 2016 - 17:27:17 PDT)
[AMBER] cpptraj.hbond: water in the complex chemjxn (Thu Jun 30 2016 - 18:10:42 PDT)
- Re: [AMBER] cpptraj.hbond: water in the complex Daniel Roe (Fri Jul 01 2016 - 10:37:12 PDT)
[AMBER] Help: make test fails during parallel amber installation Dr. M. K. Yadav (Thu Jun 30 2016 - 20:52:03 PDT)
- Re: [AMBER] Help: make test fails during parallel amber installation Hai Nguyen (Thu Jun 30 2016 - 22:34:47 PDT)
[AMBER] Regarding GIST calculation ATUL KUMAR (Thu Jun 30 2016 - 22:51:58 PDT)
- Re: [AMBER] Regarding GIST calculation Steven Ramsey (Fri Jul 01 2016 - 07:12:03 PDT)
[AMBER] can MCPB build non amino-acid containing complex? Zhenyu Meng (Fri Jul 01 2016 - 05:37:26 PDT)
- Re: [AMBER] can MCPB build non amino-acid containing complex? zoran matovic (Fri Jul 01 2016 - 08:13:32 PDT)
  - Re: [AMBER] can MCPB build non amino-acid containing complex? Pengfei Li (Fri Jul 01 2016 - 08:54:08 PDT)
    - Re: [AMBER] can MCPB build non amino-acid containing complex? Zhenyu Meng (Sat Jul 02 2016 - 06:49:56 PDT)
  - Re: [AMBER] can MCPB build non amino-acid containing complex? Zhenyu Meng (Sat Jul 02 2016 - 03:02:03 PDT)
[AMBER] MMPBSA -O: command not found Thakur, Abhishek (Fri Jul 01 2016 - 12:58:38 PDT)
- Re: [AMBER] MMPBSA -O: command not found Hai Nguyen (Fri Jul 01 2016 - 13:17:11 PDT)
  - Re: [AMBER] MMPBSA -O: command not found Thakur, Abhishek (Fri Jul 01 2016 - 13:26:51 PDT)
- Re: [AMBER] MMPBSA -O: command not found David A Case (Sat Jul 02 2016 - 04:50:23 PDT)
[AMBER] convert amber topology and coordinates files into gromacs topology Ming Tang (Sun Jul 03 2016 - 17:27:47 PDT)
- Re: [AMBER] convert amber topology and coordinates files into gromacs topology Jason Swails (Sun Jul 03 2016 - 19:57:49 PDT)
- Re: [AMBER] convert amber topology and coordinates files into gromacs topology Ming Tang (Thu Jul 07 2016 - 19:06:57 PDT)
  - Re: [AMBER] convert amber topology and coordinates files into gromacs topology Ming Tang (Thu Jul 07 2016 - 19:21:35 PDT)
  - Re: [AMBER] convert amber topology and coordinates files into gromacs topology David A Case (Thu Jul 07 2016 - 20:45:20 PDT)
[AMBER] Lipid14 with ntr=1 Himanshu Joshi (Mon Jul 04 2016 - 00:17:39 PDT)
- Re: [AMBER] Lipid14 with ntr=1 Himanshu Joshi (Sat Jul 09 2016 - 12:49:24 PDT)
[AMBER] ParmEd Neha Gandhi (Mon Jul 04 2016 - 01:26:46 PDT)
- Re: [AMBER] ParmEd Hai Nguyen (Mon Jul 04 2016 - 08:34:12 PDT)
  - Re: [AMBER] ParmEd Neha Gandhi (Mon Jul 04 2016 - 18:10:04 PDT)
- Re: [AMBER] ParmEd Jason Swails (Mon Jul 04 2016 - 18:50:43 PDT)
  - Re: [AMBER] ParmEd Neha Gandhi (Mon Jul 04 2016 - 19:09:06 PDT)
    - Re: [AMBER] ParmEd Daniel Roe (Mon Jul 04 2016 - 19:22:01 PDT)
    - Re: [AMBER] ParmEd Jason Swails (Mon Jul 04 2016 - 19:30:16 PDT)
    - Re: [AMBER] ParmEd Neha Gandhi (Mon Jul 04 2016 - 20:37:26 PDT)
[AMBER] Ambertool16 - MCPB.py angle cut off and Error with Pdbsearcher.py Bilal Nizami (Mon Jul 04 2016 - 01:39:33 PDT)
- Re: [AMBER] Ambertool16 - MCPB.py angle cut off and Error with Pdbsearcher.py Pengfei Li (Tue Jul 05 2016 - 18:30:50 PDT)
  - Re: [AMBER] Ambertool16 - MCPB.py angle cut off and Error with Pdbsearcher.py Bilal Nizami (Wed Jul 06 2016 - 05:37:19 PDT)
    - Re: [AMBER] Ambertool16 - MCPB.py angle cut off and Error with Pdbsearcher.py Pengfei Li (Sat Jul 09 2016 - 14:30:09 PDT)
[AMBER] Question about Charge derivation for GLYCAM force field Casalini Tommaso (Mon Jul 04 2016 - 07:03:00 PDT)
- Re: [AMBER] Question about Charge derivation for GLYCAM force field Lachele Foley (Mon Jul 04 2016 - 22:44:00 PDT)
[AMBER] Potential on each atom Elisa Pieri (Mon Jul 04 2016 - 07:43:20 PDT)
- Re: [AMBER] Potential on each atom Adrian Roitberg (Mon Jul 04 2016 - 09:23:33 PDT)
  - Re: [AMBER] Potential on each atom Elisa Pieri (Tue Jul 05 2016 - 09:20:24 PDT)
    - Re: [AMBER] Potential on each atom Jason Swails (Tue Jul 05 2016 - 11:17:49 PDT)
    - Re: [AMBER] Potential on each atom Adrian Roitberg (Tue Jul 05 2016 - 11:21:39 PDT)
    - Re: [AMBER] Potential on each atom Elisa Pieri (Wed Jul 06 2016 - 07:17:51 PDT)
    - Re: [AMBER] Potential on each atom Jason Swails (Wed Jul 06 2016 - 07:38:05 PDT)
  - Re: [AMBER] Potential on each atom Elisa Pieri (Wed Jul 06 2016 - 02:11:55 PDT)
[AMBER] SMD at constant force Ming Tang (Mon Jul 04 2016 - 19:06:25 PDT)
- Re: [AMBER] SMD at constant force Jason Swails (Mon Jul 04 2016 - 19:34:12 PDT)
- Re: [AMBER] SMD at constant force Ming Tang (Thu Jul 21 2016 - 04:01:19 PDT)
[AMBER] MCPB.py cannot recognize Cl Zhenyu Meng (Mon Jul 04 2016 - 20:00:11 PDT)
- Re: [AMBER] MCPB.py cannot recognize Cl Pengfei Li (Mon Jul 04 2016 - 20:07:43 PDT)
  - Re: [AMBER] MCPB.py cannot recognize Cl Zhenyu Meng (Mon Jul 04 2016 - 20:14:32 PDT)
    - Re: [AMBER] MCPB.py cannot recognize Cl Pengfei Li (Mon Jul 04 2016 - 20:17:21 PDT)
    - Re: [AMBER] MCPB.py cannot recognize Cl Zhenyu Meng (Mon Jul 04 2016 - 20:23:43 PDT)
    - Re: [AMBER] MCPB.py cannot recognize Cl Zhenyu Meng (Mon Jul 04 2016 - 20:38:31 PDT)
    - Re: [AMBER] MCPB.py cannot recognize Cl zoran matovic (Mon Jul 04 2016 - 23:12:58 PDT)
    - Re: [AMBER] MCPB.py cannot recognize Cl Zhenyu Meng (Mon Jul 04 2016 - 23:29:43 PDT)
    - Re: [AMBER] MCPB.py cannot recognize Cl Pengfei Li (Tue Jul 05 2016 - 18:21:11 PDT)
    - Re: [AMBER] MCPB.py cannot recognize Cl Zhenyu Meng (Fri Jul 08 2016 - 00:22:47 PDT)
    - Re: [AMBER] MCPB.py cannot recognize Cl zoran matovic (Fri Jul 08 2016 - 01:16:13 PDT)
    - Re: [AMBER] MCPB.py cannot recognize Cl Zhenyu Meng (Fri Jul 08 2016 - 01:55:21 PDT)
    - Re: [AMBER] MCPB.py cannot recognize Cl zoran matovic (Fri Jul 08 2016 - 02:06:05 PDT)
    - Re: [AMBER] MCPB.py cannot recognize Cl zoran matovic (Fri Jul 08 2016 - 02:10:08 PDT)
    - Re: [AMBER] MCPB.py cannot recognize Cl Pengfei Li (Sat Jul 09 2016 - 08:50:56 PDT)
    - Re: [AMBER] MCPB.py cannot recognize Cl Zhenyu Meng (Mon Jul 11 2016 - 01:16:20 PDT)
    - Re: [AMBER] MCPB.py cannot recognize Cl Pengfei Li (Mon Jul 11 2016 - 12:18:19 PDT)
- Re: [AMBER] MCPB.py cannot recognize Cl zoran matovic (Mon Jul 04 2016 - 23:37:28 PDT)
  - Re: [AMBER] MCPB.py cannot recognize Cl Zhenyu Meng (Mon Jul 04 2016 - 23:44:08 PDT)
[AMBER] iwrap=0 Ming Tang (Tue Jul 05 2016 - 04:25:13 PDT)
- Re: [AMBER] iwrap=0 Daniel Roe (Tue Jul 05 2016 - 04:56:49 PDT)
Re: [AMBER] Error during amber 12 installation bharat gupta (Tue Jul 05 2016 - 06:07:37 PDT)
- Re: [AMBER] Error during amber 12 installation Daniel Roe (Tue Jul 05 2016 - 06:38:04 PDT)
Re: [AMBER] Help with Umbrella Sampling bharat gupta (Tue Jul 05 2016 - 22:31:57 PDT)
[AMBER] Amber12 or lated on POWER8 platform Sanman Sabane (Wed Jul 06 2016 - 03:22:40 PDT)
- Re: [AMBER] Amber12 or lated on POWER8 platform Jason Swails (Wed Jul 06 2016 - 05:50:54 PDT)
[AMBER] Problem to extending Simulation ATUL KUMAR (Wed Jul 06 2016 - 04:38:16 PDT)
- Re: [AMBER] Problem to extending Simulation Jason Swails (Wed Jul 06 2016 - 05:53:00 PDT)
  - Re: [AMBER] Problem to extending Simulation ATUL KUMAR (Wed Jul 06 2016 - 06:43:27 PDT)
    - Re: [AMBER] Problem to extending Simulation Daniel Roe (Wed Jul 06 2016 - 08:32:18 PDT)
    - Re: [AMBER] Problem to extending Simulation ATUL KUMAR (Wed Jul 06 2016 - 23:23:27 PDT)
    - Re: [AMBER] Problem to extending Simulation Bill Ross (Thu Jul 07 2016 - 01:37:41 PDT)
    - Re: [AMBER] Problem to extending Simulation David A Case (Thu Jul 07 2016 - 05:43:22 PDT)
[AMBER] Multiplicity in antechamber Fabrício Bracht (Wed Jul 06 2016 - 11:22:44 PDT)
- Re: [AMBER] Multiplicity in antechamber Jason Swails (Wed Jul 06 2016 - 13:35:12 PDT)
[AMBER] Amber16 tutorials Corum, Katharine W (Wed Jul 06 2016 - 14:07:01 PDT)
- Re: [AMBER] Amber16 tutorials Corum, Katharine W (Wed Jul 06 2016 - 14:11:37 PDT)
- Re: [AMBER] Amber16 tutorials Hai Nguyen (Wed Jul 06 2016 - 14:14:49 PDT)
  - Re: [AMBER] Amber16 tutorials Corum, Katharine W (Wed Jul 06 2016 - 14:16:06 PDT)
    - Re: [AMBER] Amber16 tutorials Corum, Katharine W (Thu Jul 07 2016 - 07:43:36 PDT)
    - Re: [AMBER] Amber16 tutorials Hirdesh Kumar (Thu Jul 07 2016 - 07:52:20 PDT)
    - Re: [AMBER] Amber16 tutorials Corum, Katharine W (Thu Jul 07 2016 - 07:54:12 PDT)
    - Re: [AMBER] Amber16 tutorials Daniel Roe (Thu Jul 07 2016 - 08:03:53 PDT)
    - Re: [AMBER] Amber16 tutorials Corum, Katharine W (Thu Jul 07 2016 - 08:13:15 PDT)
    - Re: [AMBER] Amber16 tutorials Hai Nguyen (Thu Jul 07 2016 - 08:20:39 PDT)
    - Re: [AMBER] Amber16 tutorials Daniel Roe (Thu Jul 07 2016 - 08:23:46 PDT)
    - Re: [AMBER] Amber16 tutorials Corum, Katharine W (Thu Jul 07 2016 - 08:26:02 PDT)
[AMBER] DPPC simulation temperature gsottile.unq.edu.ar (Wed Jul 06 2016 - 14:15:35 PDT)
[AMBER] Question on SMD Ming Tang (Wed Jul 06 2016 - 14:46:02 PDT)
[AMBER] Query on SMD Ming Tang (Wed Jul 06 2016 - 14:49:02 PDT)
[AMBER] A question on SMD simulations Ming Tang (Wed Jul 06 2016 - 14:59:42 PDT)
- Re: [AMBER] A question on SMD simulations Hai Nguyen (Wed Jul 06 2016 - 15:11:21 PDT)
[AMBER] Stuck somewhere using antechamber Xiaoyu Wang (Wed Jul 06 2016 - 16:00:37 PDT)
- Re: [AMBER] Stuck somewhere using antechamber Hai Nguyen (Wed Jul 06 2016 - 16:03:56 PDT)
- Re: [AMBER] Stuck somewhere using antechamber David A Case (Thu Jul 07 2016 - 05:40:13 PDT)
Re: [AMBER] Defining reaction coordinate for US bharat gupta (Thu Jul 07 2016 - 01:38:33 PDT)
[AMBER] Gunning GIST in parallel ATUL KUMAR (Thu Jul 07 2016 - 03:05:07 PDT)
- Re: [AMBER] Gunning GIST in parallel Daniel Roe (Thu Jul 07 2016 - 08:04:56 PDT)
[AMBER] An attempt for TI with QM/MM Hamiltonian Xiangyu Jia (Thu Jul 07 2016 - 06:13:51 PDT)
[AMBER] VMD Thakur, Abhishek (Thu Jul 07 2016 - 09:44:53 PDT)
- Re: [AMBER] VMD Daniel Roe (Thu Jul 07 2016 - 09:48:08 PDT)
- Re: [AMBER] VMD Nhai (Thu Jul 07 2016 - 09:57:02 PDT)
[AMBER] Calculating lipid diffusion using stfcdiffusion Amy Rice (Thu Jul 07 2016 - 10:49:07 PDT)
- Re: [AMBER] Calculating lipid diffusion using stfcdiffusion Amy Rice (Thu Jul 14 2016 - 09:13:57 PDT)
  - Re: [AMBER] Calculating lipid diffusion using stfcdiffusion Dickson, Callum J (Mon Jul 18 2016 - 13:25:17 PDT)
- Re: [AMBER] Calculating lipid diffusion using stfcdiffusion Daniel Roe (Tue Jul 19 2016 - 08:26:01 PDT)
  - Re: [AMBER] Calculating lipid diffusion using stfcdiffusion Amy Rice (Wed Jul 20 2016 - 11:34:14 PDT)
    - Re: [AMBER] Calculating lipid diffusion using stfcdiffusion Amy Rice (Wed Jul 20 2016 - 11:57:32 PDT)
    - Re: [AMBER] Calculating lipid diffusion using stfcdiffusion Dickson, Callum J (Wed Jul 20 2016 - 14:25:40 PDT)
    - Re: [AMBER] Calculating lipid diffusion using stfcdiffusion Amy Rice (Mon Jul 25 2016 - 09:24:04 PDT)
    - Re: [AMBER] Calculating lipid diffusion using stfcdiffusion Dickson, Callum J (Mon Jul 25 2016 - 13:14:42 PDT)
    - Re: [AMBER] Calculating lipid diffusion using stfcdiffusion Daniel Roe (Tue Jul 26 2016 - 12:53:14 PDT)
    - Re: [AMBER] Calculating lipid diffusion using stfcdiffusion Daniel Roe (Thu Jul 28 2016 - 13:21:23 PDT)
    - Re: [AMBER] Calculating lipid diffusion using stfcdiffusion Amy Rice (Mon Aug 01 2016 - 12:06:53 PDT)
    - Re: [AMBER] Calculating lipid diffusion using stfcdiffusion Daniel Roe (Mon Aug 01 2016 - 12:24:37 PDT)
    - Re: [AMBER] Calculating lipid diffusion using stfcdiffusion Amy Rice (Mon Aug 01 2016 - 12:35:03 PDT)
[AMBER] GLYCAM naming Fabrício Bracht (Thu Jul 07 2016 - 11:56:05 PDT)
- Re: [AMBER] GLYCAM naming Lachele Foley (Thu Jul 07 2016 - 12:45:13 PDT)
[AMBER] QM/MM issue Morteza Chehel Amirani (Thu Jul 07 2016 - 14:13:10 PDT)
- Re: [AMBER] QM/MM issue Dr. Andreas W. Goetz (Thu Jul 07 2016 - 21:41:22 PDT)
[AMBER] QM/MM simulations with Amber/deMon2k Morteza Chehel Amirani (Thu Jul 07 2016 - 14:19:53 PDT)
- Re: [AMBER] QM/MM simulations with Amber/deMon2k Andreas Goetz (Thu Jul 07 2016 - 21:04:52 PDT)
- Re: [AMBER] QM/MM simulations with Amber/deMon2k Joan Torras (Thu Jul 07 2016 - 23:18:29 PDT)
Re: [AMBER] Patching Plumed 1.3 with Amber12 bharat gupta (Thu Jul 07 2016 - 18:04:39 PDT)
[AMBER] rmsd plot error Saman Yousuf ali (Fri Jul 08 2016 - 03:55:51 PDT)
- Re: [AMBER] rmsd plot error zoran matovic (Fri Jul 08 2016 - 04:17:00 PDT)
  - Re: [AMBER] rmsd plot error Saman Yousuf ali (Fri Jul 08 2016 - 04:42:08 PDT)
    - Re: [AMBER] rmsd plot error Vlad Cojocaru (Fri Jul 08 2016 - 05:17:23 PDT)
    - Re: [AMBER] rmsd plot error Saman Yousuf ali (Fri Jul 08 2016 - 05:28:28 PDT)
    - Re: [AMBER] rmsd plot error Vlad Cojocaru (Fri Jul 08 2016 - 05:47:48 PDT)
    - Re: [AMBER] rmsd plot error Saman Yousuf ali (Fri Jul 08 2016 - 05:58:19 PDT)
    - Re: [AMBER] rmsd plot error zoran matovic (Fri Jul 08 2016 - 07:13:07 PDT)
    - Re: [AMBER] rmsd plot error Vlad Cojocaru (Fri Jul 08 2016 - 07:29:45 PDT)
    - Re: [AMBER] rmsd plot error zoran matovic (Fri Jul 08 2016 - 07:48:24 PDT)
    - Re: [AMBER] rmsd plot error Vlad Cojocaru (Fri Jul 08 2016 - 08:17:34 PDT)
    - Re: [AMBER] rmsd plot error Daniel Roe (Fri Jul 08 2016 - 07:47:46 PDT)
[AMBER] how to fix COM of a group of atoms? Ming Tang (Fri Jul 08 2016 - 06:01:05 PDT)
- Re: [AMBER] how to fix COM of a group of atoms? Himanshu Joshi (Sat Jul 09 2016 - 22:02:10 PDT)
  - Re: [AMBER] how to fix COM of a group of atoms? Ming Tang (Sun Jul 10 2016 - 17:45:19 PDT)
    - Re: [AMBER] how to fix COM of a group of atoms? Jason Swails (Mon Jul 11 2016 - 10:34:35 PDT)
    - Re: [AMBER] how to fix COM of a group of atoms? Thakur, Abhishek (Mon Jul 11 2016 - 13:51:31 PDT)
    - Re: [AMBER] how to fix COM of a group of atoms? Ming Tang (Fri Jul 15 2016 - 00:03:56 PDT)
    - Re: [AMBER] how to fix COM of a group of atoms? Ming Tang (Tue Jul 19 2016 - 15:50:45 PDT)
[AMBER] MMPBSA Thakur, Abhishek (Fri Jul 08 2016 - 09:57:16 PDT)
- Re: [AMBER] MMPBSA Nhai (Fri Jul 08 2016 - 10:03:40 PDT)
  - Re: [AMBER] MMPBSA Thakur, Abhishek (Fri Jul 08 2016 - 11:02:45 PDT)
    - Re: [AMBER] MMPBSA Hai Nguyen (Fri Jul 08 2016 - 11:07:46 PDT)
    - Re: [AMBER] MMPBSA Thakur, Abhishek (Fri Jul 08 2016 - 11:20:25 PDT)
    - Re: [AMBER] MMPBSA Thakur, Abhishek (Fri Jul 08 2016 - 11:38:34 PDT)
- Re: [AMBER] MMPBSA Thakur, Abhishek (Fri Jul 08 2016 - 11:42:13 PDT)
  - Re: [AMBER] MMPBSA Daniel Roe (Fri Jul 08 2016 - 13:09:46 PDT)
    - Re: [AMBER] MMPBSA Thakur, Abhishek (Fri Jul 08 2016 - 14:14:08 PDT)
[AMBER] ligand bond distortion during MD run. Saman Yousuf ali (Fri Jul 08 2016 - 10:48:21 PDT)
- Re: [AMBER] ligand bond distortion during MD run. zoran matovic (Fri Jul 08 2016 - 11:20:04 PDT)
- Re: [AMBER] ligand bond distortion during MD run. Daniel Roe (Fri Jul 08 2016 - 13:12:26 PDT)
[AMBER] MD of an elongated active site protein. Saman Yousuf ali (Sat Jul 09 2016 - 07:58:02 PDT)
[AMBER] adding non-standard residue to RNA strand Martina Devi (Sat Jul 09 2016 - 10:21:28 PDT)
- Re: [AMBER] adding non-standard residue to RNA strand David A Case (Sat Jul 09 2016 - 15:29:41 PDT)
- Re: [AMBER] adding non-standard residue to RNA strand FyD (Tue Jul 12 2016 - 14:03:16 PDT)
[AMBER] Restrain COM of a group of atoms Ming Tang (Sat Jul 09 2016 - 18:18:11 PDT)
[AMBER] mmpbsa.py to calculate binding energy between protein and a ligand when there are two ligands combined with the protein. 朱婧涵 (Mon Jul 11 2016 - 02:19:28 PDT)
- Re: [AMBER] mmpbsa.py to calculate binding energy between protein and a ligand when there are two ligands combined with the protein. Thakur, Abhishek (Mon Jul 11 2016 - 08:50:46 PDT)
- Re: [AMBER] mmpbsa.py to calculate binding energy between protein and a ligand when there are two ligands combined with the protein. Jason Swails (Mon Jul 11 2016 - 10:33:02 PDT)
- Re: [AMBER] mmpbsa.py to calculate binding energy between protein and a ligand when there are two ligands combined with the protein. ZHU JH (Mon Jul 11 2016 - 19:55:27 PDT)
  - Re: [AMBER] mmpbsa.py to calculate binding energy between protein and a ligand when there are two ligands combined with the protein. Jason Swails (Mon Jul 11 2016 - 20:13:12 PDT)
    - Re: [AMBER] mmpbsa.py to calculate binding energy between protein and a ligand when there are two ligands combined with the protein. Thakur, Abhishek (Mon Jul 11 2016 - 21:21:20 PDT)
    - Re: [AMBER] mmpbsa.py to calculate binding energy between protein and a ligand when there are two ligands combined with the protein. Hai Nguyen (Mon Jul 11 2016 - 21:36:02 PDT)
    - Re: [AMBER] mmpbsa.py to calculate binding energy between protein and a ligand when there are two ligands combined with the protein. Hai Nguyen (Mon Jul 11 2016 - 21:56:28 PDT)
[AMBER] predicting RDCs for un-restrained bonds Thomas Pochapsky (Mon Jul 11 2016 - 06:23:03 PDT)
- Re: [AMBER] predicting RDCs for un-restrained bonds David A Case (Mon Jul 11 2016 - 18:36:38 PDT)
  - Re: [AMBER] predicting RDCs for un-restrained bonds Thomas Pochapsky (Tue Jul 12 2016 - 05:36:35 PDT)
[AMBER] Steered Molecular Dynamics Fair, Ryan (Mon Jul 11 2016 - 09:05:38 PDT)
- Re: [AMBER] Steered Molecular Dynamics bharat gupta (Mon Jul 25 2016 - 00:00:26 PDT)
  - Re: [AMBER] Steered Molecular Dynamics Adrian Roitberg (Mon Jul 25 2016 - 00:06:11 PDT)
[AMBER] MMPBSA Thakur, Abhishek (Mon Jul 11 2016 - 13:31:32 PDT)
- Re: [AMBER] MMPBSA Hai Nguyen (Mon Jul 11 2016 - 13:41:40 PDT)
  - Re: [AMBER] MMPBSA Thakur, Abhishek (Mon Jul 11 2016 - 13:46:54 PDT)
    - Re: [AMBER] MMPBSA Hai Nguyen (Mon Jul 11 2016 - 13:49:37 PDT)
    - Re: [AMBER] MMPBSA Thakur, Abhishek (Mon Jul 11 2016 - 13:53:27 PDT)
    - Re: [AMBER] MMPBSA Hai Nguyen (Mon Jul 11 2016 - 13:57:53 PDT)
    - Re: [AMBER] MMPBSA Thakur, Abhishek (Mon Jul 11 2016 - 14:33:41 PDT)
[AMBER] rism1d convergence for solvent mixtures Shijie Sheng (Mon Jul 11 2016 - 16:30:42 PDT)
- Re: [AMBER] rism1d convergence for solvent mixtures Tyler Luchko (Lists) (Mon Jul 11 2016 - 19:18:25 PDT)
  - Re: [AMBER] rism1d convergence for solvent mixtures sshen004.ucr.edu (Mon Jul 11 2016 - 19:32:55 PDT)
Re: [AMBER] Help with SMD bharat gupta (Tue Jul 12 2016 - 01:02:31 PDT)
- Re: [AMBER] Help with SMD Feng Pan (Tue Jul 12 2016 - 10:21:08 PDT)
[AMBER] QM/MM problems with Amber/Gaussian Allen Zou (Tue Jul 12 2016 - 08:11:25 PDT)
- Re: [AMBER] QM/MM problems with Amber/Gaussian Adrian Roitberg (Tue Jul 12 2016 - 08:17:23 PDT)
[AMBER] Born Mayer Potential Vivien Ramothe (Tue Jul 12 2016 - 08:36:22 PDT)
- Re: [AMBER] Born Mayer Potential Hai Nguyen (Tue Jul 12 2016 - 09:53:57 PDT)
- Re: [AMBER] Born Mayer Potential David A Case (Tue Jul 12 2016 - 18:37:30 PDT)
  - Re: [AMBER] Born Mayer Potential Jason Swails (Tue Jul 12 2016 - 19:28:25 PDT)
[AMBER] Decomposition in minimization step Atila Petrosian (Tue Jul 12 2016 - 23:14:57 PDT)
- Re: [AMBER] Decomposition in minimization step Daniel Roe (Wed Jul 13 2016 - 07:22:10 PDT)
[AMBER] strategies to speed up MM/GBSA screening Thomas Evangelidis (Wed Jul 13 2016 - 04:08:31 PDT)
- Re: [AMBER] strategies to speed up MM/GBSA screening Jason Swails (Wed Jul 13 2016 - 05:14:24 PDT)
  - Re: [AMBER] strategies to speed up MM/GBSA screening Thomas Evangelidis (Wed Jul 13 2016 - 16:09:31 PDT)
    - Re: [AMBER] strategies to speed up MM/GBSA screening Carlos Simmerling (Wed Jul 13 2016 - 18:23:54 PDT)
    - Re: [AMBER] strategies to speed up MM/GBSA screening Jason Swails (Wed Jul 13 2016 - 18:38:44 PDT)
    - Re: [AMBER] strategies to speed up MM/GBSA screening Thomas Evangelidis (Thu Jul 14 2016 - 07:29:12 PDT)
    - Re: [AMBER] strategies to speed up MM/GBSA screening Jason Swails (Thu Jul 14 2016 - 13:22:34 PDT)
[AMBER] a question about resp restraints strength Bahaa Mostafa (Wed Jul 13 2016 - 05:40:44 PDT)
- Re: [AMBER] a question about resp restraints strength David A Case (Thu Jul 14 2016 - 04:26:48 PDT)
  - Re: [AMBER] a question about resp restraints strength Bahaa Mostafa (Thu Jul 14 2016 - 05:56:24 PDT)
[AMBER] WHAM-2D analysis Alessandra Lacetera (Wed Jul 13 2016 - 09:55:20 PDT)
- Re: [AMBER] WHAM-2D analysis Amy Rice (Wed Jul 13 2016 - 10:02:03 PDT)
- Re: [AMBER] WHAM-2D analysis Christina Bergonzo (Wed Jul 13 2016 - 10:03:21 PDT)
- Re: [AMBER] WHAM-2D analysis Alessandra Lacetera (Thu Jul 14 2016 - 02:31:55 PDT)
[AMBER] Compute SASA through molsurf Francesco Gentile (Wed Jul 13 2016 - 15:02:21 PDT)
[AMBER] carbon nanotube Neha Gandhi (Wed Jul 13 2016 - 18:18:31 PDT)
- Re: [AMBER] carbon nanotube Carlos Simmerling (Wed Jul 13 2016 - 18:20:18 PDT)
  - Re: [AMBER] carbon nanotube Neha Gandhi (Wed Jul 13 2016 - 18:43:15 PDT)
    - Re: [AMBER] carbon nanotube Jason Swails (Wed Jul 13 2016 - 19:12:59 PDT)
    - Re: [AMBER] carbon nanotube Neha Gandhi (Wed Jul 13 2016 - 19:15:55 PDT)
    - Re: [AMBER] carbon nanotube Jason Swails (Thu Jul 14 2016 - 06:30:22 PDT)
- Re: [AMBER] carbon nanotube FyD (Fri Jul 15 2016 - 10:17:39 PDT)
[AMBER] Generating a HETATM database to use with reduce Kucharski Jr., Amir N (Wed Jul 13 2016 - 21:01:37 PDT)
- Re: [AMBER] Generating a HETATM database to use with reduce David A Case (Thu Jul 14 2016 - 17:51:23 PDT)
  - Re: [AMBER] Generating a HETATM database to use with reduce Kucharski Jr., Amir N (Thu Jul 14 2016 - 18:04:54 PDT)
    - Re: [AMBER] Generating a HETATM database to use with reduce David A Case (Fri Jul 15 2016 - 05:12:18 PDT)
    - Re: [AMBER] Generating a HETATM database to use with reduce Kucharski Jr., Amir N (Fri Jul 15 2016 - 09:51:46 PDT)
    - Re: [AMBER] Generating a HETATM database to use with reduce David A Case (Fri Jul 15 2016 - 11:30:31 PDT)
    - Re: [AMBER] Generating a HETATM database to use with reduce Kucharski Jr., Amir N (Fri Jul 15 2016 - 13:58:00 PDT)
[AMBER] ff99SB*-ildn again Neha Gandhi (Wed Jul 13 2016 - 23:47:07 PDT)
- Re: [AMBER] ff99SB*-ildn again Vlad Cojocaru (Thu Jul 14 2016 - 00:56:23 PDT)
  - Re: [AMBER] ff99SB*-ildn again Neha Gandhi (Thu Jul 14 2016 - 02:45:37 PDT)
    - Re: [AMBER] ff99SB*-ildn again Alessandro Contini (Thu Jul 14 2016 - 02:57:24 PDT)
    - Re: [AMBER] ff99SB*-ildn again Vlad Cojocaru (Thu Jul 14 2016 - 03:28:54 PDT)
    - Re: [AMBER] ff99SB*-ildn again Vlad Cojocaru (Thu Jul 14 2016 - 03:31:22 PDT)
  - Re: [AMBER] ff99SB*-ildn again Thomas Evangelidis (Thu Jul 14 2016 - 04:40:37 PDT)
    - Re: [AMBER] ff99SB*-ildn again Vlad Cojocaru (Thu Jul 14 2016 - 04:59:25 PDT)
  - Re: [AMBER] ff99SB*-ildn again Jason Swails (Thu Jul 14 2016 - 06:58:00 PDT)
    - Re: [AMBER] ff99SB*-ildn again Vlad Cojocaru (Thu Jul 14 2016 - 07:45:45 PDT)
- Re: [AMBER] ff99SB*-ildn again David A Case (Thu Jul 14 2016 - 04:50:28 PDT)
  - Re: [AMBER] ff99SB*-ildn again Vlad Cojocaru (Thu Jul 14 2016 - 05:03:27 PDT)
    - Re: [AMBER] ff99SB*-ildn again Neha Gandhi (Thu Jul 14 2016 - 05:10:15 PDT)
    - Re: [AMBER] ff99SB*-ildn again Vlad Cojocaru (Thu Jul 14 2016 - 05:21:29 PDT)
[AMBER] Is the surf or the molsurf calculate the protein surface? windy (Thu Jul 14 2016 - 01:44:08 PDT)
[AMBER] NEW parameters with AMBER Anna Cebrian Prats (Thu Jul 14 2016 - 02:55:16 PDT)
- Re: [AMBER] NEW parameters with AMBER David A Case (Thu Jul 14 2016 - 04:59:06 PDT)
  - Re: [AMBER] NEW parameters with AMBER Anna Cebrian Prats (Thu Jul 14 2016 - 06:52:43 PDT)
[AMBER] a question about resp restraints strength Bahaa Mostafa (Thu Jul 14 2016 - 04:04:13 PDT)
- Re: [AMBER] a question about resp restraints strength FyD (Fri Jul 15 2016 - 10:22:13 PDT)
  - Re: [AMBER] a question about resp restraints strength Bahaa Mostafa (Sat Jul 16 2016 - 09:43:55 PDT)
[AMBER] a question about resp restraints strength Bahaa Mostafa (Thu Jul 14 2016 - 04:10:27 PDT)
[AMBER] Problem with Gaussian09 with B97D/def2TZVPPD basis set from EMSL Indrajit Deb (Thu Jul 14 2016 - 05:55:07 PDT)
- Re: [AMBER] Problem with Gaussian09 with B97D/def2TZVPPD basis set fromEMSL zoran matovic (Thu Jul 14 2016 - 06:22:32 PDT)
[AMBER] RMSD plot query esther nehu (Thu Jul 14 2016 - 07:29:41 PDT)
- Re: [AMBER] RMSD plot query Hai Nguyen (Thu Jul 14 2016 - 07:57:10 PDT)
[AMBER] Is the surf or the molsurf calculate the protein surface? windy (Thu Jul 14 2016 - 19:08:02 PDT)
- Re: [AMBER] Is the surf or the molsurf calculate the protein surface? David A Case (Sun Jul 17 2016 - 04:27:27 PDT)
[AMBER] REMD Reg Annie Ancy (Fri Jul 15 2016 - 04:23:18 PDT)
- Re: [AMBER] REMD Reg Hai Nguyen (Mon Jul 18 2016 - 20:33:22 PDT)
[AMBER] MMPBSA.py for complex or receptor or ligand only Bruno Falcone (Fri Jul 15 2016 - 07:10:17 PDT)
- Re: [AMBER] MMPBSA.py for complex or receptor or ligand only Jason Swails (Fri Jul 15 2016 - 10:53:38 PDT)
[AMBER] MMPBSA (inp=1 or inp=2)?? Thakur, Abhishek (Fri Jul 15 2016 - 08:53:44 PDT)
- Re: [AMBER] MMPBSA (inp=1 or inp=2)?? Thakur, Abhishek (Fri Jul 15 2016 - 09:16:14 PDT)
  - Re: [AMBER] MMPBSA (inp=1 or inp=2)?? Ray Luo (Fri Jul 15 2016 - 13:30:27 PDT)
- Re: [AMBER] MMPBSA (inp=1 or inp=2)?? Ray Luo (Fri Jul 15 2016 - 13:27:42 PDT)
[AMBER] HMR 4fs failure? Gerald Monard (Fri Jul 15 2016 - 12:54:29 PDT)
- Re: [AMBER] HMR 4fs failure? Hai Nguyen (Fri Jul 15 2016 - 12:56:10 PDT)
  - Re: [AMBER] HMR 4fs failure? David Cerutti (Fri Jul 15 2016 - 12:57:50 PDT)
  - Re: [AMBER] HMR 4fs failure? Gerald Monard (Fri Jul 15 2016 - 14:14:44 PDT)
    - Re: [AMBER] HMR 4fs failure? Adrian Roitberg (Fri Jul 15 2016 - 14:18:14 PDT)
    - Re: [AMBER] HMR 4fs failure? David Cerutti (Fri Jul 15 2016 - 14:53:32 PDT)
    - Re: [AMBER] HMR 4fs failure? Gerald Monard (Fri Jul 15 2016 - 15:12:48 PDT)
    - Re: [AMBER] HMR 4fs failure? Gerald Monard (Fri Jul 15 2016 - 14:56:11 PDT)
[AMBER] ff14SB compatible with Glycam_06j-1? yunshi11 . (Sat Jul 16 2016 - 03:06:13 PDT)
- Re: [AMBER] ff14SB compatible with Glycam_06j-1? David A Case (Sat Jul 16 2016 - 05:42:27 PDT)
[AMBER] Cpptraj Dd H (Sun Jul 17 2016 - 05:57:55 PDT)
- Re: [AMBER] Cpptraj Hai Nguyen (Sun Jul 17 2016 - 09:24:22 PDT)
  - Re: [AMBER] Cpptraj Hai Nguyen (Sun Jul 17 2016 - 09:25:25 PDT)
    - Re: [AMBER] Cpptraj Dd H (Sun Jul 17 2016 - 18:13:15 PDT)
    - Re: [AMBER] Cpptraj Hai Nguyen (Sun Jul 17 2016 - 22:15:12 PDT)
[AMBER] Regarding Parameter file not saved Vishal Nemaysh (Sun Jul 17 2016 - 10:52:32 PDT)
- Re: [AMBER] Regarding Parameter file not saved Hai Nguyen (Sun Jul 17 2016 - 11:15:28 PDT)
  - Re: [AMBER] Regarding Parameter file not saved Vishal Nemaysh (Mon Jul 18 2016 - 02:31:42 PDT)
    - Re: [AMBER] Regarding Parameter file not saved Vishal Nemaysh (Mon Jul 18 2016 - 03:09:37 PDT)
    - Re: [AMBER] Regarding Parameter file not saved Bilal Nizami (Mon Jul 18 2016 - 04:58:42 PDT)
    - Re: [AMBER] Regarding Parameter file not saved Aleksandra Skoric (Mon Jul 18 2016 - 06:21:31 PDT)
    - Re: [AMBER] Regarding Parameter file not saved Vishal Nemaysh (Mon Jul 18 2016 - 08:17:02 PDT)
    - Re: [AMBER] Regarding Parameter file not saved Thakur, Abhishek (Mon Jul 18 2016 - 09:06:41 PDT)
    - Re: [AMBER] Regarding Parameter file not saved Nhai (Mon Jul 18 2016 - 09:06:52 PDT)
    - Re: [AMBER] Regarding Parameter file not saved zoran matovic (Mon Jul 18 2016 - 14:10:43 PDT)
    - Re: [AMBER] Regarding Parameter file not saved zoran matovic (Mon Jul 18 2016 - 11:58:58 PDT)
    - Re: [AMBER] Regarding Parameter file not saved zoran matovic (Tue Jul 19 2016 - 01:00:24 PDT)
[AMBER] Discrepancy between mdcrd and output files for MD run jandre17 (Sun Jul 17 2016 - 13:21:31 PDT)
- Re: [AMBER] Discrepancy between mdcrd and output files for MD run Carlos Simmerling (Sun Jul 17 2016 - 14:08:21 PDT)
[AMBER] Amber 16 Installation Beale, John (Mon Jul 18 2016 - 00:17:35 PDT)
- Re: [AMBER] Amber 16 Installation Bill Ross (Mon Jul 18 2016 - 00:43:31 PDT)
  - Re: [AMBER] Amber 16 Installation Beale, John (Mon Jul 18 2016 - 00:44:27 PDT)
- Re: [AMBER] Amber 16 Installation David A Case (Mon Jul 18 2016 - 06:07:11 PDT)
- Re: [AMBER] Amber 16 Installation Hai Nguyen (Mon Jul 18 2016 - 07:24:45 PDT)
  - Re: [AMBER] Amber 16 Installation Corum, Katharine W (Mon Jul 18 2016 - 12:39:56 PDT)
    - Re: [AMBER] Amber 16 Installation David A Case (Mon Jul 18 2016 - 17:13:55 PDT)
[AMBER] Ligand RMSD anu chandra (Mon Jul 18 2016 - 10:27:26 PDT)
- Re: [AMBER] Ligand RMSD David A Case (Mon Jul 18 2016 - 12:49:48 PDT)
  - Re: [AMBER] Ligand RMSD anu chandra (Tue Jul 19 2016 - 07:59:01 PDT)
[AMBER] RDF Mahmood Jasim (Mon Jul 18 2016 - 10:32:45 PDT)
- Re: [AMBER] RDF David A Case (Mon Jul 18 2016 - 12:56:03 PDT)
[AMBER] phosphorylated residues Neha Gandhi (Mon Jul 18 2016 - 23:40:36 PDT)
- Re: [AMBER] phosphorylated residues Bill Ross (Fri Dec 10 2010 - 10:07:16 PST)
  - Re: [AMBER] phosphorylated residues Jason Swails (Fri Dec 10 2010 - 11:01:50 PST)
- Re: [AMBER] phosphorylated residues Bill Ross (Fri Dec 10 2010 - 11:13:42 PST)
  - Re: [AMBER] phosphorylated residues Jason Swails (Fri Dec 10 2010 - 11:30:55 PST)
    - Re: [AMBER] phosphorylated residues baljinder (Fri Dec 10 2010 - 21:57:12 PST)
- Re: [AMBER] phosphorylated residues Carlos Simmerling (Tue Jul 19 2016 - 03:38:35 PDT)
[AMBER] Proton wanders away from tryptophan and histadine sidechain carbon Ross Cheloha (Tue Jul 19 2016 - 07:50:53 PDT)
- Re: [AMBER] Proton wanders away from tryptophan and histadine sidechain carbon Carlos Simmerling (Tue Jul 19 2016 - 08:23:06 PDT)
  - Re: [AMBER] Proton wanders away from tryptophan and histidine sidechain carbon Ross Cheloha (Wed Jul 20 2016 - 07:53:04 PDT)
    - Re: [AMBER] Proton wanders away from tryptophan and histidine sidechain carbon David A Case (Wed Jul 20 2016 - 14:40:58 PDT)
[AMBER] aMD with chloroform Stephan Schott (Tue Jul 19 2016 - 08:19:24 PDT)
[AMBER] Multiple Replicas on a Single GPU Bin Sun (Tue Jul 19 2016 - 18:12:32 PDT)
[AMBER] Is the surf or the molsurf calculate the protein surface? Windy CC (Tue Jul 19 2016 - 19:46:15 PDT)
- Re: [AMBER] Is the surf or the molsurf calculate the protein surface? David A Case (Wed Jul 20 2016 - 06:46:27 PDT)
[AMBER] Dielectric asymptotic parameter of mixtures for DRISM in rism1d Shijie Sheng (Tue Jul 19 2016 - 23:14:25 PDT)
- Re: [AMBER] Dielectric asymptotic parameter of mixtures for DRISM in rism1d Tyler Luchko (Lists) (Wed Jul 20 2016 - 10:48:34 PDT)
  - Re: [AMBER] Dielectric asymptotic parameter of mixtures for DRISM in rism1d Shijie Sheng (Wed Jul 20 2016 - 16:01:48 PDT)
    - Re: [AMBER] Dielectric asymptotic parameter of mixtures for DRISM in rism1d Tyler Luchko (Lists) (Wed Jul 20 2016 - 16:28:46 PDT)
    - Re: [AMBER] Dielectric asymptotic parameter of mixtures for DRISM in rism1d Shijie Sheng (Wed Jul 20 2016 - 17:14:41 PDT)
[AMBER] sander QM/MM MD Masoud Kazemi (Wed Jul 20 2016 - 05:26:50 PDT)
- Re: [AMBER] sander QM/MM MD Dr. Andreas W. Goetz (Wed Jul 20 2016 - 11:23:30 PDT)
[AMBER] MCPB.py - coordinate sphere FE Anna Cebrian Prats (Wed Jul 20 2016 - 05:44:01 PDT)
- Re: [AMBER] MCPB.py - coordinate sphere FE Pengfei Li (Wed Jul 20 2016 - 07:16:34 PDT)
  - Re: [AMBER] MCPB.py - coordinate sphere FE Anna Cebrian Prats (Wed Jul 20 2016 - 07:35:15 PDT)
[AMBER] NMR restraint Ming Tang (Wed Jul 20 2016 - 06:18:07 PDT)
- Re: [AMBER] NMR restraint David A Case (Wed Jul 20 2016 - 14:31:39 PDT)
  - Re: [AMBER] NMR restraint Ming Tang (Wed Jul 20 2016 - 18:10:54 PDT)
  - Re: [AMBER] NMR restraint Ming Tang (Wed Jul 20 2016 - 18:21:19 PDT)
[AMBER] MCPB.py Anna Cebrian Prats (Wed Jul 20 2016 - 06:44:08 PDT)
- Re: [AMBER] MCPB.py Marcelo Andrade Chagas (Wed Jul 20 2016 - 06:53:33 PDT)
[AMBER] Binding deltaG in ligand pose selction anu chandra (Wed Jul 20 2016 - 09:14:03 PDT)
- Re: [AMBER] Binding deltaG in ligand pose selction David A Case (Thu Jul 21 2016 - 08:30:05 PDT)
[AMBER] Remove rotation in postoprocess Fabrício Bracht (Wed Jul 20 2016 - 13:15:31 PDT)
- Re: [AMBER] Remove rotation in postoprocess Jean-Marc Billod (Wed Jul 20 2016 - 13:25:49 PDT)
[AMBER] Amber16 Parallel CUDA Tests Steven Ford (Wed Jul 20 2016 - 13:19:16 PDT)
- Re: [AMBER] Amber16 Parallel CUDA Tests Ross Walker (Thu Jul 21 2016 - 02:34:19 PDT)
- Re: [AMBER] Amber16 Parallel CUDA Tests Ross Walker (Sat Jul 23 2016 - 15:32:59 PDT)
  - Re: [AMBER] Amber16 Parallel CUDA Tests Steven Ford (Mon Jul 25 2016 - 12:06:20 PDT)
    - Re: [AMBER] Amber16 Parallel CUDA Tests Steven Ford (Thu Aug 11 2016 - 19:54:15 PDT)
    - Re: [AMBER] Amber16 Parallel CUDA Tests Ross Walker (Thu Aug 11 2016 - 20:17:16 PDT)
    - Re: [AMBER] Amber16 Parallel CUDA Tests Steven Ford (Thu Aug 11 2016 - 21:21:52 PDT)
    - Re: [AMBER] Amber16 Parallel CUDA Tests Ross Walker (Thu Aug 11 2016 - 21:29:05 PDT)
    - Re: [AMBER] Amber16 Parallel CUDA Tests Steven Ford (Thu Aug 11 2016 - 21:33:15 PDT)
    - Re: [AMBER] Amber16 Parallel CUDA Tests Steven Ford (Thu Aug 11 2016 - 21:38:10 PDT)
    - Re: [AMBER] Amber16 Parallel CUDA Tests Ross Walker (Thu Aug 11 2016 - 21:39:19 PDT)
    - Re: [AMBER] Amber16 Parallel CUDA Tests Steven Ford (Fri Aug 12 2016 - 09:44:54 PDT)
[AMBER] Difference of two trajectories C.D. Okafor (Wed Jul 20 2016 - 14:25:54 PDT)
- Re: [AMBER] Difference of two trajectories Daniel Roe (Mon Aug 01 2016 - 10:27:33 PDT)
[AMBER] CPPTRAJ Anna Cebrian Prats (Thu Jul 21 2016 - 03:30:20 PDT)
- Re: [AMBER] CPPTRAJ Jason Swails (Mon Jul 25 2016 - 08:10:08 PDT)
[AMBER] MD simulation can not proceed normally 乔艳 (Thu Jul 21 2016 - 04:31:22 PDT)
- Re: [AMBER] MD simulation can not proceed normally Carlos Simmerling (Thu Jul 21 2016 - 04:54:41 PDT)
  - [AMBER] 回复： Re: MD simulation can not proceed normally 乔艳 (Thu Jul 21 2016 - 07:28:13 PDT)
    - Re: [AMBER] 回复： Re: MD simulation can not proceed normally Carlos Simmerling (Thu Jul 21 2016 - 07:45:51 PDT)
[AMBER] Save individual PDBs from MD trajectory Iqbal, Muhammad Sajid (Thu Jul 21 2016 - 06:52:50 PDT)
- Re: [AMBER] Save individual PDBs from MD trajectory Carlos Simmerling (Thu Jul 21 2016 - 06:55:07 PDT)
Re: [AMBER] SMD and free energy value bharat gupta (Thu Jul 21 2016 - 07:20:47 PDT)
[AMBER] Amber with Amoeba force field Xiaoliu Zhang (Thu Jul 21 2016 - 08:26:38 PDT)
- Re: [AMBER] Amber with Amoeba force field David A Case (Fri Jul 22 2016 - 05:23:21 PDT)
[AMBER] Minimization of a small molecule in gas phase Tiffani Rovira (Thu Jul 21 2016 - 08:31:38 PDT)
- Re: [AMBER] Minimization of a small molecule in gas phase David A Case (Thu Jul 21 2016 - 18:22:45 PDT)
- Re: [AMBER] Minimization of a small molecule in gas phase David A Case (Thu Jul 21 2016 - 18:23:46 PDT)
[AMBER] Energy overflow in MD with distance restraint under PBC (aMD problem?) Stephan Schott (Thu Jul 21 2016 - 10:25:49 PDT)
- Re: [AMBER] Energy overflow in MD with distance restraint under PBC (aMD problem?) David A Case (Fri Jul 22 2016 - 09:36:56 PDT)
- Re: [AMBER] Energy overflow in MD with distance restraint under PBC (aMD problem?) Stephan Schott (Tue Aug 02 2016 - 07:00:29 PDT)
- Re: [AMBER] Energy overflow in MD with distance restraint under PBC (aMD problem?) Daniel Roe (Tue Aug 02 2016 - 08:25:42 PDT)
[AMBER] Wierd line in amber-TI output Files Khabiri, Morteza (Thu Jul 21 2016 - 10:52:53 PDT)
- Re: [AMBER] Wierd line in amber-TI output Files Scott Brozell (Fri Jul 22 2016 - 14:10:40 PDT)
  - Re: [AMBER] Wierd line in amber-TI output Files Thomas Fox (Fri Nov 25 2016 - 04:37:22 PST)
[AMBER] selecting frames with distribution Neha Gandhi (Thu Jul 21 2016 - 22:02:45 PDT)
- Re: [AMBER] selecting frames with distribution Nhai (Thu Jul 21 2016 - 23:08:31 PDT)
[AMBER] Gaussian error with MCPB ion modeling calculation Bilal Nizami (Fri Jul 22 2016 - 01:19:36 PDT)
[AMBER] MDCRD nida baig (Fri Jul 22 2016 - 04:19:49 PDT)
- Re: [AMBER] MDCRD David A Case (Fri Jul 22 2016 - 05:29:04 PDT)
- Re: [AMBER] MDCRD nida baig (Sat Jul 23 2016 - 00:46:45 PDT)
  - Re: [AMBER] MDCRD David A Case (Sat Jul 23 2016 - 07:11:01 PDT)
[AMBER] parmed chamber Neha Gandhi (Fri Jul 22 2016 - 04:58:50 PDT)
- Re: [AMBER] parmed chamber David A Case (Fri Jul 22 2016 - 05:33:02 PDT)
  - Re: [AMBER] parmed chamber Neha Gandhi (Fri Jul 22 2016 - 05:35:23 PDT)
- Re: [AMBER] parmed chamber Song-Ho Chong (Fri Jul 22 2016 - 05:57:13 PDT)
  - Re: [AMBER] parmed chamber Neha Gandhi (Fri Jul 22 2016 - 06:14:30 PDT)
[AMBER] Cpptraj - Stat bug? Markus Schneider (Fri Jul 22 2016 - 05:22:44 PDT)
- Re: [AMBER] Cpptraj - Stat bug? Daniel Roe (Thu Jul 28 2016 - 14:05:17 PDT)
  - Re: [AMBER] Cpptraj - Stat bug? Daniel Roe (Thu Jul 28 2016 - 15:03:33 PDT)
    - Re: [AMBER] Cpptraj - Stat bug? Daniel Roe (Thu Jul 28 2016 - 16:00:16 PDT)
    - Re: [AMBER] Cpptraj - Stat bug? Markus Schneider (Fri Jul 29 2016 - 06:56:43 PDT)
    - Re: [AMBER] Cpptraj - Stat bug? Daniel Roe (Fri Jul 29 2016 - 07:17:48 PDT)
[AMBER] NMR restraints not responding to 'value' flags in AMBER16 (pmemd.cuda) Wesley Michael Botello-Smith (Fri Jul 22 2016 - 16:01:12 PDT)
- Re: [AMBER] NMR restraints not responding to 'value' flags in AMBER16 (pmemd.cuda) ankita mehta (Sat Jul 23 2016 - 01:09:16 PDT)
  - Re: [AMBER] NMR restraints not responding to 'value' flags in AMBER16 (pmemd.cuda) ankita mehta (Mon Jul 25 2016 - 00:32:58 PDT)
- Re: [AMBER] NMR restraints not responding to 'value' flags in AMBER16 (pmemd.cuda) David A Case (Sat Jul 23 2016 - 07:05:33 PDT)
- Re: [AMBER] NMR restraints not responding to 'value' flags in AMBER16 (pmemd.cuda) Wesley Michael Botello-Smith (Sat Jul 23 2016 - 09:39:05 PDT)
  - Re: [AMBER] NMR restraints not responding to 'value' flags in AMBER16 (pmemd.cuda) ankita mehta (Sat Jul 23 2016 - 10:39:23 PDT)
  - Re: [AMBER] NMR restraints not responding to 'value' flags in AMBER16 (pmemd.cuda) David A Case (Sat Jul 23 2016 - 15:22:44 PDT)
- Re: [AMBER] NMR restraints not responding to 'value' flags in AMBER16 (pmemd.cuda) ankita mehta (Mon Jul 25 2016 - 00:34:56 PDT)
  - Re: [AMBER] NMR restraints not responding to 'value' flags in AMBER16 (pmemd.cuda) Wesley Michael Botello-Smith (Mon Jul 25 2016 - 10:21:31 PDT)
    - Re: [AMBER] NMR restraints not responding to 'value' flags in AMBER16 (pmemd.cuda) Adrian Roitberg (Mon Jul 25 2016 - 10:23:20 PDT)
    - Re: [AMBER] NMR restraints not responding to 'value' flags in AMBER16 (pmemd.cuda) Wesley Michael Botello-Smith (Mon Jul 25 2016 - 10:52:11 PDT)
    - Re: [AMBER] NMR restraints not responding to 'value' flags in AMBER16 (pmemd.cuda) Wesley Michael Botello-Smith (Mon Jul 25 2016 - 16:17:14 PDT)
    - Re: [AMBER] NMR restraints not responding to 'value' flags in AMBER16 (pmemd.cuda) David A Case (Mon Jul 25 2016 - 19:13:47 PDT)
- Re: [AMBER] NMR restraints not responding to 'value' flags in AMBER16 (pmemd.cuda) Wesley Michael Botello-Smith (Mon Jul 25 2016 - 14:29:00 PDT)
- Re: [AMBER] NMR restraints not responding to 'value' flags in AMBER16 (pmemd.cuda) Wesley Michael Botello-Smith (Tue Jul 26 2016 - 11:11:37 PDT)
  - Re: [AMBER] NMR restraints not responding to 'value' flags in AMBER16 (pmemd.cuda) David A Case (Tue Jul 26 2016 - 13:40:52 PDT)
[AMBER] NMode binding entropy Error -- Line minimizer aborted 康宁 (Sat Jul 23 2016 - 03:16:24 PDT)
- Re: [AMBER] NMode binding entropy Error -- Line minimizer aborted David A Case (Sat Jul 23 2016 - 07:14:18 PDT)
[AMBER] NAB ABHIJEET CHOWDHURY (Sat Jul 23 2016 - 05:02:06 PDT)
- Re: [AMBER] NAB Indrajit Deb (Sat Jul 23 2016 - 05:07:57 PDT)
  - Re: [AMBER] NAB ABHIJEET CHOWDHURY (Sat Jul 23 2016 - 06:23:04 PDT)
[AMBER] Create x.out and x.rst from x.mdcrd Mijiddorj Batsaikhan (Sat Jul 23 2016 - 06:27:54 PDT)
- Re: [AMBER] Create x.out and x.rst from x.mdcrd David A Case (Sat Jul 23 2016 - 07:17:02 PDT)
[AMBER] SMD simulation protocols Ibrahim Said (Sun Jul 24 2016 - 09:25:47 PDT)
- Re: [AMBER] SMD simulation protocols Adrian Roitberg (Sun Jul 24 2016 - 10:35:50 PDT)
  - Re: [AMBER] SMD simulation protocols Ibrahim Said (Sun Jul 24 2016 - 13:08:28 PDT)
    - Re: [AMBER] SMD simulation protocols Dwight McGee (Sun Jul 24 2016 - 14:55:41 PDT)
[AMBER] restraintmask: select residues around the coordinates of a point Thomas Evangelidis (Sun Jul 24 2016 - 16:51:43 PDT)
- Re: [AMBER] restraintmask: select residues around the coordinates of a point David A Case (Mon Jul 25 2016 - 07:05:18 PDT)
  - Re: [AMBER] restraintmask: select residues around the coordinates of a point Thomas Evangelidis (Mon Jul 25 2016 - 11:03:11 PDT)
    - Re: [AMBER] restraintmask: select residues around the coordinates of a point David A Case (Mon Jul 25 2016 - 14:03:06 PDT)
    - Re: [AMBER] restraintmask: select residues around the coordinates of a point Thomas Evangelidis (Mon Jul 25 2016 - 15:02:09 PDT)
    - Re: [AMBER] restraintmask: select residues around the coordinates of a point David A Case (Mon Jul 25 2016 - 18:47:32 PDT)
[AMBER] NMR restraint Ming Tang (Sun Jul 24 2016 - 17:51:17 PDT)
[AMBER] Implicit solvent with Glycam force field yunshi11 . (Sun Jul 24 2016 - 17:58:48 PDT)
- Re: [AMBER] Implicit solvent with Glycam force field Lachele Foley (Sun Jul 24 2016 - 19:27:01 PDT)
  - Re: [AMBER] Implicit solvent with Glycam force field Carlos Simmerling (Mon Jul 25 2016 - 04:00:56 PDT)
- Re: [AMBER] Implicit solvent with Glycam force field David A Case (Mon Jul 25 2016 - 07:08:52 PDT)
[AMBER] charmmlipid2amber not found Kshatresh Dutta Dubey (Mon Jul 25 2016 - 01:08:23 PDT)
- Re: [AMBER] charmmlipid2amber not found David A Case (Mon Jul 25 2016 - 07:16:43 PDT)
  - Re: [AMBER] charmmlipid2amber not found Kshatresh Dutta Dubey (Mon Jul 25 2016 - 08:26:03 PDT)
    - Re: [AMBER] charmmlipid2amber not found Adrian Roitberg (Mon Jul 25 2016 - 09:14:31 PDT)
[AMBER] ibelly to fix protein. Saman Yousuf ali (Mon Jul 25 2016 - 05:21:49 PDT)
[AMBER] Applying different restraints to different sets of atoms Dmitry Suplatov (Mon Jul 25 2016 - 05:38:52 PDT)
- Re: [AMBER] Applying different restraints to different sets of atoms David A Case (Mon Jul 25 2016 - 09:50:47 PDT)
[AMBER] Creating topology file in MMPBSA Anwesha Sarkar (Mon Jul 25 2016 - 05:51:35 PDT)
- Re: [AMBER] Creating topology file in MMPBSA Hirdesh Kumar (Mon Jul 25 2016 - 07:25:39 PDT)
- Re: [AMBER] Creating topology file in MMPBSA Jason Swails (Mon Jul 25 2016 - 08:05:41 PDT)
[AMBER] Error MCPB when send the input Tiffani Rovira (Mon Jul 25 2016 - 10:05:23 PDT)
- Re: [AMBER] Error MCPB when send the input Pengfei Li (Tue Jul 26 2016 - 07:28:45 PDT)
[AMBER] average pdb distorted Thakur, Abhishek (Mon Jul 25 2016 - 12:20:34 PDT)
- Re: [AMBER] average pdb distorted Hai Nguyen (Mon Jul 25 2016 - 12:28:34 PDT)
  - Re: [AMBER] average pdb distorted Thakur, Abhishek (Mon Jul 25 2016 - 12:33:42 PDT)
    - Re: [AMBER] average pdb distorted David A Case (Mon Jul 25 2016 - 18:43:48 PDT)
    - Re: [AMBER] average pdb distorted Marc van der Kamp (Tue Jul 26 2016 - 00:55:05 PDT)
    - Re: [AMBER] average pdb distorted Thakur, Abhishek (Tue Jul 26 2016 - 11:24:29 PDT)
    - Re: [AMBER] average pdb distorted kenfack cyril (Sat Jul 30 2016 - 12:27:10 PDT)
    - [AMBER] EVB calculations of proton transfer David A Case (Mon Aug 01 2016 - 07:52:43 PDT)
    - Re: [AMBER] EVB calculations of proton transfer kenfack cyril (Mon Aug 01 2016 - 14:05:09 PDT)
    - Re: [AMBER] EVB calculations of proton transfer David A Case (Tue Aug 02 2016 - 07:38:37 PDT)
[AMBER] MDGX tutorial? Dickson, Callum J (Mon Jul 25 2016 - 13:20:01 PDT)
- Re: [AMBER] MDGX tutorial? David Cerutti (Mon Jul 25 2016 - 13:50:24 PDT)
  - Re: [AMBER] MDGX tutorial? Dickson, Callum J (Mon Jul 25 2016 - 15:40:42 PDT)
Re: [AMBER] AMBER Digest, Vol 1646, Issue 1 bharat gupta (Mon Jul 25 2016 - 22:21:49 PDT)
[AMBER] ntr vs ibelly. Saman Yousuf ali (Tue Jul 26 2016 - 02:38:42 PDT)
- Re: [AMBER] ntr vs ibelly. Barbault Florent (Tue Jul 26 2016 - 03:13:21 PDT)
  - Re: [AMBER] ntr vs ibelly. Adrian Roitberg (Tue Jul 26 2016 - 03:28:16 PDT)
- Re: [AMBER] ntr vs ibelly. Barbault Florent (Tue Jul 26 2016 - 03:56:24 PDT)
  - Re: [AMBER] ntr vs ibelly. David A Case (Tue Jul 26 2016 - 07:40:17 PDT)
[AMBER] ntr vs ibelly. Saman Yousuf ali (Tue Jul 26 2016 - 03:45:06 PDT)
[AMBER] Failed to solvate the molecule during the TUTORIAL A8 Nikolay N. Kuzmich (Tue Jul 26 2016 - 04:18:49 PDT)
- Re: [AMBER] Failed to solvate the molecule during the TUTORIAL A8 Kenneth Huang (Tue Jul 26 2016 - 06:14:33 PDT)
[AMBER] Error cuda Anna Cebrian Prats (Tue Jul 26 2016 - 07:33:39 PDT)
[AMBER] cpptraj grid command multiple trajectories Sarah Graham (Tue Jul 26 2016 - 10:17:47 PDT)
- Re: [AMBER] cpptraj grid command multiple trajectories Daniel Roe (Tue Jul 26 2016 - 12:11:19 PDT)
  - Re: [AMBER] cpptraj grid command multiple trajectories Sarah Graham (Tue Jul 26 2016 - 13:26:12 PDT)
    - Re: [AMBER] cpptraj grid command multiple trajectories Daniel Roe (Tue Jul 26 2016 - 13:31:34 PDT)
[AMBER] How to modify forcefield to use TIP4P-D water model Suguru ASAI (Wed Jul 27 2016 - 03:24:29 PDT)
- Re: [AMBER] How to modify forcefield to use TIP4P-D water model David A Case (Wed Jul 27 2016 - 05:44:05 PDT)
  - Re: [AMBER] How to modify forcefield to use TIP4P-D water model Suguru ASAI (Wed Jul 27 2016 - 20:03:17 PDT)
[AMBER] paramfit Igor Marques (Wed Jul 27 2016 - 09:34:45 PDT)
- Re: [AMBER] paramfit David Cerutti (Wed Jul 27 2016 - 10:02:02 PDT)
  - Re: [AMBER] paramfit Robin Betz (Fri Jul 29 2016 - 13:31:54 PDT)
[AMBER] make test.cuda failed Nikolay N. Kuzmich (Thu Jul 28 2016 - 06:50:52 PDT)
- Re: [AMBER] make test.cuda failed Marcos Serrou do Amaral (Thu Jul 28 2016 - 07:53:03 PDT)
[AMBER] EEL become ****** in minimization Suguru ASAI (Thu Jul 28 2016 - 07:04:56 PDT)
- Re: [AMBER] EEL become ****** in minimization David Cerutti (Thu Jul 28 2016 - 07:44:08 PDT)
  - Re: [AMBER] EEL become ****** in minimization Osman, Roman (Thu Jul 28 2016 - 08:00:56 PDT)
  - Re: [AMBER] EEL become ****** in minimization Suguru ASAI (Thu Jul 28 2016 - 08:15:55 PDT)
    - Re: [AMBER] EEL become ****** in minimization Thakur, Abhishek (Thu Jul 28 2016 - 11:37:42 PDT)
- Re: [AMBER] EEL become ****** in minimization David A Case (Thu Jul 28 2016 - 15:46:38 PDT)
  - Re: [AMBER] EEL become ****** in minimization Suguru ASAI (Sun Jul 31 2016 - 21:10:44 PDT)
    - Re: [AMBER] EEL become ****** in minimization David Cerutti (Sun Jul 31 2016 - 22:04:36 PDT)
    - Re: [AMBER] EEL become ****** in minimization David A Case (Mon Aug 01 2016 - 08:04:15 PDT)
[AMBER] Sander bomb: how to create a larger box Ruth Helena Tichauer (Thu Jul 28 2016 - 07:48:43 PDT)
- Re: [AMBER] Sander bomb: how to create a larger box Bilal Nizami (Sat Jul 30 2016 - 13:58:29 PDT)
  - Re: [AMBER] Sander bomb: how to create a larger box Ruth Helena Tichauer (Mon Aug 01 2016 - 03:53:51 PDT)
    - Re: [AMBER] Sander bomb: how to create a larger box Bill Ross (Mon Aug 01 2016 - 04:32:22 PDT)
    - Re: [AMBER] Sander bomb: how to create a larger box Ruth Helena Tichauer (Mon Aug 01 2016 - 04:42:28 PDT)
    - Re: [AMBER] Sander bomb: how to create a larger box Bill Ross (Mon Aug 01 2016 - 05:11:10 PDT)
    - Re: [AMBER] Sander bomb: how to create a larger box Ruth Helena Tichauer (Mon Aug 01 2016 - 05:38:12 PDT)
    - Re: [AMBER] Sander bomb: how to create a larger box David A Case (Mon Aug 01 2016 - 07:57:05 PDT)
    - Re: [AMBER] Sander bomb: how to create a larger box Ruth Helena Tichauer (Tue Aug 02 2016 - 07:14:33 PDT)
[AMBER] NMR restraint Ming Tang (Thu Jul 28 2016 - 17:36:35 PDT)
- Re: [AMBER] NMR restraint David A Case (Fri Jul 29 2016 - 06:35:08 PDT)
[AMBER] InVacuoWithDielc JAIME RUBIO MARTINEZ (Thu Jul 28 2016 - 23:38:17 PDT)
- Re: [AMBER] InVacuoWithDielc David A Case (Sat Jul 30 2016 - 07:51:01 PDT)
  - Re: [AMBER] InVacuoWithDielc JAIME RUBIO MARTINEZ (Tue Aug 02 2016 - 00:32:58 PDT)
[AMBER] can amber14 be run with gtx1060 xjq (Fri Jul 29 2016 - 02:43:08 PDT)
- Re: [AMBER] can amber14 be run with gtx1060 Ross Walker (Fri Jul 29 2016 - 05:03:59 PDT)
[AMBER] rmsd calculations on multiple trajectories Hirdesh Kumar (Fri Jul 29 2016 - 05:26:54 PDT)
- Re: [AMBER] rmsd calculations on multiple trajectories Daniel Roe (Fri Jul 29 2016 - 07:31:56 PDT)
  - Re: [AMBER] rmsd calculations on multiple trajectories Hirdesh Kumar (Fri Jul 29 2016 - 08:00:03 PDT)
    - Re: [AMBER] rmsd calculations on multiple trajectories Daniel Roe (Fri Jul 29 2016 - 08:34:25 PDT)
- Re: [AMBER] rmsd calculations on multiple trajectories Carlos Simmerling (Fri Jul 29 2016 - 08:04:33 PDT)
  - Re: [AMBER] rmsd calculations on multiple trajectories Hirdesh Kumar (Fri Jul 29 2016 - 08:08:34 PDT)
    - Re: [AMBER] rmsd calculations on multiple trajectories Carlos Simmerling (Fri Jul 29 2016 - 08:30:34 PDT)
    - Re: [AMBER] rmsd calculations on multiple trajectories Daniel Roe (Fri Jul 29 2016 - 08:36:35 PDT)
    - Re: [AMBER] rmsd calculations on multiple trajectories Carlos Simmerling (Fri Jul 29 2016 - 08:47:23 PDT)
    - Re: [AMBER] rmsd calculations on multiple trajectories Hai Nguyen (Fri Jul 29 2016 - 12:02:38 PDT)
    - Re: [AMBER] rmsd calculations on multiple trajectories Hirdesh Kumar (Fri Jul 29 2016 - 12:52:31 PDT)
    - Re: [AMBER] rmsd calculations on multiple trajectories Daniel Roe (Fri Jul 29 2016 - 13:45:57 PDT)
    - Re: [AMBER] rmsd calculations on multiple trajectories Hirdesh Kumar (Fri Jul 29 2016 - 14:09:45 PDT)
    - Re: [AMBER] rmsd calculations on multiple trajectories Daniel Roe (Fri Jul 29 2016 - 14:20:36 PDT)
    - Re: [AMBER] rmsd calculations on multiple trajectories Hirdesh Kumar (Fri Jul 29 2016 - 14:25:26 PDT)
    - Re: [AMBER] rmsd calculations on multiple trajectories Daniel Roe (Fri Jul 29 2016 - 14:27:59 PDT)
    - Re: [AMBER] rmsd calculations on multiple trajectories Hirdesh Kumar (Fri Jul 29 2016 - 14:33:19 PDT)
    - Re: [AMBER] rmsd calculations on multiple trajectories Daniel Roe (Fri Jul 29 2016 - 14:52:49 PDT)
[AMBER] Question about QM/MM Anna Cebrian Prats (Fri Jul 29 2016 - 06:45:19 PDT)
- Re: [AMBER] Question about QM/MM Dr. Andreas W. Goetz (Fri Jul 29 2016 - 18:14:30 PDT)
  - Re: [AMBER] Question about QM/MM Anna Cebrian Prats (Fri Sep 02 2016 - 02:01:06 PDT)
    - Re: [AMBER] Question about QM/MM Adrian Roitberg (Fri Sep 02 2016 - 08:27:46 PDT)
    - Re: [AMBER] Question about QM/MM Anna Cebrian Prats (Mon Sep 05 2016 - 09:14:31 PDT)
    - Re: [AMBER] Question about QM/MM David A Case (Tue Sep 06 2016 - 04:17:09 PDT)
    - Re: [AMBER] Question about QM/MM Anna Cebrian Prats (Tue Sep 06 2016 - 05:57:54 PDT)
    - Re: [AMBER] Question about QM/MM Adrian Roitberg (Tue Sep 06 2016 - 07:44:25 PDT)
    - Re: [AMBER] Question about QM/MM Anna Cebrian Prats (Tue Sep 06 2016 - 08:26:29 PDT)
    - Re: [AMBER] Question about QM/MM Adrian Roitberg (Tue Sep 06 2016 - 08:36:18 PDT)
    - Re: [AMBER] Question about QM/MM Anna Cebrian Prats (Wed Sep 07 2016 - 07:48:00 PDT)
    - Re: [AMBER] Question about QM/MM Gustavo Seabra (Fri Sep 02 2016 - 09:17:30 PDT)
    - Re: [AMBER] Question about QM/MM Fabrício Bracht (Fri Sep 02 2016 - 10:03:30 PDT)
    - Re: [AMBER] Question about QM/MM Adrian Roitberg (Fri Sep 02 2016 - 10:09:35 PDT)
    - Re: [AMBER] Question about QM/MM Fabrício Bracht (Fri Sep 02 2016 - 10:34:20 PDT)
    - Re: [AMBER] Question about QM/MM Adrian Roitberg (Fri Sep 02 2016 - 10:37:53 PDT)
    - Re: [AMBER] Question about QM/MM Fabrício Bracht (Fri Sep 02 2016 - 10:46:06 PDT)
    - Re: [AMBER] Question about QM/MM Adrian Roitberg (Fri Sep 02 2016 - 10:54:07 PDT)
    - Re: [AMBER] Question about QM/MM Fabrício Bracht (Fri Sep 02 2016 - 10:57:31 PDT)
    - Re: [AMBER] Question about QM/MM Adrian Roitberg (Fri Sep 02 2016 - 10:59:31 PDT)
    - Re: [AMBER] Question about QM/MM Marc van der Kamp (Fri Sep 02 2016 - 12:09:18 PDT)
[AMBER] modified potentials Irem Altan (Fri Jul 29 2016 - 06:52:07 PDT)
- Re: [AMBER] modified potentials David Cerutti (Fri Jul 29 2016 - 07:55:31 PDT)
  - Re: [AMBER] modified potentials Irem Altan (Fri Jul 29 2016 - 08:38:13 PDT)
    - Re: [AMBER] modified potentials Carlos Simmerling (Fri Jul 29 2016 - 08:46:14 PDT)
    - Re: [AMBER] modified potentials David Cerutti (Fri Jul 29 2016 - 09:33:22 PDT)
[AMBER] Problem setting AMBERHOME as environment variable Ambertools 16 Linux Elissa Fink (Fri Jul 29 2016 - 09:15:59 PDT)
- Re: [AMBER] Problem setting AMBERHOME as environment variable Ambertools 16 Linux Daniel Roe (Fri Jul 29 2016 - 09:24:25 PDT)
[AMBER] MMPBSA (MD or aMD) Thakur, Abhishek (Fri Jul 29 2016 - 12:27:21 PDT)
- Re: [AMBER] MMPBSA (MD or aMD) Jason Swails (Fri Jul 29 2016 - 12:56:39 PDT)
  - Re: [AMBER] MMPBSA (MD or aMD) Thakur, Abhishek (Fri Jul 29 2016 - 13:04:38 PDT)
  - Re: [AMBER] MMPBSA (MD or aMD) Thakur, Abhishek (Fri Jul 29 2016 - 13:40:11 PDT)
    - Re: [AMBER] MMPBSA (MD or aMD) Jason Swails (Fri Jul 29 2016 - 17:43:05 PDT)
    - Re: [AMBER] MMPBSA (MD or aMD) Daniel Roe (Fri Jul 29 2016 - 19:13:46 PDT)
[AMBER] figure legend problem in the tutorial? Albert (Fri Jul 29 2016 - 12:50:53 PDT)
- Re: [AMBER] figure legend problem in the tutorial? Robin Betz (Fri Jul 29 2016 - 13:25:33 PDT)
[AMBER] Exposed hydrophobic surface area anu chandra (Fri Jul 29 2016 - 16:50:43 PDT)
- Re: [AMBER] Exposed hydrophobic surface area Daniel Roe (Fri Jul 29 2016 - 19:15:05 PDT)
[AMBER] where is amber.jupyter? Albert (Sat Jul 30 2016 - 00:17:08 PDT)
- Re: [AMBER] where is amber.jupyter? Hai Nguyen (Sat Jul 30 2016 - 00:26:42 PDT)
  - Re: [AMBER] where is amber.jupyter? Albert (Sat Jul 30 2016 - 00:59:24 PDT)
    - Re: [AMBER] where is amber.jupyter? Hai Nguyen (Sat Jul 30 2016 - 01:11:21 PDT)
    - Re: [AMBER] where is amber.jupyter? Albert (Sat Jul 30 2016 - 01:32:47 PDT)
    - Re: [AMBER] where is amber.jupyter? Albert (Sat Jul 30 2016 - 01:35:19 PDT)
    - Re: [AMBER] where is amber.jupyter? Hai Nguyen (Sat Jul 30 2016 - 01:47:09 PDT)
    - Re: [AMBER] where is amber.jupyter? Albert (Sat Jul 30 2016 - 01:59:30 PDT)
[AMBER] Calculating Salt bridge interactions- Protein and RNA Muthukumaran R (Sat Jul 30 2016 - 00:27:51 PDT)
- Re: [AMBER] Calculating Salt bridge interactions- Protein and RNA Daniel Roe (Mon Aug 01 2016 - 10:26:14 PDT)
[AMBER] dssp xlabel conversion. Saman Yousuf ali (Sat Jul 30 2016 - 00:38:04 PDT)
- Re: [AMBER] dssp xlabel conversion. Daniel Roe (Sat Jul 30 2016 - 07:41:26 PDT)
[AMBER] hydrogen bond occupancy plot cpptraj Saman Yousuf ali (Sat Jul 30 2016 - 15:15:59 PDT)
- Re: [AMBER] hydrogen bond occupancy plot cpptraj Daniel Roe (Mon Aug 01 2016 - 10:23:57 PDT)
[AMBER] Hii ankita mehta (Sun Jul 31 2016 - 06:22:34 PDT)
- Re: [AMBER] Hii Daniel Roe (Sun Jul 31 2016 - 06:58:12 PDT)
[AMBER] EEL energy of QM/MM-GBSA 张姝姝 (Sun Jul 31 2016 - 20:11:42 PDT)
- Re: [AMBER] EEL energy of QM/MM-GBSA David A Case (Mon Aug 01 2016 - 07:58:39 PDT)
[AMBER] Use two different force fields in Amber Xiaoliu Zhang (Mon Aug 01 2016 - 07:41:19 PDT)
- Re: [AMBER] Use two different force fields in Amber David A Case (Tue Aug 02 2016 - 07:34:33 PDT)
- Re: [AMBER] Use two different force fields in Amber Xiaoliu Zhang (Fri Aug 05 2016 - 08:30:56 PDT)
[AMBER] subject: parametrization of Force field DOCENTE ANTISTIO ANIBAL ALVIS AMADOR (Mon Aug 01 2016 - 07:50:08 PDT)
- Re: [AMBER] subject: parametrization of Force field David A Case (Tue Aug 02 2016 - 07:36:09 PDT)
[AMBER] tinker_to_amber error Xiaoliu Zhang (Mon Aug 01 2016 - 08:52:17 PDT)
- Re: [AMBER] tinker_to_amber error Ray Luo (Mon Aug 01 2016 - 10:40:08 PDT)
- Re: [AMBER] tinker_to_amber error Xiaoliu Zhang (Wed Aug 03 2016 - 07:46:04 PDT)
[AMBER] default value (inp= 0,1,2)? MMPBSA Thakur, Abhishek (Mon Aug 01 2016 - 09:35:16 PDT)
- Re: [AMBER] default value (inp= 0,1,2)? MMPBSA Ray Luo (Mon Aug 01 2016 - 10:35:04 PDT)
  - Re: [AMBER] default value (inp= 0,1,2)? MMPBSA Thakur, Abhishek (Mon Aug 01 2016 - 11:42:29 PDT)
    - Re: [AMBER] default value (inp= 0,1,2)? MMPBSA Ray Luo (Mon Aug 01 2016 - 12:25:42 PDT)
[AMBER] which forcefield it is? Albert (Mon Aug 01 2016 - 23:38:43 PDT)
- Re: [AMBER] which forcefield it is? Amy Rice (Tue Aug 02 2016 - 09:17:43 PDT)
  - Re: [AMBER] which forcefield it is? Ross Walker (Tue Aug 02 2016 - 09:22:05 PDT)
[AMBER] HBond command Sidhu, Khushwant (Dr.) (Tue Aug 02 2016 - 05:50:08 PDT)
- Re: [AMBER] HBond command Daniel Roe (Tue Aug 02 2016 - 08:49:18 PDT)
[AMBER] interaction entropy instead of normal mode analysis diaby (Tue Aug 02 2016 - 06:57:10 PDT)
- Re: [AMBER] interaction entropy instead of normal mode analysis Jason Swails (Thu Aug 04 2016 - 11:03:44 PDT)
[AMBER] correlated dihedral force constant Chi Jin (Tue Aug 02 2016 - 12:46:23 PDT)
[AMBER] EM in vacuum Dmitry Suplatov (Tue Aug 02 2016 - 13:52:17 PDT)
- Re: [AMBER] EM in vacuum David A Case (Wed Aug 03 2016 - 16:22:18 PDT)
[AMBER] running RISM/MD on multi processors Jingyi Yan (Tue Aug 02 2016 - 14:26:16 PDT)
- Re: [AMBER] running RISM/MD on multi processors Tyler Luchko (Lists) (Tue Aug 02 2016 - 14:46:02 PDT)
[AMBER] the phosphoric acid group is deformed 乔艳 (Tue Aug 02 2016 - 16:40:30 PDT)
[AMBER] the end phosphoric acid group is deformed during simulation rain (Tue Aug 02 2016 - 17:12:34 PDT)
[AMBER] parmchk vs parmchk2 Andrew.Warden.csiro.au (Tue Aug 02 2016 - 21:53:09 PDT)
- Re: [AMBER] parmchk vs parmchk2 David A Case (Wed Aug 03 2016 - 16:34:34 PDT)
  - Re: [AMBER] parmchk vs parmchk2 Hannes Loeffler (Mon Aug 15 2016 - 00:39:45 PDT)
- Re: [AMBER] parmchk vs parmchk2 Andrew.Warden.csiro.au (Thu Aug 04 2016 - 18:08:21 PDT)
[AMBER] Amber´14 Solvent box simulation, something went wrong!! Stregone (Wed Aug 03 2016 - 06:43:18 PDT)
- Re: [AMBER] Amber´14 Solvent box simulation, something went wrong!! Daniel Roe (Wed Aug 03 2016 - 12:30:45 PDT)
  - Re: [AMBER] Amber´14 Solvent box simulation, something went wrong!! Stregone (Thu Aug 04 2016 - 02:08:37 PDT)
    - Re: [AMBER] Amber´14 Solvent box simulation, something went wrong!! Daniel Roe (Thu Aug 04 2016 - 08:02:28 PDT)
[AMBER] Cyana3.97 to Amber15 pdb conversion Erik Davis (Wed Aug 03 2016 - 08:09:35 PDT)
- Re: [AMBER] Cyana3.97 to Amber15 pdb conversion Daniel Roe (Wed Aug 03 2016 - 12:26:52 PDT)
- Re: [AMBER] Cyana3.97 to Amber15 pdb conversion David A Case (Wed Aug 03 2016 - 16:41:13 PDT)
  - Re: [AMBER] Cyana3.97 to Amber15 pdb conversion Erik Davis (Fri Aug 05 2016 - 11:01:46 PDT)
[AMBER] gbsa parameter Thomas Evangelidis (Wed Aug 03 2016 - 08:54:11 PDT)
- Re: [AMBER] gbsa parameter Hai Nguyen (Wed Aug 03 2016 - 09:33:14 PDT)
- Re: [AMBER] gbsa parameter Daniel Roe (Wed Aug 03 2016 - 12:23:03 PDT)
[AMBER] save Hessian nmode mmpbsa Bruno Falcone (Wed Aug 03 2016 - 09:51:23 PDT)
- Re: [AMBER] save Hessian nmode mmpbsa Bruno Falcone (Thu Aug 04 2016 - 08:45:51 PDT)
  - Re: [AMBER] save Hessian nmode mmpbsa Jason Swails (Thu Aug 04 2016 - 10:56:37 PDT)
[AMBER] Generate Polymer parameters konda003 . (Wed Aug 03 2016 - 12:58:24 PDT)
- Re: [AMBER] Generate Polymer parameters David A Case (Wed Aug 03 2016 - 16:47:17 PDT)
[AMBER] 180 degrees of angle in AMBER 10 Pengzhi Zhang (Wed Aug 03 2016 - 13:07:26 PDT)
- Re: [AMBER] 180 degrees of angle in AMBER 10 Jason Swails (Thu Aug 04 2016 - 13:30:36 PDT)
[AMBER] Getting free energy (difference) from GPU simulations yunshi11 . (Wed Aug 03 2016 - 16:18:05 PDT)
- Re: [AMBER] Getting free energy (difference) from GPU simulations Jason Swails (Thu Aug 04 2016 - 11:09:44 PDT)
[AMBER] error in runing mdout_analyzer.py nida baig (Wed Aug 03 2016 - 21:10:04 PDT)
- Re: [AMBER] error in runing mdout_analyzer.py Daniel Roe (Wed Aug 03 2016 - 21:25:23 PDT)
  - Re: [AMBER] error in runing mdout_analyzer.py nida baig (Wed Aug 03 2016 - 21:39:05 PDT)
    - Re: [AMBER] error in runing mdout_analyzer.py Daniel Roe (Thu Aug 04 2016 - 08:05:51 PDT)
[AMBER] error running production with restraint. Saman Yousuf ali (Wed Aug 03 2016 - 22:16:51 PDT)
- Re: [AMBER] error running production with restraint. Daniel Roe (Thu Aug 04 2016 - 08:04:48 PDT)
- Re: [AMBER] error running production with restraint. zoran matovic (Thu Aug 04 2016 - 11:27:49 PDT)
  - Re: [AMBER] error running production with restraint. zoran matovic (Thu Aug 04 2016 - 11:38:52 PDT)
- Re: [AMBER] error running production with restraint. zoran matovic (Fri Aug 05 2016 - 00:14:00 PDT)
- Re: [AMBER] error running production with restraint. Saman Yousuf ali (Fri Aug 05 2016 - 02:04:39 PDT)
  - Re: [AMBER] error running production with restraint. David A Case (Fri Aug 05 2016 - 04:55:29 PDT)
    - Re: [AMBER] error running production with restraint. Saman Yousuf ali (Sat Aug 06 2016 - 02:29:13 PDT)
[AMBER] solvate hexagonal box Neha Gandhi (Wed Aug 03 2016 - 22:29:52 PDT)
[AMBER] Is there a way to disable electrostatic solute-solvent interactions in PMEMD? Plotnikov, Nikolay (Thu Aug 04 2016 - 08:27:25 PDT)
- Re: [AMBER] Is there a way to disable electrostatic solute-solvent interactions in PMEMD? Jason Swails (Thu Aug 04 2016 - 11:02:00 PDT)
[AMBER] Question about usage of external QM in QM/MM Fabrício Bracht (Thu Aug 04 2016 - 10:59:10 PDT)
- Re: [AMBER] Question about usage of external QM in QM/MM Dr. Andreas W. Goetz (Thu Aug 04 2016 - 12:17:15 PDT)
  - Re: [AMBER] Question about usage of external QM in QM/MM Fabrício Bracht (Thu Aug 04 2016 - 12:29:35 PDT)
    - Re: [AMBER] Question about usage of external QM in QM/MM Fabrício Bracht (Thu Aug 04 2016 - 13:03:56 PDT)
    - Re: [AMBER] Question about usage of external QM in QM/MM David A Case (Thu Aug 04 2016 - 14:38:07 PDT)
    - Re: [AMBER] Question about usage of external QM in QM/MM Fabrício Bracht (Thu Aug 04 2016 - 19:04:46 PDT)
    - Re: [AMBER] Question about usage of external QM in QM/MM Dr. Andreas W. Goetz (Thu Aug 04 2016 - 23:15:40 PDT)
    - Re: [AMBER] Question about usage of external QM in QM/MM David A Case (Fri Aug 05 2016 - 06:50:55 PDT)
    - Re: [AMBER] Question about usage of external QM in QM/MM Fabrício Bracht (Fri Aug 05 2016 - 11:06:18 PDT)
    - Re: [AMBER] Question about usage of external QM in QM/MM Dr. Andreas W. Goetz (Fri Aug 05 2016 - 14:17:21 PDT)
    - Re: [AMBER] Question about usage of external QM in QM/MM Fabrício Bracht (Fri Aug 05 2016 - 18:30:56 PDT)
    - Re: [AMBER] Question about usage of external QM in QM/MM Dr. Andreas W. Goetz (Sat Aug 06 2016 - 13:18:13 PDT)
    - Re: [AMBER] Question about usage of external QM in QM/MM Fabrício Bracht (Tue Aug 09 2016 - 07:07:55 PDT)
    - Re: [AMBER] Question about usage of external QM in QM/MM Fabrício Bracht (Tue Aug 09 2016 - 07:13:42 PDT)
    - Re: [AMBER] Question about usage of external QM in QM/MM David A Case (Tue Aug 09 2016 - 12:27:00 PDT)
    - Re: [AMBER] Question about usage of external QM in QM/MM Fabrício Bracht (Tue Aug 09 2016 - 13:26:01 PDT)
    - Re: [AMBER] Question about usage of external QM in QM/MM Dr. Andreas W. Goetz (Tue Aug 09 2016 - 15:39:00 PDT)
[AMBER] unreadable crd files macc_200 (Thu Aug 04 2016 - 14:47:48 PDT)
- Re: [AMBER] unreadable crd files Adrian Roitberg (Thu Aug 04 2016 - 15:31:29 PDT)
  - Re: [AMBER] unreadable crd files Hai Nguyen (Thu Aug 04 2016 - 21:05:07 PDT)
[AMBER] MMPBSA.py TrajError: Could not find number of frames in .mdcrd maryam azimzadehirani (Thu Aug 04 2016 - 20:52:07 PDT)
- Re: [AMBER] MMPBSA.py TrajError: Could not find number of frames in .mdcrd David A Case (Fri Aug 05 2016 - 04:49:56 PDT)
  - Re: [AMBER] MMPBSA.py TrajError: Could not find number of frames in .mdcrd maryam azimzadehirani (Mon Aug 08 2016 - 00:27:58 PDT)
[AMBER] amber16/test/qmmm_DFTB Markus Kaukonen (Thu Aug 04 2016 - 23:13:12 PDT)
- Re: [AMBER] amber16/test/qmmm_DFTB Dr. Andreas W. Goetz (Thu Aug 04 2016 - 23:27:47 PDT)
[AMBER] QMMM MD, Simulation does not start Stregone (Fri Aug 05 2016 - 06:29:59 PDT)
- Re: [AMBER] QMMM MD, Simulation does not start Dr. Andreas W. Goetz (Fri Aug 05 2016 - 14:31:45 PDT)
  - Re: [AMBER] QMMM MD, Simulation does not start Stregone (Sun Aug 07 2016 - 04:01:57 PDT)
    - Re: [AMBER] QMMM MD, Simulation does not start Daniel Roe (Sun Aug 07 2016 - 14:42:01 PDT)
    - Re: [AMBER] QMMM MD, Simulation does not start Stregone (Mon Aug 08 2016 - 01:20:03 PDT)
[AMBER] Cpptraj-PCA Warning Ilkow, Veronica (Fri Aug 05 2016 - 07:15:50 PDT)
- Re: [AMBER] Cpptraj-PCA Warning Daniel Roe (Thu Oct 13 2016 - 06:14:51 PDT)
[AMBER] Amber14 FEW for 3 trajectory free energy JoAnne Babula (Fri Aug 05 2016 - 07:32:22 PDT)
- Re: [AMBER] Amber14 FEW for 3 trajectory free energy Amy Rice (Fri Aug 05 2016 - 08:21:50 PDT)
  - Re: [AMBER] Amber14 FEW for 3 trajectory free energy JoAnne Babula (Tue Aug 09 2016 - 11:02:24 PDT)
[AMBER] Implicit solvent in pmemd.cuda Chitrak Gupta (Fri Aug 05 2016 - 08:54:58 PDT)
- Re: [AMBER] Implicit solvent in pmemd.cuda Hai Nguyen (Fri Aug 05 2016 - 09:05:47 PDT)
  - Re: [AMBER] Implicit solvent in pmemd.cuda Carlos Simmerling (Fri Aug 05 2016 - 09:31:42 PDT)
    - Re: [AMBER] Implicit solvent in pmemd.cuda Ross Walker (Fri Aug 05 2016 - 09:39:36 PDT)
[AMBER] Error with nmode calculations Praneeth Bommisetti (Fri Aug 05 2016 - 11:10:32 PDT)
- Re: [AMBER] Error with nmode calculations Jason Swails (Fri Aug 05 2016 - 12:10:33 PDT)
[AMBER] restraining mean square displacements Irem Altan (Fri Aug 05 2016 - 12:52:35 PDT)
- Re: [AMBER] restraining mean square displacements Adrian Roitberg (Fri Aug 05 2016 - 12:54:33 PDT)
[AMBER] box of polar molecules using amoeba force field Xiaoliu Zhang (Fri Aug 05 2016 - 14:32:46 PDT)
[AMBER] Extend of manual modulation-Connecting two molecules methodology Kostas Bourandas (Sat Aug 06 2016 - 13:32:44 PDT)
- Re: [AMBER] Extend of manual modulation-Connecting two molecules methodology David A Case (Sat Aug 06 2016 - 19:27:23 PDT)
  - Re: [AMBER] Extend of manual modulation-Connecting two molecules methodology Kostas Bourandas (Mon Aug 08 2016 - 19:56:53 PDT)
[AMBER] How to fix the wall of the water box in amber Ming Tang (Sat Aug 06 2016 - 18:17:18 PDT)
- Re: [AMBER] How to fix the wall of the water box in amber Bill Ross (Sat Aug 06 2016 - 18:59:00 PDT)
  - Re: [AMBER] How to fix the wall of the water box in amber Ming Tang (Sat Aug 06 2016 - 22:34:11 PDT)
    - Re: [AMBER] How to fix the wall of the water box in amber Bill Ross (Sun Aug 07 2016 - 02:01:46 PDT)
[AMBER] copy charges using Python API Thomas Evangelidis (Sun Aug 07 2016 - 04:28:38 PDT)
- Re: [AMBER] copy charges using Python API Jason Swails (Sun Aug 07 2016 - 06:05:35 PDT)
  - Re: [AMBER] copy charges using Python API Thomas Evangelidis (Sun Aug 07 2016 - 06:50:23 PDT)
    - Re: [AMBER] copy charges using Python API Hai Nguyen (Mon Aug 08 2016 - 12:06:07 PDT)
  - Re: [AMBER] copy charges using Python API William Lees (Tue Aug 09 2016 - 02:07:50 PDT)
- Re: [AMBER] copy charges using Python API David A Case (Sun Aug 07 2016 - 09:13:06 PDT)
  - Re: [AMBER] copy charges using Python API Thomas Evangelidis (Mon Aug 08 2016 - 03:00:44 PDT)
    - Re: [AMBER] copy charges using Python API David A Case (Mon Aug 08 2016 - 05:16:13 PDT)
Re: [AMBER] SMD simulation bharat gupta (Sun Aug 07 2016 - 22:44:08 PDT)
[AMBER] intel MPI failed Albert (Mon Aug 08 2016 - 06:40:54 PDT)
- Re: [AMBER] intel MPI failed Daniel Roe (Mon Aug 08 2016 - 07:16:04 PDT)
  - Re: [AMBER] intel MPI failed Albert (Mon Aug 08 2016 - 07:26:47 PDT)
    - Re: [AMBER] intel MPI failed Daniel Roe (Mon Aug 08 2016 - 07:37:26 PDT)
    - Re: [AMBER] intel MPI failed Albert (Mon Aug 08 2016 - 07:39:38 PDT)
    - Re: [AMBER] intel MPI failed Albert (Mon Aug 08 2016 - 23:12:00 PDT)
    - Re: [AMBER] intel MPI failed David A Case (Tue Aug 09 2016 - 04:55:04 PDT)
    - Re: [AMBER] intel MPI failed Albert (Tue Aug 09 2016 - 06:00:17 PDT)
[AMBER] reweighting scheme Thakur, Abhishek (Mon Aug 08 2016 - 12:02:00 PDT)
[AMBER] phi-psi distribution Thakur, Abhishek (Mon Aug 08 2016 - 13:54:24 PDT)
[AMBER] Setting up a pdb file for a QM/MM calculation with explicit water Corum, Katharine W (Mon Aug 08 2016 - 14:33:12 PDT)
- Re: [AMBER] Setting up a pdb file for a QM/MM calculation with explicit water Ayesha Fatima (Mon Aug 08 2016 - 16:36:48 PDT)
- Re: [AMBER] Setting up a pdb file for a QM/MM calculation with explicit water David A Case (Tue Aug 09 2016 - 04:52:06 PDT)
  - Re: [AMBER] Setting up a pdb file for a QM/MM calculation with explicit water Corum, Katharine W (Tue Aug 09 2016 - 07:20:05 PDT)
    - Re: [AMBER] Setting up a pdb file for a QM/MM calculation with explicit water Marc van der Kamp (Tue Aug 09 2016 - 07:43:13 PDT)
    - Re: [AMBER] Setting up a pdb file for a QM/MM calculation with explicit water Corum, Katharine W (Tue Aug 09 2016 - 07:53:51 PDT)
    - Re: [AMBER] Setting up a pdb file for a QM/MM calculation with explicit water David A Case (Tue Aug 09 2016 - 12:30:04 PDT)
[AMBER] query regarding restraint on specific residues. Saman Yousuf ali (Tue Aug 09 2016 - 00:00:57 PDT)
- Re: [AMBER] query regarding restraint on specific residues. David A Case (Tue Aug 09 2016 - 05:02:10 PDT)
  - Re: [AMBER] query regarding restraint on specific residues. Saman Yousuf ali (Tue Aug 09 2016 - 08:08:10 PDT)
[AMBER] {AMBER} installation on mac osx 10.11.6 hanging when configuring NetCDF mirko hennig (Tue Aug 09 2016 - 00:53:23 PDT)
- Re: [AMBER] {AMBER} installation on mac osx 10.11.6 hanging when configuring NetCDF David A Case (Tue Aug 09 2016 - 05:00:39 PDT)
  - Re: [AMBER] {AMBER} installation on mac osx 10.11.6 hanging when configuring NetCDF mirko hennig (Tue Aug 09 2016 - 08:29:50 PDT)
[AMBER] Off , mol2 and frcmod files Christopher Jesudason (Tue Aug 09 2016 - 04:40:25 PDT)
- Re: [AMBER] Off , mol2 and frcmod files David A Case (Tue Aug 09 2016 - 06:56:40 PDT)
[AMBER] for what kind of post simulation analysis I need to do reweighing? Thakur, Abhishek (Tue Aug 09 2016 - 08:01:27 PDT)
- Re: [AMBER] for what kind of post simulation analysis I need to do reweighing? Adrian Roitberg (Tue Aug 09 2016 - 08:04:05 PDT)
  - Re: [AMBER] for what kind of post simulation analysis I need to do reweighing? Thakur, Abhishek (Tue Aug 09 2016 - 08:08:32 PDT)
    - Re: [AMBER] for what kind of post simulation analysis I need to do reweighing? Christina Bergonzo (Tue Aug 09 2016 - 09:18:41 PDT)
[AMBER] simultaneous use of ibelly=1 and ntr=1 Saman Yousuf ali (Tue Aug 09 2016 - 08:54:47 PDT)
- Re: [AMBER] simultaneous use of ibelly=1 and ntr=1 David A Case (Tue Aug 09 2016 - 12:33:05 PDT)
  - Re: [AMBER] simultaneous use of ibelly=1 and ntr=1 Saman Yousuf ali (Tue Aug 09 2016 - 12:41:00 PDT)
[AMBER] Converting rst to pdb Corum, Katharine W (Tue Aug 09 2016 - 14:01:58 PDT)
- Re: [AMBER] Converting rst to pdb Hai Nguyen (Tue Aug 09 2016 - 14:09:46 PDT)
- Re: [AMBER] Converting rst to pdb Daniel Roe (Tue Aug 09 2016 - 14:22:17 PDT)
  - Re: [AMBER] Converting rst to pdb Corum, Katharine W (Tue Aug 09 2016 - 16:26:09 PDT)
[AMBER] Amber 14.13 pmemd.cuda: Error: invalid configuration argument launching kernel kPMEReduceChargeGridBuffer William Lees (Wed Aug 10 2016 - 02:02:59 PDT)
- Re: [AMBER] Amber 14.13 pmemd.cuda: Error: invalid configuration argument launching kernel kPMEReduceChargeGridBuffer Ross Walker (Wed Aug 10 2016 - 20:01:52 PDT)
  - Re: [AMBER] Amber 14.13 pmemd.cuda: Error: invalid configuration argument launching kernel kPMEReduceChargeGridBuffer William Lees (Fri Aug 12 2016 - 06:19:05 PDT)
[AMBER] does AMBER already have Pt parameters for modeling cisplatin like compounds? Vaibhav Dixit (Wed Aug 10 2016 - 04:49:05 PDT)
- Re: [AMBER] does AMBER already have Pt parameters for modeling cisplatin like compounds? Pengfei Li (Wed Aug 10 2016 - 06:37:06 PDT)
[AMBER] 3 trajectory MMPBSA free energy calculation JoAnne Babula (Wed Aug 10 2016 - 07:47:45 PDT)
- Re: [AMBER] 3 trajectory MMPBSA free energy calculation Amy Rice (Wed Aug 10 2016 - 08:34:15 PDT)
  - Re: [AMBER] 3 trajectory MMPBSA free energy calculation JoAnne Babula (Wed Aug 10 2016 - 11:04:44 PDT)
[AMBER] Regarding antechamber command Error Vishal Nemaysh (Wed Aug 10 2016 - 08:47:05 PDT)
- [AMBER] Fwd: Regarding antechamber command Error Vishal Nemaysh (Thu Aug 11 2016 - 00:10:40 PDT)
- Re: [AMBER] Regarding antechamber command Error David A Case (Thu Aug 11 2016 - 04:52:43 PDT)
  - Re: [AMBER] Regarding antechamber command Error Vishal Nemaysh (Thu Aug 11 2016 - 06:07:53 PDT)
    - Re: [AMBER] Regarding antechamber command Error David A Case (Thu Aug 11 2016 - 12:38:51 PDT)
    - Re: [AMBER] Regarding antechamber command Error Vishal Nemaysh (Thu Aug 11 2016 - 23:36:29 PDT)
    - Re: [AMBER] Regarding antechamber command Error David A Case (Fri Aug 12 2016 - 05:34:01 PDT)
[AMBER] paper describing the ff15ipq protein force field is now available David A Case (Wed Aug 10 2016 - 11:11:08 PDT)
- Re: [AMBER] paper describing the ff15ipq protein force field is now available David Cerutti (Wed Aug 10 2016 - 11:55:11 PDT)
[AMBER] antechamber cannot match patching atoms of amino acid Chitrak Gupta (Wed Aug 10 2016 - 15:26:24 PDT)
- Re: [AMBER] antechamber cannot match patching atoms of amino acid David A Case (Thu Aug 11 2016 - 05:05:53 PDT)
- Re: [AMBER] antechamber cannot match patching atoms of amino acid FyD (Fri Aug 12 2016 - 01:12:01 PDT)
[AMBER] GPU MPI failed Albert (Thu Aug 11 2016 - 01:37:52 PDT)
- Re: [AMBER] GPU MPI failed David A Case (Thu Aug 11 2016 - 05:15:16 PDT)
  - Re: [AMBER] GPU MPI failed Albert (Thu Aug 11 2016 - 06:20:37 PDT)
[AMBER] Amber16 installation error. Abhilash J (Thu Aug 11 2016 - 07:55:00 PDT)
- Re: [AMBER] Amber16 installation error. Hai Nguyen (Thu Aug 11 2016 - 11:54:41 PDT)
  - Re: [AMBER] Amber16 installation error. Abhilash J (Thu Aug 11 2016 - 12:06:33 PDT)
    - Re: [AMBER] Amber16 installation error. Hai Nguyen (Thu Aug 11 2016 - 12:12:35 PDT)
    - Re: [AMBER] Amber16 installation error. Abhilash J (Thu Aug 11 2016 - 12:18:33 PDT)
    - Re: [AMBER] Amber16 installation error. Hai Nguyen (Thu Aug 11 2016 - 12:41:34 PDT)
    - Re: [AMBER] Amber16 installation error. Abhilash J (Thu Aug 11 2016 - 12:45:35 PDT)
    - Re: [AMBER] Amber16 installation error. Hai Nguyen (Thu Aug 11 2016 - 12:52:46 PDT)
    - Re: [AMBER] Amber16 installation error. Abhilash J (Thu Aug 11 2016 - 13:04:45 PDT)
    - Re: [AMBER] Amber16 installation error. Hai Nguyen (Thu Aug 11 2016 - 13:13:53 PDT)
    - Re: [AMBER] Amber16 installation error. Hai Nguyen (Thu Aug 11 2016 - 13:16:30 PDT)
    - Re: [AMBER] Amber16 installation error. Abhilash J (Thu Aug 11 2016 - 13:27:52 PDT)
    - Re: [AMBER] Amber16 installation error. Hai Nguyen (Thu Aug 11 2016 - 13:36:56 PDT)
    - Re: [AMBER] Amber16 installation error. Abhilash J (Thu Aug 11 2016 - 13:44:56 PDT)
    - Re: [AMBER] Amber16 installation error. Abhilash J (Thu Aug 11 2016 - 14:00:32 PDT)
    - Re: [AMBER] Amber16 installation error. Hai Nguyen (Thu Aug 11 2016 - 14:06:31 PDT)
    - Re: [AMBER] Amber16 installation error. Abhilash J (Thu Aug 11 2016 - 14:19:11 PDT)
[AMBER] error in mdcrd box coordinates during MMPBSA calculation JoAnne Babula (Thu Aug 11 2016 - 08:21:11 PDT)
- Re: [AMBER] error in mdcrd box coordinates during MMPBSA calculation Hai Nguyen (Thu Aug 11 2016 - 11:32:25 PDT)
  - Re: [AMBER] error in mdcrd box coordinates during MMPBSA calculation JoAnne Babula (Thu Aug 11 2016 - 11:41:31 PDT)
    - Re: [AMBER] error in mdcrd box coordinates during MMPBSA calculation Hai Nguyen (Thu Aug 11 2016 - 11:49:15 PDT)
    - Re: [AMBER] error in mdcrd box coordinates during MMPBSA calculation Bilal Nizami (Fri Aug 12 2016 - 00:15:01 PDT)
    - Re: [AMBER] error in mdcrd box coordinates during MMPBSA calculation JoAnne Babula (Fri Aug 12 2016 - 10:34:41 PDT)
    - Re: [AMBER] error in mdcrd box coordinates during MMPBSA calculation JoAnne Babula (Fri Aug 12 2016 - 10:38:24 PDT)
    - Re: [AMBER] error in mdcrd box coordinates during MMPBSA calculation Amy Rice (Fri Aug 12 2016 - 10:46:30 PDT)
    - Re: [AMBER] error in mdcrd box coordinates during MMPBSA calculation JoAnne Babula (Fri Aug 12 2016 - 11:41:21 PDT)
    - Re: [AMBER] error in mdcrd box coordinates during MMPBSA calculation Hai Nguyen (Fri Aug 12 2016 - 11:49:05 PDT)
    - Re: [AMBER] error in mdcrd box coordinates during MMPBSA calculation Bilal Nizami (Sat Aug 13 2016 - 01:11:11 PDT)
    - Re: [AMBER] error in mdcrd box coordinates during MMPBSA calculation JoAnne Babula (Mon Aug 22 2016 - 07:19:03 PDT)
    - Re: [AMBER] error in mdcrd box coordinates during MMPBSA calculation Nhai (Mon Aug 22 2016 - 08:31:42 PDT)
    - Re: [AMBER] error in mdcrd box coordinates during MMPBSA calculation JoAnne Babula (Mon Aug 22 2016 - 08:33:56 PDT)
    - Re: [AMBER] error in mdcrd box coordinates during MMPBSA calculation Nhai (Mon Aug 22 2016 - 08:38:38 PDT)
    - Re: [AMBER] error in mdcrd box coordinates during MMPBSA calculation JoAnne Babula (Mon Aug 22 2016 - 08:54:16 PDT)
    - Re: [AMBER] error in mdcrd box coordinates during MMPBSA calculation JoAnne Babula (Mon Aug 22 2016 - 09:04:27 PDT)
    - Re: [AMBER] error in mdcrd box coordinates during MMPBSA calculation Hai Nguyen (Mon Aug 22 2016 - 09:40:38 PDT)
    - Re: [AMBER] error in mdcrd box coordinates during MMPBSA calculation JoAnne Babula (Mon Aug 22 2016 - 09:58:21 PDT)
    - Re: [AMBER] error in mdcrd box coordinates during MMPBSA calculation Hai Nguyen (Mon Aug 22 2016 - 10:17:51 PDT)
    - Re: [AMBER] error in mdcrd box coordinates during MMPBSA calculation JoAnne Babula (Mon Aug 22 2016 - 17:56:23 PDT)
    - Re: [AMBER] error in mdcrd box coordinates during MMPBSA calculation Jason Swails (Tue Aug 23 2016 - 09:25:45 PDT)
[AMBER] secondary structure graph vs Time Parviz Seifpanahi Shabane (Thu Aug 11 2016 - 09:03:01 PDT)
- Re: [AMBER] secondary structure graph vs Time Adrian Roitberg (Thu Aug 11 2016 - 09:05:01 PDT)
  - Re: [AMBER] secondary structure graph vs Time Parviz Seifpanahi Shabane (Thu Aug 11 2016 - 09:16:59 PDT)
    - Re: [AMBER] secondary structure graph vs Time Adrian Roitberg (Thu Aug 11 2016 - 09:26:20 PDT)
    - Re: [AMBER] secondary structure graph vs Time Prajwal Nandekar (Fri Aug 12 2016 - 01:58:20 PDT)
    - Re: [AMBER] secondary structure graph vs Time Parviz Seifpanahi Shabane (Mon Aug 15 2016 - 13:28:43 PDT)
    - Re: [AMBER] secondary structure graph vs Time Daniel Roe (Mon Aug 15 2016 - 14:15:24 PDT)
    - Re: [AMBER] secondary structure graph vs Time Parviz Seifpanahi Shabane (Tue Aug 16 2016 - 08:45:59 PDT)
[AMBER] Running tleap with old prmtop Taylor Quinn (Thu Aug 11 2016 - 10:13:09 PDT)
- Re: [AMBER] Running tleap with old prmtop Samuel Bowerman (Thu Aug 11 2016 - 10:30:18 PDT)
[AMBER] GPU peer support disabled Hirdesh Kumar (Thu Aug 11 2016 - 13:53:22 PDT)
- Re: [AMBER] GPU peer support disabled Ross Walker (Thu Aug 11 2016 - 14:01:33 PDT)
  - Re: [AMBER] GPU peer support disabled Hirdesh Kumar (Thu Aug 11 2016 - 14:11:38 PDT)
[AMBER] LINMIN FAILURE on large protein minimization with GB and explicit SUNHEE CHO (Thu Aug 11 2016 - 18:25:19 PDT)
- Re: [AMBER] LINMIN FAILURE on large protein minimization with GB and explicit Ross Walker (Thu Aug 11 2016 - 18:47:20 PDT)
- Re: [AMBER] LINMIN FAILURE on large protein minimization with GB and explicit David A Case (Fri Aug 12 2016 - 05:27:23 PDT)
[AMBER] not sure if this is an ERROR in installation please suggest Vaibhav Dixit (Thu Aug 11 2016 - 20:44:07 PDT)
- Re: [AMBER] not sure if this is an ERROR in installation please suggest Ross Walker (Thu Aug 11 2016 - 21:32:26 PDT)
  - Re: [AMBER] not sure if this is an ERROR in installation please suggest Hai Nguyen (Thu Aug 11 2016 - 22:11:31 PDT)
    - Re: [AMBER] not sure if this is an ERROR in installation please suggest Vaibhav Dixit (Fri Aug 12 2016 - 00:43:29 PDT)
    - Re: [AMBER] not sure if this is an ERROR in installation please suggest Hai Nguyen (Fri Aug 12 2016 - 06:36:34 PDT)
[AMBER] amber pdb > 100,000 atoms Neha Gandhi (Fri Aug 12 2016 - 00:53:28 PDT)
- Re: [AMBER] amber pdb > 100,000 atoms Marc van der Kamp (Fri Aug 12 2016 - 01:19:18 PDT)
- Re: [AMBER] amber pdb > 100,000 atoms David A Case (Fri Aug 12 2016 - 05:42:19 PDT)
[AMBER] modeling flexible loops in protein-DNA complexes Vlad Cojocaru (Fri Aug 12 2016 - 01:43:23 PDT)
[AMBER] Optimal force constant for AMBER Stregone (Fri Aug 12 2016 - 06:29:15 PDT)
- Re: [AMBER] Optimal force constant for AMBER David A Case (Fri Aug 12 2016 - 07:40:46 PDT)
[AMBER] job suspended Albert (Fri Aug 12 2016 - 06:33:22 PDT)
- Re: [AMBER] job suspended David A Case (Fri Aug 12 2016 - 08:11:28 PDT)
  - Re: [AMBER] job suspended Albert (Fri Aug 12 2016 - 08:15:42 PDT)
    - Re: [AMBER] job suspended Nhai (Fri Aug 12 2016 - 08:26:09 PDT)
[AMBER] MASK with distance in AMBER. Parviz Seifpanahi Shabane (Fri Aug 12 2016 - 08:48:32 PDT)
- Re: [AMBER] MASK with distance in AMBER. Daniel Roe (Fri Aug 12 2016 - 10:54:05 PDT)
  - Re: [AMBER] MASK with distance in AMBER. Parviz Seifpanahi Shabane (Tue Aug 16 2016 - 11:23:32 PDT)
    - Re: [AMBER] MASK with distance in AMBER. Daniel Roe (Wed Aug 17 2016 - 09:38:20 PDT)
[AMBER] umbrella sampling restraining both angle and distance Thakur, Abhishek (Fri Aug 12 2016 - 09:50:11 PDT)
- Re: [AMBER] umbrella sampling restraining both angle and distance Carlos Simmerling (Fri Aug 12 2016 - 15:22:27 PDT)
  - Re: [AMBER] umbrella sampling restraining both angle and distance Thakur, Abhishek (Fri Aug 12 2016 - 15:49:30 PDT)
    - Re: [AMBER] umbrella sampling restraining both angle and distance Carlos Simmerling (Sun Aug 14 2016 - 07:55:57 PDT)
[AMBER] cpptraj issues Thomas Pochapsky (Fri Aug 12 2016 - 09:52:19 PDT)
- Re: [AMBER] cpptraj issues Daniel Roe (Fri Aug 12 2016 - 10:56:20 PDT)
- [AMBER] Fwd: cpptraj issues Thomas Pochapsky (Mon Aug 15 2016 - 08:02:22 PDT)
  - Re: [AMBER] Fwd: cpptraj issues Daniel Roe (Mon Aug 15 2016 - 10:45:40 PDT)
- [AMBER] Fwd: cpptraj issues Thomas Pochapsky (Tue Aug 16 2016 - 07:20:30 PDT)
  - Re: [AMBER] Fwd: cpptraj issues Daniel Roe (Tue Aug 16 2016 - 07:56:01 PDT)
    - Re: [AMBER] Fwd: cpptraj issues Thomas Pochapsky (Tue Aug 16 2016 - 08:23:25 PDT)
[AMBER] Two ion problem with mcpb.py Abhilash J (Fri Aug 12 2016 - 10:11:55 PDT)
- Re: [AMBER] Two ion problem with mcpb.py sunita guptacDgug (Fri Aug 12 2016 - 12:50:46 PDT)
  - Re: [AMBER] Two ion problem with mcpb.py Pengfei Li (Tue Aug 16 2016 - 07:40:46 PDT)
    - Re: [AMBER] Two ion problem with mcpb.py Abhilash J (Thu Aug 18 2016 - 12:17:50 PDT)
    - Re: [AMBER] Two ion problem with mcpb.py Pengfei Li (Thu Aug 18 2016 - 18:18:35 PDT)
    - Re: [AMBER] Two ion problem with mcpb.py Abhilash J (Thu Aug 18 2016 - 21:19:44 PDT)
[AMBER] Amber B5 tutorial Chitrak Gupta (Fri Aug 12 2016 - 11:10:05 PDT)
- Re: [AMBER] Amber B5 tutorial David A Case (Fri Aug 12 2016 - 12:22:25 PDT)
[AMBER] Accelerated MD -- cudaMemcpy error Dmitry Suplatov (Fri Aug 12 2016 - 13:53:07 PDT)
- Re: [AMBER] Accelerated MD -- cudaMemcpy error DmitryASuplatov (Mon Aug 15 2016 - 03:52:14 PDT)
  - Re: [AMBER] Accelerated MD -- cudaMemcpy error Daniel Roe (Mon Aug 15 2016 - 11:01:27 PDT)
- Re: [AMBER] Accelerated MD -- cudaMemcpy error DmitryASuplatov (Tue Aug 16 2016 - 04:05:38 PDT)
  - Re: [AMBER] Accelerated MD -- cudaMemcpy error Daniel Roe (Tue Aug 16 2016 - 07:58:59 PDT)
[AMBER] Question of Parameter Defaults Robert Molt (Fri Aug 12 2016 - 18:00:57 PDT)
- Re: [AMBER] Question of Parameter Defaults Carlos Simmerling (Sat Aug 13 2016 - 07:37:00 PDT)
- Re: [AMBER] Question of Parameter Defaults David A Case (Sat Aug 13 2016 - 12:48:59 PDT)
  - Re: [AMBER] Question of Parameter Defaults Robert Molt (Mon Aug 15 2016 - 10:49:12 PDT)
[AMBER] job failed Albert (Sat Aug 13 2016 - 23:37:26 PDT)
- Re: [AMBER] job failed David A Case (Sun Aug 14 2016 - 06:03:23 PDT)
[AMBER] error in sander and sander.mpi running leila karami (Sun Aug 14 2016 - 04:11:11 PDT)
[AMBER] error in sander and sander.mpi running leila karami (Sun Aug 14 2016 - 05:24:31 PDT)
- Re: [AMBER] error in sander and sander.mpi running Daniel Roe (Tue Aug 16 2016 - 07:52:01 PDT)
[AMBER] solid surface simulation in amber Neha Gandhi (Sun Aug 14 2016 - 23:59:57 PDT)
- Re: [AMBER] solid surface simulation in amber David A Case (Mon Aug 15 2016 - 04:39:23 PDT)
  - Re: [AMBER] solid surface simulation in amber Neha Gandhi (Mon Aug 15 2016 - 22:25:46 PDT)
    - Re: [AMBER] solid surface simulation in amber Bill Ross (Tue Aug 16 2016 - 00:33:02 PDT)
    - Re: [AMBER] solid surface simulation in amber Neha Gandhi (Tue Aug 16 2016 - 01:00:20 PDT)
    - Re: [AMBER] solid surface simulation in amber Bill Ross (Tue Aug 16 2016 - 01:27:51 PDT)
    - Re: [AMBER] solid surface simulation in amber David A Case (Tue Aug 16 2016 - 05:04:29 PDT)
    - Re: [AMBER] solid surface simulation in amber Neha Gandhi (Tue Aug 16 2016 - 06:17:47 PDT)
    - Re: [AMBER] solid surface simulation in amber Daniel Roe (Tue Aug 16 2016 - 07:58:05 PDT)
    - Re: [AMBER] solid surface simulation in amber Neha Gandhi (Thu Aug 18 2016 - 01:27:28 PDT)
    - Re: [AMBER] solid surface simulation in amber Bill Ross (Thu Aug 18 2016 - 01:36:32 PDT)
    - Re: [AMBER] solid surface simulation in amber Neha Gandhi (Thu Aug 18 2016 - 01:48:12 PDT)
    - Re: [AMBER] solid surface simulation in amber Bill Ross (Thu Aug 18 2016 - 01:55:20 PDT)
    - Re: [AMBER] solid surface simulation in amber David A Case (Thu Aug 18 2016 - 06:13:05 PDT)
    - Re: [AMBER] solid surface simulation in amber Neha Gandhi (Fri Aug 19 2016 - 01:57:24 PDT)
    - Re: [AMBER] solid surface simulation in amber David A Case (Fri Aug 19 2016 - 07:54:01 PDT)
    - Re: [AMBER] solid surface simulation in amber Bill Ross (Fri Aug 19 2016 - 14:06:40 PDT)
    - Re: [AMBER] solid surface simulation in amber Neha Gandhi (Fri Aug 19 2016 - 18:28:18 PDT)
    - Re: [AMBER] solid surface simulation in amber Bill Ross (Fri Aug 19 2016 - 18:35:12 PDT)
    - Re: [AMBER] solid surface simulation in amber Neha Gandhi (Mon Aug 22 2016 - 02:00:52 PDT)
    - Re: [AMBER] solid surface simulation in amber Bill Ross (Mon Aug 22 2016 - 03:07:59 PDT)
    - Re: [AMBER] solid surface simulation in amber Neha Gandhi (Mon Aug 22 2016 - 03:17:23 PDT)
[AMBER] parmchk2 issue Hannes Loeffler (Mon Aug 15 2016 - 08:06:38 PDT)
- Re: [AMBER] parmchk2 issue David A Case (Mon Aug 15 2016 - 09:06:35 PDT)
  - Re: [AMBER] parmchk2 issue Hannes Loeffler (Tue Aug 16 2016 - 01:35:08 PDT)
    - Re: [AMBER] parmchk2 issue David A Case (Tue Aug 16 2016 - 05:09:37 PDT)
    - Re: [AMBER] parmchk2 issue Hannes Loeffler (Tue Aug 16 2016 - 06:47:21 PDT)
    - Re: [AMBER] parmchk2 issue David A Case (Tue Aug 16 2016 - 14:15:52 PDT)
[AMBER] QM/MM stops at step 2114 Corum, Katharine W (Mon Aug 15 2016 - 08:08:25 PDT)
- Re: [AMBER] QM/MM stops at step 2114 David A Case (Mon Aug 15 2016 - 09:13:44 PDT)
  - Re: [AMBER] QM/MM stops at step 2114 Corum, Katharine W (Tue Aug 16 2016 - 06:40:23 PDT)
[AMBER] [AMBER} NetCDF installation problem on mac OS X El Capitan mirko hennig (Mon Aug 15 2016 - 09:26:56 PDT)
- Re: [AMBER] [AMBER} NetCDF installation problem on mac OS X El Capitan Hai Nguyen (Mon Aug 15 2016 - 09:50:41 PDT)
  - Re: [AMBER] [AMBER} NetCDF installation problem on mac OS X El Capitan mirko hennig (Mon Aug 15 2016 - 10:03:04 PDT)
    - Re: [AMBER] [AMBER} NetCDF installation problem on mac OS X El Capitan Hai Nguyen (Mon Aug 15 2016 - 10:15:04 PDT)
- Re: [AMBER] [AMBER} NetCDF installation problem on mac OS X El Capitan David A Case (Mon Aug 15 2016 - 10:00:30 PDT)
  - Re: [AMBER] [AMBER} NetCDF installation problem on mac OS X El Capitan mirko hennig (Mon Aug 15 2016 - 11:00:40 PDT)
    - Re: [AMBER] [AMBER} NetCDF installation problem on mac OS X El Capitan David A Case (Mon Aug 15 2016 - 13:32:38 PDT)
    - Re: [AMBER] [AMBER} NetCDF installation problem on mac OS X El Capitan Jason Swails (Mon Aug 15 2016 - 18:56:04 PDT)
    - Re: [AMBER] [AMBER} NetCDF installation problem on mac OS X El Capitan mirko hennig (Tue Aug 16 2016 - 00:18:10 PDT)
    - Re: [AMBER] [AMBER} NetCDF installation problem on mac OS X El Capitan David A Case (Tue Aug 16 2016 - 04:57:21 PDT)
    - Re: [AMBER] [AMBER} NetCDF installation problem on mac OS X El Capitan mirko hennig (Tue Aug 16 2016 - 07:53:42 PDT)
    - Re: [AMBER] [AMBER} NetCDF installation problem on mac OS X El Capitan Jason Swails (Thu Aug 18 2016 - 05:18:47 PDT)
- Re: [AMBER] [AMBER} NetCDF installation problem on mac OS X El Capitan Jason Swails (Fri Aug 19 2016 - 05:51:35 PDT)
  - Re: [AMBER] [AMBER} NetCDF installation problem on mac OS X El Capitan mirko hennig (Sat Aug 27 2016 - 09:52:04 PDT)
    - Re: [AMBER] [AMBER} NetCDF installation problem on mac OS X El Capitan Nhai (Sat Aug 27 2016 - 15:07:14 PDT)
    - Re: [AMBER] [AMBER} NetCDF installation problem on mac OS X El Capitan mirko hennig (Sat Aug 27 2016 - 15:32:25 PDT)
    - Re: [AMBER] [AMBER} NetCDF installation problem on mac OS X El Capitan Bill Ross (Sat Aug 27 2016 - 15:33:52 PDT)
[AMBER] CHARM force field Chi Jin (Mon Aug 15 2016 - 13:48:12 PDT)
- Re: [AMBER] CHARM force field Jason Swails (Mon Aug 15 2016 - 18:50:22 PDT)
[AMBER] bellymask option. Saman Yousuf ali (Mon Aug 15 2016 - 19:24:05 PDT)
- Re: [AMBER] bellymask option. David A Case (Tue Aug 16 2016 - 04:59:16 PDT)
  - Re: [AMBER] bellymask option. Saman Yousuf ali (Tue Aug 16 2016 - 07:48:26 PDT)
[AMBER] lipid simulation with Lipid14 FF failed Albert (Tue Aug 16 2016 - 03:00:50 PDT)
- Re: [AMBER] lipid simulation with Lipid14 FF failed David A Case (Tue Aug 16 2016 - 05:11:16 PDT)
  - Re: [AMBER] lipid simulation with Lipid14 FF failed Albert (Tue Aug 16 2016 - 06:07:56 PDT)
    - Re: [AMBER] lipid simulation with Lipid14 FF failed Ross Walker (Tue Aug 16 2016 - 07:07:30 PDT)
[AMBER] Water flexibility in QM/MM simulation Ruth Helena Tichauer (Tue Aug 16 2016 - 09:27:14 PDT)
[AMBER] Restarting a crushed run DmitryASuplatov (Tue Aug 16 2016 - 09:43:44 PDT)
- Re: [AMBER] Restarting a crushed run Bill Ross (Tue Aug 16 2016 - 12:12:05 PDT)
  - Re: [AMBER] Restarting a crushed run Bill Ross (Tue Aug 16 2016 - 12:40:07 PDT)
    - Re: [AMBER] Restarting a crushed run Dmitry Suplatov (Tue Aug 16 2016 - 12:45:23 PDT)
    - Re: [AMBER] Restarting a crushed run Dmitry Suplatov (Tue Aug 16 2016 - 13:27:34 PDT)
    - Re: [AMBER] Restarting a crushed run Bill Ross (Tue Aug 16 2016 - 14:24:52 PDT)
    - Re: [AMBER] Restarting a crushed run Ross Walker (Tue Aug 16 2016 - 15:53:43 PDT)
[AMBER] Regarding the free energy calculation Sivanandam M (Tue Aug 16 2016 - 11:00:06 PDT)
- Re: [AMBER] Regarding the free energy calculation Daniel Mermelstein (Fri Aug 19 2016 - 11:32:23 PDT)
[AMBER] Combining single structure NMR pdb files into an ensemble. Erik Davis (Tue Aug 16 2016 - 13:38:05 PDT)
- Re: [AMBER] Combining single structure NMR pdb files into an ensemble. Hai Nguyen (Tue Aug 16 2016 - 13:45:14 PDT)
  - Re: [AMBER] Combining single structure NMR pdb files into an ensemble. Erik Davis (Wed Aug 17 2016 - 06:05:24 PDT)
[AMBER] about lipids retrain Albert (Wed Aug 17 2016 - 02:45:19 PDT)
- Re: [AMBER] about lipids retrain David A Case (Wed Aug 17 2016 - 04:48:00 PDT)
  - Re: [AMBER] about lipids retrain Albert (Wed Aug 17 2016 - 05:26:59 PDT)
[AMBER] MD simulation with non natural amino acid, parameterized using the RED server Cecilia Lindgren (Wed Aug 17 2016 - 05:56:24 PDT)
- Re: [AMBER] MD simulation with non natural amino acid, parameterized using the RED server David A Case (Wed Aug 17 2016 - 07:13:46 PDT)
  - Re: [AMBER] MD simulation with non natural amino acid, parameterized using the RED server Cecilia Lindgren (Wed Aug 17 2016 - 23:11:15 PDT)
    - Re: [AMBER] MD simulation with non natural amino acid, parameterized using the RED server Bill Ross (Wed Aug 17 2016 - 23:40:44 PDT)
    - Re: [AMBER] MD simulation with non natural amino acid, parameterized using the RED server Cecilia Lindgren (Thu Aug 18 2016 - 01:35:54 PDT)
    - Re: [AMBER] MD simulation with non natural amino acid, parameterized using the RED server Bill Ross (Thu Aug 18 2016 - 01:49:43 PDT)
    - Re: [AMBER] MD simulation with non natural amino acid, parameterized using the RED server Cecilia Lindgren (Thu Aug 18 2016 - 02:03:43 PDT)
    - Re: [AMBER] MD simulation with non natural amino acid, parameterized using the RED server Bill Ross (Thu Aug 18 2016 - 02:17:30 PDT)
    - Re: [AMBER] MD simulation with non natural amino acid, parameterized using the RED server Hannes Loeffler (Thu Aug 18 2016 - 02:19:35 PDT)
    - Re: [AMBER] MD simulation with non natural amino acid, parameterized using the RED server Bill Ross (Thu Aug 18 2016 - 02:24:14 PDT)
    - Re: [AMBER] MD simulation with non natural amino acid, parameterized using the RED server Cecilia Lindgren (Thu Aug 18 2016 - 03:40:21 PDT)
- Re: [AMBER] MD simulation with non natural amino acid, parameterized using the RED server FyD (Sat Aug 20 2016 - 01:55:11 PDT)
[AMBER] Is there any CG martini parameter for K+? li he (Wed Aug 17 2016 - 11:18:34 PDT)
- Re: [AMBER] Is there any CG martini parameter for K+? Pengfei Li (Wed Aug 17 2016 - 13:40:33 PDT)
[AMBER] Problem when visualizing bonds in VMD Xiaoliu Zhang (Wed Aug 17 2016 - 12:40:22 PDT)
- Re: [AMBER] Problem when visualizing bonds in VMD Jason Swails (Wed Aug 17 2016 - 13:17:27 PDT)
- Re: [AMBER] Problem when visualizing bonds in VMD Xiaoliu Zhang (Thu Aug 18 2016 - 14:56:00 PDT)
  - Re: [AMBER] Problem when visualizing bonds in VMD Hai Nguyen (Thu Aug 18 2016 - 15:12:22 PDT)
- Re: [AMBER] Problem when visualizing bonds in VMD Xiaoliu Zhang (Fri Aug 19 2016 - 13:30:22 PDT)
  - Re: [AMBER] Problem when visualizing bonds in VMD Nhai (Fri Aug 19 2016 - 14:53:17 PDT)
[AMBER] QM region has an odd number of electrons Corum, Katharine W (Wed Aug 17 2016 - 14:22:53 PDT)
- Re: [AMBER] QM region has an odd number of electrons Dr. Andreas W. Goetz (Wed Aug 17 2016 - 16:33:24 PDT)
[AMBER] RMSd Wong Li Zhe (Wed Aug 17 2016 - 21:08:05 PDT)
- Re: [AMBER] RMSd Hai Nguyen (Wed Aug 17 2016 - 21:11:05 PDT)
  - Re: [AMBER] RMSd Wong Li Zhe (Wed Aug 17 2016 - 21:12:52 PDT)
    - Re: [AMBER] RMSd Wong Li Zhe (Wed Aug 17 2016 - 22:50:22 PDT)
    - Re: [AMBER] RMSd Bill Ross (Wed Aug 17 2016 - 23:18:53 PDT)
[AMBER] LEaP and PARMSETs Aronica, Pietro (Thu Aug 18 2016 - 01:49:50 PDT)
- Re: [AMBER] LEaP and PARMSETs David A Case (Fri Sep 30 2016 - 04:57:06 PDT)
[AMBER] a bug in leaprc.gaff2 file Ye Mei (Thu Aug 18 2016 - 02:21:16 PDT)
- Re: [AMBER] a bug in leaprc.gaff2 file David A Case (Thu Aug 18 2016 - 06:22:25 PDT)
  - Re: [AMBER] a bug in leaprc.gaff2 file David A Case (Thu Aug 18 2016 - 11:07:07 PDT)
[AMBER] Problem in charge generation through antechamber ATUL KUMAR (Thu Aug 18 2016 - 11:53:45 PDT)
- Re: [AMBER] Problem in charge generation through antechamber Bruno Falcone (Thu Aug 18 2016 - 12:33:49 PDT)
  - Re: [AMBER] Problem in charge generation through antechamber ATUL KUMAR (Thu Aug 18 2016 - 12:43:07 PDT)
    - Re: [AMBER] Problem in charge generation through antechamber Bruno Falcone (Thu Aug 18 2016 - 12:58:42 PDT)
    - Re: [AMBER] Problem in charge generation through antechamber ATUL KUMAR (Thu Aug 18 2016 - 23:11:14 PDT)
    - Re: [AMBER] Problem in charge generation through antechamber Bruno Falcone (Fri Aug 19 2016 - 07:47:05 PDT)
- Re: [AMBER] Problem in charge generation through antechamber David A Case (Thu Aug 18 2016 - 12:43:09 PDT)
- Re: [AMBER] Problem in charge generation through antechamber FyD (Sat Aug 20 2016 - 02:08:20 PDT)
[AMBER] percentages of protein secondary structure. Saman Yousuf ali (Thu Aug 18 2016 - 21:17:59 PDT)
- Re: [AMBER] percentages of protein secondary structure. Nhai (Thu Aug 18 2016 - 22:32:00 PDT)
- Re: [AMBER] percentages of protein secondary structure. Hai Nguyen (Fri Aug 19 2016 - 07:51:53 PDT)
[AMBER] Does Scaled MD require NVT ensemble? Harshavardhan Khare (Thu Aug 18 2016 - 23:20:40 PDT)
- Re: [AMBER] Does Scaled MD require NVT ensemble? Ross Walker (Fri Aug 19 2016 - 07:13:12 PDT)
  - Re: [AMBER] Does Scaled MD require NVT ensemble? Harshavardhan Khare (Fri Aug 19 2016 - 22:01:53 PDT)
[AMBER] Temperature Shoot-up in TMD Aravind Ravichandran (Fri Aug 19 2016 - 00:26:24 PDT)
- Re: [AMBER] Temperature Shoot-up in TMD Bill Ross (Fri Aug 19 2016 - 00:20:52 PDT)
- Re: [AMBER] Temperature Shoot-up in TMD Carlos Simmerling (Fri Aug 19 2016 - 04:50:38 PDT)
[AMBER] What cutoff you use in Amber simulations? DmitryASuplatov (Fri Aug 19 2016 - 04:35:40 PDT)
- Re: [AMBER] What cutoff you use in Amber simulations? Jason Swails (Fri Aug 19 2016 - 05:57:48 PDT)
[AMBER] Tutorial B5 - Loading CRO from ccif file Alfredo Quevedo (Fri Aug 19 2016 - 07:26:42 PDT)
- Re: [AMBER] Tutorial B5 - Loading CRO from ccif file David A Case (Fri Aug 19 2016 - 10:43:15 PDT)
  - Re: [AMBER] Tutorial B5 - Loading CRO from ccif file Alfredo Quevedo (Fri Aug 19 2016 - 10:49:05 PDT)
[AMBER] concerns on membrane protein restrain Albert (Fri Aug 19 2016 - 11:39:35 PDT)
[AMBER] WHAM analysis Thakur, Abhishek (Fri Aug 19 2016 - 14:55:16 PDT)
- Re: [AMBER] WHAM analysis Chi Jin (Sat Aug 20 2016 - 00:30:05 PDT)
  - Re: [AMBER] WHAM analysis Amy Rice (Sat Aug 20 2016 - 08:41:00 PDT)
    - Re: [AMBER] WHAM analysis Chi Jin (Sat Aug 20 2016 - 11:13:41 PDT)
    - Re: [AMBER] WHAM analysis Adrian Roitberg (Sat Aug 20 2016 - 11:17:23 PDT)
[AMBER] minimum restraint_wt. Saman Yousuf ali (Sun Aug 21 2016 - 00:05:43 PDT)
- Re: [AMBER] minimum restraint_wt. David A Case (Tue Aug 23 2016 - 04:49:54 PDT)
[AMBER] Frac in cpptraj hydrogen bond command. Saman Yousuf ali (Sun Aug 21 2016 - 05:25:42 PDT)
- Re: [AMBER] Frac in cpptraj hydrogen bond command. Daniel Roe (Sun Aug 21 2016 - 05:55:13 PDT)
[AMBER] Adaptively Biased MD Simulations of type "distance" using "FLOODING" Emmanuel (Mon Aug 22 2016 - 03:32:05 PDT)
- Re: [AMBER] Adaptively Biased MD Simulations of type "distance" using "FLOODING" Bill Ross (Mon Aug 22 2016 - 03:45:53 PDT)
  - Re: [AMBER] Adaptively Biased MD Simulations of type "distance" using "FLOODING" Bill Ross (Mon Aug 22 2016 - 03:54:06 PDT)
- Re: [AMBER] Adaptively Biased MD Simulations of type "distance" using "FLOODING" Feng Pan (Mon Aug 22 2016 - 08:25:24 PDT)
[AMBER] Sigma and epsilon vdw parameters Neha Gandhi (Mon Aug 22 2016 - 15:28:44 PDT)
- Re: [AMBER] Sigma and epsilon vdw parameters Bill Ross (Mon Aug 22 2016 - 15:58:45 PDT)
[AMBER] Output Files Wong Li Zhe (Mon Aug 22 2016 - 18:03:36 PDT)
- Re: [AMBER] Output Files Hai Nguyen (Mon Aug 22 2016 - 20:33:37 PDT)
[AMBER] Simulation Time Wong Li Zhe (Mon Aug 22 2016 - 22:00:03 PDT)
- Re: [AMBER] Simulation Time Dd H (Wed Aug 24 2016 - 04:31:07 PDT)
[AMBER] Alanine scan of nonnatural amino acid Aronica, Pietro (Tue Aug 23 2016 - 02:21:37 PDT)
- Re: [AMBER] Alanine scan of nonnatural amino acid Jason Swails (Tue Aug 23 2016 - 09:21:07 PDT)
[AMBER] Copper +1 and membrane with LJ 12-6-4 potential Stephan Schott (Tue Aug 23 2016 - 07:37:52 PDT)
- Re: [AMBER] Copper +1 and membrane with LJ 12-6-4 potential Pengfei Li (Sat Aug 27 2016 - 13:48:22 PDT)
[AMBER] Problem with atommap function in cpptraj (v16) Samuel Bowerman (Tue Aug 23 2016 - 12:23:56 PDT)
- Re: [AMBER] Problem with atommap function in cpptraj (v16) Daniel Roe (Fri Aug 26 2016 - 13:40:24 PDT)
  - Re: [AMBER] Problem with atommap function in cpptraj (v16) Samuel Bowerman (Tue Aug 30 2016 - 12:39:05 PDT)
    - Re: [AMBER] Problem with atommap function in cpptraj (v16) Daniel Roe (Wed Aug 31 2016 - 06:12:00 PDT)
    - Re: [AMBER] Problem with atommap function in cpptraj (v16) Daniel Roe (Tue Sep 20 2016 - 07:06:49 PDT)
    - Re: [AMBER] Problem with atommap function in cpptraj (v16) Samuel Bowerman (Tue Sep 20 2016 - 08:01:29 PDT)
    - Re: [AMBER] Problem with atommap function in cpptraj (v16) Daniel Roe (Tue Sep 20 2016 - 08:11:15 PDT)
[AMBER] Generating parameter and topology files for a protein with multiple Zinc ions Aditya Padhi (Tue Aug 23 2016 - 18:00:15 PDT)
- Re: [AMBER] Generating parameter and topology files for a protein with multiple Zinc ions Bill Ross (Wed Aug 24 2016 - 21:19:37 PDT)
- Re: [AMBER] Generating parameter and topology files for a protein with multiple Zinc ions Pengfei Li (Sat Aug 27 2016 - 13:55:54 PDT)
[AMBER] Checking modeling after MCPB and unable to fix atom order using cpptraj Andrew Schaub (Tue Aug 23 2016 - 22:15:58 PDT)
- Re: [AMBER] Checking modeling after MCPB and unable to fix atom order using cpptraj Hai Nguyen (Tue Aug 23 2016 - 22:44:43 PDT)
  - Re: [AMBER] Checking modeling after MCPB and unable to fix atom order using cpptraj Andrew Schaub (Tue Aug 23 2016 - 22:56:02 PDT)
[AMBER] Generating topology and parameter file for a peptide pratibha sharma (Tue Aug 23 2016 - 23:34:57 PDT)
- Re: [AMBER] Generating topology and parameter file for a peptide Hai Nguyen (Tue Aug 23 2016 - 23:37:14 PDT)
- Re: [AMBER] Generating topology and parameter file for a peptide Bill Ross (Wed Aug 24 2016 - 00:57:27 PDT)
[AMBER] 22.1.6.1. Free Energy using linear scaling 22.1.6.2.Absolute free energy using soft core, Markus Kaukonen (Wed Aug 24 2016 - 01:01:45 PDT)
- Re: [AMBER] 22.1.6.1. Free Energy using linear scaling 22.1.6.2.Absolute free energy using soft core, Hannes Loeffler (Wed Aug 24 2016 - 04:58:58 PDT)
[AMBER] cpptraj on pH-REMD Elisa Pieri (Wed Aug 24 2016 - 04:19:10 PDT)
- Re: [AMBER] cpptraj on pH-REMD Jason Swails (Wed Aug 24 2016 - 19:34:16 PDT)
[AMBER] Regarding hbond bridgeout Indrajit Deb (Wed Aug 24 2016 - 09:04:17 PDT)
- Re: [AMBER] Regarding hbond bridgeout Daniel Roe (Fri Aug 26 2016 - 13:24:08 PDT)
[AMBER] Issues compiling Amber with CUDA support Sivy, Shawn (Wed Aug 24 2016 - 11:47:10 PDT)
- Re: [AMBER] Issues compiling Amber with CUDA support Ross Walker (Thu Aug 25 2016 - 04:30:46 PDT)
  - Re: [AMBER] Issues compiling Amber with CUDA support Baker, Joseph (Sat Aug 27 2016 - 13:10:31 PDT)
    - Re: [AMBER] Issues compiling Amber with CUDA support Ross Walker (Sat Aug 27 2016 - 15:53:28 PDT)
    - Re: [AMBER] Issues compiling Amber with CUDA support Baker, Joseph (Sat Aug 27 2016 - 21:48:21 PDT)
[AMBER] SEP parameter with ff15ipq vadiraj kurdekar (Thu Aug 25 2016 - 00:08:31 PDT)
- Re: [AMBER] SEP parameter with ff15ipq David A Case (Thu Aug 25 2016 - 06:33:47 PDT)
  - Re: [AMBER] SEP parameter with ff15ipq David Cerutti (Thu Aug 25 2016 - 07:18:37 PDT)
- Re: [AMBER] SEP parameter with ff15ipq vadiraj kurdekar (Thu Aug 25 2016 - 21:43:22 PDT)
- Re: [AMBER] SEP parameter with ff15ipq Carlos Simmerling (Fri Aug 26 2016 - 06:35:52 PDT)
[AMBER] Problem with rst7 Elisa Pieri (Thu Aug 25 2016 - 02:12:46 PDT)
- Re: [AMBER] Problem with rst7 Bill Ross (Thu Aug 25 2016 - 02:41:46 PDT)
  - Re: [AMBER] Problem with rst7 Elisa Pieri (Thu Aug 25 2016 - 04:04:18 PDT)
    - Re: [AMBER] Problem with rst7 Carlos Simmerling (Thu Aug 25 2016 - 04:31:25 PDT)
- Re: [AMBER] Problem with rst7 Carlos Simmerling (Thu Aug 25 2016 - 03:33:54 PDT)
[AMBER] Fw: Problems to calculate frequencies Stregone (Thu Aug 25 2016 - 03:14:42 PDT)
- Re: [AMBER] Fw: Problems to calculate frequencies David A Case (Thu Aug 25 2016 - 06:40:56 PDT)
[AMBER] output of MMPBSA.py Markus Kaukonen (Thu Aug 25 2016 - 03:43:20 PDT)
- Re: [AMBER] output of MMPBSA.py Bilal Nizami (Thu Aug 25 2016 - 03:54:19 PDT)
[AMBER] MMPBSA.py CalcError on ligand contribution only Leandro Bortot (Thu Aug 25 2016 - 07:43:11 PDT)
- Re: [AMBER] MMPBSA.py CalcError on ligand contribution only Jason Swails (Thu Aug 25 2016 - 10:35:26 PDT)
  - Re: [AMBER] MMPBSA.py CalcError on ligand contribution only Leandro Bortot (Thu Aug 25 2016 - 12:51:54 PDT)
    - Re: [AMBER] MMPBSA.py CalcError on ligand contribution only Jason Swails (Thu Aug 25 2016 - 17:19:27 PDT)
[AMBER] problem upon optimization giulia palermo (Thu Aug 25 2016 - 08:12:39 PDT)
- Re: [AMBER] problem upon optimization Adrian Roitberg (Thu Aug 25 2016 - 08:14:34 PDT)
- Re: [AMBER] problem upon optimization Jason Swails (Thu Aug 25 2016 - 10:34:44 PDT)
  - Re: [AMBER] problem upon optimization giulia palermo (Thu Aug 25 2016 - 15:34:15 PDT)
[AMBER] Checking AmberTools16 installation Bence Hégely (Thu Aug 25 2016 - 11:53:11 PDT)
- Re: [AMBER] Checking AmberTools16 installation Hai Nguyen (Thu Aug 25 2016 - 12:45:01 PDT)
  - Re: [AMBER] Checking AmberTools16 installation Bence Hégely (Fri Aug 26 2016 - 07:19:10 PDT)
    - Re: [AMBER] Checking AmberTools16 installation Hai Nguyen (Mon Aug 29 2016 - 10:09:08 PDT)
    - Re: [AMBER] Checking AmberTools16 installation Bence Hégely (Tue Aug 30 2016 - 07:37:58 PDT)
    - Re: [AMBER] Checking AmberTools16 installation Hai Nguyen (Tue Aug 30 2016 - 09:30:49 PDT)
    - Re: [AMBER] Checking AmberTools16 installation Hai Nguyen (Tue Aug 30 2016 - 10:07:17 PDT)
    - Re: [AMBER] Checking AmberTools16 installation Bence Hégely (Tue Sep 06 2016 - 05:24:34 PDT)
    - Re: [AMBER] Checking AmberTools16 installation David A Case (Tue Sep 06 2016 - 05:52:56 PDT)
[AMBER] repair mdcrd? Bill Ross (Thu Aug 25 2016 - 13:26:01 PDT)
- Re: [AMBER] repair mdcrd? Hai Nguyen (Thu Aug 25 2016 - 13:47:07 PDT)
  - Re: [AMBER] repair mdcrd? Bill Ross (Thu Aug 25 2016 - 15:48:11 PDT)
    - Re: [AMBER] repair mdcrd? Daniel Roe (Thu Aug 25 2016 - 16:56:44 PDT)
[AMBER] begin time read from input coords Hannes Loeffler (Fri Aug 26 2016 - 01:10:09 PDT)
- Re: [AMBER] begin time read from input coords Daniel Roe (Fri Aug 26 2016 - 03:17:33 PDT)
  - Re: [AMBER] begin time read from input coords Hannes Loeffler (Fri Aug 26 2016 - 05:01:40 PDT)
- Re: [AMBER] begin time read from input coords David A Case (Fri Aug 26 2016 - 06:11:04 PDT)
  - Re: [AMBER] begin time read from input coords Hannes Loeffler (Fri Aug 26 2016 - 08:34:45 PDT)
[AMBER] Multihist in watershell command Damiano Spadoni (Fri Aug 26 2016 - 05:26:24 PDT)
- Re: [AMBER] Multihist in watershell command Hai Nguyen (Fri Aug 26 2016 - 10:35:39 PDT)
- Re: [AMBER] Multihist in watershell command Daniel Roe (Fri Aug 26 2016 - 11:11:06 PDT)
  - Re: [AMBER] Multihist in watershell command Damiano Spadoni (Wed Aug 31 2016 - 08:45:21 PDT)
[AMBER] (no subject) Amrullah13 (Sat Aug 27 2016 - 18:51:50 PDT)
- Re: [AMBER] (no subject) waleed zalloum (Wed Apr 29 2009 - 11:06:44 PDT)
- Re: [AMBER] (no subject) Bill Ross (Thu Jun 24 2010 - 11:27:28 PDT)
- Re: [AMBER] (no subject) Bill Ross (Sat Nov 06 2010 - 19:15:41 PDT)
- Re: [AMBER] (no subject) Hai Nguyen (Sat Aug 27 2016 - 20:34:02 PDT)
- Re: [AMBER] (no subject) Jason Swails (Mon Aug 29 2016 - 08:27:33 PDT)
[AMBER] autoimage bug? Filip Persson (Mon Aug 29 2016 - 05:36:24 PDT)
- Re: [AMBER] autoimage bug? Daniel Roe (Wed Aug 31 2016 - 06:22:55 PDT)
  - Re: [AMBER] autoimage bug? Filip Persson (Thu Sep 08 2016 - 05:32:36 PDT)
    - Re: [AMBER] autoimage bug? Daniel Roe (Mon Sep 19 2016 - 07:20:50 PDT)
    - Re: [AMBER] autoimage bug? Filip Persson (Tue Sep 27 2016 - 23:48:13 PDT)
    - Re: [AMBER] autoimage bug? Daniel Roe (Wed Sep 28 2016 - 06:53:45 PDT)
  - Re: [AMBER] autoimage bug? Filip Persson (Thu Sep 08 2016 - 05:34:09 PDT)
[AMBER] autocorr of hydrogen bonds Osman, Roman (Mon Aug 29 2016 - 06:05:06 PDT)
- Re: [AMBER] autocorr of hydrogen bonds Tom Kurtzman (Tue Aug 30 2016 - 08:07:36 PDT)
  - Re: [AMBER] autocorr of hydrogen bonds Osman, Roman (Tue Aug 30 2016 - 14:41:38 PDT)
  - Re: [AMBER] autocorr of hydrogen bonds Osman, Roman (Thu Sep 01 2016 - 09:06:44 PDT)
    - Re: [AMBER] autocorr of hydrogen bonds Roitberg,Adrian E (Thu Sep 01 2016 - 09:27:06 PDT)
    - Re: [AMBER] autocorr of hydrogen bonds David A Case (Thu Sep 01 2016 - 09:46:22 PDT)
[AMBER] errors in doing TI tutorial calculation 张姝姝 (Mon Aug 29 2016 - 07:26:56 PDT)
- Re: [AMBER] errors in doing TI tutorial calculation David A Case (Mon Aug 29 2016 - 12:25:59 PDT)
- Re: [AMBER] errors in doing TI tutorial calculation Hannes Loeffler (Mon Aug 29 2016 - 12:26:33 PDT)
[AMBER] restraint does not work in mininmization Michael Shokhen (Tue Aug 30 2016 - 00:48:54 PDT)
- Re: [AMBER] restraint does not work in mininmization Hirdesh Kumar (Tue Aug 30 2016 - 01:02:56 PDT)
[AMBER] frozen geometry setting? Michael Shokhen (Tue Aug 30 2016 - 07:32:09 PDT)
- Re: [AMBER] frozen geometry setting? David A Case (Tue Aug 30 2016 - 08:26:12 PDT)
  - Re: [AMBER] frozen geometry setting? Michael Shokhen (Tue Aug 30 2016 - 11:55:56 PDT)
    - Re: [AMBER] frozen geometry setting? Bill Ross (Tue Aug 30 2016 - 11:59:10 PDT)
    - Re: [AMBER] frozen geometry setting? Michael Shokhen (Tue Aug 30 2016 - 12:12:33 PDT)
    - Re: [AMBER] frozen geometry setting? Adrian Roitberg (Tue Aug 30 2016 - 12:14:29 PDT)
- Re: [AMBER] frozen geometry setting? Bill Ross (Tue Aug 30 2016 - 12:32:16 PDT)
  - Re: [AMBER] frozen geometry setting? Michael Shokhen (Wed Aug 31 2016 - 06:34:36 PDT)
[AMBER] Parameters for modified nucleosides Tomek Wlodarski (Tue Aug 30 2016 - 10:34:09 PDT)
[AMBER] lowering the temperature Thomas Evangelidis (Tue Aug 30 2016 - 16:51:40 PDT)
- Re: [AMBER] lowering the temperature Carlos Simmerling (Tue Aug 30 2016 - 17:19:14 PDT)
  - Re: [AMBER] lowering the temperature Thomas Evangelidis (Wed Aug 31 2016 - 03:33:26 PDT)
    - Re: [AMBER] lowering the temperature Carlos Simmerling (Wed Aug 31 2016 - 04:02:04 PDT)
[AMBER] change the atom charge in a restart simulations windy (Wed Aug 31 2016 - 01:49:25 PDT)
- Re: [AMBER] change the atom charge in a restart simulations Bill Ross (Wed Aug 31 2016 - 02:54:44 PDT)
  - Re: [AMBER] change the atom charge in a restart simulations windy (Wed Aug 31 2016 - 18:53:55 PDT)
- Re: [AMBER] change the atom charge in a restart simulations David A Case (Wed Aug 31 2016 - 05:32:25 PDT)
[AMBER] changing atom type Jacopo Sgrignani (Wed Aug 31 2016 - 08:16:37 PDT)
- Re: [AMBER] changing atom type Hai Nguyen (Wed Aug 31 2016 - 08:41:22 PDT)
  - Re: [AMBER] changing atom type Jason Swails (Wed Aug 31 2016 - 09:00:20 PDT)
    - Re: [AMBER] changing atom type Dr. Andreas W. Goetz (Wed Aug 31 2016 - 14:15:35 PDT)
    - Re: [AMBER] changing atom type Jacopo Sgrignani (Thu Sep 01 2016 - 01:43:19 PDT)
[AMBER] QM/MM energy units? Corum, Katharine W (Wed Aug 31 2016 - 08:52:45 PDT)
- Re: [AMBER] QM/MM energy units? Jacopo Sgrignani (Wed Aug 31 2016 - 08:56:24 PDT)
- Re: [AMBER] QM/MM energy units? Adrian Roitberg (Wed Aug 31 2016 - 08:56:48 PDT)
  - Re: [AMBER] QM/MM energy units? Corum, Katharine W (Wed Aug 31 2016 - 08:58:56 PDT)
[AMBER] File redirection commands with targeted MD Sonia Ziada (Wed Aug 31 2016 - 09:10:52 PDT)
- [AMBER] Fwd: File redirection commands with targeted MD Sonia Ziada (Fri Sep 02 2016 - 00:03:35 PDT)
  - Re: [AMBER] Fwd: File redirection commands with targeted MD Sonia Ziada (Thu Sep 08 2016 - 06:11:32 PDT)
    - Re: [AMBER] Fwd: File redirection commands with targeted MD Carlos Simmerling (Thu Sep 08 2016 - 06:26:31 PDT)
    - Re: [AMBER] Fwd: File redirection commands with targeted MD Sonia Ziada (Thu Sep 08 2016 - 06:37:39 PDT)
    - Re: [AMBER] Fwd: File redirection commands with targeted MD Florent Barbault (Thu Sep 08 2016 - 07:24:02 PDT)
    - Re: [AMBER] Fwd: File redirection commands with targeted MD Sonia Ziada (Thu Sep 08 2016 - 07:45:22 PDT)
    - Re: [AMBER] Fwd: File redirection commands with targeted MD Bill Ross (Thu Sep 08 2016 - 10:03:56 PDT)
    - Re: [AMBER] Fwd: File redirection commands with targeted MD Michael Shokhen (Fri Sep 09 2016 - 01:36:01 PDT)
[AMBER] Amber Force Fields amir sadeghi (Wed Aug 31 2016 - 12:33:48 PDT)
- Re: [AMBER] Amber Force Fields Hai Nguyen (Wed Aug 31 2016 - 12:40:45 PDT)
- Re: [AMBER] Amber Force Fields Carlos Simmerling (Wed Aug 31 2016 - 17:34:12 PDT)
[AMBER] Regarding the use of sed command to replace water Budhathoki, Dipesh (Wed Aug 31 2016 - 12:52:37 PDT)
- Re: [AMBER] Regarding the use of sed command to replace water Corum, Katharine W (Wed Aug 31 2016 - 12:57:43 PDT)
- Re: [AMBER] Regarding the use of sed command to replace water Adrian Roitberg (Wed Aug 31 2016 - 12:58:29 PDT)
  - Re: [AMBER] Regarding the use of sed command to replace water David A Case (Wed Aug 31 2016 - 13:38:16 PDT)
    - Re: [AMBER] Regarding the use of sed command to replace water Budhathoki, Dipesh (Wed Aug 31 2016 - 14:54:40 PDT)
    - Re: [AMBER] Regarding the use of sed command to replace water MOHD HOMAIDUR RAHMAN (Wed Aug 31 2016 - 21:29:51 PDT)
    - Re: [AMBER] Regarding the use of sed command to replace water David A Case (Thu Sep 01 2016 - 04:30:01 PDT)
[AMBER] Fwd: MD stop at different time period without giving any error Garima Singh (Thu Sep 01 2016 - 01:39:30 PDT)
- Re: [AMBER] Fwd: MD stop at different time period without giving any error David A Case (Thu Sep 01 2016 - 04:35:05 PDT)
[AMBER] error in sander minimization Prayagraj Fandilolu (Thu Sep 01 2016 - 04:45:13 PDT)
- Re: [AMBER] error in sander minimization David A Case (Thu Sep 01 2016 - 09:41:54 PDT)
  - Re: [AMBER] error in sander minimization Prayagraj Fandilolu (Fri Sep 02 2016 - 07:30:45 PDT)
[AMBER] how to center a polipeptide inside a solvent box Elisa Pieri (Thu Sep 01 2016 - 05:27:59 PDT)
- Re: [AMBER] how to center a polipeptide inside a solvent box Jason Swails (Thu Sep 01 2016 - 17:47:04 PDT)
  - Re: [AMBER] how to center a polipeptide inside a solvent box Elisa Pieri (Fri Sep 02 2016 - 03:01:02 PDT)
    - Re: [AMBER] how to center a polipeptide inside a solvent box David A Case (Fri Sep 02 2016 - 05:37:57 PDT)
[AMBER] Unable to find mopac charges in mopac.out Sneha Rai (Thu Sep 01 2016 - 05:29:18 PDT)
- Re: [AMBER] Unable to find mopac charges in mopac.out Marcelo Andrade Chagas (Thu Sep 01 2016 - 05:42:09 PDT)
  - Re: [AMBER] Unable to find mopac charges in mopac.out Sneha Rai (Thu Sep 01 2016 - 10:55:58 PDT)
    - Re: [AMBER] Unable to find mopac charges in mopac.out Hannes Loeffler (Thu Sep 01 2016 - 11:01:23 PDT)
    - Re: [AMBER] Unable to find mopac charges in mopac.out Sneha Rai (Thu Sep 01 2016 - 11:31:16 PDT)
    - Re: [AMBER] Unable to find mopac charges in mopac.out Marcelo Andrade Chagas (Thu Sep 01 2016 - 11:37:16 PDT)
    - Re: [AMBER] Unable to find mopac charges in mopac.out David A Case (Thu Sep 01 2016 - 11:49:57 PDT)
- Re: [AMBER] Unable to find mopac charges in mopac.out Ashutosh Shandilya (Thu Sep 01 2016 - 23:46:15 PDT)
  - Re: [AMBER] Unable to find mopac charges in mopac.out Sneha Rai (Fri Sep 02 2016 - 00:00:45 PDT)
    - Re: [AMBER] Unable to find mopac charges in mopac.out David A Case (Fri Sep 02 2016 - 05:31:07 PDT)
[AMBER] noshakemask and qmshake Fabrício Bracht (Thu Sep 01 2016 - 11:34:47 PDT)
[AMBER] radial distribution function from 1drism calculation Jingyi Yan (Thu Sep 01 2016 - 12:21:32 PDT)
- Re: [AMBER] radial distribution function from 1drism calculation Tyler Luchko (Lists) (Thu Sep 01 2016 - 13:26:05 PDT)
[AMBER] Any idea about this Amber compile bug? David Cerutti (Thu Sep 01 2016 - 13:45:35 PDT)
- Re: [AMBER] Any idea about this Amber compile bug? Jason Swails (Thu Sep 01 2016 - 17:53:07 PDT)
  - Re: [AMBER] Any idea about this Amber compile bug? Scott Brozell (Thu Sep 01 2016 - 20:13:28 PDT)
[AMBER] accelerated MD Neha Gandhi (Thu Sep 01 2016 - 14:55:27 PDT)
[AMBER] QMMM simulation with user-specified basis set in amber zycz138.126.com (Thu Sep 01 2016 - 20:31:59 PDT)
[AMBER] query regaridng unrestarint minimization step Saman Yousuf ali (Fri Sep 02 2016 - 00:29:56 PDT)
[AMBER] Which is the best thermostat for cMD? Dd H (Fri Sep 02 2016 - 01:15:21 PDT)
- Re: [AMBER] Which is the best thermostat for cMD? David A Case (Tue Sep 06 2016 - 06:41:37 PDT)
  - Re: [AMBER] Which is the best thermostat for cMD? Dd H (Tue Sep 06 2016 - 19:11:46 PDT)
[AMBER] RMS-fit during PCA Anasuya Dighe (Fri Sep 02 2016 - 02:38:31 PDT)
- Re: [AMBER] RMS-fit during PCA Hai Nguyen (Fri Sep 02 2016 - 08:42:03 PDT)
[AMBER] Trajectory analysis Anna Cebrian Prats (Fri Sep 02 2016 - 08:05:39 PDT)
- Re: [AMBER] Trajectory analysis Hai Nguyen (Fri Sep 02 2016 - 09:45:57 PDT)
[AMBER] lig.frcmod file is not formed Vishal Nemaysh (Sat Sep 03 2016 - 07:37:58 PDT)
- [AMBER] Fwd: lig.frcmod file is not formed Vishal Nemaysh (Mon Sep 05 2016 - 00:08:32 PDT)
[AMBER] why does my computer cannot access to Internet after Installing ambertool 16 sunyeping (Sun Sep 04 2016 - 01:35:20 PDT)
- Re: [AMBER] why does my computer cannot access to Internet after Installing ambertool 16 Bill Ross (Sun Sep 04 2016 - 02:22:56 PDT)
- Re: [AMBER] why does my computer cannot access to Internet after Installing ambertool 16 David A Case (Sun Sep 04 2016 - 15:01:02 PDT)
- Re: [AMBER] why does my computer cannot access to Internet after Installing ambertool 16 sunyeping (Sun Sep 04 2016 - 16:30:20 PDT)
  - Re: [AMBER] why does my computer cannot access to Internet after Installing ambertool 16 Jason Swails (Mon Sep 05 2016 - 18:03:36 PDT)
    - Re: [AMBER] why does my computer cannot access to Internet after Installing ambertool 16 Bill Ross (Mon Sep 05 2016 - 18:20:12 PDT)
- Re: [AMBER] why does my computer cannot access to Internet after Installing ambertool 16 Bill Ross (Sun Sep 04 2016 - 17:53:08 PDT)
- Re: [AMBER] why does my computer cannot access to Internet after Installing ambertool 16 sunyeping (Sun Sep 04 2016 - 21:39:21 PDT)
  - Re: [AMBER] why does my computer cannot access to Internet after Installing ambertool 16 Bill Ross (Sun Sep 04 2016 - 21:44:16 PDT)
- Re: [AMBER] why does my computer cannot access to Internet after Installing ambertool 16 sunyeping (Mon Sep 05 2016 - 07:24:23 PDT)
  - Re: [AMBER] why does my computer cannot access to Internet after Installing ambertool 16 Bill Ross (Mon Sep 05 2016 - 10:11:01 PDT)
[AMBER] Hydrophobic interactions in MM-GBSA Atila Petrosian (Sun Sep 04 2016 - 13:37:01 PDT)
- Re: [AMBER] Hydrophobic interactions in MM-GBSA Carlos Simmerling (Sun Sep 04 2016 - 14:02:44 PDT)
  - Re: [AMBER] Hydrophobic interactions in MM-GBSA Atila Petrosian (Sun Sep 04 2016 - 14:14:37 PDT)
    - Re: [AMBER] Hydrophobic interactions in MM-GBSA Nhai (Sun Sep 04 2016 - 14:56:29 PDT)
    - Re: [AMBER] Hydrophobic interactions in MM-GBSA Carlos Simmerling (Sun Sep 04 2016 - 16:37:44 PDT)
[AMBER] Parmed.py, deleteBond and setBond Aronica, Pietro (Sun Sep 04 2016 - 21:18:05 PDT)
[AMBER] Select a snapshot Anna Cebrian Prats (Mon Sep 05 2016 - 02:42:24 PDT)
- Re: [AMBER] Select a snapshot Daniel Roe (Mon Sep 05 2016 - 18:41:40 PDT)
[AMBER] Temperature connected to the dipole convergence in the output BLEY Michael (Mon Sep 05 2016 - 07:39:57 PDT)
- Re: [AMBER] Temperature connected to the dipole convergence in the output David A Case (Tue Sep 06 2016 - 06:57:15 PDT)
[AMBER] historical changes to LYN charges in amber03 Mark Abraham (Mon Sep 05 2016 - 08:40:38 PDT)
- Re: [AMBER] historical changes to LYN charges in amber03 Carlos Simmerling (Mon Sep 05 2016 - 08:56:47 PDT)
  - Re: [AMBER] historical changes to LYN charges in amber03 Mark Abraham (Mon Sep 05 2016 - 09:05:44 PDT)
    - Re: [AMBER] historical changes to LYN charges in amber03 Carlos Simmerling (Mon Sep 05 2016 - 09:41:43 PDT)
    - Re: [AMBER] historical changes to LYN charges in amber03 David A Case (Mon Sep 05 2016 - 17:45:05 PDT)
    - Re: [AMBER] historical changes to LYN charges in amber03 Mark Abraham (Tue Sep 06 2016 - 07:08:24 PDT)
[AMBER] How to fixed residues in amber? windy (Mon Sep 05 2016 - 19:32:36 PDT)
- Re: [AMBER] How to fixed residues in amber? David A Case (Tue Sep 06 2016 - 04:20:40 PDT)
[AMBER] resp charges in LIPID14 jojartb.jgypk.u-szeged.hu (Tue Sep 06 2016 - 04:55:21 PDT)
- Re: [AMBER] resp charges in LIPID14 Dickson, Callum J (Tue Sep 06 2016 - 06:43:36 PDT)
[AMBER] about print_res in MMPBSA.py Thomas Evangelidis (Tue Sep 06 2016 - 08:37:34 PDT)
- Re: [AMBER] about print_res in MMPBSA.py Jason Swails (Tue Sep 06 2016 - 09:37:57 PDT)
  - Re: [AMBER] about print_res in MMPBSA.py Thomas Evangelidis (Tue Sep 06 2016 - 10:44:46 PDT)
    - Re: [AMBER] about print_res in MMPBSA.py Jason Swails (Tue Sep 06 2016 - 13:37:58 PDT)
[AMBER] [Amber] Periodic Box Issue Chase Zagorec-Marks (Tue Sep 06 2016 - 09:04:41 PDT)
- Re: [AMBER] [Amber] Periodic Box Issue Adrian Roitberg (Tue Sep 06 2016 - 09:07:34 PDT)
  - Re: [AMBER] [Amber] Periodic Box Issue Chase Zagorec-Marks (Tue Sep 06 2016 - 09:31:14 PDT)
[AMBER] query regarding radial distribution function plot. Saman Yousuf ali (Tue Sep 06 2016 - 14:08:46 PDT)
- Re: [AMBER] query regarding radial distribution function plot. Daniel Roe (Tue Sep 06 2016 - 18:26:53 PDT)
[AMBER] MMPBSA analysis for a heme protein Smriti Sharma (Tue Sep 06 2016 - 22:07:34 PDT)
- Re: [AMBER] MMPBSA analysis for a heme protein David A Case (Wed Sep 07 2016 - 04:50:03 PDT)
[AMBER] How to assign frame range for cpptraj analysis? sunyeping (Wed Sep 07 2016 - 02:04:30 PDT)
- Re: [AMBER] How to assign frame range for cpptraj analysis? Anna Cebrian Prats (Wed Sep 07 2016 - 02:21:06 PDT)
- Re: [AMBER] How to assign frame range for cpptraj analysis? sunyeping (Wed Sep 07 2016 - 02:44:36 PDT)
[AMBER] Problem with MCPB.py workflow after calculation of force constants. Abhi Acharya (Wed Sep 07 2016 - 02:15:49 PDT)
- Re: [AMBER] Problem with MCPB.py workflow after calculation of force constants. Marcelo Andrade Chagas (Wed Sep 07 2016 - 08:16:23 PDT)
  - Re: [AMBER] Problem with MCPB.py workflow after calculation of force constants. Pengfei Li (Thu Sep 08 2016 - 07:58:24 PDT)
[AMBER] changepot Xiaoliu Zhang (Wed Sep 07 2016 - 11:49:10 PDT)
- Re: [AMBER] changepot Adrian Roitberg (Wed Sep 07 2016 - 11:53:17 PDT)
[AMBER] distance based mask Kris Feher (Wed Sep 07 2016 - 12:09:24 PDT)
- Re: [AMBER] distance based mask Daniel Roe (Wed Sep 07 2016 - 12:26:07 PDT)
  - Re: [AMBER] distance based mask Kris Feher (Wed Sep 07 2016 - 12:52:08 PDT)
[AMBER] Switching from PM3-PDDG to SCC-DFT method Thakur, Abhishek (Wed Sep 07 2016 - 14:02:20 PDT)
- Re: [AMBER] Switching from PM3-PDDG to SCC-DFT method Adrian Roitberg (Wed Sep 07 2016 - 15:29:56 PDT)
[AMBER] Upgrade AMBER 14 to 16 Anton Perera (Thu Sep 08 2016 - 01:44:52 PDT)
- Re: [AMBER] Upgrade AMBER 14 to 16 David A Case (Thu Sep 08 2016 - 04:58:06 PDT)
[AMBER] On the simulation of phosphate ions in water solution Casalini Tommaso (Thu Sep 08 2016 - 01:49:56 PDT)
- Re: [AMBER] On the simulation of phosphate ions in water solution Niel Henriksen (Thu Sep 08 2016 - 19:08:17 PDT)
[AMBER] question on the reference data of GIST Shunsuke Mizutani (Thu Sep 08 2016 - 01:54:31 PDT)
- Re: [AMBER] question on the reference data of GIST David A Case (Thu Sep 08 2016 - 05:02:01 PDT)
  - Re: [AMBER] question on the reference data of GIST Tom Kurtzman (Thu Sep 08 2016 - 08:04:18 PDT)
[AMBER] Radial Distribution Function Fatema Al-Haddad [fy14fmah] (Thu Sep 08 2016 - 02:27:02 PDT)
- Re: [AMBER] Radial Distribution Function David A Case (Thu Sep 08 2016 - 05:04:40 PDT)
[AMBER] Problem with CRD files dhanasekar.mbu.iisc.ernet.in (Thu Sep 08 2016 - 08:05:38 PDT)
- Re: [AMBER] Problem with CRD files Nhai (Thu Sep 08 2016 - 10:25:25 PDT)
- Re: [AMBER] Problem with CRD files Nhai (Thu Sep 08 2016 - 10:35:36 PDT)
- Re: [AMBER] Problem with CRD files Hai Nguyen (Thu Sep 15 2016 - 07:22:15 PDT)
[AMBER] PME calculation for Vacuum? Mochena, Mogus D. (Fri Sep 09 2016 - 11:36:27 PDT)
- Re: [AMBER] PME calculation for Vacuum? Bill Ross (Fri Sep 09 2016 - 11:49:06 PDT)
- Re: [AMBER] PME calculation for Vacuum? Charles Lin (Fri Sep 09 2016 - 11:51:12 PDT)
  - Re: [AMBER] PME calculation for Vacuum? Mochena, Mogus D. (Fri Sep 09 2016 - 14:10:53 PDT)
    - Re: [AMBER] PME calculation for Vacuum? Bill Ross (Fri Sep 09 2016 - 14:19:10 PDT)
    - Re: [AMBER] PME calculation for Vacuum? Bill Ross (Fri Sep 09 2016 - 14:35:24 PDT)
    - Re: [AMBER] PME calculation for Vacuum? David A Case (Sat Sep 10 2016 - 09:19:07 PDT)
    - Re: [AMBER] PME calculation for Vacuum? Mochena, Mogus D. (Sat Sep 10 2016 - 09:30:55 PDT)
    - [AMBER] Follow up Mochena, Mogus D. (Thu Sep 15 2016 - 14:15:48 PDT)
    - Re: [AMBER] Follow up David A Case (Fri Sep 16 2016 - 02:13:40 PDT)
[AMBER] generating topology file for non-standard amino acid Chitrak Gupta (Fri Sep 09 2016 - 15:17:06 PDT)
- Re: [AMBER] generating topology file for non-standard amino acid David A Case (Sat Sep 10 2016 - 09:40:36 PDT)
[AMBER] Calculations of dG for protein-ions James Starlight (Sat Sep 10 2016 - 13:57:36 PDT)
[AMBER] lipid bilayer Sofia Vasilakaki (Sat Sep 10 2016 - 16:17:05 PDT)
[AMBER] Add Molecule symmetry to sander tanfei777.sina.cn (Sat Sep 10 2016 - 17:58:28 PDT)
- Re: [AMBER] Add Molecule symmetry to sander Carlos Simmerling (Sun Sep 11 2016 - 04:39:29 PDT)
[AMBER] Speed issue with Accelerated molecular dynamics. Abhilash J (Sun Sep 11 2016 - 00:35:47 PDT)
- Re: [AMBER] Speed issue with Accelerated molecular dynamics. Marc van der Kamp (Sun Sep 11 2016 - 01:33:48 PDT)
  - Re: [AMBER] Speed issue with Accelerated molecular dynamics. Abhilash J (Sun Sep 11 2016 - 01:54:44 PDT)
[AMBER] PCA plotting waleed zalloum (Sun Sep 11 2016 - 04:00:32 PDT)
- Re: [AMBER] PCA plotting Jason Swails (Mon Sep 12 2016 - 05:36:11 PDT)
[AMBER] 回复：Re: Add Molecule symmetry to sander tanfei777.sina.cn (Sun Sep 11 2016 - 06:53:00 PDT)
- Re: [AMBER] 回复：Re: Add Molecule symmetry to sander Jason Swails (Tue Sep 13 2016 - 05:30:11 PDT)
[AMBER] 回复： Enforced Symmetry? tanfei777.sina.cn (Sun Sep 11 2016 - 18:02:50 PDT)
[AMBER] Problems about creating ligand leap input files 康宁 (Sun Sep 11 2016 - 20:37:20 PDT)
- Re: [AMBER] Problems about creating ligand leap input files Bill Ross (Sun Sep 11 2016 - 21:14:47 PDT)
[AMBER] cpptraj Beale, John (Mon Sep 12 2016 - 02:16:14 PDT)
- Re: [AMBER] cpptraj Bill Ross (Mon Sep 12 2016 - 02:28:11 PDT)
- Re: [AMBER] cpptraj Daniel Roe (Mon Sep 12 2016 - 10:43:31 PDT)
[AMBER] MMPBSA with different external Dielectric Constant Elvis Martis (Mon Sep 12 2016 - 03:15:25 PDT)
- Re: [AMBER] MMPBSA with different external Dielectric Constant Jason Swails (Mon Sep 12 2016 - 05:28:21 PDT)
  - Re: [AMBER] MMPBSA with different external Dielectric Constant Adrian Roitberg (Mon Sep 12 2016 - 08:29:04 PDT)
- Re: [AMBER] MMPBSA with different external Dielectric Constant Elvis Martis (Mon Sep 12 2016 - 20:12:03 PDT)
  - Re: [AMBER] MMPBSA with different external Dielectric Constant Jason Swails (Mon Sep 12 2016 - 20:41:56 PDT)
[AMBER] cpinutil.py describe flag Elisa Pieri (Mon Sep 12 2016 - 07:47:03 PDT)
- Re: [AMBER] cpinutil.py describe flag Jason Swails (Mon Sep 12 2016 - 08:15:32 PDT)
- Re: [AMBER] cpinutil.py describe flag Elisa Pieri (Mon Sep 12 2016 - 08:44:48 PDT)
  - Re: [AMBER] cpinutil.py describe flag Jason Swails (Mon Sep 12 2016 - 12:30:41 PDT)
[AMBER] pmemd Segmentation fault on Tutorial A27 liu junjun (Mon Sep 12 2016 - 09:01:33 PDT)
- Re: [AMBER] pmemd Segmentation fault on Tutorial A27 liu junjun (Mon Sep 12 2016 - 15:08:19 PDT)
[AMBER] SCC-DFTB Thakur, Abhishek (Mon Sep 12 2016 - 09:04:01 PDT)
- Re: [AMBER] SCC-DFTB Adrian Roitberg (Mon Sep 12 2016 - 09:09:22 PDT)
[AMBER] NVIDIA GTX-970 Class Action Suit $30 settlement link Ross Walker (Mon Sep 12 2016 - 12:03:23 PDT)
[AMBER] bad atom type: Mn Thomas Evangelidis (Mon Sep 12 2016 - 18:08:07 PDT)
[AMBER] How by residue decomposition in MMPBSA.py is performed? Irina Ivanova (Mon Sep 12 2016 - 21:53:48 PDT)
- Re: [AMBER] How by residue decomposition in MMPBSA.py is performed? Jason Swails (Tue Sep 13 2016 - 05:28:40 PDT)
[AMBER] comparing pytraj vs. sander output Niel Henriksen (Mon Sep 12 2016 - 22:07:57 PDT)
- Re: [AMBER] comparing pytraj vs. sander output Hai Nguyen (Mon Sep 12 2016 - 22:52:13 PDT)
- Re: [AMBER] comparing pytraj vs. sander output Jason Swails (Tue Sep 13 2016 - 03:48:01 PDT)
  - Re: [AMBER] comparing pytraj vs. sander output Niel Henriksen (Tue Sep 13 2016 - 07:34:19 PDT)
    - Re: [AMBER] comparing pytraj vs. sander output Nhai (Tue Sep 13 2016 - 07:40:38 PDT)
    - Re: [AMBER] comparing pytraj vs. sander output Daniel Roe (Tue Sep 13 2016 - 07:53:19 PDT)
    - Re: [AMBER] comparing pytraj vs. sander output Niel Henriksen (Tue Sep 13 2016 - 08:10:23 PDT)
    - Re: [AMBER] comparing pytraj vs. sander output Daniel Roe (Tue Sep 13 2016 - 08:29:42 PDT)
    - Re: [AMBER] comparing pytraj vs. sander output Hai Nguyen (Tue Sep 13 2016 - 09:06:56 PDT)
    - Re: [AMBER] comparing pytraj vs. sander output Jason Swails (Tue Sep 13 2016 - 09:19:18 PDT)
    - Re: [AMBER] comparing pytraj vs. sander output Hai Nguyen (Tue Sep 13 2016 - 09:39:52 PDT)
  - Re: [AMBER] comparing pytraj vs. sander output Hai Nguyen (Tue Sep 13 2016 - 09:41:44 PDT)
    - Re: [AMBER] comparing pytraj vs. sander output Niel Henriksen (Tue Sep 13 2016 - 09:48:25 PDT)
    - Re: [AMBER] comparing pytraj vs. sander output Hai Nguyen (Tue Sep 13 2016 - 09:52:49 PDT)
    - Re: [AMBER] comparing pytraj vs. sander output Niel Henriksen (Tue Sep 13 2016 - 09:56:36 PDT)
    - Re: [AMBER] comparing pytraj vs. sander output Jason Swails (Tue Sep 13 2016 - 10:36:39 PDT)
[AMBER] Error: cannot run "/share/apps/amber/amber14/bin/sqm -O -i sqm.in -o sqm.out" of bcc() in charge.c properly, exit shahab shariati (Tue Sep 13 2016 - 04:25:41 PDT)
- Re: [AMBER] Error: cannot run "/share/apps/amber/amber14/bin/sqm -O -i sqm.in -o sqm.out" of bcc() in charge.c properly, exit shahab shariati (Tue Sep 13 2016 - 04:28:03 PDT)
  - Re: [AMBER] Error: cannot run "/share/apps/amber/amber14/bin/sqm -O -i sqm.in -o sqm.out" of bcc() in charge.c properly, exit shahab shariati (Tue Sep 13 2016 - 04:31:45 PDT)
    - Re: [AMBER] Error: cannot run "/share/apps/amber/amber14/bin/sqm -O -i sqm.in -o sqm.out" of bcc() in charge.c properly, exit Samuel Bowerman (Tue Sep 13 2016 - 11:00:05 PDT)
[AMBER] Fullerene RESP charges derivation Fabio Bologna (Tue Sep 13 2016 - 06:04:41 PDT)
- Re: [AMBER] Fullerene RESP charges derivation David A Case (Wed Sep 14 2016 - 06:36:42 PDT)
  - [AMBER] R: Fullerene RESP charges derivation Fabio Bologna (Wed Sep 14 2016 - 07:18:52 PDT)
- Re: [AMBER] Fullerene RESP charges derivation FyD (Tue Sep 20 2016 - 02:01:13 PDT)
[AMBER] FATAL: Atom .R<CLEU 124>.A<H13 34> does not have a type. Failed to generate parameters Parameter file was not saved. shahab shariati (Tue Sep 13 2016 - 22:29:57 PDT)
- Re: [AMBER] FATAL: Atom .R<CLEU 124>.A<H13 34> does not have a type. Failed to generate parameters Parameter file was not saved. Bill Ross (Tue Sep 13 2016 - 23:32:36 PDT)
- Re: [AMBER] FATAL: Atom .R<CLEU 124>.A<H13 34> does not have a type. Failed to generate parameters Parameter file was not saved. David A Case (Wed Sep 14 2016 - 06:40:52 PDT)
 - Re: [AMBER] FATAL: Atom .R<CLEU 124>.A<H13 34> does not have a type. Failed to generate parameters Parameter file was not saved. Yeng-Tseng Wang (Wed Sep 14 2016 - 15:03:29 PDT)
[AMBER] MM-PBSA, Protein-nucleic acids free energy calculations hari krishna (Tue Sep 13 2016 - 22:30:10 PDT)
- Re: [AMBER] MM-PBSA, Protein-nucleic acids free energy calculations Carlos Simmerling (Wed Sep 14 2016 - 03:02:12 PDT)
- Re: [AMBER] MM-PBSA, Protein-nucleic acids free energy calculations David A Case (Wed Sep 14 2016 - 06:49:43 PDT)
  - Re: [AMBER] MM-PBSA, Protein-nucleic acids free energy calculations Vlad Cojocaru (Wed Sep 14 2016 - 07:57:36 PDT)
- Re: [AMBER] MM-PBSA, Protein-nucleic acids free energy calculations hari krishna (Wed Sep 14 2016 - 10:54:13 PDT)
  - Re: [AMBER] MM-PBSA, Protein-nucleic acids free energy calculations Jiri Sponer (Wed Sep 14 2016 - 11:27:16 PDT)
[AMBER] Fwd: query with amber Pooja Kesari (Tue Sep 13 2016 - 23:00:50 PDT)
- Re: [AMBER] Fwd: query with amber Bill Ross (Tue Sep 13 2016 - 23:39:41 PDT)
  - Re: [AMBER] Fwd: query with amber Pooja Kesari (Wed Sep 14 2016 - 00:12:40 PDT)
    - Re: [AMBER] Fwd: query with amber Bill Ross (Wed Sep 14 2016 - 01:27:07 PDT)
    - Re: [AMBER] Fwd: query with amber Pooja Kesari (Wed Sep 14 2016 - 21:47:20 PDT)
    - Re: [AMBER] Fwd: query with amber Bill Ross (Wed Sep 14 2016 - 23:26:03 PDT)
- Re: [AMBER] Fwd: query with amber David A Case (Wed Sep 14 2016 - 06:54:41 PDT)
[AMBER] How to "not" strip an ion (say Mg) in MMPBSA Hirdesh Kumar (Wed Sep 14 2016 - 03:06:57 PDT)
- Re: [AMBER] How to "not" strip an ion (say Mg) in MMPBSA Bruno Falcone (Wed Sep 14 2016 - 08:13:52 PDT)
- Re: [AMBER] How to "not" strip an ion (say Mg) in MMPBSA Jason Swails (Wed Sep 14 2016 - 08:58:20 PDT)
[AMBER] Force field ff14SB Anna Cebrian Prats (Wed Sep 14 2016 - 04:06:44 PDT)
- Re: [AMBER] Force field ff14SB Jason Swails (Wed Sep 14 2016 - 09:00:34 PDT)
  - Re: [AMBER] Force field ff14SB Carlos Simmerling (Wed Sep 14 2016 - 09:05:33 PDT)
    - Re: [AMBER] Force field ff14SB Anna Cebrian Prats (Wed Sep 14 2016 - 09:11:16 PDT)
[AMBER] Parameters for GppNHp ligand. Dd H (Wed Sep 14 2016 - 07:31:29 PDT)
[AMBER] Potential Energy in 3D-RISM Maksim Mišin (Wed Sep 14 2016 - 12:16:29 PDT)
- Re: [AMBER] Potential Energy in 3D-RISM Tyler Luchko (Lists) (Wed Sep 14 2016 - 15:07:03 PDT)
[AMBER] Problem with CRD files dhanasekar.mbu.iisc.ernet.in (Wed Sep 14 2016 - 23:24:10 PDT)
- Re: [AMBER] Problem with CRD files dhanasekar.mbu.iisc.ernet.in (Fri Sep 16 2016 - 02:55:38 PDT)
- Re: [AMBER] Problem with CRD files Daniel Roe (Mon Sep 19 2016 - 07:12:24 PDT)
  - Re: [AMBER] Problem with CRD files Daniel Roe (Tue Sep 20 2016 - 08:24:35 PDT)
[AMBER] Glaycam04 version for q4md-CD FF Helen Lvy (Thu Sep 15 2016 - 07:20:41 PDT)
- Re: [AMBER] Glaycam04 version for q4md-CD FF FyD (Tue Sep 20 2016 - 01:57:00 PDT)
  - Re: [AMBER] Glaycam04 version for q4md-CD FF Lachele Foley (Tue Sep 20 2016 - 02:08:41 PDT)
    - Re: [AMBER] Glaycam04 version for q4md-CD FF FyD (Tue Sep 20 2016 - 05:43:19 PDT)
[AMBER] Continue a simulation run Pooja Kesari (Thu Sep 15 2016 - 08:18:47 PDT)
- Re: [AMBER] Continue a simulation run Bilal Nizami (Thu Sep 15 2016 - 10:13:58 PDT)
  - Re: [AMBER] Continue a simulation run David A Case (Fri Sep 16 2016 - 02:05:49 PDT)
    - Re: [AMBER] Continue a simulation run Pooja Kesari (Fri Sep 16 2016 - 03:40:41 PDT)
    - Re: [AMBER] Continue a simulation run Hai Nguyen (Fri Sep 16 2016 - 10:51:20 PDT)
[AMBER] WARNING: The unperturbed charge of the unit: -0.99 is not zero. shahab shariati (Thu Sep 15 2016 - 11:41:22 PDT)
- Re: [AMBER] WARNING: The unperturbed charge of the unit: -0.99 is not zero. David A Case (Fri Sep 16 2016 - 02:08:28 PDT)
[AMBER] changeLJPair/pmemd.cuda Batuhan Kav (Thu Sep 15 2016 - 13:32:23 PDT)
- Re: [AMBER] changeLJPair/pmemd.cuda David A Case (Fri Sep 16 2016 - 02:10:27 PDT)
[AMBER] DNA residue atom names. Christian Schafmeister (Thu Sep 15 2016 - 17:57:41 PDT)
- Re: [AMBER] DNA residue atom names. David A Case (Fri Sep 16 2016 - 02:19:51 PDT)
- Re: [AMBER] DNA residue atom names. Bill Ross (Fri Sep 16 2016 - 13:14:43 PDT)
[AMBER] hbond and autoimage Francesco Gentile (Thu Sep 15 2016 - 23:24:29 PDT)
- Re: [AMBER] hbond and autoimage Daniel Roe (Fri Sep 16 2016 - 06:17:11 PDT)
[AMBER] aromatic ring plane distorted Thomas Evangelidis (Fri Sep 16 2016 - 04:03:03 PDT)
- Re: [AMBER] aromatic ring plane distorted Carlos Simmerling (Fri Sep 16 2016 - 04:41:00 PDT)
  - Re: [AMBER] aromatic ring plane distorted Thomas Evangelidis (Fri Sep 16 2016 - 09:26:35 PDT)
- Re: [AMBER] aromatic ring plane distorted Bill Ross (Fri Sep 16 2016 - 10:26:40 PDT)
[AMBER] "ATTN, need revision" in frcmod file / Could not find bond parameter & Could not find angle parameter shahab shariati (Fri Sep 16 2016 - 11:25:50 PDT)
- Re: [AMBER] "ATTN, need revision" in frcmod file / Could not find bond parameter & Could not find angle parameter ABEL Stephane 175950 (Fri Sep 16 2016 - 12:12:10 PDT)
- Re: [AMBER] "ATTN, need revision" in frcmod file / Could not find bond parameter & Could not find angle parameter Hannes Loeffler (Fri Sep 16 2016 - 12:16:22 PDT)
[AMBER] How to get GppNHp parameters. Dd H (Fri Sep 16 2016 - 19:44:46 PDT)
[AMBER] Simulation of protein complex with four protein chains Jag Silwal (Sat Sep 17 2016 - 12:30:01 PDT)
[AMBER] AMBER installation help Huma Tahir (Sat Sep 17 2016 - 12:58:22 PDT)
- Re: [AMBER] AMBER installation help Bill Ross (Sat Sep 17 2016 - 13:19:09 PDT)
  - Re: [AMBER] AMBER installation help Hai Nguyen (Sat Sep 17 2016 - 15:37:02 PDT)
    - Re: [AMBER] AMBER installation help Huma Tahir (Sun Sep 18 2016 - 02:49:14 PDT)
[AMBER] Installing amber tools on ubuntu neelam wafa (Sat Sep 17 2016 - 13:07:37 PDT)
- Re: [AMBER] Installing amber tools on ubuntu Bill Ross (Sat Sep 17 2016 - 13:20:31 PDT)
  - Re: [AMBER] Installing amber tools on ubuntu chandan patel (Sat Sep 17 2016 - 15:30:22 PDT)
[AMBER] chamber in parmed (Amber16) Song-Ho Chong (Sun Sep 18 2016 - 09:21:18 PDT)
- Re: [AMBER] chamber in parmed (Amber16) Jason Swails (Sun Sep 18 2016 - 11:04:32 PDT)
  - Re: [AMBER] chamber in parmed (Amber16) Song-Ho Chong (Sun Sep 18 2016 - 17:52:22 PDT)
[AMBER] delete residue in tleap Thomas Evangelidis (Sun Sep 18 2016 - 15:46:19 PDT)
- Re: [AMBER] delete residue in tleap Bill Ross (Sun Sep 18 2016 - 16:33:20 PDT)
  - Re: [AMBER] delete residue in tleap Thomas Evangelidis (Sun Sep 18 2016 - 16:55:35 PDT)
    - Re: [AMBER] delete residue in tleap Bill Ross (Sun Sep 18 2016 - 17:24:58 PDT)
[AMBER] adaptive qm/mm NVT, number of quantum atoms outside the legal range Stregone (Mon Sep 19 2016 - 05:12:19 PDT)
- Re: [AMBER] adaptive qm/mm NVT, number of quantum atoms outside the legal range Dr. Andreas W. Goetz (Mon Sep 19 2016 - 20:46:27 PDT)
[AMBER] SCC-DFTB Thakur, Abhishek (Mon Sep 19 2016 - 07:44:03 PDT)
- Re: [AMBER] SCC-DFTB Dr. Andreas W. Goetz (Mon Sep 19 2016 - 20:53:29 PDT)
[AMBER] Parmchk - missing nitro improper Miha Purg (Mon Sep 19 2016 - 11:50:37 PDT)
[AMBER] what is DFTB and SCC-DFTB Thakur, Abhishek (Tue Sep 20 2016 - 07:55:50 PDT)
- Re: [AMBER] what is DFTB and SCC-DFTB Marc van der Kamp (Tue Sep 20 2016 - 11:41:08 PDT)
  - Re: [AMBER] what is DFTB and SCC-DFTB Thakur, Abhishek (Tue Sep 20 2016 - 12:29:18 PDT)
[AMBER] fixing concentration in implicit solvent simulation Chitrak Gupta (Tue Sep 20 2016 - 08:12:48 PDT)
- Re: [AMBER] fixing concentration in implicit solvent simulation Carlos Simmerling (Tue Sep 20 2016 - 08:42:49 PDT)
- Re: [AMBER] fixing concentration in implicit solvent simulation Chitrak Gupta (Wed Sep 21 2016 - 13:11:51 PDT)
  - Re: [AMBER] fixing concentration in implicit solvent simulation Jason Swails (Wed Sep 21 2016 - 17:58:00 PDT)
  - Re: [AMBER] fixing concentration in implicit solvent simulation David A Case (Thu Sep 22 2016 - 06:10:20 PDT)
[AMBER] positive electrostatic energy MM-PBSA Trang Nguyen (Tue Sep 20 2016 - 22:03:34 PDT)
- Re: [AMBER] positive electrostatic energy MM-PBSA David A Case (Wed Sep 21 2016 - 04:38:36 PDT)
[AMBER] Parmchk - missing improper parameter for nitro group Miha Purg (Wed Sep 21 2016 - 00:25:45 PDT)
- Re: [AMBER] Parmchk - missing improper parameter for nitro group David A Case (Thu Sep 22 2016 - 06:34:00 PDT)
[AMBER] frame wise MMPBSA energy difference Hirdesh Kumar (Wed Sep 21 2016 - 02:15:07 PDT)
- Re: [AMBER] frame wise MMPBSA energy difference Jason Swails (Wed Sep 21 2016 - 06:46:53 PDT)
  - Re: [AMBER] frame wise MMPBSA energy difference Hirdesh Kumar (Wed Sep 21 2016 - 07:12:39 PDT)
[AMBER] DFTB and slater koster files Markus Kaukonen (Wed Sep 21 2016 - 02:30:58 PDT)
[AMBER] A refresher on how non-bonding terms are represented in a topology file. Christian Schafmeister (Wed Sep 21 2016 - 10:10:42 PDT)
- Re: [AMBER] A refresher on how non-bonding terms are represented in a topology file. Daniel Roe (Wed Sep 21 2016 - 13:09:14 PDT)
  - Re: [AMBER] A refresher on how non-bonding terms are represented in a topology file. Christian Schafmeister (Wed Sep 21 2016 - 13:13:07 PDT)
  - Re: [AMBER] A refresher on how non-bonding terms are represented in a topology file. Jason Swails (Wed Sep 21 2016 - 17:48:31 PDT)
    - Re: [AMBER] A refresher on how non-bonding terms are represented in a topology file. David A Case (Wed Sep 21 2016 - 19:29:18 PDT)
    - Re: [AMBER] A refresher on how non-bonding terms are represented in a topology file. Jason Swails (Thu Sep 22 2016 - 07:24:49 PDT)
    - Re: [AMBER] A refresher on how non-bonding terms are represented in a topology file. Bill Ross (Wed Sep 21 2016 - 19:44:36 PDT)
[AMBER] setup time with pmemd.cuda Hannes Loeffler (Wed Sep 21 2016 - 11:06:34 PDT)
- Re: [AMBER] setup time with pmemd.cuda Ross Walker (Wed Sep 21 2016 - 12:16:40 PDT)
  - Re: [AMBER] setup time with pmemd.cuda Hannes Loeffler (Wed Sep 21 2016 - 13:01:38 PDT)
    - Re: [AMBER] setup time with pmemd.cuda Ross Walker (Wed Sep 21 2016 - 13:08:11 PDT)
    - Re: [AMBER] setup time with pmemd.cuda Hannes Loeffler (Wed Sep 21 2016 - 13:17:38 PDT)
    - Re: [AMBER] setup time with pmemd.cuda Ross Walker (Wed Sep 21 2016 - 15:23:39 PDT)
    - Re: [AMBER] setup time with pmemd.cuda Hannes Loeffler (Thu Sep 22 2016 - 03:10:34 PDT)
    - Re: [AMBER] setup time with pmemd.cuda Scott Brozell (Thu Sep 22 2016 - 06:17:00 PDT)
    - Re: [AMBER] setup time with pmemd.cuda Hannes Loeffler (Sat Sep 24 2016 - 02:05:46 PDT)
    - Re: [AMBER] setup time with pmemd.cuda Daniel Mermelstein (Sat Sep 24 2016 - 10:54:43 PDT)
    - Re: [AMBER] setup time with pmemd.cuda Hannes Loeffler (Mon Oct 03 2016 - 01:07:02 PDT)
[AMBER] Segmentation fault in tleap when using "sequence" command Lane Votapka (Wed Sep 21 2016 - 13:31:58 PDT)
- Re: [AMBER] Segmentation fault in tleap when using "sequence" command Daniel Roe (Wed Sep 21 2016 - 17:11:17 PDT)
  - Re: [AMBER] Segmentation fault in tleap when using "sequence" command Daniel Roe (Wed Sep 21 2016 - 17:12:34 PDT)
    - Re: [AMBER] Segmentation fault in tleap when using "sequence" command Bill Ross (Wed Sep 21 2016 - 17:34:26 PDT)
    - Re: [AMBER] Segmentation fault in tleap when using "sequence" command Lane Votapka (Thu Sep 22 2016 - 08:14:07 PDT)
    - Re: [AMBER] Segmentation fault in tleap when using "sequence" command Carlos Simmerling (Thu Sep 22 2016 - 08:17:20 PDT)
    - Re: [AMBER] Segmentation fault in tleap when using "sequence" command Lane Votapka (Thu Sep 22 2016 - 08:21:00 PDT)
    - Re: [AMBER] Segmentation fault in tleap when using "sequence" command Daniel Roe (Thu Sep 22 2016 - 08:51:36 PDT)
    - Re: [AMBER] Segmentation fault in tleap when using "sequence" command Lane Votapka (Thu Sep 22 2016 - 09:12:22 PDT)
    - Re: [AMBER] Segmentation fault in tleap when using "sequence" command Lane Votapka (Thu Sep 22 2016 - 08:01:08 PDT)
[AMBER] dihedral PCA amber Neha Gandhi (Wed Sep 21 2016 - 20:08:10 PDT)
- Re: [AMBER] dihedral PCA amber Daniel Roe (Thu Sep 22 2016 - 12:16:11 PDT)
  - Re: [AMBER] dihedral PCA amber Neha Gandhi (Thu Sep 22 2016 - 19:00:41 PDT)
    - Re: [AMBER] dihedral PCA amber Bill Ross (Thu Sep 22 2016 - 19:14:46 PDT)
    - Re: [AMBER] dihedral PCA amber Daniel Roe (Fri Sep 23 2016 - 05:11:42 PDT)
    - Re: [AMBER] dihedral PCA amber Neha Gandhi (Mon Sep 26 2016 - 21:09:08 PDT)
    - Re: [AMBER] dihedral PCA amber Daniel Roe (Tue Sep 27 2016 - 05:42:11 PDT)
    - Re: [AMBER] dihedral PCA amber Neha Gandhi (Wed Sep 28 2016 - 03:19:46 PDT)
[AMBER] Plot activesite water vs time. Saman Yousuf ali (Wed Sep 21 2016 - 21:24:38 PDT)
- Re: [AMBER] Plot activesite water vs time. mmaestre (Wed Sep 21 2016 - 21:49:10 PDT)
  - Re: [AMBER] Plot activesite water vs time. Saman Yousuf ali (Wed Sep 21 2016 - 22:00:29 PDT)
    - Re: [AMBER] Plot activesite water vs time. mmaestre (Wed Sep 21 2016 - 22:15:46 PDT)
[AMBER] Implicit solvent with GPU AMBER and Pulling direction in SMD Ana Bergues (Thu Sep 22 2016 - 00:38:16 PDT)
[AMBER] How to 2D-RDF in cpptraj. Saman Yousuf ali (Thu Sep 22 2016 - 01:05:25 PDT)
[AMBER] Fw:car_to_files.py in AMBER16 is not available. Jinfeng Huang (Thu Sep 22 2016 - 02:23:43 PDT)
[AMBER] Unstable SHAKE ABHIJEET CHOWDHURY (Thu Sep 22 2016 - 08:49:51 PDT)
- Re: [AMBER] Unstable SHAKE Daniel Roe (Thu Sep 22 2016 - 08:52:17 PDT)
  - Re: [AMBER] Unstable SHAKE ABHIJEET CHOWDHURY (Thu Sep 22 2016 - 08:53:49 PDT)
- Re: [AMBER] Unstable SHAKE Carlos Simmerling (Thu Sep 22 2016 - 08:52:35 PDT)
[AMBER] minimzation & MD in vacuo Thomas Evangelidis (Thu Sep 22 2016 - 09:54:48 PDT)
- Re: [AMBER] minimzation & MD in vacuo Thomas Evangelidis (Thu Sep 22 2016 - 16:01:03 PDT)
[AMBER] cpptraj gist core dumped peter.schmidtke.discngine.servier.com (Thu Sep 22 2016 - 23:40:23 PDT)
- Re: [AMBER] cpptraj gist core dumped Nhai (Fri Sep 23 2016 - 00:11:21 PDT)
- Re: [AMBER] cpptraj gist core dumped Daniel Roe (Fri Sep 23 2016 - 05:22:11 PDT)
  - Re: [AMBER] cpptraj gist core dumped Steven Ramsey (Fri Sep 23 2016 - 08:34:48 PDT)
[AMBER] netcdf trajectory Andrew Bostick (Fri Sep 23 2016 - 01:28:50 PDT)
- Re: [AMBER] netcdf trajectory Daniel Roe (Fri Sep 23 2016 - 05:17:38 PDT)
- Re: [AMBER] netcdf trajectory David A Case (Fri Sep 23 2016 - 05:23:52 PDT)
[AMBER] MM-PBSA calculation in different temprature shahab shariati (Fri Sep 23 2016 - 05:07:04 PDT)
- Re: [AMBER] MM-PBSA calculation in different temprature Adrian Roitberg (Fri Sep 23 2016 - 05:45:58 PDT)
  - Re: [AMBER] MM-PBSA calculation in different temprature shahab shariati (Fri Sep 23 2016 - 07:03:32 PDT)
    - Re: [AMBER] MM-PBSA calculation in different temprature shahab shariati (Tue Oct 25 2016 - 03:29:30 PDT)
    - Re: [AMBER] MM-PBSA calculation in different temprature shahab shariati (Wed Oct 26 2016 - 11:18:15 PDT)
    - Re: [AMBER] MM-PBSA calculation in different temprature Hai Nguyen (Wed Oct 26 2016 - 11:24:55 PDT)
    - Re: [AMBER] MM-PBSA calculation in different temprature shahab shariati (Thu Oct 27 2016 - 09:13:50 PDT)
    - Re: [AMBER] MM-PBSA calculation in different temprature Hai Nguyen (Thu Oct 27 2016 - 10:06:56 PDT)
[AMBER] strip waters using distance criteria Thomas Evangelidis (Fri Sep 23 2016 - 06:23:07 PDT)
- Re: [AMBER] strip waters using distance criteria Daniel Roe (Fri Sep 23 2016 - 12:45:09 PDT)
  - Re: [AMBER] strip waters using distance criteria Thomas Evangelidis (Sat Sep 24 2016 - 17:14:13 PDT)
    - Re: [AMBER] strip waters using distance criteria Hai Nguyen (Sat Sep 24 2016 - 23:13:04 PDT)
[AMBER] How aggressively should bond, angle, torsion parameters be coalesced? Christian Schafmeister (Sat Sep 24 2016 - 06:58:11 PDT)
- Re: [AMBER] How aggressively should bond, angle, torsion parameters be coalesced? W. Andeas Svrcek-Seiler (Sat Sep 24 2016 - 12:26:07 PDT)
  - Re: [AMBER] How aggressively should bond, angle, torsion parameters be coalesced? Christian Schafmeister (Sat Sep 24 2016 - 13:03:34 PDT)
[AMBER] netcdf trajectory Andrew Bostick (Sat Sep 24 2016 - 13:39:38 PDT)
- Re: [AMBER] netcdf trajectory Bill Ross (Sat Sep 24 2016 - 13:53:48 PDT)
  - Re: [AMBER] netcdf trajectory Hirdesh Kumar (Sat Sep 24 2016 - 23:06:38 PDT)
[AMBER] netcdf trajectory Andrew Bostick (Sun Sep 25 2016 - 00:09:01 PDT)
- Re: [AMBER] netcdf trajectory Bill Ross (Sun Sep 25 2016 - 00:30:14 PDT)
  - Re: [AMBER] netcdf trajectory Bill Ross (Sun Sep 25 2016 - 00:44:48 PDT)
- Re: [AMBER] netcdf trajectory Andrew Bostick (Sun Sep 25 2016 - 01:20:29 PDT)
  - Re: [AMBER] netcdf trajectory TERREUX RAPHAEL (Sun Sep 25 2016 - 01:28:09 PDT)
    - Re: [AMBER] netcdf trajectory Bill Ross (Sun Sep 25 2016 - 09:45:24 PDT)
  - Re: [AMBER] netcdf trajectory Bill Ross (Sun Sep 25 2016 - 09:31:08 PDT)
  - Re: [AMBER] netcdf trajectory Jason Swails (Sun Sep 25 2016 - 09:58:10 PDT)
    - Re: [AMBER] netcdf trajectory Kshatresh Dutta Dubey (Mon Sep 26 2016 - 06:25:19 PDT)
    - Re: [AMBER] netcdf trajectory Hai Nguyen (Mon Sep 26 2016 - 10:31:39 PDT)
    - Re: [AMBER] netcdf trajectory Markowska (Fri Sep 30 2016 - 01:29:50 PDT)
    - Re: [AMBER] netcdf trajectory Daniel Roe (Fri Sep 30 2016 - 05:28:58 PDT)
    - Re: [AMBER] netcdf trajectory Markowska (Fri Sep 30 2016 - 06:08:08 PDT)
[AMBER] Signal: Segmentation fault (11) shahab shariati (Sun Sep 25 2016 - 02:10:03 PDT)
- Re: [AMBER] Signal: Segmentation fault (11) David A Case (Sun Sep 25 2016 - 13:38:58 PDT)
  - Re: [AMBER] Signal: Segmentation fault (11) shahab shariati (Mon Sep 26 2016 - 12:01:40 PDT)
    - Re: [AMBER] Signal: Segmentation fault (11) David A Case (Mon Sep 26 2016 - 18:04:26 PDT)
    - Re: [AMBER] Signal: Segmentation fault (11) shahab shariati (Wed Sep 28 2016 - 05:35:08 PDT)
    - Re: [AMBER] Signal: Segmentation fault (11) David A Case (Wed Sep 28 2016 - 11:53:28 PDT)
[AMBER] Restrain in Umbrella Sampling ATUL KUMAR (Sun Sep 25 2016 - 07:12:10 PDT)
[AMBER] 2 ns heating in constant pH tutorial inquiry Andrew Schaub (Sun Sep 25 2016 - 08:56:29 PDT)
- Re: [AMBER] 2 ns heating in constant pH tutorial inquiry Jason Swails (Mon Sep 26 2016 - 08:45:48 PDT)
[AMBER] create a cubic box of 4.5 nm Jesmita Dhar (Mon Sep 26 2016 - 01:39:18 PDT)
- Re: [AMBER] create a cubic box of 4.5 nm David A Case (Mon Sep 26 2016 - 05:17:59 PDT)
[AMBER] problem about Using ParmEd or xParmEd 杨金鹏 (Mon Sep 26 2016 - 04:06:02 PDT)
- Re: [AMBER] problem about Using ParmEd or xParmEd Jason Swails (Mon Sep 26 2016 - 08:32:52 PDT)
[AMBER] PGI Fortran/C/C++ workstation Hector A. Baldoni (Mon Sep 26 2016 - 05:29:32 PDT)
- Re: [AMBER] PGI Fortran/C/C++ workstation Hector A. Baldoni (Mon Sep 26 2016 - 05:51:34 PDT)
[AMBER] pmemd.cuda: multiple bonds illegal for SHAKEH Hannes Loeffler (Mon Sep 26 2016 - 07:57:31 PDT)
- Re: [AMBER] pmemd.cuda: multiple bonds illegal for SHAKEH Jason Swails (Mon Sep 26 2016 - 08:36:55 PDT)
[AMBER] RESP charge fitting error in MCPB.py zycz138.126.com (Mon Sep 26 2016 - 17:54:06 PDT)
[AMBER] Issue regarding parametrization Mahrukh Imtiaz (Tue Sep 27 2016 - 04:22:41 PDT)
- Re: [AMBER] Issue regarding parametrization David A Case (Tue Sep 27 2016 - 05:11:46 PDT)
[AMBER] tleap cannot solvate unit in amber16 windy (Tue Sep 27 2016 - 05:53:00 PDT)
- Re: [AMBER] tleap cannot solvate unit in amber16 Christina Bergonzo (Tue Sep 27 2016 - 06:25:26 PDT)
  - Re: [AMBER] tleap cannot solvate unit in amber16 windy (Tue Sep 27 2016 - 22:33:39 PDT)
[AMBER] Tcl problem Elisa Pieri (Tue Sep 27 2016 - 06:59:02 PDT)
- Re: [AMBER] Tcl problem Jason Swails (Tue Sep 27 2016 - 07:26:59 PDT)
  - Re: [AMBER] Tcl problem Elisa Pieri (Tue Sep 27 2016 - 07:40:19 PDT)
    - Re: [AMBER] Tcl problem Jason Swails (Tue Sep 27 2016 - 08:40:12 PDT)
- Re: [AMBER] Tcl problem Hai Nguyen (Tue Sep 27 2016 - 08:37:47 PDT)
  - Re: [AMBER] Tcl problem Jason Swails (Tue Sep 27 2016 - 08:41:47 PDT)
    - Re: [AMBER] Tcl problem Elisa Pieri (Wed Sep 28 2016 - 00:58:19 PDT)
[AMBER] Amber NaN error DIAO Jianxiong (Tue Sep 27 2016 - 15:53:13 PDT)
- Re: [AMBER] Amber NaN error David A Case (Wed Sep 28 2016 - 06:04:45 PDT)
  - [AMBER] 答复: Amber NaN error DIAO Jianxiong (Wed Sep 28 2016 - 14:24:12 PDT)
    - Re: [AMBER] 答复: Amber NaN error David A Case (Thu Sep 29 2016 - 11:57:18 PDT)
[AMBER] Can amber handle carbon -- nitrogen double and single bond? Ming Tang (Wed Sep 28 2016 - 01:43:52 PDT)
- Re: [AMBER] Can amber handle carbon -- nitrogen double and single bond? Bill Ross (Wed Sep 28 2016 - 02:38:18 PDT)
[AMBER] ACS COMP award deadline for Spring 2017 Carlos Simmerling (Wed Sep 28 2016 - 03:48:05 PDT)
[AMBER] mdin for LIO interface Hector A. Baldoni (Wed Sep 28 2016 - 04:03:53 PDT)
[AMBER] invoking MPI_ABORT causes Open MPI to kill all MPI processes. Pooja Kesari (Wed Sep 28 2016 - 04:38:28 PDT)
- Re: [AMBER] invoking MPI_ABORT causes Open MPI to kill all MPI processes. David A Case (Wed Sep 28 2016 - 06:09:46 PDT)
  - Re: [AMBER] invoking MPI_ABORT causes Open MPI to kill all MPI processes. Pooja Kesari (Wed Sep 28 2016 - 07:47:42 PDT)
    - Re: [AMBER] invoking MPI_ABORT causes Open MPI to kill all MPI processes. Nhai (Wed Sep 28 2016 - 08:12:47 PDT)
    - Re: [AMBER] invoking MPI_ABORT causes Open MPI to kill all MPI processes. David A Case (Wed Sep 28 2016 - 11:53:52 PDT)
[AMBER] MMPBSA.py error Your ligand residues must be sequential in your complex maryam azimzadehirani (Wed Sep 28 2016 - 06:06:42 PDT)
- Re: [AMBER] MMPBSA.py error Your ligand residues must be sequential in your complex Dwight McGee (Wed Sep 28 2016 - 07:19:12 PDT)
  - Re: [AMBER] MMPBSA.py error Your ligand residues must be sequential in your complex maryam azimzadehirani (Sun Oct 02 2016 - 17:53:23 PDT)
    - Re: [AMBER] MMPBSA.py error Your ligand residues must be sequential in your complex Jason Swails (Mon Oct 03 2016 - 08:00:04 PDT)
    - Re: [AMBER] MMPBSA.py error Your ligand residues must be sequential in your complex maryam azimzadehirani (Mon Oct 03 2016 - 20:11:51 PDT)
[AMBER] scaling of mpi version of pmemd.mpi (AMBER14) and that of the MMPBSA.py.MPI Kris Feher (Wed Sep 28 2016 - 12:40:37 PDT)
- Re: [AMBER] scaling of mpi version of pmemd.mpi (AMBER14) and that of the MMPBSA.py.MPI Jason Swails (Thu Sep 29 2016 - 11:26:07 PDT)
[AMBER] on periodic conditions and unspecified launch failure Elisa Pieri (Wed Sep 28 2016 - 13:46:26 PDT)
- Re: [AMBER] on periodic conditions and unspecified launch failure Jason Swails (Thu Sep 29 2016 - 09:40:28 PDT)
- Re: [AMBER] on periodic conditions and unspecified launch failure David A Case (Thu Sep 29 2016 - 11:53:59 PDT)
  - Re: [AMBER] on periodic conditions and unspecified launch failure Elisa Pieri (Fri Sep 30 2016 - 04:42:21 PDT)
    - Re: [AMBER] on periodic conditions and unspecified launch failure Jason Swails (Fri Sep 30 2016 - 05:06:03 PDT)
    - Re: [AMBER] on periodic conditions and unspecified launch failure Elisa Pieri (Sun Oct 02 2016 - 11:02:25 PDT)
    - Re: [AMBER] on periodic conditions and unspecified launch failure Jason Swails (Mon Oct 03 2016 - 06:24:04 PDT)
[AMBER] FMN parameters ruqaiya khalil (Wed Sep 28 2016 - 22:46:13 PDT)
- Re: [AMBER] FMN parameters Bill Ross (Wed Sep 28 2016 - 23:47:46 PDT)
  - Re: [AMBER] FMN parameters Bill Ross (Thu Sep 29 2016 - 00:48:34 PDT)
    - Re: [AMBER] FMN parameters ruqaiya khalil (Thu Sep 29 2016 - 02:51:05 PDT)
[AMBER] Disparities in H-bond lifetimes calculated through different approaches Praneeth Bommisetti (Wed Sep 28 2016 - 23:03:25 PDT)
- Re: [AMBER] Disparities in H-bond lifetimes calculated through different approaches Daniel Roe (Thu Sep 29 2016 - 06:22:42 PDT)
  - Re: [AMBER] Disparities in H-bond lifetimes calculated through different approaches Daniel Roe (Wed Oct 12 2016 - 07:07:25 PDT)
[AMBER] Error in the second step using MCPB.py Tiffani Rovira (Thu Sep 29 2016 - 02:26:41 PDT)
- Re: [AMBER] Error in the second step using MCPB.py Pengfei Li (Fri Sep 30 2016 - 19:49:17 PDT)
[AMBER] using boundary information from previous run Hirdesh Kumar (Thu Sep 29 2016 - 04:45:46 PDT)
- Re: [AMBER] using boundary information from previous run Daniel Roe (Thu Sep 29 2016 - 06:38:42 PDT)
- Re: [AMBER] using boundary information from previous run David A Case (Thu Sep 29 2016 - 12:05:29 PDT)
  - Re: [AMBER] using boundary information from previous run Hirdesh Kumar (Fri Sep 30 2016 - 01:53:31 PDT)
    - Re: [AMBER] using boundary information from previous run David A Case (Fri Sep 30 2016 - 04:22:09 PDT)
    - Re: [AMBER] using boundary information from previous run Hirdesh Kumar (Fri Sep 30 2016 - 05:19:48 PDT)
    - Re: [AMBER] using boundary information from previous run David A Case (Fri Sep 30 2016 - 07:17:45 PDT)
    - Re: [AMBER] using boundary information from previous run Daniel Roe (Fri Sep 30 2016 - 05:25:10 PDT)
    - Re: [AMBER] using boundary information from previous run Hirdesh Kumar (Fri Sep 30 2016 - 05:54:46 PDT)
[AMBER] Pressure of the system during equilibration Debodyuti Dutta (Thu Sep 29 2016 - 06:01:20 PDT)
- Re: [AMBER] Pressure of the system during equilibration Daniel Roe (Thu Sep 29 2016 - 06:28:17 PDT)
[AMBER] Problem regarding sccdftb not converging amitosh gautam (Thu Sep 29 2016 - 22:36:34 PDT)
- Re: [AMBER] Problem regarding sccdftb not converging Thakur, Abhishek (Fri Sep 30 2016 - 09:07:04 PDT)
[AMBER] How to read prmtop file flag pointer section Xiaoyu Wang (Fri Sep 30 2016 - 11:43:05 PDT)
- Re: [AMBER] How to read prmtop file flag pointer section Jason Swails (Fri Sep 30 2016 - 12:35:02 PDT)
[AMBER] Save the average structure from two pdb files Iqbal, Muhammad Sajid (Fri Sep 30 2016 - 15:22:11 PDT)
- Re: [AMBER] Save the average structure from two pdb files Hai Nguyen (Fri Sep 30 2016 - 15:47:01 PDT)
[AMBER] SHAKE problem ABHIJEET CHOWDHURY (Sat Oct 01 2016 - 04:40:07 PDT)
- Re: [AMBER] SHAKE problem Carlos Simmerling (Sat Oct 01 2016 - 05:29:31 PDT)
- Re: [AMBER] SHAKE problem Bill Ross (Sat Oct 01 2016 - 05:32:45 PDT)
  - Re: [AMBER] SHAKE problem ABHIJEET CHOWDHURY (Sat Oct 01 2016 - 07:41:21 PDT)
[AMBER] MMPBSA.py TrajError: Could not find number of frames in MMPBSA.mdcrd maryam azimzadehirani (Sun Oct 02 2016 - 18:01:24 PDT)
- Re: [AMBER] MMPBSA.py TrajError: Could not find number of frames in MMPBSA.mdcrd Hai Nguyen (Sun Oct 02 2016 - 18:21:30 PDT)
[AMBER] Got an error on tleap Elka Firmanda (Sun Oct 02 2016 - 22:31:34 PDT)
- Re: [AMBER] Got an error on tleap Bill Ross (Sun Oct 02 2016 - 22:46:15 PDT)
- Re: [AMBER] Got an error on tleap David A Case (Mon Oct 03 2016 - 04:36:49 PDT)
[AMBER] MM-PBSA result for small molecule-receptor complex Maryam Hamzehee (Sun Oct 02 2016 - 23:49:20 PDT)
- Re: [AMBER] MM-PBSA result for small molecule-receptor complex David A Case (Mon Oct 03 2016 - 04:44:02 PDT)
  - Re: [AMBER] MM-PBSA result for small molecule-receptor complex Bruno Falcone (Mon Oct 03 2016 - 10:07:14 PDT)
    - Re: [AMBER] MM-PBSA result for small molecule-receptor complex Maryam Hamzehee (Tue Oct 04 2016 - 01:25:47 PDT)
    - Re: [AMBER] MM-PBSA result for small molecule-receptor complex David A Case (Tue Oct 04 2016 - 05:17:07 PDT)
    - Re: [AMBER] MM-PBSA result for small molecule-receptor complex Bruno Falcone (Tue Oct 04 2016 - 06:58:31 PDT)
[AMBER] Increase titratable groups Orion Shih (Mon Oct 03 2016 - 02:54:20 PDT)
- Re: [AMBER] Increase titratable groups Jason Swails (Mon Oct 03 2016 - 06:24:35 PDT)
[AMBER] WHAM_ANALYSIS Thakur, Abhishek (Mon Oct 03 2016 - 12:49:46 PDT)
[AMBER] missing windows qm/mm Thakur, Abhishek (Mon Oct 03 2016 - 13:50:22 PDT)
[AMBER] Failing to compile AmberTools16 on Mac Sierra with Fink Alan (Mon Oct 03 2016 - 14:26:26 PDT)
- Re: [AMBER] Failing to compile AmberTools16 on Mac Sierra with Fink Jason Swails (Mon Oct 03 2016 - 16:32:12 PDT)
[AMBER] did not find amber.python xwnail2003.163.com (Tue Oct 04 2016 - 04:38:12 PDT)
- Re: [AMBER] did not find amber.python Bill Ross (Tue Oct 04 2016 - 04:54:19 PDT)
- Re: [AMBER] did not find amber.python David A Case (Tue Oct 04 2016 - 18:00:13 PDT)
[AMBER] time step changes during long simulation run Hirdesh Kumar (Tue Oct 04 2016 - 05:48:27 PDT)
- Re: [AMBER] time step changes during long simulation run Jason Swails (Tue Oct 04 2016 - 06:21:55 PDT)
  - Re: [AMBER] time step changes during long simulation run Hirdesh Kumar (Tue Oct 04 2016 - 06:26:40 PDT)
[AMBER] MD simulation by amber Atila Petrosian (Tue Oct 04 2016 - 09:52:25 PDT)
- Re: [AMBER] MD simulation by amber Hai Nguyen (Tue Nov 15 2016 - 18:40:12 PST)
  - Re: [AMBER] MD simulation by amber David A Case (Wed Nov 16 2016 - 06:00:38 PST)
[AMBER] drmsd to reference with different mask Vlad Cojocaru (Tue Oct 04 2016 - 14:14:28 PDT)
- Re: [AMBER] drmsd to reference with different mask Daniel Roe (Wed Oct 05 2016 - 05:56:06 PDT)
  - Re: [AMBER] drmsd to reference with different mask Vlad Cojocaru (Wed Oct 05 2016 - 06:13:24 PDT)
    - Re: [AMBER] drmsd to reference with different mask Daniel Roe (Wed Oct 05 2016 - 06:48:38 PDT)
Re: [AMBER] AMBER Digest, Vol 1717, Issue 1 xwnail2003.163.com (Tue Oct 04 2016 - 15:50:45 PDT)
[AMBER] Amber14 using triple GTX 1080 Yohanes Gultom (Wed Oct 05 2016 - 04:59:09 PDT)
- Re: [AMBER] Amber14 using triple GTX 1080 Elka Firmanda (Wed Oct 05 2016 - 06:04:25 PDT)
- Re: [AMBER] Amber14 using triple GTX 1080 David A Case (Wed Oct 05 2016 - 07:18:24 PDT)
  - Re: [AMBER] Amber14 using triple GTX 1080 Yohanes Gultom (Wed Oct 05 2016 - 07:50:04 PDT)
[AMBER] hbond cutoff for %occupancy in series data (.gnu file) Hirdesh Kumar (Wed Oct 05 2016 - 05:10:45 PDT)
- Re: [AMBER] hbond cutoff for %occupancy in series data (.gnu file) Daniel Roe (Thu Oct 13 2016 - 06:26:32 PDT)
[AMBER] QM/MM calculation on protein+ligand (covalently bond) Corum, Katharine W (Wed Oct 05 2016 - 08:05:19 PDT)
[AMBER] update the reference structure along trajectory kurisaki (Wed Oct 05 2016 - 23:12:55 PDT)
- Re: [AMBER] update the reference structure along trajectory Daniel Roe (Thu Oct 13 2016 - 06:30:31 PDT)
[AMBER] issue regarding GLYCAM and amber FF Mahrukh Imtiaz (Wed Oct 05 2016 - 23:46:10 PDT)
- Re: [AMBER] issue regarding GLYCAM and amber FF David A Case (Thu Oct 06 2016 - 05:11:03 PDT)
  - Re: [AMBER] issue regarding GLYCAM and amber FF Mahrukh Imtiaz (Thu Oct 06 2016 - 05:19:11 PDT)
  - Re: [AMBER] issue regarding GLYCAM and amber FF Lachele Foley (Thu Oct 06 2016 - 08:45:07 PDT)
[AMBER] zn parameters Stefania Mirabella (Thu Oct 06 2016 - 06:34:06 PDT)
- Re: [AMBER] zn parameters Jacopo Sgrignani (Thu Oct 06 2016 - 06:53:10 PDT)
  - Re: [AMBER] zn parameters Stefania Mirabella (Thu Oct 13 2016 - 05:37:51 PDT)
[AMBER] Creating an AMBER input to Gaussian Aseel Bala (Thu Oct 06 2016 - 09:27:00 PDT)
- Re: [AMBER] Creating an AMBER input to Gaussian Daniel Roe (Thu Oct 06 2016 - 17:45:46 PDT)
[AMBER] Best practice for charmm to AMBER conversion with HEME group Korey M Reid (Thu Oct 06 2016 - 11:08:08 PDT)
- Re: [AMBER] Best practice for charmm to AMBER conversion with HEME group David A Case (Fri Oct 07 2016 - 08:55:27 PDT)
  - Re: [AMBER] Best practice for charmm to AMBER conversion with HEME group Korey M Reid (Fri Oct 07 2016 - 16:09:42 PDT)
    - Re: [AMBER] Best practice for charmm to AMBER conversion with HEME group David A Case (Sat Oct 08 2016 - 17:45:46 PDT)
[AMBER] Amber compilation problems Fabrício Bracht (Thu Oct 06 2016 - 13:01:34 PDT)
- Re: [AMBER] Amber compilation problems David A Case (Fri Oct 07 2016 - 08:48:43 PDT)
[AMBER] AF-NMR (Shifts5.1) for Nonstandard Residue Eleftherios A P Lambros (Thu Oct 06 2016 - 18:42:06 PDT)
[AMBER] GIST hydration analysis of big interface Sergey Samsonov (Fri Oct 07 2016 - 07:22:53 PDT)
- Re: [AMBER] GIST hydration analysis of big interface Steven Ramsey (Fri Oct 07 2016 - 07:56:43 PDT)
  - Re: [AMBER] GIST hydration analysis of big interface Steven Ramsey (Fri Oct 07 2016 - 08:31:39 PDT)
    - Re: [AMBER] GIST hydration analysis of big interface Sergey Samsonov (Sun Oct 09 2016 - 22:57:44 PDT)
[AMBER] Compiling Amber16 Daniel G. Oblinsky (Fri Oct 07 2016 - 08:21:06 PDT)
- Re: [AMBER] Compiling Amber16 Hai Nguyen (Fri Oct 07 2016 - 08:31:23 PDT)
[AMBER] Bug report for pdb4amber code (amber16) Yusuf Simsek (Fri Oct 07 2016 - 14:37:17 PDT)
- Re: [AMBER] Bug report for pdb4amber code (amber16) Hai Nguyen (Sat Oct 08 2016 - 10:11:53 PDT)
[AMBER] AmberTools16 Installation with openMPI fails? Ucisik, Melek Nihan (Fri Oct 07 2016 - 15:23:44 PDT)
- Re: [AMBER] AmberTools16 Installation with openMPI fails? Hai Nguyen (Fri Oct 07 2016 - 15:26:54 PDT)
- Re: [AMBER] AmberTools16 Installation with openMPI fails? Charles Lin (Fri Oct 07 2016 - 15:30:32 PDT)
  - Re: [AMBER] AmberTools16 Installation with openMPI fails? Ucisik, Melek Nihan (Sat Oct 08 2016 - 09:56:31 PDT)
    - Re: [AMBER] AmberTools16 Installation with openMPI fails? Ucisik, Melek Nihan (Mon Oct 10 2016 - 10:39:55 PDT)
    - Re: [AMBER] AmberTools16 Installation with openMPI fails? Marcelo Andrade Chagas (Mon Oct 10 2016 - 10:53:42 PDT)
    - Re: [AMBER] AmberTools16 Installation with openMPI fails? Gulsevin,Alican (Mon Oct 10 2016 - 11:02:44 PDT)
    - Re: [AMBER] AmberTools16 Installation with openMPI fails? Hai Nguyen (Mon Oct 10 2016 - 11:09:21 PDT)
    - Re: [AMBER] AmberTools16 Installation with openMPI fails? Daniel Roe (Wed Oct 12 2016 - 06:30:32 PDT)
[AMBER] Problem with aMD on membrane protein and/or the amd.log file filip fratev (Fri Oct 07 2016 - 20:02:36 PDT)
- Re: [AMBER] Problem with aMD on membrane protein and/or the amd.log file Samuel Bowerman (Sat Oct 08 2016 - 05:39:51 PDT)
  - Re: [AMBER] Problem with aMD on membrane protein and/or the amd.log file Filip Fratev (Sat Oct 08 2016 - 13:31:46 PDT)
[AMBER] mm_pbsa.pl error: Found unknown atflg DC 康宁 (Sat Oct 08 2016 - 02:04:06 PDT)
- Re: [AMBER] mm_pbsa.pl error: Found unknown atflg DC Hai Nguyen (Tue Nov 15 2016 - 18:42:37 PST)
[AMBER] cpptraj and selection Dhiraj Srivastava (Sun Oct 09 2016 - 18:56:08 PDT)
- Re: [AMBER] cpptraj and selection Daniel Roe (Thu Oct 13 2016 - 05:50:40 PDT)
[AMBER] Steered MD collective variables abdennour braka (Mon Oct 10 2016 - 00:46:39 PDT)
- Re: [AMBER] Steered MD collective variables Feng Pan (Mon Oct 10 2016 - 13:51:52 PDT)
- [AMBER] Question about the implementation of the Steered MD abdennour braka (Thu Mar 09 2017 - 23:26:36 PST)
  - Re: [AMBER] Question about the implementation of the Steered MD Feng Pan (Fri Mar 10 2017 - 08:45:31 PST)
[AMBER] mmpbsa with atomic radii for ff14SB and parmbsc1 atom types Vlad Cojocaru (Tue Oct 11 2016 - 05:36:50 PDT)
- Re: [AMBER] mmpbsa with atomic radii for ff14SB and parmbsc1 atom types Vlad Cojocaru (Tue Oct 11 2016 - 05:42:25 PDT)
- Re: [AMBER] mmpbsa with atomic radii for ff14SB and parmbsc1 atom types Carlos Simmerling (Tue Oct 11 2016 - 05:57:04 PDT)
  - Re: [AMBER] mmpbsa with atomic radii for ff14SB and parmbsc1 atom types Vlad Cojocaru (Tue Oct 11 2016 - 06:12:19 PDT)
    - Re: [AMBER] mmpbsa with atomic radii for ff14SB and parmbsc1 atom types Niel Henriksen (Tue Oct 11 2016 - 07:10:54 PDT)
[AMBER] amb2gmx.pl (sh: rdparm: command not found) shahab shariati (Tue Oct 11 2016 - 09:32:40 PDT)
- Re: [AMBER] amb2gmx.pl (sh: rdparm: command not found) David A Case (Tue Oct 11 2016 - 10:52:22 PDT)
  - Re: [AMBER] amb2gmx.pl (sh: rdparm: command not found) Lorenzo Gontrani (Tue Oct 11 2016 - 11:17:52 PDT)
  - Re: [AMBER] amb2gmx.pl (sh: rdparm: command not found) shahab shariati (Tue Oct 11 2016 - 11:50:17 PDT)
    - Re: [AMBER] amb2gmx.pl (sh: rdparm: command not found) Alan (Tue Oct 11 2016 - 14:48:22 PDT)
    - Re: [AMBER] amb2gmx.pl (sh: rdparm: command not found) David A Case (Tue Oct 11 2016 - 17:59:33 PDT)
    - Re: [AMBER] amb2gmx.pl (sh: rdparm: command not found) shahab shariati (Wed Oct 12 2016 - 05:18:15 PDT)
    - Re: [AMBER] amb2gmx.pl (sh: rdparm: command not found) Daniel Roe (Wed Oct 12 2016 - 06:32:06 PDT)
    - Re: [AMBER] amb2gmx.pl (sh: rdparm: command not found) shahab shariati (Wed Oct 12 2016 - 12:19:51 PDT)
- Re: [AMBER] amb2gmx.pl (sh: rdparm: command not found) Hai Nguyen (Tue Oct 11 2016 - 10:59:39 PDT)
[AMBER] tleap loadamberparams failing on OSX Stefan Doerr (Tue Oct 11 2016 - 09:48:13 PDT)
- Re: [AMBER] tleap loadamberparams failing on OSX Gulsevin,Alican (Tue Oct 11 2016 - 09:58:01 PDT)
  - Re: [AMBER] tleap loadamberparams failing on OSX Stefan Doerr (Tue Oct 11 2016 - 14:43:23 PDT)
    - Re: [AMBER] tleap loadamberparams failing on OSX Bill Ross (Tue Oct 11 2016 - 15:03:34 PDT)
    - Re: [AMBER] tleap loadamberparams failing on OSX Hai Nguyen (Tue Oct 11 2016 - 15:08:49 PDT)
    - Re: [AMBER] tleap loadamberparams failing on OSX Jason Swails (Wed Oct 12 2016 - 05:09:04 PDT)
    - Re: [AMBER] tleap loadamberparams failing on OSX Stefan Doerr (Wed Oct 12 2016 - 06:13:00 PDT)
[AMBER] Ligand across membrane Fabrício Bracht (Tue Oct 11 2016 - 14:06:40 PDT)
- Re: [AMBER] Ligand across membrane Charles Lin (Tue Oct 11 2016 - 14:14:24 PDT)
  - Re: [AMBER] Ligand across membrane Fabrício Bracht (Tue Oct 11 2016 - 17:26:15 PDT)
    - Re: [AMBER] Ligand across membrane Dickson, Callum J (Wed Oct 12 2016 - 06:52:03 PDT)
    - Re: [AMBER] Ligand across membrane Fabrício Bracht (Thu Oct 13 2016 - 07:40:18 PDT)
    - Re: [AMBER] Ligand across membrane zoran matovic (Sun Nov 06 2016 - 23:38:25 PST)
[AMBER] MMPBSA results with Amber 12 versus Amber 16 Vlad Cojocaru (Wed Oct 12 2016 - 01:31:57 PDT)
- Re: [AMBER] MMPBSA results with Amber 12 versus Amber 16 Ray Luo (Wed Oct 12 2016 - 01:44:09 PDT)
  - Re: [AMBER] MMPBSA results with Amber 12 versus Amber 16 Vlad Cojocaru (Thu Oct 13 2016 - 01:47:29 PDT)
    - Re: [AMBER] MMPBSA results with Amber 12 versus Amber 16 Vlad Cojocaru (Thu Oct 13 2016 - 08:43:47 PDT)
    - Re: [AMBER] MMPBSA results with Amber 12 versus Amber 16 Ray Luo (Thu Oct 13 2016 - 15:23:27 PDT)
    - Re: [AMBER] MMPBSA results with Amber 12 versus Amber 16 Vlad Cojocaru (Fri Oct 14 2016 - 01:42:44 PDT)
    - Re: [AMBER] MMPBSA results with Amber 12 versus Amber 16 Ray Luo (Fri Oct 14 2016 - 08:44:17 PDT)
    - Re: [AMBER] MMPBSA results with Amber 12 versus Amber 16 Ray Luo (Fri Oct 14 2016 - 09:34:23 PDT)
    - Re: [AMBER] MMPBSA results with Amber 12 versus Amber 16 Vlad Cojocaru (Fri Oct 14 2016 - 10:35:02 PDT)
    - Re: [AMBER] MMPBSA results with Amber 12 versus Amber 16 Ray Luo (Fri Oct 14 2016 - 11:29:14 PDT)
    - Re: [AMBER] MMPBSA results with Amber 12 versus Amber 16 Vlad Cojocaru (Fri Oct 14 2016 - 11:38:49 PDT)
    - Re: [AMBER] MMPBSA results with Amber 12 versus Amber 16 Ray Luo (Tue Oct 18 2016 - 10:47:30 PDT)
    - Re: [AMBER] MMPBSA results with Amber 12 versus Amber 16 Vlad Cojocaru (Tue Oct 18 2016 - 14:21:51 PDT)
    - Re: [AMBER] MMPBSA results with Amber 12 versus Amber 16 Ray Luo (Tue Oct 18 2016 - 16:26:43 PDT)
    - Re: [AMBER] MMPBSA results with Amber 12 versus Amber 16 Vlad Cojocaru (Wed Oct 19 2016 - 02:19:57 PDT)
    - Re: [AMBER] MMPBSA results with Amber 12 versus Amber 16 Vlad Cojocaru (Wed Oct 19 2016 - 02:28:33 PDT)
    - Re: [AMBER] MMPBSA results with Amber 12 versus Amber 16 Vlad Cojocaru (Fri Oct 14 2016 - 10:40:23 PDT)
[AMBER] pbsa eneopt = 4 option Vlad Cojocaru (Wed Oct 12 2016 - 07:44:58 PDT)
- Re: [AMBER] pbsa eneopt = 4 option Ray Luo (Wed Oct 12 2016 - 08:32:36 PDT)
  - Re: [AMBER] pbsa eneopt = 4 option Vlad Cojocaru (Wed Oct 12 2016 - 10:03:51 PDT)
    - Re: [AMBER] pbsa eneopt = 4 option Ray Luo (Wed Oct 12 2016 - 11:41:18 PDT)
[AMBER] cpptraj grid output George Tzotzos (Wed Oct 12 2016 - 08:39:01 PDT)
- Re: [AMBER] cpptraj grid output Daniel Roe (Thu Oct 13 2016 - 05:45:04 PDT)
[AMBER] Correctly defining keywords in cpptraj - radial Stregone (Wed Oct 12 2016 - 15:45:36 PDT)
- Re: [AMBER] Correctly defining keywords in cpptraj - radial Daniel Roe (Thu Oct 13 2016 - 05:41:15 PDT)
  - Re: [AMBER] Correctly defining keywords in cpptraj - radial Stregone (Fri Oct 14 2016 - 05:19:36 PDT)
    - Re: [AMBER] Correctly defining keywords in cpptraj - radial Daniel Roe (Fri Oct 14 2016 - 06:41:08 PDT)
    - Re: [AMBER] Correctly defining keywords in cpptraj - radial Stregone (Fri Oct 14 2016 - 07:24:51 PDT)
[AMBER] cpptraj rmsd unit nm. Saman Yousuf ali (Thu Oct 13 2016 - 04:27:47 PDT)
- Re: [AMBER] cpptraj rmsd unit nm. Daniel Roe (Thu Oct 13 2016 - 05:32:53 PDT)
- Re: [AMBER] cpptraj rmsd unit nm. Daniel Roe (Fri Oct 14 2016 - 06:53:40 PDT)
[AMBER] cpptraj nativecontacts George Tzotzos (Thu Oct 13 2016 - 06:57:29 PDT)
- Re: [AMBER] cpptraj nativecontacts Daniel Roe (Thu Oct 13 2016 - 07:17:11 PDT)
[AMBER] How to get average from 3 repeated tracjectory Setyanto Md (Thu Oct 13 2016 - 07:50:09 PDT)
- Re: [AMBER] How to get average from 3 repeated tracjectory Nhai (Thu Oct 13 2016 - 08:00:22 PDT)
  - Re: [AMBER] How to get average from 3 repeated tracjectory Setyanto Md (Thu Oct 13 2016 - 08:08:45 PDT)
    - Re: [AMBER] How to get average from 3 repeated tracjectory Carlos Simmerling (Thu Oct 13 2016 - 08:16:00 PDT)
    - Re: [AMBER] How to get average from 3 repeated tracjectory Setyanto Md (Thu Oct 13 2016 - 16:25:41 PDT)
[AMBER] Parmchk2 - Atom type of CX does not shown up in PARMCHK.DAT Miha Purg (Thu Oct 13 2016 - 08:42:00 PDT)
- Re: [AMBER] Parmchk2 - Atom type of CX does not shown up in PARMCHK.DAT David A Case (Thu Oct 13 2016 - 09:11:12 PDT)
  - Re: [AMBER] Parmchk2 - Atom type of CX does not shown up in PARMCHK.DAT Carlos Simmerling (Thu Oct 13 2016 - 09:27:49 PDT)
[AMBER] QM/MM MD with Amber-Gaussian interface Monsurat Lawal (Thu Oct 13 2016 - 12:41:49 PDT)
- Re: [AMBER] QM/MM MD with Amber-Gaussian interface Dr. Andreas W. Goetz (Thu Oct 13 2016 - 12:55:59 PDT)
[AMBER] Pure POPC Membrane Expands and Crashes Rodriguez, Yoel (Thu Oct 13 2016 - 13:33:07 PDT)
- Re: [AMBER] Pure POPC Membrane Expands and Crashes Dickson, Callum J (Thu Oct 13 2016 - 14:11:13 PDT)
  - Re: [AMBER] Pure POPC Membrane Expands and Crashes Rodriguez, Yoel (Thu Oct 13 2016 - 15:34:43 PDT)
[AMBER] Amber and gaff atom types Aditya G Rao (Thu Oct 13 2016 - 14:12:18 PDT)
- Re: [AMBER] Amber and gaff atom types David A Case (Sun Oct 16 2016 - 05:35:06 PDT)
[AMBER] extract frame from mdcrd file. Saman Yousuf ali (Fri Oct 14 2016 - 02:59:18 PDT)
- Re: [AMBER] extract frame from mdcrd file. Daniel Roe (Fri Oct 14 2016 - 05:00:57 PDT)
[AMBER] ACE and NME terminal add Mijiddorj Batsaikhan (Sat Oct 15 2016 - 09:45:57 PDT)
- Re: [AMBER] ACE and NME terminal add David A Case (Sat Oct 15 2016 - 17:50:04 PDT)
[AMBER] Error in equilibration steps after minimization Prayagraj Fandilolu (Sun Oct 16 2016 - 02:10:01 PDT)
- Re: [AMBER] Error in equilibration steps after minimization Bill Ross (Sun Oct 16 2016 - 03:08:33 PDT)
  - Re: [AMBER] Error in equilibration steps after minimization Prayagraj Fandilolu (Wed Oct 19 2016 - 03:06:47 PDT)
- Re: [AMBER] Error in equilibration steps after minimization Carlos Simmerling (Sun Oct 16 2016 - 05:01:45 PDT)
  - Re: [AMBER] Error in equilibration steps after minimization Prayagraj Fandilolu (Wed Oct 19 2016 - 03:08:33 PDT)
    - Re: [AMBER] Error in equilibration steps after minimization Carlos Simmerling (Wed Oct 19 2016 - 04:58:30 PDT)
    - Re: [AMBER] Error in equilibration steps after minimization David A Case (Wed Oct 19 2016 - 05:03:16 PDT)
[AMBER] LEaP error Paul Meister (Sun Oct 16 2016 - 13:09:29 PDT)
- Re: [AMBER] LEaP error Bill Ross (Sun Oct 16 2016 - 13:42:01 PDT)
  - Re: [AMBER] LEaP error Bill Ross (Sun Oct 16 2016 - 16:09:04 PDT)
[AMBER] Analysis of results Stacyann Nelson (Sun Oct 16 2016 - 20:14:49 PDT)
- Re: [AMBER] Analysis of results Hai Nguyen (Sun Oct 16 2016 - 20:36:12 PDT)
  - Re: [AMBER] Analysis of results Stacyann Nelson (Sun Oct 16 2016 - 20:49:32 PDT)
    - Re: [AMBER] Analysis of results Gulsevin,Alican (Sun Oct 16 2016 - 20:54:29 PDT)
    - Re: [AMBER] Analysis of results Hai Nguyen (Sun Oct 16 2016 - 20:58:25 PDT)
    - Re: [AMBER] Analysis of results Stacyann Nelson (Sun Oct 16 2016 - 21:04:01 PDT)
    - Re: [AMBER] Analysis of results Hai Nguyen (Sun Oct 16 2016 - 21:07:36 PDT)
    - Re: [AMBER] Analysis of results David A Case (Mon Oct 17 2016 - 04:36:45 PDT)
    - Re: [AMBER] Analysis of results Stacyann Nelson (Mon Oct 17 2016 - 05:06:48 PDT)
    - Re: [AMBER] Analysis of results David A Case (Mon Oct 17 2016 - 09:00:55 PDT)
    - Re: [AMBER] Analysis of results Stacyann Nelson (Mon Oct 17 2016 - 09:17:39 PDT)
[AMBER] compile Amber16 with the intel compiler Vlad Cojocaru (Mon Oct 17 2016 - 04:56:43 PDT)
- Re: [AMBER] compile Amber16 with the intel compiler David A Case (Mon Oct 17 2016 - 09:12:59 PDT)
  - Re: [AMBER] compile Amber16 with the intel compiler Vlad Cojocaru (Mon Oct 17 2016 - 09:22:14 PDT)
    - Re: [AMBER] compile Amber16 with the intel compiler David A Case (Mon Oct 17 2016 - 10:56:25 PDT)
    - Re: [AMBER] compile Amber16 with the intel compiler Vlad Cojocaru (Mon Oct 17 2016 - 11:20:39 PDT)
    - Re: [AMBER] compile Amber16 with the intel compiler David A Case (Tue Oct 18 2016 - 05:49:50 PDT)
    - Re: [AMBER] compile Amber16 with the intel compiler Vlad Cojocaru (Tue Oct 18 2016 - 06:01:58 PDT)
    - Re: [AMBER] compile Amber16 with the intel compiler David A Case (Tue Oct 18 2016 - 08:25:59 PDT)
- Re: [AMBER] compile Amber16 with the intel compiler Vlad Cojocaru (Tue Oct 18 2016 - 05:31:23 PDT)
  - Re: [AMBER] compile Amber16 with the intel compiler Vlad Cojocaru (Tue Oct 18 2016 - 07:57:18 PDT)
[AMBER] An issue with conformational changes during MD. Abhilash J (Mon Oct 17 2016 - 06:24:21 PDT)
- Re: [AMBER] An issue with conformational changes during MD. Hai Nguyen (Sun Oct 23 2016 - 10:22:30 PDT)
[AMBER] Small bug in MMPBSA/input_parser.py William Lees (Mon Oct 17 2016 - 07:17:34 PDT)
- Re: [AMBER] Small bug in MMPBSA/input_parser.py Hai Nguyen (Mon Oct 17 2016 - 13:06:16 PDT)
[AMBER] The value of NONBONDED_PARM_INDEX pointer Meiting Wang (Mon Oct 17 2016 - 07:57:17 PDT)
- Re: [AMBER] The value of NONBONDED_PARM_INDEX pointer David A Case (Mon Oct 17 2016 - 09:45:33 PDT)
[AMBER] UnitCell problem:Anisotropy records cannot be placed Zhou, Weijiang (Mon Oct 17 2016 - 08:03:56 PDT)
- Re: [AMBER] UnitCell problem:Anisotropy records cannot be placed David A Case (Mon Oct 17 2016 - 09:37:36 PDT)
[AMBER] native contacts Parviz Seifpanahi Shabane (Mon Oct 17 2016 - 09:25:33 PDT)
- Re: [AMBER] native contacts Daniel Roe (Mon Oct 17 2016 - 10:02:57 PDT)
  - Re: [AMBER] native contacts Parviz Seifpanahi Shabane (Mon Oct 17 2016 - 11:27:09 PDT)
    - Re: [AMBER] native contacts Parviz Seifpanahi Shabane (Mon Oct 17 2016 - 11:37:45 PDT)
    - Re: [AMBER] native contacts Daniel Roe (Mon Oct 17 2016 - 11:55:27 PDT)
    - Re: [AMBER] native contacts Parviz Seifpanahi Shabane (Mon Oct 17 2016 - 12:09:02 PDT)
    - Re: [AMBER] native contacts Daniel Roe (Mon Oct 17 2016 - 12:16:22 PDT)
[AMBER] Autoimage Error Life Sciences Inc (Mon Oct 17 2016 - 09:26:04 PDT)
- Re: [AMBER] Autoimage Error Daniel Roe (Mon Oct 17 2016 - 10:32:14 PDT)
[AMBER] WHAM analysis Thakur, Abhishek (Mon Oct 17 2016 - 14:20:58 PDT)
- Re: [AMBER] WHAM analysis Marc van der Kamp (Mon Oct 17 2016 - 14:34:26 PDT)
- Re: [AMBER] WHAM analysis Hai Nguyen (Mon Oct 17 2016 - 14:45:31 PDT)
  - Re: [AMBER] WHAM analysis Thakur, Abhishek (Mon Oct 17 2016 - 15:22:37 PDT)
    - Re: [AMBER] WHAM analysis Hai Nguyen (Mon Oct 17 2016 - 15:26:03 PDT)
[AMBER] update.4 of Amber16 and update.9 of AmberTools are not available jacky zhao (Mon Oct 17 2016 - 18:03:39 PDT)
- Re: [AMBER] update.4 of Amber16 and update.9 of AmberTools are not available Hai Nguyen (Mon Oct 17 2016 - 18:10:24 PDT)
  - Re: [AMBER] update.4 of Amber16 and update.9 of AmberTools are not available Hai Nguyen (Mon Oct 17 2016 - 18:17:33 PDT)
    - Re: [AMBER] update.4 of Amber16 and update.9 of AmberTools are not available jacky zhao (Mon Oct 17 2016 - 18:49:53 PDT)
[AMBER] update error of Amber16 and Tools jacky zhao (Mon Oct 17 2016 - 18:44:44 PDT)
- Re: [AMBER] update error of Amber16 and Tools Hai Nguyen (Mon Oct 17 2016 - 19:42:14 PDT)
  - Re: [AMBER] update error of Amber16 and Tools jacky zhao (Tue Oct 18 2016 - 03:01:40 PDT)
[AMBER] Scaling of Non-Bonding Potential for Specific Atom Pairs Samuel Walpole (PHA) (Tue Oct 18 2016 - 00:52:27 PDT)
- Re: [AMBER] Scaling of Non-Bonding Potential for Specific Atom Pairs David A Case (Tue Oct 18 2016 - 06:02:06 PDT)
[AMBER] configuration file for amber16 on IBM power Ye Mei (Tue Oct 18 2016 - 01:19:16 PDT)
- Re: [AMBER] configuration file for amber16 on IBM power jacky zhao (Tue Oct 18 2016 - 04:20:40 PDT)
[AMBER] Charmm to amber conversion of lipid Mahrukh Imtiaz (Tue Oct 18 2016 - 02:08:57 PDT)
[AMBER] cpptraj reimaging: frame reading issue. Saman Yousuf ali (Tue Oct 18 2016 - 02:44:58 PDT)
- Re: [AMBER] cpptraj reimaging: frame reading issue. Daniel Roe (Tue Oct 18 2016 - 05:49:31 PDT)
[AMBER] A question about PCA analysis Markowska (Tue Oct 18 2016 - 03:06:27 PDT)
- Re: [AMBER] A question about PCA analysis Hai Nguyen (Mon Oct 24 2016 - 14:48:59 PDT)
- Re: [AMBER] A question about PCA analysis Daniel Roe (Tue Oct 25 2016 - 05:28:16 PDT)
[AMBER] PBSA: sasopt=0 incompatible with eneopt=4, frcopt=5 Vlad Cojocaru (Tue Oct 18 2016 - 03:23:42 PDT)
- Re: [AMBER] PBSA: sasopt=0 incompatible with eneopt=4, frcopt=5 Ray Luo (Tue Oct 18 2016 - 08:39:31 PDT)
  - Re: [AMBER] PBSA: sasopt=0 incompatible with eneopt=4, frcopt=5 Vlad Cojocaru (Tue Oct 18 2016 - 14:23:43 PDT)
    - Re: [AMBER] PBSA: sasopt=0 incompatible with eneopt=4, frcopt=5 Ray Luo (Thu Oct 20 2016 - 09:22:40 PDT)
[AMBER] error of amber16 mpi version using open-mpi jacky zhao (Tue Oct 18 2016 - 03:41:32 PDT)
- Re: [AMBER] error of amber16 mpi version using open-mpi David A Case (Tue Oct 18 2016 - 06:08:14 PDT)
  - Re: [AMBER] error of amber16 mpi version using open-mpi Daniel Roe (Tue Oct 18 2016 - 06:22:06 PDT)
    - Re: [AMBER] error of amber16 mpi version using open-mpi jacky zhao (Tue Oct 18 2016 - 07:01:21 PDT)
    - Re: [AMBER] error of amber16 mpi version using open-mpi jacky zhao (Tue Oct 18 2016 - 07:02:50 PDT)
    - Re: [AMBER] error of amber16 mpi version using open-mpi jacky zhao (Tue Oct 18 2016 - 07:24:08 PDT)
    - Re: [AMBER] error of amber16 mpi version using open-mpi Daniel Roe (Tue Oct 18 2016 - 07:47:04 PDT)
    - Re: [AMBER] error of amber16 mpi version using open-mpi jacky zhao (Tue Oct 18 2016 - 08:27:30 PDT)
    - Re: [AMBER] error of amber16 mpi version using open-mpi jacky zhao (Tue Oct 18 2016 - 09:03:17 PDT)
    - Re: [AMBER] error of amber16 mpi version using open-mpi Ross Walker (Tue Oct 18 2016 - 09:34:53 PDT)
    - Re: [AMBER] error of amber16 mpi version using open-mpi jacky zhao (Tue Oct 18 2016 - 20:35:10 PDT)
[AMBER] Request for help for installing Amber Tools 16 Yogendra Ramtirtha (Tue Oct 18 2016 - 04:48:35 PDT)
- Re: [AMBER] Request for help for installing Amber Tools 16 Vlad Cojocaru (Tue Oct 18 2016 - 05:02:34 PDT)
  - Re: [AMBER] Request for help for installing Amber Tools 16 Yogendra Ramtirtha (Thu Oct 20 2016 - 09:30:38 PDT)
[AMBER] Bugs in CPPTRAJ V16.14 MOHD HOMAIDUR RAHMAN (Tue Oct 18 2016 - 04:56:47 PDT)
- Re: [AMBER] Bugs in CPPTRAJ V16.14 Daniel Roe (Tue Oct 18 2016 - 05:44:31 PDT)
Re: [AMBER] protein drift during NPT equilibrium David A Case (Tue Oct 18 2016 - 05:57:32 PDT)
[AMBER] FEW TI and calulation absolute free energy using soft core Cockroft, Nicholas T. (Tue Oct 18 2016 - 11:20:34 PDT)
- Re: [AMBER] FEW TI and calulation absolute free energy using soft core Hannes Loeffler (Tue Oct 18 2016 - 11:58:13 PDT)
  - Re: [AMBER] FEW TI and calulation absolute free energy using soft core Cockroft, Nicholas T. (Tue Oct 18 2016 - 12:50:37 PDT)
    - Re: [AMBER] FEW TI and calulation absolute free energy using soft core Hannes Loeffler (Tue Oct 18 2016 - 23:22:19 PDT)
[AMBER] how to make peptide Thakur, Abhishek (Tue Oct 18 2016 - 14:51:59 PDT)
- Re: [AMBER] how to make peptide Carlos Simmerling (Tue Oct 18 2016 - 14:54:03 PDT)
  - Re: [AMBER] how to make peptide Thakur, Abhishek (Tue Oct 18 2016 - 15:19:33 PDT)
    - Re: [AMBER] how to make peptide Carlos Simmerling (Tue Oct 18 2016 - 15:21:08 PDT)
    - Re: [AMBER] how to make peptide Thakur, Abhishek (Tue Oct 18 2016 - 15:26:39 PDT)
    - Re: [AMBER] how to make peptide Hai Nguyen (Tue Oct 18 2016 - 15:37:46 PDT)
    - Re: [AMBER] how to make peptide Thakur, Abhishek (Tue Oct 18 2016 - 16:24:18 PDT)
    - Re: [AMBER] how to make peptide Nhai (Tue Oct 18 2016 - 16:28:39 PDT)
    - Re: [AMBER] how to make peptide Carlos Simmerling (Tue Oct 18 2016 - 16:43:47 PDT)
    - Re: [AMBER] how to make peptide Thakur, Abhishek (Tue Oct 18 2016 - 16:55:51 PDT)
    - Re: [AMBER] how to make peptide Carlos Simmerling (Tue Oct 18 2016 - 18:05:40 PDT)
    - Re: [AMBER] how to make peptide Thakur, Abhishek (Wed Oct 19 2016 - 06:09:41 PDT)
    - Re: [AMBER] how to make peptide Carlos Simmerling (Wed Oct 19 2016 - 06:23:42 PDT)
    - Re: [AMBER] how to make peptide Thakur, Abhishek (Wed Oct 19 2016 - 06:54:47 PDT)
[AMBER] heating step: volume, density and pressure plots. Saman Yousuf ali (Wed Oct 19 2016 - 00:54:45 PDT)
- Re: [AMBER] heating step: volume, density and pressure plots. David A Case (Wed Oct 19 2016 - 04:54:17 PDT)
  - Re: [AMBER] heating step: volume, density and pressure plots. Ruth Helena Tichauer (Fri Oct 21 2016 - 02:52:04 PDT)
    - Re: [AMBER] heating step: volume, density and pressure plots. Daniel Roe (Fri Oct 21 2016 - 07:56:26 PDT)
- Re: [AMBER] heating step: volume, density and pressure plots. ruqaiya khalil (Wed Oct 19 2016 - 10:30:19 PDT)
[AMBER] How to make replicas using leap Stacyann Nelson (Wed Oct 19 2016 - 06:38:24 PDT)
[AMBER] Update 16 for AmberTools 16 CPPTRAJ Daniel Roe (Wed Oct 19 2016 - 06:55:42 PDT)
- Re: [AMBER] Update 16 for AmberTools 16 CPPTRAJ jacky zhao (Thu Oct 20 2016 - 04:11:56 PDT)
[AMBER] Help with GIST analysis Sérgio Marques (Wed Oct 19 2016 - 08:31:59 PDT)
- Re: [AMBER] Help with GIST analysis Steven Ramsey (Wed Oct 19 2016 - 13:56:41 PDT)
  - Re: [AMBER] Help with GIST analysis Sérgio Marques (Thu Oct 20 2016 - 02:18:02 PDT)
  - Re: [AMBER] Help with GIST analysis Daniel Roe (Thu Oct 20 2016 - 06:33:10 PDT)
    - Re: [AMBER] Help with GIST analysis Sérgio Marques (Thu Oct 20 2016 - 08:38:47 PDT)
    - Re: [AMBER] Help with GIST analysis Jonathan Gough (Thu Oct 20 2016 - 08:51:35 PDT)
    - Re: [AMBER] Help with GIST analysis Sérgio Marques (Fri Oct 21 2016 - 04:13:16 PDT)
    - Re: [AMBER] Help with GIST analysis Jonathan Gough (Fri Oct 21 2016 - 11:17:19 PDT)
    - Re: [AMBER] Help with GIST analysis Sérgio Marques (Mon Oct 24 2016 - 00:22:30 PDT)
    - Re: [AMBER] Help with GIST analysis Steven Ramsey (Mon Oct 24 2016 - 10:13:26 PDT)
    - Re: [AMBER] Help with GIST analysis Sérgio Marques (Mon Oct 24 2016 - 11:44:03 PDT)
[AMBER] frcmod file error Thakur, Abhishek (Wed Oct 19 2016 - 09:06:22 PDT)
- Re: [AMBER] frcmod file error Bill Ross (Wed Oct 19 2016 - 09:16:42 PDT)
  - Re: [AMBER] frcmod file error Bill Ross (Wed Oct 19 2016 - 09:18:29 PDT)
- Re: [AMBER] frcmod file error Bill Ross (Wed Oct 19 2016 - 09:35:57 PDT)
- Re: [AMBER] frcmod file error David A Case (Wed Oct 19 2016 - 12:27:20 PDT)
  - Re: [AMBER] frcmod file error Thakur, Abhishek (Wed Oct 19 2016 - 14:28:50 PDT)
    - Re: [AMBER] frcmod file error David A Case (Wed Oct 19 2016 - 17:06:36 PDT)
    - Re: [AMBER] frcmod file error Thakur, Abhishek (Thu Oct 20 2016 - 07:37:37 PDT)
    - Re: [AMBER] frcmod file error Carlos Simmerling (Thu Oct 20 2016 - 07:40:39 PDT)
    - Re: [AMBER] frcmod file error Thakur, Abhishek (Thu Oct 20 2016 - 07:46:03 PDT)
    - Re: [AMBER] frcmod file error Carlos Simmerling (Thu Oct 20 2016 - 07:54:36 PDT)
    - Re: [AMBER] frcmod file error Thakur, Abhishek (Thu Oct 20 2016 - 08:04:09 PDT)
    - Re: [AMBER] frcmod file error Carlos Simmerling (Thu Oct 20 2016 - 08:11:05 PDT)
    - Re: [AMBER] frcmod file error Thakur, Abhishek (Thu Oct 20 2016 - 08:17:58 PDT)
    - Re: [AMBER] frcmod file error Carlos Simmerling (Thu Oct 20 2016 - 08:26:51 PDT)
    - Re: [AMBER] frcmod file error Thakur, Abhishek (Thu Oct 20 2016 - 08:35:08 PDT)
    - Re: [AMBER] frcmod file error Carlos Simmerling (Thu Oct 20 2016 - 08:39:43 PDT)
    - Re: [AMBER] frcmod file error Thakur, Abhishek (Thu Oct 20 2016 - 08:59:19 PDT)
    - Re: [AMBER] frcmod file error Carlos Simmerling (Thu Oct 20 2016 - 09:14:53 PDT)
    - Re: [AMBER] frcmod file error Thakur, Abhishek (Thu Oct 20 2016 - 09:29:19 PDT)
    - Re: [AMBER] frcmod file error Carlos Simmerling (Thu Oct 20 2016 - 09:33:09 PDT)
    - Re: [AMBER] frcmod file error Thakur, Abhishek (Thu Oct 20 2016 - 09:40:21 PDT)
    - Re: [AMBER] frcmod file error David A Case (Thu Oct 20 2016 - 09:35:44 PDT)
    - Re: [AMBER] frcmod file error Thakur, Abhishek (Thu Oct 20 2016 - 09:57:17 PDT)
    - Re: [AMBER] frcmod file error Thakur, Abhishek (Thu Oct 20 2016 - 11:28:33 PDT)
    - Re: [AMBER] frcmod file error David A Case (Fri Oct 21 2016 - 05:14:41 PDT)
    - Re: [AMBER] frcmod file error Bill Ross (Fri Oct 21 2016 - 05:43:38 PDT)
    - Re: [AMBER] frcmod file error Thakur, Abhishek (Fri Oct 21 2016 - 07:02:57 PDT)
    - Re: [AMBER] frcmod file error Carlos Simmerling (Fri Oct 21 2016 - 07:23:25 PDT)
    - Re: [AMBER] frcmod file error David A Case (Fri Oct 21 2016 - 11:21:33 PDT)
    - Re: [AMBER] frcmod file error Bill Ross (Fri Oct 21 2016 - 12:09:07 PDT)
    - Re: [AMBER] frcmod file error Thakur, Abhishek (Sat Oct 22 2016 - 11:17:38 PDT)
    - Re: [AMBER] frcmod file error Carlos Simmerling (Fri Oct 21 2016 - 07:19:48 PDT)
    - Re: [AMBER] frcmod file error Thakur, Abhishek (Fri Oct 21 2016 - 07:25:16 PDT)
- Re: [AMBER] frcmod file error Hector A. Baldoni (Fri Oct 21 2016 - 08:42:29 PDT)
[AMBER] Difference between POPI and DOPI membranes? and about lipid headgroups Mijiddorj Batsaikhan (Wed Oct 19 2016 - 09:25:21 PDT)
[AMBER] help in solvent box Robin Jain (Wed Oct 19 2016 - 23:37:21 PDT)
[AMBER] cpptraj: format of diagmatrix output Marc van der Kamp (Thu Oct 20 2016 - 04:20:04 PDT)
- Re: [AMBER] cpptraj: format of diagmatrix output Daniel Roe (Thu Oct 20 2016 - 05:06:56 PDT)
  - Re: [AMBER] cpptraj: format of diagmatrix output Marc van der Kamp (Thu Oct 20 2016 - 09:19:31 PDT)
[AMBER] Adding a Dummy Atom to Benzene Samuel Walpole (PHA) (Thu Oct 20 2016 - 07:59:17 PDT)
- Re: [AMBER] Adding a Dummy Atom to Benzene Carlos Simmerling (Thu Oct 20 2016 - 08:03:13 PDT)
  - Re: [AMBER] Adding a Dummy Atom to Benzene Samuel Walpole (PHA) (Thu Oct 20 2016 - 10:02:57 PDT)
    - Re: [AMBER] Adding a Dummy Atom to Benzene Carlos Simmerling (Fri Oct 21 2016 - 05:13:38 PDT)
    - Re: [AMBER] Adding a Dummy Atom to Benzene David A Case (Fri Oct 21 2016 - 05:19:06 PDT)
    - Re: [AMBER] Adding a Dummy Atom to Benzene Samuel Walpole (PHA) (Fri Oct 21 2016 - 05:36:16 PDT)
[AMBER] ambmask and periodic boundaries Aseel Bala (Thu Oct 20 2016 - 11:41:12 PDT)
- Re: [AMBER] ambmask and periodic boundaries Daniel Roe (Thu Oct 20 2016 - 11:45:20 PDT)
  - Re: [AMBER] ambmask and periodic boundaries Aseel Bala (Thu Oct 20 2016 - 12:53:02 PDT)
[AMBER] uneven bond formed after cyclization of peptide Thakur, Abhishek (Thu Oct 20 2016 - 16:32:57 PDT)
- Re: [AMBER] uneven bond formed after cyclization of peptide Andy Watkins (Thu Oct 20 2016 - 17:38:00 PDT)
  - Re: [AMBER] uneven bond formed after cyclization of peptide Xu Dong (Mon Oct 24 2016 - 06:51:56 PDT)
[AMBER] cpptraj Saman Yousuf ali (Thu Oct 20 2016 - 21:12:47 PDT)
[AMBER] Methyl groups Imma Speciale (Fri Oct 21 2016 - 07:26:42 PDT)
- Re: [AMBER] Methyl groups Elvis Martis (Fri Oct 21 2016 - 07:42:12 PDT)
  - Re: [AMBER] Methyl groups Imma Speciale (Fri Oct 21 2016 - 07:57:04 PDT)
- Re: [AMBER] Methyl groups Elvis Martis (Fri Oct 21 2016 - 08:07:20 PDT)
[AMBER] problem with STRIP command. Parviz Seifpanahi Shabane (Fri Oct 21 2016 - 08:23:58 PDT)
- Re: [AMBER] problem with STRIP command. Daniel Roe (Fri Oct 21 2016 - 09:06:41 PDT)
[AMBER] Regarding Hydroxyproline parameter Saikat Dutta chowdhury (Fri Oct 21 2016 - 21:42:23 PDT)
- Re: [AMBER] Regarding Hydroxyproline parameter David A Case (Sat Oct 22 2016 - 17:14:27 PDT)
  - Re: [AMBER] Regarding Hydroxyproline parameter Saikat Dutta chowdhury (Sat Oct 22 2016 - 19:47:36 PDT)
    - Re: [AMBER] Regarding Hydroxyproline parameter Hai Nguyen (Sat Oct 22 2016 - 21:30:44 PDT)
[AMBER] The error of 'RESTARTED DUE to LINMIN FAILURE' and the 'cudaFree GpuBuffer::Deallocate failed unspecified launch failure' windy (Fri Oct 21 2016 - 23:09:26 PDT)
- Re: [AMBER] The error of 'RESTARTED DUE to LINMIN FAILURE' and the 'cudaFree GpuBuffer::Deallocate failed unspecified launch failure' Bill Ross (Fri Oct 21 2016 - 23:26:07 PDT)
  - Re: [AMBER] The error of 'RESTARTED DUE to LINMIN FAILURE' and the 'cudaFree GpuBuffer::Deallocate failed unspecified launch failure' windy (Sat Oct 22 2016 - 00:21:15 PDT)
    - Re: [AMBER] The error of 'RESTARTED DUE to LINMIN FAILURE' and the 'cudaFree GpuBuffer::Deallocate failed unspecified launch failure' Bill Ross (Sat Oct 22 2016 - 00:42:08 PDT)
    - Re: [AMBER] The error of 'RESTARTED DUE to LINMIN FAILURE' and the 'cudaFree GpuBuffer::Deallocate failed unspecified launch failure' windy (Sat Oct 22 2016 - 02:03:01 PDT)
    - Re: [AMBER] The error of 'RESTARTED DUE to LINMIN FAILURE' and the 'cudaFree GpuBuffer::Deallocate failed unspecified launch failure' Bill Ross (Sat Oct 22 2016 - 16:14:38 PDT)
    - Re: [AMBER] The error of 'RESTARTED DUE to LINMIN FAILURE' and the 'cudaFree GpuBuffer::Deallocate failed unspecified launch failure' windy (Sun Oct 23 2016 - 02:03:14 PDT)
    - Re: [AMBER] The error of 'RESTARTED DUE to LINMIN FAILURE' and the 'cudaFree GpuBuffer::Deallocate failed unspecified launch failure' Bill Ross (Sun Oct 23 2016 - 10:06:18 PDT)
- Re: [AMBER] The error of 'RESTARTED DUE to LINMIN FAILURE' and the 'cudaFree GpuBuffer::Deallocate failed unspecified launch failure' David A Case (Sun Oct 23 2016 - 18:12:23 PDT)
  - Re: [AMBER] The error of 'RESTARTED DUE to LINMIN FAILURE' and the 'cudaFree GpuBuffer::Deallocate failed unspecified launch failure' XP Chen (Mon Oct 24 2016 - 23:28:22 PDT)
[AMBER] cpptraj: ligand and active site rmsd Saman Yousuf ali (Sat Oct 22 2016 - 01:42:01 PDT)
- Re: [AMBER] cpptraj: ligand and active site rmsd Hai Nguyen (Sun Oct 23 2016 - 10:17:08 PDT)
[AMBER] VMD hydrogen bonds calculation Pooja Kesari (Sat Oct 22 2016 - 23:21:45 PDT)
- Re: [AMBER] VMD hydrogen bonds calculation Bill Ross (Sat Oct 22 2016 - 23:27:20 PDT)
  - Re: [AMBER] VMD hydrogen bonds calculation Pooja Kesari (Sun Oct 23 2016 - 21:06:29 PDT)
[AMBER] cpptraj readdata bad_alloc Niel Henriksen (Sun Oct 23 2016 - 12:01:42 PDT)
- Re: [AMBER] cpptraj readdata bad_alloc Daniel Roe (Mon Oct 24 2016 - 08:10:08 PDT)
  - Re: [AMBER] cpptraj readdata bad_alloc Daniel Roe (Mon Oct 24 2016 - 08:22:50 PDT)
    - Re: [AMBER] cpptraj readdata bad_alloc Daniel Roe (Mon Oct 24 2016 - 09:45:12 PDT)
    - Re: [AMBER] cpptraj readdata bad_alloc Niel Henriksen (Mon Oct 24 2016 - 10:02:47 PDT)
[AMBER] problem equilibrating the structure giulia palermo (Sun Oct 23 2016 - 13:43:25 PDT)
- Re: [AMBER] problem equilibrating the structure Carlos Simmerling (Sun Oct 23 2016 - 15:30:22 PDT)
- Re: [AMBER] problem equilibrating the structure David A Case (Sun Oct 23 2016 - 18:17:22 PDT)
  - Re: [AMBER] problem equilibrating the structure giulia palermo (Tue Oct 25 2016 - 08:21:39 PDT)
[AMBER] centering a molecule in a frame with command line cpptraj Aseel Bala Ahmed (Sun Oct 23 2016 - 15:25:15 PDT)
- Re: [AMBER] centering a molecule in a frame with command line cpptraj Nhai (Sun Oct 23 2016 - 15:33:15 PDT)
  - Re: [AMBER] centering a molecule in a frame with command line cpptraj Aseel Bala Ahmed (Sun Oct 23 2016 - 18:27:14 PDT)
[AMBER] time of MD Stefania Mirabella (Mon Oct 24 2016 - 01:33:42 PDT)
- Re: [AMBER] time of MD Jacopo Sgrignani (Mon Oct 24 2016 - 01:47:21 PDT)
- Re: [AMBER] time of MD David A Case (Mon Oct 24 2016 - 04:58:53 PDT)
  - Re: [AMBER] time of MD Stefania Mirabella (Mon Oct 24 2016 - 05:58:26 PDT)
[AMBER] Setting MM-PBSA script Jag Silwal (Mon Oct 24 2016 - 11:03:57 PDT)
- Re: [AMBER] Setting MM-PBSA script Hai Nguyen (Mon Oct 24 2016 - 11:15:46 PDT)
  - Re: [AMBER] Setting MM-PBSA script Jag Silwal (Mon Oct 24 2016 - 16:14:40 PDT)
- Re: [AMBER] Setting MM-PBSA script William Lees (Tue Oct 25 2016 - 03:12:14 PDT)
  - Re: [AMBER] Setting MM-PBSA script Jag Silwal (Tue Oct 25 2016 - 06:56:16 PDT)
    - Re: [AMBER] Setting MM-PBSA script William Lees (Wed Oct 26 2016 - 07:14:01 PDT)
[AMBER] aMD used for simulated small peptide with non-standard residues Gabriel Jara (Mon Oct 24 2016 - 11:38:42 PDT)
- Re: [AMBER] aMD used for simulated small peptide with non-standard residues David A Case (Tue Oct 25 2016 - 05:21:22 PDT)
- Re: [AMBER] aMD used for simulated small peptide with non-standard residues Gabriel Jara (Fri Oct 28 2016 - 10:16:31 PDT)
[AMBER] Gaussian through sander-cutoffs Aseel Bala (Mon Oct 24 2016 - 12:11:44 PDT)
[AMBER] cpptraj: rms around 5 angstrom of ligand issue. Saman Yousuf ali (Mon Oct 24 2016 - 22:01:07 PDT)
- Re: [AMBER] cpptraj: rms around 5 angstrom of ligand issue. Nhai (Mon Oct 24 2016 - 22:07:41 PDT)
- Re: [AMBER] cpptraj: rms around 5 angstrom of ligand issue. Saman Yousuf ali (Mon Oct 24 2016 - 22:23:37 PDT)
  - Re: [AMBER] cpptraj: rms around 5 angstrom of ligand issue. Daniel Roe (Tue Oct 25 2016 - 05:14:31 PDT)
[AMBER] Deprotonated serine residue. Dd H (Tue Oct 25 2016 - 01:06:55 PDT)
- Re: [AMBER] Deprotonated serine residue. David A Case (Tue Oct 25 2016 - 05:17:42 PDT)
- Re: [AMBER] Deprotonated serine residue. FyD (Wed Oct 26 2016 - 01:27:42 PDT)
  - Re: [AMBER] Deprotonated serine residue. Dd H (Thu Oct 27 2016 - 05:06:40 PDT)
[AMBER] replicating a box in all direction Aseel Bala (Tue Oct 25 2016 - 11:47:48 PDT)
[AMBER] Zinc ion visualization from Amber trajectory Aditya Padhi (Tue Oct 25 2016 - 17:45:38 PDT)
- Re: [AMBER] Zinc ion visualization from Amber trajectory Eiros Zamora, Juan (Wed Oct 26 2016 - 04:37:34 PDT)
  - Re: [AMBER] Zinc ion visualization from Amber trajectory Aditya Padhi (Wed Oct 26 2016 - 19:11:31 PDT)
[AMBER] Van der waals and electrostatic energy calculations using cpptraj? Aishani Prem (Wed Oct 26 2016 - 11:27:41 PDT)
- Re: [AMBER] Van der waals and electrostatic energy calculations using cpptraj? Daniel Roe (Wed Oct 26 2016 - 11:33:32 PDT)
- Re: [AMBER] Van der waals and electrostatic energy calculations using cpptraj? Hai Nguyen (Wed Oct 26 2016 - 17:13:50 PDT)
  - Re: [AMBER] Van der waals and electrostatic energy calculations using cpptraj? Aishani Prem (Wed Oct 26 2016 - 17:31:09 PDT)
[AMBER] Issue with parametrization of lipid using lipid14 forcefield Mahrukh Imtiaz (Wed Oct 26 2016 - 23:33:05 PDT)
- Re: [AMBER] Issue with parametrization of lipid using lipid14 forcefield Bill Ross (Thu Oct 27 2016 - 01:55:32 PDT)
[AMBER] Explicit solvent CpHMD - Are protonation state evaluations done on the GPU in Amber 16? Eric Lang (Thu Oct 27 2016 - 01:13:17 PDT)
- Re: [AMBER] Explicit solvent CpHMD - Are protonation state evaluations done on the GPU in Amber 16? Adrian Roitberg (Thu Oct 27 2016 - 07:36:13 PDT)
- Re: [AMBER] Explicit solvent CpHMD - Are protonation state evaluations done on the GPU in Amber 16? Jason Swails (Thu Oct 27 2016 - 12:58:59 PDT)
[AMBER] cannot find Chamber in Amber16 Abhishek TYAGI (Thu Oct 27 2016 - 04:25:41 PDT)
- Re: [AMBER] cannot find Chamber in Amber16 Daniel Roe (Thu Oct 27 2016 - 04:56:38 PDT)
- Re: [AMBER] cannot find Chamber in Amber16 David A Case (Thu Oct 27 2016 - 05:18:52 PDT)
[AMBER] editing checkpoint name Aseel Bala (Thu Oct 27 2016 - 09:11:50 PDT)
[AMBER] Can we combine amber and gaff atom types? Aditya G Rao (Thu Oct 27 2016 - 09:20:48 PDT)
- Re: [AMBER] Can we combine amber and gaff atom types? Carlos Simmerling (Thu Oct 27 2016 - 09:38:30 PDT)
  - Re: [AMBER] Can we combine amber and gaff atom types? Aditya G Rao (Thu Oct 27 2016 - 10:31:52 PDT)
    - Re: [AMBER] Can we combine amber and gaff atom types? David Cerutti (Thu Oct 27 2016 - 11:45:15 PDT)
    - Re: [AMBER] Can we combine amber and gaff atom types? Aditya G Rao (Wed Nov 02 2016 - 06:55:12 PDT)
    - Re: [AMBER] Can we combine amber and gaff atom types? Carlos Simmerling (Wed Nov 02 2016 - 07:16:29 PDT)
    - Re: [AMBER] Can we combine amber and gaff atom types? David Cerutti (Wed Nov 02 2016 - 13:44:42 PDT)
    - Re: [AMBER] Can we combine amber and gaff atom types? Aditya G Rao (Thu Nov 03 2016 - 09:39:58 PDT)
    - Re: [AMBER] Can we combine amber and gaff atom types? David Cerutti (Thu Nov 03 2016 - 10:13:21 PDT)
[AMBER] number of bins used in wham analysis Thakur, Abhishek (Thu Oct 27 2016 - 13:11:54 PDT)
[AMBER] Separate forcefield for oligosaccharide residues? Nikolay N. Kuzmich (Fri Oct 28 2016 - 03:21:05 PDT)
- Re: [AMBER] Separate forcefield for oligosaccharide residues? David A Case (Fri Oct 28 2016 - 06:44:30 PDT)
- Re: [AMBER] Separate forcefield for oligosaccharide residues? FyD (Sat Oct 29 2016 - 03:27:47 PDT)
  - Re: [AMBER] Separate forcefield for oligosaccharide residues? Lachele Foley (Sat Oct 29 2016 - 13:14:02 PDT)
    - Re: [AMBER] Separate forcefield for oligosaccharide residues? FyD (Mon Oct 31 2016 - 09:22:48 PDT)
[AMBER] pH calculation of site in md simulation Shilpa Gupta (Fri Oct 28 2016 - 03:51:41 PDT)
- Re: [AMBER] pH calculation of site in md simulation Bill Ross (Fri Oct 28 2016 - 04:27:31 PDT)
[AMBER] dysprosium vdw parameters Florent Barbault (Fri Oct 28 2016 - 05:12:13 PDT)
- Re: [AMBER] dysprosium vdw parameters Pengfei Li (Fri Oct 28 2016 - 11:18:02 PDT)
  - Re: [AMBER] dysprosium vdw parameters Barbault Florent (Sat Oct 29 2016 - 09:43:41 PDT)
[AMBER] MCPB.py Mahmood Jasim (Fri Oct 28 2016 - 11:21:36 PDT)
- Re: [AMBER] MCPB.py Pengfei Li (Fri Oct 28 2016 - 13:25:40 PDT)
  - Re: [AMBER] MCPB.py Pengfei Li (Sat Oct 29 2016 - 20:33:03 PDT)
    - Re: [AMBER] MCPB.py Mahmood Jasim (Mon Oct 31 2016 - 09:21:46 PDT)
    - Re: [AMBER] MCPB.py Pengfei Li (Mon Oct 31 2016 - 17:46:43 PDT)
    - Re: [AMBER] MCPB.py Mahmood Jasim (Thu Nov 03 2016 - 03:02:59 PDT)
    - Re: [AMBER] MCPB.py Pengfei Li (Tue Nov 08 2016 - 10:53:11 PST)
[AMBER] 126_parmed.in in tutorial A20. Jun Doo (Sun Oct 30 2016 - 03:26:22 PDT)
- Re: [AMBER] 126_parmed.in in tutorial A20. Pengfei Li (Mon Oct 31 2016 - 18:10:44 PDT)
[AMBER] REMD hang without error 宁璐璐 (Sun Oct 30 2016 - 19:37:06 PDT)
[AMBER] amber 杨满意 (Sun Oct 30 2016 - 20:23:05 PDT)
[AMBER] semiempirical MD simulation for systems contain metal atoms 杨满意 (Sun Oct 30 2016 - 20:45:52 PDT)
- Re: [AMBER] semiempirical MD simulation for systems contain metal atoms Elvis Martis (Sun Oct 30 2016 - 20:59:40 PDT)
  - Re: [AMBER] semiempirical MD simulation for systems contain metal atoms 杨满意 (Mon Oct 31 2016 - 00:41:37 PDT)
[AMBER] Regarding multipl cutoffs Sudhanshu Shanker (Sun Oct 30 2016 - 22:13:32 PDT)
- Re: [AMBER] Regarding multipl cutoffs Jason Swails (Mon Oct 31 2016 - 03:53:18 PDT)
[AMBER] deal with organometaliic with MCPB.py 杨满意 (Mon Oct 31 2016 - 03:24:44 PDT)
[AMBER] Change in dihedral angle Sudip Das (Mon Oct 31 2016 - 04:07:57 PDT)
- Re: [AMBER] Change in dihedral angle Carlos Simmerling (Mon Oct 31 2016 - 04:53:30 PDT)
  - Re: [AMBER] Change in dihedral angle Sudip Das (Mon Oct 31 2016 - 05:20:13 PDT)
[AMBER] [mdout_analyzer.py] Problem with OS X El Capitan Eiros Zamora, Juan (Mon Oct 31 2016 - 05:09:27 PDT)
- Re: [AMBER] [mdout_analyzer.py] Problem with OS X El Capitan Jason Swails (Mon Oct 31 2016 - 11:48:49 PDT)
  - Re: [AMBER] [mdout_analyzer.py] Problem with OS X El Capitan Eiros Zamora, Juan (Tue Nov 01 2016 - 05:59:46 PDT)
    - Re: [AMBER] [mdout_analyzer.py] Problem with OS X El Capitan Eiros Zamora, Juan (Tue Nov 01 2016 - 06:11:45 PDT)
    - Re: [AMBER] [mdout_analyzer.py] Problem with OS X El Capitan Jason Swails (Tue Nov 01 2016 - 06:13:49 PDT)
[AMBER] Problem reading coordinates or velocities from *.rst, GB solvation model Nikolay N. Kuzmich (Mon Oct 31 2016 - 11:34:35 PDT)
- Re: [AMBER] Problem reading coordinates or velocities from *.rst, GB solvation model Carlos Simmerling (Mon Oct 31 2016 - 11:43:15 PDT)
[AMBER] mmpbsa error 东不拉 (Tue Nov 01 2016 - 01:31:34 PDT)
- Re: [AMBER] mmpbsa error Ray Luo (Tue Nov 01 2016 - 10:35:45 PDT)
[AMBER] MCPB problems Fabrício Bracht (Tue Nov 01 2016 - 07:58:42 PDT)
- Re: [AMBER] MCPB problems Pengfei Li (Tue Nov 01 2016 - 09:16:21 PDT)
  - Re: [AMBER] MCPB problems Fabrício Bracht (Tue Nov 01 2016 - 09:28:47 PDT)
    - Re: [AMBER] MCPB problems Fabrício Bracht (Tue Nov 01 2016 - 09:49:35 PDT)
    - Re: [AMBER] MCPB problems Pengfei Li (Wed Nov 02 2016 - 19:13:42 PDT)
[AMBER] problem with MMPBSApy in Amber 16 Marek Maly (Tue Nov 01 2016 - 08:54:04 PDT)
- Re: [AMBER] problem with MMPBSApy in Amber 16 Ray Luo (Tue Nov 01 2016 - 09:14:50 PDT)
  - Re: [AMBER] problem with MMPBSApy in Amber 16 Marek Maly (Tue Nov 01 2016 - 10:36:24 PDT)
    - Re: [AMBER] problem with MMPBSApy in Amber 16 Ray Luo (Tue Nov 01 2016 - 10:49:36 PDT)
    - Re: [AMBER] problem with MMPBSApy in Amber 16 Marek Maly (Tue Nov 01 2016 - 12:14:55 PDT)
    - Re: [AMBER] problem with MMPBSApy in Amber 16 Ray Luo (Tue Nov 01 2016 - 13:29:22 PDT)
    - Re: [AMBER] problem with MMPBSApy in Amber 16 Ray Luo (Tue Nov 01 2016 - 14:34:01 PDT)
    - Re: [AMBER] problem with MMPBSApy in Amber 16 Marek Maly (Tue Nov 01 2016 - 15:20:40 PDT)
[AMBER] The ultimate temperature is 11K instead of 100K in heating simulation Nikolay N. Kuzmich (Tue Nov 01 2016 - 10:34:22 PDT)
- Re: [AMBER] The ultimate temperature is 11K instead of 100K in heating simulation Ross Walker (Tue Nov 01 2016 - 10:38:51 PDT)
[AMBER] Gromber failed. Dd H (Wed Nov 02 2016 - 01:43:51 PDT)
- Re: [AMBER] Gromber failed. Jason Swails (Wed Nov 02 2016 - 05:14:09 PDT)
  - Re: [AMBER] Gromber failed. Dd H (Wed Nov 02 2016 - 17:56:48 PDT)
    - Re: [AMBER] Gromber failed. Hai Nguyen (Wed Nov 02 2016 - 18:00:20 PDT)
    - Re: [AMBER] Gromber failed. Dd H (Wed Nov 02 2016 - 18:13:16 PDT)
    - Re: [AMBER] Gromber failed. Nhai (Wed Nov 02 2016 - 18:58:03 PDT)
    - Re: [AMBER] Gromber failed. Dd H (Wed Nov 02 2016 - 19:05:40 PDT)
    - Re: [AMBER] Gromber failed. Jason Swails (Thu Nov 03 2016 - 03:18:04 PDT)
    - Re: [AMBER] Gromber failed. Dd H (Thu Nov 03 2016 - 05:31:14 PDT)
[AMBER] Simulation of protein in lipid blayer using GB solvation model Nikolay N. Kuzmich (Wed Nov 02 2016 - 03:49:34 PDT)
- Re: [AMBER] Simulation of protein in lipid blayer using GB solvation model Carlos Simmerling (Wed Nov 02 2016 - 04:34:49 PDT)
[AMBER] Problem installing Amber 16 on mac OS El Capitan Ruth Helena Tichauer (Wed Nov 02 2016 - 06:32:15 PDT)
- Re: [AMBER] Problem installing Amber 16 on mac OS El Capitan Hai Nguyen (Wed Nov 02 2016 - 07:14:09 PDT)
  - Re: [AMBER] Problem installing Amber 16 on mac OS El Capitan Ruth Helena Tichauer (Wed Nov 02 2016 - 08:13:25 PDT)
[AMBER] MMGBSA: estimating "effective energy" convergence George Tzotzos (Wed Nov 02 2016 - 06:38:36 PDT)
- Re: [AMBER] MMGBSA: estimating "effective energy" convergence Casalini Tommaso (Wed Nov 02 2016 - 06:44:17 PDT)
  - Re: [AMBER] MMGBSA: estimating "effective energy" convergence George Tzotzos (Wed Nov 02 2016 - 07:30:42 PDT)
[AMBER] micro iterations in QM/MM optimization. Yigal Lahav (Wed Nov 02 2016 - 07:28:57 PDT)
- Re: [AMBER] micro iterations in QM/MM optimization. Dr. Andreas W. Goetz (Wed Nov 02 2016 - 09:28:47 PDT)
[AMBER] Problem with bonds in NAB Vladislav Sláma (Wed Nov 02 2016 - 08:39:12 PDT)
- Re: [AMBER] Problem with bonds in NAB David A Case (Thu Nov 03 2016 - 04:44:35 PDT)
- Re: [AMBER] Problem with bonds in NAB Vladislav Sláma (Tue Nov 08 2016 - 09:24:20 PST)
  - Re: [AMBER] Problem with bonds in NAB David A Case (Tue Nov 08 2016 - 12:24:35 PST)
- Re: [AMBER] Problem with bonds in NAB Vladislav Sláma (Thu Nov 24 2016 - 06:58:16 PST)
  - Re: [AMBER] Problem with bonds in NAB David A Case (Thu Nov 24 2016 - 10:58:09 PST)
[AMBER] Generating parameters of HEME Ramin Ekhteiari (Wed Nov 02 2016 - 10:32:11 PDT)
- Re: [AMBER] Generating parameters of HEME Hai Nguyen (Wed Nov 02 2016 - 10:48:15 PDT)
- Re: [AMBER] Generating parameters of HEME David A Case (Wed Nov 02 2016 - 12:35:55 PDT)
- Re: [AMBER] Generating parameters of HEME Elvis Martis (Wed Nov 02 2016 - 16:59:52 PDT)
[AMBER] How to visualize modes obtained from NMA The Cromicus Productions (Wed Nov 02 2016 - 11:23:30 PDT)
[AMBER] Software announcement: Release of PUPIL 3.1 Joan Torras (Wed Nov 02 2016 - 13:33:54 PDT)
[AMBER] Error in the production of heat.rst file Stacyann Nelson (Wed Nov 02 2016 - 17:32:33 PDT)
- Re: [AMBER] Error in the production of heat.rst file Elvis Martis (Wed Nov 02 2016 - 20:08:18 PDT)
  - Re: [AMBER] Error in the production of heat.rst file Stacyann Nelson (Wed Nov 02 2016 - 20:44:47 PDT)
    - Re: [AMBER] Error in the production of heat.rst file Elvis Martis (Wed Nov 02 2016 - 21:05:26 PDT)
- Re: [AMBER] Error in the production of heat.rst file David A Case (Thu Nov 03 2016 - 04:48:33 PDT)
  - Re: [AMBER] Error in the production of heat.rst file Stacyann Nelson (Thu Nov 03 2016 - 17:20:51 PDT)
    - Re: [AMBER] Error in the production of heat.rst file Hai Nguyen (Thu Nov 03 2016 - 17:55:16 PDT)
[AMBER] RESP routine not found Marcelo Depólo (Thu Nov 03 2016 - 05:09:32 PDT)
- Re: [AMBER] RESP routine not found Hai Nguyen (Thu Nov 03 2016 - 09:52:52 PDT)
[AMBER] cudaMemcpy GpuBuffer::Download failed an illegal memory access was encountered Andreas Tosstorff (Thu Nov 03 2016 - 05:15:47 PDT)
- [AMBER] Potential energy fluctuation of NVT ensemble Zhe Li (Thu Nov 03 2016 - 18:45:22 PDT)
- Re: [AMBER] cudaMemcpy GpuBuffer::Download failed an illegal memory access was encountered David A Case (Fri Nov 04 2016 - 04:58:41 PDT)
[AMBER] cpptraj error: 'cluster': Command not found. Ruth Helena Tichauer (Thu Nov 03 2016 - 08:59:45 PDT)
- Re: [AMBER] cpptraj error: 'cluster': Command not found. Daniel Roe (Thu Nov 03 2016 - 18:41:21 PDT)
  - Re: [AMBER] cpptraj error: 'cluster': Command not found. Ruth Helena Tichauer (Fri Nov 04 2016 - 01:51:17 PDT)
[AMBER] MD simulations, DDR4 2133MHz vs 3200MHz Nikolay N. Kuzmich (Thu Nov 03 2016 - 10:53:17 PDT)
- Re: [AMBER] MD simulations, DDR4 2133MHz vs 3200MHz David Cerutti (Thu Nov 03 2016 - 11:23:01 PDT)
[AMBER] Failed to install mpirun Nikolay N. Kuzmich (Thu Nov 03 2016 - 10:58:30 PDT)
- Re: [AMBER] Failed to install mpirun Adrian Roitberg (Thu Nov 03 2016 - 11:00:19 PDT)
  - Re: [AMBER] Failed to install mpirun Charles Lin (Thu Nov 03 2016 - 11:35:02 PDT)
    - Re: [AMBER] Failed to install mpirun Charles Lin (Thu Nov 03 2016 - 11:39:02 PDT)
    - [AMBER] Are Intel compilers free for academics? David A Case (Fri Nov 04 2016 - 05:08:32 PDT)
[AMBER] Quenstions about pmemd.cuda.MPI Pengfei Li (Thu Nov 03 2016 - 20:20:41 PDT)
- Re: [AMBER] Quenstions about pmemd.cuda.MPI Ross Walker (Thu Nov 03 2016 - 20:48:16 PDT)
- Re: [AMBER] Quenstions about pmemd.cuda.MPI Pengfei Li (Sun Nov 06 2016 - 22:27:21 PST)
  - Re: [AMBER] Quenstions about pmemd.cuda.MPI Ross Walker (Mon Nov 07 2016 - 06:29:29 PST)
- Re: [AMBER] Quenstions about pmemd.cuda.MPI Pengfei Li (Thu Nov 10 2016 - 17:48:11 PST)
  - Re: [AMBER] Quenstions about pmemd.cuda.MPI Ross Walker (Thu Nov 10 2016 - 18:33:32 PST)
[AMBER] do_debugf changes energy Ulf Ryde (Thu Nov 03 2016 - 23:25:11 PDT)
- Re: [AMBER] do_debugf changes energy David Cerutti (Thu Nov 03 2016 - 23:43:37 PDT)
  - Re: [AMBER] do_debugf changes energy Ulf Ryde (Fri Nov 04 2016 - 00:25:27 PDT)
[AMBER] Fw:problems for running step 2 of MCPB.py 杨满意 (Fri Nov 04 2016 - 00:00:56 PDT)
[AMBER] ntt = 6 and ibelly = 1 Xiangyu Jia (Fri Nov 04 2016 - 01:50:03 PDT)
[AMBER] virtual box in gas phase simulation Xiangyu Jia (Fri Nov 04 2016 - 02:07:25 PDT)
[AMBER] Umbrella simulation with an arbitrary bias potential diego.soler.uam.es (Fri Nov 04 2016 - 03:02:04 PDT)
- Re: [AMBER] Umbrella simulation with an arbitrary bias potential David A Case (Mon Nov 07 2016 - 05:48:07 PST)
  - Re: [AMBER] Umbrella simulation with an arbitrary bias potential Vlad Cojocaru (Mon Nov 07 2016 - 06:01:43 PST)
- Re: [AMBER] Umbrella simulation with an arbitrary bias potential Feng Pan (Mon Nov 07 2016 - 11:44:10 PST)
  - Re: [AMBER] Umbrella simulation with an arbitrary bias potential diego.soler.uam.es (Tue Nov 15 2016 - 02:53:15 PST)
[AMBER] Uridine diphosphate (UDP) - tleap Anna Cebrian Prats (Fri Nov 04 2016 - 04:58:51 PDT)
- Re: [AMBER] Uridine diphosphate (UDP) - tleap David A Case (Fri Nov 04 2016 - 10:07:21 PDT)
- Re: [AMBER] Uridine diphosphate (UDP) - tleap FyD (Wed Nov 09 2016 - 02:58:18 PST)
[AMBER] RNA backbone dihedral restraints question Kasprzak, Wojciech (NIH/NCI) [C] (Fri Nov 04 2016 - 07:05:25 PDT)
- Re: [AMBER] RNA backbone dihedral restraints question Carlos Simmerling (Fri Nov 04 2016 - 07:10:31 PDT)
  - Re: [AMBER] RNA backbone dihedral restraints question Kasprzak, Wojciech (NIH/NCI) [C] (Fri Nov 04 2016 - 07:41:00 PDT)
    - Re: [AMBER] RNA backbone dihedral restraints question Carlos Simmerling (Tue Nov 08 2016 - 03:39:27 PST)
[AMBER] Can ff14SB be used instead of ff10 for CpHMD simulations? Eric Lang (Fri Nov 04 2016 - 08:08:55 PDT)
- Re: [AMBER] Can ff14SB be used instead of ff10 for CpHMD simulations? Carlos Simmerling (Fri Nov 04 2016 - 08:22:16 PDT)
- Re: [AMBER] Can ff14SB be used instead of ff10 for CpHMD simulations? Jason Swails (Fri Nov 04 2016 - 12:52:26 PDT)
  - Re: [AMBER] Can ff14SB be used instead of ff10 for CpHMD simulations? Eric Lang (Mon Nov 07 2016 - 03:29:57 PST)
    - Re: [AMBER] Can ff14SB be used instead of ff10 for CpHMD simulations? Adrian Roitberg (Mon Nov 07 2016 - 06:02:17 PST)
    - Re: [AMBER] Can ff14SB be used instead of ff10 for CpHMD simulations? Carlos Simmerling (Mon Nov 07 2016 - 06:10:11 PST)
[AMBER] can not find chamber in amber16? Neale, Christopher Andrew (Fri Nov 04 2016 - 09:25:51 PDT)
- Re: [AMBER] can not find chamber in amber16? Nhai (Fri Nov 04 2016 - 09:34:04 PDT)
[AMBER] Potential energy fluctuation of NVT ensemble Zhe Li (Fri Nov 04 2016 - 15:15:49 PDT)
- Re: [AMBER] Potential energy fluctuation of NVT ensemble Niel Henriksen (Fri Nov 04 2016 - 17:25:22 PDT)
- Re: [AMBER] Potential energy fluctuation of NVT ensemble diego.soler.uam.es (Sat Nov 05 2016 - 01:29:38 PDT)
  - Re: [AMBER] Potential energy fluctuation of NVT ensemble Zhe Li (Sat Nov 05 2016 - 10:30:47 PDT)
[AMBER] Hello! Distance restraint problems in SANDER tanfei777.sina.cn (Sat Nov 05 2016 - 01:11:18 PDT)
- Re: [AMBER] Hello! Distance restraint problems in SANDER David A Case (Sat Nov 05 2016 - 17:35:33 PDT)
[AMBER] MM-PBSA calculation for HEME-contained protein Ramin Ekhteiari (Sat Nov 05 2016 - 05:14:47 PDT)
- Re: [AMBER] MM-PBSA calculation for HEME-contained protein Elvis Martis (Sat Nov 05 2016 - 05:42:36 PDT)
[AMBER] enhanced sampling conformations by AMD Kat G (Mon Nov 07 2016 - 09:03:29 PST)
- Re: [AMBER] enhanced sampling conformations by AMD Eric Lang (Wed Nov 09 2016 - 01:50:10 PST)
[AMBER] Performance drop for large systems Andreas Tosstorff (Tue Nov 08 2016 - 02:11:46 PST)
- Re: [AMBER] Performance drop for large systems Ross Walker (Tue Nov 08 2016 - 05:48:08 PST)
[AMBER] Coordinates for PEG4K, Folic acid and chitin Abdul Ajees (Tue Nov 08 2016 - 03:02:37 PST)
[AMBER] CPPTRAJ cluster analysis: Segmentation fault (core dumped) Michael Shokhen (Tue Nov 08 2016 - 05:28:06 PST)
- Re: [AMBER] CPPTRAJ cluster analysis: Segmentation fault (core dumped) Samuel Bowerman (Tue Nov 08 2016 - 06:23:31 PST)
- Re: [AMBER] CPPTRAJ cluster analysis: Segmentation fault (core dumped) Daniel Roe (Tue Nov 08 2016 - 06:56:51 PST)
  - Re: [AMBER] CPPTRAJ cluster analysis: Segmentation fault (core dumped) Michael Shokhen (Tue Nov 08 2016 - 07:38:40 PST)
    - Re: [AMBER] CPPTRAJ cluster analysis: Segmentation fault (core dumped) Daniel Roe (Tue Nov 08 2016 - 08:17:35 PST)
[AMBER] Error in running FEW calculations Miguel Rivera (Tue Nov 08 2016 - 12:50:23 PST)
- Re: [AMBER] Error in running FEW calculations Hannes Loeffler (Wed Nov 09 2016 - 00:21:39 PST)
  - Re: [AMBER] Error in running FEW calculations Miguel Rivera (Wed Nov 09 2016 - 00:26:49 PST)
    - Re: [AMBER] Error in running FEW calculations Hannes Loeffler (Wed Nov 09 2016 - 00:39:31 PST)
    - Re: [AMBER] Error in running FEW calculations Miguel Rivera (Wed Nov 09 2016 - 00:44:34 PST)
    - Re: [AMBER] Error in running FEW calculations Hannes Loeffler (Wed Nov 09 2016 - 00:51:25 PST)
[AMBER] number of cpus in parallel GPU jobs Neha Gandhi (Tue Nov 08 2016 - 17:42:03 PST)
- Re: [AMBER] number of cpus in parallel GPU jobs Ross Walker (Tue Nov 08 2016 - 19:08:08 PST)
[AMBER] AMBER FF for intrinsically disordered protein giulia palermo (Tue Nov 08 2016 - 19:53:35 PST)
- Re: [AMBER] AMBER FF for intrinsically disordered protein Neha Gandhi (Tue Nov 08 2016 - 19:56:46 PST)
[AMBER] log file in aMD Neha Gandhi (Wed Nov 09 2016 - 02:50:12 PST)
[AMBER] Mapping back the original PDB numbering and chain IDs when analysing Amber trajectories Eric Lang (Wed Nov 09 2016 - 03:44:02 PST)
- Re: [AMBER] Mapping back the original PDB numbering and chain IDs when analysing Amber trajectories Nhai (Wed Nov 09 2016 - 07:07:40 PST)
  - Re: [AMBER] Mapping back the original PDB numbering and chain IDs when analysing Amber trajectories Eric Lang (Wed Nov 09 2016 - 09:16:08 PST)
    - Re: [AMBER] Mapping back the original PDB numbering and chain IDs when analysing Amber trajectories William Lees (Thu Nov 10 2016 - 02:00:46 PST)
- Re: [AMBER] Mapping back the original PDB numbering and chain IDs when analysing Amber trajectories David A Case (Wed Nov 09 2016 - 10:32:20 PST)
  - Re: [AMBER] Mapping back the original PDB numbering and chain IDs when analysing Amber trajectories Daniel Roe (Wed Nov 09 2016 - 10:57:59 PST)
[AMBER] PCA trajectories give unrealistic structures Gulsevin,Alican (Wed Nov 09 2016 - 08:06:43 PST)
- Re: [AMBER] PCA trajectories give unrealistic structures Daniel Roe (Wed Nov 09 2016 - 12:33:36 PST)
[AMBER] integer limit for nstlim Neale, Christopher Andrew (Wed Nov 09 2016 - 14:14:12 PST)
- Re: [AMBER] integer limit for nstlim David A Case (Wed Nov 09 2016 - 14:41:58 PST)
[AMBER] compute RESP charges asdda asa (Wed Nov 09 2016 - 14:16:45 PST)
- Re: [AMBER] compute RESP charges Dr. Anselm Horn (Thu Nov 10 2016 - 02:21:31 PST)
  - Re: [AMBER] compute RESP charges asdda asa (Thu Nov 10 2016 - 14:14:00 PST)
[AMBER] CUDA version for Amber14 Sofia Vasilakaki (Wed Nov 09 2016 - 14:17:39 PST)
- Re: [AMBER] CUDA version for Amber14 Ross Walker (Thu Nov 10 2016 - 06:57:27 PST)
[AMBER] recompile Sander suite Ibrahim Said (Thu Nov 10 2016 - 02:56:34 PST)
- Re: [AMBER] recompile Sander suite Dr. Anselm Horn (Thu Nov 10 2016 - 03:13:48 PST)
[AMBER] MCPB.py error in Step 2 Jon Mujika (Thu Nov 10 2016 - 03:25:11 PST)
- Re: [AMBER] MCPB.py error in Step 2 Pengfei Li (Fri Nov 11 2016 - 09:52:42 PST)
[AMBER] Constant pH charge set Fabrício Bracht (Thu Nov 10 2016 - 06:05:42 PST)
- Re: [AMBER] Constant pH charge set Jason Swails (Thu Nov 10 2016 - 06:22:12 PST)
[AMBER] Parameters for selenocysteine Paul Meister (Thu Nov 10 2016 - 06:06:54 PST)
- Re: [AMBER] Parameters for selenocysteine David A Case (Thu Nov 10 2016 - 07:43:51 PST)
  - Re: [AMBER] Parameters for selenocysteine David A Case (Thu Nov 10 2016 - 10:14:14 PST)
[AMBER] Missing dispersion parameters for Mg2+ in QM/MM MD with DFTB Ruth Helena Tichauer (Thu Nov 10 2016 - 06:07:29 PST)
- Re: [AMBER] Missing dispersion parameters for Mg2+ in QM/MM MD with DFTB Gustavo Seabra (Thu Nov 10 2016 - 09:44:45 PST)
  - Re: [AMBER] Missing dispersion parameters for Mg2+ in QM/MM MD with DFTB Ruth Helena Tichauer (Tue Nov 15 2016 - 01:47:37 PST)
    - Re: [AMBER] Missing dispersion parameters for Mg2+ in QM/MM MD with DFTB David A Case (Tue Nov 15 2016 - 05:04:53 PST)
    - Re: [AMBER] Missing dispersion parameters for Mg2+ in QM/MM MD with DFTB Ruth Helena Tichauer (Tue Nov 15 2016 - 05:16:42 PST)
    - Re: [AMBER] Missing dispersion parameters for Mg2+ in QM/MM MD with DFTB Gustavo Seabra (Wed Nov 16 2016 - 04:26:41 PST)
    - Re: [AMBER] Missing dispersion parameters for Mg2+ in QM/MM MD with DFTB Ruth Helena Tichauer (Wed Nov 16 2016 - 04:32:01 PST)
    - Re: [AMBER] Missing dispersion parameters for Mg2+ in QM/MM MD with DFTB Hector A. Baldoni (Wed Nov 16 2016 - 05:06:59 PST)
    - Re: [AMBER] Missing dispersion parameters for Mg2+ in QM/MM MD with DFTB Ruth Helena Tichauer (Fri Nov 18 2016 - 07:16:57 PST)
[AMBER] Problem with Parmed-generated chamber prmtop Marc van der Kamp (Thu Nov 10 2016 - 07:01:48 PST)
- Re: [AMBER] Problem with Parmed-generated chamber prmtop Hai Nguyen (Tue Nov 15 2016 - 18:50:32 PST)
- Re: [AMBER] Problem with Parmed-generated chamber prmtop Jason Swails (Fri Nov 18 2016 - 11:45:19 PST)
  - Re: [AMBER] Problem with Parmed-generated chamber prmtop Marc van der Kamp (Fri Nov 18 2016 - 14:39:40 PST)
    - Re: [AMBER] Problem with Parmed-generated chamber prmtop Jason Swails (Fri Nov 18 2016 - 16:49:07 PST)
    - Re: [AMBER] Problem with Parmed-generated chamber prmtop Jason Swails (Wed Nov 23 2016 - 08:47:58 PST)
    - Re: [AMBER] Problem with Parmed-generated chamber prmtop Marc van der Kamp (Thu Nov 24 2016 - 02:34:37 PST)
[AMBER] ambmask issue Aseel Bala (Thu Nov 10 2016 - 15:08:01 PST)
- Re: [AMBER] ambmask issue Hai Nguyen (Thu Nov 10 2016 - 15:11:29 PST)
  - Re: [AMBER] ambmask issue Aseel Bala (Thu Nov 10 2016 - 15:22:18 PST)
[AMBER] cpptraj: RMSD vs Residue Number. Saman Yousuf ali (Fri Nov 11 2016 - 00:48:23 PST)
- Re: [AMBER] cpptraj: RMSD vs Residue Number. Daniel Roe (Fri Nov 11 2016 - 04:10:26 PST)
[AMBER] GIST: convergence of the translational entropy term Sergey Samsonov (Fri Nov 11 2016 - 06:28:26 PST)
- Re: [AMBER] GIST: convergence of the translational entropy term Steven Ramsey (Fri Nov 11 2016 - 08:43:15 PST)
  - Re: [AMBER] GIST: convergence of the translational entropy term Tom Kurtzman (Fri Nov 11 2016 - 10:26:13 PST)
[AMBER] Constraints Ol Sta (Fri Nov 11 2016 - 06:34:07 PST)
- Re: [AMBER] Constraints David A Case (Tue Nov 15 2016 - 05:19:34 PST)
  - Re: [AMBER] Constraints Roitberg,Adrian E (Tue Nov 15 2016 - 06:21:01 PST)
    - Re: [AMBER] Constraints Jason Swails (Tue Nov 15 2016 - 11:20:07 PST)
[AMBER] NPT equilibration at constant pH with protonation states allowed to change Eric Lang (Fri Nov 11 2016 - 09:31:56 PST)
- Re: [AMBER] NPT equilibration at constant pH with protonation states allowed to change Jason Swails (Fri Nov 11 2016 - 09:39:05 PST)
  - Re: [AMBER] NPT equilibration at constant pH with protonation states allowed to change Eric Lang (Fri Nov 11 2016 - 13:18:50 PST)
- Re: [AMBER] NPT equilibration at constant pH with protonation states allowed to change Eric Lang (Mon Nov 14 2016 - 02:12:46 PST)
[AMBER] length of restraintmask Ignacio J. General (Fri Nov 11 2016 - 09:51:50 PST)
- Re: [AMBER] length of restraintmask David A Case (Fri Nov 11 2016 - 17:09:29 PST)
[AMBER] MMGBSA decomposition analysis George Tzotzos (Fri Nov 11 2016 - 13:16:41 PST)
- Re: [AMBER] MMGBSA decomposition analysis Carlos Simmerling (Fri Nov 11 2016 - 13:27:51 PST)
  - Re: [AMBER] MMGBSA decomposition analysis George Tzotzos (Fri Nov 11 2016 - 13:30:46 PST)
[AMBER] error in antechamber Nehad Elsalamouny (Fri Nov 11 2016 - 16:10:17 PST)
- Re: [AMBER] error in antechamber David A Case (Fri Nov 11 2016 - 17:14:55 PST)
[AMBER] Query regarding the MCPB.py workflow Abhi Acharya (Sat Nov 12 2016 - 01:09:19 PST)
- Re: [AMBER] Query regarding the MCPB.py workflow Abhi Acharya (Wed Nov 16 2016 - 02:45:23 PST)
  - Re: [AMBER] Query regarding the MCPB.py workflow Pengfei Li (Wed Nov 16 2016 - 17:07:22 PST)
  - Re: [AMBER] Query regarding the MCPB.py workflow Abhi Acharya (Sat Nov 19 2016 - 22:34:34 PST)
    - Re: [AMBER] Query regarding the MCPB.py workflow Pengfei Li (Mon Nov 21 2016 - 14:27:34 PST)
- Re: [AMBER] Query regarding the MCPB.py workflow Pengfei Li (Wed Nov 16 2016 - 17:05:31 PST)
[AMBER] Generation of parameter files of transmembrane protein system via xleap Mahrukh Imtiaz (Mon Nov 14 2016 - 01:05:39 PST)
- Re: [AMBER] Generation of parameter files of transmembrane protein system via xleap Bill Ross (Mon Nov 14 2016 - 01:21:21 PST)
- Re: [AMBER] Generation of parameter files of transmembrane protein system via xleap David A Case (Mon Nov 14 2016 - 04:47:21 PST)
[AMBER] dlpc membrane jojartb.jgypk.u-szeged.hu (Mon Nov 14 2016 - 01:45:03 PST)
- Re: [AMBER] dlpc membrane Batuhan Kav (Mon Nov 14 2016 - 02:36:05 PST)
  - Re: [AMBER] dlpc membrane jojartb.jgypk.u-szeged.hu (Mon Nov 14 2016 - 03:05:17 PST)
    - Re: [AMBER] dlpc membrane David A Case (Mon Nov 14 2016 - 04:51:26 PST)
    - Re: [AMBER] dlpc membrane jojartb.jgypk.u-szeged.hu (Mon Nov 14 2016 - 05:38:28 PST)
    - Re: [AMBER] dlpc membrane David A Case (Mon Nov 14 2016 - 08:18:07 PST)
    - Re: [AMBER] dlpc membrane jojartb.jgypk.u-szeged.hu (Mon Nov 14 2016 - 08:41:16 PST)
    - Re: [AMBER] dlpc membrane Nhai (Mon Nov 14 2016 - 08:55:48 PST)
    - Re: [AMBER] dlpc membrane jojartb.jgypk.u-szeged.hu (Mon Nov 14 2016 - 09:26:22 PST)
    - Re: [AMBER] dlpc membrane David A Case (Mon Nov 14 2016 - 18:00:17 PST)
    - Re: [AMBER] dlpc membrane jojartb.jgypk.u-szeged.hu (Mon Nov 14 2016 - 21:17:49 PST)
    - Re: [AMBER] dlpc membrane David A Case (Tue Nov 15 2016 - 06:29:16 PST)
[AMBER] Targeted molecular dynamics on GPU Sonia Ziada (Mon Nov 14 2016 - 07:14:34 PST)
[AMBER] how to neutralize protein when using intrinsic water model Thakur, Abhishek (Mon Nov 14 2016 - 08:00:46 PST)
- Re: [AMBER] how to neutralize protein when using intrinsic water model David A Case (Mon Nov 14 2016 - 08:22:34 PST)
[AMBER] Filename being truncated by pmemd.cuda Andreas Tosstorff (Mon Nov 14 2016 - 08:14:03 PST)
- Re: [AMBER] Filename being truncated by pmemd.cuda Adrian Roitberg (Mon Nov 14 2016 - 08:16:25 PST)
  - Re: [AMBER] Filename being truncated by pmemd.cuda Andreas Tosstorff (Mon Nov 14 2016 - 08:19:56 PST)
- Re: [AMBER] Filename being truncated by pmemd.cuda David A Case (Mon Nov 14 2016 - 12:31:53 PST)
[AMBER] covalently bound ligand Ahsan Mohd (Mon Nov 14 2016 - 10:20:14 PST)
- Re: [AMBER] covalently bound ligand David A Case (Mon Nov 14 2016 - 18:08:18 PST)
- Re: [AMBER] covalently bound ligand FyD (Mon Nov 14 2016 - 23:36:17 PST)
Re: [AMBER] Negative interaction energy between Sodium ions? Oliver Emil Skytte Glue (Mon Nov 14 2016 - 14:29:17 PST)
- Re: [AMBER] Negative interaction energy between Sodium ions? David Cerutti (Mon Nov 14 2016 - 14:46:16 PST)
[AMBER] Restraints not working, What Am I doing Wrong? The Cromicus Productions (Mon Nov 14 2016 - 23:28:17 PST)
- Re: [AMBER] Restraints not working, What Am I doing Wrong? Dr. Anselm Horn (Tue Nov 15 2016 - 00:45:07 PST)
  - Re: [AMBER] Restraints not working, What Am I doing Wrong? The Cromicus Productions (Fri Nov 18 2016 - 10:26:46 PST)
[AMBER] Methylated adenine parameter Kshatresh Dutta Dubey (Tue Nov 15 2016 - 02:45:07 PST)
- Re: [AMBER] Methylated adenine parameter David A Case (Tue Nov 15 2016 - 05:15:59 PST)
[AMBER] simulating with "gbsa=1" on gpu give only 0.18ns per/day Thakur, Abhishek (Tue Nov 15 2016 - 07:01:41 PST)
- Re: [AMBER] simulating with "gbsa=1" on gpu give only 0.18ns per/day Adrian Roitberg (Tue Nov 15 2016 - 07:06:36 PST)
- Re: [AMBER] simulating with "gbsa=1" on gpu give only 0.18ns per/day Hai Nguyen (Tue Nov 15 2016 - 07:13:20 PST)
  - Re: [AMBER] simulating with "gbsa=1" on gpu give only 0.18ns per/day Thakur, Abhishek (Tue Nov 15 2016 - 09:12:37 PST)
[AMBER] Compatibility of Amber parameters for FF99 and FF14SB forcefields DmitryASuplatov (Tue Nov 15 2016 - 08:12:45 PST)
- Re: [AMBER] Compatibility of Amber parameters for FF99 and FF14SB forcefields Carlos Simmerling (Tue Nov 15 2016 - 08:25:12 PST)
[AMBER] Help Constant pH MD calculations Tsibela German Tebello Mofokeng (Tue Nov 15 2016 - 08:32:45 PST)
- Re: [AMBER] Help Constant pH MD calculations Jason Swails (Tue Nov 15 2016 - 11:24:25 PST)
  - Re: [AMBER] Help Constant pH MD calculations Tsibela German Tebello Mofokeng (Wed Nov 16 2016 - 01:06:46 PST)
[AMBER] Energy decomposition of free energy profiles wjli (Tue Nov 15 2016 - 17:46:53 PST)
[AMBER] MM-GBSA calculation in temperature other than 298.15 K Atila Petrosian (Tue Nov 15 2016 - 21:42:37 PST)
- Re: [AMBER] MM-GBSA calculation in temperature other than 298.15 K Carlos Simmerling (Wed Nov 16 2016 - 03:12:43 PST)
  - Re: [AMBER] MM-GBSA calculation in temperature other than 298.15 K Atila Petrosian (Wed Nov 16 2016 - 22:46:26 PST)
    - Re: [AMBER] MM-GBSA calculation in temperature other than 298.15 K Carlos Simmerling (Thu Nov 17 2016 - 04:35:32 PST)
    - Re: [AMBER] MM-GBSA calculation in temperature other than 298.15 K Atila Petrosian (Thu Nov 17 2016 - 05:12:09 PST)
    - Re: [AMBER] MM-GBSA calculation in temperature other than 298.15 K Carlos Simmerling (Thu Nov 17 2016 - 05:18:35 PST)
    - Re: [AMBER] MM-GBSA calculation in temperature other than 298.15 K Atila Petrosian (Thu Nov 17 2016 - 05:22:17 PST)
    - Re: [AMBER] MM-GBSA calculation in temperature other than 298.15 K Carlos Simmerling (Thu Nov 17 2016 - 05:44:36 PST)
    - Re: [AMBER] MM-GBSA calculation in temperature other than 298.15 K Daniel Roe (Thu Nov 17 2016 - 08:11:13 PST)
    - Re: [AMBER] MM-GBSA calculation in temperature other than 298.15 K Jason Swails (Thu Nov 17 2016 - 09:55:37 PST)
    - Re: [AMBER] MM-GBSA calculation in temperature other than 298.15 K Atila Petrosian (Sun Nov 20 2016 - 00:52:52 PST)
    - Re: [AMBER] MM-GBSA calculation in temperature other than 298.15 K Daniel Roe (Sun Nov 20 2016 - 04:05:06 PST)
[AMBER] GaMD patches to Amber 14 and PME's gridhi parameter Kasprzak, Wojciech (NIH/NCI) [C] (Wed Nov 16 2016 - 06:07:03 PST)
- Re: [AMBER] GaMD patches to Amber 14 and PME's gridhi parameter David A Case (Wed Nov 16 2016 - 06:56:09 PST)
  - Re: [AMBER] GaMD patches to Amber 14 and PME's gridhi parameter Kasprzak, Wojciech (NIH/NCI) [C] (Wed Nov 16 2016 - 07:36:06 PST)
[AMBER] HMassRepartition Thakur, Abhishek (Wed Nov 16 2016 - 07:38:23 PST)
- Re: [AMBER] HMassRepartition Elvis Martis (Wed Nov 16 2016 - 07:43:39 PST)
- Re: [AMBER] HMassRepartition David Cerutti (Wed Nov 16 2016 - 07:46:06 PST)
  - Re: [AMBER] HMassRepartition Thakur, Abhishek (Wed Nov 16 2016 - 07:55:45 PST)
    - Re: [AMBER] HMassRepartition Elvis Martis (Wed Nov 16 2016 - 07:58:39 PST)
    - Re: [AMBER] HMassRepartition David Cerutti (Wed Nov 16 2016 - 08:04:22 PST)
    - Re: [AMBER] HMassRepartition Hai Nguyen (Wed Nov 16 2016 - 08:11:24 PST)
    - Re: [AMBER] HMassRepartition Thakur, Abhishek (Wed Nov 16 2016 - 08:41:02 PST)
    - Re: [AMBER] HMassRepartition Adrian Roitberg (Wed Nov 16 2016 - 09:59:54 PST)
    - Re: [AMBER] HMassRepartition Thakur, Abhishek (Wed Nov 16 2016 - 10:31:28 PST)
    - Re: [AMBER] HMassRepartition Adrian Roitberg (Wed Nov 16 2016 - 10:38:58 PST)
    - Re: [AMBER] HMassRepartition Thakur, Abhishek (Wed Nov 16 2016 - 11:02:17 PST)
- Re: [AMBER] HMassRepartition Daniel Roe (Wed Nov 16 2016 - 07:54:11 PST)
  - Re: [AMBER] HMassRepartition Thakur, Abhishek (Wed Nov 16 2016 - 07:57:42 PST)
- Re: [AMBER] HMassRepartition Adrian Roitberg (Wed Nov 16 2016 - 09:54:34 PST)
[AMBER] compatibility Magno . (Wed Nov 16 2016 - 10:13:16 PST)
[AMBER] MD under external electric field Hector A. Baldoni (Wed Nov 16 2016 - 13:36:05 PST)
- Re: [AMBER] MD under external electric field Charles Lin (Wed Nov 16 2016 - 14:18:46 PST)
  - Re: [AMBER] MD under external electric field Hector A. Baldoni (Thu Nov 17 2016 - 05:56:13 PST)
    - Re: [AMBER] MD under external electric field Charles Lin (Thu Nov 17 2016 - 12:48:12 PST)
[AMBER] ATP Parameters for ff14SB Stevens, David Ryan (Wed Nov 16 2016 - 13:57:21 PST)
- Re: [AMBER] ATP Parameters for ff14SB David Cerutti (Wed Nov 16 2016 - 14:07:23 PST)
- Re: [AMBER] ATP Parameters for ff14SB David A Case (Wed Nov 16 2016 - 17:38:13 PST)
[AMBER] cpptraj RMSD calculation with mismatch residue numbers anu chandra (Wed Nov 16 2016 - 15:02:04 PST)
- Re: [AMBER] cpptraj RMSD calculation with mismatch residue numbers Nhai (Wed Nov 16 2016 - 15:26:16 PST)
  - Re: [AMBER] cpptraj RMSD calculation with mismatch residue numbers anu chandra (Fri Nov 18 2016 - 05:12:32 PST)
- Re: [AMBER] cpptraj RMSD calculation with mismatch residue numbers Daniel Roe (Wed Nov 30 2016 - 13:07:00 PST)
[AMBER] Phosphoryated amino acids Beale, John (Thu Nov 17 2016 - 01:10:30 PST)
- Re: [AMBER] Phosphoryated amino acids Bill Ross (Thu Nov 17 2016 - 01:12:58 PST)
  - Re: [AMBER] Phosphoryated amino acids Bill Ross (Thu Nov 17 2016 - 01:25:12 PST)
- Re: [AMBER] Phosphoryated amino acids Neha Gandhi (Thu Nov 17 2016 - 01:35:20 PST)
  - Re: [AMBER] Phosphoryated amino acids Eiros Zamora, Juan (Thu Nov 17 2016 - 02:21:26 PST)
    - Re: [AMBER] Phosphoryated amino acids David A Case (Thu Nov 17 2016 - 05:39:19 PST)
[AMBER] No output_file during SMD with LCOD Ruth Helena Tichauer (Thu Nov 17 2016 - 02:45:47 PST)
- Re: [AMBER] No output_file during SMD with LCOD Feng Pan (Thu Nov 17 2016 - 09:03:08 PST)
  - Re: [AMBER] No output_file during SMD with LCOD Ruth Helena Tichauer (Fri Nov 18 2016 - 07:04:06 PST)
[AMBER] Converting coordinate file generated into pdb format for nuparm ABHIJEET CHOWDHURY (Thu Nov 17 2016 - 04:43:59 PST)
- Re: [AMBER] Converting coordinate file generated into pdb format for nuparm David A Case (Thu Nov 17 2016 - 05:45:46 PST)
  - Re: [AMBER] Converting coordinate file generated into pdb format for nuparm ABHIJEET CHOWDHURY (Thu Nov 17 2016 - 06:39:02 PST)
    - Re: [AMBER] Converting coordinate file generated into pdb format for nuparm Nhai (Thu Nov 17 2016 - 06:44:11 PST)
    - Re: [AMBER] Converting coordinate file generated into pdb format for nuparm ABHIJEET CHOWDHURY (Thu Nov 17 2016 - 06:52:33 PST)
[AMBER] Fwd: Normal Mode Analysis Imma Speciale (Thu Nov 17 2016 - 05:47:45 PST)
- Re: [AMBER] Fwd: Normal Mode Analysis Nhai (Thu Nov 17 2016 - 06:54:09 PST)
  - Re: [AMBER] Fwd: Normal Mode Analysis Imma Speciale (Tue Nov 22 2016 - 02:42:02 PST)
    - Re: [AMBER] Fwd: Normal Mode Analysis David A Case (Tue Nov 22 2016 - 05:14:38 PST)
    - Re: [AMBER] Fwd: Normal Mode Analysis The Cromicus Productions (Tue Nov 22 2016 - 06:29:34 PST)
    - Re: [AMBER] Fwd: Normal Mode Analysis Imma Speciale (Tue Nov 22 2016 - 06:33:07 PST)
[AMBER] creating parameters for integrins Tsibela German Tebello Mofokeng (Thu Nov 17 2016 - 09:22:03 PST)
- Re: [AMBER] creating parameters for integrins Nhai (Thu Nov 17 2016 - 09:44:00 PST)
  - Re: [AMBER] creating parameters for integrins Tsibela German Tebello Mofokeng (Thu Nov 17 2016 - 23:40:38 PST)
[AMBER] ImportError: Could not import Amber Python modules Thakur, Abhishek (Thu Nov 17 2016 - 09:42:56 PST)
- Re: [AMBER] ImportError: Could not import Amber Python modules Nhai (Thu Nov 17 2016 - 09:47:27 PST)
  - Re: [AMBER] ImportError: Could not import Amber Python modules Thakur, Abhishek (Thu Nov 17 2016 - 11:02:40 PST)
    - Re: [AMBER] ImportError: Could not import Amber Python modules Nhai (Thu Nov 17 2016 - 11:48:37 PST)
    - Re: [AMBER] ImportError: Could not import Amber Python modules Thakur, Abhishek (Thu Nov 17 2016 - 11:51:06 PST)
    - Re: [AMBER] ImportError: Could not import Amber Python modules David A Case (Thu Nov 17 2016 - 12:35:53 PST)
    - Re: [AMBER] ImportError: Could not import Amber Python modules Daniel Roe (Thu Nov 17 2016 - 12:40:10 PST)
    - Re: [AMBER] ImportError: Could not import Amber Python modules Thakur, Abhishek (Thu Nov 17 2016 - 12:52:31 PST)
    - Re: [AMBER] ImportError: Could not import Amber Python modules Jason Swails (Thu Nov 17 2016 - 13:23:48 PST)
    - Re: [AMBER] ImportError: Could not import Amber Python modules David A Case (Fri Nov 18 2016 - 06:13:46 PST)
    - Re: [AMBER] ImportError: Could not import Amber Python modules Niel Henriksen (Thu Nov 17 2016 - 13:28:36 PST)
    - Re: [AMBER] ImportError: Could not import Amber Python modules David A Case (Fri Nov 18 2016 - 06:14:38 PST)
[AMBER] ambmask issue Aseel Bala (Thu Nov 17 2016 - 10:21:11 PST)
[AMBER] extracting velocities from rst7 file giulia palermo (Thu Nov 17 2016 - 10:55:59 PST)
- Re: [AMBER] extracting velocities from rst7 file Hai Nguyen (Thu Nov 17 2016 - 12:58:09 PST)
  - Re: [AMBER] extracting velocities from rst7 file giulia palermo (Thu Nov 17 2016 - 13:39:07 PST)
    - Re: [AMBER] extracting velocities from rst7 file Nhai (Thu Nov 17 2016 - 14:54:24 PST)
    - Re: [AMBER] extracting velocities from rst7 file Daniel Roe (Thu Nov 17 2016 - 15:05:18 PST)
- Re: [AMBER] extracting velocities from rst7 file Daniel Roe (Thu Nov 17 2016 - 13:00:12 PST)
[AMBER] Issue with addAtomType: Syntax Error Korey M Reid (Thu Nov 17 2016 - 12:14:36 PST)
- Re: [AMBER] Issue with addAtomType: Syntax Error Bill Ross (Thu Nov 17 2016 - 12:22:00 PST)
  - Re: [AMBER] Issue with addAtomType: Syntax Error Korey M Reid (Thu Nov 17 2016 - 13:01:23 PST)
    - Re: [AMBER] Issue with addAtomType: Syntax Error Bill Ross (Thu Nov 17 2016 - 13:21:45 PST)
- Re: [AMBER] Issue with addAtomType: Syntax Error David A Case (Fri Nov 18 2016 - 06:18:05 PST)
  - Re: [AMBER] Issue with addAtomType: Syntax Error Korey M Reid (Fri Nov 18 2016 - 13:57:34 PST)
[AMBER] strange format of .rst file Thakur, Abhishek (Fri Nov 18 2016 - 07:53:41 PST)
- Re: [AMBER] strange format of .rst file Daniel Roe (Fri Nov 18 2016 - 08:20:42 PST)
  - Re: [AMBER] strange format of .rst file Thakur, Abhishek (Fri Nov 18 2016 - 09:04:15 PST)
    - Re: [AMBER] strange format of .rst file Jason Swails (Fri Nov 18 2016 - 09:13:43 PST)
[AMBER] [Amber] How to convert vector files (.pev) into coordinate files (.pdb) The Cromicus Productions (Fri Nov 18 2016 - 10:26:21 PST)
- Re: [AMBER] [Amber] How to convert vector files (.pev) into coordinate files (.pdb) Hai Nguyen (Fri Nov 18 2016 - 10:30:01 PST)
  - Re: [AMBER] [Amber] How to convert vector files (.pev) into coordinate files (.pdb) The Cromicus Productions (Fri Nov 18 2016 - 13:02:11 PST)
    - Re: [AMBER] [Amber] How to convert vector files (.pev) into coordinate files (.pdb) Hai Nguyen (Fri Nov 18 2016 - 13:06:33 PST)
    - Re: [AMBER] [Amber] How to convert vector files (.pev) into coordinate files (.pdb) The Cromicus Productions (Fri Nov 18 2016 - 16:29:10 PST)
    - Re: [AMBER] [Amber] How to convert vector files (.pev) into coordinate files (.pdb) Hai Nguyen (Fri Nov 18 2016 - 17:09:35 PST)
    - Re: [AMBER] [Amber] How to convert vector files (.pev) into coordinate files (.pdb) The Cromicus Productions (Fri Nov 18 2016 - 17:12:39 PST)
[AMBER] Converting a PDB Collection to a NetCDF trajectory Dmitry Suplatov (Fri Nov 18 2016 - 12:11:41 PST)
- Re: [AMBER] Converting a PDB Collection to a NetCDF trajectory Hai Nguyen (Fri Nov 18 2016 - 12:19:33 PST)
- Re: [AMBER] Converting a PDB Collection to a NetCDF trajectory Christina Bergonzo (Fri Nov 18 2016 - 12:30:48 PST)
[AMBER] generated correct inputfiles(.iprmtop and .inpcrd ) files 杨满意 (Fri Nov 18 2016 - 19:12:20 PST)
- Re: [AMBER] generated correct inputfiles(.iprmtop and .inpcrd ) files David A Case (Tue Nov 22 2016 - 05:21:42 PST)
[AMBER] TUTORIAL B5: Simulating the Green Fluorescent Protein -PREPGEN Error Taylor, Miles (Sat Nov 19 2016 - 16:50:20 PST)
- Re: [AMBER] TUTORIAL B5: Simulating the Green Fluorescent Protein -PREPGEN Error Brent Krueger (Sun Nov 20 2016 - 06:31:59 PST)
- Re: [AMBER] TUTORIAL B5: Simulating the Green Fluorescent Protein -PREPGEN Error David A Case (Mon Nov 21 2016 - 06:11:38 PST)
[AMBER] How to change the dielectric constant in the electrostatic energy term? 冯国强 (Sun Nov 20 2016 - 08:02:05 PST)
- Re: [AMBER] How to change the dielectric constant in the electrostatic energy term? David A Case (Sun Nov 20 2016 - 12:55:47 PST)
[AMBER] The parameters for the fully protonated phosphate group jinfeng liu (Sun Nov 20 2016 - 18:45:31 PST)
- Re: [AMBER] The parameters for the fully protonated phosphate group David Cerutti (Sun Nov 20 2016 - 19:22:47 PST)
  - Re: [AMBER] The parameters for the fully protonated phosphate group Dd H (Sun Nov 20 2016 - 22:56:37 PST)
- Re: [AMBER] The parameters for the fully protonated phosphate group David A Case (Mon Nov 21 2016 - 06:08:04 PST)
- Re: [AMBER] The parameters for the fully protonated phosphate group David Cerutti (Mon Nov 21 2016 - 08:55:32 PST)
[AMBER] MMPBSA Calculation Preeti Pandey (Mon Nov 21 2016 - 08:49:43 PST)
[AMBER] Lifetime Analysis in cpptraj MOHD HOMAIDUR RAHMAN (Mon Nov 21 2016 - 11:20:06 PST)
- Re: [AMBER] Lifetime Analysis in cpptraj Daniel Roe (Tue Nov 22 2016 - 06:36:25 PST)
[AMBER] Convert prm into prmtop - from NAMD to AMBER The Cromicus Productions (Mon Nov 21 2016 - 11:21:43 PST)
- Re: [AMBER] Convert prm into prmtop - from NAMD to AMBER Hai Nguyen (Mon Nov 21 2016 - 11:29:31 PST)
  - Re: [AMBER] Convert prm into prmtop - from NAMD to AMBER The Cromicus Productions (Mon Nov 21 2016 - 11:36:27 PST)
  - Re: [AMBER] Convert prm into prmtop - from NAMD to AMBER Amy Rice (Mon Nov 21 2016 - 11:39:05 PST)
    - Re: [AMBER] Convert prm into prmtop - from NAMD to AMBER The Cromicus Productions (Mon Nov 21 2016 - 11:43:44 PST)
[AMBER] cap the 5' phosphate of a RNA Mohaddeseh Habibzadeh (Mon Nov 21 2016 - 11:48:23 PST)
[AMBER] 20161121141138.GE88784.scarletmail.rutgers.edu Taylor, Miles (Mon Nov 21 2016 - 12:36:36 PST)
- Re: [AMBER] 20161121141138.GE88784.scarletmail.rutgers.edu David Cerutti (Mon Nov 21 2016 - 13:20:57 PST)
[AMBER] implicit water model in aMD Thakur, Abhishek (Mon Nov 21 2016 - 13:45:04 PST)
[AMBER] creating 5' phosphate groups David A Case (Mon Nov 21 2016 - 14:36:13 PST)
- Re: [AMBER] creating 5' phosphate groups Mohaddeseh Habibzadeh (Sun Nov 27 2016 - 03:12:22 PST)
  - Re: [AMBER] creating 5' phosphate groups David A Case (Sun Nov 27 2016 - 05:44:06 PST)
    - Re: [AMBER] creating 5' phosphate groups Mohaddeseh Habibzadeh (Sun Nov 27 2016 - 10:05:57 PST)
[AMBER] [Amber] Calculating Normal Modes with Restrictions The Cromicus Productions (Mon Nov 21 2016 - 17:00:26 PST)
- Re: [AMBER] [Amber] Calculating Normal Modes with Restrictions David A Case (Tue Nov 22 2016 - 05:11:35 PST)
  - Re: [AMBER] [Amber] Calculating Normal Modes with Restrictions The Cromicus Productions (Tue Nov 22 2016 - 06:30:50 PST)
    - Re: [AMBER] [Amber] Calculating Normal Modes with Restrictions The Cromicus Productions (Tue Nov 22 2016 - 06:49:26 PST)
Re: [AMBER] AMBER Digest, Vol 1763, Issue 1 冯国强 (Tue Nov 22 2016 - 00:52:41 PST)
[AMBER] Protein path error Arthi Venkat (Tue Nov 22 2016 - 01:52:18 PST)
- Re: [AMBER] Protein path error Elvis Martis (Tue Nov 22 2016 - 02:08:26 PST)
  - Re: [AMBER] Protein path error Arthi Venkat (Tue Nov 22 2016 - 02:23:50 PST)
- Re: [AMBER] Protein path error Elvis Martis (Tue Nov 22 2016 - 02:31:01 PST)
  - Re: [AMBER] Protein path error Arthi Venkat (Tue Nov 22 2016 - 02:58:02 PST)
- Re: [AMBER] Protein path error Elvis Martis (Tue Nov 22 2016 - 03:30:32 PST)
[AMBER] Modes associated to the principal components? The Cromicus Productions (Tue Nov 22 2016 - 06:54:45 PST)
- Re: [AMBER] Modes associated to the principal components? Jason Swails (Tue Nov 22 2016 - 09:26:31 PST)
  - Re: [AMBER] Modes associated to the principal components? The Cromicus Productions (Tue Nov 22 2016 - 10:52:36 PST)
- Re: [AMBER] Modes associated to the principal components? David A Case (Tue Nov 22 2016 - 11:00:16 PST)
[AMBER] Could not find enough velocities in .rst Ruth Helena Tichauer (Tue Nov 22 2016 - 09:21:32 PST)
- Re: [AMBER] Could not find enough velocities in .rst Daniel Roe (Tue Nov 22 2016 - 10:28:08 PST)
  - Re: [AMBER] Could not find enough velocities in .rst Ruth Helena Tichauer (Wed Nov 23 2016 - 01:52:23 PST)
    - Re: [AMBER] Could not find enough velocities in .rst Daniel Roe (Wed Nov 23 2016 - 05:02:42 PST)
    - Re: [AMBER] Could not find enough velocities in .rst Ruth Helena Tichauer (Wed Nov 23 2016 - 05:33:33 PST)
[AMBER] DIfferences between thermostats Markowska (Tue Nov 22 2016 - 11:31:18 PST)
- Re: [AMBER] DIfferences between thermostats Gustavo Seabra (Tue Nov 22 2016 - 11:38:06 PST)
- Re: [AMBER] DIfferences between thermostats Geoffrey Gray (Tue Nov 22 2016 - 11:38:30 PST)
- Re: [AMBER] DIfferences between thermostats Markowska (Tue Nov 22 2016 - 12:06:24 PST)
  - Re: [AMBER] DIfferences between thermostats Gustavo Seabra (Tue Nov 22 2016 - 12:13:11 PST)
  - Re: [AMBER] DIfferences between thermostats Geoffrey Gray (Tue Nov 22 2016 - 14:09:32 PST)
    - Re: [AMBER] DIfferences between thermostats David Cerutti (Tue Nov 22 2016 - 14:42:05 PST)
    - Re: [AMBER] DIfferences between thermostats Adrian Roitberg (Tue Nov 22 2016 - 15:28:14 PST)
    - Re: [AMBER] DIfferences between thermostats David Cerutti (Tue Nov 22 2016 - 15:40:04 PST)
    - Re: [AMBER] DIfferences between thermostats David A Case (Tue Nov 22 2016 - 17:36:46 PST)
    - Re: [AMBER] DIfferences between thermostats Markowska (Wed Nov 23 2016 - 00:14:47 PST)
    - Re: [AMBER] DIfferences between thermostats David Cerutti (Wed Nov 23 2016 - 07:48:24 PST)
    - Re: [AMBER] DIfferences between thermostats Nhai (Wed Nov 23 2016 - 07:57:59 PST)
    - Re: [AMBER] DIfferences between thermostats Gustavo Seabra (Wed Nov 23 2016 - 08:45:47 PST)
    - Re: [AMBER] DIfferences between thermostats Markowska (Wed Nov 23 2016 - 10:54:16 PST)
    - Re: [AMBER] DIfferences between thermostats Gustavo Seabra (Wed Nov 23 2016 - 13:22:32 PST)
    - Re: [AMBER] DIfferences between thermostats Markowska (Wed Nov 23 2016 - 13:26:54 PST)
    - Re: [AMBER] DIfferences between thermostats David Cerutti (Wed Nov 23 2016 - 14:04:48 PST)
    - Re: [AMBER] DIfferences between thermostats Marc van der Kamp (Wed Nov 23 2016 - 07:53:48 PST)
- Re: [AMBER] DIfferences between thermostats Markowska (Wed Nov 23 2016 - 14:45:17 PST)
  - Re: [AMBER] DIfferences between thermostats Gustavo Seabra (Thu Nov 24 2016 - 04:58:43 PST)
    - Re: [AMBER] DIfferences between thermostats Markowska (Thu Nov 24 2016 - 05:10:43 PST)
    - Re: [AMBER] DIfferences between thermostats Gustavo Seabra (Thu Nov 24 2016 - 05:23:58 PST)
[AMBER] is it possible to run aMD in implicit water model? Thakur, Abhishek (Tue Nov 22 2016 - 12:51:26 PST)
- Re: [AMBER] is it possible to run aMD in implicit water model? Pengfei Li (Tue Nov 22 2016 - 12:54:33 PST)
  - Re: [AMBER] is it possible to run aMD in implicit water model? Thakur, Abhishek (Tue Nov 22 2016 - 14:36:52 PST)
    - Re: [AMBER] is it possible to run aMD in implicit water model? Pengfei Li (Tue Nov 22 2016 - 16:58:16 PST)
    - Re: [AMBER] is it possible to run aMD in implicit water model? Thakur, Abhishek (Tue Nov 22 2016 - 17:46:36 PST)
[AMBER] Paramfit for multiple molecules Sven Hackbusch (Tue Nov 22 2016 - 15:59:22 PST)
- Re: [AMBER] Paramfit for multiple molecules Robin Betz (Mon Nov 28 2016 - 15:47:05 PST)
  - Re: [AMBER] Paramfit for multiple molecules Robin Betz (Mon Dec 05 2016 - 16:56:00 PST)
[AMBER] How to generated correct inputfiles(.iprmtop and .inpcrd ) files 杨满意 (Tue Nov 22 2016 - 17:11:13 PST)
[AMBER] simulation running error. Saman Yousuf ali (Tue Nov 22 2016 - 21:31:15 PST)
- Re: [AMBER] simulation running error. Elvis Martis (Tue Nov 22 2016 - 21:41:39 PST)
  - Re: [AMBER] simulation running error. Saman Yousuf ali (Tue Nov 22 2016 - 21:49:50 PST)
- Re: [AMBER] simulation running error. Bill Ross (Tue Nov 22 2016 - 21:55:08 PST)
  - Re: [AMBER] simulation running error. Saman Yousuf ali (Tue Nov 22 2016 - 22:02:30 PST)
[AMBER] rmsf problem Sepideh Jafari (Wed Nov 23 2016 - 02:07:27 PST)
- Re: [AMBER] rmsf problem Elvis Martis (Wed Nov 23 2016 - 02:14:08 PST)
- Re: [AMBER] rmsf problem Eiros Zamora, Juan (Wed Nov 23 2016 - 04:42:39 PST)
- Re: [AMBER] rmsf problem Daniel Roe (Wed Nov 23 2016 - 05:06:31 PST)
[AMBER] Error, charge not integral Fabrício Bracht (Wed Nov 23 2016 - 02:26:46 PST)
- Re: [AMBER] Error, charge not integral Fabrício Bracht (Wed Nov 23 2016 - 02:39:39 PST)
  - Re: [AMBER] Error, charge not integral Bill Ross (Wed Nov 23 2016 - 02:59:32 PST)
    - Re: [AMBER] Error, charge not integral Lachele Foley (Wed Nov 23 2016 - 03:01:13 PST)
    - Re: [AMBER] Error, charge not integral Fabrício Bracht (Wed Nov 23 2016 - 03:29:12 PST)
[AMBER] aMD with dt=0.004 Thakur, Abhishek (Wed Nov 23 2016 - 06:53:34 PST)
- Re: [AMBER] aMD with dt=0.004 Nhai (Wed Nov 23 2016 - 07:47:16 PST)
[AMBER] About multiconformations RESP fitting Marion, Antoine (Wed Nov 23 2016 - 07:39:16 PST)
- Re: [AMBER] About multiconformations RESP fitting David Cerutti (Wed Nov 23 2016 - 08:27:01 PST)
  - Re: [AMBER] About multiconformations RESP fitting Marion, Antoine (Wed Nov 23 2016 - 09:29:29 PST)
    - Re: [AMBER] About multiconformations RESP fitting David Cerutti (Wed Nov 23 2016 - 10:40:17 PST)
    - Re: [AMBER] About multiconformations RESP fitting Marion, Antoine (Thu Nov 24 2016 - 01:06:32 PST)
- Re: [AMBER] About multiconformations RESP fitting FyD (Thu Nov 24 2016 - 02:32:38 PST)
  - Re: [AMBER] About multiconformations RESP fitting Marion, Antoine (Thu Nov 24 2016 - 05:38:45 PST)
    - Re: [AMBER] About multiconformations RESP fitting FyD (Fri Nov 25 2016 - 00:07:34 PST)
    - Re: [AMBER] About multiconformations RESP fitting Marion, Antoine (Fri Nov 25 2016 - 01:40:07 PST)
[AMBER] 20161121141138.GE88784.scarletmail.rutgers.edu Taylor, Miles (Wed Nov 23 2016 - 07:56:48 PST)
[AMBER] more on the Berendsen thermostat David A Case (Wed Nov 23 2016 - 10:44:29 PST)
- Re: [AMBER] more on the Berendsen thermostat Adrian Roitberg (Wed Nov 23 2016 - 10:48:49 PST)
  - Re: [AMBER] more on the Berendsen thermostat Markowska (Wed Nov 23 2016 - 11:07:59 PST)
[AMBER] Hydrophobic and covalent interactions bond length and stability muhammad tahir ayub (Wed Nov 23 2016 - 21:46:04 PST)
Re: [AMBER] Distorsion in water box size and shape Mahrukh Imtiaz (Wed Nov 23 2016 - 22:13:14 PST)
[AMBER] Optimal values for harm and output_freq in SMD Ruth Helena Tichauer (Thu Nov 24 2016 - 03:34:04 PST)
- Re: [AMBER] Optimal values for harm and output_freq in SMD Feng Pan (Thu Nov 24 2016 - 10:55:04 PST)
  - Re: [AMBER] Optimal values for harm and output_freq in SMD Ruth Helena Tichauer (Fri Nov 25 2016 - 03:47:37 PST)
    - Re: [AMBER] Optimal values for harm and output_freq in SMD Feng Pan (Mon Nov 28 2016 - 18:16:18 PST)
    - Re: [AMBER] Optimal values for harm and output_freq in SMD Ruth Helena Tichauer (Tue Nov 29 2016 - 07:59:07 PST)
    - Re: [AMBER] Optimal values for harm and output_freq in SMD Feng Pan (Tue Nov 29 2016 - 17:22:30 PST)
    - Re: [AMBER] Optimal values for harm and output_freq in SMD Ruth Helena Tichauer (Wed Nov 30 2016 - 01:32:31 PST)
[AMBER] GlcNAc-UDP problem with frcmod file Sonia Romero (Fri Nov 25 2016 - 02:15:41 PST)
- Re: [AMBER] GlcNAc-UDP problem with frcmod file Hannes Loeffler (Fri Nov 25 2016 - 03:28:02 PST)
- Re: [AMBER] GlcNAc-UDP problem with frcmod file David A Case (Mon Nov 28 2016 - 11:57:23 PST)
  - Re: [AMBER] GlcNAc-UDP problem with frcmod file Lachele Foley (Mon Nov 28 2016 - 23:40:16 PST)
[AMBER] Problem to submit a pH-REMD on a GPU node Yong Wang (Fri Nov 25 2016 - 02:54:49 PST)
- Re: [AMBER] Problem to submit a pH-REMD on a GPU node Ross Walker (Fri Nov 25 2016 - 07:57:16 PST)
[AMBER] Extract temperature of a subsytem diego.soler.uam.es (Fri Nov 25 2016 - 03:22:15 PST)
- Re: [AMBER] Extract temperature of a subsytem Gustavo Seabra (Fri Nov 25 2016 - 05:24:19 PST)
  - Re: [AMBER] Extract temperature of a subsytem diego.soler.uam.es (Fri Nov 25 2016 - 06:15:53 PST)
    - Re: [AMBER] Extract temperature of a subsytem Nhai (Fri Nov 25 2016 - 07:54:46 PST)
    - Re: [AMBER] Extract temperature of a subsytem Daniel Roe (Fri Nov 25 2016 - 07:55:40 PST)
[AMBER] Dynamic at high temperature Imma Speciale (Fri Nov 25 2016 - 03:49:01 PST)
- Re: [AMBER] Dynamic at high temperature David A Case (Fri Nov 25 2016 - 05:44:21 PST)
  - Re: [AMBER] Dynamic at high temperature Carlos Simmerling (Fri Nov 25 2016 - 10:24:13 PST)
[AMBER] instal aamber "mpich2" Sepideh Jafari (Fri Nov 25 2016 - 09:23:44 PST)
- Re: [AMBER] instal aamber "mpich2" Nhai (Fri Nov 25 2016 - 09:37:15 PST)
  - Re: [AMBER] instal aamber "mpich2" Sepideh Jafari (Fri Nov 25 2016 - 09:51:54 PST)
    - Re: [AMBER] instal aamber "mpich2" David A Case (Fri Nov 25 2016 - 11:29:39 PST)
[AMBER] Tools for calculation of interaction energy Andrew Bostick (Fri Nov 25 2016 - 09:41:26 PST)
- Re: [AMBER] Tools for calculation of interaction energy Nhai (Fri Nov 25 2016 - 12:57:48 PST)
[AMBER] Convert mdcrd files into pbd files The Cromicus Productions (Fri Nov 25 2016 - 14:47:00 PST)
- Re: [AMBER] Convert mdcrd files into pbd files Nhai (Fri Nov 25 2016 - 14:52:28 PST)
- Re: [AMBER] Convert mdcrd files into pbd files Daniel Roe (Sun Nov 27 2016 - 11:01:15 PST)
[AMBER] Obtaining infrared/Raman spectra The Cromicus Productions (Sat Nov 26 2016 - 00:36:22 PST)
- Re: [AMBER] Obtaining infrared/Raman spectra case (Sat Nov 26 2016 - 05:24:13 PST)
  - Re: [AMBER] Obtaining infrared/Raman spectra Brent Krueger (Sat Nov 26 2016 - 13:45:07 PST)
[AMBER] MCPB.py and MMPBSA issue 庄灿波 (Sat Nov 26 2016 - 01:32:53 PST)
- Re: [AMBER] MCPB.py and MMPBSA issue Pengfei Li (Mon Nov 28 2016 - 13:09:46 PST)
- Re: [AMBER] MCPB.py and MMPBSA issue Jason Swails (Tue Nov 29 2016 - 09:17:33 PST)
[AMBER] recipe for target "parallel" failed Mohaddeseh Habibzadeh (Sat Nov 26 2016 - 10:08:58 PST)
- Re: [AMBER] recipe for target "parallel" failed Elvis Martis (Sat Nov 26 2016 - 10:31:43 PST)
  - Re: [AMBER] recipe for target "parallel" failed Mohaddeseh Habibzadeh (Sat Nov 26 2016 - 11:03:35 PST)
- Re: [AMBER] recipe for target "parallel" failed David A Case (Sat Nov 26 2016 - 17:52:07 PST)
  - Re: [AMBER] recipe for target "parallel" failed Mohaddeseh Habibzadeh (Sat Nov 26 2016 - 22:38:56 PST)
  - Re: [AMBER] recipe for target "parallel" failed Mohaddeseh Habibzadeh (Sat Nov 26 2016 - 23:03:56 PST)
- Re: [AMBER] recipe for target "parallel" failed Elvis Martis (Sat Nov 26 2016 - 23:13:53 PST)
  - Re: [AMBER] recipe for target "parallel" failed Mohaddeseh Habibzadeh (Sun Nov 27 2016 - 00:07:24 PST)
- Re: [AMBER] recipe for target "parallel" failed Elvis Martis (Sun Nov 27 2016 - 00:14:51 PST)
[AMBER] How to create the .off/.lib file of the equilibrated non-aqueous solvent box? Yew Mun Yip (Sat Nov 26 2016 - 22:05:12 PST)
- Re: [AMBER] How to create the .off/.lib file of the equilibrated non-aqueous solvent box? David A Case (Sun Nov 27 2016 - 13:16:12 PST)
[AMBER] NAB input file containing first and second structure of RNA Mohaddeseh Habibzadeh (Sat Nov 26 2016 - 22:56:16 PST)
- Re: [AMBER] NAB input file containing first and second structure of RNA David A Case (Sun Nov 27 2016 - 09:40:13 PST)
  - Re: [AMBER] NAB input file containing first and second structure of RNA Mohaddeseh Habibzadeh (Sun Nov 27 2016 - 09:56:59 PST)
    - Re: [AMBER] NAB input file containing first and second structure of RNA David A Case (Sun Nov 27 2016 - 13:06:55 PST)
    - Re: [AMBER] NAB input file containing first and second structure of RNA Mohaddeseh Habibzadeh (Mon Nov 28 2016 - 01:32:20 PST)
[AMBER] Regarding integration of my code with CPPTRAJ Nikhil Chowdary (Sun Nov 27 2016 - 21:35:46 PST)
- Re: [AMBER] Regarding integration of my code with CPPTRAJ Hai Nguyen (Sun Nov 27 2016 - 21:47:06 PST)
- Re: [AMBER] Regarding integration of my code with CPPTRAJ Daniel Roe (Mon Nov 28 2016 - 05:16:03 PST)
[AMBER] AMBER Materials modelling- periodic image Neha Gandhi (Sun Nov 27 2016 - 21:41:46 PST)
- Re: [AMBER] AMBER Materials modelling- periodic image Pengfei Li (Mon Nov 28 2016 - 13:17:21 PST)
[AMBER] cudaMemcpyToSymbol Error cuiyinglukitty (Mon Nov 28 2016 - 00:45:48 PST)
- Re: [AMBER] cudaMemcpyToSymbol Error Charles Lin (Mon Nov 28 2016 - 01:27:35 PST)
  - Re: [AMBER] cudaMemcpyToSymbol Error Charles Lin (Mon Nov 28 2016 - 01:28:46 PST)
    - Re: [AMBER] cudaMemcpyToSymbol Error Ross Walker (Mon Nov 28 2016 - 05:46:45 PST)
[AMBER] Questions concerning charges calculated by antechamber Andreas Gavrielides (Mon Nov 28 2016 - 04:36:19 PST)
- Re: [AMBER] Questions concerning charges calculated by antechamber Daniel Roe (Mon Nov 28 2016 - 05:35:35 PST)
[AMBER] solvate box of long length and short width Lara rajam (Mon Nov 28 2016 - 06:58:31 PST)
- Re: [AMBER] solvate box of long length and short width David A Case (Mon Nov 28 2016 - 11:40:47 PST)
  - Re: [AMBER] solvate box of long length and short width Lara rajam (Mon Nov 28 2016 - 12:22:12 PST)
[AMBER] Etot = ************** with dtt=0.004 Thakur, Abhishek (Mon Nov 28 2016 - 08:29:40 PST)
- Re: [AMBER] Etot = ************** with dtt=0.004 Carlos Simmerling (Mon Nov 28 2016 - 08:39:05 PST)
  - Re: [AMBER] Etot = ************** with dtt=0.004 Thakur, Abhishek (Mon Nov 28 2016 - 08:43:09 PST)
    - Re: [AMBER] Etot = ************** with dtt=0.004 Roitberg,Adrian E (Mon Nov 28 2016 - 08:47:43 PST)
    - Re: [AMBER] Etot = ************** with dtt=0.004 Thakur, Abhishek (Mon Nov 28 2016 - 09:06:21 PST)
    - Re: [AMBER] Etot = ************** with dtt=0.004 Thakur, Abhishek (Mon Nov 28 2016 - 09:15:12 PST)
    - Re: [AMBER] Etot = ************** with dtt=0.004 Carlos Simmerling (Mon Nov 28 2016 - 09:22:13 PST)
    - Re: [AMBER] Etot = ************** with dtt=0.004 Thakur, Abhishek (Mon Nov 28 2016 - 09:45:25 PST)
    - Re: [AMBER] Etot = ************** with dtt=0.004 Nhai (Mon Nov 28 2016 - 10:01:38 PST)
    - Re: [AMBER] Etot = ************** with dtt=0.004 Ross Walker (Mon Nov 28 2016 - 12:21:35 PST)
[AMBER] MM-GBSA calculation in temperature other than 298 K Atila Petrosian (Mon Nov 28 2016 - 10:47:36 PST)
- Re: [AMBER] MM-GBSA calculation in temperature other than 298 K Hai Nguyen (Mon Nov 28 2016 - 11:13:06 PST)
[AMBER] RMSD for two different MDs Haining Liu (Mon Nov 28 2016 - 12:49:02 PST)
- Re: [AMBER] RMSD for two different MDs Thakur, Abhishek (Mon Nov 28 2016 - 13:27:53 PST)
  - Re: [AMBER] RMSD for two different MDs Adrian Roitberg (Mon Nov 28 2016 - 13:32:23 PST)
    - Re: [AMBER] RMSD for two different MDs David Cerutti (Mon Nov 28 2016 - 13:46:32 PST)
- Re: [AMBER] RMSD for two different MDs Daniel Roe (Tue Nov 29 2016 - 05:34:07 PST)
[AMBER] Fw: Problems with imaging Mark Waterhouse [RPG] (Mon Nov 28 2016 - 12:49:09 PST)
- Re: [AMBER] Fw: Problems with imaging Daniel Roe (Tue Nov 29 2016 - 05:59:31 PST)
  - Re: [AMBER] Fw: Problems with imaging Mark Waterhouse [RPG] (Wed Nov 30 2016 - 01:08:00 PST)
    - Re: [AMBER] Fw: Problems with imaging Daniel Roe (Wed Nov 30 2016 - 10:24:32 PST)
    - Re: [AMBER] Fw: Problems with imaging Mark Waterhouse [RPG] (Thu Dec 01 2016 - 03:37:35 PST)
    - Re: [AMBER] Fw: Problems with imaging Daniel Roe (Mon Jan 09 2017 - 06:25:41 PST)
[AMBER] cpptraj - trouble with autoimage and triclinic truncated octahedron DCD from NAMD Brian Radak (Tue Nov 29 2016 - 10:24:05 PST)
- Re: [AMBER] cpptraj - trouble with autoimage and triclinic truncated octahedron DCD from NAMD Daniel Roe (Tue Nov 29 2016 - 10:48:38 PST)
  - Re: [AMBER] cpptraj - trouble with autoimage and triclinic truncated octahedron DCD from NAMD Brian Radak (Tue Nov 29 2016 - 10:56:50 PST)
    - Re: [AMBER] cpptraj - trouble with autoimage and triclinic truncated octahedron DCD from NAMD Daniel Roe (Tue Nov 29 2016 - 11:26:29 PST)
    - Re: [AMBER] cpptraj - trouble with autoimage and triclinic truncated octahedron DCD from NAMD Brian Radak (Tue Nov 29 2016 - 11:34:18 PST)
    - Re: [AMBER] cpptraj - trouble with autoimage and triclinic truncated octahedron DCD from NAMD Daniel Roe (Tue Nov 29 2016 - 13:02:44 PST)
    - Re: [AMBER] cpptraj - trouble with autoimage and triclinic truncated octahedron DCD from NAMD Daniel Roe (Wed Nov 30 2016 - 11:18:17 PST)
    - Re: [AMBER] cpptraj - trouble with autoimage and triclinic truncated octahedron DCD from NAMD Brian Radak (Fri Dec 02 2016 - 13:47:45 PST)
    - Re: [AMBER] cpptraj - trouble with autoimage and triclinic truncated octahedron DCD from NAMD Daniel Roe (Tue Dec 06 2016 - 12:05:52 PST)
[AMBER] Error for copper atom type Shreeramesh (Tue Nov 29 2016 - 18:26:02 PST)
- Re: [AMBER] Error for copper atom type Elvis Martis (Tue Nov 29 2016 - 21:40:10 PST)
[AMBER] Force field files for ff99IDPs barsha bharadwaz (Wed Nov 30 2016 - 05:04:49 PST)
- Re: [AMBER] Force field files for ff99IDPs Carlos Simmerling (Wed Nov 30 2016 - 05:10:12 PST)
[AMBER] Issue with the gaff parameters for "nh" atom type Prajwal Nandekar (Wed Nov 30 2016 - 05:58:45 PST)
- Re: [AMBER] Issue with the gaff parameters for "nh" atom type Hirdesh Kumar (Wed Nov 30 2016 - 11:13:35 PST)
- Re: [AMBER] Issue with the gaff parameters for "nh" atom type David Case (Mon Dec 19 2016 - 05:22:13 PST)
[AMBER] question about calculated density in sander output file amaury paquet (Wed Nov 30 2016 - 06:22:01 PST)
- Re: [AMBER] question about calculated density in sander output file David A Case (Wed Nov 30 2016 - 11:39:05 PST)
[AMBER] selection of the residues when using MM-GBSA Hyun (Wed Nov 30 2016 - 08:38:08 PST)
- Re: [AMBER] selection of the residues when using MM-GBSA Jason Swails (Wed Nov 30 2016 - 13:31:39 PST)
[AMBER] mdfil: Error unknown flag: pdb_wat.prmtop Aishani Prem (Wed Nov 30 2016 - 15:32:29 PST)
- Re: [AMBER] mdfil: Error unknown flag: pdb_wat.prmtop Hai Nguyen (Wed Nov 30 2016 - 15:33:47 PST)
[AMBER] Collective Variable not "Strictly" Enforced: Adaptively Biased MD Simulations of type "COM_ANGLE" using "FLOODING" Emmanuel (Wed Nov 30 2016 - 22:08:29 PST)
- Re: [AMBER] Collective Variable not "Strictly" Enforced: Adaptively Biased MD Simulations of type "COM_ANGLE" using "FLOODING" Feng Pan (Fri Dec 02 2016 - 12:26:25 PST)
[AMBER] clustering doubt Mary Varughese (Wed Nov 30 2016 - 23:26:29 PST)
- Re: [AMBER] clustering doubt Achim Sandmann (Thu Dec 01 2016 - 02:26:24 PST)
  - Re: [AMBER] clustering doubt Mary Varughese (Thu Dec 01 2016 - 02:43:32 PST)
    - Re: [AMBER] clustering doubt Achim Sandmann (Thu Dec 01 2016 - 03:29:44 PST)
    - Re: [AMBER] clustering doubt Daniel Roe (Tue Dec 06 2016 - 12:09:21 PST)
    - Re: [AMBER] clustering doubt Mary Varughese (Tue Dec 06 2016 - 20:48:58 PST)
    - Re: [AMBER] clustering doubt Mary Varughese (Wed Dec 14 2016 - 02:34:34 PST)
    - Re: [AMBER] clustering doubt Daniel Roe (Wed Dec 14 2016 - 10:44:07 PST)
    - Re: [AMBER] clustering doubt Mary Varughese (Thu Dec 15 2016 - 01:54:37 PST)
    - Re: [AMBER] clustering doubt Nhai (Thu Dec 15 2016 - 05:51:11 PST)
    - Re: [AMBER] clustering doubt Daniel Roe (Thu Dec 15 2016 - 07:49:19 PST)
[AMBER] Atom type for middle nitrogen in dycyanamide? Mohd Farid Ismail (Thu Dec 01 2016 - 00:59:47 PST)
- Re: [AMBER] Atom type for middle nitrogen in dycyanamide? David A Case (Thu Dec 01 2016 - 10:28:09 PST)
[AMBER] question about pol_h in ambertool15 Thibaud von Erlach (Thu Dec 01 2016 - 02:30:32 PST)
- Re: [AMBER] question about pol_h in ambertool15 David A Case (Thu Dec 01 2016 - 18:54:30 PST)
  - Re: [AMBER] question about pol_h in ambertool15 Anon (Thu Dec 01 2016 - 19:13:20 PST)
- Re: [AMBER] question about pol_h in ambertool15 Thibaud von Erlach (Fri Dec 02 2016 - 00:24:45 PST)
[AMBER] trajectory analysis Carlos Romero (Thu Dec 01 2016 - 22:39:53 PST)
- Re: [AMBER] trajectory analysis Elvis Martis (Thu Dec 01 2016 - 22:45:38 PST)
[AMBER] multiple residues and solvatebox command Azade Yazdan Yar (Fri Dec 02 2016 - 04:24:22 PST)
- Re: [AMBER] multiple residues and solvatebox command David A Case (Fri Dec 02 2016 - 04:56:10 PST)
[AMBER] Slowly reducing restraints Dd H (Fri Dec 02 2016 - 05:28:05 PST)
- Re: [AMBER] Slowly reducing restraints Elvis Martis (Fri Dec 02 2016 - 05:36:30 PST)
[AMBER] ReCpHMD Optimal values of ntcnstph, ntrelax, nstlim and numexchg Fabrício Bracht (Mon Dec 05 2016 - 04:46:15 PST)
- Re: [AMBER] ReCpHMD Optimal values of ntcnstph, ntrelax, nstlim and numexchg Jason Swails (Mon Dec 05 2016 - 07:56:45 PST)
  - Re: [AMBER] ReCpHMD Optimal values of ntcnstph, ntrelax, nstlim and numexchg Adrian Roitberg (Mon Dec 05 2016 - 08:12:43 PST)
    - Re: [AMBER] ReCpHMD Optimal values of ntcnstph, ntrelax, nstlim and numexchg Jason Swails (Mon Dec 05 2016 - 08:28:40 PST)
[AMBER] CpHMD tutorial: how to generate the titration_curves.dat file in an automated way Eric Lang (Mon Dec 05 2016 - 08:36:38 PST)
- Re: [AMBER] CpHMD tutorial: how to generate the titration_curves.dat file in an automated way Fabrício Bracht (Mon Dec 05 2016 - 08:50:23 PST)
- Re: [AMBER] CpHMD tutorial: how to generate the titration_curves.dat file in an automated way Jason Swails (Mon Dec 05 2016 - 10:48:15 PST)
  - Re: [AMBER] CpHMD tutorial: how to generate the titration_curves.dat file in an automated way Eric Lang (Mon Dec 05 2016 - 12:25:14 PST)
[AMBER] MMGBSA vs MMPBSA Aronica, Pietro (Mon Dec 05 2016 - 20:10:48 PST)
- Re: [AMBER] MMGBSA vs MMPBSA Hai Nguyen (Mon Dec 05 2016 - 20:15:02 PST)
  - [AMBER] GIST: nan (not a number) in unreferenced water-water energy of the grid Bruno Falcone (Tue Dec 06 2016 - 06:40:18 PST)
    - Re: [AMBER] GIST: nan (not a number) in unreferenced water-water energy of the grid Steven Ramsey (Tue Dec 06 2016 - 08:59:50 PST)
    - Re: [AMBER] GIST: nan (not a number) in unreferenced water-water energy of the grid Bruno Falcone (Tue Dec 06 2016 - 09:27:54 PST)
    - Re: [AMBER] GIST: nan (not a number) in unreferenced water-water energy of the grid Steven Ramsey (Tue Dec 06 2016 - 09:41:38 PST)
    - Re: [AMBER] GIST: nan (not a number) in unreferenced water-water energy of the grid Daniel Roe (Tue Dec 06 2016 - 10:38:05 PST)
    - Re: [AMBER] GIST: nan (not a number) in unreferenced water-water energy of the grid Bruno Falcone (Tue Dec 06 2016 - 10:44:06 PST)
    - Re: [AMBER] GIST: nan (not a number) in unreferenced water-water energy of the grid Bruno Falcone (Wed Dec 07 2016 - 11:41:36 PST)
    - Re: [AMBER] GIST: nan (not a number) in unreferenced water-water energy of the grid Daniel Roe (Wed Dec 07 2016 - 13:07:50 PST)
  - Re: [AMBER] MMGBSA vs MMPBSA Ray Luo (Tue Dec 06 2016 - 09:03:46 PST)
    - Re: [AMBER] MMGBSA vs MMPBSA Aronica, Pietro (Tue Dec 06 2016 - 18:14:13 PST)
    - Re: [AMBER] MMGBSA vs MMPBSA Ray Luo (Wed Dec 07 2016 - 10:01:32 PST)
[AMBER] Parmchk2 and dihedral parameters Andreas Gavrielides (Tue Dec 06 2016 - 02:28:37 PST)
- Re: [AMBER] Parmchk2 and dihedral parameters David A Case (Tue Dec 06 2016 - 04:45:47 PST)
  - Re: [AMBER] Parmchk2 and dihedral parameters Andreas Gavrielides (Tue Dec 06 2016 - 05:02:49 PST)
    - Re: [AMBER] Parmchk2 and dihedral parameters David A Case (Tue Dec 06 2016 - 07:02:26 PST)
[AMBER] How to turn off non-bonded interactions A kS (Tue Dec 06 2016 - 03:36:43 PST)
- Re: [AMBER] How to turn off non-bonded interactions David A Case (Tue Dec 06 2016 - 04:48:43 PST)
Re: [AMBER] Paramfit for multiple molecules (Robin Betz) Sven Hackbusch (Tue Dec 06 2016 - 13:44:35 PST)
[AMBER] Amber 16: ** NFE-Error ** : Cannot read &colvar namelist! Ruth Helena Tichauer (Wed Dec 07 2016 - 04:32:09 PST)
- Re: [AMBER] Amber 16: ** NFE-Error ** : Cannot read &colvar namelist! Daniel Roe (Wed Dec 07 2016 - 07:07:36 PST)
  - Re: [AMBER] Amber 16: ** NFE-Error ** : Cannot read &colvar namelist! Ruth Helena Tichauer (Wed Dec 07 2016 - 10:08:26 PST)
    - Re: [AMBER] Amber 16: ** NFE-Error ** : Cannot read &colvar namelist! Feng Pan (Wed Dec 07 2016 - 10:26:03 PST)
    - Re: [AMBER] Amber 16: ** NFE-Error ** : Cannot read &colvar namelist! Ruth Helena Tichauer (Thu Dec 08 2016 - 09:40:28 PST)
[AMBER] Explicit solvent CpHMD calculation with Amber14 Tsibela German Tebello Mofokeng (Wed Dec 07 2016 - 05:23:24 PST)
- Re: [AMBER] Explicit solvent CpHMD calculation with Amber14 Jason Swails (Wed Dec 07 2016 - 05:35:57 PST)
  - Re: [AMBER] Explicit solvent CpHMD calculation with Amber14 Carlos Simmerling (Wed Dec 07 2016 - 05:38:30 PST)
    - Re: [AMBER] Explicit solvent CpHMD calculation with Amber14 Tsibela German Tebello Mofokeng (Wed Dec 07 2016 - 05:49:02 PST)
[AMBER] The AmberTools 16 build errors Juwen (Wed Dec 07 2016 - 16:35:23 PST)
- Re: [AMBER] The AmberTools 16 build errors Nhai (Wed Dec 07 2016 - 16:39:13 PST)
  - Re: [AMBER] The AmberTools 16 build errors Nhai (Wed Dec 07 2016 - 16:40:45 PST)
  - Re: [AMBER] The AmberTools 16 build errors Juwen (Wed Dec 07 2016 - 16:46:48 PST)
    - Re: [AMBER] The AmberTools 16 build errors Nhai (Wed Dec 07 2016 - 16:51:32 PST)
[AMBER] Query regarding Ligand Binding Metalloprotein with MCPB.py Abhilash J (Wed Dec 07 2016 - 21:34:21 PST)
[AMBER] Parallel installation of MMPBSA.py.MPI failed MOHD HOMAIDUR RAHMAN (Thu Dec 08 2016 - 02:03:37 PST)
- Re: [AMBER] Parallel installation of MMPBSA.py.MPI failed Jason Swails (Thu Dec 08 2016 - 08:35:42 PST)
[AMBER] NADH antechamber Andreas Tosstorff (Thu Dec 08 2016 - 07:45:17 PST)
- Re: [AMBER] NADH antechamber FyD (Thu Dec 08 2016 - 08:26:16 PST)
- Re: [AMBER] NADH antechamber David A Case (Thu Dec 08 2016 - 11:37:15 PST)
  - Re: [AMBER] NADH antechamber Andreas Tosstorff (Fri Dec 09 2016 - 00:31:37 PST)
[AMBER] QM/MM/MD g09 interface issues, David Poole (Thu Dec 08 2016 - 08:01:14 PST)
- Re: [AMBER] QM/MM/MD g09 interface issues, Fabrício Bracht (Thu Dec 08 2016 - 08:46:25 PST)
[AMBER] Installation of AMBER on Centos Rocks 6.2 Yasir Israr (Thu Dec 08 2016 - 18:23:09 PST)
- Re: [AMBER] Installation of AMBER on Centos Rocks 6.2 Elvis Martis (Thu Dec 08 2016 - 19:08:16 PST)
  - Re: [AMBER] Installation of AMBER on Centos Rocks 6.2 Yasir Israr (Thu Dec 08 2016 - 20:09:02 PST)
- Re: [AMBER] Installation of AMBER on Centos Rocks 6.2 Elvis Martis (Thu Dec 08 2016 - 21:26:12 PST)
  - Re: [AMBER] Installation of AMBER on Centos Rocks 6.2 yasir.orionsolutions.co.in (Sat Dec 10 2016 - 00:36:32 PST)
    - Re: [AMBER] Installation of AMBER on Centos Rocks 6.2 Hai Nguyen (Sat Dec 10 2016 - 00:39:55 PST)
    - Re: [AMBER] Installation of AMBER on Centos Rocks 6.2 yasir.orionsolutions.co.in (Sat Dec 10 2016 - 00:43:21 PST)
    - Re: [AMBER] Installation of AMBER on Centos Rocks 6.2 Hai Nguyen (Sat Dec 10 2016 - 00:48:08 PST)
    - Re: [AMBER] Installation of AMBER on Centos Rocks 6.2 yasir.orionsolutions.co.in (Sat Dec 10 2016 - 00:53:23 PST)
    - Re: [AMBER] Installation of AMBER on Centos Rocks 6.2 yasir.orionsolutions.co.in (Sat Dec 10 2016 - 00:57:55 PST)
    - Re: [AMBER] Installation of AMBER on Centos Rocks 6.2 yasir.orionsolutions.co.in (Sat Dec 10 2016 - 02:36:19 PST)
    - Re: [AMBER] Installation of AMBER on Centos Rocks 6.2 David A Case (Sat Dec 10 2016 - 06:44:52 PST)
[AMBER] Fitting of rms2d Mike Nemec (Fri Dec 09 2016 - 05:56:23 PST)
- Re: [AMBER] Fitting of rms2d Carlos Simmerling (Fri Dec 09 2016 - 05:58:45 PST)
[AMBER] Eigenvector visualization in Nmode JPB (Fri Dec 09 2016 - 07:32:36 PST)
- Re: [AMBER] Eigenvector visualization in Nmode The Cromicus Productions (Fri Dec 09 2016 - 14:41:23 PST)
  - Re: [AMBER] Eigenvector visualization in Nmode The Cromicus Productions (Fri Dec 09 2016 - 14:43:51 PST)
- Re: [AMBER] Eigenvector visualization in Nmode David A Case (Fri Dec 09 2016 - 18:25:40 PST)
[AMBER] HMR with ParmEd for PSF/PDB inputs? Brian Radak (Fri Dec 09 2016 - 07:59:21 PST)
- Re: [AMBER] HMR with ParmEd for PSF/PDB inputs? Hai Nguyen (Fri Dec 09 2016 - 09:07:02 PST)
  - Re: [AMBER] HMR with ParmEd for PSF/PDB inputs? Brian Radak (Fri Dec 09 2016 - 09:18:32 PST)
    - Re: [AMBER] HMR with ParmEd for PSF/PDB inputs? Hai Nguyen (Fri Dec 09 2016 - 09:25:45 PST)
    - Re: [AMBER] HMR with ParmEd for PSF/PDB inputs? Brian Radak (Fri Dec 09 2016 - 09:28:05 PST)
    - Re: [AMBER] HMR with ParmEd for PSF/PDB inputs? Hai Nguyen (Fri Dec 09 2016 - 09:34:10 PST)
    - Re: [AMBER] HMR with ParmEd for PSF/PDB inputs? Jason Swails (Sat Dec 10 2016 - 19:46:57 PST)
    - Re: [AMBER] HMR with ParmEd for PSF/PDB inputs? Brian Radak (Sun Dec 11 2016 - 10:21:23 PST)
    - Re: [AMBER] HMR with ParmEd for PSF/PDB inputs? Jason Swails (Sun Dec 11 2016 - 14:15:10 PST)
    - Re: [AMBER] HMR with ParmEd for PSF/PDB inputs? Brian Radak (Mon Dec 12 2016 - 07:50:51 PST)
    - Re: [AMBER] HMR with ParmEd for PSF/PDB inputs? Nhai (Mon Dec 12 2016 - 07:52:39 PST)
    - Re: [AMBER] HMR with ParmEd for PSF/PDB inputs? Nhai (Mon Dec 12 2016 - 07:53:35 PST)
    - Re: [AMBER] HMR with ParmEd for PSF/PDB inputs? Jason Swails (Tue Dec 13 2016 - 06:47:04 PST)
[AMBER] Freeze Atoms in Nab The Cromicus Productions (Fri Dec 09 2016 - 13:05:12 PST)
- Re: [AMBER] Freeze Atoms in Nab David A Case (Fri Dec 09 2016 - 18:17:27 PST)
[AMBER] error 睿 ? (Fri Dec 09 2016 - 18:11:09 PST)
- Re: [AMBER] error Hai Nguyen (Fri Dec 09 2016 - 21:55:33 PST)
  - Re: [AMBER] error 睿翟 (Fri Dec 09 2016 - 22:02:44 PST)
- Re: [AMBER] error David A Case (Sat Dec 10 2016 - 06:35:07 PST)
[AMBER] 10. QM/MM/MD g09 interface issues, now tleap David Poole (Sun Dec 11 2016 - 10:42:03 PST)
- Re: [AMBER] 10. QM/MM/MD g09 interface issues, now tleap David Case (Mon Dec 19 2016 - 05:16:23 PST)
- Re: [AMBER] 10. QM/MM/MD g09 interface issues, now tleap David Poole (Tue Dec 20 2016 - 12:11:39 PST)
  - Re: [AMBER] 10. QM/MM/MD g09 interface issues, now tleap David Case (Tue Dec 20 2016 - 18:09:50 PST)
[AMBER] Questions regarding Installation of AMBER 16 James Kress (Sun Dec 11 2016 - 13:07:50 PST)
- Re: [AMBER] Questions regarding Installation of AMBER 16 Hai Nguyen (Sun Dec 11 2016 - 13:22:48 PST)
- Re: [AMBER] Questions regarding Installation of AMBER 16 Daniel Roe (Mon Dec 12 2016 - 11:52:07 PST)
[AMBER] [Amber] Calculation of Velocity Autocorrelation Function The Cromicus Productions (Sun Dec 11 2016 - 14:10:04 PST)
- Re: [AMBER] [Amber] Calculation of Velocity Autocorrelation Function Daniel Roe (Mon Dec 12 2016 - 05:15:06 PST)
[AMBER] Untwisting a molecule The Cromicus Productions (Sun Dec 11 2016 - 14:50:07 PST)
- Re: [AMBER] Untwisting a molecule David A Case (Sun Dec 11 2016 - 18:05:21 PST)
  - Re: [AMBER] Untwisting a molecule Bill Ross (Sun Dec 11 2016 - 18:12:28 PST)
    - Re: [AMBER] Untwisting a molecule The Cromicus Productions (Sun Dec 11 2016 - 18:15:45 PST)
    - Re: [AMBER] Untwisting a molecule Bill Ross (Sun Dec 11 2016 - 18:31:41 PST)
    - Re: [AMBER] Untwisting a molecule Josh Berryman (Mon Dec 12 2016 - 02:41:20 PST)
    - Re: [AMBER] Untwisting a molecule Christina Bergonzo (Mon Dec 12 2016 - 04:38:14 PST)
    - Re: [AMBER] Untwisting a molecule Daniel Roe (Mon Dec 12 2016 - 05:04:06 PST)
[AMBER] different frequencies for mdout/mdinfo writes? Bill Ross (Sun Dec 11 2016 - 17:13:42 PST)
- Re: [AMBER] different frequencies for mdout/mdinfo writes? Daniel Roe (Mon Dec 12 2016 - 11:46:25 PST)
- Re: [AMBER] different frequencies for mdout/mdinfo writes? Lorenzo Gontrani (Mon Dec 12 2016 - 11:54:24 PST)
[AMBER] Magnesium ion and MMPBSA/GBSA Francesco Gentile (Sun Dec 11 2016 - 23:44:04 PST)
- Re: [AMBER] Magnesium ion and MMPBSA/GBSA Elvis Martis (Sun Dec 11 2016 - 23:55:59 PST)
- Re: [AMBER] Magnesium ion and MMPBSA/GBSA David A Case (Mon Dec 12 2016 - 08:34:10 PST)
- Re: [AMBER] Magnesium ion and MMPBSA/GBSA Ray Luo (Mon Dec 12 2016 - 08:52:48 PST)
  - Re: [AMBER] Magnesium ion and MMPBSA/GBSA Brian Radak (Mon Dec 12 2016 - 09:11:11 PST)
[AMBER] AmberTools16 installation problem a.jarmula.nencki.gov.pl (Mon Dec 12 2016 - 04:19:52 PST)
- Re: [AMBER] AmberTools16 installation problem David A Case (Mon Dec 12 2016 - 04:46:29 PST)
  - Re: [AMBER] AmberTools16 installation problem David A Case (Mon Dec 12 2016 - 04:48:03 PST)
    - Re: [AMBER] AmberTools16 installation problem a.jarmula.nencki.gov.pl (Mon Dec 19 2016 - 18:34:42 PST)
[AMBER] acdoctor: Warning: There are no hydrogen and halogens in this molecule, it is highly possible that this molecule has open valence Andreas Tosstorff (Mon Dec 12 2016 - 05:12:11 PST)
- Re: [AMBER] acdoctor: Warning: There are no hydrogen and halogens in this molecule, it is highly possible that this molecule has open valence David A Case (Mon Dec 12 2016 - 08:27:10 PST)
  - Re: [AMBER] acdoctor: Warning: There are no hydrogen and halogens in this molecule, it is highly possible that this molecule has open valence Andreas Tosstorff (Tue Dec 13 2016 - 00:40:52 PST)
    - Re: [AMBER] acdoctor: Warning: There are no hydrogen and halogens in this molecule, it is highly possible that this molecule has open valence Andreas Tosstorff (Tue Dec 13 2016 - 01:01:37 PST)
    - Re: [AMBER] acdoctor: Warning: There are no hydrogen and halogens in this molecule, it is highly possible that this molecule has open valence David A Case (Tue Dec 13 2016 - 06:07:10 PST)
    - Re: [AMBER] acdoctor: Warning: There are no hydrogen and halogens in this molecule, it is highly possible that this molecule has open valence Andreas Tosstorff (Tue Dec 13 2016 - 06:14:12 PST)
    - Re: [AMBER] acdoctor: Warning: There are no hydrogen and halogens in this molecule, it is highly possible that this molecule has open valence Bruno Falcone (Tue Dec 13 2016 - 06:33:25 PST)
    - Re: [AMBER] acdoctor: Warning: There are no hydrogen and halogens in this molecule, it is highly possible that this molecule has open valence Andreas Tosstorff (Tue Dec 13 2016 - 06:43:25 PST)
[AMBER] Editing residue in PDB file Nikolay N. Kuzmich (Mon Dec 12 2016 - 07:03:56 PST)
- Re: [AMBER] Editing residue in PDB file David A Case (Mon Dec 12 2016 - 08:17:50 PST)
[AMBER] pka of CYS Sowmya Indrakumar (Mon Dec 12 2016 - 12:14:03 PST)
- Re: [AMBER] pka of CYS Eric Lang (Mon Dec 12 2016 - 23:33:05 PST)
- Re: [AMBER] pka of CYS Carlos Simmerling (Tue Dec 13 2016 - 03:09:57 PST)
  - Re: [AMBER] pka of CYS Eric Lang (Tue Dec 13 2016 - 05:43:44 PST)
    - Re: [AMBER] pka of CYS Adrian Roitberg (Tue Dec 13 2016 - 06:18:36 PST)
    - Re: [AMBER] pka of CYS Sowmya Indrakumar (Tue Dec 13 2016 - 07:21:59 PST)
    - Re: [AMBER] pka of CYS Andreas Tosstorff (Tue Dec 13 2016 - 07:28:10 PST)
    - Re: [AMBER] pka of CYS Sowmya Indrakumar (Tue Dec 13 2016 - 08:07:58 PST)
    - Re: [AMBER] pka of CYS Jason Swails (Tue Dec 13 2016 - 09:42:35 PST)
    - Re: [AMBER] pka of CYS Carlos Simmerling (Tue Dec 13 2016 - 10:22:53 PST)
    - Re: [AMBER] pka of CYS Jason Swails (Tue Dec 13 2016 - 10:55:55 PST)
    - Re: [AMBER] pka of CYS Carlos Simmerling (Tue Dec 13 2016 - 11:27:36 PST)
    - Re: [AMBER] pka of CYS Sowmya Indrakumar (Fri Dec 16 2016 - 07:33:28 PST)
    - Re: [AMBER] pka of CYS Eric Lang (Fri Dec 16 2016 - 07:59:11 PST)
[AMBER] REMD with pressure coupling Neale, Christopher Andrew (Mon Dec 12 2016 - 12:44:24 PST)
- Re: [AMBER] REMD with pressure coupling Daniel Roe (Mon Dec 12 2016 - 13:06:02 PST)
- Re: [AMBER] REMD with pressure coupling Adrian Roitberg (Tue Dec 13 2016 - 06:23:39 PST)
- Re: [AMBER] REMD with pressure coupling Neale, Christopher Andrew (Wed Dec 14 2016 - 14:48:37 PST)
  - Re: [AMBER] REMD with pressure coupling Giovanni Bussi (Thu Dec 15 2016 - 00:07:17 PST)
    - Re: [AMBER] REMD with pressure coupling Jason Swails (Thu Dec 15 2016 - 18:35:17 PST)
    - Re: [AMBER] REMD with pressure coupling Giovanni Bussi (Fri Dec 16 2016 - 00:21:19 PST)
- Re: [AMBER] REMD with pressure coupling Neale, Christopher Andrew (Mon Dec 19 2016 - 09:12:50 PST)
- Re: [AMBER] REMD with pressure coupling Neale, Christopher Andrew (Tue Dec 20 2016 - 09:09:43 PST)
  - Re: [AMBER] REMD with pressure coupling Feng Pan (Thu Dec 22 2016 - 08:35:20 PST)
    - Re: [AMBER] REMD with pressure coupling Chris Neale (Thu Dec 22 2016 - 09:43:17 PST)
    - Re: [AMBER] REMD with pressure coupling Feng Pan (Thu Dec 22 2016 - 18:47:25 PST)
    - Re: [AMBER] REMD with pressure coupling Chris Neale (Thu Dec 22 2016 - 19:02:08 PST)
    - Re: [AMBER] REMD with pressure coupling Feng Pan (Thu Dec 22 2016 - 19:25:26 PST)
  - Re: [AMBER] REMD with pressure coupling Jason Swails (Thu Dec 22 2016 - 13:26:23 PST)
    - Re: [AMBER] REMD with pressure coupling Chris Neale (Thu Dec 22 2016 - 19:10:06 PST)
[AMBER] Problems during solvation of molecule from Protein Data Bank The Cromicus Productions (Mon Dec 12 2016 - 13:52:15 PST)
- Re: [AMBER] Problems during solvation of molecule from Protein Data Bank The Cromicus Productions (Mon Dec 12 2016 - 13:53:04 PST)
- Re: [AMBER] Problems during solvation of molecule from Protein Data Bank Carlos Simmerling (Mon Dec 12 2016 - 16:14:47 PST)
- Re: [AMBER] Problems during solvation of molecule from Protein Data Bank David A Case (Mon Dec 12 2016 - 17:52:49 PST)
  - Re: [AMBER] Problems during solvation of molecule from Protein Data Bank Sowmya Indrakumar (Tue Dec 13 2016 - 03:05:03 PST)
[AMBER] MMPBSA Quasi-Harmonic Entropy Sachin Natesh (Mon Dec 12 2016 - 20:16:26 PST)
[AMBER] Zinc Oxide and protein simulation with AMBER vivek m (Tue Dec 13 2016 - 01:35:19 PST)
- Re: [AMBER] Zinc Oxide and protein simulation with AMBER David A Case (Tue Dec 13 2016 - 07:34:53 PST)
  - Re: [AMBER] Zinc Oxide and protein simulation with AMBER vivek m (Tue Dec 13 2016 - 09:50:41 PST)
    - Re: [AMBER] Zinc Oxide and protein simulation with AMBER Pengfei Li (Tue Dec 13 2016 - 11:47:10 PST)
    - Re: [AMBER] Zinc Oxide and protein simulation with AMBER vivek m (Wed Dec 21 2016 - 10:17:57 PST)
    - Re: [AMBER] Zinc Oxide and protein simulation with AMBER Pengfei Li (Thu Dec 22 2016 - 08:46:49 PST)
[AMBER] Minimum distance between imgaes A kS (Tue Dec 13 2016 - 05:39:07 PST)
- Re: [AMBER] Minimum distance between imgaes Daniel Roe (Tue Dec 13 2016 - 05:44:41 PST)
  - Re: [AMBER] Minimum distance between imgaes A kS (Tue Dec 13 2016 - 05:48:05 PST)
    - Re: [AMBER] Minimum distance between imgaes Daniel Roe (Tue Dec 13 2016 - 05:51:13 PST)
    - Re: [AMBER] Minimum distance between imgaes A kS (Tue Dec 13 2016 - 06:02:21 PST)
[AMBER] Re_Re: Editing residue in PDB file Nikolay N. Kuzmich (Tue Dec 13 2016 - 06:27:10 PST)
- Re: [AMBER] Re_Re: Editing residue in PDB file David A Case (Tue Dec 13 2016 - 07:30:41 PST)
[AMBER] The right character for logical AND in mask definition in MMPBSA ? Marek Maly (Tue Dec 13 2016 - 09:40:59 PST)
- Re: [AMBER] The right character for logical AND in mask definition in MMPBSA ? Jason Swails (Tue Dec 13 2016 - 09:47:29 PST)
  - Re: [AMBER] The right character for logical AND in mask definition in MMPBSA ? Marek Maly (Tue Dec 13 2016 - 13:28:15 PST)
[AMBER] Fwd: AmberTools 16: IBM XL Compiler Support James Ostrander (Tue Dec 13 2016 - 12:52:02 PST)
- Re: [AMBER] Fwd: AmberTools 16: IBM XL Compiler Support Jason Swails (Tue Dec 13 2016 - 22:14:38 PST)
  - Re: [AMBER] Fwd: AmberTools 16: IBM XL Compiler Support James Ostrander (Tue Dec 20 2016 - 11:29:34 PST)
    - Re: [AMBER] Fwd: AmberTools 16: IBM XL Compiler Support James Ostrander (Tue Dec 20 2016 - 11:37:58 PST)
    - Re: [AMBER] Fwd: AmberTools 16: IBM XL Compiler Support Hai Nguyen (Tue Dec 20 2016 - 13:32:43 PST)
    - Re: [AMBER] Fwd: AmberTools 16: IBM XL Compiler Support Jason Swails (Tue Dec 20 2016 - 13:36:58 PST)
[AMBER] Hydrogen bond calculataion richa anand (Tue Dec 13 2016 - 23:01:08 PST)
- Re: [AMBER] Hydrogen bond calculataion Daniel Roe (Wed Dec 14 2016 - 10:39:24 PST)
[AMBER] mmpbsa snapshots Mary Varughese (Wed Dec 14 2016 - 00:18:31 PST)
- Re: [AMBER] mmpbsa snapshots Elvis Martis (Wed Dec 14 2016 - 01:10:06 PST)
  - Re: [AMBER] mmpbsa snapshots Mary Varughese (Wed Dec 14 2016 - 01:51:19 PST)
- Re: [AMBER] mmpbsa snapshots Elvis Martis (Wed Dec 14 2016 - 02:46:28 PST)
  - Re: [AMBER] mmpbsa snapshots Mary Varughese (Wed Dec 14 2016 - 02:58:47 PST)
[AMBER] Frequencies in AMBER, obtaining the hessian Stregone (Wed Dec 14 2016 - 03:14:20 PST)
- Re: [AMBER] Frequencies in AMBER, obtaining the hessian David A Case (Wed Dec 14 2016 - 05:06:20 PST)
[AMBER] Uridine diphosphate rhamnose (UDP-Rha) Imma Speciale (Wed Dec 14 2016 - 07:10:13 PST)
- Re: [AMBER] Uridine diphosphate rhamnose (UDP-Rha) David A Case (Wed Dec 14 2016 - 08:16:03 PST)
- Re: [AMBER] Uridine diphosphate rhamnose (UDP-Rha) FyD (Thu Dec 15 2016 - 10:06:29 PST)
[AMBER] sviol script error ? Benjamin Chagot (Wed Dec 14 2016 - 08:08:52 PST)
- Re: [AMBER] sviol script error ? David A Case (Thu Dec 15 2016 - 06:13:29 PST)
[AMBER] cpptraj cluster -representative structure Thomas Pochapsky (Wed Dec 14 2016 - 08:13:54 PST)
- Re: [AMBER] cpptraj cluster -representative structure Elvis Martis (Wed Dec 14 2016 - 08:23:46 PST)
- Re: [AMBER] cpptraj cluster -representative structure Thomas Cheatham (Wed Dec 14 2016 - 10:38:55 PST)
  - Re: [AMBER] cpptraj cluster -representative structure Thomas Pochapsky (Wed Dec 14 2016 - 11:29:32 PST)
[AMBER] Constant pH across membrane Fabrício Bracht (Wed Dec 14 2016 - 15:49:34 PST)
- Re: [AMBER] Constant pH across membrane Jason Swails (Wed Dec 14 2016 - 20:22:20 PST)
  - Re: [AMBER] Constant pH across membrane Fabrício Bracht (Thu Dec 15 2016 - 04:58:06 PST)
    - Re: [AMBER] Constant pH across membrane Adrian Roitberg (Thu Dec 15 2016 - 06:01:10 PST)
    - Re: [AMBER] Constant pH across membrane Fabrício Bracht (Thu Dec 15 2016 - 06:45:14 PST)
[AMBER] About Constant pH Molecular Dynamics 上海科技大学吴萌 (Wed Dec 14 2016 - 17:49:50 PST)
[AMBER] Two different graphics cards in the same PC for pmemd.cuda Anton Perera (Wed Dec 14 2016 - 20:09:28 PST)
- Re: [AMBER] Two different graphics cards in the same PC for pmemd.cuda Elvis Martis (Wed Dec 14 2016 - 20:17:09 PST)
- Re: [AMBER] Two different graphics cards in the same PC for pmemd.cuda Elvis Martis (Wed Dec 14 2016 - 20:23:25 PST)
[AMBER] difference between %occupied and lifetime in hydrogen bond analysis Andrew Bostick (Thu Dec 15 2016 - 00:17:32 PST)
- Re: [AMBER] difference between %occupied and lifetime in hydrogen bond analysis Daniel Roe (Thu Dec 15 2016 - 08:18:01 PST)
[AMBER] pmemd.cuda incomplete output file Andreas Tosstorff (Thu Dec 15 2016 - 06:59:43 PST)
- Re: [AMBER] pmemd.cuda incomplete output file Andreas Tosstorff (Thu Dec 15 2016 - 13:31:30 PST)
  - Re: [AMBER] pmemd.cuda incomplete output file Niel Henriksen (Thu Dec 15 2016 - 16:39:56 PST)
    - Re: [AMBER] pmemd.cuda incomplete output file Andreas Tosstorff (Thu Dec 15 2016 - 23:15:59 PST)
    - Re: [AMBER] pmemd.cuda incomplete output file Hai Nguyen (Thu Dec 15 2016 - 23:32:28 PST)
    - Re: [AMBER] pmemd.cuda incomplete output file Andreas Tosstorff (Thu Dec 15 2016 - 23:46:47 PST)
    - Re: [AMBER] pmemd.cuda incomplete output file Niel Henriksen (Fri Dec 16 2016 - 05:51:51 PST)
- Re: [AMBER] pmemd.cuda incomplete output file David A Case (Fri Dec 16 2016 - 06:01:50 PST)
  - Re: [AMBER] pmemd.cuda incomplete output file Andreas Tosstorff (Sun Dec 18 2016 - 05:27:12 PST)
    - Re: [AMBER] pmemd.cuda incomplete output file David Case (Sun Dec 18 2016 - 05:45:01 PST)
    - Re: [AMBER] pmemd.cuda incomplete output file Andreas Tosstorff (Thu Dec 22 2016 - 07:39:27 PST)
    - Re: [AMBER] pmemd.cuda incomplete output file Niel Henriksen (Thu Dec 22 2016 - 07:58:17 PST)
[AMBER] Remove water from mdvel file The Cromicus Productions (Thu Dec 15 2016 - 13:25:16 PST)
- Re: [AMBER] Remove water from mdvel file Nhai (Thu Dec 15 2016 - 16:20:12 PST)
  - Re: [AMBER] Remove water from mdvel file The Cromicus Productions (Thu Dec 15 2016 - 17:30:16 PST)
[AMBER] Specify Grid Origin in 3D-RISM - Is it possible? Lucia Fusani (Fri Dec 16 2016 - 06:45:16 PST)
- Re: [AMBER] Specify Grid Origin in 3D-RISM - Is it possible? George Giambasu (Fri Dec 16 2016 - 07:19:50 PST)
[AMBER] ensuring lack of non-equilibrium jolt on restart Neale, Christopher Andrew (Fri Dec 16 2016 - 10:30:02 PST)
- Re: [AMBER] ensuring lack of non-equilibrium jolt on restart David Case (Sun Dec 18 2016 - 05:52:09 PST)
[AMBER] Unknown atom type EP A kS (Sat Dec 17 2016 - 03:53:09 PST)
- Re: [AMBER] Unknown atom type EP David Case (Sat Dec 17 2016 - 07:49:16 PST)
  - Re: [AMBER] Unknown atom type EP A kS (Sun Dec 18 2016 - 06:34:32 PST)
[AMBER] Constant pH Molecular Dynamics for membrane protein 上海科技大学吴萌 (Sun Dec 18 2016 - 18:01:43 PST)
- Re: [AMBER] Constant pH Molecular Dynamics for membrane protein Jason Swails (Sun Dec 18 2016 - 20:57:07 PST)
[AMBER] TI calculation problem in pmemd cuiyinglukitty (Sun Dec 18 2016 - 22:34:12 PST)
- Re: [AMBER] TI calculation problem in pmemd Hannes Loeffler (Sun Dec 18 2016 - 23:48:53 PST)
[AMBER] parmchk2 multiple parameters Andreas Gavrielides (Mon Dec 19 2016 - 06:53:01 PST)
- Re: [AMBER] parmchk2 multiple parameters David Case (Mon Dec 19 2016 - 09:39:24 PST)
  - Re: [AMBER] parmchk2 multiple parameters Andreas Gavrielides (Mon Dec 19 2016 - 09:47:51 PST)
[AMBER] Error in rst file Mohaddeseh Habibzadeh (Mon Dec 19 2016 - 07:54:53 PST)
- Re: [AMBER] Error in rst file Nhai (Mon Dec 19 2016 - 08:11:19 PST)
  - Re: [AMBER] Error in rst file Mohaddeseh Habibzadeh (Mon Dec 19 2016 - 08:26:22 PST)
    - Re: [AMBER] Error in rst file Nhai (Mon Dec 19 2016 - 08:41:01 PST)
    - Re: [AMBER] Error in rst file Mohaddeseh Habibzadeh (Mon Dec 19 2016 - 09:34:05 PST)
    - Re: [AMBER] Error in rst file Mohaddeseh Habibzadeh (Tue Dec 20 2016 - 00:45:04 PST)
    - Re: [AMBER] Error in rst file David Case (Tue Dec 20 2016 - 05:27:34 PST)
    - Re: [AMBER] Error in rst file Mohaddeseh Habibzadeh (Tue Dec 20 2016 - 07:26:59 PST)
[AMBER] Amber16 on GPUs and speed differences between CUDA_VISIBLE_DEVICES=0, 1 or 0, 2 Neale, Christopher Andrew (Mon Dec 19 2016 - 10:09:00 PST)
[AMBER] Amber16 on GPUs and speed differences between CUDA_VISIBLE_DEVICES=0, 1 or 0, 2 Neale, Christopher Andrew (Mon Dec 19 2016 - 10:31:19 PST)
- Re: [AMBER] Amber16 on GPUs and speed differences between CUDA_VISIBLE_DEVICES=0, 1 or 0, 2 Andreas Tosstorff (Mon Dec 19 2016 - 13:32:17 PST)
[AMBER] Amber16 on GPUs and speed differences between CUDA_VISIBLE_DEVICES=0, 1 or 0, 2 Neale, Christopher Andrew (Mon Dec 19 2016 - 11:22:21 PST)
[AMBER] locating cpinutil.py file Tsibela German Tebello Mofokeng (Mon Dec 19 2016 - 11:29:00 PST)
- Re: [AMBER] locating cpinutil.py file Hai Nguyen (Mon Dec 19 2016 - 11:32:52 PST)
[AMBER] Benign typo for a constant in barostats.F90 Neale, Christopher Andrew (Mon Dec 19 2016 - 13:52:00 PST)
[AMBER] ERROR no map function for HH12 ARG srinivas penumutchu (Mon Dec 19 2016 - 13:53:11 PST)
- Re: [AMBER] ERROR no map function for HH12 ARG David Case (Tue Dec 20 2016 - 05:20:13 PST)
[AMBER] Error: The system has extended beyond the extent of the virtual box. Taylor, Miles (Mon Dec 19 2016 - 19:11:00 PST)
- Re: [AMBER] Error: The system has extended beyond the extent of the virtual box. Nhai (Mon Dec 19 2016 - 22:11:41 PST)
[AMBER] bad atom type MN2+ ions in the binding free energy decomposition (Amber14) 袁浩亮 (Tue Dec 20 2016 - 06:25:27 PST)
- Re: [AMBER] bad atom type MN2+ ions in the binding free energy decomposition (Amber14) Elvis Martis (Tue Dec 20 2016 - 07:43:58 PST)
- Re: [AMBER] bad atom type MN2+ ions in the binding free energy decomposition (Amber14) 袁浩亮 (Tue Dec 20 2016 - 19:33:22 PST)
[AMBER] How to have a certain number of water molecules? Azade Yazdan Yar (Tue Dec 20 2016 - 07:39:07 PST)
- Re: [AMBER] How to have a certain number of water molecules? David Case (Tue Dec 20 2016 - 10:15:35 PST)
  - Re: [AMBER] How to have a certain number of water molecules? Azade Yazdan Yar (Fri Jan 13 2017 - 02:57:49 PST)
    - Re: [AMBER] How to have a certain number of water molecules? David Case (Fri Jan 13 2017 - 10:29:43 PST)
[AMBER] problem building Amber 16 with Intel compilers Susan Chacko (Tue Dec 20 2016 - 08:42:19 PST)
- Re: [AMBER] problem building Amber 16 with Intel compilers Hai Nguyen (Tue Dec 20 2016 - 08:52:35 PST)
  - Re: [AMBER] problem building Amber 16 with Intel compilers Hai Nguyen (Tue Dec 20 2016 - 08:56:43 PST)
    - Re: [AMBER] problem building Amber 16 with Intel compilers Susan Chacko (Tue Dec 20 2016 - 09:10:20 PST)
  - Re: [AMBER] problem building Amber 16 with Intel compilers Susan Chacko (Tue Dec 20 2016 - 08:59:31 PST)
    - Re: [AMBER] problem building Amber 16 with Intel compilers Hai Nguyen (Tue Dec 20 2016 - 09:21:29 PST)
    - Re: [AMBER] problem building Amber 16 with Intel compilers Susan Chacko (Tue Dec 20 2016 - 10:45:35 PST)
    - Re: [AMBER] problem building Amber 16 with Intel compilers Hai Nguyen (Tue Dec 20 2016 - 10:50:57 PST)
    - Re: [AMBER] problem building Amber 16 with Intel compilers Daniel Roe (Tue Dec 20 2016 - 11:04:39 PST)
    - Re: [AMBER] problem building Amber 16 with Intel compilers Yeng-Tseng Wang (Tue Dec 20 2016 - 11:18:58 PST)
    - Re: [AMBER] problem building Amber 16 with Intel compilers Susan Chacko (Tue Dec 20 2016 - 13:24:48 PST)
    - Re: [AMBER] problem building Amber 16 with Intel compilers Hai Nguyen (Tue Dec 20 2016 - 13:27:35 PST)
- [AMBER] van der Waals parameters GAFF UFF OPLS Bruno Falcone (Tue Dec 20 2016 - 08:58:01 PST)
  - Re: [AMBER] van der Waals parameters GAFF UFF OPLS David Case (Tue Dec 20 2016 - 10:31:42 PST)
[AMBER] addion issue Hirdesh Kumar (Tue Dec 20 2016 - 10:15:58 PST)
- Re: [AMBER] addion issue Hai Nguyen (Tue Dec 20 2016 - 10:19:39 PST)
  - Re: [AMBER] addion issue Hirdesh Kumar (Tue Dec 20 2016 - 10:25:47 PST)
    - Re: [AMBER] addion issue Hai Nguyen (Tue Dec 20 2016 - 10:27:49 PST)
    - Re: [AMBER] addion issue Hirdesh Kumar (Tue Dec 20 2016 - 10:45:28 PST)
    - Re: [AMBER] addion issue Prajwal Nandekar (Wed Dec 21 2016 - 04:12:25 PST)
    - Re: [AMBER] addion issue Hirdesh Kumar (Wed Dec 21 2016 - 07:35:10 PST)
[AMBER] Problem building FEW and mmpbsa.pl in Amber16 Tong Zhu (Tue Dec 20 2016 - 19:13:00 PST)
- Re: [AMBER] Problem building FEW and mmpbsa.pl in Amber16 Nhai (Tue Dec 20 2016 - 19:17:21 PST)
  - Re: [AMBER] Problem building FEW and mmpbsa.pl in Amber16 Tong Zhu (Tue Dec 20 2016 - 22:57:23 PST)
- Re: [AMBER] Problem building FEW and mmpbsa.pl in Amber16 David A Case (Fri Dec 23 2016 - 08:08:29 PST)
[AMBER] Possible conformations predicted by MD from NMR data (RDC, dihedral) Trang Nguyen (Tue Dec 20 2016 - 22:42:10 PST)
- Re: [AMBER] Possible conformations predicted by MD from NMR data (RDC, dihedral) David A Case (Wed Dec 21 2016 - 05:02:47 PST)
[AMBER] rdf_with_center_in_cpptraj_16 JAIME RUBIO MARTINEZ (Wed Dec 21 2016 - 05:01:57 PST)
- Re: [AMBER] rdf_with_center_in_cpptraj_16 Daniel Roe (Wed Dec 21 2016 - 06:59:26 PST)
  - Re: [AMBER] rdf_with_center_in_cpptraj_16 JAIME RUBIO MARTINEZ (Wed Dec 21 2016 - 08:20:24 PST)
    - Re: [AMBER] rdf_with_center_in_cpptraj_16 JAIME RUBIO MARTINEZ (Sun Dec 25 2016 - 09:54:26 PST)
    - Re: [AMBER] rdf_with_center_in_cpptraj_16 Daniel Roe (Fri Dec 30 2016 - 10:02:20 PST)
    - Re: [AMBER] rdf_with_center_in_cpptraj_16 Daniel Roe (Mon Mar 06 2017 - 05:21:05 PST)
[AMBER] Problem about one GPU & multiple CPUs 吴萌 (Wed Dec 21 2016 - 05:38:21 PST)
- Re: [AMBER] Problem about one GPU & multiple CPUs Daniel Roe (Wed Dec 21 2016 - 06:56:39 PST)
[AMBER] cpptraj LIE on a ghost-atom Elisa Pieri (Wed Dec 21 2016 - 06:45:22 PST)
- Re: [AMBER] cpptraj LIE on a ghost-atom Jason Swails (Thu Dec 22 2016 - 13:34:27 PST)
  - Re: [AMBER] cpptraj LIE on a ghost-atom Elisa Pieri (Tue Jan 03 2017 - 03:36:25 PST)
[AMBER] Force field modifications Jonathan Huihui (Wed Dec 21 2016 - 11:48:58 PST)
- Re: [AMBER] Force field modifications David Cerutti (Wed Dec 21 2016 - 11:57:51 PST)
  - Re: [AMBER] Force field modifications Jonathan Huihui (Thu Dec 22 2016 - 03:18:20 PST)
    - Re: [AMBER] Force field modifications David A Case (Thu Dec 22 2016 - 05:18:25 PST)
    - Re: [AMBER] Force field modifications Jonathan Huihui (Fri Jan 06 2017 - 13:09:26 PST)
    - Re: [AMBER] Force field modifications Carlos Simmerling (Fri Jan 06 2017 - 13:22:47 PST)
    - Re: [AMBER] Force field modifications Jonathan Huihui (Fri Jan 06 2017 - 13:25:14 PST)
    - Re: [AMBER] Force field modifications Carlos Simmerling (Fri Jan 06 2017 - 13:28:42 PST)
    - Re: [AMBER] Force field modifications Jonathan Huihui (Fri Jan 06 2017 - 13:36:58 PST)
    - Re: [AMBER] Force field modifications David Case (Fri Jan 06 2017 - 14:38:14 PST)
[AMBER] solvatebox command Mohaddeseh Habibzadeh (Thu Dec 22 2016 - 01:36:46 PST)
- Re: [AMBER] solvatebox command David A Case (Thu Dec 22 2016 - 05:11:12 PST)
[AMBER] How to perform energy decomposition in Thermodynamic integration with Sander in Amber 14? Stefan Ivanov (Thu Dec 22 2016 - 02:55:49 PST)
- Re: [AMBER] How to perform energy decomposition in Thermodynamic integration with Sander in Amber 14? Dwight McGee (Thu Dec 22 2016 - 06:44:44 PST)
  - Re: [AMBER] How to perform energy decomposition in Thermodynamic integration with Sander in Amber 14? Stefan Ivanov (Fri Dec 23 2016 - 08:01:45 PST)
[AMBER] neutralization and Salt concentration for DNA simulations Muthukumaran R (Thu Dec 22 2016 - 05:25:18 PST)
- Re: [AMBER] neutralization and Salt concentration for DNA simulations Rodrigo Galindo-Murillo (Thu Dec 22 2016 - 08:07:17 PST)
[AMBER] error in amber 16 mpi installation Michael Shokhen (Thu Dec 22 2016 - 10:35:30 PST)
- Re: [AMBER] error in amber 16 mpi installation Daniel Roe (Thu Dec 22 2016 - 11:00:04 PST)
  - Re: [AMBER] error in amber 16 mpi installation Michael Shokhen (Thu Dec 22 2016 - 11:31:23 PST)
- Re: [AMBER] error in amber 16 mpi installation Hai Nguyen (Thu Dec 22 2016 - 11:15:49 PST)
[AMBER] Amber16 configure: error: could not find mpi library for --enable-mpi Michael Shokhen (Thu Dec 22 2016 - 12:07:34 PST)
- Re: [AMBER] Amber16 configure: error: could not find mpi library for --enable-mpi Nhai (Thu Dec 22 2016 - 12:14:58 PST)
- Re: [AMBER] Amber16 configure: error: could not find mpi library for --enable-mpi Lucas (Mon May 29 2017 - 13:19:27 PDT)
  - Re: [AMBER] Amber16 configure: error: could not find mpi library for --enable-mpi David Case (Mon May 29 2017 - 16:55:42 PDT)
[AMBER] failed testing cuda Michael Shokhen (Sun Dec 25 2016 - 10:36:48 PST)
- Re: [AMBER] failed testing cuda David A Case (Tue Dec 27 2016 - 08:55:58 PST)
[AMBER] Problem in not defining the hybridization of a atomtype A kS (Mon Dec 26 2016 - 07:37:16 PST)
- Re: [AMBER] Problem in not defining the hybridization of a atomtype David A Case (Tue Dec 27 2016 - 09:02:14 PST)
  - Re: [AMBER] Problem in not defining the hybridization of a atomtype A kS (Mon Jan 02 2017 - 08:33:24 PST)
    - Re: [AMBER] Problem in not defining the hybridization of a atomtype David Case (Mon Jan 02 2017 - 08:49:57 PST)
[AMBER] 2D distance plots Abhilash J (Mon Dec 26 2016 - 10:18:59 PST)
[AMBER] SEP non-standard phosphoserine issue. Saman Yousuf ali (Mon Dec 26 2016 - 23:02:47 PST)
- Re: [AMBER] SEP non-standard phosphoserine issue. Hai Nguyen (Mon Dec 26 2016 - 23:22:21 PST)
  - Re: [AMBER] SEP non-standard phosphoserine issue. Hai Nguyen (Mon Dec 26 2016 - 23:23:07 PST)
- [AMBER] Molecular Modelling Workshop: March 27-29, 2017 in Erlangen, Germany Dr. Anselm Horn (Tue Jan 24 2017 - 00:20:22 PST)
[AMBER] Distance diffusion calculation in ptraj and cpptraj wei (Mon Dec 26 2016 - 23:58:46 PST)
- Re: [AMBER] Distance diffusion calculation in ptraj and cpptraj Huang Jing (Tue Dec 27 2016 - 05:04:07 PST)
- Re: [AMBER] Distance diffusion calculation in ptraj and cpptraj Daniel Roe (Wed Dec 28 2016 - 09:31:03 PST)
[AMBER] Water density near the protein suspiciously low I Lőrincz (Tue Dec 27 2016 - 13:54:53 PST)
- Re: [AMBER] Water density near the protein suspiciously low Hai Nguyen (Tue Dec 27 2016 - 14:00:09 PST)
- Re: [AMBER] Water density near the protein suspiciously low Bill Ross (Tue Dec 27 2016 - 14:00:22 PST)
- Re: [AMBER] Water density near the protein suspiciously low Chris Moth (Tue Dec 27 2016 - 14:42:07 PST)
  - Re: [AMBER] Water density near the protein suspiciously low David Case (Tue Dec 27 2016 - 18:08:34 PST)
    - Re: [AMBER] Water density near the protein suspiciously low I Lőrincz (Wed Dec 28 2016 - 00:45:16 PST)
    - Re: [AMBER] Water density near the protein suspiciously low I Lőrincz (Tue Jan 03 2017 - 15:46:04 PST)
[AMBER] 回复：Re: Distance diffusion calculation in ptraj and cpptraj wei (Tue Dec 27 2016 - 18:07:51 PST)
- Re: [AMBER] 回复：Re: Distance diffusion calculation in ptraj and cpptraj Daniel Roe (Wed Dec 28 2016 - 09:43:06 PST)
[AMBER] Proplem about how to set substrate concentration Shanghaitech University WuMeng (Tue Dec 27 2016 - 23:38:54 PST)
- Re: [AMBER] Proplem about how to set substrate concentration Huang Jing (Tue Dec 27 2016 - 23:54:27 PST)
- Re: [AMBER] Proplem about how to set substrate concentration Sérgio Marques (Wed Dec 28 2016 - 05:09:08 PST)
[AMBER] cuda.h: No such file or directory Elka Firmanda (Wed Dec 28 2016 - 17:16:25 PST)
- Re: [AMBER] cuda.h: No such file or directory David Case (Wed Dec 28 2016 - 18:12:01 PST)
[AMBER] help in restart file Robin Jain (Thu Dec 29 2016 - 22:14:33 PST)
- Re: [AMBER] help in restart file Hai Nguyen (Thu Dec 29 2016 - 22:51:01 PST)
- Re: [AMBER] help in restart file David A Case (Fri Dec 30 2016 - 04:47:20 PST)
[AMBER] Should I image atoms when I calculate translational and rotational diffusion constants with cpptraj? wei (Thu Dec 29 2016 - 22:51:27 PST)
- Re: [AMBER] Should I image atoms when I calculate translational and rotational diffusion constants with cpptraj? David A Case (Fri Dec 30 2016 - 04:50:50 PST)
[AMBER] Umbrella sampling (US) along RMSD-based coordinates using targeted MD script Tarsis (Fri Dec 30 2016 - 07:49:51 PST)
[AMBER] Principal Component Analysis (PCA) query. Abhilash J (Fri Dec 30 2016 - 09:39:21 PST)
- Re: [AMBER] Principal Component Analysis (PCA) query. Daniel Roe (Fri Dec 30 2016 - 10:01:13 PST)
  - Re: [AMBER] Principal Component Analysis (PCA) query. Abhilash J (Fri Dec 30 2016 - 10:28:05 PST)
[AMBER] Remove motion of center of mass after obtaining trajectory The Cromicus Productions (Fri Dec 30 2016 - 11:54:25 PST)
- Re: [AMBER] Remove motion of center of mass after obtaining trajectory Hai Nguyen (Fri Dec 30 2016 - 13:21:51 PST)
  - Re: [AMBER] Remove motion of center of mass after obtaining trajectory The Cromicus Productions (Fri Dec 30 2016 - 18:23:20 PST)
    - Re: [AMBER] Remove motion of center of mass after obtaining trajectory The Cromicus Productions (Fri Dec 30 2016 - 23:32:06 PST)
    - Re: [AMBER] Remove motion of center of mass after obtaining trajectory Daniel Roe (Tue Jan 03 2017 - 06:06:17 PST)
[AMBER] failed to visualize trajectories in vmd. Saman Yousuf ali (Mon Jan 02 2017 - 02:02:25 PST)
- Re: [AMBER] failed to visualize trajectories in vmd. David Case (Mon Jan 02 2017 - 06:14:03 PST)
  - Re: [AMBER] failed to visualize trajectories in vmd. Saman Yousuf ali (Mon Jan 02 2017 - 07:08:41 PST)
    - Re: [AMBER] failed to visualize trajectories in vmd. David Case (Mon Jan 02 2017 - 07:20:20 PST)
    - Re: [AMBER] failed to visualize trajectories in vmd. Saman Yousuf ali (Mon Jan 02 2017 - 07:32:57 PST)
    - Re: [AMBER] failed to visualize trajectories in vmd. Saman Yousuf ali (Mon Jan 02 2017 - 07:46:31 PST)
    - Re: [AMBER] failed to visualize trajectories in vmd. Nhai (Mon Jan 02 2017 - 07:56:57 PST)
    - Re: [AMBER] failed to visualize trajectories in vmd. Elvis Martis (Mon Jan 02 2017 - 08:20:07 PST)
    - Re: [AMBER] failed to visualize trajectories in vmd. Saman Yousuf ali (Mon Jan 02 2017 - 08:59:17 PST)
    - Re: [AMBER] failed to visualize trajectories in vmd. Daniel Roe (Tue Jan 03 2017 - 05:31:39 PST)
[AMBER] partial replica exchange molecular dynamics Johannes Loeffler (Mon Jan 02 2017 - 06:09:30 PST)
- Re: [AMBER] partial replica exchange molecular dynamics Huang Jing (Tue Jan 03 2017 - 08:50:28 PST)
[AMBER] how to use depreciated cpptraj code Chris Neale (Mon Jan 02 2017 - 11:21:24 PST)
- Re: [AMBER] how to use depreciated cpptraj code Hai Nguyen (Mon Jan 02 2017 - 11:33:16 PST)
  - Re: [AMBER] how to use depreciated cpptraj code Hai Nguyen (Mon Jan 02 2017 - 11:36:51 PST)
- Re: [AMBER] how to use depreciated cpptraj code Daniel Roe (Tue Jan 03 2017 - 05:24:28 PST)
[AMBER] Error in reordering pH-REMD trajectories Elisa Pieri (Mon Jan 02 2017 - 12:31:16 PST)
- Re: [AMBER] Error in reordering pH-REMD trajectories Jason Swails (Mon Jan 02 2017 - 12:33:52 PST)
  - Re: [AMBER] Error in reordering pH-REMD trajectories Elisa Pieri (Tue Jan 03 2017 - 04:09:30 PST)
    - Re: [AMBER] Error in reordering pH-REMD trajectories Daniel Roe (Tue Jan 03 2017 - 05:15:59 PST)
    - Re: [AMBER] Error in reordering pH-REMD trajectories Elisa Pieri (Tue Jan 03 2017 - 05:22:25 PST)
[AMBER] Amber16 on K80 GPUs --poor performance on multiple GPUs Susan Chacko (Tue Jan 03 2017 - 08:00:09 PST)
- Re: [AMBER] Amber16 on K80 GPUs --poor performance on multiple GPUs Daniel Roe (Tue Jan 03 2017 - 08:25:24 PST)
  - Re: [AMBER] Amber16 on K80 GPUs --poor performance on multiple GPUs Huang Jing (Tue Jan 03 2017 - 08:32:23 PST)
    - Re: [AMBER] Amber16 on K80 GPUs --poor performance on multiple GPUs Ross Walker (Wed Jan 04 2017 - 05:03:50 PST)
  - Re: [AMBER] Amber16 on K80 GPUs --poor performance on multiple GPUs Susan Chacko (Tue Jan 03 2017 - 09:36:21 PST)
    - Re: [AMBER] Amber16 on K80 GPUs --poor performance on multiple GPUs Ross Walker (Wed Jan 04 2017 - 05:05:08 PST)
    - Re: [AMBER] Amber16 on K80 GPUs --poor performance on multiple GPUs Susan Chacko (Thu Jan 05 2017 - 08:41:00 PST)
    - Re: [AMBER] Amber16 on K80 GPUs --poor performance on multiple GPUs Susan Chacko (Thu Jan 05 2017 - 11:15:30 PST)
    - Re: [AMBER] Amber16 on K80 GPUs --poor performance on multiple GPUs Jason Swails (Thu Jan 05 2017 - 12:44:24 PST)
    - Re: [AMBER] Amber16 on K80 GPUs --poor performance on multiple GPUs Huang Jing (Thu Jan 05 2017 - 13:46:28 PST)
[AMBER] Question about Empirical Valence Bond(EVB) simulation 没关系 (Tue Jan 03 2017 - 18:21:21 PST)
- Re: [AMBER] Question about Empirical Valence Bond(EVB) simulation Huang Jing (Tue Jan 03 2017 - 20:48:27 PST)
  - [AMBER] 回复： Question about Empirical Valence Bond(EVB) simulation 没关系 (Tue Jan 03 2017 - 22:55:31 PST)
- Re: [AMBER] Question about Empirical Valence Bond(EVB) simulation David Case (Thu Jan 05 2017 - 18:17:18 PST)
[AMBER] Zinc +2 SMD pulling Fabian gmail (Wed Jan 04 2017 - 01:33:29 PST)
- Re: [AMBER] Zinc +2 SMD pulling Huang Jing (Wed Jan 04 2017 - 02:07:18 PST)
  - Re: [AMBER] Zinc +2 SMD pulling Fabian gmail (Wed Jan 04 2017 - 02:24:44 PST)
    - Re: [AMBER] Zinc +2 SMD pulling Huang Jing (Wed Jan 04 2017 - 03:34:19 PST)
- Re: [AMBER] Zinc +2 SMD pulling Fabian Glaser (Wed Jan 04 2017 - 03:39:17 PST)
  - [AMBER] ZINC PERMEATION PATHWAY Fabian gmail (Wed Jan 04 2017 - 05:09:53 PST)
    - Re: [AMBER] ZINC PERMEATION PATHWAY Daniel Roe (Wed Jan 04 2017 - 06:13:49 PST)
    - Re: [AMBER] ZINC PERMEATION PATHWAY Fabian gmail (Wed Jan 04 2017 - 06:59:02 PST)
[AMBER] tLeap adding non-library hydrogens David Poole (Wed Jan 04 2017 - 02:07:31 PST)
- Re: [AMBER] tLeap adding non-library hydrogens Huang Jing (Wed Jan 04 2017 - 02:16:38 PST)
- Re: [AMBER] tLeap adding non-library hydrogens David Case (Wed Jan 04 2017 - 05:20:47 PST)
- Re: [AMBER] tLeap adding non-library hydrogens David Poole (Sat Jan 07 2017 - 04:07:10 PST)
  - Re: [AMBER] tLeap adding non-library hydrogens Huang Jing (Sat Jan 07 2017 - 04:41:52 PST)
  - Re: [AMBER] tLeap adding non-library hydrogens David Case (Sat Jan 07 2017 - 14:58:10 PST)
- Re: [AMBER] tLeap adding non-library hydrogens David Poole (Sun Jan 08 2017 - 12:41:46 PST)
  - Re: [AMBER] tLeap adding non-library hydrogens David Case (Sun Jan 08 2017 - 18:43:32 PST)
[AMBER] tLeap and acetonitrile/chloroform solvation Luka Bilić (Wed Jan 04 2017 - 06:12:51 PST)
- Re: [AMBER] tLeap and acetonitrile/chloroform solvation Huang Jing (Wed Jan 04 2017 - 07:33:25 PST)
  - Re: [AMBER] tLeap and acetonitrile/chloroform solvation Luka Bilić (Thu Jan 05 2017 - 00:17:51 PST)
- Re: [AMBER] tLeap and acetonitrile/chloroform solvation David Case (Wed Jan 04 2017 - 18:51:18 PST)
  - Re: [AMBER] tLeap and acetonitrile/chloroform solvation Luka Bilić (Thu Jan 05 2017 - 00:09:41 PST)
[AMBER] mmCIF from amber Thomas Pochapsky (Wed Jan 04 2017 - 06:34:22 PST)
- Re: [AMBER] mmCIF from amber Nhai (Wed Jan 04 2017 - 09:00:28 PST)
[AMBER] Problems about membrane protein simulation Shanghaitech University WuMeng (Wed Jan 04 2017 - 06:44:22 PST)
- Re: [AMBER] Problems about membrane protein simulation Huang Jing (Wed Jan 04 2017 - 07:13:16 PST)
- Re: [AMBER] Problems about membrane protein simulation 吴萌 (Thu Jan 05 2017 - 00:14:51 PST)
  - Re: [AMBER] Problems about membrane protein simulation Huang Jing (Thu Jan 05 2017 - 01:31:40 PST)
  - Re: [AMBER] Problems about membrane protein simulation Daniel Roe (Thu Jan 05 2017 - 06:14:14 PST)
[AMBER] compatibility issues erik rp zuiderweg (Wed Jan 04 2017 - 09:54:18 PST)
- Re: [AMBER] compatibility issues Hai Nguyen (Wed Jan 04 2017 - 10:00:00 PST)
  - Re: [AMBER] compatibility issues Huang Jing (Wed Jan 04 2017 - 10:13:30 PST)
    - Re: [AMBER] compatibility issues Hai Nguyen (Wed Jan 04 2017 - 10:25:14 PST)
    - Re: [AMBER] compatibility issues Huang Jing (Wed Jan 04 2017 - 10:43:10 PST)
    - Re: [AMBER] compatibility issues erik rp zuiderweg (Wed Jan 04 2017 - 10:50:08 PST)
    - Re: [AMBER] compatibility issues David Case (Wed Jan 04 2017 - 19:06:03 PST)
    - Re: [AMBER] compatibility issues erik rp zuiderweg (Thu Jan 05 2017 - 09:33:53 PST)
    - Re: [AMBER] compatibility issues Hai Nguyen (Thu Jan 05 2017 - 09:45:05 PST)
    - Re: [AMBER] compatibility issues David Case (Thu Jan 05 2017 - 17:34:31 PST)
    - Re: [AMBER] compatibility issues Hai Nguyen (Wed Jan 04 2017 - 11:06:31 PST)
    - Re: [AMBER] compatibility issues Huang Jing (Wed Jan 04 2017 - 11:34:31 PST)
    - Re: [AMBER] compatibility issues Jason Swails (Thu Jan 05 2017 - 18:35:22 PST)
    - [AMBER] Some notes erik rp zuiderweg (Sat Jan 14 2017 - 11:12:01 PST)
    - Re: [AMBER] Some notes David Case (Sat Jan 14 2017 - 12:41:03 PST)
  - Re: [AMBER] compatibility issues David Case (Wed Jan 04 2017 - 18:58:33 PST)
[AMBER] antechamber: why the net charge does not sum up to zero? Azade Yazdan Yar (Thu Jan 05 2017 - 02:52:34 PST)
- Re: [AMBER] antechamber: why the net charge does not sum up to zero? Hannes Loeffler (Thu Jan 05 2017 - 03:06:06 PST)
- Re: [AMBER] antechamber: why the net charge does not sum up to zero? Jason Swails (Thu Jan 05 2017 - 09:55:23 PST)
- Re: [AMBER] antechamber: why the net charge does not sum up to zero? FyD (Sat Jan 07 2017 - 10:33:39 PST)
  - Re: [AMBER] antechamber: why the net charge does not sum up to zero? Huang Jing (Sat Jan 07 2017 - 12:26:54 PST)
    - Re: [AMBER] antechamber: why the net charge does not sum up to zero? FyD (Sun Jan 08 2017 - 10:25:07 PST)
    - Re: [AMBER] antechamber: why the net charge does not sum up to zero? David Case (Sun Jan 08 2017 - 18:41:56 PST)
    - Re: [AMBER] antechamber: why the net charge does not sum up to zero? FyD (Mon Jan 16 2017 - 06:51:38 PST)
    - Re: [AMBER] antechamber: why the net charge does not sum up to zero? FyD (Mon Jan 16 2017 - 22:04:01 PST)
  - Re: [AMBER] antechamber: why the net charge does not sum up to zero? David Case (Sat Jan 07 2017 - 15:12:49 PST)
[AMBER] cpptraj clustering doubt Mary Varughese (Thu Jan 05 2017 - 02:59:52 PST)
- Re: [AMBER] cpptraj clustering doubt Elvis Martis (Thu Jan 05 2017 - 03:41:22 PST)
- Re: [AMBER] cpptraj clustering doubt Christina Bergonzo (Thu Jan 05 2017 - 04:48:21 PST)
  - Re: [AMBER] cpptraj clustering doubt Daniel Roe (Thu Jan 05 2017 - 05:30:50 PST)
    - Re: [AMBER] cpptraj clustering doubt Mary Varughese (Thu Jan 05 2017 - 07:23:38 PST)
    - Re: [AMBER] cpptraj clustering doubt Mary Varughese (Sat Jan 07 2017 - 02:33:17 PST)
    - Re: [AMBER] cpptraj clustering doubt Elvis Martis (Sat Jan 07 2017 - 06:56:27 PST)
    - Re: [AMBER] cpptraj clustering doubt Daniel Roe (Sun Jan 08 2017 - 10:32:26 PST)
    - Re: [AMBER] cpptraj clustering doubt Mary Varughese (Sun Jan 08 2017 - 20:55:11 PST)
    - Re: [AMBER] cpptraj clustering doubt Daniel Roe (Mon Jan 09 2017 - 06:05:53 PST)
[AMBER] 'Diffusion' calculation in Ptraj - could not understand a description of Ptraj code in Amber14 wei (Thu Jan 05 2017 - 04:39:40 PST)
- Re: [AMBER] 'Diffusion' calculation in Ptraj - could not understand a description of Ptraj code in Amber14 Daniel Roe (Thu Jan 05 2017 - 05:52:17 PST)
[AMBER] VMD/netcdf Adrian Roitberg (Thu Jan 05 2017 - 07:09:50 PST)
[AMBER] cpptraj PCA of crystal structure anu chandra (Thu Jan 05 2017 - 08:25:48 PST)
- Re: [AMBER] cpptraj PCA of crystal structure Daniel Roe (Thu Jan 05 2017 - 08:30:14 PST)
  - Re: [AMBER] cpptraj PCA of crystal structure anu chandra (Tue Jan 10 2017 - 02:50:23 PST)
    - Re: [AMBER] cpptraj PCA of crystal structure Daniel Roe (Tue Jan 10 2017 - 05:03:48 PST)
    - Re: [AMBER] cpptraj PCA of crystal structure anu chandra (Thu Jan 12 2017 - 05:00:09 PST)
[AMBER] /dev/hfi1_0 device failed to appear after 15 seconds: Connection timed out jacky zhao (Thu Jan 05 2017 - 08:34:46 PST)
[AMBER] Ion Parameters for tip4pfb Samaneh Ghassabi Kondalaji (Thu Jan 05 2017 - 09:44:25 PST)
- Re: [AMBER] Ion Parameters for tip4pfb Huang Jing (Thu Jan 05 2017 - 13:40:51 PST)
- Re: [AMBER] Ion Parameters for tip4pfb David Case (Thu Jan 05 2017 - 17:19:14 PST)
[AMBER] Amber16 benchmark suite error jacky zhao (Thu Jan 05 2017 - 22:51:31 PST)
- Re: [AMBER] Amber16 benchmark suite error Ross Walker (Fri Jan 06 2017 - 11:55:14 PST)
  - Re: [AMBER] Amber16 benchmark suite error jacky zhao (Fri Jan 06 2017 - 23:16:46 PST)
    - Re: [AMBER] Amber16 benchmark suite error Ross Walker (Sat Jan 07 2017 - 15:06:57 PST)
    - Re: [AMBER] Amber16 benchmark suite error David Case (Sun Jan 08 2017 - 05:25:45 PST)
    - Re: [AMBER] Amber16 benchmark suite error jacky zhao (Sun Jan 08 2017 - 06:37:50 PST)
    - Re: [AMBER] Amber16 benchmark suite error jacky zhao (Sun Jan 08 2017 - 22:02:11 PST)
    - Re: [AMBER] Amber16 benchmark suite error jacky zhao (Tue Jan 10 2017 - 07:26:19 PST)
[AMBER] xmin and QM/MM Åsmund Kjendseth Røhr (Fri Jan 06 2017 - 01:19:33 PST)
- Re: [AMBER] xmin and QM/MM Goetz, Andreas (Fri Jan 06 2017 - 02:37:44 PST)
[AMBER] 回复：AMBER Digest, Vol 1806, Issue 1 wei (Fri Jan 06 2017 - 21:42:38 PST)
[AMBER] Simple normal mode analysis in amber Ella Gale (Sat Jan 07 2017 - 09:15:45 PST)
- Re: [AMBER] Simple normal mode analysis in amber Huang Jing (Sat Jan 07 2017 - 12:18:53 PST)
- Re: [AMBER] Simple normal mode analysis in amber David Case (Sat Jan 07 2017 - 15:09:10 PST)
- Re: [AMBER] Simple normal mode analysis in amber Lorena.Rosaleny.uv.es (Sun Apr 15 2018 - 23:08:57 PDT)
  - Re: [AMBER] Simple normal mode analysis in amber David A Case (Mon Apr 16 2018 - 05:59:11 PDT)
- Re: [AMBER] Simple normal mode analysis in amber Lorena.Rosaleny.uv.es (Tue Apr 17 2018 - 07:20:02 PDT)
  - Re: [AMBER] Simple normal mode analysis in amber David A Case (Tue Apr 17 2018 - 07:50:15 PDT)
- Re: [AMBER] Simple normal mode analysis in amber Lorena.Rosaleny.uv.es (Thu Apr 19 2018 - 00:49:05 PDT)
- Re: [AMBER] Simple normal mode analysis in amber Lorena.Rosaleny.uv.es (Mon Apr 23 2018 - 12:42:43 PDT)
  - Re: [AMBER] Simple normal mode analysis in amber David A Case (Mon Apr 23 2018 - 18:11:11 PDT)
[AMBER] autoimage colvin (Mon Jan 09 2017 - 00:10:57 PST)
- Re: [AMBER] autoimage Daniel Roe (Mon Jan 09 2017 - 06:40:52 PST)
  - Re: [AMBER] autoimage colvin (Thu Jan 12 2017 - 21:09:00 PST)
    - Re: [AMBER] autoimage Daniel Roe (Fri Jan 13 2017 - 10:50:01 PST)
    - Re: [AMBER] autoimage Daniel Roe (Tue Jan 17 2017 - 06:38:19 PST)
    - Re: [AMBER] autoimage Daniel Roe (Tue Jan 17 2017 - 07:35:21 PST)
[AMBER] 2nd eChemInfo Training and Innovation Course in Drug Design 2017 in Milano Thomas Exner (Mon Jan 09 2017 - 01:17:00 PST)
[AMBER] Split trajectory by atom The Cromicus Productions (Mon Jan 09 2017 - 02:22:41 PST)
- Re: [AMBER] Split trajectory by atom Hai Nguyen (Mon Jan 09 2017 - 06:26:30 PST)
  - Re: [AMBER] Split trajectory by atom The Cromicus Productions (Tue Jan 10 2017 - 00:01:25 PST)
[AMBER] Python Programs Chase Zagorec-Marks (Mon Jan 09 2017 - 12:53:28 PST)
- Re: [AMBER] Python Programs Hai Nguyen (Mon Jan 09 2017 - 13:05:50 PST)
  - Re: [AMBER] Python Programs Chase Zagorec-Marks (Mon Jan 09 2017 - 13:13:06 PST)
    - Re: [AMBER] Python Programs Hai Nguyen (Mon Jan 09 2017 - 13:20:43 PST)
    - Re: [AMBER] Python Programs Chase Zagorec-Marks (Mon Jan 09 2017 - 13:29:43 PST)
    - Re: [AMBER] Python Programs Hai Nguyen (Mon Jan 09 2017 - 13:41:48 PST)
    - Re: [AMBER] Python Programs Chase Zagorec-Marks (Mon Jan 09 2017 - 16:56:35 PST)
[AMBER] Error in leaprc.ff14SB (Amber14) Subashini .K (Mon Jan 09 2017 - 21:29:03 PST)
- Re: [AMBER] Error in leaprc.ff14SB (Amber14) Hai Nguyen (Mon Jan 09 2017 - 21:39:46 PST)
  - Re: [AMBER] Error in leaprc.ff14SB (Amber14) Subashini .K (Mon Jan 09 2017 - 22:28:06 PST)
[AMBER] ACPYPE ERROR Subashini .K (Tue Jan 10 2017 - 00:28:51 PST)
- Re: [AMBER] ACPYPE ERROR Alan (Tue Jan 10 2017 - 00:38:38 PST)
  - Re: [AMBER] ACPYPE ERROR Subashini .K (Tue Jan 10 2017 - 01:11:22 PST)
    - Re: [AMBER] ACPYPE ERROR Alan (Tue Jan 10 2017 - 09:24:55 PST)
    - Re: [AMBER] ACPYPE ERROR Subashini .K (Tue Jan 10 2017 - 09:57:39 PST)
- Re: [AMBER] ACPYPE ERROR Subashini .K (Tue Jan 10 2017 - 01:12:55 PST)
[AMBER] restrain protein with two different force constant Khabiri, Morteza (Tue Jan 10 2017 - 06:58:47 PST)
- Re: [AMBER] restrain protein with two different force constant Elvis Martis (Tue Jan 10 2017 - 07:11:26 PST)
[AMBER] QMMM with MOPAC2016 Carlos SOTO GARZA (Tue Jan 10 2017 - 15:06:10 PST)
- Re: [AMBER] QMMM with MOPAC2016 Adrian Roitberg (Tue Jan 10 2017 - 15:35:30 PST)
- Re: [AMBER] QMMM with MOPAC2016 Goetz, Andreas (Tue Jan 10 2017 - 15:37:30 PST)
  - Re: [AMBER] QMMM with MOPAC2016 Carlos SOTO GARZA (Tue Jan 10 2017 - 15:52:23 PST)
- Re: [AMBER] QMMM with MOPAC2016 Joan Torras (Tue Jan 10 2017 - 22:38:13 PST)
[AMBER] verification of ligand rmsd script. Saman Yousuf ali (Wed Jan 11 2017 - 03:11:53 PST)
- Re: [AMBER] verification of ligand rmsd script. Elvis Martis (Wed Jan 11 2017 - 06:38:15 PST)
- Re: [AMBER] verification of ligand rmsd script. Daniel Roe (Wed Jan 11 2017 - 06:46:41 PST)
- Re: [AMBER] verification of ligand rmsd script. Daniel Roe (Thu Jan 12 2017 - 06:05:11 PST)
[AMBER] All working now, except some trajectories erik rp zuiderweg (Wed Jan 11 2017 - 07:48:22 PST)
- Re: [AMBER] All working now, except some trajectories Daniel Roe (Wed Jan 11 2017 - 08:47:00 PST)
- Re: [AMBER] All working now, except some trajectories David Case (Wed Jan 11 2017 - 11:57:32 PST)
[AMBER] /tmp/sh24281: Permission denied. Thakur, Abhishek (Wed Jan 11 2017 - 07:48:18 PST)
- Re: [AMBER] /tmp/sh24281: Permission denied. Hai Nguyen (Wed Jan 11 2017 - 08:05:12 PST)
  - Re: [AMBER] /tmp/sh24281: Permission denied. Thakur, Abhishek (Wed Jan 11 2017 - 08:07:56 PST)
- Re: [AMBER] /tmp/sh24281: Permission denied. Hannes Loeffler (Wed Jan 11 2017 - 08:26:42 PST)
  - Re: [AMBER] /tmp/sh24281: Permission denied. Thakur, Abhishek (Wed Jan 11 2017 - 08:34:58 PST)
    - Re: [AMBER] /tmp/sh24281: Permission denied. Hannes Loeffler (Wed Jan 11 2017 - 08:38:05 PST)
    - Re: [AMBER] /tmp/sh24281: Permission denied. Thakur, Abhishek (Wed Jan 11 2017 - 08:40:13 PST)
[AMBER] minimum distance between two sets of atoms anu chandra (Wed Jan 11 2017 - 08:55:03 PST)
- Re: [AMBER] minimum distance between two sets of atoms Hai Nguyen (Wed Jan 11 2017 - 09:20:22 PST)
  - Re: [AMBER] minimum distance between two sets of atoms anu chandra (Thu Jan 12 2017 - 04:59:38 PST)
[AMBER] Sander input into Gaussian Aseel Bala (Wed Jan 11 2017 - 13:55:58 PST)
- Re: [AMBER] Sander input into Gaussian Huang Jing (Wed Jan 11 2017 - 14:33:17 PST)
  - Re: [AMBER] Sander input into Gaussian Aseel Bala (Thu Jan 12 2017 - 10:17:37 PST)
    - Re: [AMBER] Sander input into Gaussian Adrian Roitberg (Thu Jan 12 2017 - 10:23:48 PST)
    - Re: [AMBER] Sander input into Gaussian Aseel Bala (Thu Jan 12 2017 - 13:02:07 PST)
[AMBER] New user needs help imam siswanto (Wed Jan 11 2017 - 20:23:26 PST)
- Re: [AMBER] New user needs help Hai Nguyen (Wed Jan 11 2017 - 20:49:21 PST)
  - Re: [AMBER] New user needs help imam siswanto (Wed Jan 11 2017 - 21:24:17 PST)
[AMBER] TLEAP error Subashini .K (Thu Jan 12 2017 - 00:15:54 PST)
- Re: [AMBER] TLEAP error Huang Jing (Thu Jan 12 2017 - 02:28:00 PST)
- Re: [AMBER] TLEAP error David Case (Thu Jan 12 2017 - 05:17:22 PST)
  - Re: [AMBER] TLEAP error Subashini .K (Thu Jan 12 2017 - 06:39:55 PST)
    - Re: [AMBER] TLEAP error David Case (Thu Jan 12 2017 - 08:57:27 PST)
[AMBER] RDF between centers of mass/geometry Lorenzo Gontrani (Thu Jan 12 2017 - 02:36:43 PST)
[AMBER] Issues for updating AmberTools 16 - update.14 Kihoon.Yoon.dell.com (Thu Jan 12 2017 - 09:03:59 PST)
- Re: [AMBER] Issues for updating AmberTools 16 - update.14 Daniel Roe (Thu Jan 12 2017 - 10:36:47 PST)
  - Re: [AMBER] Issues for updating AmberTools 16 - update.14 Kihoon.Yoon.dell.com (Thu Jan 12 2017 - 11:20:35 PST)
[AMBER] csh to bash Thakur, Abhishek (Thu Jan 12 2017 - 09:11:12 PST)
- Re: [AMBER] csh to bash Nhai (Thu Jan 12 2017 - 09:18:44 PST)
  - Re: [AMBER] csh to bash Huang Jing (Thu Jan 12 2017 - 09:57:47 PST)
[AMBER] LJ parameters in frcmod files Jacob Monroe (Thu Jan 12 2017 - 10:34:37 PST)
- Re: [AMBER] LJ parameters in frcmod files Pengfei Li (Thu Jan 12 2017 - 11:11:19 PST)
  - Re: [AMBER] LJ parameters in frcmod files Jacob Monroe (Thu Jan 12 2017 - 11:53:09 PST)
    - Re: [AMBER] LJ parameters in frcmod files Pengfei Li (Thu Jan 12 2017 - 12:12:59 PST)
[AMBER] MD for covalent inhibitors Ren Jinhong (Thu Jan 12 2017 - 14:23:58 PST)
- Re: [AMBER] MD for covalent inhibitors Huang Jing (Thu Jan 12 2017 - 15:12:15 PST)
[AMBER] Radius of gyration for the hydrophobic core Aishani Prem (Thu Jan 12 2017 - 15:51:38 PST)
- Re: [AMBER] Radius of gyration for the hydrophobic core Nhai (Thu Jan 12 2017 - 15:56:58 PST)
[AMBER] potential energy Albert (Fri Jan 13 2017 - 00:42:08 PST)
- Re: [AMBER] potential energy Carlos Simmerling (Fri Jan 13 2017 - 03:11:20 PST)
  - Re: [AMBER] potential energy Albert (Fri Jan 13 2017 - 03:12:11 PST)
    - Re: [AMBER] potential energy Carlos Simmerling (Fri Jan 13 2017 - 03:14:55 PST)
    - Re: [AMBER] potential energy Albert (Fri Jan 13 2017 - 03:16:48 PST)
    - Re: [AMBER] potential energy Carlos Simmerling (Fri Jan 13 2017 - 03:35:26 PST)
[AMBER] amber14 parallel build problems Ada Sedova (Fri Jan 13 2017 - 09:52:40 PST)
- Re: [AMBER] amber14 parallel build problems Scott Brozell (Fri Jan 13 2017 - 11:35:07 PST)
  - Re: [AMBER] amber14 parallel build problems Ada Sedova (Fri Jan 13 2017 - 12:12:43 PST)
    - Re: [AMBER] amber14 parallel build problems Hai Nguyen (Fri Jan 13 2017 - 12:23:38 PST)
    - Re: [AMBER] amber14 parallel build problems Ada Sedova (Fri Jan 13 2017 - 12:25:11 PST)
    - Re: [AMBER] amber14 parallel build problems Hai Nguyen (Fri Jan 13 2017 - 12:26:40 PST)
    - Re: [AMBER] amber14 parallel build problems Ada Sedova (Fri Jan 13 2017 - 12:29:48 PST)
    - Re: [AMBER] amber14 parallel build problems Hai Nguyen (Fri Jan 13 2017 - 12:34:31 PST)
    - Re: [AMBER] amber14 parallel build problems Ada Sedova (Fri Jan 13 2017 - 20:22:09 PST)
    - Re: [AMBER] amber14 parallel build problems Hai Nguyen (Fri Jan 13 2017 - 21:07:51 PST)
    - Re: [AMBER] amber14 parallel build problems Ada Sedova (Sat Jan 14 2017 - 06:22:58 PST)
    - Re: [AMBER] amber14 parallel build problems Ada Sedova (Sat Jan 14 2017 - 07:22:41 PST)
    - Re: [AMBER] amber14 parallel build problems Hai Nguyen (Sat Jan 14 2017 - 08:07:22 PST)
    - Re: [AMBER] amber14 parallel build problems Ada Sedova (Sat Jan 14 2017 - 08:48:25 PST)
    - Re: [AMBER] amber14 parallel build problems Nhai (Sat Jan 14 2017 - 08:59:26 PST)
    - Re: [AMBER] amber14 parallel build problems David Case (Sat Jan 14 2017 - 11:50:20 PST)
    - Re: [AMBER] amber14 parallel build problems Ada Sedova (Sat Jan 14 2017 - 09:01:04 PST)
    - Re: [AMBER] amber14 parallel build problems Nhai (Sat Jan 14 2017 - 09:09:30 PST)
    - Re: [AMBER] amber14 parallel build problems Ada Sedova (Sat Jan 14 2017 - 09:14:36 PST)
    - Re: [AMBER] amber14 parallel build problems Nhai (Sat Jan 14 2017 - 09:27:25 PST)
    - Re: [AMBER] amber14 parallel build problems Ada Sedova (Sat Jan 14 2017 - 09:33:28 PST)
    - Re: [AMBER] amber14 parallel build problems David Case (Sat Jan 14 2017 - 12:05:59 PST)
    - Re: [AMBER] amber14 parallel build problems Ada Sedova (Sat Jan 14 2017 - 20:01:57 PST)
    - Re: [AMBER] amber14 parallel build problems David Case (Sun Jan 15 2017 - 10:42:00 PST)
    - Re: [AMBER] amber14 parallel build problems Ada Sedova (Sun Jan 15 2017 - 11:18:23 PST)
    - Re: [AMBER] amber14 parallel build problems Ada Sedova (Sun Jan 15 2017 - 11:32:04 PST)
[AMBER] Handling modified residues asdda asa (Sat Jan 14 2017 - 01:12:46 PST)
- Re: [AMBER] Handling modified residues Huang Jing (Sat Jan 14 2017 - 03:36:17 PST)
  - Re: [AMBER] Handling modified residues asdda asa (Sat Jan 14 2017 - 04:10:59 PST)
    - Re: [AMBER] Handling modified residues Huang Jing (Sat Jan 14 2017 - 04:26:09 PST)
    - Re: [AMBER] Handling modified residues asdda asa (Sat Jan 14 2017 - 04:50:18 PST)
[AMBER] Single-Point MM-PBSA/GBSA Energy Calculations Naiem Issa (Sat Jan 14 2017 - 08:20:10 PST)
- Re: [AMBER] Single-Point MM-PBSA/GBSA Energy Calculations Hai Nguyen (Sat Jan 14 2017 - 08:31:01 PST)
  - Re: [AMBER] Single-Point MM-PBSA/GBSA Energy Calculations Naiem Issa (Sat Jan 14 2017 - 08:38:43 PST)
    - Re: [AMBER] Single-Point MM-PBSA/GBSA Energy Calculations Nhai (Sat Jan 14 2017 - 08:55:29 PST)
    - Re: [AMBER] Single-Point MM-PBSA/GBSA Energy Calculations Huang Jing (Sat Jan 14 2017 - 08:59:24 PST)
[AMBER] Continue running an incomplete MD with NMR restraints Kat G (Sat Jan 14 2017 - 22:43:04 PST)
- Re: [AMBER] Continue running an incomplete MD with NMR restraints Bill Ross (Sat Jan 14 2017 - 23:18:54 PST)
- Re: [AMBER] Continue running an incomplete MD with NMR restraints David Case (Sun Jan 15 2017 - 10:44:18 PST)
[AMBER] CpHREMD (explicit solvent) parameter settings inquiry Andrew Schaub (Sun Jan 15 2017 - 01:39:41 PST)
- Re: [AMBER] CpHREMD (explicit solvent) parameter settings inquiry Jason Swails (Mon Jan 16 2017 - 17:30:19 PST)
  - Re: [AMBER] CpHREMD (explicit solvent) parameter settings inquiry Andrew Schaub (Mon Jan 16 2017 - 17:50:57 PST)
    - Re: [AMBER] CpHREMD (explicit solvent) parameter settings inquiry Jason Swails (Mon Jan 16 2017 - 19:46:13 PST)
[AMBER] alpha helical content as reaction coordinate Bin Sun (Sun Jan 15 2017 - 09:28:15 PST)
- Re: [AMBER] alpha helical content as reaction coordinate David Case (Sun Jan 15 2017 - 10:52:42 PST)
[AMBER] intermolecular hydrogen bonding. Saman Yousuf ali (Mon Jan 16 2017 - 02:50:55 PST)
- Re: [AMBER] intermolecular hydrogen bonding. Daniel Roe (Tue Jan 17 2017 - 06:20:05 PST)
- Re: [AMBER] intermolecular hydrogen bonding. Daniel Roe (Wed Jan 25 2017 - 05:53:10 PST)
[AMBER] lipid membrane tleap problem amber16 Sofia Vasilakaki (Mon Jan 16 2017 - 12:32:21 PST)
- Re: [AMBER] lipid membrane tleap problem amber16 Dickson, Callum J (Tue Jan 17 2017 - 06:29:45 PST)
[AMBER] ambmask issue Aseel Bala (Mon Jan 16 2017 - 13:50:20 PST)
- Re: [AMBER] ambmask issue Huang Jing (Mon Jan 16 2017 - 14:37:20 PST)
- Re: [AMBER] ambmask issue Hai Nguyen (Tue Jan 17 2017 - 11:15:08 PST)
  - Re: [AMBER] ambmask issue Aseel Bala (Wed Jan 18 2017 - 12:53:44 PST)
    - Re: [AMBER] ambmask issue Hai Nguyen (Wed Jan 18 2017 - 12:59:09 PST)
    - Re: [AMBER] ambmask issue Aseel Bala (Wed Jan 18 2017 - 14:20:15 PST)
    - Re: [AMBER] ambmask issue Hai Nguyen (Wed Jan 18 2017 - 14:23:09 PST)
    - Re: [AMBER] ambmask issue Hai Nguyen (Wed Jan 18 2017 - 14:38:37 PST)
    - Re: [AMBER] ambmask issue David Case (Thu Jan 19 2017 - 05:25:36 PST)
    - Re: [AMBER] ambmask issue Aseel Bala (Thu Jan 19 2017 - 07:20:56 PST)
    - Re: [AMBER] ambmask issue Daniel Roe (Thu Jan 19 2017 - 07:34:17 PST)
    - Re: [AMBER] ambmask issue Aseel Bala (Thu Jan 19 2017 - 10:16:48 PST)
    - Re: [AMBER] ambmask issue Hai Nguyen (Thu Jan 19 2017 - 10:52:17 PST)
    - Re: [AMBER] ambmask issue Aseel Bala (Thu Jan 19 2017 - 11:06:13 PST)
[AMBER] Modified residue separated in leap module asdda asa (Mon Jan 16 2017 - 17:16:10 PST)
- Re: [AMBER] Modified residue separated in leap module David Case (Tue Jan 17 2017 - 05:53:56 PST)
[AMBER] Fwd: [AMBER-Developers] non-neutral ethane from antechamber FyD (Mon Jan 16 2017 - 21:40:17 PST)
[AMBER] pmemd.cuda.MPI not running well with SGE Wang, Yin (Tue Jan 17 2017 - 03:22:54 PST)
- Re: [AMBER] pmemd.cuda.MPI not running well with SGE Daniel Roe (Tue Jan 17 2017 - 06:07:29 PST)
  - Re: [AMBER] pmemd.cuda.MPI not running well with SGE Ross Walker (Tue Jan 17 2017 - 17:51:40 PST)
    - Re: [AMBER] pmemd.cuda.MPI not running well with SGE Scott Le Grand (Wed Jan 18 2017 - 10:00:51 PST)
  - Re: [AMBER] pmemd.cuda.MPI not running well with SGE Chris Neale (Wed Jan 18 2017 - 10:06:59 PST)
  - Re: [AMBER] pmemd.cuda.MPI not running well with SGE Wang, Yin (Tue Feb 14 2017 - 08:12:15 PST)
[AMBER] TIP4P-Ew vs TIP3 vs TIP5 DmitryASuplatov (Tue Jan 17 2017 - 07:21:30 PST)
- Re: [AMBER] TIP4P-Ew vs TIP3 vs TIP5 Elvis Martis (Tue Jan 17 2017 - 21:03:57 PST)
- Re: [AMBER] TIP4P-Ew vs TIP3 vs TIP5 Saeed Izadi (Tue Jan 17 2017 - 21:13:41 PST)
  - Re: [AMBER] TIP4P-Ew vs TIP3 vs TIP5 DmitrySuplatov (Wed Jan 18 2017 - 03:13:35 PST)
    - Re: [AMBER] TIP4P-Ew vs TIP3 vs TIP5 Saeed Izadi (Wed Jan 18 2017 - 13:17:45 PST)
[AMBER] matching times from .out with frames from .mdcrd Chris Neale (Tue Jan 17 2017 - 10:00:30 PST)
- Re: [AMBER] matching times from .out with frames from .mdcrd Daniel Roe (Tue Jan 17 2017 - 10:19:21 PST)
- Re: [AMBER] matching times from .out with frames from .mdcrd David A Case (Wed Jan 18 2017 - 12:37:06 PST)
[AMBER] ACPYPE now works with GAFF2 Alan (Tue Jan 17 2017 - 10:42:26 PST)
[AMBER] Reference for GAFF2? Alan (Tue Jan 17 2017 - 14:36:34 PST)
- Re: [AMBER] Reference for GAFF2? Albert (Tue Jan 17 2017 - 22:53:44 PST)
  - Re: [AMBER] Reference for GAFF2? Alan (Wed Jan 18 2017 - 00:04:06 PST)
    - Re: [AMBER] Reference for GAFF2? Albert (Wed Jan 18 2017 - 00:16:07 PST)
[AMBER] rmsf value for 2 chains Hirdesh Kumar (Tue Jan 17 2017 - 15:08:59 PST)
- Re: [AMBER] rmsf value for 2 chains Daniel Roe (Fri Jan 20 2017 - 13:56:55 PST)
[AMBER] amber16 Centos 7 Coleman, Marcus [JRDUS Non-J&J] (Tue Jan 17 2017 - 15:50:54 PST)
- Re: [AMBER] amber16 Centos 7 Nhai (Tue Jan 17 2017 - 16:05:19 PST)
  - Re: [AMBER] amber16 Centos 7 Coleman, Marcus [JRDUS Non-J&J] (Tue Jan 17 2017 - 16:17:13 PST)
- Re: [AMBER] amber16 Centos 7 Daniel Roe (Tue Jan 17 2017 - 16:23:45 PST)
  - Re: [AMBER] amber16 Centos 7 Coleman, Marcus [JRDUS Non-J&J] (Tue Jan 17 2017 - 19:08:57 PST)
    - Re: [AMBER] amber16 Centos 7 Hai Nguyen (Tue Jan 17 2017 - 19:17:07 PST)
    - Re: [AMBER] amber16 Centos 7 Coleman, Marcus [JRDUS Non-J&J] (Tue Jan 17 2017 - 19:23:04 PST)
    - Re: [AMBER] amber16 Centos 7 Coleman, Marcus [JRDUS Non-J&J] (Tue Jan 17 2017 - 19:24:06 PST)
    - Re: [AMBER] amber16 Centos 7 Hai Nguyen (Tue Jan 17 2017 - 19:35:29 PST)
    - Re: [AMBER] amber16 Centos 7 Coleman, Marcus [JRDUS Non-J&J] (Tue Jan 17 2017 - 19:45:20 PST)
    - Re: [AMBER] amber16 Centos 7 Hai Nguyen (Tue Jan 17 2017 - 19:46:52 PST)
    - Re: [AMBER] amber16 Centos 7 Jason Swails (Tue Jan 17 2017 - 19:55:33 PST)
    - Re: [AMBER] amber16 Centos 7 Coleman, Marcus [JRDUS Non-J&J] (Tue Jan 17 2017 - 21:03:57 PST)
  - Re: [AMBER] amber16 Centos 7 James Kress (Wed Jan 18 2017 - 08:22:23 PST)
    - Re: [AMBER] amber16 Centos 7 Hai Nguyen (Wed Jan 18 2017 - 08:36:35 PST)
[AMBER] antechamber syntax error Aseel Bala Ahmed (Tue Jan 17 2017 - 17:38:03 PST)
- Re: [AMBER] antechamber syntax error Hai Nguyen (Tue Jan 17 2017 - 19:45:05 PST)
- Re: [AMBER] antechamber syntax error David A Case (Wed Jan 18 2017 - 05:27:06 PST)
  - Re: [AMBER] antechamber syntax error Aseel Bala (Wed Jan 18 2017 - 07:25:52 PST)
    - Re: [AMBER] antechamber syntax error David A Case (Wed Jan 18 2017 - 12:18:51 PST)
[AMBER] Model Folding Wong Li Zhe (Tue Jan 17 2017 - 18:49:02 PST)
- Re: [AMBER] Model Folding Nhai (Tue Jan 17 2017 - 19:10:19 PST)
  - Re: [AMBER] Model Folding Wong Li Zhe (Tue Jan 17 2017 - 22:23:16 PST)
    - Re: [AMBER] Model Folding Nhai (Tue Jan 17 2017 - 22:43:38 PST)
[AMBER] Installing Amber Karla Galdamez (Tue Jan 17 2017 - 22:24:50 PST)
- Re: [AMBER] Installing Amber Nhai (Tue Jan 17 2017 - 22:47:23 PST)
  - Re: [AMBER] Installing Amber Karla Galdamez (Fri Jan 20 2017 - 21:53:30 PST)
    - Re: [AMBER] Installing Amber Hai Nguyen (Fri Jan 20 2017 - 21:58:11 PST)
    - Re: [AMBER] Installing Amber Karla Galdamez (Fri Jan 20 2017 - 23:28:48 PST)
    - Re: [AMBER] Installing Amber Hai Nguyen (Fri Jan 20 2017 - 23:43:13 PST)
    - Re: [AMBER] Installing Amber Karla Galdamez (Sat Jan 21 2017 - 21:44:14 PST)
    - Re: [AMBER] Installing Amber Hai Nguyen (Sat Jan 21 2017 - 21:55:26 PST)
    - Re: [AMBER] Installing Amber Karla Galdamez (Tue Jan 24 2017 - 22:29:22 PST)
    - Re: [AMBER] Installing Amber David A Case (Wed Jan 25 2017 - 05:03:35 PST)
    - Re: [AMBER] Installing Amber Karla Galdamez (Wed Jan 25 2017 - 23:08:38 PST)
    - Re: [AMBER] Installing Amber David Case (Thu Jan 26 2017 - 05:21:50 PST)
    - Re: [AMBER] Installing Amber Karla Galdamez (Thu Jan 26 2017 - 23:08:06 PST)
    - Re: [AMBER] Installing Amber Bill Ross (Sat Jan 21 2017 - 01:10:55 PST)
[AMBER] Kmeans-clustering : AvgDist query Bala subramanian (Wed Jan 18 2017 - 02:51:04 PST)
- Re: [AMBER] Kmeans-clustering : AvgDist query Daniel Roe (Fri Jan 20 2017 - 13:54:29 PST)
[AMBER] Error while creation topology and coordinate files in tleap Manjula Saravanan (Wed Jan 18 2017 - 02:53:24 PST)
- Re: [AMBER] Error while creation topology and coordinate files in tleap Elvis Martis (Wed Jan 18 2017 - 03:06:13 PST)
- Re: [AMBER] Error while creation topology and coordinate files in tleap David A Case (Wed Jan 18 2017 - 12:32:50 PST)
[AMBER] REMD_suggestion Thakur, Abhishek (Wed Jan 18 2017 - 07:03:26 PST)
- Re: [AMBER] REMD_suggestion Hai Nguyen (Wed Jan 18 2017 - 08:33:45 PST)
[AMBER] Center atoms (translate & rotate reference) abdennour braka (Wed Jan 18 2017 - 08:40:07 PST)
- Re: [AMBER] Center atoms (translate & rotate reference) Daniel Roe (Thu Jan 19 2017 - 07:00:02 PST)
[AMBER] Fwd: some clues about yacc errors on OLCF rhea Ada Sedova (Wed Jan 18 2017 - 10:19:24 PST)
- Re: [AMBER] Fwd: some clues about yacc errors on OLCF rhea Scott Brozell (Wed Jan 18 2017 - 10:44:41 PST)
  - Re: [AMBER] Fwd: some clues about yacc errors on OLCF rhea Scott Brozell (Wed Jan 18 2017 - 11:06:33 PST)
    - Re: [AMBER] Fwd: some clues about yacc errors on OLCF rhea Ada Sedova (Wed Jan 18 2017 - 11:41:22 PST)
- Re: [AMBER] Fwd: some clues about yacc errors on OLCF rhea Hai Nguyen (Wed Jan 18 2017 - 10:44:51 PST)
  - Re: [AMBER] Fwd: some clues about yacc errors on OLCF rhea Ada Sedova (Wed Jan 18 2017 - 11:43:37 PST)
  - Re: [AMBER] Fwd: some clues about yacc errors on OLCF rhea David A Case (Wed Jan 18 2017 - 12:25:21 PST)
    - Re: [AMBER] Fwd: some clues about yacc errors on OLCF rhea Ada Sedova (Wed Jan 18 2017 - 13:29:37 PST)
    - Re: [AMBER] Fwd: some clues about yacc errors on OLCF rhea Scott Brozell (Wed Jan 18 2017 - 13:57:55 PST)
    - Re: [AMBER] Fwd: some clues about yacc errors on OLCF rhea Ada Sedova (Wed Jan 18 2017 - 20:04:45 PST)
[AMBER] Fwd: amber14 parallel build problems Ada Sedova (Wed Jan 18 2017 - 11:44:38 PST)
- Re: [AMBER] Fwd: amber14 parallel build problems Hai Nguyen (Wed Jan 18 2017 - 11:54:20 PST)
  - Re: [AMBER] Fwd: amber14 parallel build problems Ada Sedova (Wed Jan 18 2017 - 11:58:35 PST)
    - Re: [AMBER] Fwd: amber14 parallel build problems Ada Sedova (Wed Jan 18 2017 - 12:05:50 PST)
    - Re: [AMBER] Fwd: amber14 parallel build problems Hai Nguyen (Wed Jan 18 2017 - 12:09:32 PST)
    - Re: [AMBER] Fwd: amber14 parallel build problems Ada Sedova (Wed Jan 18 2017 - 12:20:31 PST)
    - Re: [AMBER] Fwd: amber14 parallel build problems Hai Nguyen (Wed Jan 18 2017 - 12:23:37 PST)
    - Re: [AMBER] Fwd: amber14 parallel build problems Ada Sedova (Wed Jan 18 2017 - 12:30:21 PST)
  - Re: [AMBER] Fwd: amber14 parallel build problems Hai Nguyen (Wed Jan 18 2017 - 12:00:09 PST)
[AMBER] constrain nitrate as bound and neutral Liyang Zhu (Wed Jan 18 2017 - 12:22:03 PST)
- Re: [AMBER] constrain nitrate as bound and neutral David Case (Sat Jan 21 2017 - 19:24:47 PST)
  - Re: [AMBER] constrain nitrate as bound and neutral Liyang Zhu (Sat Jan 21 2017 - 19:57:45 PST)
    - Re: [AMBER] constrain nitrate as bound and neutral Pengfei Li (Sat Jan 21 2017 - 20:11:30 PST)
    - Re: [AMBER] constrain nitrate as bound and neutral Liyang Zhu (Sun Jan 22 2017 - 16:01:44 PST)
    - Re: [AMBER] constrain nitrate as bound and neutral Pengfei Li (Wed Jan 25 2017 - 07:54:29 PST)
    - Re: [AMBER] constrain nitrate as bound and neutral Liyang Zhu (Wed Jan 25 2017 - 10:54:04 PST)
    - Re: [AMBER] constrain nitrate as bound and neutral Pengfei Li (Wed Jan 25 2017 - 13:56:42 PST)
    - Re: [AMBER] constrain nitrate as bound and neutral Pengfei Li (Wed Feb 01 2017 - 07:48:35 PST)
[AMBER] About constraints on QM system of QM/MM simulation Pengfei Li (Wed Jan 18 2017 - 14:04:07 PST)
- Re: [AMBER] About constraints on QM system of QM/MM simulation Marc van der Kamp (Wed Jan 18 2017 - 14:14:24 PST)
- Re: [AMBER] About constraints on QM system of QM/MM simulation Goetz, Andreas (Wed Jan 18 2017 - 14:14:30 PST)
  - Re: [AMBER] About constraints on QM system of QM/MM simulation Pengfei Li (Wed Jan 18 2017 - 14:33:06 PST)
[AMBER] REGARDING ACPYPE GENERATED TOPOLOGY FILE Subashini .K (Wed Jan 18 2017 - 21:24:05 PST)
[AMBER] Regarding trajectory analysis Debodyuti Dutta (Wed Jan 18 2017 - 21:24:48 PST)
- Re: [AMBER] Regarding trajectory analysis Daniel Roe (Thu Jan 19 2017 - 06:57:15 PST)
[AMBER] cpptraj: list command throws seqfault Thomas Fox (Thu Jan 19 2017 - 04:58:36 PST)
- Re: [AMBER] cpptraj: list command throws seqfault Daniel Roe (Thu Jan 19 2017 - 05:22:20 PST)
  - Re: [AMBER] cpptraj: list command throws seqfault Daniel Roe (Thu Jan 19 2017 - 06:42:36 PST)
[AMBER] valiine chirality inversion Thomas Pochapsky (Thu Jan 19 2017 - 05:52:10 PST)
- Re: [AMBER] valiine chirality inversion David Case (Sat Jan 21 2017 - 19:09:18 PST)
[AMBER] REMD_Multiple_GPU Thakur, Abhishek (Thu Jan 19 2017 - 08:29:57 PST)
- Re: [AMBER] REMD_Multiple_GPU Hai Nguyen (Thu Jan 19 2017 - 08:36:17 PST)
[AMBER] Amber tutorial of APR(attach-pull-release) approach Jian Yin (Thu Jan 19 2017 - 10:58:52 PST)
[AMBER] Distance between the center of gravities of tow molecules-CPPTRAJ konda003 . (Thu Jan 19 2017 - 11:01:06 PST)
- Re: [AMBER] Distance between the center of gravities of tow molecules-CPPTRAJ Daniel Roe (Thu Jan 19 2017 - 11:21:24 PST)
[AMBER] setup_equilibrate_input.x Thakur, Abhishek (Thu Jan 19 2017 - 11:40:09 PST)
- Re: [AMBER] setup_equilibrate_input.x Hai Nguyen (Thu Jan 19 2017 - 14:15:14 PST)
[AMBER] cpptraj: segfault after list command Thomas Fox (Fri Jan 20 2017 - 05:07:53 PST)
[AMBER] adqmmm with PM6 for copper complex M_Chikira (Fri Jan 20 2017 - 05:13:46 PST)
- Re: [AMBER] adqmmm with PM6 for copper complex Dr. Robert Molt (Fri Jan 20 2017 - 05:25:34 PST)
  - Re: [AMBER] adqmmm with PM6 for copper complex M_Chikira (Fri Jan 20 2017 - 20:46:45 PST)
[AMBER] Interpreting energy decomposition in Amber thermodynamic integration Stefan Ivanov (Fri Jan 20 2017 - 07:28:00 PST)
- Re: [AMBER] Interpreting energy decomposition in Amber thermodynamic integration David A Case (Fri Jan 20 2017 - 09:25:05 PST)
  - Re: [AMBER] Interpreting energy decomposition in Amber thermodynamic integration Stefan Ivanov (Fri Jan 20 2017 - 09:56:06 PST)
    - Re: [AMBER] Interpreting energy decomposition in Amber thermodynamic integration David Case (Sat Jan 21 2017 - 19:05:02 PST)
    - Re: [AMBER] Interpreting energy decomposition in Amber thermodynamic integration Stefan Ivanov (Sun Jan 22 2017 - 02:31:05 PST)
    - Re: [AMBER] Interpreting energy decomposition in Amber thermodynamic integration David Case (Mon Jan 23 2017 - 04:45:53 PST)
    - Re: [AMBER] Interpreting energy decomposition in Amber thermodynamic integration Stefan Ivanov (Mon Jan 23 2017 - 11:27:38 PST)
[AMBER] Ntt value for Nose-hoover chain thermostat Samaneh Ghassabi Kondalaji (Fri Jan 20 2017 - 12:46:39 PST)
- Re: [AMBER] Ntt value for Nose-hoover chain thermostat David Case (Sat Jan 21 2017 - 19:15:11 PST)
  - Re: [AMBER] Ntt value for Nose-hoover chain thermostat Samaneh Ghassabi Kondalaji (Mon Jan 23 2017 - 08:01:33 PST)
[AMBER] Pure POPC Membrane Tilts during MD simulation Rodriguez, Yoel (Sat Jan 21 2017 - 16:21:52 PST)
- Re: [AMBER] Pure POPC Membrane Tilts during MD simulation Dickson, Callum J (Mon Jan 23 2017 - 14:41:28 PST)
  - Re: [AMBER] Pure POPC Membrane Tilts during MD simulation Rodriguez, Yoel (Tue Jan 24 2017 - 07:41:26 PST)
- Re: [AMBER] Pure POPC Membrane Tilts during MD simulation Daniel Roe (Tue Jan 24 2017 - 05:23:29 PST)
  - Re: [AMBER] Pure POPC Membrane Tilts during MD simulation Rodriguez, Yoel (Tue Jan 24 2017 - 07:48:17 PST)
    - Re: [AMBER] Pure POPC Membrane Tilts during MD simulation Daniel Roe (Tue Jan 24 2017 - 10:53:54 PST)
    - Re: [AMBER] Pure POPC Membrane Tilts during MD simulation Rodriguez, Yoel (Tue Jan 24 2017 - 11:20:07 PST)
[AMBER] [david.case.rutgers.edu: Re: Modified residue separated in leap module] David Case (Mon Jan 23 2017 - 04:52:52 PST)
- Re: [AMBER] [david.case.rutgers.edu: Re: Modified residue separated in leap module] asdda asa (Mon Jan 23 2017 - 12:34:29 PST)
  - Re: [AMBER] [david.case.rutgers.edu: Re: Modified residue separated in leap module] Bill Ross (Mon Jan 23 2017 - 15:33:24 PST)
    - Re: [AMBER] [david.case.rutgers.edu: Re: Modified residue separated in leap module] asdda asa (Mon Jan 23 2017 - 17:00:27 PST)
[AMBER] INCREASING BOX SIZE Subashini .K (Mon Jan 23 2017 - 08:05:51 PST)
- Re: [AMBER] INCREASING BOX SIZE David Case (Mon Jan 23 2017 - 18:48:58 PST)
[AMBER] REMD_suggestion Thakur, Abhishek (Mon Jan 23 2017 - 08:46:51 PST)
- Re: [AMBER] REMD_suggestion Adrian Roitberg (Mon Jan 23 2017 - 08:50:29 PST)
  - Re: [AMBER] REMD_suggestion Thakur, Abhishek (Mon Jan 23 2017 - 08:59:45 PST)
    - Re: [AMBER] REMD_suggestion Adrian Roitberg (Mon Jan 23 2017 - 09:01:31 PST)
    - Re: [AMBER] REMD_suggestion Thakur, Abhishek (Mon Jan 23 2017 - 09:05:23 PST)
[AMBER] From PMF to free energy of binding Andreas Tosstorff (Mon Jan 23 2017 - 09:03:17 PST)
- Re: [AMBER] From PMF to free energy of binding Niel Henriksen (Mon Jan 23 2017 - 11:51:09 PST)
  - Re: [AMBER] From PMF to free energy of binding Andreas Tosstorff (Tue Jan 24 2017 - 00:53:30 PST)
- Re: [AMBER] From PMF to free energy of binding David Case (Tue Jan 24 2017 - 05:46:20 PST)
  - Re: [AMBER] From PMF to free energy of binding Andreas Tosstorff (Tue Jan 24 2017 - 07:42:39 PST)
[AMBER] In REMD there is two irest=0 in amber tut Thakur, Abhishek (Mon Jan 23 2017 - 09:18:38 PST)
- Re: [AMBER] In REMD there is two irest=0 in amber tut Bill Ross (Mon Jan 23 2017 - 11:16:47 PST)
[AMBER] Simulating lipid bilayer below phase transition temperature Casalini Tommaso (Mon Jan 23 2017 - 14:12:24 PST)
- Re: [AMBER] Simulating lipid bilayer below phase transition temperature Dickson, Callum J (Mon Jan 23 2017 - 14:37:52 PST)
  - Re: [AMBER] Simulating lipid bilayer below phase transition temperature Casalini Tommaso (Tue Jan 24 2017 - 07:41:32 PST)
    - Re: [AMBER] Simulating lipid bilayer below phase transition temperature Dickson, Callum J (Tue Jan 24 2017 - 11:06:28 PST)
[AMBER] Error opening unit 15: File "remd.groupfile" is missing or unreadable Thakur, Abhishek (Mon Jan 23 2017 - 14:25:19 PST)
- Re: [AMBER] Error opening unit 15: File "remd.groupfile" is missing or unreadable Nhai (Mon Jan 23 2017 - 14:58:58 PST)
  - Re: [AMBER] Error opening unit 15: File "remd.groupfile" is missing or unreadable Thakur, Abhishek (Mon Jan 23 2017 - 15:15:31 PST)
    - Re: [AMBER] Error opening unit 15: File "remd.groupfile" is missing or unreadable Adrian Roitberg (Mon Jan 23 2017 - 15:31:05 PST)
[AMBER] Regarding forcefields for Z-DNA Yogeeshwar Ajjugal (Tue Jan 24 2017 - 01:53:24 PST)
- Re: [AMBER] Regarding forcefields for Z-DNA Jiri Sponer (Tue Jan 24 2017 - 02:12:35 PST)
  - Re: [AMBER] Regarding forcefields for Z-DNA Yogeeshwar Ajjugal (Tue Jan 24 2017 - 04:01:44 PST)
    - Re: [AMBER] Regarding forcefields for Z-DNA Yogeeshwar Ajjugal (Thu Jan 26 2017 - 05:55:02 PST)
    - Re: [AMBER] Regarding forcefields for Z-DNA Debayan Chakraborty (Sat Jan 28 2017 - 12:29:24 PST)
    - Re: [AMBER] Regarding forcefields for Z-DNA Josh Berryman (Wed Feb 01 2017 - 01:38:24 PST)
    - Re: [AMBER] Regarding forcefields for Z-DNA Jiri Sponer (Sat Feb 04 2017 - 03:13:55 PST)
[AMBER] error in finding vdW (or other) parameters for type Fatemeh Fatemi (Tue Jan 24 2017 - 03:42:54 PST)
- Re: [AMBER] error in finding vdW (or other) parameters for type David Case (Tue Jan 24 2017 - 05:52:20 PST)
[AMBER] paramfit stephanie.essafi.ens.fr (Tue Jan 24 2017 - 05:23:03 PST)
[AMBER] QM method used for force constants derivation in GAFF2 ? Marek Maly (Tue Jan 24 2017 - 09:47:19 PST)
- Re: [AMBER] QM method used for force constants derivation in GAFF2 ? David Case (Tue Jan 24 2017 - 10:44:34 PST)
  - Re: [AMBER] QM method used for force constants derivation in GAFF2 ? Marek Maly (Tue Jan 24 2017 - 17:24:19 PST)
    - Re: [AMBER] QM method used for force constants derivation in GAFF2 ? Junmei Wang (Thu Jan 26 2017 - 10:04:30 PST)
    - Re: [AMBER] QM method used for force constants derivation in GAFF2 ? Marek Maly (Thu Jan 26 2017 - 16:02:29 PST)
    - Re: [AMBER] QM method used for force constants derivation in GAFF2 ? Marek Maly (Sat Feb 04 2017 - 19:24:56 PST)
    - Re: [AMBER] QM method used for force constants derivation in GAFF2 ? Karl Kirschner (Mon Feb 06 2017 - 01:48:03 PST)
    - Re: [AMBER] QM method used for force constants derivation in GAFF2 ? Marek Maly (Thu Feb 09 2017 - 18:20:19 PST)
[AMBER] REMD_just_1.10ns/day Thakur, Abhishek (Tue Jan 24 2017 - 10:53:26 PST)
- Re: [AMBER] REMD_just_1.10ns/day Hai Nguyen (Tue Jan 24 2017 - 11:01:44 PST)
  - Re: [AMBER] REMD_just_1.10ns/day Thakur, Abhishek (Tue Jan 24 2017 - 11:15:12 PST)
    - Re: [AMBER] REMD_just_1.10ns/day Hai Nguyen (Tue Jan 24 2017 - 11:33:43 PST)
- Re: [AMBER] REMD_just_1.10ns/day Carlos Simmerling (Tue Jan 24 2017 - 12:50:28 PST)
  - Re: [AMBER] REMD_just_1.10ns/day Thakur, Abhishek (Tue Jan 24 2017 - 12:58:37 PST)
    - Re: [AMBER] REMD_just_1.10ns/day Adrian Roitberg (Tue Jan 24 2017 - 13:09:35 PST)
    - Re: [AMBER] REMD_just_1.10ns/day Thakur, Abhishek (Tue Jan 24 2017 - 15:11:57 PST)
    - Re: [AMBER] REMD_just_1.10ns/day Hai Nguyen (Tue Jan 24 2017 - 15:21:34 PST)
    - Re: [AMBER] REMD_just_1.10ns/day Carlos Simmerling (Tue Jan 24 2017 - 16:37:40 PST)
[AMBER] Reproduce tetraalanine Phi and Psi amplitudes ff99SB with Paramfit BOSISIO Stefano (Tue Jan 24 2017 - 11:07:29 PST)
- Re: [AMBER] Reproduce tetraalanine Phi and Psi amplitudes ff99SB with Paramfit Robin Betz (Tue Jan 24 2017 - 11:35:16 PST)
  - Re: [AMBER] Reproduce tetraalanine Phi and Psi amplitudes ff99SB with Paramfit Carlos Simmerling (Tue Jan 24 2017 - 12:49:13 PST)
    - Re: [AMBER] Reproduce tetraalanine Phi and Psi amplitudes ff99SB with Paramfit Robin Betz (Tue Jan 24 2017 - 14:43:43 PST)
[AMBER] Issue with solvateOct for a large system benedikt.diewald.fau.de (Wed Jan 25 2017 - 07:03:34 PST)
- Re: [AMBER] Issue with solvateOct for a large system David Case (Wed Jan 25 2017 - 11:10:12 PST)
[AMBER] distance restraints failed Qinghua Liao (Wed Jan 25 2017 - 07:44:55 PST)
- Re: [AMBER] distance restraints failed Carlos Simmerling (Wed Jan 25 2017 - 07:49:42 PST)
  - Re: [AMBER] distance restraints failed Nhai (Wed Jan 25 2017 - 07:52:37 PST)
    - Re: [AMBER] distance restraints failed Qinghua Liao (Wed Jan 25 2017 - 08:15:10 PST)
    - Re: [AMBER] distance restraints failed Thakur, Abhishek (Wed Jan 25 2017 - 08:37:51 PST)
    - Re: [AMBER] distance restraints failed Qinghua Liao (Wed Jan 25 2017 - 11:11:50 PST)
  - Re: [AMBER] distance restraints failed Qinghua Liao (Wed Jan 25 2017 - 08:10:59 PST)
    - Re: [AMBER] distance restraints failed Carlos Simmerling (Wed Jan 25 2017 - 09:46:53 PST)
    - Re: [AMBER] distance restraints failed Adrian Roitberg (Wed Jan 25 2017 - 09:52:16 PST)
    - Re: [AMBER] distance restraints failed Qinghua Liao (Wed Jan 25 2017 - 10:40:51 PST)
    - Re: [AMBER] distance restraints failed Adrian Roitberg (Wed Jan 25 2017 - 10:45:44 PST)
    - Re: [AMBER] distance restraints failed Qinghua Liao (Wed Jan 25 2017 - 10:50:13 PST)
    - Re: [AMBER] distance restraints failed Qinghua Liao (Wed Jan 25 2017 - 10:32:23 PST)
- Re: [AMBER] distance restraints failed David Case (Wed Jan 25 2017 - 11:06:12 PST)
  - Re: [AMBER] distance restraints failed Qinghua Liao (Wed Jan 25 2017 - 11:31:51 PST)
[AMBER] Give the correct charge to heme using antechamber Matteo Uggeri (Thu Jan 26 2017 - 06:15:44 PST)
- Re: [AMBER] Give the correct charge to heme using antechamber David Case (Thu Jan 26 2017 - 09:11:44 PST)
  - Re: [AMBER] Give the correct charge to heme using antechamber Elvis Martis (Thu Jan 26 2017 - 20:22:38 PST)
    - Re: [AMBER] Give the correct charge to heme using antechamber Matteo Uggeri (Wed Feb 01 2017 - 06:36:41 PST)
[AMBER] Split a trajectory into frames Elisa Pieri (Thu Jan 26 2017 - 06:35:11 PST)
- Re: [AMBER] Split a trajectory into frames Kenneth Huang (Thu Jan 26 2017 - 06:50:51 PST)
  - Re: [AMBER] Split a trajectory into frames Daniel Roe (Thu Jan 26 2017 - 07:09:47 PST)
  - Re: [AMBER] Split a trajectory into frames Elisa Pieri (Thu Jan 26 2017 - 07:10:19 PST)
    - Re: [AMBER] Split a trajectory into frames Nhai (Thu Jan 26 2017 - 07:26:01 PST)
    - Re: [AMBER] Split a trajectory into frames Elisa Pieri (Thu Jan 26 2017 - 07:30:26 PST)
    - Re: [AMBER] Split a trajectory into frames Nhai (Thu Jan 26 2017 - 07:38:17 PST)
    - Re: [AMBER] Split a trajectory into frames Elisa Pieri (Thu Jan 26 2017 - 07:42:31 PST)
    - Re: [AMBER] Split a trajectory into frames Casalini Tommaso (Thu Jan 26 2017 - 07:45:55 PST)
    - Re: [AMBER] Split a trajectory into frames Adrian Roitberg (Thu Jan 26 2017 - 07:47:47 PST)
    - Re: [AMBER] Split a trajectory into frames Elisa Pieri (Thu Jan 26 2017 - 07:53:45 PST)
    - Re: [AMBER] Split a trajectory into frames Nhai (Thu Jan 26 2017 - 07:57:27 PST)
    - Re: [AMBER] Split a trajectory into frames Daniel Roe (Thu Jan 26 2017 - 08:00:38 PST)
    - Re: [AMBER] Split a trajectory into frames Elisa Pieri (Thu Jan 26 2017 - 08:12:59 PST)
    - Re: [AMBER] Split a trajectory into frames Kenneth Huang (Thu Jan 26 2017 - 07:48:10 PST)
[AMBER] 5' Terminal Phosphate Parameters Paul Meister (Thu Jan 26 2017 - 06:54:30 PST)
- Re: [AMBER] 5' Terminal Phosphate Parameters Qinghua Liao (Thu Jan 26 2017 - 06:57:06 PST)
  - Re: [AMBER] 5' Terminal Phosphate Parameters Paul Meister (Thu Jan 26 2017 - 07:49:19 PST)
- Re: [AMBER] 5' Terminal Phosphate Parameters David Case (Thu Jan 26 2017 - 09:21:00 PST)
  - Re: [AMBER] 5' Terminal Phosphate Parameters Paul Meister (Thu Jan 26 2017 - 11:28:19 PST)
    - Re: [AMBER] 5' Terminal Phosphate Parameters David Case (Thu Jan 26 2017 - 19:05:11 PST)
    - Re: [AMBER] 5' Terminal Phosphate Parameters David Case (Fri Jan 27 2017 - 06:30:01 PST)
    - Re: [AMBER] 5' Terminal Phosphate Parameters FyD (Thu Jan 26 2017 - 22:47:42 PST)
[AMBER] How to make restrt file for specific step Thakur, Abhishek (Thu Jan 26 2017 - 11:52:58 PST)
- Re: [AMBER] How to make restrt file for specific step Hai Nguyen (Thu Jan 26 2017 - 11:56:29 PST)
  - Re: [AMBER] How to make restrt file for specific step Thakur, Abhishek (Thu Jan 26 2017 - 12:08:26 PST)
    - Re: [AMBER] How to make restrt file for specific step Hai Nguyen (Thu Jan 26 2017 - 12:11:14 PST)
    - Re: [AMBER] How to make restrt file for specific step Bill Ross (Thu Jan 26 2017 - 12:13:10 PST)
    - Re: [AMBER] How to make restrt file for specific step Thakur, Abhishek (Thu Jan 26 2017 - 12:16:44 PST)
    - Re: [AMBER] How to make restrt file for specific step Daniel Roe (Thu Jan 26 2017 - 12:30:16 PST)
    - Re: [AMBER] How to make restrt file for specific step Thakur, Abhishek (Thu Jan 26 2017 - 12:57:33 PST)
    - Re: [AMBER] How to make restrt file for specific step Bill Ross (Thu Jan 26 2017 - 13:13:01 PST)
    - Re: [AMBER] How to make restrt file for specific step Bill Ross (Thu Jan 26 2017 - 15:34:33 PST)
    - Re: [AMBER] How to make restrt file for specific step Thakur, Abhishek (Thu Jan 26 2017 - 15:54:20 PST)
    - Re: [AMBER] How to make restrt file for specific step Thakur, Abhishek (Fri Jan 27 2017 - 06:47:09 PST)
    - Re: [AMBER] How to make restrt file for specific step Bill Ross (Fri Jan 27 2017 - 09:01:57 PST)
    - Re: [AMBER] How to make restrt file for specific step Daniel Roe (Fri Jan 27 2017 - 10:18:15 PST)
[AMBER] Implicit Solvent CpHMD Chase Zagorec-Marks (Thu Jan 26 2017 - 12:29:21 PST)
- Re: [AMBER] Implicit Solvent CpHMD Jason Swails (Thu Jan 26 2017 - 17:51:34 PST)
  - Re: [AMBER] Implicit Solvent CpHMD Chase Zagorec-Marks (Fri Jan 27 2017 - 17:52:17 PST)
[AMBER] Thermodynamic Integration on GPU in AMBER16? Hadházi Ádám (Thu Jan 26 2017 - 13:30:12 PST)
- Re: [AMBER] Thermodynamic Integration on GPU in AMBER16? Daniel Mermelstein (Thu Jan 26 2017 - 18:58:21 PST)
[AMBER] Fw: Process exclusive mode and GPU peer-to-peer communication Matthew Harrigan (Thu Jan 26 2017 - 14:12:39 PST)
- Re: [AMBER] Process exclusive mode and GPU peer-to-peer communication Ross Walker (Fri Jan 27 2017 - 04:54:13 PST)
  - Re: [AMBER] Process exclusive mode and GPU peer-to-peer communication Scott Le Grand (Fri Jan 27 2017 - 08:43:03 PST)
    - Re: [AMBER] Process exclusive mode and GPU peer-to-peer communication Matthew Harrigan (Fri Jan 27 2017 - 08:58:34 PST)
[AMBER] the formatting of the CPPTRAJ-generated restart files Vlad Cojocaru (Fri Jan 27 2017 - 01:56:54 PST)
- Re: [AMBER] the formatting of the CPPTRAJ-generated restart files Hannes Loeffler (Fri Jan 27 2017 - 02:12:46 PST)
  - Re: [AMBER] the formatting of the CPPTRAJ-generated restart files Vlad Cojocaru (Fri Jan 27 2017 - 02:26:08 PST)
[AMBER] how to Neutralize system automatically? Albert (Fri Jan 27 2017 - 02:00:37 PST)
- Re: [AMBER] how to Neutralize system automatically? Eric Lang (Fri Jan 27 2017 - 03:34:35 PST)
[AMBER] Free energy techniques for conformational changes and alchemical mutations Hadházi Ádám (Fri Jan 27 2017 - 02:25:20 PST)
[AMBER] Peptide with non-standard residues Andreas Tosstorff (Fri Jan 27 2017 - 03:03:36 PST)
- Re: [AMBER] Peptide with non-standard residues David Case (Fri Jan 27 2017 - 06:39:27 PST)
  - Re: [AMBER] Peptide with non-standard residues Andreas Tosstorff (Fri Jan 27 2017 - 07:47:59 PST)
    - Re: [AMBER] Peptide with non-standard residues David Case (Fri Jan 27 2017 - 12:46:33 PST)
[AMBER] TI simulations blowing up with clambda = 1 with pmemd Stefan Ivanov (Fri Jan 27 2017 - 03:15:02 PST)
- Re: [AMBER] TI simulations blowing up with clambda = 1 with pmemd Hannes Loeffler (Fri Jan 27 2017 - 03:30:46 PST)
- Re: [AMBER] TI simulations blowing up with clambda = 1 with pmemd Hannes Loeffler (Fri Jan 27 2017 - 06:04:07 PST)
  - Re: [AMBER] TI simulations blowing up with clambda = 1 with pmemd Stefan Ivanov (Fri Jan 27 2017 - 06:54:38 PST)
    - Re: [AMBER] TI simulations blowing up with clambda = 1 with pmemd Hannes Loeffler (Fri Jan 27 2017 - 07:46:01 PST)
    - Re: [AMBER] TI simulations blowing up with clambda = 1 with pmemd Stefan Ivanov (Fri Jan 27 2017 - 08:00:21 PST)
    - Re: [AMBER] TI simulations blowing up with clambda = 1 with pmemd Stefan Ivanov (Fri Jan 27 2017 - 08:09:16 PST)
    - Re: [AMBER] TI simulations blowing up with clambda = 1 with pmemd Hannes Loeffler (Fri Jan 27 2017 - 08:13:53 PST)
    - Re: [AMBER] TI simulations blowing up with clambda = 1 with pmemd Stefan Ivanov (Fri Jan 27 2017 - 08:17:55 PST)
    - Re: [AMBER] TI simulations blowing up with clambda = 1 with pmemd David Case (Fri Jan 27 2017 - 12:42:19 PST)
    - Re: [AMBER] TI simulations blowing up with clambda = 1 with pmemd Stefan Ivanov (Sun Jan 29 2017 - 07:07:13 PST)
    - Re: [AMBER] TI simulations blowing up with clambda = 1 with pmemd Hannes Loeffler (Mon Jan 30 2017 - 01:02:58 PST)
    - Re: [AMBER] TI simulations blowing up with clambda = 1 with pmemd Stefan Ivanov (Mon Jan 30 2017 - 02:22:04 PST)
    - Re: [AMBER] TI simulations blowing up with clambda = 1 with pmemd Hannes Loeffler (Mon Jan 30 2017 - 03:11:23 PST)
- Re: [AMBER] TI simulations blowing up with clambda = 1 with pmemd Stefan Ivanov (Mon Jan 30 2017 - 06:20:43 PST)
[AMBER] Is there any command in tleap by which I can change Met to Leu Thakur, Abhishek (Fri Jan 27 2017 - 08:04:41 PST)
- Re: [AMBER] Is there any command in tleap by which I can change Met to Leu David Case (Fri Jan 27 2017 - 12:47:43 PST)
  - Re: [AMBER] Is there any command in tleap by which I can change Met to Leu Hai Nguyen (Fri Jan 27 2017 - 13:06:53 PST)
[AMBER] Parameters Anna Cebrian Prats (Fri Jan 27 2017 - 09:00:24 PST)
- Re: [AMBER] Parameters David Case (Fri Jan 27 2017 - 12:49:51 PST)
  - Re: [AMBER] Parameters FyD (Mon Jan 30 2017 - 00:25:08 PST)
    - Re: [AMBER] Parameters FyD (Mon Jan 30 2017 - 01:12:16 PST)
[AMBER] is there any way by which I can use tleap to do mutation? Thakur, Abhishek (Fri Jan 27 2017 - 10:00:10 PST)
- Re: [AMBER] is there any way by which I can use tleap to do mutation? Elvis Martis (Sat Jan 28 2017 - 21:12:56 PST)
- Re: [AMBER] is there any way by which I can use tleap to do mutation? Gustavo Seabra (Mon Jan 30 2017 - 06:24:41 PST)
[AMBER] amber installation test failure Hirdesh Kumar (Fri Jan 27 2017 - 10:20:41 PST)
- Re: [AMBER] amber installation test failure David Case (Fri Jan 27 2017 - 12:52:11 PST)
  - Re: [AMBER] amber installation test failure Hirdesh Kumar (Mon Jan 30 2017 - 08:06:38 PST)
[AMBER] amber16 on parallel GPUs Hirdesh Kumar (Fri Jan 27 2017 - 13:06:23 PST)
- Re: [AMBER] amber16 on parallel GPUs Ross Walker (Fri Jan 27 2017 - 17:04:26 PST)
  - Re: [AMBER] amber16 on parallel GPUs Hirdesh Kumar (Mon Jan 30 2017 - 08:10:03 PST)
    - Re: [AMBER] amber16 on parallel GPUs Ross Walker (Mon Jan 30 2017 - 16:30:33 PST)
[AMBER] amber installation test question James Kress (Fri Jan 27 2017 - 20:11:04 PST)
- Re: [AMBER] amber installation test question David Case (Sat Jan 28 2017 - 07:01:15 PST)
  - Re: [AMBER] amber installation test question James Kress (Sat Jan 28 2017 - 12:25:40 PST)
    - Re: [AMBER] amber installation test question David Case (Sat Jan 28 2017 - 17:48:17 PST)
    - Re: [AMBER] amber installation test question James Kress (Sun Jan 29 2017 - 12:51:48 PST)
[AMBER] problems with input file preparation sunyeping (Sat Jan 28 2017 - 12:23:56 PST)
- Re: [AMBER] problems with input file preparation Elvis Martis (Sat Jan 28 2017 - 21:07:34 PST)
- Re: [AMBER] problems with input file preparation sunyeping (Sat Jan 28 2017 - 21:39:27 PST)
- Re: [AMBER] problems with input file preparation David Case (Sun Jan 29 2017 - 10:44:28 PST)
[AMBER] hbond Backbone CPPTRAJ. Saman Yousuf ali (Sun Jan 29 2017 - 08:19:38 PST)
- Re: [AMBER] hbond Backbone CPPTRAJ. Daniel Roe (Mon Jan 30 2017 - 08:53:15 PST)
[AMBER] pH-REMD explicit solvent Sowmya Indrakumar (Sun Jan 29 2017 - 12:59:57 PST)
- Re: [AMBER] pH-REMD explicit solvent Jason Swails (Sun Jan 29 2017 - 13:31:03 PST)
[AMBER] VMD not working after parmed Andreas Tosstorff (Mon Jan 30 2017 - 02:33:56 PST)
[AMBER] CpHMD – Effect of explicit ions when calculating the pKa of model compounds Eric Lang (Mon Jan 30 2017 - 04:33:37 PST)
- Re: [AMBER] CpHMD – Effect of explicit ions when calculating the pKa of model compounds Eric Lang (Tue Feb 07 2017 - 05:22:16 PST)
  - Re: [AMBER] CpHMD – Effect of explicit ions when calculating the pKa of model compounds Adrian Roitberg (Tue Feb 07 2017 - 05:28:11 PST)
    - Re: [AMBER] CpHMD – Effect of explicit ions when calculating the pKa of model compounds Eric Lang (Wed Feb 08 2017 - 04:16:24 PST)
  - Re: [AMBER] CpHMD – Effect of explicit ions when calculating the pKa of model compounds Jason Swails (Wed Feb 08 2017 - 19:19:24 PST)
    - Re: [AMBER] CpHMD – Effect of explicit ions when calculating the pKa of model compounds Eric Lang (Fri Feb 10 2017 - 02:34:56 PST)
    - Re: [AMBER] CpHMD – Effect of explicit ions when calculating the pKa of model compounds Eric Lang (Fri Mar 03 2017 - 06:33:24 PST)
    - Re: [AMBER] CpHMD – Effect of explicit ions when calculating the pKa of model compounds Jason Swails (Fri Mar 03 2017 - 06:47:53 PST)
    - Re: [AMBER] CpHMD – Effect of explicit ions when calculating the pKa of model compounds Adrian Roitberg (Fri Mar 03 2017 - 06:51:50 PST)
    - Re: [AMBER] CpHMD – Effect of explicit ions when calculating the pKa of model compounds Eric Lang (Fri Mar 03 2017 - 07:01:36 PST)
    - Re: [AMBER] CpHMD – Effect of explicit ions when calculating the pKa of model compounds Adrian Roitberg (Fri Mar 03 2017 - 07:02:52 PST)
    - Re: [AMBER] CpHMD – Effect of explicit ions when calculating the pKa of model compounds Eric Lang (Fri Mar 03 2017 - 06:52:38 PST)
    - Re: [AMBER] CpHMD – Effect of explicit ions when calculating the pKa of model compounds Eric Lang (Tue Mar 14 2017 - 07:40:22 PDT)
    - Re: [AMBER] CpHMD – Effect of explicit ions when calculating the pKa of model compounds Jason Swails (Tue Mar 14 2017 - 10:53:25 PDT)
    - Re: [AMBER] CpHMD – Effect of explicit ions when calculating the pKa of model compounds Eric Lang (Wed Mar 15 2017 - 01:49:03 PDT)
[AMBER] script to run background job? Michael Shokhen (Mon Jan 30 2017 - 08:31:50 PST)
- Re: [AMBER] script to run background job? Hai Nguyen (Mon Jan 30 2017 - 08:34:10 PST)
- Re: [AMBER] script to run background job? Elvis Martis (Mon Jan 30 2017 - 08:35:26 PST)
  - Re: [AMBER] script to run background job? Michael Shokhen (Mon Jan 30 2017 - 08:56:33 PST)
    - Re: [AMBER] script to run background job? Andrea Spitaleri (Tue Jan 31 2017 - 00:04:09 PST)
    - Re: [AMBER] script to run background job? Hannes Loeffler (Tue Jan 31 2017 - 00:23:00 PST)
  - Re: [AMBER] script to run background job? Hannes Loeffler (Tue Jan 31 2017 - 00:53:32 PST)
[AMBER] mpi error in Amber16 Hirdesh Kumar (Mon Jan 30 2017 - 12:26:34 PST)
- Re: [AMBER] mpi error in Amber16 case (Mon Jan 30 2017 - 14:52:46 PST)
  - Re: [AMBER] mpi error in Amber16 Hirdesh Kumar (Mon Jan 30 2017 - 14:56:11 PST)
    - Re: [AMBER] mpi error in Amber16 Hirdesh Kumar (Mon Jan 30 2017 - 15:45:20 PST)
[AMBER] MMPBSA failed Albert (Mon Jan 30 2017 - 23:28:55 PST)
- Re: [AMBER] MMPBSA failed Albert (Tue Jan 31 2017 - 00:00:31 PST)
  - Re: [AMBER] MMPBSA failed Elvis Martis (Tue Jan 31 2017 - 01:12:49 PST)
    - Re: [AMBER] MMPBSA failed Vlad Cojocaru (Tue Jan 31 2017 - 01:25:54 PST)
    - Re: [AMBER] MMPBSA failed Albert (Tue Jan 31 2017 - 01:27:37 PST)
    - Re: [AMBER] MMPBSA failed Vlad Cojocaru (Tue Jan 31 2017 - 01:38:32 PST)
    - Re: [AMBER] MMPBSA failed Albert (Tue Jan 31 2017 - 05:36:24 PST)
    - Re: [AMBER] MMPBSA failed Albert (Tue Jan 31 2017 - 05:38:27 PST)
    - Re: [AMBER] MMPBSA failed Vlad Cojocaru (Tue Jan 31 2017 - 06:28:56 PST)
    - Re: [AMBER] MMPBSA failed Albert (Tue Jan 31 2017 - 06:42:21 PST)
    - Re: [AMBER] MMPBSA failed Vlad Cojocaru (Tue Jan 31 2017 - 06:55:40 PST)
    - Re: [AMBER] MMPBSA failed Albert (Tue Jan 31 2017 - 06:57:07 PST)
    - Re: [AMBER] MMPBSA failed Vlad Cojocaru (Tue Jan 31 2017 - 07:07:23 PST)
    - Re: [AMBER] MMPBSA failed Albert (Tue Jan 31 2017 - 07:41:15 PST)
    - Re: [AMBER] MMPBSA failed Dwight McGee (Tue Jan 31 2017 - 08:31:35 PST)
    - Re: [AMBER] MMPBSA failed Albert (Tue Jan 31 2017 - 23:46:48 PST)
    - Re: [AMBER] MMPBSA failed Albert (Wed Feb 01 2017 - 03:11:12 PST)
    - Re: [AMBER] MMPBSA failed Vlad Cojocaru (Wed Feb 01 2017 - 03:21:27 PST)
    - Re: [AMBER] MMPBSA failed Albert (Wed Feb 01 2017 - 03:46:10 PST)
    - Re: [AMBER] MMPBSA failed Vlad Cojocaru (Wed Feb 01 2017 - 04:37:32 PST)
    - Re: [AMBER] MMPBSA failed Albert (Wed Feb 01 2017 - 06:18:38 PST)
    - Re: [AMBER] MMPBSA failed Vlad Cojocaru (Wed Feb 01 2017 - 06:35:00 PST)
    - Re: [AMBER] MMPBSA failed Jason Swails (Wed Feb 08 2017 - 21:00:28 PST)
[AMBER] strip inpcrd Saman Yousuf ali (Tue Jan 31 2017 - 00:58:53 PST)
- Re: [AMBER] strip inpcrd Elvis Martis (Tue Jan 31 2017 - 01:33:17 PST)
  - Re: [AMBER] strip inpcrd Saman Yousuf ali (Tue Jan 31 2017 - 02:46:44 PST)
- Re: [AMBER] strip inpcrd Daniel Roe (Tue Jan 31 2017 - 05:10:32 PST)
[AMBER] cpptraj: autoimage DCD trajectories (with Amber topology) Vlad Cojocaru (Tue Jan 31 2017 - 01:10:02 PST)
- Re: [AMBER] cpptraj: autoimage DCD trajectories (with Amber topology) Daniel Roe (Tue Jan 31 2017 - 03:54:53 PST)
  - Re: [AMBER] cpptraj: autoimage DCD trajectories (with Amber topology) Vlad Cojocaru (Tue Jan 31 2017 - 04:16:23 PST)
    - Re: [AMBER] cpptraj: autoimage DCD trajectories (with Amber topology) Vlad Cojocaru (Tue Jan 31 2017 - 04:32:37 PST)
    - Re: [AMBER] cpptraj: autoimage DCD trajectories (with Amber topology) Daniel Roe (Tue Jan 31 2017 - 05:07:59 PST)
    - Re: [AMBER] cpptraj: autoimage DCD trajectories (with Amber topology) Vlad Cojocaru (Tue Jan 31 2017 - 06:16:20 PST)
    - Re: [AMBER] cpptraj: autoimage DCD trajectories (with Amber topology) Daniel Roe (Tue Jan 31 2017 - 09:48:08 PST)
    - Re: [AMBER] cpptraj: autoimage DCD trajectories (with Amber topology) vlad.cojocaru.mpi-muenster.mpg.de (Tue Jan 31 2017 - 09:59:57 PST)
[AMBER] lj1264 pmemd.cuda Andreas Tosstorff (Tue Jan 31 2017 - 01:40:32 PST)
- Re: [AMBER] lj1264 pmemd.cuda Ross Walker (Tue Jan 31 2017 - 04:24:24 PST)
  - Re: [AMBER] lj1264 pmemd.cuda Marcelo Andrade Chagas (Tue Jan 31 2017 - 04:53:51 PST)
    - Re: [AMBER] lj1264 pmemd.cuda Ross Walker (Tue Jan 31 2017 - 05:08:08 PST)
    - Re: [AMBER] lj1264 pmemd.cuda Qinghua Liao (Tue Jan 31 2017 - 05:11:50 PST)
    - Re: [AMBER] lj1264 pmemd.cuda Andreas Tosstorff (Tue Jan 31 2017 - 05:18:48 PST)
    - Re: [AMBER] lj1264 pmemd.cuda Marcelo Andrade Chagas (Tue Jan 31 2017 - 05:36:59 PST)
    - Re: [AMBER] lj1264 pmemd.cuda Christina Bergonzo (Tue Jan 31 2017 - 06:11:59 PST)
    - Re: [AMBER] lj1264 pmemd.cuda Marcelo Andrade Chagas (Tue Jan 31 2017 - 06:57:01 PST)
- Re: [AMBER] lj1264 pmemd.cuda Jason Swails (Thu Feb 02 2017 - 18:27:23 PST)
  - Re: [AMBER] lj1264 pmemd.cuda Pengfei Li (Sat Feb 04 2017 - 14:20:55 PST)
    - Re: [AMBER] lj1264 pmemd.cuda Jason Swails (Sun Feb 05 2017 - 21:50:03 PST)
[AMBER] Fwd: Error during installation process Danu Fajar (Tue Jan 31 2017 - 06:25:07 PST)
- Re: [AMBER] Fwd: Error during installation process Hai Nguyen (Tue Jan 31 2017 - 06:29:46 PST)
  - Re: [AMBER] Fwd: Error during installation process Danu Fajar (Tue Jan 31 2017 - 09:37:49 PST)
    - Re: [AMBER] Fwd: Error during installation process Danu Fajar (Tue Jan 31 2017 - 09:46:54 PST)
    - Re: [AMBER] Fwd: Error during installation process Hai Nguyen (Tue Jan 31 2017 - 09:58:15 PST)
    - Re: [AMBER] Fwd: Error during installation process Danu Fajar (Tue Jan 31 2017 - 19:28:45 PST)
    - Re: [AMBER] Fwd: Error during installation process Hai Nguyen (Tue Jan 31 2017 - 20:12:26 PST)
    - Re: [AMBER] Fwd: Error during installation process Danu Fajar (Wed Feb 01 2017 - 18:03:57 PST)
    - Re: [AMBER] Fwd: Error during installation process David Case (Thu Feb 02 2017 - 05:08:31 PST)
- Re: [AMBER] Fwd: Error during installation process David Case (Thu Feb 02 2017 - 05:21:34 PST)
[AMBER] Radical Carbon Anna Cebrian Prats (Tue Jan 31 2017 - 06:54:58 PST)
- Re: [AMBER] Radical Carbon David Case (Wed Feb 01 2017 - 05:04:07 PST)
  - Re: [AMBER] Radical Carbon Anna Cebrian Prats (Wed Feb 01 2017 - 06:42:14 PST)
[AMBER] clustering Sowmya Indrakumar (Tue Jan 31 2017 - 07:03:32 PST)
- Re: [AMBER] clustering Daniel Roe (Tue Jan 31 2017 - 09:59:59 PST)
  - Re: [AMBER] clustering Bill Ross (Tue Jan 31 2017 - 10:11:20 PST)
    - Re: [AMBER] clustering Sowmya Indrakumar (Wed Feb 01 2017 - 03:41:39 PST)
    - Re: [AMBER] clustering Ravi Abrol (Wed Feb 01 2017 - 15:08:37 PST)
    - Re: [AMBER] clustering Sowmya Indrakumar (Thu Feb 02 2017 - 00:46:57 PST)
    - Re: [AMBER] clustering Daniel Roe (Thu Feb 02 2017 - 06:46:02 PST)
[AMBER] DFTB3 in Amber is not there, but it may be in gromacs. Markus Kaukonen (Tue Jan 31 2017 - 08:06:54 PST)
- Re: [AMBER] DFTB3 in Amber is not there, but it may be in gromacs. Goetz, Andreas (Tue Jan 31 2017 - 10:59:52 PST)
  - Re: [AMBER] DFTB3 in Amber is not there, but it may be in gromacs. Markus Kaukonen (Tue Feb 07 2017 - 03:04:17 PST)
[AMBER] visualization problem Albert (Tue Jan 31 2017 - 08:09:13 PST)
- Re: [AMBER] visualization problem Hai Nguyen (Tue Jan 31 2017 - 08:11:19 PST)
  - Re: [AMBER] visualization problem Albert (Tue Jan 31 2017 - 08:13:49 PST)
    - Re: [AMBER] visualization problem Hai Nguyen (Tue Jan 31 2017 - 08:15:03 PST)
    - Re: [AMBER] visualization problem Albert (Tue Jan 31 2017 - 08:17:05 PST)
    - Re: [AMBER] visualization problem Andreas Tosstorff (Tue Jan 31 2017 - 08:21:32 PST)
    - Re: [AMBER] visualization problem Albert (Tue Jan 31 2017 - 08:18:21 PST)
- Re: [AMBER] visualization problem Daniel Roe (Tue Jan 31 2017 - 09:22:10 PST)
  - Re: [AMBER] visualization problem Adrian Roitberg (Tue Jan 31 2017 - 09:24:42 PST)
[AMBER] Multiple ligands in MMGBSA Abhilash J (Tue Jan 31 2017 - 08:20:05 PST)
- Re: [AMBER] Multiple ligands in MMGBSA Elvis Martis (Tue Jan 31 2017 - 19:13:13 PST)
  - Re: [AMBER] Multiple ligands in MMGBSA Abhilash J (Wed Feb 01 2017 - 02:39:06 PST)
    - Re: [AMBER] Multiple ligands in MMGBSA Elvis Martis (Wed Feb 01 2017 - 04:29:57 PST)
    - Re: [AMBER] Multiple ligands in MMGBSA Abhilash J (Thu Feb 02 2017 - 00:22:36 PST)
[AMBER] Methods to count the different species Liyang Zhu (Tue Jan 31 2017 - 12:32:23 PST)
- Re: [AMBER] Methods to count the different species Daniel Roe (Thu Feb 02 2017 - 06:59:17 PST)
  - Re: [AMBER] Methods to count the different species Liyang Zhu (Tue Feb 28 2017 - 10:59:53 PST)
    - Re: [AMBER] Methods to count the different species Daniel Roe (Wed Mar 01 2017 - 08:13:56 PST)
    - Re: [AMBER] Methods to count the different species Liyang Zhu (Wed Mar 01 2017 - 18:24:39 PST)
[AMBER] Differences using leaprc.ff14SB from AmberTools15 and oldff/leaprc.ff14SB from AmberTools16 Joao Damas (Tue Jan 31 2017 - 12:33:16 PST)
- Re: [AMBER] Differences using leaprc.ff14SB from AmberTools15 and oldff/leaprc.ff14SB from AmberTools16 Daniel Roe (Tue Jan 31 2017 - 17:27:18 PST)
  - Re: [AMBER] Differences using leaprc.ff14SB from AmberTools15 and oldff/leaprc.ff14SB from AmberTools16 Joao Damas (Wed Feb 01 2017 - 13:27:46 PST)
[AMBER] APR - atom selection Andreas Tosstorff (Wed Feb 01 2017 - 05:05:56 PST)
- Re: [AMBER] APR - atom selection Daniel Roe (Wed Feb 01 2017 - 06:52:56 PST)
  - Re: [AMBER] APR - atom selection Andreas Tosstorff (Wed Feb 01 2017 - 07:10:57 PST)
- Re: [AMBER] APR - atom selection Jian Yin (Thu Feb 02 2017 - 12:46:22 PST)
  - Re: [AMBER] APR - atom selection Andreas Tosstorff (Tue Feb 07 2017 - 05:38:03 PST)
[AMBER] [MMPBSA.py.MPI] Two questions (autoimage and parsing of output) Eiros Zamora, Juan (Wed Feb 01 2017 - 05:09:02 PST)
- Re: [AMBER] [MMPBSA.py.MPI] Two questions (autoimage and parsing of output) Daniel Roe (Thu Feb 02 2017 - 06:52:24 PST)
  - Re: [AMBER] [MMPBSA.py.MPI] Two questions (autoimage and parsing of output) Jason Swails (Fri Feb 03 2017 - 05:06:23 PST)
    - Re: [AMBER] [MMPBSA.py.MPI] Two questions (autoimage and parsing of output) Eiros Zamora, Juan (Fri Feb 03 2017 - 08:11:01 PST)
    - Re: [AMBER] [MMPBSA.py.MPI] Two questions (autoimage and parsing of output) Eiros Zamora, Juan (Mon Feb 06 2017 - 04:16:26 PST)
    - Re: [AMBER] [MMPBSA.py.MPI] Two questions (autoimage and parsing of output) Eiros Zamora, Juan (Mon Feb 06 2017 - 06:30:11 PST)
[AMBER] Thiophosphate paramters - AMBER Balaji Selvam (Wed Feb 01 2017 - 10:33:12 PST)
- Re: [AMBER] Thiophosphate paramters - AMBER Elvis Martis (Wed Feb 01 2017 - 19:53:02 PST)
  - Re: [AMBER] Thiophosphate paramters - AMBER Abhilash J (Thu Feb 02 2017 - 05:41:23 PST)
[AMBER] Two Ph.D. positions in molecular simulations Jan Brezovsky (Wed Feb 01 2017 - 13:35:12 PST)
[AMBER] cannot add bond Thakur, Abhishek (Wed Feb 01 2017 - 14:26:09 PST)
- Re: [AMBER] cannot add bond Elvis Martis (Wed Feb 01 2017 - 19:51:04 PST)
  - Re: [AMBER] cannot add bond Sowmya Indrakumar (Thu Feb 02 2017 - 00:49:20 PST)
[AMBER] Error in compiling pmemd.cuda Anton Perera (Wed Feb 01 2017 - 20:06:12 PST)
- Re: [AMBER] Error in compiling pmemd.cuda Elvis Martis (Wed Feb 01 2017 - 20:11:13 PST)
- Re: [AMBER] Error in compiling pmemd.cuda Ross Walker (Wed Feb 01 2017 - 20:14:28 PST)
  - Re: [AMBER] Error in compiling pmemd.cuda Ross Walker (Wed Feb 01 2017 - 20:15:21 PST)
[AMBER] Amber16 installation error SeungHyun Kim (Wed Feb 01 2017 - 22:39:28 PST)
- Re: [AMBER] Amber16 installation error Nhai (Wed Feb 01 2017 - 22:47:19 PST)
- Re: [AMBER] Amber16 installation error David Case (Thu Feb 02 2017 - 05:17:59 PST)
[AMBER] changing water molecules in water box Lara rajam (Thu Feb 02 2017 - 07:24:08 PST)
- Re: [AMBER] changing water molecules in water box David Case (Thu Feb 02 2017 - 12:54:38 PST)
  - Re: [AMBER] changing water molecules in water box Lara rajam (Thu Feb 02 2017 - 13:07:45 PST)
[AMBER] Parameters for nucelotides Buteler,Maria del Pilar (Thu Feb 02 2017 - 08:15:12 PST)
- Re: [AMBER] Parameters for nucelotides FyD (Fri Feb 03 2017 - 00:53:50 PST)
[AMBER] MTKpp.pdf manual Corum, Katharine W (Thu Feb 02 2017 - 09:08:19 PST)
- Re: [AMBER] MTKpp.pdf manual Pengfei Li (Thu Feb 02 2017 - 09:10:23 PST)
  - Re: [AMBER] MTKpp.pdf manual Corum, Katharine W (Thu Feb 02 2017 - 09:11:42 PST)
  - Re: [AMBER] MTKpp.pdf manual Hai Nguyen (Thu Feb 02 2017 - 09:13:02 PST)
[AMBER] Tleap is making C instaed of Cl Thakur, Abhishek (Thu Feb 02 2017 - 09:09:45 PST)
- Re: [AMBER] Tleap is making C instaed of Cl David Case (Thu Feb 02 2017 - 09:37:35 PST)
  - Re: [AMBER] Tleap is making C instaed of Cl Thakur, Abhishek (Thu Feb 02 2017 - 09:46:30 PST)
    - Re: [AMBER] Tleap is making C instaed of Cl David Case (Thu Feb 02 2017 - 12:51:31 PST)
    - Re: [AMBER] Tleap is making C instaed of Cl Thakur, Abhishek (Thu Feb 02 2017 - 13:56:50 PST)
    - Re: [AMBER] Tleap is making C instaed of Cl Thakur, Abhishek (Thu Feb 02 2017 - 14:22:23 PST)
    - Re: [AMBER] Tleap is making C instaed of Cl Thakur, Abhishek (Thu Feb 02 2017 - 14:23:57 PST)
    - Re: [AMBER] Tleap is making C instaed of Cl James Kress (Thu Feb 02 2017 - 16:00:19 PST)
    - Re: [AMBER] Tleap is making C instaed of Cl Thakur, Abhishek (Thu Feb 02 2017 - 16:45:00 PST)
- Re: [AMBER] Tleap is making C instaed of Cl James Kress (Thu Feb 02 2017 - 19:14:04 PST)
  - Re: [AMBER] Tleap is making C instaed of Cl Daniel Roe (Fri Feb 03 2017 - 05:47:29 PST)
    - Re: [AMBER] Tleap is making C instaed of Cl Thakur, Abhishek (Fri Feb 03 2017 - 06:49:10 PST)
[AMBER] binding energy decomposition Jacopo Sgrignani (Thu Feb 02 2017 - 12:44:37 PST)
- Re: [AMBER] binding energy decomposition Bruno Falcone (Fri Feb 03 2017 - 06:03:13 PST)
[AMBER] protocol for simulating a system in NaCl using xleaP module zeba firdows (Thu Feb 02 2017 - 23:27:08 PST)
- Re: [AMBER] protocol for simulating a system in NaCl using xleaP module Elvis Martis (Fri Feb 03 2017 - 03:21:14 PST)
  - Re: [AMBER] protocol for simulating a system in NaCl using xleaP module zeba firdows (Fri Feb 03 2017 - 03:25:58 PST)
    - Re: [AMBER] protocol for simulating a system in NaCl using xleaP module Elvis Martis (Fri Feb 03 2017 - 03:30:24 PST)
    - Re: [AMBER] protocol for simulating a system in NaCl using xleaP module zeba firdows (Fri Feb 03 2017 - 03:33:42 PST)
[AMBER] Force Field for Ammonia? Gustavo Seabra (Fri Feb 03 2017 - 08:37:44 PST)
- Re: [AMBER] Force Field for Ammonia? Andrew Schaub (Fri Feb 03 2017 - 20:18:22 PST)
  - Re: [AMBER] Force Field for Ammonia? jojartb.jgypk.u-szeged.hu (Fri Feb 03 2017 - 22:10:21 PST)
  - Re: [AMBER] Force Field for Ammonia? Gustavo Seabra (Mon Feb 06 2017 - 07:00:24 PST)
[AMBER] parmed gromber issues inappropriate disulfide warning based on CYS/MET approach Chris Neale (Fri Feb 03 2017 - 13:57:39 PST)
[AMBER] Number of threads in MMGBSA/MMPBSA calculations. Abhilash J (Fri Feb 03 2017 - 22:27:05 PST)
- Re: [AMBER] Number of threads in MMGBSA/MMPBSA calculations. Elvis Martis (Sat Feb 04 2017 - 00:25:57 PST)
  - Re: [AMBER] Number of threads in MMGBSA/MMPBSA calculations. Abhilash J (Sat Feb 04 2017 - 05:59:06 PST)
    - Re: [AMBER] Number of threads in MMGBSA/MMPBSA calculations. Jason Swails (Mon Feb 06 2017 - 17:52:06 PST)
[AMBER] ADDING WATER MOLECULES Subashini .K (Sat Feb 04 2017 - 02:54:49 PST)
- Re: [AMBER] ADDING WATER MOLECULES Elvis Martis (Sat Feb 04 2017 - 03:18:34 PST)
- Re: [AMBER] ADDING WATER MOLECULES David Case (Sun Feb 05 2017 - 05:31:31 PST)
[AMBER] parmed add12_6_4 command error Marek Havrila (Sat Feb 04 2017 - 13:41:19 PST)
- Re: [AMBER] parmed add12_6_4 command error Pengfei Li (Sat Feb 04 2017 - 14:03:21 PST)
  - Re: [AMBER] parmed add12_6_4 command error Marek Havrila (Sat Feb 04 2017 - 14:25:14 PST)
[AMBER] EPM2 Force field for CO2 Liyang Zhu (Sun Feb 05 2017 - 17:34:59 PST)
- Re: [AMBER] EPM2 Force field for CO2 David Case (Mon Feb 06 2017 - 08:03:16 PST)
  - Re: [AMBER] EPM2 Force field for CO2 Liyang Zhu (Mon Feb 06 2017 - 13:28:43 PST)
- Re: [AMBER] EPM2 Force field for CO2 David Case (Wed Feb 08 2017 - 16:17:14 PST)
  - Re: [AMBER] EPM2 Force field for CO2 Liyang Zhu (Thu Feb 09 2017 - 09:54:25 PST)
    - Re: [AMBER] EPM2 Force field for CO2 David Case (Thu Feb 09 2017 - 13:09:03 PST)
    - Re: [AMBER] EPM2 Force field for CO2 Liyang Zhu (Thu Feb 09 2017 - 15:42:21 PST)
[AMBER] Cannot open the main chain file after prepgen command Nikolay N. Kuzmich (Mon Feb 06 2017 - 04:09:52 PST)
- Re: [AMBER] Cannot open the main chain file after prepgen command David Case (Mon Feb 06 2017 - 08:08:00 PST)
[AMBER] MMPBSA error konda003 . (Mon Feb 06 2017 - 09:08:42 PST)
- Re: [AMBER] MMPBSA error Ray Luo (Mon Feb 06 2017 - 10:31:26 PST)
[AMBER] 8 GPU single pmemd run with amber 16? Chris Neale (Mon Feb 06 2017 - 12:31:12 PST)
- Re: [AMBER] 8 GPU single pmemd run with amber 16? Ross Walker (Mon Feb 06 2017 - 12:56:13 PST)
  - Re: [AMBER] 8 GPU single pmemd run with amber 16? Scott Le Grand (Mon Feb 06 2017 - 12:59:33 PST)
  - Re: [AMBER] 8 GPU single pmemd run with amber 16? Chris Neale (Mon Feb 06 2017 - 13:09:28 PST)
[AMBER] how to solve syntax error issue Ayesha Kanwal (Tue Feb 07 2017 - 02:09:57 PST)
- Re: [AMBER] how to solve syntax error issue Elvis Martis (Tue Feb 07 2017 - 04:15:27 PST)
- Re: [AMBER] how to solve syntax error issue David Case (Tue Feb 07 2017 - 05:50:43 PST)
[AMBER] Amber16 -mpt-2.15-gcc/6.1.0-RHEL7.3- compilation error Sudhakar Lakkaraju (Wed Feb 08 2017 - 07:07:58 PST)
- Re: [AMBER] Amber16 -mpt-2.15-gcc/6.1.0-RHEL7.3- compilation error David Case (Wed Feb 08 2017 - 07:42:55 PST)
  - Re: [AMBER] Amber16 -mpt-2.15-gcc/6.1.0-RHEL7.3- compilation error Sudhakar Lakkaraju (Wed Feb 08 2017 - 09:56:14 PST)
    - Re: [AMBER] Amber16 -mpt-2.15-gcc/6.1.0-RHEL7.3- compilation error Feng Pan (Thu Feb 09 2017 - 08:09:49 PST)
    - Re: [AMBER] Amber16 -mpt-2.15-gcc/6.1.0-RHEL7.3- compilation error Sudhakar Lakkaraju (Thu Feb 09 2017 - 09:43:43 PST)
    - Re: [AMBER] Amber16 -mpt-2.15-gcc/6.1.0-RHEL7.3- compilation error Sudhakar Lakkaraju (Thu Feb 16 2017 - 09:23:50 PST)
    - Re: [AMBER] Amber16 -mpt-2.15-gcc/6.1.0-RHEL7.3- compilation error Feng Pan (Thu Feb 16 2017 - 11:12:04 PST)
[AMBER] How to download patches and updates manually Elisa Pieri (Wed Feb 08 2017 - 07:49:21 PST)
- Re: [AMBER] How to download patches and updates manually Chris Neale (Wed Feb 08 2017 - 07:56:29 PST)
- Re: [AMBER] How to download patches and updates manually Hai Nguyen (Wed Feb 08 2017 - 08:52:35 PST)
  - Re: [AMBER] How to download patches and updates manually Jason Swails (Wed Feb 08 2017 - 19:24:10 PST)
[AMBER] VdW parameters in AMBER Andreas Gavrielides (Wed Feb 08 2017 - 08:48:12 PST)
- Re: [AMBER] VdW parameters in AMBER David Case (Wed Feb 08 2017 - 10:28:42 PST)
  - Re: [AMBER] VdW parameters in AMBER Andreas Gavrielides (Thu Feb 09 2017 - 03:25:25 PST)
[AMBER] Failed to calculate entropy with mm_pbsa.pl in AMBER14, with no error informations reported in nmode_com.1.out wei (Wed Feb 08 2017 - 20:36:47 PST)
- Re: [AMBER] Failed to calculate entropy with mm_pbsa.pl in AMBER14, with no error informations reported in nmode_com.1.out Hai Nguyen (Wed Feb 08 2017 - 20:49:05 PST)
- Re: [AMBER] Failed to calculate entropy with mm_pbsa.pl in AMBER14, with no error informations reported in nmode_com.1.out Elvis Martis (Thu Feb 09 2017 - 04:08:37 PST)
- Re: [AMBER] Failed to calculate entropy with mm_pbsa.pl in AMBER14, with no error informations reported in nmode_com.1.out David Case (Thu Feb 09 2017 - 06:02:35 PST)
[AMBER] CHARMM36 force field Shanghaitech University WuMeng (Thu Feb 09 2017 - 05:08:38 PST)
- Re: [AMBER] CHARMM36 force field Dickson, Callum J (Fri Feb 10 2017 - 08:41:45 PST)
[AMBER] PCA analysis Thakur, Abhishek (Thu Feb 09 2017 - 06:58:24 PST)
- Re: [AMBER] PCA analysis Elvis Martis (Thu Feb 09 2017 - 07:02:25 PST)
- Re: [AMBER] PCA analysis Elvis Martis (Thu Feb 09 2017 - 07:06:41 PST)
  - Re: [AMBER] PCA analysis Thakur, Abhishek (Thu Feb 09 2017 - 07:30:02 PST)
[AMBER] Possible BUG in pmemd.cuda - minimization with igb eq 6 Marek Maly (Thu Feb 09 2017 - 07:09:32 PST)
- Re: [AMBER] Possible BUG in pmemd.cuda - minimization with igb eq 6 Ross Walker (Thu Feb 09 2017 - 07:43:18 PST)
  - Re: [AMBER] Possible BUG in pmemd.cuda - minimization with igb eq 6 Marek Maly (Thu Feb 09 2017 - 07:58:12 PST)
    - Re: [AMBER] Possible BUG in pmemd.cuda - minimization with igb eq 6 Ross Walker (Thu Feb 09 2017 - 08:43:07 PST)
    - Re: [AMBER] Possible BUG in pmemd.cuda - minimization with igb eq 6 Marek Maly (Thu Feb 09 2017 - 09:24:22 PST)
[AMBER] custom directory for DFTB parameter files Alfredo Quevedo (Thu Feb 09 2017 - 07:41:36 PST)
- Re: [AMBER] custom directory for DFTB parameter files Gustavo Seabra (Thu Feb 09 2017 - 10:37:23 PST)
  - Re: [AMBER] custom directory for DFTB parameter files Alfredo Quevedo (Thu Feb 09 2017 - 10:45:23 PST)
[AMBER] Obtain dynamical matrix away from equilibrium The Cromicus Productions (Thu Feb 09 2017 - 10:00:37 PST)
- Re: [AMBER] Obtain dynamical matrix away from equilibrium Adrian Roitberg (Thu Feb 09 2017 - 10:10:48 PST)
[AMBER] PCA Thakur, Abhishek (Thu Feb 09 2017 - 14:20:48 PST)
- Re: [AMBER] PCA Elvis Martis (Thu Feb 09 2017 - 17:26:36 PST)
- Re: [AMBER] PCA Daniel Roe (Mon Feb 13 2017 - 12:15:35 PST)
[AMBER] RE：RE: Failed to calculate entropy with mm_pbsa.pl in AMBER14, with no error informations reported in nmode_com.1.out wei (Thu Feb 09 2017 - 15:48:42 PST)
- Re: [AMBER] RE：RE: Failed to calculate entropy with mm_pbsa.pl in AMBER14, with no error informations reported in nmode_com.1.out Daniel Roe (Thu Feb 09 2017 - 17:16:32 PST)
- Re: [AMBER] RE：RE: Failed to calculate entropy with mm_pbsa.pl in AMBER14, with no error informations reported in nmode_com.1.out Elvis Martis (Thu Feb 09 2017 - 17:31:08 PST)
[AMBER] Explicity solvent CpHD, -cprestrt .cpin file Tsibela German Tebello Mofokeng (Fri Feb 10 2017 - 06:40:18 PST)
- Re: [AMBER] Explicity solvent CpHD, -cprestrt .cpin file Eric Lang (Fri Feb 10 2017 - 06:56:17 PST)
  - Re: [AMBER] Explicity solvent CpHD, -cprestrt .cpin file Tsibela German Tebello Mofokeng (Fri Feb 10 2017 - 07:33:12 PST)
    - Re: [AMBER] Explicity solvent CpHD, -cprestrt .cpin file Eric Lang (Fri Feb 10 2017 - 13:10:00 PST)
[AMBER] ZAFF LEAP Carbonic Anhydrase II Protein Topology & Coordinate Preparation Naiem Issa (Fri Feb 10 2017 - 12:43:53 PST)
- Re: [AMBER] ZAFF LEAP Carbonic Anhydrase II Protein Topology & Coordinate Preparation Pengfei Li (Fri Feb 10 2017 - 12:50:57 PST)
  - Re: [AMBER] ZAFF LEAP Carbonic Anhydrase II Protein Topology & Coordinate Preparation Naiem Issa (Fri Feb 10 2017 - 13:04:53 PST)
    - Re: [AMBER] ZAFF LEAP Carbonic Anhydrase II Protein Topology & Coordinate Preparation Pengfei Li (Fri Feb 10 2017 - 14:56:56 PST)
    - Re: [AMBER] ZAFF LEAP Carbonic Anhydrase II Protein Topology & Coordinate Preparation nti.georgetown.edu (Mon Feb 13 2017 - 09:03:49 PST)
Re: [AMBER] Re：Re: RE：RE: Failed to calculate entropy with mm_pbsa.pl in AMBER14, with no error_informations_reported_in_nmode_com.1.out Elvis Martis (Fri Feb 10 2017 - 21:25:07 PST)
[AMBER] H_bond Thakur, Abhishek (Sun Feb 12 2017 - 08:22:13 PST)
- Re: [AMBER] H_bond Daniel Roe (Mon Feb 13 2017 - 12:12:08 PST)
[AMBER] Compilation errors Sudhakar Lakkaraju (Sun Feb 12 2017 - 18:06:07 PST)
- Re: [AMBER] Compilation errors Jason Swails (Sun Feb 12 2017 - 18:37:39 PST)
[AMBER] CPPTRAJ combined clustering with different topologies Jan Ludwiczak (Mon Feb 13 2017 - 04:59:02 PST)
- Re: [AMBER] CPPTRAJ combined clustering with different topologies Daniel Roe (Mon Feb 13 2017 - 06:16:32 PST)
[AMBER] Should ig value be set explicitly? Azade Yazdan Yar (Mon Feb 13 2017 - 08:17:41 PST)
- Re: [AMBER] Should ig value be set explicitly? Hai Nguyen (Mon Feb 13 2017 - 08:40:24 PST)
  - Re: [AMBER] Should ig value be set explicitly? Azade Yazdan Yar (Mon Feb 13 2017 - 08:45:11 PST)
- Re: [AMBER] Should ig value be set explicitly? Adrian Roitberg (Mon Feb 13 2017 - 08:42:18 PST)
[AMBER] Velocity file output AMBER16 Korey M Reid (Mon Feb 13 2017 - 13:14:46 PST)
- Re: [AMBER] Velocity file output AMBER16 Elvis Martis (Mon Feb 13 2017 - 20:00:55 PST)
- Re: [AMBER] Velocity file output AMBER16 David Case (Tue Feb 14 2017 - 06:10:49 PST)
  - Re: [AMBER] Velocity file output AMBER16 Korey M Reid (Tue Feb 14 2017 - 11:39:04 PST)
    - Re: [AMBER-Developers] [AMBER] Velocity file output AMBER16 David Case (Sat Feb 18 2017 - 12:34:09 PST)
[AMBER] production error. Saman Yousuf ali (Mon Feb 13 2017 - 21:37:46 PST)
- Re: [AMBER] production error. Elvis Martis (Mon Feb 13 2017 - 23:04:32 PST)
- Re: [AMBER] production error. David Case (Tue Feb 14 2017 - 06:15:29 PST)
  - Re: [AMBER] production error. Saman Yousuf ali (Tue Feb 14 2017 - 07:50:26 PST)
    - Re: [AMBER] production error. David Case (Tue Feb 14 2017 - 09:15:36 PST)
    - Re: [AMBER] production error. Saman Yousuf ali (Tue Feb 14 2017 - 09:42:42 PST)
    - Re: [AMBER] production error. Hai Nguyen (Tue Feb 14 2017 - 10:09:42 PST)
[AMBER] Amber Energy Unit Meaning Eugene Cha (Mon Feb 13 2017 - 22:47:34 PST)
- Re: [AMBER] Amber Energy Unit Meaning Bill Ross (Mon Feb 13 2017 - 23:02:29 PST)
  - Re: [AMBER] Amber Energy Unit Meaning Bill Ross (Mon Feb 13 2017 - 23:06:03 PST)
  - Re: [AMBER] Amber Energy Unit Meaning Ross Walker (Tue Feb 14 2017 - 04:40:45 PST)
[AMBER] [Amber] Frequencies from normal mode analysis in nab The Cromicus Productions (Tue Feb 14 2017 - 00:03:38 PST)
- Re: [AMBER] [Amber] Frequencies from normal mode analysis in nab David Case (Sat Feb 18 2017 - 12:33:57 PST)
  - Re: [AMBER] [Amber] Frequencies from normal mode analysis in nab James Kress (Sun Feb 19 2017 - 10:07:15 PST)
[AMBER] PLUMED Meeting 2017 Giovanni Bussi (Tue Feb 14 2017 - 01:03:01 PST)
[AMBER] Amber15 Cpinutil.py Bug Chase Zagorec-Marks (Tue Feb 14 2017 - 13:19:09 PST)
- Re: [AMBER] Amber15 Cpinutil.py Bug Jason Swails (Tue Feb 14 2017 - 19:39:20 PST)
[AMBER] binding free energy- error calculation Mary Varughese (Tue Feb 14 2017 - 21:01:57 PST)
- [AMBER] Fwd: binding free energy- error calculation Mary Varughese (Thu Feb 16 2017 - 19:02:04 PST)
  - Re: [AMBER] Fwd: binding free energy- error calculation Hai Nguyen (Thu Feb 16 2017 - 19:19:57 PST)
[AMBER] help in parameters Robin Jain (Tue Feb 14 2017 - 22:08:34 PST)
- Re: [AMBER] help in parameters Bill Ross (Tue Feb 14 2017 - 22:32:21 PST)
- Re: [AMBER] help in parameters David Case (Thu Feb 16 2017 - 05:11:43 PST)
[AMBER] building premed for Intel Xeon Phi coprocessors (offload mode) Song-Ho Chong (Tue Feb 14 2017 - 23:04:21 PST)
[AMBER] constant pH caluculations with pmemd.cuda.MPI Hofer, Florian (Wed Feb 15 2017 - 04:50:44 PST)
- Re: [AMBER] constant pH caluculations with pmemd.cuda.MPI Adrian Roitberg (Wed Feb 15 2017 - 06:15:32 PST)
  - Re: [AMBER] constant pH caluculations with pmemd.cuda.MPI Florian Hofer (Wed Feb 15 2017 - 06:19:34 PST)
[AMBER] Installation problem with miniconda ABHIJEET CHOWDHURY (Wed Feb 15 2017 - 05:13:36 PST)
- Re: [AMBER] Installation problem with miniconda Hai Nguyen (Wed Feb 15 2017 - 05:26:47 PST)
  - Re: [AMBER] Installation problem with miniconda ABHIJEET CHOWDHURY (Wed Feb 15 2017 - 09:27:58 PST)
    - Re: [AMBER] Installation problem with miniconda Hai Nguyen (Wed Feb 15 2017 - 10:09:04 PST)
    - Re: [AMBER] Installation problem with miniconda ABHIJEET CHOWDHURY (Fri Feb 17 2017 - 04:53:15 PST)
[AMBER] frequency contact maps antonio.coluccia.uniroma1.it (Wed Feb 15 2017 - 06:28:05 PST)
- Re: [AMBER] frequency contact maps Daniel Roe (Wed Feb 15 2017 - 07:38:57 PST)
  - Re: [AMBER] frequency contact maps Antonio Coluccia (Wed Feb 15 2017 - 08:15:50 PST)
    - Re: [AMBER] frequency contact maps Alejandro Sosa (Thu Feb 16 2017 - 13:38:27 PST)
  - Re: [AMBER] frequency contact maps Antonio Coluccia (Fri Feb 17 2017 - 01:04:42 PST)
    - Re: [AMBER] frequency contact maps Daniel Roe (Fri Feb 17 2017 - 06:48:19 PST)
    - Re: [AMBER] frequency contact maps Antonio Coluccia (Tue Feb 21 2017 - 06:45:00 PST)
    - Re: [AMBER] frequency contact maps Daniel Roe (Tue Feb 21 2017 - 07:16:06 PST)
[AMBER] Hydrophobic and pi-pi interaction Thakur, Abhishek (Wed Feb 15 2017 - 07:40:14 PST)
- [AMBER] Fw: Hydrophobic and pi-pi interaction Thakur, Abhishek (Thu Feb 16 2017 - 05:08:58 PST)
  - Re: [AMBER] Fw: Hydrophobic and pi-pi interaction chemocev marker (Thu Feb 16 2017 - 08:05:57 PST)
[AMBER] Creating a double bond in a pdb file with xleap Aseel Bala (Wed Feb 15 2017 - 11:08:03 PST)
- Re: [AMBER] Creating a double bond in a pdb file with xleap David Case (Wed Feb 15 2017 - 18:31:24 PST)
  - Re: [AMBER] Creating a double bond in a pdb file with xleap Aseel Bala (Thu Feb 16 2017 - 12:47:27 PST)
    - Re: [AMBER] Creating a double bond in a pdb file with xleap David Case (Thu Feb 16 2017 - 13:50:32 PST)
- Re: [AMBER] Creating a double bond in a pdb file with xleap Vaibhav Dixit (Thu Feb 16 2017 - 22:40:03 PST)
  - Re: [AMBER] Creating a double bond in a pdb file with xleap Bill Ross (Thu Feb 16 2017 - 22:54:10 PST)
    - Re: [AMBER] Creating a double bond in a pdb file with xleap Aseel Bala (Tue Feb 21 2017 - 08:40:10 PST)
  - Re: [AMBER] Creating a double bond in a pdb file with xleap Aseel Bala (Tue Feb 21 2017 - 08:40:21 PST)
[AMBER] Simulations with R_OF_GYRATION Osman, Roman (Wed Feb 15 2017 - 11:29:30 PST)
- Re: [AMBER] Simulations with R_OF_GYRATION Adrian Roitberg (Wed Feb 15 2017 - 11:31:14 PST)
  - Re: [AMBER] Simulations with R_OF_GYRATION Osman, Roman (Wed Feb 15 2017 - 11:34:10 PST)
    - Re: [AMBER] Simulations with R_OF_GYRATION Feng Pan (Wed Feb 15 2017 - 13:56:40 PST)
    - Re: [AMBER] Simulations with R_OF_GYRATION Osman, Roman (Wed Feb 15 2017 - 16:53:15 PST)
    - Re: [AMBER] Simulations with R_OF_GYRATION Osman, Roman (Wed Feb 15 2017 - 16:53:12 PST)
[AMBER] LES, Umbrella sampling and/or NEB Stregone (Thu Feb 16 2017 - 03:50:59 PST)
[AMBER] density and concentration of 8Mureabox Jorge Iulek (Thu Feb 16 2017 - 08:44:18 PST)
[AMBER] Problem using nmropt=1 with CUDA - AMBER 14 Jenner Bonanata (Thu Feb 16 2017 - 09:09:16 PST)
- Re: [AMBER] Problem using nmropt=1 with CUDA - AMBER 14 David Case (Thu Feb 16 2017 - 19:34:57 PST)
[AMBER] MMPBSA error konda003 . (Thu Feb 16 2017 - 12:02:35 PST)
[AMBER] IERR CPU hang needing support please Curtis Walker (Thu Feb 16 2017 - 14:11:17 PST)
- Re: [AMBER] IERR CPU hang needing support please Ross Walker (Fri Feb 17 2017 - 08:35:57 PST)
[AMBER] makeDIST_RST issue Miguel Garavís (Fri Feb 17 2017 - 04:29:00 PST)
- Re: [AMBER] makeDIST_RST issue David Case (Fri Feb 17 2017 - 05:24:03 PST)
  - Re: [AMBER] makeDIST_RST issue Miguel Garavís (Fri Feb 17 2017 - 05:32:48 PST)
[AMBER] LeAP and FFs for Hybrid DNA/RNA structure Kasprzak, Wojciech (NIH/NCI) [C] (Fri Feb 17 2017 - 12:09:39 PST)
- Re: [AMBER] LeAP and FFs for Hybrid DNA/RNA structure David Case (Sat Feb 18 2017 - 12:33:35 PST)
  - Re: [AMBER] LeAP and FFs for Hybrid DNA/RNA structure Kasprzak, Wojciech (NIH/NCI) [C] (Mon Feb 20 2017 - 10:36:18 PST)
    - Re: [AMBER] LeAP and FFs for Hybrid DNA/RNA structure Hai Nguyen (Mon Feb 20 2017 - 11:46:02 PST)
[AMBER] Na cation drifts away from metal chelating protein Michael Shokhen (Sun Feb 19 2017 - 01:45:13 PST)
- Re: [AMBER] Na cation drifts away from metal chelating protein Elvis Martis (Sun Feb 19 2017 - 02:41:16 PST)
  - Re: [AMBER] Na cation drifts away from metal chelating protein Bill Ross (Sun Feb 19 2017 - 02:49:09 PST)
    - Re: [AMBER] Na cation drifts away from metal chelating protein Michael Shokhen (Sun Feb 19 2017 - 02:59:11 PST)
[AMBER] Distance between of each residues of two chains within trajectory Jesmita Dhar (Mon Feb 20 2017 - 01:22:33 PST)
- Re: [AMBER] Distance between of each residues of two chains within trajectory Daniel Roe (Tue Feb 21 2017 - 08:52:03 PST)
[AMBER] SO4 molecule xleap ARMIN HODAEI (Mon Feb 20 2017 - 02:53:06 PST)
- Re: [AMBER] SO4 molecule xleap Elvis Martis (Mon Feb 20 2017 - 03:35:02 PST)
[AMBER] Problem with mmpbsa Tiffani Rovira (Mon Feb 20 2017 - 04:11:04 PST)
- Re: [AMBER] Problem with mmpbsa Elvis Martis (Mon Feb 20 2017 - 04:15:15 PST)
- Re: [AMBER] Problem with mmpbsa Bill Ross (Mon Feb 20 2017 - 04:46:38 PST)
- Re: [AMBER] Problem with mmpbsa David Case (Mon Feb 20 2017 - 07:33:18 PST)
[AMBER] error in the input file Michael Shokhen (Mon Feb 20 2017 - 04:47:03 PST)
- Re: [AMBER] error in the input file Bill Ross (Mon Feb 20 2017 - 04:50:26 PST)
  - Re: [AMBER] error in the input file Michael Shokhen (Mon Feb 20 2017 - 05:11:57 PST)
    - Re: [AMBER] error in the input file Bill Ross (Mon Feb 20 2017 - 05:23:08 PST)
    - Re: [AMBER] error in the input file Michael Shokhen (Mon Feb 20 2017 - 05:31:26 PST)
    - Re: [AMBER] error in the input file Bill Ross (Mon Feb 20 2017 - 05:36:25 PST)
    - Re: [AMBER] error in the input file Michael Shokhen (Mon Feb 20 2017 - 05:47:09 PST)
    - Re: [AMBER] error in the input file Qinghua Liao (Mon Feb 20 2017 - 05:51:16 PST)
- Re: [AMBER] error in the input file Hannes Loeffler (Mon Feb 20 2017 - 05:58:44 PST)
  - Re: [AMBER] error in the input file Michael Shokhen (Mon Feb 20 2017 - 06:38:08 PST)
[AMBER] changing chirality with ParmEd? Thomas Pochapsky (Mon Feb 20 2017 - 07:14:48 PST)
- Re: [AMBER] changing chirality with ParmEd? Hai Nguyen (Mon Feb 20 2017 - 11:42:18 PST)
  - Re: [AMBER] changing chirality with ParmEd? Lachele Foley (Tue Feb 21 2017 - 13:26:32 PST)
    - Re: [AMBER] changing chirality with ParmEd? Carlos Simmerling (Tue Feb 21 2017 - 13:33:23 PST)
    - Re: [AMBER] changing chirality with ParmEd? Hai Nguyen (Tue Feb 21 2017 - 13:39:06 PST)
    - Re: [AMBER] changing chirality with ParmEd? Osman, Roman (Tue Feb 21 2017 - 13:39:13 PST)
    - Re: [AMBER] changing chirality with ParmEd? Carlos Simmerling (Tue Feb 21 2017 - 13:41:36 PST)
Re: [AMBER] Using CHARMM 36 force field in AMBER Brian Radak (Mon Feb 20 2017 - 07:55:56 PST)
- [AMBER] 回复： Using CHARMM 36 force field in AMBER Shanghaitech University WuMeng (Tue Feb 21 2017 - 17:56:37 PST)
  - Re: [AMBER] 回复： Using CHARMM 36 force field in AMBER Jason Swails (Tue Feb 21 2017 - 19:25:52 PST)
    - Re: [AMBER] 回复： Using CHARMM 36 force field in AMBER Chris Neale (Tue Feb 21 2017 - 19:50:02 PST)
    - Re: [AMBER-Developers] [AMBER] 回复： Using CHARMM 36 force field in AMBER David Case (Thu Feb 23 2017 - 05:28:52 PST)
[AMBER] 12-6-4 potential in TI Qinghua Liao (Mon Feb 20 2017 - 14:37:24 PST)
- Re: [AMBER] 12-6-4 potential in TI Hannes Loeffler (Tue Feb 21 2017 - 01:06:03 PST)
  - Re: [AMBER] 12-6-4 potential in TI Qinghua Liao (Tue Feb 21 2017 - 02:09:00 PST)
[AMBER] minimization issue (**** in rst file) Chinh Su Tran To (Mon Feb 20 2017 - 19:07:46 PST)
- Re: [AMBER] minimization issue (**** in rst file) Hai Nguyen (Mon Feb 20 2017 - 19:33:27 PST)
  - Re: [AMBER] minimization issue (**** in rst file) Bill Ross (Mon Feb 20 2017 - 19:50:52 PST)
    - Re: [AMBER] minimization issue (**** in rst file) Chinh Su Tran To (Mon Feb 20 2017 - 21:55:14 PST)
    - Re: [AMBER] minimization issue (**** in rst file) Bill Ross (Mon Feb 20 2017 - 22:19:23 PST)
    - Re: [AMBER] minimization issue (**** in rst file) Bill Ross (Mon Feb 20 2017 - 22:28:26 PST)
    - Re: [AMBER] minimization issue (**** in rst file) Chinh Su Tran To (Mon Feb 20 2017 - 23:18:53 PST)
    - Re: [AMBER] minimization issue (**** in rst file) David Case (Tue Feb 21 2017 - 05:15:23 PST)
[AMBER] tleap error Manjula Saravanan (Mon Feb 20 2017 - 22:48:03 PST)
- Re: [AMBER] tleap error Bill Ross (Mon Feb 20 2017 - 22:53:16 PST)
- Re: [AMBER] tleap error Elvis Martis (Tue Feb 21 2017 - 02:06:14 PST)
[AMBER] binding free energy- error calculation doubt Mary Varughese (Tue Feb 21 2017 - 02:08:15 PST)
- Re: [AMBER] binding free energy- error calculation doubt David Case (Tue Feb 21 2017 - 05:19:54 PST)
  - Re: [AMBER] binding free energy- error calculation doubt Mary Varughese (Wed Feb 22 2017 - 03:00:02 PST)
    - Re: [AMBER] binding free energy- error calculation doubt Elvis Martis (Wed Feb 22 2017 - 04:21:12 PST)
Re: [AMBER] AMBER Digest, Vol 1852, Issue 1 Tiffani Rovira (Tue Feb 21 2017 - 02:41:48 PST)
- Re: [AMBER] AMBER Digest, Vol 1852, Issue 1 Bill Ross (Tue Feb 21 2017 - 03:04:41 PST)
[AMBER] problem with CpHMD Michael Shokhen (Tue Feb 21 2017 - 04:03:39 PST)
- Re: [AMBER] problem with CpHMD Roitberg,Adrian E (Tue Feb 21 2017 - 04:36:47 PST)
  - Re: [AMBER] problem with CpHMD Michael Shokhen (Tue Feb 21 2017 - 05:19:07 PST)
    - Re: [AMBER] problem with CpHMD Roitberg,Adrian E (Tue Feb 21 2017 - 05:23:58 PST)
    - Re: [AMBER] problem with CpHMD Michael Shokhen (Tue Feb 21 2017 - 05:31:21 PST)
- Re: [AMBER] problem with CpHMD David Case (Tue Feb 21 2017 - 05:22:40 PST)
[AMBER] Memory usage of NMR center of mass restreaints on GPUs paul (Tue Feb 21 2017 - 05:33:15 PST)
[AMBER] > source leaprc.water.tip3p chemocev marker (Tue Feb 21 2017 - 05:35:57 PST)
- Re: [AMBER] > source leaprc.water.tip3p David Case (Tue Feb 21 2017 - 06:28:05 PST)
  - Re: [AMBER] > source leaprc.water.tip3p chemocev marker (Tue Feb 21 2017 - 07:17:01 PST)
    - Re: [AMBER] > source leaprc.water.tip3p David Case (Tue Feb 21 2017 - 11:05:22 PST)
[AMBER] ParmEd problem: LJ12_6_4Error: Could not find parameters for ATOM_TYPE CL 杨金鹏 (Tue Feb 21 2017 - 05:42:20 PST)
- Re: [AMBER] ParmEd problem: LJ12_6_4Error: Could not find parameters for ATOM_TYPE CL Pengfei Li (Tue Feb 21 2017 - 13:33:46 PST)
[AMBER] When does cpptraj use information from the original pdb file? Markowska (Tue Feb 21 2017 - 05:54:17 PST)
- Re: [AMBER] When does cpptraj use information from the original pdb file? Daniel Roe (Tue Feb 21 2017 - 06:30:27 PST)
  - Re: [AMBER] When does cpptraj use information from the original pdb file? Daniel Roe (Fri Mar 03 2017 - 07:02:11 PST)
    - Re: [AMBER] When does cpptraj use information from the original pdb file? Markowska (Fri Mar 03 2017 - 09:57:56 PST)
[AMBER] Segmentation fault when starting parmchk2 for a modified aminoacid residue Nikolay N. Kuzmich (Tue Feb 21 2017 - 06:03:32 PST)
- Re: [AMBER] Segmentation fault when starting parmchk2 for a modified aminoacid residue David Case (Tue Feb 21 2017 - 06:32:02 PST)
- Re: [AMBER] Segmentation fault when starting parmchk2 for a modified aminoacid residue Elvis Martis (Tue Feb 21 2017 - 08:21:23 PST)
- Re: [AMBER] Segmentation fault when starting parmchk2 for a modified aminoacid residue Nikolay N. Kuzmich (Wed Feb 22 2017 - 07:20:16 PST)
  - Re: [AMBER] Segmentation fault when starting parmchk2 for a modified aminoacid residue Elvis Martis (Wed Feb 22 2017 - 08:25:20 PST)
  - Re: [AMBER] Segmentation fault when starting parmchk2 for a modified aminoacid residue David Case (Wed Feb 22 2017 - 11:27:21 PST)
- Re: [AMBER] Segmentation fault when starting parmchk2 for a modified aminoacid residue Nikolay N. Kuzmich (Thu Feb 23 2017 - 06:49:01 PST)
  - Re: [AMBER] Segmentation fault when starting parmchk2 for a modified aminoacid residue Elvis Martis (Thu Feb 23 2017 - 08:35:11 PST)
  - Re: [AMBER-Developers] [AMBER] Segmentation fault when starting parmchk2 for a modified aminoacid residue David Case (Fri Feb 24 2017 - 04:54:24 PST)
- Re: [AMBER] Segmentation fault when starting parmchk2 for a modified aminoacid residue Junmei Wang (Thu Mar 02 2017 - 08:13:04 PST)
[AMBER] antechamber warning Saman Yousuf ali (Tue Feb 21 2017 - 08:16:31 PST)
[AMBER] AMBER 16 problem with LEaP's addIons command Kasprzak, Wojciech (NIH/NCI) [C] (Tue Feb 21 2017 - 13:20:31 PST)
- Re: [AMBER] AMBER 16 problem with LEaP's addIons command Hai Nguyen (Tue Feb 21 2017 - 13:23:22 PST)
  - Re: [AMBER] AMBER 16 problem with LEaP's addIons command Kasprzak, Wojciech (NIH/NCI) [C] (Tue Feb 21 2017 - 14:58:11 PST)
    - Re: [AMBER] AMBER 16 problem with LEaP's addIons command Nhai (Tue Feb 21 2017 - 15:05:34 PST)
[AMBER] antechamber warning Saman Yousuf ali (Tue Feb 21 2017 - 22:18:13 PST)
- Re: [AMBER] antechamber warning Scott Brozell (Tue Feb 21 2017 - 23:11:36 PST)
  - Re: [AMBER] antechamber warning Saman Yousuf ali (Wed Feb 22 2017 - 00:11:57 PST)
    - Re: [AMBER] antechamber warning Scott Brozell (Wed Feb 22 2017 - 11:22:58 PST)
    - Re: [AMBER] antechamber warning Saman Yousuf ali (Wed Feb 22 2017 - 20:08:12 PST)
[AMBER] Fwd: SQM Error Mitul Srivastava (Tue Feb 21 2017 - 22:53:01 PST)
- Re: [AMBER] Fwd: SQM Error Bill Ross (Tue Feb 21 2017 - 23:28:00 PST)
  - Re: [AMBER] Fwd: SQM Error Goetz, Andreas (Tue Feb 21 2017 - 23:42:16 PST)
    - Re: [AMBER] Fwd: SQM Error Mitul Srivastava (Tue Feb 21 2017 - 23:52:04 PST)
    - Re: [AMBER] Fwd: SQM Error Bill Ross (Tue Feb 21 2017 - 23:57:13 PST)
    - Re: [AMBER] Fwd: SQM Error Mitul Srivastava (Wed Feb 22 2017 - 00:00:22 PST)
    - Re: [AMBER] Fwd: SQM Error Bill Ross (Wed Feb 22 2017 - 00:05:14 PST)
    - Re: [AMBER] Fwd: SQM Error Goetz, Andreas (Wed Feb 22 2017 - 00:09:05 PST)
    - Re: [AMBER] Fwd: SQM Error Mitul Srivastava (Wed Feb 22 2017 - 00:24:37 PST)
    - Re: [AMBER] Fwd: SQM Error Bill Ross (Wed Feb 22 2017 - 00:27:11 PST)
    - Re: [AMBER] Fwd: SQM Error Mitul Srivastava (Wed Feb 22 2017 - 00:28:48 PST)
    - Re: [AMBER] Fwd: SQM Error Bill Ross (Wed Feb 22 2017 - 00:40:30 PST)
    - Re: [AMBER] Fwd: SQM Error Mitul Srivastava (Wed Feb 22 2017 - 00:45:30 PST)
    - Re: [AMBER] Fwd: SQM Error Goetz, Andreas (Wed Feb 22 2017 - 00:54:26 PST)
    - Re: [AMBER] Fwd: SQM Error Bill Ross (Wed Feb 22 2017 - 00:54:44 PST)
    - Re: [AMBER] Fwd: SQM Error Bill Ross (Wed Feb 22 2017 - 01:00:22 PST)
    - Re: [AMBER] Fwd: SQM Error Bill Ross (Wed Feb 22 2017 - 00:30:38 PST)
    - Re: [AMBER] Fwd: SQM Error Mitul Srivastava (Wed Feb 22 2017 - 00:36:12 PST)
[AMBER] Minimisation error and system blowup for a large protein using implicit solvent Joseph Salmon (Wed Feb 22 2017 - 06:54:03 PST)
- Re: [AMBER] Minimisation error and system blowup for a large protein using implicit solvent Nhai (Wed Feb 22 2017 - 08:44:13 PST)
- Re: [AMBER] Minimisation error and system blowup for a large protein using implicit solvent Nhai (Wed Feb 22 2017 - 09:12:13 PST)
  - Re: [AMBER] Minimisation error and system blowup for a large protein using implicit solvent Joseph Salmon (Wed Feb 22 2017 - 10:37:16 PST)
    - Re: [AMBER] Minimisation error and system blowup for a large protein using implicit solvent Hai Nguyen (Wed Feb 22 2017 - 10:46:41 PST)
    - Re: [AMBER] Minimisation error and system blowup for a large protein using implicit solvent Joseph Salmon (Thu Feb 23 2017 - 07:08:17 PST)
[AMBER] problems with heating Alicia Merlino (Wed Feb 22 2017 - 11:24:34 PST)
- Re: [AMBER] problems with heating Hai Nguyen (Wed Feb 22 2017 - 11:29:42 PST)
- Re: [AMBER] problems with heating David Case (Wed Feb 22 2017 - 12:49:35 PST)
  - Re: [AMBER] problems with heating Alicia Merlino (Wed Feb 22 2017 - 14:57:40 PST)
    - Re: [AMBER] problems with heating Alicia Merlino (Wed Feb 22 2017 - 15:13:10 PST)
    - Re: [AMBER-Developers] [AMBER] problems with heating David Case (Wed Feb 22 2017 - 18:26:12 PST)
    - Re: [AMBER] problems with heating Alicia Merlino (Wed Feb 22 2017 - 19:30:41 PST)
    - Re: [AMBER] problems with heating Alicia Merlino (Wed Feb 22 2017 - 20:00:23 PST)
    - Re: [AMBER] problems with heating Alicia Merlino (Wed Feb 22 2017 - 20:32:36 PST)
    - Re: [AMBER] problems with heating Bill Ross (Wed Feb 22 2017 - 20:38:06 PST)
    - Re: [AMBER] problems with heating Alicia Merlino (Wed Feb 22 2017 - 21:01:14 PST)
    - Re: [AMBER] problems with heating Alicia Merlino (Thu Feb 23 2017 - 18:23:04 PST)
    - Re: [AMBER] problems with heating Bill Ross (Thu Feb 23 2017 - 19:12:33 PST)
    - Re: [AMBER] problems with heating Alicia Merlino (Thu Feb 23 2017 - 20:05:04 PST)
    - Re: [AMBER] problems with heating Alicia Merlino (Thu Feb 23 2017 - 20:09:37 PST)
    - Re: [AMBER] problems with heating Bill Ross (Thu Feb 23 2017 - 20:18:23 PST)
    - Re: [AMBER] problems with heating Alicia Merlino (Thu Feb 23 2017 - 20:52:53 PST)
    - Re: [AMBER] problems with heating Bill Ross (Fri Feb 24 2017 - 01:22:23 PST)
    - Re: [AMBER] problems with heating Bill Ross (Fri Feb 24 2017 - 02:00:14 PST)
    - Re: [AMBER] problems with heating David Case (Sat Feb 25 2017 - 06:33:31 PST)
    - Re: [AMBER] problems with heating Alicia Merlino (Mon Mar 06 2017 - 20:44:37 PST)
    - Re: [AMBER] problems with heating David Case (Tue Mar 07 2017 - 05:04:43 PST)
[AMBER] Amber force filed parameter Statics Eng (Wed Feb 22 2017 - 14:30:14 PST)
- Re: [AMBER] Amber force filed parameter Adrian Roitberg (Wed Feb 22 2017 - 14:32:09 PST)
- Re: [AMBER] Amber force filed parameter Bill Ross (Wed Feb 22 2017 - 14:58:32 PST)
  - Re: [AMBER] Amber force filed parameter Bill Ross (Wed Feb 22 2017 - 15:13:42 PST)
- Re: [AMBER] Amber force filed parameter Statics Eng (Thu Feb 23 2017 - 04:29:29 PST)
  - Re: [AMBER] Amber force filed parameter David Case (Thu Feb 23 2017 - 05:22:48 PST)
[AMBER] Antechamber Gaff Am1-bcc charges Neha Gandhi (Thu Feb 23 2017 - 00:22:07 PST)
- Re: [AMBER] Antechamber Gaff Am1-bcc charges Mitul Srivastava (Thu Feb 23 2017 - 00:38:43 PST)
- Re: [AMBER] Antechamber Gaff Am1-bcc charges David Case (Thu Feb 23 2017 - 05:16:40 PST)
[AMBER] This error may be due to faulty Connection atoms when using cationic dummy model JinpengYang (Thu Feb 23 2017 - 03:59:05 PST)
- Re: [AMBER] This error may be due to faulty Connection atoms when using cationic dummy model Qinghua Liao (Thu Feb 23 2017 - 04:11:37 PST)
[AMBER] scale part of the system with Parmed Qinghua Liao (Thu Feb 23 2017 - 04:42:11 PST)
[AMBER] DIMENSION OF BOX Subashini .K (Thu Feb 23 2017 - 04:58:15 PST)
- Re: [AMBER] DIMENSION OF BOX Daniel Roe (Thu Feb 23 2017 - 05:40:37 PST)
[AMBER] pbsa EDISPER with radiopt=0 vs radiopt=1 Paulo Costa (Thu Feb 23 2017 - 06:57:40 PST)
[AMBER] Sander python API problem (?) Elisa Pieri (Thu Feb 23 2017 - 07:05:15 PST)
- Re: [AMBER] Sander python API problem (?) Nhai (Thu Feb 23 2017 - 07:36:37 PST)
  - Re: [AMBER] Sander python API problem (?) Elisa Pieri (Thu Feb 23 2017 - 07:43:05 PST)
    - Re: [AMBER] Sander python API problem (?) Elisa Pieri (Thu Feb 23 2017 - 07:54:52 PST)
    - Re: [AMBER] Sander python API problem (?) Nhai (Thu Feb 23 2017 - 08:10:14 PST)
    - Re: [AMBER] Sander python API problem (?) Elisa Pieri (Thu Feb 23 2017 - 08:18:05 PST)
    - Re: [AMBER] Sander python API problem (?) Hai Nguyen (Thu Feb 23 2017 - 09:55:53 PST)
    - Re: [AMBER] Sander python API problem (?) Elisa Pieri (Fri Feb 24 2017 - 06:23:19 PST)
    - Re: [AMBER] Sander python API problem (?) Hai Nguyen (Fri Feb 24 2017 - 06:35:20 PST)
    - Re: [AMBER] Sander python API problem (?) Hai Nguyen (Fri Feb 24 2017 - 06:38:02 PST)
    - Re: [AMBER] Sander python API problem (?) Elisa Pieri (Fri Feb 24 2017 - 06:40:46 PST)
    - Re: [AMBER] Sander python API problem (?) Daniel Roe (Fri Feb 24 2017 - 06:42:38 PST)
    - Re: [AMBER] Sander python API problem (?) Daniel Roe (Fri Feb 24 2017 - 11:27:43 PST)
- Re: [AMBER] Sander python API problem (?) Elisa Pieri (Fri Feb 24 2017 - 02:24:33 PST)
[AMBER] Alternatives to ambmask that might work with parmed/gromber generated .prmtop files? Chris Neale (Thu Feb 23 2017 - 10:13:16 PST)
- Re: [AMBER] Alternatives to ambmask that might work with parmed/gromber generated .prmtop files? Daniel Roe (Thu Feb 23 2017 - 11:38:50 PST)
  - Re: [AMBER] Alternatives to ambmask that might work with parmed/gromber generated .prmtop files? Chris Neale (Thu Feb 23 2017 - 12:29:02 PST)
[AMBER] pbsa EDISPER with radiopt=0 vs radiopt=1 Paulo Costa (Fri Feb 24 2017 - 01:32:23 PST)
- Re: [AMBER] pbsa EDISPER with radiopt=0 vs radiopt=1 Ray Luo (Fri Feb 24 2017 - 08:35:37 PST)
[AMBER] REMD potential energy fluctuation sarah colin (Fri Feb 24 2017 - 03:18:15 PST)
[AMBER] Free energy calculation SHAKE's failure when heating. Artem Shekhovtsov (Fri Feb 24 2017 - 08:11:53 PST)
- Re: [AMBER] Free energy calculation SHAKE's failure when heating. Hannes Loeffler (Fri Feb 24 2017 - 08:35:23 PST)
- Re: [AMBER] Free energy calculation SHAKE's failure when heating. Hannes Loeffler (Fri Feb 24 2017 - 08:47:42 PST)
  - Re: [AMBER] Free energy calculation SHAKE's failure when heating. Artem Shekhovtsov (Fri Feb 24 2017 - 11:06:00 PST)
    - Re: [AMBER] Free energy calculation SHAKE's failure when heating. Hannes Loeffler (Sat Feb 25 2017 - 01:35:04 PST)
[AMBER] Charge error in Antechamber. Vatsal Purohit (Fri Feb 24 2017 - 08:50:57 PST)
- Re: [AMBER] Charge error in Antechamber. Bruno Falcone (Fri Feb 24 2017 - 09:04:54 PST)
  - Re: [AMBER] Charge error in Antechamber. Vatsal Purohit (Fri Feb 24 2017 - 09:28:16 PST)
    - Re: [AMBER] Charge error in Antechamber. Hannes Loeffler (Fri Feb 24 2017 - 09:36:25 PST)
    - Re: [AMBER] Charge error in Antechamber. Bruno Falcone (Fri Feb 24 2017 - 10:13:13 PST)
[AMBER] Non standrad residue unknown parameters and atomtypes Maral Aminpour (Fri Feb 24 2017 - 09:22:37 PST)
[AMBER] STRIP Thakur, Abhishek (Fri Feb 24 2017 - 11:36:55 PST)
- Re: [AMBER] STRIP Daniel Roe (Fri Feb 24 2017 - 11:40:16 PST)
[AMBER] pi-pi interaction and hydrophobic Thakur, Abhishek (Fri Feb 24 2017 - 12:59:02 PST)
- Re: [AMBER] pi-pi interaction and hydrophobic Kenneth McGuinness (Fri Feb 24 2017 - 14:17:40 PST)
  - Re: [AMBER] pi-pi interaction and hydrophobic Jianping Lin (Fri Feb 24 2017 - 14:35:08 PST)
  - Re: [AMBER] pi-pi interaction and hydrophobic Chris Neale (Fri Feb 24 2017 - 14:46:58 PST)
    - Re: [AMBER] pi-pi interaction and hydrophobic Jiri Sponer (Sat Feb 25 2017 - 01:05:39 PST)
[AMBER] How to define a "Dihedral parameters" crossing a C-C triple bond? (Due to two fragment's interaction) Siwei Wang (Fri Feb 24 2017 - 18:32:11 PST)
[AMBER] Call for awards applications for ACS COMP Division Fall meeting in DC Carlos Simmerling (Sat Feb 25 2017 - 03:08:05 PST)
Re: [AMBER] [q4md-fft] Unknown parameters frcmod.unknown FyD (Sun Feb 26 2017 - 02:05:02 PST)
[AMBER] Problems reading in TIP3P parameters Geoffrey Gray (Sun Feb 26 2017 - 09:51:33 PST)
- Re: [AMBER] Problems reading in TIP3P parameters Daniel Roe (Sun Feb 26 2017 - 10:57:46 PST)
[AMBER] MM energy contributions of atoms in a molecule Jas Kalayan (Mon Feb 27 2017 - 08:52:51 PST)
- Re: [AMBER] MM energy contributions of atoms in a molecule Bruno Falcone (Wed Mar 01 2017 - 06:43:33 PST)
[AMBER] Cannot convert rst to pdb file after md simulation. Vatsal Purohit (Mon Feb 27 2017 - 09:29:13 PST)
- Re: [AMBER] Cannot convert rst to pdb file after md simulation. Daniel Roe (Mon Feb 27 2017 - 09:40:44 PST)
  - Re: [AMBER] Cannot convert rst to pdb file after md simulation. Vatsal Purohit (Mon Feb 27 2017 - 09:52:04 PST)
    - Re: [AMBER] Cannot convert rst to pdb file after md simulation. Bill Ross (Mon Feb 27 2017 - 10:03:02 PST)
    - Re: [AMBER] Cannot convert rst to pdb file after md simulation. Daniel Roe (Mon Feb 27 2017 - 10:23:20 PST)
    - Re: [AMBER] Cannot convert rst to pdb file after md simulation. Vatsal Purohit (Mon Feb 27 2017 - 10:54:52 PST)
[AMBER] request for input files Adrian Roitberg (Mon Feb 27 2017 - 10:24:56 PST)
- Re: [AMBER] request for input files Hannes Loeffler (Mon Feb 27 2017 - 10:43:51 PST)
[AMBER] periodic boundary conditions Neha Gandhi (Mon Feb 27 2017 - 17:19:56 PST)
[AMBER] problem about pressure setting 吴萌 (Mon Feb 27 2017 - 19:40:24 PST)
- Re: [AMBER] problem about pressure setting David Case (Tue Feb 28 2017 - 05:16:15 PST)
[AMBER] cpptraj: dihcovar and projection need trajin to work properly? Thomas Fox (Tue Feb 28 2017 - 07:33:54 PST)
- [AMBER] cpptraj: dihcovar and projection need trajin to work properly? - FollowUp Thomas Fox (Tue Feb 28 2017 - 07:42:48 PST)
- Re: [AMBER] cpptraj: dihcovar and projection need trajin to work properly? Daniel Roe (Wed Mar 01 2017 - 08:26:10 PST)
  - Re: [AMBER] cpptraj: dihcovar and projection need trajin to work properly? Thomas Fox (Wed Mar 01 2017 - 09:54:04 PST)
    - Re: [AMBER] cpptraj: dihcovar and projection need trajin to work properly? Daniel Roe (Wed Mar 01 2017 - 10:01:44 PST)
[AMBER] Holes/bubbles in water during NVT (fix atoms) Neha Gandhi (Tue Feb 28 2017 - 23:35:53 PST)
- Re: [AMBER] Holes/bubbles in water during NVT (fix atoms) David Cerutti (Wed Mar 01 2017 - 02:33:00 PST)
- Re: [AMBER] Holes/bubbles in water during NVT (fix atoms) Daniel Roe (Wed Mar 01 2017 - 08:17:51 PST)
[AMBER] pmemd.cuda and taskset on K80 Diego Gomes (Wed Mar 01 2017 - 08:10:24 PST)
- Re: [AMBER] pmemd.cuda and taskset on K80 Ross Walker (Wed Mar 01 2017 - 17:22:05 PST)
[AMBER] Distance between benzene ring of one molecule and centre of mass of other molecule konda003 . (Wed Mar 01 2017 - 13:54:53 PST)
- Re: [AMBER] Distance between benzene ring of one molecule and centre of mass of other molecule Nhai (Wed Mar 01 2017 - 17:38:36 PST)
[AMBER] REMD processor number Andreas Tosstorff (Thu Mar 02 2017 - 09:04:47 PST)
[AMBER] H-bonds matrix giulia palermo (Thu Mar 02 2017 - 09:26:11 PST)
- [AMBER] Fwd: H-bonds matrix giulia palermo (Thu Mar 02 2017 - 11:59:33 PST)
[AMBER] 1-4 VDW and 1-4 EEL Energy Components in mm-gbsa Atila Petrosian (Fri Mar 03 2017 - 01:01:24 PST)
- Re: [AMBER] 1-4 VDW and 1-4 EEL Energy Components in mm-gbsa Jason Swails (Fri Mar 03 2017 - 06:09:00 PST)
[AMBER] How to make rst file by using ptraj Vishal Nemaysh (Sat Mar 04 2017 - 07:24:09 PST)
- Re: [AMBER] How to make rst file by using ptraj Daniel Roe (Sat Mar 04 2017 - 12:19:13 PST)
- Re: [AMBER] How to make rst file by using ptraj David Case (Sat Mar 04 2017 - 12:51:02 PST)
  - Re: [AMBER] How to make rst file by using ptraj Daniel Roe (Sun Mar 05 2017 - 04:40:32 PST)
[AMBER] Amber 16 MD simulation Problems 杨满意 (Sat Mar 04 2017 - 20:11:03 PST)
- Re: [AMBER] Amber 16 MD simulation Problems Elvis Martis (Sun Mar 05 2017 - 02:28:54 PST)
  - Re: [AMBER] Amber 16 MD simulation Problems 杨满意 (Mon Mar 06 2017 - 02:53:46 PST)
    - Re: [AMBER] Amber 16 MD simulation Problems Elvis Martis (Mon Mar 06 2017 - 03:22:26 PST)
    - Re: [AMBER] Amber 16 MD simulation Problems 杨满意 (Mon Mar 06 2017 - 03:38:14 PST)
    - Re: [AMBER] Amber 16 MD simulation Problems David Case (Mon Mar 06 2017 - 18:39:03 PST)
- Re: [AMBER] Amber 16 MD simulation Problems David Case (Sun Mar 05 2017 - 10:21:47 PST)
[AMBER] dUMP parameters Mrinal Arandhara (Sun Mar 05 2017 - 07:20:35 PST)
- Re: [AMBER] dUMP parameters Elvis Martis (Sun Mar 05 2017 - 07:34:01 PST)
- Re: [AMBER] dUMP parameters Elvis Martis (Sun Mar 05 2017 - 07:37:07 PST)
  - Re: [AMBER] dUMP parameters Mrinal Arandhara (Sun Mar 05 2017 - 07:53:42 PST)
    - Re: [AMBER] dUMP parameters Elvis Martis (Sun Mar 05 2017 - 07:58:29 PST)
    - Re: [AMBER] dUMP parameters Mrinal Arandhara (Sun Mar 05 2017 - 08:06:14 PST)
    - Re: [AMBER] dUMP parameters ABEL Stephane (Sun Mar 05 2017 - 09:03:19 PST)
- Re: [AMBER] dUMP parameters David Case (Sun Mar 05 2017 - 10:17:09 PST)
- Re: [AMBER] dUMP parameters FyD (Mon Mar 06 2017 - 22:57:11 PST)
[AMBER] prepare prepin file from MCPB results Abhilash J (Mon Mar 06 2017 - 00:34:14 PST)
- Re: [AMBER] prepare prepin file from MCPB results Elvis Martis (Mon Mar 06 2017 - 02:38:50 PST)
- Re: [AMBER] prepare prepin file from MCPB results Pengfei Li (Mon Mar 06 2017 - 20:00:18 PST)
  - Re: [AMBER] prepare prepin file from MCPB results Abhilash J (Wed Mar 08 2017 - 01:31:34 PST)
[AMBER] reg "rel delta G binding computation using TIMD" Smriti Sharma (Mon Mar 06 2017 - 02:12:32 PST)
- Re: [AMBER] reg "rel delta G binding computation using TIMD" Hannes Loeffler (Mon Mar 06 2017 - 03:43:40 PST)
  - Re: [AMBER] reg "rel delta G binding computation using TIMD" Smriti Sharma (Mon Mar 06 2017 - 19:37:43 PST)
[AMBER] Simulating a protein with modified amino acid residue, the saga continues. Atom ... does not have a type. Nikolay N. Kuzmich (Mon Mar 06 2017 - 09:16:33 PST)
- Re: [AMBER] Simulating a protein with modified amino acid residue, the saga continues. Atom ... does not have a type. Thakur, Abhishek (Mon Mar 06 2017 - 11:32:51 PST)
- Re: [AMBER] Simulating a protein with modified amino acid residue, the saga continues. Atom ... does not have a type. David Case (Mon Mar 06 2017 - 18:36:03 PST)
- Re: [AMBER] Simulating a protein with modified amino acid residue, the saga continues. Atom ... does not have a type. FyD (Tue Mar 07 2017 - 01:30:34 PST)
- Re: [AMBER] Simulating a protein with modified amino acid residue, the saga continues. Atom ... does not have a type. Nikolay N. Kuzmich (Fri Mar 10 2017 - 08:35:09 PST)
  - Re: [AMBER] Simulating a protein with modified amino acid residue, the saga continues. Atom ... does not have a type. FyD (Fri Mar 10 2017 - 09:30:22 PST)
  - Re: [AMBER] Simulating a protein with modified amino acid residue, the saga continues. Atom ... does not have a type. David Case (Fri Mar 10 2017 - 11:13:03 PST)
[AMBER] Query regarding extension of Molecular dynamics simulation from 50ns to 100ns Lovika Mittal (Mon Mar 06 2017 - 20:26:12 PST)
- Re: [AMBER] Query regarding extension of Molecular dynamics simulation from 50ns to 100ns Elvis Martis (Mon Mar 06 2017 - 20:35:14 PST)
  - Re: [AMBER] Query regarding extension of Molecular dynamics simulation from 50ns to 100ns Lovika Mittal (Mon Mar 06 2017 - 20:59:15 PST)
    - Re: [AMBER] Query regarding extension of Molecular dynamics simulation from 50ns to 100ns Elvis Martis (Mon Mar 06 2017 - 21:04:21 PST)
    - Re: [AMBER] Query regarding extension of Molecular dynamics simulation from 50ns to 100ns Elvis Martis (Mon Mar 06 2017 - 21:07:32 PST)
    - Re: [AMBER] Query regarding extension of Molecular dynamics simulation from 50ns to 100ns Bill Ross (Mon Mar 06 2017 - 21:09:10 PST)
[AMBER] error explicit solvent CpHMD production run EGIDEA PUTI DEVINA (Mon Mar 06 2017 - 22:05:05 PST)
- Re: [AMBER] error explicit solvent CpHMD production run Adrian Roitberg (Tue Mar 07 2017 - 05:25:14 PST)
  - Re: [AMBER] error explicit solvent CpHMD production run EGIDEA PUTI DEVINA (Wed Mar 08 2017 - 01:41:11 PST)
    - Re: [AMBER] error explicit solvent CpHMD production run Adrian Roitberg (Wed Mar 08 2017 - 07:30:21 PST)
[AMBER] how to use TImerge to do TI simulations Sowmya Indrakumar (Tue Mar 07 2017 - 06:55:53 PST)
- Re: [AMBER] how to use TImerge to do TI simulations Sowmya Indrakumar (Tue Mar 07 2017 - 07:01:07 PST)
  - Re: [AMBER] how to use TImerge to do TI simulations Hannes Loeffler (Tue Mar 07 2017 - 07:25:51 PST)
    - Re: [AMBER] how to use TImerge to do TI simulations Sowmya Indrakumar (Tue Mar 07 2017 - 07:44:46 PST)
[AMBER] Application of external electric field with QM/MM in Amber Kshatresh Dutta Dubey (Tue Mar 07 2017 - 12:47:15 PST)
[AMBER] Error in Cobalt parameters in CO-METHYLCOBALAMIN with MCPB.py Abhilash J (Wed Mar 08 2017 - 01:45:50 PST)
- Re: [AMBER] Error in Cobalt parameters in CO-METHYLCOBALAMIN with MCPB.py Pengfei Li (Tue Mar 14 2017 - 14:19:26 PDT)
  - Re: [AMBER] Error in Cobalt parameters in CO-METHYLCOBALAMIN with MCPB.py Abhilash J (Wed Mar 15 2017 - 04:42:47 PDT)
[AMBER] OPEN SHELL MOLECULES Stellamaris Sotomayor Burneo (Wed Mar 08 2017 - 14:19:29 PST)
- Re: [AMBER] OPEN SHELL MOLECULES Hai Nguyen (Wed Mar 08 2017 - 14:38:30 PST)
- Re: [AMBER] OPEN SHELL MOLECULES David Case (Wed Mar 08 2017 - 18:57:47 PST)
[AMBER] cudaMemcpy GpuBuffer::Download failed an illegal memory access was encountered kungking Hanpaibool (Thu Mar 09 2017 - 01:59:04 PST)
- Re: [AMBER] cudaMemcpy GpuBuffer::Download failed an illegal memory access was encountered Andreas Tosstorff (Thu Mar 09 2017 - 02:29:59 PST)
- Re: [AMBER] cudaMemcpy GpuBuffer::Download failed an illegal memory access was encountered David Case (Thu Mar 09 2017 - 05:07:12 PST)
[AMBER] Accelerated MD Beale, John (Thu Mar 09 2017 - 02:51:12 PST)
- Re: [AMBER] Accelerated MD Jeff Wereszczynski (Sun Apr 27 2014 - 12:16:34 PDT)
  - Re: [AMBER] Accelerated MD Vlad Cojocaru (Sun Apr 27 2014 - 14:50:59 PDT)
    - Re: [AMBER] Accelerated MD Thomas Evangelidis (Sun Apr 27 2014 - 16:26:29 PDT)
    - Re: [AMBER] Accelerated MD Daniel Roe (Sun Apr 27 2014 - 17:26:08 PDT)
    - Re: [AMBER] Accelerated MD Vlad Cojocaru (Sun Apr 27 2014 - 22:15:35 PDT)
    - Re: [AMBER] Accelerated MD Thomas Evangelidis (Mon Apr 28 2014 - 14:42:16 PDT)
    - Re: [AMBER] Accelerated MD Vlad Cojocaru (Mon Apr 28 2014 - 15:06:07 PDT)
- Re: [AMBER] Accelerated MD Neha Gandhi (Thu Mar 09 2017 - 04:46:09 PST)
  - Re: [AMBER] Accelerated MD Beale, John (Thu Mar 09 2017 - 04:47:56 PST)
  - Re: [AMBER] Accelerated MD Beale, John (Thu Mar 09 2017 - 04:49:36 PST)
- Re: [AMBER] Accelerated MD Daniel Roe (Thu Mar 09 2017 - 05:36:51 PST)
[AMBER] Generate psf file for chamber Shanghaitech University WuMeng (Thu Mar 09 2017 - 02:56:23 PST)
- Re: [AMBER] Generate psf file for chamber Amy Rice (Thu Mar 09 2017 - 09:04:04 PST)
[AMBER] AmberTools compilation Tom Dreyfus (Thu Mar 09 2017 - 05:04:44 PST)
- Re: [AMBER] AmberTools compilation Daniel Roe (Thu Mar 09 2017 - 05:33:00 PST)
  - Re: [AMBER] AmberTools compilation Tom Dreyfus (Thu Mar 09 2017 - 05:45:18 PST)
    - Re: [AMBER] AmberTools compilation Daniel Roe (Thu Mar 09 2017 - 05:48:02 PST)
    - Re: [AMBER] AmberTools compilation Nhai (Thu Mar 09 2017 - 05:51:03 PST)
    - Re: [AMBER] AmberTools compilation Tom Dreyfus (Thu Mar 09 2017 - 05:56:15 PST)
    - Re: [AMBER] AmberTools compilation Daniel Roe (Thu Mar 09 2017 - 06:08:32 PST)
    - Re: [AMBER] AmberTools compilation David Case (Thu Mar 09 2017 - 06:16:50 PST)
    - Re: [AMBER] AmberTools compilation Tom Dreyfus (Thu Mar 09 2017 - 06:41:44 PST)
    - Re: [AMBER] AmberTools compilation Hai Nguyen (Thu Mar 09 2017 - 07:23:15 PST)
    - Re: [AMBER] AmberTools compilation Tom Dreyfus (Thu Mar 09 2017 - 07:36:09 PST)
    - Re: [AMBER] AmberTools compilation Hai Nguyen (Thu Mar 09 2017 - 07:40:25 PST)
    - Re: [AMBER] AmberTools compilation Tom Dreyfus (Thu Mar 09 2017 - 07:54:24 PST)
    - Re: [AMBER] AmberTools compilation Tom Dreyfus (Thu Mar 09 2017 - 07:22:47 PST)
    - Re: [AMBER] AmberTools compilation Hai Nguyen (Thu Mar 09 2017 - 07:30:23 PST)
[AMBER] anionic Ser ? Michael Shokhen (Thu Mar 09 2017 - 05:23:25 PST)
- Re: [AMBER] anionic Ser ? David Case (Thu Mar 09 2017 - 06:21:12 PST)
  - Re: [AMBER] anionic Ser ? Michael Shokhen (Thu Mar 09 2017 - 07:38:20 PST)
- Re: [AMBER] anionic Ser ? FyD (Fri Mar 10 2017 - 06:08:38 PST)
Re: [AMBER] Distance constraint Thakur, Abhishek (Thu Mar 09 2017 - 07:53:35 PST)
[AMBER] hydophobic Thakur, Abhishek (Thu Mar 09 2017 - 12:28:58 PST)
[AMBER] Problem in configuring+compiling cpptraj development version with Sander compiled with AmberTools16 SHAILESH KUMAR (Fri Mar 10 2017 - 02:50:34 PST)
- Re: [AMBER] Problem in configuring+compiling cpptraj development version with Sander compiled with AmberTools16 Daniel Roe (Fri Mar 10 2017 - 05:05:24 PST)
  - Re: [AMBER] Problem in configuring+compiling cpptraj development version with Sander compiled with AmberTools16 SHAILESH KUMAR (Fri Mar 10 2017 - 05:35:04 PST)
    - Re: [AMBER] Problem in configuring+compiling cpptraj development version with Sander compiled with AmberTools16 Daniel Roe (Fri Mar 10 2017 - 05:38:59 PST)
    - Re: [AMBER] Problem in configuring+compiling cpptraj development version with Sander compiled with AmberTools16 SHAILESH KUMAR (Fri Mar 10 2017 - 06:25:56 PST)
    - Re: [AMBER] Problem in configuring+compiling cpptraj development version with Sander compiled with AmberTools16 Hai Nguyen (Fri Mar 10 2017 - 07:26:32 PST)
    - Re: [AMBER] Problem in configuring+compiling cpptraj development version with Sander compiled with AmberTools16 SHAILESH KUMAR (Fri Mar 10 2017 - 07:51:54 PST)
[AMBER] Boron's parameter jinfeng liu (Fri Mar 10 2017 - 04:35:54 PST)
- Re: [AMBER] Boron's parameter David Case (Fri Mar 10 2017 - 07:27:07 PST)
[AMBER] Potential on QM atoms - details about cutoff Elisa Pieri (Fri Mar 10 2017 - 07:13:19 PST)
[AMBER] maximum distance for protein-ligand interactions in MM/GBSA Thomas Evangelidis (Sat Mar 11 2017 - 07:34:05 PST)
[AMBER] Memory footprint goes on increasing: pytraj traj.iterchunk used, distances between bonds calculation SHAILESH KUMAR (Sun Mar 12 2017 - 13:17:30 PDT)
- Re: [AMBER] Memory footprint goes on increasing: pytraj traj.iterchunk used, distances between bonds calculation Nhai (Sun Mar 12 2017 - 13:41:00 PDT)
  - Re: [AMBER] Memory footprint goes on increasing: pytraj traj.iterchunk used, distances between bonds calculation SHAILESH KUMAR (Sun Mar 12 2017 - 14:13:51 PDT)
    - Re: [AMBER] Memory footprint goes on increasing: pytraj traj.iterchunk used, distances between bonds calculation Hai Nguyen (Sun Mar 12 2017 - 14:30:15 PDT)
    - Re: [AMBER] Memory footprint goes on increasing: pytraj traj.iterchunk used, distances between bonds calculation Hai Nguyen (Sun Mar 12 2017 - 14:34:49 PDT)
[AMBER] How to use MCPB.py to generate OH parameters Alice Zeng (Sun Mar 12 2017 - 21:25:36 PDT)
- Re: [AMBER] How to use MCPB.py to generate OH parameters Pengfei Li (Tue Mar 14 2017 - 14:09:38 PDT)
[AMBER] Unperturbed charge of the unit is not zero Eugene Cha (Mon Mar 13 2017 - 07:09:29 PDT)
- Re: [AMBER] Unperturbed charge of the unit is not zero David Case (Mon Mar 13 2017 - 19:03:40 PDT)
Re: [AMBER] Error for reading the amber rst file David Case (Mon Mar 13 2017 - 08:02:23 PDT)
[AMBER] Installing AmberTools16 - ld library issue Giannis Gl (Mon Mar 13 2017 - 10:32:43 PDT)
- Re: [AMBER] Installing AmberTools16 - ld library issue Daniel Roe (Mon Mar 13 2017 - 10:37:58 PDT)
  - Re: [AMBER] Installing AmberTools16 - ld library issue Hai Nguyen (Mon Mar 13 2017 - 11:03:14 PDT)
    - Re: [AMBER] Installing AmberTools16 - ld library issue Giannis Gl (Mon Mar 13 2017 - 11:14:52 PDT)
[AMBER] Installing AmberTools16 - Sierra MacOs Giannis Gl (Mon Mar 13 2017 - 12:10:49 PDT)
- Re: [AMBER] Installing AmberTools16 - Sierra MacOs Hai Nguyen (Mon Mar 13 2017 - 13:27:09 PDT)
  - Re: [AMBER] Installing AmberTools16 - Sierra MacOs Hai Nguyen (Mon Mar 13 2017 - 13:27:50 PDT)
    - Re: [AMBER] Installing AmberTools16 - Sierra MacOs Giannis Gl (Mon Mar 13 2017 - 13:32:11 PDT)
    - Re: [AMBER] Installing AmberTools16 - Sierra MacOs Hai Nguyen (Mon Mar 13 2017 - 13:37:37 PDT)
    - Re: [AMBER] Installing AmberTools16 - Sierra MacOs Giannis Gl (Mon Mar 13 2017 - 13:46:28 PDT)
    - Re: [AMBER] Installing AmberTools16 - Sierra MacOs Hai Nguyen (Mon Mar 13 2017 - 13:51:56 PDT)
    - Re: [AMBER] Installing AmberTools16 - Sierra MacOs Giannis Gl (Mon Mar 13 2017 - 14:00:24 PDT)
    - Re: [AMBER] Installing AmberTools16 - Sierra MacOs Giannis Gl (Mon Mar 13 2017 - 14:01:56 PDT)
    - Re: [AMBER] Installing AmberTools16 - Sierra MacOs Hai Nguyen (Mon Mar 13 2017 - 14:11:56 PDT)
    - Re: [AMBER] Installing AmberTools16 - Sierra MacOs Hai Nguyen (Mon Mar 13 2017 - 14:23:25 PDT)
    - Re: [AMBER] Installing AmberTools16 - Sierra MacOs Bill Ross (Mon Mar 13 2017 - 14:02:44 PDT)
    - Re: [AMBER] Installing AmberTools16 - Sierra MacOs Giannis Gl (Mon Mar 13 2017 - 14:08:14 PDT)
    - Re: [AMBER] Installing AmberTools16 - Sierra MacOs Bill Ross (Mon Mar 13 2017 - 14:30:10 PDT)
    - Re: [AMBER] Installing AmberTools16 - Sierra MacOs Hai Nguyen (Mon Mar 13 2017 - 13:57:06 PDT)
[AMBER] Discrepancy between gaff.dat and leaprc.gaff hybridization Maral Aminpour (Mon Mar 13 2017 - 13:17:52 PDT)
[AMBER] A problem about the frcmod produced by ParmChk JinpengYang (Mon Mar 13 2017 - 18:07:16 PDT)
- Re: [AMBER] A problem about the frcmod produced by ParmChk David Case (Mon Mar 13 2017 - 19:15:23 PDT)
[AMBER] Error when running QM/MM MD for actinide and lanthanide system by amber 鲁俊波 (Mon Mar 13 2017 - 19:22:19 PDT)
- Re: [AMBER] Error when running QM/MM MD for actinide and lanthanide system by amber Goetz, Andreas (Mon Mar 13 2017 - 20:30:27 PDT)
[AMBER] problem with solvation Maryam Hamzehee (Tue Mar 14 2017 - 00:21:18 PDT)
- Re: [AMBER] problem with solvation David Case (Tue Mar 14 2017 - 07:27:52 PDT)
[AMBER] Intel Xeon Phi 7120P Sofia Vasilakaki (Tue Mar 14 2017 - 07:26:43 PDT)
- Re: [AMBER] Intel Xeon Phi 7120P Elvis Martis (Wed Mar 15 2017 - 00:03:44 PDT)
[AMBER] prepc vs prepi Yong Duan (Tue Mar 14 2017 - 12:36:07 PDT)
- Re: [AMBER] prepc vs prepi Yong Duan (Tue Mar 14 2017 - 12:55:51 PDT)
- Re: [AMBER] prepc vs prepi David Case (Tue Mar 14 2017 - 14:43:28 PDT)
[AMBER] How to generate inputfile 杨满意 (Tue Mar 14 2017 - 20:37:08 PDT)
- Re: [AMBER] How to generate inputfile David Case (Wed Mar 15 2017 - 07:19:25 PDT)
  - Re: [AMBER] How to generate inputfile 杨满意 (Wed Mar 15 2017 - 18:49:43 PDT)
    - Re: [AMBER] How to generate inputfile David Case (Thu Mar 16 2017 - 05:54:26 PDT)
    - Re: [AMBER] How to generate inputfile 杨满意 (Fri Mar 17 2017 - 05:34:59 PDT)
    - Re: [AMBER] How to generate inputfile David Case (Fri Mar 17 2017 - 07:12:57 PDT)
    - Re: [AMBER] How to generate inputfile 杨满意 (Wed Mar 22 2017 - 05:48:51 PDT)
[AMBER] How to get parmed.py script? Sowmya Indrakumar (Wed Mar 15 2017 - 02:31:05 PDT)
- Re: [AMBER] How to get parmed.py script? Karl Kirschner (Wed Mar 15 2017 - 03:25:13 PDT)
  - Re: [AMBER] How to get parmed.py script? Sowmya Indrakumar (Wed Mar 15 2017 - 03:30:37 PDT)
- Re: [AMBER] How to get parmed.py script? Hai Nguyen (Wed Mar 15 2017 - 06:11:40 PDT)
[AMBER] Help with reconstructing pH-based mdcrd (trajectory) files Ingvild Isaksen (Wed Mar 15 2017 - 05:13:32 PDT)
- Re: [AMBER] Help with reconstructing pH-based mdcrd (trajectory) files Daniel Roe (Wed Mar 15 2017 - 06:15:05 PDT)
  - Re: [AMBER] Help with reconstructing pH-based mdcrd (trajectory) files Ingvild Isaksen (Wed Mar 15 2017 - 06:42:21 PDT)
    - Re: [AMBER] Help with reconstructing pH-based mdcrd (trajectory) files Daniel Roe (Wed Mar 15 2017 - 07:17:10 PDT)
    - Re: [AMBER] Help with reconstructing pH-based mdcrd (trajectory) files Ingvild Isaksen (Wed Mar 15 2017 - 07:26:26 PDT)
[AMBER] Problems in using Parmchk2 杨满意 (Wed Mar 15 2017 - 07:08:58 PDT)
- Re: [AMBER] Problems in using Parmchk2 David Case (Wed Mar 15 2017 - 15:10:50 PDT)
  - Re: [AMBER] Problems in using Parmchk2 杨满意 (Wed Mar 15 2017 - 19:09:35 PDT)
    - Re: [AMBER] Problems in using Parmchk2 David Case (Thu Mar 16 2017 - 05:50:56 PDT)
    - Re: [AMBER] Problems in using Parmchk2 杨满意 (Thu Mar 16 2017 - 07:13:06 PDT)
    - Re: [AMBER] Problems in using Parmchk2 David Case (Tue Mar 21 2017 - 07:15:51 PDT)
[AMBER] About PCA with cpptraj Elvis Martis (Wed Mar 15 2017 - 09:34:00 PDT)
- Re: [AMBER] About PCA with cpptraj Daniel Roe (Wed Mar 15 2017 - 10:03:19 PDT)
  - Re: [AMBER] About PCA with cpptraj Elvis Martis (Wed Mar 15 2017 - 10:06:26 PDT)
[AMBER] Issues running TI simulations Sowmya Indrakumar (Thu Mar 16 2017 - 02:10:04 PDT)
- Re: [AMBER] Issues running TI simulations Bill Ross (Thu Mar 16 2017 - 02:24:42 PDT)
  - Re: [AMBER] Issues running TI simulations Sowmya Indrakumar (Thu Mar 16 2017 - 02:30:37 PDT)
    - Re: [AMBER] Issues running TI simulations Bill Ross (Thu Mar 16 2017 - 02:36:50 PDT)
    - Re: [AMBER] Issues running TI simulations Sowmya Indrakumar (Thu Mar 16 2017 - 05:21:07 PDT)
[AMBER] distance calculations - Protein-RNA Sidhu, Khushwant (Dr.) (Thu Mar 16 2017 - 03:36:26 PDT)
- Re: [AMBER] distance calculations - Protein-RNA Daniel Roe (Thu Mar 16 2017 - 05:41:05 PDT)
  - Re: [AMBER] distance calculations - Protein-RNA Sidhu, Khushwant (Dr.) (Tue Apr 04 2017 - 01:50:01 PDT)
    - Re: [AMBER] distance calculations - Protein-RNA Bill Ross (Tue Apr 04 2017 - 01:59:59 PDT)
    - Re: [AMBER] distance calculations - Protein-RNA Daniel Roe (Tue Apr 04 2017 - 05:17:02 PDT)
[AMBER] Generating topology from Gaussian 09 Vijay Achari (Thu Mar 16 2017 - 05:08:25 PDT)
- Re: [AMBER] Generating topology from Gaussian 09 Elvis Martis (Thu Mar 16 2017 - 07:25:26 PDT)
[AMBER] converting trajectory file from NAMD to AMBER Oleksii Zdorevskyi (Thu Mar 16 2017 - 07:43:12 PDT)
- Re: [AMBER] converting trajectory file from NAMD to AMBER Elvis Martis (Thu Mar 16 2017 - 07:45:43 PDT)
- Re: [AMBER] converting trajectory file from NAMD to AMBER Daniel Roe (Thu Mar 16 2017 - 08:05:45 PDT)
  - Re: [AMBER] converting trajectory file from NAMD to AMBER Oleksii Zdorevskyi (Thu Mar 16 2017 - 08:40:12 PDT)
    - Re: [AMBER] converting trajectory file from NAMD to AMBER Oleksii Zdorevskyi (Thu Mar 16 2017 - 09:31:21 PDT)
    - Re: [AMBER] converting trajectory file from NAMD to AMBER Elvis Martis (Thu Mar 16 2017 - 09:37:06 PDT)
    - Re: [AMBER] converting trajectory file from NAMD to AMBER Hai Nguyen (Thu Mar 16 2017 - 09:49:09 PDT)
[AMBER] timerge question Adrian Roitberg (Thu Mar 16 2017 - 07:48:09 PDT)
- Re: [AMBER] timerge question Daniel Mermelstein (Thu Mar 16 2017 - 15:47:31 PDT)
  - Re: [AMBER] timerge question Hannes Loeffler (Fri Mar 17 2017 - 02:38:06 PDT)
    - Re: [AMBER] timerge question Jason Swails (Sat Mar 18 2017 - 11:33:10 PDT)
[AMBER] RE : suitable basis sets for QM/MM Budhathoki, Dipesh (Thu Mar 16 2017 - 10:49:00 PDT)
- Re: [AMBER] RE : suitable basis sets for QM/MM Goetz, Andreas (Thu Mar 16 2017 - 12:25:00 PDT)
  - Re: [AMBER] RE : suitable basis sets for QM/MM Budhathoki, Dipesh (Thu Mar 16 2017 - 13:51:04 PDT)
    - Re: [AMBER] RE : suitable basis sets for QM/MM Vaibhav Dixit (Thu Mar 16 2017 - 22:01:28 PDT)
Re: [AMBER] How to generate inputfile (???) David Poole (Thu Mar 16 2017 - 12:08:50 PDT)
- Re: [AMBER] How to generate inputfile (???) 杨满意 (Fri Mar 17 2017 - 06:09:32 PDT)
[AMBER] Generate DNA sequence with a mismatch diego.soler.uam.es (Fri Mar 17 2017 - 04:39:43 PDT)
[AMBER] MM/GBSA residual decomposition issue Bharatham, Nagakumar (Fri Mar 17 2017 - 05:29:57 PDT)
- [AMBER] Fw: MM/GBSA residual decomposition issue Bharatham, Nagakumar (Fri Mar 17 2017 - 07:50:48 PDT)
  - Re: [AMBER] Fw: MM/GBSA residual decomposition issue Hai Nguyen (Fri Mar 17 2017 - 08:13:18 PDT)
[AMBER] issues generating parameter files for the ligands- FEW Sowmya Indrakumar (Fri Mar 17 2017 - 08:13:03 PDT)
[AMBER] MM/GBSA residual decomposition issue nagakumarb.ccamp.res.in (Fri Mar 17 2017 - 08:13:20 PDT)
[AMBER] C/Fortran compilation Kanin Wichapong (Fri Mar 17 2017 - 08:42:27 PDT)
- Re: [AMBER] C/Fortran compilation Hai Nguyen (Fri Mar 17 2017 - 09:00:15 PDT)
[AMBER] NMODE ERROR MESSAGE konda003 . (Fri Mar 17 2017 - 09:02:46 PDT)
[AMBER] [MTKPP & pmemd error]: Installation of Amber 12 with Amber-too13 on Fedora25-64bit Vasantha Kumar (Fri Mar 17 2017 - 23:33:42 PDT)
- Re: [AMBER] [MTKPP & pmemd error]: Installation of Amber 12 with Amber-too13 on Fedora25-64bit Bill Ross (Fri Mar 17 2017 - 23:55:50 PDT)
  - Re: [AMBER] [MTKPP & pmemd error]: Installation of Amber 12 with Amber-too13 on Fedora25-64bit Vasantha Kumar (Mon Mar 20 2017 - 08:49:48 PDT)
- Re: [AMBER] [MTKPP & pmemd error]: Installation of Amber 12 with Amber-too13 on Fedora25-64bit David Case (Sat Mar 18 2017 - 08:22:33 PDT)
  - Re: [AMBER] [MTKPP & pmemd error]: Installation of Amber 12 with Amber-too13 on Fedora25-64bit Vasantha Kumar (Sat Mar 18 2017 - 19:12:19 PDT)
    - Re: [AMBER] [MTKPP & pmemd error]: Installation of Amber 12 with Amber-too13 on Fedora25-64bit Vasantha Kumar (Sat Mar 18 2017 - 19:19:19 PDT)
    - Re: [AMBER] [MTKPP & pmemd error]: Installation of Amber 12 with Amber-too13 on Fedora25-64bit Bill Ross (Sat Mar 18 2017 - 22:46:07 PDT)
    - Re: [AMBER] [MTKPP & pmemd error]: Installation of Amber 12 with Amber-too13 on Fedora25-64bit Hai Nguyen (Sat Mar 18 2017 - 23:19:36 PDT)
    - Re: [AMBER] [MTKPP & pmemd error]: Installation of Amber 12 with Amber-too13 on Fedora25-64bit Vasantha Kumar (Mon Mar 20 2017 - 08:38:01 PDT)
    - Re: [AMBER] [MTKPP & pmemd error]: Installation of Amber 12 with Amber-too13 on Fedora25-64bit Hai Nguyen (Mon Mar 20 2017 - 08:46:30 PDT)
[AMBER] 2D rms plot doubt Mary Varughese (Sat Mar 18 2017 - 02:56:00 PDT)
- Re: [AMBER] 2D rms plot doubt Elvis Martis (Sat Mar 18 2017 - 03:11:19 PDT)
  - Re: [AMBER] 2D rms plot doubt SHAILESH KUMAR (Sat Mar 18 2017 - 06:58:01 PDT)
    - Re: [AMBER] 2D rms plot doubt Daniel Roe (Sat Mar 18 2017 - 09:36:55 PDT)
    - Re: [AMBER] 2D rms plot doubt SHAILESH KUMAR (Sat Mar 18 2017 - 10:10:05 PDT)
    - Re: [AMBER] 2D rms plot doubt Mary Varughese (Sat Mar 18 2017 - 10:14:55 PDT)
    - Re: [AMBER] 2D rms plot doubt Daniel Roe (Mon Mar 20 2017 - 05:27:20 PDT)
    - Re: [AMBER] 2D rms plot doubt SHAILESH KUMAR (Mon Mar 20 2017 - 09:57:35 PDT)
    - Re: [AMBER] 2D rms plot doubt Daniel Roe (Mon Mar 20 2017 - 05:23:33 PDT)
[AMBER] pmemd.MPI error on lonestar5 super comp. Miguel Rivera (Sun Mar 19 2017 - 15:48:00 PDT)
- Re: [AMBER] pmemd.MPI error on lonestar5 super comp. Daniel Roe (Mon Mar 20 2017 - 05:30:49 PDT)
  - Re: [AMBER] pmemd.MPI error on lonestar5 super comp. Miguel Rivera (Wed Jun 07 2017 - 12:19:24 PDT)
[AMBER] Issue regarding ligand parameterization Nirupma Singh (Sun Mar 19 2017 - 22:55:18 PDT)
- Re: [AMBER] Issue regarding ligand parameterization David Case (Mon Mar 20 2017 - 05:06:17 PDT)
  - Re: [AMBER] Issue regarding ligand parameterization Bruno Falcone (Mon Mar 20 2017 - 07:21:22 PDT)
[AMBER] install AMBER16 GTX480 Kanin Wichapong (Mon Mar 20 2017 - 06:46:54 PDT)
- Re: [AMBER] install AMBER16 GTX480 Jason Swails (Mon Mar 20 2017 - 11:29:30 PDT)
  - Re: [AMBER] install AMBER16 GTX480 Ross Walker (Tue Mar 21 2017 - 17:09:38 PDT)
[AMBER] Memory usage of NMR COM restraints 4 times larger in amber 16? paul (Mon Mar 20 2017 - 07:02:10 PDT)
- Re: [AMBER] Memory usage of NMR COM restraints 4 times larger in amber 16? David Case (Mon Mar 20 2017 - 07:44:01 PDT)
  - Re: [AMBER] Memory usage of NMR COM restraints 4 times larger in amber 16? paul (Mon Mar 20 2017 - 09:01:53 PDT)
    - Re: [AMBER] Memory usage of NMR COM restraints 4 times larger in amber 16? Jason Swails (Mon Mar 20 2017 - 11:24:28 PDT)
    - Re: [AMBER] Memory usage of NMR COM restraints 4 times larger in amber 16? paul (Tue Mar 21 2017 - 04:35:39 PDT)
    - Re: [AMBER] Memory usage of NMR COM restraints 4 times larger in amber 16? Paul Westphälinger (Wed Mar 22 2017 - 00:42:22 PDT)
    - Re: [AMBER] Memory usage of NMR COM restraints 4 times larger in amber 16? David Case (Wed Mar 22 2017 - 08:24:20 PDT)
    - Re: [AMBER] Memory usage of NMR COM restraints 4 times larger in amber 16? Paul Westphälinger (Wed Mar 22 2017 - 09:17:27 PDT)
    - Re: [AMBER] Memory usage of NMR COM restraints 4 times larger in amber 16? Paul Westphälinger (Thu Mar 23 2017 - 03:38:38 PDT)
    - Re: [AMBER] Memory usage of NMR COM restraints 4 times larger in amber 16? Paul Westphaelinger (Fri Mar 24 2017 - 01:53:43 PDT)
    - Re: [AMBER] Memory usage of NMR COM restraints 4 times larger in amber 16? Paul Westphaelinger (Tue Mar 28 2017 - 08:29:14 PDT)
[AMBER] Memory usage of NMR COM restraints 4 times larger in amber 16? paul (Mon Mar 20 2017 - 07:12:48 PDT)
[AMBER] Antechamber Error luca maggi (Mon Mar 20 2017 - 23:56:51 PDT)
- Re: [AMBER] Antechamber Error Elvis Martis (Tue Mar 21 2017 - 00:15:27 PDT)
  - Re: [AMBER] Antechamber Error luca maggi (Thu Mar 23 2017 - 00:09:58 PDT)
    - Re: [AMBER] Antechamber Error Elvis Martis (Thu Mar 23 2017 - 01:58:53 PDT)
    - Re: [AMBER] Antechamber Error luca maggi (Thu Mar 23 2017 - 02:28:17 PDT)
    - Re: [AMBER] Antechamber Error Elvis Martis (Thu Mar 23 2017 - 02:59:26 PDT)
    - Re: [AMBER] Antechamber Error Andrew Schaub (Sat Mar 25 2017 - 00:30:38 PDT)
    - Re: [AMBER] Antechamber Error David Case (Sat Mar 25 2017 - 08:21:09 PDT)
[AMBER] Issue generating parameter files - FEW Sowmya Indrakumar (Tue Mar 21 2017 - 08:06:10 PDT)
[AMBER] help in RDF Robin Jain (Tue Mar 21 2017 - 08:19:44 PDT)
- Re: [AMBER] help in RDF Daniel Roe (Tue Mar 21 2017 - 08:30:33 PDT)
  - [AMBER] Is it possible to create a bugreport.ambermd.org mailinglist? Paul Westphälinger (Tue Mar 21 2017 - 11:56:41 PDT)
    - Re: [AMBER] Is it possible to create a bugreport.ambermd.org mailinglist? Hai Nguyen (Tue Mar 21 2017 - 13:23:07 PDT)
    - Re: [AMBER] Is it possible to create a bugreport.ambermd.org mailinglist? Paul Westphälinger (Wed Mar 22 2017 - 00:39:01 PDT)
    - Re: [AMBER] Is it possible to create a bugreport.ambermd.org mailinglist? Daniel Roe (Wed Mar 22 2017 - 06:04:30 PDT)
[AMBER] Questions about Amber TI tutorial Sadegh Faramarzi Ganjabad (Tue Mar 21 2017 - 12:50:28 PDT)
- Re: [AMBER] Questions about Amber TI tutorial Hannes Loeffler (Tue Mar 21 2017 - 13:56:48 PDT)
  - Re: [AMBER] Questions about Amber TI tutorial Hannes Loeffler (Wed Mar 22 2017 - 01:19:25 PDT)
[AMBER] multinode pmemd.cuda.MPI jac9999 behavior Scott Brozell (Tue Mar 21 2017 - 12:52:34 PDT)
- Re: [AMBER] multinode pmemd.cuda.MPI jac9999 behavior Niel Henriksen (Tue Mar 21 2017 - 13:50:00 PDT)
  - Re: [AMBER] multinode pmemd.cuda.MPI jac9999 behavior Scott Brozell (Thu Mar 23 2017 - 15:58:52 PDT)
    - Re: [AMBER] multinode pmemd.cuda.MPI jac9999 behavior Ross Walker (Thu Mar 23 2017 - 16:18:41 PDT)
    - Re: [AMBER] multinode pmemd.cuda.MPI jac9999 behavior Scott Brozell (Mon Apr 24 2017 - 13:26:21 PDT)
    - Re: [AMBER] multinode pmemd.cuda.MPI jac9999 behavior Daniel Roe (Tue Apr 25 2017 - 06:09:14 PDT)
    - Re: [AMBER] multinode pmemd.cuda.MPI jac9999 behavior Scott Brozell (Tue Apr 25 2017 - 08:44:50 PDT)
    - Re: [AMBER] multinode pmemd.cuda.MPI jac9999 behavior David Case (Tue Apr 25 2017 - 10:27:45 PDT)
    - Re: [AMBER] multinode pmemd.cuda.MPI jac9999 behavior Scott Brozell (Tue Apr 25 2017 - 10:48:19 PDT)
    - Re: [AMBER] multinode pmemd.cuda.MPI jac9999 behavior Ross Walker (Tue Apr 25 2017 - 12:32:21 PDT)
    - Re: [AMBER] multinode pmemd.cuda.MPI jac9999 behavior Daniel Roe (Tue Apr 25 2017 - 13:02:46 PDT)
    - Re: [AMBER] multinode pmemd.cuda.MPI jac9999 behavior Nhai (Tue Apr 25 2017 - 16:10:53 PDT)
[AMBER] Select specific frames within cpptraj? Kenneth Huang (Tue Mar 21 2017 - 13:03:03 PDT)
- Re: [AMBER] Select specific frames within cpptraj? Daniel Roe (Tue Mar 21 2017 - 13:17:37 PDT)
Re: [AMBER] Nmode using MMPBSA.py konda003 . (Tue Mar 21 2017 - 14:06:36 PDT)
- Re: [AMBER] Nmode using MMPBSA.py David Case (Wed Mar 22 2017 - 08:12:42 PDT)
  - Re: [AMBER] Nmode using MMPBSA.py Dwight McGee (Wed Mar 22 2017 - 09:29:52 PDT)
[AMBER] Error Importing pytraj to Python 2.7 Program Samuel Bowerman (Tue Mar 21 2017 - 14:20:40 PDT)
- Re: [AMBER] Error Importing pytraj to Python 2.7 Program Hai Nguyen (Tue Mar 21 2017 - 14:35:38 PDT)
  - Re: [AMBER] Error Importing pytraj to Python 2.7 Program Samuel Bowerman (Tue Mar 21 2017 - 15:02:21 PDT)
- Re: [AMBER] Error Importing pytraj to Python 2.7 Program Hai Nguyen (Tue Mar 21 2017 - 14:59:53 PDT)
  - Re: [AMBER] Error Importing pytraj to Python 2.7 Program Samuel Bowerman (Tue Mar 21 2017 - 15:05:00 PDT)
    - Re: [AMBER] Error Importing pytraj to Python 2.7 Program Nhai (Tue Mar 21 2017 - 15:31:31 PDT)
[AMBER] unable to solvate a polymer Jon Mujika (Tue Mar 21 2017 - 16:00:19 PDT)
- Re: [AMBER] unable to solvate a polymer Bill Ross (Tue Mar 21 2017 - 16:12:29 PDT)
- Re: [AMBER] unable to solvate a polymer David Case (Wed Mar 22 2017 - 08:18:00 PDT)
- Re: [AMBER] unable to solvate a polymer Nhai (Wed Mar 22 2017 - 09:00:13 PDT)
[AMBER] Difficulty using noshakemask in Amber15 Chase Zagorec-Marks (Tue Mar 21 2017 - 16:43:03 PDT)
- Re: [AMBER] Difficulty using noshakemask in Amber15 Bill Ross (Tue Mar 21 2017 - 16:49:00 PDT)
  - Re: [AMBER] Difficulty using noshakemask in Amber15 Chase Zagorec-Marks (Wed Mar 22 2017 - 10:16:25 PDT)
[AMBER] Problem with keyboard in xleap Miguel Garavís (Wed Mar 22 2017 - 03:59:30 PDT)
- Re: [AMBER] Problem with keyboard in xleap Andreas Tosstorff (Wed Mar 22 2017 - 04:33:18 PDT)
  - Re: [AMBER] Problem with keyboard in xleap Miguel Garavís (Wed Mar 22 2017 - 05:07:33 PDT)
    - Re: [AMBER] Problem with keyboard in xleap Elvis Martis (Wed Mar 22 2017 - 05:23:41 PDT)
- Re: [AMBER] Problem with keyboard in xleap Daniel Roe (Wed Mar 22 2017 - 05:38:21 PDT)
  - Re: [AMBER] Problem with keyboard in xleap Miguel Garavís (Wed Mar 22 2017 - 05:59:59 PDT)
    - Re: [AMBER] Problem with keyboard in xleap David Case (Wed Mar 22 2017 - 08:40:36 PDT)
[AMBER] CpHMD: how is the charged system treated? Elisa Pieri (Wed Mar 22 2017 - 06:33:30 PDT)
- Re: [AMBER] CpHMD: how is the charged system treated? Adrian Roitberg (Wed Mar 22 2017 - 07:18:23 PDT)
[AMBER] 来自zengxitao的邮件 zengxitao (Wed Mar 22 2017 - 10:28:16 PDT)
- Re: [AMBER] 来自zengxitao的邮件 Adrian Roitberg (Wed Mar 22 2017 - 10:30:23 PDT)
[AMBER] AWS GPU node crashes with AMBER 16 Arnoult, Eric [JRDUS] (Wed Mar 22 2017 - 10:35:11 PDT)
[AMBER] Chamber error; No NONBONDED Sadegh Faramarzi Ganjabad (Wed Mar 22 2017 - 11:34:47 PDT)
- Re: [AMBER] Chamber error; No NONBONDED Jason Swails (Thu Mar 23 2017 - 20:22:38 PDT)
[AMBER] Count number of water molecules in minor groove of DNA The Cromicus Productions (Wed Mar 22 2017 - 12:33:02 PDT)
[AMBER] DU issue with Antechamber Abhilash J (Wed Mar 22 2017 - 21:21:37 PDT)
- Re: [AMBER] DU issue with Antechamber David Case (Thu Mar 23 2017 - 06:32:47 PDT)
  - Re: [AMBER] DU issue with Antechamber Abhilash J (Sat Mar 25 2017 - 00:16:26 PDT)
    - Re: [AMBER] DU issue with Antechamber David Case (Tue Mar 28 2017 - 10:01:36 PDT)
    - Re: [AMBER] DU issue with Antechamber Abhilash J (Thu Mar 30 2017 - 03:21:14 PDT)
[AMBER] Why molecular dynamics simulation was stopped without giving any error Garima Singh (Wed Mar 22 2017 - 23:36:01 PDT)
- Re: [AMBER] Why molecular dynamics simulation was stopped without giving any error Bill Ross (Thu Mar 23 2017 - 00:42:16 PDT)
- Re: [AMBER] Why molecular dynamics simulation was stopped without giving any error David Case (Thu Mar 23 2017 - 06:36:02 PDT)
[AMBER] cpptraj distance between centroid of a ring and an atom Neha Gandhi (Thu Mar 23 2017 - 00:41:54 PDT)
- Re: [AMBER] cpptraj distance between centroid of a ring and an atom Daniel Roe (Thu Mar 23 2017 - 05:11:36 PDT)
[AMBER] How to perform Newton-Raphson minimization to protein 巩梦雪 (Thu Mar 23 2017 - 05:22:59 PDT)
- Re: [AMBER] How to perform Newton-Raphson minimization to protein David Case (Thu Mar 23 2017 - 06:38:01 PDT)
  - Re: [AMBER] How to perform Newton-Raphson minimization to protein 巩梦雪 (Fri Mar 24 2017 - 06:53:26 PDT)
    - Re: [AMBER] How to perform Newton-Raphson minimization to protein David Case (Fri Mar 24 2017 - 07:20:28 PDT)
[AMBER] 发自刘兰茹的邮件 刘兰茹 (Fri Mar 24 2017 - 01:42:12 PDT)
- Re: [AMBER] 发自刘兰茹的邮件 Vlad Cojocaru (Fri Mar 24 2017 - 01:53:00 PDT)
- Re: [AMBER] 发自刘兰茹的邮件 liulr13.mails.jlu.edu.cn (Fri Mar 24 2017 - 02:30:36 PDT)
  - Re: [AMBER] 发自刘兰茹的邮件 Vlad Cojocaru (Fri Mar 24 2017 - 03:14:26 PDT)
    - Re: [AMBER] 发自刘兰茹的邮件 David Case (Fri Mar 24 2017 - 05:19:58 PDT)
    - Re: [AMBER] 发自刘兰茹的邮件 Vlad Cojocaru (Fri Mar 24 2017 - 06:50:38 PDT)
[AMBER] residue contribution for covalent inhibitor nagakumarb.ccamp.res.in (Fri Mar 24 2017 - 06:54:34 PDT)
- [AMBER] residue contribution calculation for covalent inhibitor--- Technical challenge??? nagakumarb.ccamp.res.in (Fri Apr 14 2017 - 22:02:36 PDT)
  - Re: [AMBER] residue contribution calculation for covalent inhibitor--- Technical challenge??? Bill Ross (Fri Apr 14 2017 - 22:22:34 PDT)
    - Re: [AMBER] residue contribution calculation for covalent inhibitor--- Technical challenge??? nagakumarb.ccamp.res.in (Fri Apr 14 2017 - 22:47:49 PDT)
    - Re: [AMBER] residue contribution calculation for covalent inhibitor--- Technical challenge??? Bill Ross (Fri Apr 14 2017 - 23:01:41 PDT)
    - Re: [AMBER] residue contribution calculation for covalent inhibitor--- Technical challenge??? nagakumarb.ccamp.res.in (Fri Apr 14 2017 - 23:32:09 PDT)
    - Re: [AMBER] residue contribution calculation for covalent inhibitor--- Technical challenge??? Bill Ross (Fri Apr 14 2017 - 23:48:34 PDT)
    - Re: [AMBER] residue contribution calculation for covalent inhibitor--- Technical challenge??? nagakumarb.ccamp.res.in (Sat Apr 15 2017 - 05:24:45 PDT)
[AMBER] renumber residues Thakur, Abhishek (Fri Mar 24 2017 - 07:15:15 PDT)
- Re: [AMBER] renumber residues Daniel Roe (Fri Mar 24 2017 - 08:01:16 PDT)
- Re: [AMBER] renumber residues David Case (Fri Mar 24 2017 - 11:05:59 PDT)
[AMBER] Restraint on Z-projection of a distance Chitrak Gupta (Fri Mar 24 2017 - 11:44:53 PDT)
- Re: [AMBER] Restraint on Z-projection of a distance Feng Pan (Fri Mar 24 2017 - 12:15:50 PDT)
[AMBER] Installation issue George Tzotzos (Sat Mar 25 2017 - 05:37:03 PDT)
- Re: [AMBER] Installation issue Bill Ross (Tue Sep 22 2009 - 10:50:28 PDT)
- Re: [AMBER] Installation issue Bill Ross (Tue Sep 22 2009 - 10:55:34 PDT)
  - Re: [AMBER] Installation issue Ashveen Seenauth (Tue Sep 22 2009 - 10:59:46 PDT)
    - Re: [AMBER] Installation issue Tom Joseph (Tue Sep 22 2009 - 11:16:01 PDT)
- Re: [AMBER] Installation issue Bill Ross (Tue Sep 22 2009 - 10:59:22 PDT)
- Re: [AMBER] Installation issue Bill Ross (Tue Sep 22 2009 - 11:28:43 PDT)
  - Re: [AMBER] Installation issue Ashveen Seenauth (Wed Sep 23 2009 - 08:28:55 PDT)
    - Re: [AMBER] Installation issue Tom Joseph (Wed Sep 23 2009 - 08:35:44 PDT)
    - Re: [AMBER] Installation issue Ashveen Seenauth (Wed Sep 23 2009 - 08:41:53 PDT)
    - Re: [AMBER] Installation issue Tom Joseph (Wed Sep 23 2009 - 08:43:42 PDT)
    - Re: [AMBER] Installation issue Ashveen Seenauth (Wed Sep 23 2009 - 08:54:27 PDT)
    - Re: [AMBER] Installation issue Tom Joseph (Wed Sep 23 2009 - 09:08:33 PDT)
- Re: [AMBER] Installation issue Bill Ross (Wed Sep 23 2009 - 09:29:28 PDT)
- Re: [AMBER] Installation issue Bill Ross (Wed Sep 23 2009 - 09:36:59 PDT)
- Re: [AMBER] Installation issue Daniel Roe (Sat Mar 25 2017 - 05:59:51 PDT)
[AMBER] Force/energy vs extension curve in steered MD Ramin Salimi (Sat Mar 25 2017 - 10:02:22 PDT)
[AMBER] Force/Energy vs extension curve from Steered MD Ramin Salimi (Sat Mar 25 2017 - 10:36:15 PDT)
- Re: [AMBER] Force/Energy vs extension curve from Steered MD Adrian Roitberg (Sat Mar 25 2017 - 11:03:39 PDT)
  - Re: [AMBER] Force/Energy vs extension curve from Steered MD Ramin Salimi (Sat Mar 25 2017 - 11:15:19 PDT)
    - Re: [AMBER] Force/Energy vs extension curve from Steered MD Adrian Roitberg (Sat Mar 25 2017 - 11:31:03 PDT)
    - Re: [AMBER] Force/Energy vs extension curve from Steered MD Ramin Salimi (Sat Mar 25 2017 - 12:05:03 PDT)
    - Re: [AMBER] Force/Energy vs extension curve from Steered MD Jason Swails (Sun Mar 26 2017 - 17:27:26 PDT)
    - Re: [AMBER] Force/Energy vs extension curve from Steered MD Ramin Salimi (Sun Mar 26 2017 - 21:48:49 PDT)
    - Re: [AMBER] Force/Energy vs extension curve from Steered MD Ramin Salimi (Mon Mar 27 2017 - 11:13:07 PDT)
    - Re: [AMBER] Force/Energy vs extension curve from Steered MD Ramin Salimi (Sun Mar 26 2017 - 14:21:49 PDT)
[AMBER] Force/Energy vs extension curve from Steered MD Ramin Salimi (Sat Mar 25 2017 - 10:50:05 PDT)
[AMBER] restarting Amber calculations gives abnormal structures Sadegh Faramarzi Ganjabad (Sat Mar 25 2017 - 20:53:09 PDT)
- Re: [AMBER] restarting Amber calculations gives abnormal structures David Case (Tue Mar 28 2017 - 09:47:13 PDT)
- Re: [AMBER] restarting Amber calculations gives abnormal structures Sadegh Faramarzi Ganjabad (Tue Mar 28 2017 - 13:29:49 PDT)
  - Re: [AMBER] restarting Amber calculations gives abnormal structures David Case (Wed Mar 29 2017 - 04:50:28 PDT)
- Re: [AMBER] restarting Amber calculations gives abnormal structures Sadegh Faramarzi Ganjabad (Wed Mar 29 2017 - 12:26:56 PDT)
  - Re: [AMBER] restarting Amber calculations gives abnormal structures Chris Neale (Wed Mar 29 2017 - 12:36:15 PDT)
- Re: [AMBER] restarting Amber calculations gives abnormal structures Sadegh Faramarzi Ganjabad (Thu Mar 30 2017 - 22:17:15 PDT)
  - Re: [AMBER] restarting Amber calculations gives abnormal structures Marc van der Kamp (Thu Mar 30 2017 - 23:58:25 PDT)
    - Re: [AMBER] restarting Amber calculations gives abnormal structures Chris Neale (Fri Mar 31 2017 - 09:30:34 PDT)
    - Re: [AMBER] restarting Amber calculations gives abnormal structures Marc van der Kamp (Fri Mar 31 2017 - 09:37:53 PDT)
    - Re: [AMBER] restarting Amber calculations gives abnormal structures Daniel Roe (Fri Mar 31 2017 - 09:57:01 PDT)
    - Re: [AMBER] restarting Amber calculations gives abnormal structures Chris Neale (Fri Mar 31 2017 - 10:01:10 PDT)
    - Re: [AMBER] restarting Amber calculations gives abnormal structures David Case (Fri Mar 31 2017 - 11:18:31 PDT)
- Re: [AMBER] restarting Amber calculations gives abnormal structures Sadegh Faramarzi Ganjabad (Sun Apr 02 2017 - 23:28:02 PDT)
- Re: [AMBER] restarting Amber calculations gives abnormal structures Sadegh Faramarzi Ganjabad (Sun Apr 02 2017 - 23:37:09 PDT)
  - Re: [AMBER] restarting Amber calculations gives abnormal structures Chris Neale (Sun Apr 02 2017 - 23:45:00 PDT)
    - Re: [AMBER] restarting Amber calculations gives abnormal structures David Case (Mon Apr 03 2017 - 18:43:03 PDT)
[AMBER] Thermodynamic integration simulations issues Szymon Żaczek (Sun Mar 26 2017 - 13:02:04 PDT)
- Re: [AMBER] Thermodynamic integration simulations issues Hannes Loeffler (Tue Mar 28 2017 - 06:21:26 PDT)
[AMBER] surf cpptraj non-standard residue Andreas Tosstorff (Mon Mar 27 2017 - 05:29:01 PDT)
- Re: [AMBER] surf cpptraj non-standard residue Elvis Martis (Mon Mar 27 2017 - 05:38:39 PDT)
  - Re: [AMBER] surf cpptraj non-standard residue Andreas Tosstorff (Mon Mar 27 2017 - 05:50:18 PDT)
    - Re: [AMBER] surf cpptraj non-standard residue Elvis Martis (Mon Mar 27 2017 - 06:24:50 PDT)
    - Re: [AMBER] surf cpptraj non-standard residue Andreas Tosstorff (Mon Mar 27 2017 - 07:56:27 PDT)
    - Re: [AMBER] surf cpptraj non-standard residue Daniel Roe (Mon Mar 27 2017 - 08:02:25 PDT)
[AMBER] FEW- issues generating parameter files for MD Sowmya Indrakumar (Mon Mar 27 2017 - 06:57:49 PDT)
- Re: [AMBER] FEW- issues generating parameter files for MD Andreas Tosstorff (Mon Mar 27 2017 - 07:20:53 PDT)
  - Re: [AMBER] FEW- issues generating parameter files for MD Sowmya Indrakumar (Mon Mar 27 2017 - 08:18:40 PDT)
    - Re: [AMBER] FEW- issues generating parameter files for MD Andreas Tosstorff (Mon Mar 27 2017 - 08:28:06 PDT)
- Re: [AMBER] FEW- issues generating parameter files for MD Andreas Tosstorff (Tue Mar 28 2017 - 07:24:31 PDT)
  - Re: [AMBER] FEW- issues generating parameter files for MD Sowmya Indrakumar (Tue Mar 28 2017 - 08:37:45 PDT)
    - Re: [AMBER] FEW- issues generating parameter files for MD Andreas Tosstorff (Tue Mar 28 2017 - 08:45:41 PDT)
    - Re: [AMBER] FEW- issues generating parameter files for MD Sowmya Indrakumar (Tue Mar 28 2017 - 08:59:19 PDT)
    - Re: [AMBER] FEW- issues generating parameter files for MD Andreas Tosstorff (Wed Mar 29 2017 - 00:50:05 PDT)
    - Re: [AMBER] FEW- issues generating parameter files for MD Sowmya Indrakumar (Wed Mar 29 2017 - 01:27:02 PDT)
Re: [AMBER-Developers] web site inaccessible? David Case (Mon Mar 27 2017 - 07:31:14 PDT)
- Re: [AMBER-Developers] web site inaccessible? Hai Nguyen (Mon Mar 27 2017 - 07:54:20 PDT)
[AMBER] water bridge Ming Tang (Tue Mar 28 2017 - 02:24:20 PDT)
- Re: [AMBER] water bridge Daniel Roe (Tue Mar 28 2017 - 06:20:22 PDT)
[AMBER] RDF plot Sowmya Indrakumar (Tue Mar 28 2017 - 03:35:39 PDT)
- Re: [AMBER] RDF plot Ming Tang (Tue Mar 28 2017 - 03:41:17 PDT)
  - Re: [AMBER] RDF plot Sowmya Indrakumar (Tue Mar 28 2017 - 03:51:28 PDT)
- Re: [AMBER] RDF plot Gustavo Seabra (Tue Mar 28 2017 - 04:26:15 PDT)
  - Re: [AMBER] RDF plot Sowmya Indrakumar (Tue Mar 28 2017 - 05:49:36 PDT)
    - Re: [AMBER] RDF plot Gustavo Seabra (Tue Mar 28 2017 - 05:55:07 PDT)
    - Re: [AMBER] RDF plot Sowmya Indrakumar (Tue Mar 28 2017 - 06:03:19 PDT)
  - Re: [AMBER] RDF plot Daniel Roe (Tue Mar 28 2017 - 06:59:32 PDT)
    - Re: [AMBER] RDF plot Sowmya Indrakumar (Tue Mar 28 2017 - 09:18:32 PDT)
    - Re: [AMBER] RDF plot Daniel Roe (Tue Mar 28 2017 - 09:55:37 PDT)
    - Re: [AMBER] RDF plot Sowmya Indrakumar (Tue Mar 28 2017 - 10:04:57 PDT)
    - Re: [AMBER] RDF plot Daniel Roe (Tue Mar 28 2017 - 10:16:47 PDT)
    - Re: [AMBER] RDF plot Sowmya Indrakumar (Tue Mar 28 2017 - 10:28:18 PDT)
    - Re: [AMBER] RDF plot Daniel Roe (Tue Mar 28 2017 - 10:49:46 PDT)
    - Re: [AMBER] RDF plot Sowmya Indrakumar (Tue Mar 28 2017 - 11:17:06 PDT)
[AMBER] Linkage problem in branched oligosaccharide Manju Sah (Tue Mar 28 2017 - 05:36:34 PDT)
- Re: [AMBER] Linkage problem in branched oligosaccharide Daniel Roe (Tue Mar 28 2017 - 06:22:22 PDT)
  - Re: [AMBER] Linkage problem in branched oligosaccharide Sangeetha B (Wed Mar 29 2017 - 02:09:13 PDT)
    - Re: [AMBER] Linkage problem in branched oligosaccharide David Case (Wed Mar 29 2017 - 04:57:40 PDT)
    - Re: [AMBER] Linkage problem in branched oligosaccharide Manju Sah (Wed Mar 29 2017 - 05:32:14 PDT)
    - Re: [AMBER] Linkage problem in branched oligosaccharide Lachele Foley (Thu Mar 30 2017 - 05:39:52 PDT)
    - Re: [AMBER] Linkage problem in branched oligosaccharide Manju Sah (Sat Apr 01 2017 - 03:10:13 PDT)
Re: [AMBER] Question about the propagation of error in MM/PBSA binding free energy calculation. Adrian Roitberg (Tue Mar 28 2017 - 10:11:17 PDT)
[AMBER] Preparation of ligand enantiomers George Tzotzos (Tue Mar 28 2017 - 10:14:45 PDT)
[AMBER] what hardware is required for gou peer-ro-peer an how imporant is gpu-to-gpu nvlink Chris Neale (Tue Mar 28 2017 - 17:38:22 PDT)
- Re: [AMBER] what hardware is required for gou peer-ro-peer an how imporant is gpu-to-gpu nvlink Jason Swails (Tue Mar 28 2017 - 19:09:22 PDT)
  - Re: [AMBER] what hardware is required for gou peer-ro-peer an how imporant is gpu-to-gpu nvlink Chris Neale (Tue Mar 28 2017 - 19:27:43 PDT)
    - Re: [AMBER] what hardware is required for gou peer-ro-peer an how imporant is gpu-to-gpu nvlink Jason Swails (Tue Mar 28 2017 - 21:19:54 PDT)
    - Re: [AMBER] what hardware is required for gou peer-ro-peer an how imporant is gpu-to-gpu nvlink Jason Swails (Tue Mar 28 2017 - 21:27:13 PDT)
    - Re: [AMBER] what hardware is required for gou peer-ro-peer an how imporant is gpu-to-gpu nvlink Chris Neale (Tue Mar 28 2017 - 22:07:13 PDT)
[AMBER] Error: FATAL: Atom .R<ZN 2>.A<ZN 1> does not have a type. Aishani Prem (Tue Mar 28 2017 - 18:22:06 PDT)
- Re: [AMBER] Error: FATAL: Atom .R<ZN 2>.A<ZN 1> does not have a type. Andrew Schaub (Tue Mar 28 2017 - 20:47:47 PDT)
- Re: [AMBER] Error: FATAL: Atom .R<ZN 2>.A<ZN 1> does not have a type. Elvis Martis (Tue Mar 28 2017 - 21:28:23 PDT)
[AMBER] Cpptraj problems 杨满意 (Tue Mar 28 2017 - 20:43:52 PDT)
- Re: [AMBER] Cpptraj problems Daniel Roe (Thu Mar 30 2017 - 05:03:10 PDT)
[AMBER] Split a Large trajectory into smaller trajectory Vishal Nemaysh (Tue Mar 28 2017 - 21:30:33 PDT)
- Re: [AMBER] Split a Large trajectory into smaller trajectory Andreas Tosstorff (Wed Mar 29 2017 - 00:38:14 PDT)
[AMBER] Oligosaccharide linkage breaking problem during Solvent minimization Manju Sah (Wed Mar 29 2017 - 02:53:19 PDT)
[AMBER] Dimer trajectory analysis Andreas Tosstorff (Wed Mar 29 2017 - 09:34:23 PDT)
- Re: [AMBER] Dimer trajectory analysis Bill Ross (Wed Mar 29 2017 - 09:41:22 PDT)
- Re: [AMBER] Dimer trajectory analysis Daniel Roe (Thu Mar 30 2017 - 05:16:58 PDT)
[AMBER] constraint residues while enhanced sampling simulation Kat G (Wed Mar 29 2017 - 13:40:43 PDT)
[AMBER] Questions about MCPB.py Mingyuan_xu (Wed Mar 29 2017 - 18:57:03 PDT)
[AMBER] autoimage for a protein filament Baker, Joseph (Wed Mar 29 2017 - 19:10:08 PDT)
- Re: [AMBER] autoimage for a protein filament Daniel Roe (Thu Mar 30 2017 - 05:20:20 PDT)
  - Re: [AMBER] autoimage for a protein filament Baker, Joseph (Thu Mar 30 2017 - 10:44:22 PDT)
- Re: [AMBER] autoimage for a protein filament Baker, Joseph (Wed Dec 13 2017 - 14:32:59 PST)
  - Re: [AMBER] autoimage for a protein filament Daniel Roe (Thu Dec 14 2017 - 07:30:50 PST)
    - Re: [AMBER] autoimage for a protein filament Baker, Joseph (Sat Dec 16 2017 - 15:56:43 PST)
[AMBER] Installing Amber14 and AmberTools15 Error Erma Fatiha Muhammad (Wed Mar 29 2017 - 19:59:11 PDT)
- Re: [AMBER] Installing Amber14 and AmberTools15 Error Scott Brozell (Thu Mar 30 2017 - 00:00:27 PDT)
[AMBER] Water molecules show three bonds in VMD 吴萌 (Thu Mar 30 2017 - 04:04:57 PDT)
- Re: [AMBER] Water molecules show three bonds in VMD Andreas Tosstorff (Thu Mar 30 2017 - 04:20:20 PDT)
- Re: [AMBER] Water molecules show three bonds in VMD Daniel Roe (Thu Mar 30 2017 - 05:23:00 PDT)
  - Re: [AMBER] Water molecules show three bonds in VMD MOHD HOMAIDUR RAHMAN (Thu Mar 30 2017 - 21:03:46 PDT)
[AMBER] Amber Mailing List problem George Tzotzos (Thu Mar 30 2017 - 06:59:43 PDT)
- Re: [AMBER] Amber Mailing List problem Marcos Serrou do Amaral (Thu Mar 30 2017 - 07:02:09 PDT)
[AMBER] 4.5 fold increase in memory consumption for nmr restraints going from amber14 to amber16 Paul Westphälinger (Thu Mar 30 2017 - 07:57:04 PDT)
- Re: [AMBER] 4.5 fold increase in memory consumption for nmr restraints going from amber14 to amber16 Charles Lin (Thu Mar 30 2017 - 12:26:04 PDT)
  - Re: [AMBER] 4.5 fold increase in memory consumption for nmr restraints going from amber14 to amber16 Paul Westphaelinger (Thu Mar 30 2017 - 12:46:48 PDT)
    - Re: [AMBER] 4.5 fold increase in memory consumption for nmr restraints going from amber14 to amber16 Charles Lin (Wed Apr 05 2017 - 12:46:03 PDT)
    - Re: [AMBER] 4.5 fold increase in memory consumption for nmr restraints going from amber14 to amber16 Paul Westphaelinger (Wed Apr 05 2017 - 13:03:53 PDT)
    - Re: [AMBER] 4.5 fold increase in memory consumption for nmr restraints going from amber14 to amber16 Paul Westphaelinger (Tue May 09 2017 - 01:00:06 PDT)
    - Re: [AMBER] 4.5 fold increase in memory consumption for nmr restraints going from amber14 to amber16 Charles Lin (Tue May 09 2017 - 08:24:56 PDT)
    - Re: [AMBER] 4.5 fold increase in memory consumption for nmr restraints going from amber14 to amber16 Pratul K. Agarwal (Tue May 09 2017 - 08:36:26 PDT)
    - Re: [AMBER] 4.5 fold increase in memory consumption for nmr restraints going from amber14 to amber16 Charles Lin (Tue May 09 2017 - 09:02:45 PDT)
    - Re: [AMBER] 4.5 fold increase in memory consumption for nmr restraints going from amber14 to amber16 Paul Westphälinger (Thu Oct 04 2018 - 02:34:30 PDT)
    - Re: [AMBER] 4.5 fold increase in memory consumption for nmr restraints going from amber14 to amber16 Charles Lin (Mon Oct 08 2018 - 07:19:11 PDT)
    - Re: [AMBER] 4.5 fold increase in memory consumption for nmr restraints going from amber14 to amber16 Paul Westphälinger (Tue Sep 25 2018 - 03:43:55 PDT)
    - Re: [AMBER] 4.5 fold increase in memory consumption for nmr restraints going from amber14 to amber16 James Kress (Tue Sep 25 2018 - 09:49:54 PDT)
    - Re: [AMBER] 4.5 fold increase in memory consumption for nmr restraints going from amber14 to amber16 Paul Westphälinger (Wed Sep 26 2018 - 04:10:04 PDT)
    - Re: [AMBER] 4.5 fold increase in memory consumption for nmr restraints going from amber14 to amber16 Paul Westphälinger (Tue Oct 02 2018 - 02:33:18 PDT)
[AMBER] coordinates in restraint mast Thomas Evangelidis (Fri Mar 31 2017 - 06:13:37 PDT)
- Re: [AMBER] coordinates in restraint mast Hannes Loeffler (Fri Mar 31 2017 - 06:35:34 PDT)
  - Re: [AMBER] coordinates in restraint mast Thomas Evangelidis (Fri Mar 31 2017 - 07:54:22 PDT)
    - Re: [AMBER] coordinates in restraint mast Daniel Roe (Fri Mar 31 2017 - 08:14:53 PDT)
    - Re: [AMBER] coordinates in restraint mast Thomas Evangelidis (Fri Mar 31 2017 - 08:44:06 PDT)
    - Re: [AMBER] coordinates in restraint mast Daniel Roe (Fri Mar 31 2017 - 09:24:20 PDT)
    - Re: [AMBER] coordinates in restraint mast Thomas Evangelidis (Sun Apr 02 2017 - 09:25:48 PDT)
    - Re: [AMBER] coordinates in restraint mast Daniel Roe (Mon Apr 03 2017 - 10:29:24 PDT)
[AMBER] Issues Regaring the PDB files from Trajectory frames Ramin Salimi (Fri Mar 31 2017 - 14:23:52 PDT)
- Re: [AMBER] Issues Regaring the PDB files from Trajectory frames Hai Nguyen (Fri Mar 31 2017 - 14:27:14 PDT)
  - Re: [AMBER] Issues Regaring the PDB files from Trajectory frames Ramin Salimi (Fri Mar 31 2017 - 14:30:29 PDT)
    - Re: [AMBER] Issues Regaring the PDB files from Trajectory frames Hai Nguyen (Fri Mar 31 2017 - 14:37:45 PDT)
    - Re: [AMBER] Issues Regaring the PDB files from Trajectory frames Ramin Salimi (Fri Mar 31 2017 - 16:03:33 PDT)
[AMBER] How to perform good quality local optimization with Sander danil kutov (Sat Apr 01 2017 - 00:48:50 PDT)
- Re: [AMBER] How to perform good quality local optimization with Sander David Case (Sat Apr 01 2017 - 06:17:22 PDT)
[AMBER] mmpbsa - stability calculation Mary Varughese (Mon Apr 03 2017 - 00:12:32 PDT)
- Re: [AMBER] mmpbsa - stability calculation David Case (Mon Apr 03 2017 - 05:11:33 PDT)
[AMBER] placing water at specified coordinates with tleap Thomas Evangelidis (Mon Apr 03 2017 - 08:14:51 PDT)
- Re: [AMBER] placing water at specified coordinates with tleap David Case (Mon Apr 03 2017 - 09:49:00 PDT)
[AMBER] GB Methodology for Nucleic Acid to calculate Internal energy Ramin Salimi (Mon Apr 03 2017 - 18:02:46 PDT)
- Re: [AMBER] GB Methodology for Nucleic Acid to calculate Internal energy David A Case (Tue Apr 04 2017 - 05:17:39 PDT)
  - Re: [AMBER] GB Methodology for Nucleic Acid to calculate Internal energy Ramin Salimi (Tue Apr 04 2017 - 10:50:13 PDT)
    - Re: [AMBER] GB Methodology for Nucleic Acid to calculate Internal energy Carlos Simmerling (Tue Apr 04 2017 - 14:19:54 PDT)
    - Re: [AMBER] GB Methodology for Nucleic Acid to calculate Internal energy David Case (Tue Apr 04 2017 - 18:44:22 PDT)
    - Re: [AMBER] GB Methodology for Nucleic Acid to calculate Internal energy Ramin Salimi (Tue Apr 04 2017 - 19:13:38 PDT)
    - Re: [AMBER] GB Methodology for Nucleic Acid to calculate Internal energy Bill Ross (Tue Apr 04 2017 - 21:17:26 PDT)
    - Re: [AMBER] GB Methodology for Nucleic Acid to calculate Internal energy Ramin Salimi (Wed Apr 05 2017 - 03:01:25 PDT)
    - Re: [AMBER] GB Methodology for Nucleic Acid to calculate Internal energy Bill Ross (Wed Apr 05 2017 - 10:35:51 PDT)
    - Re: [AMBER] GB Methodology for Nucleic Acid to calculate Internal energy Ramin Salimi (Wed Apr 05 2017 - 19:54:43 PDT)
    - Re: [AMBER] GB Methodology for Nucleic Acid to calculate Internal energy Bill Ross (Thu Apr 06 2017 - 00:41:25 PDT)
    - Re: [AMBER] GB Methodology for Nucleic Acid to calculate Internal energy Bill Ross (Thu Apr 06 2017 - 01:57:08 PDT)
    - Re: [AMBER] GB Methodology for Nucleic Acid to calculate Internal energy Daniel Roe (Wed Apr 05 2017 - 09:20:33 PDT)
[AMBER] 3 GPUs ? Chris Neale (Mon Apr 03 2017 - 19:43:01 PDT)
- Re: [AMBER] 3 GPUs ? Andreas Tosstorff (Tue Apr 04 2017 - 00:18:53 PDT)
- Re: [AMBER] 3 GPUs ? Ross Walker (Tue Apr 04 2017 - 08:26:57 PDT)
  - Re: [AMBER] 3 GPUs ? Chris Neale (Tue Apr 04 2017 - 13:28:43 PDT)
    - Re: [AMBER] 3 GPUs ? Ross Walker (Tue Apr 04 2017 - 16:46:34 PDT)
    - Re: [AMBER] 3 GPUs ? Chris Neale (Tue Apr 04 2017 - 17:06:04 PDT)
    - Re: [AMBER] 3 GPUs ? Ross Walker (Wed Apr 05 2017 - 12:41:33 PDT)
    - Re: [AMBER] 3 GPUs ? Chris Neale (Wed Apr 05 2017 - 17:04:27 PDT)
[AMBER] eChemInfo Training and Innovation Course in Drug Design Thomas Exner (Tue Apr 04 2017 - 02:51:20 PDT)
- [AMBER] Early-bird and bursary deadline April 30: eChemInfo Training and Innovation Course in Drug Design Thomas Exner (Mon Apr 24 2017 - 04:09:50 PDT)
[AMBER] mmpbsa- binding energy between ligand-receptor Anna Cebrian Prats (Tue Apr 04 2017 - 06:27:06 PDT)
[AMBER] You won't believe what happens with maximum coordination limits... David Poole (Tue Apr 04 2017 - 07:23:11 PDT)
- Re: [AMBER] You won't believe what happens with maximum coordination limits... Hannes Loeffler (Tue Apr 04 2017 - 07:50:27 PDT)
- Re: [AMBER] You won't believe what happens with maximum coordination limits... Ben Roberts (Tue Apr 04 2017 - 12:53:23 PDT)
  - Re: [AMBER] You won't believe what happens with maximum coordination limits... Marek Maly (Tue Apr 04 2017 - 14:49:21 PDT)
- Re: [AMBER] You won't believe what happens with maximum coordination limits... David Poole (Thu Apr 06 2017 - 03:22:04 PDT)
[AMBER] Creating a pdb of only certain molecules from a frame Aseel Bala (Tue Apr 04 2017 - 09:46:37 PDT)
- Re: [AMBER] Creating a pdb of only certain molecules from a frame Daniel Roe (Mon Apr 10 2017 - 11:46:20 PDT)
[AMBER] Atom types for Baaden Hydronium Ion Samaneh Ghassabi Kondalaji (Tue Apr 04 2017 - 18:51:26 PDT)
- Re: [AMBER] Atom types for Baaden Hydronium Ion David A Case (Wed Apr 05 2017 - 04:51:49 PDT)
  - Re: [AMBER] Atom types for Baaden Hydronium Ion Samaneh Ghassabi Kondalaji (Wed Apr 05 2017 - 09:06:39 PDT)
    - Re: [AMBER] Atom types for Baaden Hydronium Ion David A Case (Wed Apr 05 2017 - 12:17:21 PDT)
    - Re: [AMBER] Atom types for Baaden Hydronium Ion Samaneh Ghassabi Kondalaji (Wed Apr 05 2017 - 13:11:21 PDT)
[AMBER] density plot of Na+ ions using grid Mary Varughese (Tue Apr 04 2017 - 23:17:14 PDT)
[AMBER] How to distinguish between water molecules? Markowska (Wed Apr 05 2017 - 02:11:03 PDT)
- Re: [AMBER] How to distinguish between water molecules? Hannes Loeffler (Wed Apr 05 2017 - 02:53:06 PDT)
  - Re: [AMBER] How to distinguish between water molecules? Markowska (Wed Apr 05 2017 - 04:32:05 PDT)
    - Re: [AMBER] How to distinguish between water molecules? Hannes Loeffler (Wed Apr 05 2017 - 04:50:34 PDT)
    - Re: [AMBER] How to distinguish between water molecules? David A Case (Wed Apr 05 2017 - 04:55:30 PDT)
    - Re: [AMBER] How to distinguish between water molecules? Markowska (Wed Apr 05 2017 - 05:11:07 PDT)
    - Re: [AMBER] How to distinguish between water molecules? Hannes Loeffler (Wed Apr 05 2017 - 05:42:57 PDT)
    - Re: [AMBER] How to distinguish between water molecules? Markowska (Wed Apr 05 2017 - 05:52:05 PDT)
    - Re: [AMBER] How to distinguish between water molecules? Jason Swails (Wed Apr 05 2017 - 05:53:56 PDT)
[AMBER] CPPTRAJ Cluster d00b46022 (Wed Apr 05 2017 - 02:26:09 PDT)
- Re: [AMBER] CPPTRAJ Cluster Daniel Roe (Wed Apr 05 2017 - 10:08:46 PDT)
[AMBER] ptraj hbonds Mary Varughese (Wed Apr 05 2017 - 03:33:55 PDT)
- Re: [AMBER] ptraj hbonds Daniel Roe (Wed Apr 05 2017 - 09:45:58 PDT)
[AMBER] Acetonitrile Water Mix Andreas Tosstorff (Wed Apr 05 2017 - 05:35:31 PDT)
- Re: [AMBER] Acetonitrile Water Mix Marcos Serrou do Amaral (Wed Apr 05 2017 - 05:46:25 PDT)
  - Re: [AMBER] Acetonitrile Water Mix Andreas Tosstorff (Wed Apr 05 2017 - 05:50:55 PDT)
- Re: [AMBER] Acetonitrile Water Mix David A Case (Wed Apr 05 2017 - 07:37:58 PDT)
  - Re: [AMBER] Acetonitrile Water Mix Sowmya Indrakumar (Wed Apr 05 2017 - 07:48:34 PDT)
    - Re: [AMBER] Acetonitrile Water Mix David Cerutti (Wed Apr 05 2017 - 08:00:55 PDT)
    - Re: [AMBER] Acetonitrile Water Mix Andreas Tosstorff (Wed Apr 05 2017 - 09:08:53 PDT)
    - [AMBER] How to write an frcmod file Andreas Tosstorff (Thu Apr 06 2017 - 01:13:23 PDT)
    - Re: [AMBER] How to write an frcmod file Hannes Loeffler (Thu Apr 06 2017 - 02:15:43 PDT)
    - Re: [AMBER] Acetonitrile Water Mix Marcos Serrou do Amaral (Fri Apr 07 2017 - 05:58:51 PDT)
    - Re: [AMBER] Acetonitrile Water Mix Andreas Tosstorff (Fri Apr 07 2017 - 06:32:01 PDT)
    - Re: [AMBER] Acetonitrile Water Mix Marcos Serrou do Amaral (Fri Apr 07 2017 - 06:44:44 PDT)
[AMBER] GPU performance Sofia Vasilakaki (Wed Apr 05 2017 - 07:27:35 PDT)
- Re: [AMBER] GPU performance Andreas Tosstorff (Wed Apr 05 2017 - 07:35:54 PDT)
  - Re: [AMBER] GPU performance Ross Walker (Wed Apr 05 2017 - 16:26:41 PDT)
[AMBER] Binding site volume calculation Thakur, Abhishek (Wed Apr 05 2017 - 08:45:53 PDT)
- Re: [AMBER] Binding site volume calculation David A Case (Wed Apr 05 2017 - 12:14:29 PDT)
[AMBER] parmed doesn't give any output or error message Sadegh Faramarzi Ganjabad (Wed Apr 05 2017 - 10:55:59 PDT)
[AMBER] Diffusion and permeability coefficients Fabrício Bracht (Thu Apr 06 2017 - 12:01:19 PDT)
- Re: [AMBER] Diffusion and permeability coefficients Chris Neale (Thu Apr 06 2017 - 12:16:12 PDT)
  - Re: [AMBER] Diffusion and permeability coefficients Fabrício Bracht (Thu Apr 06 2017 - 13:21:14 PDT)
[AMBER] GTX 1080 error Jacopo Sgrignani (Thu Apr 06 2017 - 13:41:57 PDT)
- Re: [AMBER] GTX 1080 error Paul Westphaelinger (Thu Apr 06 2017 - 13:49:44 PDT)
- Re: [AMBER] GTX 1080 error Ross Walker (Thu Apr 06 2017 - 14:30:04 PDT)
[AMBER] Tleap error. Vatsal Purohit (Thu Apr 06 2017 - 17:11:45 PDT)
- Re: [AMBER] Tleap error. Scott Brozell (Thu Apr 06 2017 - 19:26:42 PDT)
- Re: [AMBER] Tleap error. David A Case (Thu Apr 06 2017 - 20:36:43 PDT)
[AMBER] Periodic box error for restarting simulations with restraints Sadegh Faramarzi Ganjabad (Fri Apr 07 2017 - 00:44:28 PDT)
- Re: [AMBER] Periodic box error for restarting simulations with restraints Daniel Roe (Fri Apr 07 2017 - 06:08:09 PDT)
- Re: [AMBER] Periodic box error for restarting simulations with restraints Sadegh Faramarzi Ganjabad (Fri Apr 07 2017 - 22:05:37 PDT)
  - Re: [AMBER] Periodic box error for restarting simulations with restraints Bill Ross (Fri Apr 07 2017 - 22:13:48 PDT)
- Re: [AMBER] Periodic box error for restarting simulations with restraints Sadegh Faramarzi Ganjabad (Tue Apr 11 2017 - 12:39:12 PDT)
  - Re: [AMBER] Periodic box error for restarting simulations with restraints Bill Ross (Tue Apr 11 2017 - 13:15:59 PDT)
- Re: [AMBER] Periodic box error for restarting simulations with restraints Sadegh Faramarzi Ganjabad (Thu Apr 13 2017 - 13:12:21 PDT)
  - Re: [AMBER] Periodic box error for restarting simulations with restraints Chris Neale (Thu Apr 13 2017 - 13:19:14 PDT)
- Re: [AMBER] Periodic box error for restarting simulations with restraints Sadegh Faramarzi Ganjabad (Sun Apr 16 2017 - 00:24:41 PDT)
[AMBER] Steered MD using two reaction coordinates Suchetana Gupta (Fri Apr 07 2017 - 21:27:26 PDT)
- Re: [AMBER] Steered MD using two reaction coordinates Hannes Loeffler (Fri Apr 07 2017 - 23:28:52 PDT)
[AMBER] Query regarding output of 3D-RISM in Amber. Rakesh Srivastava (Fri Apr 07 2017 - 21:48:22 PDT)
- Re: [AMBER] Query regarding output of 3D-RISM in Amber. David Case (Sun Apr 09 2017 - 17:26:28 PDT)
  - Re: [AMBER] Query regarding output of 3D-RISM in Amber. Rakesh Srivastava (Mon Apr 10 2017 - 02:10:38 PDT)
[AMBER] cpptraj analysis of two different dsDNA strands. James Kress (Sat Apr 08 2017 - 11:31:57 PDT)
- Re: [AMBER] cpptraj analysis of two different dsDNA strands. Nhai (Sun Apr 09 2017 - 01:35:49 PDT)
  - Re: [AMBER] cpptraj analysis of two different dsDNA strands. James Kress (Sun Apr 09 2017 - 08:43:57 PDT)
[AMBER] Minimization fails when switching from steepest descent to conjugate gradient Andreas Tosstorff (Sat Apr 08 2017 - 16:08:36 PDT)
- Re: [AMBER] Minimization fails when switching from steepest descent to conjugate gradient Elvis Martis (Sat Apr 08 2017 - 22:23:07 PDT)
- Re: [AMBER] Minimization fails when switching from steepest descent to conjugate gradient Hai Nguyen (Sat Apr 08 2017 - 22:43:42 PDT)
  - Re: [AMBER] Minimization fails when switching from steepest descent to conjugate gradient Chris Moth (Sun Apr 09 2017 - 14:06:06 PDT)
    - Re: [AMBER] Minimization fails when switching from steepest descent to conjugate gradient Andreas Tosstorff (Sun Apr 09 2017 - 14:40:02 PDT)
[AMBER] Regarding REMD simulations of Proteins MOHD HOMAIDUR RAHMAN (Sun Apr 09 2017 - 08:35:32 PDT)
- Re: [AMBER] Regarding REMD simulations of Proteins Carlos Simmerling (Sun Apr 09 2017 - 09:22:24 PDT)
[AMBER] MMPBSA entropy calculation help Mary Varughese (Mon Apr 10 2017 - 04:02:21 PDT)
- Re: [AMBER] MMPBSA entropy calculation help David Case (Mon Apr 10 2017 - 05:29:00 PDT)
[AMBER] QM/MM equilibration before SMD in vacuum Samaneh Ghassabi Kondalaji (Mon Apr 10 2017 - 09:04:21 PDT)
- Re: [AMBER] QM/MM equilibration before SMD in vacuum Samaneh Ghassabi Kondalaji (Mon Apr 10 2017 - 09:58:49 PDT)
[AMBER] simulation energies are exploding giulia palermo (Mon Apr 10 2017 - 17:30:28 PDT)
- Re: [AMBER] simulation energies are exploding David Case (Tue Apr 11 2017 - 05:12:59 PDT)
  - Re: [AMBER] simulation energies are exploding giulia palermo (Tue Apr 11 2017 - 14:44:28 PDT)
[AMBER] problem about amber install of MMPBSA.py.mpi 白正亚 (Tue Apr 11 2017 - 00:38:27 PDT)
[AMBER] DNA Tutorial B1 - Temperature Drop Johannes Kalliauer (Tue Apr 11 2017 - 02:42:42 PDT)
- Re: [AMBER] DNA Tutorial B1 - Temperature Drop Johannes Kalliauer (Wed May 03 2017 - 03:57:37 PDT)
  - Re: [AMBER] DNA Tutorial B1 - Temperature Drop David Case (Wed May 03 2017 - 05:37:42 PDT)
[AMBER] cpptraj creates pdb file it cannot read James Kress (Tue Apr 11 2017 - 12:29:13 PDT)
- Re: [AMBER] cpptraj creates pdb file it cannot read Hai Nguyen (Tue Apr 11 2017 - 13:07:16 PDT)
  - Re: [AMBER] cpptraj creates pdb file it cannot read James Kress (Tue Apr 11 2017 - 13:44:09 PDT)
    - Re: [AMBER] cpptraj creates pdb file it cannot read Hai Nguyen (Tue Apr 11 2017 - 13:51:49 PDT)
    - Re: [AMBER] cpptraj creates pdb file it cannot read James Kress (Tue Apr 11 2017 - 14:03:17 PDT)
    - Re: [AMBER] cpptraj creates pdb file it cannot read James Kress (Tue Apr 11 2017 - 14:37:10 PDT)
    - Re: [AMBER] cpptraj creates pdb file it cannot read Elka Firmanda (Tue Apr 11 2017 - 23:00:55 PDT)
    - Re: [AMBER] cpptraj creates pdb file it cannot read James Kress (Wed Apr 12 2017 - 07:28:47 PDT)
    - Re: [AMBER] cpptraj creates pdb file it cannot read Hai Nguyen (Wed Apr 12 2017 - 07:47:21 PDT)
    - Re: [AMBER] cpptraj creates pdb file it cannot read Daniel Roe (Wed Apr 12 2017 - 08:05:56 PDT)
    - Re: [AMBER] cpptraj creates pdb file it cannot read James Kress (Sat Apr 15 2017 - 14:09:56 PDT)
    - Re: [AMBER] cpptraj creates pdb file it cannot read Daniel Roe (Sun Apr 16 2017 - 08:17:09 PDT)
    - Re: [AMBER] cpptraj creates pdb file it cannot read James Kress (Sun Apr 16 2017 - 11:41:41 PDT)
    - Re: [AMBER] cpptraj creates pdb file it cannot read Jason Swails (Sun Apr 16 2017 - 19:56:34 PDT)
    - Re: [AMBER] cpptraj creates pdb file it cannot read Daniel Roe (Mon Apr 17 2017 - 05:40:13 PDT)
    - Re: [AMBER] cpptraj creates pdb file it cannot read James Kress (Mon Apr 17 2017 - 13:26:03 PDT)
[AMBER] Discrepancy in delta G total and per residues decomposition results in MMPBSA.py mish (Wed Apr 12 2017 - 01:35:32 PDT)
[AMBER] antechamber problem Maura Malinska (Wed Apr 12 2017 - 06:59:37 PDT)
- Re: [AMBER] antechamber problem David Case (Wed Apr 12 2017 - 07:47:07 PDT)
  - Re: [AMBER] antechamber problem Gerald Monard (Wed Apr 12 2017 - 08:00:39 PDT)
  - Re: [AMBER] antechamber problem Niel Henriksen (Wed Apr 12 2017 - 09:54:53 PDT)
    - Re: [AMBER] antechamber problem Maura Malinska (Thu Apr 13 2017 - 00:25:10 PDT)
- [AMBER] APR method in CHCl3 Maura Malinska (Wed Oct 18 2017 - 09:34:01 PDT)
  - Re: [AMBER] APR method in CHCl3 Jian Yin (Wed Oct 18 2017 - 13:51:34 PDT)
  - Re: [AMBER] APR method in CHCl3 Jian Yin (Fri Oct 20 2017 - 14:02:53 PDT)
[AMBER] using pmemd.MPI for REMD Kris Feher (Wed Apr 12 2017 - 09:48:36 PDT)
- Re: [AMBER] using pmemd.MPI for REMD Hannes Loeffler (Wed Apr 12 2017 - 10:31:25 PDT)
  - Re: [AMBER] using pmemd.MPI for REMD Kris Feher (Thu Apr 13 2017 - 03:38:41 PDT)
  - Re: [AMBER] using pmemd.MPI for REMD Kris Feher (Thu Apr 13 2017 - 04:01:15 PDT)
[AMBER] reorientation in rmsd James Kress (Wed Apr 12 2017 - 10:32:31 PDT)
- Re: [AMBER] reorientation in rmsd Bill Ross (Wed Apr 12 2017 - 11:28:35 PDT)
  - Re: [AMBER] reorientation in rmsd Jason Swails (Wed Apr 12 2017 - 11:41:06 PDT)
    - Re: [AMBER] reorientation in rmsd James Kress (Wed Apr 12 2017 - 12:08:37 PDT)
- Re: [AMBER] reorientation in rmsd David Case (Wed Apr 12 2017 - 19:06:13 PDT)
  - Re: [AMBER] reorientation in rmsd James Kress (Wed Apr 12 2017 - 19:55:08 PDT)
    - Re: [AMBER] reorientation in rmsd Andy Watkins (Wed Apr 12 2017 - 20:18:23 PDT)
    - Re: [AMBER] reorientation in rmsd Andy Watkins (Wed Apr 12 2017 - 20:18:26 PDT)
  - Re: [AMBER] reorientation in rmsd Jason Swails (Thu Apr 13 2017 - 06:21:19 PDT)
[AMBER] ERROR in load_lbfgs(): YS=0. 杨满意 (Wed Apr 12 2017 - 20:46:26 PDT)
- Re: [AMBER] ERROR in load_lbfgs(): YS=0. David A Case (Thu Apr 13 2017 - 04:49:29 PDT)
  - Re: [AMBER] ERROR in load_lbfgs(): YS=0. 杨满意 (Thu Apr 13 2017 - 19:20:45 PDT)
[AMBER] problem with temperature after rst Jorgen Simonsen (Wed Apr 12 2017 - 22:03:57 PDT)
- Re: [AMBER] problem with temperature after rst Bill Ross (Wed Apr 12 2017 - 22:15:49 PDT)
  - Re: [AMBER] problem with temperature after rst Jorgen Simonsen (Wed Apr 12 2017 - 22:41:45 PDT)
    - Re: [AMBER] problem with temperature after rst Bill Ross (Wed Apr 12 2017 - 22:52:51 PDT)
    - Re: [AMBER] problem with temperature after rst Bill Ross (Wed Apr 12 2017 - 22:57:25 PDT)
    - Re: [AMBER] problem with temperature after rst Jorgen Simonsen (Wed Apr 12 2017 - 23:10:51 PDT)
    - Re: [AMBER] problem with temperature after rst Bill Ross (Wed Apr 12 2017 - 23:44:36 PDT)
    - Re: [AMBER] problem with temperature after rst Bill Ross (Wed Apr 12 2017 - 23:52:25 PDT)
- Re: [AMBER] problem with temperature after rst David A Case (Thu Apr 13 2017 - 04:55:54 PDT)
[AMBER] AMBER umbrella sampling 吴萌 (Thu Apr 13 2017 - 02:27:20 PDT)
- Re: [AMBER] AMBER umbrella sampling Hannes Loeffler (Thu Apr 13 2017 - 06:04:10 PDT)
  - Re: [AMBER] AMBER umbrella sampling Andreas Tosstorff (Thu Apr 13 2017 - 09:59:01 PDT)
- Re: [AMBER] AMBER umbrella sampling Feng Pan (Thu Apr 13 2017 - 13:04:56 PDT)
- Re: [AMBER] AMBER umbrella sampling 吴萌 (Fri Apr 14 2017 - 20:02:07 PDT)
[AMBER] solvateBox for large size of RNA Li, Wen (Thu Apr 13 2017 - 07:03:15 PDT)
- Re: [AMBER] solvateBox for large size of RNA David Case (Thu Apr 13 2017 - 07:20:39 PDT)
  - Re: [AMBER] solvateBox for large size of RNA George Giambasu (Thu Apr 13 2017 - 09:59:52 PDT)
[AMBER] Amber 16 does not read the "ncsu_smd" from a QMMM input file Samaneh Ghassabi Kondalaji (Thu Apr 13 2017 - 08:29:59 PDT)
- Re: [AMBER] Amber 16 does not read the "ncsu_smd" from a QMMM input file Hannes Loeffler (Thu Apr 13 2017 - 08:40:22 PDT)
  - Re: [AMBER] Amber 16 does not read the "ncsu_smd" from a QMMM input file Samaneh Ghassabi Kondalaji (Thu Apr 13 2017 - 09:01:35 PDT)
    - Re: [AMBER] Amber 16 does not read the "ncsu_smd" from a QMMM input file Hannes Loeffler (Thu Apr 13 2017 - 09:35:02 PDT)
    - Re: [AMBER] Amber 16 does not read the "ncsu_smd" from a QMMM input file Samaneh Ghassabi Kondalaji (Thu Apr 13 2017 - 09:56:02 PDT)
    - Re: [AMBER] Amber 16 does not read the "ncsu_smd" from a QMMM input file Samaneh Ghassabi Kondalaji (Mon Apr 17 2017 - 09:50:20 PDT)
    - Re: [AMBER] Amber 16 does not read the "ncsu_smd" from a QMMM input file Feng Pan (Mon Apr 17 2017 - 10:11:22 PDT)
    - Re: [AMBER] Amber 16 does not read the "ncsu_smd" from a QMMM input file Goetz, Andreas (Mon Apr 17 2017 - 10:15:17 PDT)
    - Re: [AMBER] Amber 16 does not read the "ncsu_smd" from a QMMM input file Samaneh Ghassabi Kondalaji (Mon Apr 17 2017 - 10:19:55 PDT)
    - Re: [AMBER] Amber 16 does not read the "ncsu_smd" from a QMMM input file Samaneh Ghassabi Kondalaji (Mon Apr 17 2017 - 10:40:37 PDT)
    - Re: [AMBER] Amber 16 does not read the "ncsu_smd" from a QMMM input file Goetz, Andreas (Mon Apr 17 2017 - 11:21:32 PDT)
    - Re: [AMBER] Amber 16 does not read the "ncsu_smd" from a QMMM input file Samaneh Ghassabi Kondalaji (Mon Apr 17 2017 - 11:36:58 PDT)
[AMBER] Incorrect ligand parameterization using GAFF Emilia Pecora-de-barros (Thu Apr 13 2017 - 10:16:07 PDT)
- Re: [AMBER] Incorrect ligand parameterization using GAFF David Case (Thu Apr 13 2017 - 18:40:41 PDT)
  - [AMBER] RES: Incorrect ligand parameterization using GAFF Emilia Pecora-de-barros (Thu Apr 13 2017 - 18:53:54 PDT)
- Re: [AMBER] Incorrect ligand parameterization using GAFF Hannes Loeffler (Fri Apr 14 2017 - 01:23:26 PDT)
  - [AMBER] RES: Incorrect ligand parameterization using GAFF Emilia Pecora-de-barros (Fri Apr 14 2017 - 13:50:05 PDT)
    - Re: [AMBER] RES: Incorrect ligand parameterization using GAFF Hannes Loeffler (Sat Apr 15 2017 - 03:32:12 PDT)
[AMBER] About Tutorial B3 Hadeer ELHabashy (Thu Apr 13 2017 - 15:40:12 PDT)
- Re: [AMBER] About Tutorial B3 David Case (Thu Apr 13 2017 - 18:44:17 PDT)
[AMBER] Compilation of MPI 3D-RISM issue in amber1 4 Rakesh Srivastava (Thu Apr 13 2017 - 21:54:07 PDT)
- Re: [AMBER] Compilation of MPI 3D-RISM issue in amber1 4 Tyler Luchko (Lists) (Thu Apr 13 2017 - 22:03:50 PDT)
- Re: [AMBER] Compilation of MPI 3D-RISM issue in amber1 4 Nhai (Thu Apr 13 2017 - 22:13:26 PDT)
[AMBER] BCC charge for my HEME Thakur, Abhishek (Fri Apr 14 2017 - 07:12:51 PDT)
- Re: [AMBER] BCC charge for my HEME Elvis Martis (Fri Apr 14 2017 - 08:29:23 PDT)
  - Re: [AMBER] BCC charge for my HEME Thakur, Abhishek (Fri Apr 14 2017 - 09:16:23 PDT)
    - Re: [AMBER] BCC charge for my HEME Elvis Martis (Fri Apr 14 2017 - 09:42:25 PDT)
    - Re: [AMBER] BCC charge for my HEME David Case (Fri Apr 14 2017 - 11:34:28 PDT)
[AMBER] Format error in frcmod file of HEME Thakur, Abhishek (Fri Apr 14 2017 - 09:42:46 PDT)
- Re: [AMBER] Format error in frcmod file of HEME Marcos Serrou do Amaral (Fri Apr 14 2017 - 09:50:57 PDT)
- Re: [AMBER] Format error in frcmod file of HEME David Case (Fri Apr 14 2017 - 11:41:09 PDT)
  - Re: [AMBER] Format error in frcmod file of HEME Thakur, Abhishek (Fri Apr 14 2017 - 11:46:25 PDT)
[AMBER] coordinate bond between them and S and FE Thakur, Abhishek (Fri Apr 14 2017 - 12:18:37 PDT)
- Re: [AMBER] coordinate bond between them and S and FE Marcos Serrou do Amaral (Fri Apr 14 2017 - 12:24:54 PDT)
  - Re: [AMBER] coordinate bond between them and S and FE Thakur, Abhishek (Fri Apr 14 2017 - 13:44:44 PDT)
    - Re: [AMBER] coordinate bond between them and S and FE Adrian Roitberg (Fri Apr 14 2017 - 13:48:37 PDT)
    - Re: [AMBER] coordinate bond between them and S and FE Thakur, Abhishek (Mon Apr 17 2017 - 07:45:31 PDT)
    - Re: [AMBER] coordinate bond between them and S and FE Adrian Roitberg (Mon Apr 17 2017 - 08:14:58 PDT)
    - Re: [AMBER] coordinate bond between them and S and FE Thakur, Abhishek (Mon Apr 17 2017 - 08:38:55 PDT)
    - Re: [AMBER] coordinate bond between them and S and FE David Case (Mon Apr 17 2017 - 09:00:50 PDT)
    - Re: [AMBER] coordinate bond between them and S and FE Andrew Schaub (Fri Apr 14 2017 - 14:23:27 PDT)
[AMBER] weird asymmetries in solvent box Thomas Charles Pochapsky (Sat Apr 15 2017 - 05:52:11 PDT)
- Re: [AMBER] weird asymmetries in solvent box David Case (Mon Apr 17 2017 - 04:43:39 PDT)
  - Re: [AMBER] weird asymmetries in solvent box Thomas Pochapsky (Mon Apr 17 2017 - 06:57:34 PDT)
    - Re: [AMBER] weird asymmetries in solvent box David Case (Mon Apr 17 2017 - 07:32:23 PDT)
    - Re: [AMBER] weird asymmetries in solvent box Thomas Pochapsky (Wed Apr 19 2017 - 12:03:18 PDT)
[AMBER] How to calculate the solvation free energy using Amber? JinpengYang (Mon Apr 17 2017 - 01:05:07 PDT)
- Re: [AMBER] How to calculate the solvation free energy using Amber? Bill Ross (Mon Apr 17 2017 - 01:52:51 PDT)
- Re: [AMBER] How to calculate the solvation free energy using Amber? hannes.loeffler.stfc.ac.uk (Mon Apr 17 2017 - 03:19:43 PDT)
[AMBER] PCA - concatenating trajectories George Tzotzos (Mon Apr 17 2017 - 06:19:03 PDT)
- Re: [AMBER] PCA - concatenating trajectories Adrian Roitberg (Mon Apr 17 2017 - 06:21:50 PDT)
  - Re: [AMBER] PCA - concatenating trajectories George Tzotzos (Mon Apr 17 2017 - 06:23:53 PDT)
- Re: [AMBER] PCA - concatenating trajectories Daniel Roe (Mon Apr 17 2017 - 06:25:47 PDT)
  - Re: [AMBER] PCA - concatenating trajectories Chris Neale (Mon Apr 17 2017 - 06:58:57 PDT)
    - Re: [AMBER] PCA - concatenating trajectories George Tzotzos (Mon Apr 17 2017 - 07:12:23 PDT)
[AMBER] HEME-CYS Thakur, Abhishek (Mon Apr 17 2017 - 09:45:38 PDT)
- Re: [AMBER] HEME-CYS Elvis Martis (Mon Apr 17 2017 - 10:10:21 PDT)
  - Re: [AMBER] HEME-CYS Thakur, Abhishek (Mon Apr 17 2017 - 10:56:41 PDT)
    - Re: [AMBER] HEME-CYS Elvis Martis (Mon Apr 17 2017 - 20:31:14 PDT)
- Re: [AMBER] HEME-CYS Thakur, Abhishek (Mon Apr 17 2017 - 11:37:43 PDT)
  - Re: [AMBER] HEME-CYS Elvis Martis (Mon Apr 17 2017 - 20:30:25 PDT)
- Re: [AMBER] HEME-CYS Elvis Martis (Tue Apr 18 2017 - 08:22:26 PDT)
  - Re: [AMBER] HEME-CYS Thakur, Abhishek (Tue Apr 18 2017 - 09:10:04 PDT)
    - Re: [AMBER] HEME-CYS Elvis Martis (Tue Apr 18 2017 - 21:44:33 PDT)
    - Re: [AMBER] HEME-CYS Thakur, Abhishek (Wed Apr 19 2017 - 07:19:20 PDT)
    - Re: [AMBER] HEME-CYS Elvis Martis (Wed Apr 19 2017 - 09:35:02 PDT)
    - Re: [AMBER] HEME-CYS Thakur, Abhishek (Wed Apr 19 2017 - 09:42:58 PDT)
    - Re: [AMBER] HEME-CYS Elvis Martis (Wed Apr 19 2017 - 09:50:05 PDT)
[AMBER] Release of AmberTools17 David Case (Mon Apr 17 2017 - 18:28:04 PDT)
- Re: [AMBER] Release of AmberTools17 James Kress (Wed Apr 19 2017 - 11:22:54 PDT)
  - Re: [AMBER] Release of AmberTools17 David Case (Wed Apr 19 2017 - 12:27:36 PDT)
    - Re: [AMBER] Release of AmberTools17 James Kress (Wed Apr 19 2017 - 13:52:36 PDT)
    - Re: [AMBER] Release of AmberTools17 James Kress (Wed Apr 19 2017 - 13:55:22 PDT)
    - Re: [AMBER] Release of AmberTools17 Bill Ross (Wed Apr 19 2017 - 14:08:30 PDT)
    - Re: [AMBER] Release of AmberTools17 James Kress (Wed Apr 19 2017 - 19:11:09 PDT)
[AMBER] Adding hydrogens to a ligand jacob wick (Tue Apr 18 2017 - 01:57:34 PDT)
- Re: [AMBER] Adding hydrogens to a ligand Bill Ross (Tue Apr 18 2017 - 02:22:20 PDT)
- Re: [AMBER] Adding hydrogens to a ligand Hannes Loeffler (Tue Apr 18 2017 - 02:22:38 PDT)
  - Re: [AMBER] Adding hydrogens to a ligand jacob wick (Tue Apr 18 2017 - 03:27:54 PDT)
[AMBER] Quasi-harmonic entropy calculation ---- Vibrational component of entropy George Tzotzos (Tue Apr 18 2017 - 04:42:20 PDT)
- Re: [AMBER] Quasi-harmonic entropy calculation ---- Vibrational component of entropy David Case (Tue Apr 18 2017 - 05:02:39 PDT)
- Re: [AMBER] Quasi-harmonic entropy calculation ---- Vibrational component of entropy David Case (Tue Apr 18 2017 - 05:06:20 PDT)
[AMBER] pmemd.cuda on an Amber Certified High-End workstation Li, Wen (Tue Apr 18 2017 - 09:02:52 PDT)
- Re: [AMBER] pmemd.cuda on an Amber Certified High-End workstation Ross Walker (Tue Apr 18 2017 - 10:20:31 PDT)
- Re: [AMBER] pmemd.cuda on an Amber Certified High-End workstation David Case (Tue Apr 18 2017 - 10:29:26 PDT)
  - Re: [AMBER] pmemd.cuda on an Amber Certified High-End workstation Li, Wen (Thu Apr 20 2017 - 12:52:43 PDT)
[AMBER] Discussion questions regarding PyRED FF development Iqbal, Muhammad Sajid (Tue Apr 18 2017 - 10:28:40 PDT)
[AMBER] Error with MMPSA.py calculation Praneeth Bommisetti (Tue Apr 18 2017 - 14:22:16 PDT)
- Re: [AMBER] Error with MMPSA.py calculation Jason Swails (Wed Apr 19 2017 - 17:20:59 PDT)
[AMBER] AmberTools17 + intel17 = bug Hector A. Baldoni (Tue Apr 18 2017 - 16:02:39 PDT)
- Re: [AMBER] AmberTools17 + intel17 = bug Hector A. Baldoni (Tue Apr 18 2017 - 16:30:05 PDT)
- Re: [AMBER] AmberTools17 + intel17 = bug Daniel Roe (Tue Apr 18 2017 - 17:34:24 PDT)
- Re: [AMBER] AmberTools17 + intel17 = bug David Case (Tue Apr 18 2017 - 18:19:19 PDT)
  - Re: [AMBER] AmberTools17 + intel17 = bug Hector A. Baldoni (Wed Apr 19 2017 - 06:09:50 PDT)
[AMBER] EVB with RPMD Rob Arbon (Wed Apr 19 2017 - 08:25:33 PDT)
- Re: [AMBER] EVB with RPMD David Case (Wed Apr 19 2017 - 08:59:58 PDT)
[AMBER] Post MD minimization Manjula Saravanan (Thu Apr 20 2017 - 02:33:48 PDT)
- Re: [AMBER] Post MD minimization Bill Ross (Thu Apr 20 2017 - 02:51:25 PDT)
- Re: [AMBER] Post MD minimization David Case (Thu Apr 20 2017 - 08:07:50 PDT)
[AMBER] Run NPT in a small periodic box Xiaoliu Zhang (Thu Apr 20 2017 - 07:44:37 PDT)
- Re: [AMBER] Run NPT in a small periodic box David Case (Thu Apr 20 2017 - 09:48:44 PDT)
[AMBER] MMPBSA - error Anna Cebrian Prats (Thu Apr 20 2017 - 08:02:45 PDT)
- Re: [AMBER] MMPBSA - error Ray Luo (Thu Apr 20 2017 - 09:06:20 PDT)
[AMBER] Membrane Protein Simulation Methodology Gulsevin,Alican (Thu Apr 20 2017 - 08:53:30 PDT)
- Re: [AMBER] Membrane Protein Simulation Methodology Edson Katekawa (Thu Apr 20 2017 - 11:18:24 PDT)
- Re: [AMBER] Membrane Protein Simulation Methodology Elvis Martis (Thu Apr 20 2017 - 22:13:20 PDT)
[AMBER] Recommended LJ parameters for divalent cations used for negatively charged lipid bilayers simulations ? Marek Maly (Thu Apr 20 2017 - 09:02:08 PDT)
[AMBER] 3D-RISM centering 0 Lucia Fusani (Thu Apr 20 2017 - 10:05:42 PDT)
- Re: [AMBER] 3D-RISM centering 0 Tyler Luchko (Lists) (Thu Apr 20 2017 - 11:18:04 PDT)
  - Re: [AMBER] 3D-RISM centering 0 Lucia Fusani (Wed Apr 26 2017 - 08:45:30 PDT)
[AMBER] Internal dielectric constant and pmemd Samaneh Ghassabi Kondalaji (Thu Apr 20 2017 - 11:02:59 PDT)
- Re: [AMBER] Internal dielectric constant and pmemd David Case (Fri Apr 21 2017 - 05:04:49 PDT)
  - Re: [AMBER] Internal dielectric constant and pmemd Samaneh Ghassabi Kondalaji (Fri Apr 21 2017 - 06:11:47 PDT)
    - Re: [AMBER] Internal dielectric constant and pmemd Adrian Roitberg (Fri Apr 21 2017 - 06:14:52 PDT)
    - Re: [AMBER] Internal dielectric constant and pmemd Samaneh Ghassabi Kondalaji (Fri Apr 21 2017 - 06:21:45 PDT)
    - Re: [AMBER] Internal dielectric constant and pmemd Adrian Roitberg (Fri Apr 21 2017 - 06:26:37 PDT)
    - Re: [AMBER] Internal dielectric constant and pmemd Samaneh Ghassabi Kondalaji (Fri Apr 21 2017 - 06:36:17 PDT)
    - Re: [AMBER] Internal dielectric constant and pmemd James Kress (Fri Apr 21 2017 - 09:53:13 PDT)
    - Re: [AMBER] Internal dielectric constant and pmemd Samaneh Ghassabi Kondalaji (Fri Apr 21 2017 - 11:04:34 PDT)
    - Re: [AMBER] Internal dielectric constant and pmemd James Kress (Fri Apr 21 2017 - 11:19:43 PDT)
    - Re: [AMBER] Internal dielectric constant and pmemd Thomas Cheatham (Fri Apr 21 2017 - 13:48:22 PDT)
    - Re: [AMBER] Internal dielectric constant and pmemd Samaneh Ghassabi Kondalaji (Fri Apr 21 2017 - 14:23:48 PDT)
- Re: [AMBER] Internal dielectric constant and pmemd James Kress (Fri Apr 21 2017 - 09:55:38 PDT)
[AMBER] How to make sure there is bond in my complex Thakur, Abhishek (Thu Apr 20 2017 - 11:56:22 PDT)
- Re: [AMBER] How to make sure there is bond in my complex Hai Nguyen (Thu Apr 20 2017 - 11:59:20 PDT)
  - Re: [AMBER] How to make sure there is bond in my complex Thakur, Abhishek (Thu Apr 20 2017 - 12:06:48 PDT)
    - Re: [AMBER] How to make sure there is bond in my complex Hai Nguyen (Thu Apr 20 2017 - 12:17:09 PDT)
    - Re: [AMBER] How to make sure there is bond in my complex Thakur, Abhishek (Thu Apr 20 2017 - 12:23:09 PDT)
[AMBER] Minor bug with updating Amber/AmberTools with Python3 Rohith Mohan (Thu Apr 20 2017 - 13:52:35 PDT)
- Re: [AMBER] Minor bug with updating Amber/AmberTools with Python3 Hai Nguyen (Thu Apr 20 2017 - 13:57:28 PDT)
[AMBER] PMEMD should halt with error exit after netcdf write failure Chris Moth (Thu Apr 20 2017 - 15:30:25 PDT)
[AMBER] Is Hvib (vibration contribution to enthalpy) considered/calculated in NMA in NAB program? Guqin Shi (Thu Apr 20 2017 - 15:59:14 PDT)
- Re: [AMBER] Is Hvib (vibration contribution to enthalpy) considered/calculated in NMA in NAB program? David Case (Thu Apr 20 2017 - 18:48:12 PDT)
  - Re: [AMBER] Is Hvib (vibration contribution to enthalpy) considered/calculated in NMA in NAB program? Guqin Shi (Fri Apr 21 2017 - 07:58:01 PDT)
    - Re: [AMBER] Is Hvib (vibration contribution to enthalpy) considered/calculated in NMA in NAB program? David Case (Fri Apr 21 2017 - 19:34:03 PDT)
    - Re: [AMBER] Is Hvib (vibration contribution to enthalpy) considered/calculated in NMA in NAB program? Guqin Shi (Fri Apr 21 2017 - 21:05:34 PDT)
    - Re: [AMBER] Is Hvib (vibration contribution to enthalpy) considered/calculated in NMA in NAB program? David Case (Sat Apr 22 2017 - 05:38:53 PDT)
    - Re: [AMBER] Is Hvib (vibration contribution to enthalpy) considered/calculated in NMA in NAB program? Guqin Shi (Sat Apr 22 2017 - 13:43:33 PDT)
[AMBER] Can't not run cpptraj Khatcharin Siriwong (Thu Apr 20 2017 - 19:13:06 PDT)
- Re: [AMBER] Can't not run cpptraj Hai Nguyen (Thu Apr 20 2017 - 19:15:51 PDT)
  - Re: [AMBER] Can't not run cpptraj Khatcharin Siriwong (Thu Apr 20 2017 - 19:21:13 PDT)
- Re: [AMBER] Can't not run cpptraj Gulsevin,Alican (Thu Apr 20 2017 - 19:45:42 PDT)
  - Re: [AMBER] Can't not run cpptraj Khatcharin Siriwong (Thu Apr 20 2017 - 20:04:39 PDT)
[AMBER] Segmentation fault sylvester kisembo (Fri Apr 21 2017 - 06:35:04 PDT)
- Re: [AMBER] Segmentation fault Adrian Roitberg (Fri Apr 21 2017 - 06:40:34 PDT)
- Re: [AMBER] Segmentation fault David Case (Fri Apr 21 2017 - 07:49:16 PDT)
  - Re: [AMBER] Segmentation fault sylvester kisembo (Fri Apr 21 2017 - 16:50:39 PDT)
    - Re: [AMBER] Segmentation fault David Case (Fri Apr 21 2017 - 19:17:50 PDT)
[AMBER] residue-based dielectric model in MMGBSA Mrinda Jones (Fri Apr 21 2017 - 11:28:44 PDT)
- Re: [AMBER] residue-based dielectric model in MMGBSA David Case (Fri Apr 21 2017 - 18:25:25 PDT)
  - Re: [AMBER] residue-based dielectric model in MMGBSA Thomas Cheatham (Fri Apr 21 2017 - 18:32:27 PDT)
    - Re: [AMBER] residue-based dielectric model in MMGBSA David Case (Sat Apr 22 2017 - 05:32:02 PDT)
    - Re: [AMBER] residue-based dielectric model in MMGBSA Jaime Rubio Martinez (Mon Apr 24 2017 - 00:45:47 PDT)
- Re: [AMBER] residue-based dielectric model in MMGBSA Thomas Cheatham (Fri Apr 21 2017 - 18:26:13 PDT)
[AMBER] Warning message in AmberTools17 upgrade Baker, Joseph (Fri Apr 21 2017 - 11:41:19 PDT)
- Re: [AMBER] Warning message in AmberTools17 upgrade Baker, Joseph (Fri Apr 21 2017 - 11:53:11 PDT)
- Re: [AMBER] Warning message in AmberTools17 upgrade Nhai (Fri Apr 21 2017 - 12:07:29 PDT)
  - Re: [AMBER] Warning message in AmberTools17 upgrade Baker, Joseph (Fri Apr 21 2017 - 12:17:52 PDT)
    - Re: [AMBER] Warning message in AmberTools17 upgrade Baker, Joseph (Fri Apr 21 2017 - 12:23:51 PDT)
    - Re: [AMBER] Warning message in AmberTools17 upgrade Nhai (Fri Apr 21 2017 - 12:27:24 PDT)
    - Re: [AMBER] Warning message in AmberTools17 upgrade Baker, Joseph (Fri Apr 21 2017 - 12:30:27 PDT)
    - Re: [AMBER] Warning message in AmberTools17 upgrade Baker, Joseph (Fri Apr 21 2017 - 12:36:56 PDT)
    - Re: [AMBER] Warning message in AmberTools17 upgrade Hai Nguyen (Fri Apr 21 2017 - 12:39:59 PDT)
    - Re: [AMBER] Warning message in AmberTools17 upgrade Baker, Joseph (Fri Apr 21 2017 - 12:43:43 PDT)
    - Re: [AMBER] Warning message in AmberTools17 upgrade Hai Nguyen (Fri Apr 21 2017 - 12:46:30 PDT)
    - Re: [AMBER] Warning message in AmberTools17 upgrade Baker, Joseph (Fri Apr 21 2017 - 13:23:13 PDT)
    - Re: [AMBER] Warning message in AmberTools17 upgrade Jason Swails (Fri Apr 21 2017 - 13:48:47 PDT)
    - Re: [AMBER] Warning message in AmberTools17 upgrade Baker, Joseph (Fri Apr 21 2017 - 13:53:04 PDT)
    - Re: [AMBER] Warning message in AmberTools17 upgrade Hai Nguyen (Fri Apr 21 2017 - 20:49:02 PDT)
    - Re: [AMBER] Warning message in AmberTools17 upgrade Baker, Joseph (Mon Apr 24 2017 - 09:41:09 PDT)
    - Re: [AMBER] Warning message in AmberTools17 upgrade Hai Nguyen (Mon Apr 24 2017 - 09:54:08 PDT)
    - Re: [AMBER] Warning message in AmberTools17 upgrade Baker, Joseph (Mon Apr 24 2017 - 11:53:37 PDT)
[AMBER] AmberTools17: test of mpi configuration with pnetcdf failed on Mac OS X 10.10 Mooers, Blaine H.M. (HSC) (Fri Apr 21 2017 - 12:36:27 PDT)
- Re: [AMBER] AmberTools17: test of mpi configuration with pnetcdf failed on Mac OS X 10.10 David Case (Fri Apr 21 2017 - 18:42:49 PDT)
  - Re: [AMBER] AmberTools17: test of mpi configuration with pnetcdf failed on Mac OS X 10.10 Mooers, Blaine H.M. (HSC) (Sat Apr 22 2017 - 14:01:02 PDT)
    - Re: [AMBER] AmberTools17: test of mpi configuration with pnetcdf failed on Mac OS X 10.10 David Case (Sun Apr 23 2017 - 06:00:41 PDT)
    - Re: [AMBER] AmberTools17: test of mpi configuration with pnetcdf failed on Mac OS X 10.10 Mooers, Blaine H.M. (HSC) (Sun Apr 23 2017 - 09:10:44 PDT)
    - Re: [AMBER] AmberTools17: test of mpi configuration with pnetcdf failed on Mac OS X 10.10 David Case (Sun Apr 23 2017 - 14:57:40 PDT)
    - Re: [AMBER] AmberTools17: test of mpi configuration with pnetcdf failed on Mac OS X 10.10 Mooers, Blaine H.M. (HSC) (Wed Apr 26 2017 - 08:06:50 PDT)
[AMBER] failed to generate parameter and topology file for protein-ligand complex containing zinc Sharon D. Morris (Sat Apr 22 2017 - 02:00:17 PDT)
- Re: [AMBER] failed to generate parameter and topology file for protein-ligand complex containing zinc Elvis Martis (Sat Apr 22 2017 - 05:53:17 PDT)
- Re: [AMBER] failed to generate parameter and topology file for protein-ligand complex containing zinc Elvis Martis (Mon Apr 24 2017 - 00:24:14 PDT)
[AMBER] cpptraj configure may fail in AmberTools17 Hannes Loeffler (Sat Apr 22 2017 - 03:38:57 PDT)
- Re: [AMBER] cpptraj configure may fail in AmberTools17 Daniel Roe (Tue Apr 25 2017 - 06:16:46 PDT)
[AMBER] Query regarding convergence issue of 3D-RISM Rakesh Srivastava (Sun Apr 23 2017 - 23:28:53 PDT)
- Re: [AMBER] Query regarding convergence issue of 3D-RISM David Case (Mon Apr 24 2017 - 04:50:45 PDT)
[AMBER] Query regarding energy calcuation using 3D-RISM Vertika Gautam (Mon Apr 24 2017 - 01:50:11 PDT)
- Re: [AMBER] Query regarding energy calcuation using 3D-RISM David Case (Mon Apr 24 2017 - 04:55:40 PDT)
  - Re: [AMBER] Query regarding energy calcuation using 3D-RISM Vertika Gautam (Sat May 20 2017 - 13:44:54 PDT)
    - Re: [AMBER] Query regarding energy calcuation using 3D-RISM David Case (Sat May 20 2017 - 21:23:57 PDT)
[AMBER] Membrane Protein Simulation Methodology Gulsevin,Alican (Mon Apr 24 2017 - 04:10:18 PDT)
[AMBER] antechamber convergence problem. Vatsal Purohit (Mon Apr 24 2017 - 13:32:52 PDT)
- Re: [AMBER] antechamber convergence problem. David Case (Tue Apr 25 2017 - 05:07:34 PDT)
[AMBER] Pairwise energy calculations in cpptraj Aishani Prem (Mon Apr 24 2017 - 20:07:52 PDT)
- Re: [AMBER] Pairwise energy calculations in cpptraj Daniel Roe (Tue Apr 25 2017 - 06:33:09 PDT)
[AMBER] Stricter convergence Criterion for stretching Ramin Salimi (Tue Apr 25 2017 - 10:57:29 PDT)
- Re: [AMBER] Stricter convergence Criterion for stretching Adrian Roitberg (Tue Apr 25 2017 - 11:01:02 PDT)
  - Re: [AMBER] Stricter convergence Criterion for stretching Ramin Salimi (Tue Apr 25 2017 - 11:26:43 PDT)
  - Re: [AMBER] Stricter convergence Criterion for stretching Ramin Salimi (Tue Apr 25 2017 - 16:18:14 PDT)
[AMBER] Regarding gaussian namelist error Budhathoki, Dipesh (Tue Apr 25 2017 - 16:35:45 PDT)
- Re: [AMBER] Regarding gaussian namelist error David Case (Tue Apr 25 2017 - 17:22:08 PDT)
  - Re: [AMBER] Regarding gaussian namelist error Budhathoki, Dipesh (Tue Apr 25 2017 - 20:48:12 PDT)
[AMBER] Trouble with simple MD simulation of short peptide and Cu2+ ion Eugene Cha (Tue Apr 25 2017 - 20:34:27 PDT)
- Re: [AMBER] Trouble with simple MD simulation of short peptide and Cu2+ ion Bill Ross (Tue Apr 25 2017 - 20:54:58 PDT)
  - Re: [AMBER] Trouble with simple MD simulation of short peptide and Cu2+ ion MOHD HOMAIDUR RAHMAN (Tue Apr 25 2017 - 21:29:30 PDT)
    - Re: [AMBER] Trouble with simple MD simulation of short peptide and Cu2+ ion Bill Ross (Tue Apr 25 2017 - 21:33:07 PDT)
[AMBER] consult about LEaP in amber 张壮壮 (Tue Apr 25 2017 - 20:49:48 PDT)
- Re: [AMBER] consult about LEaP in amber Elvis Martis (Wed Apr 26 2017 - 03:39:01 PDT)
  - Re: [AMBER] [SPAM] Re: consult about LEaP in amber 张壮壮 (Mon May 01 2017 - 07:28:07 PDT)
    - [AMBER] Question about the pairwise option in cpptraj David Case (Wed May 03 2017 - 18:30:21 PDT)
    - Re: [AMBER] Question about the pairwise option in cpptraj Daniel Roe (Fri May 05 2017 - 11:48:45 PDT)
[AMBER] intra-residue water bridge with cpptraj Joanna Sarzynska (Wed Apr 26 2017 - 07:27:36 PDT)
- Re: [AMBER] intra-residue water bridge with cpptraj Daniel Roe (Wed Apr 26 2017 - 08:25:49 PDT)
  - Re: [AMBER] intra-residue water bridge with cpptraj Joanna Sarzynska (Fri Apr 28 2017 - 03:22:09 PDT)
    - Re: [AMBER] intra-residue water bridge with cpptraj Joanna Sarzynska (Fri May 05 2017 - 01:17:20 PDT)
    - Re: [AMBER] intra-residue water bridge with cpptraj Daniel Roe (Fri May 05 2017 - 06:00:04 PDT)
[AMBER] Release of AmberTools17 binary Hai Nguyen (Wed Apr 26 2017 - 07:30:04 PDT)
- Re: [AMBER] Release of AmberTools17 binary David Case (Wed Apr 26 2017 - 12:22:25 PDT)
[AMBER] Post Doc position in Munich, German required Andreas Tosstorff (Wed Apr 26 2017 - 09:01:44 PDT)
[AMBER] barostat=1 error at Stampede Tarsis (Wed Apr 26 2017 - 13:10:05 PDT)
- Re: [AMBER] barostat=1 error at Stampede Elvis Martis (Wed Apr 26 2017 - 23:51:56 PDT)
  - Re: [AMBER] barostat=1 error at Stampede Elvis Martis (Wed Apr 26 2017 - 23:53:12 PDT)
    - Re: [AMBER] barostat=1 error at Stampede Bill Ross (Thu Apr 27 2017 - 00:23:15 PDT)
    - Re: [AMBER] barostat=1 error at Stampede Ross Walker (Thu Apr 27 2017 - 04:33:35 PDT)
    - Re: [AMBER] barostat=1 error at Stampede Elvis Martis (Thu Apr 27 2017 - 07:05:42 PDT)
[AMBER] Tutorial - 3 / MM-PBSA Marcelo Andrade Chagas (Wed Apr 26 2017 - 14:19:55 PDT)
- Re: [AMBER] Tutorial - 3 / MM-PBSA Hai Nguyen (Wed Apr 26 2017 - 14:26:51 PDT)
[AMBER] Error with 'surf' and acetonitrile-water solvent mixture Marcel Passon (Thu Apr 27 2017 - 01:21:32 PDT)
- Re: [AMBER] Error with 'surf' and acetonitrile-water solvent mixture Daniel Roe (Tue May 02 2017 - 10:45:28 PDT)
  - Re: [AMBER] Error with 'surf' and acetonitrile-water solvent mixture Daniel Roe (Thu May 04 2017 - 08:00:55 PDT)
    - Re: [AMBER] Error with 'surf' and acetonitrile-water solvent mixture Daniel Roe (Thu May 04 2017 - 08:54:32 PDT)
    - Re: [AMBER] Error with 'surf' and acetonitrile-water solvent mixture Marcel Passon (Fri May 05 2017 - 07:43:06 PDT)
    - Re: [AMBER] Error with 'surf' and acetonitrile-water solvent mixture Daniel Roe (Mon Jul 03 2017 - 12:14:26 PDT)
[AMBER] tleap input file that fails following upgrade to AmberTools17 Adams, John E. (Thu Apr 27 2017 - 08:45:51 PDT)
- Re: [AMBER] tleap input file that fails following upgrade to AmberTools17 Scott Brozell (Fri Apr 28 2017 - 09:21:35 PDT)
  - Re: [AMBER] tleap input file that fails following upgrade to AmberTools17 Adams, John E. (Fri Apr 28 2017 - 11:03:36 PDT)
    - Re: [AMBER] tleap input file that fails following upgrade to AmberTools17 Hai Nguyen (Fri Apr 28 2017 - 11:50:48 PDT)
    - Re: [AMBER] tleap input file that fails following upgrade to AmberTools17 Hai Nguyen (Fri Apr 28 2017 - 11:55:22 PDT)
    - Re: [AMBER] tleap input file that fails following upgrade to AmberTools17 Adams, John E. (Fri Apr 28 2017 - 14:59:15 PDT)
    - Re: [AMBER] tleap input file that fails following upgrade to AmberTools17 Hai Nguyen (Fri Apr 28 2017 - 15:15:20 PDT)
    - Re: [AMBER] tleap input file that fails following upgrade to AmberTools17 Adams, John E. (Fri Apr 28 2017 - 15:24:10 PDT)
    - Re: [AMBER] tleap input file that fails following upgrade to AmberTools17 Adams, John E. (Fri Apr 28 2017 - 15:49:46 PDT)
    - Re: [AMBER] tleap input file that fails following upgrade to AmberTools17 Nhai (Fri Apr 28 2017 - 15:58:05 PDT)
    - Re: [AMBER] tleap input file that fails following upgrade to AmberTools17 David Case (Sat Apr 29 2017 - 05:20:13 PDT)
    - Re: [AMBER] tleap input file that fails following upgrade to AmberTools17 Adams, John E. (Sat Apr 29 2017 - 09:43:27 PDT)
[AMBER] Announcement: Release of DOCK 6.8 Scott Brozell (Thu Apr 27 2017 - 13:23:57 PDT)
[AMBER] Quenstions about Constraints in AMBER Pengfei Li (Thu Apr 27 2017 - 21:05:26 PDT)
- Re: [AMBER] Quenstions about Constraints in AMBER Hannes Loeffler (Fri Apr 28 2017 - 00:31:50 PDT)
- Re: [AMBER] Quenstions about Constraints in AMBER David Case (Sun Apr 30 2017 - 17:14:40 PDT)
[AMBER] Error when running MMPBSA calculation using Force field from CHARMM GUI membrane builder running on amber. Miguel Rivera (Fri Apr 28 2017 - 15:12:18 PDT)
- Re: [AMBER] Error when running MMPBSA calculation using Force field from CHARMM GUI membrane builder running on amber. David Case (Sat Apr 29 2017 - 05:28:00 PDT)
  - Re: [AMBER] Error when running MMPBSA calculation using Force field from CHARMM GUI membrane builder running on amber. Miguel Rivera (Thu May 04 2017 - 15:18:54 PDT)
- Re: [AMBER] Error when running MMPBSA calculation using Force field from CHARMM GUI membrane builder running on amber. Daniel Roe (Fri May 05 2017 - 11:29:08 PDT)
  - Re: [AMBER] Error when running MMPBSA calculation using Force field from CHARMM GUI membrane builder running on amber. Miguel Rivera (Wed Jun 07 2017 - 12:22:21 PDT)
    - Re: [AMBER] Error when running MMPBSA calculation using Force field from CHARMM GUI membrane builder running on amber. Jason Swails (Wed Jun 14 2017 - 13:08:12 PDT)
[AMBER] Using AmberTools17 and Amber14 David Adrian Saez San Martin (Fri Apr 28 2017 - 20:40:38 PDT)
- Re: [AMBER] Using AmberTools17 and Amber14 Hai Nguyen (Fri Apr 28 2017 - 22:00:48 PDT)
[AMBER] Too many iterations in routine! in RMSD calculation kungking Hanpaibool (Sat Apr 29 2017 - 02:16:06 PDT)
- Re: [AMBER] Too many iterations in routine! in RMSD calculation Daniel Roe (Mon May 01 2017 - 08:29:09 PDT)
  - Re: [AMBER] Too many iterations in routine! in RMSD calculation kungking Hanpaibool (Mon May 01 2017 - 08:50:42 PDT)
    - Re: [AMBER] Too many iterations in routine! in RMSD calculation Daniel Roe (Mon May 01 2017 - 08:55:58 PDT)
    - Re: [AMBER] Too many iterations in routine! in RMSD calculation kungking Hanpaibool (Mon May 01 2017 - 08:59:59 PDT)
    - Re: [AMBER] Too many iterations in routine! in RMSD calculation kungking Hanpaibool (Mon May 01 2017 - 09:09:42 PDT)
    - Re: [AMBER] Too many iterations in routine! in RMSD calculation Daniel Roe (Mon May 01 2017 - 09:23:09 PDT)
[AMBER] Restraint in Steered MD/Jarzynski method Ramin Salimi (Sat Apr 29 2017 - 04:02:01 PDT)
[AMBER] Restraint in Steered MD/Jarzynski method Ramin Salimi (Sat Apr 29 2017 - 10:55:20 PDT)
- Re: [AMBER] Restraint in Steered MD/Jarzynski method Hannes Loeffler (Sun Apr 30 2017 - 09:05:15 PDT)
  - Re: [AMBER] Restraint in Steered MD/Jarzynski method Ramin Salimi (Sun Apr 30 2017 - 11:41:18 PDT)
    - Re: [AMBER] Restraint in Steered MD/Jarzynski method Hannes Loeffler (Mon May 01 2017 - 00:11:42 PDT)
    - Re: [AMBER] Restraint in Steered MD/Jarzynski method Ramin Salimi (Mon May 01 2017 - 09:10:04 PDT)
[AMBER] Dftb3 Jacopo Sgrignani (Sat Apr 29 2017 - 13:40:28 PDT)
- Re: [AMBER] Dftb3 David Case (Sat Apr 29 2017 - 14:33:59 PDT)
[AMBER] External electric fields on CUDA enabled PMEMD Neville Bethel (Sun Apr 30 2017 - 13:14:00 PDT)
- Re: [AMBER] External electric fields on CUDA enabled PMEMD Charles Lin (Sun Apr 30 2017 - 19:32:00 PDT)
- Re: [AMBER] External electric fields on CUDA enabled PMEMD Neville Bethel (Wed May 10 2017 - 18:54:11 PDT)
  - Re: [AMBER] External electric fields on CUDA enabled PMEMD Charles Lin (Wed May 10 2017 - 21:37:02 PDT)
[AMBER] Missing File: charmmlipid2amber.csv Alexander Adams (Sun Apr 30 2017 - 23:28:02 PDT)
- Re: [AMBER] Missing File: charmmlipid2amber.csv Elvis Martis (Mon May 01 2017 - 00:03:57 PDT)
Re: [AMBER] does not have a type Sowmya Indrakumar (Mon May 01 2017 - 07:56:14 PDT)
- Re: [AMBER] does not have a type Thakur, Abhishek (Mon May 01 2017 - 07:58:44 PDT)
- Re: [AMBER] does not have a type David Case (Mon May 01 2017 - 07:59:23 PDT)
[AMBER] Find entropy from non-equilibrium free energy calculation Ramin Salimi (Mon May 01 2017 - 10:50:48 PDT)
- Re: [AMBER] Find entropy from non-equilibrium free energy calculation Hannes Loeffler (Tue May 02 2017 - 00:08:52 PDT)
  - Re: [AMBER] Find entropy from non-equilibrium free energy calculation Ramin Salimi (Tue May 02 2017 - 00:53:18 PDT)
[AMBER] acdoctor: fatal error when reading carboxylates from .mol2 files Niel Henriksen (Mon May 01 2017 - 15:09:32 PDT)
- Re: [AMBER] acdoctor: fatal error when reading carboxylates from .mol2 files Scott Brozell (Tue May 02 2017 - 00:20:56 PDT)
[AMBER] glycoprotein Neha Gandhi (Mon May 01 2017 - 23:49:10 PDT)
- Re: [AMBER] glycoprotein Neha Gandhi (Tue May 02 2017 - 00:08:48 PDT)
[AMBER] MD under external electric field & GPUs parallel problem 吴萌 (Tue May 02 2017 - 02:28:29 PDT)
[AMBER] Fwd: failed to generate parameter and topology file for protein-ligand complex containing zinc Sharon D. Morris (Tue May 02 2017 - 05:22:55 PDT)
- Re: [AMBER] Fwd: failed to generate parameter and topology file for protein-ligand complex containing zinc Elvis Martis (Tue May 02 2017 - 07:24:02 PDT)
[AMBER] AddtoBox failure sylvester kisembo (Tue May 02 2017 - 07:21:22 PDT)
- Re: [AMBER] AddtoBox failure David Case (Tue May 02 2017 - 18:24:55 PDT)
  - Re: [AMBER] AddtoBox failure David Cerutti (Tue May 02 2017 - 19:50:52 PDT)
[AMBER] Regarding amber-gaussian QM/MM problem Budhathoki, Dipesh (Tue May 02 2017 - 15:35:08 PDT)
- Re: [AMBER] Regarding amber-gaussian QM/MM problem Goetz, Andreas (Tue May 02 2017 - 16:07:24 PDT)
  - Re: [AMBER] Regarding amber-gaussian QM/MM problem Budhathoki, Dipesh (Fri May 05 2017 - 10:24:57 PDT)
[AMBER] Ambertools coulomb constant Gard Nelson (Tue May 02 2017 - 16:55:28 PDT)
- Re: [AMBER] Ambertools coulomb constant David Case (Wed May 03 2017 - 10:30:22 PDT)
[AMBER] ntx=5 and ntx=7 (Sanderinput) Johannes Kalliauer (Wed May 03 2017 - 00:16:49 PDT)
- Re: [AMBER] ntx=5 and ntx=7 (Sanderinput) Hannes Loeffler (Wed May 03 2017 - 00:31:05 PDT)
- Re: [AMBER] ntx=5 and ntx=7 (Sanderinput) David Case (Wed May 03 2017 - 05:27:41 PDT)
[AMBER] Question on implementing igb=8, along with mbondi3 Ramin Salimi (Wed May 03 2017 - 00:26:23 PDT)
- Re: [AMBER] Question on implementing igb=8, along with mbondi3 Carlos Simmerling (Wed May 03 2017 - 03:28:58 PDT)
Re: [AMBER] AddToBox Failure David Case (Wed May 03 2017 - 10:20:16 PDT)
[AMBER] LEaP failing after update to AmberTools17 Charles-Alexandre Mattelaer (Wed May 03 2017 - 10:35:19 PDT)
- Re: [AMBER] LEaP failing after update to AmberTools17 David Case (Wed May 03 2017 - 11:18:10 PDT)
  - Re: [AMBER] LEaP failing after update to AmberTools17 Charles-Alexandre Mattelaer (Wed May 03 2017 - 11:39:08 PDT)
[AMBER] The problem for image tool in AMBER 鲁俊波 (Wed May 03 2017 - 20:20:58 PDT)
- Re: [AMBER] The problem for image tool in AMBER Daniel Roe (Thu May 04 2017 - 08:49:53 PDT)
  - Re: [AMBER] The problem for image tool in AMBER 鲁俊波 (Thu May 04 2017 - 09:37:35 PDT)
- Re: [AMBER] The problem for image tool in AMBER Daniel Roe (Fri May 05 2017 - 06:14:01 PDT)
[AMBER] How to restart MD Garima Singh (Wed May 03 2017 - 23:48:32 PDT)
- Re: [AMBER] How to restart MD Andreas Tosstorff (Thu May 04 2017 - 00:11:52 PDT)
- Re: [AMBER] How to restart MD Elvis Martis (Thu May 04 2017 - 00:12:58 PDT)
[AMBER] GPUs parallel problem Meng Wu (Thu May 04 2017 - 01:26:20 PDT)
- Re: [AMBER] GPUs parallel problem Andreas Tosstorff (Thu May 04 2017 - 02:21:41 PDT)
  - Re: [AMBER] GPUs parallel problem Gulsevin,Alican (Thu May 04 2017 - 02:29:26 PDT)
    - Re: [AMBER] GPUs parallel problem Ross Walker (Thu May 04 2017 - 08:16:03 PDT)
- Re: [AMBER] GPUs parallel problem Meng Wu (Fri May 05 2017 - 02:36:59 PDT)
  - Re: [AMBER] GPUs parallel problem Ross Walker (Fri May 05 2017 - 05:05:58 PDT)
[AMBER] aMD and cpH-MD Hofer, Florian (Thu May 04 2017 - 01:45:42 PDT)
[AMBER] ff parameters Andrea Spitaleri (Fri May 05 2017 - 00:38:28 PDT)
- Re: [AMBER] ff parameters David Case (Fri May 05 2017 - 05:05:31 PDT)
- Re: [AMBER] ff parameters Jason Swails (Fri May 05 2017 - 11:31:13 PDT)
  - Re: [AMBER] ff parameters Andrea Spitaleri (Fri May 05 2017 - 12:46:19 PDT)
    - Re: [AMBER] ff parameters Hai Nguyen (Fri May 05 2017 - 13:17:49 PDT)
    - Re: [AMBER] ff parameters David Case (Sat May 06 2017 - 05:19:20 PDT)
    - Re: [AMBER] ff parameters Jason Swails (Mon May 08 2017 - 05:39:40 PDT)
[AMBER] Fast 3-point water residue error for coordinates generated with parmed Sadegh Faramarzi Ganjabad (Fri May 05 2017 - 11:32:46 PDT)
- Re: [AMBER] Fast 3-point water residue error for coordinates generated with parmed Daniel Roe (Fri May 05 2017 - 12:15:57 PDT)
[AMBER] Cellulose simulation luca maggi (Sun May 07 2017 - 07:37:18 PDT)
- Re: [AMBER] Cellulose simulation Lachele Foley (Mon May 08 2017 - 01:06:26 PDT)
  - Re: [AMBER] Cellulose simulation luca maggi (Mon May 08 2017 - 01:17:52 PDT)
[AMBER] Molecule with glyco - single amino acid linkage? yunshi11 . (Sun May 07 2017 - 20:25:23 PDT)
- Re: [AMBER] Molecule with glyco - single amino acid linkage? Lachele Foley (Sun May 07 2017 - 21:32:46 PDT)
  - Re: [AMBER] Molecule with glyco - single amino acid linkage? yunshi11 . (Mon May 08 2017 - 15:18:09 PDT)
[AMBER] Atom type assignment by Antechamber Matsuura, Azuma (Sun May 07 2017 - 22:13:13 PDT)
- Re: [AMBER] Atom type assignment by Antechamber Junmei Wang (Mon May 08 2017 - 08:19:48 PDT)
  - Re: [AMBER] Atom type assignment by Antechamber Matsuura, Azuma (Mon May 08 2017 - 18:14:22 PDT)
Re: [AMBER] Fast 3-point water residue error for coordinates Sadegh Faramarzi Ganjabad (Sun May 07 2017 - 23:46:54 PDT)
- Re: [AMBER] Fast 3-point water residue error for coordinates Song-Ho Chong (Mon May 08 2017 - 08:22:53 PDT)
- Re: [AMBER] Fast 3-point water residue error for coordinates Sadegh Faramarzi Ganjabad (Mon May 08 2017 - 13:09:40 PDT)
[AMBER] Parameterization Ligand Boron Pedro Fernandes (Mon May 08 2017 - 06:09:46 PDT)
- Re: [AMBER] Parameterization Ligand Boron Elvis Martis (Mon May 08 2017 - 07:45:48 PDT)
[AMBER] Cpptraj calculates only three PHI-PSI angles in a 18-residue long peptide Chetna Tyagi (Mon May 08 2017 - 08:07:34 PDT)
- Re: [AMBER] Cpptraj calculates only three PHI-PSI angles in a 18-residue long peptide Daniel Roe (Mon May 08 2017 - 08:14:26 PDT)
- Re: [AMBER] Cpptraj calculates only three PHI-PSI angles in a 18-residue long peptide Elvis Martis (Mon May 08 2017 - 09:51:27 PDT)
  - Re: [AMBER] Cpptraj calculates only three PHI-PSI angles in a 18-residue long peptide Chetna Tyagi (Mon May 08 2017 - 10:37:53 PDT)
    - Re: [AMBER] Cpptraj calculates only three PHI-PSI angles in a 18-residue long peptide Daniel Roe (Mon May 08 2017 - 13:04:18 PDT)
[AMBER] tleap-incorpoarating .frcmod, .prep files for unnatural nucleotides p.kartheek (Mon May 08 2017 - 10:33:43 PDT)
- Re: [AMBER] tleap-incorpoarating .frcmod, .prep files for unnatural nucleotides Elvis Martis (Mon May 08 2017 - 21:11:43 PDT)
[AMBER] Possible bug in the GPU code Pratul K. Agarwal (Mon May 08 2017 - 15:35:44 PDT)
- Re: [AMBER] Possible bug in the GPU code David Case (Mon May 08 2017 - 18:14:57 PDT)
[AMBER] Amber parameters for CPD and 6-4PP p.kartheek (Tue May 09 2017 - 02:50:28 PDT)
- Re: [AMBER] Amber parameters for CPD and 6-4PP Elvis Martis (Tue May 09 2017 - 04:21:58 PDT)
[AMBER] Problem in splitting mdcrd file with cpptraj Manjula Saravanan (Tue May 09 2017 - 23:11:11 PDT)
- Re: [AMBER] Problem in splitting mdcrd file with cpptraj Daniel Roe (Wed May 10 2017 - 08:48:56 PDT)
- [AMBER] Fwd: Problem in splitting mdcrd file with cpptraj Manjula Saravanan (Thu May 11 2017 - 22:20:31 PDT)
[AMBER] Two questions for GAFF Matsuura, Azuma (Wed May 10 2017 - 00:58:16 PDT)
- Re: [AMBER] Two questions for GAFF Junmei Wang (Wed May 10 2017 - 05:39:55 PDT)
  - Re: [AMBER] Two questions for GAFF Matsuura, Azuma (Wed May 10 2017 - 18:01:15 PDT)
[AMBER] Distance regarding to interface between two solvents Habib Rozale (Wed May 10 2017 - 02:00:40 PDT)
[AMBER] fcc_metals.lib is not a valid databae Sohag Biswas (Wed May 10 2017 - 04:58:24 PDT)
[AMBER] how to draw Radial Distribution Functions? Yang Jinpeng (Wed May 10 2017 - 05:15:30 PDT)
- Re: [AMBER] how to draw Radial Distribution Functions? Daniel Roe (Wed May 10 2017 - 10:11:19 PDT)
[AMBER] MG angle parameter Tommaso Biagini (Wed May 10 2017 - 05:37:58 PDT)
- Re: [AMBER] MG angle parameter Elvis Martis (Wed May 10 2017 - 07:21:49 PDT)
  - Re: [AMBER] MG angle parameter Tommaso Biagini (Wed May 10 2017 - 08:15:22 PDT)
    - Re: [AMBER] MG angle parameter kungking Hanpaibool (Wed May 10 2017 - 08:25:07 PDT)
    - Re: [AMBER] MG angle parameter Tommaso Biagini (Wed May 10 2017 - 21:17:17 PDT)
    - Re: [AMBER] MG angle parameter Elvis Martis (Wed May 10 2017 - 21:48:00 PDT)
    - Re: [AMBER] MG angle parameter Tommaso Biagini (Wed May 10 2017 - 22:47:11 PDT)
[AMBER] question about commutation of sub-trajectories and frame aligning Gordon Richard Chalmers (Wed May 10 2017 - 05:56:42 PDT)
- Re: [AMBER] question about commutation of sub-trajectories and frame aligning Daniel Roe (Wed May 10 2017 - 08:46:12 PDT)
  - Re: [AMBER] question about commutation of sub-trajectories and frame aligning Gordon Richard Chalmers (Wed May 10 2017 - 10:36:08 PDT)
[AMBER] CX1 missing connect0 atom._MCPB Thakur, Abhishek (Wed May 10 2017 - 12:24:55 PDT)
- Re: [AMBER] CX1 missing connect0 atom._MCPB Pengfei Li (Wed May 10 2017 - 15:45:08 PDT)
[AMBER] ERROR: Could not read coords from .rst file Vishal Nemaysh (Thu May 11 2017 - 00:23:45 PDT)
- Re: [AMBER] ERROR: Could not read coords from .rst file Szymon Żaczek (Thu May 11 2017 - 01:01:36 PDT)
[AMBER] Water Analysis with SPAM julian.zachmann selvita.home.pl (Thu May 11 2017 - 07:29:58 PDT)
- Re: [AMBER] Water Analysis with SPAM julian.zachmann selvita.home.pl (Mon May 15 2017 - 01:55:38 PDT)
  - Re: [AMBER] Water Analysis with SPAM Bill Ross (Mon May 15 2017 - 02:09:32 PDT)
    - Re: [AMBER] Water Analysis with SPAM julian.zachmann selvita.home.pl (Mon May 15 2017 - 02:20:43 PDT)
    - Re: [AMBER] Water Analysis with SPAM Bill Ross (Mon May 15 2017 - 02:54:51 PDT)
    - Re: [AMBER] Water Analysis with SPAM Bill Ross (Mon May 15 2017 - 03:16:53 PDT)
    - Re: [AMBER] Water Analysis with SPAM Bill Ross (Mon May 15 2017 - 03:22:45 PDT)
    - Re: [AMBER] Water Analysis with SPAM julian.zachmann selvita.home.pl (Mon May 15 2017 - 04:27:48 PDT)
    - Re: [AMBER] Water Analysis with SPAM Bill Ross (Mon May 15 2017 - 04:47:34 PDT)
    - Re: [AMBER] Water Analysis with SPAM julian.zachmann selvita.home.pl (Mon May 15 2017 - 04:56:15 PDT)
    - Re: [AMBER] Water Analysis with SPAM Bill Ross (Mon May 15 2017 - 11:34:14 PDT)
    - Re: [AMBER] Water Analysis with SPAM Daniel Roe (Tue May 16 2017 - 07:49:58 PDT)
    - Re: [AMBER] Water Analysis with SPAM julian.zachmann selvita.home.pl (Tue May 16 2017 - 08:09:24 PDT)
    - Re: [AMBER] Water Analysis with SPAM Daniel Roe (Tue May 16 2017 - 08:19:50 PDT)
    - Re: [AMBER] Water Analysis with SPAM julian.zachmann selvita.home.pl (Tue May 16 2017 - 08:40:07 PDT)
    - Re: [AMBER] Water Analysis with SPAM Daniel Roe (Tue May 16 2017 - 09:08:23 PDT)
[AMBER] Tip3p water box size for two different systems. Saman Yousuf ali (Thu May 11 2017 - 07:57:17 PDT)
- Re: [AMBER] Tip3p water box size for two different systems. Elvis Martis (Thu May 11 2017 - 22:18:59 PDT)
  - Re: [AMBER] Tip3p water box size for two different systems. Saman Yousuf ali (Thu May 11 2017 - 22:30:43 PDT)
    - Re: [AMBER] Tip3p water box size for two different systems. Elvis Martis (Thu May 11 2017 - 22:42:34 PDT)
    - Re: [AMBER] Tip3p water box size for two different systems. Bill Ross (Thu May 11 2017 - 22:52:06 PDT)
[AMBER] <Na 1> Could not find vdW (or other) parameters for type: Na Thakur, Abhishek (Thu May 11 2017 - 09:10:52 PDT)
- Re: [AMBER] <Na 1> Could not find vdW (or other) parameters for type: Na David A Case (Thu May 11 2017 - 12:02:00 PDT)
 - Re: [AMBER] <Na 1> Could not find vdW (or other) parameters for type: Na Thakur, Abhishek (Thu May 11 2017 - 14:37:54 PDT)
 - Re: [AMBER] <Na 1> Could not find vdW (or other) parameters for type: Na David A Case (Fri May 12 2017 - 05:33:34 PDT)
 - Re: [AMBER] <Na 1> Could not find vdW (or other) parameters for type: Na Thakur, Abhishek (Mon May 15 2017 - 09:01:42 PDT)
 - Re: [AMBER] <Na 1> Could not find vdW (or other) parameters for type: Na Bill Ross (Mon May 15 2017 - 11:52:00 PDT)
[AMBER] How to use Amber in HPC Garima Singh (Fri May 12 2017 - 03:53:49 PDT)
- Re: [AMBER] How to use Amber in HPC Elvis Martis (Fri May 12 2017 - 04:40:31 PDT)
[AMBER] EEL and VDW Notification on minimization with sander/pmemd Charles Mariasoosai (Fri May 12 2017 - 09:57:53 PDT)
- Re: [AMBER] EEL and VDW Notification on minimization with sander/pmemd Elvis Martis (Sat May 13 2017 - 01:11:17 PDT)
- Re: [AMBER] EEL and VDW Notification on minimization with sander/pmemd David Case (Sun May 14 2017 - 05:29:46 PDT)
[AMBER] Has Hessian printing been added? Eric Hansen (Fri May 12 2017 - 12:47:17 PDT)
- Re: [AMBER] Has Hessian printing been added? David Case (Sun May 14 2017 - 05:36:43 PDT)
[AMBER] error: At line 551 of file mdin_ctrl_dat.F90 (unit = 5, file = 'heat.mdin') Ramin Salimi (Sat May 13 2017 - 05:21:35 PDT)
- Re: [AMBER] error: At line 551 of file mdin_ctrl_dat.F90 (unit = 5, file = 'heat.mdin') Elvis Martis (Sat May 13 2017 - 06:17:22 PDT)
- Re: [AMBER] error: At line 551 of file mdin_ctrl_dat.F90 (unit = 5, file = 'heat.mdin') Elvis Martis (Sat May 13 2017 - 06:21:00 PDT)
  - Re: [AMBER] error: At line 551 of file mdin_ctrl_dat.F90 (unit = 5, file = 'heat.mdin') Ramin Salimi (Sat May 13 2017 - 06:43:56 PDT)
    - Re: [AMBER] error: At line 551 of file mdin_ctrl_dat.F90 (unit = 5, file = 'heat.mdin') Elvis Martis (Sat May 13 2017 - 07:33:06 PDT)
[AMBER] MCPB and Can not run MD simulation; some residue move out of protein kungking Hanpaibool (Sat May 13 2017 - 13:05:59 PDT)
- Re: [AMBER] MCPB and Can not run MD simulation; some residue move out of protein Elvis Martis (Sat May 13 2017 - 22:11:16 PDT)
  - Re: [AMBER] MCPB and Can not run MD simulation; some residue move out of protein kungking Hanpaibool (Sat May 13 2017 - 23:36:57 PDT)
    - Re: [AMBER] MCPB and Can not run MD simulation; some residue move out of protein Bill Ross (Sat May 13 2017 - 23:51:19 PDT)
- Re: [AMBER] MCPB and Can not run MD simulation; some residue move out of protein David Case (Sun May 14 2017 - 05:42:31 PDT)
- Re: [AMBER] MCPB and Can not run MD simulation; some residue move out of protein Pengfei Li (Thu May 18 2017 - 09:45:22 PDT)
[AMBER] dimer rmsd issue. Saman Yousuf ali (Sun May 14 2017 - 10:13:54 PDT)
- Re: [AMBER] dimer rmsd issue. Elvis Martis (Sun May 14 2017 - 10:44:13 PDT)
- Re: [AMBER] dimer rmsd issue. Bill Ross (Sun May 14 2017 - 12:16:55 PDT)
- Re: [AMBER] dimer rmsd issue. Daniel Roe (Tue May 16 2017 - 08:16:36 PDT)
[AMBER] Fwd: Request for troubleshoot in MAWS (igem software from Heidelberg) based on AMBER Abudhahir Buhari (Mon May 15 2017 - 01:24:23 PDT)
[AMBER] Partial Mini error Nikita Devnarain (Mon May 15 2017 - 05:33:02 PDT)
- Re: [AMBER] Partial Mini error David Case (Mon May 15 2017 - 19:15:50 PDT)
[AMBER] Ante_R.E.D script files. Vatsal Purohit (Mon May 15 2017 - 11:10:25 PDT)
[AMBER] Reference structure for targeted MD Francesco Gentile (Mon May 15 2017 - 19:26:39 PDT)
- Re: [AMBER] Reference structure for targeted MD David Case (Tue May 16 2017 - 05:28:30 PDT)
- Re: [AMBER] Reference structure for targeted MD Daniel Roe (Tue May 16 2017 - 09:02:15 PDT)
[AMBER] convergence question about xmin liu junjun (Tue May 16 2017 - 02:53:21 PDT)
- Re: [AMBER] convergence question about xmin liu junjun (Wed May 17 2017 - 10:22:00 PDT)
  - Re: [AMBER] convergence question about xmin Scott Brozell (Wed May 17 2017 - 11:30:05 PDT)
  - Re: [AMBER] convergence question about xmin David Case (Mon May 29 2017 - 13:06:40 PDT)
[AMBER] sander API data structure Brent Krueger (Tue May 16 2017 - 06:43:26 PDT)
- Re: [AMBER] sander API data structure Daniel Roe (Tue May 16 2017 - 08:03:21 PDT)
  - Re: [AMBER] sander API data structure Hai Nguyen (Tue May 16 2017 - 08:32:34 PDT)
    - Re: [AMBER] sander API data structure Brent Krueger (Tue May 16 2017 - 09:15:59 PDT)
    - Re: [AMBER] sander API data structure Bill Ross (Tue May 16 2017 - 10:52:24 PDT)
    - Re: [AMBER] sander API data structure Brent Krueger (Mon May 22 2017 - 07:39:02 PDT)
    - Re: [AMBER] sander API data structure Hai Nguyen (Mon May 22 2017 - 19:20:46 PDT)
  - Re: [AMBER] sander API data structure Jason Swails (Tue May 16 2017 - 10:39:10 PDT)
[AMBER] Building distributable executable D'Auria, Raffaella (Tue May 16 2017 - 12:24:09 PDT)
- Re: [AMBER] Building distributable executable David Case (Wed May 17 2017 - 05:52:30 PDT)
  - Re: [AMBER] Building distributable executable Scott Brozell (Wed May 17 2017 - 09:21:59 PDT)
    - Re: [AMBER] Building distributable executable Jason Swails (Wed May 17 2017 - 10:40:08 PDT)
    - Re: [AMBER] Building distributable executable Scott Brozell (Wed May 17 2017 - 11:20:26 PDT)
    - Re: [AMBER] Building distributable executable Daniel Roe (Wed May 17 2017 - 11:49:49 PDT)
    - Re: [AMBER] Building distributable executable D'Auria, Raffaella (Wed May 17 2017 - 18:05:47 PDT)
    - Re: [AMBER] Building distributable executable Scott Brozell (Wed May 17 2017 - 18:40:22 PDT)
- Re: [AMBER] Building distributable executable Scott Brozell (Thu May 18 2017 - 12:07:07 PDT)
[AMBER] addions doubt Mary Varughese (Wed May 17 2017 - 00:05:22 PDT)
- Re: [AMBER] addions doubt Bill Ross (Wed May 17 2017 - 01:13:54 PDT)
[AMBER] resp charges Jacopo Sgrignani (Wed May 17 2017 - 01:11:21 PDT)
- Re: [AMBER] resp charges Alessandro Contini (Wed May 17 2017 - 01:27:19 PDT)
  - Re: [AMBER] resp charges Andrea Spitaleri (Wed May 17 2017 - 01:50:22 PDT)
    - Re: [AMBER] resp charges David Cerutti (Wed May 17 2017 - 02:58:48 PDT)
- Re: [AMBER] resp charges Artem Shekhovtsov (Wed May 17 2017 - 01:34:05 PDT)
- Re: [AMBER] resp charges Jones de Andrade (Wed May 17 2017 - 06:01:45 PDT)
- Re: [AMBER] resp charges FyD (Thu May 18 2017 - 04:50:46 PDT)
[AMBER] Statistically estimating the error and data reliability for Jarzynski Method Ramin Salimi (Wed May 17 2017 - 01:24:54 PDT)
- Re: [AMBER] Statistically estimating the error and data reliability for Jarzynski Method Hannes Loeffler (Wed May 17 2017 - 01:52:54 PDT)
  - Re: [AMBER] Statistically estimating the error and data reliability for Jarzynski Method Ramin Salimi (Wed May 17 2017 - 02:00:54 PDT)
    - Re: [AMBER] Statistically estimating the error and data reliability for Jarzynski Method Hannes Loeffler (Wed May 17 2017 - 02:12:44 PDT)
    - Re: [AMBER] Statistically estimating the error and data reliability for Jarzynski Method Ramin Salimi (Wed May 17 2017 - 10:21:41 PDT)
    - Re: [AMBER] Statistically estimating the error and data reliability for Jarzynski Method Adrian Roitberg (Wed May 17 2017 - 10:30:22 PDT)
    - Re: [AMBER] Statistically estimating the error and data reliability for Jarzynski Method Ramin Salimi (Wed May 17 2017 - 10:50:16 PDT)
    - [AMBER] Statistically estimating the error and data reliability for Jarzynski Method Ramin Salimi (Wed May 17 2017 - 13:26:41 PDT)
    - Re: [AMBER] Statistically estimating the error and data reliability for Jarzynski Method Hannes Loeffler (Thu May 18 2017 - 00:40:15 PDT)
[AMBER] Problem with parmed Qinghua Liao (Wed May 17 2017 - 03:00:42 PDT)
- Re: [AMBER] Problem with parmed Hannes Loeffler (Wed May 17 2017 - 03:08:37 PDT)
  - Re: [AMBER] Problem with parmed Qinghua Liao (Wed May 17 2017 - 03:16:54 PDT)
- Re: [AMBER] Problem with parmed Jason Swails (Wed May 17 2017 - 04:17:00 PDT)
  - Re: [AMBER] Problem with parmed Qinghua Liao (Wed May 17 2017 - 04:23:59 PDT)
[AMBER] early bird deadline extended Thomas Exner (Wed May 17 2017 - 08:56:52 PDT)
[AMBER] Doubt about EVB/LES-PIMD Stregone (Wed May 17 2017 - 11:06:07 PDT)
- Re: [AMBER] Doubt about EVB/LES-PIMD David A Case (Thu May 18 2017 - 06:30:40 PDT)
[AMBER] understanding results Carlos Romero (Wed May 17 2017 - 11:46:28 PDT)
- Re: [AMBER] understanding results David A Case (Thu May 18 2017 - 06:35:19 PDT)
  - Re: [AMBER] understanding results Carlos Romero (Thu May 18 2017 - 20:06:38 PDT)
[AMBER] Implicit solvation method giving the error number of triangulated 3-point waters found: 0 Ramin Salimi (Wed May 17 2017 - 12:51:28 PDT)
- Re: [AMBER] Implicit solvation method giving the error number of triangulated 3-point waters found: 0 Adrian Roitberg (Wed May 17 2017 - 12:53:28 PDT)
  - Re: [AMBER] Implicit solvation method giving the error number of triangulated 3-point waters found: 0 Ramin Salimi (Wed May 17 2017 - 13:25:19 PDT)
    - Re: [AMBER] Implicit solvation method giving the error number of triangulated 3-point waters found: 0 David Case (Wed May 17 2017 - 18:14:31 PDT)
- Re: [AMBER] Implicit solvation method giving the error number of triangulated 3-point waters found: 0 David Case (Wed May 17 2017 - 18:17:40 PDT)
[AMBER] [Amber16]"cudaMemcpyToSymbol: SetSim copy to cSim failed invalid device symbol" 冯国强 (Wed May 17 2017 - 23:18:10 PDT)
[AMBER] [Amber16]"cudaMemcpyToSymbol: SetSim copy to cSim failed invalid device symbol" 冯国强 (Wed May 17 2017 - 23:23:58 PDT)
- Re: [AMBER] [Amber16]"cudaMemcpyToSymbol: SetSim copy to cSim failed invalid device symbol" Elvis Martis (Thu May 18 2017 - 05:58:15 PDT)
- Re: [AMBER] [Amber16]"cudaMemcpyToSymbol: SetSim copy to cSim failed invalid device symbol" David A Case (Thu May 18 2017 - 06:42:34 PDT)
  - Re: [AMBER] [Amber16]"cudaMemcpyToSymbol: SetSim copy to cSim failed invalid device symbol" Scott Brozell (Thu May 18 2017 - 11:57:11 PDT)
- Re: [AMBER] [Amber16]"cudaMemcpyToSymbol: SetSim copy to cSim failed invalid device symbol" Ross Walker (Thu May 18 2017 - 14:46:15 PDT)
  - Re: [AMBER] [Amber16]"cudaMemcpyToSymbol: SetSim copy to cSim failed invalid device symbol" Scott Le Grand (Thu May 18 2017 - 15:16:01 PDT)
[AMBER] reference or custom GPUs? Hadházi Ádám (Thu May 18 2017 - 03:00:57 PDT)
- Re: [AMBER] reference or custom GPUs? Ross Walker (Thu May 18 2017 - 14:50:10 PDT)
  - Re: [AMBER] reference or custom GPUs? Scott Le Grand (Thu May 18 2017 - 15:14:59 PDT)
    - Re: [AMBER] reference or custom GPUs? Ross Walker (Thu May 18 2017 - 17:22:11 PDT)
[AMBER] Could not find vdW (or other) parameters for type: Na+ Michael Shokhen (Thu May 18 2017 - 04:13:40 PDT)
- Re: [AMBER] Could not find vdW (or other) parameters for type: Na+ Elvis Martis (Thu May 18 2017 - 05:56:25 PDT)
- Re: [AMBER] Could not find vdW (or other) parameters for type: Na+ David A Case (Thu May 18 2017 - 06:51:14 PDT)
[AMBER] phosaa10 reference Jacopo Sgrignani (Thu May 18 2017 - 07:30:39 PDT)
- Re: [AMBER] phosaa10 reference David A Case (Thu May 18 2017 - 08:06:13 PDT)
[AMBER] possible bug for reading &qmmm after &lmod liu junjun (Thu May 18 2017 - 09:00:01 PDT)
- Re: [AMBER] possible bug for reading &qmmm after &lmod Scott Brozell (Thu May 18 2017 - 11:34:07 PDT)
- Re: [AMBER] possible bug for reading &qmmm after &lmod David Case (Mon May 29 2017 - 12:34:07 PDT)
[AMBER] cpptraj nastruct local helical vectors? Kenneth Huang (Thu May 18 2017 - 12:03:55 PDT)
- Re: [AMBER] cpptraj nastruct local helical vectors? Daniel Roe (Fri May 19 2017 - 08:33:55 PDT)
[AMBER] Help with PB simulations using MPI Jake (Thu May 18 2017 - 12:34:54 PDT)
- Re: [AMBER] Help with PB simulations using MPI Ray Luo (Thu May 18 2017 - 14:11:25 PDT)
[AMBER] Amber Error Jerrano Bowleg (Thu May 18 2017 - 12:48:22 PDT)
- Re: [AMBER] Amber Error Bill Ross (Thu May 18 2017 - 13:00:19 PDT)
- Re: [AMBER] Amber Error David Case (Thu May 18 2017 - 19:00:52 PDT)
[AMBER] Unstable umbrella simulation with Amber16 in GTX1080 kurisaki (Thu May 18 2017 - 15:41:03 PDT)
- Re: [AMBER] Unstable umbrella simulation with Amber16 in GTX1080 David Case (Sun May 21 2017 - 16:31:08 PDT)
[AMBER] How to use Amber GAFF force field for methylated DNA MINGREN SHEN (Thu May 18 2017 - 20:03:15 PDT)
- Re: [AMBER] How to use Amber GAFF force field for methylated DNA Hannes Loeffler (Fri May 19 2017 - 00:36:15 PDT)
[AMBER] calculation of the binding energy in amber 12 or 14 Saikat Pal (Thu May 18 2017 - 22:33:30 PDT)
- Re: [AMBER] calculation of the binding energy in amber 12 or 14 David A Case (Sat May 20 2017 - 06:26:27 PDT)
  - Re: [AMBER] calculation of the binding energy in amber 12 or 14 Saikat Pal (Tue May 23 2017 - 22:09:30 PDT)
    - Re: [AMBER] calculation of the binding energy in amber 12 or 14 David Case (Thu May 25 2017 - 10:28:42 PDT)
[AMBER] GAFF parameters in amber16 and amber14 Meiting Wang (Fri May 19 2017 - 00:14:19 PDT)
- Re: [AMBER] GAFF parameters in amber16 and amber14 Hannes Loeffler (Fri May 19 2017 - 00:21:17 PDT)
[AMBER] Input case causing NaN in sander (and possibly pmemd) (Ambertools17) Åke Sandgren (Fri May 19 2017 - 00:32:43 PDT)
- Re: [AMBER] Input case causing NaN in sander (and possibly pmemd) (Ambertools17) David Case (Mon May 29 2017 - 12:43:31 PDT)
  - Re: [AMBER] Input case causing NaN in sander (and possibly pmemd) (Ambertools17) Åke Sandgren (Mon May 29 2017 - 13:18:48 PDT)
    - Re: [AMBER] Input case causing NaN in sander (and possibly pmemd) (Ambertools17) David Case (Mon May 29 2017 - 16:32:38 PDT)
[AMBER] mdgx configuration sampling CA gmail (Fri May 19 2017 - 04:55:05 PDT)
- Re: [AMBER] mdgx configuration sampling David Cerutti (Fri May 19 2017 - 08:33:34 PDT)
  - Re: [AMBER] mdgx configuration sampling David Cerutti (Fri May 19 2017 - 10:23:13 PDT)
    - Re: [AMBER] mdgx configuration sampling CA gmail (Mon May 22 2017 - 00:36:22 PDT)
[AMBER] Distance based mask and reference Marion, Antoine (Fri May 19 2017 - 09:15:21 PDT)
- Re: [AMBER] Distance based mask and reference David Case (Sat May 20 2017 - 06:19:52 PDT)
  - Re: [AMBER] Distance based mask and reference Marion, Antoine (Sat May 20 2017 - 06:44:48 PDT)
[AMBER] A9 tutorial analyse.sh problem Robert Wohlhueter (Fri May 19 2017 - 17:37:18 PDT)
- Re: [AMBER] A9 tutorial analyse.sh problem Hai Nguyen (Fri May 19 2017 - 17:58:45 PDT)
  - Re: [AMBER] A9 tutorial analyse.sh problem Hai Nguyen (Fri May 19 2017 - 18:05:47 PDT)
  - Re: [AMBER] A9 tutorial analyse.sh problem David Case (Sat May 20 2017 - 06:31:19 PDT)
    - Re: [AMBER] A9 tutorial analyse.sh problem Robert Wohlhueter (Sat May 20 2017 - 09:06:58 PDT)
    - Re: [AMBER-Developers] [AMBER] A9 tutorial analyse.sh problem David Case (Sat May 20 2017 - 21:38:52 PDT)
    - Re: [AMBER] A9 tutorial analyse.sh problem Robert Wohlhueter (Sun May 21 2017 - 08:40:55 PDT)
[AMBER] NetCDF error: Invalid argument xu qingliang (Sat May 20 2017 - 06:03:18 PDT)
- Re: [AMBER] NetCDF error: Invalid argument David Case (Sat May 20 2017 - 21:45:58 PDT)
[AMBER] Unable to view the box coordinates in VMD Ramin Salimi (Sun May 21 2017 - 10:55:32 PDT)
- Re: [AMBER] Unable to view the box coordinates in VMD David Case (Sun May 21 2017 - 16:23:54 PDT)
  - Re: [AMBER] Unable to view the box coordinates in VMD Ramin Salimi (Sun May 21 2017 - 22:51:55 PDT)
    - Re: [AMBER] Unable to view the box coordinates in VMD David Case (Mon May 22 2017 - 06:06:28 PDT)
    - Re: [AMBER] Unable to view the box coordinates in VMD Ramin Salimi (Mon May 22 2017 - 08:35:12 PDT)
[AMBER] NetCDF error: Invalid argument xu qingliang (Sun May 21 2017 - 23:28:03 PDT)
- Re: [AMBER] NetCDF error: Invalid argument Daniel Roe (Mon May 22 2017 - 07:17:27 PDT)
- Re: [AMBER] NetCDF error: Invalid argument David Case (Mon May 22 2017 - 21:20:22 PDT)
[AMBER] Minimisation of a complex Nikita Devnarain (Mon May 22 2017 - 00:54:09 PDT)
- Re: [AMBER] Minimisation of a complex Bill Ross (Mon May 22 2017 - 01:12:00 PDT)
  - Re: [AMBER] Minimisation of a complex Nikita Devnarain (Mon May 22 2017 - 01:19:04 PDT)
    - Re: [AMBER] Minimisation of a complex Bill Ross (Mon May 22 2017 - 01:27:23 PDT)
    - Re: [AMBER] Minimisation of a complex Nikita Devnarain (Mon May 22 2017 - 01:34:07 PDT)
[AMBER] Wrong Quotation marks in Manual in several examplecodes Johannes Kalliauer (Mon May 22 2017 - 01:59:09 PDT)
- Re: [AMBER] Wrong Quotation marks in Manual in several examplecodes Hai Nguyen (Tue May 23 2017 - 21:06:28 PDT)
[AMBER] Regarding Native Contacts Suchetana Gupta (Mon May 22 2017 - 03:28:01 PDT)
- Re: [AMBER] Regarding Native Contacts Daniel Roe (Mon May 22 2017 - 07:12:01 PDT)
[AMBER] Which Linux distro for Amber16? Hadházi Ádám (Mon May 22 2017 - 05:00:20 PDT)
- Re: [AMBER] Which Linux distro for Amber16? Hai Nguyen (Tue May 23 2017 - 20:57:18 PDT)
- Re: [AMBER] Which Linux distro for Amber16? Jason Swails (Tue May 23 2017 - 21:28:19 PDT)
  - Re: [AMBER] Which Linux distro for Amber16? Bill Ross (Tue May 23 2017 - 21:33:47 PDT)
[AMBER] MD Simulation of chemical complex ruqaiya khalil (Mon May 22 2017 - 06:18:15 PDT)
- Re: [AMBER] MD Simulation of chemical complex David Case (Thu May 25 2017 - 10:31:59 PDT)
Re: [AMBER] AMBER Digest, Vol 1932, Issue 1 Garima Singh (Tue May 23 2017 - 00:17:18 PDT)
- Re: [AMBER] AMBER Digest, Vol 1932, Issue 1 Elvis Martis (Tue May 23 2017 - 01:27:02 PDT)
- Re: [AMBER] AMBER Digest, Vol 1932, Issue 1 Garima Singh (Tue Jun 06 2017 - 01:54:36 PDT)
  - Re: [AMBER] AMBER Digest, Vol 1932, Issue 1 Elvis Martis (Tue Jun 06 2017 - 02:43:21 PDT)
[AMBER] Virial and Kinetic energy Iain Bethune (Tue May 23 2017 - 03:47:10 PDT)
[AMBER] .prmtop file not saved Shafaq Muzammal (Tue May 23 2017 - 05:33:51 PDT)
- Re: [AMBER] .prmtop file not saved David Case (Tue May 23 2017 - 20:34:18 PDT)
  - Re: [AMBER] .prmtop file not saved Shafaq Muzammal (Tue May 30 2017 - 01:40:28 PDT)
[AMBER] Installation of AMBER 16 Vidhya Srivatsan (Tue May 23 2017 - 06:26:15 PDT)
- Re: [AMBER] Installation of AMBER 16 Nhai (Tue May 23 2017 - 06:37:06 PDT)
- Re: [AMBER] Installation of AMBER 16 Hai Nguyen (Tue May 23 2017 - 07:01:39 PDT)
[AMBER] Libgfortran error during amber tools install Van Rompaey Dries (Tue May 23 2017 - 10:57:43 PDT)
- Re: [AMBER] Libgfortran error during amber tools install Hai Nguyen (Tue May 23 2017 - 15:24:41 PDT)
- Re: [AMBER] Libgfortran error during amber tools install David Case (Tue May 23 2017 - 20:41:10 PDT)
  - Re: [AMBER] Libgfortran error during amber tools install Hai Nguyen (Tue May 23 2017 - 20:52:19 PDT)
[AMBER] . Re: NetCDF error: Invalid argument (David Case) xu qingliang (Wed May 24 2017 - 01:39:17 PDT)
- Re: [AMBER] . Re: NetCDF error: Invalid argument (David Case) David Case (Wed May 24 2017 - 17:26:42 PDT)
[AMBER] Translate the center of mass of the protein to the origin (0, 0, 0) Meng Wu (Wed May 24 2017 - 02:47:27 PDT)
- Re: [AMBER] Translate the center of mass of the protein to the origin (0, 0, 0) Daniel Roe (Wed May 24 2017 - 06:23:32 PDT)
[AMBER] Error while upgrading to AmberTools 17 Chetna Tyagi (Wed May 24 2017 - 03:29:51 PDT)
- Re: [AMBER] Error while upgrading to AmberTools 17 Hai Nguyen (Wed May 24 2017 - 06:03:55 PDT)
  - Re: [AMBER] Error while upgrading to AmberTools 17 Chetna Tyagi (Thu May 25 2017 - 04:15:11 PDT)
    - Re: [AMBER] Error while upgrading to AmberTools 17 Hai Nguyen (Thu May 25 2017 - 05:56:30 PDT)
[AMBER] finding number of atoms within a radius Debodyuti Dutta (Wed May 24 2017 - 04:45:20 PDT)
- Re: [AMBER] finding number of atoms within a radius Elvis Martis (Wed May 24 2017 - 05:54:34 PDT)
[AMBER] Reg residue selection in trajectory Vidhya Srivatsan (Wed May 24 2017 - 11:07:12 PDT)
- Re: [AMBER] Reg residue selection in trajectory Irfan Alibay (Wed May 24 2017 - 11:34:17 PDT)
  - Re: [AMBER] Reg residue selection in trajectory Vidhya Srivatsan (Wed May 24 2017 - 12:08:24 PDT)
[AMBER] AMBER error Neha Gandhi (Wed May 24 2017 - 20:28:10 PDT)
- Re: [AMBER] AMBER error Bill Ross (Wed May 24 2017 - 21:01:42 PDT)
- Re: [AMBER] AMBER error David Case (Thu May 25 2017 - 07:54:44 PDT)
  - Re: [AMBER] AMBER error Neha Gandhi (Thu May 25 2017 - 17:11:20 PDT)
[AMBER] amino-cyclopropyl parameters Loris Moretti (Fri May 26 2017 - 00:32:30 PDT)
- Re: [AMBER] amino-cyclopropyl parameters Thakur, Abhishek (Fri May 26 2017 - 06:00:04 PDT)
  - Re: [AMBER] amino-cyclopropyl parameters Loris Moretti (Tue May 30 2017 - 05:39:51 PDT)
    - Re: [AMBER] amino-cyclopropyl parameters David A Case (Tue May 30 2017 - 06:52:05 PDT)
    - Re: [AMBER] amino-cyclopropyl parameters Loris Moretti (Wed May 31 2017 - 00:32:48 PDT)
    - Re: [AMBER] amino-cyclopropyl parameters David A Case (Wed May 31 2017 - 05:20:21 PDT)
- Re: [AMBER] amino-cyclopropyl parameters Loris Moretti (Thu Jun 01 2017 - 00:37:05 PDT)
- Re: [AMBER] amino-cyclopropyl parameters Loris Moretti (Thu Jun 01 2017 - 06:07:48 PDT)
[AMBER] add ligand parameters Loris Moretti (Fri May 26 2017 - 01:45:01 PDT)
- Re: [AMBER] add ligand parameters Bill Ross (Fri May 26 2017 - 01:50:10 PDT)
  - Re: [AMBER] add ligand parameters Loris Moretti (Fri May 26 2017 - 03:19:32 PDT)
    - Re: [AMBER] add ligand parameters Bill Ross (Fri May 26 2017 - 03:37:43 PDT)
    - Re: [AMBER] add ligand parameters Brent Krueger (Fri May 26 2017 - 04:04:53 PDT)
    - Re: [AMBER] add ligand parameters Loris Moretti (Tue May 30 2017 - 05:39:59 PDT)
[AMBER] cpptraj GIST Gabriel Jara (Fri May 26 2017 - 10:49:54 PDT)
- Re: [AMBER] cpptraj GIST Daniel Roe (Fri May 26 2017 - 10:54:29 PDT)
  - Re: [AMBER] cpptraj GIST Tom Kurtzman (Wed May 31 2017 - 05:52:27 PDT)
[AMBER] random coil in the protein secondary structure analysis leila karami (Sat May 27 2017 - 09:04:03 PDT)
- Re: [AMBER] random coil in the protein secondary structure analysis Daniel Roe (Tue May 30 2017 - 07:06:22 PDT)
[AMBER] Question about RMSD "jumps" Ly, Thu Ngoc Anh (Sat May 27 2017 - 16:26:55 PDT)
- Re: [AMBER] Question about RMSD "jumps" Bill Ross (Sat May 27 2017 - 17:48:05 PDT)
[AMBER] Spherical flat bottom restraint M. Wong (Sat May 27 2017 - 20:41:16 PDT)
- Re: [AMBER] Spherical flat bottom restraint David Case (Sun May 28 2017 - 09:02:45 PDT)
[AMBER] Fwd: Error while preparing docked complex for minimization NADIA RAHMAH (Sun May 28 2017 - 03:59:59 PDT)
- Re: [AMBER] Fwd: Error while preparing docked complex for minimization Elvis Martis (Sun May 28 2017 - 04:40:29 PDT)
- Re: [AMBER] Fwd: Error while preparing docked complex for minimization David Case (Sun May 28 2017 - 09:09:10 PDT)
  - Re: [AMBER] Fwd: Error while preparing docked complex for minimization NADIA RAHMAH (Mon May 29 2017 - 16:03:23 PDT)
- Re: [AMBER] Fwd: Error while preparing docked complex for minimization Bill Ross (Sun May 28 2017 - 13:53:17 PDT)
[AMBER] MMGBSA energy decomposition per frame Thomas Evangelidis (Sun May 28 2017 - 06:29:19 PDT)
- Re: [AMBER] MMGBSA energy decomposition per frame Jason Swails (Tue May 30 2017 - 07:47:17 PDT)
[AMBER] Water Geometry in SPCBOX Inconsistent with Literatures Changhao Wang (Mon May 29 2017 - 00:30:23 PDT)
- Re: [AMBER] Water Geometry in SPCBOX Inconsistent with Literatures David Cerutti (Mon May 29 2017 - 01:24:54 PDT)
  - Re: [AMBER] Water Geometry in SPCBOX Inconsistent with Literatures Chris Moth (Tue May 30 2017 - 09:57:04 PDT)
[AMBER] RESP charge for protonated cytosine ribonucleotide xuzhh (Mon May 29 2017 - 03:42:02 PDT)
- Re: [AMBER] RESP charge for protonated cytosine ribonucleotide David Case (Mon May 29 2017 - 12:46:34 PDT)
[AMBER] KeyError: 'A' (MCPB.py) Sushi Shilpa (Mon May 29 2017 - 05:35:33 PDT)
- Re: [AMBER] KeyError: 'A' (MCPB.py) Pengfei Li (Tue May 30 2017 - 10:09:52 PDT)
  - Re: [AMBER] KeyError: 'A' (MCPB.py) Sushi Shilpa (Tue May 30 2017 - 21:15:34 PDT)
    - Re: [AMBER] KeyError: 'A' (MCPB.py) Pengfei Li (Wed May 31 2017 - 14:58:21 PDT)
[AMBER] Dummy atoms when running antechamber in B4 (sustiva) tutorial Nikolay N. Kuzmich (Mon May 29 2017 - 06:08:32 PDT)
- Re: [AMBER] Dummy atoms when running antechamber in B4 (sustiva) tutorial David Case (Mon May 29 2017 - 09:17:56 PDT)
- Re: [AMBER] Dummy atoms when running antechamber in B4 (sustiva) tutorial Nikolay N. Kuzmich (Wed May 31 2017 - 04:43:20 PDT)
  - Re: [AMBER] Dummy atoms when running antechamber in B4 (sustiva) tutorial David A Case (Wed May 31 2017 - 05:15:22 PDT)
- Re: [AMBER] Dummy atoms when running antechamber in B4 (sustiva) tutorial Nikolay N. Kuzmich (Thu Jun 01 2017 - 09:50:28 PDT)
  - Re: [AMBER] Dummy atoms when running antechamber in B4 (sustiva) tutorial Bill Ross (Thu Jun 01 2017 - 10:09:24 PDT)
  - Re: [AMBER] Dummy atoms when running antechamber in B4 (sustiva) tutorial David A Case (Thu Jun 01 2017 - 12:23:22 PDT)
[AMBER] Wrong quotation marks in manual David Case (Mon May 29 2017 - 09:07:50 PDT)
[AMBER] fcc_metals.lib not found Sohag Biswas (Mon May 29 2017 - 21:24:47 PDT)
- Re: [AMBER] fcc_metals.lib not found Pengfei Li (Tue May 30 2017 - 10:40:09 PDT)
[AMBER] No Torsion terms sylvester kisembo (Tue May 30 2017 - 06:15:39 PDT)
- Re: [AMBER] No Torsion terms Elvis Martis (Tue May 30 2017 - 06:26:07 PDT)
  - Re: [AMBER] No Torsion terms Chris Moth (Thu Jun 01 2017 - 08:46:19 PDT)
[AMBER] external electric field in Amber 16 michal biler (Tue May 30 2017 - 07:39:20 PDT)
- Re: [AMBER] external electric field in Amber 16 Carlos Simmerling (Tue May 30 2017 - 07:43:23 PDT)
- Re: [AMBER] external electric field in Amber 16 michal biler (Tue May 30 2017 - 14:06:04 PDT)
  - Re: [AMBER] external electric field in Amber 16 Bill Ross (Tue May 30 2017 - 14:46:57 PDT)
- Re: [AMBER] external electric field in Amber 16 michal biler (Wed May 31 2017 - 14:22:24 PDT)
  - Re: [AMBER] external electric field in Amber 16 Bill Ross (Wed May 31 2017 - 17:00:06 PDT)
    - Re: [AMBER] external electric field in Amber 16 Charles Lin (Wed May 31 2017 - 19:02:47 PDT)
    - Re: [AMBER] external electric field in Amber 16 David A Case (Thu Jun 01 2017 - 06:16:12 PDT)
[AMBER] Citation for frcmod.parmbsc0, frcmod.ionsjc_tip3p Ramin Salimi (Tue May 30 2017 - 17:33:58 PDT)
- Re: [AMBER] Citation for frcmod.parmbsc0, frcmod.ionsjc_tip3p Saeed Izadi (Tue May 30 2017 - 18:12:58 PDT)
- Re: [AMBER] Citation for frcmod.parmbsc0, frcmod.ionsjc_tip3p David A Case (Wed May 31 2017 - 05:25:43 PDT)
  - Re: [AMBER] Citation for frcmod.parmbsc0, frcmod.ionsjc_tip3p Ramin Salimi (Wed May 31 2017 - 05:41:36 PDT)
[AMBER] Antechamber can't transform Gaussian output file into *.mol2 Nikolay N. Kuzmich (Wed May 31 2017 - 05:06:28 PDT)
- Re: [AMBER] Antechamber can't transform Gaussian output file into *.mol2 Bill Ross (Wed May 31 2017 - 05:09:59 PDT)
  - Re: [AMBER] Antechamber can't transform Gaussian output file into *.mol2 Scott Brozell (Wed May 31 2017 - 11:24:36 PDT)
[AMBER] High pressure fluctuation in isothermal-isobaric ensemble Ramin Salimi (Wed May 31 2017 - 09:12:03 PDT)
- Re: [AMBER] High pressure fluctuation in isothermal-isobaric ensemble Daniel Roe (Wed May 31 2017 - 12:09:44 PDT)
  - Re: [AMBER] High pressure fluctuation in isothermal-isobaric ensemble Ramin Salimi (Thu Jun 01 2017 - 07:36:39 PDT)
    - Re: [AMBER] High pressure fluctuation in isothermal-isobaric ensemble Irfan Alibay (Thu Jun 01 2017 - 11:05:18 PDT)
[AMBER] Input case causing NaN in sander David Case (Wed May 31 2017 - 19:10:34 PDT)
[AMBER] Error during the installion Jeyaram R A (Thu Jun 01 2017 - 05:25:29 PDT)
- Re: [AMBER] Error during the installion Daniel Roe (Thu Jun 01 2017 - 05:44:52 PDT)
  - Re: [AMBER] Error during the installion Jeyaram R A (Thu Jun 01 2017 - 06:05:23 PDT)
    - Re: [AMBER] Error during the installion Daniel Roe (Thu Jun 01 2017 - 06:05:01 PDT)
- Re: [AMBER] Error during the installion David A Case (Thu Jun 01 2017 - 06:34:02 PDT)
Re: [AMBER] Questions about special periodic boundary conditions. Bill Ross (Thu Jun 01 2017 - 10:11:21 PDT)
[AMBER] TI free energy calculation errors Sumudu Leelananda (Thu Jun 01 2017 - 11:16:38 PDT)
- Re: [AMBER] TI free energy calculation errors Hannes Loeffler (Thu Jun 01 2017 - 11:56:00 PDT)
  - Re: [AMBER] TI free energy calculation errors Sumudu Leelananda (Thu Jun 01 2017 - 12:22:53 PDT)
    - Re: [AMBER] TI free energy calculation errors Hannes Loeffler (Fri Jun 02 2017 - 00:19:54 PDT)
    - Re: [AMBER] TI free energy calculation errors Sumudu Leelananda (Wed Jun 28 2017 - 09:18:26 PDT)
    - Re: [AMBER] TI free energy calculation errors Sumudu Leelananda (Wed Jun 28 2017 - 12:05:13 PDT)
    - Re: [AMBER] TI free energy calculation errors Bill Ross (Wed Jun 28 2017 - 12:08:37 PDT)
    - Re: [AMBER] TI free energy calculation errors Sumudu Leelananda (Wed Jun 28 2017 - 12:29:38 PDT)
    - Re: [AMBER] TI free energy calculation errors Bill Ross (Wed Jun 28 2017 - 12:43:20 PDT)
    - Re: [AMBER] TI free energy calculation errors Sumudu Leelananda (Wed Jun 28 2017 - 12:47:04 PDT)
    - Re: [AMBER] TI free energy calculation errors Bill Ross (Wed Jun 28 2017 - 12:51:35 PDT)
    - Re: [AMBER] TI free energy calculation errors Sumudu Leelananda (Wed Jun 28 2017 - 12:53:32 PDT)
    - Re: [AMBER] TI free energy calculation errors Bill Ross (Wed Jun 28 2017 - 12:58:33 PDT)
    - Re: [AMBER] TI free energy calculation errors Scott Brozell (Thu Jun 29 2017 - 20:03:35 PDT)
[AMBER] TI MD simulation Sowmya Indrakumar (Fri Jun 02 2017 - 03:24:48 PDT)
- Re: [AMBER] TI MD simulation Hannes Loeffler (Fri Jun 02 2017 - 03:35:51 PDT)
  - Re: [AMBER] TI MD simulation Sowmya Indrakumar (Fri Jun 02 2017 - 03:57:33 PDT)
    - Re: [AMBER] TI MD simulation Hannes Loeffler (Fri Jun 02 2017 - 04:14:00 PDT)
    - Re: [AMBER] TI MD simulation Markowska (Fri Jun 02 2017 - 04:25:15 PDT)
    - Re: [AMBER] TI MD simulation Sowmya Indrakumar (Fri Jun 02 2017 - 05:28:15 PDT)
[AMBER] center of mass of Guanine Saikat Pal (Fri Jun 02 2017 - 05:25:42 PDT)
- Re: [AMBER] center of mass of Guanine Pratul K. Agarwal (Fri Jun 02 2017 - 06:16:38 PDT)
- Re: [AMBER] center of mass of Guanine Daniel Roe (Fri Jun 02 2017 - 06:33:36 PDT)
[AMBER] Linear energy decrease in the JAC_production_NVE_4fs benchmark on SDSC Comet (GPU) Marat Talipov (Fri Jun 02 2017 - 07:39:48 PDT)
[AMBER] How to set substrate concentration gradient difference acorss membrane Meng Wu (Fri Jun 02 2017 - 21:37:19 PDT)
[AMBER] error in qmmm Ayesha Fatima (Sat Jun 03 2017 - 06:58:44 PDT)
- Re: [AMBER] error in qmmm Goetz, Andreas (Sat Jun 03 2017 - 08:55:43 PDT)
[AMBER] Accelerated MD: How to reweight secondary structure propensities and radial distribution function? Harshavardhan Khare (Sun Jun 04 2017 - 02:29:55 PDT)
[AMBER] accelerated molecular dynamics when iamd=1 or iamd=3 Sonia Ziada (Sun Jun 04 2017 - 08:39:21 PDT)
[AMBER] cuda vs. mpi vs. mpi-cuda Robert Wohlhueter (Sun Jun 04 2017 - 12:17:34 PDT)
- Re: [AMBER] cuda vs. mpi vs. mpi-cuda David Cerutti (Sun Jun 04 2017 - 13:11:13 PDT)
- Re: [AMBER] cuda vs. mpi vs. mpi-cuda Vidhya Srivatsan (Mon Jun 05 2017 - 04:39:15 PDT)
  - Re: [AMBER] cuda vs. mpi vs. mpi-cuda Daniel Roe (Mon Jun 05 2017 - 05:15:31 PDT)
  - Re: [AMBER] cuda vs. mpi vs. mpi-cuda David A Case (Mon Jun 05 2017 - 05:17:57 PDT)
    - Re: [AMBER] cuda vs. mpi vs. mpi-cuda Vidhya Srivatsan (Mon Jun 05 2017 - 06:23:53 PDT)
[AMBER] MMPBSA.py with non-standard residues? Marc van der Kamp (Mon Jun 05 2017 - 07:35:19 PDT)
- Re: [AMBER] MMPBSA.py with non-standard residues? Jason Swails (Wed Jun 07 2017 - 20:55:52 PDT)
  - Re: [AMBER] MMPBSA.py with non-standard residues? Marc van der Kamp (Wed Jun 07 2017 - 23:42:19 PDT)
    - Re: [AMBER] MMPBSA.py with non-standard residues? Marc van der Kamp (Mon Jun 12 2017 - 04:55:07 PDT)
    - Re: [AMBER] MMPBSA.py with non-standard residues? Jason Swails (Wed Jun 14 2017 - 13:05:40 PDT)
Re: [AMBER] AMBER Digest, Vol 1946, Issue 1 Gabriel Jara (Mon Jun 05 2017 - 08:33:43 PDT)
Re: [AMBER] AMBER Digest, Vol 1951, Issue 1 Gabriel Jara (Mon Jun 05 2017 - 11:28:49 PDT)
[AMBER] RMSD Thakur, Abhishek (Mon Jun 05 2017 - 14:19:23 PDT)
- Re: [AMBER] RMSD Carlos Simmerling (Mon Jun 05 2017 - 14:20:51 PDT)
- Re: [AMBER] RMSD Daniel Roe (Tue Jun 06 2017 - 08:07:09 PDT)
[AMBER] set substrate concentration gradient difference acorss membrane Meng Wu (Mon Jun 05 2017 - 18:07:47 PDT)
- Re: [AMBER] set substrate concentration gradient difference acorss membrane Chris Neale (Mon Jun 05 2017 - 20:29:05 PDT)
[AMBER] MD simulation of the whole protein or just its ligand-binding domain Nikolay N. Kuzmich (Tue Jun 06 2017 - 02:02:51 PDT)
- Re: [AMBER] MD simulation of the whole protein or just its ligand-binding domain Billy Williams-Noonan (Tue Jun 06 2017 - 02:39:39 PDT)
- Re: [AMBER] MD simulation of the whole protein or just its ligand-binding domain Marcos Serrou do Amaral (Tue Jun 06 2017 - 06:45:49 PDT)
- Re: [AMBER] MD simulation of the whole protein or just its ligand-binding domain Nikolay N. Kuzmich (Thu Jun 08 2017 - 08:09:23 PDT)
[AMBER] Weighting factors in multi conformational resp fitting Eiros Zamora, Juan (Tue Jun 06 2017 - 04:05:16 PDT)
- Re: [AMBER] Weighting factors in multi conformational resp fitting Brent Krueger (Tue Jun 06 2017 - 04:57:49 PDT)
  - Re: [AMBER] Weighting factors in multi conformational resp fitting Eiros Zamora, Juan (Tue Jun 06 2017 - 07:05:57 PDT)
[AMBER] average no. of H bond between ligand-solvent. Saman Yousuf ali (Tue Jun 06 2017 - 05:02:31 PDT)
- Re: [AMBER] average no. of H bond between ligand-solvent. Elvis Martis (Tue Jun 06 2017 - 05:16:56 PDT)
- Re: [AMBER] average no. of H bond between ligand-solvent. Daniel Roe (Tue Jun 06 2017 - 05:25:56 PDT)
[AMBER] Calculation of Volume fraction Supriyo Naskar (Tue Jun 06 2017 - 06:12:51 PDT)
- Re: [AMBER] Calculation of Volume fraction David Case (Wed Jun 07 2017 - 09:26:53 PDT)
[AMBER] Center of mass Saikat Pal (Tue Jun 06 2017 - 07:56:22 PDT)
- Re: [AMBER] Center of mass Daniel Roe (Tue Jun 06 2017 - 08:59:22 PDT)
  - Re: [AMBER] Center of mass Saikat Pal (Tue Jun 06 2017 - 21:34:28 PDT)
[AMBER] Regarding empty lig.frcmod file Vishal Nemaysh (Tue Jun 06 2017 - 09:27:45 PDT)
- Re: [AMBER] Regarding empty lig.frcmod file Elvis Martis (Tue Jun 06 2017 - 09:32:04 PDT)
  - Re: [AMBER] Regarding empty lig.frcmod file Vishal Nemaysh (Fri Jun 09 2017 - 00:20:58 PDT)
    - Re: [AMBER] Regarding empty lig.frcmod file Elvis Martis (Fri Jun 09 2017 - 04:30:34 PDT)
    - Re: [AMBER] Regarding empty lig.frcmod file Vishal Nemaysh (Fri Jun 09 2017 - 04:44:51 PDT)
    - Re: [AMBER] Regarding empty lig.frcmod file Elvis Martis (Fri Jun 09 2017 - 05:29:36 PDT)
    - Re: [AMBER] Regarding empty lig.frcmod file Vishal Nemaysh (Fri Jun 09 2017 - 05:45:54 PDT)
    - Re: [AMBER] Regarding empty lig.frcmod file Elvis Martis (Fri Jun 09 2017 - 06:06:38 PDT)
    - Re: [AMBER] Regarding empty lig.frcmod file Vishal Nemaysh (Thu Jun 15 2017 - 10:35:51 PDT)
    - Re: [AMBER] Regarding empty lig.frcmod file Elvis Martis (Thu Jun 15 2017 - 23:55:20 PDT)
    - Re: [AMBER] Regarding empty lig.frcmod file Vishal Nemaysh (Fri Jun 16 2017 - 00:30:55 PDT)
    - Re: [AMBER] Regarding empty lig.frcmod file Elvis Martis (Fri Jun 16 2017 - 02:16:18 PDT)
    - Re: [AMBER] Regarding empty lig.frcmod file Vishal Nemaysh (Fri Jun 16 2017 - 05:44:10 PDT)
    - Re: [AMBER] Regarding empty lig.frcmod file David Case (Fri Jun 16 2017 - 08:08:38 PDT)
    - Re: [AMBER] Regarding empty lig.frcmod file David A Case (Fri Jun 09 2017 - 05:56:23 PDT)
[AMBER] pmemd: posixio...failed Andreas Tosstorff (Tue Jun 06 2017 - 09:49:26 PDT)
- Re: [AMBER] pmemd: posixio...failed Daniel Roe (Tue Jun 06 2017 - 10:14:30 PDT)
  - Re: [AMBER] pmemd: posixio...failed Andreas Tosstorff (Thu Jun 08 2017 - 05:31:04 PDT)
[AMBER] Normal mode entropy calculations for active site residues Manjula Saravanan (Tue Jun 06 2017 - 19:22:01 PDT)
- Re: [AMBER] Normal mode entropy calculations for active site residues Elvis Martis (Tue Jun 06 2017 - 21:18:05 PDT)
- Re: [AMBER] Normal mode entropy calculations for active site residues David A Case (Thu Jun 08 2017 - 05:40:34 PDT)
[AMBER] External electric fields support for GPU and how to set the parameters in mdin files? Jianing Song (Tue Jun 06 2017 - 21:49:45 PDT)
- Re: [AMBER] External electric fields support for GPU and how to set the parameters in mdin files? Charles Lin (Tue Jun 06 2017 - 23:21:35 PDT)
  - Re: [AMBER] External electric fields support for GPU and how to set the parameters in mdin files? Jianing Song (Tue Jun 06 2017 - 23:59:55 PDT)
    - Re: [AMBER] External electric fields support for GPU and how to set the parameters in mdin files? Bill Ross (Wed Jun 07 2017 - 00:02:03 PDT)
[AMBER] Is explicit solvent more accurate than implicit solvent? Dd H (Wed Jun 07 2017 - 01:06:46 PDT)
- Re: [AMBER] Is explicit solvent more accurate than implicit solvent? Bill Ross (Wed Jun 07 2017 - 01:09:55 PDT)
  - Re: [AMBER] Is explicit solvent more accurate than implicit solvent? Dd H (Wed Jun 07 2017 - 01:38:00 PDT)
    - Re: [AMBER] Is explicit solvent more accurate than implicit solvent? diego.soler.uam.es (Wed Jun 07 2017 - 03:00:14 PDT)
    - Re: [AMBER] Is explicit solvent more accurate than implicit solvent? Daniel Roe (Wed Jun 07 2017 - 06:52:09 PDT)
    - Re: [AMBER] Is explicit solvent more accurate than implicit solvent? Robert Molt (Wed Jun 07 2017 - 17:13:12 PDT)
    - Re: [AMBER] Is explicit solvent more accurate than implicit solvent? David Case (Wed Jun 07 2017 - 18:19:03 PDT)
    - Re: [AMBER] Is explicit solvent more accurate than implicit solvent? Dd H (Wed Jun 07 2017 - 19:07:12 PDT)
    - Re: [AMBER] Is explicit solvent more accurate than implicit solvent? Hai Nguyen (Wed Jun 07 2017 - 21:28:39 PDT)
[AMBER] Center of mass Saikat Pal (Wed Jun 07 2017 - 03:51:55 PDT)
- Re: [AMBER] Center of mass Daniel Roe (Wed Jun 07 2017 - 06:39:33 PDT)
  - Re: [AMBER] Center of mass Saikat Pal (Wed Jun 07 2017 - 09:29:22 PDT)
    - Re: [AMBER] Center of mass Daniel Roe (Wed Jun 07 2017 - 09:33:16 PDT)
[AMBER] Velocity autocorrelation ATUL KUMAR (Wed Jun 07 2017 - 04:22:37 PDT)
- Re: [AMBER] Velocity autocorrelation George Giambasu (Wed Jun 07 2017 - 06:13:22 PDT)
  - Re: [AMBER] Velocity autocorrelation Daniel Roe (Wed Jun 07 2017 - 06:35:43 PDT)
    - Re: [AMBER] Velocity autocorrelation ATUL KUMAR (Wed Jun 07 2017 - 09:37:46 PDT)
    - Re: [AMBER] Velocity autocorrelation Adrian Roitberg (Wed Jun 07 2017 - 09:41:54 PDT)
[AMBER] Neutral N-terminal proline in AMBER force field Yue Qian (Wed Jun 07 2017 - 07:48:51 PDT)
[AMBER] TI in dimeric enzyme carmine marco morgillo (Wed Jun 07 2017 - 09:44:00 PDT)
- Re: [AMBER] TI in dimeric enzyme hannes.loeffler.stfc.ac.uk (Thu Jun 08 2017 - 00:30:39 PDT)
[AMBER] Poor performance of REMD simulation MOHD HOMAIDUR RAHMAN (Wed Jun 07 2017 - 13:54:23 PDT)
- Re: [AMBER] Poor performance of REMD simulation Adrian Roitberg (Wed Jun 07 2017 - 13:58:02 PDT)
  - Re: [AMBER] Poor performance of REMD simulation MOHD HOMAIDUR RAHMAN (Wed Jun 07 2017 - 14:43:58 PDT)
    - Re: [AMBER] Poor performance of REMD simulation Thomas Cheatham (Wed Jun 07 2017 - 20:00:55 PDT)
[AMBER] ERROR: nfft1 must be in the range of 6 to 512! Andreas Tosstorff (Thu Jun 08 2017 - 05:38:36 PDT)
- Re: [AMBER] ERROR: nfft1 must be in the range of 6 to 512! David A Case (Thu Jun 08 2017 - 08:15:55 PDT)
[AMBER] PCA analysis Thakur, Abhishek (Thu Jun 08 2017 - 09:52:06 PDT)
- Re: [AMBER] PCA analysis Adrian Roitberg (Thu Jun 08 2017 - 09:55:54 PDT)
  - Re: [AMBER] PCA analysis Thakur, Abhishek (Thu Jun 08 2017 - 11:33:58 PDT)
    - Re: [AMBER] PCA analysis Elvis Martis (Thu Jun 08 2017 - 21:45:58 PDT)
[AMBER] visualizing first mode of motion from PCA analysis in chimera or vmd Thakur, Abhishek (Thu Jun 08 2017 - 14:16:38 PDT)
- Re: [AMBER] visualizing first mode of motion from PCA analysis in chimera or vmd Elvis Martis (Thu Jun 08 2017 - 21:46:55 PDT)
Re: [AMBER] set substrate concentration gradient difference Meng Wu (Thu Jun 08 2017 - 19:26:45 PDT)
[AMBER] SASA calculation Garima Singh (Thu Jun 08 2017 - 22:40:05 PDT)
- Re: [AMBER] SASA calculation Elvis Martis (Fri Jun 09 2017 - 00:04:07 PDT)
- Re: [AMBER] SASA calculation David A Case (Fri Jun 09 2017 - 05:49:26 PDT)
- [AMBER] Fwd: SASA calculation Garima Singh (Mon Jun 12 2017 - 00:07:13 PDT)
  - Re: [AMBER] Fwd: SASA calculation Elvis Martis (Mon Jun 12 2017 - 00:17:05 PDT)
  - Re: [AMBER] Fwd: SASA calculation David Case (Mon Jun 12 2017 - 04:41:43 PDT)
[AMBER] Retrieve amd.log/ gamd.log files Kat G (Fri Jun 09 2017 - 21:00:52 PDT)
- Re: [AMBER] Retrieve amd.log/ gamd.log files Irfan Alibay (Mon Jun 12 2017 - 05:37:04 PDT)
[AMBER] How restart md simulation Mustafa Alhaji Isa (Sat Jun 10 2017 - 03:48:55 PDT)
- Re: [AMBER] How restart md simulation Shafaq Muzammal (Sat Jun 10 2017 - 04:07:43 PDT)
  - Re: [AMBER] How restart md simulation Mustafa Alhaji Isa (Sat Jun 10 2017 - 05:24:47 PDT)
[AMBER] Problem in creating topology and coordinate files Mustafa Alhaji Isa (Sat Jun 10 2017 - 22:49:59 PDT)
- Re: [AMBER] Problem in creating topology and coordinate files Bill Ross (Sat Jun 10 2017 - 22:53:34 PDT)
- Re: [AMBER] Problem in creating topology and coordinate files David Case (Sun Jun 11 2017 - 05:06:47 PDT)
[AMBER] Accelerated MD when iamd=1 or 3 Sonia Ziada (Sun Jun 11 2017 - 02:38:56 PDT)
- [AMBER] Fwd: Accelerated MD when iamd=1 or 3 Sonia Ziada (Mon Jun 12 2017 - 04:45:41 PDT)
  - Re: [AMBER] Fwd: Accelerated MD when iamd=1 or 3 Irfan Alibay (Mon Jun 12 2017 - 05:02:53 PDT)
    - Re: [AMBER] Fwd: Accelerated MD when iamd=1 or 3 Sonia Ziada (Mon Jun 12 2017 - 05:53:01 PDT)
    - Re: [AMBER] Fwd: Accelerated MD when iamd=1 or 3 Irfan Alibay (Mon Jun 12 2017 - 06:31:01 PDT)
    - Re: [AMBER] Fwd: Accelerated MD when iamd=1 or 3 Sonia Ziada (Mon Jun 12 2017 - 07:36:55 PDT)
    - Re: [AMBER] Fwd: Accelerated MD when iamd=1 or 3 Hagrouna sadiki (Mon Jun 12 2017 - 07:42:54 PDT)
    - Re: [AMBER] Fwd: Accelerated MD when iamd=1 or 3 Sonia Ziada (Mon Jun 12 2017 - 08:08:00 PDT)
[AMBER] Split trajectory Shafaq Muzammal (Sun Jun 11 2017 - 05:32:43 PDT)
- Re: [AMBER] Split trajectory Elvis Martis (Sun Jun 11 2017 - 05:48:31 PDT)
  - Re: [AMBER] Split trajectory Shafaq Muzammal (Sun Jun 11 2017 - 09:29:55 PDT)
[AMBER] RNA parameters for wc_helix Supriyo Naskar (Mon Jun 12 2017 - 02:11:53 PDT)
- Re: [AMBER] RNA parameters for wc_helix David Case (Mon Jun 12 2017 - 04:38:53 PDT)
  - Re: [AMBER] RNA parameters for wc_helix Supriyo Naskar (Mon Jun 12 2017 - 07:10:02 PDT)
    - Re: [AMBER] RNA parameters for wc_helix David Case (Mon Jun 12 2017 - 17:12:47 PDT)
    - Re: [AMBER] RNA parameters for wc_helix Supriyo Naskar (Tue Jun 13 2017 - 00:13:25 PDT)
[AMBER] mdgx extracting energies Charles-Alexandre Mattelaer (Mon Jun 12 2017 - 06:36:27 PDT)
- Re: [AMBER] mdgx extracting energies David Cerutti (Mon Jun 12 2017 - 21:23:53 PDT)
  - Re: [AMBER] mdgx extracting energies David Cerutti (Mon Jun 12 2017 - 21:46:32 PDT)
    - Re: [AMBER] mdgx extracting energies Charles-Alexandre Mattelaer (Wed Jun 14 2017 - 07:56:14 PDT)
[AMBER] Formula/reference for ambertools native contact calculations Julio Dominguez (Mon Jun 12 2017 - 09:27:54 PDT)
- Re: [AMBER] Formula/reference for ambertools native contact calculations Daniel Roe (Mon Jun 12 2017 - 10:02:35 PDT)
- Re: [AMBER] Formula/reference for ambertools native contact calculations Julio Dominguez (Tue Jun 13 2017 - 19:26:16 PDT)
[AMBER] inpcrd file format in AmberTools16 Dr. Robert Molt (Mon Jun 12 2017 - 10:45:33 PDT)
- Re: [AMBER] inpcrd file format in AmberTools16 David Case (Mon Jun 12 2017 - 17:28:14 PDT)
- Re: [AMBER] inpcrd file format in AmberTools16 Chris Moth (Tue Jun 13 2017 - 09:55:59 PDT)
Re: [AMBER] Neutral N-terminal proline parameter in AMBER force field David Case (Tue Jun 13 2017 - 07:00:37 PDT)
- Re: [AMBER] Neutral N-terminal proline parameter in AMBER force field Yue Qian (Tue Jun 13 2017 - 07:05:47 PDT)
[AMBER] NFE dihedral Fabrício Bracht (Tue Jun 13 2017 - 13:55:15 PDT)
- Re: [AMBER] NFE dihedral Feng Pan (Tue Jun 13 2017 - 14:48:43 PDT)
  - Re: [AMBER] NFE dihedral Fabrício Bracht (Wed Jun 14 2017 - 08:47:01 PDT)
    - Re: [AMBER] NFE dihedral Feng Pan (Wed Jun 14 2017 - 10:13:23 PDT)
    - Re: [AMBER] NFE dihedral Fabrício Bracht (Wed Jun 14 2017 - 11:36:49 PDT)
    - Re: [AMBER] NFE dihedral Fabrício Bracht (Fri Jun 16 2017 - 16:05:13 PDT)
    - Re: [AMBER] NFE dihedral Feng Pan (Fri Jun 16 2017 - 16:41:19 PDT)
    - Re: [AMBER] NFE dihedral Fabrício Bracht (Sun Jun 18 2017 - 13:47:57 PDT)
    - Re: [AMBER] NFE dihedral Bill Ross (Sun Jun 18 2017 - 15:16:13 PDT)
    - Re: [AMBER] NFE dihedral Feng Pan (Sun Jun 18 2017 - 19:14:26 PDT)
[AMBER] LAMMPS data file to PDB file (off topic) Sushi Shilpa (Tue Jun 13 2017 - 21:29:22 PDT)
- Re: [AMBER] LAMMPS data file to PDB file (off topic) James Kress (Wed Jun 14 2017 - 08:52:24 PDT)
[AMBER] convert .nc trajectories to .xyz Shafaq Muzammal (Wed Jun 14 2017 - 01:29:15 PDT)
- Re: [AMBER] convert .nc trajectories to .xyz Elvis Martis (Wed Jun 14 2017 - 02:39:34 PDT)
  - Re: [AMBER] convert .nc trajectories to .xyz Shafaq Muzammal (Fri Jun 16 2017 - 08:19:59 PDT)
    - Re: [AMBER] convert .nc trajectories to .xyz Daniel Roe (Mon Jun 19 2017 - 11:10:58 PDT)
    - Re: [AMBER] convert .nc trajectories to .xyz Hai Nguyen (Mon Jun 19 2017 - 12:06:16 PDT)
[AMBER] A conceptual question on MMGBSA binding and RMSF analysis Abhilash J (Wed Jun 14 2017 - 04:42:23 PDT)
- Re: [AMBER] A conceptual question on MMGBSA binding and RMSF analysis Elvis Martis (Wed Jun 14 2017 - 08:25:15 PDT)
  - Re: [AMBER] A conceptual question on MMGBSA binding and RMSF analysis Abhilash J (Wed Jun 14 2017 - 09:08:31 PDT)
    - Re: [AMBER] A conceptual question on MMGBSA binding and RMSF analysis David Case (Thu Jun 15 2017 - 08:08:19 PDT)
[AMBER] Fwd: test serial amber 14 and ambertool15 co nguyentruong (Wed Jun 14 2017 - 07:58:38 PDT)
- Re: [AMBER] Fwd: test serial amber 14 and ambertool15 Elvis Martis (Wed Jun 14 2017 - 08:27:44 PDT)
  - Re: [AMBER] Fwd: test serial amber 14 and ambertool15 co nguyentruong (Wed Jun 14 2017 - 16:02:52 PDT)
- Re: [AMBER] Fwd: test serial amber 14 and ambertool15 Bill Ross (Wed Jun 14 2017 - 10:55:43 PDT)
  - Re: [AMBER] Fwd: test serial amber 14 and ambertool15 co nguyentruong (Wed Jun 14 2017 - 15:55:11 PDT)
    - Re: [AMBER] Fwd: test serial amber 14 and ambertool15 David Case (Thu Jun 15 2017 - 08:13:12 PDT)
[AMBER] deleting water with ParmEd Hector A. Baldoni (Wed Jun 14 2017 - 12:44:36 PDT)
- Re: [AMBER] deleting water with ParmEd Jason Swails (Wed Jun 14 2017 - 13:03:25 PDT)
  - Re: [AMBER] deleting water with ParmEd Hector A. Baldoni (Wed Jun 14 2017 - 13:56:01 PDT)
[AMBER] Warning during minimization Ramin Salimi (Wed Jun 14 2017 - 18:14:57 PDT)
- Re: [AMBER] Warning during minimization Bill Ross (Wed Jun 14 2017 - 18:20:07 PDT)
  - Re: [AMBER] Warning during minimization Ramin Salimi (Wed Jun 14 2017 - 18:28:17 PDT)
    - Re: [AMBER] Warning during minimization Bill Ross (Wed Jun 14 2017 - 18:30:49 PDT)
    - Re: [AMBER] Warning during minimization Ramin Salimi (Wed Jun 14 2017 - 22:20:27 PDT)
    - Re: [AMBER] Warning during minimization Bill Ross (Wed Jun 14 2017 - 23:20:52 PDT)
- Re: [AMBER] Warning during minimization David Case (Thu Jun 15 2017 - 08:01:43 PDT)
  - Re: [AMBER] Warning during minimization Ramin Salimi (Thu Jun 15 2017 - 21:23:25 PDT)
    - Re: [AMBER] Warning during minimization Bill Ross (Thu Jun 15 2017 - 21:27:40 PDT)
[AMBER] problem regarding ACE capping of the protein terminal of the PDB Saikat Pal (Thu Jun 15 2017 - 00:29:46 PDT)
- Re: [AMBER] problem regarding ACE capping of the protein terminal of the PDB Bill Ross (Thu Jun 15 2017 - 01:33:48 PDT)
  - Re: [AMBER] problem regarding ACE capping of the protein terminal of the PDB Saikat Pal (Thu Jun 15 2017 - 03:38:27 PDT)
    - Re: [AMBER] problem regarding ACE capping of the protein terminal of the PDB David Case (Thu Jun 15 2017 - 07:24:14 PDT)
    - Re: [AMBER] problem regarding ACE capping of the protein terminal of the PDB Saikat Pal (Thu Jun 15 2017 - 07:39:33 PDT)
    - Re: [AMBER] problem regarding ACE capping of the protein terminal of the PDB David Case (Thu Jun 15 2017 - 12:34:28 PDT)
    - Re: [AMBER] problem regarding ACE capping of the protein terminal of the PDB Saikat Pal (Fri Jun 16 2017 - 00:04:48 PDT)
    - Re: [AMBER] problem regarding ACE capping of the protein terminal of the PDB David Case (Fri Jun 16 2017 - 07:53:10 PDT)
    - Re: [AMBER] problem regarding ACE capping of the protein terminal of the PDB Andrew Schaub (Wed Jun 21 2017 - 09:35:46 PDT)
[AMBER] Selecting histidine Protonation state for simulation Jag Silwal (Thu Jun 15 2017 - 08:43:53 PDT)
- Re: [AMBER] Selecting histidine Protonation state for simulation Dean Cuebas (Thu Jun 15 2017 - 16:30:36 PDT)
[AMBER] Weired behaviour during Heating Ramin Salimi (Thu Jun 15 2017 - 21:55:02 PDT)
- Re: [AMBER] Weired behaviour during Heating David Case (Fri Jun 16 2017 - 07:26:39 PDT)
  - Re: [AMBER] Weired behaviour during Heating Carlos Simmerling (Fri Jun 16 2017 - 07:31:52 PDT)
    - Re: [AMBER] Weired behaviour during Heating Ramin Salimi (Fri Jun 16 2017 - 10:52:08 PDT)
    - Re: [AMBER] Weired behaviour during Heating Carlos Simmerling (Fri Jun 16 2017 - 11:41:46 PDT)
[AMBER] Ramin Salimi wants to share the file Heat.tar.gz with you Ramin Salimi (Thu Jun 15 2017 - 21:55:14 PDT)
[AMBER] Issue installing Amber16 cuda Alexander Martin Spring-Connell (Fri Jun 16 2017 - 05:05:38 PDT)
- Re: [AMBER] Issue installing Amber16 cuda Dr. M. Shahid (Fri Jun 16 2017 - 06:08:17 PDT)
- Re: [AMBER] Issue installing Amber16 cuda David Case (Fri Jun 16 2017 - 08:00:38 PDT)
  - Re: [AMBER] Issue installing Amber16 cuda Alexander Martin Spring-Connell (Fri Jun 16 2017 - 08:49:09 PDT)
[AMBER] Specific GPU for running pmemd.cuda Krantzman, Kristin D (Fri Jun 16 2017 - 12:48:05 PDT)
- Re: [AMBER] Specific GPU for running pmemd.cuda Jerrano Bowleg (Fri Jun 16 2017 - 13:03:48 PDT)
  - Re: [AMBER] Specific GPU for running pmemd.cuda Krantzman, Kristin D (Fri Jun 16 2017 - 15:05:14 PDT)
- Re: [AMBER] Specific GPU for running pmemd.cuda David Cerutti (Fri Jun 16 2017 - 13:08:31 PDT)
- Re: [AMBER] Specific GPU for running pmemd.cuda Hector A. Baldoni (Fri Jun 16 2017 - 16:52:49 PDT)
[AMBER] relaxation time to maintain quasi-static condition Ramin Salimi (Mon Jun 19 2017 - 18:06:12 PDT)
- Re: [AMBER] relaxation time to maintain quasi-static condition David Case (Tue Jun 20 2017 - 05:28:24 PDT)
  - Re: [AMBER] relaxation time to maintain quasi-static condition Adrian Roitberg (Tue Jun 20 2017 - 05:48:05 PDT)
    - Re: [AMBER] relaxation time to maintain quasi-static condition Ramin Salimi (Tue Jun 20 2017 - 09:40:45 PDT)
    - Re: [AMBER] relaxation time to maintain quasi-static condition Adrian Roitberg (Tue Jun 20 2017 - 11:29:56 PDT)
    - Re: [AMBER] relaxation time to maintain quasi-static condition Ramin Salimi (Tue Jun 20 2017 - 12:15:53 PDT)
[AMBER] Free energy path waleed zalloum (Mon Jun 19 2017 - 18:22:28 PDT)
- Re: [AMBER] Free energy path David A Case (Wed Jun 21 2017 - 06:02:39 PDT)
  - Re: [AMBER] Free energy path Carlos Simmerling (Fri Jun 23 2017 - 06:45:03 PDT)
[AMBER] Duplicate random seeds with ig=-1 Code enhancement to think about, perhaps Chris Moth (Tue Jun 20 2017 - 11:29:41 PDT)
- Re: [AMBER] Duplicate random seeds with ig=-1 Code enhancement to think about, perhaps David Cerutti (Tue Jun 20 2017 - 11:39:52 PDT)
- Re: [AMBER] Duplicate random seeds with ig=-1 Code enhancement to think about, perhaps Adrian Roitberg (Tue Jun 20 2017 - 11:45:43 PDT)
  - Re: [AMBER] Duplicate random seeds with ig=-1 Code enhancement to think about, perhaps Chris Moth (Tue Jun 20 2017 - 12:27:08 PDT)
    - Re: [AMBER] Duplicate random seeds with ig=-1 Code enhancement to think about, perhaps Bill Ross (Tue Jun 20 2017 - 12:34:45 PDT)
    - Re: [AMBER] Duplicate random seeds with ig=-1 Code enhancement to think about, perhaps Adrian Roitberg (Tue Jun 20 2017 - 12:38:41 PDT)
    - Re: [AMBER] Duplicate random seeds with ig=-1 Code enhancement to think about, perhaps David Case (Tue Jun 20 2017 - 13:20:28 PDT)
    - Re: [AMBER] Duplicate random seeds with ig=-1 Code enhancement to think about, perhaps Adrian Roitberg (Tue Jun 20 2017 - 13:30:00 PDT)
    - Re: [AMBER] Duplicate random seeds with ig=-1 Code enhancement to think about, perhaps Bill Ross (Tue Jun 20 2017 - 13:51:50 PDT)
    - Re: [AMBER] Duplicate random seeds with ig=-1 Code enhancement to think about, perhaps Bill Ross (Tue Jun 20 2017 - 13:50:18 PDT)
    - Re: [AMBER] Duplicate random seeds with ig=-1 Code enhancement to think about, perhaps Bill Ross (Tue Jun 20 2017 - 13:55:08 PDT)
    - Re: [AMBER] Duplicate random seeds with ig=-1 Code enhancement to think about, perhaps Bill Ross (Tue Jun 20 2017 - 13:57:37 PDT)
    - Re: [AMBER] Duplicate random seeds with ig=-1 Code enhancement to think about, perhaps Bill Ross (Tue Jun 20 2017 - 16:41:56 PDT)
    - Re: [AMBER] Duplicate random seeds with ig=-1 Code enhancement to think about, perhaps Daniel Roe (Wed Jun 21 2017 - 05:42:11 PDT)
    - Re: [AMBER] Duplicate random seeds with ig=-1 Code enhancement to think about, perhaps Chris Moth (Wed Jun 21 2017 - 14:37:43 PDT)
[AMBER] LEAP Merging Atom Types Govind Hegde (Tue Jun 20 2017 - 14:10:25 PDT)
- Re: [AMBER] LEAP Merging Atom Types Alexander Martin Spring-Connell (Tue Jun 20 2017 - 15:14:09 PDT)
  - Re: [AMBER] LEAP Merging Atom Types Alexander Martin Spring-Connell (Tue Jun 20 2017 - 15:40:06 PDT)
    - Re: [AMBER] LEAP Merging Atom Types Govind Hegde (Wed Jun 21 2017 - 09:12:30 PDT)
    - Re: [AMBER] LEAP Merging Atom Types Bill Ross (Wed Jun 21 2017 - 09:19:28 PDT)
- Re: [AMBER] LEAP Merging Atom Types David A Case (Wed Jun 21 2017 - 05:27:24 PDT)
  - Re: [AMBER] LEAP Merging Atom Types Govind Hegde (Wed Jun 21 2017 - 08:52:56 PDT)
    - Re: [AMBER] LEAP Merging Atom Types David Case (Fri Jun 23 2017 - 07:57:13 PDT)
[AMBER] Hydrogen bond Average distance Jag Silwal (Tue Jun 20 2017 - 19:14:12 PDT)
- Re: [AMBER] Hydrogen bond Average distance Daniel Roe (Wed Jun 21 2017 - 06:23:31 PDT)
  - Re: [AMBER] Hydrogen bond Average distance Hai Nguyen (Thu Jun 22 2017 - 22:22:48 PDT)
[AMBER] Question about ergodicity and MD Andreas Tosstorff (Wed Jun 21 2017 - 02:09:34 PDT)
- Re: [AMBER] Question about ergodicity and MD diego.soler.uam.es (Wed Jun 21 2017 - 04:03:49 PDT)
[AMBER] invoking MPI_ABORT causes Open MPI to kill all MPI processes Maryam Hamzehee (Wed Jun 21 2017 - 02:23:10 PDT)
- Re: [AMBER] invoking MPI_ABORT causes Open MPI to kill all MPI processes Daniel Roe (Wed Jun 21 2017 - 05:33:18 PDT)
- Re: [AMBER] invoking MPI_ABORT causes Open MPI to kill all MPI processes David A Case (Wed Jun 21 2017 - 05:34:49 PDT)
  - Re: [AMBER] invoking MPI_ABORT causes Open MPI to kill all MPI processes Daniel Roe (Wed Jun 21 2017 - 05:38:03 PDT)
[AMBER] "Abort trap 6" error message with tLeap and xLeap Xichong Liu (Wed Jun 21 2017 - 04:36:11 PDT)
- Re: [AMBER] "Abort trap 6" error message with tLeap and xLeap Bill Ross (Wed Jun 21 2017 - 04:54:09 PDT)
- Re: [AMBER] "Abort trap 6" error message with tLeap and xLeap David A Case (Wed Jun 21 2017 - 05:45:24 PDT)
  - Re: [AMBER] "Abort trap 6" error message with tLeap and xLeap Xichong Liu (Wed Jun 21 2017 - 06:53:20 PDT)
    - Re: [AMBER] "Abort trap 6" error message with tLeap and xLeap Hai Nguyen (Wed Jun 21 2017 - 07:37:50 PDT)
    - Re: [AMBER] "Abort trap 6" error message with tLeap and xLeap Xichong Liu (Wed Jun 21 2017 - 13:53:23 PDT)
[AMBER] issue in antechamber17 bcc charges with mopac Alessandro Contini (Wed Jun 21 2017 - 04:48:17 PDT)
- Re: [AMBER] issue in antechamber17 bcc charges with mopac David A Case (Wed Jun 21 2017 - 05:57:37 PDT)
  - Re: [AMBER] issue in antechamber17 bcc charges with mopac Alessandro Contini (Wed Jun 21 2017 - 07:04:11 PDT)
[AMBER] What nVidia driver for GTX 1080TI? Hadházi Ádám (Wed Jun 21 2017 - 06:22:46 PDT)
- Re: [AMBER] What nVidia driver for GTX 1080TI? Gould, Ian R (Wed Jun 21 2017 - 07:01:14 PDT)
[AMBER] " possible FAILURE " messages Núbia Prates (Wed Jun 21 2017 - 06:41:16 PDT)
- Re: [AMBER] " possible FAILURE " messages Daniel Roe (Wed Jun 21 2017 - 06:42:59 PDT)
[AMBER] Leap: Periodic Boundary of DNA Johannes Kalliauer (Wed Jun 21 2017 - 06:44:45 PDT)
- Re: [AMBER] Leap: Periodic Boundary of DNA David Case (Wed Jun 21 2017 - 17:52:43 PDT)
[AMBER] A question about handling constraints/restraints with AMBER Jewgeni Starikow (Wed Jun 21 2017 - 06:51:08 PDT)
[AMBER] convert psf to top of gmx with parmed Qinghua Liao (Wed Jun 21 2017 - 09:42:48 PDT)
- Re: [AMBER] convert psf to top of gmx with parmed Jason Swails (Sun Jun 25 2017 - 12:18:37 PDT)
[AMBER] correlated dihedrals in ff parameterization Bala subramanian (Thu Jun 22 2017 - 01:42:58 PDT)
- Re: [AMBER] correlated dihedrals in ff parameterization Karl Kirschner (Thu Jun 22 2017 - 03:40:20 PDT)
[AMBER] Amber md in HPC : Job terminated Garima Singh (Thu Jun 22 2017 - 03:26:49 PDT)
- Re: [AMBER] Amber md in HPC : Job terminated Elvis Martis (Thu Jun 22 2017 - 04:35:59 PDT)
- Re: [AMBER] Amber md in HPC : Job terminated David A Case (Thu Jun 22 2017 - 05:17:46 PDT)
[AMBER] Problem Imaging atoms of system crossing the PBC box from opposite faces of box at the same time SHAILESH KUMAR (Thu Jun 22 2017 - 06:51:00 PDT)
- Re: [AMBER] Problem Imaging atoms of system crossing the PBC box from opposite faces of box at the same time Daniel Roe (Thu Jun 22 2017 - 08:55:07 PDT)
  - Re: [AMBER] Problem Imaging atoms of system crossing the PBC box from opposite faces of box at the same time SHAILESH KUMAR (Thu Jun 22 2017 - 09:47:41 PDT)
    - Re: [AMBER] Problem Imaging atoms of system crossing the PBC box from opposite faces of box at the same time Daniel Roe (Thu Jun 22 2017 - 12:52:24 PDT)
    - Re: [AMBER] Problem Imaging atoms of system crossing the PBC box from opposite faces of box at the same time SHAILESH KUMAR (Fri Jun 23 2017 - 03:55:27 PDT)
    - Re: [AMBER] Problem Imaging atoms of system crossing the PBC box from opposite faces of box at the same time Daniel Roe (Mon Jun 26 2017 - 09:06:15 PDT)
    - Re: [AMBER] Problem Imaging atoms of system crossing the PBC box from opposite faces of box at the same time Daniel Roe (Wed Jun 28 2017 - 05:45:56 PDT)
    - Re: [AMBER] Problem Imaging atoms of system crossing the PBC box from opposite faces of box at the same time SHAILESH KUMAR (Wed Jun 28 2017 - 11:02:22 PDT)
    - Re: [AMBER] Problem Imaging atoms of system crossing the PBC box from opposite faces of box at the same time SHAILESH KUMAR (Thu Jul 13 2017 - 14:01:47 PDT)
[AMBER] error running mmpbsa giulia palermo (Fri Jun 23 2017 - 13:32:54 PDT)
- Re: [AMBER] error running mmpbsa Elvis Martis (Fri Jun 23 2017 - 18:09:56 PDT)
  - Re: [AMBER] error running mmpbsa Elvis Martis (Fri Jun 23 2017 - 20:43:49 PDT)
    - Re: [AMBER] error running mmpbsa giulia palermo (Sat Jun 24 2017 - 10:56:40 PDT)
    - Re: [AMBER] error running mmpbsa Elvis Martis (Sat Jun 24 2017 - 20:35:48 PDT)
    - Re: [AMBER] error running mmpbsa giulia palermo (Mon Jun 26 2017 - 16:53:59 PDT)
    - Re: [AMBER] error running mmpbsa Elvis Martis (Mon Jun 26 2017 - 18:18:13 PDT)
    - Re: [AMBER] error running mmpbsa giulia palermo (Tue Jun 27 2017 - 10:53:06 PDT)
    - Re: [AMBER] error running mmpbsa Elvis Martis (Tue Jun 27 2017 - 21:25:49 PDT)
    - Re: [AMBER] error running mmpbsa giulia palermo (Thu Jun 29 2017 - 11:50:00 PDT)
    - Re: [AMBER] error running mmpbsa Elvis Martis (Sun Jul 02 2017 - 23:41:39 PDT)
    - Re: [AMBER] error running mmpbsa Daniel Roe (Mon Jun 26 2017 - 05:54:47 PDT)
[AMBER] Problem of running ANTECHAMBER Mustafa Alhaji Isa (Fri Jun 23 2017 - 21:19:30 PDT)
- Re: [AMBER] Problem of running ANTECHAMBER Elvis Martis (Fri Jun 23 2017 - 22:18:53 PDT)
- Re: [AMBER] Problem of running ANTECHAMBER David Case (Sat Jun 24 2017 - 05:46:22 PDT)
[AMBER] problem in creating topology and coordinate files Mustafa Alhaji Isa (Fri Jun 23 2017 - 21:51:35 PDT)
- Re: [AMBER] problem in creating topology and coordinate files Elvis Martis (Fri Jun 23 2017 - 22:17:40 PDT)
[AMBER] Download and installing cpptraj sub-application Mustafa Alhaji Isa (Sat Jun 24 2017 - 03:56:01 PDT)
- Re: [AMBER] Download and installing cpptraj sub-application Elvis Martis (Sat Jun 24 2017 - 04:06:00 PDT)
  - Re: [AMBER] Download and installing cpptraj sub-application Daniel Roe (Mon Jun 26 2017 - 05:55:34 PDT)
[AMBER] Download and installing cpptraj sub-application Mustafa Alhaji Isa (Sat Jun 24 2017 - 03:56:00 PDT)
[AMBER] AMber trajectory to Gromacs trajectory Saikat Pal (Sat Jun 24 2017 - 04:55:25 PDT)
- Re: [AMBER] AMber trajectory to Gromacs trajectory Daniel Roe (Sat Jun 24 2017 - 04:57:32 PDT)
  - Re: [AMBER] AMber trajectory to Gromacs trajectory Qinghua Liao (Sat Jun 24 2017 - 05:02:03 PDT)
  - Re: [AMBER] AMber trajectory to Gromacs trajectory Saikat Pal (Sun Jun 25 2017 - 22:06:07 PDT)
    - Re: [AMBER] AMber trajectory to Gromacs trajectory Daniel Roe (Mon Jun 26 2017 - 05:50:20 PDT)
    - Re: [AMBER] AMber trajectory to Gromacs trajectory Saikat Pal (Mon Jun 26 2017 - 06:30:27 PDT)
    - Re: [AMBER] AMber trajectory to Gromacs trajectory Daniel Roe (Wed Jul 05 2017 - 05:54:14 PDT)
[AMBER] mbondi set up Jag Silwal (Sun Jun 25 2017 - 04:45:15 PDT)
- Re: [AMBER] mbondi set up Elvis Martis (Sun Jun 25 2017 - 05:18:36 PDT)
  - Re: [AMBER] mbondi set up Arati Paudyal (Sun Jun 25 2017 - 05:22:07 PDT)
[AMBER] An off topic survey request Karl Kirschner (Mon Jun 26 2017 - 04:36:29 PDT)
[AMBER] SN is required in naa_mol2files but not provided Eugene Cha (Mon Jun 26 2017 - 06:04:14 PDT)
- Re: [AMBER] SN is required in naa_mol2files but not provided Pengfei Li (Mon Jun 26 2017 - 08:25:51 PDT)
[AMBER] how heme force field combine with amber 99 ff Rana Rehan Khalid (Mon Jun 26 2017 - 13:44:56 PDT)
- Re: [AMBER] how heme force field combine with amber 99 ff Elvis Martis (Mon Jun 26 2017 - 18:24:08 PDT)
  - Re: [AMBER] how heme force field combine with amber 99 ff Rana Rehan Khalid (Mon Jun 26 2017 - 19:03:23 PDT)
    - Re: [AMBER] how heme force field combine with amber 99 ff Elvis Martis (Tue Jun 27 2017 - 00:03:08 PDT)
[AMBER] mmpbsa Baker, Joseph (Mon Jun 26 2017 - 14:50:30 PDT)
- Re: [AMBER] mmpbsa Ray Luo (Mon Jun 26 2017 - 15:48:26 PDT)
  - Re: [AMBER] mmpbsa Baker, Joseph (Mon Jun 26 2017 - 18:15:09 PDT)
[AMBER] can't mutated Pro to Ala correctly during generating snapshots 刘兰茹 (Mon Jun 26 2017 - 20:32:30 PDT)
- Re: [AMBER] can't mutated Pro to Ala correctly during generating snapshots Daniel Roe (Wed Jul 05 2017 - 05:30:34 PDT)
[AMBER] Parabolic restraint with nmropt Ramin Salimi (Tue Jun 27 2017 - 02:07:50 PDT)
- Re: [AMBER] Parabolic restraint with nmropt David Case (Tue Jun 27 2017 - 08:17:56 PDT)
[AMBER] using mmgbsa for dna/protein Baker, Joseph (Tue Jun 27 2017 - 20:18:11 PDT)
- Re: [AMBER] using mmgbsa for dna/protein Hai Nguyen (Tue Jun 27 2017 - 20:26:54 PDT)
  - Re: [AMBER] using mmgbsa for dna/protein Baker, Joseph (Tue Jun 27 2017 - 20:41:29 PDT)
    - Re: [AMBER] using mmgbsa for dna/protein Hai Nguyen (Tue Jun 27 2017 - 21:00:44 PDT)
    - Re: [AMBER] using mmgbsa for dna/protein Hai Nguyen (Tue Jun 27 2017 - 21:02:35 PDT)
[AMBER] how can i use two force field one is ff14sb other is not in leaprc source to produce prmtop and inpcrd files for protein Rana Rehan Khalid (Tue Jun 27 2017 - 20:54:07 PDT)
- Re: [AMBER] how can i use two force field one is ff14sb other is not in leaprc source to produce prmtop and inpcrd files for protein Elvis Martis (Tue Jun 27 2017 - 21:27:59 PDT)
  - Re: [AMBER] how can i use two force field one is ff14sb other is not in leaprc source to produce prmtop and inpcrd files for protein Rana Rehan Khalid (Tue Jun 27 2017 - 22:11:11 PDT)
    - Re: [AMBER] how can i use two force field one is ff14sb other is not in leaprc source to produce prmtop and inpcrd files for protein Rana Rehan Khalid (Tue Jun 27 2017 - 22:33:54 PDT)
    - Re: [AMBER] how can i use two force field one is ff14sb other is not in leaprc source to produce prmtop and inpcrd files for protein Elvis Martis (Tue Jun 27 2017 - 22:36:28 PDT)
    - Re: [AMBER] how can i use two force field one is ff14sb other is not in leaprc source to produce prmtop and inpcrd files for protein Rana Rehan Khalid (Tue Jun 27 2017 - 22:43:59 PDT)
    - Re: [AMBER] how can i use two force field one is ff14sb other is not in leaprc source to produce prmtop and inpcrd files for protein Rana Rehan Khalid (Tue Jun 27 2017 - 22:59:58 PDT)
    - Re: [AMBER] how can i use two force field one is ff14sb other is not in leaprc source to produce prmtop and inpcrd files for protein Bill Ross (Tue Jun 27 2017 - 23:50:01 PDT)
    - Re: [AMBER] how can i use two force field one is ff14sb other is not in leaprc source to produce prmtop and inpcrd files for protein Elvis Martis (Tue Jun 27 2017 - 23:57:20 PDT)
    - Re: [AMBER] how can i use two force field one is ff14sb other is not in leaprc source to produce prmtop and inpcrd files for protein Rana Rehan Khalid (Wed Jun 28 2017 - 10:17:39 PDT)
    - Re: [AMBER] how can i use two force field one is ff14sb other is not in leaprc source to produce prmtop and inpcrd files for protein Elvis Martis (Wed Jun 28 2017 - 12:06:18 PDT)
    - Re: [AMBER] how can i use two force field one is ff14sb other is not in leaprc source to produce prmtop and inpcrd files for protein Rana Rehan Khalid (Wed Jun 28 2017 - 12:18:46 PDT)
    - Re: [AMBER] how can i use two force field one is ff14sb other is not in leaprc source to produce prmtop and inpcrd files for protein Rana Rehan Khalid (Wed Jun 28 2017 - 13:27:25 PDT)
    - Re: [AMBER] how can i use two force field one is ff14sb other is not in leaprc source to produce prmtop and inpcrd files for protein Rana Rehan Khalid (Wed Jun 28 2017 - 15:34:13 PDT)
    - Re: [AMBER] how can i use two force field one is ff14sb other is not in leaprc source to produce prmtop and inpcrd files for protein Elvis Martis (Wed Jun 28 2017 - 20:26:31 PDT)
    - Re: [AMBER] how can i use two force field one is ff14sb other is not in leaprc source to produce prmtop and inpcrd files for protein Andrew Schaub (Wed Jun 28 2017 - 21:16:13 PDT)
    - Re: [AMBER] how can i use two force field one is ff14sb other is not in leaprc source to produce prmtop and inpcrd files for protein Rana Rehan Khalid (Wed Jun 28 2017 - 21:23:05 PDT)
    - Re: [AMBER] how can i use two force field one is ff14sb other is not in leaprc source to produce prmtop and inpcrd files for protein Elvis Martis (Wed Jun 28 2017 - 21:32:37 PDT)
    - Re: [AMBER] how can i use two force field one is ff14sb other is not in leaprc source to produce prmtop and inpcrd files for protein Rana Rehan Khalid (Thu Jun 29 2017 - 12:05:31 PDT)
    - Re: [AMBER] how can i use two force field one is ff14sb other is not in leaprc source to produce prmtop and inpcrd files for protein Bill Ross (Thu Jun 29 2017 - 13:20:50 PDT)
    - Re: [AMBER] how can i use two force field one is ff14sb other is not in leaprc source to produce prmtop and inpcrd files for protein Rana Rehan Khalid (Thu Jun 29 2017 - 13:33:28 PDT)
    - Re: [AMBER] how can i use two force field one is ff14sb other is not in leaprc source to produce prmtop and inpcrd files for protein Rana Rehan Khalid (Thu Jun 29 2017 - 20:09:31 PDT)
    - Re: [AMBER] how can i use two force field one is ff14sb other is not in leaprc source to produce prmtop and inpcrd files for protein Rana Rehan Khalid (Wed Jun 28 2017 - 10:28:43 PDT)
- Re: [AMBER] how can i use two force field one is ff14sb other is not in leaprc source to produce prmtop and inpcrd files for protein Rana Rehan Khalid (Wed Jun 28 2017 - 17:45:46 PDT)
[AMBER] ambpdb- Segmentation fault (core dumped) Jag Silwal (Wed Jun 28 2017 - 05:16:12 PDT)
- Re: [AMBER] ambpdb- Segmentation fault (core dumped) Elvis Martis (Wed Jun 28 2017 - 05:46:58 PDT)
- Re: [AMBER] ambpdb- Segmentation fault (core dumped) Daniel Roe (Wed Jun 28 2017 - 08:22:53 PDT)
[AMBER] Cluster analysis Elisa Pieri (Wed Jun 28 2017 - 08:51:00 PDT)
- Re: [AMBER] Cluster analysis Elvis Martis (Wed Jun 28 2017 - 09:29:28 PDT)
[AMBER] sander do not write rst and mdcrd files Núbia Prates (Wed Jun 28 2017 - 10:19:01 PDT)
- Re: [AMBER] sander do not write rst and mdcrd files Bill Ross (Wed Jun 28 2017 - 10:27:11 PDT)
  - Re: [AMBER] sander do not write rst and mdcrd files Rana Rehan Khalid (Wed Jun 28 2017 - 10:30:11 PDT)
    - Re: [AMBER] sander do not write rst and mdcrd files Bill Ross (Wed Jun 28 2017 - 10:34:36 PDT)
    - Re: [AMBER] sander do not write rst and mdcrd files Rana Rehan Khalid (Wed Jun 28 2017 - 10:49:53 PDT)
    - Re: [AMBER] sander do not write rst and mdcrd files Bill Ross (Wed Jun 28 2017 - 10:46:40 PDT)
  - Re: [AMBER] sander do not write rst and mdcrd files Núbia Prates (Wed Jun 28 2017 - 10:42:01 PDT)
    - Re: [AMBER] sander do not write rst and mdcrd files Bill Ross (Wed Jun 28 2017 - 10:44:27 PDT)
    - Re: [AMBER] sander do not write rst and mdcrd files Núbia Prates (Wed Jun 28 2017 - 10:52:00 PDT)
    - Re: [AMBER] sander do not write rst and mdcrd files Rana Rehan Khalid (Wed Jun 28 2017 - 10:54:22 PDT)
    - Re: [AMBER] sander do not write rst and mdcrd files Bill Ross (Wed Jun 28 2017 - 10:55:58 PDT)
    - Re: [AMBER] sander do not write rst and mdcrd files Rana Rehan Khalid (Wed Jun 28 2017 - 11:04:55 PDT)
    - Re: [AMBER] sander do not write rst and mdcrd files Bill Ross (Wed Jun 28 2017 - 11:08:09 PDT)
    - Re: [AMBER] sander do not write rst and mdcrd files Núbia Prates (Wed Jun 28 2017 - 11:06:34 PDT)
    - Re: [AMBER] sander do not write rst and mdcrd files SHAILESH KUMAR (Wed Jun 28 2017 - 11:12:16 PDT)
    - Re: [AMBER] sander do not write rst and mdcrd files Rana Rehan Khalid (Wed Jun 28 2017 - 11:14:30 PDT)
    - Re: [AMBER] sander do not write rst and mdcrd files Bill Ross (Wed Jun 28 2017 - 11:21:56 PDT)
    - Re: [AMBER] sander do not write rst and mdcrd files Rana Rehan Khalid (Wed Jun 28 2017 - 11:25:20 PDT)
    - Re: [AMBER] sander do not write rst and mdcrd files Núbia Prates (Wed Jun 28 2017 - 11:29:45 PDT)
    - Re: [AMBER] sander do not write rst and mdcrd files Núbia Prates (Wed Jun 28 2017 - 10:53:40 PDT)
    - Re: [AMBER] sander do not write rst and mdcrd files Rana Rehan Khalid (Wed Jun 28 2017 - 11:24:00 PDT)
[AMBER] Force LEaP to use impose on atoms with LOOP or improper torsions in prep file Gorday, Kent M. (Wed Jun 28 2017 - 11:55:12 PDT)
[AMBER] steps to prepare prmtop and inpcrd for heme containing protein (ff for fe----O2 is present ) Rana Rehan Khalid (Wed Jun 28 2017 - 12:03:02 PDT)
[AMBER] antechamber Rana Rehan Khalid (Wed Jun 28 2017 - 15:37:12 PDT)
- Re: [AMBER] antechamber Elvis Martis (Wed Jun 28 2017 - 20:29:04 PDT)
  - Re: [AMBER] antechamber Rana Rehan Khalid (Wed Jun 28 2017 - 21:08:54 PDT)
  - Re: [AMBER] antechamber Rana Rehan Khalid (Wed Jun 28 2017 - 21:31:42 PDT)
    - Re: [AMBER] antechamber Elvis Martis (Wed Jun 28 2017 - 21:37:52 PDT)
    - Re: [AMBER] antechamber Rana Rehan Khalid (Wed Jun 28 2017 - 21:56:59 PDT)
    - Re: [AMBER] antechamber Rana Rehan Khalid (Wed Jun 28 2017 - 22:13:59 PDT)
    - Re: [AMBER] antechamber Rana Rehan Khalid (Wed Jun 28 2017 - 22:42:20 PDT)
    - Re: [AMBER] antechamber Elvis Martis (Wed Jun 28 2017 - 22:52:13 PDT)
    - Re: [AMBER] antechamber Elvis Martis (Wed Jun 28 2017 - 22:56:13 PDT)
    - Re: [AMBER] antechamber Bill Ross (Wed Jun 28 2017 - 22:59:06 PDT)
    - Re: [AMBER] antechamber Rana Rehan Khalid (Wed Jun 28 2017 - 23:06:03 PDT)
    - Re: [AMBER] antechamber Rana Rehan Khalid (Wed Jun 28 2017 - 23:07:18 PDT)
    - Re: [AMBER] antechamber Elvis Martis (Wed Jun 28 2017 - 23:16:20 PDT)
    - Re: [AMBER] antechamber Rana Rehan Khalid (Wed Jun 28 2017 - 23:23:21 PDT)
    - Re: [AMBER] antechamber Rana Rehan Khalid (Wed Jun 28 2017 - 23:27:13 PDT)
    - Re: [AMBER] antechamber Bill Ross (Wed Jun 28 2017 - 23:52:38 PDT)
    - Re: [AMBER] antechamber Bill Ross (Wed Jun 28 2017 - 23:19:58 PDT)
    - Re: [AMBER] antechamber Bill Ross (Wed Jun 28 2017 - 21:57:52 PDT)
- Re: [AMBER] antechamber Andrew Schaub (Wed Jun 28 2017 - 20:55:52 PDT)
  - Re: [AMBER] antechamber Rana Rehan Khalid (Thu Jun 29 2017 - 14:16:58 PDT)
- Re: [AMBER] antechamber David Case (Thu Jun 29 2017 - 07:27:57 PDT)
[AMBER] Heme parameter error Rana Rehan Khalid (Wed Jun 28 2017 - 17:58:03 PDT)
- Re: [AMBER] Heme parameter error Andrew Schaub (Wed Jun 28 2017 - 21:19:36 PDT)
[AMBER] MCPB step 2 local variable 'ban' referenced before assignment Eugene Cha (Wed Jun 28 2017 - 23:15:55 PDT)
- Re: [AMBER] MCPB step 2 local variable 'ban' referenced before assignment Scott Brozell (Thu Jun 29 2017 - 12:24:02 PDT)
- Re: [AMBER] MCPB step 2 local variable 'ban' referenced before assignment Pengfei Li (Fri Jun 30 2017 - 14:26:47 PDT)
[AMBER] constant pH MD question Michael Shokhen (Thu Jun 29 2017 - 02:17:58 PDT)
- Re: [AMBER] constant pH MD question Monsurat Lawal (Thu Jun 29 2017 - 02:31:43 PDT)
  - Re: [AMBER] constant pH MD question Andrew Schaub (Thu Jun 29 2017 - 06:46:47 PDT)
- Re: [AMBER] constant pH MD question Adrian Roitberg (Thu Jun 29 2017 - 07:39:32 PDT)
  - Re: [AMBER] constant pH MD question Michael Shokhen (Thu Jun 29 2017 - 10:15:20 PDT)
    - Re: [AMBER] constant pH MD question Jason Swails (Thu Jun 29 2017 - 18:53:06 PDT)
Re: [AMBER] AMBER Digest, Vol 1973, Issue 1 Garima Singh (Thu Jun 29 2017 - 04:31:19 PDT)
- Re: [AMBER] AMBER Digest, Vol 1973, Issue 1 David Case (Thu Jun 29 2017 - 07:35:50 PDT)
[AMBER] Parametrization of a phosphorylated small molecule Andreas Tosstorff (Thu Jun 29 2017 - 05:31:54 PDT)
- Re: [AMBER] Parametrization of a phosphorylated small molecule David A Case (Fri Jun 30 2017 - 11:16:26 PDT)
[AMBER] Is there any analysis of the stability of DNA in presence of Divalent cation?? Saikat Pal (Thu Jun 29 2017 - 06:58:11 PDT)
- Re: [AMBER] Is there any analysis of the stability of DNA in presence of Divalent cation?? David Case (Thu Jun 29 2017 - 10:09:04 PDT)
[AMBER] adding dummy atom using Parmed API Thomas Evangelidis (Thu Jun 29 2017 - 16:08:52 PDT)
- Re: [AMBER] adding dummy atom using Parmed API Jason Swails (Thu Jun 29 2017 - 18:50:58 PDT)
[AMBER] kindly see the leap.log for fe---02 Rana Rehan Khalid (Thu Jun 29 2017 - 17:16:42 PDT)
- Re: [AMBER] kindly see the leap.log for fe---02 Elvis Martis (Thu Jun 29 2017 - 20:58:41 PDT)
  - Re: [AMBER] kindly see the leap.log for fe---02 Rana Rehan Khalid (Thu Jun 29 2017 - 21:11:44 PDT)
    - Re: [AMBER] kindly see the leap.log for fe---02 Elvis Martis (Thu Jun 29 2017 - 21:17:02 PDT)
[AMBER] MCPB.py warning meaning is this mol2 file correct?? Rana Rehan Khalid (Thu Jun 29 2017 - 18:07:09 PDT)
- Re: [AMBER] MCPB.py warning meaning is this mol2 file correct?? Rana Rehan Khalid (Thu Jun 29 2017 - 18:12:44 PDT)
  - Re: [AMBER] MCPB.py warning meaning is this mol2 file correct?? Pengfei Li (Fri Jun 30 2017 - 13:56:03 PDT)
[AMBER] how we can find that metal residue protonation state Rana Rehan Khalid (Thu Jun 29 2017 - 19:15:48 PDT)
[AMBER] MCPB.py error (MCPB.py -i 4ZF6.in -s 1) use default ions 7440 Rana Rehan Khalid (Thu Jun 29 2017 - 19:44:36 PDT)
- Re: [AMBER] MCPB.py error (MCPB.py -i 4ZF6.in -s 1) use default ions 7440 Andrew Schaub (Thu Jun 29 2017 - 20:18:45 PDT)
  - Re: [AMBER] MCPB.py error (MCPB.py -i 4ZF6.in -s 1) use default ions 7440 Rana Rehan Khalid (Thu Jun 29 2017 - 20:30:14 PDT)
    - Re: [AMBER] MCPB.py error (MCPB.py -i 4ZF6.in -s 1) use default ions 7440 Rana Rehan Khalid (Thu Jun 29 2017 - 21:15:47 PDT)
    - Re: [AMBER] MCPB.py error (MCPB.py -i 4ZF6.in -s 1) use default ions 7440 Elvis Martis (Thu Jun 29 2017 - 21:19:13 PDT)
    - Re: [AMBER] MCPB.py error (MCPB.py -i 4ZF6.in -s 1) use default ions 7440 Rana Rehan Khalid (Thu Jun 29 2017 - 21:26:12 PDT)
    - Re: [AMBER] MCPB.py error (MCPB.py -i 4ZF6.in -s 1) use default ions 7440 Andrew Schaub (Thu Jun 29 2017 - 21:31:46 PDT)
    - Re: [AMBER] MCPB.py error (MCPB.py -i 4ZF6.in -s 1) use default ions 7440 Rana Rehan Khalid (Mon Jul 17 2017 - 12:45:35 PDT)
    - Re: [AMBER] MCPB.py error (MCPB.py -i 4ZF6.in -s 1) use default ions 7440 Pengfei Li (Thu Jul 27 2017 - 12:15:48 PDT)
    - Re: [AMBER] MCPB.py error (MCPB.py -i 4ZF6.in -s 1) use default ions 7440 Andrew Schaub (Thu Jun 29 2017 - 21:30:00 PDT)
    - Re: [AMBER] MCPB.py error (MCPB.py -i 4ZF6.in -s 1) use default ions 7440 Rana Rehan Khalid (Thu Jun 29 2017 - 21:38:56 PDT)
    - Re: [AMBER] MCPB.py error (MCPB.py -i 4ZF6.in -s 1) use default ions 7440 Rana Rehan Khalid (Thu Jun 29 2017 - 22:03:39 PDT)
    - Re: [AMBER] MCPB.py error (MCPB.py -i 4ZF6.in -s 1) use default ions 7440 Andrew Schaub (Thu Jun 29 2017 - 23:35:55 PDT)
    - Re: [AMBER] MCPB.py error (MCPB.py -i 4ZF6.in -s 1) use default ions 7440 Rana Rehan Khalid (Sat Jul 01 2017 - 17:47:52 PDT)
    - Re: [AMBER] MCPB.py error (MCPB.py -i 4ZF6.in -s 1) use default ions 7440 Andrew Schaub (Sat Jul 01 2017 - 17:57:12 PDT)
    - Re: [AMBER] MCPB.py error (MCPB.py -i 4ZF6.in -s 1) use default ions 7440 Rana Rehan Khalid (Sat Jul 01 2017 - 18:40:45 PDT)
    - Re: [AMBER] MCPB.py error (MCPB.py -i 4ZF6.in -s 1) use default ions 7440 Pengfei Li (Mon Jul 03 2017 - 10:05:26 PDT)
    - Re: [AMBER] MCPB.py error (MCPB.py -i 4ZF6.in -s 1) use default ions 7440 Rana Rehan Khalid (Mon Jul 03 2017 - 11:23:21 PDT)
    - Re: [AMBER] MCPB.py error (MCPB.py -i 4ZF6.in -s 1) use default ions 7440 Andrew Schaub (Mon Jul 03 2017 - 11:31:52 PDT)
    - Re: [AMBER] MCPB.py error (MCPB.py -i 4ZF6.in -s 1) use default ions 7440 Rana Rehan Khalid (Mon Jul 03 2017 - 11:51:57 PDT)
    - Re: [AMBER] MCPB.py error (MCPB.py -i 4ZF6.in -s 1) use default ions 7440 Andrew Schaub (Mon Jul 03 2017 - 12:18:46 PDT)
    - Re: [AMBER] MCPB.py error (MCPB.py -i 4ZF6.in -s 1) use default ions 7440 Rana Rehan Khalid (Mon Jul 03 2017 - 12:30:55 PDT)
    - Re: [AMBER] MCPB.py error (MCPB.py -i 4ZF6.in -s 1) use default ions 7440 Rana Rehan Khalid (Tue Jul 04 2017 - 19:49:14 PDT)
    - Re: [AMBER] MCPB.py error (MCPB.py -i 4ZF6.in -s 1) use default ions 7440 David A Case (Wed Jul 05 2017 - 04:49:37 PDT)
    - Re: [AMBER] MCPB.py error (MCPB.py -i 4ZF6.in -s 1) use default ions 7440 Rana Rehan Khalid (Wed Jul 05 2017 - 07:31:03 PDT)
    - Re: [AMBER] MCPB.py error (MCPB.py -i 4ZF6.in -s 1) use default ions 7440 David A Case (Wed Jul 05 2017 - 09:19:41 PDT)
    - Re: [AMBER] MCPB.py error (MCPB.py -i 4ZF6.in -s 1) use default ions 7440 Andrew Schaub (Wed Jul 05 2017 - 09:57:10 PDT)
    - Re: [AMBER] MCPB.py error (MCPB.py -i 4ZF6.in -s 1) use default ions 7440 Rana Rehan Khalid (Wed Jul 05 2017 - 10:22:59 PDT)
    - Re: [AMBER] MCPB.py error (MCPB.py -i 4ZF6.in -s 1) use default ions 7440 Rana Rehan Khalid (Wed Jul 05 2017 - 11:16:54 PDT)
    - Re: [AMBER] MCPB.py error (MCPB.py -i 4ZF6.in -s 1) use default ions 7440 Rana Rehan Khalid (Wed Jul 05 2017 - 11:21:10 PDT)
    - Re: [AMBER] MCPB.py error (MCPB.py -i 4ZF6.in -s 1) use default ions 7440 Rana Rehan Khalid (Wed Jul 05 2017 - 12:48:45 PDT)
    - Re: [AMBER] MCPB.py error (MCPB.py -i 4ZF6.in -s 1) use default ions 7440 Rana Rehan Khalid (Wed Jul 05 2017 - 07:44:55 PDT)
[AMBER] Mm_pbsa.pl using netcdf trajectory Elvis Martis (Fri Jun 30 2017 - 01:18:14 PDT)
- Re: [AMBER] Mm_pbsa.pl using netcdf trajectory Daniel Roe (Fri Jun 30 2017 - 07:49:11 PDT)
  - Re: [AMBER] Mm_pbsa.pl using netcdf trajectory Elvis Martis (Fri Jun 30 2017 - 08:22:00 PDT)
[AMBER] amber installations error in cygwin venkat (Fri Jun 30 2017 - 06:30:01 PDT)
- Re: [AMBER] amber installations error in cygwin Hai Nguyen (Fri Jun 30 2017 - 06:37:09 PDT)
- Re: [AMBER] amber installations error in cygwin venkat (Fri Jun 30 2017 - 22:53:25 PDT)
  - Re: [AMBER] amber installations error in cygwin Hai Nguyen (Sat Jul 01 2017 - 09:04:46 PDT)
[AMBER] problem of installing amber17 in window 10 using cygwin Mustafa Alhaji Isa (Fri Jun 30 2017 - 08:28:55 PDT)
- Re: [AMBER] problem of installing amber17 in window 10 using cygwin David A Case (Fri Jun 30 2017 - 11:02:59 PDT)
[AMBER] TI/FEP on GPU in Amber? Hadházi Ádám (Fri Jun 30 2017 - 09:15:48 PDT)
- Re: [AMBER] TI/FEP on GPU in Amber? Adrian Roitberg (Fri Jun 30 2017 - 09:17:24 PDT)
- Re: [AMBER] TI/FEP on GPU in Amber? Ross Walker (Fri Jun 30 2017 - 12:59:09 PDT)
  - Re: [AMBER] TI/FEP on GPU in Amber? liu junjun (Mon Jul 03 2017 - 01:41:16 PDT)
[AMBER] Amber14 compatible with TITAN X Pascal? Thakur, Abhishek (Fri Jun 30 2017 - 09:43:38 PDT)
- Re: [AMBER] Amber14 compatible with TITAN X Pascal? Ross Walker (Fri Jun 30 2017 - 12:54:58 PDT)
[AMBER] problem in setting AMBERHOME environment variable using cygwin Mustafa Alhaji Isa (Fri Jun 30 2017 - 10:08:10 PDT)
- Re: [AMBER] problem in setting AMBERHOME environment variable using cygwin Hai Nguyen (Fri Jun 30 2017 - 10:11:21 PDT)
- Re: [AMBER] problem in setting AMBERHOME environment variable using cygwin Bill Ross (Fri Jun 30 2017 - 10:38:57 PDT)
  - Re: [AMBER] problem in setting AMBERHOME environment variable using cygwin Mustafa Alhaji Isa (Fri Jun 30 2017 - 11:10:47 PDT)
    - Re: [AMBER] problem in setting AMBERHOME environment variable using cygwin David A Case (Fri Jun 30 2017 - 14:08:33 PDT)
    - Re: [AMBER] problem in setting AMBERHOME environment variable using cygwin Bill Ross (Fri Jun 30 2017 - 14:10:37 PDT)
    - Re: [AMBER] problem in setting AMBERHOME environment variable using cygwin Pratul K. Agarwal (Fri Jun 30 2017 - 17:53:05 PDT)
[AMBER] cphstats Error: Could not open or parse cpin file Vincent Ustach (Fri Jun 30 2017 - 15:54:52 PDT)
- Re: [AMBER] cphstats Error: Could not open or parse cpin file Jason Swails (Fri Jun 30 2017 - 20:42:18 PDT)
[AMBER] error with MMPBSA Mohammad Salem (Fri Jun 30 2017 - 21:22:54 PDT)
- Re: [AMBER] error with MMPBSA Elvis Martis (Fri Jun 30 2017 - 21:41:45 PDT)
  - Re: [AMBER] error with MMPBSA Mohammad Salem (Fri Jun 30 2017 - 21:50:35 PDT)
    - Re: [AMBER] error with MMPBSA Mohammad Salem (Fri Jun 30 2017 - 21:56:09 PDT)
[AMBER] Principal component analysis with CPPTRAJ - PCA Marcelo Andrade Chagas (Sat Jul 01 2017 - 10:40:16 PDT)
- Re: [AMBER] Principal component analysis with CPPTRAJ - PCA Daniel Roe (Mon Jul 03 2017 - 06:36:56 PDT)
  - Re: [AMBER] Principal component analysis with CPPTRAJ - PCA Marcelo Andrade Chagas (Mon Jul 03 2017 - 09:45:49 PDT)
    - Re: [AMBER] Principal component analysis with CPPTRAJ - PCA Daniel Roe (Wed Jul 05 2017 - 05:45:00 PDT)
    - [AMBER] I have generated an AMBER trajectory with coordinates, velocities and forces. How can I place the relevant data sets in the text file? Jewgeni Starikow (Sun Aug 27 2017 - 14:41:29 PDT)
    - Re: [AMBER] I have generated an AMBER trajectory with coordinates, velocities and forces. How can I place the relevant data sets in the text file? Bill Ross (Sun Aug 27 2017 - 15:38:45 PDT)
    - Re: [AMBER] I have generated an AMBER trajectory with coordinates, velocities and forces. How can I place the relevant data sets in the text file? Jewgeni Starikow (Sun Aug 27 2017 - 22:24:26 PDT)
    - Re: [AMBER] I have generated an AMBER trajectory with coordinates, velocities and forces. How can I place the relevant data sets in the text file? Bill Ross (Sun Aug 27 2017 - 23:16:21 PDT)
    - Re: [AMBER] I have generated an AMBER trajectory with coordinates, velocities and forces. How can I place the relevant data sets in the text file? Jewgeni Starikow (Mon Aug 28 2017 - 00:26:42 PDT)
    - Re: [AMBER] I have generated an AMBER trajectory with coordinates, velocities and forces. How can I place the relevant data sets in the text file? Bill Ross (Mon Aug 28 2017 - 01:44:35 PDT)
    - Re: [AMBER] I have generated an AMBER trajectory with coordinates, velocities and forces. How can I place the relevant data sets in the text file? Hai Nguyen (Sun Aug 27 2017 - 19:01:01 PDT)
    - Re: [AMBER] I have generated an AMBER trajectory with coordinates, velocities and forces. How can I place the relevant data sets in the text file? Jewgeni Starikow (Sun Aug 27 2017 - 22:22:29 PDT)
    - Re: [AMBER] I have generated an AMBER trajectory with coordinates, velocities and forces. How can I place the relevant data sets in the text file? Daniel Roe (Mon Aug 28 2017 - 05:39:36 PDT)
    - Re: [AMBER] I have generated an AMBER trajectory with coordinates, velocities and forces. How can I place the relevant data sets in the text file? Jewgeni Starikow (Mon Aug 28 2017 - 06:45:45 PDT)
[AMBER] amber error Rana Rehan Khalid (Sat Jul 01 2017 - 13:08:13 PDT)
[AMBER] Construction of a large non-standard residue Andrew Schaub (Sat Jul 01 2017 - 17:52:55 PDT)
[AMBER] MMPBSA maxitn warning with protein/dna complex Baker, Joseph (Sat Jul 01 2017 - 19:19:07 PDT)
- Re: [AMBER] MMPBSA maxitn warning with protein/dna complex Ray Luo (Sun Jul 02 2017 - 08:35:59 PDT)
[AMBER] Frcmod and prepin from inpcrd Hirdesh Kumar (Sat Jul 01 2017 - 20:43:17 PDT)
- Re: [AMBER] Frcmod and prepin from inpcrd Bill Ross (Sat Jul 01 2017 - 23:20:51 PDT)
  - Re: [AMBER] Frcmod and prepin from inpcrd Lorenzo Gontrani (Sun Jul 02 2017 - 01:21:22 PDT)
    - Re: [AMBER] Frcmod and prepin from inpcrd Bill Ross (Sun Jul 02 2017 - 10:58:37 PDT)
- Re: [AMBER] Frcmod and prepin from inpcrd David Case (Sun Jul 02 2017 - 13:22:48 PDT)
[AMBER] questions on MMPBSA giulia palermo (Sun Jul 02 2017 - 10:51:21 PDT)
[AMBER] how can i remove this error Rana Rehan Khalid (Sun Jul 02 2017 - 13:53:15 PDT)
- Re: [AMBER] how can i remove this error Bill Ross (Sun Jul 02 2017 - 13:55:18 PDT)
  - Re: [AMBER] how can i remove this error Rana Rehan Khalid (Sun Jul 02 2017 - 13:58:52 PDT)
    - Re: [AMBER] how can i remove this error Bill Ross (Sun Jul 02 2017 - 14:16:06 PDT)
  - Re: [AMBER] how can i remove this error Rana Rehan Khalid (Sun Jul 02 2017 - 14:20:30 PDT)
    - Re: [AMBER] how can i remove this error Rana Rehan Khalid (Sun Jul 02 2017 - 14:23:00 PDT)
    - Re: [AMBER] how can i remove this error Bill Ross (Sun Jul 02 2017 - 14:42:57 PDT)
    - Re: [AMBER] how can i remove this error Rana Rehan Khalid (Sun Jul 02 2017 - 15:02:01 PDT)
    - Re: [AMBER] how can i remove this error Bill Ross (Sun Jul 02 2017 - 15:05:55 PDT)
    - Re: [AMBER] how can i remove this error Rana Rehan Khalid (Sun Jul 02 2017 - 15:12:22 PDT)
    - Re: [AMBER] how can i remove this error Rana Rehan Khalid (Sun Jul 02 2017 - 15:21:44 PDT)
    - Re: [AMBER] how can i remove this error Bill Ross (Sun Jul 02 2017 - 15:23:58 PDT)
[AMBER] Problem in cuda for AMBER 14 Mahendra B Thapa (Sun Jul 02 2017 - 19:09:31 PDT)
- Re: [AMBER] Problem in cuda for AMBER 14 Bill Ross (Sun Jul 02 2017 - 19:23:18 PDT)
Re: [AMBER] FW: Problem in cuda for AMBER 14 Mahendra B Thapa (Sun Jul 02 2017 - 19:30:52 PDT)
- Re: [AMBER] FW: Problem in cuda for AMBER 14 Bill Ross (Sun Jul 02 2017 - 19:33:20 PDT)
[AMBER] abmer error Rana Rehan Khalid (Sun Jul 02 2017 - 20:57:43 PDT)
- Re: [AMBER] abmer error Rana Rehan Khalid (Sun Jul 02 2017 - 21:11:06 PDT)
  - Re: [AMBER] abmer error Bill Ross (Sun Jul 02 2017 - 21:14:26 PDT)
    - Re: [AMBER] abmer error Rana Rehan Khalid (Sun Jul 02 2017 - 21:27:58 PDT)
    - Re: [AMBER] abmer error Bill Ross (Sun Jul 02 2017 - 22:06:09 PDT)
[AMBER] using PCA to find entropy Ramin Salimi (Sun Jul 02 2017 - 23:06:54 PDT)
- Re: [AMBER] using PCA to find entropy David A Case (Mon Jul 03 2017 - 05:17:49 PDT)
[AMBER] QM/MM with Gaussian Xichong Liu (Mon Jul 03 2017 - 02:24:38 PDT)
- Re: [AMBER] QM/MM with Gaussian liu junjun (Mon Jul 03 2017 - 02:51:11 PDT)
  - Re: [AMBER] QM/MM with Gaussian Xichong Liu (Mon Jul 03 2017 - 02:53:57 PDT)
    - Re: [AMBER] QM/MM with Gaussian liu junjun (Mon Jul 03 2017 - 06:15:26 PDT)
    - Re: [AMBER] QM/MM with Gaussian Xichong Liu (Mon Jul 03 2017 - 06:51:34 PDT)
[AMBER] How continue a crached minimization step? Núbia Prates (Mon Jul 03 2017 - 07:38:34 PDT)
- Re: [AMBER] How continue a crached minimization step? Elvis Martis (Mon Jul 03 2017 - 08:04:30 PDT)
- Re: [AMBER] How continue a crached minimization step? Bill Ross (Mon Jul 03 2017 - 11:21:05 PDT)
  - Re: [AMBER] How continue a crached minimization step? Núbia Prates (Mon Jul 03 2017 - 12:11:50 PDT)
    - Re: [AMBER] How continue a crached minimization step? Bill Ross (Mon Jul 03 2017 - 13:50:52 PDT)
    - Re: [AMBER] How continue a crached minimization step? Núbia Prates (Tue Jul 04 2017 - 07:24:10 PDT)
    - Re: [AMBER] How continue a crached minimization step? Bill Ross (Tue Jul 04 2017 - 08:01:03 PDT)
    - Re: [AMBER] How continue a crached minimization step? Núbia Prates (Tue Jul 04 2017 - 09:33:44 PDT)
    - Re: [AMBER] How continue a crached minimization step? Bill Ross (Tue Jul 04 2017 - 09:36:35 PDT)
[AMBER] Selecting solvationBox size to simulate a mobile multidomain protein Dmitry Suplatov (Mon Jul 03 2017 - 11:32:49 PDT)
- Re: [AMBER] Selecting solvationBox size to simulate a mobile multidomain protein Dmitry Suplatov (Wed Jul 05 2017 - 10:26:19 PDT)
  - Re: [AMBER] Selecting solvationBox size to simulate a mobile multidomain protein Daniel Roe (Mon Jul 10 2017 - 06:01:11 PDT)
[AMBER] xleap editor Rana Rehan Khalid (Mon Jul 03 2017 - 21:42:46 PDT)
- Re: [AMBER] xleap editor Bill Ross (Mon Jul 03 2017 - 23:25:41 PDT)
  - Re: [AMBER] xleap editor Rana Rehan Khalid (Tue Jul 04 2017 - 00:14:21 PDT)
    - Re: [AMBER] xleap editor Bill Ross (Tue Jul 04 2017 - 00:33:38 PDT)
    - Re: [AMBER] xleap editor Elvis Martis (Tue Jul 04 2017 - 00:34:03 PDT)
    - Re: [AMBER] xleap editor Rana Rehan Khalid (Tue Jul 04 2017 - 00:38:57 PDT)
[AMBER] Question about installing Amber16 on the intel Xeon phi computational server Mingyuan (Mon Jul 03 2017 - 23:44:32 PDT)
- Re: [AMBER] Question about installing Amber16 on the intel Xeon phi computational server Bill Ross (Mon Jul 03 2017 - 23:47:42 PDT)
[AMBER] Amber md in HPC Garima Singh (Mon Jul 03 2017 - 23:53:42 PDT)
- Re: [AMBER] Amber md in HPC Elvis Martis (Tue Jul 04 2017 - 00:31:41 PDT)
  - Re: [AMBER] Amber md in HPC Bill Ross (Tue Jul 04 2017 - 00:36:04 PDT)
- Re: [AMBER] Amber md in HPC David Case (Tue Jul 04 2017 - 06:57:28 PDT)
[AMBER] MPI error when trying to run heating Daniela Rivas (Tue Jul 04 2017 - 03:34:27 PDT)
- Re: [AMBER] MPI error when trying to run heating Bill Ross (Tue Jul 04 2017 - 03:49:08 PDT)
  - Re: [AMBER] MPI error when trying to run heating Daniela Rivas (Tue Jul 04 2017 - 04:36:45 PDT)
    - Re: [AMBER] MPI error when trying to run heating Bill Ross (Tue Jul 04 2017 - 04:57:50 PDT)
- Re: [AMBER] MPI error when trying to run heating David Case (Tue Jul 04 2017 - 07:02:42 PDT)
  - Re: [AMBER] MPI error when trying to run heating Daniela Rivas (Tue Jul 04 2017 - 17:18:37 PDT)
    - Re: [AMBER] MPI error when trying to run heating Daniela Rivas (Tue Jul 04 2017 - 23:04:55 PDT)
[AMBER] MCPB.py error step 2 Lizelle Lubbe (Tue Jul 04 2017 - 04:05:55 PDT)
- Re: [AMBER] MCPB.py error step 2 Dr. M. Shahid (Tue Jul 04 2017 - 07:25:52 PDT)
  - Re: [AMBER] MCPB.py error step 2 Pengfei Li (Wed Jul 05 2017 - 20:24:42 PDT)
[AMBER] Reproduction of MMPBSA Calculations on Processed Trajectories Guqin Shi (Tue Jul 04 2017 - 06:17:33 PDT)
[AMBER] Residue number in tleap not appropriate with residue number in pdb file NADIA RAHMAH (Tue Jul 04 2017 - 08:00:44 PDT)
- Re: [AMBER] Residue number in tleap not appropriate with residue number in pdb file Bill Ross (Tue Jul 04 2017 - 08:49:32 PDT)
  - Re: [AMBER] Residue number in tleap not appropriate with residue number in pdb file NADIA RAHMAH (Tue Jul 04 2017 - 17:16:56 PDT)
    - Re: [AMBER] Residue number in tleap not appropriate with residue number in pdb file David A Case (Wed Jul 05 2017 - 04:40:52 PDT)
    - Re: [AMBER] Residue number in tleap not appropriate with residue number in pdb file NADIA RAHMAH (Thu Jul 06 2017 - 19:47:29 PDT)
[AMBER] RED ESP not working in these days Rana Rehan Khalid (Tue Jul 04 2017 - 10:23:42 PDT)
- Re: [AMBER] RED ESP not working in these days David Cerutti (Tue Jul 04 2017 - 10:56:19 PDT)
[AMBER] pull a dimer apart in AMBER? Xing (Tue Jul 04 2017 - 19:24:12 PDT)
- Re: [AMBER] pull a dimer apart in AMBER? Elvis Martis (Tue Jul 04 2017 - 20:52:42 PDT)
  - Re: [AMBER] pull a dimer apart in AMBER? Xing (Wed Jul 19 2017 - 17:07:57 PDT)
    - Re: [AMBER] pull a dimer apart in AMBER? Thakur, Abhishek (Wed Jul 19 2017 - 17:52:09 PDT)
    - Re: [AMBER] pull a dimer apart in AMBER? Xing (Wed Jul 19 2017 - 18:27:11 PDT)
    - Re: [AMBER] pull a dimer apart in AMBER? Elvis Martis (Thu Jul 20 2017 - 03:23:30 PDT)
    - Re: [AMBER] pull a dimer apart in AMBER? Xing (Thu Jul 20 2017 - 14:44:02 PDT)
    - Re: [AMBER] pull a dimer apart in AMBER? David Case (Fri Jul 21 2017 - 05:38:33 PDT)
    - Re: [AMBER] pull a dimer apart in AMBER? Xing (Sun Jul 23 2017 - 21:48:56 PDT)
[AMBER] Osmotic Pressure Calculation in AMBER Xiaocong Wang (Tue Jul 04 2017 - 20:27:17 PDT)
- Re: [AMBER] Osmotic Pressure Calculation in AMBER David A Case (Wed Jul 05 2017 - 04:52:21 PDT)
[AMBER] MCPB.py error Rana Rehan Khalid (Tue Jul 04 2017 - 20:32:38 PDT)
[AMBER] icc version 17 Fabrício Bracht (Tue Jul 04 2017 - 20:41:07 PDT)
- Re: [AMBER] icc version 17 Ross Walker (Wed Jul 05 2017 - 04:48:59 PDT)
- Re: [AMBER] icc version 17 David A Case (Wed Jul 05 2017 - 04:59:36 PDT)
  - Re: [AMBER] icc version 17 Hector A. Baldoni (Wed Jul 05 2017 - 06:27:49 PDT)
    - Re: [AMBER] icc version 17 Daniel Roe (Wed Jul 05 2017 - 06:42:42 PDT)
- Re: [AMBER] icc version 17 Ryan Novosielski (Thu Jul 06 2017 - 09:13:27 PDT)
[AMBER] Generation of Topology and coordinate file for ionic liquid. Vidya Sundaram (Tue Jul 04 2017 - 22:22:04 PDT)
- Re: [AMBER] Generation of Topology and coordinate file for ionic liquid. Lorenzo Gontrani (Tue Jul 04 2017 - 22:28:54 PDT)
  - Re: [AMBER] Generation of Topology and coordinate file for ionic liquid. Lorenzo Gontrani (Tue Jul 04 2017 - 22:29:37 PDT)
    - Re: [AMBER] Generation of Topology and coordinate file for ionic liquid. Vidya Sundaram (Wed Jul 05 2017 - 01:05:57 PDT)
[AMBER] aMD Hamiltonian replica exchange Qinghua Liao (Wed Jul 05 2017 - 06:06:16 PDT)
- Re: [AMBER] aMD Hamiltonian replica exchange Daniel Roe (Wed Jul 05 2017 - 06:51:34 PDT)
  - Re: [AMBER] aMD Hamiltonian replica exchange Qinghua Liao (Wed Jul 05 2017 - 07:55:06 PDT)
[AMBER] Amber Installation Rana Rehan Khalid (Wed Jul 05 2017 - 22:09:43 PDT)
- Re: [AMBER] Amber Installation Bill Ross (Wed Jul 05 2017 - 22:11:54 PDT)
  - Re: [AMBER] Amber Installation Rana Rehan Khalid (Wed Jul 05 2017 - 22:22:33 PDT)
    - Re: [AMBER] Amber Installation Hai Nguyen (Wed Jul 05 2017 - 22:34:29 PDT)
    - Re: [AMBER] Amber Installation Rana Rehan Khalid (Wed Jul 05 2017 - 23:31:08 PDT)
    - Re: [AMBER] Amber Installation Bill Ross (Wed Jul 05 2017 - 23:33:27 PDT)
    - Re: [AMBER] Amber Installation Rana Rehan Khalid (Wed Jul 05 2017 - 23:35:18 PDT)
    - Re: [AMBER] Amber Installation Bill Ross (Wed Jul 05 2017 - 23:37:39 PDT)
    - Re: [AMBER] Amber Installation Rana Rehan Khalid (Wed Jul 05 2017 - 23:41:38 PDT)
    - Re: [AMBER] Amber Installation Bill Ross (Wed Jul 05 2017 - 23:50:02 PDT)
    - Re: [AMBER] Amber Installation Rana Rehan Khalid (Thu Jul 06 2017 - 00:18:12 PDT)
    - Re: [AMBER] Amber Installation Bill Ross (Thu Jul 06 2017 - 00:54:10 PDT)
  - Re: [AMBER] Amber Installation David A Case (Thu Jul 06 2017 - 04:26:40 PDT)
    - Re: [AMBER] Amber Installation Rana Rehan Khalid (Thu Jul 06 2017 - 07:55:30 PDT)
- Re: [AMBER] Amber Installation David A Case (Tue Mar 19 2019 - 06:50:10 PDT)
[AMBER] MMPBSA Delta total results NADIA RAHMAH (Thu Jul 06 2017 - 00:15:40 PDT)
- Re: [AMBER] MMPBSA Delta total results Elvis Martis (Thu Jul 06 2017 - 02:27:53 PDT)
  - Re: [AMBER] MMPBSA Delta total results NADIA RAHMAH (Thu Jul 06 2017 - 02:49:42 PDT)
    - Re: [AMBER] MMPBSA Delta total results Elvis Martis (Thu Jul 06 2017 - 03:29:21 PDT)
    - Re: [AMBER] MMPBSA Delta total results Ray Luo (Thu Jul 06 2017 - 12:34:10 PDT)
    - Re: [AMBER] MMPBSA Delta total results Elvis Martis (Thu Jul 06 2017 - 19:03:10 PDT)
    - Re: [AMBER] MMPBSA Delta total results NADIA RAHMAH (Thu Jul 06 2017 - 19:38:20 PDT)
    - Re: [AMBER] MMPBSA Delta total results Elvis Martis (Thu Jul 06 2017 - 20:19:41 PDT)
    - Re: [AMBER] MMPBSA Delta total results David Case (Fri Jul 07 2017 - 06:32:45 PDT)
    - Re: [AMBER] MMPBSA Delta total results Ray Luo (Fri Jul 07 2017 - 12:17:25 PDT)
[AMBER] Using AMBER FF in NAMD to study Steered Molecular Dynamics (SMD) Bharat Manna (Thu Jul 06 2017 - 03:00:40 PDT)
- Re: [AMBER] Using AMBER FF in NAMD to study Steered Molecular Dynamics (SMD) David A Case (Thu Jul 06 2017 - 04:32:22 PDT)
[AMBER] pytraj multihedral attributes Robert Wohlhueter (Thu Jul 06 2017 - 08:00:45 PDT)
- Re: [AMBER] pytraj multihedral attributes Hai Nguyen (Thu Jul 06 2017 - 09:09:07 PDT)
[AMBER] CPPTRAJ question: How to do RMS on a trajectory fragment? Jose Borreguero (Thu Jul 06 2017 - 11:41:58 PDT)
- Re: [AMBER] CPPTRAJ question: How to do RMS on a trajectory fragment? Hai Nguyen (Thu Jul 06 2017 - 11:49:38 PDT)
  - Re: [AMBER] CPPTRAJ question: How to do RMS on a trajectory fragment? Jose Borreguero (Thu Jul 06 2017 - 13:22:25 PDT)
- Re: [AMBER] CPPTRAJ question: How to do RMS on a trajectory fragment? Daniel Roe (Thu Jul 06 2017 - 13:13:48 PDT)
  - Re: [AMBER] CPPTRAJ question: How to do RMS on a trajectory fragment? Jose Borreguero (Thu Jul 06 2017 - 13:26:35 PDT)
[AMBER] non-realistic energies in MMPBSA giulia palermo (Thu Jul 06 2017 - 11:45:31 PDT)
- Re: [AMBER] non-realistic energies in MMPBSA Jason Swails (Thu Jul 06 2017 - 19:58:04 PDT)
  - Re: [AMBER] non-realistic energies in MMPBSA giulia palermo (Sat Jul 08 2017 - 10:09:44 PDT)
[AMBER] mismatch NTYPES for mixtures of 2 molecules Quynh Vo (Thu Jul 06 2017 - 16:28:30 PDT)
- Re: [AMBER] mismatch NTYPES for mixtures of 2 molecules Bill Ross (Thu Jul 06 2017 - 17:10:42 PDT)
- Re: [AMBER] mismatch NTYPES for mixtures of 2 molecules David Case (Fri Jul 07 2017 - 06:41:46 PDT)
- Re: [AMBER] mismatch NTYPES for mixtures of 2 molecules Quynh Vo (Fri Jul 07 2017 - 15:06:37 PDT)
  - Re: [AMBER] mismatch NTYPES for mixtures of 2 molecules Bill Ross (Fri Jul 07 2017 - 15:55:46 PDT)
[AMBER] Free energy calculation of Metalloprotein Garima Singh (Fri Jul 07 2017 - 04:02:29 PDT)
- Re: [AMBER] Free energy calculation of Metalloprotein David Case (Fri Jul 07 2017 - 06:50:18 PDT)
- Re: [AMBER] Free energy calculation of Metalloprotein Garima Singh (Sun Jul 09 2017 - 17:26:56 PDT)
  - Re: [AMBER] Free energy calculation of Metalloprotein Hai Nguyen (Sun Jul 09 2017 - 18:43:23 PDT)
Re: [AMBER] AMBER Digest, Vol 1985, Issue 1 Garima Singh (Fri Jul 07 2017 - 04:23:24 PDT)
- Re: [AMBER] AMBER Digest, Vol 1985, Issue 1 Elvis Martis (Fri Jul 07 2017 - 09:56:10 PDT)
[AMBER] RESP charge fitting error in MCPB.py V3.0 abdennour braka (Fri Jul 07 2017 - 07:34:08 PDT)
- Re: [AMBER] RESP charge fitting error in MCPB.py V3.0 abdennour braka (Mon Jul 10 2017 - 00:45:47 PDT)
  - Re: [AMBER] RESP charge fitting error in MCPB.py V3.0 liu junjun (Mon Jul 10 2017 - 02:23:38 PDT)
    - Re: [AMBER] RESP charge fitting error in MCPB.py V3.0 Pengfei Li (Mon Jul 10 2017 - 19:22:42 PDT)
[AMBER] GPUs job and GUI issue Hirdesh Kumar (Fri Jul 07 2017 - 10:28:49 PDT)
- Re: [AMBER] GPUs job and GUI issue Pratul K. Agarwal (Fri Jul 07 2017 - 10:33:53 PDT)
- Re: [AMBER] GPUs job and GUI issue Ross Walker (Fri Jul 07 2017 - 11:28:12 PDT)
  - Re: [AMBER] GPUs job and GUI issue Hirdesh Kumar (Fri Jul 07 2017 - 14:14:57 PDT)
    - Re: [AMBER] GPUs job and GUI issue Pratul K. Agarwal (Fri Jul 07 2017 - 17:02:21 PDT)
    - Re: [AMBER] GPUs job and GUI issue Ross Walker (Sat Jul 08 2017 - 21:28:53 PDT)
- Re: [AMBER] GPUs job and GUI issue Dow Hurst (Sun Jul 09 2017 - 16:41:53 PDT)
  - Re: [AMBER] GPUs job and GUI issue Hirdesh Kumar (Mon Jul 10 2017 - 09:52:46 PDT)
[AMBER] HIE CONVERT INTO HID Rana Rehan Khalid (Fri Jul 07 2017 - 12:44:11 PDT)
- Re: [AMBER] HIE CONVERT INTO HID Bill Ross (Fri Jul 07 2017 - 12:51:10 PDT)
  - Re: [AMBER] HIE CONVERT INTO HID Rana Rehan Khalid (Fri Jul 07 2017 - 13:14:54 PDT)
    - Re: [AMBER] HIE CONVERT INTO HID Bill Ross (Fri Jul 07 2017 - 13:27:14 PDT)
    - Re: [AMBER] HIE CONVERT INTO HID Rana Rehan Khalid (Fri Jul 07 2017 - 14:20:19 PDT)
    - Re: [AMBER] HIE CONVERT INTO HID Bill Ross (Fri Jul 07 2017 - 14:30:22 PDT)
[AMBER] MMPBSA.py.MPI errors with prmtop files on PBS platform Guqin Shi (Fri Jul 07 2017 - 15:47:10 PDT)
- Re: [AMBER] MMPBSA.py.MPI errors with prmtop files on PBS platform Elvis Martis (Fri Jul 07 2017 - 20:39:10 PDT)
  - Re: [AMBER] MMPBSA.py.MPI errors with prmtop files on PBS platform Guqin Shi (Sat Jul 08 2017 - 07:43:25 PDT)
    - Re: [AMBER] MMPBSA.py.MPI errors with prmtop files on PBS platform Elvis Martis (Sat Jul 08 2017 - 08:52:27 PDT)
    - Re: [AMBER] MMPBSA.py.MPI errors with prmtop files on PBS platform Guqin Shi (Sat Jul 08 2017 - 13:11:31 PDT)
[AMBER] Suggestions about Center and Image for multiple-molecule complex Guqin Shi (Sat Jul 08 2017 - 15:58:53 PDT)
- Re: [AMBER] Suggestions about Center and Image for multiple-molecule complex Daniel Roe (Sat Jul 08 2017 - 17:02:23 PDT)
  - Re: [AMBER] Suggestions about Center and Image for multiple-molecule complex Guqin Shi (Sat Jul 08 2017 - 19:06:46 PDT)
    - Re: [AMBER] Suggestions about Center and Image for multiple-molecule complex Bill Ross (Sat Jul 08 2017 - 19:22:02 PDT)
    - Re: [AMBER] Suggestions about Center and Image for multiple-molecule complex Guqin Shi (Sat Jul 08 2017 - 20:34:45 PDT)
    - Re: [AMBER] Suggestions about Center and Image for multiple-molecule complex Bill Ross (Sat Jul 08 2017 - 21:00:06 PDT)
    - Re: [AMBER] Suggestions about Center and Image for multiple-molecule complex Bill Ross (Sat Jul 08 2017 - 21:01:43 PDT)
    - Re: [AMBER] Suggestions about Center and Image for multiple-molecule complex Bill Ross (Sat Jul 08 2017 - 23:31:54 PDT)
    - Re: [AMBER] Suggestions about Center and Image for multiple-molecule complex Guqin Shi (Sun Jul 09 2017 - 19:31:42 PDT)
    - Re: [AMBER] Suggestions about Center and Image for multiple-molecule complex Bill Ross (Sun Jul 09 2017 - 21:51:01 PDT)
    - Re: [AMBER] Suggestions about Center and Image for multiple-molecule complex David Case (Mon Jul 10 2017 - 05:51:08 PDT)
    - Re: [AMBER] Suggestions about Center and Image for multiple-molecule complex Daniel Roe (Mon Jul 10 2017 - 05:32:15 PDT)
- Re: [AMBER] Suggestions about Center and Image for multiple-molecule complex Guqin Shi (Mon Jul 10 2017 - 09:15:29 PDT)
  - Re: [AMBER] Suggestions about Center and Image for multiple-molecule complex Daniel Roe (Mon Jul 10 2017 - 09:29:15 PDT)
    - Re: [AMBER] Suggestions about Center and Image for multiple-molecule complex Guqin Shi (Mon Jul 10 2017 - 10:05:17 PDT)
    - Re: [AMBER] Suggestions about Center and Image for multiple-molecule complex Daniel Roe (Tue Jul 11 2017 - 06:00:47 PDT)
    - Re: [AMBER] Suggestions about Center and Image for multiple-molecule complex Guqin Shi (Tue Jul 11 2017 - 06:43:51 PDT)
    - Re: [AMBER] Suggestions about Center and Image for multiple-molecule complex Guqin Shi (Tue Jul 11 2017 - 08:46:39 PDT)
    - Re: [AMBER] Suggestions about Center and Image for multiple-molecule complex Daniel Roe (Tue Jul 11 2017 - 12:52:14 PDT)
    - Re: [AMBER] Suggestions about Center and Image for multiple-molecule complex Guqin Shi (Tue Jul 11 2017 - 13:35:27 PDT)
    - Re: [AMBER] Suggestions about Center and Image for multiple-molecule complex Daniel Roe (Wed Jul 12 2017 - 05:07:22 PDT)
    - Re: [AMBER] Suggestions about Center and Image for multiple-molecule complex Guqin Shi (Wed Jul 12 2017 - 06:53:39 PDT)
    - Re: [AMBER] Suggestions about Center and Image for multiple-molecule complex Daniel Roe (Wed Jul 12 2017 - 07:01:49 PDT)
    - Re: [AMBER] Suggestions about Center and Image for multiple-molecule complex Guqin Shi (Wed Jul 12 2017 - 06:55:15 PDT)
    - Re: [AMBER] Suggestions about Center and Image for multiple-molecule complex Daniel Roe (Wed Jul 12 2017 - 07:03:12 PDT)
    - Re: [AMBER] Suggestions about Center and Image for multiple-molecule complex Guqin Shi (Wed Jul 12 2017 - 07:32:10 PDT)
    - Re: [AMBER] Suggestions about Center and Image for multiple-molecule complex Daniel Roe (Wed Jul 12 2017 - 07:39:37 PDT)
    - Re: [AMBER] Suggestions about Center and Image for multiple-molecule complex Guqin Shi (Wed Jul 12 2017 - 14:34:02 PDT)
    - Re: [AMBER] Suggestions about Center and Image for multiple-molecule complex Bill Ross (Wed Jul 12 2017 - 14:37:58 PDT)
    - Re: [AMBER] Suggestions about Center and Image for multiple-molecule complex Guqin Shi (Wed Jul 12 2017 - 14:54:34 PDT)
    - Re: [AMBER] Suggestions about Center and Image for multiple-molecule complex Bill Ross (Wed Jul 12 2017 - 15:07:02 PDT)
    - Re: [AMBER] Suggestions about Center and Image for multiple-molecule complex Hai Nguyen (Wed Jul 12 2017 - 15:18:06 PDT)
    - Re: [AMBER] Suggestions about Center and Image for multiple-molecule complex Hai Nguyen (Wed Jul 12 2017 - 15:20:12 PDT)
    - Re: [AMBER] Suggestions about Center and Image for multiple-molecule complex Bill Ross (Wed Jul 12 2017 - 15:36:52 PDT)
    - Re: [AMBER] Suggestions about Center and Image for multiple-molecule complex Guqin Shi (Wed Jul 12 2017 - 15:57:26 PDT)
    - Re: [AMBER] Suggestions about Center and Image for multiple-molecule complex David Case (Tue Jul 11 2017 - 10:16:59 PDT)
    - Re: [AMBER] Suggestions about Center and Image for multiple-molecule complex Guqin Shi (Tue Jul 11 2017 - 10:41:58 PDT)
[AMBER] problem with cpptraj saving the average structure Ramin Salimi (Mon Jul 10 2017 - 03:07:21 PDT)
- Re: [AMBER] problem with cpptraj saving the average structure Daniel Roe (Mon Jul 10 2017 - 05:45:15 PDT)
[AMBER] tleap atom type and hybridization Lizelle Lubbe (Mon Jul 10 2017 - 05:04:06 PDT)
- [AMBER] tleap atom type and hybridization Lizelle Lubbe (Mon Jul 10 2017 - 05:13:25 PDT)
  - Re: [AMBER] tleap atom type and hybridization Pengfei Li (Mon Jul 10 2017 - 19:27:58 PDT)
- Re: [AMBER] tleap atom type and hybridization David Case (Mon Jul 10 2017 - 19:05:39 PDT)
  - Re: [AMBER] tleap atom type and hybridization Lizelle Lubbe (Tue Jul 11 2017 - 03:56:58 PDT)
- Re: [AMBER] tleap atom type and hybridization Pengfei Li (Thu Jul 13 2017 - 12:25:38 PDT)
[AMBER] charm-gui pdb incompatible with xleap Robert Wohlhueter (Mon Jul 10 2017 - 09:51:21 PDT)
- Re: [AMBER] charm-gui pdb incompatible with xleap David Case (Mon Jul 10 2017 - 19:20:07 PDT)
[AMBER] xleap fonts Robert Wohlhueter (Mon Jul 10 2017 - 11:51:14 PDT)
- Re: [AMBER] xleap fonts David Case (Fri Jul 14 2017 - 18:03:29 PDT)
[AMBER] About steered MD with pmemd and NMR restraints Yao Xiao (Mon Jul 10 2017 - 14:32:50 PDT)
- Re: [AMBER] About steered MD with pmemd and NMR restraints Adrian Roitberg (Mon Jul 10 2017 - 14:35:58 PDT)
  - [AMBER] 答复: About steered MD with pmemd and NMR restraints Yao Xiao (Thu Jul 13 2017 - 09:21:55 PDT)
[AMBER] gamess installation Rana Rehan Khalid (Mon Jul 10 2017 - 19:19:41 PDT)
- Re: [AMBER] gamess installation James Kress (Mon Jul 10 2017 - 19:55:47 PDT)
[AMBER] parmed validity off-diagonal LJ parameters Lizelle Lubbe (Tue Jul 11 2017 - 08:00:59 PDT)
- Re: [AMBER] parmed validity off-diagonal LJ parameters Lizelle Lubbe (Wed Jul 12 2017 - 05:23:24 PDT)
  - Re: [AMBER] parmed validity off-diagonal LJ parameters Daniel Roe (Wed Jul 12 2017 - 06:30:05 PDT)
    - Re: [AMBER] parmed validity off-diagonal LJ parameters Lizelle Lubbe (Thu Jul 13 2017 - 02:03:31 PDT)
    - Re: [AMBER] parmed validity off-diagonal LJ parameters Lizelle Lubbe (Thu Jul 13 2017 - 03:58:08 PDT)
    - Re: [AMBER] parmed validity off-diagonal LJ parameters Jason Swails (Sun Jul 23 2017 - 20:21:54 PDT)
    - Re: [AMBER] parmed validity off-diagonal LJ parameters Lizelle Lubbe (Sun Jul 23 2017 - 20:30:10 PDT)
    - Re: [AMBER] parmed validity off-diagonal LJ parameters Daniel Roe (Mon Jul 24 2017 - 05:55:56 PDT)
[AMBER] error Rana Rehan Khalid (Tue Jul 11 2017 - 09:22:55 PDT)
- Re: [AMBER] error Rana Rehan Khalid (Tue Jul 11 2017 - 09:48:19 PDT)
  - Re: [AMBER] error Rana Rehan Khalid (Tue Jul 11 2017 - 14:05:07 PDT)
    - Re: [AMBER] error Bill Ross (Tue Jul 11 2017 - 14:20:37 PDT)
    - Re: [AMBER] error Rana Rehan Khalid (Tue Jul 11 2017 - 14:23:29 PDT)
    - Re: [AMBER] error Bill Ross (Tue Jul 11 2017 - 14:24:38 PDT)
    - Re: [AMBER] error Rana Rehan Khalid (Tue Jul 11 2017 - 14:30:00 PDT)
    - Re: [AMBER] error Bill Ross (Tue Jul 11 2017 - 14:36:01 PDT)
    - Re: [AMBER] error Rana Rehan Khalid (Tue Jul 11 2017 - 14:52:30 PDT)
    - Re: [AMBER] error Bill Ross (Tue Jul 11 2017 - 14:57:20 PDT)
    - Re: [AMBER] error Rana Rehan Khalid (Tue Jul 11 2017 - 15:07:37 PDT)
- Re: [AMBER] error Daniel Roe (Wed Jul 12 2017 - 06:08:08 PDT)
[AMBER] addAtomType Rana Rehan Khalid (Tue Jul 11 2017 - 19:20:32 PDT)
- Re: [AMBER] addAtomType Hai Nguyen (Tue Jul 11 2017 - 19:25:51 PDT)
  - Re: [AMBER] addAtomType Rana Rehan Khalid (Tue Jul 11 2017 - 20:36:25 PDT)
    - Re: [AMBER] addAtomType Hai Nguyen (Tue Jul 11 2017 - 21:23:43 PDT)
    - Re: [AMBER] addAtomType Rana Rehan Khalid (Tue Jul 11 2017 - 21:38:49 PDT)
    - Re: [AMBER] addAtomType Bill Ross (Tue Jul 11 2017 - 21:52:48 PDT)
    - Re: [AMBER] addAtomType Rana Rehan Khalid (Tue Jul 11 2017 - 22:08:29 PDT)
    - Re: [AMBER] addAtomType Hai Nguyen (Tue Jul 11 2017 - 21:55:00 PDT)
    - Re: [AMBER] addAtomType Rana Rehan Khalid (Tue Jul 11 2017 - 22:09:38 PDT)
[AMBER] How to perform analysis using ptraj Mustafa Alhaji Isa (Tue Jul 11 2017 - 23:01:53 PDT)
- Re: [AMBER] How to perform analysis using ptraj Hai Nguyen (Tue Jul 11 2017 - 23:07:30 PDT)
- Re: [AMBER] How to perform analysis using ptraj Luka Bilić (Wed Jul 12 2017 - 01:14:03 PDT)
[AMBER] A good multi GPU work-station James Starlight (Wed Jul 12 2017 - 01:46:40 PDT)
- Re: [AMBER] A good multi GPU work-station Luka Bilić (Wed Jul 12 2017 - 04:54:15 PDT)
- Re: [AMBER] A good multi GPU work-station Ross Walker (Wed Jul 12 2017 - 05:59:22 PDT)
  - Re: [AMBER] A good multi GPU work-station James Starlight (Wed Jul 12 2017 - 06:47:58 PDT)
    - Re: [AMBER] A good multi GPU work-station James Starlight (Wed Jul 12 2017 - 06:53:37 PDT)
[AMBER] micelle simulation Meng Wu (Wed Jul 12 2017 - 05:26:01 PDT)
- Re: [AMBER] micelle simulation Qinghua Liao (Wed Jul 12 2017 - 05:47:49 PDT)
- Re: [AMBER] micelle simulation ABEL Stephane (Wed Jul 12 2017 - 07:20:28 PDT)
[AMBER] no output files of umbrella_file in ABMD Qinghua Liao (Wed Jul 12 2017 - 05:37:29 PDT)
- Re: [AMBER] no output files of umbrella_file in ABMD Feng Pan (Thu Jul 13 2017 - 14:24:44 PDT)
  - Re: [AMBER] no output files of umbrella_file in ABMD Qinghua Liao (Thu Jul 13 2017 - 14:45:04 PDT)
    - Re: [AMBER] no output files of umbrella_file in ABMD Fabrício Bracht (Thu Jul 13 2017 - 17:59:17 PDT)
- Re: [AMBER] no output files of umbrella_file in ABMD Qinghua Liao (Sat Jul 15 2017 - 02:04:11 PDT)
[AMBER] SDF (Spatial Distribution Function) calculation Saikat Pal (Wed Jul 12 2017 - 06:06:00 PDT)
- Re: [AMBER] SDF (Spatial Distribution Function) calculation Daniel Roe (Wed Jul 12 2017 - 06:10:23 PDT)
  - Re: [AMBER] SDF (Spatial Distribution Function) calculation Saikat Pal (Wed Jul 12 2017 - 07:29:35 PDT)
    - Re: [AMBER] SDF (Spatial Distribution Function) calculation Daniel Roe (Wed Jul 12 2017 - 07:46:23 PDT)
[AMBER] Sander MPI running over multiple nodes. Robinson, Roger (Wed Jul 12 2017 - 06:45:44 PDT)
- Re: [AMBER] Sander MPI running over multiple nodes. Daniel Roe (Wed Jul 12 2017 - 07:08:48 PDT)
[AMBER] Amber installation Saikat Pal (Wed Jul 12 2017 - 08:01:30 PDT)
- Re: [AMBER] Amber installation Daniel Roe (Wed Jul 12 2017 - 08:21:14 PDT)
  - Re: [AMBER] Amber installation Saikat Pal (Wed Jul 12 2017 - 23:18:51 PDT)
    - Re: [AMBER] Amber installation Bill Ross (Thu Jul 13 2017 - 01:35:07 PDT)
    - Re: [AMBER] Amber installation Saikat Pal (Thu Jul 13 2017 - 04:08:17 PDT)
    - Re: [AMBER] Amber installation Bill Ross (Thu Jul 13 2017 - 11:23:16 PDT)
    - Re: [AMBER] Amber installation Saikat Pal (Fri Jul 14 2017 - 05:16:20 PDT)
    - Re: [AMBER] Amber installation David Case (Fri Jul 14 2017 - 17:38:35 PDT)
    - Re: [AMBER] Amber installation Daniel Roe (Thu Jul 13 2017 - 05:04:44 PDT)
    - Re: [AMBER] Amber installation Saikat Pal (Thu Jul 13 2017 - 05:32:21 PDT)
    - Re: [AMBER] Amber installation Daniel Roe (Thu Jul 13 2017 - 10:18:19 PDT)
    - Re: [AMBER] Amber installation Hai Nguyen (Thu Jul 13 2017 - 10:24:58 PDT)
[AMBER] cudaGetDeviceCount failed unknown error AMBER16 Hector Velazquez (Wed Jul 12 2017 - 12:16:18 PDT)
- Re: [AMBER] cudaGetDeviceCount failed unknown error AMBER16 Daniel Roe (Wed Jul 12 2017 - 12:36:32 PDT)
- Re: [AMBER] cudaGetDeviceCount failed unknown error AMBER16 Ross Walker (Wed Jul 12 2017 - 12:44:58 PDT)
[AMBER] A DNA-based short-term memory for biological deep learning Bill Ross (Wed Jul 12 2017 - 14:46:54 PDT)
[AMBER] Problem with running mdout_analyzer.py Krantzman, Kristin D (Wed Jul 12 2017 - 15:40:42 PDT)
- Re: [AMBER] Problem with running mdout_analyzer.py Bill Ross (Wed Jul 12 2017 - 15:43:02 PDT)
  - Re: [AMBER] Problem with running mdout_analyzer.py Bill Ross (Wed Jul 12 2017 - 15:44:56 PDT)
    - Re: [AMBER] Problem with running mdout_analyzer.py Krantzman, Kristin D (Wed Jul 12 2017 - 15:55:41 PDT)
    - Re: [AMBER] Problem with running mdout_analyzer.py Bill Ross (Wed Jul 12 2017 - 16:02:02 PDT)
    - Re: [AMBER] Problem with running mdout_analyzer.py Bill Ross (Wed Jul 12 2017 - 16:07:44 PDT)
    - Re: [AMBER] Problem with running mdout_analyzer.py Hai Nguyen (Wed Jul 12 2017 - 16:06:01 PDT)
    - Re: [AMBER] Problem with running mdout_analyzer.py Krantzman, Kristin D (Wed Jul 12 2017 - 16:18:58 PDT)
[AMBER] MCPB.py issue Aldo Segura Cabrera (Wed Jul 12 2017 - 19:47:45 PDT)
- Re: [AMBER] MCPB.py issue Pengfei Li (Thu Jul 13 2017 - 12:09:09 PDT)
  - Re: [AMBER] MCPB.py issue Aldo Segura Cabrera (Thu Jul 13 2017 - 13:06:09 PDT)
    - Re: [AMBER] MCPB.py issue Pengfei Li (Thu Jul 13 2017 - 13:10:18 PDT)
    - Re: [AMBER] MCPB.py issue Aldo Segura Cabrera (Thu Jul 13 2017 - 13:16:15 PDT)
    - Re: [AMBER] MCPB.py issue Pengfei Li (Fri Jul 14 2017 - 13:42:25 PDT)
[AMBER] antechamber problem Michael Shokhen (Thu Jul 13 2017 - 02:15:28 PDT)
- Re: [AMBER] antechamber problem Changqing Yan (Fri Jan 11 2013 - 21:31:47 PST)
- Re: [AMBER] antechamber problem Prayagraj Fandilolu (Thu Jul 13 2017 - 02:42:44 PDT)
  - Re: [AMBER] antechamber problem Michael Shokhen (Thu Jul 13 2017 - 03:22:32 PDT)
[AMBER] prepin file for CMP ligand ARMIN HODAEI (Thu Jul 13 2017 - 04:40:29 PDT)
- Re: [AMBER] prepin file for CMP ligand Prayagraj Fandilolu (Thu Jul 13 2017 - 05:25:37 PDT)
[AMBER] cpptraj hbond Martina Devi (Thu Jul 13 2017 - 09:12:16 PDT)
- Re: [AMBER] cpptraj hbond Daniel Roe (Thu Jul 13 2017 - 10:12:00 PDT)
[AMBER] ERROR: The unperturbed charge of the unit: is not integral Li, Wen (Thu Jul 13 2017 - 11:38:01 PDT)
- Re: [AMBER] ERROR: The unperturbed charge of the unit: is not integral David Case (Thu Jul 13 2017 - 14:01:10 PDT)
  - Re: [AMBER] ERROR: The unperturbed charge of the unit: is not integral Li, Wen (Fri Jul 14 2017 - 06:39:45 PDT)
    - Re: [AMBER] ERROR: The unperturbed charge of the unit: is not integral Qinghua Liao (Fri Jul 14 2017 - 06:50:21 PDT)
    - Re: [AMBER] ERROR: The unperturbed charge of the unit: is not integral Li, Wen (Tue Jul 18 2017 - 07:33:44 PDT)
    - Re: [AMBER] ERROR: The unperturbed charge of the unit: is not integral David Case (Fri Jul 14 2017 - 17:41:58 PDT)
[AMBER] cphstats Error: Could not open or parse cpin file Vincent Ustach (Thu Jul 13 2017 - 12:12:59 PDT)
- Re: [AMBER] cphstats Error: Could not open or parse cpin file Eric Lang (Fri Jul 14 2017 - 01:48:40 PDT)
  - Re: [AMBER] cphstats Error: Could not open or parse cpin file Vincent Ustach (Fri Jul 14 2017 - 09:34:08 PDT)
    - Re: [AMBER] cphstats Error: Could not open or parse cpin file Vincent Ustach (Thu Aug 24 2017 - 20:22:28 PDT)
    - Re: [AMBER] cphstats Error: Could not open or parse cpin file Jason Swails (Mon Aug 28 2017 - 18:52:15 PDT)
[AMBER] PCA - first mode of motion Thakur, Abhishek (Thu Jul 13 2017 - 14:46:25 PDT)
- Re: [AMBER] PCA - first mode of motion Elvis Martis (Thu Jul 13 2017 - 20:27:42 PDT)
[AMBER] PMEMD module for Umbrella sampling Supriyo Naskar (Thu Jul 13 2017 - 21:45:42 PDT)
- Re: [AMBER] PMEMD module for Umbrella sampling Feng Pan (Fri Jul 14 2017 - 20:36:36 PDT)
  - Re: [AMBER] PMEMD module for Umbrella sampling Supriyo Naskar (Tue Jul 18 2017 - 21:46:37 PDT)
    - Re: [AMBER] PMEMD module for Umbrella sampling Feng Pan (Tue Jul 18 2017 - 22:05:43 PDT)
    - Re: [AMBER] PMEMD module for Umbrella sampling Supriyo Naskar (Tue Jul 18 2017 - 22:12:03 PDT)
[AMBER] parmchk2 closing loop error CA gmail (Fri Jul 14 2017 - 02:08:43 PDT)
- Re: [AMBER] parmchk2 closing loop error David Case (Fri Jul 14 2017 - 17:45:00 PDT)
[AMBER] Umbrella sampling and weighted histogram analysis for binding energy calculation Investigador Química (Fri Jul 14 2017 - 11:40:04 PDT)
[AMBER] micelle simulation problem Meng Wu (Sat Jul 15 2017 - 01:03:46 PDT)
- Re: [AMBER] micelle simulation problem Bill Ross (Sat Jul 15 2017 - 02:16:42 PDT)
[AMBER] gcc error while compiling Amber16 on ubuntu16.04 Vivek Bharadwaj (Sat Jul 15 2017 - 14:17:17 PDT)
- Re: [AMBER] gcc error while compiling Amber16 on ubuntu16.04 Bill Ross (Sat Jul 15 2017 - 14:27:37 PDT)
- Re: [AMBER] gcc error while compiling Amber16 on ubuntu16.04 David Case (Sun Jul 16 2017 - 10:03:18 PDT)
  - Re: [AMBER] gcc error while compiling Amber16 on ubuntu16.04 Hai Nguyen (Sun Jul 16 2017 - 10:13:03 PDT)
[AMBER] FW: hbond analysis with CPPTRAJ Al Muhit, Baig Abdullah (Sat Jul 15 2017 - 17:05:43 PDT)
[AMBER] hbond analysis with CPPTRAJ Al Muhit, Baig Abdullah (Sat Jul 15 2017 - 23:59:01 PDT)
[AMBER] problem in CUDA-enabled Amber11 Pooja Kesari (Sun Jul 16 2017 - 06:35:36 PDT)
- Re: [AMBER] problem in CUDA-enabled Amber11 David Case (Sun Jul 16 2017 - 10:15:18 PDT)
[AMBER] Set-up the GPU cluster for AMBER James Starlight (Sun Jul 16 2017 - 06:49:25 PDT)
- Re: [AMBER] Set-up the GPU cluster for AMBER David Case (Sun Jul 16 2017 - 10:31:41 PDT)
[AMBER] hbond analysis with CPPTRAJ Baig abdullah Al muhit (Sun Jul 16 2017 - 08:19:19 PDT)
- Re: [AMBER] hbond analysis with CPPTRAJ Hai Nguyen (Sun Jul 16 2017 - 08:55:17 PDT)
  - Re: [AMBER] hbond analysis with CPPTRAJ Baig abdullah Al muhit (Sun Jul 16 2017 - 09:01:37 PDT)
    - Re: [AMBER] hbond analysis with CPPTRAJ Hai Nguyen (Sun Jul 16 2017 - 09:54:37 PDT)
    - Re: [AMBER] hbond analysis with CPPTRAJ Al Muhit, Baig Abdullah (Sun Jul 16 2017 - 10:01:07 PDT)
- Re: [AMBER] hbond analysis with CPPTRAJ Daniel Roe (Mon Jul 17 2017 - 10:23:32 PDT)
  - Re: [AMBER] hbond analysis with CPPTRAJ Baig abdullah Al muhit (Mon Jul 17 2017 - 14:19:19 PDT)
    - Re: [AMBER] hbond analysis with CPPTRAJ Daniel Roe (Thu Jul 20 2017 - 06:34:01 PDT)
    - Re: [AMBER] hbond analysis with CPPTRAJ Daniel Roe (Thu Jul 20 2017 - 07:08:13 PDT)
[AMBER] Simulation of the mechanical stress in Amber James Starlight (Mon Jul 17 2017 - 00:53:32 PDT)
[AMBER] pmemd.cuda vs pmemd.cuda.MPI Saikat Pal (Mon Jul 17 2017 - 05:03:21 PDT)
- Re: [AMBER] pmemd.cuda vs pmemd.cuda.MPI Charles Lin (Mon Jul 17 2017 - 08:16:17 PDT)
[AMBER] Error in LEaP Dey, S. (Mon Jul 17 2017 - 08:55:10 PDT)
- Re: [AMBER] Error in LEaP Thakur, Abhishek (Mon Jul 17 2017 - 09:02:42 PDT)
  - Re: [AMBER] Error in LEaP Dey, S. (Tue Jul 18 2017 - 02:11:42 PDT)
- Re: [AMBER] Error in LEaP Bill Ross (Mon Jul 17 2017 - 09:54:29 PDT)
- Re: [AMBER] Error in LEaP Bill Ross (Tue Jul 18 2017 - 08:29:33 PDT)
[AMBER] NVIDIA quadro 5000 with Intel Xeon server for Amber-16 James Starlight (Mon Jul 17 2017 - 09:01:07 PDT)
- Re: [AMBER] NVIDIA quadro 5000 with Intel Xeon server for Amber-16 Daniel Roe (Mon Jul 17 2017 - 10:13:27 PDT)
- Re: [AMBER] NVIDIA quadro 5000 with Intel Xeon server for Amber-16 David A Case (Mon Jul 17 2017 - 10:30:22 PDT)
[AMBER] G09 Error Rana Rehan Khalid (Mon Jul 17 2017 - 11:38:12 PDT)
- Re: [AMBER] G09 Error Gorday, Kent M. (Mon Jul 17 2017 - 11:57:07 PDT)
  - Re: [AMBER] G09 Error Rana Rehan Khalid (Mon Jul 17 2017 - 12:51:20 PDT)
    - Re: [AMBER] G09 Error Gorday, Kent M. (Mon Jul 17 2017 - 13:20:15 PDT)
    - Re: [AMBER] G09 Error Rana Rehan Khalid (Mon Jul 17 2017 - 13:26:55 PDT)
[AMBER] MCPB.py tutorial - numbering issues Szymon Żaczek (Mon Jul 17 2017 - 11:54:33 PDT)
- Re: [AMBER] MCPB.py tutorial - numbering issues Daniel Roe (Mon Jul 17 2017 - 16:09:09 PDT)
  - Re: [AMBER] MCPB.py tutorial - numbering issues Szymon Żaczek (Tue Jul 18 2017 - 01:07:23 PDT)
    - Re: [AMBER] MCPB.py tutorial - numbering issues Daniel Roe (Tue Jul 18 2017 - 07:21:24 PDT)
    - Re: [AMBER] MCPB.py tutorial - numbering issues Pengfei Li (Thu Jul 27 2017 - 12:52:26 PDT)
Re: [AMBER] AMBER Digest, Vol 1994, Issue 1 Hector Velazquez (Mon Jul 17 2017 - 12:44:21 PDT)
[AMBER] Log file for Reweighting Parthiban Marimuthu (Mon Jul 17 2017 - 14:58:50 PDT)
[AMBER] CPPTRAJ analysis on PDB trajectory with TIP4P water from GROMACS Ming Tang (Mon Jul 17 2017 - 19:08:13 PDT)
- Re: [AMBER] CPPTRAJ analysis on PDB trajectory with TIP4P water from GROMACS Daniel Roe (Tue Jul 18 2017 - 07:11:15 PDT)
  - Re: [AMBER] CPPTRAJ analysis on PDB trajectory with TIP4P water from GROMACS Ming Tang (Tue Jul 18 2017 - 14:56:41 PDT)
    - Re: [AMBER] CPPTRAJ analysis on PDB trajectory with TIP4P water from GROMACS Chris Neale (Tue Jul 18 2017 - 21:04:46 PDT)
    - Re: [AMBER] CPPTRAJ analysis on PDB trajectory with TIP4P water from GROMACS Daniel Roe (Wed Jul 19 2017 - 03:16:32 PDT)
- Re: [AMBER] CPPTRAJ analysis on PDB trajectory with TIP4P water from GROMACS Daniel Roe (Thu Jul 20 2017 - 06:24:18 PDT)
  - Re: [AMBER] CPPTRAJ analysis on PDB trajectory with TIP4P water from GROMACS Neha Gandhi (Fri Jul 21 2017 - 02:43:19 PDT)
[AMBER] Chi plot tryptophan. Saman Yousuf ali (Mon Jul 17 2017 - 22:07:16 PDT)
- Re: [AMBER] Chi plot tryptophan. Hai Nguyen (Mon Jul 17 2017 - 22:10:16 PDT)
[AMBER] amber12 cpptraj runanalysis Martina Devi (Tue Jul 18 2017 - 07:21:29 PDT)
- Re: [AMBER] amber12 cpptraj runanalysis Daniel Roe (Tue Jul 18 2017 - 07:38:52 PDT)
  - Re: [AMBER] amber12 cpptraj runanalysis Martina Devi (Tue Jul 18 2017 - 09:18:39 PDT)
[AMBER] parmed/intermol gromacs to amber Neha Gandhi (Tue Jul 18 2017 - 17:56:38 PDT)
- Re: [AMBER] parmed/intermol gromacs to amber Daniel Roe (Thu Jul 20 2017 - 06:26:25 PDT)
[AMBER] Error come after executing this command MCPB.py -i 4ZF6.in -s 2 Rana Rehan Khalid (Tue Jul 18 2017 - 20:38:51 PDT)
- Re: [AMBER] Error come after executing this command MCPB.py -i 4ZF6.in -s 2 Pengfei Li (Thu Jul 27 2017 - 12:31:46 PDT)
[AMBER] problem Finding entropy Ramin Salimi (Tue Jul 18 2017 - 21:33:47 PDT)
- Re: [AMBER] problem Finding entropy David A Case (Wed Jul 19 2017 - 05:33:09 PDT)
  - Re: [AMBER] problem Finding entropy Ramin Salimi (Wed Jul 19 2017 - 19:27:50 PDT)
    - Re: [AMBER] problem Finding entropy Daniel Roe (Thu Jul 20 2017 - 06:21:58 PDT)
    - Re: [AMBER] problem Finding entropy Ramin Salimi (Thu Jul 20 2017 - 06:46:21 PDT)
    - Re: [AMBER] problem Finding entropy Adrian Roitberg (Thu Jul 20 2017 - 06:50:28 PDT)
    - Re: [AMBER] problem Finding entropy Ramin Salimi (Thu Jul 20 2017 - 06:54:00 PDT)
    - Re: [AMBER] problem Finding entropy Ramin Salimi (Thu Jul 20 2017 - 06:57:16 PDT)
    - Re: [AMBER] problem Finding entropy David A Case (Thu Jul 20 2017 - 08:16:47 PDT)
    - Re: [AMBER] problem Finding entropy Ramin Salimi (Thu Jul 20 2017 - 08:48:01 PDT)
- Re: [AMBER] problem Finding entropy Ramin Salimi (Thu Jul 20 2017 - 05:37:49 PDT)
  - Re: [AMBER] problem Finding entropy Gustavo Seabra (Thu Jul 20 2017 - 11:47:30 PDT)
- Re: [AMBER] problem Finding entropy Ramin Salimi (Thu Jul 20 2017 - 10:40:28 PDT)
  - Re: [AMBER] problem Finding entropy David A Case (Thu Jul 20 2017 - 11:51:23 PDT)
[AMBER] How do I perform LIE analysis for a metalloprotein containing Cd using Amber ? Garima Singh (Wed Jul 19 2017 - 02:50:39 PDT)
- Re: [AMBER] How do I perform LIE analysis for a metalloprotein containing Cd using Amber ? Daniel Roe (Thu Jul 20 2017 - 06:32:00 PDT)
[AMBER] amb2gmx.pl script not working Dey, S. (Wed Jul 19 2017 - 05:27:17 PDT)
- Re: [AMBER] amb2gmx.pl script not working Hai Nguyen (Wed Jul 19 2017 - 05:34:14 PDT)
[AMBER] QM/MM Minimization with restraints Sonia Romero (Wed Jul 19 2017 - 06:07:45 PDT)
- Re: [AMBER] QM/MM Minimization with restraints diego.soler.uam.es (Wed Jul 19 2017 - 06:23:34 PDT)
  - Re: [AMBER] QM/MM Minimization with restraints Sonia Romero (Wed Jul 19 2017 - 07:26:21 PDT)
[AMBER] vlimit error sangita kachhap (Wed Jul 19 2017 - 07:54:01 PDT)
- Re: [AMBER] vlimit error David A Case (Wed Jul 19 2017 - 08:51:04 PDT)
  - Re: [AMBER] vlimit error sangita kachhap (Wed Jul 19 2017 - 14:09:39 PDT)
[AMBER] Orca interface for QM/MM James Kress (Wed Jul 19 2017 - 10:03:28 PDT)
- Re: [AMBER] Orca interface for QM/MM Goetz, Andreas (Wed Jul 19 2017 - 13:28:49 PDT)
  - Re: [AMBER] Orca interface for QM/MM James Kress (Thu Jul 20 2017 - 09:30:04 PDT)
    - Re: [AMBER] Orca interface for QM/MM Goetz, Andreas (Thu Jul 20 2017 - 17:20:31 PDT)
[AMBER] Log file for Reweighting Parthiban Marimuthu (Wed Jul 19 2017 - 12:48:12 PDT)
- Re: [AMBER] Log file for Reweighting Daniel Roe (Thu Jul 20 2017 - 06:27:56 PDT)
- Re: [AMBER] Log file for Reweighting Parthiban Marimuthu (Thu Jul 20 2017 - 13:23:55 PDT)
  - Re: [AMBER] Log file for Reweighting Daniel Roe (Thu Jul 20 2017 - 14:16:08 PDT)
- Re: [AMBER] Log file for Reweighting Parthiban Marimuthu (Mon Jul 24 2017 - 11:51:21 PDT)
[AMBER] Use energy fluctuations as the criterion of equilibrium in the NPT ensembles? Xing (Wed Jul 19 2017 - 17:02:33 PDT)
- Re: [AMBER] Use energy fluctuations as the criterion of equilibrium in the NPT ensembles? Daniel Roe (Thu Jul 20 2017 - 06:29:28 PDT)
[AMBER] ion distribution-doubt Mary Varughese (Wed Jul 19 2017 - 23:38:29 PDT)
- Re: [AMBER] ion distribution-doubt David A Case (Thu Jul 20 2017 - 04:49:15 PDT)
[AMBER] Simulation of the mechanical stress James Starlight (Thu Jul 20 2017 - 02:14:23 PDT)
- Re: [AMBER] Simulation of the mechanical stress David A Case (Thu Jul 20 2017 - 04:52:29 PDT)
  - Re: [AMBER] Simulation of the mechanical stress James Starlight (Thu Jul 20 2017 - 05:30:34 PDT)
- Re: [AMBER] Simulation of the mechanical stress James Starlight (Fri Jul 21 2017 - 01:44:48 PDT)
  - Re: [AMBER] Simulation of the mechanical stress James Starlight (Fri Jul 21 2017 - 04:40:59 PDT)
[AMBER] Sander doing the minimisation but stopping at the first heating step, not generating rst or nc files Alonso Martinez, Diego (Thu Jul 20 2017 - 06:05:39 PDT)
- Re: [AMBER] Sander doing the minimisation but stopping at the first heating step, not generating rst or nc files Adrian Roitberg (Thu Jul 20 2017 - 06:22:36 PDT)
  - Re: [AMBER] Sander doing the minimisation but stopping at the first heating step, not generating rst or nc files Carlos Simmerling (Thu Jul 20 2017 - 06:40:57 PDT)
    - Re: [AMBER] Sander doing the minimisation but stopping at the first heating step, not generating rst or nc files Alonso Martinez, Diego (Thu Jul 20 2017 - 11:58:46 PDT)
    - Re: [AMBER] Sander doing the minimisation but stopping at the first heating step, not generating rst or nc files Adrian Roitberg (Thu Jul 20 2017 - 12:04:35 PDT)
    - Re: [AMBER] Sander doing the minimisation but stopping at the first heating step, not generating rst or nc files Alonso Martinez, Diego (Thu Jul 20 2017 - 12:19:39 PDT)
    - Re: [AMBER] Sander doing the minimisation but stopping at the first heating step, not generating rst or nc files Adrian Roitberg (Thu Jul 20 2017 - 12:23:34 PDT)
    - Re: [AMBER] Sander doing the minimisation but stopping at the first heating step, not generating rst or nc files Bill Ross (Thu Jul 20 2017 - 12:23:55 PDT)
    - Re: [AMBER] Sander doing the minimisation but stopping at the first heating step, not generating rst or nc files Alonso Martinez, Diego (Thu Jul 20 2017 - 12:33:00 PDT)
    - Re: [AMBER] Sander doing the minimisation but stopping at the first heating step, not generating rst or nc files Hai Nguyen (Thu Jul 20 2017 - 12:38:41 PDT)
- Re: [AMBER] Sander doing the minimisation but stopping at the first heating step, not generating rst or nc files Bill Ross (Thu Jul 20 2017 - 13:00:24 PDT)
  - Re: [AMBER] Sander doing the minimisation but stopping at the first heating step, not generating rst or nc files Alonso Martinez, Diego (Tue Aug 01 2017 - 07:48:34 PDT)
    - Re: [AMBER] Sander doing the minimisation but stopping at the first heating step, not generating rst or nc files Carlos Simmerling (Tue Aug 01 2017 - 07:54:17 PDT)
    - Re: [AMBER] Sander doing the minimisation but stopping at the first heating step, not generating rst or nc files Alonso Martinez, Diego (Tue Aug 01 2017 - 09:49:42 PDT)
    - Re: [AMBER] Sander doing the minimisation but stopping at the first heating step, not generating rst or nc files Szymon Żaczek (Tue Aug 01 2017 - 11:17:17 PDT)
    - Re: [AMBER] Sander doing the minimisation but stopping at the first heating step, not generating rst or nc files Bill Ross (Tue Aug 01 2017 - 11:23:02 PDT)
[AMBER] Buying-renting GPU/CPU time for amber MD simulations George Tzotzos (Thu Jul 20 2017 - 08:38:16 PDT)
- Re: [AMBER] Buying-renting GPU/CPU time for amber MD simulations Chris Neale (Thu Jul 20 2017 - 08:53:27 PDT)
  - Re: [AMBER] Buying-renting GPU/CPU time for amber MD simulations Kenneth Huang (Thu Jul 20 2017 - 09:05:10 PDT)
    - Re: [AMBER] Buying-renting GPU/CPU time for amber MD simulations George Tzotzos (Thu Jul 20 2017 - 09:27:21 PDT)
- Re: [AMBER] Buying-renting GPU/CPU time for amber MD simulations Ross Walker (Thu Jul 20 2017 - 08:56:48 PDT)
[AMBER] Functions in NAB Akshar Sharma (Thu Jul 20 2017 - 08:54:23 PDT)
- Re: [AMBER] Functions in NAB David A Case (Thu Jul 20 2017 - 10:33:35 PDT)
  - Re: [AMBER] Functions in NAB Akshar Sharma (Thu Jul 20 2017 - 21:20:50 PDT)
    - Re: [AMBER] Functions in NAB David Case (Fri Jul 21 2017 - 06:03:10 PDT)
    - Re: [AMBER] Functions in NAB Akshar Sharma (Fri Jul 21 2017 - 11:14:17 PDT)
    - Re: [AMBER] Functions in NAB Akshar Sharma (Fri Jul 21 2017 - 11:18:14 PDT)
    - Re: [AMBER] Functions in NAB David Case (Tue Jul 25 2017 - 17:02:07 PDT)
    - Re: [AMBER] Functions in NAB Akshar Sharma (Tue Jul 25 2017 - 21:14:22 PDT)
    - Re: [AMBER] Functions in NAB Hai Nguyen (Tue Jul 25 2017 - 21:18:18 PDT)
[AMBER] His getting protonated to HIP Thakur, Abhishek (Thu Jul 20 2017 - 15:26:50 PDT)
- Re: [AMBER] His getting protonated to HIP Adrian Roitberg (Thu Jul 20 2017 - 15:29:44 PDT)
- Re: [AMBER] His getting protonated to HIP Hai Nguyen (Thu Jul 20 2017 - 15:32:49 PDT)
  - Re: [AMBER] His getting protonated to HIP Thakur, Abhishek (Thu Jul 20 2017 - 15:52:27 PDT)
    - Re: [AMBER] His getting protonated to HIP Hai Nguyen (Thu Jul 20 2017 - 16:00:06 PDT)
    - Re: [AMBER] His getting protonated to HIP Thakur, Abhishek (Thu Jul 20 2017 - 16:06:04 PDT)
    - Re: [AMBER] His getting protonated to HIP Hai Nguyen (Thu Jul 20 2017 - 16:22:21 PDT)
    - Re: [AMBER] His getting protonated to HIP Thakur, Abhishek (Thu Jul 20 2017 - 18:23:29 PDT)
    - Re: [AMBER] His getting protonated to HIP Hirdesh Kumar (Thu Jul 20 2017 - 20:13:00 PDT)
    - Re: [AMBER] His getting protonated to HIP David Case (Fri Jul 21 2017 - 05:50:34 PDT)
[AMBER] Problems in using GLYCAM force field Meng Wu (Fri Jul 21 2017 - 05:17:32 PDT)
- Re: [AMBER] Problems in using GLYCAM force field Lachele Foley (Fri Jul 21 2017 - 05:39:14 PDT)
- Re: [AMBER] Problems in using GLYCAM force field Meng Wu (Sun Jul 23 2017 - 04:16:31 PDT)
[AMBER] Distance restraint during production md Lizelle Lubbe (Sat Jul 22 2017 - 10:51:43 PDT)
- Re: [AMBER] Distance restraint during production md David Case (Sun Jul 23 2017 - 04:33:06 PDT)
[AMBER] INSTALLING AMBER IN WINDOWS K. Subashini (Sun Jul 23 2017 - 01:08:49 PDT)
- Re: [AMBER] INSTALLING AMBER IN WINDOWS David Case (Sun Jul 23 2017 - 04:37:13 PDT)
[AMBER] Use of DFTB3 with Dispersion Correction Christian Wiebeler (Sun Jul 23 2017 - 10:36:21 PDT)
[AMBER] Extracting trajectory without the periodic boundary conditions usng ptraj Shilpa Gupta (Sun Jul 23 2017 - 10:55:18 PDT)
- Re: [AMBER] Extracting trajectory without the periodic boundary conditions usng ptraj David Case (Sun Jul 23 2017 - 12:44:28 PDT)
[AMBER] Mcpbpy empirical method Lizelle Lubbe (Mon Jul 24 2017 - 04:32:19 PDT)
- Re: [AMBER] Mcpbpy empirical method Pengfei Li (Thu Jul 27 2017 - 12:11:15 PDT)
[AMBER] SASA calculation using LCPO method Garima Singh (Mon Jul 24 2017 - 04:34:58 PDT)
- Re: [AMBER] SASA calculation using LCPO method Daniel Roe (Mon Jul 24 2017 - 05:47:31 PDT)
[AMBER] gpu %utils vs mem used Meij, Henk (Mon Jul 24 2017 - 11:20:39 PDT)
- Re: [AMBER] gpu %utils vs mem used Ross Walker (Mon Jul 24 2017 - 12:16:09 PDT)
  - Re: [AMBER] gpu %utils vs mem used Meij, Henk (Tue Jul 25 2017 - 06:06:17 PDT)
    - Re: [AMBER] gpu %utils vs mem used Ross Walker (Tue Jul 25 2017 - 07:31:16 PDT)
    - Re: [AMBER] gpu %utils vs mem used Meij, Henk (Tue Jul 25 2017 - 10:49:58 PDT)
    - Re: [AMBER] gpu %utils vs mem used Mark Abraham (Tue Jul 25 2017 - 11:48:40 PDT)
    - Re: [AMBER] gpu %utils vs mem used Ross Walker (Tue Jul 25 2017 - 12:02:55 PDT)
    - Re: [AMBER] gpu %utils vs mem used Mark Abraham (Tue Jul 25 2017 - 14:19:42 PDT)
    - Re: [AMBER] gpu %utils vs mem used James Kress (Tue Jul 25 2017 - 16:18:21 PDT)
    - Re: [AMBER] gpu %utils vs mem used Ross Walker (Tue Jul 25 2017 - 16:38:20 PDT)
    - Re: [AMBER] gpu %utils vs mem used Mark Abraham (Tue Jul 25 2017 - 18:24:33 PDT)
    - Re: [AMBER] gpu %utils vs mem used Ross Walker (Tue Jul 25 2017 - 18:44:21 PDT)
    - Re: [AMBER] gpu %utils vs mem used Ryan Novosielski (Tue Jul 25 2017 - 18:58:00 PDT)
- Re: [AMBER] gpu %utils vs mem used Scott Le Grand (Tue Jul 25 2017 - 19:04:31 PDT)
[AMBER] Is it possible to align frames? Elisa Pieri (Mon Jul 24 2017 - 12:59:17 PDT)
- Re: [AMBER] Is it possible to align frames? Xing (Mon Jul 24 2017 - 14:09:04 PDT)
  - Re: [AMBER] Is it possible to align frames? Elisa Pieri (Mon Jul 24 2017 - 14:56:47 PDT)
    - Re: [AMBER] Is it possible to align frames? Bill Ross (Mon Jul 24 2017 - 15:10:10 PDT)
    - Re: [AMBER] Is it possible to align frames? Elisa Pieri (Mon Jul 24 2017 - 15:19:47 PDT)
- Re: [AMBER] Is it possible to align frames? Daniel Roe (Tue Jul 25 2017 - 05:34:56 PDT)
[AMBER] ncsu_smd codes with pmemd in Amber 16 Yao Xiao (Mon Jul 24 2017 - 13:58:51 PDT)
- Re: [AMBER] ncsu_smd codes with pmemd in Amber 16 Feng Pan (Mon Jul 24 2017 - 14:11:33 PDT)
  - [AMBER] 答复: ncsu_smd codes with pmemd in Amber 16 Yao Xiao (Mon Jul 24 2017 - 14:55:16 PDT)
    - Re: [AMBER] 答复: ncsu_smd codes with pmemd in Amber 16 Feng Pan (Mon Jul 24 2017 - 19:27:45 PDT)
    - [AMBER] 答复: 答复: ncsu_smd codes with pmemd in Amber 16 Yao Xiao (Tue Jul 25 2017 - 12:47:59 PDT)
    - Re: [AMBER] 答复: 答复: ncsu_smd codes with pmemd in Amber 16 Feng Pan (Wed Jul 26 2017 - 10:37:38 PDT)
[AMBER] Grid visualization for ions- doubt maryvj1985 (Mon Jul 24 2017 - 22:54:05 PDT)
[AMBER] Free Energy, mutating an amino acid Johannes Loeffler (Mon Jul 24 2017 - 23:09:11 PDT)
[AMBER] MPI Error in Amber Installation Debasish Mandal (Tue Jul 25 2017 - 02:10:05 PDT)
- Re: [AMBER] MPI Error in Amber Installation Daniel Roe (Tue Jul 25 2017 - 05:29:00 PDT)
- Re: [AMBER] MPI Error in Amber Installation Hai Nguyen (Tue Jul 25 2017 - 05:42:20 PDT)
[AMBER] wheel representation of torsional angle Saikat Pal (Tue Jul 25 2017 - 06:28:47 PDT)
[AMBER] Mcpb.py prepared .com input small file MCPB.py -i 4ZF6.in -s 1 Rana Rehan Khalid (Tue Jul 25 2017 - 15:30:26 PDT)
[AMBER] Query regarding 3D-RISM Rakesh Srivastava (Tue Jul 25 2017 - 22:55:57 PDT)
- Re: [AMBER] Query regarding 3D-RISM David Cerutti (Wed Jul 26 2017 - 00:11:19 PDT)
  - Re: [AMBER] Query regarding 3D-RISM Rakesh Srivastava (Wed Jul 26 2017 - 00:13:52 PDT)
    - Re: [AMBER] Query regarding 3D-RISM Tyler Luchko (Lists) (Wed Jul 26 2017 - 09:01:42 PDT)
    - Re: [AMBER] Query regarding 3D-RISM Rakesh Srivastava (Wed Jul 26 2017 - 21:55:14 PDT)
[AMBER] counting ions - doubt-urgent Mary Varughese (Wed Jul 26 2017 - 03:05:15 PDT)
- Re: [AMBER] counting ions - doubt-urgent George Giambasu (Wed Jul 26 2017 - 06:46:03 PDT)
  - Re: [AMBER] counting ions - doubt-urgent Christina Bergonzo (Wed Jul 26 2017 - 06:55:20 PDT)
- Re: [AMBER] counting ions - doubt-urgent Daniel Roe (Wed Jul 26 2017 - 06:55:39 PDT)
- Re: [AMBER] counting ions - doubt-urgent maryvj1985 (Wed Jul 26 2017 - 07:55:37 PDT)
  - Re: [AMBER] counting ions - doubt-urgent Daniel Roe (Wed Jul 26 2017 - 08:33:32 PDT)
- Re: [AMBER] counting ions - doubt-urgent maryvj1985 (Wed Jul 26 2017 - 11:33:15 PDT)
  - Re: [AMBER] counting ions - doubt-urgent George Giambasu (Wed Jul 26 2017 - 12:10:08 PDT)
[AMBER] Difference between AMBER 14 pmemd.cuda and AMBER 12 pmemd.cuda Saikat Pal (Wed Jul 26 2017 - 07:34:36 PDT)
- Re: [AMBER] Difference between AMBER 14 pmemd.cuda and AMBER 12 pmemd.cuda David A Case (Sat Jul 29 2017 - 06:24:49 PDT)
[AMBER] Mutating DNA bases Debostuti Ghoshdastidar (Thu Jul 27 2017 - 05:12:08 PDT)
- Re: [AMBER] Mutating DNA bases Vlad Cojocaru (Thu Jul 27 2017 - 05:18:59 PDT)
  - Re: [AMBER] Mutating DNA bases Debostuti Ghoshdastidar (Thu Jul 27 2017 - 22:02:16 PDT)
- Re: [AMBER] Mutating DNA bases Yogeeshwar Ajjugal (Thu Jul 27 2017 - 23:12:36 PDT)
  - Re: [AMBER] Mutating DNA bases Yogeeshwar Ajjugal (Thu Jul 27 2017 - 23:37:02 PDT)
    - Re: [AMBER] Mutating DNA bases Debostuti Ghoshdastidar (Thu Jul 27 2017 - 23:44:44 PDT)
[AMBER] Manual parameterization of the TIP4P/2005 water model Hannes Konegger (Thu Jul 27 2017 - 07:13:41 PDT)
- Re: [AMBER] Manual parameterization of the TIP4P/2005 water model David A Case (Sat Jul 29 2017 - 06:20:05 PDT)
- Re: [AMBER] Manual parameterization of the TIP4P/2005 water model Hannes Konegger (Wed Aug 02 2017 - 01:27:32 PDT)
[AMBER] adaptive biasing force (ABF) method in AMBER? Xing (Thu Jul 27 2017 - 10:44:52 PDT)
[AMBER] How to make a phenol monolayer Ramin Salimi (Thu Jul 27 2017 - 14:36:55 PDT)
- Re: [AMBER] How to make a phenol monolayer Elvis Martis (Thu Jul 27 2017 - 20:48:29 PDT)
  - Re: [AMBER] How to make a phenol monolayer Ramin Salimi (Fri Jul 28 2017 - 08:48:30 PDT)
    - Re: [AMBER] How to make a phenol monolayer Elvis Martis (Fri Jul 28 2017 - 08:52:31 PDT)
    - Re: [AMBER] How to make a phenol monolayer Ramin Salimi (Fri Jul 28 2017 - 09:01:25 PDT)
    - Re: [AMBER] How to make a phenol monolayer Elvis Martis (Fri Jul 28 2017 - 09:35:46 PDT)
    - Re: [AMBER] How to make a phenol monolayer Ramin Salimi (Fri Jul 28 2017 - 10:54:23 PDT)
    - Re: [AMBER] How to make a phenol monolayer ABEL Stephane (Sat Jul 29 2017 - 05:48:46 PDT)
[AMBER] gaff Milo Westler (Thu Jul 27 2017 - 16:17:16 PDT)
- Re: [AMBER] gaff David A Case (Fri Jul 28 2017 - 10:51:53 PDT)
[AMBER] PBC problem with autoimage&image Meng Wu (Thu Jul 27 2017 - 21:37:06 PDT)
- Re: [AMBER] PBC problem with autoimage&image Hai Nguyen (Thu Jul 27 2017 - 21:40:44 PDT)
- Re: [AMBER] PBC problem with autoimage&image Meng Wu (Sun Jul 30 2017 - 20:33:49 PDT)
  - Re: [AMBER] PBC problem with autoimage&image Daniel Roe (Mon Jul 31 2017 - 05:34:07 PDT)
[AMBER] question about the error when I start up the xleap 方煜 (Thu Jul 27 2017 - 21:42:14 PDT)
- Re: [AMBER] question about the error when I start up the xleap Elvis Martis (Thu Jul 27 2017 - 21:47:39 PDT)
- Re: [AMBER] question about the error when I start up the xleap Ryan Novosielski (Thu Jul 27 2017 - 23:39:36 PDT)
[AMBER] Error analyzing temperature Núbia Prates (Fri Jul 28 2017 - 08:16:13 PDT)
- Re: [AMBER] Error analyzing temperature Daniel Roe (Fri Jul 28 2017 - 09:07:17 PDT)
[AMBER] Atoms do not have type Error for G-quadruplex DNA. Jerrano Bowleg (Sun Jul 30 2017 - 09:12:07 PDT)
- Re: [AMBER] Atoms do not have type Error for G-quadruplex DNA. David A Case (Sun Jul 30 2017 - 18:21:26 PDT)
[AMBER] "Length of coordinates and ESP charges are different" in MCPB.py -s3 Eugene Cha (Mon Jul 31 2017 - 03:59:56 PDT)
- Re: [AMBER] "Length of coordinates and ESP charges are different" in MCPB.py -s3 Pengfei Li (Mon Jul 31 2017 - 14:29:46 PDT)
[AMBER] How to use cpptraj in AMBER10 to generate RMSD and RMSF Mustafa Alhaji Isa (Mon Jul 31 2017 - 07:35:19 PDT)
- Re: [AMBER] How to use cpptraj in AMBER10 to generate RMSD and RMSF Christina Bergonzo (Mon Jul 31 2017 - 07:47:21 PDT)
[AMBER] If I use source leaprc.gaff command for DNA and protein is it load gaff forcefield or ff14SB force field?? Saikat Pal (Tue Aug 01 2017 - 03:54:10 PDT)
- Re: [AMBER] If I use source leaprc.gaff command for DNA and protein is it load gaff forcefield or ff14SB force field?? Daniel Roe (Tue Aug 01 2017 - 05:13:12 PDT)
- Re: [AMBER] If I use source leaprc.gaff command for DNA and protein is it load gaff forcefield or ff14SB force field?? David A Case (Tue Aug 01 2017 - 05:21:25 PDT)
[AMBER] Tleap parametrisation of NA+ bound proteins James Starlight (Tue Aug 01 2017 - 06:56:25 PDT)
- Re: [AMBER] Tleap parametrisation of NA+ bound proteins David A Case (Tue Aug 01 2017 - 10:23:42 PDT)
  - Re: [AMBER] Tleap parametrisation of NA+ bound proteins James Starlight (Wed Aug 02 2017 - 03:47:22 PDT)
- Re: [AMBER] Tleap parametrisation of NA+ bound proteins James Starlight (Wed Aug 02 2017 - 06:29:45 PDT)
[AMBER] string methods in AMBER16 Chunli Yan (Tue Aug 01 2017 - 12:00:33 PDT)
- Re: [AMBER] string methods in AMBER16 Scott Brozell (Tue Aug 01 2017 - 12:59:07 PDT)
- Re: [AMBER] string methods in AMBER16 Feng Pan (Tue Aug 01 2017 - 12:59:28 PDT)
  - Re: [AMBER] string methods in AMBER16 Chunli Yan (Tue Aug 01 2017 - 13:07:35 PDT)
    - Re: [AMBER] string methods in AMBER16 Feng Pan (Tue Aug 01 2017 - 13:37:33 PDT)
    - Re: [AMBER] string methods in AMBER16 Chunli Yan (Tue Aug 01 2017 - 13:58:10 PDT)
    - Re: [AMBER] string methods in AMBER16 Chunli Yan (Tue Aug 01 2017 - 17:32:58 PDT)
[AMBER] GaMD Neha Gandhi (Tue Aug 01 2017 - 16:00:55 PDT)
[AMBER] External force apply along a particular direction Sanjib Paul (Wed Aug 02 2017 - 00:21:30 PDT)
[AMBER] Tleap processing of membrane protein in amber-16 James Starlight (Wed Aug 02 2017 - 03:52:14 PDT)
- Re: [AMBER] Tleap processing of membrane protein in amber-16 David A Case (Wed Aug 02 2017 - 06:42:27 PDT)
  - Re: [AMBER] Tleap processing of membrane protein in amber-16 James Starlight (Wed Aug 02 2017 - 06:56:45 PDT)
[AMBER] Building of beta strand Rajarshi Roy (Wed Aug 02 2017 - 07:51:19 PDT)
- Re: [AMBER] Building of beta strand Hai Nguyen (Wed Aug 02 2017 - 09:27:47 PDT)
  - Re: [AMBER] Building of beta strand Rajarshi Roy (Wed Aug 02 2017 - 09:32:52 PDT)
    - Re: [AMBER] Building of beta strand Hai Nguyen (Wed Aug 02 2017 - 10:24:54 PDT)
- Re: [AMBER] Building of beta strand Rajarshi Roy (Wed Aug 02 2017 - 21:34:08 PDT)
  - Re: [AMBER] Building of beta strand Daniel Roe (Mon Aug 07 2017 - 07:28:37 PDT)
    - Re: [AMBER] Building of beta strand Hai Nguyen (Mon Aug 07 2017 - 12:23:58 PDT)
    - Re: [AMBER] Building of beta strand Rajarshi Roy (Tue Aug 08 2017 - 03:40:34 PDT)
[AMBER] Barostat options for membrane protein simulations in NPT James Starlight (Wed Aug 02 2017 - 08:21:15 PDT)
[AMBER] A bug with unperturbed charge during tleap processing James Starlight (Wed Aug 02 2017 - 11:16:02 PDT)
- Re: [AMBER] A bug with unperturbed charge during tleap processing Bill Ross (Wed Aug 02 2017 - 21:31:28 PDT)
  - Re: [AMBER] A bug with unperturbed charge during tleap processing James Starlight (Thu Aug 03 2017 - 01:27:19 PDT)
    - Re: [AMBER] A bug with unperturbed charge during tleap processing David A Case (Thu Aug 03 2017 - 04:55:44 PDT)
    - Re: [AMBER] A bug with unperturbed charge during tleap processing James Starlight (Thu Aug 03 2017 - 06:38:34 PDT)
    - Re: [AMBER] A bug with unperturbed charge during tleap processing David A Case (Thu Aug 03 2017 - 18:07:42 PDT)
    - Re: [AMBER] A bug with unperturbed charge during tleap processing James Starlight (Fri Aug 04 2017 - 00:19:27 PDT)
- Re: [AMBER] A bug with unperturbed charge during tleap processing James Starlight (Fri Aug 04 2017 - 05:34:02 PDT)
  - Re: [AMBER] A bug with unperturbed charge during tleap processing James Starlight (Fri Aug 04 2017 - 11:50:25 PDT)
    - Re: [AMBER] A bug with unperturbed charge during tleap processing Bill Ross (Fri Aug 04 2017 - 12:00:01 PDT)
    - Re: [AMBER] A bug with unperturbed charge during tleap processing James Starlight (Mon Aug 07 2017 - 08:00:19 PDT)
    - Re: [AMBER] A bug with unperturbed charge during tleap processing Daniel Roe (Mon Aug 07 2017 - 09:13:32 PDT)
    - Re: [AMBER] A bug with unperturbed charge during tleap processing James Starlight (Mon Aug 07 2017 - 09:28:15 PDT)
    - Re: [AMBER] A bug with unperturbed charge during tleap processing Daniel Roe (Mon Aug 07 2017 - 09:29:37 PDT)
    - Re: [AMBER] A bug with unperturbed charge during tleap processing James Starlight (Mon Aug 07 2017 - 11:07:31 PDT)
    - Re: [AMBER] A bug with unperturbed charge during tleap processing James Starlight (Wed Aug 09 2017 - 02:21:12 PDT)
    - Re: [AMBER] A bug with unperturbed charge during tleap processing Bill Ross (Wed Aug 09 2017 - 04:03:29 PDT)
[AMBER] pbc box information missing Albert (Wed Aug 02 2017 - 13:13:44 PDT)
- Re: [AMBER] pbc box information missing David A Case (Thu Aug 03 2017 - 04:59:00 PDT)
[AMBER] -rem flags in string method with swarms of trajectories amber Chunli Yan (Wed Aug 02 2017 - 14:49:22 PDT)
- Re: [AMBER] -rem flags in string method with swarms of trajectories amber Feng Pan (Wed Aug 02 2017 - 15:18:46 PDT)
  - Re: [AMBER] -rem flags in string method with swarms of trajectories amber Feng Pan (Wed Aug 02 2017 - 15:24:59 PDT)
  - Re: [AMBER] -rem flags in string method with swarms of trajectories amber Chunli Yan (Wed Aug 02 2017 - 19:02:31 PDT)
[AMBER] amber install Mohammad Zahidul Hossain Khan (Wed Aug 02 2017 - 15:04:19 PDT)
- Re: [AMBER] amber install David A Case (Thu Aug 03 2017 - 05:02:01 PDT)
[AMBER] amber install Mohammad Zahidul Hossain Khan (Wed Aug 02 2017 - 19:06:31 PDT)
- Re: [AMBER] amber install liu junjun (Wed Aug 02 2017 - 20:00:36 PDT)
- Re: [AMBER] amber install Hai Nguyen (Wed Aug 02 2017 - 21:34:18 PDT)
[AMBER] different crd format? Albert (Thu Aug 03 2017 - 00:46:25 PDT)
- Re: [AMBER] different crd format? David A Case (Thu Aug 03 2017 - 05:06:31 PDT)
- Re: [AMBER] different crd format? Daniel Roe (Mon Aug 07 2017 - 07:25:42 PDT)
[AMBER] amber frcmod file Neha Gandhi (Thu Aug 03 2017 - 01:51:40 PDT)
[AMBER] Number of triangulated 3-point waters found: 0 Shilpa Gupta (Thu Aug 03 2017 - 03:50:59 PDT)
- Re: [AMBER] Number of triangulated 3-point waters found: 0 David A Case (Thu Aug 03 2017 - 05:09:32 PDT)
[AMBER] Applying external force along a particular direction Sanjib Paul (Thu Aug 03 2017 - 05:45:29 PDT)
[AMBER] Compilation of Amber 14 Milo Westler (Thu Aug 03 2017 - 13:01:10 PDT)
- Re: [AMBER] Compilation of Amber 14 David A Case (Thu Aug 03 2017 - 18:20:59 PDT)
  - Re: [AMBER] Compilation of Amber 14 Milo Westler (Fri Aug 04 2017 - 09:00:39 PDT)
    - Re: [AMBER] Compilation of Amber 14 Daniel Roe (Fri Aug 04 2017 - 11:24:34 PDT)
    - Re: [AMBER] Compilation of Amber 14 Milo Westler (Fri Aug 04 2017 - 12:44:56 PDT)
[AMBER] Using polarizable force field ff02 in AMBER 14 Aishwarya Venkatramani (Thu Aug 03 2017 - 17:00:00 PDT)
[AMBER] Using polarizable force field ff02 in AMBER 14 Aishwarya Venkatramani (Thu Aug 03 2017 - 20:15:17 PDT)
- Re: [AMBER] Using polarizable force field ff02 in AMBER 14 Carlos Simmerling (Fri Aug 04 2017 - 05:40:05 PDT)
  - Re: [AMBER] Using polarizable force field ff02 in AMBER 14 Aishwarya Venkatramani (Fri Aug 04 2017 - 05:47:34 PDT)
    - Re: [AMBER] Using polarizable force field ff02 in AMBER 14 David A Case (Fri Aug 04 2017 - 08:18:42 PDT)
    - Re: [AMBER] Using polarizable force field ff02 in AMBER 14 Aishwarya Venkatramani (Mon Aug 07 2017 - 11:41:23 PDT)
    - Re: [AMBER] Using polarizable force field ff02 in AMBER 14 Anthony Cruz-Balberdy (Mon Aug 07 2017 - 12:41:04 PDT)
    - Re: [AMBER] Using polarizable force field ff02 in AMBER 14 David A Case (Mon Aug 07 2017 - 12:54:42 PDT)
[AMBER] RDF for dendrimer Christopher Gorman (Fri Aug 04 2017 - 14:18:33 PDT)
- Re: [AMBER] RDF for dendrimer Hai Nguyen (Fri Aug 04 2017 - 14:34:55 PDT)
- Re: [AMBER] RDF for dendrimer Daniel Roe (Mon Aug 07 2017 - 08:56:16 PDT)
[AMBER] parametrization of an RNA base giulia palermo (Fri Aug 04 2017 - 14:48:01 PDT)
- Re: [AMBER] parametrization of an RNA base Bill Ross (Fri Aug 04 2017 - 15:29:03 PDT)
  - Re: [AMBER] parametrization of an RNA base Andrew Schaub (Sat Aug 05 2017 - 00:47:50 PDT)
- Re: [AMBER] parametrization of an RNA base David A Case (Sun Aug 06 2017 - 11:33:40 PDT)
[AMBER] QM/MM calculation in Amber Albert (Fri Aug 04 2017 - 23:39:52 PDT)
- Re: [AMBER] QM/MM calculation in Amber David A Case (Sun Aug 06 2017 - 11:37:38 PDT)
[AMBER] Parameters for HEME-CYS covalent bond Avijit Rakshit (Sat Aug 05 2017 - 00:29:21 PDT)
- Re: [AMBER] Parameters for HEME-CYS covalent bond Andrew Schaub (Sat Aug 05 2017 - 00:43:18 PDT)
  - Re: [AMBER] Parameters for HEME-CYS covalent bond Avijit Rakshit (Sat Aug 05 2017 - 00:56:42 PDT)
    - Re: [AMBER] Parameters for HEME-CYS covalent bond Thomas Charles Pochapsky (Sat Aug 05 2017 - 05:25:31 PDT)
    - Re: [AMBER] Parameters for HEME-CYS covalent bond Pengfei Li (Sat Aug 05 2017 - 20:16:24 PDT)
[AMBER] Amber Atom Types for Non-standard Residue david kastner (Sat Aug 05 2017 - 18:08:23 PDT)
[AMBER] How best to build a solvent box for a solute with changing dimensions? Kasprzak, Wojciech (NIH/NCI) [C] (Mon Aug 07 2017 - 08:53:57 PDT)
- Re: [AMBER] How best to build a solvent box for a solute with changing dimensions? Daniel Roe (Mon Aug 07 2017 - 09:26:13 PDT)
[AMBER] gaff2 atom type (cs) is not in PARMCHK.DAT Tsai Kun-Lin (Mon Aug 07 2017 - 17:51:44 PDT)
- Re: [AMBER] gaff2 atom type (cs) is not in PARMCHK.DAT Scott Brozell (Tue Aug 08 2017 - 14:22:54 PDT)
  - Re: [AMBER] gaff2 atom type (cs) is not in PARMCHK.DAT Scott Brozell (Tue Aug 08 2017 - 20:06:29 PDT)
    - Re: [AMBER] gaff2 atom type (cs) is not in PARMCHK.DAT David A Case (Wed Aug 09 2017 - 04:42:57 PDT)
- Re: [AMBER] gaff2 atom type (cs) is not in PARMCHK.DAT Junmei Wang (Tue Aug 15 2017 - 04:51:09 PDT)
[AMBER] results for string methods Chunli Yan (Mon Aug 07 2017 - 18:49:45 PDT)
- Re: [AMBER] results for string methods Feng Pan (Tue Aug 08 2017 - 10:27:38 PDT)
  - Re: [AMBER] results for string methods Chunli Yan (Tue Aug 08 2017 - 10:33:36 PDT)
[AMBER] About common Gromacs and Amber Benchmarks Vlad (Tue Aug 08 2017 - 00:38:55 PDT)
- Re: [AMBER] About common Gromacs and Amber Benchmarks Hannes Loeffler (Tue Aug 08 2017 - 00:45:01 PDT)
[AMBER] polarization force field sangita kachhap (Tue Aug 08 2017 - 03:25:12 PDT)
- Re: [AMBER] polarization force field David A Case (Tue Aug 08 2017 - 04:19:40 PDT)
  - Re: [AMBER] polarization force field sangita kachhap (Tue Aug 08 2017 - 05:50:46 PDT)
[AMBER] Problem with leaprc.ff14SB George Tzotzos (Tue Aug 08 2017 - 10:50:59 PDT)
- Re: [AMBER] Problem with leaprc.ff14SB David A Case (Tue Aug 08 2017 - 12:55:00 PDT)
  - Re: [AMBER] Problem with leaprc.ff14SB George Tzotzos (Wed Aug 09 2017 - 08:20:53 PDT)
[AMBER] Error in hbond lifetime analysis Baig abdullah Al muhit (Tue Aug 08 2017 - 13:17:41 PDT)
- Re: [AMBER] Error in hbond lifetime analysis Daniel Roe (Thu Aug 10 2017 - 12:29:17 PDT)
[AMBER] adQMMM overheating Artur Przydacz (Tue Aug 08 2017 - 14:03:40 PDT)
- Re: [AMBER] adQMMM overheating Goetz, Andreas (Tue Aug 08 2017 - 14:58:20 PDT)
  - Re: [AMBER] adQMMM overheating Artur Przydacz (Wed Aug 09 2017 - 05:28:39 PDT)
    - Re: [AMBER] adQMMM overheating Goetz, Andreas (Thu Aug 10 2017 - 00:41:04 PDT)
[AMBER] iat >= 3 in PMEMD and PMEMD.cuda kurisaki (Tue Aug 08 2017 - 18:09:51 PDT)
[AMBER] Error in leap on using divalent ion Chayya Bhargac (Wed Aug 09 2017 - 06:23:42 PDT)
- Re: [AMBER] Error in leap on using divalent ion David A Case (Wed Aug 09 2017 - 08:35:44 PDT)
[AMBER] Use of param.Frosst parameters to prepare a ligand in Ambertools? Anne Nierobisch (Wed Aug 09 2017 - 06:57:57 PDT)
- Re: [AMBER] Use of param.Frosst parameters to prepare a ligand in Ambertools? David A Case (Thu Aug 10 2017 - 10:47:54 PDT)
[AMBER] ... RESTARTED DUE TO LINMIN FAILURE ... Malay Raul (Wed Aug 09 2017 - 08:23:31 PDT)
- Re: [AMBER] ... RESTARTED DUE TO LINMIN FAILURE ... Jason Swails (Mon Aug 28 2017 - 19:02:11 PDT)
[AMBER] problems with the HAP tutorial Kris Feher (Thu Aug 10 2017 - 03:25:06 PDT)
[AMBER] Query about SPC and SPCE water model Saikat Pal (Thu Aug 10 2017 - 04:03:35 PDT)
- Re: [AMBER] Query about SPC and SPCE water model David A Case (Thu Aug 10 2017 - 04:18:12 PDT)
[AMBER] Is this necessary HOH=SPC command Saikat Pal (Thu Aug 10 2017 - 05:32:52 PDT)
- Re: [AMBER] Is this necessary HOH=SPC command David A Case (Thu Aug 10 2017 - 10:24:21 PDT)
[AMBER] QMMM error: "| Flags: getting box info from netcdf restart file" Charles Mariasoosai (Thu Aug 10 2017 - 09:20:24 PDT)
- Re: [AMBER] QMMM error: "| Flags: getting box info from netcdf restart file" Goetz, Andreas (Thu Aug 10 2017 - 09:52:58 PDT)
[AMBER] QM/MM calculation Amber16/DFTB Amani Eshtiwi (Thu Aug 10 2017 - 17:38:48 PDT)
[AMBER] fixing backbone dihedral angles in RNA structure Asmita Gupta (Thu Aug 10 2017 - 17:58:58 PDT)
- Re: [AMBER] fixing backbone dihedral angles in RNA structure Bill Ross (Thu Aug 10 2017 - 18:08:23 PDT)
  - Re: [AMBER] fixing backbone dihedral angles in RNA structure Daniel Roe (Fri Aug 11 2017 - 10:08:09 PDT)
[AMBER] Decomposition Energy Problem with Aspartic Acid only Jag Silwal (Fri Aug 11 2017 - 09:18:45 PDT)
[AMBER] Error-Calculating distance between two atoms in CPPTRAJ Jag Silwal (Fri Aug 11 2017 - 09:42:21 PDT)
- Re: [AMBER] Error-Calculating distance between two atoms in CPPTRAJ Hai Nguyen (Fri Aug 11 2017 - 09:52:26 PDT)
- Re: [AMBER] Error-Calculating distance between two atoms in CPPTRAJ Daniel Roe (Fri Aug 11 2017 - 09:52:39 PDT)
  - Re: [AMBER] Error-Calculating distance between two atoms in CPPTRAJ Jag Silwal (Fri Aug 11 2017 - 10:00:21 PDT)
    - Re: [AMBER] Error-Calculating distance between two atoms in CPPTRAJ Daniel Roe (Fri Aug 11 2017 - 10:03:44 PDT)
[AMBER] The Amber web site is down.... David A Case (Fri Aug 11 2017 - 09:54:54 PDT)
[AMBER] SASA energy Mohammad Zahidul Hossain Khan (Fri Aug 11 2017 - 10:17:57 PDT)
- Re: [AMBER] SASA energy Elvis Martis (Fri Aug 11 2017 - 12:06:40 PDT)
  - Re: [AMBER] SASA energy Mohammad Zahidul Hossain Khan (Fri Aug 11 2017 - 12:17:08 PDT)
    - Re: [AMBER] SASA energy Elvis Martis (Fri Aug 11 2017 - 20:13:53 PDT)
    - Re: [AMBER] SASA energy David A Case (Sat Aug 12 2017 - 06:32:57 PDT)
    - Re: [AMBER] SASA energy Mohammad Zahidul Hossain Khan (Wed Aug 16 2017 - 11:09:14 PDT)
    - Re: [AMBER] SASA energy Daniel Roe (Wed Aug 16 2017 - 11:39:26 PDT)
    - Re: [AMBER] SASA energy Mohammad Zahidul Hossain Khan (Wed Aug 16 2017 - 11:41:12 PDT)
    - Re: [AMBER] SASA energy Daniel Roe (Wed Aug 16 2017 - 11:51:02 PDT)
[AMBER] Cpptraj to center molecules Aseel Bala (Fri Aug 11 2017 - 12:36:06 PDT)
- Re: [AMBER] Cpptraj to center molecules Daniel Roe (Sat Aug 12 2017 - 10:50:17 PDT)
  - Re: [AMBER] Cpptraj to center molecules Aseel Bala Ahmed (Sat Aug 12 2017 - 12:55:32 PDT)
    - Re: [AMBER] Cpptraj to center molecules Bill Ross (Sat Aug 12 2017 - 13:04:17 PDT)
    - Re: [AMBER] Cpptraj to center molecules Bill Ross (Sat Aug 12 2017 - 13:09:27 PDT)
    - Re: [AMBER] Cpptraj to center molecules Aseel Bala Ahmed (Sat Aug 12 2017 - 13:13:49 PDT)
    - Re: [AMBER] Cpptraj to center molecules Bill Ross (Sat Aug 12 2017 - 13:22:38 PDT)
    - Re: [AMBER] Cpptraj to center molecules Aseel Bala Ahmed (Sat Aug 12 2017 - 14:38:56 PDT)
    - Re: [AMBER] Cpptraj to center molecules David A Case (Sun Aug 13 2017 - 05:32:15 PDT)
    - Re: [AMBER] Cpptraj to center molecules Aseel Bala Ahmed (Sun Aug 13 2017 - 13:27:22 PDT)
[AMBER] Pairwise-Decomposition Energy Jag Silwal (Mon Aug 14 2017 - 07:45:08 PDT)
[AMBER] Periodicity of metal bond Lizelle Lubbe (Tue Aug 15 2017 - 06:28:22 PDT)
- Re: [AMBER] Periodicity of metal bond Pengfei Li (Tue Aug 15 2017 - 07:50:00 PDT)
[AMBER] Amber web site is back up David A Case (Tue Aug 15 2017 - 06:49:49 PDT)
[AMBER] Amber TI accuracy Nikolay N. Kuzmich (Tue Aug 15 2017 - 08:36:59 PDT)
- Re: [AMBER] Amber TI accuracy Adrian Roitberg (Tue Aug 15 2017 - 08:42:38 PDT)
[AMBER] Pairwise Decomposition-Mask not wroking? Jag Silwal (Tue Aug 15 2017 - 09:09:21 PDT)
[AMBER] Amber Install Failure - update does not work James Kress (Tue Aug 15 2017 - 15:47:52 PDT)
- Re: [AMBER] Amber Install Failure - update does not work David A Case (Tue Aug 15 2017 - 20:41:03 PDT)
  - Re: [AMBER] Amber Install Failure - update does not work David A Case (Wed Aug 16 2017 - 07:06:32 PDT)
    - Re: [AMBER] Amber Install Failure - update does not work James Kress (Wed Aug 16 2017 - 08:45:27 PDT)
    - Re: [AMBER] Amber Install Failure - update does not work Leandro Bortot (Thu Aug 17 2017 - 06:21:43 PDT)
[AMBER] How to cross-corrlation matrix betwern 3 Calpha atom Arpita Goswami (Tue Aug 15 2017 - 22:34:37 PDT)
[AMBER] Error in Amber16 documentation Paul Westphälinger (Wed Aug 16 2017 - 03:30:01 PDT)
- Re: [AMBER] Error in Amber16 documentation Paul Westphälinger (Wed Aug 16 2017 - 07:32:18 PDT)
[AMBER] grid command in cpptraj 沖本憲明 (Wed Aug 16 2017 - 07:23:10 PDT)
- Re: [AMBER] grid command in cpptraj Daniel Roe (Wed Aug 16 2017 - 07:56:10 PDT)
[AMBER] charmmlipid2amber.py with Charm-gui lipids James Starlight (Wed Aug 16 2017 - 08:54:01 PDT)
- Re: [AMBER] charmmlipid2amber.py with Charm-gui lipids ABEL Stephane (Wed Aug 16 2017 - 09:18:54 PDT)
  - Re: [AMBER] charmmlipid2amber.py with Charm-gui lipids James Starlight (Wed Aug 16 2017 - 10:57:40 PDT)
    - Re: [AMBER] charmmlipid2amber.py with Charm-gui lipids ABEL Stephane (Wed Aug 16 2017 - 11:07:34 PDT)
    - Re: [AMBER] charmmlipid2amber.py with Charm-gui lipids James Starlight (Thu Aug 17 2017 - 01:44:42 PDT)
    - Re: [AMBER] charmmlipid2amber.py with Charm-gui lipids ABEL Stephane (Thu Aug 17 2017 - 04:16:30 PDT)
    - Re: [AMBER] charmmlipid2amber.py with Charm-gui lipids James Starlight (Thu Aug 17 2017 - 04:25:35 PDT)
[AMBER] Can pmemd.cuda.MPI do SMD on GPUs? Xing (Wed Aug 16 2017 - 14:16:47 PDT)
- Re: [AMBER] Can pmemd.cuda.MPI do SMD on GPUs? Adrian Roitberg (Wed Aug 16 2017 - 14:55:10 PDT)
  - Re: [AMBER] Can pmemd.cuda.MPI do SMD on GPUs? Xing (Thu Aug 17 2017 - 13:59:12 PDT)
[AMBER] calculate PMF in string methods Chunli Yan (Wed Aug 16 2017 - 16:42:03 PDT)
- Re: [AMBER] calculate PMF in string methods Feng Pan (Thu Aug 17 2017 - 15:48:55 PDT)
  - Re: [AMBER] calculate PMF in string methods Chunli Yan (Thu Aug 17 2017 - 19:22:45 PDT)
    - Re: [AMBER] calculate PMF in string methods Chunli Yan (Thu Aug 17 2017 - 19:25:57 PDT)
    - Re: [AMBER] calculate PMF in string methods Carlos Simmerling (Fri Aug 18 2017 - 12:40:19 PDT)
    - Re: [AMBER] calculate PMF in string methods Chunli Yan (Fri Aug 18 2017 - 14:43:41 PDT)
    - Re: [AMBER] calculate PMF in string methods Feng Pan (Sat Aug 19 2017 - 00:28:35 PDT)
[AMBER] how to implement GEN keyword in QM/MM with external program chemist zobia (Wed Aug 16 2017 - 22:31:16 PDT)
- Re: [AMBER] how to implement GEN keyword in QM/MM with external program Goetz, Andreas (Fri Aug 18 2017 - 11:33:04 PDT)
[AMBER] Install in gpu AMBER14 for high performance computer Saikat Pal (Thu Aug 17 2017 - 08:46:02 PDT)
- Re: [AMBER] Install in gpu AMBER14 for high performance computer David A Case (Thu Aug 17 2017 - 11:57:18 PDT)
  - Re: [AMBER] Install in gpu AMBER14 for high performance computer Saikat Pal (Thu Aug 17 2017 - 23:57:46 PDT)
[AMBER] Thermodynamic Integration using PMEMD Roma Mukhopadhyay (Thu Aug 17 2017 - 11:24:00 PDT)
- Re: [AMBER] Thermodynamic Integration using PMEMD Hannes Loeffler (Fri Aug 18 2017 - 00:09:45 PDT)
  - Re: [AMBER] Thermodynamic Integration using PMEMD Roma Mukhopadhyay (Fri Aug 18 2017 - 06:34:32 PDT)
    - Re: [AMBER] Thermodynamic Integration using PMEMD Hannes Loeffler (Fri Aug 18 2017 - 07:20:10 PDT)
    - Re: [AMBER] Thermodynamic Integration using PMEMD Roma Mukhopadhyay (Fri Aug 18 2017 - 09:13:46 PDT)
    - Re: [AMBER] Thermodynamic Integration using PMEMD Hannes Loeffler (Fri Aug 18 2017 - 09:36:24 PDT)
    - [AMBER] TImask command for PMEMD Roma Mukhopadhyay (Mon Oct 02 2017 - 10:01:12 PDT)
    - Re: [AMBER] TImask command for PMEMD David A Case (Mon Oct 02 2017 - 14:26:26 PDT)
[AMBER] Amber16/DFTB and bromine Amani Eshtiwi (Thu Aug 17 2017 - 12:32:01 PDT)
- Re: [AMBER] Amber16/DFTB and bromine Goetz, Andreas (Thu Aug 17 2017 - 12:53:05 PDT)
  - Re: [AMBER] Amber16/DFTB and bromine Amani Eshtiwi (Thu Aug 17 2017 - 13:20:17 PDT)
    - Re: [AMBER] Amber16/DFTB and bromine Goetz, Andreas (Fri Aug 18 2017 - 12:19:55 PDT)
    - Re: [AMBER] Amber16/DFTB and bromine Gustavo Seabra (Fri Aug 18 2017 - 13:02:26 PDT)
    - Re: [AMBER] Amber16/DFTB and bromine Amani Eshtiwi (Fri Aug 18 2017 - 15:37:35 PDT)
    - Re: [AMBER] Amber16/DFTB and bromine Amani Eshtiwi (Fri Aug 18 2017 - 15:46:46 PDT)
    - Re: [AMBER] Amber16/DFTB and bromine Amani Eshtiwi (Fri Aug 18 2017 - 16:26:55 PDT)
    - Re: [AMBER] Amber16/DFTB and bromine Amani Eshtiwi (Fri Aug 18 2017 - 16:44:18 PDT)
    - Re: [AMBER] Amber16/DFTB and bromine Gustavo Seabra (Fri Aug 18 2017 - 18:51:19 PDT)
    - Re: [AMBER] Amber16/DFTB and bromine Amani Eshtiwi (Fri Aug 18 2017 - 19:04:12 PDT)
    - Re: [AMBER] Amber16/DFTB and bromine Gustavo Seabra (Fri Aug 18 2017 - 19:06:32 PDT)
    - Re: [AMBER] Amber16/DFTB and bromine Amani Eshtiwi (Fri Aug 18 2017 - 19:11:18 PDT)
    - Re: [AMBER] Amber16/DFTB and bromine Amani Eshtiwi (Fri Aug 18 2017 - 19:32:43 PDT)
[AMBER] An equilibration of the membrane protein prepared by charmm-gui James Starlight (Fri Aug 18 2017 - 00:23:24 PDT)
- Re: [AMBER] An equilibration of the membrane protein prepared by charmm-gui ABEL Stephane (Fri Aug 18 2017 - 03:30:45 PDT)
  - Re: [AMBER] An equilibration of the membrane protein prepared by charmm-gui James Starlight (Fri Aug 18 2017 - 06:36:28 PDT)
    - Re: [AMBER] An equilibration of the membrane protein prepared by charmm-gui ABEL Stephane (Fri Aug 18 2017 - 07:28:23 PDT)
    - Re: [AMBER] An equilibration of the membrane protein prepared by charmm-gui James Starlight (Fri Aug 18 2017 - 07:33:21 PDT)
    - Re: [AMBER] An equilibration of the membrane protein prepared by charmm-gui ABEL Stephane (Fri Aug 18 2017 - 07:51:13 PDT)
    - Re: [AMBER] An equilibration of the membrane protein prepared by charmm-gui James Starlight (Tue Aug 22 2017 - 07:26:11 PDT)
    - Re: [AMBER] An equilibration of the membrane protein prepared by charmm-gui James Starlight (Wed Aug 23 2017 - 08:50:58 PDT)
    - Re: [AMBER] An equilibration of the membrane protein prepared by charmm-gui James Starlight (Fri Aug 25 2017 - 14:26:46 PDT)
    - Re: [AMBER] An equilibration of the membrane protein prepared by charmm-gui James Starlight (Thu Aug 31 2017 - 07:52:04 PDT)
    - Re: [AMBER] An equilibration of the membrane protein prepared by charmm-gui Amy Rice (Thu Aug 31 2017 - 08:23:31 PDT)
    - Re: [AMBER] An equilibration of the membrane protein prepared by charmm-gui James Starlight (Thu Aug 31 2017 - 09:31:12 PDT)
    - Re: [AMBER] An equilibration of the membrane protein prepared by charmm-gui James Starlight (Thu Aug 31 2017 - 09:57:38 PDT)
    - Re: [AMBER] An equilibration of the membrane protein prepared by charmm-gui James Kress (Thu Aug 31 2017 - 13:28:38 PDT)
    - Re: [AMBER] An equilibration of the membrane protein prepared by charmm-gui James Starlight (Fri Sep 01 2017 - 00:52:56 PDT)
    - Re: [AMBER] An equilibration of the membrane protein prepared by charmm-gui ABEL Stephane (Fri Sep 01 2017 - 02:23:11 PDT)
    - Re: [AMBER] An equilibration of the membrane protein prepared by charmm-gui James Starlight (Fri Sep 01 2017 - 06:08:35 PDT)
    - Re: [AMBER] An equilibration of the membrane protein prepared by charmm-gui ABEL Stephane (Fri Sep 01 2017 - 07:23:54 PDT)
[AMBER] How many GPU card is working Saikat Pal (Fri Aug 18 2017 - 04:33:47 PDT)
- Re: [AMBER] How many GPU card is working Daniel Roe (Fri Aug 18 2017 - 05:15:09 PDT)
  - Re: [AMBER] How many GPU card is working Saikat Pal (Fri Aug 18 2017 - 05:35:48 PDT)
    - Re: [AMBER] How many GPU card is working Daniel Roe (Fri Aug 18 2017 - 06:09:12 PDT)
    - Re: [AMBER] How many GPU card is working Saikat Pal (Fri Aug 18 2017 - 06:50:13 PDT)
    - Re: [AMBER] How many GPU card is working Daniel Roe (Fri Aug 18 2017 - 07:13:37 PDT)
    - Re: [AMBER] How many GPU card is working Saikat Pal (Fri Aug 18 2017 - 07:33:34 PDT)
[AMBER] A restrain mask for membrane protein simulation James Starlight (Fri Aug 18 2017 - 07:17:05 PDT)
- Re: [AMBER] A restrain mask for membrane protein simulation ABEL Stephane (Fri Aug 18 2017 - 07:31:24 PDT)
  - Re: [AMBER] A restrain mask for membrane protein simulation James Starlight (Fri Aug 18 2017 - 07:34:41 PDT)
[AMBER] Problem with tleap (non atom type) Parviz Seifpanahi Shabane (Fri Aug 18 2017 - 07:51:06 PDT)
- Re: [AMBER] Problem with tleap (non atom type) Bill Ross (Fri Aug 18 2017 - 10:20:39 PDT)
- Re: [AMBER] Problem with tleap (non atom type) David A Case (Fri Aug 18 2017 - 13:44:33 PDT)
  - Re: [AMBER] Problem with tleap (non atom type) Bill Ross (Fri Aug 18 2017 - 13:48:09 PDT)
[AMBER] Deprotonation of Tyr Sowmya Indrakumar (Fri Aug 18 2017 - 08:24:46 PDT)
- Re: [AMBER] Deprotonation of Tyr Adrian Roitberg (Fri Aug 18 2017 - 08:38:10 PDT)
  - Re: [AMBER] Deprotonation of Tyr Sowmya Indrakumar (Fri Aug 18 2017 - 08:57:44 PDT)
- Re: [AMBER] Deprotonation of Tyr Sowmya Indrakumar (Sun Aug 20 2017 - 06:45:32 PDT)
  - Re: [AMBER] Deprotonation of Tyr pancham lal Gupta (Wed Aug 30 2017 - 08:40:08 PDT)
[AMBER] Impose bond lengths RYDER WHITTAKER HAWKINS (Fri Aug 18 2017 - 08:35:58 PDT)
- Re: [AMBER] Impose bond lengths Bill Ross (Fri Aug 18 2017 - 10:18:30 PDT)
[AMBER] Performed MMPBSA.py.MPI failed in Amber16 with Ambertools 17 JiYuan Liu (Fri Aug 18 2017 - 10:28:05 PDT)
- Re: [AMBER] Performed MMPBSA.py.MPI failed in Amber16 with Ambertools 17 David A Case (Fri Aug 18 2017 - 13:59:41 PDT)
  - Re: [AMBER] Performed MMPBSA.py.MPI failed in Amber16 with Ambertools 17 Jiyuan Liu (Sat Aug 19 2017 - 05:48:07 PDT)
- Re: [AMBER] Performed MMPBSA.py.MPI failed in Amber16 with Ambertools 17 Jiyuan Liu (Sun Aug 20 2017 - 07:35:09 PDT)
- Re: [AMBER] Performed MMPBSA.py.MPI failed in Amber16 with Ambertools 17 Jiyuan Liu (Mon Aug 21 2017 - 07:22:48 PDT)
[AMBER] Install amber 14 in nvidia gpu tesla k40 Saikat Pal (Sat Aug 19 2017 - 00:24:36 PDT)
- Re: [AMBER] Install amber 14 in nvidia gpu tesla k40 David A Case (Sat Aug 19 2017 - 09:04:59 PDT)
[AMBER] Analyzing the aMD results - Tutorial 22 carmine marco morgillo (Sat Aug 19 2017 - 08:51:37 PDT)
[AMBER] How to move the protein to the corner of the box. Parviz Seifpanahi Shabane (Sat Aug 19 2017 - 13:49:37 PDT)
- Re: [AMBER] How to move the protein to the corner of the box. David A Case (Sun Aug 20 2017 - 06:05:52 PDT)
[AMBER] Calculation the Area per lipids using cpptraj James Starlight (Mon Aug 21 2017 - 01:19:35 PDT)
- Re: [AMBER] Calculation the Area per lipids using cpptraj Daniel Roe (Mon Aug 21 2017 - 06:28:04 PDT)
  - Re: [AMBER] Calculation the Area per lipids using cpptraj James Starlight (Wed Aug 23 2017 - 06:33:35 PDT)
    - Re: [AMBER] Calculation the Area per lipids using cpptraj Daniel Roe (Tue Aug 29 2017 - 12:35:33 PDT)
    - Re: [AMBER] Calculation the Area per lipids using cpptraj James Starlight (Wed Aug 30 2017 - 01:00:03 PDT)
    - Re: [AMBER] Calculation the Area per lipids using cpptraj Daniel Roe (Fri Sep 01 2017 - 06:13:58 PDT)
[AMBER] mpirun -np 1 and mpirun -np 2 Peer to Peer support problem Saikat Pal (Mon Aug 21 2017 - 03:22:17 PDT)
[AMBER] Deprotonation of Tyr Sowmya Indrakumar (Mon Aug 21 2017 - 08:37:54 PDT)
- Re: [AMBER] Deprotonation of Tyr Marcos Serrou do Amaral (Mon Aug 21 2017 - 12:34:52 PDT)
  - Re: [AMBER] Deprotonation of Tyr Sowmya Indrakumar (Mon Aug 21 2017 - 13:19:15 PDT)
    - Re: [AMBER] Deprotonation of Tyr Marcos Serrou do Amaral (Mon Aug 21 2017 - 16:25:46 PDT)
[AMBER] (kein Betreff) Traeg, Johannes (Tue Aug 22 2017 - 01:47:49 PDT)
- Re: [AMBER] (kein Betreff) Hannes Loeffler (Tue Aug 22 2017 - 01:56:40 PDT)
  - Re: [AMBER] (kein Betreff) Traeg, Johannes (Tue Aug 22 2017 - 03:31:48 PDT)
- Re: [AMBER] (kein Betreff) David A Case (Tue Aug 22 2017 - 05:14:16 PDT)
- Re: [AMBER] (kein Betreff) Junmei Wang (Tue Aug 29 2017 - 06:54:03 PDT)
  - Re: [AMBER] (kein Betreff) Junmei Wang (Tue Aug 29 2017 - 07:02:48 PDT)
    - Re: [AMBER] (kein Betreff) Traeg, Johannes (Wed Aug 30 2017 - 02:28:48 PDT)
    - Re: [AMBER] (kein Betreff) Junmei Wang (Wed Aug 30 2017 - 08:27:44 PDT)
    - Re: [AMBER] (kein Betreff) Traeg, Johannes (Thu Aug 31 2017 - 01:11:33 PDT)
Re: [AMBER] Deprotonation of Tyr using Parmed Sowmya Indrakumar (Tue Aug 22 2017 - 06:41:11 PDT)
- Re: [AMBER] Deprotonation of Tyr using Parmed Sowmya Indrakumar (Tue Aug 22 2017 - 07:08:06 PDT)
- Re: [AMBER] Deprotonation of Tyr using Parmed Jason Swails (Thu Aug 24 2017 - 02:01:16 PDT)
  - Re: [AMBER] Deprotonation of Tyr using Parmed Sowmya Indrakumar (Thu Aug 24 2017 - 06:04:32 PDT)
    - Re: [AMBER] Deprotonation of Tyr using Parmed Jason Swails (Mon Aug 28 2017 - 18:57:59 PDT)
[AMBER] Thermodynamic Integration question Lin Song (Tue Aug 22 2017 - 15:51:08 PDT)
- Re: [AMBER] Thermodynamic Integration question David Cerutti (Tue Aug 22 2017 - 16:01:29 PDT)
  - Re: [AMBER] Thermodynamic Integration question Lin Song (Tue Aug 22 2017 - 16:33:43 PDT)
[AMBER] angle of domain movement calculation sangita kachhap (Wed Aug 23 2017 - 03:05:29 PDT)
- Re: [AMBER] angle of domain movement calculation Carlos Simmerling (Wed Aug 23 2017 - 08:58:53 PDT)
[AMBER] Binding free energy for dimeric form Maryam Hamzehee (Wed Aug 23 2017 - 04:55:07 PDT)
[AMBER] Amber workshop? Georg Kuenze (Wed Aug 23 2017 - 14:51:23 PDT)
- Re: [AMBER] Amber workshop? Ross Walker (Thu Aug 24 2017 - 09:54:28 PDT)
[AMBER] Regarding GPU card MOHD HOMAIDUR RAHMAN (Thu Aug 24 2017 - 07:32:10 PDT)
- Re: [AMBER] Regarding GPU card Alessandro Contini (Thu Aug 24 2017 - 07:41:11 PDT)
- Re: [AMBER] Regarding GPU card Ross Walker (Thu Aug 24 2017 - 09:58:30 PDT)
- Re: [AMBER] Regarding GPU card Scott Le Grand (Thu Aug 24 2017 - 11:25:17 PDT)
[AMBER] Closest velocities Pär Håkansson (Thu Aug 24 2017 - 12:20:04 PDT)
- Re: [AMBER] Closest velocities Daniel Roe (Thu Aug 24 2017 - 13:00:49 PDT)
  - Re: [AMBER] Closest velocities Pär Håkansson (Tue Aug 29 2017 - 00:31:23 PDT)
    - Re: [AMBER] Closest velocities Daniel Roe (Tue Aug 29 2017 - 12:26:03 PDT)
[AMBER] RMSD colvar Chunli Yan (Thu Aug 24 2017 - 12:57:01 PDT)
- Re: [AMBER] RMSD colvar Feng Pan (Sun Aug 27 2017 - 21:09:03 PDT)
[AMBER] Discrepancies in MMPBSA calculations for the same trajectory Andrew.Warden.csiro.au (Thu Aug 24 2017 - 21:42:06 PDT)
[AMBER] LINMIN Error while minimizing Chayya Bhargac (Thu Aug 24 2017 - 23:05:10 PDT)
- Re: [AMBER] LINMIN Error while minimizing Bill Ross (Thu Aug 24 2017 - 23:10:23 PDT)
  - Re: [AMBER] LINMIN Error while minimizing Chayya Bhargac (Fri Aug 25 2017 - 08:19:38 PDT)
    - Re: [AMBER] LINMIN Error while minimizing Bill Ross (Fri Aug 25 2017 - 09:58:51 PDT)
    - Re: [AMBER] LINMIN Error while minimizing James Kress (Fri Aug 25 2017 - 10:36:32 PDT)
    - Re: [AMBER] LINMIN Error while minimizing David A Case (Fri Aug 25 2017 - 13:07:09 PDT)
[AMBER] RESP calculation in MCPBpy Lizelle Lubbe (Fri Aug 25 2017 - 03:39:18 PDT)
[AMBER] TIP3p lennard jones parameters Lizelle Lubbe (Fri Aug 25 2017 - 08:19:10 PDT)
- Re: [AMBER] TIP3p lennard jones parameters David A Case (Fri Aug 25 2017 - 13:17:08 PDT)
  - Re: [AMBER] TIP3p lennard jones parameters Lizelle Lubbe (Thu Aug 31 2017 - 01:45:57 PDT)
    - Re: [AMBER] TIP3p lennard jones parameters Pengfei Li (Mon Sep 11 2017 - 09:28:01 PDT)
[AMBER] Hybridization problem in Amber Julian Stys (Fri Aug 25 2017 - 12:14:24 PDT)
- Re: [AMBER] Hybridization problem in Amber David A Case (Sun Aug 27 2017 - 14:08:55 PDT)
  - Re: [AMBER] Hybridization problem in Amber Julian Stys (Mon Aug 28 2017 - 15:11:08 PDT)
[AMBER] Fw: Ambermd Error: an illegal memory access was encountered launching kernel kClearForces Silvana Valdebenito Silva (Sat Aug 26 2017 - 10:13:16 PDT)
- Re: [AMBER] Fw: Ambermd Error: an illegal memory access was encountered launching kernel kClearForces David A Case (Sun Aug 27 2017 - 13:49:16 PDT)
[AMBER] wrong ligand geometry Thomas Evangelidis (Sat Aug 26 2017 - 12:41:33 PDT)
- Re: [AMBER] wrong ligand geometry David A Case (Sun Aug 27 2017 - 05:40:51 PDT)
[AMBER] Error while running antechamber for modified amino acid residue Rajarshi Roy (Sun Aug 27 2017 - 04:50:28 PDT)
- Re: [AMBER] Error while running antechamber for modified amino acid residue David A Case (Sun Aug 27 2017 - 05:57:40 PDT)
  - Re: [AMBER] Error while running antechamber for modified amino acid residue Rajarshi Roy (Sun Aug 27 2017 - 09:22:33 PDT)
[AMBER] How to put the restrain on just part of the system. Parviz Seifpanahi Shabane (Sun Aug 27 2017 - 08:05:24 PDT)
- Re: [AMBER] How to put the restrain on just part of the system. David A Case (Sun Aug 27 2017 - 13:45:10 PDT)
  - Re: [AMBER] How to put the restrain on just part of the system. Parviz Seifpanahi Shabane (Sun Aug 27 2017 - 15:57:17 PDT)
    - Re: [AMBER] How to put the restrain on just part of the system. Daniel Roe (Mon Aug 28 2017 - 05:42:13 PDT)
  - Re: [AMBER] How to put the restrain on just part of the system. James Kress (Mon Aug 28 2017 - 15:33:13 PDT)
[AMBER] Segmentation error in minimization Lizelle Lubbe (Mon Aug 28 2017 - 05:49:06 PDT)
- Re: [AMBER] Segmentation error in minimization David A Case (Mon Aug 28 2017 - 08:03:23 PDT)
[AMBER] Creation of coordinate and topology file for protei-ligand complex Ashok Kumar (Mon Aug 28 2017 - 09:03:00 PDT)
- Re: [AMBER] Creation of coordinate and topology file for protei-ligand complex Bill Ross (Mon Aug 28 2017 - 09:06:28 PDT)
  - Re: [AMBER] Creation of coordinate and topology file for protei-ligand complex Bill Ross (Mon Aug 28 2017 - 09:08:38 PDT)
- Re: [AMBER] Creation of coordinate and topology file for protei-ligand complex David A Case (Mon Aug 28 2017 - 10:42:34 PDT)
[AMBER] problem in minimization and heating Saikat Pal (Tue Aug 29 2017 - 00:42:37 PDT)
- Re: [AMBER] problem in minimization and heating Bill Ross (Tue Aug 29 2017 - 00:50:46 PDT)
- Re: [AMBER] problem in minimization and heating David A Case (Tue Aug 29 2017 - 04:53:28 PDT)
[AMBER] Query regarding water-water interaction potential in GIST output Rakesh Srivastava (Tue Aug 29 2017 - 04:56:54 PDT)
- Re: [AMBER] Query regarding water-water interaction potential in GIST output Steven Ramsey (Tue Aug 29 2017 - 07:03:40 PDT)
  - Re: [AMBER] Query regarding water-water interaction potential in GIST output Rakesh Srivastava (Tue Aug 29 2017 - 21:22:07 PDT)
[AMBER] Distance Restraint using COM for Umbrella Sampling Suchetana Gupta (Tue Aug 29 2017 - 05:56:49 PDT)
- Re: [AMBER] Distance Restraint using COM for Umbrella Sampling Daniel Roe (Tue Aug 29 2017 - 12:29:06 PDT)
[AMBER] For restraint heating Saikat Pal (Tue Aug 29 2017 - 07:06:08 PDT)
- Re: [AMBER] For restraint heating Bill Ross (Tue Aug 29 2017 - 07:13:34 PDT)
  - Re: [AMBER] For restraint heating Saikat Pal (Tue Aug 29 2017 - 07:29:41 PDT)
[AMBER] Clarification about Gnp settings in MM/PBSA Guqin Shi (Tue Aug 29 2017 - 11:35:51 PDT)
- Re: [AMBER] Clarification about Gnp settings in MM/PBSA Guqin Shi (Tue Aug 29 2017 - 13:00:47 PDT)
[AMBER] TIP3PBOX for membrane system James Starlight (Wed Aug 30 2017 - 02:25:00 PDT)
- Re: [AMBER] TIP3PBOX for membrane system Bill Ross (Wed Aug 30 2017 - 02:30:58 PDT)
  - Re: [AMBER] TIP3PBOX for membrane system James Starlight (Wed Aug 30 2017 - 02:39:21 PDT)
    - Re: [AMBER] TIP3PBOX for membrane system Bill Ross (Wed Aug 30 2017 - 02:41:50 PDT)
    - Re: [AMBER] TIP3PBOX for membrane system James Starlight (Wed Aug 30 2017 - 02:42:57 PDT)
    - Re: [AMBER] TIP3PBOX for membrane system Bill Ross (Wed Aug 30 2017 - 02:43:17 PDT)
    - Re: [AMBER] TIP3PBOX for membrane system James Starlight (Wed Aug 30 2017 - 02:54:33 PDT)
[AMBER] Calculate lateral self-diffusion coefficient for POPE embedded protein system carmine marco morgillo (Wed Aug 30 2017 - 15:51:20 PDT)
- Re: [AMBER] Calculate lateral self-diffusion coefficient for POPE embedded protein system Daniel Roe (Thu Aug 31 2017 - 06:03:18 PDT)
[AMBER] convert .mae topology to .prmtop topology? Marcelo Andrade Chagas (Wed Aug 30 2017 - 20:14:56 PDT)
- Re: [AMBER] convert .mae topology to .prmtop topology? Daniel Roe (Thu Aug 31 2017 - 06:15:31 PDT)
[AMBER] frcmod file format Lizelle Lubbe (Thu Aug 31 2017 - 03:03:45 PDT)
- Re: [AMBER] frcmod file format Pengfei Li (Thu Aug 31 2017 - 07:48:34 PDT)
Re: [AMBER] AMBER Digest, Vol 2042, Issue 1 Suchetana Gupta (Thu Aug 31 2017 - 03:13:38 PDT)
[AMBER] How to add the charged sphere (ion) with arbitrary charge to my PDB file. Parviz Seifpanahi Shabane (Thu Aug 31 2017 - 08:11:44 PDT)
- Re: [AMBER] How to add the charged sphere (ion) with arbitrary charge to my PDB file. Bill Ross (Thu Aug 31 2017 - 10:02:55 PDT)
  - Re: [AMBER] How to add the charged sphere (ion) with arbitrary charge to my PDB file. Parviz Seifpanahi Shabane (Thu Aug 31 2017 - 10:11:49 PDT)
    - Re: [AMBER] How to add the charged sphere (ion) with arbitrary charge to my PDB file. Bill Ross (Thu Aug 31 2017 - 12:50:42 PDT)
    - Re: [AMBER] How to add the charged sphere (ion) with arbitrary charge to my PDB file. Parviz Seifpanahi Shabane (Fri Sep 01 2017 - 16:57:38 PDT)
    - Re: [AMBER] How to add the charged sphere (ion) with arbitrary charge to my PDB file. Bill Ross (Fri Sep 01 2017 - 17:01:45 PDT)
    - Re: [AMBER] How to add the charged sphere (ion) with arbitrary charge to my PDB file. Bill Ross (Fri Sep 01 2017 - 17:03:12 PDT)
    - Re: [AMBER] How to add the charged sphere (ion) with arbitrary charge to my PDB file. Parviz Seifpanahi Shabane (Sun Sep 03 2017 - 18:10:13 PDT)
    - Re: [AMBER] How to add the charged sphere (ion) with arbitrary charge to my PDB file. Bill Ross (Sun Sep 03 2017 - 18:11:50 PDT)
    - Re: [AMBER] How to add the charged sphere (ion) with arbitrary charge to my PDB file. Parviz Seifpanahi Shabane (Sun Sep 03 2017 - 18:12:55 PDT)
    - Re: [AMBER] How to add the charged sphere (ion) with arbitrary charge to my PDB file. Bill Ross (Sun Sep 03 2017 - 18:14:11 PDT)
    - Re: [AMBER] How to add the charged sphere (ion) with arbitrary charge to my PDB file. Parviz Seifpanahi Shabane (Sun Sep 03 2017 - 18:15:32 PDT)
    - Re: [AMBER] How to add the charged sphere (ion) with arbitrary charge to my PDB file. Bill Ross (Sun Sep 03 2017 - 18:17:29 PDT)
    - Re: [AMBER] How to add the charged sphere (ion) with arbitrary charge to my PDB file. Parviz Seifpanahi Shabane (Sun Sep 03 2017 - 18:19:56 PDT)
[AMBER] Webinar: “An AI Quantum Breakthrough: ANAKIN-ME” Mark Berger (Thu Aug 31 2017 - 13:33:34 PDT)
[AMBER] Pressure tensor Sonata Kvedaravičiūtė (Fri Sep 01 2017 - 01:43:48 PDT)
[AMBER] ACE and NME capping protein is essential for protein simulation jacky zhao (Fri Sep 01 2017 - 03:30:57 PDT)
- Re: [AMBER] ACE and NME capping protein is essential for protein simulation David A Case (Fri Sep 01 2017 - 05:42:20 PDT)
  - Re: [AMBER] ACE and NME capping protein is essential for protein simulation Carlos Simmerling (Fri Sep 01 2017 - 06:29:04 PDT)
    - Re: [AMBER] ACE and NME capping protein is essential for protein simulation jacky zhao (Fri Sep 01 2017 - 08:55:56 PDT)
  - Re: [AMBER] ACE and NME capping protein is essential for protein simulation jacky zhao (Fri Sep 01 2017 - 08:50:19 PDT)
[AMBER] significance of iwrap Saikat Pal (Fri Sep 01 2017 - 04:59:28 PDT)
- Re: [AMBER] significance of iwrap Daniel Roe (Fri Sep 01 2017 - 05:22:06 PDT)
[AMBER] H++ salinity Andreas Tosstorff (Fri Sep 01 2017 - 05:38:46 PDT)
[AMBER] Missing amino acids preparation for long-term simulation jacky zhao (Fri Sep 01 2017 - 09:31:43 PDT)
[AMBER] Cpptraj and parmwrite and strip Khabiri, Morteza (Fri Sep 01 2017 - 11:16:16 PDT)
- Re: [AMBER] Cpptraj and parmwrite and strip Daniel Roe (Fri Sep 01 2017 - 12:05:44 PDT)
- Re: [AMBER] Cpptraj and parmwrite and strip Khabiri, Morteza (Fri Sep 01 2017 - 12:37:58 PDT)
  - Re: [AMBER] Cpptraj and parmwrite and strip Khabiri, Morteza (Fri Sep 01 2017 - 12:44:20 PDT)
    - Re: [AMBER] Cpptraj and parmwrite and strip Daniel Roe (Fri Sep 01 2017 - 13:27:18 PDT)
[AMBER] Explicit solvent CpHMD: seeking clarifications George Tzotzos (Sat Sep 02 2017 - 10:07:21 PDT)
- Re: [AMBER] Explicit solvent CpHMD: seeking clarifications Jason Swails (Sun Sep 03 2017 - 04:42:40 PDT)
  - Re: [AMBER] Explicit solvent CpHMD: seeking clarifications George Tzotzos (Sun Sep 03 2017 - 04:57:44 PDT)
    - Re: [AMBER] Explicit solvent CpHMD: seeking clarifications Cruzeiro,Vinicius Wilian D (Sun Sep 03 2017 - 06:26:13 PDT)
    - Re: [AMBER] Explicit solvent CpHMD: seeking clarifications George Tzotzos (Mon Sep 04 2017 - 08:56:36 PDT)
    - Re: [AMBER] Explicit solvent CpHMD: seeking clarifications George Tzotzos (Mon Sep 04 2017 - 04:09:30 PDT)
[AMBER] amberlite p38 tutorial: Failure of final step of "pymdpbsa" in amberlite Bartberger, Michael (Sun Sep 03 2017 - 09:25:31 PDT)
- Re: [AMBER] amberlite p38 tutorial: Failure of final step of "pymdpbsa" in amberlite David A Case (Sun Sep 03 2017 - 18:27:21 PDT)
  - Re: [AMBER] amberlite p38 tutorial: Failure of final step of "pymdpbsa" in amberlite Bartberger, Michael (Sat Sep 09 2017 - 14:57:41 PDT)
[AMBER] Error bad atom Br Fábio Jorge (Sun Sep 03 2017 - 12:43:58 PDT)
- Re: [AMBER] Error bad atom Br James Kress (Sun Sep 03 2017 - 16:35:42 PDT)
[AMBER] Binding Free Energy Calculation in Ionic Liquid Debasish Mandal (Sun Sep 03 2017 - 21:57:09 PDT)
- Re: [AMBER] Binding Free Energy Calculation in Ionic Liquid Bill Ross (Sun Sep 03 2017 - 22:17:51 PDT)
- Re: [AMBER] Binding Free Energy Calculation in Ionic Liquid David A Case (Mon Sep 04 2017 - 05:39:56 PDT)
[AMBER] Moldeling with MCPB.py Lê Ngọc Chính (Mon Sep 04 2017 - 04:09:45 PDT)
- Re: [AMBER] Moldeling with MCPB.py Pengfei Li (Tue Sep 05 2017 - 05:33:26 PDT)
  - Re: [AMBER] Moldeling with MCPB.py Lê Ngọc Chính (Sun Sep 10 2017 - 09:22:02 PDT)
[AMBER] Question about MM/PBSA idecomp=1: Eelec from receptor and ligand don't add up Guqin Shi (Mon Sep 04 2017 - 17:13:25 PDT)
[AMBER] Residue wise energy decomposition via MM-PBSA Rajarshi Roy (Mon Sep 04 2017 - 21:06:49 PDT)
- Re: [AMBER] Residue wise energy decomposition via MM-PBSA Elvis Martis (Tue Sep 05 2017 - 23:37:16 PDT)
  - Re: [AMBER] Residue wise energy decomposition via MM-PBSA Rajarshi Roy (Wed Sep 06 2017 - 00:20:34 PDT)
[AMBER] Rebuilt missing amino acid gap is critical for long-time MD simulation by Amber jacky zhao (Mon Sep 04 2017 - 22:00:53 PDT)
- Re: [AMBER] Rebuilt missing amino acid gap is critical for long-time MD simulation by Amber jacky zhao (Fri Sep 08 2017 - 07:28:56 PDT)
  - Re: [AMBER] Rebuilt missing amino acid gap is critical for long-time MD simulation by Amber Carlos Simmerling (Fri Sep 08 2017 - 07:39:14 PDT)
    - Re: [AMBER] Rebuilt missing amino acid gap is critical for long-time MD simulation by Amber jacky zhao (Sat Sep 09 2017 - 00:25:57 PDT)
    - Re: [AMBER] Rebuilt missing amino acid gap is critical for long-time MD simulation by Amber Carlos Simmerling (Sat Sep 09 2017 - 04:16:12 PDT)
    - Re: [AMBER] Rebuilt missing amino acid gap is critical for long-time MD simulation by Amber jacky zhao (Wed Sep 13 2017 - 05:13:13 PDT)
[AMBER] .crd file format error Thakur, Abhishek (Tue Sep 05 2017 - 08:37:15 PDT)
- Re: [AMBER] .crd file format error Daniel Roe (Tue Sep 05 2017 - 08:46:41 PDT)
Re: [AMBER] Question about MM/PBSA idecomp=1: decomposed Eelec stays the same when internal dielec constant increases. Is this a bug? Guqin Shi (Tue Sep 05 2017 - 08:54:40 PDT)
[AMBER] Zinc dummy atom error in MMPBSA calculation Sharon D. Morris (Tue Sep 05 2017 - 22:26:13 PDT)
- Re: [AMBER] Zinc dummy atom error in MMPBSA calculation Bill Ross (Wed Sep 06 2017 - 10:05:06 PDT)
[AMBER] MD terminate in HPC Garima Singh (Wed Sep 06 2017 - 03:49:05 PDT)
- Re: [AMBER] MD terminate in HPC Elvis Martis (Wed Sep 06 2017 - 05:42:58 PDT)
- Re: [AMBER] MD terminate in HPC David A Case (Wed Sep 06 2017 - 05:43:06 PDT)
[AMBER] Oct 2 deadline for awards applications, Computers in Chemistry Division of ACS Carlos Simmerling (Wed Sep 06 2017 - 05:27:12 PDT)
[AMBER] Error in MM-PBSA -- BondError: Cannot exclude an atom from itself 康宁 (Thu Sep 07 2017 - 00:47:07 PDT)
- Re: [AMBER] Error in MM-PBSA -- BondError: Cannot exclude an atom from itself Bill Ross (Thu Sep 07 2017 - 01:11:27 PDT)
- Re: [AMBER] Error in MM-PBSA -- BondError: Cannot exclude an atom from itself 康宁 (Fri Sep 08 2017 - 18:04:24 PDT)
- Re: [AMBER] Error in MM-PBSA -- BondError: Cannot exclude an atom from itself Jason Swails (Sat Sep 09 2017 - 19:18:54 PDT)
- Re: [AMBER] Error in MM-PBSA -- BondError: Cannot exclude an atom from itself 康宁 (Sun Sep 17 2017 - 18:47:37 PDT)
[AMBER] Error after using Parmed: A residue defined as "fast 3-point water"... David Sáez (Thu Sep 07 2017 - 16:07:32 PDT)
- Re: [AMBER] Error after using Parmed: A residue defined as "fast 3-point water"... Bill Ross (Thu Sep 07 2017 - 16:23:39 PDT)
[AMBER] Fixed links and files: Error in parmed: A residue defined as "fast 3-point water"... David Adrian Saez San Martin (Thu Sep 07 2017 - 17:14:24 PDT)
- Re: [AMBER] Fixed links and files: Error in parmed: A residue defined as "fast 3-point water"... Bill Ross (Thu Sep 07 2017 - 17:25:17 PDT)
- Re: [AMBER] Fixed links and files: Error in parmed: A residue defined as "fast 3-point water"... David Adrian Saez San Martin (Fri Sep 08 2017 - 12:31:39 PDT)
- Re: [AMBER] Fixed links and files: Error in parmed: A residue defined as "fast 3-point water"... David Adrian Saez San Martin (Fri Sep 08 2017 - 12:58:25 PDT)
[AMBER] umbrella sampling - restraint problem Nisha Amarnath Jonniya (Fri Sep 08 2017 - 04:37:14 PDT)
- Re: [AMBER] umbrella sampling - restraint problem diego.soler.uam.es (Fri Sep 08 2017 - 05:50:17 PDT)
  - Re: [AMBER] umbrella sampling - restraint problem Nisha Amarnath Jonniya (Fri Sep 08 2017 - 07:57:10 PDT)
    - Re: [AMBER] umbrella sampling - restraint problem Carlos Simmerling (Fri Sep 08 2017 - 08:20:04 PDT)
    - Re: [AMBER] umbrella sampling - restraint problem Nisha Amarnath Jonniya (Sun Sep 10 2017 - 22:21:44 PDT)
    - Re: [AMBER] umbrella sampling - restraint problem Daniel Roe (Mon Sep 11 2017 - 06:04:06 PDT)
[AMBER] Problem in restarting pH-REMD CpHMD Elisa Pieri (Fri Sep 08 2017 - 05:43:56 PDT)
- Re: [AMBER] Problem in restarting pH-REMD CpHMD Daniel Roe (Fri Sep 08 2017 - 11:09:08 PDT)
  - Re: [AMBER] Problem in restarting pH-REMD CpHMD Elisa Pieri (Sat Sep 09 2017 - 01:14:12 PDT)
[AMBER] Frcmod file for ionic liquids guptashilpa_91.yahoo.com (Fri Sep 08 2017 - 07:42:13 PDT)
- Re: [AMBER] Frcmod file for ionic liquids Bill Ross (Fri Sep 08 2017 - 12:22:46 PDT)
[AMBER] I only receive a digest, but not specific answers to my posts David Adrian Saez San Martin (Fri Sep 08 2017 - 12:36:40 PDT)
- Re: [AMBER] I only receive a digest, but not specific answers to my posts David Adrian Saez San Martin (Fri Sep 08 2017 - 12:49:26 PDT)
[AMBER] Frcmod file for ionic liquids Shilpa Gupta (Fri Sep 08 2017 - 21:43:05 PDT)
[AMBER] Regarding Glucose naming Aashish Bhatt (Sat Sep 09 2017 - 08:02:12 PDT)
- Re: [AMBER] Regarding Glucose naming Elvis Martis (Sat Sep 09 2017 - 20:06:26 PDT)
  - Re: [AMBER] Regarding Glucose naming Aashish Bhatt (Sun Sep 10 2017 - 00:57:44 PDT)
    - Re: [AMBER] Regarding Glucose naming Hector A. Baldoni (Sun Sep 10 2017 - 11:02:38 PDT)
    - Re: [AMBER] Regarding Glucose naming Aashish Bhatt (Tue Sep 12 2017 - 08:00:12 PDT)
[AMBER] Error in quasiharmonic calculation: prmtop file? Nada Afiva (Sat Sep 09 2017 - 19:50:48 PDT)
- Re: [AMBER] Error in quasiharmonic calculation: prmtop file? Hai Nguyen (Sat Sep 09 2017 - 19:52:44 PDT)
  - Re: [AMBER] Error in quasiharmonic calculation: prmtop file? Nada Afiva (Sat Sep 09 2017 - 20:55:07 PDT)
    - Re: [AMBER] Error in quasiharmonic calculation: prmtop file? Daniel Roe (Mon Sep 11 2017 - 09:07:38 PDT)
[AMBER] Obtaining AM1-BCC charges in Antechamber Zachary Smithline (Sat Sep 09 2017 - 23:33:14 PDT)
- Re: [AMBER] Obtaining AM1-BCC charges in Antechamber David A Case (Mon Sep 11 2017 - 05:19:18 PDT)
[AMBER] index error -reg Jeyaram R A (Sun Sep 10 2017 - 04:54:00 PDT)
- Re: [AMBER] index error -reg David A Case (Sun Sep 10 2017 - 08:15:04 PDT)
[AMBER] tleap atom numbering Neha Gandhi (Sun Sep 10 2017 - 18:38:03 PDT)
- Re: [AMBER] tleap atom numbering David A Case (Mon Sep 11 2017 - 05:07:13 PDT)
  - Re: [AMBER] tleap atom numbering Neha Gandhi (Mon Sep 11 2017 - 14:38:23 PDT)
    - Re: [AMBER] tleap atom numbering Bill Ross (Mon Sep 11 2017 - 16:24:40 PDT)
[AMBER] CNT hongping zhang (Sun Sep 10 2017 - 18:58:34 PDT)
[AMBER] rmsf < 5A colvin (Mon Sep 11 2017 - 01:11:46 PDT)
- Re: [AMBER] rmsf < 5A Daniel Roe (Mon Sep 11 2017 - 06:07:34 PDT)
[AMBER] MMPBSA.py failing with topologies Sebastian Franco Ulloa (Mon Sep 11 2017 - 01:46:18 PDT)
- Re: [AMBER] MMPBSA.py failing with topologies Dwight McGee (Wed Sep 13 2017 - 22:29:16 PDT)
  - Re: [AMBER] MMPBSA.py failing with topologies Sebastian Franco Ulloa (Wed Sep 13 2017 - 23:42:48 PDT)
  - Re: [AMBER] MMPBSA.py failing with topologies Sebastian Franco Ulloa (Thu Sep 14 2017 - 00:17:44 PDT)
[AMBER] MMPBSA error Sebastian Franco Ulloa (Mon Sep 11 2017 - 02:10:18 PDT)
[AMBER] gamd.log for multiple runs Battocchio, Giovanni (Mon Sep 11 2017 - 02:37:35 PDT)
- Re: [AMBER] gamd.log for multiple runs Ross Walker (Tue Sep 12 2017 - 09:15:18 PDT)
  - Re: [AMBER] gamd.log for multiple runs Yinglong Miao (Tue Sep 12 2017 - 11:28:40 PDT)
    - Re: [AMBER] gamd.log for multiple runs Battocchio, Giovanni (Wed Sep 13 2017 - 01:05:26 PDT)
[AMBER] TLEAP generation of ionized amino acid residue? Michael Shokhen (Mon Sep 11 2017 - 03:38:55 PDT)
Re: [AMBER] Minimization error due to modified residue Bill Ross (Mon Sep 11 2017 - 06:09:40 PDT)
- Re: [AMBER] Minimization error due to modified residue Lizelle Lubbe (Mon Sep 11 2017 - 06:12:46 PDT)
  - Re: [AMBER] Minimization error due to modified residue Lizelle Lubbe (Mon Sep 11 2017 - 07:03:57 PDT)
    - Re: [AMBER] Minimization error due to modified residue Lizelle Lubbe (Mon Sep 11 2017 - 07:21:05 PDT)
    - Re: [AMBER] Minimization error due to modified residue Bill Ross (Mon Sep 11 2017 - 07:28:24 PDT)
    - Re: [AMBER] Minimization error due to modified residue Lizelle Lubbe (Mon Sep 11 2017 - 07:30:29 PDT)
    - Re: [AMBER] Minimization error due to modified residue Bill Ross (Mon Sep 11 2017 - 07:37:24 PDT)
    - Re: [AMBER] Minimization error due to modified residue Lizelle Lubbe (Mon Sep 11 2017 - 07:48:26 PDT)
    - Re: [AMBER] Minimization error due to modified residue Bill Ross (Mon Sep 11 2017 - 07:55:16 PDT)
    - Re: [AMBER] Minimization error due to modified residue Bill Ross (Mon Sep 11 2017 - 07:57:24 PDT)
    - Re: [AMBER] Minimization error due to modified residue Lizelle Lubbe (Tue Sep 12 2017 - 05:05:32 PDT)
    - Re: [AMBER] Minimization error due to modified residue Lizelle Lubbe (Tue Sep 12 2017 - 07:43:13 PDT)
    - Re: [AMBER] Minimization error due to modified residue Shafaq Muzammal (Mon Sep 11 2017 - 07:57:48 PDT)
    - Re: [AMBER] Minimization error due to modified residue Lizelle Lubbe (Mon Sep 11 2017 - 07:59:38 PDT)
    - Re: [AMBER] Minimization error due to modified residue Shafaq Muzammal (Mon Sep 11 2017 - 08:09:24 PDT)
    - Re: [AMBER] Minimization error due to modified residue Bill Ross (Mon Sep 11 2017 - 08:32:01 PDT)
    - Re: [AMBER] Minimization error due to modified residue Lizelle Lubbe (Mon Sep 11 2017 - 08:43:07 PDT)
    - Re: [AMBER] Minimization error due to modified residue Ross Walker (Mon Sep 11 2017 - 10:05:21 PDT)
[AMBER] How to use two different force fields for a molecule? Anhui Wang (Mon Sep 11 2017 - 07:09:05 PDT)
- Re: [AMBER] How to use two different force fields for a molecule? Hai Nguyen (Mon Sep 11 2017 - 09:09:51 PDT)
- Re: [AMBER] How to use two different force fields for a molecule? David A Case (Tue Sep 12 2017 - 04:16:11 PDT)
[AMBER] Atom does not have file type -reg. Jeyaram R A (Mon Sep 11 2017 - 08:04:39 PDT)
- Re: [AMBER] Atom does not have file type -reg. Bill Ross (Mon Sep 11 2017 - 08:07:51 PDT)
- Re: [AMBER] Atom does not have file type -reg. David A Case (Tue Sep 12 2017 - 04:21:04 PDT)
  - Re: [AMBER] Atom does not have file type -reg. Jeyaram R A (Tue Sep 12 2017 - 07:21:01 PDT)
    - Re: [AMBER] Atom does not have file type -reg. Aashish Bhatt (Tue Sep 12 2017 - 08:09:33 PDT)
    - Re: [AMBER] Atom does not have file type -reg. Jeyaram R A (Tue Sep 12 2017 - 08:34:02 PDT)
    - Re: [AMBER] Atom does not have file type -reg. Aashish Bhatt (Tue Sep 12 2017 - 08:51:37 PDT)
[AMBER] pmemd and sander simulations different - sander equilibration crashes Chayya Bhargac (Mon Sep 11 2017 - 09:34:14 PDT)
- Re: [AMBER] pmemd and sander simulations different - sander equilibration crashes Chayya Bhargac (Mon Sep 11 2017 - 10:51:32 PDT)
- Re: [AMBER] pmemd and sander simulations different - sander equilibration crashes David A Case (Tue Sep 12 2017 - 04:25:07 PDT)
  - Re: [AMBER] pmemd and sander simulations different - sander equilibration crashes Chayya Bhargac (Wed Sep 13 2017 - 09:25:38 PDT)
    - Re: [AMBER] pmemd and sander simulations different - sander equilibration crashes Chayya Bhargac (Wed Sep 13 2017 - 09:30:11 PDT)
[AMBER] Can we specify the length and width of the water box in LEaP ? Xing (Mon Sep 11 2017 - 16:27:45 PDT)
- Re: [AMBER] Can we specify the length and width of the water box in LEaP ? Robin Betz (Mon Sep 11 2017 - 16:35:54 PDT)
  - Re: [AMBER] Can we specify the length and width of the water box in LEaP ? Xing (Mon Sep 11 2017 - 16:53:29 PDT)
[AMBER] NEW machine need help with GPU choice. Mohit Mazumder (Mon Sep 11 2017 - 18:46:02 PDT)
- Re: [AMBER] NEW machine need help with GPU choice. David Cerutti (Mon Sep 11 2017 - 19:25:06 PDT)
- Re: [AMBER] NEW machine need help with GPU choice. Ross Walker (Tue Sep 12 2017 - 06:09:01 PDT)
[AMBER] Could not import Amber Python modules when using mdout_analyzer.py jacky zhao (Mon Sep 11 2017 - 21:31:50 PDT)
- Re: [AMBER] Could not import Amber Python modules when using mdout_analyzer.py Hai Nguyen (Mon Sep 11 2017 - 21:39:44 PDT)
  - Re: [AMBER] Could not import Amber Python modules when using mdout_analyzer.py jacky zhao (Tue Sep 12 2017 - 02:07:28 PDT)
    - Re: [AMBER] Could not import Amber Python modules when using mdout_analyzer.py Hai Nguyen (Tue Sep 12 2017 - 05:25:30 PDT)
    - Re: [AMBER] Could not import Amber Python modules when using mdout_analyzer.py jacky zhao (Tue Sep 12 2017 - 05:39:23 PDT)
    - Re: [AMBER] Could not import Amber Python modules when using mdout_analyzer.py Hai Nguyen (Tue Sep 12 2017 - 05:45:00 PDT)
    - Re: [AMBER] Could not import Amber Python modules when using mdout_analyzer.py jacky zhao (Tue Sep 12 2017 - 05:54:12 PDT)
    - Re: [AMBER] Could not import Amber Python modules when using mdout_analyzer.py jacky zhao (Tue Sep 12 2017 - 05:55:21 PDT)
    - Re: [AMBER] Could not import Amber Python modules when using mdout_analyzer.py Hai Nguyen (Tue Sep 12 2017 - 05:57:25 PDT)
    - Re: [AMBER] Could not import Amber Python modules when using mdout_analyzer.py jacky zhao (Tue Sep 12 2017 - 18:52:04 PDT)
    - Re: [AMBER] Could not import Amber Python modules when using mdout_analyzer.py Hai Nguyen (Tue Sep 12 2017 - 19:10:26 PDT)
    - Re: [AMBER] Could not import Amber Python modules when using mdout_analyzer.py Hai Nguyen (Tue Sep 12 2017 - 19:18:03 PDT)
    - Re: [AMBER] Could not import Amber Python modules when using mdout_analyzer.py jacky zhao (Tue Sep 12 2017 - 19:36:23 PDT)
    - Re: [AMBER] Could not import Amber Python modules when using mdout_analyzer.py Hai Nguyen (Tue Sep 12 2017 - 19:39:10 PDT)
    - Re: [AMBER] Could not import Amber Python modules when using mdout_analyzer.py Hai Nguyen (Tue Sep 12 2017 - 19:43:50 PDT)
    - Re: [AMBER] Could not import Amber Python modules when using mdout_analyzer.py jacky zhao (Tue Sep 12 2017 - 19:45:30 PDT)
    - Re: [AMBER] Could not import Amber Python modules when using mdout_analyzer.py Hai Nguyen (Tue Sep 12 2017 - 19:48:50 PDT)
    - Re: [AMBER] Could not import Amber Python modules when using mdout_analyzer.py Hai Nguyen (Tue Sep 12 2017 - 19:49:03 PDT)
    - Re: [AMBER] Could not import Amber Python modules when using mdout_analyzer.py jacky zhao (Tue Sep 12 2017 - 19:52:44 PDT)
    - Re: [AMBER] Could not import Amber Python modules when using mdout_analyzer.py Hai Nguyen (Tue Sep 12 2017 - 19:58:04 PDT)
    - Re: [AMBER] Could not import Amber Python modules when using mdout_analyzer.py jacky zhao (Tue Sep 12 2017 - 20:06:00 PDT)
    - Re: [AMBER] Could not import Amber Python modules when using mdout_analyzer.py jacky zhao (Tue Sep 12 2017 - 05:31:26 PDT)
[AMBER] GPU-accelerated thermodynamic integration available in Amber Darrin York (Tue Sep 12 2017 - 06:01:40 PDT)
- Re: [AMBER] GPU-accelerated thermodynamic integration available in Amber Ross Walker (Tue Sep 12 2017 - 06:43:50 PDT)
  - Re: [AMBER] GPU-accelerated thermodynamic integration available in Amber Hadházi Ádám (Wed Sep 13 2017 - 11:33:49 PDT)
    - Re: [AMBER] GPU-accelerated thermodynamic integration available in Amber Daniel Mermelstein (Wed Sep 13 2017 - 13:16:39 PDT)
    - Re: [AMBER] GPU-accelerated thermodynamic integration available in Amber Hadházi Ádám (Wed Sep 13 2017 - 14:33:30 PDT)
    - Re: [AMBER] GPU-accelerated thermodynamic integration available in Amber Jason Swails (Wed Sep 13 2017 - 19:52:00 PDT)
    - [AMBER] TI where charges change David A Case (Thu Sep 14 2017 - 04:51:26 PDT)
    - Re: [AMBER] TI where charges change Adrian Roitberg (Thu Sep 14 2017 - 05:38:53 PDT)
    - Re: [AMBER] TI where charges change Hadházi Ádám (Thu Sep 14 2017 - 06:10:46 PDT)
    - Re: [AMBER] TI where charges change David A Case (Thu Sep 14 2017 - 08:05:13 PDT)
    - Re: [AMBER] TI where charges change Hadházi Ádám (Thu Sep 14 2017 - 10:44:15 PDT)
[AMBER] Etot and TEMP become NaN during a simulation on commodity GPUs Chris Neale (Tue Sep 12 2017 - 09:28:30 PDT)
- Re: [AMBER] Etot and TEMP become NaN during a simulation on commodity GPUs Ross Walker (Tue Sep 12 2017 - 09:43:34 PDT)
  - Re: [AMBER] Etot and TEMP become NaN during a simulation on commodity GPUs Chris Neale (Tue Sep 12 2017 - 10:16:47 PDT)
    - Re: [AMBER] Etot and TEMP become NaN during a simulation on commodity GPUs Chris Neale (Fri Sep 15 2017 - 11:09:34 PDT)
    - Re: [AMBER] Etot and TEMP become NaN during a simulation on commodity GPUs Ross Walker (Sat Sep 16 2017 - 07:00:21 PDT)
[AMBER] Creation of unusual bonding via pdb4amber. Rajarshi Roy (Tue Sep 12 2017 - 11:18:18 PDT)
- Re: [AMBER] Creation of unusual bonding via pdb4amber. Hai Nguyen (Tue Sep 12 2017 - 18:37:39 PDT)
  - Re: [AMBER] Creation of unusual bonding via pdb4amber. Hai Nguyen (Tue Sep 12 2017 - 19:36:38 PDT)
    - Re: [AMBER] Creation of unusual bonding via pdb4amber. Rajarshi Roy (Tue Sep 12 2017 - 20:56:29 PDT)
    - Re: [AMBER] Creation of unusual bonding via pdb4amber. Hai Nguyen (Tue Sep 12 2017 - 21:16:50 PDT)
    - Re: [AMBER] Creation of unusual bonding via pdb4amber. Rajarshi Roy (Tue Sep 12 2017 - 22:52:43 PDT)
[AMBER] How to calculate RDF with 'radial' 杨满意 (Tue Sep 12 2017 - 20:58:06 PDT)
- Re: [AMBER] How to calculate RDF with 'radial' Daniel Roe (Wed Sep 13 2017 - 06:39:48 PDT)
  - Re: [AMBER] How to calculate RDF with 'radial' 杨满意 (Wed Sep 13 2017 - 18:49:49 PDT)
    - Re: [AMBER] How to calculate RDF with 'radial' Daniel Roe (Mon Sep 18 2017 - 11:22:15 PDT)
    - Re: [AMBER] How to calculate RDF with 'radial' 杨满意 (Mon Sep 25 2017 - 04:44:12 PDT)
[AMBER] tleap error jacky zhao (Wed Sep 13 2017 - 03:28:24 PDT)
- Re: [AMBER] tleap error jacky zhao (Wed Sep 13 2017 - 05:15:56 PDT)
- Re: [AMBER] tleap error David A Case (Wed Sep 13 2017 - 06:27:46 PDT)
  - Re: [AMBER] tleap error jacky zhao (Wed Sep 13 2017 - 06:48:03 PDT)
[AMBER] Amber16 archive corrupted? Casalini Tommaso (Wed Sep 13 2017 - 03:30:01 PDT)
- Re: [AMBER] Amber16 archive corrupted? Elvis Martis (Wed Sep 13 2017 - 04:05:47 PDT)
  - Re: [AMBER] Amber16 archive corrupted? Casalini Tommaso (Wed Sep 13 2017 - 04:07:57 PDT)
[AMBER] REMD one long or many short runs? Andreas Tosstorff (Wed Sep 13 2017 - 06:18:02 PDT)
- Re: [AMBER] REMD one long or many short runs? Carlos Simmerling (Wed Sep 13 2017 - 06:37:28 PDT)
[AMBER] Deprotonated SER side residue by AMBER? Michael Shokhen (Wed Sep 13 2017 - 10:18:07 PDT)
- Re: [AMBER] Deprotonated SER side residue by AMBER? David A Case (Thu Sep 14 2017 - 05:02:06 PDT)
  - Re: [AMBER] Deprotonated SER side residue by AMBER? Michael Shokhen (Thu Sep 14 2017 - 06:25:52 PDT)
[AMBER] Total energy of peptide simulation is positive Chetna Tyagi (Thu Sep 14 2017 - 05:51:00 PDT)
- Re: [AMBER] Total energy of peptide simulation is positive David A Case (Thu Sep 14 2017 - 08:11:57 PDT)
  - Re: [AMBER] Total energy of peptide simulation is positive Chetna Tyagi (Thu Sep 14 2017 - 08:31:06 PDT)
[AMBER] cpptraj SPAM error George Tzotzos (Thu Sep 14 2017 - 08:13:50 PDT)
- Re: [AMBER] cpptraj SPAM error Daniel Roe (Thu Sep 14 2017 - 08:16:55 PDT)
  - Re: [AMBER] cpptraj SPAM error George Tzotzos (Thu Sep 14 2017 - 08:30:48 PDT)
    - Re: [AMBER] cpptraj SPAM error George Tzotzos (Thu Sep 14 2017 - 08:33:07 PDT)
    - Re: [AMBER] cpptraj SPAM error Daniel Roe (Thu Sep 14 2017 - 08:49:37 PDT)
    - Re: [AMBER] cpptraj SPAM error George Tzotzos (Thu Sep 14 2017 - 09:04:09 PDT)
    - Re: [AMBER] cpptraj SPAM error Daniel Roe (Thu Sep 14 2017 - 09:34:56 PDT)
    - Re: [AMBER] cpptraj SPAM error George Tzotzos (Thu Sep 14 2017 - 09:42:20 PDT)
[AMBER] Installing Compiling Errors Timothy Schutt (Thu Sep 14 2017 - 13:30:10 PDT)
- Re: [AMBER] Installing Compiling Errors Hai Nguyen (Thu Sep 14 2017 - 13:39:30 PDT)
  - Re: [AMBER] Installing Compiling Errors Timothy Schutt (Thu Sep 14 2017 - 15:00:25 PDT)
    - Re: [AMBER] Installing Compiling Errors David A Case (Thu Sep 14 2017 - 17:58:07 PDT)
    - Re: [AMBER] Installing Compiling Errors Timothy Schutt (Fri Sep 15 2017 - 09:56:08 PDT)
[AMBER] New Phospho Amino Acids Parameters? martin.lepsik.uochb.cas.cz (Fri Sep 15 2017 - 01:32:46 PDT)
- Re: [AMBER] New Phospho Amino Acids Parameters? Carlos Simmerling (Fri Sep 15 2017 - 09:29:51 PDT)
[AMBER] cpptraj volmap: some questions George Tzotzos (Fri Sep 15 2017 - 06:54:25 PDT)
- Re: [AMBER] cpptraj volmap: some questions Daniel Roe (Wed Sep 20 2017 - 09:26:59 PDT)
  - Re: [AMBER] cpptraj volmap: some questions George Tzotzos (Wed Sep 20 2017 - 11:36:05 PDT)
[AMBER] Is geometric center of atoms same as center of mass ? Saikat Pal (Sat Sep 16 2017 - 00:28:39 PDT)
- Re: [AMBER] Is geometric center of atoms same as center of mass ? Daniel Roe (Sat Sep 16 2017 - 04:46:09 PDT)
- Re: [AMBER] Is geometric center of atoms same as center of mass ? Daniel Roe (Mon Sep 18 2017 - 11:11:21 PDT)
[AMBER] simulation time Rana Rehan Khalid (Sat Sep 16 2017 - 09:52:51 PDT)
- Re: [AMBER] simulation time Elvis Martis (Sat Sep 16 2017 - 11:14:40 PDT)
  - Re: [AMBER] simulation time Rana Rehan Khalid (Sat Sep 16 2017 - 11:31:29 PDT)
    - Re: [AMBER] simulation time Elvis Martis (Sat Sep 16 2017 - 11:34:34 PDT)
    - Re: [AMBER] simulation time Hai Nguyen (Sat Sep 16 2017 - 11:39:04 PDT)
    - Re: [AMBER] simulation time Rana Rehan Khalid (Sat Sep 16 2017 - 12:07:45 PDT)
    - Re: [AMBER] simulation time Elvis Martis (Sat Sep 16 2017 - 20:22:16 PDT)
    - Re: [AMBER] simulation time Pengfei Li (Tue Sep 19 2017 - 19:25:05 PDT)
    - Re: [AMBER] simulation time Pengfei Li (Tue Sep 19 2017 - 19:25:23 PDT)
    - Re: [AMBER] simulation time Chris Neale (Tue Sep 19 2017 - 19:53:55 PDT)
[AMBER] Mcpb.py for bay60 compound Rana Rehan Khalid (Sat Sep 16 2017 - 10:43:17 PDT)
- Re: [AMBER] Mcpb.py for bay60 compound Rana Rehan Khalid (Sat Sep 16 2017 - 12:20:08 PDT)
  - Re: [AMBER] Mcpb.py for bay60 compound Pengfei Li (Tue Sep 19 2017 - 20:08:41 PDT)
[AMBER] MCPB.py hbay.in input (system does not have metal ion) Rana Rehan Khalid (Sat Sep 16 2017 - 12:19:05 PDT)
- Re: [AMBER] MCPB.py hbay.in input (system does not have metal ion) Rana Rehan Khalid (Sat Sep 16 2017 - 12:30:28 PDT)
  - Re: [AMBER] MCPB.py hbay.in input (system does not have metal ion) Bill Ross (Sat Sep 16 2017 - 12:46:09 PDT)
    - Re: [AMBER] MCPB.py hbay.in input (system does not have metal ion) Rana Rehan Khalid (Sat Sep 16 2017 - 23:58:25 PDT)
    - Re: [AMBER] MCPB.py hbay.in input (system does not have metal ion) Bill Ross (Sun Sep 17 2017 - 00:04:23 PDT)
    - Re: [AMBER] MCPB.py hbay.in input (system does not have metal ion) David A Case (Sun Sep 17 2017 - 09:25:44 PDT)
[AMBER] cpptraj: modification of topologies/trajectories George Tzotzos (Sun Sep 17 2017 - 08:02:43 PDT)
- Re: [AMBER] cpptraj: modification of topologies/trajectories Daniel Roe (Mon Sep 18 2017 - 05:38:21 PDT)
  - Re: [AMBER] cpptraj: modification of topologies/trajectories George Tzotzos (Mon Sep 18 2017 - 05:53:02 PDT)
    - Re: [AMBER] cpptraj: modification of topologies/trajectories Daniel Roe (Mon Sep 18 2017 - 06:01:14 PDT)
    - Re: [AMBER] cpptraj: modification of topologies/trajectories George Tzotzos (Mon Sep 18 2017 - 06:04:24 PDT)
    - Re: [AMBER] cpptraj: modification of topologies/trajectories Daniel Roe (Mon Sep 18 2017 - 12:23:03 PDT)
[AMBER] Manually set residues Protonation states for HIS and CYS Rana Rehan Khalid (Sun Sep 17 2017 - 12:27:46 PDT)
- Re: [AMBER] Manually set residues Protonation states for HIS and CYS Rana Rehan Khalid (Sun Sep 17 2017 - 12:30:16 PDT)
- Re: [AMBER] Manually set residues Protonation states for HIS and CYS David A Case (Mon Sep 18 2017 - 08:19:11 PDT)
  - Re: [AMBER] Manually set residues Protonation states for HIS and CYS Rana Rehan Khalid (Mon Sep 18 2017 - 09:46:15 PDT)
[AMBER] How to specify the liquid-liquid interface 鲁俊波 (Mon Sep 18 2017 - 01:45:49 PDT)
[AMBER] CpHMD and cys residues Angus Voice (Mon Sep 18 2017 - 03:55:42 PDT)
[AMBER] AmberTools 17 incomplete compilation D L S Dinuka (Mon Sep 18 2017 - 05:31:04 PDT)
- Re: [AMBER] AmberTools 17 incomplete compilation Daniel Roe (Mon Sep 18 2017 - 05:41:02 PDT)
  - Re: [AMBER] AmberTools 17 incomplete compilation Hai Nguyen (Mon Sep 18 2017 - 15:19:58 PDT)
[AMBER] improper torsion terms Lizelle Lubbe (Mon Sep 18 2017 - 09:07:08 PDT)
- Re: [AMBER] improper torsion terms Pengfei Li (Tue Sep 19 2017 - 19:20:45 PDT)
  - Re: [AMBER] improper torsion terms Lizelle Lubbe (Wed Sep 20 2017 - 00:57:16 PDT)
[AMBER] Problem with parallel install Maria Clelia Milletti (Mon Sep 18 2017 - 09:18:47 PDT)
- Re: [AMBER] Problem with parallel install David A Case (Mon Sep 18 2017 - 13:33:30 PDT)
  - Re: [AMBER] Problem with parallel install Maria Clelia Milletti (Tue Sep 19 2017 - 07:35:58 PDT)
    - Re: [AMBER] Problem with parallel install Daniel Roe (Tue Sep 19 2017 - 07:42:47 PDT)
    - Re: [AMBER] Problem with parallel install Maria Clelia Milletti (Tue Sep 19 2017 - 08:53:20 PDT)
    - Re: [AMBER] Problem with parallel install Daniel Roe (Tue Sep 19 2017 - 10:26:06 PDT)
    - Re: [AMBER] Problem with parallel install Maria Clelia Milletti (Wed Sep 20 2017 - 12:30:25 PDT)
    - Re: [AMBER] Problem with parallel install Bill Ross (Wed Sep 20 2017 - 12:33:18 PDT)
    - Re: [AMBER] Problem with parallel install Maria Clelia Milletti (Wed Sep 20 2017 - 13:13:55 PDT)
    - Re: [AMBER] Problem with parallel install Bill Ross (Wed Sep 20 2017 - 13:44:00 PDT)
    - Re: [AMBER] Problem with parallel install Maria Clelia Milletti (Wed Sep 20 2017 - 13:54:28 PDT)
    - Re: [AMBER] Problem with parallel install Bill Ross (Wed Sep 20 2017 - 16:49:02 PDT)
    - Re: [AMBER] Problem with parallel install Maria Clelia Milletti (Thu Sep 21 2017 - 06:54:18 PDT)
    - Re: [AMBER] Problem with parallel install Daniel Roe (Thu Sep 21 2017 - 08:01:37 PDT)
    - Re: [AMBER] Problem with parallel install Bill Ross (Thu Sep 21 2017 - 09:57:09 PDT)
    - Re: [AMBER] Problem with parallel install Maria Clelia Milletti (Thu Sep 21 2017 - 10:35:45 PDT)
- Re: [AMBER] Problem with parallel install Maria Clelia Milletti (Mon Feb 26 2018 - 14:04:25 PST)
  - Re: [AMBER] Problem with parallel install Kevin Keane (Mon Feb 26 2018 - 17:04:20 PST)
    - Re: [AMBER] Problem with parallel install Maria Clelia Milletti (Mon Apr 02 2018 - 12:59:52 PDT)
  - Re: [AMBER] Problem with parallel install David A Case (Mon Feb 26 2018 - 18:30:05 PST)
[AMBER] cpptraj: usage of strip and parmstrip George Tzotzos (Mon Sep 18 2017 - 11:15:45 PDT)
- Re: [AMBER] cpptraj: usage of strip and parmstrip Daniel Roe (Mon Sep 18 2017 - 11:38:18 PDT)
[AMBER] How tleap read a Ruthenium complex solvent box generated by packmol? Sanaa ALAbbad (Mon Sep 18 2017 - 15:18:03 PDT)
- Re: [AMBER] How tleap read a Ruthenium complex solvent box generated by packmol? David A Case (Tue Sep 19 2017 - 02:39:54 PDT)
  - Re: [AMBER] How tleap read a Ruthenium complex solvent box generated by packmol? Sanaa ALAbbad (Tue Sep 19 2017 - 15:32:31 PDT)
[AMBER] Hoogsteen base pair using "useboundsfrom" Mandar Kulkarni (Tue Sep 19 2017 - 02:42:05 PDT)
[AMBER] Pytraj Gyration Tensor Domenico Marson (Tue Sep 19 2017 - 03:18:19 PDT)
- Re: [AMBER] Pytraj Gyration Tensor Hai Nguyen (Tue Sep 19 2017 - 05:49:25 PDT)
- Re: [AMBER] Pytraj Gyration Tensor Domenico Marson (Thu Sep 21 2017 - 04:29:54 PDT)
  - Re: [AMBER] Pytraj Gyration Tensor Hai Nguyen (Thu Sep 21 2017 - 05:33:22 PDT)
    - Re: [AMBER] Pytraj Gyration Tensor Domenico Marson (Thu Sep 21 2017 - 06:32:28 PDT)
    - Re: [AMBER] Pytraj Gyration Tensor Domenico Marson (Thu Sep 21 2017 - 10:08:04 PDT)
    - Re: [AMBER] Pytraj Gyration Tensor Hai Nguyen (Thu Sep 21 2017 - 10:28:13 PDT)
    - Re: [AMBER] Pytraj Gyration Tensor Daniel Roe (Thu Sep 21 2017 - 12:35:56 PDT)
    - Re: [AMBER] Pytraj Gyration Tensor Hai Nguyen (Thu Sep 21 2017 - 12:38:32 PDT)
    - Re: [AMBER] Pytraj Gyration Tensor Hai Nguyen (Thu Sep 21 2017 - 21:43:16 PDT)
[AMBER] angle between two subdomains Sowmya Indrakumar (Tue Sep 19 2017 - 06:44:11 PDT)
- Re: [AMBER] angle between two subdomains Daniel Roe (Tue Sep 19 2017 - 07:44:44 PDT)
[AMBER] reduce command warnings Rana Rehan Khalid (Tue Sep 19 2017 - 08:13:30 PDT)
[AMBER] converting crd to pdb Rana Rehan Khalid (Tue Sep 19 2017 - 10:05:21 PDT)
- Re: [AMBER] converting crd to pdb Bill Ross (Tue Sep 19 2017 - 10:09:02 PDT)
  - Re: [AMBER] converting crd to pdb Rana Rehan Khalid (Tue Sep 19 2017 - 10:12:12 PDT)
- Re: [AMBER] converting crd to pdb Hai Nguyen (Tue Sep 19 2017 - 10:11:45 PDT)
[AMBER] ambertools install issue Eric Smoll (Tue Sep 19 2017 - 10:50:30 PDT)
- Re: [AMBER] ambertools install issue Hai Nguyen (Tue Sep 19 2017 - 11:07:04 PDT)
[AMBER] Restart Simulation Rana Rehan Khalid (Tue Sep 19 2017 - 11:29:44 PDT)
- Re: [AMBER] Restart Simulation Daniel Roe (Tue Sep 19 2017 - 11:39:45 PDT)
Re: [AMBER] ambertools install issue (Eric Smoll) Eric Smoll (Tue Sep 19 2017 - 12:38:21 PDT)
- Re: [AMBER] ambertools install issue (Eric Smoll) Hai Nguyen (Tue Sep 19 2017 - 14:11:12 PDT)
- Re: [AMBER] ambertools install issue (Eric Smoll) David A Case (Wed Sep 20 2017 - 08:21:49 PDT)
[AMBER] .com file creation Rana Rehan Khalid (Tue Sep 19 2017 - 13:21:41 PDT)
- Re: [AMBER] .com file creation pancham lal Gupta (Tue Sep 19 2017 - 17:30:49 PDT)
- Re: [AMBER] .com file creation Rana Rehan Khalid (Fri Sep 22 2017 - 14:34:32 PDT)
[AMBER] Error in pmemd.cuda David Sáez (Tue Sep 19 2017 - 22:58:39 PDT)
[AMBER] Protein drifts out of the periodic cell Michael Shokhen (Wed Sep 20 2017 - 02:21:07 PDT)
- Re: [AMBER] Protein drifts out of the periodic cell Daniel Roe (Wed Sep 20 2017 - 05:35:22 PDT)
  - Re: [AMBER] Protein drifts out of the periodic cell Michael Shokhen (Wed Sep 20 2017 - 08:35:22 PDT)
    - Re: [AMBER] Protein drifts out of the periodic cell Daniel Roe (Wed Sep 20 2017 - 08:56:16 PDT)
    - Re: [AMBER] Protein drifts out of the periodic cell Michael Shokhen (Wed Sep 20 2017 - 09:03:24 PDT)
[AMBER] Distance restraint Lizelle Lubbe (Wed Sep 20 2017 - 07:26:44 PDT)
[AMBER] protein-membrane visualize in VMD Kanin Wichapong (Wed Sep 20 2017 - 09:00:05 PDT)
[AMBER] simulation of docked domains of protein Rana Rehan Khalid (Wed Sep 20 2017 - 09:26:30 PDT)
- Re: [AMBER] simulation of docked domains of protein Elvis Martis (Wed Sep 20 2017 - 09:36:07 PDT)
  - Re: [AMBER] simulation of docked domains of protein Rana Rehan Khalid (Wed Sep 20 2017 - 12:45:17 PDT)
    - Re: [AMBER] simulation of docked domains of protein Bill Ross (Wed Sep 20 2017 - 12:49:30 PDT)
    - Re: [AMBER] simulation of docked domains of protein Elvis Martis (Wed Sep 20 2017 - 23:03:05 PDT)
    - Re: [AMBER] simulation of docked domains of protein David A Case (Thu Sep 21 2017 - 13:16:55 PDT)
[AMBER] Antechamber Rana Rehan Khalid (Wed Sep 20 2017 - 09:46:19 PDT)
- Re: [AMBER] Antechamber Rana Rehan Khalid (Wed Sep 20 2017 - 09:57:09 PDT)
  - Re: [AMBER] Antechamber Rana Rehan Khalid (Wed Sep 20 2017 - 11:02:02 PDT)
    - Re: [AMBER] Antechamber Bill Ross (Wed Sep 20 2017 - 11:07:26 PDT)
    - Re: [AMBER] Antechamber Robin Betz (Wed Sep 20 2017 - 11:14:07 PDT)
    - Re: [AMBER] Antechamber Rana Rehan Khalid (Wed Sep 20 2017 - 11:22:23 PDT)
    - Re: [AMBER] Antechamber David A Case (Thu Sep 21 2017 - 13:20:32 PDT)
    - Re: [AMBER] Antechamber Rana Rehan Khalid (Thu Sep 21 2017 - 13:57:20 PDT)
[AMBER] Inverting a selection in NAB atom expression? Istvan Kolossvary (Wed Sep 20 2017 - 13:47:52 PDT)
[AMBER] Question about MCPB.py Lê Ngọc Chính (Thu Sep 21 2017 - 00:07:33 PDT)
- Re: [AMBER] Question about MCPB.py Pengfei Li (Sat Sep 23 2017 - 15:14:04 PDT)
[AMBER] Amber16 electric field parameters Alessandro Mariani (Thu Sep 21 2017 - 02:22:33 PDT)
- Re: [AMBER] Amber16 electric field parameters Pengfei Li (Sat Sep 23 2017 - 15:35:06 PDT)
  - Re: [AMBER] Amber16 electric field parameters Alessandro Mariani (Mon Oct 02 2017 - 01:18:57 PDT)
    - Re: [AMBER] Amber16 electric field parameters David A Case (Mon Oct 02 2017 - 06:46:12 PDT)
    - Re: [AMBER] Amber16 electric field parameters Ross Walker (Mon Oct 02 2017 - 06:52:14 PDT)
    - Re: [AMBER] Amber16 electric field parameters Pengfei Li (Tue Oct 03 2017 - 19:10:00 PDT)
    - Re: [AMBER] Amber16 electric field parameters Pengfei Li (Thu Oct 05 2017 - 18:15:47 PDT)
[AMBER] simulation stop due to size limit exceed Rana Rehan Khalid (Thu Sep 21 2017 - 05:36:43 PDT)
- Re: [AMBER] simulation stop due to size limit exceed Chris Neale (Thu Sep 21 2017 - 09:16:05 PDT)
  - Re: [AMBER] simulation stop due to size limit exceed Rana Rehan Khalid (Thu Sep 21 2017 - 09:17:54 PDT)
[AMBER] Antechamber error Rana Rehan Khalid (Thu Sep 21 2017 - 07:34:08 PDT)
- Re: [AMBER] Antechamber error Elvis Martis (Thu Sep 21 2017 - 07:39:14 PDT)
  - Re: [AMBER] Antechamber error Scott Brozell (Thu Sep 21 2017 - 08:59:19 PDT)
  - Re: [AMBER] Antechamber error Rana Rehan Khalid (Thu Sep 21 2017 - 09:03:28 PDT)
[AMBER] Quasi-Harmonic Analysis and Entropy Calculations in cpptraj - Help Requested Mo Rahman (Thu Sep 21 2017 - 08:36:55 PDT)
- Re: [AMBER] Quasi-Harmonic Analysis and Entropy Calculations in cpptraj - Help Requested Daniel Roe (Thu Sep 21 2017 - 08:53:44 PDT)
  - Re: [AMBER] Quasi-Harmonic Analysis and Entropy Calculations in cpptraj - Help Requested Mo Rahman (Thu Sep 21 2017 - 10:16:43 PDT)
    - Re: [AMBER] Quasi-Harmonic Analysis and Entropy Calculations in cpptraj - Help Requested Daniel Roe (Thu Sep 21 2017 - 12:43:10 PDT)
    - Re: [AMBER] Quasi-Harmonic Analysis and Entropy Calculations in cpptraj - Help Requested Mo Rahman (Thu Sep 21 2017 - 13:15:56 PDT)
  - Re: [AMBER] Quasi-Harmonic Analysis and Entropy Calculations in cpptraj - Help Requested Celeste Saguí (Thu Sep 21 2017 - 20:23:38 PDT)
[AMBER] Setting water box with fix dimension Ashutosh Shandilya (Thu Sep 21 2017 - 09:13:45 PDT)
- Re: [AMBER] Setting water box with fix dimension Daniel Roe (Thu Sep 21 2017 - 12:46:09 PDT)
  - Re: [AMBER] Setting water box with fix dimension Ashutosh Shandilya (Thu Sep 21 2017 - 12:55:39 PDT)
    - Re: [AMBER] Setting water box with fix dimension Bill Ross (Thu Sep 21 2017 - 12:58:27 PDT)
    - Re: [AMBER] Setting water box with fix dimension Bill Ross (Thu Sep 21 2017 - 13:00:01 PDT)
    - Re: [AMBER] Setting water box with fix dimension Daniel Roe (Thu Sep 21 2017 - 12:58:59 PDT)
- Re: [AMBER] Setting water box with fix dimension David A Case (Thu Sep 21 2017 - 13:30:33 PDT)
[AMBER] Question about MCPB.py Lê Ngọc Chính (Thu Sep 21 2017 - 09:26:05 PDT)
- Re: [AMBER] Question about MCPB.py Hai Nguyen (Thu Sep 21 2017 - 09:49:12 PDT)
  - Re: [AMBER] Question about MCPB.py Lê Ngọc Chính (Thu Sep 21 2017 - 09:57:27 PDT)
[AMBER] MCPB.py AmberTools17 Amani Eshtiwi (Thu Sep 21 2017 - 09:36:18 PDT)
- Re: [AMBER] MCPB.py AmberTools17 Pengfei Li (Sat Sep 23 2017 - 15:28:56 PDT)
[AMBER] Reduce command warnings Skipped hydrogen Rana Rehan Khalid (Thu Sep 21 2017 - 10:55:00 PDT)
- Re: [AMBER] Reduce command warnings Skipped hydrogen Rana Rehan Khalid (Thu Sep 21 2017 - 11:21:42 PDT)
[AMBER] Is it possible to compile without linking C++ and fortran? Timothy Schutt (Thu Sep 21 2017 - 10:56:19 PDT)
- Re: [AMBER] Is it possible to compile without linking C++ and fortran? Daniel Roe (Thu Sep 21 2017 - 12:26:29 PDT)
- Re: [AMBER] Is it possible to compile without linking C++ and fortran? Timothy Schutt (Thu Sep 21 2017 - 15:12:04 PDT)
  - Re: [AMBER] Is it possible to compile without linking C++ and fortran? Daniel Roe (Thu Sep 21 2017 - 17:07:21 PDT)
[AMBER] cpinutil.py Pacheco, Sayuri (Thu Sep 21 2017 - 12:45:40 PDT)
- Re: [AMBER] cpinutil.py Adrian Roitberg (Thu Sep 21 2017 - 13:24:13 PDT)
  - Re: [AMBER] cpinutil.py Pacheco, Sayuri (Thu Sep 21 2017 - 13:56:31 PDT)
    - Re: [AMBER] cpinutil.py Hai Nguyen (Thu Sep 21 2017 - 21:40:38 PDT)
    - Re: [AMBER] cpinutil.py Pacheco, Sayuri (Mon Sep 25 2017 - 10:47:39 PDT)
    - Re: [AMBER] cpinutil.py Hai Nguyen (Mon Sep 25 2017 - 10:57:46 PDT)
[AMBER] Split the image to run in the string method Chunli Yan (Thu Sep 21 2017 - 12:50:50 PDT)
- Re: [AMBER] Split the image to run in the string method Feng Pan (Thu Sep 21 2017 - 15:06:13 PDT)
[AMBER] [david.case.rutgers.edu: Re: Is it possible to compile without linking C++ and fortran?] David A Case (Thu Sep 21 2017 - 13:46:29 PDT)
- Re: [AMBER] [david.case.rutgers.edu: Re: Is it possible to compile without linking C++ and fortran?] Timothy Schutt (Thu Sep 21 2017 - 14:15:31 PDT)
  - Re: [AMBER] [david.case.rutgers.edu: Re: Is it possible to compile without linking C++ and fortran?] Daniel Roe (Fri Sep 22 2017 - 06:59:31 PDT)
[AMBER] simulations crash Ana Luisa Novo de Oliveira (Fri Sep 22 2017 - 04:50:07 PDT)
- Re: [AMBER] simulations crash Carlos Simmerling (Fri Sep 22 2017 - 05:12:44 PDT)
  - Re: [AMBER] simulations crash Ana Luisa Novo de Oliveira (Fri Sep 22 2017 - 05:18:30 PDT)
    - Re: [AMBER] simulations crash Carlos Simmerling (Fri Sep 22 2017 - 05:48:16 PDT)
    - Re: [AMBER] simulations crash Daniel Roe (Fri Sep 22 2017 - 07:03:02 PDT)
[AMBER] SHAKE failure Lizelle Lubbe (Fri Sep 22 2017 - 05:30:13 PDT)
- Re: [AMBER] SHAKE failure Daniel Roe (Fri Sep 22 2017 - 07:08:39 PDT)
  - Re: [AMBER] SHAKE failure Bill Ross (Fri Sep 22 2017 - 07:18:42 PDT)
    - Re: [AMBER] SHAKE failure Lizelle Lubbe (Fri Sep 22 2017 - 11:37:05 PDT)
    - Re: [AMBER] SHAKE failure Lizelle Lubbe (Fri Sep 22 2017 - 11:40:36 PDT)
    - Re: [AMBER] SHAKE failure Pengfei Li (Sat Sep 23 2017 - 14:34:31 PDT)
    - Re: [AMBER] SHAKE failure Lizelle Lubbe (Tue Sep 26 2017 - 03:34:12 PDT)
- Re: [AMBER] SHAKE failure Lizelle Lubbe (Tue Sep 26 2017 - 05:56:35 PDT)
  - Re: [AMBER] SHAKE failure Lizelle Lubbe (Tue Sep 26 2017 - 06:14:46 PDT)
[AMBER] PMEMD TERMINATED ABNORMALLY (But simulation run with sander command) Rana Rehan Khalid (Fri Sep 22 2017 - 08:04:55 PDT)
- Re: [AMBER] PMEMD TERMINATED ABNORMALLY (But simulation run with sander command) Bill Ross (Fri Sep 22 2017 - 08:07:12 PDT)
  - Re: [AMBER] PMEMD TERMINATED ABNORMALLY (But simulation run with sander command) Rana Rehan Khalid (Fri Sep 22 2017 - 09:30:42 PDT)
- Re: [AMBER] PMEMD TERMINATED ABNORMALLY (But simulation run with sander command) David A Case (Sat Sep 23 2017 - 14:30:19 PDT)
  - Re: [AMBER] PMEMD TERMINATED ABNORMALLY (But simulation run with sander command) Rana Rehan Khalid (Sat Sep 23 2017 - 14:39:07 PDT)
[AMBER] cluster analysis of protein complex simulation jacky zhao (Fri Sep 22 2017 - 08:10:09 PDT)
- Re: [AMBER] cluster analysis of protein complex simulation Hai Nguyen (Fri Sep 22 2017 - 09:13:03 PDT)
  - Re: [AMBER] cluster analysis of protein complex simulation Daniel Roe (Fri Sep 22 2017 - 09:36:12 PDT)
    - Re: [AMBER] cluster analysis of protein complex simulation jacky zhao (Fri Sep 22 2017 - 18:22:43 PDT)
[AMBER] mdcrd file not open in vmd Rana Rehan Khalid (Fri Sep 22 2017 - 10:47:51 PDT)
- Re: [AMBER] mdcrd file not open in vmd Daniel Roe (Fri Sep 22 2017 - 11:04:27 PDT)
  - Re: [AMBER] mdcrd file not open in vmd Rana Rehan Khalid (Fri Sep 22 2017 - 11:23:13 PDT)
[AMBER] How to compare the difference between two trajectories with two very similar parm files jacky zhao (Fri Sep 22 2017 - 18:32:12 PDT)
[AMBER] Antechamber RESP calculation error Rana Rehan Khalid (Sat Sep 23 2017 - 10:05:26 PDT)
- Re: [AMBER] Antechamber RESP calculation error Pengfei Li (Sat Sep 23 2017 - 14:24:35 PDT)
  - Re: [AMBER] Antechamber RESP calculation error Rana Rehan Khalid (Sat Sep 23 2017 - 14:36:21 PDT)
    - Re: [AMBER] Antechamber RESP calculation error Pengfei Li (Sat Sep 23 2017 - 15:31:57 PDT)
[AMBER] Different production speeds at different pHs when doing explicit constant pH simulations Andrew Schaub (Sat Sep 23 2017 - 23:47:36 PDT)
- Re: [AMBER] Different production speeds at different pHs when doing explicit constant pH simulations Adrian Roitberg (Sun Sep 24 2017 - 09:15:45 PDT)
  - Re: [AMBER] Different production speeds at different pHs when doing explicit constant pH simulations Andrew Schaub (Mon Sep 25 2017 - 14:52:49 PDT)
    - Re: [AMBER] Different production speeds at different pHs when doing explicit constant pH simulations Jason Swails (Tue Sep 26 2017 - 12:27:06 PDT)
[AMBER] CpHMD: seeking clarification George Tzotzos (Sun Sep 24 2017 - 10:41:05 PDT)
- Re: [AMBER] CpHMD: seeking clarification Eric Lang (Mon Sep 25 2017 - 03:29:50 PDT)
  - Re: [AMBER] CpHMD: seeking clarification George Tzotzos (Mon Sep 25 2017 - 07:36:01 PDT)
[AMBER] cluster analysis using cpptraj Sowmya Indrakumar (Mon Sep 25 2017 - 02:22:33 PDT)
- Re: [AMBER] cluster analysis using cpptraj Bill Ross (Mon Sep 25 2017 - 02:28:23 PDT)
  - Re: [AMBER] cluster analysis using cpptraj Bill Ross (Mon Sep 25 2017 - 02:30:48 PDT)
    - Re: [AMBER] cluster analysis using cpptraj Sowmya Indrakumar (Mon Sep 25 2017 - 02:38:52 PDT)
    - Re: [AMBER] cluster analysis using cpptraj Sowmya Indrakumar (Mon Sep 25 2017 - 02:47:51 PDT)
- Re: [AMBER] cluster analysis using cpptraj Bill Ross (Mon Sep 25 2017 - 02:29:18 PDT)
- Re: [AMBER] cluster analysis using cpptraj Thomas Cheatham (Mon Sep 25 2017 - 02:47:51 PDT)
  - Re: [AMBER] cluster analysis using cpptraj Sowmya Indrakumar (Mon Sep 25 2017 - 02:55:57 PDT)
  - Re: [AMBER] cluster analysis using cpptraj Bill Ross (Mon Sep 25 2017 - 03:00:38 PDT)
- Re: [AMBER] cluster analysis using cpptraj Daniel Roe (Mon Sep 25 2017 - 05:42:29 PDT)
- Re: [AMBER] cluster analysis using cpptraj Elvis Martis (Mon Sep 25 2017 - 06:38:10 PDT)
  - Re: [AMBER] cluster analysis using cpptraj Sowmya Indrakumar (Mon Sep 25 2017 - 07:00:20 PDT)
[AMBER] Using FEW with a transmembrane protein Tarsis (Mon Sep 25 2017 - 10:34:32 PDT)
[AMBER] water bridge analysis Thakur, Abhishek (Mon Sep 25 2017 - 15:17:00 PDT)
- Re: [AMBER] water bridge analysis pancham lal Gupta (Mon Sep 25 2017 - 17:22:09 PDT)
[AMBER] analysizing the trajectory for water interaction Thakur, Abhishek (Mon Sep 25 2017 - 15:31:00 PDT)
[AMBER] PyRed Steven M. Graham (Mon Sep 25 2017 - 18:42:18 PDT)
- Re: [AMBER] PyRed FyD (Mon Oct 02 2017 - 23:10:11 PDT)
[AMBER] How to save reimaged trajectory file during MD? Ravi Abrol (Mon Sep 25 2017 - 22:51:57 PDT)
- Re: [AMBER] How to save reimaged trajectory file during MD? Elvis Martis (Tue Sep 26 2017 - 00:37:11 PDT)
  - Re: [AMBER] How to save reimaged trajectory file during MD? Ravi Abrol (Tue Sep 26 2017 - 06:37:27 PDT)
    - Re: [AMBER] How to save reimaged trajectory file during MD? David A Case (Tue Sep 26 2017 - 10:17:15 PDT)
    - Re: [AMBER] How to save reimaged trajectory file during MD? Ravi Abrol (Wed Sep 27 2017 - 11:35:41 PDT)
    - Re: [AMBER] How to save reimaged trajectory file during MD? Daniel Roe (Mon Oct 02 2017 - 06:05:16 PDT)
[AMBER] Problem with MM-GBSA decomposition Sergey Samsonov (Tue Sep 26 2017 - 00:13:59 PDT)
- Re: [AMBER] Problem with MM-GBSA decomposition Daniel Roe (Wed Sep 27 2017 - 10:22:47 PDT)
  - Re: [AMBER] Problem with MM-GBSA decomposition Sergey Samsonov (Thu Sep 28 2017 - 00:05:20 PDT)
[AMBER] A query about coordinate saving frequency for solvation entropy calculation using GIST SHAILESH KUMAR (Tue Sep 26 2017 - 00:37:13 PDT)
[AMBER] Problem in analysing radius of gyration value in CPPTRAJ krishna.2015.iitg.ernet.in (Tue Sep 26 2017 - 09:07:04 PDT)
- Re: [AMBER] Problem in analysing radius of gyration value in CPPTRAJ Daniel Roe (Wed Sep 27 2017 - 06:00:24 PDT)
  - Re: [AMBER] Problem in analysing radius of gyration value in CPPTRAJ krishna.2015.iitg.ernet.in (Thu Sep 28 2017 - 04:01:40 PDT)
- Re: [AMBER] Problem in analysing radius of gyration value in CPPTRAJ Hai Nguyen (Wed Sep 27 2017 - 06:21:30 PDT)
[AMBER] cpptraj distance: error George Tzotzos (Tue Sep 26 2017 - 09:41:37 PDT)
- Re: [AMBER] cpptraj distance: error Daniel Roe (Tue Sep 26 2017 - 09:46:05 PDT)
  - Re: [AMBER] cpptraj distance: error George Tzotzos (Tue Sep 26 2017 - 10:02:45 PDT)
    - Re: [AMBER] cpptraj distance: error Daniel Roe (Tue Sep 26 2017 - 10:10:40 PDT)
[AMBER] Air-water interface jesus berlanga (Tue Sep 26 2017 - 22:58:12 PDT)
- Re: [AMBER] Air-water interface Bill Ross (Tue Sep 26 2017 - 23:03:46 PDT)
  - Re: [AMBER] Air-water interface jesus berlanga (Wed Sep 27 2017 - 09:44:32 PDT)
    - Re: [AMBER] Air-water interface Bill Ross (Wed Sep 27 2017 - 09:58:25 PDT)
[AMBER] Error with MMGBSA/PBSA jacob wick (Wed Sep 27 2017 - 08:38:17 PDT)
- Re: [AMBER] Error with MMGBSA/PBSA Elvis Martis (Wed Sep 27 2017 - 09:28:17 PDT)
  - Re: [AMBER] Error with MMGBSA/PBSA jacob wick (Wed Sep 27 2017 - 09:34:06 PDT)
    - Re: [AMBER] Error with MMGBSA/PBSA Elvis Martis (Wed Sep 27 2017 - 09:53:44 PDT)
    - Re: [AMBER] Error with MMGBSA/PBSA jacob wick (Thu Sep 28 2017 - 07:01:01 PDT)
    - Re: [AMBER] Error with MMGBSA/PBSA Elvis Martis (Thu Sep 28 2017 - 12:21:52 PDT)
[AMBER] [Fwd: Re: Problem in analysing radius of gyration value in CPPTRAJ] krishna.2015.iitg.ernet.in (Wed Sep 27 2017 - 11:35:23 PDT)
[AMBER] Avoid pH Titration of LYS and TYR R zu (Wed Sep 27 2017 - 12:17:21 PDT)
- Re: [AMBER] Avoid pH Titration of LYS and TYR Adrian Roitberg (Wed Sep 27 2017 - 12:48:29 PDT)
  - Re: [AMBER] Avoid pH Titration of LYS and TYR R zu (Thu Sep 28 2017 - 11:26:45 PDT)
[AMBER] Dr. Nick Riviera Eric Pettersen (Wed Sep 27 2017 - 12:43:21 PDT)
- Re: [AMBER] Dr. Nick Riviera Eric Pettersen (Wed Sep 27 2017 - 12:49:31 PDT)
  - Re: [AMBER] Dr. Nick Riviera Niel Henriksen (Wed Sep 27 2017 - 13:20:07 PDT)
  - Re: [AMBER] Dr. Nick Riviera Eric Pettersen (Wed Sep 27 2017 - 13:29:13 PDT)
    - Re: [AMBER] Dr. Nick Riviera Scott Brozell (Wed Sep 27 2017 - 18:18:20 PDT)
    - Re: [AMBER] Dr. Nick Riviera Junmei Wang (Thu Oct 05 2017 - 08:47:29 PDT)
[AMBER] moveanchor waleed zalloum (Thu Sep 28 2017 - 04:41:55 PDT)
- Re: [AMBER] moveanchor Daniel Roe (Thu Sep 28 2017 - 09:13:24 PDT)
[AMBER] RAC_analysis jacky zhao (Thu Sep 28 2017 - 06:53:27 PDT)
- Re: [AMBER] RAC_analysis Daniel Roe (Thu Sep 28 2017 - 09:08:44 PDT)
[AMBER] leaprc.constph and ff14sb R zu (Thu Sep 28 2017 - 08:06:18 PDT)
- Re: [AMBER] leaprc.constph and ff14sb R zu (Thu Sep 28 2017 - 11:16:48 PDT)
  - Re: [AMBER] leaprc.constph and ff14sb Carlos Simmerling (Thu Sep 28 2017 - 18:59:12 PDT)
    - Re: [AMBER] leaprc.constph and ff14sb Jason Swails (Sun Oct 01 2017 - 20:29:41 PDT)
[AMBER] Cpptraj Sayuri Pacheco (Thu Sep 28 2017 - 09:01:42 PDT)
- Re: [AMBER] Cpptraj Daniel Roe (Thu Sep 28 2017 - 09:07:24 PDT)
  - Re: [AMBER] Cpptraj Sayuri Pacheco (Thu Sep 28 2017 - 09:12:19 PDT)
    - Re: [AMBER] Cpptraj Pacheco, Sayuri (Thu Sep 28 2017 - 14:52:09 PDT)
    - Re: [AMBER] Cpptraj Pacheco, Sayuri (Thu Sep 28 2017 - 14:59:02 PDT)
[AMBER] trajout last x frames cpptraj Hughes, Travis (Thu Sep 28 2017 - 11:23:06 PDT)
- Re: [AMBER] trajout last x frames cpptraj R zu (Thu Sep 28 2017 - 18:45:58 PDT)
  - Re: [AMBER] trajout last x frames cpptraj R zu (Thu Sep 28 2017 - 18:52:15 PDT)
- Re: [AMBER] trajout last x frames cpptraj Hai Nguyen (Thu Sep 28 2017 - 20:27:32 PDT)
  - Re: [AMBER] trajout last x frames cpptraj Hai Nguyen (Thu Sep 28 2017 - 20:28:55 PDT)
    - Re: [AMBER] trajout last x frames cpptraj Hughes, Travis (Fri Sep 29 2017 - 07:34:35 PDT)
- Re: [AMBER] trajout last x frames cpptraj Daniel Roe (Mon Oct 02 2017 - 05:31:23 PDT)
  - Re: [AMBER] trajout last x frames cpptraj Hughes, Travis (Mon Oct 02 2017 - 07:16:01 PDT)
    - Re: [AMBER] trajout last x frames cpptraj Daniel Roe (Mon Jul 23 2018 - 10:34:57 PDT)
[AMBER] identiy the step of interaction from an entire trajectory Thakur, Abhishek (Thu Sep 28 2017 - 12:10:47 PDT)
- Re: [AMBER] identiy the step of interaction from an entire trajectory Daniel Roe (Mon Oct 02 2017 - 05:55:48 PDT)
[AMBER] barostat with large coupling constant R zu (Thu Sep 28 2017 - 18:14:57 PDT)
- Re: [AMBER] barostat with large coupling constant Jason Swails (Sun Oct 01 2017 - 20:37:57 PDT)
  - Re: [AMBER] barostat with large coupling constant R zu (Wed Oct 04 2017 - 08:49:22 PDT)
    - Re: [AMBER] barostat with large coupling constant R zu (Wed Oct 04 2017 - 09:16:53 PDT)
    - Re: [AMBER] barostat with large coupling constant Jason Swails (Wed Oct 04 2017 - 12:58:20 PDT)
[AMBER] identifying the step of hbond interaction from trajectories Thakur, Abhishek (Fri Sep 29 2017 - 11:20:24 PDT)
[AMBER] Multiple Simulations on One GPU R zu (Fri Sep 29 2017 - 14:58:43 PDT)
- Re: [AMBER] Multiple Simulations on One GPU Ross Walker (Sat Sep 30 2017 - 05:43:28 PDT)
[AMBER] Thermodynamic Integration with pmemd, for explicit solvent models Roma Mukhopadhyay (Sat Sep 30 2017 - 19:48:47 PDT)
- Re: [AMBER] Thermodynamic Integration with pmemd, for explicit solvent models David A Case (Sun Oct 01 2017 - 13:08:25 PDT)
  - Re: [AMBER] Thermodynamic Integration with pmemd, for explicit solvent models Roma Mukhopadhyay (Sun Oct 01 2017 - 16:54:40 PDT)
[AMBER] total frames for hbond Thakur, Abhishek (Sun Oct 01 2017 - 12:16:42 PDT)
- Re: [AMBER] total frames for hbond Elvis Martis (Sun Oct 01 2017 - 20:30:15 PDT)
[AMBER] Current rmsd from reference in targeted MD Sonia Ziada (Tue Oct 03 2017 - 04:36:33 PDT)
- Re: [AMBER] Current rmsd from reference in targeted MD Carlos Simmerling (Tue Oct 03 2017 - 09:44:00 PDT)
  - Re: [AMBER] Current rmsd from reference in targeted MD Sonia Ziada (Tue Oct 03 2017 - 14:05:04 PDT)
    - Re: [AMBER] Current rmsd from reference in targeted MD Hai Nguyen (Tue Oct 03 2017 - 16:22:38 PDT)
    - Re: [AMBER] Current rmsd from reference in targeted MD Sonia Ziada (Wed Oct 04 2017 - 00:10:11 PDT)
    - Re: [AMBER] Current rmsd from reference in targeted MD Carlos Simmerling (Wed Oct 04 2017 - 03:30:59 PDT)
    - Re: [AMBER] Current rmsd from reference in targeted MD Sonia Ziada (Wed Oct 04 2017 - 05:25:36 PDT)
    - Re: [AMBER] Current rmsd from reference in targeted MD Carlos Simmerling (Wed Oct 04 2017 - 05:38:13 PDT)
    - Re: [AMBER] Current rmsd from reference in targeted MD Sonia Ziada (Wed Oct 04 2017 - 05:45:34 PDT)
    - Re: [AMBER] Current rmsd from reference in targeted MD Carlos Simmerling (Wed Oct 04 2017 - 06:04:55 PDT)
    - Re: [AMBER] Current rmsd from reference in targeted MD Sonia Ziada (Wed Oct 04 2017 - 08:16:55 PDT)
[AMBER] DPPG lipid bilayer simulation using Lipid17 - too small area per lipid ? Marek Maly (Tue Oct 03 2017 - 08:52:41 PDT)
- Re: [AMBER] DPPG lipid bilayer simulation using Lipid17 - too small area per lipid ? Batuhan Kav (Wed Oct 04 2017 - 11:41:43 PDT)
  - Re: [AMBER] DPPG lipid bilayer simulation using Lipid17 - too small area per lipid ? Marek Maly (Wed Oct 04 2017 - 16:44:02 PDT)
[AMBER] Is it possible to simulate Indium (coupled with sulpher and copper) nano material in amber? Charles Mariasoosai (Tue Oct 03 2017 - 09:33:25 PDT)
- Re: [AMBER] Is it possible to simulate Indium (coupled with sulpher and copper) nano material in amber? David A Case (Tue Oct 03 2017 - 10:15:49 PDT)
[AMBER] Vector math: a couple of questions George Tzotzos (Tue Oct 03 2017 - 11:42:09 PDT)
- Re: [AMBER] Vector math: a couple of questions Daniel Roe (Wed Oct 04 2017 - 09:30:02 PDT)
  - Re: [AMBER] Vector math: a couple of questions George Tzotzos (Wed Oct 04 2017 - 09:43:20 PDT)
    - Re: [AMBER] Vector math: a couple of questions Daniel Roe (Wed Oct 04 2017 - 09:54:11 PDT)
    - Re: [AMBER] Vector math: a couple of questions George Tzotzos (Wed Oct 04 2017 - 09:56:04 PDT)
[AMBER] force distribution analysis and Ewald Thomas Pochapsky (Tue Oct 03 2017 - 11:57:01 PDT)
- Re: [AMBER] force distribution analysis and Ewald Jason Swails (Tue Oct 03 2017 - 12:37:44 PDT)
  - Re: [AMBER] force distribution analysis and Ewald David Cerutti (Tue Oct 03 2017 - 19:09:42 PDT)
[AMBER] vague error when running constant ph simulations Andrew Schaub (Tue Oct 03 2017 - 21:08:01 PDT)
- Re: [AMBER] vague error when running constant ph simulations David A Case (Wed Oct 04 2017 - 05:44:57 PDT)
  - Re: [AMBER] vague error when running constant ph simulations Andrew Schaub (Wed Oct 11 2017 - 12:24:13 PDT)
    - Re: [AMBER] vague error when running constant ph simulations Andrew Schaub (Wed Oct 11 2017 - 13:06:45 PDT)
[AMBER] TI calculations using pmemd Roma Mukhopadhyay (Wed Oct 04 2017 - 13:00:22 PDT)
[AMBER] Constant pH Explicit Solvent Pacheco, Sayuri (Wed Oct 04 2017 - 18:22:18 PDT)
[AMBER] colvar in string methods Chunli Yan (Wed Oct 04 2017 - 19:57:27 PDT)
- Re: [AMBER] colvar in string methods Feng Pan (Wed Oct 04 2017 - 20:33:26 PDT)
  - Re: [AMBER] colvar in string methods Chunli Yan (Wed Oct 04 2017 - 20:51:16 PDT)
[AMBER] Independent MD runs colvin (Wed Oct 04 2017 - 20:11:19 PDT)
- Re: [AMBER] Independent MD runs Elvis Martis (Wed Oct 04 2017 - 21:58:33 PDT)
  - Re: [AMBER] Independent MD runs Chris Neale (Wed Oct 04 2017 - 22:30:01 PDT)
[AMBER] Generating a dimer starting from monomers using MD jacob wick (Thu Oct 05 2017 - 02:26:48 PDT)
- Re: [AMBER] Generating a dimer starting from monomers using MD Karl Kirschner (Thu Oct 05 2017 - 03:57:46 PDT)
  - Re: [AMBER] Generating a dimer starting from monomers using MD jacob wick (Thu Oct 05 2017 - 05:47:40 PDT)
[AMBER] AMBER Hossein Geraili (Thu Oct 05 2017 - 02:44:50 PDT)
- Re: [AMBER] AMBER Bill Ross (Mon May 24 2010 - 23:01:29 PDT)
  - Re: [AMBER] AMBER Asfa Ali (Mon May 24 2010 - 23:31:08 PDT)
    - Re: [AMBER] AMBER Jason Swails (Tue May 25 2010 - 05:04:23 PDT)
    - Re: [AMBER] AMBER (will two K+ ions retain their numbering?) Thomas Cheatham III (Tue May 25 2010 - 08:40:33 PDT)
- Re: [AMBER] AMBER Bill Ross (Tue May 25 2010 - 09:57:28 PDT)
- Re: [AMBER] AMBER Bill Ross (Mon Jan 17 2011 - 14:32:01 PST)
  - Re: [AMBER] AMBER Shesh Nath (Mon Jan 17 2011 - 19:55:50 PST)
- Re: [AMBER] AMBER Chris Moth (Thu Oct 05 2017 - 05:16:11 PDT)
[AMBER] AmberTools17 and shape.h Christopher Benjamin Coffey (Thu Oct 05 2017 - 07:11:55 PDT)
- Re: [AMBER] AmberTools17 and shape.h David A Case (Thu Oct 05 2017 - 10:53:04 PDT)
  - Re: [AMBER] AmberTools17 and shape.h Christopher Benjamin Coffey (Thu Oct 05 2017 - 16:26:09 PDT)
    - Re: [AMBER] AmberTools17 and shape.h Bill Ross (Thu Oct 05 2017 - 16:51:02 PDT)
    - Re: [AMBER] AmberTools17 and shape.h Bill Ross (Thu Oct 05 2017 - 16:53:21 PDT)
    - Re: [AMBER] AmberTools17 and shape.h Christopher Benjamin Coffey (Fri Oct 06 2017 - 11:01:03 PDT)
    - Re: [AMBER] AmberTools17 and shape.h Hai Nguyen (Thu Oct 05 2017 - 17:28:56 PDT)
[AMBER] AMBER16 parallelisation and fftw3 error Shirin Jamshidi (Thu Oct 05 2017 - 14:41:57 PDT)
- Re: [AMBER] AMBER16 parallelisation and fftw3 error Hai Nguyen (Thu Oct 05 2017 - 15:20:47 PDT)
  - Re: [AMBER] AMBER16 parallelisation and fftw3 error Shirin Jamshidi (Thu Oct 05 2017 - 15:24:08 PDT)
    - Re: [AMBER] AMBER16 parallelisation and fftw3 error Hai Nguyen (Thu Oct 05 2017 - 15:57:17 PDT)
    - Re: [AMBER] AMBER16 parallelisation and fftw3 error Shirin Jamshidi (Fri Oct 06 2017 - 04:24:57 PDT)
    - Re: [AMBER] AMBER16 parallelisation and fftw3 error David A Case (Fri Oct 06 2017 - 05:08:24 PDT)
    - Re: [AMBER] AMBER16 parallelisation and fftw3 error Shirin Jamshidi (Fri Oct 06 2017 - 06:37:20 PDT)
    - Re: [AMBER] AMBER16 parallelisation and fftw3 error Hai Nguyen (Fri Oct 06 2017 - 14:25:32 PDT)
    - Re: [AMBER] AMBER16 parallelisation and fftw3 error Shirin Jamshidi (Fri Oct 06 2017 - 14:45:02 PDT)
[AMBER] net charge problem of Amber Lipid14 Force Field Xibing He (Thu Oct 05 2017 - 15:03:47 PDT)
- Re: [AMBER] net charge problem of Amber Lipid14 Force Field Bill Ross (Thu Oct 05 2017 - 15:56:08 PDT)
  - Re: [AMBER] net charge problem of Amber Lipid14 Force Field Bill Ross (Thu Oct 05 2017 - 16:08:48 PDT)
[AMBER] Error in preparation of Zn.lib Anton Perera (Fri Oct 06 2017 - 01:12:44 PDT)
- Re: [AMBER] Error in preparation of Zn.lib Pengfei Li (Fri Oct 06 2017 - 07:45:49 PDT)
[AMBER] System preparation for protein with Multiple Zn-CCCC Parthiban Marimuthu (Fri Oct 06 2017 - 09:16:07 PDT)
- Re: [AMBER] System preparation for protein with Multiple Zn-CCCC Amani Eshtiwi (Fri Oct 06 2017 - 19:59:06 PDT)
- Re: [AMBER] System preparation for protein with Multiple Zn-CCCC Parthiban Marimuthu (Sat Oct 07 2017 - 13:58:49 PDT)
  - Re: [AMBER] System preparation for protein with Multiple Zn-CCCC Bill Ross (Sat Oct 07 2017 - 16:37:08 PDT)
  - Re: [AMBER] System preparation for protein with Multiple Zn-CCCC Pengfei Li (Thu Oct 12 2017 - 19:59:28 PDT)
[AMBER] Thermodynamic integration/switch off/on cloumbic and vdw interactions Khabiri, Morteza (Fri Oct 06 2017 - 11:05:54 PDT)
- Re: [AMBER] Thermodynamic integration/switch off/on cloumbic and vdw interactions Daniel Mermelstein (Mon Oct 09 2017 - 10:40:02 PDT)
[AMBER] about Paramfit Albert (Fri Oct 06 2017 - 14:03:21 PDT)
- Re: [AMBER] about Paramfit Robin Betz (Fri Oct 06 2017 - 14:22:43 PDT)
  - Re: [AMBER] about Paramfit Albert (Fri Oct 06 2017 - 23:59:56 PDT)
[AMBER] chamber is unavailable from terminal MacOS Sundar (Fri Oct 06 2017 - 15:02:47 PDT)
- Re: [AMBER] chamber is unavailable from terminal MacOS Hai Nguyen (Fri Oct 06 2017 - 15:31:18 PDT)
[AMBER] striping correctly with ante-MMPBSA.py Sundar (Mon Oct 09 2017 - 01:24:38 PDT)
[AMBER] Hydrogen Bond ATUL KUMAR (Mon Oct 09 2017 - 04:54:07 PDT)
- Re: [AMBER] Hydrogen Bond Daniel Roe (Tue Oct 10 2017 - 12:16:35 PDT)
[AMBER] How to put anchor_position for RMSD collective variable Value in string methods Chunli Yan (Mon Oct 09 2017 - 05:45:01 PDT)
- Re: [AMBER] How to put anchor_position for RMSD collective variable Value in string methods Feng Pan (Fri Oct 13 2017 - 09:06:52 PDT)
  - Re: [AMBER] How to put anchor_position for RMSD collective variable Value in string methods Chunli Yan (Fri Oct 13 2017 - 09:37:00 PDT)
[AMBER] Hydrogen Bond ATUL KUMAR (Mon Oct 09 2017 - 05:48:23 PDT)
[AMBER] MMPBSA error sangita kachhap (Mon Oct 09 2017 - 07:27:26 PDT)
- Re: [AMBER] MMPBSA error Ray Luo (Mon Oct 09 2017 - 20:20:37 PDT)
  - Re: [AMBER] MMPBSA error sangita kachhap (Wed Oct 11 2017 - 03:37:25 PDT)
    - Re: [AMBER] MMPBSA error Ray Luo (Wed Oct 11 2017 - 07:58:55 PDT)
[AMBER] MCPB.py issue - add_bonded_pairs Szymon Żaczek (Mon Oct 09 2017 - 08:37:38 PDT)
- Re: [AMBER] MCPB.py issue - add_bonded_pairs Miha Purg (Mon Oct 09 2017 - 10:53:04 PDT)
  - Re: [AMBER] MCPB.py issue - add_bonded_pairs Szymon Żaczek (Mon Oct 09 2017 - 13:00:18 PDT)
    - Re: [AMBER] MCPB.py issue - add_bonded_pairs Pengfei Li (Thu Oct 12 2017 - 19:53:18 PDT)
[AMBER] Question regarding protonated CP in pH dependent REMD Paul Freidhoff (Mon Oct 09 2017 - 09:04:09 PDT)
[AMBER] Ruthenium complex MD simulation ERROR: the combination ntb != 0, ntp != 0, ifbox == 0 is not supported! Sanaa ALAbbad (Mon Oct 09 2017 - 16:44:24 PDT)
- Re: [AMBER] Ruthenium complex MD simulation ERROR: the combination ntb != 0, ntp != 0, ifbox == 0 is not supported! Adrian Roitberg (Mon Oct 09 2017 - 16:48:50 PDT)
  - Re: [AMBER] Ruthenium complex MD simulation ERROR: the combination ntb != 0, ntp != 0, ifbox == 0 is not supported! Sanaa ALAbbad (Mon Oct 09 2017 - 16:52:01 PDT)
    - Re: [AMBER] Ruthenium complex MD simulation ERROR: the combination ntb != 0, ntp != 0, ifbox == 0 is not supported! Carlos Simmerling (Mon Oct 09 2017 - 16:54:47 PDT)
[AMBER] Fwd: Error with AMBER/Charmm-GUI output Mac Kevin Braza (Mon Oct 09 2017 - 22:57:33 PDT)
[AMBER] Fwd: Error with AMBER/Charmm-GUI output Mac Kevin Braza (Mon Oct 09 2017 - 22:57:59 PDT)
[AMBER] pmemd.cuda and rigid CH2Cl2 Alain Chaumont (Tue Oct 10 2017 - 04:31:12 PDT)
- Re: [AMBER] pmemd.cuda and rigid CH2Cl2 David A Case (Sat Oct 14 2017 - 06:35:17 PDT)
- Re: [AMBER] pmemd.cuda and rigid CH2Cl2 Thomas Fox (Fri Jan 12 2018 - 00:38:48 PST)
[AMBER] query regarding the restart file of molecular dynamics simulation Leena Aggarwal (Tue Oct 10 2017 - 05:40:03 PDT)
- Re: [AMBER] query regarding the restart file of molecular dynamics simulation Elvis Martis (Tue Oct 10 2017 - 06:09:39 PDT)
  - Re: [AMBER] query regarding the restart file of molecular dynamics simulation Leena Aggarwal (Tue Oct 10 2017 - 06:47:19 PDT)
    - Re: [AMBER] query regarding the restart file of molecular dynamics simulation Bill Ross (Tue Oct 10 2017 - 08:05:03 PDT)
    - Re: [AMBER] query regarding the restart file of molecular dynamics simulation Leena Aggarwal (Tue Oct 10 2017 - 21:17:59 PDT)
    - Re: [AMBER] query regarding the restart file of molecular dynamics simulation Bill Ross (Tue Oct 10 2017 - 23:05:47 PDT)
    - Re: [AMBER] query regarding the restart file of molecular dynamics simulation Leena Aggarwal (Wed Oct 11 2017 - 00:03:36 PDT)
    - Re: [AMBER] query regarding the restart file of molecular dynamics simulation Bill Ross (Wed Oct 11 2017 - 00:05:25 PDT)
    - Re: [AMBER] query regarding the restart file of molecular dynamics simulation Leena Aggarwal (Wed Oct 11 2017 - 00:09:08 PDT)
    - Re: [AMBER] query regarding the restart file of molecular dynamics simulation Leena Aggarwal (Wed Oct 11 2017 - 00:11:12 PDT)
    - Re: [AMBER] query regarding the restart file of molecular dynamics simulation Elvis Martis (Wed Oct 11 2017 - 00:33:43 PDT)
    - Re: [AMBER] query regarding the restart file of molecular dynamics simulation Leena Aggarwal (Wed Oct 11 2017 - 01:04:09 PDT)
    - Re: [AMBER] query regarding the restart file of molecular dynamics simulation Elvis Martis (Wed Oct 11 2017 - 02:25:21 PDT)
    - Re: [AMBER] query regarding the restart file of molecular dynamics simulation Bill Ross (Wed Oct 11 2017 - 10:31:45 PDT)
    - Re: [AMBER] query regarding the restart file of molecular dynamics simulation Leena Aggarwal (Wed Oct 11 2017 - 21:24:17 PDT)
    - Re: [AMBER] query regarding the restart file of molecular dynamics simulation Bill Ross (Wed Oct 11 2017 - 21:27:32 PDT)
    - Re: [AMBER] query regarding the restart file of molecular dynamics simulation Leena Aggarwal (Thu Oct 12 2017 - 02:00:28 PDT)
    - Re: [AMBER] query regarding the restart file of molecular dynamics simulation Bill Ross (Thu Oct 12 2017 - 02:11:08 PDT)
    - Re: [AMBER] query regarding the restart file of molecular dynamics simulation Leena Aggarwal (Thu Oct 12 2017 - 05:12:51 PDT)
    - Re: [AMBER] query regarding the restart file of molecular dynamics simulation Elvis Martis (Thu Oct 12 2017 - 06:59:13 PDT)
    - Re: [AMBER] query regarding the restart file of molecular dynamics simulation Leena Aggarwal (Thu Oct 12 2017 - 22:49:18 PDT)
    - Re: [AMBER] query regarding the restart file of molecular dynamics simulation Bill Ross (Thu Oct 12 2017 - 22:52:13 PDT)
    - Re: [AMBER] query regarding the restart file of molecular dynamics simulation Elvis Martis (Fri Oct 13 2017 - 01:01:54 PDT)
    - Re: [AMBER] query regarding the restart file of molecular dynamics simulation Leena Aggarwal (Sun Oct 15 2017 - 21:38:15 PDT)
    - Re: [AMBER] query regarding the restart file of molecular dynamics simulation Bill Ross (Sun Oct 15 2017 - 21:41:18 PDT)
    - Re: [AMBER] query regarding the restart file of molecular dynamics simulation Leena Aggarwal (Sun Oct 15 2017 - 22:06:56 PDT)
    - Re: [AMBER] query regarding the restart file of molecular dynamics simulation Bill Ross (Sun Oct 15 2017 - 22:12:03 PDT)
    - Re: [AMBER] query regarding the restart file of molecular dynamics simulation Leena Aggarwal (Sun Oct 15 2017 - 22:26:53 PDT)
    - Re: [AMBER] query regarding the restart file of molecular dynamics simulation Bill Ross (Sun Oct 15 2017 - 22:29:02 PDT)
    - Re: [AMBER] query regarding the restart file of molecular dynamics simulation Leena Aggarwal (Sun Oct 15 2017 - 22:37:01 PDT)
    - Re: [AMBER] query regarding the restart file of molecular dynamics simulation Bill Ross (Sun Oct 15 2017 - 22:38:23 PDT)
    - Re: [AMBER] query regarding the restart file of molecular dynamics simulation Leena Aggarwal (Sun Oct 15 2017 - 22:46:11 PDT)
    - Re: [AMBER] query regarding the restart file of molecular dynamics simulation Bill Ross (Sun Oct 15 2017 - 22:48:17 PDT)
    - Re: [AMBER] query regarding the restart file of molecular dynamics simulation Leena Aggarwal (Sun Oct 15 2017 - 23:07:56 PDT)
    - Re: [AMBER] query regarding the restart file of molecular dynamics simulation Leena Aggarwal (Sun Oct 15 2017 - 23:08:20 PDT)
    - Re: [AMBER] query regarding the restart file of molecular dynamics simulation Bill Ross (Sun Oct 15 2017 - 23:11:06 PDT)
    - Re: [AMBER] query regarding the restart file of molecular dynamics simulation Bill Ross (Sun Oct 15 2017 - 23:09:37 PDT)
    - Re: [AMBER] query regarding the restart file of molecular dynamics simulation Leena Aggarwal (Sun Oct 15 2017 - 23:15:29 PDT)
    - Re: [AMBER] query regarding the restart file of molecular dynamics simulation Bill Ross (Sun Oct 15 2017 - 23:18:32 PDT)
    - Re: [AMBER] query regarding the restart file of molecular dynamics simulation Leena Aggarwal (Sun Oct 15 2017 - 23:23:08 PDT)
    - Re: [AMBER] query regarding the restart file of molecular dynamics simulation Bill Ross (Sun Oct 15 2017 - 23:25:21 PDT)
- Re: [AMBER] query regarding the restart file of molecular dynamics simulation David A Case (Tue Oct 10 2017 - 06:55:29 PDT)
- Re: [AMBER] query regarding the restart file of molecular dynamics simulation Leena Aggarwal (Mon Oct 16 2017 - 03:50:44 PDT)
  - Re: [AMBER] query regarding the restart file of molecular dynamics simulation David A Case (Mon Oct 16 2017 - 05:03:23 PDT)
[AMBER] REMD job failed Albert (Tue Oct 10 2017 - 07:34:32 PDT)
- Re: [AMBER] REMD job failed Cruzeiro,Vinicius Wilian D (Tue Oct 10 2017 - 07:41:03 PDT)
  - Re: [AMBER] REMD job failed Albert (Tue Oct 10 2017 - 07:44:56 PDT)
    - Re: [AMBER] REMD job failed Daniel Roe (Tue Oct 10 2017 - 10:15:37 PDT)
[AMBER] Problem with charges - Unable to recover LYS charges from AmberFF Nicolas Cheron (Wed Oct 11 2017 - 03:13:59 PDT)
- Re: [AMBER] Problem with charges - Unable to recover LYS charges from AmberFF David A Case (Wed Oct 11 2017 - 05:38:32 PDT)
  - Re: [AMBER] Problem with charges - Unable to recover LYS charges from AmberFF Nicolas Cheron (Mon Oct 16 2017 - 00:50:46 PDT)
[AMBER] output file .out file deleted mistakenly Rana Rehan Khalid (Wed Oct 11 2017 - 10:35:48 PDT)
- Re: [AMBER] output file .out file deleted mistakenly Bill Ross (Wed Oct 11 2017 - 11:04:25 PDT)
  - Re: [AMBER] output file .out file deleted mistakenly Bill Ross (Wed Oct 11 2017 - 11:06:30 PDT)
    - Re: [AMBER] output file .out file deleted mistakenly Rana Rehan Khalid (Wed Oct 11 2017 - 11:13:49 PDT)
    - Re: [AMBER] output file .out file deleted mistakenly Bill Ross (Wed Oct 11 2017 - 11:15:25 PDT)
- Re: [AMBER] output file .out file deleted mistakenly Daniel Roe (Thu Oct 12 2017 - 06:02:55 PDT)
[AMBER] getting MC barostat to print less Smith, Louis (Wed Oct 11 2017 - 21:36:58 PDT)
- Re: [AMBER] getting MC barostat to print less Jason Swails (Thu Oct 12 2017 - 19:36:26 PDT)
  - Re: [AMBER] getting MC barostat to print less Smith, Louis (Thu Oct 12 2017 - 22:14:25 PDT)
[AMBER] making 6M GDMCl box ATUL KUMAR (Thu Oct 12 2017 - 02:58:08 PDT)
- Re: [AMBER] making 6M GDMCl box Bill Ross (Thu Oct 12 2017 - 03:02:03 PDT)
  - Re: [AMBER] making 6M GDMCl box ATUL KUMAR (Thu Oct 12 2017 - 03:34:07 PDT)
    - Re: [AMBER] making 6M GDMCl box Bill Ross (Thu Oct 12 2017 - 12:06:25 PDT)
[AMBER] Restarting pH-REMD simulations after abnormal termination Eric Lang (Thu Oct 12 2017 - 06:55:28 PDT)
- Re: [AMBER] Restarting pH-REMD simulations after abnormal termination Cruzeiro,Vinicius Wilian D (Fri Oct 13 2017 - 07:07:18 PDT)
  - Re: [AMBER] Restarting pH-REMD simulations after abnormal termination Eric Lang (Fri Oct 13 2017 - 09:11:32 PDT)
[AMBER] Error reading Ruthenium complex residue Sanaa ALAbbad (Thu Oct 12 2017 - 08:27:17 PDT)
- Re: [AMBER] Error reading Ruthenium complex residue Szymon Żaczek (Thu Oct 12 2017 - 09:51:35 PDT)
  - Re: [AMBER] Error reading Ruthenium complex residue Sanaa ALAbbad (Thu Oct 12 2017 - 09:56:11 PDT)
    - Re: [AMBER] Error reading Ruthenium complex residue Pengfei Li (Thu Oct 12 2017 - 19:47:11 PDT)
    - Re: [AMBER] Error reading Ruthenium complex residue Sanaa ALAbbad (Fri Oct 13 2017 - 06:18:03 PDT)
- Re: [AMBER] Error reading Ruthenium complex residue Bill Ross (Thu Oct 12 2017 - 14:57:24 PDT)
[AMBER] parmstrip with cpptraj in Ambertools 17 Li, Wen (Thu Oct 12 2017 - 10:12:37 PDT)
- Re: [AMBER] parmstrip with cpptraj in Ambertools 17 Daniel Roe (Thu Oct 12 2017 - 17:35:39 PDT)
  - Re: [AMBER] parmstrip with cpptraj in Ambertools 17 Daniel Roe (Fri Oct 13 2017 - 07:25:43 PDT)
    - Re: [AMBER] parmstrip with cpptraj in Ambertools 17 Li, Wen (Fri Oct 13 2017 - 08:48:54 PDT)
    - Re: [AMBER] parmstrip with cpptraj in Ambertools 17 Daniel Roe (Fri Oct 13 2017 - 09:54:59 PDT)
[AMBER] Wham analysis Thakur, Abhishek (Thu Oct 12 2017 - 14:02:35 PDT)
- [AMBER] Wham analysis Thakur, Abhishek (Fri Oct 13 2017 - 07:32:40 PDT)
  - Re: [AMBER] Wham analysis diego.soler.uam.es (Sat Oct 14 2017 - 12:42:13 PDT)
[AMBER] help for the installation of Ambertools 17 on Mac huangwc8 (Thu Oct 12 2017 - 22:40:50 PDT)
- Re: [AMBER] help for the installation of Ambertools 17 on Mac David A Case (Fri Oct 13 2017 - 05:08:18 PDT)
  - Re: [AMBER] help for the installation of Ambertools 17 on Mac Andrew Schaub (Mon Oct 16 2017 - 14:42:49 PDT)
[AMBER] Restarting REMD Andreas Tosstorff (Fri Oct 13 2017 - 01:13:54 PDT)
- Re: [AMBER] Restarting REMD Andreas Tosstorff (Fri Oct 13 2017 - 01:17:37 PDT)
- Re: [AMBER] Restarting REMD Carlos Simmerling (Fri Oct 13 2017 - 03:34:15 PDT)
  - Re: [AMBER] Restarting REMD Andreas Tosstorff (Fri Oct 13 2017 - 03:43:02 PDT)
[AMBER] problem with AMBER TUTORIAL A1 Michael Shokhen (Fri Oct 13 2017 - 05:27:12 PDT)
- Re: [AMBER] problem with AMBER TUTORIAL A1 David A Case (Sat Oct 14 2017 - 06:31:18 PDT)
[AMBER] Metal site hybrid bonded model Lizelle Lubbe (Fri Oct 13 2017 - 05:45:30 PDT)
[AMBER] Converting atom names from NAMD to AMBER Eiros Zamora, Juan (Fri Oct 13 2017 - 10:10:54 PDT)
- Re: [AMBER] Converting atom names from NAMD to AMBER Daniel Roe (Fri Oct 13 2017 - 10:32:16 PDT)
- Re: [AMBER] Converting atom names from NAMD to AMBER Bill Ross (Fri Oct 13 2017 - 13:36:55 PDT)
[AMBER] mdfrc for a single ion in vacuum William Marquardt (Fri Oct 13 2017 - 11:24:46 PDT)
- Re: [AMBER] mdfrc for a single ion in vacuum David A Case (Fri Oct 13 2017 - 13:43:55 PDT)
[AMBER] SCEE incorrectly set for certain dihedral parameter comments Niel Henriksen (Fri Oct 13 2017 - 12:05:00 PDT)
[AMBER] How to show double bond connection between N=O2 Rana Rehan Khalid (Sat Oct 14 2017 - 07:31:29 PDT)
- Re: [AMBER] How to show double bond connection between N=O2 Bill Ross (Sat Oct 14 2017 - 15:47:40 PDT)
[AMBER] Specify amount of memory David Sáez (Sun Oct 15 2017 - 00:20:44 PDT)
- Re: [AMBER] Specify amount of memory Bill Ross (Sun Oct 15 2017 - 01:39:11 PDT)
- Re: [AMBER] Specify amount of memory David A Case (Sun Oct 15 2017 - 10:28:45 PDT)
[AMBER] Vector command in cpptraj Pietro Aronica (Sun Oct 15 2017 - 21:14:22 PDT)
- Re: [AMBER] Vector command in cpptraj Daniel Roe (Mon Oct 16 2017 - 06:23:37 PDT)
  - Re: [AMBER] Vector command in cpptraj Pietro Aronica (Mon Oct 16 2017 - 20:39:44 PDT)
[AMBER] Running Explicit pH MD Pacheco, Sayuri (Mon Oct 16 2017 - 08:26:33 PDT)
- Re: [AMBER] Running Explicit pH MD Adrian Roitberg (Mon Oct 16 2017 - 08:31:03 PDT)
  - Re: [AMBER] Running Explicit pH MD Pacheco, Sayuri (Tue Oct 24 2017 - 21:54:54 PDT)
- [AMBER] Running Explicit pH MD Pacheco, Sayuri (Mon Oct 30 2017 - 07:31:36 PDT)
  - Re: [AMBER] Running Explicit pH MD Cruzeiro,Vinicius Wilian D (Mon Oct 30 2017 - 08:14:03 PDT)
    - Re: [AMBER] Running Explicit pH MD Pacheco, Sayuri (Mon Oct 30 2017 - 08:20:52 PDT)
    - Re: [AMBER] Running Explicit pH MD Cruzeiro,Vinicius Wilian D (Mon Oct 30 2017 - 08:24:00 PDT)
    - Re: [AMBER] Running Explicit pH MD Pacheco, Sayuri (Thu Nov 09 2017 - 22:56:59 PST)
    - Re: [AMBER] Running Explicit pH MD Cruzeiro,Vinicius Wilian D (Fri Nov 10 2017 - 08:00:38 PST)
- Re: [AMBER] Running Explicit pH MD Pacheco, Sayuri (Fri Nov 10 2017 - 10:56:28 PST)
  - Re: [AMBER] Running Explicit pH MD Cruzeiro,Vinicius Wilian D (Fri Nov 10 2017 - 12:54:10 PST)
    - Re: [AMBER] Running Explicit pH MD Pacheco, Sayuri (Fri Nov 10 2017 - 13:06:04 PST)
    - Re: [AMBER] Running Explicit pH MD Cruzeiro,Vinicius Wilian D (Thu Nov 16 2017 - 12:00:27 PST)
    - Re: [AMBER] Running Explicit pH MD Pacheco, Sayuri (Thu Nov 16 2017 - 14:48:26 PST)
[AMBER] Question on GPUs and OS George Tzotzos (Mon Oct 16 2017 - 11:15:38 PDT)
- Re: [AMBER] Question on GPUs and OS Hai Nguyen (Mon Oct 16 2017 - 11:20:50 PDT)
  - Re: [AMBER] Question on GPUs and OS George Tzotzos (Mon Oct 16 2017 - 11:28:00 PDT)
[AMBER] RESP charges for a peptide-bound probe with R.E.D. Seth Axen (Mon Oct 16 2017 - 16:00:30 PDT)
- Re: [AMBER] RESP charges for a peptide-bound probe with R.E.D. Andrew Schaub (Mon Oct 16 2017 - 17:15:44 PDT)
  - Re: [AMBER] RESP charges for a peptide-bound probe with R.E.D. Seth Axen (Tue Oct 17 2017 - 08:54:39 PDT)
[AMBER] trajout format with cpptraj in Ambertools 17 Li, Wen (Tue Oct 17 2017 - 08:40:28 PDT)
- Re: [AMBER] trajout format with cpptraj in Ambertools 17 Daniel Roe (Tue Oct 17 2017 - 08:52:07 PDT)
  - Re: [AMBER] trajout format with cpptraj in Ambertools 17 Li, Wen (Tue Oct 17 2017 - 10:57:26 PDT)
- Re: [AMBER] trajout format with cpptraj in Ambertools 17 Elvis Martis (Tue Oct 17 2017 - 08:53:16 PDT)
  - Re: [AMBER] trajout format with cpptraj in Ambertools 17 Li, Wen (Tue Oct 17 2017 - 08:54:53 PDT)
[AMBER] Cannot create Ru-ligands bonds using genMetalFF.sh Sanaa ALAbbad (Tue Oct 17 2017 - 16:10:44 PDT)
- Re: [AMBER] Cannot create Ru-ligands bonds using genMetalFF.sh Pengfei Li (Wed Oct 18 2017 - 09:19:19 PDT)
  - Re: [AMBER] Cannot create Ru-ligands bonds using genMetalFF.sh Pengfei Li (Wed Oct 18 2017 - 09:21:34 PDT)
    - Re: [AMBER] Cannot create Ru-ligands bonds using genMetalFF.sh Sanaa ALAbbad (Wed Oct 18 2017 - 17:14:09 PDT)
    - Re: [AMBER] Cannot create Ru-ligands bonds using genMetalFF.sh Sanaa ALAbbad (Thu Oct 19 2017 - 06:39:47 PDT)
[AMBER] Bias Towards the Periodic Boundary Timothy Schutt (Wed Oct 18 2017 - 10:37:56 PDT)
- Re: [AMBER] Bias Towards the Periodic Boundary Adrian Roitberg (Wed Oct 18 2017 - 11:22:01 PDT)
- Re: [AMBER] Bias Towards the Periodic Boundary David A Case (Wed Oct 18 2017 - 13:03:02 PDT)
  - Re: [AMBER] Bias Towards the Periodic Boundary Timothy Schutt (Wed Oct 18 2017 - 13:11:43 PDT)
[AMBER] How to add the deprotonated SER residue to the ff14SB leap library? Michael Shokhen (Thu Oct 19 2017 - 05:42:38 PDT)
- Re: [AMBER] How to add the deprotonated SER residue to the ff14SB leap library? Pietro Aronica (Thu Oct 19 2017 - 06:44:17 PDT)
- Re: [AMBER] How to add the deprotonated SER residue to the ff14SB leap library? Carlos Simmerling (Thu Oct 19 2017 - 06:46:13 PDT)
  - Re: [AMBER] How to add the deprotonated SER residue to the ff14SB leap library? Michael Shokhen (Thu Oct 19 2017 - 07:27:17 PDT)
    - Re: [AMBER] How to add the deprotonated SER residue to the ff14SB leap library? David A Case (Thu Oct 19 2017 - 09:06:36 PDT)
    - Re: [AMBER] How to add the deprotonated SER residue to the ff14SB leap library? Michael Shokhen (Mon Oct 23 2017 - 06:51:58 PDT)
- Re: [AMBER] How to add the deprotonated SER residue to the ff14SB leap library? Cruzeiro,Vinicius Wilian D (Thu Oct 19 2017 - 07:28:38 PDT)
[AMBER] Protein drift from solvent box Lizelle Lubbe (Thu Oct 19 2017 - 05:44:48 PDT)
- Re: [AMBER] Protein drift from solvent box Thakur, Abhishek (Thu Oct 19 2017 - 07:06:42 PDT)
  - Re: [AMBER] Protein drift from solvent box Bill Ross (Thu Oct 19 2017 - 07:29:39 PDT)
    - Re: [AMBER] Protein drift from solvent box Lizelle Lubbe (Thu Oct 19 2017 - 07:58:51 PDT)
    - Re: [AMBER] Protein drift from solvent box David A Case (Thu Oct 19 2017 - 09:11:11 PDT)
    - Re: [AMBER] Protein drift from solvent box Lizelle Lubbe (Thu Oct 19 2017 - 09:14:32 PDT)
    - Re: [AMBER] Protein drift from solvent box Lizelle Lubbe (Fri Oct 20 2017 - 01:13:38 PDT)
    - Re: [AMBER] Protein drift from solvent box Daniel Roe (Fri Oct 20 2017 - 11:43:08 PDT)
[AMBER] Dummy Atoms in CP Paul Freidhoff (Thu Oct 19 2017 - 06:34:57 PDT)
[AMBER] WHAM, DHAM, MBAR, BAR, TI... Andreas Tosstorff (Thu Oct 19 2017 - 09:04:22 PDT)
- Re: [AMBER] WHAM, DHAM, MBAR, BAR, TI... Niel Henriksen (Thu Oct 19 2017 - 12:24:19 PDT)
[AMBER] how we can visualized the bonds after saving on of the MD frame into pdb file. Rana Rehan Khalid (Thu Oct 19 2017 - 11:16:51 PDT)
- Re: [AMBER] how we can visualized the bonds after saving on of the MD frame into pdb file. Carlos Simmerling (Thu Oct 19 2017 - 11:19:00 PDT)
  - Re: [AMBER] how we can visualized the bonds after saving on of the MD frame into pdb file. Rana Rehan Khalid (Thu Oct 19 2017 - 11:22:46 PDT)
- Re: [AMBER] how we can visualized the bonds after saving on of the MD frame into pdb file. Bill Ross (Thu Oct 19 2017 - 12:06:43 PDT)
[AMBER] effect of MPI problem on MD calculations sangita kachhap (Fri Oct 20 2017 - 01:25:20 PDT)
- Re: [AMBER] effect of MPI problem on MD calculations David A Case (Fri Oct 20 2017 - 05:21:48 PDT)
- Re: [AMBER] effect of MPI problem on MD calculations Bill Ross (Fri Oct 20 2017 - 10:05:29 PDT)
[AMBER] Force field parameters for Magnesium and Calcium in Amber Nadine Schwierz-Neumann (Fri Oct 20 2017 - 03:35:06 PDT)
- Re: [AMBER] Force field parameters for Magnesium and Calcium in Amber David A Case (Fri Oct 20 2017 - 05:26:40 PDT)
[AMBER] how to generated data for plot? Albert (Fri Oct 20 2017 - 04:17:17 PDT)
- Re: [AMBER] how to generated data for plot? Daniel Roe (Fri Oct 20 2017 - 06:39:31 PDT)
  - Re: [AMBER] how to generated data for plot? Albert (Wed Oct 25 2017 - 11:50:18 PDT)
[AMBER] Independent production runs Lizelle Lubbe (Fri Oct 20 2017 - 04:28:34 PDT)
- Re: [AMBER] Independent production runs Carlos Simmerling (Fri Oct 20 2017 - 05:08:22 PDT)
  - Re: [AMBER] Independent production runs Lizelle Lubbe (Fri Oct 20 2017 - 05:44:53 PDT)
[AMBER] Center of mass restraint on GPU? Lin Song (Fri Oct 20 2017 - 08:12:50 PDT)
- Re: [AMBER] Center of mass restraint on GPU? Ross Walker (Fri Oct 20 2017 - 10:28:31 PDT)
  - Re: [AMBER] Center of mass restraint on GPU? Lin Song (Fri Oct 20 2017 - 11:39:59 PDT)
[AMBER] hydrogenbond calculations megha vaishnavi (Sun Oct 22 2017 - 20:11:44 PDT)
- Re: [AMBER] hydrogenbond calculations Hai Nguyen (Sun Oct 22 2017 - 21:53:36 PDT)
[AMBER] difficulty reading a frcmod file in amber Eugene Cha (Sun Oct 22 2017 - 23:41:42 PDT)
- Re: [AMBER] difficulty reading a frcmod file in amber Elvis Martis (Mon Oct 23 2017 - 02:24:27 PDT)
[AMBER] About penalty scores Arun Srikanth (Mon Oct 23 2017 - 17:02:08 PDT)
- Re: [AMBER] About penalty scores David A Case (Tue Oct 24 2017 - 05:09:55 PDT)
  - Re: [AMBER] About penalty scores Arun Srikanth (Tue Oct 24 2017 - 07:29:15 PDT)
[AMBER] Can we use OPLS force field in AMBER Shilpa Gupta (Tue Oct 24 2017 - 05:35:52 PDT)
- Re: [AMBER] Can we use OPLS force field in AMBER David A Case (Tue Oct 24 2017 - 06:34:59 PDT)
  - Re: [AMBER] Can we use OPLS force field in AMBER Shilpa Gupta (Tue Oct 24 2017 - 06:57:11 PDT)
    - Re: [AMBER] Can we use OPLS force field in AMBER Bill Ross (Tue Oct 24 2017 - 07:01:47 PDT)
    - Re: [AMBER] Can we use OPLS force field in AMBER Shilpa Gupta (Tue Oct 24 2017 - 21:06:17 PDT)
    - Re: [AMBER] Can we use OPLS force field in AMBER Bill Ross (Wed Oct 25 2017 - 00:11:27 PDT)
  - Re: [AMBER] Can we use OPLS force field in AMBER Jason Swails (Fri Oct 27 2017 - 04:56:54 PDT)
[AMBER] MM/PBSA or MM/GBSA sangita kachhap (Tue Oct 24 2017 - 06:47:21 PDT)
- Re: [AMBER] MM/PBSA or MM/GBSA Carlos Simmerling (Tue Oct 24 2017 - 06:51:48 PDT)
  - Re: [AMBER] MM/PBSA or MM/GBSA sangita kachhap (Tue Oct 24 2017 - 07:00:07 PDT)
    - Re: [AMBER] MM/PBSA or MM/GBSA Alessandro Contini (Tue Oct 24 2017 - 08:06:50 PDT)
    - Re: [AMBER] MM/PBSA or MM/GBSA sangita kachhap (Tue Oct 24 2017 - 12:46:57 PDT)
    - Re: [AMBER] MM/PBSA or MM/GBSA Alessandro Contini (Wed Oct 25 2017 - 00:03:03 PDT)
[AMBER] disulfide bonds braking during MD simulation Michael Shokhen (Tue Oct 24 2017 - 07:59:52 PDT)
- Re: [AMBER] disulfide bonds braking during MD simulation Carlos Simmerling (Tue Oct 24 2017 - 08:07:21 PDT)
  - Re: [AMBER] disulfide bonds braking during MD simulation Michael Shokhen (Tue Oct 24 2017 - 08:50:17 PDT)
- Re: [AMBER] disulfide bonds braking during MD simulation David A Case (Tue Oct 24 2017 - 17:39:09 PDT)
  - Re: [AMBER] disulfide bonds braking during MD simulation Michael Shokhen (Wed Oct 25 2017 - 11:37:47 PDT)
    - Re: [AMBER] disulfide bonds braking during MD simulation Carlos Simmerling (Wed Oct 25 2017 - 11:44:55 PDT)
    - Re: [AMBER] disulfide bonds braking during MD simulation Michael Shokhen (Wed Oct 25 2017 - 11:51:29 PDT)
    - Re: [AMBER] disulfide bonds braking during MD simulation Michael Shokhen (Wed Oct 25 2017 - 12:39:14 PDT)
    - Re: [AMBER] disulfide bonds braking during MD simulation Carlos Simmerling (Wed Oct 25 2017 - 12:59:28 PDT)
    - Re: [AMBER] disulfide bonds braking during MD simulation Michael Shokhen (Wed Oct 25 2017 - 13:26:36 PDT)
    - Re: [AMBER] disulfide bonds braking during MD simulation Adrian Roitberg (Wed Oct 25 2017 - 13:31:58 PDT)
    - Re: [AMBER] disulfide bonds braking during MD simulation Bill Ross (Wed Oct 25 2017 - 13:33:06 PDT)
    - Re: [AMBER] disulfide bonds braking during MD simulation Carlos Simmerling (Wed Oct 25 2017 - 13:56:03 PDT)
    - Re: [AMBER] disulfide bonds braking during MD simulation Michael Shokhen (Wed Oct 25 2017 - 14:05:50 PDT)
[AMBER] Are RNA with ligand system and a GB neck2 protocol compatible Kasprzak, Wojciech (NIH/NCI) [C] (Tue Oct 24 2017 - 10:57:29 PDT)
- Re: [AMBER] Are RNA with ligand system and a GB neck2 protocol compatible Hai Nguyen (Tue Oct 24 2017 - 19:31:20 PDT)
  - [AMBER] RNA with ligand - a follow-up ANTECHAMBER question Kasprzak, Wojciech (NIH/NCI) [C] (Wed Oct 25 2017 - 14:00:06 PDT)
    - Re: [AMBER] RNA with ligand - a follow-up ANTECHAMBER question David A Case (Wed Oct 25 2017 - 19:35:50 PDT)
    - Re: [AMBER] RNA with ligand - a follow-up ANTECHAMBER question Kasprzak, Wojciech (NIH/NCI) [C] (Thu Oct 26 2017 - 08:10:22 PDT)
    - Re: [AMBER] RNA with ligand - a follow-up ANTECHAMBER question Junmei Wang (Thu Oct 26 2017 - 08:51:43 PDT)
[AMBER] About paramfit 1-4 scaling Arun Srikanth (Tue Oct 24 2017 - 17:47:18 PDT)
- Re: [AMBER] About paramfit 1-4 scaling David Cerutti (Wed Oct 25 2017 - 13:08:09 PDT)
[AMBER] Forecefield error Arthi Venkat (Tue Oct 24 2017 - 20:05:28 PDT)
- Re: [AMBER] Forecefield error Hai Nguyen (Tue Oct 24 2017 - 20:09:53 PDT)
  - Re: [AMBER] Forecefield error Arthi Venkat (Tue Oct 24 2017 - 20:16:41 PDT)
    - Re: [AMBER] Forecefield error Hai Nguyen (Tue Oct 24 2017 - 20:20:26 PDT)
- Re: [AMBER] Forecefield error Arthi Venkat (Tue Oct 24 2017 - 20:30:39 PDT)
  - Re: [AMBER] Forecefield error Carlos Simmerling (Wed Oct 25 2017 - 03:40:25 PDT)
[AMBER] Cpptraj HBond salt bridge output question Amy Rice (Wed Oct 25 2017 - 08:22:27 PDT)
- Re: [AMBER] Cpptraj HBond salt bridge output question Daniel Roe (Wed Oct 25 2017 - 08:39:56 PDT)
  - Re: [AMBER] Cpptraj HBond salt bridge output question Amy Rice (Wed Oct 25 2017 - 08:57:15 PDT)
[AMBER] error with restraint distance minimization Michael Shokhen (Wed Oct 25 2017 - 09:02:52 PDT)
- Re: [AMBER] error with restraint distance minimization Adrian Roitberg (Wed Oct 25 2017 - 09:08:57 PDT)
  - Re: [AMBER] error with restraint distance minimization Michael Shokhen (Wed Oct 25 2017 - 09:31:00 PDT)
[AMBER] STOP PMEMD Terminated Abnormally! Jeyaram R A (Thu Oct 26 2017 - 05:01:21 PDT)
- Re: [AMBER] STOP PMEMD Terminated Abnormally! Carlos Simmerling (Thu Oct 26 2017 - 05:23:44 PDT)
[AMBER] reference for long-range van der Waals interactions Wook Lee (Thu Oct 26 2017 - 08:16:06 PDT)
[AMBER] Use of pmemd for minimisation and equilibration Suchetana Gupta (Fri Oct 27 2017 - 05:52:56 PDT)
- Re: [AMBER] Use of pmemd for minimisation and equilibration Elvis Martis (Fri Oct 27 2017 - 07:05:49 PDT)
  - Re: [AMBER] Use of pmemd for minimisation and equilibration Ross Walker (Fri Oct 27 2017 - 08:06:34 PDT)
- Re: [AMBER] Use of pmemd for minimisation and equilibration David A Case (Fri Oct 27 2017 - 07:09:14 PDT)
  - Re: [AMBER] Use of pmemd for minimisation and equilibration David A Case (Fri Oct 27 2017 - 09:01:35 PDT)
    - Re: [AMBER] Use of pmemd for minimisation and equilibration Carlos Simmerling (Fri Oct 27 2017 - 09:06:47 PDT)
[AMBER] parmed.py and xparmed.py problem Michael Shokhen (Fri Oct 27 2017 - 05:58:50 PDT)
- Re: [AMBER] parmed.py and xparmed.py problem Hai Nguyen (Fri Oct 27 2017 - 06:06:06 PDT)
  - Re: [AMBER] parmed.py and xparmed.py problem mirzo (Fri Oct 27 2017 - 06:36:29 PDT)
    - Re: [AMBER] parmed.py and xparmed.py problem Michael Shokhen (Fri Oct 27 2017 - 06:40:18 PDT)
[AMBER] Binding affinity of different small molecules to a complex of metal + protein + DNA Alonso Martinez, Diego (Fri Oct 27 2017 - 06:17:57 PDT)
- Re: [AMBER] Binding affinity of different small molecules to a complex of metal + protein + DNA Elvis Martis (Fri Oct 27 2017 - 08:06:07 PDT)
- Re: [AMBER] Binding affinity of different small molecules to a complex of metal + protein + DNA Thomas Cheatham (Fri Oct 27 2017 - 15:20:03 PDT)
[AMBER] MM-PBSA calculation Mustafa Alhaji Isa (Fri Oct 27 2017 - 08:22:33 PDT)
- Re: [AMBER] MM-PBSA calculation Elvis Martis (Fri Oct 27 2017 - 08:53:02 PDT)
[AMBER] frozen atoms. danilo gonzalez (Fri Oct 27 2017 - 09:14:30 PDT)
- Re: [AMBER] frozen atoms. Cruzeiro,Vinicius Wilian D (Fri Oct 27 2017 - 09:28:32 PDT)
  - Re: [AMBER] frozen atoms. danilo gonzalez (Fri Oct 27 2017 - 11:40:25 PDT)
    - Re: [AMBER] frozen atoms. Cruzeiro,Vinicius Wilian D (Fri Oct 27 2017 - 12:30:14 PDT)
- Re: [AMBER] frozen atoms. David A Case (Fri Oct 27 2017 - 12:23:44 PDT)
[AMBER] Error Due to Duplicate residues atoms Rana Rehan Khalid (Fri Oct 27 2017 - 11:15:16 PDT)
- Re: [AMBER] Error Due to Duplicate residues atoms David A Case (Fri Oct 27 2017 - 12:15:49 PDT)
- Re: [AMBER] Error Due to Duplicate residues atoms Rana Rehan Khalid (Sat Oct 28 2017 - 09:31:48 PDT)
[AMBER] Wrong connectivity after antechamber/Gaussian16 Andreas Tosstorff (Fri Oct 27 2017 - 11:19:04 PDT)
- Re: [AMBER] Wrong connectivity after antechamber/Gaussian16 David A Case (Fri Oct 27 2017 - 12:20:59 PDT)
  - Re: [AMBER] Wrong connectivity after antechamber/Gaussian16 Andreas Tosstorff (Sat Oct 28 2017 - 02:24:57 PDT)
    - Re: [AMBER] Wrong connectivity after antechamber/Gaussian16 David A Case (Sat Oct 28 2017 - 05:16:25 PDT)
    - Re: [AMBER] Wrong connectivity after antechamber/Gaussian16 Junmei Wang (Sat Oct 28 2017 - 06:23:26 PDT)
    - Re: [AMBER] Wrong connectivity after antechamber/Gaussian16 Andreas Tosstorff (Sat Oct 28 2017 - 13:47:33 PDT)
    - Re: [AMBER] Wrong connectivity after antechamber/Gaussian16 David A Case (Sat Oct 28 2017 - 17:31:21 PDT)
    - Re: [AMBER] Wrong connectivity after antechamber/Gaussian16 Junmei Wang (Sat Oct 28 2017 - 18:02:13 PDT)
    - Re: [AMBER] Wrong connectivity after antechamber/Gaussian16 Andreas Tosstorff (Tue Nov 07 2017 - 02:22:39 PST)
[AMBER] Error in calculating MM-PBSA Mustafa Alhaji Isa (Sun Oct 29 2017 - 01:11:59 PDT)
- Re: [AMBER] Error in calculating MM-PBSA Elvis Martis (Sun Oct 29 2017 - 03:34:10 PDT)
- Re: [AMBER] Error in calculating MM-PBSA David A Case (Sun Oct 29 2017 - 05:14:01 PDT)
[AMBER] AM1-BCC for charge derivation Shilpa Gupta (Sun Oct 29 2017 - 12:22:40 PDT)
[AMBER] positive electrostatic energy Sharon D. Morris (Mon Oct 30 2017 - 03:35:18 PDT)
[AMBER] warning Close contact Shilpa Gupta (Mon Oct 30 2017 - 03:56:13 PDT)
- Re: [AMBER] warning Close contact David A Case (Mon Oct 30 2017 - 05:02:26 PDT)
[AMBER] positional restraint to optimize crystal structure M P (Mon Oct 30 2017 - 04:12:40 PDT)
[AMBER] restraint_wt applied to wrong atoms sangita kachhap (Mon Oct 30 2017 - 05:14:11 PDT)
- Re: [AMBER] restraint_wt applied to wrong atoms Carlos Simmerling (Mon Oct 30 2017 - 05:22:20 PDT)
  - Re: [AMBER] restraint_wt applied to wrong atoms sangita kachhap (Mon Oct 30 2017 - 06:02:50 PDT)
[AMBER] problem with TUTORAL C5: Hydrogen Bond Analysis with CPPTRAJ Setyanto Md (Mon Oct 30 2017 - 05:16:23 PDT)
- Re: [AMBER] problem with TUTORAL C5: Hydrogen Bond Analysis with CPPTRAJ Rodrigo Galindo-Murillo (Mon Oct 30 2017 - 06:25:58 PDT)
  - Re: [AMBER] problem with TUTORAL C5: Hydrogen Bond Analysis with CPPTRAJ Setyanto Md (Mon Oct 30 2017 - 07:07:55 PDT)
    - Re: [AMBER] problem with TUTORAL C5: Hydrogen Bond Analysis with CPPTRAJ Rodrigo Galindo-Murillo (Fri Nov 03 2017 - 15:53:23 PDT)
    - Re: [AMBER] problem with TUTORAL C5: Hydrogen Bond Analysis with CPPTRAJ Setyanto Md (Fri Nov 03 2017 - 16:17:07 PDT)
[AMBER] disulfide bonds braking during MD simulation Michael Shokhen (Mon Oct 30 2017 - 05:23:00 PDT)
[AMBER] pdb4amber bug - incorrect "CONECT" between chains Diego Gomes (Mon Oct 30 2017 - 10:49:33 PDT)
- Re: [AMBER] pdb4amber bug - incorrect "CONECT" between chains Hai Nguyen (Mon Oct 30 2017 - 19:46:32 PDT)
  - Re: [AMBER] pdb4amber bug - incorrect "CONECT" between chains Hai Nguyen (Mon Oct 30 2017 - 20:21:27 PDT)
    - Re: [AMBER] pdb4amber bug - incorrect "CONECT" between chains David A Case (Tue Oct 31 2017 - 05:12:23 PDT)
    - Re: [AMBER] pdb4amber bug - incorrect "CONECT" between chains Hai Nguyen (Tue Oct 31 2017 - 05:39:30 PDT)
    - Re: [AMBER] pdb4amber bug - incorrect "CONECT" between chains Daniel Roe (Tue Oct 31 2017 - 06:07:05 PDT)
    - Re: [AMBER] pdb4amber bug - incorrect "CONECT" between chains Hai Nguyen (Tue Oct 31 2017 - 06:12:11 PDT)
[AMBER] Possible concerns regarding future availability of cost effective NVIDIA GPU systems for running AMBER Ross Walker (Mon Oct 30 2017 - 11:57:47 PDT)
- Re: [AMBER] Possible concerns regarding future availability of cost effective NVIDIA GPU systems for running AMBER Scott Le Grand (Mon Oct 30 2017 - 12:29:30 PDT)
  - Re: [AMBER] Possible concerns regarding future availability of cost effective NVIDIA GPU systems for running AMBER David Cerutti (Mon Oct 30 2017 - 13:21:06 PDT)
- Re: [AMBER] Possible concerns regarding future availability of cost effective NVIDIA GPU systems for running AMBER Robert Molt (Mon Oct 30 2017 - 12:59:43 PDT)
- Re: [AMBER] Possible concerns regarding future availability of cost effective NVIDIA GPU systems for running AMBER Bill Ross (Mon Oct 30 2017 - 14:10:45 PDT)
  - Re: [AMBER] Possible concerns regarding future availability of cost effective NVIDIA GPU systems for running AMBER Bill Ross (Mon Oct 30 2017 - 14:57:33 PDT)
- Re: [AMBER] Possible concerns regarding future availability of cost effective NVIDIA GPU systems for running AMBER Gerald Monard (Mon Oct 30 2017 - 14:29:33 PDT)
  - Re: [AMBER] Possible concerns regarding future availability of cost effective NVIDIA GPU systems for running AMBER Dow Hurst (Mon Oct 30 2017 - 16:10:34 PDT)
- Re: [AMBER] Possible concerns regarding future availability of cost effective NVIDIA GPU systems for running AMBER Marek Maly (Mon Oct 30 2017 - 18:15:10 PDT)
  - Re: [AMBER] Possible concerns regarding future availability of cost effective NVIDIA GPU systems for running AMBER Scott Le Grand (Tue Oct 31 2017 - 08:30:51 PDT)
- Re: [AMBER] Possible concerns regarding future availability of cost effective NVIDIA GPU systems for running AMBER Dow Hurst (Fri Dec 08 2017 - 11:34:47 PST)
  - Re: [AMBER] Possible concerns regarding future availability of cost effective NVIDIA GPU systems for running AMBER David Cerutti (Fri Dec 08 2017 - 12:18:39 PST)
  - Re: [AMBER] Possible concerns regarding future availability of cost effective NVIDIA GPU systems for running AMBER Ross Walker (Sat Dec 09 2017 - 09:53:31 PST)
  - Re: [AMBER] Possible concerns regarding future availability of cost effective NVIDIA GPU systems for running AMBER Scott Le Grand (Sat Dec 09 2017 - 11:35:18 PST)
[AMBER] Constant temperature is not constant from the beginning David Sáez (Mon Oct 30 2017 - 21:32:29 PDT)
- Re: [AMBER] Constant temperature is not constant from the beginning Bill Ross (Mon Oct 30 2017 - 22:16:08 PDT)
  - Re: [AMBER] Constant temperature is not constant from the beginning David Sáez (Tue Oct 31 2017 - 14:31:22 PDT)
[AMBER] contributing code Holger Kruse (Tue Oct 31 2017 - 06:19:43 PDT)
[AMBER] PB Bomb in pb_aaradi() Urszula Uciechowska (Tue Oct 31 2017 - 06:41:15 PDT)
[AMBER] SCC-DFTB for iron Àngels González Lafont (Tue Oct 31 2017 - 09:04:43 PDT)
- Re: [AMBER] SCC-DFTB for iron Goetz, Andreas (Tue Oct 31 2017 - 14:20:21 PDT)
[AMBER] CUDA 9 Weinzierl, Robert O J (Tue Oct 31 2017 - 10:11:52 PDT)
- Re: [AMBER] CUDA 9 Ross Walker (Tue Oct 31 2017 - 10:53:58 PDT)
  - Re: [AMBER] CUDA 9 Scott Le Grand (Tue Oct 31 2017 - 12:36:33 PDT)
[AMBER] Test failed after installing Amber Tools 17 Crystal Vander Zanden (Tue Oct 31 2017 - 13:18:24 PDT)
- Re: [AMBER] Test failed after installing Amber Tools 17 David A Case (Tue Oct 31 2017 - 17:36:14 PDT)
[AMBER] PB Bomb in pb_aaradi() while running mmpbsa.py Urszula Uciechowska (Wed Nov 01 2017 - 03:39:04 PDT)
[AMBER] pulling along RMSD Qinghua Liao (Wed Nov 01 2017 - 05:07:06 PDT)
- [AMBER] protein && DNA in implicit solvents Qinghua Liao (Wed Nov 01 2017 - 05:15:26 PDT)
  - Re: [AMBER] protein && DNA in implicit solvents Carlos Simmerling (Wed Nov 01 2017 - 07:31:57 PDT)
    - Re: [AMBER] protein && DNA in implicit solvents Qinghua Liao (Wed Nov 01 2017 - 14:19:45 PDT)
[AMBER] the best APS is not zero, bonds involved by this atom are frozen Shilpa Gupta (Wed Nov 01 2017 - 07:40:59 PDT)
- Re: [AMBER] the best APS is not zero, bonds involved by this atom are frozen David A Case (Wed Nov 01 2017 - 14:06:04 PDT)
[AMBER] energy minimum vs binding pose for charge calculation Thomas Evangelidis (Wed Nov 01 2017 - 07:45:32 PDT)
- Re: [AMBER] energy minimum vs binding pose for charge calculation David A Case (Wed Nov 01 2017 - 10:56:07 PDT)
  - Re: [AMBER] energy minimum vs binding pose for charge calculation Thomas Evangelidis (Wed Nov 01 2017 - 11:20:50 PDT)
  - Re: [AMBER] energy minimum vs binding pose for charge calculation Thomas Evangelidis (Wed Nov 01 2017 - 15:16:07 PDT)
[AMBER] MCPB.py step 1 help please Eugene Cha (Wed Nov 01 2017 - 12:14:31 PDT)
- Re: [AMBER] MCPB.py step 1 help please Pengfei Li (Wed Nov 08 2017 - 06:51:26 PST)
[AMBER] How to generate inpcrd and prmtop files for A and B mixed solution 杨满意 (Wed Nov 01 2017 - 18:52:38 PDT)
- Re: [AMBER] How to generate inpcrd and prmtop files for A and B mixed solution David A Case (Thu Nov 02 2017 - 04:51:15 PDT)
  - Re: [AMBER] How to generate inpcrd and prmtop files for A and B mixed solution 杨满意 (Thu Nov 02 2017 - 05:52:03 PDT)
    - Re: [AMBER] How to generate inpcrd and prmtop files for A and B mixed solution David A Case (Thu Nov 02 2017 - 11:13:45 PDT)
    - Re: [AMBER] How to generate inpcrd and prmtop files for A and B mixed solution 杨满意 (Thu Nov 02 2017 - 18:13:53 PDT)
[AMBER] Miniconda gives error while compiling AmberTools-17 Biplab Ghosh (Thu Nov 02 2017 - 04:46:21 PDT)
- Re: [AMBER] Miniconda gives error while compiling AmberTools-17 Hai Nguyen (Thu Nov 02 2017 - 05:47:34 PDT)
[AMBER] Acetate ion using xleap Shilpa Gupta (Thu Nov 02 2017 - 21:19:00 PDT)
- Re: [AMBER] Acetate ion using xleap Bill Ross (Thu Nov 02 2017 - 21:36:45 PDT)
  - Re: [AMBER] Acetate ion using xleap Shilpa Gupta (Thu Nov 02 2017 - 21:48:50 PDT)
    - Re: [AMBER] Acetate ion using xleap Bill Ross (Thu Nov 02 2017 - 21:55:35 PDT)
    - Re: [AMBER] Acetate ion using xleap Shilpa Gupta (Thu Nov 02 2017 - 22:11:52 PDT)
    - Re: [AMBER] Acetate ion using xleap Bill Ross (Thu Nov 02 2017 - 22:37:11 PDT)
[AMBER] mmpbsa.py error Urszula Uciechowska (Fri Nov 03 2017 - 00:22:15 PDT)
- Re: [AMBER] mmpbsa.py error Ray Luo (Fri Nov 03 2017 - 10:30:36 PDT)
[AMBER] chloride as anion Shilpa Gupta (Fri Nov 03 2017 - 03:16:28 PDT)
- Re: [AMBER] chloride as anion Carlos Simmerling (Fri Nov 03 2017 - 03:35:45 PDT)
  - Re: [AMBER] chloride as anion Shilpa Gupta (Fri Nov 03 2017 - 03:38:34 PDT)
[AMBER] H-REMD Dr. MANAS MONDAL (Fri Nov 03 2017 - 03:53:22 PDT)
- Re: [AMBER] H-REMD Feng Pan (Fri Nov 03 2017 - 17:47:37 PDT)
  - Re: [AMBER] H-REMD Dr. MANAS MONDAL (Fri Nov 03 2017 - 20:29:17 PDT)
    - Re: [AMBER] H-REMD Feng Pan (Fri Nov 03 2017 - 20:48:14 PDT)
[AMBER] 1-4 scaling factors in case of GAFF-GLYCAM mixed dihedral terms ? Marek Maly (Fri Nov 03 2017 - 15:28:32 PDT)
- Re: [AMBER] 1-4 scaling factors in case of GAFF-GLYCAM mixed dihedral terms ? Lachele Foley (Sat Nov 04 2017 - 03:02:38 PDT)
  - Re: [AMBER] 1-4 scaling factors in case of GAFF-GLYCAM mixed dihedral terms ? Marek Maly (Sat Nov 04 2017 - 07:07:59 PDT)
    - Re: [AMBER] 1-4 scaling factors in case of GAFF-GLYCAM mixed dihedral terms ? Lachele Foley (Sun Nov 05 2017 - 02:34:59 PST)
    - Re: [AMBER] 1-4 scaling factors in case of GAFF-GLYCAM mixed dihedral terms ? Marek Maly (Sun Nov 05 2017 - 16:15:41 PST)
[AMBER] Automatic rotation of the protein by LEAP to minimize the periodic cell dimensions? Dmitry Suplatov (Sat Nov 04 2017 - 02:34:58 PDT)
- Re: [AMBER] Automatic rotation of the protein by LEAP to minimize the periodic cell dimensions? Bill Ross (Sat Nov 04 2017 - 02:38:54 PDT)
[AMBER] Distance restrain usage for fixing distance between two atoms jacob wick (Sat Nov 04 2017 - 06:43:02 PDT)
- Re: [AMBER] Distance restrain usage for fixing distance between two atoms David A Case (Mon Nov 06 2017 - 00:33:37 PST)
[AMBER] Free Energy GPU Johannes Löffler (Mon Nov 06 2017 - 00:57:19 PST)
- Re: [AMBER] Free Energy GPU Ross Walker (Mon Nov 06 2017 - 05:13:50 PST)
- Re: [AMBER] Free Energy GPU Taisung Lee (Mon Nov 06 2017 - 04:36:50 PST)
- Re: [AMBER] Free Energy GPU Feng Pan (Mon Nov 06 2017 - 09:55:06 PST)
- Re: [AMBER] Free Energy GPU Darrin Y (Mon Nov 06 2017 - 13:30:51 PST)
[AMBER] Unknown flag error - sander Mo Rahman (Mon Nov 06 2017 - 05:55:00 PST)
- Re: [AMBER] Unknown flag error - sander Hai Nguyen (Mon Nov 06 2017 - 06:18:48 PST)
  - Re: [AMBER] Unknown flag error - sander Hai Nguyen (Mon Nov 06 2017 - 06:20:27 PST)
[AMBER] Hydrogen atom SHAKEH problem sangita kachhap (Mon Nov 06 2017 - 08:18:15 PST)
[AMBER] No Cartesian force constants found Sushi Shilpa (Mon Nov 06 2017 - 21:20:32 PST)
- Re: [AMBER] No Cartesian force constants found Pengfei Li (Wed Nov 08 2017 - 06:46:11 PST)
[AMBER] Need information regarding frcmod.urea Saikat Pal (Mon Nov 06 2017 - 23:14:12 PST)
[AMBER] New ligand [antechamber->prepgen->parmchk2->xLeap] Taylor, Miles (Tue Nov 07 2017 - 13:53:42 PST)
- Re: [AMBER] New ligand [antechamber->prepgen->parmchk2->xLeap] David A Case (Wed Nov 08 2017 - 00:31:04 PST)
[AMBER] change in density on multiple gpus Neha Gandhi (Tue Nov 07 2017 - 22:15:27 PST)
- Re: [AMBER] change in density on multiple gpus Ross Walker (Wed Nov 08 2017 - 06:21:19 PST)
  - Re: [AMBER] change in density on multiple gpus Neha Gandhi (Wed Nov 08 2017 - 13:24:48 PST)
    - Re: [AMBER] change in density on multiple gpus Ross Walker (Wed Nov 08 2017 - 13:33:15 PST)
    - Re: [AMBER] change in density on multiple gpus Neha Gandhi (Wed Nov 08 2017 - 16:22:48 PST)
    - Re: [AMBER] change in density on multiple gpus Ross Walker (Fri Nov 10 2017 - 03:08:30 PST)
    - Re: [AMBER] change in density on multiple gpus Neha Gandhi (Fri Nov 10 2017 - 17:26:51 PST)
[AMBER] error: Atom does not have type Shilpa Gupta (Tue Nov 07 2017 - 23:32:57 PST)
- Re: [AMBER] error: Atom does not have type Bill Ross (Tue Nov 07 2017 - 23:42:16 PST)
[AMBER] No torsion terms error even though I specified them in frcmod file Adebayo Adeniyi (Wed Nov 08 2017 - 03:10:05 PST)
[AMBER] H-bond analysis Mustafa Alhaji Isa (Wed Nov 08 2017 - 04:17:45 PST)
- Re: [AMBER] H-bond analysis Daniel Roe (Wed Nov 08 2017 - 08:31:32 PST)
[AMBER] Fwd: Can't load MEOHBOX as solvent Chetna Tyagi (Wed Nov 08 2017 - 08:08:50 PST)
- Re: [AMBER] Fwd: Can't load MEOHBOX as solvent David A Case (Wed Nov 08 2017 - 17:15:44 PST)
  - Re: [AMBER] Fwd: Can't load MEOHBOX as solvent Chetna Tyagi (Thu Nov 09 2017 - 04:29:13 PST)
[AMBER] mmpbsa.py Urszula Uciechowska (Thu Nov 09 2017 - 01:22:30 PST)
- Re: [AMBER] mmpbsa.py Ray Luo (Thu Nov 09 2017 - 05:40:47 PST)
  - Re: [AMBER] mmpbsa.py Urszula Uciechowska (Thu Nov 09 2017 - 07:06:35 PST)
    - Re: [AMBER] mmpbsa.py Ray Luo (Thu Nov 09 2017 - 13:29:41 PST)
[AMBER] solvation box Shilpa Gupta (Thu Nov 09 2017 - 01:32:13 PST)
- Re: [AMBER] solvation box Bill Ross (Thu Nov 09 2017 - 02:02:55 PST)
- Re: [AMBER] solvation box David A Case (Thu Nov 09 2017 - 04:44:40 PST)
[AMBER] Computer for running MD simulation using Amber Ashok Kumar (Thu Nov 09 2017 - 03:26:05 PST)
- Re: [AMBER] Computer for running MD simulation using Amber Bill Ross (Thu Nov 09 2017 - 03:40:26 PST)
- Re: [AMBER] Computer for running MD simulation using Amber Marek Havrila (Thu Nov 09 2017 - 04:15:15 PST)
[AMBER] Energy Calculations by cpptraj sylvester kisembo (Thu Nov 09 2017 - 05:56:01 PST)
- Re: [AMBER] Energy Calculations by cpptraj Daniel Roe (Thu Nov 09 2017 - 06:36:47 PST)
[AMBER] REMD jobs slowing down unexpectedly Andreas Tosstorff (Fri Nov 10 2017 - 00:47:36 PST)
- Re: [AMBER] REMD jobs slowing down unexpectedly Thomas Cheatham (Fri Nov 10 2017 - 12:41:05 PST)
[AMBER] UREA PDB file from xleap Saikat Pal (Fri Nov 10 2017 - 02:46:59 PST)
- Re: [AMBER] UREA PDB file from xleap David A Case (Fri Nov 10 2017 - 05:18:22 PST)
  - Re: [AMBER] UREA PDB file from xleap Saikat Pal (Fri Nov 10 2017 - 21:18:31 PST)
    - Re: [AMBER] UREA PDB file from xleap Bill Ross (Fri Nov 10 2017 - 23:40:44 PST)
[AMBER] Is accelerated MD suitable for DFG-flip simulation in kinase? 张姝姝 (Fri Nov 10 2017 - 07:51:06 PST)
[AMBER] Amber GCC 6.4.0 and MKL 2017.3.196 build failing Joachim Hein (Fri Nov 10 2017 - 08:32:36 PST)
- Re: [AMBER] Amber GCC 6.4.0 and MKL 2017.3.196 build failing Joachim Hein (Fri Nov 10 2017 - 08:35:14 PST)
  - Re: [AMBER] Amber GCC 6.4.0 and MKL 2017.3.196 build failing Daniel Roe (Tue Nov 14 2017 - 09:27:09 PST)
[AMBER] ntxo option in amber Leena Aggarwal (Sat Nov 11 2017 - 02:36:59 PST)
- Re: [AMBER] ntxo option in amber Bill Ross (Sat Nov 11 2017 - 02:39:57 PST)
  - Re: [AMBER] ntxo option in amber Leena Aggarwal (Sat Nov 11 2017 - 02:45:09 PST)
    - Re: [AMBER] ntxo option in amber Bill Ross (Sat Nov 11 2017 - 02:48:00 PST)
- Re: [AMBER] ntxo option in amber David A Case (Sat Nov 11 2017 - 06:27:21 PST)
[AMBER] suggestion for a GTX 1080 ilhan.yavuz (Sat Nov 11 2017 - 10:41:04 PST)
- Re: [AMBER] suggestion for a GTX 1080 Ross Walker (Sun Nov 12 2017 - 16:06:38 PST)
  - Re: [AMBER] suggestion for a GTX 1080 Scott Le Grand (Sun Nov 12 2017 - 17:34:41 PST)
    - Re: [AMBER] suggestion for a GTX 1080 ilhan.yavuz (Mon Nov 13 2017 - 00:29:34 PST)
    - Re: [AMBER] suggestion for a GTX 1080 Ross Walker (Mon Nov 13 2017 - 04:40:03 PST)
[AMBER] error of pdb4amber jacky zhao (Sun Nov 12 2017 - 08:03:39 PST)
- Re: [AMBER] error of pdb4amber Hai Nguyen (Sun Nov 12 2017 - 08:44:56 PST)
  - Re: [AMBER] error of pdb4amber jacky zhao (Sun Nov 12 2017 - 13:51:19 PST)
    - Re: [AMBER] error of pdb4amber Hai Nguyen (Sun Nov 12 2017 - 16:23:54 PST)
    - Re: [AMBER] error of pdb4amber jacky zhao (Mon Nov 13 2017 - 09:14:05 PST)
[AMBER] force field for xylose Osman, Roman (Sun Nov 12 2017 - 11:58:34 PST)
- Re: [AMBER] force field for xylose Hector A. Baldoni (Sun Nov 12 2017 - 14:58:57 PST)
[AMBER] the CYX problem of generation parm7 crd files by AT17 jacky zhao (Sun Nov 12 2017 - 15:14:49 PST)
- Re: [AMBER] the CYX problem of generation parm7 crd files by AT17 Hai Nguyen (Sun Nov 12 2017 - 16:33:40 PST)
  - Re: [AMBER] the CYX problem of generation parm7 crd files by AT17 Hai Nguyen (Sun Nov 12 2017 - 16:40:35 PST)
    - Re: [AMBER] the CYX problem of generation parm7 crd files by AT17 Hai Nguyen (Sun Nov 12 2017 - 16:43:44 PST)
[AMBER] error of pdb4amber Lei Zhao (Sun Nov 12 2017 - 08:02:59 PST)
[AMBER] cpptraj error Rana Rehan Khalid (Mon Nov 13 2017 - 03:24:22 PST)
- Re: [AMBER] cpptraj error Bill Ross (Mon Nov 13 2017 - 03:26:42 PST)
  - Re: [AMBER] cpptraj error Rana Rehan Khalid (Mon Nov 13 2017 - 03:32:00 PST)
    - Re: [AMBER] cpptraj error Bill Ross (Mon Nov 13 2017 - 03:33:48 PST)
    - Re: [AMBER] cpptraj error Rana Rehan Khalid (Mon Nov 13 2017 - 04:22:31 PST)
    - Re: [AMBER] cpptraj error Bill Ross (Mon Nov 13 2017 - 04:24:37 PST)
    - Re: [AMBER] cpptraj error Rana Rehan Khalid (Mon Nov 13 2017 - 04:30:24 PST)
    - Re: [AMBER] cpptraj error Rana Rehan Khalid (Mon Nov 13 2017 - 04:32:24 PST)
    - Re: [AMBER] cpptraj error Rana Rehan Khalid (Mon Nov 13 2017 - 04:36:08 PST)
    - Re: [AMBER] cpptraj error Bill Ross (Mon Nov 13 2017 - 04:39:01 PST)
    - Re: [AMBER] cpptraj error Rana Rehan Khalid (Mon Nov 13 2017 - 04:41:25 PST)
    - Re: [AMBER] cpptraj error Rana Rehan Khalid (Mon Nov 13 2017 - 05:03:25 PST)
    - Re: [AMBER] cpptraj error Bill Ross (Mon Nov 13 2017 - 05:41:11 PST)
- Re: [AMBER] cpptraj error Daniel Roe (Tue Nov 14 2017 - 09:36:47 PST)
[AMBER] Single long pH-REMD simulation vs. several short pH-REMD simulations Eric Lang (Mon Nov 13 2017 - 03:46:01 PST)
- Re: [AMBER] Single long pH-REMD simulation vs. several short pH-REMD simulations Bill Ross (Mon Nov 13 2017 - 04:04:57 PST)
  - Re: [AMBER] Single long pH-REMD simulation vs. several short pH-REMD simulations Eric Lang (Mon Nov 13 2017 - 08:07:46 PST)
    - Re: [AMBER] Single long pH-REMD simulation vs. several short pH-REMD simulations Bill Ross (Mon Nov 13 2017 - 12:50:24 PST)
- Re: [AMBER] Single long pH-REMD simulation vs. several short pH-REMD simulations Cruzeiro,Vinicius Wilian D (Mon Nov 13 2017 - 06:51:07 PST)
  - Re: [AMBER] Single long pH-REMD simulation vs. several short pH-REMD simulations Eric Lang (Mon Nov 13 2017 - 08:00:47 PST)
    - Re: [AMBER] Single long pH-REMD simulation vs. several short pH-REMD simulations Cruzeiro,Vinicius Wilian D (Mon Nov 13 2017 - 08:20:29 PST)
    - Re: [AMBER] Single long pH-REMD simulation vs. several short pH-REMD simulations Eric Lang (Tue Nov 14 2017 - 03:20:27 PST)
[AMBER] Cross-vendor GPU layer for Machine Learning Bill Ross (Mon Nov 13 2017 - 03:58:16 PST)
[AMBER] Cpptraj pdb snapshots Lizelle Lubbe (Mon Nov 13 2017 - 04:28:32 PST)
- Re: [AMBER] Cpptraj pdb snapshots David A Case (Mon Nov 13 2017 - 05:01:41 PST)
  - Re: [AMBER] Cpptraj pdb snapshots Lizelle Lubbe (Mon Nov 13 2017 - 05:07:18 PST)
[AMBER] Convert prmtop Lizelle Lubbe (Mon Nov 13 2017 - 04:48:54 PST)
- Re: [AMBER] Convert prmtop David A Case (Mon Nov 13 2017 - 07:18:09 PST)
  - Re: [AMBER] Convert prmtop Lizelle Lubbe (Mon Nov 13 2017 - 07:25:10 PST)
[AMBER] MMPBSA.py error: “Could not set up '_MMPBSA_receptor.mdcrd.0' for reading” Alonso Martinez, Diego (Mon Nov 13 2017 - 06:16:56 PST)
[AMBER] Regarding MCPB.py error Aashish Bhatt (Mon Nov 13 2017 - 07:42:25 PST)
- Re: [AMBER] Regarding MCPB.py error Pengfei Li (Mon Nov 13 2017 - 08:07:21 PST)
  - Re: [AMBER] Regarding MCPB.py error Pengfei Li (Mon Nov 13 2017 - 08:08:46 PST)
[AMBER] Domain domain interaction study Rana Rehan Khalid (Mon Nov 13 2017 - 09:42:37 PST)
[AMBER] MC barostat filip (Tue Nov 14 2017 - 03:09:59 PST)
- Re: [AMBER] MC barostat Niel Henriksen (Tue Nov 14 2017 - 10:17:16 PST)
  - Re: [AMBER] MC barostat David Cerutti (Tue Nov 14 2017 - 11:18:26 PST)
    - Re: [AMBER] MC barostat filip (Wed Nov 15 2017 - 00:13:14 PST)
    - Re: [AMBER] MC barostat David Cerutti (Wed Nov 15 2017 - 00:27:34 PST)
    - Re: [AMBER] MC barostat filip (Wed Nov 15 2017 - 01:39:55 PST)
[AMBER] pdb snapshots Lizelle Lubbe (Tue Nov 14 2017 - 04:49:39 PST)
- Re: [AMBER] pdb snapshots David A Case (Tue Nov 14 2017 - 05:26:08 PST)
  - Re: [AMBER] pdb snapshots Lizelle Lubbe (Wed Nov 15 2017 - 04:16:13 PST)
    - Re: [AMBER] pdb snapshots Daniel Roe (Wed Nov 15 2017 - 08:22:32 PST)
[AMBER] Regarding Glucose dynamics Aashish Bhatt (Tue Nov 14 2017 - 06:48:06 PST)
- Re: [AMBER] Regarding Glucose dynamics Lachele Foley (Tue Nov 14 2017 - 06:55:38 PST)
  - Re: [AMBER] Regarding Glucose dynamics Aashish Bhatt (Tue Nov 14 2017 - 07:02:29 PST)
- Re: [AMBER] Regarding Glucose dynamics Carlos Simmerling (Tue Nov 14 2017 - 07:03:40 PST)
  - Re: [AMBER] Regarding Glucose dynamics Aashish Bhatt (Tue Nov 14 2017 - 07:14:10 PST)
    - Re: [AMBER] Regarding Glucose dynamics Carlos Simmerling (Tue Nov 14 2017 - 07:23:36 PST)
    - Re: [AMBER] Regarding Glucose dynamics Bill Ross (Tue Nov 14 2017 - 07:26:29 PST)
    - Re: [AMBER] Regarding Glucose dynamics Aashish Bhatt (Tue Nov 14 2017 - 07:27:59 PST)
    - Re: [AMBER] Regarding Glucose dynamics Lachele Foley (Tue Nov 14 2017 - 08:16:26 PST)
    - Re: [AMBER] Regarding Glucose dynamics Bill Ross (Tue Nov 14 2017 - 07:24:09 PST)
[AMBER] Help Yuliia Varenyk (Tue Nov 14 2017 - 07:16:36 PST)
- Re: [AMBER] Help Daniel Roe (Tue Nov 14 2017 - 09:33:36 PST)
[AMBER] restrain charge during MCPB.py parametrization Antonija Tomić (Tue Nov 14 2017 - 08:22:00 PST)
- Re: [AMBER] restrain charge during MCPB.py parametrization Pengfei Li (Tue Nov 14 2017 - 12:43:26 PST)
  - Re: [AMBER] restrain charge during MCPB.py parametrization Antonija Tomić (Tue Nov 14 2017 - 23:10:30 PST)
[AMBER] The strange way of paramfit working process viktor drobot (Tue Nov 14 2017 - 13:32:33 PST)
- Re: [AMBER] The strange way of paramfit working process David Cerutti (Wed Nov 15 2017 - 00:08:10 PST)
  - Re: [AMBER] The strange way of paramfit working process viktor drobot (Wed Nov 15 2017 - 04:14:55 PST)
    - Re: [AMBER] The strange way of paramfit working process viktor drobot (Wed Nov 15 2017 - 07:19:14 PST)
    - Re: [AMBER] The strange way of paramfit working process Robin Betz (Thu Nov 16 2017 - 16:26:07 PST)
    - Re: [AMBER] The strange way of paramfit working process David Cerutti (Thu Nov 16 2017 - 16:42:28 PST)
    - Re: [AMBER] The strange way of paramfit working process viktor drobot (Fri Nov 17 2017 - 12:25:29 PST)
    - Re: [AMBER] The strange way of paramfit working process David Cerutti (Fri Nov 17 2017 - 13:45:10 PST)
[AMBER] Confusion in urea Model Saikat Pal (Tue Nov 14 2017 - 22:47:53 PST)
- Re: [AMBER] Confusion in urea Model David A Case (Wed Nov 15 2017 - 04:26:15 PST)
  - Re: [AMBER] Confusion in urea Model mirzo (Wed Nov 15 2017 - 06:27:05 PST)
[AMBER] Cpptraj Rana Rehan Khalid (Tue Nov 14 2017 - 23:51:46 PST)
- Re: [AMBER] Cpptraj Daniel Roe (Wed Nov 15 2017 - 07:31:36 PST)
[AMBER] Analysis of percentage contact in residue-ligand interaction with CPPTRAJ anu chandra (Wed Nov 15 2017 - 21:36:19 PST)
- Re: [AMBER] Analysis of percentage contact in residue-ligand interaction with CPPTRAJ Wesley Michael Botello-Smith (Mon Nov 20 2017 - 17:25:44 PST)
  - Re: [AMBER] Analysis of percentage contact in residue-ligand interaction with CPPTRAJ anu chandra (Mon Nov 20 2017 - 20:51:40 PST)
  - Re: [AMBER] Analysis of percentage contact in residue-ligand interaction with CPPTRAJ Daniel Roe (Tue Nov 21 2017 - 05:48:08 PST)
[AMBER] Query regarding MCPB.py force constant Abhilash J (Thu Nov 16 2017 - 00:20:56 PST)
- Re: [AMBER] Query regarding MCPB.py force constant Abhilash J (Thu Nov 16 2017 - 01:48:26 PST)
[AMBER] MMPBSA.py calculations on protein domain Prithvi Raj Pandey (Thu Nov 16 2017 - 01:05:35 PST)
[AMBER] PCA scree plots Lizelle Lubbe (Thu Nov 16 2017 - 02:27:47 PST)
- Re: [AMBER] PCA scree plots Lizelle Lubbe (Thu Nov 16 2017 - 02:40:28 PST)
- Re: [AMBER] PCA scree plots Daniel Roe (Thu Feb 01 2018 - 06:26:10 PST)
[AMBER] All interactions fraction analysis Ruchika Bhat (Thu Nov 16 2017 - 03:14:21 PST)
[AMBER] Parameterizing cardiolipins in Lipid17 force field Prunotto Alessio (Thu Nov 16 2017 - 03:35:52 PST)
[AMBER] DFTB3 Holger Kruse (Thu Nov 16 2017 - 04:10:18 PST)
[AMBER] Distorted peptide Chetna Tyagi (Thu Nov 16 2017 - 07:12:27 PST)
- Re: [AMBER] Distorted peptide Carlos Simmerling (Thu Nov 16 2017 - 08:26:50 PST)
[AMBER] Fw(4): sudipta.mml.gmail.com sudipta.mml (Thu Nov 16 2017 - 08:55:47 PST)
[AMBER] simulations of enzyme with ligand Qinghua Liao (Thu Nov 16 2017 - 08:51:19 PST)
- [AMBER] Fwd: simulations of enzyme with ligand Qinghua Liao (Sun Nov 19 2017 - 06:58:47 PST)
  - Re: [AMBER] Fwd: simulations of enzyme with ligand Daniel Roe (Mon Nov 20 2017 - 07:59:11 PST)
    - Re: [AMBER] Fwd: simulations of enzyme with ligand Qinghua Liao (Mon Nov 20 2017 - 08:09:25 PST)
[AMBER] How to extract one frame from a trajectory to use as input file for new MD run? James Kress (Thu Nov 16 2017 - 18:25:53 PST)
- Re: [AMBER] How to extract one frame from a trajectory to use as input file for new MD run? Bill Ross (Thu Nov 16 2017 - 18:32:15 PST)
- Re: [AMBER] How to extract one frame from a trajectory to use as input file for new MD run? David A Case (Thu Nov 16 2017 - 19:20:54 PST)
  - Re: [AMBER] How to extract one frame from a trajectory to use as input file for new MD run? James Kress (Fri Nov 17 2017 - 15:29:14 PST)
  - Re: [AMBER] How to extract one frame from a trajectory to use as input file for new MD run? Daniel Roe (Mon Nov 20 2017 - 08:28:44 PST)
[AMBER] What does "NRF ne Abs NRFX" error (Gaussian 09) mean? Rinsha Chk (Thu Nov 16 2017 - 21:41:47 PST)
[AMBER] MMPBSA's output: Which atoms are treated as Backbone Atoms (and Side Chain Atoms) for Nucleic Acids? Emmanuel (Fri Nov 17 2017 - 00:22:24 PST)
[AMBER] AMBER QM/MM Point charges daniele selli (Fri Nov 17 2017 - 02:05:11 PST)
- Re: [AMBER] AMBER QM/MM Point charges Gustavo Seabra (Fri Nov 17 2017 - 03:49:08 PST)
  - Re: [AMBER] AMBER QM/MM Point charges daniele selli (Fri Nov 17 2017 - 05:10:56 PST)
    - Re: [AMBER] AMBER QM/MM Point charges Gustavo Seabra (Fri Nov 17 2017 - 13:46:52 PST)
[AMBER] Is GAFF polarizable forcefield ?? Saikat Pal (Fri Nov 17 2017 - 02:16:22 PST)
- Re: [AMBER] Is GAFF polarizable forcefield ?? David A Case (Fri Nov 17 2017 - 04:54:15 PST)
[AMBER] PCA eigenvalues Lizelle Lubbe (Sat Nov 18 2017 - 07:05:51 PST)
- Re: [AMBER] PCA eigenvalues Daniel Roe (Mon Nov 20 2017 - 07:53:21 PST)
  - Re: [AMBER] PCA eigenvalues Lizelle Lubbe (Thu Nov 23 2017 - 10:56:12 PST)
    - Re: [AMBER] PCA eigenvalues Nisha Amarnath Jonniya (Fri Nov 24 2017 - 03:39:01 PST)
    - Re: [AMBER] PCA eigenvalues Elvis Martis (Fri Nov 24 2017 - 04:15:33 PST)
    - Re: [AMBER] PCA eigenvalues Nisha Amarnath Jonniya (Mon Nov 27 2017 - 00:45:38 PST)
    - Re: [AMBER] PCA eigenvalues Bill Ross (Mon Nov 27 2017 - 00:58:19 PST)
    - Re: [AMBER] PCA eigenvalues Bill Ross (Mon Nov 27 2017 - 02:20:09 PST)
    - Re: [AMBER] PCA eigenvalues Elvis Martis (Mon Nov 27 2017 - 04:05:47 PST)
    - Re: [AMBER] PCA eigenvalues Nisha Amarnath Jonniya (Mon Nov 27 2017 - 04:20:46 PST)
    - Re: [AMBER] PCA eigenvalues Marcelo Andrade Chagas (Mon Nov 27 2017 - 07:52:09 PST)
    - Re: [AMBER] PCA eigenvalues Daniel Roe (Mon Nov 27 2017 - 08:24:03 PST)
    - Re: [AMBER] PCA eigenvalues Nisha Amarnath Jonniya (Tue Nov 28 2017 - 00:40:59 PST)
    - Re: [AMBER] PCA eigenvalues Nisha Amarnath Jonniya (Wed Nov 29 2017 - 03:24:50 PST)
    - Re: [AMBER] PCA eigenvalues Daniel Roe (Mon Nov 27 2017 - 08:09:18 PST)
[AMBER] Equilibration sara.iti.lk (Sun Nov 19 2017 - 22:20:22 PST)
- Re: [AMBER] Equilibration Bill Ross (Mon Nov 20 2017 - 00:25:09 PST)
- Re: [AMBER] Equilibration sara.iti.lk (Tue Nov 21 2017 - 23:03:07 PST)
  - Re: [AMBER] Equilibration Bill Ross (Wed Nov 22 2017 - 01:51:30 PST)
- Re: [AMBER] Equilibration sara.iti.lk (Wed Nov 22 2017 - 22:30:54 PST)
  - Re: [AMBER] Equilibration Bill Ross (Wed Nov 22 2017 - 22:39:42 PST)
  - Re: [AMBER] Equilibration Lizelle Lubbe (Wed Nov 22 2017 - 23:23:36 PST)
[AMBER] problem in minimization Carlos Romero (Sun Nov 19 2017 - 23:16:28 PST)
- Re: [AMBER] problem in minimization Bill Ross (Mon Nov 20 2017 - 00:27:36 PST)
  - Re: [AMBER] problem in minimization Carlos Romero (Mon Nov 20 2017 - 08:12:36 PST)
[AMBER] Query about the Glucose Parameters Aashish Bhatt (Mon Nov 20 2017 - 04:00:08 PST)
- Re: [AMBER] Query about the Glucose Parameters Lachele Foley (Tue Nov 21 2017 - 05:56:16 PST)
  - Re: [AMBER] Query about the Glucose Parameters Aashish Bhatt (Tue Nov 21 2017 - 20:48:15 PST)
    - Re: [AMBER] Query about the Glucose Parameters Lachele Foley (Wed Nov 22 2017 - 07:12:12 PST)
    - Re: [AMBER] Query about the Glucose Parameters Aashish Bhatt (Thu Nov 23 2017 - 21:48:32 PST)
    - Re: [AMBER] Query about the Glucose Parameters David A Case (Fri Nov 24 2017 - 14:11:03 PST)
    - Re: [AMBER] Query about the Glucose Parameters Lachele Foley (Fri Nov 24 2017 - 21:37:47 PST)
    - Re: [AMBER] Query about the Glucose Parameters mirzo (Fri Nov 24 2017 - 23:11:55 PST)
    - Re: [AMBER] Query about the Glucose Parameters Marcelo Andrade Chagas (Sat Nov 25 2017 - 04:21:20 PST)
[AMBER] Help Regarding Amber Tools Jerrano Bowleg (Mon Nov 20 2017 - 08:15:41 PST)
[AMBER] Can't find pad4amber module. minyuan.mail.ustc.edu.cn (Mon Nov 20 2017 - 17:37:58 PST)
- Re: [AMBER] Can't find pad4amber module. Hai Nguyen (Mon Nov 20 2017 - 22:21:38 PST)
Re: [AMBER] [SPAM] Re: Can't find pad4amber module. minyuan.mail.ustc.edu.cn (Mon Nov 20 2017 - 23:01:24 PST)
[AMBER] Does amber16 support gaussian16? minyuan.mail.ustc.edu.cn (Tue Nov 21 2017 - 00:39:27 PST)
- Re: [AMBER] Does amber16 support gaussian16? Pengfei Li (Tue Nov 21 2017 - 07:15:17 PST)
- Re: [AMBER] Does amber16 support gaussian16? minyuan.mail.ustc.edu.cn (Wed Nov 22 2017 - 01:59:20 PST)
  - Re: [AMBER] Does amber16 support gaussian16? Pengfei Li (Tue Nov 28 2017 - 18:10:38 PST)
[AMBER] How to generate a cis-isomoerization of PRO? Wenbo Zhang (Tue Nov 21 2017 - 01:05:37 PST)
[AMBER] SHAKEH problem in GPU calculation sangita kachhap (Tue Nov 21 2017 - 02:08:32 PST)
- Re: [AMBER] SHAKEH problem in GPU calculation David A Case (Tue Nov 21 2017 - 05:17:11 PST)
[AMBER] SHAKEH problem in GPU calculation sangita kachhap (Tue Nov 21 2017 - 02:30:25 PST)
[AMBER] 回复: Re: Does amber16 support gaussian16? 闵媛 (Tue Nov 21 2017 - 07:37:37 PST)
- Re: [AMBER] Does amber16 support gaussian16? Pengfei Li (Tue Nov 21 2017 - 15:44:21 PST)
[AMBER] T.I. - single topology HIP <-> HIE Andrew Schaub (Tue Nov 21 2017 - 08:53:39 PST)
[AMBER] SCEE/SCNB zeros Stefan Doerr (Wed Nov 22 2017 - 02:11:00 PST)
- Re: [AMBER] SCEE/SCNB zeros David A Case (Wed Nov 22 2017 - 04:33:05 PST)
- Re: [AMBER] SCEE/SCNB zeros Ross Walker (Wed Nov 22 2017 - 05:29:00 PST)
  - Re: [AMBER] SCEE/SCNB zeros Stefan Doerr (Wed Nov 22 2017 - 07:17:04 PST)
[AMBER] cpptraj: partial charges missing from mol2 file Thomas Evangelidis (Wed Nov 22 2017 - 08:04:07 PST)
- Re: [AMBER] cpptraj: partial charges missing from mol2 file Daniel Roe (Wed Nov 22 2017 - 09:44:43 PST)
  - Re: [AMBER] cpptraj: partial charges missing from mol2 file Thomas Evangelidis (Wed Nov 22 2017 - 17:04:37 PST)
    - Re: [AMBER] cpptraj: partial charges missing from mol2 file Daniel Roe (Mon Nov 27 2017 - 08:29:34 PST)
[AMBER] About position restrains Pablo Galaz-Davison (Wed Nov 22 2017 - 12:25:20 PST)
- Re: [AMBER] About position restrains Thomas Cheatham (Wed Nov 22 2017 - 14:22:09 PST)
[AMBER] how to set hetrodimer for MD Simulation Rana Rehan Khalid (Wed Nov 22 2017 - 13:13:49 PST)
- Re: [AMBER] how to set hetrodimer for MD Simulation David A Case (Thu Nov 23 2017 - 05:21:54 PST)
[AMBER] cudaGetDeviceCount failed unknown error Ercig Bogac (BIOCH) (Thu Nov 23 2017 - 05:29:42 PST)
- Re: [AMBER] cudaGetDeviceCount failed unknown error Ross Walker (Thu Nov 23 2017 - 08:08:13 PST)
  - Re: [AMBER] cudaGetDeviceCount failed unknown error Ercig Bogac (BIOCH) (Thu Nov 23 2017 - 10:51:25 PST)
    - Re: [AMBER] cudaGetDeviceCount failed unknown error Ross Walker (Sat Nov 25 2017 - 12:33:16 PST)
- Re: [AMBER] cudaGetDeviceCount failed unknown error Taisung Lee (Thu Nov 23 2017 - 14:18:12 PST)
  - Re: [AMBER] cudaGetDeviceCount failed unknown error Ercig Bogac (BIOCH) (Thu Nov 23 2017 - 14:29:35 PST)
Re: [AMBER] Equiliibration sara.iti.lk (Thu Nov 23 2017 - 21:13:10 PST)
- Re: [AMBER] Equiliibration sara.iti.lk (Thu Nov 23 2017 - 21:20:15 PST)
[AMBER] Can we study the bond breaking event through Md simulation Rana Rehan Khalid (Thu Nov 23 2017 - 21:51:39 PST)
- Re: [AMBER] Can we study the bond breaking event through Md simulation Elvis Martis (Thu Nov 23 2017 - 22:52:44 PST)
  - Re: [AMBER] Can we study the bond breaking event through Md simulation Rana Rehan Khalid (Thu Nov 23 2017 - 22:59:35 PST)
    - Re: [AMBER] Can we study the bond breaking event through Md simulation Bill Ross (Thu Nov 23 2017 - 23:40:45 PST)
    - Re: [AMBER] Can we study the bond breaking event through Md simulation Rana Rehan Khalid (Thu Nov 23 2017 - 23:46:32 PST)
- Re: [AMBER] Can we study the bond breaking event through Md simulation Ercig Bogac (BIOCH) (Fri Nov 24 2017 - 00:58:37 PST)
  - Re: [AMBER] Can we study the bond breaking event through Md simulation Rana Rehan Khalid (Fri Nov 24 2017 - 01:14:01 PST)
    - Re: [AMBER] Can we study the bond breaking event through Md simulation Szymon Żaczek (Fri Nov 24 2017 - 02:50:08 PST)
    - Re: [AMBER] Can we study the bond breaking event through Md simulation Rana Rehan Khalid (Sat Nov 25 2017 - 04:38:15 PST)
[AMBER] Regarding Resp charge Aashish Bhatt (Sat Nov 25 2017 - 06:18:09 PST)
[AMBER] What forcefield does the DHFR JAC benchmark system use? John Chodera (Sat Nov 25 2017 - 11:12:55 PST)
- Re: [AMBER] What forcefield does the DHFR JAC benchmark system use? Ross Walker (Sat Nov 25 2017 - 12:42:52 PST)
- Re: [AMBER] What forcefield does the DHFR JAC benchmark system use? David Cerutti (Sat Nov 25 2017 - 12:44:19 PST)
  - Re: [AMBER] What forcefield does the DHFR JAC benchmark system use? David Cerutti (Sat Nov 25 2017 - 12:46:06 PST)
    - Re: [AMBER] What forcefield does the DHFR JAC benchmark system use? John Chodera (Sun Nov 26 2017 - 10:26:49 PST)
[AMBER] Batch Minimization Abdul-Rashid III Sampaco (Sat Nov 25 2017 - 19:24:56 PST)
- Re: [AMBER] Batch Minimization Daniel Roe (Sat Nov 25 2017 - 19:34:43 PST)
  - Re: [AMBER] Batch Minimization Abdul-Rashid III Sampaco (Sat Nov 25 2017 - 19:44:54 PST)
[AMBER] Hydrogen bond analysis Through CPPTRAJ Rana Rehan Khalid (Sun Nov 26 2017 - 06:03:15 PST)
- Re: [AMBER] Hydrogen bond analysis Through CPPTRAJ Daniel Roe (Mon Nov 27 2017 - 08:27:28 PST)
  - Re: [AMBER] Hydrogen bond analysis Through CPPTRAJ Rana Rehan Khalid (Mon Nov 27 2017 - 08:58:22 PST)
[AMBER] any opportunity of using the pmemd.cuda if one cannot afford the fee MinYuan (Sun Nov 26 2017 - 22:08:15 PST)
- Re: [AMBER] any opportunity of using the pmemd.cuda if one cannot afford the fee David A Case (Mon Nov 27 2017 - 04:30:59 PST)
[AMBER] STOP PMEMD Terminated Abnormally MinYuan (Mon Nov 27 2017 - 08:08:08 PST)
- Re: [AMBER] STOP PMEMD Terminated Abnormally Elvis Martis (Mon Nov 27 2017 - 08:10:36 PST)
  - Re: [AMBER] STOP PMEMD Terminated Abnormally MinYuan (Mon Nov 27 2017 - 16:17:15 PST)
    - Re: [AMBER] STOP PMEMD Terminated Abnormally Hai Nguyen (Mon Nov 27 2017 - 16:27:48 PST)
    - Re: [AMBER] STOP PMEMD Terminated Abnormally MinYuan (Mon Nov 27 2017 - 16:35:52 PST)
[AMBER] Multidomain protein Simulation Rana Rehan Khalid (Mon Nov 27 2017 - 14:50:11 PST)
[AMBER] cannot fix the problem LD_LIBRARY_PATH does not include $AMBERHOME/lib MinYuan (Tue Nov 28 2017 - 01:24:11 PST)
- Re: [AMBER] cannot fix the problem LD_LIBRARY_PATH does not include $AMBERHOME/lib Bill Ross (Tue Nov 28 2017 - 02:35:35 PST)
  - Re: [AMBER] cannot fix the problem LD_LIBRARY_PATH does not include $AMBERHOME/lib MinYuan (Tue Nov 28 2017 - 22:42:23 PST)
    - Re: [AMBER] cannot fix the problem LD_LIBRARY_PATH does not include $AMBERHOME/lib David A Case (Wed Nov 29 2017 - 04:28:08 PST)
- Re: [AMBER] cannot fix the problem LD_LIBRARY_PATH does not include $AMBERHOME/lib David A Case (Tue Nov 28 2017 - 05:41:45 PST)
- Re: [AMBER] cannot fix the problem LD_LIBRARY_PATH does not include $AMBERHOME/lib Daniel Roe (Tue Nov 28 2017 - 05:49:44 PST)
  - Re: [AMBER] [SPAM] Re: cannot fix the problem LD_LIBRARY_PATH does not include $AMBERHOME/lib MinYuan (Tue Nov 28 2017 - 17:28:40 PST)
- Re: [AMBER] cannot fix the problem LD_LIBRARY_PATH does not include $AMBERHOME/lib minyuan.mail.ustc.edu.cn (Wed Nov 29 2017 - 06:23:04 PST)
[AMBER] structure minimization Rana Rehan Khalid (Tue Nov 28 2017 - 03:01:12 PST)
- Re: [AMBER] structure minimization Marcelo Andrade Chagas (Tue Nov 28 2017 - 03:10:56 PST)
  - Re: [AMBER] structure minimization Rana Rehan Khalid (Tue Nov 28 2017 - 03:13:23 PST)
- Re: [AMBER] structure minimization Bill Ross (Tue Nov 28 2017 - 03:27:10 PST)
  - Re: [AMBER] structure minimization Rana Rehan Khalid (Tue Nov 28 2017 - 03:28:51 PST)
- Re: [AMBER] structure minimization David A Case (Tue Nov 28 2017 - 05:44:57 PST)
  - Re: [AMBER] structure minimization Rana Rehan Khalid (Tue Nov 28 2017 - 06:05:59 PST)
[AMBER] APR error Maura Malinska (Tue Nov 28 2017 - 03:25:14 PST)
- Re: [AMBER] APR error Bill Ross (Tue Nov 28 2017 - 03:34:12 PST)
- Re: [AMBER] APR error Jian Yin (Tue Nov 28 2017 - 14:57:27 PST)
- Re: [AMBER] APR error Jian Yin (Tue Nov 28 2017 - 15:08:56 PST)
[AMBER] Centriod in clustering sangita kachhap (Tue Nov 28 2017 - 07:09:41 PST)
- Re: [AMBER] Centriod in clustering Daniel Roe (Tue Nov 28 2017 - 07:27:25 PST)
  - Re: [AMBER] Centriod in clustering sangita kachhap (Tue Nov 28 2017 - 08:28:46 PST)
[AMBER] About PCA and pi-stacking Elisa Pieri (Tue Nov 28 2017 - 08:51:43 PST)
[AMBER] aMD- alphaD- what does solute residues mean? Thakur, Abhishek (Tue Nov 28 2017 - 12:36:51 PST)
- Re: [AMBER] aMD- alphaD- what does solute residues mean? Elvis Martis (Wed Nov 29 2017 - 03:45:57 PST)
[AMBER] how to generate the force fied file of AsO3H3? minyuan.mail.ustc.edu.cn (Tue Nov 28 2017 - 23:50:58 PST)
- Re: [AMBER] how to generate the force fied file of AsO3H3? Bill Ross (Wed Nov 29 2017 - 00:05:41 PST)
  - Re: [AMBER] how to generate the force fied file of AsO3H3? MinYuan (Wed Nov 29 2017 - 02:31:04 PST)
  - Re: [AMBER] how to generate the force fied file of AsO3H3? David A Case (Wed Nov 29 2017 - 04:38:49 PST)
- Re: [AMBER] how to generate the force fied file of AsO3H3? minyuan.mail.ustc.edu.cn (Wed Nov 29 2017 - 06:20:50 PST)
  - Re: [AMBER] how to generate the force fied file of AsO3H3? Andrew Schaub (Wed Nov 29 2017 - 08:57:55 PST)
    - Re: [AMBER] how to generate the force fied file of AsO3H3? MinYuan (Wed Nov 29 2017 - 19:37:54 PST)
    - Re: [AMBER] how to generate the force fied file of AsO3H3? Pengfei Li (Wed Nov 29 2017 - 20:14:10 PST)
[AMBER] mpirun Error opening unit 5 MinYuan (Wed Nov 29 2017 - 02:00:00 PST)
- Re: [AMBER] mpirun Error opening unit 5 Bill Ross (Wed Nov 29 2017 - 02:13:55 PST)
[AMBER] Fw: mpirun Error opening unit 5 MinYuan (Wed Nov 29 2017 - 02:22:44 PST)
[AMBER] Using soft-core potentials to run TI simulations Yang Jinpeng (Wed Nov 29 2017 - 02:50:12 PST)
[AMBER] Trouble installing amber tools on new OSX 10.13.1 Eiros Zamora, Juan (Wed Nov 29 2017 - 04:35:00 PST)
- Re: [AMBER] Trouble installing amber tools on new OSX 10.13.1 Daniel Roe (Wed Nov 29 2017 - 05:25:54 PST)
- Re: [AMBER] Trouble installing amber tools on new OSX 10.13.1 Hai Nguyen (Wed Nov 29 2017 - 05:40:17 PST)
- Re: [AMBER] Trouble installing amber tools on new OSX 10.13.1 David A Case (Wed Nov 29 2017 - 10:43:13 PST)
[AMBER] Post processing of trajectory Sowmya Indrakumar (Wed Nov 29 2017 - 05:04:42 PST)
- Re: [AMBER] Post processing of trajectory Abdul-Rashid III Sampaco (Wed Nov 29 2017 - 05:22:37 PST)
  - Re: [AMBER] Post processing of trajectory Sowmya Indrakumar (Wed Nov 29 2017 - 05:39:31 PST)
[AMBER] imin=5 not working in AMBER16? Paul Mortenson (Wed Nov 29 2017 - 07:19:37 PST)
- Re: [AMBER] imin=5 not working in AMBER16? Cruzeiro,Vinicius Wilian D (Wed Nov 29 2017 - 07:27:03 PST)
  - Re: [AMBER] imin=5 not working in AMBER16? Paul Mortenson (Wed Nov 29 2017 - 07:51:25 PST)
    - Re: [AMBER] imin=5 not working in AMBER16? Cruzeiro,Vinicius Wilian D (Wed Nov 29 2017 - 09:04:46 PST)
    - Re: [AMBER] imin=5 not working in AMBER16? Paul Mortenson (Wed Nov 29 2017 - 23:52:08 PST)
- Re: [AMBER] imin=5 not working in AMBER16? Daniel Roe (Thu Nov 30 2017 - 10:57:44 PST)
  - Re: [AMBER] imin=5 not working in AMBER16? Paul Mortenson (Thu Nov 30 2017 - 23:52:26 PST)
    - Re: [AMBER] imin=5 not working in AMBER16? Daniel Roe (Fri Dec 01 2017 - 05:39:05 PST)
    - Re: [AMBER] imin=5 not working in AMBER16? Paul Mortenson (Fri Dec 01 2017 - 07:08:44 PST)
    - Re: [AMBER] imin=5 not working in AMBER16? David A Case (Fri Dec 01 2017 - 09:40:52 PST)
    - Re: [AMBER] imin=5 not working in AMBER16? Paul Mortenson (Mon Dec 04 2017 - 06:04:04 PST)
[AMBER] lipid 14 compatibility with FF14SB Chitrak Gupta (Wed Nov 29 2017 - 10:05:31 PST)
- Re: [AMBER] lipid 14 compatibility with FF14SB Ross Walker (Wed Nov 29 2017 - 11:36:33 PST)
[AMBER] Protein-Ligand Energy Minimization Kadir Tung (Wed Nov 29 2017 - 10:14:58 PST)
- Re: [AMBER] Protein-Ligand Energy Minimization Daniel Roe (Thu Nov 30 2017 - 12:02:59 PST)
  - Re: [AMBER] Protein-Ligand Energy Minimization Carlos Simmerling (Thu Nov 30 2017 - 12:10:42 PST)
[AMBER] MCPB.py how to insert the heteroatom heme in the one domain of macromolecule Rana Rehan Khalid (Thu Nov 30 2017 - 06:44:54 PST)
- Re: [AMBER] MCPB.py how to insert the heteroatom heme in the one domain of macromolecule Pengfei Li (Mon Dec 04 2017 - 14:22:19 PST)
[AMBER] antechamber: prepgen mainchain file character limit Markus Schneider (Thu Nov 30 2017 - 07:36:02 PST)
- Re: [AMBER] antechamber: prepgen mainchain file character limit Junmei Wang (Thu Nov 30 2017 - 07:54:48 PST)
  - Re: [AMBER] antechamber: prepgen mainchain file character limit Markus Schneider (Thu Nov 30 2017 - 09:10:52 PST)
- Re: [AMBER] antechamber: prepgen mainchain file character limit Junmei Wang (Fri Dec 01 2017 - 11:35:35 PST)
[AMBER] Error: No module named parmed.scripts Setyanto Md (Thu Nov 30 2017 - 15:12:49 PST)
- Re: [AMBER] Error: No module named parmed.scripts Jason Swails (Sun Dec 03 2017 - 20:43:17 PST)
  - Re: [AMBER] Error: No module named parmed.scripts Setyanto Md (Mon Dec 04 2017 - 06:50:00 PST)
[AMBER] PF6- octahedral geometry change during equilibration!! Sanaa ALAbbad (Thu Nov 30 2017 - 16:00:48 PST)
- Re: [AMBER] PF6- octahedral geometry change during equilibration!! junmwang.gmail.com (Thu Nov 30 2017 - 18:20:12 PST)
- Re: [AMBER] PF6- octahedral geometry change during equilibration!! Gustavo Seabra (Fri Dec 01 2017 - 03:23:40 PST)
- Re: [AMBER] PF6- octahedral geometry change during equilibration!! Junmei Wang (Fri Dec 01 2017 - 09:29:41 PST)
  - Re: [AMBER] PF6- octahedral geometry change during equilibration!! Sanaa ALAbbad (Fri Dec 01 2017 - 09:41:17 PST)
    - Re: [AMBER] PF6- octahedral geometry change during equilibration!! Sanaa ALAbbad (Fri Dec 01 2017 - 11:13:57 PST)
    - Re: [AMBER] PF6- octahedral geometry change during equilibration!! Junmei Wang (Fri Dec 01 2017 - 11:30:46 PST)
    - Re: [AMBER] PF6- octahedral geometry change during equilibration!! mirzo (Fri Dec 01 2017 - 11:43:57 PST)
    - Re: [AMBER] PF6- octahedral geometry change during equilibration!! Sanaa ALAbbad (Fri Dec 01 2017 - 15:54:41 PST)
[AMBER] Problems with the "conbine" conmmand in LEaP 杨满意 (Thu Nov 30 2017 - 16:56:33 PST)
- Re: [AMBER] Problems with the "conbine" conmmand in LEaP Daniel Roe (Fri Dec 01 2017 - 05:30:14 PST)
  - Re: [AMBER] Problems with the "conbine" conmmand in LEaP 杨满意 (Fri Dec 01 2017 - 17:23:16 PST)
[AMBER] implicit models for other solvents and non-standard solvents Vaibhav Dixit (Fri Dec 01 2017 - 04:35:11 PST)
[AMBER] Residue Protonation State Rana Rehan Khalid (Sat Dec 02 2017 - 01:07:50 PST)
- Re: [AMBER] Residue Protonation State Schmid, Ralf (Dr.) (Sat Dec 02 2017 - 09:08:40 PST)
[AMBER] lipid 14 compatibility with FF14SB Chitrak Gupta (Sat Dec 02 2017 - 11:17:33 PST)
- Re: [AMBER] lipid 14 compatibility with FF14SB Chitrak Gupta (Thu Nov 30 2017 - 08:53:40 PST)
- Re: [AMBER] lipid 14 compatibility with FF14SB David A Case (Sun Dec 03 2017 - 05:39:45 PST)
[AMBER] Problem with running Example2 from MCPB.py reference SI file MinYuan (Sat Dec 02 2017 - 19:25:29 PST)
- Re: [AMBER] Problem with running Example2 from MCPB.py reference SI file Pengfei Li (Mon Dec 04 2017 - 14:12:11 PST)
  - Re: [AMBER] Problem with running Example2 from MCPB.py reference SI file MinYuan (Tue Dec 05 2017 - 03:33:18 PST)
[AMBER] MCPB.py to generate force field parameter for metal ion As3+ MinYuan (Sat Dec 02 2017 - 19:49:17 PST)
- Re: [AMBER] MCPB.py to generate force field parameter for metal ion As3+ Lorenzo Gontrani (Sun Dec 03 2017 - 02:19:42 PST)
- Re: [AMBER] MCPB.py to generate force field parameter for metal ion As3+ minyuan.mail.ustc.edu.cn (Sun Dec 03 2017 - 02:33:18 PST)
  - Re: [AMBER] MCPB.py to generate force field parameter for metal ion As3+ Lorenzo Gontrani (Sun Dec 03 2017 - 02:49:49 PST)
- Re: [AMBER] MCPB.py to generate force field parameter for metal ion As3+ Lorenzo Gontrani (Sun Dec 03 2017 - 02:51:17 PST)
- Re: [AMBER] MCPB.py to generate force field parameter for metal ion As3+ minyuan.mail.ustc.edu.cn (Sun Dec 03 2017 - 02:56:59 PST)
- Re: [AMBER] MCPB.py to generate force field parameter for metal ion As3+ Lorenzo Gontrani (Sun Dec 03 2017 - 03:10:43 PST)
  - Re: [AMBER] MCPB.py to generate force field parameter for metal ion As3+ MinYuan (Sun Dec 03 2017 - 03:57:24 PST)
    - Re: [AMBER] MCPB.py to generate force field parameter for metal ion As3+ Pengfei Li (Mon Dec 04 2017 - 14:07:12 PST)
    - Re: [AMBER] MCPB.py to generate force field parameter for metal ion As3+ MinYuan (Mon Dec 04 2017 - 18:09:03 PST)
    - Re: [AMBER] MCPB.py to generate force field parameter for metal ion As3+ MinYuan (Mon Dec 04 2017 - 18:12:48 PST)
    - Re: [AMBER] MCPB.py to generate force field parameter for metal ion As3+ Lorenzo Gontrani (Mon Dec 04 2017 - 22:17:54 PST)
    - Re: [AMBER] MCPB.py to generate force field parameter for metal ion As3+ MinYuan (Tue Dec 05 2017 - 03:31:48 PST)
[AMBER] Normalization of radial distribution function Szymon Żaczek (Sun Dec 03 2017 - 10:38:08 PST)
- Re: [AMBER] Normalization of radial distribution function George M. Giambasu (Mon Dec 04 2017 - 07:28:33 PST)
  - Re: [AMBER] Normalization of radial distribution function Szymon Żaczek (Tue Dec 05 2017 - 00:09:38 PST)
    - Re: [AMBER] Normalization of radial distribution function Batuhan Kav (Tue Dec 05 2017 - 01:40:54 PST)
    - Re: [AMBER] Normalization of radial distribution function Szymon Żaczek (Tue Dec 05 2017 - 03:31:08 PST)
[AMBER] helix broken during minimization step Rana Rehan Khalid (Mon Dec 04 2017 - 06:52:34 PST)
[AMBER] GPU workstation with 8 x nVidia GTX 1080 Ti Hadházi Ádám (Mon Dec 04 2017 - 10:41:10 PST)
- Re: [AMBER] GPU workstation with 8 x nVidia GTX 1080 Ti Ross Walker (Mon Dec 04 2017 - 10:48:15 PST)
- Re: [AMBER] GPU workstation with 8 x nVidia GTX 1080 Ti Carlos Simmerling (Mon Dec 04 2017 - 11:32:22 PST)
  - Re: [AMBER] GPU workstation with 8 x nVidia GTX 1080 Ti Ross Walker (Mon Dec 04 2017 - 11:38:14 PST)
[AMBER] To calculate TI using soft-core potential or not Yang Jinpeng (Tue Dec 05 2017 - 00:35:09 PST)
- Re: [AMBER] To calculate TI using soft-core potential or not Daniel Mermelstein (Tue Dec 05 2017 - 13:54:40 PST)
[AMBER] how to generate paramaters for GlcNH3 Tarsis (Tue Dec 05 2017 - 14:19:25 PST)
- Re: [AMBER] how to generate paramaters for GlcNH3 Bill Ross (Tue Dec 05 2017 - 14:29:28 PST)
- Re: [AMBER] how to generate paramaters for GlcNH3 Tarsis (Thu Dec 07 2017 - 11:37:09 PST)
- Re: [AMBER] how to generate paramaters for GlcNH3 Tarsis Ferreira (Fri Dec 08 2017 - 09:34:17 PST)
  - Re: [AMBER] how to generate paramaters for GlcNH3 Lachele Foley (Fri Dec 08 2017 - 15:01:39 PST)
[AMBER] generation of topology and coordinate for glycan Rajarshi Roy (Tue Dec 05 2017 - 20:56:41 PST)
- Re: [AMBER] generation of topology and coordinate for glycan Bill Ross (Tue Dec 05 2017 - 21:15:08 PST)
  - Re: [AMBER] generation of topology and coordinate for glycan Rajarshi Roy (Tue Dec 05 2017 - 22:14:02 PST)
    - Re: [AMBER] generation of topology and coordinate for glycan Bill Ross (Tue Dec 05 2017 - 22:32:03 PST)
    - Re: [AMBER] generation of topology and coordinate for glycan Lachele Foley (Thu Dec 07 2017 - 19:09:31 PST)
[AMBER] Problem in visualizing Amber16 trajecories in VMD Biplab Ghosh (Tue Dec 05 2017 - 22:57:23 PST)
- Re: [AMBER] Problem in visualizing Amber16 trajecories in VMD Bill Ross (Tue Dec 05 2017 - 23:11:14 PST)
  - Re: [AMBER] Problem in visualizing Amber16 trajecories in VMD Abdul-Rashid III Sampaco (Tue Dec 05 2017 - 23:55:18 PST)
- Re: [AMBER] Problem in visualizing Amber16 trajecories in VMD David A Case (Wed Dec 06 2017 - 05:08:36 PST)
[AMBER] Amber Protonate for H++ Andreas Tosstorff (Wed Dec 06 2017 - 09:58:19 PST)
- Re: [AMBER] Amber Protonate for H++ David A Case (Wed Dec 06 2017 - 11:14:48 PST)
  - Re: [AMBER] Amber Protonate for H++ Andreas Tosstorff (Thu Dec 07 2017 - 01:45:03 PST)
    - Re: [AMBER] Amber Protonate for H++ David A Case (Fri Dec 08 2017 - 06:14:58 PST)
- Re: [AMBER] Amber Protonate for H++ Setyanto Md (Wed Dec 06 2017 - 19:17:44 PST)
  - Re: [AMBER] Amber Protonate for H++ Andreas Tosstorff (Thu Dec 07 2017 - 00:28:16 PST)
    - Re: [AMBER] Amber Protonate for H++ Setyanto Md (Thu Dec 07 2017 - 05:30:43 PST)
[AMBER] The paramters of frcmod.chcl3 Yang Jinpeng (Wed Dec 06 2017 - 19:25:50 PST)
[AMBER] force addions to avoid replacing specific solvent molecules by ions Vlad Cojocaru (Thu Dec 07 2017 - 02:14:41 PST)
- Re: [AMBER] force addions to avoid replacing specific solvent molecules by ions Bill Ross (Thu Dec 07 2017 - 02:24:31 PST)
  - Re: [AMBER] force addions to avoid replacing specific solvent molecules by ions Vlad Cojocaru (Thu Dec 07 2017 - 02:35:58 PST)
    - Re: [AMBER] force addions to avoid replacing specific solvent molecules by ions Bill Ross (Thu Dec 07 2017 - 02:39:20 PST)
    - Re: [AMBER] force addions to avoid replacing specific solvent molecules by ions Vlad Cojocaru (Thu Dec 07 2017 - 02:52:10 PST)
[AMBER] Modified amino acid Rajarshi Roy (Thu Dec 07 2017 - 03:37:22 PST)
- Re: [AMBER] Modified amino acid junmwang.gmail.com (Thu Dec 07 2017 - 04:29:44 PST)
  - Re: [AMBER] Modified amino acid Rajarshi Roy (Thu Dec 07 2017 - 05:25:20 PST)
    - Re: [AMBER] Modified amino acid Junmei Wang (Thu Dec 07 2017 - 07:49:49 PST)
    - Re: [AMBER] Modified amino acid Rajarshi Roy (Fri Dec 08 2017 - 02:24:06 PST)
[AMBER] pdf of O-GlcNAc Ser and Thr Yin, Guowei (Thu Dec 07 2017 - 07:57:35 PST)
- [AMBER] pdf of O-GlcNAc Ser and Thr Yin, Guowei (Thu Dec 07 2017 - 09:42:50 PST)
[AMBER] End-of-File error occurring for Minimization run using Amoeba Force Field Chase Zagorec-Marks (Thu Dec 07 2017 - 09:48:28 PST)
- Re: [AMBER] End-of-File error occurring for Minimization run using Amoeba Force Field David A Case (Fri Dec 08 2017 - 06:24:29 PST)
[AMBER] pdf of O-GlcNAc Ser and Thr Li, Xinghui (Thu Dec 07 2017 - 11:15:07 PST)
- Re: [AMBER] pdf of O-GlcNAc Ser and Thr Lachele Foley (Thu Dec 07 2017 - 19:11:34 PST)
[AMBER] Bonds between residues are broken Shilpa Gupta (Thu Dec 07 2017 - 21:33:59 PST)
- Re: [AMBER] Bonds between residues are broken David A Case (Fri Dec 08 2017 - 06:27:28 PST)
  - Re: [AMBER] Bonds between residues are broken Shilpa Gupta (Fri Dec 08 2017 - 08:22:18 PST)
[AMBER] Does pmemd.cuda support QM/MM MinYuan (Fri Dec 08 2017 - 00:03:47 PST)
- Re: [AMBER] Does pmemd.cuda support QM/MM Elvis Martis (Fri Dec 08 2017 - 02:27:12 PST)
  - Re: [AMBER] Does pmemd.cuda support QM/MM MinYuan (Sat Dec 09 2017 - 04:15:03 PST)
    - Re: [AMBER] Does pmemd.cuda support QM/MM Rivera, Miguel (Tue Dec 12 2017 - 04:20:32 PST)
    - Re: [AMBER] Does pmemd.cuda support QM/MM David Cerutti (Tue Dec 12 2017 - 05:01:19 PST)
    - Re: [AMBER] Does pmemd.cuda support QM/MM Elvis Martis (Tue Dec 12 2017 - 05:03:18 PST)
[AMBER] Problem of loading complex Mustafa Alhaji Isa (Fri Dec 08 2017 - 12:48:55 PST)
- Re: [AMBER] Problem of loading complex Carlos Simmerling (Fri Dec 08 2017 - 12:51:33 PST)
  - Re: [AMBER] Problem of loading complex Mustafa Alhaji Isa (Fri Dec 08 2017 - 13:08:31 PST)
    - Re: [AMBER] Problem of loading complex Carlos Simmerling (Fri Dec 08 2017 - 15:19:01 PST)
    - Re: [AMBER] Problem of loading complex David A Case (Fri Dec 08 2017 - 17:51:32 PST)
[AMBER] Solvating a molecule in amber Shilpa Gupta (Sun Dec 10 2017 - 20:37:41 PST)
- Re: [AMBER] Solvating a molecule in amber Bill Ross (Sun Dec 10 2017 - 22:05:02 PST)
  - Re: [AMBER] Solvating a molecule in amber Shilpa Gupta (Sun Dec 10 2017 - 22:09:28 PST)
    - Re: [AMBER] Solvating a molecule in amber Bill Ross (Sun Dec 10 2017 - 22:42:52 PST)
    - Re: [AMBER] Solvating a molecule in amber Shilpa Gupta (Mon Dec 11 2017 - 04:20:48 PST)
    - Re: [AMBER] Solvating a molecule in amber Bill Ross (Mon Dec 11 2017 - 05:05:31 PST)
    - Re: [AMBER] Solvating a molecule in amber Shilpa Gupta (Mon Dec 11 2017 - 05:17:58 PST)
[AMBER] Queries about aMD simulation of metal-bound membrane protein and anu chandra (Mon Dec 11 2017 - 01:59:43 PST)
[AMBER] MCPB HEME Rana Rehan Khalid (Mon Dec 11 2017 - 03:00:11 PST)
- Re: [AMBER] MCPB HEME Bill Ross (Mon Dec 11 2017 - 03:02:14 PST)
- Re: [AMBER] MCPB HEME Marcos Serrou do Amaral (Mon Dec 11 2017 - 05:53:14 PST)
  - Re: [AMBER] MCPB HEME Rana Rehan Khalid (Mon Dec 11 2017 - 06:33:52 PST)
[AMBER] cpptraj segmentation fault Andreas Tosstorff (Mon Dec 11 2017 - 07:12:31 PST)
- Re: [AMBER] cpptraj segmentation fault Daniel Roe (Mon Dec 11 2017 - 07:41:10 PST)
  - Re: [AMBER] cpptraj segmentation fault Andreas Tosstorff (Mon Dec 11 2017 - 07:47:12 PST)
    - Re: [AMBER] cpptraj segmentation fault Daniel Roe (Mon Dec 11 2017 - 07:53:48 PST)
    - Re: [AMBER] cpptraj segmentation fault Andreas Tosstorff (Mon Dec 11 2017 - 08:07:21 PST)
    - Re: [AMBER] cpptraj segmentation fault Daniel Roe (Mon Dec 11 2017 - 08:38:35 PST)
    - Re: [AMBER] cpptraj segmentation fault Daniel Roe (Mon Dec 11 2017 - 08:39:22 PST)
[AMBER] MCPB.py deal with two metal-like sites simultaneously MinYuan (Tue Dec 12 2017 - 02:14:52 PST)
- Re: [AMBER] MCPB.py deal with two metal-like sites simultaneously Pengfei Li (Wed Dec 13 2017 - 08:54:11 PST)
[AMBER] Too large numbers in PDB when using CPPtraj to generate PDB Myron (Tue Dec 12 2017 - 04:26:16 PST)
- Re: [AMBER] Too large numbers in PDB when using CPPtraj to generate PDB Carlos Simmerling (Tue Dec 12 2017 - 05:23:38 PST)
  - Re: [AMBER] Too large numbers in PDB when using CPPtraj to generate PDB Myron (Tue Dec 12 2017 - 08:07:10 PST)
    - Re: [AMBER] Too large numbers in PDB when using CPPtraj to generate PDB Carlos Simmerling (Tue Dec 12 2017 - 09:39:28 PST)
- Re: [AMBER] Too large numbers in PDB when using CPPtraj to generate PDB Daniel Roe (Tue Dec 12 2017 - 05:52:05 PST)
  - Re: [AMBER] Too large numbers in PDB when using CPPtraj to generate PDB Myron (Tue Dec 12 2017 - 08:15:48 PST)
[AMBER] error when running tleap from script, works fine from shell Andreas Tosstorff (Tue Dec 12 2017 - 05:52:58 PST)
- Re: [AMBER] error when running tleap from script, works fine from shell David A Case (Wed Dec 13 2017 - 06:14:30 PST)
[AMBER] MMPBSA.py and S-S bonds between different chains Sergey Samsonov (Tue Dec 12 2017 - 07:58:59 PST)
[AMBER] Error with installation, amber 17 on centos server Praneeth Bommisetti (Tue Dec 12 2017 - 09:16:03 PST)
- Re: [AMBER] Error with installation, amber 17 on centos server Hai Nguyen (Tue Dec 12 2017 - 09:22:14 PST)
- Re: [AMBER] Error with installation, amber 17 on centos server Tru Huynh (Tue Dec 12 2017 - 10:23:34 PST)
[AMBER] Fwd: Re: Error with installation, amber 17 on centos server Praneeth Bommisetti (Tue Dec 12 2017 - 10:05:54 PST)
[AMBER] simulate free metal ion, which is not included in $AMBERHOME/dat/leap/lib/atomic_ions.lib MinYuan (Tue Dec 12 2017 - 19:11:20 PST)
- Re: [AMBER] simulate free metal ion, which is not included in $AMBERHOME/dat/leap/lib/atomic_ions.lib Pengfei Li (Wed Dec 13 2017 - 08:54:52 PST)
  - Re: [AMBER] simulate free metal ion, which is not included in $AMBERHOME/dat/leap/lib/atomic_ions.lib MinYuan (Fri Dec 15 2017 - 06:04:19 PST)
    - Re: [AMBER] simulate free metal ion, which is not included in $AMBERHOME/dat/leap/lib/atomic_ions.lib Bill Ross (Fri Dec 15 2017 - 06:12:23 PST)
    - Re: [AMBER] simulate free metal ion, which is not included in $AMBERHOME/dat/leap/lib/atomic_ions.lib Pengfei Li (Fri Dec 15 2017 - 07:58:53 PST)
- Re: [AMBER] simulate free metal ion, which is not included in $AMBERHOME/dat/leap/lib/atomic_ions.lib minyuan.mail.ustc.edu.cn (Sun Dec 17 2017 - 22:49:02 PST)
  - Re: [AMBER] simulate free metal ion, which is not included in $AMBERHOME/dat/leap/lib/atomic_ions.lib Pengfei Li (Wed Dec 20 2017 - 14:57:29 PST)
[AMBER] Parmed topology file have ifbox=0 Shilpa Gupta (Wed Dec 13 2017 - 00:36:57 PST)
[AMBER] MM-GBSA, acquire the value of each frame Giovanni Grazioso (Wed Dec 13 2017 - 07:56:30 PST)
- Re: [AMBER] MM-GBSA, acquire the value of each frame Casalini Tommaso (Wed Dec 13 2017 - 08:00:26 PST)
- Re: [AMBER] MM-GBSA, acquire the value of each frame Dolivier (Wed Dec 13 2017 - 08:00:47 PST)
[AMBER] T.I. Sidechain setup (softcore potential) based off of A9 tutorial Andrew Schaub (Wed Dec 13 2017 - 11:17:58 PST)
- Re: [AMBER] T.I. Sidechain setup (softcore potential) based off of A9 tutorial Daniel Mermelstein (Sun Dec 17 2017 - 14:49:24 PST)
[AMBER] PCA.CPPTRAJ Rana Rehan Khalid (Wed Dec 13 2017 - 13:58:26 PST)
- Re: [AMBER] PCA.CPPTRAJ Daniel Roe (Thu Dec 14 2017 - 10:21:41 PST)
  - Re: [AMBER] PCA.CPPTRAJ Rana Rehan Khalid (Thu Dec 14 2017 - 13:03:41 PST)
    - Re: [AMBER] PCA.CPPTRAJ Daniel Roe (Fri Dec 15 2017 - 06:39:03 PST)
  - Re: [AMBER] PCA.CPPTRAJ Rana Rehan Khalid (Sat Dec 16 2017 - 00:05:12 PST)
    - Re: [AMBER] PCA.CPPTRAJ Rana Rehan Khalid (Sat Dec 16 2017 - 05:38:13 PST)
    - Re: [AMBER] PCA.CPPTRAJ Rana Rehan Khalid (Sat Dec 16 2017 - 07:25:38 PST)
    - Re: [AMBER] PCA.CPPTRAJ Daniel Roe (Mon Dec 18 2017 - 10:58:06 PST)
    - Re: [AMBER] PCA.CPPTRAJ Rana Rehan Khalid (Mon Dec 18 2017 - 13:16:27 PST)
    - Re: [AMBER] PCA.CPPTRAJ Rana Rehan Khalid (Mon Dec 18 2017 - 13:43:33 PST)
    - Re: [AMBER] PCA.CPPTRAJ Daniel Roe (Tue Dec 19 2017 - 06:23:37 PST)
    - Re: [AMBER] PCA.CPPTRAJ Rana Rehan Khalid (Tue Dec 19 2017 - 06:24:51 PST)
    - Re: [AMBER] PCA.CPPTRAJ Rana Rehan Khalid (Thu Dec 21 2017 - 04:36:13 PST)
[AMBER] query regarding restraint_wt Leena Aggarwal (Thu Dec 14 2017 - 01:57:34 PST)
- Re: [AMBER] query regarding restraint_wt Bill Ross (Thu Dec 14 2017 - 02:15:21 PST)
  - Re: [AMBER] query regarding restraint_wt Leena Aggarwal (Thu Dec 14 2017 - 02:18:42 PST)
    - Re: [AMBER] query regarding restraint_wt Bill Ross (Thu Dec 14 2017 - 02:24:56 PST)
    - Re: [AMBER] query regarding restraint_wt Carlos Simmerling (Thu Dec 14 2017 - 03:51:48 PST)
[AMBER] TI softcore single topology (HIE to HIP) - How do I generate a new lib file for an existing residue? Andrew Schaub (Thu Dec 14 2017 - 09:58:50 PST)
- Re: [AMBER] TI softcore single topology (HIE to HIP) - How do I generate a new lib file for an existing residue? Andrew Schaub (Thu Dec 14 2017 - 10:03:56 PST)
  - Re: [AMBER] TI softcore single topology (HIE to HIP) - How do I generate a new lib file for an existing residue? Andrew Schaub (Thu Dec 14 2017 - 10:28:42 PST)
[AMBER] Trouble with running AMBER16 (MM/PBSA): extract_coords Investigador Química (Thu Dec 14 2017 - 16:42:23 PST)
- Re: [AMBER] Trouble with running AMBER16 (MM/PBSA): extract_coords David A Case (Fri Dec 15 2017 - 05:43:20 PST)
  - Re: [AMBER] Trouble with running AMBER16 (MM/PBSA): extract_coords Elvis Martis (Fri Dec 15 2017 - 06:07:14 PST)
  - Re: [AMBER] Trouble with running AMBER16 (MM/PBSA): extract_coords Investigador Química (Tue Dec 19 2017 - 03:27:19 PST)
[AMBER] HREMD run Dr. MANAS MONDAL (Thu Dec 14 2017 - 17:47:56 PST)
- Re: [AMBER] HREMD run Daniel Roe (Fri Dec 15 2017 - 06:38:10 PST)
  - Re: [AMBER] HREMD run Dr. MANAS MONDAL (Mon Dec 18 2017 - 03:28:23 PST)
    - Re: [AMBER] HREMD run Daniel Roe (Mon Dec 18 2017 - 10:50:19 PST)
    - Re: [AMBER] HREMD run Dr. MANAS MONDAL (Mon Dec 18 2017 - 18:32:45 PST)
    - Re: [AMBER] HREMD run Hai Nguyen (Mon Dec 18 2017 - 18:40:45 PST)
[AMBER] Leap not running Naina Singh (Sat Dec 16 2017 - 04:10:18 PST)
- Re: [AMBER] Leap not running Bill Ross (Sat Dec 16 2017 - 04:13:02 PST)
- Re: [AMBER] Leap not running David A Case (Sat Dec 16 2017 - 05:20:35 PST)
[AMBER] CPPTRAJ hbond Analysis Rana Rehan Khalid (Sun Dec 17 2017 - 13:17:13 PST)
- Re: [AMBER] CPPTRAJ hbond Analysis Hai Nguyen (Mon Dec 18 2017 - 02:47:52 PST)
  - Re: [AMBER] CPPTRAJ hbond Analysis Rana Rehan Khalid (Mon Dec 18 2017 - 03:04:23 PST)
    - Re: [AMBER] CPPTRAJ hbond Analysis Daniel Roe (Mon Dec 18 2017 - 10:52:03 PST)
    - Re: [AMBER] CPPTRAJ hbond Analysis Rana Rehan Khalid (Mon Dec 18 2017 - 14:36:49 PST)
    - Re: [AMBER] CPPTRAJ hbond Analysis Daniel Roe (Tue Dec 19 2017 - 06:23:10 PST)
    - Re: [AMBER] CPPTRAJ hbond Analysis Rana Rehan Khalid (Wed Dec 20 2017 - 08:05:26 PST)
[AMBER] cpptraj multiple trajectories Andreas Tosstorff (Mon Dec 18 2017 - 02:14:31 PST)
- Re: [AMBER] cpptraj multiple trajectories Daniel Roe (Mon Dec 18 2017 - 10:48:15 PST)
[AMBER] Several questions about Amber adaptive QM/MM MD. Mingyuan_xu (Mon Dec 18 2017 - 08:39:00 PST)
- Re: [AMBER] Several questions about Amber adaptive QM/MM MD. Goetz, Andreas (Fri Dec 22 2017 - 17:45:39 PST)
[AMBER] Water-slab at constant pressure jesus berlanga (Mon Dec 18 2017 - 18:38:52 PST)
- Re: [AMBER] Water-slab at constant pressure David A Case (Tue Dec 19 2017 - 05:21:58 PST)
[AMBER] box coordinates of the trajectory Leena Aggarwal (Mon Dec 18 2017 - 20:44:32 PST)
- Re: [AMBER] box coordinates of the trajectory Bill Ross (Mon Dec 18 2017 - 20:47:51 PST)
- [AMBER] [MGMS-DS]: Molecular Modelling Workshop March 12-14, 2018 in Erlangen, Germany Dr. Anselm Horn (Tue Dec 19 2017 - 01:36:28 PST)
- Re: [AMBER] box coordinates of the trajectory Daniel Roe (Tue Dec 19 2017 - 06:19:43 PST)
[AMBER] more than 100% hydrogen bond population Thakur, Abhishek (Wed Dec 20 2017 - 12:38:59 PST)
- Re: [AMBER] more than 100% hydrogen bond population Daniel Roe (Tue Jan 16 2018 - 06:57:32 PST)
[AMBER] error in distance restraints Michael Shokhen (Wed Dec 20 2017 - 13:40:03 PST)
- Re: [AMBER] error in distance restraints David A Case (Wed Dec 20 2017 - 18:53:56 PST)
[AMBER] Function name not recognized in RdPar Rinsha Chk (Thu Dec 21 2017 - 00:24:53 PST)
- Re: [AMBER] Function name not recognized in RdPar David A Case (Thu Dec 21 2017 - 05:13:14 PST)
  - Re: [AMBER] Function name not recognized in RdPar Rinsha Chk (Thu Dec 21 2017 - 05:20:48 PST)
    - Re: [AMBER] Function name not recognized in RdPar Rinsha Chk (Thu Dec 21 2017 - 05:21:45 PST)
[AMBER] parmed error Thakur, Abhishek (Thu Dec 21 2017 - 10:44:56 PST)
- Re: [AMBER] parmed error p.kartheek (Thu Dec 21 2017 - 11:26:16 PST)
- Re: [AMBER] parmed error Hai Nguyen (Thu Dec 21 2017 - 18:53:52 PST)
[AMBER] Binding energy of ligand with homology model Morrow,John Kenneth (Thu Dec 21 2017 - 11:45:31 PST)
- Re: [AMBER] Binding energy of ligand with homology model Daniel Mermelstein (Wed Jan 03 2018 - 13:31:50 PST)
[AMBER] Atom restraints in AMBER Nikolay N. Kuzmich (Fri Dec 22 2017 - 00:29:09 PST)
[AMBER] Meltcurve cpptraj Andreas Tosstorff (Fri Dec 22 2017 - 02:17:26 PST)
- Re: [AMBER] Meltcurve cpptraj Daniel Roe (Fri Dec 22 2017 - 05:34:42 PST)
[AMBER] hbond occupancy plot cpptraj Rana Rehan Khalid (Sat Dec 23 2017 - 17:38:35 PST)
- Re: [AMBER] hbond occupancy plot cpptraj Rana Rehan Khalid (Sun Dec 24 2017 - 04:45:38 PST)
[AMBER] Can tLeap read SCNB and SCEE vales from frcmod file ? mish (Tue Dec 26 2017 - 00:09:35 PST)
- Re: [AMBER] Can tLeap read SCNB and SCEE vales from frcmod file ? David Cerutti (Tue Dec 26 2017 - 06:12:01 PST)
  - Re: [AMBER] Can tLeap read SCNB and SCEE vales from frcmod file ? mish (Tue Dec 26 2017 - 16:12:02 PST)
    - Re: [AMBER] Can tLeap read SCNB and SCEE vales from frcmod file ? Bill Ross (Tue Dec 26 2017 - 16:14:03 PST)
    - Re: [AMBER] Can tLeap read SCNB and SCEE vales from frcmod file ? mish (Tue Dec 26 2017 - 16:27:32 PST)
    - Re: [AMBER] Can tLeap read SCNB and SCEE vales from frcmod file ? Lachele Foley (Tue Dec 26 2017 - 19:51:32 PST)
    - Re: [AMBER] Can tLeap read SCNB and SCEE vales from frcmod file ? mish (Tue Dec 26 2017 - 20:10:40 PST)
    - Re: [AMBER] Can tLeap read SCNB and SCEE vales from frcmod file ? Lachele Foley (Tue Dec 26 2017 - 20:22:42 PST)
    - Re: [AMBER] Can tLeap read SCNB and SCEE vales from frcmod file ? mish (Tue Dec 26 2017 - 20:36:44 PST)
    - Re: [AMBER] Can tLeap read SCNB and SCEE vales from frcmod file ? Lachele Foley (Tue Dec 26 2017 - 20:42:38 PST)
    - Re: [AMBER] Can tLeap read SCNB and SCEE vales from frcmod file ? mish (Tue Dec 26 2017 - 20:56:13 PST)
    - Re: [AMBER] Can tLeap read SCNB and SCEE vales from frcmod file ? Bill Ross (Tue Dec 26 2017 - 21:06:38 PST)
    - Re: [AMBER] Can tLeap read SCNB and SCEE vales from frcmod file ? mish (Tue Dec 26 2017 - 21:09:11 PST)
    - Re: [AMBER] Can tLeap read SCNB and SCEE vales from frcmod file ? Lachele Foley (Wed Dec 27 2017 - 00:36:04 PST)
    - Re: [AMBER] Can tLeap read SCNB and SCEE vales from frcmod file ? Bill Ross (Wed Dec 27 2017 - 00:44:40 PST)
    - Re: [AMBER] Can tLeap read SCNB and SCEE vales from frcmod file ? Lachele Foley (Wed Dec 27 2017 - 00:55:41 PST)
    - Re: [AMBER] Can tLeap read SCNB and SCEE vales from frcmod file ? mish (Wed Dec 27 2017 - 04:23:05 PST)
    - Re: [AMBER] Can tLeap read SCNB and SCEE vales from frcmod file ? Lachele Foley (Wed Dec 27 2017 - 22:46:35 PST)
    - Re: [AMBER] Can tLeap read SCNB and SCEE vales from frcmod file ? mish (Thu Dec 28 2017 - 00:49:43 PST)
    - Re: [AMBER] Can tLeap read SCNB and SCEE vales from frcmod file ? Lachele Foley (Thu Dec 28 2017 - 22:30:44 PST)
[AMBER] Fwd: A small but fatal Typo in "LEaP Tutorial" Gao Zhenting (Tue Dec 26 2017 - 01:01:24 PST)
- Re: [AMBER] A small but fatal Typo in "LEaP Tutorial" Pengfei Li (Tue Dec 26 2017 - 09:49:18 PST)
  - Re: [AMBER] A small but fatal Typo in "LEaP Tutorial" Gao Zhenting (Tue Dec 26 2017 - 18:16:48 PST)
[AMBER] Unable to compile mixed C/Fortran code. suma jayakrishnan (Tue Dec 26 2017 - 03:53:18 PST)
- Re: [AMBER] Unable to compile mixed C/Fortran code. Bill Ross (Tue Dec 26 2017 - 04:18:48 PST)
- Re: [AMBER] Unable to compile mixed C/Fortran code. David A Case (Tue Dec 26 2017 - 06:04:03 PST)
[AMBER] Troubling changes to NVIDIA Driver EULA Ross Walker (Tue Dec 26 2017 - 08:07:25 PST)
- Re: [AMBER] Troubling changes to NVIDIA Driver EULA Charles-Alexandre Mattelaer (Tue Dec 26 2017 - 08:29:27 PST)
  - Re: [AMBER] Troubling changes to NVIDIA Driver EULA David Cerutti (Tue Dec 26 2017 - 09:54:02 PST)
  - Re: [AMBER] Troubling changes to NVIDIA Driver EULA Ross Walker (Tue Dec 26 2017 - 11:57:10 PST)
    - Re: [AMBER] Troubling changes to NVIDIA Driver EULA David Cerutti (Tue Dec 26 2017 - 12:11:26 PST)
    - Re: [AMBER] Troubling changes to NVIDIA Driver EULA Ross Walker (Tue Dec 26 2017 - 15:43:22 PST)
    - Re: [AMBER] Troubling changes to NVIDIA Driver EULA Bill Ross (Tue Dec 26 2017 - 16:01:20 PST)
    - Re: [AMBER] Troubling changes to NVIDIA Driver EULA Robert Molt (Tue Dec 26 2017 - 17:24:57 PST)
    - Re: [AMBER] Troubling changes to NVIDIA Driver EULA Bill Ross (Tue Dec 26 2017 - 16:09:58 PST)
[AMBER] Which potential is used in TIP3P (How to calculate EPot by hand) Johannes Kalliauer (Wed Dec 27 2017 - 05:00:32 PST)
- Re: [AMBER] Which potential is used in TIP3P (How to calculate EPot by hand) David Cerutti (Wed Dec 27 2017 - 05:34:42 PST)
- Re: [AMBER] Which potential is used in TIP3P (How to calculate EPot by hand) David A Case (Wed Dec 27 2017 - 06:00:58 PST)
[AMBER] NTWR,NTWX, NTPR increases for rest of simulation. Rana Rehan Khalid (Wed Dec 27 2017 - 12:47:14 PST)
- Re: [AMBER] NTWR,NTWX, NTPR increases for rest of simulation. David A Case (Wed Dec 27 2017 - 14:16:55 PST)
  - Re: [AMBER] NTWR,NTWX, NTPR increases for rest of simulation. Rana Rehan Khalid (Wed Dec 27 2017 - 14:19:44 PST)
[AMBER] Phosphohistidine residues Jan Ludwiczak (Thu Dec 28 2017 - 08:34:50 PST)
[AMBER] CPPTRAJ HBOND Rana Rehan Khalid (Fri Dec 29 2017 - 05:40:31 PST)
- Re: [AMBER] CPPTRAJ HBOND Daniel Roe (Fri Dec 29 2017 - 05:51:28 PST)
  - Re: [AMBER] CPPTRAJ HBOND Charles-Alexandre Mattelaer (Fri Dec 29 2017 - 05:58:47 PST)
    - Re: [AMBER] CPPTRAJ HBOND Rana Rehan Khalid (Fri Dec 29 2017 - 08:26:26 PST)
    - Re: [AMBER] CPPTRAJ HBOND Daniel Roe (Tue Jan 02 2018 - 10:21:00 PST)
[AMBER] DSSP CPPtraj Rana Rehan Khalid (Sun Dec 31 2017 - 06:27:35 PST)
- Re: [AMBER] DSSP CPPtraj Rana Rehan Khalid (Sun Dec 31 2017 - 07:05:20 PST)
  - Re: [AMBER] DSSP CPPtraj Daniel Roe (Tue Jan 02 2018 - 10:12:51 PST)
[AMBER] AMBER intelmpi installation on cluster Simon Kit Sang Chu (Mon Jan 01 2018 - 22:31:51 PST)
- Re: [AMBER] AMBER intelmpi installation on cluster Qinghua Liao (Tue Jan 02 2018 - 02:30:24 PST)
- Re: [AMBER] AMBER intelmpi installation on cluster Simon Kit Sang Chu (Tue Jan 02 2018 - 19:48:28 PST)
[AMBER] LIPID17 reference ? Marek Maly (Wed Jan 03 2018 - 05:37:01 PST)
- Re: [AMBER] LIPID17 reference ? Ross Walker (Wed Jan 03 2018 - 06:32:42 PST)
  - Re: [AMBER] LIPID17 reference ? Marek Maly (Wed Jan 03 2018 - 07:32:39 PST)
[AMBER] Trying to use AMBER parameters in GROMACS Crystal Vander Zanden (Wed Jan 03 2018 - 08:49:35 PST)
- Re: [AMBER] Trying to use AMBER parameters in GROMACS Jason Swails (Fri Jan 05 2018 - 21:18:04 PST)
  - Re: [AMBER] Trying to use AMBER parameters in GROMACS Jason Swails (Fri Jan 05 2018 - 21:18:37 PST)
[AMBER] Distance calculation between atoms from two different frames using CPPTRAJ anu chandra (Thu Jan 04 2018 - 03:41:56 PST)
- Re: [AMBER] Distance calculation between atoms from two different frames using CPPTRAJ Daniel Roe (Thu Jan 04 2018 - 06:00:38 PST)
  - Re: [AMBER] Distance calculation between atoms from two different frames using CPPTRAJ anu chandra (Fri Jan 05 2018 - 02:35:32 PST)
[AMBER] Which command to use for printing X Y Z coordinates of the given atom ? Marek Maly (Thu Jan 04 2018 - 17:54:07 PST)
- Re: [AMBER] Which command to use for printing X Y Z coordinates of the given atom ? Hai Nguyen (Thu Jan 04 2018 - 19:09:03 PST)
- Re: [AMBER] Which command to use for printing X Y Z coordinates of the given atom ? Daniel Roe (Fri Jan 05 2018 - 06:02:50 PST)
[AMBER] Problem regarding compiling in cpptraj with openmp Saikat Pal (Thu Jan 04 2018 - 22:54:54 PST)
- Re: [AMBER] Problem regarding compiling in cpptraj with openmp Bill Ross (Thu Jan 04 2018 - 22:58:35 PST)
- Re: [AMBER] Problem regarding compiling in cpptraj with openmp Bill Ross (Thu Jan 04 2018 - 23:05:53 PST)
  - Re: [AMBER] Problem regarding compiling in cpptraj with openmp Saikat Pal (Thu Jan 04 2018 - 23:32:17 PST)
    - Re: [AMBER] Problem regarding compiling in cpptraj with openmp Bill Ross (Thu Jan 04 2018 - 23:58:52 PST)
- Re: [AMBER] Problem regarding compiling in cpptraj with openmp Daniel Roe (Fri Jan 05 2018 - 05:37:47 PST)
[AMBER] Density equilibration Thomas Exner (Fri Jan 05 2018 - 07:21:47 PST)
- Re: [AMBER] Density equilibration Thomas Exner (Sat Jan 06 2018 - 04:23:48 PST)
[AMBER] qm2_extern_gau_module Thakur, Abhishek (Fri Jan 05 2018 - 11:46:50 PST)
- Re: [AMBER] qm2_extern_gau_module David A Case (Fri Jan 05 2018 - 12:04:18 PST)
  - Re: [AMBER] qm2_extern_gau_module Thakur, Abhishek (Fri Jan 05 2018 - 12:12:03 PST)
    - Re: [AMBER] qm2_extern_gau_module Goetz, Andreas (Fri Jan 05 2018 - 13:37:55 PST)
- Re: [AMBER] qm2_extern_gau_module David Poole (Sat Jan 06 2018 - 14:42:09 PST)
  - Re: [AMBER] qm2_extern_gau_module David Poole (Sat Jan 06 2018 - 14:48:40 PST)
    - Re: [AMBER] qm2_extern_gau_module Thakur, Abhishek (Tue Jan 09 2018 - 08:49:59 PST)
- Re: [AMBER] qm2_extern_gau_module Thakur, Abhishek (Tue Jan 09 2018 - 09:11:29 PST)
[AMBER] xmgr x-axis change to ns. Rana Rehan Khalid (Sat Jan 06 2018 - 08:30:31 PST)
- Re: [AMBER] xmgr x-axis change to ns. MOHD HOMAIDUR RAHMAN (Sun Jan 07 2018 - 01:26:07 PST)
  - Re: [AMBER] xmgr x-axis change to ns. Rana Rehan Khalid (Sun Jan 07 2018 - 06:55:43 PST)
  - Re: [AMBER] xmgr x-axis change to ns. Rana Rehan Khalid (Sun Jan 07 2018 - 09:25:41 PST)
[AMBER] Minimization Problem(error shows "... RESTARTED DUE TO LINMIN FAILURE ..." ) Malay Raul (Sat Jan 06 2018 - 13:05:13 PST)
- Re: [AMBER] Minimization Problem(error shows "... RESTARTED DUE TO LINMIN FAILURE ..." ) David A Case (Sun Jan 07 2018 - 05:37:14 PST)
- Re: [AMBER] Minimization Problem(error shows "... RESTARTED DUE TO LINMIN FAILURE ..." ) Malay Raul (Sun Jan 07 2018 - 12:28:38 PST)
  - Re: [AMBER] Minimization Problem(error shows "... RESTARTED DUE TO LINMIN FAILURE ..." ) David A Case (Sun Jan 07 2018 - 17:41:19 PST)
[AMBER] Announcement: AMBER Molecular Dynamics Workshop 2018 Fabian Glaser (Sun Jan 07 2018 - 06:37:11 PST)
[AMBER] resources for summer researches Mahendra B Thapa (Mon Jan 08 2018 - 10:35:33 PST)
[AMBER] REMD job stops on loadleveler Andreas Tosstorff (Mon Jan 08 2018 - 11:56:21 PST)
- Re: [AMBER] REMD job stops on loadleveler David A Case (Tue Jan 09 2018 - 08:23:42 PST)
[AMBER] Error during the MMPBSA calculation -reg. Jeyaram R A (Mon Jan 08 2018 - 20:34:04 PST)
[AMBER] Regarding error in preparation of HEME via MCPB.py Aashish Bhatt (Mon Jan 08 2018 - 20:47:34 PST)
- Re: [AMBER] Regarding error in preparation of HEME via MCPB.py Pengfei Li (Tue Jan 16 2018 - 12:07:04 PST)
  - Re: [AMBER] Regarding error in preparation of HEME via MCPB.py Aashish Bhatt (Mon Jan 22 2018 - 03:33:43 PST)
    - Re: [AMBER] Regarding error in preparation of HEME via MCPB.py Pengfei Li (Thu Jan 25 2018 - 10:34:38 PST)
    - Re: [AMBER] Regarding error in preparation of HEME via MCPB.py Aashish Bhatt (Thu Jan 25 2018 - 22:47:02 PST)
    - Re: [AMBER] Regarding error in preparation of HEME via MCPB.py Pengfei Li (Wed Jan 31 2018 - 07:37:11 PST)
[AMBER] DNA melting temperature Marie Brut (Tue Jan 09 2018 - 01:16:13 PST)
- Re: [AMBER] DNA melting temperature matheus froeyen (Tue Jan 09 2018 - 02:56:32 PST)
[AMBER] prmtop.pdf %FLAG SCREEN Johannes Kalliauer (Tue Jan 09 2018 - 04:53:21 PST)
- Re: [AMBER] prmtop.pdf %FLAG SCREEN David A Case (Wed Jan 10 2018 - 10:53:08 PST)
[AMBER] Hydrophobic interaction VS time in protein interfaces Jag Silwal (Tue Jan 09 2018 - 08:45:38 PST)
[AMBER] Atom restraints in AMBER Nikolay N. Kuzmich (Tue Jan 09 2018 - 18:33:02 PST)
[AMBER] AMBER workshop registration opened, 4-8 March, Technion, Israel Fabian Glaser (Wed Jan 10 2018 - 00:07:14 PST)
[AMBER] cpptraj.OMP vs cpptraj Saikat Pal (Wed Jan 10 2018 - 03:06:25 PST)
- Re: [AMBER] cpptraj.OMP vs cpptraj Daniel Roe (Wed Jan 10 2018 - 06:20:43 PST)
[AMBER] ligand outside the binding site - vmd visualisation problem M. Pyrka (Wed Jan 10 2018 - 03:47:50 PST)
- Re: [AMBER] ligand outside the binding site - vmd visualisation problem David A Case (Wed Jan 10 2018 - 05:19:08 PST)
[AMBER] gnuplot x-axis represented the number of frames how to convert it in nano second time. Rana Rehan Khalid (Wed Jan 10 2018 - 05:44:48 PST)
- Re: [AMBER] gnuplot x-axis represented the number of frames how to convert it in nano second time. Qinghua Liao (Wed Jan 10 2018 - 05:47:34 PST)
- Re: [AMBER] gnuplot x-axis represented the number of frames how to convert it in nano second time. Daniel Roe (Wed Jan 10 2018 - 06:13:52 PST)
  - Re: [AMBER] gnuplot x-axis represented the number of frames how to convert it in nano second time. Rana Rehan Khalid (Wed Jan 10 2018 - 06:53:21 PST)
    - Re: [AMBER] gnuplot x-axis represented the number of frames how to convert it in nano second time. Daniel Roe (Wed Jan 10 2018 - 07:00:13 PST)
    - Re: [AMBER] gnuplot x-axis represented the number of frames how to convert it in nano second time. Rana Rehan Khalid (Wed Jan 10 2018 - 07:02:00 PST)
[AMBER] use_template = 0 Thakur, Abhishek (Wed Jan 10 2018 - 08:34:27 PST)
- Re: [AMBER] use_template = 0 David A Case (Wed Jan 10 2018 - 08:43:19 PST)
  - Re: [AMBER] use_template = 0 Thakur, Abhishek (Wed Jan 10 2018 - 09:02:54 PST)
  - Re: [AMBER] use_template = 0 Thakur, Abhishek (Wed Jan 10 2018 - 09:04:20 PST)
[AMBER] pseudo-trajectory in pytraj Abdul-Rashid III Sampaco (Wed Jan 10 2018 - 09:04:17 PST)
- Re: [AMBER] pseudo-trajectory in pytraj Hai Nguyen (Wed Jan 10 2018 - 09:54:33 PST)
[AMBER] QM/MM MD B3LYP Thakur, Abhishek (Wed Jan 10 2018 - 09:25:05 PST)
[AMBER] QM/MM MD B3LYP Thakur, Abhishek (Wed Jan 10 2018 - 09:35:29 PST)
- Re: [AMBER] QM/MM MD B3LYP Marcelo Andrade Chagas (Wed Jan 10 2018 - 09:43:58 PST)
  - Re: [AMBER] QM/MM MD B3LYP Thakur, Abhishek (Wed Jan 10 2018 - 10:02:51 PST)
    - Re: [AMBER] QM/MM MD B3LYP Goetz, Andreas (Wed Jan 10 2018 - 21:00:20 PST)
[AMBER] OS High Sierra Hallel Freedman (Wed Jan 10 2018 - 16:36:51 PST)
- Re: [AMBER] OS High Sierra David A Case (Thu Jan 11 2018 - 04:32:41 PST)
  - Re: [AMBER] OS High Sierra Hallel Freedman (Fri Jan 26 2018 - 07:32:39 PST)
[AMBER] error during MMPBSA calculation -reg. Jeyaram R A (Wed Jan 10 2018 - 23:06:16 PST)
[AMBER] constant pH md Maciej Maciejczyk (Wed Jan 10 2018 - 23:44:21 PST)
- Re: [AMBER] constant pH md Cruzeiro,Vinicius Wilian D (Thu Jan 11 2018 - 04:04:06 PST)
  - Re: [AMBER] constant pH md Maciej Maciejczyk (Thu Jan 11 2018 - 04:52:16 PST)
- Re: [AMBER] constant pH md Jason Swails (Mon Jan 15 2018 - 18:33:10 PST)
  - Re: [AMBER] constant pH md Daniel Roe (Tue Jan 16 2018 - 06:44:08 PST)
    - Re: [AMBER] constant pH md Jason Swails (Tue Jan 16 2018 - 06:59:52 PST)
[AMBER] MMGBSA calculation gives very high positive free energy of binding!!! Sandip Mondal (Thu Jan 11 2018 - 01:41:12 PST)
- Re: [AMBER] MMGBSA calculation gives very high positive free energy of binding!!! David A Case (Thu Jan 11 2018 - 04:38:49 PST)
[AMBER] scaling of electrostatic interactions Antonija Tomić (Thu Jan 11 2018 - 02:18:00 PST)
- Re: [AMBER] scaling of electrostatic interactions Lorenzo Gontrani (Thu Jan 11 2018 - 02:19:49 PST)
  - Re: [AMBER] scaling of electrostatic interactions Antonija Tomić (Thu Jan 11 2018 - 02:49:12 PST)
[AMBER] error 12-6-4 LJ with the last update (November 2017) Davide Sala (Thu Jan 11 2018 - 02:53:31 PST)
- Re: [AMBER] error 12-6-4 LJ with the last update (November 2017) David A Case (Thu Jan 11 2018 - 04:52:39 PST)
  - Re: [AMBER] error 12-6-4 LJ with the last update (November 2017) Davide Sala (Thu Jan 11 2018 - 05:49:23 PST)
    - Re: [AMBER] error 12-6-4 LJ with the last update (November 2017) Qinghua Liao (Thu Jan 11 2018 - 05:51:52 PST)
    - Re: [AMBER] error 12-6-4 LJ with the last update (November 2017) David Cerutti (Thu Jan 11 2018 - 10:55:34 PST)
    - Re: [AMBER] error 12-6-4 LJ with the last update (November 2017) Pengfei Li (Tue Jan 16 2018 - 13:54:47 PST)
    - Re: [AMBER] error 12-6-4 LJ with the last update (November 2017) Pengfei Li (Tue Jan 16 2018 - 14:01:32 PST)
    - Re: [AMBER] error 12-6-4 LJ with the last update (November 2017) Jason Swails (Thu Jan 18 2018 - 10:49:44 PST)
[AMBER] AMBER GPU-TI implementation - paper? Hadházi Ádám (Thu Jan 11 2018 - 05:37:07 PST)
- Re: [AMBER] AMBER GPU-TI implementation - paper? Darrin York (Thu Jan 11 2018 - 06:16:02 PST)
  - Re: [AMBER] AMBER GPU-TI implementation - paper? Hadházi Ádám (Thu Jan 11 2018 - 06:26:51 PST)
    - Re: [AMBER] AMBER GPU-TI implementation - paper? Darrin York (Thu Jan 11 2018 - 06:46:03 PST)
[AMBER] Replica exchange thermodynamic integration in AMBER Roma Mukhopadhyay (Thu Jan 11 2018 - 15:45:55 PST)
- Re: [AMBER] Replica exchange thermodynamic integration in AMBER Jason Swails (Thu Jan 18 2018 - 10:51:15 PST)
[AMBER] Amber 16.12 and 12-6-4 force field Problem Guanglin Kuang (Thu Jan 11 2018 - 18:49:22 PST)
- Re: [AMBER] Amber 16.12 and 12-6-4 force field Problem David Cerutti (Thu Jan 11 2018 - 21:11:55 PST)
  - Re: [AMBER] Amber 16.12 and 12-6-4 force field Problem Guanglin Kuang (Thu Jan 11 2018 - 22:01:56 PST)
    - Re: [AMBER] Amber 16.12 and 12-6-4 force field Problem Ross Walker (Sat Jan 13 2018 - 12:10:01 PST)
    - Re: [AMBER] Amber 16.12 and 12-6-4 force field Problem Pengfei Li (Sat Jan 13 2018 - 18:40:07 PST)
    - Re: [AMBER] Amber 16.12 and 12-6-4 force field Problem Chris Neale (Sat Jan 13 2018 - 19:01:44 PST)
    - Re: [AMBER] Amber 16.12 and 12-6-4 force field Problem Ross Walker (Sat Jan 13 2018 - 20:19:32 PST)
    - Re: [AMBER] Amber 16.12 and 12-6-4 force field Problem Jason Swails (Thu Jan 18 2018 - 19:14:06 PST)
[AMBER] Amber mailing list Angela dos Reis (Fri Jan 12 2018 - 17:54:16 PST)
- Re: [AMBER] Amber mailing list David A Case (Sat Jan 13 2018 - 06:01:31 PST)
[AMBER] going away for now Bill Ross (Fri Jan 12 2018 - 18:26:01 PST)
[AMBER] RESP charges for capped C termimal glycine: NHCH2CONH2 ABEL Stephane (Sat Jan 13 2018 - 05:50:17 PST)
- Re: [AMBER] RESP charges for capped C termimal glycine: NHCH2CONH2 David Cerutti (Sat Jan 13 2018 - 20:33:57 PST)
  - Re: [AMBER] RESP charges for capped C termimal glycine: NHCH2CONH2 ABEL Stephane (Sun Jan 14 2018 - 04:02:05 PST)
  - Re: [AMBER] RESP charges for capped C termimal glycine: NHCH2CONH2 David A Case (Sun Jan 14 2018 - 06:01:30 PST)
Re: [AMBER] Fwd: Hydrophobic interaction VS time in protein interfaces Jag Silwal (Sun Jan 14 2018 - 09:06:44 PST)
- Re: [AMBER] Fwd: Hydrophobic interaction VS time in protein interfaces Szymon Żaczek (Mon Jan 15 2018 - 03:10:45 PST)
- Re: [AMBER] Fwd: Hydrophobic interaction VS time in protein interfaces Daniel Roe (Tue Jan 16 2018 - 06:41:52 PST)
[AMBER] H-bond analysis in tetrameric protein complexes Jag Silwal (Mon Jan 15 2018 - 13:09:44 PST)
- Re: [AMBER] H-bond analysis in tetrameric protein complexes Daniel Roe (Tue Jan 16 2018 - 06:42:37 PST)
[AMBER] distance to center of geometry Meng Wu (Mon Jan 15 2018 - 19:27:06 PST)
- Re: [AMBER] distance to center of geometry David Cerutti (Mon Jan 15 2018 - 21:31:05 PST)
- Re: [AMBER] distance to center of geometry Daniel Roe (Tue Jan 16 2018 - 06:46:05 PST)
[AMBER] email khair.bux.iccs.edu (Tue Jan 16 2018 - 01:58:45 PST)
[AMBER] Reorienting the protein during simulation Ahmed Mashaly (Tue Jan 16 2018 - 02:52:20 PST)
- Re: [AMBER] Reorienting the protein during simulation Daniel Roe (Tue Jan 16 2018 - 06:54:33 PST)
  - Re: [AMBER] Reorienting the protein during simulation Ahmed Mashaly (Wed Jan 17 2018 - 02:39:01 PST)
    - Re: [AMBER] Reorienting the protein during simulation Daniel Roe (Wed Jan 17 2018 - 07:55:13 PST)
    - Re: [AMBER] Reorienting the protein during simulation Ahmed Mashaly (Fri Jan 19 2018 - 08:25:22 PST)
    - Re: [AMBER] Reorienting the protein during simulation Daniel Roe (Thu Feb 01 2018 - 05:59:19 PST)
[AMBER] leap Lara rajam (Tue Jan 16 2018 - 09:26:39 PST)
- Re: [AMBER] leap Szymon Żaczek (Tue Jan 16 2018 - 11:32:33 PST)
[AMBER] MD run saving only 250 frames Paul Meister (Tue Jan 16 2018 - 11:58:00 PST)
- Re: [AMBER] MD run saving only 250 frames Jeyaram R A (Tue Jan 16 2018 - 23:14:29 PST)
[AMBER] Errors in my installation Bhargava Sai M (Tue Jan 16 2018 - 20:52:23 PST)
- Re: [AMBER] Errors in my installation Hai Nguyen (Wed Jan 17 2018 - 14:38:08 PST)
  - Re: [AMBER] Errors in my installation Bhargava Sai M (Wed Jan 17 2018 - 21:29:09 PST)
[AMBER] Error during MMPBSA calculation -reg. Jeyaram R A (Wed Jan 17 2018 - 03:40:01 PST)
[AMBER] AMBER tools 17 installation problem maryam azimzadehirani (Wed Jan 17 2018 - 08:20:45 PST)
- Re: [AMBER] AMBER tools 17 installation problem Hai Nguyen (Wed Jan 17 2018 - 14:36:02 PST)
- Re: [AMBER] AMBER tools 17 installation problem David A Case (Wed Jan 17 2018 - 15:52:33 PST)
[AMBER] umbrella sampling process krishna.2015.iitg.ernet.in (Wed Jan 17 2018 - 10:04:33 PST)
- Re: [AMBER] umbrella sampling process Andreas Tosstorff (Wed Jan 17 2018 - 10:22:50 PST)
[AMBER] Crystal water in Amber 16 Yuliana Bosken (Wed Jan 17 2018 - 21:12:45 PST)
- Re: [AMBER] Crystal water in Amber 16 Hai Nguyen (Wed Jan 17 2018 - 22:05:47 PST)
  - Re: [AMBER] Crystal water in Amber 16 Yuliana Bosken (Thu Jan 18 2018 - 04:33:10 PST)
    - Re: [AMBER] Crystal water in Amber 16 David A Case (Thu Jan 18 2018 - 05:23:47 PST)
    - Re: [AMBER] Crystal water in Amber 16 Yuliana Bosken (Sun Jan 21 2018 - 13:14:33 PST)
[AMBER] Change a residue in a protein David Sáez (Thu Jan 18 2018 - 00:45:47 PST)
[AMBER] AMBER - QMMM with DFTB daniele selli (Thu Jan 18 2018 - 01:59:50 PST)
- Re: [AMBER] AMBER - QMMM with DFTB Gustavo Seabra (Thu Jan 18 2018 - 05:22:47 PST)
  - Re: [AMBER] AMBER - QMMM with DFTB Goetz, Andreas (Thu Jan 18 2018 - 11:29:21 PST)
[AMBER] AmberTools with Amber11 Jennifer L. Muzyka (Thu Jan 18 2018 - 11:35:22 PST)
- Re: [AMBER] AmberTools with Amber11 Jason Swails (Thu Jan 18 2018 - 18:58:47 PST)
[AMBER] MMGBSA calculations with explicit water molecules Marawan Hussien (Thu Jan 18 2018 - 12:14:15 PST)
- Re: [AMBER] MMGBSA calculations with explicit water molecules Jason Swails (Sat Jan 20 2018 - 18:06:23 PST)
[AMBER] MCPB Thakur, Abhishek (Thu Jan 18 2018 - 14:23:49 PST)
- Re: [AMBER] MCPB Pengfei Li (Fri Jan 19 2018 - 11:21:05 PST)
[AMBER] Patent to solve floating point errors Kenneth McGuinness (Thu Jan 18 2018 - 14:41:33 PST)
[AMBER] Ligand modifying softwares. Vatsal Purohit (Thu Jan 18 2018 - 20:23:21 PST)
- Re: [AMBER] Ligand modifying softwares. Bakary N'tji Diallo (Fri Jan 19 2018 - 01:21:54 PST)
- Re: [AMBER] Ligand modifying softwares. Luka Bilić (Fri Jan 19 2018 - 01:28:01 PST)
[AMBER] Mail from "Dr. MANAS MONDAL" <manas.pku.edu.cn>. Dr. MANAS MONDAL (Fri Jan 19 2018 - 01:48:01 PST)
- Re: [AMBER] Mail from "Dr. MANAS MONDAL" <manas.pku.edu.cn>. Daniel Roe (Fri Jan 19 2018 - 05:31:13 PST)
[AMBER] Parametrization of new amino acid in methanol solvent Chetna Tyagi (Fri Jan 19 2018 - 04:10:51 PST)
- Re: [AMBER] Parametrization of new amino acid in methanol solvent Alessandro Contini (Fri Jan 19 2018 - 05:03:50 PST)
[AMBER] Amber 18 Qinghua Liao (Fri Jan 19 2018 - 04:47:44 PST)
- Re: [AMBER] Amber 18 David A Case (Fri Jan 19 2018 - 06:55:56 PST)
  - Re: [AMBER] Amber 18 Qinghua Liao (Fri Jan 19 2018 - 07:32:36 PST)
[AMBER] error during MMPBSA-reg Jeyaram R A (Fri Jan 19 2018 - 06:47:34 PST)
[AMBER] CPPTRAJ-Angle between two Helices Jag Silwal (Fri Jan 19 2018 - 10:23:06 PST)
- Re: [AMBER] CPPTRAJ-Angle between two Helices Daniel Roe (Fri Jan 19 2018 - 12:24:10 PST)
  - Re: [AMBER] CPPTRAJ-Angle between two Helices Arati Paudyal (Fri Jan 19 2018 - 13:15:42 PST)
    - Re: [AMBER] CPPTRAJ-Angle between two Helices Daniel Roe (Fri Jan 19 2018 - 14:39:24 PST)
  - Re: [AMBER] CPPTRAJ-Angle between two Helices Jag Silwal (Fri Jan 19 2018 - 13:17:03 PST)
[AMBER] Installation - NetCDF C compile failed Jiří Dluhoš (Fri Jan 19 2018 - 10:23:31 PST)
- Re: [AMBER] Installation - NetCDF C compile failed Hai Nguyen (Fri Jan 19 2018 - 10:25:13 PST)
- Re: [AMBER] Installation - NetCDF C compile failed Jiří Dluhoš (Fri Jan 19 2018 - 10:35:27 PST)
  - Re: [AMBER] Installation - NetCDF C compile failed Daniel Roe (Fri Jan 19 2018 - 11:35:03 PST)
- Re: [AMBER] Installation - NetCDF C compile failed Jiří Dluhoš (Fri Jan 19 2018 - 12:13:19 PST)
  - Re: [AMBER] Installation - NetCDF C compile failed Daniel Roe (Fri Jan 19 2018 - 12:30:06 PST)
    - Re: [AMBER] Installation - NetCDF C compile failed David A Case (Sat Jan 20 2018 - 07:29:35 PST)
    - Re: [AMBER] Installation - NetCDF C compile failed David A Case (Sat Jan 20 2018 - 14:41:41 PST)
- Re: [AMBER] Installation - NetCDF C compile failed Jiří Dluhoš (Sat Jan 20 2018 - 14:15:12 PST)
  - Re: [AMBER] Installation - NetCDF C compile failed Hai Nguyen (Sat Jan 20 2018 - 15:39:06 PST)
[AMBER] PB Bomb in pb_aaradi(): No radius assigned for atom 7 CB 3C Morrow,John Kenneth (Fri Jan 19 2018 - 15:14:12 PST)
- Re: [AMBER] PB Bomb in pb_aaradi(): No radius assigned for atom 7 CB 3C Ray Luo (Fri Jan 19 2018 - 15:57:11 PST)
  - Re: [AMBER] PB Bomb in pb_aaradi(): No radius assigned for atom 7 CB 3C Morrow,John Kenneth (Sat Jan 27 2018 - 06:03:46 PST)
    - Re: [AMBER] PB Bomb in pb_aaradi(): No radius assigned for atom 7 CB 3C Morrow,John Kenneth (Sun Feb 11 2018 - 14:08:57 PST)
    - Re: [AMBER] PB Bomb in pb_aaradi(): No radius assigned for atom 7 CB 3C Ray Luo (Sun Feb 11 2018 - 17:40:18 PST)
    - Re: [AMBER] PB Bomb in pb_aaradi(): No radius assigned for atom 7 CB 3C Morrow,John Kenneth (Thu Mar 01 2018 - 14:15:24 PST)
    - Re: [AMBER] PB Bomb in pb_aaradi(): No radius assigned for atom 7 CB 3C Ray Luo (Thu Mar 01 2018 - 16:56:52 PST)
[AMBER] fatty acid ligand comes out of binding site during md. Saman Yousuf ali (Sat Jan 20 2018 - 05:43:11 PST)
- Re: [AMBER] fatty acid ligand comes out of binding site during md. Daniel Roe (Tue Jan 23 2018 - 08:36:47 PST)
[AMBER] PROBLEM ENCOUNTERED WHILE UNDERGOING TUTUORIAL FOR ROOM TEMPERATURE IONIC LIQUID. Suman Bhaumik (Sun Jan 21 2018 - 01:46:05 PST)
- Re: [AMBER] PROBLEM ENCOUNTERED WHILE UNDERGOING TUTUORIAL FOR ROOM TEMPERATURE IONIC LIQUID. David A Case (Mon Jan 22 2018 - 05:33:32 PST)
- Re: [AMBER] PROBLEM ENCOUNTERED WHILE UNDERGOING TUTUORIAL FOR ROOM TEMPERATURE IONIC LIQUID. Markowska (Mon Jan 22 2018 - 05:55:55 PST)
[AMBER] Non-PBC simulation in a droplet made of organic solvent Veronika Jurásková (Mon Jan 22 2018 - 02:13:49 PST)
- Re: [AMBER] Non-PBC simulation in a droplet made of organic solvent David A Case (Tue Jan 23 2018 - 12:38:12 PST)
- Re: [AMBER] Non-PBC simulation in a droplet made of organic solvent Veronika Jurásková (Wed Jan 24 2018 - 02:45:23 PST)
[AMBER] Writing mdcrd to inpcrd Simon Kit Sang Chu (Mon Jan 22 2018 - 03:29:09 PST)
- Re: [AMBER] Writing mdcrd to inpcrd Batuhan Kav (Mon Jan 22 2018 - 05:20:44 PST)
- Re: [AMBER] Writing mdcrd to inpcrd David A Case (Mon Jan 22 2018 - 05:31:02 PST)
- Re: [AMBER] Writing mdcrd to inpcrd Jeyaram R A (Mon Jan 22 2018 - 08:32:08 PST)
[AMBER] Best practices for lipid equilibration - Amber parameters in Gromacs Crystal Vander Zanden (Mon Jan 22 2018 - 08:13:30 PST)
[AMBER] Transformation from cartesian to torsion space Siddhartha Jain (Mon Jan 22 2018 - 12:00:39 PST)
- Re: [AMBER] Transformation from cartesian to torsion space David Cerutti (Mon Jan 22 2018 - 13:39:50 PST)
[AMBER] Amber16 installation: Segmentation fault (core dumped) error when execute antechamber Yuan Hu (Mon Jan 22 2018 - 16:03:01 PST)
- Re: [AMBER] Amber16 installation: Segmentation fault (core dumped) error when execute antechamber David A Case (Mon Jan 22 2018 - 18:44:45 PST)
  - Re: [AMBER] Amber16 installation: Segmentation fault (core dumped) error when execute antechamber Yuan Hu (Mon Jan 22 2018 - 22:41:28 PST)
    - Re: [AMBER] Amber16 installation: Segmentation fault (core dumped) error when execute antechamber Scott Brozell (Tue Jan 23 2018 - 12:12:14 PST)
    - Re: [AMBER] Amber16 installation: Segmentation fault (core dumped) error when execute antechamber Yuan Hu (Tue Jan 23 2018 - 13:27:41 PST)
    - Re: [AMBER] Amber16 installation: Segmentation fault (core dumped) error when execute antechamber Scott Brozell (Tue Jan 23 2018 - 16:13:24 PST)
    - Re: [AMBER] Amber16 installation: Segmentation fault (core dumped) error when execute antechamber Yuan Hu (Tue Jan 23 2018 - 19:06:11 PST)
    - Re: [AMBER] Amber16 installation: Segmentation fault (core dumped) error when execute antechamber Hai Nguyen (Tue Jan 23 2018 - 19:30:35 PST)
    - Re: [AMBER] Amber16 installation: Segmentation fault (core dumped) error when execute antechamber Yuan Hu (Wed Jan 24 2018 - 05:19:13 PST)
    - Re: [AMBER] Amber16 installation: Segmentation fault (core dumped) error when execute antechamber Scott Brozell (Thu Jan 25 2018 - 10:51:01 PST)
    - Re: [AMBER] Amber16 installation: Segmentation fault (core dumped) error when execute antechamber Yuan Hu (Fri Jan 26 2018 - 05:17:29 PST)
    - Re: [AMBER] Amber16 installation: Segmentation fault (core dumped) error when execute antechamber Scott Brozell (Fri Jan 26 2018 - 10:40:41 PST)
    - Re: [AMBER] Amber16 installation: Segmentation fault (core dumped) error when execute antechamber Hai Nguyen (Fri Jan 26 2018 - 11:09:42 PST)
    - Re: [AMBER] Amber16 installation: Segmentation fault (core dumped) error when execute antechamber Yuan Hu (Fri Jan 26 2018 - 11:43:06 PST)
    - Re: [AMBER] Amber16 installation: Segmentation fault (core dumped) error when execute antechamber Yuan Hu (Fri Jan 26 2018 - 11:50:44 PST)
    - Re: [AMBER] Amber16 installation: Segmentation fault (core dumped) error when execute antechamber Scott Brozell (Fri Jan 26 2018 - 12:09:07 PST)
    - Re: [AMBER] Amber16 installation: Segmentation fault (core dumped) error when execute antechamber Yuan Hu (Fri Jan 26 2018 - 12:15:53 PST)
    - Re: [AMBER] Amber16 installation: Segmentation fault (core dumped) error when execute antechamber Scott Brozell (Mon Jan 29 2018 - 11:56:28 PST)
    - Re: [AMBER] Amber16 installation: Segmentation fault (core dumped) error when execute antechamber Yuan Hu (Mon Jan 29 2018 - 12:35:45 PST)
    - Re: [AMBER] Amber16 installation: Segmentation fault (core dumped) error when execute antechamber Scott Brozell (Mon Jan 29 2018 - 13:49:15 PST)
    - Re: [AMBER] Amber16 installation: Segmentation fault (core dumped) error when execute antechamber Yuan Hu (Tue Jan 30 2018 - 07:09:16 PST)
[AMBER] How to perform Newton-Raphson minimization to protein 巩梦雪 (Mon Jan 22 2018 - 23:30:22 PST)
- Re: [AMBER] How to perform Newton-Raphson minimization to protein David A Case (Tue Jan 23 2018 - 05:26:46 PST)
  - Re: [AMBER] How to perform Newton-Raphson minimization to protein 巩梦雪 (Fri Jan 26 2018 - 01:38:55 PST)
[AMBER] Unreplicable AMBER tutorial 3 Audrius Laurynėnas (Tue Jan 23 2018 - 04:22:21 PST)
[AMBER] Avoiding pdb4amber renumbering Sundar (Tue Jan 23 2018 - 10:04:22 PST)
- Re: [AMBER] Avoiding pdb4amber renumbering Hai Nguyen (Tue Jan 23 2018 - 11:11:42 PST)
- Re: [AMBER] Avoiding pdb4amber renumbering David A Case (Tue Jan 23 2018 - 12:14:22 PST)
  - Re: [AMBER] Avoiding pdb4amber renumbering Sundar (Tue Jan 23 2018 - 12:55:32 PST)
[AMBER] EVB xch_* values Stregone (Tue Jan 23 2018 - 11:44:07 PST)
- Re: [AMBER] EVB xch_* values David A Case (Mon Jan 29 2018 - 09:14:51 PST)
[AMBER] Amber16+AT17: Several checks failing w/Intel Parallel Studio XE 2018.1 Patrice Peterson (Tue Jan 23 2018 - 12:18:30 PST)
- Re: [AMBER] Amber16+AT17: Several checks failing w/Intel Parallel Studio XE 2018.1 Patrice Peterson (Tue Jan 23 2018 - 12:24:20 PST)
- Re: [AMBER] Amber16+AT17: Several checks failing w/Intel Parallel Studio XE 2018.1 Patrice Peterson (Tue Jan 23 2018 - 12:55:00 PST)
- Re: [AMBER] Amber16+AT17: Several checks failing w/Intel Parallel Studio XE 2018.1 David A Case (Mon Jan 29 2018 - 09:10:39 PST)
- Re: [AMBER] Amber16+AT17: Several checks failing w/Intel Parallel Studio XE 2018.1 David A Case (Mon Apr 09 2018 - 06:14:20 PDT)
[AMBER] cpptraj long writing queue Simon Kit Sang Chu (Wed Jan 24 2018 - 00:03:49 PST)
- Re: [AMBER] cpptraj long writing queue Daniel Roe (Wed Jan 24 2018 - 03:10:58 PST)
  - Re: [AMBER] cpptraj long writing queue Simon Kit Sang Chu (Wed Jan 24 2018 - 06:40:32 PST)
[AMBER] Cannot match namelist object name 0 Núbia Prates (Wed Jan 24 2018 - 08:26:33 PST)
- Re: [AMBER] Cannot match namelist object name 0 Batuhan Kav (Wed Jan 24 2018 - 09:52:34 PST)
  - Re: [AMBER] Cannot match namelist object name 0 Núbia Prates (Thu Jan 25 2018 - 05:23:02 PST)
[AMBER] Acpype and Gromacs Ahmed Mashaly (Wed Jan 24 2018 - 12:42:11 PST)
- Re: [AMBER] Acpype and Gromacs Alan (Thu Jan 25 2018 - 00:57:16 PST)
[AMBER] KeyError: 'HIE-HD1' MCPB.py Thakur, Abhishek (Wed Jan 24 2018 - 12:43:10 PST)
- Re: [AMBER] KeyError: 'HIE-HD1' MCPB.py Pengfei Li (Thu Jan 25 2018 - 10:39:40 PST)
[AMBER] Extract Velocity (and Force) from Gromacs .trr trajectory using cpptraj Mohd Farid Ismail (Thu Jan 25 2018 - 02:19:19 PST)
- Re: [AMBER] Extract Velocity (and Force) from Gromacs .trr trajectory using cpptraj Daniel Roe (Thu Feb 01 2018 - 06:03:48 PST)
[AMBER] Metadynamics in pmemd Hannes Konegger (Thu Jan 25 2018 - 05:13:39 PST)
- Re: [AMBER] Metadynamics in pmemd Celeste Sagui (Thu Jan 25 2018 - 14:51:20 PST)
- Re: [AMBER] Metadynamics in pmemd David A Case (Mon Jan 29 2018 - 09:01:42 PST)
[AMBER] Protonated cytosine and adenine: Parameter file was not saved Amen Shamim (Thu Jan 25 2018 - 05:15:28 PST)
- Re: [AMBER] Protonated cytosine and adenine: Parameter file was not saved David A Case (Thu Jan 25 2018 - 06:52:16 PST)
[AMBER] CPPTRAJ HBond analysis Segmentation fault (core dumped) 姚永霖 (Thu Jan 25 2018 - 06:54:00 PST)
[AMBER] Problem to convert Alberto Bencomo (Thu Jan 25 2018 - 08:23:31 PST)
- Re: [AMBER] Problem to convert David A Case (Fri Jan 26 2018 - 04:51:31 PST)
[AMBER] CPPTRAJ HBond analysis Segmentation fault (core dumped) 姚永霖 (Thu Jan 25 2018 - 17:33:30 PST)
- Re: [AMBER] CPPTRAJ HBond analysis Segmentation fault (core dumped) Daniel Roe (Thu Feb 01 2018 - 05:58:10 PST)
[AMBER] QM/MM metadynamics with external QM code Qinghua Liao (Fri Jan 26 2018 - 01:42:22 PST)
- Re: [AMBER] QM/MM metadynamics with external QM code Goetz, Andreas (Fri Jan 26 2018 - 02:20:18 PST)
  - Re: [AMBER] QM/MM metadynamics with external QM code Qinghua Liao (Fri Jan 26 2018 - 02:36:47 PST)
    - Re: [AMBER] QM/MM metadynamics with external QM code Jacopo Sgrignani (Fri Jan 26 2018 - 03:26:44 PST)
    - Re: [AMBER] QM/MM metadynamics with external QM code Qinghua Liao (Fri Jan 26 2018 - 04:05:53 PST)
[AMBER] Compressing trajectory file Setyanto Md (Fri Jan 26 2018 - 04:16:07 PST)
- Re: [AMBER] Compressing trajectory file Elvis Martis (Fri Jan 26 2018 - 05:56:25 PST)
- Re: [AMBER] Compressing trajectory file David A Case (Fri Jan 26 2018 - 18:09:34 PST)
  - Re: [AMBER] Compressing trajectory file Setyanto Md (Tue Jan 30 2018 - 22:37:32 PST)
    - Re: [AMBER] Compressing trajectory file Daniel Roe (Thu Feb 01 2018 - 06:10:06 PST)
[AMBER] QM/MM SMD with 'external' theory and PBCs Ruth Helena Tichauer (Fri Jan 26 2018 - 06:33:05 PST)
- Re: [AMBER] QM/MM SMD with 'external' theory and PBCs Goetz, Andreas (Fri Jan 26 2018 - 15:20:53 PST)
  - Re: [AMBER] QM/MM SMD with 'external' theory and PBCs Ruth Helena Tichauer (Fri Jan 26 2018 - 21:40:46 PST)
[AMBER] Can amber16 pmemd rigorously combine position restraints with pressure coupling on GPUs ? Chris Neale (Fri Jan 26 2018 - 11:48:09 PST)
- Re: [AMBER] Can amber16 pmemd rigorously combine position restraints with pressure coupling on GPUs ? David A Case (Mon Jan 29 2018 - 08:45:36 PST)
[AMBER] GBSA parameters Siddhartha Jain (Sat Jan 27 2018 - 17:11:57 PST)
- Re: [AMBER] GBSA parameters Carlos Simmerling (Sun Jan 28 2018 - 06:59:49 PST)
  - Re: [AMBER] GBSA parameters Siddhartha Jain (Sun Jan 28 2018 - 11:22:32 PST)
    - Re: [AMBER] GBSA parameters Siddhartha Jain (Sun Jan 28 2018 - 13:09:06 PST)
    - Re: [AMBER] GBSA parameters Carlos Simmerling (Sun Jan 28 2018 - 13:27:17 PST)
    - Re: [AMBER] GBSA parameters Hai Nguyen (Sun Jan 28 2018 - 17:26:34 PST)
    - Re: [AMBER] GBSA parameters David A Case (Sun Jan 28 2018 - 18:32:21 PST)
[AMBER] parmchk Yuliana Bosken (Sat Jan 27 2018 - 20:18:41 PST)
- Re: [AMBER] parmchk Kellon Belfon (Sat Jan 27 2018 - 22:37:40 PST)
  - Re: [AMBER] parmchk Yuliana Bosken (Sun Jan 28 2018 - 05:01:42 PST)
[AMBER] box size and SMD simulation Ibrahim Said (Sun Jan 28 2018 - 10:18:46 PST)
- Re: [AMBER] box size and SMD simulation David A Case (Sun Jan 28 2018 - 18:44:47 PST)
[AMBER] command problem SHALJA VERMA (Mon Jan 29 2018 - 02:27:46 PST)
- Re: [AMBER] command problem David A Case (Mon Jan 29 2018 - 05:09:44 PST)
[AMBER] command not working SHALJA VERMA (Mon Jan 29 2018 - 02:28:34 PST)
- Re: [AMBER] command not working David A Case (Mon Jan 29 2018 - 05:12:58 PST)
  - Re: [AMBER] command not working SHALJA VERMA (Mon Jan 29 2018 - 05:50:38 PST)
[AMBER] dftb_chg not working David Sáez (Mon Jan 29 2018 - 03:54:55 PST)
- Re: [AMBER] dftb_chg not working David Sáez (Mon Jan 29 2018 - 04:18:53 PST)
[AMBER] hbond analysis on DNA-protein complex Kenneth Huang (Mon Jan 29 2018 - 07:26:47 PST)
- Re: [AMBER] hbond analysis on DNA-protein complex Daniel Roe (Thu Feb 01 2018 - 06:05:41 PST)
[AMBER] MCPB.py error with ion id Thakur, Abhishek (Mon Jan 29 2018 - 07:37:07 PST)
- Re: [AMBER] MCPB.py error with ion id Pengfei Li (Wed Jan 31 2018 - 07:36:12 PST)
  - Re: [AMBER] MCPB.py error with ion id Thakur, Abhishek (Wed Jan 31 2018 - 08:54:07 PST)
[AMBER] Use amber output velocity for different system Khabiri, Morteza (Mon Jan 29 2018 - 08:48:11 PST)
- Re: [AMBER] Use amber output velocity for different system David A Case (Mon Jan 29 2018 - 11:57:58 PST)
  - Re: [AMBER] Use amber output velocity for different system Daniel Roe (Thu Feb 01 2018 - 06:06:48 PST)
[AMBER] Empty .frcmod file roja rahmani (Tue Jan 30 2018 - 05:39:56 PST)
- Re: [AMBER] Empty .frcmod file Elvis Martis (Tue Jan 30 2018 - 05:51:43 PST)
  - Re: [AMBER] Empty .frcmod file roja rahmani (Tue Jan 30 2018 - 06:19:16 PST)
    - Re: [AMBER] Empty .frcmod file roja rahmani (Tue Jan 30 2018 - 06:20:11 PST)
    - Re: [AMBER] Empty .frcmod file Elvis Martis (Tue Jan 30 2018 - 06:30:53 PST)
    - Re: [AMBER] Empty .frcmod file ABEL Stephane (Tue Jan 30 2018 - 06:31:39 PST)
    - Re: [AMBER] Empty .frcmod file ABEL Stephane (Tue Jan 30 2018 - 06:34:45 PST)
    - Re: [AMBER] Empty .frcmod file roja rahmani (Tue Jan 30 2018 - 06:50:10 PST)
    - Re: [AMBER] Empty .frcmod file ABEL Stephane (Tue Jan 30 2018 - 07:38:51 PST)
    - Re: [AMBER] Empty .frcmod file roja rahmani (Tue Jan 30 2018 - 08:09:18 PST)
    - Re: [AMBER] Empty .frcmod file roja rahmani (Tue Jan 30 2018 - 08:15:59 PST)
    - Re: [AMBER] Empty .frcmod file ABEL Stephane (Tue Jan 30 2018 - 09:36:02 PST)
[AMBER] Query regarding the ff99SB*ildn force field Leena Aggarwal (Tue Jan 30 2018 - 20:53:26 PST)
- Re: [AMBER] Query regarding the ff99SB*ildn force field David A Case (Wed Jan 31 2018 - 05:32:55 PST)
  - Re: [AMBER] Query regarding the ff99SB*ildn force field Vlad Cojocaru (Wed Jan 31 2018 - 05:55:45 PST)
    - Re: [AMBER] Query regarding the ff99SB*ildn force field Carlos Simmerling (Wed Jan 31 2018 - 06:01:54 PST)
[AMBER] Compiling AMBER16 with Open MPI 3.x Jonas Mansoor (Wed Jan 31 2018 - 01:15:09 PST)
[AMBER] Query on thermodynamic integration of complexes involving metal ions Muthukumaran Rajagopalan (Wed Jan 31 2018 - 04:24:55 PST)
- Re: [AMBER] Query on thermodynamic integration of complexes involving metal ions David A Case (Thu Feb 01 2018 - 04:25:28 PST)
  - Re: [AMBER] Query on thermodynamic integration of complexes involving metal ions muthu kumaran (Thu Feb 01 2018 - 20:32:53 PST)
[AMBER] Query on thermodynamic integration of complexes involving metal ions Muthukumaran Rajagopalan (Wed Jan 31 2018 - 05:16:02 PST)
[AMBER] About rerun the same trajectory David Sáez (Wed Jan 31 2018 - 07:20:54 PST)
- Re: [AMBER] About rerun the same trajectory David Sáez (Wed Jan 31 2018 - 07:49:42 PST)
  - Re: [AMBER] About rerun the same trajectory David Sáez (Wed Jan 31 2018 - 09:40:32 PST)
[AMBER] Is there anyway to recover the potential energies obtained after running md Shamsi, Zahra (Wed Jan 31 2018 - 08:20:57 PST)
- Re: [AMBER] Is there anyway to recover the potential energies obtained after running md Carlos Simmerling (Wed Jan 31 2018 - 08:36:23 PST)
- Re: [AMBER] Is there anyway to recover the potential energies obtained after running md Alberto Bencomo (Wed Jan 31 2018 - 08:39:44 PST)
  - Re: [AMBER] Is there anyway to recover the potential energies obtained after running md ABEL Stephane (Wed Jan 31 2018 - 09:23:57 PST)
[AMBER] distance restrain for group of residues ARMIN HODAEI (Wed Jan 31 2018 - 15:19:56 PST)
- Re: [AMBER] distance restrain for group of residues David A Case (Thu Feb 01 2018 - 04:31:00 PST)
  - Re: [AMBER] distance restrain for group of residues ARMIN HODAEI (Thu Feb 01 2018 - 04:39:22 PST)
    - Re: [AMBER] distance restrain for group of residues David A Case (Thu Feb 01 2018 - 10:17:05 PST)
    - Re: [AMBER] distance restrain for group of residues Armin Hodaei (Mon Feb 26 2018 - 02:01:08 PST)
[AMBER] Query on thermodynamic integration of complexes involving metal ions muthu kumaran (Wed Jan 31 2018 - 21:33:20 PST)
[AMBER] by MM-PBSA binding energy at 310K? Michael Shokhen (Thu Feb 01 2018 - 00:00:16 PST)
[AMBER] Regarding vdW (or other) parameters for type: Pb Garima Singh (Thu Feb 01 2018 - 02:03:48 PST)
- Re: [AMBER] Regarding vdW (or other) parameters for type: Pb Lorenzo Gontrani (Thu Feb 01 2018 - 02:19:42 PST)
  - Re: [AMBER] Regarding vdW (or other) parameters for type: Pb Pengfei Li (Thu Feb 01 2018 - 08:27:59 PST)
[AMBER] CPPTRAJ ERROR-Reg. Manjula Saravanan (Thu Feb 01 2018 - 02:26:52 PST)
- Re: [AMBER] CPPTRAJ ERROR-Reg. Daniel Roe (Thu Feb 01 2018 - 05:50:28 PST)
Re: [AMBER] AMBER16 and intel 2017, possible to compile? David A Case (Thu Feb 01 2018 - 04:24:40 PST)
- Re: [AMBER] AMBER16 and intel 2017, possible to compile? Patrice Peterson (Thu Feb 01 2018 - 04:51:26 PST)
[AMBER] printcharges not working when imin=5 and maxcyc=0 David Sáez (Thu Feb 01 2018 - 05:48:36 PST)
Re: [AMBER] CPPTRAJ: How to project trajectories of one simulation onto principal components (PCs) of another simulation? Daniel Roe (Thu Feb 01 2018 - 06:20:05 PST)
[AMBER] is that possible to change the size of the box in one direction in simulation? Parviz Seifpanahi Shabane (Thu Feb 01 2018 - 08:55:23 PST)
[AMBER] BASIC information for AMBER Vikram Dalal (Thu Feb 01 2018 - 10:35:13 PST)
- Re: [AMBER] BASIC information for AMBER Leena Aggarwal (Thu Feb 01 2018 - 21:09:50 PST)
[AMBER] Thermodynamic Integration query Sowmya Indrakumar (Fri Feb 02 2018 - 02:15:48 PST)
- Re: [AMBER] Thermodynamic Integration query Daniel Mermelstein (Tue Feb 13 2018 - 22:03:47 PST)
  - Re: [AMBER] Thermodynamic Integration query Sowmya Indrakumar (Wed Feb 14 2018 - 01:19:53 PST)
[AMBER] path_mode variable in SMD David Sáez (Fri Feb 02 2018 - 06:29:46 PST)
- Re: [AMBER] path_mode variable in SMD Feng Pan (Sat Feb 03 2018 - 16:52:15 PST)
[AMBER] setbox for octahedral Andrew Schaub (Fri Feb 02 2018 - 10:07:57 PST)
- Re: [AMBER] setbox for octahedral accuratefreeenergy.gmail.com (Fri Feb 02 2018 - 14:08:53 PST)
- Re: [AMBER] setbox for octahedral David A Case (Sun Feb 04 2018 - 05:29:15 PST)
- Re: [AMBER] setbox for octahedral Daniel Roe (Fri Feb 09 2018 - 04:21:42 PST)
[AMBER] amb2gmx roja rahmani (Fri Feb 02 2018 - 23:15:46 PST)
- Re: [AMBER] amb2gmx Jason Swails (Sat Feb 03 2018 - 21:55:18 PST)
  - Re: [AMBER] amb2gmx Roja (Mon Feb 05 2018 - 05:55:24 PST)
    - Re: [AMBER] amb2gmx Soumendranath Bhakat (Mon Feb 05 2018 - 06:01:58 PST)
    - Re: [AMBER] amb2gmx Jason Swails (Mon Feb 05 2018 - 06:10:16 PST)
    - Re: [AMBER] amb2gmx roja rahmani (Mon Feb 05 2018 - 06:14:52 PST)
    - Re: [AMBER] amb2gmx Jason Swails (Mon Feb 05 2018 - 06:23:22 PST)
    - Re: [AMBER] amb2gmx roja rahmani (Mon Feb 05 2018 - 06:58:54 PST)
    - Re: [AMBER] amb2gmx roja rahmani (Mon Feb 05 2018 - 07:34:31 PST)
    - Re: [AMBER] amb2gmx Jason Swails (Mon Feb 05 2018 - 07:54:07 PST)
    - Re: [AMBER] amb2gmx Roja (Mon Feb 05 2018 - 08:51:39 PST)
[AMBER] Units used in ff14sb Siddhartha Jain (Sun Feb 04 2018 - 14:16:41 PST)
- Re: [AMBER] Units used in ff14sb Carlos Simmerling (Mon Feb 05 2018 - 08:06:47 PST)
  - Re: [AMBER] Units used in ff14sb Siddhartha Jain (Mon Feb 05 2018 - 08:15:35 PST)
    - Re: [AMBER] Units used in ff14sb Carlos Simmerling (Mon Feb 05 2018 - 08:30:37 PST)
    - Re: [AMBER] Units used in ff14sb Siddhartha Jain (Mon Feb 05 2018 - 08:40:50 PST)
    - Re: [AMBER] Units used in ff14sb John Chodera (Tue Feb 06 2018 - 15:18:47 PST)
[AMBER] amber workshop reminder Fabian Glaser (Mon Feb 05 2018 - 02:02:59 PST)
[AMBER] adding ions Krystyna Zakrzewska (Mon Feb 05 2018 - 02:15:38 PST)
- Re: [AMBER] adding ions David A Case (Mon Feb 05 2018 - 06:08:23 PST)
  - Re: [AMBER] adding ions Krystyna Zakrzewska (Mon Feb 05 2018 - 06:46:54 PST)
    - Re: [AMBER] adding ions Daniel Roe (Tue Feb 06 2018 - 06:37:06 PST)
    - Re: [AMBER] adding ions Krystyna Zakrzewska (Tue Feb 06 2018 - 07:33:14 PST)
[AMBER] Extracting lowest energy snapshot from trajectory MOHD HOMAIDUR RAHMAN (Mon Feb 05 2018 - 08:28:04 PST)
- Re: [AMBER] Extracting lowest energy snapshot from trajectory Daniel Roe (Fri Feb 09 2018 - 04:27:38 PST)
[AMBER] Jobs and Evens in CHARMM-GUI Jumin Lee (Mon Feb 05 2018 - 14:00:04 PST)
[AMBER] EULA/NVIDIA Adrian Roitberg (Mon Feb 05 2018 - 14:31:20 PST)
- Re: [AMBER] EULA/NVIDIA Chris Neale (Wed Feb 07 2018 - 19:27:40 PST)
  - Re: [AMBER] EULA/NVIDIA Ross Walker (Fri Feb 09 2018 - 04:50:35 PST)
[AMBER] Quasi-harmonic analysis Chetna Tyagi (Tue Feb 06 2018 - 06:50:52 PST)
- Re: [AMBER] Quasi-harmonic analysis Daniel Roe (Fri Feb 09 2018 - 04:35:09 PST)
  - Re: [AMBER] Quasi-harmonic analysis Chetna Tyagi (Fri Feb 09 2018 - 07:12:39 PST)
[AMBER] how to run/install leap Mike Mazanetz (Tue Feb 06 2018 - 08:39:54 PST)
- Re: [AMBER] how to run/install leap Mike Mazanetz (Tue Feb 06 2018 - 10:00:22 PST)
  - Re: [AMBER] how to run/install leap David A Case (Tue Feb 06 2018 - 10:59:23 PST)
Re: [AMBER] how to run/install leap - help needed Mike Mazanetz (Tue Feb 06 2018 - 11:04:12 PST)
Re: [AMBER] how to run/install leap - solved Mike Mazanetz (Tue Feb 06 2018 - 12:04:30 PST)
[AMBER] gist analysis Sofia Vasilakaki (Tue Feb 06 2018 - 16:14:58 PST)
- Re: [AMBER] gist analysis Steven Ramsey (Tue Feb 06 2018 - 17:47:52 PST)
[AMBER] Constant Redox potential MD simulations Tarsis (Tue Feb 06 2018 - 16:19:00 PST)
- Re: [AMBER] Constant Redox potential MD simulations Roitberg,Adrian E (Tue Feb 06 2018 - 16:43:35 PST)
[AMBER] Problem in installing Amber16 Tasneem Kausar (Wed Feb 07 2018 - 00:43:25 PST)
- Re: [AMBER] Problem in installing Amber16 Tasneem Kausar (Wed Feb 07 2018 - 19:14:29 PST)
  - Re: [AMBER] Problem in installing Amber16 Elvis Martis (Wed Feb 07 2018 - 19:26:33 PST)
    - Re: [AMBER] Problem in installing Amber16 Tasneem Kausar (Wed Feb 07 2018 - 19:42:18 PST)
- Re: [AMBER] Problem in installing Amber16 Daniel Roe (Thu Feb 08 2018 - 04:03:36 PST)
  - Re: [AMBER] Problem in installing Amber16 Tasneem Kausar (Fri Feb 09 2018 - 02:18:41 PST)
[AMBER] Certain statistics from the trajectory Nikolay N. Kuzmich (Wed Feb 07 2018 - 03:54:56 PST)
- Re: [AMBER] Certain statistics from the trajectory Daniel Roe (Fri Feb 09 2018 - 05:40:49 PST)
- Re: [AMBER] Certain statistics from the trajectory Nikolay N. Kuzmich (Mon Feb 12 2018 - 01:10:47 PST)
[AMBER] Paramfit WRITE_ENERGY CA gmail (Wed Feb 07 2018 - 05:35:25 PST)
[AMBER] solvatebox iso error Ahmed Mashaly (Wed Feb 07 2018 - 10:10:21 PST)
- Re: [AMBER] solvatebox iso error Daniel Roe (Thu Feb 08 2018 - 04:14:37 PST)
  - Re: [AMBER] solvatebox iso error Ahmed Mashaly (Thu Feb 08 2018 - 05:16:17 PST)
  - Re: [AMBER] solvatebox iso error Ahmed Mashaly (Thu Feb 08 2018 - 08:32:58 PST)
    - Re: [AMBER] solvatebox iso error Daniel Roe (Fri Feb 09 2018 - 06:02:16 PST)
- Re: [AMBER] solvatebox iso error Daniel Roe (Fri Feb 09 2018 - 08:10:46 PST)
  - Re: [AMBER] solvatebox iso error Ahmed Mashaly (Fri Feb 09 2018 - 08:23:48 PST)
    - Re: [AMBER] solvatebox iso error Daniel Roe (Fri Feb 09 2018 - 08:38:40 PST)
[AMBER] lipidorder in cpptraj Chitrak Gupta (Wed Feb 07 2018 - 16:13:59 PST)
- Re: [AMBER] lipidorder in cpptraj Daniel Roe (Thu Feb 08 2018 - 03:55:16 PST)
- Re: [AMBER] lipidorder in cpptraj Chitrak Gupta (Fri Feb 09 2018 - 11:27:17 PST)
  - Re: [AMBER] lipidorder in cpptraj Daniel Roe (Fri Feb 09 2018 - 12:48:03 PST)
[AMBER] Regarding termination of pmemd.cuda Rajarshi Roy (Thu Feb 08 2018 - 00:41:25 PST)
[AMBER] Ion dissociation computed by umbrella sampling Veronika Jurásková (Thu Feb 08 2018 - 02:21:52 PST)
- Re: [AMBER] Ion dissociation computed by umbrella sampling David A Case (Mon Feb 12 2018 - 04:30:17 PST)
[AMBER] Ph.D. and Post-doc positions in molecular simulations and structural bioinformatics Jan Brezovsky (Thu Feb 08 2018 - 05:16:42 PST)
[AMBER] Adding divalent ions in LEaP Nikolay N. Kuzmich (Thu Feb 08 2018 - 06:19:36 PST)
- Re: [AMBER] Adding divalent ions in LEaP Christina Bergonzo (Thu Feb 08 2018 - 06:42:41 PST)
- Re: [AMBER] Adding divalent ions in LEaP David A Case (Thu Feb 08 2018 - 12:36:43 PST)
- Re: [AMBER] Adding divalent ions in LEaP Nikolay N. Kuzmich (Fri Feb 09 2018 - 03:04:02 PST)
  - Re: [AMBER] Adding divalent ions in LEaP Hector A. Baldoni (Fri Feb 09 2018 - 04:28:58 PST)
  - Re: [AMBER] Adding divalent ions in LEaP David A Case (Fri Feb 09 2018 - 04:46:51 PST)
- Re: [AMBER] Adding divalent ions in LEaP Nikolay N. Kuzmich (Thu Feb 15 2018 - 06:45:24 PST)
[AMBER] Forcefield for methylated and acetylated amino acids Shahryar Alavi (Thu Feb 08 2018 - 07:55:27 PST)
- Re: [AMBER] Forcefield for methylated and acetylated amino acids Junmei Wang (Thu Feb 08 2018 - 08:12:20 PST)
[AMBER] SMD using Orca for QM region unknown atom specifier Ruth Helena Tichauer (Thu Feb 08 2018 - 12:37:28 PST)
- Re: [AMBER] SMD using Orca for QM region unknown atom specifier Goetz, Andreas (Thu Feb 08 2018 - 13:52:56 PST)
  - Re: [AMBER] SMD using Orca for QM region unknown atom specifier Ruth Helena Tichauer (Fri Feb 09 2018 - 02:03:57 PST)
    - Re: [AMBER] SMD using Orca for QM region unknown atom specifier David A Case (Mon Feb 12 2018 - 04:44:22 PST)
    - Re: [AMBER] SMD using Orca for QM region unknown atom specifier Ruth Helena Tichauer (Mon Feb 12 2018 - 05:57:23 PST)
    - Re: [AMBER] SMD using Orca for QM region unknown atom specifier Ruth Helena Tichauer (Mon Feb 12 2018 - 06:10:51 PST)
[AMBER] Trajectory processing Ming Tang (Thu Feb 08 2018 - 16:39:51 PST)
- Re: [AMBER] Trajectory processing Daniel Roe (Fri Feb 09 2018 - 05:48:13 PST)
[AMBER] AMBER on AWS - Beta testers wanted. Mike Mazanetz (Thu Feb 08 2018 - 17:10:36 PST)
[AMBER] B-factor Values Mac Kevin Braza (Thu Feb 08 2018 - 23:12:34 PST)
- [AMBER] Fwd: B-factor Values Mac Kevin Braza (Thu Feb 08 2018 - 23:13:44 PST)
- Re: [AMBER] B-factor Values Daniel Roe (Fri Feb 09 2018 - 05:50:18 PST)
[AMBER] Strong Na+-ASP interactions Rui, Huan (Fri Feb 09 2018 - 06:57:14 PST)
- Re: [AMBER] Strong Na+-ASP interactions Carlos Simmerling (Fri Feb 09 2018 - 07:00:43 PST)
  - Re: [AMBER] Strong Na+-ASP interactions Rui, Huan (Fri Feb 09 2018 - 08:39:06 PST)
- Re: [AMBER] Strong Na+-ASP interactions David A Case (Mon Feb 12 2018 - 04:50:46 PST)
  - Re: [AMBER] Strong Na+-ASP interactions Rui, Huan (Mon Feb 12 2018 - 06:33:29 PST)
[AMBER] RMSD with cpptraj Rui, Huan (Fri Feb 09 2018 - 11:38:32 PST)
- Re: [AMBER] RMSD with cpptraj Carlos Simmerling (Fri Feb 09 2018 - 11:40:48 PST)
  - Re: [AMBER] RMSD with cpptraj Rui, Huan (Fri Feb 09 2018 - 11:46:21 PST)
- Re: [AMBER] RMSD with cpptraj Rui, Huan (Fri Feb 09 2018 - 11:50:37 PST)
- Re: [AMBER] RMSD with cpptraj Rui, Huan (Fri Feb 09 2018 - 13:29:17 PST)
  - Re: [AMBER] RMSD with cpptraj Daniel Roe (Fri Feb 09 2018 - 13:36:20 PST)
    - Re: [AMBER] RMSD with cpptraj Rui, Huan (Fri Feb 09 2018 - 13:54:37 PST)
[AMBER] Information required about the potential of Amber software. Ubaid Ullah (Fri Feb 09 2018 - 20:10:56 PST)
- Re: [AMBER] Information required about the potential of Amber software. David A Case (Mon Feb 12 2018 - 04:57:41 PST)
[AMBER] MPI error in running a multi-sander job for TI calculation Ahsan Mohd (Sat Feb 10 2018 - 11:27:42 PST)
- Re: [AMBER] MPI error in running a multi-sander job for TI calculation David A Case (Sun Feb 11 2018 - 05:30:12 PST)
[AMBER] STSM sample files Szymon Żaczek (Mon Feb 12 2018 - 00:48:31 PST)
- Re: [AMBER] STSM sample files Feng Pan (Mon Feb 12 2018 - 11:26:01 PST)
[AMBER] Regarding error in frcmod file Aashish Bhatt (Mon Feb 12 2018 - 05:46:53 PST)
- Re: [AMBER] Regarding error in frcmod file Aashish Bhatt (Tue Feb 13 2018 - 07:30:23 PST)
  - Re: [AMBER] Regarding error in frcmod file David A Case (Tue Feb 13 2018 - 09:34:11 PST)
[AMBER] Question about how to compute kinetic energy from velocity trajectory Lee-Ping Wang (Mon Feb 12 2018 - 12:04:21 PST)
- Re: [AMBER] Question about how to compute kinetic energy from velocity trajectory Daniel Roe (Tue Feb 20 2018 - 12:36:38 PST)
  - Re: [AMBER] Question about how to compute kinetic energy from velocity trajectory Lee-Ping Wang (Tue Feb 20 2018 - 15:38:46 PST)
[AMBER] Problem calculating energies using cpptraj and sander API Lee-Ping Wang (Mon Feb 12 2018 - 14:16:27 PST)
- Re: [AMBER] Problem calculating energies using cpptraj and sander API Jason Swails (Mon Feb 12 2018 - 19:31:23 PST)
  - Re: [AMBER] Problem calculating energies using cpptraj and sander API Lee-Ping Wang (Mon Feb 12 2018 - 19:40:36 PST)
[AMBER] some programs do not appear Ibrahim Said (Mon Feb 12 2018 - 14:50:09 PST)
- Re: [AMBER] some programs do not appear Hai Nguyen (Mon Feb 12 2018 - 14:55:23 PST)
- Re: [AMBER] some programs do not appear David A Case (Tue Feb 13 2018 - 07:13:09 PST)
[AMBER] ff15ipq and divalent ions Neha Gandhi (Mon Feb 12 2018 - 22:05:15 PST)
- Re: [AMBER] ff15ipq and divalent ions David Cerutti (Mon Feb 12 2018 - 23:04:59 PST)
[AMBER] Problem with Atomtype of ligand in protein-ligand complex Sivasudhan R (Mon Feb 12 2018 - 23:22:33 PST)
- Re: [AMBER] Problem with Atomtype of ligand in protein-ligand complex Daniel Roe (Tue Feb 13 2018 - 05:47:23 PST)
  - Re: [AMBER] Problem with Atomtype of ligand in protein-ligand complex Sivasudhan R (Tue Feb 13 2018 - 06:43:52 PST)
    - Re: [AMBER] Problem with Atomtype of ligand in protein-ligand complex David A Case (Tue Feb 13 2018 - 09:40:19 PST)
[AMBER] PatchingError: No changes made from this patch Elisa Pieri (Tue Feb 13 2018 - 01:27:26 PST)
- Re: [AMBER] PatchingError: No changes made from this patch Daniel Roe (Tue Feb 13 2018 - 05:46:01 PST)
  - Re: [AMBER] PatchingError: No changes made from this patch Elisa Pieri (Tue Feb 13 2018 - 06:32:19 PST)
[AMBER] Make install Error Elisa Pieri (Tue Feb 13 2018 - 01:46:05 PST)
- Re: [AMBER] Make install Error Hai Nguyen (Tue Feb 13 2018 - 04:30:55 PST)
  - Re: [AMBER] Make install Error Elisa Pieri (Tue Feb 13 2018 - 05:11:03 PST)
    - Re: [AMBER] Make install Error Hai Nguyen (Tue Feb 13 2018 - 05:22:57 PST)
    - Re: [AMBER] Make install Error Hai Nguyen (Tue Feb 13 2018 - 05:27:41 PST)
    - Re: [AMBER] Make install Error Elisa Pieri (Tue Feb 13 2018 - 06:03:00 PST)
    - Re: [AMBER] Make install Error Elisa Pieri (Tue Feb 13 2018 - 06:57:28 PST)
[AMBER] Question about proper usage of pysander Lee-Ping Wang (Tue Feb 13 2018 - 07:31:06 PST)
- Re: [AMBER] Question about proper usage of pysander Hai Nguyen (Tue Feb 13 2018 - 09:32:59 PST)
  - Re: [AMBER] Question about proper usage of pysander Hai Nguyen (Tue Feb 13 2018 - 09:34:07 PST)
    - Re: [AMBER] Question about proper usage of pysander Lee-Ping Wang (Tue Feb 13 2018 - 10:49:54 PST)
    - Re: [AMBER] Question about proper usage of pysander Jason Swails (Tue Feb 13 2018 - 13:05:30 PST)
- Re: [AMBER] Question about proper usage of pysander David A Case (Tue Feb 13 2018 - 09:53:54 PST)
  - Re: [AMBER] Question about proper usage of pysander Lee-Ping Wang (Tue Feb 13 2018 - 10:47:13 PST)
[AMBER] AMBER disk usage on CPU or GPU nodes Lenz, Stefan (Tue Feb 13 2018 - 09:27:53 PST)
- Re: [AMBER] AMBER disk usage on CPU or GPU nodes Ross Walker (Wed Feb 14 2018 - 06:58:43 PST)
  - Re: [AMBER] AMBER disk usage on CPU or GPU nodes Lenz, Stefan (Wed Feb 14 2018 - 08:11:06 PST)
[AMBER] Dendrogram from cpptraj clustering? Gustavo Seabra (Thu Feb 15 2018 - 06:51:00 PST)
- Re: [AMBER] Dendrogram from cpptraj clustering? George M. Giambasu (Thu Feb 15 2018 - 16:37:45 PST)
  - Re: [AMBER] Dendrogram from cpptraj clustering? Gustavo Seabra (Fri Feb 16 2018 - 05:15:07 PST)
[AMBER] Torsion angle frequency Lizelle Lubbe (Thu Feb 15 2018 - 23:56:30 PST)
- Re: [AMBER] Torsion angle frequency Yuliana Bosken (Fri Feb 16 2018 - 11:35:56 PST)
  - Re: [AMBER] Torsion angle frequency Roitberg,Adrian E (Fri Feb 16 2018 - 11:45:45 PST)
[AMBER] 3 GPUs and replica exchange MD Nikolay N. Kuzmich (Fri Feb 16 2018 - 01:27:01 PST)
- Re: [AMBER] 3 GPUs and replica exchange MD Cruzeiro,Vinicius Wilian D (Fri Feb 16 2018 - 03:37:33 PST)
  - Re: [AMBER] 3 GPUs and replica exchange MD James Kress (Fri Feb 16 2018 - 10:27:51 PST)
    - Re: [AMBER] 3 GPUs and replica exchange MD Cruzeiro,Vinicius Wilian D (Fri Feb 16 2018 - 16:49:46 PST)
[AMBER] MD simulation of a protein at pH 3.0 Rakesh Srivastava (Fri Feb 16 2018 - 04:15:48 PST)
- Re: [AMBER] MD simulation of a protein at pH 3.0 Cruzeiro,Vinicius Wilian D (Fri Feb 16 2018 - 06:01:48 PST)
  - Re: [AMBER] MD simulation of a protein at pH 3.0 Rakesh Srivastava (Fri Feb 16 2018 - 20:46:16 PST)
[AMBER] sander API does not support EP with igb 6 Lee-Ping Wang (Fri Feb 16 2018 - 05:44:16 PST)
- Re: [AMBER] sander API does not support EP with igb 6 David Cerutti (Fri Feb 16 2018 - 07:01:08 PST)
[AMBER] Amber16 pmemd.cuda on Tesla M2075 Richard Smith (Fri Feb 16 2018 - 08:46:59 PST)
[AMBER] "Issue" with hbond Núbia Prates (Fri Feb 16 2018 - 13:57:29 PST)
- Re: [AMBER] "Issue" with hbond Daniel Roe (Tue Feb 20 2018 - 09:18:31 PST)
  - Re: [AMBER] "Issue" with hbond Núbia Prates (Tue Feb 20 2018 - 10:00:51 PST)
[AMBER] Updated Website James Kress (Mon Feb 05 2018 - 11:47:42 PST)
[AMBER] Problem with using Monte Carlo Barostat algorithm in pmemd cuda Roma Mukhopadhyay (Fri Feb 16 2018 - 20:07:06 PST)
- Re: [AMBER] Problem with using Monte Carlo Barostat algorithm in pmemd cuda Andreas Tosstorff (Sat Feb 17 2018 - 00:09:17 PST)
  - Re: [AMBER] Problem with using Monte Carlo Barostat algorithm in pmemd cuda Roma Mukhopadhyay (Sat Feb 17 2018 - 08:53:55 PST)
    - Re: [AMBER] Problem with using Monte Carlo Barostat algorithm in pmemd cuda David A Case (Sun Feb 18 2018 - 17:22:16 PST)
    - Re: [AMBER] Problem with using Monte Carlo Barostat algorithm in pmemd cuda David Cerutti (Sun Feb 18 2018 - 17:48:36 PST)
    - Re: [AMBER] Problem with using Monte Carlo Barostat algorithm in pmemd cuda Roma Mukhopadhyay (Sun Feb 18 2018 - 20:31:40 PST)
    - Re: [AMBER] Problem with using Monte Carlo Barostat algorithm in pmemd cuda David Cerutti (Sun Feb 18 2018 - 21:25:16 PST)
[AMBER] eChemInfo 2018 workshop on drug design in Milano Thomas Exner (Sat Feb 17 2018 - 02:51:15 PST)
[AMBER] 3D-RISM calculation at pH 3.0 Rakesh Srivastava (Sun Feb 18 2018 - 21:55:12 PST)
- Re: [AMBER] 3D-RISM calculation at pH 3.0 Tyler Luchko (Lists) (Mon Feb 19 2018 - 14:58:23 PST)
  - Re: [AMBER] 3D-RISM calculation at pH 3.0 Rakesh Srivastava (Mon Feb 19 2018 - 19:59:13 PST)
[AMBER] "The unperturbed charge of the unit is not integral": really nothing to care about? Nikolay N. Kuzmich (Mon Feb 19 2018 - 01:09:32 PST)
- Re: [AMBER] "The unperturbed charge of the unit is not integral": really nothing to care about? David A Case (Mon Feb 19 2018 - 18:22:01 PST)
- Re: [AMBER] "The unperturbed charge of the unit is not integral": really nothing to care about? Nikolay N. Kuzmich (Wed Feb 21 2018 - 01:23:13 PST)
  - Re: [AMBER] "The unperturbed charge of the unit is not integral": really nothing to care about? David A Case (Wed Feb 21 2018 - 04:48:24 PST)
[AMBER] add vertical lines for initial and final angle Rosellen, Martin (Mon Feb 19 2018 - 04:41:27 PST)
- Re: [AMBER] add vertical lines for initial and final angle Daniel Roe (Tue Feb 20 2018 - 09:13:02 PST)
[AMBER] Scaling QM energy/forces Raimon Fabregat (Mon Feb 19 2018 - 06:50:16 PST)
- Re: [AMBER] Scaling QM energy/forces Goetz, Andreas (Tue Feb 20 2018 - 12:29:34 PST)
[AMBER] workshop amber Technion Israel Fabian Glaser (Mon Feb 19 2018 - 23:41:38 PST)
[AMBER] OL15 (leaprc.DNA.OL15) vs bsc1 (leaprc.DNA.bsc1). Saikat Pal (Tue Feb 20 2018 - 04:41:06 PST)
- Re: [AMBER] OL15 (leaprc.DNA.OL15) vs bsc1 (leaprc.DNA.bsc1). Vlad Cojocaru (Tue Feb 20 2018 - 05:33:35 PST)
  - Re: [AMBER] OL15 (leaprc.DNA.OL15) vs bsc1 (leaprc.DNA.bsc1). Saikat Pal (Tue Feb 20 2018 - 09:23:52 PST)
[AMBER] Mask building problems James Kress (Tue Feb 20 2018 - 16:14:44 PST)
[AMBER] visualization of long simulation data with out downloading .mdcrd file Rana Rehan Khalid (Wed Feb 21 2018 - 05:23:27 PST)
- Re: [AMBER] visualization of long simulation data with out downloading .mdcrd file Elvis Martis (Wed Feb 21 2018 - 05:43:37 PST)
[AMBER] Amber16/AmberTools17 CUDA version Baker D.J. (Wed Feb 21 2018 - 08:28:09 PST)
- Re: [AMBER] Amber16/AmberTools17 CUDA version David A Case (Mon Mar 05 2018 - 05:17:28 PST)
[AMBER] Combining coordinate files + Renumbering residues Jag Silwal (Wed Feb 21 2018 - 12:07:05 PST)
[AMBER] Amber16/AmberTools17 CUDA version Baker D.J. (Wed Feb 21 2018 - 12:53:42 PST)
[AMBER] Is there a bug in how Amber16 handles qmmask and WAT? James Kress (Wed Feb 21 2018 - 13:25:25 PST)
- Re: [AMBER] Is there a bug in how Amber16 handles qmmask and WAT? James Kress (Sun Feb 25 2018 - 11:03:06 PST)
  - Re: [AMBER] Is there a bug in how Amber16 handles qmmask and WAT? Chris Neale (Sun Feb 25 2018 - 11:05:54 PST)
    - Re: [AMBER] Is there a bug in how Amber16 handles qmmask and WAT? James Kress (Sun Feb 25 2018 - 12:55:27 PST)
- Re: [AMBER] Is there a bug in how Amber16 handles qmmask and WAT? James Kress (Tue Feb 27 2018 - 10:48:51 PST)
  - Re: [AMBER] Is there a bug in how Amber16 handles qmmask and WAT? Carlos Simmerling (Tue Feb 27 2018 - 10:54:33 PST)
    - Re: [AMBER] Is there a bug in how Amber16 handles qmmask and WAT? James Kress (Tue Feb 27 2018 - 12:01:37 PST)
    - Re: [AMBER] Is there a bug in how Amber16 handles qmmask and WAT? Goetz, Andreas (Tue Feb 27 2018 - 17:43:23 PST)
- Re: [AMBER] Is there a bug in how Amber16 handles qmmask and WAT? David A Case (Tue Feb 27 2018 - 17:33:59 PST)
  - Re: [AMBER] Is there a bug in how Amber16 handles qmmask and WAT? James Kress (Tue Feb 27 2018 - 19:06:03 PST)
[AMBER] amber coordinates in VMD Stefano Guglielmo (Wed Feb 21 2018 - 16:17:54 PST)
- Re: [AMBER] amber coordinates in VMD pancham lal Gupta (Thu Feb 22 2018 - 06:30:28 PST)
- Re: [AMBER] amber coordinates in VMD Carlos Simmerling (Thu Feb 22 2018 - 06:42:23 PST)
  - Re: [AMBER] amber coordinates in VMD Stefano Guglielmo (Mon Feb 26 2018 - 17:06:41 PST)
[AMBER] Enquiry on ntt Ming Tang (Thu Feb 22 2018 - 03:22:08 PST)
- Re: [AMBER] Enquiry on ntt Tom Kurtzman (Thu Feb 22 2018 - 04:52:11 PST)
  - Re: [AMBER] Enquiry on ntt Ming Tang (Thu Feb 22 2018 - 14:40:41 PST)
  - Re: [AMBER] Enquiry on ntt Ming Tang (Fri Feb 23 2018 - 14:50:13 PST)
    - Re: [AMBER] Enquiry on ntt David A Case (Fri Feb 23 2018 - 18:56:35 PST)
    - Re: [AMBER] Enquiry on ntt Ming Tang (Fri Feb 23 2018 - 19:28:40 PST)
  - Re: [AMBER] Enquiry on ntt Chris Neale (Fri Feb 23 2018 - 15:00:25 PST)
Re: [AMBER] The unperturbed charge of the unit is not integral": really nothing to care about? Nikolay N. Kuzmich (Thu Feb 22 2018 - 08:18:49 PST)
- Re: [AMBER] The unperturbed charge of the unit is not integral": really nothing to care about? David A Case (Thu Feb 22 2018 - 09:33:36 PST)
[AMBER] Using solvatebox with a SO2 molecule - difficulties in adding duplicate oxygen atoms in .pdb M Conte (Thu Feb 22 2018 - 08:52:48 PST)
- Re: [AMBER] Using solvatebox with a SO2 molecule - difficulties in adding duplicate oxygen atoms in .pdb David A Case (Thu Feb 22 2018 - 09:36:45 PST)
[AMBER] Is there a bug in how Amber16 handles qmmask and WAT? James Kress (Thu Feb 22 2018 - 11:58:54 PST)
- Re: [AMBER] Is there a bug in how Amber16 handles qmmask and WAT? Daniel Roe (Thu Feb 22 2018 - 12:19:59 PST)
  - Re: [AMBER] Is there a bug in how Amber16 handles qmmask and WAT? James Kress (Thu Feb 22 2018 - 14:10:31 PST)
[AMBER] selection of the type of box in molecular dynamics in AMBER Vikram Dalal (Thu Feb 22 2018 - 13:22:38 PST)
- Re: [AMBER] selection of the type of box in molecular dynamics in AMBER David A Case (Fri Feb 23 2018 - 05:14:54 PST)
[AMBER] Coordinate resetting (SHAKE) cannot be accomplished, deviation is too large NITTER, NIT, LL and J are 0 1 151 KRIPI TOMAR (Thu Feb 22 2018 - 23:24:35 PST)
- Re: [AMBER] Coordinate resetting (SHAKE) cannot be accomplished, deviation is too large NITTER, NIT, LL and J are 0 1 151 David A Case (Fri Feb 23 2018 - 05:18:05 PST)
[AMBER] Simulation does not restart from restart file written in previous step. Abhilash J (Fri Feb 23 2018 - 04:49:29 PST)
- Re: [AMBER] Simulation does not restart from restart file written in previous step. David A Case (Fri Feb 23 2018 - 10:29:25 PST)
  - Re: [AMBER] Simulation does not restart from restart file written in previous step. Abhilash J (Sat Feb 24 2018 - 05:52:52 PST)
    - Re: [AMBER] Simulation does not restart from restart file written in previous step. Abhilash J (Tue Mar 06 2018 - 05:53:01 PST)
    - Re: [AMBER] Simulation does not restart from restart file written in previous step. David A Case (Tue Mar 06 2018 - 15:53:39 PST)
    - Re: [AMBER] Simulation does not restart from restart file written in previous step. Ruchika Bhat (Tue Mar 06 2018 - 23:13:49 PST)
    - Re: [AMBER] Simulation does not restart from restart file written in previous step. Abhilash J (Wed Mar 07 2018 - 02:37:22 PST)
    - Re: [AMBER] Simulation does not restart from restart file written in previous step. David A Case (Wed Mar 07 2018 - 05:52:36 PST)
    - Re: [AMBER] Simulation does not restart from restart file written in previous step. Abhilash J (Thu Mar 08 2018 - 04:31:25 PST)
    - Re: [AMBER] Simulation does not restart from restart file written in previous step. Abhilash J (Fri May 04 2018 - 05:19:38 PDT)
Re: [AMBER] The unperturbed charge of the unit is not integral: really nothing to care about? Nikolay N. Kuzmich (Fri Feb 23 2018 - 09:33:07 PST)
[AMBER] RDF Marcelo Andrade Chagas (Fri Feb 23 2018 - 10:39:06 PST)
- Re: [AMBER] RDF Gustavo Seabra (Fri Feb 23 2018 - 11:13:46 PST)
[AMBER] trouble with pdb4amber Jennifer L. Muzyka (Sun Feb 25 2018 - 09:18:12 PST)
- Re: [AMBER] trouble with pdb4amber David A Case (Sun Feb 25 2018 - 09:52:45 PST)
  - Re: [AMBER] trouble with pdb4amber Jennifer L. Muzyka (Mon Feb 26 2018 - 06:18:52 PST)
  - Re: [AMBER] trouble with pdb4amber Jennifer L. Muzyka (Mon Feb 26 2018 - 06:49:42 PST)
    - Re: [AMBER] trouble with pdb4amber Hai Nguyen (Mon Feb 26 2018 - 07:45:03 PST)
- Re: [AMBER] trouble with pdb4amber Hai Nguyen (Sun Feb 25 2018 - 10:38:50 PST)
  - Re: [AMBER] trouble with pdb4amber Jennifer L. Muzyka (Mon Feb 26 2018 - 06:20:01 PST)
    - Re: [AMBER] trouble with pdb4amber Jennifer L. Muzyka (Mon Feb 26 2018 - 06:44:25 PST)
    - Re: [AMBER] trouble with pdb4amber David A Case (Mon Feb 26 2018 - 14:50:57 PST)
[AMBER] Placing ions within a maximum distance from the solute Nikolay N. Kuzmich (Mon Feb 26 2018 - 00:14:24 PST)
- Re: [AMBER] Placing ions within a maximum distance from the solute David A Case (Mon Feb 26 2018 - 04:47:18 PST)
[AMBER] AMBER/ORCA for QM/MM minyuan.mail.ustc.edu.cn (Mon Feb 26 2018 - 06:24:29 PST)
- Re: [AMBER] AMBER/ORCA for QM/MM Goetz, Andreas (Mon Feb 26 2018 - 13:04:01 PST)
- Re: [AMBER] AMBER/ORCA for QM/MM minyuan.mail.ustc.edu.cn (Mon Feb 26 2018 - 17:13:21 PST)
  - Re: [AMBER] AMBER/ORCA for QM/MM Goetz, Andreas (Mon Feb 26 2018 - 17:56:12 PST)
    - Re: [AMBER] AMBER/ORCA for QM/MM MinYuan (Wed Feb 28 2018 - 04:26:38 PST)
- Re: [AMBER] AMBER/ORCA for QM/MM minyuan.mail.ustc.edu.cn (Wed Feb 28 2018 - 19:23:16 PST)
  - Re: [AMBER] AMBER/ORCA for QM/MM Goetz, Andreas (Wed Feb 28 2018 - 20:10:34 PST)
- Re: [AMBER] AMBER/ORCA for QM/MM minyuan.mail.ustc.edu.cn (Thu Mar 01 2018 - 00:09:39 PST)
  - Re: [AMBER] AMBER/ORCA for QM/MM Goetz, Andreas (Thu Mar 01 2018 - 00:25:54 PST)
- Re: [AMBER] AMBER/ORCA for QM/MM minyuan.mail.ustc.edu.cn (Thu Mar 01 2018 - 01:45:40 PST)
  - Re: [AMBER] AMBER/ORCA for QM/MM Charles-Alexandre Mattelaer (Thu Mar 01 2018 - 01:54:03 PST)
  - Re: [AMBER] AMBER/ORCA for QM/MM Goetz, Andreas (Thu Mar 01 2018 - 03:02:35 PST)
    - Re: [AMBER] AMBER/ORCA for QM/MM MinYuan (Thu Mar 01 2018 - 17:13:59 PST)
    - Re: [AMBER] AMBER/ORCA for QM/MM Goetz, Andreas (Thu Mar 01 2018 - 18:04:23 PST)
    - Re: [AMBER] AMBER/ORCA for QM/MM MinYuan (Fri Mar 02 2018 - 02:22:38 PST)
    - Re: [AMBER] AMBER/ORCA for QM/MM Goetz, Andreas (Fri Mar 02 2018 - 23:29:31 PST)
- Re: [AMBER] AMBER/ORCA for QM/MM minyuan.mail.ustc.edu.cn (Sat Mar 03 2018 - 16:53:58 PST)
  - Re: [AMBER] AMBER/ORCA for QM/MM Goetz, Andreas (Sat Mar 03 2018 - 19:35:30 PST)
- Re: [AMBER] AMBER/ORCA for QM/MM minyuan.mail.ustc.edu.cn (Sun Mar 04 2018 - 04:18:38 PST)
[AMBER] How to generate parameters for two MG 2+ ions ---GTP Rana Rehan Khalid (Mon Feb 26 2018 - 08:02:02 PST)
- Re: [AMBER] How to generate parameters for two MG 2+ ions ---GTP David A Case (Mon Feb 26 2018 - 14:55:31 PST)
  - Re: [AMBER] How to generate parameters for two MG 2+ ions ---GTP Rana Rehan Khalid (Thu Mar 01 2018 - 08:09:52 PST)
[AMBER] Interface with DFTB+ Raimon Fabregat (Tue Feb 27 2018 - 02:26:55 PST)
- Re: [AMBER] Interface with DFTB+ Holger Kruse (Tue Feb 27 2018 - 06:11:53 PST)
[AMBER] "refc" file Armin Hodaei (Tue Feb 27 2018 - 02:45:29 PST)
- Re: [AMBER] "refc" file David A Case (Tue Feb 27 2018 - 04:36:47 PST)
  - Re: [AMBER] "refc" file Armin Hodaei (Tue Feb 27 2018 - 05:43:39 PST)
[AMBER] Has anyone determined a fix for QM_CHECK_PERIODIC or inability to include solvent in qmmask error James Kress (Tue Feb 27 2018 - 12:02:30 PST)
- Re: [AMBER] Has anyone determined a fix for QM_CHECK_PERIODIC or inability to include solvent in qmmask error Gustavo Seabra (Tue Feb 27 2018 - 12:13:51 PST)
- Re: [AMBER] Has anyone determined a fix for QM_CHECK_PERIODIC or inability to include solvent in qmmask error David A Case (Tue Feb 27 2018 - 17:50:13 PST)
  - Re: [AMBER] Has anyone determined a fix for QM_CHECK_PERIODIC or inability to include solvent in qmmask error James Kress (Tue Feb 27 2018 - 19:26:53 PST)
    - Re: [AMBER] Has anyone determined a fix for QM_CHECK_PERIODIC or inability to include solvent in qmmask error Goetz, Andreas (Tue Feb 27 2018 - 23:59:18 PST)
[AMBER] Adding a new atom type - ATTN, no polarizability parameter Henrik Hariman (Tue Feb 27 2018 - 12:21:59 PST)
[AMBER] Can I include Mg ions in receptor mask when using MMPBSA.py Jie Zhu (Tue Feb 27 2018 - 14:19:04 PST)
- Re: [AMBER] Can I include Mg ions in receptor mask when using MMPBSA.py Pengfei Li (Mon Mar 19 2018 - 15:29:59 PDT)
  - Re: [AMBER] Can I include Mg ions in receptor mask when using MMPBSA.py Pengfei Li (Mon Mar 19 2018 - 16:08:30 PDT)
[AMBER] leap (UNKNOWN ATOM TYPE: O3) Ruth Helena Tichauer (Wed Feb 28 2018 - 04:46:59 PST)
- Re: [AMBER] leap (UNKNOWN ATOM TYPE: O3) Markowska (Wed Feb 28 2018 - 04:55:15 PST)
  - Re: [AMBER] leap (UNKNOWN ATOM TYPE: O3) Ruth Helena Tichauer (Wed Feb 28 2018 - 05:01:08 PST)
    - Re: [AMBER] leap (UNKNOWN ATOM TYPE: O3) Kellon Belfon (Wed Feb 28 2018 - 09:59:52 PST)
    - Re: [AMBER] leap (UNKNOWN ATOM TYPE: O3) Ruth Helena Tichauer (Wed Feb 28 2018 - 11:18:45 PST)
[AMBER] Question about using cpptraj - Script Marcelo Andrade Chagas (Wed Feb 28 2018 - 11:28:02 PST)
- Re: [AMBER] Question about using cpptraj - Script Gustavo Seabra (Wed Feb 28 2018 - 12:59:51 PST)
- Re: [AMBER] Question about using cpptraj - Script Daniel Roe (Thu Mar 01 2018 - 03:30:53 PST)
[AMBER] ABMD write error to MDOUT Hugo Macdermott-Opeskin (Wed Feb 28 2018 - 20:28:49 PST)
- Re: [AMBER] ABMD write error to MDOUT Feng Pan (Wed Feb 28 2018 - 20:45:24 PST)
[AMBER] Creating gaff-suitable PDB file for SO2 M Conte (Wed Feb 28 2018 - 22:24:30 PST)
- Re: [AMBER] Creating gaff-suitable PDB file for SO2 David A Case (Mon Mar 05 2018 - 05:13:25 PST)
  - Re: [AMBER] Creating gaff-suitable PDB file for SO2 M Conte (Mon Mar 05 2018 - 23:27:39 PST)
[AMBER] vlimit exceeded for step ASMITA SEN (Thu Mar 01 2018 - 05:31:26 PST)
- Re: [AMBER] vlimit exceeded for step David A Case (Mon Mar 05 2018 - 05:09:28 PST)
- Re: [AMBER] vlimit exceeded for step ASMITA SEN (Fri Mar 09 2018 - 12:11:00 PST)
  - Re: [AMBER] vlimit exceeded for step David A Case (Fri Mar 09 2018 - 18:37:00 PST)
[AMBER] vlimit exceeded for step ASMITA SEN (Thu Mar 01 2018 - 05:32:53 PST)
[AMBER] Question about Parmbsc1 Force Field Dan Gil (Thu Mar 01 2018 - 07:09:53 PST)
- Re: [AMBER] Question about Parmbsc1 Force Field Vlad Cojocaru (Thu Mar 01 2018 - 08:09:35 PST)
- Re: [AMBER] Question about Parmbsc1 Force Field ABEL Stephane (Thu Mar 01 2018 - 08:32:54 PST)
  - Re: [AMBER] Question about Parmbsc1 Force Field Dan Gil (Thu Mar 01 2018 - 11:38:39 PST)
    - Re: [AMBER] Question about Parmbsc1 Force Field Dan Gil (Fri Mar 02 2018 - 07:24:45 PST)
    - Re: [AMBER] Question about Parmbsc1 Force Field Vlad Cojocaru (Fri Mar 02 2018 - 07:44:21 PST)
    - Re: [AMBER] Question about Parmbsc1 Force Field Dan Gil (Fri Mar 02 2018 - 08:11:30 PST)
    - Re: [AMBER] Question about Parmbsc1 Force Field David A Case (Sat Mar 03 2018 - 05:59:36 PST)
[AMBER] After running MD, the number of atom in mdcrd file becomes 0 Gu, Wenze (Thu Mar 01 2018 - 11:16:09 PST)
- Re: [AMBER] After running MD, the number of atom in mdcrd file becomes 0 Carlos Simmerling (Thu Mar 01 2018 - 11:37:46 PST)
  - Re: [AMBER] After running MD, the number of atom in mdcrd file becomes 0 Gu, Wenze (Thu Mar 01 2018 - 15:43:56 PST)
    - Re: [AMBER] After running MD, the number of atom in mdcrd file becomes 0 Carlos Simmerling (Thu Mar 01 2018 - 16:02:16 PST)
    - Re: [AMBER] After running MD, the number of atom in mdcrd file becomes 0 Carlos Simmerling (Thu Mar 01 2018 - 16:02:45 PST)
    - Re: [AMBER] After running MD, the number of atom in mdcrd file becomes 0 Gu, Wenze (Thu Mar 01 2018 - 16:20:21 PST)
    - Re: [AMBER] After running MD, the number of atom in mdcrd file becomes 0 Carlos Simmerling (Fri Mar 02 2018 - 14:51:06 PST)
    - Re: [AMBER] After running MD, the number of atom in mdcrd file becomes 0 koushik kasavajhala (Fri Mar 02 2018 - 14:57:50 PST)
    - Re: [AMBER] After running MD, the number of atom in mdcrd file becomes 0 Gu, Wenze (Sat Mar 03 2018 - 06:57:22 PST)
    - Re: [AMBER] After running MD, the number of atom in mdcrd file becomes 0 David A Case (Sat Mar 03 2018 - 14:07:35 PST)
    - Re: [AMBER] After running MD, the number of atom in mdcrd file becomes 0 Gu, Wenze (Sun Mar 04 2018 - 07:45:20 PST)
[AMBER] Turn of SMD after reaching target. David Sáez (Fri Mar 02 2018 - 08:19:40 PST)
- Re: [AMBER] Turn of SMD after reaching target. Feng Pan (Fri Mar 02 2018 - 15:55:55 PST)
[AMBER] Replica Exchange Cut > 999.0 - Necessitates Very Large Water Box? Jason Ku Wang (Fri Mar 02 2018 - 14:42:31 PST)
- Re: [AMBER] Replica Exchange Cut > 999.0 - Necessitates Very Large Water Box? Carlos Simmerling (Fri Mar 02 2018 - 14:49:41 PST)
[AMBER] Using center of mass dihedral restraints using PMEMD Lenz, Stefan (Fri Mar 02 2018 - 15:34:42 PST)
- Re: [AMBER] Using center of mass dihedral restraints using PMEMD David A Case (Sat Mar 03 2018 - 06:06:47 PST)
  - Re: [AMBER] Using center of mass dihedral restraints using PMEMD Stefan Lenz (Sat Mar 03 2018 - 06:19:37 PST)
[AMBER] created a new atom named (is an error or we can ignore it) Rana Rehan Khalid (Sat Mar 03 2018 - 02:43:16 PST)
- Re: [AMBER] created a new atom named (is an error or we can ignore it) Carlos Simmerling (Sat Mar 03 2018 - 04:27:35 PST)
  - Re: [AMBER] created a new atom named (is an error or we can ignore it) Rana Rehan Khalid (Sat Mar 03 2018 - 09:56:12 PST)
    - Re: [AMBER] created a new atom named (is an error or we can ignore it) David A Case (Sat Mar 03 2018 - 14:25:37 PST)
    - Re: [AMBER] created a new atom named (is an error or we can ignore it) Rana Rehan Khalid (Sat Mar 03 2018 - 14:47:11 PST)
[AMBER] Regarding PLP and Lys parameter Aashish Bhatt (Sat Mar 03 2018 - 03:35:05 PST)
- Re: [AMBER] Regarding PLP and Lys parameter Aashish Bhatt (Thu Mar 08 2018 - 06:38:57 PST)
  - Re: [AMBER] Regarding PLP and Lys parameter David A Case (Fri Mar 09 2018 - 05:06:58 PST)
[AMBER] Created a new atom named: Rana Rehan Khalid (Sat Mar 03 2018 - 06:23:22 PST)
- Re: [AMBER] Created a new atom named: Carlos Simmerling (Sat Mar 03 2018 - 06:27:58 PST)
  - Re: [AMBER] Created a new atom named: Rana Rehan Khalid (Sat Mar 03 2018 - 06:40:15 PST)
    - Re: [AMBER] Created a new atom named: Carlos Simmerling (Sat Mar 03 2018 - 06:57:27 PST)
[AMBER] How to Develop New Amber ForceField For Borons Barış Kurt (Sat Mar 03 2018 - 08:00:20 PST)
- Re: [AMBER] How to Develop New Amber ForceField For Borons David A Case (Sat Mar 03 2018 - 14:14:26 PST)
- Re: [AMBER] How to Develop New Amber ForceField For Borons FyD (Sat Mar 03 2018 - 22:44:48 PST)
  - Re: [AMBER] How to Develop New Amber ForceField For Borons Barış Kurt (Thu Mar 08 2018 - 05:58:25 PST)
    - Re: [AMBER] How to Develop New Amber ForceField For Borons David Cerutti (Thu Mar 08 2018 - 09:40:10 PST)
    - Re: [AMBER] How to Develop New Amber ForceField For Borons FyD (Thu Mar 08 2018 - 11:14:44 PST)
[AMBER] mm_pbsa.pl error Wu Xu (Sat Mar 03 2018 - 08:08:26 PST)
- Re: [AMBER] mm_pbsa.pl error liu junjun (Sat Mar 03 2018 - 08:17:21 PST)
  - Re: [AMBER] mm_pbsa.pl error Wu Xu (Sat Mar 03 2018 - 10:01:16 PST)
    - Re: [AMBER] mm_pbsa.pl error David A Case (Sat Mar 03 2018 - 14:21:38 PST)
    - Re: [AMBER] mm_pbsa.pl error Wu Xu (Sun Mar 04 2018 - 16:25:47 PST)
[AMBER] Penalty score Henrik Hariman (Sat Mar 03 2018 - 11:24:34 PST)
- Re: [AMBER] Penalty score David A Case (Sat Mar 03 2018 - 14:29:40 PST)
  - Re: [AMBER] Penalty score Henrik Hariman (Sun Mar 04 2018 - 07:15:18 PST)
[AMBER] reaidt.f problem Barış Kurt (Sat Mar 03 2018 - 14:50:40 PST)
- Re: [AMBER] reaidt.f problem David A Case (Sun Mar 04 2018 - 05:41:43 PST)
  - Re: [AMBER] reaidt.f problem Barış Kurt (Sun Mar 04 2018 - 12:11:35 PST)
    - Re: [AMBER] reaidt.f problem Barış Kurt (Sun Mar 04 2018 - 12:19:12 PST)
    - Re: [AMBER] reaidt.f problem Premila Samuel Mohan Dass (Sun Mar 04 2018 - 12:26:52 PST)
    - Re: [AMBER] reaidt.f problem Premila Samuel Mohan Dass (Sun Mar 04 2018 - 12:54:10 PST)
[AMBER] Energy Calculations in Amber minyuan.mail.ustc.edu.cn (Sun Mar 04 2018 - 06:10:54 PST)
- Re: [AMBER] Energy Calculations in Amber David A Case (Mon Mar 05 2018 - 05:04:30 PST)
[AMBER] disulfide bridge -reg Jeyaram R A (Mon Mar 05 2018 - 01:46:14 PST)
- Re: [AMBER] disulfide bridge -reg Abdul-Rashid III Sampaco (Mon Mar 05 2018 - 01:58:55 PST)
- Re: [AMBER] disulfide bridge -reg David A Case (Mon Mar 05 2018 - 05:00:46 PST)
  - Re: [AMBER] disulfide bridge -reg Jeyaram R A (Mon Mar 05 2018 - 21:56:51 PST)
[AMBER] Additional Ph.D. and Post-doc positions in MD simulations of enzymes Jan Brezovsky (Mon Mar 05 2018 - 09:04:16 PST)
[AMBER] Slab of water M Conte (Mon Mar 05 2018 - 15:28:18 PST)
[AMBER] vlimit exceed error sangita kachhap (Tue Mar 06 2018 - 07:47:16 PST)
- Re: [AMBER] vlimit exceed error Daniel Roe (Wed Mar 07 2018 - 10:07:09 PST)
[AMBER] van der Waals interactions, electrostatic interactions and long-range corrections balaahme (Tue Mar 06 2018 - 12:37:42 PST)
- Re: [AMBER] van der Waals interactions, electrostatic interactions and long-range corrections David A Case (Tue Mar 06 2018 - 15:47:57 PST)
[AMBER] Force Fields and Water Models meryem m'hachi (Wed Mar 07 2018 - 02:08:07 PST)
- Re: [AMBER] Force Fields and Water Models Vlad Cojocaru (Wed Mar 07 2018 - 03:17:54 PST)
Re: [AMBER] amber16 sander can't read the box information from restart file David A Case (Wed Mar 07 2018 - 05:47:41 PST)
[AMBER] Suitability of amber force fields for very low temperature MD simulations? Carolin Berner (Wed Mar 07 2018 - 06:28:43 PST)
- Re: [AMBER] Suitability of amber force fields for very low temperature MD simulations? David A Case (Thu Mar 08 2018 - 11:10:56 PST)
  - Re: [AMBER] Suitability of amber force fields for very low temperature MD simulations? Andreas Tosstorff (Sun Mar 11 2018 - 00:31:45 PST)
[AMBER] can't compile Ryan Richter (Wed Mar 07 2018 - 07:02:05 PST)
- Re: [AMBER] can't compile Daniel Roe (Wed Mar 07 2018 - 07:20:35 PST)
[AMBER] QM/MM with Orca: selected input parameters not taken into account Ruth Helena Tichauer (Thu Mar 08 2018 - 01:54:35 PST)
- Re: [AMBER] QM/MM with Orca: selected input parameters not taken into account James Kress (Thu Mar 08 2018 - 09:03:15 PST)
  - Re: [AMBER] QM/MM with Orca: selected input parameters not taken into account Ruth Helena Tichauer (Fri Mar 09 2018 - 00:44:28 PST)
    - Re: [AMBER] QM/MM with Orca: selected input parameters not taken into account Ruth Helena Tichauer (Mon Mar 12 2018 - 03:51:51 PDT)
- Re: [AMBER] QM/MM with Orca: selected input parameters not taken into account Goetz, Andreas (Thu Mar 08 2018 - 12:01:57 PST)
  - Re: [AMBER] QM/MM with Orca: selected input parameters not taken into account Ruth Helena Tichauer (Thu Mar 08 2018 - 14:11:55 PST)
[AMBER] When will you update this tutorial? Barış Kurt (Thu Mar 08 2018 - 06:04:12 PST)
- Re: [AMBER] When will you update this tutorial? David A Case (Fri Mar 09 2018 - 04:53:29 PST)
- Re: [AMBER] When will you update this tutorial? Barış Kurt (Fri Mar 09 2018 - 09:58:26 PST)
  - Re: [AMBER] When will you update this tutorial? Barış Kurt (Fri Mar 09 2018 - 10:01:37 PST)
[AMBER] constant pH simulations pemed.cuda Jacopo Sgrignani (Thu Mar 08 2018 - 07:45:53 PST)
- Re: [AMBER] constant pH simulations pemed.cuda Cruzeiro,Vinicius Wilian D (Thu Mar 08 2018 - 07:48:02 PST)
  - Re: [AMBER] constant pH simulations pemed.cuda Jacopo Sgrignani (Thu Mar 08 2018 - 07:50:53 PST)
    - Re: [AMBER] constant pH simulations pemed.cuda Cruzeiro,Vinicius Wilian D (Thu Mar 08 2018 - 08:13:43 PST)
    - Re: [AMBER] constant pH simulations pemed.cuda Eric Lang (Thu Mar 08 2018 - 08:19:10 PST)
[AMBER] radial distribution function results Lizelle Lubbe (Thu Mar 08 2018 - 09:52:45 PST)
- Re: [AMBER] radial distribution function results Daniel Roe (Tue Mar 13 2018 - 10:44:04 PDT)
  - Re: [AMBER] radial distribution function results Lizelle Lubbe (Tue Mar 13 2018 - 12:16:17 PDT)
[AMBER] FW: AMBER support and extra-point of charge (RESP) issue Jonathan David (Thu Mar 08 2018 - 23:33:53 PST)
- Re: [AMBER] FW: AMBER support and extra-point of charge (RESP) issue Mahmoud A. A. Ibrahim (Thu Mar 15 2018 - 06:46:13 PDT)
  - Re: [AMBER] FW: AMBER support and extra-point of charge (RESP) issue Jonathan David (Sun Mar 18 2018 - 23:21:37 PDT)
[AMBER] How to Convert gaussian force constant to Gaff? Barış Kurt (Fri Mar 09 2018 - 08:02:05 PST)
- Re: [AMBER] How to Convert gaussian force constant to Gaff? Pengfei Li (Mon Mar 19 2018 - 15:43:30 PDT)
  - Re: [AMBER] How to Convert gaussian force constant to Gaff? Pengfei Li (Mon Mar 19 2018 - 15:52:13 PDT)
    - Re: [AMBER] How to Convert gaussian force constant to Gaff? Hector A. Baldoni (Mon Mar 19 2018 - 18:44:54 PDT)
    - Re: [AMBER] How to Convert gaussian force constant to Gaff? Pengfei Li (Tue Mar 20 2018 - 06:14:03 PDT)
[AMBER] Lennard Jones 12-6-4 with Multiple Ion Types Seitz, Anthony Joseph (Fri Mar 09 2018 - 11:28:19 PST)
- Re: [AMBER] Lennard Jones 12-6-4 with Multiple Ion Types Jason Swails (Sun Mar 18 2018 - 15:07:13 PDT)
  - Re: [AMBER] Lennard Jones 12-6-4 with Multiple Ion Types Pengfei Li (Mon Mar 19 2018 - 16:03:36 PDT)
[AMBER] Help With tinker_to_amber Angelo Rossi (Sat Mar 10 2018 - 10:49:03 PST)
- Re: [AMBER] Help With tinker_to_amber David A Case (Sat Mar 10 2018 - 12:57:07 PST)
- Re: [AMBER] Help With tinker_to_amber Angelo Rossi (Sun Mar 11 2018 - 14:48:15 PDT)
[AMBER] Problem with cphstat Tasneem Kausar (Sun Mar 11 2018 - 22:29:49 PDT)
- Re: [AMBER] Problem with cphstat Eric Lang (Mon Mar 12 2018 - 05:14:15 PDT)
  - Re: [AMBER] Problem with cphstat Tasneem Kausar (Mon Mar 12 2018 - 07:53:28 PDT)
    - Re: [AMBER] Problem with cphstat Eric Lang (Mon Mar 12 2018 - 08:33:03 PDT)
    - Re: [AMBER] Problem with cphstat Tasneem Kausar (Mon Mar 12 2018 - 09:12:09 PDT)
[AMBER] error while installing AMBER for GPU malkeet singh Bahia (Mon Mar 12 2018 - 07:59:33 PDT)
- Re: [AMBER] error while installing AMBER for GPU David A Case (Mon Mar 12 2018 - 10:22:33 PDT)
- Re: [AMBER] error while installing AMBER for GPU David A Case (Mon Mar 12 2018 - 10:24:15 PDT)
  - Re: [AMBER] error while installing AMBER for GPU malkeet singh Bahia (Tue Mar 13 2018 - 09:14:47 PDT)
    - Re: [AMBER] error while installing AMBER for GPU Daniel Roe (Tue Mar 13 2018 - 09:34:30 PDT)
    - Re: [AMBER] error while installing AMBER for GPU malkeet singh Bahia (Tue Mar 13 2018 - 11:08:29 PDT)
    - Re: [AMBER] error while installing AMBER for GPU malkeet singh Bahia (Tue Mar 13 2018 - 11:28:15 PDT)
    - Re: [AMBER] error while installing AMBER for GPU malkeet singh Bahia (Tue Mar 13 2018 - 11:31:15 PDT)
    - Re: [AMBER] error while installing AMBER for GPU malkeet singh Bahia (Wed Mar 14 2018 - 07:53:09 PDT)
    - Re: [AMBER] error while installing AMBER for GPU Dr. M. Shahid (Wed Mar 14 2018 - 08:49:29 PDT)
    - Re: [AMBER] error while installing AMBER for GPU malkeet singh Bahia (Wed Mar 14 2018 - 11:08:59 PDT)
    - Re: [AMBER] error while installing AMBER for GPU malkeet singh Bahia (Wed Mar 14 2018 - 11:10:45 PDT)
    - Re: [AMBER] error while installing AMBER for GPU Roitberg,Adrian E (Wed Mar 14 2018 - 11:15:36 PDT)
    - Re: [AMBER] error while installing AMBER for GPU malkeet singh Bahia (Wed Mar 14 2018 - 11:47:51 PDT)
    - Re: [AMBER] error while installing AMBER for GPU malkeet singh Bahia (Wed Mar 14 2018 - 11:59:46 PDT)
    - Re: [AMBER] error while installing AMBER for GPU David A Case (Wed Mar 14 2018 - 13:07:36 PDT)
    - Re: [AMBER] error while installing AMBER for GPU malkeet singh Bahia (Mon Mar 19 2018 - 11:11:23 PDT)
    - Re: [AMBER] error while installing AMBER for GPU malkeet singh Bahia (Mon Mar 19 2018 - 11:14:23 PDT)
    - Re: [AMBER] error while installing AMBER for GPU Ross Walker (Tue Mar 20 2018 - 07:46:36 PDT)
    - Re: [AMBER] error while installing AMBER for GPU malkeet singh Bahia (Tue Mar 20 2018 - 07:51:30 PDT)
    - [AMBER] Fwd: error while installing AMBER for GPU malkeet singh Bahia (Mon Mar 19 2018 - 23:29:40 PDT)
    - Re: [AMBER] Fwd: error while installing AMBER for GPU Luka Bilić (Tue Mar 20 2018 - 00:12:36 PDT)
    - Re: [AMBER] Fwd: error while installing AMBER for GPU malkeet singh Bahia (Tue Mar 20 2018 - 03:13:47 PDT)
    - Re: [AMBER] Fwd: error while installing AMBER for GPU David A Case (Tue Mar 20 2018 - 05:04:09 PDT)
    - Re: [AMBER] Fwd: error while installing AMBER for GPU Maciej Maciejczyk (Tue Mar 20 2018 - 05:15:36 PDT)
    - Re: [AMBER] error while installing AMBER for GPU David A Case (Wed Mar 14 2018 - 13:01:57 PDT)
[AMBER] TI simulation with a solvateCap: vlimit exceeded for step Meiting Wang (Tue Mar 13 2018 - 08:31:38 PDT)
- Re: [AMBER] TI simulation with a solvateCap: vlimit exceeded for step David A Case (Sun Mar 18 2018 - 12:00:28 PDT)
[AMBER] Fwd: ACS COMP Boston awards deadline set Carlos Simmerling (Tue Mar 13 2018 - 12:00:21 PDT)
[AMBER] NFE, PMD, and MULTI_RMSD questions Russell Davidson (Tue Mar 13 2018 - 16:26:53 PDT)
- Re: [AMBER] NFE, PMD, and MULTI_RMSD questions Feng Pan (Wed Mar 14 2018 - 11:31:32 PDT)
[AMBER] restraintmask, error in reading namelist cntrl Nikolay N. Kuzmich (Wed Mar 14 2018 - 08:10:37 PDT)
- Re: [AMBER] restraintmask, error in reading namelist cntrl Dr. M. Shahid (Wed Mar 14 2018 - 08:51:25 PDT)
- Re: [AMBER] restraintmask, error in reading namelist cntrl David A Case (Wed Mar 14 2018 - 13:09:39 PDT)
- Re: [AMBER] restraintmask, error in reading namelist cntrl Nikolay N. Kuzmich (Fri Mar 16 2018 - 08:53:38 PDT)
  - Re: [AMBER] restraintmask, error in reading namelist cntrl David A Case (Sat Mar 17 2018 - 06:28:30 PDT)
- Re: [AMBER] restraintmask, error in reading namelist cntrl Nikolay N. Kuzmich (Mon Mar 19 2018 - 02:14:17 PDT)
[AMBER] Reaction Coordinate that is the Difference of two Distances diego.soler.uam.es (Wed Mar 14 2018 - 08:24:01 PDT)
- Re: [AMBER] Reaction Coordinate that is the Difference of two Distances Ruth Helena Tichauer (Wed Mar 14 2018 - 08:40:23 PDT)
  - Re: [AMBER] Reaction Coordinate that is the Difference of two Distances diego.soler.uam.es (Wed Mar 14 2018 - 09:19:21 PDT)
[AMBER] Query regarding minimization Rakesh Srivastava (Thu Mar 15 2018 - 00:37:44 PDT)
- Re: [AMBER] Query regarding minimization David A Case (Thu Mar 15 2018 - 04:50:02 PDT)
  - Re: [AMBER] Query regarding minimization Rakesh Srivastava (Thu Mar 15 2018 - 05:17:24 PDT)
[AMBER] center of mass restraint in pmemd.cuda Rajarshi Roy (Thu Mar 15 2018 - 03:07:49 PDT)
- Re: [AMBER] center of mass restraint in pmemd.cuda David A Case (Sun Mar 18 2018 - 11:52:25 PDT)
  - Re: [AMBER] center of mass restraint in pmemd.cuda Rajarshi Roy (Mon Mar 19 2018 - 03:39:57 PDT)
    - Re: [AMBER] center of mass restraint in pmemd.cuda Ross Walker (Tue Mar 20 2018 - 07:42:42 PDT)
- Re: [AMBER] center of mass restraint in pmemd.cuda Rajarshi Roy (Tue Mar 20 2018 - 08:15:25 PDT)
  - Re: [AMBER] center of mass restraint in pmemd.cuda Feng Pan (Tue Mar 20 2018 - 14:46:49 PDT)
    - Re: [AMBER] center of mass restraint in pmemd.cuda Rajarshi Roy (Tue Mar 20 2018 - 18:34:08 PDT)
    - Re: [AMBER] center of mass restraint in pmemd.cuda Feng Pan (Tue Mar 20 2018 - 18:44:30 PDT)
    - Re: [AMBER] center of mass restraint in pmemd.cuda Rajarshi Roy (Tue Mar 20 2018 - 20:39:05 PDT)
    - Re: [AMBER] center of mass restraint in pmemd.cuda Feng Pan (Tue Mar 20 2018 - 20:41:50 PDT)
    - Re: [AMBER] center of mass restraint in pmemd.cuda Rajarshi Roy (Tue Mar 20 2018 - 20:54:15 PDT)
    - Re: [AMBER] center of mass restraint in pmemd.cuda Rajarshi Roy (Wed Mar 21 2018 - 04:41:17 PDT)
    - Re: [AMBER] center of mass restraint in pmemd.cuda Feng Pan (Mon Mar 26 2018 - 12:35:39 PDT)
    - Re: [AMBER] center of mass restraint in pmemd.cuda Rajarshi Roy (Tue Apr 03 2018 - 23:27:13 PDT)
[AMBER] Count water in active site Lizelle Lubbe (Thu Mar 15 2018 - 06:22:57 PDT)
- Re: [AMBER] Count water in active site Daniel Roe (Tue Apr 10 2018 - 06:17:39 PDT)
[AMBER] Volume occupied during MD Lizelle Lubbe (Thu Mar 15 2018 - 06:31:28 PDT)
- Re: [AMBER] Volume occupied during MD Daniel Roe (Tue Apr 10 2018 - 06:24:00 PDT)
[AMBER] Convertion between Gaussian and Gaff ANGULAR Force Constant Units micheal lop (Thu Mar 15 2018 - 09:43:15 PDT)
[AMBER] Inconsistency with the number of counter ions required for neutralization maryam azimzadehirani (Mon Mar 19 2018 - 04:01:35 PDT)
- Re: [AMBER] Inconsistency with the number of counter ions required for neutralization David A Case (Mon Mar 19 2018 - 05:07:34 PDT)
  - Re: [AMBER] Inconsistency with the number of counter ions required for neutralization maryam azimzadehirani (Mon Mar 19 2018 - 07:48:16 PDT)
[AMBER] 3D-RISM solvation free energy of a molecule in an organic solvent (not water) Smith, Micholas D. (Mon Mar 19 2018 - 07:40:12 PDT)
- Re: [AMBER] 3D-RISM solvation free energy of a molecule in an organic solvent (not water) Tyler Luchko (Lists) (Mon Mar 19 2018 - 10:53:36 PDT)
  - Re: [AMBER] 3D-RISM solvation free energy of a molecule in an organic solvent (not water) Smith, Micholas D. (Mon Mar 19 2018 - 10:59:09 PDT)
[AMBER] force-filed parametrization for dichloromethane daniele selli (Wed Mar 21 2018 - 02:27:08 PDT)
- Re: [AMBER] force-filed parametrization for dichloromethane David A Case (Fri Mar 23 2018 - 04:43:27 PDT)
[AMBER] Sudden termination of the heating simulation with sander.MPI Nikolay N. Kuzmich (Wed Mar 21 2018 - 05:24:44 PDT)
- Re: [AMBER] Sudden termination of the heating simulation with sander.MPI malkeet singh Bahia (Wed Mar 21 2018 - 05:47:44 PDT)
- Re: [AMBER] Sudden termination of the heating simulation with sander.MPI Carlos Simmerling (Wed Mar 21 2018 - 05:52:51 PDT)
- Re: [AMBER] Sudden termination of the heating simulation with sander.MPI Nikolay N. Kuzmich (Thu Mar 22 2018 - 08:42:47 PDT)
[AMBER] upper limit of water with solvateBox Ikuo KURISAKI (Wed Mar 21 2018 - 06:06:28 PDT)
- Re: [AMBER] upper limit of water with solvateBox Ahmed Mashaly (Wed Mar 21 2018 - 07:07:18 PDT)
  - Re: [AMBER] upper limit of water with solvateBox Ikuo KURISAKI (Wed Mar 21 2018 - 17:54:18 PDT)
- Re: [AMBER] upper limit of water with solvateBox David A Case (Wed Mar 21 2018 - 07:35:21 PDT)
- Re: [AMBER] upper limit of water with solvateBox Scott Brozell (Fri Mar 23 2018 - 09:38:23 PDT)
[AMBER] Resume AMD simulation Rosellen, Martin (Wed Mar 21 2018 - 06:24:35 PDT)
- Re: [AMBER] Resume AMD simulation Daniel Roe (Tue Apr 10 2018 - 06:25:58 PDT)
Re: [AMBER] FE atom in PARMCHK.DAT file David A Case (Wed Mar 21 2018 - 07:32:20 PDT)
[AMBER] PMEMD error: "Increase lin__limit in nb_pairlist.F90!!!" Colin Brown (Wed Mar 21 2018 - 07:42:01 PDT)
[AMBER] Temperature-Based Replica Exchange: Number of Replicas Jason Ku Wang (Wed Mar 21 2018 - 16:15:12 PDT)
- Re: [AMBER] Temperature-Based Replica Exchange: Number of Replicas Cruzeiro,Vinicius Wilian D (Wed Mar 21 2018 - 16:37:47 PDT)
  - Re: [AMBER] Temperature-Based Replica Exchange: Number of Replicas Chris Neale (Wed Mar 21 2018 - 19:40:58 PDT)
[AMBER] MM-GBSA for membrane protein jixiaofeng (Wed Mar 21 2018 - 18:59:02 PDT)
[AMBER] Normal Mode Analysis in Amber Robert DeLisle (Wed Mar 21 2018 - 19:59:24 PDT)
- Re: [AMBER] Normal Mode Analysis in Amber David A Case (Thu Mar 22 2018 - 05:30:41 PDT)
  - Re: [AMBER] Normal Mode Analysis in Amber Robert DeLisle (Thu Mar 22 2018 - 07:59:25 PDT)
[AMBER] prep to mol2 conversion Rana Rehan Khalid (Thu Mar 22 2018 - 04:45:03 PDT)
- Re: [AMBER] prep to mol2 conversion David A Case (Thu Mar 22 2018 - 05:34:39 PDT)
  - Re: [AMBER] prep to mol2 conversion Rana Rehan Khalid (Thu Mar 22 2018 - 05:55:42 PDT)
    - Re: [AMBER] prep to mol2 conversion Rana Rehan Khalid (Thu Mar 22 2018 - 06:12:05 PDT)
    - Re: [AMBER] prep to mol2 conversion Rana Rehan Khalid (Thu Mar 22 2018 - 07:11:15 PDT)
Re: [AMBER] pysmst code David A Case (Thu Mar 22 2018 - 05:21:00 PDT)
[AMBER] Accelerated MD - Please advice maryam azimzadehirani (Thu Mar 22 2018 - 07:41:41 PDT)
[AMBER] MCPB.py Thakur, Abhishek (Thu Mar 22 2018 - 12:12:54 PDT)
- Re: [AMBER] MCPB.py Pengfei Li (Mon Mar 26 2018 - 09:24:03 PDT)
  - Re: [AMBER] MCPB.py Thakur, Abhishek (Mon Mar 26 2018 - 09:39:25 PDT)
    - Re: [AMBER] MCPB.py Pengfei Li (Tue Mar 27 2018 - 14:13:27 PDT)
[AMBER] generating solvated Fe2+ Thomas Pochapsky (Thu Mar 22 2018 - 12:48:53 PDT)
- Re: [AMBER] generating solvated Fe2+ Pengfei Li (Mon Mar 26 2018 - 09:30:56 PDT)
[AMBER] pmemd.MPI with a single-entry group file? Kevin Keane (Thu Mar 22 2018 - 16:12:25 PDT)
- Re: [AMBER] pmemd.MPI with a single-entry group file? David A Case (Thu Mar 22 2018 - 18:52:30 PDT)
  - Re: [AMBER] pmemd.MPI with a single-entry group file? Kevin Keane (Thu Mar 22 2018 - 20:30:02 PDT)
[AMBER] which geometry is used in am1bcc charge in antechamber in amber tools 17? Dai, Shuo (Thu Mar 22 2018 - 17:03:06 PDT)
- Re: [AMBER] which geometry is used in am1bcc charge in antechamber in amber tools 17? David A Case (Thu Mar 22 2018 - 18:27:17 PDT)
  - Re: [AMBER] which geometry is used in am1bcc charge in antechamber in amber tools 17? Dai, Shuo (Fri Mar 23 2018 - 01:35:00 PDT)
[AMBER] Problems with creating prmtop file from Charmm-GUI generated membrane system Chetna Tyagi (Fri Mar 23 2018 - 03:55:00 PDT)
[AMBER] AMBER qualitatively compared to other packages Dmitry Suplatov (Fri Mar 23 2018 - 04:24:37 PDT)
- Re: [AMBER] AMBER qualitatively compared to other packages David A Case (Tue Mar 27 2018 - 06:53:51 PDT)
  - Re: [AMBER] AMBER qualitatively compared to other packages Thomas Evangelidis (Wed Mar 28 2018 - 04:38:44 PDT)
    - Re: [AMBER] AMBER qualitatively compared to other packages George M. Giambasu (Wed Mar 28 2018 - 06:35:21 PDT)
[AMBER] ERROR TUTORIAL AMBER - creating PDB files from the AMBER coordinate files Edjan Silva (Fri Mar 23 2018 - 10:16:30 PDT)
- Re: [AMBER] ERROR TUTORIAL AMBER - creating PDB files from the AMBER coordinate files Yuliana Bosken (Fri Mar 23 2018 - 15:41:52 PDT)
  - Re: [AMBER] ERROR TUTORIAL AMBER - creating PDB files from the AMBER coordinate files Edjan Silva (Fri Mar 23 2018 - 22:47:14 PDT)
[AMBER] Position of amino acid from surface roja rahmani (Sat Mar 24 2018 - 05:21:46 PDT)
[AMBER] Normal Mode Analysis - output from nmode? Robert DeLisle (Sat Mar 24 2018 - 10:42:51 PDT)
- Re: [AMBER] Normal Mode Analysis - output from nmode? David A Case (Sun Mar 25 2018 - 08:13:41 PDT)
[AMBER] Calculating ligand contribution is failing- MMPBSA method varun dewaker (Sun Mar 25 2018 - 22:20:24 PDT)
- Re: [AMBER] Calculating ligand contribution is failing- MMPBSA method George Tzotzos (Tue Mar 27 2018 - 03:15:05 PDT)
[AMBER] Calculate water density in the protein water channel by Amber 16 张玥 (Mon Mar 26 2018 - 06:20:26 PDT)
- Re: [AMBER] Calculate water density in the protein water channel by Amber 16 Daniel Roe (Tue Apr 10 2018 - 06:32:05 PDT)
[AMBER] Selection of interactions that persisted for over 75% of MD time Manivel Panneerselvam (Mon Mar 26 2018 - 22:39:30 PDT)
[AMBER] Calculate water density in the protein water channel by Amber 16 张玥 (Mon Mar 26 2018 - 22:52:22 PDT)
[AMBER] WESTPA workshop August 2-3, 2018 Lillian Chong (Tue Mar 27 2018 - 10:54:13 PDT)
[AMBER] RMSD of individual sub unit of a protein complex. Jag Silwal (Tue Mar 27 2018 - 14:40:20 PDT)
- Re: [AMBER] RMSD of individual sub unit of a protein complex. David A Case (Tue Mar 27 2018 - 15:15:14 PDT)
[AMBER] peptide and bilayer membrane simulations Chetna Tyagi (Wed Mar 28 2018 - 02:30:27 PDT)
- Re: [AMBER] peptide and bilayer membrane simulations Beale, John (Wed Mar 28 2018 - 02:41:50 PDT)
  - Re: [AMBER] peptide and bilayer membrane simulations Chetna Tyagi (Wed Mar 28 2018 - 02:46:39 PDT)
- Re: [AMBER] peptide and bilayer membrane simulations David A Case (Wed Mar 28 2018 - 06:56:07 PDT)
  - Re: [AMBER] peptide and bilayer membrane simulations Chetna Tyagi (Wed Mar 28 2018 - 08:54:51 PDT)
[AMBER] Random seed reproducibility Sergey Samsonov (Thu Mar 29 2018 - 01:32:04 PDT)
- Re: [AMBER] Random seed reproducibility Daniel Roe (Thu Mar 29 2018 - 06:17:41 PDT)
[AMBER] MacOS pmemd.cuda Kadir Ozcan (Thu Mar 29 2018 - 12:21:22 PDT)
- Re: [AMBER] MacOS pmemd.cuda David Cerutti (Thu Mar 29 2018 - 12:54:34 PDT)
[AMBER] cpptraj mask for hbond analysis Michael Yonkunas (Fri Mar 30 2018 - 09:09:27 PDT)
- Re: [AMBER] cpptraj mask for hbond analysis David A Case (Fri Mar 30 2018 - 11:58:07 PDT)
- Re: [AMBER] cpptraj mask for hbond analysis Daniel Roe (Fri Mar 30 2018 - 12:00:15 PDT)
[AMBER] CUDA (GPU): Implementation does not currently support the use of COM simulations.Require iat(1) >= 0. rabi1993.iitg.ernet.in (Fri Mar 30 2018 - 22:03:23 PDT)
- Re: [AMBER] CUDA (GPU): Implementation does not currently support the use of COM simulations.Require iat(1) >= 0. Ross Walker (Sat Mar 31 2018 - 06:06:05 PDT)
[AMBER] Query for force field parameters of 'R' and 'S' enantiomers rabi1993.iitg.ernet.in (Fri Mar 30 2018 - 22:05:17 PDT)
- Re: [AMBER] Query for force field parameters of 'R' and 'S' enantiomers Chetna Tyagi (Sun Apr 01 2018 - 03:32:55 PDT)
  - Re: [AMBER] Query for force field parameters of 'R' and 'S' enantiomers FyD (Wed Apr 04 2018 - 01:47:39 PDT)
    - Re: [AMBER] Query for force field parameters of 'R' and 'S' enantiomers Carlos Simmerling (Wed Apr 04 2018 - 05:27:14 PDT)
- Re: [AMBER] Query for force field parameters of 'R' and 'S' enantiomers David A Case (Sun Apr 01 2018 - 08:17:12 PDT)
- Re: [AMBER] Query for force field parameters of 'R' and 'S' enantiomers FyD (Wed Apr 04 2018 - 02:01:07 PDT)
[AMBER] Need advice with GPU choice. Setyanto Md (Sat Mar 31 2018 - 01:54:08 PDT)
[AMBER] Help with mdcrd in VMD Vikram Dalal (Sat Mar 31 2018 - 10:16:49 PDT)
- Re: [AMBER] Help with mdcrd in VMD Abdul-Rashid III Sampaco (Sat Mar 31 2018 - 10:35:54 PDT)
[AMBER] superimpose two atoms in cpptraj Mark Rance (Sun Apr 01 2018 - 05:55:34 PDT)
- Re: [AMBER] superimpose two atoms in cpptraj David A Case (Sun Apr 01 2018 - 08:29:21 PDT)
[AMBER] ZnS force field parameters roja rahmani (Sun Apr 01 2018 - 11:17:43 PDT)
- Re: [AMBER] ZnS force field parameters David A Case (Mon Apr 02 2018 - 07:57:47 PDT)
[AMBER] no output results for heating process wangjy.dicp.ac.cn (Mon Apr 02 2018 - 01:47:11 PDT)
- Re: [AMBER] no output results for heating process Carlos Simmerling (Mon Apr 02 2018 - 06:13:08 PDT)
- Re: [AMBER] no output results for heating process David A Case (Tue Apr 03 2018 - 08:23:58 PDT)
[AMBER] Fwd: Postdoctoral Positions in Computational Biophysics at Westlake University Pengfei Li (Tue Apr 03 2018 - 09:00:38 PDT)
[AMBER] Converting gromacs TRX file to mdcrd.nc and mdvel.nc Mohd Farid Ismail (Wed Apr 04 2018 - 03:20:15 PDT)
- Re: [AMBER] Converting gromacs TRX file to mdcrd.nc and mdvel.nc Daniel Roe (Tue Apr 10 2018 - 06:34:05 PDT)
[AMBER] RNA with Amber16 Elisa FREZZA (Wed Apr 04 2018 - 04:05:57 PDT)
- Re: [AMBER] RNA with Amber16 Christina Bergonzo (Wed Apr 04 2018 - 05:58:36 PDT)
[AMBER] A Problem about Alanine Scan of Proline 忠彦 (Wed Apr 04 2018 - 04:55:01 PDT)
[AMBER] When did SCEE and SCNB make it into the force-field files Karl Kirschner (Wed Apr 04 2018 - 06:28:08 PDT)
- Re: [AMBER] When did SCEE and SCNB make it into the force-field files David Cerutti (Wed Apr 04 2018 - 16:37:09 PDT)
  - Re: [AMBER] When did SCEE and SCNB make it into the force-field files Ross Walker (Thu Apr 05 2018 - 13:18:42 PDT)
    - Re: [AMBER] When did SCEE and SCNB make it into the force-field files Karl Kirschner (Thu Apr 05 2018 - 23:49:26 PDT)
[AMBER] Are the equations for FF14SB and FF15IPQ same or different Dmitry Suplatov (Wed Apr 04 2018 - 06:32:52 PDT)
- Re: [AMBER] Are the equations for FF14SB and FF15IPQ same or different David A Case (Wed Apr 04 2018 - 08:05:55 PDT)
[AMBER] parmed CharmmError: Could not convert dihedral phase to <type 'float'> Sadegh Faramarzi Ganjabad (Wed Apr 04 2018 - 11:05:50 PDT)
- Re: [AMBER] parmed CharmmError: Could not convert dihedral phase to <type 'float'> David A Case (Mon Apr 09 2018 - 06:04:19 PDT)
- Re: [AMBER] parmed CharmmError: Could not convert dihedral phase to <type 'float'> Sadegh Faramarzi Ganjabad (Tue Apr 10 2018 - 09:42:45 PDT)
[AMBER] Changing box size M Conte (Wed Apr 04 2018 - 17:47:13 PDT)
- Re: [AMBER] Changing box size David A Case (Thu Apr 05 2018 - 07:53:23 PDT)
[AMBER] Fix for fixed sized cmd in nab Åke Sandgren (Thu Apr 05 2018 - 03:35:29 PDT)
- Re: [AMBER] Fix for fixed sized cmd in nab Åke Sandgren (Thu Apr 05 2018 - 09:56:23 PDT)
- Re: [AMBER] Fix for fixed sized cmd in nab David A Case (Mon Apr 09 2018 - 06:01:43 PDT)
[AMBER] Query about Constant pH cpout file Saikat Dutta chowdhury (Thu Apr 05 2018 - 05:33:07 PDT)
- Re: [AMBER] Query about Constant pH cpout file Cruzeiro,Vinicius Wilian D (Thu Apr 05 2018 - 10:04:20 PDT)
[AMBER] Replica Exchange: an illegal memory access was encountered launching kernel kClearForces Jason Ku Wang (Thu Apr 05 2018 - 13:58:35 PDT)
[AMBER] Calculate minimum distance between two groups of atoms David Sáez (Thu Apr 05 2018 - 14:13:55 PDT)
- Re: [AMBER] Calculate minimum distance between two groups of atoms Daniel Roe (Thu Apr 05 2018 - 14:31:42 PDT)
  - Re: [AMBER] Calculate minimum distance between two groups of atoms David Sáez (Sat Apr 07 2018 - 05:09:34 PDT)
    - Re: [AMBER] Calculate minimum distance between two groups of atoms Daniel Roe (Tue Apr 10 2018 - 06:36:32 PDT)
[AMBER] Replica Exchange: an illegal memory access was encountered launching kernel kClearForces Jason Ku Wang (Thu Apr 05 2018 - 14:37:46 PDT)
[AMBER] Temperatured-Based Replica Exchange: an illegal memory access was encountered launching kernel kClearForces Jason Ku Wang (Thu Apr 05 2018 - 14:45:06 PDT)
[AMBER] Questions about SEBOMD with Divide and Conqure method Mingyuan_xu (Fri Apr 06 2018 - 04:35:07 PDT)
- [AMBER] Questions about SEBOMD with Divide and Conqure method Mingyuan (Fri Apr 06 2018 - 04:47:10 PDT)
  - Re: [AMBER] Questions about SEBOMD with Divide and Conqure method Gerald Monard (Fri Apr 06 2018 - 08:18:17 PDT)
[AMBER] ERROR TUTORIAL AMBER --- Step 3.3.3) "Visualizing the trajectories with VMD" Edjan Silva (Fri Apr 06 2018 - 05:07:09 PDT)
- Re: [AMBER] ERROR TUTORIAL AMBER --- Step 3.3.3) "Visualizing the trajectories with VMD" Diego Gomes (Fri Apr 06 2018 - 05:20:12 PDT)
  - Re: [AMBER] ERROR TUTORIAL AMBER --- Step 3.3.3) "Visualizing the trajectories with VMD" Edjan Silva (Thu Apr 12 2018 - 08:05:41 PDT)
- Re: [AMBER] ERROR TUTORIAL AMBER --- Step 3.3.3) "Visualizing the trajectories with VMD" David A Case (Sat Apr 07 2018 - 08:02:11 PDT)
[AMBER] atomic radius data in amber library Rakesh Srivastava (Sat Apr 07 2018 - 03:51:09 PDT)
- Re: [AMBER] atomic radius data in amber library David A Case (Sat Apr 07 2018 - 08:09:03 PDT)
  - Re: [AMBER] atomic radius data in amber library Rakesh Srivastava (Sat Apr 07 2018 - 21:49:10 PDT)
[AMBER] MMGBSA calculation for complex with two ligangs using three trajectoris cuiyinglukitty (Sun Apr 08 2018 - 01:36:55 PDT)
[AMBER] RED Server deriving charges for hybrid molecule using GLYCAM ff Neha Gandhi (Sun Apr 08 2018 - 23:26:32 PDT)
- Re: [AMBER] RED Server deriving charges for hybrid molecule using GLYCAM ff FyD (Tue Apr 10 2018 - 05:36:17 PDT)
[AMBER] Unable to perform MD because of Fortran runtime error: End of file Sehrish Naz (Mon Apr 09 2018 - 03:28:18 PDT)
- Re: [AMBER] Unable to perform MD because of Fortran runtime error: End of file David A Case (Mon Apr 09 2018 - 05:50:08 PDT)
[AMBER] Extracting forces from the mdcrd file Nikolay N. Kuzmich (Mon Apr 09 2018 - 04:28:06 PDT)
- Re: [AMBER] Extracting forces from the mdcrd file Daniel Roe (Mon Apr 09 2018 - 05:13:08 PDT)
- Re: [AMBER] Extracting forces from the mdcrd file Nikolay N. Kuzmich (Mon Apr 09 2018 - 10:09:01 PDT)
  - Re: [AMBER] Extracting forces from the mdcrd file Daniel Roe (Mon Apr 09 2018 - 11:53:54 PDT)
- Re: [AMBER] Extracting forces from the mdcrd file Nikolay N. Kuzmich (Tue Apr 10 2018 - 03:41:16 PDT)
  - Re: [AMBER] Extracting forces from the mdcrd file Daniel Roe (Tue Apr 10 2018 - 06:14:12 PDT)
- Re: [AMBER] Extracting forces from the mdcrd file Nikolay N. Kuzmich (Wed Apr 11 2018 - 06:09:49 PDT)
  - Re: [AMBER] Extracting forces from the mdcrd file Daniel Roe (Thu Apr 12 2018 - 08:28:02 PDT)
- Re: [AMBER] Extracting forces from the mdcrd file Nikolay N. Kuzmich (Fri Apr 13 2018 - 15:08:14 PDT)
[AMBER] residue looks like it is not a part of protein Thakur, Abhishek (Mon Apr 09 2018 - 14:54:27 PDT)
- Re: [AMBER] residue looks like it is not a part of protein David A Case (Mon Apr 09 2018 - 18:34:09 PDT)
- Re: [AMBER] residue looks like it is not a part of protein Rajarshi Roy (Mon Apr 09 2018 - 20:21:11 PDT)
  - Re: [AMBER] residue looks like it is not a part of protein Thakur, Abhishek (Thu Apr 12 2018 - 08:41:55 PDT)
    - Re: [AMBER] residue looks like it is not a part of protein Carlos Simmerling (Thu Apr 12 2018 - 08:56:27 PDT)
[AMBER] protons Carlos Romero (Mon Apr 09 2018 - 16:36:13 PDT)
- Re: [AMBER] protons David A Case (Mon Apr 09 2018 - 18:42:38 PDT)
  - Re: [AMBER] protons Carlos Romero (Mon Apr 09 2018 - 21:45:54 PDT)
[AMBER] Regarding input files Midhun K Madhu (Mon Apr 09 2018 - 23:45:01 PDT)
- Re: [AMBER] Regarding input files David A Case (Tue Apr 10 2018 - 04:28:12 PDT)
  - Re: [AMBER] Regarding input files Daniel Roe (Tue Apr 10 2018 - 06:40:09 PDT)
Re: [AMBER] AMBER Digest, Vol 2256, Issue 1 Sehrish Naz (Tue Apr 10 2018 - 07:01:01 PDT)
[AMBER] PB calculation is failing varun dewaker (Tue Apr 10 2018 - 07:54:38 PDT)
[AMBER] Cpptraj and Sander Question Portillo, Jennifer (Tue Apr 10 2018 - 17:24:58 PDT)
- Re: [AMBER] Cpptraj and Sander Question David A Case (Wed Apr 11 2018 - 05:15:53 PDT)
  - Re: [AMBER] Cpptraj and Sander Question Portillo, Jennifer (Mon Apr 16 2018 - 14:10:42 PDT)
[AMBER] Problem building Amber16 with -cuda Ryan Novosielski (Wed Apr 11 2018 - 00:28:19 PDT)
- Re: [AMBER] Problem building Amber16 with -cuda David A Case (Wed Apr 11 2018 - 05:19:39 PDT)
  - Re: [AMBER] Problem building Amber16 with -cuda Ryan Novosielski (Wed Apr 11 2018 - 07:53:42 PDT)
    - Re: [AMBER] Problem building Amber16 with -cuda Ryan Novosielski (Wed Apr 11 2018 - 07:57:57 PDT)
[AMBER] ATP hydrolysis Abhilash J (Wed Apr 11 2018 - 00:42:36 PDT)
[AMBER] Thioester Bond:leap Aravind Ravichandran (Wed Apr 11 2018 - 02:54:12 PDT)
- Re: [AMBER] Thioester Bond:leap David A Case (Wed Apr 11 2018 - 05:23:04 PDT)
[AMBER] Problem in disance restraints for atom groups Huan He (Wed Apr 11 2018 - 04:00:36 PDT)
- Re: [AMBER] Problem in disance restraints for atom groups Huan He (Wed Apr 11 2018 - 04:20:42 PDT)
  - Re: [AMBER] Problem in disance restraints for atom groups David A Case (Wed Apr 11 2018 - 05:28:37 PDT)
    - Re: [AMBER] Problem in disance restraints for atom groups Huan He (Wed Apr 11 2018 - 06:37:02 PDT)
[AMBER] MMPBSA runs GB but fails in PB for RNA-ligand complex Kasprzak, Wojciech (NIH/NCI) [C] (Wed Apr 11 2018 - 07:47:44 PDT)
- Re: [AMBER] MMPBSA runs GB but fails in PB for RNA-ligand complex Ray Luo (Wed Apr 11 2018 - 09:46:32 PDT)
  - Re: [AMBER] MMPBSA runs GB but fails in PB for RNA-ligand complex Kasprzak, Wojciech (NIH/NCI) [C] (Wed Apr 11 2018 - 12:47:02 PDT)
    - Re: [AMBER] MMPBSA runs GB but fails in PB for RNA-ligand complex Ray Luo (Wed Apr 11 2018 - 18:54:47 PDT)
[AMBER] Help with building a non-standard RNA structure Debostuti Ghoshdastidar (Wed Apr 11 2018 - 23:52:47 PDT)
[AMBER] Ambertools17 error: 3D-RISM calculation Fabian Herrera Olivares (Thu Apr 12 2018 - 00:49:40 PDT)
- Re: [AMBER] Ambertools17 error: 3D-RISM calculation Leena Aggarwal (Thu Apr 12 2018 - 04:51:08 PDT)
- Re: [AMBER] Ambertools17 error: 3D-RISM calculation David A Case (Thu Apr 12 2018 - 04:51:56 PDT)
[AMBER] How can I run PMEMD with multiple distance restraints? Markowska (Thu Apr 12 2018 - 06:32:17 PDT)
- Re: [AMBER] How can I run PMEMD with multiple distance restraints? David A Case (Thu Apr 12 2018 - 09:55:20 PDT)
[AMBER] MM-GBSA on pH constant MD simulations Giovanni Grazioso (Thu Apr 12 2018 - 07:27:43 PDT)
[AMBER] Simulation between DNA and small molecules. Edjan Silva (Thu Apr 12 2018 - 08:35:37 PDT)
- Re: [AMBER] Simulation between DNA and small molecules. David A Case (Thu Apr 12 2018 - 09:58:48 PDT)
  - Re: [AMBER] Simulation between DNA and small molecules. Edjan Silva (Mon Apr 16 2018 - 05:44:46 PDT)
- Re: [AMBER] Simulation between DNA and small molecules. Edjan Silva (Mon Apr 16 2018 - 11:49:13 PDT)
[AMBER] Building Amber16 CPU with Intel Compiler and GPU with GNU Compiler vs. MPI Ryan Novosielski (Thu Apr 12 2018 - 10:14:20 PDT)
- Re: [AMBER] Building Amber16 CPU with Intel Compiler and GPU with GNU Compiler vs. MPI Daniel Roe (Fri Apr 13 2018 - 08:05:22 PDT)
  - Re: [AMBER] Building Amber16 CPU with Intel Compiler and GPU with GNU Compiler vs. MPI Scott Brozell (Sat Apr 14 2018 - 14:36:28 PDT)
[AMBER] Two-Dimensional Replica Exchange in AMBER Jason Ku Wang (Fri Apr 13 2018 - 00:56:17 PDT)
- Re: [AMBER] Two-Dimensional Replica Exchange in AMBER Cruzeiro,Vinicius Wilian D (Fri Apr 13 2018 - 04:15:53 PDT)
  - Re: [AMBER] Two-Dimensional Replica Exchange in AMBER Daniel Roe (Fri Apr 13 2018 - 07:55:13 PDT)
[AMBER] Replica exchange in explicit solvent Maya Hauss (Fri Apr 13 2018 - 12:23:12 PDT)
- Re: [AMBER] Replica exchange in explicit solvent Cruzeiro,Vinicius Wilian D (Fri Apr 13 2018 - 12:36:20 PDT)
  - Re: [AMBER] Replica exchange in explicit solvent Maya Hauss (Tue Apr 17 2018 - 05:59:02 PDT)
    - Re: [AMBER] Replica exchange in explicit solvent Cruzeiro,Vinicius Wilian D (Tue Apr 17 2018 - 07:49:47 PDT)
    - Re: [AMBER] Replica exchange in explicit solvent Maya Hauss (Wed Apr 18 2018 - 08:15:04 PDT)
[AMBER] "bad atom type: DU" error Sharon D. Morris (Fri Apr 13 2018 - 21:25:35 PDT)
- Re: [AMBER] "bad atom type: DU" error Elvis Martis (Fri Apr 13 2018 - 21:43:04 PDT)
[AMBER] Amber94 charges for neutral amino acids Rinsha Chk (Fri Apr 13 2018 - 21:33:23 PDT)
- Re: [AMBER] Amber94 charges for neutral amino acids FyD (Fri Apr 13 2018 - 21:58:18 PDT)
[AMBER] md simulation of modified nucleotides in RNA leila karami (Sat Apr 14 2018 - 08:47:19 PDT)
- Re: [AMBER] md simulation of modified nucleotides in RNA David A Case (Sat Apr 14 2018 - 18:18:36 PDT)
- Re: [AMBER] md simulation of modified nucleotides in RNA FyD (Mon Apr 16 2018 - 21:30:41 PDT)
[AMBER] GPU Atila Petrosian (Sat Apr 14 2018 - 08:59:32 PDT)
- Re: [AMBER] GPU Scott Brozell (Sat Apr 14 2018 - 14:06:49 PDT)
  - Re: [AMBER] GPU Atila Petrosian (Sat Apr 14 2018 - 22:57:53 PDT)
    - Re: [AMBER] GPU Setyanto Md (Sun Apr 15 2018 - 15:22:42 PDT)
    - Re: [AMBER] GPU Atila Petrosian (Mon Apr 16 2018 - 11:13:23 PDT)
    - Re: [AMBER] GPU David Cerutti (Mon Apr 16 2018 - 11:55:36 PDT)
    - Re: [AMBER] GPU Scott Brozell (Mon Apr 16 2018 - 11:56:25 PDT)
[AMBER] (pmemd.cuda.MPI) Note: The following floating-point exceptions are signalling: IEEE_UNDERFLOW_FLAG IEEE_DENORMAL Amen Shamim (Sun Apr 15 2018 - 06:30:42 PDT)
- Re: [AMBER] (pmemd.cuda.MPI) Note: The following floating-point exceptions are signalling: IEEE_UNDERFLOW_FLAG IEEE_DENORMAL David A Case (Sun Apr 15 2018 - 13:36:37 PDT)
[AMBER] query regarding nonlinear pbsa Rakesh Srivastava (Mon Apr 16 2018 - 01:02:15 PDT)
[AMBER] Regarding AuCl force field Aashish Bhatt (Mon Apr 16 2018 - 06:58:08 PDT)
- Re: [AMBER] Regarding AuCl force field David A Case (Mon Apr 16 2018 - 18:15:47 PDT)
  - Re: [AMBER] Regarding AuCl force field Pengfei Li (Wed Apr 18 2018 - 14:27:17 PDT)
[AMBER] Configure cuda Kadir Ozcan (Mon Apr 16 2018 - 16:53:15 PDT)
- Re: [AMBER] Configure cuda David A Case (Mon Apr 16 2018 - 17:58:16 PDT)
- Re: [AMBER] Configure cuda Kadir Ozcan (Thu Apr 19 2018 - 07:26:50 PDT)
  - Re: [AMBER] Configure cuda David A Case (Fri Apr 20 2018 - 05:22:20 PDT)
- Re: [AMBER] Configure cuda Kadir Ozcan (Mon Apr 23 2018 - 11:41:27 PDT)
  - Re: [AMBER] Configure cuda David A Case (Mon Apr 23 2018 - 17:51:51 PDT)
- Re: [AMBER] Configure cuda Kadir Ozcan (Thu Apr 26 2018 - 12:38:26 PDT)
  - Re: [AMBER] Configure cuda David A Case (Fri Apr 27 2018 - 05:07:31 PDT)
[AMBER] convert psf to prmtop Ashutosh Shandilya (Mon Apr 16 2018 - 17:00:04 PDT)
- Re: [AMBER] convert psf to prmtop David A Case (Mon Apr 16 2018 - 18:06:55 PDT)
  - Re: [AMBER] convert psf to prmtop Jason Swails (Tue Apr 17 2018 - 05:52:35 PDT)
[AMBER] Weight the xyz components of restraints Huan He (Tue Apr 17 2018 - 06:24:03 PDT)
[AMBER] QMMM Replica exchange with TeraChem Raimon Fabregat (Tue Apr 17 2018 - 08:12:58 PDT)
- Re: [AMBER] QMMM Replica exchange with TeraChem Goetz, Andreas (Wed Apr 18 2018 - 13:30:19 PDT)
[AMBER] How fast is Amber's new GPU code? Are CPUs ever coming back? David Cerutti (Tue Apr 17 2018 - 08:40:14 PDT)
- Re: [AMBER] How fast is Amber's new GPU code? Are CPUs ever coming back? David A Case (Tue Apr 17 2018 - 13:40:18 PDT)
  - Re: [AMBER] How fast is Amber's new GPU code? Are CPUs ever coming back? Ross Walker (Wed Apr 18 2018 - 06:34:19 PDT)
Re: [AMBER] Configure cuda (David A Case) Kadir Ozcan (Tue Apr 17 2018 - 12:27:37 PDT)
- Re: [AMBER] Configure cuda (David A Case) David A Case (Tue Apr 17 2018 - 13:45:33 PDT)
[AMBER] Release of Amber18 and AmberTools18 David A Case (Tue Apr 17 2018 - 14:28:42 PDT)
[AMBER] Multisander: No scale up Aravind Ravichandran (Tue Apr 17 2018 - 23:31:57 PDT)
- Re: [AMBER] Multisander: No scale up David A Case (Wed Apr 18 2018 - 06:09:21 PDT)
[AMBER] How to solve the problem of molecule box jumping? golshan bakrani (Wed Apr 18 2018 - 21:42:54 PDT)
[AMBER] Brand new GPU card testing Nikolay N. Kuzmich (Thu Apr 19 2018 - 00:28:06 PDT)
- Re: [AMBER] Brand new GPU card testing Ross Walker (Thu Apr 19 2018 - 05:11:50 PDT)
- Re: [AMBER] Brand new GPU card testing Nikolay N. Kuzmich (Fri Apr 20 2018 - 04:25:41 PDT)
  - Re: [AMBER] Brand new GPU card testing Ross Walker (Fri Apr 20 2018 - 14:43:34 PDT)
- Re: [AMBER] Brand new GPU card testing Nikolay N. Kuzmich (Mon Apr 23 2018 - 03:09:21 PDT)
[AMBER] Python installation while installing AmberTools18 Debostuti Ghoshdastidar (Thu Apr 19 2018 - 02:04:22 PDT)
- Re: [AMBER] Python installation while installing AmberTools18 David A Case (Thu Apr 19 2018 - 05:46:48 PDT)
[AMBER] Error generating gau_job.inp Giovanni Grazioso (Thu Apr 19 2018 - 03:16:47 PDT)
[AMBER] eCheminfo Milano July 16-29, Training and Innovation Course in Drug Design 2018, bursary and early-bird deadline ending soon Thomas Exner (Thu Apr 19 2018 - 03:40:13 PDT)
- Re: [AMBER] eCheminfo Milano July 16-29, Training and Innovation Course in Drug Design 2018, bursary and early-bird deadline ending soon Thomas Exner (Thu May 24 2018 - 04:43:18 PDT)
  - Re: [AMBER] eCheminfo Oxford, UK Training and Innovation Course in Drug Design 2018, first announcement Thomas Exner (Wed May 30 2018 - 02:59:48 PDT)
  - Re: [AMBER] eCheminfo Milano July 16-29, Training and Innovation Course in Drug Design 2018, bursary and early-bird deadline ending soon Thomas Exner (Mon Jul 02 2018 - 03:05:47 PDT)
    - [AMBER] eCheminfo Oxford 3-7 Sep., Training and Innovation Course in Drug Design, bursary and early-bird deadline approaching quickly Thomas Exner (Mon Jul 23 2018 - 05:53:12 PDT)
    - Re: [AMBER] eCheminfo Oxford 3-7 Sep., Training and Innovation Course in Drug Design, bursary and early-bird deadline approaching quickly Thomas Exner (Fri Aug 03 2018 - 04:07:56 PDT)
[AMBER] Error compiling AmberTools18 cpptraj with Intel 16 Niel Henriksen (Thu Apr 19 2018 - 07:34:38 PDT)
- Re: [AMBER] Error compiling AmberTools18 cpptraj with Intel 16 David A Case (Fri Apr 20 2018 - 04:58:36 PDT)
  - Re: [AMBER] Error compiling AmberTools18 cpptraj with Intel 16 Daniel Roe (Fri Apr 20 2018 - 05:37:09 PDT)
    - Re: [AMBER] Error compiling AmberTools18 cpptraj with Intel 16 Niel Henriksen (Fri Apr 20 2018 - 10:10:39 PDT)
[AMBER] native contacts Sowmya Indrakumar (Thu Apr 19 2018 - 09:26:27 PDT)
[AMBER] Aligning frames and printing pdb files Christopher Warren (Thu Apr 19 2018 - 10:04:05 PDT)
- Re: [AMBER] Aligning frames and printing pdb files David A Case (Thu Apr 19 2018 - 10:58:43 PDT)
[AMBER] mac installation problem Jiyong Su (Thu Apr 19 2018 - 21:54:22 PDT)
- Re: [AMBER] mac installation problem David A Case (Fri Apr 20 2018 - 04:44:28 PDT)
- Re: [AMBER] mac installation problem Jiyong Su (Sun Apr 22 2018 - 00:21:32 PDT)
  - Re: [AMBER] mac installation problem Hai Nguyen (Sun Apr 22 2018 - 14:07:22 PDT)
    - Re: [AMBER] mac installation problem Jiyong Su (Sun Apr 22 2018 - 18:41:28 PDT)
- Re: [AMBER] mac installation problem Jiyong Su (Sun Apr 22 2018 - 00:22:20 PDT)
[AMBER] installation problem wuxc (Fri Apr 20 2018 - 01:53:06 PDT)
- Re: [AMBER] installation problem David A Case (Fri Apr 20 2018 - 04:50:56 PDT)
[AMBER] NEB simulations: Inputs from TMD ? Aravind Ravichandran (Fri Apr 20 2018 - 02:33:41 PDT)
- Re: [AMBER] NEB simulations: Inputs from TMD ? Carlos Simmerling (Fri Apr 20 2018 - 04:50:26 PDT)
  - Re: [AMBER] NEB simulations: Inputs from TMD ? Aravind Ravichandran (Sat Apr 21 2018 - 02:10:43 PDT)
[AMBER] NEB simulations: Inputs from TMD ? Aravind Ravichandran (Fri Apr 20 2018 - 02:36:24 PDT)
[AMBER] Amber18 and Amber14 Günther H.J. Peters (Fri Apr 20 2018 - 08:48:56 PDT)
- Re: [AMBER] Amber18 and Amber14 David A Case (Fri Apr 20 2018 - 09:13:47 PDT)
[AMBER] pmemd.cuda error; Exiting due to the presence of inconsistent SHAKEH hydrogen clusters Sadegh Faramarzi Ganjabad (Fri Apr 20 2018 - 10:49:31 PDT)
- Re: [AMBER] pmemd.cuda error; Exiting due to the presence of inconsistent SHAKEH hydrogen clusters David A Case (Sat Apr 21 2018 - 06:07:37 PDT)
- Re: [AMBER] pmemd.cuda error; Exiting due to the presence of inconsistent SHAKEH hydrogen clusters Sadegh Faramarzi Ganjabad (Mon Apr 23 2018 - 09:17:29 PDT)
[AMBER] pH as a Dimension in Multidimensional (2D) Replica Exchange Jason Ku Wang (Fri Apr 20 2018 - 11:08:57 PDT)
- Re: [AMBER] pH as a Dimension in Multidimensional (2D) Replica Exchange Cruzeiro,Vinicius Wilian D (Fri Apr 20 2018 - 11:59:24 PDT)
[AMBER] accelerated MD cudaMemcpy GpuBuffer::Download failed an illegal memory access was encountered Ashutosh Shandilya (Fri Apr 20 2018 - 14:59:09 PDT)
- Re: [AMBER] accelerated MD cudaMemcpy GpuBuffer::Download failed an illegal memory access was encountered David Cerutti (Fri Apr 20 2018 - 20:08:30 PDT)
- Re: [AMBER] accelerated MD cudaMemcpy GpuBuffer::Download failed an illegal memory access was encountered David A Case (Sat Apr 21 2018 - 06:02:10 PDT)
[AMBER] How to solve the problem of molecule box jumping? g.bakrani.sci.ui.ac.ir (Fri Apr 20 2018 - 23:39:54 PDT)
- Re: [AMBER] How to solve the problem of molecule box jumping? Daniel Roe (Sat Apr 21 2018 - 09:52:27 PDT)
[AMBER] Constant Redox potential MD simulations Fernando Ogata (Sat Apr 21 2018 - 14:20:51 PDT)
- Re: [AMBER] Constant Redox potential MD simulations Cruzeiro,Vinicius Wilian D (Sun Apr 22 2018 - 12:15:23 PDT)
[AMBER] Jumping from simulation box g.bakrani.sci.ui.ac.ir (Sun Apr 22 2018 - 12:49:33 PDT)
- Re: [AMBER] Jumping from simulation box Daniel Roe (Mon Apr 23 2018 - 06:50:01 PDT)
[AMBER] average between structures with different residue numbering Rosellen, Martin (Mon Apr 23 2018 - 04:31:52 PDT)
- Re: [AMBER] average between structures with different residue numbering Daniel Roe (Mon Apr 23 2018 - 06:43:24 PDT)
  - Re: [AMBER] average between structures with different residue numbering Rosellen, Martin (Mon Apr 23 2018 - 07:22:22 PDT)
    - Re: [AMBER] average between structures with different residue numbering Daniel Roe (Mon Apr 23 2018 - 07:30:48 PDT)
    - Re: [AMBER] average between structures with different residue numbering Rosellen, Martin (Mon Apr 23 2018 - 07:43:54 PDT)
    - Re: [AMBER] average between structures with different residue numbering Daniel Roe (Mon Apr 23 2018 - 07:58:19 PDT)
    - Re: [AMBER] average between structures with different residue numbering Rosellen, Martin (Mon Apr 23 2018 - 08:03:35 PDT)
  - Re: [AMBER] average between structures with different residue numbering Rosellen, Martin (Mon Apr 23 2018 - 08:30:37 PDT)
[AMBER] Amber18 and Titan V graphic cards Nikolay N. Kuzmich (Mon Apr 23 2018 - 05:24:48 PDT)
- Re: [AMBER] Amber18 and Titan V graphic cards David Cerutti (Mon Apr 23 2018 - 05:59:46 PDT)
- Re: [AMBER] Amber18 and Titan V graphic cards Nikolay N. Kuzmich (Thu Apr 26 2018 - 06:19:50 PDT)
[AMBER] Amino acid GROMACS topology file roja rahmani (Mon Apr 23 2018 - 06:50:41 PDT)
- Re: [AMBER] Amino acid GROMACS topology file roja rahmani (Mon Apr 23 2018 - 13:08:01 PDT)
- Re: [AMBER] Amino acid GROMACS topology file David A Case (Mon Apr 23 2018 - 14:41:48 PDT)
  - Re: [AMBER] Amino acid GROMACS topology file roja rahmani (Mon Apr 23 2018 - 22:09:37 PDT)
[AMBER] Problem with g++ compiler with boost (AmberTools18) Abdul-Rashid III Sampaco (Mon Apr 23 2018 - 22:48:11 PDT)
- Re: [AMBER] Problem with g++ compiler with boost (AmberTools18) David A Case (Tue Apr 24 2018 - 05:11:13 PDT)
- Re: [AMBER] Problem with g++ compiler with boost (AmberTools18) Stephan Schott (Wed Apr 25 2018 - 09:08:48 PDT)
  - Re: [AMBER] Problem with g++ compiler with boost (AmberTools18) Abdul-Rashid III Sampaco (Wed Apr 25 2018 - 14:49:09 PDT)
- Re: [AMBER] Problem with g++ compiler with boost (AmberTools18) Stephan Schott (Wed Apr 25 2018 - 16:23:53 PDT)
  - Re: [AMBER] Problem with g++ compiler with boost (AmberTools18) Abdul-Rashid III Sampaco (Thu Apr 26 2018 - 02:30:06 PDT)
- Re: [AMBER] Problem with g++ compiler with boost (AmberTools18) Matias Machado (Wed May 30 2018 - 19:12:28 PDT)
  - Re: [AMBER] Problem with g++ compiler with boost (AmberTools18) David A Case (Thu May 31 2018 - 04:21:47 PDT)
    - Re: [AMBER] Problem with g++ compiler with boost (AmberTools18) Matias Machado (Thu May 31 2018 - 05:10:54 PDT)
[AMBER] Charmm36 modified forcefield in Amber Midhun K Madhu (Tue Apr 24 2018 - 03:05:10 PDT)
- Re: [AMBER] Charmm36 modified forcefield in Amber David A Case (Tue Apr 24 2018 - 05:19:22 PDT)
[AMBER] PMF analysis Tousif Hossen (Tue Apr 24 2018 - 04:06:16 PDT)
- Re: [AMBER] PMF analysis David A Case (Tue Apr 24 2018 - 05:25:51 PDT)
  - Re: [AMBER] PMF analysis Tousif Hossen (Wed Apr 25 2018 - 07:13:38 PDT)
[AMBER] Trouble Running/Understanding Wavelet Analysis Moataz Noureddine (Tue Apr 24 2018 - 10:42:01 PDT)
- Re: [AMBER] Trouble Running/Understanding Wavelet Analysis Daniel Roe (Thu Apr 26 2018 - 10:40:36 PDT)
[AMBER] Atom position changes when setting up QM/MM calculation James Kress (Tue Apr 24 2018 - 11:37:54 PDT)
- Re: [AMBER] Atom position changes when setting up QM/MM calculation David A Case (Tue Apr 24 2018 - 18:09:52 PDT)
  - Re: [AMBER] Atom position changes when setting up QM/MM calculation Goetz, Andreas (Tue Apr 24 2018 - 22:26:38 PDT)
    - Re: [AMBER] Atom position changes when setting up QM/MM calculation James Kress (Wed Apr 25 2018 - 11:19:03 PDT)
[AMBER] Parmchk roja rahmani (Tue Apr 24 2018 - 11:52:40 PDT)
- Re: [AMBER] Parmchk David A Case (Tue Apr 24 2018 - 18:13:02 PDT)
  - Re: [AMBER] Parmchk roja rahmani (Tue Apr 24 2018 - 21:11:57 PDT)
    - Re: [AMBER] Parmchk Premila Samuel Mohan Dass (Tue Apr 24 2018 - 21:55:06 PDT)
[AMBER] Issue running alanine scanning Núbia Prates (Tue Apr 24 2018 - 14:49:23 PDT)
- Re: [AMBER] Issue running alanine scanning David A Case (Tue Apr 24 2018 - 18:15:57 PDT)
  - Re: [AMBER] Issue running alanine scanning Núbia Prates (Wed Apr 25 2018 - 12:00:00 PDT)
    - Re: [AMBER] Issue running alanine scanning pancham lal Gupta (Thu Apr 26 2018 - 08:35:36 PDT)
[AMBER] Boost not linking when compiling on Mac Gustaf Olsson (Wed Apr 25 2018 - 02:53:11 PDT)
- Re: [AMBER] Boost not linking when compiling on Mac David A Case (Wed Apr 25 2018 - 05:53:46 PDT)
  - Re: [AMBER] Boost not linking when compiling on Mac Gustaf Olsson (Wed Apr 25 2018 - 06:25:42 PDT)
- Re: [AMBER] Boost not linking when compiling on Mac Stephan Schott (Wed Apr 25 2018 - 07:53:54 PDT)
  - Re: [AMBER] Boost not linking when compiling on Mac Gustaf Olsson (Thu Apr 26 2018 - 00:32:52 PDT)
- Re: [AMBER] Boost not linking when compiling on Mac Hai Nguyen (Wed Apr 25 2018 - 16:26:55 PDT)
- Re: [AMBER] Boost not linking when compiling on Mac Stephan Schott (Thu Apr 26 2018 - 01:59:24 PDT)
  - Re: [AMBER] Boost not linking when compiling on Mac Gustaf Olsson (Thu Apr 26 2018 - 02:38:52 PDT)
  - Re: [AMBER] Boost not linking when compiling on Mac Gustaf Olsson (Thu Apr 26 2018 - 02:43:58 PDT)
- Re: [AMBER] Boost not linking when compiling on Mac Stephan Schott (Thu Apr 26 2018 - 10:21:37 PDT)
  - Re: [AMBER] Boost not linking when compiling on Mac David A Case (Thu Apr 26 2018 - 11:24:36 PDT)
    - Re: [AMBER] Boost not linking when compiling on Mac Hai Nguyen (Thu Apr 26 2018 - 12:18:14 PDT)
  - Re: [AMBER] Boost not linking when compiling on Mac Gustaf Olsson (Thu Apr 26 2018 - 23:37:05 PDT)
    - Re: [AMBER] Boost not linking when compiling on Mac Scott Brozell (Fri Apr 27 2018 - 11:12:45 PDT)
    - Re: [AMBER] Boost not linking when compiling on Mac Gustaf Olsson (Tue May 01 2018 - 23:44:30 PDT)
    - Re: [AMBER] Boost not linking when compiling on Mac David A Case (Wed May 02 2018 - 04:48:41 PDT)
    - Re: [AMBER] Boost not linking when compiling on Mac Gustaf Olsson (Wed May 02 2018 - 05:53:36 PDT)
    - Re: [AMBER] Boost not linking when compiling on Mac Scott Brozell (Wed May 02 2018 - 17:30:23 PDT)
- Re: [AMBER] Boost not linking when compiling on Mac Stephan Schott (Fri Apr 27 2018 - 04:11:18 PDT)
  - Re: [AMBER] Boost not linking when compiling on Mac Gustaf Olsson (Fri Apr 27 2018 - 06:55:43 PDT)
[AMBER] Analyzing Multidimensional REMD Simulations Jason Ku Wang (Wed Apr 25 2018 - 02:58:06 PDT)
- Re: [AMBER] Analyzing Multidimensional REMD Simulations Christina Bergonzo (Wed Apr 25 2018 - 05:51:39 PDT)
[AMBER] Call for Papers, GCC 2018, 14th German Conference on Chemoinformatics Stefan.Guessregen.sanofi.com (Wed Apr 25 2018 - 05:35:41 PDT)
[AMBER] topology file roja rahmani (Wed Apr 25 2018 - 05:51:18 PDT)
- Re: [AMBER] topology file David A Case (Thu Apr 26 2018 - 04:20:39 PDT)
  - Re: [AMBER] topology file roja rahmani (Mon Apr 30 2018 - 03:41:46 PDT)
[AMBER] simulation with duration of 5000 Ps Edjan Silva (Wed Apr 25 2018 - 06:52:29 PDT)
- Re: [AMBER] simulation with duration of 5000 Ps Gustaf Olsson (Wed Apr 25 2018 - 07:20:29 PDT)
  - Re: [AMBER] simulation with duration of 5000 Ps Edjan Silva (Wed Apr 25 2018 - 08:21:36 PDT)
[AMBER] Paramfit issues - Improvement of R^2 value Alechania Misturini (Wed Apr 25 2018 - 07:51:54 PDT)
[AMBER] QM/MM-MD charges Thakur, Abhishek (Wed Apr 25 2018 - 08:38:17 PDT)
- Re: [AMBER] QM/MM-MD charges Goetz, Andreas (Wed Apr 25 2018 - 12:34:34 PDT)
[AMBER] Solvateoct Distance Parameter Kung, Ryan (Wed Apr 25 2018 - 15:42:09 PDT)
[AMBER] Multi-Dimensional REMD: rem.log shows exchanges along Hamiltonian dimension, but .mdout files do not Jason Ku Wang (Wed Apr 25 2018 - 17:44:45 PDT)
- Re: [AMBER] Multi-Dimensional REMD: rem.log shows exchanges along Hamiltonian dimension, but .mdout files do not Cruzeiro,Vinicius Wilian D (Wed Apr 25 2018 - 18:29:08 PDT)
  - Re: [AMBER] Multi-Dimensional REMD: rem.log shows exchanges along Hamiltonian dimension, but .mdout files do not Jason Ku Wang (Fri Apr 27 2018 - 10:54:23 PDT)
    - Re: [AMBER] Multi-Dimensional REMD: rem.log shows exchanges along Hamiltonian dimension, but .mdout files do not Cruzeiro,Vinicius Wilian D (Fri Apr 27 2018 - 11:43:20 PDT)
    - Re: [AMBER] Multi-Dimensional REMD: rem.log shows exchanges along Hamiltonian dimension, but .mdout files do not Jason Ku Wang (Fri Apr 27 2018 - 13:20:20 PDT)
[AMBER] AmberError: FLAG ATOMIC_NUMBER Sharon D. Morris (Wed Apr 25 2018 - 23:14:24 PDT)
[AMBER] Simulation of bilayer with negative pressure Debostuti Ghoshdastidar (Thu Apr 26 2018 - 02:13:10 PDT)
[AMBER] packmol-memgen and parmed packages import error Chetna Tyagi (Thu Apr 26 2018 - 03:04:09 PDT)
- Re: [AMBER] packmol-memgen and parmed packages import error Stephan Schott (Thu Apr 26 2018 - 03:25:44 PDT)
  - Re: [AMBER] packmol-memgen and parmed packages import error Chetna Tyagi (Thu Apr 26 2018 - 04:16:58 PDT)
Re: [AMBER] AMBER Digest, Vol 2271, Issue 1 Kadir Ozcan (Thu Apr 26 2018 - 09:07:59 PDT)
- Re: [AMBER] AMBER Digest, Vol 2271, Issue 1 David A Case (Thu Apr 26 2018 - 10:12:21 PDT)
[AMBER] QM/MM-MD Mulliken Charge calculation output atom name changed Thakur, Abhishek (Thu Apr 26 2018 - 11:50:54 PDT)
- Re: [AMBER] QM/MM-MD Mulliken Charge calculation output atom name changed Goetz, Andreas (Thu Apr 26 2018 - 13:20:23 PDT)
  - Re: [AMBER] QM/MM-MD Mulliken Charge calculation output atom name changed Thakur, Abhishek (Thu Apr 26 2018 - 13:41:48 PDT)
[AMBER] Amber Lipid Force Field Tutorial: update? Matthias.Nachtschatt.csiro.au (Thu Apr 26 2018 - 19:35:23 PDT)
[AMBER] Suggestions to pick up right methodology anu chandra (Fri Apr 27 2018 - 02:52:00 PDT)
[AMBER] Fwd: Paramfit issues - Improvement of R^2 value. Alechania Misturini (Fri Apr 27 2018 - 07:29:19 PDT)
- Re: [AMBER] Fwd: Paramfit issues - Improvement of R^2 value. David Cerutti (Fri Apr 27 2018 - 07:43:58 PDT)
- Re: [AMBER] Fwd: Paramfit issues - Improvement of R^2 value. David Cerutti (Mon Apr 30 2018 - 20:05:25 PDT)
[AMBER] Segmentation fault - invalid memory reference, during the minimization Nikolay N. Kuzmich (Fri Apr 27 2018 - 08:20:27 PDT)
- Re: [AMBER] Segmentation fault - invalid memory reference, during the minimization David A Case (Fri Apr 27 2018 - 09:02:11 PDT)
[AMBER] Forces on atoms Yuliana Bosken (Sat Apr 28 2018 - 01:29:54 PDT)
- Re: [AMBER] Forces on atoms David A Case (Sat Apr 28 2018 - 04:12:17 PDT)
[AMBER] Continuous hydrogen bond time correlation function S(t) Tousif Hossen (Sat Apr 28 2018 - 04:07:06 PDT)
[AMBER] variety of errors in membrane/umbrella sampling simulations Baker, Joseph (Sat Apr 28 2018 - 11:51:13 PDT)
- [AMBER] problem with membrane embedding Mohammad Salem (Sat Apr 28 2018 - 15:29:12 PDT)
  - Re: [AMBER] problem with membrane embedding Stephan Schott (Sat Apr 28 2018 - 17:17:26 PDT)
    - Re: [AMBER] problem with membrane embedding Gould, Ian R (Sun Apr 29 2018 - 02:00:47 PDT)
- Re: [AMBER] variety of errors in membrane/umbrella sampling simulations Stephan Schott (Sat Apr 28 2018 - 17:13:42 PDT)
  - Re: [AMBER] variety of errors in membrane/umbrella sampling simulations Baker, Joseph (Sat Apr 28 2018 - 19:08:31 PDT)
- Re: [AMBER] variety of errors in membrane/umbrella sampling simulations Gould, Ian R (Sun Apr 29 2018 - 02:28:43 PDT)
  - Re: [AMBER] variety of errors in membrane/umbrella sampling simulations Baker, Joseph (Sun Apr 29 2018 - 11:47:40 PDT)
- Re: [AMBER] variety of errors in membrane/umbrella sampling simulations David A Case (Sun Apr 29 2018 - 14:00:42 PDT)
  - Re: [AMBER] variety of errors in membrane/umbrella sampling simulations Baker, Joseph (Sun Apr 29 2018 - 17:39:55 PDT)
    - Re: [AMBER] variety of errors in membrane/umbrella sampling simulations David Cerutti (Sun Apr 29 2018 - 18:15:26 PDT)
    - Re: [AMBER] variety of errors in membrane/umbrella sampling simulations Baker, Joseph (Sun Apr 29 2018 - 19:09:10 PDT)
- Re: [AMBER] variety of errors in membrane/umbrella sampling simulations Stephan Schott (Mon Apr 30 2018 - 00:49:08 PDT)
[AMBER] GTX 1080Ti Problem. 汪盛 (Sun Apr 29 2018 - 03:16:54 PDT)
- Re: [AMBER] GTX 1080Ti Problem. David Cerutti (Sun Apr 29 2018 - 05:42:51 PDT)
[AMBER] QM/MM minimization issue using sander (AMBER 18) Abhilash J (Mon Apr 30 2018 - 01:16:17 PDT)
- Re: [AMBER] QM/MM minimization issue using sander (AMBER 18) Goetz, Andreas (Mon Apr 30 2018 - 17:01:55 PDT)
  - Re: [AMBER] QM/MM minimization issue using sander (AMBER 18) Abhilash J (Tue May 01 2018 - 06:03:28 PDT)
    - Re: [AMBER] QM/MM minimization issue using sander (AMBER 18) Abhilash J (Tue May 01 2018 - 08:47:49 PDT)
[AMBER] MMPBSA.py.MPI TypeError when using &pb Eiros Zamora, Juan (Mon Apr 30 2018 - 10:49:48 PDT)
[AMBER] Thermodynamic integration with sander + using nosoftcore Khabiri, Morteza (Mon Apr 30 2018 - 10:58:32 PDT)
- Re: [AMBER] Thermodynamic integration with sander + using nosoftcore David A Case (Mon Apr 30 2018 - 17:11:43 PDT)
[AMBER] Cremer Pucker values using Pytraj Vivek Bharadwaj (Mon Apr 30 2018 - 11:13:38 PDT)
- Re: [AMBER] Cremer Pucker values using Pytraj Hai Nguyen (Mon Apr 30 2018 - 14:26:32 PDT)
  - Re: [AMBER] Cremer Pucker values using Pytraj Vivek Bharadwaj (Tue May 01 2018 - 07:31:34 PDT)
[AMBER] Computing interaction energies from trajectory Aravind Ravichandran (Tue May 01 2018 - 06:59:32 PDT)
[AMBER] Using infe = 1, &pmd, and pmemd.cuda (AMBER16) Lenz, Stefan (Tue May 01 2018 - 09:04:27 PDT)
- Re: [AMBER] Using infe = 1, &pmd, and pmemd.cuda (AMBER16) Feng Pan (Wed May 02 2018 - 13:40:13 PDT)
[AMBER] CPPTRAJ Ensemble Keyword: "Too Many Open Files" Jason Ku Wang (Tue May 01 2018 - 16:55:15 PDT)
- Re: [AMBER] CPPTRAJ Ensemble Keyword: "Too Many Open Files" Daniel Roe (Thu May 03 2018 - 07:28:19 PDT)
[AMBER] GPU benchmark - Amber18 Hadházi Ádám (Wed May 02 2018 - 02:00:19 PDT)
- Re: [AMBER] GPU benchmark - Amber18 David A Case (Wed May 02 2018 - 05:18:39 PDT)
[AMBER] update ambertools Tousif Hossen (Wed May 02 2018 - 02:28:52 PDT)
- Re: [AMBER] update ambertools David A Case (Wed May 02 2018 - 05:26:34 PDT)
  - Re: [AMBER] update ambertools Kevin Keane (Wed May 02 2018 - 10:20:30 PDT)
[AMBER] update Ambertools Tousif Hossen (Wed May 02 2018 - 02:33:16 PDT)
[AMBER] PhD/Junior position, AMBER sims DNA/RNA Jiri Sponer (Wed May 02 2018 - 03:54:35 PDT)
[AMBER] How to extract frames with particular hydrogen bonds only Stejskal, Lenka (Wed May 02 2018 - 08:31:59 PDT)
- Re: [AMBER] How to extract frames with particular hydrogen bonds only Daniel Roe (Thu May 03 2018 - 07:42:05 PDT)
Re: [AMBER] .rst and .mdcrd file outputted in ascii David A Case (Wed May 02 2018 - 11:36:59 PDT)
[AMBER] need QMMM interface for TURBOMOLE 陈金峰 (Wed May 02 2018 - 16:38:09 PDT)
- Re: [AMBER] need QMMM interface for TURBOMOLE David A Case (Mon May 07 2018 - 04:39:11 PDT)
  - Re: [AMBER] need QMMM interface for TURBOMOLE Goetz, Andreas (Mon May 07 2018 - 10:26:15 PDT)
    - Re: [AMBER] need QMMM interface for TURBOMOLE Antoine MARION (Tue May 08 2018 - 08:19:17 PDT)
    - Re: [AMBER] need QMMM interface for TURBOMOLE Scott Brozell (Tue May 08 2018 - 12:47:04 PDT)
    - Re: [AMBER] need QMMM interface for TURBOMOLE Holger Kruse (Wed May 09 2018 - 05:26:25 PDT)
[AMBER] Multiple temperature groups I Lőrincz (Thu May 03 2018 - 07:03:13 PDT)
- Re: [AMBER] Multiple temperature groups David A Case (Wed May 09 2018 - 18:52:59 PDT)
[AMBER] input files from AmberTools 16/17 run on Amber14 pmemd.cuda engine problem Chetna Tyagi (Thu May 03 2018 - 07:18:54 PDT)
- Re: [AMBER] input files from AmberTools 16/17 run on Amber14 pmemd.cuda engine problem Gustaf Olsson (Thu May 03 2018 - 07:28:47 PDT)
- Re: [AMBER] input files from AmberTools 16/17 run on Amber14 pmemd.cuda engine problem Daniel Roe (Thu May 03 2018 - 07:32:30 PDT)
  - Re: [AMBER] input files from AmberTools 16/17 run on Amber14 pmemd.cuda engine problem Chetna Tyagi (Thu May 03 2018 - 07:36:12 PDT)
Re: [AMBER] Configure CUDA issues Kadir Ozcan (Thu May 03 2018 - 08:55:34 PDT)
- Re: [AMBER] Configure CUDA issues David A Case (Thu May 03 2018 - 10:35:32 PDT)
Re: [AMBER] AMBER Digest, Vol 2280, Issue 1 Kadir Ozcan (Thu May 03 2018 - 15:19:23 PDT)
- Re: [AMBER] AMBER Digest, Vol 2280, Issue 1 David A Case (Fri May 04 2018 - 05:21:02 PDT)
[AMBER] calculation of cavity water Tousif Hossen (Fri May 04 2018 - 04:11:33 PDT)
- Re: [AMBER] calculation of cavity water Kenneth Huang (Fri May 04 2018 - 13:15:16 PDT)
  - Re: [AMBER] calculation of cavity water Leena Aggarwal (Fri May 04 2018 - 21:13:08 PDT)
    - Re: [AMBER] calculation of cavity water Tousif Hossen (Sat May 05 2018 - 23:29:43 PDT)
    - Re: [AMBER] calculation of cavity water Kenneth Huang (Sun May 06 2018 - 07:28:37 PDT)
    - Re: [AMBER] calculation of cavity water Tousif Hossen (Sun May 06 2018 - 22:41:24 PDT)
    - Re: [AMBER] calculation of cavity water Tousif Hossen (Mon May 07 2018 - 06:38:35 PDT)
    - Re: [AMBER] calculation of cavity water Kenneth Huang (Mon May 07 2018 - 07:47:36 PDT)
    - Re: [AMBER] calculation of cavity water Tousif Hossen (Mon May 07 2018 - 08:22:41 PDT)
    - Re: [AMBER] calculation of cavity water Tom Kurtzman (Mon May 07 2018 - 09:13:15 PDT)
    - Re: [AMBER] calculation of cavity water Tousif Hossen (Mon May 07 2018 - 11:09:26 PDT)
    - Re: [AMBER] calculation of cavity water Kenneth Huang (Sun May 06 2018 - 07:35:01 PDT)
[AMBER] Problem in distance restraint Kshatresh Dutta Dubey (Fri May 04 2018 - 05:01:57 PDT)
- Re: [AMBER] Problem in distance restraint David A Case (Fri May 04 2018 - 10:47:07 PDT)
[AMBER] Setting initial velocities diego.soler.uam.es (Fri May 04 2018 - 05:42:39 PDT)
- Re: [AMBER] Setting initial velocities Hai Nguyen (Tue May 08 2018 - 20:18:27 PDT)
  - Re: [AMBER] Setting initial velocities Hai Nguyen (Tue May 08 2018 - 20:22:29 PDT)
  - Re: [AMBER] Setting initial velocities David A Case (Wed May 09 2018 - 05:27:58 PDT)
[AMBER] SGLD Piotr Fajer (Sat May 05 2018 - 12:52:40 PDT)
- Re: [AMBER] SGLD David A Case (Sat May 05 2018 - 19:10:14 PDT)
  - Re: [AMBER] SGLD Piotr Fajer (Sat May 05 2018 - 19:19:12 PDT)
[AMBER] Poly amino acid helix form topology files roja rahmani (Sat May 05 2018 - 23:53:31 PDT)
- Re: [AMBER] Poly amino acid helix form topology files Carlos Simmerling (Sun May 06 2018 - 06:01:08 PDT)
  - Re: [AMBER] Poly amino acid helix form topology files roja rahmani (Sun May 06 2018 - 06:15:12 PDT)
    - Re: [AMBER] Poly amino acid helix form topology files Carlos Simmerling (Sun May 06 2018 - 06:20:18 PDT)
    - Re: [AMBER] Poly amino acid helix form topology files roja rahmani (Sun May 06 2018 - 06:29:52 PDT)
    - Re: [AMBER] Poly amino acid helix form topology files ABEL Stephane (Mon May 07 2018 - 03:02:53 PDT)
    - Re: [AMBER] Poly amino acid helix form topology files roja rahmani (Mon May 07 2018 - 03:19:01 PDT)
    - Re: [AMBER] Poly amino acid helix form topology files ABEL Stephane (Mon May 07 2018 - 04:00:58 PDT)
    - Re: [AMBER] Poly amino acid helix form topology files Carlos Simmerling (Mon May 07 2018 - 04:59:51 PDT)
[AMBER] nativecontacts command in CPPTRAJ Ruth Helena Tichauer (Sun May 06 2018 - 03:31:06 PDT)
- Re: [AMBER] nativecontacts command in CPPTRAJ Andreas Tosstorff (Sun May 06 2018 - 05:05:41 PDT)
  - Re: [AMBER] nativecontacts command in CPPTRAJ Ruth Helena Tichauer (Sun May 06 2018 - 07:57:01 PDT)
- Re: [AMBER] nativecontacts command in CPPTRAJ Sowmya Indrakumar (Sun May 06 2018 - 08:13:32 PDT)
  - Re: [AMBER] nativecontacts command in CPPTRAJ Ruth Helena Tichauer (Sun May 06 2018 - 08:58:09 PDT)
    - Re: [AMBER] nativecontacts command in CPPTRAJ Sowmya Indrakumar (Sun May 06 2018 - 09:26:52 PDT)
    - Re: [AMBER] nativecontacts command in CPPTRAJ Ruth Helena Tichauer (Tue May 22 2018 - 06:25:33 PDT)
    - Re: [AMBER] nativecontacts command in CPPTRAJ Daniel Roe (Tue May 22 2018 - 06:33:38 PDT)
    - Re: [AMBER] nativecontacts command in CPPTRAJ Ruth Helena Tichauer (Wed May 23 2018 - 01:09:47 PDT)
    - Re: [AMBER] nativecontacts command in CPPTRAJ Andreas Tosstorff (Wed May 23 2018 - 01:15:51 PDT)
    - Re: [AMBER] nativecontacts command in CPPTRAJ Ruth Helena Tichauer (Wed May 23 2018 - 01:43:43 PDT)
    - Re: [AMBER] nativecontacts command in CPPTRAJ Ruth Helena Tichauer (Wed May 23 2018 - 08:28:49 PDT)
[AMBER] PC modes per residue from existing evecs file? Kenneth Huang (Mon May 07 2018 - 08:15:27 PDT)
[AMBER] Amber 18 Thermodynamic integration question David Wifling (Mon May 07 2018 - 12:27:18 PDT)
- Re: [AMBER] Amber 18 Thermodynamic integration question David A Case (Wed May 09 2018 - 07:29:18 PDT)
[AMBER] Advice on SMD QM/MM for Cyanogenic Glucoside senal dinuka (Mon May 07 2018 - 23:34:21 PDT)
[AMBER] GBNSR6 with MMPBSA.py Jose Manuel Granadino Roldán (Tue May 08 2018 - 02:08:38 PDT)
[AMBER] MMPBSA.py.MPI and matching topology files a problem Kasprzak, Wojciech (NIH/NCI) [C] (Tue May 08 2018 - 09:17:21 PDT)
[AMBER] Parametrization: consistency with gaff force field Alechania Misturini (Tue May 08 2018 - 11:25:50 PDT)
- Re: [AMBER] Parametrization: consistency with gaff force field David A Case (Mon May 14 2018 - 07:25:43 PDT)
  - Re: [AMBER] Parametrization: consistency with gaff force field Alechania Misturini (Tue May 15 2018 - 04:55:07 PDT)
[AMBER] amber18 pmemd.MPI compile fails with Fatal Error: Can't delete temporary module file 'memory_module.mod0': No such file or directory Chris Neale (Tue May 08 2018 - 16:58:41 PDT)
- Re: [AMBER] amber18 pmemd.MPI compile fails with Fatal Error: Can't delete temporary module file 'memory_module.mod0': No such file or directory David A Case (Wed May 09 2018 - 05:20:48 PDT)
  - Re: [AMBER] amber18 pmemd.MPI compile fails with Fatal Error: Can't delete temporary module file 'memory_module.mod0': No such file or directory Chris Neale (Thu May 10 2018 - 12:16:16 PDT)
    - Re: [AMBER] amber18 pmemd.MPI compile fails with Fatal Error: Can't delete temporary module file 'memory_module.mod0': No such file or directory Dow Hurst (Wed Oct 31 2018 - 21:23:59 PDT)
    - Re: [AMBER] amber18 pmemd.MPI compile fails with Fatal Error: Can't delete temporary module file 'memory_module.mod0': No such file or directory Dow Hurst (Wed Oct 31 2018 - 22:42:14 PDT)
[AMBER] what are the benefits of cuda9 vs. 8 with amber 18? Chris Neale (Tue May 08 2018 - 21:41:11 PDT)
- Re: [AMBER] what are the benefits of cuda9 vs. 8 with amber 18? David A Case (Wed May 09 2018 - 07:18:28 PDT)
  - Re: [AMBER] what are the benefits of cuda9 vs. 8 with amber 18? Chris Neale (Wed May 09 2018 - 08:32:08 PDT)
[AMBER] Extracting infromation from topology file anu chandra (Tue May 08 2018 - 22:36:23 PDT)
- Re: [AMBER] Extracting infromation from topology file Hai Nguyen (Tue May 08 2018 - 22:47:07 PDT)
[AMBER] Query related to the Umbrella sampling method Saikat Pal (Tue May 08 2018 - 23:00:50 PDT)
[AMBER] adding NME and ACE terminals roja rahmani (Wed May 09 2018 - 03:40:10 PDT)
- Re: [AMBER] adding NME and ACE terminals Juan Eiros (Wed May 09 2018 - 03:56:23 PDT)
  - Re: [AMBER] adding NME and ACE terminals roja rahmani (Wed May 09 2018 - 05:08:59 PDT)
  - Re: [AMBER] adding NME and ACE terminals roja rahmani (Wed May 09 2018 - 05:21:18 PDT)
    - Re: [AMBER] adding NME and ACE terminals David A Case (Wed May 09 2018 - 07:23:48 PDT)
    - Re: [AMBER] adding NME and ACE terminals roja rahmani (Wed May 09 2018 - 08:53:15 PDT)
    - Re: [AMBER] adding NME and ACE terminals ABEL Stephane (Wed May 09 2018 - 10:36:28 PDT)
    - Re: [AMBER] adding NME and ACE terminals roja rahmani (Wed May 09 2018 - 10:41:15 PDT)
    - Re: [AMBER] adding NME and ACE terminals ABEL Stephane (Wed May 09 2018 - 10:45:59 PDT)
[AMBER] Different outputs of external electric field Meng Wu (Wed May 09 2018 - 04:05:42 PDT)
- Re: [AMBER] Different outputs of external electric field David A Case (Wed May 09 2018 - 07:20:33 PDT)
- Re: [AMBER] Different outputs of external electric field Meng Wu (Wed May 09 2018 - 20:16:44 PDT)
  - Re: [AMBER] Different outputs of external electric field David A Case (Thu May 10 2018 - 04:17:56 PDT)
    - Re: [AMBER] Different outputs of external electric field David A Case (Thu May 10 2018 - 06:05:56 PDT)
[AMBER] Error: No data sets selected - Problem or not? Gustaf Olsson (Wed May 09 2018 - 04:15:55 PDT)
- Re: [AMBER] Error: No data sets selected - Problem or not? Daniel Roe (Wed May 09 2018 - 05:25:27 PDT)
  - Re: [AMBER] Error: No data sets selected - Problem or not? Gustaf Olsson (Wed May 09 2018 - 05:34:07 PDT)
[AMBER] QM/MM issue with boron containing compound (AMBER16) Bodee Nutho (Thu May 10 2018 - 08:04:32 PDT)
- Re: [AMBER] QM/MM issue with boron containing compound (AMBER16) David A Case (Thu May 10 2018 - 11:48:01 PDT)
  - Re: [AMBER] QM/MM issue with boron containing compound (AMBER16) Bodee Nutho (Thu May 10 2018 - 19:02:07 PDT)
[AMBER] MMPBSA.py execution error Jose Manuel Granadino Roldán (Thu May 10 2018 - 09:14:27 PDT)
- Re: [AMBER] MMPBSA.py execution error Daniel Roe (Thu May 10 2018 - 11:15:38 PDT)
- Re: [AMBER] MMPBSA.py execution error David A Case (Thu May 10 2018 - 12:11:56 PDT)
  - Re: [AMBER] MMPBSA.py execution error Hai Nguyen (Thu May 10 2018 - 13:24:22 PDT)
    - Re: [AMBER] MMPBSA.py execution error Jose Manuel Granadino Roldán (Fri May 11 2018 - 00:27:52 PDT)
[AMBER] Angle calculation between three amino acids maryam azimzadehirani (Thu May 10 2018 - 23:45:27 PDT)
- Re: [AMBER] Angle calculation between three amino acids Daniel Roe (Fri May 11 2018 - 06:10:00 PDT)
  - Re: [AMBER] Angle calculation between three amino acids maryam azimzadehirani (Fri May 11 2018 - 06:35:05 PDT)
[AMBER] MMPBSA.py.MPI: questions about output warnings and discrepancies Kasprzak, Wojciech (NIH/NCI) [C] (Fri May 11 2018 - 06:59:40 PDT)
[AMBER] TMD : Doubts regarding TGTMDFRC Aravind Ravichandran (Fri May 11 2018 - 23:25:58 PDT)
- Re: [AMBER] TMD : Doubts regarding TGTMDFRC Carlos Simmerling (Sat May 12 2018 - 10:58:54 PDT)
  - Re: [AMBER] TMD : Doubts regarding TGTMDFRC Aravind Ravichandran (Sun May 13 2018 - 23:44:25 PDT)
    - Re: [AMBER] TMD : Doubts regarding TGTMDFRC Carlos Simmerling (Mon May 14 2018 - 05:12:01 PDT)
[AMBER] change the charge of the chlorine ion Saikat Pal (Sat May 12 2018 - 05:13:21 PDT)
- Re: [AMBER] change the charge of the chlorine ion David A Case (Sat May 12 2018 - 10:13:23 PDT)
  - Re: [AMBER] change the charge of the chlorine ion Saikat Pal (Sun May 13 2018 - 21:43:43 PDT)
[AMBER] lipid MSD values for lipid 14 FF Chitrak Gupta (Sat May 12 2018 - 14:56:12 PDT)
Re: [AMBER] Novice Question: MD Visualisation in VMD Horn, Anselm (Sun May 13 2018 - 05:07:40 PDT)
- Re: [AMBER] Novice Question: MD Visualisation in VMD David A Case (Sun May 13 2018 - 10:59:33 PDT)
  - Re: [AMBER] Novice Question: MD Visualisation in VMD James Kress (Sun May 13 2018 - 12:18:14 PDT)
[AMBER] lipid 14 MSD with OPC water Chitrak Gupta (Sun May 13 2018 - 12:30:48 PDT)
[AMBER] tleap error 'FATAL: Atom .R<NMET 1>.A<CAY 20> does not have a type' Midhun K Madhu (Mon May 14 2018 - 00:26:01 PDT)
- Re: [AMBER] tleap error 'FATAL: Atom .R<NMET 1>.A<CAY 20> does not have a type' David A Case (Mon May 14 2018 - 05:06:22 PDT)
[AMBER] combining trajectories with different parameter files Chetna Tyagi (Mon May 14 2018 - 04:31:36 PDT)
- Re: [AMBER] combining trajectories with different parameter files David A Case (Mon May 14 2018 - 05:09:20 PDT)
  - Re: [AMBER] combining trajectories with different parameter files Chetna Tyagi (Mon May 14 2018 - 05:17:12 PDT)
    - Re: [AMBER] combining trajectories with different parameter files Daniel Roe (Mon May 14 2018 - 06:18:23 PDT)
[AMBER] GUI for TI setup Hadházi Ádám (Mon May 14 2018 - 06:38:43 PDT)
- Re: [AMBER] GUI for TI setup Charles Lin (Mon May 14 2018 - 12:53:58 PDT)
  - Re: [AMBER] GUI for TI setup James Kress (Mon May 14 2018 - 14:11:00 PDT)
[AMBER] autoimage problem Ming Tang (Mon May 14 2018 - 06:59:14 PDT)
- Re: [AMBER] autoimage problem David A Case (Wed May 16 2018 - 05:59:17 PDT)
- Re: [AMBER] autoimage problem Daniel Roe (Wed May 16 2018 - 06:46:09 PDT)
[AMBER] NetCDF error: NetCDF: Not a valid ID Midhun K Madhu (Mon May 14 2018 - 14:12:46 PDT)
- Re: [AMBER] NetCDF error: NetCDF: Not a valid ID David A Case (Fri May 18 2018 - 05:34:43 PDT)
[AMBER] Creating a Gold surface library file Timothy Cholko (Mon May 14 2018 - 17:35:06 PDT)
- Re: [AMBER] Creating a Gold surface library file David A Case (Mon May 14 2018 - 18:20:45 PDT)
- Re: [AMBER] Creating a Gold surface library file Timothy Cholko (Thu May 17 2018 - 14:49:53 PDT)
  - Re: [AMBER] Creating a Gold surface library file David A Case (Fri May 18 2018 - 04:51:42 PDT)
- Re: [AMBER] Creating a Gold surface library file Timothy Cholko (Fri May 18 2018 - 15:03:41 PDT)
  - Re: [AMBER] Creating a Gold surface library file David A Case (Sat May 19 2018 - 06:53:59 PDT)
- Re: [AMBER] Creating a Gold surface library file Timothy Cholko (Tue May 22 2018 - 15:37:29 PDT)
  - Re: [AMBER] Creating a Gold surface library file David A Case (Tue May 22 2018 - 17:43:01 PDT)
[AMBER] Exiting due to the presence of inconsistent SHAKEH hydrogen clusters. with pmemd.cuda David Sáez (Mon May 14 2018 - 18:49:05 PDT)
- Re: [AMBER] Exiting due to the presence of inconsistent SHAKEH hydrogen clusters. with pmemd.cuda David Adrian Saez San Martin (Mon May 14 2018 - 18:58:02 PDT)
  - Re: [AMBER] Exiting due to the presence of inconsistent SHAKEH hydrogen clusters. with pmemd.cuda David A Case (Tue May 15 2018 - 13:12:53 PDT)
- Re: [AMBER] Exiting due to the presence of inconsistent SHAKEH hydrogen clusters. with pmemd.cuda David A Case (Tue May 22 2018 - 12:21:31 PDT)
[AMBER] MMPBSA.py - PrmtopError: Inconsistent charge definition for atom Rodrigo Galindo-Murillo (Tue May 15 2018 - 14:41:50 PDT)
- Re: [AMBER] MMPBSA.py - PrmtopError: Inconsistent charge definition for atom David A Case (Wed May 16 2018 - 05:49:18 PDT)
[AMBER] Electrostatic potential calculation Meng Wu (Tue May 15 2018 - 19:52:18 PDT)
- Re: [AMBER] Electrostatic potential calculation Meng Wu (Thu May 17 2018 - 23:45:54 PDT)
- Re: [AMBER] Electrostatic potential calculation Daniel Roe (Fri May 18 2018 - 07:49:11 PDT)
[AMBER] pmemd.MPI compatible for REMD simulation IN AMBER package Saikat Pal (Tue May 15 2018 - 22:48:07 PDT)
- Re: [AMBER] pmemd.MPI compatible for REMD simulation IN AMBER package Cruzeiro,Vinicius Wilian D (Wed May 16 2018 - 05:39:37 PDT)
[AMBER] I: help please giuseppe gatti (Wed May 16 2018 - 08:10:19 PDT)
- Re: [AMBER] I: help please David A Case (Fri May 18 2018 - 05:18:16 PDT)
[AMBER] MMPBSA energy decomposition Yuxin Xie (Wed May 16 2018 - 11:38:47 PDT)
[AMBER] Reservoir REMD using GPUs Hurst, Travis C (MU-Student) (Wed May 16 2018 - 15:25:55 PDT)
- Re: [AMBER] Reservoir REMD using GPUs Carlos Simmerling (Fri May 25 2018 - 10:07:02 PDT)
  - Re: [AMBER] Reservoir REMD using GPUs Hurst, Travis C (MU-Student) (Tue May 29 2018 - 08:09:01 PDT)
    - Re: [AMBER] Reservoir REMD using GPUs koushik kasavajhala (Thu May 31 2018 - 12:47:15 PDT)
[AMBER] Reg. AMBER ff14SB force filed / GAFF (recent version). DHEERAJ CHITARA (Thu May 17 2018 - 01:04:54 PDT)
- Re: [AMBER] Reg. AMBER ff14SB force filed / GAFF (recent version). Carlos Simmerling (Thu May 17 2018 - 04:27:37 PDT)
  - Re: [AMBER] Reg. AMBER ff14SB force filed / GAFF (recent version). DHEERAJ CHITARA (Thu May 17 2018 - 04:41:08 PDT)
- Re: [AMBER] Reg. AMBER ff14SB force filed / GAFF (recent version). David A Case (Thu May 17 2018 - 05:02:00 PDT)
  - Re: [AMBER] Reg. AMBER ff14SB force filed / GAFF (recent version). DHEERAJ CHITARA (Thu May 17 2018 - 05:08:50 PDT)
[AMBER] MD stops due to the distortion of a molecule Sergey Samsonov (Thu May 17 2018 - 01:23:57 PDT)
- Re: [AMBER] MD stops due to the distortion of a molecule David A Case (Thu May 17 2018 - 05:11:48 PDT)
  - Re: [AMBER] MD stops due to the distortion of a molecule Sergey Samsonov (Thu May 17 2018 - 23:13:43 PDT)
[AMBER] 1D-RISM: "ERROR> RXRISM: reached steps limit Maxstep=10000 STOP 1" PRITI ROY (Thu May 17 2018 - 02:45:51 PDT)
- Re: [AMBER] 1D-RISM: "ERROR> RXRISM: reached steps limit Maxstep=10000 STOP 1" Leena Aggarwal (Thu May 17 2018 - 05:06:37 PDT)
  - Re: [AMBER] 1D-RISM: "ERROR> RXRISM: reached steps limit Maxstep=10000 STOP 1" PRITI ROY (Thu May 17 2018 - 06:04:08 PDT)
    - Re: [AMBER] 1D-RISM: "ERROR> RXRISM: reached steps limit Maxstep=10000 STOP 1" Leena Aggarwal (Thu May 17 2018 - 06:23:15 PDT)
    - Re: [AMBER] 1D-RISM: "ERROR> RXRISM: reached steps limit Maxstep=10000 STOP 1" Tyler Luchko (Lists) (Thu May 17 2018 - 08:47:57 PDT)
    - Re: [AMBER] 1D-RISM: "ERROR> RXRISM: reached steps limit Maxstep=10000 STOP 1" PRITI ROY (Thu May 17 2018 - 09:18:50 PDT)
    - Re: [AMBER] 1D-RISM: "ERROR> RXRISM: reached steps limit Maxstep=10000 STOP 1" Leena Aggarwal (Thu May 17 2018 - 21:36:09 PDT)
- Re: [AMBER] 1D-RISM: "ERROR> RXRISM: reached steps limit Maxstep=10000 STOP 1" David A Case (Thu May 17 2018 - 09:11:23 PDT)
  - Re: [AMBER] 1D-RISM: "ERROR> RXRISM: reached steps limit Maxstep=10000 STOP 1" PRITI ROY (Thu May 17 2018 - 22:22:51 PDT)
[AMBER] DFT method for calculating amino acids partial charges in AMBER99 roja rahmani (Thu May 17 2018 - 03:10:43 PDT)
- Re: [AMBER] DFT method for calculating amino acids partial charges in AMBER99 FyD (Thu May 17 2018 - 03:19:32 PDT)
- Re: [AMBER] DFT method for calculating amino acids partial charges in AMBER99 David A Case (Fri May 18 2018 - 05:10:07 PDT)
  - Re: [AMBER] DFT method for calculating amino acids partial charges in AMBER99 roja rahmani (Fri May 18 2018 - 05:33:26 PDT)
[AMBER] Reg. generating empty frcmod file for ligand molecule DHEERAJ CHITARA (Thu May 17 2018 - 05:03:01 PDT)
- Re: [AMBER] Reg. generating empty frcmod file for ligand molecule Aashish Bhatt (Thu May 17 2018 - 05:16:09 PDT)
  - Re: [AMBER] Reg. generating empty frcmod file for ligand molecule DHEERAJ CHITARA (Thu May 17 2018 - 05:40:57 PDT)
[AMBER] GPU questions 陈金峰 (Thu May 17 2018 - 07:54:17 PDT)
- Re: [AMBER] GPU questions Daniel Roe (Thu May 17 2018 - 08:25:32 PDT)
[AMBER] Parametrization of Small Molecules Johannes Loeffler (Fri May 18 2018 - 02:44:56 PDT)
- Re: [AMBER] Parametrization of Small Molecules David A Case (Fri May 18 2018 - 04:58:13 PDT)
[AMBER] [cpptraj] Angle between atom and two centroids Eiros Zamora, Juan (Fri May 18 2018 - 04:14:11 PDT)
- Re: [AMBER] [cpptraj] Angle between atom and two centroids David A Case (Fri May 18 2018 - 05:04:34 PDT)
- Re: [AMBER] [cpptraj] Angle between atom and two centroids Daniel Roe (Fri May 18 2018 - 05:05:26 PDT)
[AMBER] Facing problem to generate ala10_chir.dat in REMD tutorial Saikat Pal (Fri May 18 2018 - 05:29:21 PDT)
- Re: [AMBER] Facing problem to generate ala10_chir.dat in REMD tutorial David A Case (Fri May 18 2018 - 07:03:50 PDT)
[AMBER] QMMM surface scan 陈金峰 (Fri May 18 2018 - 07:55:39 PDT)
[AMBER] Amber16 pmemd.cuda.MPI simulation can drop a frame with an inopportune node crash Chris Neale (Sat May 19 2018 - 00:07:06 PDT)
- Re: [AMBER] Amber16 pmemd.cuda.MPI simulation can drop a frame with an inopportune node crash David Cerutti (Sat May 19 2018 - 04:30:27 PDT)
  - Re: [AMBER] Amber16 pmemd.cuda.MPI simulation can drop a frame with an inopportune node crash Chris Neale (Sat May 19 2018 - 15:04:04 PDT)
[AMBER] Restart From Check point File Midhun K Madhu (Sun May 20 2018 - 05:47:24 PDT)
- Re: [AMBER] Restart From Check point File Stephan Schott (Sun May 20 2018 - 08:27:10 PDT)
- Re: [AMBER] Restart From Check point File Midhun K Madhu (Mon May 21 2018 - 22:22:46 PDT)
- Re: [AMBER] Restart From Check point File Stephan Schott (Tue May 22 2018 - 05:36:12 PDT)
[AMBER] Total Energy Decomposition daniele selli (Mon May 21 2018 - 04:06:56 PDT)
- Re: [AMBER] Total Energy Decomposition David A Case (Tue May 22 2018 - 05:12:46 PDT)
  - Re: [AMBER] Total Energy Decomposition daniele selli (Wed May 23 2018 - 05:06:43 PDT)
[AMBER] info grafic about MD Rosellen, Martin (Mon May 21 2018 - 05:45:42 PDT)
[AMBER] SHAKEH: Extra bond between hydrogen atoms of TIP3 water model Sadegh Faramarzi Ganjabad (Mon May 21 2018 - 11:24:52 PDT)
- Re: [AMBER] SHAKEH: Extra bond between hydrogen atoms of TIP3 water model Karla Galdamez (Mon May 21 2018 - 18:54:49 PDT)
- Re: [AMBER] SHAKEH: Extra bond between hydrogen atoms of TIP3 water model David A Case (Tue May 22 2018 - 05:15:20 PDT)
  - Re: [AMBER] SHAKEH: Extra bond between hydrogen atoms of TIP3 water model David A Case (Tue May 22 2018 - 12:53:54 PDT)
- Re: [AMBER] SHAKEH: Extra bond between hydrogen atoms of TIP3 water model Sadegh Faramarzi Ganjabad (Wed May 23 2018 - 12:36:30 PDT)
  - Re: [AMBER] SHAKEH: Extra bond between hydrogen atoms of TIP3 water model Sadegh Faramarzi Ganjabad (Mon May 28 2018 - 13:29:46 PDT)
[AMBER] 1x PCI-E Riser card for MD/TI? Hadházi Ádám (Tue May 22 2018 - 07:20:46 PDT)
- Re: [AMBER] 1x PCI-E Riser card for MD/TI? Ross Walker (Tue May 22 2018 - 14:08:48 PDT)
  - Re: [AMBER] 1x PCI-E Riser card for MD/TI? Hadházi Ádám (Tue May 22 2018 - 14:42:29 PDT)
[AMBER] Possible memory leak with LMOD Charo del Genio (Tue May 22 2018 - 09:39:08 PDT)
- Re: [AMBER] Possible memory leak with LMOD David A Case (Tue May 22 2018 - 13:08:59 PDT)
  - Re: [AMBER] Possible memory leak with LMOD Charo del Genio (Wed May 23 2018 - 10:31:11 PDT)
    - Re: [AMBER] Possible memory leak with LMOD David A Case (Thu May 24 2018 - 04:31:06 PDT)
    - Re: [AMBER] Possible memory leak with LMOD David A Case (Thu May 31 2018 - 12:43:12 PDT)
[AMBER] Scabilility of the code in cpus Ana Luisa Novo de Oliveira (Tue May 22 2018 - 09:45:39 PDT)
- Re: [AMBER] Scabilility of the code in cpus David A Case (Tue May 22 2018 - 13:38:59 PDT)
[AMBER] Hydrogen Bond Occupancy Jerrano Bowleg (Tue May 22 2018 - 10:13:42 PDT)
- Re: [AMBER] Hydrogen Bond Occupancy David A Case (Tue May 22 2018 - 17:46:00 PDT)
- Re: [AMBER] Hydrogen Bond Occupancy Gustaf Olsson (Tue May 22 2018 - 23:27:45 PDT)
- Re: [AMBER] Hydrogen Bond Occupancy Jerrano Bowleg (Wed May 23 2018 - 06:44:22 PDT)
[AMBER] R: Re: SHAKEH: Extra bond between hydrogen atoms of TIP3 water model Sadegh Faramarzi Ganjabad (Tue May 22 2018 - 12:59:21 PDT)
- Re: [AMBER] R: Re: SHAKEH: Extra bond between hydrogen atoms of TIP3 water model David A Case (Tue May 22 2018 - 17:32:17 PDT)
[AMBER] VMD window Karla Galdamez (Tue May 22 2018 - 20:43:23 PDT)
- Re: [AMBER] VMD window Gustaf Olsson (Tue May 22 2018 - 23:05:11 PDT)
  - Re: [AMBER] VMD window Karla Galdamez (Tue May 22 2018 - 23:53:14 PDT)
    - Re: [AMBER] VMD window Gustaf Olsson (Wed May 23 2018 - 00:48:40 PDT)
    - Re: [AMBER] VMD window Karla Galdamez (Wed May 23 2018 - 07:24:27 PDT)
[AMBER] update_amber URL time out problem Meng Wu (Wed May 23 2018 - 01:29:11 PDT)
- Re: [AMBER] update_amber URL time out problem David A Case (Wed May 23 2018 - 05:13:09 PDT)
- Re: [AMBER] update_amber URL time out problem Meng Wu (Wed May 23 2018 - 20:07:55 PDT)
  - Re: [AMBER] update_amber URL time out problem David A Case (Thu May 24 2018 - 04:45:05 PDT)
[AMBER] S-S bond roja rahmani (Wed May 23 2018 - 02:47:29 PDT)
- Re: [AMBER] S-S bond FyD (Wed May 23 2018 - 22:24:55 PDT)
  - Re: [AMBER] S-S bond roja rahmani (Wed May 23 2018 - 22:45:13 PDT)
    - Re: [AMBER] S-S bond FyD (Thu May 31 2018 - 22:22:31 PDT)
[AMBER] Use of Amber12 and 14 on the same simulation JoAnne Babula (Wed May 23 2018 - 09:09:08 PDT)
- Re: [AMBER] Use of Amber12 and 14 on the same simulation David A Case (Thu May 24 2018 - 04:28:45 PDT)
[AMBER] parmed/chamber verify including CMAP corrections David Sáez (Wed May 23 2018 - 12:00:26 PDT)
- Re: [AMBER] parmed/chamber verify including CMAP corrections Robin Betz (Wed May 23 2018 - 12:06:19 PDT)
[AMBER] Amber 18 manual shows TI as not supported in pmemd.cuda Patricio German Barletta Roldan (Wed May 23 2018 - 13:47:48 PDT)
- Re: [AMBER] Amber 18 manual shows TI as not supported in pmemd.cuda David A Case (Thu May 24 2018 - 04:34:27 PDT)
[AMBER] pmemd.MPI won't work in Amber 18 Hai Long (Wed May 23 2018 - 14:37:27 PDT)
- Re: [AMBER] pmemd.MPI won't work in Amber 18 David A Case (Thu May 24 2018 - 04:38:09 PDT)
  - Re: [AMBER] pmemd.MPI won't work in Amber 18 Hai Long (Thu May 24 2018 - 14:44:40 PDT)
    - Re: [AMBER] pmemd.MPI won't work in Amber 18 Ross Walker (Thu May 24 2018 - 15:08:11 PDT)
    - Re: [AMBER] pmemd.MPI won't work in Amber 18 Hai Long (Wed Oct 03 2018 - 19:57:17 PDT)
    - Re: [AMBER] pmemd.MPI won't work in Amber 18 Ross Walker (Thu Oct 04 2018 - 05:31:06 PDT)
[AMBER] optimization of QM zone in QM/MM-GBSA calculations. mish (Thu May 24 2018 - 00:10:19 PDT)
- Re: [AMBER] optimization of QM zone in QM/MM-GBSA calculations. David A Case (Thu May 24 2018 - 04:46:03 PDT)
[AMBER] Error in using pdb4amber command senal dinuka (Thu May 24 2018 - 03:14:03 PDT)
- Re: [AMBER] Error in using pdb4amber command David A Case (Thu May 24 2018 - 04:49:10 PDT)
  - Re: [AMBER] Error in using pdb4amber command senal dinuka (Thu May 24 2018 - 04:55:14 PDT)
    - Re: [AMBER] Error in using pdb4amber command Aashish Bhatt (Thu May 24 2018 - 06:04:45 PDT)
    - Re: [AMBER] Error in using pdb4amber command Hai Nguyen (Sat Jun 02 2018 - 20:58:05 PDT)
[AMBER] How to prepare prmtop and inpcrd files from a PDB file? Markowska (Thu May 24 2018 - 05:07:20 PDT)
- Re: [AMBER] How to prepare prmtop and inpcrd files from a PDB file? Gustaf Olsson (Thu May 24 2018 - 05:15:47 PDT)
- Re: [AMBER] How to prepare prmtop and inpcrd files from a PDB file? Carlos Simmerling (Thu May 24 2018 - 05:17:26 PDT)
  - Re: [AMBER] How to prepare prmtop and inpcrd files from a PDB file? Markowska (Thu May 24 2018 - 05:52:59 PDT)
    - Re: [AMBER] How to prepare prmtop and inpcrd files from a PDB file? Carlos Simmerling (Thu May 24 2018 - 05:56:20 PDT)
    - Re: [AMBER] How to prepare prmtop and inpcrd files from a PDB file? Markowska (Thu May 24 2018 - 06:07:13 PDT)
    - Re: [AMBER] How to prepare prmtop and inpcrd files from a PDB file? Carlos Simmerling (Thu May 24 2018 - 06:53:04 PDT)
    - Re: [AMBER] How to prepare prmtop and inpcrd files from a PDB file? Markowska (Fri May 25 2018 - 05:37:18 PDT)
- Re: [AMBER] How to prepare prmtop and inpcrd files from a PDB file? Gustaf Olsson (Thu May 24 2018 - 05:19:18 PDT)
  - Re: [AMBER] How to prepare prmtop and inpcrd files from a PDB file? Kshatresh Dutta Dubey (Thu May 24 2018 - 06:27:03 PDT)
[AMBER] Plotting phi-psi plots with free energy scale Chetna Tyagi (Thu May 24 2018 - 07:01:19 PDT)
- Re: [AMBER] Plotting phi-psi plots with free energy scale Carlos Simmerling (Thu May 24 2018 - 07:13:33 PDT)
[AMBER] How to evaluate the impact of PH on protein structures by Amber Lei Zhao (Thu May 24 2018 - 07:49:38 PDT)
[AMBER] AMBER TI more examples Omoto, Kiyoyuki (Thu May 24 2018 - 08:30:55 PDT)
- Re: [AMBER] AMBER TI more examples David A Case (Tue May 29 2018 - 06:24:41 PDT)
[AMBER] ABMD with multiple walkers Qinghua Liao (Fri May 25 2018 - 16:00:01 PDT)
- Re: [AMBER] ABMD with multiple walkers Feng Pan (Sat May 26 2018 - 19:16:09 PDT)
  - Re: [AMBER] ABMD with multiple walkers Qinghua Liao (Sun May 27 2018 - 14:08:12 PDT)
    - Re: [AMBER] ABMD with multiple walkers Feng Pan (Sun May 27 2018 - 19:05:45 PDT)
    - Re: [AMBER] ABMD with multiple walkers Qinghua Liao (Mon May 28 2018 - 05:36:21 PDT)
    - Re: [AMBER] ABMD with multiple walkers Feng Pan (Mon May 28 2018 - 18:01:21 PDT)
    - Re: [AMBER] ABMD with multiple walkers Qinghua Liao (Tue May 29 2018 - 00:31:31 PDT)
[AMBER] CUDA v9.0 with AMBER16 Question Korey M Reid (Fri May 25 2018 - 16:56:43 PDT)
- Re: [AMBER] CUDA v9.0 with AMBER16 Question David A Case (Sat May 26 2018 - 06:14:01 PDT)
[AMBER] Using multiple CPU threads senal dinuka (Sat May 26 2018 - 01:17:55 PDT)
- Re: [AMBER] Using multiple CPU threads David A Case (Sat May 26 2018 - 06:19:21 PDT)
[AMBER] Troubleshooting SHAKE problems in minimization Alen Ahmetovic (Sat May 26 2018 - 21:07:29 PDT)
- Re: [AMBER] Troubleshooting SHAKE problems in minimization David A Case (Sun May 27 2018 - 06:06:47 PDT)
[AMBER] DEADLINE EXTENDED: Call for Papers, GCC 2018, 14th German Conference on Chemoinformatics Stefan.Guessregen.sanofi.com (Mon May 28 2018 - 04:56:58 PDT)
[AMBER] error in rst file during Minimization Subrata Paul (Mon May 28 2018 - 05:37:08 PDT)
- Re: [AMBER] error in rst file during Minimization Stephan Schott (Mon May 28 2018 - 06:03:57 PDT)
  - Re: [AMBER] error in rst file during Minimization Subrata Paul (Mon May 28 2018 - 09:04:38 PDT)
[AMBER] AMBER NFE SMD calculation with new collective variable georg.kuenze.vanderbilt.edu (Mon May 28 2018 - 13:51:41 PDT)
- Re: [AMBER] AMBER NFE SMD calculation with new collective variable Feng Pan (Wed May 30 2018 - 11:20:39 PDT)
[AMBER] AMBER: trouble while running constant pH simulation 李耀 (Mon May 28 2018 - 19:35:06 PDT)
- Re: [AMBER] AMBER: trouble while running constant pH simulation 李耀 (Tue May 29 2018 - 00:54:18 PDT)
  - Re: [AMBER] AMBER: trouble while running constant pH simulation Cruzeiro,Vinicius Wilian D (Tue May 29 2018 - 05:58:06 PDT)
[AMBER] Automatic patching failed! senal dinuka (Tue May 29 2018 - 21:10:54 PDT)
- Re: [AMBER] Automatic patching failed! Charles Lin (Tue May 29 2018 - 21:24:18 PDT)
  - Re: [AMBER] Automatic patching failed! senal dinuka (Tue May 29 2018 - 21:30:50 PDT)
    - Re: [AMBER] Automatic patching failed! Charles Lin (Tue May 29 2018 - 22:11:09 PDT)
    - Re: [AMBER] Automatic patching failed! senal dinuka (Wed May 30 2018 - 00:49:40 PDT)
    - Re: [AMBER] Automatic patching failed! David A Case (Wed May 30 2018 - 05:42:42 PDT)
[AMBER] Request of help on Leap PDB preparation error "atom does not have a type" 符哲瀚 (Tue May 29 2018 - 21:32:33 PDT)
- Re: [AMBER] Request of help on Leap PDB preparation error "atom does not have a type" Gustaf Olsson (Tue May 29 2018 - 23:36:40 PDT)
- Re: [AMBER] Request of help on Leap PDB preparation error "atom does not have a type" Carlos Simmerling (Wed May 30 2018 - 05:09:31 PDT)
- Re: [AMBER] Request of help on Leap PDB preparation error "atom does not have a type" David A Case (Wed May 30 2018 - 05:46:50 PDT)
[AMBER] sander failed with prmtop complex.top! Urszula Uciechowska (Tue May 29 2018 - 23:52:54 PDT)
[AMBER] TI for side chain mutation in dimer protein Josephine la sala (Wed May 30 2018 - 02:55:48 PDT)
[AMBER] problems with MCPY.py step 2 Cristián Ferretti (Wed May 30 2018 - 03:03:02 PDT)
- Re: [AMBER] problems with MCPY.py step 2 Pengfei Li (Sat Jun 02 2018 - 11:58:52 PDT)
[AMBER] TiMergeError: Cannot have dihedral cross through softcore region Jissy Akkarapattiakal Kuriappan (Wed May 30 2018 - 06:07:15 PDT)
[AMBER] TI for side chain mutation in dimer protein Josephine la sala (Wed May 30 2018 - 06:29:22 PDT)
Re: [AMBER] AMBER: trouble while running constant pH simulation > (Cruzeiro, Vinicius Wilian D) 李耀 (Wed May 30 2018 - 08:48:29 PDT)
- Re: [AMBER] AMBER: trouble while running constant pH simulation > (Cruzeiro, Vinicius Wilian D) Cruzeiro,Vinicius Wilian D (Wed May 30 2018 - 09:03:55 PDT)
[AMBER] Conda Installation error andreas.tosstorff.cup.uni-muenchen.de (Wed May 30 2018 - 10:51:25 PDT)
- Re: [AMBER] Conda Installation error Hai Nguyen (Thu May 31 2018 - 07:18:30 PDT)
  - Re: [AMBER] Conda Installation error Scott Brozell (Thu May 31 2018 - 09:06:54 PDT)
    - Re: [AMBER] Conda Installation error Hai Nguyen (Thu May 31 2018 - 09:11:38 PDT)
    - Re: [AMBER] Conda Installation error Scott Brozell (Thu May 31 2018 - 09:18:24 PDT)
    - Re: [AMBER] Conda Installation error andreas.tosstorff.cup.uni-muenchen.de (Wed Jun 06 2018 - 00:41:44 PDT)
    - Re: [AMBER] Conda Installation error David A Case (Wed Jun 06 2018 - 05:08:02 PDT)
    - Re: [AMBER] Conda Installation error Hai Nguyen (Wed Jun 06 2018 - 17:51:43 PDT)
    - Re: [AMBER] Conda Installation error andreas.tosstorff.cup.uni-muenchen.de (Thu Jun 07 2018 - 00:42:21 PDT)
[AMBER] Dimension Box visualization Aashish Bhatt (Wed May 30 2018 - 23:00:50 PDT)
- Re: [AMBER] Dimension Box visualization David A Case (Thu May 31 2018 - 04:29:35 PDT)
  - Re: [AMBER] Dimension Box visualization Matias Machado (Thu May 31 2018 - 04:45:13 PDT)
    - Re: [AMBER] Dimension Box visualization Aashish Bhatt (Tue Jun 05 2018 - 03:09:48 PDT)
[AMBER] Ubuntu 18 Sepideh Jafari (Thu May 31 2018 - 06:22:00 PDT)
- Re: [AMBER] Ubuntu 18 David A Case (Thu May 31 2018 - 07:10:58 PDT)
  - Re: [AMBER] Ubuntu 18 Sepideh Jafari (Thu May 31 2018 - 07:29:24 PDT)
    - Re: [AMBER] Ubuntu 18 Scott Brozell (Thu May 31 2018 - 08:55:40 PDT)
[AMBER] Initial configuration of ADP and ion simulation using AMBER. Abhilash J (Thu May 31 2018 - 09:45:12 PDT)
- Re: [AMBER] Initial configuration of ADP and ion simulation using AMBER. Pengfei Li (Sat Jun 02 2018 - 15:07:44 PDT)
  - Re: [AMBER] Initial configuration of ADP and ion simulation using AMBER. Chris Neale (Sat Jun 02 2018 - 16:04:57 PDT)
    - Re: [AMBER] Initial configuration of ADP and ion simulation using AMBER. Abhilash J (Tue Jun 05 2018 - 11:38:47 PDT)
    - Re: [AMBER] Initial configuration of ADP and ion simulation using AMBER. Pengfei Li (Tue Jun 12 2018 - 12:52:30 PDT)
    - Re: [AMBER] Initial configuration of ADP and ion simulation using AMBER. Abhilash J (Wed Jun 13 2018 - 09:46:09 PDT)
[AMBER] Clarification on forming covalent linkages senal dinuka (Fri Jun 01 2018 - 02:00:35 PDT)
- Re: [AMBER] Clarification on forming covalent linkages David A Case (Fri Jun 01 2018 - 05:26:00 PDT)
[AMBER] lifetime analysis of native/nonnative contacts data Ruth Helena Tichauer (Fri Jun 01 2018 - 04:28:46 PDT)
[AMBER] high values of RMSD during the simulation of molecular dynamics between DNA and small molecule. Does anyone explain? Edjan Silva (Fri Jun 01 2018 - 07:26:20 PDT)
- Re: [AMBER] high values of RMSD during the simulation of molecular dynamics between DNA and small molecule. Does anyone explain? Carlos Simmerling (Fri Jun 01 2018 - 07:33:14 PDT)
- Re: [AMBER] high values of RMSD during the simulation of molecular dynamics between DNA and small molecule. Does anyone explain? ABEL Stephane (Fri Jun 01 2018 - 07:35:54 PDT)
  - Re: [AMBER] high values of RMSD during the simulation of molecular dynamics between DNA and small molecule. Does anyone explain? Carlos Simmerling (Fri Jun 01 2018 - 08:17:01 PDT)
    - Re: [AMBER] high values of RMSD during the simulation of molecular dynamics between DNA and small molecule. Does anyone explain? Edjan Silva (Fri Jun 01 2018 - 18:15:09 PDT)
    - Re: [AMBER] high values of RMSD during the simulation of molecular dynamics between DNA and small molecule. Does anyone explain? Carlos Simmerling (Fri Jun 01 2018 - 18:20:13 PDT)
    - Re: [AMBER] high values of RMSD during the simulation of molecular dynamics between DNA and small molecule. Does anyone explain? Edjan Silva (Fri Jun 01 2018 - 18:38:42 PDT)
    - Re: [AMBER] high values of RMSD during the simulation of molecular dynamics between DNA and small molecule. Does anyone explain? Akash Deep Biswas (Fri Jun 01 2018 - 18:57:10 PDT)
    - Re: [AMBER] high values of RMSD during the simulation of molecular dynamics between DNA and small molecule. Does anyone explain? Carlos Simmerling (Sat Jun 02 2018 - 04:03:31 PDT)
[AMBER] Calculation of the REMD exchange rate in amber 14 RITUPARNA (Fri Jun 01 2018 - 08:04:03 PDT)
- Re: [AMBER] Calculation of the REMD exchange rate in amber 14 Carlos Simmerling (Fri Jun 01 2018 - 08:17:26 PDT)
[AMBER] Are 1070Ti GPUs Supported? Zachary Fallon (Fri Jun 01 2018 - 09:24:16 PDT)
- Re: [AMBER] Are 1070Ti GPUs Supported? Ross Walker (Sun Jun 03 2018 - 05:05:35 PDT)
  - Re: [AMBER] Are 1070Ti GPUs Supported? Zachary Fallon (Sun Jun 03 2018 - 12:50:39 PDT)
[AMBER] box size Qinghua Liao (Fri Jun 01 2018 - 10:10:57 PDT)
- Re: [AMBER] box size Carlos Simmerling (Fri Jun 01 2018 - 10:59:54 PDT)
  - Re: [AMBER] box size Qinghua Liao (Fri Jun 01 2018 - 11:12:40 PDT)
    - Re: [AMBER] box size David A Case (Sat Jun 02 2018 - 05:39:08 PDT)
    - Re: [AMBER] box size Qinghua Liao (Sat Jun 02 2018 - 05:46:33 PDT)
[AMBER] Question about how to calculate the mass center distance between adjacent repeat units of one polymer chain 唐元晖 (Fri Jun 01 2018 - 14:19:26 PDT)
[AMBER] Using Pytraj to read and write velocity files Korey M Reid (Fri Jun 01 2018 - 21:08:03 PDT)
- Re: [AMBER] Using Pytraj to read and write velocity files Hai Nguyen (Sat Jun 02 2018 - 15:44:59 PDT)
  - Re: [AMBER] Using Pytraj to read and write velocity files Korey M Reid (Tue Jun 05 2018 - 21:03:40 PDT)
    - Re: [AMBER] Using Pytraj to read and write velocity files Hai Nguyen (Tue Jun 05 2018 - 21:21:08 PDT)
    - Re: [AMBER] Using Pytraj to read and write velocity files Korey M Reid (Wed Jun 06 2018 - 00:50:32 PDT)
[AMBER] Accelerated MD re-weighting---- very high PMF values Chetna Tyagi (Sun Jun 03 2018 - 07:25:54 PDT)
- Re: [AMBER] Accelerated MD re-weighting---- very high PMF values Chetna Tyagi (Sun Jun 03 2018 - 07:27:10 PDT)
  - [AMBER] Fwd: Accelerated MD re-weighting---- very high PMF values Chetna Tyagi (Mon Jun 11 2018 - 05:33:42 PDT)
Re: [AMBER] A question about force-field parameters for organic compounds related to the purchase of AMBER-Certified EXXACT machine David A Case (Sun Jun 03 2018 - 09:21:23 PDT)
- Re: [AMBER] A question about force-field parameters for organic compounds related to the purchase of AMBER-Certified EXXACT machine Ross Walker (Sun Jun 03 2018 - 10:02:23 PDT)
[AMBER] Atom Mask in QMMM calculation emanuele (Sun Jun 03 2018 - 13:29:48 PDT)
- Re: [AMBER] Atom Mask in QMMM calculation Goetz, Andreas (Sun Jun 03 2018 - 18:29:59 PDT)
  - Re: [AMBER] Atom Mask in QMMM calculation emanuele falbo (Mon Jun 04 2018 - 02:31:48 PDT)
[AMBER] Query regarding 3D-RISM output Rakesh Srivastava (Sun Jun 03 2018 - 23:45:39 PDT)
- Re: [AMBER] Query regarding 3D-RISM output David A Case (Mon Jun 04 2018 - 12:21:56 PDT)
  - Re: [AMBER] Query regarding 3D-RISM output Rakesh Srivastava (Mon Jun 04 2018 - 21:51:02 PDT)
[AMBER] Radial distribution function of waters diego.soler.uam.es (Mon Jun 04 2018 - 08:08:24 PDT)
- Re: [AMBER] Radial distribution function of waters David A Case (Mon Jun 04 2018 - 12:24:35 PDT)
- Re: [AMBER] Radial distribution function of waters Gustaf Olsson (Mon Jun 04 2018 - 23:12:25 PDT)
  - Re: [AMBER] Radial distribution function of waters diego.soler.uam.es (Tue Jun 05 2018 - 05:53:00 PDT)
    - Re: [AMBER] Radial distribution function of waters Daniel Roe (Tue Jun 05 2018 - 06:05:34 PDT)
    - Re: [AMBER] Radial distribution function of waters Gustaf Olsson (Tue Jun 05 2018 - 06:09:01 PDT)
[AMBER] make test error: make: *** [test.serial] Error 2 ersin gündeğer (Tue Jun 05 2018 - 00:41:32 PDT)
- Re: [AMBER] make test error: make: *** [test.serial] Error 2 David A Case (Tue Jun 05 2018 - 04:39:39 PDT)
  - Re: [AMBER] make test error: make: *** [test.serial] Error 2 ersin gündeğer (Thu Jun 07 2018 - 06:21:05 PDT)
[AMBER] Installing GPU version Amber18 juan.franco.uam.es (Tue Jun 05 2018 - 01:12:30 PDT)
- Re: [AMBER] Installing GPU version Amber18 Stephan Schott (Tue Jun 05 2018 - 02:30:44 PDT)
  - Re: [AMBER] Installing GPU version Amber18 David A Case (Tue Jun 05 2018 - 04:45:16 PDT)
    - Re: [AMBER] Installing GPU version Amber18 Felipe Franco Gonzalez (Tue Jun 05 2018 - 06:46:47 PDT)
[AMBER] Converting atom naming to GLYCAM senal dinuka (Tue Jun 05 2018 - 01:50:11 PDT)
- Re: [AMBER] Converting atom naming to GLYCAM Lachele Foley (Tue Jun 05 2018 - 07:55:07 PDT)
[AMBER] compatibility of graphic card and Amber Andrea H. Kasun (Tue Jun 05 2018 - 02:25:06 PDT)
- Re: [AMBER] compatibility of graphic card and Amber Zachary Fallon (Tue Jun 05 2018 - 06:52:33 PDT)
  - Re: [AMBER] compatibility of graphic card and Amber Andrea H. Kasun (Tue Jun 05 2018 - 07:12:49 PDT)
    - Re: [AMBER] compatibility of graphic card and Amber Carlos Simmerling (Tue Jun 05 2018 - 07:21:43 PDT)
    - Re: [AMBER] compatibility of graphic card and Amber Ross Walker (Wed Jun 06 2018 - 07:10:10 PDT)
[AMBER] how to calculate the mass center distance between adjacent repeat units of one polymer chain 唐元晖 (Tue Jun 05 2018 - 09:53:49 PDT)
- Re: [AMBER] how to calculate the mass center distance between adjacent repeat units of one polymer chain Wesley Michael Botello-Smith (Tue Jun 05 2018 - 10:13:23 PDT)
  - Re: [AMBER] how to calculate the mass center distance between adjacent repeat units of one polymer chain 唐元晖 (Tue Jun 05 2018 - 13:09:17 PDT)
- Re: [AMBER] how to calculate the mass center distance between adjacent repeat units of one polymer chain Daniel Roe (Tue Jun 05 2018 - 12:11:53 PDT)
[AMBER] protein sampling efficacy Lei Zhao (Tue Jun 05 2018 - 20:10:31 PDT)
[AMBER] NaN in NEB output Aravind Ravichandran (Tue Jun 05 2018 - 21:41:51 PDT)
- Re: [AMBER] NaN in NEB output Carlos Simmerling (Wed Jun 06 2018 - 05:20:37 PDT)
[AMBER] Queries regarding bond command in leap Aravind Ravichandran (Tue Jun 05 2018 - 22:06:34 PDT)
- Re: [AMBER] Queries regarding bond command in leap Bill Ross (Tue Jun 05 2018 - 22:21:44 PDT)
  - Re: [AMBER] Queries regarding bond command in leap Aravind Ravichandran (Tue Jun 05 2018 - 22:43:43 PDT)
[AMBER] Amber18 and CUDA 9.2 Nikolay N. Kuzmich (Wed Jun 06 2018 - 02:08:10 PDT)
- Re: [AMBER] Amber18 and CUDA 9.2 David A Case (Wed Jun 06 2018 - 05:15:20 PDT)
- Re: [AMBER] Amber18 and CUDA 9.2 Nikolay N. Kuzmich (Fri Jun 08 2018 - 04:53:00 PDT)
  - Re: [AMBER] Amber18 and CUDA 9.2 David A Case (Sat Jun 09 2018 - 05:59:25 PDT)
[AMBER] Advanced restraints in protein mutation Simon Kit Sang Chu (Wed Jun 06 2018 - 02:21:10 PDT)
[AMBER] Amber DSSP : Secondary structure Garima Singh (Wed Jun 06 2018 - 04:17:18 PDT)
- Re: [AMBER] Amber DSSP : Secondary structure Daniel Roe (Wed Jun 06 2018 - 10:07:01 PDT)
[AMBER] Carbon-nanotube topology construction Shilpa Gupta (Thu Jun 07 2018 - 02:44:10 PDT)
- Re: [AMBER] Carbon-nanotube topology construction David A Case (Thu Jun 07 2018 - 04:24:14 PDT)
  - Re: [AMBER] Carbon-nanotube topology construction Shilpa Gupta (Thu Jun 07 2018 - 06:04:32 PDT)
[AMBER] MM-GBSA for recptor-magnesium-ligand complex Urszula Uciechowska (Thu Jun 07 2018 - 03:24:23 PDT)
- Re: [AMBER] MM-GBSA for recptor-magnesium-ligand complex David A Case (Thu Jun 07 2018 - 04:28:20 PDT)
  - Re: [AMBER] MM-GBSA for recptor-magnesium-ligand complex Urszula Uciechowska (Wed Jun 13 2018 - 06:07:36 PDT)
Re: [AMBER] AMBER Digest, Vol 2314, Issue 1 Garima Singh (Thu Jun 07 2018 - 03:34:01 PDT)
[AMBER] CPPTRAJ H-bond Plot Rana Rehan Khalid (Thu Jun 07 2018 - 04:33:42 PDT)
- Re: [AMBER] CPPTRAJ H-bond Plot Daniel Roe (Mon Jun 11 2018 - 12:28:13 PDT)
[AMBER] change x-axis to time for gnuplot using cpptraj Krantzman, Kristin D (Thu Jun 07 2018 - 12:19:09 PDT)
[AMBER] conversion of MG ions in parmed Holly Freedman (Thu Jun 07 2018 - 16:49:28 PDT)
[AMBER] psf from parmed Stefano Guglielmo (Thu Jun 07 2018 - 16:56:46 PDT)
- Re: [AMBER] psf from parmed Pengfei Li (Tue Jun 12 2018 - 13:02:01 PDT)
  - Re: [AMBER] psf from parmed Stefano Guglielmo (Tue Jun 12 2018 - 13:33:53 PDT)
    - Re: [AMBER] psf from parmed Jason Swails (Wed Jun 13 2018 - 19:38:19 PDT)
    - Re: [AMBER] psf from parmed Stefano Guglielmo (Wed Jun 13 2018 - 23:59:29 PDT)
[AMBER] Bonds across the periodic boundaries Xiaoyu Wang (Thu Jun 07 2018 - 20:32:57 PDT)
- Re: [AMBER] Bonds across the periodic boundaries David Cerutti (Thu Jun 07 2018 - 20:53:33 PDT)
  - Re: [AMBER] Bonds across the periodic boundaries Thomas C Bishop (Fri Jun 08 2018 - 09:53:09 PDT)
[AMBER] Distance restraint not working Simon Kit Sang Chu (Fri Jun 08 2018 - 04:13:07 PDT)
- Re: [AMBER] Distance restraint not working Bill Ross (Fri Jun 08 2018 - 04:32:11 PDT)
- Re: [AMBER] Distance restraint not working Stephan Schott (Fri Jun 08 2018 - 04:40:13 PDT)
  - Re: [AMBER] Distance restraint not working Simon Kit Sang Chu (Fri Jun 08 2018 - 04:50:53 PDT)
    - Re: [AMBER] Distance restraint not working Bill Ross (Fri Jun 08 2018 - 05:18:32 PDT)
    - Re: [AMBER] Distance restraint not working Simon Kit Sang Chu (Fri Jun 08 2018 - 05:22:20 PDT)
    - Re: [AMBER] Distance restraint not working Bill Ross (Fri Jun 08 2018 - 05:42:46 PDT)
    - Re: [AMBER] Distance restraint not working Simon Kit Sang Chu (Fri Jun 08 2018 - 07:31:43 PDT)
- Re: [AMBER] Distance restraint not working Stephan Schott (Fri Jun 08 2018 - 10:16:59 PDT)
  - Re: [AMBER] Distance restraint not working Simon Kit Sang Chu (Sat Jun 09 2018 - 03:29:28 PDT)
- Re: [AMBER] Distance restraint not working Stephan Schott (Mon Jun 11 2018 - 02:07:28 PDT)
  - Re: [AMBER] Distance restraint not working Simon Kit Sang Chu (Mon Jun 11 2018 - 08:15:09 PDT)
[AMBER] Error at runtime running AMBER18 with CUDA91 on GTX980 Wesley Michael Botello-Smith (Fri Jun 08 2018 - 10:36:54 PDT)
- Re: [AMBER] Error at runtime running AMBER18 with CUDA91 on GTX980 Stephan Schott (Fri Jun 08 2018 - 11:07:36 PDT)
  - Re: [AMBER] Error at runtime running AMBER18 with CUDA91 on GTX980 Wesley Michael Botello-Smith (Fri Jun 08 2018 - 11:30:47 PDT)
[AMBER] water box with 64 molecules 赵东波 (Sun Jun 10 2018 - 18:22:47 PDT)
- Re: [AMBER] water box with 64 molecules Bill Ross (Sun Jun 10 2018 - 19:14:48 PDT)
- Re: [AMBER] water box with 64 molecules David A Case (Mon Jun 11 2018 - 04:58:18 PDT)
[AMBER] TrajError: start frame (51021) > total frames (5000) 岡部勇二 (Mon Jun 11 2018 - 00:52:22 PDT)
- Re: [AMBER] TrajError: start frame (51021) > total frames (5000) David A Case (Mon Jun 11 2018 - 05:03:49 PDT)
  - Re: [AMBER] TrajError: start frame (51021) > total frames (5000) y-okabe.cc.miyakonojo-nct.ac.jp (Mon Jun 11 2018 - 07:26:22 PDT)
[AMBER] Running QMMM on Iron Core enzyme Devashish_Das (Mon Jun 11 2018 - 02:59:41 PDT)
- Re: [AMBER] Running QMMM on Iron Core enzyme David A Case (Mon Jun 11 2018 - 05:08:25 PDT)
[AMBER] QMMM problem 陈金峰 (Mon Jun 11 2018 - 06:59:45 PDT)
- Re: [AMBER] QMMM problem emanuele falbo (Mon Jun 11 2018 - 07:34:50 PDT)
[AMBER] Change x-axis from frame # to time in gnu plot created with secstruct command using cpptraj Krantzman, Kristin D (Mon Jun 11 2018 - 12:07:31 PDT)
- Re: [AMBER] Change x-axis from frame # to time in gnu plot created with secstruct command using cpptraj Daniel Roe (Mon Jun 11 2018 - 12:20:21 PDT)
  - Re: [AMBER] Change x-axis from frame # to time in gnu plot created with secstruct command using cpptraj Krantzman, Kristin D (Mon Jun 11 2018 - 12:29:08 PDT)
[AMBER] Free Energy landscape (FEL) Facundo Gomes (Mon Jun 11 2018 - 19:58:46 PDT)
[AMBER] Simulating drug molecules in lipid bilayers Christopher Faulkner (Tue Jun 12 2018 - 05:29:47 PDT)
- [AMBER] Including C4 terms LJ12-6-4 Pooria Farahani (Tue Jun 12 2018 - 05:41:53 PDT)
  - Re: [AMBER] Including C4 terms LJ12-6-4 Pengfei Li (Tue Jun 12 2018 - 13:11:51 PDT)
    - Re: [AMBER] Including C4 terms LJ12-6-4 Pooria Farahani (Wed Jun 13 2018 - 04:00:52 PDT)
- Re: [AMBER] Simulating drug molecules in lipid bilayers Dickson, Callum (Wed Jun 13 2018 - 16:24:22 PDT)
  - Re: [AMBER] Simulating drug molecules in lipid bilayers Christopher Faulkner (Thu Jun 14 2018 - 02:36:37 PDT)
[AMBER] Charm-gui and water models Danial Pourjafar-Dehkordi (Tue Jun 12 2018 - 08:56:10 PDT)
- Re: [AMBER] Charm-gui and water models Bill Ross (Tue Jun 12 2018 - 13:28:34 PDT)
- Re: [AMBER] Charm-gui and water models Danial Pourjafar-Dehkordi (Fri Jun 15 2018 - 06:02:41 PDT)
[AMBER] GaMD Not Running in GPU Midhun K Madhu (Tue Jun 12 2018 - 09:25:41 PDT)
- Re: [AMBER] GaMD Not Running in GPU ATUL KUMAR (Mon Aug 05 2019 - 22:13:49 PDT)
[AMBER] Periodic boundary conditions and N_OF_BONDS_COLVAR Hugo Macdermott-Opeskin (Tue Jun 12 2018 - 18:51:01 PDT)
- Re: [AMBER] Periodic boundary conditions and N_OF_BONDS_COLVAR Feng Pan (Tue Jun 12 2018 - 21:04:15 PDT)
[AMBER] AMBER performance degradation on CPU compared to GPU Dmitry Suplatov (Wed Jun 13 2018 - 02:46:00 PDT)
- Re: [AMBER] AMBER performance degradation on CPU compared to GPU David A Case (Wed Jun 13 2018 - 05:52:51 PDT)
[AMBER] NetCDF trajectories in lower precision Markowska (Wed Jun 13 2018 - 03:17:21 PDT)
- Re: [AMBER] NetCDF trajectories in lower precision Gustaf Olsson (Wed Jun 13 2018 - 03:32:44 PDT)
  - Re: [AMBER] NetCDF trajectories in lower precision Markowska (Wed Jun 13 2018 - 03:41:52 PDT)
    - Re: [AMBER] NetCDF trajectories in lower precision David A Case (Wed Jun 13 2018 - 05:35:14 PDT)
[AMBER] CPPTRAJ: Wildcards for the frames to extract Nikolay N. Kuzmich (Wed Jun 13 2018 - 05:12:19 PDT)
- Re: [AMBER] CPPTRAJ: Wildcards for the frames to extract David A Case (Wed Jun 13 2018 - 05:37:18 PDT)
- Re: [AMBER] CPPTRAJ: Wildcards for the frames to extract Nikolay N. Kuzmich (Fri Jun 15 2018 - 08:15:01 PDT)
[AMBER] Net salt ions ouside the solvent box after AddIons Kasprzak, Wojciech (NIH/NCI) [C] (Wed Jun 13 2018 - 12:11:55 PDT)
- Re: [AMBER] Net salt ions ouside the solvent box after AddIons Parviz Seifpanahi Shabane (Wed Jun 13 2018 - 12:20:00 PDT)
  - Re: [AMBER] Net salt ions ouside the solvent box after AddIons Kasprzak, Wojciech (NIH/NCI) [C] (Wed Jun 13 2018 - 12:53:27 PDT)
    - Re: [AMBER] Net salt ions ouside the solvent box after AddIons David A Case (Wed Jun 13 2018 - 13:10:01 PDT)
    - Re: [AMBER] Net salt ions ouside the solvent box after AddIons Kasprzak, Wojciech (NIH/NCI) [C] (Wed Jun 13 2018 - 13:25:51 PDT)
    - Re: [AMBER] Net salt ions ouside the solvent box after AddIons Matias Machado (Thu Jun 14 2018 - 11:27:11 PDT)
    - Re: [AMBER] Net salt ions ouside the solvent box after AddIons Bill Ross (Thu Jun 14 2018 - 11:43:40 PDT)
    - Re: [AMBER] Net salt ions - Thank you! Kasprzak, Wojciech (NIH/NCI) [C] (Thu Jun 14 2018 - 13:10:19 PDT)
[AMBER] direction in SMD Qinghua Liao (Thu Jun 14 2018 - 06:59:19 PDT)
[AMBER] Amber16 + Ambertools17 + CUDA 9.0 + NVIDIA 390 Installation Guide BERGY (Thu Jun 14 2018 - 10:10:17 PDT)
- Re: [AMBER] Amber16 + Ambertools17 + CUDA 9.0 + NVIDIA 390 Installation Guide Lod King (Mon Jun 18 2018 - 19:03:25 PDT)
  - Re: [AMBER] Amber16 + Ambertools17 + CUDA 9.0 + NVIDIA 390 Installation Guide David A Case (Wed Jun 20 2018 - 04:03:46 PDT)
[AMBER] MMGBSA error FATAL: NATOM mismatch in coord and topology files Urszula Uciechowska (Thu Jun 14 2018 - 22:45:55 PDT)
- Re: [AMBER] MMGBSA error FATAL: NATOM mismatch in coord and topology files David A Case (Fri Jun 15 2018 - 04:46:05 PDT)
  - [AMBER] Progress bar will not be used during Run [strip :WAT, Cl*, CIO, Cs+, IB, K*, Li+, MG*, Na+ ...] Urszula Uciechowska (Tue Jun 19 2018 - 02:55:12 PDT)
[AMBER] Trajectory format ATUL KUMAR (Fri Jun 15 2018 - 06:02:36 PDT)
- Re: [AMBER] Trajectory format emanuele falbo (Fri Jun 15 2018 - 06:16:28 PDT)
  - Re: [AMBER] Trajectory format ATUL KUMAR (Fri Jun 15 2018 - 22:09:29 PDT)
    - Re: [AMBER] Trajectory format Rodrigo Galindo (Sat Jun 16 2018 - 07:06:48 PDT)
    - Re: [AMBER] Trajectory format ATUL KUMAR (Sat Jun 16 2018 - 07:23:07 PDT)
    - Re: [AMBER] Trajectory format Bill Ross (Sat Jun 16 2018 - 07:31:26 PDT)
    - Re: [AMBER] Trajectory format ATUL KUMAR (Sat Jun 16 2018 - 07:36:45 PDT)
    - Re: [AMBER] Trajectory format Bill Ross (Sat Jun 16 2018 - 07:56:23 PDT)
    - Re: [AMBER] Trajectory format Matias Machado (Sat Jun 16 2018 - 11:13:19 PDT)
    - Re: [AMBER] Trajectory format ATUL KUMAR (Sat Jun 16 2018 - 11:26:29 PDT)
- Re: [AMBER] Trajectory format Daniel Roe (Fri Jun 15 2018 - 09:54:28 PDT)
  - Re: [AMBER] Trajectory format ATUL KUMAR (Fri Jun 15 2018 - 22:00:39 PDT)
[AMBER] Deal with trajectoy PBC 陈金峰 (Fri Jun 15 2018 - 06:59:39 PDT)
- Re: [AMBER] Deal with trajectoy PBC Stephan Schott (Fri Jun 15 2018 - 08:15:40 PDT)
- Re: [AMBER] Deal with trajectoy PBC Wesley Michael Botello-Smith (Fri Jun 15 2018 - 09:54:48 PDT)
[AMBER] Idea of equilibration in MD before production? senal dinuka (Sun Jun 17 2018 - 20:54:37 PDT)
- Re: [AMBER] Idea of equilibration in MD before production? David A Case (Mon Jun 18 2018 - 05:48:08 PDT)
  - Re: [AMBER] Idea of equilibration in MD before production? senal dinuka (Mon Jun 18 2018 - 08:53:16 PDT)
[AMBER] Implicit solvent TI calculations with soft core potentials Srinivasaraghavan KANNAN (Sun Jun 17 2018 - 21:11:54 PDT)
- Re: [AMBER] Implicit solvent TI calculations with soft core potentials David A Case (Wed Jun 20 2018 - 04:07:07 PDT)
[AMBER] Problems in running MMPBSA.py: undefined symbol: __libm_feature_flag Qing Lv (Sun Jun 17 2018 - 21:56:07 PDT)
- Re: [AMBER] Problems in running MMPBSA.py: undefined symbol: __libm_feature_flag Ray Luo (Mon Jun 18 2018 - 10:07:32 PDT)
  - Re: [AMBER] Problems in running MMPBSA.py: undefined symbol: __libm_feature_flag Qing Lv (Fri Jun 22 2018 - 20:33:58 PDT)
    - [AMBER] How to read .nc file in VMD Qing Lv (Sat Jun 23 2018 - 23:36:04 PDT)
    - Re: [AMBER] How to read .nc file in VMD Markowska (Sun Jun 24 2018 - 05:14:51 PDT)
    - Re: [AMBER] How to read .nc file in VMD Qing Lv (Sun Jun 24 2018 - 06:01:58 PDT)
- Re: [AMBER] Problems in running MMPBSA.py: undefined symbol: __libm_feature_flag David A Case (Wed Jun 20 2018 - 04:05:11 PDT)
- Re: [AMBER] Problems in running MMPBSA.py: undefined symbol: __libm_feature_flag Daniel Roe (Wed Jun 20 2018 - 05:28:01 PDT)
[AMBER] Defining aMD Boost Parameters (Range and Distribution) for Hamiltonian Replica Exchange Jason Ku Wang (Mon Jun 18 2018 - 18:09:18 PDT)
[AMBER] Implicit solvent TI calculations with soft core potentials Srinivasaraghavan KANNAN (Mon Jun 18 2018 - 19:51:13 PDT)
[AMBER] restarting REMD vacuum simulation with watercap Duy Tran Phuoc (Mon Jun 18 2018 - 20:25:56 PDT)
- Re: [AMBER] restarting REMD vacuum simulation with watercap Cruzeiro,Vinicius Wilian D (Tue Jun 19 2018 - 13:43:54 PDT)
[AMBER] AMBER: targeted MD 李耀 (Tue Jun 19 2018 - 22:03:47 PDT)
- Re: [AMBER] AMBER: targeted MD Charles Lin (Thu Jun 21 2018 - 09:45:33 PDT)
[AMBER] Reg. esander or energy command not found. DHEERAJ CHITARA (Wed Jun 20 2018 - 00:30:53 PDT)
- Re: [AMBER] Reg. esander or energy command not found. David A Case (Wed Jun 20 2018 - 03:58:36 PDT)
- Re: [AMBER] Reg. esander or energy command not found. Daniel Roe (Wed Jun 20 2018 - 05:32:21 PDT)
[AMBER] How to "un-strip" the MG* atom from mmpbsa Urszula Uciechowska (Wed Jun 20 2018 - 02:41:08 PDT)
- Re: [AMBER] How to "un-strip" the MG* atom from mmpbsa Thomas Cheatham (Wed Jun 20 2018 - 03:42:53 PDT)
  - Re: [AMBER] How to "un-strip" the MG* atom from mmpbsa Urszula Uciechowska (Wed Jun 20 2018 - 03:50:11 PDT)
- Re: [AMBER] How to "un-strip" the MG* atom from mmpbsa Daniel Roe (Wed Jun 20 2018 - 05:35:42 PDT)
[AMBER] bad atom type for Mn after running mmpbsa Urszula Uciechowska (Wed Jun 20 2018 - 02:49:15 PDT)
- Re: [AMBER] bad atom type for Mn after running mmpbsa Thomas Cheatham (Wed Jun 20 2018 - 03:53:35 PDT)
[AMBER] script for converting amber parameters into CNS file Urszula Uciechowska (Wed Jun 20 2018 - 04:31:00 PDT)
- Re: [AMBER] script for converting amber parameters into CNS file David A Case (Fri Jun 22 2018 - 05:43:19 PDT)
[AMBER] GIST preparetion error Gamze Özbay (Wed Jun 20 2018 - 05:19:19 PDT)
- Re: [AMBER] GIST preparetion error Daniel Roe (Wed Jun 20 2018 - 05:25:36 PDT)
  - Re: [AMBER] GIST preparetion error Tom Kurtzman (Wed Jun 20 2018 - 06:28:44 PDT)
    - Re: [AMBER] GIST preparetion error Gamze Özbay (Thu Jun 21 2018 - 02:31:31 PDT)
    - Re: [AMBER] GIST preparetion error Tom Kurtzman (Thu Jun 21 2018 - 09:21:54 PDT)
[AMBER] Cpptraj h-bond Rana Rehan Khalid (Wed Jun 20 2018 - 10:37:26 PDT)
- Re: [AMBER] Cpptraj h-bond Rana Rehan Khalid (Thu Jun 21 2018 - 08:05:55 PDT)
[AMBER] why tleap adds TER in the middle of a DNA sequence Kat G (Wed Jun 20 2018 - 11:40:52 PDT)
- Re: [AMBER] why tleap adds TER in the middle of a DNA sequence Bill Ross (Wed Jun 20 2018 - 19:05:40 PDT)
- Re: [AMBER] why tleap adds TER in the middle of a DNA sequence David A Case (Fri Jun 22 2018 - 05:40:23 PDT)
[AMBER] Amber14-GIST Berkant Düzgün (Thu Jun 21 2018 - 01:42:52 PDT)
- Re: [AMBER] Amber14-GIST Tom Kurtzman (Thu Jun 21 2018 - 09:18:38 PDT)
[AMBER] Problem in Membrane Simulation : water molecules are out of box somdev pahari (Thu Jun 21 2018 - 07:21:45 PDT)
- Re: [AMBER] Problem in Membrane Simulation : water molecules are out of box David Cerutti (Thu Jun 21 2018 - 07:41:18 PDT)
[AMBER] AMBER18 pmemd.cuda running error for divalent metal ions represented using multisite (dummy) atom model with the 12-6-4 LJ potential Zuo, Zhicheng (Thu Jun 21 2018 - 14:45:16 PDT)
- Re: [AMBER] AMBER18 pmemd.cuda running error for divalent metal ions represented using multisite (dummy) atom model with the 12-6-4 LJ potential Qinghua Liao (Thu Jun 21 2018 - 15:42:22 PDT)
  - Re: [AMBER] AMBER18 pmemd.cuda running error for divalent metal ions represented using multisite (dummy) atom model with the 12-6-4 LJ potential Zuo, Zhicheng (Sat Jun 23 2018 - 07:51:11 PDT)
    - Re: [AMBER] AMBER18 pmemd.cuda running error for divalent metal ions represented using multisite (dummy) atom model with the 12-6-4 LJ potential Qinghua Liao (Tue Jun 26 2018 - 14:50:41 PDT)
[AMBER] Question on writing clustering information Subha Kalyaanamoorthy (Thu Jun 21 2018 - 17:57:31 PDT)
[AMBER] Lipid diffusion COM drift Christopher Faulkner (Fri Jun 22 2018 - 01:43:22 PDT)
- Re: [AMBER] Lipid diffusion COM drift Stephan Schott (Fri Jun 22 2018 - 03:44:42 PDT)
  - Re: [AMBER] Lipid diffusion COM drift Christopher Faulkner (Mon Jun 25 2018 - 04:39:27 PDT)
- Re: [AMBER] Lipid diffusion COM drift Stephan Schott (Mon Jun 25 2018 - 06:00:25 PDT)
[AMBER] Multi GPU performance 陈金峰 (Fri Jun 22 2018 - 04:58:58 PDT)
- Re: [AMBER] Multi GPU performance David Cerutti (Fri Jun 22 2018 - 07:08:32 PDT)
- Re: [AMBER] Multi GPU performance James Kress (Fri Jun 22 2018 - 07:54:26 PDT)
  - Re: [AMBER] Multi GPU performance David Cerutti (Fri Jun 22 2018 - 08:00:01 PDT)
[AMBER] Difference between frcmod and mdl parameters Rakesh Srivastava (Fri Jun 22 2018 - 10:16:43 PDT)
- Re: [AMBER] Difference between frcmod and mdl parameters David A Case (Fri Jun 22 2018 - 11:02:29 PDT)
  - Re: [AMBER] Difference between frcmod and mdl parameters Rakesh Srivastava (Fri Jun 22 2018 - 21:14:12 PDT)
[AMBER] Question on writing clustering information with cpptraj Subha Kalyaanamoorthy (Fri Jun 22 2018 - 11:04:30 PDT)
- Re: [AMBER] Question on writing clustering information with cpptraj Daniel Roe (Tue Jun 26 2018 - 06:35:29 PDT)
  - Re: [AMBER] Question on writing clustering information with cpptraj Subha Kalyaanamoorthy (Tue Jun 26 2018 - 10:29:58 PDT)
    - Re: [AMBER] Question on writing clustering information with cpptraj Daniel Roe (Tue Jun 26 2018 - 10:53:52 PDT)
    - Re: [AMBER] Question on writing clustering information with cpptraj Subha Kalyaanamoorthy (Tue Jun 26 2018 - 11:50:12 PDT)
[AMBER] AMBER18 pmemd.cuda TI generates Error: an illegal memory access was encountered launching kernel kNLSkinTest Maximilian Ebert (Sat Jun 23 2018 - 07:53:35 PDT)
- Re: [AMBER] AMBER18 pmemd.cuda TI generates Error: an illegal memory access was encountered launching kernel kNLSkinTest David Cerutti (Sat Jun 23 2018 - 15:10:26 PDT)
  - Re: [AMBER] AMBER18 pmemd.cuda TI generates Error: an illegal memory access was encountered launching kernel kNLSkinTest Maximilian Ebert (Sun Jun 24 2018 - 07:58:22 PDT)
    - Re: [AMBER] AMBER18 pmemd.cuda TI generates Error: an illegal memory access was encountered launching kernel kNLSkinTest Darrin York (Mon Jun 25 2018 - 11:00:24 PDT)
    - Re: [AMBER] AMBER18 pmemd.cuda TI generates Error: an illegal memory access was encountered launching kernel kNLSkinTest Maximilian Ebert (Tue Jun 26 2018 - 13:50:20 PDT)
[AMBER] Extract force for every atom in a 100ns MD run trajectory Lod King (Sun Jun 24 2018 - 00:04:17 PDT)
- Re: [AMBER] Extract force for every atom in a 100ns MD run trajectory David A Case (Sun Jun 24 2018 - 13:18:15 PDT)
  - Re: [AMBER] Extract force for every atom in a 100ns MD run trajectory Lod King (Sun Jun 24 2018 - 13:45:49 PDT)
    - Re: [AMBER] Extract force for every atom in a 100ns MD run trajectory Kellon Belfon (Sun Jun 24 2018 - 17:58:33 PDT)
[AMBER] Fwd: increase speed in amber using implcit solvent model Chhaya Singh (Sun Jun 24 2018 - 00:26:33 PDT)
- Re: [AMBER] Fwd: increase speed in amber using implcit solvent model Carlos Simmerling (Sun Jun 24 2018 - 04:18:56 PDT)
- Re: [AMBER] Fwd: increase speed in amber using implcit solvent model David A Case (Sun Jun 24 2018 - 11:49:08 PDT)
  - Re: [AMBER] Fwd: increase speed in amber using implcit solvent model Chhaya Singh (Sun Jun 24 2018 - 23:44:06 PDT)
    - Re: [AMBER] Fwd: increase speed in amber using implcit solvent model Chhaya Singh (Sun Jun 24 2018 - 23:57:37 PDT)
    - Re: [AMBER] Fwd: increase speed in amber using implcit solvent model Matias Machado (Tue Jun 26 2018 - 09:27:58 PDT)
    - Re: [AMBER] Fwd: increase speed in amber using implcit solvent model Chhaya Singh (Wed Jun 27 2018 - 11:26:23 PDT)
[AMBER] Unit 5 Error on OPEN:mdin on clustuer with pmemd.cuda Meng Wu (Sun Jun 24 2018 - 02:23:11 PDT)
- Re: [AMBER] Unit 5 Error on OPEN:mdin on clustuer with pmemd.cuda David A Case (Sun Jun 24 2018 - 11:54:01 PDT)
[AMBER] Fortran runtime error: Cannot write to file opened for READ Lod King (Sun Jun 24 2018 - 22:33:39 PDT)
- Re: [AMBER] Fortran runtime error: Cannot write to file opened for READ David A Case (Mon Jun 25 2018 - 04:59:02 PDT)
  - Re: [AMBER] Fortran runtime error: Cannot write to file opened for READ Lod King (Mon Jun 25 2018 - 09:02:57 PDT)
[AMBER] QMMM interface for TURBOMOLE Francesca Lønstad Bleken (Mon Jun 25 2018 - 01:49:56 PDT)
[AMBER] radial distribution from center of mass of solute Shilpa Gupta (Mon Jun 25 2018 - 02:57:42 PDT)
- Re: [AMBER] radial distribution from center of mass of solute emanuele falbo (Mon Jun 25 2018 - 03:29:22 PDT)
  - Re: [AMBER] radial distribution from center of mass of solute Shilpa Gupta (Mon Jun 25 2018 - 03:37:20 PDT)
    - Re: [AMBER] radial distribution from center of mass of solute emanuele falbo (Mon Jun 25 2018 - 03:50:12 PDT)
[AMBER] Problem regarding running independent parallel simulations in AMBER14 using -rem<#> RITUPARNA ROY (Mon Jun 25 2018 - 07:56:07 PDT)
- Re: [AMBER] Problem regarding running independent parallel simulations in AMBER14 using -rem<#> Cruzeiro,Vinicius Wilian D (Mon Jun 25 2018 - 08:01:14 PDT)
 - Re: [AMBER] Problem regarding running independent parallel simulations in AMBER14 using -rem<#> RITUPARNA ROY (Mon Jun 25 2018 - 08:43:52 PDT)
 - Re: [AMBER] Problem regarding running independent parallel simulations in AMBER14 using -rem<#> Cruzeiro,Vinicius Wilian D (Mon Jun 25 2018 - 08:48:17 PDT)
[AMBER] Time averaged mean squared displacement Christopher Faulkner (Mon Jun 25 2018 - 08:50:34 PDT)
[AMBER] Amber16 (with AmberToos16) install problems. Seibold, Steve Allan (Mon Jun 25 2018 - 08:55:07 PDT)
- Re: [AMBER] Amber16 (with AmberToos16) install problems. David A Case (Mon Jun 25 2018 - 11:31:34 PDT)
[AMBER] Install problems fftw for AMBER16 Seibold, Steve Allan (Tue Jun 26 2018 - 11:10:22 PDT)
- Re: [AMBER] Install problems fftw for AMBER16 David A Case (Wed Jun 27 2018 - 08:34:43 PDT)
[AMBER] rism1d query Rakesh Srivastava (Tue Jun 26 2018 - 22:34:22 PDT)
- Re: [AMBER] rism1d query Leena Aggarwal (Wed Jun 27 2018 - 02:12:39 PDT)
  - Re: [AMBER] rism1d query Rakesh Srivastava (Wed Jun 27 2018 - 03:24:28 PDT)
    - Re: [AMBER] rism1d query Leena Aggarwal (Wed Jun 27 2018 - 05:30:25 PDT)
    - Re: [AMBER] rism1d query Rakesh Srivastava (Wed Jun 27 2018 - 05:37:21 PDT)
    - Re: [AMBER] rism1d query Leena Aggarwal (Wed Jun 27 2018 - 06:18:46 PDT)
    - Re: [AMBER] rism1d query Tyler Luchko (Lists) (Wed Jun 27 2018 - 09:52:09 PDT)
    - Re: [AMBER] rism1d query Rakesh Srivastava (Wed Jun 27 2018 - 22:01:21 PDT)
[AMBER] rism1d convergence query Rakesh Srivastava (Tue Jun 26 2018 - 23:14:17 PDT)
- Re: [AMBER] rism1d convergence query Tyler Luchko (Lists) (Wed Jun 27 2018 - 10:00:19 PDT)
  - Re: [AMBER] rism1d convergence query Rakesh Srivastava (Wed Jun 27 2018 - 22:00:16 PDT)
    - Re: [AMBER] rism1d convergence query Rakesh Srivastava (Wed Jun 27 2018 - 23:02:32 PDT)
    - Re: [AMBER] rism1d convergence query Tyler Luchko (Lists) (Thu Jun 28 2018 - 09:20:29 PDT)
    - Re: [AMBER] rism1d convergence query Rakesh Srivastava (Fri Jun 29 2018 - 00:36:11 PDT)
[AMBER] query regarding the Amber 12 compatibility with RHEL upgraded versions Leena Aggarwal (Wed Jun 27 2018 - 23:50:17 PDT)
- Re: [AMBER] query regarding the Amber 12 compatibility with RHEL upgraded versions David A Case (Thu Jun 28 2018 - 03:51:08 PDT)
  - Re: [AMBER] query regarding the Amber 12 compatibility with RHEL upgraded versions Leena Aggarwal (Thu Jun 28 2018 - 03:55:33 PDT)
[AMBER] Amber16 with AmberTools18 Shirin Jamshidi (Thu Jun 28 2018 - 02:13:53 PDT)
[AMBER] Regarding the MPI error in parallel running of 3D-RISM PRITI ROY (Thu Jun 28 2018 - 04:35:13 PDT)
- Re: [AMBER] Regarding the MPI error in parallel running of 3D-RISM George M. Giambasu (Thu Jun 28 2018 - 07:03:40 PDT)
  - Re: [AMBER] Regarding the MPI error in parallel running of 3D-RISM PRITI ROY (Thu Jun 28 2018 - 10:49:24 PDT)
    - Re: [AMBER] Regarding the MPI error in parallel running of 3D-RISM David A Case (Thu Jun 28 2018 - 11:26:17 PDT)
    - Re: [AMBER] Regarding the MPI error in parallel running of 3D-RISM PRITI ROY (Thu Jun 28 2018 - 21:52:02 PDT)
    - Re: [AMBER] Regarding the MPI error in parallel running of 3D-RISM George M. Giambasu (Fri Jun 29 2018 - 07:02:53 PDT)
    - Re: [AMBER] Regarding the MPI error in parallel running of 3D-RISM PRITI ROY (Wed Jul 04 2018 - 12:52:43 PDT)
    - Re: [AMBER] Regarding the MPI error in parallel running of 3D-RISM David A Case (Wed Jul 04 2018 - 18:47:44 PDT)
    - Re: [AMBER] Regarding the MPI error in parallel running of 3D-RISM PRITI ROY (Thu Jul 05 2018 - 03:39:32 PDT)
    - Re: [AMBER] Regarding the MPI error in parallel running of 3D-RISM Tyler Luchko (Lists) (Fri Jul 06 2018 - 16:17:48 PDT)
    - Re: [AMBER] Regarding the MPI error in parallel running of 3D-RISM PRITI ROY (Mon Jul 23 2018 - 04:00:40 PDT)
    - Re: [AMBER] Regarding the MPI error in parallel running of 3D-RISM David A Case (Mon Jul 23 2018 - 08:50:33 PDT)
    - Re: [AMBER] Regarding the MPI error in parallel running of 3D-RISM PRITI ROY (Wed Jul 25 2018 - 22:13:13 PDT)
    - Re: [AMBER] Regarding the MPI error in parallel running of 3D-RISM Tyler Luchko (Lists) (Wed Aug 01 2018 - 15:55:25 PDT)
[AMBER] REF_ENERGY in Titratable_residues.py Nuno Barbosa (Thu Jun 28 2018 - 06:52:35 PDT)
[AMBER] Using chirality restraints for modified residues Baptiste Legrand (Thu Jun 28 2018 - 09:03:11 PDT)
- Re: [AMBER] Using chirality restraints for modified residues Carlos Simmerling (Thu Jun 28 2018 - 09:15:21 PDT)
- Re: [AMBER] Using chirality restraints for modified residues David A Case (Thu Jun 28 2018 - 11:31:13 PDT)
  - Re: [AMBER] Using chirality restraints for modified residues Baptiste Legrand (Fri Jun 29 2018 - 01:32:33 PDT)
    - Re: [AMBER] Using chirality restraints for modified residues Bill Ross (Fri Jun 29 2018 - 01:52:44 PDT)
    - Re: [AMBER] Using chirality restraints for modified residues Baptiste Legrand (Fri Jun 29 2018 - 02:43:44 PDT)
    - Re: [AMBER] Using chirality restraints for modified residues Bill Ross (Fri Jun 29 2018 - 03:21:41 PDT)
[AMBER] calculating force correlation in trajectory Lod King (Thu Jun 28 2018 - 10:55:21 PDT)
- Re: [AMBER] calculating force correlation in trajectory David A Case (Thu Jun 28 2018 - 11:37:13 PDT)
  - Re: [AMBER] calculating force correlation in trajectory Lod King (Thu Jun 28 2018 - 11:47:14 PDT)
    - Re: [AMBER] calculating force correlation in trajectory David A Case (Thu Jun 28 2018 - 15:04:51 PDT)
    - Re: [AMBER] calculating force correlation in trajectory Lod King (Thu Jun 28 2018 - 16:30:06 PDT)
[AMBER] implicit solvent Chhaya Singh (Thu Jun 28 2018 - 11:07:42 PDT)
- Re: [AMBER] implicit solvent Chhaya Singh (Thu Jun 28 2018 - 11:28:40 PDT)
- Re: [AMBER] implicit solvent David A Case (Thu Jun 28 2018 - 11:40:31 PDT)
  - Re: [AMBER] implicit solvent Chhaya Singh (Thu Jun 28 2018 - 11:42:31 PDT)
    - Re: [AMBER] implicit solvent Chhaya Singh (Fri Jun 29 2018 - 12:29:24 PDT)
    - Re: [AMBER] implicit solvent Carlos Simmerling (Fri Jun 29 2018 - 12:33:30 PDT)
    - Re: [AMBER] implicit solvent Chhaya Singh (Fri Jun 29 2018 - 12:37:05 PDT)
    - Re: [AMBER] implicit solvent Chhaya Singh (Fri Jun 29 2018 - 12:33:23 PDT)
[AMBER] Gaussian aMD in Amber14 anu chandra (Fri Jun 29 2018 - 00:22:54 PDT)
[AMBER] Geforce GTX 1080Ti testing on Amber18/CUDA 9.2 Nikolay N. Kuzmich (Fri Jun 29 2018 - 04:58:17 PDT)
- Re: [AMBER] Geforce GTX 1080Ti testing on Amber18/CUDA 9.2 Dow Hurst (Fri Jun 29 2018 - 11:28:45 PDT)
- Re: [AMBER] Geforce GTX 1080Ti testing on Amber18/CUDA 9.2 Ross Walker (Mon Jul 02 2018 - 04:57:26 PDT)
- Re: [AMBER] Geforce GTX 1080Ti testing on Amber18/CUDA 9.2 Nikolay N. Kuzmich (Wed Jul 04 2018 - 12:15:00 PDT)
[AMBER] cpptraj and sander Portillo, Jennifer (Fri Jun 29 2018 - 07:15:05 PDT)
- Re: [AMBER] cpptraj and sander David A Case (Fri Jun 29 2018 - 18:03:09 PDT)
[AMBER] Individual bridging water lifetimes by closest? Kenneth Huang (Fri Jun 29 2018 - 12:21:19 PDT)
- Re: [AMBER] Individual bridging water lifetimes by closest? Daniel Roe (Mon Jul 02 2018 - 06:25:19 PDT)
  - Re: [AMBER] Individual bridging water lifetimes by closest? Kenneth Huang (Mon Jul 02 2018 - 13:18:46 PDT)
    - Re: [AMBER] Individual bridging water lifetimes by closest? Daniel Roe (Tue Jul 03 2018 - 05:38:45 PDT)
    - Re: [AMBER] Individual bridging water lifetimes by closest? Kenneth Huang (Tue Jul 03 2018 - 10:16:30 PDT)
    - Re: [AMBER] Individual bridging water lifetimes by closest? Daniel Roe (Tue Jul 03 2018 - 10:21:02 PDT)
[AMBER] implicit solvent simmulation Chhaya Singh (Fri Jun 29 2018 - 12:26:24 PDT)
- Re: [AMBER] implicit solvent simmulation Chhaya Singh (Fri Jun 29 2018 - 14:40:04 PDT)
- Re: [AMBER] implicit solvent simmulation Charles-Alexandre Mattelaer (Sat Jun 30 2018 - 05:55:23 PDT)
[AMBER] Cuda Zahra Khatti (Sat Jun 30 2018 - 05:47:33 PDT)
- Re: [AMBER] Cuda Ross Walker (Mon Jul 02 2018 - 05:02:14 PDT)
  - Re: [AMBER] Cuda Zahra Khatti (Tue Jul 03 2018 - 08:14:20 PDT)
[AMBER] Extraction of atomic charges. Vishal Kumar (Sun Jul 01 2018 - 05:32:44 PDT)
- Re: [AMBER] Extraction of atomic charges. Jissy Akkarapattiakal Kuriappan (Mon Jul 02 2018 - 02:41:38 PDT)
[AMBER] Query about Salt-Concentration (soltcon) for Constant pH MD Bharat Manna (Sun Jul 01 2018 - 22:51:09 PDT)
- Re: [AMBER] Query about Salt-Concentration (soltcon) for Constant pH MD Cruzeiro,Vinicius Wilian D (Tue Jul 03 2018 - 07:03:18 PDT)
[AMBER] Tutorial B1 problems Jennifer L. Muzyka (Mon Jul 02 2018 - 08:46:58 PDT)
- Re: [AMBER] Tutorial B1 problems David A Case (Wed Jul 04 2018 - 18:19:38 PDT)
[AMBER] How to specify the protein position in box while using tleap Jinfeng Chen (Mon Jul 02 2018 - 18:15:25 PDT)
- Re: [AMBER] How to specify the protein position in box while using tleap Bill Ross (Mon Jul 02 2018 - 18:58:11 PDT)
- Re: [AMBER] How to specify the protein position in box while using tleap David A Case (Tue Jul 03 2018 - 05:49:35 PDT)
[AMBER] How should I perform a long-time Simulated Annealing MD? xmgign.126.com (Tue Jul 03 2018 - 01:32:16 PDT)
- Re: [AMBER] How should I perform a long-time Simulated Annealing MD? David A Case (Tue Jul 03 2018 - 15:53:27 PDT)
- Re: [AMBER] How should I perform a long-time Simulated Annealing MD? xmgign.126.com (Tue Jul 03 2018 - 19:06:14 PDT)
  - Re: [AMBER] How should I perform a long-time Simulated Annealing MD? David A Case (Wed Jul 04 2018 - 05:41:42 PDT)
    - Re: [AMBER] How should I perform a long-time Simulated Annealing MD? Robert Molt (Wed Jul 04 2018 - 15:22:39 PDT)
    - Re: [AMBER] How should I perform a long-time Simulated Annealing MD? David A Case (Wed Jul 04 2018 - 19:06:11 PDT)
[AMBER] Tleap Impose Doesn't work for defining some angle/diedral Alechania Misturini (Tue Jul 03 2018 - 04:57:37 PDT)
- Re: [AMBER] Tleap Impose Doesn't work for defining some angle/diedral Daniel Roe (Tue Jul 03 2018 - 05:43:46 PDT)
- Re: [AMBER] Tleap Impose Doesn't work for defining some angle/diedral David A Case (Tue Jul 03 2018 - 06:00:40 PDT)
  - Re: [AMBER] Tleap Impose Doesn't work for defining some angle/diedral Alechania Misturini (Tue Jul 03 2018 - 06:28:26 PDT)
[AMBER] global scaling of vdW Korey M Reid (Tue Jul 03 2018 - 11:10:02 PDT)
- Re: [AMBER] global scaling of vdW David A Case (Thu Jul 05 2018 - 05:35:59 PDT)
[AMBER] AMBER: QM/MM calculations using GPU Witkin, Katharine R (Tue Jul 03 2018 - 12:52:07 PDT)
- Re: [AMBER] AMBER: QM/MM calculations using GPU Qinghua Liao (Tue Jul 03 2018 - 13:02:45 PDT)
- Re: [AMBER] AMBER: QM/MM calculations using GPU Goetz, Andreas (Tue Jul 03 2018 - 13:05:01 PDT)
  - Re: [AMBER] AMBER: QM/MM calculations using GPU Witkin, Katharine R (Tue Jul 03 2018 - 13:07:50 PDT)
    - Re: [AMBER] AMBER: QM/MM calculations using GPU Goetz, Andreas (Tue Jul 03 2018 - 14:58:57 PDT)
    - Re: [AMBER] AMBER: QM/MM calculations using GPU Witkin, Katharine R (Tue Jul 03 2018 - 16:10:35 PDT)
[AMBER] premed.cuda.MPI Shirin Jamshidi (Tue Jul 03 2018 - 16:40:40 PDT)
[AMBER] pmemd.cuda.MPI Shirin Jamshidi (Tue Jul 03 2018 - 16:41:54 PDT)
[AMBER] packmol error Gustaf Olsson (Wed Jul 04 2018 - 00:29:32 PDT)
- Re: [AMBER] packmol error David A Case (Thu Jul 05 2018 - 05:37:37 PDT)
  - Re: [AMBER] packmol error Gould, Ian R (Thu Jul 05 2018 - 05:43:04 PDT)
[AMBER] TI calculations emanuele (Wed Jul 04 2018 - 03:15:35 PDT)
- Re: [AMBER] TI calculations David A Case (Wed Jul 04 2018 - 05:47:19 PDT)
[AMBER] Ph.D. candidate position in biomolecular modeling or bioinformatics Jan Brezovsky (Wed Jul 04 2018 - 03:26:44 PDT)
[AMBER] Regarding installation problem in CUDA 9.2 Debasish Mandal (Wed Jul 04 2018 - 03:37:39 PDT)
- Re: [AMBER] Regarding installation problem in CUDA 9.2 Matias Machado (Wed Jul 04 2018 - 07:01:22 PDT)
[AMBER] How to reference the integration algorithm? Elisa Pieri (Wed Jul 04 2018 - 10:31:42 PDT)
- Re: [AMBER] How to reference the integration algorithm? David A Case (Thu Jul 05 2018 - 05:42:29 PDT)
  - Re: [AMBER] How to reference the integration algorithm? Elisa Pieri (Thu Jul 05 2018 - 05:44:24 PDT)
[AMBER] Interpretation the result of pairwise per-residue MM/PB(GB)SA decomposition. walkingintheair (Wed Jul 04 2018 - 20:18:04 PDT)
[AMBER] Error while perform ALA Scanning Mutageneis Mitul Srivastava (Thu Jul 05 2018 - 00:42:41 PDT)
[AMBER] RST file setting in SMD Meng Wu (Thu Jul 05 2018 - 05:56:06 PDT)
- Re: [AMBER] RST file setting in SMD David A Case (Thu Jul 05 2018 - 15:31:22 PDT)
[AMBER] setting ionic strength in leap Kris Feher (Thu Jul 05 2018 - 13:45:26 PDT)
- Re: [AMBER] setting ionic strength in leap Thomas Cheatham (Thu Jul 05 2018 - 16:44:04 PDT)
  - Re: [AMBER] setting ionic strength in leap Kris Feher (Fri Jul 06 2018 - 06:32:28 PDT)
  - Re: [AMBER] setting ionic strength in leap Thomas C Bishop (Fri Jul 06 2018 - 08:51:14 PDT)
    - Re: [AMBER] setting ionic strength in leap George M. Giambasu (Fri Jul 06 2018 - 21:34:45 PDT)
    - Re: [AMBER] setting ionic strength in leap Kris Feher (Thu Jul 12 2018 - 12:02:30 PDT)
    - Re: [AMBER] setting ionic strength in leap Kris Feher (Thu Jul 12 2018 - 11:52:39 PDT)
[AMBER] Need help regarding Constant pH MD in pmemd.cuda Bharat Manna (Thu Jul 05 2018 - 23:37:08 PDT)
[AMBER] huge difference in GB and PB energies calculated with MMPBSA.py Charles Mariasoosai (Fri Jul 06 2018 - 00:55:49 PDT)
- Re: [AMBER] huge difference in GB and PB energies calculated with MMPBSA.py David A Case (Fri Jul 06 2018 - 05:29:57 PDT)
- Re: [AMBER] huge difference in GB and PB energies calculated with MMPBSA.py Ray Luo (Fri Jul 06 2018 - 08:20:18 PDT)
- Re: [AMBER] huge difference in GB and PB energies calculated with MMPBSA.py Wesley Michael Botello-Smith (Fri Jul 06 2018 - 12:17:40 PDT)
[AMBER] Need help regarding CpHMD with T-REMD Saikat Dutta chowdhury (Fri Jul 06 2018 - 03:52:10 PDT)
- Re: [AMBER] Need help regarding CpHMD with T-REMD Cruzeiro,Vinicius Wilian D (Fri Jul 06 2018 - 07:29:53 PDT)
  - Re: [AMBER] Need help regarding CpHMD with T-REMD Saikat Dutta chowdhury (Mon Jul 09 2018 - 07:58:42 PDT)
[AMBER] Fit the trajectory to the original inpcrd file Meng Wu (Fri Jul 06 2018 - 05:40:31 PDT)
- Re: [AMBER] Fit the trajectory to the original inpcrd file Daniel Roe (Fri Jul 06 2018 - 06:26:51 PDT)
[AMBER] Calcutaion of the observed acceptance ratio from simulation RITUPARNA ROY (Fri Jul 06 2018 - 06:07:46 PDT)
- Re: [AMBER] Calcutaion of the observed acceptance ratio from simulation Daniel Roe (Fri Jul 06 2018 - 06:23:08 PDT)
[AMBER] Si bonded parameters GAFF compatible Alechania Misturini (Fri Jul 06 2018 - 11:17:23 PDT)
[AMBER] Some Parameters In MM_PB/GBSA 龚乾坤 (Sat Jul 07 2018 - 04:10:07 PDT)
- Re: [AMBER] Some Parameters In MM_PB/GBSA David A Case (Sat Jul 07 2018 - 04:35:04 PDT)
[AMBER] Regarding simulation of Organometallic compounds dhaval patel (Sat Jul 07 2018 - 04:11:52 PDT)
[AMBER] Energy file generation problem of pmemd.cuda Meng Wu (Sat Jul 07 2018 - 06:02:17 PDT)
- Re: [AMBER] Energy file generation problem of pmemd.cuda David A Case (Sat Jul 07 2018 - 15:34:56 PDT)
[AMBER] distance restraints and accelerated MD giulia palermo (Sun Jul 08 2018 - 17:08:00 PDT)
- Re: [AMBER] distance restraints and accelerated MD Carlos Simmerling (Sun Jul 08 2018 - 17:14:33 PDT)
[AMBER] Puckering parameters for pyranose ring Rajarshi Roy (Sun Jul 08 2018 - 22:40:34 PDT)
- Re: [AMBER] Puckering parameters for pyranose ring Charles-Alexandre Mattelaer (Sun Jul 08 2018 - 22:52:25 PDT)
- Re: [AMBER] Puckering parameters for pyranose ring Rajarshi Roy (Mon Jul 09 2018 - 03:47:43 PDT)
  - Re: [AMBER] Puckering parameters for pyranose ring David A Case (Mon Jul 09 2018 - 05:41:59 PDT)
[AMBER] The Calculate Formula of Ionic strength in MM_PBSA/GBSA 龚乾坤 (Mon Jul 09 2018 - 01:40:56 PDT)
- Re: [AMBER] The Calculate Formula of Ionic strength in MM_PBSA/GBSA David A Case (Mon Jul 09 2018 - 05:44:53 PDT)
  - Re: [AMBER] The Calculate Formula of Ionic strength in MM_PBSA/GBSA Wesley Michael Botello-Smith (Mon Jul 09 2018 - 09:45:13 PDT)
[AMBER] Question about equilibration of membrane protein MD 鲍劲霄 (Mon Jul 09 2018 - 02:14:56 PDT)
- Re: [AMBER] Question about equilibration of membrane protein MD Wesley Michael Botello-Smith (Mon Jul 09 2018 - 09:55:10 PDT)
[AMBER] How to provide the CPIN input file argument for CpHMD in pmemd.cuda? Bharat Manna (Mon Jul 09 2018 - 03:31:39 PDT)
- Re: [AMBER] How to provide the CPIN input file argument for CpHMD in pmemd.cuda? Eric Lang (Mon Jul 09 2018 - 04:58:23 PDT)
- Re: [AMBER] How to provide the CPIN input file argument for CpHMD in pmemd.cuda? Bharat Manna (Mon Jul 09 2018 - 21:24:41 PDT)
  - Re: [AMBER] How to provide the CPIN input file argument for CpHMD in pmemd.cuda? Cruzeiro,Vinicius Wilian D (Tue Jul 10 2018 - 06:38:25 PDT)
- Re: [AMBER] How to provide the CPIN input file argument for CpHMD in pmemd.cuda? Bharat Manna (Wed Jul 11 2018 - 05:49:59 PDT)
[AMBER] Help on Elisa Pieri (Mon Jul 09 2018 - 06:12:07 PDT)
- Re: [AMBER] Help on Kenneth Huang (Mon Jul 09 2018 - 10:20:08 PDT)
- Re: [AMBER] Help on Stephan Schott (Mon Jul 09 2018 - 10:32:21 PDT)
  - Re: [AMBER] Help on Wesley Michael Botello-Smith (Mon Jul 09 2018 - 10:46:23 PDT)
[AMBER] implicit solvent remd simulation Chhaya Singh (Mon Jul 09 2018 - 09:37:55 PDT)
[AMBER] issues with accelerated MD in chloroform Chetna Tyagi (Mon Jul 09 2018 - 11:37:11 PDT)
- [AMBER] Fwd: issues with accelerated MD in chloroform Chetna Tyagi (Fri Jul 13 2018 - 03:48:15 PDT)
[AMBER] MM_PBSA/GBSA 龚乾坤 (Tue Jul 10 2018 - 04:51:15 PDT)
[AMBER] Lipid NMR order parameters Christopher Faulkner (Tue Jul 10 2018 - 05:53:30 PDT)
- Re: [AMBER] Lipid NMR order parameters Daniel Roe (Tue Jul 10 2018 - 09:12:38 PDT)
  - Re: [AMBER] Lipid NMR order parameters Christopher Faulkner (Thu Jul 12 2018 - 00:16:17 PDT)
    - Re: [AMBER] Lipid NMR order parameters Baker, Joseph (Sun Dec 16 2018 - 16:59:48 PST)
    - Re: [AMBER] Lipid NMR order parameters Daniel Roe (Fri Dec 21 2018 - 11:46:00 PST)
[AMBER] Xleap does not (?) loadoff lib files Sebastian Muraru (Tue Jul 10 2018 - 06:46:33 PDT)
- Re: [AMBER] Xleap does not (?) loadoff lib files Matias Machado (Tue Jul 10 2018 - 08:01:14 PDT)
- Re: [AMBER] Xleap does not (?) loadoff lib files Sebastian Muraru (Wed Jul 11 2018 - 06:20:58 PDT)
[AMBER] Error: an illegal memory access was encountered launching kernel kClearForces Kandes, Martin (Tue Jul 10 2018 - 16:46:35 PDT)
- Re: [AMBER] Error: an illegal memory access was encountered launching kernel kClearForces David Cerutti (Tue Jul 10 2018 - 19:02:50 PDT)
  - Re: [AMBER] Error: an illegal memory access was encountered launching kernel kClearForces Kandes, Martin (Tue Jul 10 2018 - 23:37:37 PDT)
[AMBER] Ionic strength in MM_PBSA 龚乾坤 (Tue Jul 10 2018 - 19:39:35 PDT)
- Re: [AMBER] Ionic strength in MM_PBSA David A Case (Wed Jul 11 2018 - 06:40:24 PDT)
[AMBER] PCA multiple trajectories for mutants and wild type Stejskal, Lenka (Wed Jul 11 2018 - 04:48:26 PDT)
- Re: [AMBER] PCA multiple trajectories for mutants and wild type Wesley Michael Botello-Smith (Wed Jul 11 2018 - 11:07:36 PDT)
- Re: [AMBER] PCA multiple trajectories for mutants and wild type Daniel Roe (Thu Jul 12 2018 - 15:12:52 PDT)
[AMBER] Regarding Force constants from Mopac Devashish_Das (Wed Jul 11 2018 - 09:30:22 PDT)
- Re: [AMBER] Regarding Force constants from Mopac David A Case (Thu Jul 12 2018 - 05:34:37 PDT)
[AMBER] H-REMD ligand binding Milo Westler (Wed Jul 11 2018 - 11:16:45 PDT)
[AMBER] Cannot run pdb4amber Alen Ahmetovic (Wed Jul 11 2018 - 21:27:24 PDT)
- Re: [AMBER] Cannot run pdb4amber Hai Nguyen (Wed Jul 11 2018 - 21:37:25 PDT)
  - Re: [AMBER] Cannot run pdb4amber Alen Ahmetovic (Thu Jul 12 2018 - 13:56:58 PDT)
- Re: [AMBER] Cannot run pdb4amber David A Case (Thu Jul 12 2018 - 05:48:08 PDT)
[AMBER] Replica Exchange with Solute Tempering implementation in AMBER14/16/18 on GPUs Alan Hicks (Thu Jul 12 2018 - 10:38:15 PDT)
[AMBER] Error in MCPB.py step 2 dhaval patel (Thu Jul 12 2018 - 12:36:06 PDT)
- Re: [AMBER] Error in MCPB.py step 2 Pengfei Li (Thu Jul 12 2018 - 14:22:43 PDT)
[AMBER] Amber16 to Amber18 upgrade? Hirdesh Kumar (Thu Jul 12 2018 - 13:46:13 PDT)
- Re: [AMBER] Amber16 to Amber18 upgrade? Pengfei Li (Thu Jul 12 2018 - 14:24:11 PDT)
[AMBER] peptide bond restraints lucrecia bogado (Thu Jul 12 2018 - 15:19:50 PDT)
- Re: [AMBER] peptide bond restraints Wesley Michael Botello-Smith (Thu Jul 12 2018 - 15:32:58 PDT)
- Re: [AMBER] peptide bond restraints Carlos Simmerling (Thu Jul 12 2018 - 16:08:22 PDT)
  - Re: [AMBER] peptide bond restraints lucrecia bogado (Fri Jul 13 2018 - 11:23:26 PDT)
    - Re: [AMBER] peptide bond restraints Carlos Simmerling (Fri Jul 13 2018 - 11:30:54 PDT)
    - Re: [AMBER] peptide bond restraints lucrecia bogado (Wed Jul 18 2018 - 14:40:25 PDT)
    - Re: [AMBER] peptide bond restraints David A Case (Thu Jul 19 2018 - 05:53:37 PDT)
    - Re: [AMBER] peptide bond restraints lucrecia bogado (Thu Jul 19 2018 - 15:50:14 PDT)
[AMBER] translational diffusion coefficient from MSD Kris Feher (Thu Jul 12 2018 - 15:44:36 PDT)
- Re: [AMBER] translational diffusion coefficient from MSD Daniel Roe (Sat Jul 14 2018 - 09:42:23 PDT)
  - Re: [AMBER] translational diffusion coefficient from MSD Kris Feher (Sun Jul 15 2018 - 15:04:33 PDT)
    - Re: [AMBER] translational diffusion coefficient from MSD Daniel Roe (Fri Jul 20 2018 - 08:01:20 PDT)
[AMBER] Reduced GPU Performance Midhun K Madhu (Fri Jul 13 2018 - 03:40:54 PDT)
- Re: [AMBER] Reduced GPU Performance Matias Machado (Fri Jul 13 2018 - 04:44:15 PDT)
- Re: [AMBER] Reduced GPU Performance Ross Walker (Fri Jul 13 2018 - 11:45:47 PDT)
[AMBER] Single Point Calculation on trajectory Raimon Fabregat (Fri Jul 13 2018 - 06:12:50 PDT)
[AMBER] Per-residue energy decomposition by MMPBSA.pl Syeda (Fri Jul 13 2018 - 09:51:05 PDT)
[AMBER] convert trajectories files in AMBER Chhaya Singh (Fri Jul 13 2018 - 10:31:00 PDT)
- Re: [AMBER] convert trajectories files in AMBER Charles-Alexandre Mattelaer (Fri Jul 13 2018 - 10:43:34 PDT)
[AMBER] calculating headgroup ion-ion and ion-dipole contacts for lipid bilayers Sally Pias (Fri Jul 13 2018 - 15:14:33 PDT)
- Re: [AMBER] calculating headgroup ion-ion and ion-dipole contacts for lipid bilayers Daniel Roe (Fri Jul 20 2018 - 08:03:41 PDT)
- Re: [AMBER] calculating headgroup ion-ion and ion-dipole contacts for lipid bilayers Wesley Michael Botello-Smith (Fri Jul 20 2018 - 16:56:51 PDT)
  - Re: [AMBER] calculating headgroup ion-ion and ion-dipole contacts for lipid bilayers Hai Nguyen (Fri Jul 20 2018 - 17:01:18 PDT)
    - Re: [AMBER] calculating headgroup ion-ion and ion-dipole contacts for lipid bilayers Sally Pias (Tue Jul 24 2018 - 10:16:58 PDT)
    - Re: [AMBER] calculating headgroup ion-ion and ion-dipole contacts for lipid bilayers Wesley Michael Botello-Smith (Tue Jul 24 2018 - 10:32:46 PDT)
    - Re: [AMBER] calculating headgroup ion-ion and ion-dipole contacts for lipid bilayers Wesley Michael Botello-Smith (Tue Jul 24 2018 - 12:06:54 PDT)
[AMBER] Per-residue energy decomposition by MMPBSA.pl S (Fri Jul 13 2018 - 23:30:40 PDT)
[AMBER] error in leap prmtop incprd preparation senal dinuka (Sun Jul 15 2018 - 08:10:59 PDT)
- Re: [AMBER] error in leap prmtop incprd preparation Bill Ross (Sun Jul 15 2018 - 13:37:16 PDT)
- Re: [AMBER] error in leap prmtop incprd preparation Matias Machado (Sun Jul 15 2018 - 15:59:11 PDT)
[AMBER] Determination of pmf, diffuse, permeability and resistance in case of lipid molecule? zmatovic.kg.ac.rs (Mon Jul 16 2018 - 02:33:26 PDT)
- Re: [AMBER] Determination of pmf, diffuse, permeability and resistance in case of lipid molecule? Dickson, Callum (Tue Jul 17 2018 - 07:47:22 PDT)
  - Re: [AMBER] Determination of pmf, diffuse, permeability and resistance in case of lipid molecule? zmatovic.kg.ac.rs (Tue Jul 17 2018 - 09:03:11 PDT)
[AMBER] Distance between two different solvent mask MOHD HOMAIDUR RAHMAN (Mon Jul 16 2018 - 03:23:53 PDT)
- Re: [AMBER] Distance between two different solvent mask Daniel Roe (Fri Jul 20 2018 - 07:55:14 PDT)
  - Re: [AMBER] Distance between two different solvent mask MOHD HOMAIDUR RAHMAN (Sat Jul 21 2018 - 02:04:03 PDT)
[AMBER] CUDA and Amber 18 Beale, John (Mon Jul 16 2018 - 05:15:46 PDT)
- Re: [AMBER] CUDA and Amber 18 Darrin York (Mon Jul 16 2018 - 05:36:55 PDT)
- Re: [AMBER] CUDA and Amber 18 David A Case (Mon Jul 16 2018 - 13:00:11 PDT)
[AMBER] Au+++ ion parameter Aashish Bhatt (Tue Jul 17 2018 - 04:18:36 PDT)
- Re: [AMBER] Au+++ ion parameter Pengfei Li (Sat Sep 08 2018 - 12:18:52 PDT)
  - Re: [AMBER] Au+++ ion parameter Pengfei Li (Sat Sep 08 2018 - 12:49:12 PDT)
Re: [AMBER] AMBER Digest, Vol 2349, Issue 1 Stejskal, Lenka (Tue Jul 17 2018 - 07:46:17 PDT)
- Re: [AMBER] AMBER Digest, Vol 2349, Issue 1 Daniel Roe (Fri Jul 20 2018 - 07:25:36 PDT)
[AMBER] Calcium forcefields Piotr Fajer (Tue Jul 17 2018 - 10:36:55 PDT)
- Re: [AMBER] Calcium forcefields Aashish Bhatt (Tue Jul 17 2018 - 22:35:59 PDT)
  - Re: [AMBER] Calcium forcefields Zuo, Zhicheng (Wed Jul 18 2018 - 07:30:39 PDT)
[AMBER] Problem with NaN and Asteriks Jorge Curima (Tue Jul 17 2018 - 11:59:01 PDT)
- Re: [AMBER] Problem with NaN and Asteriks Bill Ross (Tue Jul 17 2018 - 12:24:37 PDT)
  - Re: [AMBER] Problem with NaN and Asteriks Jorge Curima (Tue Jul 17 2018 - 13:44:07 PDT)
- Re: [AMBER] Problem with NaN and Asteriks Bill Ross (Tue Jul 17 2018 - 13:58:00 PDT)
  - Re: [AMBER] Problem with NaN and Asteriks Jorge Curima (Tue Jul 17 2018 - 14:25:44 PDT)
- Re: [AMBER] Problem with NaN and Asteriks Bill Ross (Tue Jul 17 2018 - 15:27:26 PDT)
  - Re: [AMBER] Problem with NaN and Asteriks Jorge Curima (Sat Jul 21 2018 - 00:12:47 PDT)
    - Re: [AMBER] Problem with NaN and Asteriks Bill Ross (Sat Jul 21 2018 - 11:05:36 PDT)
[AMBER] Neural net timestep integration diagram Bill Ross (Tue Jul 17 2018 - 17:54:58 PDT)
[AMBER] Advice on using GLYCAM parameters senal dinuka (Tue Jul 17 2018 - 23:51:08 PDT)
- Re: [AMBER] Advice on using GLYCAM parameters Lachele Foley (Tue Jul 24 2018 - 08:34:00 PDT)
[AMBER] Calcium force fields David A Case (Wed Jul 18 2018 - 04:16:10 PDT)
- Re: [AMBER] Calcium force fields Piotr Fajer (Wed Jul 18 2018 - 08:53:39 PDT)
  - Re: [AMBER] Calcium force fields Qinghua Liao (Wed Jul 18 2018 - 09:29:47 PDT)
[AMBER] Amber on GTX 1-5- / 1050 TI ? Gustavo Seabra (Wed Jul 18 2018 - 08:06:12 PDT)
[AMBER] How to analyse the PCA results? Markowska (Wed Jul 18 2018 - 09:01:59 PDT)
- Re: [AMBER] How to analyse the PCA results? Daniel Roe (Fri Jul 20 2018 - 07:20:21 PDT)
  - Re: [AMBER] How to analyse the PCA results? Daniel Roe (Fri Jul 20 2018 - 07:23:58 PDT)
    - Re: [AMBER] How to analyse the PCA results? Markowska (Thu Jul 26 2018 - 06:10:42 PDT)
    - Re: [AMBER] How to analyse the PCA results? Markowska (Thu Jul 26 2018 - 06:41:40 PDT)
[AMBER] mask behavior with ions? Kenneth Huang (Wed Jul 18 2018 - 10:37:01 PDT)
- Re: [AMBER] mask behavior with ions? Daniel Roe (Fri Jul 20 2018 - 07:06:55 PDT)
[AMBER] ACE_NME_TLEAP Antonio Carlesso (Wed Jul 18 2018 - 23:38:43 PDT)
- Re: [AMBER] ACE_NME_TLEAP Bill Ross (Thu Jul 19 2018 - 10:32:16 PDT)
  - Re: [AMBER] ACE_NME_TLEAP Antonio Carlesso (Thu Jul 19 2018 - 12:56:16 PDT)
[AMBER] Amber on GTX 1050 / 1050 TI Gustavo Seabra (Thu Jul 19 2018 - 02:26:35 PDT)
- Re: [AMBER] Amber on GTX 1050 / 1050 TI Jinfeng Chen (Thu Jul 19 2018 - 04:08:03 PDT)
  - Re: [AMBER] Amber on GTX 1050 / 1050 TI Gustavo Seabra (Thu Jul 19 2018 - 04:17:22 PDT)
[AMBER] Distance restraint for PMEMD Abir Ganguly (Thu Jul 19 2018 - 05:48:20 PDT)
- Re: [AMBER] Distance restraint for PMEMD David A Case (Thu Jul 19 2018 - 12:38:47 PDT)
- Re: [AMBER] Distance restraint for PMEMD Feng Pan (Thu Jul 19 2018 - 14:13:59 PDT)
- Re: [AMBER] Distance restraint for PMEMD Abir Ganguly (Fri Jul 20 2018 - 07:18:23 PDT)
[AMBER] Diffusion coefficient from Terachem emanuele falbo (Thu Jul 19 2018 - 07:52:43 PDT)
[AMBER] CPPTRAJ read different frames Rana Rehan Khalid (Thu Jul 19 2018 - 10:08:23 PDT)
- Re: [AMBER] CPPTRAJ read different frames Daniel Roe (Thu Jul 19 2018 - 10:40:09 PDT)
  - Re: [AMBER] CPPTRAJ read different frames Rana Rehan Khalid (Thu Jul 19 2018 - 15:45:01 PDT)
    - Re: [AMBER] CPPTRAJ read different frames Daniel Roe (Fri Jul 20 2018 - 07:01:23 PDT)
[AMBER] Amber targeted MD restraintmask 李耀 (Thu Jul 19 2018 - 19:57:33 PDT)
- Re: [AMBER] Amber targeted MD restraintmask Carlos Simmerling (Fri Jul 20 2018 - 05:00:20 PDT)
[AMBER] Arsenous acid (H3AsO3) parameterization Zuo, Zhicheng (Thu Jul 19 2018 - 21:25:32 PDT)
- Re: [AMBER] Arsenous acid (H3AsO3) parameterization Pengfei Li (Sat Sep 08 2018 - 12:10:41 PDT)
[AMBER] amber test run ilhan.yavuz (Fri Jul 20 2018 - 05:59:53 PDT)
- Re: [AMBER] amber test run Bill Ross (Fri Jul 20 2018 - 06:23:19 PDT)
[AMBER] Papers that use RPMD in AMBER Rodrigo Pérez Cossio (Fri Jul 20 2018 - 06:08:16 PDT)
Re: [AMBER] Is Amber18 compatible with GCC-7.x? Mirza Ahmed Hammad (Fri Jul 20 2018 - 23:59:29 PDT)
- Re: [AMBER] Is Amber18 compatible with GCC-7.x? David A Case (Mon Jul 23 2018 - 07:55:58 PDT)
- Re: [AMBER] Is Amber18 compatible with GCC-7.x? Mirza Ahmed Hammad (Mon Jul 23 2018 - 20:50:41 PDT)
  - Re: [AMBER] Is Amber18 compatible with GCC-7.x? David A Case (Tue Jul 24 2018 - 05:07:36 PDT)
  - Re: [AMBER] Is Amber18 compatible with GCC-7.x? Ross Walker (Tue Jul 24 2018 - 08:19:53 PDT)
    - Re: [AMBER] Is Amber18 compatible with GCC-7.x? David A Case (Tue Jul 24 2018 - 16:26:28 PDT)
[AMBER] partial molar volume of hypothetical protein molecule without atomic charges Leena Aggarwal (Sat Jul 21 2018 - 02:45:51 PDT)
- Re: [AMBER] partial molar volume of hypothetical protein molecule without atomic charges David A Case (Fri Jul 27 2018 - 05:25:13 PDT)
  - Re: [AMBER] partial molar volume of hypothetical protein molecule without atomic charges Leena Aggarwal (Fri Jul 27 2018 - 07:05:37 PDT)
    - Re: [AMBER] partial molar volume of hypothetical protein molecule without atomic charges Tyler Luchko (Lists) (Fri Jul 27 2018 - 09:33:27 PDT)
[AMBER] error in antechamber Andrew Bostick (Sat Jul 21 2018 - 13:15:41 PDT)
- Re: [AMBER] error in antechamber Bill Ross (Sat Jul 21 2018 - 13:27:26 PDT)
[AMBER] Question about implicit solvation: DNA-linker conjugate Supriyo Bhattacharya (Sun Jul 22 2018 - 11:30:07 PDT)
- Re: [AMBER] Question about implicit solvation: DNA-linker conjugate Hai Nguyen (Mon Jul 23 2018 - 11:06:32 PDT)
  - Re: [AMBER] Question about implicit solvation: DNA-linker conjugate Carlos Simmerling (Mon Jul 23 2018 - 11:11:26 PDT)
    - Re: [AMBER] Question about implicit solvation: DNA-linker conjugate Supriyo Bhattacharya (Mon Jul 23 2018 - 13:53:50 PDT)
    - Re: [AMBER] Question about implicit solvation: DNA-linker conjugate Matias Machado (Tue Jul 24 2018 - 07:43:10 PDT)
    - Re: [AMBER] Question about implicit solvation: DNA-linker conjugate Supriyo Bhattacharya (Wed Jul 25 2018 - 10:32:20 PDT)
  - Re: [AMBER] Question about implicit solvation: DNA-linker conjugate Supriyo Bhattacharya (Mon Jul 23 2018 - 13:44:32 PDT)
[AMBER] Amber targeted MD variables 李耀 (Mon Jul 23 2018 - 02:57:44 PDT)
- Re: [AMBER] Amber targeted MD variables Carlos Simmerling (Mon Jul 23 2018 - 03:42:07 PDT)
[AMBER] Soft-core alchemical transformation in TI Simon Kit Sang Chu (Mon Jul 23 2018 - 08:11:35 PDT)
- Re: [AMBER] Soft-core alchemical transformation in TI David Cerutti (Mon Jul 23 2018 - 09:57:24 PDT)
  - Re: [AMBER] Soft-core alchemical transformation in TI Simon Kit Sang Chu (Mon Jul 23 2018 - 19:44:28 PDT)
    - Re: [AMBER] Soft-core alchemical transformation in TI accuratefreeenergy.gmail.com (Tue Jul 24 2018 - 05:49:47 PDT)
    - Re: [AMBER] Soft-core alchemical transformation in TI Simon Kit Sang Chu (Wed Jul 25 2018 - 01:58:32 PDT)
    - Re: [AMBER] Soft-core alchemical transformation in TI accuratefreeenergy.gmail.com (Wed Jul 25 2018 - 09:10:48 PDT)
    - Re: [AMBER] Soft-core alchemical transformation in TI Simon Kit Sang Chu (Wed Jul 25 2018 - 09:17:52 PDT)
    - Re: [AMBER] Soft-core alchemical transformation in TI Simon Kit Sang Chu (Wed Jul 25 2018 - 01:21:36 PDT)
    - Re: [AMBER] Soft-core alchemical transformation in TI accuratefreeenergy.gmail.com (Wed Jul 25 2018 - 09:37:30 PDT)
    - Re: [AMBER] Soft-core alchemical transformation in TI Simon Kit Sang Chu (Sat Jul 28 2018 - 08:17:47 PDT)
[AMBER] LJEDIT syntax Matias Machado (Mon Jul 23 2018 - 11:15:50 PDT)
- Re: [AMBER] LJEDIT syntax David Cerutti (Mon Jul 23 2018 - 12:09:38 PDT)
  - Re: [AMBER] LJEDIT syntax Matias Machado (Tue Jul 24 2018 - 13:58:15 PDT)
    - Re: [AMBER] LJEDIT syntax Matias Machado (Tue Jul 24 2018 - 14:01:45 PDT)
    - Re: [AMBER] LJEDIT syntax David Cerutti (Tue Jul 24 2018 - 17:05:22 PDT)
[AMBER] analyze force on selected atoms James Kress (Mon Jul 23 2018 - 12:22:20 PDT)
[AMBER] Query regarding multiplication of LJ parameters by a constant in topology file using parmed Leena Aggarwal (Tue Jul 24 2018 - 06:06:56 PDT)
- Re: [AMBER] Query regarding multiplication of LJ parameters by a constant in topology file using parmed David A Case (Tue Jul 24 2018 - 16:28:52 PDT)
  - Re: [AMBER] Query regarding multiplication of LJ parameters by a constant in topology file using parmed Leena Aggarwal (Tue Jul 24 2018 - 21:36:27 PDT)
    - Re: [AMBER] Query regarding multiplication of LJ parameters by a constant in topology file using parmed Jason Swails (Thu Jul 26 2018 - 10:30:17 PDT)
    - Re: [AMBER] Query regarding multiplication of LJ parameters by a constant in topology file using parmed Leena Aggarwal (Thu Jul 26 2018 - 21:31:10 PDT)
Re: [AMBER] Is Amber18 compatible with GCC-7.x Nikolay N. Kuzmich (Tue Jul 24 2018 - 14:41:19 PDT)
- Re: [AMBER] Is Amber18 compatible with GCC-7.x Mirza Ahmed Hammad (Wed Jul 25 2018 - 20:15:27 PDT)
  - Re: [AMBER] Is Amber18 compatible with GCC-7.x David A Case (Thu Jul 26 2018 - 07:00:58 PDT)
[AMBER] problem preparing n-terminus with tleap (?) Julia Belk (Tue Jul 24 2018 - 18:32:26 PDT)
- Re: [AMBER] problem preparing n-terminus with tleap (?) Matias Machado (Tue Jul 24 2018 - 20:07:18 PDT)
[AMBER] Problem in chamber Suzan Bose (Tue Jul 24 2018 - 21:10:45 PDT)
- Re: [AMBER] Problem in chamber Jason Swails (Thu Jul 26 2018 - 10:26:12 PDT)
[AMBER] Reading grid data from standard datafile I Lőrincz (Wed Jul 25 2018 - 04:55:09 PDT)
- Re: [AMBER] Reading grid data from standard datafile Daniel Roe (Wed Jul 25 2018 - 06:25:07 PDT)
  - Re: [AMBER] Reading grid data from standard datafile Daniel Roe (Fri Jul 27 2018 - 09:27:49 PDT)
    - Re: [AMBER] Reading grid data from standard datafile I Lőrincz (Fri Aug 03 2018 - 10:35:38 PDT)
[AMBER] MCBP force constants Seibold, Steve Allan (Wed Jul 25 2018 - 10:23:02 PDT)
- Re: [AMBER] MCBP force constants Pengfei Li (Thu Jul 26 2018 - 08:08:38 PDT)
  - Re: [AMBER] MCBP force constants Seibold, Steve Allan (Wed Aug 01 2018 - 08:18:14 PDT)
[AMBER] Extract Force from MDCRD/DCD trj Lod King (Wed Jul 25 2018 - 17:50:09 PDT)
- Re: [AMBER] Extract Force from MDCRD/DCD trj Hai Nguyen (Wed Jul 25 2018 - 20:33:47 PDT)
  - Re: [AMBER] Extract Force from MDCRD/DCD trj Lod King (Thu Jul 26 2018 - 23:40:21 PDT)
    - Re: [AMBER] Extract Force from MDCRD/DCD trj David A Case (Fri Jul 27 2018 - 05:21:12 PDT)
    - Re: [AMBER] Extract Force from MDCRD/DCD trj James Kress (Fri Jul 27 2018 - 15:07:40 PDT)
[AMBER] The instructions of the .out file Zhonghua Xia (Fri Jul 27 2018 - 03:48:05 PDT)
- Re: [AMBER] The instructions of the .out file Thomas Cheatham (Fri Jul 27 2018 - 13:37:27 PDT)
  - Re: [AMBER] The instructions of the .out file Zhonghua Xia (Fri Aug 17 2018 - 06:19:34 PDT)
[AMBER] The instructions of the .out file Zhonghua Xia (Fri Jul 27 2018 - 03:57:25 PDT)
[AMBER] The instructions of the .out file Zhonghua Xia (Fri Jul 27 2018 - 04:04:35 PDT)
[AMBER] The right syntax for creating the given mask using logical operators - Not all arguments handled Marek Maly (Fri Jul 27 2018 - 06:18:27 PDT)
- Re: [AMBER] The right syntax for creating the given mask using logical operators - Not all arguments handled Daniel Roe (Fri Jul 27 2018 - 08:51:28 PDT)
  - Re: [AMBER] The right syntax for creating the given mask using logical operators - Not all arguments handled Marek Maly (Sat Jul 28 2018 - 05:39:02 PDT)
    - Re: [AMBER] The right syntax for creating the given mask using logical operators - Not all arguments handled David A Case (Sat Jul 28 2018 - 06:06:44 PDT)
    - Re: [AMBER] The right syntax for creating the given mask using logical operators - Not all arguments handled Marek Maly (Sat Jul 28 2018 - 06:31:07 PDT)
[AMBER] CPPTRAJ contacts and nativecontacts PAQUET Amaury (Fri Jul 27 2018 - 07:16:35 PDT)
- Re: [AMBER] CPPTRAJ contacts and nativecontacts Wesley Michael Botello-Smith (Fri Jul 27 2018 - 08:41:22 PDT)
- Re: [AMBER] CPPTRAJ contacts and nativecontacts Wesley Michael Botello-Smith (Fri Jul 27 2018 - 08:47:45 PDT)
  - Re: [AMBER] CPPTRAJ contacts and nativecontacts PAQUET Amaury (Tue Jul 31 2018 - 04:11:52 PDT)
- Re: [AMBER] CPPTRAJ contacts and nativecontacts Daniel Roe (Fri Jul 27 2018 - 08:53:27 PDT)
[AMBER] Thermodyncamic Integration (TI) emanuele falbo (Fri Jul 27 2018 - 08:45:14 PDT)
- Re: [AMBER] Thermodyncamic Integration (TI) David A Case (Fri Jul 27 2018 - 12:04:51 PDT)
  - Re: [AMBER] Thermodyncamic Integration (TI) emanuele falbo (Mon Jul 30 2018 - 01:37:53 PDT)
[AMBER] very slow implicit simulation on GPU!!! Parviz Seifpanahi Shabane (Fri Jul 27 2018 - 13:15:26 PDT)
- Re: [AMBER] very slow implicit simulation on GPU!!! Bill Ross (Fri Jul 27 2018 - 13:34:56 PDT)
  - Re: [AMBER] very slow implicit simulation on GPU!!! Parviz Seifpanahi Shabane (Fri Jul 27 2018 - 13:46:23 PDT)
    - Re: [AMBER] very slow implicit simulation on GPU!!! David Cerutti (Fri Jul 27 2018 - 14:03:09 PDT)
    - Re: [AMBER] very slow implicit simulation on GPU!!! Bill Ross (Fri Jul 27 2018 - 14:09:04 PDT)
  - Re: [AMBER] very slow implicit simulation on GPU!!! Supriyo Bhattacharya (Fri Jul 27 2018 - 14:05:42 PDT)
    - Re: [AMBER] very slow implicit simulation on GPU!!! Bill Ross (Fri Jul 27 2018 - 14:10:42 PDT)
    - Re: [AMBER] very slow implicit simulation on GPU!!! Parviz Seifpanahi Shabane (Fri Jul 27 2018 - 16:01:47 PDT)
    - Re: [AMBER] very slow implicit simulation on GPU!!! Supriyo Bhattacharya (Fri Jul 27 2018 - 16:07:08 PDT)
    - Re: [AMBER] very slow implicit simulation on GPU!!! Parviz Seifpanahi Shabane (Fri Jul 27 2018 - 16:13:09 PDT)
    - Re: [AMBER] very slow implicit simulation on GPU!!! Parviz Seifpanahi Shabane (Fri Jul 27 2018 - 16:16:13 PDT)
    - Re: [AMBER] very slow implicit simulation on GPU!!! Matias Machado (Fri Jul 27 2018 - 23:17:56 PDT)
    - Re: [AMBER] very slow implicit simulation on GPU!!! Matias Machado (Sat Jul 28 2018 - 08:37:07 PDT)
    - Re: [AMBER] very slow implicit simulation on GPU!!! Supriyo Bhattacharya (Sat Jul 28 2018 - 09:53:12 PDT)
- Re: [AMBER] very slow implicit simulation on GPU!!! Roitberg,Adrian E (Fri Jul 27 2018 - 16:12:13 PDT)
  - Re: [AMBER] very slow implicit simulation on GPU!!! Jason Swails (Wed Aug 01 2018 - 14:22:54 PDT)
[AMBER] Possible bug on addLJType command of Parmed Matias Machado (Fri Jul 27 2018 - 20:20:19 PDT)
- Re: [AMBER] Possible bug on addLJType command of Parmed Jason Swails (Wed Aug 01 2018 - 14:20:07 PDT)
  - Re: [AMBER] Possible bug on addLJType command of Parmed Matias Machado (Thu Aug 02 2018 - 12:52:06 PDT)
[AMBER] Inquries about Non-periodic PMF profile Meng Wu (Sat Jul 28 2018 - 07:26:37 PDT)
- [AMBER] Inquries about Non-periodic PMF profile Meng Wu (Sun Jul 29 2018 - 18:54:15 PDT)
  - Re: [AMBER] Inquries about Non-periodic PMF profile Dickson, Callum (Mon Jul 30 2018 - 11:39:10 PDT)
  - Re: [AMBER] Inquries about Non-periodic PMF profile Feng Pan (Mon Jul 30 2018 - 12:06:30 PDT)
  - Re: [AMBER] Inquries about Non-periodic PMF profile Meng Wu (Mon Jul 30 2018 - 19:02:18 PDT)
[AMBER] Amber targeted MD tgtmdfrc 李耀 (Sat Jul 28 2018 - 09:59:25 PDT)
- Re: [AMBER] Amber targeted MD tgtmdfrc Carlos Simmerling (Sat Jul 28 2018 - 10:50:21 PDT)
[AMBER] Gaff vs Gaff2 when using antechamber to generate charges Yuliana Bosken (Sat Jul 28 2018 - 15:31:48 PDT)
- Re: [AMBER] Gaff vs Gaff2 when using antechamber to generate charges Yuliana Bosken (Sun Jul 29 2018 - 04:44:41 PDT)
- Re: [AMBER] Gaff vs Gaff2 when using antechamber to generate charges David A Case (Sun Jul 29 2018 - 05:13:16 PDT)
  - Re: [AMBER] Gaff vs Gaff2 when using antechamber to generate charges Yuliana Bosken (Sun Jul 29 2018 - 10:23:42 PDT)
    - Re: [AMBER] Gaff vs Gaff2 when using antechamber to generate charges Yuliana Bosken (Mon Jul 30 2018 - 11:16:28 PDT)
    - Re: [AMBER] Gaff vs Gaff2 when using antechamber to generate charges Junmei Wang (Mon Jul 30 2018 - 12:50:33 PDT)
    - Re: [AMBER] Gaff vs Gaff2 when using antechamber to generate charges Yuliana Bosken (Mon Jul 30 2018 - 13:06:11 PDT)
[AMBER] Amber targeted MD tgtmdfrc 李耀 (Sat Jul 28 2018 - 22:29:19 PDT)
[AMBER] Amber ff for oniom method roja rahmani (Sun Jul 29 2018 - 21:15:22 PDT)
- Re: [AMBER] Amber ff for oniom method Rinsha Chk (Sun Jul 29 2018 - 21:26:36 PDT)
  - Re: [AMBER] Amber ff for oniom method Rinsha Chk (Sun Jul 29 2018 - 21:27:07 PDT)
- Re: [AMBER] Amber ff for oniom method David A Case (Mon Jul 30 2018 - 04:18:47 PDT)
  - Re: [AMBER] Amber ff for oniom method roja rahmani (Mon Jul 30 2018 - 04:41:08 PDT)
- Re: [AMBER] Amber ff for oniom method Hector A. Baldoni (Mon Jul 30 2018 - 05:09:43 PDT)
[AMBER] SANDER BOMB in subroutine qm2_extern_get_qm_forces Devashish_Das (Mon Jul 30 2018 - 01:07:32 PDT)
- Re: [AMBER] SANDER BOMB in subroutine qm2_extern_get_qm_forces Goetz, Andreas (Mon Jul 30 2018 - 10:17:05 PDT)
[AMBER] Cpptraj PCA analysis - correlation between PCs? Markowska (Tue Jul 31 2018 - 01:28:55 PDT)
- Re: [AMBER] Cpptraj PCA analysis - correlation between PCs? Markowska (Tue Jul 31 2018 - 06:22:35 PDT)
[AMBER] QM/MM link atoms emanuele falbo (Tue Jul 31 2018 - 04:09:10 PDT)
- Re: [AMBER] QM/MM link atoms Gustavo Seabra (Tue Jul 31 2018 - 05:12:16 PDT)
  - Re: [AMBER] QM/MM link atoms emanuele falbo (Thu Aug 02 2018 - 07:59:08 PDT)
    - Re: [AMBER] QM/MM link atoms Gustavo Seabra (Thu Aug 02 2018 - 08:25:00 PDT)
    - Re: [AMBER] QM/MM link atoms Goetz, Andreas (Thu Aug 02 2018 - 12:14:19 PDT)
    - Re: [AMBER] QM/MM link atoms James Kress (Thu Aug 02 2018 - 14:12:53 PDT)
    - Re: [AMBER] QM/MM link atoms Goetz, Andreas (Thu Aug 02 2018 - 15:46:30 PDT)
[AMBER] TIP4P inputs and tests Brian Radak (Tue Jul 31 2018 - 07:13:04 PDT)
[AMBER] Running a small minimization with amber 16 package Debarati DasGupta (Tue Jul 31 2018 - 09:34:26 PDT)
- Re: [AMBER] Running a small minimization with amber 16 package David A Case (Tue Jul 31 2018 - 11:33:06 PDT)
  - Re: [AMBER] Running a small minimization with amber 16 package Debarati DasGupta (Tue Jul 31 2018 - 14:51:56 PDT)
    - Re: [AMBER] Running a small minimization with amber 16 package Scott Brozell (Mon Aug 06 2018 - 16:42:16 PDT)
  - Re: [AMBER] Running a small minimization with amber 16 package Debarati DasGupta (Mon Aug 06 2018 - 14:38:36 PDT)
[AMBER] FMNH2 parameters Maximilian Ebert (Tue Jul 31 2018 - 20:31:28 PDT)
[AMBER] Constant pH simulation in explicit solvent Nikolay N. Kuzmich (Wed Aug 01 2018 - 02:32:06 PDT)
- Re: [AMBER] Constant pH simulation in explicit solvent Eric Lang (Wed Aug 01 2018 - 03:19:53 PDT)
- Re: [AMBER] Constant pH simulation in explicit solvent Nikolay N. Kuzmich (Thu Aug 02 2018 - 03:32:35 PDT)
[AMBER] Eigenvalues from PCA in cpptraj Adam Jo Elatico (Wed Aug 01 2018 - 04:39:50 PDT)
- Re: [AMBER] Eigenvalues from PCA in cpptraj Daniel Roe (Wed Aug 01 2018 - 09:12:48 PDT)
  - Re: [AMBER] Eigenvalues from PCA in cpptraj Adam Jo Elatico (Wed Aug 01 2018 - 09:49:36 PDT)
    - Re: [AMBER] Eigenvalues from PCA in cpptraj Daniel Roe (Wed Aug 01 2018 - 09:59:16 PDT)
[AMBER] asking about PBRadii in MMPBSA an other else Setyanto Md (Wed Aug 01 2018 - 04:49:16 PDT)
[AMBER] Multiple PDB files to a MDCRD file Alechania Misturini (Wed Aug 01 2018 - 06:58:26 PDT)
- Re: [AMBER] Multiple PDB files to a MDCRD file Daniel Roe (Wed Aug 01 2018 - 09:15:12 PDT)
  - Re: [AMBER] Multiple PDB files to a MDCRD file Charles-Alexandre Mattelaer (Wed Aug 01 2018 - 09:22:17 PDT)
    - Re: [AMBER] Multiple PDB files to a MDCRD file Daniel Roe (Wed Aug 01 2018 - 09:44:30 PDT)
  - Re: [AMBER] Multiple PDB files to a MDCRD file Alechania Misturini (Wed Aug 01 2018 - 10:10:41 PDT)
    - Re: [AMBER] Multiple PDB files to a MDCRD file David A Case (Wed Aug 01 2018 - 17:09:28 PDT)
    - Re: [AMBER] Multiple PDB files to a MDCRD file Alechania Misturini (Thu Aug 02 2018 - 08:00:37 PDT)
    - Re: [AMBER] Multiple PDB files to a MDCRD file Alechania Misturini (Thu Aug 02 2018 - 08:05:58 PDT)
[AMBER] Fwd: Issue with imploding structure during heating and equilibration David Stevens (Wed Aug 01 2018 - 10:45:46 PDT)
- Re: [AMBER] Fwd: Issue with imploding structure during heating and equilibration Carlos Simmerling (Thu Aug 02 2018 - 05:18:22 PDT)
[AMBER] GPUs Alexandra Carvalho (Wed Aug 01 2018 - 14:11:49 PDT)
- Re: [AMBER] GPUs David Cerutti (Wed Aug 01 2018 - 16:13:10 PDT)
[AMBER] Reproduce part of AMBER trajectory Supriyo Bhattacharya (Wed Aug 01 2018 - 16:36:03 PDT)
[AMBER] Calculate protein energy from simulation trajectory Adam Jo Elatico (Thu Aug 02 2018 - 01:10:28 PDT)
[AMBER] Velocity Format in AMBER BLEY Michael (Thu Aug 02 2018 - 06:58:24 PDT)
- Re: [AMBER] Velocity Format in AMBER David A Case (Thu Aug 02 2018 - 09:21:56 PDT)
[AMBER] System density decrease during accelerated MD: why? Nikolay N. Kuzmich (Thu Aug 02 2018 - 07:13:59 PDT)
[AMBER] Free energy landscape on principal components Adam Jo Elatico (Thu Aug 02 2018 - 08:34:04 PDT)
[AMBER] MCPB.py with G09 rev. B.01 Jinfeng Chen (Thu Aug 02 2018 - 18:26:49 PDT)
- Re: [AMBER] MCPB.py with G09 rev. B.01 Pengfei Li (Tue Aug 07 2018 - 12:16:31 PDT)
[AMBER] COM pulling in direction Meng Wu (Fri Aug 03 2018 - 02:52:24 PDT)
- Re: [AMBER] COM pulling in direction Meng Wu (Sat Aug 04 2018 - 02:08:56 PDT)
  - [AMBER] COM pulling in direction Meng Wu (Mon Aug 06 2018 - 18:51:28 PDT)
    - Re: [AMBER] COM pulling in direction Feng Pan (Tue Aug 07 2018 - 05:54:52 PDT)
    - Re: [AMBER] COM pulling in direction Meng Wu (Tue Aug 07 2018 - 18:59:31 PDT)
[AMBER] Amber16 Installation error Sushi Shilpa (Fri Aug 03 2018 - 03:46:33 PDT)
- Re: [AMBER] Amber16 Installation error Matias Machado (Fri Aug 03 2018 - 04:38:15 PDT)
  - Re: [AMBER] Amber16 Installation error Sushi Shilpa (Fri Aug 03 2018 - 04:44:20 PDT)
    - Re: [AMBER] Amber16 Installation error Matias Machado (Fri Aug 03 2018 - 05:04:44 PDT)
    - Re: [AMBER] Amber16 Installation error Matias Machado (Fri Aug 03 2018 - 05:08:17 PDT)
    - Re: [AMBER] Amber16 Installation error Sushi Shilpa (Fri Aug 03 2018 - 05:14:15 PDT)
    - Re: [AMBER] Amber16 Installation error Sushi Shilpa (Fri Aug 03 2018 - 05:15:08 PDT)
    - Re: [AMBER] Amber16 Installation error Sushi Shilpa (Fri Aug 03 2018 - 23:43:37 PDT)
[AMBER] Error for Amber16 and Amber tools 17 installation maryam azimzadehirani (Fri Aug 03 2018 - 05:16:11 PDT)
- Re: [AMBER] Error for Amber16 and Amber tools 17 installation Josh Berryman (Fri Aug 03 2018 - 12:34:42 PDT)
  - Re: [AMBER] Error for Amber16 and Amber tools 17 installation maryam azimzadehirani (Sat Aug 04 2018 - 03:19:12 PDT)
    - Re: [AMBER] Error for Amber16 and Amber tools 17 installation David A Case (Sat Aug 04 2018 - 06:41:34 PDT)
    - Re: [AMBER] Error for Amber16 and Amber tools 17 installation Kevin Keane (USD) (Sun Aug 05 2018 - 00:03:41 PDT)
    - Re: [AMBER] Error for Amber16 and Amber tools 17 installation maryam azimzadehirani (Tue Aug 07 2018 - 05:56:28 PDT)
[AMBER] Solute-solvent hydrogen bond lifetime ATUL KUMAR (Fri Aug 03 2018 - 06:01:36 PDT)
- Re: [AMBER] Solute-solvent hydrogen bond lifetime Daniel Roe (Mon Aug 06 2018 - 06:18:27 PDT)
  - Re: [AMBER] Solute-solvent hydrogen bond lifetime ATUL KUMAR (Tue Aug 07 2018 - 00:03:29 PDT)
[AMBER] error_antechamber (QMMM: ERROR!) Atila Petrosian (Fri Aug 03 2018 - 07:11:30 PDT)
- Re: [AMBER] error_antechamber (QMMM: ERROR!) Gustavo Seabra (Fri Aug 03 2018 - 08:23:28 PDT)
[AMBER] Change in boxlength during memebrane simulation somdev pahari (Fri Aug 03 2018 - 07:59:19 PDT)
- Re: [AMBER] Change in boxlength during memebrane simulation David Cerutti (Fri Aug 03 2018 - 08:19:00 PDT)
  - Re: [AMBER] Change in boxlength during memebrane simulation somdev pahari (Fri Aug 03 2018 - 10:05:05 PDT)
- Re: [AMBER] Change in boxlength during memebrane simulation Sally Pias (Fri Aug 03 2018 - 14:55:35 PDT)
  - Re: [AMBER] Change in boxlength during memebrane simulation David Cerutti (Fri Aug 03 2018 - 15:22:06 PDT)
    - Re: [AMBER] Change in boxlength during memebrane simulation Chris Neale (Fri Aug 03 2018 - 15:50:40 PDT)
    - Re: [AMBER] Change in boxlength during memebrane simulation David Cerutti (Fri Aug 03 2018 - 17:07:33 PDT)
    - Re: [AMBER] Change in boxlength during memebrane simulation Sally Pias (Fri Aug 10 2018 - 15:13:08 PDT)
[AMBER] error_antechamber (QMMM: ERROR!) Atila Petrosian (Fri Aug 03 2018 - 08:52:17 PDT)
- Re: [AMBER] error_antechamber (QMMM: ERROR!) Goetz, Andreas (Fri Aug 03 2018 - 10:57:31 PDT)
- [AMBER] RES: error_antechamber (QMMM: ERROR!) gustavo.seabra.gmail.com (Fri Aug 03 2018 - 11:56:45 PDT)
  - Re: [AMBER] RES: error_antechamber (QMMM: ERROR!) Atila Petrosian (Fri Aug 03 2018 - 12:28:07 PDT)
[AMBER] counterions_automatic Antonio Amber Carlesso (Sun Aug 05 2018 - 08:56:50 PDT)
- Re: [AMBER] counterions_automatic Matias Machado (Sun Aug 05 2018 - 13:31:24 PDT)
  - Re: [AMBER] counterions_automatic Antonio Amber Carlesso (Tue Aug 07 2018 - 07:59:26 PDT)
[AMBER] Adding box dimension Simon Kit Sang Chu (Sun Aug 05 2018 - 09:31:19 PDT)
- Re: [AMBER] Adding box dimension David A Case (Mon Aug 06 2018 - 05:00:41 PDT)
  - Re: [AMBER] Adding box dimension Simon Kit Sang Chu (Mon Aug 06 2018 - 05:04:14 PDT)
    - Re: [AMBER] Adding box dimension David Cerutti (Mon Aug 06 2018 - 11:50:14 PDT)
[AMBER] Atom Types for carbons with unsaturated bond Vijay Achari (Mon Aug 06 2018 - 01:37:22 PDT)
[AMBER] Parameters for non-standard residues Anuja Ware (Mon Aug 06 2018 - 02:49:13 PDT)
- Re: [AMBER] Parameters for non-standard residues Zhonghua Xia (Mon Aug 06 2018 - 04:47:52 PDT)
- Re: [AMBER] Parameters for non-standard residues David A Case (Mon Aug 06 2018 - 05:04:12 PDT)
  - Re: [AMBER] Parameters for non-standard residues Junmei Wang (Mon Aug 06 2018 - 05:57:13 PDT)
    - Re: [AMBER] Parameters for non-standard residues Anuja Ware (Mon Sep 03 2018 - 04:10:19 PDT)
[AMBER] RDCs in pmemd? Thomas Pochapsky (Mon Aug 06 2018 - 09:02:32 PDT)
- Re: [AMBER] RDCs in pmemd? David A Case (Tue Aug 14 2018 - 08:03:03 PDT)
[AMBER] .frcmod_file_generation Antonio Amber Carlesso (Tue Aug 07 2018 - 07:57:39 PDT)
- Re: [AMBER] .frcmod_file_generation David A Case (Tue Aug 07 2018 - 13:07:52 PDT)
  - Re: [AMBER] .frcmod_file_generation Antonio Amber Carlesso (Tue Aug 07 2018 - 22:59:40 PDT)
[AMBER] max# cpu's for sander, specify which gpu runs a job David Christopher Schröder (Tue Aug 07 2018 - 09:40:56 PDT)
- Re: [AMBER] max# cpu's for sander, specify which gpu runs a job David A Case (Tue Aug 07 2018 - 13:19:26 PDT)
  - Re: [AMBER] max# cpu's for sander, specify which gpu runs a job David Christopher Schröder (Tue Aug 14 2018 - 00:28:32 PDT)
[AMBER] Restraints on a system Debarati DasGupta (Tue Aug 07 2018 - 14:15:06 PDT)
- Re: [AMBER] Restraints on a system Matias Machado (Sat Aug 11 2018 - 13:06:43 PDT)
  - Re: [AMBER] Restraints on a system Matias Machado (Sat Aug 11 2018 - 13:11:48 PDT)
[AMBER] problem with amber 16 giovanna rogati (Wed Aug 08 2018 - 01:29:38 PDT)
- Re: [AMBER] problem with amber 16 David A Case (Wed Aug 08 2018 - 06:41:51 PDT)
  - Re: [AMBER] problem with amber 16 giovanna rogati (Wed Aug 15 2018 - 23:04:20 PDT)
[AMBER] number of interconversions from free energy landscape (FEL) plot Chetna Tyagi (Wed Aug 08 2018 - 05:54:17 PDT)
[AMBER] checkmolecule.c John L. Kulp, Jr. (Wed Aug 08 2018 - 06:10:13 PDT)
- Re: [AMBER] checkmolecule.c David A Case (Wed Aug 08 2018 - 11:35:50 PDT)
- Re: [AMBER] checkmolecule.c David A Case (Wed Aug 08 2018 - 11:56:04 PDT)
  - Re: [AMBER] checkmolecule.c Scott Brozell (Wed Aug 15 2018 - 10:48:41 PDT)
    - Re: [AMBER] checkmolecule.c John Kulp (Thu Aug 16 2018 - 05:35:27 PDT)
[AMBER] Speeding up sqm, PM6 vs AM1 for am1-bcc John L. Kulp, Jr. (Wed Aug 08 2018 - 06:13:14 PDT)
- Re: [AMBER] Speeding up sqm, PM6 vs AM1 for am1-bcc David A Case (Wed Aug 08 2018 - 11:59:07 PDT)
[AMBER] Amber18 on NVIDIA Quadro Cards mish (Wed Aug 08 2018 - 08:51:02 PDT)
- Re: [AMBER] Amber18 on NVIDIA Quadro Cards Ross Walker (Wed Aug 08 2018 - 09:55:17 PDT)
  - Re: [AMBER] Amber18 on NVIDIA Quadro Cards James Kress (Wed Aug 08 2018 - 10:22:54 PDT)
    - Re: [AMBER] Amber18 on NVIDIA Quadro Cards David Cerutti (Wed Aug 08 2018 - 10:48:01 PDT)
    - Re: [AMBER] Amber18 on NVIDIA Quadro Cards Ross Walker (Wed Aug 08 2018 - 11:53:49 PDT)
    - Re: [AMBER] Amber18 on NVIDIA Quadro Cards James Kress (Wed Aug 08 2018 - 12:13:27 PDT)
    - Re: [AMBER] Amber18 on NVIDIA Quadro Cards mish (Thu Aug 09 2018 - 01:54:41 PDT)
    - Re: [AMBER] Amber18 on NVIDIA Quadro Cards malkeet singh Bahia (Thu Aug 09 2018 - 02:09:27 PDT)
    - Re: [AMBER] Amber18 on NVIDIA Quadro Cards mish (Thu Aug 09 2018 - 02:10:14 PDT)
    - Re: [AMBER] Amber18 on NVIDIA Quadro Cards Ross Walker (Thu Aug 09 2018 - 06:56:20 PDT)
    - Re: [AMBER] Amber18 on NVIDIA Quadro Cards mish (Fri Aug 10 2018 - 04:01:41 PDT)
    - Re: [AMBER] Amber18 on NVIDIA Quadro Cards Ross Walker (Thu Aug 09 2018 - 06:40:16 PDT)
    - Re: [AMBER] Amber18 on NVIDIA Quadro Cards Ross Walker (Wed Aug 08 2018 - 11:52:50 PDT)
[AMBER] Erreneous PMF Stefan Ivanov (Wed Aug 08 2018 - 23:21:14 PDT)
- Re: [AMBER] Erreneous PMF Dickson, Callum (Thu Aug 09 2018 - 06:21:22 PDT)
  - Re: [AMBER] Erreneous PMF Stefan Ivanov (Thu Aug 09 2018 - 18:31:15 PDT)
    - Re: [AMBER] Erreneous PMF Dickson, Callum (Fri Aug 10 2018 - 10:53:16 PDT)
    - Re: [AMBER] Erreneous PMF Stefan Ivanov (Fri Aug 10 2018 - 16:57:20 PDT)
[AMBER] how to install PTRAJ and CPPTRAJ Subrata Paul (Thu Aug 09 2018 - 00:17:30 PDT)
- Re: [AMBER] how to install PTRAJ and CPPTRAJ Rodrigo Galindo-Murillo (Thu Aug 09 2018 - 00:27:39 PDT)
  - Re: [AMBER] how to install PTRAJ and CPPTRAJ Subrata Paul (Thu Aug 09 2018 - 00:36:39 PDT)
    - Re: [AMBER] how to install PTRAJ and CPPTRAJ Daniel Roe (Thu Aug 09 2018 - 06:30:08 PDT)
[AMBER] Cpptraj not working Subrata Paul (Thu Aug 09 2018 - 03:38:53 PDT)
- Re: [AMBER] Cpptraj not working Marcelo Andrade Chagas (Thu Aug 09 2018 - 04:52:16 PDT)
  - Re: [AMBER] Cpptraj not working Subrata Paul (Thu Aug 09 2018 - 09:33:42 PDT)
- Re: [AMBER] Cpptraj not working Daniel Roe (Thu Aug 09 2018 - 09:37:09 PDT)
[AMBER] mistake in source-code in egb.F90 Johannes Kalliauer (Thu Aug 09 2018 - 04:15:45 PDT)
[AMBER] PrmtopError: Inconsistent charge definition for atom Santanu Santra (Thu Aug 09 2018 - 06:40:08 PDT)
- Re: [AMBER] PrmtopError: Inconsistent charge definition for atom Jason Swails (Tue Aug 14 2018 - 19:27:45 PDT)
[AMBER] miRNA-mRNA structure / NAB Atila Petrosian (Thu Aug 09 2018 - 08:59:49 PDT)
- Re: [AMBER] miRNA-mRNA structure / NAB David A Case (Thu Aug 09 2018 - 11:18:25 PDT)
[AMBER] cpptraj / ambpdb only selected atoms / residues Simon Kit Sang Chu (Thu Aug 09 2018 - 09:04:36 PDT)
- Re: [AMBER] cpptraj / ambpdb only selected atoms / residues Daniel Roe (Thu Aug 09 2018 - 09:23:54 PDT)
  - Re: [AMBER] cpptraj / ambpdb only selected atoms / residues Simon Kit Sang Chu (Thu Aug 09 2018 - 10:30:54 PDT)
    - Re: [AMBER] cpptraj / ambpdb only selected atoms / residues Daniel Roe (Thu Aug 09 2018 - 11:19:35 PDT)
[AMBER] X-mer analysis or statistics ? Marek Maly (Thu Aug 09 2018 - 16:49:29 PDT)
[AMBER] Amber Installation: MPI Error Aravind Ravichandran (Fri Aug 10 2018 - 00:07:24 PDT)
- Re: [AMBER] Amber Installation: MPI Error David A Case (Fri Aug 10 2018 - 05:10:56 PDT)
[AMBER] command not found Sushi Shilpa (Fri Aug 10 2018 - 04:47:41 PDT)
- Re: [AMBER] command not found David A Case (Fri Aug 10 2018 - 05:14:22 PDT)
[AMBER] How to use filter command to find the structures of high density during PCA analysis? Markowska (Fri Aug 10 2018 - 05:08:41 PDT)
[AMBER] Research Programmers Positions Available João Ribeiro (Fri Aug 10 2018 - 11:35:23 PDT)
[AMBER] sander.MPI running on only one node Leena Aggarwal (Sat Aug 11 2018 - 03:01:15 PDT)
- Re: [AMBER] sander.MPI running on only one node Matias Machado (Sat Aug 11 2018 - 08:20:20 PDT)
[AMBER] # of Coordinates Mismatch in PCA Robert Molt (Sat Aug 11 2018 - 22:04:35 PDT)
- Re: [AMBER] # of Coordinates Mismatch in PCA Kenneth Huang (Sun Aug 12 2018 - 20:21:38 PDT)
  - Re: [AMBER] # of Coordinates Mismatch in PCA Robert Molt (Mon Aug 13 2018 - 18:07:24 PDT)
    - Re: [AMBER] # of Coordinates Mismatch in PCA Kenneth Huang (Tue Aug 14 2018 - 13:20:34 PDT)
- Re: [AMBER] # of Coordinates Mismatch in PCA Jason Swails (Tue Aug 14 2018 - 16:55:05 PDT)
  - Re: [AMBER] # of Coordinates Mismatch in PCA Robert Molt (Tue Aug 14 2018 - 18:21:41 PDT)
  - Re: [AMBER] # of Coordinates Mismatch in PCA Robert Molt (Mon Aug 20 2018 - 13:50:18 PDT)
    - Re: [AMBER] # of Coordinates Mismatch in PCA Jason Swails (Mon Aug 20 2018 - 19:54:01 PDT)
    - Re: [AMBER] # of Coordinates Mismatch in PCA Daniel Roe (Tue Aug 21 2018 - 06:39:30 PDT)
    - Re: [AMBER] # of Coordinates Mismatch in PCA Robert Molt (Tue Aug 21 2018 - 09:09:43 PDT)
    - Re: [AMBER] # of Coordinates Mismatch in PCA Daniel Roe (Tue Aug 21 2018 - 09:29:22 PDT)
    - Re: [AMBER] # of Coordinates Mismatch in PCA Robert Molt (Tue Aug 21 2018 - 09:57:35 PDT)
    - Re: [AMBER] # of Coordinates Mismatch in PCA Jason Swails (Tue Aug 21 2018 - 15:15:07 PDT)
[AMBER] Warning: DISABLING BOX in topology '<name>.pdb'! Dmitry Suplatov (Sun Aug 12 2018 - 04:04:19 PDT)
- Re: [AMBER] Warning: DISABLING BOX in topology '<name>.pdb'! Daniel Roe (Mon Aug 20 2018 - 11:12:05 PDT)
[AMBER] alkyl chain unsaturated bond Vijay Achari (Sun Aug 12 2018 - 14:58:42 PDT)
- Re: [AMBER] alkyl chain unsaturated bond Dickson, Callum (Mon Aug 13 2018 - 07:03:18 PDT)
  - Re: [AMBER] alkyl chain unsaturated bond Vijay Achari (Thu Aug 16 2018 - 05:26:46 PDT)
    - Re: [AMBER] alkyl chain unsaturated bond Dickson, Callum (Thu Aug 16 2018 - 07:16:44 PDT)
[AMBER] MMPBSA.PY 龚乾坤 (Sun Aug 12 2018 - 19:37:37 PDT)
- Re: [AMBER] MMPBSA.PY Jason Swails (Tue Aug 14 2018 - 19:20:33 PDT)
[AMBER] Can I calculate the domain-domain interaction energy using the MMPBSA.py tool? maryam azimzadehirani (Mon Aug 13 2018 - 03:35:43 PDT)
[AMBER] amber18 and amazon aws Luca Codutti (Mon Aug 13 2018 - 08:37:44 PDT)
- Re: [AMBER] amber18 and amazon aws David Cerutti (Mon Aug 13 2018 - 08:57:32 PDT)
- Re: [AMBER] amber18 and amazon aws Luca Codutti (Wed Aug 22 2018 - 03:45:47 PDT)
[AMBER] A question about tleap 龚乾坤 (Tue Aug 14 2018 - 01:01:56 PDT)
- Re: [AMBER] A question about tleap Nisha Amarnath Jonniya (Tue Aug 14 2018 - 01:50:04 PDT)
[AMBER] tleap_protein_preparation_general_rule Antonio Amber Carlesso (Tue Aug 14 2018 - 01:06:07 PDT)
- Re: [AMBER] tleap_protein_preparation_general_rule David A Case (Tue Aug 14 2018 - 07:33:22 PDT)
  - Re: [AMBER] tleap_protein_preparation_general_rule Antonio Amber Carlesso (Tue Aug 14 2018 - 11:20:17 PDT)
    - Re: [AMBER] tleap_protein_preparation_general_rule Matias Machado (Tue Aug 14 2018 - 13:48:08 PDT)
    - Re: [AMBER] tleap_protein_preparation_general_rule Antonio Amber Carlesso (Tue Aug 14 2018 - 14:41:27 PDT)
[AMBER] QM/MM Thermodynamic Integration emanuele (Tue Aug 14 2018 - 03:44:46 PDT)
- Re: [AMBER] QM/MM Thermodynamic Integration David A Case (Tue Aug 14 2018 - 07:37:09 PDT)
  - Re: [AMBER] QM/MM Thermodynamic Integration emanuele falbo (Thu Sep 20 2018 - 04:29:22 PDT)
    - Re: [AMBER] QM/MM Thermodynamic Integration Goetz, Andreas (Thu Sep 20 2018 - 09:50:57 PDT)
- Re: [AMBER] QM/MM Thermodynamic Integration James Kress (Tue Aug 14 2018 - 08:16:45 PDT)
[AMBER] Problem with QMMM with Amber/Gaussian interface. Sadra Aghajani (Tue Aug 14 2018 - 20:53:47 PDT)
- Re: [AMBER] Problem with QMMM with Amber/Gaussian interface. Goetz, Andreas (Tue Aug 14 2018 - 22:33:57 PDT)
[AMBER] HOW to type a free CYS molecule MinYuan (Wed Aug 15 2018 - 06:57:13 PDT)
- Re: [AMBER] HOW to type a free CYS molecule David A Case (Wed Aug 15 2018 - 09:48:56 PDT)
  - Re: [AMBER] HOW to type a free CYS molecule MinYuan (Wed Aug 15 2018 - 19:26:00 PDT)
- Re: [AMBER] HOW to type a free CYS molecule Matias Machado (Wed Aug 15 2018 - 14:59:18 PDT)
  - Re: [AMBER] HOW to type a free CYS molecule MinYuan (Wed Aug 15 2018 - 19:38:04 PDT)
[AMBER] Multiple trajectory analysis with CPPTRAJ and getting output for each of them separately Luka Bilić (Thu Aug 16 2018 - 00:06:23 PDT)
- Re: [AMBER] Multiple trajectory analysis with CPPTRAJ and getting output for each of them separately Daniel Roe (Mon Aug 20 2018 - 11:07:24 PDT)
[AMBER] implement_revised_RNA_force_field_general rule? Antonio Amber Carlesso (Thu Aug 16 2018 - 01:57:47 PDT)
- Re: [AMBER] implement_revised_RNA_force_field_general rule? Matias Machado (Thu Aug 16 2018 - 08:09:58 PDT)
- Re: [AMBER] implement_revised_RNA_force_field_general rule? David A Case (Thu Aug 16 2018 - 08:57:49 PDT)
  - Re: [AMBER] implement_revised_RNA_force_field_general rule? Antonio Amber Carlesso (Sat Aug 18 2018 - 09:59:45 PDT)
    - Re: [AMBER] implement_revised_RNA_force_field_general rule? David A Case (Sat Aug 18 2018 - 17:01:22 PDT)
    - Re: [AMBER] implement_revised_RNA_force_field_general rule? Antonio Amber Carlesso (Sun Aug 19 2018 - 04:41:52 PDT)
[AMBER] cpptraj segmentation fault when using avgout in cluster Charo del Genio (Thu Aug 16 2018 - 03:55:11 PDT)
- Re: [AMBER] cpptraj segmentation fault when using avgout in cluster Daniel Roe (Tue Aug 21 2018 - 08:27:08 PDT)
  - Re: [AMBER] cpptraj segmentation fault when using avgout in cluster Charo del Genio (Tue Aug 21 2018 - 10:21:36 PDT)
  - Re: [AMBER] cpptraj segmentation fault when using avgout in cluster Charo del Genio (Mon Sep 03 2018 - 07:07:27 PDT)
[AMBER] AM1BCC challenge with atomic types recognition and convertion of .ac to .mol2 Sergey Samsonov (Thu Aug 16 2018 - 08:05:29 PDT)
- Re: [AMBER] AM1BCC challenge with atomic types recognition and convertion of .ac to .mol2 David A Case (Thu Aug 16 2018 - 08:46:20 PDT)
  - Re: [AMBER] AM1BCC challenge with atomic types recognition and convertion of .ac to .mol2 Sergey Samsonov (Fri Aug 17 2018 - 00:03:21 PDT)
[AMBER] About calculating entropy in MM_PB/GBSA using mm_pbsa.pl 龚乾坤 (Fri Aug 17 2018 - 00:17:32 PDT)
- Re: [AMBER] About calculating entropy in MM_PB/GBSA using mm_pbsa.pl David A Case (Fri Aug 17 2018 - 06:12:45 PDT)
[AMBER] MMPBSA.PY 龚乾坤 (Fri Aug 17 2018 - 00:21:07 PDT)
[AMBER] Where is the source code adjusting the size of the periodic boundary condition box in NPT ensemble ? jinfeng liu (Fri Aug 17 2018 - 01:15:40 PDT)
- Re: [AMBER] Where is the source code adjusting the size of the periodic boundary condition box in NPT ensemble ? David A Case (Fri Aug 17 2018 - 06:34:22 PDT)
  - Re: [AMBER] Where is the source code adjusting the size of the periodic boundary condition box in NPT ensemble ? jinfeng liu (Fri Aug 17 2018 - 07:04:58 PDT)
[AMBER] Mutation Free Energy hosein geraili (Fri Aug 17 2018 - 03:28:22 PDT)
- Re: [AMBER] Mutation Free Energy David A Case (Fri Aug 17 2018 - 06:21:48 PDT)
[AMBER] TLEAP script Keiran Corbett (Fri Aug 17 2018 - 03:58:59 PDT)
- Re: [AMBER] TLEAP script David A Case (Fri Aug 17 2018 - 06:29:37 PDT)
  - Re: [AMBER] TLEAP script Keiran Corbett (Mon Aug 20 2018 - 02:20:34 PDT)
[AMBER] Error in Running heating in GPU enabled AMBER kuldeep singh (Fri Aug 17 2018 - 10:50:02 PDT)
- Re: [AMBER] Error in Running heating in GPU enabled AMBER David A Case (Fri Aug 17 2018 - 18:28:41 PDT)
[AMBER] SCF convergence problems and write density matrix Anaid Flores (Fri Aug 17 2018 - 15:08:39 PDT)
- Re: [AMBER] SCF convergence problems and write density matrix Gerald Monard (Sat Aug 18 2018 - 00:55:01 PDT)
  - Re: [AMBER] SCF convergence problems and write density matrix Sadra Aghajani (Sat Aug 18 2018 - 09:34:38 PDT)
  - Re: [AMBER] SCF convergence problems and write density matrix Anaid Flores (Sun Aug 19 2018 - 20:57:22 PDT)
[AMBER] update to Amber18's pmemd.cuda code David A Case (Sat Aug 18 2018 - 06:08:35 PDT)
[AMBER] How to convert QM parameters to AMBER force field parameters MinYuan (Sat Aug 18 2018 - 06:40:40 PDT)
[AMBER] cpptraj and ptraj not installed Subrata Paul (Sun Aug 19 2018 - 04:49:54 PDT)
- Re: [AMBER] cpptraj and ptraj not installed Hai Nguyen (Sun Aug 19 2018 - 08:04:40 PDT)
[AMBER] Scripting Bash to tleap Keiran Corbett (Mon Aug 20 2018 - 02:39:32 PDT)
- Re: [AMBER] Scripting Bash to tleap David A Case (Mon Aug 20 2018 - 04:39:57 PDT)
- Re: [AMBER] Scripting Bash to tleap Wesley Michael Botello-Smith (Mon Aug 20 2018 - 05:45:04 PDT)
  - Re: [AMBER] Scripting Bash to tleap Wesley Michael Botello-Smith (Mon Aug 20 2018 - 05:48:50 PDT)
[AMBER] metalParm2.xml or metalParm.xml Seibold, Steve Allan (Mon Aug 20 2018 - 08:47:27 PDT)
- Re: [AMBER] metalParm2.xml or metalParm.xml Pengfei Li (Sat Sep 08 2018 - 11:46:38 PDT)
[AMBER] How to calculate SASA for an arbitrary solvent Kasprzak, Wojciech (NIH/NCI) [C] (Mon Aug 20 2018 - 13:37:19 PDT)
[AMBER] Umbrella sampling run error Rakesh Srivastava (Mon Aug 20 2018 - 21:43:37 PDT)
- Re: [AMBER] Umbrella sampling run error Bill Ross (Mon Aug 20 2018 - 22:44:46 PDT)
  - Re: [AMBER] Umbrella sampling run error Rakesh Srivastava (Mon Aug 20 2018 - 23:23:28 PDT)
[AMBER] ASMD for decrease in distance between ligand and catalytic site sangita kachhap (Tue Aug 21 2018 - 03:42:04 PDT)
- Re: [AMBER] ASMD for decrease in distance between ligand and catalytic site Feng Pan (Tue Aug 21 2018 - 20:35:23 PDT)
  - Re: [AMBER] ASMD for decrease in distance between ligand and catalytic site sangita kachhap (Wed Aug 22 2018 - 03:59:22 PDT)
[AMBER] H-bond between the substrate molecule and protein in the MD traj Meng Wu (Wed Aug 22 2018 - 01:18:13 PDT)
- Re: [AMBER] H-bond between the substrate molecule and protein in the MD traj Daniel Roe (Thu Aug 30 2018 - 06:34:51 PDT)
[AMBER] Umbrella sampling rst file error M RCC (Wed Aug 22 2018 - 12:02:38 PDT)
- Re: [AMBER] Umbrella sampling rst file error David A Case (Thu Aug 23 2018 - 05:04:02 PDT)
[AMBER] restraintmask input setup Lod King (Wed Aug 22 2018 - 18:26:43 PDT)
- Re: [AMBER] restraintmask input setup David A Case (Thu Aug 23 2018 - 05:10:58 PDT)
[AMBER] Need help regarding Lifetime Curve of Hydrogen bond analysis Bharat Manna (Wed Aug 22 2018 - 22:32:25 PDT)
- Re: [AMBER] Need help regarding Lifetime Curve of Hydrogen bond analysis Daniel Roe (Thu Aug 30 2018 - 06:15:52 PDT)
[AMBER] Problems with constant pH production step Helena Damtoft Tjørnelund (Thu Aug 23 2018 - 01:18:27 PDT)
- Re: [AMBER] Problems with constant pH production step Bill Ross (Thu Aug 23 2018 - 01:25:46 PDT)
- Re: [AMBER] Problems with constant pH production step Jason Swails (Thu Aug 23 2018 - 07:48:45 PDT)
  - Re: [AMBER] Problems with constant pH production step Helena Damtoft Tjørnelund (Thu Aug 23 2018 - 23:41:15 PDT)
    - Re: [AMBER] Problems with constant pH production step Cruzeiro,Vinicius Wilian D (Fri Aug 24 2018 - 01:52:42 PDT)
    - Re: [AMBER] Problems with constant pH production step Helena Damtoft Tjørnelund (Fri Aug 24 2018 - 02:47:18 PDT)
    - Re: [AMBER] Problems with constant pH production step Cruzeiro,Vinicius Wilian D (Fri Aug 24 2018 - 03:11:30 PDT)
    - Re: [AMBER] Problems with constant pH production step Jason Swails (Fri Aug 24 2018 - 07:25:12 PDT)
[AMBER] Need help regarding calculation of Coordination number from RDF Profile Bharat Manna (Fri Aug 24 2018 - 03:21:02 PDT)
- Re: [AMBER] Need help regarding calculation of Coordination number from RDF Profile Daniel Roe (Fri Aug 24 2018 - 10:02:34 PDT)
- Re: [AMBER] Need help regarding calculation of Coordination number from RDF Profile Bharat Manna (Tue Sep 04 2018 - 06:35:59 PDT)
[AMBER] MG Coordination System: Nonbonded Cationic Dummy Model Aravind Ravichandran (Wed Feb 27 153518 - 00:00:00 PST)
[AMBER] Thank you Tai Tze Hong (Fri Aug 24 2018 - 19:10:56 PDT)
- Re: [AMBER] Thank you elias_christoforides (Mon Aug 27 2018 - 06:57:28 PDT)
[AMBER] Amber18 error: an illegal memory access was encountered launching kernel kNLSkinTest 李耀 (Sat Aug 25 2018 - 06:22:32 PDT)
- Re: [AMBER] Amber18 error: an illegal memory access was encountered launching kernel kNLSkinTest accuratefreeenergy.gmail.com (Sat Aug 25 2018 - 06:30:40 PDT)
- Re: [AMBER] Amber18 error: an illegal memory access was encountered launching kernel kNLSkinTest David A Case (Sun Aug 26 2018 - 06:10:01 PDT)
[AMBER] NCSU_SMD for protein-ligand complex pulling M RCC (Sat Aug 25 2018 - 08:15:08 PDT)
- Re: [AMBER] NCSU_SMD for protein-ligand complex pulling Feng Pan (Sat Aug 25 2018 - 09:11:21 PDT)
- Re: [AMBER] NCSU_SMD for protein-ligand complex pulling M RCC (Sat Sep 01 2018 - 03:25:20 PDT)
[AMBER] MG Coordination System: Nonbonded Cationic Dummy Model Aravind Ravichandran (Sun Aug 26 2018 - 22:57:15 PDT)
- Re: [AMBER] MG Coordination System: Nonbonded Cationic Dummy Model Qinghua Liao (Mon Aug 27 2018 - 02:29:26 PDT)
[AMBER] GIST calculation M RCC (Sun Aug 26 2018 - 23:32:07 PDT)
- Re: [AMBER] GIST calculation Steven Ramsey (Tue Aug 28 2018 - 08:31:02 PDT)
- Re: [AMBER] GIST calculation Daniel Roe (Tue Aug 28 2018 - 09:30:00 PDT)
[AMBER] Amber 18 targeted MD errorin input::atommask.f::pop_evalstack stack underflow 李耀 (Mon Aug 27 2018 - 00:24:27 PDT)
- Re: [AMBER] Amber 18 targeted MD errorin input::atommask.f::pop_evalstack stack underflow Daniel Roe (Mon Aug 27 2018 - 09:38:45 PDT)
[AMBER] Error: System density has likely changed M RCC (Mon Aug 27 2018 - 02:40:07 PDT)
- Re: [AMBER] Error: System density has likely changed David A Case (Mon Aug 27 2018 - 05:08:53 PDT)
  - Re: [AMBER] Error: System density has likely changed David Cerutti (Mon Aug 27 2018 - 10:49:14 PDT)
    - Re: [AMBER] Error: System density has likely changed David Cerutti (Mon Aug 27 2018 - 10:51:49 PDT)
[AMBER] A part of protein molecule moving out of the box Sanjib Paul (Sun Aug 26 2018 - 23:16:36 PDT)
- Re: [AMBER] A part of protein molecule moving out of the box Carlos Simmerling (Mon Aug 27 2018 - 05:49:48 PDT)
[AMBER] Best Methods Leon Hardy (Mon Aug 27 2018 - 06:01:58 PDT)
- Re: [AMBER] Best Methods Alechania Misturini (Mon Aug 27 2018 - 09:28:00 PDT)
[AMBER] Are there any forcefield present of bio-organic polyphosphate in AMBER ?? Saikat Pal (Mon Aug 27 2018 - 08:10:06 PDT)
- Re: [AMBER] Are there any forcefield present of bio-organic polyphosphate in AMBER ?? Alechania Misturini (Mon Aug 27 2018 - 08:52:21 PDT)
[AMBER] Amber16 installation error Renato Araujo (Mon Aug 27 2018 - 16:50:44 PDT)
- Re: [AMBER] Amber16 installation error Bill Ross (Mon Aug 27 2018 - 17:07:35 PDT)
  - Re: [AMBER] Amber16 installation error Renato Araujo (Mon Aug 27 2018 - 17:13:47 PDT)
  - Re: [AMBER] Amber16 installation error Renato Araujo (Mon Aug 27 2018 - 17:35:08 PDT)
- Re: [AMBER] Amber16 installation error David A Case (Mon Aug 27 2018 - 18:04:03 PDT)
[AMBER] Protein_ligand_preparation_general_rule Antonio Amber Carlesso (Tue Aug 28 2018 - 05:59:28 PDT)
- Re: [AMBER] Protein_ligand_preparation_general_rule Keiran Corbett (Tue Aug 28 2018 - 06:41:51 PDT)
- Re: [AMBER] Protein_ligand_preparation_general_rule David A Case (Tue Aug 28 2018 - 14:35:25 PDT)
  - Re: [AMBER] Protein_ligand_preparation_general_rule Antonio Amber Carlesso (Wed Aug 29 2018 - 02:56:00 PDT)
[AMBER] R.E.D. Server is down Anthony Bogetti (Tue Aug 28 2018 - 10:13:00 PDT)
- Re: [AMBER] R.E.D. Server is down Stéphane Téletchéa (Thu Oct 04 2018 - 07:43:25 PDT)
[AMBER] I want to calculate electrostatic and van der Waals energy Saikat Pal (Wed Aug 29 2018 - 03:44:03 PDT)
[AMBER] How to define the speed of pulling ligand in SMD? M RCC (Wed Aug 29 2018 - 06:39:41 PDT)
[AMBER] RED SERVER DOWN Corinn Durham (Wed Aug 29 2018 - 09:44:23 PDT)
[AMBER] The R.E.D. server is down Bellesis, Andrew G (Wed Aug 29 2018 - 09:36:01 PDT)
[AMBER] Heating error in complex sandeep singh (Wed Aug 29 2018 - 12:52:45 PDT)
- Re: [AMBER] Heating error in complex David A Case (Thu Aug 30 2018 - 05:55:57 PDT)
- Re: [AMBER] Heating error in complex sandeep singh (Thu Aug 30 2018 - 13:37:23 PDT)
  - Re: [AMBER] Heating error in complex David A Case (Fri Aug 31 2018 - 06:47:36 PDT)
[AMBER] How to use cpptraj to wrap protein Yang, Tianyi (Wed Aug 29 2018 - 17:12:19 PDT)
- Re: [AMBER] How to use cpptraj to wrap protein Daniel Roe (Thu Aug 30 2018 - 05:59:36 PDT)
  - Re: [AMBER] How to use cpptraj to wrap protein Yang, Tianyi (Fri Aug 31 2018 - 13:04:10 PDT)
    - Re: [AMBER] How to use cpptraj to wrap protein Daniel Roe (Fri Aug 31 2018 - 16:31:57 PDT)
[AMBER] Steered molecular dynamics..... pulling force is not decreasing M RCC (Thu Aug 30 2018 - 03:01:51 PDT)
- Re: [AMBER] Steered molecular dynamics..... pulling force is not decreasing Feng Pan (Fri Aug 31 2018 - 15:14:33 PDT)
[AMBER] CPPTRAJ issues parsing NETCDF RST file Gustaf Olsson (Thu Aug 30 2018 - 05:20:09 PDT)
- Re: [AMBER] CPPTRAJ issues parsing NETCDF RST file Daniel Roe (Thu Aug 30 2018 - 05:46:59 PDT)
  - Re: [AMBER] CPPTRAJ issues parsing NETCDF RST file Gustaf Olsson (Thu Aug 30 2018 - 07:35:15 PDT)
    - Re: [AMBER] CPPTRAJ issues parsing NETCDF RST file Daniel Roe (Thu Aug 30 2018 - 08:43:43 PDT)
    - Re: [AMBER] CPPTRAJ issues parsing NETCDF RST file Gustaf Olsson (Thu Aug 30 2018 - 23:20:07 PDT)
[AMBER] Normal mode calculation on a truncated system Marko Tomin (Thu Aug 30 2018 - 08:13:33 PDT)
- Re: [AMBER] Normal mode calculation on a truncated system David A Case (Mon Sep 03 2018 - 04:46:07 PDT)
[AMBER] minimization restrain in Qm-mm/MD Thakur, Abhishek (Thu Aug 30 2018 - 12:05:50 PDT)
- Re: [AMBER] minimization restrain in Qm-mm/MD Szymon Żaczek (Thu Aug 30 2018 - 13:29:30 PDT)
[AMBER] Distance HH TIP3P David Sáez (Fri Aug 31 2018 - 12:55:49 PDT)
- Re: [AMBER] Distance HH TIP3P David A Case (Mon Sep 03 2018 - 04:47:40 PDT)
[AMBER] KDE analysis, (P) greater than one Mac Kevin Braza (Fri Aug 31 2018 - 20:24:19 PDT)
- Re: [AMBER] KDE analysis, (P) greater than one Daniel Roe (Sat Sep 01 2018 - 05:48:25 PDT)
  - Re: [AMBER] KDE analysis, (P) greater than one Adrian Roitberg (Mon Sep 03 2018 - 06:34:24 PDT)
    - Re: [AMBER] KDE analysis, (P) greater than one Mac Kevin Braza (Mon Sep 03 2018 - 18:25:25 PDT)
    - Re: [AMBER] KDE analysis, (P) greater than one Jason Swails (Wed Sep 05 2018 - 20:49:34 PDT)
[AMBER] Constant velocity pulling in SMD M RCC (Fri Aug 31 2018 - 23:49:50 PDT)
[AMBER] Temperature calculaton by CPPTRAJ Ikuo KURISAKI (Sat Sep 01 2018 - 01:34:48 PDT)
- Re: [AMBER] Temperature calculaton by CPPTRAJ Daniel Roe (Sat Sep 01 2018 - 05:46:25 PDT)
[AMBER] Temperature calculaton by CPPTRAJ Ikuo KURISAKI (Sat Sep 01 2018 - 03:32:08 PDT)
- Re: [AMBER] Temperature calculaton by CPPTRAJ Ikuo KURISAKI (Mon Sep 03 2018 - 06:38:34 PDT)
[AMBER] Constant pH and Redox Potential MD tutorial Cruzeiro,Vinicius Wilian D (Sat Sep 01 2018 - 05:41:44 PDT)
[AMBER] Regarding error in MCPB.py dhaval patel (Sun Sep 02 2018 - 02:18:23 PDT)
- Re: [AMBER] Regarding error in MCPB.py Pengfei Li (Tue Sep 04 2018 - 07:12:38 PDT)
[AMBER] Help in COM pulling M RCC (Sun Sep 02 2018 - 09:25:52 PDT)
[AMBER] Subtracting the forces from harmonic restraints Nikolay N. Kuzmich (Mon Sep 03 2018 - 01:52:57 PDT)
[AMBER] Format of cpptraj pairwise distance file when clustering Charo del Genio (Mon Sep 03 2018 - 07:18:02 PDT)
- Re: [AMBER] Format of cpptraj pairwise distance file when clustering Daniel Roe (Mon Sep 03 2018 - 11:49:34 PDT)
  - Re: [AMBER] Format of cpptraj pairwise distance file when clustering Charo del Genio (Tue Sep 04 2018 - 01:00:48 PDT)
    - Re: [AMBER] Format of cpptraj pairwise distance file when clustering Daniel Roe (Tue Sep 04 2018 - 08:02:53 PDT)
    - Re: [AMBER] Format of cpptraj pairwise distance file when clustering Daniel Roe (Tue Sep 04 2018 - 12:26:16 PDT)
[AMBER] parameterizing the covalently bonded ligand hosein geraili (Mon Sep 03 2018 - 09:25:24 PDT)
[AMBER] Coordinate messed up after tleap set box Simon Kit Sang Chu (Mon Sep 03 2018 - 12:31:32 PDT)
- Re: [AMBER] Coordinate messed up after tleap set box David A Case (Tue Sep 04 2018 - 05:28:36 PDT)
  - Re: [AMBER] Coordinate messed up after tleap set box Simon Kit Sang Chu (Tue Sep 04 2018 - 09:58:33 PDT)
    - Re: [AMBER] Coordinate messed up after tleap set box David A Case (Tue Sep 04 2018 - 10:37:20 PDT)
    - Re: [AMBER] Coordinate messed up after tleap set box Simon Kit Sang Chu (Tue Sep 04 2018 - 11:39:48 PDT)
[AMBER] Regarding output file in REMD Rajarshi Roy (Mon Sep 03 2018 - 21:47:10 PDT)
[AMBER] [david.case.rutgers.edu: Re: Coordinate messed up after tleap set box] David A Case (Tue Sep 04 2018 - 05:31:36 PDT)
[AMBER] Reg: antechamber net charge calculation -nc Samdani A (Tue Sep 04 2018 - 07:22:40 PDT)
- Re: [AMBER] Reg: antechamber net charge calculation -nc David A Case (Tue Sep 04 2018 - 10:46:58 PDT)
[AMBER] GTX-2080 benchmarks Piotr Fajer (Tue Sep 04 2018 - 10:04:49 PDT)
- Re: [AMBER] GTX-2080 benchmarks David Cerutti (Tue Sep 04 2018 - 10:24:06 PDT)
[AMBER] RMS is zero Hadi Rahmaninejad (Tue Sep 04 2018 - 13:34:23 PDT)
- Re: [AMBER] RMS is zero Stephan Schott (Tue Sep 04 2018 - 13:58:04 PDT)
  - Re: [AMBER] RMS is zero Hadi Rahmaninejad (Tue Sep 04 2018 - 14:19:08 PDT)
[AMBER] Restraining forces for atoms Nikolay N. Kuzmich (Wed Sep 05 2018 - 01:06:12 PDT)
- Re: [AMBER] Restraining forces for atoms Bill Ross (Wed Sep 05 2018 - 01:17:52 PDT)
- Re: [AMBER] Restraining forces for atoms Nikolay N. Kuzmich (Thu Sep 06 2018 - 05:46:42 PDT)
  - Re: [AMBER] Restraining forces for atoms Bill Ross (Thu Sep 06 2018 - 09:07:23 PDT)
[AMBER] Fwd: Problem with energy minimization sander.MPI maryam azimzadehirani (Wed Sep 05 2018 - 01:54:14 PDT)
- Re: [AMBER] Fwd: Problem with energy minimization sander.MPI Bill Ross (Wed Sep 05 2018 - 02:03:25 PDT)
  - Re: [AMBER] Fwd: Problem with energy minimization sander.MPI maryam azimzadehirani (Wed Sep 05 2018 - 02:34:17 PDT)
    - Re: [AMBER] Fwd: Problem with energy minimization sander.MPI David A Case (Wed Sep 05 2018 - 05:10:03 PDT)
    - Re: [AMBER] Fwd: Problem with energy minimization sander.MPI maryam azimzadehirani (Wed Sep 05 2018 - 07:03:20 PDT)
[AMBER] covalently bonded ligand hosein geraili (Wed Sep 05 2018 - 05:40:54 PDT)
- Re: [AMBER] covalently bonded ligand Pengfei Li (Sat Sep 08 2018 - 11:30:14 PDT)
[AMBER] MCPB.py error (not reading chk file) Sushi Shilpa (Thu Sep 06 2018 - 01:58:22 PDT)
- Re: [AMBER] MCPB.py error (not reading chk file) Pengfei Li (Sat Sep 08 2018 - 11:38:13 PDT)
[AMBER] Couldn't find VdW parameters Sushi Shilpa (Thu Sep 06 2018 - 05:20:02 PDT)
- Re: [AMBER] Couldn't find VdW parameters Jason Swails (Thu Sep 06 2018 - 05:56:23 PDT)
  - Re: [AMBER] Couldn't find VdW parameters Sushi Shilpa (Fri Sep 07 2018 - 01:51:10 PDT)
[AMBER] Energy uints in mden file and mdout_analyzer.py Meng Wu (Thu Sep 06 2018 - 06:17:41 PDT)
- Re: [AMBER] Energy uints in mden file and mdout_analyzer.py David A Case (Thu Sep 06 2018 - 11:59:39 PDT)
- Re: [AMBER] Energy uints in mden file and mdout_analyzer.py Meng Wu (Thu Sep 06 2018 - 19:14:59 PDT)
  - Re: [AMBER] Energy uints in mden file and mdout_analyzer.py Meng Wu (Fri Sep 07 2018 - 20:42:52 PDT)
[AMBER] parmed pdb to crd Neha Gandhi (Fri Sep 07 2018 - 02:04:34 PDT)
- Re: [AMBER] parmed pdb to crd Jason Swails (Fri Sep 07 2018 - 20:09:32 PDT)
[AMBER] CUDA and driver version for Nvidia Titan Black and Titan Z GPUs cluster Markowska (Fri Sep 07 2018 - 10:37:06 PDT)
- Re: [AMBER] CUDA and driver version for Nvidia Titan Black and Titan Z GPUs cluster David Cerutti (Fri Sep 07 2018 - 10:46:41 PDT)
  - Re: [AMBER] CUDA and driver version for Nvidia Titan Black and Titan Z GPUs cluster Markowska (Fri Sep 07 2018 - 11:17:42 PDT)
- Re: [AMBER] CUDA and driver version for Nvidia Titan Black and Titan Z GPUs cluster David A Case (Mon Sep 10 2018 - 08:20:55 PDT)
  - Re: [AMBER] CUDA and driver version for Nvidia Titan Black and Titan Z GPUs cluster Ryan Novosielski (Mon Sep 10 2018 - 13:33:09 PDT)
    - Re: [AMBER] CUDA and driver version for Nvidia Titan Black and Titan Z GPUs cluster Ross Walker (Mon Sep 10 2018 - 15:12:49 PDT)
[AMBER] Leap: Nuleotides addition Aravind Ravichandran (Sat Sep 08 2018 - 04:32:36 PDT)
- Re: [AMBER] Leap: Nuleotides addition David A Case (Sat Sep 08 2018 - 07:31:39 PDT)
[AMBER] A error about Minimize structure and calc entropy IN MM_PBSA.PL 龚乾坤 (Tue Sep 11 2018 - 05:26:36 PDT)
- Re: [AMBER] A error about Minimize structure and calc entropy IN MM_PBSA.PL David A Case (Tue Sep 11 2018 - 09:11:25 PDT)
  - Re: [AMBER] A error about Minimize structure and calc entropy IN MM_PBSA.PL 龚乾坤 (Tue Sep 11 2018 - 18:06:48 PDT)
- Re: [AMBER] A error about Minimize structure and calc entropy IN MM_PBSA.PL 龚乾坤 (Tue Sep 11 2018 - 23:59:41 PDT)
[AMBER] RMS rotate about z-axis only Wesley Michael Botello-Smith (Tue Sep 11 2018 - 13:02:49 PDT)
- Re: [AMBER] RMS rotate about z-axis only Hai Nguyen (Fri Sep 14 2018 - 08:07:01 PDT)
- Re: [AMBER] RMS rotate about z-axis only Daniel Roe (Thu Sep 20 2018 - 08:25:03 PDT)
[AMBER] Question about configure Ambertool18 on Mac tang.xiaping.outlook.com (Tue Sep 11 2018 - 22:35:25 PDT)
- Re: [AMBER] Question about configure Ambertool18 on Mac Bill Ross (Tue Sep 11 2018 - 22:46:11 PDT)
  - Re: [AMBER] Question about configure Ambertool18 on Mac tang.xiaping.outlook.com (Wed Sep 12 2018 - 00:29:08 PDT)
    - Re: [AMBER] Question about configure Ambertool18 on Mac Bill Ross (Wed Sep 12 2018 - 00:38:43 PDT)
    - Re: [AMBER] Question about configure Ambertool18 on Mac tang.xiaping.outlook.com (Wed Sep 12 2018 - 00:50:49 PDT)
    - Re: [AMBER] Question about configure Ambertool18 on Mac Bill Ross (Wed Sep 12 2018 - 01:06:26 PDT)
- Re: [AMBER] Question about configure Ambertool18 on Mac David A Case (Wed Sep 12 2018 - 05:08:42 PDT)
[AMBER] Query for umbrella sampling Saikat Pal (Wed Sep 12 2018 - 00:09:01 PDT)
- [AMBER] Query for umbrella sampling Saikat Pal (Wed Sep 12 2018 - 13:36:57 PDT)
  - Re: [AMBER] Query for umbrella sampling Bill Ross (Wed Sep 12 2018 - 13:41:32 PDT)
[AMBER] Residue mutation and side chains Benjamin Clausen (Wed Sep 12 2018 - 04:01:50 PDT)
- Re: [AMBER] Residue mutation and side chains Carlos Simmerling (Wed Sep 12 2018 - 09:25:16 PDT)
  - Re: [AMBER] Residue mutation and side chains Benjamin Clausen (Thu Sep 13 2018 - 00:15:57 PDT)
    - Re: [AMBER] Residue mutation and side chains Bill Ross (Thu Sep 13 2018 - 00:23:03 PDT)
    - Re: [AMBER] Residue mutation and side chains Carlos Simmerling (Thu Sep 13 2018 - 08:41:48 PDT)
[AMBER] difference of distances using cpptraj in free energy plot Nisha Amarnath Jonniya (Wed Sep 12 2018 - 05:07:10 PDT)
- Re: [AMBER] difference of distances using cpptraj in free energy plot Daniel Roe (Wed Sep 12 2018 - 10:55:23 PDT)
  - Re: [AMBER] difference of distances using cpptraj in free energy plot Nisha Amarnath Jonniya (Thu Sep 13 2018 - 00:34:53 PDT)
[AMBER] CPPTRAJ: extracting the restraining forces Nikolay N. Kuzmich (Wed Sep 12 2018 - 06:02:47 PDT)
- Re: [AMBER] CPPTRAJ: extracting the restraining forces Daniel Roe (Thu Sep 20 2018 - 08:45:32 PDT)
[AMBER] A confusion about the binding energy calculated by pbsa with implicit membrane model 高振梅 (Wed Sep 12 2018 - 06:15:50 PDT)
- Re: [AMBER] A confusion about the binding energy calculated by pbsa with implicit membrane model Ray Luo (Wed Sep 12 2018 - 10:35:32 PDT)
[AMBER] Amber constraint SMD 李耀 (Wed Sep 12 2018 - 08:17:30 PDT)
[AMBER] more about gfortran8.2 and clang9.1: no cpptraj problems here David A Case (Wed Sep 12 2018 - 13:28:34 PDT)
- Re: [AMBER] more about gfortran8.2 and clang9.1: no cpptraj problems here Bill Ross (Wed Sep 12 2018 - 13:35:08 PDT)
  - Re: [AMBER] more about gfortran8.2 and clang9.1: no cpptraj problems here Bill Ross (Wed Sep 12 2018 - 13:38:55 PDT)
[AMBER] H-bond between the substrate molecule and protein in the MD traj Meng Wu (Wed Sep 12 2018 - 18:30:49 PDT)
- Re: [AMBER] H-bond between the substrate molecule and protein in the MD traj Gustaf Olsson (Wed Sep 12 2018 - 23:16:14 PDT)
- Re: [AMBER] H-bond between the substrate molecule and protein in the MD traj Daniel Roe (Thu Sep 13 2018 - 06:09:18 PDT)
[AMBER] Some questions about mmpbsa.py 龚乾坤 (Thu Sep 13 2018 - 00:01:12 PDT)
- Re: [AMBER] Some questions about mmpbsa.py David A Case (Thu Sep 13 2018 - 04:32:04 PDT)
[AMBER] Compression of CDF coordinate files to gzip AMBER18. DHEERAJ CHITARA (Thu Sep 13 2018 - 01:12:44 PDT)
- Re: [AMBER] Compression of CDF coordinate files to gzip AMBER18. David A Case (Thu Sep 13 2018 - 04:39:00 PDT)
[AMBER] Distance based energy calculation MOHD HOMAIDUR RAHMAN (Thu Sep 13 2018 - 06:45:52 PDT)
- [AMBER] Fwd: Distance based energy calculation MOHD HOMAIDUR RAHMAN (Tue Sep 18 2018 - 23:32:03 PDT)
- Re: [AMBER] Distance based energy calculation Daniel Roe (Thu Sep 20 2018 - 08:13:41 PDT)
[AMBER] How to calculate Coordination number from RDF Profile using CPPTRAJ ? Bharat Manna (Thu Sep 13 2018 - 11:48:48 PDT)
- Re: [AMBER] How to calculate Coordination number from RDF Profile using CPPTRAJ ? Matias Machado (Sun Sep 16 2018 - 07:50:47 PDT)
- Re: [AMBER] How to calculate Coordination number from RDF Profile using CPPTRAJ ? Bharat Manna (Thu Sep 20 2018 - 20:30:19 PDT)
[AMBER] a error about MMPBSA.PY 龚乾坤 (Thu Sep 13 2018 - 17:29:07 PDT)
- Re: [AMBER] a error about MMPBSA.PY David A Case (Fri Sep 14 2018 - 05:40:24 PDT)
[AMBER] Query regarding the number of cores for running sander.MPI Leena Aggarwal (Fri Sep 14 2018 - 01:25:42 PDT)
- Re: [AMBER] Query regarding the number of cores for running sander.MPI Stephan Schott (Fri Sep 14 2018 - 01:43:18 PDT)
[AMBER] Question about Amber. Asier Zorrilla (Fri Sep 14 2018 - 05:08:37 PDT)
- Re: [AMBER] Question about Amber. Carlos Simmerling (Fri Sep 14 2018 - 05:17:15 PDT)
- Re: [AMBER] Question about Amber. Adrian Roitberg (Fri Sep 14 2018 - 05:39:51 PDT)
- Re: [AMBER] Question about Amber. David A Case (Fri Sep 14 2018 - 05:53:49 PDT)
  - Re: [AMBER] Question about Amber. Asier Zorrilla (Mon Sep 17 2018 - 01:25:00 PDT)
    - Re: [AMBER] Question about Amber. Bill Ross (Mon Sep 17 2018 - 01:40:01 PDT)
    - Re: [AMBER] Question about Amber. Asier Zorrilla (Fri Sep 21 2018 - 05:00:42 PDT)
[AMBER] A confusion about the binding energy calculated by pbsa with implicit membrane model 高振梅 (Fri Sep 14 2018 - 06:25:56 PDT)
[AMBER] Error in umbrella sampling Saikat Pal (Fri Sep 14 2018 - 07:26:14 PDT)
- Re: [AMBER] Error in umbrella sampling Bill Ross (Fri Sep 14 2018 - 09:47:11 PDT)
  - Re: [AMBER] Error in umbrella sampling Saikat Pal (Mon Sep 17 2018 - 08:50:53 PDT)
    - Re: [AMBER] Error in umbrella sampling David A Case (Mon Sep 17 2018 - 10:10:20 PDT)
    - Re: [AMBER] Error in umbrella sampling Saikat Pal (Mon Sep 17 2018 - 10:23:41 PDT)
    - Re: [AMBER] Error in umbrella sampling Saikat Pal (Tue Sep 18 2018 - 07:30:02 PDT)
[AMBER] Protein "jumping" during SMD run Cory Ayres (Fri Sep 14 2018 - 08:13:16 PDT)
- Re: [AMBER] Protein "jumping" during SMD run Carlos Simmerling (Fri Sep 14 2018 - 13:32:53 PDT)
[AMBER] rdf in one dimmension Hadi Rahmaninejad (Fri Sep 14 2018 - 13:29:25 PDT)
- Re: [AMBER] rdf in one dimmension Tom Kurtzman (Fri Sep 14 2018 - 18:36:17 PDT)
  - Re: [AMBER] rdf in one dimmension Tom Kurtzman (Fri Sep 14 2018 - 18:48:20 PDT)
    - Re: [AMBER] rdf in one dimmension Hadi Rahmaninejad (Sun Sep 16 2018 - 17:32:30 PDT)
    - Re: [AMBER] rdf in one dimmension Daniel Roe (Mon Sep 17 2018 - 04:22:57 PDT)
    - Re: [AMBER] rdf in one dimmension Tom Kurtzman (Mon Sep 17 2018 - 19:49:35 PDT)
[AMBER] why not free QM software？ Albert (Sat Sep 15 2018 - 07:42:01 PDT)
- Re: [AMBER] why not free QM software？ Charles-Alexandre Mattelaer (Sat Sep 15 2018 - 07:47:41 PDT)
- Re: [AMBER] why not free QM software？ Gustavo Seabra (Sun Sep 16 2018 - 11:49:33 PDT)
  - Re: [AMBER] why not free QM software？ Albert (Sun Sep 16 2018 - 12:23:19 PDT)
    - Re: [AMBER] why not free QM software？ Gustavo Seabra (Sun Sep 16 2018 - 12:33:38 PDT)
[AMBER] Newbie question about installing AmberTool18 in Linux (VirtualBox) leifepeterson.sbcglobal.net (Sat Sep 15 2018 - 09:28:16 PDT)
- Re: [AMBER] Newbie question about installing AmberTool18 in Linux (VirtualBox) Hai Nguyen (Sun Sep 16 2018 - 15:00:46 PDT)
[AMBER] Installing fortran in Ubuntu-64 for Sander leifepeterson.sbcglobal.net (Sat Sep 15 2018 - 13:03:50 PDT)
- Re: [AMBER] Installing fortran in Ubuntu-64 for Sander Dwight McGee (Sat Sep 15 2018 - 17:35:31 PDT)
[AMBER] RESOLVED: Installing fortran in Ubuntu-64 for Sander leifepeterson.sbcglobal.net (Sat Sep 15 2018 - 19:15:25 PDT)
[AMBER] Sander 01_Min.out error leifepeterson.sbcglobal.net (Sat Sep 15 2018 - 19:23:44 PDT)
[AMBER] RESOLVED: peek_ewald_inpcrd: Box info not found in inpcrd leifepeterson.sbcglobal.net (Sat Sep 15 2018 - 20:24:35 PDT)
- Re: [AMBER] RESOLVED: peek_ewald_inpcrd: Box info not found in inpcrd Matias Machado (Sun Sep 16 2018 - 08:35:10 PDT)
[AMBER] unwrap problem in the liquid water dynamics trajectory analysis jinfeng liu (Sat Sep 15 2018 - 22:43:13 PDT)
- Re: [AMBER] unwrap problem in the liquid water dynamics trajectory analysis Matias Machado (Sun Sep 16 2018 - 06:52:54 PDT)
  - Re: [AMBER] unwrap problem in the liquid water dynamics trajectory analysis Matias Machado (Sun Sep 16 2018 - 07:04:09 PDT)
    - Re: [AMBER] unwrap problem in the liquid water dynamics trajectory analysis jinfeng liu (Sun Sep 16 2018 - 18:21:31 PDT)
- Re: [AMBER] unwrap problem in the liquid water dynamics trajectory analysis David A Case (Sun Sep 16 2018 - 17:59:18 PDT)
  - Re: [AMBER] unwrap problem in the liquid water dynamics trajectory analysis jinfeng liu (Sun Sep 16 2018 - 18:47:44 PDT)
- Re: [AMBER] unwrap problem in the liquid water dynamics trajectory analysis Daniel Roe (Mon Sep 17 2018 - 04:21:51 PDT)
[AMBER] Clustering_distance_metric_option_general_rule Antonio Amber Carlesso (Sun Sep 16 2018 - 01:26:25 PDT)
- Re: [AMBER] Clustering_distance_metric_option_general_rule Daniel Roe (Thu Sep 20 2018 - 08:21:26 PDT)
  - Re: [AMBER] Clustering_distance_metric_option_general_rule Christina Bergonzo (Thu Sep 20 2018 - 08:47:55 PDT)
    - Re: [AMBER] Clustering_distance_metric_option_general_rule Antonio Amber Carlesso (Thu Sep 27 2018 - 14:07:15 PDT)
[AMBER] Adding 12_6_4 LJ parameters in prmtop file Deepika Sardana (Sun Sep 16 2018 - 09:33:18 PDT)
- Re: [AMBER] Adding 12_6_4 LJ parameters in prmtop file Pengfei Li (Sat Sep 22 2018 - 07:41:42 PDT)
  - Re: [AMBER] Adding 12_6_4 LJ parameters in prmtop file Pengfei Li (Sat Sep 22 2018 - 07:42:55 PDT)
[AMBER] AMBER Alanine tutorial (different outputs from AMBER15 and AMBER18) leifepeterson.sbcglobal.net (Sun Sep 16 2018 - 12:30:24 PDT)
- Re: [AMBER] AMBER Alanine tutorial (different outputs from AMBER15 and AMBER18) Matias Machado (Sun Sep 16 2018 - 13:18:29 PDT)
[AMBER] Options for nonpolar solvation free energy calculation with mm_pbsa.pl 龚乾坤 (Sun Sep 16 2018 - 19:50:56 PDT)
- Re: [AMBER] Options for nonpolar solvation free energy calculation with mm_pbsa.pl David A Case (Mon Sep 24 2018 - 04:32:26 PDT)
[AMBER] RESOLVED: AMBER Alanine tutorial (need to replace .mdcrd with .nc) leifepeterson.sbcglobal.net (Mon Sep 17 2018 - 06:36:34 PDT)
[AMBER] test errors of amber18 Lei Zhao (Mon Sep 17 2018 - 06:41:34 PDT)
- Re: [AMBER] test errors of amber18 David Case (Thu Sep 27 2018 - 04:51:59 PDT)
[AMBER] pbsa:cannot match namelist object name mprob 高振梅 (Mon Sep 17 2018 - 07:00:46 PDT)
- Re: [AMBER] pbsa:cannot match namelist object name mprob Ray Luo (Mon Sep 17 2018 - 10:15:21 PDT)
[AMBER] Contact Map Sourav Purohit (Mon Sep 17 2018 - 15:59:06 PDT)
- Re: [AMBER] Contact Map Daniel Roe (Thu Sep 20 2018 - 06:00:58 PDT)
  - Re: [AMBER] Contact Map Sourav Purohit (Thu Sep 20 2018 - 11:24:01 PDT)
    - Re: [AMBER] Contact Map Daniel Roe (Mon Sep 24 2018 - 08:46:58 PDT)
    - Re: [AMBER] Contact Map Daniel Roe (Mon Sep 24 2018 - 08:48:33 PDT)
[AMBER] Amber16 cuda compiling error senal dinuka (Mon Sep 17 2018 - 20:43:19 PDT)
- Re: [AMBER] Amber16 cuda compiling error David Cerutti (Mon Sep 17 2018 - 20:47:11 PDT)
  - Re: [AMBER] Amber16 cuda compiling error senal dinuka (Mon Sep 17 2018 - 21:13:58 PDT)
    - Re: [AMBER] Amber16 cuda compiling error David Cerutti (Mon Sep 17 2018 - 21:33:00 PDT)
    - Re: [AMBER] Amber16 cuda compiling error David Case (Tue Sep 18 2018 - 06:18:54 PDT)
[AMBER] Amber Installation Error Yuthika Dholey (Mon Sep 17 2018 - 22:46:02 PDT)
- Re: [AMBER] Amber Installation Error David Case (Tue Sep 18 2018 - 06:21:49 PDT)
[AMBER] Regarding nastruct command in cpptraj Rajarshi Roy (Tue Sep 18 2018 - 10:39:41 PDT)
- Re: [AMBER] Regarding nastruct command in cpptraj Daniel Roe (Thu Sep 20 2018 - 07:40:39 PDT)
  - Re: [AMBER] Regarding nastruct command in cpptraj Rajarshi Roy (Fri Sep 21 2018 - 00:35:42 PDT)
    - Re: [AMBER] Regarding nastruct command in cpptraj Daniel Roe (Fri Sep 21 2018 - 09:09:47 PDT)
    - Re: [AMBER] Regarding nastruct command in cpptraj Rajarshi Roy (Fri Sep 21 2018 - 22:01:54 PDT)
[AMBER] atomic fluctuation vs residue Avirup Ghosh (Tue Sep 18 2018 - 19:26:19 PDT)
- Re: [AMBER] atomic fluctuation vs residue Daniel Roe (Thu Sep 20 2018 - 07:42:08 PDT)
[AMBER] Problem in testing the Zinc enzyme example using MCPB.py Alex Schwartz (Tue Sep 18 2018 - 20:55:07 PDT)
- Re: [AMBER] Problem in testing the Zinc enzyme example using MCPB.py Pengfei Li (Sat Sep 22 2018 - 07:31:16 PDT)
[AMBER] Unknown keyword Sushi Shilpa (Wed Sep 19 2018 - 02:55:54 PDT)
- Re: [AMBER] Unknown keyword Bill Ross (Wed Sep 19 2018 - 03:04:48 PDT)
[AMBER] Problem with stripping with a condition Hadi Rahmaninejad (Wed Sep 19 2018 - 08:56:43 PDT)
- Re: [AMBER] Problem with stripping with a condition Daniel Roe (Thu Sep 20 2018 - 05:49:44 PDT)
[AMBER] Running GIST calculation in parallel M RCC (Thu Sep 20 2018 - 02:57:44 PDT)
- Re: [AMBER] Running GIST calculation in parallel Daniel Roe (Thu Sep 20 2018 - 08:37:37 PDT)
- Re: [AMBER] Running GIST calculation in parallel M RCC (Fri Sep 21 2018 - 07:53:03 PDT)
  - Re: [AMBER] Running GIST calculation in parallel Daniel Roe (Fri Sep 21 2018 - 10:18:41 PDT)
    - Re: [AMBER] Running GIST calculation in parallel Matias Machado (Fri Sep 21 2018 - 11:16:07 PDT)
    - Re: [AMBER] Running GIST calculation in parallel Tom Kurtzman (Fri Sep 21 2018 - 15:35:32 PDT)
    - Re: [AMBER] Running GIST calculation in parallel Matias Machado (Sun Sep 23 2018 - 06:08:22 PDT)
[AMBER] Amber on GPU emanuele falbo (Thu Sep 20 2018 - 03:13:40 PDT)
- Re: [AMBER] Amber on GPU David A Case (Thu Sep 20 2018 - 04:14:54 PDT)
  - Re: [AMBER] Amber on GPU emanuele falbo (Thu Sep 20 2018 - 04:23:04 PDT)
[AMBER] Temperature RMS, ntslim limit Nikolay N. Kuzmich (Thu Sep 20 2018 - 05:29:24 PDT)
- Re: [AMBER] Temperature RMS, ntslim limit Matias Machado (Thu Sep 20 2018 - 07:48:35 PDT)
[AMBER] Seeking clarification regarding Calculation of Linear Interaction Energy (lie) Bharat Manna (Thu Sep 20 2018 - 20:25:51 PDT)
Re: [AMBER] AMBER ntslim limit Nikolay N. Kuzmich (Fri Sep 21 2018 - 02:34:30 PDT)
- Re: [AMBER] AMBER ntslim limit Bill Ross (Fri Sep 21 2018 - 02:46:10 PDT)
- Re: [AMBER] AMBER ntslim limit Matias Machado (Fri Sep 21 2018 - 05:06:16 PDT)
[AMBER] cuda 10 support Waqas Takkar (Fri Sep 21 2018 - 03:42:04 PDT)
- Re: [AMBER] cuda 10 support David Cerutti (Fri Sep 21 2018 - 08:41:57 PDT)
[AMBER] Query on 2DRMSD Saikat Pal (Fri Sep 21 2018 - 05:03:09 PDT)
- Re: [AMBER] Query on 2DRMSD Thomas Cheatham (Fri Sep 21 2018 - 17:09:41 PDT)
[AMBER] setting of different concentration of Nacl Nisha Amarnath Jonniya (Fri Sep 21 2018 - 05:40:52 PDT)
- Re: [AMBER] setting of different concentration of Nacl Matias Machado (Fri Sep 21 2018 - 07:10:30 PDT)
- Re: [AMBER] setting of different concentration of Nacl Stephan Schott (Fri Sep 21 2018 - 07:49:30 PDT)
  - Re: [AMBER] setting of different concentration of Nacl Matias Machado (Fri Sep 21 2018 - 07:58:16 PDT)
- Re: [AMBER] setting of different concentration of Nacl Stephan Schott (Fri Sep 21 2018 - 08:13:31 PDT)
[AMBER] Critical Isoform selectivity in MD M RCC (Sun Sep 23 2018 - 23:15:49 PDT)
- Re: [AMBER] Critical Isoform selectivity in MD David Case (Thu Sep 27 2018 - 04:46:52 PDT)
[AMBER] Error while creating topology file(HMassRepartition) in parmed Aravind Ravichandran (Mon Sep 24 2018 - 03:39:09 PDT)
- Re: [AMBER] Error while creating topology file(HMassRepartition) in parmed David A Case (Mon Sep 24 2018 - 04:39:26 PDT)
  - Re: [AMBER] Error while creating topology file(HMassRepartition) in parmed Aravind Ravichandran (Fri Oct 22 153779 - 00:00:00 PST)
    - Re: [AMBER] Error while creating topology file(HMassRepartition) in parmed David Case (Mon Sep 24 2018 - 16:11:47 PDT)
- Re: [AMBER] Error while creating topology file(HMassRepartition) in parmed David A Case (Mon Sep 24 2018 - 04:42:28 PDT)
[AMBER] SMD free energy inferred from work Ruth Helena Tichauer (Mon Sep 24 2018 - 06:46:42 PDT)
- Re: [AMBER] SMD free energy inferred from work Feng Pan (Mon Sep 24 2018 - 08:38:09 PDT)
  - Re: [AMBER] SMD free energy inferred from work Ruth Helena Tichauer (Mon Sep 24 2018 - 13:16:10 PDT)
[AMBER] nVidia Webinar: Achievable Free Energy Calculations through GPU-Accelerated AMBER accuratefreeenergy.gmail.com (Mon Sep 24 2018 - 10:28:14 PDT)
[AMBER] PBC error. Amber force field in NAMD M RCC (Tue Sep 25 2018 - 04:34:54 PDT)
- Re: [AMBER] PBC error. Amber force field in NAMD Eric Lang (Tue Sep 25 2018 - 06:34:28 PDT)
[AMBER] Calculating residence times with cpptraj Stefan Ivanov (Tue Sep 25 2018 - 21:52:54 PDT)
- Re: [AMBER] Calculating residence times with cpptraj Daniel Roe (Wed Sep 26 2018 - 12:08:57 PDT)
[AMBER] Reducing memory usage in lifetime analyses Gustaf Olsson (Tue Sep 25 2018 - 23:15:29 PDT)
- Re: [AMBER] Reducing memory usage in lifetime analyses Daniel Roe (Wed Sep 26 2018 - 12:14:10 PDT)
  - Re: [AMBER] Reducing memory usage in lifetime analyses Gustaf Olsson (Fri Sep 28 2018 - 00:20:42 PDT)
    - Re: [AMBER] Reducing memory usage in lifetime analyses Daniel Roe (Tue Oct 02 2018 - 11:20:34 PDT)
    - Re: [AMBER] Reducing memory usage in lifetime analyses Gustaf Olsson (Wed Oct 03 2018 - 03:23:52 PDT)
[AMBER] Problem with antechamber/acdoctor Sarah Fegan - UKRI STFC (Wed Sep 26 2018 - 03:15:11 PDT)
- Re: [AMBER] Problem with antechamber/acdoctor David Case (Sat Oct 06 2018 - 05:54:35 PDT)
Re: [AMBER] Re-scaling masses and kinetic energy in TI calculations David Case (Thu Sep 27 2018 - 04:42:42 PDT)
- Re: [AMBER] Re-scaling masses and kinetic energy in TI calculations Tom Kurtzman (Thu Sep 27 2018 - 05:29:51 PDT)
[AMBER] Counter Ions in X-Ray structure. Keiran Corbett (Thu Sep 27 2018 - 04:55:35 PDT)
- Re: [AMBER] Counter Ions in X-Ray structure. David Case (Thu Sep 27 2018 - 05:53:16 PDT)
  - Re: [AMBER] Counter Ions in X-Ray structure. Keiran Corbett (Thu Sep 27 2018 - 07:08:27 PDT)
    - Re: [AMBER] Counter Ions in X-Ray structure. Keiran Corbett (Thu Sep 27 2018 - 07:38:52 PDT)
    - Re: [AMBER] Counter Ions in X-Ray structure. Matias Machado (Thu Sep 27 2018 - 09:24:24 PDT)
    - Re: [AMBER] Counter Ions in X-Ray structure. Matias Machado (Thu Sep 27 2018 - 10:25:17 PDT)
    - Re: [AMBER] Counter Ions in X-Ray structure. David Case (Thu Sep 27 2018 - 13:29:38 PDT)
[AMBER] annoying elapsed time in mdout of amber18 Song-Ho Chong (Thu Sep 27 2018 - 05:57:00 PDT)
- Re: [AMBER] annoying elapsed time in mdout of amber18 David Case (Thu Sep 27 2018 - 13:36:36 PDT)
  - Re: [AMBER] annoying elapsed time in mdout of amber18 Song-Ho Chong (Thu Sep 27 2018 - 20:38:57 PDT)
  - Re: [AMBER] annoying elapsed time in mdout of amber18 Song-Ho Chong (Fri Sep 28 2018 - 00:15:24 PDT)
    - Re: [AMBER] annoying elapsed time in mdout of amber18 James Kress (Fri Sep 28 2018 - 09:18:53 PDT)
    - Re: [AMBER] annoying elapsed time in mdout of amber18 Song-Ho Chong (Fri Sep 28 2018 - 09:23:26 PDT)
[AMBER] Umbrella sampling scripts emanuele falbo (Thu Sep 27 2018 - 06:33:59 PDT)
- Re: [AMBER] Umbrella sampling scripts Marcos Serrou do Amaral (Thu Sep 27 2018 - 06:51:27 PDT)
  - Re: [AMBER] Umbrella sampling scripts emanuele falbo (Thu Sep 27 2018 - 06:56:58 PDT)
    - Re: [AMBER] Umbrella sampling scripts emanuele falbo (Thu Sep 27 2018 - 07:14:28 PDT)
    - Re: [AMBER] Umbrella sampling scripts Marcos Serrou do Amaral (Thu Sep 27 2018 - 07:54:03 PDT)
    - Re: [AMBER] Umbrella sampling scripts emanuele falbo (Thu Sep 27 2018 - 11:43:50 PDT)
[AMBER] NVIDIA GPU RTX 2080 / RTX 2080 Ti Alain Chaumont (Thu Sep 27 2018 - 09:55:11 PDT)
- Re: [AMBER] NVIDIA GPU RTX 2080 / RTX 2080 Ti David Cerutti (Thu Sep 27 2018 - 10:18:50 PDT)
[AMBER] Problems with MPI compilation gb_force.F90 Ruben Ramos Horta (Fri Sep 28 2018 - 01:05:10 PDT)
- Re: [AMBER] Problems with MPI compilation gb_force.F90 David Case (Fri Sep 28 2018 - 04:28:31 PDT)
  - Re: [AMBER] Problems with MPI compilation gb_force.F90 James Kress (Fri Sep 28 2018 - 09:16:49 PDT)
- Re: [AMBER] Problems with MPI compilation gb_force.F90 Ruben Ramos Horta (Wed Oct 03 2018 - 10:10:58 PDT)
[AMBER] How to computing peptide partial charges with antechamber? yulongsun.nwpu.edu.cn (Sat Sep 29 2018 - 06:59:53 PDT)
- Re: [AMBER] How to computing peptide partial charges with antechamber? David Case (Sat Sep 29 2018 - 10:54:01 PDT)
[AMBER] Regarding calculation of RMSD DHEERAJ CHITARA (Mon Oct 01 2018 - 05:38:49 PDT)
[AMBER] Query regarding Amber installation Rakesh Srivastava (Mon Oct 01 2018 - 05:49:29 PDT)
- Re: [AMBER] Query regarding Amber installation Hai Nguyen (Mon Oct 01 2018 - 05:59:23 PDT)
- Re: [AMBER] Query regarding Amber installation David A Case (Mon Oct 01 2018 - 08:42:49 PDT)
  - Re: [AMBER] Query regarding Amber installation Rakesh Srivastava (Mon Oct 01 2018 - 09:21:31 PDT)
    - Re: [AMBER] Query regarding Amber installation Rakesh Srivastava (Thu Oct 04 2018 - 22:07:38 PDT)
[AMBER] Water Density Seibold, Steve Allan (Mon Oct 01 2018 - 12:03:00 PDT)
- Re: [AMBER] Water Density David Case (Mon Oct 01 2018 - 16:32:22 PDT)
  - Re: [AMBER] Water Density Seibold, Steve Allan (Tue Oct 02 2018 - 05:57:30 PDT)
[AMBER] Total system charge and TI simulations Veenis, Andrew Jay (Mon Oct 01 2018 - 12:29:05 PDT)
- Re: [AMBER] Total system charge and TI simulations David Case (Mon Oct 01 2018 - 16:49:24 PDT)
[AMBER] ligand_preparation_general_rule Antonio Amber Carlesso (Tue Oct 02 2018 - 00:31:14 PDT)
- Re: [AMBER] ligand_preparation_general_rule Bill Ross (Tue Oct 02 2018 - 00:52:14 PDT)
- Re: [AMBER] ligand_preparation_general_rule David Case (Tue Oct 02 2018 - 04:37:58 PDT)
  - Re: [AMBER] ligand_preparation_general_rule Antonio Amber Carlesso (Wed Oct 03 2018 - 02:51:37 PDT)
    - Re: [AMBER] ligand_preparation_general_rule David Case (Wed Oct 03 2018 - 04:40:13 PDT)
    - Re: [AMBER] ligand_preparation_general_rule David Case (Wed Oct 03 2018 - 04:50:35 PDT)
    - Re: [AMBER] ligand_preparation_general_rule Antonio Amber Carlesso (Wed Oct 03 2018 - 07:07:05 PDT)
    - Re: [AMBER] ligand_preparation_general_rule David A Case (Thu Oct 04 2018 - 05:43:46 PDT)
    - Re: [AMBER] ligand_preparation_general_rule Antonio Amber Carlesso (Fri Oct 05 2018 - 13:02:33 PDT)
[AMBER] add12_6_4 Parmed error Nikolay N. Kuzmich (Tue Oct 02 2018 - 10:06:28 PDT)
- Re: [AMBER] add12_6_4 Parmed error Pengfei Li (Tue Oct 02 2018 - 12:03:46 PDT)
- Re: [AMBER] add12_6_4 Parmed error Nikolay N. Kuzmich (Thu Oct 04 2018 - 04:26:08 PDT)
[AMBER] NFE _Lib error Hugo Macdermott-Opeskin (Tue Oct 02 2018 - 17:19:16 PDT)
- Re: [AMBER] NFE _Lib error Feng Pan (Wed Oct 03 2018 - 07:02:12 PDT)
[AMBER] Number of inter-conversions between minima on a FEL Chetna Tyagi (Wed Oct 03 2018 - 04:59:35 PDT)
- Re: [AMBER] Number of inter-conversions between minima on a FEL Daniel Roe (Wed Oct 03 2018 - 08:03:06 PDT)
[AMBER] AMBER18 compilation using intel compiler pavel.banas.upol.cz (Wed Oct 03 2018 - 06:13:47 PDT)
- Re: [AMBER] AMBER18 compilation using intel compiler David A Case (Wed Oct 03 2018 - 07:03:17 PDT)
  - Re: [AMBER] AMBER18 compilation using intel compiler pavel.banas.upol.cz (Wed Oct 03 2018 - 08:35:38 PDT)
[AMBER] get energy of some residues of the molecule Johannes Kalliauer (Wed Oct 03 2018 - 07:13:44 PDT)
[AMBER] Cpptraj bond deforming Aashish Bhatt (Wed Oct 03 2018 - 07:52:42 PDT)
- Re: [AMBER] Cpptraj bond deforming Daniel Roe (Wed Oct 03 2018 - 09:43:33 PDT)
  - Re: [AMBER] Cpptraj bond deforming Aashish Bhatt (Wed Oct 03 2018 - 10:10:15 PDT)
    - Re: [AMBER] Cpptraj bond deforming Daniel Roe (Wed Oct 03 2018 - 10:16:34 PDT)
    - Re: [AMBER] Cpptraj bond deforming Aashish Bhatt (Wed Oct 03 2018 - 10:41:53 PDT)
    - Re: [AMBER] Cpptraj bond deforming Daniel Roe (Wed Oct 03 2018 - 10:59:53 PDT)
    - Re: [AMBER] Cpptraj bond deforming Aashish Bhatt (Wed Oct 03 2018 - 22:56:42 PDT)
[AMBER] Part of protein going out of the box Leena Aggarwal (Wed Oct 03 2018 - 07:57:32 PDT)
- Re: [AMBER] Part of protein going out of the box Daniel Roe (Wed Oct 03 2018 - 10:21:38 PDT)
[AMBER] Problem in saving amber prmtop file from DNA pdb file creacted using server http://structure.usc.edu/make-na/server.html) ? Subrata Paul (Thu Oct 04 2018 - 00:37:08 PDT)
- Re: [AMBER] Problem in saving amber prmtop file from DNA pdb file creacted using server http://structure.usc.edu/make-na/server.html) ? Bill Ross (Thu Oct 04 2018 - 01:09:22 PDT)
- Re: [AMBER] Problem in saving amber prmtop file from DNA pdb file creacted using server http://structure.usc.edu/make-na/server.html) ? David A Case (Thu Oct 04 2018 - 05:54:50 PDT)
[AMBER] Amber 18 installation problem MR. RABINDRANATH PAUL (Thu Oct 04 2018 - 00:44:25 PDT)
- Re: [AMBER] Amber 18 installation problem Bill Ross (Thu Oct 04 2018 - 01:08:05 PDT)
  - Re: [AMBER] Amber 18 installation problem MR. RABINDRANATH PAUL (Thu Oct 04 2018 - 01:25:10 PDT)
    - Re: [AMBER] Amber 18 installation problem Bill Ross (Thu Oct 04 2018 - 10:35:25 PDT)
    - Re: [AMBER] Amber 18 installation problem MR. RABINDRANATH PAUL (Thu Oct 04 2018 - 22:02:46 PDT)
- Re: [AMBER] Amber 18 installation problem Daniel Roe (Thu Oct 04 2018 - 05:45:34 PDT)
  - Re: [AMBER] Amber 18 installation problem MR. RABINDRANATH PAUL (Thu Oct 04 2018 - 08:41:08 PDT)
    - Re: [AMBER] Amber 18 installation problem Hai Nguyen (Thu Oct 04 2018 - 08:42:47 PDT)
[AMBER] How to run the test in HPC cluster and GPU Saikat Pal (Thu Oct 04 2018 - 04:15:53 PDT)
- Re: [AMBER] How to run the test in HPC cluster and GPU Charles Lin (Fri Oct 05 2018 - 08:14:49 PDT)
[AMBER] Amber to gromacs topology Saikat Pal (Thu Oct 04 2018 - 04:37:46 PDT)
- Re: [AMBER] Amber to gromacs topology Matias Machado (Thu Oct 04 2018 - 07:19:12 PDT)
  - Re: [AMBER] Amber to gromacs topology Saikat Pal (Thu Oct 04 2018 - 07:34:34 PDT)
    - Re: [AMBER] Amber to gromacs topology Matias Machado (Thu Oct 04 2018 - 08:16:21 PDT)
    - Re: [AMBER] Amber to gromacs topology Saikat Pal (Thu Oct 04 2018 - 08:20:09 PDT)
    - Re: [AMBER] Amber to gromacs topology David A Case (Thu Oct 04 2018 - 08:27:43 PDT)
[AMBER] FW: Problem running the adqmmm test, one mdcrd file only Dreab, Ana (Thu Oct 04 2018 - 06:17:30 PDT)
- Re: [AMBER] FW: Problem running the adqmmm test, one mdcrd file only David A Case (Thu Oct 04 2018 - 08:21:11 PDT)
  - Re: [AMBER] FW: Problem running the adqmmm test, one mdcrd file only Dreab, Ana (Sat Oct 06 2018 - 20:46:47 PDT)
    - Re: [AMBER] FW: Problem running the adqmmm test, one mdcrd file only Goetz, Andreas (Sat Oct 06 2018 - 23:01:20 PDT)
    - Re: [AMBER] FW: Problem running the adqmmm test, one mdcrd file only Dreab, Ana (Sun Oct 07 2018 - 14:17:10 PDT)
[AMBER] Setting up parameters for a simulation at 350K Dmitry Suplatov (Thu Oct 04 2018 - 08:39:51 PDT)
- Re: [AMBER] Setting up parameters for a simulation at 350K David Cerutti (Thu Oct 04 2018 - 08:45:24 PDT)
  - Re: [AMBER] Setting up parameters for a simulation at 350K Dmitry Suplatov (Thu Oct 04 2018 - 08:54:02 PDT)
- Re: [AMBER] Setting up parameters for a simulation at 350K Bill Ross (Thu Oct 04 2018 - 10:30:05 PDT)
  - Re: [AMBER] Setting up parameters for a simulation at 350K David Cerutti (Thu Oct 04 2018 - 10:35:28 PDT)
[AMBER] Provisional RTX2080 AMBER 18 Performance Numbers Ross Walker (Fri Oct 05 2018 - 05:32:07 PDT)
- Re: [AMBER] Provisional RTX2080 AMBER 18 Performance Numbers Marek Maly (Fri Oct 05 2018 - 06:17:19 PDT)
  - Re: [AMBER] Provisional RTX2080 AMBER 18 Performance Numbers Ross Walker (Fri Oct 05 2018 - 06:39:30 PDT)
    - Re: [AMBER] Provisional RTX2080 AMBER 18 Performance Numbers David Cerutti (Fri Oct 05 2018 - 07:11:14 PDT)
    - Re: [AMBER] Provisional RTX2080 AMBER 18 Performance Numbers Ross Walker (Sat Oct 06 2018 - 08:30:40 PDT)
    - Re: [AMBER] Provisional RTX2080 AMBER 18 Performance Numbers Ross Walker (Sat Oct 06 2018 - 14:03:11 PDT)
    - Re: [AMBER] Provisional RTX2080 AMBER 18 Performance Numbers David Cerutti (Sat Oct 06 2018 - 14:53:43 PDT)
    - Re: [AMBER] Provisional RTX2080 AMBER 18 Performance Numbers Charles-Alexandre Mattelaer (Tue Nov 19 2019 - 14:49:20 PST)
    - Re: [AMBER] Provisional RTX2080 AMBER 18 Performance Numbers Ross Walker (Wed Nov 20 2019 - 08:53:46 PST)
    - Re: [AMBER] Provisional RTX2080 AMBER 18 Performance Numbers Charles-Alexandre Mattelaer (Wed Nov 20 2019 - 09:55:15 PST)
    - Re: [AMBER] Provisional RTX2080 AMBER 18 Performance Numbers Daniel Roe (Mon Nov 25 2019 - 05:31:23 PST)
    - Re: [AMBER] Provisional RTX2080 AMBER 18 Performance Numbers Marek Maly (Mon Oct 08 2018 - 03:15:37 PDT)
    - Re: [AMBER] Provisional RTX2080 AMBER 18 Performance Numbers David Cerutti (Mon Oct 08 2018 - 04:28:08 PDT)
    - Re: [AMBER] Provisional RTX2080 AMBER 18 Performance Numbers Marek Maly (Mon Oct 08 2018 - 11:44:13 PDT)
    - Re: [AMBER] Provisional RTX2080 AMBER 18 Performance Numbers David Cerutti (Mon Oct 08 2018 - 12:46:47 PDT)
    - Re: [AMBER] Provisional RTX2080 AMBER 18 Performance Numbers Marek Maly (Tue Oct 09 2018 - 02:39:23 PDT)
    - Re: [AMBER] Provisional RTX2080 AMBER 18 Performance Numbers Ross Walker (Tue Oct 09 2018 - 06:14:20 PDT)
    - Re: [AMBER] Provisional RTX2080 AMBER 18 Performance Numbers Marek Maly (Tue Oct 09 2018 - 06:18:29 PDT)
[AMBER] number of reaction coordinate in a ASMD run sangita kachhap (Fri Oct 05 2018 - 06:14:38 PDT)
[AMBER] questions on pmemd.cuda for thermodynamic integration Song-Ho Chong (Fri Oct 05 2018 - 08:06:49 PDT)
[AMBER] acpype_error Antonio Amber Carlesso (Fri Oct 05 2018 - 11:11:06 PDT)
- Re: [AMBER] acpype_error dhaval patel (Fri Oct 05 2018 - 11:49:08 PDT)
  - Re: [AMBER] acpype_error Antonio Amber Carlesso (Fri Oct 05 2018 - 12:15:38 PDT)
    - Re: [AMBER] acpype_error Alan (Fri Oct 05 2018 - 13:25:38 PDT)
    - Re: [AMBER] acpype_error Antonio Amber Carlesso (Fri Oct 05 2018 - 14:25:39 PDT)
[AMBER] Warning for MMPBSA.py calculation maryam azimzadehirani (Sat Oct 06 2018 - 00:01:19 PDT)
[AMBER] Lipid Order Parameters somdev pahari (Sat Oct 06 2018 - 08:03:48 PDT)
- [AMBER] Fwd: Lipid Order Parameters somdev pahari (Wed Oct 10 2018 - 08:39:36 PDT)
- Re: [AMBER] Lipid Order Parameters Daniel Roe (Wed Oct 10 2018 - 09:07:20 PDT)
[AMBER] Amber Install on Mojave (ld: library not found for -lmc) Fix Andrew Schaub (Sun Oct 07 2018 - 17:02:03 PDT)
- Re: [AMBER] Amber Install on Mojave (ld: library not found for -lmc) Fix Andrew Schaub (Mon Oct 08 2018 - 06:09:28 PDT)
  - Re: [AMBER] Amber Install on Mojave (ld: library not found for -lmc) Fix Gustaf Olsson (Mon Oct 08 2018 - 07:54:11 PDT)
    - Re: [AMBER] Amber Install on Mojave (ld: library not found for -lmc) Fix Andrew Schaub (Mon Oct 08 2018 - 09:33:00 PDT)
    - Re: [AMBER] Amber Install on Mojave (ld: library not found for -lmc) Fix Andrew Schaub (Mon Oct 08 2018 - 09:39:51 PDT)
    - Re: [AMBER] Amber Install on Mojave David A Case (Fri Oct 12 2018 - 05:13:45 PDT)
[AMBER] Testing C++11 support: Not present Gustaf Olsson (Mon Oct 08 2018 - 01:04:12 PDT)
- Re: [AMBER] Testing C++11 support: Not present Bill Ross (Mon Oct 08 2018 - 01:54:37 PDT)
  - Re: [AMBER] Testing C++11 support: Not present Gustaf Olsson (Mon Oct 08 2018 - 02:07:32 PDT)
  - Re: [AMBER] Testing C++11 support: Not present Gustaf Olsson (Mon Oct 08 2018 - 04:25:00 PDT)
    - Re: [AMBER] Testing C++11 support: Not present Gustaf Olsson (Mon Oct 08 2018 - 05:21:10 PDT)
    - Re: [AMBER] Testing C++11 support: Not present Gustaf Olsson (Mon Oct 08 2018 - 07:55:10 PDT)
- Re: [AMBER] Testing C++11 support: Not present Gustaf Olsson (Mon Oct 08 2018 - 22:52:45 PDT)
  - Re: [AMBER] Testing C++11 support: Not present Daniel Roe (Tue Oct 09 2018 - 07:17:27 PDT)
    - Re: [AMBER] Testing C++11 support: Not present Gustaf Olsson (Tue Oct 09 2018 - 07:34:55 PDT)
    - Re: [AMBER] Testing C++11 support: Not present Daniel Roe (Tue Oct 09 2018 - 08:45:09 PDT)
    - Re: [AMBER] Testing C++11 support: Not present Gustaf Olsson (Tue Oct 09 2018 - 23:00:52 PDT)
    - Re: [AMBER] Testing C++11 support: Not present Daniel Roe (Wed Oct 10 2018 - 06:52:17 PDT)
    - Re: [AMBER] Testing C++11 support: Not present Andrew Schaub (Thu Oct 11 2018 - 13:20:57 PDT)
    - Re: [AMBER] Testing C++11 support: Not present Gustaf Olsson (Thu Oct 11 2018 - 23:28:25 PDT)
    - Re: [AMBER] Testing C++11 support: Not present Gustaf Olsson (Fri Oct 12 2018 - 00:54:13 PDT)
    - Re: [AMBER] Testing C++11 support: Not present Daniel Roe (Fri Oct 12 2018 - 05:41:29 PDT)
    - Re: [AMBER] Testing C++11 support: Not present Gustaf Olsson (Fri Oct 12 2018 - 05:55:23 PDT)
[AMBER] Parameters for atom CE in lj_1264_pol.dat Nikolay N. Kuzmich (Mon Oct 08 2018 - 02:20:52 PDT)
[AMBER] Full: Parameters for atom CE in lj_1264_pol.dat Nikolay N. Kuzmich (Mon Oct 08 2018 - 02:29:17 PDT)
- Re: [AMBER] Full: Parameters for atom CE in lj_1264_pol.dat Pengfei Li (Tue Oct 09 2018 - 16:59:30 PDT)
- Re: [AMBER] Full: Parameters for atom CE in lj_1264_pol.dat Nikolay N. Kuzmich (Fri Oct 12 2018 - 08:42:16 PDT)
[AMBER] Antechamber on unknown residue Keiran Corbett (Mon Oct 08 2018 - 03:44:25 PDT)
- Re: [AMBER] Antechamber on unknown residue David Case (Mon Oct 08 2018 - 06:29:41 PDT)
[AMBER] GPU memory usage with center-of-mass restratints David Case (Mon Oct 08 2018 - 06:08:03 PDT)
[AMBER] Restrain distance for Umbrella Sampling emanuele falbo (Mon Oct 08 2018 - 07:03:44 PDT)
- Re: [AMBER] Restrain distance for Umbrella Sampling David A Case (Mon Oct 08 2018 - 08:08:08 PDT)
  - Re: [AMBER] Restrain distance for Umbrella Sampling emanuele falbo (Mon Oct 08 2018 - 08:28:08 PDT)
[AMBER] torsion angles of carbon allotropes Ibrahim Said (Mon Oct 08 2018 - 11:57:08 PDT)
- Re: [AMBER] torsion angles of carbon allotropes David Case (Mon Oct 08 2018 - 18:04:27 PDT)
  - Re: [AMBER] torsion angles of carbon allotropes Ibrahim Said (Tue Oct 09 2018 - 03:56:34 PDT)
[AMBER] RTX 2080 Benchmarks Bisignano, Paola (Mon Oct 08 2018 - 13:05:14 PDT)
- Re: [AMBER] RTX 2080 Benchmarks David Cerutti (Mon Oct 08 2018 - 13:13:40 PDT)
  - Re: [AMBER] RTX 2080 Benchmarks Bisignano, Paola (Mon Oct 08 2018 - 13:21:24 PDT)
[AMBER] constant pH pmemd.cuda error andreas.tosstorff.cup.uni-muenchen.de (Mon Oct 08 2018 - 13:20:30 PDT)
- Re: [AMBER] constant pH pmemd.cuda error Cruzeiro,Vinicius Wilian D (Mon Oct 08 2018 - 13:34:09 PDT)
  - Re: [AMBER] constant pH pmemd.cuda error andreas.tosstorff.cup.uni-muenchen.de (Mon Oct 08 2018 - 14:03:26 PDT)
    - Re: [AMBER] constant pH pmemd.cuda error Cruzeiro,Vinicius Wilian D (Mon Oct 08 2018 - 14:20:08 PDT)
[AMBER] Errors when installing with MPI Felipe Franco Gonzalez (Mon Oct 08 2018 - 13:49:03 PDT)
- Re: [AMBER] Errors when installing with MPI David Case (Mon Oct 08 2018 - 18:09:39 PDT)
[AMBER] Regarding Leap Charu Sharma (JRF) (Mon Oct 08 2018 - 21:33:15 PDT)
- Re: [AMBER] Regarding Leap Elvis Martis (Mon Oct 08 2018 - 22:41:36 PDT)
  - Re: [AMBER] Regarding Leap Charu Sharma (JRF) (Wed Oct 10 2018 - 04:01:24 PDT)
    - Re: [AMBER] Regarding Leap Elvis Martis (Wed Oct 10 2018 - 08:15:02 PDT)
    - Re: [AMBER] Regarding Leap Charu Sharma (JRF) (Fri Oct 12 2018 - 22:58:52 PDT)
    - Re: [AMBER] Regarding Leap Elvis Martis (Sat Oct 13 2018 - 00:31:40 PDT)
    - Re: [AMBER] Regarding Leap Charu Sharma (JRF) (Sat Oct 13 2018 - 03:46:17 PDT)
    - Re: [AMBER] Regarding Leap Elvis Martis (Sun Oct 14 2018 - 00:58:56 PDT)
    - Re: [AMBER] Regarding Leap Charu Sharma (JRF) (Wed Oct 17 2018 - 04:30:14 PDT)
    - Re: [AMBER] Regarding Leap Chetna Tyagi (Wed Oct 17 2018 - 04:24:19 PDT)
    - Re: [AMBER] Regarding Leap Charu Sharma (JRF) (Wed Oct 17 2018 - 04:49:02 PDT)
    - Re: [AMBER] Regarding Leap Charu Sharma (JRF) (Wed Oct 17 2018 - 04:50:56 PDT)
    - Re: [AMBER] Regarding Leap Chetna Tyagi (Wed Oct 17 2018 - 04:42:37 PDT)
    - Re: [AMBER] Regarding Leap Charu Sharma (JRF) (Wed Oct 17 2018 - 05:05:22 PDT)
    - Re: [AMBER] Regarding Leap Chetna Tyagi (Wed Oct 17 2018 - 05:52:03 PDT)
    - Re: [AMBER] Regarding Leap Charu Sharma (JRF) (Tue Oct 30 2018 - 08:49:49 PDT)
    - Re: [AMBER] Regarding Leap David A Case (Tue Oct 30 2018 - 09:24:46 PDT)
    - Re: [AMBER] Regarding Leap Charu Sharma (JRF) (Tue Oct 30 2018 - 09:40:15 PDT)
- Re: [AMBER] Regarding Leap Charu Sharma (JRF) (Tue Oct 30 2018 - 09:40:38 PDT)
[AMBER] Fwd: The results of your email commands Charu Sharma (JRF) (Mon Oct 08 2018 - 21:35:22 PDT)
[AMBER] Rigid body simulation of Nitrogenase's FeMo cluster Sadra Aghajani (Tue Oct 09 2018 - 00:32:17 PDT)
- Re: [AMBER] Rigid body simulation of Nitrogenase's FeMo cluster David A Case (Tue Oct 09 2018 - 05:17:47 PDT)
[AMBER] Selecting specific set of molecules for output trajectory anu chandra (Tue Oct 09 2018 - 04:29:36 PDT)
- Re: [AMBER] Selecting specific set of molecules for output trajectory David A Case (Tue Oct 09 2018 - 05:20:53 PDT)
[AMBER] viscosity calculation Lorenzo Gontrani (Tue Oct 09 2018 - 07:48:45 PDT)
- Re: [AMBER] viscosity calculation David A Case (Fri Oct 12 2018 - 04:56:52 PDT)
  - Re: [AMBER] viscosity calculation Arun Srikanth (Fri Oct 12 2018 - 10:59:25 PDT)
[AMBER] hydrogen bond analysis Qinghua Liao (Tue Oct 09 2018 - 16:03:44 PDT)
- Re: [AMBER] hydrogen bond analysis Zuo, Zhicheng (Tue Oct 09 2018 - 17:15:22 PDT)
  - Re: [AMBER] hydrogen bond analysis Qinghua Liao (Wed Oct 10 2018 - 02:51:39 PDT)
- Re: [AMBER] hydrogen bond analysis Daniel Roe (Wed Oct 10 2018 - 05:23:13 PDT)
  - Re: [AMBER] hydrogen bond analysis Qinghua Liao (Wed Oct 10 2018 - 08:40:03 PDT)
[AMBER] Regarding calculation of RMSD using AMBER-18 CPPTRAJ V-18.01 DHEERAJ CHITARA (Tue Oct 09 2018 - 23:15:50 PDT)
- Re: [AMBER] Regarding calculation of RMSD using AMBER-18 CPPTRAJ V-18.01 Daniel Roe (Wed Oct 10 2018 - 05:20:11 PDT)
  - Re: [AMBER] Regarding calculation of RMSD using AMBER-18 CPPTRAJ V-18.01 DHEERAJ CHITARA (Thu Oct 11 2018 - 01:23:10 PDT)
    - Re: [AMBER] Regarding calculation of RMSD using AMBER-18 CPPTRAJ V-18.01 Daniel Roe (Thu Oct 11 2018 - 05:13:17 PDT)
[AMBER] Unkown residue to AMBER Keiran Corbett (Wed Oct 10 2018 - 00:55:52 PDT)
- Re: [AMBER] Unkown residue to AMBER David A Case (Wed Oct 10 2018 - 04:31:27 PDT)
[AMBER] Striping distance based water residues Kshatresh Dutta Dubey (Wed Oct 10 2018 - 03:29:30 PDT)
- Re: [AMBER] Striping distance based water residues Daniel Roe (Wed Oct 10 2018 - 05:17:50 PDT)
  - Re: [AMBER] Striping distance based water residues Kshatresh Dutta Dubey (Wed Oct 10 2018 - 08:48:06 PDT)
[AMBER] Cationic dummy Zinc atom in accelerated molecular dynamics M RCC (Wed Oct 10 2018 - 06:06:18 PDT)
[AMBER] FW: Fatal error in RESP calculation fateme haghighi (Wed Oct 10 2018 - 06:52:52 PDT)
- Re: [AMBER] FW: Fatal error in RESP calculation David A Case (Wed Oct 10 2018 - 07:40:02 PDT)
[AMBER] Water do not see the system.... Vito GENNA (Wed Oct 10 2018 - 09:18:40 PDT)
- Re: [AMBER] Water do not see the system.... David A Case (Wed Oct 10 2018 - 13:16:03 PDT)
  - Re: [AMBER] Water do not see the system.... Vito GENNA (Wed Oct 10 2018 - 13:48:20 PDT)
    - Re: [AMBER] Water do not see the system.... Vito GENNA (Thu Oct 11 2018 - 01:48:44 PDT)
    - Re: [AMBER] Water do not see the system.... Matias Machado (Thu Oct 11 2018 - 08:48:45 PDT)
    - Re: [AMBER] Water do not see the system.... Vito GENNA (Thu Oct 11 2018 - 08:56:10 PDT)
    - Re: [AMBER] Water do not see the system.... Daniel Roe (Thu Oct 11 2018 - 08:59:04 PDT)
    - Re: [AMBER] Water do not see the system.... Daniel Roe (Thu Oct 11 2018 - 09:20:19 PDT)
    - Re: [AMBER] Water do not see the system.... Vito GENNA (Thu Oct 11 2018 - 10:25:29 PDT)
[AMBER] .gesp file is not generated for Antechamber M RCC (Wed Oct 10 2018 - 09:43:37 PDT)
[AMBER] AMBER and plumed Pierre GIRARD (Wed Oct 10 2018 - 11:05:05 PDT)
- Re: [AMBER] AMBER and plumed Qinghua Liao (Wed Oct 10 2018 - 12:23:24 PDT)
  - Re: [AMBER] AMBER and plumed Pierre GIRARD (Wed Oct 10 2018 - 13:35:26 PDT)
    - Re: [AMBER] AMBER and plumed Qinghua Liao (Wed Oct 10 2018 - 13:42:21 PDT)
    - Re: [AMBER] AMBER and plumed Pierre GIRARD (Wed Oct 10 2018 - 14:03:31 PDT)
[AMBER] RTX2080 Performance Update for AMBER 18 Ross Walker (Wed Oct 10 2018 - 20:15:37 PDT)
[AMBER] AMBER 18 INSTALLATION ON CLUSTER - ERROR Midhun K Madhu (Wed Oct 10 2018 - 22:32:49 PDT)
- Re: [AMBER] AMBER 18 INSTALLATION ON CLUSTER - ERROR David A Case (Thu Oct 11 2018 - 06:30:27 PDT)
[AMBER] error in RESP calculation fateme haghighi (Thu Oct 11 2018 - 00:36:23 PDT)
- Re: [AMBER] error in RESP calculation David A Case (Thu Oct 11 2018 - 06:35:22 PDT)
[AMBER] RTX2080TI Performance Ross Walker (Thu Oct 11 2018 - 04:19:47 PDT)
- Re: [AMBER] RTX2080TI Performance David Cerutti (Thu Oct 11 2018 - 07:46:21 PDT)
  - Re: [AMBER] RTX2080TI Performance Ross Walker (Fri Oct 12 2018 - 07:27:59 PDT)
- Re: [AMBER] RTX2080TI Performance Marek Maly (Thu Oct 11 2018 - 09:58:50 PDT)
[AMBER] calculation of free binding energy when a residue is mutated to residues other than alanine? ali akbar (Thu Oct 11 2018 - 05:08:27 PDT)
[AMBER] SIRAH 2.0: a finer taste in coarse-grained protiens Matias Machado (Thu Oct 11 2018 - 08:17:17 PDT)
[AMBER] Installation issues on Mac OSX 10.14 Matthew Fisher (Thu Oct 11 2018 - 10:02:18 PDT)
- Re: [AMBER] Installation issues on Mac OSX 10.14 David Case (Thu Oct 11 2018 - 19:15:10 PDT)
  - Re: [AMBER] Installation issues on Mac OSX 10.14 Gustaf Olsson (Thu Oct 11 2018 - 23:17:04 PDT)
    - Re: [AMBER] Installation issues on Mac OSX 10.14 Matthew Fisher (Mon Oct 15 2018 - 07:49:28 PDT)
[AMBER] Commented AmberTools functions Ruben Ramos Horta (Thu Oct 11 2018 - 10:09:21 PDT)
Re: [AMBER] AMBER Digest, Vol 2436, Issue 1 Midhun K Madhu (Fri Oct 12 2018 - 01:36:25 PDT)
[AMBER] How to use ff99SB-ILDN in Amber16 Yang, Tianyi (Fri Oct 12 2018 - 14:26:13 PDT)
- Re: [AMBER] How to use ff99SB-ILDN in Amber16 Qinghua Liao (Fri Oct 12 2018 - 14:29:28 PDT)
  - Re: [AMBER] How to use ff99SB-ILDN in Amber16 Vito GENNA (Fri Oct 12 2018 - 15:02:02 PDT)
[AMBER] Fondaparinux Amber Force Field Marcelo Andrade Chagas (Sun Oct 14 2018 - 07:31:42 PDT)
[AMBER] GAMD not running in CPU cluster Midhun K Madhu (Mon Oct 15 2018 - 04:19:18 PDT)
[AMBER] more on building Amber18 on Mojave David A Case (Mon Oct 15 2018 - 07:39:27 PDT)
- Re: [AMBER] more on building Amber18 on Mojave Gustaf Olsson (Tue Oct 16 2018 - 03:47:06 PDT)
- Re: [AMBER] more on building Amber18 on Mojave David A Case (Wed Oct 17 2018 - 10:25:29 PDT)
  - Re: [AMBER] more on building Amber18 on Mojave Gustaf Olsson (Thu Oct 18 2018 - 00:00:14 PDT)
    - Re: [AMBER] more on building Amber18 on Mojave Daniel Roe (Thu Oct 18 2018 - 16:07:57 PDT)
    - Re: [AMBER] more on building Amber18 on Mojave Gustaf Olsson (Thu Oct 18 2018 - 22:56:29 PDT)
[AMBER] GLYCAM Amber Force Field to Fondaparinux...? Marcelo Andrade Chagas (Mon Oct 15 2018 - 13:24:14 PDT)
- Re: [AMBER] GLYCAM Amber Force Field to Fondaparinux...? Lachele Foley (Tue Oct 16 2018 - 07:11:20 PDT)
Re: [AMBER] Using custom non-bonding potential, drude oscillator in Amber18 Kyeong-jun Jeong (Mon Oct 15 2018 - 15:46:22 PDT)
- Re: [AMBER] Using custom non-bonding potential, drude oscillator in Amber18 David A Case (Tue Oct 16 2018 - 06:22:43 PDT)
[AMBER] Using custom non-bonding potential, drude oscillator in Amber18 Kyeong-jun Jeong (Tue Oct 16 2018 - 10:11:42 PDT)
[AMBER] using parmed (python api) to merge two parm7 files for TI Wesley Michael Botello-Smith (Tue Oct 16 2018 - 13:35:33 PDT)
- Re: [AMBER] using parmed (python api) to merge two parm7 files for TI Wesley Michael Botello-Smith (Tue Oct 16 2018 - 13:43:22 PDT)
  - Re: [AMBER] using parmed (python api) to merge two parm7 files for TI Jason Swails (Fri Oct 19 2018 - 11:39:27 PDT)
[AMBER] does surf command use for stripped trajectory? g.bakrani.sci.ui.ac.ir (Wed Oct 17 2018 - 04:30:56 PDT)
- Re: [AMBER] does surf command use for stripped trajectory? Daniel Roe (Wed Oct 17 2018 - 07:27:56 PDT)
[AMBER] error in Resp fateme haghighi (Wed Oct 17 2018 - 05:33:22 PDT)
- [AMBER] FW: fatal error in Resp fateme haghighi (Thu Oct 18 2018 - 00:52:22 PDT)
  - [AMBER] FW: fatal error in Resp fateme haghighi (Thu Oct 18 2018 - 14:33:00 PDT)
  - Re: [AMBER] FW: fatal error in Resp David Case (Fri Oct 19 2018 - 04:28:03 PDT)
[AMBER] Problem with tleap Ali Khodayari (Wed Oct 17 2018 - 11:05:01 PDT)
- Re: [AMBER] Problem with tleap Bill Ross (Wed Oct 17 2018 - 11:22:43 PDT)
[AMBER] sugar derivatives parametrization Bisignano, Paola (Wed Oct 17 2018 - 15:49:34 PDT)
- Re: [AMBER] sugar derivatives parametrization David Case (Thu Oct 18 2018 - 11:09:42 PDT)
  - Re: [AMBER] sugar derivatives parametrization Lachele Foley (Thu Oct 18 2018 - 20:00:27 PDT)
    - Re: [AMBER] sugar derivatives parametrization Bisignano, Paola (Fri Oct 19 2018 - 08:34:14 PDT)
    - Re: [AMBER] sugar derivatives parametrization Lachele Foley (Thu Oct 25 2018 - 08:29:58 PDT)
- Re: [AMBER] sugar derivatives parametrization Lachele Foley (Thu Oct 18 2018 - 19:58:32 PDT)
[AMBER] Parametarization error senal dinuka (Wed Oct 17 2018 - 21:34:09 PDT)
- Re: [AMBER] Parametarization error Bill Ross (Wed Oct 17 2018 - 21:45:59 PDT)
  - Re: [AMBER] Parametarization error senal dinuka (Thu Oct 18 2018 - 00:18:16 PDT)
    - Re: [AMBER] Parametarization error Bill Ross (Thu Oct 18 2018 - 00:29:49 PDT)
    - Re: [AMBER] Parametarization error senal dinuka (Thu Oct 18 2018 - 00:58:25 PDT)
    - Re: [AMBER] Parametarization error Bill Ross (Thu Oct 18 2018 - 02:19:37 PDT)
- Re: [AMBER] Parametarization error David Case (Thu Oct 18 2018 - 11:09:55 PDT)
  - Re: [AMBER] Parametarization error senal dinuka (Thu Oct 18 2018 - 20:47:59 PDT)
[AMBER] Amber workshop in Europe? Albert (Wed Oct 17 2018 - 23:31:44 PDT)
[AMBER] Question about stripping waters Maria Clelia Milletti (Thu Oct 18 2018 - 10:22:31 PDT)
- Re: [AMBER] Question about stripping waters Daniel Roe (Thu Oct 18 2018 - 16:00:58 PDT)
  - Re: [AMBER] Question about stripping waters Maria Clelia Milletti (Fri Oct 19 2018 - 13:42:24 PDT)
    - Re: [AMBER] Question about stripping waters David Case (Sat Oct 20 2018 - 14:23:30 PDT)
    - Re: [AMBER] Question about stripping waters Maria Clelia Milletti (Tue Oct 23 2018 - 08:24:37 PDT)
[AMBER] Alternative way to do targeted MD Xiaoling Leng (Thu Oct 18 2018 - 11:53:33 PDT)
- Re: [AMBER] Alternative way to do targeted MD Feng Pan (Thu Oct 18 2018 - 15:17:34 PDT)
  - Re: [AMBER] Alternative way to do targeted MD Xiaoling Leng (Wed Oct 24 2018 - 07:55:15 PDT)
    - Re: [AMBER] Alternative way to do targeted MD Feng Pan (Wed Oct 24 2018 - 11:01:35 PDT)
    - Re: [AMBER] Alternative way to do targeted MD Xiaoling Leng (Thu Oct 25 2018 - 12:43:42 PDT)
    - Re: [AMBER] Alternative way to do targeted MD Feng Pan (Thu Oct 25 2018 - 13:47:46 PDT)
    - Re: [AMBER] Alternative way to do targeted MD Xiaoling Leng (Fri Oct 26 2018 - 13:49:09 PDT)
    - Re: [AMBER] Alternative way to do targeted MD Feng Pan (Sun Oct 28 2018 - 12:41:07 PDT)
[AMBER] pi-pi And Aromatic Interactions Meng Wu (Thu Oct 18 2018 - 19:11:02 PDT)
- Re: [AMBER] pi-pi And Aromatic Interactions Chris Neale (Thu Oct 18 2018 - 20:27:05 PDT)
  - Re: [AMBER] pi-pi And Aromatic Interactions Christina Bergonzo (Fri Oct 19 2018 - 05:49:58 PDT)
    - Re: [AMBER] pi-pi And Aromatic Interactions Chris Neale (Fri Oct 19 2018 - 13:37:57 PDT)
    - Re: [AMBER] pi-pi And Aromatic Interactions Carlos Simmerling (Fri Oct 19 2018 - 14:03:26 PDT)
    - Re: [AMBER] pi-pi And Aromatic Interactions Chris Neale (Fri Oct 19 2018 - 14:15:23 PDT)
    - Re: [AMBER] pi-pi And Aromatic Interactions Carlos Simmerling (Fri Oct 19 2018 - 14:21:48 PDT)
    - Re: [AMBER] pi-pi And Aromatic Interactions Jiri Sponer (Fri Oct 19 2018 - 15:56:19 PDT)
    - Re: [AMBER] pi-pi And Aromatic Interactions Jiri Sponer (Fri Oct 19 2018 - 16:25:06 PDT)
[AMBER] Constrained QM.MM minimization Vito GENNA (Fri Oct 19 2018 - 06:29:12 PDT)
- Re: [AMBER] Constrained QM.MM minimization Zuo, Zhicheng (Fri Oct 19 2018 - 07:23:00 PDT)
  - Re: [AMBER] Constrained QM.MM minimization Vito GENNA (Fri Oct 19 2018 - 07:28:37 PDT)
    - Re: [AMBER] Constrained QM.MM minimization Timothy Schutt (Fri Oct 19 2018 - 07:52:17 PDT)
    - Re: [AMBER] Constrained QM.MM minimization Timothy Schutt (Fri Oct 19 2018 - 08:01:28 PDT)
    - Re: [AMBER] Constrained QM.MM minimization Vito GENNA (Fri Oct 19 2018 - 09:12:31 PDT)
- Re: [AMBER] Constrained QM.MM minimization Vito GENNA (Fri Oct 19 2018 - 08:20:41 PDT)
  - Re: [AMBER] Constrained QM.MM minimization David Case (Fri Oct 19 2018 - 11:50:53 PDT)
    - Re: [AMBER] Constrained QM.MM minimization Vito GENNA (Fri Oct 19 2018 - 13:37:02 PDT)
[AMBER] Amber force field for non-natural amino acids Mijiddorj B (Fri Oct 19 2018 - 21:53:42 PDT)
- Re: [AMBER] Amber force field for non-natural amino acids Carlos Simmerling (Sat Oct 20 2018 - 03:11:19 PDT)
  - Re: [AMBER] Amber force field for non-natural amino acids Mijiddorj B (Mon Oct 22 2018 - 06:46:19 PDT)
- Re: [AMBER] Amber force field for non-natural amino acids Thomas Fox (Tue Oct 23 2018 - 14:24:20 PDT)
  - Re: [AMBER] Amber force field for non-natural amino acids Carlos Simmerling (Tue Oct 23 2018 - 14:44:15 PDT)
- Re: [AMBER] Amber force field for non-natural amino acids Thomas Fox (Tue Oct 23 2018 - 14:53:01 PDT)
  - Re: [AMBER] Amber force field for non-natural amino acids Carlos Simmerling (Tue Oct 23 2018 - 15:06:35 PDT)
[AMBER] tleap gamma-carboxyglutamic acid linkage error Rajbinder Kaur Virk (Sun Oct 21 2018 - 20:06:30 PDT)
- Re: [AMBER] tleap gamma-carboxyglutamic acid linkage error Matias Machado (Tue Oct 23 2018 - 15:26:52 PDT)
  - Re: [AMBER] tleap gamma-carboxyglutamic acid linkage error Rajbinder Kaur Virk (Wed Oct 24 2018 - 22:39:03 PDT)
    - Re: [AMBER] tleap gamma-carboxyglutamic acid linkage error Matias Machado (Fri Oct 26 2018 - 11:45:20 PDT)
    - Re: [AMBER] tleap gamma-carboxyglutamic acid linkage error Rajbinder Kaur Virk (Tue Oct 30 2018 - 10:27:15 PDT)
    - Re: [AMBER] tleap gamma-carboxyglutamic acid linkage error David Case (Tue Oct 30 2018 - 18:40:59 PDT)
    - Re: [AMBER] tleap gamma-carboxyglutamic acid linkage error Rajbinder Kaur Virk (Wed Oct 31 2018 - 02:13:58 PDT)
    - Re: [AMBER] tleap gamma-carboxyglutamic acid linkage error Bill Ross (Wed Oct 31 2018 - 02:30:25 PDT)
    - Re: [AMBER] tleap gamma-carboxyglutamic acid linkage error Bill Ross (Wed Oct 31 2018 - 02:40:02 PDT)
    - Re: [AMBER] tleap gamma-carboxyglutamic acid linkage error Matias Machado (Wed Oct 31 2018 - 10:26:15 PDT)
    - Re: [AMBER] tleap gamma-carboxyglutamic acid linkage error Rajbinder Kaur Virk (Sat Nov 03 2018 - 01:01:01 PDT)
[AMBER] The make_na web service, and corresponding code David A Case (Mon Oct 22 2018 - 06:27:48 PDT)
[AMBER] Error in Running tLEaP for Protein File Amartya Pradhan (Mon Oct 22 2018 - 11:30:00 PDT)
- Re: [AMBER] Error in Running tLEaP for Protein File David A Case (Mon Oct 22 2018 - 11:55:09 PDT)
[AMBER] Simulating a covalently bound ligand senal dinuka (Mon Oct 22 2018 - 21:48:53 PDT)
- Re: [AMBER] Simulating a covalently bound ligand David A Case (Tue Oct 23 2018 - 04:39:42 PDT)
  - Re: [AMBER] Simulating a covalently bound ligand senal dinuka (Fri Oct 26 2018 - 04:03:22 PDT)
[AMBER] Effective born radii calculations - No correct statistics returned at the end of the mdout file Eric Lang (Tue Oct 23 2018 - 08:28:16 PDT)
- Re: [AMBER] Effective born radii calculations - No correct statistics returned at the end of the mdout file David A Case (Tue Oct 23 2018 - 09:48:40 PDT)
  - Re: [AMBER] Effective born radii calculations - No correct statistics returned at the end of the mdout file Eric Lang (Wed Oct 24 2018 - 02:00:08 PDT)
[AMBER] Struggling to convert AMBER .frcmod and .mol2 to GROMACS for HEME Matthew Fisher (Tue Oct 23 2018 - 14:10:32 PDT)
- Re: [AMBER] Struggling to convert AMBER .frcmod and .mol2 to GROMACS for HEME Bill Ross (Tue Oct 23 2018 - 14:47:38 PDT)
- Re: [AMBER] Struggling to convert AMBER .frcmod and .mol2 to GROMACS for HEME David Case (Tue Oct 23 2018 - 17:08:56 PDT)
- Re: [AMBER] Struggling to convert AMBER .frcmod and .mol2 to GROMACS for HEME ABEL Stephane (Wed Oct 24 2018 - 01:45:55 PDT)
  - [AMBER] TR : Struggling to convert AMBER .frcmod and .mol2 to GROMACS for HEME ABEL Stephane (Wed Oct 24 2018 - 01:50:20 PDT)
[AMBER] Material simulation using Amber and Interface FF Sundar (Tue Oct 23 2018 - 14:42:51 PDT)
- Re: [AMBER] Material simulation using Amber and Interface FF Pengfei Li (Fri Oct 26 2018 - 14:48:46 PDT)
[AMBER] Topological error for Mg in .prepin file. Anuja Ware (Wed Oct 24 2018 - 06:22:55 PDT)
- Re: [AMBER] Topological error for Mg in .prepin file. ABEL Stephane (Wed Oct 24 2018 - 06:41:03 PDT)
  - Re: [AMBER] Topological error for Mg in .prepin file. Anuja Ware (Wed Oct 24 2018 - 06:54:19 PDT)
    - Re: [AMBER] Topological error for Mg in .prepin file. ABEL Stephane (Wed Oct 24 2018 - 07:11:39 PDT)
- Re: [AMBER] Topological error for Mg in .prepin file. David Case (Wed Oct 24 2018 - 17:58:31 PDT)
- Re: [AMBER] Topological error for Mg in .prepin file. Pengfei Li (Fri Oct 26 2018 - 14:57:39 PDT)
[AMBER] Temperature-Replica Exchange MD Gilberto Pereira (Wed Oct 24 2018 - 07:26:32 PDT)
- Re: [AMBER] Temperature-Replica Exchange MD Alessandro Contini (Wed Oct 24 2018 - 07:53:00 PDT)
  - Re: [AMBER] Temperature-Replica Exchange MD Cruzeiro,Vinicius Wilian D (Wed Oct 24 2018 - 08:00:01 PDT)
[AMBER] MD_Box_size_and_counterions_counting_general_rule Antonio Amber Carlesso (Thu Oct 25 2018 - 04:54:55 PDT)
- Re: [AMBER] MD_Box_size_and_counterions_counting_general_rule David A Case (Thu Oct 25 2018 - 07:18:59 PDT)
  - Re: [AMBER] MD_Box_size_and_counterions_counting_general_rule Matias Machado (Wed Oct 31 2018 - 07:04:29 PDT)
    - Re: [AMBER] MD_Box_size_and_counterions_counting_general_rule Antonio Amber Carlesso (Thu Nov 08 2018 - 01:43:16 PST)
[AMBER] Ca ion bond distances restraints with chelator ? Michael Shokhen (Thu Oct 25 2018 - 05:25:35 PDT)
- Re: [AMBER] Ca ion bond distances restraints with chelator ? David A Case (Thu Oct 25 2018 - 07:26:03 PDT)
[AMBER] Measuring Membrane Curvature somdev pahari (Thu Oct 25 2018 - 11:31:05 PDT)
[AMBER] Sander and Thermodynamic integration and softcore Khabiri, Morteza (Thu Oct 25 2018 - 12:07:24 PDT)
- Re: [AMBER] Sander and Thermodynamic integration and softcore David A Case (Fri Oct 26 2018 - 05:06:55 PDT)
[AMBER] Na+ ion got stuck at one C-terminal end Rakesh Srivastava (Thu Oct 25 2018 - 23:25:13 PDT)
- Re: [AMBER] Na+ ion got stuck at one C-terminal end Pengfei Li (Fri Oct 26 2018 - 15:03:42 PDT)
  - Re: [AMBER] Na+ ion got stuck at one C-terminal end Rakesh Srivastava (Fri Oct 26 2018 - 21:30:09 PDT)
[AMBER] error in distance restraint input file Michael Shokhen (Fri Oct 26 2018 - 03:31:12 PDT)
- Re: [AMBER] error in distance restraint input file David A Case (Fri Oct 26 2018 - 05:12:09 PDT)
  - Re: [AMBER] error in distance restraint input file Michael Shokhen (Fri Oct 26 2018 - 05:34:53 PDT)
[AMBER] parmchk2 frcmod file Jon Uranga (Fri Oct 26 2018 - 03:36:12 PDT)
- Re: [AMBER] parmchk2 frcmod file David A Case (Fri Oct 26 2018 - 05:30:45 PDT)
  - Re: [AMBER] parmchk2 frcmod file Jon Uranga (Fri Oct 26 2018 - 05:57:34 PDT)
[AMBER] Question Regarding GRID Saikat Pal (Fri Oct 26 2018 - 07:44:09 PDT)
[AMBER] non-bonded params hosein geraili (Fri Oct 26 2018 - 09:30:36 PDT)
- Re: [AMBER] non-bonded params Matias Machado (Fri Oct 26 2018 - 11:23:36 PDT)
  - Re: [AMBER] non-bonded params hosein geraili (Fri Nov 02 2018 - 09:50:47 PDT)
    - Re: [AMBER] non-bonded params Matias Machado (Fri Nov 02 2018 - 12:11:26 PDT)
    - Re: [AMBER] non-bonded params hosein geraili (Wed Nov 07 2018 - 00:31:31 PST)
    - Re: [AMBER] non-bonded params Matias Machado (Fri Nov 09 2018 - 07:32:01 PST)
[AMBER] Post-process calculation of atomic forces SARAH JEANNE LEFAVE (Fri Oct 26 2018 - 17:00:10 PDT)
- Re: [AMBER] Post-process calculation of atomic forces Daniel Roe (Tue Oct 30 2018 - 08:20:34 PDT)
  - Re: [AMBER] Post-process calculation of atomic forces SARAH JEANNE LEFAVE (Wed Oct 31 2018 - 10:58:35 PDT)
[AMBER] the unperturbed charge of the unit is not zero soukaina louerdi (Sat Oct 27 2018 - 16:17:49 PDT)
- Re: [AMBER] the unperturbed charge of the unit is not zero David Case (Sat Oct 27 2018 - 18:10:49 PDT)
  - Re: [AMBER] the unperturbed charge of the unit is not zero soukaina louerdi (Sun Oct 28 2018 - 11:37:32 PDT)
    - Re: [AMBER] the unperturbed charge of the unit is not zero David A Case (Mon Oct 29 2018 - 05:07:46 PDT)
    - Re: [AMBER] the unperturbed charge of the unit is not zero soukaina louerdi (Tue Oct 30 2018 - 03:59:25 PDT)
    - Re: [AMBER] the unperturbed charge of the unit is not zero David A Case (Tue Oct 30 2018 - 05:08:03 PDT)
    - Re: [AMBER] the unperturbed charge of the unit is not zero soukaina louerdi (Tue Oct 30 2018 - 05:18:04 PDT)
    - Re: [AMBER] the unperturbed charge of the unit is not zero David A Case (Tue Oct 30 2018 - 08:52:25 PDT)
    - Re: [AMBER] the unperturbed charge of the unit is not zero Charu Sharma (JRF) (Tue Oct 30 2018 - 09:26:11 PDT)
    - Re: [AMBER] the unperturbed charge of the unit is not zero soukaina louerdi (Thu Nov 01 2018 - 12:15:15 PDT)
[AMBER] Interplane angles using vector and vectormath in cpptraj Matthew Turner (Mon Oct 29 2018 - 15:35:09 PDT)
- Re: [AMBER] Interplane angles using vector and vectormath in cpptraj Wesley Michael Botello-Smith (Mon Oct 29 2018 - 17:45:48 PDT)
- Re: [AMBER] Interplane angles using vector and vectormath in cpptraj Daniel Roe (Tue Oct 30 2018 - 05:53:35 PDT)
  - Re: [AMBER] Interplane angles using vector and vectormath in cpptraj Daniel Roe (Wed Nov 07 2018 - 05:54:30 PST)
[AMBER] AMBER18: user-defined reaction coordinate in umbrella sampling 李耀 (Tue Oct 30 2018 - 07:06:20 PDT)
[AMBER] Fortran runtime error: Bad value during integer read Thomas Evangelidis (Tue Oct 30 2018 - 15:55:14 PDT)
- Re: [AMBER] Fortran runtime error: Bad value during integer read David Case (Tue Oct 30 2018 - 18:45:37 PDT)
  - Re: [AMBER] Fortran runtime error: Bad value during integer read Thomas Evangelidis (Wed Oct 31 2018 - 04:14:06 PDT)
    - Re: [AMBER] Fortran runtime error: Bad value during integer read Carlos Simmerling (Wed Oct 31 2018 - 04:22:24 PDT)
    - Re: [AMBER] Fortran runtime error: Bad value during integer read Thomas Evangelidis (Wed Oct 31 2018 - 04:36:17 PDT)
    - Re: [AMBER] Fortran runtime error: Bad value during integer read Carlos Simmerling (Wed Oct 31 2018 - 04:42:00 PDT)
[AMBER] Amber Error (an illegal memory access) Avirup Ghosh (Tue Oct 30 2018 - 21:22:45 PDT)
[AMBER] amber18 installation problem Mary Dutta (Wed Oct 31 2018 - 03:48:13 PDT)
- Re: [AMBER] amber18 installation problem David A Case (Wed Oct 31 2018 - 05:04:17 PDT)
- Re: [AMBER] amber18 installation problem David A Case (Wed Oct 31 2018 - 05:06:00 PDT)
[AMBER] Problem regarding radial command Saikat Pal (Wed Oct 31 2018 - 05:01:13 PDT)
- Re: [AMBER] Problem regarding radial command Daniel Roe (Mon Nov 05 2018 - 07:12:29 PST)
[AMBER] CUDA 10.0 vs CUDA 9.2 for Amber18&1080Ti GTX - any gain in performance? Nikolay N. Kuzmich (Wed Oct 31 2018 - 07:31:56 PDT)
- Re: [AMBER] CUDA 10.0 vs CUDA 9.2 for Amber18&1080Ti GTX - any gain in performance? Ross Walker (Wed Oct 31 2018 - 13:12:54 PDT)
- Re: [AMBER] CUDA 10.0 vs CUDA 9.2 for Amber18&1080Ti GTX - any gain in performance? Nikolay N. Kuzmich (Fri Nov 02 2018 - 02:12:44 PDT)
[AMBER] CpH simulation- error reading charges in long cpin file Amy Rice (Thu Nov 01 2018 - 09:28:54 PDT)
- Re: [AMBER] CpH simulation- error reading charges in long cpin file Cruzeiro,Vinicius Wilian D (Thu Nov 01 2018 - 12:33:52 PDT)
  - Re: [AMBER] CpH simulation- error reading charges in long cpin file Amy Rice (Thu Nov 01 2018 - 12:49:47 PDT)
    - Re: [AMBER] CpH simulation- error reading charges in long cpin file Cruzeiro,Vinicius Wilian D (Thu Nov 01 2018 - 12:57:38 PDT)
[AMBER] Protein residues CA atoms treated as sidechain in binding energy decomposition? 鲍劲霄 (Fri Nov 02 2018 - 07:58:31 PDT)
[AMBER] Non-convergence when calculating partial charges for aromatic-adjacent nitriles Jeffrey Wagner (Fri Nov 02 2018 - 10:50:49 PDT)
- Re: [AMBER] Non-convergence when calculating partial charges for aromatic-adjacent nitriles James Kress (Fri Nov 02 2018 - 12:02:27 PDT)
- Re: [AMBER] Non-convergence when calculating partial charges for aromatic-adjacent nitriles David A Case (Mon Nov 05 2018 - 11:11:22 PST)
  - Re: [AMBER] Non-convergence when calculating partial charges for aromatic-adjacent nitriles Jeffrey Wagner (Tue Nov 06 2018 - 08:06:02 PST)
[AMBER] Postdoctoral position in the area of FFT-based binding free energy calculations David Minh (Fri Nov 02 2018 - 10:59:01 PDT)
[AMBER] ligand force field hosein geraili (Fri Nov 02 2018 - 11:22:13 PDT)
- Re: [AMBER] ligand force field Matias Machado (Fri Nov 09 2018 - 07:41:26 PST)
[AMBER] 回复： non-bonded params 201612095.mail.sdu.edu.cn (Fri Nov 02 2018 - 16:06:10 PDT)
[AMBER] 02_03.rms problem simon chapman (Sat Nov 03 2018 - 02:08:29 PDT)
- Re: [AMBER] 02_03.rms problem Daniel Roe (Sat Nov 03 2018 - 06:41:53 PDT)
  - Re: [AMBER] 02_03.rms problem simon chapman (Sat Nov 03 2018 - 07:49:19 PDT)
    - Re: [AMBER] 02_03.rms problem Daniel Roe (Mon Nov 05 2018 - 06:39:48 PST)
    - Re: [AMBER] 02_03.rms problem simon chapman (Mon Nov 05 2018 - 14:09:42 PST)
    - Re: [AMBER] 02_03.rms problem Daniel Roe (Thu Nov 08 2018 - 05:08:49 PST)
    - Re: [AMBER] 02_03.rms problem simon chapman (Wed Nov 07 2018 - 13:16:08 PST)
[AMBER] regarding ter Charu Sharma (JRF) (Sat Nov 03 2018 - 22:39:15 PDT)
- Re: [AMBER] regarding ter Vaibhav Dixit (Sat Nov 03 2018 - 22:49:47 PDT)
[AMBER] IR Spectra Abdullah Bin Faheem (Sun Nov 04 2018 - 22:07:16 PST)
- Re: [AMBER] IR Spectra David Case (Mon Nov 05 2018 - 17:40:00 PST)
[AMBER] Accelerated MD stopped with Cuda GPU error. M RCC (Sun Nov 04 2018 - 23:10:11 PST)
- Re: [AMBER] Accelerated MD stopped with Cuda GPU error. Bill Ross (Mon Nov 05 2018 - 00:08:43 PST)
  - Re: [AMBER] Accelerated MD stopped with Cuda GPU error. Bill Ross (Mon Nov 05 2018 - 00:25:41 PST)
- Re: [AMBER] Accelerated MD stopped with Cuda GPU error. M RCC (Wed Nov 07 2018 - 01:32:57 PST)
  - Re: [AMBER] Accelerated MD stopped with Cuda GPU error. Bill Ross (Wed Nov 07 2018 - 01:53:54 PST)
  - Re: [AMBER] Accelerated MD stopped with Cuda GPU error. M RCC (Wed Nov 07 2018 - 19:21:54 PST)
    - Re: [AMBER] Accelerated MD stopped with Cuda GPU error. Bill Ross (Wed Nov 07 2018 - 20:23:34 PST)
    - Re: [AMBER] Accelerated MD stopped with Cuda GPU error. accuratefreeenergy.gmail.com (Wed Nov 07 2018 - 20:31:34 PST)
    - Re: [AMBER] Accelerated MD stopped with Cuda GPU error. David Case (Thu Nov 08 2018 - 05:49:37 PST)
[AMBER] Acpype error. No such file or directory neelam wafa (Mon Nov 05 2018 - 07:18:51 PST)
[AMBER] Implicit solvent simulation effects for the folding Mijiddorj B (Mon Nov 05 2018 - 19:17:47 PST)
- Re: [AMBER] Implicit solvent simulation effects for the folding Hai Nguyen (Mon Nov 05 2018 - 20:16:50 PST)
  - Re: [AMBER] Implicit solvent simulation effects for the folding Mijiddorj B (Mon Nov 05 2018 - 20:50:14 PST)
    - Re: [AMBER] Implicit solvent simulation effects for the folding Carlos Simmerling (Tue Nov 06 2018 - 03:32:54 PST)
[AMBER] Help regarding AMBER16 CUDA installation Saikat Dutta chowdhury (Tue Nov 06 2018 - 05:13:29 PST)
- Re: [AMBER] Help regarding AMBER16 CUDA installation David Case (Tue Nov 06 2018 - 16:54:16 PST)
  - Re: [AMBER] Help regarding AMBER16 CUDA installation Saikat Dutta chowdhury (Tue Nov 06 2018 - 20:04:48 PST)
    - Re: [AMBER] Help regarding AMBER16 CUDA installation Hai Nguyen (Tue Nov 06 2018 - 20:46:13 PST)
    - Re: [AMBER] Help regarding AMBER16 CUDA installation Saikat Dutta chowdhury (Wed Nov 07 2018 - 00:29:44 PST)
    - Re: [AMBER] Help regarding AMBER16 CUDA installation Bill Ross (Wed Nov 07 2018 - 00:55:35 PST)
    - Re: [AMBER] Help regarding AMBER16 CUDA installation David A Case (Wed Nov 07 2018 - 04:43:28 PST)
[AMBER] amber 18 compilation issue Vlad Cojocaru (Tue Nov 06 2018 - 06:29:54 PST)
- Re: [AMBER] amber 18 compilation issue David A Case (Wed Nov 07 2018 - 05:05:23 PST)
- Re: [AMBER] amber 18 compilation issue Stephan Schott (Wed Nov 07 2018 - 07:21:54 PST)
  - Re: [AMBER] amber 18 compilation issue Vlad Cojocaru (Wed Nov 07 2018 - 07:54:51 PST)
- Re: [AMBER] amber 18 compilation issue Stephan Schott (Wed Nov 07 2018 - 08:57:07 PST)
[AMBER] different residue numbering Rosellen, Martin (Tue Nov 06 2018 - 07:27:37 PST)
- Re: [AMBER] different residue numbering Daniel Roe (Tue Nov 06 2018 - 12:59:28 PST)
  - Re: [AMBER] different residue numbering Daniel Roe (Wed Nov 14 2018 - 15:33:38 PST)
[AMBER] Generating topologies with antechamber and acpype neelam wafa (Wed Nov 07 2018 - 01:37:16 PST)
[AMBER] Geometric hard constraints Charo del Genio (Wed Nov 07 2018 - 02:44:16 PST)
[AMBER] Generation of velocities depends on conformation? Nicolas Cheron (Wed Nov 07 2018 - 02:44:11 PST)
- Re: [AMBER] Generation of velocities depends on conformation? Thomas Cheatham (Wed Nov 07 2018 - 04:15:05 PST)
- Re: [AMBER] Generation of velocities depends on conformation? David A Case (Wed Nov 07 2018 - 04:52:24 PST)
  - Re: [AMBER] Generation of velocities depends on conformation? Nicolas Cheron (Thu Nov 08 2018 - 00:54:59 PST)
[AMBER] MCPB.py Viviani, Lucas (Wed Nov 07 2018 - 02:49:48 PST)
- Re: [AMBER] MCPB.py Pengfei Li (Sat Nov 10 2018 - 15:18:59 PST)
[AMBER] Files work with sander and not pmemd Nicolas Cheron (Wed Nov 07 2018 - 03:12:38 PST)
- Re: [AMBER] Files work with sander and not pmemd David Case (Mon Nov 12 2018 - 14:20:22 PST)
  - Re: [AMBER] Files work with sander and not pmemd Nicolas Cheron (Tue Nov 13 2018 - 02:03:57 PST)
[AMBER] REMD: What can I do with much larger replicas than the number of processors Zhonghua Xia (Wed Nov 07 2018 - 07:22:51 PST)
- Re: [AMBER] REMD: What can I do with much larger replicas than the number of processors Cruzeiro,Vinicius Wilian D (Wed Nov 07 2018 - 07:50:20 PST)
  - Re: [AMBER] REMD: What can I do with much larger replicas than the number of processors Carlos Simmerling (Wed Nov 07 2018 - 11:37:29 PST)
- Re: [AMBER] REMD: What can I do with much larger replicas than the number of processors Qinghua Liao (Wed Nov 07 2018 - 11:43:00 PST)
- Re: [AMBER] REMD: What can I do with much larger replicas than the number of processors Wesley Michael Botello-Smith (Wed Nov 07 2018 - 14:40:14 PST)
  - Re: [AMBER] REMD: What can I do with much larger replicas than the number of processors Zhonghua Xia (Fri Nov 09 2018 - 05:27:07 PST)
[AMBER] problem of GPU with ibelly Hadi Rahmaninejad (Wed Nov 07 2018 - 08:05:44 PST)
- Re: [AMBER] problem of GPU with ibelly David A Case (Wed Nov 07 2018 - 11:50:30 PST)
  - Re: [AMBER] problem of GPU with ibelly Hadi Rahmaninejad (Wed Nov 07 2018 - 15:59:19 PST)
    - Re: [AMBER] problem of GPU with ibelly David Case (Thu Nov 08 2018 - 05:41:39 PST)
[AMBER] Error while using antechamber (AMBER 18) RITUPARNA ROY (Wed Nov 07 2018 - 23:08:13 PST)
- Re: [AMBER] Error while using antechamber (AMBER 18) David Case (Thu Nov 08 2018 - 05:52:54 PST)
[AMBER] Problem with obtaining iodine parameters via R.E.D. Server Markowska (Thu Nov 08 2018 - 04:29:21 PST)
- Re: [AMBER] Problem with obtaining iodine parameters via R.E.D. Server Markowska (Sun Nov 18 2018 - 23:32:33 PST)
[AMBER] post-simulation thermodynamic integration calculations Veenis, Andrew Jay (Thu Nov 08 2018 - 12:17:03 PST)
- Re: [AMBER] post-simulation thermodynamic integration calculations David A Case (Fri Nov 09 2018 - 05:26:04 PST)
  - Re: [AMBER] post-simulation thermodynamic integration calculations Veenis, Andrew Jay (Fri Nov 09 2018 - 09:57:29 PST)
[AMBER] CPPTRAJ "usefrcascoords" SARAH JEANNE LEFAVE (Thu Nov 08 2018 - 12:33:36 PST)
- Re: [AMBER] CPPTRAJ "usefrcascoords" Daniel Roe (Thu Nov 08 2018 - 12:46:45 PST)
  - Re: [AMBER] CPPTRAJ "usefrcascoords" SARAH JEANNE LEFAVE (Thu Nov 08 2018 - 12:50:44 PST)
    - Re: [AMBER] CPPTRAJ "usefrcascoords" Daniel Roe (Thu Nov 08 2018 - 12:56:10 PST)
    - Re: [AMBER] CPPTRAJ "usefrcascoords" SARAH JEANNE LEFAVE (Thu Nov 08 2018 - 13:31:37 PST)
    - Re: [AMBER] CPPTRAJ "usefrcascoords" Daniel Roe (Fri Nov 09 2018 - 12:17:20 PST)
    - Re: [AMBER-Developers] [AMBER] CPPTRAJ "usefrcascoords" Daniel Roe (Fri Nov 09 2018 - 12:22:56 PST)
    - Re: [AMBER] CPPTRAJ "usefrcascoords" SARAH JEANNE LEFAVE (Fri Nov 09 2018 - 12:35:37 PST)
    - Re: [AMBER] CPPTRAJ "usefrcascoords" SARAH JEANNE LEFAVE (Mon Nov 26 2018 - 09:31:26 PST)
Re: [AMBER] phosphorylated peptide with implicit solvent David A Case (Fri Nov 09 2018 - 05:17:44 PST)
[AMBER] Post-doctoral position in MD at UC Riverside giulia palermo (Fri Nov 09 2018 - 23:57:30 PST)
[AMBER] tLeap sequence overlap with new residues David Poole (Sat Nov 10 2018 - 06:45:13 PST)
- Re: [AMBER] tLeap sequence overlap with new residues David A Case (Mon Nov 12 2018 - 05:18:50 PST)
[AMBER] leap warning: The unperturbed charge of the unit: -0.388000 is not integral, can I proceed for MD with such warning? maryam azimzadehirani (Sun Nov 11 2018 - 04:40:39 PST)
- Re: [AMBER] leap warning: The unperturbed charge of the unit: -0.388000 is not integral, can I proceed for MD with such warning? David Cerutti (Sun Nov 11 2018 - 23:03:04 PST)
  - Re: [AMBER] leap warning: The unperturbed charge of the unit: -0.388000 is not integral, can I proceed for MD with such warning? maryam azimzadehirani (Mon Nov 12 2018 - 04:05:02 PST)
    - Re: [AMBER] leap warning: The unperturbed charge of the unit: -0.388000 is not integral, can I proceed for MD with such warning? ABEL Stephane (Mon Nov 12 2018 - 05:23:17 PST)
    - Re: [AMBER] leap warning: The unperturbed charge of the unit: -0.388000 is not integral, can I proceed for MD with such warning? maryam azimzadehirani (Mon Nov 12 2018 - 06:10:17 PST)
    - Re: [AMBER] leap warning: The unperturbed charge of the unit: -0.388000 is not integral, can I proceed for MD with such warning? David Cerutti (Mon Nov 12 2018 - 23:24:20 PST)
    - Re: [AMBER] leap warning: The unperturbed charge of the unit: -0.388000 is not integral, can I proceed for MD with such warning? Casalini Tommaso (Mon Nov 12 2018 - 23:39:40 PST)
    - Re: [AMBER] leap warning: The unperturbed charge of the unit: -0.388000 is not integral, can I proceed for MD with such warning? maryam azimzadehirani (Mon Nov 12 2018 - 23:41:42 PST)
    - Re: [AMBER] leap warning: The unperturbed charge of the unit: -0.388000 is not integral, can I proceed for MD with such warning? David Cerutti (Mon Nov 12 2018 - 23:49:45 PST)
    - Re: [AMBER] leap warning: The unperturbed charge of the unit: -0.388000 is not integral, can I proceed for MD with such warning? Dr. Anselm Horn (Tue Nov 13 2018 - 04:50:58 PST)
    - Re: [AMBER] leap warning: The unperturbed charge of the unit: -0.388000 is not integral, can I proceed for MD with such warning? Lachele Foley (Tue Nov 13 2018 - 05:57:59 PST)
    - Re: [AMBER] leap warning: The unperturbed charge of the unit: -0.388000 is not integral, can I proceed for MD with such warning? maryam azimzadehirani (Tue Nov 13 2018 - 06:06:15 PST)
    - Re: [AMBER] leap warning: The unperturbed charge of the unit: -0.388000 is not integral, can I proceed for MD with such warning? maryam azimzadehirani (Tue Nov 13 2018 - 23:10:11 PST)
    - Re: [AMBER] leap warning: The unperturbed charge of the unit: -0.388000 is not integral, can I proceed for MD with such warning? David A Case (Mon Nov 12 2018 - 05:26:58 PST)
    - Re: [AMBER] leap warning: The unperturbed charge of the unit: -0.388000 is not integral, can I proceed for MD with such warning? Casalini Tommaso (Mon Nov 12 2018 - 05:36:45 PST)
[AMBER] Preparation of force field of zwitterion glycine molecule euq1702 (Sun Nov 11 2018 - 08:14:49 PST)
- Re: [AMBER] Preparation of force field of zwitterion glycine molecule David A Case (Mon Nov 12 2018 - 05:36:44 PST)
  - Re: [AMBER] Preparation of force field of zwitterion glycine molecule euq1702 (Mon Nov 12 2018 - 06:20:44 PST)
[AMBER] How long should a NPT equilibrium take in QM/MM MD? Meng Wu (Mon Nov 12 2018 - 02:28:14 PST)
- Re: [AMBER] How long should a NPT equilibrium take in QM/MM MD? David Case (Mon Nov 12 2018 - 14:16:48 PST)
  - Re: [AMBER] How long should a NPT equilibrium take in QM/MM MD? David Case (Mon Nov 12 2018 - 17:22:17 PST)
Re: [AMBER] Energies SARAH JEANNE LEFAVE (Mon Nov 12 2018 - 08:14:56 PST)
- Re: [AMBER] Energies David A Case (Mon Nov 12 2018 - 10:03:25 PST)
[AMBER] how long should a NPT equilibrium take in QM/MM MD? 郭昱 (Mon Nov 12 2018 - 17:17:56 PST)
- Re: [AMBER] how long should a NPT equilibrium take in QM/MM MD? Joan Torras (Mon Nov 12 2018 - 18:05:11 PST)
[AMBER] regarding tutorials Charu Sharma (JRF) (Mon Nov 12 2018 - 21:41:28 PST)
- Re: [AMBER] regarding tutorials Bill Ross (Mon Nov 12 2018 - 22:26:12 PST)
[AMBER] query Charu Sharma (JRF) (Mon Nov 12 2018 - 22:27:35 PST)
- Re: [AMBER] query Keiran Corbett (Tue Nov 13 2018 - 00:40:59 PST)
[AMBER] RMSD mask selection and closestwater clarification Korey M Reid (Tue Nov 13 2018 - 14:17:06 PST)
- Re: [AMBER] RMSD mask selection and closestwater clarification Korey M Reid (Tue Nov 13 2018 - 14:40:05 PST)
- Re: [AMBER] RMSD mask selection and closestwater clarification Daniel Roe (Thu Nov 15 2018 - 05:12:01 PST)
  - Re: [AMBER] RMSD mask selection and closestwater clarification Korey M Reid (Thu Nov 15 2018 - 14:18:28 PST)
[AMBER] Radial Distribution Function of Waters with respect to a particular Atom diego.soler.uam.es (Wed Nov 14 2018 - 02:11:06 PST)
- Re: [AMBER] Radial Distribution Function of Waters with respect to a particular Atom Daniel Roe (Wed Nov 14 2018 - 15:57:35 PST)
[AMBER] regarding MD simulation Charu Sharma (JRF) (Wed Nov 14 2018 - 02:57:36 PST)
[AMBER] Regarding output file processing of temperature replica exchange Rajarshi Roy (Wed Nov 14 2018 - 04:01:50 PST)
- Re: [AMBER] Regarding output file processing of temperature replica exchange Daniel Roe (Wed Nov 14 2018 - 06:10:06 PST)
  - Re: [AMBER] Regarding output file processing of temperature replica exchange Rajarshi Roy (Fri Nov 16 2018 - 00:13:36 PST)
    - Re: [AMBER] Regarding output file processing of temperature replica exchange Daniel Roe (Fri Nov 16 2018 - 06:59:13 PST)
    - Re: [AMBER] Regarding output file processing of temperature replica exchange Rajarshi Roy (Fri Nov 16 2018 - 09:46:50 PST)
    - Re: [AMBER] Regarding output file processing of temperature replica exchange Daniel Roe (Mon Nov 19 2018 - 06:34:30 PST)
    - Re: [AMBER] Regarding output file processing of temperature replica exchange Rajarshi Roy (Sat Nov 24 2018 - 09:45:51 PST)
    - Re: [AMBER] Regarding output file processing of temperature replica exchange Thomas Cheatham (Sat Nov 24 2018 - 18:53:20 PST)
    - Re: [AMBER] Regarding output file processing of temperature replica exchange Rajarshi Roy (Mon Nov 26 2018 - 08:37:42 PST)
    - Re: [AMBER] Regarding output file processing of temperature replica exchange Carlos Simmerling (Mon Nov 26 2018 - 09:10:21 PST)
[AMBER] reconstruction of pH-based trajectory files Elvira Tarasova (Wed Nov 14 2018 - 20:25:15 PST)
- Re: [AMBER] reconstruction of pH-based trajectory files Daniel Roe (Thu Nov 15 2018 - 05:15:21 PST)
  - Re: [AMBER] reconstruction of pH-based trajectory files Elvira Tarasova (Thu Nov 15 2018 - 20:21:36 PST)
    - Re: [AMBER] reconstruction of pH-based trajectory files Daniel Roe (Fri Nov 16 2018 - 07:11:03 PST)
    - Re: [AMBER] reconstruction of pH-based trajectory files Elvira Tarasova (Sat Nov 17 2018 - 05:09:41 PST)
[AMBER] Antechamber with protonated arginine Jose Manuel Granadino Roldán (Wed Nov 14 2018 - 23:05:12 PST)
- Re: [AMBER] Antechamber with protonated arginine David Case (Thu Nov 15 2018 - 05:41:30 PST)
  - Re: [AMBER] Antechamber with protonated arginine Jaime Rubio Martinez (Tue Nov 20 2018 - 08:47:34 PST)
    - Re: [AMBER] Antechamber with protonated arginine Junmei Wang (Tue Nov 20 2018 - 12:50:52 PST)
[AMBER] Amber 18 memory Beale, John (Thu Nov 15 2018 - 01:05:19 PST)
- [AMBER] new amber mailing list for beginner questions Paul Westphälinger (Thu Nov 15 2018 - 03:19:28 PST)
  - Re: [AMBER] new amber mailing list for beginner questions Luca Codutti (Thu Nov 15 2018 - 04:05:02 PST)
- Re: [AMBER] Amber 18 memory Bill Ross (Thu Nov 15 2018 - 13:40:15 PST)
[AMBER] GPU card for AMBER Fabian Glaser (Thu Nov 15 2018 - 03:16:43 PST)
- Re: [AMBER] GPU card for AMBER Ross Walker (Sat Nov 17 2018 - 02:15:02 PST)
  - Re: [AMBER] GPU card for AMBER Fabian Glaser (Sun Nov 18 2018 - 08:20:36 PST)
[AMBER] Antechamber for PCBM soukaina louerdi (Thu Nov 15 2018 - 05:07:50 PST)
- Re: [AMBER] Antechamber for PCBM David A Case (Mon Nov 19 2018 - 05:28:36 PST)
  - Re: [AMBER] Antechamber for PCBM soukaina louerdi (Mon Nov 19 2018 - 11:17:19 PST)
    - Re: [AMBER] Antechamber for PCBM David Case (Mon Nov 19 2018 - 14:22:58 PST)
    - Re: [AMBER] Antechamber for PCBM David Case (Mon Nov 19 2018 - 14:27:18 PST)
    - Re: [AMBER] Antechamber for PCBM soukaina louerdi (Fri Nov 23 2018 - 07:37:24 PST)
    - Re: [AMBER] Antechamber for PCBM Maura Malinska (Fri Nov 23 2018 - 09:01:20 PST)
    - Re: [AMBER] Antechamber for PCBM soukaina louerdi (Fri Nov 23 2018 - 14:12:04 PST)
[AMBER] very high values of "wrapping mol" when potential boost applied to chloroform solvent system Chetna Tyagi (Thu Nov 15 2018 - 05:24:53 PST)
- Re: [AMBER] very high values of "wrapping mol" when potential boost applied to chloroform solvent system David Case (Thu Nov 15 2018 - 13:30:24 PST)
  - Re: [AMBER] very high values of "wrapping mol" when potential boost applied to chloroform solvent system Chetna Tyagi (Fri Nov 16 2018 - 02:40:39 PST)
    - Re: [AMBER] very high values of "wrapping mol" when potential boost applied to chloroform solvent system Chetna Tyagi (Fri Nov 16 2018 - 02:58:58 PST)
[AMBER] Building crystal structures Ali Khodayari (Thu Nov 15 2018 - 11:28:52 PST)
- Re: [AMBER] Building crystal structures David Cerutti (Thu Nov 15 2018 - 11:41:54 PST)
  - Re: [AMBER] Building crystal structures Ali Khodayari (Thu Nov 15 2018 - 13:16:12 PST)
    - Re: [AMBER] Building crystal structures David Cerutti (Thu Nov 15 2018 - 13:25:26 PST)
[AMBER] Problem in designing MD simulation based on Experimental data Bharat Manna (Fri Nov 16 2018 - 07:53:12 PST)
- Re: [AMBER] Problem in designing MD simulation based on Experimental data Chris Moth (Fri Nov 16 2018 - 06:16:40 PST)
[AMBER] regarding creation of production MD output Charu Sharma (JRF) (Fri Nov 16 2018 - 08:33:23 PST)
- Re: [AMBER] regarding creation of production MD output Chetna Tyagi (Fri Nov 16 2018 - 08:27:29 PST)
- Re: [AMBER] regarding creation of production MD output Charu Sharma (JRF) (Fri Nov 16 2018 - 08:48:52 PST)
[AMBER] md production Charu Sharma (JRF) (Fri Nov 16 2018 - 21:07:57 PST)
[AMBER] xmgrace Charu Sharma (JRF) (Fri Nov 16 2018 - 21:23:11 PST)
- Re: [AMBER] xmgrace mathew k varghese (Fri Mar 20 2009 - 22:18:32 PDT)
  - Re:Re: [AMBER] xmgrace Nancy (Fri Mar 20 2009 - 22:42:48 PDT)
- Re: [AMBER] xmgrace Premila Samuel Mohan Dass (Fri Nov 16 2018 - 21:35:20 PST)
- Re: [AMBER] xmgrace Daniel Roe (Mon Nov 19 2018 - 06:27:10 PST)
[AMBER] graph Charu Sharma (JRF) (Fri Nov 16 2018 - 22:01:24 PST)
- Re: [AMBER] graph Markowska (Fri Nov 16 2018 - 22:43:50 PST)
[AMBER] regarding ambpdb Charu Sharma (JRF) (Sun Nov 18 2018 - 01:22:59 PST)
- Re: [AMBER] regarding ambpdb Elvis Martis (Sun Nov 18 2018 - 03:13:42 PST)
  - Re: [AMBER] regarding ambpdb Charu Sharma (JRF) (Sun Nov 18 2018 - 03:45:51 PST)
    - Re: [AMBER] regarding ambpdb Bill Ross (Sun Nov 18 2018 - 05:12:43 PST)
    - Re: [AMBER-Developers] [AMBER] regarding ambpdb David Case (Sun Nov 18 2018 - 05:23:12 PST)
[AMBER] cpptraj eroor Rajbinder Kaur Virk (Sun Nov 18 2018 - 05:33:03 PST)
[AMBER] Post_analysis_Amber_tools_suggestion Antonio Amber Carlesso (Sun Nov 18 2018 - 06:09:51 PST)
[AMBER] Errors regarding generation of parameter file shivangi agarwal (Sun Nov 18 2018 - 19:15:50 PST)
- Re: [AMBER] Errors regarding generation of parameter file David A Case (Mon Nov 19 2018 - 05:20:23 PST)
  - Re: [AMBER] Errors regarding generation of parameter file shivangi agarwal (Mon Nov 19 2018 - 06:54:54 PST)
[AMBER] CUDA problems in Amber18 Julio Dominguez (Sun Nov 18 2018 - 19:33:30 PST)
- Re: [AMBER] CUDA problems in Amber18 Ross Walker (Mon Nov 19 2018 - 18:14:40 PST)
- Re: [AMBER] CUDA problems in Amber18 Julio Dominguez (Wed Nov 21 2018 - 14:09:06 PST)
[AMBER] antechamber soukaina louerdi (Mon Nov 19 2018 - 03:29:51 PST)
- Re: [AMBER] antechamber R. A. (Wed Jul 01 2009 - 17:46:19 PDT)
  - Re: [AMBER] antechamber FyD (Wed Jul 01 2009 - 23:33:46 PDT)
    - Re: [AMBER] antechamber Alan (Thu Jul 02 2009 - 03:16:55 PDT)
- Re: [AMBER] antechamber R. A. (Thu Jul 02 2009 - 17:35:42 PDT)
  - 回复： [AMBER] antechamber 廖青华 (Thu Jul 02 2009 - 17:45:41 PDT)
    - 回复：回复： [AMBER] antechamber 廖青华 (Thu Jul 02 2009 - 17:53:06 PDT)
- Re: [AMBER] antechamber David A Case (Mon Nov 19 2018 - 05:27:18 PST)
[AMBER] cpptraj error Rajbinder Kaur Virk (Mon Nov 19 2018 - 04:59:02 PST)
- Re: [AMBER] cpptraj error Daniel Roe (Mon Nov 19 2018 - 06:00:25 PST)
  - Re: [AMBER] cpptraj error Charu Sharma (JRF) (Mon Nov 19 2018 - 09:22:15 PST)
    - Re: [AMBER] cpptraj error Carlos Simmerling (Mon Nov 19 2018 - 09:31:27 PST)
    - Re: [AMBER] cpptraj error Daniel Roe (Mon Nov 19 2018 - 10:04:59 PST)
  - Re: [AMBER] cpptraj error Rajbinder Kaur Virk (Sun Dec 02 2018 - 22:16:28 PST)
    - Re: [AMBER] cpptraj error Daniel Roe (Mon Dec 03 2018 - 11:23:50 PST)
    - Re: [AMBER] cpptraj error Rajbinder Kaur Virk (Tue Dec 04 2018 - 01:18:29 PST)
[AMBER] About dpeaks implementation in cpptraj Casalini Tommaso (Mon Nov 19 2018 - 05:49:19 PST)
- Re: [AMBER] About dpeaks implementation in cpptraj Daniel Roe (Mon Nov 19 2018 - 06:23:26 PST)
  - Re: [AMBER] About dpeaks implementation in cpptraj Casalini Tommaso (Mon Nov 19 2018 - 07:47:10 PST)
[AMBER] Correction needed for output of energy action command in cpptraj Veenis, Andrew Jay (Mon Nov 19 2018 - 10:02:18 PST)
- Re: [AMBER] Correction needed for output of energy action command in cpptraj Daniel Roe (Mon Nov 19 2018 - 10:14:58 PST)
  - Re: [AMBER] Correction needed for output of energy action command in cpptraj Daniel Roe (Wed Nov 28 2018 - 07:49:25 PST)
[AMBER] REGARDING TUTORIAL Charu Sharma (JRF) (Tue Nov 20 2018 - 15:39:07 PST)
- Re: [AMBER] REGARDING TUTORIAL David A Case (Wed Nov 21 2018 - 06:46:10 PST)
[AMBER] CPPTRAJ/PnetCDF error Nikolay N. Kuzmich (Wed Nov 21 2018 - 01:34:37 PST)
- Re: [AMBER] CPPTRAJ/PnetCDF error Daniel Roe (Mon Nov 26 2018 - 06:39:23 PST)
[AMBER] RTX 2080 slower then 1080 Ti with pmemd 18 ? Alain Chaumont (Wed Nov 21 2018 - 11:24:29 PST)
- Re: [AMBER] RTX 2080 slower then 1080 Ti with pmemd 18 ? Ross Walker (Wed Nov 21 2018 - 12:37:27 PST)
  - Re: [AMBER] RTX 2080 slower then 1080 Ti with pmemd 18 ? Ross Walker (Wed Nov 21 2018 - 12:43:35 PST)
  - Re: [AMBER] RTX 2080 slower then 1080 Ti with pmemd 18 ? Charles-Alexandre Mattelaer (Sat Oct 05 2019 - 14:11:52 PDT)
    - Re: [AMBER] RTX 2080 slower then 1080 Ti with pmemd 18 ? Ross Walker (Sun Oct 06 2019 - 13:22:33 PDT)
    - Re: [AMBER] RTX 2080 slower then 1080 Ti with pmemd 18 ? Charles-Alexandre Mattelaer (Sun Oct 06 2019 - 23:01:19 PDT)
[AMBER] The interaction energy between substrate molecule and protein Meng Wu (Thu Nov 22 2018 - 02:44:55 PST)
[AMBER] polymer state hosein geraili (Thu Nov 22 2018 - 07:35:38 PST)
- Re: [AMBER] polymer state andreas.tosstorff.cup.uni-muenchen.de (Thu Nov 22 2018 - 10:00:46 PST)
  - Re: [AMBER] polymer state hosein geraili (Thu Nov 22 2018 - 12:26:26 PST)
[AMBER] Getting error for MMPB/GBSA calculaton Saikat Pal (Thu Nov 22 2018 - 07:44:49 PST)
- Re: [AMBER] Getting error for MMPB/GBSA calculaton David Case (Fri Nov 23 2018 - 06:47:34 PST)
[AMBER] Obtaining contact maps with cpptraj Stefan Ivanov (Thu Nov 22 2018 - 20:47:59 PST)
- Re: [AMBER] Obtaining contact maps with cpptraj Daniel Roe (Mon Dec 03 2018 - 12:14:13 PST)
  - Re: [AMBER] Obtaining contact maps with cpptraj Alex Spasic (Tue Dec 04 2018 - 12:25:22 PST)
[AMBER] Running tleap for topology generation of a list of pdb files. Leena Aggarwal (Fri Nov 23 2018 - 02:44:39 PST)
- Re: [AMBER] Running tleap for topology generation of a list of pdb files. Alechania Misturini (Fri Nov 23 2018 - 03:33:56 PST)
  - Re: [AMBER] Running tleap for topology generation of a list of pdb files. Alechania Misturini (Fri Nov 23 2018 - 03:39:57 PST)
    - Re: [AMBER] Running tleap for topology generation of a list of pdb files. Leena Aggarwal (Fri Nov 23 2018 - 21:42:01 PST)
[AMBER] Hamiltonian Replica Exchange with Amber 18 Bruno Falcone (Fri Nov 23 2018 - 07:28:29 PST)
- Re: [AMBER] Hamiltonian Replica Exchange with Amber 18 Jason Swails (Mon Nov 26 2018 - 08:20:36 PST)
  - Re: [AMBER] Hamiltonian Replica Exchange with Amber 18 Bruno Falcone (Mon Nov 26 2018 - 13:22:48 PST)
[AMBER] RMSF Charu Sharma (JRF) (Sat Nov 24 2018 - 03:25:44 PST)
- Re: [AMBER] RMSF David Case (Sat Nov 24 2018 - 06:41:26 PST)
  - Re: [AMBER] RMSF Charu Sharma (JRF) (Sun Nov 25 2018 - 20:34:12 PST)
[AMBER] Parametrs for Targeted MD Mohamad Reza G. (Sat Nov 24 2018 - 03:52:26 PST)
[AMBER] Latest force field shivangi agarwal (Sat Nov 24 2018 - 09:15:50 PST)
- Re: [AMBER] Latest force field andreas.tosstorff.cup.uni-muenchen.de (Sun Nov 25 2018 - 09:28:27 PST)
[AMBER] Ante-MMPBSA.py error jacky zhao (Sat Nov 24 2018 - 19:05:54 PST)
- Re: [AMBER] Ante-MMPBSA.py error David Case (Sun Nov 25 2018 - 12:06:45 PST)
[AMBER] RMSD Charu Sharma (JRF) (Sun Nov 25 2018 - 22:01:47 PST)
[AMBER] new amber mailing list for beginner questions/mailing list for advanced users&bug reports Paul Westphälinger (Mon Nov 26 2018 - 01:15:01 PST)
- Re: [AMBER] new amber mailing list for beginner questions/mailing list for advanced users&bug reports Jason Swails (Mon Nov 26 2018 - 08:44:44 PST)
  - Re: [AMBER] new amber mailing list for beginner questions/mailing list for advanced users&bug reports Paul Westphälinger (Tue Nov 27 2018 - 03:18:07 PST)
    - Re: [AMBER] new amber mailing list for beginner questions/mailing list for advanced users&bug reports Daniel Roe (Tue Nov 27 2018 - 06:34:31 PST)
    - Re: [AMBER] new amber mailing list for beginner questions/mailing list for advanced users&bug reports Lachele Foley (Tue Nov 27 2018 - 12:49:29 PST)
[AMBER] RESP charge calculation Aashish Bhatt (Mon Nov 26 2018 - 04:43:09 PST)
- Re: [AMBER] RESP charge calculation Pengfei Li (Sat Dec 08 2018 - 18:27:17 PST)
  - Re: [AMBER] RESP charge calculation Aashish Bhatt (Mon Dec 10 2018 - 02:54:14 PST)
[AMBER] Regarding the Targeted MD M. Reza Ganjalikhany (Mon Nov 26 2018 - 12:21:59 PST)
- Re: [AMBER] Regarding the Targeted MD M. Reza Ganjalikhany (Mon Nov 26 2018 - 12:25:11 PST)
- Re: [AMBER] Regarding the Targeted MD Carlos Simmerling (Mon Nov 26 2018 - 12:52:42 PST)
  - Re: [AMBER] Regarding the Targeted MD Carlos Simmerling (Mon Nov 26 2018 - 12:53:42 PST)
    - Re: [AMBER] Regarding the Targeted MD M. Reza Ganjalikhany (Thu Nov 29 2018 - 05:31:29 PST)
    - Re: [AMBER] Regarding the Targeted MD Carlos Simmerling (Thu Nov 29 2018 - 14:38:11 PST)
    - Re: [AMBER] Regarding the Targeted MD M. Reza Ganjalikhany (Fri Nov 30 2018 - 01:22:00 PST)
    - Re: [AMBER] Regarding the Targeted MD Carlos Simmerling (Fri Nov 30 2018 - 04:29:03 PST)
    - Re: [AMBER] Regarding the Targeted MD M. Reza Ganjalikhany (Fri Nov 30 2018 - 05:25:08 PST)
[AMBER] QMMM free energy calculations for alchemical changes using a coupling parameter in amber 18 Braden Kelly (Tue Nov 27 2018 - 00:10:01 PST)
- Re: [AMBER] QMMM free energy calculations for alchemical changes using a coupling parameter in amber 18 Brian Radak (Tue Nov 27 2018 - 08:51:35 PST)
- Re: [AMBER] QMMM free energy calculations for alchemical changes using a coupling parameter in amber 18 David Case (Tue Nov 27 2018 - 18:51:46 PST)
  - Re: [AMBER] QMMM free energy calculations for alchemical changes using a coupling parameter in amber 18 Braden Kelly (Wed Nov 28 2018 - 13:15:14 PST)
    - Re: [AMBER] QMMM free energy calculations for alchemical changes using a coupling parameter in amber 18 Brian Radak (Thu Nov 29 2018 - 07:18:06 PST)
    - Re: [AMBER] QMMM free energy calculations for alchemical changes using a coupling parameter in amber 18 Braden Kelly (Thu Nov 29 2018 - 10:35:40 PST)
    - Re: [AMBER] QMMM free energy calculations for alchemical changes using a coupling parameter in amber 18 Adrian Roitberg (Thu Nov 29 2018 - 10:46:48 PST)
    - Re: [AMBER] QMMM free energy calculations for alchemical changes using a coupling parameter in amber 18 Goetz, Andreas (Thu Nov 29 2018 - 11:23:14 PST)
    - Re: [AMBER] QMMM free energy calculations for alchemical changes using a coupling parameter in amber 18 Adrian Roitberg (Thu Nov 29 2018 - 11:31:18 PST)
    - Re: [AMBER] QMMM free energy calculations for alchemical changes using a coupling parameter in amber 18 Brian Radak (Thu Nov 29 2018 - 13:56:36 PST)
    - Re: [AMBER] QMMM free energy calculations for alchemical changes using a coupling parameter in amber 18 E. Kuechler (Thu Nov 29 2018 - 17:13:32 PST)
    - Re: [AMBER] QMMM free energy calculations for alchemical changes using a coupling parameter in amber 18 David A Case (Fri Nov 30 2018 - 05:15:20 PST)
[AMBER] Failed to merge the protein-ligand amoeba parameters 王茜茜 (Tue Nov 27 2018 - 00:46:01 PST)
- Re: [AMBER] Failed to merge the protein-ligand amoeba parameters David A Case (Wed Nov 28 2018 - 04:43:48 PST)
  - Re: [AMBER] Failed to merge the protein-ligand amoeba parameters 王茜茜 (Wed Nov 28 2018 - 05:38:18 PST)
[AMBER] Why does makeCHIR_RST create restraints for side chains? Stefan Ivanov (Tue Nov 27 2018 - 01:11:39 PST)
- Re: [AMBER] Why does makeCHIR_RST create restraints for side chains? David A Case (Tue Nov 27 2018 - 10:08:38 PST)
  - Re: [AMBER] Why does makeCHIR_RST create restraints for side chains? Stefan Ivanov (Tue Nov 27 2018 - 10:35:46 PST)
[AMBER] Velocity autocorrelation function(VACF) Aashish Bhatt (Tue Nov 27 2018 - 04:24:28 PST)
- Re: [AMBER] Velocity autocorrelation function(VACF) Daniel Roe (Tue Nov 27 2018 - 05:58:36 PST)
[AMBER] Announcement: Release of DOCK 6.9 Scott Brozell (Tue Nov 27 2018 - 17:29:21 PST)
[AMBER] thermostat on solvent hosein geraili (Tue Nov 27 2018 - 23:47:19 PST)
- Re: [AMBER] thermostat on solvent David Case (Thu Dec 06 2018 - 19:04:46 PST)
[AMBER] Combining GAFF and GLYCAM force fields to describe a non-natural sugar José Daniel Martinez (Wed Nov 28 2018 - 08:50:38 PST)
- Re: [AMBER] Combining GAFF and GLYCAM force fields to describe a non-natural sugar David Cerutti (Wed Nov 28 2018 - 10:53:58 PST)
  - Re: [AMBER] Combining GAFF and GLYCAM force fields to describe a non-natural sugar Lachele Foley (Wed Nov 28 2018 - 11:19:14 PST)
    - Re: [AMBER] Combining GAFF and GLYCAM force fields to describe a non-natural sugar José Daniel Martinez (Thu Nov 29 2018 - 00:52:44 PST)
    - Re: [AMBER] Combining GAFF and GLYCAM force fields to describe a non-natural sugar David Cerutti (Thu Nov 29 2018 - 08:59:30 PST)
  - Re: [AMBER] Combining GAFF and GLYCAM force fields to describe a non-natural sugar José Daniel Martinez (Thu Nov 29 2018 - 00:52:14 PST)
[AMBER] Minimisation and periodic boundaries. Stejskal, Lenka (Wed Nov 28 2018 - 09:56:30 PST)
- Re: [AMBER] Minimisation and periodic boundaries. Sally Pias (Wed Nov 28 2018 - 10:53:55 PST)
- Re: [AMBER] Minimisation and periodic boundaries. Stejskal, Lenka (Wed Nov 28 2018 - 12:17:14 PST)
  - Re: [AMBER] Minimisation and periodic boundaries. Daniel Roe (Mon Dec 03 2018 - 12:21:16 PST)
- [AMBER] Linear Interaction Energy Pietro Aronica (Thu Nov 29 2018 - 01:43:51 PST)
  - [AMBER] Head-to-tail cyclized Peptides Pietro Aronica (Thu Nov 29 2018 - 20:46:30 PST)
    - Re: [AMBER] Head-to-tail cyclized Peptides Bill Ross (Thu Nov 29 2018 - 21:11:57 PST)
    - Re: [AMBER] Head-to-tail cyclized Peptides Pietro Aronica (Thu Nov 29 2018 - 21:37:21 PST)
    - Re: [AMBER] Head-to-tail cyclized Peptides Dr. Anselm Horn (Fri Nov 30 2018 - 07:16:27 PST)
    - Re: [AMBER] Head-to-tail cyclized Peptides David A Case (Fri Nov 30 2018 - 05:06:06 PST)
  - Re: [AMBER] Linear Interaction Energy Daniel Roe (Mon Dec 03 2018 - 12:50:03 PST)
[AMBER] equilibration of Packmol generated boxes Arkajyoti Sengupta (Wed Nov 28 2018 - 15:30:31 PST)
[AMBER] Choosing a temperature schedule for Simulated annealing Rajbinder Kaur Virk (Wed Nov 28 2018 - 23:19:39 PST)
Re: [AMBER] reminder Chhaya Singh (Thu Nov 29 2018 - 09:13:50 PST)
[AMBER] free energy calculation for restraining ligand Sukanya Sasmal (Thu Nov 29 2018 - 18:27:53 PST)
[AMBER] Installation & testing of AMBER18 parallel GPU problem Ibrahim M. Moustafa (Fri Nov 30 2018 - 09:38:11 PST)
[AMBER] Extracting PDBs every 'N" ns Jag Silwal (Sun Dec 02 2018 - 07:16:15 PST)
- [AMBER] Ris: Extracting PDBs every 'N" ns Casalini Tommaso (Sun Dec 02 2018 - 07:45:16 PST)
  - Re: [AMBER] Ris: Extracting PDBs every 'N" ns Jag Silwal (Sun Dec 02 2018 - 07:54:44 PST)
    - [AMBER] Ris: Ris: Extracting PDBs every 'N" ns Casalini Tommaso (Sun Dec 02 2018 - 08:02:03 PST)
- Re: [AMBER] Extracting PDBs every 'N" ns David Case (Sun Dec 02 2018 - 11:40:27 PST)
  - Re: [AMBER] Extracting PDBs every 'N" ns Jag Silwal (Mon Dec 03 2018 - 02:25:11 PST)
    - Re: [AMBER] Extracting PDBs every 'N" ns Daniel Roe (Mon Dec 03 2018 - 11:14:20 PST)
[AMBER] RMSD vs RMSF Xiaoyu Wang (Sun Dec 02 2018 - 16:28:45 PST)
- Re: [AMBER] RMSD vs RMSF Elvis Martis (Sun Dec 02 2018 - 20:51:24 PST)
[AMBER] TUTORIAL Charu Sharma (JRF) (Mon Dec 03 2018 - 01:54:35 PST)
- Re: [AMBER] TUTORIAL Bill Ross (Mon Dec 03 2018 - 02:24:26 PST)
  - Re: [AMBER] TUTORIAL Charu Sharma (JRF) (Mon Dec 03 2018 - 02:34:12 PST)
    - Re: [AMBER] TUTORIAL Bill Ross (Mon Dec 03 2018 - 02:44:42 PST)
    - Re: [AMBER] TUTORIAL Charu Sharma (JRF) (Mon Dec 03 2018 - 02:53:05 PST)
    - Re: [AMBER] TUTORIAL Bill Ross (Mon Dec 03 2018 - 03:05:37 PST)
[AMBER] minimization difficulties Kimia Sh (Mon Dec 03 2018 - 02:46:16 PST)
- Re: [AMBER] minimization difficulties Bill Ross (Mon Dec 03 2018 - 03:10:05 PST)
- Re: [AMBER] minimization difficulties David A Case (Mon Dec 03 2018 - 07:05:32 PST)
[AMBER] MCPB.py problems For atom (.R<AL1 380>.A<CL2 1>) could not find vdW (or other) parameters for type (Y1) Jinfeng Chen (Mon Dec 03 2018 - 03:42:29 PST)
- Re: [AMBER] MCPB.py problems For atom (.R<AL1 380>.A<CL2 1>) could not find vdW (or other) parameters for type (Y1) Pengfei Li (Sat Dec 08 2018 - 18:34:00 PST)
[AMBER] Delta G pb and Delta G Sa Keiran Corbett (Mon Dec 03 2018 - 08:00:11 PST)
- Re: [AMBER] Delta G pb and Delta G Sa Wesley Michael Botello-Smith (Mon Dec 03 2018 - 10:19:41 PST)
[AMBER] stapled peptide- PDB bond atom problem Angew Chemie (Mon Dec 03 2018 - 08:45:08 PST)
- Re: [AMBER] stapled peptide- PDB bond atom problem David A Case (Mon Dec 03 2018 - 10:17:07 PST)
[AMBER] QM/MM using Amber and Gaussian: Discrepancies between the QM energy from the gaussian output file and the energy reported in the mdout file as EXTERNESCF Eric Lang (Tue Dec 04 2018 - 03:36:20 PST)
- Re: [AMBER] QM/MM using Amber and Gaussian: Discrepancies between the QM energy from the gaussian output file and the energy reported in the mdout file as EXTERNESCF Antoine MARION (Tue Dec 04 2018 - 06:22:56 PST)
  - Re: [AMBER] QM/MM using Amber and Gaussian: Discrepancies between the QM energy from the gaussian output file and the energy reported in the mdout file as EXTERNESCF Eric Lang (Tue Dec 04 2018 - 08:10:14 PST)
    - Re: [AMBER] QM/MM using Amber and Gaussian: Discrepancies between the QM energy from the gaussian output file and the energy reported in the mdout file as EXTERNESCF Goetz, Andreas (Tue Dec 04 2018 - 11:48:59 PST)
    - Re: [AMBER] QM/MM using Amber and Gaussian: Discrepancies between the QM energy from the gaussian output file and the energy reported in the mdout file as EXTERNESCF Eric Lang (Wed Dec 05 2018 - 01:55:43 PST)
    - Re: [AMBER] QM/MM using Amber and Gaussian: Discrepancies between the QM energy from the gaussian output file and the energy reported in the mdout file as EXTERNESCF Antoine MARION (Wed Dec 05 2018 - 02:16:12 PST)
    - Re: [AMBER] QM/MM using Amber and Gaussian: Discrepancies between the QM energy from the gaussian output file and the energy reported in the mdout file as EXTERNESCF Goetz, Andreas (Wed Dec 05 2018 - 11:38:02 PST)
[AMBER] Antechamber give a different total charge from net charge that I specified by -nc Jinfeng Huang (Tue Dec 04 2018 - 10:42:41 PST)
[AMBER] Cpptraj usage Chhaya Singh (Tue Dec 04 2018 - 14:16:01 PST)
- Re: [AMBER] Cpptraj usage Daniel Roe (Mon Dec 10 2018 - 06:34:28 PST)
[AMBER] Backbone position restraints as a group lorenaz (Wed Dec 05 2018 - 00:49:57 PST)
- Re: [AMBER] Backbone position restraints as a group David A Case (Thu Dec 06 2018 - 06:12:04 PST)
  - Re: [AMBER] Backbone position restraints as a group lorenaz (Thu Dec 06 2018 - 06:33:07 PST)
[AMBER] regarding graph saving in JPEG Charu Sharma (JRF) (Wed Dec 05 2018 - 03:41:05 PST)
- Re: [AMBER] regarding graph saving in JPEG David A Case (Wed Dec 05 2018 - 05:08:50 PST)
[AMBER] water-induced force on substrate along time Meng Wu (Wed Dec 05 2018 - 04:27:45 PST)
- Re: [AMBER] water-induced force on substrate along time Meng Wu (Wed Dec 05 2018 - 17:31:15 PST)
Re: [AMBER] Minimisation and periodic boundaries Stejskal, Lenka (Wed Dec 05 2018 - 08:11:44 PST)
- Re: [AMBER] Minimisation and periodic boundaries Daniel Roe (Mon Dec 10 2018 - 06:37:06 PST)
[AMBER] Include bound ions as part of the receptor molecule in MMPBSA.py Nanjie Deng (Wed Dec 05 2018 - 13:27:11 PST)
- Re: [AMBER] Include bound ions as part of the receptor molecule in MMPBSA.py Keiran Corbett (Thu Dec 06 2018 - 00:11:17 PST)
  - Re: [AMBER] Include bound ions as part of the receptor molecule in MMPBSA.py Christina Bergonzo (Thu Dec 06 2018 - 05:34:21 PST)
    - Re: [AMBER] Include bound ions as part of the receptor molecule in MMPBSA.py Nanjie Deng (Thu Dec 06 2018 - 19:44:42 PST)
[AMBER] Ambiguous interfaces in generic interface Pedro H. Oliveira (Wed Dec 05 2018 - 13:36:24 PST)
- Re: [AMBER] Ambiguous interfaces in generic interface David Case (Wed Dec 05 2018 - 18:14:38 PST)
[AMBER] tleap does not add OXT when I load a crystal structure Thomas Evangelidis (Wed Dec 05 2018 - 15:23:47 PST)
- Re: [AMBER] tleap does not add OXT when I load a crystal structure David Cerutti (Wed Dec 05 2018 - 16:40:21 PST)
- Re: [AMBER] tleap does not add OXT when I load a crystal structure David Case (Wed Dec 05 2018 - 18:22:26 PST)
  - Re: [AMBER] tleap does not add OXT when I load a crystal structure Thomas Evangelidis (Thu Dec 06 2018 - 02:09:31 PST)
    - Re: [AMBER] tleap does not add OXT when I load a crystal structure David A Case (Thu Dec 06 2018 - 05:57:53 PST)
[AMBER] numpy related problem in amber Seketoulie Keretsu (Wed Dec 05 2018 - 20:05:22 PST)
- Re: [AMBER] numpy related problem in amber Elvis Martis (Wed Dec 05 2018 - 20:52:32 PST)
- Re: [AMBER] numpy related problem in amber David A Case (Thu Dec 06 2018 - 06:01:57 PST)
  - Re: [AMBER] numpy related problem in amber Seketoulie Keretsu (Thu Dec 06 2018 - 22:02:39 PST)
    - Re: [AMBER] numpy related problem in amber Hai Nguyen (Thu Dec 06 2018 - 23:30:28 PST)
    - Re: [AMBER] numpy related problem in amber Seketoulie Keretsu (Fri Dec 07 2018 - 03:05:46 PST)
[AMBER] Strange TIP3P solvent box distortions in Amber 18 with Mg2+ Kasprzak, Wojciech (NIH/NCI) [C] (Thu Dec 06 2018 - 12:21:19 PST)
- Re: [AMBER] Strange TIP3P solvent box distortions in Amber 18 with Mg2+ David Cerutti (Thu Dec 06 2018 - 12:32:55 PST)
  - Re: [AMBER] Strange TIP3P solvent box distortions in Amber 18 with Mg2+, but no MG Kasprzak, Wojciech (NIH/NCI) [C] (Thu Dec 06 2018 - 13:56:21 PST)
    - Re: [AMBER] Strange TIP3P solvent box distortions in Amber 18 with Mg2+, but no MG David Case (Thu Dec 06 2018 - 19:02:59 PST)
    - Re: [AMBER] Strange TIP3P solvent box - reference to the tutorial Kasprzak, Wojciech (NIH/NCI) [C] (Fri Dec 07 2018 - 05:25:54 PST)
[AMBER] Calculate the conduct rate from PMF Meng Wu (Thu Dec 06 2018 - 18:51:13 PST)
- Re: [AMBER] Calculate the conduct rate from PMF David A Case (Mon Dec 10 2018 - 10:41:29 PST)
[AMBER] AMBER18 Update Fail (AmberTools Update.10) Rui Sun (Fri Dec 07 2018 - 01:31:50 PST)
- Re: [AMBER] AMBER18 Update Fail (AmberTools Update.10) Seketoulie Keretsu (Fri Dec 07 2018 - 03:04:19 PST)
- Re: [AMBER] AMBER18 Update Fail (AmberTools Update.10) Daniel Roe (Fri Dec 07 2018 - 05:21:33 PST)
  - Re: [AMBER] AMBER18 Update Fail (AmberTools Update.10) Rui Sun (Fri Dec 07 2018 - 11:28:56 PST)
- Re: [AMBER] AMBER18 Update Fail (AmberTools Update.10) David Case (Sat Dec 08 2018 - 08:09:00 PST)
[AMBER] vdwmeth Hosein Geraili Daronkola (Fri Dec 07 2018 - 06:58:46 PST)
- Re: [AMBER] vdwmeth Hosein Geraili Daronkola (Fri Dec 07 2018 - 07:55:42 PST)
  - Re: [AMBER] vdwmeth Hosein Geraili Daronkola (Fri Dec 07 2018 - 10:16:49 PST)
    - Re: [AMBER] vdwmeth Brian Radak (Fri Dec 07 2018 - 11:44:59 PST)
    - Re: [AMBER] vdwmeth Hosein Geraili Daronkola (Fri Dec 07 2018 - 14:46:04 PST)
    - Re: [AMBER] vdwmeth Brian Radak (Sat Dec 08 2018 - 07:15:34 PST)
    - Re: [AMBER] vdwmeth David Case (Sat Dec 08 2018 - 08:11:02 PST)
[AMBER] Can a Nudged elastic band (NEB) job run on a single GPU? Li, Dailin (Fri Dec 07 2018 - 11:11:49 PST)
- Re: [AMBER] Can a Nudged elastic band (NEB) job run on a single GPU? Ghoreishi, Delaram (Fri Dec 07 2018 - 11:49:08 PST)
  - [AMBER] 答复: Can a Nudged elastic band (NEB) job run on a single GPU? Li, Dailin (Fri Dec 07 2018 - 12:09:15 PST)
    - Re: [AMBER] Can a Nudged elastic band (NEB) job run on a single GPU? Ghoreishi, Delaram (Fri Dec 07 2018 - 13:10:03 PST)
    - [AMBER] 答复: Can a Nudged elastic band (NEB) job run on a single GPU? Li, Dailin (Fri Dec 07 2018 - 14:16:11 PST)
[AMBER] Dear AMBER members, 대학원/일반대학원 생명과학부 (Sat Dec 08 2018 - 07:46:31 PST)
- Re: [AMBER] Dear AMBER members, David Case (Sun Dec 09 2018 - 05:39:56 PST)
[AMBER] ligand charges for md Fabian Glaser (Sun Dec 09 2018 - 08:15:56 PST)
- Re: [AMBER] ligand charges for md David Case (Sun Dec 09 2018 - 13:08:51 PST)
  - Re: [AMBER] ligand charges for md Fabian Glaser (Tue Dec 11 2018 - 08:33:08 PST)
    - Re: [AMBER] ligand charges for md dhaval patel (Fri Dec 21 2018 - 21:23:04 PST)
[AMBER] Ptraj Command not found. Pavithra Support (Sun Dec 09 2018 - 18:37:37 PST)
- Re: [AMBER] Ptraj Command not found. Pratul Agarwal (Sun Dec 09 2018 - 18:59:43 PST)
  - Re: [AMBER] Ptraj Command not found. Daniel Roe (Mon Dec 10 2018 - 06:04:30 PST)
[AMBER] Problems with installation on Mac with Mojave. (cpptraj??) Margarita I. Bernal-Uruchurtu (Mon Dec 10 2018 - 03:18:10 PST)
- Re: [AMBER] Problems with installation on Mac with Mojave. (cpptraj??) Bill Ross (Mon Dec 10 2018 - 03:22:59 PST)
- Re: [AMBER] Problems with installation on Mac with Mojave. (cpptraj??) Gustaf Olsson (Mon Dec 10 2018 - 04:32:36 PST)
- Re: [AMBER] Problems with installation on Mac with Mojave. (cpptraj??) Margarita I. Bernal-Uruchurtu (Tue Dec 11 2018 - 05:26:28 PST)
- Re: [AMBER] Problems with installation on Mac with Mojave. (cpptraj??) Margarita I. Bernal-Uruchurtu (Tue Dec 11 2018 - 05:35:29 PST)
  - Re: [AMBER] Problems with installation on Mac with Mojave. (cpptraj??) Gustaf Olsson (Tue Dec 11 2018 - 05:41:57 PST)
    - Re: [AMBER] Problems with installation on Mac with Mojave. (cpptraj??) David A Case (Tue Dec 11 2018 - 10:31:15 PST)
    - Re: [AMBER] Problems with installation on Mac with Mojave. (cpptraj??) Gustaf Olsson (Mon Dec 17 2018 - 06:21:04 PST)
[AMBER] Size limit for amber Ibrahim M. Moustafa (Mon Dec 10 2018 - 09:27:09 PST)
- Re: [AMBER] Size limit for amber David A Case (Mon Dec 10 2018 - 10:34:30 PST)
- Re: [AMBER] Size limit for amber Ibrahim M. Moustafa (Mon Dec 10 2018 - 10:44:41 PST)
  - Re: [AMBER] Size limit for amber Daniel Roe (Wed Dec 12 2018 - 08:01:26 PST)
- Re: [AMBER] Size limit for amber Ibrahim M. Moustafa (Wed Dec 12 2018 - 10:42:14 PST)
[AMBER] amber12 install problem Qasim Pars (Mon Dec 10 2018 - 11:46:57 PST)
- Re: [AMBER] amber12 install problem David A Case (Tue Dec 11 2018 - 04:41:21 PST)
[AMBER] Fatty acid ester parameter file andreas.tosstorff.cup.uni-muenchen.de (Mon Dec 10 2018 - 13:28:06 PST)
[AMBER] How to get the jac.restrt？ 王茜茜 (Mon Dec 10 2018 - 19:37:04 PST)
- [AMBER] Re: How to get the jac.restrt？ Elvis Martis (Mon Dec 10 2018 - 20:48:15 PST)
  - Re: [AMBER] How to get the jac.restrt？ 王茜茜 (Mon Dec 10 2018 - 22:53:26 PST)
    - [AMBER] Re: How to get the jac.restrt？ Elvis Martis (Tue Dec 11 2018 - 00:53:45 PST)
    - Re: [AMBER] How to get the jac.restrt？ 王茜茜 (Tue Dec 11 2018 - 01:08:18 PST)
- Re: [AMBER] How to get the jac.restrt？ David A Case (Tue Dec 11 2018 - 04:46:36 PST)
  - Re: [AMBER] How to get the jac.restrt？ 王茜茜 (Tue Dec 11 2018 - 06:14:24 PST)
[AMBER] Reading Amber-generated NetCDF files using python Debostuti Ghoshdastidar (Mon Dec 10 2018 - 23:16:28 PST)
- Re: [AMBER] Reading Amber-generated NetCDF files using python Pratul Agarwal (Tue Dec 11 2018 - 04:18:26 PST)
  - Re: [AMBER] Reading Amber-generated NetCDF files using python Debostuti Ghoshdastidar (Tue Dec 11 2018 - 04:22:39 PST)
    - Re: [AMBER] Reading Amber-generated NetCDF files using python Pratul Agarwal (Tue Dec 11 2018 - 04:33:57 PST)
    - Re: [AMBER] Reading Amber-generated NetCDF files using python Debostuti Ghoshdastidar (Tue Dec 11 2018 - 22:21:03 PST)
- Re: [AMBER] Reading Amber-generated NetCDF files using python David A Case (Tue Dec 11 2018 - 04:49:04 PST)
  - Re: [AMBER] Reading Amber-generated NetCDF files using python Debostuti Ghoshdastidar (Tue Dec 11 2018 - 22:17:10 PST)
[AMBER] GBSA error jacob wick (Tue Dec 11 2018 - 00:49:15 PST)
- [AMBER] GBSA error jacob wick (Tue Dec 11 2018 - 21:45:32 PST)
- Re: [AMBER] GBSA error Daniel Roe (Wed Dec 12 2018 - 08:45:20 PST)
[AMBER] GIST calculation on NAMD-generated trajectory Bin Sun (Tue Dec 11 2018 - 11:52:48 PST)
- Re: [AMBER] GIST calculation on NAMD-generated trajectory Daniel Roe (Wed Dec 12 2018 - 07:58:30 PST)
- Re: [AMBER] GIST calculation on NAMD-generated trajectory anthonycruzpr (Wed Dec 12 2018 - 15:42:11 PST)
  - Re: [AMBER] GIST calculation on NAMD-generated trajectory Daniel Roe (Wed Dec 12 2018 - 17:40:08 PST)
    - Re: [AMBER] GIST calculation on NAMD-generated trajectory Bin Sun (Thu Dec 13 2018 - 11:55:14 PST)
    - Re: [AMBER] GIST calculation on NAMD-generated trajectory Daniel Roe (Thu Dec 13 2018 - 11:59:00 PST)
    - Re: [AMBER] GIST calculation on NAMD-generated trajectory Tom Kurtzman (Tue Dec 18 2018 - 10:26:27 PST)
  - Re: [AMBER] GIST calculation on NAMD-generated trajectory Bin Sun (Thu Dec 13 2018 - 11:57:19 PST)
[AMBER] PSF file generation for heme and hydrogen peroxide 대학원/일반대학원 생명과학부 (Wed Dec 12 2018 - 18:37:09 PST)
- Re: [AMBER] PSF file generation for heme and hydrogen peroxide David A Case (Thu Dec 13 2018 - 05:25:10 PST)
[AMBER] strange line between protein chains Núbia Prates (Thu Dec 13 2018 - 07:20:42 PST)
- Re: [AMBER] strange line between protein chains Pratul Agarwal (Thu Dec 13 2018 - 09:25:19 PST)
  - Re: [AMBER] strange line between protein chains Núbia Prates (Fri Dec 14 2018 - 04:54:40 PST)
    - Re: [AMBER] strange line between protein chains Pratul Agarwal (Fri Dec 14 2018 - 12:18:02 PST)
- Re: [AMBER] strange line between protein chains David A Case (Thu Dec 13 2018 - 09:45:30 PST)
- Re: [AMBER] strange line between protein chains Bill Ross (Thu Dec 13 2018 - 10:25:55 PST)
[AMBER] mmpbsa Farial Tavakoli (Thu Dec 13 2018 - 08:59:04 PST)
[AMBER] using sander in Xeon Phi Alfredo Quevedo (Wed Dec 12 2018 - 13:29:12 PST)
- Re: [AMBER] using sander in Xeon Phi David A Case (Thu Dec 13 2018 - 09:42:41 PST)
  - Re: [AMBER] using sander in Xeon Phi Alfredo Quevedo (Wed Dec 12 2018 - 14:03:07 PST)
[AMBER] Error when installing AMBER16 Bellesis, Andrew G (Thu Dec 13 2018 - 09:55:38 PST)
[AMBER] sander: command not found maya nair (Fri Dec 14 2018 - 04:54:50 PST)
- Re: [AMBER] sander: command not found Gustaf Olsson (Fri Dec 14 2018 - 05:14:10 PST)
[AMBER] MMPBSA Farial Tavakoli (Fri Dec 14 2018 - 07:26:48 PST)
[AMBER] resp charge fitting Thomas Fox (Fri Dec 14 2018 - 08:14:41 PST)
[AMBER] AMBER18 on RTX 2080Ti Rui Sun (Fri Dec 14 2018 - 14:53:23 PST)
- Re: [AMBER] AMBER18 on RTX 2080Ti David Cerutti (Fri Dec 14 2018 - 15:09:21 PST)
  - Re: [AMBER] AMBER18 on RTX 2080Ti Rui Sun (Mon Dec 17 2018 - 16:46:59 PST)
    - Re: [AMBER] AMBER18 on RTX 2080Ti Pratul Agarwal (Mon Dec 17 2018 - 17:16:31 PST)
    - Re: [AMBER] AMBER18 on RTX 2080Ti Ross Walker (Mon Dec 17 2018 - 17:55:22 PST)
    - Re: [AMBER] AMBER18 on RTX 2080Ti David Cerutti (Mon Dec 17 2018 - 19:37:48 PST)
    - Re: [AMBER] AMBER18 on RTX 2080Ti Rui Sun (Tue Dec 18 2018 - 02:56:02 PST)
    - Re: [AMBER] AMBER18 on RTX 2080Ti Pratul Agarwal (Tue Dec 18 2018 - 09:43:59 PST)
    - Re: [AMBER] AMBER18 on RTX 2080Ti Mlynsky Vojtech (Fri Dec 21 2018 - 07:25:43 PST)
- Re: [AMBER] AMBER18 on RTX 2080Ti Pratul Agarwal (Fri Dec 14 2018 - 15:29:57 PST)
  - Re: [AMBER] AMBER18 on RTX 2080Ti David Cerutti (Fri Dec 14 2018 - 18:01:31 PST)
[AMBER] Query regarding force field Rakesh Srivastava (Sat Dec 15 2018 - 08:05:19 PST)
- Re: [AMBER] Query regarding force field David Case (Sat Dec 15 2018 - 18:04:32 PST)
  - Re: [AMBER] Query regarding force field Rakesh Srivastava (Sat Dec 15 2018 - 22:46:30 PST)
[AMBER] Acpype related problem : topology for GROMACS Seketoulie Keretsu (Sun Dec 16 2018 - 05:58:08 PST)
- Re: [AMBER] Acpype related problem : topology for GROMACS Bill Ross (Sun Dec 16 2018 - 06:10:07 PST)
  - Re: [AMBER] Acpype related problem : topology for GROMACS Seketoulie Keretsu (Sun Dec 16 2018 - 16:31:42 PST)
    - Re: [AMBER] Acpype related problem : topology for GROMACS Bill Ross (Sun Dec 16 2018 - 18:48:27 PST)
    - Re: [AMBER] Acpype related problem : topology for GROMACS Seketoulie Keretsu (Sun Dec 16 2018 - 21:11:33 PST)
    - Re: [AMBER] Acpype related problem : topology for GROMACS Alan (Mon Dec 17 2018 - 01:24:12 PST)
    - Re: [AMBER] Acpype related problem : topology for GROMACS David A Case (Mon Dec 17 2018 - 05:13:01 PST)
    - Re: [AMBER] Acpype related problem : topology for GROMACS Seketoulie Keretsu (Mon Dec 17 2018 - 05:20:09 PST)
    - Re: [AMBER] Acpype related problem : topology for GROMACS Alan (Mon Dec 17 2018 - 07:26:36 PST)
    - Re: [AMBER] Acpype related problem : topology for GROMACS Seketoulie Keretsu (Mon Dec 17 2018 - 08:04:12 PST)
[AMBER] DOi for Amber 2017 David Sáez (Sun Dec 16 2018 - 12:30:41 PST)
- Re: [AMBER] DOi for Amber 2017 David A Case (Mon Dec 17 2018 - 05:13:28 PST)
[AMBER] MCPB.py Modelling Question Hunter Wilson (Sun Dec 16 2018 - 12:48:07 PST)
- Re: [AMBER] MCPB.py Modelling Question Pengfei Li (Fri Dec 21 2018 - 14:21:27 PST)
  - Re: [AMBER] MCPB.py Modelling Question Hunter Wilson (Sat Dec 29 2018 - 14:17:11 PST)
    - Re: [AMBER] MCPB.py Modelling Question Pengfei Li (Thu Jan 10 2019 - 07:35:29 PST)
[AMBER] is acpype compatible with amber 2018?? parmchk2 and not parmchk available Seketoulie Keretsu (Sun Dec 16 2018 - 21:07:04 PST)
[AMBER] CUDA test failure Asma Abro (Sun Dec 16 2018 - 23:22:47 PST)
- Re: [AMBER] CUDA test failure Bill Ross (Sun Dec 16 2018 - 23:42:35 PST)
- Re: [AMBER] CUDA test failure David A Case (Mon Dec 17 2018 - 05:21:33 PST)
- Re: [AMBER] CUDA test failure Pratul Agarwal (Mon Dec 17 2018 - 06:10:09 PST)
  - Re: [AMBER] CUDA test failure Asma Abro (Mon Dec 17 2018 - 06:33:42 PST)
[AMBER] AMBER16 re-installation problem ilhan.yavuz (Mon Dec 17 2018 - 01:06:30 PST)
- Re: [AMBER] AMBER16 re-installation problem David A Case (Mon Dec 17 2018 - 05:31:09 PST)
[AMBER] Query regarding the internal energy of protein. Leena Aggarwal (Mon Dec 17 2018 - 02:09:29 PST)
- Re: [AMBER] Query regarding the internal energy of protein. David A Case (Mon Dec 17 2018 - 05:34:56 PST)
- Re: [AMBER] Query regarding the internal energy of protein. Pratul Agarwal (Mon Dec 17 2018 - 07:37:58 PST)
  - Re: [AMBER] Query regarding the internal energy of protein. Leena Aggarwal (Mon Dec 17 2018 - 22:14:46 PST)
[AMBER] lambda option in SEBOMD Margarita I. Bernal-Uruchurtu (Mon Dec 17 2018 - 05:15:38 PST)
[AMBER] Problems modifing box lengths in a .rst file. Lucas Bandeira (Mon Dec 17 2018 - 08:43:04 PST)
- Re: [AMBER] Problems modifing box lengths in a .rst file. Lucas Bandeira (Mon Dec 17 2018 - 08:45:46 PST)
- Re: [AMBER] Problems modifing box lengths in a .rst file. Daniel Roe (Mon Dec 17 2018 - 09:13:53 PST)
  - Re: [AMBER] Problems modifing box lengths in a .rst file. Lucas Bandeira (Mon Dec 17 2018 - 10:18:00 PST)
    - Re: [AMBER] Problems modifing box lengths in a .rst file. Daniel Roe (Mon Dec 17 2018 - 10:59:54 PST)
- Re: [AMBER] Problems modifing box lengths in a .rst file. David A Case (Tue Dec 18 2018 - 05:18:52 PST)
  - Re: [AMBER] Problems modifing box lengths in a .rst file. Lucas Bandeira (Tue Dec 18 2018 - 07:29:31 PST)
    - Re: [AMBER] Problems modifing box lengths in a .rst file. Daniel Roe (Tue Dec 18 2018 - 09:18:14 PST)
    - Re: [AMBER] Problems modifing box lengths in a .rst file. David Cerutti (Tue Dec 18 2018 - 09:44:56 PST)
    - Re: [AMBER] Problems modifing box lengths in a .rst file. Lucas Bandeira (Wed Dec 19 2018 - 07:25:34 PST)
[AMBER] Missing gaff parameters for epoxy ring Chang Woon Jang (Mon Dec 17 2018 - 15:07:09 PST)
- Re: [AMBER] Missing gaff parameters for epoxy ring David A Case (Tue Dec 18 2018 - 05:21:49 PST)
- Re: [AMBER] Missing gaff parameters for epoxy ring Chang Woon Jang (Tue Dec 18 2018 - 09:29:23 PST)
[AMBER] amd running error Nisha Amarnath Jonniya (Mon Dec 17 2018 - 22:01:20 PST)
- Re: [AMBER] amd running error Gustaf Olsson (Mon Dec 17 2018 - 23:25:57 PST)
  - Re: [AMBER] amd running error Bill Ross (Mon Dec 17 2018 - 23:52:38 PST)
[AMBER] Too much comparisons failed for test_at_parallel changseo park (Tue Dec 18 2018 - 04:07:28 PST)
- Re: [AMBER] Too much comparisons failed for test_at_parallel David A Case (Tue Dec 18 2018 - 09:15:46 PST)
[AMBER] error on equilibriation Akshay Prabhakant (Tue Dec 18 2018 - 07:55:10 PST)
- Re: [AMBER] error on equilibriation Pratul Agarwal (Tue Dec 18 2018 - 08:09:00 PST)
[AMBER] Simulating a DNA Double helix with a mutated base pair Anthony Bogetti (Tue Dec 18 2018 - 08:43:11 PST)
- Re: [AMBER] Simulating a DNA Double helix with a mutated base pair Pratul Agarwal (Tue Dec 18 2018 - 09:07:55 PST)
- Re: [AMBER] Simulating a DNA Double helix with a mutated base pair David A Case (Tue Dec 18 2018 - 09:10:33 PST)
[AMBER] info on trajectory files Akshay Prabhakant (Wed Dec 19 2018 - 01:14:59 PST)
- Re: [AMBER] info on trajectory files Dr. Anselm Horn (Wed Dec 19 2018 - 02:12:01 PST)
[AMBER] Problems calculating self diffusion coefficient of water Lucas Bandeira (Wed Dec 19 2018 - 09:13:07 PST)
- Re: [AMBER] Problems calculating self diffusion coefficient of water Saeed Izadi (Wed Dec 19 2018 - 12:52:06 PST)
  - Re: [AMBER] Problems calculating self diffusion coefficient of water Lucas Bandeira (Thu Dec 20 2018 - 02:21:04 PST)
  - Re: [AMBER] Problems calculating self diffusion coefficient of water Tom Kurtzman (Thu Dec 20 2018 - 05:13:30 PST)
    - Re: [AMBER] Problems calculating self diffusion coefficient of water Daniel Roe (Fri Dec 21 2018 - 12:04:39 PST)
    - Re: [AMBER] Problems calculating self diffusion coefficient of water Lucas Bandeira (Sat Dec 22 2018 - 05:30:37 PST)
[AMBER] CUDA bootstrap site Bill Ross (Wed Dec 19 2018 - 20:05:59 PST)
[AMBER] cation-pi and amber FF Sundar (Wed Dec 19 2018 - 21:36:45 PST)
[AMBER] Amber18 compilation error on a Linux CPU cluster Sundar (Wed Dec 19 2018 - 21:47:23 PST)
- Re: [AMBER] Amber18 compilation error on a Linux CPU cluster David A Case (Thu Dec 20 2018 - 04:54:07 PST)
- Re: [AMBER] Amber18 compilation error on a Linux CPU cluster Sundar (Sat Dec 22 2018 - 20:21:07 PST)
- Re: [AMBER] Amber18 compilation error on a Linux CPU cluster Sundar (Sun Dec 23 2018 - 10:40:59 PST)
- Re: [AMBER] Amber18 compilation error on a Linux CPU cluster Bill Ross (Sun Dec 23 2018 - 11:17:50 PST)
- Re: [AMBER] Amber18 compilation error on a Linux CPU cluster Sundar (Mon Dec 24 2018 - 17:16:49 PST)
  - Re: [AMBER] Amber18 compilation error on a Linux CPU cluster Daniel Roe (Fri Dec 28 2018 - 06:24:47 PST)
[AMBER] ACE Keiran Corbett (Thu Dec 20 2018 - 00:22:58 PST)
- Re: [AMBER] ACE Bill Ross (Thu Dec 20 2018 - 02:39:23 PST)
  - Re: [AMBER] ACE David Cerutti (Thu Dec 20 2018 - 02:44:02 PST)
    - Re: [AMBER] ACE Bill Ross (Thu Dec 20 2018 - 03:05:42 PST)
  - [AMBER] error with HEM parm Mohammad Salem (Tue Jan 01 2019 - 20:21:02 PST)
    - Re: [AMBER] error with HEM parm David A Case (Wed Jan 02 2019 - 05:37:33 PST)
    - Re: [AMBER] error with HEM parm Matthew Fisher (Wed Jan 02 2019 - 06:16:29 PST)
[AMBER] Axis of a helix as a collective variable Akshay Prabhakant (Thu Dec 20 2018 - 09:13:26 PST)
- Re: [AMBER] Axis of a helix as a collective variable Akshay Prabhakant (Thu Dec 20 2018 - 09:30:14 PST)
  - Re: [AMBER] Axis of a helix as a collective variable Wesley Michael Botello-Smith (Thu Dec 20 2018 - 10:37:24 PST)
    - Re: [AMBER] Axis of a helix as a collective variable Osman, Roman (Thu Dec 20 2018 - 10:54:03 PST)
- Re: [AMBER] Axis of a helix as a collective variable Pratul Agarwal (Thu Dec 20 2018 - 12:23:53 PST)
  - Re: [AMBER] Axis of a helix as a collective variable Wesley Michael Botello-Smith (Thu Dec 20 2018 - 15:11:25 PST)
    - Re: [AMBER] Axis of a helix as a collective variable Pratul Agarwal (Thu Dec 20 2018 - 15:19:18 PST)
    - Re: [AMBER] Axis of a helix as a collective variable Akshay Prabhakant (Thu Dec 20 2018 - 19:24:06 PST)
    - Re: [AMBER] Axis of a helix as a collective variable Pratul Agarwal (Thu Dec 20 2018 - 21:35:17 PST)
[AMBER] ff12pol in Amber 18 Han, Jaebeom (Thu Dec 20 2018 - 12:37:34 PST)
- Re: [AMBER] ff12pol in Amber 18 Ray Luo (Thu Dec 20 2018 - 14:51:45 PST)
[AMBER] mpi Charu Sharma (JRF) (Thu Dec 20 2018 - 22:04:44 PST)
- Re: [AMBER] mpi Elvis Martis (Thu Dec 20 2018 - 22:08:08 PST)
- Re: [AMBER] mpi David A Case (Fri Dec 21 2018 - 05:57:34 PST)
[AMBER] Total energy of glycan simulation is postive Rajarshi Roy (Fri Dec 21 2018 - 03:38:30 PST)
- Re: [AMBER] Total energy of glycan simulation is postive Daniel Roe (Fri Dec 21 2018 - 05:49:55 PST)
- Re: [AMBER] Total energy of glycan simulation is postive David A Case (Fri Dec 21 2018 - 06:00:12 PST)
  - Re: [AMBER] Total energy of glycan simulation is postive Rajarshi Roy (Sat Dec 22 2018 - 02:26:38 PST)
[AMBER] cpin file format issue in production run Manju Sah (Fri Dec 21 2018 - 03:45:32 PST)
- Re: [AMBER] cpin file format issue in production run Cruzeiro,Vinicius Wilian D (Fri Dec 21 2018 - 06:58:25 PST)
[AMBER] How to add ff99sb*ildn? Midhun K Madhu (Fri Dec 21 2018 - 07:22:33 PST)
- Re: [AMBER] How to add ff99sb*ildn? Vlad Cojocaru (Fri Dec 21 2018 - 07:43:22 PST)
  - Re: [AMBER] How to add ff99sb*ildn? Leena Aggarwal (Fri Dec 21 2018 - 20:51:50 PST)
[AMBER] Problem running tiMerge (parmed) Wesley Michael Botello-Smith (Fri Dec 21 2018 - 09:15:47 PST)
[AMBER] Testing AMBER16 installation in parallel; possible bug in testing scripts Bellesis, Andrew G (Fri Dec 21 2018 - 12:56:46 PST)
- Re: [AMBER] Testing AMBER16 installation in parallel; possible bug in testing scripts Pratul Agarwal (Fri Dec 21 2018 - 15:04:38 PST)
- Re: [AMBER] Testing AMBER16 installation in parallel; possible bug in testing scripts David Case (Sat Dec 22 2018 - 14:22:54 PST)
- Re: [AMBER] Testing AMBER16 installation in parallel; possible bug in testing scripts Bellesis, Andrew G (Thu Jan 03 2019 - 08:26:19 PST)
[AMBER] multiconformational respgen with fixed charges and gcc 4.8 Stephan Schott (Sat Dec 22 2018 - 15:39:56 PST)
- Re: [AMBER] multiconformational respgen with fixed charges and gcc 4.8 David Case (Sun Dec 30 2018 - 06:06:28 PST)
- Re: [AMBER] multiconformational respgen with fixed charges and gcc 4.8 Stephan Schott (Sun Dec 30 2018 - 16:38:16 PST)
[AMBER] MD Analysis - Consistency senal dinuka (Sat Dec 22 2018 - 22:10:44 PST)
- Re: [AMBER] MD Analysis - Consistency Daniel Roe (Fri Dec 28 2018 - 06:33:39 PST)
[AMBER] regarding G-quadraplex Charu Sharma (JRF) (Mon Dec 24 2018 - 04:31:18 PST)
- Re: [AMBER] regarding G-quadraplex Bill Ross (Mon Dec 24 2018 - 05:12:36 PST)
[AMBER] constant dieletcric Farial Tavakoli (Tue Dec 25 2018 - 05:05:23 PST)
- [AMBER] Fwd: constant dieletcric Farial Tavakoli (Thu Dec 27 2018 - 22:15:25 PST)
- Re: [AMBER] constant dieletcric Daniel Roe (Fri Dec 28 2018 - 06:06:51 PST)
[AMBER] All Energy Calculations in AMBER18. DHEERAJ CHITARA (Tue Dec 25 2018 - 05:58:19 PST)
- Re: [AMBER] All Energy Calculations in AMBER18. Daniel Roe (Fri Dec 28 2018 - 06:21:01 PST)
[AMBER] Calculation of Hbond energy MOHD HOMAIDUR RAHMAN (Tue Dec 25 2018 - 07:33:58 PST)
- Re: [AMBER] Calculation of Hbond energy David Case (Tue Dec 25 2018 - 14:42:48 PST)
[AMBER] FATAL Error: Atom does not have a type Mac Kevin Braza (Tue Dec 25 2018 - 20:36:55 PST)
- [AMBER] Fwd: FATAL Error: Atom does not have a type Mac Kevin Braza (Tue Dec 25 2018 - 20:38:01 PST)
- Re: [AMBER] FATAL Error: Atom does not have a type Elvis Martis (Tue Dec 25 2018 - 20:57:22 PST)
- Re: [AMBER] FATAL Error: Atom does not have a type David Case (Wed Dec 26 2018 - 18:35:33 PST)
  - Re: [AMBER] FATAL Error: Atom does not have a type Mac Kevin Braza (Thu Dec 27 2018 - 02:58:26 PST)
    - Re: [AMBER] FATAL Error: Atom does not have a type Bill Ross (Thu Dec 27 2018 - 04:07:32 PST)
[AMBER] GPU download(upload) only a small subset of coordinates 张浩淼 (Wed Dec 26 2018 - 01:12:02 PST)
- Re: [AMBER] GPU download(upload) only a small subset of coordinates Ghoreishi, Delaram (Wed Dec 26 2018 - 10:22:41 PST)
[AMBER] TI method with combination of restrained MD in pmemd.cuda of AMBER18 kegohda2kegohda.mx5.canvas.ne.jp (Wed Dec 26 2018 - 05:11:59 PST)
- Re: [AMBER] TI method with combination of restrained MD in pmemd.cuda of AMBER18 David Case (Thu Dec 27 2018 - 06:25:54 PST)
  - Re: [AMBER] TI method with combination of restrained MD in pmemd.cuda of AMBER18 kegohda2kegohda.mx5.canvas.ne.jp (Fri Dec 28 2018 - 04:41:53 PST)
[AMBER] compilation error AMBER16 Seibold, Steve Allan (Thu Dec 27 2018 - 11:31:20 PST)
- Re: [AMBER] compilation error AMBER16 David Case (Thu Dec 27 2018 - 12:56:06 PST)
  - Re: [AMBER] compilation error AMBER16 Seibold, Steve Allan (Fri Dec 28 2018 - 07:52:56 PST)
[AMBER] q wangjianing_mail (Sat Dec 29 2018 - 04:19:24 PST)
[AMBER] HMR 4fs error. M RCC (Mon Dec 31 2018 - 02:06:51 PST)
- Re: [AMBER] HMR 4fs error. David A Case (Mon Dec 31 2018 - 04:49:22 PST)
[AMBER] Obtaining necessary *.top for MMPBSA.py Sundar (Mon Dec 31 2018 - 06:08:46 PST)
- Re: [AMBER] Obtaining necessary *.top for MMPBSA.py Qinghua Liao (Mon Dec 31 2018 - 07:12:16 PST)
  - Re: [AMBER] Obtaining necessary *.top for MMPBSA.py Elvis Martis (Mon Dec 31 2018 - 21:05:54 PST)
[AMBER] orca failure in mdgx: QM grid file not found Anthony Bogetti (Tue Jan 01 2019 - 18:10:04 PST)
[AMBER] Understanding Distance Restraint Ara R (Wed Jan 02 2019 - 06:19:54 PST)
- Re: [AMBER] Understanding Distance Restraint Charles Lin (Wed Jan 02 2019 - 08:43:04 PST)
- Re: [AMBER] Understanding Distance Restraint Stephan Schott (Thu Jan 03 2019 - 02:21:54 PST)
[AMBER] Calculated dipole moment in AMBER Xiaocong Wang (Wed Jan 02 2019 - 07:22:25 PST)
- Re: [AMBER] Calculated dipole moment in AMBER Daniel Roe (Wed Jan 02 2019 - 10:52:13 PST)
  - Re: [AMBER] Calculated dipole moment in AMBER Xiaocong Wang (Wed Jan 02 2019 - 17:45:15 PST)
    - Re: [AMBER] Calculated dipole moment in AMBER Fulbabu Sk (Wed Jan 02 2019 - 20:39:01 PST)
    - Re: [AMBER] Calculated dipole moment in AMBER Daniel Roe (Thu Jan 03 2019 - 05:26:13 PST)
    - Re: [AMBER] Calculated dipole moment in AMBER Fulbabu Sk (Thu Jan 03 2019 - 19:21:14 PST)
[AMBER] Amber Restraint output from Kung, Ryan (Wed Jan 02 2019 - 14:29:35 PST)
[AMBER] DMF Arkajyoti Sengupta (Wed Jan 02 2019 - 15:37:25 PST)
- Re: [AMBER] DMF Thomas Cheatham (Wed Jan 02 2019 - 19:21:23 PST)
[AMBER] Error with mdnab from amberlite Sundar (Wed Jan 02 2019 - 17:30:57 PST)
- Re: [AMBER-Developers] [AMBER] Error with mdnab from amberlite David A Case (Thu Jan 03 2019 - 06:09:33 PST)
  - Re: [AMBER] Error with mdnab from amberlite Sundar (Fri Jan 04 2019 - 21:08:06 PST)
Re: [AMBER] Literature about magnesium ion parameters in tutorial A8 Zuo, Zhicheng (Thu Jan 03 2019 - 12:19:03 PST)
- Re: [AMBER] Literature about magnesium ion parameters in tutorial A8 Mauricio Esguerra (Fri Jan 04 2019 - 03:00:17 PST)
[AMBER] Zeolite simulations Sundar (Thu Jan 03 2019 - 21:06:06 PST)
- Re: [AMBER] Zeolite simulations Pengfei Li (Thu Jan 10 2019 - 07:45:45 PST)
  - Re: [AMBER] Zeolite simulations Sundar (Mon Jan 14 2019 - 06:42:09 PST)
    - Re: [AMBER] Zeolite simulations Pengfei Li (Sat Jan 19 2019 - 13:56:28 PST)
    - Re: [AMBER] Zeolite simulations Sundar (Sat Jan 19 2019 - 19:54:38 PST)
    - Re: [AMBER] Zeolite simulations David A Case (Fri Jan 25 2019 - 07:59:49 PST)
    - Re: [AMBER] Zeolite simulations Pengfei Li (Fri Jan 25 2019 - 08:34:30 PST)
[AMBER] CUDA and Restraint Error Kung, Ryan (Fri Jan 04 2019 - 13:51:18 PST)
- Re: [AMBER] CUDA and Restraint Error David Case (Sat Jan 05 2019 - 06:40:39 PST)
  - Re: [AMBER] CUDA and Restraint Error Pratul Agarwal (Sat Jan 05 2019 - 07:05:51 PST)
    - Re: [AMBER] CUDA and Restraint Error Mehreen Ghufran (Sat Jan 05 2019 - 09:08:01 PST)
    - Re: [AMBER] CUDA and Restraint Error Daniel Roe (Mon Jan 07 2019 - 09:02:44 PST)
- Re: [AMBER] CUDA and Restraint Error Stephan Schott (Sat Jan 05 2019 - 06:55:49 PST)
[AMBER] Si and Al parameters Sundar (Sat Jan 05 2019 - 14:17:44 PST)
[AMBER] QM/MM-GBSA results Sundar (Sat Jan 05 2019 - 14:21:55 PST)
[AMBER] RMSF in amber Akshay Prabhakant (Sun Jan 06 2019 - 01:23:41 PST)
- Re: [AMBER] RMSF in amber Elvis Martis (Sun Jan 06 2019 - 03:01:49 PST)
  - Re: [AMBER] RMSF in amber Daniel Roe (Mon Jan 07 2019 - 07:31:05 PST)
    - Re: [AMBER] RMSF in amber Elvis Martis (Mon Jan 07 2019 - 20:46:36 PST)
[AMBER] Amber installation Yazan Haddad (Mon Jan 07 2019 - 08:07:07 PST)
- Re: [AMBER] Amber installation Yazan Haddad (Mon Jan 07 2019 - 23:48:58 PST)
  - Re: [AMBER] Amber installation David A Case (Tue Jan 08 2019 - 05:56:16 PST)
    - Re: [AMBER] Amber installation Yazan Haddad (Tue Jan 08 2019 - 07:59:28 PST)
[AMBER] average mulliken charges Thakur, Abhishek (Mon Jan 07 2019 - 08:50:35 PST)
[AMBER] Problem with AMP atom separating in equilibration Kasprzak, Wojciech (NIH/NCI) [C] (Mon Jan 07 2019 - 13:13:57 PST)
- Re: [AMBER] Problem with AMP atom separating in equilibration David A Case (Tue Jan 08 2019 - 06:01:02 PST)
[AMBER] Clipping radius in AddToBox Lucas Bandeira (Tue Jan 08 2019 - 04:02:24 PST)
- Re: [AMBER] Clipping radius in AddToBox David A Case (Tue Jan 08 2019 - 06:07:09 PST)
  - Re: [AMBER] Clipping radius in AddToBox David Cerutti (Tue Jan 08 2019 - 06:26:38 PST)
    - Re: [AMBER] Clipping radius in AddToBox Lucas Bandeira (Tue Jan 08 2019 - 06:58:58 PST)
    - Re: [AMBER] Clipping radius in AddToBox David Cerutti (Tue Jan 08 2019 - 07:13:18 PST)
[AMBER] "vlimit exceeded" in NVT simulation Lucas Bandeira (Tue Jan 08 2019 - 07:07:03 PST)
- Re: [AMBER] "vlimit exceeded" in NVT simulation Pratul Agarwal (Tue Jan 08 2019 - 07:24:14 PST)
[AMBER] makeDIST_RST Sundar (Tue Jan 08 2019 - 13:51:54 PST)
- Re: [AMBER] makeDIST_RST David A Case (Wed Jan 09 2019 - 05:45:28 PST)
  - Re: [AMBER] makeDIST_RST Sundar (Wed Jan 09 2019 - 12:13:16 PST)
[AMBER] steered md at constant force Batuhan Kav (Wed Jan 09 2019 - 03:00:56 PST)
- Re: [AMBER] steered md at constant force Jason Swails (Thu Jan 10 2019 - 13:23:13 PST)
  - Re: [AMBER] steered md at constant force Wesley Michael Botello-Smith (Thu Nov 07 2019 - 16:15:58 PST)
[AMBER] Cpptraj: std::bad_alloc error Nikolay N. Kuzmich (Wed Jan 09 2019 - 03:33:45 PST)
- Re: [AMBER] Cpptraj: std::bad_alloc error Pratul Agarwal (Wed Jan 09 2019 - 05:36:16 PST)
- Re: [AMBER] Cpptraj: std::bad_alloc error Daniel Roe (Wed Jan 09 2019 - 06:48:05 PST)
  - Re: [AMBER] Cpptraj: std::bad_alloc error Pratul Agarwal (Wed Jan 09 2019 - 09:27:41 PST)
- Re: [AMBER] Cpptraj: std::bad_alloc error Nikolay N. Kuzmich (Thu Jan 10 2019 - 02:30:20 PST)
[AMBER] How to load and visualize large trajectories? Chetna Tyagi (Wed Jan 09 2019 - 04:22:29 PST)
- Re: [AMBER] How to load and visualize large trajectories? Qinghua Liao (Wed Jan 09 2019 - 04:38:41 PST)
  - Re: [AMBER] How to load and visualize large trajectories? Mehreen Ghufran (Wed Jan 09 2019 - 04:59:17 PST)
    - Re: [AMBER] How to load and visualize large trajectories? Chetna Tyagi (Wed Jan 09 2019 - 04:58:53 PST)
  - Re: [AMBER] How to load and visualize large trajectories? Chetna Tyagi (Wed Jan 09 2019 - 04:32:41 PST)
    - Re: [AMBER] How to load and visualize large trajectories? Daniel Roe (Wed Jan 09 2019 - 08:13:52 PST)
    - Re: [AMBER] How to load and visualize large trajectories? Chetna Tyagi (Wed Jan 09 2019 - 08:09:51 PST)
- Re: [AMBER] How to load and visualize large trajectories? Hai Nguyen (Fri Jan 18 2019 - 12:46:26 PST)
  - Re: [AMBER] How to load and visualize large trajectories? James Kress (Fri Jan 18 2019 - 13:50:55 PST)
    - Re: [AMBER] How to load and visualize large trajectories? Chetna Tyagi (Mon Jan 21 2019 - 01:08:11 PST)
    - Re: [AMBER] How to load and visualize large trajectories? Hai Nguyen (Tue Jan 22 2019 - 20:55:04 PST)
[AMBER] TMD and pmemd Sundar (Wed Jan 09 2019 - 12:15:06 PST)
- Re: [AMBER] TMD and pmemd Wesley Michael Botello-Smith (Wed Jan 09 2019 - 12:25:43 PST)
[AMBER] Virtual Spin Labels in Amber Kari Gaalswyk (Thu Jan 10 2019 - 07:56:30 PST)
- Re: [AMBER] Virtual Spin Labels in Amber David Case (Sat Jan 12 2019 - 14:00:57 PST)
[AMBER] MMPBSA.py- bad atom type "I" Subha Kalyaanamoorthy (Thu Jan 10 2019 - 11:20:33 PST)
[AMBER] Installation error on cray machine Sundar (Thu Jan 10 2019 - 12:23:58 PST)
- Re: [AMBER] Installation error on cray machine Daniel Roe (Fri Jan 11 2019 - 05:52:16 PST)
  - Re: [AMBER] Installation error on cray machine Sundar (Fri Jan 11 2019 - 09:34:38 PST)
    - Re: [AMBER] Installation error on cray machine Daniel Roe (Fri Jan 11 2019 - 17:06:31 PST)
[AMBER] NO and CO parameters from Antechamber Markowska (Thu Jan 10 2019 - 13:17:06 PST)
- Re: [AMBER] NO and CO parameters from Antechamber David A Case (Fri Jan 11 2019 - 05:49:50 PST)
[AMBER] Amber energy minimization and the energy unit Vasantha Kumar (Thu Jan 10 2019 - 20:45:10 PST)
- Re: [AMBER] Amber energy minimization and the energy unit Pratul Agarwal (Fri Jan 11 2019 - 04:19:26 PST)
[AMBER] Problems with cutoff (?) Margarita I. Bernal-Uruchurtu (Fri Jan 11 2019 - 01:48:21 PST)
- Re: [AMBER] Problems with cutoff (?) David Case (Sat Jan 12 2019 - 13:45:47 PST)
[AMBER] reweighting aMD Núbia Prates (Fri Jan 11 2019 - 04:17:43 PST)
[AMBER] "make test" 1 errors occur changseo park (Fri Jan 11 2019 - 04:30:31 PST)
- Re: [AMBER] "make test" 1 errors occur David Case (Sat Jan 12 2019 - 13:48:30 PST)
  - Re: [AMBER] "make test" 1 errors occur changseo park (Tue Jan 15 2019 - 04:16:46 PST)
[AMBER] Constant external force in the given space zone ? Thermostat working just on selected part of simulated system ? Marek Maly (Fri Jan 11 2019 - 06:38:54 PST)
[AMBER] TMD reporting force profile Sundar (Fri Jan 11 2019 - 08:04:40 PST)
[AMBER] Modifying mdread2.F90 for bad atom type: "I" MMPBSA error Subha Kalyaanamoorthy (Fri Jan 11 2019 - 10:29:45 PST)
[AMBER] gpu_shuttle_post_data can't work in the implicit solvent 张浩淼 (Fri Jan 11 2019 - 21:23:22 PST)
- Re: [AMBER] gpu_shuttle_post_data can't work in the implicit solvent David Cerutti (Sat Jan 12 2019 - 02:08:26 PST)
[AMBER] DMF Arkajyoti Sengupta (Sun Jan 13 2019 - 03:59:43 PST)
[AMBER] calculating am1-bcc charges from user generated mulliken charges Braden Kelly (Sun Jan 13 2019 - 14:32:19 PST)
- Re: [AMBER] calculating am1-bcc charges from user generated mulliken charges Braden Kelly (Sun Jan 13 2019 - 19:10:47 PST)
[AMBER] Using Distance Restraints in TMD Aravind R (Mon Jan 14 2019 - 06:40:13 PST)
[AMBER] mutation using pdb4amber Sundar (Mon Jan 14 2019 - 10:51:36 PST)
- Re: [AMBER] mutation using pdb4amber Hai Nguyen (Mon Jan 14 2019 - 16:26:29 PST)
[AMBER] RMSD of independent trajectories using cpptraj Hunter Wilson (Mon Jan 14 2019 - 13:24:30 PST)
- Re: [AMBER] RMSD of independent trajectories using cpptraj Daniel Roe (Mon Jan 14 2019 - 16:41:58 PST)
  - Re: [AMBER] RMSD of independent trajectories using cpptraj Hunter Wilson (Tue Jan 15 2019 - 05:51:24 PST)
    - Re: [AMBER] RMSD of independent trajectories using cpptraj Daniel Roe (Tue Jan 15 2019 - 06:27:50 PST)
    - Re: [AMBER] RMSD of independent trajectories using cpptraj Hunter Wilson (Tue Jan 15 2019 - 12:09:20 PST)
[AMBER] Metal center molecule gaohanlu (Mon Jan 14 2019 - 19:22:02 PST)
- Re: [AMBER] Metal center molecule Saikat Pal (Tue Jan 15 2019 - 05:24:23 PST)
  - Re: [AMBER] Metal center molecule 高含露 (Tue Jan 15 2019 - 19:41:47 PST)
    - Re: [AMBER] Metal center molecule Pengfei Li (Sat Jan 19 2019 - 08:28:55 PST)
[AMBER] Autoimage command not working Martín Pettinati (Tue Jan 15 2019 - 10:40:44 PST)
- Re: [AMBER] Autoimage command not working Premila Samuel Mohan Dass (Tue Jan 15 2019 - 10:50:47 PST)
  - Re: [AMBER] Autoimage command not working Martín Pettinati (Tue Jan 15 2019 - 13:26:03 PST)
- Re: [AMBER] Autoimage command not working Daniel Roe (Tue Jan 15 2019 - 10:51:52 PST)
  - Re: [AMBER] Autoimage command not working Martín Pettinati (Tue Jan 15 2019 - 11:35:04 PST)
    - Re: [AMBER] Autoimage command not working Daniel Roe (Tue Jan 15 2019 - 11:46:23 PST)
[AMBER] Printing distance values to a file Sundar (Tue Jan 15 2019 - 14:18:29 PST)
- Re: [AMBER] Printing distance values to a file David A Case (Wed Jan 16 2019 - 07:17:44 PST)
  - Re: [AMBER] Printing distance values to a file Sundar (Wed Jan 16 2019 - 07:29:52 PST)
[AMBER] simulation with glycans Jacopo Sgrignani (Wed Jan 16 2019 - 02:47:44 PST)
- Re: [AMBER] simulation with glycans Sundar (Wed Jan 16 2019 - 07:14:33 PST)
[AMBER] Separate work values for each restraint in SMD Sundar (Wed Jan 16 2019 - 07:10:17 PST)
- Re: [AMBER] Separate work values for each restraint in SMD Adrian Roitberg (Wed Jan 16 2019 - 07:15:05 PST)
  - Re: [AMBER] Separate work values for each restraint in SMD Sundar (Wed Jan 16 2019 - 07:38:30 PST)
[AMBER] Can't put position restrains on ions Andrea H. Kasun (Wed Jan 16 2019 - 07:33:48 PST)
- Re: [AMBER] Can't put position restrains on ions David A Case (Wed Jan 16 2019 - 10:28:24 PST)
- Re: [AMBER] Can't put position restrains on ions Pratul Agarwal (Wed Jan 16 2019 - 10:49:26 PST)
  - Re: [AMBER] Can't put position restrains on ions Andrea H. Kasun (Wed Jan 16 2019 - 11:02:45 PST)
    - Re: [AMBER] Can't put position restrains on ions Pratul Agarwal (Wed Jan 16 2019 - 11:09:53 PST)
[AMBER] Introduction to dummy atoms needed Markowska (Wed Jan 16 2019 - 09:30:54 PST)
- Re: [AMBER] Introduction to dummy atoms needed Emmett Leddin (Wed Jan 16 2019 - 09:39:14 PST)
- Re: [AMBER] Introduction to dummy atoms needed Pengfei Li (Fri Jan 25 2019 - 08:31:19 PST)
[AMBER] Abrupt peaks in the RMSD plot of heating trajectory Amartya Pradhan (Wed Jan 16 2019 - 10:29:36 PST)
- Re: [AMBER] Abrupt peaks in the RMSD plot of heating trajectory Adrian Roitberg (Wed Jan 16 2019 - 10:31:42 PST)
- Re: [AMBER] Abrupt peaks in the RMSD plot of heating trajectory ABEL Stephane (Wed Jan 16 2019 - 10:40:05 PST)
[AMBER] MCPB.py problem gaohanlu (Wed Jan 16 2019 - 17:46:53 PST)
- Re: [AMBER] MCPB.py problem Pengfei Li (Sat Jan 19 2019 - 08:30:39 PST)
  - Re: [AMBER] MCPB.py problem 高含露 (Mon Jan 21 2019 - 04:49:25 PST)
[AMBER] Amber parameters for Boron atom Vincenzo Maria D'Amore (Thu Jan 17 2019 - 05:48:46 PST)
- Re: [AMBER] Amber parameters for Boron atom David Case (Sat Jan 19 2019 - 06:34:42 PST)
  - [AMBER] Fwd: Amber parameters for Boron atom Vincenzo Maria D'Amore (Sat Jan 19 2019 - 10:23:51 PST)
    - Re: [AMBER] Fwd: Amber parameters for Boron atom David Case (Sat Jan 19 2019 - 17:47:46 PST)
    - Re: [AMBER] Fwd: Amber parameters for Boron atom Vincenzo Maria D'Amore (Mon Jan 21 2019 - 02:17:43 PST)
[AMBER] pytraj Error: No reference set, cannot select by distance. Thomas Evangelidis (Thu Jan 17 2019 - 07:48:46 PST)
- Re: [AMBER] pytraj Error: No reference set, cannot select by distance. Hai Nguyen (Fri Jan 18 2019 - 12:38:44 PST)
[AMBER] time-dependent distance restraints Sundar (Thu Jan 17 2019 - 08:07:47 PST)
- Re: [AMBER] time-dependent distance restraints David A Case (Fri Jan 18 2019 - 05:51:47 PST)
[AMBER] Post to amber mailing list Debarati DasGupta (Thu Jan 17 2019 - 12:31:31 PST)
[AMBER] LIE calculation in FEW workflow Debarati DasGupta (Thu Jan 17 2019 - 12:46:36 PST)
[AMBER] How to convert a NetCDF format trajectory to separate PDB files in sequential order frame by frame Li, Dailin (Thu Jan 17 2019 - 15:10:19 PST)
- Re: [AMBER] How to convert a NetCDF format trajectory to separate PDB files in sequential order frame by frame Alechania Misturini (Thu Jan 17 2019 - 15:35:57 PST)
[AMBER] AMBER v18 on BG/Q Pratul Agarwal (Thu Jan 17 2019 - 15:36:04 PST)
- Re: [AMBER] AMBER v18 on BG/Q David A Case (Fri Jan 18 2019 - 05:57:09 PST)
[AMBER] [MGMS-DS]: Molecular Modelling Workshop + Tim Clark Birthday Symposium: April 08-11, 2019 in Erlangen, Germany Dr. Anselm Horn (Fri Jan 18 2019 - 01:13:18 PST)
- [AMBER] recovering amber binaries Andreas Tosstorff (Tue Jan 22 2019 - 04:12:17 PST)
  - Re: [AMBER] recovering amber binaries Gustaf Olsson (Tue Jan 22 2019 - 05:20:54 PST)
  - Re: [AMBER] recovering amber binaries Pratul Agarwal (Tue Jan 22 2019 - 05:41:03 PST)
    - Re: [AMBER] recovering amber binaries Andreas Tosstorff (Tue Jan 22 2019 - 06:56:31 PST)
    - Re: [AMBER] recovering amber binaries Daniel Roe (Tue Jan 22 2019 - 16:28:54 PST)
[AMBER] detecting bridging waters and ions with cpptraj Stefan Ivanov (Fri Jan 18 2019 - 02:48:17 PST)
- Re: [AMBER] detecting bridging waters and ions with cpptraj Daniel Roe (Thu Jan 24 2019 - 08:16:07 PST)
[AMBER] Water bridge analysis using cpptraj (hbond) Abhilash J (Fri Jan 18 2019 - 06:04:06 PST)
[AMBER] Xplor file generation Debarati DasGupta (Fri Jan 18 2019 - 07:47:28 PST)
- Re: [AMBER] Xplor file generation Daniel Roe (Thu Jan 24 2019 - 08:08:38 PST)
[AMBER] Entropy calculation with Interaction Entropy (IE) method Fulbabu Sk (Fri Jan 18 2019 - 12:03:36 PST)
[AMBER] pmemd18 mpi installation error Kateryna Miroshnychenko (Fri Jan 18 2019 - 13:38:18 PST)
- Re: [AMBER] pmemd18 mpi installation error David Case (Sat Jan 19 2019 - 06:26:20 PST)
  - Re: [AMBER] pmemd18 mpi installation error Kateryna Miroshnychenko (Mon Jan 21 2019 - 13:38:17 PST)
[AMBER] DNA-ligand system maya nair (Sun Jan 20 2019 - 22:42:50 PST)
- Re: [AMBER] DNA-ligand system Bill Ross (Sun Jan 20 2019 - 23:20:04 PST)
- Re: [AMBER] DNA-ligand system David A Case (Mon Jan 21 2019 - 05:52:36 PST)
[AMBER] regarding change in time Charu Sharma (JRF) (Mon Jan 21 2019 - 00:36:19 PST)
- Re: [AMBER] regarding change in time David A Case (Mon Jan 21 2019 - 05:54:52 PST)
[AMBER] MD with different velocities. Rinsha Chk (Mon Jan 21 2019 - 04:47:51 PST)
- Re: [AMBER] MD with different velocities. David A Case (Mon Jan 21 2019 - 06:01:23 PST)
[AMBER] Suggestions on MM-(GB)PBSA Sundar (Mon Jan 21 2019 - 23:20:56 PST)
[AMBER] Using Distance Restraints in TMD Aravind R (Tue Jan 22 2019 - 00:30:25 PST)
[AMBER] PCA Analyze mode evec.pev Shirin Jamshidi (Tue Jan 22 2019 - 03:01:25 PST)
- Re: [AMBER] PCA Analyze mode evec.pev Daniel Roe (Thu Jan 24 2019 - 08:28:44 PST)
- Re: [AMBER] PCA Analyze mode evec.pev Shirin Jamshidi (Fri Feb 01 2019 - 04:12:17 PST)
  - Re: [AMBER] PCA Analyze mode evec.pev Daniel Roe (Fri Feb 01 2019 - 05:01:27 PST)
[AMBER] lipidscd S.D. Stephan Schott (Tue Jan 22 2019 - 06:44:27 PST)
- Re: [AMBER] lipidscd S.D. Daniel Roe (Tue Jan 22 2019 - 16:19:50 PST)
  - Re: [AMBER] lipidscd S.D. Daniel Roe (Mon Jan 28 2019 - 08:53:42 PST)
- Re: [AMBER] lipidscd S.D. Stephan Schott (Mon Jan 28 2019 - 09:26:24 PST)
  - Re: [AMBER] lipidscd S.D. Daniel Roe (Mon Jan 28 2019 - 11:57:29 PST)
- Re: [AMBER] lipidscd S.D. Stephan Schott (Tue Jan 29 2019 - 08:21:42 PST)
[AMBER] MCPB.py Error Dylan Novack (Tue Jan 22 2019 - 16:53:40 PST)
- Re: [AMBER] MCPB.py Error Pengfei Li (Fri Jan 25 2019 - 08:23:27 PST)
  - Re: [AMBER] MCPB.py Error Dylan Novack (Wed Jan 30 2019 - 07:29:55 PST)
    - Re: [AMBER] MCPB.py Error Pengfei Li (Tue Feb 05 2019 - 09:03:59 PST)
[AMBER] 2 types of Chlorine atom (one charge is -1 and other is -0.8) Saikat Pal (Tue Jan 22 2019 - 22:13:49 PST)
- Re: [AMBER] 2 types of Chlorine atom (one charge is -1 and other is -0.8) David A Case (Wed Jan 23 2019 - 04:46:10 PST)
[AMBER] Creating a coarse-grained trajectory from an all atomistic simulation SARAH JEANNE LEFAVE (Wed Jan 23 2019 - 07:22:01 PST)
- Re: [AMBER] Creating a coarse-grained trajectory from an all atomistic simulation David A Case (Wed Jan 23 2019 - 10:32:44 PST)
  - Re: [AMBER] Creating a coarse-grained trajectory from an all atomistic simulation SARAH JEANNE LEFAVE (Wed Jan 23 2019 - 11:18:35 PST)
  - Re: [AMBER] Creating a coarse-grained trajectory from an all atomistic simulation Daniel Roe (Thu Jan 24 2019 - 07:50:36 PST)
[AMBER] pytraj native contacts Rosellen, Martin (Wed Jan 23 2019 - 07:55:34 PST)
- Re: [AMBER] pytraj native contacts Hai Nguyen (Wed Jan 23 2019 - 08:31:44 PST)
  - Re: [AMBER] pytraj native contacts Daniel Roe (Thu Jan 24 2019 - 07:55:04 PST)
- Re: [AMBER] pytraj native contacts Wesley Michael Botello-Smith (Wed Jan 23 2019 - 10:35:02 PST)
[AMBER] GPU cards RTX 2080Ti and Nvidia quadro 16GB RTX 5000 madhumalar arumugam (Thu Jan 24 2019 - 03:35:39 PST)
[AMBER] Lifetime structural waters CPPTRAJ error Pedro Miguel Reis Figueiredo (Thu Jan 24 2019 - 04:24:10 PST)
- Re: [AMBER] Lifetime structural waters CPPTRAJ error Daniel Roe (Thu Jan 24 2019 - 07:45:05 PST)
[AMBER] Combining CpHMD and aMD Cecilia Lindgren (Thu Jan 24 2019 - 07:37:26 PST)
- Re: [AMBER] Combining CpHMD and aMD Cruzeiro,Vinicius Wilian D (Fri Jan 25 2019 - 14:00:13 PST)
  - Re: [AMBER] Combining CpHMD and aMD Cecilia Lindgren (Sun Jan 27 2019 - 23:26:49 PST)
    - Re: [AMBER] Combining CpHMD and aMD Cruzeiro,Vinicius Wilian D (Mon Jan 28 2019 - 04:36:28 PST)
    - Re: [AMBER] Combining CpHMD and aMD Cecilia Lindgren (Mon Jan 28 2019 - 05:13:49 PST)
    - Re: [AMBER] Combining CpHMD and aMD Cruzeiro,Vinicius Wilian D (Mon Jan 28 2019 - 06:22:58 PST)
[AMBER] Simulation setup for LIE Debarati DasGupta (Thu Jan 24 2019 - 11:27:04 PST)
- Re: [AMBER] Simulation setup for LIE Bill Ross (Thu Jan 24 2019 - 12:23:19 PST)
  - Re: [AMBER] Simulation setup for LIE Bill Ross (Thu Jan 24 2019 - 13:08:21 PST)
[AMBER] Unnatural nucleic acid in DNA chain Anthony Bogetti (Thu Jan 24 2019 - 12:52:19 PST)
- Re: [AMBER] Unnatural nucleic acid in DNA chain Bill Ross (Thu Jan 24 2019 - 13:15:04 PST)
- Re: [AMBER] Unnatural nucleic acid in DNA chain David A Case (Fri Jan 25 2019 - 04:53:26 PST)
[AMBER] Error in conversion from charmmgui to AMBER format Souvik Dey (Thu Jan 24 2019 - 16:21:03 PST)
- Re: [AMBER] Error in conversion from charmmgui to AMBER format Sally Pias (Mon Jan 28 2019 - 13:35:09 PST)
[AMBER] NMOD is not running for MM PBSA Santanu Santra (Thu Jan 24 2019 - 23:20:12 PST)
- Re: [AMBER] NMOD is not running for MM PBSA David A Case (Fri Jan 25 2019 - 04:56:15 PST)
[AMBER] Failed to compile mcres.F90 of Amber18+update.10 with ifort Motoshi Kamiya (Fri Jan 25 2019 - 00:58:21 PST)
- Re: [AMBER] Failed to compile mcres.F90 of Amber18+update.10 with ifort Charles Lin (Fri Jan 25 2019 - 07:09:19 PST)
- Re: [AMBER] Failed to compile mcres.F90 of Amber18+update.10 with ifort David A Case (Fri Jan 25 2019 - 07:36:09 PST)
[AMBER] questions on VDW parameters Qinghua Liao (Fri Jan 25 2019 - 03:06:02 PST)
- Re: [AMBER] questions on VDW parameters David A Case (Fri Jan 25 2019 - 07:56:52 PST)
[AMBER] Program received signal SIGSEGV: Segmentation fault - invalid memory reference. Qinghua Liao (Fri Jan 25 2019 - 04:46:20 PST)
- Re: [AMBER] Program received signal SIGSEGV: Segmentation fault - invalid memory reference. David A Case (Mon Jan 28 2019 - 04:59:18 PST)
Re: [AMBER] simple minimization error of a acetonitrile molecule in water (TIP3P water) Debarati DasGupta (Fri Jan 25 2019 - 08:00:31 PST)
- Re: [AMBER] simple minimization error of a acetonitrile molecule in water (TIP3P water) Bill Ross (Fri Jan 25 2019 - 08:31:11 PST)
- Re: [AMBER] simple minimization error of a acetonitrile molecule in water (TIP3P water) Bill Ross (Fri Jan 25 2019 - 09:35:43 PST)
  - Re: [AMBER] simple minimization error of a acetonitrile molecule in water (TIP3P water) Debarati DasGupta (Fri Jan 25 2019 - 11:54:12 PST)
- Re: [AMBER] simple minimization error of a acetonitrile molecule in water (TIP3P water) Bill Ross (Fri Jan 25 2019 - 14:59:33 PST)
- Re: [AMBER] simple minimization error of a acetonitrile molecule in water (TIP3P water) David A Case (Mon Jan 28 2019 - 04:57:05 PST)
- Re: [AMBER] simple minimization error of a acetonitrile molecule in water (TIP3P water) David Case (Tue Jan 29 2019 - 18:10:52 PST)
Re: [AMBER] MCPB.py error with HEME containing protein Pengfei Li (Fri Jan 25 2019 - 08:21:16 PST)
- Re: [AMBER] MCPB.py error with HEME containing protein Prasanth G, Research Scholar (Sun Jan 27 2019 - 03:06:44 PST)
  - Re: [AMBER] MCPB.py error with HEME containing protein Pengfei Li (Tue Feb 05 2019 - 08:00:19 PST)
[AMBER] QM/MM dynamics: metal oxides emanuele falbo (Fri Jan 25 2019 - 09:03:49 PST)
- Re: [AMBER] QM/MM dynamics: metal oxides emanuele falbo (Fri Jan 25 2019 - 12:57:23 PST)
  - Re: [AMBER] QM/MM dynamics: metal oxides David Case (Sat Jan 26 2019 - 07:18:27 PST)
    - Re: [AMBER] QM/MM dynamics: metal oxides emanuele (Sun Jan 27 2019 - 03:43:17 PST)
[AMBER] Error Amber18 installation with Intel 19 compiler Bundit BOONYARIT (Fri Jan 25 2019 - 12:56:55 PST)
- Re: [AMBER] Error Amber18 installation with Intel 19 compiler David Case (Sat Jan 26 2019 - 14:02:25 PST)
[AMBER] Unusual separation between protein and ligand Rajarshi Roy (Fri Jan 25 2019 - 23:11:34 PST)
- Re: [AMBER] Unusual separation between protein and ligand ABEL Stephane (Sat Jan 26 2019 - 04:36:28 PST)
  - Re: [AMBER] Unusual separation between protein and ligand Rajarshi Roy (Sat Jan 26 2019 - 10:22:44 PST)
- Re: [AMBER] Unusual separation between protein and ligand Stephan Schott (Sat Jan 26 2019 - 11:41:30 PST)
[AMBER] Interpreting MM-(GB)PBSA results Sundar (Sat Jan 26 2019 - 17:43:57 PST)
- Re: [AMBER] Interpreting MM-(GB)PBSA results David A Case (Mon Jan 28 2019 - 04:54:33 PST)
  - Re: [AMBER] Interpreting MM-(GB)PBSA results Josh Berryman (Mon Jan 28 2019 - 07:53:15 PST)
    - Re: [AMBER] Interpreting MM-(GB)PBSA results Sundar (Wed Jan 30 2019 - 10:22:22 PST)
    - Re: [AMBER] Interpreting MM-(GB)PBSA results Wesley Michael Botello-Smith (Wed Jan 30 2019 - 10:41:07 PST)
[AMBER] Calculation of binding energy associated with a single water molecule Leena Aggarwal (Sun Jan 27 2019 - 22:04:40 PST)
- Re: [AMBER] Calculation of binding energy associated with a single water molecule Pratul Agarwal (Mon Jan 28 2019 - 08:47:24 PST)
[AMBER] Amber force-filed parameters for amino-acid side chain analogues mish (Mon Jan 28 2019 - 09:15:24 PST)
- Re: [AMBER] Amber force-filed parameters for amino-acid side chain analogues Pratul Agarwal (Tue Jan 29 2019 - 06:18:12 PST)
- Re: [AMBER] Amber force-filed parameters for amino-acid side chain analogues mish (Thu Jan 31 2019 - 04:00:29 PST)
  - Re: [AMBER] Amber force-filed parameters for amino-acid side chain analogues David A Case (Thu Jan 31 2019 - 04:46:22 PST)
    - Re: [AMBER] Amber force-filed parameters for amino-acid side chain analogues mish (Thu Jan 31 2019 - 05:07:56 PST)
    - Re: [AMBER] Amber force-filed parameters for amino-acid side chain analogues David Cerutti (Thu Jan 31 2019 - 05:34:13 PST)
[AMBER] Energy Calculation Mathematical Formula. DHEERAJ CHITARA (Tue Jan 29 2019 - 03:57:32 PST)
- Re: [AMBER] Energy Calculation Mathematical Formula. Daniel Roe (Tue Jan 29 2019 - 05:21:51 PST)
[AMBER] Set the correct number of CPUs and GPU - benchmark - Amber 14 Eduardo Almeida Costa (Tue Jan 29 2019 - 10:34:02 PST)
- Re: [AMBER] Set the correct number of CPUs and GPU - benchmark - Amber 14 Ross Walker (Wed Jan 30 2019 - 07:33:17 PST)
[AMBER] email MYRIAN TORRES RICO (Wed Jan 30 2019 - 07:22:07 PST)
[AMBER] dihedral angles MYRIAN TORRES RICO (Wed Jan 30 2019 - 07:49:46 PST)
- Re: [AMBER] dihedral angles Hai Nguyen (Wed Jan 30 2019 - 07:57:52 PST)
- Re: [AMBER] dihedral angles diego.soler.uam.es (Wed Jan 30 2019 - 08:03:55 PST)
  - Re: [AMBER] dihedral angles Charles-Alexandre Mattelaer (Wed Jan 30 2019 - 08:17:55 PST)
[AMBER] Error while running MMPBSA.py Shagun Krishna (Wed Jan 30 2019 - 10:08:37 PST)
[AMBER] Problem regarding RMSD Saikat Pal (Thu Jan 31 2019 - 06:50:03 PST)
- Re: [AMBER] Problem regarding RMSD Saikat Pal (Thu Jan 31 2019 - 06:54:44 PST)
- Re: [AMBER] Problem regarding RMSD Daniel Roe (Fri Feb 01 2019 - 12:48:30 PST)
  - Re: [AMBER] Problem regarding RMSD Saikat Pal (Fri Feb 01 2019 - 20:46:21 PST)
[AMBER] pytraj time Shayna Hilburg (Thu Jan 31 2019 - 11:44:26 PST)
- Re: [AMBER] pytraj time Daniel Roe (Thu Jan 31 2019 - 12:32:17 PST)
  - Re: [AMBER] pytraj time Shayna Hilburg (Thu Jan 31 2019 - 12:48:29 PST)
[AMBER] MCPB.py and ambmask for IRON Prasanth G, Research Scholar (Fri Feb 01 2019 - 01:58:13 PST)
- Re: [AMBER] MCPB.py and ambmask for IRON Pengfei Li (Tue Feb 05 2019 - 08:27:20 PST)
- Re: [AMBER] MCPB.py and ambmask for IRON Prasanth G, Research Scholar (Tue Feb 05 2019 - 20:36:38 PST)
[AMBER] Adding an atom to a residue by parmed mish (Fri Feb 01 2019 - 07:46:40 PST)
- Re: [AMBER] Adding an atom to a residue by parmed mish (Sat Feb 02 2019 - 06:40:19 PST)
  - Re: [AMBER] Adding an atom to a residue by parmed Jason Swails (Mon Feb 18 2019 - 12:37:39 PST)
    - Re: [AMBER] Adding an atom to a residue by parmed mish (Tue Feb 19 2019 - 10:18:25 PST)
[AMBER] QMMM differences between AMBER PM3 and Orca PM3 GiovanniMaria Piccini (Fri Feb 01 2019 - 08:55:57 PST)
- Re: [AMBER] QMMM differences between AMBER PM3 and Orca PM3 Goetz, Andreas (Fri Feb 01 2019 - 11:07:42 PST)
  - Re: [AMBER] QMMM differences between AMBER PM3 and Orca PM3 GiovanniMaria Piccini (Sat Feb 02 2019 - 04:08:50 PST)
    - Re: [AMBER] QMMM differences between AMBER PM3 and Orca PM3 Goetz, Andreas (Sat Feb 02 2019 - 16:45:23 PST)
    - Re: [AMBER] QMMM differences between AMBER PM3 and Orca PM3 Ross Walker (Sun Feb 03 2019 - 07:34:11 PST)
    - Re: [AMBER] QMMM differences between AMBER PM3 and Orca PM3 GiovanniMaria Piccini (Sun Feb 03 2019 - 09:32:58 PST)
    - Re: [AMBER] QMMM differences between AMBER PM3 and Orca PM3 David Case (Sun Feb 03 2019 - 17:21:50 PST)
    - Re: [AMBER] QMMM differences between AMBER PM3 and Orca PM3 GiovanniMaria Piccini (Mon Feb 04 2019 - 02:46:21 PST)
[AMBER] mpi installation problem Prabir Khatua (Fri Feb 01 2019 - 11:02:42 PST)
- Re: [AMBER] mpi installation problem David Case (Sat Feb 02 2019 - 09:07:51 PST)
  - Re: [AMBER] mpi installation problem Prabir Khatua (Mon Feb 04 2019 - 09:06:12 PST)
    - Re: [AMBER] mpi installation problem Prabir Khatua (Mon Feb 04 2019 - 09:21:32 PST)
    - Re: [AMBER] mpi installation problem Daniel Roe (Mon Feb 04 2019 - 09:35:26 PST)
    - Re: [AMBER] mpi installation problem Prabir Khatua (Mon Feb 04 2019 - 14:17:18 PST)
    - Re: [AMBER] mpi installation problem David Case (Mon Feb 04 2019 - 17:38:03 PST)
    - Re: [AMBER] mpi installation problem Prabir Khatua (Tue Feb 05 2019 - 09:22:50 PST)
    - Re: [AMBER] mpi installation problem Prabir Khatua (Wed Feb 06 2019 - 11:40:38 PST)
[AMBER] vdw radii of sodium ion in GAFF Qasim Pars (Fri Feb 01 2019 - 16:34:55 PST)
- Re: [AMBER] vdw radii of sodium ion in GAFF David Case (Sat Feb 02 2019 - 09:14:53 PST)
  - Re: [AMBER] vdw radii of sodium ion in GAFF Thomas Cheatham (Sat Feb 02 2019 - 10:31:25 PST)
[AMBER] merging molecules Stefano Guglielmo (Sat Feb 02 2019 - 09:10:11 PST)
- Re: [AMBER] merging molecules Daniel Roe (Mon Feb 04 2019 - 10:23:18 PST)
- Re: [AMBER] merging molecules Jason Swails (Mon Feb 18 2019 - 12:50:21 PST)
  - Re: [AMBER] merging molecules Wesley Michael Botello-Smith (Mon Feb 18 2019 - 13:10:46 PST)
[AMBER] MCPB.py & error: coordinates number in fchk file are not consistent with the atom number Prasanth G, Research Scholar (Mon Feb 04 2019 - 05:43:32 PST)
- Re: [AMBER] MCPB.py & error: coordinates number in fchk file are not consistent with the atom number Pengfei Li (Tue Feb 05 2019 - 08:31:40 PST)
- Re: [AMBER] MCPB.py & error: coordinates number in fchk file are not consistent with the atom number Prasanth G, Research Scholar (Wed Feb 06 2019 - 02:06:02 PST)
  - Re: [AMBER] MCPB.py & error: coordinates number in fchk file are not consistent with the atom number Pengfei Li (Fri Feb 08 2019 - 19:03:02 PST)
[AMBER] RMSD of single residue, fit to main structure Rosellen, Martin (Mon Feb 04 2019 - 06:33:18 PST)
- Re: [AMBER] RMSD of single residue, fit to main structure Daniel Roe (Mon Feb 04 2019 - 10:26:14 PST)
[AMBER] NaN in QM-MMPBSA results Sundar (Mon Feb 04 2019 - 11:13:57 PST)
[AMBER] Wham analysis on amber18 (pmemd.cuda) output file mish (Tue Feb 05 2019 - 03:05:32 PST)
- Re: [AMBER] Wham analysis on amber18 (pmemd.cuda) output file mish (Tue Feb 05 2019 - 03:07:17 PST)
[AMBER] Cpptraj hist command Pablo Palomino (Tue Feb 05 2019 - 03:23:22 PST)
- Re: [AMBER] Cpptraj hist command Daniel Roe (Tue Feb 05 2019 - 06:08:24 PST)
- Re: [AMBER] Cpptraj hist command Pablo Palomino (Mon Feb 11 2019 - 05:08:50 PST)
  - Re: [AMBER] Cpptraj hist command LuxStyle International (Mon Feb 11 2019 - 05:10:18 PST)
  - Re: [AMBER] Cpptraj hist command Daniel Roe (Wed Feb 13 2019 - 05:36:00 PST)
[AMBER] pairwise command in cpptraj Leena Aggarwal (Tue Feb 05 2019 - 04:27:22 PST)
- Re: [AMBER] pairwise command in cpptraj Daniel Roe (Tue Feb 05 2019 - 09:44:39 PST)
[AMBER] Graphs Keiran Corbett (Tue Feb 05 2019 - 05:56:06 PST)
- Re: [AMBER] Graphs Gustaf Olsson (Tue Feb 05 2019 - 06:42:12 PST)
- Re: [AMBER] Graphs Daniel Roe (Tue Feb 05 2019 - 08:57:12 PST)
[AMBER] Ca in Amber14 vs Amber18 Keiran Corbett (Tue Feb 05 2019 - 06:07:53 PST)
- Re: [AMBER] Ca in Amber14 vs Amber18 Pengfei Li (Tue Feb 05 2019 - 08:37:26 PST)
[AMBER] hbonds solute with residue Rosellen, Martin (Tue Feb 05 2019 - 06:29:26 PST)
- Re: [AMBER] hbonds solute with residue Daniel Roe (Tue Feb 05 2019 - 08:34:54 PST)
[AMBER] cpptraj MYRIAN TORRES RICO (Tue Feb 05 2019 - 06:51:05 PST)
- Re: [AMBER] cpptraj Daniel Roe (Tue Feb 05 2019 - 08:17:36 PST)
[AMBER] Use of LIE command in cpptraj error Debarati DasGupta (Tue Feb 05 2019 - 12:28:50 PST)
- Re: [AMBER] Use of LIE command in cpptraj error Debarati DasGupta (Tue Feb 05 2019 - 12:31:58 PST)
[AMBER] chamber problem Prabir Khatua (Tue Feb 05 2019 - 13:46:38 PST)
- Re: [AMBER] chamber problem Jason Swails (Wed Feb 06 2019 - 20:58:41 PST)
  - Re: [AMBER] chamber problem Prabir Khatua (Tue Feb 12 2019 - 10:30:22 PST)
    - Re: [AMBER] chamber problem David Case (Tue Feb 12 2019 - 14:34:45 PST)
    - Re: [AMBER] chamber problem Prabir Khatua (Wed Feb 13 2019 - 10:31:03 PST)
    - Re: [AMBER] chamber problem Jason Swails (Mon Feb 18 2019 - 12:32:46 PST)
    - Re: [AMBER] chamber problem Prabir Khatua (Tue Feb 19 2019 - 08:33:33 PST)
    - Re: [AMBER] chamber problem Jason Swails (Tue Feb 19 2019 - 19:37:38 PST)
    - Re: [AMBER] chamber problem Prabir Khatua (Wed Feb 20 2019 - 08:16:07 PST)
[AMBER] Creating PRMTOP and INPCRD in Amber 16 Fulbabu Sk (Wed Feb 06 2019 - 01:30:55 PST)
- Re: [AMBER] Creating PRMTOP and INPCRD in Amber 16 Pengfei Li (Fri Feb 08 2019 - 18:35:13 PST)
Re: [AMBER] FW: Building topology of a molecule with Antechamber David A Case (Wed Feb 06 2019 - 04:56:02 PST)
[AMBER] Change simulation box size Anthony Cruz-Balberdy (Wed Feb 06 2019 - 05:24:24 PST)
- Re: [AMBER] Change simulation box size David A Case (Wed Feb 06 2019 - 07:59:00 PST)
[AMBER] RESP charges for atoms/molecules which not included gaff, gaff2, exc..? Erdem Yeler (Wed Feb 06 2019 - 05:49:32 PST)
[AMBER] mmpbsa error Mehreen Ghufran (Wed Feb 06 2019 - 08:19:55 PST)
- [AMBER] mmpbsa error Mehreen Ghufran (Wed Feb 06 2019 - 08:28:29 PST)
[AMBER] The 3D-RISM-PC+ information for each atoms Eugene huh (Wed Feb 06 2019 - 23:49:04 PST)
- Re: [AMBER] The 3D-RISM-PC+ information for each atoms Tyler Luchko (Lists) (Thu Feb 07 2019 - 11:38:29 PST)
[AMBER] FW: Running Tempered + Hamiltonian replica exchange using pmemd.cuda.MPI BLUNTZER Marie (Thu Feb 07 2019 - 03:28:17 PST)
- Re: [AMBER] FW: Running Tempered + Hamiltonian replica exchange using pmemd.cuda.MPI Daniel Roe (Fri Feb 08 2019 - 07:30:59 PST)
[AMBER] Regarding constant pH MD Saikat Pal (Fri Feb 08 2019 - 07:29:38 PST)
- Re: [AMBER] Regarding constant pH MD Saikat Pal (Sun Feb 10 2019 - 23:07:30 PST)
  - Re: [AMBER] Regarding constant pH MD LuxStyle International (Sun Feb 10 2019 - 23:08:05 PST)
    - Re: [AMBER] Regarding constant pH MD Bill Ross (Sun Feb 10 2019 - 23:33:58 PST)
- Re: [AMBER] Regarding constant pH MD Cruzeiro,Vinicius Wilian D (Mon Feb 11 2019 - 07:08:59 PST)
[AMBER] amber installation problem Rimon Riju (Fri Feb 08 2019 - 23:19:03 PST)
- Re: [AMBER] amber installation problem David Case (Sat Feb 09 2019 - 18:09:04 PST)
  - Re: [AMBER] amber installation problem Rimon Riju (Sat Feb 09 2019 - 22:05:16 PST)
[AMBER] Convert prmtop to PSF file in Cpptraj Fulbabu Sk (Sat Feb 09 2019 - 12:39:50 PST)
- Re: [AMBER] Convert prmtop to PSF file in Cpptraj Daniel Roe (Wed Feb 13 2019 - 05:34:42 PST)
  - Re: [AMBER] Convert prmtop to PSF file in Cpptraj Fulbabu Sk (Wed Feb 13 2019 - 06:10:37 PST)
    - Re: [AMBER] Convert prmtop to PSF file in Cpptraj Daniel Roe (Wed Feb 13 2019 - 06:29:58 PST)
    - Re: [AMBER] Convert prmtop to PSF file in Cpptraj Fulbabu Sk (Wed Feb 13 2019 - 06:58:22 PST)
[AMBER] 1D-RISM: *.xvv generation error Eugene huh (Mon Feb 11 2019 - 01:31:43 PST)
- Re: [AMBER] 1D-RISM: *.xvv generation error LuxStyle International (Mon Feb 11 2019 - 01:32:17 PST)
- Re: [AMBER] 1D-RISM: *.xvv generation error Tyler Luchko (Lists) (Mon Feb 11 2019 - 10:02:20 PST)
- Re: [AMBER] 1D-RISM: *.xvv generation error Eugene huh (Thu Feb 14 2019 - 02:08:01 PST)
  - Re: [AMBER] 1D-RISM: *.xvv generation error Tyler Luchko (Lists) (Thu Feb 14 2019 - 08:52:55 PST)
[AMBER] Behavior of MSD at different collision frequency values Abdullah Bin Faheem (Mon Feb 11 2019 - 02:13:07 PST)
- Re: [AMBER] Behavior of MSD at different collision frequency values LuxStyle International (Mon Feb 11 2019 - 02:13:28 PST)
- Re: [AMBER] Behavior of MSD at different collision frequency values David A Case (Mon Feb 11 2019 - 05:23:46 PST)
  - Re: [AMBER] Behavior of MSD at different collision frequency values Abdullah Bin Faheem (Mon Feb 11 2019 - 18:57:14 PST)
    - Re: [AMBER] Behavior of MSD at different collision frequency values Daniel Roe (Fri Feb 15 2019 - 05:24:05 PST)
[AMBER] Planarity of bound versus unbound ligand Tye Martin (Mon Feb 11 2019 - 12:36:42 PST)
- Re: [AMBER] Planarity of bound versus unbound ligand David Case (Mon Feb 11 2019 - 17:57:39 PST)
[AMBER] charmm psf to amber prmtop conversion problem Prabir Khatua (Mon Feb 11 2019 - 13:09:31 PST)
- Re: [AMBER] charmm psf to amber prmtop conversion problem David Case (Mon Feb 11 2019 - 18:00:54 PST)
[AMBER] Atom type of Calcium Sunita Patel (Mon Feb 11 2019 - 23:22:24 PST)
- Re: [AMBER] Atom type of Calcium Bill Ross (Mon Feb 11 2019 - 23:37:28 PST)
  - Re: [AMBER] Atom type of Calcium Sunita Patel (Mon Feb 11 2019 - 23:47:12 PST)
    - Re: [AMBER] Atom type of Calcium David Case (Tue Feb 12 2019 - 06:26:18 PST)
    - Re: [AMBER] Atom type of Calcium Sunita Patel (Wed Feb 20 2019 - 04:05:06 PST)
    - Re: [AMBER] Atom type of Calcium David A Case (Wed Feb 20 2019 - 07:35:54 PST)
    - Re: [AMBER] Atom type of Calcium Sunita Patel (Thu Feb 28 2019 - 04:21:23 PST)
    - Re: [AMBER] Atom type of Calcium Daniel Roe (Fri Mar 01 2019 - 07:10:01 PST)
    - Re: [AMBER] Atom type of Calcium Sunita Patel (Fri Mar 01 2019 - 23:26:23 PST)
    - Re: [AMBER] Atom type of Calcium Pengfei Li (Sat Mar 02 2019 - 19:14:17 PST)
  - Re: [AMBER] Atom type of Calcium Bill Ross (Mon Feb 11 2019 - 23:52:33 PST)
    - Re: [AMBER] Atom type of Calcium Sunita Patel (Tue Feb 12 2019 - 02:13:00 PST)
[AMBER] Restart file is not formed until the simulation finishes Chetna Tyagi (Tue Feb 12 2019 - 02:55:30 PST)
- Re: [AMBER] Restart file is not formed until the simulation finishes Pratul Agarwal (Tue Feb 12 2019 - 05:03:24 PST)
- Re: [AMBER] Restart file is not formed until the simulation finishes Shayna Hilburg (Tue Feb 12 2019 - 06:23:49 PST)
  - Re: [AMBER] Restart file is not formed until the simulation finishes Chetna Tyagi (Wed Feb 13 2019 - 02:54:05 PST)
[AMBER] MM-GBSA for protein-sugar complex James Starlight (Tue Feb 12 2019 - 07:30:10 PST)
[AMBER] Cpptraj: PC1 and PC1 as function of residue number calculation Fulbabu Sk (Tue Feb 12 2019 - 11:30:42 PST)
- Re: [AMBER] Cpptraj: PC1 and PC1 as function of residue number calculation Daniel Roe (Wed Feb 13 2019 - 05:06:42 PST)
[AMBER] Interpreting QM MMPBSA results Sundar (Tue Feb 12 2019 - 14:50:25 PST)
- Re: [AMBER] Interpreting QM MMPBSA results David A Case (Mon Feb 18 2019 - 05:09:00 PST)
[AMBER] cpptraj PCA error Alen Ahmetovic (Tue Feb 12 2019 - 16:27:22 PST)
- Re: [AMBER] cpptraj PCA error Daniel Roe (Wed Feb 13 2019 - 05:11:02 PST)
[AMBER] Regarding population of hydrogen bond MOHD HOMAIDUR RAHMAN (Tue Feb 12 2019 - 17:24:14 PST)
- Re: [AMBER] Regarding population of hydrogen bond Wesley Michael Botello-Smith (Wed Feb 13 2019 - 11:24:31 PST)
[AMBER] Amber installation on Ubuntu 18.04 Rajarshi Roy (Tue Feb 12 2019 - 20:32:32 PST)
- Re: [AMBER] Amber installation on Ubuntu 18.04 Bill Ross (Tue Feb 12 2019 - 21:50:12 PST)
- Re: [AMBER] Amber installation on Ubuntu 18.04 David A Case (Wed Feb 13 2019 - 10:09:11 PST)
  - Re: [AMBER] Amber installation on Ubuntu 18.04 Rajarshi Roy (Wed Feb 13 2019 - 20:15:24 PST)
[AMBER] Amber18 TI on K10 - any known problem? Thomas Fox (Wed Feb 13 2019 - 04:06:28 PST)
- Re: [AMBER] Amber18 TI on K10 - any known problem? David A Case (Mon Feb 18 2019 - 05:07:45 PST)
[AMBER] gromacs .top file error fateme haghighi (Wed Feb 13 2019 - 06:52:06 PST)
- Re: [AMBER] gromacs .top file error Jason Swails (Tue Feb 19 2019 - 19:39:10 PST)
- Re: [AMBER] gromacs .top file error dhaval patel (Tue Feb 19 2019 - 20:45:50 PST)
[AMBER] A few issues Paul, Austin (Wed Feb 13 2019 - 06:55:12 PST)
- Re: [AMBER] A few issues Hai Nguyen (Wed Feb 13 2019 - 07:31:10 PST)
  - Re: [AMBER] A few issues Hai Nguyen (Thu Feb 14 2019 - 20:48:02 PST)
    - Re: [AMBER] A few issues David A Case (Fri Feb 15 2019 - 05:25:29 PST)
    - Re: [AMBER] A few issues Hai Nguyen (Fri Feb 15 2019 - 09:51:31 PST)
    - Re: [AMBER] A few issues Paul, Austin (Tue Feb 19 2019 - 11:59:42 PST)
    - Re: [AMBER] A few issues Hai Nguyen (Tue Feb 19 2019 - 12:59:29 PST)
    - Re: [AMBER] A few issues Hai Nguyen (Tue Feb 19 2019 - 16:29:35 PST)
- Re: [AMBER] A few issues David Case (Wed Feb 13 2019 - 18:18:07 PST)
[AMBER] reference.frc file from MMPBSA calculations Sundar (Wed Feb 13 2019 - 10:02:55 PST)
[AMBER] NMR restraints in AmberTools? Istvan Kolossvary (Wed Feb 13 2019 - 15:34:45 PST)
- Re: [AMBER] NMR restraints in AmberTools? David Case (Wed Feb 13 2019 - 18:30:31 PST)
  - Re: [AMBER] NMR restraints in AmberTools? Istvan Kolossvary (Wed Feb 13 2019 - 18:38:31 PST)
[AMBER] Dihedral configuration entropy Lod King (Wed Feb 13 2019 - 16:02:50 PST)
- Re: [AMBER] Dihedral configuration entropy Daniel Roe (Tue Feb 19 2019 - 11:41:56 PST)
[AMBER] Calculation of Entropy using MMPBSA AMBER 18 DHEERAJ CHITARA (Wed Feb 13 2019 - 21:43:48 PST)
- Re: [AMBER] Calculation of Entropy using MMPBSA AMBER 18 David A Case (Thu Feb 14 2019 - 06:04:58 PST)
[AMBER] MMPBSA Nisha Amarnath Jonniya (Wed Feb 13 2019 - 23:06:08 PST)
- Re: [AMBER] MMPBSA David A Case (Mon Feb 18 2019 - 04:55:49 PST)
  - Re: [AMBER] MMPBSA Nisha Amarnath Jonniya (Mon Feb 18 2019 - 05:42:04 PST)
[AMBER] making force fields files from topology Hadi Rahmaninejad (Thu Feb 14 2019 - 07:31:45 PST)
- [AMBER] Fwd: making force fields files from topology Hadi Rahmaninejad (Sun Feb 17 2019 - 15:22:21 PST)
- [AMBER] Fwd: making force fields files from topology Hadi Rahmaninejad (Sun Feb 17 2019 - 15:28:06 PST)
- Re: [AMBER] making force fields files from topology David A Case (Mon Feb 18 2019 - 04:51:58 PST)
[AMBER] MBAR from TI on pmemd Hosein Geraili Daronkola (Thu Feb 14 2019 - 08:36:17 PST)
- Re: [AMBER] MBAR from TI on pmemd Jason Swails (Wed Feb 27 2019 - 22:13:56 PST)
Re: [AMBER] OpenMPI 4.0.0 support Stephan Schott (Thu Feb 14 2019 - 16:54:02 PST)
- Re: [AMBER] OpenMPI 4.0.0 support viktor drobot (Thu Feb 14 2019 - 22:32:03 PST)
- Re: [AMBER] OpenMPI 4.0.0 support David A Case (Fri Feb 15 2019 - 05:16:01 PST)
- Re: [AMBER] OpenMPI 4.0.0 support David A Case (Fri Feb 15 2019 - 11:07:29 PST)
- Re: [AMBER] OpenMPI 4.0.0 support Stephan Schott (Fri Feb 15 2019 - 11:28:49 PST)
[AMBER] Dihedral configuration entropy Lod King (Thu Feb 14 2019 - 17:48:27 PST)
- Re: [AMBER] Dihedral configuration entropy Daniel Roe (Fri Feb 15 2019 - 10:33:45 PST)
[AMBER] Generating spherical macro-ion in amber ATUL KUMAR (Thu Feb 14 2019 - 23:20:18 PST)
- Re: [AMBER] Generating spherical macro-ion in amber David A Case (Fri Feb 15 2019 - 05:29:16 PST)
  - Re: [AMBER] Generating spherical macro-ion in amber ATUL KUMAR (Fri Feb 15 2019 - 05:55:22 PST)
[AMBER] MBAR from TI on pmemd Hosein Geraili Daronkola (Fri Feb 15 2019 - 00:38:46 PST)
[AMBER] xleap "impose" and addAtomtypes command for paramfit gen_conformers.sh Erdem Yeler (Sat Feb 16 2019 - 20:54:52 PST)
- Re: [AMBER] xleap "impose" and addAtomtypes command for paramfit gen_conformers.sh Robin Betz (Mon Feb 18 2019 - 13:51:52 PST)
  - Re: [AMBER] xleap "impose" and addAtomtypes command for paramfit gen_conformers.sh Erdem Yeler (Tue Feb 19 2019 - 01:49:52 PST)
- Re: [AMBER] xleap "impose" and addAtomtypes command for paramfit gen_conformers.sh Daniel Roe (Thu Feb 21 2019 - 07:43:02 PST)
  - Re: [AMBER] xleap "impose" and addAtomtypes command for paramfit gen_conformers.sh Erdem Yeler (Fri Feb 22 2019 - 02:33:30 PST)
[AMBER] peptide-bilayer MD simulation analysis golshan bakrani (Sun Feb 17 2019 - 21:50:35 PST)
[AMBER] Speed-up calculation of Entropy with MMPBSA James Starlight (Mon Feb 18 2019 - 01:34:22 PST)
- Re: [AMBER] Speed-up calculation of Entropy with MMPBSA David A Case (Mon Feb 18 2019 - 04:50:12 PST)
  - Re: [AMBER] Speed-up calculation of Entropy with MMPBSA James Starlight (Mon Feb 18 2019 - 05:16:41 PST)
[AMBER] Umbrella Sampling and WHAM analysis mish (Mon Feb 18 2019 - 03:29:31 PST)
[AMBER] MBAR from TI on pmemd Hosein Geraili Daronkola (Mon Feb 18 2019 - 04:57:17 PST)
[AMBER] ChamberParm objects are not supported by this action Hadi Rahmaninejad (Mon Feb 18 2019 - 09:13:22 PST)
- Re: [AMBER] ChamberParm objects are not supported by this action David A Case (Mon Feb 18 2019 - 11:21:07 PST)
  - Re: [AMBER] ChamberParm objects are not supported by this action Jason Swails (Mon Feb 18 2019 - 12:26:44 PST)
    - Re: [AMBER] ChamberParm objects are not supported by this action Hadi Rahmaninejad (Mon Feb 18 2019 - 13:07:12 PST)
[AMBER] puckering coordinates MYRIAN TORRES RICO (Mon Feb 18 2019 - 09:54:13 PST)
- Re: [AMBER] puckering coordinates Pratul Agarwal (Tue Feb 19 2019 - 05:52:31 PST)
  - Re: [AMBER] puckering coordinates mish (Tue Feb 19 2019 - 08:02:25 PST)
    - Re: [AMBER] puckering coordinates MYRIAN TORRES RICO (Tue Feb 19 2019 - 08:25:03 PST)
    - Re: [AMBER] puckering coordinates Daniel Roe (Tue Feb 19 2019 - 08:42:24 PST)
    - Re: [AMBER] puckering coordinates mish (Tue Feb 19 2019 - 08:58:22 PST)
    - Re: [AMBER] puckering coordinates MYRIAN TORRES RICO (Tue Feb 19 2019 - 09:47:44 PST)
    - Re: [AMBER] puckering coordinates Charles-Alexandre Mattelaer (Tue Feb 19 2019 - 09:54:27 PST)
    - Re: [AMBER] puckering coordinates mish (Tue Feb 19 2019 - 10:04:23 PST)
    - Re: [AMBER] puckering coordinates mish (Tue Feb 19 2019 - 10:09:38 PST)
    - Re: [AMBER] puckering coordinates Daniel Roe (Tue Feb 19 2019 - 10:42:57 PST)
    - Re: [AMBER] puckering coordinates Pratul Agarwal (Tue Feb 19 2019 - 10:19:18 PST)
Re: [AMBER] Speed-up calculation of Entropy with MMPBSA (James Starlight) David Minh (Mon Feb 18 2019 - 12:22:08 PST)
[AMBER] ff99SBi force field in Amber Advanced Tutorial A22 Michiel de Hoon (Mon Feb 18 2019 - 18:30:06 PST)
[AMBER] Problem during parallel installation Sunita Patel (Tue Feb 19 2019 - 07:05:49 PST)
- Re: [AMBER] Problem during parallel installation Pratul Agarwal (Tue Feb 19 2019 - 05:45:39 PST)
- Re: [AMBER] Problem during parallel installation David A Case (Tue Feb 19 2019 - 05:50:49 PST)
  - Re: [AMBER] Problem during parallel installation Sunita Patel (Wed Feb 20 2019 - 03:04:47 PST)
[AMBER] Bad atom type i Keiran Corbett (Tue Feb 19 2019 - 02:04:52 PST)
- Re: [AMBER] Bad atom type i David Case (Wed Feb 20 2019 - 18:11:13 PST)
[AMBER] puckering MYRIAN TORRES RICO (Tue Feb 19 2019 - 07:23:43 PST)
[AMBER] gas phase TI Hosein Geraili Daronkola (Tue Feb 19 2019 - 07:37:39 PST)
- Re: [AMBER] gas phase TI David A Case (Tue Feb 19 2019 - 10:35:43 PST)
  - Re: [AMBER] gas phase TI Hosein Geraili Daronkola (Wed Feb 20 2019 - 06:33:17 PST)
[AMBER] gas phase TI Hosein Geraili Daronkola (Tue Feb 19 2019 - 07:42:00 PST)
[AMBER] gas phase TI Hosein Geraili Daronkola (Tue Feb 19 2019 - 07:52:58 PST)
[AMBER] gas phase TI Hosein Geraili Daronkola (Tue Feb 19 2019 - 08:06:54 PST)
[AMBER] MMPBSA Calculation Error: Order of protein and ligand M RCC (Tue Feb 19 2019 - 09:17:07 PST)
- Re: [AMBER] MMPBSA Calculation Error: Order of protein and ligand Sundar (Tue Feb 19 2019 - 09:35:52 PST)
- Re: [AMBER] MMPBSA Calculation Error: Order of protein and ligand David A Case (Tue Feb 19 2019 - 10:39:34 PST)
- Re: [AMBER] MMPBSA Calculation Error: Order of protein and ligand M RCC (Wed Feb 20 2019 - 03:32:50 PST)
[AMBER] Silica in antechamber Hadi Rahmaninejad (Tue Feb 19 2019 - 09:46:42 PST)
- Re: [AMBER] Silica in antechamber David A Case (Tue Feb 19 2019 - 10:42:51 PST)
  - Re: [AMBER] Silica in antechamber Hadi Rahmaninejad (Tue Feb 19 2019 - 11:23:27 PST)
[AMBER] Protein_plus_ADP_plus_Mg2+_preparation_general_rule Antonio Amber Carlesso (Tue Feb 19 2019 - 10:57:26 PST)
- Re: [AMBER] Protein_plus_ADP_plus_Mg2+_preparation_general_rule Christina Bergonzo (Thu Feb 21 2019 - 07:01:52 PST)
  - Re: [AMBER] Protein_plus_ADP_plus_Mg2+_preparation_general_rule Adrian Roitberg (Thu Feb 21 2019 - 11:41:01 PST)
[AMBER] Ovito visualization Shayna Hilburg (Tue Feb 19 2019 - 12:48:46 PST)
[AMBER] Suggestions for Analysis Souvik Dey (Tue Feb 19 2019 - 15:49:27 PST)
- Re: [AMBER] Suggestions for Analysis dhaval patel (Tue Feb 19 2019 - 20:49:58 PST)
  - Re: [AMBER] Suggestions for Analysis Souvik Dey (Thu Feb 21 2019 - 11:50:00 PST)
[AMBER] MMGBSA Angew Chemie (Tue Feb 19 2019 - 20:21:34 PST)
[AMBER] overestimate hydrogen bonding distance Niko Prasetyo (Wed Feb 20 2019 - 01:36:40 PST)
- Re: [AMBER] overestimate hydrogen bonding distance Maciej Maciejczyk (Wed Feb 20 2019 - 02:22:48 PST)
  - Re: [AMBER] overestimate hydrogen bonding distance Niko Prasetyo (Wed Feb 20 2019 - 02:47:40 PST)
    - Re: [AMBER] overestimate hydrogen bonding distance Daniel Roe (Mon Feb 25 2019 - 05:31:58 PST)
[AMBER] puckering coordinates MYRIAN TORRES RICO (Wed Feb 20 2019 - 03:17:48 PST)
- Re: [AMBER] puckering coordinates Daniel Roe (Wed Feb 20 2019 - 04:51:57 PST)
[AMBER] Bond breakage modelling Ali Khodayari (Wed Feb 20 2019 - 05:04:13 PST)
[AMBER] puckering coordinates MYRIAN TORRES RICO (Wed Feb 20 2019 - 06:22:34 PST)
- Re: [AMBER] puckering coordinates Daniel Roe (Thu Feb 21 2019 - 11:18:29 PST)
[AMBER] Amber14 installation issue Alexey Orlov (Wed Feb 20 2019 - 09:56:56 PST)
- Re: [AMBER] Amber14 installation issue David A Case (Wed Feb 20 2019 - 11:14:19 PST)
[AMBER] XMIN internal output suppressed Istvan Kolossvary (Wed Feb 20 2019 - 15:45:51 PST)
- Re: [AMBER] XMIN internal output suppressed David Case (Wed Feb 20 2019 - 18:03:34 PST)
  - Re: [AMBER] XMIN internal output suppressed Istvan Kolossvary (Wed Feb 20 2019 - 19:19:00 PST)
[AMBER] Can cpptraj multidihedral use nonbonded atoms? Michael F. Bruist (Wed Feb 20 2019 - 15:48:29 PST)
- Re: [AMBER] Can cpptraj multidihedral use nonbonded atoms? Daniel Roe (Thu Feb 21 2019 - 11:16:25 PST)
  - Re: [AMBER] Can cpptraj multidihedral use nonbonded atoms? Michael F. Bruist (Thu Feb 28 2019 - 15:01:15 PST)
[AMBER] About clusterdihedral Gilberto Pereira (Thu Feb 21 2019 - 01:06:47 PST)
- Re: [AMBER] About clusterdihedral Daniel Roe (Thu Feb 21 2019 - 11:12:10 PST)
[AMBER] Error and sudden halt in equilibration senal dinuka (Thu Feb 21 2019 - 03:00:00 PST)
- Re: [AMBER] Error and sudden halt in equilibration Bill Ross (Thu Feb 21 2019 - 03:32:19 PST)
- Re: [AMBER] Error and sudden halt in equilibration David A Case (Thu Feb 21 2019 - 05:22:24 PST)
  - Re: [AMBER] Error and sudden halt in equilibration senal dinuka (Thu Feb 21 2019 - 20:07:35 PST)
    - Re: [AMBER] Error and sudden halt in equilibration Bill Ross (Thu Feb 21 2019 - 21:47:04 PST)
- Re: [AMBER] Error and sudden halt in equilibration Stephan Schott (Fri Feb 22 2019 - 10:21:32 PST)
[AMBER] Problem in running pmemd.cuda ATUL KUMAR (Thu Feb 21 2019 - 03:00:03 PST)
- Re: [AMBER] Problem in running pmemd.cuda David A Case (Thu Feb 21 2019 - 05:27:53 PST)
- Re: [AMBER] Problem in running pmemd.cuda Stejskal, Lenka (Thu Feb 21 2019 - 13:16:05 PST)
  - Re: [AMBER] Problem in running pmemd.cuda ATUL KUMAR (Thu Feb 21 2019 - 22:43:23 PST)
[AMBER] Reference energies in CpHMD (constant pH MD) for HIP Rodrigo Pérez Cossio (Thu Feb 21 2019 - 16:16:48 PST)
- Re: [AMBER] Reference energies in CpHMD (constant pH MD) for HIP Cruzeiro,Vinicius Wilian D (Thu Feb 21 2019 - 17:41:16 PST)
  - Re: [AMBER] Reference energies in CpHMD (constant pH MD) for HIP Cruzeiro,Vinicius Wilian D (Thu Feb 21 2019 - 18:11:17 PST)
    - Re: [AMBER] Reference energies in CpHMD (constant pH MD) for HIP Jason Swails (Wed Feb 27 2019 - 22:08:33 PST)
    - Re: [AMBER] Reference energies in CpHMD (constant pH MD) for HIP Brian Radak (Thu Feb 28 2019 - 09:14:41 PST)
    - Re: [AMBER] Reference energies in CpHMD (constant pH MD) for HIP Jason Swails (Sat Mar 02 2019 - 06:54:39 PST)
    - Re: [AMBER] Reference energies in CpHMD (constant pH MD) for HIP Brian Radak (Sat Mar 02 2019 - 08:39:54 PST)
  - Re: [AMBER] Reference energies in CpHMD (constant pH MD) for HIP Jason Swails (Wed Feb 27 2019 - 22:00:26 PST)
[AMBER] Does NVIDIA RTX 2080 Ti support Amber16 with cuda-8? M RCC (Fri Feb 22 2019 - 00:20:29 PST)
- Re: [AMBER] Does NVIDIA RTX 2080 Ti support Amber16 with cuda-8? Ross Walker (Fri Feb 22 2019 - 13:05:08 PST)
[AMBER] puckering coordinates MYRIAN TORRES RICO (Fri Feb 22 2019 - 01:40:41 PST)
[AMBER] MBAR from TI on pmemd Hosein Geraili Daronkola (Fri Feb 22 2019 - 02:33:31 PST)
- Re: [AMBER] MBAR from TI on pmemd accuratefreeenergy.gmail.com (Fri Feb 22 2019 - 06:25:23 PST)
[AMBER] Dihedral Kb Value when IDIVF=1 Erdem Yeler (Fri Feb 22 2019 - 03:17:57 PST)
[AMBER] QM/MM - gaussian interface query Abhilash J (Sat Feb 23 2019 - 04:02:31 PST)
[AMBER] Potential bug in sander/LMOD Istvan Kolossvary (Sun Feb 24 2019 - 14:29:11 PST)
- Re: [AMBER] Potential bug in sander/LMOD Charles Lin (Fri Mar 08 2019 - 11:05:50 PST)
- Re: [AMBER] Potential bug in sander/LMOD Scott Brozell (Fri Mar 08 2019 - 18:02:40 PST)
[AMBER] Protein-ligand simulation and help w.r.t files for carrying out simulation Prasanth G, Research Scholar (Mon Feb 25 2019 - 04:53:34 PST)
- Re: [AMBER] Protein-ligand simulation and help w.r.t files for carrying out simulation David A Case (Mon Feb 25 2019 - 08:07:47 PST)
[AMBER] pytraj distance image Antoine MARION (Mon Feb 25 2019 - 07:53:56 PST)
- Re: [AMBER] pytraj distance image Hai Nguyen (Mon Feb 25 2019 - 08:36:19 PST)
  - Re: [AMBER] pytraj distance image Hai Nguyen (Mon Feb 25 2019 - 11:23:54 PST)
- Re: [AMBER] pytraj distance image Hai Nguyen (Mon Feb 25 2019 - 15:47:37 PST)
  - Re: [AMBER] pytraj distance image Antoine MARION (Tue Feb 26 2019 - 02:29:02 PST)
    - Re: [AMBER] pytraj distance image Hai Nguyen (Tue Feb 26 2019 - 06:10:43 PST)
    - Re: [AMBER] pytraj distance image Antoine MARION (Wed Feb 27 2019 - 00:02:02 PST)
[AMBER] Nothing returned in aMD simulation of membrane protein Meng Wu (Mon Feb 25 2019 - 21:42:52 PST)
[AMBER] confusion of choosing force field Sasthi Charan Mandal (Tue Feb 26 2019 - 04:54:13 PST)
- Re: [AMBER] confusion of choosing force field David A Case (Tue Feb 26 2019 - 06:13:50 PST)
- Re: [AMBER] confusion of choosing force field Pavlína Pokorná (Tue Feb 26 2019 - 06:41:19 PST)
  - Re: [AMBER] confusion of choosing force field Sasthi Charan Mandal (Tue Feb 26 2019 - 09:18:32 PST)
    - Re: [AMBER] confusion of choosing force field David Case (Thu Feb 28 2019 - 15:48:15 PST)
[AMBER] Changing ligand coordinates D. Yousefi (Tue Feb 26 2019 - 05:29:04 PST)
- Re: [AMBER] Changing ligand coordinates Daniel Roe (Tue Feb 26 2019 - 07:08:19 PST)
  - Re: [AMBER] Changing ligand coordinates D. Yousefi (Wed Feb 27 2019 - 03:33:10 PST)
[AMBER] command from ambertools tutorial does not working Sasthi Charan Mandal (Tue Feb 26 2019 - 09:29:30 PST)
- Re: [AMBER] command from ambertools tutorial does not working Daniel Roe (Tue Feb 26 2019 - 09:41:38 PST)
  - Re: [AMBER] command from ambertools tutorial does not working Sasthi Charan Mandal (Tue Feb 26 2019 - 09:48:51 PST)
    - Re: [AMBER] command from ambertools tutorial does not working David A Case (Wed Feb 27 2019 - 11:10:37 PST)
    - Re: [AMBER] command from ambertools tutorial does not working Erdem Yeler (Wed Feb 27 2019 - 13:45:54 PST)
    - Re: [AMBER] command from ambertools tutorial does not working Sasthi Charan Mandal (Thu Feb 28 2019 - 00:12:26 PST)
[AMBER] protein function Hosein Geraili Daronkola (Tue Feb 26 2019 - 10:30:12 PST)
[AMBER] Error in generating the residue topology for non-standard amino acid residues RITUPARNA ROY (Wed Feb 27 2019 - 06:48:10 PST)
- Re: [AMBER] Error in generating the residue topology for non-standard amino acid residues David Case (Thu Feb 28 2019 - 15:40:58 PST)
[AMBER] antechamber error Chang Woon Jang (Wed Feb 27 2019 - 09:38:14 PST)
- Re: [AMBER] antechamber error David A Case (Wed Feb 27 2019 - 11:17:08 PST)
[AMBER] is this reference energy dG ~34 kcal/mol reasonable for acetic acid? Feng, Zimin (Wed Feb 27 2019 - 12:25:02 PST)
- Re: [AMBER] is this reference energy dG ~34 kcal/mol reasonable for acetic acid? Cruzeiro,Vinicius Wilian D (Wed Feb 27 2019 - 14:41:43 PST)
  - Re: [AMBER] is this reference energy dG ~34 kcal/mol reasonable for acetic acid? Feng, Zimin (Fri Mar 01 2019 - 07:47:20 PST)
    - Re: [AMBER] is this reference energy dG ~34 kcal/mol reasonable for acetic acid? Cruzeiro,Vinicius Wilian D (Fri Mar 01 2019 - 12:00:31 PST)
    - Re: [AMBER] is this reference energy dG ~34 kcal/mol reasonable for acetic acid? Feng, Zimin (Fri Mar 01 2019 - 12:28:39 PST)
    - Re: [AMBER] is this reference energy dG ~34 kcal/mol reasonable for acetic acid? Feng, Zimin (Fri Mar 01 2019 - 12:32:39 PST)
    - Re: [AMBER] is this reference energy dG ~34 kcal/mol reasonable for acetic acid? Feng, Zimin (Fri Mar 01 2019 - 12:35:23 PST)
    - Re: [AMBER] is this reference energy dG ~34 kcal/mol reasonable for acetic acid? Cruzeiro,Vinicius Wilian D (Fri Mar 01 2019 - 14:38:17 PST)
[AMBER] CPPTRAJ Center of Mass binning Debarati DasGupta (Wed Feb 27 2019 - 12:49:54 PST)
[AMBER] CPPTRAJ grid unknown command Debarati DasGupta (Wed Feb 27 2019 - 14:11:54 PST)
- Re: [AMBER] CPPTRAJ grid unknown command Daniel Roe (Wed Feb 27 2019 - 14:21:00 PST)
  - Re: [AMBER] CPPTRAJ grid unknown command Debarati DasGupta (Thu Feb 28 2019 - 07:31:10 PST)
    - Re: [AMBER] CPPTRAJ grid unknown command Daniel Roe (Fri Mar 01 2019 - 07:08:17 PST)
    - Re: [AMBER] CPPTRAJ grid unknown command Debarati DasGupta (Fri Mar 01 2019 - 09:17:44 PST)
    - Re: [AMBER] CPPTRAJ grid unknown command Debarati DasGupta (Fri Mar 01 2019 - 09:23:50 PST)
    - Re: [AMBER] CPPTRAJ grid unknown command Debarati DasGupta (Fri Mar 01 2019 - 09:41:16 PST)
    - Re: [AMBER] CPPTRAJ grid unknown command Daniel Roe (Mon Mar 11 2019 - 12:17:28 PDT)
[AMBER] Two dimensional replica exchange MD: Success rate Stephan Eismann (Wed Feb 27 2019 - 17:30:20 PST)
- Re: [AMBER] Two dimensional replica exchange MD: Success rate Daniel Roe (Mon Mar 04 2019 - 11:58:09 PST)
[AMBER] alchemical_analysis Hosein Geraili Daronkola (Thu Feb 28 2019 - 08:24:01 PST)
- Re: [AMBER] alchemical_analysis accuratefreeenergy.gmail.com (Thu Feb 28 2019 - 10:55:21 PST)
Re: [AMBER] Ligand autoimaging issue Amber18 David A Case (Fri Mar 01 2019 - 05:41:03 PST)
[AMBER] Doubt regarding input files in NMR refinement RITUPARNA ROY (Fri Mar 01 2019 - 06:34:13 PST)
- Re: [AMBER] Doubt regarding input files in NMR refinement Christina Bergonzo (Fri Mar 01 2019 - 06:51:30 PST)
[AMBER] 1/2 term in dihdral Mayank Dixit (Fri Mar 01 2019 - 14:27:36 PST)
- Re: [AMBER] 1/2 term in dihdral David A Case (Thu Mar 07 2019 - 08:54:17 PST)
[AMBER] distance restraint Sunita Patel (Sat Mar 02 2019 - 04:00:15 PST)
- Re: [AMBER] distance restraint Sundar (Wed Mar 06 2019 - 07:57:38 PST)
  - Re: [AMBER] distance restraint Sunita Patel (Wed Mar 06 2019 - 19:58:55 PST)
    - Re: [AMBER] distance restraint Sundar (Thu Mar 07 2019 - 06:29:09 PST)
    - Re: [AMBER] distance restraint Sunita Patel (Thu Mar 07 2019 - 20:12:15 PST)
[AMBER] [error] The system has extended beyond the extent of the virtual box Xiaocong Wang (Sun Mar 03 2019 - 00:37:41 PST)
- Re: [AMBER] [error] The system has extended beyond the extent of the virtual box Bill Ross (Sun Mar 03 2019 - 01:20:06 PST)
  - Re: [AMBER] [error] The system has extended beyond the extent of the virtual box Xiaocong Wang (Sun Mar 03 2019 - 02:17:15 PST)
    - Re: [AMBER] [error] The system has extended beyond the extent of the virtual box Bill Ross (Sun Mar 03 2019 - 03:18:30 PST)
- Re: [AMBER] [error] The system has extended beyond the extent of the virtual box David A Case (Tue Mar 05 2019 - 06:35:42 PST)
[AMBER] MM/PBSA topfile question Manyi Yang (Sun Mar 03 2019 - 17:35:51 PST)
- Re: [AMBER] MM/PBSA topfile question David A Case (Tue Mar 05 2019 - 06:38:01 PST)
[AMBER] Solvating a Lipid bilayer in Amber Souvik Dey (Sun Mar 03 2019 - 18:13:59 PST)
[AMBER] how to make sure .prmtop is the same for NEB calculation when using explicit solvent? 郭昱 (Sun Mar 03 2019 - 19:06:08 PST)
- Re: [AMBER] how to make sure .prmtop is the same for NEB calculation when using explicit solvent? Ghoreishi, Delaram (Sun Mar 03 2019 - 23:11:02 PST)
[AMBER] How can I generate of force field parameter for nano-material? xmgign.126.com (Sun Mar 03 2019 - 22:00:57 PST)
[AMBER] Message-ID: <20190301134103.u232i6wjibdt4cav@godel.rutgers.edu> zaid kamal (Mon Mar 04 2019 - 00:37:49 PST)
- Re: [AMBER] Message-ID: <20190301134103.u232i6wjibdt4cav@godel.rutgers.edu> Daniel Roe (Mon Mar 04 2019 - 12:00:06 PST)
[AMBER] Retrieving topology file emanuele falbo (Mon Mar 04 2019 - 02:08:01 PST)
- Re: [AMBER] Retrieving topology file Daniel Roe (Mon Mar 04 2019 - 05:53:38 PST)
  - Re: [AMBER] Retrieving topology file emanuele falbo (Mon Mar 04 2019 - 06:57:27 PST)
    - Re: [AMBER] Retrieving topology file Daniel Roe (Tue Mar 26 2019 - 12:16:08 PDT)
[AMBER] CPPTRAJ SPAM error while executing the input file Debarati DasGupta (Mon Mar 04 2019 - 09:14:52 PST)
- Re: [AMBER] CPPTRAJ SPAM error while executing the input file Daniel Roe (Mon Mar 04 2019 - 11:31:25 PST)
  - Re: [AMBER] CPPTRAJ SPAM error while executing the input file Daniel Roe (Tue Mar 05 2019 - 05:41:17 PST)
    - Re: [AMBER] CPPTRAJ SPAM error while executing the input file Daniel Roe (Tue Mar 05 2019 - 09:09:44 PST)
[AMBER] Converting Charmm forcefileld to Amber Hadi Rahmaninejad (Mon Mar 04 2019 - 09:23:26 PST)
- Re: [AMBER] Converting Charmm forcefileld to Amber Daniel Roe (Mon Mar 04 2019 - 11:36:03 PST)
  - Re: [AMBER] Converting Charmm forcefileld to Amber Hadi Rahmaninejad (Mon Mar 04 2019 - 12:43:49 PST)
    - Re: [AMBER] Converting Charmm forcefileld to Amber Daniel Roe (Tue Mar 05 2019 - 06:21:29 PST)
    - Re: [AMBER] Converting Charmm forcefileld to Amber Jason Swails (Tue Mar 05 2019 - 15:02:19 PST)
[AMBER] Use of amber force field in gromacs Akshay Prabhakant (Tue Mar 05 2019 - 01:39:49 PST)
- Re: [AMBER] Use of amber force field in gromacs Mayank Dixit (Tue Mar 05 2019 - 06:16:49 PST)
- Re: [AMBER] Use of amber force field in gromacs David A Case (Tue Mar 05 2019 - 06:46:23 PST)
[AMBER] Amber18 pmemd TI Hosein Geraili Daronkola (Tue Mar 05 2019 - 06:12:43 PST)
[AMBER] simulating a box of pure TIP3P water Debarati DasGupta (Tue Mar 05 2019 - 07:32:16 PST)
- Re: [AMBER] simulating a box of pure TIP3P water Daniel Roe (Mon Mar 11 2019 - 12:30:28 PDT)
  - Re: [AMBER] simulating a box of pure TIP3P water Daniel Roe (Mon Mar 11 2019 - 12:31:50 PDT)
[AMBER] improper dihedral Mayank Dixit (Tue Mar 05 2019 - 08:59:58 PST)
- Re: [AMBER] improper dihedral David Case (Thu Mar 07 2019 - 06:17:07 PST)
[AMBER] One query about SPAM type calculations Debarati DasGupta (Tue Mar 05 2019 - 09:45:26 PST)
- Re: [AMBER] One query about SPAM type calculations Daniel Roe (Mon Mar 11 2019 - 12:15:14 PDT)
[AMBER] What does "0 Kb value" mean in dihedrals Erdem Yeler (Tue Mar 05 2019 - 11:35:33 PST)
- Re: [AMBER] What does "0 Kb value" mean in dihedrals David Case (Wed Mar 06 2019 - 14:27:08 PST)
  - Re: [AMBER] What does "0 Kb value" mean in dihedrals Erdem Yeler (Sat Mar 09 2019 - 05:47:12 PST)
[AMBER] SPAM analysis Debarati DasGupta (Tue Mar 05 2019 - 14:05:41 PST)
- Re: [AMBER] SPAM analysis Daniel Roe (Mon Mar 11 2019 - 12:14:34 PDT)
[AMBER] Error in REMD with pmemd.cuda.MPI Ikuo KURISAKI (Wed Mar 06 2019 - 00:24:07 PST)
- Re: [AMBER] Error in REMD with pmemd.cuda.MPI Cruzeiro,Vinicius Wilian D (Wed Mar 06 2019 - 06:58:25 PST)
- Re: [AMBER] Error in REMD with pmemd.cuda.MPI Ikuo KURISAKI (Wed Mar 06 2019 - 22:05:10 PST)
[AMBER] Problem with distance restraints in membrane system with pmemd.cuda David Bickel (Wed Mar 06 2019 - 01:18:40 PST)
- Re: [AMBER] Problem with distance restraints in membrane system with pmemd.cuda David Bickel (Fri Mar 08 2019 - 07:29:28 PST)
- Re: [AMBER] Problem with distance restraints in membrane system with pmemd.cuda David Case (Sat Mar 09 2019 - 06:01:53 PST)
  - Re: [AMBER] Problem with distance restraints in membrane system with pmemd.cuda David Bickel (Mon Mar 11 2019 - 05:10:32 PDT)
    - Re: [AMBER] Problem with distance restraints in membrane system with pmemd.cuda Charles Lin (Mon Mar 11 2019 - 08:44:58 PDT)
[AMBER] Protein - Ligand simulation on amber and PBSA Prasanth G, Research Scholar (Wed Mar 06 2019 - 05:35:34 PST)
[AMBER] chi1 angle of amino acids not having a CG atom Rosellen, Martin (Wed Mar 06 2019 - 09:21:34 PST)
- Re: [AMBER] chi1 angle of amino acids not having a CG atom Daniel Roe (Mon Mar 11 2019 - 12:07:20 PDT)
[AMBER] Chirality Restraint on a Part of Replica Ikuo KURISAKI (Wed Mar 06 2019 - 22:19:51 PST)
[AMBER] Query about metal RMSD regarding residue number or atom number shahid khan (Thu Mar 07 2019 - 03:21:39 PST)
- Re: [AMBER] Query about metal RMSD regarding residue number or atom number Dr. Anselm Horn (Thu Mar 07 2019 - 04:09:55 PST)
[AMBER] Help regarding protein DNA MD in AMBER Vikram Dalal (Thu Mar 07 2019 - 03:25:19 PST)
- Re: [AMBER] Help regarding protein DNA MD in AMBER David A Case (Thu Mar 07 2019 - 06:09:15 PST)
[AMBER] Running a MMPBSA calculation on only the structure Keiran Corbett (Thu Mar 07 2019 - 06:32:17 PST)
[AMBER] Setbox and ChBox Lin Song (Thu Mar 07 2019 - 09:48:14 PST)
[AMBER] system explosion Hadi Rahmaninejad (Thu Mar 07 2019 - 15:18:30 PST)
- Re: [AMBER] system explosion David A Case (Fri Mar 08 2019 - 06:04:02 PST)
[AMBER] ValueError: invalid literal for int() with base 10: '-3.0' SATYAJIT KHATUA (Thu Mar 07 2019 - 20:29:11 PST)
- Re: [AMBER] ValueError: invalid literal for int() with base 10: '-3.0' SATYAJIT KHATUA (Wed Mar 13 2019 - 21:19:19 PDT)
  - [AMBER] [MGMS-DS]: Molecular Modelling Workshop + Tim Clark Birthday Symposium: April 08-11, 2019 in Erlangen, Germany Dr. Anselm Horn (Thu Mar 14 2019 - 02:24:46 PDT)
  - Re: [AMBER] ValueError: invalid literal for int() with base 10: '-3.0' Daniel Roe (Thu Mar 14 2019 - 05:26:50 PDT)
[AMBER] MMPBSA.py Calculation error Rinsha Chk (Thu Mar 07 2019 - 21:52:40 PST)
- Re: [AMBER] MMPBSA.py Calculation error David A Case (Fri Mar 08 2019 - 06:06:45 PST)
  - Re: [AMBER] MMPBSA.py Calculation error Rinsha Chk (Fri Mar 08 2019 - 06:21:05 PST)
[AMBER] calculate RDF using COM Saikat Pal (Thu Mar 07 2019 - 22:57:51 PST)
- Re: [AMBER] calculate RDF using COM Daniel Roe (Mon Mar 11 2019 - 11:12:25 PDT)
[AMBER] Error in Minimization Zhonghua Xia (Fri Mar 08 2019 - 01:18:57 PST)
- Re: [AMBER] Error in Minimization Bill Ross (Fri Mar 08 2019 - 02:21:21 PST)
- Re: [AMBER] Error in Minimization David A Case (Fri Mar 08 2019 - 06:13:54 PST)
  - Re: [AMBER] Error in Minimization Zhonghua Xia (Fri Mar 15 2019 - 08:37:48 PDT)
    - Re: [AMBER] Error in Minimization Zhonghua Xia (Fri Mar 15 2019 - 09:48:21 PDT)
[AMBER] Query about protein DNA MD Vikram Dalal (Fri Mar 08 2019 - 09:29:34 PST)
- Re: [AMBER] Query about protein DNA MD David A Case (Fri Mar 08 2019 - 11:00:35 PST)
[AMBER] write equilibrium bond lengths, angles and dihedrals from a ligand structure file to a frcmod file Thomas Evangelidis (Fri Mar 08 2019 - 10:08:14 PST)
- Re: [AMBER] write equilibrium bond lengths, angles and dihedrals from a ligand structure file to a frcmod file Dickson, Callum (Sat Mar 09 2019 - 19:03:29 PST)
  - Re: [AMBER] write equilibrium bond lengths, angles and dihedrals from a ligand structure file to a frcmod file Thomas Evangelidis (Sun Mar 10 2019 - 03:49:56 PDT)
[AMBER] CUDA COM distance restraint (v18 with patch.7 applied) Pratul Agarwal (Sun Mar 10 2019 - 11:48:33 PDT)
- Re: [AMBER] CUDA COM distance restraint (v18 with patch.7 applied) Stephan Schott (Sun Mar 10 2019 - 12:10:57 PDT)
  - Re: [AMBER] CUDA COM distance restraint (v18 with patch.7 applied) Pratul Agarwal (Sun Mar 10 2019 - 13:38:51 PDT)
  - Re: [AMBER] CUDA COM distance restraint (v18 with patch.7 applied) Kellon Belfon (Sun Mar 10 2019 - 13:44:31 PDT)
    - Re: [AMBER] CUDA COM distance restraint (v18 with patch.7 applied) Pratul Agarwal (Sun Mar 10 2019 - 16:19:06 PDT)
    - Re: [AMBER] CUDA COM distance restraint (v18 with patch.7 applied) Charles Lin (Mon Mar 11 2019 - 08:05:29 PDT)
[AMBER] antechamber bcc error Michael Shokhen (Mon Mar 11 2019 - 04:09:32 PDT)
- Re: [AMBER] antechamber bcc error David A Case (Mon Mar 11 2019 - 07:36:40 PDT)
- Re: [AMBER] antechamber bcc error Michael Shokhen (Tue Mar 12 2019 - 06:16:19 PDT)
[AMBER] metal parameters Fabian Glaser (Tue Mar 12 2019 - 07:00:06 PDT)
- Re: [AMBER] metal parameters Pengfei Li (Sat Mar 16 2019 - 08:19:13 PDT)
  - Re: [AMBER] metal parameters Marcelo Andrade Chagas (Sat Mar 16 2019 - 08:49:45 PDT)
  - Re: [AMBER] metal parameters Fabian Glaser (Fri Apr 05 2019 - 21:56:51 PDT)
    - Re: [AMBER] metal parameters Pengfei Li (Sat Apr 06 2019 - 14:39:29 PDT)
[AMBER] Metal parameters method Fabian Glaser (Tue Mar 12 2019 - 09:09:27 PDT)
[AMBER] Research Programmer for VMD/NAMD at UIUC João Ribeiro (Tue Mar 12 2019 - 11:33:01 PDT)
[AMBER] Directly Set Restraint for Chilarity to Prmtop File Ikuo KURISAKI (Tue Mar 12 2019 - 18:16:01 PDT)
- Re: [AMBER] Directly Set Restraint for Chilarity to Prmtop File David Case (Wed Mar 13 2019 - 08:39:54 PDT)
[AMBER] Quantitative measurement of hydrophobic and polar contacts Rakesh Srivastava (Wed Mar 13 2019 - 00:13:07 PDT)
[AMBER] Job terminated during TI calculation in pmemd.cuda 강무석 (Wed Mar 13 2019 - 01:13:42 PDT)
[AMBER] nmode_com.96 高含露 (Wed Mar 13 2019 - 01:24:58 PDT)
[AMBER] DSSP residue vs time graph Myriam Hanna (Wed Mar 13 2019 - 08:30:27 PDT)
- Re: [AMBER] DSSP residue vs time graph Premila Samuel Mohan Dass (Wed Mar 13 2019 - 09:18:21 PDT)
  - Re: [AMBER] DSSP residue vs time graph Myriam Hanna (Wed Mar 13 2019 - 09:54:12 PDT)
- Re: [AMBER] DSSP residue vs time graph Daniel Roe (Thu Mar 14 2019 - 05:20:47 PDT)
  - Re: [AMBER] DSSP residue vs time graph Myriam Hanna (Thu Mar 14 2019 - 06:44:14 PDT)
[AMBER] CPPTRAJ Grid with COM Kung, Ryan (Wed Mar 13 2019 - 09:03:55 PDT)
- Re: [AMBER] CPPTRAJ Grid with COM Daniel Roe (Wed Mar 13 2019 - 09:08:55 PDT)
  - Re: [AMBER] CPPTRAJ Grid with COM Kung, Ryan (Wed Mar 13 2019 - 09:57:16 PDT)
    - Re: [AMBER] CPPTRAJ Grid with COM Daniel Roe (Wed Mar 13 2019 - 10:03:09 PDT)
[AMBER] velocities from and velocityautocorr Ruth Helena Tichauer (Wed Mar 13 2019 - 09:07:37 PDT)
- Re: [AMBER] velocities from and velocityautocorr Ruth Helena Tichauer (Wed Mar 13 2019 - 09:25:43 PDT)
- Re: [AMBER] velocities from and velocityautocorr Daniel Roe (Wed Mar 13 2019 - 10:17:47 PDT)
  - Re: [AMBER] velocities from and velocityautocorr Ruth Helena Tichauer (Wed Mar 13 2019 - 13:56:51 PDT)
    - Re: [AMBER] velocities from and velocityautocorr Ruth Helena Tichauer (Fri Mar 15 2019 - 07:08:02 PDT)
    - Re: [AMBER] velocities from and velocityautocorr Daniel Roe (Fri Mar 15 2019 - 12:30:59 PDT)
    - Re: [AMBER] velocities from and velocityautocorr Ruth Helena Tichauer (Mon Mar 18 2019 - 00:36:08 PDT)
[AMBER] parameters for cc and cd Träg, Johannes (Wed Mar 13 2019 - 10:27:19 PDT)
- Re: [AMBER] parameters for cc and cd David Case (Wed Mar 13 2019 - 16:46:18 PDT)
[AMBER] Jar pulling Gerardo Zerbetto De Palma (Wed Mar 13 2019 - 10:21:47 PDT)
- Re: [AMBER] Jar pulling Pratul Agarwal (Wed Mar 13 2019 - 13:46:49 PDT)
- Re: [AMBER] Jar pulling Stephan Schott (Fri Mar 15 2019 - 07:15:17 PDT)
  - Re: [AMBER] Jar pulling Gerardo Zerbetto De Palma (Fri Mar 15 2019 - 05:00:28 PDT)
[AMBER] PNEB simulation transition Ashutosh Shandilya (Thu Mar 14 2019 - 09:04:18 PDT)
- Re: [AMBER] PNEB simulation transition Ghoreishi, Delaram (Thu Mar 14 2019 - 11:23:14 PDT)
  - Re: [AMBER] PNEB simulation transition Ashutosh Shandilya (Thu Mar 14 2019 - 12:11:39 PDT)
[AMBER] MMPBSA.py.MPI error Prabir Khatua (Thu Mar 14 2019 - 15:24:21 PDT)
[AMBER] the question of calculate the binding free energy by MMPBSA.py bjyx20090941 (Fri Mar 15 2019 - 00:28:05 PDT)
[AMBER] charged residue mutation free energy Hosein Geraili Daronkola (Fri Mar 15 2019 - 06:32:43 PDT)
- Re: [AMBER] charged residue mutation free energy Hosein Geraili Daronkola (Fri Apr 12 2019 - 00:04:12 PDT)
[AMBER] gaff2 parameters of c3-c3-os-c3 Träg, Johannes (Fri Mar 15 2019 - 08:21:05 PDT)
- Re: [AMBER] gaff2 parameters of c3-c3-os-c3 David Case (Fri Mar 15 2019 - 12:20:19 PDT)
  - Re: [AMBER] gaff2 parameters of c3-c3-os-c3 Träg, Johannes (Mon Mar 18 2019 - 03:41:46 PDT)
    - Re: [AMBER] gaff2 parameters of c3-c3-os-c3 Song, Lin (Mon Aug 05 2019 - 12:51:36 PDT)
    - Re: [AMBER] gaff2 parameters of c3-c3-os-c3 David Cerutti (Mon Aug 05 2019 - 13:04:28 PDT)
    - Re: [AMBER] gaff2 parameters of c3-c3-os-c3 David Case (Mon Aug 05 2019 - 18:27:36 PDT)
    - Re: [AMBER] gaff2 parameters of c3-c3-os-c3 Song, Lin (Fri Aug 09 2019 - 08:30:28 PDT)
    - Re: [AMBER] gaff2 parameters of c3-c3-os-c3 Junmei Wang (Fri Aug 09 2019 - 13:03:14 PDT)
[AMBER] Restraint and ambmask syntax issue Xiaoyu Wang (Fri Mar 15 2019 - 11:36:13 PDT)
- Re: [AMBER] Restraint and ambmask syntax issue David Case (Fri Mar 15 2019 - 12:29:20 PDT)
[AMBER] Amber18 STSM 李耀 (Sat Mar 16 2019 - 06:38:45 PDT)
- Re: [AMBER] Amber18 STSM Feng Pan (Sun Mar 17 2019 - 21:48:00 PDT)
[AMBER] Homodimerization of IRF3 protein Debarati DasGupta (Sat Mar 16 2019 - 14:38:05 PDT)
[AMBER] A confused question about calculate the binding free energy from MMPBSA.py bjyx20090941 (Sun Mar 17 2019 - 18:13:28 PDT)
[AMBER] pdb file with 4 atoms coordinates of water molecules with TIP4PFB model bjyx20090941 (Mon Mar 18 2019 - 05:41:16 PDT)
- Re: [AMBER] pdb file with 4 atoms coordinates of water molecules with TIP4PFB model Daniel Roe (Mon Mar 18 2019 - 05:49:47 PDT)
[AMBER] Assigning protonation states manually to the amino vs CpH MD simulation Bharat Manna (Mon Mar 18 2019 - 11:50:23 PDT)
- Re: [AMBER] Assigning protonation states manually to the amino vs CpH MD simulation Carlos Simmerling (Mon Mar 18 2019 - 07:05:15 PDT)
[AMBER] Nastruct vs 3DNA Jason Imamoto (Mon Mar 18 2019 - 10:12:37 PDT)
- Re: [AMBER] Nastruct vs 3DNA Daniel Roe (Mon Mar 18 2019 - 10:37:04 PDT)
- Re: [AMBER] Nastruct vs 3DNA Jason Imamoto (Mon Mar 18 2019 - 12:14:24 PDT)
  - Re: [AMBER] Nastruct vs 3DNA Daniel Roe (Mon Mar 18 2019 - 12:33:47 PDT)
[AMBER] Input Reservoir REMD Raimon Fabregat (Tue Mar 19 2019 - 01:17:13 PDT)
- Re: [AMBER] Input Reservoir REMD koushik kasavajhala (Tue Mar 19 2019 - 02:47:31 PDT)
Re: [AMBER] Installation problem AMBER16 David A Case (Tue Mar 19 2019 - 06:51:50 PDT)
[AMBER] Hyaluronic acid using Glycam06 monia kam (Tue Mar 19 2019 - 08:15:18 PDT)
- Re: [AMBER] Hyaluronic acid using Glycam06 Casalini Tommaso (Wed Mar 20 2019 - 04:00:26 PDT)
[AMBER] Query regarding secondary structure Saikat Pal (Tue Mar 19 2019 - 22:08:42 PDT)
- Re: [AMBER] Query regarding secondary structure Daniel Roe (Wed Mar 20 2019 - 05:09:21 PDT)
[AMBER] Gpu illegal memory code accessed Debarati DasGupta (Wed Mar 20 2019 - 07:39:25 PDT)
- Re: [AMBER] Gpu illegal memory code accessed Brian Radak (Wed Mar 20 2019 - 07:53:17 PDT)
  - Re: [AMBER] Gpu illegal memory code accessed Debarati DasGupta (Thu Mar 21 2019 - 07:03:35 PDT)
    - Re: [AMBER] Gpu illegal memory code accessed David A Case (Thu Mar 21 2019 - 11:38:16 PDT)
[AMBER] Amber18: cv_min and cv_max for periodic cv in ABMD 李耀 (Wed Mar 20 2019 - 09:25:26 PDT)
[AMBER] Installation error AmberTools18 - [test.rism1d] Error Mariana Simões Ferreira (Wed Mar 20 2019 - 10:02:37 PDT)
- Re: [AMBER] Installation error AmberTools18 - [test.rism1d] Error David A Case (Wed Mar 20 2019 - 13:25:08 PDT)
- Re: [AMBER] Installation error AmberTools18 - [test.rism1d] Error Daniel Roe (Thu Mar 21 2019 - 07:50:03 PDT)
[AMBER] cuda test failing after installation Ravi Abrol (Wed Mar 20 2019 - 10:09:32 PDT)
- Re: [AMBER] cuda test failing after installation David Case (Sun Mar 24 2019 - 05:35:00 PDT)
  - Re: [AMBER] cuda test failing after installation Ravi Abrol (Sun Mar 24 2019 - 22:35:49 PDT)
    - Re: [AMBER] cuda test failing after installation Ravi Abrol (Tue May 07 2019 - 10:26:54 PDT)
    - Re: [AMBER] cuda test failing after installation David Cerutti (Tue May 07 2019 - 11:02:48 PDT)
    - Re: [AMBER] cuda test failing after installation Ravi Abrol (Tue May 07 2019 - 12:43:28 PDT)
    - Re: [AMBER] cuda test failing after installation Ravi Abrol (Mon May 13 2019 - 11:52:43 PDT)
Re: [AMBER] Nastruct vs 3DNA: Files used for analysis and the output Jason Imamoto (Wed Mar 20 2019 - 11:00:51 PDT)
- Re: [AMBER] Nastruct vs 3DNA: Files used for analysis and the output Daniel Roe (Wed Mar 20 2019 - 12:23:59 PDT)
[AMBER] using amber parameters in namd Akshay Prabhakant (Thu Mar 21 2019 - 06:27:22 PDT)
- Re: [AMBER] using amber parameters in namd David A Case (Thu Mar 21 2019 - 11:34:07 PDT)
[AMBER] FEW amber- LIE analysis Sowmya Indrakumar (Thu Mar 21 2019 - 06:38:37 PDT)
- Re: [AMBER] FEW amber- LIE analysis Sowmya Indrakumar (Wed Mar 27 2019 - 03:36:06 PDT)
[AMBER] Amber18: Adaptively Biased MD (Metadynalmics) 李耀 (Thu Mar 21 2019 - 08:49:56 PDT)
- Re: [AMBER] Amber18: Adaptively Biased MD (Metadynalmics) Feng Pan (Sun Mar 24 2019 - 20:37:50 PDT)
[AMBER] DFTB3/MM simulations of CCCC zinc finger Dreab, Ana (Thu Mar 21 2019 - 09:18:35 PDT)
- Re: [AMBER] DFTB3/MM simulations of CCCC zinc finger Pengfei Li (Sat Mar 23 2019 - 12:35:59 PDT)
  - Re: [AMBER] DFTB3/MM simulations of CCCC zinc finger Dreab, Ana (Thu Mar 28 2019 - 08:27:33 PDT)
    - Re: [AMBER] DFTB3/MM simulations of CCCC zinc finger Pengfei Li (Thu Mar 28 2019 - 09:09:44 PDT)
[AMBER] CEMD protcnt meaning Feng, Zimin (Thu Mar 21 2019 - 09:31:40 PDT)
- Re: [AMBER] CEMD protcnt meaning Cruzeiro,Vinicius Wilian D (Thu Mar 21 2019 - 09:41:42 PDT)
  - Re: [AMBER] CEMD protcnt meaning Feng, Zimin (Thu Mar 21 2019 - 10:18:48 PDT)
[AMBER] Incorrect electric field Ashutosh Mishra (Thu Mar 21 2019 - 23:26:14 PDT)
- Re: [AMBER] Incorrect electric field Bill Ross (Thu Mar 21 2019 - 23:40:21 PDT)
  - Re: [AMBER] Incorrect electric field Ashutosh Mishra (Thu Mar 21 2019 - 23:43:27 PDT)
    - Re: [AMBER] Incorrect electric field Bill Ross (Thu Mar 21 2019 - 23:45:34 PDT)
    - Re: [AMBER] Incorrect electric field Ashutosh Mishra (Thu Mar 21 2019 - 23:48:05 PDT)
    - Re: [AMBER] Incorrect electric field Bill Ross (Fri Mar 22 2019 - 00:40:31 PDT)
    - Re: [AMBER] Incorrect electric field Charles Lin (Mon Mar 25 2019 - 08:28:12 PDT)
    - Re: [AMBER] Incorrect electric field Bill Ross (Mon Mar 25 2019 - 12:18:47 PDT)
- [AMBER] installation error ilhan.yavuz (Tue Sep 24 2019 - 07:13:08 PDT)
  - Re: [AMBER] installation error David Mathog (Tue Sep 24 2019 - 09:34:58 PDT)
  - Re: [AMBER] installation error David Case (Wed Sep 25 2019 - 06:08:43 PDT)
[AMBER] Closest command in cpptraj for non aqeous solvents Debarati DasGupta (Fri Mar 22 2019 - 12:23:32 PDT)
- Re: [AMBER] Closest command in cpptraj for non aqeous solvents Daniel Roe (Fri Mar 22 2019 - 12:32:04 PDT)
  - Re: [AMBER] Closest command in cpptraj for non aqeous solvents Debarati DasGupta (Fri Mar 22 2019 - 13:09:10 PDT)
    - Re: [AMBER] Closest command in cpptraj for non aqeous solvents Debarati DasGupta (Fri Mar 22 2019 - 13:40:58 PDT)
    - Re: [AMBER] Closest command in cpptraj for non aqeous solvents Daniel Roe (Tue Mar 26 2019 - 08:32:06 PDT)
[AMBER] Occupancy values in pseudo PDB from CPPRAJ grid analysis anu chandra (Fri Mar 22 2019 - 14:42:04 PDT)
- Re: [AMBER] Occupancy values in pseudo PDB from CPPRAJ grid analysis Daniel Roe (Tue Mar 26 2019 - 05:34:54 PDT)
[AMBER] PCA analysis of NM maya nair (Mon Mar 25 2019 - 05:05:01 PDT)
- Re: [AMBER] PCA analysis of NM Daniel Roe (Tue Mar 26 2019 - 12:09:37 PDT)
[AMBER] Single point energy calculation SCC-DFTB Anthony Bogetti (Mon Mar 25 2019 - 05:40:28 PDT)
- Re: [AMBER] Single point energy calculation SCC-DFTB Setyanto Md (Mon Mar 25 2019 - 05:47:53 PDT)
- Re: [AMBER] Single point energy calculation SCC-DFTB David A Case (Mon Mar 25 2019 - 07:33:45 PDT)
[AMBER] Simulation of spherical macroion system Rakesh Srivastava (Mon Mar 25 2019 - 06:17:24 PDT)
[AMBER] locating the single probe out of 80000 snapshots Debarati DasGupta (Mon Mar 25 2019 - 07:58:20 PDT)
- Re: [AMBER] locating the single probe out of 80000 snapshots Daniel Roe (Tue Mar 26 2019 - 12:12:30 PDT)
  - Re: [AMBER] locating the single probe out of 80000 snapshots Debarati DasGupta (Tue Mar 26 2019 - 14:05:36 PDT)
    - Re: [AMBER] locating the single probe out of 80000 snapshots Daniel Roe (Tue Mar 26 2019 - 17:36:02 PDT)
    - Re: [AMBER] locating the single probe out of 80000 snapshots Debarati DasGupta (Wed Mar 27 2019 - 06:12:45 PDT)
    - Re: [AMBER] locating the single probe out of 80000 snapshots Daniel Roe (Wed Mar 27 2019 - 06:23:30 PDT)
    - Re: [AMBER] locating the single probe out of 80000 snapshots Debarati DasGupta (Wed Mar 27 2019 - 06:24:59 PDT)
    - Re: [AMBER] locating the single probe out of 80000 snapshots Daniel Roe (Wed Mar 27 2019 - 06:42:56 PDT)
    - Re: [AMBER] locating the single probe out of 80000 snapshots Debarati DasGupta (Wed Mar 27 2019 - 07:02:18 PDT)
[AMBER] Problems calculating density over distance Lucas Bandeira (Mon Mar 25 2019 - 10:41:48 PDT)
- Re: [AMBER] Problems calculating density over distance Daniel Roe (Tue Mar 26 2019 - 12:08:03 PDT)
  - Re: [AMBER] Problems calculating density over distance Lucas Bandeira (Mon Apr 01 2019 - 09:13:25 PDT)
[AMBER] varying pressure conditions? Shayna Hilburg (Mon Mar 25 2019 - 11:06:06 PDT)
- Re: [AMBER] varying pressure conditions? David Case (Sat Mar 30 2019 - 13:53:00 PDT)
  - Re: [AMBER] varying pressure conditions? Shayna Hilburg (Mon Apr 01 2019 - 08:21:07 PDT)
    - Re: [AMBER] varying pressure conditions? Carlos Simmerling (Mon Apr 01 2019 - 08:23:06 PDT)
[AMBER] AMBER 18 error in QM region of QMMM Abhilash J (Tue Mar 26 2019 - 02:27:05 PDT)
- Re: [AMBER] AMBER 18 error in QM region of QMMM Szymon Żaczek (Tue Mar 26 2019 - 02:45:10 PDT)
  - Re: [AMBER] AMBER 18 error in QM region of QMMM Bill Ross (Tue Mar 26 2019 - 03:39:46 PDT)
    - Re: [AMBER] AMBER 18 error in QM region of QMMM Abhilash J (Tue Mar 26 2019 - 06:33:03 PDT)
    - Re: [AMBER] AMBER 18 error in QM region of QMMM Goetz, Andreas (Tue Mar 26 2019 - 14:49:26 PDT)
    - Re: [AMBER] AMBER 18 error in QM region of QMMM Abhilash J (Tue Mar 26 2019 - 19:21:31 PDT)
    - Re: [AMBER] AMBER 18 error in QM region of QMMM Abhilash J (Tue Mar 26 2019 - 23:02:49 PDT)
[AMBER] Solvate with methanol and acetone using free energy methods? Defrese, Matthew (Tue Mar 26 2019 - 08:27:31 PDT)
- Re: [AMBER] Solvate with methanol and acetone using free energy methods? Debarati DasGupta (Tue Mar 26 2019 - 09:53:33 PDT)
- Re: [AMBER] Solvate with methanol and acetone using free energy methods? Stephan Schott (Sat Mar 30 2019 - 14:47:07 PDT)
[AMBER] Question about Amber TUTORIAL B5: Simulating the Green Fluorescent Protein A K (Tue Mar 26 2019 - 10:12:13 PDT)
- Re: [AMBER] Question about Amber TUTORIAL B5: Simulating the Green Fluorescent Protein Debarati DasGupta (Tue Mar 26 2019 - 10:17:13 PDT)
- Re: [AMBER] Question about Amber TUTORIAL B5: Simulating the Green Fluorescent Protein David A Case (Wed Mar 27 2019 - 04:28:35 PDT)
[AMBER] TIP4P Ice1h phase initial structure Mohd moid khan (Tue Mar 26 2019 - 13:11:14 PDT)
[AMBER] Error in `sander': malloc(): smallbin double linked list corrupted: Margarita I. Bernal-Uruchurtu (Tue Mar 26 2019 - 14:53:00 PDT)
[AMBER] metal-oxide-metal interactions Arun Srikanth (Tue Mar 26 2019 - 15:34:21 PDT)
- Re: [AMBER] metal-oxide-metal interactions Pengfei Li (Thu Apr 04 2019 - 17:44:44 PDT)
[AMBER] Design of graphene quantum dots RITUPARNA ROY (Tue Mar 26 2019 - 20:50:50 PDT)
- Re: [AMBER] Design of graphene quantum dots pavel.banas.upol.cz (Wed Mar 27 2019 - 01:35:55 PDT)
[AMBER] TI atom limit Andrea Cavalli (Wed Mar 27 2019 - 01:14:32 PDT)
- Re: [AMBER] TI atom limit accuratefreeenergy.gmail.com (Wed Mar 27 2019 - 04:53:19 PDT)
  - Re: [AMBER] TI atom limit Andrea Cavalli (Wed Mar 27 2019 - 05:37:46 PDT)
    - Re: [AMBER] TI atom limit accuratefreeenergy.gmail.com (Wed Mar 27 2019 - 06:27:26 PDT)
[AMBER] how to get unbiased trajectories from biased trajectories Mayank Dixit (Wed Mar 27 2019 - 07:33:36 PDT)
[AMBER] Installation of AmberTools18 in macOS Mojave Reza Esmaeeli (Wed Mar 27 2019 - 11:48:21 PDT)
- Re: [AMBER] Installation of AmberTools18 in macOS Mojave David Case (Wed Mar 27 2019 - 19:02:52 PDT)
- Re: [AMBER] Installation of AmberTools18 in macOS Mojave Gustaf Olsson (Wed Mar 27 2019 - 23:41:42 PDT)
  - Re: [AMBER] Installation of AmberTools18 in macOS Mojave Reza Esmaeeli (Wed Mar 27 2019 - 23:59:26 PDT)
    - Re: [AMBER] Installation of AmberTools18 in macOS Mojave Gustaf Olsson (Thu Mar 28 2019 - 04:32:42 PDT)
    - Re: [AMBER] Installation of AmberTools18 in macOS Mojave Gustaf Olsson (Thu Mar 28 2019 - 07:08:46 PDT)
    - Re: [AMBER] Installation of AmberTools18 in macOS Mojave Gustaf Olsson (Thu Mar 28 2019 - 07:58:26 PDT)
    - Re: [AMBER] Installation of AmberTools18 in macOS Mojave Gustaf Olsson (Thu Mar 28 2019 - 08:18:33 PDT)
    - Re: [AMBER] Installation of AmberTools18 in macOS Mojave Reza Esmaeeli (Thu Mar 28 2019 - 08:21:37 PDT)
    - Re: [AMBER] Installation of AmberTools18 in macOS Mojave Gustaf Olsson (Fri Mar 29 2019 - 07:22:10 PDT)
    - Re: [AMBER] Installation of AmberTools18 in macOS Mojave Daniel Roe (Fri Mar 29 2019 - 07:41:49 PDT)
    - Re: [AMBER] Installation of AmberTools18 in macOS Mojave Gustaf Olsson (Fri Mar 29 2019 - 08:15:17 PDT)
    - Re: [AMBER] Installation of AmberTools18 in macOS Mojave Reza Esmaeeli (Thu Mar 28 2019 - 07:15:01 PDT)
[AMBER] NMR order parameters from MD trajectories giulia palermo (Wed Mar 27 2019 - 18:41:09 PDT)
- Re: [AMBER] NMR order parameters from MD trajectories George M. Giambasu (Wed Mar 27 2019 - 19:36:50 PDT)
[AMBER] Regarding solvated interaction energy (SIE) method in Amber 16 Fulbabu Sk (Thu Mar 28 2019 - 03:27:00 PDT)
[AMBER] Building pmemd.cuda.MPI error in amber18 Meng Wu (Thu Mar 28 2019 - 04:11:23 PDT)
- [AMBER] Building pmemd.cuda.MPI error in amber18 Meng Wu (Fri Mar 29 2019 - 01:13:48 PDT)
- Re: [AMBER] Building pmemd.cuda.MPI error in amber18 David Case (Fri Mar 29 2019 - 04:15:39 PDT)
[AMBER] A confused question about calculate the binding free energy from MMPBSA.py bjyx20090941 (Thu Mar 28 2019 - 05:29:53 PDT)
- Re: [AMBER] A confused question about calculate the binding free energy from MMPBSA.py Ray Luo (Fri Mar 29 2019 - 07:38:02 PDT)
[AMBER] Job position Ganesh Kamath (Thu Mar 28 2019 - 18:31:02 PDT)
- Re: [AMBER] Job position David Case (Sat Mar 30 2019 - 13:30:02 PDT)
[AMBER] regarding simulation angad sharma (Thu Mar 28 2019 - 23:59:05 PDT)
- Re: [AMBER] regarding simulation Carlos Simmerling (Fri Mar 29 2019 - 04:43:17 PDT)
[AMBER] Query about plotting/visualizing the lifetime curve from H-Bond analysis using CPPTRAJ SATYAJIT KHATUA (Fri Mar 29 2019 - 07:12:27 PDT)
- Re: [AMBER] Query about plotting/visualizing the lifetime curve from H-Bond analysis using CPPTRAJ Daniel Roe (Fri Mar 29 2019 - 07:34:55 PDT)
[AMBER] nativecontacs in ccptraj Debarati DasGupta (Fri Mar 29 2019 - 10:49:51 PDT)
- Re: [AMBER] nativecontacs in ccptraj Daniel Roe (Sat Mar 30 2019 - 06:03:30 PDT)
[AMBER] MMPBSA Prabir Khatua (Fri Mar 29 2019 - 14:14:33 PDT)
- Re: [AMBER] MMPBSA Vijay Singh (Sat Mar 15 2014 - 20:33:05 PDT)
- Re: [AMBER] MMPBSA Elvis Martis (Fri Mar 29 2019 - 21:38:19 PDT)
  - Re: [AMBER] MMPBSA Prabir Khatua (Fri Mar 29 2019 - 22:46:23 PDT)
    - Re: [AMBER] MMPBSA Abhilash J (Sat Mar 30 2019 - 01:42:49 PDT)
    - Re: [AMBER] MMPBSA Prabir Khatua (Sat Mar 30 2019 - 09:39:40 PDT)
    - Re: [AMBER] MMPBSA Wesley Michael Botello-Smith (Sat Mar 30 2019 - 12:43:38 PDT)
    - Re: [AMBER] MMPBSA Wesley Michael Botello-Smith (Sat Mar 30 2019 - 12:58:42 PDT)
    - Re: [AMBER] MMPBSA Prabir Khatua (Sat Mar 30 2019 - 16:12:36 PDT)
[AMBER] NFE error: Cannot read &abmd namelist Jason Imamoto (Sat Mar 30 2019 - 04:26:33 PDT)
- Re: [AMBER] NFE error: Cannot read &abmd namelist Feng Pan (Sat Mar 30 2019 - 20:52:49 PDT)
- Re: [AMBER] NFE error: Cannot read &abmd namelist Jason Imamoto (Mon Apr 01 2019 - 00:54:59 PDT)
  - Re: [AMBER] NFE error: Cannot read &abmd namelist Feng Pan (Tue Apr 02 2019 - 16:56:47 PDT)
[AMBER] huge reference.frc in MMPBSA Antoine MARION (Sun Mar 31 2019 - 10:44:56 PDT)
- Re: [AMBER] huge reference.frc in MMPBSA Ray Luo (Sun Mar 31 2019 - 13:51:03 PDT)
  - Re: [AMBER] huge reference.frc in MMPBSA Antoine Marion (Sun Mar 31 2019 - 21:20:27 PDT)
[AMBER] How the instantaneous temperature is calculated in Amber ? Marek Maly (Sun Mar 31 2019 - 17:35:05 PDT)
- Re: [AMBER] How the instantaneous temperature is calculated in Amber ? Bill Ross (Sun Mar 31 2019 - 17:57:02 PDT)
  - Re: [AMBER] How the instantaneous temperature is calculated in Amber ? Marek Maly (Sun Mar 31 2019 - 20:20:18 PDT)
    - Re: [AMBER] How the instantaneous temperature is calculated in Amber ? Bill Ross (Sun Mar 31 2019 - 21:51:19 PDT)
    - Re: [AMBER] How the instantaneous temperature is calculated in Amber ? Carlos Simmerling (Mon Apr 01 2019 - 04:16:16 PDT)
    - Re: [AMBER] How the instantaneous temperature is calculated in Amber ? Marek Maly (Mon Apr 01 2019 - 10:37:31 PDT)
- Re: [AMBER] How the instantaneous temperature is calculated in Amber ? Marek Maly (Sun Mar 31 2019 - 20:02:36 PDT)
[AMBER] How to build the central fragment of a modified nucleotide in the AMBER force fields 21818674.zju.edu.cn (Sun Mar 31 2019 - 19:28:55 PDT)
[AMBER] Fwd: AMBER Digest, Vol 2600, Issue 1 SATYAJIT KHATUA (Mon Apr 01 2019 - 00:45:18 PDT)
[AMBER] Equilibration in multiple steps with decrement in force constants Priyabrata Das (Mon Apr 01 2019 - 03:19:34 PDT)
- Re: [AMBER] Equilibration in multiple steps with decrement in force constants Carlos Simmerling (Mon Apr 01 2019 - 04:11:30 PDT)
  - Re: [AMBER] Equilibration in multiple steps with decrement in force constants Priyabrata Das (Mon Apr 01 2019 - 04:30:14 PDT)
    - Re: [AMBER] Equilibration in multiple steps with decrement in force constants Carlos Simmerling (Mon Apr 01 2019 - 06:29:41 PDT)
    - Re: [AMBER] Equilibration in multiple steps with decrement in force constants Priyabrata Das (Mon Apr 01 2019 - 10:04:08 PDT)
    - Re: [AMBER] Equilibration in multiple steps with decrement in force constants Carlos Simmerling (Mon Apr 01 2019 - 11:38:16 PDT)
[AMBER] New compile-issue macOS, CPPTRAJ Gustaf Olsson (Mon Apr 01 2019 - 05:04:14 PDT)
- Re: [AMBER] New compile-issue macOS, CPPTRAJ David A Case (Mon Apr 01 2019 - 07:45:28 PDT)
- Re: [AMBER] New compile-issue macOS, CPPTRAJ Daniel Roe (Mon Apr 01 2019 - 08:18:46 PDT)
  - Re: [AMBER] New compile-issue macOS, CPPTRAJ Gustaf Olsson (Tue Apr 02 2019 - 00:27:58 PDT)
    - Re: [AMBER] New compile-issue macOS, CPPTRAJ Gustaf Olsson (Tue Apr 02 2019 - 06:23:48 PDT)
    - Re: [AMBER] New compile-issue macOS, CPPTRAJ Hai Nguyen (Tue Apr 02 2019 - 06:26:56 PDT)
    - Re: [AMBER] New compile-issue macOS, CPPTRAJ Gustaf Olsson (Tue Apr 02 2019 - 06:40:03 PDT)
    - Re: [AMBER] New compile-issue macOS, CPPTRAJ Hai Nguyen (Tue Apr 02 2019 - 07:20:23 PDT)
    - Re: [AMBER] New compile-issue macOS, CPPTRAJ Gustaf Olsson (Tue Apr 02 2019 - 23:36:19 PDT)
    - Re: [AMBER] New compile-issue macOS, CPPTRAJ David A Case (Wed Apr 03 2019 - 07:36:59 PDT)
    - Re: [AMBER] New compile-issue macOS, CPPTRAJ Gustaf Olsson (Thu Apr 04 2019 - 06:16:01 PDT)
    - Re: [AMBER] New compile-issue macOS, CPPTRAJ Daniel Roe (Thu Apr 04 2019 - 06:30:51 PDT)
    - Re: [AMBER] New compile-issue macOS, CPPTRAJ Gustaf Olsson (Thu Apr 04 2019 - 06:54:53 PDT)
    - Re: [AMBER] New compile-issue macOS, CPPTRAJ David A Case (Fri Apr 05 2019 - 06:01:56 PDT)
    - Re: [AMBER] New compile-issue macOS, CPPTRAJ David A Case (Mon Apr 08 2019 - 04:57:11 PDT)
    - Re: [AMBER] New compile-issue macOS, CPPTRAJ Gustaf Olsson (Mon Apr 08 2019 - 06:48:20 PDT)
    - Re: [AMBER] New compile-issue macOS, CPPTRAJ David A Case (Wed Apr 03 2019 - 05:24:27 PDT)
    - Re: [AMBER] New compile-issue macOS, CPPTRAJ Hai Nguyen (Wed Apr 03 2019 - 05:54:30 PDT)
    - Re: [AMBER] New compile-issue macOS, CPPTRAJ Hai Nguyen (Wed Apr 03 2019 - 05:59:45 PDT)
[AMBER] regarding simulation Charu Sharma (JRF) (Tue Apr 02 2019 - 00:55:53 PDT)
- Re: [AMBER] regarding simulation David A Case (Tue Apr 02 2019 - 05:20:38 PDT)
[AMBER] Box with a “separator” Alessandro Mariani (Tue Apr 02 2019 - 02:59:01 PDT)
[AMBER] Negative dihedral angle n glycan simulation Rajarshi Roy (Tue Apr 02 2019 - 04:04:58 PDT)
- Re: [AMBER] Negative dihedral angle n glycan simulation Lachele Foley (Mon Apr 08 2019 - 08:24:16 PDT)
  - Re: [AMBER] Negative dihedral angle n glycan simulation Lachele Foley (Mon Apr 08 2019 - 08:49:58 PDT)
- Re: [AMBER] Negative dihedral angle n glycan simulation Rajarshi Roy (Tue Apr 09 2019 - 00:55:44 PDT)
  - Re: [AMBER] Negative dihedral angle n glycan simulation Lachele Foley (Tue Apr 09 2019 - 10:32:58 PDT)
    - Re: [AMBER] Negative dihedral angle n glycan simulation Lachele Foley (Wed Apr 10 2019 - 12:13:57 PDT)
    - Re: [AMBER] Negative dihedral angle n glycan simulation Irfan Alibay (Thu Apr 11 2019 - 04:43:51 PDT)
    - Re: [AMBER] Negative dihedral angle n glycan simulation Rajarshi Roy (Thu Apr 11 2019 - 09:45:11 PDT)
    - Re: [AMBER] Negative dihedral angle n glycan simulation Rajarshi Roy (Thu Apr 11 2019 - 10:01:20 PDT)
    - Re: [AMBER] Negative dihedral angle n glycan simulation Lachele Foley (Fri Apr 26 2019 - 18:10:18 PDT)
    - Re: [AMBER] Negative dihedral angle n glycan simulation Rajarshi Roy (Fri Apr 26 2019 - 19:20:08 PDT)
[AMBER] leap duplicates bond ('triangular' bond) warning Fabian Glaser (Tue Apr 02 2019 - 05:16:39 PDT)
- Re: [AMBER] leap duplicates bond ('triangular' bond) warning Pietro Aronica (Tue Apr 02 2019 - 05:45:04 PDT)
[AMBER] rms2d analysis Debarati DasGupta (Tue Apr 02 2019 - 11:38:26 PDT)
- Re: [AMBER] rms2d analysis Daniel Roe (Tue Apr 02 2019 - 12:43:54 PDT)
  - Re: [AMBER] rms2d analysis Debarati DasGupta (Wed Apr 03 2019 - 06:20:20 PDT)
[AMBER] KeyError: 4018 for iron containing enzyme (prolyl hydroxylase) Mahesh kumar Teli (Tue Apr 02 2019 - 22:06:32 PDT)
- Re: [AMBER] KeyError: 4018 for iron containing enzyme (prolyl hydroxylase) Aashish Bhatt (Wed Apr 03 2019 - 05:48:11 PDT)
  - Re: [AMBER] KeyError: 4018 for iron containing enzyme (prolyl hydroxylase) Mahesh kumar Teli (Wed Apr 03 2019 - 19:14:48 PDT)
[AMBER] tests with different # of threads Vaibhav Dixit (Wed Apr 03 2019 - 03:26:04 PDT)
- Re: [AMBER] tests with different # of threads David A Case (Wed Apr 03 2019 - 05:30:44 PDT)
  - Re: [AMBER] tests with different # of threads Vaibhav Dixit (Thu Apr 04 2019 - 08:11:38 PDT)
[AMBER] cudaMemcpyToSymbol: SetSim copy to cSim failed invalid device symbol ( GeForce RTX 2080) bjyx20090941 (Wed Apr 03 2019 - 07:24:23 PDT)
- Re: [AMBER] cudaMemcpyToSymbol: SetSim copy to cSim failed invalid device symbol ( GeForce RTX 2080) accuratefreeenergy.gmail.com (Wed Apr 03 2019 - 07:36:36 PDT)
Re: [AMBER] cudaMemcpyToSymbol: SetSim copy to cSim failed bjyx20090941 (Wed Apr 03 2019 - 20:21:49 PDT)
- Re: [AMBER] cudaMemcpyToSymbol: SetSim copy to cSim failed Ross Walker (Thu Apr 04 2019 - 07:36:32 PDT)
[AMBER] mmpbsa error MYRIAN TORRES RICO (Thu Apr 04 2019 - 01:08:44 PDT)
[AMBER] mmpbsa error MYRIAN TORRES RICO (Thu Apr 04 2019 - 02:07:07 PDT)
- Re: [AMBER] mmpbsa error Daniel Roe (Fri Apr 05 2019 - 08:06:08 PDT)
[AMBER] Problem calculating water density over distance Lucas Bandeira (Thu Apr 04 2019 - 13:35:38 PDT)
[AMBER] location related redox-potential? Feng, Zimin (Fri Apr 05 2019 - 09:15:00 PDT)
- Re: [AMBER] location related redox-potential? Cruzeiro,Vinicius Wilian D (Fri Apr 05 2019 - 16:31:36 PDT)
  - Re: [AMBER] location related redox-potential? Feng, Zimin (Sun Apr 07 2019 - 14:34:05 PDT)
[AMBER] Can Amber constant pH run with CHARMM force field? Chen Yifan (Fri Apr 05 2019 - 11:51:35 PDT)
- Re: [AMBER] Can Amber constant pH run with CHARMM force field? Feng, Zimin (Fri Apr 05 2019 - 13:56:57 PDT)
- Re: [AMBER] Can Amber constant pH run with CHARMM force field? Cruzeiro,Vinicius Wilian D (Fri Apr 05 2019 - 16:15:16 PDT)
  - Re: [AMBER] Can Amber constant pH run with CHARMM force field? Chen Yifan (Fri Apr 05 2019 - 19:12:56 PDT)
- Re: [AMBER] Can Amber constant pH run with CHARMM force field? Jason Swails (Sun Apr 07 2019 - 17:19:37 PDT)
[AMBER] 2 job positions InterX Inc. Molecular Simulation and Molecular ForceField Scientists Ganesh Kamath (Fri Apr 05 2019 - 12:58:51 PDT)
[AMBER] outtraj question Xiaoyu Wang (Fri Apr 05 2019 - 15:35:10 PDT)
- Re: [AMBER] outtraj question Daniel Roe (Tue Apr 30 2019 - 07:23:30 PDT)
[AMBER] pmemd.CUDA vs pmemd.MPI for equilibration of protein-ligand and trajectory identification for mmpbsa Prasanth G, Research Scholar (Fri Apr 05 2019 - 23:47:01 PDT)
[AMBER] 2 job positions InterX Inc. Molecular Simulation and Molecular ForceField Scientists Ganesh Kamath (Sat Apr 06 2019 - 08:00:24 PDT)
Re: [AMBER] preparing a new pdb Boutheïna KERKENI (Sun Apr 07 2019 - 03:56:11 PDT)
[AMBER] Ligand Splitting Issue Tamsila Parveen (Sun Apr 07 2019 - 04:21:59 PDT)
- Re: [AMBER] Ligand Splitting Issue David Case (Sun Apr 07 2019 - 18:22:03 PDT)
[AMBER] Error working with pytleap ARITRA MITRA (Mon Apr 08 2019 - 03:58:33 PDT)
- Re: [AMBER] Error working with pytleap David A Case (Mon Apr 08 2019 - 04:44:42 PDT)
[AMBER] Problem in setting parameters for the modified nucleotide Xiaoting Mao (Mon Apr 08 2019 - 06:10:58 PDT)
[AMBER] Creating a water model from scratch Gustavo Seabra (Mon Apr 08 2019 - 11:55:39 PDT)
- Re: [AMBER] Creating a water model from scratch David Cerutti (Mon Apr 08 2019 - 12:36:46 PDT)
[AMBER] secstruct issue in CPPTRAJ SARAH JEANNE LEFAVE (Mon Apr 08 2019 - 13:22:18 PDT)
- Re: [AMBER] secstruct issue in CPPTRAJ Daniel Roe (Wed Apr 10 2019 - 11:28:42 PDT)
  - Re: [AMBER] secstruct issue in CPPTRAJ Daniel Roe (Wed Apr 10 2019 - 12:16:06 PDT)
    - Re: [AMBER] secstruct issue in CPPTRAJ Daniel Roe (Tue Apr 16 2019 - 05:26:58 PDT)
    - Re: [AMBER] [UCE] Re: secstruct issue in CPPTRAJ SARAH JEANNE LEFAVE (Tue Apr 16 2019 - 05:44:35 PDT)
[AMBER] Question about QM/MM simulation in vacuum connecting Amber and Gaussian 09 package 王婷婷 (Mon Apr 08 2019 - 17:36:31 PDT)
- Re: [AMBER] Question about QM/MM simulation in vacuum connecting Amber and Gaussian 09 package Roitberg,Adrian E (Mon Apr 08 2019 - 17:41:56 PDT)
[AMBER] mmpbsa MYRIAN TORRES RICO (Tue Apr 09 2019 - 01:22:16 PDT)
- Re: [AMBER] mmpbsa Chris Moth (Tue Apr 09 2019 - 19:30:18 PDT)
[AMBER] Calculate zero point energy for a protein (no ligand) system Akshay Prabhakant (Tue Apr 09 2019 - 04:42:58 PDT)
- Re: [AMBER] Calculate zero point energy for a protein (no ligand) system Carlos Simmerling (Tue Apr 09 2019 - 04:47:57 PDT)
  - Re: [AMBER] Calculate zero point energy for a protein (no ligand) system Robert Molt (Tue Apr 09 2019 - 05:26:43 PDT)
  - Re: [AMBER] Calculate zero point energy for a protein (no ligand) system Akshay Prabhakant (Tue Apr 09 2019 - 05:32:19 PDT)
    - Re: [AMBER] Calculate zero point energy for a protein (no ligand) system Carlos Simmerling (Tue Apr 09 2019 - 05:36:05 PDT)
    - Re: [AMBER] Calculate zero point energy for a protein (no ligand) system Akshay Prabhakant (Tue Apr 09 2019 - 05:46:42 PDT)
    - Re: [AMBER] Calculate zero point energy for a protein (no ligand) system MOHD HOMAIDUR RAHMAN (Tue Apr 09 2019 - 11:49:17 PDT)
[AMBER] Force field parameters for modified amino acid residues (carboxy glutamates) Tanusree S (Tue Apr 09 2019 - 21:42:30 PDT)
[AMBER] Patches for AmberTools18 viktor drobot (Wed Apr 10 2019 - 04:26:12 PDT)
- Re: [AMBER] Patches for AmberTools18 Stephan Schott (Wed Apr 10 2019 - 05:38:58 PDT)
  - Re: [AMBER] Patches for AmberTools18 Hai Nguyen (Wed Apr 10 2019 - 13:19:11 PDT)
[AMBER] REGARDING MPI Charu Sharma (JRF) (Wed Apr 10 2019 - 11:06:10 PDT)
[AMBER] Question about chemical reaction in vacuum with adding an extra reaction field (Specify dielectric constant in vacuum) 王婷婷 (Wed Apr 10 2019 - 18:03:59 PDT)
- Re: [AMBER] Question about chemical reaction in vacuum with adding an extra reaction field (Specify dielectric constant in vacuum) David A Case (Thu Apr 11 2019 - 06:57:52 PDT)
  - Re: [AMBER] Question about chemical reaction in vacuum with adding an extra reaction field (Specify dielectric constant in vacuum) 王婷婷 (Thu Apr 11 2019 - 18:40:46 PDT)
[AMBER] parameters for isolated zwitter ion tyrosine angad sharma (Wed Apr 10 2019 - 23:15:25 PDT)
- Re: [AMBER] parameters for isolated zwitter ion tyrosine Elvis Martis (Wed Apr 10 2019 - 23:50:29 PDT)
[AMBER] Capping RNA Mihaljevic-Juric Paula (Mme) (Thu Apr 11 2019 - 02:56:08 PDT)
- [AMBER] cReAtInG PDB Boutheïna KERKENI (Thu Apr 11 2019 - 03:13:20 PDT)
  - Re: [AMBER] cReAtInG PDB David A Case (Thu Apr 11 2019 - 07:06:11 PDT)
- Re: [AMBER] Capping RNA David A Case (Thu Apr 11 2019 - 07:03:46 PDT)
[AMBER] T4 vs RTX2080Ti Giovanni Grazioso (Thu Apr 11 2019 - 08:00:42 PDT)
- Re: [AMBER] T4 vs RTX2080Ti Shenglong Wang (Thu Apr 11 2019 - 08:03:00 PDT)
  - Re: [AMBER] T4 vs RTX2080Ti David Cerutti (Fri Apr 12 2019 - 08:21:38 PDT)
[AMBER] COM Dihedral Restraint Kung, Ryan (Thu Apr 11 2019 - 08:23:17 PDT)
- Re: [AMBER] COM Dihedral Restraint Kellon Belfon (Thu Apr 11 2019 - 09:34:45 PDT)
[AMBER] Problem calculating water mass density over distance Lucas Bandeira (Thu Apr 11 2019 - 09:00:23 PDT)
- Re: [AMBER] Problem calculating water mass density over distance Gerardo Zerbetto De Palma (Thu Apr 11 2019 - 09:05:18 PDT)
  - Re: [AMBER] Problem calculating water mass density over distance Lucas Bandeira (Thu Apr 11 2019 - 09:08:47 PDT)
    - Re: [AMBER] Problem calculating water mass density over distance Gerardo Zerbetto De Palma (Thu Apr 11 2019 - 09:37:30 PDT)
    - Re: [AMBER] Problem calculating water mass density over distance Lucas Bandeira (Thu Apr 11 2019 - 09:48:23 PDT)
    - Re: [AMBER] Problem calculating water mass density over distance Gerardo Zerbetto De Palma (Thu Apr 11 2019 - 07:54:08 PDT)
[AMBER] Electrostatic interactions in LIE method Debarati DasGupta (Thu Apr 11 2019 - 10:57:19 PDT)
[AMBER] namd and amber md energies do not match Akshay Prabhakant (Thu Apr 11 2019 - 11:33:01 PDT)
- Re: [AMBER] namd and amber md energies do not match David A Case (Fri Apr 12 2019 - 05:37:56 PDT)
  - Re: [AMBER] namd and amber md energies do not match Akshay Prabhakant (Mon Apr 15 2019 - 23:00:28 PDT)
[AMBER] Confusion regarding ff14SB and ff99SBildn forcefields RITUPARNA ROY (Fri Apr 12 2019 - 00:09:12 PDT)
- Re: [AMBER] Confusion regarding ff14SB and ff99SBildn forcefields David Cerutti (Fri Apr 12 2019 - 00:36:01 PDT)
[AMBER] How to source oldff in tleap Saikat Pal (Fri Apr 12 2019 - 04:32:54 PDT)
- Re: [AMBER] How to source oldff in tleap Saikat Pal (Fri Apr 12 2019 - 04:43:24 PDT)
- Re: [AMBER] How to source oldff in tleap Carlos Simmerling (Fri Apr 12 2019 - 05:00:25 PDT)
- Re: [AMBER] How to source oldff in tleap David A Case (Fri Apr 12 2019 - 05:47:29 PDT)
[AMBER] Question about NEB Lillian Chong (Fri Apr 12 2019 - 06:02:57 PDT)
[AMBER] Problems in setting parameters for the modified nucleotide Xiaoting Mao (Fri Apr 12 2019 - 06:08:43 PDT)
[AMBER] silver parameters Uroš Javornik (Fri Apr 12 2019 - 06:29:12 PDT)
- Re: [AMBER] silver parameters Christina Bergonzo (Fri Apr 12 2019 - 06:48:50 PDT)
[AMBER] pdb4amber install w/ conda Paul, Austin (Fri Apr 12 2019 - 09:16:21 PDT)
- Re: [AMBER] pdb4amber install w/ conda Hai Nguyen (Fri Apr 12 2019 - 09:49:23 PDT)
  - Re: [AMBER] pdb4amber install w/ conda Hai Nguyen (Fri Apr 12 2019 - 23:14:10 PDT)
[AMBER] Save RST from mdcrd containing velocities Yuliana Bosken (Sat Apr 13 2019 - 02:40:05 PDT)
- Re: [AMBER] Save RST from mdcrd containing velocities Daniel Roe (Thu Apr 18 2019 - 10:59:21 PDT)
[AMBER] Guidance on WHAM Daniel Fernández Remacha (Sat Apr 13 2019 - 06:19:01 PDT)
- Re: [AMBER] Guidance on WHAM Zachary Fallon (Tue Apr 16 2019 - 12:23:01 PDT)
  - Re: [AMBER] Guidance on WHAM Carlos Simmerling (Tue Apr 16 2019 - 12:43:34 PDT)
  - Re: [AMBER] Guidance on WHAM Daniel Fernández Remacha (Wed Apr 17 2019 - 03:59:17 PDT)
    - Re: [AMBER] Guidance on WHAM Zachary Fallon (Wed Apr 17 2019 - 10:21:56 PDT)
    - Re: [AMBER] Guidance on WHAM Daniel Fernández Remacha (Thu Apr 18 2019 - 11:28:40 PDT)
    - Re: [AMBER] Guidance on WHAM Zachary Fallon (Thu Apr 18 2019 - 12:35:43 PDT)
    - Re: [AMBER] Guidance on WHAM Ruth Helena Tichauer (Fri May 03 2019 - 08:09:38 PDT)
    - Re: [AMBER] Guidance on WHAM Carlos Simmerling (Fri May 03 2019 - 08:14:49 PDT)
    - Re: [AMBER] Guidance on WHAM Ruth Helena Tichauer (Fri May 03 2019 - 08:18:48 PDT)
- Re: [AMBER] Guidance on WHAM Daniel Fernández Remacha (Tue May 07 2019 - 11:46:45 PDT)
[AMBER] RTX 2070 GPU Card Ajeet Kumar Yadav (Mon Apr 15 2019 - 03:02:01 PDT)
[AMBER] Atoms per processor Charo del Genio (Mon Apr 15 2019 - 04:36:10 PDT)
- Re: [AMBER] Atoms per processor David A Case (Mon Apr 15 2019 - 07:37:15 PDT)
[AMBER] mdgx CreateBellyMask error Anthony Bogetti (Mon Apr 15 2019 - 07:50:02 PDT)
- Re: [AMBER] mdgx CreateBellyMask error David Cerutti (Mon Apr 15 2019 - 08:02:08 PDT)
[AMBER] Fixing few box dimensions in semiisotropic/anisotropic pressure scaling Kyeong-jun Jeong (Mon Apr 15 2019 - 13:56:54 PDT)
- Re: [AMBER] Fixing few box dimensions in semiisotropic/anisotropic pressure scaling David A Case (Tue Apr 16 2019 - 06:12:08 PDT)
[AMBER] How to use GaMD in amber16 ATUL KUMAR (Tue Apr 16 2019 - 01:35:25 PDT)
[AMBER] Problems in forcefield parameterization of Mercury Muthukumaran Rajagopalan (Tue Apr 16 2019 - 10:24:35 PDT)
- Re: [AMBER] Problems in forcefield parameterization of Mercury Pengfei Li (Tue Apr 16 2019 - 18:31:35 PDT)
  - Re: [AMBER] Problems in forcefield parameterization of Mercury Muthukumaran Rajagopalan (Tue Apr 16 2019 - 22:36:14 PDT)
    - Re: [AMBER] Problems in forcefield parameterization of Mercury Pengfei Li (Fri Apr 19 2019 - 08:42:20 PDT)
[AMBER] How to select dihedral angles to reweight accelerated molecular dynamics simulation of protein Mayank Dixit (Tue Apr 16 2019 - 17:48:47 PDT)
- Re: [AMBER] How to select dihedral angles to reweight accelerated molecular dynamics simulation of protein Chetna Tyagi (Wed Apr 17 2019 - 00:57:18 PDT)
  - Re: [AMBER] How to select dihedral angles to reweight accelerated molecular dynamics simulation of protein Mayank Dixit (Thu Apr 18 2019 - 07:47:04 PDT)
[AMBER] pKa calculation Tanmoy Paul (Tue Apr 16 2019 - 23:18:58 PDT)
[AMBER] mol2 files for FEW Zhonghua Xia (Wed Apr 17 2019 - 01:33:24 PDT)
- Re: [AMBER] mol2 files for FEW David A Case (Wed Apr 17 2019 - 05:06:50 PDT)
  - Re: [AMBER] mol2 files for FEW Zhonghua Xia (Tue Apr 30 2019 - 07:48:28 PDT)
    - Re: [AMBER] mol2 files for FEW David A Case (Wed May 01 2019 - 10:50:43 PDT)
- Re: [AMBER] mol2 files for FEW Nadine Homeyer (Mon May 20 2019 - 11:10:56 PDT)
[AMBER] Mg2+_preparation_general_rule Antonio Amber Carlesso (Wed Apr 17 2019 - 08:27:11 PDT)
- Re: [AMBER] Mg2+_preparation_general_rule Antonio Amber Carlesso (Wed Apr 17 2019 - 09:53:47 PDT)
[AMBER] More macOS compilation issues.... Gustaf Olsson (Thu Apr 18 2019 - 01:20:39 PDT)
- Re: [AMBER] More macOS compilation issues.... Hai Nguyen (Thu Apr 18 2019 - 06:47:08 PDT)
  - Re: [AMBER] More macOS compilation issues.... Gustaf Olsson (Sun Apr 21 2019 - 03:31:39 PDT)
    - Re: [AMBER] More macOS compilation issues.... Gustaf Olsson (Sun Apr 21 2019 - 13:37:05 PDT)
    - Re: [AMBER] More macOS compilation issues.... David A Case (Mon Apr 22 2019 - 13:07:11 PDT)
    - Re: [AMBER] More macOS compilation issues.... Gustaf Olsson (Mon Apr 22 2019 - 22:20:11 PDT)
    - Re: [AMBER] More macOS compilation issues.... Gustaf Olsson (Thu Apr 25 2019 - 13:08:51 PDT)
    - Re: [AMBER] More macOS compilation issues.... Gustaf Olsson (Thu Apr 25 2019 - 23:49:37 PDT)
    - Re: [AMBER] More macOS compilation issues.... David A Case (Fri Apr 26 2019 - 06:48:32 PDT)
    - Re: [AMBER] More macOS compilation issues.... Gustaf Olsson (Fri Apr 26 2019 - 22:48:25 PDT)
- Re: [AMBER] More macOS compilation issues.... David A Case (Thu Apr 18 2019 - 10:33:25 PDT)
[AMBER] AMBER - Heating MD Systems An Ta (Thu Apr 18 2019 - 05:48:37 PDT)
- Re: [AMBER] AMBER - Heating MD Systems Carlos Simmerling (Thu Apr 18 2019 - 06:03:41 PDT)
  - Re: [AMBER] AMBER - Heating MD Systems An Ta (Thu Apr 18 2019 - 06:23:32 PDT)
    - Re: [AMBER] AMBER - Heating MD Systems Carlos Simmerling (Thu Apr 18 2019 - 08:43:54 PDT)
    - Re: [AMBER] AMBER - Heating MD Systems An Ta (Thu Apr 18 2019 - 10:58:58 PDT)
- Re: [AMBER] AMBER - Heating MD Systems Lin Song (Thu Apr 18 2019 - 08:38:30 PDT)
[AMBER] "Problem installing Miniconda" Seibold, Steve Allan (Thu Apr 18 2019 - 08:43:30 PDT)
- Re: [AMBER] "Problem installing Miniconda" Hai Nguyen (Thu Apr 18 2019 - 08:57:55 PDT)
  - Re: [AMBER] "Problem installing Miniconda" David A Case (Thu Apr 18 2019 - 10:55:27 PDT)
    - Re: [AMBER] "Problem installing Miniconda" Hai Nguyen (Thu Apr 18 2019 - 11:00:05 PDT)
    - Re: [AMBER] "Problem installing Miniconda" Seibold, Steve Allan (Thu Apr 18 2019 - 11:44:39 PDT)
[AMBER] Force field for C-C Di-Tyrosine Linkage Bharat Manna (Thu Apr 18 2019 - 03:45:55 PDT)
[AMBER] RTX-2070 supported(untested)? Yeyue Xiong (Thu Apr 18 2019 - 13:29:28 PDT)
- Re: [AMBER] RTX-2070 supported(untested)? David Cerutti (Thu Apr 18 2019 - 14:28:33 PDT)
  - Re: [AMBER] RTX-2070 supported(untested)? Carlos Simmerling (Fri Apr 19 2019 - 05:05:48 PDT)
    - Re: [AMBER] RTX-2070 supported(untested)? Bill Ross (Fri Apr 19 2019 - 05:11:25 PDT)
[AMBER] MM PBSA - clarification Prasanth G, Research Scholar (Fri Apr 19 2019 - 06:14:33 PDT)
- Re: [AMBER] MM PBSA - clarification Ray Luo (Fri Apr 19 2019 - 06:35:12 PDT)
- Re: [AMBER] MM PBSA - clarification Prasanth G, Research Scholar (Sun Apr 21 2019 - 23:17:41 PDT)
  - Re: [AMBER] MM PBSA - clarification Thomas Evangelidis (Mon Apr 22 2019 - 06:31:00 PDT)
[AMBER] smflags in configure script viktor drobot (Fri Apr 19 2019 - 07:19:24 PDT)
- Re: [AMBER] smflags in configure script Charles Lin (Mon Apr 22 2019 - 12:52:10 PDT)
- Re: [AMBER] smflags in configure script David A Case (Mon Apr 22 2019 - 13:03:56 PDT)
[AMBER] trouble in amberFATA: Atom doesn't have a type Maximilien BERNE (Fri Apr 19 2019 - 09:19:14 PDT)
- Re: [AMBER] trouble in amberFATA: Atom doesn't have a type Sally Pias (Fri Apr 19 2019 - 12:09:19 PDT)
[AMBER] Change the trajectory format. Parviz Seifpanahi Shabane (Fri Apr 19 2019 - 12:12:39 PDT)
- Re: [AMBER] Change the trajectory format. Thomas Cheatham (Wed Apr 24 2019 - 23:15:14 PDT)
  - Re: [AMBER] Change the trajectory format. Daniel Roe (Thu Apr 25 2019 - 04:54:18 PDT)
[AMBER] possible bug in charmmlipid2amber.py liu junjun (Mon Apr 22 2019 - 00:14:17 PDT)
[AMBER] Suggestions on running a qm-mm simulation for studying a group transfer reaction Prayagraj Fandilolu (Mon Apr 22 2019 - 05:43:24 PDT)
[AMBER] regarding radius of gyration angad sharma (Mon Apr 22 2019 - 06:03:04 PDT)
- Re: [AMBER] regarding radius of gyration Carlos Simmerling (Mon Apr 22 2019 - 07:02:36 PDT)
[AMBER] Computing forces by trajectory post-processing with sander Casalini Tommaso (Mon Apr 22 2019 - 12:54:10 PDT)
- Re: [AMBER] Computing forces by trajectory post-processing with sander Alen Ahmetovic (Mon Apr 22 2019 - 16:50:40 PDT)
  - Re: [AMBER] Computing forces by trajectory post-processing with sander Yuliana Bosken (Mon Apr 22 2019 - 20:44:34 PDT)
- Re: [AMBER] Computing forces by trajectory post-processing with sander Daniel Roe (Tue Apr 23 2019 - 06:56:30 PDT)
  - Re: [AMBER] Computing forces by trajectory post-processing with sander Casalini Tommaso (Wed Apr 24 2019 - 01:09:51 PDT)
[AMBER] problem in locating Aqvist Mg2+ parameter in amber ATUL KUMAR (Mon Apr 22 2019 - 21:52:18 PDT)
- Re: [AMBER] problem in locating Aqvist Mg2+ parameter in amber David Case (Tue Apr 23 2019 - 05:23:49 PDT)
[AMBER] A-DNA Charu Sharma (JRF) (Mon Apr 22 2019 - 22:17:26 PDT)
- Re: [AMBER] A-DNA David Case (Tue Apr 23 2019 - 05:13:52 PDT)
  - Re: [AMBER] A-DNA Charu Sharma (JRF) (Tue Apr 23 2019 - 11:51:09 PDT)
[AMBER] Issue with cpptraj.MPI Benard, Dany (Tue Apr 23 2019 - 05:44:23 PDT)
- Re: [AMBER] Issue with cpptraj.MPI Pratul Agarwal (Tue Apr 23 2019 - 05:52:05 PDT)
  - Re: [AMBER] Issue with cpptraj.MPI Pratul Agarwal (Tue Apr 23 2019 - 05:58:41 PDT)
  - Re: [AMBER] Issue with cpptraj.MPI Benard, Dany (Tue Apr 23 2019 - 06:01:36 PDT)
    - Re: [AMBER] Issue with cpptraj.MPI Daniel Roe (Tue Apr 23 2019 - 06:34:31 PDT)
- Re: [AMBER] Issue with cpptraj.MPI Daniel Roe (Tue Apr 23 2019 - 05:52:46 PDT)
[AMBER] saving output of Gaussian accelerated MD Qinghua Liao (Tue Apr 23 2019 - 07:41:28 PDT)
[AMBER] charge in constant redox cein file vs. prmtop file Feng, Zimin (Tue Apr 23 2019 - 15:03:24 PDT)
- Re: [AMBER] charge in constant redox cein file vs. prmtop file Cruzeiro,Vinicius Wilian D (Tue Apr 23 2019 - 15:51:31 PDT)
  - Re: [AMBER] charge in constant redox cein file vs. prmtop file Feng, Zimin (Wed Apr 24 2019 - 09:14:30 PDT)
    - Re: [AMBER] charge in constant redox cein file vs. prmtop file Cruzeiro,Vinicius Wilian D (Wed Apr 24 2019 - 09:51:12 PDT)
    - Re: [AMBER] charge in constant redox cein file vs. prmtop file Feng, Zimin (Wed Apr 24 2019 - 11:10:41 PDT)
[AMBER] styrene sulfonate molecule building using xleap Shilpa Gupta (Tue Apr 23 2019 - 23:32:36 PDT)
- Re: [AMBER] styrene sulfonate molecule building using xleap David A Case (Wed Apr 24 2019 - 04:45:08 PDT)
[AMBER] Problem with heating the system ATUL KUMAR (Wed Apr 24 2019 - 01:57:34 PDT)
- Re: [AMBER] Problem with heating the system Bill Ross (Wed Apr 24 2019 - 01:49:56 PDT)
  - Re: [AMBER] Problem with heating the system ATUL KUMAR (Wed Apr 24 2019 - 02:06:52 PDT)
- Re: [AMBER] Problem with heating the system David A Case (Wed Apr 24 2019 - 04:47:18 PDT)
  - Re: [AMBER] Problem with heating the system ATUL KUMAR (Wed Apr 24 2019 - 04:53:58 PDT)
    - Re: [AMBER] Problem with heating the system Pratul Agarwal (Wed Apr 24 2019 - 05:14:12 PDT)
[AMBER] secondary structure angad sharma (Wed Apr 24 2019 - 04:32:53 PDT)
- Re: [AMBER] secondary structure Carlos Simmerling (Wed Apr 24 2019 - 04:59:50 PDT)
[AMBER] Targeted MD Elena Gomez (Thu Apr 25 2019 - 01:08:18 PDT)
- Re: [AMBER] Targeted MD Carlos Simmerling (Thu Apr 25 2019 - 05:01:37 PDT)
[AMBER] issues with pmemd.cuda Veenis, Andrew Jay (Thu Apr 25 2019 - 08:11:46 PDT)
- Re: [AMBER] issues with pmemd.cuda David A Case (Thu Apr 25 2019 - 10:43:32 PDT)
  - Re: [AMBER] issues with pmemd.cuda Veenis, Andrew Jay (Fri Apr 26 2019 - 07:08:02 PDT)
    - Re: [AMBER] issues with pmemd.cuda Veenis, Andrew Jay (Fri May 03 2019 - 12:20:43 PDT)
[AMBER] processing trajectories subjected to GIST analysis Alfredo Quevedo (Tue Apr 23 2019 - 23:19:47 PDT)
- Re: [AMBER] processing trajectories subjected to GIST analysis Daniel Roe (Tue Apr 30 2019 - 06:58:42 PDT)
[AMBER] Simulation with Protein, cofactor and Ligand Prasanth G, Research Scholar (Thu Apr 25 2019 - 11:41:05 PDT)
- Re: [AMBER] Simulation with Protein, cofactor and Ligand David A Case (Wed May 01 2019 - 10:53:53 PDT)
[AMBER] Antechamber question David Poole (Thu Apr 25 2019 - 16:03:37 PDT)
[AMBER] setting up triplicate runs Yin, Guowei (Thu Apr 25 2019 - 18:08:00 PDT)
- Re: [AMBER] setting up triplicate runs David Cerutti (Thu Apr 25 2019 - 19:02:45 PDT)
[AMBER] dihedral scanning with GAFF and GAFF2 Qasim Pars (Fri Apr 26 2019 - 03:22:33 PDT)
[AMBER] Any help on how to implement it in cpptraj? Debarati DasGupta (Fri Apr 26 2019 - 09:25:11 PDT)
- Re: [AMBER] Any help on how to implement it in cpptraj? Daniel Roe (Tue Apr 30 2019 - 06:43:21 PDT)
  - Re: [AMBER] Any help on how to implement it in cpptraj? Debarati DasGupta (Mon May 06 2019 - 13:27:46 PDT)
    - Re: [AMBER] Any help on how to implement it in cpptraj? Daniel Roe (Thu May 09 2019 - 11:54:48 PDT)
[AMBER] Release of AmberTools19 David Case (Fri Apr 26 2019 - 17:59:43 PDT)
[AMBER] AmberTools19 - macOS 10.14.4 - Xcode 10.2.1 - clang Gustaf Olsson (Sat Apr 27 2019 - 05:58:27 PDT)
- Re: [AMBER] AmberTools19 - macOS 10.14.4 - Xcode 10.2.1 - clang Hai Nguyen (Sat Apr 27 2019 - 09:36:49 PDT)
  - Re: [AMBER] AmberTools19 - macOS 10.14.4 - Xcode 10.2.1 - clang Gustaf Olsson (Sat Apr 27 2019 - 11:25:03 PDT)
- Re: [AMBER] AmberTools19 - macOS 10.14.4 - Xcode 10.2.1 - clang David Case (Sun Apr 28 2019 - 09:49:13 PDT)
  - Re: [AMBER] AmberTools19 - macOS 10.14.4 - Xcode 10.2.1 - clang Gustaf Olsson (Sun Apr 28 2019 - 14:12:38 PDT)
[AMBER] NpT simulations in interfacial system Lucas Bandeira (Sat Apr 27 2019 - 07:38:33 PDT)
- Re: [AMBER] NpT simulations in interfacial system David Case (Sun Apr 28 2019 - 09:56:50 PDT)
[AMBER] AmberTools19 - macOS 10.14.4 - Xcode 10.2.1 - GCC8.3 Gustaf Olsson (Sat Apr 27 2019 - 11:44:00 PDT)
[AMBER] xleap display Yin, Guowei (Sat Apr 27 2019 - 14:49:20 PDT)
- Re: [AMBER] xleap display Bill Ross (Sat Apr 27 2019 - 15:49:56 PDT)
  - Re: [AMBER] xleap display Bill Ross (Sat Apr 27 2019 - 15:57:41 PDT)
  - Re: [AMBER] xleap display Yin, Guowei (Sat Apr 27 2019 - 19:54:15 PDT)
    - Re: [AMBER] xleap display Bill Ross (Sat Apr 27 2019 - 21:28:56 PDT)
- Re: [AMBER] xleap display Pratul Agarwal (Sat Apr 27 2019 - 16:02:31 PDT)
  - Re: [AMBER] xleap display Bill Ross (Sat Apr 27 2019 - 16:31:50 PDT)
- Re: [AMBER] xleap display Gustaf Olsson (Sun Apr 28 2019 - 05:58:47 PDT)
[AMBER] Novel Force Field Parameters for Aromatic Dihedrals Erdem Yeler (Sun Apr 28 2019 - 13:09:41 PDT)
- Re: [AMBER] Novel Force Field Parameters for Aromatic Dihedrals Carlos Simmerling (Thu May 02 2019 - 09:36:00 PDT)
  - Re: [AMBER] Novel Force Field Parameters for Aromatic Dihedrals Erdem Yeler (Fri May 03 2019 - 02:25:00 PDT)
[AMBER] WHAM umbrella PMF of ligand Z diffusion on lipid molecule zmatovic.kg.ac.rs (Mon Apr 29 2019 - 04:05:27 PDT)
[AMBER] constant-pressure equilibration with a water droplet Anthony Bogetti (Mon Apr 29 2019 - 08:37:40 PDT)
- Re: [AMBER] constant-pressure equilibration with a water droplet Carlos Simmerling (Mon Apr 29 2019 - 09:07:25 PDT)
- Re: [AMBER] constant-pressure equilibration with a water droplet David A Case (Mon Apr 29 2019 - 11:06:09 PDT)
[AMBER] Why is SPAM throwing errors when I see none in my input files or trajectories. Debarati DasGupta (Mon Apr 29 2019 - 13:25:58 PDT)
- Re: [AMBER] Why is SPAM throwing errors when I see none in my input files or trajectories. Daniel Roe (Tue Apr 30 2019 - 06:12:07 PDT)
[AMBER] Regarding cosine content calculation in AMBER Rajarshi Roy (Mon Apr 29 2019 - 22:22:40 PDT)
- Re: [AMBER] Regarding cosine content calculation in AMBER Daniel Roe (Tue Apr 30 2019 - 06:16:45 PDT)
  - Re: [AMBER] Regarding cosine content calculation in AMBER Rajarshi Roy (Tue Apr 30 2019 - 08:47:39 PDT)
    - Re: [AMBER] Regarding cosine content calculation in AMBER Pratul Agarwal (Tue Apr 30 2019 - 08:53:56 PDT)
    - Re: [AMBER] Regarding cosine content calculation in AMBER Rajarshi Roy (Tue Apr 30 2019 - 09:14:09 PDT)
    - Re: [AMBER] Regarding cosine content calculation in AMBER Pratul Agarwal (Tue Apr 30 2019 - 09:46:56 PDT)
    - Re: [AMBER] Regarding cosine content calculation in AMBER Rajarshi Roy (Tue Apr 30 2019 - 10:39:37 PDT)
[AMBER] mmpbsa error MYRIAN TORRES RICO (Tue Apr 30 2019 - 02:01:54 PDT)
- Re: [AMBER] mmpbsa error David A Case (Tue Apr 30 2019 - 04:28:17 PDT)
  - Re: [AMBER] mmpbsa error MYRIAN TORRES RICO (Tue Apr 30 2019 - 09:28:57 PDT)
[AMBER] CPPTRAJ gnu extension not working anu chandra (Tue Apr 30 2019 - 10:00:08 PDT)
- Re: [AMBER] CPPTRAJ gnu extension not working Daniel Roe (Thu May 02 2019 - 05:34:12 PDT)
[AMBER] [rok.ucsd.edu: AT19 cpptraj MPI build issue (Linux, x86_64, gnu)] David A Case (Tue Apr 30 2019 - 12:55:23 PDT)
[AMBER] Vina Zinc Beale, John (Wed May 01 2019 - 04:05:56 PDT)
Re: [AMBER] Library for Phosphate ion David A Case (Wed May 01 2019 - 04:44:06 PDT)
- Re: [AMBER] Library for Phosphate ion Sowmya Indrakumar (Wed May 01 2019 - 06:19:14 PDT)
[AMBER] SMD using contact number Chem Jubilant (Wed May 01 2019 - 07:40:46 PDT)
- Re: [AMBER] SMD using contact number Feng Pan (Thu May 02 2019 - 08:50:29 PDT)
[AMBER] CPPTRAJ average residue-wise contact map anu chandra (Wed May 01 2019 - 12:06:24 PDT)
- Re: [AMBER] CPPTRAJ average residue-wise contact map Daniel Roe (Thu May 02 2019 - 05:25:25 PDT)
  - Re: [AMBER] CPPTRAJ average residue-wise contact map anu chandra (Thu May 02 2019 - 08:30:48 PDT)
[AMBER] Error using mm_pbsa.pl binding energy calculations Jaimes, Luis (Wed May 01 2019 - 17:44:23 PDT)
[AMBER] Random segfaults (invalid memory reference) in sander Charo del Genio (Thu May 02 2019 - 01:43:19 PDT)
- Re: [AMBER] Random segfaults (invalid memory reference) in sander James Kress (Thu May 02 2019 - 10:28:48 PDT)
  - Re: [AMBER] Random segfaults (invalid memory reference) in sander Charo del Genio (Thu May 02 2019 - 10:51:31 PDT)
- Re: [AMBER] Random segfaults (invalid memory reference) in sander Daniel Roe (Fri May 03 2019 - 05:27:15 PDT)
[AMBER] FEW not producing *.lib file for ligand ali akbar (Thu May 02 2019 - 02:50:12 PDT)
[AMBER] Distance calculation and distance matrix giving discrepant results Jonathan Huihui (Thu May 02 2019 - 09:25:55 PDT)
- Re: [AMBER] Distance calculation and distance matrix giving discrepant results Daniel Roe (Fri May 03 2019 - 09:14:29 PDT)
  - Re: [AMBER] Distance calculation and distance matrix giving discrepant results Jonathan Huihui (Fri May 03 2019 - 10:01:27 PDT)
[AMBER] Force field for nucleobases, nucleosides and nucleotides Elisa Pieri (Thu May 02 2019 - 14:10:06 PDT)
- Re: [AMBER] Force field for nucleobases, nucleosides and nucleotides Elisa Pieri (Thu May 02 2019 - 15:31:19 PDT)
- Re: [AMBER] Force field for nucleobases, nucleosides and nucleotides David A Case (Fri May 03 2019 - 06:40:36 PDT)
[AMBER] Random segfaults (invalid memory reference) in sander Margarita I. Bernal-Uruchurtu (Fri May 03 2019 - 02:11:59 PDT)
- Re: [AMBER] Random segfaults (invalid memory reference) in sander Daniel Roe (Fri May 03 2019 - 05:29:15 PDT)
  - Re: [AMBER] Random segfaults (invalid memory reference) in sander Charo del Genio (Fri May 03 2019 - 07:08:31 PDT)
  - Re: [AMBER] Random segfaults (invalid memory reference) in sander scanya.interia.eu (Fri May 03 2019 - 07:23:10 PDT)
  - Re: [AMBER] Random segfaults (invalid memory reference) in sander Charo del Genio (Mon May 06 2019 - 02:37:34 PDT)
    - Re: [AMBER] Random segfaults (invalid memory reference) in sander David A Case (Mon May 06 2019 - 07:52:18 PDT)
    - Re: [AMBER] Random segfaults (invalid memory reference) in sander Charo del Genio (Wed May 15 2019 - 08:45:27 PDT)
    - Re: [AMBER] Random segfaults (invalid memory reference) in sander Daniel Roe (Wed May 15 2019 - 08:52:10 PDT)
[AMBER] Files for Tutorial 32 (Deriving bonded parameters with mdgx) Michiel de Hoon (Fri May 03 2019 - 02:26:58 PDT)
[AMBER] Rotating and Obtaining Dihedral Energies [DISANG keyword] Erdem Yeler (Fri May 03 2019 - 02:36:48 PDT)
- Re: [AMBER] Rotating and Obtaining Dihedral Energies [DISANG keyword] Kellon Belfon (Fri May 03 2019 - 08:22:22 PDT)
  - Re: [AMBER] Rotating and Obtaining Dihedral Energies [DISANG keyword] Kellon Belfon (Fri May 03 2019 - 08:49:00 PDT)
    - Re: [AMBER] Rotating and Obtaining Dihedral Energies [DISANG keyword] Erdem Yeler (Sat May 04 2019 - 02:56:05 PDT)
    - Re: [AMBER] Rotating and Obtaining Dihedral Energies [DISANG keyword] Erdem Yeler (Sat May 04 2019 - 02:57:44 PDT)
    - Re: [AMBER] Rotating and Obtaining Dihedral Energies [DISANG keyword] Carlos Simmerling (Sat May 04 2019 - 03:39:42 PDT)
    - Re: [AMBER] Rotating and Obtaining Dihedral Energies [DISANG keyword] Erdem Yeler (Sun May 05 2019 - 03:03:59 PDT)
    - Re: [AMBER] Rotating and Obtaining Dihedral Energies [DISANG keyword] Carlos Simmerling (Sun May 05 2019 - 03:57:32 PDT)
    - Re: [AMBER] Rotating and Obtaining Dihedral Energies [DISANG keyword] Erdem Yeler (Sun May 05 2019 - 04:30:44 PDT)
[AMBER] FLAG_POINTERS in prmtop file Feng, Zimin (Fri May 03 2019 - 08:10:33 PDT)
- Re: [AMBER] FLAG_POINTERS in prmtop file Feng, Zimin (Fri May 03 2019 - 09:11:09 PDT)
  - Re: [AMBER] FLAG_POINTERS in prmtop file Jason Swails (Fri May 10 2019 - 12:25:48 PDT)
Re: [AMBER] [mjldehoon.yahoo.com: Files for Tutorial 32 (Deriving bonded parameters with mdgx)] David Cerutti (Fri May 03 2019 - 08:30:40 PDT)
[AMBER] Are R.E.D. tools still a thing? Luca Codutti (Fri May 03 2019 - 10:17:35 PDT)
- Re: [AMBER] Are R.E.D. tools still a thing? Feng, Zimin (Fri May 03 2019 - 10:52:09 PDT)
- Re: [AMBER] Are R.E.D. tools still a thing? Jason Swails (Fri May 10 2019 - 12:23:47 PDT)
[AMBER] Question regarding compatibility of Temperature replica exchange MD (TREMD) with constant pH MD Pacheco, Sayuri (Fri May 03 2019 - 11:48:35 PDT)
- Re: [AMBER] Question regarding compatibility of Temperature replica exchange MD (TREMD) with constant pH MD Cruzeiro,Vinicius Wilian D (Fri May 03 2019 - 12:14:45 PDT)
  - Re: [AMBER] Question regarding compatibility of Temperature replica exchange MD (TREMD) with constant pH MD Pacheco, Sayuri (Fri May 03 2019 - 13:02:06 PDT)
[AMBER] SIRAH force field goes quantum in AMBER Matias Machado (Fri May 03 2019 - 13:12:34 PDT)
[AMBER] FEW- an issue generating *.lib for ligand ali akbar (Sat May 04 2019 - 00:39:44 PDT)
[AMBER] AmberTools hardcodes library names into binaries viktor drobot (Sat May 04 2019 - 03:57:57 PDT)
- Re: [AMBER] AmberTools hardcodes library names into binaries David Case (Sat May 04 2019 - 19:19:14 PDT)
[AMBER] check version Akshay Prabhakant (Sun May 05 2019 - 05:29:29 PDT)
- Re: [AMBER] check version Pratul Agarwal (Sun May 05 2019 - 07:51:40 PDT)
- Re: [AMBER] check version David Case (Sun May 05 2019 - 13:38:36 PDT)
[AMBER] umbrella sampling using pmemd in amber/2016 Akshay Prabhakant (Sun May 05 2019 - 08:30:04 PDT)
- Re: [AMBER] umbrella sampling using pmemd in amber/2016 Feng Pan (Tue May 07 2019 - 09:26:58 PDT)
[AMBER] Ambertools2018/SQM installation Sina (Mon May 06 2019 - 01:59:31 PDT)
- Re: [AMBER] Ambertools2018/SQM installation Gustaf Olsson (Mon May 06 2019 - 03:36:28 PDT)
  - Re: [AMBER] Ambertools2018/SQM installation Sina (Mon May 06 2019 - 09:24:44 PDT)
- Re: [AMBER] Ambertools2018/SQM installation David A Case (Mon May 06 2019 - 07:43:50 PDT)
[AMBER] matching energies betwen amber-md and gromacs using amber parameters in both Akshay Prabhakant (Mon May 06 2019 - 02:59:06 PDT)
- Re: [AMBER] matching energies betwen amber-md and gromacs using amber parameters in both Karl Kirschner (Mon May 06 2019 - 03:32:28 PDT)
  - Re: [AMBER] matching energies betwen amber-md and gromacs using amber parameters in both Akshay Prabhakant (Mon May 06 2019 - 04:11:58 PDT)
    - Re: [AMBER] matching energies betwen amber-md and gromacs using amber parameters in both Karl Kirschner (Tue May 07 2019 - 00:21:37 PDT)
[AMBER] three letter code for unprotonated carboxyglutamates Tanusree S (Tue May 07 2019 - 02:45:25 PDT)
- Re: [AMBER] three letter code for unprotonated carboxyglutamates Pietro Aronica (Tue May 07 2019 - 02:52:12 PDT)
[AMBER] running qsub files in a single standalone workstation ali akbar (Tue May 07 2019 - 03:28:21 PDT)
- Re: [AMBER] running qsub files in a single standalone workstation David A Case (Tue May 07 2019 - 04:16:58 PDT)
[AMBER] different energy values from mdout and cpptraj Batuhan Kav (Tue May 07 2019 - 05:24:18 PDT)
- Re: [AMBER] different energy values from mdout and cpptraj David A Case (Tue May 07 2019 - 06:01:20 PDT)
[AMBER] SPAM bulk solvent free energy parameters Debarati DasGupta (Tue May 07 2019 - 06:36:51 PDT)
- Re: [AMBER] SPAM bulk solvent free energy parameters Daniel Roe (Thu May 09 2019 - 11:39:26 PDT)
[AMBER] NVidia backwards compatibility James Kress (Tue May 07 2019 - 12:43:34 PDT)
- Re: [AMBER] NVidia backwards compatibility David A Case (Wed May 08 2019 - 05:14:42 PDT)
  - Re: [AMBER] NVidia backwards compatibility James Kress (Wed May 08 2019 - 06:43:11 PDT)
[AMBER] Unequal distribution of water Piotr Fajer (Tue May 07 2019 - 14:26:29 PDT)
- Re: [AMBER] Unequal distribution of water Carlos Simmerling (Tue May 07 2019 - 15:41:04 PDT)
[AMBER] distance restraint failed in minimization and MD wujue (Tue May 07 2019 - 19:38:40 PDT)
- Re: [AMBER] distance restraint failed in minimization and MD David A Case (Wed May 08 2019 - 05:09:24 PDT)
Re: [AMBER] AMBER Digest, Vol 2638, Issue 1 ali akbar (Tue May 07 2019 - 22:07:54 PDT)
[AMBER] running qsub files in a single standalone workstation ali akbar (Tue May 07 2019 - 22:32:49 PDT)
- Re: [AMBER] running qsub files in a single standalone workstation Nadine Homeyer (Tue May 07 2019 - 23:09:28 PDT)
[AMBER] Thermostat question Markowska (Tue May 07 2019 - 23:51:52 PDT)
- Re: [AMBER] Thermostat question David Cerutti (Wed May 08 2019 - 00:22:16 PDT)
- Re: [AMBER] Thermostat question Daniel Roe (Wed May 08 2019 - 05:55:08 PDT)
  - Re: [AMBER] Thermostat question Markowska (Wed May 08 2019 - 13:32:46 PDT)
    - Re: [AMBER] Thermostat question Daniel Roe (Thu May 09 2019 - 11:21:10 PDT)
[AMBER] CPPTRAJ OPENMP - MPI Lorenzo Gontrani (Wed May 08 2019 - 02:51:34 PDT)
- Re: [AMBER] CPPTRAJ OPENMP - MPI Daniel Roe (Wed May 08 2019 - 04:23:21 PDT)
[AMBER] Capping a dipeptide with Boc Saikat Pal (Wed May 08 2019 - 04:04:50 PDT)
- Re: [AMBER] Capping a dipeptide with Boc Alessandro Contini (Wed May 08 2019 - 04:14:46 PDT)
  - Re: [AMBER] Capping a dipeptide with Boc Saikat Pal (Wed May 08 2019 - 05:15:12 PDT)
    - Re: [AMBER] Capping a dipeptide with Boc Alessandro Contini (Wed May 08 2019 - 07:33:38 PDT)
    - Re: [AMBER] Capping a dipeptide with Boc Saikat Pal (Wed May 08 2019 - 09:16:24 PDT)
    - Re: [AMBER] Capping a dipeptide with Boc Alessandro Contini (Wed May 08 2019 - 09:29:09 PDT)
    - Re: [AMBER] Capping a dipeptide with Boc Saikat Pal (Wed May 08 2019 - 09:44:32 PDT)
[AMBER] pmemd.cuda "cudaMemcpy GpuBuffer::Download failed an illegal memory access was encountered" Akshay Prabhakant (Wed May 08 2019 - 08:50:21 PDT)
- Re: [AMBER] pmemd.cuda "cudaMemcpy GpuBuffer::Download failed an illegal memory access was encountered" Pratul Agarwal (Wed May 08 2019 - 09:09:44 PDT)
[AMBER] AMBER 16 vs 18 on different cuda Xiaoyu Wang (Wed May 08 2019 - 13:08:11 PDT)
- Re: [AMBER] AMBER 16 vs 18 on different cuda David Cerutti (Wed May 08 2019 - 13:17:12 PDT)
[AMBER] continuous DNA Qinghua Liao (Thu May 09 2019 - 06:39:00 PDT)
- Re: [AMBER] continuous DNA David A Case (Thu May 09 2019 - 10:44:04 PDT)
- Re: [AMBER] continuous DNA Thomas C. Bishop (Thu May 09 2019 - 12:33:40 PDT)
[AMBER] GPU versions: pmemd.cuda* Yin, Guowei (Thu May 09 2019 - 08:11:05 PDT)
- Re: [AMBER] GPU versions: pmemd.cuda* Pratul Agarwal (Thu May 09 2019 - 08:17:08 PDT)
[AMBER] Energy shifted energy term Debarati DasGupta (Thu May 09 2019 - 13:48:42 PDT)
- Re: [AMBER] Energy shifted energy term Jason Swails (Fri May 10 2019 - 12:04:04 PDT)
  - Re: [AMBER] Energy shifted energy term Debarati DasGupta (Fri May 10 2019 - 13:13:59 PDT)
[AMBER] Fwd: August 5-8.SBU: 2019 Summer School Parallel Computing in Molecular Sciences Carlos Simmerling (Fri May 10 2019 - 07:09:40 PDT)
[AMBER] Regarding GTX 1050 Ti Rajarshi Roy (Fri May 10 2019 - 20:22:09 PDT)
- Re: [AMBER] Regarding GTX 1050 Ti Ross Walker (Sat May 11 2019 - 11:23:40 PDT)
  - Re: [AMBER] Regarding GTX 1050 Ti Rajarshi Roy (Sat May 11 2019 - 11:51:28 PDT)
[AMBER] Fwd: The unperturbed charge of the unit: 4.003000 is not zero Sadaf Rani (Sat May 11 2019 - 04:16:07 PDT)
- Re: [AMBER] Fwd: The unperturbed charge of the unit: 4.003000 is not zero Bill Ross (Sat May 11 2019 - 12:36:57 PDT)
[AMBER] Failed to generate parameters Sadaf Rani (Sat May 11 2019 - 08:48:41 PDT)
[AMBER] MC barostat cause the system to stuck indefinitely Zhiyi Wu (Sat May 11 2019 - 14:10:13 PDT)
- Re: [AMBER] MC barostat cause the system to stuck indefinitely David A Case (Mon May 13 2019 - 05:44:29 PDT)
[AMBER] Problem with preparing parameters with antechamber for modified amino acid Saikat Dutta chowdhury (Sat May 11 2019 - 23:40:19 PDT)
- Re: [AMBER] Problem with preparing parameters with antechamber for modified amino acid Bill Ross (Sun May 12 2019 - 01:52:59 PDT)
  - Re: [AMBER] Problem with preparing parameters with antechamber for modified amino acid Saikat Dutta chowdhury (Mon May 13 2019 - 00:46:40 PDT)
    - Re: [AMBER] Problem with preparing parameters with antechamber for modified amino acid Bill Ross (Mon May 13 2019 - 00:56:07 PDT)
    - Re: [AMBER] Problem with preparing parameters with antechamber for modified amino acid Bill Ross (Mon May 13 2019 - 01:05:59 PDT)
    - Re: [AMBER] Problem with preparing parameters with antechamber for modified amino acid Saikat Dutta chowdhury (Mon May 13 2019 - 03:41:15 PDT)
- Re: [AMBER] Problem with preparing parameters with antechamber for modified amino acid David A Case (Mon May 13 2019 - 05:51:38 PDT)
  - Re: [AMBER] Problem with preparing parameters with antechamber for modified amino acid Saikat Dutta chowdhury (Mon May 13 2019 - 21:23:06 PDT)
[AMBER] Residence time around ions Reber, David (Sun May 12 2019 - 03:58:43 PDT)
[AMBER] Center of mass velocity autocorrelation function Reber, David (Sun May 12 2019 - 18:29:33 PDT)
[AMBER] tleap split lipid when it shouldn't Maximilien BERNE (Mon May 13 2019 - 05:41:42 PDT)
- Re: [AMBER] tleap split lipid when it shouldn't David A Case (Mon May 13 2019 - 06:50:41 PDT)
  - Re: [AMBER] tleap split lipid when it shouldn't Maximilien BERNE (Mon May 13 2019 - 07:32:03 PDT)
  - Re: [AMBER] tleap split lipid when it shouldn't Maximilien BERNE (Mon May 13 2019 - 07:37:09 PDT)
    - Re: [AMBER] tleap split lipid when it shouldn't Dickson, Callum (Mon May 13 2019 - 07:49:49 PDT)
  - Re: [AMBER] tleap split lipid when it shouldn't Maximilien BERNE (Mon May 13 2019 - 08:23:28 PDT)
    - Re: [AMBER] tleap split lipid when it shouldn't Dickson, Callum (Mon May 13 2019 - 08:57:36 PDT)
  - Re: [AMBER] tleap split lipid when it shouldn't Maximilien BERNE (Wed May 15 2019 - 03:18:29 PDT)
    - Re: [AMBER] tleap split lipid when it shouldn't David A Case (Wed May 15 2019 - 06:08:40 PDT)
    - Re: [AMBER] tleap split lipid when it shouldn't Maximilien BERNE (Wed May 15 2019 - 07:17:52 PDT)
    - Re: [AMBER] tleap split lipid when it shouldn't Matias Machado (Wed May 15 2019 - 10:15:32 PDT)
    - Re: [AMBER] tleap split lipid when it shouldn't Maximilien BERNE (Mon May 20 2019 - 07:48:12 PDT)
    - Re: [AMBER] tleap split lipid when it shouldn't Sally Pias (Wed May 15 2019 - 15:12:15 PDT)
  - Re: [AMBER] tleap split lipid when it shouldn't Stephan Schott (Wed May 15 2019 - 10:35:22 PDT)
  - Re: [AMBER] tleap split lipid when it shouldn't Stephan Schott (Wed May 15 2019 - 10:42:50 PDT)
- Re: [AMBER] tleap split lipid when it shouldn't Dickson, Callum (Mon May 13 2019 - 06:56:21 PDT)
[AMBER] Treat alpha helix as a rigid body during umbrella sampling simulations in amber/2016 Akshay Prabhakant (Mon May 13 2019 - 06:53:49 PDT)
- Re: [AMBER] Treat alpha helix as a rigid body during umbrella sampling simulations in amber/2016 Akshay Prabhakant (Mon May 13 2019 - 07:01:26 PDT)
  - Re: [AMBER] Treat alpha helix as a rigid body during umbrella sampling simulations in amber/2016 Pratul Agarwal (Mon May 13 2019 - 07:24:10 PDT)
    - Re: [AMBER] Treat alpha helix as a rigid body during umbrella sampling simulations in amber/2016 Akshay Prabhakant (Tue May 14 2019 - 03:03:12 PDT)
    - Re: [AMBER] Treat alpha helix as a rigid body during umbrella sampling simulations in amber/2016 Pratul Agarwal (Tue May 14 2019 - 06:31:01 PDT)
[AMBER] Atom type (C.2) is not in PARMCHK.DAT Segmentation fault (core dumped) Sadaf Rani (Mon May 13 2019 - 08:56:06 PDT)
- Re: [AMBER] Atom type (C.2) is not in PARMCHK.DAT Segmentation fault (core dumped) David A Case (Tue May 14 2019 - 05:55:43 PDT)
  - Re: [AMBER] Atom type (C.2) is not in PARMCHK.DAT Segmentation fault (core dumped) Sadaf Rani (Wed May 15 2019 - 11:00:28 PDT)
[AMBER] MMPBSA radiopt effect on EDISPER Thomas Gaillard (Mon May 13 2019 - 09:40:57 PDT)
- Re: [AMBER] MMPBSA radiopt effect on EDISPER Thomas Gaillard (Tue Jun 11 2019 - 06:49:08 PDT)
  - Re: [AMBER] MMPBSA radiopt effect on EDISPER Ray Luo (Mon Jun 17 2019 - 16:20:12 PDT)
    - Re: [AMBER] MMPBSA radiopt effect on EDISPER Thomas Gaillard (Wed Jun 19 2019 - 07:49:20 PDT)
    - Re: [AMBER] MMPBSA radiopt effect on EDISPER Ray Luo (Wed Jun 19 2019 - 07:51:24 PDT)
    - Re: [AMBER] MMPBSA radiopt effect on EDISPER Ray Luo (Wed Jun 19 2019 - 14:14:11 PDT)
    - Re: [AMBER] MMPBSA radiopt effect on EDISPER Thomas Gaillard (Wed Jun 19 2019 - 15:34:50 PDT)
    - Re: [AMBER] MMPBSA radiopt effect on EDISPER Ray Luo (Wed Jun 19 2019 - 15:54:28 PDT)
    - Re: [AMBER] MMPBSA radiopt effect on EDISPER Thomas Gaillard (Mon Jun 24 2019 - 03:46:15 PDT)
    - Re: [AMBER] MMPBSA radiopt effect on EDISPER Ray Luo (Mon Jun 24 2019 - 14:23:14 PDT)
[AMBER] amber18 parallel cpu make test hanging at first test Ravi Abrol (Mon May 13 2019 - 11:47:18 PDT)
- Re: [AMBER] amber18 parallel cpu make test hanging at first test David A Case (Tue May 14 2019 - 06:02:37 PDT)
  - Re: [AMBER] amber18 parallel cpu make test hanging at first test Ravi Abrol (Tue May 14 2019 - 17:55:22 PDT)
[AMBER] Average structure vs Individual frames Yin, Guowei (Mon May 13 2019 - 18:16:59 PDT)
- Re: [AMBER] Average structure vs Individual frames Bill Ross (Mon May 13 2019 - 18:50:15 PDT)
  - Re: [AMBER] Average structure vs Individual frames Yin, Guowei (Mon May 13 2019 - 19:19:16 PDT)
    - Re: [AMBER] Average structure vs Individual frames Bill Ross (Mon May 13 2019 - 19:53:18 PDT)
- Re: [AMBER] Average structure vs Individual frames David A Case (Tue May 14 2019 - 06:09:05 PDT)
Re: [AMBER] Building inpcrd and prmtop for a non-standard residue containing cyclic peptide Pietro Aronica (Tue May 14 2019 - 02:19:31 PDT)
- Re: [AMBER] Building inpcrd and prmtop for a non-standard residue containing cyclic peptide David A Case (Tue May 14 2019 - 06:12:31 PDT)
- Re: [AMBER] Building inpcrd and prmtop for a non-standard residue containing cyclic peptide Schröder, David Christopher (Tue May 14 2019 - 07:20:27 PDT)
[AMBER] Solute free non-water solvent razie yousefi (Tue May 14 2019 - 08:01:17 PDT)
- Re: [AMBER] Solute free non-water solvent David A Case (Tue May 14 2019 - 10:34:58 PDT)
[AMBER] 3D-RISM options Ryan Pavlovicz (Tue May 14 2019 - 14:45:27 PDT)
- Re: [AMBER] 3D-RISM options Tyler Luchko (Lists) (Tue May 14 2019 - 15:44:24 PDT)
  - Re: [AMBER] 3D-RISM options Ryan Pavlovicz (Tue May 14 2019 - 17:10:31 PDT)
    - Re: [AMBER] 3D-RISM options Tyler Luchko (Lists) (Tue May 14 2019 - 17:17:38 PDT)
    - Re: [AMBER] 3D-RISM options Ryan Pavlovicz (Tue May 14 2019 - 23:01:18 PDT)
    - Re: [AMBER] 3D-RISM options David A Case (Wed May 15 2019 - 05:46:55 PDT)
    - Re: [AMBER] 3D-RISM options Ryan Pavlovicz (Wed May 15 2019 - 07:45:41 PDT)
    - Re: [AMBER] 3D-RISM options Tyler Luchko (Lists) (Wed May 15 2019 - 10:17:12 PDT)
[AMBER] Entropy calculation for a protein homodimerization Rakesh Srivastava (Wed May 15 2019 - 01:47:53 PDT)
- Re: [AMBER] Entropy calculation for a protein homodimerization Pratul Agarwal (Wed May 15 2019 - 04:47:16 PDT)
  - Re: [AMBER] Entropy calculation for a protein homodimerization Rakesh Srivastava (Wed May 15 2019 - 05:20:31 PDT)
[AMBER] hbond lifetime filesize issues Reber, David (Wed May 15 2019 - 02:53:13 PDT)
- Re: [AMBER] hbond lifetime filesize issues Daniel Roe (Wed May 15 2019 - 06:36:27 PDT)
  - Re: [AMBER] hbond lifetime filesize issues Reber, David (Wed May 15 2019 - 18:52:17 PDT)
    - Re: [AMBER] hbond lifetime filesize issues Reber, David (Wed May 15 2019 - 22:02:36 PDT)
    - Re: [AMBER] hbond lifetime filesize issues Daniel Roe (Tue May 21 2019 - 09:50:58 PDT)
    - Re: [AMBER] hbond lifetime filesize issues Reber, David (Tue May 21 2019 - 19:09:20 PDT)
[AMBER] set RA, RT and n_partition in adQM/MM run Ruth Helena Tichauer (Wed May 15 2019 - 03:57:38 PDT)
- Re: [AMBER] set RA, RT and n_partition in adQM/MM run Ruth Helena Tichauer (Wed Jul 10 2019 - 03:41:39 PDT)
[AMBER] Crashed dynamics : connectivity emanuele falbo (Wed May 15 2019 - 05:59:49 PDT)
- Re: [AMBER] Crashed dynamics : connectivity David A Case (Wed May 15 2019 - 07:50:27 PDT)
[AMBER] nvidia tesla-t4 and amber Luca Codutti (Wed May 15 2019 - 08:46:36 PDT)
- Re: [AMBER] nvidia tesla-t4 and amber Shenglong Wang (Wed May 15 2019 - 08:52:12 PDT)
  - Re: [AMBER] nvidia tesla-t4 and amber David Cerutti (Wed May 15 2019 - 08:58:45 PDT)
    - Re: [AMBER] nvidia tesla-t4 and amber Luca Codutti (Wed May 15 2019 - 09:28:01 PDT)
[AMBER] Missing file amber tutorial Sadaf Rani (Wed May 15 2019 - 11:06:10 PDT)
- Re: [AMBER] Missing file amber tutorial Pratul Agarwal (Wed May 15 2019 - 11:12:02 PDT)
  - Re: [AMBER] Missing file amber tutorial Pratul Agarwal (Wed May 15 2019 - 11:32:55 PDT)
    - Re: [AMBER] Missing file amber tutorial Sadaf Rani (Tue May 28 2019 - 02:01:02 PDT)
[AMBER] NetCDF trajectory file does not contain information about time/timestep Markowska (Wed May 15 2019 - 11:12:57 PDT)
- Re: [AMBER] NetCDF trajectory file does not contain information about time/timestep Daniel Roe (Fri May 17 2019 - 07:25:00 PDT)
  - Re: [AMBER] NetCDF trajectory file does not contain information about time/timestep Markowska (Sat May 18 2019 - 12:46:30 PDT)
    - Re: [AMBER] NetCDF trajectory file does not contain information about time/timestep Daniel Roe (Mon May 20 2019 - 11:08:54 PDT)
[AMBER] Releasing SIRAH lipids! A complete coarse-grained force field running on AMBER Matias Machado (Wed May 15 2019 - 11:30:57 PDT)
[AMBER] ELECTRIC_FIELD in md.out file does not match with md.in file Gargi Borgohain (Thu May 16 2019 - 02:38:29 PDT)
- Re: [AMBER] ELECTRIC_FIELD in md.out file does not match with md.in file Bill Ross (Thu May 16 2019 - 03:03:55 PDT)
  - Re: [AMBER] ELECTRIC_FIELD in md.out file does not match with md.in file Charles Lin (Thu May 16 2019 - 08:06:50 PDT)
- Re: [AMBER] ELECTRIC_FIELD in md.out file does not match with md.in file Gargi Borgohain (Fri May 17 2019 - 02:45:31 PDT)
  - Re: [AMBER] ELECTRIC_FIELD in md.out file does not match with md.in file Joan Torras (Fri May 17 2019 - 03:47:00 PDT)
[AMBER] Bubbles during NPT and NVT simulations Stefano Motta (Thu May 16 2019 - 02:56:24 PDT)
- Re: [AMBER] Bubbles during NPT and NVT simulations Carlos Simmerling (Thu May 16 2019 - 03:02:03 PDT)
- Re: [AMBER] Bubbles during NPT and NVT simulations Bill Ross (Thu May 16 2019 - 03:13:54 PDT)
- Re: [AMBER] Bubbles during NPT and NVT simulations David A Case (Thu May 16 2019 - 05:05:25 PDT)
[AMBER] RMSF of combined trajectory Rinsha Chk (Thu May 16 2019 - 04:43:37 PDT)
- Re: [AMBER] RMSF of combined trajectory Bill Ross (Thu May 16 2019 - 04:59:21 PDT)
  - Re: [AMBER] RMSF of combined trajectory Rinsha Chk (Thu May 16 2019 - 22:26:58 PDT)
    - Re: [AMBER] RMSF of combined trajectory Bill Ross (Thu May 16 2019 - 23:16:02 PDT)
    - Re: [AMBER] RMSF of combined trajectory Bill Ross (Thu May 16 2019 - 23:17:31 PDT)
    - Re: [AMBER] RMSF of combined trajectory Rinsha Chk (Fri May 17 2019 - 00:08:53 PDT)
    - Re: [AMBER] RMSF of combined trajectory Daniel Roe (Fri May 17 2019 - 05:23:23 PDT)
    - Re: [AMBER] RMSF of combined trajectory Rinsha Chk (Sun May 19 2019 - 21:23:40 PDT)
[AMBER] Simulating Water Exchange to Buried Binding Sites Debarati DasGupta (Thu May 16 2019 - 06:21:44 PDT)
- Re: [AMBER] Simulating Water Exchange to Buried Binding Sites Matias Machado (Fri May 17 2019 - 07:14:06 PDT)
  - Re: [AMBER] Simulating Water Exchange to Buried Binding Sites Charles Lin (Fri May 17 2019 - 10:45:25 PDT)
    - Re: [AMBER] Simulating Water Exchange to Buried Binding Sites Debarati DasGupta (Fri May 17 2019 - 11:18:09 PDT)
    - Re: [AMBER] Simulating Water Exchange to Buried Binding Sites Charles Lin (Mon May 20 2019 - 10:09:22 PDT)
    - Re: [AMBER] Simulating Water Exchange to Buried Binding Sites Matias Machado (Fri May 17 2019 - 11:22:10 PDT)
    - Re: [AMBER] Simulating Water Exchange to Buried Binding Sites Charles Lin (Mon May 20 2019 - 10:10:56 PDT)
[AMBER] Error in step 3 of MCPB.py Shahila Muhammed (Fri May 17 2019 - 01:02:55 PDT)
- Re: [AMBER] Error in step 3 of MCPB.py Pengfei Li (Tue May 21 2019 - 08:50:36 PDT)
  - Re: [AMBER] Error in step 3 of MCPB.py Shahila Muhammed (Wed May 22 2019 - 05:20:42 PDT)
    - Re: [AMBER] Error in step 3 of MCPB.py Pengfei Li (Sat Jun 01 2019 - 12:27:26 PDT)
[AMBER] Selecting number of waters in tleap Elena Gomez (Fri May 17 2019 - 01:09:35 PDT)
- Re: [AMBER] Selecting number of waters in tleap Matias Machado (Fri May 17 2019 - 07:19:02 PDT)
  - Re: [AMBER] Selecting number of waters in tleap Kellon Belfon (Fri May 17 2019 - 11:07:00 PDT)
[AMBER] Open position for doctoral candidate in biomolecular simulations Jan Brezovsky (Fri May 17 2019 - 02:17:10 PDT)
[AMBER] Suggestion about proper ANTECHAMBER usage Saikat Dutta chowdhury (Fri May 17 2019 - 04:38:52 PDT)
- Re: [AMBER] Suggestion about proper ANTECHAMBER usage David A Case (Fri May 17 2019 - 06:25:17 PDT)
  - Re: [AMBER] Suggestion about proper ANTECHAMBER usage Saikat Dutta chowdhury (Fri May 17 2019 - 06:54:27 PDT)
[AMBER] Velocity rescaling between different temperatures? Kenneth Huang (Fri May 17 2019 - 12:18:15 PDT)
- Re: [AMBER] Velocity rescaling between different temperatures? Daniel Roe (Mon May 20 2019 - 05:28:04 PDT)
  - Re: [AMBER] Velocity rescaling between different temperatures? Kenneth Huang (Mon May 20 2019 - 09:25:38 PDT)
    - Re: [AMBER] Velocity rescaling between different temperatures? Daniel Roe (Mon May 20 2019 - 09:33:25 PDT)
[AMBER] DRMSD utility in cpptraj Debarati DasGupta (Fri May 17 2019 - 13:45:30 PDT)
- Re: [AMBER] DRMSD utility in cpptraj Daniel Roe (Mon May 20 2019 - 12:33:46 PDT)
  - Re: [AMBER] DRMSD utility in cpptraj Debarati DasGupta (Tue May 21 2019 - 06:15:48 PDT)
[AMBER] Force field for intrinsically disordered proteins Markowska (Sat May 18 2019 - 05:11:46 PDT)
- Re: [AMBER] Force field for intrinsically disordered proteins David Case (Sun May 19 2019 - 05:24:37 PDT)
[AMBER] Catalysis mechanism of ATPase sunyeping (Sun May 19 2019 - 04:29:35 PDT)
- Re: [AMBER] Catalysis mechanism of ATPase Pratul Agarwal (Mon May 20 2019 - 15:59:27 PDT)
[AMBER] Regarding building of parallel version of AMBER18 in centos 7 Rajarshi Roy (Tue May 21 2019 - 20:49:41 PDT)
- Re: [AMBER] Regarding building of parallel version of AMBER18 in centos 7 David A Case (Wed May 22 2019 - 05:03:30 PDT)
  - Re: [AMBER] Regarding building of parallel version of AMBER18 in centos 7 Rajarshi Roy (Thu May 23 2019 - 06:40:42 PDT)
[AMBER] Temperature variation in QM/MM simulation with AMBER18/G09 Abhilash J (Wed May 22 2019 - 11:38:05 PDT)
- Re: [AMBER] Temperature variation in QM/MM simulation with AMBER18/G09 David A Case (Thu May 23 2019 - 06:00:40 PDT)
  - Re: [AMBER] Temperature variation in QM/MM simulation with AMBER18/G09 Abhilash J (Fri May 24 2019 - 22:53:38 PDT)
[AMBER] amber inputs Sina (Thu May 23 2019 - 06:44:31 PDT)
- Re: [AMBER] amber inputs David A Case (Thu May 23 2019 - 07:59:33 PDT)
[AMBER] Volmap command in cpptraj followed by SPAM Debarati DasGupta (Thu May 23 2019 - 06:59:28 PDT)
[AMBER] Lennard Jones parameters in frcmod Stefano Motta (Thu May 23 2019 - 07:31:17 PDT)
- Re: [AMBER] Lennard Jones parameters in frcmod Matias Machado (Thu May 23 2019 - 08:21:56 PDT)
[AMBER] Different potential energies between recomputed and original simulations from PMEMD? 杨明俊 (Fri May 24 2019 - 03:14:32 PDT)
- Re: [AMBER] Different potential energies between recomputed and original simulations from PMEMD? 杨明俊 (Fri May 24 2019 - 05:02:28 PDT)
[AMBER] Qm minimization, Sina (Fri May 24 2019 - 03:22:47 PDT)
- Re: [AMBER] Qm minimization, David Case (Fri May 24 2019 - 04:42:33 PDT)
[AMBER] Some basic question Sina (Fri May 24 2019 - 09:18:41 PDT)
- Re: [AMBER] Some basic question David A Case (Tue May 28 2019 - 10:51:29 PDT)
[AMBER] jobs getting cancelled on cuda7 gpus maryam azimzadehirani (Fri May 24 2019 - 22:59:14 PDT)
[AMBER] PCA with a really giant trajectory David Cerutti (Sat May 25 2019 - 12:31:54 PDT)
- Re: [AMBER] PCA with a really giant trajectory Chris Neale (Mon May 27 2019 - 00:29:24 PDT)
  - Re: [AMBER] PCA with a really giant trajectory David Cerutti (Tue May 28 2019 - 10:49:15 PDT)
- Re: [AMBER] PCA with a really giant trajectory Daniel Roe (Tue May 28 2019 - 11:41:52 PDT)
  - Re: [AMBER] PCA with a really giant trajectory David Cerutti (Tue May 28 2019 - 11:47:56 PDT)
[AMBER] Print Hessian matrix in (3,3) dimension Bouibes Amine (Sun May 26 2019 - 01:03:55 PDT)
- Re: [AMBER] Print Hessian matrix in (3,3) dimension David Case (Mon May 27 2019 - 18:30:38 PDT)
[AMBER] How to generate the correct force field parameter for a large molecule? xmgign.126.com (Sun May 26 2019 - 23:27:44 PDT)
- Re: [AMBER] How to generate the correct force field parameter for a large molecule? Bill Ross (Mon May 27 2019 - 00:52:02 PDT)
[AMBER] graph Charu Sharma (JRF) (Mon May 27 2019 - 04:06:01 PDT)
- Re: [AMBER] graph Daniel Roe (Thu May 30 2019 - 08:08:20 PDT)
[AMBER] compiling Amber Tools 19 Vlad Cojocaru (Mon May 27 2019 - 04:42:38 PDT)
- Re: [AMBER] compiling Amber Tools 19 Vlad Cojocaru (Mon May 27 2019 - 05:14:32 PDT)
- Re: [AMBER] compiling Amber Tools 19 David Case (Mon May 27 2019 - 18:45:21 PDT)
  - Re: [AMBER] compiling Amber Tools 19 Vlad Cojocaru (Tue May 28 2019 - 01:33:15 PDT)
    - Re: [AMBER] compiling Amber Tools 19 David A Case (Tue May 28 2019 - 04:38:55 PDT)
    - Re: [AMBER] compiling Amber Tools 19 Vlad Cojocaru (Tue May 28 2019 - 05:37:07 PDT)
- Re: [AMBER] compiling Amber Tools 19 Hashemi, Mohtadin (Thu May 30 2019 - 06:59:59 PDT)
  - Re: [AMBER] compiling Amber Tools 19 Hai Nguyen (Thu May 30 2019 - 11:22:52 PDT)
    - Re: [AMBER] compiling Amber Tools 19 Hashemi, Mohtadin (Thu May 30 2019 - 12:12:16 PDT)
[AMBER] Protein-Lipid Bilayer PDB preparation Issue(s) Abhishek Sirohiwal (Mon May 27 2019 - 09:48:32 PDT)
- Re: [AMBER] Protein-Lipid Bilayer PDB preparation Issue(s) Stephan Schott (Mon May 27 2019 - 10:17:42 PDT)
  - Re: [AMBER] Protein-Lipid Bilayer PDB preparation Issue(s) Abhishek Sirohiwal (Mon May 27 2019 - 11:31:10 PDT)
- Re: [AMBER] Protein-Lipid Bilayer PDB preparation Issue(s) Stephan Schott (Mon May 27 2019 - 11:49:56 PDT)
[AMBER] rmsd Hirdesh Kumar (Mon May 27 2019 - 11:35:16 PDT)
- Re: [AMBER] rmsd 김준기 (Fri Sep 06 2013 - 19:57:20 PDT)
  - Re: [AMBER] rmsd Daniel Roe (Fri Sep 06 2013 - 20:37:30 PDT)
- Re: [AMBER] rmsd Kenneth Huang (Mon May 27 2019 - 18:18:27 PDT)
- Re: [AMBER] rmsd David Case (Mon May 27 2019 - 18:49:22 PDT)
[AMBER] GCC 2019, November 3-5 in Mainz, Deadline extendend to June 23, 2019 Stefan.Guessregen.sanofi.com (Mon May 27 2019 - 23:20:14 PDT)
[AMBER] Problem in simulating peptide with modified amino acid - vlimit exceeded Saikat Dutta chowdhury (Tue May 28 2019 - 04:07:07 PDT)
- Re: [AMBER] Problem in simulating peptide with modified amino acid - vlimit exceeded David A Case (Tue May 28 2019 - 04:45:22 PDT)
[AMBER] reduce info.log Sadaf Rani (Tue May 28 2019 - 04:38:07 PDT)
- Re: [AMBER] reduce info.log David A Case (Tue May 28 2019 - 10:35:07 PDT)
  - Re: [AMBER] reduce info.log Sadaf Rani (Wed May 29 2019 - 03:08:02 PDT)
Re: [AMBER] Installation of AMBER 18 regarding David A Case (Tue May 28 2019 - 10:43:50 PDT)
[AMBER] Changes to AmberTools antechamber Makefile Jocelyn Sunseri (Tue May 28 2019 - 10:58:47 PDT)
- Re: [AMBER] Changes to AmberTools antechamber Makefile David A Case (Wed May 29 2019 - 04:57:05 PDT)
[AMBER] amber 16 installation on Ubuntu 18 Ming Tang (Tue May 28 2019 - 21:45:12 PDT)
- Re: [AMBER] amber 16 installation on Ubuntu 18 David A Case (Wed May 29 2019 - 04:58:12 PDT)
[AMBER] Minimization input Sadaf Rani (Wed May 29 2019 - 03:29:46 PDT)
- Re: [AMBER] Minimization input Carlos Simmerling (Wed May 29 2019 - 03:47:35 PDT)
[AMBER] problem of srun Albert (Wed May 29 2019 - 05:51:46 PDT)
- Re: [AMBER] problem of srun David A Case (Wed May 29 2019 - 06:45:22 PDT)
[AMBER] phosphor tyrosine bound to C5' terminal DA5 Fabian Glaser (Wed May 29 2019 - 07:04:19 PDT)
- Re: [AMBER] phosphor tyrosine bound to C5' terminal DA5 Bill Ross (Wed May 29 2019 - 07:12:15 PDT)
  - Re: [AMBER] phosphor tyrosine bound to C5' terminal DA5 Fabian Glaser (Wed May 29 2019 - 10:54:14 PDT)
    - Re: [AMBER] phosphor tyrosine bound to C5' terminal DA5 Bill Ross (Wed May 29 2019 - 12:09:53 PDT)
    - Re: [AMBER] phosphor tyrosine bound to C5' terminal DA5 Fabian Glaser (Wed May 29 2019 - 12:15:15 PDT)
- Re: [AMBER] phosphor tyrosine bound to C5' terminal DA5 David Case (Thu May 30 2019 - 18:20:12 PDT)
  - Re: [AMBER] phosphor tyrosine bound to C5' terminal DA5 Fabian Glaser (Sun Jun 02 2019 - 06:21:58 PDT)
[AMBER] error with loading HEM parameters for constph redox calcuations Vaibhav Dixit (Wed May 29 2019 - 07:53:28 PDT)
- Re: [AMBER] error with loading HEM parameters for constph redox calcuations David A Case (Wed May 29 2019 - 09:03:23 PDT)
  - Re: [AMBER] error with loading HEM parameters for constph redox calcuations Vaibhav Dixit (Wed May 29 2019 - 13:52:32 PDT)
    - Re: [AMBER] error with loading HEM parameters for constph redox calcuations Vaibhav Dixit (Thu May 30 2019 - 02:35:41 PDT)
- Re: [AMBER] error with loading HEM parameters for constph redox calcuations Vaibhav Dixit (Fri May 31 2019 - 12:05:26 PDT)
  - Re: [AMBER] error with loading HEM parameters for constph redox calcuations Vaibhav Dixit (Fri May 31 2019 - 12:32:03 PDT)
    - Re: [AMBER] error with loading HEM parameters for constph redox calcuations David Case (Fri May 31 2019 - 17:57:39 PDT)
    - Re: [AMBER] error with loading HEM parameters for constph redox calcuations Matias Machado (Mon Jun 03 2019 - 16:10:13 PDT)
[AMBER] deselect residues for step1 model in MCPB.py SARAH JEANNE LEFAVE (Wed May 29 2019 - 09:39:30 PDT)
- Re: [AMBER] deselect residues for step1 model in MCPB.py Pengfei Li (Sat Jun 01 2019 - 12:33:12 PDT)
[AMBER] Help compiling AMBER18 GPU Code- Cannot find compiler cl.exe in PATH Jay Spencer (Wed May 29 2019 - 19:01:53 PDT)
- Re: [AMBER] Help compiling AMBER18 GPU Code- Cannot find compiler cl.exe in PATH David A Case (Thu May 30 2019 - 03:58:58 PDT)
[AMBER] Radgyr or distance averages Reber, David (Wed May 29 2019 - 20:24:20 PDT)
- Re: [AMBER] Radgyr or distance averages Daniel Roe (Thu May 30 2019 - 08:03:21 PDT)
  - Re: [AMBER] Radgyr or distance averages Reber, David (Thu May 30 2019 - 17:31:45 PDT)
    - Re: [AMBER] Radgyr or distance averages Daniel Roe (Thu May 30 2019 - 18:15:29 PDT)
    - Re: [AMBER] Radgyr or distance averages Reber, David (Thu May 30 2019 - 18:23:39 PDT)
    - Re: [AMBER] Radgyr or distance averages Daniel Roe (Thu May 30 2019 - 18:29:13 PDT)
    - Re: [AMBER] Radgyr or distance averages Reber, David (Thu May 30 2019 - 18:33:31 PDT)
    - Re: [AMBER] Radgyr or distance averages Daniel Roe (Thu May 30 2019 - 18:39:12 PDT)
    - Re: [AMBER] Radgyr or distance averages Reber, David (Thu May 30 2019 - 18:46:20 PDT)
    - Re: [AMBER] Radgyr or distance averages Thomas Cheatham (Thu May 30 2019 - 19:07:01 PDT)
    - Re: [AMBER] Radgyr or distance averages Reber, David (Thu May 30 2019 - 19:17:53 PDT)
    - Re: [AMBER] Radgyr or distance averages Thomas Cheatham (Thu May 30 2019 - 19:23:11 PDT)
    - Re: [AMBER] Radgyr or distance averages Reber, David (Thu May 30 2019 - 19:33:47 PDT)
    - Re: [AMBER] Radgyr or distance averages Thomas Cheatham (Thu May 30 2019 - 19:43:02 PDT)
    - Re: [AMBER] Radgyr or distance averages Reber, David (Thu May 30 2019 - 20:03:49 PDT)
    - Re: [AMBER] Radgyr or distance averages Thomas Cheatham (Thu May 30 2019 - 20:07:06 PDT)
    - Re: [AMBER] Radgyr or distance averages Reber, David (Thu May 30 2019 - 20:55:32 PDT)
    - Re: [AMBER] Radgyr or distance averages Daniel Roe (Fri May 31 2019 - 07:17:28 PDT)
[AMBER] Optimization of geometry in xleap Shilpa Gupta (Wed May 29 2019 - 23:21:05 PDT)
- Re: [AMBER] Optimization of geometry in xleap Bill Ross (Wed May 29 2019 - 23:36:14 PDT)
[AMBER] anybody has any idea? Albert (Thu May 30 2019 - 00:17:35 PDT)
- Re: [AMBER] anybody has any idea? David A Case (Thu May 30 2019 - 04:04:26 PDT)
  - Re: [AMBER] anybody has any idea? Albert (Thu May 30 2019 - 04:14:51 PDT)
[AMBER] How to generate boron atom force field parameters Meng Wu (Thu May 30 2019 - 03:53:24 PDT)
- Re: [AMBER] How to generate boron atom force field parameters David Case (Thu May 30 2019 - 18:24:54 PDT)
[AMBER] empty cein file redox potential calculations Vaibhav Dixit (Thu May 30 2019 - 04:36:37 PDT)
- Re: [AMBER] empty cein file redox potential calculations Marcos Serrou do Amaral (Thu May 30 2019 - 05:03:43 PDT)
  - Re: [AMBER] empty cein file redox potential calculations Vaibhav Dixit (Thu May 30 2019 - 05:16:45 PDT)
    - Re: [AMBER] empty cein file redox potential calculations Marcos Serrou do Amaral (Thu May 30 2019 - 05:38:51 PDT)
    - Re: [AMBER] empty cein file redox potential calculations Vaibhav Dixit (Thu May 30 2019 - 07:38:16 PDT)
    - Re: [AMBER] empty cein file redox potential calculations Cruzeiro,Vinicius Wilian D (Thu May 30 2019 - 12:29:15 PDT)
    - Re: [AMBER] empty cein file redox potential calculations Vaibhav Dixit (Mon Jun 03 2019 - 09:08:58 PDT)
    - Re: [AMBER] empty cein file redox potential calculations Cruzeiro,Vinicius Wilian D (Mon Jun 03 2019 - 10:20:55 PDT)
    - Re: [AMBER] empty cein file redox potential calculations Vaibhav Dixit (Mon Jun 03 2019 - 10:23:34 PDT)
    - Re: [AMBER] empty cein file redox potential calculations Cruzeiro,Vinicius Wilian D (Mon Jun 03 2019 - 10:33:50 PDT)
    - Re: [AMBER] empty cein file redox potential calculations Vaibhav Dixit (Mon Jan 06 2020 - 00:59:37 PST)
    - Re: [AMBER] empty cein file redox potential calculations Cruzeiro,Vinicius Wilian D (Thu Jan 09 2020 - 07:01:11 PST)
[AMBER] parameter file for dUTP sunyeping (Thu May 30 2019 - 06:03:54 PDT)
- Re: [AMBER] parameter file for dUTP Zachary Fallon (Thu May 30 2019 - 10:55:20 PDT)
  - Re: [AMBER] parameter file for dUTP sunyeping (Thu May 30 2019 - 14:38:11 PDT)
    - Re: [AMBER] parameter file for dUTP Zachary Fallon (Thu May 30 2019 - 15:12:07 PDT)
    - Re: [AMBER] parameter file for dUTP sunyeping (Tue Jun 04 2019 - 12:51:29 PDT)
    - Re: [AMBER] parameter file for dUTP Zachary Fallon (Tue Jun 04 2019 - 15:34:36 PDT)
    - Re: [AMBER] parameter file for dUTP David Case (Thu May 30 2019 - 18:43:37 PDT)
[AMBER] Using a box of organic solvent Alessandro LANDI (Fri May 31 2019 - 03:42:08 PDT)
- Re: [AMBER] Using a box of organic solvent David A Case (Fri May 31 2019 - 05:14:51 PDT)
[AMBER] Boron QM/MM Pär Håkansson (Fri May 31 2019 - 04:08:00 PDT)
- Re: [AMBER] Boron QM/MM Pär Håkansson (Fri May 31 2019 - 05:55:05 PDT)
[AMBER] make test fail Sadaf Rani (Fri May 31 2019 - 09:24:55 PDT)
- Re: [AMBER] make test fail David A Case (Fri May 31 2019 - 10:21:31 PDT)
[AMBER] Question about sander running parallel Sadaf Rani (Fri May 31 2019 - 09:39:23 PDT)
- Re: [AMBER] Question about sander running parallel David A Case (Fri May 31 2019 - 10:31:08 PDT)
  - Re: [AMBER] Question about sander running parallel Charo del Genio (Fri May 31 2019 - 12:19:27 PDT)
  - Re: [AMBER] Question about sander running parallel Sadaf Rani (Tue Jun 04 2019 - 02:53:09 PDT)
[AMBER] Dealing with non standard amino acid hii (Fri May 31 2019 - 22:03:20 PDT)
[AMBER] temperature not reaching target value in heating simulation Vaibhav Dixit (Sun Jun 02 2019 - 02:07:29 PDT)
- Re: [AMBER] temperature not reaching target value in heating simulation Bill Ross (Sun Jun 02 2019 - 05:00:05 PDT)
  - Re: [AMBER] temperature not reaching target value in heating simulation Bill Ross (Sun Jun 02 2019 - 05:06:35 PDT)
    - Re: [AMBER] temperature not reaching target value in heating simulation Vaibhav Dixit (Sun Jun 02 2019 - 09:00:44 PDT)
    - Re: [AMBER] temperature not reaching target value in heating simulation David A Case (Mon Jun 03 2019 - 04:58:06 PDT)
    - Re: [AMBER] temperature not reaching target value in heating simulation Vaibhav Dixit (Mon Jun 03 2019 - 05:22:23 PDT)
    - Re: [AMBER] temperature not reaching target value in heating simulation David A Case (Mon Jun 03 2019 - 08:59:26 PDT)
    - Re: [AMBER] temperature not reaching target value in heating simulation Vaibhav Dixit (Mon Jun 03 2019 - 11:27:12 PDT)
    - Re: [AMBER] temperature not reaching target value in heating simulation David A Case (Tue Jun 04 2019 - 05:05:30 PDT)
[AMBER] Error analysis of a trajetory Keiran Corbett (Sun Jun 02 2019 - 07:00:26 PDT)
- Re: [AMBER] Error analysis of a trajetory David A Case (Mon Jun 03 2019 - 05:03:39 PDT)
[AMBER] Paramfit non-gaff atom problem Erdem Yeler (Sun Jun 02 2019 - 08:22:06 PDT)
[AMBER] Some errors for the membrane system xmgign.126.com (Sun Jun 02 2019 - 20:32:00 PDT)
- Re: [AMBER] Some errors for the membrane system Maximilien BERNE (Mon Jun 03 2019 - 02:28:05 PDT)
[AMBER] Ab initio MD in AMBER Nikolay N. Kuzmich (Mon Jun 03 2019 - 06:19:01 PDT)
- Re: [AMBER] Ab initio MD in AMBER David A Case (Mon Jun 03 2019 - 09:04:33 PDT)
- Re: [AMBER] Ab initio MD in AMBER Nikolay N. Kuzmich (Tue Jun 04 2019 - 05:45:37 PDT)
  - Re: [AMBER] Ab initio MD in AMBER Pratul Agarwal (Tue Jun 04 2019 - 06:03:46 PDT)
- Re: [AMBER] Ab initio MD in AMBER Nikolay N. Kuzmich (Wed Jun 05 2019 - 05:10:39 PDT)
  - Re: [AMBER] Ab initio MD in AMBER Pratul Agarwal (Wed Jun 05 2019 - 08:32:32 PDT)
[AMBER] tleap ERROR Sadaf Rani (Mon Jun 03 2019 - 07:24:51 PDT)
- Re: [AMBER] tleap ERROR Gerardo Zerbetto De Palma (Mon Jun 03 2019 - 08:54:51 PDT)
  - Re: [AMBER] tleap ERROR Aidan Reynolds (Mon Jun 03 2019 - 08:57:43 PDT)
    - Re: [AMBER] tleap ERROR Sadaf Rani (Mon Jun 03 2019 - 10:19:45 PDT)
    - Re: [AMBER] tleap ERROR Gerardo Zerbetto De Palma (Mon Jun 03 2019 - 10:31:18 PDT)
    - Re: [AMBER] tleap ERROR Gerardo Zerbetto De Palma (Mon Jun 03 2019 - 10:32:56 PDT)
    - Re: [AMBER] tleap ERROR Sadaf Rani (Tue Jun 04 2019 - 05:15:01 PDT)
    - Re: [AMBER] tleap ERROR Matias Machado (Tue Jun 04 2019 - 09:11:42 PDT)
    - Re: [AMBER] tleap ERROR David A Case (Tue Jun 04 2019 - 12:31:07 PDT)
    - Re: [AMBER] tleap ERROR Vaibhav Dixit (Mon Jun 03 2019 - 10:30:09 PDT)
    - Re: [AMBER] tleap ERROR Matias Machado (Mon Jun 03 2019 - 15:27:19 PDT)
- Re: [AMBER] tleap ERROR David A Case (Mon Jun 03 2019 - 09:06:21 PDT)
[AMBER] AMBER to RCSB pdb format for analysis in other tools like LeView Vaibhav Dixit (Tue Jun 04 2019 - 03:00:27 PDT)
- Re: [AMBER] AMBER to RCSB pdb format for analysis in other tools like LeView David A Case (Tue Jun 04 2019 - 05:11:39 PDT)
  - Re: [AMBER] AMBER to RCSB pdb format for analysis in other tools like LeView Vaibhav Dixit (Tue Jun 04 2019 - 06:12:24 PDT)
    - Re: [AMBER] AMBER to RCSB pdb format for analysis in other tools like LeView Vaibhav Dixit (Wed Jun 19 2019 - 06:11:48 PDT)
    - Re: [AMBER] AMBER to RCSB pdb format for analysis in other tools like LeView Vaibhav Dixit (Wed Jun 19 2019 - 14:42:25 PDT)
[AMBER] Double metal ion parameterization using MCPB.py Abhilash J (Tue Jun 04 2019 - 03:02:26 PDT)
- Re: [AMBER] Double metal ion parameterization using MCPB.py Pengfei Li (Sat Jun 15 2019 - 17:57:07 PDT)
[AMBER] File missing in the apr tutorial Zhiyi Wu (Tue Jun 04 2019 - 03:53:51 PDT)
- Re: [AMBER] File missing in the apr tutorial David Case (Sat Jun 15 2019 - 05:56:13 PDT)
- Re: [AMBER] File missing in the apr tutorial David Slochower (Wed Jun 19 2019 - 11:26:34 PDT)
[AMBER] Convergence issues in QM/MM simulations involving charge separation Anthony Bogetti (Tue Jun 04 2019 - 07:29:01 PDT)
- Re: [AMBER] Convergence issues in QM/MM simulations involving charge separation David A Case (Fri Jun 07 2019 - 11:24:50 PDT)
[AMBER] Cpptraj RMSF Lod King (Tue Jun 04 2019 - 10:10:49 PDT)
- Re: [AMBER] Cpptraj RMSF Daniel Roe (Tue Jun 04 2019 - 10:29:15 PDT)
[AMBER] Write out box dimensions in the trajectory Yuan Hu (Tue Jun 04 2019 - 10:43:35 PDT)
- Re: [AMBER] Write out box dimensions in the trajectory Daniel Roe (Tue Jun 04 2019 - 11:56:52 PDT)
  - Re: [AMBER] Write out box dimensions in the trajectory Yuan Hu (Wed Jun 05 2019 - 08:16:13 PDT)
[AMBER] Quantum mechanical models for proton transfer studies in AMBER Margarita I. Bernal-Uruchurtu (Wed Jun 05 2019 - 02:27:50 PDT)
[AMBER] Most recent GAFF version to use? Melania T (Wed Jun 05 2019 - 14:17:18 PDT)
- Re: [AMBER] Most recent GAFF version to use? David A Case (Thu Jun 06 2019 - 06:55:34 PDT)
  - Re: [AMBER] Most recent GAFF version to use? Matias Machado (Thu Jun 06 2019 - 08:50:28 PDT)
    - Re: [AMBER] Most recent GAFF version to use? Niel Henriksen (Fri Jun 07 2019 - 12:01:49 PDT)
    - Re: [AMBER] Most recent GAFF version to use? Matias Machado (Fri Jun 07 2019 - 13:12:51 PDT)
  - Re: [AMBER] Most recent GAFF version to use? Melania T (Thu Jun 06 2019 - 22:54:37 PDT)
[AMBER] How to Calculate Frequency Analysis and Intermolecular Energies by Using Amber Erdem Yeler (Wed Jun 05 2019 - 14:59:21 PDT)
[AMBER] Amber 18 licence Sadaf Rani (Thu Jun 06 2019 - 05:01:57 PDT)
- Re: [AMBER] Amber 18 licence Carlos Simmerling (Thu Jun 06 2019 - 05:27:40 PDT)
  - Re: [AMBER] Amber 18 licence Sadaf Rani (Thu Jun 06 2019 - 14:40:40 PDT)
[AMBER] convert AMBER files to CHARMM emanuele falbo (Thu Jun 06 2019 - 06:06:36 PDT)
[AMBER] multi gpu run using MPI Hossein Pourreza (Thu Jun 06 2019 - 13:35:20 PDT)
- Re: [AMBER] multi gpu run using MPI Ross Walker (Tue Jun 11 2019 - 06:10:30 PDT)
  - Re: [AMBER] multi gpu run using MPI Hossein Pourreza (Tue Jun 11 2019 - 06:12:33 PDT)
[AMBER] Costant ph simulation for Small molecules Stefano Motta (Fri Jun 07 2019 - 02:22:23 PDT)
- Re: [AMBER] Costant ph simulation for Small molecules Marcos Serrou do Amaral (Fri Jun 07 2019 - 03:31:12 PDT)
[AMBER] CpHMD usage cpimenta (Fri Jun 07 2019 - 03:08:03 PDT)
- Re: [AMBER] CpHMD usage Cruzeiro,Vinicius Wilian D (Fri Jun 07 2019 - 10:10:27 PDT)
[AMBER] propka web server Sadaf Rani (Fri Jun 07 2019 - 10:17:55 PDT)
- Re: [AMBER] propka web server Matias Machado (Fri Jun 07 2019 - 10:29:31 PDT)
  - Re: [AMBER] propka web server Sadaf Rani (Sat Jun 08 2019 - 05:27:11 PDT)
    - Re: [AMBER] propka web server Matias Machado (Sat Jun 08 2019 - 13:30:47 PDT)
[AMBER] Regular Ewald calculations on GPU Nikolay N. Kuzmich (Fri Jun 07 2019 - 10:35:33 PDT)
- Re: [AMBER] Regular Ewald calculations on GPU David A Case (Fri Jun 07 2019 - 11:19:45 PDT)
- Re: [AMBER] Regular Ewald calculations on GPU Nikolay N. Kuzmich (Sat Jun 08 2019 - 07:26:36 PDT)
[AMBER] cpptraj hbond between ligand protein/wat Vaibhav Dixit (Sat Jun 08 2019 - 05:24:37 PDT)
- Re: [AMBER] cpptraj hbond between ligand protein/wat Daniel Roe (Mon Jun 10 2019 - 05:32:29 PDT)
[AMBER] Gromacs-4.6 to Amber Parameter Conversion Mohammed I Sorour (Sun Jun 09 2019 - 16:03:05 PDT)
[AMBER] substitution of fluorine atom at o9 hydroxyl group sialic acid by using glycam force field -reg Jeyaram R A (Sun Jun 09 2019 - 22:30:32 PDT)
[AMBER] ff14IDPs and ffIDPSFF Lod King (Tue Jun 11 2019 - 01:12:55 PDT)
- Re: [AMBER] ff14IDPs and ffIDPSFF Carlos Simmerling (Fri Jun 14 2019 - 06:50:54 PDT)
[AMBER] Atom type for fluorine atom in glycam force field -reg. Jeyaram R A (Tue Jun 11 2019 - 05:39:49 PDT)
- Re: [AMBER] Atom type for fluorine atom in glycam force field -reg. Stephan Schott (Tue Jun 11 2019 - 06:33:45 PDT)
- Re: [AMBER] Atom type for fluorine atom in glycam force field -reg. David Case (Tue Jun 11 2019 - 08:30:35 PDT)
- Re: [AMBER] Atom type for fluorine atom in glycam force field -reg. Stephan Schott (Tue Jun 11 2019 - 09:32:52 PDT)
  - Re: [AMBER] Atom type for fluorine atom in glycam force field -reg. Jeyaram R A (Tue Jun 11 2019 - 21:45:28 PDT)
[AMBER] Urea water mixture Nora Kremer (Tue Jun 11 2019 - 07:16:25 PDT)
- Re: [AMBER] Urea water mixture Matias Machado (Tue Jun 11 2019 - 08:54:06 PDT)
  - Re: [AMBER] Urea water mixture Nora Kremer (Wed Jun 12 2019 - 07:13:58 PDT)
[AMBER] Higher level spline correction to PMF obtain from low-level QM/MM umbrella impelling MOHD HOMAIDUR RAHMAN (Tue Jun 11 2019 - 08:44:11 PDT)
[AMBER] Fwd: Charu Sharma (JRF) (Tue Jun 11 2019 - 11:10:19 PDT)
- Re: [AMBER] Fwd: David Cerutti (Tue Jun 11 2019 - 11:18:40 PDT)
- [AMBER] Fwd: Fwd: please clarify this answer Charu Sharma (JRF) (Wed Jul 03 2019 - 10:22:52 PDT)
  - Re: [AMBER] Fwd: Fwd: please clarify this answer David Case (Wed Jul 03 2019 - 10:48:02 PDT)
[AMBER] AMD with GB solvation Supriyo Bhattacharya (Tue Jun 11 2019 - 12:08:33 PDT)
[AMBER] I have a problem in using LEaP. Rui Chen (Tue Jun 11 2019 - 18:24:45 PDT)
- Re: [AMBER] I have a problem in using LEaP. Rui Chen (Tue Jun 11 2019 - 19:57:48 PDT)
  - Re: [AMBER] I have a problem in using LEaP. Gustaf Olsson (Tue Jun 11 2019 - 21:53:49 PDT)
    - Re: [AMBER] I have a problem in using LEaP. Rui Chen (Wed Jun 12 2019 - 06:12:08 PDT)
    - Re: [AMBER] I have a problem in using LEaP. Gustaf Olsson (Wed Jun 12 2019 - 07:07:51 PDT)
    - Re: [AMBER] I have a problem in using LEaP. Rui Chen (Wed Jun 12 2019 - 08:30:09 PDT)
  - Re: [AMBER] I have a problem in using LEaP. David A Case (Wed Jun 12 2019 - 04:35:47 PDT)
    - Re: [AMBER] I have a problem in using LEaP. Rui Chen (Wed Jun 12 2019 - 05:54:14 PDT)
[AMBER] Non-integer charge problem with tleap using GLYCAM_06EPb but not GLYCAM_06j-1 Barb, Adam [BBMBS] (Wed Jun 12 2019 - 07:12:03 PDT)
- Re: [AMBER] Non-integer charge problem with tleap using GLYCAM_06EPb but not GLYCAM_06j-1 Lachele Foley (Wed Aug 21 2019 - 12:36:10 PDT)
[AMBER] Tleap impose command for boron Erdem Yeler (Wed Jun 12 2019 - 08:21:38 PDT)
- Re: [AMBER] Tleap impose command for boron David A Case (Wed Jun 12 2019 - 09:57:15 PDT)
[AMBER] cpptraj hbond calculation Stefano Motta (Wed Jun 12 2019 - 09:14:09 PDT)
- Re: [AMBER] cpptraj hbond calculation Daniel Roe (Wed Jun 12 2019 - 10:22:22 PDT)
  - Re: [AMBER] cpptraj hbond calculation Daniel Roe (Thu Jun 13 2019 - 06:43:55 PDT)
[AMBER] counting water molecules through transmembrane pore Chetna Tyagi (Wed Jun 12 2019 - 09:09:54 PDT)
- Re: [AMBER] counting water molecules through transmembrane pore Wesley Michael Botello-Smith (Wed Jun 12 2019 - 13:14:38 PDT)
- Re: [AMBER] counting water molecules through transmembrane pore Markowska (Wed Jun 12 2019 - 13:40:04 PDT)
  - Re: [AMBER] counting water molecules through transmembrane pore Chetna Tyagi (Thu Jun 13 2019 - 01:32:42 PDT)
[AMBER] [Amber]-help-messy rst output using Sander Yuwei Song (Wed Jun 12 2019 - 11:13:26 PDT)
- Re: [AMBER] [Amber]-help-messy rst output using Sander David Cerutti (Wed Jun 12 2019 - 12:35:29 PDT)
  - Re: [AMBER] [Amber]-help-messy rst output using Sander David A Case (Thu Jun 13 2019 - 05:00:27 PDT)
[AMBER] Installing amber with CUDA as local user on supercomputer Francesca Lønstad Bleken (Thu Jun 13 2019 - 04:55:30 PDT)
- Re: [AMBER] Installing amber with CUDA as local user on supercomputer Ross Walker (Thu Jun 13 2019 - 07:42:51 PDT)
- Re: [AMBER] Installing amber with CUDA as local user on supercomputer David A Case (Thu Jun 13 2019 - 09:20:12 PDT)
[AMBER] Amber installation error Nisha Amarnath Jonniya (Thu Jun 13 2019 - 05:06:29 PDT)
- Re: [AMBER] Amber installation error David A Case (Thu Jun 13 2019 - 09:25:54 PDT)
  - Re: [AMBER] Amber installation error Nisha Amarnath Jonniya (Fri Jun 14 2019 - 04:38:01 PDT)
[AMBER] Fw: Ligand Parameterization Hira Jabeen (Thu Jun 13 2019 - 05:53:14 PDT)
- Re: [AMBER] Fw: Ligand Parameterization David A Case (Thu Jun 13 2019 - 09:29:54 PDT)
[AMBER] hbond somdev pahari (Thu Jun 13 2019 - 07:39:32 PDT)
- Re: [AMBER] hbond Stefano Motta (Thu Jun 13 2019 - 08:32:31 PDT)
- Re: [AMBER] hbond Daniel Roe (Thu Jun 13 2019 - 08:55:07 PDT)
  - Re: [AMBER] hbond somdev pahari (Thu Jun 13 2019 - 21:56:45 PDT)
    - Re: [AMBER] hbond somdev pahari (Thu Jun 13 2019 - 10:41:47 PDT)
    - Re: [AMBER] hbond Daniel Roe (Thu Jun 13 2019 - 10:57:59 PDT)
    - Re: [AMBER] hbond somdev pahari (Thu Jun 13 2019 - 16:50:59 PDT)
    - Re: [AMBER] hbond Daniel Roe (Thu Jun 13 2019 - 16:26:16 PDT)
    - Re: [AMBER] hbond somdev pahari (Thu Jun 13 2019 - 23:04:51 PDT)
[AMBER] Problem with mol2 file generated by Antechamber Alessandro LANDI (Thu Jun 13 2019 - 07:51:10 PDT)
- Re: [AMBER] Problem with mol2 file generated by Antechamber sribone.fcq.unc.edu.ar (Thu Jun 13 2019 - 08:35:38 PDT)
  - Re: [AMBER] Problem with mol2 file generated by Antechamber Matias Machado (Thu Jun 13 2019 - 09:02:35 PDT)
- Re: [AMBER] Problem with mol2 file generated by Antechamber David Case (Sat Jun 15 2019 - 05:51:31 PDT)
  - Re: [AMBER] Problem with mol2 file generated by Antechamber Alessandro LANDI (Thu Jun 27 2019 - 07:24:24 PDT)
    - Re: [AMBER] Problem with mol2 file generated by Antechamber Matias Machado (Thu Jun 27 2019 - 08:04:28 PDT)
    - Re: [AMBER] Problem with mol2 file generated by Antechamber Daniel Roe (Thu Jun 27 2019 - 08:10:19 PDT)
[AMBER] CU library file Fabian Glaser (Thu Jun 13 2019 - 08:09:25 PDT)
- Re: [AMBER] CU library file Matias Machado (Thu Jun 13 2019 - 08:38:30 PDT)
[AMBER] "Official" / valid Amber-GAFF parameters for 1-octanol Fotis Baltoumas (Thu Jun 13 2019 - 09:45:54 PDT)
[AMBER] DBSCAN CLUSTERING STARTS AT 0 CLUSTERS dnlfr1994.gmail.com (Thu Jun 13 2019 - 10:04:33 PDT)
- Re: [AMBER] DBSCAN CLUSTERING STARTS AT 0 CLUSTERS Daniel Roe (Thu Jun 13 2019 - 12:12:00 PDT)
  - Re: [AMBER] [UCE] Re: DBSCAN CLUSTERING STARTS AT 0 CLUSTERS Thomas Cheatham (Thu Jun 13 2019 - 12:45:45 PDT)
    - Re: [AMBER] [UCE] Re: DBSCAN CLUSTERING STARTS AT 0 CLUSTERS Daniel Roe (Thu Jun 13 2019 - 12:49:45 PDT)
    - Re: [AMBER] [UCE] Re: DBSCAN CLUSTERING STARTS AT 0 CLUSTERS Daniel Fernández Remacha (Thu Jun 13 2019 - 15:01:25 PDT)
    - Re: [AMBER] [UCE] Re: DBSCAN CLUSTERING STARTS AT 0 CLUSTERS Daniel Roe (Fri Jun 14 2019 - 06:46:27 PDT)
    - Re: [AMBER] [UCE] Re: DBSCAN CLUSTERING STARTS AT 0 CLUSTERS dnlfr1994.gmail.com (Mon Jun 17 2019 - 04:43:06 PDT)
    - Re: [AMBER] [UCE] Re: DBSCAN CLUSTERING STARTS AT 0 CLUSTERS Daniel Roe (Tue Jun 18 2019 - 09:19:20 PDT)
[AMBER] Problems using stfcdiffusion Lucas Bandeira (Thu Jun 13 2019 - 11:27:07 PDT)
- Re: [AMBER] Problems using stfcdiffusion Daniel Roe (Thu Jun 13 2019 - 12:53:52 PDT)
  - Re: [AMBER] Problems using stfcdiffusion Lucas Bandeira (Fri Jun 14 2019 - 09:32:21 PDT)
[AMBER] bash: leaprc.protein.ff14SB: No such file or directory Gert Kruger (Thu Jun 13 2019 - 23:17:15 PDT)
- Re: [AMBER] bash: leaprc.protein.ff14SB: No such file or directory Elvis Martis (Thu Jun 13 2019 - 23:40:07 PDT)
  - Re: [AMBER] bash: leaprc.protein.ff14SB: No such file or directory Gert Kruger (Fri Jun 14 2019 - 03:11:23 PDT)
[AMBER] Antechamber Error Akinpelu Olayinka (Fri Jun 14 2019 - 02:44:01 PDT)
- Re: [AMBER] Antechamber Error Elvis Martis (Fri Jun 14 2019 - 04:13:21 PDT)
- Re: [AMBER] Antechamber Error David A Case (Fri Jun 14 2019 - 04:51:45 PDT)
[AMBER] parameterization of ligand+protein complex Hira Jabeen (Fri Jun 14 2019 - 09:09:45 PDT)
- [AMBER] Fw: parameterization of ligand+protein complex Hira Jabeen (Tue Jun 18 2019 - 03:27:53 PDT)
  - Re: [AMBER] Fw: parameterization of ligand+protein complex Daniel Roe (Tue Jun 18 2019 - 09:10:29 PDT)
    - Re: [AMBER] Fw: parameterization of ligand+protein complex Hira Jabeen (Tue Jun 18 2019 - 09:13:58 PDT)
    - Re: [AMBER] Fw: parameterization of ligand+protein complex Daniel Roe (Tue Jun 18 2019 - 09:31:56 PDT)
    - Re: [AMBER] Fw: parameterization of ligand+protein complex Hira Jabeen (Wed Jun 19 2019 - 04:20:19 PDT)
    - Re: [AMBER] Fw: parameterization of ligand+protein complex Matias Machado (Wed Jun 19 2019 - 07:36:34 PDT)
    - Re: [AMBER] Fw: parameterization of ligand+protein complex Hira Jabeen (Thu Jun 20 2019 - 03:54:49 PDT)
    - Re: [AMBER] Fw: parameterization of ligand+protein complex Hira Jabeen (Thu Jun 20 2019 - 04:04:27 PDT)
    - Re: [AMBER] Fw: parameterization of ligand+protein complex David Case (Thu Jun 20 2019 - 06:37:06 PDT)
[AMBER] RMSF phi angle Lod King (Fri Jun 14 2019 - 09:24:18 PDT)
- Re: [AMBER] RMSF phi angle Daniel Roe (Fri Jun 14 2019 - 11:26:27 PDT)
  - Re: [AMBER] RMSF phi angle Lod King (Fri Jun 14 2019 - 11:41:39 PDT)
[AMBER] RMSF CPPTRAJ Lod King (Fri Jun 14 2019 - 09:59:04 PDT)
- Re: [AMBER] RMSF CPPTRAJ Daniel Roe (Thu Jun 20 2019 - 05:41:34 PDT)
  - Re: [AMBER] RMSF CPPTRAJ Lod King (Wed Jun 26 2019 - 18:46:18 PDT)
    - Re: [AMBER] RMSF CPPTRAJ Daniel Roe (Thu Jun 27 2019 - 08:17:59 PDT)
[AMBER] Problems using stfcdiffusion Lucas Bandeira (Fri Jun 14 2019 - 11:22:19 PDT)
[AMBER] Unit of pucker amplitude Charles-Alexandre Mattelaer (Fri Jun 14 2019 - 23:30:33 PDT)
[AMBER] Amplitude of ring puckering Charles-Alexandre Mattelaer (Sat Jun 15 2019 - 05:59:44 PDT)
- Re: [AMBER] Amplitude of ring puckering Daniel Roe (Mon Jun 17 2019 - 12:41:23 PDT)
  - Re: [AMBER] Amplitude of ring puckering Charles-Alexandre Mattelaer (Mon Jun 17 2019 - 12:43:56 PDT)
    - Re: [AMBER] Amplitude of ring puckering Steven M. Graham (Mon Jun 17 2019 - 12:48:07 PDT)
    - Re: [AMBER] Amplitude of ring puckering Daniel Roe (Tue Jun 18 2019 - 09:13:25 PDT)
[AMBER] solvateoct and sovlatebox errors while solvating ligand Vaibhav Dixit (Sun Jun 16 2019 - 01:47:28 PDT)
- Re: [AMBER] solvateoct and sovlatebox errors while solvating ligand David Case (Sun Jun 16 2019 - 06:13:24 PDT)
  - Re: [AMBER] solvateoct and sovlatebox errors while solvating ligand Vaibhav Dixit (Sun Jun 16 2019 - 09:46:47 PDT)
[AMBER] qmmm error Sina (Sun Jun 16 2019 - 08:01:05 PDT)
- Re: [AMBER] qmmm error David A Case (Mon Jun 17 2019 - 04:56:56 PDT)
[AMBER] Using Gaussian 16 as external QM software with amber 14 Anuja Ware (Mon Jun 17 2019 - 04:08:01 PDT)
- Re: [AMBER] Using Gaussian 16 as external QM software with amber 14 Gert Kruger (Mon Jun 17 2019 - 23:19:54 PDT)
  - Re: [AMBER] Using Gaussian 16 as external QM software with amber 14 Anuja Ware (Tue Jun 18 2019 - 09:59:16 PDT)
[AMBER] incorrect dispersion term when radiopt=0: bug found and solved Thomas Gaillard (Mon Jun 17 2019 - 06:18:27 PDT)
[AMBER] Constant pH simulation of PyroPhosphate in Explicit solvent Yuvraj Singh (Mon Jun 17 2019 - 08:58:45 PDT)
- Re: [AMBER] Constant pH simulation of PyroPhosphate in Explicit solvent Cruzeiro,Vinicius Wilian D (Mon Jun 17 2019 - 10:52:03 PDT)
[AMBER] Loop of H1-H2 in ZN6 of ZAFF Hosein Geraili Daronkola (Mon Jun 17 2019 - 09:10:56 PDT)
- Re: [AMBER] Loop of H1-H2 in ZN6 of ZAFF Pengfei Li (Thu Jun 20 2019 - 13:44:42 PDT)
[AMBER] Description of atom types for Ergosterol Lutimba-Stuart (Mon Jun 17 2019 - 12:13:34 PDT)
[AMBER] Problem in creating topology and coordinate files Mustafa Alhaji Isa (Mon Jun 17 2019 - 22:45:20 PDT)
- Re: [AMBER] Problem in creating topology and coordinate files Bill Ross (Mon Jun 17 2019 - 22:47:39 PDT)
  - Re: [AMBER] Problem in creating topology and coordinate files Bill Ross (Mon Jun 17 2019 - 22:49:25 PDT)
- Re: [AMBER] Problem in creating topology and coordinate files Carlos Simmerling (Wed Jun 19 2019 - 04:35:19 PDT)
- Re: [AMBER] Problem in creating topology and coordinate files David Case (Mon Jun 24 2019 - 19:03:50 PDT)
[AMBER] The membran-water system ran out of the box xmgign.126.com (Mon Jun 17 2019 - 23:41:40 PDT)
- Re: [AMBER] The membran-water system ran out of the box Daniel Roe (Tue Jun 18 2019 - 09:09:28 PDT)
[AMBER] QMMM, with NWChem and Amber Francesca Lønstad Bleken (Tue Jun 18 2019 - 05:04:28 PDT)
- Re: [AMBER] QMMM, with NWChem and Amber James Kress (Tue Jun 18 2019 - 09:50:15 PDT)
- Re: [AMBER] QMMM, with NWChem and Amber Francesca Lønstad Bleken (Wed Jun 19 2019 - 00:21:07 PDT)
  - Re: [AMBER] QMMM, with NWChem and Amber Joan Torras (Wed Jun 19 2019 - 06:52:55 PDT)
[AMBER] MM-PBSA Thakur, Abhishek (Tue Jun 18 2019 - 11:09:07 PDT)
- Re: [AMBER] MM-PBSA Xia, Zhonghua (Tue Jun 18 2019 - 11:19:43 PDT)
  - Re: [AMBER] MM-PBSA Thakur, Abhishek (Tue Jun 18 2019 - 11:31:45 PDT)
    - Re: [AMBER] MM-PBSA Xia, Zhonghua (Tue Jun 18 2019 - 11:42:16 PDT)
[AMBER] Adding disulphide bonds. Rui Chen (Tue Jun 18 2019 - 16:21:43 PDT)
- Re: [AMBER] Adding disulphide bonds. David Case (Wed Jun 19 2019 - 09:10:43 PDT)
  - Re: [AMBER] Adding disulphide bonds. Rui Chen (Wed Jun 19 2019 - 14:22:52 PDT)
[AMBER] hbond 谭畅 (Tue Jun 18 2019 - 23:25:51 PDT)
- Re: [AMBER] hbond Daniel Roe (Wed Jun 19 2019 - 03:24:56 PDT)
[AMBER] ff19SB forcefield Nikolay N. Kuzmich (Wed Jun 19 2019 - 01:46:39 PDT)
- Re: [AMBER] ff19SB forcefield Matias Machado (Wed Jun 19 2019 - 09:35:11 PDT)
  - Re: [AMBER] ff19SB forcefield Carlos Simmerling (Wed Jun 19 2019 - 10:27:07 PDT)
[AMBER] Immediate postdoc opening in Bio-molecular simulation, University of Alberta, Canada Marawan Hussien (Wed Jun 19 2019 - 17:17:19 PDT)
[AMBER] problem of CUDA MPI Albert (Thu Jun 20 2019 - 04:08:50 PDT)
- Re: [AMBER] problem of CUDA MPI David Case (Wed Jun 19 2019 - 22:48:53 PDT)
  - Re: [AMBER] problem of CUDA MPI Albert (Thu Jun 20 2019 - 05:39:53 PDT)
    - Re: [AMBER] problem of CUDA MPI Albert (Fri Jun 21 2019 - 08:27:52 PDT)
    - Re: [AMBER] problem of CUDA MPI Daniel Roe (Fri Jun 21 2019 - 11:43:56 PDT)
[AMBER] framed parameters Fabian Glaser (Thu Jun 20 2019 - 05:41:26 PDT)
- Re: [AMBER] framed parameters David Case (Thu Jun 20 2019 - 07:01:40 PDT)
[AMBER] NaN Error Paula Mihaljevic-Juric (Thu Jun 20 2019 - 06:34:50 PDT)
- Re: [AMBER] NaN Error Carlos Simmerling (Thu Jun 20 2019 - 06:52:09 PDT)
  - Re: [AMBER] NaN Error Paula Mihaljevic-Juric (Thu Jun 20 2019 - 07:09:26 PDT)
    - Re: [AMBER] NaN Error Carlos Simmerling (Thu Jun 20 2019 - 07:15:14 PDT)
    - Re: [AMBER] NaN Error Paula Mihaljevic-Juric (Thu Jun 20 2019 - 07:20:52 PDT)
    - Re: [AMBER] NaN Error Josh Berryman (Thu Jun 20 2019 - 07:28:41 PDT)
    - Re: [AMBER] NaN Error Paula Mihaljevic-Juric (Thu Jun 20 2019 - 08:00:11 PDT)
    - Re: [AMBER] NaN Error Josh Berryman (Thu Jun 20 2019 - 08:16:26 PDT)
    - Re: [AMBER] NaN Error Paula Mihaljevic-Juric (Thu Jun 20 2019 - 08:28:41 PDT)
    - Re: [AMBER] NaN Error Carlos Simmerling (Thu Jun 20 2019 - 08:31:11 PDT)
    - Re: [AMBER] NaN Error Thomas Cheatham (Thu Jun 20 2019 - 09:28:02 PDT)
    - Re: [AMBER] NaN Error Josh Berryman (Thu Jun 20 2019 - 11:06:51 PDT)
    - Re: [AMBER] NaN Error Carlos Simmerling (Thu Jun 20 2019 - 07:33:11 PDT)
[AMBER] Insight into CMAP corrections ARITRA MITRA (Thu Jun 20 2019 - 22:40:53 PDT)
- Re: [AMBER] Insight into CMAP corrections Carlos Simmerling (Fri Jun 21 2019 - 07:09:57 PDT)
[AMBER] external electric field Maryam (Fri Jun 21 2019 - 09:22:47 PDT)
[AMBER] Recommended CUDA version for Amber18-19 on RTX GPUs? Yeyue Xiong (Fri Jun 21 2019 - 13:01:53 PDT)
- Re: [AMBER] Recommended CUDA version for Amber18-19 on RTX GPUs? Ross Walker (Sun Jun 23 2019 - 16:21:54 PDT)
[AMBER] GAFF2 Missing parameters - Melania T (Fri Jun 21 2019 - 23:05:57 PDT)
- Re: [AMBER] GAFF2 Missing parameters - David Case (Sun Jun 23 2019 - 06:12:34 PDT)
  - Re: [AMBER] GAFF2 Missing parameters - Melania T (Sun Jun 23 2019 - 10:23:01 PDT)
[AMBER] Antechamber (sqm) charge generation Melania T (Fri Jun 21 2019 - 23:46:25 PDT)
- Re: [AMBER] Antechamber (sqm) charge generation David Case (Sun Jun 23 2019 - 06:05:54 PDT)
  - Re: [AMBER] Antechamber (sqm) charge generation Melania T (Sun Jun 23 2019 - 10:15:48 PDT)
    - Re: [AMBER] Antechamber (sqm) charge generation Melania T (Sun Jun 23 2019 - 12:13:17 PDT)
[AMBER] ambpdb hetatm connectivity only Vaibhav Dixit (Sat Jun 22 2019 - 03:28:54 PDT)
- Re: [AMBER] ambpdb hetatm connectivity only Daniel Roe (Sat Jun 22 2019 - 04:55:59 PDT)
  - Re: [AMBER] ambpdb hetatm connectivity only Vaibhav Dixit (Sat Jun 22 2019 - 07:05:57 PDT)
[AMBER] open valance problem Sadaf Rani (Sat Jun 22 2019 - 06:26:25 PDT)
- Re: [AMBER] open valance problem Elvis Martis (Sat Jun 22 2019 - 20:56:57 PDT)
  - Re: [AMBER] open valance problem Sadaf Rani (Mon Jun 24 2019 - 13:25:51 PDT)
    - Re: [AMBER] open valance problem David Case (Mon Jun 24 2019 - 18:59:20 PDT)
    - Re: [AMBER] open valance problem Sadaf Rani (Tue Jun 25 2019 - 07:34:51 PDT)
    - Re: [AMBER] open valance problem Elvis Martis (Mon Jun 24 2019 - 22:11:29 PDT)
    - Re: [AMBER] open valance problem Sadaf Rani (Tue Jun 25 2019 - 06:47:31 PDT)
    - Re: [AMBER] open valance problem Sadaf Rani (Tue Jun 25 2019 - 09:29:33 PDT)
    - Re: [AMBER] open valance problem Elvis Martis (Tue Jun 25 2019 - 21:53:03 PDT)
    - Re: [AMBER] open valance problem Sadaf Rani (Wed Jun 26 2019 - 14:30:53 PDT)
    - Re: [AMBER] open valance problem Elvis Martis (Wed Jun 26 2019 - 22:02:44 PDT)
[AMBER] sqm.pdb structure Sadaf Rani (Sat Jun 22 2019 - 07:24:59 PDT)
- Re: [AMBER] sqm.pdb structure zmatovic.kg.ac.rs (Sat Jun 22 2019 - 08:18:42 PDT)
  - Re: [AMBER] sqm.pdb structure Sadaf Rani (Sat Jun 22 2019 - 08:35:50 PDT)
    - Re: [AMBER] sqm.pdb structure zmatovic.kg.ac.rs (Sat Jun 22 2019 - 17:26:02 PDT)
    - Re: [AMBER] sqm.pdb structure Sadaf Rani (Mon Jun 24 2019 - 01:59:19 PDT)
[AMBER] Amber mask for harmonic restraints James Starlight (Sun Jun 23 2019 - 11:49:27 PDT)
- Re: [AMBER] Amber mask for harmonic restraints Carlos Simmerling (Mon Jun 24 2019 - 04:18:26 PDT)
- Re: [AMBER] Amber mask for harmonic restraints David A Case (Mon Jun 24 2019 - 05:12:07 PDT)
  - Re: [AMBER] Amber mask for harmonic restraints James Starlight (Mon Jun 24 2019 - 05:39:43 PDT)
[AMBER] Dihedral parameters in a small molecule Prashanth Athri (Sun Jun 23 2019 - 18:18:18 PDT)
[AMBER] Issue installing Amber18 cuda Mahesh kumar Teli (Mon Jun 24 2019 - 02:09:31 PDT)
- Re: [AMBER] Issue installing Amber18 pbsa.cuda David A Case (Mon Jun 24 2019 - 05:18:14 PDT)
  - Re: [AMBER] Issue installing Amber18 pbsa.cuda Mahesh kumar Teli (Mon Jun 24 2019 - 20:03:10 PDT)
    - Re: [AMBER] Issue installing Amber18 pbsa.cuda David A Case (Tue Jun 25 2019 - 05:04:16 PDT)
    - Re: [AMBER] Issue installing Amber18 pbsa.cuda Ray Luo (Tue Jun 25 2019 - 05:51:18 PDT)
    - Re: [AMBER] Issue installing Amber18 pbsa.cuda Ruxi Qi (Wed Jul 10 2019 - 20:34:08 PDT)
[AMBER] Pressure regulation with position restraints Franz Waibl (Mon Jun 24 2019 - 04:07:33 PDT)
- Re: [AMBER] Pressure regulation with position restraints Daniel Roe (Mon Jun 24 2019 - 04:31:01 PDT)
  - Re: [AMBER] Pressure regulation with position restraints Franz Waibl (Mon Jun 24 2019 - 07:13:02 PDT)
    - Re: [AMBER] Pressure regulation with position restraints Jacob Monroe (Mon Jun 24 2019 - 08:13:02 PDT)
    - Re: [AMBER] Pressure regulation with position restraints Franz Waibl (Mon Jun 24 2019 - 11:07:18 PDT)
    - Re: [AMBER] Pressure regulation with position restraints Jacob Monroe (Mon Jun 24 2019 - 11:20:53 PDT)
    - Re: [AMBER] Pressure regulation with position restraints Franz Waibl (Mon Jun 24 2019 - 11:45:08 PDT)
- Re: [AMBER] Pressure regulation with position restraints David A Case (Mon Jun 24 2019 - 05:24:22 PDT)
[AMBER] cyclen derived copper ligand parametrisation Fabian Glaser (Mon Jun 24 2019 - 05:11:27 PDT)
[AMBER] MD Simulation in DMSO Rodriguez, Yoel (Mon Jun 24 2019 - 05:11:53 PDT)
- Re: [AMBER] MD Simulation in DMSO Rodriguez, Yoel (Tue Jul 02 2019 - 01:14:18 PDT)
- Re: [AMBER] MD Simulation in DMSO Gould, Ian R (Tue Jul 02 2019 - 01:23:24 PDT)
  - Re: [AMBER] MD Simulation in DMSO Rodriguez, Yoel (Tue Jul 02 2019 - 11:43:17 PDT)
[AMBER] Heating Error Akinpelu Olayinka (Mon Jun 24 2019 - 07:03:45 PDT)
- Re: [AMBER] Heating Error David A Case (Mon Jun 24 2019 - 08:39:19 PDT)
[AMBER] cuda 10.1 compile warnings Luca Codutti (Mon Jun 24 2019 - 09:19:52 PDT)
- Re: [AMBER] cuda 10.1 compile warnings accuratefreeenergy.gmail.com (Mon Jun 24 2019 - 10:23:27 PDT)
[AMBER] What is the effect of 150mM of salt in simulations? M RCC (Mon Jun 24 2019 - 11:38:50 PDT)
- Re: [AMBER] What is the effect of 150mM of salt in simulations? David Cerutti (Mon Jun 24 2019 - 12:07:20 PDT)
- Re: [AMBER] What is the effect of 150mM of salt in simulations? David A Case (Mon Jun 24 2019 - 12:12:44 PDT)
[AMBER] error in REMD on GPUs Marcela Madrid (Mon Jun 24 2019 - 20:36:11 PDT)
- Re: [AMBER] error in REMD on GPUs Bill Ross (Mon Jun 24 2019 - 21:01:19 PDT)
  - Re: [AMBER] error in REMD on GPUs Bill Ross (Mon Jun 24 2019 - 21:05:10 PDT)
    - Re: [AMBER] error in REMD on GPUs Marcela Madrid (Tue Jun 25 2019 - 06:31:59 PDT)
[AMBER] SPAM calculations in cpptraj Debarati DasGupta (Tue Jun 25 2019 - 06:32:13 PDT)
[AMBER] Correct procedure to perform CpHMD simulations jacob wick (Tue Jun 25 2019 - 06:56:36 PDT)
- Re: [AMBER] Correct procedure to perform CpHMD simulations Cruzeiro, Vinicius (Tue Jun 25 2019 - 10:35:18 PDT)
  - Re: [AMBER] Correct procedure to perform CpHMD simulations jacob wick (Wed Jun 26 2019 - 03:28:09 PDT)
[AMBER] Modeling of flexible enzyme: on the selection of the thermostat James Starlight (Tue Jun 25 2019 - 11:20:29 PDT)
- Re: [AMBER] Modeling of flexible enzyme: on the selection of the thermostat David Cerutti (Tue Jun 25 2019 - 11:51:15 PDT)
- Re: [AMBER] Modeling of flexible enzyme: on the selection of the thermostat James Starlight (Tue Jun 25 2019 - 23:39:33 PDT)
  - Re: [AMBER] Modeling of flexible enzyme: on the selection of the thermostat Matias Machado (Wed Jun 26 2019 - 10:54:33 PDT)
    - Re: [AMBER] Modeling of flexible enzyme: on the selection of the thermostat David Cerutti (Wed Jun 26 2019 - 12:09:07 PDT)
    - Re: [AMBER] Modeling of flexible enzyme: on the selection of the thermostat James Starlight (Thu Jun 27 2019 - 01:18:14 PDT)
    - Re: [AMBER] Modeling of flexible enzyme: on the selection of the thermostat David Cerutti (Thu Jun 27 2019 - 08:34:24 PDT)
    - Re: [AMBER] Modeling of flexible enzyme: on the selection of the thermostat James Starlight (Wed Jul 03 2019 - 06:10:47 PDT)
    - Re: [AMBER] Modeling of flexible enzyme: on the selection of the thermostat David A Case (Wed Jul 03 2019 - 06:54:15 PDT)
    - Re: [AMBER] Modeling of flexible enzyme: on the selection of the thermostat James Starlight (Wed Jul 03 2019 - 06:59:01 PDT)
- Re: [AMBER] Modeling of flexible enzyme: on the selection of the thermostat James Starlight (Thu Jul 04 2019 - 01:05:38 PDT)
[AMBER] how to check if bad contacts exsist after min heat jobs Vaibhav Dixit (Wed Jun 26 2019 - 07:48:24 PDT)
- Re: [AMBER] how to check if bad contacts exsist after min heat jobs Matias Machado (Wed Jun 26 2019 - 11:40:39 PDT)
- Re: [AMBER] how to check if bad contacts exsist after min heat jobs David Case (Wed Jun 26 2019 - 19:11:11 PDT)
  - Re: [AMBER] how to check if bad contacts exsist after min heat jobs Vaibhav Dixit (Thu Jun 27 2019 - 01:11:16 PDT)
    - Re: [AMBER] how to check if bad contacts exsist after min heat jobs Daniel Roe (Thu Jun 27 2019 - 08:14:44 PDT)
    - Re: [AMBER] how to check if bad contacts exsist after min heat jobs Vaibhav Dixit (Thu Jun 27 2019 - 08:46:46 PDT)
- Re: [AMBER] how to check if bad contacts exsist after min heat jobs Vaibhav Dixit (Thu Jun 27 2019 - 07:32:26 PDT)
[AMBER] Problems with iwrap Lucas Bandeira (Wed Jun 26 2019 - 11:26:26 PDT)
- Re: [AMBER] Problems with iwrap Thomas Cheatham (Wed Jun 26 2019 - 16:14:45 PDT)
[AMBER] ntt=9 in pmemd? Kenneth Huang (Wed Jun 26 2019 - 13:07:04 PDT)
- Re: [AMBER] ntt=9 in pmemd? David Cerutti (Wed Jun 26 2019 - 13:15:52 PDT)
  - Re: [AMBER] ntt=9 in pmemd? Kenneth Huang (Wed Jun 26 2019 - 14:08:42 PDT)
    - Re: [AMBER] ntt=9 in pmemd? David Cerutti (Wed Jun 26 2019 - 18:45:24 PDT)
[AMBER] RESTARTED DUE TO LINMIN FAILURE Sadaf Rani (Thu Jun 27 2019 - 08:56:55 PDT)
- Re: [AMBER] RESTARTED DUE TO LINMIN FAILURE Elvis Martis (Thu Jun 27 2019 - 09:23:53 PDT)
  - Re: [AMBER] RESTARTED DUE TO LINMIN FAILURE Sadaf Rani (Thu Jun 27 2019 - 10:58:50 PDT)
    - Re: [AMBER] RESTARTED DUE TO LINMIN FAILURE David Case (Thu Jun 27 2019 - 13:01:09 PDT)
  - Re: [AMBER] RESTARTED DUE TO LINMIN FAILURE Sadaf Rani (Tue Jul 02 2019 - 11:23:31 PDT)
    - Re: [AMBER] RESTARTED DUE TO LINMIN FAILURE David A Case (Wed Jul 03 2019 - 04:49:25 PDT)
    - Re: [AMBER] RESTARTED DUE TO LINMIN FAILURE Sadaf Rani (Thu Jul 04 2019 - 11:59:20 PDT)
- Re: [AMBER] RESTARTED DUE TO LINMIN FAILURE David Case (Fri Jun 28 2019 - 05:24:07 PDT)
[AMBER] Adding inhomogeneous force Mohammad Hassan Khatami (Thu Jun 27 2019 - 10:59:40 PDT)
- [AMBER] Adding external forces to amber Mohammad Hassan Khatami (Sat Jul 06 2019 - 06:59:49 PDT)
  - Re: [AMBER] Adding external forces to amber Matias Machado (Sat Jul 06 2019 - 12:22:22 PDT)
    - Re: [AMBER] Adding external forces to amber Mohammad Hassan Khatami (Sat Jul 06 2019 - 12:47:17 PDT)
    - Re: [AMBER] Adding external forces to amber Mohammad Hassan Khatami (Mon Jul 08 2019 - 06:25:22 PDT)
    - Re: [AMBER] Adding external forces to amber Matias Machado (Mon Jul 08 2019 - 13:13:59 PDT)
    - Re: [AMBER] Adding external forces to amber David Case (Tue Jul 09 2019 - 06:27:10 PDT)
    - Re: [AMBER] Adding external forces to amber Mohammad Hassan Khatami (Tue Jul 09 2019 - 06:30:43 PDT)
    - [AMBER] Confined box for implicit solvent simulations Mohammad Hassan Khatami (Tue Jul 23 2019 - 11:10:06 PDT)
    - Re: [AMBER] Confined box for implicit solvent simulations David Cerutti (Tue Jul 23 2019 - 11:49:37 PDT)
    - Re: [AMBER] Confined box for implicit solvent simulations Mohammad Hassan Khatami (Tue Jul 23 2019 - 12:23:27 PDT)
    - Re: [AMBER] Confined box for implicit solvent simulations David Cerutti (Tue Jul 23 2019 - 12:42:48 PDT)
[AMBER] Program received signal SIGSEGV: Segmentation fault - invalid memory reference. error Sadaf Rani (Thu Jun 27 2019 - 12:09:22 PDT)
- Re: [AMBER] Program received signal SIGSEGV: Segmentation fault - invalid memory reference. error David Case (Fri Jun 28 2019 - 05:27:07 PDT)
[AMBER] mmpbsa/entropy frames Alen Ahmetovic (Thu Jun 27 2019 - 20:15:31 PDT)
- Re: [AMBER] mmpbsa/entropy frames David Case (Fri Jun 28 2019 - 05:37:57 PDT)
  - Re: [AMBER] mmpbsa/entropy frames Alen Ahmetovic (Fri Jun 28 2019 - 13:27:37 PDT)
[AMBER] How can we simulate only the ligand-bound domain of the protein? Chetna Tyagi (Fri Jun 28 2019 - 05:15:59 PDT)
- Re: [AMBER] How can we simulate only the ligand-bound domain of the protein? David Case (Sun Jun 30 2019 - 05:32:31 PDT)
- Re: [AMBER] How can we simulate only the ligand-bound domain of the protein? Supriyo Bhattacharya (Sun Jun 30 2019 - 11:43:41 PDT)
  - Re: [AMBER] How can we simulate only the ligand-bound domain of the protein? Supriyo Bhattacharya (Sun Jun 30 2019 - 12:04:52 PDT)
[AMBER] stopping antechamber Andrew Bostick (Fri Jun 28 2019 - 08:50:47 PDT)
- Re: [AMBER] stopping antechamber zmatovic.kg.ac.rs (Fri Jun 28 2019 - 12:41:51 PDT)
[AMBER] Extract potential energy of ligand Akshay Prabhakant (Fri Jun 28 2019 - 11:51:29 PDT)
[AMBER] changes in periodic box dimensions after pmemd.cuda run Violeta Burns Casamayor (Fri Jun 28 2019 - 17:26:42 PDT)
- Re: [AMBER] changes in periodic box dimensions after pmemd.cuda run Chris Neale (Fri Jun 28 2019 - 23:46:57 PDT)
  - Re: [AMBER] changes in periodic box dimensions after pmemd.cuda run Violeta Burns Casamayor (Mon Jul 01 2019 - 10:12:29 PDT)
[AMBER] Error: "System must be very inhomogeneous" Lucas Bandeira (Sat Jun 29 2019 - 09:59:13 PDT)
- Re: [AMBER] Error: "System must be very inhomogeneous" Gustaf Olsson (Sat Jun 29 2019 - 23:43:34 PDT)
- Re: [AMBER] Error: "System must be very inhomogeneous" David Case (Sun Jun 30 2019 - 05:28:02 PDT)
  - Re: [AMBER] Error: "System must be very inhomogeneous" Lucas Bandeira (Mon Jul 01 2019 - 09:33:42 PDT)
    - Re: [AMBER] Error: "System must be very inhomogeneous" Gustaf Olsson (Mon Jul 01 2019 - 22:16:38 PDT)
[AMBER] leap chirally mirrored and flipped the first half of my weekend Bill Ross (Sun Jun 30 2019 - 03:04:51 PDT)
[AMBER] Regarding nmode error Rajarshi Roy (Sun Jun 30 2019 - 07:24:31 PDT)
- Re: [AMBER] Regarding nmode error David A Case (Mon Jul 01 2019 - 05:57:14 PDT)
  - Re: [AMBER] Regarding nmode error Rajarshi Roy (Mon Jul 01 2019 - 06:49:01 PDT)
[AMBER] RESP charge calculation Sadaf Rani (Mon Jul 01 2019 - 03:39:39 PDT)
- Re: [AMBER] RESP charge calculation Elvis Martis (Mon Jul 01 2019 - 04:21:09 PDT)
  - Re: [AMBER] RESP charge calculation Sadaf Rani (Mon Jul 01 2019 - 07:35:11 PDT)
    - Re: [AMBER] RESP charge calculation Elvis Martis (Mon Jul 01 2019 - 08:24:42 PDT)
    - Re: [AMBER] RESP charge calculation Sadaf Rani (Mon Jul 01 2019 - 09:37:22 PDT)
    - Re: [AMBER] RESP charge calculation David Cerutti (Mon Jul 01 2019 - 09:56:40 PDT)
    - Re: [AMBER] RESP charge calculation Sadaf Rani (Mon Jul 01 2019 - 12:34:40 PDT)
    - Re: [AMBER] RESP charge calculation David Cerutti (Mon Jul 01 2019 - 12:38:15 PDT)
    - Re: [AMBER] RESP charge calculation Premila Samuel Mohan Dass (Mon Jul 01 2019 - 17:43:40 PDT)
[AMBER] Thermodynamic information of RISM Eugene huh (Mon Jul 01 2019 - 04:12:20 PDT)
- Re: [AMBER] Thermodynamic information of RISM Tyler Luchko (Lists) (Mon Jul 01 2019 - 10:09:15 PDT)
[AMBER] AMBER G09 RESP Calculation problem Gustaf Olsson (Mon Jul 01 2019 - 04:22:54 PDT)
- Re: [AMBER] AMBER G09 RESP Calculation problem Gustaf Olsson (Mon Jul 01 2019 - 05:07:30 PDT)
[AMBER] Antechamber Charge Methods Sofia Vasilakaki (Mon Jul 01 2019 - 07:26:10 PDT)
- Re: [AMBER] Antechamber Charge Methods David A Case (Mon Jul 01 2019 - 13:20:06 PDT)
  - Re: [AMBER] Antechamber Charge Methods Sofia Vasilakaki (Mon Jul 01 2019 - 14:08:02 PDT)
    - Re: [AMBER] Antechamber Charge Methods Melania T (Mon Jul 01 2019 - 16:56:53 PDT)
[AMBER] REMD error Marcela Madrid (Mon Jul 01 2019 - 17:13:24 PDT)
- Re: [AMBER] REMD error David A Case (Tue Jul 02 2019 - 06:01:15 PDT)
  - Re: [AMBER] REMD error Marcela Madrid (Tue Jul 02 2019 - 06:57:43 PDT)
    - Re: [AMBER] REMD error koushik kasavajhala (Tue Jul 02 2019 - 08:56:32 PDT)
    - Re: [AMBER] REMD error Marcela Madrid (Tue Jul 02 2019 - 11:59:04 PDT)
    - Re: [AMBER] REMD error koushik kasavajhala (Tue Jul 02 2019 - 13:23:29 PDT)
    - Re: [AMBER] REMD error Marcela Madrid (Wed Jul 03 2019 - 12:44:47 PDT)
    - Re: [AMBER] REMD error koushik kasavajhala (Wed Jul 03 2019 - 12:55:59 PDT)
    - Re: [AMBER] REMD error Marcela Madrid (Wed Jul 03 2019 - 13:24:45 PDT)
    - Re: [AMBER] REMD error koushik kasavajhala (Wed Jul 03 2019 - 13:53:44 PDT)
    - Re: [AMBER] REMD error koushik kasavajhala (Wed Jul 03 2019 - 14:21:52 PDT)
    - Re: [AMBER] REMD error Marcela Madrid (Wed Jul 03 2019 - 14:38:25 PDT)
    - Re: [AMBER] REMD error koushik kasavajhala (Wed Jul 03 2019 - 14:49:51 PDT)
    - Re: [AMBER] REMD error Marcela Madrid (Wed Jul 03 2019 - 14:52:19 PDT)
[AMBER] R . E. D Kolattukudy P. Santo (Tue Jul 02 2019 - 06:47:00 PDT)
- Re: [AMBER] R . E. D David A Case (Tue Jul 02 2019 - 10:05:00 PDT)
  - Re: [AMBER] R . E. D Kolattukudy P. Santo (Tue Jul 02 2019 - 10:22:27 PDT)
    - Re: [AMBER] R . E. D ABEL Stephane (Tue Jul 02 2019 - 10:28:30 PDT)
    - Re: [AMBER] R . E. D Kolattukudy P. Santo (Tue Jul 02 2019 - 10:41:40 PDT)
    - Re: [AMBER] R . E. D ABEL Stephane (Tue Jul 02 2019 - 11:03:29 PDT)
    - Re: [AMBER] R . E. D Lachele Foley (Wed Aug 21 2019 - 12:34:09 PDT)
[AMBER] Amberff14sb Dylan Tasse (Tue Jul 02 2019 - 07:52:07 PDT)
[AMBER] memtestG80 alternative ? - testing actual GPUs regarding soft errors Marek Maly (Tue Jul 02 2019 - 08:37:55 PDT)
- Re: [AMBER] memtestG80 alternative ? - testing actual GPUs regarding soft errors Ross Walker (Tue Jul 02 2019 - 18:52:02 PDT)
  - Re: [AMBER] memtestG80 alternative ? - testing actual GPUs regarding soft errors Marek Maly (Wed Jul 03 2019 - 01:41:13 PDT)
  - Re: [AMBER] memtestG80 alternative ? - testing actual GPUs regarding soft errors Dow Hurst (Mon Jul 15 2019 - 11:32:21 PDT)
[AMBER] unwrap in pytraj? Shayna Hilburg (Tue Jul 02 2019 - 13:49:59 PDT)
- Re: [AMBER] unwrap in pytraj? Hai Nguyen (Tue Jul 02 2019 - 13:57:52 PDT)
  - Re: [AMBER] unwrap in pytraj? Shayna Hilburg (Tue Jul 02 2019 - 14:32:04 PDT)
    - Re: [AMBER] unwrap in pytraj? Hai Nguyen (Tue Jul 02 2019 - 15:13:46 PDT)
[AMBER] problem about print_res 谭畅 (Tue Jul 02 2019 - 18:15:52 PDT)
[AMBER] SIGSEVV error on test_at_serial for QMMM interface and miniconda installation problem thrugh amberTools Francesca Lønstad Bleken (Wed Jul 03 2019 - 01:28:11 PDT)
- Re: [AMBER] SIGSEVV error on test_at_serial for QMMM interface and miniconda installation problem thrugh amberTools David A Case (Wed Jul 03 2019 - 05:04:36 PDT)
[AMBER] install Amber16 Bacaita Simona (Wed Jul 03 2019 - 04:47:53 PDT)
- [AMBER] Problems with the miniconda installation David Case (Wed Jul 03 2019 - 11:34:05 PDT)
- Re: [AMBER] install Amber16 David Case (Fri Jul 05 2019 - 05:16:47 PDT)
[AMBER] on the choosing of the cut-off value for PME with Amber14SB James Starlight (Wed Jul 03 2019 - 06:16:52 PDT)
- Re: [AMBER] on the choosing of the cut-off value for PME with Amber14SB David A Case (Wed Jul 03 2019 - 07:03:11 PDT)
[AMBER] Error in prmtop and inpcrd atom shivangi agarwal (Wed Jul 03 2019 - 10:06:19 PDT)
- Re: [AMBER] Error in prmtop and inpcrd atom David Case (Wed Jul 03 2019 - 10:44:59 PDT)
  - Re: [AMBER] Error in prmtop and inpcrd atom shivangi agarwal (Mon Jul 08 2019 - 00:34:23 PDT)
    - Re: [AMBER] Error in prmtop and inpcrd atom Daniel Roe (Mon Jul 08 2019 - 06:28:17 PDT)
    - Re: [AMBER] Error in prmtop and inpcrd atom shivangi agarwal (Mon Jul 08 2019 - 21:03:46 PDT)
    - Re: [AMBER] Error in prmtop and inpcrd atom Elvis Martis (Mon Jul 08 2019 - 21:43:39 PDT)
    - Re: [AMBER] Error in prmtop and inpcrd atom somdev pahari (Mon Jul 08 2019 - 21:54:36 PDT)
    - Re: [AMBER] Error in prmtop and inpcrd atom shivangi agarwal (Tue Jul 09 2019 - 05:45:52 PDT)
    - Re: [AMBER] Error in prmtop and inpcrd atom Santanu Santra (Tue Jul 09 2019 - 05:34:14 PDT)
    - Re: [AMBER] Error in prmtop and inpcrd atom shivangi agarwal (Tue Jul 09 2019 - 06:04:07 PDT)
    - Re: [AMBER] Error in prmtop and inpcrd atom Violeta Burns Casamayor (Tue Jul 09 2019 - 06:20:53 PDT)
    - Re: [AMBER] Error in prmtop and inpcrd atom Santanu Santra (Tue Jul 09 2019 - 06:06:25 PDT)
    - Re: [AMBER] Error in prmtop and inpcrd atom shivangi agarwal (Wed Jul 10 2019 - 00:00:37 PDT)
[AMBER] Glycan naming problem Rui Chen (Wed Jul 03 2019 - 21:28:32 PDT)
- Re: [AMBER] Glycan naming problem Dr. Anselm Horn (Thu Jul 04 2019 - 04:42:37 PDT)
  - Re: [AMBER] Glycan naming problem Rui Chen (Thu Jul 04 2019 - 09:56:37 PDT)
    - Re: [AMBER] Glycan naming problem David A Case (Fri Jul 05 2019 - 08:01:23 PDT)
    - Re: [AMBER] Glycan naming problem Rui Chen (Fri Jul 05 2019 - 08:24:56 PDT)
    - Re: [AMBER] Glycan naming problem Lachele Foley (Wed Aug 21 2019 - 12:40:17 PDT)
    - Re: [AMBER] Glycan naming problem Rui Chen (Wed Aug 21 2019 - 12:51:37 PDT)
    - Re: [AMBER] Glycan naming problem Lachele Foley (Wed Aug 21 2019 - 12:53:42 PDT)
Re: [AMBER] SIGSEVV error on test_at_serial for QMMM Francesca Lønstad Bleken (Wed Jul 03 2019 - 22:42:38 PDT)
- Re: [AMBER] SIGSEVV error on test_at_serial for QMMM David Case (Fri Jul 05 2019 - 05:33:04 PDT)
[AMBER] How to print the total Potential Energy for an atom? Biplab Ghosh (Thu Jul 04 2019 - 02:09:05 PDT)
- Re: [AMBER] How to print the total Potential Energy for an atom? David A Case (Fri Jul 05 2019 - 07:57:03 PDT)
  - Re: [AMBER] How to print the total Potential Energy for an atom? Matias Machado (Fri Jul 05 2019 - 13:57:27 PDT)
[AMBER] How to replicate the number of lipids in bilayer for membrane dynamics Maria Bzówka (Fri Jul 05 2019 - 01:46:01 PDT)
- Re: [AMBER] How to replicate the number of lipids in bilayer for membrane dynamics Vítor Felix (Fri Jul 05 2019 - 02:02:29 PDT)
  - Re: [AMBER] How to replicate the number of lipids in bilayer for membrane dynamics Gustaf Olsson (Fri Jul 05 2019 - 04:10:17 PDT)
[AMBER] parmchk2 and acceptable penalty score Prasanth G, Research Scholar (Fri Jul 05 2019 - 10:08:49 PDT)
- Re: [AMBER] parmchk2 and acceptable penalty score David Case (Mon Jul 08 2019 - 08:27:13 PDT)
- Re: [AMBER] parmchk2 and acceptable penalty score Prasanth G, Research Scholar (Wed Jul 10 2019 - 09:37:18 PDT)
[AMBER] MCPB.py generated parameters in leap SARAH JEANNE LEFAVE (Fri Jul 05 2019 - 10:13:18 PDT)
- Re: [AMBER] MCPB.py generated parameters in leap Pengfei Li (Tue Jul 09 2019 - 19:45:33 PDT)
  - Re: [AMBER] MCPB.py generated parameters in leap SARAH JEANNE LEFAVE (Mon Jul 15 2019 - 15:59:42 PDT)
    - Re: [AMBER] MCPB.py generated parameters in leap Pengfei Li (Mon Jul 22 2019 - 18:48:21 PDT)
    - Re: [AMBER] MCPB.py generated parameters in leap Pengfei Li (Mon Jul 22 2019 - 18:55:03 PDT)
    - Re: [AMBER] MCPB.py generated parameters in leap Pengfei Li (Mon Jul 22 2019 - 18:56:01 PDT)
[AMBER] Fwd: amber installation problem Charu Sharma (JRF) (Sat Jul 06 2019 - 00:26:21 PDT)
- [AMBER] Fwd: amber installation problem Elvis Martis (Sat Jul 06 2019 - 00:32:51 PDT)
  - Re: [AMBER] Fwd: amber installation problem Charu Sharma (JRF) (Sat Jul 06 2019 - 00:34:35 PDT)
    - Re: [AMBER] Fwd: amber installation problem Elvis Martis (Sat Jul 06 2019 - 00:44:28 PDT)
    - Re: [AMBER] Fwd: amber installation problem Charu Sharma (JRF) (Sat Jul 06 2019 - 00:49:35 PDT)
    - Re: [AMBER] Fwd: amber installation problem Elvis Martis (Sat Jul 06 2019 - 00:54:25 PDT)
    - Re: [AMBER] Fwd: amber installation problem Charu Sharma (JRF) (Sat Jul 06 2019 - 03:23:29 PDT)
- Re: [AMBER] Fwd: amber installation problem Charu Sharma (JRF) (Sat Jul 06 2019 - 03:24:15 PDT)
  - Re: [AMBER] Fwd: amber installation problem Bill Ross (Sat Jul 06 2019 - 03:32:51 PDT)
    - Re: [AMBER] Fwd: amber installation problem Charu Sharma (JRF) (Sat Jul 06 2019 - 04:08:23 PDT)
    - Re: [AMBER] Fwd: amber installation problem Elvis Martis (Sat Jul 06 2019 - 04:15:51 PDT)
[AMBER] Fwd: Charu Sharma (JRF) (Sat Jul 06 2019 - 04:20:57 PDT)
- Re: [AMBER] Fwd: Elvis Martis (Sat Jul 06 2019 - 04:34:47 PDT)
  - Re: [AMBER] Fwd: Bill Ross (Sat Jul 06 2019 - 05:23:13 PDT)
- Re: [AMBER] Fwd: Bill Ross (Sat Jul 06 2019 - 05:20:30 PDT)
- Re: [AMBER] Fwd: Gustaf Olsson (Mon Jul 08 2019 - 02:10:31 PDT)
[AMBER] GROMACS to AMBER .top and .pdb conversion using gromber cpimenta (Sat Jul 06 2019 - 04:56:44 PDT)
- Re: [AMBER] GROMACS to AMBER .top and .pdb conversion using gromber Jason Swails (Mon Sep 09 2019 - 08:57:50 PDT)
Re: [AMBER] Perturbing residue co-ordinates within a solvated truncated octohedral box David Case (Sun Jul 07 2019 - 04:34:41 PDT)
[AMBER] RESP charges Sadaf Rani (Sun Jul 07 2019 - 11:45:38 PDT)
- Re: [AMBER] RESP charges David Case (Tue Jul 09 2019 - 06:28:40 PDT)
  - Re: [AMBER] RESP charges Sadaf Rani (Thu Jul 11 2019 - 05:36:52 PDT)
    - Re: [AMBER] RESP charges Kellon Belfon (Thu Jul 11 2019 - 07:18:53 PDT)
    - Re: [AMBER] RESP charges Kellon Belfon (Thu Jul 11 2019 - 07:27:23 PDT)
    - Re: [AMBER] RESP charges Sadaf Rani (Thu Jul 11 2019 - 08:49:25 PDT)
    - Re: [AMBER] RESP charges Kellon Belfon (Thu Jul 11 2019 - 09:51:48 PDT)
[AMBER] closest distance between ligand and particular amino-acid residues during MD simulation Rinsha Chk (Mon Jul 08 2019 - 04:28:44 PDT)
- Re: [AMBER] closest distance between ligand and particular amino-acid residues during MD simulation Daniel Roe (Mon Jul 08 2019 - 06:32:10 PDT)
  - Re: [AMBER] closest distance between ligand and particular amino-acid residues during MD simulation Rinsha Chk (Tue Jul 09 2019 - 03:20:17 PDT)
[AMBER] EPW "ATOMS Moving too fast" - TIP4PEW Bowman, Jacob (Mon Jul 08 2019 - 10:25:03 PDT)
- Re: [AMBER] EPW "ATOMS Moving too fast" - TIP4PEW Carlos Simmerling (Mon Jul 08 2019 - 10:29:40 PDT)
  - Re: [AMBER] EPW "ATOMS Moving too fast" - TIP4PEW Bowman, Jacob (Mon Jul 08 2019 - 10:33:24 PDT)
    - Re: [AMBER] EPW "ATOMS Moving too fast" - TIP4PEW Carlos Simmerling (Mon Jul 08 2019 - 11:41:15 PDT)
- Re: [AMBER] EPW "ATOMS Moving too fast" - TIP4PEW David Case (Mon Jul 08 2019 - 15:02:49 PDT)
[AMBER] Export command not found (export CUDA_VISIBLE_DEVICES) Amen Shamim (Mon Jul 08 2019 - 11:05:54 PDT)
- Re: [AMBER] Export command not found (export CUDA_VISIBLE_DEVICES) Supriyo Bhattacharya (Mon Jul 08 2019 - 11:44:27 PDT)
  - Re: [AMBER] Export command not found (export CUDA_VISIBLE_DEVICES) Bill Ross (Mon Jul 08 2019 - 13:40:56 PDT)
- Re: [AMBER] Export command not found (export CUDA_VISIBLE_DEVICES) Ross Walker (Mon Jul 08 2019 - 19:24:39 PDT)
[AMBER] Fwd: Charu Sharma (JRF) (Tue Jul 09 2019 - 01:08:47 PDT)
- Re: [AMBER] Fwd: Bill Ross (Tue Jul 09 2019 - 01:58:07 PDT)
  - Re: [AMBER] Fwd: Charu Sharma (JRF) (Tue Jul 09 2019 - 04:02:23 PDT)
    - Re: [AMBER] Fwd: Roitberg,Adrian E (Tue Jul 09 2019 - 04:06:54 PDT)
    - [AMBER] Fwd: Fwd: Charu Sharma (JRF) (Tue Jul 09 2019 - 04:08:47 PDT)
    - Re: [AMBER] Fwd: Elvis Martis (Tue Jul 09 2019 - 05:06:08 PDT)
[AMBER] Constant pH MD + HMR Nikolay N. Kuzmich (Tue Jul 09 2019 - 04:43:25 PDT)
- Re: [AMBER] Constant pH MD + HMR Marcos Serrou do Amaral (Tue Jul 30 2019 - 10:04:40 PDT)
- Re: [AMBER] Constant pH MD + HMR Jason Swails (Fri Aug 02 2019 - 21:50:07 PDT)
[AMBER] Fwd: Charu Sharma (JRF) (Tue Jul 09 2019 - 06:43:31 PDT)
- Re: [AMBER] Fwd: ATUL KUMAR (Tue Jul 09 2019 - 06:47:49 PDT)
[AMBER] mpirun <defunct> with pmemd.cuda.MPI on EXXACT systems Jardin, Christophe Dr. (Tue Jul 09 2019 - 06:57:48 PDT)
[AMBER] amber14sb.ff Dylan Tasse (Tue Jul 09 2019 - 07:41:45 PDT)
- Re: [AMBER] amber14sb.ff David Cerutti (Tue Jul 09 2019 - 07:53:48 PDT)
  - Re: [AMBER] amber14sb.ff Dylan Tasse (Tue Jul 09 2019 - 08:00:39 PDT)
  - Re: [AMBER] amber14sb.ff Carlos Simmerling (Tue Jul 09 2019 - 08:26:39 PDT)
[AMBER] There is a bond of 8.882728 angstroms between: [Blank] Anthony Bogetti (Tue Jul 09 2019 - 08:40:58 PDT)
- Re: [AMBER] There is a bond of 8.882728 angstroms between: [Blank] Carlos Simmerling (Tue Jul 09 2019 - 08:43:42 PDT)
  - Re: [AMBER] There is a bond of 8.882728 angstroms between: [Blank] Anthony Bogetti (Tue Jul 09 2019 - 08:49:23 PDT)
    - Re: [AMBER] There is a bond of 8.882728 angstroms between: [Blank] Anthony Bogetti (Tue Jul 09 2019 - 08:52:26 PDT)
    - Re: [AMBER] There is a bond of 8.882728 angstroms between: [Blank] Carlos Simmerling (Tue Jul 09 2019 - 09:15:54 PDT)
    - Re: [AMBER] There is a bond of 8.882728 angstroms between: [Blank] David Cerutti (Tue Jul 09 2019 - 09:34:23 PDT)
    - Re: [AMBER] There is a bond of 8.882728 angstroms between: [Blank] Carlos Simmerling (Tue Jul 09 2019 - 10:04:15 PDT)
    - Re: [AMBER] There is a bond of 8.882728 angstroms between: [Blank] Anthony Bogetti (Tue Jul 09 2019 - 10:34:58 PDT)
    - Re: [AMBER] There is a bond of 8.882728 angstroms between: [Blank] David Case (Wed Jul 10 2019 - 09:30:20 PDT)
- Re: [AMBER] There is a bond of 8.882728 angstroms between: [Blank] David Cerutti (Tue Jul 09 2019 - 08:44:19 PDT)
[AMBER] electrostatic energy of mmgbsa decomposition 谭畅 (Wed Jul 10 2019 - 00:49:48 PDT)
- Re: [AMBER] electrostatic energy of mmgbsa decomposition Josh Berryman (Wed Jul 10 2019 - 02:38:04 PDT)
  - Re: [AMBER] electrostatic energy of mmgbsa decomposition 谭畅 (Wed Jul 10 2019 - 04:06:37 PDT)
    - Re: [AMBER] electrostatic energy of mmgbsa decomposition Josh Berryman (Thu Jul 11 2019 - 04:49:10 PDT)
[AMBER] Compiling MPI 3D-RISM Rakesh Srivastava (Wed Jul 10 2019 - 03:50:07 PDT)
- Re: [AMBER] Compiling MPI 3D-RISM Tyler Luchko (Wed Jul 10 2019 - 08:02:59 PDT)
  - Re: [AMBER] Compiling MPI 3D-RISM Rakesh Srivastava (Wed Jul 10 2019 - 11:07:51 PDT)
    - Re: [AMBER] Compiling MPI 3D-RISM David Case (Wed Jul 10 2019 - 14:45:01 PDT)
[AMBER] To stop the message service Vishnudatt Pandey (Wed Jul 10 2019 - 03:57:29 PDT)
[AMBER] About -dr option in Antechamber Alan (Wed Jul 10 2019 - 04:53:19 PDT)
- Re: [AMBER] About -dr option in Antechamber David Case (Wed Jul 10 2019 - 09:34:38 PDT)
  - Re: [AMBER] About -dr option in Antechamber Alan (Wed Jul 10 2019 - 14:25:35 PDT)
[AMBER] How to generate topology file for protein-ATP complex 李耀 (Wed Jul 10 2019 - 07:51:54 PDT)
- Re: [AMBER] How to generate topology file for protein-ATP complex Zachary Fallon (Wed Jul 10 2019 - 09:54:24 PDT)
[AMBER] Significant deviation in electrostatics, (EEL/EGL values) Aswin Hanagal (Wed Jul 10 2019 - 08:11:56 PDT)
[AMBER] salt concentration in the production run and MMPBSA Prasanth G, Research Scholar (Wed Jul 10 2019 - 09:50:55 PDT)
[AMBER] conformational sampling for organic/drug-like compounds Vaibhav Dixit (Wed Jul 10 2019 - 11:16:12 PDT)
[AMBER] Cluster Analysis with CPPTRAJ Lod King (Wed Jul 10 2019 - 19:39:45 PDT)
- Re: [AMBER] Cluster Analysis with CPPTRAJ Elvis Martis (Wed Jul 10 2019 - 20:09:07 PDT)
  - Re: [AMBER] Cluster Analysis with CPPTRAJ Lod King (Wed Jul 10 2019 - 22:02:52 PDT)
    - Re: [AMBER] Cluster Analysis with CPPTRAJ Elvis Martis (Wed Jul 10 2019 - 22:14:57 PDT)
[AMBER] Query regarding 3D-RISM thermodynamic output format Leena Aggarwal (Wed Jul 10 2019 - 23:46:08 PDT)
- Re: [AMBER] Query regarding 3D-RISM thermodynamic output format Rakesh Srivastava (Wed Jul 10 2019 - 23:51:49 PDT)
  - Re: [AMBER] Query regarding 3D-RISM thermodynamic output format Leena Aggarwal (Wed Jul 10 2019 - 23:56:46 PDT)
[AMBER] vlimit exceeded and volume of ucell too big, too many subcells during adQM/MM dynamics Ruth Helena Tichauer (Thu Jul 11 2019 - 00:36:30 PDT)
- Re: [AMBER] vlimit exceeded and volume of ucell too big, too many subcells during adQM/MM dynamics Ruth Helena Tichauer (Thu Jul 11 2019 - 00:39:25 PDT)
[AMBER] PM6 charges for MD with AMBER Thomas Evangelidis (Thu Jul 11 2019 - 02:52:34 PDT)
- Re: [AMBER] PM6 charges for MD with AMBER David Case (Thu Jul 11 2019 - 06:39:37 PDT)
[AMBER] Error in saving prmtop and inpcrd shivangi agarwal (Fri Jul 12 2019 - 01:42:24 PDT)
- Re: [AMBER] Error in saving prmtop and inpcrd Elvis Martis (Fri Jul 12 2019 - 02:14:44 PDT)
  - Re: [AMBER] Error in saving prmtop and inpcrd shivangi agarwal (Fri Jul 12 2019 - 02:11:25 PDT)
    - Re: [AMBER] Error in saving prmtop and inpcrd Aashish Bhatt (Fri Jul 12 2019 - 02:26:55 PDT)
    - Re: [AMBER] Error in saving prmtop and inpcrd Elvis Martis (Fri Jul 12 2019 - 02:34:22 PDT)
    - Re: [AMBER] Error in saving prmtop and inpcrd shivangi agarwal (Fri Jul 12 2019 - 04:15:03 PDT)
    - Re: [AMBER] Error in saving prmtop and inpcrd David Case (Fri Jul 12 2019 - 06:40:33 PDT)
- Re: [AMBER] Error in saving prmtop and inpcrd David Case (Fri Jul 12 2019 - 12:36:21 PDT)
  - Re: [AMBER] Error in saving prmtop and inpcrd shivangi agarwal (Fri Jul 12 2019 - 21:05:59 PDT)
    - Re: [AMBER] Error in saving prmtop and inpcrd Elvis Martis (Fri Jul 12 2019 - 21:22:43 PDT)
    - Re: [AMBER] Error in saving prmtop and inpcrd shivangi agarwal (Fri Jul 12 2019 - 21:17:39 PDT)
    - Re: [AMBER] Error in saving prmtop and inpcrd Elvis Martis (Fri Jul 12 2019 - 21:54:36 PDT)
- Re: [AMBER] Error in saving prmtop and inpcrd shivangi agarwal (Sun Jul 14 2019 - 22:53:27 PDT)
  - Re: [AMBER] Error in saving prmtop and inpcrd David A Case (Mon Jul 15 2019 - 04:21:37 PDT)
[AMBER] Problem with Phenylphosphonic acid Gustaf Olsson (Fri Jul 12 2019 - 06:15:34 PDT)
- Re: [AMBER] Problem with Phenylphosphonic acid David Case (Sun Jul 14 2019 - 05:50:51 PDT)
  - Re: [AMBER] Problem with Phenylphosphonic acid Gustaf Olsson (Sat Jul 20 2019 - 04:51:12 PDT)
    - Re: [AMBER] Problem with Phenylphosphonic acid Gustaf Olsson (Tue Jul 30 2019 - 03:43:46 PDT)
[AMBER] CUDA errors on a 700k system Dmitry Suplatov (Sun Jul 14 2019 - 11:00:51 PDT)
- Re: [AMBER] CUDA errors on a 700k system Bill Ross (Sun Jul 14 2019 - 11:07:55 PDT)
  - Re: [AMBER] CUDA errors on a 700k system David Cerutti (Sun Jul 14 2019 - 14:25:53 PDT)
[AMBER] Force field for Cecl3, Lacl3 and Prcl3 Satyaseelan C (Mon Jul 15 2019 - 02:04:16 PDT)
- [AMBER] Trajout by distance Pietro Aronica (Mon Jul 15 2019 - 04:03:58 PDT)
  - Re: [AMBER] Trajout by distance Daniel Roe (Mon Jul 15 2019 - 06:31:32 PDT)
- Re: [AMBER] Force field for Cecl3, Lacl3 and Prcl3 David A Case (Mon Jul 15 2019 - 04:30:45 PDT)
  - Re: [AMBER] Force field for Cecl3, Lacl3 and Prcl3 Satyaseelan C (Tue Jul 16 2019 - 03:14:03 PDT)
    - Re: [AMBER] Force field for Cecl3, Lacl3 and Prcl3 Pengfei Li (Wed Aug 14 2019 - 19:15:07 PDT)
[AMBER] How to change the coordinates of the system Maria Bzówka (Mon Jul 15 2019 - 04:32:32 PDT)
- Re: [AMBER] How to change the coordinates of the system Daniel Roe (Mon Jul 15 2019 - 06:26:36 PDT)
  - Re: [AMBER] How to change the coordinates of the system Maria Bzówka (Mon Jul 15 2019 - 06:52:56 PDT)
    - Re: [AMBER] How to change the coordinates of the system ABEL Stephane (Mon Jul 15 2019 - 07:06:24 PDT)
    - Re: [AMBER] How to change the coordinates of the system Daniel Roe (Mon Jul 15 2019 - 07:39:06 PDT)
    - Re: [AMBER] How to change the coordinates of the system Maria Bzówka (Fri Jul 19 2019 - 01:17:05 PDT)
    - Re: [AMBER] How to change the coordinates of the system Daniel Roe (Fri Jul 19 2019 - 02:13:59 PDT)
    - Re: [AMBER] How to change the coordinates of the system Maria Bzówka (Fri Jul 19 2019 - 04:34:55 PDT)
    - Re: [AMBER] How to change the coordinates of the system Daniel Roe (Fri Jul 19 2019 - 05:10:22 PDT)
    - Re: [AMBER] How to change the coordinates of the system Maria Bzówka (Mon Jul 22 2019 - 00:08:36 PDT)
[AMBER] close contact between atoms Sadaf Rani (Mon Jul 15 2019 - 13:22:05 PDT)
- Re: [AMBER] close contact between atoms David A Case (Tue Jul 16 2019 - 04:34:16 PDT)
  - Re: [AMBER] close contact between atoms Sadaf Rani (Tue Jul 16 2019 - 11:38:19 PDT)
    - Re: [AMBER] close contact between atoms Elvis Martis (Tue Jul 16 2019 - 19:30:36 PDT)
[AMBER] Error in MMPBSA calculation Shilpa Gupta (Tue Jul 16 2019 - 00:03:02 PDT)
- Re: [AMBER] Error in MMPBSA calculation rluo.uci.edu (Sat Aug 17 2019 - 06:21:04 PDT)
  - Re: [AMBER] Error in MMPBSA calculation Lei Zhao (Sat Aug 17 2019 - 19:57:54 PDT)
    - Re: [AMBER] Error in MMPBSA calculation Ray Luo (Sun Aug 18 2019 - 07:08:27 PDT)
[AMBER] Recent Force Fields for nucleotides Alessandro LANDI (Tue Jul 16 2019 - 04:11:14 PDT)
- Re: [AMBER] Recent Force Fields for nucleotides Matias Machado (Tue Jul 16 2019 - 08:52:54 PDT)
  - Re: [AMBER] Recent Force Fields for nucleotides David A Case (Tue Jul 16 2019 - 12:26:13 PDT)
  - Re: [AMBER] Recent Force Fields for nucleotides David Cerutti (Tue Jul 16 2019 - 12:29:46 PDT)
    - Re: [AMBER] Recent Force Fields for nucleotides Alessandro LANDI (Wed Jul 17 2019 - 02:24:02 PDT)
[AMBER] Umbrella Sampling: frequency restraint emanuele falbo (Wed Jul 17 2019 - 02:21:35 PDT)
[AMBER] Print out velocities from a restart-crd file Felipe Franco (Wed Jul 17 2019 - 04:36:15 PDT)
- Re: [AMBER] Print out velocities from a restart-crd file Daniel Roe (Thu Jul 18 2019 - 05:07:31 PDT)
[AMBER] Problem with barostat during the production stage (membrane simulation) Maria Bzówka (Wed Jul 17 2019 - 06:10:52 PDT)
- Re: [AMBER] Problem with barostat during the production stage (membrane simulation) David A Case (Wed Jul 17 2019 - 09:18:03 PDT)
  - Re: [AMBER] Problem with barostat during the production stage (membrane simulation) Maria Bzówka (Wed Jul 17 2019 - 09:42:46 PDT)
[AMBER] Covariance Matrix of residues center of mass Guadalupe Alvarez (Wed Jul 17 2019 - 07:42:01 PDT)
- Re: [AMBER] Covariance Matrix of residues center of mass David A Case (Wed Jul 17 2019 - 09:30:56 PDT)
  - Re: [AMBER] Covariance Matrix of residues center of mass Guadalupe Alvarez (Thu Jul 18 2019 - 09:51:39 PDT)
[AMBER] Adding Na+ Anuja Ware (Wed Jul 17 2019 - 08:21:03 PDT)
- Re: [AMBER] Adding Na+ David A Case (Wed Jul 17 2019 - 09:34:24 PDT)
- Re: [AMBER] Adding Na+ emanuele falbo (Wed Jul 17 2019 - 09:40:22 PDT)
  - Re: [AMBER] Adding Na+ Matias Machado (Wed Jul 17 2019 - 10:30:28 PDT)
[AMBER] How to prepare correct gaussian input for RESP charge calculation? Sadaf Rani (Wed Jul 17 2019 - 12:03:34 PDT)
- Re: [AMBER] How to prepare correct gaussian input for RESP charge calculation? David A Case (Thu Jul 18 2019 - 05:22:51 PDT)
  - Re: [AMBER] How to prepare correct gaussian input for RESP charge calculation? Dr. Anselm Horn (Thu Jul 18 2019 - 06:24:54 PDT)
    - Re: [AMBER] How to prepare correct gaussian input for RESP charge calculation? Sadaf Rani (Thu Jul 18 2019 - 13:49:35 PDT)
[AMBER] Error with make test after installing Amber14 and AmberTools15 A K (Wed Jul 17 2019 - 17:30:05 PDT)
- Re: [AMBER] Error with make test after installing Amber14 and AmberTools15 David A Case (Thu Jul 18 2019 - 05:16:19 PDT)
  - Re: [AMBER] Error with make test after installing Amber14 and AmberTools15 A K (Thu Jul 18 2019 - 07:04:18 PDT)
[AMBER] Posits preparing to pounce on Floating Point Bill Ross (Wed Jul 17 2019 - 20:29:52 PDT)
- Re: [AMBER] Posits preparing to pounce on Floating Point Matias Machado (Fri Jul 19 2019 - 09:59:38 PDT)
  - Re: [AMBER] Posits preparing to pounce on Floating Point David Cerutti (Fri Jul 19 2019 - 10:44:02 PDT)
[AMBER] pca - Projecting vectors onto a trajectory Prasanth G, Research Scholar (Thu Jul 18 2019 - 03:40:34 PDT)
[AMBER] Help with parameters for iron centers Sérgio Marques (Thu Jul 18 2019 - 05:00:39 PDT)
- [AMBER] Hydrogen atomic charges of PRO Dr. Anselm Horn (Thu Jul 18 2019 - 07:00:55 PDT)
[AMBER] error in mmpbsa Fransiska Kurniawan (Fri Jul 19 2019 - 02:24:16 PDT)
[AMBER] Error: "Bad data for namelist object statene" with constant pH RE simulation Jardin, Christophe Dr. (Fri Jul 19 2019 - 04:30:12 PDT)
- Re: [AMBER] Error: "Bad data for namelist object statene" with constant pH RE simulation Cruzeiro, Vinicius (Sat Jul 20 2019 - 11:03:14 PDT)
[AMBER] Energy different between igb=0 and igb=6 during vacuum minimization with sander Jingxiao Bao (Fri Jul 19 2019 - 06:52:44 PDT)
Re: [AMBER] New ACPYPE server Matias Machado (Fri Jul 19 2019 - 11:30:51 PDT)
[AMBER] Parameter file for GTP or GMP containing tRNA student_cbc_1 nnlab (Sun Jul 21 2019 - 08:38:11 PDT)
- Re: [AMBER] Parameter file for GTP or GMP containing tRNA Ahmed Elrashedy (Mon Jul 22 2019 - 03:20:06 PDT)
[AMBER] hbond 谭畅 (Mon Jul 22 2019 - 08:45:37 PDT)
[AMBER] Ligand-Resp-Gaussian Prasanth G, Research Scholar (Mon Jul 22 2019 - 09:26:31 PDT)
- Re: [AMBER] Ligand-Resp-Gaussian David Case (Mon Jul 22 2019 - 13:33:51 PDT)
[AMBER] Error in preparing system using AmberTools19 shivangi agarwal (Mon Jul 22 2019 - 09:29:44 PDT)
- Re: [AMBER] Error in preparing system using AmberTools19 James Kress (Mon Jul 22 2019 - 10:55:16 PDT)
  - Re: [AMBER] Error in preparing system using AmberTools19 shivangi agarwal (Mon Jul 22 2019 - 11:00:51 PDT)
    - Re: [AMBER] Error in preparing system using AmberTools19 Bill Ross (Mon Jul 22 2019 - 12:50:10 PDT)
    - Re: [AMBER] Error in preparing system using AmberTools19 David Case (Mon Jul 22 2019 - 13:39:21 PDT)
    - Re: [AMBER] Error in preparing system using AmberTools19 Matias Machado (Mon Jul 22 2019 - 13:46:12 PDT)
    - Re: [AMBER] Error in preparing system using AmberTools19 shivangi agarwal (Tue Jul 23 2019 - 00:02:34 PDT)
    - Re: [AMBER] Error in preparing system using AmberTools19 Bill Ross (Tue Jul 23 2019 - 00:13:52 PDT)
    - Re: [AMBER] Error in preparing system using AmberTools19 Bill Ross (Tue Jul 23 2019 - 00:18:35 PDT)
    - Re: [AMBER] Error in preparing system using AmberTools19 Elvis Martis (Tue Jul 23 2019 - 00:17:53 PDT)
    - Re: [AMBER] Error in preparing system using AmberTools19 Bill Ross (Tue Jul 23 2019 - 00:19:14 PDT)
    - Re: [AMBER] Error in preparing system using AmberTools19 Matias Machado (Tue Jul 23 2019 - 06:20:38 PDT)
    - Re: [AMBER] Error in preparing system using AmberTools19 shivangi agarwal (Tue Jul 23 2019 - 09:55:09 PDT)
    - Re: [AMBER] Error in preparing system using AmberTools19 David Case (Tue Jul 23 2019 - 15:10:14 PDT)
    - Re: [AMBER] Error in preparing system using AmberTools19 shivangi agarwal (Tue Jul 23 2019 - 20:50:12 PDT)
    - Re: [AMBER] Error in preparing system using AmberTools19 Matias Machado (Wed Jul 24 2019 - 11:58:53 PDT)
    - Re: [AMBER] Error in preparing system using AmberTools19 Matias Machado (Wed Jul 24 2019 - 12:21:35 PDT)
    - Re: [AMBER] Error in preparing system using AmberTools19 Matias Machado (Wed Jul 24 2019 - 12:30:44 PDT)
    - Re: [AMBER] Error in preparing system using AmberTools19 shivangi agarwal (Sun Jul 28 2019 - 21:51:30 PDT)
    - Re: [AMBER] Error in preparing system using AmberTools19 Bill Ross (Sun Jul 28 2019 - 22:19:46 PDT)
    - Re: [AMBER] Error in preparing system using AmberTools19 shivangi agarwal (Sun Jul 28 2019 - 22:34:03 PDT)
    - Re: [AMBER] Error in preparing system using AmberTools19 Matias Machado (Sun Jul 28 2019 - 22:51:48 PDT)
    - Re: [AMBER] Error in preparing system using AmberTools19 shivangi agarwal (Wed Jul 31 2019 - 00:23:52 PDT)
    - Re: [AMBER] Error in preparing system using AmberTools19 Matias Machado (Sun Jul 28 2019 - 22:41:19 PDT)
[AMBER] Error in resp charge calculation Sadaf Rani (Mon Jul 22 2019 - 13:20:46 PDT)
[AMBER] Calculating area per lipid for system with different numbers of lipids on leaflets Maria Bzówka (Tue Jul 23 2019 - 02:24:03 PDT)
- Re: [AMBER] Calculating area per lipid for system with different numbers of lipids on leaflets Prajwal Nandekar (Tue Jul 23 2019 - 02:32:00 PDT)
- Re: [AMBER] Calculating area per lipid for system with different numbers of lipids on leaflets Daniel Roe (Tue Jul 23 2019 - 09:15:52 PDT)
[AMBER] Large increase in polarization energy during MD CROUZY Serge 119222 (Tue Jul 23 2019 - 04:39:59 PDT)
- Re: [AMBER] Large increase in polarization energy during MD David Case (Tue Jul 23 2019 - 15:16:49 PDT)
[AMBER] Problems with RTX2080Ti Giovanni Grazioso (Tue Jul 23 2019 - 05:55:58 PDT)
- Re: [AMBER] Problems with RTX2080Ti David Cerutti (Tue Jul 23 2019 - 09:36:56 PDT)
  - Re: [AMBER] Problems with RTX2080Ti Giovanni Grazioso (Tue Jul 23 2019 - 09:56:59 PDT)
    - Re: [AMBER] Problems with RTX2080Ti David Cerutti (Tue Jul 23 2019 - 11:53:08 PDT)
    - Re: [AMBER] Problems with RTX2080Ti David Cerutti (Tue Jul 23 2019 - 15:26:36 PDT)
[AMBER] Can't load trajectory in coordinate formate from amber in VMD Xikun Liu (Tue Jul 23 2019 - 18:35:46 PDT)
- Re: [AMBER] Can't load trajectory in coordinate formate from amber in VMD Chetna Tyagi (Wed Jul 24 2019 - 04:21:56 PDT)
[AMBER] Combing trajectoty mwli.mail.ustc.edu.cn (Tue Jul 23 2019 - 18:46:18 PDT)
- Re: [AMBER] Combing trajectoty Chetna Tyagi (Wed Jul 24 2019 - 04:29:59 PDT)
[AMBER] Reference for External electric field implementation in Amber Kshatresh Dutta Dubey (Tue Jul 23 2019 - 21:15:00 PDT)
- Re: [AMBER] Reference for External electric field implementation in Amber Chetna Tyagi (Wed Jul 24 2019 - 04:17:46 PDT)
  - Re: [AMBER] Reference for External electric field implementation in Amber Kshatresh Dutta Dubey (Wed Jul 24 2019 - 04:55:38 PDT)
    - Re: [AMBER] Reference for External electric field implementation in Amber Chetna Tyagi (Wed Jul 24 2019 - 04:44:49 PDT)
[AMBER] -regarding failure in addition of Na+ ions in tleap Patil Pranita Uttamrao (Wed Jul 24 2019 - 07:26:22 PDT)
- Re: [AMBER] -regarding failure in addition of Na+ ions in tleap David Case (Wed Jul 24 2019 - 10:24:44 PDT)
[AMBER] problem with building cpptraj in AmberTools19 David Case (Wed Jul 24 2019 - 10:17:52 PDT)
- Re: [AMBER] problem with building cpptraj in AmberTools19 Daniel Roe (Wed Jul 24 2019 - 12:01:19 PDT)
  - Re: [AMBER] problem with building cpptraj in AmberTools19 A K (Mon Jul 29 2019 - 10:50:04 PDT)
    - Re: [AMBER] problem with building cpptraj in AmberTools19 Daniel Roe (Mon Jul 29 2019 - 12:10:07 PDT)
    - Re: [AMBER] problem with building cpptraj in AmberTools19 A K (Mon Jul 29 2019 - 12:26:18 PDT)
    - Re: [AMBER] problem with building cpptraj in AmberTools19 Daniel Roe (Wed Jul 31 2019 - 05:09:58 PDT)
    - Re: [AMBER] problem with building cpptraj in AmberTools19 A K (Thu Aug 15 2019 - 13:04:03 PDT)
    - Re: [AMBER] problem with building cpptraj in AmberTools19 Daniel Roe (Mon Aug 19 2019 - 06:40:34 PDT)
- Re: [AMBER] problem with building cpptraj in AmberTools19 A K (Thu Jul 25 2019 - 14:26:25 PDT)
[AMBER] Query on linear interaction energy (lie) calculation using CPPTRAJ Bharat Manna (Wed Jul 24 2019 - 21:49:16 PDT)
[AMBER] reg: residue number order like pdb Lara rajam (Thu Jul 25 2019 - 11:23:07 PDT)
- Re: [AMBER] reg: residue number order like pdb David A Case (Fri Jul 26 2019 - 05:33:01 PDT)
[AMBER] Amber installation problem Debasish Mandal (Fri Jul 26 2019 - 03:03:25 PDT)
- Re: [AMBER] Amber installation problem David A Case (Fri Jul 26 2019 - 05:42:40 PDT)
[AMBER] MMPBSA for Absolute free energy Lod King (Fri Jul 26 2019 - 12:00:50 PDT)
- Re: [AMBER] MMPBSA for Absolute free energy David A Case (Fri Jul 26 2019 - 12:21:47 PDT)
  - Re: [AMBER] MMPBSA for Absolute free energy Lod King (Fri Jul 26 2019 - 17:25:13 PDT)
[AMBER] Switch function in NAMDEnergy cooresponds to AMBER input flag Lod King (Fri Jul 26 2019 - 13:38:50 PDT)
- Re: [AMBER] Switch function in NAMDEnergy cooresponds to AMBER input flag David Case (Sat Jul 27 2019 - 06:08:52 PDT)
  - Re: [AMBER] Switch function in NAMDEnergy cooresponds to AMBER input flag Lod King (Sat Jul 27 2019 - 08:23:15 PDT)
[AMBER] Kinetic Energy is zero in production run. Amit Kumar (Sat Jul 27 2019 - 04:38:18 PDT)
- Re: [AMBER] Kinetic Energy is zero in production run. Matias Machado (Sat Jul 27 2019 - 14:13:18 PDT)
[AMBER] General questions regarding MMPBSA in AMBER Lod King (Sat Jul 27 2019 - 10:19:25 PDT)
[AMBER] Using pmemd.gem (Amoeba) with nmropt=1 Luboš Plamitzer (Sat Jul 27 2019 - 12:33:16 PDT)
[AMBER] Regarding cut-off distance in hydrogen bond richa anand (Sun Jul 28 2019 - 07:32:03 PDT)
- Re: [AMBER] Regarding cut-off distance in hydrogen bond Daniel Roe (Mon Jul 29 2019 - 06:11:41 PDT)
[AMBER] Swarms-of-trajectories example files Federico Olivieri (Sun Jul 28 2019 - 18:34:12 PDT)
- Re: [AMBER] Swarms-of-trajectories example files Feng Pan (Tue Jul 30 2019 - 08:13:44 PDT)
[AMBER] TI for mutation of charged residues Hosein Geraili Daronkola (Mon Jul 29 2019 - 00:17:05 PDT)
- Re: [AMBER] TI for mutation of charged residues Hosein Geraili Daronkola (Tue Jul 30 2019 - 01:33:24 PDT)
  - Re: [AMBER] TI for mutation of charged residues Matias Machado (Tue Jul 30 2019 - 12:16:05 PDT)
[AMBER] missing bond parameter for Mg ion Chen, Wei (Mon Jul 29 2019 - 14:35:22 PDT)
- Re: [AMBER] missing bond parameter for Mg ion David A Case (Tue Jul 30 2019 - 07:53:01 PDT)
- Re: [AMBER] missing bond parameter for Mg ion Chen, Wei (Tue Jul 30 2019 - 15:04:32 PDT)
[AMBER] pbsa calculation Lod King (Mon Jul 29 2019 - 17:38:24 PDT)
- Re: [AMBER] pbsa calculation Ray Luo (Mon Jul 29 2019 - 20:49:21 PDT)
[AMBER] modelling of a penta coordination around zinc ion (+2) using MCPB.py SATYAJIT KHATUA (Mon Jul 29 2019 - 22:22:50 PDT)
- Re: [AMBER] modelling of a penta coordination around zinc ion (+2) using MCPB.py Pengfei Li (Wed Aug 07 2019 - 19:56:47 PDT)
  - [AMBER] How to deal with Dummy atoms of 4-coordinated Zinc in QM/MM Qing Lv (Fri Dec 20 2019 - 23:13:44 PST)
[AMBER] question about GIST calculation Aliakbartehrani Zahra (Tue Jul 30 2019 - 03:17:04 PDT)
- Re: [AMBER] question about GIST calculation Steven Ramsey (Tue Jul 30 2019 - 07:39:01 PDT)
[AMBER] Non-standard Hydrogen Bonding Loris Moretti (Tue Jul 30 2019 - 05:25:46 PDT)
- Re: [AMBER] Non-standard Hydrogen Bonding David A Case (Tue Jul 30 2019 - 13:11:34 PDT)
[AMBER] Simulating Water-Metal Interface with NPT Ensemble Lucas Bandeira (Tue Jul 30 2019 - 12:31:32 PDT)
[AMBER] MCPB.py showing error in the step: MCPB.py -i 1OKL.in -s 2 Divya Rai (Wed Jul 31 2019 - 05:09:24 PDT)
- Re: [AMBER] MCPB.py showing error in the step: MCPB.py -i 1OKL.in -s 2 Pengfei Li (Wed Aug 07 2019 - 19:49:23 PDT)
[AMBER] Problem running Antechamber for GTP Akinpelu Olayinka (Wed Jul 31 2019 - 11:12:37 PDT)
- Re: [AMBER] Problem running Antechamber for GTP David A Case (Wed Jul 31 2019 - 13:17:46 PDT)
[AMBER] error in Cuda installtion Karim Mahnam (Thu Aug 01 2019 - 03:41:04 PDT)
- Re: [AMBER] error in Cuda installtion Daniel Roe (Thu Aug 01 2019 - 04:57:57 PDT)
- Re: [AMBER] error in Cuda installtion David A Case (Thu Aug 01 2019 - 05:23:48 PDT)
[AMBER] 1-4 EvdW and 1-4 EEL Lod King (Thu Aug 01 2019 - 14:24:56 PDT)
- Re: [AMBER] 1-4 EvdW and 1-4 EEL David A Case (Fri Aug 02 2019 - 05:42:17 PDT)
  - Re: [AMBER] 1-4 EvdW and 1-4 EEL David Cerutti (Fri Aug 02 2019 - 11:51:42 PDT)
    - Re: [AMBER] 1-4 EvdW and 1-4 EEL Lod King (Fri Aug 02 2019 - 11:54:43 PDT)
[AMBER] RTX 5000 cards and AMBER 16 compatibility Laura Furge (Fri Aug 02 2019 - 14:17:05 PDT)
- Re: [AMBER] RTX 5000 cards and AMBER 16 compatibility Hashemi, Mohtadin (Fri Aug 02 2019 - 20:38:12 PDT)
[AMBER] Simulations without PME Tom Kurtzman (Mon Aug 05 2019 - 12:45:49 PDT)
- Re: [AMBER] Simulations without PME David Case (Mon Aug 05 2019 - 18:18:50 PDT)
  - Re: [AMBER] Simulations without PME Bill Ross (Mon Aug 05 2019 - 18:43:09 PDT)
    - Re: [AMBER] Simulations without PME Tom Kurtzman (Tue Aug 06 2019 - 09:03:27 PDT)
[AMBER] $AMBERHOME vs $AMBER_PREFIX Pete Biggs (Tue Aug 06 2019 - 01:23:19 PDT)
- Re: [AMBER] $AMBERHOME vs $AMBER_PREFIX Hai Nguyen (Tue Aug 06 2019 - 04:55:15 PDT)
  - Re: [AMBER] $AMBERHOME vs $AMBER_PREFIX Pete Biggs (Tue Aug 06 2019 - 08:40:59 PDT)
[AMBER] error during the calculation of MMPBSA Jeyaram R A (Tue Aug 06 2019 - 06:03:44 PDT)
- Re: [AMBER] error during the calculation of MMPBSA rluo.uci.edu (Tue Aug 06 2019 - 06:50:54 PDT)
  - Re: [AMBER] error during the calculation of MMPBSA Jeyaram R A (Tue Aug 06 2019 - 08:24:47 PDT)
  - Re: [AMBER] error during the calculation of MMPBSA Thomas Gaillard (Wed Aug 07 2019 - 02:30:47 PDT)
- Re: [AMBER] error during the calculation of MMPBSA Elvis Martis (Tue Aug 06 2019 - 06:54:02 PDT)
  - Re: [AMBER] error during the calculation of MMPBSA Jeyaram R A (Tue Aug 06 2019 - 08:14:22 PDT)
    - Re: [AMBER] error during the calculation of MMPBSA Elvis Martis (Tue Aug 06 2019 - 08:21:33 PDT)
    - Re: [AMBER] error during the calculation of MMPBSA Jeyaram R A (Tue Aug 06 2019 - 08:26:31 PDT)
    - Re: [AMBER] error during the calculation of MMPBSA Jeyaram R A (Tue Aug 06 2019 - 09:50:38 PDT)
    - Re: [AMBER] error during the calculation of MMPBSA Jeyaram R A (Tue Aug 06 2019 - 09:51:51 PDT)
    - Re: [AMBER] error during the calculation of MMPBSA Elvis Martis (Tue Aug 06 2019 - 19:33:31 PDT)
    - Re: [AMBER] error during the calculation of MMPBSA Jeyaram R A (Tue Aug 06 2019 - 22:33:25 PDT)
    - Re: [AMBER] error during the calculation of MMPBSA Elvis Martis (Tue Aug 06 2019 - 22:37:57 PDT)
[AMBER] T-leap. Parviz Seifpanahi Shabane (Tue Aug 06 2019 - 07:01:25 PDT)
- Re: [AMBER] T-leap. David A Case (Tue Aug 06 2019 - 09:24:16 PDT)
[AMBER] Specifying size of truncated octahedron box manually Bellesis, Andrew G (Tue Aug 06 2019 - 07:29:57 PDT)
- Re: [AMBER] Specifying size of truncated octahedron box manually David Case (Tue Aug 20 2019 - 19:33:01 PDT)
  - Re: [AMBER] Specifying size of truncated octahedron box manually Matias Machado (Fri Aug 23 2019 - 13:32:20 PDT)
[AMBER] Alanine scan issue YOGESH NARKHEDE (Tue Aug 06 2019 - 10:59:51 PDT)
[AMBER] How to generate Free energy landscape for amber trajectory? M RCC (Tue Aug 06 2019 - 22:10:14 PDT)
- Re: [AMBER] How to generate Free energy landscape for amber trajectory? Carlos Simmerling (Wed Aug 07 2019 - 04:58:07 PDT)
  - Re: [AMBER] How to generate Free energy landscape for amber trajectory? Daniel Roe (Thu Aug 08 2019 - 05:00:21 PDT)
[AMBER] Imaging-rst file error Hira Jabeen (Wed Aug 07 2019 - 03:34:59 PDT)
- Re: [AMBER] Imaging-rst file error Carlos Simmerling (Wed Aug 07 2019 - 04:41:27 PDT)
  - Re: [AMBER] Imaging-rst file error Hira Jabeen (Wed Aug 07 2019 - 05:56:44 PDT)
    - Re: [AMBER] Imaging-rst file error Carlos Simmerling (Wed Aug 07 2019 - 06:19:59 PDT)
    - Re: [AMBER] Imaging-rst file error Hira Jabeen (Wed Aug 07 2019 - 06:51:30 PDT)
    - Re: [AMBER] Imaging-rst file error Daniel Roe (Thu Aug 08 2019 - 05:38:38 PDT)
    - Re: [AMBER] Imaging-rst file error David A Case (Thu Aug 08 2019 - 08:41:50 PDT)
    - Re: [AMBER] Imaging-rst file error Daniel Roe (Thu Aug 08 2019 - 10:31:46 PDT)
[AMBER] Lazy Question: File conversion NCRST to RST Gustaf Olsson (Wed Aug 07 2019 - 04:40:51 PDT)
- Re: [AMBER] Lazy Question: File conversion NCRST to RST Carlos Simmerling (Wed Aug 07 2019 - 04:41:58 PDT)
- Re: [AMBER] Lazy Question: File conversion NCRST to RST Daniel Roe (Wed Aug 07 2019 - 05:06:37 PDT)
  - Re: [AMBER] Lazy Question: File conversion NCRST to RST Gustaf Olsson (Wed Aug 07 2019 - 05:58:53 PDT)
  - Re: [AMBER] Lazy Question: File conversion NCRST to RST Gustaf Olsson (Wed Aug 07 2019 - 06:43:41 PDT)
    - Re: [AMBER] Lazy Question: File conversion NCRST to RST Daniel Roe (Mon Aug 12 2019 - 11:05:31 PDT)
    - Re: [AMBER] Lazy Question: File conversion NCRST to RST Gustaf Olsson (Mon Aug 12 2019 - 22:42:01 PDT)
    - Re: [AMBER] Lazy Question: File conversion NCRST to RST Gustaf Olsson (Wed Aug 14 2019 - 02:32:32 PDT)
    - Re: [AMBER] Lazy Question: File conversion NCRST to RST Daniel Roe (Wed Aug 14 2019 - 04:30:10 PDT)
    - Re: [AMBER] Lazy Question: File conversion NCRST to RST Gustaf Olsson (Wed Aug 14 2019 - 05:28:44 PDT)
    - Re: [AMBER] Lazy Question: File conversion NCRST to RST Gustaf Olsson (Wed Aug 14 2019 - 06:06:35 PDT)
[AMBER] Difference in velocity values between parmed and pytraj Irfan Alibay (Wed Aug 07 2019 - 08:13:12 PDT)
- Re: [AMBER] Difference in velocity values between parmed and pytraj Hai Nguyen (Wed Aug 07 2019 - 08:47:37 PDT)
  - Re: [AMBER] Difference in velocity values between parmed and pytraj Irfan Alibay (Thu Aug 08 2019 - 12:06:34 PDT)
    - Re: [AMBER] Difference in velocity values between parmed and pytraj Hai Nguyen (Thu Aug 08 2019 - 12:14:26 PDT)
    - Re: [AMBER] Difference in velocity values between parmed and pytraj Daniel Roe (Thu Aug 08 2019 - 12:23:05 PDT)
    - Re: [AMBER] Difference in velocity values between parmed and pytraj Jason Swails (Mon Sep 09 2019 - 08:56:34 PDT)
[AMBER] problems with Miniconda installation Elvis Martis (Wed Aug 07 2019 - 23:52:40 PDT)
- Re: [AMBER] problems with Miniconda installation David A Case (Thu Aug 08 2019 - 08:39:10 PDT)
  - Re: [AMBER] problems with Miniconda installation Elvis Martis (Thu Aug 08 2019 - 08:50:07 PDT)
  - Re: [AMBER] problems with Miniconda installation Sunita Patel (Thu Aug 08 2019 - 23:43:27 PDT)
    - Re: [AMBER] problems with Miniconda installation Sunita Patel (Fri Aug 09 2019 - 01:52:59 PDT)
    - Re: [AMBER] problems with Miniconda installation Elvis Martis (Fri Aug 09 2019 - 03:44:09 PDT)
    - Re: [AMBER] problems with Miniconda installation Sunita Patel (Fri Aug 09 2019 - 04:44:39 PDT)
[AMBER] Transcription factor DNA binding - Gibbs of activation charalamm.cheng.auth.gr (Wed Aug 07 2019 - 23:58:27 PDT)
- [AMBER] ΑΠ: Transcription factor DNA binding - Gibbs of activation Antonios Kolocouris (Thu Aug 08 2019 - 00:41:43 PDT)
- Re: [AMBER] Transcription factor DNA binding - Gibbs of activation Kevin Hauser (Thu Aug 08 2019 - 07:38:03 PDT)
[AMBER-Developers] AMBER developer job opening and TI/FEP calculation postdoc opening coming up Christian Schafmeister (Thu Aug 08 2019 - 10:17:44 PDT)
[AMBER] Issues in AMBER-18 Installation Deepika Sardana (Fri Aug 09 2019 - 00:25:40 PDT)
[AMBER] How to calculate the tilt angle of TM helix Maria Bzówka (Fri Aug 09 2019 - 01:17:53 PDT)
- Re: [AMBER] How to calculate the tilt angle of TM helix Dickson, Callum (Fri Aug 09 2019 - 13:49:44 PDT)
  - Re: [AMBER] How to calculate the tilt angle of TM helix Prajwal Nandekar (Fri Aug 09 2019 - 21:56:17 PDT)
- Re: [AMBER] How to calculate the tilt angle of TM helix Daniel Roe (Sat Aug 10 2019 - 06:25:38 PDT)
  - Re: [AMBER] How to calculate the tilt angle of TM helix Maria Bzówka (Mon Aug 12 2019 - 01:57:36 PDT)
- Re: [AMBER] How to calculate the tilt angle of TM helix Stephan Schott (Mon Aug 12 2019 - 03:37:26 PDT)
  - Re: [AMBER] How to calculate the tilt angle of TM helix Maria Bzówka (Mon Aug 12 2019 - 04:22:47 PDT)
[AMBER] T-leap "does not have a type" Parviz Seifpanahi Shabane (Fri Aug 09 2019 - 09:47:14 PDT)
- Re: [AMBER] T-leap "does not have a type" Matias Machado (Sat Aug 10 2019 - 12:39:12 PDT)
  - Re: [AMBER] T-leap "does not have a type" Matias Machado (Sat Aug 10 2019 - 13:18:17 PDT)
    - Re: [AMBER] T-leap "does not have a type" David Case (Sun Aug 11 2019 - 05:36:06 PDT)
[AMBER] DNA force field. Parviz Seifpanahi Shabane (Fri Aug 09 2019 - 09:54:06 PDT)
- Re: [AMBER] DNA force field. Matias Machado (Sat Aug 10 2019 - 13:01:51 PDT)
[AMBER] MM-PBSA Alanine scanning issue YOGESH NARKHEDE (Fri Aug 09 2019 - 10:44:00 PDT)
- Re: [AMBER] MM-PBSA Alanine scanning issue Elvis Martis (Fri Aug 09 2019 - 21:23:18 PDT)
[AMBER] MD on small molecules, The file contained 8 atoms not in residue templates Amen Shamim (Fri Aug 09 2019 - 11:17:52 PDT)
- Re: [AMBER] MD on small molecules, The file contained 8 atoms not in residue templates David Case (Tue Aug 20 2019 - 19:29:47 PDT)
[AMBER] Installaiton of pmemd for Amber16 Ryoichi Utsumi (Sat Aug 10 2019 - 04:18:40 PDT)
- Re: [AMBER] Installaiton of pmemd for Amber16 David Case (Wed Aug 14 2019 - 18:32:57 PDT)
  - Re: [AMBER] Installaiton of pmemd for Amber16 Ryoichi Utsumi (Wed Sep 25 2019 - 06:16:40 PDT)
    - Re: [AMBER] Installaiton of pmemd for Amber16 Ryoichi Utsumi (Mon Sep 30 2019 - 19:31:35 PDT)
[AMBER] Error iin running mmpbsa shivangi agarwal (Sat Aug 10 2019 - 09:36:39 PDT)
[AMBER] Question about DFTB3 method with dispersion correction Rajiv (Sun Aug 11 2019 - 09:55:33 PDT)
- Re: [AMBER] Question about DFTB3 method with dispersion correction Pavlína Pokorná (Mon Aug 12 2019 - 07:43:40 PDT)
[AMBER] sander engine problem Rui Chen (Mon Aug 12 2019 - 07:24:43 PDT)
- Re: [AMBER] sander engine problem Pratul Agarwal (Mon Aug 12 2019 - 07:28:24 PDT)
[AMBER] atom numbering in cpptraj and pytraj Rosellen, Martin (Mon Aug 12 2019 - 07:38:29 PDT)
- Re: [AMBER] atom numbering in cpptraj and pytraj Hai Nguyen (Mon Aug 12 2019 - 07:45:44 PDT)
  - Re: [AMBER] atom numbering in cpptraj and pytraj Hai Nguyen (Mon Aug 12 2019 - 07:49:09 PDT)
[AMBER] OpenMPI 4 and pmemd.cuda.MPI Jose Christian Flores Canales (Tue Aug 13 2019 - 04:20:31 PDT)
- Re: [AMBER] OpenMPI 4 and pmemd.cuda.MPI Jose Christian Flores Canales (Tue Aug 13 2019 - 04:22:58 PDT)
- Re: [AMBER] OpenMPI 4 and pmemd.cuda.MPI David Case (Tue Aug 13 2019 - 06:25:54 PDT)
[AMBER] NH-pi interaction using ff14SB forcefield Saikat Pal (Tue Aug 13 2019 - 04:44:50 PDT)
- Re: [AMBER] NH-pi interaction using ff14SB forcefield Carlos Simmerling (Tue Aug 13 2019 - 06:56:35 PDT)
[AMBER] Problem for the frcmod file from the amber tutorial 辛志宏 (Tue Aug 13 2019 - 09:14:27 PDT)
- Re: [AMBER] Problem for the frcmod file from the amber tutorial David Case (Tue Aug 20 2019 - 19:24:16 PDT)
[AMBER] AmberTools19/AMBER18 - FFTW3 and MKL compiling issues viktor drobot (Tue Aug 13 2019 - 13:28:50 PDT)
- Re: [AMBER] AmberTools19/AMBER18 - FFTW3 and MKL compiling issues David Case (Wed Aug 14 2019 - 18:12:48 PDT)
  - Re: [AMBER] AmberTools19/AMBER18 - FFTW3 and MKL compiling issues viktor drobot (Thu Aug 15 2019 - 07:26:49 PDT)
- Re: [AMBER] AmberTools19/AMBER18 - FFTW3 and MKL compiling issues viktor drobot (Fri Aug 16 2019 - 06:57:58 PDT)
  - Re: [AMBER] AmberTools19/AMBER18 - FFTW3 and MKL compiling issues David Case (Fri Aug 16 2019 - 13:54:31 PDT)
    - Re: [AMBER] AmberTools19/AMBER18 - FFTW3 and MKL compiling issues Tyler Luchko (Lists) (Fri Aug 16 2019 - 16:54:35 PDT)
    - Re: [AMBER] AmberTools19/AMBER18 - FFTW3 and MKL compiling issues viktor drobot (Sat Aug 17 2019 - 03:29:38 PDT)
    - Re: [AMBER] AmberTools19/AMBER18 - FFTW3 and MKL compiling issues David Case (Sat Aug 17 2019 - 06:03:37 PDT)
    - Re: [AMBER] AmberTools19/AMBER18 - FFTW3 and MKL compiling issues viktor drobot (Sat Aug 17 2019 - 06:29:57 PDT)
[AMBER] Amber16 + AmberTools19 Jose Javier Muñoz Criollo (Wed Aug 14 2019 - 08:39:27 PDT)
- Re: [AMBER] Amber16 + AmberTools19 David Case (Wed Aug 14 2019 - 18:06:57 PDT)
  - Re: [AMBER] Amber16 + AmberTools19 Jose Javier Muñoz Criollo (Fri Aug 16 2019 - 05:29:05 PDT)
    - Re: [AMBER] Amber16 + AmberTools19 David Case (Fri Aug 16 2019 - 13:56:44 PDT)
[AMBER] How can I calculate RDF only in a specific region of my system? Lucas Bandeira (Wed Aug 14 2019 - 09:57:28 PDT)
- Re: [AMBER] How can I calculate RDF only in a specific region of my system? emanuele falbo (Wed Aug 14 2019 - 10:16:30 PDT)
[AMBER] Segmentation Fault Parviz Seifpanahi Shabane (Wed Aug 14 2019 - 13:53:15 PDT)
- Re: [AMBER] Segmentation Fault Bill Ross (Wed Aug 14 2019 - 14:16:22 PDT)
- Re: [AMBER] Segmentation Fault David Case (Wed Aug 14 2019 - 18:20:51 PDT)
[AMBER] probelm -- QMMM-MD with ZN（Znic atom）in QM region 东庚 (Wed Aug 14 2019 - 23:20:20 PDT)
- [AMBER] probelm -- QMMM-MD with ZN（Znic atom）in QM region 东庚 (Fri Aug 16 2019 - 19:10:11 PDT)
  - Re: [AMBER] probelm -- QMMM-MD with ZN（Znic atom）in QM region Pengfei Li (Fri Aug 16 2019 - 20:12:00 PDT)
  - [AMBER] 答复: probelm -- QMMM-MD with ZN（Znic atom）in QM region 东庚 (Sat Aug 17 2019 - 19:20:03 PDT)
    - [AMBER] 答复: probelm -- QMMM-MD with ZN（Znic atom）in QM region 东庚 (Mon Aug 19 2019 - 01:51:21 PDT)
    - Re: [AMBER] 答复: probelm -- QMMM-MD with ZN（Znic atom）in QM region Pengfei Li (Tue Aug 20 2019 - 12:28:59 PDT)
    - Re: [AMBER] 答复: probelm -- QMMM-MD with ZN（Znic atom）in QM region Pengfei Li (Mon Aug 26 2019 - 14:55:58 PDT)
[AMBER] Problem Running Antechamber for GTP Akinpelu Olayinka (Thu Aug 15 2019 - 00:21:48 PDT)
- Re: [AMBER] Problem Running Antechamber for GTP Elvis Martis (Thu Aug 15 2019 - 00:47:32 PDT)
- Re: [AMBER] Problem Running Antechamber for GTP Gustaf Olsson (Thu Aug 15 2019 - 01:14:40 PDT)
[AMBER] Installing Amber parallel option Roy Ashworth (Thu Aug 15 2019 - 04:00:40 PDT)
- Re: [AMBER] Installing Amber parallel option Elvis Martis (Thu Aug 15 2019 - 04:08:38 PDT)
  - Re: [AMBER] Installing Amber parallel option Roy Ashworth (Thu Aug 15 2019 - 07:45:27 PDT)
    - Re: [AMBER] Installing Amber parallel option Elvis Martis (Thu Aug 15 2019 - 07:48:44 PDT)
    - Re: [AMBER] Installing Amber parallel option David Case (Thu Aug 15 2019 - 18:05:43 PDT)
[AMBER] Lateral diffusion of lipid head groups Maria Bzówka (Thu Aug 15 2019 - 04:12:21 PDT)
- Re: [AMBER] Lateral diffusion of lipid head groups Daniel Roe (Tue Sep 03 2019 - 10:46:56 PDT)
[AMBER] mmPBSA error in Amber19 suite jacky zhao (Thu Aug 15 2019 - 10:10:25 PDT)
- Re: [AMBER] mmPBSA error in Amber19 suite jacky zhao (Sat Aug 17 2019 - 04:40:29 PDT)
  - Re: [AMBER] mmPBSA error in Amber19 suite David Case (Sat Aug 17 2019 - 06:11:31 PDT)
    - Re: [AMBER] mmPBSA error in Amber19 suite Lei Zhao (Sat Aug 17 2019 - 19:55:45 PDT)
    - Re: [AMBER] mmPBSA error in Amber19 suite jacky zhao (Sat Aug 17 2019 - 22:12:33 PDT)
[AMBER] WaterBox is getting distorted while running PMF Airy Sanjeev (Thu Aug 15 2019 - 21:17:45 PDT)
- Re: [AMBER] WaterBox is getting distorted while running PMF David Cerutti (Fri Aug 16 2019 - 10:10:56 PDT)
  - Re: [AMBER] WaterBox is getting distorted while running PMF Airy Sanjeev (Sun Aug 18 2019 - 23:50:37 PDT)
[AMBER] Error in MMPBSA calculation shivangi agarwal (Fri Aug 16 2019 - 01:14:43 PDT)
- Re: [AMBER] Error in MMPBSA calculation Ray Luo (Fri Aug 16 2019 - 02:27:20 PDT)
  - Re: [AMBER] Error in MMPBSA calculation shivangi agarwal (Fri Aug 16 2019 - 04:52:13 PDT)
    - Re: [AMBER] Error in MMPBSA calculation Elvis Martis (Fri Aug 16 2019 - 05:17:46 PDT)
    - Re: [AMBER] Error in MMPBSA calculation shivangi agarwal (Fri Aug 16 2019 - 05:40:39 PDT)
    - Re: [AMBER] Error in MMPBSA calculation RAY LUO, Ph.D. (Fri Aug 16 2019 - 13:29:34 PDT)
- Re: [AMBER] Error in MMPBSA calculation jacky zhao (Sat Aug 17 2019 - 04:44:03 PDT)
[AMBER] error with CPPTRAj Mohammad Salem (Fri Aug 16 2019 - 03:44:50 PDT)
- Re: [AMBER] error with CPPTRAj Mohammad Salem (Fri Aug 16 2019 - 04:25:01 PDT)
[AMBER] volume in pytraj? Shayna Hilburg (Fri Aug 16 2019 - 14:56:12 PDT)
- Re: [AMBER] volume in pytraj? Hai Nguyen (Fri Aug 16 2019 - 15:29:58 PDT)
  - Re: [AMBER] volume in pytraj? Shayna Hilburg (Sun Aug 18 2019 - 18:03:44 PDT)
    - Re: [AMBER] volume in pytraj? Hai Nguyen (Sun Aug 18 2019 - 21:28:43 PDT)
    - Re: [AMBER] volume in pytraj? Shayna Hilburg (Mon Aug 19 2019 - 06:51:13 PDT)
    - Re: [AMBER] volume in pytraj? Hai Nguyen (Mon Aug 19 2019 - 09:06:45 PDT)
[AMBER] Question about running MMPBSA.py with a mask to exclude certain residues A K (Fri Aug 16 2019 - 17:05:26 PDT)
- Re: [AMBER] Question about running MMPBSA.py with a mask to exclude certain residues A K (Fri Aug 23 2019 - 09:22:53 PDT)
  - Re: [AMBER] Question about running MMPBSA.py with a mask to exclude certain residues A K (Fri Aug 23 2019 - 14:03:55 PDT)
    - Re: [AMBER] Question about running MMPBSA.py with a mask to exclude certain residues David Case (Fri Aug 23 2019 - 18:58:53 PDT)
    - Re: [AMBER] Question about running MMPBSA.py with a mask to exclude certain residues A K (Fri Aug 23 2019 - 20:03:32 PDT)
- Re: [AMBER] Question about running MMPBSA.py with a mask to exclude certain residues Supriyo Bhattacharya (Fri Aug 23 2019 - 11:07:03 PDT)
[AMBER] mismatch between parm files from CHARMM-GUI and chamber Quynh Vo (Fri Aug 16 2019 - 17:13:52 PDT)
[AMBER] Error searching for compatible GPU in Amber18 Karim Mahnam (Sat Aug 17 2019 - 00:47:18 PDT)
- Re: [AMBER] Error searching for compatible GPU in Amber18 James Kress (Sat Aug 17 2019 - 09:16:20 PDT)
  - Re: [AMBER] Error searching for compatible GPU in Amber18 Karim Mahnam (Sun Aug 18 2019 - 19:22:38 PDT)
    - Re: [AMBER] Error searching for compatible GPU in Amber18 Daniel Roe (Mon Aug 19 2019 - 05:13:12 PDT)
    - Re: [AMBER] Error searching for compatible GPU in Amber18 Karim Mahnam (Mon Aug 19 2019 - 06:44:43 PDT)
    - Re: [AMBER] Error searching for compatible GPU in Amber18 Ross Walker (Mon Aug 19 2019 - 19:59:54 PDT)
[AMBER] Restraint ramp Dhananjay (Sat Aug 17 2019 - 09:58:03 PDT)
- Re: [AMBER] Restraint ramp David Case (Sat Aug 17 2019 - 18:16:40 PDT)
[AMBER] MMPBSA using amberTools19 shivangi agarwal (Sun Aug 18 2019 - 00:39:28 PDT)
- Re: [AMBER] MMPBSA using amberTools19 Ray Luo (Sun Aug 18 2019 - 07:10:58 PDT)
- Re: [AMBER] MMPBSA using amberTools19 Hai Nguyen (Sun Aug 18 2019 - 08:27:14 PDT)
[AMBER] Amber installation error Vivek Junghare (Mon Aug 19 2019 - 00:57:09 PDT)
- Re: [AMBER] Amber installation error Daniel Roe (Mon Aug 19 2019 - 05:35:33 PDT)
[AMBER] Graphene residue name Tleap Nora Kremer (Mon Aug 19 2019 - 01:03:12 PDT)
- Re: [AMBER] Graphene residue name Tleap Matias Machado (Fri Aug 23 2019 - 10:57:33 PDT)
[AMBER] Regarding restarting from RST files using pmemd.cuda Midhun K Madhu (Mon Aug 19 2019 - 03:53:03 PDT)
- Re: [AMBER] Regarding restarting from RST files using pmemd.cuda Daniel Roe (Mon Aug 19 2019 - 05:22:51 PDT)
  - Re: [AMBER] Regarding restarting from RST files using pmemd.cuda Akinpelu Olayinka (Mon Aug 19 2019 - 06:39:03 PDT)
  - Re: [AMBER] Regarding restarting from RST files using pmemd.cuda David Cerutti (Mon Aug 19 2019 - 09:55:18 PDT)
[AMBER] AccelleratedMD production Giulia Paiardi (Mon Aug 19 2019 - 04:01:36 PDT)
- Re: [AMBER] AccelleratedMD production Jacopo Sgrignani (Mon Aug 19 2019 - 04:06:50 PDT)
  - Re: [AMBER] AccelleratedMD production Giulia Paiardi (Mon Aug 19 2019 - 05:55:03 PDT)
    - Re: [AMBER] AccelleratedMD production David Cerutti (Mon Aug 19 2019 - 09:59:37 PDT)
    - Re: [AMBER] AccelleratedMD production Elvis Martis (Mon Aug 19 2019 - 10:15:09 PDT)
[AMBER] CHARMM forcefield Hira Jabeen (Mon Aug 19 2019 - 06:59:31 PDT)
- Re: [AMBER] CHARMM forcefield David Case (Tue Aug 20 2019 - 19:20:00 PDT)
[AMBER] How does PMEMD handle duplicates in GROUP? Quynh N. Vo (Mon Aug 19 2019 - 12:04:01 PDT)
- Re: [AMBER] How does PMEMD handle duplicates in GROUP? David Case (Tue Aug 20 2019 - 19:17:02 PDT)
[AMBER] Could not import Amber Python modules! error during parallel test of Amber18 Sunita Patel (Mon Aug 19 2019 - 22:41:59 PDT)
- Re: [AMBER] Could not import Amber Python modules! error during parallel test of Amber18 Bill Ross (Mon Aug 19 2019 - 22:49:40 PDT)
  - Re: [AMBER] Could not import Amber Python modules! error during parallel test of Amber18 Sunita Patel (Mon Aug 19 2019 - 22:54:23 PDT)
- Re: [AMBER] Could not import Amber Python modules! error during parallel test of Amber18 David A Case (Tue Aug 20 2019 - 05:21:19 PDT)
  - Re: [AMBER] Could not import Amber Python modules! error during parallel test of Amber18 Sunita Patel (Tue Aug 20 2019 - 22:26:41 PDT)
    - Re: [AMBER] Could not import Amber Python modules! error during parallel test of Amber18 Sunita Patel (Tue Aug 20 2019 - 22:41:08 PDT)
    - Re: [AMBER] Could not import Amber Python modules! error during parallel test of Amber18 Hai Nguyen (Tue Aug 20 2019 - 23:10:51 PDT)
    - Re: [AMBER] Could not import Amber Python modules! error during parallel test of Amber18 Sunita Patel (Wed Aug 21 2019 - 01:20:21 PDT)
    - Re: [AMBER] Could not import Amber Python modules! error during parallel test of Amber18 Sunita Patel (Wed Aug 21 2019 - 04:52:06 PDT)
    - Re: [AMBER] Could not import Amber Python modules! error during parallel test of Amber18 Hai Nguyen (Wed Aug 21 2019 - 05:33:39 PDT)
[AMBER] Amberff99sb topology for phosphorylated tyrosine residue in GROMACS Seketoulie Keretsu (Tue Aug 20 2019 - 02:22:09 PDT)
- Re: [AMBER] Amberff99sb topology for phosphorylated tyrosine residue in GROMACS David A Case (Tue Aug 20 2019 - 05:24:42 PDT)
[AMBER] Not able to load Amber trajectories in VMD shivangi agarwal (Tue Aug 20 2019 - 09:50:35 PDT)
- Re: [AMBER] Not able to load Amber trajectories in VMD Daniel Roe (Tue Aug 20 2019 - 10:15:20 PDT)
[AMBER] vlimit exceeded for step Sadaf Rani (Tue Aug 20 2019 - 15:54:12 PDT)
- Re: [AMBER] vlimit exceeded for step Bill Ross (Wed Jun 30 2010 - 16:48:38 PDT)
  - Re: [AMBER] vlimit exceeded for step Homa Azizian (Wed Jun 30 2010 - 22:22:04 PDT)
- Re: [AMBER] vlimit exceeded for step Fatemeh Sadat Alavi (Mon Feb 23 2015 - 04:06:55 PST)
  - Re: [AMBER] vlimit exceeded for step Jason Swails (Mon Feb 23 2015 - 05:22:21 PST)
  - Re: [AMBER] vlimit exceeded for step David A Case (Mon Feb 23 2015 - 05:41:01 PST)
- Re: [AMBER] vlimit exceeded for step David Case (Tue Aug 20 2019 - 19:12:58 PDT)
  - Re: [AMBER] vlimit exceeded for step Sadaf Rani (Wed Aug 21 2019 - 02:02:36 PDT)
Re: [AMBER] MMPBSA.py code Error: unknown keyword or invalid value: --closureorder David Case (Tue Aug 20 2019 - 19:30:46 PDT)
[AMBER] PDB file carbohydrates naming problem Rui Chen (Tue Aug 20 2019 - 20:43:45 PDT)
- Re: [AMBER] PDB file carbohydrates naming problem Rui Chen (Tue Aug 20 2019 - 20:49:26 PDT)
  - Re: [AMBER] PDB file carbohydrates naming problem Lachele Foley (Tue Aug 20 2019 - 21:07:18 PDT)
    - Re: [AMBER] PDB file carbohydrates naming problem Rui Chen (Tue Aug 20 2019 - 21:32:14 PDT)
    - Re: [AMBER] PDB file carbohydrates naming problem Lachele Foley (Tue Aug 20 2019 - 22:32:14 PDT)
    - Re: [AMBER] PDB file carbohydrates naming problem Rui Chen (Wed Aug 21 2019 - 16:02:22 PDT)
    - Re: [AMBER] PDB file carbohydrates naming problem Lachele Foley (Wed Aug 21 2019 - 18:35:32 PDT)
    - Re: [AMBER] PDB file carbohydrates naming problem Rui Chen (Wed Aug 21 2019 - 19:17:53 PDT)
    - Re: [AMBER] PDB file carbohydrates naming problem Lachele Foley (Thu Aug 22 2019 - 07:24:07 PDT)
    - Re: [AMBER] PDB file carbohydrates naming problem Rui Chen (Thu Aug 22 2019 - 08:45:11 PDT)
    - Re: [AMBER] PDB file carbohydrates naming problem Rui Chen (Thu Aug 22 2019 - 19:21:03 PDT)
    - Re: [AMBER] PDB file carbohydrates naming problem Lachele Foley (Fri Aug 23 2019 - 05:59:04 PDT)
    - Re: [AMBER] PDB file carbohydrates naming problem Rui Chen (Fri Aug 23 2019 - 21:44:51 PDT)
    - Re: [AMBER] PDB file carbohydrates naming problem Rui Chen (Fri Aug 23 2019 - 21:53:24 PDT)
    - Re: [AMBER] PDB file carbohydrates naming problem Lachele Foley (Mon Aug 26 2019 - 11:30:22 PDT)
    - Re: [AMBER] PDB file carbohydrates naming problem Rui Chen (Mon Aug 26 2019 - 12:23:20 PDT)
    - Re: [AMBER] PDB file carbohydrates naming problem Rui Chen (Fri Aug 30 2019 - 14:37:52 PDT)
    - Re: [AMBER] PDB file carbohydrates naming problem Lachele Foley (Sat Aug 31 2019 - 02:51:35 PDT)
    - Re: [AMBER] PDB file carbohydrates naming problem Rui Chen (Sat Aug 31 2019 - 09:59:27 PDT)
[AMBER] Preparation of trajectory for stfc diffusion calculations Maria Bzówka (Wed Aug 21 2019 - 06:37:34 PDT)
- Re: [AMBER] Preparation of trajectory for stfc diffusion calculations Daniel Roe (Tue Sep 03 2019 - 10:42:46 PDT)
[AMBER] Did I miss anyone? Sorry I was gone so long Lachele Foley (Wed Aug 21 2019 - 12:44:58 PDT)
[AMBER] Regarding heating equilibration Midhun K Madhu (Wed Aug 21 2019 - 16:11:09 PDT)
- Re: [AMBER] Regarding heating equilibration David A Case (Thu Aug 22 2019 - 06:31:00 PDT)
[AMBER] CHARMM 3 extra energy terms in AMBER dynamic engines (SANDER&PMEMD) Lod King (Wed Aug 21 2019 - 20:52:39 PDT)
- Re: [AMBER] CHARMM 3 extra energy terms in AMBER dynamic engines (SANDER&PMEMD) David A Case (Thu Aug 22 2019 - 06:35:19 PDT)
  - Re: [AMBER] CHARMM 3 extra energy terms in AMBER dynamic engines (SANDER&PMEMD) Lod King (Thu Aug 22 2019 - 08:14:46 PDT)
[AMBER] mdgx, improper terms and multifit viktor drobot (Thu Aug 22 2019 - 10:23:06 PDT)
- Re: [AMBER] mdgx, improper terms and multifit David Cerutti (Thu Aug 22 2019 - 10:45:22 PDT)
[AMBER] Error in running simulation in HPC using AMBER-18 Deepika Sardana (Thu Aug 22 2019 - 21:48:23 PDT)
- Re: [AMBER] Error in running simulation in HPC using AMBER-18 Elvis Martis (Thu Aug 22 2019 - 23:07:48 PDT)
[AMBER] Glycolipid Simulation Rajarshi Roy (Fri Aug 23 2019 - 05:07:40 PDT)
- Re: [AMBER] Glycolipid Simulation Lachele Foley (Sat Aug 24 2019 - 13:17:52 PDT)
  - Re: [AMBER] Glycolipid Simulation Horn, Anselm (Tue Aug 27 2019 - 00:28:31 PDT)
    - Re: [AMBER] Glycolipid Simulation Rajarshi Roy (Tue Aug 27 2019 - 04:27:46 PDT)
[AMBER] PIMD is not compatible with the MC Barostat jinfeng liu (Fri Aug 23 2019 - 17:29:19 PDT)
- Re: [AMBER] PIMD is not compatible with the MC Barostat David Case (Fri Aug 23 2019 - 19:07:28 PDT)
[AMBER] Testing New Parameters For a Novel boron Force Field.. is my advisors' strange approach true? Erdem Yeler (Sat Aug 24 2019 - 04:18:49 PDT)
- Re: [AMBER] Testing New Parameters For a Novel boron Force Field.. is my advisors' strange approach true? Bill Ross (Sat Aug 24 2019 - 04:44:18 PDT)
  - Re: [AMBER] Testing New Parameters For a Novel boron Force Field.. is my advisors' strange approach true? Bill Ross (Sat Aug 24 2019 - 04:57:15 PDT)
    - Re: [AMBER] Testing New Parameters For a Novel boron Force Field.. is my advisors' strange approach true? Erdem Yeler (Tue Aug 27 2019 - 14:32:59 PDT)
    - Re: [AMBER] Testing New Parameters For a Novel boron Force Field.. is my advisors' strange approach true? Bill Ross (Tue Aug 27 2019 - 16:06:55 PDT)
    - Re: [AMBER] Testing New Parameters For a Novel boron Force Field.. is my advisors' strange approach true? Erdem Yeler (Thu Aug 29 2019 - 13:42:26 PDT)
[AMBER] MAWS_Amber/antechamber assistance Bruno Cramer (Sun Aug 25 2019 - 13:06:23 PDT)
- Re: [AMBER] MAWS_Amber/antechamber assistance Gerald Monard (Mon Aug 26 2019 - 06:49:18 PDT)
[AMBER] Regarding setting up FEP calculations in AMBER18 Debarati DasGupta (Mon Aug 26 2019 - 11:59:52 PDT)
- Re: [AMBER] Regarding setting up FEP calculations in AMBER18 Sadaf Rani (Fri Sep 06 2019 - 04:42:48 PDT)
[AMBER] Error "forrtl: severe (174) : SIGSEGV, segmentation fault" while running MD simulation production run Leena Aggarwal (Tue Aug 27 2019 - 07:02:15 PDT)
- Re: [AMBER] Error "forrtl: severe (174) : SIGSEGV, segmentation fault" while running MD simulation production run Andrew Sugarman (Tue Aug 27 2019 - 08:13:16 PDT)
  - Re: [AMBER] Error "forrtl: severe (174) : SIGSEGV, segmentation fault" while running MD simulation production run Leena Aggarwal (Wed Aug 28 2019 - 00:31:31 PDT)
    - Re: [AMBER] Error "forrtl: severe (174) : SIGSEGV, segmentation fault" while running MD simulation production run Horn, Anselm (Wed Aug 28 2019 - 01:56:06 PDT)
    - Re: [AMBER] Error "forrtl: severe (174) : SIGSEGV, segmentation fault" while running MD simulation production run Leena Aggarwal (Wed Aug 28 2019 - 04:49:01 PDT)
[AMBER] Combining sevaral frcmods into single file viktor drobot (Tue Aug 27 2019 - 07:16:13 PDT)
- Re: [AMBER] Combining sevaral frcmods into single file Matias Machado (Tue Aug 27 2019 - 08:20:28 PDT)
  - Re: [AMBER] Combining sevaral frcmods into single file viktor drobot (Tue Aug 27 2019 - 08:31:58 PDT)
[AMBER] Fwd: evec.pev file in essential dynamics analysis Shirin Jamshidi (Tue Aug 27 2019 - 08:39:24 PDT)
- Re: [AMBER] Fwd: evec.pev file in essential dynamics analysis Daniel Roe (Tue Aug 27 2019 - 10:29:50 PDT)
- Re: [AMBER] evec.pev file in essential dynamics analysis Shirin Jamshidi (Thu Aug 29 2019 - 03:24:49 PDT)
  - Re: [AMBER] evec.pev file in essential dynamics analysis Shirin Jamshidi (Thu Aug 29 2019 - 08:14:44 PDT)
[AMBER] building amber 16 parallel with MPI Sadaf Rani (Tue Aug 27 2019 - 09:57:42 PDT)
- Re: [AMBER] building amber 16 parallel with MPI Gustaf Olsson (Tue Aug 27 2019 - 22:43:39 PDT)
[AMBER] MAWS/Amber and python program adjustment Bruno Cramer (Tue Aug 27 2019 - 15:53:53 PDT)
[AMBER] Calculation of ΔG from PMF Airy Sanjeev (Tue Aug 27 2019 - 21:41:06 PDT)
- Re: [AMBER] Calculation of ΔG from PMF Carlos Simmerling (Wed Aug 28 2019 - 08:19:14 PDT)
- Re: [AMBER] Calculation of ΔG from PMF David A Case (Wed Aug 28 2019 - 08:35:29 PDT)
[AMBER] MMPBS.py error: IOError: [Errno 2] No such file or directory maryam azimzadehirani (Wed Aug 28 2019 - 00:48:45 PDT)
[AMBER] nmropt problems Andrea H. Kasun (Wed Aug 28 2019 - 06:50:38 PDT)
- Re: [AMBER] nmropt problems David A Case (Wed Aug 28 2019 - 08:15:12 PDT)
  - Re: [AMBER] nmropt problems Andrea H. Kasun (Thu Aug 29 2019 - 09:02:06 PDT)
[AMBER] using accelerated MD on membrane proteins? Homeo Morphism (Wed Aug 28 2019 - 09:09:15 PDT)
- Re: [AMBER] using accelerated MD on membrane proteins? Robin Betz (Wed Aug 28 2019 - 10:39:36 PDT)
[AMBER] question about bond command in tleap Rui Chen (Wed Aug 28 2019 - 13:47:11 PDT)
- Re: [AMBER] question about bond command in tleap Matias Machado (Wed Aug 28 2019 - 14:33:44 PDT)
[AMBER] per residue decompose energy error Nisha Amarnath Jonniya (Thu Aug 29 2019 - 02:07:09 PDT)
[AMBER] periodic box size Rui Chen (Thu Aug 29 2019 - 17:58:54 PDT)
- Re: [AMBER] periodic box size David A Case (Fri Aug 30 2019 - 04:30:27 PDT)
  - Re: [AMBER] periodic box size Rui Chen (Fri Aug 30 2019 - 08:42:13 PDT)
[AMBER] Small molecule break after minimization Amen Shamim (Fri Aug 30 2019 - 06:16:46 PDT)
[AMBER] equilirbration at constant volume Sadaf Rani (Fri Aug 30 2019 - 07:48:24 PDT)
- Re: [AMBER] equilirbration at constant volume David A Case (Fri Aug 30 2019 - 09:30:19 PDT)
[AMBER] Constant PH simulations for non-proteins and nonstandard residues Kolattukudy P. Santo (Fri Aug 30 2019 - 09:00:26 PDT)
- Re: [AMBER] Constant PH simulations for non-proteins and nonstandard residues Cruzeiro,Vinicius Wilian D (Fri Aug 30 2019 - 11:03:56 PDT)
  - Re: [AMBER] Constant PH simulations for non-proteins and nonstandard residues Kolattukudy P. Santo (Tue Sep 03 2019 - 13:08:05 PDT)
[AMBER] Print non bonded pair list Song, Lin (Fri Aug 30 2019 - 09:39:54 PDT)
- Re: [AMBER] Print non bonded pair list David Cerutti (Fri Aug 30 2019 - 09:59:34 PDT)
  - Re: [AMBER] Print non bonded pair list Song, Lin (Tue Sep 03 2019 - 12:09:06 PDT)
    - Re: [AMBER] Print non bonded pair list David Cerutti (Tue Sep 03 2019 - 14:08:05 PDT)
    - Re: [AMBER] Print non bonded pair list Song, Lin (Tue Sep 03 2019 - 14:26:01 PDT)
    - Re: [AMBER] Print non bonded pair list David Cerutti (Tue Sep 03 2019 - 15:36:52 PDT)
[AMBER] Bug in ambpdb in anaconda distribution? Nathan Guerin (Fri Aug 30 2019 - 10:27:17 PDT)
- Re: [AMBER] Bug in ambpdb in anaconda distribution? viktor drobot (Fri Aug 30 2019 - 10:36:38 PDT)
  - Re: [AMBER] Bug in ambpdb in anaconda distribution? Nathan Guerin (Fri Aug 30 2019 - 10:42:22 PDT)
    - Re: [AMBER] Bug in ambpdb in anaconda distribution? Nathan Guerin (Fri Aug 30 2019 - 10:58:25 PDT)
    - Re: [AMBER] Bug in ambpdb in anaconda distribution? viktor drobot (Fri Aug 30 2019 - 11:13:29 PDT)
[AMBER] H - bond calculations shivangi agarwal (Fri Aug 30 2019 - 10:20:31 PDT)
- Re: [AMBER] H - bond calculations shivangi agarwal (Mon Sep 02 2019 - 06:16:25 PDT)
  - Re: [AMBER] H - bond calculations Gustaf Olsson (Mon Sep 02 2019 - 06:47:04 PDT)
[AMBER] running NAMD with AMBER inputs Rui Chen (Sun Sep 01 2019 - 10:29:28 PDT)
- Re: [AMBER] running NAMD with AMBER inputs David Case (Sun Sep 01 2019 - 13:00:43 PDT)
  - Re: [AMBER] running NAMD with AMBER inputs David Case (Sun Sep 01 2019 - 13:02:37 PDT)
[AMBER] MMGBSA.py lignad maryam azimzadehirani (Sun Sep 01 2019 - 22:49:40 PDT)
- Re: [AMBER] MMGBSA.py lignad Elvis Martis (Sun Sep 01 2019 - 23:42:05 PDT)
  - Re: [AMBER] MMGBSA.py lignad maryam azimzadehirani (Sun Sep 01 2019 - 23:56:17 PDT)
    - Re: [AMBER] MMGBSA.py lignad Elvis Martis (Sun Sep 01 2019 - 23:59:21 PDT)
    - Re: [AMBER] MMGBSA.py lignad Elvis Martis (Mon Sep 02 2019 - 00:01:15 PDT)
    - Re: [AMBER] MMGBSA.py lignad maryam azimzadehirani (Mon Sep 02 2019 - 00:09:37 PDT)
[AMBER] Cpptraj watershell CUDA Max Knicker (Mon Sep 02 2019 - 02:29:54 PDT)
- Re: [AMBER] Cpptraj watershell CUDA Elvis Martis (Mon Sep 02 2019 - 03:50:46 PDT)
- Re: [AMBER] Cpptraj watershell CUDA Daniel Roe (Tue Sep 03 2019 - 07:00:29 PDT)
[AMBER] Error creating topology and coordinates file charalamm.cheng.auth.gr (Mon Sep 02 2019 - 02:42:20 PDT)
- Re: [AMBER] Error creating topology and coordinates file charalamm.cheng.auth.gr (Mon Sep 02 2019 - 02:58:21 PDT)
  - Re: [AMBER] Error creating topology and coordinates file Matias Machado (Thu Sep 12 2019 - 07:01:46 PDT)
    - Re: [AMBER] Error creating topology and coordinates file Matias Machado (Thu Sep 12 2019 - 07:16:19 PDT)
[AMBER] Installing on Mac - Back at it Gustaf Olsson (Mon Sep 02 2019 - 06:43:55 PDT)
[AMBER] issue during TI minimisation Núbia Prates (Mon Sep 02 2019 - 07:02:42 PDT)
- Re: [AMBER] issue during TI minimisation David Case (Mon Sep 02 2019 - 09:02:26 PDT)
  - Re: [AMBER] issue during TI minimisation Núbia Prates (Tue Sep 03 2019 - 03:23:04 PDT)
[AMBER] restraintmask (Cannot match namelist object name :1-294) Parviz Seifpanahi Shabane (Mon Sep 02 2019 - 09:22:06 PDT)
- Re: [AMBER] restraintmask (Cannot match namelist object name :1-294) Adrian Roitberg (Mon Sep 02 2019 - 09:29:21 PDT)
[AMBER] Generating parameters for iron-sulfur protein 崔佳文 (Mon Sep 02 2019 - 21:11:10 PDT)
- Re: [AMBER] Generating parameters for iron-sulfur protein Pengfei Li (Sat Sep 07 2019 - 15:03:05 PDT)
  - Re: [AMBER] Generating parameters for iron-sulfur protein Baker, Joseph (Tue Jan 14 2020 - 20:51:28 PST)
    - Re: [AMBER] Generating parameters for iron-sulfur protein Pengfei Li (Sat Jan 18 2020 - 16:39:57 PST)
[AMBER] Problem with CPPTRAJ (RMSD) Rui Chen (Mon Sep 02 2019 - 22:21:47 PDT)
- Re: [AMBER] Problem with CPPTRAJ (RMSD) Daniel Roe (Tue Sep 03 2019 - 05:38:40 PDT)
  - Re: [AMBER] Problem with CPPTRAJ (RMSD) Rui Chen (Tue Sep 03 2019 - 08:18:57 PDT)
    - Re: [AMBER] Problem with CPPTRAJ (RMSD) Daniel Roe (Tue Sep 03 2019 - 10:05:59 PDT)
    - Re: [AMBER] Problem with CPPTRAJ (RMSD) Rui Chen (Tue Sep 03 2019 - 10:10:11 PDT)
[AMBER] AMBER18 installation error xmgign.126.com (Tue Sep 03 2019 - 00:33:15 PDT)
- Re: [AMBER] AMBER18 installation error Daniel Roe (Tue Sep 03 2019 - 05:31:01 PDT)
- Re: [AMBER] AMBER18 installation error David A Case (Tue Sep 03 2019 - 06:29:50 PDT)
  - Re: [AMBER] AMBER18 installation error aa (Tue Sep 03 2019 - 08:31:25 PDT)
[AMBER] Ligand parameterization Hira Jabeen (Tue Sep 03 2019 - 03:56:42 PDT)
- Re: [AMBER] Ligand parameterization Gerald Monard (Tue Sep 03 2019 - 06:17:16 PDT)
  - Re: [AMBER] Ligand parameterization Hira Jabeen (Tue Sep 03 2019 - 08:49:01 PDT)
    - Re: [AMBER] Ligand parameterization David A Case (Tue Sep 03 2019 - 09:51:31 PDT)
[AMBER-Developers] Job opening for AMBER developer. Christian Schafmeister (Tue Sep 03 2019 - 10:30:03 PDT)
[AMBER] lipid order per leaflet Violeta Burns Casamayor (Tue Sep 03 2019 - 10:49:08 PDT)
- Re: [AMBER] lipid order per leaflet Daniel Roe (Fri Sep 13 2019 - 09:22:40 PDT)
  - Re: [AMBER] lipid order per leaflet Violeta Burns Casamayor (Mon Sep 16 2019 - 09:36:21 PDT)
    - Re: [AMBER] lipid order per leaflet Daniel Roe (Mon Sep 16 2019 - 10:08:05 PDT)
[AMBER] ff14SB overestimation of helical comformation Lod King (Tue Sep 03 2019 - 10:49:41 PDT)
- Re: [AMBER] ff14SB overestimation of helical comformation Carlos Simmerling (Tue Sep 03 2019 - 11:17:14 PDT)
  - Re: [AMBER] ff14SB overestimation of helical comformation Lod King (Tue Sep 03 2019 - 11:46:14 PDT)
[AMBER] GBSA Kolattukudy P. Santo (Tue Sep 03 2019 - 13:13:35 PDT)
- Re: [AMBER] GBSA David Case (Tue Sep 03 2019 - 18:18:46 PDT)
  - Re: [AMBER] GBSA Kolattukudy P. Santo (Tue Sep 03 2019 - 18:45:42 PDT)
    - Re: [AMBER] GBSA Matias Machado (Thu Sep 12 2019 - 07:37:47 PDT)
    - Re: [AMBER] GBSA Carlos Simmerling (Fri Sep 13 2019 - 06:13:48 PDT)
    - Re: [AMBER] GBSA Kolattukudy P. Santo (Fri Sep 13 2019 - 07:40:40 PDT)
[AMBER] Amber 18 installation Sunita Patel (Wed Sep 04 2019 - 02:51:58 PDT)
- Re: [AMBER] Amber 18 installation Daniel Roe (Mon Sep 16 2019 - 07:39:28 PDT)
  - Re: [AMBER] Amber 18 installation David A Case (Tue Sep 17 2019 - 05:36:46 PDT)
[AMBER] how to load amber rst file in vmd for observing box size Sadaf Rani (Wed Sep 04 2019 - 08:04:52 PDT)
- Re: [AMBER] how to load amber rst file in vmd for observing box size Elvis Martis (Wed Sep 04 2019 - 08:21:15 PDT)
  - Re: [AMBER] how to load amber rst file in vmd for observing box size Sadaf Rani (Wed Sep 04 2019 - 09:03:12 PDT)
    - Re: [AMBER] how to load amber rst file in vmd for observing box size Elvis Martis (Wed Sep 04 2019 - 09:22:50 PDT)
    - Re: [AMBER] how to load amber rst file in vmd for observing box size Sadaf Rani (Wed Sep 04 2019 - 09:45:55 PDT)
    - Re: [AMBER] how to load amber rst file in vmd for observing box size Elvis Martis (Wed Sep 04 2019 - 10:07:17 PDT)
    - Re: [AMBER] how to load amber rst file in vmd for observing box size Sadaf Rani (Wed Sep 04 2019 - 10:21:25 PDT)
    - Re: [AMBER] how to load amber rst file in vmd for observing box size Sadaf Rani (Wed Sep 04 2019 - 10:25:38 PDT)
    - Re: [AMBER] how to load amber rst file in vmd for observing box size Gustaf Olsson (Wed Sep 04 2019 - 23:06:12 PDT)
    - Re: [AMBER] how to load amber rst file in vmd for observing box size Sadaf Rani (Fri Sep 06 2019 - 12:55:30 PDT)
    - Re: [AMBER] how to load amber rst file in vmd for observing box size Gustaf Olsson (Sat Sep 07 2019 - 01:14:22 PDT)
    - Re: [AMBER] how to load amber rst file in vmd for observing box size Gustaf Olsson (Mon Sep 09 2019 - 06:29:44 PDT)
- Re: [AMBER] how to load amber rst file in vmd for observing box size Fabian Glaser (Wed Sep 04 2019 - 09:09:41 PDT)
[AMBER] cloud vs purchase Fabian Glaser (Thu Sep 05 2019 - 00:25:38 PDT)
- Re: [AMBER] cloud vs purchase Gustaf Olsson (Thu Sep 05 2019 - 02:16:01 PDT)
- Re: [AMBER] cloud vs purchase Ross Walker (Thu Sep 05 2019 - 06:13:13 PDT)
  - Re: [AMBER] cloud vs purchase Fabian Glaser (Thu Sep 05 2019 - 07:32:54 PDT)
- Re: [AMBER] cloud vs purchase Thomas Cheatham (Wed Sep 18 2019 - 14:22:29 PDT)
[AMBER] how to read the outup file of QMMM MD simulation with Amber combined with Gaussian (Geng Dong) 东庚 (Thu Sep 05 2019 - 02:50:36 PDT)
- Re: [AMBER] how to read the outup file of QMMM MD simulation with Amber combined with Gaussian (Geng Dong) David A Case (Thu Sep 05 2019 - 05:40:28 PDT)
[AMBER] Recent updates to how Amber carries out softcore free energy calculations David A Case (Thu Sep 05 2019 - 06:40:38 PDT)
- Re: [AMBER] Recent updates to how Amber carries out softcore free energy calculations Ruxi Qi (Wed Sep 11 2019 - 23:36:21 PDT)
[AMBER] Calculating RMSF Martín Pettinati (Thu Sep 05 2019 - 08:20:40 PDT)
- Re: [AMBER] Calculating RMSF Daniel Roe (Thu Sep 05 2019 - 08:34:52 PDT)
[AMBER] How to generate parameter files of modified terminal amino acid residue using Antechamber Shankha Banerjee (Thu Sep 05 2019 - 11:19:51 PDT)
- Re: [AMBER] How to generate parameter files of modified terminal amino acid residue using Antechamber David Case (Fri Sep 06 2019 - 05:19:47 PDT)
- Re: [AMBER] How to generate parameter files of modified terminal amino acid residue using Antechamber Shankha Banerjee (Fri Sep 06 2019 - 23:00:26 PDT)
[AMBER] Explicit understanding the force computed from U(CMAP) term Lod King (Thu Sep 05 2019 - 15:34:34 PDT)
- Re: [AMBER] Explicit understanding the force computed from U(CMAP) term David Cerutti (Fri Sep 06 2019 - 01:28:58 PDT)
  - Re: [AMBER] Explicit understanding the force computed from U(CMAP) term Lod King (Fri Sep 06 2019 - 02:03:58 PDT)
  - Re: [AMBER] Explicit understanding the force computed from U(CMAP) term Lod King (Fri Sep 06 2019 - 17:20:48 PDT)
    - Re: [AMBER] Explicit understanding the force computed from U(CMAP) term David Cerutti (Mon Sep 09 2019 - 10:13:06 PDT)
    - Re: [AMBER] Explicit understanding the force computed from U(CMAP) term Lod King (Mon Sep 09 2019 - 10:53:56 PDT)
[AMBER] Recent Enhancements to secstruct/dssp in Cpptraj Daniel Roe (Fri Sep 06 2019 - 12:47:12 PDT)
[AMBER] Generating the parameters for non-standard amino-acid residue RITUPARNA ROY (Sat Sep 07 2019 - 00:37:24 PDT)
- Re: [AMBER] Generating the parameters for non-standard amino-acid residue David A Case (Mon Sep 09 2019 - 05:50:53 PDT)
  - Re: [AMBER] Generating the parameters for non-standard amino-acid residue RITUPARNA ROY (Mon Sep 09 2019 - 07:01:53 PDT)
    - Re: [AMBER] Generating the parameters for non-standard amino-acid residue Carlos Simmerling (Mon Sep 09 2019 - 08:18:40 PDT)
    - Re: [AMBER] Generating the parameters for non-standard amino-acid residue RITUPARNA ROY (Mon Sep 09 2019 - 09:25:58 PDT)
    - Re: [AMBER] Generating the parameters for non-standard amino-acid residue Carlos Simmerling (Mon Sep 09 2019 - 10:21:49 PDT)
[AMBER] Error in calculation of per residue decomposition shivangi agarwal (Sat Sep 07 2019 - 12:42:35 PDT)
- Re: [AMBER] Error in calculation of per residue decomposition shivangi agarwal (Mon Sep 09 2019 - 08:13:24 PDT)
  - Re: [AMBER] Error in calculation of per residue decomposition koushik kasavajhala (Mon Sep 09 2019 - 08:39:05 PDT)
[AMBER] bad atom type i Johnny Guevara (Sun Sep 08 2019 - 12:49:15 PDT)
- Re: [AMBER] bad atom type i Elvis Martis (Sun Sep 08 2019 - 22:53:37 PDT)
[AMBER] Energy minimization in Implicit solvent for Langevin dynamics simulation Vishal Singh (Mon Sep 09 2019 - 00:21:04 PDT)
- Re: [AMBER] Energy minimization in Implicit solvent for Langevin dynamics simulation David A Case (Mon Sep 09 2019 - 05:58:23 PDT)
[AMBER] tMD and free energy calculation Elena Gomez (Mon Sep 09 2019 - 01:38:22 PDT)
- Re: [AMBER] tMD and free energy calculation Bill Ross (Mon Sep 09 2019 - 02:03:58 PDT)
Re: [AMBER] Force conversion David A Case (Mon Sep 09 2019 - 05:57:07 PDT)
[AMBER] Implicit solvent simulation. Parviz Seifpanahi Shabane (Mon Sep 09 2019 - 15:13:39 PDT)
- Re: [AMBER] Implicit solvent simulation. David A Case (Tue Sep 10 2019 - 05:35:55 PDT)
- Re: [AMBER] Implicit solvent simulation. Saeed Izadi (Tue Sep 10 2019 - 12:16:51 PDT)
[AMBER] Query regarding plot Airy Sanjeev (Tue Sep 10 2019 - 04:44:19 PDT)
[AMBER] Small Molecules parameters Alaa Abdelrahman (Tue Sep 10 2019 - 08:51:10 PDT)
- Re: [AMBER] Small Molecules parameters David Case (Sat Sep 28 2019 - 05:52:08 PDT)
[AMBER] Amber_Cpptraj Avirup Ghosh (Tue Sep 10 2019 - 09:12:24 PDT)
- Re: [AMBER] Amber_Cpptraj Daniel Roe (Fri Sep 13 2019 - 09:26:42 PDT)
[AMBER] Force field for aMD cpimenta (Tue Sep 10 2019 - 09:56:25 PDT)
- Re: [AMBER] Force field for aMD Carlos Simmerling (Tue Sep 10 2019 - 10:01:50 PDT)
[AMBER] titratable residues cuda M. Pyrka (Wed Sep 11 2019 - 00:27:35 PDT)
[AMBER] PCA calculation projection Aashish Bhatt (Wed Sep 11 2019 - 03:22:35 PDT)
- Re: [AMBER] PCA calculation projection Pratul Agarwal (Wed Sep 11 2019 - 05:59:51 PDT)
  - Re: [AMBER] PCA calculation projection Aashish Bhatt (Wed Sep 11 2019 - 22:15:26 PDT)
    - Re: [AMBER] PCA calculation projection Pratul Agarwal (Thu Sep 12 2019 - 05:52:24 PDT)
[AMBER] Helix Structures Lost during Heating and Equilibrium Steps Bharat Manna (Wed Sep 11 2019 - 03:43:38 PDT)
- Re: [AMBER] Helix Structures Lost during Heating and Equilibrium Steps Carlos Simmerling (Wed Sep 11 2019 - 03:56:51 PDT)
[AMBER] problem with random seed Jinfeng Huang (Wed Sep 11 2019 - 07:44:17 PDT)
- Re: [AMBER] problem with random seed Carlos Simmerling (Wed Sep 11 2019 - 07:56:36 PDT)
- Re: [AMBER] problem with random seed diane lynch (Wed Sep 11 2019 - 08:08:22 PDT)
[AMBER] PNEB--"vlimit exceeded" error Anthony Bogetti (Wed Sep 11 2019 - 08:03:46 PDT)
[AMBER] error regarding MCPB.py Hemant Kisan (Wed Sep 11 2019 - 08:59:16 PDT)
- Re: [AMBER] error regarding MCPB.py Aashish Bhatt (Wed Sep 11 2019 - 21:50:41 PDT)
[AMBER] optimizing GAFF2 torsional parameters Christos Deligkaris (Wed Sep 11 2019 - 11:22:38 PDT)
- Re: [AMBER] optimizing GAFF2 torsional parameters Karl Kirschner (Thu Sep 12 2019 - 00:06:56 PDT)
[AMBER] Protein-ligand simulation and help w.r.t files for carrying out simulation Renato Araujo (Wed Sep 11 2019 - 15:06:04 PDT)
- Re: [AMBER] Protein-ligand simulation and help w.r.t files for carrying out simulation Gustaf Olsson (Wed Sep 11 2019 - 22:38:18 PDT)
[AMBER] Fwd: AmberTools19 installation error 174026008.iitb.ac.in (Wed Sep 11 2019 - 22:57:00 PDT)
- Re: [AMBER] Fwd: AmberTools19 installation error David Case (Thu Sep 12 2019 - 06:30:37 PDT)
[AMBER] How to generate parameter files of N-terminal modified amino acid residue? Shankha Banerjee (Thu Sep 12 2019 - 00:56:30 PDT)
[AMBER] ASMD iat define Nisha Amarnath Jonniya (Thu Sep 12 2019 - 05:46:17 PDT)
[AMBER] the structure of cellulose II in Glycam-06h force field 冷灿 (Thu Sep 12 2019 - 18:00:44 PDT)
[AMBER] AmberTools19 installation error 174026008.iitb.ac.in (Thu Sep 12 2019 - 22:10:18 PDT)
- Re: [AMBER] AmberTools19 installation error Tyler Luchko (Lists) (Fri Sep 13 2019 - 09:47:17 PDT)
[AMBER] Amber not working after installation - Help from github charalamm.cheng.auth.gr (Fri Sep 13 2019 - 02:59:24 PDT)
- Re: [AMBER] Amber not working after installation - Help from github Elvis Martis (Fri Sep 13 2019 - 04:11:39 PDT)
  - Re: [AMBER] Amber not working after installation - Help from github charalamm.cheng.auth.gr (Fri Sep 13 2019 - 06:05:08 PDT)
    - Re: [AMBER] Amber not working after installation - Help from github Elvis Martis (Fri Sep 13 2019 - 06:49:31 PDT)
    - Re: [AMBER] Amber not working after installation - Help from github charalamm.cheng.auth.gr (Fri Sep 13 2019 - 09:56:04 PDT)
    - Re: [AMBER] Amber not working after installation - Help from github Elvis Martis (Fri Sep 13 2019 - 10:12:20 PDT)
    - Re: [AMBER] Amber not working after installation - Help from github Hai Nguyen (Fri Sep 13 2019 - 12:45:03 PDT)
- Re: [AMBER] Amber not working after installation - Help from github Hai Nguyen (Fri Sep 13 2019 - 12:44:04 PDT)
  - Re: [AMBER] Amber not working after installation - Help from github charalamm.cheng.auth.gr (Sat Sep 14 2019 - 01:36:17 PDT)
    - Re: [AMBER] Amber not working after installation - Help from github Hai Nguyen (Sat Sep 14 2019 - 11:37:08 PDT)
    - Re: [AMBER] Amber not working after installation - Help from github charalamm.cheng.auth.gr (Sun Sep 15 2019 - 01:24:38 PDT)
    - Re: [AMBER] Amber not working after installation - Help from github Elvis Martis (Sun Sep 15 2019 - 05:02:29 PDT)
    - Re: [AMBER] Amber not working after installation - Help from github Hai Nguyen (Sun Sep 15 2019 - 12:27:13 PDT)
[AMBER] Bug in Amber-Orca communication ? Åsmund Røhr Kjendseth (Fri Sep 13 2019 - 02:59:56 PDT)
[AMBER] Fwd: tutorial for finding binding free energies Sadaf Rani (Fri Sep 13 2019 - 08:45:07 PDT)
- Re: [AMBER] Fwd: tutorial for finding binding free energies David Case (Fri Sep 13 2019 - 14:39:00 PDT)
[AMBER] sqm error 174026008.iitb.ac.in (Sat Sep 14 2019 - 04:51:44 PDT)
- Re: [AMBER] sqm error David Case (Sat Sep 14 2019 - 09:28:55 PDT)
[AMBER] sander.MPI gives segfault if compiled with Intel compilers viktor drobot (Sun Sep 15 2019 - 06:34:55 PDT)
- Re: [AMBER] sander.MPI gives segfault if compiled with Intel compilers David A Case (Mon Sep 16 2019 - 05:21:16 PDT)
  - Re: [AMBER] sander.MPI gives segfault if compiled with Intel compilers viktor drobot (Mon Sep 16 2019 - 05:32:25 PDT)
    - Re: [AMBER] sander.MPI gives segfault if compiled with Intel compilers Scott Brozell (Wed Sep 18 2019 - 13:16:37 PDT)
    - Re: [AMBER] sander.MPI gives segfault if compiled with Intel compilers viktor drobot (Wed Sep 18 2019 - 14:45:32 PDT)
    - Re: [AMBER] sander.MPI gives segfault if compiled with Intel compilers David Case (Wed Sep 18 2019 - 18:06:45 PDT)
[AMBER] How can I make the initial configuration and topology with polarizable force field? 조준범 (Sun Sep 15 2019 - 20:25:18 PDT)
- Re: [AMBER] How can I make the initial configuration and topology with polarizable force field? David A Case (Mon Sep 16 2019 - 05:24:57 PDT)
[AMBER] AMBER: error in reading namelist cntrl 조준범 (Mon Sep 16 2019 - 00:14:05 PDT)
- Re: [AMBER] AMBER: error in reading namelist cntrl Elvis Martis (Mon Sep 16 2019 - 00:24:43 PDT)
  - Re: [AMBER] AMBER: error in reading namelist cntrl 조준범 (Mon Sep 16 2019 - 00:40:20 PDT)
    - Re: [AMBER] AMBER: error in reading namelist cntrl Elvis Martis (Mon Sep 16 2019 - 00:46:31 PDT)
- Re: [AMBER] AMBER: error in reading namelist cntrl David A Case (Mon Sep 16 2019 - 05:29:13 PDT)
[AMBER] AMBER: Segmentation fault 조준범 (Mon Sep 16 2019 - 01:19:35 PDT)
- Re: [AMBER] AMBER: Segmentation fault Bill Ross (Mon Sep 16 2019 - 01:26:22 PDT)
  - Re: [AMBER] AMBER: Segmentation fault David A Case (Mon Sep 16 2019 - 05:31:45 PDT)
[AMBER] Modified variables in cphstats cpimenta (Mon Sep 16 2019 - 05:36:33 PDT)
- Re: [AMBER] Modified variables in cphstats Daniel Roe (Mon Sep 16 2019 - 06:33:17 PDT)
[AMBER] Question about unusual RMSD behaviour Amit Kumar (Mon Sep 16 2019 - 06:19:48 PDT)
- Re: [AMBER] Question about unusual RMSD behaviour Carlos Simmerling (Mon Sep 16 2019 - 06:26:55 PDT)
  - Re: [AMBER] Question about unusual RMSD behaviour Amit Kumar (Tue Sep 17 2019 - 02:14:25 PDT)
    - Re: [AMBER] Question about unusual RMSD behaviour Carlos Simmerling (Tue Sep 17 2019 - 03:58:13 PDT)
    - Re: [AMBER] Question about unusual RMSD behaviour Amit Kumar (Tue Sep 17 2019 - 06:14:18 PDT)
    - Re: [AMBER] Question about unusual RMSD behaviour Carlos Simmerling (Tue Sep 17 2019 - 08:45:39 PDT)
[AMBER] Hybrid topology for mutating residue Aashish Bhatt (Mon Sep 16 2019 - 08:37:37 PDT)
- Re: [AMBER] Hybrid topology for mutating residue David A Case (Tue Sep 17 2019 - 05:43:11 PDT)
[AMBER] Coordinate resetting (SHAKE) can not be accomplished Sunita Patel (Mon Sep 16 2019 - 23:30:26 PDT)
- Re: [AMBER] Coordinate resetting (SHAKE) can not be accomplished Ahmed Elrashedy (Tue Sep 17 2019 - 00:30:29 PDT)
[AMBER] Small ligand activators molecule shivangi agarwal (Tue Sep 17 2019 - 05:15:14 PDT)
- Re: [AMBER] Small ligand activators molecule David A Case (Wed Sep 18 2019 - 06:31:07 PDT)
[AMBER] Error installing Amber on Centos 7 Juan Etchart (Tue Sep 17 2019 - 05:19:53 PDT)
- Re: [AMBER] Error installing Amber on Centos 7 David A Case (Tue Sep 17 2019 - 12:18:56 PDT)
[AMBER] seek for how to calculate the binding free energy of a covalent inhibitor 石娜 (Tue Sep 17 2019 - 05:24:50 PDT)
- Re: [AMBER] seek for how to calculate the binding free energy of a covalent inhibitor Ahmed Elrashedy (Tue Sep 17 2019 - 05:46:57 PDT)
  - Re: [AMBER] seek for how to calculate the binding free energy of a covalent inhibitor Carlos Simmerling (Tue Sep 17 2019 - 08:46:21 PDT)
- Re: [AMBER] seek for how to calculate the binding free energy of a covalent inhibitor David A Case (Tue Sep 17 2019 - 12:20:30 PDT)
[AMBER] problem with random seed Jinfeng Huang (Tue Sep 17 2019 - 06:57:30 PDT)
- Re: [AMBER] problem with random seed Carlos Simmerling (Tue Sep 17 2019 - 09:17:22 PDT)
[AMBER] Amber17 to Amber18 considerations and archive? Shayna Hilburg (Tue Sep 17 2019 - 13:59:18 PDT)
- Re: [AMBER] Amber17 to Amber18 considerations and archive? David Case (Wed Sep 18 2019 - 18:12:59 PDT)
[AMBER] unit conversion during umbrella sampling and then PMF calculation SATYAJIT KHATUA (Wed Sep 18 2019 - 01:06:34 PDT)
- Re: [AMBER] unit conversion during umbrella sampling and then PMF calculation Song, Lin (Wed Sep 18 2019 - 09:27:28 PDT)
[AMBER] Cpptraj RDF onlyframes Nikolay N. Kuzmich (Wed Sep 18 2019 - 05:07:41 PDT)
- Re: [AMBER] Cpptraj RDF onlyframes Gustaf Olsson (Wed Sep 18 2019 - 06:15:12 PDT)
- Re: [AMBER] Cpptraj RDF onlyframes Elvis Martis (Wed Sep 18 2019 - 06:15:22 PDT)
- Re: [AMBER] Cpptraj RDF onlyframes Nikolay N. Kuzmich (Thu Sep 19 2019 - 09:02:17 PDT)
[AMBER] Trouble installing Amber 18 Groner, Rob (Wed Sep 18 2019 - 06:43:47 PDT)
- Re: [AMBER] Trouble installing Amber 18 Daniel Roe (Wed Sep 18 2019 - 08:22:15 PDT)
  - Re: [AMBER] Trouble installing Amber 18 Scott Brozell (Wed Sep 18 2019 - 12:48:00 PDT)
[AMBER] How big a molecule can antechamber (sqm) put charges on? Liao (Wed Sep 18 2019 - 18:29:24 PDT)
- Re: [AMBER] How big a molecule can antechamber (sqm) put charges on? David A Case (Thu Sep 19 2019 - 06:57:43 PDT)
[AMBER] Cpptraj extracting coordinate data of a projectile Hadi Rahmaninejad (Wed Sep 18 2019 - 21:04:44 PDT)
- Re: [AMBER] Cpptraj extracting coordinate data of a projectile Daniel Roe (Thu Sep 19 2019 - 03:55:12 PDT)
  - Re: [AMBER] Cpptraj extracting coordinate data of a projectile Hadi Rahmaninejad (Thu Sep 19 2019 - 07:14:36 PDT)
    - Re: [AMBER] Cpptraj extracting coordinate data of a projectile Daniel Roe (Thu Sep 19 2019 - 11:08:43 PDT)
[AMBER] ambpdb error while conversion Sunita Patel (Thu Sep 19 2019 - 04:25:29 PDT)
- Re: [AMBER] ambpdb error while conversion Elvis Martis (Thu Sep 19 2019 - 04:41:07 PDT)
  - Re: [AMBER] ambpdb error while conversion Sunita Patel (Tue Sep 24 2019 - 04:23:10 PDT)
    - Re: [AMBER] ambpdb error while conversion Elvis Martis (Tue Sep 24 2019 - 04:42:42 PDT)
    - Re: [AMBER] ambpdb error while conversion Sunita Patel (Tue Sep 24 2019 - 04:45:51 PDT)
    - Re: [AMBER] ambpdb error while conversion Elvis Martis (Tue Sep 24 2019 - 04:58:21 PDT)
    - Re: [AMBER] ambpdb error while conversion Sunita Patel (Wed Sep 25 2019 - 01:06:22 PDT)
    - Re: [AMBER] ambpdb error while conversion Bill Ross (Wed Sep 25 2019 - 01:16:43 PDT)
    - Re: [AMBER] ambpdb error while conversion Sunita Patel (Wed Sep 25 2019 - 01:29:15 PDT)
    - Re: [AMBER] ambpdb error while conversion Elvis Martis (Wed Sep 25 2019 - 01:42:53 PDT)
    - Re: [AMBER] ambpdb error while conversion Bill Ross (Wed Sep 25 2019 - 03:11:41 PDT)
    - Re: [AMBER] ambpdb error while conversion Sunita Patel (Wed Sep 25 2019 - 04:35:20 PDT)
    - Re: [AMBER] ambpdb error while conversion Bill Ross (Wed Sep 25 2019 - 05:15:53 PDT)
- Re: [AMBER] ambpdb error while conversion David Case (Fri Sep 20 2019 - 06:13:57 PDT)
  - Re: [AMBER] ambpdb error while conversion Sunita Patel (Tue Sep 24 2019 - 04:12:54 PDT)
    - Re: [AMBER] ambpdb error while conversion Bill Ross (Tue Sep 24 2019 - 04:25:00 PDT)
    - Re: [AMBER] ambpdb error while conversion Carlos Simmerling (Tue Sep 24 2019 - 04:26:47 PDT)
    - Re: [AMBER] ambpdb error while conversion David Case (Wed Sep 25 2019 - 05:59:07 PDT)
- Re: [AMBER] ambpdb error while conversion Daniel Roe (Mon Sep 23 2019 - 06:21:45 PDT)
[AMBER] ANTECHAMBER_AC 2018808152.njau.edu.cn (Thu Sep 19 2019 - 05:38:07 PDT)
- Re: [AMBER] ANTECHAMBER_AC Matias Machado (Thu Sep 19 2019 - 06:51:27 PDT)
- Re: [AMBER] ANTECHAMBER_AC David A Case (Thu Sep 19 2019 - 07:08:07 PDT)
  - Re: [AMBER] ANTECHAMBER_AC Matias Machado (Thu Sep 19 2019 - 07:36:48 PDT)
[AMBER] Force field problem : Acyl tail fragments parameters Pierre Leprovost (Thu Sep 19 2019 - 05:46:03 PDT)
[AMBER] trajectory coordinate out of box Hadi Rahmaninejad (Thu Sep 19 2019 - 09:47:31 PDT)
- Re: [AMBER] trajectory coordinate out of box Daniel Roe (Thu Sep 19 2019 - 10:49:36 PDT)
  - Re: [AMBER] trajectory coordinate out of box Hadi Rahmaninejad (Thu Sep 19 2019 - 11:40:09 PDT)
- Re: [AMBER] trajectory coordinate out of box David A Case (Thu Sep 19 2019 - 12:48:42 PDT)
[AMBER] Error: an illegal memory access was encountered launching kernel kClearForces cudaFree GpuBuffer::Deallocate failed an illegal memory access was encountered 石娜 (Fri Sep 20 2019 - 00:27:20 PDT)
- Re: [AMBER] Error: an illegal memory access was encountered launching kernel kClearForces cudaFree GpuBuffer::Deallocate failed an illegal memory access was encountered Bill Ross (Fri Sep 20 2019 - 02:53:26 PDT)
- Re: [AMBER] Error: an illegal memory access was encountered launching kernel kClearForces cudaFree GpuBuffer::Deallocate failed an illegal memory access was encountered David Case (Fri Sep 20 2019 - 05:40:26 PDT)
[AMBER] EstJ6_DBP_bound_sus 2018808152.njau.edu.cn (Fri Sep 20 2019 - 02:18:46 PDT)
- Re: [AMBER] EstJ6_DBP_bound_sus Bill Ross (Fri Sep 20 2019 - 02:50:34 PDT)
- Re: [AMBER] EstJ6_DBP_bound_sus David Case (Fri Sep 20 2019 - 05:43:41 PDT)
[AMBER] Replica Exchange pH simulations with explicit solvent Jon Uranga (Fri Sep 20 2019 - 03:07:55 PDT)
[AMBER] TI residue mutation with pmemd on GPU Hosein Geraili Daronkola (Fri Sep 20 2019 - 03:18:11 PDT)
- Re: [AMBER] TI residue mutation with pmemd on GPU David Case (Fri Sep 20 2019 - 05:56:16 PDT)
- Re: [AMBER] TI residue mutation with pmemd on GPU Premila Samuel Mohan Dass (Fri Sep 20 2019 - 06:15:19 PDT)
- Re: [AMBER] TI residue mutation with pmemd on GPU Hosein Geraili Daronkola (Thu Sep 26 2019 - 07:33:59 PDT)
[AMBER] cpptraj rms with different pdb Lenka (Fri Sep 20 2019 - 12:24:59 PDT)
- Re: [AMBER] cpptraj rms with different pdb Elvis Martis (Fri Sep 20 2019 - 22:29:43 PDT)
- Re: [AMBER] cpptraj rms with different pdb Lenka (Sat Sep 21 2019 - 05:59:23 PDT)
  - Re: [AMBER] cpptraj rms with different pdb Elvis Martis (Sat Sep 21 2019 - 21:31:43 PDT)
- Re: [AMBER] cpptraj rms with different pdb Lenka (Sun Sep 22 2019 - 05:15:24 PDT)
- Re: [AMBER] cpptraj rms with different pdb Daniel Roe (Mon Sep 23 2019 - 06:16:48 PDT)
- Re: [AMBER] cpptraj rms with different pdb Lenka (Mon Sep 23 2019 - 07:49:02 PDT)
  - Re: [AMBER] cpptraj rms with different pdb Daniel Roe (Thu Sep 26 2019 - 10:58:30 PDT)
[AMBER] angles analysis Fabian Glaser (Sun Sep 22 2019 - 05:15:44 PDT)
[AMBER] MD distorted MYRIAN TORRES RICO (Mon Sep 23 2019 - 02:41:40 PDT)
- Re: [AMBER] MD distorted Bill Ross (Mon Sep 23 2019 - 02:51:28 PDT)
[AMBER] md distorted MYRIAN TORRES RICO (Mon Sep 23 2019 - 03:54:20 PDT)
- Re: [AMBER] md distorted Bill Ross (Mon Sep 23 2019 - 04:27:42 PDT)
[AMBER] DNA methylation parameters 李振东 (Mon Sep 23 2019 - 06:10:17 PDT)
- Re: [AMBER] DNA methylation parameters David Case (Sat Sep 28 2019 - 05:49:17 PDT)
  - Re: [AMBER] DNA methylation parameters Zhendong Li (Tue Oct 01 2019 - 07:50:20 PDT)
[AMBER] Unable to generate parameters of modified amino acids using LEAP Shankha Banerjee (Mon Sep 23 2019 - 07:04:07 PDT)
- Re: [AMBER] Unable to generate parameters of modified amino acids using LEAP David Case (Mon Sep 23 2019 - 08:31:24 PDT)
[AMBER] PARAMFIT David Ricardo Figueroa Blanco (Mon Sep 23 2019 - 08:28:15 PDT)
- Re: [AMBER] PARAMFIT Robin Betz (Mon Sep 23 2019 - 16:05:18 PDT)
[AMBER] many failures on "make test" David Mathog (Mon Sep 23 2019 - 13:18:45 PDT)
- Re: [AMBER] many failures on "make test" Hai Nguyen (Mon Sep 23 2019 - 13:47:51 PDT)
  - Re: [AMBER] many failures on "make test" David Mathog (Mon Sep 23 2019 - 13:57:17 PDT)
    - Re: [AMBER] many failures on "make test" Hai Nguyen (Mon Sep 23 2019 - 15:03:26 PDT)
  - Re: [AMBER] many failures on "make test" David Mathog (Mon Sep 23 2019 - 16:46:46 PDT)
[AMBER] About Thermodynamic Integration tutorial (A9) with pmemd.cuda (GPU) HOCHEOL LIM (Mon Sep 23 2019 - 18:35:20 PDT)
- Re: [AMBER] About Thermodynamic Integration tutorial (A9) with pmemd.cuda (GPU) Hosein Geraili Daronkola (Mon Sep 23 2019 - 23:37:03 PDT)
[AMBER] EstJ6_DBP_bound_sus 2018808152.njau.edu.cn (Tue Sep 24 2019 - 01:34:36 PDT)
- Re: [AMBER] EstJ6_DBP_bound_sus Elvis Martis (Tue Sep 24 2019 - 01:48:43 PDT)
- Re: [AMBER] EstJ6_DBP_bound_sus David Case (Tue Sep 24 2019 - 04:55:54 PDT)
[AMBER] restraints error MYRIAN TORRES RICO (Tue Sep 24 2019 - 01:36:50 PDT)
- Re: [AMBER] restraints error David Case (Tue Sep 24 2019 - 05:03:45 PDT)
  - Re: [AMBER] restraints error MYRIAN TORRES RICO (Tue Sep 24 2019 - 06:39:33 PDT)
[AMBER] Packmol and Amber emanuele falbo (Tue Sep 24 2019 - 06:33:12 PDT)
- Re: [AMBER] Packmol and Amber David Case (Wed Sep 25 2019 - 06:03:09 PDT)
  - Re: [AMBER] Packmol and Amber Matias Machado (Wed Sep 25 2019 - 07:01:40 PDT)
[AMBER] MMPBSA.py -> FATAL: NATOM mismatch in coord and topology files charalamm.cheng.auth.gr (Tue Sep 24 2019 - 09:50:57 PDT)
[AMBER] up to date CUDA versions? Shayna Hilburg (Tue Sep 24 2019 - 13:07:28 PDT)
- Re: [AMBER] up to date CUDA versions? Ross Walker (Wed Sep 25 2019 - 03:25:52 PDT)
[AMBER] On AWS instance, MD stops running after sometime without producing any error neha rana (Tue Sep 24 2019 - 13:28:32 PDT)
[AMBER] Problem in calculating MMPBSA-GBSA Airy Sanjeev (Tue Sep 24 2019 - 22:53:46 PDT)
- Re: [AMBER] Problem in calculating MMPBSA-GBSA Ray Luo (Wed Sep 25 2019 - 08:30:52 PDT)
[AMBER] aMD on a protein-protein complex maryam azimzadehirani (Wed Sep 25 2019 - 01:27:05 PDT)
[AMBER] which force field should be used for proteins when phosaa10 is used for phosphorylated serine? Ming Tang (Wed Sep 25 2019 - 01:36:14 PDT)
[AMBER] Question regarding ntx and irest Gustaf Olsson (Wed Sep 25 2019 - 03:09:58 PDT)
- Re: [AMBER] Question regarding ntx and irest David Case (Wed Sep 25 2019 - 06:43:35 PDT)
  - Re: [AMBER] Question regarding ntx and irest Gustaf Olsson (Wed Sep 25 2019 - 13:01:19 PDT)
[AMBER] MMGBSA energy calculation problem for RNA Liao (Wed Sep 25 2019 - 03:49:23 PDT)
- Re: [AMBER] MMGBSA energy calculation problem for RNA David Case (Wed Sep 25 2019 - 06:54:17 PDT)
  - Re: [AMBER] MMGBSA energy calculation problem for RNA Liao (Wed Sep 25 2019 - 08:18:38 PDT)
    - Re: [AMBER] MMGBSA energy calculation problem for RNA Carlos Simmerling (Wed Sep 25 2019 - 09:06:16 PDT)
    - Re: [AMBER] MMGBSA energy calculation problem for RNA Hai Nguyen (Wed Sep 25 2019 - 09:13:00 PDT)
    - Re: [AMBER] MMGBSA energy calculation problem for RNA Liao (Wed Sep 25 2019 - 19:13:53 PDT)
- [AMBER] Self-update: MMGBSA energy calculation problem for RNA Liao (Wed Sep 25 2019 - 08:12:55 PDT)
[AMBER] Please how to solve the unfilled valence problem in antechamber Renato Araujo (Wed Sep 25 2019 - 10:27:40 PDT)
- Re: [AMBER] Please how to solve the unfilled valence problem in antechamber Liao (Wed Sep 25 2019 - 19:10:46 PDT)
- Re: [AMBER] Please how to solve the unfilled valence problem in antechamber David Case (Sat Sep 28 2019 - 05:46:49 PDT)
[AMBER] How can I change the default unit of density? 조준범 (Wed Sep 25 2019 - 22:13:02 PDT)
- Re: [AMBER] How can I change the default unit of density? Adrian Roitberg (Thu Sep 26 2019 - 01:02:58 PDT)
[AMBER] -Antechamber error for modified residues Patil Pranita Uttamrao (Wed Sep 25 2019 - 23:16:49 PDT)
- Re: [AMBER] -Antechamber error for modified residues David Case (Sat Sep 28 2019 - 05:44:55 PDT)
[AMBER] Rotational/torsion energy Gustaf Olsson (Wed Sep 25 2019 - 23:30:31 PDT)
- Re: [AMBER] Rotational/torsion energy Karl Kirschner (Thu Sep 26 2019 - 00:48:13 PDT)
  - Re: [AMBER] Rotational/torsion energy Gustaf Olsson (Thu Sep 26 2019 - 03:13:36 PDT)
    - Re: [AMBER] Rotational/torsion energy Daniel Roe (Thu Oct 03 2019 - 12:33:08 PDT)
    - Re: [AMBER] Rotational/torsion energy Gustaf Olsson (Thu Oct 03 2019 - 23:01:10 PDT)
[AMBER] Compilation of Amber on Cray Suman Chakrabarty (Thu Sep 26 2019 - 01:53:28 PDT)
- Re: [AMBER] Compilation of Amber on Cray David Case (Thu Sep 26 2019 - 07:07:00 PDT)
  - Re: [AMBER] Compilation of Amber on Cray Hai Nguyen (Thu Sep 26 2019 - 07:52:57 PDT)
    - Re: [AMBER] Compilation of Amber on Cray Jason Swails (Sun Sep 29 2019 - 19:27:50 PDT)
  - Re: [AMBER] Compilation of Amber on Cray Suman Chakrabarty (Thu Sep 26 2019 - 09:30:22 PDT)
    - Re: [AMBER] Compilation of Amber on Cray David Case (Thu Sep 26 2019 - 12:41:30 PDT)
    - Re: [AMBER] Compilation of Amber on Cray Suman Chakrabarty (Sun Sep 29 2019 - 01:07:32 PDT)
    - Re: [AMBER] Compilation of Amber on Cray David Case (Sun Sep 29 2019 - 05:21:48 PDT)
    - Re: [AMBER] Compilation of Amber on Cray Suman Chakrabarty (Mon Sep 30 2019 - 04:05:40 PDT)
    - Re: [AMBER] Compilation of Amber on Cray Daniel Roe (Mon Sep 30 2019 - 04:48:00 PDT)
    - Re: [AMBER] Compilation of Amber on Cray Suman Chakrabarty (Mon Sep 30 2019 - 10:42:13 PDT)
[AMBER] BORON parameters Monika Choudhary (Thu Sep 26 2019 - 02:41:29 PDT)
- Re: [AMBER] BORON parameters David Case (Thu Sep 26 2019 - 07:09:29 PDT)
Re: [AMBER] not able to install python...using cygwin David Case (Thu Sep 26 2019 - 07:11:23 PDT)
- Re: [AMBER] not able to install python...using cygwin David Case (Thu Sep 26 2019 - 07:13:26 PDT)
[AMBER] free energy calculation Sadaf Rani (Thu Sep 26 2019 - 07:25:56 PDT)
- Re: [AMBER] free energy calculation David Case (Thu Sep 26 2019 - 13:04:16 PDT)
Re: [AMBER] problem installing miniconda ABEL Stephane (Thu Sep 26 2019 - 08:41:20 PDT)
Re: [AMBER] imin=5 fails to produce output Casalini Tommaso (Thu Sep 26 2019 - 08:41:14 PDT)
- Re: [AMBER] imin=5 fails to produce output Casalini Tommaso (Thu Sep 26 2019 - 11:52:53 PDT)
  - Re: [AMBER] imin=5 fails to produce output Daniel Roe (Fri Sep 27 2019 - 11:39:33 PDT)
    - Re: [AMBER] imin=5 fails to produce output Daniel Roe (Sat Sep 28 2019 - 05:46:19 PDT)
    - Re: [AMBER] imin=5 fails to produce output Casalini Tommaso (Fri Dec 20 2019 - 01:29:12 PST)
[AMBER] PCA reweighting Aswin Hanagal (Thu Sep 26 2019 - 23:51:37 PDT)
[AMBER] problem with heavy atom (Cl atom) of ligand in tleap Seketoulie Keretsu (Fri Sep 27 2019 - 04:52:02 PDT)
- Re: [AMBER] problem with heavy atom (Cl atom) of ligand in tleap Elvis Martis (Fri Sep 27 2019 - 04:51:50 PDT)
  - Re: [AMBER] problem with heavy atom (Cl atom) of ligand in tleap Seketoulie Keretsu (Fri Sep 27 2019 - 05:34:57 PDT)
    - Re: [AMBER] problem with heavy atom (Cl atom) of ligand in tleap Elvis Martis (Fri Sep 27 2019 - 05:27:35 PDT)
[AMBER] avoiding protein residue renumbering during tleap processing Seketoulie Keretsu (Fri Sep 27 2019 - 07:04:38 PDT)
- Re: [AMBER] avoiding protein residue renumbering during tleap processing David A Case (Fri Sep 27 2019 - 13:15:22 PDT)
[AMBER] How to incorporate new lipid molecules through packmol-memgen Chetna Tyagi (Fri Sep 27 2019 - 09:00:32 PDT)
- Re: [AMBER] How to incorporate new lipid molecules through packmol-memgen Stephan Schott (Mon Sep 30 2019 - 01:44:13 PDT)
  - Re: [AMBER] How to incorporate new lipid molecules through packmol-memgen Chetna Tyagi (Mon Sep 30 2019 - 04:33:30 PDT)
- Re: [AMBER] How to incorporate new lipid molecules through packmol-memgen Stephan Schott (Mon Sep 30 2019 - 06:05:22 PDT)
  - Re: [AMBER] How to incorporate new lipid molecules through packmol-memgen Chetna Tyagi (Tue Oct 01 2019 - 02:54:35 PDT)
[AMBER] Restart file format. Parviz Seifpanahi Shabane (Fri Sep 27 2019 - 10:45:33 PDT)
- Re: [AMBER] Restart file format. Elvis Martis (Fri Sep 27 2019 - 10:52:33 PDT)
- Re: [AMBER] Restart file format. Daniel Roe (Fri Sep 27 2019 - 11:09:23 PDT)
[AMBER] Query regarding mmgbsa Saikat Pal (Fri Sep 27 2019 - 21:52:22 PDT)
- Re: [AMBER] Query regarding mmgbsa David Case (Sat Sep 28 2019 - 05:35:24 PDT)
[AMBER] Free energy calculation Sadaf Rani (Mon Sep 30 2019 - 03:56:07 PDT)
- Re: [AMBER] Free energy calculation David Case (Mon Sep 30 2019 - 05:12:11 PDT)
Re: [AMBER] Amber18 installation Sunita Patel (Mon Sep 30 2019 - 04:27:42 PDT)
- Re: [AMBER] Amber18 installation David Case (Mon Sep 30 2019 - 05:14:25 PDT)
  - Re: [AMBER] Amber18 installation Sunita Patel (Mon Sep 30 2019 - 22:14:43 PDT)
[AMBER] netcdf: issue with timestamp Sarath Dantu (Staff) (Tue Oct 01 2019 - 06:26:27 PDT)
- Re: [AMBER] netcdf: issue with timestamp Daniel Roe (Tue Oct 01 2019 - 09:59:41 PDT)
[AMBER] Is there any standard set of parameters to build the topology Iron Sulfur clusters? David Sáez (Tue Oct 01 2019 - 06:37:24 PDT)
[AMBER] I add Ions to the system and they don't show up!!! Parviz Seifpanahi Shabane (Tue Oct 01 2019 - 08:34:22 PDT)
- Re: [AMBER] I add Ions to the system and they don't show up!!! Daniel Roe (Tue Oct 01 2019 - 10:01:36 PDT)
- Re: [AMBER] I add Ions to the system and they don't show up!!! David Case (Tue Oct 01 2019 - 18:07:05 PDT)
  - Re: [AMBER] I add Ions to the system and they don't show up!!! Parviz Seifpanahi Shabane (Wed Oct 02 2019 - 06:59:22 PDT)
    - Re: [AMBER] I add Ions to the system and they don't show up!!! Bill Ross (Wed Oct 02 2019 - 17:08:58 PDT)
    - Re: [AMBER] I add Ions to the system and they don't show up!!! Parviz Seifpanahi Shabane (Fri Oct 04 2019 - 09:25:34 PDT)
[AMBER] regarding amber licensed version and free version. Seketoulie Keretsu (Tue Oct 01 2019 - 09:06:48 PDT)
- Re: [AMBER] regarding amber licensed version and free version. Carlos Simmerling (Tue Oct 01 2019 - 09:09:55 PDT)
[AMBER] Thermodynamic integration Debarati DasGupta (Tue Oct 01 2019 - 13:25:59 PDT)
- Re: [AMBER] Thermodynamic integration Charles Lin (Wed Oct 02 2019 - 08:19:52 PDT)
  - Re: [AMBER] Thermodynamic integration Debarati DasGupta (Thu Oct 03 2019 - 06:41:17 PDT)
    - Re: [AMBER] Thermodynamic integration Charles Lin (Thu Oct 03 2019 - 09:15:51 PDT)
    - Re: [AMBER] Thermodynamic integration Debarati DasGupta (Thu Oct 03 2019 - 10:48:49 PDT)
    - Re: [AMBER] Thermodynamic integration Charles Lin (Thu Oct 03 2019 - 12:23:16 PDT)
    - Re: [AMBER] Thermodynamic integration David Case (Thu Oct 03 2019 - 12:59:54 PDT)
    - Re: [AMBER] Thermodynamic integration Debarati DasGupta (Wed Oct 09 2019 - 11:36:18 PDT)
  - Re: [AMBER] Thermodynamic integration Sadaf Rani (Thu Oct 03 2019 - 08:06:17 PDT)
    - Re: [AMBER] Thermodynamic integration Charles Lin (Thu Oct 03 2019 - 09:13:44 PDT)
    - Re: [AMBER] Thermodynamic integration Sadaf Rani (Thu Oct 10 2019 - 05:16:31 PDT)
    - Re: [AMBER] Thermodynamic integration Charles Lin (Thu Oct 10 2019 - 06:13:11 PDT)
    - Re: [AMBER] Thermodynamic integration Sadaf Rani (Thu Oct 10 2019 - 07:45:13 PDT)
    - Re: [AMBER] Thermodynamic integration Charles Lin (Thu Oct 10 2019 - 11:51:20 PDT)
    - Re: [AMBER] Thermodynamic integration Sadaf Rani (Mon Oct 14 2019 - 03:59:22 PDT)
    - Re: [AMBER] Thermodynamic integration Charles Lin (Mon Oct 14 2019 - 07:20:10 PDT)
    - Re: [AMBER] Thermodynamic integration Sadaf Rani (Mon Oct 14 2019 - 08:10:46 PDT)
    - Re: [AMBER] Thermodynamic integration Charles Lin (Mon Oct 14 2019 - 09:58:35 PDT)
    - Re: [AMBER] Thermodynamic integration Sadaf Rani (Mon Oct 14 2019 - 12:02:52 PDT)
    - Re: [AMBER] Thermodynamic integration Charles Lin (Mon Oct 14 2019 - 13:03:26 PDT)
    - Re: [AMBER] Thermodynamic integration Sadaf Rani (Thu Oct 17 2019 - 04:19:01 PDT)
    - Re: [AMBER] Thermodynamic integration Charles Lin (Thu Oct 17 2019 - 07:26:50 PDT)
[AMBER] ABMD COM_DISTANCE Help Kyle Ghaby (Tue Oct 01 2019 - 14:16:37 PDT)
- Re: [AMBER] ABMD COM_DISTANCE Help Feng Pan (Wed Oct 02 2019 - 08:17:04 PDT)
  - Re: [AMBER] ABMD COM_DISTANCE Help Kyle Ghaby (Wed Oct 02 2019 - 08:41:12 PDT)
    - Re: [AMBER] ABMD COM_DISTANCE Help Feng Pan (Thu Oct 03 2019 - 08:57:51 PDT)
    - Re: [AMBER] ABMD COM_DISTANCE Help Kyle Ghaby (Thu Oct 03 2019 - 09:17:04 PDT)
    - Re: [AMBER] ABMD COM_DISTANCE Help Feng Pan (Thu Oct 03 2019 - 10:26:37 PDT)
[AMBER] CPPTRAJ parameter file error Rui Chen (Tue Oct 01 2019 - 15:36:19 PDT)
- Re: [AMBER] CPPTRAJ parameter file error Daniel Roe (Wed Oct 02 2019 - 06:31:48 PDT)
  - Re: [AMBER] CPPTRAJ parameter file error Rui Chen (Wed Oct 02 2019 - 07:41:54 PDT)
    - Re: [AMBER] CPPTRAJ parameter file error Rui Chen (Wed Oct 02 2019 - 15:18:04 PDT)
    - Re: [AMBER] CPPTRAJ parameter file error Daniel Roe (Thu Oct 03 2019 - 05:42:13 PDT)
  - Re: [AMBER] CPPTRAJ parameter file error Rui Chen (Wed Oct 09 2019 - 15:41:30 PDT)
    - Re: [AMBER] CPPTRAJ parameter file error Daniel Roe (Thu Oct 10 2019 - 07:16:33 PDT)
    - Re: [AMBER] CPPTRAJ parameter file error Rui Chen (Thu Oct 10 2019 - 15:49:43 PDT)
- Re: [AMBER] CPPTRAJ parameter file error Rui Chen (Fri Oct 04 2019 - 10:31:35 PDT)
  - Re: [AMBER] CPPTRAJ parameter file error Daniel Roe (Mon Oct 07 2019 - 07:47:13 PDT)
    - Re: [AMBER] CPPTRAJ parameter file error Rui Chen (Mon Oct 07 2019 - 21:27:20 PDT)
[AMBER] seek help for mmpbsa 石娜 (Wed Oct 02 2019 - 03:42:48 PDT)
- Re: [AMBER] seek help for mmpbsa Liao (Wed Oct 02 2019 - 04:47:52 PDT)
[AMBER] WHere do I modify the charge of a standard residue? David Sáez (Wed Oct 02 2019 - 06:42:54 PDT)
- Re: [AMBER] WHere do I modify the charge of a standard residue? David Case (Wed Oct 02 2019 - 11:48:03 PDT)
[AMBER] restraining a peptide to devoid of any secondary structure Vlad Cojocaru (Wed Oct 02 2019 - 07:11:06 PDT)
[AMBER] Error during the test of amber 18 installation Sunita Patel (Wed Oct 02 2019 - 07:18:35 PDT)
- Re: [AMBER] Error during the test of amber 18 installation David Case (Wed Oct 02 2019 - 12:02:34 PDT)
- Re: [AMBER] Error during the test of amber 18 installation Daniel Roe (Thu Oct 03 2019 - 10:49:53 PDT)
  - Re: [AMBER] Error during the test of amber 18 installation Sunita Patel (Fri Oct 04 2019 - 00:10:00 PDT)
- Re: [AMBER] Error during the test of amber 18 installation Sunita Patel (Mon Oct 07 2019 - 04:30:33 PDT)
  - Re: [AMBER] Error during the test of amber 18 installation David A Case (Mon Oct 07 2019 - 05:25:35 PDT)
  - Re: [AMBER] Error during the test of amber 18 installation David A Case (Mon Oct 07 2019 - 05:26:29 PDT)
[AMBER] Gtx 16-series Charles-Alexandre Mattelaer (Wed Oct 02 2019 - 09:40:51 PDT)
- Re: [AMBER] Gtx 16-series Gerardo Zerbetto De Palma (Thu Oct 03 2019 - 07:33:28 PDT)
[AMBER] ERROR: NaNs found in input coordinates. HOCHEOL LIM (Wed Oct 02 2019 - 17:13:05 PDT)
- Re: [AMBER] ERROR: NaNs found in input coordinates. Daniel Roe (Thu Oct 03 2019 - 05:37:58 PDT)
[AMBER] Calculation of stacking energy of a RNA containing UUCG tetra loop Swagata Halder (Thu Oct 03 2019 - 00:58:58 PDT)
- Re: [AMBER] Calculation of stacking energy of a RNA containing UUCG tetra loop Bill Ross (Thu Oct 03 2019 - 02:09:12 PDT)
  - Re: [AMBER] Calculation of stacking energy of a RNA containing UUCG tetra loop Swagata Halder (Thu Oct 03 2019 - 23:20:45 PDT)
    - Re: [AMBER] Calculation of stacking energy of a RNA containing UUCG tetra loop Bill Ross (Thu Oct 03 2019 - 23:37:51 PDT)
    - Re: [AMBER] Calculation of stacking energy of a RNA containing UUCG tetra loop Jiri Sponer (Fri Oct 04 2019 - 00:55:12 PDT)
[AMBER] Amber Installation Problem on Mac Fanglue Ni (Thu Oct 03 2019 - 16:35:23 PDT)
- Re: [AMBER] Amber Installation Problem on Mac Ray Luo (Thu Oct 03 2019 - 16:50:23 PDT)
- Re: [AMBER] Amber Installation Problem on Mac Gustaf Olsson (Thu Oct 03 2019 - 23:06:43 PDT)
- Re: [AMBER] Amber Installation Problem on Mac David A Case (Fri Oct 04 2019 - 07:10:13 PDT)
  - Re: [AMBER] Amber Installation Problem on Mac: update David A Case (Fri Oct 04 2019 - 09:17:08 PDT)
[AMBER] CHARMM-GUI now supports Amber Paul Westphälinger (Fri Oct 04 2019 - 04:47:48 PDT)
[AMBER] Calculate MMGBSA keeping water in binding site Rosellen, Martin (Fri Oct 04 2019 - 06:27:27 PDT)
- Re: [AMBER] Calculate MMGBSA keeping water in binding site Carlos Simmerling (Fri Oct 04 2019 - 06:35:40 PDT)
- Re: [AMBER] Calculate MMGBSA keeping water in binding site Rosellen, Martin (Sat Oct 05 2019 - 06:40:18 PDT)
  - Re: [AMBER] Calculate MMGBSA keeping water in binding site Carlos Simmerling (Thu Oct 10 2019 - 11:06:05 PDT)
- Re: [AMBER] Calculate MMGBSA keeping water in binding site Rosellen, Martin (Mon Oct 21 2019 - 04:39:17 PDT)
  - Re: [AMBER] Calculate MMGBSA keeping water in binding site Carlos Simmerling (Mon Oct 21 2019 - 05:48:24 PDT)
- Re: [AMBER] Calculate MMGBSA keeping water in binding site Rosellen, Martin (Fri Nov 01 2019 - 10:24:54 PDT)
Re: [AMBER] Amber Installation Problem on Mac: me too Mooers, Blaine H.M. (HSC) (Fri Oct 04 2019 - 15:29:15 PDT)
[AMBER] About STOP PMEMD Terminated Abnormally! HOCHEOL LIM (Sat Oct 05 2019 - 02:33:19 PDT)
- Re: [AMBER] About STOP PMEMD Terminated Abnormally! David Case (Sat Oct 05 2019 - 05:58:36 PDT)
[AMBER] tleap hangs when tries to read new residue Dawid das (Sun Oct 06 2019 - 10:09:05 PDT)
- Re: [AMBER] tleap hangs when tries to read new residue Bill Ross (Sun Oct 06 2019 - 12:48:28 PDT)
  - Re: [AMBER] tleap hangs when tries to read new residue Bill Ross (Sun Oct 06 2019 - 12:49:51 PDT)
    - Re: [AMBER] tleap hangs when tries to read new residue Dawid das (Mon Oct 07 2019 - 02:40:27 PDT)
    - Re: [AMBER] tleap hangs when tries to read new residue Bill Ross (Mon Oct 07 2019 - 02:52:14 PDT)
    - Re: [AMBER] tleap hangs when tries to read new residue Dawid das (Mon Oct 07 2019 - 05:31:01 PDT)
    - Re: [AMBER] tleap hangs when tries to read new residue Matias Machado (Mon Oct 07 2019 - 14:35:45 PDT)
    - Re: [AMBER] tleap hangs when tries to read new residue Dawid das (Mon Oct 07 2019 - 14:52:30 PDT)
- Re: [AMBER] tleap hangs when tries to read new residue David A Case (Mon Oct 07 2019 - 05:21:41 PDT)
[AMBER] hydroxyapatite force field parameters Tal Duanias (Mon Oct 07 2019 - 00:20:47 PDT)
- Re: [AMBER] hydroxyapatite force field parameters Pengfei Li (Mon Oct 07 2019 - 07:13:38 PDT)
  - Re: [AMBER] hydroxyapatite force field parameters Tal Duanias (Mon Oct 07 2019 - 10:09:23 PDT)
[AMBER] Force extension curve from ASMD Aravind R (Mon Oct 07 2019 - 00:27:12 PDT)
[AMBER] How can I use modified GAFF? 조준범 (Mon Oct 07 2019 - 00:40:13 PDT)
- Re: [AMBER] How can I use modified GAFF? Bill Ross (Mon Oct 07 2019 - 00:59:25 PDT)
  - Re: [AMBER] How can I use modified GAFF? Bill Ross (Mon Oct 07 2019 - 01:00:51 PDT)
[AMBER] Error using MCPB.py Hafiz Saqib Ali (Mon Oct 07 2019 - 03:58:32 PDT)
- Re: [AMBER] Error using MCPB.py Pengfei Li (Mon Oct 07 2019 - 07:16:26 PDT)
[AMBER] mmpbsa MYRIAN TORRES RICO (Mon Oct 07 2019 - 08:27:12 PDT)
[AMBER] cpptraj.MPI error Debarati DasGupta (Mon Oct 07 2019 - 12:33:50 PDT)
- Re: [AMBER] cpptraj.MPI error Daniel Roe (Mon Oct 07 2019 - 12:42:46 PDT)
[AMBER] Question about ff14SB and parameter files Nate Guerin (Mon Oct 07 2019 - 17:45:40 PDT)
- Re: [AMBER] Question about ff14SB and parameter files Carlos Simmerling (Mon Oct 07 2019 - 18:09:20 PDT)
[AMBER] H - bond tools shivangi agarwal (Mon Oct 07 2019 - 23:10:05 PDT)
- Re: [AMBER] H - bond tools Elvis Martis (Mon Oct 07 2019 - 23:22:51 PDT)
  - Re: [AMBER] H - bond tools shivangi agarwal (Mon Oct 07 2019 - 23:31:05 PDT)
    - Re: [AMBER] H - bond tools Daniel Roe (Thu Oct 10 2019 - 08:00:03 PDT)
    - Re: [AMBER] H - bond tools shivangi agarwal (Sat Oct 12 2019 - 22:08:11 PDT)
[AMBER] Imaging issue Hira Jabeen (Tue Oct 08 2019 - 03:58:06 PDT)
- Re: [AMBER] Imaging issue David A Case (Tue Oct 08 2019 - 04:49:53 PDT)
[AMBER] Gaff v2.1 Force Field for n4 chaumont (Tue Oct 08 2019 - 05:29:45 PDT)
- Re: [AMBER] Gaff v2.1 Force Field for n4 Junmei Wang (Wed Oct 09 2019 - 10:51:22 PDT)
[AMBER] could not find vdW (or other) parameters for type for virtually every amino acid atom Dawid das (Tue Oct 08 2019 - 09:03:59 PDT)
- Re: [AMBER] could not find vdW (or other) parameters for type for virtually every amino acid atom Carlos Simmerling (Tue Oct 08 2019 - 10:33:18 PDT)
  - Re: [AMBER] could not find vdW (or other) parameters for type for virtually every amino acid atom Dawid das (Tue Oct 08 2019 - 11:00:25 PDT)
    - Re: [AMBER] could not find vdW (or other) parameters for type for virtually every amino acid atom Carlos Simmerling (Tue Oct 08 2019 - 11:46:37 PDT)
    - Re: [AMBER] could not find vdW (or other) parameters for type for virtually every amino acid atom Dawid das (Tue Oct 08 2019 - 11:58:29 PDT)
    - Re: [AMBER] could not find vdW (or other) parameters for type for virtually every amino acid atom Carlos Simmerling (Tue Oct 08 2019 - 12:01:05 PDT)
    - Re: [AMBER] could not find vdW (or other) parameters for type for virtually every amino acid atom Dawid das (Wed Oct 09 2019 - 01:54:52 PDT)
    - Re: [AMBER] could not find vdW (or other) parameters for type for virtually every amino acid atom Bill Ross (Wed Oct 09 2019 - 02:03:51 PDT)
    - Re: [AMBER] could not find vdW (or other) parameters for type for virtually every amino acid atom Dawid das (Wed Oct 09 2019 - 02:05:55 PDT)
[AMBER] amber99sb-disp forcefield in Amber Prithvi Raj Pandey (Tue Oct 08 2019 - 10:25:46 PDT)
- Re: [AMBER] amber99sb-disp forcefield in Amber Carlos Simmerling (Tue Oct 08 2019 - 11:40:36 PDT)
- Re: [AMBER] amber99sb-disp forcefield in Amber Supriyo Bhattacharya (Tue Oct 08 2019 - 12:02:51 PDT)
[AMBER] Problem in MMPBSA analysis 崔佳文 (Tue Oct 08 2019 - 19:39:30 PDT)
[AMBER] Error during the test of amber 18 installation Sunita Patel (Wed Oct 09 2019 - 04:33:53 PDT)
- Re: [AMBER] Error during the test of amber 18 installation Daniel Roe (Thu Oct 10 2019 - 09:06:57 PDT)
  - Re: [AMBER] Error during the test of amber 18 installation Sunita Patel (Thu Oct 10 2019 - 22:43:42 PDT)
[AMBER] "Could not import Amber Python modules!" error sunyeping (Wed Oct 09 2019 - 05:28:52 PDT)
- Re: [AMBER] "Could not import Amber Python modules!" error Hai Nguyen (Wed Oct 09 2019 - 05:59:38 PDT)
- Re: [AMBER] "Could not import Amber Python modules!" error Anthony Cruz-Balberdy (Wed Oct 09 2019 - 06:47:11 PDT)
  - Re: [AMBER] "Could not import Amber Python modules!" error sunyeping (Wed Oct 09 2019 - 07:43:49 PDT)
    - Re: [AMBER] "Could not import Amber Python modules!" error Mijiddorj B (Wed Oct 09 2019 - 07:54:22 PDT)
- Re: [AMBER] "Could not import Amber Python modules!" error David A Case (Wed Oct 09 2019 - 08:30:19 PDT)
  - Re: [AMBER] "Could not import Amber Python modules!" error sunyeping (Fri Oct 11 2019 - 03:55:21 PDT)
[AMBER] mmpbsa MYRIAN TORRES RICO (Thu Oct 10 2019 - 01:16:59 PDT)
[AMBER] tleap changes order of atoms in the parm file Dawid das (Thu Oct 10 2019 - 07:09:16 PDT)
- Re: [AMBER] tleap changes order of atoms in the parm file Bill Ross (Thu Oct 10 2019 - 07:13:08 PDT)
  - Re: [AMBER] tleap changes order of atoms in the parm file Dawid das (Thu Oct 10 2019 - 07:36:12 PDT)
    - Re: [AMBER] tleap changes order of atoms in the parm file Bill Ross (Thu Oct 10 2019 - 07:46:50 PDT)
    - Re: [AMBER] tleap changes order of atoms in the parm file Dawid das (Thu Oct 10 2019 - 08:14:53 PDT)
    - Re: [AMBER] tleap changes order of atoms in the parm file Bill Ross (Thu Oct 10 2019 - 11:48:34 PDT)
- Re: [AMBER] tleap changes order of atoms in the parm file David A Case (Thu Oct 10 2019 - 09:50:54 PDT)
[AMBER] Generating the parameters of a peptide sequence consisting of non-standard amino-acid RITUPARNA ROY (Thu Oct 10 2019 - 08:37:12 PDT)
[AMBER] PDB CONECT issues with OpenBabel 3.0 and antechamber Miroslav Suruzhon (Thu Oct 10 2019 - 08:41:57 PDT)
- Re: [AMBER] PDB CONECT issues with OpenBabel 3.0 and antechamber Elvis Martis (Thu Oct 10 2019 - 08:53:44 PDT)
- Re: [AMBER] PDB CONECT issues with OpenBabel 3.0 and antechamber David A Case (Fri Oct 11 2019 - 07:24:45 PDT)
  - Re: [AMBER] PDB CONECT issues with OpenBabel 3.0 and antechamber Suruzhon M. (Fri Oct 11 2019 - 07:31:11 PDT)
  - Re: [AMBER] PDB CONECT issues with OpenBabel 3.0 and antechamber Hai Nguyen (Fri Oct 11 2019 - 07:32:31 PDT)
[AMBER] Is it necessary to set "baroscalingdir" in the membrane system? xmgign.126.com (Fri Oct 11 2019 - 01:29:06 PDT)
[AMBER] Query regarding DNA Saikat Pal (Fri Oct 11 2019 - 08:21:20 PDT)
- Re: [AMBER] Query regarding DNA David A Case (Fri Oct 11 2019 - 10:31:52 PDT)
  - Re: [AMBER] Query regarding DNA Matias Machado (Fri Oct 11 2019 - 14:10:47 PDT)
[AMBER] What is the correction in amber99SB-*-ILDN? Dawid das (Fri Oct 11 2019 - 08:23:57 PDT)
- Re: [AMBER] What is the correction in amber99SB-*-ILDN? Carlos Simmerling (Fri Oct 11 2019 - 08:29:08 PDT)
  - Re: [AMBER] What is the correction in amber99SB-*-ILDN? Dawid das (Sat Oct 12 2019 - 09:33:06 PDT)
    - Re: [AMBER] What is the correction in amber99SB-*-ILDN? David A Case (Mon Oct 14 2019 - 05:40:09 PDT)
[AMBER] Adding OH⁻ in a water box Lucas Bandeira (Fri Oct 11 2019 - 10:11:33 PDT)
- Re: [AMBER] Adding OH⁻ in a water box Matias Machado (Fri Oct 11 2019 - 13:37:18 PDT)
- Re: [AMBER] Adding OH⁻ in a water box David Case (Fri Oct 11 2019 - 18:45:12 PDT)
  - Re: [AMBER] Adding OH⁻ in a water box Lucas Bandeira (Sat Oct 12 2019 - 14:05:44 PDT)
[AMBER] Problems in compilation: fftw3.a ?? Margarita I. Bernal-Uruchurtu (Fri Oct 11 2019 - 13:05:19 PDT)
- Re: [AMBER] Problems in compilation: fftw3.a ?? David Cerutti (Fri Oct 11 2019 - 13:12:49 PDT)
- Re: [AMBER] Problems in compilation: fftw3.a ?? David Case (Sat Oct 12 2019 - 05:22:38 PDT)
[AMBER] Trouble Installing Amber on Mac Faisal Malik (Fri Oct 11 2019 - 21:19:09 PDT)
- Re: [AMBER] Trouble Installing Amber on Mac Bill Ross (Fri Oct 11 2019 - 22:31:39 PDT)
  - Re: [AMBER] Trouble Installing Amber on Mac Faisal Malik (Fri Oct 11 2019 - 23:35:18 PDT)
    - Re: [AMBER] Trouble Installing Amber on Mac Bill Ross (Sat Oct 12 2019 - 00:23:09 PDT)
- Re: [AMBER] Trouble Installing Amber on Mac David A Case (Mon Oct 14 2019 - 05:25:11 PDT)
[AMBER] Adding OH- to a water box David Case (Sun Oct 13 2019 - 05:16:49 PDT)
- Re: [AMBER] Adding OH- to a water box Lucas Bandeira (Sun Oct 13 2019 - 10:50:48 PDT)
  - Re: [AMBER] Adding OH- to a water box Matias Machado (Thu Oct 17 2019 - 06:20:19 PDT)
    - Re: [AMBER] Adding OH- to a water box Lucas Bandeira (Fri Oct 18 2019 - 10:53:06 PDT)
[AMBER] Cataline Gustaf Olsson (Sun Oct 13 2019 - 13:01:37 PDT)
- Re: [AMBER] Cataline Bill Ross (Sun Oct 13 2019 - 14:52:55 PDT)
  - Re: [AMBER] Cataline Gustaf Olsson (Sun Oct 13 2019 - 23:48:31 PDT)
    - Re: [AMBER] Cataline Bill Ross (Mon Oct 14 2019 - 00:34:38 PDT)
    - Re: [AMBER] Cataline Gustaf Olsson (Wed Oct 16 2019 - 12:48:34 PDT)
    - Re: [AMBER] Cataline Hai Nguyen (Wed Oct 16 2019 - 13:00:47 PDT)
    - Re: [AMBER] Cataline Gustaf Olsson (Wed Oct 16 2019 - 13:43:41 PDT)
    - Re: [AMBER] Cataline David Case (Wed Oct 16 2019 - 19:19:16 PDT)
- Re: [AMBER] Cataline David A Case (Mon Oct 14 2019 - 05:52:25 PDT)
  - Re: [AMBER] Cataline Gustaf Olsson (Mon Oct 14 2019 - 13:34:00 PDT)
[AMBER] MMPBSA.py resulted in DELTA TOTAL= 1414 kcal/mole Seketoulie Keretsu (Sun Oct 13 2019 - 16:55:20 PDT)
[AMBER] Problem in extracting pdb file from mdcrd file Airy Sanjeev (Mon Oct 14 2019 - 01:07:15 PDT)
- Re: [AMBER] Problem in extracting pdb file from mdcrd file Elvis Martis (Mon Oct 14 2019 - 01:21:43 PDT)
- Re: [AMBER] Problem in extracting pdb file from mdcrd file Daniel Roe (Wed Oct 16 2019 - 07:48:28 PDT)
[AMBER] symmetry corrected rms fitting Venkata Krishnan Ramaswamy (Mon Oct 14 2019 - 06:30:56 PDT)
[AMBER] More ... problems in compilation: fftw3a | Case1 - Using GNU Margarita I. Bernal-Uruchurtu (Mon Oct 14 2019 - 10:12:03 PDT)
[AMBER] More ... problems in compilation: fftw3a | Case2 - Using intel Margarita I. Bernal-Uruchurtu (Mon Oct 14 2019 - 10:42:36 PDT)
- Re: [AMBER] More ... problems in compilation: fftw3a | Case2 - Using intel David A Case (Tue Oct 15 2019 - 05:05:12 PDT)
[AMBER] make install errors Alen Ahmetovic (Mon Oct 14 2019 - 19:28:33 PDT)
- Re: [AMBER] make install errors Hai Nguyen (Mon Oct 14 2019 - 20:27:24 PDT)
  - Re: [AMBER] make install errors Alen Ahmetovic (Wed Oct 16 2019 - 15:34:49 PDT)
    - Re: [AMBER] make install errors Alen Ahmetovic (Wed Oct 16 2019 - 15:44:52 PDT)
    - Re: [AMBER] make install errors Alen Ahmetovic (Tue Oct 29 2019 - 16:49:24 PDT)
    - Re: [AMBER] make install errors David Case (Tue Oct 29 2019 - 18:59:16 PDT)
    - Re: [AMBER] make install errors Hai Nguyen (Tue Oct 29 2019 - 19:15:06 PDT)
[AMBER] (long) OSX/catalina Ambertools19 building success with brew Tru Huynh (Tue Oct 15 2019 - 03:05:31 PDT)
- Re: [AMBER] (long) OSX/catalina Ambertools19 building success with brew Hai Nguyen (Tue Oct 15 2019 - 08:08:11 PDT)
  - Re: [AMBER] (long) OSX/catalina Ambertools19 building success with brew Gustaf Olsson (Wed Oct 16 2019 - 13:46:00 PDT)
    - Re: [AMBER] (long) OSX/catalina Ambertools19 building success with brew Tru Huynh (Thu Oct 17 2019 - 08:36:36 PDT)
    - [AMBER] Some short Catalina experience David A Case (Thu Oct 17 2019 - 10:49:13 PDT)
    - Re: [AMBER] Some short Catalina experience Scott Brozell (Thu Oct 17 2019 - 11:02:02 PDT)
    - Re: [AMBER] Some short Catalina experience Hai Nguyen (Thu Oct 17 2019 - 11:41:13 PDT)
    - Re: [AMBER] Some short Catalina experience David Case (Thu Oct 17 2019 - 18:42:18 PDT)
    - Re: [AMBER] Some short Catalina experience Gustaf Olsson (Thu Oct 17 2019 - 23:57:22 PDT)
    - Re: [AMBER] Some short Catalina experience David A Case (Tue Oct 29 2019 - 05:59:41 PDT)
    - Re: [AMBER] Some short Catalina experience Gustaf Olsson (Tue Oct 29 2019 - 06:09:05 PDT)
    - Re: [AMBER] (long) OSX/catalina Ambertools19 building success with brew Gustaf Olsson (Thu Oct 17 2019 - 12:02:02 PDT)
    - Re: [AMBER] (long) OSX/catalina Ambertools19 building success with brew David A Case (Fri Oct 18 2019 - 08:13:07 PDT)
[AMBER] Paste command for xleap Gert Kruger (Tue Oct 15 2019 - 04:13:28 PDT)
- Re: [AMBER] Paste command for xleap Bill Ross (Tue Oct 15 2019 - 06:17:09 PDT)
  - Re: [AMBER] Paste command for xleap Gert Kruger (Thu Oct 17 2019 - 23:45:01 PDT)
[AMBER] PTRAJ (clustering)-Segmentation fault Rui Chen (Tue Oct 15 2019 - 08:35:56 PDT)
- Re: [AMBER] PTRAJ (clustering)-Segmentation fault Thomas Cheatham (Tue Oct 15 2019 - 13:11:10 PDT)
[AMBER] minimize protein with a small molecule tethered at a fixed location Debarati DasGupta (Tue Oct 15 2019 - 16:34:01 PDT)
- Re: [AMBER] minimize protein with a small molecule tethered at a fixed location David A Case (Wed Oct 16 2019 - 05:22:46 PDT)
  - Re: [AMBER] minimize protein with a small molecule tethered at a fixed location Debarati DasGupta (Wed Oct 16 2019 - 06:32:02 PDT)
    - Re: [AMBER] minimize protein with a small molecule tethered at a fixed location Bill Ross (Wed Oct 16 2019 - 06:34:58 PDT)
    - Re: [AMBER] minimize protein with a small molecule tethered at a fixed location Debarati DasGupta (Wed Oct 16 2019 - 06:40:42 PDT)
    - Re: [AMBER] minimize protein with a small molecule tethered at a fixed location Bill Ross (Wed Oct 16 2019 - 06:47:21 PDT)
[AMBER] Problem in running MMPBSA Airy Sanjeev (Wed Oct 16 2019 - 02:23:43 PDT)
- Re: [AMBER] Problem in running MMPBSA Bill Ross (Wed Oct 16 2019 - 02:34:47 PDT)
  - Re: [AMBER] Problem in running MMPBSA Airy Sanjeev (Wed Oct 16 2019 - 02:47:10 PDT)
- Re: [AMBER] Problem in running MMPBSA David A Case (Wed Oct 16 2019 - 05:27:13 PDT)
[AMBER] ff19SB update Åsmund Røhr Kjendseth (Wed Oct 16 2019 - 06:10:05 PDT)
- Re: [AMBER] ff19SB update Chuan Tian (Wed Oct 16 2019 - 07:04:06 PDT)
- Re: [AMBER] ff19SB update David A Case (Wed Oct 16 2019 - 07:51:14 PDT)
  - Re: [AMBER] ff19SB update Åsmund Røhr Kjendseth (Thu Oct 17 2019 - 23:47:44 PDT)
    - Re: [AMBER] ff19SB update David A Case (Fri Oct 18 2019 - 06:49:50 PDT)
[AMBER] minimization using restrain weight Debarati DasGupta (Wed Oct 16 2019 - 06:54:50 PDT)
- Re: [AMBER] minimization using restrain weight David A Case (Wed Oct 16 2019 - 07:56:53 PDT)
[AMBER] Check for updates failed Gustaf Olsson (Wed Oct 16 2019 - 13:21:15 PDT)
- Re: [AMBER] Check for updates failed David Case (Wed Oct 16 2019 - 19:31:03 PDT)
  - Re: [AMBER] Check for updates failed Gustaf Olsson (Wed Oct 16 2019 - 23:00:32 PDT)
  - Re: [AMBER] Check for updates failed David A Case (Thu Oct 17 2019 - 06:02:23 PDT)
    - Re: [AMBER] Check for updates failed Gustaf Olsson (Thu Oct 17 2019 - 06:25:22 PDT)
[AMBER] Incorrect instructions in tutorial B1 Cavender, Chapin (Wed Oct 16 2019 - 16:23:27 PDT)
[AMBER] more efficient TI rerun over existing trajectory 杨明俊 (Wed Oct 16 2019 - 20:25:04 PDT)
- Re: [AMBER] more efficient TI rerun over existing trajectory Carlos Simmerling (Thu Oct 17 2019 - 03:54:45 PDT)
  - Re: [AMBER] more efficient TI rerun over existing trajectory 杨明俊 (Thu Oct 17 2019 - 06:35:27 PDT)
    - Re: [AMBER] more efficient TI rerun over existing trajectory Charles Lin (Thu Oct 17 2019 - 07:37:35 PDT)
    - Re: [AMBER] more efficient TI rerun over existing trajectory Carlos Simmerling (Thu Oct 17 2019 - 10:44:04 PDT)
    - Re: [AMBER] more efficient TI rerun over existing trajectory 杨明俊 (Mon Oct 28 2019 - 06:12:56 PDT)
    - Re: [AMBER] more efficient TI rerun over existing trajectory David A Case (Tue Oct 29 2019 - 05:42:47 PDT)
[AMBER] Convergence value for GMAX Anuja Ware (Thu Oct 17 2019 - 06:48:53 PDT)
- Re: [AMBER] Convergence value for GMAX David A Case (Thu Oct 17 2019 - 10:36:04 PDT)
[AMBER] Problem with Installation of AMBER 조준범 (Sat Oct 19 2019 - 08:02:01 PDT)
- Re: [AMBER] Problem with Installation of AMBER David Case (Sat Oct 19 2019 - 09:46:51 PDT)
[AMBER] clustering using distance matrix file only Tim Davis (Sat Oct 19 2019 - 15:26:51 PDT)
- Re: [AMBER] clustering using distance matrix file only Matias Machado (Mon Oct 21 2019 - 20:12:09 PDT)
- Re: [AMBER] clustering using distance matrix file only Daniel Roe (Tue Oct 22 2019 - 05:55:23 PDT)
  - Re: [AMBER] clustering using distance matrix file only Tim Davis (Tue Oct 22 2019 - 14:09:54 PDT)
[AMBER] TI tutorial for preparation of ligand Debarati DasGupta (Sun Oct 20 2019 - 09:03:15 PDT)
[AMBER] Post-doc position in molecular simulations and structural bioinformatics Jan Brezovsky (Mon Oct 21 2019 - 02:35:18 PDT)
[AMBER] Problem with installation of AMBER 조준범 (Mon Oct 21 2019 - 02:56:02 PDT)
- Re: [AMBER] Problem with installation of AMBER David A Case (Mon Oct 21 2019 - 05:30:20 PDT)
  - Re: [AMBER] Problem with installation of AMBER Bill Ross (Mon Oct 21 2019 - 05:38:15 PDT)
[AMBER] NAN error Hira Jabeen (Mon Oct 21 2019 - 06:13:32 PDT)
- Re: [AMBER] NAN error Bill Ross (Mon Oct 21 2019 - 06:17:54 PDT)
  - Re: [AMBER] NAN error Hira Jabeen (Mon Oct 21 2019 - 06:33:56 PDT)
    - Re: [AMBER] NAN error Bill Ross (Mon Oct 21 2019 - 06:45:48 PDT)
    - Re: [AMBER] NAN error Hira Jabeen (Mon Oct 21 2019 - 07:14:14 PDT)
    - Re: [AMBER] NAN error Bill Ross (Mon Oct 21 2019 - 08:01:50 PDT)
    - Re: [AMBER] NAN error Hira Jabeen (Mon Oct 21 2019 - 09:41:44 PDT)
    - Re: [AMBER] NAN error Bill Ross (Mon Oct 21 2019 - 14:22:50 PDT)
- Re: [AMBER] NAN error David A Case (Wed Oct 23 2019 - 05:01:17 PDT)
  - Re: [AMBER] NAN error Hira Jabeen (Thu Oct 24 2019 - 03:56:06 PDT)
[AMBER] sander/lmod parallel execution Charles-Alexandre Mattelaer (Mon Oct 21 2019 - 07:07:29 PDT)
- Re: [AMBER] sander/lmod parallel execution Scott Brozell (Mon Oct 21 2019 - 11:20:49 PDT)
  - Re: [AMBER] sander/lmod parallel execution Charles-Alexandre Mattelaer (Tue Oct 22 2019 - 00:39:09 PDT)
[AMBER] Error adding OH⁻ ions in a simulation box Lucas Bandeira (Mon Oct 21 2019 - 13:44:54 PDT)
- Re: [AMBER] Error adding OH⁻ ions in a simulation box Matias Machado (Mon Oct 21 2019 - 20:05:17 PDT)
- Re: [AMBER] Error adding OH⁻ ions in a simulation box David A Case (Tue Oct 22 2019 - 05:42:47 PDT)
  - Re: [AMBER] Error adding OH⁻ ions in a simulation box Lucas Bandeira (Tue Oct 22 2019 - 14:09:50 PDT)
[AMBER] How to obtain the pressure in NVT ensemble jinfeng liu (Mon Oct 21 2019 - 23:37:09 PDT)
- Re: [AMBER] How to obtain the pressure in NVT ensemble Bill Ross (Tue Oct 22 2019 - 00:44:00 PDT)
- Re: [AMBER] How to obtain the pressure in NVT ensemble David A Case (Tue Oct 22 2019 - 05:03:32 PDT)
[AMBER] Regarding GIST analysis MR. RABINDRANATH PAUL (Tue Oct 22 2019 - 00:11:44 PDT)
- Re: [AMBER] Regarding GIST analysis Steven Ramsey (Tue Oct 22 2019 - 08:23:47 PDT)
[AMBER] error while running pmemd.cuda after reinstallation of amber 16 Schröder, David Christopher (Tue Oct 22 2019 - 01:36:16 PDT)
- Re: [AMBER] error while running pmemd.cuda after reinstallation of amber 16 David A Case (Tue Oct 22 2019 - 05:16:30 PDT)
  - Re: [AMBER] error while running pmemd.cuda after reinstallation of amber 16 Schröder, David Christopher (Wed Oct 23 2019 - 09:16:42 PDT)
[AMBER] iwrap Andrea H. Kasun (Tue Oct 22 2019 - 03:11:50 PDT)
- Re: [AMBER] iwrap Carlos Simmerling (Tue Oct 22 2019 - 03:21:48 PDT)
  - Re: [AMBER] iwrap Andrea H. Kasun (Tue Oct 22 2019 - 03:55:21 PDT)
- Re: [AMBER] iwrap David A Case (Tue Oct 22 2019 - 05:34:24 PDT)
[AMBER] thermodynamic integration parameters in input file Debarati DasGupta (Tue Oct 22 2019 - 08:44:41 PDT)
- Re: [AMBER] thermodynamic integration parameters in input file David A Case (Tue Oct 22 2019 - 11:17:23 PDT)
[AMBER] free energy calculation and leap error Sadaf Rani (Tue Oct 22 2019 - 09:03:04 PDT)
- Re: [AMBER] free energy calculation and leap error David A Case (Tue Oct 22 2019 - 11:20:23 PDT)
[AMBER] Prmtop file creation for thermodynamic integration Debarati DasGupta (Tue Oct 22 2019 - 10:50:56 PDT)
- Re: [AMBER] Prmtop file creation for thermodynamic integration Sadaf Rani (Tue Oct 22 2019 - 11:07:42 PDT)
  - Re: [AMBER] Prmtop file creation for thermodynamic integration Debarati DasGupta (Tue Oct 22 2019 - 13:51:12 PDT)
[AMBER] compiling with -noX11 option Swantje Mohr (Tue Oct 22 2019 - 11:22:16 PDT)
[AMBER] constraining ligands to some distance from a target molecule on pmemd.cuda Homeo Morphism (Tue Oct 22 2019 - 13:11:36 PDT)
- Re: [AMBER] constraining ligands to some distance from a target molecule on pmemd.cuda Carlos Simmerling (Tue Oct 22 2019 - 14:01:53 PDT)
[AMBER] Extract the last 90ns trajectory Airy Sanjeev (Wed Oct 23 2019 - 02:29:14 PDT)
- Re: [AMBER] Extract the last 90ns trajectory Carlos Simmerling (Wed Oct 23 2019 - 03:10:59 PDT)
  - Re: [AMBER] Extract the last 90ns trajectory Daniel Roe (Wed Oct 23 2019 - 10:12:50 PDT)
[AMBER] Thermodynamic integration more questions! Debarati DasGupta (Wed Oct 23 2019 - 06:50:29 PDT)
[AMBER] Combining FF14Sb and ForceField_PTM (FF03)... What could possibly go wrong? Gustavo Seabra (Wed Oct 23 2019 - 12:21:55 PDT)
- Re: [AMBER] Combining FF14Sb and ForceField_PTM (FF03)... What could possibly go wrong? Carlos Simmerling (Wed Oct 23 2019 - 15:28:22 PDT)
  - Re: [AMBER] Combining FF14Sb and ForceField_PTM (FF03)... What could possibly go wrong? Gustavo Seabra (Wed Oct 23 2019 - 17:28:59 PDT)
[AMBER] Problem in Leap PDB Reading Robert Molt (Wed Oct 23 2019 - 19:13:41 PDT)
- Re: [AMBER] Problem in Leap PDB Reading Bill Ross (Wed Oct 23 2019 - 21:53:37 PDT)
- Re: [AMBER] Problem in Leap PDB Reading David A Case (Fri Oct 25 2019 - 09:09:18 PDT)
  - Re: [AMBER] Problem in Leap PDB Reading Robert Molt (Sun Nov 03 2019 - 14:25:08 PST)
    - Re: [AMBER] Problem in Leap PDB Reading Yong Duan (Sun Nov 03 2019 - 15:07:38 PST)
    - Re: [AMBER] Problem in Leap PDB Reading Robert Molt (Sun Nov 03 2019 - 16:31:04 PST)
    - Re: [AMBER] Problem in Leap PDB Reading Yong Duan (Tue Nov 05 2019 - 21:48:40 PST)
[AMBER] Lennard-Jones parameters in amber and gromacs Hadi Rahmaninejad (Thu Oct 24 2019 - 08:58:09 PDT)
- Re: [AMBER] Lennard-Jones parameters in amber and gromacs Carlos Simmerling (Thu Oct 24 2019 - 09:55:02 PDT)
[AMBER] TI on gpus Debarati DasGupta (Thu Oct 24 2019 - 10:45:55 PDT)
- Re: [AMBER] TI on gpus Ross Walker (Thu Oct 24 2019 - 17:56:06 PDT)
  - Re: [AMBER] TI on gpus Debarati DasGupta (Fri Oct 25 2019 - 06:26:43 PDT)
    - Re: [AMBER] TI on gpus David A Case (Fri Oct 25 2019 - 08:59:58 PDT)
    - Re: [AMBER] TI on gpus Debarati DasGupta (Fri Oct 25 2019 - 12:51:01 PDT)
    - Re: [AMBER] TI on gpus Debarati DasGupta (Wed Dec 04 2019 - 10:01:14 PST)
    - Re: [AMBER] TI on gpus David A Case (Thu Dec 05 2019 - 05:58:10 PST)
[AMBER] PARMFIT and CHARMM David Ricardo Figueroa Blanco (Thu Oct 24 2019 - 12:55:47 PDT)
[AMBER] REMD Error Rinsha Chk (Thu Oct 24 2019 - 21:23:26 PDT)
- Re: [AMBER] REMD Error Elvis Martis (Thu Oct 24 2019 - 22:09:30 PDT)
  - Re: [AMBER] REMD Error Rinsha Chk (Thu Oct 24 2019 - 22:19:55 PDT)
- Re: [AMBER] REMD Error Carlos Simmerling (Fri Oct 25 2019 - 12:33:46 PDT)
  - Re: [AMBER] REMD Error Rinsha Chk (Fri Oct 25 2019 - 20:34:01 PDT)
    - Re: [AMBER] REMD Error Carlos Simmerling (Sat Oct 26 2019 - 03:26:35 PDT)
    - Re: [AMBER] REMD Error Rinsha Chk (Sat Oct 26 2019 - 04:10:44 PDT)
    - Re: [AMBER] REMD Error Carlos Simmerling (Sat Oct 26 2019 - 04:33:43 PDT)
    - Re: [AMBER] REMD Error Rinsha Chk (Sun Oct 27 2019 - 20:42:42 PDT)
    - Re: [AMBER] REMD Error Rinsha Chk (Sun Oct 27 2019 - 20:42:57 PDT)
    - Re: [AMBER] REMD Error Carlos Simmerling (Mon Oct 28 2019 - 07:23:07 PDT)
    - Re: [AMBER] REMD Error Rinsha Chk (Mon Oct 28 2019 - 20:57:23 PDT)
    - Re: [AMBER] REMD Error Carlos Simmerling (Tue Oct 29 2019 - 10:35:08 PDT)
    - Re: [AMBER] REMD Error Rinsha Chk (Tue Oct 29 2019 - 20:21:23 PDT)
[AMBER] strip problem in cpptraj Sadaf Rani (Fri Oct 25 2019 - 10:58:30 PDT)
- Re: [AMBER] strip problem in cpptraj Daniel Roe (Tue Nov 12 2019 - 05:52:07 PST)
[AMBER] atomicfluct/rmsf time Shayna Hilburg (Fri Oct 25 2019 - 13:40:45 PDT)
- Re: [AMBER] atomicfluct/rmsf time David Case (Sat Oct 26 2019 - 05:11:16 PDT)
  - Re: [AMBER] atomicfluct/rmsf time Shayna Hilburg (Sat Oct 26 2019 - 16:18:39 PDT)
    - Re: [AMBER] atomicfluct/rmsf time Daniel Roe (Wed Oct 30 2019 - 07:18:25 PDT)
[AMBER] How to check the convergence of NEB calculation? Yang JIANG (Fri Oct 25 2019 - 15:19:09 PDT)
- Re: [AMBER] How to check the convergence of NEB calculation? Charles-Alexandre Mattelaer (Mon Nov 11 2019 - 00:33:05 PST)
  - Re: [AMBER] How to check the convergence of NEB calculation? Bill Ross (Mon Nov 11 2019 - 03:40:58 PST)
    - Re: [AMBER] How to check the convergence of NEB calculation? Charles-Alexandre Mattelaer (Mon Nov 11 2019 - 04:16:37 PST)
[AMBER] Assigning am1-bcc charges to a whole library of ligands Liao (Sat Oct 26 2019 - 06:31:56 PDT)
- Re: [AMBER] Assigning am1-bcc charges to a whole library of ligands Elvis Martis (Sat Oct 26 2019 - 06:39:23 PDT)
- Re: [AMBER] Assigning am1-bcc charges to a whole library of ligands David Case (Sun Oct 27 2019 - 19:12:13 PDT)
  - Re: [AMBER] Assigning am1-bcc charges to a whole library of ligands Liao (Sun Oct 27 2019 - 22:55:21 PDT)
[AMBER] MD simulation system Sudad Dayl (Sat Oct 26 2019 - 07:26:36 PDT)
[AMBER] About the unit of the pressure in the md.out file? 邸春艳 (Mon Oct 28 2019 - 00:35:14 PDT)
[AMBER] compiling Amber with gcc 9.2 and intel mpi 2019 Vlad Cojocaru (Mon Oct 28 2019 - 07:57:51 PDT)
- Re: [AMBER] compiling Amber with gcc 9.2 and intel mpi 2019 David A Case (Mon Oct 28 2019 - 11:48:46 PDT)
- Re: [AMBER] compiling Amber with gcc 9.2 and intel mpi 2019 Daniel Roe (Wed Oct 30 2019 - 07:03:59 PDT)
- Re: [AMBER] compiling Amber with gcc 9.2 and intel mpi 2019 Vlad Cojocaru (Thu Nov 07 2019 - 06:47:09 PST)
  - Re: [AMBER] compiling Amber with gcc 9.2 and intel mpi 2019 David A Case (Thu Nov 07 2019 - 11:50:49 PST)
    - Re: [AMBER] compiling Amber with gcc 9.2 and intel mpi 2019 Vlad Cojocaru (Thu Nov 07 2019 - 11:56:57 PST)
[AMBER] Problem in the x-axis of SASA analysis Airy Sanjeev (Mon Oct 28 2019 - 22:47:03 PDT)
- Re: [AMBER] Problem in the x-axis of SASA analysis David A Case (Tue Oct 29 2019 - 05:32:45 PDT)
- Re: [AMBER] Problem in the x-axis of SASA analysis Daniel Roe (Wed Oct 30 2019 - 06:56:06 PDT)
[AMBER] if the ligand doesn't bind when it should, what does it say about quality of my simulations and what can I do? Homeo Morphism (Tue Oct 29 2019 - 07:10:49 PDT)
- Re: [AMBER] if the ligand doesn't bind when it should, what does it say about quality of my simulations and what can I do? Carlos Simmerling (Tue Oct 29 2019 - 10:33:46 PDT)
- Re: [AMBER] if the ligand doesn't bind when it should, what does it say about quality of my simulations and what can I do? Wesley Michael Botello-Smith (Tue Oct 29 2019 - 14:37:07 PDT)
[AMBER] Multiple simulations on one GPU Aiden Aceves (Tue Oct 29 2019 - 08:55:12 PDT)
- Re: [AMBER] Multiple simulations on one GPU Piotr Fajer (Tue Oct 29 2019 - 09:59:54 PDT)
  - Re: [AMBER] Multiple simulations on one GPU David Cerutti (Tue Oct 29 2019 - 10:46:10 PDT)
    - Re: [AMBER] Multiple simulations on one GPU Aiden Aceves (Wed Oct 30 2019 - 07:27:54 PDT)
[AMBER] Thermodynamic integration questions questions and questions Debarati DasGupta (Tue Oct 29 2019 - 08:59:12 PDT)
[AMBER] umbrella sampling question 钟海洋 (Tue Oct 29 2019 - 23:59:38 PDT)
- Re: [AMBER] umbrella sampling question diego.soler.uam.es (Wed Oct 30 2019 - 07:10:23 PDT)
  - Re: [AMBER] umbrella sampling question 钟海洋 (Wed Oct 30 2019 - 20:45:42 PDT)
[AMBER] Error in Step two of MCPB Sodiq Waheed (Wed Oct 30 2019 - 05:15:04 PDT)
- Re: [AMBER] Error in Step two of MCPB Akinpelu Olayinka (Wed Oct 30 2019 - 06:23:22 PDT)
[AMBER] tip4pew water module in different version performs different 钟海洋 (Thu Oct 31 2019 - 01:54:42 PDT)
[AMBER] Any ideas what may be wrong Debarati DasGupta (Thu Oct 31 2019 - 05:58:19 PDT)
[AMBER] reinstallation of amber 14 Sruthi Sudhakar (Fri Nov 01 2019 - 22:41:49 PDT)
[AMBER] Parameter file not saved student_cbc_1 nnlab (Sun Nov 03 2019 - 03:11:19 PST)
- Re: [AMBER] Parameter file not saved Bill Ross (Sun Nov 03 2019 - 03:47:49 PST)
- Re: [AMBER] Parameter file not saved Carlos Simmerling (Sun Nov 03 2019 - 04:47:19 PST)
- Re: [AMBER] Parameter file not saved David Case (Sun Nov 03 2019 - 04:54:31 PST)
[AMBER] Problem with ABMD simulation Federico Iacovelli (Sun Nov 03 2019 - 06:47:39 PST)
- Re: [AMBER] Problem with ABMD simulation Feng Pan (Sun Nov 03 2019 - 11:39:16 PST)
[AMBER] cpptraj.MPI query Debarati DasGupta (Sun Nov 03 2019 - 09:39:14 PST)
- Re: [AMBER] cpptraj.MPI query Daniel Roe (Sun Nov 03 2019 - 17:00:50 PST)
  - Re: [AMBER] cpptraj.MPI query Debarati DasGupta (Mon Nov 04 2019 - 06:01:28 PST)
    - Re: [AMBER] cpptraj.MPI query Daniel Roe (Mon Nov 04 2019 - 07:20:00 PST)
    - Re: [AMBER] cpptraj.MPI query Debarati DasGupta (Mon Nov 04 2019 - 07:34:59 PST)
    - Re: [AMBER] cpptraj.MPI query Daniel Roe (Mon Nov 04 2019 - 11:17:11 PST)
    - Re: [AMBER] cpptraj.MPI query Debarati DasGupta (Mon Nov 04 2019 - 11:41:05 PST)
    - Re: [AMBER] cpptraj.MPI query Daniel Roe (Mon Nov 04 2019 - 11:54:10 PST)
    - Re: [AMBER] cpptraj.MPI query Debarati DasGupta (Mon Nov 04 2019 - 12:07:53 PST)
    - Re: [AMBER] cpptraj.MPI query Daniel Roe (Mon Nov 04 2019 - 12:28:49 PST)
    - Re: [AMBER] cpptraj.MPI query Debarati DasGupta (Mon Nov 04 2019 - 12:38:13 PST)
    - Re: [AMBER] cpptraj.MPI query Debarati DasGupta (Mon Nov 04 2019 - 12:50:11 PST)
[AMBER] velocity autocorrelation Ajeet Kumar Yadav (Sun Nov 03 2019 - 10:00:28 PST)
- Re: [AMBER] velocity autocorrelation Daniel Roe (Mon Nov 04 2019 - 11:27:17 PST)
[AMBER] Parameter file GTP or GMP containing tRNA student_cbc_1 nnlab (Mon Nov 04 2019 - 02:27:35 PST)
- Re: [AMBER] Parameter file GTP or GMP containing tRNA David A Case (Mon Nov 04 2019 - 04:36:17 PST)
[AMBER] Open Scientific Computing Roles at GSK. Ross Walker (Mon Nov 04 2019 - 12:48:59 PST)
[AMBER] problem with MM/PB(GB)SA (Geng Dong) 东庚 (Tue Nov 05 2019 - 00:21:53 PST)
- Re: [AMBER] problem with MM/PB(GB)SA (Geng Dong) Ray Luo (Wed Nov 06 2019 - 09:28:37 PST)
[AMBER] md simulation with GPU （Geng Dong）东庚 (Tue Nov 05 2019 - 00:44:27 PST)
- Re: [AMBER] md simulation with GPU （Geng Dong） Gerardo Zerbetto De Palma (Tue Nov 05 2019 - 05:18:57 PST)
[AMBER] Large GPU performance difference for umbrella sampling methods: (infe=1 and &pmd) vs (nmropt=1 and disang-rst) Åsmund Røhr Kjendseth (Tue Nov 05 2019 - 01:13:23 PST)
- Re: [AMBER] Large GPU performance difference for umbrella sampling methods: (infe=1 and &pmd) vs (nmropt=1 and disang-rst) accuratefreeenergy.gmail.com (Tue Nov 05 2019 - 04:55:49 PST)
[AMBER] error in namelist Debarati DasGupta (Tue Nov 05 2019 - 06:29:22 PST)
- Re: [AMBER] error in namelist David A Case (Tue Nov 05 2019 - 09:47:52 PST)
[AMBER] mmbpsa.py error Alen Ahmetovic (Tue Nov 05 2019 - 16:25:26 PST)
- Re: [AMBER] mmbpsa.py error David Case (Tue Nov 05 2019 - 17:45:29 PST)
[AMBER] md simulation with GPU -Geng Dong 东庚 (Tue Nov 05 2019 - 18:03:07 PST)
- Re: [AMBER] md simulation with GPU -Geng Dong Ross Walker (Tue Nov 05 2019 - 18:09:35 PST)
[AMBER] mac os catalina..... (oh my god) Fabian Glaser (Wed Nov 06 2019 - 00:07:55 PST)
- Re: [AMBER] mac os catalina..... (oh my god) Gustaf Olsson (Wed Nov 06 2019 - 00:40:52 PST)
  - Re: [AMBER] mac os catalina..... (oh my god) Fabian Glaser (Wed Nov 06 2019 - 00:58:05 PST)
[AMBER] jump in monomer position Fabian Glaser (Wed Nov 06 2019 - 00:55:55 PST)
- Re: [AMBER] jump in monomer position Carlos Simmerling (Wed Nov 06 2019 - 13:02:50 PST)
  - Re: [AMBER] jump in monomer position Fabian Glaser (Wed Nov 06 2019 - 23:26:23 PST)
Re: [AMBER] Minimization of ethanol in water David Case (Wed Nov 06 2019 - 14:25:17 PST)
[AMBER] tleap error MYRIAN TORRES RICO (Fri Nov 08 2019 - 03:31:02 PST)
- Re: [AMBER] tleap error Akinpelu Olayinka (Fri Nov 08 2019 - 03:50:09 PST)
- Re: [AMBER] tleap error David A Case (Fri Nov 08 2019 - 05:25:11 PST)
[AMBER] tleap error MYRIAN TORRES RICO (Fri Nov 08 2019 - 03:31:45 PST)
- Re: [AMBER] tleap error Bill Ross (Fri Nov 08 2019 - 04:14:30 PST)
[AMBER] tleap error MYRIAN TORRES RICO (Fri Nov 08 2019 - 04:11:38 PST)
[AMBER] building openMP cpptraj with intel compiler Vlad Cojocaru (Fri Nov 08 2019 - 05:13:14 PST)
- Re: [AMBER] building openMP cpptraj with intel compiler Vlad Cojocaru (Fri Nov 08 2019 - 05:34:36 PST)
  - Re: [AMBER] building openMP cpptraj with intel compiler Daniel Roe (Tue Nov 12 2019 - 06:49:44 PST)
    - Re: [AMBER] building openMP cpptraj with intel compiler Vlad Cojocaru (Tue Nov 12 2019 - 06:59:38 PST)
    - Re: [AMBER] building openMP cpptraj with intel compiler Daniel Roe (Tue Nov 12 2019 - 07:03:42 PST)
- Re: [AMBER] building openMP cpptraj with intel compiler Vlad Cojocaru (Tue Nov 12 2019 - 10:13:26 PST)
  - Re: [AMBER] building openMP cpptraj with intel compiler Daniel Roe (Tue Nov 12 2019 - 10:26:10 PST)
[AMBER] Metal ion parameterization using MCPB.py Abhilash J (Sat Nov 09 2019 - 10:42:25 PST)
- Re: [AMBER] Metal ion parameterization using MCPB.py Pengfei Li (Sat Nov 16 2019 - 20:20:08 PST)
[AMBER] How can I calculate dihedral distribution through CPPTRAJ 조준범 (Mon Nov 11 2019 - 03:21:01 PST)
- Re: [AMBER] How can I calculate dihedral distribution through CPPTRAJ David A Case (Mon Nov 11 2019 - 04:50:07 PST)
  - Re: [AMBER] How can I calculate dihedral distribution through CPPTRAJ 조준범 (Mon Nov 11 2019 - 18:23:40 PST)
    - Re: [AMBER] How can I calculate dihedral distribution through CPPTRAJ Elvis Martis (Mon Nov 11 2019 - 19:32:48 PST)
    - Re: [AMBER] How can I calculate dihedral distribution through CPPTRAJ 조준범 (Tue Nov 12 2019 - 00:16:39 PST)
    - Re: [AMBER] How can I calculate dihedral distribution through CPPTRAJ Elvis Martis (Tue Nov 12 2019 - 02:00:53 PST)
- Re: [AMBER] How can I calculate dihedral distribution through CPPTRAJ Daniel Roe (Tue Nov 12 2019 - 08:21:14 PST)
[AMBER] Making ParmEd play nice with OpenEye? Brian Radak (Mon Nov 11 2019 - 07:52:58 PST)
[AMBER] how to cluster by cpptraj 石娜 (Mon Nov 11 2019 - 17:12:22 PST)
- Re: [AMBER] how to cluster by cpptraj Daniel Roe (Tue Nov 12 2019 - 07:58:52 PST)
[AMBER] cpptraj msd of center -of-mass motion 조준범 (Mon Nov 11 2019 - 18:11:02 PST)
- Re: [AMBER] cpptraj msd of center -of-mass motion David A Case (Tue Nov 12 2019 - 05:43:00 PST)
- Re: [AMBER] cpptraj msd of center -of-mass motion Daniel Roe (Tue Nov 12 2019 - 08:22:29 PST)
[AMBER] AMBER18/16 12-6-4LJ Sander TI problem Paulius Kantakevicius (Tue Nov 12 2019 - 02:58:51 PST)
- Re: [AMBER] AMBER18/16 12-6-4LJ Sander TI problem Pengfei Li (Fri Nov 15 2019 - 15:32:10 PST)
  - Re: [AMBER] AMBER18/16 12-6-4LJ Sander TI problem Paulius Kantakevicius (Sat Nov 16 2019 - 03:20:35 PST)
    - Re: [AMBER] AMBER18/16 12-6-4LJ Sander TI problem Pengfei Li (Sat Nov 16 2019 - 18:13:15 PST)
[AMBER] NMR refined MD maya nair (Tue Nov 12 2019 - 09:20:03 PST)
- Re: [AMBER] NMR refined MD Christina Bergonzo (Tue Nov 12 2019 - 10:18:39 PST)
  - Re: [AMBER] NMR refined MD maya nair (Tue Nov 12 2019 - 23:28:11 PST)
- Re: [AMBER] NMR refined MD David A Case (Tue Nov 12 2019 - 10:50:37 PST)
  - Re: [AMBER] NMR refined MD maya nair (Tue Nov 12 2019 - 23:31:08 PST)
[AMBER] Using the polarizable FF GolP Lucas Bandeira (Tue Nov 12 2019 - 11:42:18 PST)
[AMBER] Modification of gaff 조준범 (Tue Nov 12 2019 - 19:02:10 PST)
- Re: [AMBER] Modification of gaff David A Case (Wed Nov 13 2019 - 04:42:21 PST)
[AMBER] 2D graphic visualisation Giulia Paiardi (Wed Nov 13 2019 - 08:42:54 PST)
[AMBER] question about prmtop file 조준범 (Thu Nov 14 2019 - 01:22:43 PST)
- Re: [AMBER] question about prmtop file David A Case (Thu Nov 14 2019 - 05:38:23 PST)
[AMBER] Workshop on Free Energy calculations in Muenster March 11-13 2020 Vlad Cojocaru (Thu Nov 14 2019 - 02:41:29 PST)
[AMBER] Charge neutrality in QM/MM system James Kress (Thu Nov 14 2019 - 06:46:21 PST)
[AMBER] Calculation Tetrahedral Order Parameter of Water Ajeet Kumar Yadav (Thu Nov 14 2019 - 10:22:44 PST)
[AMBER] different radii sets and GB models Neha Gandhi (Thu Nov 14 2019 - 18:21:57 PST)
- Re: [AMBER] different radii sets and GB models Pietro Aronica (Thu Nov 14 2019 - 18:29:23 PST)
[AMBER] Does amber work with NVIDIA RTX6000? Shenglong Wang (Fri Nov 15 2019 - 08:35:56 PST)
- Re: [AMBER] Does amber work with NVIDIA RTX6000? David Cerutti (Fri Nov 15 2019 - 19:16:01 PST)
  - Re: [AMBER] Does amber work with NVIDIA RTX6000? Shenglong Wang (Fri Nov 15 2019 - 19:33:27 PST)
    - Re: [AMBER] Does amber work with NVIDIA RTX6000? David Cerutti (Sat Nov 16 2019 - 09:05:16 PST)
[AMBER] Broken AmberTools19 cpptraj compilation for GNU, Intel and PGI on a Cray with -crayxt5 flag Victor Holanda Rusu (Fri Nov 15 2019 - 08:42:20 PST)
- Re: [AMBER] Broken AmberTools19 cpptraj compilation for GNU, Intel and PGI on a Cray with -crayxt5 flag Daniel Roe (Fri Nov 15 2019 - 11:50:58 PST)
[AMBER] decompose MMGBSA error Nisha Amarnath Jonniya (Fri Nov 15 2019 - 21:58:59 PST)
- Re: [AMBER] decompose MMGBSA error Elvis Martis (Fri Nov 15 2019 - 22:21:15 PST)
  - Re: [AMBER] decompose MMGBSA error Nisha Amarnath Jonniya (Sat Nov 16 2019 - 18:53:35 PST)
    - Re: [AMBER] decompose MMGBSA error Elvis Martis (Sun Nov 17 2019 - 22:07:41 PST)
    - Re: [AMBER] decompose MMGBSA error Nisha Amarnath Jonniya (Mon Nov 18 2019 - 00:19:05 PST)
    - Re: [AMBER] decompose MMGBSA error Elvis Martis (Mon Nov 18 2019 - 00:45:20 PST)
    - Re: [AMBER] decompose MMGBSA error David Case (Mon Nov 18 2019 - 04:35:12 PST)
    - Re: [AMBER] decompose MMGBSA error Nisha Amarnath Jonniya (Mon Nov 18 2019 - 20:50:34 PST)
    - Re: [AMBER] decompose MMGBSA error Nisha Amarnath Jonniya (Wed Nov 20 2019 - 03:43:21 PST)
    - Re: [AMBER] decompose MMGBSA error Elvis Martis (Wed Nov 20 2019 - 04:38:41 PST)
    - Re: [AMBER] decompose MMGBSA error Nisha Amarnath Jonniya (Wed Nov 20 2019 - 22:46:36 PST)
    - Re: [AMBER] decompose MMGBSA error David A Case (Thu Nov 21 2019 - 05:36:03 PST)
    - Re: [AMBER] decompose MMGBSA error Nisha Amarnath Jonniya (Thu Nov 21 2019 - 20:27:25 PST)
    - Re: [AMBER] decompose MMGBSA error Elvis Martis (Thu Nov 21 2019 - 20:32:48 PST)
- Re: [AMBER] decompose MMGBSA error Nisha Amarnath Jonniya (Thu Nov 28 2019 - 04:56:40 PST)
  - Re: [AMBER] decompose MMGBSA error Elvis Martis (Thu Nov 28 2019 - 05:12:04 PST)
[AMBER] Problem running production run Airy Sanjeev (Sat Nov 16 2019 - 00:48:04 PST)
- Re: [AMBER] Problem running production run Bill Ross (Sat Nov 16 2019 - 00:54:11 PST)
- Re: [AMBER] Problem running production run Bill Ross (Sat Nov 16 2019 - 01:33:23 PST)
[AMBER] There is an bug in how Amber preserves charge neutrality in QM/MM system when ORCA is the targeted QM tool. James Kress (Sat Nov 16 2019 - 08:08:40 PST)
[AMBER] Error in PMEMD installation with MPI Rahul Verma (Sun Nov 17 2019 - 21:01:52 PST)
- Re: [AMBER] Error in PMEMD installation with MPI David Case (Mon Nov 18 2019 - 04:22:38 PST)
[AMBER] Simulation run issue Sayan Poddar (Sun Nov 17 2019 - 22:03:03 PST)
- Re: [AMBER] Simulation run issue David Case (Mon Nov 18 2019 - 04:27:52 PST)
[AMBER] Error in themodynamic integration with PMEMD.CUDA HOCHEOL LIM (Mon Nov 18 2019 - 04:37:49 PST)
[AMBER] MD CYT C : heme bound emanuele falbo (Mon Nov 18 2019 - 07:58:40 PST)
[AMBER] amber maillist Q Yu (Mon Nov 18 2019 - 08:41:09 PST)
[AMBER] Conformation of NEB end states changing during 1HEAT Madhur Aggarwal (Mon Nov 18 2019 - 09:09:59 PST)
- Re: [AMBER] Conformation of NEB end states changing during 1HEAT Ghoreishi, Delaram (Mon Nov 18 2019 - 09:29:36 PST)
- Re: [AMBER] Conformation of NEB end states changing during 1HEAT Carlos Simmerling (Mon Nov 18 2019 - 09:40:13 PST)
- Re: [AMBER] Conformation of NEB end states changing during 1HEAT Madhur Aggarwal (Mon Nov 18 2019 - 11:44:29 PST)
  - Re: [AMBER] Conformation of NEB end states changing during 1HEAT Ghoreishi, Delaram (Mon Nov 18 2019 - 22:55:15 PST)
    - Re: [AMBER] Conformation of NEB end states changing during 1HEAT Madhur Aggarwal (Tue Nov 19 2019 - 06:51:36 PST)
    - Re: [AMBER] Conformation of NEB end states changing during 1HEAT Ghoreishi, Delaram (Tue Nov 19 2019 - 07:48:53 PST)
    - Re: [AMBER] Conformation of NEB end states changing during 1HEAT Carlos Simmerling (Tue Nov 19 2019 - 07:53:13 PST)
    - Re: [AMBER] Conformation of NEB end states changing during 1HEAT Madhur Aggarwal (Wed Nov 20 2019 - 00:15:46 PST)
Re: [AMBER] amber15 cpptraj closest Q Yu (Mon Nov 18 2019 - 10:34:43 PST)
- Re: [AMBER] amber15 cpptraj closest Daniel Roe (Thu Nov 21 2019 - 08:52:18 PST)
  - Re: [AMBER] amber15 cpptraj closest Q Yu (Fri Nov 22 2019 - 08:55:56 PST)
- Re: [AMBER] amber15 cpptraj closest Daniel Roe (Fri Nov 22 2019 - 09:07:35 PST)
  - [AMBER] ATP gamma phosphate distorted in MD Qing Lv (Fri Nov 22 2019 - 10:11:23 PST)
    - Re: [AMBER] ATP gamma phosphate distorted in MD Zachary Fallon (Fri Nov 22 2019 - 10:26:28 PST)
    - Re: [AMBER] ATP gamma phosphate distorted in MD Qing Lv (Fri Nov 22 2019 - 22:04:09 PST)
[AMBER] Charge neutrality in QM/MM system James Kress (Mon Nov 18 2019 - 15:13:42 PST)
- Re: [AMBER] Charge neutrality in QM/MM system David Case (Mon Nov 18 2019 - 18:25:13 PST)
  - Re: [AMBER] Charge neutrality in QM/MM system James Kress (Mon Nov 18 2019 - 20:51:09 PST)
[AMBER] PIMD restart error in Amber18 jinfeng liu (Mon Nov 18 2019 - 19:36:35 PST)
- Re: [AMBER] PIMD restart error in Amber18 David A Case (Thu Nov 21 2019 - 11:56:49 PST)
[AMBER] Problem in generating the .rst file Airy Sanjeev (Mon Nov 18 2019 - 21:44:33 PST)
- Re: [AMBER] Problem in generating the .rst file Carlos Simmerling (Tue Nov 19 2019 - 02:42:40 PST)
[AMBER] Error with addIons 조준범 (Mon Nov 18 2019 - 22:10:09 PST)
- Re: [AMBER] Error with addIons Bill Ross (Mon Nov 18 2019 - 22:17:02 PST)
  - Re: [AMBER] Error with addIons 조준범 (Mon Nov 18 2019 - 22:45:54 PST)
    - Re: [AMBER] Error with addIons 조준범 (Mon Nov 18 2019 - 22:49:37 PST)
    - Re: [AMBER] Error with addIons Bill Ross (Mon Nov 18 2019 - 22:56:45 PST)
    - Re: [AMBER] Error with addIons 조준범 (Mon Nov 18 2019 - 23:09:33 PST)
    - Re: [AMBER] Error with addIons 조준범 (Mon Nov 18 2019 - 23:22:03 PST)
    - Re: [AMBER] Error with addIons Bill Ross (Mon Nov 18 2019 - 23:22:42 PST)
    - Re: [AMBER] Error with addIons David Case (Tue Nov 19 2019 - 05:14:10 PST)
[AMBER] amber 16 with nVIDIA Tesla T4 GPU Schröder, David Christopher (Tue Nov 19 2019 - 03:51:35 PST)
[AMBER] RROR: I could not understand line - during US Fabian Glaser (Tue Nov 19 2019 - 07:55:59 PST)
- Re: [AMBER] RROR: I could not understand line - during US David Case (Tue Nov 19 2019 - 12:41:43 PST)
  - Re: [AMBER] RROR: I could not understand line - during US Fabian Glaser (Wed Nov 20 2019 - 03:44:35 PST)
    - Re: [AMBER] RROR: I could not understand line - during US Bill Ross (Wed Nov 20 2019 - 03:50:16 PST)
    - Re: [AMBER] RROR: I could not understand line - during US Fabian Glaser (Wed Nov 20 2019 - 05:16:10 PST)
    - Re: [AMBER] RROR: I could not understand line - during US David A Case (Wed Nov 20 2019 - 06:04:59 PST)
    - Re: [AMBER] RROR: I could not understand line - during US Fabian Glaser (Wed Nov 20 2019 - 06:57:09 PST)
    - Re: [AMBER] RROR: I could not understand line - during US David A Case (Wed Nov 20 2019 - 10:46:49 PST)
[AMBER] Error parameterizing a heme using MCPB Mohamed M. Aboelnga (Tue Nov 19 2019 - 09:20:01 PST)
- Re: [AMBER] Error parameterizing a heme using MCPB Pengfei Li (Wed Nov 20 2019 - 19:29:33 PST)
  - Re: [AMBER] Error parameterizing a heme using MCPB Mohamed M. Aboelnga (Thu Nov 21 2019 - 05:50:13 PST)
    - Re: [AMBER] Error parameterizing a heme using MCPB Pengfei Li (Mon Nov 25 2019 - 18:04:28 PST)
[AMBER] Amber updates brings duplicate patch viktor drobot (Wed Nov 20 2019 - 01:50:44 PST)
- Re: [AMBER] Amber updates brings duplicate patch David A Case (Wed Nov 20 2019 - 06:21:41 PST)
  - Re: [AMBER] Amber updates brings duplicate patch viktor drobot (Wed Nov 20 2019 - 06:27:24 PST)
    - Re: [AMBER] Amber updates brings duplicate patch David A Case (Wed Nov 20 2019 - 10:57:07 PST)
    - Re: [AMBER] Amber updates brings duplicate patch viktor drobot (Thu Nov 21 2019 - 04:03:52 PST)
    - Re: [AMBER] Amber updates brings duplicate patch David A Case (Thu Nov 21 2019 - 05:29:41 PST)
[AMBER] Using NetCDF trajectory files as ParmEd structure Brian Radak (Wed Nov 20 2019 - 07:44:15 PST)
- Re: [AMBER] Using NetCDF trajectory files as ParmEd structure Jason Swails (Wed Nov 27 2019 - 10:58:18 PST)
[AMBER] Fwd: Error in PMEMD installation with MPI Rahul Verma (Wed Nov 20 2019 - 19:42:30 PST)
[AMBER] antechamber QM calculation/qmcharge error Rui Chen (Wed Nov 20 2019 - 21:25:53 PST)
- Re: [AMBER] antechamber QM calculation/qmcharge error David A Case (Thu Nov 21 2019 - 05:34:06 PST)
  - Re: [AMBER] antechamber QM calculation/qmcharge error Rui Chen (Thu Nov 21 2019 - 08:48:38 PST)
[AMBER] Force-field with only Bond parameters Stefano Motta (Thu Nov 21 2019 - 02:04:44 PST)
- Re: [AMBER] Force-field with only Bond parameters Carlos Simmerling (Thu Nov 21 2019 - 02:12:33 PST)
  - Re: [AMBER] Force-field with only Bond parameters Stefano Motta (Thu Nov 21 2019 - 02:48:57 PST)
    - Re: [AMBER] Force-field with only Bond parameters Carlos Simmerling (Thu Nov 21 2019 - 02:59:24 PST)
    - Re: [AMBER] Force-field with only Bond parameters Stefano Motta (Thu Nov 21 2019 - 03:12:33 PST)
    - Re: [AMBER] Force-field with only Bond parameters Carlos Simmerling (Thu Nov 21 2019 - 03:21:37 PST)
    - Re: [AMBER] Force-field with only Bond parameters Stefano Motta (Thu Nov 21 2019 - 03:27:39 PST)
    - Re: [AMBER] Force-field with only Bond parameters Carlos Simmerling (Thu Nov 21 2019 - 03:59:52 PST)
    - Re: [AMBER] Force-field with only Bond parameters Stefano Motta (Thu Nov 21 2019 - 05:19:53 PST)
    - Re: [AMBER] Force-field with only Bond parameters David A Case (Thu Nov 21 2019 - 11:47:45 PST)
    - Re: [AMBER] Force-field with only Bond parameters Stefano Motta (Fri Nov 22 2019 - 01:07:02 PST)
[AMBER] Error in themodynamic integration with PMEMD.CUDA HOCHEOL LIM (Thu Nov 21 2019 - 07:06:28 PST)
- Re: [AMBER] Error in themodynamic integration with PMEMD.CUDA David A Case (Thu Nov 21 2019 - 11:53:55 PST)
[AMBER] Error in themodynamic integration with PMEMD.CUDA HOCHEOL LIM (Thu Nov 21 2019 - 07:32:29 PST)
[AMBER] Error in the namelist cntrl Airy Sanjeev (Thu Nov 21 2019 - 22:04:00 PST)
- Re: [AMBER] Error in the namelist cntrl David A Case (Fri Nov 22 2019 - 05:30:33 PST)
[AMBER] absolute binding free energy calculations Debarati DasGupta (Fri Nov 22 2019 - 10:37:22 PST)
[AMBER] List of GAF2 atom types? Gustavo Seabra (Fri Nov 22 2019 - 13:19:28 PST)
- Re: [AMBER] List of GAF2 atom types? David Case (Fri Nov 22 2019 - 18:55:26 PST)
[AMBER] [Bug-Report] NAB: TER record need a serial number Johannes Kalliauer (Mon Nov 25 2019 - 03:06:57 PST)
- Re: [AMBER] [Bug-Report] NAB: TER record need a serial number Daniel Roe (Mon Nov 25 2019 - 05:21:42 PST)
[AMBER] Finding radial distribution function using cpptraj Raghav Arora (Mon Nov 25 2019 - 03:57:22 PST)
- Re: [AMBER] Finding radial distribution function using cpptraj Daniel Roe (Mon Nov 25 2019 - 05:16:02 PST)
[AMBER] Citation for GAFF2 Gustaf Olsson (Mon Nov 25 2019 - 07:02:59 PST)
[AMBER] umbrella box size for protein-protein Fabian Glaser (Tue Nov 26 2019 - 01:38:39 PST)
[AMBER] Regarding Amber16 installation dilrajl.bii.a-star.edu.sg (Tue Nov 26 2019 - 04:15:09 PST)
- Re: [AMBER] Regarding Amber16 installation David Case (Tue Nov 26 2019 - 04:57:34 PST)
[AMBER] Tleap-complex PDB problem Rui Chen (Tue Nov 26 2019 - 17:52:10 PST)
- Re: [AMBER] Tleap-complex PDB problem Lachele Foley (Tue Nov 26 2019 - 21:07:36 PST)
  - Re: [AMBER] Tleap-complex PDB problem Rui Chen (Wed Nov 27 2019 - 07:37:19 PST)
    - Re: [AMBER] Tleap-complex PDB problem David A Case (Wed Nov 27 2019 - 08:42:31 PST)
    - Re: [AMBER] Tleap-complex PDB problem Rui Chen (Wed Nov 27 2019 - 08:52:12 PST)
- Re: [AMBER] Tleap-complex PDB problem Rui Chen (Wed Nov 27 2019 - 14:01:40 PST)
[AMBER] ff19SB inpcrd test file missing David Wang (Wed Nov 27 2019 - 11:57:37 PST)
- Re: [AMBER] ff19SB inpcrd test file missing Chuan Tian (Wed Nov 27 2019 - 14:48:39 PST)
  - Re: [AMBER] ff19SB inpcrd test file missing David Case (Thu Nov 28 2019 - 05:48:07 PST)
[AMBER] Obtaining excess molar volumes using Molecular Dynamics Raghav Arora (Thu Nov 28 2019 - 02:58:30 PST)
- Re: [AMBER] Obtaining excess molar volumes using Molecular Dynamics David Case (Tue Dec 03 2019 - 05:51:28 PST)
[AMBER] HTTP Error 500 - download Mattia Pini (Fri Nov 29 2019 - 00:16:59 PST)
- Re: [AMBER] HTTP Error 500 - download Hai Nguyen (Fri Nov 29 2019 - 08:42:07 PST)
[AMBER] help on this error Debarati DasGupta (Fri Nov 29 2019 - 06:29:45 PST)
- Re: [AMBER] help on this error David Case (Fri Nov 29 2019 - 18:10:18 PST)
  - Re: [AMBER] help on this error Debarati DasGupta (Tue Dec 03 2019 - 14:06:17 PST)
    - Re: [AMBER] help on this error Josh Berryman (Fri Dec 06 2019 - 03:21:58 PST)
    - Re: [AMBER] help on this error Debarati DasGupta (Fri Dec 06 2019 - 05:24:08 PST)
    - Re: [AMBER] help on this error Debarati DasGupta (Fri Dec 06 2019 - 13:08:29 PST)
    - Re: [AMBER] help on this error David Case (Sat Dec 07 2019 - 06:03:43 PST)
[AMBER] MMGBSA error RITUPARNA ROY (Sat Nov 30 2019 - 08:48:26 PST)
[AMBER] On deprotonated Tyr David Sáez (Sun Dec 01 2019 - 20:39:54 PST)
[AMBER] sequence command ankita mehta (Sun Dec 01 2019 - 22:28:03 PST)
- Re: [AMBER] sequence command ankita mehta (Mon Dec 02 2019 - 02:15:44 PST)
[AMBER] Charge distribution in molecule Aashish Bhatt (Sun Dec 01 2019 - 23:04:21 PST)
- Re: [AMBER] Charge distribution in molecule Horn, Anselm (Sun Dec 01 2019 - 23:37:51 PST)
  - [AMBER] Announcement: 34th Molecular Modelling Workshop (MMWS) Feb 17-19, 2020 in Erlangen, Germany Dr. Anselm Horn (Wed Dec 04 2019 - 05:13:39 PST)
- Re: [AMBER] Charge distribution in molecule Bill Ross (Mon Dec 02 2019 - 05:42:54 PST)
  - Re: [AMBER] Charge distribution in molecule Aashish Bhatt (Thu Dec 05 2019 - 04:09:00 PST)
[AMBER] cpptraj RMS calculations appear to be incorrect Bellesis, Andrew G (Mon Dec 02 2019 - 09:02:50 PST)
- Re: [AMBER] cpptraj RMS calculations appear to be incorrect Carlos Simmerling (Mon Dec 02 2019 - 10:18:09 PST)
- Re: [AMBER] cpptraj RMS calculations appear to be incorrect Bellesis, Andrew G (Tue Dec 03 2019 - 08:00:41 PST)
[AMBER] Chemical education for MD articles Lod King (Mon Dec 02 2019 - 12:21:12 PST)
- Re: [AMBER] Chemical education for MD articles Joanna Michelle E. Chua (Mon Dec 02 2019 - 18:25:19 PST)
  - [AMBER] MMPBSA mmpbsa_py_energy failed with prmtop Qing Lv (Wed Dec 04 2019 - 20:32:05 PST)
    - Re: [AMBER] MMPBSA mmpbsa_py_energy failed with prmtop Qing Lv (Wed Dec 04 2019 - 23:41:02 PST)
- Re: [AMBER] Chemical education for MD articles Daniel Roe (Tue Dec 03 2019 - 05:02:31 PST)
  - Re: [AMBER] Chemical education for MD articles Joanna Michelle E. Chua (Tue Dec 03 2019 - 05:18:00 PST)
[AMBER] 34th Molecular Modelling Workshop (MMWS) February 17-19, 2020 in Erlangen, Germany Dr. Anselm Horn (Tue Dec 03 2019 - 01:56:09 PST)
[AMBER] TI support for CHARMM FF Jose Christian Flores Canales (Tue Dec 03 2019 - 04:58:02 PST)
[AMBER] Table 21.1 in Thermodynamic Integration section of amber18 manual Debarati DasGupta (Wed Dec 04 2019 - 07:17:42 PST)
[AMBER] Sequential equilibration versus parallel runs in TI Debarati DasGupta (Wed Dec 04 2019 - 07:45:05 PST)
- Re: [AMBER] Sequential equilibration versus parallel runs in TI Debarati DasGupta (Wed Dec 04 2019 - 07:45:57 PST)
- Re: [AMBER] Sequential equilibration versus parallel runs in TI David A Case (Thu Dec 05 2019 - 05:54:39 PST)
[AMBER] Fixed Minimization emanuele falbo (Thu Dec 05 2019 - 06:15:49 PST)
- Re: [AMBER] Fixed Minimization David A Case (Fri Dec 06 2019 - 05:26:13 PST)
  - Re: [AMBER] Fixed Minimization emanuele falbo (Fri Dec 06 2019 - 07:05:14 PST)
[AMBER] TI calculation steps Debarati DasGupta (Thu Dec 05 2019 - 12:24:56 PST)
- Re: [AMBER] TI calculation steps Song, Lin (Thu Dec 05 2019 - 13:25:39 PST)
  - Re: [AMBER] TI calculation steps Debarati DasGupta (Thu Dec 05 2019 - 13:39:29 PST)
    - Re: [AMBER] TI calculation steps Song, Lin (Thu Dec 05 2019 - 13:45:55 PST)
    - Re: [AMBER] TI calculation steps Debarati DasGupta (Thu Dec 05 2019 - 13:46:44 PST)
[AMBER] Equilibriation input file for TI Debarati DasGupta (Thu Dec 05 2019 - 14:35:23 PST)
- Re: [AMBER] Equilibriation input file for TI David A Case (Fri Dec 06 2019 - 05:28:04 PST)
  - Re: [AMBER] Equilibriation input file for TI Debarati DasGupta (Fri Dec 06 2019 - 07:57:28 PST)
[AMBER] TI calculations linear scaling of atoms! Debarati DasGupta (Thu Dec 05 2019 - 15:01:21 PST)
[AMBER] fxyz and outxyz Baker, Joseph (Thu Dec 05 2019 - 19:09:11 PST)
[AMBER] Warning: 2 or more molecules (3 and 4) share residue numbers (1003). David Sáez (Thu Dec 05 2019 - 21:08:38 PST)
- Re: [AMBER] Warning: 2 or more molecules (3 and 4) share residue numbers (1003). Bill Ross (Thu Dec 05 2019 - 21:27:39 PST)
- Re: [AMBER] Warning: 2 or more molecules (3 and 4) share residue numbers (1003). David A Case (Fri Dec 06 2019 - 05:32:42 PST)
[AMBER] Conference Announcement: Molecular Modeling Workshop, Feb 17-19, 2020 in Erlangen, Germany Dr. Anselm Horn (Fri Dec 06 2019 - 01:41:01 PST)
[AMBER] How can I get solute-solute energy information? Zhonghua Xia (Fri Dec 06 2019 - 04:04:38 PST)
[AMBER] How can I get solute-solute energy information? Zhonghua Xia (Fri Dec 06 2019 - 05:36:35 PST)
[AMBER] Segmentation Fault when running constant pH Replica Exchange on GPUs Hofer, Florian (Fri Dec 06 2019 - 07:52:01 PST)
[AMBER] Problems adding molecule on Metal-Water system Lucas Bandeira (Fri Dec 06 2019 - 11:22:44 PST)
- Re: [AMBER] Problems adding molecule on Metal-Water system David Case (Sat Dec 07 2019 - 06:07:01 PST)
  - Re: [AMBER] Problems adding molecule on Metal-Water system Lucas Bandeira (Sun Dec 08 2019 - 16:59:40 PST)
- Re: [AMBER] Problems adding molecule on Metal-Water system David Case (Mon Dec 09 2019 - 09:46:38 PST)
  - Re: [AMBER] Problems adding molecule on Metal-Water system Lucas Bandeira (Thu Dec 12 2019 - 06:19:09 PST)
[AMBER] problem of compiling Albert (Sat Dec 07 2019 - 20:23:04 PST)
- Re: [AMBER] problem of compiling Charo del Genio (Sun Dec 08 2019 - 00:46:19 PST)
- Re: [AMBER] problem of compiling Gerald Monard (Mon Dec 09 2019 - 01:48:53 PST)
- [AMBER] Fwd: problem of compiling Albert (Wed Dec 11 2019 - 16:21:54 PST)
  - Re: [AMBER] Fwd: problem of compiling David A Case (Thu Dec 12 2019 - 06:05:15 PST)
  - Re: [AMBER] Fwd: problem of compiling Gerald Monard (Thu Dec 12 2019 - 10:46:44 PST)
    - Re: [AMBER] Fwd: problem of compiling Albert (Thu Dec 12 2019 - 16:44:36 PST)
    - Re: [AMBER] Fwd: problem of compiling Gerald Monard (Thu Dec 12 2019 - 23:01:45 PST)
    - Re: [AMBER] Fwd: problem of compiling Albert (Thu Dec 12 2019 - 23:16:59 PST)
    - Re: [AMBER] Fwd: problem of compiling Gerald Monard (Fri Dec 13 2019 - 00:38:05 PST)
[AMBER] Timestep (dt) in TI calculations Debarati DasGupta (Sun Dec 08 2019 - 06:30:03 PST)
Re: [AMBER] PrmtopError: Complex natom != receptor natom + ligand natom Bill Ross (Sun Dec 08 2019 - 18:02:59 PST)
- Re: [AMBER] PrmtopError: Complex natom != receptor natom + ligand natom David Case (Mon Dec 09 2019 - 05:28:18 PST)
[AMBER] error MYRIAN TORRES RICO (Tue Dec 10 2019 - 04:27:02 PST)
- Re: [AMBER] error David A Case (Tue Dec 10 2019 - 04:46:18 PST)
  - Re: [AMBER] error MYRIAN TORRES RICO (Tue Dec 10 2019 - 06:59:45 PST)
- Re: [AMBER] error Daniel Roe (Tue Dec 10 2019 - 09:01:45 PST)
  - Re: [AMBER] error MYRIAN TORRES RICO (Wed Dec 11 2019 - 08:05:49 PST)
    - Re: [AMBER] error David A Case (Wed Dec 11 2019 - 08:40:39 PST)
    - Re: [AMBER] error James Kress (Wed Dec 11 2019 - 09:36:15 PST)
    - Re: [AMBER] error Carlos Simmerling (Wed Dec 11 2019 - 11:28:32 PST)
    - Re: [AMBER] error Bill Ross (Wed Dec 11 2019 - 14:54:52 PST)
    - Re: [AMBER] error MYRIAN TORRES RICO (Thu Dec 12 2019 - 01:13:39 PST)
    - Re: [AMBER] error Bill Ross (Thu Dec 12 2019 - 11:26:17 PST)
    - Re: [AMBER] error MYRIAN TORRES RICO (Wed Jan 08 2020 - 07:07:38 PST)
    - Re: [AMBER] error Gustaf Olsson (Wed Jan 08 2020 - 22:54:22 PST)
    - Re: [AMBER] error Daniel Roe (Sun Dec 15 2019 - 12:10:09 PST)
[AMBER] Molecular dynamics of tripeptide like organic molecule Debasish Mandal (Tue Dec 10 2019 - 20:18:56 PST)
- Re: [AMBER] Molecular dynamics of tripeptide like organic molecule Petro (Tue Dec 10 2019 - 22:19:35 PST)
[AMBER] ff19SB with end-caps pmemd.cuda problem Pavlína Pokorná (Wed Dec 11 2019 - 02:37:55 PST)
- Re: [AMBER] ff19SB with end-caps pmemd.cuda problem Carlos Simmerling (Wed Dec 11 2019 - 03:53:44 PST)
  - Re: [AMBER] ff19SB with end-caps pmemd.cuda problem Pavlína Pokorná (Wed Dec 11 2019 - 05:34:28 PST)
    - Re: [AMBER] ff19SB with end-caps pmemd.cuda problem Carlos Simmerling (Wed Dec 11 2019 - 06:02:22 PST)
    - Re: [AMBER] ff19SB with end-caps pmemd.cuda problem Pavlína Pokorná (Wed Dec 11 2019 - 06:40:06 PST)
    - Re: [AMBER] ff19SB with end-caps pmemd.cuda problem Carlos Simmerling (Wed Dec 11 2019 - 07:10:18 PST)
    - Re: [AMBER] ff19SB with end-caps pmemd.cuda problem Pavlína Pokorná (Wed Dec 11 2019 - 08:50:41 PST)
    - Re: [AMBER] ff19SB with end-caps pmemd.cuda problem Carlos Simmerling (Wed Dec 11 2019 - 08:54:39 PST)
    - Re: [AMBER] ff19SB with end-caps pmemd.cuda problem Pavlína Pokorná (Wed Dec 11 2019 - 09:07:30 PST)
    - Re: [AMBER] ff19SB with end-caps pmemd.cuda problem Pavlína Pokorná (Mon Dec 16 2019 - 01:59:01 PST)
    - Re: [AMBER] ff19SB with end-caps pmemd.cuda problem Carlos Simmerling (Tue Dec 17 2019 - 06:04:13 PST)
    - Re: [AMBER] ff19SB with end-caps pmemd.cuda problem Pavlína Pokorná (Tue Dec 17 2019 - 06:21:57 PST)
    - Re: [AMBER] ff19SB with end-caps pmemd.cuda problem Carlos Simmerling (Tue Dec 17 2019 - 08:21:16 PST)
    - [AMBER] Problems installing Amber 18 Billiot, Eugene (Tue Dec 17 2019 - 13:54:07 PST)
    - Re: [AMBER] Problems installing Amber 18 Billiot, Eugene (Tue Dec 17 2019 - 13:58:14 PST)
    - [AMBER] installing Amber 18 issues Billiot, Eugene (Tue Dec 17 2019 - 15:46:00 PST)
    - Re: [AMBER] installing Amber 18 issues Joanna Michelle E. Chua (Tue Dec 17 2019 - 18:50:24 PST)
    - Re: [AMBER] installing Amber 18 issues Joanna Michelle E. Chua (Tue Dec 17 2019 - 19:01:26 PST)
    - Re: [AMBER] installing Amber 18 issues Billiot, Eugene (Tue Dec 17 2019 - 19:17:58 PST)
    - Re: [AMBER] installing Amber 18 issues David Case (Wed Dec 18 2019 - 06:34:38 PST)
    - Re: [AMBER] Problems installing Amber 18 Gustaf Olsson (Tue Dec 17 2019 - 22:49:14 PST)
    - Re: [AMBER] Problems installing Amber 18 Billiot, Eugene (Wed Dec 18 2019 - 06:46:38 PST)
[AMBER] Found an invalid periodicity in the prmtop file : MMPBSA venkat (Wed Dec 11 2019 - 08:13:02 PST)
- Re: [AMBER] Found an invalid periodicity in the prmtop file : MMPBSA David A Case (Wed Dec 11 2019 - 10:42:09 PST)
[AMBER] GPU installation error Sruthi Sudhakar (Wed Dec 11 2019 - 09:47:45 PST)
- Re: [AMBER] GPU installation error David A Case (Wed Dec 11 2019 - 10:39:38 PST)
  - Re: [AMBER] GPU installation error Sruthi Sudhakar (Wed Dec 11 2019 - 19:41:30 PST)
[AMBER] Time shift. Petro (Wed Dec 11 2019 - 23:40:55 PST)
- Re: [AMBER] Time shift. Bill Ross (Thu Dec 12 2019 - 00:17:03 PST)
[AMBER] User-defined high precision AMBER trajectory file formats Xin Bai (Thu Dec 12 2019 - 03:12:01 PST)
- Re: [AMBER] User-defined high precision AMBER trajectory file formats Daniel Roe (Sun Dec 15 2019 - 12:14:13 PST)
[AMBER] Found an invalid periodicity in the prmtop file : MMPBSA venkat (Thu Dec 12 2019 - 03:31:40 PST)
- Re: [AMBER] Found an invalid periodicity in the prmtop file : MMPBSA venkat (Thu Dec 12 2019 - 03:57:16 PST)
[AMBER] Ti on pmemd.CUDA Hosein Geraili Daronkola (Thu Dec 12 2019 - 07:22:04 PST)
- Re: [AMBER] Ti on pmemd.CUDA Carlos Simmerling (Thu Dec 12 2019 - 09:36:18 PST)
[AMBER] Flexible protein! Debarati DasGupta (Thu Dec 12 2019 - 10:26:20 PST)
- Re: [AMBER] Flexible protein! David A Case (Fri Dec 13 2019 - 04:17:10 PST)
  - Re: [AMBER] Flexible protein! Debarati DasGupta (Fri Dec 13 2019 - 11:37:26 PST)
    - [AMBER] Problems installing mpi for AMBER 18. Billiot, Eugene (Sun Dec 15 2019 - 17:08:03 PST)
    - Re: [AMBER] Problems installing mpi for AMBER 18. Bill Ross (Sun Dec 15 2019 - 17:31:03 PST)
    - Re: [AMBER] Problems installing mpi for AMBER 18. Billiot, Eugene (Sun Dec 15 2019 - 18:04:35 PST)
    - Re: [AMBER] Problems installing mpi for AMBER 18. Billiot, Eugene (Mon Dec 16 2019 - 07:42:07 PST)
    - Re: [AMBER] Problems installing mpi for AMBER 18. Bill Ross (Mon Dec 16 2019 - 07:45:51 PST)
    - Re: [AMBER] Problems installing mpi for AMBER 18. I was trying to install mpi I was typing in Billiot, Eugene (Mon Dec 16 2019 - 08:07:21 PST)
[AMBER] GaMD problems with different computers. Seibold, Steve Allan (Thu Dec 12 2019 - 11:12:25 PST)
- Re: [AMBER] GaMD problems with different computers. David A Case (Fri Dec 13 2019 - 04:22:32 PST)
[AMBER] mm-gbsa with more than one receptor Neha Gandhi (Thu Dec 12 2019 - 15:50:11 PST)
[AMBER] mm-gbsa with more than one receptor Liao (Thu Dec 12 2019 - 17:42:08 PST)
[AMBER] mm-gbsa with more than one receptor Liao (Thu Dec 12 2019 - 17:37:41 PST)
[AMBER] mm-gbsa with more than one receptor Liao (Thu Dec 12 2019 - 17:39:01 PST)
[AMBER] mm-gbsa with more than one receptor Liao (Thu Dec 12 2019 - 17:42:54 PST)
[AMBER] MM-GBSA error Rui Chen (Thu Dec 12 2019 - 18:31:57 PST)
- Re: [AMBER] MM-GBSA error Rui Chen (Fri Dec 13 2019 - 19:49:26 PST)
  - Re: [AMBER] MM-GBSA error David Case (Sat Dec 14 2019 - 06:47:27 PST)
    - Re: [AMBER] MM-GBSA error Rui Chen (Wed Dec 18 2019 - 09:06:07 PST)
[AMBER] intel compiling failed Albert (Thu Dec 12 2019 - 19:47:28 PST)
- Re: [AMBER] intel compiling failed David A Case (Fri Dec 13 2019 - 04:30:52 PST)
[AMBER] Error when running MD maya nair (Fri Dec 13 2019 - 09:51:34 PST)
- Re: [AMBER] Error when running MD David Case (Fri Dec 13 2019 - 10:42:10 PST)
- Re: [AMBER] Error when running MD Bill Ross (Fri Dec 13 2019 - 11:02:13 PST)
[AMBER] Any way of making protein rigid in MD simulation? Liao (Fri Dec 13 2019 - 20:59:40 PST)
- Re: [AMBER] Any way of making protein rigid in MD simulation? Gustaf Olsson (Sun Dec 15 2019 - 23:14:30 PST)
  - Re: [AMBER] Any way of making protein rigid in MD simulation? Brian Radak (Mon Dec 16 2019 - 07:13:30 PST)
[AMBER] FESetup Debarati DasGupta (Sun Dec 15 2019 - 14:14:34 PST)
- Re: [AMBER] FESetup Sushil Mishra (Sun Dec 15 2019 - 22:12:32 PST)
  - Re: [AMBER] FESetup Sarah Fegan - UKRI STFC (Mon Dec 16 2019 - 00:56:53 PST)
[AMBER] Virtual box with imin = 1 or imin = 5 Jerome Eberhardt (Sun Dec 15 2019 - 21:24:26 PST)
- Re: [AMBER] Virtual box with imin = 1 or imin = 5 Bill Ross (Sun Dec 15 2019 - 21:59:49 PST)
- Re: [AMBER] Virtual box with imin = 1 or imin = 5 Carlos Simmerling (Mon Dec 16 2019 - 05:16:32 PST)
  - Re: [AMBER] Virtual box with imin = 1 or imin = 5 Jerome Eberhardt (Mon Dec 16 2019 - 10:34:52 PST)
    - Re: [AMBER] Virtual box with imin = 1 or imin = 5 David Case (Mon Dec 16 2019 - 12:40:13 PST)
    - Re: [AMBER] Virtual box with imin = 1 or imin = 5 Jerome Eberhardt (Mon Dec 16 2019 - 16:38:15 PST)
- Re: [AMBER] Virtual box with imin = 1 or imin = 5 David Case (Mon Dec 16 2019 - 12:15:34 PST)
  - Re: [AMBER] Virtual box with imin = 1 or imin = 5 Jerome Eberhardt (Mon Dec 16 2019 - 16:38:09 PST)
[AMBER] NVT equilibriation followed by NPT in TI Debarati DasGupta (Mon Dec 16 2019 - 06:30:48 PST)
- Re: [AMBER] NVT equilibriation followed by NPT in TI David Case (Tue Dec 17 2019 - 05:38:58 PST)
  - Re: [AMBER] NVT equilibriation followed by NPT in TI Debarati DasGupta (Tue Dec 17 2019 - 06:54:15 PST)
[AMBER] question about Tleap Rui Chen (Mon Dec 16 2019 - 10:19:27 PST)
[AMBER] Any idea on this error and how to troubleshoot Debarati DasGupta (Mon Dec 16 2019 - 10:43:46 PST)
- Re: [AMBER] Any idea on this error and how to troubleshoot Cruzeiro,Vinicius Wilian D (Mon Dec 16 2019 - 13:09:49 PST)
[AMBER] MMGBSA script file Rui Chen (Mon Dec 16 2019 - 16:27:40 PST)
- Re: [AMBER] MMGBSA script file Rui Chen (Mon Dec 16 2019 - 19:57:47 PST)
[AMBER] nuc.nab:no such file found error Sruthi Sudhakar (Mon Dec 16 2019 - 20:44:15 PST)
- Re: [AMBER] nuc.nab:no such file found error Bill Ross (Mon Dec 16 2019 - 22:52:19 PST)
- Re: [AMBER] nuc.nab:no such file found error David Case (Tue Dec 17 2019 - 05:30:32 PST)
  - Re: [AMBER] nuc.nab:no such file found error Sruthi Sudhakar (Tue Dec 17 2019 - 20:23:51 PST)
[AMBER] tip4p-d water forcefield parameters Luca Codutti (Tue Dec 17 2019 - 08:03:25 PST)
- Re: [AMBER] tip4p-d water forcefield parameters Luca Codutti (Tue Dec 17 2019 - 08:06:23 PST)
- Re: [AMBER] tip4p-d water forcefield parameters David Case (Wed Dec 18 2019 - 06:41:11 PST)
[AMBER] If there is a method that can just use the soft-core potential for VDW interaction but not for electrostatic part wangjianing_mail (Tue Dec 17 2019 - 22:17:07 PST)
- Re: [AMBER] If there is a method that can just use the soft-core potential for VDW interaction but not for electrostatic part David Case (Wed Dec 18 2019 - 06:44:15 PST)
[AMBER] Attaching Methoxy (OMe) Capping at C-terminal Pallab Dutta (Thu Dec 19 2019 - 04:15:47 PST)
- Re: [AMBER] Attaching Methoxy (OMe) Capping at C-terminal David Case (Thu Dec 19 2019 - 05:01:15 PST)
  - Re: [AMBER] Attaching Methoxy (OMe) Capping at C-terminal Pallab Dutta (Thu Dec 19 2019 - 06:40:47 PST)
[AMBER] cpptraj.MPI versus cpptraj Debarati DasGupta (Thu Dec 19 2019 - 11:51:47 PST)
- Re: [AMBER] cpptraj.MPI versus cpptraj David Case (Thu Dec 19 2019 - 19:00:25 PST)
  - Re: [AMBER] cpptraj.MPI versus cpptraj Debarati DasGupta (Fri Dec 20 2019 - 05:18:43 PST)
- Re: [AMBER] cpptraj.MPI versus cpptraj Daniel Roe (Fri Dec 20 2019 - 05:22:39 PST)
  - Re: [AMBER] cpptraj.MPI versus cpptraj Daniel Roe (Fri Dec 20 2019 - 05:23:54 PST)
  - Re: [AMBER] cpptraj.MPI versus cpptraj Debarati DasGupta (Fri Dec 20 2019 - 05:24:54 PST)
  - Re: [AMBER] cpptraj.MPI versus cpptraj Debarati DasGupta (Fri Dec 20 2019 - 05:26:26 PST)
[AMBER] amber 18 installation error Saikat Pal (Thu Dec 19 2019 - 22:46:05 PST)
- Re: [AMBER] amber 18 installation error Gustaf Olsson (Thu Dec 19 2019 - 22:59:18 PST)
[AMBER] amber update issue Saikat Pal (Thu Dec 19 2019 - 23:39:52 PST)
- Re: [AMBER] amber update issue David Case (Fri Dec 20 2019 - 09:18:56 PST)
[AMBER] Amber18 installation problem Billiot, Eugene (Fri Dec 20 2019 - 13:22:02 PST)
- Re: [AMBER] Amber18 installation problem David Case (Fri Dec 20 2019 - 14:05:03 PST)
Re: [AMBER] Amber18 download instructions Billiot, Eugene (Fri Dec 20 2019 - 14:10:18 PST)
- Re: [AMBER] Amber18 download instructions Billiot, Eugene (Fri Dec 20 2019 - 14:16:01 PST)
[AMBER] How to use AMBER on Supercomputer MUHAMMAD KHATTAB FATHI KHATTAB (Fri Dec 20 2019 - 22:49:44 PST)
- Re: [AMBER] How to use AMBER on Supercomputer Liao (Sat Dec 21 2019 - 07:28:20 PST)
  - Re: [AMBER] How to use AMBER on Supercomputer MUHAMMAD KHATTAB FATHI KHATTAB (Sat Dec 21 2019 - 07:51:15 PST)
    - Re: [AMBER] How to use AMBER on Supercomputer Liao (Sat Dec 21 2019 - 08:07:36 PST)
    - Re: [AMBER] How to use AMBER on Supercomputer MUHAMMAD KHATTAB FATHI KHATTAB (Sat Dec 21 2019 - 09:11:32 PST)
[AMBER] Definition of restraints to avoid ligand aggregation Giulio RASTELLI (Sun Dec 22 2019 - 08:06:16 PST)
- [AMBER] help needed for failed installation of CUDA for GPU-accelerated versions of pmemd for AMBER 18 Billiot, Eugene (Sun Dec 22 2019 - 14:30:26 PST)
  - Re: [AMBER] help needed for failed installation of CUDA for GPU-accelerated versions of pmemd for AMBER 18 David Case (Mon Dec 23 2019 - 18:40:33 PST)
    - Re: [AMBER] help needed for failed installation of CUDA for GPU-accelerated versions of pmemd for AMBER 18 Billiot, Eugene (Tue Dec 24 2019 - 10:19:16 PST)
[AMBER] AMBER 18 cuda installation Saikat Pal (Mon Dec 23 2019 - 05:33:19 PST)
- Re: [AMBER] AMBER 18 cuda installation David Case (Tue Jan 07 2020 - 18:47:26 PST)
- Re: [AMBER] AMBER 18 cuda installation ChenXingqiang (Sat Apr 11 2020 - 08:11:42 PDT)
  - Re: [AMBER] AMBER 18 cuda installation Ray Luo (Sat Apr 11 2020 - 09:59:12 PDT)
    - Re: [AMBER] AMBER 18 cuda installation ChenXingqiang (Sat Apr 11 2020 - 22:55:56 PDT)
[AMBER] MMGB/PBSA parameters Rui Chen (Mon Dec 23 2019 - 09:12:44 PST)
- Re: [AMBER] MMGB/PBSA parameters Carlos Simmerling (Mon Dec 23 2019 - 10:33:36 PST)
  - Re: [AMBER] MMGB/PBSA parameters Rui Chen (Mon Dec 23 2019 - 10:57:21 PST)
[AMBER] Minimization equilibration of protein+ligand prior to TI setup Debarati DasGupta (Mon Dec 23 2019 - 12:33:03 PST)
- Re: [AMBER] Minimization equilibration of protein+ligand prior to TI setup David Case (Mon Dec 23 2019 - 18:36:42 PST)
  - Re: [AMBER] Minimization equilibration of protein+ligand prior to TI setup Debarati DasGupta (Tue Dec 24 2019 - 06:44:24 PST)
    - Re: [AMBER] Minimization equilibration of protein+ligand prior to TI setup Carlos Simmerling (Wed Dec 25 2019 - 03:51:15 PST)
    - Re: [AMBER] Minimization equilibration of protein+ligand prior to TI setup Debarati DasGupta (Fri Dec 27 2019 - 08:07:29 PST)
[AMBER] Amber18-bash: logFile: command not found... 辛志宏 (Mon Dec 23 2019 - 19:03:49 PST)
- Re: [AMBER] Amber18-bash: logFile: command not found... David Case (Tue Dec 24 2019 - 06:43:07 PST)
[AMBER] Error during installation ARITRA MITRA (Tue Dec 24 2019 - 01:23:12 PST)
- Re: [AMBER] Error during installation David Case (Tue Dec 24 2019 - 06:52:26 PST)
[AMBER] Interaction entropy program （Geng Dong）东庚 (Wed Dec 25 2019 - 17:52:55 PST)
[AMBER] Tleap naming problem Rui Chen (Wed Dec 25 2019 - 19:53:49 PST)
- Re: [AMBER] Tleap naming problem David Case (Thu Dec 26 2019 - 06:35:43 PST)
  - Re: [AMBER] Tleap naming problem Rui Chen (Wed Jan 01 2020 - 13:19:00 PST)
    - Re: [AMBER] Tleap naming problem David Case (Thu Jan 02 2020 - 05:30:41 PST)
[AMBER] Which language could tleap know? mwli.mail.ustc.edu.cn (Thu Dec 26 2019 - 00:06:22 PST)
- Re: [AMBER] Which language could tleap know? David Case (Thu Dec 26 2019 - 06:39:08 PST)
[AMBER] Parameters to be used for protein in implicit solvent SHAUNAK BADANI (Fri Dec 27 2019 - 03:54:08 PST)
- Re: [AMBER] Parameters to be used for protein in implicit solvent Carlos Simmerling (Fri Dec 27 2019 - 05:35:41 PST)
[AMBER] some queries Ayesha Fatima (Sun Dec 29 2019 - 08:41:39 PST)
- Re: [AMBER] some queries David Case (Mon Dec 30 2019 - 06:13:58 PST)
  - Re: [AMBER] some queries Ayesha Fatima (Mon Dec 30 2019 - 06:24:29 PST)
[AMBER] reinstalling Amber 16 + Ambertools 16 on a Mac erik zuiderweg (Mon Dec 30 2019 - 03:38:59 PST)
[AMBER] Figured Amber 16 installation on Mac Erik Zuiderweg (Mon Dec 30 2019 - 04:44:19 PST)
[AMBER] ligand clustering Neha Gandhi (Wed Jan 01 2020 - 21:47:51 PST)
[AMBER] Regarding clustering using mmtsb toolkit Sruthi Sudhakar (Wed Jan 01 2020 - 22:37:22 PST)
- Re: [AMBER] Regarding clustering using mmtsb toolkit Carlos Simmerling (Thu Jan 02 2020 - 04:58:17 PST)
- Re: [AMBER] Regarding clustering using mmtsb toolkit David Case (Thu Jan 02 2020 - 05:35:57 PST)
[AMBER] NMR distance restrained MD maya nair (Wed Jan 01 2020 - 23:56:32 PST)
- Re: [AMBER] NMR distance restrained MD David Case (Thu Jan 02 2020 - 05:41:00 PST)
  - Re: [AMBER] NMR distance restrained MD maya nair (Mon Jan 06 2020 - 04:21:57 PST)
- Re: [AMBER] NMR distance restrained MD Christina Bergonzo (Thu Jan 02 2020 - 05:45:30 PST)
  - Re: [AMBER] NMR distance restrained MD maya nair (Mon Jan 06 2020 - 04:17:14 PST)
- Re: [AMBER] NMR distance restrained MD maya nair (Tue Jan 28 2020 - 23:44:59 PST)
[AMBER] query ankita mehta (Thu Jan 02 2020 - 08:45:08 PST)
- Re: [AMBER] query Pansy Patel (Fri Jul 31 2009 - 07:41:05 PDT)
  - Re: [AMBER] query Ashish Runthala (Fri Jul 31 2009 - 18:23:07 PDT)
- Re: [AMBER] query David Case (Thu Jan 02 2020 - 12:13:55 PST)
  - Re: [AMBER] query ankita mehta (Fri Jan 03 2020 - 02:50:20 PST)
[AMBER] MMPBSA error Rui Chen (Thu Jan 02 2020 - 16:27:54 PST)
- Re: [AMBER] MMPBSA error Abhishek TYAGI (Wed Apr 08 2015 - 20:50:51 PDT)
  - Re: [AMBER] MMPBSA error Jason Swails (Thu Apr 09 2015 - 04:32:40 PDT)
  - Re: [AMBER] MMPBSA error Daniel Roe (Thu Apr 09 2015 - 07:16:41 PDT)
- Re: [AMBER] MMPBSA error Abhishek TYAGI (Tue Apr 14 2015 - 17:43:19 PDT)
- Re: [AMBER] MMPBSA error konda003 . (Mon Feb 06 2017 - 12:43:36 PST)
- Re: [AMBER] MMPBSA error Ray Luo (Thu Jan 02 2020 - 16:37:15 PST)
  - Re: [AMBER] MMPBSA error Rui Chen (Thu Jan 02 2020 - 21:37:14 PST)
    - Re: [AMBER] MMPBSA error Ray Luo (Thu Jan 02 2020 - 22:15:58 PST)
    - Re: [AMBER] MMPBSA error Rui Chen (Fri Jan 03 2020 - 08:58:42 PST)
    - Re: [AMBER] MMPBSA error Ray Luo (Fri Jan 03 2020 - 12:05:06 PST)
    - Re: [AMBER] MMPBSA error Rui Chen (Fri Jan 03 2020 - 12:59:10 PST)
    - Re: [AMBER] MMPBSA error Ray Luo (Sat Jan 04 2020 - 17:41:50 PST)
[AMBER] Semi-empirical QMMD on all molecules Abdullah Faheem (Thu Jan 02 2020 - 23:43:39 PST)
- Re: [AMBER] Semi-empirical QMMD on all molecules Goetz, Andreas (Fri Jan 03 2020 - 03:36:43 PST)
[AMBER] Query ankita mehta (Fri Jan 03 2020 - 02:42:39 PST)
[AMBER] Drug parameter generation Madhur Aggarwal (Fri Jan 03 2020 - 10:09:16 PST)
- Re: [AMBER] Drug parameter generation Carlos Simmerling (Fri Jan 03 2020 - 10:22:19 PST)
[AMBER] Glycosylation issue: Atom xx was assigned a lower molecule # than previous atom. zizhang sheng (Fri Jan 03 2020 - 13:44:04 PST)
- Re: [AMBER] Glycosylation issue: Atom xx was assigned a lower molecule # than previous atom. Lachele Foley (Fri Jan 03 2020 - 14:44:14 PST)
  - Re: [AMBER] Glycosylation issue: Atom xx was assigned a lower molecule # than previous atom. zz sheng (Fri Jan 03 2020 - 15:43:14 PST)
    - Re: [AMBER] Glycosylation issue: Atom xx was assigned a lower molecule # than previous atom. Lachele Foley (Fri Jan 03 2020 - 15:49:35 PST)
[AMBER] esp charge Rui Chen (Fri Jan 03 2020 - 16:49:52 PST)
[AMBER] Problems using groups to provide centre for solvent caps in tLeap David Wright (Sat Jan 04 2020 - 05:10:03 PST)
- [AMBER] Fwd: Problems using groups to provide centre for solvent caps in tLeap David Wright (Mon Jan 06 2020 - 03:37:59 PST)
  - Re: [AMBER] Fwd: Problems using groups to provide centre for solvent caps in tLeap David Case (Mon Jan 06 2020 - 06:34:20 PST)
    - Re: [AMBER] Fwd: Problems using groups to provide centre for solvent caps in tLeap David Wright (Tue Jan 07 2020 - 03:41:40 PST)
[AMBER] parmed issue Ayesha Fatima (Sat Jan 04 2020 - 05:50:11 PST)
- Re: [AMBER] parmed issue David Case (Sat Jan 04 2020 - 14:16:27 PST)
[AMBER] hiii ankita mehta (Sat Jan 04 2020 - 05:54:40 PST)
- Re: [AMBER] hiii David Case (Sat Jan 04 2020 - 14:18:12 PST)
[AMBER] hiiiiii ankita mehta (Sat Jan 04 2020 - 07:17:42 PST)
[AMBER] hiiiii ankita mehta (Sat Jan 04 2020 - 23:01:39 PST)
- Re: [AMBER] hiiiii David Case (Sun Jan 05 2020 - 05:47:26 PST)
[AMBER] pmemd.cuda:command not found Sruthi Sudhakar (Sat Jan 04 2020 - 23:28:32 PST)
- Re: [AMBER] pmemd.cuda:command not found Liao (Sat Jan 04 2020 - 23:56:35 PST)
[AMBER] MMPBSA standard deviation (Geng Dong) 东庚 (Sun Jan 05 2020 - 03:30:01 PST)
- Re: [AMBER] MMPBSA standard deviation (Geng Dong) Ray Luo (Sun Jan 05 2020 - 07:46:29 PST)
[AMBER] hiiiii ankita mehta (Sun Jan 05 2020 - 06:18:43 PST)
- Re: [AMBER] hiiiii Carlos Simmerling (Sun Jan 05 2020 - 06:32:56 PST)
  - Re: [AMBER] hiiiii ankita mehta (Sun Jan 05 2020 - 07:20:44 PST)
    - Re: [AMBER] hiiiii Carlos Simmerling (Sun Jan 05 2020 - 07:28:38 PST)
    - Re: [AMBER] hiiiii ankita mehta (Sun Jan 05 2020 - 07:37:54 PST)
    - Re: [AMBER] hiiiii David Case (Sun Jan 05 2020 - 10:32:44 PST)
    - Re: [AMBER] hiiiii ankita mehta (Sun Jan 05 2020 - 20:02:52 PST)
    - Re: [AMBER] hiiiii Cory Ayres (Mon Jan 06 2020 - 03:19:12 PST)
    - Re: [AMBER] hiiiii ankita mehta (Sun Jan 05 2020 - 23:43:51 PST)
[AMBER] gaff with and without gaff atom types Erdem Yeler (Sun Jan 05 2020 - 08:32:08 PST)
- Re: [AMBER] gaff with and without gaff atom types David Case (Sun Jan 05 2020 - 10:42:28 PST)
  - Re: [AMBER] gaff with and without gaff atom types Erdem Yeler (Tue Jan 07 2020 - 00:27:24 PST)
[AMBER] Molecule is wrapped out of the cell. Petro (Mon Jan 06 2020 - 02:44:51 PST)
- Re: [AMBER] Molecule is wrapped out of the cell. David Case (Mon Jan 06 2020 - 07:07:43 PST)
  - Re: [AMBER] Molecule is wrapped out of the cell. Petro (Tue Jan 07 2020 - 09:32:41 PST)
[AMBER] Umbrella sampling sufficient overlap test Martin Rosellen (Mon Jan 06 2020 - 04:20:06 PST)
[AMBER] printing charges in pdb Vaibhav Dixit (Mon Jan 06 2020 - 01:44:53 PST)
- Re: [AMBER] printing charges in pdb David Case (Mon Jan 06 2020 - 07:04:07 PST)
  - Re: [AMBER] printing charges in pdb Vaibhav Dixit (Mon Jan 06 2020 - 09:04:05 PST)
[AMBER] Any help on the error Debarati DasGupta (Mon Jan 06 2020 - 12:22:52 PST)
- [AMBER] Amber 18 installation error Billiot, Eugene (Mon Jan 06 2020 - 14:29:11 PST)
  - Re: [AMBER] Amber 18 installation error David Case (Tue Jan 07 2020 - 06:09:08 PST)
    - Re: [AMBER] Amber 18 installation error Billiot, Eugene (Tue Jan 07 2020 - 09:19:04 PST)
- Re: [AMBER] Any help on the error David Case (Tue Jan 07 2020 - 05:59:45 PST)
[AMBER] [ Lone pair electron & Polymer ] 조준범 (Mon Jan 06 2020 - 22:06:13 PST)
[AMBER] [ Polymer with Extra Points ] 조준범 (Mon Jan 06 2020 - 22:40:38 PST)
- Re: [AMBER] [ Polymer with Extra Points ] David Cerutti (Mon Jan 06 2020 - 23:56:54 PST)
  - Re: [AMBER] [ Polymer with Extra Points ] 조준범 (Tue Jan 07 2020 - 01:04:40 PST)
    - Re: [AMBER] [ Polymer with Extra Points ] David Cerutti (Thu Jan 09 2020 - 00:02:47 PST)
    - Re: [AMBER] [ Polymer with Extra Points ] 조준범 (Thu Jan 09 2020 - 21:29:10 PST)
[AMBER] DOPC lipid bilayer deformation in Implicit MD simulation using Lipid14 force field in Amber18 Bhat Zahoor (Mon Jan 06 2020 - 23:16:55 PST)
- Re: [AMBER] DOPC lipid bilayer deformation in Implicit MD simulation using Lipid14 force field in Amber18 Gould, Ian R (Tue Jan 07 2020 - 00:37:25 PST)
[AMBER] Glycoprotein MD error in Amber18: an illegal memory access was encountered launching kernel kNLSkinTest zizhang sheng (Tue Jan 07 2020 - 07:47:45 PST)
[AMBER] TI data collection of DU/Dlambda at constant volume Debarati DasGupta (Tue Jan 07 2020 - 09:00:20 PST)
[AMBER] P2 correlation functions questions erik zuiderweg (Tue Jan 07 2020 - 09:08:28 PST)
- Re: [AMBER] P2 correlation functions questions David Case (Tue Jan 07 2020 - 18:29:27 PST)
[AMBER] saxs Adrian Roitberg (Tue Jan 07 2020 - 12:41:25 PST)
[AMBER] Question about addtobox Petro (Tue Jan 07 2020 - 22:28:09 PST)
- Re: [AMBER] Question about addtobox David Case (Wed Jan 08 2020 - 07:22:21 PST)
  - Re: [AMBER] Question about addtobox Petro (Wed Jan 08 2020 - 15:19:41 PST)
- Re: [AMBER] Question about addtobox David Cerutti (Thu Jan 09 2020 - 06:52:13 PST)
  - Re: [AMBER] Question about addtobox David Case (Thu Jan 09 2020 - 10:03:14 PST)
[AMBER] Adjacent cell molecules appear in the trajectory after autoimaging in cpptraj [ DOPC lipid bilayer simulation with lipid14 force field] Bhat Zahoor (Wed Jan 08 2020 - 01:46:26 PST)
[AMBER] Generalized Born and entropy Martin Rosellen (Wed Jan 08 2020 - 06:03:51 PST)
- Re: [AMBER] Generalized Born and entropy David Case (Wed Jan 08 2020 - 07:30:25 PST)
- Re: [AMBER] Generalized Born and entropy Rosellen, Martin (Mon Jan 13 2020 - 04:48:19 PST)
  - Re: [AMBER] Generalized Born and entropy Carlos Simmerling (Mon Jan 13 2020 - 05:04:43 PST)
[AMBER] saxs_md Buteler,Maria del Pilar (Wed Jan 08 2020 - 08:49:02 PST)
- Re: [AMBER] saxs_md Christina Bergonzo (Wed Jan 08 2020 - 09:25:11 PST)
[AMBER] NPT density equilibration Debarati DasGupta (Wed Jan 08 2020 - 12:43:00 PST)
- [AMBER] FW: NPT density equilibration Debarati DasGupta (Wed Jan 08 2020 - 12:44:41 PST)
[AMBER] [ Polymer ] Parameter Modification 조준범 (Wed Jan 08 2020 - 21:17:32 PST)
- Re: [AMBER] [ Polymer ] Parameter Modification David Cerutti (Wed Jan 08 2020 - 21:56:12 PST)
[AMBER] Resolving overlapping atoms. Petro (Thu Jan 09 2020 - 01:54:12 PST)
- Re: [AMBER] Resolving overlapping atoms. David Case (Thu Jan 09 2020 - 06:23:04 PST)
  - Re: [AMBER] Resolving overlapping atoms. Petro (Thu Jan 09 2020 - 10:19:36 PST)
- Re: [AMBER] Resolving overlapping atoms. Petro (Tue Feb 04 2020 - 04:50:23 PST)
[AMBER] charting Ligand's movement in the binding pocket Prasanth G, Research Scholar (Thu Jan 09 2020 - 02:58:01 PST)
- Re: [AMBER] charting Ligand's movement in the binding pocket Markowska (Thu Jan 09 2020 - 12:02:08 PST)
[AMBER] [ inpcrd file ] 조준범 (Thu Jan 09 2020 - 03:09:29 PST)
- Re: [AMBER] [ inpcrd file ] Gustaf Olsson (Thu Jan 09 2020 - 03:40:35 PST)
[AMBER] Lipid bilayer imaging problem Bhat Zahoor (Thu Jan 09 2020 - 03:58:07 PST)
- Re: [AMBER] Lipid bilayer imaging problem Chetna Tyagi (Thu Jan 09 2020 - 03:48:47 PST)
  - Re: [AMBER] Lipid bilayer imaging problem Bhat Zahoor (Thu Jan 09 2020 - 04:59:41 PST)
- Re: [AMBER] Lipid bilayer imaging problem Daniel Roe (Tue Aug 04 2020 - 07:29:01 PDT)
[AMBER] MD error in Amber18: an illegal memory access was encountered launching kernel kNLSkinTest zizhang sheng (Thu Jan 09 2020 - 06:18:32 PST)
- Re: [AMBER] MD error in Amber18: an illegal memory access was encountered launching kernel kNLSkinTest David Case (Thu Jan 09 2020 - 10:01:48 PST)
- Re: [AMBER] MD error in Amber18: an illegal memory access was encountered launching kernel kNLSkinTest zizhang sheng (Fri Jan 10 2020 - 09:29:32 PST)
  - Re: [AMBER] MD error in Amber18: an illegal memory access was encountered launching kernel kNLSkinTest David Case (Fri Jan 10 2020 - 12:54:26 PST)
    - Re: [AMBER] MD error in Amber18: an illegal memory access was encountered launching kernel kNLSkinTest zizhang sheng (Fri Jan 10 2020 - 13:43:01 PST)
[AMBER] weights for the lambda values Debarati DasGupta (Thu Jan 09 2020 - 11:30:49 PST)
- Re: [AMBER] weights for the lambda values Carlos Simmerling (Fri Jan 10 2020 - 03:30:35 PST)
[AMBER] Cpptraj - Density Action Command Units An Ta (Thu Jan 09 2020 - 13:11:53 PST)
[AMBER] [ prmtop ] SOLVENT_POINTERS 조준범 (Thu Jan 09 2020 - 21:15:18 PST)
- Re: [AMBER] [ prmtop ] SOLVENT_POINTERS Carlos Simmerling (Fri Jan 10 2020 - 03:31:25 PST)
[AMBER] [ Error with MD ] Energetics of the system 조준범 (Thu Jan 09 2020 - 23:35:38 PST)
- Re: [AMBER] [ Error with MD ] Energetics of the system David Case (Fri Jan 10 2020 - 05:43:39 PST)
  - [AMBER] Is minimization and equilibration needed in umbrella sampling? Qing Lv (Fri Jan 10 2020 - 07:46:29 PST)
    - [AMBER] Is NPT ensemble necessary for the protein-water system? Qing Lv (Fri Jan 10 2020 - 07:55:57 PST)
    - [AMBER] Is error bar necessary for umbrella sampling? Qing Lv (Mon Jan 13 2020 - 06:36:15 PST)
    - Re: [AMBER] Is error bar necessary for umbrella sampling? Carlos Simmerling (Mon Jan 13 2020 - 06:42:49 PST)
    - Re: [AMBER] Is error bar necessary for umbrella sampling? Qing Lv (Mon Jan 13 2020 - 18:48:06 PST)
    - Re: [AMBER] Is error bar necessary for umbrella sampling? Carlos Simmerling (Tue Jan 14 2020 - 03:30:35 PST)
[AMBER] ff99SBnmr2 Force field implemented in AMBER18 Lod King (Fri Jan 10 2020 - 17:41:14 PST)
- Re: [AMBER] ff99SBnmr2 Force field implemented in AMBER18 Carlos Simmerling (Fri Jan 10 2020 - 17:58:30 PST)
[AMBER] Tracking ligand position throughout equilibration stages Debarati DasGupta (Sat Jan 11 2020 - 07:21:37 PST)
- Re: [AMBER] Tracking ligand position throughout equilibration stages Dr. Anselm Horn (Mon Jan 13 2020 - 01:34:40 PST)
  - Re: [AMBER] Tracking ligand position throughout equilibration stages Carlos Simmerling (Mon Jan 13 2020 - 02:29:32 PST)
[AMBER] Custom language module(s) for AMBER file types for common text editors? Makay Murray (Sat Jan 11 2020 - 18:17:06 PST)
- Re: [AMBER] Custom language module(s) for AMBER file types for common text editors? Matias Machado (Wed Jan 15 2020 - 12:23:52 PST)
[AMBER] installing amber on wsl Ayesha Fatima (Sun Jan 12 2020 - 05:29:26 PST)
- Re: [AMBER] installing amber on wsl David Case (Sun Jan 12 2020 - 11:56:35 PST)
  - Re: [AMBER] installing amber on wsl Ayesha Fatima (Sun Jan 12 2020 - 22:54:28 PST)
  - Re: [AMBER] installing amber on wsl Ayesha Fatima (Mon Jan 13 2020 - 06:59:49 PST)
- Re: [AMBER] installing amber on wsl ALAMGIR KHAN (Sun Jan 12 2020 - 20:04:17 PST)
[AMBER] [ MD Failure ] 조준범 (Sun Jan 12 2020 - 08:19:33 PST)
- Re: [AMBER] [ MD Failure ] David Case (Mon Jan 13 2020 - 06:27:42 PST)
[AMBER] compatible graphics card Antonio Bauzá (Sun Jan 12 2020 - 09:01:29 PST)
[AMBER] Fwd: Periodic box problem when simulating Membrane system Tiejun Wei (Mon Jan 13 2020 - 06:26:41 PST)
- Re: [AMBER] Periodic box problem when simulating Membrane system Gustaf Olsson (Mon Jan 13 2020 - 06:44:36 PST)
  - Re: [AMBER] Periodic box problem when simulating Membrane system Bhat Zahoor (Mon Jan 13 2020 - 07:09:40 PST)
[AMBER] CPPTRAJ-Hbonds Rui Chen (Mon Jan 13 2020 - 07:49:11 PST)
- Re: [AMBER] CPPTRAJ-Hbonds Daniel Roe (Mon Jan 13 2020 - 09:08:01 PST)
[AMBER] parameters for Si3N4 Akshay Prabhakant (Mon Jan 13 2020 - 08:38:24 PST)
- Re: [AMBER] parameters for Si3N4 Pengfei Li (Mon Feb 03 2020 - 18:13:34 PST)
  - Re: [AMBER] parameters for Si3N4 Akshay Prabhakant (Mon Mar 16 2020 - 21:11:06 PDT)
[AMBER] Error with using dpeaks clustering in CPPTRAJ yinglong.miao.gmail.com (Mon Jan 13 2020 - 15:50:49 PST)
- Re: [AMBER] Error with using dpeaks clustering in CPPTRAJ Daniel Roe (Mon Jan 13 2020 - 16:20:42 PST)
  - Re: [AMBER] Error with using dpeaks clustering in CPPTRAJ Yinglong Miao (Mon Jan 13 2020 - 17:10:04 PST)
    - Re: [AMBER] Error with using dpeaks clustering in CPPTRAJ Daniel Roe (Tue Jan 14 2020 - 07:46:30 PST)
    - Re: [AMBER] Error with using dpeaks clustering in CPPTRAJ Yinglong Miao (Tue Jan 14 2020 - 08:05:11 PST)
    - Re: [AMBER] Error with using dpeaks clustering in CPPTRAJ yinglong.miao.gmail.com (Tue Jan 14 2020 - 09:34:22 PST)
    - Re: [AMBER] Error with using dpeaks clustering in CPPTRAJ Daniel Roe (Fri Jan 17 2020 - 06:34:12 PST)
    - Re: [AMBER] Error with using dpeaks clustering in CPPTRAJ Daniel Roe (Fri Jan 17 2020 - 06:37:12 PST)
    - Re: [AMBER] Error with using dpeaks clustering in CPPTRAJ Daniel Roe (Fri Jan 17 2020 - 06:41:09 PST)
    - Re: [AMBER] Error with using dpeaks clustering in CPPTRAJ Yinglong Miao (Fri Jan 17 2020 - 07:09:34 PST)
    - Re: [AMBER] Error with using dpeaks clustering in CPPTRAJ Daniel Roe (Fri Jan 17 2020 - 07:35:57 PST)
    - Re: [AMBER] Error with using dpeaks clustering in CPPTRAJ Yinglong Miao (Fri Jan 17 2020 - 07:45:10 PST)
[AMBER] ligand split MYRIAN TORRES RICO (Tue Jan 14 2020 - 09:07:35 PST)
- Re: [AMBER] ligand split David Case (Tue Jan 14 2020 - 11:25:48 PST)
  - Re: [AMBER] ligand split MYRIAN TORRES RICO (Wed Jan 15 2020 - 02:26:22 PST)
    - Re: [AMBER] ligand split Carlos Simmerling (Wed Jan 15 2020 - 02:31:48 PST)
    - Re: [AMBER] ligand split MYRIAN TORRES RICO (Wed Jan 15 2020 - 02:44:40 PST)
    - Re: [AMBER] ligand split Carlos Simmerling (Wed Jan 15 2020 - 03:07:00 PST)
    - Re: [AMBER] ligand split MYRIAN TORRES RICO (Wed Jan 15 2020 - 04:52:20 PST)
    - Re: [AMBER] ligand split Carlos Simmerling (Wed Jan 15 2020 - 10:22:33 PST)
    - Re: [AMBER] ligand split MYRIAN TORRES RICO (Fri Jan 17 2020 - 07:15:52 PST)
    - Re: [AMBER] ligand split Carlos Simmerling (Fri Jan 17 2020 - 07:24:07 PST)
    - Re: [AMBER] ligand split MYRIAN TORRES RICO (Fri Jan 17 2020 - 07:32:27 PST)
[AMBER] modeling a Schiff base with GAFF atom types Sally Pias (Tue Jan 14 2020 - 15:16:57 PST)
- Re: [AMBER] modeling a Schiff base with GAFF atom types David Case (Wed Jan 15 2020 - 05:54:42 PST)
[AMBER] RESP fitting Sruthi Sudhakar (Wed Jan 15 2020 - 04:58:56 PST)
- Re: [AMBER] RESP fitting Elvis Martis (Wed Jan 15 2020 - 04:53:12 PST)
[AMBER] How to use polarizable water model in Amber 18? Markowska (Wed Jan 15 2020 - 05:39:39 PST)
- Re: [AMBER] How to use polarizable water model in Amber 18? Matias Machado (Wed Jan 15 2020 - 08:46:11 PST)
  - Re: [AMBER] How to use polarizable water model in Amber 18? Carlos Simmerling (Wed Jan 15 2020 - 10:23:48 PST)
    - Re: [AMBER] How to use polarizable water model in Amber 18? Markowska (Fri Jan 17 2020 - 00:22:11 PST)
    - Re: [AMBER] How to use polarizable water model in Amber 18? Markowska (Sat Jan 18 2020 - 10:01:14 PST)
    - Re: [AMBER] How to use polarizable water model in Amber 18? David Case (Sun Jan 19 2020 - 17:46:57 PST)
[AMBER] Harmless bug in Lipid11-17 residue libraries causing tleap to split fragments in saved PDB Matias Machado (Wed Jan 15 2020 - 08:32:38 PST)
[AMBER] Membrane simulation with PSM cpimenta (Wed Jan 15 2020 - 11:09:24 PST)
[AMBER] ValueError: could not convert string to float: ********* Error occured on rank 0. Exiting. All files have been retained. Neha Gandhi (Wed Jan 15 2020 - 20:35:09 PST)
- Re: [AMBER] ValueError: could not convert string to float: ********* Error occured on rank 0. Exiting. All files have been retained. David Case (Thu Jan 16 2020 - 05:36:00 PST)
[AMBER] Reg. Centering of Molecule and Periodic Boundary Conditions DHEERAJ CHITARA (Thu Jan 16 2020 - 00:46:32 PST)
- Re: [AMBER] Reg. Centering of Molecule and Periodic Boundary Conditions Daniel Roe (Thu Jan 16 2020 - 12:26:02 PST)
[AMBER] Issues with Umbrella Sampling Simulations involving lipid bilayer Casalini Tommaso (Thu Jan 16 2020 - 01:30:58 PST)
- Re: [AMBER] Issues with Umbrella Sampling Simulations involving lipid bilayer Stephan Schott (Thu Jan 16 2020 - 04:13:59 PST)
  - Re: [AMBER] Issues with Umbrella Sampling Simulations involving lipid bilayer Casalini Tommaso (Thu Jan 16 2020 - 04:37:26 PST)
- Re: [AMBER] Issues with Umbrella Sampling Simulations involving lipid bilayer Stephan Schott (Thu Jan 16 2020 - 14:37:43 PST)
  - Re: [AMBER] Issues with Umbrella Sampling Simulations involving lipid bilayer Casalini Tommaso (Fri Jan 17 2020 - 01:24:23 PST)
- Re: [AMBER] Issues with Umbrella Sampling Simulations involving lipid bilayer Stephan Schott (Mon Jan 20 2020 - 07:01:36 PST)
  - Re: [AMBER] Issues with Umbrella Sampling Simulations involving lipid bilayer Charles Lin (Tue Jan 21 2020 - 06:30:36 PST)
[AMBER] vanilla Nose-Hoover thermostat availability Sally Pias (Thu Jan 16 2020 - 14:19:39 PST)
- Re: [AMBER] vanilla Nose-Hoover thermostat availability David Case (Fri Jan 17 2020 - 06:43:07 PST)
  - Re: [AMBER] vanilla Nose-Hoover thermostat availability Sally Pias (Wed Jan 22 2020 - 17:41:00 PST)
[AMBER] pdb to mol2 conversion via antechamber Sruthi Sudhakar (Thu Jan 16 2020 - 22:54:51 PST)
- Re: [AMBER] pdb to mol2 conversion via antechamber Liao (Fri Jan 17 2020 - 00:20:02 PST)
[AMBER] Workshop on Free Energy calculations in Muenster March 11-13 2020 Vlad Cojocaru (Fri Jan 17 2020 - 01:32:27 PST)
[AMBER] RDF: corrupted trajectory emanuele falbo (Fri Jan 17 2020 - 08:02:09 PST)
- Re: [AMBER] RDF: corrupted trajectory Daniel Roe (Fri Jan 17 2020 - 10:47:57 PST)
  - Re: [AMBER] RDF: corrupted trajectory emanuele falbo (Mon Jan 20 2020 - 02:24:06 PST)
    - Re: [AMBER] RDF: corrupted trajectory Daniel Roe (Tue Jan 21 2020 - 11:00:46 PST)
    - Re: [AMBER] RDF: corrupted trajectory emanuele falbo (Wed Jan 22 2020 - 01:40:51 PST)
[AMBER] Long syntax error on complex molecule Manisha Yadav (Fri Jan 17 2020 - 20:00:20 PST)
- Re: [AMBER] Long syntax error on complex molecule Thomas Cheatham (Fri Jan 17 2020 - 20:11:19 PST)
[AMBER] Problem in Amber update Kshatresh Dutta Dubey (Sat Jan 18 2020 - 00:07:50 PST)
- Re: [AMBER] Problem in Amber update David Case (Sat Jan 18 2020 - 05:27:10 PST)
  - Re: [AMBER] Problem in Amber update Kshatresh Dutta Dubey (Sun Jan 19 2020 - 05:14:27 PST)
[AMBER] GPU-AMBER18 installation on RTX2080Ti ke.gohda.camm-kansai.org (Sat Jan 18 2020 - 02:29:48 PST)
- Re: [AMBER] GPU-AMBER18 installation on RTX2080Ti Ross Walker (Sat Jan 18 2020 - 11:32:13 PST)
  - Re: [AMBER] GPU-AMBER18 installation on RTX2080Ti ke.gohda.camm-kansai.org (Mon Jan 20 2020 - 03:30:38 PST)
[AMBER] rror: an illegal memory access was encountered launching kernel kNLSkinTest Sruthi Sudhakar (Sat Jan 18 2020 - 04:30:58 PST)
- [AMBER] MMPBSA run failure Billiot, Eugene (Sat Jan 18 2020 - 04:45:31 PST)
- Re: [AMBER] rror: an illegal memory access was encountered launching kernel kNLSkinTest David Case (Sat Jan 18 2020 - 05:31:36 PST)
[AMBER] defining a progress variable to be the z-component of some atom or group of atoms? David Case (Sat Jan 18 2020 - 05:14:29 PST)
- Re: [AMBER] defining a progress variable to be the z-component of some atom or group of atoms? Goetz, Andreas (Sat Jan 18 2020 - 18:01:59 PST)
  - Re: [AMBER] defining a progress variable to be the z-component of some atom or group of atoms? Gerardo Zerbetto De Palma (Sat Jan 18 2020 - 18:26:19 PST)
- Re: [AMBER] defining a progress variable to be the z-component of some atom or group of atoms? Feng Pan (Sun Jan 19 2020 - 08:31:08 PST)
- Re: [AMBER] defining a progress variable to be the z-component of some atom or group of atoms? Stephan Schott (Mon Jan 20 2020 - 07:12:55 PST)
[AMBER] Problem regarding umbrella sampling roomno sixtysix (Sun Jan 19 2020 - 06:45:41 PST)
[AMBER] Problem regarding umbrella sampling Rituparna Roy (Sun Jan 19 2020 - 20:31:13 PST)
- Re: [AMBER] Problem regarding umbrella sampling David Case (Mon Jan 20 2020 - 05:44:45 PST)
[AMBER] About ions coordinated to Zinc MENDOZA Cesar (Mon Jan 20 2020 - 06:45:22 PST)
- Re: [AMBER] About ions coordinated to Zinc MENDOZA Cesar (Thu Jan 23 2020 - 07:23:05 PST)
  - Re: [AMBER] About ions coordinated to Zinc MENDOZA Cesar (Fri Jan 24 2020 - 15:18:38 PST)
[AMBER] sqm calculation with external charges not working Anthony Bogetti (Mon Jan 20 2020 - 07:53:08 PST)
- Re: [AMBER] sqm calculation with external charges not working Goetz, Andreas (Tue Jan 21 2020 - 21:58:43 PST)
[AMBER] convergence of Ref energies in cpHMD Kolattukudy P. Santo (Mon Jan 20 2020 - 10:43:20 PST)
- Re: [AMBER] convergence of Ref energies in cpHMD Cruzeiro,Vinicius Wilian D (Mon Jan 20 2020 - 12:15:54 PST)
  - Re: [AMBER] convergence of Ref energies in cpHMD Kolattukudy P. Santo (Mon Jan 20 2020 - 12:41:18 PST)
    - Re: [AMBER] convergence of Ref energies in cpHMD Cruzeiro,Vinicius Wilian D (Mon Jan 20 2020 - 14:27:11 PST)
    - Re: [AMBER] convergence of Ref energies in cpHMD Kolattukudy P. Santo (Tue Jan 21 2020 - 06:13:47 PST)
    - Re: [AMBER] convergence of Ref energies in cpHMD Cruzeiro,Vinicius Wilian D (Tue Jan 21 2020 - 23:43:35 PST)
    - Re: [AMBER] convergence of Ref energies in cpHMD Kolattukudy P. Santo (Wed Jan 22 2020 - 06:37:44 PST)
    - Re: [AMBER] convergence of Ref energies in cpHMD Cruzeiro,Vinicius Wilian D (Thu Jan 23 2020 - 14:38:23 PST)
[AMBER] Is there any sense in even trying to model large conformational dynamics with molecular dynamics? Homeo Morphism (Mon Jan 20 2020 - 11:15:52 PST)
- Re: [AMBER] Is there any sense in even trying to model large conformational dynamics with molecular dynamics? Gerardo Zerbetto De Palma (Mon Jan 20 2020 - 11:24:30 PST)
  - Re: [AMBER] Is there any sense in even trying to model large conformational dynamics with molecular dynamics? Carlos Simmerling (Mon Jan 20 2020 - 11:59:07 PST)
[AMBER] NEB Simulations in Amber SHAUNAK BADANI (Mon Jan 20 2020 - 12:25:26 PST)
- Re: [AMBER] NEB Simulations in Amber Carlos Simmerling (Mon Jan 20 2020 - 13:55:31 PST)
[AMBER] DUMPAVE digits Santiago Movilla (Mon Jan 20 2020 - 14:29:33 PST)
[AMBER] Reg. working of Periodic Boundary Conditions DHEERAJ CHITARA (Tue Jan 21 2020 - 06:25:23 PST)
- Re: [AMBER] Reg. working of Periodic Boundary Conditions David Case (Tue Jan 21 2020 - 09:38:10 PST)
[AMBER] cpptraj_clucster Lod King (Tue Jan 21 2020 - 19:16:44 PST)
- Re: [AMBER] cpptraj_clucster Thayer, Kelly (Wed Jan 29 2020 - 07:13:49 PST)
  - Re: [AMBER] cpptraj_clucster Lod King (Sat Feb 01 2020 - 10:47:56 PST)
- Re: [AMBER] cpptraj_clucster Daniel Roe (Sat Feb 01 2020 - 11:05:57 PST)
[AMBER] generating g-quadruplex DNA structures from a sequence Vaibhav Dixit (Tue Jan 21 2020 - 22:51:39 PST)
- Re: [AMBER] generating g-quadruplex DNA structures from a sequence David Case (Wed Jan 22 2020 - 05:05:18 PST)
  - Re: [AMBER] generating g-quadruplex DNA structures from a sequence Vaibhav Dixit (Wed Jan 22 2020 - 21:09:14 PST)
- Re: [AMBER] generating g-quadruplex DNA structures from a sequence Satyaseelan C (Thu Jan 23 2020 - 00:53:24 PST)
[AMBER] Wanting to get synchronized trajectory files Abdullah Bin Faheem (Wed Jan 22 2020 - 02:53:50 PST)
- Re: [AMBER] Wanting to get synchronized trajectory files David Case (Wed Jan 22 2020 - 05:09:18 PST)
  - Re: [AMBER] Wanting to get synchronized trajectory files Abdullah Bin Faheem (Wed Jan 22 2020 - 07:05:28 PST)
    - Re: [AMBER] Wanting to get synchronized trajectory files Carlos Simmerling (Wed Jan 22 2020 - 07:43:43 PST)
    - Re: [AMBER] Wanting to get synchronized trajectory files Abdullah Bin Faheem (Wed Jan 22 2020 - 08:06:01 PST)
    - Re: [AMBER] Wanting to get synchronized trajectory files Carlos Simmerling (Wed Jan 22 2020 - 09:10:16 PST)
    - Re: [AMBER] Wanting to get synchronized trajectory files Abdullah Bin Faheem (Wed Jan 22 2020 - 10:58:14 PST)
- Re: [AMBER] Wanting to get synchronized trajectory files Gustaf Olsson (Wed Jan 22 2020 - 05:47:36 PST)
[AMBER] Multiple GPU imstallation of AMBER 18 error Sruthi Sudhakar (Wed Jan 22 2020 - 22:54:08 PST)
- Re: [AMBER] Multiple GPU imstallation of AMBER 18 error Elvis Martis (Thu Jan 23 2020 - 00:06:36 PST)
  - Re: [AMBER] Multiple GPU imstallation of AMBER 18 error Sruthi Sudhakar (Thu Jan 23 2020 - 00:17:11 PST)
    - Re: [AMBER] Multiple GPU imstallation of AMBER 18 error Elvis Martis (Thu Jan 23 2020 - 01:33:20 PST)
    - Re: [AMBER] Multiple GPU imstallation of AMBER 18 error Sruthi Sudhakar (Thu Jan 23 2020 - 02:08:46 PST)
    - Re: [AMBER] Multiple GPU imstallation of AMBER 18 error Sruthi Sudhakar (Thu Jan 23 2020 - 02:10:05 PST)
    - Re: [AMBER] Multiple GPU imstallation of AMBER 18 error Sruthi Sudhakar (Thu Jan 23 2020 - 03:39:54 PST)
    - Re: [AMBER] Multiple GPU imstallation of AMBER 18 error Elvis Martis (Thu Jan 23 2020 - 05:15:11 PST)
- Re: [AMBER] Multiple GPU imstallation of AMBER 18 error David Case (Thu Jan 23 2020 - 06:39:31 PST)
  - Re: [AMBER] Multiple GPU imstallation of AMBER 18 error Sruthi Sudhakar (Thu Jan 23 2020 - 07:24:01 PST)
    - Re: [AMBER] Multiple GPU imstallation of AMBER 18 error Elvis Martis (Thu Jan 23 2020 - 07:38:03 PST)
    - Re: [AMBER] Multiple GPU imstallation of AMBER 18 error Sruthi Sudhakar (Thu Jan 23 2020 - 07:53:41 PST)
    - Re: [AMBER] Multiple GPU imstallation of AMBER 18 error Sruthi Sudhakar (Fri Jan 24 2020 - 02:13:20 PST)
    - Re: [AMBER] Multiple GPU imstallation of AMBER 18 error Elvis Martis (Fri Jan 24 2020 - 03:51:15 PST)
    - Re: [AMBER] Multiple GPU imstallation of AMBER 18 error Sruthi Sudhakar (Fri Jan 24 2020 - 20:48:14 PST)
    - Re: [AMBER] Multiple GPU imstallation of AMBER 18 error Sruthi Sudhakar (Fri Jan 24 2020 - 22:25:09 PST)
    - Re: [AMBER] Multiple GPU imstallation of AMBER 18 error Elvis Martis (Sat Jan 25 2020 - 18:45:45 PST)
[AMBER] Normal mode analysis using trajectory files Divya Rai (Wed Jan 22 2020 - 22:26:31 PST)
- Re: [AMBER] Normal mode analysis using trajectory files Elvis Martis (Thu Jan 23 2020 - 00:08:52 PST)
[AMBER] Parameter Files for Nanopore made of Si3N4(Silicon Nitride) Vishal Reddy (Thu Jan 23 2020 - 02:05:25 PST)
[AMBER] Does anyone here use a99SB-disp force field and how did you obtain it? Homeo Morphism (Thu Jan 23 2020 - 02:44:52 PST)
- Re: [AMBER] Does anyone here use a99SB-disp force field and how did you obtain it? Anthony Cruz-Balberdy (Thu Jan 23 2020 - 04:56:36 PST)
  - Re: [AMBER] Does anyone here use a99SB-disp force field and how did you obtain it? Casalini Tommaso (Thu Jan 23 2020 - 07:05:43 PST)
[AMBER] steered MD question Baker, Joseph (Thu Jan 23 2020 - 12:10:50 PST)
[AMBER] Shaw DE RNA ff in Amber format amirhossein taghavi (Thu Jan 23 2020 - 13:59:17 PST)
- Re: [AMBER] Shaw DE RNA ff in Amber format Josh Berryman (Thu Feb 06 2020 - 05:34:00 PST)
- Re: [AMBER] Shaw DE RNA ff in Amber format Cavender, Chapin (Thu Feb 06 2020 - 13:23:53 PST)
[AMBER] Autoimage problem Agata Sowińska I34 (Fri Jan 24 2020 - 08:41:14 PST)
[AMBER] pmemd.cuda.MPI run error Sruthi Sudhakar (Mon Jan 27 2020 - 04:21:04 PST)
- Re: [AMBER] pmemd.cuda.MPI run error Gerardo Zerbetto De Palma (Mon Jan 27 2020 - 03:52:05 PST)
- Re: [AMBER] pmemd.cuda.MPI run error Elvis Martis (Mon Jan 27 2020 - 03:58:28 PST)
  - Re: [AMBER] pmemd.cuda.MPI run error Sruthi Sudhakar (Mon Jan 27 2020 - 04:49:12 PST)
    - Re: [AMBER] pmemd.cuda.MPI run error Sruthi Sudhakar (Mon Jan 27 2020 - 04:55:00 PST)
    - Re: [AMBER] pmemd.cuda.MPI run error Gerardo Zerbetto De Palma (Mon Jan 27 2020 - 04:31:08 PST)
    - Re: [AMBER] pmemd.cuda.MPI run error Sruthi Sudhakar (Mon Jan 27 2020 - 05:11:08 PST)
[AMBER] Fwd: CalcError: /truba/sw/centos6.4/app/amber/amber14/bin/sander failed with prmtop gas.complex.prmtop! Rana Rehan Khalid (Mon Jan 27 2020 - 08:51:02 PST)
[AMBER] About ferrocene MENDOZA Cesar (Mon Jan 27 2020 - 08:54:45 PST)
[AMBER] Calculation of mask for TI input Airy Sanjeev (Mon Jan 27 2020 - 20:22:34 PST)
- Re: [AMBER] Calculation of mask for TI input Carlos Simmerling (Tue Jan 28 2020 - 02:40:09 PST)
[AMBER] Several alpha-helices stitched together - how would you stress-test it with MD? Homeo Morphism (Tue Jan 28 2020 - 02:48:35 PST)
- Re: [AMBER] Several alpha-helices stitched together - how would you stress-test it with MD? Carlos Simmerling (Tue Jan 28 2020 - 02:52:49 PST)
[AMBER] Amber on windows 10 Nicolas Feldman (Tue Jan 28 2020 - 04:14:39 PST)
- Re: [AMBER] Amber on windows 10 Elvis Martis (Tue Jan 28 2020 - 04:19:42 PST)
  - Re: [AMBER] Amber on windows 10 Nicolas Feldman (Tue Jan 28 2020 - 04:33:33 PST)
- Re: [AMBER] Amber on windows 10 Gustaf Olsson (Tue Jan 28 2020 - 04:22:32 PST)
  - Re: [AMBER] Amber on windows 10 Nicolas Feldman (Tue Jan 28 2020 - 04:27:06 PST)
    - Re: [AMBER] Amber on windows 10 Gustaf Olsson (Tue Jan 28 2020 - 05:21:47 PST)
    - Re: [AMBER] Amber on windows 10 Gustaf Olsson (Tue Jan 28 2020 - 07:08:14 PST)
    - Re: [AMBER] Amber on windows 10 Nicolas Feldman (Tue Jan 28 2020 - 07:13:37 PST)
    - Re: [AMBER] Amber on windows 10 Elvis Martis (Tue Jan 28 2020 - 07:22:22 PST)
[AMBER] About utilities to convert Amber input files for MD into the Tinker, NAMD, Genesis, or Desmond input files Vlad (Tue Jan 28 2020 - 20:00:19 PST)
- Re: [AMBER] About utilities to convert Amber input files for MD into the Tinker, NAMD, Genesis, or Desmond input files Elvis Martis (Tue Jan 28 2020 - 20:17:49 PST)
  - Re: [AMBER] About utilities to convert Amber input files for MD into the Tinker, NAMD, Genesis, or Desmond input files Pengfei Li (Mon Feb 03 2020 - 18:09:05 PST)
[AMBER] kindly guide me ALAMGIR KHAN (Tue Jan 28 2020 - 21:00:54 PST)
- Re: [AMBER] kindly guide me Gustaf Olsson (Tue Jan 28 2020 - 22:42:49 PST)
  - Re: [AMBER] kindly guide me ALAMGIR KHAN (Wed Jan 29 2020 - 01:43:08 PST)
[AMBER] gnuplot MYRIAN TORRES RICO (Wed Jan 29 2020 - 02:17:48 PST)
[AMBER] gnuplot MYRIAN TORRES RICO (Wed Jan 29 2020 - 02:18:56 PST)
[AMBER] sulfonamide parameters for correct geometry Annachiara TINIVELLA (Wed Jan 29 2020 - 04:31:25 PST)
- Re: [AMBER] sulfonamide parameters for correct geometry Junmei Wang (Mon Feb 03 2020 - 10:01:45 PST)
  - Re: [AMBER] sulfonamide parameters for correct geometry Annachiara TINIVELLA (Thu Feb 06 2020 - 08:17:36 PST)
[AMBER] how does one reply to a thread in a mailing list Homeo Morphism (Wed Jan 29 2020 - 07:26:57 PST)
- Re: [AMBER] how does one reply to a thread in a mailing list David Case (Wed Jan 29 2020 - 11:08:18 PST)
[AMBER] Help building a model of a 2F-2S protein with MDPB.py Gustavo Seabra (Wed Jan 29 2020 - 10:57:18 PST)
- Re: [AMBER] Help building a model of a 2F-2S protein with MDPB.py MENDOZA Cesar (Wed Jan 29 2020 - 12:25:47 PST)
  - Re: [AMBER] Help building a model of a 2F-2S protein with MDPB.py MENDOZA Cesar (Wed Jan 29 2020 - 12:27:36 PST)
  - Re: [AMBER] Help building a model of a 2F-2S protein with MDPB.py Gustavo Seabra (Mon Feb 03 2020 - 11:46:12 PST)
- Re: [AMBER] Help building a model of a 2F-2S protein with MDPB.py Pengfei Li (Mon Feb 03 2020 - 18:02:20 PST)
[AMBER] Error in installing parallel version of AMBER18 dilrajl.bii.a-star.edu.sg (Thu Jan 30 2020 - 06:51:57 PST)
- Re: [AMBER] Error in installing parallel version of AMBER18 Scott Brozell (Thu Jan 30 2020 - 11:55:53 PST)
[AMBER] postdoc DNA/RNA simulations Jiri Sponer (Thu Jan 30 2020 - 09:36:31 PST)
- Re: [AMBER] postdoc DNA/RNA simulations Nicolas Feldman (Thu Jan 30 2020 - 10:14:06 PST)
[AMBER] usefrcascoords calculations Lambach, Lauren (Thu Jan 30 2020 - 14:25:28 PST)
[AMBER] Doubt regarding Collision frequency during NEB simulations SHAUNAK BADANI (Fri Jan 31 2020 - 11:37:03 PST)
[AMBER] ante-MMPBSA.py Rui Chen (Sat Feb 01 2020 - 13:20:17 PST)
- Re: [AMBER] ante-MMPBSA.py Elvis Martis (Sat Feb 01 2020 - 18:56:38 PST)
  - Re: [AMBER] ante-MMPBSA.py Rui Chen (Sat Feb 01 2020 - 19:02:53 PST)
    - Re: [AMBER] ante-MMPBSA.py Elvis Martis (Sat Feb 01 2020 - 20:15:41 PST)
    - Re: [AMBER] ante-MMPBSA.py Elvis Martis (Sat Feb 01 2020 - 20:16:16 PST)
    - Re: [AMBER] ante-MMPBSA.py Rui Chen (Sat Feb 01 2020 - 20:26:33 PST)
[AMBER] installation of amber 18 failed - CUDA_HOME not set (although not true) Bisignano, Paola (Sat Feb 01 2020 - 20:09:08 PST)
- Re: [AMBER] installation of amber 18 failed - CUDA_HOME not set (although not true) Elvis Martis (Sat Feb 01 2020 - 20:17:56 PST)
  - Re: [AMBER] installation of amber 18 failed - CUDA_HOME not set (although not true) Bisignano, Paola (Sat Feb 01 2020 - 20:19:20 PST)
    - Re: [AMBER] installation of amber 18 failed - CUDA_HOME not set (although not true) Gerardo Zerbetto De Palma (Sat Feb 01 2020 - 20:31:17 PST)
- Re: [AMBER] installation of amber 18 failed - CUDA_HOME not set (although not true) David Case (Sun Feb 02 2020 - 05:34:52 PST)
[AMBER] "Bad inpcrd file!" when running pmemd.MPI but not pmemd Johannes Blaschke (Sun Feb 02 2020 - 09:09:13 PST)
- Re: [AMBER] "Bad inpcrd file!" when running pmemd.MPI but not pmemd Daniel Roe (Mon Feb 03 2020 - 05:15:30 PST)
- Re: [AMBER] "Bad inpcrd file!" when running pmemd.MPI but not pmemd David A Case (Mon Feb 03 2020 - 05:17:58 PST)
[AMBER] .crd error MYRIAN TORRES RICO (Mon Feb 03 2020 - 01:16:16 PST)
- Re: [AMBER] .crd error Daniel Roe (Mon Feb 03 2020 - 05:08:08 PST)
  - Re: [AMBER] .crd error MYRIAN TORRES RICO (Tue Feb 04 2020 - 01:12:18 PST)
    - Re: [AMBER] .crd error Gustaf Olsson (Tue Feb 04 2020 - 03:11:51 PST)
    - Re: [AMBER] .crd error MYRIAN TORRES RICO (Tue Feb 04 2020 - 04:57:09 PST)
    - Re: [AMBER] .crd error David A Case (Tue Feb 04 2020 - 05:34:13 PST)
    - Re: [AMBER] .crd error MYRIAN TORRES RICO (Tue Feb 04 2020 - 06:26:53 PST)
    - Re: [AMBER] .crd error Carlos Simmerling (Tue Feb 04 2020 - 07:00:40 PST)
    - Re: [AMBER] .crd error MYRIAN TORRES RICO (Tue Feb 04 2020 - 07:37:17 PST)
    - Re: [AMBER] .crd error Gustaf Olsson (Tue Feb 04 2020 - 06:35:45 PST)
    - Re: [AMBER] .crd error Daniel Roe (Tue Feb 04 2020 - 11:37:04 PST)
- Re: [AMBER] .crd error David A Case (Mon Feb 03 2020 - 05:24:22 PST)
[AMBER] Reading Frames from Trajectory File Catherine Jenifer Rajam Rajendran (Mon Feb 03 2020 - 10:12:50 PST)
- Re: [AMBER] Reading Frames from Trajectory File Carlos Simmerling (Mon Feb 03 2020 - 10:39:22 PST)
  - Re: [AMBER] [External] Re: Reading Frames from Trajectory File Catherine Jenifer Rajam Rajendran (Mon Feb 03 2020 - 10:51:00 PST)
    - Re: [AMBER] [External] Re: Reading Frames from Trajectory File Carlos Simmerling (Mon Feb 03 2020 - 10:55:41 PST)
    - Re: [AMBER] [External] Re: Reading Frames from Trajectory File Catherine Jenifer Rajam Rajendran (Mon Feb 03 2020 - 11:03:48 PST)
- Re: [AMBER] Reading Frames from Trajectory File Daniel Roe (Mon Feb 03 2020 - 11:12:38 PST)
  - Re: [AMBER] [External] Re: Reading Frames from Trajectory File Catherine Jenifer Rajam Rajendran (Mon Feb 03 2020 - 11:45:02 PST)
[AMBER] heme B parameter by mcpb PRAGYA PRIYADARSHINI (Mon Feb 03 2020 - 20:39:48 PST)
- Re: [AMBER] heme B parameter by mcpb Pengfei Li (Fri Mar 27 2020 - 13:54:42 PDT)
[AMBER] pdb4amber strips atoms Petro (Tue Feb 04 2020 - 04:47:23 PST)
- Re: [AMBER] pdb4amber strips atoms Petro (Tue Feb 04 2020 - 04:58:19 PST)
[AMBER] CPPTRAJ hydrogen bond analysis Rui Chen (Tue Feb 04 2020 - 07:21:53 PST)
- Re: [AMBER] CPPTRAJ hydrogen bond analysis Daniel Roe (Tue Feb 04 2020 - 11:42:26 PST)
  - Re: [AMBER] CPPTRAJ hydrogen bond analysis Rui Chen (Tue Feb 04 2020 - 12:45:54 PST)
Re: [AMBER] CalcError: /truba/sw/centos6.4/app/amber/amber14/bin/sander failed with prmtop gas.complex.prmtop! Rana Rehan Khalid (Tue Feb 04 2020 - 12:24:37 PST)
[AMBER] Gas phase simulation for heat of vaporization calculation wijaya.t.aa.m.titech.ac.jp (Wed Feb 05 2020 - 00:18:20 PST)
[AMBER] Reg. Periodic Boundary Conditions DHEERAJ CHITARA (Wed Feb 05 2020 - 04:20:36 PST)
- Re: [AMBER] Reg. Periodic Boundary Conditions Carlos Simmerling (Wed Feb 05 2020 - 04:39:26 PST)
- Re: [AMBER] Reg. Periodic Boundary Conditions David A Case (Wed Feb 05 2020 - 04:52:47 PST)
  - Re: [AMBER] (no subject) mirzo (Wed Feb 05 2020 - 05:11:50 PST)
[AMBER] counterions present in topology files for the MMPSA calculation Shilpa Gupta (Wed Feb 05 2020 - 05:43:46 PST)
- Re: [AMBER] counterions present in topology files for the MMPSA calculation Elvis Martis (Wed Feb 05 2020 - 05:51:33 PST)
[AMBER] Several FAILED tests for AmberTools19 and Amber18 zmatovic.kg.ac.rs (Wed Feb 05 2020 - 06:12:02 PST)
[AMBER] AQUA-DUCT Summer School 22-25 June, Gliwice, Poland Markowska (Wed Feb 05 2020 - 07:08:02 PST)
[AMBER] hiii ankita mehta (Wed Feb 05 2020 - 10:27:00 PST)
- Re: [AMBER] hiii David A Case (Wed Feb 05 2020 - 10:46:28 PST)
  - Re: [AMBER] hiii ankita mehta (Wed Feb 05 2020 - 11:00:02 PST)
    - Re: [AMBER] hiii ankita mehta (Wed Feb 05 2020 - 11:09:51 PST)
    - Re: [AMBER] hiii Daniel Roe (Thu Feb 06 2020 - 05:16:02 PST)
[AMBER] MMPBSA calculations Baptiste Legrand (Thu Feb 06 2020 - 03:14:17 PST)
- Re: [AMBER] MMPBSA calculations Elvis Martis (Thu Feb 06 2020 - 20:54:18 PST)
[AMBER] Question about LSC-IVR keep running without any output information after PIMD sampling wangjianing_mail (Thu Feb 06 2020 - 05:51:55 PST)
[AMBER] On QM/MM dummy atom and deprotonated TYR David Sáez (Thu Feb 06 2020 - 14:38:55 PST)
- Re: [AMBER] On QM/MM dummy atom and deprotonated TYR Clorice Reinhardt (Thu Feb 06 2020 - 15:27:38 PST)
  - Re: [AMBER] On QM/MM dummy atom and deprotonated TYR David Sáez (Thu Feb 06 2020 - 18:36:44 PST)
  - Re: [AMBER] On QM/MM dummy atom and deprotonated TYR David Sáez (Tue Feb 11 2020 - 07:28:29 PST)
    - Re: [AMBER] On QM/MM dummy atom and deprotonated TYR Clorice Reinhardt (Tue Feb 11 2020 - 07:34:51 PST)
    - Re: [AMBER] On QM/MM dummy atom and deprotonated TYR Clorice Reinhardt (Tue Feb 11 2020 - 07:47:35 PST)
[AMBER] tleap/xleap performance enhancement Himanshu Joshi (Thu Feb 06 2020 - 14:48:58 PST)
- Re: [AMBER] tleap/xleap performance enhancement David A Case (Fri Feb 07 2020 - 05:00:10 PST)
  - Re: [AMBER] tleap/xleap performance enhancement Himanshu Joshi (Fri Feb 07 2020 - 09:08:39 PST)
    - Re: [AMBER] tleap/xleap performance enhancement Himanshu Joshi (Fri Feb 07 2020 - 12:12:44 PST)
    - Re: [AMBER] tleap/xleap performance enhancement Matias Machado (Mon Feb 10 2020 - 07:35:05 PST)
    - Re: [AMBER] tleap/xleap performance enhancement Himanshu Joshi (Wed Mar 04 2020 - 10:13:11 PST)
[AMBER] [LEaP] Atom does not have a type Johannes Kalliauer (Fri Feb 07 2020 - 06:09:29 PST)
- Re: [AMBER] [LEaP] Atom does not have a type Gustavo Seabra (Fri Feb 07 2020 - 08:02:01 PST)
  - Re: [AMBER] [LEaP] Atom does not have a type mirzo (Fri Feb 07 2020 - 08:32:54 PST)
  - Re: [AMBER] [LEaP] Atom does not have a type David A Case (Fri Feb 07 2020 - 15:06:13 PST)
[AMBER] question about pressure and sensible MD trajectories Gordon Richard Chalmers (Fri Feb 07 2020 - 19:38:43 PST)
- Re: [AMBER] question about pressure and sensible MD trajectories Gordon Richard Chalmers (Fri Feb 07 2020 - 19:53:39 PST)
[AMBER] query on a script called getdvdl.py in AMBER TI tutorial section Debarati DasGupta (Sat Feb 08 2020 - 06:50:39 PST)
[AMBER] Regarding RMSD calculation and Clustering Manish Kumar Mohanty (Sat Feb 08 2020 - 21:10:09 PST)
- Re: [AMBER] Regarding RMSD calculation and Clustering Daniel Roe (Tue Aug 04 2020 - 07:54:54 PDT)
[AMBER] TI on pmemd CUDA, AMBER18 Hosein Geraili Daronkola (Mon Feb 10 2020 - 02:13:48 PST)
- Re: [AMBER] TI on pmemd CUDA, AMBER18 Taisung Lee (Tue Feb 11 2020 - 06:39:33 PST)
  - Re: [AMBER] TI on pmemd CUDA, AMBER18 Hosein Geraili Daronkola (Fri Feb 21 2020 - 01:57:41 PST)
[AMBER] DOCKED LIGAND CONFORMATION INTO AMBER MD Sruthi Sudhakar (Mon Feb 10 2020 - 02:56:43 PST)
- Re: [AMBER] DOCKED LIGAND CONFORMATION INTO AMBER MD Elvis Martis (Mon Feb 10 2020 - 04:13:14 PST)
[AMBER] kindly guide me. ALAMGIR KHAN (Mon Feb 10 2020 - 21:25:00 PST)
- Re: [AMBER] kindly guide me. David A Case (Tue Feb 11 2020 - 04:49:07 PST)
[AMBER] how to treat capped non-standard AA residue Vaibhav Dixit (Tue Feb 11 2020 - 02:07:04 PST)
[AMBER] pmemd.cuda installation Bacaita Simona (Tue Feb 11 2020 - 11:40:44 PST)
- Re: [AMBER] pmemd.cuda installation David A Case (Wed Feb 12 2020 - 06:08:46 PST)
[AMBER] AMBER 18 installation issue Abhilash J (Tue Feb 11 2020 - 17:09:56 PST)
- Re: [AMBER] AMBER 18 installation issue David A Case (Wed Feb 12 2020 - 06:16:36 PST)
  - Re: [AMBER] AMBER 18 installation issue Abhilash J (Wed Feb 12 2020 - 08:44:32 PST)
[AMBER] Query regarding 3DRISM in Amber with CHARMM force field Rakesh Srivastava (Tue Feb 11 2020 - 22:46:07 PST)
- Re: [AMBER] Query regarding 3DRISM in Amber with CHARMM force field Tyler Luchko (Lists) (Wed Feb 12 2020 - 10:05:06 PST)
  - Re: [AMBER] Query regarding 3DRISM in Amber with CHARMM force field Rakesh Srivastava (Fri Mar 06 2020 - 22:20:51 PST)
Re: [AMBER] Amber install error David A Case (Wed Feb 12 2020 - 06:11:53 PST)
[AMBER] Simulation of an asymmetric membrane model Eduardo R. Almeida (Wed Feb 12 2020 - 11:38:07 PST)
- Re: [AMBER] Simulation of an asymmetric membrane model ABEL Stephane (Thu Feb 13 2020 - 01:37:43 PST)
  - Re: [AMBER] Simulation of an asymmetric membrane model Matias Machado (Thu Feb 13 2020 - 11:37:33 PST)
[AMBER] Representative structures from `clusterdihedral`? Gustavo Seabra (Wed Feb 12 2020 - 13:43:52 PST)
[AMBER] BMRB Chemical shift values Lod King (Wed Feb 12 2020 - 15:21:29 PST)
- Re: [AMBER] BMRB Chemical shift values Christina Bergonzo (Thu Feb 13 2020 - 05:50:58 PST)
  - Re: [AMBER] BMRB Chemical shift values Gordon Richard Chalmers (Thu Feb 13 2020 - 07:07:49 PST)
    - Re: [AMBER] BMRB Chemical shift values Lod King (Thu Feb 13 2020 - 08:05:15 PST)
    - Re: [AMBER] BMRB Chemical shift values Adrian Roitberg (Thu Feb 13 2020 - 08:29:02 PST)
[AMBER] counter ions in TI calculations Maier, Sarah (Wed Feb 12 2020 - 16:03:49 PST)
- Re: [AMBER] counter ions in TI calculations Josh Berryman (Wed Feb 12 2020 - 23:45:58 PST)
[AMBER] QM/MM AMBER/ORCA: output emanuele falbo (Thu Feb 13 2020 - 01:21:40 PST)
- Re: [AMBER] QM/MM AMBER/ORCA: output Goetz, Andreas (Thu Feb 13 2020 - 02:20:45 PST)
  - Re: [AMBER] QM/MM AMBER/ORCA: output emanuele falbo (Thu Feb 13 2020 - 06:25:39 PST)
    - Re: [AMBER] QM/MM AMBER/ORCA: output Goetz, Andreas (Thu Feb 13 2020 - 23:07:09 PST)
    - Re: [AMBER] QM/MM AMBER/ORCA: output emanuele falbo (Wed Feb 19 2020 - 08:27:15 PST)
    - Re: [AMBER] QM/MM AMBER/ORCA: output Goetz, Andreas (Wed Feb 19 2020 - 09:11:20 PST)
[AMBER] Compatibility issue of Atom type naming in AMBER Lod King (Thu Feb 13 2020 - 14:57:38 PST)
- Re: [AMBER] Compatibility issue of Atom type naming in AMBER David A Case (Fri Feb 14 2020 - 04:36:48 PST)
[AMBER] H++ processing non-standard amino acids: Atom does not have a type Wei-Tse Hsu (Thu Feb 13 2020 - 21:16:35 PST)
- Re: [AMBER] H++ processing non-standard amino acids: Atom does not have a type Ramu Anandakrishnan (Fri Feb 14 2020 - 05:27:16 PST)
[AMBER] combination of MD simulations with NMR Vlad Cojocaru (Fri Feb 14 2020 - 01:07:33 PST)
[AMBER] Production run in NVT ensemble Baptiste Legrand (Fri Feb 14 2020 - 03:04:18 PST)
- Re: [AMBER] Production run in NVT ensemble Carlos Simmerling (Fri Feb 14 2020 - 03:34:51 PST)
  - Re: [AMBER] Production run in NVT ensemble Baptiste Legrand (Wed Feb 19 2020 - 00:13:03 PST)
[AMBER] how to locate all parameters for specific AA in parm directory Vaibhav Dixit (Thu Feb 13 2020 - 23:41:12 PST)
- Re: [AMBER] how to locate all parameters for specific AA in parm directory Carlos Simmerling (Fri Feb 14 2020 - 03:31:18 PST)
  - Re: [AMBER] how to locate all parameters for specific AA in parm directory Vaibhav Dixit (Fri Feb 14 2020 - 00:38:11 PST)
    - Re: [AMBER] how to locate all parameters for specific AA in parm directory Vaibhav Dixit (Fri Feb 14 2020 - 08:21:20 PST)
    - Re: [AMBER] how to locate all parameters for specific AA in parm directory Carlos Simmerling (Fri Feb 14 2020 - 08:43:58 PST)
[AMBER] Dihedral restraint problems in AMBER16/18 Rebecca Twidale (Fri Feb 14 2020 - 04:33:56 PST)
- Re: [AMBER] Dihedral restraint problems in AMBER16/18 Kellon Belfon (Fri Feb 14 2020 - 19:12:52 PST)
[AMBER] GLYCAM Topology for alfa-cyclodextrin, beta-cyclodextrin and gama-cyclodextrin. Marcelo Andrade Chagas (Fri Feb 14 2020 - 12:41:32 PST)
- Re: [AMBER] GLYCAM Topology for alfa-cyclodextrin, beta-cyclodextrin and gama-cyclodextrin. Lachele Foley (Fri Feb 14 2020 - 16:24:55 PST)
  - Re: [AMBER] GLYCAM Topology for alfa-cyclodextrin, beta-cyclodextrin and gama-cyclodextrin. Marcelo Andrade Chagas (Sun Feb 16 2020 - 09:49:41 PST)
    - Re: [AMBER] GLYCAM Topology for alfa-cyclodextrin, beta-cyclodextrin and gama-cyclodextrin. Oliver Grant (Mon Feb 17 2020 - 08:20:04 PST)
    - Re: [AMBER] GLYCAM Topology for alfa-cyclodextrin, beta-cyclodextrin and gama-cyclodextrin. Marcelo Andrade Chagas (Mon Feb 17 2020 - 08:56:37 PST)
    - Re: [AMBER] GLYCAM Topology for alfa-cyclodextrin, beta-cyclodextrin and gama-cyclodextrin. Karl Kirschner (Mon Feb 17 2020 - 11:33:30 PST)
    - Re: [AMBER] GLYCAM Topology for alfa-cyclodextrin, beta-cyclodextrin and gama-cyclodextrin. Lachele Foley (Tue Feb 18 2020 - 08:20:41 PST)
    - Re: [AMBER] GLYCAM Topology for alfa-cyclodextrin, beta-cyclodextrin and gama-cyclodextrin. Lachele Foley (Wed Feb 19 2020 - 19:27:03 PST)
[AMBER] tLEaP error of the N-terminal OXT atom Wei-Tse Hsu (Sat Feb 15 2020 - 11:55:04 PST)
- Re: [AMBER] tLEaP error of the N-terminal OXT atom Carlos Simmerling (Sat Feb 15 2020 - 15:34:20 PST)
[AMBER] no bonds formed between AA and non-standard residue Vaibhav Dixit (Sun Feb 16 2020 - 03:30:32 PST)
- Re: [AMBER] no bonds formed between AA and non-standard residue Clorice Reinhardt (Sun Feb 16 2020 - 07:24:57 PST)
  - Re: [AMBER] no bonds formed between AA and non-standard residue Vaibhav Dixit (Sun Feb 16 2020 - 08:14:51 PST)
- Re: [AMBER] no bonds formed between AA and non-standard residue Carlos Simmerling (Sun Feb 16 2020 - 07:29:21 PST)
  - Re: [AMBER] no bonds formed between AA and non-standard residue Vaibhav Dixit (Sun Feb 16 2020 - 08:27:52 PST)
    - Re: [AMBER] no bonds formed between AA and non-standard residue Busra Demir (Sun Feb 16 2020 - 10:55:23 PST)
    - Re: [AMBER] no bonds formed between AA and non-standard residue Vaibhav Dixit (Sun Feb 16 2020 - 18:25:51 PST)
    - Re: [AMBER] no bonds formed between AA and non-standard residue Busra Demir (Mon Feb 17 2020 - 00:12:54 PST)
    - Re: [AMBER] no bonds formed between AA and non-standard residue Vaibhav Dixit (Mon Feb 17 2020 - 00:45:45 PST)
    - Re: [AMBER] no bonds formed between AA and non-standard residue David A Case (Mon Feb 17 2020 - 04:38:01 PST)
    - Re: [AMBER] no bonds formed between AA and non-standard residue Vaibhav Dixit (Mon Feb 17 2020 - 01:41:12 PST)
    - Re: [AMBER] no bonds formed between AA and non-standard residue Vaibhav Dixit (Mon Feb 17 2020 - 01:48:10 PST)
- Re: [AMBER] no bonds formed between AA and non-standard residue Vaibhav Dixit (Mon Feb 17 2020 - 16:08:48 PST)
- Re: [AMBER] no bonds formed between AA and non-standard residue Vaibhav Dixit (Tue Feb 18 2020 - 18:19:28 PST)
  - Re: [AMBER] no bonds formed between AA and non-standard residue David A Case (Wed Feb 19 2020 - 05:55:28 PST)
    - Re: [AMBER] no bonds formed between AA and non-standard residue Vaibhav Dixit (Wed Feb 19 2020 - 16:16:46 PST)
    - Re: [AMBER] no bonds formed between AA and non-standard residue Vaibhav Dixit (Thu Feb 20 2020 - 00:52:16 PST)
- Re: [AMBER] no bonds formed between AA and non-standard residue Vaibhav Dixit (Thu Feb 20 2020 - 17:48:32 PST)
  - Re: [AMBER] no bonds formed between AA and non-standard residue Vaibhav Dixit (Thu Feb 20 2020 - 18:15:29 PST)
[AMBER] MMPBSA.py error Sruthi Sudhakar (Mon Feb 17 2020 - 02:57:54 PST)
- Re: [AMBER] MMPBSA.py error Pietro Aronica (Mon Feb 17 2020 - 02:42:44 PST)
[AMBER] install amber Nicolas Feldman (Mon Feb 17 2020 - 08:07:51 PST)
- Re: [AMBER] install amber Elvis Martis (Mon Feb 17 2020 - 08:13:56 PST)
  - Re: [AMBER] install amber Nicolas Feldman (Mon Feb 17 2020 - 08:19:47 PST)
[AMBER] installing Nicolas Feldman (Mon Feb 17 2020 - 12:35:38 PST)
- Re: [AMBER] installing Gerardo Zerbetto De Palma (Mon Feb 17 2020 - 12:38:31 PST)
  - Re: [AMBER] installing Nicolas Feldman (Mon Feb 17 2020 - 12:41:02 PST)
    - Re: [AMBER] installing Gerardo Zerbetto De Palma (Mon Feb 17 2020 - 12:48:29 PST)
    - Re: [AMBER] installing Gerardo Zerbetto De Palma (Mon Feb 17 2020 - 12:49:28 PST)
    - Re: [AMBER] installing Nicolas Feldman (Mon Feb 17 2020 - 12:56:45 PST)
    - Re: [AMBER] installing Gerardo Zerbetto De Palma (Mon Feb 17 2020 - 13:07:11 PST)
    - Re: [AMBER] installing Nicolas Feldman (Mon Feb 17 2020 - 13:10:08 PST)
    - Re: [AMBER] installing Nicolas Feldman (Mon Feb 17 2020 - 13:11:07 PST)
    - Re: [AMBER] installing Gerardo Zerbetto De Palma (Mon Feb 17 2020 - 13:32:30 PST)
    - Re: [AMBER] installing Gustaf Olsson (Mon Feb 17 2020 - 14:47:26 PST)
    - Re: [AMBER] installing Nicolas Feldman (Mon Feb 17 2020 - 14:53:36 PST)
    - Re: [AMBER] installing Gustaf Olsson (Mon Feb 17 2020 - 14:56:12 PST)
    - Re: [AMBER] installing Gerardo Zerbetto De Palma (Mon Feb 17 2020 - 15:20:54 PST)
    - Re: [AMBER] installing Nicolas Feldman (Mon Feb 17 2020 - 15:28:13 PST)
    - Re: [AMBER] installing Gerardo Zerbetto De Palma (Mon Feb 17 2020 - 16:10:45 PST)
    - Re: [AMBER] installing Nicolas Feldman (Mon Feb 17 2020 - 16:14:09 PST)
    - Re: [AMBER] installing Gerardo Zerbetto De Palma (Mon Feb 17 2020 - 16:17:17 PST)
    - Re: [AMBER] installing Nicolas Feldman (Mon Feb 17 2020 - 16:20:38 PST)
    - Re: [AMBER] installing Daniel Roe (Tue Feb 18 2020 - 06:02:37 PST)
    - Re: [AMBER] installing Nicolas Feldman (Tue Feb 18 2020 - 06:33:55 PST)
    - Re: [AMBER] installing Gerardo Zerbetto De Palma (Tue Feb 18 2020 - 03:44:33 PST)
    - Re: [AMBER] installing Nicolas Feldman (Tue Feb 18 2020 - 06:55:15 PST)
    - Re: [AMBER] installing Gerardo Zerbetto De Palma (Tue Feb 18 2020 - 04:04:43 PST)
    - Re: [AMBER] installing Nicolas Feldman (Tue Feb 18 2020 - 07:07:31 PST)
    - Re: [AMBER] installing Gerardo Zerbetto De Palma (Tue Feb 18 2020 - 04:08:44 PST)
[AMBER] suggest an article for MD for covalent inhibitors ALAMGIR KHAN (Mon Feb 17 2020 - 21:44:04 PST)
[AMBER] Force field for terminal phosphorylated residues Ming Tang (Mon Feb 17 2020 - 23:11:57 PST)
- Re: [AMBER] Force field for terminal phosphorylated residues David A Case (Tue Feb 18 2020 - 05:35:16 PST)
  - Re: [AMBER] Force field for terminal phosphorylated residues Ming Tang (Tue Feb 18 2020 - 14:50:33 PST)
  - Re: [AMBER] Force field for terminal phosphorylated residues Ming Tang (Tue Feb 18 2020 - 21:37:23 PST)
[AMBER] What Can I do for Mixture of Solutions simulation and what should I assign epsilon value for this? Erdem Yeler (Tue Feb 18 2020 - 02:19:47 PST)
- Re: [AMBER] What Can I do for Mixture of Solutions simulation and what should I assign epsilon value for this? David A Case (Tue Feb 18 2020 - 08:17:33 PST)
[AMBER] mmpbsa.py Sruthi Sudhakar (Tue Feb 18 2020 - 05:34:27 PST)
- Re: [AMBER] mmpbsa.py David A Case (Tue Feb 18 2020 - 05:39:31 PST)
  - Re: [AMBER] mmpbsa.py Sruthi Sudhakar (Tue Feb 18 2020 - 07:07:14 PST)
    - Re: [AMBER] mmpbsa.py Ray Luo (Tue Feb 18 2020 - 07:03:05 PST)
    - Re: [AMBER] mmpbsa.py Sruthi Sudhakar (Tue Feb 18 2020 - 07:05:35 PST)
[AMBER] Shearing useful tips for adding ions to biomolecular simulations Matias Machado (Tue Feb 18 2020 - 10:13:54 PST)
[AMBER] kindly guide me ALAMGIR KHAN (Wed Feb 19 2020 - 03:33:59 PST)
- Re: [AMBER] kindly guide me Pietro Aronica (Wed Feb 19 2020 - 03:43:27 PST)
- Re: [AMBER] kindly guide me David A Case (Wed Feb 19 2020 - 05:56:47 PST)
[AMBER] Running Amber in a GPU cluster Aravind R (Wed Feb 19 2020 - 04:23:35 PST)
- Re: [AMBER] Running Amber in a GPU cluster Carlos Simmerling (Wed Feb 19 2020 - 04:26:49 PST)
[AMBER] facing problem in installation of Amber18 with CUDA support SATYAJIT KHATUA (Wed Feb 19 2020 - 06:12:21 PST)
[AMBER] Doubt in running mmpbsa Sruthi Sudhakar (Wed Feb 19 2020 - 07:32:11 PST)
- Re: [AMBER] Doubt in running mmpbsa Elvis Martis (Wed Feb 19 2020 - 07:27:28 PST)
  - Re: [AMBER] Doubt in running mmpbsa Sruthi Sudhakar (Wed Feb 19 2020 - 08:23:03 PST)
    - Re: [AMBER] Doubt in running mmpbsa Elvis Martis (Wed Feb 19 2020 - 08:25:43 PST)
    - Re: [AMBER] Doubt in running mmpbsa Sruthi Sudhakar (Wed Feb 19 2020 - 08:30:35 PST)
[AMBER] amber18 tests failures Antonio Bauzá Riera (Wed Feb 19 2020 - 07:46:51 PST)
- Re: [AMBER] amber18 tests failures David Cerutti (Wed Feb 19 2020 - 08:02:41 PST)
[AMBER] Versions of AMBER Frederico Henrique (Wed Feb 19 2020 - 11:17:57 PST)
- Re: [AMBER] Versions of AMBER David A Case (Wed Feb 19 2020 - 12:14:23 PST)
  - [AMBER] Unexpected reaction occurred in QM/MM umbrella sampling Qing Lv (Wed Feb 19 2020 - 17:56:18 PST)
    - Re: [AMBER] Unexpected reaction occurred in QM/MM umbrella sampling Goetz, Andreas (Wed Feb 19 2020 - 18:41:06 PST)
    - Re: [AMBER] Unexpected reaction occurred in QM/MM umbrella sampling Qing Lv (Thu Feb 20 2020 - 02:59:38 PST)
[AMBER] facing problem in installation of Amber18 with CUDA support SATYAJIT KHATUA (Wed Feb 19 2020 - 22:56:48 PST)
- Re: [AMBER] facing problem in installation of Amber18 with CUDA support David Cerutti (Wed Feb 19 2020 - 22:58:28 PST)
[AMBER] amber18 tests failure Antonio Bauzá (Thu Feb 20 2020 - 01:37:39 PST)
[AMBER] facing problem in installation of Amber18 with CUDA SATYAJIT KHATUA (Thu Feb 20 2020 - 22:56:34 PST)
[AMBER] Using cutoffs smaller than 8 A Abdullah Bin Faheem (Thu Feb 20 2020 - 23:51:23 PST)
[AMBER] Amber 16 or 20 Fabian Glaser (Sat Feb 22 2020 - 00:32:22 PST)
- Re: [AMBER] Amber 16 or 20 David A Case (Sat Feb 22 2020 - 05:17:57 PST)
  - Re: [AMBER] Amber 16 or 20 Vaibhav Dixit (Sat Feb 22 2020 - 19:17:27 PST)
[AMBER] Are benchmarks/tests on NVidia RTX 2080 Super available? Pietro Amodeo (Sat Feb 22 2020 - 05:05:32 PST)
- Re: [AMBER] Are benchmarks/tests on NVidia RTX 2080 Super available? Abhilash J (Thu Feb 27 2020 - 08:06:27 PST)
  - Re: [AMBER] Are benchmarks/tests on NVidia RTX 2080 Super available? Ross Walker (Thu Feb 27 2020 - 09:13:47 PST)
    - Re: [AMBER] Are benchmarks/tests on NVidia RTX 2080 Super available? Ross Walker (Thu Feb 27 2020 - 09:42:18 PST)
    - Re: [AMBER] Are benchmarks/tests on NVidia RTX 2080 Super available? Abhilash J (Thu Feb 27 2020 - 09:42:40 PST)
    - Re: [AMBER] Are benchmarks/tests on NVidia RTX 2080 Super available? Ross Walker (Thu Feb 27 2020 - 09:45:36 PST)
    - Re: [AMBER] Are benchmarks/tests on NVidia RTX 2080 Super available? Abhilash J (Thu Feb 27 2020 - 09:48:41 PST)
- Re: [AMBER] Are benchmarks/tests on NVidia RTX 2080 Super available? Pietro Amodeo (Sat Feb 29 2020 - 12:26:38 PST)
[AMBER] Regarding compatibility of PLUMED with the MPI and CUDA versions of pmemd SATYAJIT KHATUA (Sat Feb 22 2020 - 21:58:43 PST)
[AMBER] vmd progress time Fabian Glaser (Sun Feb 23 2020 - 07:11:53 PST)
- Re: [AMBER] vmd progress time James Kress (Sun Feb 23 2020 - 10:19:33 PST)
  - Re: [AMBER] vmd progress time Fabian Glaser (Tue Feb 25 2020 - 23:50:03 PST)
    - Re: [AMBER] vmd progress time Gustaf Olsson (Wed Feb 26 2020 - 00:59:45 PST)
    - Re: [AMBER] vmd progress time Fabian Glaser (Wed Feb 26 2020 - 01:44:05 PST)
    - Re: [AMBER] vmd progress time Gustaf Olsson (Wed Feb 26 2020 - 02:58:04 PST)
    - Re: [AMBER] vmd progress time Arun Srikanth (Wed Feb 26 2020 - 03:04:10 PST)
    - Re: [AMBER] vmd progress time Fabian Glaser (Wed Feb 26 2020 - 05:52:39 PST)
[AMBER] inquiry regarding minimum-image convention in cpptraj Akshay Prabhakant (Sun Feb 23 2020 - 11:13:03 PST)
- Re: [AMBER] inquiry regarding minimum-image convention in cpptraj Daniel Roe (Mon Feb 24 2020 - 06:39:51 PST)
[AMBER] frcmod.urea Parameters for urea (or urea-water mixtures). Fabian Glaser (Mon Feb 24 2020 - 07:25:41 PST)
[AMBER] Clustering logistics Debarati DasGupta (Mon Feb 24 2020 - 09:27:01 PST)
- Re: [AMBER] Clustering logistics Daniel Roe (Mon Feb 24 2020 - 09:59:02 PST)
[AMBER] make test MPI don't continue Nicolas Feldman (Tue Feb 25 2020 - 05:51:17 PST)
- Re: [AMBER] make test MPI don't continue Gustaf Olsson (Thu Feb 27 2020 - 04:48:26 PST)
  - Re: [AMBER] make test MPI don't continue Gustaf Olsson (Thu Feb 27 2020 - 05:15:40 PST)
[AMBER] Single ion solvation free energy calculations. Akhilesh Paspureddi (Wed Feb 26 2020 - 13:33:30 PST)
- Re: [AMBER] Single ion solvation free energy calculations. Tyler Luchko (Lists) (Thu Feb 27 2020 - 10:07:01 PST)
[AMBER] Weird error with antechamber for metal ion / MCPB tutorial Gustavo Seabra (Wed Feb 26 2020 - 14:01:03 PST)
- Re: [AMBER] Weird error with antechamber for metal ion / MCPB tutorial David A Case (Wed Feb 26 2020 - 18:17:50 PST)
- Re: [AMBER] Weird error with antechamber for metal ion / MCPB tutorial David A Case (Wed Feb 26 2020 - 18:18:50 PST)
  - Re: [AMBER] Weird error with antechamber for metal ion / MCPB tutorial Marcelo Andrade Chagas (Thu Feb 27 2020 - 00:49:37 PST)
    - Re: [AMBER] Weird error with antechamber for metal ion / MCPB tutorial Gustavo Seabra (Thu Feb 27 2020 - 06:10:03 PST)
    - Re: [AMBER] Weird error with antechamber for metal ion / MCPB tutorial Pengfei Li (Fri Mar 27 2020 - 13:57:51 PDT)
    - Re: [AMBER] Weird error with antechamber for metal ion / MCPB tutorial Gustavo Seabra (Fri Mar 27 2020 - 21:31:38 PDT)
    - Re: [AMBER] Weird error with antechamber for metal ion / MCPB tutorial Pengfei Li (Thu Apr 09 2020 - 08:24:20 PDT)
[AMBER] lack scripts for Continuous constant pH molecular dynamics Yingang Feng (Thu Feb 27 2020 - 01:23:04 PST)
[AMBER] MCPB.py with mixed valence di-iron system? Gustavo Seabra (Thu Feb 27 2020 - 14:11:06 PST)
- Re: [AMBER] MCPB.py with mixed valence di-iron system? Marcelo Andrade Chagas (Thu Feb 27 2020 - 17:47:58 PST)
[AMBER] generate ligand frcmod and lib files Madhur Aggarwal (Fri Feb 28 2020 - 03:44:33 PST)
- Re: [AMBER] generate ligand frcmod and lib files Elvis Martis (Fri Feb 28 2020 - 04:07:42 PST)
[AMBER] Tutorial A08 Nicolas Feldman (Fri Feb 28 2020 - 08:23:16 PST)
[AMBER] TI calculations in AMBER18 Debarati DasGupta (Fri Feb 28 2020 - 11:23:45 PST)
[AMBER] G quadruplex simulation Sruthi Sudhakar (Fri Feb 28 2020 - 22:13:16 PST)
- Re: [AMBER] G quadruplex simulation Sruthi Sudhakar (Sat Feb 29 2020 - 02:02:22 PST)
[AMBER] Amber and Domains Conformational Dynamics mario (Sat Feb 29 2020 - 11:00:01 PST)
Re: [AMBER] Issue in drug parameter David A Case (Sun Mar 01 2020 - 05:32:04 PST)
[AMBER] Issue in drug parameter SHAUNAK BADANI (Sun Mar 01 2020 - 10:13:45 PST)
- Re: [AMBER] Issue in drug parameter David A Case (Sun Mar 01 2020 - 14:28:39 PST)
  - Re: [AMBER] Issue in drug parameter Carlos Simmerling (Sun Mar 01 2020 - 14:34:48 PST)
[AMBER] AMBER 18 compilation error with CUDA 10.2 Abhilash J (Sun Mar 01 2020 - 17:08:23 PST)
- Re: [AMBER] AMBER 18 compilation error with CUDA 10.2 Ruxi Qi (Wed Mar 04 2020 - 06:22:27 PST)
[AMBER] g09 genecp in QM/MM MD in amber Vaibhav Dixit (Sun Mar 01 2020 - 19:48:01 PST)
- Re: [AMBER] g09 genecp in QM/MM MD in amber James Kress (Mon Mar 02 2020 - 11:22:30 PST)
  - Re: [AMBER] g09 genecp in QM/MM MD in amber Vaibhav Dixit (Mon Mar 02 2020 - 19:30:11 PST)
[AMBER] problem adding MG.off file Nicolas Feldman (Mon Mar 02 2020 - 04:31:19 PST)
[AMBER] Question of units James Kress (Mon Mar 02 2020 - 14:19:12 PST)
- Re: [AMBER] Question of units David A Case (Mon Mar 02 2020 - 18:36:25 PST)
  - Re: [AMBER] Question of units James Kress (Mon Mar 02 2020 - 18:47:26 PST)
[AMBER] tar-MD with custom J-coupling relation Dieter Buyst (Tue Mar 03 2020 - 05:37:30 PST)
- Re: [AMBER] tar-MD with custom J-coupling relation Christina Bergonzo (Tue Mar 03 2020 - 06:02:34 PST)
[AMBER] CUDA single gpu usage issue Nicholas Moyer (Tue Mar 03 2020 - 06:03:58 PST)
- Re: [AMBER] CUDA single gpu usage issue David A Case (Tue Mar 03 2020 - 07:09:18 PST)
  - Re: [AMBER] CUDA single gpu usage issue Nicholas Moyer (Tue Mar 03 2020 - 10:20:30 PST)
    - Re: [AMBER] CUDA single gpu usage issue Nicholas Moyer (Tue Mar 03 2020 - 10:21:56 PST)
    - Re: [AMBER] CUDA single gpu usage issue Ray Luo (Tue Mar 03 2020 - 10:26:35 PST)
    - Re: [AMBER] CUDA single gpu usage issue Abhilash J (Tue Mar 03 2020 - 13:58:03 PST)
    - Re: [AMBER] CUDA single gpu usage issue Nicholas Moyer (Tue Mar 03 2020 - 14:04:07 PST)
    - Re: [AMBER] CUDA single gpu usage issue Ray Luo (Tue Mar 03 2020 - 19:06:19 PST)
    - Re: [AMBER] CUDA single gpu usage issue Manish Manish (Tue Mar 03 2020 - 21:54:16 PST)
    - Re: [AMBER] CUDA single gpu usage issue Ruxi Qi (Wed Mar 04 2020 - 01:05:57 PST)
    - Re: [AMBER] CUDA single gpu usage issue Ruxi Qi (Wed Mar 04 2020 - 01:22:42 PST)
    - Re: [AMBER] CUDA single gpu usage issue Nicholas Moyer (Wed Mar 04 2020 - 08:24:59 PST)
    - Re: [AMBER] CUDA single gpu usage issue Abhilash J (Wed Mar 04 2020 - 09:32:00 PST)
    - Re: [AMBER] CUDA single gpu usage issue Ray Luo (Wed Mar 04 2020 - 10:03:55 PST)
    - Re: [AMBER] CUDA single gpu usage issue Ray Luo (Thu Mar 05 2020 - 22:33:43 PST)
    - Re: [AMBER] CUDA single gpu usage issue Nicholas Moyer (Fri Mar 06 2020 - 06:15:43 PST)
    - Re: [AMBER] CUDA single gpu usage issue Abhilash J (Fri Mar 06 2020 - 13:48:38 PST)
- Re: [AMBER] CUDA single gpu usage issue Ray Luo (Tue Mar 03 2020 - 10:16:22 PST)
[AMBER] dvdl.dat file details AMBER18 TI Debarati DasGupta (Tue Mar 03 2020 - 07:48:35 PST)
[AMBER] adding Na, K and Cl ions matching intracellular conc Vaibhav Dixit (Wed Mar 04 2020 - 04:49:40 PST)
- Re: [AMBER] adding Na, K and Cl ions matching intracellular conc Matias Machado (Wed Mar 04 2020 - 16:23:01 PST)
  - Re: [AMBER] adding Na, K and Cl ions matching intracellular conc Matias Machado (Wed Mar 04 2020 - 16:24:40 PST)
    - Re: [AMBER] adding Na, K and Cl ions matching intracellular conc Vaibhav Dixit (Wed Mar 04 2020 - 20:19:41 PST)
    - Re: [AMBER] adding Na, K and Cl ions matching intracellular conc Matias Machado (Fri Mar 06 2020 - 07:29:54 PST)
    - Re: [AMBER] adding Na, K and Cl ions matching intracellular conc Matias Machado (Fri Mar 06 2020 - 07:32:57 PST)
    - Re: [AMBER] adding Na, K and Cl ions matching intracellular conc Vaibhav Dixit (Fri Mar 06 2020 - 07:50:09 PST)
[AMBER] KeyError: 'MG' Filipa Mendonça (Wed Mar 04 2020 - 09:00:33 PST)
- Re: [AMBER] KeyError: 'MG' Pengfei Li (Fri Mar 27 2020 - 14:21:21 PDT)
  - Re: [AMBER] KeyError: 'MG' Pengfei Li (Fri Mar 27 2020 - 14:26:40 PDT)
[AMBER] Citing DNA OL15 forcefield Sruthi Sudhakar (Wed Mar 04 2020 - 11:14:40 PST)
- Re: [AMBER] Citing DNA OL15 forcefield Christina Bergonzo (Wed Mar 04 2020 - 11:55:02 PST)
  - Re: [AMBER] Citing DNA OL15 forcefield Sruthi Sudhakar (Thu Mar 05 2020 - 01:00:18 PST)
[AMBER] Are the 6-character atom types of CGenFF compatible with parmed-chamber David Sáez (Wed Mar 04 2020 - 11:33:42 PST)
- Re: [AMBER] Are the 6-character atom types of CGenFF compatible with parmed-chamber David Sáez (Thu Mar 05 2020 - 13:40:46 PST)
  - Re: [AMBER] Are the 6-character atom types of CGenFF compatible with parmed-chamber David Sáez (Thu Mar 05 2020 - 15:58:18 PST)
[AMBER] problem in MCPB.py wujue (Wed Mar 04 2020 - 19:41:49 PST)
- Re: [AMBER] problem in MCPB.py Pengfei Li (Fri Mar 27 2020 - 14:05:29 PDT)
[AMBER] QM/MM Convergence questions 辛志宏 (Thu Mar 05 2020 - 01:07:44 PST)
- Re: [AMBER] QM/MM Convergence questions Busra Demir (Thu Mar 05 2020 - 03:41:27 PST)
- Re: [AMBER] QM/MM Convergence questions 辛志宏 (Thu Mar 05 2020 - 18:22:32 PST)
  - Re: [AMBER] QM/MM Convergence questions David A Case (Fri Mar 06 2020 - 04:51:58 PST)
- Re: [AMBER] QM/MM Convergence questions 辛志宏 (Mon Mar 09 2020 - 02:55:21 PDT)
  - Re: [AMBER] QM/MM Convergence questions Goetz, Andreas (Mon Mar 09 2020 - 12:17:48 PDT)
[AMBER] error job.sh MYRIAN TORRES RICO (Thu Mar 05 2020 - 09:05:40 PST)
- Re: [AMBER] error job.sh Gustaf Olsson (Thu Mar 05 2020 - 09:35:29 PST)
[AMBER] TI production error in nstep =1 Debarati DasGupta (Thu Mar 05 2020 - 13:38:21 PST)
- Re: [AMBER] TI production error in nstep =1 David A Case (Fri Mar 06 2020 - 04:48:17 PST)
  - Re: [AMBER] TI production error in nstep =1 Debarati DasGupta (Fri Mar 06 2020 - 06:46:40 PST)
[AMBER] Modified force fields ankita mehta (Thu Mar 05 2020 - 20:34:37 PST)
- Re: [AMBER] Modified force fields David A Case (Fri Mar 06 2020 - 05:00:25 PST)
  - Re: [AMBER] Modified force fields ankita mehta (Sun Mar 08 2020 - 10:59:09 PDT)
    - Re: [AMBER] Modified force fields Kellon Belfon (Sun Mar 08 2020 - 15:23:08 PDT)
    - Re: [AMBER] Modified force fields ankita mehta (Sun Mar 08 2020 - 20:52:39 PDT)
    - [AMBER] Modified force fields ankita mehta (Mon Mar 09 2020 - 09:40:12 PDT)
    - Re: [AMBER] Modified force fields Carlos Simmerling (Mon Mar 09 2020 - 09:45:00 PDT)
    - Re: [AMBER] Modified force fields ankita mehta (Tue Mar 10 2020 - 10:26:47 PDT)
    - Re: [AMBER] Modified force fields Kellon Belfon (Tue Mar 10 2020 - 10:48:50 PDT)
    - Re: [AMBER] Modified force fields Carlos Simmerling (Tue Mar 10 2020 - 10:53:10 PDT)
    - Re: [AMBER] Modified force fields David A Case (Tue Mar 10 2020 - 11:38:36 PDT)
[AMBER] linear interaction energy tool in AMBER Akshay Prabhakant (Thu Mar 05 2020 - 21:24:01 PST)
- Re: [AMBER] linear interaction energy tool in AMBER Adrian Roitberg (Fri Mar 06 2020 - 08:47:52 PST)
[AMBER] Amber parameters for heme b / d coordinated with deprotonated tyrosine HOCHEOL LIM (Thu Mar 05 2020 - 22:45:31 PST)
[AMBER] When I use fitted parameters as initial parameters in paramfit, I am getting different results? Erdem Yeler (Fri Mar 06 2020 - 04:11:20 PST)
- Re: [AMBER] When I use fitted parameters as initial parameters in paramfit, I am getting different results? David Cerutti (Fri Mar 06 2020 - 11:10:49 PST)
- Re: [AMBER] When I use fitted parameters as initial parameters in paramfit, I am getting different results? Robin Betz (Fri Mar 06 2020 - 13:08:21 PST)
  - Re: [AMBER] When I use fitted parameters as initial parameters in paramfit, I am getting different results? Erdem Yeler (Mon Mar 09 2020 - 02:10:48 PDT)
    - Re: [AMBER] When I use fitted parameters as initial parameters in paramfit, I am getting different results? Erdem Yeler (Mon Mar 09 2020 - 05:34:01 PDT)
    - Re: [AMBER] When I use fitted parameters as initial parameters in paramfit, I am getting different results? David Cerutti (Mon Mar 09 2020 - 10:36:58 PDT)
    - Re: [AMBER] When I use fitted parameters as initial parameters in paramfit, I am getting different results? Erdem Yeler (Thu Mar 12 2020 - 00:33:01 PDT)
[AMBER] Unavailability of the file related to -cprestrt flag in equilibration (NPT) step of constant pH MD in Amber14 with AmberTools15 SATYAJIT KHATUA (Fri Mar 06 2020 - 23:14:32 PST)
[AMBER] Inconsistency in energy values between out files and cpptraj SHAUNAK BADANI (Sat Mar 07 2020 - 03:56:38 PST)
- Re: [AMBER] Inconsistency in energy values between out files and cpptraj Daniel Roe (Tue Mar 10 2020 - 09:07:51 PDT)
[AMBER] 2DRMS before clustering Debarati DasGupta (Sat Mar 07 2020 - 08:46:56 PST)
- Re: [AMBER] 2DRMS before clustering Rodrigo Galindo-Murillo (Sat Mar 07 2020 - 13:10:01 PST)
[AMBER] AmberTools19 install error Raman Preet Singh (Sun Mar 08 2020 - 07:03:00 PDT)
- Re: [AMBER] AmberTools19 install error David A Case (Sun Mar 08 2020 - 09:39:48 PDT)
  - Re: [AMBER] AmberTools19 install error Raman Preet Singh (Sun Mar 08 2020 - 10:59:22 PDT)
    - Re: [AMBER] AmberTools19 install error Gustaf Olsson (Sun Mar 08 2020 - 14:37:42 PDT)
    - Re: [AMBER] AmberTools19 install error Raman Preet Singh (Mon Mar 09 2020 - 05:40:06 PDT)
[AMBER] AMBER19: error in reading namelist cntrl geyushu.ustc.edu.cn (Mon Mar 09 2020 - 03:04:38 PDT)
- Re: [AMBER] AMBER19: error in reading namelist cntrl Gustaf Olsson (Mon Mar 09 2020 - 03:10:58 PDT)
[AMBER] Question about MMPBSA calculation Rinsha Chk (Mon Mar 09 2020 - 03:06:13 PDT)
- Re: [AMBER] Question about MMPBSA calculation Elvis Martis (Mon Mar 09 2020 - 03:41:42 PDT)
  - Re: [AMBER] Question about MMPBSA calculation Rinsha Chk (Mon Mar 09 2020 - 06:31:50 PDT)
[AMBER] QM/MM Convergence questions 辛志宏 (Mon Mar 09 2020 - 20:02:03 PDT)
[AMBER] AmberTools on Ubuntu 19.04: compilation emanuele falbo (Tue Mar 10 2020 - 03:16:28 PDT)
- Re: [AMBER] AmberTools on Ubuntu 19.04: compilation David A Case (Tue Mar 10 2020 - 05:25:52 PDT)
  - Re: [AMBER] AmberTools on Ubuntu 19.04: compilation emanuele falbo (Tue Mar 10 2020 - 08:43:32 PDT)
[AMBER] sieve keyword in cpptraj clustering Debarati DasGupta (Tue Mar 10 2020 - 06:36:59 PDT)
- Re: [AMBER] sieve keyword in cpptraj clustering Daniel Roe (Wed Mar 25 2020 - 12:16:43 PDT)
[AMBER] Incosistency in energy values from out files and cpptraj energy tools SHAUNAK BADANI (Tue Mar 10 2020 - 08:20:02 PDT)
- Re: [AMBER] Incosistency in energy values from out files and cpptraj energy tools Daniel Roe (Tue Mar 10 2020 - 08:54:41 PDT)
[AMBER] Found an invalid periodicity in the prmtop file: ... CalcError: bin/mmpbsa_py_energy failed with prmtop .prmtop! Harold Grosjean (Tue Mar 10 2020 - 10:47:02 PDT)
- Re: [AMBER] Found an invalid periodicity in the prmtop file: ... CalcError: bin/mmpbsa_py_energy failed with prmtop .prmtop! David A Case (Tue Mar 10 2020 - 11:44:31 PDT)
[AMBER] REMD hybrid solvent model Hosein Geraili Daronkola (Tue Mar 10 2020 - 13:09:00 PDT)
- Re: [AMBER] REMD hybrid solvent model koushik kasavajhala (Tue Mar 10 2020 - 13:24:06 PDT)
  - Re: [AMBER] REMD hybrid solvent model Carlos Simmerling (Tue Mar 10 2020 - 19:09:09 PDT)
  - Re: [AMBER] REMD hybrid solvent model Hosein Geraili Daronkola (Wed Mar 11 2020 - 08:35:21 PDT)
    - Re: [AMBER] REMD hybrid solvent model Carlos Simmerling (Wed Mar 11 2020 - 08:39:32 PDT)
    - Re: [AMBER] REMD hybrid solvent model Hosein Geraili Daronkola (Wed Mar 11 2020 - 10:13:35 PDT)
    - Re: [AMBER] REMD hybrid solvent model Carlos Simmerling (Wed Mar 11 2020 - 10:32:33 PDT)
    - Re: [AMBER] REMD hybrid solvent model koushik (Wed Mar 11 2020 - 10:35:51 PDT)
[AMBER] What is the default pH when loading a protein in Amber environment Siavoush Dastmalchi (Wed Mar 11 2020 - 04:20:41 PDT)
- Re: [AMBER] What is the default pH when loading a protein in Amber environment Carlos Simmerling (Wed Mar 11 2020 - 04:48:30 PDT)
[AMBER] DBscan gives me errors in clustering Debarati DasGupta (Wed Mar 11 2020 - 08:40:34 PDT)
- Re: [AMBER] DBscan gives me errors in clustering Daniel Roe (Wed Mar 25 2020 - 12:18:53 PDT)
[AMBER] Reg: MMGBSA for NAMD trajectory Lara rajam (Wed Mar 11 2020 - 10:25:51 PDT)
- Re: [AMBER] Reg: MMGBSA for NAMD trajectory David A Case (Wed Mar 11 2020 - 11:20:43 PDT)
[AMBER] units of the calculated diffusion coefficient Chetna Tyagi (Wed Mar 11 2020 - 10:54:27 PDT)
- Re: [AMBER] units of the calculated diffusion coefficient Daniel Roe (Thu Mar 12 2020 - 10:48:55 PDT)
[AMBER] EXTRACTING A PARTICULAR FRAME Sruthi Sudhakar (Thu Mar 12 2020 - 00:41:28 PDT)
- Re: [AMBER] EXTRACTING A PARTICULAR FRAME Gustaf Olsson (Thu Mar 12 2020 - 01:00:21 PDT)
  - Re: [AMBER] EXTRACTING A PARTICULAR FRAME Sruthi Sudhakar (Thu Mar 12 2020 - 01:12:32 PDT)
    - Re: [AMBER] EXTRACTING A PARTICULAR FRAME Gustaf Olsson (Thu Mar 12 2020 - 02:06:09 PDT)
    - Re: [AMBER] EXTRACTING A PARTICULAR FRAME Sruthi Sudhakar (Thu Mar 12 2020 - 04:14:38 PDT)
- Re: [AMBER] EXTRACTING A PARTICULAR FRAME Daniel Roe (Thu Mar 12 2020 - 10:45:38 PDT)
  - Re: [AMBER] EXTRACTING A PARTICULAR FRAME koushik kasavajhala (Thu Mar 12 2020 - 10:49:12 PDT)
    - Re: [AMBER] EXTRACTING A PARTICULAR FRAME Daniel Roe (Thu Mar 12 2020 - 10:53:29 PDT)
[AMBER] simulations of proteins with 2 domains connected by a linker Vlad Cojocaru (Thu Mar 12 2020 - 02:57:47 PDT)
- Re: [AMBER] simulations of proteins with 2 domains connected by a linker Carlos Simmerling (Thu Mar 12 2020 - 06:58:25 PDT)
  - Re: [AMBER] simulations of proteins with 2 domains connected by a linker Vlad Cojocaru (Thu Mar 12 2020 - 11:03:40 PDT)
    - Re: [AMBER] simulations of proteins with 2 domains connected by a linker Vlad Cojocaru (Thu Apr 16 2020 - 02:35:57 PDT)
[AMBER] Modified AA residue without NH2 end. Petro (Thu Mar 12 2020 - 03:41:16 PDT)
- Re: [AMBER] Modified AA residue without NH2 end. Carlos Simmerling (Thu Mar 12 2020 - 03:51:55 PDT)
[AMBER] What's the least biased way to stop a molecule from crossing a periodic boundary? Homeo Morphism (Thu Mar 12 2020 - 04:16:23 PDT)
- Re: [AMBER] What's the least biased way to stop a molecule from crossing a periodic boundary? Carlos Simmerling (Thu Mar 12 2020 - 04:21:40 PDT)
  - Re: [AMBER] What's the least biased way to stop a molecule from crossing a periodic boundary? Carlos Simmerling (Thu Mar 12 2020 - 04:48:44 PDT)
[AMBER] unusual planarity change during md. Sruthi Sudhakar (Thu Mar 12 2020 - 08:25:40 PDT)
- Re: [AMBER] unusual planarity change during md. Adrian Roitberg (Thu Mar 12 2020 - 08:38:14 PDT)
[AMBER] mmpbsa_py_energy failed with prmtop dim_gas.prmtop Azahara.Doncel.uv.es (Thu Mar 12 2020 - 08:58:17 PDT)
[AMBER] problems implementing tiMerge for base pair mutation Gabriel Jara (Thu Mar 12 2020 - 10:18:00 PDT)
Re: [AMBER] AMBER Digest, Vol 2934, Issue 1 SATYAJIT KHATUA (Thu Mar 12 2020 - 12:51:53 PDT)
[AMBER] AmberTools19 serial installation test errors Mariana Simoes Ferreira (Thu Mar 12 2020 - 12:57:39 PDT)
- Re: [AMBER] AmberTools19 serial installation test errors Gustaf Olsson (Fri Mar 13 2020 - 01:52:28 PDT)
[AMBER] TI runs on GPU Debarati DasGupta (Thu Mar 12 2020 - 13:48:29 PDT)
- Re: [AMBER] TI runs on GPU David A Case (Fri Mar 13 2020 - 04:24:39 PDT)
  - Re: [AMBER] TI runs on GPU Debarati DasGupta (Sun Mar 15 2020 - 06:56:06 PDT)
[AMBER] Questions on force field Sasthi Mandal (Fri Mar 13 2020 - 00:03:28 PDT)
- Re: [AMBER] Questions on force field David A Case (Fri Mar 13 2020 - 04:28:59 PDT)
[AMBER] Not recognising output file for N_OF_BONDS reaction coordinate Vishal Reddy (Fri Mar 13 2020 - 12:07:31 PDT)
[AMBER] information regarding space filling visualization Prasanth G, Research Scholar (Sat Mar 14 2020 - 02:18:55 PDT)
- Re: [AMBER] information regarding space filling visualization Elvis Martis (Sat Mar 14 2020 - 02:49:08 PDT)
- Re: [AMBER] information regarding space filling visualization Carlos Simmerling (Sat Mar 14 2020 - 02:50:36 PDT)
  - Re: [AMBER] information regarding space filling visualization Ahmed Elrashedy (Sat Mar 14 2020 - 06:04:43 PDT)
[AMBER] Lone Pairs in AMBER FF 杨明俊 (Sat Mar 14 2020 - 07:35:18 PDT)
- Re: [AMBER] Lone Pairs in AMBER FF Carlos Simmerling (Sat Mar 14 2020 - 08:18:40 PDT)
  - Re: [AMBER] Lone Pairs in AMBER FF 杨明俊 (Sat Mar 14 2020 - 20:06:23 PDT)
    - Re: [AMBER] Lone Pairs in AMBER FF David A Case (Sun Mar 15 2020 - 06:03:55 PDT)
    - Re: [AMBER] Lone Pairs in AMBER FF 杨明俊 (Thu Mar 19 2020 - 03:57:52 PDT)
[AMBER] Boron compunds with "pdb" file with novel frcmod file Erdem Yeler (Sat Mar 14 2020 - 13:43:33 PDT)
- Re: [AMBER] Boron compunds with "pdb" file with novel frcmod file David A Case (Sun Mar 15 2020 - 09:41:26 PDT)
  - Re: [AMBER] Boron compunds with "pdb" file with novel frcmod file Erdem Yeler (Tue Mar 17 2020 - 05:56:31 PDT)
[AMBER] GAFF/AMBER peptide bond Petro (Sat Mar 14 2020 - 14:21:40 PDT)
- Re: [AMBER] GAFF/AMBER peptide bond Song, Lin (Sat Mar 14 2020 - 14:33:03 PDT)
  - Re: [AMBER] GAFF/AMBER peptide bond Petro (Sat Mar 14 2020 - 14:43:35 PDT)
    - Re: [AMBER] GAFF/AMBER peptide bond Song, Lin (Sat Mar 14 2020 - 14:56:15 PDT)
    - Re: [AMBER] GAFF/AMBER peptide bond Petro (Sat Mar 14 2020 - 15:16:45 PDT)
- Re: [AMBER] GAFF/AMBER peptide bond Carlos Simmerling (Sat Mar 14 2020 - 15:06:51 PDT)
[AMBER] how to turned off C N terminal amino in tleap Yeng-Tseng Wang (Sun Mar 15 2020 - 00:21:06 PDT)
- Re: [AMBER] how to turned off C N terminal amino in tleap Petro (Sun Mar 15 2020 - 02:51:19 PDT)
[AMBER] About the D form amino amber force field Yeng-Tseng Wang (Sun Mar 15 2020 - 01:53:07 PDT)
- Re: [AMBER] About the D form amino amber force field Carlos Simmerling (Sun Mar 15 2020 - 03:42:44 PDT)
  - Re: [AMBER] About the D form amino amber force field Yeng-Tseng Wang (Sun Mar 15 2020 - 07:30:20 PDT)
[AMBER] CUDA version for AMBER 16 and 20? Michael Shokhen (Sun Mar 15 2020 - 10:56:00 PDT)
[AMBER] Texas red force field Tiejun Wei (Mon Mar 16 2020 - 08:27:20 PDT)
[AMBER] If a non-standard force field is used for proteins, how would you approach parameterization of lipids and ligands? Homeo Morphism (Tue Mar 17 2020 - 01:24:28 PDT)
- Re: [AMBER] If a non-standard force field is used for proteins, how would you approach parameterization of lipids and ligands? Carlos Simmerling (Tue Mar 17 2020 - 03:18:53 PDT)
[AMBER] issue while installing AMBER tools on windows10 Linux subsystem Ana Ziad (Tue Mar 17 2020 - 14:35:54 PDT)
- Re: [AMBER] issue while installing AMBER tools on windows10 Linux subsystem Gustaf Olsson (Wed Mar 18 2020 - 14:03:04 PDT)
- Re: [AMBER] issue while installing AMBER tools on windows10 Linux subsystem Ana Ziad (Fri Mar 20 2020 - 09:20:00 PDT)
  - Re: [AMBER] issue while installing AMBER tools on windows10 Linux subsystem David A Case (Fri Mar 20 2020 - 10:09:23 PDT)
  - Re: [AMBER] issue while installing AMBER tools on windows10 Linux subsystem Ana Ziad (Fri Mar 20 2020 - 10:29:33 PDT)
    - Re: [AMBER] issue while installing AMBER tools on windows10 Linux subsystem Gustaf Olsson (Fri Mar 20 2020 - 15:49:39 PDT)
    - Re: [AMBER] issue while installing AMBER tools on windows10 Linux subsystem Ana Ziad (Sat Mar 21 2020 - 08:50:07 PDT)
[AMBER] A problem of "Could not import Amber Python modules" 唐元晖 (Tue Mar 17 2020 - 23:48:43 PDT)
- Re: [AMBER] A problem of "Could not import Amber Python modules" 唐元晖 (Wed Mar 18 2020 - 05:45:34 PDT)
- Re: [AMBER] A problem of "Could not import Amber Python modules" David A Case (Wed Mar 18 2020 - 05:51:21 PDT)
[AMBER] Clustering analysis Debarati DasGupta (Wed Mar 18 2020 - 15:33:59 PDT)
- Re: [AMBER] Clustering analysis Daniel Roe (Wed Mar 25 2020 - 12:27:27 PDT)
  - Re: [AMBER] Clustering analysis Debarati DasGupta (Wed Apr 15 2020 - 07:38:37 PDT)
[AMBER] Ambmask Error in group input::atommask.f::pop_evalstack stack underflow Oliver Grant (Fri Mar 20 2020 - 02:35:20 PDT)
- Re: [AMBER] Ambmask Error in group input::atommask.f::pop_evalstack stack underflow Daniel Roe (Wed Mar 25 2020 - 12:30:44 PDT)
[AMBER] about TREE_CHAIN_CLASSIFICATION Thomas Gaillard (Fri Mar 20 2020 - 05:16:40 PDT)
- Re: [AMBER] about TREE_CHAIN_CLASSIFICATION David A Case (Fri Mar 20 2020 - 06:11:51 PDT)
[AMBER] setting pdb file Nicolas Feldman (Fri Mar 20 2020 - 11:49:46 PDT)
- Re: [AMBER] setting pdb file Daniel Roe (Fri Mar 20 2020 - 12:29:27 PDT)
  - Re: [AMBER] setting pdb file Nicolas Feldman (Fri Mar 20 2020 - 12:41:57 PDT)
  - Re: [AMBER] setting pdb file Carlos Simmerling (Fri Mar 20 2020 - 12:55:57 PDT)
    - Re: [AMBER] setting pdb file Nicolas Feldman (Fri Mar 20 2020 - 13:01:15 PDT)
    - Re: [AMBER] setting pdb file Gustaf Olsson (Fri Mar 20 2020 - 15:31:17 PDT)
    - Re: [AMBER] setting pdb file Nicolas Feldman (Fri Mar 20 2020 - 15:44:02 PDT)
    - Re: [AMBER] setting pdb file Gustaf Olsson (Fri Mar 20 2020 - 15:52:25 PDT)
    - Re: [AMBER] setting pdb file Nicolas Feldman (Fri Mar 20 2020 - 15:57:24 PDT)
    - Re: [AMBER] setting pdb file Carlos Simmerling (Fri Mar 20 2020 - 16:55:37 PDT)
    - Re: [AMBER] setting pdb file Nicolas Feldman (Sat Mar 21 2020 - 10:03:59 PDT)
[AMBER] "Error of reading the .dat file" in MCPB.py step 2 Gustavo Seabra (Fri Mar 20 2020 - 14:42:18 PDT)
- Re: [AMBER] "Error of reading the .dat file" in MCPB.py step 2 Pengfei Li (Fri Mar 27 2020 - 15:14:19 PDT)
[AMBER] RTX 2020 Super GPU Random Memorry Errors Giorgos Lambrinidis (Sat Mar 21 2020 - 12:36:07 PDT)
[AMBER] RTX 2020 Super GPU Random Memory Errors Giorgos Lambrinidis (Sat Mar 21 2020 - 12:43:43 PDT)
- Re: [AMBER] RTX 2020 Super GPU Random Memory Errors David Cerutti (Sat Mar 21 2020 - 15:54:50 PDT)
- Re: [AMBER] RTX 2020 Super GPU Random Memory Errors Stephan Schott (Sat Mar 21 2020 - 16:44:27 PDT)
  - Re: [AMBER] RTX 2020 Super GPU Random Memory Errors Giorgos Lambrinidis (Sun Mar 22 2020 - 02:56:10 PDT)
    - Re: [AMBER] RTX 2020 Super GPU Random Memory Errors Giorgos Lambrinidis (Wed Apr 01 2020 - 00:21:50 PDT)
    - Re: [AMBER] RTX 2020 Super GPU Random Memory Errors Dow Hurst (Mon Apr 20 2020 - 10:30:53 PDT)
[AMBER] Clustering query Debarati DasGupta (Sun Mar 22 2020 - 10:37:06 PDT)
- Re: [AMBER] Clustering query Elvis Martis (Sun Mar 22 2020 - 11:14:19 PDT)
[AMBER] questions about paramfit and frcmod file ttz (Sun Mar 22 2020 - 15:11:30 PDT)
- Re: [AMBER] questions about paramfit and frcmod file David Cerutti (Sun Mar 22 2020 - 23:36:44 PDT)
- Re: [AMBER] questions about paramfit and frcmod file ttz (Mon Mar 23 2020 - 21:00:34 PDT)
[AMBER] Installation problem for a parallel version of Amber18/AmberTools19 Kosuke Tachibana (Sun Mar 22 2020 - 21:02:09 PDT)
- Re: [AMBER] Installation problem for a parallel version of Amber18/AmberTools19 David A Case (Mon Mar 23 2020 - 06:38:48 PDT)
- Re: [AMBER] Installation problem for a parallel version of Amber18/AmberTools19 Kosuke Tachibana (Tue Mar 24 2020 - 08:57:37 PDT)
  - Re: [AMBER] Installation problem for a parallel version of Amber18/AmberTools19 Gustaf Olsson (Tue Mar 24 2020 - 23:46:19 PDT)
    - Re: [AMBER] Installation problem for a parallel version of Amber18/AmberTools19 Kosuke Tachibana (Wed Mar 25 2020 - 04:26:47 PDT)
- Re: [AMBER] Installation problem for a parallel version of Amber18/AmberTools19 Kosuke Tachibana (Wed Mar 25 2020 - 02:57:54 PDT)
[AMBER] ** NFE-Error ** : Cannot read &colvar namelist! Vishal Reddy (Mon Mar 23 2020 - 05:56:37 PDT)
- Re: [AMBER] ** NFE-Error ** : Cannot read &colvar namelist! Feng Pan (Mon Mar 23 2020 - 12:18:32 PDT)
[AMBER] GPU support information Serena Vittorio (Tue Mar 24 2020 - 03:12:26 PDT)
[AMBER] cross angle analysis Antonio Amber Carlesso (Tue Mar 24 2020 - 05:56:28 PDT)
- Re: [AMBER] cross angle analysis Daniel Roe (Wed Mar 25 2020 - 12:39:23 PDT)
[AMBER] MM-PB(GB)/SA error message Antonio Amber Carlesso (Tue Mar 24 2020 - 07:41:12 PDT)
[AMBER] tleap for Mg2+ data type Sunita Patel (Wed Mar 25 2020 - 07:15:44 PDT)
- Re: [AMBER] tleap for Mg2+ data type Stephan Schott (Wed Mar 25 2020 - 07:36:52 PDT)
  - Re: [AMBER] tleap for Mg2+ data type Sunita Patel (Wed Mar 25 2020 - 17:32:05 PDT)
    - Re: [AMBER] tleap for Mg2+ data type David A Case (Wed Mar 25 2020 - 19:09:01 PDT)
    - Re: [AMBER] tleap for Mg2+ data type Sunita Patel (Thu Mar 26 2020 - 20:19:21 PDT)
    - Re: [AMBER] tleap for Mg2+ data type Sunita Patel (Thu Mar 26 2020 - 20:26:25 PDT)
- Re: [AMBER] tleap for Mg2+ data type Pengfei Li (Thu Apr 09 2020 - 09:19:19 PDT)
  - Re: [AMBER] tleap for Mg2+ data type Sunita Patel (Thu Apr 09 2020 - 19:39:05 PDT)
[AMBER] Writing Trajectories as netcdf files Hunter Wilson (Wed Mar 25 2020 - 10:11:08 PDT)
- Re: [AMBER] Writing Trajectories as netcdf files emanuele falbo (Wed Mar 25 2020 - 10:16:46 PDT)
  - Re: [AMBER] Writing Trajectories as netcdf files Hunter Wilson (Wed Mar 25 2020 - 12:19:46 PDT)
- Re: [AMBER] Writing Trajectories as netcdf files Stephan Schott (Wed Mar 25 2020 - 10:22:26 PDT)
[AMBER] parameterization with crystal water Hira Jabeen (Wed Mar 25 2020 - 10:53:52 PDT)
- Re: [AMBER] parameterization with crystal water David A Case (Wed Mar 25 2020 - 18:41:55 PDT)
[AMBER] nastruct and modified base pairs Kenneth Huang (Wed Mar 25 2020 - 11:47:01 PDT)
- Re: [AMBER] nastruct and modified base pairs Daniel Roe (Wed Mar 25 2020 - 12:42:00 PDT)
  - Re: [AMBER] nastruct and modified base pairs Kenneth Huang (Wed Mar 25 2020 - 14:10:44 PDT)
    - Re: [AMBER] nastruct and modified base pairs Daniel Roe (Thu Mar 26 2020 - 12:30:55 PDT)
    - Re: [AMBER] nastruct and modified base pairs Kenneth Huang (Thu Mar 26 2020 - 17:47:02 PDT)
    - Re: [AMBER] nastruct and modified base pairs Daniel Roe (Fri Mar 27 2020 - 06:00:00 PDT)
[AMBER] FATAL Error: Atom does not have a type (Cation) Yoanes Vianney (Wed Mar 25 2020 - 13:28:33 PDT)
- Re: [AMBER] FATAL Error: Atom does not have a type (Cation) Thomas Cheatham (Wed Mar 25 2020 - 14:09:54 PDT)
  - Re: [AMBER] FATAL Error: Atom does not have a type (Cation) Yoanes Vianney (Wed Mar 25 2020 - 14:56:43 PDT)
    - Re: [AMBER] FATAL Error: Atom does not have a type (Cation) David A Case (Wed Mar 25 2020 - 19:01:11 PDT)
  - Re: [AMBER] FATAL Error: Atom does not have a type (Cation) David A Case (Wed Mar 25 2020 - 18:51:25 PDT)
[AMBER] SImulation prepared using CHARMM GUI terminates with no error at the NTP step Lenka (Wed Mar 25 2020 - 16:16:37 PDT)
- Re: [AMBER] SImulation prepared using CHARMM GUI terminates with no error at the NTP step Gustaf Olsson (Wed Mar 25 2020 - 23:58:56 PDT)
[AMBER] residue library for na_link AmberTools19 Gül Zerze (Wed Mar 25 2020 - 18:38:27 PDT)
- Re: [AMBER] residue library for na_link AmberTools19 David A Case (Thu Mar 26 2020 - 05:10:41 PDT)
  - Re: [AMBER] residue library for na_link AmberTools19 Gül Zerze (Thu Mar 26 2020 - 10:33:34 PDT)
[AMBER] Problems with Nvidia Drivers Andrea H. Kasun (Thu Mar 26 2020 - 10:25:16 PDT)
- Re: [AMBER] Problems with Nvidia Drivers Ross Walker (Thu Mar 26 2020 - 12:49:14 PDT)
  - Re: [AMBER] Problems with Nvidia Drivers Andrea H. Kasun (Sat Mar 28 2020 - 03:21:02 PDT)
    - Re: [AMBER] Problems with Nvidia Drivers Ross Walker (Sat Mar 28 2020 - 07:32:07 PDT)
    - Re: [AMBER] Problems with Nvidia Drivers Andrea H. Kasun (Sun Mar 29 2020 - 04:14:24 PDT)
[AMBER] How to setup a QM/MM calculation in Amber Sadaf Rani (Fri Mar 27 2020 - 02:36:32 PDT)
- Re: [AMBER] How to setup a QM/MM calculation in Amber James Kress (Fri Mar 27 2020 - 11:57:17 PDT)
  - Re: [AMBER] How to setup a QM/MM calculation in Amber Sadaf Rani (Fri Mar 27 2020 - 16:39:12 PDT)
    - Re: [AMBER] How to setup a QM/MM calculation in Amber Goetz, Andreas (Fri Mar 27 2020 - 17:23:32 PDT)
    - Re: [AMBER] How to setup a QM/MM calculation in Amber Sadaf Rani (Fri Mar 27 2020 - 17:55:11 PDT)
[AMBER] mmpbsa_py_energy failed with prmtop dim_gas.prmtop Azahara.Doncel.uv.es (Fri Mar 27 2020 - 09:11:29 PDT)
- Re: [AMBER] mmpbsa_py_energy failed with prmtop dim_gas.prmtop Ray Luo (Fri Mar 27 2020 - 09:35:16 PDT)
[AMBER] Simulations Without Network Garcia, Mauro (Fri Mar 27 2020 - 09:34:57 PDT)
- Re: [AMBER] Simulations Without Network David Cerutti (Fri Mar 27 2020 - 09:56:55 PDT)
  - Re: [AMBER] Simulations Without Network Gustaf Olsson (Fri Mar 27 2020 - 13:21:09 PDT)
    - Re: [AMBER] Simulations Without Network Garcia, Mauro (Fri Mar 27 2020 - 15:31:29 PDT)
[AMBER] AmberTools19 update.8 fails to install mark.bergman.uphs.upenn.edu (Fri Mar 27 2020 - 14:49:04 PDT)
- Re: [AMBER] AmberTools19 update.8 fails to install David A Case (Sat Mar 28 2020 - 08:21:49 PDT)
[AMBER] Error while amber installation ankita mehta (Sat Mar 28 2020 - 10:12:56 PDT)
- Re: [AMBER] Error while amber installation David A Case (Sat Mar 28 2020 - 16:47:06 PDT)
  - Re: [AMBER] Error while amber installation mirzo (Sat Mar 28 2020 - 21:57:58 PDT)
  - Re: [AMBER] Error while amber installation ankita mehta (Sat Mar 28 2020 - 23:26:38 PDT)
[AMBER] NPT equilibration is crashing Sunita Patel (Sat Mar 28 2020 - 21:11:36 PDT)
- Re: [AMBER] NPT equilibration is crashing David Sáez (Sat Mar 28 2020 - 22:01:24 PDT)
  - Re: [AMBER] NPT equilibration is crashing Carlos Simmerling (Sun Mar 29 2020 - 03:19:23 PDT)
  - Re: [AMBER] NPT equilibration is crashing Sunita Patel (Sun Mar 29 2020 - 03:37:43 PDT)
- Re: [AMBER] NPT equilibration is crashing David Sáez (Sun Mar 29 2020 - 23:52:27 PDT)
  - Re: [AMBER] NPT equilibration is crashing Sunita Patel (Wed Apr 01 2020 - 05:45:40 PDT)
    - Re: [AMBER] NPT equilibration is crashing Carlos Simmerling (Wed Apr 01 2020 - 06:14:04 PDT)
    - Re: [AMBER] NPT equilibration is crashing David Sáez (Wed Apr 01 2020 - 06:44:25 PDT)
    - Re: [AMBER] NPT equilibration is crashing Sunita Patel (Wed Apr 01 2020 - 09:41:43 PDT)
    - Re: [AMBER] NPT equilibration is crashing Carlos Simmerling (Wed Apr 01 2020 - 10:01:49 PDT)
    - Re: [AMBER] NPT equilibration is crashing Sunita Patel (Fri Apr 03 2020 - 18:23:34 PDT)
    - Re: [AMBER] NPT equilibration is crashing David Sáez (Fri Apr 03 2020 - 18:56:44 PDT)
    - Re: [AMBER] NPT equilibration is crashing Sunita Patel (Sat Apr 04 2020 - 11:22:13 PDT)
    - Re: [AMBER] NPT equilibration is crashing Carlos Simmerling (Sat Apr 04 2020 - 11:30:29 PDT)
    - Re: [AMBER] NPT equilibration is crashing Sunita Patel (Sat Apr 04 2020 - 19:53:31 PDT)
    - Re: [AMBER] NPT equilibration is crashing Carlos Simmerling (Sun Apr 05 2020 - 04:41:13 PDT)
[AMBER] ff19SB + BSC1 + OPC + which ions ? Vlad Cojocaru (Sun Mar 29 2020 - 05:36:41 PDT)
- Re: [AMBER] ff19SB + BSC1 + OPC + which ions ? David A Case (Sun Mar 29 2020 - 07:36:29 PDT)
  - Re: [AMBER] ff19SB + BSC1 + OPC + which ions ? Vlad Cojocaru (Sun Mar 29 2020 - 08:27:36 PDT)
    - Re: [AMBER] ff19SB + BSC1 + OPC + which ions ? Christina Bergonzo (Sun Mar 29 2020 - 14:28:35 PDT)
[AMBER] Error: Could not find angle parameter Rosellen, Martin (Sun Mar 29 2020 - 05:41:59 PDT)
- Re: [AMBER] Error: Could not find angle parameter David A Case (Sun Mar 29 2020 - 07:41:39 PDT)
- Re: [AMBER] Error: Could not find angle parameter Rosellen, Martin (Fri Apr 03 2020 - 01:04:51 PDT)
[AMBER] checkstructure with cpptraj Nicolas Feldman (Sun Mar 29 2020 - 08:26:34 PDT)
- Re: [AMBER] checkstructure with cpptraj Gustaf Olsson (Sun Mar 29 2020 - 12:47:08 PDT)
  - Re: [AMBER] checkstructure with cpptraj Nicolas Feldman (Sun Mar 29 2020 - 16:18:02 PDT)
    - Re: [AMBER] checkstructure with cpptraj David Sáez (Tue Mar 31 2020 - 12:55:49 PDT)
    - Re: [AMBER] checkstructure with cpptraj Nicolas Feldman (Tue Mar 31 2020 - 13:00:19 PDT)
- Re: [AMBER] checkstructure with cpptraj Daniel Roe (Tue Mar 31 2020 - 10:31:51 PDT)
  - Re: [AMBER] checkstructure with cpptraj Nicolas Feldman (Tue Mar 31 2020 - 11:08:08 PDT)
    - Re: [AMBER] checkstructure with cpptraj Ahmed Elrashedy (Tue Mar 31 2020 - 11:29:41 PDT)
    - Re: [AMBER] checkstructure with cpptraj Nicolas Feldman (Tue Mar 31 2020 - 12:58:17 PDT)
[AMBER] PDB Modification ankita mehta (Mon Mar 30 2020 - 06:43:50 PDT)
- Re: [AMBER] PDB Modification Osman, Roman (Mon Mar 30 2020 - 08:30:39 PDT)
  - Re: [AMBER] PDB Modification ankita mehta (Mon Mar 30 2020 - 08:55:23 PDT)
    - Re: [AMBER] PDB Modification Osman, Roman (Mon Mar 30 2020 - 09:08:00 PDT)
[AMBER] Abasic Site and Leap Polymerization Robert Molt (Mon Mar 30 2020 - 07:35:44 PDT)
- Re: [AMBER] Abasic Site and Leap Polymerization Christina Bergonzo (Mon Mar 30 2020 - 08:07:58 PDT)
  - Re: [AMBER] Abasic Site and Leap Polymerization Robert Molt (Mon Mar 30 2020 - 10:08:06 PDT)
    - Re: [AMBER] Abasic Site and Leap Polymerization Carlos Simmerling (Mon Mar 30 2020 - 10:14:03 PDT)
    - Re: [AMBER] Abasic Site and Leap Polymerization Christina Bergonzo (Mon Mar 30 2020 - 11:21:43 PDT)
    - Re: [AMBER] Abasic Site and Leap Polymerization Robert Molt (Sat Apr 04 2020 - 08:56:33 PDT)
    - Re: [AMBER] Abasic Site and Leap Polymerization Christina Bergonzo (Sat Apr 04 2020 - 09:42:11 PDT)
    - Re: [AMBER] Abasic Site and Leap Polymerization Robert Molt (Sat Apr 04 2020 - 13:01:13 PDT)
    - Re: [AMBER] Abasic Site and Leap Polymerization Christina Bergonzo (Sat Apr 04 2020 - 14:37:10 PDT)
    - Re: [AMBER] Abasic Site and Leap Polymerization Robert Molt (Sun Apr 05 2020 - 10:22:40 PDT)
    - Re: [AMBER] Abasic Site and Leap Polymerization Christina Bergonzo (Sun Apr 05 2020 - 12:43:27 PDT)
[AMBER] Differences in Lennard-Jones interactions in CPU vs GPU pmemd? Hanne Antila (Mon Mar 30 2020 - 09:26:43 PDT)
- Re: [AMBER] Differences in Lennard-Jones interactions in CPU vs GPU pmemd? David A Case (Sun Apr 05 2020 - 10:15:15 PDT)
[AMBER] MPI+threads in Amber Rohit Zambre (Mon Mar 30 2020 - 10:01:21 PDT)
- Re: [AMBER] MPI+threads in Amber Daniel Roe (Tue Mar 31 2020 - 10:35:49 PDT)
[AMBER] Amber restart simulation SUNITA MUDULI (Tue Mar 31 2020 - 04:55:33 PDT)
- Re: [AMBER] Amber restart simulation Carlos Simmerling (Tue Mar 31 2020 - 04:57:19 PDT)
[AMBER] sum of charges from parm file Lenka (Tue Mar 31 2020 - 15:27:36 PDT)
- Re: [AMBER] sum of charges from parm file Clorice Reinhardt (Tue Mar 31 2020 - 15:40:38 PDT)
- Re: [AMBER] sum of charges from parm file Lenka (Tue Mar 31 2020 - 15:47:47 PDT)
  - Re: [AMBER] sum of charges from parm file Pengfei Li (Thu Apr 09 2020 - 09:12:11 PDT)
[AMBER] Remove restraint mohamed marzouk (Wed Apr 01 2020 - 05:50:33 PDT)
- Re: [AMBER] Remove restraint Ahmed Elrashedy (Wed Apr 01 2020 - 05:57:23 PDT)
- Re: [AMBER] Remove restraint David A Case (Wed Apr 01 2020 - 07:02:20 PDT)
[AMBER] Running Steered MD Simulations using GPU Souvik Dey (Wed Apr 01 2020 - 08:48:18 PDT)
- Re: [AMBER] Running Steered MD Simulations using GPU Gerardo Zerbetto De Palma (Wed Apr 01 2020 - 08:51:51 PDT)
[AMBER] Problem in configuring Sapna Shedge (Wed Apr 01 2020 - 21:34:48 PDT)
- Re: [AMBER] Problem in configuring David A Case (Thu Apr 02 2020 - 04:50:43 PDT)
Re: [AMBER] [External] Re: AmberTools19 update.8 fails to install mark.bergman.uphs.upenn.edu (Thu Apr 02 2020 - 08:29:23 PDT)
[AMBER] AMBER 18 cuda installation: error: redefinition of ‘simulationConst cSim’ Sapna Shedge (Thu Apr 02 2020 - 10:58:23 PDT)
- Re: [AMBER] AMBER 18 cuda installation: error: redefinition of ???simulationConst cSim??? Scott Brozell (Sat Apr 04 2020 - 18:09:42 PDT)
  - Re: [AMBER] AMBER 18 cuda installation: error: redefinition of ???simulationConst cSim??? David Cerutti (Sat Apr 04 2020 - 20:54:23 PDT)
[AMBER] pyramidal amide nitrogen Arnaud Bondon (Thu Apr 02 2020 - 11:17:38 PDT)
[AMBER] cellulose chain Pinky Mazumder (Thu Apr 02 2020 - 12:09:59 PDT)
- Re: [AMBER] cellulose chain David A Case (Sun Apr 05 2020 - 10:20:28 PDT)
  - Re: [AMBER] cellulose chain Raman Preet Singh (Sun Apr 05 2020 - 10:30:40 PDT)
  - Re: [AMBER] cellulose chain Pinky Mazumder (Fri May 15 2020 - 10:00:57 PDT)
    - Re: [AMBER] cellulose chain Lachele Foley (Fri May 15 2020 - 20:09:26 PDT)
    - Re: [AMBER] cellulose chain Pinky Mazumder (Fri May 15 2020 - 20:51:30 PDT)
    - Re: [AMBER] cellulose chain Pinky Mazumder (Fri May 15 2020 - 20:53:27 PDT)
    - Re: [AMBER] cellulose chain Lachele Foley (Sat May 16 2020 - 02:33:03 PDT)
    - Re: [AMBER] cellulose chain Pinky Mazumder (Fri May 29 2020 - 07:46:58 PDT)
    - Re: [AMBER] cellulose chain David A Case (Fri May 29 2020 - 09:32:06 PDT)
[AMBER] Incorrect results when running MMPBSA example. Shum, Ho Hin (Thu Apr 02 2020 - 21:48:38 PDT)
[AMBER] Amber force field for SDS and DPC detergents Ricky Nencini (Fri Apr 03 2020 - 03:17:27 PDT)
- Re: [AMBER] Amber force field for SDS and DPC detergents ABEL Stephane (Fri Apr 03 2020 - 03:25:33 PDT)
  - Re: [AMBER] Amber force field for SDS and DPC detergents Ricky Nencini (Fri Apr 03 2020 - 10:06:29 PDT)
[AMBER] nmode entropy calculations gets stuck way too often Liao (Fri Apr 03 2020 - 16:42:58 PDT)
- Re: [AMBER] nmode entropy calculations gets stuck way too often Roitberg,Adrian E (Fri Apr 03 2020 - 16:55:14 PDT)
  - Re: [AMBER] nmode entropy calculations gets stuck way too often Liao (Fri Apr 03 2020 - 18:44:22 PDT)
- Re: [AMBER] nmode entropy calculations gets stuck way too often David A Case (Sat Apr 04 2020 - 10:30:24 PDT)
  - Re: [AMBER] nmode entropy calculations gets stuck way too often Liao (Sat Apr 04 2020 - 12:26:25 PDT)
    - Re: [AMBER] nmode entropy calculations gets stuck way too often Liao (Sat Apr 11 2020 - 21:30:57 PDT)
Re: [AMBER] Contents of Amber Digest Pinky Mazumder (Sat Apr 04 2020 - 01:14:02 PDT)
[AMBER] ff_amber_to_viparr.py Error iraklis litinas (Sat Apr 04 2020 - 02:04:58 PDT)
- Re: [AMBER] ff_amber_to_viparr.py Error David A Case (Sat Apr 04 2020 - 10:22:49 PDT)
[AMBER] 12-6-4LJ for thermodynamic integration on PMEMD engine Paulius Kantakevicius (Sat Apr 04 2020 - 12:01:13 PDT)
- Re: [AMBER] 12-6-4LJ for thermodynamic integration on PMEMD engine Pengfei Li (Thu Apr 09 2020 - 08:22:55 PDT)
- Re: [AMBER] 12-6-4LJ for thermodynamic integration on PMEMD engine Song, Lin (Thu Apr 09 2020 - 08:34:22 PDT)
[AMBER] Sequence command to build the 4 - O glucuronuxylans chain Pinky Mazumder (Sat Apr 04 2020 - 19:26:03 PDT)
- Re: [AMBER] Sequence command to build the 4 - O glucuronuxylans chain Karl Kirschner (Sun Apr 05 2020 - 01:17:37 PDT)
  - Re: [AMBER] Sequence command to build the 4 - O glucuronuxylans chain Pinky Mazumder (Sun Apr 05 2020 - 15:46:10 PDT)
- Re: [AMBER] Sequence command to build the 4 - O glucuronuxylans chain Hector A. Baldoni (Sun Apr 05 2020 - 11:52:44 PDT)
  - Re: [AMBER] Sequence command to build the 4 - O glucuronuxylans chain Pinky Mazumder (Sun Apr 05 2020 - 15:00:22 PDT)
[AMBER] Help for the sequence of residue name Pinky Mazumder (Sun Apr 05 2020 - 00:09:15 PDT)
[AMBER] PrmtopError: Inconsistent charge definition for atom DHEERAJ CHITARA (Sun Apr 05 2020 - 10:20:23 PDT)
- Re: [AMBER] PrmtopError: Inconsistent charge definition for atom David A Case (Sun Apr 05 2020 - 18:06:14 PDT)
[AMBER] Installation of ambertools on 32 bit linux system Prasanth G, Research Scholar (Sun Apr 05 2020 - 22:12:12 PDT)
- Re: [AMBER] Installation of ambertools on 32 bit linux system David A Case (Mon Apr 06 2020 - 05:00:59 PDT)
[AMBER] ERROR: Calculation halted. Periodic box dimensions have changed too much from their initial values. Gallo, Angelo (Mon Apr 06 2020 - 02:12:26 PDT)
- Re: [AMBER] ERROR: Calculation halted. Periodic box dimensions have changed too much from their initial values. Carlos Simmerling (Mon Apr 06 2020 - 03:52:38 PDT)
- Re: [AMBER] ERROR: Calculation halted. Periodic box dimensions have changed too much from their initial values. David A Case (Mon Apr 06 2020 - 05:03:59 PDT)
[AMBER] command for building composite of cellulose microfibrils and hemicelullose Pinky Mazumder (Mon Apr 06 2020 - 15:05:16 PDT)
[AMBER] Penalty score in frcmod file Sruthi Sudhakar (Mon Apr 06 2020 - 23:24:47 PDT)
[AMBER] topology problems Seibold, Steve Allan (Tue Apr 07 2020 - 09:58:59 PDT)
- Re: [AMBER] topology problems Matias Machado (Tue Apr 07 2020 - 12:28:09 PDT)
- Re: [AMBER] topology problems David A Case (Wed Apr 08 2020 - 04:37:08 PDT)
[AMBER] Ligand leaving binding site at high lambdas using TI softcore Juraj Dobias (Wed Apr 08 2020 - 13:39:52 PDT)
- Re: [AMBER] Ligand leaving binding site at high lambdas using TI softcore Juraj Dobias (Thu Apr 09 2020 - 10:30:07 PDT)
  - Re: [AMBER] Ligand leaving binding site at high lambdas using TI softcore Dickson, Callum (Thu Apr 09 2020 - 12:00:30 PDT)
    - Re: [AMBER] Ligand leaving binding site at high lambdas using TI softcore Juraj Dobias (Thu Apr 09 2020 - 13:34:11 PDT)
    - Re: [AMBER] Ligand leaving binding site at high lambdas using TI softcore Debarati DasGupta (Fri Apr 10 2020 - 05:13:35 PDT)
    - Re: [AMBER] Ligand leaving binding site at high lambdas using TI softcore Qinghua Liao (Fri Apr 10 2020 - 05:44:08 PDT)
    - Re: [AMBER] Ligand leaving binding site at high lambdas using TI softcore Debarati DasGupta (Fri Apr 10 2020 - 08:46:19 PDT)
    - Re: [AMBER] Ligand leaving binding site at high lambdas using TI softcore Juraj Dobias (Sat Apr 11 2020 - 02:22:55 PDT)
    - Re: [AMBER] Ligand leaving binding site at high lambdas using TI softcore Brian Radak (Sat Apr 11 2020 - 08:13:03 PDT)
[AMBER] peek_ewald_inpcrd: Box info not found in inpcrd Sunita Patel (Wed Apr 08 2020 - 21:01:18 PDT)
- Re: [AMBER] peek_ewald_inpcrd: Box info not found in inpcrd David A Case (Thu Apr 09 2020 - 04:47:22 PDT)
  - Re: [AMBER] peek_ewald_inpcrd: Box info not found in inpcrd Sunita Patel (Thu Apr 09 2020 - 06:31:14 PDT)
    - Re: [AMBER] peek_ewald_inpcrd: Box info not found in inpcrd David A Case (Thu Apr 09 2020 - 08:24:56 PDT)
    - Re: [AMBER] peek_ewald_inpcrd: Box info not found in inpcrd Sunita Patel (Fri Apr 10 2020 - 19:49:08 PDT)
[AMBER] ImportError: Could not import Amber Python modules Renato Araujo (Thu Apr 09 2020 - 10:24:18 PDT)
- Re: [AMBER] ImportError: Could not import Amber Python modules David A Case (Thu Apr 09 2020 - 19:02:32 PDT)
[AMBER] Installing nglview Jatin Kashyap (Thu Apr 09 2020 - 20:18:53 PDT)
- Re: [AMBER] Installing nglview Hai Nguyen (Fri Apr 10 2020 - 17:11:17 PDT)
  - Re: [AMBER] Installing nglview Jatin Kashyap (Fri Apr 10 2020 - 17:30:48 PDT)
    - Re: [AMBER] Installing nglview Hai Nguyen (Fri Apr 10 2020 - 17:45:08 PDT)
[AMBER] Acetylated the truncated N- terminal Lod King (Thu Apr 09 2020 - 20:47:27 PDT)
- Re: [AMBER] Acetylated the truncated N- terminal David Sáez (Thu Apr 09 2020 - 22:02:24 PDT)
  - Re: [AMBER] Acetylated the truncated N- terminal Lod King (Thu Apr 09 2020 - 22:10:03 PDT)
    - Re: [AMBER] Acetylated the truncated N- terminal David Sáez (Thu Apr 09 2020 - 23:11:33 PDT)
    - Re: [AMBER] Acetylated the truncated N- terminal Lod King (Thu Apr 09 2020 - 23:14:53 PDT)
- Re: [AMBER] Acetylated the truncated N- terminal Abdul-Rashid III Sampaco (Thu Apr 09 2020 - 22:16:19 PDT)
[AMBER] questions about paramfit ttz (Thu Apr 09 2020 - 21:54:12 PDT)
[AMBER] Very low MMPBSA result Nada Afiva (Fri Apr 10 2020 - 14:18:47 PDT)
- Re: [AMBER] Very low MMPBSA result Ray Luo (Fri Apr 10 2020 - 15:37:31 PDT)
  - Re: [AMBER] Very low MMPBSA result Nada Afiva (Fri Apr 10 2020 - 16:46:09 PDT)
  - Re: [AMBER] Very low MMPBSA result Nada Afiva (Fri Apr 10 2020 - 17:54:22 PDT)
    - Re: [AMBER] Very low MMPBSA result Ray Luo (Fri Apr 10 2020 - 18:42:27 PDT)
    - Re: [AMBER] Very low MMPBSA result Nada Afiva (Sat Apr 11 2020 - 02:16:13 PDT)
    - Re: [AMBER] Very low MMPBSA result David A Case (Sat Apr 11 2020 - 05:00:25 PDT)
    - Re: [AMBER] Very low MMPBSA result Nada Afiva (Sat Apr 11 2020 - 23:10:28 PDT)
    - Re: [AMBER] Very low MMPBSA result Ray Luo (Sun Apr 12 2020 - 09:01:23 PDT)
    - Re: [AMBER] Very low MMPBSA result Nada Afiva (Mon Apr 13 2020 - 03:44:44 PDT)
    - Re: [AMBER] Very low MMPBSA result Ray Luo (Mon Apr 13 2020 - 13:21:22 PDT)
- Re: [AMBER] Very low MMPBSA result Nada Afiva (Mon Apr 13 2020 - 18:41:59 PDT)
- Re: [AMBER] Very low MMPBSA result Nada Afiva (Wed Apr 15 2020 - 12:36:01 PDT)
[AMBER] Why is 360 degree is not equal to 0 degree in PES Scan? Erdem Yeler (Fri Apr 10 2020 - 16:01:59 PDT)
- Re: [AMBER] Why is 360 degree is not equal to 0 degree in PES Scan? Ilyas Yildirim (Fri Apr 10 2020 - 16:15:46 PDT)
- Re: [AMBER] Why is 360 degree is not equal to 0 degree in PES Scan? Lorenzo Gontrani (Sun Apr 12 2020 - 08:11:02 PDT)
- Re: [AMBER] Why is 360 degree is not equal to 0 degree in PES Scan? Gustavo Seabra (Tue Apr 14 2020 - 07:28:12 PDT)
  - Re: [AMBER] Why is 360 degree is not equal to 0 degree in PES Scan? Steven M. Graham (Tue Apr 14 2020 - 07:35:51 PDT)
  - Re: [AMBER] Why is 360 degree is not equal to 0 degree in PES Scan? Erdem Yeler (Tue Apr 14 2020 - 13:01:14 PDT)
    - Re: [AMBER] Why is 360 degree is not equal to 0 degree in PES Scan? Erdem Yeler (Wed Apr 15 2020 - 13:59:10 PDT)
- Re: [AMBER] Why is 360 degree is not equal to 0 degree in PES Scan? Hector A. Baldoni (Tue Apr 14 2020 - 07:47:13 PDT)
[AMBER] Amber18 compiled with GCC/8.3.0 fails some DPFP tests Cong Liu (Fri Apr 10 2020 - 16:52:16 PDT)
- Re: [AMBER] Amber18 compiled with GCC/8.3.0 fails some DPFP tests David A Case (Sat Apr 11 2020 - 05:03:34 PDT)
  - Re: [AMBER] Amber18 compiled with GCC/8.3.0 fails some DPFP tests Cong Liu (Sat Apr 11 2020 - 07:25:07 PDT)
    - [AMBER] Amber install CUDA truble ChenXingqiang (Sat Apr 11 2020 - 08:04:44 PDT)
    - Re: [AMBER] Amber install CUDA truble Sapna Shedge (Mon Apr 13 2020 - 17:55:02 PDT)
    - Re: [AMBER] Amber18 compiled with GCC/8.3.0 fails some DPFP tests Cong Liu (Tue Apr 14 2020 - 08:24:37 PDT)
    - Re: [AMBER] Amber18 compiled with GCC/8.3.0 fails some DPFP tests Kellon Belfon (Tue Apr 14 2020 - 10:36:48 PDT)
    - Re: [AMBER] Amber18 compiled with GCC/8.3.0 fails some DPFP tests Cong Liu (Tue Apr 14 2020 - 11:04:08 PDT)
  - [AMBER] examination of ligand binding energy as a function of simulation time with MMPBSA calculations Billiot, Eugene (Sat Apr 11 2020 - 07:48:27 PDT)
    - Re: [AMBER] examination of ligand binding energy as a function of simulation time with MMPBSA calculations Ray Luo (Sun Apr 12 2020 - 19:33:47 PDT)
    - Re: [AMBER] examination of ligand binding energy as a function of simulation time with MMPBSA calculations Eugene.Billiot.tamucc.edu (Fri Apr 17 2020 - 08:09:42 PDT)
    - Re: [AMBER] examination of ligand binding energy as a function of simulation time with MMPBSA calculations Preeti Pandey (Fri Apr 17 2020 - 11:43:14 PDT)
    - Re: [AMBER] examination of ligand binding energy as a function of simulation time with MMPBSA calculations Eugene.Billiot.tamucc.edu (Fri Apr 17 2020 - 11:54:15 PDT)
[AMBER] Partial charge for ligand Lod King (Fri Apr 10 2020 - 17:00:05 PDT)
[AMBER] Can I use paramfit for MM scan? Elif Çiğdem Calvin (Fri Apr 10 2020 - 18:31:06 PDT)
- Re: [AMBER] Can I use paramfit for MM scan? David Cerutti (Sat Apr 11 2020 - 03:53:15 PDT)
  - Re: [AMBER] Can I use paramfit for MM scan? Erdem Yeler (Sat Apr 11 2020 - 21:35:13 PDT)
    - Re: [AMBER] Can I use paramfit for MM scan? David Cerutti (Sun Apr 12 2020 - 23:20:11 PDT)
    - Re: [AMBER] Can I use paramfit for MM scan? Erdem Yeler (Mon Apr 13 2020 - 04:37:52 PDT)
    - Re: [AMBER] Can I use paramfit for MM scan? Erdem Yeler (Wed Apr 15 2020 - 14:26:08 PDT)
    - Re: [AMBER] Can I use paramfit for MM scan? David Cerutti (Wed Apr 15 2020 - 14:44:04 PDT)
[AMBER] Help for building lignin chain Pinky Mazumder (Sat Apr 11 2020 - 00:21:32 PDT)
- Re: [AMBER] Help for building lignin chain Karl Kirschner (Sat Apr 11 2020 - 01:23:49 PDT)
  - Re: [AMBER] Help for building lignin chain Pinky Mazumder (Tue Apr 14 2020 - 20:39:45 PDT)
    - Re: [AMBER] Help for building lignin chain Carlos Simmerling (Wed Apr 15 2020 - 03:54:11 PDT)
[AMBER] Antechamber/acpype for ligand parametrization and usage of yasara autosmiles Prasanth G, Research Scholar (Sat Apr 11 2020 - 10:37:10 PDT)
- Re: [AMBER] Antechamber/acpype for ligand parametrization and usage of yasara autosmiles David A Case (Sun Apr 12 2020 - 05:49:59 PDT)
[AMBER] integration algorithm of sander? And reference of sander? Erdem Yeler (Mon Apr 13 2020 - 09:12:12 PDT)
- Re: [AMBER] integration algorithm of sander? And reference of sander? Carlos Simmerling (Mon Apr 13 2020 - 09:18:54 PDT)
  - Re: [AMBER] integration algorithm of sander? And reference of sander? Erdem Yeler (Mon Apr 13 2020 - 10:17:35 PDT)
    - Re: [AMBER] integration algorithm of sander? And reference of sander? Carlos Simmerling (Mon Apr 13 2020 - 10:27:20 PDT)
    - Re: [AMBER] integration algorithm of sander? And reference of sander? Erdem Yeler (Mon Apr 13 2020 - 10:45:26 PDT)
- Re: [AMBER] integration algorithm of sander? And reference of sander? David A Case (Mon Apr 13 2020 - 12:21:55 PDT)
  - Re: [AMBER] integration algorithm of sander? And reference of sander? Erdem Yeler (Tue Apr 14 2020 - 12:56:50 PDT)
[AMBER] Reg:MMPB(GB)SA Error Lara rajam (Mon Apr 13 2020 - 11:26:06 PDT)
- Re: [AMBER] Reg:MMPB(GB)SA Error Elvis Martis (Mon Apr 13 2020 - 11:58:21 PDT)
- Re: [AMBER] Reg:MMPB(GB)SA Error David A Case (Mon Apr 13 2020 - 12:16:12 PDT)
[AMBER] geometry of amino Song Hu (Mon Apr 13 2020 - 22:59:00 PDT)
[AMBER] Simulating magnetite surfaces with AMBER Casalini Tommaso (Tue Apr 14 2020 - 02:44:23 PDT)
[AMBER] RST File Corrupt Czarny,Ryan (Tue Apr 14 2020 - 10:54:45 PDT)
- Re: [AMBER] RST File Corrupt Carlos Simmerling (Tue Apr 14 2020 - 11:03:08 PDT)
  - Re: [AMBER] RST File Corrupt Czarny,Ryan (Tue Apr 14 2020 - 12:05:26 PDT)
[AMBER] CPPtraj PCA error Rana Rehan Khalid (Tue Apr 14 2020 - 10:57:54 PDT)
- Re: [AMBER] CPPtraj PCA error Elvis Martis (Tue Apr 14 2020 - 11:18:39 PDT)
  - Re: [AMBER] CPPtraj PCA error Rana Rehan Khalid (Tue Apr 14 2020 - 11:36:24 PDT)
    - Re: [AMBER] CPPtraj PCA error Daniel Roe (Wed Jun 24 2020 - 09:13:47 PDT)
    - Re: [AMBER] CPPtraj PCA error Rana Rehan Khalid (Wed Jun 24 2020 - 09:16:09 PDT)
[AMBER] 1 chain-1chain interactions between carbohydrates Pinky Mazumder (Tue Apr 14 2020 - 20:36:31 PDT)
- Re: [AMBER] 1 chain-1chain interactions between carbohydrates Lachele Foley (Thu Apr 16 2020 - 01:20:50 PDT)
[AMBER] Generating an asymmetric box for Steered MD Souvik Dey (Wed Apr 15 2020 - 15:43:01 PDT)
- Re: [AMBER] Generating an asymmetric box for Steered MD David A Case (Thu Apr 16 2020 - 04:54:56 PDT)
  - Re: [AMBER] Generating an asymmetric box for Steered MD Souvik Dey (Thu Apr 16 2020 - 12:33:36 PDT)
- Re: [AMBER] Generating an asymmetric box for Steered MD Souvik Dey (Fri Apr 17 2020 - 00:03:52 PDT)
[AMBER] miniconda3 AmberTools MMPBSA.py ERROR 15501908560.163.com> (Wed Apr 15 2020 - 19:06:02 PDT)
[AMBER] Interaction of cellulose-hemicellulose Pinky Mazumder (Wed Apr 15 2020 - 20:13:45 PDT)
- Re: [AMBER] Interaction of cellulose-hemicellulose Lachele Foley (Thu Apr 16 2020 - 01:22:43 PDT)
  - Re: [AMBER] Interaction of cellulose-hemicellulose Pinky Mazumder (Thu Apr 16 2020 - 22:58:54 PDT)
    - Re: [AMBER] Interaction of cellulose-hemicellulose Lachele Foley (Thu Apr 16 2020 - 23:06:01 PDT)
    - Re: [AMBER] Interaction of cellulose-hemicellulose Pinky Mazumder (Fri Apr 17 2020 - 00:45:28 PDT)
    - Re: [AMBER] Interaction of cellulose-hemicellulose Pinky Mazumder (Fri Apr 17 2020 - 07:59:54 PDT)
    - Re: [AMBER] Interaction of cellulose-hemicellulose Pinky Mazumder (Fri Apr 17 2020 - 14:28:20 PDT)
    - Re: [AMBER] Interaction of cellulose-hemicellulose Lachele Foley (Sat Apr 18 2020 - 00:21:21 PDT)
    - Re: [AMBER] Interaction of cellulose-hemicellulose Pinky Mazumder (Sun Apr 19 2020 - 22:05:17 PDT)
    - Re: [AMBER] Interaction of cellulose-hemicellulose Lachele Foley (Sun Apr 19 2020 - 23:48:13 PDT)
    - Re: [AMBER] Interaction of cellulose-hemicellulose Pinky Mazumder (Mon Apr 20 2020 - 18:30:07 PDT)
    - Re: [AMBER] Interaction of cellulose-hemicellulose Pinky Mazumder (Tue Jul 28 2020 - 08:48:49 PDT)
    - Re: [AMBER] Interaction of cellulose-hemicellulose Lachele Foley (Wed Jul 29 2020 - 00:17:07 PDT)
- Re: [AMBER] Interaction of cellulose-hemicellulose Pinky Mazumder (Fri Apr 24 2020 - 00:30:36 PDT)
  - Re: [AMBER] Interaction of cellulose-hemicellulose Lachele Foley (Fri Apr 24 2020 - 04:33:24 PDT)
    - Re: [AMBER] Interaction of cellulose-hemicellulose Pinky Mazumder (Sun Apr 26 2020 - 20:59:07 PDT)
    - Re: [AMBER] Interaction of cellulose-hemicellulose Dr. Anselm Horn (Mon Apr 27 2020 - 07:04:57 PDT)
    - Re: [AMBER] Interaction of cellulose-hemicellulose Lachele Foley (Wed Apr 29 2020 - 18:01:59 PDT)
[AMBER] protein-protein complex dissociation Núbia Toman (Thu Apr 16 2020 - 06:17:53 PDT)
- Re: [AMBER] protein-protein complex dissociation Carlos Simmerling (Thu Apr 16 2020 - 06:21:13 PDT)
  - Re: [AMBER] protein-protein complex dissociation Núbia Toman (Thu Apr 16 2020 - 06:36:13 PDT)
    - Re: [AMBER] protein-protein complex dissociation Carlos Simmerling (Thu Apr 16 2020 - 07:09:03 PDT)
    - Re: [AMBER] protein-protein complex dissociation Núbia Toman (Thu Apr 16 2020 - 09:48:20 PDT)
    - Re: [AMBER] protein-protein complex dissociation Carlos Simmerling (Thu Apr 16 2020 - 09:51:15 PDT)
    - Re: [AMBER] protein-protein complex dissociation Núbia Toman (Thu Apr 16 2020 - 10:03:52 PDT)
    - Re: [AMBER] protein-protein complex dissociation Carlos Simmerling (Thu Apr 16 2020 - 10:12:23 PDT)
    - Re: [AMBER] protein-protein complex dissociation Núbia Toman (Thu Apr 16 2020 - 10:58:14 PDT)
    - Re: [AMBER] protein-protein complex dissociation David A Case (Thu Apr 16 2020 - 11:54:03 PDT)
    - Re: [AMBER] protein-protein complex dissociation Dr. Anselm Horn (Fri Apr 17 2020 - 01:10:00 PDT)
    - Re: [AMBER] protein-protein complex dissociation Núbia Toman (Fri Apr 17 2020 - 01:50:34 PDT)
- Re: [AMBER] protein-protein complex dissociation ABEL Stephane (Thu Apr 16 2020 - 06:31:34 PDT)
  - Re: [AMBER] protein-protein complex dissociation Núbia Toman (Thu Apr 16 2020 - 06:42:45 PDT)
[AMBER] Error when installing miniconda through AmberTools19 Gardezi,Shahbaz (Thu Apr 16 2020 - 10:40:06 PDT)
- Re: [AMBER] Error when installing miniconda through AmberTools19 Abdul-Rashid III Sampaco (Thu Apr 16 2020 - 10:46:16 PDT)
  - Re: [AMBER] Error when installing miniconda through AmberTools19 Gardezi,Shahbaz (Thu Apr 16 2020 - 10:51:54 PDT)
  - Re: [AMBER] Error when installing miniconda through AmberTools19 David A Case (Thu Apr 16 2020 - 12:02:25 PDT)
    - Re: [AMBER] Error when installing miniconda through AmberTools19 Gardezi,Shahbaz (Thu Apr 16 2020 - 13:28:20 PDT)
[AMBER] Request for help in solving installation errors of Amber dhruvi.iiar.res.in (Fri Apr 17 2020 - 04:20:54 PDT)
[AMBER] Force Field for small molecule ligands Sruthi Sudhakar (Fri Apr 17 2020 - 05:17:35 PDT)
- Re: [AMBER] Force Field for small molecule ligands Carlos Simmerling (Fri Apr 17 2020 - 05:20:29 PDT)
  - Re: [AMBER] Force Field for small molecule ligands Sruthi Sudhakar (Fri Apr 17 2020 - 06:06:07 PDT)
[AMBER] thanks for the GB/SA section of the manual Antoine MARION (Fri Apr 17 2020 - 07:46:10 PDT)
- Re: [AMBER] thanks for the GB/SA section of the manual Carlos Simmerling (Fri Apr 17 2020 - 07:48:59 PDT)
  - Re: [AMBER] thanks for the GB/SA section of the manual Antoine MARION (Fri Apr 17 2020 - 07:51:18 PDT)
[AMBER] Probable bug in tleap. Hector A. Baldoni (Fri Apr 17 2020 - 11:38:41 PDT)
- Re: [AMBER] Probable bug in tleap. Scott Brozell (Fri Apr 17 2020 - 11:46:17 PDT)
- Re: [AMBER] Probable bug in tleap. Daniel Roe (Fri Apr 17 2020 - 11:47:42 PDT)
[AMBER] Amber18 PIMD tutorial Sapna Shedge (Fri Apr 17 2020 - 23:16:19 PDT)
- Re: [AMBER] Amber18 PIMD tutorial David A Case (Sat Apr 18 2020 - 05:53:07 PDT)
  - Re: [AMBER] Amber18 PIMD tutorial Sapna Shedge (Sat Apr 18 2020 - 15:56:58 PDT)
[AMBER] Request for help in solving installation errors of Amber dhruvi.iiar.res.in (Sat Apr 18 2020 - 06:13:11 PDT)
- Re: [AMBER] Request for help in solving installation errors of Amber Hai Nguyen (Sat Apr 18 2020 - 18:27:50 PDT)
  - Re: [AMBER] Request for help in solving installation errors of Amber Hai Nguyen (Sat Apr 18 2020 - 18:42:38 PDT)
    - Re: [AMBER] Request for help in solving installation errors of Amber dhruvi.iiar.res.in (Sun Apr 19 2020 - 23:57:48 PDT)
    - Re: [AMBER] Request for help in solving installation errors of Amber David A Case (Mon Apr 20 2020 - 04:59:52 PDT)
[AMBER] FRCMOD file Sruthi Sudhakar (Sat Apr 18 2020 - 07:01:46 PDT)
- Re: [AMBER] FRCMOD file Carlos Simmerling (Sat Apr 18 2020 - 07:26:57 PDT)
[AMBER] pytraj error Ravi Abrol (Mon Apr 20 2020 - 00:06:35 PDT)
- Re: [AMBER] pytraj error David A Case (Mon Apr 20 2020 - 05:05:58 PDT)
  - Re: [AMBER] pytraj error Ravi Abrol (Mon Apr 20 2020 - 14:03:47 PDT)
    - Re: [AMBER] pytraj error Hai Nguyen (Mon Apr 20 2020 - 20:56:58 PDT)
    - Re: [AMBER] pytraj error Ravi Abrol (Tue Apr 21 2020 - 04:02:03 PDT)
    - Re: [AMBER] pytraj error Hai Nguyen (Tue Apr 21 2020 - 06:55:52 PDT)
    - Re: [AMBER] pytraj error Ravi Abrol (Tue Apr 21 2020 - 14:21:36 PDT)
[AMBER] restraining many individual atoms Ignacio General (Mon Apr 20 2020 - 11:06:01 PDT)
- Re: [AMBER] restraining many individual atoms James Kress (Mon Apr 20 2020 - 12:37:44 PDT)
  - Re: [AMBER] restraining many individual atoms Ignacio J. General (Mon Apr 20 2020 - 12:48:36 PDT)
- Re: [AMBER] restraining many individual atoms David A Case (Mon Apr 20 2020 - 12:55:38 PDT)
  - Re: [AMBER] restraining many individual atoms Ignacio J. General (Mon Apr 20 2020 - 13:31:21 PDT)
[AMBER] Sander can't calculate MBAR energy swjjin0015.163.com (Mon Apr 20 2020 - 18:31:19 PDT)
[AMBER] Energy values from mdout (excluding solvent molecules) Eduardo R. Almeida (Mon Apr 20 2020 - 20:57:48 PDT)
[AMBER] Problem in calculating pairwise interaction with CPPTRAJ Prathit Chatterjee (Tue Apr 21 2020 - 02:47:42 PDT)
- Re: [AMBER] Problem in calculating pairwise interaction with CPPTRAJ Daniel Roe (Wed Jun 24 2020 - 09:07:22 PDT)
[AMBER] Restraint on certain atoms during MD Debarati DasGupta (Tue Apr 21 2020 - 05:45:15 PDT)
- Re: [AMBER] Restraint on certain atoms during MD David A Case (Tue Apr 21 2020 - 11:54:45 PDT)
  - Re: [AMBER] Restraint on certain atoms during MD Debarati DasGupta (Tue Apr 21 2020 - 11:56:46 PDT)
    - Re: [AMBER] Restraint on certain atoms during MD Carlos Simmerling (Tue Apr 21 2020 - 11:59:06 PDT)
    - Re: [AMBER] Restraint on certain atoms during MD Debarati DasGupta (Tue Apr 21 2020 - 12:02:11 PDT)
    - Re: [AMBER] Restraint on certain atoms during MD Carlos Simmerling (Wed Apr 22 2020 - 08:27:40 PDT)
    - Re: [AMBER] Restraint on certain atoms during MD Debarati DasGupta (Wed Apr 22 2020 - 08:34:38 PDT)
    - Re: [AMBER] Restraint on certain atoms during MD Debarati DasGupta (Wed Apr 22 2020 - 08:41:28 PDT)
    - Re: [AMBER] Restraint on certain atoms during MD Carlos Simmerling (Wed Apr 22 2020 - 08:52:00 PDT)
    - Re: [AMBER] Restraint on certain atoms during MD Debarati DasGupta (Wed Apr 22 2020 - 09:33:19 PDT)
    - Re: [AMBER] Restraint on certain atoms during MD Carlos Simmerling (Wed Apr 22 2020 - 09:39:34 PDT)
    - Re: [AMBER] Restraint on certain atoms during MD Debarati DasGupta (Wed Apr 22 2020 - 09:45:20 PDT)
    - Re: [AMBER] Restraint on certain atoms during MD Carlos Simmerling (Wed Apr 22 2020 - 09:48:25 PDT)
    - Re: [AMBER] Restraint on certain atoms during MD Debarati DasGupta (Wed Apr 22 2020 - 10:04:17 PDT)
    - Re: [AMBER] Restraint on certain atoms during MD Debarati DasGupta (Wed Apr 22 2020 - 10:05:59 PDT)
    - Re: [AMBER] Restraint on certain atoms during MD Daniel Roe (Wed Apr 22 2020 - 14:00:03 PDT)
    - Re: [AMBER] Restraint on certain atoms during MD Debarati DasGupta (Wed Apr 22 2020 - 15:07:16 PDT)
    - Re: [AMBER] Restraint on certain atoms during MD Carlos Simmerling (Wed Apr 22 2020 - 15:19:29 PDT)
    - Re: [AMBER] Restraint on certain atoms during MD Debarati DasGupta (Wed Apr 22 2020 - 15:22:03 PDT)
    - Re: [AMBER] Restraint on certain atoms during MD Debarati DasGupta (Wed Apr 22 2020 - 15:10:04 PDT)
    - Re: [AMBER] Restraint on certain atoms during MD David A Case (Wed Apr 22 2020 - 10:42:06 PDT)
[AMBER] Sander can't calculate Mbar energy swjjin0015.163.com (Tue Apr 21 2020 - 17:11:48 PDT)
[AMBER] Targeted MD Hector A. Baldoni (Tue Apr 21 2020 - 17:53:36 PDT)
[AMBER] Amber18, tools19, cuda 10.2 Christopher Benjamin Coffey (Wed Apr 22 2020 - 11:16:55 PDT)
- Re: [AMBER] Amber18, tools19, cuda 10.2 David A Case (Thu Apr 23 2020 - 05:49:46 PDT)
  - Re: [AMBER] Amber18, tools19, cuda 10.2 Christopher Benjamin Coffey (Thu Apr 23 2020 - 08:13:06 PDT)
- Re: [AMBER] Amber18, tools19, cuda 10.2 accuratefreeenergy.gmail.com (Thu Apr 23 2020 - 06:56:44 PDT)
[AMBER] implicit water Fabian Glaser (Wed Apr 22 2020 - 11:53:45 PDT)
[AMBER] Sander can not calculate Mbar energy Gini (Wed Apr 22 2020 - 17:21:53 PDT)
[AMBER] How to change charge value for 1 residue for MD simulation? Devashish_Das (Thu Apr 23 2020 - 00:59:57 PDT)
- Re: [AMBER] How to change charge value for 1 residue for MD simulation? David A Case (Thu Apr 23 2020 - 05:51:52 PDT)
[AMBER] FATAL: allocation failure in ivector() error while running 3D-RISM calculations Leena Aggarwal (Thu Apr 23 2020 - 04:32:16 PDT)
- Re: [AMBER] FATAL: allocation failure in ivector() error while running 3D-RISM calculations David A Case (Thu Apr 23 2020 - 05:54:19 PDT)
[AMBER] Energy values from mdout files (excluding solvent molecules) Eduardo R. Almeida (Thu Apr 23 2020 - 06:01:19 PDT)
- Re: [AMBER] Energy values from mdout files (excluding solvent molecules) Daniel Roe (Wed Jun 24 2020 - 09:04:15 PDT)
[AMBER] Run Amber as a job array Anna Sekuła (Thu Apr 23 2020 - 07:32:56 PDT)
[AMBER] Fwd: FATAL: allocation failure in ivector() error while running 3D-RISM calculations Leena Aggarwal (Thu Apr 23 2020 - 11:25:47 PDT)
[AMBER] wrong geometry amide nitrogen Arnaud Bondon (Fri Apr 24 2020 - 04:40:58 PDT)
- Re: [AMBER] wrong geometry amide nitrogen Junmei Wang (Wed Apr 29 2020 - 07:36:21 PDT)
[AMBER] wrong geometry amide nitrogen Arnaud Bondon (Fri Apr 24 2020 - 06:56:37 PDT)
- Re: [AMBER] wrong geometry amide nitrogen David A Case (Fri Apr 24 2020 - 08:01:49 PDT)
  - Re: [AMBER] wrong geometry amide nitrogen Junmei Wang (Tue Apr 28 2020 - 14:02:10 PDT)
    - Re: [AMBER] wrong geometry amide nitrogen Arnaud Bondon (Wed Apr 29 2020 - 01:43:53 PDT)
    - Re: [AMBER] wrong geometry amide nitrogen Junmei Wang (Wed Apr 29 2020 - 07:12:46 PDT)
    - Re: [AMBER] wrong geometry amide nitrogen Arnaud Bondon (Wed Apr 29 2020 - 07:52:01 PDT)
    - Re: [AMBER] wrong geometry amide nitrogen Junmei Wang (Wed Apr 29 2020 - 08:09:26 PDT)
    - Re: [AMBER] wrong geometry amide nitrogen Arnaud Bondon (Wed Apr 29 2020 - 08:13:59 PDT)
    - Re: [AMBER] wrong geometry amide nitrogen Arnaud Bondon (Wed Apr 29 2020 - 08:22:00 PDT)
    - Re: [AMBER] wrong geometry amide nitrogen Arnaud Bondon (Wed Apr 29 2020 - 09:51:08 PDT)
    - Re: [AMBER] wrong geometry amide nitrogen Junmei Wang (Wed Apr 29 2020 - 21:45:25 PDT)
    - Re: [AMBER] wrong geometry amide nitrogen Arnaud Bondon (Thu Apr 30 2020 - 01:17:37 PDT)
    - Re: [AMBER] wrong geometry amide nitrogen Junmei Wang (Thu Apr 30 2020 - 20:15:53 PDT)
    - Re: [AMBER] wrong geometry amide nitrogen Arnaud Bondon (Fri May 01 2020 - 03:54:42 PDT)
    - Re: [AMBER] wrong geometry amide nitrogen Junmei Wang (Fri May 01 2020 - 12:50:30 PDT)
    - Re: [AMBER] wrong geometry amide nitrogen Arnaud Bondon (Sat May 02 2020 - 05:30:27 PDT)
[AMBER] unsubscribe Christopher Benjamin Coffey (Fri Apr 24 2020 - 08:19:20 PDT)
[AMBER] minimizing a pyridine in water Debarati DasGupta (Sat Apr 25 2020 - 06:10:52 PDT)
- Re: [AMBER] minimizing a pyridine in water Carlos Simmerling (Sat Apr 25 2020 - 06:18:38 PDT)
  - Re: [AMBER] minimizing a pyridine in water Debarati DasGupta (Sat Apr 25 2020 - 08:38:29 PDT)
- Re: [AMBER] minimizing a pyridine in water David A Case (Sat Apr 25 2020 - 10:29:12 PDT)
  - Re: [AMBER] minimizing a pyridine in water Debarati DasGupta (Sat Apr 25 2020 - 10:35:48 PDT)
    - Re: [AMBER] minimizing a pyridine in water Debarati DasGupta (Sat Apr 25 2020 - 11:32:40 PDT)
    - Re: [AMBER] minimizing a pyridine in water James Kress (Sat Apr 25 2020 - 16:39:37 PDT)
- Re: [AMBER] minimizing a pyridine in water Debarati DasGupta (Mon Apr 27 2020 - 11:53:48 PDT)
[AMBER] DNA-RNA duplex Sruthi Sudhakar (Sat Apr 25 2020 - 07:34:30 PDT)
- Re: [AMBER] DNA-RNA duplex Satyaseelan C (Mon Apr 27 2020 - 20:37:35 PDT)
[AMBER] Ligand lose planarity Jenny 148 (Sat Apr 25 2020 - 08:09:45 PDT)
[AMBER] Recurring problem: Ligand lose planarity Jenny 148 (Sat Apr 25 2020 - 21:49:45 PDT)
- Re: [AMBER] Recurring problem: Ligand lose planarity Sruthi Sudhakar (Sun Apr 26 2020 - 08:33:44 PDT)
  - Re: [AMBER] Recurring problem: Ligand lose planarity Carlos Simmerling (Sun Apr 26 2020 - 08:49:49 PDT)
    - Re: [AMBER] Recurring problem: Ligand lose planarity Jenny 148 (Sun Apr 26 2020 - 09:33:51 PDT)
    - Re: [AMBER] Recurring problem: Ligand lose planarity Carlos Simmerling (Sun Apr 26 2020 - 10:23:54 PDT)
    - Re: [AMBER] Recurring problem: Ligand lose planarity Jenny 148 (Sun Apr 26 2020 - 11:04:32 PDT)
    - Re: [AMBER] Recurring problem: Ligand lose planarity Carlos Simmerling (Sun Apr 26 2020 - 11:24:05 PDT)
    - Re: [AMBER] Recurring problem: Ligand lose planarity Jenny 148 (Sun Apr 26 2020 - 11:28:39 PDT)
    - Re: [AMBER] Recurring problem: Ligand lose planarity Jenny 148 (Sun Apr 26 2020 - 14:15:22 PDT)
    - Re: [AMBER] Recurring problem: Ligand lose planarity David A Case (Mon Apr 27 2020 - 11:24:47 PDT)
  - Re: [AMBER] Recurring problem: Ligand lose planarity David A Case (Mon Apr 27 2020 - 11:23:18 PDT)
    - Re: [AMBER] Recurring problem: Ligand lose planarity Jenny 148 (Mon Apr 27 2020 - 11:51:53 PDT)
[AMBER] NAB to create DNA/RNA hybrid? Jisha B (Sat Apr 25 2020 - 23:21:24 PDT)
- Re: [AMBER] NAB to create DNA/RNA hybrid? David A Case (Mon Apr 27 2020 - 11:18:24 PDT)
- Re: [AMBER] NAB to create DNA/RNA hybrid? Satyaseelan C (Mon Apr 27 2020 - 20:38:27 PDT)
[AMBER] cylindrical Simulation mohamed marzouk (Sun Apr 26 2020 - 18:47:12 PDT)
- Re: [AMBER] cylindrical Simulation mohamed marzouk (Tue Apr 28 2020 - 23:26:17 PDT)
[AMBER] Tsolute and Tsolvent Eduardo R. Almeida (Mon Apr 27 2020 - 08:00:45 PDT)
[AMBER] AMBER leap issues constructing non-standard residue Siddharth marwaha (Mon Apr 27 2020 - 11:50:30 PDT)
[AMBER] How to get the eigenvalues from PCA SUNITA MUDULI (Mon Apr 27 2020 - 13:31:40 PDT)
- Re: [AMBER] How to get the eigenvalues from PCA Daniel Roe (Wed Jun 24 2020 - 08:58:00 PDT)
[AMBER] error tleap MYRIAN TORRES RICO (Tue Apr 28 2020 - 02:24:47 PDT)
- Re: [AMBER] error tleap Gustaf Olsson (Wed Sep 09 2020 - 05:21:37 PDT)
  - Re: [AMBER] error tleap MYRIAN TORRES RICO (Wed Sep 09 2020 - 11:52:24 PDT)
    - Re: [AMBER] error tleap Gustaf Olsson (Thu Sep 10 2020 - 00:19:27 PDT)
  - Re: [AMBER] error tleap MYRIAN TORRES RICO (Thu Sep 10 2020 - 02:38:29 PDT)
    - Re: [AMBER] error tleap Gustaf Olsson (Thu Sep 10 2020 - 04:28:17 PDT)
    - [AMBER] SHAKEH hydrogen clusters Pietro Aronica (Thu Sep 10 2020 - 05:19:39 PDT)
    - Re: [AMBER] SHAKEH hydrogen clusters David A Case (Thu Sep 10 2020 - 10:07:01 PDT)
    - Re: [AMBER] SHAKEH hydrogen clusters pietroa.bii.a-star.edu.sg (Thu Sep 10 2020 - 19:16:20 PDT)
    - Re: [AMBER] SHAKEH hydrogen clusters David A Case (Fri Sep 11 2020 - 08:27:15 PDT)
    - Re: [AMBER] SHAKEH hydrogen clusters pietroa.bii.a-star.edu.sg (Fri Sep 11 2020 - 22:30:55 PDT)
    - Re: [AMBER] SHAKEH hydrogen clusters David A Case (Thu Sep 17 2020 - 06:24:55 PDT)
    - Re: [AMBER] error tleap MYRIAN TORRES RICO (Fri Sep 11 2020 - 03:46:31 PDT)
    - Re: [AMBER] error tleap Gustaf Olsson (Tue Sep 15 2020 - 05:27:44 PDT)
    - Re: [AMBER] error tleap MYRIAN TORRES RICO (Wed Sep 16 2020 - 01:17:40 PDT)
    - Re: [AMBER] error tleap Gustaf Olsson (Wed Sep 16 2020 - 02:05:01 PDT)
[AMBER] tlea MYRIAN TORRES RICO (Tue Apr 28 2020 - 02:25:58 PDT)
- Re: [AMBER] tlea Lachele Foley (Wed Apr 29 2020 - 17:46:37 PDT)
  - Re: [AMBER] tlea MYRIAN TORRES RICO (Thu Apr 30 2020 - 00:55:31 PDT)
    - Re: [AMBER] tlea Lachele Foley (Sun May 10 2020 - 11:14:40 PDT)
    - Re: [AMBER] tlea David Cerutti (Sun May 10 2020 - 12:19:38 PDT)
[AMBER] Using tleap tho have the .inpcrd and crd file ABEL Stephane (Tue Apr 28 2020 - 04:51:39 PDT)
- Re: [AMBER] Using tleap tho have the .inpcrd and crd file David A Case (Wed Apr 29 2020 - 04:20:58 PDT)
  - Re: [AMBER] Using tleap tho have the .inpcrd and crd file ABEL Stephane (Thu Apr 30 2020 - 07:16:53 PDT)
[AMBER] Unavailability of AMBER tutorial on PCA Abhilash J (Tue Apr 28 2020 - 13:52:59 PDT)
- Re: [AMBER] Unavailability of AMBER tutorial on PCA James Kress (Tue Apr 28 2020 - 15:38:23 PDT)
  - Re: [AMBER] Unavailability of AMBER tutorial on PCA Abhilash J (Wed Apr 29 2020 - 10:17:57 PDT)
    - Re: [AMBER] Unavailability of AMBER tutorial on PCA Rodrigo Galindo-Murillo (Wed Apr 29 2020 - 10:27:10 PDT)
[AMBER] adding hydrogen to pdbqt ligand files Marawan Hussien (Tue Apr 28 2020 - 14:15:36 PDT)
- Re: [AMBER] adding hydrogen to pdbqt ligand files David A Case (Tue Apr 28 2020 - 16:40:40 PDT)
- Re: [AMBER] adding hydrogen to pdbqt ligand files Eduardo Mayo (Thu May 28 2020 - 23:25:00 PDT)
[AMBER] nativecontacts mohamed marzouk (Tue Apr 28 2020 - 23:35:04 PDT)
- Re: [AMBER] nativecontacts Gustavo Seabra (Wed Apr 29 2020 - 05:56:19 PDT)
- Re: [AMBER] nativecontacts Daniel Roe (Wed Jun 24 2020 - 08:52:56 PDT)
[AMBER] tleap error MYRIAN TORRES RICO (Wed Apr 29 2020 - 03:23:30 PDT)
[AMBER] Question about PCA tutorial Abhilash J (Wed Apr 29 2020 - 14:07:27 PDT)
- Re: [AMBER] Question about PCA tutorial Thomas Cheatham (Wed Apr 29 2020 - 20:24:07 PDT)
  - Re: [AMBER] Question about PCA tutorial Abhilash J (Thu Apr 30 2020 - 16:03:54 PDT)
[AMBER] tMD and pmemd Francesco Gentile (Wed Apr 29 2020 - 17:00:17 PDT)
- Re: [AMBER] tMD and pmemd Carlos Simmerling (Wed Apr 29 2020 - 17:42:35 PDT)
[AMBER] Mutations in existing DNA PDB file Jisha B (Thu Apr 30 2020 - 09:36:38 PDT)
[AMBER] TI simulations Debarati DasGupta (Thu Apr 30 2020 - 12:09:58 PDT)
- Re: [AMBER] TI simulations Song, Lin (Thu Apr 30 2020 - 17:18:02 PDT)
  - Re: [AMBER] TI simulations Debarati DasGupta (Fri May 01 2020 - 05:27:21 PDT)
[AMBER] SHAKE ALgorithm and frcmod file Elif Çiğdem Calvin (Thu Apr 30 2020 - 14:14:10 PDT)
- Re: [AMBER] SHAKE ALgorithm and frcmod file Carlos Simmerling (Thu Apr 30 2020 - 14:18:27 PDT)
  - Re: [AMBER] SHAKE ALgorithm and frcmod file Elif Çiğdem Calvin (Fri May 01 2020 - 05:22:51 PDT)
    - Re: [AMBER] SHAKE ALgorithm and frcmod file Carlos Simmerling (Fri May 01 2020 - 05:25:48 PDT)
    - Re: [AMBER] SHAKE ALgorithm and frcmod file Elif Çiğdem Calvin (Fri May 01 2020 - 05:27:35 PDT)
- Re: [AMBER] SHAKE ALgorithm and frcmod file David A Case (Fri May 01 2020 - 05:34:04 PDT)
  - Re: [AMBER] SHAKE ALgorithm and frcmod file Elif Çiğdem Calvin (Fri May 01 2020 - 05:52:30 PDT)
[AMBER] timestep dt for higher temperatures Liao (Fri May 01 2020 - 00:41:54 PDT)
- Re: [AMBER] timestep dt for higher temperatures David A Case (Fri May 01 2020 - 05:36:33 PDT)
[AMBER] QM/MM with finite temperature string Pratul Agarwal (Fri May 01 2020 - 11:17:57 PDT)
[AMBER] Leaprc error janardhanan c (Sat May 02 2020 - 03:11:07 PDT)
- Re: [AMBER] Leaprc error Daniel Roe (Sat May 02 2020 - 04:33:32 PDT)
  - Re: [AMBER] Leaprc error janardhanan c (Sun May 03 2020 - 02:58:54 PDT)
[AMBER] Simulation stops during NPT Sunita Patel (Sat May 02 2020 - 03:18:09 PDT)
- Re: [AMBER] Simulation stops during NPT Carlos Simmerling (Sat May 02 2020 - 03:30:55 PDT)
  - Re: [AMBER] Simulation stops during NPT Sunita Patel (Sat May 02 2020 - 23:11:09 PDT)
    - Re: [AMBER] Simulation stops during NPT Carlos Simmerling (Sun May 03 2020 - 05:07:25 PDT)
    - Re: [AMBER] Simulation stops during NPT Sunita Patel (Sun May 03 2020 - 11:52:50 PDT)
    - Re: [AMBER] Simulation stops during NPT Sunita Patel (Sun May 03 2020 - 18:45:07 PDT)
    - Re: [AMBER] Simulation stops during NPT David A Case (Mon May 04 2020 - 05:38:24 PDT)
[AMBER] NPT 2 ns of equilibration Debarati DasGupta (Sat May 02 2020 - 11:27:21 PDT)
- Re: [AMBER] NPT 2 ns of equilibration Carlos Simmerling (Sat May 02 2020 - 12:44:56 PDT)
[AMBER] Free energy calculation and system crash Sadaf Rani (Sat May 02 2020 - 15:54:14 PDT)
- Re: [AMBER] Free energy calculation and system crash Carlos Simmerling (Sat May 02 2020 - 16:44:52 PDT)
  - Re: [AMBER] Free energy calculation and system crash Sadaf Rani (Sat May 02 2020 - 17:29:43 PDT)
    - Re: [AMBER] Free energy calculation and system crash Sadaf Rani (Mon May 04 2020 - 06:08:01 PDT)
    - Re: [AMBER] Free energy calculation and system crash Carlos Simmerling (Mon May 04 2020 - 06:11:04 PDT)
[AMBER] CPPTRAJ: distance between atoms emanuele falbo (Mon May 04 2020 - 03:55:27 PDT)
- Re: [AMBER] CPPTRAJ: distance between atoms Daniel Roe (Mon May 04 2020 - 04:35:17 PDT)
[AMBER] Release of Amber20 and AmberTools20 David A Case (Mon May 04 2020 - 05:34:13 PDT)
- Re: [AMBER] Release of Amber20 and AmberTools20 Robert Molt (Mon May 04 2020 - 05:42:25 PDT)
  - Re: [AMBER] Release of Amber20 and AmberTools20 David A Case (Mon May 04 2020 - 07:40:01 PDT)
[AMBER] Abasic Site and Errant OH Group on Sugar Robert Molt (Mon May 04 2020 - 05:40:40 PDT)
- Re: [AMBER] Abasic Site and Errant OH Group on Sugar Christina Bergonzo (Mon May 04 2020 - 06:13:53 PDT)
- Re: [AMBER] Abasic Site and Errant OH Group on Sugar David A Case (Mon May 04 2020 - 07:44:58 PDT)
[AMBER] Mass-weighted RMSD one-liner with cpptraj - possible? Martin Mielke (Mon May 04 2020 - 06:23:09 PDT)
- Re: [AMBER] Mass-weighted RMSD one-liner with cpptraj - possible? Daniel Roe (Tue May 05 2020 - 06:08:34 PDT)
  - Re: [AMBER] Mass-weighted RMSD one-liner with cpptraj - possible? Martin Mielke (Tue May 05 2020 - 14:26:57 PDT)
    - Re: [AMBER] Mass-weighted RMSD one-liner with cpptraj - possible? Martin Mielke (Wed May 06 2020 - 06:28:27 PDT)
    - Re: [AMBER] Mass-weighted RMSD one-liner with cpptraj - possible? Daniel Roe (Wed May 06 2020 - 06:52:58 PDT)
    - Re: [AMBER] Mass-weighted RMSD one-liner with cpptraj - possible? Daniel Roe (Thu May 07 2020 - 12:47:11 PDT)
    - Re: [AMBER] Mass-weighted RMSD one-liner with cpptraj - possible? Martin Mielke (Fri May 08 2020 - 03:06:43 PDT)
[AMBER] creating parameters for a thioglycoside rosaester.forgione.unina.it (Mon May 04 2020 - 09:59:39 PDT)
- Re: [AMBER] creating parameters for a thioglycoside Karl Kirschner (Mon May 04 2020 - 11:28:22 PDT)
  - Re: [AMBER] creating parameters for a thioglycoside rosaester.forgione.unina.it (Mon May 11 2020 - 03:27:48 PDT)
[AMBER] cpptraj PCA PC-mode pseudo traj Schröder, David Christopher (Mon May 04 2020 - 13:19:23 PDT)
- Re: [AMBER] cpptraj PCA PC-mode pseudo traj Daniel Roe (Mon May 04 2020 - 13:46:52 PDT)
  - Re: [AMBER] cpptraj PCA PC-mode pseudo traj Schröder, David Christopher (Mon May 04 2020 - 13:52:47 PDT)
[AMBER] AmberTools20 comilation on macOS Gustaf Olsson (Tue May 05 2020 - 01:07:11 PDT)
- Re: [AMBER] AmberTools20 comilation on macOS Gustaf Olsson (Tue May 05 2020 - 01:22:42 PDT)
  - Re: [AMBER] AmberTools20 comilation on macOS Gustaf Olsson (Tue May 05 2020 - 01:38:13 PDT)
    - Re: [AMBER] AmberTools20 comilation on macOS Gustaf Olsson (Tue May 05 2020 - 02:33:42 PDT)
- Re: [AMBER] AmberTools20 comilation on macOS David A Case (Tue May 05 2020 - 05:58:58 PDT)
  - Re: [AMBER] AmberTools20 comilation on macOS Gustaf Olsson (Tue May 05 2020 - 09:22:03 PDT)
    - Re: [AMBER] AmberTools20 comilation on macOS Gustaf Olsson (Tue May 05 2020 - 10:03:52 PDT)
    - Re: [AMBER] AmberTools20 comilation on macOS David A Case (Tue May 05 2020 - 13:44:18 PDT)
    - Re: [AMBER] AmberTools20 comilation on macOS Gustaf Olsson (Tue May 05 2020 - 22:33:59 PDT)
    - Re: [AMBER] AmberTools20 comilation on macOS David A Case (Wed May 06 2020 - 05:31:52 PDT)
    - Re: [AMBER] AmberTools20 comilation on macOS Gustaf Olsson (Wed May 06 2020 - 06:38:14 PDT)
[AMBER] The lipid section in the 2020 manual require updating Zhiyi Wu (Tue May 05 2020 - 03:38:05 PDT)
- Re: [AMBER] The lipid section in the 2020 manual require updating David A Case (Tue May 05 2020 - 06:09:05 PDT)
- Re: [AMBER] The lipid section in the 2020 manual require updating Stephan Schott (Tue May 05 2020 - 06:45:59 PDT)
  - Re: [AMBER] The lipid section in the 2020 manual require updating Gould, Ian R (Tue May 05 2020 - 07:19:50 PDT)
    - Re: [AMBER] The lipid section in the 2020 manual require updating Ross Walker (Tue May 05 2020 - 07:30:23 PDT)
- Re: [AMBER] The lipid section in the 2020 manual require updating Stephan Schott (Tue May 05 2020 - 07:39:53 PDT)
[AMBER] C4 parameters for Au0 from INTERFACE FF sbojarowski.chem.uw.edu.pl (Tue May 05 2020 - 05:58:34 PDT)
[AMBER] CO atom type missing in PARMCHK.DAT Casalini Tommaso (Tue May 05 2020 - 11:53:42 PDT)
[AMBER] FRCMOD FILE DATABASE Jenny 148 (Tue May 05 2020 - 22:33:20 PDT)
- Re: [AMBER] FRCMOD FILE DATABASE Gustaf Olsson (Tue May 05 2020 - 22:43:24 PDT)
  - Re: [AMBER] FRCMOD FILE DATABASE Brent Krueger (Wed May 06 2020 - 05:17:17 PDT)
[AMBER] MM-PBSA calculation error Serena Vittorio (Wed May 06 2020 - 02:01:38 PDT)
- Re: [AMBER] MM-PBSA calculation error David A Case (Wed May 06 2020 - 05:36:48 PDT)
  - Re: [AMBER] [BULK] Re: MM-PBSA calculation error Serena Vittorio (Wed May 06 2020 - 08:38:01 PDT)
    - Re: [AMBER] [BULK] Re: MM-PBSA calculation error David A Case (Wed May 06 2020 - 09:32:42 PDT)
    - Re: [AMBER] [BULK] Re: [BULK] Re: MM-PBSA calculation error Serena Vittorio (Thu May 07 2020 - 02:26:12 PDT)
[AMBER] Flags to Turn off Charges in pmemd Sharif Nada (Wed May 06 2020 - 03:44:24 PDT)
[AMBER] MMGBSA-DECOM calculation Renato Araujo (Wed May 06 2020 - 04:17:46 PDT)
- Re: [AMBER] MMGBSA-DECOM calculation Elvis Martis (Wed May 06 2020 - 05:25:52 PDT)
  - Re: [AMBER] MMGBSA-DECOM calculation Renato Araujo (Wed May 06 2020 - 06:15:39 PDT)
  - Re: [AMBER] MMGBSA-DECOM calculation Renato Araujo (Wed May 06 2020 - 06:27:05 PDT)
    - Re: [AMBER] MMGBSA-DECOM calculation Elvis Martis (Wed May 06 2020 - 06:32:28 PDT)
[AMBER] Amber20 sander speed difference between cmake and old configure method Charo del Genio (Wed May 06 2020 - 05:07:51 PDT)
- Re: [AMBER] Amber20 sander speed difference between cmake and old configure method David A Case (Wed May 06 2020 - 09:22:33 PDT)
- Re: [AMBER] Amber20 sander speed difference between cmake and old configure method David A Case (Tue May 12 2020 - 05:25:39 PDT)
[AMBER] can i analysis number of water molecules in protein by watershell 石娜 (Wed May 06 2020 - 06:21:50 PDT)
- Re: [AMBER] can i analysis number of water molecules in protein by watershell Daniel Roe (Wed May 20 2020 - 09:20:05 PDT)
  - Re: [AMBER] can i analysis number of water molecules in protein by watershell Wesley Michael Botello-Smith (Wed May 20 2020 - 09:39:46 PDT)
[AMBER] Amber20 sander speed difference between cmake and old configure method (addendum) Charo del Genio (Wed May 06 2020 - 06:35:18 PDT)
[AMBER] addions Jisha B (Wed May 06 2020 - 08:55:28 PDT)
- Re: [AMBER] addions Christina Bergonzo (Wed May 06 2020 - 09:17:48 PDT)
  - Re: [AMBER] addions Robert Molt (Sat May 09 2020 - 14:35:24 PDT)
    - Re: [AMBER] addions James Kress (Sat May 09 2020 - 14:56:37 PDT)
    - Re: [AMBER] addions Robert Molt (Sat May 09 2020 - 15:13:44 PDT)
    - Re: [AMBER] addions Matias Machado (Sat May 09 2020 - 16:04:02 PDT)
    - Re: [AMBER] addions Robert Molt (Sat May 09 2020 - 17:20:10 PDT)
    - Re: [AMBER] addions James Kress (Sat May 09 2020 - 19:47:47 PDT)
- Re: [AMBER] [EXTERNAL] addions Smith, Micholas D. (Wed May 06 2020 - 10:18:27 PDT)
  - Re: [AMBER] [EXTERNAL] addions Matias Machado (Wed May 06 2020 - 10:45:46 PDT)
[AMBER] RMSD discontinuity between NPT and NVT with restraints Thomas Gaillard (Wed May 06 2020 - 08:57:00 PDT)
[AMBER] about charmmgen Francesco Pietra (Wed May 06 2020 - 09:28:01 PDT)
[AMBER] Minimum recommended hardware specs for AmberTools20 and Amber20 Adrianne Lee (Wed May 06 2020 - 14:57:49 PDT)
- Re: [AMBER] Minimum recommended hardware specs for AmberTools20 and Amber20 Martin Mielke (Thu May 07 2020 - 00:41:16 PDT)
[AMBER] How to merge GLYCAM06 and lipid17 to generate force field for simple g; ycolipids? Vijay Achari (Thu May 07 2020 - 01:30:37 PDT)
- Re: [AMBER] How to merge GLYCAM06 and lipid17 to generate force field for simple g; ycolipids? Lachele Foley (Sun May 10 2020 - 11:31:33 PDT)
[AMBER] Thermodynamic integration by parameter interpolation (PI-TI) Veenis, Andrew Jay (Thu May 07 2020 - 07:01:05 PDT)
[AMBER] MD and MD-tar restrictions MYRIAN TORRES RICO (Fri May 08 2020 - 03:53:54 PDT)
[AMBER] OHE residue and crashing Piia Kokkonen (Fri May 08 2020 - 06:49:50 PDT)
- Re: [AMBER] OHE residue and crashing David A Case (Sun May 10 2020 - 11:28:15 PDT)
  - Re: [AMBER] OHE residue and crashing Christina Bergonzo (Mon May 11 2020 - 05:48:28 PDT)
    - Re: [AMBER] OHE residue and crashing Piia Kokkonen (Mon May 11 2020 - 23:04:31 PDT)
    - Re: [AMBER] OHE residue and crashing David A Case (Tue May 12 2020 - 05:21:38 PDT)
    - Re: [AMBER] OHE residue and crashing Piia Kokkonen (Wed May 13 2020 - 05:46:18 PDT)
    - Re: [AMBER] OHE residue and crashing David A Case (Wed May 13 2020 - 13:18:59 PDT)
[AMBER] Xmin minimisation Athena N (Fri May 08 2020 - 10:18:41 PDT)
- Re: [AMBER] Xmin minimisation Scott Brozell (Fri May 08 2020 - 17:41:26 PDT)
- Re: [AMBER] Xmin minimisation David A Case (Sat May 09 2020 - 05:59:17 PDT)
[AMBER] how to compute the protein interaction surface with the ligand Thomas Evangelidis (Fri May 08 2020 - 15:57:39 PDT)
- Re: [AMBER] how to compute the protein interaction surface with the ligand Thomas Evangelidis (Mon May 18 2020 - 13:56:33 PDT)
- Re: [AMBER] how to compute the protein interaction surface with the ligand Daniel Roe (Wed May 20 2020 - 09:00:42 PDT)
  - Re: [AMBER] how to compute the protein interaction surface with the ligand David A Case (Wed May 20 2020 - 10:31:03 PDT)
    - Re: [AMBER] how to compute the protein interaction surface with the ligand Thomas Evangelidis (Wed May 20 2020 - 11:26:48 PDT)
    - Re: [AMBER] how to compute the protein interaction surface with the ligand Carlos Simmerling (Wed May 20 2020 - 12:43:24 PDT)
    - Re: [AMBER] how to compute the protein interaction surface with the ligand Thomas Evangelidis (Sat May 23 2020 - 16:32:54 PDT)
    - Re: [AMBER] how to compute the protein interaction surface with the ligand Carlos Simmerling (Sat May 23 2020 - 16:45:00 PDT)
    - Re: [AMBER] how to compute the protein interaction surface with the ligand Thomas Evangelidis (Sat May 23 2020 - 17:11:51 PDT)
[AMBER] Temperature and total energy keeps dropping with NVE ensemble Liao (Fri May 08 2020 - 21:38:15 PDT)
- Re: [AMBER] Temperature and total energy keeps dropping with NVE ensemble David A Case (Sat May 09 2020 - 06:03:05 PDT)
- Re: [AMBER] Temperature and total energy keeps dropping with NVE ensemble Adrian Roitberg (Sat May 09 2020 - 08:52:55 PDT)
  - Re: [AMBER] Temperature and total energy keeps dropping with NVE ensemble David Cerutti (Sun May 10 2020 - 22:23:53 PDT)
[AMBER] GPU based TI runs Debarati DasGupta (Sat May 09 2020 - 04:56:04 PDT)
- Re: [AMBER] GPU based TI runs David A Case (Sat May 09 2020 - 06:10:19 PDT)
  - Re: [AMBER] GPU based TI runs Debarati DasGupta (Sat May 09 2020 - 07:00:52 PDT)
    - Re: [AMBER] GPU based TI runs Song, Lin (Sat May 09 2020 - 08:41:54 PDT)
    - Re: [AMBER] GPU based TI runs Debarati DasGupta (Sat May 09 2020 - 08:57:13 PDT)
    - Re: [AMBER] GPU based TI runs Song, Lin (Sat May 09 2020 - 10:28:51 PDT)
    - Re: [AMBER] GPU based TI runs Debarati DasGupta (Sat May 09 2020 - 10:40:39 PDT)
[AMBER] the error from make test.serial 谢信锐 (Sun May 10 2020 - 05:28:34 PDT)
- Re: [AMBER] the error from make test.serial David A Case (Sun May 10 2020 - 06:19:42 PDT)
  - Re: [AMBER] the error from make test.serial 谢信锐 (Sun May 10 2020 - 07:00:09 PDT)
    - Re: [AMBER] the error from make test.serial David A Case (Sun May 10 2020 - 11:17:28 PDT)
[AMBER] Neutralizing a system Jenny 148 (Sun May 10 2020 - 05:56:45 PDT)
- Re: [AMBER] Neutralizing a system David A Case (Sun May 10 2020 - 11:17:53 PDT)
[AMBER] Ewald grid size question Yuliana Bosken (Sun May 10 2020 - 16:10:01 PDT)
- Re: [AMBER] Ewald grid size question David A Case (Sun May 10 2020 - 18:05:03 PDT)
  - Re: [AMBER] Ewald grid size question Yuliana Bosken (Sun May 10 2020 - 18:10:55 PDT)
    - Re: [AMBER] Ewald grid size question David Cerutti (Sun May 10 2020 - 21:40:13 PDT)
[AMBER] error MMPBSA MYRIAN TORRES RICO (Mon May 11 2020 - 03:12:38 PDT)
- Re: [AMBER] error MMPBSA Elvis Martis (Mon May 11 2020 - 03:59:26 PDT)
  - Re: [AMBER] error MMPBSA MYRIAN TORRES RICO (Mon May 11 2020 - 04:49:04 PDT)
    - Re: [AMBER] error MMPBSA Elvis Martis (Mon May 11 2020 - 05:53:01 PDT)
- Re: [AMBER] error MMPBSA David A Case (Mon May 11 2020 - 04:51:49 PDT)
[AMBER] MMPBSA - Ternary System = protein-ligand-1-ligand-2 Marcelo Andrade Chagas (Mon May 11 2020 - 04:17:38 PDT)
- Re: [AMBER] MMPBSA - Ternary System = protein-ligand-1-ligand-2 David A Case (Mon May 11 2020 - 04:55:47 PDT)
[AMBER] 2 aminpurine parameter from Bryce reference? Kenneth Huang (Mon May 11 2020 - 13:15:55 PDT)
- Re: [AMBER] 2 aminpurine parameter from Bryce reference? David A Case (Mon May 11 2020 - 18:12:43 PDT)
  - Re: [AMBER] 2 aminpurine parameter from Bryce reference? Kenneth Huang (Tue May 12 2020 - 14:06:34 PDT)
    - Re: [AMBER] 2 aminpurine parameter from Bryce reference? David A Case (Tue May 12 2020 - 18:47:22 PDT)
[AMBER] 2 aminpurine parameter from Bryce reference? Kenneth Huang (Mon May 11 2020 - 13:31:37 PDT)
[AMBER] How to perameterize peptide like compound Rana Rehan Khalid (Tue May 12 2020 - 05:38:00 PDT)
- Re: [AMBER] How to perameterize peptide like compound David Cerutti (Tue May 12 2020 - 08:39:01 PDT)
- Re: [AMBER] How to perameterize peptide like compound Liao (Wed May 13 2020 - 00:00:47 PDT)
[AMBER] help MYRIAN TORRES RICO (Tue May 12 2020 - 09:21:29 PDT)
- Re: [AMBER] help David A Case (Tue May 12 2020 - 18:34:27 PDT)
  - Re: [AMBER] help MYRIAN TORRES RICO (Wed May 13 2020 - 10:27:53 PDT)
    - Re: [AMBER] help David A Case (Thu May 14 2020 - 18:31:31 PDT)
    - Re: [AMBER] help MYRIAN TORRES RICO (Fri May 15 2020 - 01:58:37 PDT)
[AMBER] Topology and parameters for the T4 - Thyroxine Marcelo Andrade Chagas (Tue May 12 2020 - 15:08:35 PDT)
- Re: [AMBER] Topology and parameters for the T4 - Thyroxine David A Case (Tue May 12 2020 - 18:51:17 PDT)
[AMBER] Open a hole into an equilibrated lipid bilayer Eduardo R. Almeida (Tue May 12 2020 - 19:44:54 PDT)
[AMBER] pmemd simulation Sofia Vasilakaki (Tue May 12 2020 - 23:01:28 PDT)
- Re: [AMBER] pmemd simulation David Cerutti (Tue May 12 2020 - 23:52:06 PDT)
[AMBER] autoimage waters Hector A. Baldoni (Wed May 13 2020 - 12:46:38 PDT)
- Re: [AMBER] autoimage waters Daniel Roe (Wed May 13 2020 - 15:07:25 PDT)
  - Re: [AMBER] autoimage waters Hector A. Baldoni (Wed May 13 2020 - 16:40:35 PDT)
[AMBER] About having an auto-restart keyword for the amber/orca interface. Zhiyi Wu (Wed May 13 2020 - 14:41:11 PDT)
[AMBER] installation problem Arthur Glasfeld (Wed May 13 2020 - 16:05:06 PDT)
- Re: [AMBER] installation problem David A Case (Thu May 14 2020 - 03:56:51 PDT)
[AMBER] Steered MD with COM_ANGLE Amanda Buyan (Wed May 13 2020 - 16:32:22 PDT)
- Re: [AMBER] Steered MD with COM_ANGLE Adrian Roitberg (Wed May 13 2020 - 16:36:49 PDT)
  - Re: [AMBER] Steered MD with COM_ANGLE Amanda Buyan (Wed May 13 2020 - 16:43:06 PDT)
    - Re: [AMBER] Steered MD with COM_ANGLE Kellon Belfon (Wed May 13 2020 - 19:34:31 PDT)
    - Re: [AMBER] Steered MD with COM_ANGLE Amanda Buyan (Wed May 13 2020 - 23:18:43 PDT)
    - Re: [AMBER] Steered MD with COM_ANGLE Kellon Belfon (Thu May 14 2020 - 12:04:04 PDT)
    - Re: [AMBER] Steered MD with COM_ANGLE Amanda Buyan (Thu May 14 2020 - 19:20:28 PDT)
    - Re: [AMBER] Steered MD with COM_ANGLE Feng Pan (Mon May 18 2020 - 06:35:27 PDT)
[AMBER] AMBER 18 GPU Renato Araujo (Thu May 14 2020 - 09:53:40 PDT)
- Re: [AMBER] AMBER 18 GPU Liao (Thu May 14 2020 - 11:02:21 PDT)
[AMBER] differences in EGB energies sander vs. pmemd Niransha Kumarachchi (Thu May 14 2020 - 16:20:28 PDT)
- Re: [AMBER] differences in EGB energies sander vs. pmemd David A Case (Thu May 14 2020 - 18:28:36 PDT)
[AMBER] Fwd: Fw: Amber18 - MPI version error on HPC Cluster Sivanandam Magudeeswaran (Thu May 14 2020 - 21:04:53 PDT)
- Re: [AMBER] Fwd: Fw: Amber18 - MPI version error on HPC Cluster Gustaf Olsson (Thu May 14 2020 - 22:34:46 PDT)
- Re: [AMBER] Fwd: Fw: Amber18 - MPI version error on HPC Cluster David A Case (Fri May 15 2020 - 07:46:18 PDT)
[AMBER] Questions about PCA Kat G (Thu May 14 2020 - 21:27:24 PDT)
- Re: [AMBER] Questions about PCA Daniel Roe (Wed May 20 2020 - 09:16:42 PDT)
[AMBER] Query regarding calculating RMSF. DHEERAJ CHITARA (Thu May 14 2020 - 23:51:19 PDT)
- Re: [AMBER] Query regarding calculating RMSF. Md Fulbabu Sk (Fri May 15 2020 - 04:57:32 PDT)
- Re: [AMBER] Query regarding calculating RMSF. Daniel Roe (Mon May 18 2020 - 09:03:46 PDT)
[AMBER] Installation error Hrishikesh Dhondge (Fri May 15 2020 - 03:09:44 PDT)
- Re: [AMBER] Installation error David A Case (Fri May 15 2020 - 07:38:38 PDT)
  - Re: [AMBER] Installation error Hrishikesh Dhondge (Sat May 16 2020 - 03:14:40 PDT)
[AMBER] updating to ambertools 20 from version 19 Homeo Morphism (Fri May 15 2020 - 03:57:48 PDT)
- Re: [AMBER] updating to ambertools 20 from version 19 David A Case (Fri May 15 2020 - 07:42:04 PDT)
[AMBER] Installation Error while linking C executable xaLeap Hrishikesh Dhondge (Fri May 15 2020 - 06:33:14 PDT)
[AMBER] Similar RESP1 and RESP2 fitting outputs Kodituwakku,Dimuthu Nirmani (Fri May 15 2020 - 07:16:21 PDT)
[AMBER] Mol2 to generatee prepc and frcmod fo using Antechamer Lod King (Fri May 15 2020 - 08:36:08 PDT)
- Re: [AMBER] Mol2 to generatee prepc and frcmod fo using Antechamer Renato Araujo (Fri May 15 2020 - 16:01:40 PDT)
  - Re: [AMBER] Mol2 to generatee prepc and frcmod fo using Antechamer Lod King (Fri May 15 2020 - 21:09:20 PDT)
- Re: [AMBER] Mol2 to generatee prepc and frcmod fo using Antechamer David A Case (Sat May 16 2020 - 05:05:07 PDT)
  - Re: [AMBER] Mol2 to generatee prepc and frcmod fo using Antechamer Lod King (Sat May 16 2020 - 13:16:25 PDT)
    - Re: [AMBER] Mol2 to generatee prepc and frcmod fo using Antechamer David A Case (Sat May 16 2020 - 18:48:47 PDT)
    - Re: [AMBER] Mol2 to generatee prepc and frcmod fo using Antechamer Lod King (Sat May 16 2020 - 19:00:01 PDT)
    - Re: [AMBER] Mol2 to generatee prepc and frcmod fo using Antechamer Renato Araujo (Sun May 17 2020 - 06:12:50 PDT)
    - Re: [AMBER] Mol2 to generatee prepc and frcmod fo using Antechamer Lod King (Sun May 17 2020 - 06:40:47 PDT)
    - Re: [AMBER] Mol2 to generatee prepc and frcmod fo using Antechamer Renato Araujo (Sun May 17 2020 - 07:31:37 PDT)
    - Re: [AMBER] Mol2 to generatee prepc and frcmod fo using Antechamer David A Case (Tue May 19 2020 - 05:02:32 PDT)
    - Re: [AMBER] Mol2 to generatee prepc and frcmod fo using Antechamer Lod King (Tue May 19 2020 - 10:53:07 PDT)
    - Re: [AMBER] Mol2 to generatee prepc and frcmod fo using Antechamer David A Case (Tue May 19 2020 - 18:25:15 PDT)
[AMBER] Query regarding force fields SHAUNAK BADANI (Fri May 15 2020 - 11:10:15 PDT)
- Re: [AMBER] Query regarding force fields Carlos Simmerling (Fri May 15 2020 - 11:25:18 PDT)
[AMBER] upgrade to 19 Scott Brozell (Fri May 15 2020 - 15:01:29 PDT)
- Re: [AMBER] upgrade to 19 David A Case (Sat May 16 2020 - 05:29:36 PDT)
[AMBER] Amber20 MPIC location problem Filip Fratev (Fri May 15 2020 - 20:54:11 PDT)
- Re: [AMBER] Amber20 MPICH location problem Filip Fratev (Sat May 16 2020 - 02:57:29 PDT)
- Re: [AMBER] Amber20 MPIC location problem David A Case (Sat May 16 2020 - 05:46:43 PDT)
  - Re: [AMBER] Amber20 MPICH location problem fratev.biomed.bas.bg (Sat May 16 2020 - 20:13:19 PDT)
    - Re: [AMBER] Amber20 MPICH location problem Filip Fratev (Sun May 17 2020 - 01:25:51 PDT)
    - Re: [AMBER] Amber20 MPICH location problem David A Case (Sun May 17 2020 - 05:46:08 PDT)
- Re: [AMBER] Amber20 MPIC location problem Gerald Monard (Sun May 17 2020 - 07:26:29 PDT)
[AMBER] Could not find control namelist error Jisha B (Sat May 16 2020 - 04:31:11 PDT)
- Re: [AMBER] Could not find control namelist error Carlos Simmerling (Sat May 16 2020 - 04:39:08 PDT)
[AMBER] Absolute free energy calculation-GitHub Sadaf Rani (Sat May 16 2020 - 17:03:00 PDT)
[AMBER] Amber20 pmemd.cuda installation and performance problems Filip Fratev (Sun May 17 2020 - 01:43:26 PDT)
- Re: [AMBER] Amber20 pmemd.cuda installation and performance problems viktor drobot (Sun May 17 2020 - 01:53:21 PDT)
  - Re: [AMBER] Amber20 pmemd.cuda installation and performance problems David Cerutti (Tue May 19 2020 - 12:39:50 PDT)
    - Re: [AMBER] Amber20 pmemd.cuda installation and performance problems Filip Fratev (Wed May 27 2020 - 03:00:36 PDT)
    - Re: [AMBER] Amber20 pmemd.cuda installation and performance problems Filip Fratev (Wed May 27 2020 - 03:12:46 PDT)
    - Re: [AMBER] Amber20 pmemd.cuda installation and performance problems David Cerutti (Wed May 27 2020 - 04:54:32 PDT)
- Re: [AMBER] Amber20 pmemd.cuda installation David A Case (Sun May 17 2020 - 17:34:56 PDT)
- Re: [AMBER] Amber20 pmemd.cuda performance problems (especially on Turing-based GPUs) Thomas Zeiser (Mon May 25 2020 - 02:01:09 PDT)
  - Re: [AMBER] Amber20 pmemd.cuda performance problems (especially on Turing-based GPUs) David Cerutti (Mon May 25 2020 - 02:40:35 PDT)
    - Re: [AMBER] Amber20 pmemd.cuda performance problems (especially on Turing-based GPUs) Brent Krueger (Mon May 25 2020 - 06:04:28 PDT)
    - Re: [AMBER] Amber20 pmemd.cuda performance problems (especially on Turing-based GPUs) David Cerutti (Thu May 28 2020 - 08:34:25 PDT)
- Re: [AMBER] Amber20 pmemd.cuda installation and performance problems David Cerutti (Thu May 28 2020 - 15:51:16 PDT)
[AMBER] Galactosylation of 5-Hydroxylysine Harald Lanig (Thu May 14 2020 - 09:05:08 PDT)
- Re: [AMBER] Galactosylation of 5-Hydroxylysine Lachele Foley (Tue May 19 2020 - 13:21:50 PDT)
[AMBER] parameter for modified residue sangita kachhap (Mon May 18 2020 - 09:32:01 PDT)
- Re: [AMBER] parameter for modified residue David A Case (Tue May 19 2020 - 04:43:40 PDT)
  - Re: [AMBER] parameter for modified residue sangita kachhap (Tue May 19 2020 - 12:56:35 PDT)
[AMBER] COM position mohamed marzouk (Tue May 19 2020 - 02:41:30 PDT)
- Re: [AMBER] COM position Daniel Roe (Tue May 19 2020 - 04:30:22 PDT)
- Re: [AMBER] COM position Daniel Roe (Mon Jun 01 2020 - 12:26:00 PDT)
  - Re: [AMBER] COM position mohamed marzouk (Tue Jun 02 2020 - 16:48:06 PDT)
[AMBER] How to use set pert=true Dawid das (Wed May 20 2020 - 09:32:27 PDT)
- Re: [AMBER] How to use set pert=true David A Case (Wed May 20 2020 - 10:43:27 PDT)
  - Re: [AMBER] How to use set pert=true Dawid das (Wed May 20 2020 - 12:07:10 PDT)
    - Re: [AMBER] How to use set pert=true David A Case (Wed May 20 2020 - 18:15:53 PDT)
    - Re: [AMBER] How to use set pert=true Dawid das (Fri May 22 2020 - 07:34:35 PDT)
[AMBER] AMBER Tools 20: Bug in libraries of modified amino acids prevents force field load Matias Machado (Wed May 20 2020 - 10:13:34 PDT)
- Re: [AMBER] AMBER Tools 20: Bug in libraries of modified amino acids prevents force field load Kellon Belfon (Wed May 20 2020 - 14:13:51 PDT)
[AMBER] MMPBSA - per residue decomposition Prasanth G, Research Scholar (Thu May 21 2020 - 01:09:47 PDT)
- Re: [AMBER] MMPBSA - per residue decomposition Prasanth G, Research Scholar (Fri May 22 2020 - 23:50:47 PDT)
[AMBER] paramfit - negative energy for 1 of the 2 term Erdem Yeler (Thu May 21 2020 - 05:26:07 PDT)
- Re: [AMBER] paramfit - negative energy for 1 of the 2 term Robin Betz (Thu May 21 2020 - 14:51:02 PDT)
  - Re: [AMBER] paramfit - negative energy for 1 of the 2 term Erdem Yeler (Sat May 23 2020 - 08:17:55 PDT)
[AMBER] Amber20 serial make test FAILUREs on IBM Power9 Cong Liu (Thu May 21 2020 - 07:03:12 PDT)
- Re: [AMBER] Amber20 serial make test FAILUREs on IBM Power9 Cong Liu (Thu May 21 2020 - 07:08:05 PDT)
- Re: [AMBER] Amber20 serial make test FAILUREs on IBM Power9 David A Case (Thu May 21 2020 - 11:00:41 PDT)
  - Re: [AMBER] Amber20 serial make test FAILUREs on IBM Power9 Cong Liu (Thu May 21 2020 - 14:03:33 PDT)
[AMBER] TI production runs(20ns) NVT query Debarati DasGupta (Thu May 21 2020 - 07:05:42 PDT)
[AMBER] QM/MM MD: Error reading box emanuele falbo (Thu May 21 2020 - 07:42:33 PDT)
- Re: [AMBER] QM/MM MD: Error reading box David A Case (Thu May 21 2020 - 11:05:06 PDT)
  - Re: [AMBER] QM/MM MD: Error reading box emanuele falbo (Fri May 22 2020 - 01:23:23 PDT)
    - Re: [AMBER] QM/MM MD: Error reading box Daniel Roe (Fri May 22 2020 - 04:44:34 PDT)
    - Re: [AMBER] QM/MM MD: Error reading box David A Case (Fri May 22 2020 - 05:32:37 PDT)
    - Re: [AMBER] QM/MM MD: Error reading box emanuele falbo (Fri May 22 2020 - 06:58:27 PDT)
    - Re: [AMBER] QM/MM MD: Error reading box Daniel Roe (Fri May 22 2020 - 08:05:03 PDT)
    - Re: [AMBER] QM/MM MD: Error reading box Daniel Roe (Fri May 22 2020 - 08:55:51 PDT)
    - Re: [AMBER] QM/MM MD: Error reading box emanuele falbo (Sun May 24 2020 - 02:37:03 PDT)
    - Re: [AMBER] QM/MM MD: Error reading box David A Case (Sun May 24 2020 - 06:26:43 PDT)
    - Re: [AMBER] QM/MM MD: Error reading box emanuele falbo (Mon May 25 2020 - 02:39:39 PDT)
[AMBER] Free energy of solvation using polarizable force fields Carl Heroneme (Thu May 21 2020 - 14:11:06 PDT)
- Re: [AMBER] Free energy of solvation using polarizable force fields David A Case (Sat May 23 2020 - 09:31:35 PDT)
[AMBER] Different LJ parameters in .dat file and 'atominfo' output José Daniel Martinez (Sat May 23 2020 - 05:17:50 PDT)
- Re: [AMBER] Different LJ parameters in .dat file and 'atominfo' output Daniel Roe (Tue May 26 2020 - 08:23:36 PDT)
  - Re: [AMBER] Different LJ parameters in .dat file and 'atominfo' output José Daniel Martinez (Wed May 27 2020 - 01:25:01 PDT)
    - Re: [AMBER] Different LJ parameters in .dat file and 'atominfo' output Daniel Roe (Wed May 27 2020 - 07:59:41 PDT)
[AMBER] Changing hydrogen atom radius to optimize saltbridge in GB-OBC model Sunita Patel (Sat May 23 2020 - 07:01:04 PDT)
- Re: [AMBER] Changing hydrogen atom radius to optimize saltbridge in GB-OBC model Carlos Simmerling (Sat May 23 2020 - 07:16:56 PDT)
  - Re: [AMBER] Changing hydrogen atom radius to optimize saltbridge in GB-OBC model Sunita Patel (Sat May 23 2020 - 21:05:57 PDT)
    - Re: [AMBER] Changing hydrogen atom radius to optimize saltbridge in GB-OBC model Kellon Belfon (Sat May 23 2020 - 22:46:50 PDT)
    - Re: [AMBER] Changing hydrogen atom radius to optimize saltbridge in GB-OBC model Sunita Patel (Sun May 24 2020 - 06:07:07 PDT)
[AMBER] Amber18 with AmberTools20 test.serial FAILURES and ERRORS Samanta M (Sat May 23 2020 - 07:02:03 PDT)
- Re: [AMBER] Amber18 with AmberTools20 test.serial FAILURES and ERRORS Josh Berryman (Sat May 23 2020 - 09:03:57 PDT)
- Re: [AMBER] Amber18 with AmberTools20 test.serial FAILURES and ERRORS David A Case (Sat May 23 2020 - 09:12:29 PDT)
  - Re: [AMBER] Amber18 with AmberTools20 test.serial FAILURES and ERRORS Samanta M (Sat May 23 2020 - 11:07:50 PDT)
[AMBER] Help with Acpype on AMberTools19 Prapasiri Pongprayoon (Sun May 24 2020 - 23:02:50 PDT)
[AMBER] Help with Acpype in AmberTools19 Prapasiri Pongprayoon (Sun May 24 2020 - 23:07:32 PDT)
[AMBER] Questions about QM Ignjat Filipović (Mon May 25 2020 - 07:23:45 PDT)
[AMBER] clustering parameter files Ranim Maaieh (Mon May 25 2020 - 07:36:39 PDT)
- Re: [AMBER] clustering parameter files Daniel Roe (Tue May 26 2020 - 07:54:07 PDT)
  - Re: [AMBER] clustering parameter files Ranim Maaieh (Sun Jun 07 2020 - 16:43:21 PDT)
    - Re: [AMBER] clustering parameter files Daniel Roe (Wed Jun 24 2020 - 05:42:40 PDT)
[AMBER] What would you like to see in visualization of chemical data? Jan Mičan (Tue May 26 2020 - 09:59:39 PDT)
[AMBER] installation failed libsanderles.dir amd plumed Andrew Waight (Tue May 26 2020 - 21:07:59 PDT)
- Re: [AMBER] installation failed libsanderles.dir amd plumed David A Case (Wed May 27 2020 - 05:25:20 PDT)
  - Re: [AMBER] installation failed libsanderles.dir amd plumed Andrew Waight (Wed May 27 2020 - 07:11:45 PDT)
[AMBER] Missing bond parameters after MCPB.py Oleksandr Kravchenko (Wed May 27 2020 - 03:29:31 PDT)
- Re: [AMBER] Missing bond parameters after MCPB.py Pengfei Li (Mon Jul 20 2020 - 12:17:50 PDT)
[AMBER] Tool to calculate CSP and NOE for DNA trajectory? Kenneth Huang (Wed May 27 2020 - 16:47:41 PDT)
- Re: [AMBER] Tool to calculate CSP and NOE for DNA trajectory? Christina Bergonzo (Thu May 28 2020 - 05:42:20 PDT)
  - Re: [AMBER] Tool to calculate CSP and NOE for DNA trajectory? Kenneth Huang (Thu May 28 2020 - 20:57:59 PDT)
[AMBER] Installing latest ambertools (2020) with conda Alan (Thu May 28 2020 - 02:41:50 PDT)
- Re: [AMBER] Installing latest ambertools (2020) with conda David A Case (Thu May 28 2020 - 05:59:13 PDT)
  - Re: [AMBER] Installing latest ambertools (2020) with conda Alan (Thu May 28 2020 - 06:04:48 PDT)
    - Re: [AMBER] Installing latest ambertools (2020) with conda David A Case (Thu May 28 2020 - 08:34:10 PDT)
[AMBER] Small molecules paramters Athena N (Thu May 28 2020 - 05:47:24 PDT)
- Re: [AMBER] Small molecules paramters Gustaf Olsson (Thu May 28 2020 - 22:53:03 PDT)
- Re: [AMBER] Small molecules paramters Gustavo Seabra (Fri May 29 2020 - 09:20:56 PDT)
[AMBER] Amber99SB force field Seketoulie Keretsu (Thu May 28 2020 - 05:51:12 PDT)
- Re: [AMBER] Amber99SB force field Carlos Simmerling (Thu May 28 2020 - 06:16:02 PDT)
  - Re: [AMBER] [EXTERNAL] Re: Amber99SB force field Smith, Micholas D. (Thu May 28 2020 - 11:54:46 PDT)
- Re: [AMBER] Amber99SB force field Gustavo Seabra (Thu May 28 2020 - 06:56:08 PDT)
  - Re: [AMBER] Amber99SB force field Carlos Simmerling (Thu May 28 2020 - 07:12:52 PDT)
[AMBER] AMBER 16 NFE MULTI_RMSD Question on the Output of reaction variable Xiaoyong Zhang (Thu May 28 2020 - 08:39:38 PDT)
[AMBER] Simulating pyridine in water TIP3P Debarati DasGupta (Thu May 28 2020 - 09:22:57 PDT)
- Re: [AMBER] Simulating pyridine in water TIP3P David A Case (Thu May 28 2020 - 18:33:01 PDT)
[AMBER] Amber20 Performance on RTX (Turing): known problems, with a patch forthcoming David Cerutti (Thu May 28 2020 - 23:30:20 PDT)
- Re: [AMBER] Amber20 Performance on RTX (Turing): known problems, with a patch forthcoming Tim Travers (Tue Jul 21 2020 - 08:17:07 PDT)
  - Re: [AMBER] Amber20 Performance on RTX (Turing): known problems, with a patch forthcoming David Cerutti (Tue Jul 21 2020 - 09:06:31 PDT)
    - Re: [AMBER] Amber20 Performance on RTX (Turing): known problems, with a patch forthcoming Tim Travers (Tue Jul 21 2020 - 09:40:40 PDT)
  - Re: [AMBER] Amber20 Performance on RTX (Turing): known problems, with a patch forthcoming David A Case (Fri Aug 07 2020 - 17:41:25 PDT)
[AMBER] questions for mdgx-virtual site Gao J (Fri May 29 2020 - 01:29:44 PDT)
- Re: [AMBER] questions for mdgx-virtual site David Cerutti (Fri May 29 2020 - 02:42:42 PDT)
  - Re: [AMBER] questions for mdgx-virtual site David Cerutti (Fri May 29 2020 - 02:49:46 PDT)
[AMBER] igb for non-aqueous solvent? Timothy Schutt (Fri May 29 2020 - 06:40:59 PDT)
- Re: [AMBER] igb for non-aqueous solvent? David A Case (Mon Jun 01 2020 - 07:00:00 PDT)
  - Re: [AMBER] igb for non-aqueous solvent? Timothy Schutt (Mon Jun 01 2020 - 07:34:27 PDT)
[AMBER] how to identify lipids around a protein Sally Pias (Fri May 29 2020 - 17:53:48 PDT)
- Re: [AMBER] how to identify lipids around a protein Prajwal Nandekar (Fri May 29 2020 - 18:22:43 PDT)
Re: [AMBER] Amber for help 马海川 (Sat May 30 2020 - 06:04:02 PDT)
Re: [AMBER] AMBER Digest, Vol 3017, Issue 1 Gao J (Sat May 30 2020 - 19:18:36 PDT)
- Re: [AMBER] AMBER Digest, Vol 3017, Issue 1 David Cerutti (Sat May 30 2020 - 20:59:36 PDT)
[AMBER] amber20 output header Baker, Joseph (Sat May 30 2020 - 19:18:49 PDT)
- Re: [AMBER] amber20 output header David Cerutti (Sat May 30 2020 - 20:56:46 PDT)
  - Re: [AMBER] amber20 output header Baker, Joseph (Thu Jun 11 2020 - 06:47:05 PDT)
Re: [AMBER] Using pytraj with jupyter notebook Rangarajan, Amith (Sun May 31 2020 - 12:44:17 PDT)
- Re: [AMBER] Using pytraj with jupyter notebook Hai Nguyen (Sun May 31 2020 - 16:43:39 PDT)
Re: [AMBER] AMBER Digest, Vol 3019, Issue 1 Gao J (Sun May 31 2020 - 19:05:05 PDT)
- Re: [AMBER] AMBER Digest, Vol 3019, Issue 1 David Cerutti (Mon Jun 01 2020 - 03:28:03 PDT)
Re: [AMBER] AMBER Digest, Vol 3020, Issue 1 Gao J (Mon Jun 01 2020 - 18:17:05 PDT)
- Re: [AMBER] AMBER Digest, Vol 3020, Issue 1 Manish Manish (Mon Jun 01 2020 - 18:27:55 PDT)
[AMBER] CHARMM Forcefield in Amber - which barostat and ntp to use? Amanda Buyan (Tue Jun 02 2020 - 20:54:59 PDT)
- Re: [AMBER] CHARMM Forcefield in Amber - which barostat and ntp to use? David Cerutti (Wed Jun 03 2020 - 01:29:31 PDT)
  - Re: [AMBER] CHARMM Forcefield in Amber - which barostat and ntp to use? David A Case (Wed Jun 03 2020 - 06:17:56 PDT)
    - Re: [AMBER] CHARMM Forcefield in Amber - which barostat and ntp to use? Batuhan Kav (Wed Jun 03 2020 - 06:44:06 PDT)
    - Re: [AMBER] CHARMM Forcefield in Amber - which barostat and ntp to use? Matias Machado (Wed Jun 03 2020 - 07:51:32 PDT)
    - Re: [AMBER] CHARMM Forcefield in Amber - which barostat and ntp to use? Amanda Buyan (Wed Jun 03 2020 - 17:30:52 PDT)
    - Re: [AMBER] CHARMM Forcefield in Amber - which barostat and ntp to use? Sally Pias (Thu Jun 04 2020 - 14:08:08 PDT)
    - Re: [AMBER] CHARMM Forcefield in Amber - which barostat and ntp to use? Amanda Buyan (Thu Jun 04 2020 - 19:46:33 PDT)
    - Re: [AMBER] CHARMM Forcefield in Amber - which barostat and ntp to use? Sally Pias (Thu Jun 04 2020 - 20:16:59 PDT)
    - Re: [AMBER] CHARMM Forcefield in Amber - which barostat and ntp to use? Sally Pias (Fri Jun 05 2020 - 10:52:33 PDT)
    - Re: [AMBER] CHARMM Forcefield in Amber - which barostat and ntp to use? Amanda Buyan (Wed Jun 03 2020 - 17:15:01 PDT)
  - Re: [AMBER] CHARMM Forcefield in Amber - which barostat and ntp to use? Amanda Buyan (Wed Jun 03 2020 - 17:10:15 PDT)
[AMBER] suggestion for generation of prmtop and inpcrd file at different pH Vikram Dalal (Wed Jun 03 2020 - 14:04:52 PDT)
[AMBER] MC barostat Debarati DasGupta (Thu Jun 04 2020 - 07:25:10 PDT)
[AMBER] help with building an amino acid based surfactant molecule Billiot, Eugene (Thu Jun 04 2020 - 08:01:18 PDT)
- Re: [AMBER] help with building an amino acid based surfactant molecule Carlos Simmerling (Thu Jun 04 2020 - 08:20:24 PDT)
  - Re: [AMBER] help with building an amino acid based surfactant molecule Carlos Simmerling (Thu Jun 04 2020 - 08:21:36 PDT)
    - Re: [AMBER] help with building an amino acid based surfactant molecule Billiot, Eugene (Thu Jun 04 2020 - 08:28:57 PDT)
    - Re: [AMBER] help with building an amino acid based surfactant molecule Carlos Simmerling (Thu Jun 04 2020 - 08:56:50 PDT)
    - Re: [AMBER] help with building an amino acid based surfactant molecule Carlos Simmerling (Thu Jun 04 2020 - 09:52:10 PDT)
    - Re: [AMBER] help with building an amino acid based surfactant molecule Billiot, Eugene (Thu Jun 04 2020 - 10:12:12 PDT)
    - Re: [AMBER] help with building an amino acid based surfactant molecule Carlos Simmerling (Thu Jun 04 2020 - 10:13:21 PDT)
    - Re: [AMBER] help with building an amino acid based surfactant molecule Billiot, Eugene (Thu Jun 04 2020 - 15:55:54 PDT)
    - Re: [AMBER] help with building an amino acid based surfactant molecule Garcia, Mauro (Fri Jun 12 2020 - 11:08:54 PDT)
    - Re: [AMBER] help with building an amino acid based surfactant molecule Garcia, Mauro (Fri Jun 12 2020 - 11:22:46 PDT)
[AMBER] What is happening in my Molecular Dynamics in the beginning of every 500 steps ? Erdem Yeler (Thu Jun 04 2020 - 08:34:26 PDT)
- Re: [AMBER] What is happening in my Molecular Dynamics in the beginning of every 500 steps ? Carlos Simmerling (Thu Jun 04 2020 - 08:57:57 PDT)
  - Re: [AMBER] What is happening in my Molecular Dynamics in the beginning of every 500 steps ? David Cerutti (Thu Jun 04 2020 - 09:07:19 PDT)
    - Re: [AMBER] What is happening in my Molecular Dynamics in the beginning of every 500 steps ? Busra Demir (Thu Jun 04 2020 - 14:19:34 PDT)
    - Re: [AMBER] What is happening in my Molecular Dynamics in the beginning of every 500 steps ? Erdem Yeler (Sat Jun 06 2020 - 15:52:23 PDT)
    - Re: [AMBER] What is happening in my Molecular Dynamics in the beginning of every 500 steps ? David A Case (Sat Jun 06 2020 - 18:07:27 PDT)
    - Re: [AMBER] What is happening in my Molecular Dynamics in the beginning of every 500 steps ? Erdem Yeler (Sun Jun 07 2020 - 14:01:41 PDT)
    - Re: [AMBER] What is happening in my Molecular Dynamics in the beginning of every 500 steps ? David A Case (Sun Jun 07 2020 - 17:31:25 PDT)
    - Re: [AMBER] What is happening in my Molecular Dynamics in the beginning of every 500 steps ? Erdem Yeler (Fri Jun 12 2020 - 09:49:45 PDT)
    - Re: [AMBER] What is happening in my Molecular Dynamics in the beginning of every 500 steps ? Erdem Yeler (Fri Jun 26 2020 - 10:50:47 PDT)
    - Re: [AMBER] What is happening in my Molecular Dynamics in the beginning of every 500 steps ? Carlos Simmerling (Fri Jun 26 2020 - 11:20:39 PDT)
[AMBER] protein on gold surface Raik Grünberg (Thu Jun 04 2020 - 11:26:15 PDT)
- Re: [AMBER] protein on gold surface Casalini Tommaso (Mon Jun 08 2020 - 03:14:47 PDT)
  - Re: [AMBER] protein on gold surface Raik Grünberg (Wed Jun 10 2020 - 12:43:47 PDT)
    - Re: [AMBER] protein on gold surface Gustaf Olsson (Wed Jun 10 2020 - 22:59:27 PDT)
[AMBER] using PLUMED with pmemd.cuda? Amanda Buyan (Thu Jun 04 2020 - 19:48:31 PDT)
- Re: [AMBER] using PLUMED with pmemd.cuda? viktor drobot (Fri Jun 05 2020 - 02:34:35 PDT)
[AMBER] ambertools19 Renato Araujo (Fri Jun 05 2020 - 18:39:28 PDT)
- Re: [AMBER] ambertools19 Karl Kirschner (Fri Jun 05 2020 - 23:45:07 PDT)
- Re: [AMBER] ambertools19 David A Case (Sat Jun 06 2020 - 06:07:35 PDT)
[AMBER] Converting Amber trajectory NetCDF file to Desmond readable Nada Afiva (Sun Jun 07 2020 - 03:38:11 PDT)
[AMBER] MM/PBSA and GBSA fails Thakur, Abhishek (Sun Jun 07 2020 - 16:02:48 PDT)
- Re: [AMBER] MM/PBSA and GBSA fails David A Case (Sun Jun 07 2020 - 17:35:29 PDT)
[AMBER] Gold in PARMCHK.dat Antechamber. anirudh mantri (Mon Jun 08 2020 - 01:59:25 PDT)
- Re: [AMBER] Gold in PARMCHK.dat Antechamber. David A Case (Mon Jun 08 2020 - 06:42:09 PDT)
[AMBER] tleap splitting the lipid zhiyi wu (Mon Jun 08 2020 - 02:58:22 PDT)
- Re: [AMBER] tleap splitting the lipid David A Case (Mon Jun 08 2020 - 05:22:36 PDT)
  - Re: [AMBER] tleap splitting the lipid Matias Machado (Mon Jun 08 2020 - 06:12:34 PDT)
    - Re: [AMBER] tleap splitting the lipid Matias Machado (Mon Jun 08 2020 - 08:46:00 PDT)
[AMBER] MCPB.py problem to make step 1 works Barak Alnami (Mon Jun 08 2020 - 04:19:56 PDT)
- Re: [AMBER] MCPB.py problem to make step 1 works Pengfei Li (Thu Jun 11 2020 - 08:30:37 PDT)
[AMBER] error installation mpi Renato Araujo (Mon Jun 08 2020 - 07:18:21 PDT)
- Re: [AMBER] error installation mpi David A Case (Mon Jun 08 2020 - 07:41:09 PDT)
  - Re: [AMBER] error installation mpi Renato Araujo (Mon Jun 08 2020 - 08:29:28 PDT)
    - Re: [AMBER] error installation mpi David A Case (Mon Jun 08 2020 - 08:56:02 PDT)
[AMBER] residue renumbering in trajectory files Ranim Maaieh (Mon Jun 08 2020 - 13:40:51 PDT)
- Re: [AMBER] residue renumbering in trajectory files Kenneth Huang (Mon Jun 08 2020 - 15:51:27 PDT)
[AMBER] Individual water lifetimes within a distance cutoff? Kenneth Huang (Mon Jun 08 2020 - 16:18:17 PDT)
- Re: [AMBER] Individual water lifetimes within a distance cutoff? Markowska (Tue Jun 09 2020 - 05:49:16 PDT)
- Re: [AMBER] Individual water lifetimes within a distance cutoff? Daniel Roe (Tue Jun 09 2020 - 08:01:09 PDT)
- Re: [AMBER] Individual water lifetimes within a distance cutoff? Kenneth Huang (Tue Jun 09 2020 - 20:55:20 PDT)
[AMBER] steered MD with restraints on a selection Baker, Joseph (Mon Jun 08 2020 - 19:44:03 PDT)
- Re: [AMBER] steered MD with restraints on a selection Pinky Mazumder (Fri Jul 24 2020 - 19:51:46 PDT)
[AMBER] Charge parameters in GAFF Stefan Menzel (Mon Jun 08 2020 - 22:52:45 PDT)
- Re: [AMBER] Charge parameters in GAFF Lorenzo Gontrani (Mon Jun 08 2020 - 23:35:12 PDT)
  - Re: [AMBER] Charge parameters in GAFF Stefan Menzel (Tue Jun 09 2020 - 01:14:04 PDT)
    - Re: [AMBER] Charge parameters in GAFF Lorenzo Gontrani (Tue Jun 09 2020 - 05:18:36 PDT)
  - Re: [AMBER] Charge parameters in GAFF David A Case (Tue Jun 09 2020 - 05:00:34 PDT)
[AMBER] Parameters for sphingomyelin Jianguo Li (Tue Jun 09 2020 - 02:11:55 PDT)
[AMBER] Steered MD with highly charged species Delwakkada Liyanage, Senal Dinuka (Tue Jun 09 2020 - 08:55:06 PDT)
[AMBER] Xleap - disappearance of selection when trying to relax selection Billiot, Eugene (Tue Jun 09 2020 - 11:18:43 PDT)
- Re: [AMBER] Xleap - disappearance of selection when trying to relax selection David A Case (Tue Jun 09 2020 - 13:37:30 PDT)
  - Re: [AMBER] Xleap - disappearance of selection when trying to relax selection Billiot, Eugene (Wed Jun 10 2020 - 06:59:29 PDT)
    - Re: [AMBER] Xleap - disappearance of selection when trying to relax selection David A Case (Wed Jun 10 2020 - 08:29:07 PDT)
    - Re: [AMBER] Xleap - disappearance of selection when trying to relax selection Scott Brozell (Wed Jun 10 2020 - 23:32:57 PDT)
[AMBER] tleap - extract ion molecules and save it as pdb HOCHEOL LIM (Tue Jun 09 2020 - 16:14:02 PDT)
- Re: [AMBER] tleap - extract ion molecules and save it as pdb David A Case (Wed Jun 10 2020 - 04:33:02 PDT)
- Re: [AMBER] tleap - extract ion molecules and save it as pdb Daniel Roe (Wed Jun 10 2020 - 05:53:27 PDT)
[AMBER] atom type in a substituted pyrimidine Sofia Vasilakaki (Wed Jun 10 2020 - 00:10:50 PDT)
[AMBER] tiMerge error with ff19SB HOCHEOL LIM (Wed Jun 10 2020 - 01:30:47 PDT)
[AMBER] Python related problem running MMPBSA.py.MPI Casalini Tommaso (Wed Jun 10 2020 - 07:36:18 PDT)
- Re: [AMBER] Python related problem running MMPBSA.py.MPI David A Case (Wed Jun 10 2020 - 08:31:25 PDT)
  - Re: [AMBER] Python related problem running MMPBSA.py.MPI Casalini Tommaso (Wed Jun 10 2020 - 08:37:07 PDT)
    - Re: [AMBER] Python related problem running MMPBSA.py.MPI Casalini Tommaso (Wed Jun 10 2020 - 08:57:54 PDT)
[AMBER] Parameters for Implicit Membrane in MMPBSA.py Li,Haoxi (Wed Jun 10 2020 - 12:08:14 PDT)
- Re: [AMBER] Parameters for Implicit Membrane in MMPBSA.py Ray Luo (Thu Jun 11 2020 - 07:27:48 PDT)
  - Re: [AMBER] Parameters for Implicit Membrane in MMPBSA.py Li,Haoxi (Wed Jun 17 2020 - 14:41:35 PDT)
    - Re: [AMBER] Parameters for Implicit Membrane in MMPBSA.py Ray Luo (Thu Jun 18 2020 - 12:30:54 PDT)
[AMBER] Setting custom parameters for CpHMD simulations Jade Shi (Wed Jun 10 2020 - 15:38:59 PDT)
[AMBER] Cellulose-lignin interaction Pinky Mazumder (Wed Jun 10 2020 - 21:25:36 PDT)
- Re: [AMBER] Cellulose-lignin interaction David A Case (Thu Jun 11 2020 - 07:12:58 PDT)
  - Re: [AMBER] Cellulose-lignin interaction Pinky Mazumder (Wed Jun 17 2020 - 17:06:39 PDT)
    - Re: [AMBER] Cellulose-lignin interaction Lachele Foley (Fri Jun 19 2020 - 21:06:50 PDT)
[AMBER] Amber parameters for sphingomyelin Jianguo Li (Thu Jun 11 2020 - 01:00:14 PDT)
- Re: [AMBER] Amber parameters for sphingomyelin Gould, Ian R (Thu Jun 11 2020 - 01:10:09 PDT)
  - Re: [AMBER] Amber parameters for sphingomyelin Jianguo Li (Thu Jun 11 2020 - 01:27:52 PDT)
  - Re: [AMBER] Amber parameters for sphingomyelin Sally Pias (Thu Jun 11 2020 - 11:37:03 PDT)
[AMBER] GLYCAM and scaling of electrostatic and nonbonded interactions Jordi Bujons (Thu Jun 11 2020 - 09:17:29 PDT)
- Re: [AMBER] GLYCAM and scaling of electrostatic and nonbonded interactions David A Case (Thu Jun 11 2020 - 11:02:54 PDT)
[AMBER] Epot value in Amber TI output Eric Chen (Fri Jun 12 2020 - 10:24:20 PDT)
[AMBER] Error with MMPBSA - per residue decomposition Prasanth G, Research Scholar (Sat Jun 13 2020 - 00:51:15 PDT)
- Re: [AMBER] Error with MMPBSA - per residue decomposition Prasanth G, Research Scholar (Thu Jun 18 2020 - 10:18:51 PDT)
  - Re: [AMBER] Error with MMPBSA - per residue decomposition Prasanth G, Research Scholar (Fri Jun 19 2020 - 12:50:27 PDT)
[AMBER] adding a new covalently-linked ligand abhisek Mondal (Sat Jun 13 2020 - 03:39:57 PDT)
[AMBER] question 闫芳芳 (Sun Jun 14 2020 - 07:08:52 PDT)
- Re: [AMBER] question Elvis Martis (Sun Jun 14 2020 - 07:17:47 PDT)
  - Re: [AMBER] question James Kress (Sun Jun 14 2020 - 11:53:25 PDT)
    - Re: [AMBER] question Gustavo Seabra (Sun Jun 14 2020 - 16:32:59 PDT)
    - Re: [AMBER] question David A Case (Mon Jun 15 2020 - 05:09:18 PDT)
    - Re: [AMBER] question 闫芳芳 (Mon Jun 15 2020 - 05:52:52 PDT)
    - [AMBER] Apostrophe problems David A Case (Mon Jun 15 2020 - 11:47:13 PDT)
[AMBER] planarity issue during md Sofia Vasilakaki (Mon Jun 15 2020 - 00:23:42 PDT)
- Re: [AMBER] planarity issue during md David A Case (Mon Jun 15 2020 - 05:12:12 PDT)
  - Re: [AMBER] planarity issue during md Sofia Vasilakaki (Mon Jun 15 2020 - 07:33:55 PDT)
    - Re: [AMBER] planarity issue during md David A Case (Mon Jun 15 2020 - 11:51:16 PDT)
    - Re: [AMBER] planarity issue during md Sofia Vasilakaki (Thu Jun 18 2020 - 02:58:09 PDT)
    - Re: [AMBER] planarity issue during md David A Case (Thu Jun 18 2020 - 05:11:16 PDT)
[AMBER] MMPBSA.py error Oanh Thuy Ngoc Tran (Mon Jun 15 2020 - 14:57:20 PDT)
- Re: [AMBER] MMPBSA.py error Tony Yang (Tue Jun 16 2020 - 03:48:25 PDT)
  - Re: [AMBER] MMPBSA.py error Casalini Tommaso (Tue Jun 16 2020 - 04:09:30 PDT)
    - Re: [AMBER] MMPBSA.py error Tony Yang (Tue Jun 16 2020 - 04:23:10 PDT)
    - Re: [AMBER] MMPBSA.py error Casalini Tommaso (Tue Jun 16 2020 - 04:28:38 PDT)
    - Re: [AMBER] MMPBSA.py error Tony Yang (Tue Jun 16 2020 - 04:52:10 PDT)
  - Re: [AMBER] MMPBSA.py error Oanh Thuy Ngoc Tran (Wed Jun 17 2020 - 14:10:45 PDT)
[AMBER] mmgbsa question MYRIAN TORRES RICO (Tue Jun 16 2020 - 02:16:37 PDT)
- Re: [AMBER] mmgbsa question David A Case (Tue Jun 16 2020 - 05:02:35 PDT)
[AMBER] generating parameters for methane angad sharma (Tue Jun 16 2020 - 02:37:55 PDT)
- Re: [AMBER] generating parameters for methane Elvis Martis (Tue Jun 16 2020 - 03:04:16 PDT)
- Re: [AMBER] generating parameters for methane angad sharma (Fri Jun 19 2020 - 22:10:36 PDT)
  - Re: [AMBER] generating parameters for methane David A Case (Sat Jun 20 2020 - 04:39:48 PDT)
  - [AMBER] Fwd: generating parameters for methane angad sharma (Mon Jun 22 2020 - 08:54:13 PDT)
[AMBER] OPLS-AA/M force field Rosellen, Martin (Tue Jun 16 2020 - 03:35:36 PDT)
[AMBER] Error while using Parmchk2 Sodiq Waheed (Tue Jun 16 2020 - 09:51:22 PDT)
- Re: [AMBER] Error while using Parmchk2 David A Case (Wed Jun 17 2020 - 05:12:38 PDT)
[AMBER] Adiabatic Mapping Info Request Bowleg, Jerrano (Tue Jun 16 2020 - 10:02:23 PDT)
[AMBER] Average structure of production run Sruthi Sudhakar (Tue Jun 16 2020 - 10:26:44 PDT)
- Re: [AMBER] Average structure of production run Liao (Tue Jun 16 2020 - 13:02:32 PDT)
  - Re: [AMBER] Average structure of production run Nada Afiva (Tue Jun 16 2020 - 20:12:00 PDT)
    - Re: [AMBER] Average structure of production run Elvis Martis (Tue Jun 16 2020 - 20:36:40 PDT)
    - Re: [AMBER] Average structure of production run Nada Afiva (Tue Jun 16 2020 - 20:42:44 PDT)
    - Re: [AMBER] Average structure of production run Elvis Martis (Tue Jun 16 2020 - 21:00:45 PDT)
    - Re: [AMBER] Average structure of production run Nada Afiva (Tue Jun 16 2020 - 21:04:11 PDT)
[AMBER] how to combine several stripped trajectory netcdf files Nada Afiva (Tue Jun 16 2020 - 20:09:05 PDT)
- Re: [AMBER] how to combine several stripped trajectory netcdf files Elvis Martis (Tue Jun 16 2020 - 20:38:50 PDT)
  - Re: [AMBER] how to combine several stripped trajectory netcdf files Nada Afiva (Tue Jun 16 2020 - 20:44:22 PDT)
    - Re: [AMBER] how to combine several stripped trajectory netcdf files Elvis Martis (Tue Jun 16 2020 - 21:01:47 PDT)
    - Re: [AMBER] how to combine several stripped trajectory netcdf files Nada Afiva (Tue Jun 16 2020 - 21:03:04 PDT)
    - Re: [AMBER] how to combine several stripped trajectory netcdf files Liao (Tue Jun 16 2020 - 21:08:52 PDT)
    - Re: [AMBER] how to combine several stripped trajectory netcdf files Nada Afiva (Wed Jun 17 2020 - 00:02:02 PDT)
[AMBER] junmaozb.foxmail.com 毛君 (Tue Jun 16 2020 - 21:11:16 PDT)
[AMBER] About two amber REMD simulation problems 毛君 (Wed Jun 17 2020 - 00:26:42 PDT)
- Re: [AMBER] About two amber REMD simulation problems Alessandro Contini (Wed Jun 17 2020 - 00:54:33 PDT)
[AMBER] Error: Could not determine format of topology Jag Silwal (Wed Jun 17 2020 - 06:36:26 PDT)
- [AMBER] Fwd: Error: Could not determine format of topology Jag Silwal (Wed Jun 17 2020 - 06:37:19 PDT)
  - Re: [AMBER] Fwd: Error: Could not determine format of topology David A Case (Wed Jun 17 2020 - 12:12:16 PDT)
    - Re: [AMBER] Fwd: Error: Could not determine format of topology Jag Silwal (Fri Jun 19 2020 - 07:07:10 PDT)
    - Re: [AMBER] Fwd: Error: Could not determine format of topology David A Case (Fri Jun 19 2020 - 13:41:21 PDT)
    - Re: [AMBER] Fwd: Error: Could not determine format of topology Daniel Roe (Fri Jun 19 2020 - 14:29:58 PDT)
    - Re: [AMBER] Fwd: Error: Could not determine format of topology Jag Silwal (Fri Jun 19 2020 - 14:55:42 PDT)
    - Re: [AMBER] Fwd: Error: Could not determine format of topology Daniel Roe (Fri Jun 19 2020 - 19:05:11 PDT)
    - Re: [AMBER] Fwd: Error: Could not determine format of topology Jag Silwal (Mon Jun 22 2020 - 11:37:13 PDT)
    - Re: [AMBER] Fwd: Error: Could not determine format of topology David A Case (Mon Jun 22 2020 - 18:27:32 PDT)
    - Re: [AMBER] Fwd: Error: Could not determine format of topology Daniel Roe (Wed Jun 24 2020 - 05:33:12 PDT)
- Re: [AMBER] Error: Could not determine format of topology Alessandro Contini (Wed Jun 17 2020 - 06:50:14 PDT)
[AMBER] tleap PDB file in ORCA Benedikt Flöser (Thu Jun 18 2020 - 00:22:46 PDT)
- Re: [AMBER] tleap PDB file in ORCA David Cerutti (Thu Jun 18 2020 - 01:18:50 PDT)
- Re: [AMBER] tleap PDB file in ORCA Daniel Roe (Thu Jun 18 2020 - 04:55:15 PDT)
  - Re: [AMBER] tleap PDB file in ORCA Benedikt Flöser (Thu Jun 18 2020 - 05:02:59 PDT)
- Re: [AMBER] tleap PDB file in ORCA David A Case (Thu Jun 18 2020 - 05:04:33 PDT)
[AMBER] error: installing amber18 on MacOS gaohanlu (Thu Jun 18 2020 - 07:29:58 PDT)
- Re: [AMBER] error: installing amber18 on MacOS Gustaf Olsson (Sat Jun 20 2020 - 14:19:07 PDT)
[AMBER] Hoogsteen H-bond Jisha B (Fri Jun 19 2020 - 22:20:58 PDT)
- Re: [AMBER] Hoogsteen H-bond Daniel Roe (Wed Jun 24 2020 - 05:20:41 PDT)
  - Re: [AMBER] Hoogsteen H-bond Jisha B (Wed Jul 01 2020 - 08:18:10 PDT)
[AMBER] Cluster analysis: the result was strange Nada Afiva (Sat Jun 20 2020 - 01:57:48 PDT)
- Re: [AMBER] Cluster analysis: the result was strange Daniel Roe (Wed Jun 24 2020 - 05:15:45 PDT)
  - Re: [AMBER] Cluster analysis: the result was strange Nada Afiva (Thu Jun 25 2020 - 01:27:41 PDT)
    - Re: [AMBER] Cluster analysis: the result was strange Christina Bergonzo (Thu Jun 25 2020 - 06:22:23 PDT)
    - Re: [AMBER] Cluster analysis: the result was strange Nada Afiva (Thu Jun 25 2020 - 14:52:23 PDT)
[AMBER] Incompatibility of coordinate file with topology after minimization Houcemeddine Othman (Sat Jun 20 2020 - 06:16:13 PDT)
- Re: [AMBER] Incompatibility of coordinate file with topology after minimization David A Case (Sat Jun 20 2020 - 18:22:06 PDT)
  - Re: [AMBER] Incompatibility of coordinate file with topology after minimization Houcemeddine Othman (Sun Jun 21 2020 - 06:04:04 PDT)
    - Re: [AMBER] Incompatibility of coordinate file with topology after minimization Daniel Roe (Wed Jun 24 2020 - 05:26:02 PDT)
[AMBER] Tutorials unavailable Sruthi Sudhakar (Sat Jun 20 2020 - 08:33:32 PDT)
- Re: [AMBER] Tutorials unavailable Rodrigo Galindo-Murillo (Sat Jun 20 2020 - 08:55:26 PDT)
  - Re: [AMBER] Tutorials unavailable Preeti Pandey (Sat Jun 20 2020 - 11:46:16 PDT)
    - Re: [AMBER] Tutorials unavailable Sruthi Sudhakar (Sat Jun 20 2020 - 23:08:32 PDT)
    - Re: [AMBER] Tutorials unavailable Ahmed Elrashedy (Sat Jun 20 2020 - 23:58:38 PDT)
    - Re: [AMBER] Tutorials unavailable Rodrigo Galindo-Murillo (Sun Jun 21 2020 - 08:58:34 PDT)
[AMBER] How to install Ambertools 20 using Cygwin and CMake on windows 7? Ibrahim Mohamed (Sat Jun 20 2020 - 14:32:32 PDT)
- Re: [AMBER] How to install Ambertools 20 using Cygwin and CMake on windows 7? Daniel Roe (Wed Jun 24 2020 - 05:24:21 PDT)
[AMBER] How to use Ambertools20 parmed.py? Ibrahim Mohamed (Sun Jun 21 2020 - 00:53:49 PDT)
- Re: [AMBER] How to use Ambertools20 parmed.py? David A Case (Sun Jun 21 2020 - 07:57:26 PDT)
[AMBER] pH-REMD error Kolattukudy P. Santo (Sun Jun 21 2020 - 09:35:12 PDT)
- Re: [AMBER] pH-REMD error Cruzeiro,Vinicius Wilian D (Sun Jun 21 2020 - 11:17:13 PDT)
  - Re: [AMBER] pH-REMD error Kolattukudy P. Santo (Sun Jun 21 2020 - 11:50:54 PDT)
Re: [AMBER] contents of AMBER Digest, Vol 3040, Issue 1, message 1 gaohanlu (Sun Jun 21 2020 - 18:59:39 PDT)
- Re: [AMBER] contents of AMBER Digest, Vol 3040, Issue 1, message 1 David A Case (Mon Jun 22 2020 - 06:51:46 PDT)
[AMBER] GPU error in the heating step of PMEMD.CUDA rosaester.forgione.unina.it (Mon Jun 22 2020 - 04:05:51 PDT)
- Re: [AMBER] GPU error in the heating step of PMEMD.CUDA rosaester.forgione.unina.it (Mon Jun 22 2020 - 04:22:22 PDT)
  - Re: [AMBER] GPU error in the heating step of PMEMD.CUDA Gerardo Zerbetto De Palma (Mon Jun 22 2020 - 04:39:30 PDT)
    - Re: [AMBER] GPU error in the heating step of PMEMD.CUDA Gerardo Zerbetto De Palma (Mon Jun 22 2020 - 04:44:38 PDT)
[AMBER] RAMD implementation in the new Amber 20 package Richter, Stefan (Mon Jun 22 2020 - 08:12:36 PDT)
[AMBER] generating methane parameters angad sharma (Mon Jun 22 2020 - 08:56:55 PDT)
- Re: [AMBER] generating methane parameters David Cerutti (Mon Jun 22 2020 - 09:17:04 PDT)
[AMBER] nmropt vs infe Gard Nelson (Mon Jun 22 2020 - 14:56:17 PDT)
- Re: [AMBER] nmropt vs infe Wesley Michael Botello-Smith (Tue Jun 23 2020 - 14:11:51 PDT)
  - Re: [AMBER] nmropt vs infe Gard Nelson (Wed Jun 24 2020 - 15:58:53 PDT)
    - Re: [AMBER] nmropt vs infe Feng Pan (Thu Jul 09 2020 - 22:01:21 PDT)
[AMBER] Regarding Amber 20 License Suchetana Gupta (Tue Jun 23 2020 - 03:09:47 PDT)
[AMBER] Truncated NMODE calculation with MMPBSA.py.MPI Wan, Shunzhou (Tue Jun 23 2020 - 09:34:57 PDT)
[AMBER] Minimization erro Renato Araujo (Tue Jun 23 2020 - 12:05:59 PDT)
- Re: [AMBER] Minimization erro Debarati DasGupta (Tue Jun 23 2020 - 15:50:09 PDT)
- Re: [AMBER] Minimization erro David A Case (Tue Jun 23 2020 - 18:02:05 PDT)
  - Re: [AMBER] Minimization erro Renato Araujo (Tue Jun 23 2020 - 18:51:42 PDT)
    - Re: [AMBER] Minimization erro Debarati DasGupta (Wed Jun 24 2020 - 05:44:11 PDT)
    - Re: [AMBER] Minimization erro Renato Araujo (Wed Jun 24 2020 - 06:06:32 PDT)
[AMBER] Steered MD in AMBER using GPU Souvik Dey (Tue Jun 23 2020 - 19:30:02 PDT)
[AMBER] Amber installation error ankita mehta (Wed Jun 24 2020 - 06:41:57 PDT)
- Re: [AMBER] Amber installation error David A Case (Wed Jun 24 2020 - 11:56:25 PDT)
  - Re: [AMBER] Amber installation error ankita mehta (Wed Jul 01 2020 - 11:10:40 PDT)
    - Re: [AMBER] Amber installation error Gustaf Olsson (Wed Jul 01 2020 - 22:46:33 PDT)
[AMBER] Amber20 update failure on RHEL7/CentOS7 Peng Wang (Wed Jun 24 2020 - 11:14:29 PDT)
- Re: [AMBER] Amber20 update failure on RHEL7/CentOS7 David A Case (Wed Jun 24 2020 - 12:05:53 PDT)
- Re: [AMBER] Amber20 update failure on RHEL7/CentOS7 Ross Walker (Wed Jun 24 2020 - 12:33:56 PDT)
[AMBER] restraint 10 kcal/mol Debarati DasGupta (Wed Jun 24 2020 - 11:35:38 PDT)
- Re: [AMBER] restraint 10 kcal/mol Daniel Roe (Wed Jun 24 2020 - 13:42:12 PDT)
  - Re: [AMBER] restraint 10 kcal/mol Debarati DasGupta (Wed Jun 24 2020 - 14:54:20 PDT)
    - [AMBER] FW: restraint 10 kcal/mol Debarati DasGupta (Fri Jun 26 2020 - 05:49:49 PDT)
- Re: [AMBER] restraint 10 kcal/mol David A Case (Wed Jun 24 2020 - 18:36:37 PDT)
  - Re: [AMBER] restraint 10 kcal/mol Debarati DasGupta (Thu Jun 25 2020 - 06:12:18 PDT)
    - [AMBER] FW: restraint 10 kcal/mol Debarati DasGupta (Mon Jul 06 2020 - 08:16:07 PDT)
    - Re: [AMBER] FW: restraint 10 kcal/mol Carlos Simmerling (Mon Jul 06 2020 - 08:32:00 PDT)
    - Re: [AMBER] FW: restraint 10 kcal/mol Debarati DasGupta (Mon Jul 06 2020 - 15:57:38 PDT)
    - Re: [AMBER] FW: restraint 10 kcal/mol Debarati DasGupta (Wed Jul 15 2020 - 14:50:24 PDT)
    - Re: [AMBER] FW: restraint 10 kcal/mol Carlos Simmerling (Mon Jul 20 2020 - 07:23:54 PDT)
[AMBER] pmemd.cuda for heating and equilibration? Nada Afiva (Wed Jun 24 2020 - 18:27:34 PDT)
- Re: [AMBER] pmemd.cuda for heating and equilibration? Kenneth Huang (Wed Jun 24 2020 - 21:44:11 PDT)
  - Re: [AMBER] pmemd.cuda for heating and equilibration? Nada Afiva (Thu Jun 25 2020 - 00:06:27 PDT)
[AMBER] Problems with Make install Amber 18 Joanna Michelle E. Chua (Wed Jun 24 2020 - 20:26:44 PDT)
- Re: [AMBER] Problems with Make install Amber 18 Gustaf Olsson (Wed Jun 24 2020 - 23:15:12 PDT)
  - Re: [AMBER] Problems with Make install Amber 18 Joanna Michelle E. Chua (Thu Jun 25 2020 - 09:08:20 PDT)
    - Re: [AMBER] Problems with Make install Amber 18 Renato Araujo (Thu Jun 25 2020 - 10:32:54 PDT)
    - Re: [AMBER] Problems with Make install Amber 18 Joanna Michelle E. Chua (Thu Jun 25 2020 - 16:38:06 PDT)
    - Re: [AMBER] Problems with Make install Amber 18 Renato Araujo (Thu Jun 25 2020 - 19:02:03 PDT)
    - Re: [AMBER] Problems with Make install Amber 18 Gustaf Olsson (Thu Jun 25 2020 - 23:03:48 PDT)
    - Re: [AMBER] Problems with Make install Amber 18 Joanna Michelle E. Chua (Fri Jun 26 2020 - 00:25:15 PDT)
    - Re: [AMBER] Problems with Make install Amber 18 Gustaf Olsson (Fri Jun 26 2020 - 00:58:03 PDT)
    - Re: [AMBER] Problems with Make install Amber 18 Daniel Roe (Fri Jun 26 2020 - 03:11:32 PDT)
    - Re: [AMBER] Problems with Make install Amber 18 Joanna Michelle E. Chua (Fri Jun 26 2020 - 04:20:31 PDT)
    - Re: [AMBER] Problems with Make install Amber 18 David A Case (Fri Jun 26 2020 - 04:57:38 PDT)
    - Re: [AMBER] Problems with Make install Amber 18 Joanna Michelle E. Chua (Fri Jun 26 2020 - 05:03:03 PDT)
    - Re: [AMBER] Problems with Make install Amber 18 David A Case (Fri Jun 26 2020 - 05:38:14 PDT)
[AMBER] Compiling Amber18 AmberTools19 on CentOS 7 Gustaf Olsson (Thu Jun 25 2020 - 02:02:03 PDT)
[AMBER] ERROR:nfft1 must be in the range of 6 to 512! Rinsha Chk (Thu Jun 25 2020 - 02:28:26 PDT)
- Re: [AMBER] ERROR:nfft1 must be in the range of 6 to 512! David A Case (Thu Jun 25 2020 - 05:09:24 PDT)
[AMBER] bulding a monosaccharide with N-acetylation rosaester.forgione.unina.it (Thu Jun 25 2020 - 06:34:36 PDT)
- Re: [AMBER] bulding a monosaccharide with N-acetylation Lachele Foley (Wed Jul 01 2020 - 04:55:06 PDT)
[AMBER] nastruct command query Athena N (Thu Jun 25 2020 - 12:25:31 PDT)
- Re: [AMBER] nastruct command query Christina Bergonzo (Thu Jun 25 2020 - 12:29:01 PDT)
[AMBER] Help GPU support information Renato Araujo (Thu Jun 25 2020 - 13:45:10 PDT)
[AMBER] Positive MM-PBSA and negative MM-GBSA binding energies Nada Afiva (Thu Jun 25 2020 - 15:08:24 PDT)
- Re: [AMBER] Positive MM-PBSA and negative MM-GBSA binding energies Ray Luo (Thu Jun 25 2020 - 16:59:14 PDT)
  - Re: [AMBER] Positive MM-PBSA and negative MM-GBSA binding energies Nada Afiva (Thu Jun 25 2020 - 18:10:52 PDT)
    - Re: [AMBER] Positive MM-PBSA and negative MM-GBSA binding energies Ray Luo (Fri Jun 26 2020 - 08:19:35 PDT)
    - Re: [AMBER] Positive MM-PBSA and negative MM-GBSA binding energies Nada Afiva (Fri Jun 26 2020 - 22:59:48 PDT)
    - Re: [AMBER] Positive MM-PBSA and negative MM-GBSA binding energies Ray Luo (Sat Jun 27 2020 - 08:20:22 PDT)
    - Re: [AMBER] Positive MM-PBSA and negative MM-GBSA binding energies Nada Afiva (Sun Jun 28 2020 - 05:04:44 PDT)
    - Re: [AMBER] Positive MM-PBSA and negative MM-GBSA binding energies Elvis Martis (Sun Jun 28 2020 - 05:11:54 PDT)
    - Re: [AMBER] Positive MM-PBSA and negative MM-GBSA binding energies Ray Luo (Sun Jun 28 2020 - 09:30:41 PDT)
    - Re: [AMBER] Positive MM-PBSA and negative MM-GBSA binding energies Nada Afiva (Sun Jun 28 2020 - 15:24:36 PDT)
[AMBER] generating methane parameters angad sharma (Fri Jun 26 2020 - 00:28:56 PDT)
- Re: [AMBER] generating methane parameters David A Case (Fri Jun 26 2020 - 05:04:06 PDT)
[AMBER] Error in Antechamber Shreeramesh (Fri Jun 26 2020 - 07:38:55 PDT)
- Re: [AMBER] Error in Antechamber Scott Brozell (Fri Jun 26 2020 - 13:04:24 PDT)
  - Re: [AMBER] Error in Antechamber Shreeramesh (Sat Jun 27 2020 - 05:10:53 PDT)
    - Re: [AMBER] Error in Antechamber David A Case (Sat Jun 27 2020 - 18:07:42 PDT)
[AMBER] Problems with RMSF calculations kartik.lakshmi.gmail.com (Fri Jun 26 2020 - 11:48:47 PDT)
- Re: [AMBER] Problems with RMSF calculations Kenneth Huang (Fri Jun 26 2020 - 14:50:04 PDT)
  - Re: [AMBER] Problems with RMSF calculations kartik.lakshmi.gmail.com (Sat Jun 27 2020 - 12:56:05 PDT)
    - Re: [AMBER] Problems with RMSF calculations Kenneth Huang (Sat Jun 27 2020 - 15:58:53 PDT)
- Re: [AMBER] Problems with RMSF calculations Daniel Roe (Mon Jun 29 2020 - 09:02:27 PDT)
  - Re: [AMBER] Problems with RMSF calculations kartik.lakshmi.gmail.com (Mon Jun 29 2020 - 13:46:47 PDT)
    - Re: [AMBER] Problems with RMSF calculations Daniel Roe (Mon Jun 29 2020 - 17:58:44 PDT)
    - Re: [AMBER] Problems with RMSF calculations kartik.lakshmi.gmail.com (Mon Jun 29 2020 - 18:22:56 PDT)
[AMBER] restraining surfactant tails in micelles intact Billiot, Eugene (Fri Jun 26 2020 - 12:55:41 PDT)
- Re: [AMBER] restraining surfactant tails in micelles intact David A Case (Sat Jun 27 2020 - 04:53:01 PDT)
  - Re: [AMBER] restraining surfactant tails in micelles intact Billiot, Eugene (Sat Jun 27 2020 - 08:09:15 PDT)
[AMBER] Ligand movement w.r.t protein backbone Prasanth G, Research Scholar (Sat Jun 27 2020 - 02:29:21 PDT)
- Re: [AMBER] Ligand movement w.r.t protein backbone Daniel Roe (Mon Jun 29 2020 - 09:07:27 PDT)
  - Re: [AMBER] Ligand movement w.r.t protein backbone Debarati DasGupta (Mon Jun 29 2020 - 09:24:30 PDT)
    - Re: [AMBER] Ligand movement w.r.t protein backbone Prasanth G, Research Scholar (Mon Jun 29 2020 - 10:36:38 PDT)
    - Re: [AMBER] Ligand movement w.r.t protein backbone Daniel Roe (Mon Jun 29 2020 - 17:35:07 PDT)
    - Re: [AMBER] Ligand movement w.r.t protein backbone Debarati DasGupta (Tue Jun 30 2020 - 05:07:11 PDT)
[AMBER] Error Message while using GPU Sivanandam Magudeeswaran (Sat Jun 27 2020 - 22:53:34 PDT)
- Re: [AMBER] Error Message while using GPU David A Case (Sun Jun 28 2020 - 12:19:51 PDT)
[AMBER] Is there a method that can calculate the angle between two planes? xmgign.126.com (Sun Jun 28 2020 - 02:59:25 PDT)
- Re: [AMBER] Is there a method that can calculate the angle between two planes? David A Case (Sun Jun 28 2020 - 12:33:40 PDT)
  - Re: [AMBER] Is there a method that can calculate the angle between two planes? Daniel Roe (Mon Jun 29 2020 - 08:31:40 PDT)
- Re: [AMBER] Is there a method that can calculate the angle between two planes? Wesley Michael Botello-Smith (Mon Jun 29 2020 - 13:11:36 PDT)
[AMBER] Steered Molecular Dynamics Simulation Vishal Singh (Sun Jun 28 2020 - 11:55:13 PDT)
- Re: [AMBER] Steered molecular dynamics Simulation Pinky Mazumder (Sat Jul 25 2020 - 21:16:28 PDT)
  - Re: [AMBER] Steered molecular dynamics Simulation Pinky Mazumder (Fri Jan 15 2021 - 18:01:53 PST)
    - Re: [AMBER] Steered molecular dynamics Simulation Fabian Glaser (Sat Jan 16 2021 - 06:56:04 PST)
- Re: [AMBER] Steered molecular dynamics Simulation Pinky Mazumder (Sat Jan 16 2021 - 10:13:35 PST)
- Re: [AMBER] Steered molecular dynamics Simulation Pinky Mazumder (Sat Jan 16 2021 - 13:37:28 PST)
[AMBER] ff14SBonlysc + OPC3 Fabian Glaser (Mon Jun 29 2020 - 05:40:11 PDT)
- Re: [AMBER] ff14SBonlysc + OPC3 Daniel Roe (Mon Jun 29 2020 - 08:25:38 PDT)
  - Re: [AMBER] ff14SBonlysc + OPC3 Matias Machado (Mon Jun 29 2020 - 10:03:05 PDT)
    - Re: [AMBER] ff14SBonlysc + OPC3 Matias Machado (Mon Jun 29 2020 - 10:14:07 PDT)
    - Re: [AMBER] ff14SBonlysc + OPC3 Daniel Roe (Mon Jun 29 2020 - 10:54:57 PDT)
    - Re: [AMBER] ff14SBonlysc + OPC3 Matias Machado (Mon Jun 29 2020 - 11:33:29 PDT)
    - Re: [AMBER] ff14SBonlysc + OPC3 Daniel Roe (Mon Jun 29 2020 - 17:21:48 PDT)
- Re: [AMBER] ff14SBonlysc + OPC3 Carlos Simmerling (Mon Jun 29 2020 - 08:52:20 PDT)
  - Re: [AMBER] ff14SBonlysc + OPC3 David A Case (Mon Jun 29 2020 - 10:54:28 PDT)
    - Re: [AMBER] ff14SBonlysc + OPC3 Matias Machado (Mon Jun 29 2020 - 11:23:40 PDT)
    - Re: [AMBER] ff14SBonlysc + OPC3 David A Case (Mon Jun 29 2020 - 18:30:50 PDT)
    - Re: [AMBER] ff14SBonlysc + OPC3 Fabian Glaser (Tue Jun 30 2020 - 01:09:29 PDT)
[AMBER] error message create parameters Renato Araujo (Mon Jun 29 2020 - 05:49:42 PDT)
- Re: [AMBER] error message create parameters Elvis Martis (Mon Jun 29 2020 - 06:05:26 PDT)
  - Re: [AMBER] error message create parameters Renato Araujo (Mon Jun 29 2020 - 06:10:16 PDT)
- Re: [AMBER] error message create parameters David A Case (Mon Jun 29 2020 - 11:27:40 PDT)
[AMBER] Error in Installing Amber 20 on GPU Suchetana Gupta (Mon Jun 29 2020 - 05:55:25 PDT)
- Re: [AMBER] Error in Installing Amber 20 on GPU David A Case (Mon Jun 29 2020 - 11:04:42 PDT)
  - Re: [AMBER] Error in Installing Amber 20 on GPU Suchetana Gupta (Mon Jun 29 2020 - 20:30:46 PDT)
    - Re: [AMBER] Error in Installing Amber 20 on GPU David A Case (Tue Jun 30 2020 - 04:41:03 PDT)
    - Re: [AMBER] Error in Installing Amber 20 on GPU Suchetana Gupta (Tue Jun 30 2020 - 22:28:23 PDT)
    - Re: [AMBER] Error in Installing Amber 20 on GPU David A Case (Wed Jul 01 2020 - 08:45:01 PDT)
    - Re: [AMBER] Error in Installing Amber 20 on GPU Suchetana Gupta (Wed Jul 01 2020 - 10:39:51 PDT)
    - Re: [AMBER] Error in Installing Amber 20 on GPU Suchetana Gupta (Wed Jul 01 2020 - 11:13:29 PDT)
    - Re: [AMBER] Error in Installing Amber 20 on GPU Gustaf Olsson (Wed Jul 01 2020 - 22:55:21 PDT)
    - Re: [AMBER] Error in Installing Amber 20 on GPU Suchetana Gupta (Wed Jul 01 2020 - 22:57:41 PDT)
    - Re: [AMBER] Error in Installing Amber 20 on GPU Gustaf Olsson (Wed Jul 01 2020 - 23:44:09 PDT)
    - Re: [AMBER] Error in Installing Amber 20 on GPU David A Case (Thu Jul 02 2020 - 05:07:02 PDT)
    - Re: [AMBER] Error in Installing Amber 20 on GPU Suchetana Gupta (Thu Jul 02 2020 - 05:22:52 PDT)
    - Re: [AMBER] Error in Installing Amber 20 on GPU Gustaf Olsson (Thu Jul 02 2020 - 05:56:29 PDT)
    - Re: [AMBER] Error in Installing Amber 20 on GPU Gustaf Olsson (Thu Jul 02 2020 - 05:58:40 PDT)
    - Re: [AMBER] Error in Installing Amber 20 on GPU David A Case (Thu Jul 02 2020 - 10:11:24 PDT)
    - Re: [AMBER] Error in Installing Amber 20 on GPU Suchetana Gupta (Thu Jul 02 2020 - 21:51:54 PDT)
    - Re: [AMBER] Error in Installing Amber 20 on GPU David A Case (Fri Jul 03 2020 - 06:37:24 PDT)
    - Re: [AMBER] Error in Installing Amber 20 on GPU Suchetana Gupta (Sat Jul 04 2020 - 02:43:47 PDT)
    - Re: [AMBER] Error in Installing Amber 20 on GPU David A Case (Sat Jul 04 2020 - 05:01:40 PDT)
[AMBER] CPPTRAJ: Time Correlation Function (TCF) emanuele falbo (Mon Jun 29 2020 - 06:26:06 PDT)
- Re: [AMBER] CPPTRAJ: Time Correlation Function (TCF) Daniel Roe (Mon Jun 29 2020 - 08:16:11 PDT)
  - Re: [AMBER] CPPTRAJ: Time Correlation Function (TCF) emanuele falbo (Wed Jul 15 2020 - 07:29:40 PDT)
    - Re: [AMBER] CPPTRAJ: Time Correlation Function (TCF) Souvik (Wed Jul 15 2020 - 09:06:15 PDT)
    - Re: [AMBER] CPPTRAJ: Time Correlation Function (TCF) emanuele falbo (Thu Jul 16 2020 - 01:55:57 PDT)
    - Re: [AMBER] CPPTRAJ: Time Correlation Function (TCF) Daniel Roe (Mon Jul 20 2020 - 07:54:56 PDT)
[AMBER] centos 7 install Ambertools20 error, final link failed: Bad value He DC (Mon Jun 29 2020 - 07:50:32 PDT)
- Re: [AMBER] centos 7 install Ambertools20 error, final link failed: Bad value David A Case (Mon Jun 29 2020 - 11:15:15 PDT)
- Re: [AMBER] centos 7 install Ambertools20 error, final link failed: Bad value Gustaf Olsson (Mon Jun 29 2020 - 23:18:29 PDT)
  - Re: [AMBER] centos 7 install Ambertools20 error, final link failed: Bad value David A Case (Tue Jun 30 2020 - 04:48:35 PDT)
[AMBER] pmemd.MPI and minization trajectories Seibold, Steve Allan (Mon Jun 29 2020 - 08:09:07 PDT)
- Re: [AMBER] pmemd.MPI and minization trajectories Daniel Roe (Mon Jun 29 2020 - 08:11:05 PDT)
  - Re: [AMBER] pmemd.MPI and minization trajectories Seibold, Steve Allan (Mon Jun 29 2020 - 09:22:48 PDT)
    - Re: [AMBER] pmemd.MPI and minization trajectories Gerald Monard (Mon Jun 29 2020 - 09:53:53 PDT)
- Re: [AMBER] pmemd.MPI and minization trajectories David A Case (Mon Jun 29 2020 - 11:18:38 PDT)
  - Re: [AMBER] pmemd.MPI and minization trajectories Seibold, Steve Allan (Mon Jun 29 2020 - 11:38:51 PDT)
[AMBER] An Error with MMPBSA.py in AmberTools 17 Ibrahim Mohamed (Mon Jun 29 2020 - 15:23:34 PDT)
[AMBER] add NO3- ions 费俊文 (Mon Jun 29 2020 - 23:29:48 PDT)
[AMBER] "Does not have a type" error in tleap Jatin Kashyap (Tue Jun 30 2020 - 00:00:30 PDT)
- Re: [AMBER] "Does not have a type" error in tleap Elvis Martis (Tue Jun 30 2020 - 00:10:12 PDT)
  - Re: [AMBER] "Does not have a type" error in tleap Jatin Kashyap (Tue Jun 30 2020 - 12:48:43 PDT)
    - Re: [AMBER] "Does not have a type" error in tleap David A Case (Wed Jul 01 2020 - 08:43:20 PDT)
    - Re: [AMBER] "Does not have a type" error in tleap Jatin Kashyap (Wed Jul 01 2020 - 10:00:14 PDT)
    - [AMBER] ntx and irest David A Case (Thu Jul 02 2020 - 04:55:35 PDT)
[AMBER] Zwitter ionic form of a residue Sunita Patel (Tue Jun 30 2020 - 04:20:44 PDT)
- Re: [AMBER] Zwitter ionic form of a residue Dr. Anselm Horn (Tue Jun 30 2020 - 06:22:20 PDT)
[AMBER] interaction entropy calculation Hector A. Baldoni (Tue Jun 30 2020 - 12:41:22 PDT)
[AMBER] Caping error mohamed marzouk (Tue Jun 30 2020 - 21:38:15 PDT)
- Re: [AMBER] Caping error Elvis Martis (Tue Jun 30 2020 - 21:48:01 PDT)
  - Re: [AMBER] Caping error mohamed marzouk (Thu Aug 06 2020 - 22:39:44 PDT)
[AMBER] MBAR with Amber 18 Ulf Ryde (Wed Jul 01 2020 - 03:25:00 PDT)
- Re: [AMBER] MBAR with Amber 18 David A Case (Wed Jul 08 2020 - 05:19:59 PDT)
[AMBER] how to create nice animated videos to show simulations Chetna Tyagi (Wed Jul 01 2020 - 03:31:34 PDT)
- Re: [AMBER] how to create nice animated videos to show simulations Suchetana Gupta (Wed Jul 01 2020 - 03:34:48 PDT)
- Re: [AMBER] how to create nice animated videos to show simulations Elvis Martis (Wed Jul 01 2020 - 03:39:08 PDT)
- Re: [AMBER] how to create nice animated videos to show simulations Carlos Simmerling (Wed Jul 01 2020 - 03:40:47 PDT)
  - Re: [AMBER] how to create nice animated videos to show simulations Raman Preet Singh (Wed Jul 01 2020 - 04:56:06 PDT)
    - Re: [AMBER] how to create nice animated videos to show simulations Chetna Tyagi (Wed Jul 01 2020 - 04:54:35 PDT)
    - Re: [AMBER] how to create nice animated videos to show simulations Rodrigo Galindo-Murillo (Wed Jul 01 2020 - 06:57:01 PDT)
[AMBER] Amber20 installation Kliuchnikov, Evgenii (Wed Jul 01 2020 - 11:16:21 PDT)
- Re: [AMBER] Amber20 installation Gustaf Olsson (Wed Jul 01 2020 - 23:06:29 PDT)
- Re: [AMBER] Amber20 installation Daniel Roe (Tue Jul 07 2020 - 05:48:48 PDT)
[AMBER] How to set salt concentration Nada Afiva (Wed Jul 01 2020 - 20:54:44 PDT)
- Re: [AMBER] How to set salt concentration Gerardo Zerbetto De Palma (Wed Jul 01 2020 - 20:57:37 PDT)
- Re: [AMBER] How to set salt concentration Suchetana Gupta (Wed Jul 01 2020 - 20:59:37 PDT)
  - Re: [AMBER] How to set salt concentration Aashish Bhatt (Wed Jul 01 2020 - 21:15:29 PDT)
    - Re: [AMBER] How to set salt concentration Nada Afiva (Thu Jul 02 2020 - 01:34:28 PDT)
    - Re: [AMBER] How to set salt concentration Matias Machado (Thu Jul 02 2020 - 06:17:27 PDT)
    - Re: [AMBER] How to set salt concentration Nada Afiva (Fri Jul 03 2020 - 02:49:24 PDT)
    - Re: [AMBER] How to set salt concentration David A Case (Fri Jul 03 2020 - 06:44:48 PDT)
    - Re: [AMBER] How to set salt concentration Nada Afiva (Fri Jul 03 2020 - 12:00:43 PDT)
    - Re: [AMBER] How to set salt concentration Clorice Reinhardt (Fri Jul 03 2020 - 12:10:18 PDT)
    - Re: [AMBER] How to set salt concentration Nada Afiva (Fri Jul 03 2020 - 12:58:26 PDT)
    - Re: [AMBER] How to set salt concentration Matias Machado (Sat Jul 04 2020 - 11:17:07 PDT)
    - Re: [AMBER] How to set salt concentration Nada Afiva (Sat Jul 04 2020 - 11:42:11 PDT)
    - Re: [AMBER] How to set salt concentration Dr. Anselm Horn (Fri Jul 03 2020 - 08:59:08 PDT)
    - [AMBER] gamess/MCPB.py tutorial Arthur Glasfeld (Sat Jul 04 2020 - 11:03:32 PDT)
    - Re: [AMBER] gamess/MCPB.py tutorial Pengfei Li (Mon Jul 20 2020 - 11:14:55 PDT)
[AMBER] Amber 20 on Google Colab Suchetana Gupta (Wed Jul 01 2020 - 22:54:07 PDT)
[AMBER] calculating methane parameters using RISM angad sharma (Thu Jul 02 2020 - 01:31:03 PDT)
- Re: [AMBER] calculating methane parameters using RISM David A Case (Thu Jul 02 2020 - 05:14:52 PDT)
[AMBER] how to use triclinic box shape Nada Afiva (Thu Jul 02 2020 - 01:47:46 PDT)
- Re: [AMBER] how to use triclinic box shape David A Case (Thu Jul 02 2020 - 05:35:14 PDT)
  - Re: [AMBER] how to use triclinic box shape David Cerutti (Thu Jul 02 2020 - 05:48:10 PDT)
    - Re: [AMBER] how to use triclinic box shape Nada Afiva (Thu Jul 02 2020 - 17:38:11 PDT)
[AMBER] Problem of Steered MD Simulation for unfolding of RNA Vishal Singh (Thu Jul 02 2020 - 04:46:22 PDT)
- Re: [AMBER] Problem of Steered MD Simulation for unfolding of RNA Leena Aggarwal (Thu Jul 02 2020 - 07:43:04 PDT)
- Re: [AMBER] Problem of Steered MD Simulation for unfolding of RNA Souvik (Thu Jul 02 2020 - 09:34:22 PDT)
[AMBER] Installing Amber20 with cuda9 Schröder, David Christopher (Thu Jul 02 2020 - 06:58:38 PDT)
- Re: [AMBER] Installing Amber20 with cuda9 Schröder, David Christopher (Thu Jul 02 2020 - 08:11:36 PDT)
- Re: [AMBER] Installing Amber20 with cuda9 Schröder, David Christopher (Thu Jul 02 2020 - 10:22:44 PDT)
[AMBER] Usage of the Density Peaks Algorithm. Gilberto Pereira (Thu Jul 02 2020 - 08:34:50 PDT)
- Re: [AMBER] Usage of the Density Peaks Algorithm. Daniel Roe (Tue Aug 04 2020 - 08:13:19 PDT)
[AMBER] Defining new atoms in AMBER Kolattukudy P. Santo (Thu Jul 02 2020 - 08:47:00 PDT)
- Re: [AMBER] Defining new atoms in AMBER David A Case (Thu Jul 02 2020 - 10:20:11 PDT)
  - Re: [AMBER] Defining new atoms in AMBER Kolattukudy P. Santo (Thu Jul 02 2020 - 13:18:28 PDT)
    - Re: [AMBER] Defining new atoms in AMBER David A Case (Fri Jul 03 2020 - 06:41:54 PDT)
[AMBER] Fortran error in constant pH MD Paul Meister (Thu Jul 02 2020 - 09:28:56 PDT)
- Re: [AMBER] Fortran error in constant pH MD Cruzeiro,Vinicius Wilian D (Fri Jul 03 2020 - 08:23:37 PDT)
[AMBER] LJ potential for OPC water model Loki (Fri Jul 03 2020 - 05:07:04 PDT)
- Re: [AMBER] LJ potential for OPC water model Matias Machado (Fri Jul 03 2020 - 09:35:32 PDT)
- Re: [AMBER] LJ potential for OPC water model Loki (Fri Jul 03 2020 - 09:01:58 PDT)
- Re: [AMBER] LJ potential for OPC water model Loki (Fri Jul 03 2020 - 09:28:55 PDT)
  - Re: [AMBER] LJ potential for OPC water model David A Case (Wed Jul 08 2020 - 09:30:42 PDT)
[AMBER] Error while running Antechamber Shreeramesh (Fri Jul 03 2020 - 11:02:15 PDT)
- Re: [AMBER] Error while running Antechamber David A Case (Fri Jul 03 2020 - 14:12:24 PDT)
[AMBER] The most update force fields for DNA and RNA Nada Afiva (Fri Jul 03 2020 - 14:30:27 PDT)
- Re: [AMBER] The most update force fields for DNA and RNA David A Case (Fri Jul 03 2020 - 17:52:45 PDT)
  - Re: [AMBER] The most update force fields for DNA and RNA Nada Afiva (Fri Jul 03 2020 - 18:10:18 PDT)
[AMBER] Solvent excluded volume Shilpa Gupta (Sat Jul 04 2020 - 03:21:31 PDT)
[AMBER] generating methane parameters for rism angad sharma (Sat Jul 04 2020 - 05:22:17 PDT)
- Re: [AMBER] generating methane parameters for rism Leena Aggarwal (Sun Jul 05 2020 - 11:05:20 PDT)
  - Re: [AMBER] generating methane parameters for rism Tyler Luchko (Lists) (Sun Jul 05 2020 - 15:02:14 PDT)
[AMBER] Error in partial MINIMIZATION STEP Shreeramesh (Sat Jul 04 2020 - 09:39:01 PDT)
- Re: [AMBER] Error in partial MINIMIZATION STEP Elvis Martis (Sat Jul 04 2020 - 09:53:33 PDT)
[AMBER] MMGBSA and MMPBSA error (CalcError: failed with prmtop file complex.prmtop!) Nada Afiva (Sat Jul 04 2020 - 14:58:44 PDT)
- Re: [AMBER] MMGBSA and MMPBSA error (CalcError: failed with prmtop file complex.prmtop!) Nada Afiva (Sat Jul 04 2020 - 20:17:36 PDT)
  - Re: [AMBER] MMGBSA and MMPBSA error (CalcError: failed with prmtop file complex.prmtop!) Ray Luo (Sun Jul 05 2020 - 11:31:34 PDT)
    - Re: [AMBER] MMGBSA and MMPBSA error (CalcError: failed with prmtop file complex.prmtop!) Nada Afiva (Mon Jul 06 2020 - 14:18:44 PDT)
[AMBER] generating parameters of methane for RISM angad sharma (Sun Jul 05 2020 - 04:25:07 PDT)
[AMBER] Using ntt=10 in PMEMD Sharif Nada (Mon Jul 06 2020 - 03:29:40 PDT)
[AMBER] Question about SMD using polymer Pinky Mazumder (Mon Jul 06 2020 - 08:01:38 PDT)
- Re: [AMBER] Question about SMD using polymer Carlos Simmerling (Mon Jul 06 2020 - 08:05:08 PDT)
  - Re: [AMBER] Question about SMD using polymer Pinky Mazumder (Fri Jul 10 2020 - 13:24:35 PDT)
    - Re: [AMBER] Question about SMD using polymer Carlos Simmerling (Mon Jul 13 2020 - 07:14:24 PDT)
[AMBER] Barostat and thermostat for membrane protein-ligand simulation ANDREA PASQUADIBISCEGLIE (Mon Jul 06 2020 - 08:49:36 PDT)
- Re: [AMBER] Barostat and thermostat for membrane protein-ligand simulation Sally Pias (Tue Jul 07 2020 - 20:16:56 PDT)
- Re: [AMBER] Barostat and thermostat for membrane protein-ligand simulation Andrea Pasquadibisceglie (Thu Jul 09 2020 - 02:32:05 PDT)
  - Re: [AMBER] Barostat and thermostat for membrane protein-ligand simulation Sally Pias (Thu Jul 09 2020 - 18:27:40 PDT)
- Re: [AMBER] Barostat and thermostat for membrane protein-ligand simulation ANDREA PASQUADIBISCEGLIE (Sat Jul 11 2020 - 00:11:29 PDT)
[AMBER] Strip water job is killed after 10-40% completion Shreeramesh (Mon Jul 06 2020 - 09:23:26 PDT)
- Re: [AMBER] Strip water job is killed after 10-40% completion Dr. Anselm Horn (Tue Jul 07 2020 - 07:08:38 PDT)
- Re: [AMBER] Strip water job is killed after 10-40% completion Daniel Roe (Tue Jul 07 2020 - 07:11:16 PDT)
[AMBER] Force Trajectory Output ABMD Jonathon Ferrell (Mon Jul 06 2020 - 09:56:24 PDT)
[AMBER] Accounting for PBC in Density Plots An Ta (Mon Jul 06 2020 - 10:44:06 PDT)
- Re: [AMBER] Accounting for PBC in Density Plots An Ta (Mon Jul 06 2020 - 10:46:41 PDT)
[AMBER] Install broke and compilation fails Gustaf Olsson (Tue Jul 07 2020 - 06:58:10 PDT)
- Re: [AMBER] Install broke and compilation fails Gustaf Olsson (Tue Jul 07 2020 - 14:12:51 PDT)
[AMBER] Amber prmtop and inpcrd of complex file with a water molecular cutoff 辛志宏 (Tue Jul 07 2020 - 07:54:04 PDT)
- Re: [AMBER] Amber prmtop and inpcrd of complex file with a water molecular cutoff David A Case (Tue Jul 07 2020 - 10:56:07 PDT)
[AMBER] Atomic Polarizability Thakur, Abhishek (Tue Jul 07 2020 - 09:58:48 PDT)
- Re: [AMBER] Atomic Polarizability David A Case (Tue Jul 07 2020 - 10:58:39 PDT)
- Re: [AMBER] Atomic Polarizability Dr. Anselm Horn (Tue Jul 07 2020 - 14:24:55 PDT)
[AMBER] fixatomorder Thakur, Abhishek (Tue Jul 07 2020 - 10:38:56 PDT)
- Re: [AMBER] fixatomorder Daniel Roe (Tue Aug 04 2020 - 07:27:20 PDT)
[AMBER] Asking for help: cross linking polymer SAKO MIRZAIE (Tue Jul 07 2020 - 17:28:10 PDT)
- Re: [AMBER] Asking for help: cross linking polymer David A Case (Tue Jul 07 2020 - 18:42:53 PDT)
  - Re: [AMBER] Asking for help: cross linking polymer SAKO MIRZAIE (Tue Jul 07 2020 - 20:31:21 PDT)
    - Re: [AMBER] Asking for help: cross linking polymer Dr. Anselm Horn (Wed Jul 08 2020 - 00:56:29 PDT)
[AMBER] amber14 gpu installation failed Carlos (Tue Jul 07 2020 - 20:42:57 PDT)
- Re: [AMBER] amber14 gpu installation failed David A Case (Wed Jul 08 2020 - 05:16:50 PDT)
  - Re: [AMBER] amber14 gpu installation failed Carlos (Mon Jul 13 2020 - 12:08:47 PDT)
[AMBER] Accelerated Molecular Dynamics and convergence Rosellen, Martin (Wed Jul 08 2020 - 06:58:20 PDT)
[AMBER] Error in SMD running PRITI ROY (Wed Jul 08 2020 - 19:05:50 PDT)
- Re: [AMBER] Error in SMD running David A Case (Thu Jul 09 2020 - 05:32:53 PDT)
[AMBER] Amber prmtop and inpcrd of complex file with a water molecular cutoff 辛志宏 (Wed Jul 08 2020 - 21:11:32 PDT)
- Re: [AMBER] Amber prmtop and inpcrd of complex file with a water molecular cutoff David A Case (Thu Jul 09 2020 - 05:36:15 PDT)
[AMBER] Problem with running Python script in AMBER environment. Vishal Singh (Wed Jul 08 2020 - 23:51:52 PDT)
- Re: [AMBER] Problem with running Python script in AMBER environment. Hai Nguyen (Thu Jul 09 2020 - 14:36:02 PDT)
  - Re: [AMBER] Problem with running Python script in AMBER environment. David A Case (Thu Jul 09 2020 - 17:32:24 PDT)
[AMBER] How to deal with oxygen atom on Fe=O of Compound I (heme enzyme, P450) Thirakorn Mokkawes (Thu Jul 09 2020 - 03:59:16 PDT)
- Re: [AMBER] How to deal with oxygen atom on Fe=O of Compound I (heme enzyme, P450) Pengfei Li (Mon Jul 20 2020 - 10:53:34 PDT)
  - Re: [AMBER] How to deal with oxygen atom on Fe=O of Compound I (heme enzyme, P450) Mohamed M. Aboelnga (Tue Aug 18 2020 - 09:10:11 PDT)
    - Re: [AMBER] How to deal with oxygen atom on Fe=O of Compound I (heme enzyme, P450) Vaibhav Dixit (Tue Aug 18 2020 - 23:11:21 PDT)
    - Re: [AMBER] How to deal with oxygen atom on Fe=O of Compound I (heme enzyme, P450) Mohamed M. Aboelnga (Wed Aug 19 2020 - 06:20:40 PDT)
    - Re: [AMBER] How to deal with oxygen atom on Fe=O of Compound I (heme enzyme, P450) Vaibhav Dixit (Wed Aug 19 2020 - 06:56:04 PDT)
    - Re: [AMBER] How to deal with oxygen atom on Fe=O of Compound I (heme enzyme, P450) Pengfei Li (Thu Sep 10 2020 - 13:27:39 PDT)
    - Re: [AMBER] How to deal with oxygen atom on Fe=O of Compound I (heme enzyme, P450) Vaibhav Dixit (Fri Sep 11 2020 - 19:21:07 PDT)
    - Re: [AMBER] How to deal with oxygen atom on Fe=O of Compound I (heme enzyme, P450) Vaibhav Dixit (Sat Sep 12 2020 - 04:29:46 PDT)
    - Re: [AMBER] How to deal with oxygen atom on Fe=O of Compound I (heme enzyme, P450) Vaibhav Dixit (Sat Sep 19 2020 - 23:54:31 PDT)
    - Re: [AMBER] How to deal with oxygen atom on Fe=O of Compound I (heme enzyme, P450) Pengfei Li (Thu Oct 22 2020 - 14:36:01 PDT)
    - Re: [AMBER] How to deal with oxygen atom on Fe=O of Compound I (heme enzyme, P450) Pengfei Li (Thu Sep 10 2020 - 13:25:21 PDT)
[AMBER] Forcefield for 5' phosphate in RNA dnlfr1994.gmail.com (Thu Jul 09 2020 - 05:01:36 PDT)
- Re: [AMBER] Forcefield for 5' phosphate in RNA David A Case (Thu Jul 09 2020 - 05:42:51 PDT)
[AMBER] GPU compatible with AMBER Isabelle Navizet (Thu Jul 09 2020 - 05:34:06 PDT)
- Re: [AMBER] GPU compatible with AMBER David A Case (Fri Jul 10 2020 - 05:04:24 PDT)
[AMBER] Error pmemd.cuda amber 20 GPU Camila Clemente (Thu Jul 09 2020 - 07:11:29 PDT)
- Re: [AMBER] Error pmemd.cuda amber 20 GPU David Cerutti (Thu Jul 09 2020 - 09:30:28 PDT)
  - Re: [AMBER] Error pmemd.cuda amber 20 GPU David Cerutti (Thu Jul 09 2020 - 09:44:51 PDT)
[AMBER] attach pull release method exploration for free energy calculations Debarati DasGupta (Thu Jul 09 2020 - 12:40:32 PDT)
- Re: [AMBER] attach pull release method exploration for free energy calculations Carlos Simmerling (Thu Jul 09 2020 - 13:24:12 PDT)
- Re: [AMBER] attach pull release method exploration for free energy calculations Niel Henriksen (Thu Jul 09 2020 - 16:34:55 PDT)
[AMBER] Mask behavior vs distance measurement? Kenneth Huang (Thu Jul 09 2020 - 17:04:10 PDT)
- Re: [AMBER] Mask behavior vs distance measurement? Daniel Roe (Thu Jul 09 2020 - 19:06:18 PDT)
  - Re: [AMBER] Mask behavior vs distance measurement? Kenneth Huang (Fri Jul 10 2020 - 10:31:28 PDT)
[AMBER] REPEATED LINMIN FAILURE Akshay Prabhakant (Fri Jul 10 2020 - 04:20:12 PDT)
- Re: [AMBER] REPEATED LINMIN FAILURE Elvis Martis (Fri Jul 10 2020 - 04:27:55 PDT)
- Re: [AMBER] REPEATED LINMIN FAILURE Sharif Nada (Fri Jul 10 2020 - 14:39:32 PDT)
  - Re: [AMBER] REPEATED LINMIN FAILURE James Kress (Fri Jul 10 2020 - 15:05:27 PDT)
[AMBER] About time-dependent positional restraints David Sáez (Fri Jul 10 2020 - 18:37:45 PDT)
- Re: [AMBER] About time-dependent positional restraints David Sáez (Fri Jul 10 2020 - 18:40:27 PDT)
- Re: [AMBER] About time-dependent positional restraints Christina Bergonzo (Mon Jul 13 2020 - 05:42:04 PDT)
  - Re: [AMBER] About time-dependent positional restraints David Sáez (Mon Jul 13 2020 - 08:34:33 PDT)
[AMBER] Reg. MMGBSA Calculations DHEERAJ CHITARA (Sat Jul 11 2020 - 11:26:52 PDT)
[AMBER] Seg fault with pmemd.cuda.MPI using plumed Jacob Remington (Sat Jul 11 2020 - 12:16:54 PDT)
[AMBER] Amber vs Namd energy values are different. Vishal Reddy (Sun Jul 12 2020 - 14:24:50 PDT)
- Re: [AMBER] Amber vs Namd energy values are different. David A Case (Sun Jul 12 2020 - 18:23:52 PDT)
[AMBER] Problems with MC barostat Yessica (Sun Jul 12 2020 - 16:53:08 PDT)
- Re: [AMBER] Problems with MC barostat Gomez, Yessica (Fri Jul 31 2020 - 17:51:23 PDT)
[AMBER] Using multiple distance restraints or creating exclusion sphere Amanda Buyan (Sun Jul 12 2020 - 18:20:16 PDT)
[AMBER] XMGRACE giving error Sumra Abbasi (Mon Jul 13 2020 - 03:07:36 PDT)
- Re: [AMBER] XMGRACE giving error Elvis Martis (Mon Jul 13 2020 - 03:19:43 PDT)
  - Re: [AMBER] XMGRACE giving error Sumra Abbasi (Mon Jul 13 2020 - 03:37:50 PDT)
    - Re: [AMBER] XMGRACE giving error Elvis Martis (Mon Jul 13 2020 - 04:07:40 PDT)
- Re: [AMBER] XMGRACE giving error Tru Huynh (Mon Jul 13 2020 - 04:27:48 PDT)
  - Re: [AMBER] XMGRACE giving error Sumra Abbasi (Mon Jul 13 2020 - 22:33:20 PDT)
    - Re: [AMBER] XMGRACE giving error Elvis Martis (Mon Jul 13 2020 - 22:53:37 PDT)
[AMBER] Default temperature regulation during production run: Missed to declare ntt option Jorden Cabal (Tue Jul 14 2020 - 04:26:02 PDT)
- Re: [AMBER] Default temperature regulation during production run: Missed to declare ntt option David A Case (Tue Jul 14 2020 - 09:38:56 PDT)
  - Re: [AMBER] Default temperature regulation during production run: Missed to declare ntt option Carlos Simmerling (Tue Jul 14 2020 - 09:41:37 PDT)
    - Re: [AMBER] Default temperature regulation during production run: Missed to declare ntt option Jorden Cabal (Tue Jul 14 2020 - 20:22:14 PDT)
  - Re: [AMBER] Default temperature regulation during production run: Missed to declare ntt option Jorden Cabal (Tue Jul 14 2020 - 20:29:20 PDT)
    - Re: [AMBER] Default temperature regulation during production run: Missed to declare ntt option David A Case (Wed Jul 15 2020 - 05:08:42 PDT)
[AMBER] EAMD_BOOST and reweighting of AMD runs Rosellen, Martin (Tue Jul 14 2020 - 08:00:51 PDT)
[AMBER] Clarification of Amber Post on Heating Protocol Robert Molt (Tue Jul 14 2020 - 14:46:25 PDT)
- Re: [AMBER] Clarification of Amber Post on Heating Protocol David A Case (Tue Jul 14 2020 - 19:11:44 PDT)
[AMBER] SPLIT method doubt Camila Clemente (Tue Jul 14 2020 - 15:01:49 PDT)
- Re: [AMBER] SPLIT method doubt Dr. Anselm Horn (Wed Jul 15 2020 - 08:30:37 PDT)
  - Re: [AMBER] SPLIT method doubt Camila Clemente (Wed Jul 15 2020 - 08:45:52 PDT)
- Re: [AMBER] SPLIT method doubt Matias Machado (Wed Jul 15 2020 - 10:22:14 PDT)
  - Re: [AMBER] SPLIT method doubt Camila Mara Clemente (Wed Jul 15 2020 - 12:24:44 PDT)
[AMBER] Command for making atoms rigid Pinky Mazumder (Tue Jul 14 2020 - 15:55:40 PDT)
- Re: [AMBER] Command for making atoms rigid Dr. Anselm Horn (Wed Jul 15 2020 - 08:38:56 PDT)
[AMBER] Questions on random seed Nada Afiva (Wed Jul 15 2020 - 20:35:37 PDT)
- Re: [AMBER] Questions on random seed David A Case (Thu Jul 16 2020 - 05:25:17 PDT)
  - Re: [AMBER] Questions on random seed Nada Afiva (Thu Jul 16 2020 - 16:20:23 PDT)
[AMBER] matching paramters of methane angad sharma (Thu Jul 16 2020 - 08:27:44 PDT)
- Re: [AMBER] matching paramters of methane David A Case (Thu Jul 16 2020 - 09:36:28 PDT)
[AMBER] OT: Job Posting Lachele Foley (Thu Jul 16 2020 - 16:40:13 PDT)
[AMBER] mmpbsa error MYRIAN TORRES RICO (Fri Jul 17 2020 - 04:31:13 PDT)
- Re: [AMBER] mmpbsa error Kshatresh Dutta Dubey (Sat Jul 18 2020 - 03:19:02 PDT)
  - Re: [AMBER] mmpbsa error MYRIAN TORRES RICO (Mon Jul 20 2020 - 00:45:27 PDT)
[AMBER] Several tutorial not found Michael F. Bruist (Fri Jul 17 2020 - 08:19:56 PDT)
- Re: [AMBER] Several tutorial not found David Cerutti (Fri Jul 17 2020 - 08:59:27 PDT)
- Re: [AMBER] Several tutorial not found David A Case (Fri Jul 17 2020 - 09:53:41 PDT)
- Re: [AMBER] Several tutorial not found Michael F. Bruist (Mon Jul 20 2020 - 09:22:13 PDT)
[AMBER] Reonstructing frames from PCA projection Michael F. Bruist (Fri Jul 17 2020 - 08:24:03 PDT)
- Re: [AMBER] Reonstructing frames from PCA projection Daniel Roe (Mon Jul 20 2020 - 07:43:58 PDT)
[AMBER] Tinker_to_amber problem Kliuchnikov, Evgenii (Fri Jul 17 2020 - 12:50:01 PDT)
- Re: [AMBER] Tinker_to_amber problem David A Case (Fri Jul 17 2020 - 17:54:54 PDT)
  - Re: [AMBER] Tinker_to_amber problem Kliuchnikov, Evgenii (Fri Jul 17 2020 - 17:59:00 PDT)
[AMBER] Amber20: Error in the linking of the pysander Wim R. Cardoen (Fri Jul 17 2020 - 13:54:04 PDT)
- Re: [AMBER] Amber20: Error in the linking of the pysander Gustaf Olsson (Sat Jul 18 2020 - 12:39:37 PDT)
Re: [AMBER] Cores, CPU RAM, GPU RAM James Kress (Fri Jul 17 2020 - 15:28:37 PDT)
- Re: [AMBER] Cores, CPU RAM, GPU RAM James Kress (Wed Jul 22 2020 - 15:19:25 PDT)
[AMBER] Error in incprd file while performing steered molecular dynamics simulation Pinky Mazumder (Sat Jul 18 2020 - 00:09:30 PDT)
[AMBER] Modified cysteine parameters krishnendu sinha (Sun Jul 19 2020 - 00:49:40 PDT)
- Re: [AMBER] Modified cysteine parameters David A Case (Sun Jul 19 2020 - 04:43:13 PDT)
- Re: [AMBER] Modified cysteine parameters Dr. Anselm Horn (Mon Jul 20 2020 - 01:46:00 PDT)
[AMBER] Units from quasiharmonic analysis of Principal Components German P. Barletta (Sun Jul 19 2020 - 09:48:38 PDT)
- Re: [AMBER] Units from quasiharmonic analysis of Principal Components David A Case (Sun Jul 19 2020 - 17:57:58 PDT)
- Re: [AMBER] Units from quasiharmonic analysis of Principal Components German P. Barletta (Mon Jul 20 2020 - 12:25:23 PDT)
[AMBER] Amber SHAKE error when running REMD 변진영 (Sun Jul 19 2020 - 23:56:58 PDT)
[AMBER] What would you like to see in visualization of chemical data? Jan Mičan (Mon Jul 20 2020 - 03:48:06 PDT)
- Re: [AMBER] What would you like to see in visualization of chemical data? Robert Molt (Mon Jul 20 2020 - 04:31:50 PDT)
[AMBER] ABMD with RMSD and RoG: ** NFE-Error ** : Cannot read &colvar namelist! Diego Morone (Mon Jul 20 2020 - 06:37:31 PDT)
- Re: [AMBER] ABMD with RMSD and RoG: ** NFE-Error ** : Cannot read &colvar namelist! Feng Pan (Wed Jul 22 2020 - 18:21:51 PDT)
  - Re: [AMBER] ABMD with RMSD and RoG: ** NFE-Error ** : Cannot read &colvar namelist! Diego Morone (Thu Jul 23 2020 - 08:22:09 PDT)
[AMBER] libnetcdf.so.7 needed by /usr/local/src/amber18/lib/libcpptraj.so, not found when upgrading AT18 to AT19 Markowska (Mon Jul 20 2020 - 06:56:26 PDT)
- Re: [AMBER] libnetcdf.so.7 needed by /usr/local/src/amber18/lib/libcpptraj.so, not found when upgrading AT18 to AT19 Daniel Roe (Mon Jul 20 2020 - 06:59:36 PDT)
  - Re: [AMBER] libnetcdf.so.7 needed by /usr/local/src/amber18/lib/libcpptraj.so, not found when upgrading AT18 to AT19 Markowska (Mon Jul 20 2020 - 07:44:13 PDT)
  - Re: [AMBER] libnetcdf.so.7 needed by /usr/local/src/amber18/lib/libcpptraj.so, not found when upgrading AT18 to AT19 David A Case (Mon Jul 20 2020 - 10:05:00 PDT)
    - Re: [AMBER] libnetcdf.so.7 needed by /usr/local/src/amber18/lib/libcpptraj.so, not found when upgrading AT18 to AT19 Markowska (Mon Jul 20 2020 - 12:59:05 PDT)
[AMBER] error in 3d rism calculation angad sharma (Mon Jul 20 2020 - 10:27:05 PDT)
- Re: [AMBER] error in 3d rism calculation Tyler Luchko (Lists) (Mon Jul 20 2020 - 13:25:09 PDT)
[AMBER] amber website down? Wim R. Cardoen (Mon Jul 20 2020 - 14:07:08 PDT)
- Re: [AMBER] amber website down? Gustaf Olsson (Mon Jul 20 2020 - 14:18:29 PDT)
- Re: [AMBER] amber website down? David A Case (Mon Jul 20 2020 - 18:26:01 PDT)
[AMBER] fatal error in 3D RISM calculation angad sharma (Tue Jul 21 2020 - 01:57:07 PDT)
- Re: [AMBER] fatal error in 3D RISM calculation Leena Aggarwal (Tue Jul 21 2020 - 04:39:21 PDT)
- Re: [AMBER] fatal error in 3D RISM calculation Daniel Roe (Tue Jul 21 2020 - 10:34:04 PDT)
  - Re: [AMBER] fatal error in 3D RISM calculation Tyler Luchko (Wed Jul 22 2020 - 09:32:05 PDT)
[AMBER] AMBER20 Error: No package metadata was found for pdb4amber Huang Tao (Tue Jul 21 2020 - 19:39:21 PDT)
- Re: [AMBER] AMBER20 Error: No package metadata was found for pdb4amber David A Case (Wed Jul 22 2020 - 04:55:10 PDT)
  - Re: [AMBER] AMBER20 Error: No package metadata was found for pdb4amber Huang Tao (Wed Jul 22 2020 - 05:14:41 PDT)
[AMBER] Undefined angle parameter and torsion terms in Antechamber Razil Tahir (Tue Jul 21 2020 - 21:03:20 PDT)
- Re: [AMBER] Undefined angle parameter and torsion terms in Amber18 Razil Tahir (Wed Jul 22 2020 - 08:13:08 PDT)
[AMBER] problem with pdb4amber David A Case (Wed Jul 22 2020 - 07:59:02 PDT)
- Re: [AMBER] problem with pdb4amber Hai Nguyen (Wed Jul 22 2020 - 09:13:40 PDT)
[AMBER] Size of Solvent Box DHEERAJ CHITARA (Wed Jul 22 2020 - 11:14:20 PDT)
- Re: [AMBER] Size of Solvent Box David A Case (Wed Jul 22 2020 - 12:16:56 PDT)
[AMBER] tinker_to_amber force fields Kliuchnikov, Evgenii (Wed Jul 22 2020 - 11:37:33 PDT)
- Re: [AMBER] tinker_to_amber force fields Kliuchnikov, Evgenii (Wed Jul 22 2020 - 12:10:14 PDT)
  - Re: [AMBER] tinker_to_amber force fields David A Case (Wed Jul 22 2020 - 17:28:48 PDT)
- Re: [AMBER] tinker_to_amber force fields David A Case (Wed Jul 22 2020 - 12:24:37 PDT)
[AMBER] Amber 20 - Support Multi GPU Adriano José Ferruzzi (Wed Jul 22 2020 - 12:31:29 PDT)
- Re: [AMBER] Amber 20 - Support Multi GPU David A Case (Wed Jul 22 2020 - 17:36:38 PDT)
  - Re: [AMBER] Amber 20 - Support Multi GPU Adriano José Ferruzzi (Thu Jul 23 2020 - 07:11:26 PDT)
[AMBER] tleap does not recognize nonstandard residue from lib file JoAnne Babula (Wed Jul 22 2020 - 12:43:59 PDT)
- Re: [AMBER] tleap does not recognize nonstandard residue from lib file JoAnne Babula (Wed Jul 22 2020 - 13:49:49 PDT)
[AMBER] Problem compiling Amber20 - undefined reference to 'plumedmain_create' Amanda Buyan (Wed Jul 22 2020 - 23:07:39 PDT)
- Re: [AMBER] Problem compiling Amber20 - undefined reference to 'plumedmain_create' David A Case (Thu Jul 23 2020 - 05:05:39 PDT)
[AMBER] Download link for AmberTools17 Casalini Tommaso (Thu Jul 23 2020 - 01:44:20 PDT)
- Re: [AMBER] Download link for AmberTools17 David A Case (Thu Jul 23 2020 - 05:08:06 PDT)
[AMBER] AMBER trajectory analysis in MINT package Jisha B (Thu Jul 23 2020 - 05:40:18 PDT)
[AMBER] smooth soft core potentials Debarati DasGupta (Thu Jul 23 2020 - 13:26:32 PDT)
- Re: [AMBER] smooth soft core potentials David A Case (Thu Jul 23 2020 - 17:49:30 PDT)
[AMBER] Using Orca to develop RESP Charges Lucas Bandeira (Thu Jul 23 2020 - 13:37:56 PDT)
- Re: [AMBER] Using Orca to develop RESP Charges David Cerutti (Fri Jul 24 2020 - 11:08:22 PDT)
[AMBER] carboxylated Lys Állan Ferrari (Thu Jul 23 2020 - 14:30:32 PDT)
- Re: [AMBER] carboxylated Lys Dr. Anselm Horn (Fri Jul 24 2020 - 07:46:10 PDT)
[AMBER] Issue while installing Amber20 Alejandro Cagnoni (Fri Jul 24 2020 - 13:44:29 PDT)
- Re: [AMBER] Issue while installing Amber20 David A Case (Sat Jul 25 2020 - 05:37:24 PDT)
[AMBER] Error in Gausian file preparation using MCPB.py gagandeep singh (Fri Jul 24 2020 - 14:55:47 PDT)
- Re: [AMBER] Error in Gausian file preparation using MCPB.py gagandeep singh (Fri Jul 31 2020 - 14:01:14 PDT)
  - Re: [AMBER] Error in Gausian file preparation using MCPB.py Preeti Pandey (Fri Jul 31 2020 - 14:20:16 PDT)
    - Re: [AMBER] Error in Gausian file preparation using MCPB.py gagandeep singh (Sat Aug 01 2020 - 18:56:45 PDT)
    - [AMBER] how to calculate net charge of "molecule" using the command "netCharge" Billiot, Eugene (Sun Aug 02 2020 - 16:40:27 PDT)
    - Re: [AMBER] how to calculate net charge of "molecule" using the command "netCharge" Bill Ross (Sun Aug 02 2020 - 17:44:43 PDT)
    - Re: [AMBER] how to calculate net charge of "molecule" using the command "netCharge" David A Case (Mon Aug 03 2020 - 07:07:11 PDT)
    - Re: [AMBER] how to calculate net charge of "molecule" using the command "netCharge" Billiot, Eugene (Mon Aug 03 2020 - 11:33:59 PDT)
[AMBER] Steered molecular dynamics Simulation Pinky Mazumder (Fri Jul 24 2020 - 19:47:39 PDT)
- Re: [AMBER] Steered molecular dynamics Simulation Vishal Singh (Fri Jul 24 2020 - 21:39:40 PDT)
[AMBER] How to calculate velocity in steered simulation Pinky Mazumder (Fri Jul 24 2020 - 20:58:05 PDT)
[AMBER] cudaMemcpyToSymbol: SetSim copy to cSim failed invalid device symbol venkat (Sat Jul 25 2020 - 05:02:26 PDT)
- Re: [AMBER] cudaMemcpyToSymbol: SetSim copy to cSim failed invalid device symbol David Cerutti (Sat Jul 25 2020 - 05:40:36 PDT)
- Re: [AMBER] cudaMemcpyToSymbol: SetSim copy to cSim failed invalid device symbol mirzo (Sat Jul 25 2020 - 06:36:52 PDT)
  - Re: [AMBER] cudaMemcpyToSymbol: SetSim copy to cSim failed invalid device symbol Andrea Cavalli (Sat Jul 25 2020 - 07:26:42 PDT)
[AMBER] How to install Amber20 with pmemd.amoeba? Kliuchnikov, Evgenii (Sat Jul 25 2020 - 12:29:56 PDT)
- Re: [AMBER] How to install Amber20 with pmemd.amoeba? David A Case (Sat Jul 25 2020 - 17:36:21 PDT)
  - Re: [AMBER] How to install Amber20 with pmemd.amoeba? Kliuchnikov, Evgenii (Sat Jul 25 2020 - 21:46:59 PDT)
[AMBER] Maximum system size Jack Shepherd (Sat Jul 25 2020 - 17:57:01 PDT)
- Re: [AMBER] Maximum system size David A Case (Sun Jul 26 2020 - 17:57:50 PDT)
[AMBER] Issue about "... . RESTARTED DUE TO LINMIN FAILURE..." 辛志宏 (Sun Jul 26 2020 - 04:59:21 PDT)
- Re: [AMBER] Issue about "... . RESTARTED DUE TO LINMIN FAILURE..." Elvis Martis (Sun Jul 26 2020 - 05:43:46 PDT)
- Re: [AMBER] Issue about "... . RESTARTED DUE TO LINMIN FAILURE..." David A Case (Sun Jul 26 2020 - 17:44:15 PDT)
- Re: [AMBER] Issue about "... . RESTARTED DUE TO LINMIN FAILURE..." 辛志宏 (Mon Jul 27 2020 - 18:48:41 PDT)
  - Re: [AMBER] Issue about "... . RESTARTED DUE TO LINMIN FAILURE..." David A Case (Tue Jul 28 2020 - 06:59:16 PDT)
[AMBER] Amber20 Compiling problem with b2 and Boost.Regex Amanda Buyan (Sun Jul 26 2020 - 18:35:07 PDT)
- Re: [AMBER] Amber20 Compiling problem with b2 and Boost.Regex David A Case (Mon Jul 27 2020 - 06:10:37 PDT)
  - Re: [AMBER] Amber20 Compiling problem with b2 and Boost.Regex Amanda Buyan (Mon Jul 27 2020 - 15:50:37 PDT)
    - Re: [AMBER] Amber20 Compiling problem with b2 and Boost.Regex Amanda Buyan (Wed Jul 29 2020 - 16:40:29 PDT)
[AMBER] Charges for modified DNA base at the termini? Kenneth Huang (Sun Jul 26 2020 - 23:50:39 PDT)
[AMBER] Error building Amber Walton Smith (Mon Jul 27 2020 - 07:04:33 PDT)
- Re: [AMBER] Error building Amber David A Case (Mon Jul 27 2020 - 10:15:14 PDT)
- Re: [AMBER] Error building Amber David A Case (Mon Jul 27 2020 - 10:48:48 PDT)
  - Re: [AMBER] Error building Amber Walton Smith (Mon Jul 27 2020 - 12:50:54 PDT)
    - Re: [AMBER] Error building Amber Gustaf Olsson (Tue Jul 28 2020 - 02:14:47 PDT)
    - Re: [AMBER] Error building Amber David A Case (Tue Jul 28 2020 - 06:43:52 PDT)
    - Re: [AMBER] Error building Amber Walton Smith (Tue Jul 28 2020 - 07:03:42 PDT)
    - Re: [AMBER] Error building Amber Gustaf Olsson (Tue Jul 28 2020 - 14:35:15 PDT)
    - Re: [AMBER] Error building Amber David A Case (Tue Jul 28 2020 - 18:57:44 PDT)
    - Re: [AMBER] Error building Amber David A Case (Tue Jul 28 2020 - 20:17:05 PDT)
    - Re: [AMBER] Error building Amber Gustaf Olsson (Wed Jul 29 2020 - 04:58:32 PDT)
    - Re: [AMBER] Error building Amber Walton Smith (Wed Jul 29 2020 - 07:26:19 PDT)
    - Re: [AMBER] Error building Amber Gustaf Olsson (Wed Jul 29 2020 - 12:50:32 PDT)
    - Re: [AMBER] Error building Amber Walton Smith (Wed Jul 29 2020 - 17:09:55 PDT)
    - Re: [AMBER] Error building Amber Walton Smith (Wed Jul 29 2020 - 17:57:21 PDT)
    - Re: [AMBER] Error building Amber David A Case (Wed Jul 29 2020 - 18:21:11 PDT)
    - Re: [AMBER] Error building Amber Gustaf Olsson (Thu Jul 30 2020 - 09:56:12 PDT)
    - Re: [AMBER] Error building Amber Walton Smith (Wed Jul 29 2020 - 06:31:31 PDT)
- Re: [AMBER] Error building Amber David A Case (Thu Jul 30 2020 - 04:54:10 PDT)
  - Re: [AMBER] Error building Amber Kazuo Ohta (Tue Oct 20 2020 - 19:08:05 PDT)
[AMBER] Problems generating charges with RESP Lucas Bandeira (Mon Jul 27 2020 - 13:39:01 PDT)
[AMBER] Problem installing AmberMD with MPI support on Cray XC40 Jakub Jalowiec (Mon Jul 27 2020 - 15:27:13 PDT)
- Re: [AMBER] Problem installing AmberMD with MPI support on Cray XC40 Daniel Roe (Tue Aug 04 2020 - 06:32:11 PDT)
  - Re: [AMBER] Problem installing AmberMD with MPI support on Cray XC40 Jakub Jalowiec (Wed Aug 12 2020 - 01:33:01 PDT)
[AMBER] Problems deriving charges with RESP Lucas Bandeira (Mon Jul 27 2020 - 17:23:52 PDT)
[AMBER] ASMD equil4 not producing output files Hantz, Eric R. (Tue Jul 28 2020 - 06:51:23 PDT)
- Re: [AMBER] ASMD equil4 not producing output files Adrian Roitberg (Tue Jul 28 2020 - 09:56:35 PDT)
- Re: [AMBER] ASMD equil4 not producing output files Hantz, Eric R. (Wed Jul 29 2020 - 13:11:18 PDT)
[AMBER] Tracking lifetime distance by closest of specific water IDs? Kenneth Huang (Tue Jul 28 2020 - 07:28:51 PDT)
- Re: [AMBER] Tracking lifetime distance by closest of specific water IDs? Daniel Roe (Tue Aug 04 2020 - 06:28:49 PDT)
[AMBER] Issue heating system in equilibration step Samuel A. Ratliff (Tue Jul 28 2020 - 10:05:00 PDT)
- Re: [AMBER] Issue heating system in equilibration step Samuel A. Ratliff (Fri Jul 31 2020 - 09:58:44 PDT)
- Re: [AMBER] Issue heating system in equilibration step Carlos Simmerling (Fri Jul 31 2020 - 12:10:07 PDT)
  - Re: [AMBER] Issue heating system in equilibration step Samuel A. Ratliff (Fri Jul 31 2020 - 12:16:01 PDT)
    - Re: [AMBER] Issue heating system in equilibration step Carlos Simmerling (Fri Jul 31 2020 - 12:19:23 PDT)
    - Re: [AMBER] Issue heating system in equilibration step Samuel A. Ratliff (Fri Jul 31 2020 - 13:14:09 PDT)
    - Re: [AMBER] Issue heating system in equilibration step Samuel A. Ratliff (Thu Aug 06 2020 - 09:58:04 PDT)
[AMBER] AMD parameter: protein residue should count ligand or not Lod King (Tue Jul 28 2020 - 10:55:43 PDT)
[AMBER] 6. Re: Issue about "... . RESTARTED DUE TO LINMIN FAILURE..." (???) 辛志宏 (Wed Jul 29 2020 - 02:10:13 PDT)
- [AMBER] running QM/MM calculations David A Case (Wed Jul 29 2020 - 04:40:51 PDT)
[AMBER] Refitting charges with MCPB destabilizes the active site Casalini Tommaso (Wed Jul 29 2020 - 04:23:44 PDT)
- Re: [AMBER] Refitting charges with MCPB destabilizes the active site Pengfei Li (Thu Sep 10 2020 - 13:19:01 PDT)
[AMBER] Adding ions to implicit solvent models Conrad F Li (Wed Jul 29 2020 - 18:17:34 PDT)
- Re: [AMBER] Adding ions to implicit solvent models Bill Ross (Thu Jul 30 2020 - 02:00:18 PDT)
[AMBER] Erro Amber18 GPU Renato Araujo (Thu Jul 30 2020 - 12:55:42 PDT)
- Re: [AMBER] Erro Amber18 GPU David A Case (Thu Jul 30 2020 - 17:29:39 PDT)
  - Re: [AMBER] Erro Amber18 GPU Renato Araujo (Thu Jul 30 2020 - 18:07:17 PDT)
Re: [AMBER] Issue about "... . RESTARTED DUE TO LINMIN FAILURE..." 辛志宏 (Thu Jul 30 2020 - 20:46:21 PDT)
- Re: [AMBER] Issue about "... . RESTARTED DUE TO LINMIN FAILURE..." Daniel Roe (Fri Jul 31 2020 - 05:52:47 PDT)
[AMBER] How to make pass extra argument "--bind-to none" to mpirun for ORCA when running QMMM from sander? Francesca Lønstad Bleken (Fri Jul 31 2020 - 02:42:32 PDT)
- Re: [AMBER] How to make pass extra argument "--bind-to none" to mpirun for ORCA when running QMMM from sander? Goetz, Andreas (Fri Jul 31 2020 - 03:12:22 PDT)
[AMBER] Amber nc trajectory file analysis by x3dna Jenny 148 (Fri Jul 31 2020 - 08:05:56 PDT)
- Re: [AMBER] Amber nc trajectory file analysis by x3dna Maria Nagan (Fri Jul 31 2020 - 08:22:17 PDT)
- Re: [AMBER] Amber nc trajectory file analysis by x3dna Daniel Roe (Fri Jul 31 2020 - 08:28:19 PDT)
[AMBER] amber trajectory nc file to pdb ensemble Athena N (Fri Jul 31 2020 - 09:28:26 PDT)
- Re: [AMBER] amber trajectory nc file to pdb ensemble Thomas Cheatham (Fri Jul 31 2020 - 09:45:45 PDT)
  - Re: [AMBER] amber trajectory nc file to pdb ensemble Rodrigo Galindo-Murillo (Fri Jul 31 2020 - 10:04:00 PDT)
- Re: [AMBER] amber trajectory nc file to pdb ensemble Rodrigo Galindo-Murillo (Fri Jul 31 2020 - 10:53:30 PDT)
  - Re: [AMBER] amber trajectory nc file to pdb ensemble Rodrigo Galindo-Murillo (Fri Jul 31 2020 - 10:54:29 PDT)
[AMBER] Structure Artifact After Autoimage Mikhael, Simoun (Fri Jul 31 2020 - 14:01:52 PDT)
- Re: [AMBER] Structure Artifact After Autoimage Daniel Roe (Tue Aug 04 2020 - 06:25:10 PDT)
[AMBER] Reduced Performance with pmemd.cuda Compared With Benchmarks. 李奕言 (Sun Aug 02 2020 - 20:21:55 PDT)
- Re: [AMBER] Reduced Performance with pmemd.cuda Compared With Benchmarks. David Cerutti (Mon Aug 03 2020 - 21:40:51 PDT)
  - Re: [AMBER] Reduced Performance with pmemd.cuda Compared With Benchmarks. 李奕言 (Wed Aug 05 2020 - 18:58:58 PDT)
    - Re: [AMBER] Reduced Performance with pmemd.cuda Compared With Benchmarks. David Cerutti (Wed Aug 05 2020 - 19:48:36 PDT)
    - Re: [AMBER] Reduced Performance with pmemd.cuda Compared With Benchmarks. 李奕言 (Wed Aug 05 2020 - 23:43:57 PDT)
    - Re: [AMBER] Reduced Performance with pmemd.cuda Compared With Benchmarks. Bill Ross (Wed Aug 05 2020 - 23:52:10 PDT)
    - Re: [AMBER] Reduced Performance with pmemd.cuda Compared With Benchmarks. David Cerutti (Thu Aug 06 2020 - 02:02:27 PDT)
    - Re: [AMBER] Reduced Performance with pmemd.cuda Compared With Benchmarks. David Cerutti (Thu Aug 06 2020 - 02:03:07 PDT)
    - Re: [AMBER] Reduced Performance with pmemd.cuda Compared With Benchmarks. Bill Ross (Thu Aug 06 2020 - 02:08:33 PDT)
    - Re: [AMBER] Reduced Performance with pmemd.cuda Compared With Benchmarks. David Cerutti (Thu Aug 06 2020 - 02:11:29 PDT)
    - Re: [AMBER] Reduced Performance with pmemd.cuda Compared With Benchmarks. Bill Ross (Thu Aug 06 2020 - 02:15:36 PDT)
    - Re: [AMBER] Reduced Performance with pmemd.cuda Compared With Benchmarks. David A Case (Thu Aug 06 2020 - 04:52:31 PDT)
Re: [AMBER] Issue about "... . RESTARTED DUE TO LINMIN FAILURE..." (???) 辛志宏 (Sun Aug 02 2020 - 21:04:16 PDT)
- Re: [AMBER] Issue about "... . RESTARTED DUE TO LINMIN FAILURE..." (???) David A Case (Mon Aug 03 2020 - 07:16:16 PDT)
- Re: [AMBER] Issue about "... . RESTARTED DUE TO LINMIN FAILURE..." (???) 辛志宏 (Mon Aug 03 2020 - 18:59:17 PDT)
[AMBER] Regarding the backup of amber nc files Jenny 148 (Sun Aug 02 2020 - 22:44:34 PDT)
- Re: [AMBER] Regarding the backup of amber nc files Bill Ross (Sun Aug 02 2020 - 23:19:03 PDT)
- Re: [AMBER] Regarding the backup of amber nc files David A Case (Mon Aug 03 2020 - 07:25:23 PDT)
[AMBER] Are Amber program can running using AMD processor? Setyanto Md (Mon Aug 03 2020 - 20:25:18 PDT)
- Re: [AMBER] Are Amber program can running using AMD processor? Bill Ross (Mon Aug 03 2020 - 21:39:23 PDT)
  - Re: [AMBER] Are Amber program can running using AMD processor? Bill Ross (Mon Aug 03 2020 - 21:43:46 PDT)
    - Re: [AMBER] Are Amber program can running using AMD processor? Setyanto Md (Mon Aug 03 2020 - 22:40:31 PDT)
[AMBER] open valence problem Ayesha Fatima (Tue Aug 04 2020 - 07:34:19 PDT)
- Re: [AMBER] open valence problem David A Case (Tue Aug 04 2020 - 18:44:32 PDT)
  - Re: [AMBER] open valence problem Ayesha Fatima (Thu Aug 06 2020 - 04:10:35 PDT)
- Re: [AMBER] open valence problem Ayesha Fatima (Thu Aug 06 2020 - 05:04:23 PDT)
  - Re: [AMBER] open valence problem Ayesha Fatima (Thu Aug 06 2020 - 06:41:56 PDT)
[AMBER] conversion of tripose mol2 to amber type Nikhil Maroli (Tue Aug 04 2020 - 05:21:08 PDT)
- Re: [AMBER] conversion of tripose mol2 to amber type David A Case (Tue Aug 04 2020 - 18:37:09 PDT)
- Re: [AMBER] conversion of tripose mol2 to amber type Nikhil Maroli (Wed Aug 05 2020 - 10:30:50 PDT)
  - Re: [AMBER] conversion of tripose mol2 to amber type David A Case (Wed Aug 05 2020 - 13:07:20 PDT)
[AMBER] How to make amber/antechamber type mol2 from syble mol2 Nikhil Maroli (Wed Aug 05 2020 - 00:05:03 PDT)
[AMBER] gnuplot MYRIAN TORRES RICO (Wed Aug 05 2020 - 01:25:03 PDT)
- Re: [AMBER] gnuplot Dr. Anselm Horn (Wed Aug 05 2020 - 02:50:48 PDT)
  - Re: [AMBER] gnuplot MYRIAN TORRES RICO (Wed Aug 05 2020 - 04:23:31 PDT)
- Re: [AMBER] gnuplot Rodrigo Galindo-Murillo (Wed Aug 05 2020 - 08:38:43 PDT)
[AMBER] weird energy histograms with REMD Diego Morone (Wed Aug 05 2020 - 05:35:04 PDT)
- Re: [AMBER] weird energy histograms with REMD koushik kasavajhala (Wed Aug 05 2020 - 05:43:03 PDT)
  - Re: [AMBER] weird energy histograms with REMD Diego Morone (Wed Aug 05 2020 - 05:53:44 PDT)
- Re: [AMBER] weird energy histograms with REMD Daniel Roe (Wed Aug 05 2020 - 06:15:14 PDT)
  - Re: [AMBER] weird energy histograms with REMD Christina Bergonzo (Wed Aug 05 2020 - 06:47:31 PDT)
[AMBER] implicit solvent calculations with calcium ion Piotr Fajer (Wed Aug 05 2020 - 17:56:06 PDT)
- Re: [AMBER] implicit solvent calculations with calcium ion David A Case (Thu Aug 06 2020 - 04:46:30 PDT)
  - Re: [AMBER] implicit solvent calculations with calcium ion Bill Ross (Thu Aug 06 2020 - 04:53:24 PDT)
[AMBER] Fatal error on running GAMESS for parameters of FE ion gagandeep singh (Thu Aug 06 2020 - 08:59:52 PDT)
[AMBER] asking about "timlim" in accelerated MD Setyanto Md (Thu Aug 06 2020 - 09:22:24 PDT)
- Re: [AMBER] asking about "timlim" in accelerated MD David A Case (Thu Aug 06 2020 - 13:19:30 PDT)
  - Re: [AMBER] asking about "timlim" in accelerated MD Setyanto Md (Thu Aug 06 2020 - 16:04:22 PDT)
[AMBER] tleap.in error Ayesha Fatima (Thu Aug 06 2020 - 09:41:19 PDT)
- Re: [AMBER] tleap.in error David A Case (Thu Aug 06 2020 - 13:22:47 PDT)
- Re: [AMBER] tleap.in error Scott Brozell (Thu Aug 06 2020 - 13:26:11 PDT)
- Re: [AMBER] tleap.in error Matias Machado (Fri Aug 07 2020 - 06:00:06 PDT)
  - Re: [AMBER] tleap.in error Ayesha Fatima (Fri Aug 07 2020 - 06:14:08 PDT)
    - Re: [AMBER] tleap.in error Matias Machado (Fri Aug 07 2020 - 06:26:46 PDT)
[AMBER] Parmed: Residues cannot be part of 2 molecules! Molecule section will not be correctly set. Samuel A. Ratliff (Thu Aug 06 2020 - 10:10:58 PDT)
- Re: [AMBER] Parmed: Residues cannot be part of 2 molecules! Molecule section will not be correctly set. David A Case (Thu Aug 06 2020 - 13:30:16 PDT)
  - Re: [AMBER] Parmed: Residues cannot be part of 2 molecules! Molecule section will not be correctly set. Samuel A. Ratliff (Fri Aug 07 2020 - 08:34:26 PDT)
[AMBER] problem in 3DRISM angad sharma (Fri Aug 07 2020 - 06:32:51 PDT)
- Re: [AMBER] problem in 3DRISM ATUL KUMAR (Fri Aug 07 2020 - 06:59:41 PDT)
- Re: [AMBER] problem in 3DRISM David A Case (Fri Aug 07 2020 - 08:18:15 PDT)
[AMBER] Help with MDCRD file for calculating binding energy Ram Koganti (Fri Aug 07 2020 - 18:36:34 PDT)
[AMBER] CALL FOR PAPER - 16th German Conference on Cheminformatics (GCC) and the SAMPL satellite workshop Guessregen, Stefan /DE (Sat Aug 08 2020 - 03:45:10 PDT)
[AMBER] Problem about ADP-Protein complex simulation neildancer.sina.com (Sat Aug 08 2020 - 06:58:49 PDT)
[AMBER] Assigning new velocities from Maxwell-Boltzmann distribution (ntx = 1) German P. Barletta (Sun Aug 09 2020 - 13:43:20 PDT)
- Re: [AMBER] Assigning new velocities from Maxwell-Boltzmann distribution (ntx = 1) Bill Ross (Sun Aug 09 2020 - 23:27:45 PDT)
- Re: [AMBER] Assigning new velocities from Maxwell-Boltzmann distribution (ntx = 1) David A Case (Mon Aug 10 2020 - 04:57:40 PDT)
- Re: [AMBER] Assigning new velocities from Maxwell-Boltzmann distribution (ntx = 1) German P. Barletta (Tue Aug 11 2020 - 16:46:27 PDT)
  - Re: [AMBER] Assigning new velocities from Maxwell-Boltzmann distribution (ntx = 1) Daniel Roe (Wed Aug 12 2020 - 06:18:13 PDT)
[AMBER] Amber20 with PLUMED not working with multiple CPUs Amanda Buyan (Sun Aug 09 2020 - 16:25:13 PDT)
- Re: [AMBER] Amber20 with PLUMED not working with multiple CPUs viktor drobot (Mon Aug 10 2020 - 00:25:30 PDT)
  - Re: [AMBER] Amber20 with PLUMED not working with multiple CPUs Amanda Buyan (Mon Aug 10 2020 - 21:23:23 PDT)
    - Re: [AMBER] Amber20 with PLUMED not working with multiple CPUs viktor drobot (Tue Aug 11 2020 - 00:19:20 PDT)
    - Re: [AMBER] Amber20 with PLUMED not working with multiple CPUs Amanda Buyan (Tue Aug 11 2020 - 16:23:24 PDT)
[AMBER] about pressure calculation in Amber18 Li, Min (Sun Aug 09 2020 - 21:16:35 PDT)
[AMBER] Defining/Selecting BLAS with cmake Gustaf Olsson (Mon Aug 10 2020 - 03:19:03 PDT)
[AMBER] Using cpptraj to generate rst7 files from trajectory Liao (Tue Aug 11 2020 - 14:47:47 PDT)
- Re: [AMBER] Using cpptraj to generate rst7 files from trajectory Gustaf Olsson (Tue Aug 11 2020 - 22:57:44 PDT)
  - Re: [AMBER] Using cpptraj to generate rst7 files from trajectory Liao (Wed Aug 12 2020 - 08:59:53 PDT)
    - Re: [AMBER] Using cpptraj to generate rst7 files from trajectory Daniel Roe (Wed Aug 12 2020 - 09:04:40 PDT)
    - Re: [AMBER] Using cpptraj to generate rst7 files from trajectory Liao (Wed Aug 12 2020 - 11:25:08 PDT)
- Re: [AMBER] Using cpptraj to generate rst7 files from trajectory Daniel Roe (Wed Aug 12 2020 - 06:20:12 PDT)
[AMBER] Amazon Cloud services and Amber Debarati DasGupta (Wed Aug 12 2020 - 05:24:31 PDT)
- Re: [AMBER] Amazon Cloud services and Amber Gustaf Olsson (Wed Aug 12 2020 - 05:40:38 PDT)
  - Re: [AMBER] Amazon Cloud services and Amber Raman Preet Singh (Wed Aug 12 2020 - 05:47:36 PDT)
- Re: [AMBER] Amazon Cloud services and Amber Luca Codutti (Wed Aug 12 2020 - 05:58:40 PDT)
- Re: [AMBER] Amazon Cloud services and Amber Thomas Cheatham (Wed Aug 12 2020 - 15:37:20 PDT)
[AMBER] Compiling AmberTools on macOS Gustaf Olsson (Wed Aug 12 2020 - 07:08:23 PDT)
[AMBER] tleap error ankita mehta (Wed Aug 12 2020 - 09:43:03 PDT)
- Re: [AMBER] tleap error David A Case (Wed Aug 12 2020 - 12:30:40 PDT)
Re: [AMBER] Assigning new velocities from Maxwell-Boltzmann distribution German P. Barletta (Wed Aug 12 2020 - 12:16:19 PDT)
[AMBER] GlycoTools Webinar tomorrow Lachele Foley (Thu Aug 13 2020 - 07:34:28 PDT)
[AMBER] Running Paramfit with 300 + structures Samuel Himes (Fri Aug 14 2020 - 14:58:14 PDT)
- Re: [AMBER] Running Paramfit with 300 + structures Robin Betz (Fri Aug 14 2020 - 15:12:12 PDT)
  - Re: [AMBER] Running Paramfit with 300 + structures David Cerutti (Fri Aug 14 2020 - 15:36:18 PDT)
[AMBER] Time numbering problem with constant-pH simulations Jonee Lillard (Sat Aug 15 2020 - 07:31:14 PDT)
- Re: [AMBER] Time numbering problem with constant-pH simulations Daniel Roe (Tue Aug 18 2020 - 06:02:47 PDT)
  - Re: [AMBER] Time numbering problem with constant-pH simulations Daniel Roe (Mon Aug 24 2020 - 17:57:07 PDT)
    - Re: [AMBER] Time numbering problem with constant-pH simulations Jonee Lillard (Tue Aug 25 2020 - 08:22:01 PDT)
    - Re: [AMBER] Time numbering problem with constant-pH simulations Jonee Lillard (Tue Aug 25 2020 - 08:30:35 PDT)
    - Re: [AMBER] Time numbering problem with constant-pH simulations Daniel Roe (Tue Aug 25 2020 - 12:22:47 PDT)
    - Re: [AMBER] Time numbering problem with constant-pH simulations Jonee Lillard (Wed Aug 26 2020 - 06:03:25 PDT)
    - Re: [AMBER] Time numbering problem with constant-pH simulations Daniel Roe (Wed Aug 26 2020 - 06:47:13 PDT)
- Re: [AMBER] Time numbering problem with constant-pH simulations Jonee Lillard (Sat Aug 22 2020 - 06:04:50 PDT)
  - Re: [AMBER] Time numbering problem with constant-pH simulations Daniel Roe (Mon Aug 24 2020 - 16:57:44 PDT)
[AMBER] Error searching for compatible GPU Camila Clemente (Sat Aug 15 2020 - 18:01:37 PDT)
- Re: [AMBER] Error searching for compatible GPU David A Case (Sun Aug 16 2020 - 05:04:08 PDT)
  - Re: [AMBER] Error searching for compatible GPU Camila Clemente (Sun Aug 16 2020 - 09:00:53 PDT)
[AMBER] Number of atoms in the coordinate file does not match the parm file when assigning ntwprt value 李奕言 (Sat Aug 15 2020 - 21:00:28 PDT)
- Re: [AMBER] Number of atoms in the coordinate file does not match the parm file when assigning ntwprt value Bill Ross (Sat Aug 15 2020 - 21:21:03 PDT)
  - Re: [AMBER] Number of atoms in the coordinate file does not match the parm file when assigning ntwprt value 李奕言 (Sun Aug 16 2020 - 01:21:50 PDT)
    - Re: [AMBER] Number of atoms in the coordinate file does not match the parm file when assigning ntwprt value Bill Ross (Sun Aug 16 2020 - 01:27:22 PDT)
    - Re: [AMBER] Number of atoms in the coordinate file does not match the parm file when assigning ntwprt value Bill Ross (Sun Aug 16 2020 - 01:56:15 PDT)
    - Re: [AMBER] Number of atoms in the coordinate file does not match the parm file when assigning ntwprt value 李奕言 (Tue Aug 18 2020 - 04:31:47 PDT)
    - Re: [AMBER] Number of atoms in the coordinate file does not match the parm file when assigning ntwprt value Bill Ross (Tue Aug 18 2020 - 04:36:07 PDT)
- Re: [AMBER] Number of atoms in the coordinate file does not match the parm file when assigning ntwprt value Qinghua Liao (Sun Aug 16 2020 - 02:26:54 PDT)
[AMBER] AMBER18 pmemd.MPI installation error Shubhandra Tripathi (Mon Aug 17 2020 - 06:43:47 PDT)
- Re: [AMBER] AMBER18 pmemd.MPI installation error David A Case (Tue Aug 18 2020 - 05:45:47 PDT)
[AMBER] preparing complexes Ayesha Fatima (Mon Aug 17 2020 - 13:25:14 PDT)
- Re: [AMBER] preparing complexes neildancer (Mon Aug 17 2020 - 20:18:11 PDT)
- Re: [AMBER] preparing complexes David A Case (Tue Aug 18 2020 - 05:27:46 PDT)
[AMBER] no collective variables output for infe=1 and abfqmmm FLORA, JOSEPH (Mon Aug 17 2020 - 18:52:20 PDT)
[AMBER] Few workflow-LIE Neha Gandhi (Tue Aug 18 2020 - 06:15:04 PDT)
[AMBER] 转发: Amber20 install problem （Geng Dong）东庚 (Tue Aug 18 2020 - 18:25:04 PDT)
- Re: [AMBER] 转发: Amber20 install problem （Geng Dong） David A Case (Tue Aug 18 2020 - 19:28:34 PDT)
  - Re: [AMBER] 转发: Amber20 install problem （Geng Dong） David A Case (Wed Aug 19 2020 - 19:00:31 PDT)
    - Re: [AMBER] Amber20 install problem （Geng Dong） Gustaf Olsson (Thu Aug 20 2020 - 00:45:32 PDT)
[AMBER] Antechamber and parmchk2 problem in case of processing mol2 input files Marek Maly (Thu Aug 20 2020 - 03:21:08 PDT)
- Re: [AMBER] Antechamber and parmchk2 problem in case of processing mol2 input files Scott Brozell (Thu Aug 20 2020 - 18:02:00 PDT)
  - Re: [AMBER] Antechamber and parmchk2 problem in case of processing mol2 input files Scott Brozell (Fri Aug 21 2020 - 15:02:13 PDT)
    - Re: [AMBER] Antechamber and parmchk2 problem in case of processing mol2 input files Marek Maly (Tue Aug 25 2020 - 10:07:48 PDT)
    - Re: [AMBER] Antechamber and parmchk2 problem in case of processing mol2 input files Scott Brozell (Thu Aug 27 2020 - 14:43:01 PDT)
[AMBER] converting prmtop to psf with improper and cross-term info stripped off Lod King (Thu Aug 20 2020 - 13:22:41 PDT)
- Re: [AMBER] converting prmtop to psf with improper and cross-term info stripped off Daniel Roe (Fri Aug 21 2020 - 13:48:52 PDT)
[AMBER] Force Field ankita mehta (Fri Aug 21 2020 - 07:03:21 PDT)
- Re: [AMBER] Force Field Bowleg, Jerrano (Fri Aug 21 2020 - 07:08:07 PDT)
- Re: [AMBER] Force Field Bill Ross (Fri Aug 21 2020 - 07:11:30 PDT)
- Re: [AMBER] Force Field David A Case (Fri Aug 21 2020 - 09:47:47 PDT)
[AMBER] trouble with pdb4amber Mattia Cavallaro (Fri Aug 21 2020 - 07:10:45 PDT)
- Re: [AMBER] trouble with pdb4amber Bill Ross (Fri Aug 21 2020 - 07:15:52 PDT)
  - Re: [AMBER] trouble with pdb4amber viktor drobot (Fri Aug 21 2020 - 07:33:39 PDT)
- Re: [AMBER] trouble with pdb4amber David A Case (Fri Aug 21 2020 - 09:59:07 PDT)
  - Re: [AMBER] trouble with pdb4amber Hai Nguyen (Fri Aug 21 2020 - 19:33:42 PDT)
    - Re: [AMBER] trouble with pdb4amber Mattia Cavallaro (Sat Aug 22 2020 - 05:25:57 PDT)
[AMBER] Questions (and a small bug report) about SIRAH in Amber Charo del Genio (Fri Aug 21 2020 - 13:43:18 PDT)
- Re: [AMBER] Questions (and a small bug report) about SIRAH in Amber Scott Brozell (Fri Aug 21 2020 - 18:21:46 PDT)
- Re: [AMBER] Questions (and a small bug report) about SIRAH in Amber David A Case (Fri Aug 21 2020 - 19:06:09 PDT)
  - Re: [AMBER] Questions (and a small bug report) about SIRAH in Amber Matias Machado (Mon Aug 24 2020 - 07:26:57 PDT)
    - [AMBER] Questions (and a small bug report) about SIRAH in Amber paraw (Mon Aug 24 2020 - 08:19:42 PDT)
    - Re: [AMBER] Questions (and a small bug report) about SIRAH in Amber Matias Machado (Mon Aug 24 2020 - 09:09:09 PDT)
    - Re: [AMBER] Questions (and a small bug report) about SIRAH in Amber paraw (Mon Aug 24 2020 - 09:45:37 PDT)
    - Re: [AMBER] Questions (and a small bug report) about SIRAH in Amber David A Case (Mon Aug 24 2020 - 11:40:06 PDT)
    - Re: [AMBER] Questions (and a small bug report) about SIRAH in Amber Charo del Genio (Wed Aug 26 2020 - 02:22:59 PDT)
    - Re: [AMBER] Questions (and a small bug report) about SIRAH in Amber Matias Machado (Wed Aug 26 2020 - 06:07:09 PDT)
    - Re: [AMBER] Questions (and a small bug report) about SIRAH in Amber Charo del Genio (Wed Aug 26 2020 - 06:57:38 PDT)
    - Re: [AMBER] Questions (and a small bug report) about SIRAH in Amber Matias Machado (Wed Aug 26 2020 - 08:27:43 PDT)
    - Re: [AMBER] Questions (and a small bug report) about SIRAH in Amber Charo del Genio (Wed Aug 26 2020 - 08:38:37 PDT)
    - Re: [AMBER] Questions (and a small bug report) about SIRAH in Amber Matias Machado (Fri Aug 28 2020 - 09:57:40 PDT)
    - Re: [AMBER] Questions (and a small bug report) about SIRAH in Amber Charo del Genio (Sat Aug 29 2020 - 06:52:09 PDT)
    - Re: [AMBER] Questions (and a small bug report) about SIRAH in Amber Matias Machado (Tue Sep 01 2020 - 07:38:41 PDT)
    - Re: [AMBER] Questions (and a small bug report) about SIRAH in Amber Charo del Genio (Tue Sep 01 2020 - 08:06:44 PDT)
[AMBER] Missing (ATTN, need revision) and poor parameters (high penalty score) for small molecule parameters and hard time with paramfit Állan Ferrari (Sat Aug 22 2020 - 13:59:45 PDT)
- Re: [AMBER] Missing (ATTN, need revision) and poor parameters (high penalty score) for small molecule parameters and hard time with paramfit David Cerutti (Sun Aug 23 2020 - 15:06:46 PDT)
[AMBER] amber14 cuda code does not work Carlos (Sat Aug 22 2020 - 21:52:26 PDT)
- Re: [AMBER] amber14 cuda code does not work David A Case (Sun Aug 23 2020 - 07:33:26 PDT)
  - Re: [AMBER] amber14 cuda code does not work Bill Ross (Sun Aug 23 2020 - 08:30:19 PDT)
    - Re: [AMBER] amber14 cuda code does not work Carlos (Sun Aug 23 2020 - 12:23:10 PDT)
- Re: [AMBER] amber14 cuda code does not work Daniel Roe (Mon Aug 24 2020 - 07:46:27 PDT)
  - Re: [AMBER] amber14 cuda code does not work Carlos (Tue Aug 25 2020 - 08:28:22 PDT)
[AMBER] How to deal with oxygen atom on Fe=O of Compound I (heme enzyme) using MCPB tool Mohamed M. Aboelnga (Sun Aug 23 2020 - 08:31:58 PDT)
[AMBER] error while running tutorial B5 Ayesha Fatima (Sun Aug 23 2020 - 11:08:48 PDT)
- Re: [AMBER] error while running tutorial B5 David A Case (Sun Aug 23 2020 - 18:39:16 PDT)
  - Re: [AMBER] error while running tutorial B5 Ayesha Fatima (Sun Aug 23 2020 - 23:44:50 PDT)
  - Re: [AMBER] error while running tutorial B5 Gustaf Olsson (Mon Aug 24 2020 - 01:03:58 PDT)
  - Re: [AMBER] error while running tutorial B5 Ayesha Fatima (Mon Aug 24 2020 - 09:19:50 PDT)
    - Re: [AMBER] error while running tutorial B5 Gustaf Olsson (Tue Aug 25 2020 - 00:24:14 PDT)
[AMBER] Problem with MMPBSA.py Camila Clemente (Sun Aug 23 2020 - 21:23:36 PDT)
- Re: [AMBER] Problem with MMPBSA.py Elvis Martis (Sun Aug 23 2020 - 22:36:06 PDT)
- Re: [AMBER] Problem with MMPBSA.py Elvis Martis (Sun Aug 23 2020 - 22:37:58 PDT)
- Re: [AMBER] Problem with MMPBSA.py David A Case (Mon Aug 24 2020 - 05:04:08 PDT)
[AMBER] Request .nc to MMPBSA.py? Camila Mara Clemente (Mon Aug 24 2020 - 10:38:37 PDT)
- Re: [AMBER] Request .nc to MMPBSA.py? Elvis Martis (Mon Aug 24 2020 - 10:49:45 PDT)
  - Re: [AMBER] Request .nc to MMPBSA.py? Camila Clemente (Mon Aug 24 2020 - 10:55:59 PDT)
    - Re: [AMBER] Request .nc to MMPBSA.py? Elvis Martis (Mon Aug 24 2020 - 11:06:29 PDT)
    - Re: [AMBER] Request .nc to MMPBSA.py? Camila Mara Clemente (Mon Aug 24 2020 - 11:16:36 PDT)
    - Re: [AMBER] Request .nc to MMPBSA.py? Elvis Martis (Mon Aug 24 2020 - 11:18:20 PDT)
    - Re: [AMBER] Request .nc to MMPBSA.py? Camila Clemente (Tue Aug 25 2020 - 11:28:17 PDT)
    - Re: [AMBER] Request .nc to MMPBSA.py? Elvis Martis (Tue Aug 25 2020 - 20:03:44 PDT)
[AMBER] ANTECHAMBER error: Fatal Error! Weird atomic valence (5) for atom (ID: 7, Name: C5). Pooja Kesari (Tue Aug 25 2020 - 01:33:01 PDT)
- Re: [AMBER] ANTECHAMBER error: Fatal Error! Weird atomic valence (5) for atom (ID: 7, Name: C5). Elvis Martis (Tue Aug 25 2020 - 01:41:01 PDT)
- Re: [AMBER] ANTECHAMBER error: Fatal Error! Weird atomic valence (5) for atom (ID: 7, Name: C5). Carlos Simmerling (Tue Aug 25 2020 - 03:44:57 PDT)
[AMBER] novel residue from Glutamine alex rayevsky (Tue Aug 25 2020 - 05:24:29 PDT)
- Re: [AMBER] novel residue from Glutamine Dr. Anselm Horn (Tue Aug 25 2020 - 08:17:34 PDT)
[AMBER] Fundamentals of LEaP Tutorial Gustaf Olsson (Tue Aug 25 2020 - 05:36:19 PDT)
- Re: [AMBER] Fundamentals of LEaP Tutorial Maria Nagan (Tue Aug 25 2020 - 05:56:47 PDT)
[AMBER] plumed does not work with pmemd.cuda but it works with sander Dmitry Karlov (Wed Aug 26 2020 - 12:04:11 PDT)
- Re: [AMBER] plumed does not work with pmemd.cuda but it works with sander viktor drobot (Wed Aug 26 2020 - 12:07:10 PDT)
[AMBER] Change covar matrix precision when crdaction is used Guadalupe Alvarez (Wed Aug 26 2020 - 12:56:39 PDT)
- Re: [AMBER] Change covar matrix precision when crdaction is used Daniel Roe (Fri Sep 04 2020 - 11:07:00 PDT)
[AMBER] Help for building cross linking polymer using graphic antechamber Pinky Mazumder (Wed Aug 26 2020 - 13:16:26 PDT)
- Re: [AMBER] Help for building cross linking polymer using graphic antechamber Pinky Mazumder (Wed Aug 26 2020 - 13:17:45 PDT)
  - Re: [AMBER] Help for building cross linking polymer using graphic antechamber David A Case (Thu Aug 27 2020 - 05:10:01 PDT)
    - Re: [AMBER] Help for building cross linking polymer using graphic antechamber Pinky Mazumder (Tue Nov 10 2020 - 19:06:02 PST)
    - Re: [AMBER] Help for building cross linking polymer using graphic antechamber Gustaf Olsson (Tue Nov 10 2020 - 23:56:21 PST)
    - Re: [AMBER] Help for building cross linking polymer using graphic antechamber aishen (Wed Nov 11 2020 - 00:27:39 PST)
[AMBER] Tutorial B0 Gustaf Olsson (Thu Aug 27 2020 - 00:52:38 PDT)
[AMBER] Confusion regarding Center of mass coordinates for protein, with CPPTRAJ Prathit Chatterjee (Thu Aug 27 2020 - 04:58:48 PDT)
- Re: [AMBER] Confusion regarding Center of mass coordinates for protein, with CPPTRAJ Daniel Roe (Fri Sep 04 2020 - 11:00:41 PDT)
[AMBER] Help for building two different salt concentration system using tLeap module Fulbabu Sk (Thu Aug 27 2020 - 05:55:29 PDT)
- Re: [AMBER] Help for building two different salt concentration system using tLeap module Matias Machado (Thu Aug 27 2020 - 07:33:09 PDT)
[AMBER] MMPBSA.py with saline environment Camila Clemente (Thu Aug 27 2020 - 07:10:24 PDT)
- Re: [AMBER] MMPBSA.py with saline environment Elvis Martis (Thu Aug 27 2020 - 07:56:38 PDT)
  - Re: [AMBER] MMPBSA.py with saline environment Camila Clemente (Thu Aug 27 2020 - 10:21:20 PDT)
    - Re: [AMBER] MMPBSA.py with saline environment Elvis Martis (Thu Aug 27 2020 - 20:27:46 PDT)
    - Re: [AMBER] MMPBSA.py with saline environment Camila Clemente (Fri Aug 28 2020 - 15:41:09 PDT)
[AMBER] Unable to complete heating stage Ramanathan Rajesh (Thu Aug 27 2020 - 10:37:54 PDT)
- Re: [AMBER] Unable to complete heating stage Adrian Roitberg (Thu Aug 27 2020 - 10:00:30 PDT)
  - Re: [AMBER] Unable to complete heating stage Ramanathan Rajesh (Thu Aug 27 2020 - 10:56:05 PDT)
    - Re: [AMBER] Unable to complete heating stage Daniel Roe (Fri Sep 04 2020 - 11:08:24 PDT)
[AMBER] Fw: covalent molecule and modified residue parameters Sarah Jane (Thu Aug 27 2020 - 12:44:59 PDT)
- Re: [AMBER] Fw: covalent molecule and modified residue parameters David A Case (Thu Aug 27 2020 - 18:03:23 PDT)
  - Re: [AMBER] Fw: covalent molecule and modified residue parameters Sarah Jane (Thu Sep 03 2020 - 08:21:03 PDT)
    - Re: [AMBER] Fw: covalent molecule and modified residue parameters David A Case (Thu Sep 03 2020 - 13:29:03 PDT)
    - Re: [AMBER] Fw: covalent molecule and modified residue parameters Sarah Jane (Mon Sep 07 2020 - 04:20:19 PDT)
    - Re: [AMBER] Fw: covalent molecule and modified residue parameters David A Case (Mon Sep 07 2020 - 05:47:49 PDT)
    - Re: [AMBER] Fw: covalent molecule and modified residue parameters Sarah Jane (Mon Sep 07 2020 - 08:09:36 PDT)
    - Re: [AMBER] Fw: covalent molecule and modified residue parameters David A Case (Mon Sep 07 2020 - 08:57:45 PDT)
    - Re: [AMBER] Fw: covalent molecule and modified residue parameters Sarah Jane (Wed Sep 09 2020 - 05:22:21 PDT)
  - Re: [AMBER] Fw: covalent molecule and modified residue parameters Sarah Jane (Sun Sep 27 2020 - 17:15:48 PDT)
    - Re: [AMBER] Fw: covalent molecule and modified residue parameters David A Case (Mon Sep 28 2020 - 05:23:12 PDT)
    - Re: [AMBER] Fw: covalent molecule and modified residue parameters Sarah Jane (Mon Sep 28 2020 - 05:51:58 PDT)
[AMBER] Stripping Protocol in Cpptraj An Ta (Thu Aug 27 2020 - 12:50:39 PDT)
- Re: [AMBER] Stripping Protocol in Cpptraj Daniel Roe (Fri Sep 04 2020 - 10:55:31 PDT)
  - Re: [AMBER] Stripping Protocol in Cpptraj An Ta (Fri Sep 04 2020 - 12:40:12 PDT)
    - Re: [AMBER] Stripping Protocol in Cpptraj Daniel Roe (Fri Sep 04 2020 - 16:33:25 PDT)
[AMBER] "Atom does not have a type" despite adding .frcmod parameters Erika Davidoff (Thu Aug 27 2020 - 12:56:25 PDT)
- Re: [AMBER] "Atom does not have a type" despite adding .frcmod parameters Ayesha Fatima (Thu Aug 27 2020 - 15:42:55 PDT)
  - Re: [AMBER] "Atom does not have a type" despite adding .frcmod parameters Maria Nagan (Thu Aug 27 2020 - 16:02:21 PDT)
    - Re: [AMBER] "Atom does not have a type" despite adding .frcmod parameters Ayesha Fatima (Thu Aug 27 2020 - 17:55:26 PDT)
    - Re: [AMBER] "Atom does not have a type" despite adding .frcmod parameters Maria Nagan (Thu Aug 27 2020 - 17:59:02 PDT)
    - Re: [AMBER] "Atom does not have a type" despite adding .frcmod parameters David A Case (Fri Aug 28 2020 - 05:04:32 PDT)
[AMBER] "After the fact" lifetime analysis with CPPTRAJ Gustaf Olsson (Fri Aug 28 2020 - 05:11:52 PDT)
- Re: [AMBER] "After the fact" lifetime analysis with CPPTRAJ Gustaf Olsson (Mon Aug 31 2020 - 03:27:45 PDT)
  - Re: [AMBER] "After the fact" lifetime analysis with CPPTRAJ Daniel Roe (Fri Sep 04 2020 - 10:41:59 PDT)
[AMBER] facing problem in 3DRISM angad sharma (Fri Aug 28 2020 - 05:27:59 PDT)
- Re: [AMBER] facing problem in 3DRISM Tyler Luchko (Lists) (Fri Aug 28 2020 - 07:26:41 PDT)
[AMBER] "FATAL: Atom *** does not have a type" Error Jatin Kashyap (Fri Aug 28 2020 - 22:44:11 PDT)
- Re: [AMBER] "FATAL: Atom *** does not have a type" Error Elvis Martis (Fri Aug 28 2020 - 23:29:10 PDT)
- Re: [AMBER] "FATAL: Atom *** does not have a type" Error David A Case (Sat Aug 29 2020 - 10:23:59 PDT)
  - Re: [AMBER] "FATAL: Atom *** does not have a type" Error Kashyap, Jatin (Sat Aug 29 2020 - 21:45:39 PDT)
    - Re: [AMBER] "FATAL: Atom *** does not have a type" Error David A Case (Mon Aug 31 2020 - 05:23:29 PDT)
[AMBER] FATAL atom does not have a type crispr cas9 pdb Jisha B (Sat Aug 29 2020 - 20:37:47 PDT)
- Re: [AMBER] FATAL atom does not have a type crispr cas9 pdb David A Case (Mon Aug 31 2020 - 05:04:18 PDT)
Re: [AMBER] new to amber20 aishen (Sun Aug 30 2020 - 00:53:16 PDT)
- Re: [AMBER] new to amber20 David A Case (Mon Aug 31 2020 - 05:19:30 PDT)
[AMBER] How to select groups for energy calculations-CPPtraj Nikhil Maroli (Sun Aug 30 2020 - 12:44:25 PDT)
- Re: [AMBER] How to select groups for energy calculations-CPPtraj Daniel Roe (Fri Sep 04 2020 - 10:45:54 PDT)
[AMBER] EXTENDED DEADLINE for Submissions - 16th German Conference on Cheminformatics (GCC) and the SAMPL satellite workshop Guessregen, Stefan /DE (Sun Aug 30 2020 - 23:16:41 PDT)
[AMBER] Fatal error atom type work around Ayesha Fatima (Mon Aug 31 2020 - 04:32:19 PDT)
- Re: [AMBER] Fatal error atom type work around David A Case (Mon Aug 31 2020 - 12:53:01 PDT)
[AMBER] azobenzene atoms name in amber format Aashish Bhatt (Mon Aug 31 2020 - 04:42:26 PDT)
- Re: [AMBER] azobenzene atoms name in amber format David A Case (Mon Aug 31 2020 - 12:30:12 PDT)
  - Re: [AMBER] azobenzene atoms name in amber format Aashish Bhatt (Thu Sep 10 2020 - 04:14:30 PDT)
    - [AMBER] Fwd: azobenzene atoms name in amber format Aashish Bhatt (Fri Sep 11 2020 - 07:58:40 PDT)
    - Re: [AMBER] Fwd: azobenzene atoms name in amber format David A Case (Fri Sep 11 2020 - 08:24:26 PDT)
[AMBER] Attention: All CPPTRAJ Questions Daniel Roe (Mon Aug 31 2020 - 09:55:20 PDT)
- Re: [AMBER] Attention: All CPPTRAJ Questions aishen (Mon Aug 31 2020 - 12:35:38 PDT)
- Re: [AMBER] Attention: All CPPTRAJ Questions Gustaf Olsson (Tue Sep 01 2020 - 00:29:42 PDT)
[AMBER] Asking for Fe2-S2 cluster and Molybdopterin AMBER force field parameters Maghsoud, Yazdan (Mon Aug 31 2020 - 11:53:51 PDT)
[AMBER] How to use the ntb options in amber-cuda-version neildancer.sina.com (Mon Aug 31 2020 - 23:32:32 PDT)
- Re: [AMBER] How to use the ntb options in amber-cuda-version David Cerutti (Tue Sep 01 2020 - 00:38:48 PDT)
  - Re: [AMBER] How to use the ntb options in amber-cuda-version neildancer.sina.com (Tue Sep 01 2020 - 01:34:08 PDT)
- Re: [AMBER] How to use the ntb options in amber-cuda-version Daniel Roe (Fri Sep 04 2020 - 10:49:14 PDT)
  - Re: [AMBER] How to use the ntb options in amber-cuda-version neildancer.sina.com (Sun Sep 06 2020 - 03:35:05 PDT)
[AMBER] Enquiry Kehinde Idowu (Tue Sep 01 2020 - 02:12:22 PDT)
- Re: [AMBER] Enquiry Bill Ross (Tue Sep 01 2020 - 02:40:28 PDT)
  - Re: [AMBER] Enquiry Kehinde Idowu (Tue Sep 01 2020 - 06:12:25 PDT)
    - Re: [AMBER] Enquiry Gustaf Olsson (Tue Sep 01 2020 - 23:51:28 PDT)
[AMBER] Amber 18 generates error: an illegal memory access was encountered launching kernel kNLSkinTest Lucas, Xavier (Tue Sep 01 2020 - 05:52:51 PDT)
- Re: [AMBER] Amber 18 generates error: an illegal memory access was encountered launching kernel kNLSkinTest David A Case (Fri Sep 04 2020 - 06:21:36 PDT)
[AMBER] Questions on deriving charges for aromatic compounds using The RESP Method Lucas Bandeira (Tue Sep 01 2020 - 16:37:54 PDT)
- Re: [AMBER] Questions on deriving charges for aromatic compounds using The RESP Method David A Case (Wed Sep 02 2020 - 06:12:47 PDT)
  - Re: [AMBER] Questions on deriving charges for aromatic compounds using The RESP Method Lucas Bandeira (Wed Sep 02 2020 - 11:47:45 PDT)
[AMBER] Generating topology using tleap Lucas Bandeira (Tue Sep 01 2020 - 16:52:03 PDT)
- Re: [AMBER] Generating topology using tleap Gustaf Olsson (Tue Sep 01 2020 - 23:55:12 PDT)
  - Re: [AMBER] Generating topology using tleap Lucas Bandeira (Fri Sep 04 2020 - 10:47:41 PDT)
[AMBER] Two problems about Amber's TI totorial ecnu_wangbo (Tue Sep 01 2020 - 22:43:32 PDT)
[AMBER] MCPB parametrization for an RNA systems Claire Claire (Wed Sep 02 2020 - 02:43:38 PDT)
- Re: [AMBER] MCPB parametrization for an RNA systems Pengfei Li (Thu Sep 10 2020 - 13:49:28 PDT)
[AMBER] best way to umbrella-sample a pseudo-dihedral angle Collective Variable Akshay Prabhakant (Wed Sep 02 2020 - 04:18:17 PDT)
- Re: [AMBER] best way to umbrella-sample a pseudo-dihedral angle Collective Variable Bill Ross (Wed Sep 02 2020 - 04:57:22 PDT)
- Re: [AMBER] best way to umbrella-sample a pseudo-dihedral angle Collective Variable David A Case (Wed Sep 02 2020 - 06:10:40 PDT)
  - Re: [AMBER] best way to umbrella-sample a pseudo-dihedral angle Collective Variable Kellon Belfon (Wed Sep 02 2020 - 07:27:23 PDT)
    - Re: [AMBER] best way to umbrella-sample a pseudo-dihedral angle Collective Variable Akshay Prabhakant (Thu Sep 03 2020 - 10:49:13 PDT)
[AMBER] [MicrosoftExchange329e71ec88ae4615bbc36ab6ce41109e@rutgegetting a nucleic acid helix structure David A Case (Wed Sep 02 2020 - 06:03:58 PDT)
- Re: [AMBER] [MicrosoftExchange329e71ec88ae4615bbc36ab6ce41109e@rutgegetting a nucleic acid helix structure aishen (Wed Sep 02 2020 - 07:55:22 PDT)
  - Re: [AMBER] executable names from nab David A Case (Thu Sep 03 2020 - 07:26:30 PDT)
    - Re: [AMBER] executable names from nab aishen (Thu Sep 03 2020 - 10:16:39 PDT)
[AMBER] Fw: prepare_ligand4.py converts CA carbons to calcium atoms when doing the mol2 to pdbqt format conversion Esposito Carmen (Wed Sep 02 2020 - 06:17:09 PDT)
- Re: [AMBER] Fw: prepare_ligand4.py converts CA carbons to calcium atoms when doing the mol2 to pdbqt format conversion David A Case (Thu Sep 03 2020 - 13:36:59 PDT)
- Re: [AMBER] Fw: prepare_ligand4.py converts CA carbons to calcium atoms when doing the mol2 to pdbqt format conversion Charo del Genio (Fri Sep 04 2020 - 01:17:31 PDT)
  - Re: [AMBER] Fw: prepare_ligand4.py converts CA carbons to calcium atoms when doing the mol2 to pdbqt format conversion Esposito Carmen (Fri Sep 04 2020 - 01:26:43 PDT)
[AMBER] umbrella protein-protein Fabian Glaser (Wed Sep 02 2020 - 08:02:55 PDT)
[AMBER] cPHMD: how to define residues with two pkas Kolattukudy P. Santo (Wed Sep 02 2020 - 19:35:40 PDT)
- Re: [AMBER] cPHMD: how to define residues with two pkas Cruzeiro,Vinicius Wilian D (Wed Sep 02 2020 - 20:28:41 PDT)
  - Re: [AMBER] cPHMD: how to define residues with two pkas Kolattukudy P. Santo (Mon Sep 07 2020 - 08:45:31 PDT)
[AMBER] 30 Series GPUs from Nvidia Homeo Morphism (Thu Sep 03 2020 - 07:20:02 PDT)
- Re: [AMBER] 30 Series GPUs from Nvidia Hashemi, Mohtadin (Thu Sep 03 2020 - 12:22:39 PDT)
[AMBER] MCPB with OPC water? Gustavo Seabra (Thu Sep 03 2020 - 07:24:43 PDT)
- Re: [AMBER] MCPB with OPC water? Gustavo Seabra (Tue Sep 08 2020 - 06:09:55 PDT)
  - Re: [AMBER] MCPB with OPC water? David Cerutti (Tue Sep 08 2020 - 06:32:11 PDT)
  - Re: [AMBER] MCPB with OPC water? Casalini Tommaso (Tue Sep 08 2020 - 06:34:43 PDT)
    - Re: [AMBER] MCPB with OPC water? Gustavo Seabra (Tue Sep 08 2020 - 06:41:28 PDT)
    - Re: [AMBER] MCPB with OPC water? Pengfei Li (Thu Sep 10 2020 - 14:06:17 PDT)
    - Re: [AMBER] MCPB with OPC water? Gustavo Seabra (Fri Sep 11 2020 - 05:46:22 PDT)
    - Re: [AMBER] MCPB with OPC water? Pengfei Li (Thu Oct 22 2020 - 13:59:34 PDT)
    - Re: [AMBER] MCPB with OPC water? Gustavo Seabra (Thu Oct 22 2020 - 17:11:19 PDT)
[AMBER] Cpptraj pucker amplitude units? Kenneth Huang (Thu Sep 03 2020 - 11:09:40 PDT)
- Re: [AMBER] Cpptraj pucker amplitude units? Daniel Roe (Fri Sep 04 2020 - 10:26:23 PDT)
[AMBER] Molecular creations rather than annihilations in AMBER18/20 Debarati DasGupta (Thu Sep 03 2020 - 15:17:29 PDT)
- [AMBER] Molecular creations rather than annihilations in AMBER18/20 Debarati DasGupta (Thu Sep 03 2020 - 15:18:43 PDT)
[AMBER] | ERROR: I could not find enough velocities in 1346.rst7 Lod King (Thu Sep 03 2020 - 18:03:47 PDT)
- Re: [AMBER] | ERROR: I could not find enough velocities in 1346.rst7 Bill Ross (Thu Sep 03 2020 - 19:19:21 PDT)
  - Re: [AMBER] | ERROR: I could not find enough velocities in 1346.rst7 Lod King (Thu Sep 03 2020 - 19:45:13 PDT)
    - Re: [AMBER] | ERROR: I could not find enough velocities in 1346.rst7 Bill Ross (Thu Sep 03 2020 - 22:49:55 PDT)
    - Re: [AMBER] | ERROR: I could not find enough velocities in 1346.rst7 Daniel Roe (Fri Sep 04 2020 - 10:21:10 PDT)
[AMBER] Cyclic peptides in Amber? Alexander Izvorski (Fri Sep 04 2020 - 22:52:52 PDT)
- Re: [AMBER] Cyclic peptides in Amber? Bill Ross (Sat Sep 05 2020 - 00:59:26 PDT)
  - Re: [AMBER] Cyclic peptides in Amber? Alexander Izvorski (Sat Sep 05 2020 - 01:05:14 PDT)
    - Re: [AMBER] Cyclic peptides in Amber? Bill Ross (Sat Sep 05 2020 - 01:06:59 PDT)
    - Re: [AMBER] Cyclic peptides in Amber? Bill Ross (Sat Sep 05 2020 - 01:10:55 PDT)
- Re: [AMBER] Cyclic peptides in Amber? David A Case (Sat Sep 05 2020 - 11:40:52 PDT)
  - Re: [AMBER] Cyclic peptides in Amber? Alexander Izvorski (Sun Sep 06 2020 - 15:14:29 PDT)
[AMBER] constant pH MD in explicit solvent SATYAJIT KHATUA (Sat Sep 05 2020 - 00:15:59 PDT)
- Re: [AMBER] constant pH MD in explicit solvent Cruzeiro,Vinicius Wilian D (Sat Sep 05 2020 - 10:22:53 PDT)
[AMBER] RMSD do not increase with the increase of temperature ali akbar (Sat Sep 05 2020 - 01:00:37 PDT)
- Re: [AMBER] RMSD do not increase with the increase of temperature Bill Ross (Sat Sep 05 2020 - 01:05:12 PDT)
[AMBER] finding number of atoms within a radius Saikat Pal (Sun Sep 06 2020 - 22:25:51 PDT)
- Re: [AMBER] finding number of atoms within a radius Elvis Martis (Mon Sep 07 2020 - 00:05:26 PDT)
  - Re: [AMBER] finding number of atoms within a radius Saikat Pal (Mon Sep 07 2020 - 01:50:06 PDT)
- Re: [AMBER] finding number of atoms within a radius Daniel Roe (Fri Sep 25 2020 - 10:58:39 PDT)
[AMBER] Parametrization of GTP and terminal phosphate of DNA Jenny 148 (Mon Sep 07 2020 - 02:35:31 PDT)
- Re: [AMBER] Parametrization of GTP and terminal phosphate of DNA David A Case (Mon Sep 07 2020 - 05:31:56 PDT)
  - Re: [AMBER] Parametrization of GTP and terminal phosphate of DNA Jenny 148 (Mon Sep 07 2020 - 06:45:54 PDT)
    - Re: [AMBER] Parametrization of GTP and terminal phosphate of DNA Jenny 148 (Mon Sep 07 2020 - 09:18:03 PDT)
  - Re: [AMBER] Parametrization of GTP and terminal phosphate of DNA Jenny 148 (Mon Sep 28 2020 - 09:31:44 PDT)
    - Re: [AMBER] Parametrization of GTP and terminal phosphate of DNA David A Case (Mon Sep 28 2020 - 18:50:49 PDT)
[AMBER] Simulation of 10 ns DNA - ligand intercalation Erdem Yeler (Mon Sep 07 2020 - 02:42:23 PDT)
- Re: [AMBER] Simulation of 10 ns DNA - ligand intercalation David A Case (Mon Sep 07 2020 - 05:37:07 PDT)
  - Re: [AMBER] Simulation of 10 ns DNA - ligand intercalation Erdem Yeler (Mon Sep 07 2020 - 06:03:47 PDT)
[AMBER] Just for info aishen (Mon Sep 07 2020 - 03:03:09 PDT)
- Re: [AMBER] Just for info Bill Ross (Mon Sep 07 2020 - 03:17:18 PDT)
- Re: [AMBER] Just for info David A Case (Mon Sep 07 2020 - 05:40:20 PDT)
  - Re: [AMBER] Just for info aishen (Mon Sep 07 2020 - 08:55:31 PDT)
[AMBER] Cluster representation over trajectory Hector A. Baldoni (Mon Sep 07 2020 - 06:57:22 PDT)
- Re: [AMBER] Cluster representation over trajectory Hector A. Baldoni (Mon Sep 07 2020 - 08:36:42 PDT)
[AMBER] Combining repeated MD trajectories Nada Afiva (Mon Sep 07 2020 - 16:59:25 PDT)
- Re: [AMBER] Combining repeated MD trajectories Song, Lin (Mon Sep 07 2020 - 18:23:06 PDT)
  - Re: [AMBER] Combining repeated MD trajectories Nada Afiva (Mon Sep 07 2020 - 18:56:43 PDT)
- Re: [AMBER] Combining repeated MD trajectories Rodrigo Galindo-Murillo (Mon Sep 07 2020 - 19:51:33 PDT)
  - Re: [AMBER] Combining repeated MD trajectories Nada Afiva (Mon Sep 07 2020 - 23:46:05 PDT)
    - Re: [AMBER] Combining repeated MD trajectories Clorice Reinhardt (Tue Sep 08 2020 - 02:26:18 PDT)
    - Re: [AMBER] Combining repeated MD trajectories Setyanto Md (Tue Sep 08 2020 - 02:53:16 PDT)
    - Re: [AMBER] Combining repeated MD trajectories Nada Afiva (Tue Sep 08 2020 - 03:42:05 PDT)
[AMBER] AmberHub down ? Setyanto Md (Mon Sep 07 2020 - 17:24:59 PDT)
- Re: [AMBER] AmberHub down ? Rodrigo Galindo-Murillo (Mon Sep 07 2020 - 17:34:35 PDT)
  - Re: [AMBER] AmberHub down ? Setyanto Md (Mon Sep 07 2020 - 17:39:14 PDT)
[AMBER] free binding energy Kehinde Idowu (Mon Sep 07 2020 - 22:44:34 PDT)
- Re: [AMBER] free binding energy Song, Lin (Tue Sep 08 2020 - 01:33:04 PDT)
[AMBER] "nan" appeared in mmpbsa result Xinye Wang (Tue Sep 08 2020 - 03:32:44 PDT)
- Re: [AMBER] "nan" appeared in mmpbsa result Ray Luo (Tue Sep 08 2020 - 11:46:43 PDT)
[AMBER] Strange RMSD tower appearing in simulation Jorge da Rocha (Tue Sep 08 2020 - 08:42:51 PDT)
- Re: [AMBER] Strange RMSD tower appearing in simulation Carlos Simmerling (Tue Sep 08 2020 - 08:58:47 PDT)
  - Re: [AMBER] Strange RMSD tower appearing in simulation David Cerutti (Tue Sep 08 2020 - 09:20:49 PDT)
    - Re: [AMBER] Strange RMSD tower appearing in simulation David A Case (Tue Sep 08 2020 - 11:23:42 PDT)
    - Re: [AMBER] Strange RMSD tower appearing in simulation Dr. Anselm Horn (Wed Sep 09 2020 - 01:12:56 PDT)
- Re: [AMBER] Strange RMSD tower appearing in simulation Jorge da Rocha (Wed Sep 09 2020 - 05:09:15 PDT)
  - Re: [AMBER] Strange RMSD tower appearing in simulation David Cerutti (Wed Sep 09 2020 - 08:04:06 PDT)
Re: [AMBER] Cartesian restraints on Production phase David A Case (Tue Sep 08 2020 - 11:18:28 PDT)
[AMBER] OE Tool kit Debarati DasGupta (Tue Sep 08 2020 - 11:31:21 PDT)
- Re: [AMBER] OE Tool kit Raman Preet Singh (Wed Sep 09 2020 - 02:48:36 PDT)
[AMBER] protein-protein interaction plot Kehinde Idowu (Tue Sep 08 2020 - 13:51:13 PDT)
[AMBER] antechamber & parmck2 Lod King (Tue Sep 08 2020 - 18:25:38 PDT)
- Re: [AMBER] antechamber & parmck2 Gustaf Olsson (Wed Sep 09 2020 - 00:20:13 PDT)
  - Re: [AMBER] antechamber & parmck2 Lod King (Wed Sep 09 2020 - 07:12:30 PDT)
    - Re: [AMBER] antechamber & parmck2 Gustaf Olsson (Wed Sep 09 2020 - 23:49:53 PDT)
    - Re: [AMBER] antechamber & parmck2 Lod King (Thu Sep 10 2020 - 00:09:58 PDT)
    - Re: [AMBER] antechamber & parmck2 Gustaf Olsson (Thu Sep 10 2020 - 00:31:35 PDT)
[AMBER] Adding ions at a particular position Athena N (Tue Sep 08 2020 - 21:14:17 PDT)
- Re: [AMBER] Adding ions at a particular position Gustaf Olsson (Wed Sep 09 2020 - 00:08:27 PDT)
  - Re: [AMBER] Adding ions at a particular position Dr. Anselm Horn (Wed Sep 09 2020 - 00:57:05 PDT)
[AMBER] The status of GAFF2 Gustaf Olsson (Wed Sep 09 2020 - 01:26:00 PDT)
[AMBER] PLUMED masterclass David A Case (Wed Sep 09 2020 - 05:20:09 PDT)
[AMBER] OE tools help Debarati DasGupta (Wed Sep 09 2020 - 05:41:04 PDT)
- Re: [AMBER] OE tools help Raman Preet Singh (Thu Sep 10 2020 - 02:36:25 PDT)
  - Re: [AMBER] OE tools help Raman Preet Singh (Thu Sep 10 2020 - 02:58:58 PDT)
Re: [AMBER] AMBER Digest, Vol 3114, Issue 1 SATYAJIT KHATUA (Wed Sep 09 2020 - 09:09:06 PDT)
[AMBER] Growing of small molecules instead of annihilation of molecules in amber TI simulations Debarati DasGupta (Wed Sep 09 2020 - 15:35:40 PDT)
- Re: [AMBER] Growing of small molecules instead of annihilation of molecules in amber TI simulations David A Case (Thu Sep 10 2020 - 06:23:14 PDT)
  - Re: [AMBER] Growing of small molecules instead of annihilation of molecules in amber TI simulations Debarati DasGupta (Sat Sep 12 2020 - 06:31:01 PDT)
[AMBER] Normal Model Analysis with AmberTools20 Harley Wilson (Wed Sep 09 2020 - 16:09:46 PDT)
- Re: [AMBER] Normal Model Analysis with AmberTools20 David A Case (Thu Sep 10 2020 - 06:31:19 PDT)
[AMBER] problem with cpptraj Marko Sever (Thu Sep 10 2020 - 05:57:49 PDT)
- Re: [AMBER] problem with cpptraj Daniel Roe (Thu Sep 10 2020 - 06:13:48 PDT)
  - Re: [AMBER] problem with cpptraj Marko Sever (Thu Sep 10 2020 - 06:26:52 PDT)
    - Re: [AMBER] problem with cpptraj Daniel Roe (Thu Sep 10 2020 - 09:10:34 PDT)
[AMBER] Regarding help in installation (LINUX ubuntu) swapnil singh (Thu Sep 10 2020 - 08:13:16 PDT)
- Re: [AMBER] Regarding help in installation (LINUX ubuntu) David A Case (Thu Sep 10 2020 - 11:57:29 PDT)
  - Re: [AMBER] Regarding help in installation (LINUX ubuntu) Raman Preet Singh (Fri Sep 11 2020 - 01:19:04 PDT)
    - Re: [AMBER] Regarding help in installation (LINUX ubuntu) aishen (Fri Sep 11 2020 - 02:04:03 PDT)
    - Re: [AMBER] Regarding help in installation (LINUX ubuntu) Daniel Roe (Wed Sep 23 2020 - 03:53:43 PDT)
[AMBER] Visualizing the system trajectory from .nc file Jatin Kashyap (Thu Sep 10 2020 - 21:36:21 PDT)
- Re: [AMBER] Visualizing the system trajectory from .nc file Emmett Leddin (Thu Sep 10 2020 - 22:29:18 PDT)
  - Re: [AMBER] Visualizing the system trajectory from .nc file Jatin Kashyap (Mon Sep 14 2020 - 14:08:14 PDT)
[AMBER] Dextrins zmatovic.kg.ac.rs (Fri Sep 11 2020 - 02:24:20 PDT)
[AMBER] Dynamic cross correlation between the center of mass of two groups of atoms Jorden Cabal (Fri Sep 11 2020 - 03:56:32 PDT)
- Re: [AMBER] Dynamic cross correlation between the center of mass of two groups of atoms David A Case (Fri Sep 11 2020 - 11:22:32 PDT)
[AMBER] AQUA-DUCT Webinar 23rd September 2020 Maria Bzówka (Fri Sep 11 2020 - 06:14:52 PDT)
[AMBER] constant pH MD in explicit solvent SATYAJIT KHATUA (Mon Sep 14 2020 - 00:13:17 PDT)
- Re: [AMBER] constant pH MD in explicit solvent Cruzeiro,Vinicius Wilian D (Mon Sep 14 2020 - 08:48:45 PDT)
[AMBER] pymsmt.exp.pymsmtError: MOL is required in naa_mol2files but not provided. CHENTOUF Sara (Mon Sep 14 2020 - 07:25:09 PDT)
[AMBER] Of possible interest: Chem Faiss Bill Ross (Tue Sep 15 2020 - 04:33:28 PDT)
[AMBER] preparing parameter files for a ligand Siavoush Dastmalchi (Tue Sep 15 2020 - 09:34:27 PDT)
- Re: [AMBER] preparing parameter files for a ligand David A Case (Wed Sep 16 2020 - 05:26:30 PDT)
  - Re: [AMBER] preparing parameter files for a ligand Siavoush Dastmalchi (Wed Sep 16 2020 - 06:07:22 PDT)
[AMBER] expected average fluctuations in amino acid covalent bond distances, angle and torsion during typical md simulations Vaibhav Dixit (Tue Sep 15 2020 - 11:57:54 PDT)
- Re: [AMBER] expected average fluctuations in amino acid covalent bond distances, angle and torsion during typical md simulations David A Case (Wed Sep 16 2020 - 05:59:05 PDT)
  - Re: [AMBER] expected average fluctuations in amino acid covalent bond distances, angle and torsion during typical md simulations Vaibhav Dixit (Wed Sep 16 2020 - 08:39:41 PDT)
    - Re: [AMBER] expected average fluctuations in amino acid covalent bond distances, angle and torsion during typical md simulations David A Case (Thu Sep 17 2020 - 05:58:08 PDT)
    - Re: [AMBER] expected average fluctuations in amino acid covalent bond distances, angle and torsion during typical md simulations Vaibhav Dixit (Thu Sep 17 2020 - 10:07:44 PDT)
    - Re: [AMBER] expected average fluctuations in amino acid covalent bond distances, angle and torsion during typical md simulations Adrian Roitberg (Thu Sep 17 2020 - 10:20:47 PDT)
    - Re: [AMBER] expected average fluctuations in amino acid covalent bond distances, angle and torsion during typical md simulations Vaibhav Dixit (Fri Sep 18 2020 - 02:24:46 PDT)
    - Re: [AMBER] expected average fluctuations in amino acid covalent bond distances, angle and torsion during typical md simulations David A Case (Fri Sep 18 2020 - 04:58:57 PDT)
    - Re: [AMBER] expected average fluctuations in amino acid covalent bond distances, angle and torsion during typical md simulations Vaibhav Dixit (Fri Sep 18 2020 - 09:37:38 PDT)
[AMBER] Is it possible to run QM/MM-PIMD simulations with sander? proszx (Wed Sep 16 2020 - 02:10:52 PDT)
[AMBER] adding lysyl-phosphatidylglycerol and cardiolipin Chetna Tyagi (Wed Sep 16 2020 - 05:11:05 PDT)
- Re: [AMBER] adding lysyl-phosphatidylglycerol and cardiolipin Stephan Schott (Wed Sep 23 2020 - 08:33:07 PDT)
  - Re: [AMBER] adding lysyl-phosphatidylglycerol and cardiolipin Chetna Tyagi (Thu Sep 24 2020 - 04:30:37 PDT)
[AMBER] Query on nucleic acid force fields Jenny 148 (Wed Sep 16 2020 - 06:11:38 PDT)
- Re: [AMBER] Query on nucleic acid force fields David Cerutti (Wed Sep 16 2020 - 20:35:21 PDT)
  - Re: [AMBER] Query on nucleic acid force fields Jenny 148 (Wed Sep 16 2020 - 21:15:16 PDT)
    - Re: [AMBER] Query on nucleic acid force fields David Cerutti (Wed Sep 16 2020 - 21:28:20 PDT)
    - Re: [AMBER] Query on nucleic acid force fields Jiri Sponer (Thu Sep 17 2020 - 01:47:13 PDT)
    - Re: [AMBER] Query on nucleic acid force fields Jenny 148 (Thu Sep 17 2020 - 01:53:11 PDT)
    - Re: [AMBER] Query on nucleic acid force fields Jiri Sponer (Thu Sep 17 2020 - 02:42:20 PDT)
[AMBER] Generate deleted .rst file from coordinates? Alysia Mandato (Wed Sep 16 2020 - 06:54:41 PDT)
- Re: [AMBER] Generate deleted .rst file from coordinates? Daniel Roe (Wed Sep 16 2020 - 08:05:32 PDT)
  - Re: [AMBER] Generate deleted .rst file from coordinates? Alysia Mandato (Thu Sep 17 2020 - 07:36:34 PDT)
[AMBER] Advice on calculating binding energies of enantiomers Billiot, Eugene (Wed Sep 16 2020 - 07:05:50 PDT)
[AMBER] Tleap creates only one residue Farkhad Maksudov (Wed Sep 16 2020 - 18:43:58 PDT)
- Re: [AMBER] Tleap creates only one residue Bill Ross (Wed Sep 16 2020 - 20:10:42 PDT)
- Re: [AMBER] Tleap creates only one residue David A Case (Thu Sep 17 2020 - 05:45:26 PDT)
  - Re: [AMBER] Tleap creates only one residue Farkhad Maksudov (Thu Sep 17 2020 - 13:25:11 PDT)
[AMBER] constant pH error Kolattukudy P. Santo (Wed Sep 16 2020 - 20:18:13 PDT)
- Re: [AMBER] constant pH error Cruzeiro,Vinicius Wilian D (Thu Sep 17 2020 - 08:05:19 PDT)
  - Re: [AMBER] constant pH error Kolattukudy P. Santo (Thu Sep 17 2020 - 10:34:55 PDT)
    - Re: [AMBER] constant pH error Cruzeiro,Vinicius Wilian D (Fri Sep 18 2020 - 15:43:03 PDT)
    - Re: [AMBER] constant pH error Kolattukudy P. Santo (Sat Sep 19 2020 - 20:02:17 PDT)
[AMBER] BR atom moved out Nisha Amarnath Jonniya (Thu Sep 17 2020 - 03:46:19 PDT)
[AMBER] Perturbing charges Delwakkada Liyanage, Senal Dinuka (Thu Sep 17 2020 - 15:30:08 PDT)
- Re: [AMBER] Perturbing charges David A Case (Thu Sep 17 2020 - 19:12:15 PDT)
  - Re: [AMBER] Perturbing charges Delwakkada Liyanage, Senal Dinuka (Fri Sep 18 2020 - 05:57:58 PDT)
    - Re: [AMBER] Perturbing charges David A Case (Fri Sep 18 2020 - 08:02:40 PDT)
    - Re: [AMBER] Perturbing charges Delwakkada Liyanage, Senal Dinuka (Fri Sep 18 2020 - 14:25:23 PDT)
    - Re: [AMBER] Perturbing charges David A Case (Sun Sep 20 2020 - 06:01:40 PDT)
    - Re: [AMBER] Perturbing charges Debarati DasGupta (Sun Sep 20 2020 - 13:00:24 PDT)
    - Re: [AMBER] Perturbing charges Delwakkada Liyanage, Senal Dinuka (Mon Sep 21 2020 - 11:34:56 PDT)
    - Re: [AMBER] Perturbing charges Debarati DasGupta (Mon Sep 21 2020 - 12:54:35 PDT)
    - Re: [AMBER] Perturbing charges Delwakkada Liyanage, Senal Dinuka (Mon Sep 21 2020 - 13:16:49 PDT)
[AMBER] RMSD of nucleic acid bases Sruthi Sudhakar (Thu Sep 17 2020 - 21:05:18 PDT)
- Re: [AMBER] RMSD of nucleic acid bases Saikat Pal (Thu Sep 17 2020 - 23:10:42 PDT)
[AMBER] antechamber problem with negatively charged nitrogen Giorgos Lambrinidis (Fri Sep 18 2020 - 04:57:24 PDT)
- Re: [AMBER] antechamber problem with negatively charged nitrogen David A Case (Fri Sep 18 2020 - 07:58:30 PDT)
  - Re: [AMBER] antechamber problem with negatively charged nitrogen Giorgos Lambrinidis (Fri Sep 18 2020 - 08:29:42 PDT)
    - Re: [AMBER] antechamber problem with negatively charged nitrogen David A Case (Sun Sep 20 2020 - 07:39:05 PDT)
    - Re: [AMBER] antechamber problem with negatively charged nitrogen Giorgos Lambrinidis (Mon Sep 21 2020 - 01:07:01 PDT)
    - Re: [AMBER] antechamber problem with negatively charged nitrogen David A Case (Mon Sep 21 2020 - 05:20:29 PDT)
[AMBER] constant pH MD in explicit solvent SATYAJIT KHATUA (Fri Sep 18 2020 - 06:43:58 PDT)
- Re: [AMBER] constant pH MD in explicit solvent Cruzeiro,Vinicius Wilian D (Fri Sep 18 2020 - 15:24:03 PDT)
[AMBER] ddikick.x error during Fe3+ ion parameter derivation using Gamess gagandeep singh (Fri Sep 18 2020 - 06:47:15 PDT)
- Re: [AMBER] ddikick.x error during Fe3+ ion parameter derivation using Gamess Pengfei Li (Thu Oct 22 2020 - 14:14:09 PDT)
[AMBER] Prmtop for protein + 2 identical ligands has wrong dihedral parameters for the second ligand. LEaP bug? Mariano Curti (Fri Sep 18 2020 - 07:41:26 PDT)
- Re: [AMBER] Prmtop for protein + 2 identical ligands has wrong dihedral parameters for the second ligand. LEaP bug? Pengfei Li (Thu Oct 22 2020 - 14:19:21 PDT)
  - Re: [AMBER] Prmtop for protein + 2 identical ligands has wrong dihedral parameters for the second ligand. LEaP bug? Mariano Curti (Mon Oct 26 2020 - 02:18:33 PDT)
    - Re: [AMBER] Prmtop for protein + 2 identical ligands has wrong dihedral parameters for the second ligand. LEaP bug? Pengfei Li (Fri Nov 20 2020 - 07:14:22 PST)
[AMBER] Problem in AMBER18 Installation Mariangela Dametto (Fri Sep 18 2020 - 08:33:57 PDT)
- Re: [AMBER] Problem in AMBER18 Installation David A Case (Fri Sep 18 2020 - 13:43:51 PDT)
  - Re: [AMBER] Problem in AMBER18 Installation Mariangela Dametto (Thu Oct 01 2020 - 09:58:09 PDT)
[AMBER] Mimimization error Renato Araujo (Fri Sep 18 2020 - 14:29:10 PDT)
- Re: [AMBER] Mimimization error David A Case (Fri Sep 18 2020 - 18:29:53 PDT)
[AMBER] Is RTX 3080 compatible with Amber18 ? Setyanto Md (Fri Sep 18 2020 - 20:36:59 PDT)
[AMBER] Tri-coordination environment in zinc SATYAJIT KHATUA (Fri Sep 18 2020 - 21:36:59 PDT)
- Re: [AMBER] Tri-coordination environment in zinc Zoran (Fri Sep 18 2020 - 23:50:12 PDT)
- Re: [AMBER] Tri-coordination environment in zinc Pengfei Li (Thu Oct 22 2020 - 14:22:53 PDT)
[AMBER] Formation of a cyclic peptide RIMJHIM MORAL (Sat Sep 19 2020 - 00:58:07 PDT)
- Re: [AMBER] Formation of a cyclic peptide Bill Ross (Sat Sep 19 2020 - 02:09:00 PDT)
  - Re: [AMBER] Formation of a cyclic peptide Dr. Anselm Horn (Tue Sep 22 2020 - 01:05:59 PDT)
- Re: [AMBER] Formation of a cyclic peptide David A Case (Sat Sep 19 2020 - 05:17:46 PDT)
[AMBER] Stuck at the heating stage Jisha B (Sat Sep 19 2020 - 02:53:40 PDT)
- Re: [AMBER] Stuck at the heating stage Bill Ross (Sat Sep 19 2020 - 03:01:29 PDT)
  - Re: [AMBER] Stuck at the heating stage Jisha B (Sat Sep 19 2020 - 03:09:09 PDT)
    - Re: [AMBER] Stuck at the heating stage Bill Ross (Sat Sep 19 2020 - 05:01:27 PDT)
    - Re: [AMBER] Stuck at the heating stage David A Case (Sat Sep 19 2020 - 05:21:51 PDT)
- Re: [AMBER] Stuck at the heating stage Daniel Roe (Wed Sep 23 2020 - 03:47:47 PDT)
[AMBER] constant pH MD in explicit solvent SATYAJIT KHATUA (Sat Sep 19 2020 - 21:59:31 PDT)
[AMBER] Tri-coordination environment in zinc SATYAJIT KHATUA (Sat Sep 19 2020 - 22:07:15 PDT)
- Re: [AMBER] Tri-coordination environment in zinc SATYAJIT KHATUA (Thu Oct 29 2020 - 22:39:20 PDT)
  - Re: [AMBER] Tri-coordination environment in zinc Bill Ross (Thu Oct 29 2020 - 23:59:57 PDT)
- Re: [AMBER] Tri-coordination environment in zinc SATYAJIT KHATUA (Sun Nov 01 2020 - 09:38:42 PST)
  - Re: [AMBER] Tri-coordination environment in zinc Bill Ross (Sun Nov 01 2020 - 10:35:31 PST)
- Re: [AMBER] Tri-coordination environment in zinc SATYAJIT KHATUA (Mon Nov 02 2020 - 21:06:14 PST)
  - Re: [AMBER] Tri-coordination environment in zinc Pengfei Li (Fri Nov 20 2020 - 07:42:47 PST)
- Re: [AMBER] Tri-coordination environment in zinc SATYAJIT KHATUA (Sat Nov 21 2020 - 02:01:29 PST)
  - Re: [AMBER] Tri-coordination environment in zinc Pengfei Li (Mon Dec 07 2020 - 12:29:29 PST)
    - Re: [AMBER] Tri-coordination environment in zinc Pengfei Li (Mon Dec 07 2020 - 12:30:21 PST)
- Re: [AMBER] Tri-coordination environment in zinc SATYAJIT KHATUA (Wed Dec 09 2020 - 16:08:09 PST)
- Re: [AMBER] Tri-coordination environment in zinc SATYAJIT KHATUA (Thu Dec 10 2020 - 02:18:17 PST)
  - Re: [AMBER] Tri-coordination environment in zinc Pengfei Li (Sat Jan 16 2021 - 19:29:17 PST)
[AMBER] RMSF plot error Fatemeh Arabi (Sun Sep 20 2020 - 02:20:17 PDT)
- Re: [AMBER] RMSF plot error David A Case (Sun Sep 20 2020 - 05:53:24 PDT)
[AMBER] MMPBSA binding energy was positive for charged ligand Nada Afiva (Sun Sep 20 2020 - 19:24:56 PDT)
- Re: [AMBER] MMPBSA binding energy was positive for charged ligand David A Case (Mon Sep 21 2020 - 05:14:23 PDT)
  - Re: [AMBER] MMPBSA binding energy was positive for charged ligand Nada Afiva (Mon Sep 21 2020 - 05:45:28 PDT)
    - Re: [AMBER] MMPBSA binding energy was positive for charged ligand neildancer (Tue Sep 22 2020 - 06:11:08 PDT)
[AMBER] MMPBSA.py error Asmi Mahmood (Mon Sep 21 2020 - 03:37:35 PDT)
[AMBER] How to place oxygen molecules in tunnels of protein to calculate PMF Muhammad tariq (Mon Sep 21 2020 - 05:00:21 PDT)
[AMBER] [CPHMD] invalid reference to variable in NAMELIST input, CPIN file cprivat.ub.edu (Mon Sep 21 2020 - 07:36:48 PDT)
- Re: [AMBER] [CPHMD] invalid reference to variable in NAMELIST input, CPIN file Cruzeiro,Vinicius Wilian D (Mon Sep 21 2020 - 08:34:32 PDT)
  - Re: [AMBER] [CPHMD] invalid reference to variable in NAMELIST input, CPIN file cprivat.ub.edu (Mon Sep 21 2020 - 23:47:51 PDT)
[AMBER] How to recopile with new version of CUDA Camila Clemente (Mon Sep 21 2020 - 14:24:39 PDT)
- Re: [AMBER] How to recopile with new version of CUDA David Cerutti (Mon Sep 21 2020 - 15:05:11 PDT)
[AMBER] amber18 installation error Nisha Amarnath Jonniya (Mon Sep 21 2020 - 22:22:37 PDT)
- Re: [AMBER] amber18 installation error Gustaf Olsson (Mon Sep 21 2020 - 23:54:22 PDT)
  - Re: [AMBER] amber18 installation error Nisha Amarnath Jonniya (Mon Sep 21 2020 - 23:59:00 PDT)
    - Re: [AMBER] amber18 installation error Gustaf Olsson (Tue Sep 22 2020 - 00:05:21 PDT)
    - Re: [AMBER] amber18 installation error Nisha Amarnath Jonniya (Tue Sep 22 2020 - 00:11:09 PDT)
    - Re: [AMBER] amber18 installation error Gustaf Olsson (Tue Sep 22 2020 - 00:36:14 PDT)
    - Re: [AMBER] amber18 installation error David A Case (Tue Sep 22 2020 - 05:41:59 PDT)
    - Re: [AMBER] amber18 installation error Elvis Martis (Tue Sep 22 2020 - 06:00:00 PDT)
    - Re: [AMBER] amber18 installation error Nisha Amarnath Jonniya (Tue Sep 22 2020 - 06:03:14 PDT)
    - Re: [AMBER] amber18 installation error Elvis Martis (Tue Sep 22 2020 - 06:00:30 PDT)
[AMBER] autoimage for grid analysis with cpptraj Gustaf Olsson (Tue Sep 22 2020 - 03:05:57 PDT)
- Re: [AMBER] autoimage for grid analysis with cpptraj David A Case (Tue Sep 22 2020 - 05:45:02 PDT)
  - Re: [AMBER] autoimage for grid analysis with cpptraj Gustaf Olsson (Tue Sep 22 2020 - 06:10:27 PDT)
- Re: [AMBER] autoimage for grid analysis with cpptraj Daniel Roe (Tue Sep 22 2020 - 06:38:08 PDT)
  - Re: [AMBER] autoimage for grid analysis with cpptraj Gustaf Olsson (Tue Sep 22 2020 - 23:54:44 PDT)
    - Re: [AMBER] autoimage for grid analysis with cpptraj Daniel Roe (Wed Sep 23 2020 - 03:24:16 PDT)
[AMBER] umbrella sampling protein Ramin Mehrani (Tue Sep 22 2020 - 07:02:42 PDT)
- Re: [AMBER] umbrella sampling protein David A Case (Tue Sep 22 2020 - 08:22:11 PDT)
  - Re: [AMBER] umbrella sampling protein Feng Pan (Tue Sep 22 2020 - 12:44:23 PDT)
    - Re: [AMBER] umbrella sampling protein Ramin Mehrani (Wed Sep 23 2020 - 06:56:21 PDT)
    - Re: [AMBER] umbrella sampling protein Feng Pan (Fri Sep 25 2020 - 06:49:45 PDT)
[AMBER] How does tleap detect improper torsions? Brian Radak (Tue Sep 22 2020 - 13:57:46 PDT)
- Re: [AMBER] How does tleap detect improper torsions? David A Case (Tue Sep 22 2020 - 18:07:01 PDT)
  - Re: [AMBER] How does tleap detect improper torsions? Brian Radak (Wed Sep 23 2020 - 05:57:52 PDT)
    - Re: [AMBER] How does tleap detect improper torsions? Matias Machado (Wed Sep 23 2020 - 07:24:06 PDT)
    - Re: [AMBER] How does tleap detect improper torsions? Brian Radak (Thu Sep 24 2020 - 08:56:15 PDT)
    - Re: [AMBER] How does tleap detect improper torsions? Bill Ross (Thu Sep 24 2020 - 10:19:51 PDT)
    - Re: [AMBER] How does tleap detect improper torsions? David A Case (Thu Sep 24 2020 - 12:20:56 PDT)
    - Re: [AMBER] How does tleap detect improper torsions? Matias Machado (Thu Sep 24 2020 - 20:29:50 PDT)
    - Re: [AMBER] How does tleap detect improper torsions? Bill Ross (Thu Sep 24 2020 - 22:34:55 PDT)
[AMBER] how to keep Cl/Br/I ion in particular place Nisha Amarnath Jonniya (Tue Sep 22 2020 - 22:06:40 PDT)
[AMBER] tutorials restructured and ConstpH/redox tutorial pages not accessible Vaibhav Dixit (Tue Sep 22 2020 - 23:49:04 PDT)
- Re: [AMBER] tutorials restructured and ConstpH/redox tutorial pages not accessible Maria Nagan (Wed Sep 23 2020 - 04:08:20 PDT)
  - Re: [AMBER] tutorials restructured and ConstpH/redox tutorial pages not accessible Vaibhav Dixit (Wed Sep 23 2020 - 04:46:37 PDT)
    - Re: [AMBER] tutorials restructured and ConstpH/redox tutorial pages not accessible Daniel Roe (Wed Sep 23 2020 - 06:26:59 PDT)
    - Re: [AMBER] tutorials restructured and ConstpH/redox tutorial pages not accessible Vaibhav Dixit (Wed Sep 23 2020 - 08:01:21 PDT)
[AMBER] french version aishen (Wed Sep 23 2020 - 00:59:00 PDT)
- Re: [AMBER] french version Dr. Anselm Horn (Wed Sep 23 2020 - 06:25:41 PDT)
[AMBER] Coordinate resetting cannot be accomplished -reg R A Jeyaram 16PHD0482 (Wed Sep 23 2020 - 03:38:09 PDT)
- Re: [AMBER] Coordinate resetting cannot be accomplished -reg Daniel Roe (Wed Sep 23 2020 - 03:51:15 PDT)
- Re: [AMBER] Coordinate resetting cannot be accomplished -reg Bill Ross (Wed Sep 23 2020 - 03:54:56 PDT)
[AMBER] Heme parameters Siavoush Dastmalchi (Wed Sep 23 2020 - 08:00:19 PDT)
- Re: [AMBER] Heme parameters David A Case (Thu Sep 24 2020 - 08:05:35 PDT)
  - Re: [AMBER] Heme parameters Siavoush Dastmalchi (Thu Sep 24 2020 - 09:35:29 PDT)
[AMBER] Fwd: usage of nmr (between COMs) restraints with pmem.cuda Dmitry Karlov (Wed Sep 23 2020 - 08:28:43 PDT)
- [AMBER] usage of nmr (between COMs) restraints with pmem.cuda Dmitry Karlov (Thu Sep 24 2020 - 14:50:48 PDT)
[AMBER] xleap aishen (Wed Sep 23 2020 - 13:19:02 PDT)
- Re: [AMBER] xleap Gustaf Olsson (Thu Sep 24 2020 - 00:04:55 PDT)
  - Re: [AMBER] xleap aishen (Thu Sep 24 2020 - 00:52:29 PDT)
    - Re: [AMBER] xleap aishen (Thu Sep 24 2020 - 01:06:56 PDT)
    - Re: [AMBER] xleap Gustaf Olsson (Thu Sep 24 2020 - 01:16:39 PDT)
    - Re: [AMBER] xleap David A Case (Mon Sep 28 2020 - 19:06:32 PDT)
    - Re: [AMBER] xleap Gustaf Olsson (Tue Sep 29 2020 - 01:17:51 PDT)
    - Re: [AMBER] xleap Bill Ross (Tue Sep 29 2020 - 01:34:57 PDT)
    - Re: [AMBER] xleap Gustaf Olsson (Tue Sep 29 2020 - 02:43:34 PDT)
    - Re: [AMBER] xleap Bill Ross (Tue Sep 29 2020 - 03:05:37 PDT)
    - Re: [AMBER] xleap aishen (Tue Sep 29 2020 - 03:05:53 PDT)
    - Re: [AMBER] xleap David A Case (Tue Sep 29 2020 - 04:52:24 PDT)
    - Re: [AMBER] xleap Gustaf Olsson (Tue Sep 29 2020 - 05:22:08 PDT)
    - Re: [AMBER] xleap aishen (Tue Sep 29 2020 - 05:28:12 PDT)
    - Re: [AMBER] xleap Gustaf Olsson (Tue Sep 29 2020 - 05:45:19 PDT)
    - Re: [AMBER] xleap aishen (Tue Sep 29 2020 - 23:01:17 PDT)
    - [AMBER] Additional restraints in Umbrella sampling? Qing Lv (Thu Oct 01 2020 - 18:29:39 PDT)
    - Re: [AMBER] xleap aishen (Tue Sep 29 2020 - 05:34:35 PDT)
[AMBER] MMPBSA.py error for mismatch NATOMS Asmi Mahmood (Wed Sep 23 2020 - 23:28:10 PDT)
- Re: [AMBER] MMPBSA.py error for mismatch NATOMS Jason Swails (Sat Sep 26 2020 - 11:50:12 PDT)
[AMBER] water strip -reg R A Jeyaram 16PHD0482 (Thu Sep 24 2020 - 02:24:30 PDT)
- Re: [AMBER] water strip -reg Daniel Roe (Thu Sep 24 2020 - 05:51:03 PDT)
[AMBER] Line minimizer aborted Ramanathan Rajesh (Thu Sep 24 2020 - 07:34:34 PDT)
[AMBER] Two sets of restraints on minimization? Gustavo Seabra (Thu Sep 24 2020 - 13:49:05 PDT)
- Re: [AMBER] Two sets of restraints on minimization? David A Case (Thu Sep 24 2020 - 17:45:39 PDT)
  - Re: [AMBER] Two sets of restraints on minimization? Gustavo Seabra (Fri Sep 25 2020 - 05:22:03 PDT)
[AMBER] RESTARTED DUE TO LINMIN FAILURE Xinye Wang (Thu Sep 24 2020 - 20:06:32 PDT)
- Re: [AMBER] RESTARTED DUE TO LINMIN FAILURE Elvis Martis (Thu Sep 24 2020 - 20:20:13 PDT)
  - Re: [AMBER] RESTARTED DUE TO LINMIN FAILURE Xinye Wang (Thu Sep 24 2020 - 20:38:41 PDT)
    - Re: [AMBER] RESTARTED DUE TO LINMIN FAILURE Elvis Martis (Thu Sep 24 2020 - 21:07:57 PDT)
- Re: [AMBER] RESTARTED DUE TO LINMIN FAILURE David A Case (Fri Sep 25 2020 - 04:51:20 PDT)
  - [AMBER] Fwd: RESTARTED DUE TO LINMIN FAILURE Maschietto, Federica (Fri Sep 25 2020 - 16:52:50 PDT)
    - Re: [AMBER] Fwd: RESTARTED DUE TO LINMIN FAILURE Hector A. Baldoni (Fri Sep 25 2020 - 17:01:49 PDT)
    - Re: [AMBER] Fwd: RESTARTED DUE TO LINMIN FAILURE David A Case (Sat Sep 26 2020 - 05:21:38 PDT)
[AMBER] Netcdf trajectory in pymol? Jenny 148 (Sat Sep 26 2020 - 12:48:53 PDT)
- Re: [AMBER] Netcdf trajectory in pymol? Kenneth Huang (Sun Sep 27 2020 - 15:12:07 PDT)
[AMBER] A100 and RTX3090 Benchmarks Ross Walker (Sun Sep 27 2020 - 16:30:47 PDT)
- Re: [AMBER] A100 and RTX3090 Benchmarks xmgign.126.com (Tue Sep 29 2020 - 02:29:46 PDT)
  - Re: [AMBER] A100 and RTX3090 Benchmarks Hashemi, Mohtadin (Wed Sep 30 2020 - 08:43:03 PDT)
- Re: [AMBER] A100 and RTX3090 Benchmarks Filip Fratev (Tue Oct 06 2020 - 01:44:54 PDT)
  - Re: [AMBER] A100 and RTX3090 Benchmarks David A Case (Tue Oct 06 2020 - 05:26:26 PDT)
    - Re: [AMBER] A100 and RTX3090 Benchmarks Ross Walker (Tue Oct 06 2020 - 10:31:45 PDT)
  - Re: [AMBER] A100 and RTX3090 Benchmarks Ross Walker (Tue Oct 06 2020 - 10:13:48 PDT)
[AMBER] Make some of RNA bases as DNA in leap Athena N (Mon Sep 28 2020 - 09:23:10 PDT)
- Re: [AMBER] Make some of RNA bases as DNA in leap David A Case (Mon Sep 28 2020 - 09:56:03 PDT)
  - Re: [AMBER] Make some of RNA bases as DNA in leap Athena N (Mon Sep 28 2020 - 09:57:57 PDT)
    - Re: [AMBER] Make some of RNA bases as DNA in leap David A Case (Mon Sep 28 2020 - 18:47:12 PDT)
[AMBER] Polyproline abmd tutorial gives vlimit error SHAUNAK BADANI (Mon Sep 28 2020 - 09:32:28 PDT)
[AMBER] PMF calculation somdev pahari (Tue Sep 29 2020 - 01:25:15 PDT)
- Re: [AMBER] PMF calculation Dickson, Callum (Mon Sep 28 2020 - 13:37:53 PDT)
  - Re: [AMBER] PMF calculation somdev pahari (Tue Sep 29 2020 - 11:20:19 PDT)
    - Re: [AMBER] PMF calculation somdev pahari (Thu Oct 15 2020 - 10:11:28 PDT)
[AMBER] MMPBSA.py.MPI installation problem in Amber20 Liao (Tue Sep 29 2020 - 00:22:19 PDT)
- Re: [AMBER] MMPBSA.py.MPI installation problem in Amber20 Elvis Martis (Tue Sep 29 2020 - 00:36:16 PDT)
[AMBER] REMD Trajectory Processing Aravind R (Tue Sep 29 2020 - 00:25:32 PDT)
- Re: [AMBER] REMD Trajectory Processing Daniel Roe (Tue Sep 29 2020 - 04:42:44 PDT)
- Re: [AMBER] REMD Trajectory Processing Carlos Simmerling (Tue Sep 29 2020 - 06:18:19 PDT)
[AMBER] Query regarding Dialanine peptide 2d ABMD tutorial in the NFE category SHAUNAK BADANI (Tue Sep 29 2020 - 02:15:46 PDT)
- Re: [AMBER] Query regarding Dialanine peptide 2d ABMD tutorial in the NFE category SHAUNAK BADANI (Thu Oct 01 2020 - 13:26:28 PDT)
  - Re: [AMBER] Query regarding Dialanine peptide 2d ABMD tutorial in the NFE category David A Case (Fri Oct 02 2020 - 08:19:45 PDT)
[AMBER] Problem with metalpdb2mol2.py script Siavoush Dastmalchi (Wed Sep 30 2020 - 00:56:02 PDT)
[AMBER] Query regarding Dialanine peptide 2d ABMD tutorial in the NFE category Madhur Aggarwal (Wed Sep 30 2020 - 02:41:02 PDT)
[AMBER] AmberMdPrep github cpptraj not sourced Vaibhav Dixit (Tue Sep 29 2020 - 23:49:25 PDT)
- Re: [AMBER] AmberMdPrep github cpptraj not sourced Vaibhav Dixit (Wed Sep 30 2020 - 04:54:05 PDT)
  - Re: [AMBER] AmberMdPrep github cpptraj not sourced Daniel Roe (Wed Sep 30 2020 - 06:34:19 PDT)
    - Re: [AMBER] AmberMdPrep github cpptraj not sourced Vaibhav Dixit (Wed Sep 30 2020 - 06:53:10 PDT)
    - Re: [AMBER] AmberMdPrep github cpptraj not sourced Vaibhav Dixit (Wed Sep 30 2020 - 09:00:53 PDT)
    - Re: [AMBER] AmberMdPrep github cpptraj not sourced Vaibhav Dixit (Fri Oct 09 2020 - 17:30:17 PDT)
    - Re: [AMBER] AmberMdPrep github cpptraj not sourced Daniel Roe (Wed Oct 21 2020 - 03:38:33 PDT)
    - Re: [AMBER] AmberMdPrep github cpptraj not sourced Vaibhav Dixit (Wed Oct 21 2020 - 04:37:06 PDT)
[AMBER] Modification of dihedral torsion potential h_sahakyan.mb.sci.am (Wed Sep 30 2020 - 03:47:07 PDT)
- Re: [AMBER] Modification of dihedral torsion potential David A Case (Thu Oct 01 2020 - 05:03:36 PDT)
[AMBER] controversy in PBSA and GBSA results h_sahakyan.mb.sci.am (Wed Sep 30 2020 - 04:42:30 PDT)
- Re: [AMBER] controversy in PBSA and GBSA results Ray Luo (Wed Sep 30 2020 - 15:57:45 PDT)
  - Re: [AMBER] controversy in PBSA and GBSA results h_sahakyan.mb.sci.am (Wed Sep 30 2020 - 21:16:05 PDT)
    - Re: [AMBER] controversy in PBSA and GBSA results Ray Luo (Wed Sep 30 2020 - 22:10:53 PDT)
    - Re: [AMBER] controversy in PBSA and GBSA results h_sahakyan.mb.sci.am (Wed Sep 30 2020 - 23:32:19 PDT)
[AMBER] Conversion of Gromacs [atomtypes] and [nonbond_params] to Amber NONBON and LJEDIT Nick Palmer (Wed Sep 30 2020 - 09:40:08 PDT)
[AMBER] Conversion of Gromacs [atomtypes] and [nonbond_params] to Amber NONBON and LJEDIT Nick Palmer (Wed Sep 30 2020 - 11:46:28 PDT)
- Re: [AMBER] Conversion of Gromacs [atomtypes] and [nonbond_params] to Amber NONBON and LJEDIT Matias Machado (Thu Oct 01 2020 - 05:58:33 PDT)
  - Re: [AMBER] [External] Re: Conversion of Gromacs [atomtypes] and [nonbond_params] to Amber NONBON and LJEDIT Nick Palmer (Thu Oct 01 2020 - 16:16:21 PDT)
    - Re: [AMBER] [External] Re: Conversion of Gromacs [atomtypes] and [nonbond_params] to Amber NONBON and LJEDIT Matias Machado (Sat Oct 03 2020 - 09:00:54 PDT)
[AMBER] pmemd aishen (Thu Oct 01 2020 - 09:44:55 PDT)
- Re: [AMBER] pmemd Elvis Martis (Thu Oct 01 2020 - 09:49:36 PDT)
- Re: [AMBER] pmemd David A Case (Thu Oct 01 2020 - 13:40:41 PDT)
[AMBER] Error: Failed to generate parameters Jatin Kashyap (Thu Oct 01 2020 - 09:57:17 PDT)
- Re: [AMBER] Error: Failed to generate parameters David A Case (Thu Oct 01 2020 - 13:45:02 PDT)
  - Re: [AMBER] Error: Failed to generate parameters Jatin Kashyap (Thu Oct 01 2020 - 13:55:14 PDT)
    - Re: [AMBER] Error: Failed to generate parameters David A Case (Fri Oct 02 2020 - 08:26:38 PDT)
[AMBER] pmemd aishen (Thu Oct 01 2020 - 13:50:45 PDT)
- Re: [AMBER] pmemd Dr. Anselm Horn (Fri Oct 02 2020 - 03:20:42 PDT)
[AMBER] MMPBSA.py TypeError: a bytes-like object is required, not 'str' سید حامد سادات حیاتشاهی (Thu Oct 01 2020 - 13:52:28 PDT)
- Re: [AMBER] MMPBSA.py TypeError: a bytes-like object is required, not 'str' Ray Luo (Thu Oct 01 2020 - 20:16:16 PDT)
- Re: [AMBER] MMPBSA.py TypeError: a bytes-like object is required, not 'str' Hamed S. Hayatshahi (Mon Oct 05 2020 - 11:15:06 PDT)
[AMBER] partial charges for modified nucleotide Farkhad Maksudov (Thu Oct 01 2020 - 18:28:28 PDT)
- Re: [AMBER] partial charges for modified nucleotide David A Case (Fri Oct 02 2020 - 08:31:00 PDT)
  - Re: [AMBER] partial charges for modified nucleotide Kenneth Huang (Fri Oct 02 2020 - 17:36:31 PDT)
[AMBER] Compiling CPPTRAJ from GitHub Gustaf Olsson (Fri Oct 02 2020 - 03:53:11 PDT)
- Re: [AMBER] Compiling CPPTRAJ from GitHub Gustaf Olsson (Fri Oct 02 2020 - 05:06:43 PDT)
- Re: [AMBER] Compiling CPPTRAJ from GitHub David A Case (Fri Oct 02 2020 - 08:34:48 PDT)
  - Re: [AMBER] Compiling CPPTRAJ from GitHub Daniel Roe (Fri Oct 02 2020 - 08:41:39 PDT)
    - Re: [AMBER] Compiling CPPTRAJ from GitHub Gustaf Olsson (Mon Oct 05 2020 - 00:09:07 PDT)
    - Re: [AMBER] Compiling CPPTRAJ from GitHub David A Case (Mon Oct 05 2020 - 06:58:23 PDT)
    - Re: [AMBER] Compiling CPPTRAJ from GitHub Gustaf Olsson (Tue Oct 06 2020 - 02:00:32 PDT)
    - Re: [AMBER] Compiling CPPTRAJ from GitHub Daniel Roe (Mon Oct 05 2020 - 07:07:46 PDT)
    - Re: [AMBER] Compiling CPPTRAJ from GitHub Gustaf Olsson (Tue Oct 06 2020 - 02:22:08 PDT)
    - Re: [AMBER] Compiling CPPTRAJ from GitHub Gustaf Olsson (Tue Oct 06 2020 - 02:28:30 PDT)
    - Re: [AMBER] Compiling CPPTRAJ from GitHub Daniel Roe (Wed Oct 07 2020 - 07:47:57 PDT)
    - Re: [AMBER] Compiling CPPTRAJ from GitHub Gustaf Olsson (Thu Oct 08 2020 - 05:37:36 PDT)
[AMBER] image protein complex iwrap=1 Ari Zeida (Fri Oct 02 2020 - 07:21:41 PDT)
- Re: [AMBER] image protein complex iwrap=1 David A Case (Fri Oct 02 2020 - 08:43:53 PDT)
- Re: [AMBER] image protein complex iwrap=1 Daniel Roe (Sun Oct 04 2020 - 06:51:56 PDT)
[AMBER] how to use one prmtop for two trajectories with just one ion difference Vaibhav Dixit (Fri Oct 02 2020 - 07:55:35 PDT)
- Re: [AMBER] how to use one prmtop for two trajectories with just one ion difference Carlos Simmerling (Fri Oct 02 2020 - 08:06:47 PDT)
  - Re: [AMBER] how to use one prmtop for two trajectories with just one ion difference Vaibhav Dixit (Fri Oct 02 2020 - 08:42:28 PDT)
    - Re: [AMBER] how to use one prmtop for two trajectories with just one ion difference Carlos Simmerling (Fri Oct 02 2020 - 09:30:26 PDT)
    - Re: [AMBER] how to use one prmtop for two trajectories with just one ion difference Vaibhav Dixit (Fri Oct 02 2020 - 14:12:32 PDT)
    - Re: [AMBER] how to use one prmtop for two trajectories with just one ion difference Carlos Simmerling (Sat Oct 03 2020 - 06:16:25 PDT)
    - Re: [AMBER] how to use one prmtop for two trajectories with just one ion difference Vaibhav Dixit (Sat Oct 03 2020 - 06:29:12 PDT)
    - Re: [AMBER] how to use one prmtop for two trajectories with just one ion difference Thomas Cheatham (Wed Oct 07 2020 - 16:17:10 PDT)
    - Re: [AMBER] how to use one prmtop for two trajectories with just one ion difference Vaibhav Dixit (Wed Oct 07 2020 - 17:03:46 PDT)
    - Re: [AMBER] how to use one prmtop for two trajectories with just one ion difference Thomas Cheatham (Thu Oct 08 2020 - 16:37:23 PDT)
[AMBER] about translation aishen (Sat Oct 03 2020 - 01:21:57 PDT)
[AMBER] MMGBSA/MMPBSA Help Abdul-Rashid III Sampaco (Sat Oct 03 2020 - 04:33:44 PDT)
- Re: [AMBER] MMGBSA/MMPBSA Help Ray Luo (Fri Oct 30 2020 - 07:42:37 PDT)
  - Re: [AMBER] MMGBSA/MMPBSA Help Abdul-Rashid III Sampaco (Sun Nov 01 2020 - 21:07:56 PST)
[AMBER] RMSD of ligand in pocket Debarati DasGupta (Sat Oct 03 2020 - 08:08:20 PDT)
- Re: [AMBER] RMSD of ligand in pocket Daniel Roe (Sun Oct 04 2020 - 06:48:10 PDT)
  - Re: [AMBER] RMSD of ligand in pocket Debarati DasGupta (Sun Oct 04 2020 - 06:55:41 PDT)
    - Re: [AMBER] RMSD of ligand in pocket David A Case (Sun Oct 04 2020 - 17:54:09 PDT)
    - Re: [AMBER] RMSD of ligand in pocket Debarati DasGupta (Mon Oct 05 2020 - 05:16:53 PDT)
    - Re: [AMBER] RMSD of ligand in pocket Juraj Dobias (Mon Oct 05 2020 - 05:32:31 PDT)
    - Re: [AMBER] RMSD of ligand in pocket Daniel Roe (Wed Oct 07 2020 - 08:02:28 PDT)
    - Re: [AMBER] RMSD of ligand in pocket Debarati DasGupta (Wed Oct 07 2020 - 16:03:08 PDT)
    - Re: [AMBER] RMSD of ligand in pocket Debarati DasGupta (Sun Oct 18 2020 - 08:05:42 PDT)
[AMBER] Query regarding ion constraint in MD simulations Nisha Amarnath Jonniya (Sat Oct 03 2020 - 19:33:58 PDT)
[AMBER] cpptraj unable to write pdb files using Vaibhav Dixit (Sat Oct 03 2020 - 21:32:46 PDT)
- Re: [AMBER] cpptraj unable to write pdb files using Daniel Roe (Sun Oct 04 2020 - 06:46:05 PDT)
  - Re: [AMBER] cpptraj unable to write pdb files using Vaibhav Dixit (Sun Oct 04 2020 - 09:15:12 PDT)
    - Re: [AMBER] cpptraj unable to write pdb files using Elvis Martis (Sun Oct 04 2020 - 09:31:39 PDT)
    - Re: [AMBER] cpptraj unable to write pdb files using Vaibhav Dixit (Mon Oct 05 2020 - 20:56:51 PDT)
    - Re: [AMBER] cpptraj unable to write pdb files using Elvis Martis (Mon Oct 05 2020 - 21:06:15 PDT)
    - Re: [AMBER] cpptraj unable to write pdb files using Vaibhav Dixit (Mon Oct 05 2020 - 21:16:18 PDT)
    - Re: [AMBER] cpptraj unable to write pdb files using Vaibhav Dixit (Wed Oct 07 2020 - 01:57:52 PDT)
    - Re: [AMBER] cpptraj unable to write pdb files using Elvis Martis (Wed Oct 07 2020 - 05:40:39 PDT)
    - Re: [AMBER] cpptraj unable to write pdb files using Vaibhav Dixit (Wed Oct 07 2020 - 06:47:17 PDT)
    - Re: [AMBER] cpptraj unable to write pdb files using Elvis Martis (Wed Oct 07 2020 - 07:52:26 PDT)
    - Re: [AMBER] cpptraj unable to write pdb files using David A Case (Wed Oct 07 2020 - 08:05:22 PDT)
    - Re: [AMBER] cpptraj unable to write pdb files using Daniel Roe (Wed Oct 07 2020 - 08:35:37 PDT)
    - Re: [AMBER] cpptraj unable to write pdb files using Vaibhav Dixit (Wed Oct 07 2020 - 16:43:25 PDT)
    - Re: [AMBER] cpptraj unable to write pdb files using Daniel Roe (Wed Oct 07 2020 - 07:52:13 PDT)
    - Re: [AMBER] cpptraj unable to write pdb files using Daniel Roe (Wed Oct 07 2020 - 07:50:38 PDT)
[AMBER] usage of nmr (between COMs) restraints with pmem.cuda Dmitry Karlov (Sun Oct 04 2020 - 06:57:55 PDT)
[AMBER] controversy in PBSA and GBSA results h_sahakyan.mb.sci.am (Sun Oct 04 2020 - 22:28:30 PDT)
- Re: [AMBER] controversy in PBSA and GBSA results Ray Luo (Mon Oct 05 2020 - 07:39:59 PDT)
[AMBER] Different atomic partial charges on OD1/OD2 Margareta Hellmann (Mon Oct 05 2020 - 07:59:37 PDT)
[AMBER] Hitting the supercomputer wall limit before completion of minimization step Jatin Kashyap (Mon Oct 05 2020 - 08:28:44 PDT)
- Re: [AMBER] Hitting the supercomputer wall limit before completion of minimization step Carlos Simmerling (Mon Oct 05 2020 - 08:38:43 PDT)
  - Re: [AMBER] Hitting the supercomputer wall limit before completion of minimization step Jatin Kashyap (Mon Oct 05 2020 - 09:25:13 PDT)
    - Re: [AMBER] Hitting the supercomputer wall limit before completion of minimization step Carlos Simmerling (Mon Oct 05 2020 - 11:52:19 PDT)
[AMBER] REST2 in Amber Qinghua Liao (Mon Oct 05 2020 - 08:30:05 PDT)
[AMBER] Question about force field for proteins Asaf Farhi (Mon Oct 05 2020 - 08:31:10 PDT)
- Re: [AMBER] Question about force field for proteins Carlos Simmerling (Mon Oct 05 2020 - 08:36:49 PDT)
  - Re: [AMBER] Question about force field for proteins Asaf Farhi (Mon Oct 05 2020 - 08:42:33 PDT)
  - Re: [AMBER] Question about force field for proteins Asaf Farhi (Sat Oct 10 2020 - 11:49:32 PDT)
    - Re: [AMBER] Question about force field for proteins Carlos Simmerling (Sun Oct 11 2020 - 04:27:02 PDT)
    - Re: [AMBER] Question about force field for proteins Asaf Farhi (Fri Oct 16 2020 - 15:04:49 PDT)
[AMBER] controversy in PBSA and GBSA results h_sahakyan.mb.sci.am (Mon Oct 05 2020 - 09:04:26 PDT)
[AMBER] How does one build MMPBSA.py.MPI on a Centos 7 system? Hamed S. Hayatshahi (Mon Oct 05 2020 - 12:30:44 PDT)
- Re: [AMBER] How does one build MMPBSA.py.MPI on a Centos 7 system? David A Case (Mon Oct 05 2020 - 12:53:39 PDT)
[AMBER] Which OS/Amber combinations are supported? Kevin Keane (Mon Oct 05 2020 - 13:06:37 PDT)
- Re: [AMBER] Which OS/Amber combinations are supported? Gerald Monard (Mon Oct 05 2020 - 23:41:35 PDT)
[AMBER] Imaging issues with cpptraj Suchetana Gupta (Tue Oct 06 2020 - 00:09:41 PDT)
- [AMBER] Fwd: Imaging issues with cpptraj Suchetana Gupta (Tue Oct 06 2020 - 21:43:51 PDT)
  - Re: [AMBER] Fwd: Imaging issues with cpptraj Suchetana Gupta (Tue Oct 06 2020 - 23:56:51 PDT)
  - Re: [AMBER] Fwd: Imaging issues with cpptraj Suchetana Gupta (Wed Oct 07 2020 - 00:12:36 PDT)
    - Re: [AMBER] Fwd: Imaging issues with cpptraj Daniel Roe (Wed Oct 07 2020 - 07:53:32 PDT)
[AMBER] Amber performance Jonathan Gabriel Canan Gomez (Tue Oct 06 2020 - 15:56:22 PDT)
- Re: [AMBER] Amber performance Bill Ross (Tue Oct 06 2020 - 16:13:54 PDT)
- Re: [AMBER] Amber performance Ross Walker (Tue Oct 06 2020 - 16:19:45 PDT)
[AMBER] controversy in PBSA and GBSA results h_sahakyan.mb.sci.am (Wed Oct 07 2020 - 06:19:19 PDT)
- Re: [AMBER] controversy in PBSA and GBSA results Ray Luo (Wed Oct 07 2020 - 10:06:39 PDT)
  - Re: [AMBER] controversy in PBSA and GBSA results Ray Luo (Wed Oct 07 2020 - 10:08:33 PDT)
    - Re: [AMBER] controversy in PBSA and GBSA results Ray Luo (Wed Oct 07 2020 - 10:35:08 PDT)
[AMBER] Problems with using pdb4amber (and possibly other programs) on Ubuntu 20.04 bgostyns.cbmm.lodz.pl (Wed Oct 07 2020 - 06:52:03 PDT)
- Re: [AMBER] Problems with using pdb4amber (and possibly other programs) on Ubuntu 20.04 David A Case (Wed Oct 07 2020 - 08:15:35 PDT)
- Re: [AMBER] Problems with using pdb4amber (and possibly other programs) on Ubuntu 20.04 Hai Nguyen (Wed Oct 07 2020 - 14:36:38 PDT)
- Re: [AMBER] Problems with using pdb4amber (and possibly other programs) on Ubuntu 20.04 bgostyns.cbmm.lodz.pl (Thu Oct 08 2020 - 04:11:20 PDT)
[AMBER] Cannot run NPT mohamed marzouk (Wed Oct 07 2020 - 07:05:56 PDT)
- Re: [AMBER] Cannot run NPT David A Case (Wed Oct 07 2020 - 08:17:36 PDT)
  - Re: [AMBER] Cannot run NPT mohamed marzouk (Wed Oct 07 2020 - 19:41:01 PDT)
    - Re: [AMBER] Cannot run NPT Juraj Dobias (Thu Oct 08 2020 - 04:21:35 PDT)
    - Re: [AMBER] Cannot run NPT mohamed marzouk (Mon Oct 12 2020 - 10:45:54 PDT)
    - Re: [AMBER] Cannot run NPT David A Case (Thu Oct 08 2020 - 05:04:46 PDT)
[AMBER] QMMM SCC-DFTB: Convergence could not be achieved Sarah Jane (Wed Oct 07 2020 - 10:22:46 PDT)
[AMBER] Verbose - Output File Information Not Changing An Ta (Wed Oct 07 2020 - 11:55:43 PDT)
- Re: [AMBER] Verbose - Output File Information Not Changing An Ta (Wed Oct 07 2020 - 16:17:29 PDT)
  - Re: [AMBER] Verbose - Output File Information Not Changing An Ta (Wed Oct 07 2020 - 17:09:14 PDT)
    - Re: [AMBER] Verbose - Output File Information Not Changing David A Case (Fri Oct 09 2020 - 05:01:19 PDT)
[AMBER] Amber20 compilation issue (related to boost?) Suman Chakrabarty (Wed Oct 07 2020 - 23:07:08 PDT)
- Re: [AMBER] Amber20 compilation issue (related to boost?) George M. Giambasu (Thu Oct 08 2020 - 20:25:18 PDT)
  - Re: [AMBER] Amber20 compilation issue (related to boost?) Suman Chakrabarty (Fri Oct 09 2020 - 02:35:46 PDT)
[AMBER] not writing restart file Erik Zuiderweg (Thu Oct 08 2020 - 09:17:41 PDT)
- Re: [AMBER] not writing restart file Qinghua Liao (Thu Oct 08 2020 - 09:20:35 PDT)
  - Re: [AMBER] not writing restart file Erik Zuiderweg (Fri Oct 09 2020 - 03:57:55 PDT)
[AMBER] ERROR: The file contained 14 atoms not in residue templates Jatin Kashyap (Thu Oct 08 2020 - 12:28:14 PDT)
- Re: [AMBER] ERROR: The file contained 14 atoms not in residue templates Carlos Simmerling (Thu Oct 08 2020 - 12:48:34 PDT)
[AMBER] Permute dihedrals David Poole (Fri Oct 09 2020 - 04:40:53 PDT)
- Re: [AMBER] Permute dihedrals Daniel Roe (Fri Oct 09 2020 - 06:02:22 PDT)
[AMBER] NVIDIA GeForce RTX 3080 GPUs Mike Mazanetz (Fri Oct 09 2020 - 08:36:46 PDT)
- Re: [AMBER] NVIDIA GeForce RTX 3080 GPUs David Cerutti (Fri Oct 09 2020 - 09:41:08 PDT)
  - Re: [AMBER] NVIDIA GeForce RTX 3080 GPUs Adrian Roitberg (Fri Oct 09 2020 - 09:44:49 PDT)
    - Re: [AMBER] NVIDIA GeForce RTX 3080 GPUs Mike Mazanetz (Fri Oct 09 2020 - 10:23:33 PDT)
    - Re: [AMBER] NVIDIA GeForce RTX 3080 GPUs Ross Walker (Sat Oct 10 2020 - 06:58:21 PDT)
    - Re: [AMBER] NVIDIA GeForce RTX 3080 GPUs Mike Mazanetz (Sat Oct 10 2020 - 13:26:06 PDT)
[AMBER] CPPTRAJ: Cluster structures keeping only one water, by position? Gustavo Seabra (Fri Oct 09 2020 - 11:14:59 PDT)
- Re: [AMBER] CPPTRAJ: Cluster structures keeping only one water, by position? Niel Henriksen (Fri Oct 09 2020 - 14:41:34 PDT)
  - Re: [AMBER] CPPTRAJ: Cluster structures keeping only one water, by position? Gustavo Seabra (Fri Oct 09 2020 - 15:10:23 PDT)
Re: [AMBER] NVIDIA GeForce RTX 3080 GPUs (Ross Walker) German P. Barletta (Sat Oct 10 2020 - 12:48:39 PDT)
- Re: [AMBER] NVIDIA GeForce RTX 3080 GPUs (Ross Walker) Ross Walker (Sat Oct 10 2020 - 14:21:47 PDT)
[AMBER] Conda installation of AmberTools mukesh raval (Sat Oct 10 2020 - 21:00:54 PDT)
- Re: [AMBER] Conda installation of AmberTools Hai Nguyen (Mon Oct 12 2020 - 09:54:35 PDT)
[AMBER] NVIDIA GeForce RTX 3080 GPUs German P. Barletta (Sun Oct 11 2020 - 13:10:54 PDT)
Re: [AMBER] partial charge calculation (RESP) using gaussian09/antechamber (ambertools17) on a symmetrical molecule BLUNTZER Marie (Mon Oct 12 2020 - 04:09:32 PDT)
- [AMBER] Fw: partial charge calculation (RESP) using gaussian09/antechamber (ambertools17) on a symmetrical molecule BLUNTZER Marie (Mon Oct 12 2020 - 04:16:01 PDT)
- Re: [AMBER] partial charge calculation (RESP) using gaussian09/antechamber (ambertools17) on a symmetrical molecule David A Case (Mon Oct 12 2020 - 05:06:31 PDT)
- Re: [AMBER] partial charge calculation (RESP) using gaussian09/antechamber (ambertools17) on a symmetrical molecule BLUNTZER Marie (Mon Oct 12 2020 - 05:42:34 PDT)
  - Re: [AMBER] partial charge calculation (RESP) using gaussian09/antechamber (ambertools17) on a symmetrical molecule James Kress (Mon Oct 12 2020 - 15:52:51 PDT)
    - Re: [AMBER] partial charge calculation (RESP) using gaussian09/antechamber (ambertools17) on a symmetrical molecule BLUNTZER Marie (Tue Oct 13 2020 - 07:45:22 PDT)
[AMBER] RMSD, Rg density map mohamed marzouk (Mon Oct 12 2020 - 11:00:45 PDT)
- Re: [AMBER] RMSD, Rg density map Daniel Roe (Wed Oct 14 2020 - 11:48:51 PDT)
  - Re: [AMBER] RMSD, Rg density map mohamed marzouk (Fri Oct 16 2020 - 09:57:45 PDT)
    - Re: [AMBER] RMSD, Rg density map mohamed marzouk (Tue Oct 20 2020 - 20:17:58 PDT)
  - Re: [AMBER] RMSD, Rg density map mohamed marzouk (Tue Oct 20 2020 - 11:06:36 PDT)
[AMBER] MMGBSA Ligand Mask issues Suchetana Gupta (Tue Oct 13 2020 - 03:03:31 PDT)
- [AMBER] Fwd: MMGBSA Ligand Mask issues Suchetana Gupta (Wed Oct 14 2020 - 05:17:22 PDT)
[AMBER] Error running small molecule simulation: "RESTARTED DUE TO LINMIN FAILURE" and "an illegal memory access was encountered launching kernel kClearForces" erros Állan Ferrari (Tue Oct 13 2020 - 07:07:53 PDT)
- Re: [AMBER] Error running small molecule simulation: "RESTARTED DUE TO LINMIN FAILURE" and "an illegal memory access was encountered launching kernel kClearForces" erros David A Case (Tue Oct 13 2020 - 08:05:30 PDT)
  - Re: [AMBER] Error running small molecule simulation: "RESTARTED DUE TO LINMIN FAILURE" and "an illegal memory access was encountered launching kernel kClearForces" erros Állan Ferrari (Wed Oct 14 2020 - 12:57:44 PDT)
    - Re: [AMBER] Error running small molecule simulation: "RESTARTED DUE TO LINMIN FAILURE" and "an illegal memory access was encountered launching kernel kClearForces" erros David A Case (Thu Oct 15 2020 - 05:10:07 PDT)
    - Re: [AMBER] Error running small molecule simulation: "RESTARTED DUE TO LINMIN FAILURE" and "an illegal memory access was encountered launching kernel kClearForces" erros Állan Ferrari (Thu Oct 15 2020 - 06:26:08 PDT)
    - Re: [AMBER] Error running small molecule simulation: "RESTARTED DUE TO LINMIN FAILURE" and "an illegal memory access was encountered launching kernel kClearForces" erros David A Case (Thu Oct 15 2020 - 06:43:25 PDT)
    - Re: [AMBER] Error running small molecule simulation: "RESTARTED DUE TO LINMIN FAILURE" and "an illegal memory access was encountered launching kernel kClearForces" erros Állan Ferrari (Thu Oct 15 2020 - 07:11:40 PDT)
    - Re: [AMBER] Error running small molecule simulation: "RESTARTED DUE TO LINMIN FAILURE" and "an illegal memory access was encountered launching kernel kClearForces" erros David A Case (Sun Oct 18 2020 - 05:37:19 PDT)
[AMBER] vlimit=10 compromise for Amber 20 error: "an illegal memory access was encountered launching kernel kClearForces"? Liao (Tue Oct 13 2020 - 11:29:23 PDT)
- Re: [AMBER] vlimit=10 compromise for Amber 20 error: "an illegal memory access was encountered launching kernel kClearForces"? David A Case (Thu Oct 15 2020 - 05:13:28 PDT)
  - Re: [AMBER] vlimit=10 compromise for Amber 20 error: "an illegal memory access was encountered launching kernel kClearForces"? Liao (Thu Oct 15 2020 - 07:54:31 PDT)
    - Re: [AMBER] vlimit=10 compromise for Amber 20 error: "an illegal memory access was encountered launching kernel kClearForces"? David A Case (Thu Oct 15 2020 - 11:32:41 PDT)
    - Re: [AMBER] vlimit=10 compromise for Amber 20 error: "an illegal memory access was encountered launching kernel kClearForces"? Liao (Fri Oct 16 2020 - 14:30:45 PDT)
    - Re: [AMBER] vlimit=10 compromise for Amber 20 error: "an illegal memory access was encountered launching kernel kClearForces"? Elvis Martis (Fri Oct 16 2020 - 19:24:00 PDT)
  - Re: [AMBER] vlimit=10 compromise for Amber 20 error: "an illegal memory access was encountered launching kernel kClearForces"? Liao (Fri Nov 20 2020 - 13:18:33 PST)
    - Re: [AMBER] vlimit=10 compromise for Amber 20 error: "an illegal memory access was encountered launching kernel kClearForces"? Carlos Simmerling (Fri Nov 20 2020 - 14:29:53 PST)
    - Re: [AMBER] vlimit=10 compromise for Amber 20 error: "an illegal memory access was encountered launching kernel kClearForces"? Liao (Sun Nov 22 2020 - 16:20:43 PST)
    - Re: [AMBER] vlimit=10 compromise for Amber 20 error: "an illegal memory access was encountered launching kernel kClearForces"? David A Case (Sun Nov 22 2020 - 18:17:23 PST)
    - Re: [AMBER] vlimit=10 compromise for Amber 20 error: "an illegal memory access was encountered launching kernel kClearForces"? Liao (Sun Nov 22 2020 - 22:20:25 PST)
    - Re: [AMBER] vlimit=10 compromise for Amber 20 error: "an illegal memory access was encountered launching kernel kClearForces"? Carlos Simmerling (Mon Nov 23 2020 - 04:43:06 PST)
    - Re: [AMBER] vlimit=10 compromise for Amber 20 error: "an illegal memory access was encountered launching kernel kClearForces"? David Cerutti (Wed Dec 09 2020 - 00:57:45 PST)
    - Re: [AMBER] vlimit=10 compromise for Amber 20 error: "an illegal memory access was encountered launching kernel kClearForces"? Liao (Wed Dec 16 2020 - 09:21:12 PST)
[AMBER] Using parmchk2 with GLYCAM_06j.dat Delwakkada Liyanage, Senal Dinuka (Tue Oct 13 2020 - 12:44:58 PDT)
[AMBER] Installation of AMBER20 on CentOS 7 Pandey Anwesh (Wed Oct 14 2020 - 06:53:31 PDT)
- Re: [AMBER] Installation of AMBER20 on CentOS 7 David A Case (Wed Oct 14 2020 - 12:20:55 PDT)
[AMBER] assess which structures are similar between two MD-trajectories Vaibhav Dixit (Wed Oct 14 2020 - 20:51:04 PDT)
[AMBER] mdout issue Alejandro Cagnoni (Thu Oct 15 2020 - 07:01:53 PDT)
[AMBER] Query about using MMPBSA.py to calculate the binding free energy for a ligand bound enzyme SATYAJIT KHATUA (Thu Oct 15 2020 - 09:41:54 PDT)
- Re: [AMBER] Query about using MMPBSA.py to calculate the binding free energy for a ligand bound enzyme David A Case (Thu Oct 15 2020 - 11:29:26 PDT)
[AMBER] cpptraj's hbond shows hbonds with carbon hydrogens German P. Barletta (Thu Oct 15 2020 - 12:53:21 PDT)
- Re: [AMBER] cpptraj's hbond shows hbonds with carbon hydrogens Daniel Roe (Thu Oct 15 2020 - 15:48:27 PDT)
[AMBER] Adding catalytic Magnesium ion Jisha B (Thu Oct 15 2020 - 15:10:17 PDT)
- Re: [AMBER] Adding catalytic Magnesium ion Jisha B (Sat Oct 17 2020 - 03:22:48 PDT)
  - Re: [AMBER] Adding catalytic Magnesium ion Abhilash J (Sat Oct 17 2020 - 14:41:57 PDT)
  - Re: [AMBER] Adding catalytic Magnesium ion Juraj Dobias (Mon Oct 19 2020 - 00:27:50 PDT)
[AMBER] KeyError: 'H262' Wu Xu (Thu Oct 15 2020 - 20:25:27 PDT)
- Re: [AMBER] KeyError: 'H262' Pengfei Li (Thu Oct 22 2020 - 15:32:52 PDT)
  - Re: [AMBER] KeyError: 'H262' Wu Xu (Thu Oct 22 2020 - 20:09:03 PDT)
    - Re: [AMBER] KeyError: 'H262' Wu Xu (Fri Oct 23 2020 - 18:57:32 PDT)
[AMBER] VMD 1.9.4 could not read AMBER16 .mdcrd Wu Xu (Thu Oct 15 2020 - 21:23:17 PDT)
- Re: [AMBER] VMD 1.9.4 could not read AMBER16 .mdcrd Bill Ross (Thu Oct 15 2020 - 21:41:27 PDT)
- Re: [AMBER] VMD 1.9.4 could not read AMBER16 .mdcrd Elvis Martis (Thu Oct 15 2020 - 22:31:45 PDT)
  - Re: [AMBER] VMD 1.9.4 could not read AMBER16 .mdcrd Vaibhav Dixit (Thu Oct 15 2020 - 22:50:00 PDT)
  - Re: [AMBER] VMD 1.9.4 could not read AMBER16 .mdcrd aishen (Thu Oct 15 2020 - 23:45:47 PDT)
  - Re: [AMBER] VMD 1.9.4 could not read AMBER16 .mdcrd Mariano Curti (Fri Oct 16 2020 - 00:01:56 PDT)
    - Re: [AMBER] VMD 1.9.4 could not read AMBER16 .mdcrd Wu Xu (Fri Oct 16 2020 - 05:46:11 PDT)
    - Re: [AMBER] VMD 1.9.4 could not read AMBER16 .mdcrd aishen.free.fr (Fri Oct 16 2020 - 06:16:44 PDT)
- Re: [AMBER] VMD 1.9.4 could not read AMBER16 .mdcrd viktor (Fri Oct 16 2020 - 04:27:32 PDT)
- Re: [AMBER] VMD 1.9.4 could not read AMBER16 .mdcrd Grant Keller (Fri Oct 16 2020 - 10:40:46 PDT)
  - Re: [AMBER] VMD 1.9.4 could not read AMBER16 .mdcrd Daniel Roe (Fri Oct 16 2020 - 12:21:42 PDT)
    - Re: [AMBER] VMD 1.9.4 could not read AMBER16 .mdcrd Wu Xu (Fri Oct 16 2020 - 19:36:23 PDT)
[AMBER] Loading R.E.D server parameters into xleap Sruthi Sudhakar (Fri Oct 16 2020 - 02:50:13 PDT)
- Re: [AMBER] Loading R.E.D server parameters into xleap Emmett Leddin (Fri Oct 16 2020 - 05:05:09 PDT)
  - Re: [AMBER] Loading R.E.D server parameters into xleap Sruthi Sudhakar (Fri Oct 16 2020 - 06:12:44 PDT)
    - Re: [AMBER] Loading R.E.D server parameters into xleap Emmett Leddin (Fri Oct 16 2020 - 10:11:59 PDT)
[AMBER] Fwd: AMBER Digest, Vol 3153, Issue 1 SATYAJIT KHATUA (Thu Oct 15 2020 - 21:59:05 PDT)
- Re: [AMBER] Fwd: AMBER Digest, Vol 3153, Issue 1 David A Case (Fri Oct 16 2020 - 05:04:20 PDT)
[AMBER] mm-pbsa calculation Serena Vittorio (Fri Oct 16 2020 - 09:21:24 PDT)
- Re: [AMBER] mm-pbsa calculation Suchetana Gupta (Sun Oct 18 2020 - 00:13:36 PDT)
  - [AMBER] R: mm-pbsa calculation Serena Vittorio (Mon Oct 19 2020 - 02:36:36 PDT)
    - Re: [AMBER] R: mm-pbsa calculation Suchetana Gupta (Tue Oct 27 2020 - 22:21:26 PDT)
    - Re: [AMBER] R: mm-pbsa calculation Giulio Poli (Wed Oct 28 2020 - 01:47:20 PDT)
[AMBER] rms(d) or (f) per residue Seibold, Steve Allan (Fri Oct 16 2020 - 09:51:09 PDT)
- Re: [AMBER] rms(d) or (f) per residue Daniel Roe (Fri Oct 16 2020 - 10:06:25 PDT)
  - Re: [AMBER] rms(d) or (f) per residue Seibold, Steve Allan (Fri Oct 16 2020 - 10:21:58 PDT)
    - Re: [AMBER] rms(d) or (f) per residue Daniel Roe (Fri Oct 16 2020 - 10:32:11 PDT)
    - Re: [AMBER] rms(d) or (f) per residue Seibold, Steve Allan (Sat Oct 17 2020 - 05:01:36 PDT)
[AMBER] NAMD trajectory analysis with cpptraj sangita kachhap (Fri Oct 16 2020 - 12:35:39 PDT)
- Re: [AMBER] NAMD trajectory analysis with cpptraj Daniel Roe (Sat Oct 17 2020 - 00:05:42 PDT)
  - Re: [AMBER] NAMD trajectory analysis with cpptraj sangita kachhap (Sat Oct 17 2020 - 02:53:29 PDT)
[AMBER] cpptraj's hbond shows hbonds with carbon hydrogens German P. Barletta (Fri Oct 16 2020 - 13:03:50 PDT)
[AMBER] Creating a coordinate bond in Leap Jenny 148 (Fri Oct 16 2020 - 21:53:54 PDT)
- Re: [AMBER] Creating a coordinate bond in Leap Elvis Martis (Fri Oct 16 2020 - 22:10:59 PDT)
  - Re: [AMBER] Creating a coordinate bond in Leap Bill Ross (Sat Oct 17 2020 - 05:30:18 PDT)
- Re: [AMBER] Creating a coordinate bond in Leap Bill Ross (Fri Oct 16 2020 - 22:13:13 PDT)
[AMBER] process_mdout.perl for pmemd Jorge Iulek (Sat Oct 17 2020 - 14:31:07 PDT)
- Re: [AMBER] process_mdout.perl for pmemd Rodrigo Galindo-Murillo (Sat Oct 17 2020 - 14:45:44 PDT)
  - Re: [AMBER] process_mdout.perl for pmemd Jorge Iulek (Sun Oct 18 2020 - 10:50:59 PDT)
[AMBER] Amber20 compiling warning Tom Wang (Sun Oct 18 2020 - 05:40:44 PDT)
- Re: [AMBER] Amber20 compiling warning David A Case (Mon Oct 19 2020 - 04:29:31 PDT)
[AMBER] Bond: Maximum coordination exceeded Sarah Jane (Sun Oct 18 2020 - 11:21:45 PDT)
- Re: [AMBER] Bond: Maximum coordination exceeded David A Case (Mon Oct 19 2020 - 04:37:02 PDT)
[AMBER] Adding missing residues in a pdb file using tleap SUNITA MUDULI (Sun Oct 18 2020 - 12:14:01 PDT)
- Re: [AMBER] Adding missing residues in a pdb file using tleap David A Case (Mon Oct 19 2020 - 04:39:14 PDT)
[AMBER] RMSD (non mass-weighted) as collective variable in Amber-18 Madhur Aggarwal (Sun Oct 18 2020 - 14:20:09 PDT)
[AMBER] MD error Kehinde Idowu (Sun Oct 18 2020 - 14:24:14 PDT)
- Re: [AMBER] MD error David A Case (Mon Oct 19 2020 - 04:42:58 PDT)
  - Re: [AMBER] MD error Kehinde Idowu (Mon Oct 19 2020 - 07:58:48 PDT)
[AMBER] Metalloprotein-ligand complex modelling for MMPBSA.py SATYAJIT KHATUA (Mon Oct 19 2020 - 00:59:36 PDT)
[AMBER] mm-pbsa calculation: SA Bomb in circle(): Stored surface arcs over limit Serena Vittorio (Mon Oct 19 2020 - 01:27:56 PDT)
- Re: [AMBER] mm-pbsa calculation: SA Bomb in circle(): Stored surface arcs over limit David A Case (Mon Oct 19 2020 - 04:47:09 PDT)
[AMBER] Steered MD at constant force Vishal Singh (Mon Oct 19 2020 - 05:28:49 PDT)
[AMBER] NOE analysis with cpptraj Pavlína Pokorná (Mon Oct 19 2020 - 06:17:47 PDT)
- Re: [AMBER] NOE analysis with cpptraj Daniel Roe (Wed Nov 25 2020 - 07:24:11 PST)
  - Re: [AMBER] NOE analysis with cpptraj Pavlína Pokorná (Wed Dec 02 2020 - 04:27:56 PST)
[AMBER] Changing lj_radius without changing lj_14_radius Batuhan Kav (Mon Oct 19 2020 - 08:23:32 PDT)
- Re: [AMBER] Changing lj_radius without changing lj_14_radius Matias Machado (Wed Oct 21 2020 - 11:25:38 PDT)
  - Re: [AMBER] Changing lj_radius without changing lj_14_radius Batuhan Kav (Thu Oct 22 2020 - 01:34:22 PDT)
    - Re: [AMBER] Changing lj_radius without changing lj_14_radius Matias Machado (Thu Oct 22 2020 - 07:43:42 PDT)
    - Re: [AMBER] Changing lj_radius without changing lj_14_radius Batuhan Kav (Mon Oct 26 2020 - 09:22:52 PDT)
    - Re: [AMBER] Changing lj_radius without changing lj_14_radius Matias Machado (Mon Oct 26 2020 - 14:43:38 PDT)
[AMBER] Amber 20 compilation with the intel 2019.1.1 compiler Vlad Cojocaru (Mon Oct 19 2020 - 10:47:43 PDT)
- Re: [AMBER] Amber 20 compilation with the intel 2019.1.1 compiler Scott Brozell (Mon Oct 19 2020 - 18:44:09 PDT)
  - Re: [AMBER] Amber 20 compilation with the intel 2019.1.1 compiler Scott Brozell (Mon Oct 19 2020 - 19:10:10 PDT)
    - Re: [AMBER] Amber 20 compilation with the intel 2019.1.1 compiler Vlad Cojocaru (Tue Oct 20 2020 - 04:37:59 PDT)
    - Re: [AMBER] Amber 20 compilation with the intel 2019.1.1 compiler Vlad Cojocaru (Tue Oct 20 2020 - 07:46:37 PDT)
    - Re: [AMBER] Amber 20 compilation with the intel 2019.1.1 compiler David A Case (Tue Oct 20 2020 - 10:50:49 PDT)
    - Re: [AMBER] Amber 20 compilation with the intel 2019.1.1 compiler Scott Brozell (Tue Oct 20 2020 - 14:37:31 PDT)
    - Re: [AMBER] Amber 20 compilation with the intel 2019.1.1 compiler Vlad Cojocaru (Wed Oct 21 2020 - 04:31:27 PDT)
    - Re: [AMBER] Amber 20 compilation with the intel 2019.1.1 compiler Scott Brozell (Wed Oct 21 2020 - 16:04:20 PDT)
    - Re: [AMBER] Amber 20 compilation with the intel 2019.1.1 compiler Vlad Cojocaru (Fri Oct 23 2020 - 01:28:11 PDT)
    - Re: [AMBER] Amber 20 compilation with the intel 2019.1.1 compiler Scott Brozell (Fri Oct 30 2020 - 13:47:02 PDT)
[AMBER] Bacteria cell membrane PDB Loo Kang (Mon Oct 19 2020 - 20:06:53 PDT)
[AMBER] mdout error Alejandro Cagnoni (Tue Oct 20 2020 - 04:54:13 PDT)
[AMBER] controversy in PBSA and GBSA results h_sahakyan.mb.sci.am (Tue Oct 20 2020 - 05:27:05 PDT)
- Re: [AMBER] controversy in PBSA and GBSA results Carlos Simmerling (Tue Oct 20 2020 - 05:34:39 PDT)
- Re: [AMBER] controversy in PBSA and GBSA results Ray Luo (Tue Oct 20 2020 - 09:54:08 PDT)
[AMBER] calculating differences in binding energy for enantiomers to amino acid based surfactants Billiot, Eugene (Tue Oct 20 2020 - 05:45:16 PDT)
[AMBER] Adding Ions Gustaf Olsson (Tue Oct 20 2020 - 05:56:08 PDT)
- Re: [AMBER] Adding Ions Bill Ross (Tue Oct 20 2020 - 06:48:33 PDT)
  - Re: [AMBER] Adding Ions Gustaf Olsson (Wed Oct 21 2020 - 00:04:40 PDT)
    - Re: [AMBER] Adding Ions Gustaf Olsson (Wed Oct 21 2020 - 05:26:56 PDT)
    - Re: [AMBER] Adding Ions Matias Machado (Wed Oct 21 2020 - 10:22:20 PDT)
    - Re: [AMBER] Adding Ions Gustaf Olsson (Thu Oct 22 2020 - 01:01:09 PDT)
    - Re: [AMBER] Adding Ions David A Case (Thu Oct 22 2020 - 05:21:51 PDT)
    - Re: [AMBER] Adding Ions Gustaf Olsson (Thu Oct 22 2020 - 05:27:14 PDT)
    - Re: [AMBER] Adding Ions David A Case (Wed Oct 21 2020 - 05:40:45 PDT)
[AMBER] TI not compatible with GB on GPU Vaibhav Dixit (Tue Oct 20 2020 - 02:27:07 PDT)
- Re: [AMBER] TI not compatible with GB on GPU Debarati DasGupta (Wed Oct 21 2020 - 05:21:46 PDT)
  - Re: [AMBER] TI not compatible with GB on GPU Vaibhav Dixit (Wed Oct 21 2020 - 05:59:26 PDT)
    - Re: [AMBER] TI not compatible with GB on GPU Debarati DasGupta (Wed Oct 21 2020 - 07:45:14 PDT)
    - Re: [AMBER] TI not compatible with GB on GPU Debarati DasGupta (Wed Oct 21 2020 - 07:46:07 PDT)
    - Re: [AMBER] TI not compatible with GB on GPU Vaibhav Dixit (Wed Oct 21 2020 - 23:52:56 PDT)
    - Re: [AMBER] TI not compatible with GB on GPU David A Case (Thu Oct 22 2020 - 05:04:32 PDT)
    - Re: [AMBER] TI not compatible with GB on GPU Vaibhav Dixit (Thu Oct 22 2020 - 02:29:55 PDT)
[AMBER] AMBER16 problem Seibold, Steve Allan (Tue Oct 20 2020 - 07:56:20 PDT)
- Re: [AMBER] AMBER16 problem David A Case (Tue Oct 20 2020 - 10:59:46 PDT)
  - Re: [AMBER] AMBER16 problem Seibold, Steve Allan (Wed Oct 21 2020 - 10:08:17 PDT)
[AMBER] ff19SB and OPC, process_(min/md)out.perl and LEaP Gustaf Olsson (Wed Oct 21 2020 - 01:10:10 PDT)
- Re: [AMBER] ff19SB and OPC, process_(min/md)out.perl and LEaP Gustaf Olsson (Wed Oct 21 2020 - 05:36:30 PDT)
  - Re: [AMBER] ff19SB and OPC, process_(min/md)out.perl and LEaP Carlos Simmerling (Wed Oct 21 2020 - 06:32:50 PDT)
    - Re: [AMBER] ff19SB and OPC, process_(min/md)out.perl and LEaP Gustaf Olsson (Thu Oct 22 2020 - 00:10:34 PDT)
    - Re: [AMBER] ff19SB and OPC, process_(min/md)out.perl and LEaP Gustaf Olsson (Thu Oct 22 2020 - 01:53:17 PDT)
    - Re: [AMBER] ff19SB and OPC, process_(min/md)out.perl and LEaP Gustaf Olsson (Thu Oct 22 2020 - 02:27:13 PDT)
    - Re: [AMBER] ff19SB and OPC, process_(min/md)out.perl and LEaP David A Case (Thu Oct 22 2020 - 05:47:51 PDT)
    - Re: [AMBER] ff19SB and OPC, process_(min/md)out.perl and LEaP Carlos Simmerling (Thu Oct 22 2020 - 06:06:06 PDT)
    - Re: [AMBER] ff19SB and OPC, process_(min/md)out.perl and LEaP Gustaf Olsson (Fri Oct 23 2020 - 02:26:05 PDT)
    - Re: [AMBER] ff19SB and OPC, process_(min/md)out.perl and LEaP Daniel Roe (Fri Oct 23 2020 - 02:36:20 PDT)
    - Re: [AMBER] ff19SB and OPC, process_(min/md)out.perl and LEaP Gustaf Olsson (Fri Oct 23 2020 - 04:12:43 PDT)
    - Re: [AMBER] ff19SB and OPC, process_(min/md)out.perl and LEaP Daniel Roe (Fri Oct 23 2020 - 04:28:37 PDT)
    - Re: [AMBER] ff19SB and OPC, process_(min/md)out.perl and LEaP Daniel Roe (Fri Oct 23 2020 - 07:29:46 PDT)
    - Re: [AMBER] ff19SB and OPC, process_(min/md)out.perl and LEaP Carlos Simmerling (Fri Oct 23 2020 - 07:34:22 PDT)
    - Re: [AMBER] ff19SB and OPC, process_(min/md)out.perl and LEaP Gustaf Olsson (Fri Oct 23 2020 - 10:23:56 PDT)
    - Re: [AMBER] ff19SB and OPC, process_(min/md)out.perl and LEaP Daniel Roe (Fri Oct 23 2020 - 10:19:28 PDT)
    - Re: [AMBER] ff19SB and OPC, process_(min/md)out.perl and LEaP Gustaf Olsson (Fri Oct 23 2020 - 10:27:05 PDT)
    - Re: [AMBER] ff19SB and OPC, process_(min/md)out.perl and LEaP Carlos Simmerling (Fri Oct 23 2020 - 05:27:34 PDT)
    - Re: [AMBER] ff19SB and OPC, process_(min/md)out.perl and LEaP Carlos Simmerling (Fri Oct 23 2020 - 10:28:58 PDT)
    - Re: [AMBER] ff19SB and OPC, process_(min/md)out.perl and LEaP Gustaf Olsson (Sat Oct 24 2020 - 12:49:30 PDT)
    - Re: [AMBER] ff19SB and OPC, process_(min/md)out.perl and LEaP Carlos Simmerling (Sat Oct 24 2020 - 12:58:16 PDT)
    - Re: [AMBER] ff19SB and OPC, process_(min/md)out.perl and LEaP Gustaf Olsson (Mon Oct 26 2020 - 00:46:07 PDT)
    - Re: [AMBER] ff19SB and OPC, process_(min/md)out.perl and LEaP Gustaf Olsson (Mon Oct 26 2020 - 01:21:15 PDT)
[AMBER] MMPBS decomposition error MYRIAN TORRES RICO (Wed Oct 21 2020 - 02:05:27 PDT)
[AMBER] installing Amber18 and AmberTools20 Seibold, Steve Allan (Wed Oct 21 2020 - 10:40:43 PDT)
- Re: [AMBER] installing Amber18 and AmberTools20 David A Case (Thu Oct 22 2020 - 05:37:10 PDT)
[AMBER] drms comparison in sander during minimization? Kenneth Huang (Wed Oct 21 2020 - 15:03:40 PDT)
- Re: [AMBER] drms comparison in sander during minimization? David A Case (Thu Oct 22 2020 - 05:42:27 PDT)
  - Re: [AMBER] drms comparison in sander during minimization? Kenneth Huang (Thu Oct 22 2020 - 20:59:05 PDT)
    - Re: [AMBER] drms comparison in sander during minimization? David A Case (Fri Oct 23 2020 - 05:31:32 PDT)
Re: [AMBER] NVIDIA GeForce RTX 3090 GPUs Mike Mazanetz (Thu Oct 22 2020 - 05:11:35 PDT)
[AMBER] correct md-input & prmtop for TI calculations Vaibhav Dixit (Thu Oct 22 2020 - 02:27:55 PDT)
- Re: [AMBER] correct md-input & prmtop for TI calculations Vaibhav Dixit (Mon Oct 26 2020 - 03:47:15 PDT)
[AMBER] Is the amber website down? 9am EST Debarati DasGupta (Thu Oct 22 2020 - 06:13:12 PDT)
- Re: [AMBER] Is the amber website down? 9am EST David A Case (Thu Oct 22 2020 - 12:42:47 PDT)
[AMBER] server issues 403 on ambermd.org Mike Mazanetz (Thu Oct 22 2020 - 06:49:11 PDT)
- Re: [AMBER] server issues 403 on ambermd.org Gustaf Olsson (Thu Oct 22 2020 - 23:51:35 PDT)
[AMBER] Cannot access amber website Lang,Lijun (Thu Oct 22 2020 - 08:13:11 PDT)
- Re: [AMBER] Cannot access amber website Elvis Martis (Thu Oct 22 2020 - 08:44:27 PDT)
[AMBER] error 403 Ayesha Fatima (Thu Oct 22 2020 - 10:57:21 PDT)
[AMBER] Fwd: MMPBSA calculations with 1 explicit water molecule divyabharathi korlepara (Thu Oct 22 2020 - 11:01:31 PDT)
- Re: [AMBER] Fwd: MMPBSA calculations with 1 explicit water molecule Ray Luo (Fri Oct 30 2020 - 08:02:45 PDT)
[AMBER] Trouble installing pbsa cuda code Wesley Michael Botello-Smith (Thu Oct 22 2020 - 11:47:41 PDT)
- Re: [AMBER] Trouble installing pbsa cuda code David A Case (Thu Oct 22 2020 - 12:59:18 PDT)
  - Re: [AMBER] Trouble installing pbsa cuda code Wesley Michael Botello-Smith (Fri Oct 23 2020 - 20:32:39 PDT)
    - Re: [AMBER] Trouble installing pbsa cuda code David A Case (Sat Oct 24 2020 - 10:18:29 PDT)
- Re: [AMBER] Trouble installing pbsa cuda code Tru Huynh (Thu Oct 22 2020 - 14:09:32 PDT)
[AMBER] GaMD Neha Gandhi (Thu Oct 22 2020 - 15:30:03 PDT)
[AMBER] doubt charges MYRIAN TORRES RICO (Fri Oct 23 2020 - 01:11:27 PDT)
- Re: [AMBER] doubt charges Dr. Anselm Horn (Fri Oct 23 2020 - 01:28:05 PDT)
  - Re: [AMBER] doubt charges MYRIAN TORRES RICO (Fri Oct 23 2020 - 05:30:26 PDT)
- Re: [AMBER] doubt charges David A Case (Fri Oct 23 2020 - 05:38:41 PDT)
  - Re: [AMBER] doubt charges MYRIAN TORRES RICO (Fri Oct 23 2020 - 07:10:55 PDT)
    - Re: [AMBER] doubt charges Dr. Anselm Horn (Fri Oct 23 2020 - 08:28:58 PDT)
    - Re: [AMBER] doubt charges gagandeep singh (Fri Oct 23 2020 - 06:27:09 PDT)
    - Re: [AMBER] doubt charges MYRIAN TORRES RICO (Mon Oct 26 2020 - 02:11:53 PDT)
    - Re: [AMBER] doubt charges MYRIAN TORRES RICO (Mon Oct 26 2020 - 02:15:27 PDT)
[AMBER] Is there a way to analyze contact maps of mixtures of more than 2 components? Naxhije Berisha (Fri Oct 23 2020 - 10:44:52 PDT)
[AMBER] amber14 and amber16 are not working in new installation Marcelo Andrade Chagas (Fri Oct 23 2020 - 19:31:47 PDT)
- Re: [AMBER] amber14 and amber16 are not working in new installation David A Case (Mon Oct 26 2020 - 06:23:20 PDT)
Re: [AMBER] [GaMD-discuss] GaMD Neha Gandhi (Sun Oct 25 2020 - 17:11:36 PDT)
[AMBER] Steered MD at constant force Vishal Singh (Mon Oct 26 2020 - 05:15:01 PDT)
[AMBER] mmpbsa error MYRIAN TORRES RICO (Mon Oct 26 2020 - 05:53:47 PDT)
- Re: [AMBER] mmpbsa error David A Case (Mon Oct 26 2020 - 06:26:32 PDT)
  - Re: [AMBER] mmpbsa error MYRIAN TORRES RICO (Mon Oct 26 2020 - 10:30:43 PDT)
    - Re: [AMBER] mmpbsa error David A Case (Mon Oct 26 2020 - 17:48:53 PDT)
    - Re: [AMBER] mmpbsa error MYRIAN TORRES RICO (Tue Oct 27 2020 - 01:37:12 PDT)
[AMBER] Amber20: Ampere microarchitecture support and next Amber release Kraus, Sebastian (Mon Oct 26 2020 - 12:18:42 PDT)
- Re: [AMBER] Amber20: Ampere microarchitecture support and next Amber release David A Case (Mon Oct 26 2020 - 17:55:55 PDT)
- [AMBER] Amber20: Ampere microarchitecture support and Amber release in 2021 Kraus, Sebastian (Tue Oct 27 2020 - 00:36:28 PDT)
[AMBER] AMBER 20 Benchmarks on NVIDIA RTX 3080/3090 and more Jason Hogrefe (Mon Oct 26 2020 - 15:26:13 PDT)
- Re: [AMBER] AMBER 20 Benchmarks on NVIDIA RTX 3080/3090 and more Mike Mazanetz (Tue Oct 27 2020 - 03:40:10 PDT)
[AMBER] System preparation for MMPBSA.py SATYAJIT KHATUA (Mon Oct 26 2020 - 21:29:12 PDT)
- Re: [AMBER] System preparation for MMPBSA.py Ray Luo (Fri Oct 30 2020 - 08:07:32 PDT)
- Re: [AMBER] System preparation for MMPBSA.py SATYAJIT KHATUA (Mon Nov 02 2020 - 21:53:40 PST)
  - Re: [AMBER] System preparation for MMPBSA.py David A Case (Tue Nov 03 2020 - 05:57:32 PST)
- Re: [AMBER] System preparation for MMPBSA.py SATYAJIT KHATUA (Tue Nov 03 2020 - 21:49:38 PST)
  - Re: [AMBER] System preparation for MMPBSA.py David A Case (Wed Nov 04 2020 - 05:09:15 PST)
- Re: [AMBER] System preparation for MMPBSA.py SATYAJIT KHATUA (Wed Nov 04 2020 - 23:08:48 PST)
  - Re: [AMBER] System preparation for MMPBSA.py David A Case (Thu Nov 05 2020 - 05:37:10 PST)
    - Re: [AMBER] System preparation for MMPBSA.py Pengfei Li (Fri Nov 20 2020 - 08:02:16 PST)
[AMBER] TI calculation input clarification Delwakkada Liyanage, Senal Dinuka (Tue Oct 27 2020 - 10:00:51 PDT)
[AMBER] pmemd with hybrid mpi/mp Bill Abbott (Tue Oct 27 2020 - 12:28:53 PDT)
- Re: [AMBER] pmemd with hybrid mpi/mp David A Case (Tue Oct 27 2020 - 13:04:24 PDT)
  - Re: [AMBER] pmemd with hybrid mpi/mp Bill Abbott (Tue Oct 27 2020 - 13:13:32 PDT)
[AMBER] pmemd.cuda and CPU cores Abdul Basit (Tue Oct 27 2020 - 20:13:46 PDT)
- Re: [AMBER] pmemd.cuda and CPU cores David A Case (Wed Oct 28 2020 - 04:41:22 PDT)
[AMBER] Amber20 and RNA simulations Piia Kokkonen (Wed Oct 28 2020 - 03:31:13 PDT)
- Re: [AMBER] Amber20 and RNA simulations David A Case (Wed Oct 28 2020 - 04:58:52 PDT)
  - Re: [AMBER] Amber20 and RNA simulations Piia Kokkonen (Wed Oct 28 2020 - 05:22:05 PDT)
    - Re: [AMBER] Amber20 and RNA simulations Piia Kokkonen (Tue Nov 10 2020 - 04:38:25 PST)
[AMBER] Help with parameterization of non-standard amino acid Amit Sharma (Asstt. Prof., MCARS) (Wed Oct 28 2020 - 05:43:59 PDT)
- Re: [AMBER] Help with parameterization of non-standard amino acid Dr. Anselm Horn (Wed Oct 28 2020 - 07:57:34 PDT)
  - Re: [AMBER] Help with parameterization of non-standard amino acid Amit Sharma (Asstt. Prof., MCARS) (Wed Nov 04 2020 - 01:30:31 PST)
    - Re: [AMBER] Help with parameterization of non-standard amino acid David A Case (Wed Nov 04 2020 - 05:15:40 PST)
    - Re: [AMBER] Help with parameterization of non-standard amino acid Amit Sharma (Asstt. Prof., MCARS) (Wed Nov 04 2020 - 08:22:54 PST)
    - Re: [AMBER] Help with parameterization of non-standard amino acid Carlos Simmerling (Wed Nov 04 2020 - 08:58:12 PST)
    - Re: [AMBER] Help with parameterization of non-standard amino acid Dr. Anselm Horn (Thu Nov 05 2020 - 03:50:06 PST)
    - Re: [AMBER] Help with parameterization of non-standard amino acid Carlos Simmerling (Thu Nov 05 2020 - 10:04:43 PST)
    - Re: [AMBER] Help with parameterization of non-standard amino acid Dr. Anselm Horn (Fri Nov 06 2020 - 02:15:24 PST)
    - Re: [AMBER] Help with parameterization of non-standard amino acid Pengfei Li (Fri Nov 20 2020 - 08:24:41 PST)
[AMBER] Amber TI - crgmask Delwakkada Liyanage, Senal Dinuka (Wed Oct 28 2020 - 09:02:42 PDT)
- Re: [AMBER] Amber TI - crgmask Juraj Dobias (Thu Oct 29 2020 - 02:04:50 PDT)
  - Re: [AMBER] Amber TI - crgmask Delwakkada Liyanage, Senal Dinuka (Thu Oct 29 2020 - 08:16:23 PDT)
    - Re: [AMBER] Amber TI - crgmask Juraj Dobias (Fri Oct 30 2020 - 03:39:02 PDT)
[AMBER] CO2 Michele Vanini (Wed Oct 28 2020 - 09:55:40 PDT)
- Re: [AMBER] CO2 Raman Preet Singh (Wed Oct 28 2020 - 10:38:01 PDT)
  - Re: [AMBER] CO2 Michele Vanini (Wed Oct 28 2020 - 12:20:17 PDT)
    - Re: [AMBER] CO2 Carlos Simmerling (Wed Oct 28 2020 - 12:37:06 PDT)
    - Re: [AMBER] CO2 Raman Preet Singh (Wed Oct 28 2020 - 23:41:03 PDT)
[AMBER] a metal bound Met Wu Xu (Wed Oct 28 2020 - 12:33:18 PDT)
- Re: [AMBER] a metal bound Met Vaibhav Dixit (Wed Oct 28 2020 - 18:31:06 PDT)
  - Re: [AMBER] a metal bound Met Wu Xu (Wed Oct 28 2020 - 18:41:39 PDT)
    - Re: [AMBER] a metal bound Met Pengfei Li (Fri Nov 20 2020 - 07:25:39 PST)
    - Re: [AMBER] a metal bound Met Wu Xu (Fri Nov 20 2020 - 07:55:42 PST)
[AMBER] How to import (.pdb) files into xleap of AMBER generated by Cellulose builder Pinky Mazumder (Wed Oct 28 2020 - 22:47:59 PDT)
- Re: [AMBER] How to import (.pdb) files into xleap of AMBER generated by Cellulose builder Dr. Anselm Horn (Thu Oct 29 2020 - 03:24:11 PDT)
  - Re: [AMBER] How to import (.pdb) files into xleap of AMBER generated by Cellulose builder Pinky Mazumder (Thu Oct 29 2020 - 09:58:46 PDT)
    - Re: [AMBER] How to import (.pdb) files into xleap of AMBER generated by Cellulose builder Bill Ross (Thu Oct 29 2020 - 10:28:28 PDT)
[AMBER] cellulose crystal structure ( cellulose bundles) Pinky Mazumder (Thu Oct 29 2020 - 00:59:00 PDT)
- Re: [AMBER] cellulose crystal structure ( cellulose bundles) David A Case (Thu Oct 29 2020 - 05:05:03 PDT)
  - Re: [AMBER] cellulose crystal structure ( cellulose bundles) Pinky Mazumder (Thu Oct 29 2020 - 09:54:09 PDT)
    - Re: [AMBER] cellulose crystal structure ( cellulose bundles) Bill Ross (Thu Oct 29 2020 - 10:34:27 PDT)
    - Re: [AMBER] cellulose crystal structure ( cellulose bundles) Pinky Mazumder (Thu Dec 10 2020 - 22:50:29 PST)
[AMBER] Xleap error Jisha B (Thu Oct 29 2020 - 02:17:22 PDT)
- Re: [AMBER] Xleap error Elvis Martis (Thu Oct 29 2020 - 03:26:34 PDT)
[AMBER] Force field for IDP mohamed marzouk (Thu Oct 29 2020 - 08:31:29 PDT)
- Re: [AMBER] Force field for IDP David A Case (Fri Oct 30 2020 - 04:33:20 PDT)
[AMBER] Normalized eigen values DHEERAJ CHITARA (Thu Oct 29 2020 - 09:51:27 PDT)
[AMBER] Amber20 installation for MPI, CUDA issues. Luka Bilić (Thu Oct 29 2020 - 12:38:15 PDT)
- Re: [AMBER] Amber20 installation for MPI, CUDA issues. Luka Bilić (Fri Oct 30 2020 - 03:30:45 PDT)
[AMBER] MM/PBSA after minimization h_sahakyan.mb.sci.am (Thu Oct 29 2020 - 12:56:21 PDT)
- Re: [AMBER] MM/PBSA after minimization David A Case (Fri Oct 30 2020 - 04:38:53 PDT)
[AMBER] Constant Force SMD simulation Vishal Singh (Thu Oct 29 2020 - 21:05:24 PDT)
- Re: [AMBER] Constant Force SMD simulation MR. RABINDRANATH PAUL (Thu Oct 29 2020 - 21:55:21 PDT)
  - Re: [AMBER] Constant Force SMD simulation Vishal Singh (Thu Oct 29 2020 - 22:07:42 PDT)
[AMBER] how find Es from mdout to estimate vertical energy gap Vaibhav Dixit (Fri Oct 30 2020 - 10:05:07 PDT)
- Re: [AMBER] how find Es from mdout to estimate vertical energy gap Adrian Roitberg (Fri Oct 30 2020 - 10:11:02 PDT)
  - Re: [AMBER] how find Es from mdout to estimate vertical energy gap Vaibhav Dixit (Fri Oct 30 2020 - 13:20:58 PDT)
    - Re: [AMBER] how find Es from mdout to estimate vertical energy gap Vaibhav Dixit (Fri Oct 30 2020 - 13:56:58 PDT)
    - Re: [AMBER] how find Es from mdout to estimate vertical energy gap Adrian Roitberg (Sat Oct 31 2020 - 09:28:25 PDT)
    - Re: [AMBER] how find Es from mdout to estimate vertical energy gap Vaibhav Dixit (Sat Oct 31 2020 - 23:05:54 PDT)
[AMBER] NMR restraints Debarati DasGupta (Fri Oct 30 2020 - 12:37:48 PDT)
- Re: [AMBER] NMR restraints Carlos Simmerling (Fri Oct 30 2020 - 14:11:50 PDT)
  - Re: [AMBER] NMR restraints Debarati DasGupta (Sat Oct 31 2020 - 05:40:45 PDT)
    - Re: [AMBER] NMR restraints Carlos Simmerling (Sat Oct 31 2020 - 05:42:30 PDT)
    - Re: [AMBER] NMR restraints Debarati DasGupta (Sat Oct 31 2020 - 05:54:14 PDT)
- Re: [AMBER] NMR restraints David A Case (Fri Oct 30 2020 - 18:21:41 PDT)
  - Re: [AMBER] NMR restraints Debarati DasGupta (Sat Oct 31 2020 - 07:46:15 PDT)
    - Re: [AMBER] NMR restraints Debarati DasGupta (Sun Nov 01 2020 - 06:19:14 PST)
    - Re: [AMBER] NMR restraints David A Case (Mon Nov 02 2020 - 04:19:40 PST)
    - Re: [AMBER] NMR restraints Debarati DasGupta (Mon Nov 02 2020 - 14:19:50 PST)
- Re: [AMBER] NMR restraints Debarati DasGupta (Mon Nov 02 2020 - 14:21:27 PST)
[AMBER] Problem with acpype Michele Vanini (Sat Oct 31 2020 - 02:08:54 PDT)
- Re: [AMBER] Problem with acpype Pengfei Li (Fri Nov 20 2020 - 08:37:36 PST)
[AMBER] Aqvist force field for magnesium Jenny 148 (Sun Nov 01 2020 - 00:09:52 PDT)
- Re: [AMBER] Aqvist force field for magnesium Pengfei Li (Fri Nov 20 2020 - 08:32:28 PST)
[AMBER] RESTARTED DUE TO LINMIN FAILURE ... Sadaf Rani (Sun Nov 01 2020 - 07:21:01 PST)
- Re: [AMBER] RESTARTED DUE TO LINMIN FAILURE ... David A Case (Mon Nov 02 2020 - 04:22:52 PST)
[AMBER] Screenshots for publications Gustaf Olsson (Mon Nov 02 2020 - 02:05:28 PST)
- Re: [AMBER] Screenshots for publications David A Case (Mon Nov 02 2020 - 04:23:34 PST)
[AMBER] Understanding restraint files generated from CHARMM-GUI Souvik Dey (Mon Nov 02 2020 - 11:05:45 PST)
- Re: [AMBER] Understanding restraint files generated from CHARMM-GUI David A Case (Mon Nov 02 2020 - 13:19:20 PST)
[AMBER] MM/PBSA after minimization h_sahakyan.mb.sci.am (Mon Nov 02 2020 - 11:12:00 PST)
- Re: [AMBER] MM/PBSA after minimization Elvis Martis (Mon Nov 02 2020 - 17:35:08 PST)
[AMBER] Program received signal SIGSEGV: Segmentation fault - invalid memory reference Sarah Jane (Mon Nov 02 2020 - 16:39:05 PST)
- Re: [AMBER] Program received signal SIGSEGV: Segmentation fault - invalid memory reference David A Case (Mon Nov 02 2020 - 17:58:54 PST)
[AMBER] Protein-nucleic acid interactions Athena N (Mon Nov 02 2020 - 21:20:10 PST)
- Re: [AMBER] Protein-nucleic acid interactions Bill Ross (Mon Nov 02 2020 - 22:23:00 PST)
[AMBER] Error while running MMGBSA Suchetana Gupta (Mon Nov 02 2020 - 22:26:07 PST)
- Re: [AMBER] Error while running MMGBSA David A Case (Tue Nov 03 2020 - 06:01:37 PST)
[AMBER] installation issues with cuda 11.1 Demian Riccardi (Tue Nov 03 2020 - 10:16:57 PST)
[AMBER] PCA with multiple peaks Abhilash J (Tue Nov 03 2020 - 13:34:42 PST)
[AMBER] Question about the outfile of 'softcore part' wangjianing_mail (Wed Nov 04 2020 - 03:08:36 PST)
[AMBER] Question about the 'softcore part' of outputfile in pmemd wangjianing_mail (Wed Nov 04 2020 - 03:09:37 PST)
[AMBER] Saving pdb as parm7/prmtop file with boundary conditions Aashish Shivkumar (Thu Nov 05 2020 - 00:11:04 PST)
- Re: [AMBER] Saving pdb as parm7/prmtop file with boundary conditions Gustaf Olsson (Thu Nov 05 2020 - 03:17:09 PST)
[AMBER] Ambertools20 installation Hrvoje Brkić (Thu Nov 05 2020 - 07:31:41 PST)
- Re: [AMBER] Ambertools20 installation David A Case (Thu Nov 05 2020 - 13:56:47 PST)
[AMBER] protein folding h_sahakyan.mb.sci.am (Thu Nov 05 2020 - 08:20:43 PST)
- Re: [AMBER] protein folding Carlos Simmerling (Thu Nov 05 2020 - 08:38:04 PST)
  - [AMBER] Fwd: Re: protein folding h_sahakyan.mb.sci.am (Fri Nov 06 2020 - 06:02:34 PST)
[AMBER] using bridgebyatom keyword Samuel Holmes (Thu Nov 05 2020 - 10:22:47 PST)
- Re: [AMBER] using bridgebyatom keyword Daniel Roe (Sat Nov 07 2020 - 04:54:43 PST)
[AMBER] installing pmemd.cuda (Amber20, WSL2) Lucy Yang (Thu Nov 05 2020 - 20:46:31 PST)
- Re: [AMBER] installing pmemd.cuda (Amber20, WSL2) Lucy Yang (Thu Nov 05 2020 - 23:35:54 PST)
[AMBER] Help on understanding the errors Ayesha Fatima (Fri Nov 06 2020 - 00:23:22 PST)
- Re: [AMBER] Help on understanding the errors Dr. Anselm Horn (Fri Nov 06 2020 - 02:48:47 PST)
  - Re: [AMBER] Help on understanding the errors Ayesha Fatima (Fri Nov 06 2020 - 03:02:13 PST)
    - Re: [AMBER] Help on understanding the errors Bill Ross (Fri Nov 06 2020 - 03:06:43 PST)
    - Re: [AMBER] Help on understanding the errors Ayesha Fatima (Fri Nov 06 2020 - 03:14:36 PST)
    - Re: [AMBER] Help on understanding the errors Ayesha Fatima (Fri Nov 06 2020 - 03:21:18 PST)
[AMBER] CPPTRAJ printout auto-detected hbond donor/acceptor Gustaf Olsson (Fri Nov 06 2020 - 01:24:28 PST)
- Re: [AMBER] CPPTRAJ printout auto-detected hbond donor/acceptor Daniel Roe (Fri Nov 06 2020 - 05:53:37 PST)
  - Re: [AMBER] CPPTRAJ printout auto-detected hbond donor/acceptor Gustaf Olsson (Mon Nov 09 2020 - 00:40:53 PST)
    - Re: [AMBER] CPPTRAJ printout auto-detected hbond donor/acceptor Gustaf Olsson (Mon Nov 09 2020 - 00:45:26 PST)
    - Re: [AMBER] CPPTRAJ printout auto-detected hbond donor/acceptor Daniel Roe (Tue Nov 10 2020 - 06:26:32 PST)
    - Re: [AMBER] CPPTRAJ printout auto-detected hbond donor/acceptor Gustaf Olsson (Tue Nov 10 2020 - 23:46:37 PST)
[AMBER] protein domain "broken" MYRIAN TORRES RICO (Fri Nov 06 2020 - 02:45:06 PST)
- Re: [AMBER] protein domain "broken" Bill Ross (Fri Nov 06 2020 - 03:03:02 PST)
  - Re: [AMBER] protein domain "broken" MYRIAN TORRES RICO (Fri Nov 06 2020 - 03:21:48 PST)
    - Re: [AMBER] protein domain "broken" Dr. Anselm Horn (Fri Nov 06 2020 - 03:49:45 PST)
    - Re: [AMBER] protein domain "broken" MYRIAN TORRES RICO (Fri Nov 06 2020 - 04:11:56 PST)
    - Re: [AMBER] protein domain "broken" Carlos Simmerling (Fri Nov 06 2020 - 04:12:02 PST)
    - Re: [AMBER] protein domain "broken" MYRIAN TORRES RICO (Fri Nov 06 2020 - 04:39:16 PST)
    - Re: [AMBER] protein domain "broken" Dr. Anselm Horn (Fri Nov 06 2020 - 08:05:07 PST)
    - Re: [AMBER] protein domain "broken" MYRIAN TORRES RICO (Mon Nov 09 2020 - 00:52:22 PST)
    - Re: [AMBER] protein domain "broken" koushik kasavajhala (Mon Nov 09 2020 - 00:53:57 PST)
    - Re: [AMBER] protein domain "broken"m koushik kasavajhala (Mon Nov 09 2020 - 00:59:00 PST)
    - Re: [AMBER] protein domain "broken" koushik kasavajhala (Mon Nov 09 2020 - 01:00:20 PST)
- Re: [AMBER] protein domain "broken" Dr. Anselm Horn (Fri Nov 06 2020 - 03:03:22 PST)
  - Re: [AMBER] protein domain "broken" MYRIAN TORRES RICO (Fri Nov 06 2020 - 03:20:18 PST)
[AMBER] MMPBSA/GBSA Manisha (Fri Nov 06 2020 - 03:11:36 PST)
- Re: [AMBER] MMPBSA/GBSA Bill Ross (Fri Nov 06 2020 - 03:18:14 PST)
[AMBER] FEW: Linear interaction energy calculations. M RCC (Fri Nov 06 2020 - 03:55:46 PST)
[AMBER] Protein preparation error Ayesha Fatima (Fri Nov 06 2020 - 08:05:23 PST)
- Re: [AMBER] Protein preparation error David A Case (Fri Nov 06 2020 - 08:50:04 PST)
  - Re: [AMBER] Protein preparation error Ayesha Fatima (Fri Nov 06 2020 - 09:02:26 PST)
    - Re: [AMBER] Protein preparation error Ayesha Fatima (Fri Nov 06 2020 - 10:31:20 PST)
[AMBER] Discrepancy between interaction energy of amber coordinate trajectories of a system Prathit Chatterjee (Sat Nov 07 2020 - 05:19:17 PST)
- Re: [AMBER] Discrepancy between interaction energy of amber coordinate trajectories of a system Bill Ross (Sat Nov 07 2020 - 05:28:00 PST)
- Re: [AMBER] Discrepancy between interaction energy of amber coordinate trajectories of a system Carlos Simmerling (Sat Nov 07 2020 - 06:44:44 PST)
- Re: [AMBER] Discrepancy between interaction energy of amber coordinate trajectories of a system Prathit Chatterjee (Sun Nov 08 2020 - 19:41:40 PST)
  - Re: [AMBER] Discrepancy between interaction energy of amber coordinate trajectories of a system Carlos Simmerling (Mon Nov 09 2020 - 06:51:55 PST)
[AMBER] AMORPHOUS HEMICELLULOSE Pinky Mazumder (Sat Nov 07 2020 - 10:22:44 PST)
[AMBER] Amber 20 on AMD ryzen + Nvidia 30XX Jordi Bujons (Sun Nov 08 2020 - 10:20:17 PST)
- Re: [AMBER] Amber 20 on AMD ryzen + Nvidia 30XX Robert Konecny (Sun Nov 08 2020 - 13:08:59 PST)
- Re: [AMBER] Amber 20 on AMD ryzen + Nvidia 30XX Charo del Genio (Sun Nov 08 2020 - 13:26:56 PST)
- Re: [AMBER] Amber 20 on AMD ryzen + Nvidia 30XX Raman Preet Singh (Sun Nov 08 2020 - 23:20:57 PST)
- Re: [AMBER] Amber 20 on AMD ryzen + Nvidia 30XX Jordi Bujons (Wed Nov 11 2020 - 05:47:18 PST)
  - Re: [AMBER] Amber 20 on AMD ryzen + Nvidia 30XX Charo del Genio (Fri Nov 13 2020 - 04:17:28 PST)
  - Re: [AMBER] Amber 20 on AMD ryzen + Nvidia 30XX Jason Swails (Thu Nov 19 2020 - 16:34:20 PST)
[AMBER] Addition of polyatomic ions in Leap MADHUSMITA DEVI (Sun Nov 08 2020 - 20:57:21 PST)
- Re: [AMBER] Addition of polyatomic ions in Leap David A Case (Mon Nov 09 2020 - 05:40:09 PST)
- Re: [AMBER] Addition of polyatomic ions in Leap Bill Ross (Mon Nov 09 2020 - 06:54:22 PST)
[AMBER] CPPTRAJ returns 'Warning: Box center specified but no box information' Ikuo KURISAKI (Mon Nov 09 2020 - 22:35:21 PST)
- Re: [AMBER] CPPTRAJ returns 'Warning: Box center specified but no box information' Daniel Roe (Tue Nov 10 2020 - 06:20:54 PST)
[AMBER] iwrap/autoimage - analyses Gustaf Olsson (Tue Nov 10 2020 - 03:13:26 PST)
- Re: [AMBER] iwrap/autoimage - analyses Daniel Roe (Tue Nov 10 2020 - 06:19:32 PST)
  - Re: [AMBER] iwrap/autoimage - analyses Gustaf Olsson (Wed Nov 11 2020 - 00:27:10 PST)
[AMBER] FES (Ferredoxin) Amber Parameters Maghsoud, Yazdan (Tue Nov 10 2020 - 06:50:46 PST)
[AMBER] Query about generated (.pdb) files from GLYCAM Carbo builder Pinky Mazumder (Tue Nov 10 2020 - 11:51:59 PST)
- Re: [AMBER] Query about generated (.pdb) files from GLYCAM Carbo builder Gustaf Olsson (Tue Nov 10 2020 - 23:51:49 PST)
[AMBER] error input MYRIAN TORRES RICO (Wed Nov 11 2020 - 04:31:12 PST)
- Re: [AMBER] error input David A Case (Wed Nov 11 2020 - 05:44:02 PST)
  - Re: [AMBER] error input MYRIAN TORRES RICO (Wed Nov 11 2020 - 08:23:59 PST)
    - Re: [AMBER] error input Carlos Simmerling (Wed Nov 11 2020 - 08:35:16 PST)
    - Re: [AMBER] error input David A Case (Wed Nov 11 2020 - 19:30:32 PST)
    - Re: [AMBER] error input MYRIAN TORRES RICO (Thu Nov 12 2020 - 01:16:32 PST)
    - Re: [AMBER] error input David A Case (Thu Nov 12 2020 - 05:34:03 PST)
[AMBER] Changes in DNA sugar chilarity at NMR volume restrained simulation lomzov (Wed Nov 11 2020 - 21:45:02 PST)
- Re: [AMBER] Changes in DNA sugar chilarity at NMR volume restrained simulation David A Case (Thu Nov 12 2020 - 05:27:06 PST)
[AMBER] TI-Amber Ankita Tripathi (Thu Nov 12 2020 - 05:19:31 PST)
- Re: [AMBER] TI-Amber Ankita Tripathi (Sat Nov 14 2020 - 11:51:10 PST)
  - Re: [AMBER] TI-Amber Giorgos Lambrinidis (Sun Nov 15 2020 - 11:21:24 PST)
    - Re: [AMBER] TI-Amber Ankita Tripathi (Sun Nov 15 2020 - 11:31:58 PST)
    - Re: [AMBER] TI-Amber Giorgos Lambrinidis (Mon Nov 16 2020 - 00:18:42 PST)
    - Re: [AMBER] TI-Amber Ankita Tripathi (Tue Nov 17 2020 - 04:27:45 PST)
[AMBER] AMBER20, ff19SB and OPC Kanin Wichapong (Fri Nov 13 2020 - 02:57:49 PST)
- Re: [AMBER] AMBER20, ff19SB and OPC Stephan Schott (Sat Nov 14 2020 - 10:20:43 PST)
  - Re: [AMBER] AMBER20, ff19SB and OPC Liao (Sat Nov 14 2020 - 11:07:40 PST)
- Re: [AMBER] AMBER20, ff19SB and OPC Carlos Simmerling (Sat Nov 14 2020 - 10:38:52 PST)
  - Re: [AMBER] AMBER20, ff19SB and OPC Carlos Simmerling (Fri Nov 20 2020 - 04:24:18 PST)
[AMBER] How to correct the H atom direction in the HIE residue? 辛志宏 (Fri Nov 13 2020 - 05:41:02 PST)
- Re: [AMBER] How to correct the H atom direction in the HIE residue? Carlos Simmerling (Fri Nov 13 2020 - 05:45:39 PST)
- Re: [AMBER] How to correct the H atom direction in the HIE residue? Song, Lin (Fri Nov 13 2020 - 08:47:44 PST)
  - Re: [AMBER] How to correct the H atom direction in the HIE residue? Abdul-Rashid III Sampaco (Fri Nov 13 2020 - 10:32:27 PST)
- Re: [AMBER] How to correct the H atom direction in the HIE residue? Gustavo Seabra (Fri Nov 13 2020 - 10:42:49 PST)
  - Re: [AMBER] How to correct the H atom direction in the HIE residue? Carlos Simmerling (Fri Nov 13 2020 - 10:47:23 PST)
    - Re: [AMBER] How to correct the H atom direction in the HIE residue? Gustavo Seabra (Fri Nov 13 2020 - 10:50:15 PST)
- Re: [AMBER] How to correct the H atom direction in the HIE residue? 辛志宏 (Sat Nov 14 2020 - 05:24:07 PST)
[AMBER] Antechamber: Charge and dihedral issues Salman Zarrini (Fri Nov 13 2020 - 11:44:43 PST)
- [AMBER] Fwd: Antechamber: Charge and dihedral issues Salman Zarrini (Sun Nov 15 2020 - 10:46:12 PST)
- Re: [AMBER] Antechamber: Charge and dihedral issues David A Case (Mon Nov 16 2020 - 05:17:02 PST)
[AMBER] How to introduce repulsive force between ligands during simulation? 钟海洋 (Fri Nov 13 2020 - 23:49:58 PST)
[AMBER] GAFF.dat format: what does the second numeric column mean? Zhu Liang (Sat Nov 14 2020 - 09:35:40 PST)
- Re: [AMBER] GAFF.dat format: what does the second numeric column mean? Stephan Schott (Sat Nov 14 2020 - 09:46:35 PST)
  - Re: [AMBER] GAFF.dat format: what does the second numeric column mean? Zhu Liang (Sat Nov 14 2020 - 10:58:05 PST)
[AMBER] MMPBSA.py bad atom type: M1 error Vaibhav Dixit (Mon Nov 16 2020 - 01:23:00 PST)
- Re: [AMBER] MMPBSA.py bad atom type: M1 error Vaibhav Dixit (Thu Dec 03 2020 - 08:30:11 PST)
  - Re: [AMBER] MMPBSA.py bad atom type: M1 error Ray Luo (Thu Dec 03 2020 - 09:46:19 PST)
    - Re: [AMBER] MMPBSA.py bad atom type: M1 error Vaibhav Dixit (Thu Dec 03 2020 - 16:25:12 PST)
    - Re: [AMBER] MMPBSA.py bad atom type: M1 error Ray Luo (Thu Dec 03 2020 - 20:40:18 PST)
    - Re: [AMBER] MMPBSA.py bad atom type: M1 error Vaibhav Dixit (Thu Dec 03 2020 - 21:09:01 PST)
[AMBER] TI lambda scheduling file examples Debarati DasGupta (Mon Nov 16 2020 - 13:12:38 PST)
[AMBER] MCBP.py errors Seibold, Steve Allan (Mon Nov 16 2020 - 14:57:00 PST)
- Re: [AMBER] MCBP.py errors Pengfei Li (Fri Nov 20 2020 - 08:13:53 PST)
[AMBER] thermal averaging of properties Vaibhav Dixit (Tue Nov 17 2020 - 18:58:11 PST)
- Re: [AMBER] thermal averaging of properties David A Case (Wed Nov 18 2020 - 06:19:19 PST)
  - Re: [AMBER] thermal averaging of properties Vaibhav Dixit (Wed Nov 18 2020 - 06:24:34 PST)
[AMBER] FINAL RESULT MMPBSA QUERY Manisha (Tue Nov 17 2020 - 23:57:31 PST)
- Re: [AMBER] FINAL RESULT MMPBSA QUERY Ray Luo (Wed Nov 18 2020 - 21:47:25 PST)
[AMBER] ABMD NFE queries Victor Jun Yu Lim (Wed Nov 18 2020 - 01:40:38 PST)
- Re: [AMBER] ABMD NFE queries Feng Pan (Fri Dec 04 2020 - 17:31:31 PST)
[AMBER] Unsupported Cuda Version on Amber 20 Installation Setyanto Md (Wed Nov 18 2020 - 03:57:36 PST)
- Re: [AMBER] Unsupported Cuda Version on Amber 20 Installation David A Case (Wed Nov 18 2020 - 06:30:05 PST)
- Re: [AMBER] Unsupported Cuda Version on Amber 20 Installation viktor (Wed Nov 18 2020 - 06:31:08 PST)
  - Re: [AMBER] Unsupported Cuda Version on Amber 20 Installation Setyanto Md (Thu Nov 19 2020 - 15:35:15 PST)
    - Re: [AMBER] Unsupported Cuda Version on Amber 20 Installation David A Case (Thu Nov 19 2020 - 18:24:01 PST)
    - Re: [AMBER] Unsupported Cuda Version on Amber 20 Installation Setyanto Md (Thu Nov 19 2020 - 20:08:29 PST)
    - Re: [AMBER] Unsupported Cuda Version on Amber 20 Installation David A Case (Fri Nov 20 2020 - 04:58:36 PST)
    - Re: [AMBER] Unsupported Cuda Version on Amber 20 Installation Setyanto Md (Fri Nov 20 2020 - 06:59:42 PST)
[AMBER] cpptraj donor/acceptor definitions Gustaf Olsson (Wed Nov 18 2020 - 04:42:45 PST)
- Re: [AMBER] cpptraj donor/acceptor definitions Daniel Roe (Wed Nov 18 2020 - 06:06:44 PST)
  - Re: [AMBER] cpptraj donor/acceptor definitions Gustaf Olsson (Thu Nov 19 2020 - 02:46:00 PST)
    - Re: [AMBER] cpptraj donor/acceptor definitions Daniel Roe (Fri Nov 20 2020 - 08:13:27 PST)
    - Re: [AMBER] cpptraj donor/acceptor definitions Gustaf Olsson (Mon Nov 23 2020 - 00:11:56 PST)
    - Re: [AMBER] cpptraj donor/acceptor definitions Daniel Roe (Mon Nov 23 2020 - 05:50:11 PST)
    - Re: [AMBER] cpptraj donor/acceptor definitions Gustaf Olsson (Mon Nov 23 2020 - 06:25:26 PST)
    - Re: [AMBER] cpptraj donor/acceptor definitions Gustaf Olsson (Mon Nov 23 2020 - 06:51:37 PST)
    - Re: [AMBER] cpptraj donor/acceptor definitions Daniel Roe (Mon Nov 23 2020 - 06:56:08 PST)
    - Re: [AMBER] cpptraj donor/acceptor definitions Gustaf Olsson (Mon Nov 23 2020 - 08:22:49 PST)
[AMBER] pytraj Pietro ARONICA (Wed Nov 18 2020 - 09:03:45 PST)
- Re: [AMBER] pytraj Hai Nguyen (Wed Nov 18 2020 - 16:26:28 PST)
  - Re: [AMBER] pytraj Pietro ARONICA (Wed Nov 18 2020 - 20:22:27 PST)
    - Re: [AMBER] pytraj Hai Nguyen (Thu Nov 19 2020 - 06:43:48 PST)
    - Re: [AMBER] pytraj Pietro ARONICA (Mon Nov 23 2020 - 02:16:28 PST)
    - Re: [AMBER] pytraj Hai Nguyen (Mon Nov 23 2020 - 10:28:51 PST)
    - Re: [AMBER] pytraj Hai Nguyen (Mon Nov 23 2020 - 10:47:07 PST)
[AMBER] How can I solve the high RMS problem? 변진영 (Wed Nov 18 2020 - 22:50:09 PST)
- Re: [AMBER] How can I solve the high RMS problem? David A Case (Sun Nov 29 2020 - 10:45:07 PST)
[AMBER] jupyter notebook aishen (Wed Nov 18 2020 - 23:18:17 PST)
- Re: [AMBER] jupyter notebook Elvis Martis (Thu Nov 19 2020 - 00:35:30 PST)
- Re: [AMBER] jupyter notebook Hai Nguyen (Mon Nov 23 2020 - 17:59:56 PST)
[AMBER] Amber 18 GPU installation error Nagakumar Bharatham (Thu Nov 19 2020 - 00:56:13 PST)
- Re: [AMBER] Amber 18 GPU installation error Nagakumar Bharatham (Sun Nov 22 2020 - 23:13:30 PST)
[AMBER] Ubuntu version compatible for gpu installation of AMBER 18 Jenny 148 (Thu Nov 19 2020 - 02:26:57 PST)
- Re: [AMBER] Ubuntu version compatible for gpu installation of AMBER 18 aishen (Thu Nov 19 2020 - 03:57:12 PST)
[AMBER] molecule twisted in QM/MM simulation Qinghua Liao (Thu Nov 19 2020 - 04:26:01 PST)
- Re: [AMBER] molecule twisted in QM/MM simulation David A Case (Thu Nov 19 2020 - 08:00:25 PST)
  - Re: [AMBER] molecule twisted in QM/MM simulation Qinghua Liao (Sat Nov 21 2020 - 12:32:04 PST)
    - Re: [AMBER] molecule twisted in QM/MM simulation Goetz, Andreas (Sat Nov 21 2020 - 12:49:42 PST)
[AMBER] mdgx 'File not found' on macOS h.jolon.icloud.com (Thu Nov 19 2020 - 06:44:22 PST)
- Re: [AMBER] mdgx 'File not found' on macOS h.jolon.icloud.com (Thu Nov 19 2020 - 06:52:32 PST)
[AMBER] tinker_to_amber Michael Sonny Miller (Thu Nov 19 2020 - 13:47:09 PST)
- Re: [AMBER] tinker_to_amber Emmett Leddin (Wed Nov 25 2020 - 12:37:14 PST)
[AMBER] Question again Paul Keller (Thu Nov 19 2020 - 23:42:28 PST)
[AMBER] Amber 20 make install problem Bruno Cramer (Fri Nov 20 2020 - 06:13:41 PST)
- Re: [AMBER] Amber 20 make install problem David A Case (Sat Nov 21 2020 - 05:39:53 PST)
[AMBER] Regarding to the parameters setup in SMD simulation 辛志宏 (Sat Nov 21 2020 - 00:35:00 PST)
- Re: [AMBER] Regarding to the parameters setup in SMD simulation Feng Pan (Fri Dec 04 2020 - 17:38:11 PST)
[AMBER] antechamber error -sqm.out missing Bruno Cramer (Sat Nov 21 2020 - 04:58:27 PST)
- Re: [AMBER] antechamber error -sqm.out missing David A Case (Sat Nov 21 2020 - 05:53:17 PST)
[AMBER] Tail-to-tail peptide linker? Alexander Izvorski (Sat Nov 21 2020 - 21:53:50 PST)
- Re: [AMBER] Tail-to-tail peptide linker? David A Case (Sun Nov 22 2020 - 05:57:30 PST)
[AMBER] phi cremer MYRIAN TORRES RICO (Mon Nov 23 2020 - 04:26:51 PST)
- Re: [AMBER] phi cremer Daniel Roe (Wed Nov 25 2020 - 07:09:20 PST)
  - Re: [AMBER] phi cremer MYRIAN TORRES RICO (Wed Nov 25 2020 - 08:20:50 PST)
    - Re: [AMBER] phi cremer Daniel Roe (Fri Nov 27 2020 - 12:05:00 PST)
[AMBER] Installing AmberTools20 compile error Lennart Gundelach (Mon Nov 23 2020 - 22:55:45 PST)
- Re: [AMBER] Installing AmberTools20 compile error David A Case (Tue Nov 24 2020 - 05:13:11 PST)
  - Re: [AMBER] Installing AmberTools20 compile error Lennart Gundelach (Wed Nov 25 2020 - 04:47:32 PST)
[AMBER] MMPBSA.py: "fork()" system call to create a child process Lennart Gundelach (Mon Nov 23 2020 - 23:02:44 PST)
- Re: [AMBER] MMPBSA.py: "fork()" system call to create a child process David A Case (Tue Nov 24 2020 - 07:52:02 PST)
[AMBER] phi angle puckering MYRIAN TORRES RICO (Tue Nov 24 2020 - 00:45:52 PST)
[AMBER] System blows up when simulating under npt Amit Sharma (Asstt. Prof., MCARS) (Tue Nov 24 2020 - 03:04:38 PST)
- Re: [AMBER] System blows up when simulating under npt Carlos Simmerling (Tue Nov 24 2020 - 03:09:42 PST)
  - Re: [AMBER] System blows up when simulating under npt Juraj Dobias (Tue Nov 24 2020 - 03:35:06 PST)
  - Re: [AMBER] System blows up when simulating under npt Amit Sharma (Asstt. Prof., MCARS) (Tue Nov 24 2020 - 03:44:21 PST)
    - Re: [AMBER] System blows up when simulating under npt Carlos Simmerling (Tue Nov 24 2020 - 04:41:13 PST)
    - Re: [AMBER] System blows up when simulating under npt Daniel Roe (Wed Nov 25 2020 - 07:12:26 PST)
    - Re: [AMBER] System blows up when simulating under npt Carlos Simmerling (Wed Nov 25 2020 - 07:18:07 PST)
[AMBER] Using the rep.C0.pdb as a reference structure in RMSD analysis Soheila Shokrollahzade (Tue Nov 24 2020 - 07:56:42 PST)
- Re: [AMBER] Using the rep.C0.pdb as a reference structure in RMSD analysis Daniel Roe (Wed Nov 25 2020 - 07:18:33 PST)
[AMBER] Help in amber TI automation script Delwakkada Liyanage, Senal Dinuka (Tue Nov 24 2020 - 12:29:52 PST)
[AMBER] Fwd: System blows up when simulating under npt Amit Sharma (Asstt. Prof., MCARS) (Wed Nov 25 2020 - 09:15:47 PST)
- Re: [AMBER] Fwd: System blows up when simulating under npt Carlos Simmerling (Wed Nov 25 2020 - 09:21:19 PST)
  - Re: [AMBER] Fwd: System blows up when simulating under npt Bill Ross (Wed Nov 25 2020 - 18:12:04 PST)
[AMBER] AMBER 18 cuda installation error Mariangela Dametto (Wed Nov 25 2020 - 11:24:35 PST)
- Re: [AMBER] AMBER 18 cuda installation error Tru Huynh (Wed Nov 25 2020 - 14:40:24 PST)
- Re: [AMBER] AMBER 18 cuda installation error David A Case (Fri Nov 27 2020 - 05:14:08 PST)
  - Re: [AMBER] AMBER 18 cuda installation error Mariangela Dametto (Mon Nov 30 2020 - 04:25:25 PST)
  - Re: [AMBER] AMBER 18 cuda installation error accuratefreeenergy.gmail.com (Mon Nov 30 2020 - 05:06:20 PST)
[AMBER] Antechamber permissions issue Sam Walsworth (Researcher) (Thu Nov 26 2020 - 09:37:18 PST)
- Re: [AMBER] Antechamber permissions issue David A Case (Fri Nov 27 2020 - 04:57:29 PST)
  - Re: [AMBER] Antechamber permissions issue Sam Walsworth (Researcher) (Fri Nov 27 2020 - 06:37:44 PST)
    - Re: [AMBER] Antechamber permissions issue David A Case (Fri Nov 27 2020 - 14:10:34 PST)
    - Re: [AMBER] Antechamber permissions issue Sam Walsworth (Researcher) (Mon Nov 30 2020 - 02:22:36 PST)
    - Re: [AMBER] Antechamber permissions issue Sam Walsworth (Researcher) (Mon Nov 30 2020 - 02:48:13 PST)
    - Re: [AMBER] Antechamber permissions issue Sam Walsworth (Researcher) (Mon Nov 30 2020 - 03:23:56 PST)
[AMBER] Partial Charge with RESP (antechamber) Michele Vanini (Thu Nov 26 2020 - 09:53:57 PST)
- Re: [AMBER] Partial Charge with RESP (antechamber) David Cerutti (Thu Nov 26 2020 - 18:24:54 PST)
  - Re: [AMBER] Partial Charge with RESP (antechamber) Dr. Anselm Horn (Fri Nov 27 2020 - 00:36:54 PST)
    - Re: [AMBER] Partial Charge with RESP (antechamber) Michele Vanini (Fri Nov 27 2020 - 01:12:37 PST)
[AMBER] An error during NPT/production (GPU run) Женя Елизарова (Thu Nov 26 2020 - 10:05:33 PST)
- Re: [AMBER] An error during NPT/production (GPU run) David A Case (Fri Nov 27 2020 - 05:04:41 PST)
  - Re: [AMBER] An error during NPT/production (GPU run) Женя Елизарова (Sat Nov 28 2020 - 00:10:09 PST)
    - Re: [AMBER] An error during NPT/production (GPU run) David A Case (Sun Nov 29 2020 - 10:39:39 PST)
    - Re: [AMBER] An error during NPT/production (GPU run) Женя Елизарова (Sun Nov 29 2020 - 22:09:24 PST)
    - Re: [AMBER] An error during NPT/production (GPU run) David A Case (Fri Dec 04 2020 - 08:13:15 PST)
    - Re: [AMBER] An error during NPT/production (GPU run) David Cerutti (Wed Dec 09 2020 - 00:49:59 PST)
    - Re: [AMBER] An error during NPT/production (GPU run) Женя Елизарова (Fri Dec 11 2020 - 05:43:29 PST)
    - Re: [AMBER] An error during NPT/production (GPU run) David Cerutti (Fri Dec 11 2020 - 06:56:45 PST)
    - Re: [AMBER] An error during NPT/production (GPU run) David Cerutti (Mon Dec 14 2020 - 16:31:50 PST)
[AMBER] md simulation error Kehinde Idowu (Fri Nov 27 2020 - 08:41:08 PST)
- Re: [AMBER] md simulation error David A Case (Fri Nov 27 2020 - 14:14:23 PST)
  - Re: [AMBER] md simulation error Kehinde Idowu (Sat Nov 28 2020 - 11:34:22 PST)
    - Re: [AMBER] md simulation error David A Case (Sun Nov 29 2020 - 10:19:59 PST)
[AMBER] AMBER20 TI calculations Debarati DasGupta (Fri Nov 27 2020 - 09:15:49 PST)
- Re: [AMBER] AMBER20 TI calculations Adrian Roitberg (Fri Nov 27 2020 - 09:21:09 PST)
[AMBER] FW: AMBER20 TI calculations Debarati DasGupta (Fri Nov 27 2020 - 09:52:37 PST)
[AMBER] fail when run pmem.cuda Carlos (Sat Nov 28 2020 - 01:04:07 PST)
- Re: [AMBER] fail when run pmem.cuda David A Case (Sun Nov 29 2020 - 10:35:13 PST)
  - Re: [AMBER] fail when run pmem.cuda Carlos (Sun Nov 29 2020 - 21:56:43 PST)
[AMBER] Effective Way To Perform Molecular Dynamics Simulation Erdem Yeler (Sat Nov 28 2020 - 15:20:56 PST)
- Re: [AMBER] Effective Way To Perform Molecular Dynamics Simulation Carlos Simmerling (Sun Nov 29 2020 - 03:32:53 PST)
[AMBER] question about gaps Gordon Richard Chalmers (Sat Nov 28 2020 - 19:43:05 PST)
- Re: [AMBER] question about gaps David A Case (Sun Nov 29 2020 - 10:26:03 PST)
  - Re: [AMBER] question about gaps Gordon Richard Chalmers (Sun Nov 29 2020 - 10:41:30 PST)
[AMBER] TI electrostatic free energy Franz Waibl (Mon Nov 30 2020 - 06:34:44 PST)
- Re: [AMBER] TI electrostatic free energy David A Case (Mon Nov 30 2020 - 10:10:18 PST)
  - Re: [AMBER] TI electrostatic free energy Franz Waibl (Tue Dec 01 2020 - 04:57:37 PST)
[AMBER] pmemd.cuda: error while loading shared libraries: libgfortran.so.4: cannot open shared object file: No such file or directory Sruthi Sudhakar (Tue Dec 01 2020 - 05:29:39 PST)
- Re: [AMBER] pmemd.cuda: error while loading shared libraries: libgfortran.so.4: cannot open shared object file: No such file or directory David A Case (Tue Dec 01 2020 - 06:18:40 PST)
Re: [AMBER] TI electrostatic free energy] David A Case (Tue Dec 01 2020 - 06:08:32 PST)
- Re: [AMBER] TI electrostatic free energy] Franz Waibl (Tue Dec 01 2020 - 07:24:44 PST)
  - Re: [AMBER] TI electrostatic free energy] David A Case (Tue Dec 01 2020 - 11:07:04 PST)
[AMBER] MMBSA.py.MPI installation Jose Manuel Granadino Roldán (Tue Dec 01 2020 - 07:40:03 PST)
- Re: [AMBER] MMBSA.py.MPI installation David A Case (Fri Dec 04 2020 - 08:15:45 PST)
  - Re: [AMBER] MMBSA.py.MPI installation Jose Manuel Granadino Roldán (Fri Dec 04 2020 - 23:39:47 PST)
    - Re: [AMBER] MMBSA.py.MPI installation David A Case (Sat Dec 05 2020 - 06:03:00 PST)
[AMBER] C++ Programmer Position Lachele Foley (Tue Dec 01 2020 - 09:57:01 PST)
[AMBER] amber 20 compilation problem Jordi Bujons (Tue Dec 01 2020 - 10:14:23 PST)
- Re: [AMBER] amber 20 compilation problem David A Case (Tue Dec 01 2020 - 17:59:57 PST)
[AMBER] question about dihedral angles Gordon Richard Chalmers (Tue Dec 01 2020 - 15:43:50 PST)
- Re: [AMBER] question about dihedral angles Gordon Richard Chalmers (Tue Dec 01 2020 - 15:49:46 PST)
- Re: [AMBER] question about dihedral angles David A Case (Tue Dec 01 2020 - 18:07:17 PST)
  - Re: [AMBER] question about dihedral angles Gordon Richard Chalmers (Tue Dec 01 2020 - 20:36:39 PST)
  - Re: [AMBER] question about dihedral angles Karl Kirschner (Tue Dec 01 2020 - 23:53:32 PST)
    - Re: [AMBER] question about dihedral angles David A Case (Wed Dec 02 2020 - 05:51:08 PST)
    - Re: [AMBER] question about dihedral angles Gordon Richard Chalmers (Wed Dec 02 2020 - 06:03:51 PST)
    - Re: [AMBER] question about dihedral angles Gordon Richard Chalmers (Wed Dec 02 2020 - 06:10:11 PST)
    - Re: [AMBER] question about dihedral angles Daniel Roe (Wed Dec 02 2020 - 08:50:58 PST)
    - Re: [AMBER] question about dihedral angles Gordon Richard Chalmers (Wed Dec 02 2020 - 14:41:45 PST)
    - Re: [AMBER] question about dihedral angles Carlos Simmerling (Wed Dec 02 2020 - 14:52:48 PST)
    - Re: [AMBER] question about dihedral angles Gordon Richard Chalmers (Wed Dec 02 2020 - 14:58:04 PST)
    - Re: [AMBER] question about dihedral angles Gordon Richard Chalmers (Wed Dec 02 2020 - 15:08:32 PST)
    - Re: [AMBER] question about dihedral angles Gordon Richard Chalmers (Wed Dec 02 2020 - 16:01:59 PST)
    - Re: [AMBER] question about dihedral angles Bill Ross (Wed Dec 02 2020 - 19:15:51 PST)
    - Re: [AMBER] question about dihedral angles Bill Ross (Wed Dec 02 2020 - 19:20:38 PST)
    - Re: [AMBER] question about dihedral angles Bill Ross (Wed Dec 02 2020 - 19:25:14 PST)
    - Re: [AMBER] question about dihedral angles Gordon Richard Chalmers (Wed Dec 02 2020 - 19:57:56 PST)
    - Re: [AMBER] question about dihedral angles Gordon Richard Chalmers (Wed Dec 02 2020 - 20:09:17 PST)
- Re: [AMBER] question about dihedral angles Gordon Richard Chalmers (Wed Dec 02 2020 - 06:03:54 PST)
[AMBER] Imaging issue in DNA - cpptraj Satyaseelan C (Tue Dec 01 2020 - 23:17:22 PST)
- Re: [AMBER] Imaging issue in DNA - cpptraj Gustaf Olsson (Wed Dec 02 2020 - 00:12:38 PST)
  - Re: [AMBER] Imaging issue in DNA - cpptraj Dr. Anselm Horn (Wed Dec 02 2020 - 01:23:56 PST)
    - Re: [AMBER] Imaging issue in DNA - cpptraj lomzov (Wed Dec 02 2020 - 02:04:52 PST)
    - Re: [AMBER] Imaging issue in DNA - cpptraj David A Case (Wed Dec 02 2020 - 05:55:09 PST)
    - Re: [AMBER] Imaging issue in DNA - cpptraj Satyaseelan C (Fri Dec 04 2020 - 09:47:10 PST)
    - Re: [AMBER] Imaging issue in DNA - cpptraj Daniel Roe (Fri Dec 04 2020 - 12:27:25 PST)
[AMBER] Terminal O5'/O3' for nucleosides in ff86? Kenneth Huang (Wed Dec 02 2020 - 14:27:09 PST)
- Re: [AMBER] Terminal O5'/O3' for nucleosides in ff86? David A Case (Thu Dec 03 2020 - 05:57:40 PST)
  - Re: [AMBER] Terminal O5'/O3' for nucleosides in ff86? Kenneth Huang (Thu Dec 03 2020 - 09:02:47 PST)
[AMBER] How to use GAFF2? Alexander Izvorski (Wed Dec 02 2020 - 17:41:08 PST)
- Re: [AMBER] How to use GAFF2? Gustaf Olsson (Thu Dec 03 2020 - 00:14:33 PST)
- Re: [AMBER] How to use GAFF2? David A Case (Thu Dec 03 2020 - 05:44:42 PST)
  - Re: [AMBER] How to use GAFF2? Alexander Izvorski (Thu Dec 03 2020 - 22:11:29 PST)
    - Re: [AMBER] How to use GAFF2? Alexander Izvorski (Thu Dec 03 2020 - 22:13:37 PST)
    - Re: [AMBER] How to use GAFF2? David A Case (Fri Dec 04 2020 - 05:29:33 PST)
    - Re: [AMBER] How to use GAFF2? Alexander Izvorski (Fri Dec 04 2020 - 11:24:17 PST)
[AMBER] Unsupported CUDA version 11.1 detected during the installation of AMBER20.CUDA 贺俊宏 (Wed Dec 02 2020 - 19:29:29 PST)
- Re: [AMBER] Unsupported CUDA version 11.1 detected during the installation of AMBER20.CUDA David A Case (Thu Dec 03 2020 - 05:47:52 PST)
  - Re: [AMBER] Unsupported CUDA version 11.1 detected during the installation of AMBER20.CUDA 贺俊宏 (Thu Dec 03 2020 - 19:06:29 PST)
    - Re: [AMBER] Unsupported CUDA version 11.1 detected during the installation of AMBER20.CUDA David A Case (Fri Dec 04 2020 - 05:24:01 PST)
    - Re: [AMBER] Unsupported CUDA version 11.1 detected during the installation of AMBER20.CUDA 贺俊宏 (Sun Dec 06 2020 - 17:46:20 PST)
    - Re: [AMBER] Unsupported CUDA version 11.1 detected during the installation of AMBER20.CUDA David A Case (Mon Dec 07 2020 - 05:45:45 PST)
    - Re: [AMBER] Unsupported CUDA version 11.1 detected during the installation of AMBER20.CUDA 贺俊宏 (Mon Dec 07 2020 - 18:32:44 PST)
    - Re: [AMBER] Unsupported CUDA version 11.1 detected during the installation of AMBER20.CUDA David A Case (Tue Dec 08 2020 - 05:59:52 PST)
    - Re: [AMBER] Unsupported CUDA version 11.1 detected during the installation of AMBER20.CUDA 贺俊宏 (Tue Dec 08 2020 - 22:50:17 PST)
[AMBER] Mixing Force Constants In DISANG Files Sharif Nada (Wed Dec 02 2020 - 20:01:35 PST)
- Re: [AMBER] Mixing Force Constants In DISANG Files Carlos Simmerling (Thu Dec 03 2020 - 02:14:38 PST)
  - Re: [AMBER] Mixing Force Constants In DISANG Files Sharif Nada (Thu Dec 03 2020 - 10:43:15 PST)
    - [AMBER] Effects of scalpha in softcore runs Sharif Nada (Sun Dec 06 2020 - 17:03:43 PST)
[AMBER] app.run_mmpbsa() and mdout files were not created divyabharathi korlepara (Wed Dec 02 2020 - 23:39:11 PST)
- Re: [AMBER] app.run_mmpbsa() and mdout files were not created David A Case (Thu Dec 03 2020 - 05:54:21 PST)
  - Re: [AMBER] app.run_mmpbsa() and mdout files were not created divyabharathi korlepara (Thu Dec 03 2020 - 07:02:23 PST)
[AMBER] MMPBSA.py.MPI parallel installation using run_cmake divyabharathi korlepara (Thu Dec 03 2020 - 10:43:50 PST)
- Re: [AMBER] MMPBSA.py.MPI parallel installation using run_cmake David A Case (Fri Dec 04 2020 - 08:09:22 PST)
[AMBER] Calculation halted while running simulation angad sharma (Thu Dec 03 2020 - 11:36:21 PST)
- Re: [AMBER] Calculation halted while running simulation Carlos Simmerling (Thu Dec 03 2020 - 12:44:27 PST)
- Re: [AMBER] Calculation halted while running simulation David A Case (Fri Dec 04 2020 - 05:18:32 PST)
[AMBER] Missing Iron (Fe) DFTB3 parameters for QM/MM simulation of Enzyme Hafiz Saqib Ali (Thu Dec 03 2020 - 15:04:54 PST)
- Re: [AMBER] Missing Iron (Fe) DFTB3 parameters for QM/MM simulation of Enzyme Goetz, Andreas (Tue Jan 12 2021 - 16:15:54 PST)
[AMBER] G quadruplex ions minimization Jisha B (Thu Dec 03 2020 - 15:06:25 PST)
- Re: [AMBER] G quadruplex ions minimization Juraj Dobias (Fri Dec 04 2020 - 03:48:33 PST)
  - Re: [AMBER] G quadruplex ions minimization Bill Ross (Fri Dec 04 2020 - 09:53:49 PST)
    - Re: [AMBER] G quadruplex ions minimization Jiri Sponer (Fri Dec 04 2020 - 11:20:49 PST)
Re: [AMBER] amber 20 compilation problem (David A Case) Jordi Bujons (Fri Dec 04 2020 - 09:30:28 PST)
[AMBER] Question about atomic charges Pinky Mazumder (Fri Dec 04 2020 - 11:15:44 PST)
- Re: [AMBER] Question about atomic charges Bill Ross (Fri Dec 04 2020 - 11:19:13 PST)
- Re: [AMBER] Question about atomic charges Carlos Simmerling (Fri Dec 04 2020 - 11:45:32 PST)
[AMBER] Identifying the equilibrated production region of a MD simulation trajectory Leena Aggarwal (Fri Dec 04 2020 - 23:37:42 PST)
- Re: [AMBER] Identifying the equilibrated production region of a MD simulation trajectory Carlos Simmerling (Sat Dec 05 2020 - 18:51:47 PST)
  - Re: [AMBER] Identifying the equilibrated production region of a MD simulation trajectory Thomas Cheatham (Sat Dec 05 2020 - 21:52:07 PST)
[AMBER] error after simulation angad sharma (Mon Dec 07 2020 - 08:44:37 PST)
- Re: [AMBER] error after simulation Thomas Cheatham (Mon Dec 07 2020 - 12:40:07 PST)
[AMBER] lj1264 in vacuum Brian Radak (Tue Dec 08 2020 - 13:29:25 PST)
- Re: [AMBER] lj1264 in vacuum Brian Radak (Fri Dec 11 2020 - 13:07:36 PST)
  - Re: [AMBER] lj1264 in vacuum Pengfei Li (Sat Jan 16 2021 - 19:21:56 PST)
[AMBER] Regarding Ions renumbering. DHEERAJ CHITARA (Wed Dec 09 2020 - 12:12:18 PST)
- Re: [AMBER] Regarding Ions renumbering. Gustaf Olsson (Wed Dec 09 2020 - 01:26:15 PST)
  - Re: [AMBER] Regarding Ions renumbering. Christina Bergonzo (Wed Dec 09 2020 - 05:47:25 PST)
[AMBER] Regarding Gaussian Accelerated MD Sruthi Sudhakar (Wed Dec 09 2020 - 03:16:12 PST)
- [AMBER] Regarding Gaussian Accelerated MD Sruthi Sudhakar (Thu Dec 10 2020 - 04:29:10 PST)
[AMBER] Negative values in RDF analyses? Gustaf Olsson (Wed Dec 09 2020 - 05:44:49 PST)
- Re: [AMBER] Negative values in RDF analyses? Daniel Roe (Thu Dec 10 2020 - 03:07:46 PST)
[AMBER] B-ob-si-c3 dihedral parametization RESP/Scan problem Erdem Yeler (Thu Dec 10 2020 - 02:22:30 PST)
[AMBER] errors including MPI, OpenM, cuda OFF with run_cmake in Amber20 Vaibhav Dixit (Wed Dec 09 2020 - 23:26:05 PST)
- Re: [AMBER] errors including MPI, OpenM, cuda OFF with run_cmake in Amber20 Raman Preet Singh (Thu Dec 10 2020 - 02:58:08 PST)
  - Re: [AMBER] errors including MPI, OpenM, cuda OFF with run_cmake in Amber20 Vaibhav Dixit (Wed Dec 09 2020 - 23:31:22 PST)
    - Re: [AMBER] errors including MPI, OpenM, cuda OFF with run_cmake in Amber20 Raman Preet Singh (Thu Dec 10 2020 - 04:29:08 PST)
    - Re: [AMBER] errors including MPI, OpenM, cuda OFF with run_cmake in Amber20 Vaibhav Dixit (Thu Dec 10 2020 - 01:16:57 PST)
    - Re: [AMBER] errors including MPI, OpenM, cuda OFF with run_cmake in Amber20 Raman Preet Singh (Thu Dec 10 2020 - 04:52:57 PST)
    - Re: [AMBER] errors including MPI, OpenM, cuda OFF with run_cmake in Amber20 Vaibhav Dixit (Thu Dec 10 2020 - 01:27:01 PST)
- Re: [AMBER] errors including MPI, OpenM, cuda OFF with run_cmake in Amber20 David A Case (Thu Dec 10 2020 - 05:19:22 PST)
  - Re: [AMBER] errors including MPI, OpenM, cuda OFF with run_cmake in Amber20 Vaibhav Dixit (Thu Dec 10 2020 - 07:48:25 PST)
    - Re: [AMBER] errors including MPI, OpenM, cuda OFF with run_cmake in Amber20 Vaibhav Dixit (Thu Dec 10 2020 - 08:45:34 PST)
[AMBER] How to proceed if system charge is non-zero and non-integral Amit Sharma (Asstt. Prof., MCARS) (Thu Dec 10 2020 - 04:37:14 PST)
- Re: [AMBER] How to proceed if system charge is non-zero and non-integral David A Case (Thu Dec 10 2020 - 05:21:58 PST)
[AMBER] Bug AmberTools20 parallel installation Arsene Marian Alain (Thu Dec 10 2020 - 04:46:00 PST)
- Re: [AMBER] Bug AmberTools20 parallel installation David A Case (Thu Dec 10 2020 - 05:31:07 PST)
[AMBER] Charged species with antechamber Sam Walsworth (Researcher) (Thu Dec 10 2020 - 07:01:34 PST)
- Re: [AMBER] Charged species with antechamber Dr. Anselm Horn (Thu Dec 10 2020 - 07:48:59 PST)
- Re: [AMBER] Charged species with antechamber David A Case (Thu Dec 10 2020 - 10:00:45 PST)
  - Re: [AMBER] Charged species with antechamber Sam Walsworth (Researcher) (Thu Dec 10 2020 - 11:18:27 PST)
    - Re: [AMBER] Charged species with antechamber David A Case (Sat Dec 12 2020 - 18:39:12 PST)
- Re: [AMBER] Charged species with antechamber Gustaf Olsson (Fri Dec 11 2020 - 00:15:48 PST)
[AMBER] tleap building a peptide Seibold, Steve Allan (Thu Dec 10 2020 - 08:48:09 PST)
- Re: [AMBER] tleap building a peptide Carlos Simmerling (Thu Dec 10 2020 - 09:08:34 PST)
  - Re: [AMBER] tleap building a peptide Seibold, Steve Allan (Thu Dec 10 2020 - 10:03:33 PST)
- Re: [AMBER] tleap building a peptide Bill Ross (Thu Dec 10 2020 - 09:30:42 PST)
- Re: [AMBER] tleap building a peptide David A Case (Thu Dec 10 2020 - 10:03:49 PST)
  - Re: [AMBER] tleap building a peptide Seibold, Steve Allan (Thu Dec 10 2020 - 10:11:02 PST)
[AMBER] how to convert (psf) to (prmtop) and (incprd) Pinky Mazumder (Thu Dec 10 2020 - 22:40:38 PST)
- Re: [AMBER] how to convert (psf) to (prmtop) and (incprd) David A Case (Fri Dec 11 2020 - 06:08:52 PST)
  - Re: [AMBER] how to convert (psf) to (prmtop) and (incprd) Pinky Mazumder (Sat Dec 12 2020 - 12:05:44 PST)
    - Re: [AMBER] how to convert (psf) to (prmtop) and (incprd) Carlos Simmerling (Sat Dec 12 2020 - 12:52:18 PST)
    - Re: [AMBER] how to convert (psf) to (prmtop) and (incprd) Pinky Mazumder (Sat Dec 12 2020 - 12:55:22 PST)
    - Re: [AMBER] how to convert (psf) to (prmtop) and (incprd) David A Case (Sat Dec 12 2020 - 18:59:32 PST)
[AMBER] Box info not found in prmtop file Amit Sharma (Asstt. Prof., MCARS) (Fri Dec 11 2020 - 05:13:38 PST)
- Re: [AMBER] Box info not found in prmtop file Carlos Simmerling (Fri Dec 11 2020 - 05:29:22 PST)
  - Re: [AMBER] Box info not found in prmtop file Amit Sharma (Asstt. Prof., MCARS) (Fri Dec 11 2020 - 06:52:32 PST)
    - Re: [AMBER] Box info not found in prmtop file Carlos Simmerling (Fri Dec 11 2020 - 07:28:39 PST)
    - Re: [AMBER] Box info not found in prmtop file Amit Sharma (Asstt. Prof., MCARS) (Fri Dec 11 2020 - 08:01:07 PST)
    - Re: [AMBER] Box info not found in prmtop file Carlos Simmerling (Fri Dec 11 2020 - 08:08:15 PST)
    - Re: [AMBER] Box info not found in prmtop file Amit Sharma (Asstt. Prof., MCARS) (Fri Dec 11 2020 - 08:26:43 PST)
    - Re: [AMBER] Box info not found in prmtop file Carlos Simmerling (Fri Dec 11 2020 - 09:09:36 PST)
    - Re: [AMBER] Box info not found in prmtop file Amit Sharma (Asstt. Prof., MCARS) (Fri Dec 11 2020 - 10:21:23 PST)
    - Re: [AMBER] Box info not found in prmtop file Carlos Simmerling (Fri Dec 11 2020 - 10:43:13 PST)
    - Re: [AMBER] Box info not found in prmtop file Amit Sharma (Asstt. Prof., MCARS) (Fri Dec 11 2020 - 12:18:59 PST)
[AMBER] S2 order parameter not being calculated in IRED analysis. Chetna Tyagi (Fri Dec 11 2020 - 05:14:44 PST)
- Re: [AMBER] S2 order parameter not being calculated in IRED analysis. Gupta, Arun (Tue Dec 15 2020 - 01:11:47 PST)
- Re: [AMBER] S2 order parameter not being calculated in IRED analysis. Daniel Roe (Tue Dec 15 2020 - 07:13:59 PST)
[AMBER] tleap seems Si atom as S ... I don't know why Erdem Yeler (Fri Dec 11 2020 - 13:58:01 PST)
- Re: [AMBER] tleap seems Si atom as S ... I don't know why David A Case (Sat Dec 12 2020 - 18:50:50 PST)
  - Re: [AMBER] tleap seems Si atom as S ... I don't know why Erdem Yeler (Thu Dec 17 2020 - 04:59:56 PST)
[AMBER] MMPBSA.py.MPI not build in Amber20 Setyanto Md (Sat Dec 12 2020 - 05:08:54 PST)
- Re: [AMBER] MMPBSA.py.MPI not build in Amber20 Elvis Martis (Sat Dec 12 2020 - 05:39:47 PST)
  - Re: [AMBER] MMPBSA.py.MPI not build in Amber20 Setyanto Md (Sat Dec 12 2020 - 16:56:31 PST)
    - Re: [AMBER] MMPBSA.py.MPI not build in Amber20 Li,Haoxi (Mon Jan 04 2021 - 09:13:32 PST)
    - Re: [AMBER] MMPBSA.py.MPI not build in Amber20 Elvis A F Martis (Mon Jan 04 2021 - 09:19:43 PST)
    - Re: [AMBER] MMPBSA.py.MPI not build in Amber20 David A Case (Fri Jan 08 2021 - 07:10:57 PST)
    - Re: [AMBER] MMPBSA.py.MPI not build in Amber20 Elvis A F Martis (Fri Jan 08 2021 - 07:35:44 PST)
    - Re: [AMBER] MMPBSA.py.MPI not build in Amber20 Li,Haoxi (Fri Jan 08 2021 - 14:05:16 PST)
[AMBER] Hydrogen bond and Dissociation constant Kehinde Idowu (Sat Dec 12 2020 - 06:32:28 PST)
- Re: [AMBER] Hydrogen bond and Dissociation constant David A Case (Sat Dec 12 2020 - 18:55:36 PST)
[AMBER] How to specify SHAKE on all bonds including hydrogen in the input file Amit Sharma (Asstt. Prof., MCARS) (Sat Dec 12 2020 - 10:46:18 PST)
- Re: [AMBER] How to specify SHAKE on all bonds including hydrogen in the input file Carlos Simmerling (Sat Dec 12 2020 - 10:56:54 PST)
- Re: [AMBER] How to specify SHAKE on all bonds including hydrogen in the input file Bill Ross (Sat Dec 12 2020 - 10:57:32 PST)
[AMBER] refene2.solvent_energies refene2.dielc2_energies and refene2.dielc2.solvent_energies Luis Simon (Sat Dec 12 2020 - 15:03:01 PST)
[AMBER] parameters for benzene, pyerene, anthracene, and coronene Boutheïna KERKENI (Sat Dec 12 2020 - 15:26:24 PST)
- Re: [AMBER] parameters for benzene, pyerene, anthracene, and coronene Boutheïna KERKENI (Sun Dec 13 2020 - 05:47:39 PST)
- Re: [AMBER] parameters for benzene, pyerene, anthracene, and coronene David A Case (Mon Dec 14 2020 - 06:05:40 PST)
  - Re: [AMBER] parameters for benzene, pyerene, anthracene, and coronene Carlos Simmerling (Mon Dec 14 2020 - 06:15:19 PST)
    - Re: [AMBER] parameters for benzene, pyerene, anthracene, and coronene Boutheïna KERKENI (Mon Dec 14 2020 - 06:34:45 PST)
    - Re: [AMBER] parameters for benzene, pyerene, anthracene, and coronene Carlos Simmerling (Mon Dec 14 2020 - 06:36:33 PST)
[AMBER] Error in Quasi-Harmonic Entropy Setyanto Md (Sat Dec 12 2020 - 19:09:05 PST)
- Re: [AMBER] Error in Quasi-Harmonic Entropy David A Case (Mon Dec 14 2020 - 06:08:17 PST)
  - Re: [AMBER] Error in Quasi-Harmonic Entropy Setyanto Md (Sun Dec 20 2020 - 19:12:37 PST)
[AMBER] Stacking distance in CPPTRAJ Athena N (Sun Dec 13 2020 - 03:18:28 PST)
- Re: [AMBER] Stacking distance in CPPTRAJ Carlos Simmerling (Sun Dec 13 2020 - 03:49:43 PST)
  - Re: [AMBER] Stacking distance in CPPTRAJ Daniel Roe (Tue Dec 15 2020 - 07:30:32 PST)
[AMBER] Disulphide bonds Gustaf Olsson (Mon Dec 14 2020 - 00:54:19 PST)
- Re: [AMBER] Disulphide bonds Bill Ross (Mon Dec 14 2020 - 04:52:45 PST)
  - Re: [AMBER] Disulphide bonds Gustaf Olsson (Mon Dec 14 2020 - 05:27:18 PST)
    - Re: [AMBER] Disulphide bonds Carlos Simmerling (Mon Dec 14 2020 - 06:02:09 PST)
  - Re: [AMBER] Disulphide bonds David A Case (Mon Dec 14 2020 - 06:11:25 PST)
    - Re: [AMBER] Disulphide bonds Gustaf Olsson (Mon Dec 14 2020 - 23:43:17 PST)
[AMBER] RMSD Protein-DNA complex Plot Manisha (Mon Dec 14 2020 - 01:16:06 PST)
- Re: [AMBER] RMSD Protein-DNA complex Plot Bill Ross (Mon Dec 14 2020 - 04:15:20 PST)
  - Re: [AMBER] RMSD Protein-DNA complex Plot Dr. Anselm Horn (Tue Dec 15 2020 - 00:38:54 PST)
[AMBER] MMPBSA error with receptor prmtop but not clear how to fix Amber20 Vaibhav Dixit (Sun Dec 13 2020 - 22:31:52 PST)
- Re: [AMBER] MMPBSA error with receptor prmtop but not clear how to fix Amber20 Elvis Martis (Mon Dec 14 2020 - 02:13:45 PST)
  - Re: [AMBER] MMPBSA error with receptor prmtop but not clear how to fix Amber20 Vaibhav Dixit (Sun Dec 13 2020 - 22:56:04 PST)
    - Re: [AMBER] MMPBSA error with receptor prmtop but not clear how to fix Amber20 Elvis Martis (Mon Dec 14 2020 - 02:46:22 PST)
    - Re: [AMBER] MMPBSA error with receptor prmtop but not clear how to fix Amber20 Vaibhav Dixit (Sun Dec 13 2020 - 23:52:46 PST)
    - Re: [AMBER] MMPBSA error with receptor prmtop but not clear how to fix Amber20 Elvis Martis (Mon Dec 14 2020 - 03:35:02 PST)
    - Re: [AMBER] MMPBSA error with receptor prmtop but not clear how to fix Amber20 Elvis Martis (Mon Dec 14 2020 - 03:35:49 PST)
    - Re: [AMBER] MMPBSA error with receptor prmtop but not clear how to fix Amber20 Vaibhav Dixit (Mon Dec 14 2020 - 01:05:21 PST)
    - Re: [AMBER] MMPBSA error with receptor prmtop but not clear how to fix Amber20 Elvis Martis (Mon Dec 14 2020 - 04:53:25 PST)
    - Re: [AMBER] MMPBSA error with receptor prmtop but not clear how to fix Amber20 Vaibhav Dixit (Mon Dec 14 2020 - 01:31:57 PST)
    - Re: [AMBER] MMPBSA error with receptor prmtop but not clear how to fix Amber20 Elvis Martis (Mon Dec 14 2020 - 05:31:40 PST)
- Re: [AMBER] MMPBSA error with receptor prmtop but not clear how to fix Amber20 Vaibhav Dixit (Mon Dec 14 2020 - 19:56:32 PST)
  - Re: [AMBER] MMPBSA error with receptor prmtop but not clear how to fix Amber20 Elvis Martis (Mon Dec 14 2020 - 23:33:19 PST)
    - Re: [AMBER] MMPBSA error with receptor prmtop but not clear how to fix Amber20 Vaibhav Dixit (Mon Dec 14 2020 - 21:38:04 PST)
- Re: [AMBER] MMPBSA error with receptor prmtop but not clear how to fix Amber20 Vaibhav Dixit (Tue Dec 15 2020 - 01:36:25 PST)
[AMBER] parameters for benzene, pyerene, anthracene, and coronene Boutheïna KERKENI (Mon Dec 14 2020 - 02:20:11 PST)
[AMBER] box_dims question Carlos (Mon Dec 14 2020 - 13:06:02 PST)
- Re: [AMBER] box_dims question Daniel Roe (Thu Dec 17 2020 - 09:10:36 PST)
[AMBER] error finding MMPBSA.py.MPI redirected to amber18 instead of amber20 Vaibhav Dixit (Tue Dec 15 2020 - 09:04:26 PST)
- Re: [AMBER] error finding MMPBSA.py.MPI redirected to amber18 instead of amber20 Ray Luo (Tue Dec 15 2020 - 10:23:59 PST)
  - Re: [AMBER] error finding MMPBSA.py.MPI redirected to amber18 instead of amber20 Vaibhav Dixit (Tue Dec 15 2020 - 18:13:40 PST)
    - Re: [AMBER] error finding MMPBSA.py.MPI redirected to amber18 instead of amber20 Vaibhav Dixit (Fri Dec 18 2020 - 01:33:23 PST)
    - Re: [AMBER] error finding MMPBSA.py.MPI redirected to amber18 instead of amber20 Ray Luo (Fri Dec 18 2020 - 08:36:42 PST)
    - Re: [AMBER] error finding MMPBSA.py.MPI redirected to amber18 instead of amber20 Vaibhav Dixit (Fri Dec 18 2020 - 08:50:03 PST)
[AMBER] VDWAALS energy shoots up suddenly during transition from Minimization to Heating Chris Lee (Tue Dec 15 2020 - 15:00:32 PST)
- Re: [AMBER] VDWAALS energy shoots up suddenly during transition from Minimization to Heating Bill Ross (Tue Dec 15 2020 - 19:44:36 PST)
- Re: [AMBER] VDWAALS energy shoots up suddenly during transition from Minimization to Heating David A Case (Wed Dec 16 2020 - 06:02:54 PST)
  - Re: [AMBER] VDWAALS energy shoots up suddenly during transition from Minimization to Heating Matias Machado (Wed Dec 16 2020 - 06:45:58 PST)
    - Re: [AMBER] VDWAALS energy shoots up suddenly during transition from Minimization to Heating Matias Machado (Wed Dec 16 2020 - 07:18:44 PST)
Re: [AMBER] Amber 4/pre Amber 7 binaries? Bill Ross (Tue Dec 15 2020 - 20:20:18 PST)
- Re: [AMBER] Amber 4/pre Amber 7 binaries? Kenneth Huang (Tue Dec 15 2020 - 21:54:59 PST)
  - Re: [AMBER] Amber 4/pre Amber 7 binaries? Ryan Novosielski (Wed Dec 16 2020 - 09:35:08 PST)
    - Re: [AMBER] Amber 4/pre Amber 7 binaries? Kenneth Huang (Wed Dec 16 2020 - 12:49:02 PST)
    - Re: [AMBER] Amber 4/pre Amber 7 binaries? Ryan Novosielski (Wed Dec 16 2020 - 13:02:18 PST)
    - Re: [AMBER] Amber 4/pre Amber 7 binaries? Kenneth Huang (Wed Dec 16 2020 - 14:29:53 PST)
    - Re: [AMBER] Amber 4/pre Amber 7 binaries? Ryan Novosielski (Wed Dec 16 2020 - 14:36:33 PST)
    - Re: [AMBER] Amber 4/pre Amber 7 binaries? Bill Ross (Wed Dec 16 2020 - 14:54:17 PST)
    - Re: [AMBER] Amber 4/pre Amber 7 binaries? Bill Ross (Wed Dec 16 2020 - 15:00:29 PST)
- Re: [AMBER] Amber 4/pre Amber 7 binaries? David A Case (Wed Dec 16 2020 - 06:16:53 PST)
  - Re: [AMBER] Amber 4/pre Amber 7 binaries? Kenneth Huang (Wed Dec 16 2020 - 09:02:23 PST)
[AMBER] Getting error while compile AMBER20 with cuda support Raman Jangra (Tue Dec 15 2020 - 21:16:10 PST)
- Re: [AMBER] Getting error while compile AMBER20 with cuda support Bill Ross (Tue Dec 15 2020 - 21:24:05 PST)
- Re: [AMBER] Getting error while compile AMBER20 with cuda support David A Case (Wed Dec 16 2020 - 06:08:07 PST)
- Re: [AMBER] Getting error while compile AMBER20 with cuda support Raman Jangra (Sun Dec 20 2020 - 20:24:37 PST)
[AMBER] PROTEIN-DNA rmsd plot Syeda Amna Arshi (Tue Dec 15 2020 - 22:20:02 PST)
- Re: [AMBER] PROTEIN-DNA rmsd plot David A Case (Wed Dec 16 2020 - 06:11:58 PST)
- Re: [AMBER] PROTEIN-DNA rmsd plot Syeda Amna Arshi (Sun Dec 20 2020 - 23:09:01 PST)
  - Re: [AMBER] PROTEIN-DNA rmsd plot David A Case (Mon Dec 21 2020 - 05:12:57 PST)
  - Re: [AMBER] PROTEIN-DNA rmsd plot Syeda Amna Arshi (Wed Dec 23 2020 - 22:32:55 PST)
    - Re: [AMBER] PROTEIN-DNA rmsd plot Daniel Roe (Wed Dec 30 2020 - 06:43:05 PST)
    - Re: [AMBER] PROTEIN-DNA rmsd plot Syeda Amna Arshi (Thu Dec 31 2020 - 01:54:41 PST)
    - Re: [AMBER] PROTEIN-DNA rmsd plot Dr. Anselm Horn (Thu Dec 31 2020 - 02:21:29 PST)
    - Re: [AMBER] PROTEIN-DNA rmsd plot Syeda Amna Arshi (Mon Jan 04 2021 - 00:56:57 PST)
    - Re: [AMBER] PROTEIN-DNA rmsd plot David A Case (Mon Jan 04 2021 - 05:19:42 PST)
    - Re: [AMBER] PROTEIN-DNA rmsd plot Daniel Roe (Mon Jan 04 2021 - 06:09:10 PST)
    - Re: [AMBER] PROTEIN-DNA rmsd plot Syeda Amna Arshi (Mon Jan 04 2021 - 22:23:40 PST)
- Re: [AMBER] PROTEIN-DNA rmsd plot Syeda Amna Arshi (Thu Dec 31 2020 - 01:53:45 PST)
  - Re: [AMBER] PROTEIN-DNA rmsd plot David A Case (Thu Dec 31 2020 - 18:47:41 PST)
[AMBER] ambpdb or other scipt? Jisha B (Tue Dec 15 2020 - 23:23:23 PST)
- Re: [AMBER] ambpdb or other scipt? Bill Ross (Tue Dec 15 2020 - 23:26:43 PST)
  - Re: [AMBER] ambpdb or other scipt? Jisha B (Tue Dec 15 2020 - 23:29:16 PST)
    - Re: [AMBER] ambpdb or other scipt? Bill Ross (Tue Dec 15 2020 - 23:38:30 PST)
[AMBER] Top Mode Contribution in PCA Analysis. DHEERAJ CHITARA (Wed Dec 16 2020 - 03:53:36 PST)
- Re: [AMBER] Top Mode Contribution in PCA Analysis. Daniel Roe (Thu Dec 17 2020 - 09:08:46 PST)
  - Re: [AMBER] Top Mode Contribution in PCA Analysis. DHEERAJ CHITARA (Fri Dec 18 2020 - 09:47:02 PST)
[AMBER] positive Amber FF energies? Vaibhav Dixit (Wed Dec 16 2020 - 08:31:55 PST)
- Re: [AMBER] positive Amber FF energies? Jason Swails (Wed Dec 16 2020 - 19:59:35 PST)
  - Re: [AMBER] positive Amber FF energies? Thomas Cheatham (Wed Dec 16 2020 - 20:29:17 PST)
    - Re: [AMBER] positive Amber FF energies? Vaibhav Dixit (Wed Dec 16 2020 - 19:28:46 PST)
[AMBER] MMPBSA.py.MPI installation divyabharathi korlepara (Wed Dec 16 2020 - 10:10:14 PST)
- Re: [AMBER] MMPBSA.py.MPI installation Elvis Martis (Wed Dec 16 2020 - 17:32:19 PST)
  - Re: [AMBER] MMPBSA.py.MPI installation Jaime Rubio Martinez (Thu Dec 17 2020 - 00:40:45 PST)
  - Re: [AMBER] MMPBSA.py.MPI installation divyabharathi korlepara (Fri Dec 18 2020 - 04:47:08 PST)
    - Re: [AMBER] MMPBSA.py.MPI installation Elvis Martis (Fri Dec 18 2020 - 05:16:58 PST)
  - Re: [AMBER] MMPBSA.py.MPI installation divyabharathi korlepara (Fri Dec 18 2020 - 04:53:20 PST)
[AMBER] Antechamber vs R.E.D. Server Sam Walsworth (Researcher) (Wed Dec 16 2020 - 11:30:54 PST)
- Re: [AMBER] Antechamber vs R.E.D. Server Dr. Anselm Horn (Thu Dec 17 2020 - 07:56:31 PST)
  - Re: [AMBER] Antechamber vs R.E.D. Server Sam Walsworth (Researcher) (Thu Dec 17 2020 - 11:37:28 PST)
    - Re: [AMBER] Antechamber vs R.E.D. Server Dr. Anselm Horn (Fri Dec 18 2020 - 01:49:33 PST)
[AMBER] nc files contain lesser number of atoms compared to prmtop Sruthi Sudhakar (Wed Dec 16 2020 - 22:16:53 PST)
- Re: [AMBER] nc files contain lesser number of atoms compared to prmtop Daniel Roe (Thu Dec 17 2020 - 09:03:26 PST)
[AMBER] Renumbering Gustaf Olsson (Thu Dec 17 2020 - 02:29:26 PST)
- Re: [AMBER] Renumbering Gustaf Olsson (Thu Dec 17 2020 - 02:45:01 PST)
  - Re: [AMBER] Renumbering Carlos Simmerling (Thu Dec 17 2020 - 03:50:04 PST)
    - Re: [AMBER] Renumbering Gustaf Olsson (Thu Dec 17 2020 - 04:52:25 PST)
- Re: [AMBER] Renumbering Daniel Roe (Thu Dec 17 2020 - 08:58:53 PST)
  - Re: [AMBER] Renumbering Gustaf Olsson (Thu Dec 17 2020 - 10:07:54 PST)
[AMBER] Using sander.MPI in Docker Erdem Yeler (Thu Dec 17 2020 - 05:07:15 PST)
Re: [AMBER] AMBER Digest, Vol 3215, Issue 1 David A Case (Thu Dec 17 2020 - 05:21:27 PST)
[AMBER] cpptraj warnings topology flags being ignored Vaibhav Dixit (Thu Dec 17 2020 - 06:35:36 PST)
- Re: [AMBER] cpptraj warnings topology flags being ignored David A Case (Thu Dec 17 2020 - 08:35:00 PST)
  - Re: [AMBER] cpptraj warnings topology flags being ignored Daniel Roe (Thu Dec 17 2020 - 09:13:07 PST)
[AMBER] Conversion .rst to .inpcrd Eduardo R. Almeida (Thu Dec 17 2020 - 08:19:59 PST)
- Re: [AMBER] Conversion .rst to .inpcrd Daniel Roe (Thu Dec 17 2020 - 09:06:18 PST)
  - Re: [AMBER] Conversion .rst to .inpcrd Eduardo R. Almeida (Fri Dec 18 2020 - 05:30:37 PST)
[AMBER] pbsa calcerror Neha Gandhi (Thu Dec 17 2020 - 13:28:59 PST)
- Re: [AMBER] pbsa calcerror Ray Luo (Thu Dec 17 2020 - 17:07:40 PST)
- Re: [AMBER] pbsa calcerror Neha Gandhi (Thu Dec 17 2020 - 21:34:59 PST)
  - Re: [AMBER] pbsa calcerror Ray Luo (Fri Dec 18 2020 - 15:46:08 PST)
[AMBER] strange jump in the rmsd protein complex Vaibhav Dixit (Thu Dec 17 2020 - 23:36:25 PST)
- Re: [AMBER] strange jump in the rmsd protein complex Vaibhav Dixit (Fri Dec 18 2020 - 03:43:46 PST)
  - Re: [AMBER] strange jump in the rmsd protein complex Daniel Roe (Fri Dec 18 2020 - 06:16:02 PST)
    - Re: [AMBER] strange jump in the rmsd protein complex Vaibhav Dixit (Fri Dec 18 2020 - 08:47:21 PST)
[AMBER] Cannot minimize structure with sander George Yacu (Fri Dec 18 2020 - 09:56:28 PST)
- Re: [AMBER] Cannot minimize structure with sander David A Case (Fri Dec 18 2020 - 11:08:30 PST)
[AMBER] Molecular Dynamics Tutorial for Membrane-Bound Proteins in Amber ANDRES IBACACHE (Fri Dec 18 2020 - 12:22:05 PST)
[AMBER] Minimization Time Limit Error with Sander Aanshi Gandhi (Fri Dec 18 2020 - 12:39:57 PST)
- Re: [AMBER] Minimization Time Limit Error with Sander Carlos Simmerling (Fri Dec 18 2020 - 12:46:09 PST)
  - Re: [AMBER] Minimization Time Limit Error with Sander Aanshi Gandhi (Fri Dec 18 2020 - 12:59:33 PST)
    - Re: [AMBER] Minimization Time Limit Error with Sander Carlos Simmerling (Fri Dec 18 2020 - 13:09:09 PST)
    - Re: [AMBER] Minimization Time Limit Error with Sander Aanshi Gandhi (Fri Dec 18 2020 - 13:19:01 PST)
    - Re: [AMBER] Minimization Time Limit Error with Sander Carlos Simmerling (Fri Dec 18 2020 - 13:27:29 PST)
    - Re: [AMBER] Minimization Time Limit Error with Sander Bill Ross (Fri Dec 18 2020 - 14:28:58 PST)
    - Re: [AMBER] Minimization Time Limit Error with Sander David A Case (Fri Dec 18 2020 - 14:10:57 PST)
[AMBER] AMBER20 on Ubuntu 20.04 and CUDA 11.2? Rudy Richardson (Fri Dec 18 2020 - 15:45:57 PST)
- Re: [AMBER] AMBER20 on Ubuntu 20.04 and CUDA 11.2? David A Case (Sat Dec 19 2020 - 06:36:32 PST)
  - Re: [AMBER] AMBER20 on Ubuntu 20.04 and CUDA 11.2? Rudy Richardson (Sat Dec 19 2020 - 10:41:52 PST)
[AMBER] Cpptraj (post-processing rotation) Женя Елизарова (Mon Dec 21 2020 - 02:08:01 PST)
- Re: [AMBER] Cpptraj (post-processing rotation) Kenneth Huang (Mon Dec 21 2020 - 10:57:16 PST)
- Re: [AMBER] Cpptraj (post-processing rotation) Daniel Roe (Wed Dec 23 2020 - 06:40:13 PST)
[AMBER] question pmemd.cuda MYRIAN TORRES RICO (Mon Dec 21 2020 - 04:45:58 PST)
- Re: [AMBER] question pmemd.cuda Elvis Martis (Mon Dec 21 2020 - 04:54:22 PST)
[AMBER] Query on some old sander inputs (dele, idiel, dielc) Kenneth Huang (Mon Dec 21 2020 - 08:00:37 PST)
- Re: [AMBER] Query on some old sander inputs (dele, idiel, dielc) David A Case (Sat Dec 26 2020 - 05:58:47 PST)
  - Re: [AMBER] Query on some old sander inputs (dele, idiel, dielc) Kenneth Huang (Wed Dec 30 2020 - 08:43:49 PST)
    - Re: [AMBER] Query on some old sander inputs (dele, idiel, dielc) David Cerutti (Wed Dec 30 2020 - 09:17:02 PST)
    - Re: [AMBER] Query on some old sander inputs (dele, idiel, dielc) Kenneth Huang (Wed Dec 30 2020 - 11:55:36 PST)
[AMBER] ff15ipq-m force field for protein mimetics Lillian Chong (Mon Dec 21 2020 - 12:18:59 PST)
- [AMBER] ff15ipq-m force field for protein mimetics Lillian Chong (Tue Jan 12 2021 - 05:46:41 PST)
[AMBER] crystallographic plane Pinky Mazumder (Mon Dec 21 2020 - 21:11:50 PST)
- Re: [AMBER] crystallographic plane Bill Ross (Mon Dec 21 2020 - 21:30:10 PST)
- Re: [AMBER] crystallographic plane Daniel Roe (Wed Dec 30 2020 - 06:39:58 PST)
[AMBER] How to graph CPPTRAJ in (ns) instead of timesteps Maghsoud, Yazdan (Tue Dec 22 2020 - 10:51:03 PST)
- Re: [AMBER] How to graph CPPTRAJ in (ns) instead of timesteps Maria Nagan (Tue Dec 22 2020 - 11:09:04 PST)
- Re: [AMBER] How to graph CPPTRAJ in (ns) instead of timesteps Daniel Roe (Wed Dec 23 2020 - 06:38:32 PST)
[AMBER] Cation-pi interaction characterization Ramanathan Rajesh (Tue Dec 22 2020 - 11:43:58 PST)
- Re: [AMBER] Cation-pi interaction characterization Daniel Roe (Wed Dec 30 2020 - 06:49:51 PST)
Re: [AMBER] MD run on GPU machine Carlos Simmerling (Tue Dec 22 2020 - 14:38:31 PST)
[AMBER] Electrostatic distance plot Sruthi Sudhakar (Tue Dec 22 2020 - 19:58:14 PST)
- Re: [AMBER] Electrostatic distance plot David A Case (Wed Dec 23 2020 - 06:07:26 PST)
  - Re: [AMBER] Electrostatic distance plot Sruthi Sudhakar (Wed Dec 23 2020 - 06:19:34 PST)
    - Re: [AMBER] Electrostatic distance plot Carlos Simmerling (Wed Dec 23 2020 - 07:03:54 PST)
    - Re: [AMBER] Electrostatic distance plot Sruthi Sudhakar (Wed Dec 23 2020 - 07:44:33 PST)
    - Re: [AMBER] Electrostatic distance plot Adrian Roitberg (Wed Dec 23 2020 - 07:47:49 PST)
    - Re: [AMBER] Electrostatic distance plot Maria Nagan (Wed Dec 23 2020 - 07:56:57 PST)
    - Re: [AMBER] Electrostatic distance plot Daniel Roe (Wed Dec 30 2020 - 06:45:59 PST)
[AMBER] how to know degrees of system angad sharma (Wed Dec 23 2020 - 07:09:33 PST)
- Re: [AMBER] how to know degrees of system Carlos Simmerling (Wed Dec 23 2020 - 07:35:16 PST)
[AMBER] Parmed error Jisha B (Wed Dec 23 2020 - 09:55:50 PST)
- Re: [AMBER] Parmed error Elvis Martis (Wed Dec 23 2020 - 20:27:57 PST)
- Re: [AMBER] Parmed error Hai Nguyen (Thu Dec 24 2020 - 09:12:05 PST)
[AMBER] CPU versus GPU Divergent Minimizations Matthew Guberman-Pfeffer (Thu Dec 24 2020 - 00:22:37 PST)
- Re: [AMBER] CPU versus GPU Divergent Minimizations David A Case (Thu Dec 24 2020 - 05:57:07 PST)
[AMBER] Position of the solute (center of mass) in the simulation box Eduardo R. Almeida (Thu Dec 24 2020 - 05:07:04 PST)
- Re: [AMBER] Position of the solute (center of mass) in the simulation box Matias Machado (Thu Dec 24 2020 - 13:57:13 PST)
  - Re: [AMBER] Position of the solute (center of mass) in the simulation box Matias Machado (Thu Dec 24 2020 - 14:14:06 PST)
- Re: [AMBER] Position of the solute (center of mass) in the simulation box Daniel Roe (Wed Dec 30 2020 - 06:41:22 PST)
[AMBER] Has anyone tried and succeeded at compiling Amber 18 with CUDA 11? Homeo Morphism (Fri Dec 25 2020 - 13:23:40 PST)
[AMBER] Reweighting error in Gaussian accelerated MD- PyReweighting-1D.py Athena N (Sat Dec 26 2020 - 14:17:03 PST)
[AMBER] Problem forming circular DNA Sebastian S (Sun Dec 27 2020 - 07:52:52 PST)
- Re: [AMBER] Problem forming circular DNA David A Case (Mon Dec 28 2020 - 06:07:21 PST)
  - Re: [AMBER] Problem forming circular DNA Sebastian S (Mon Dec 28 2020 - 07:29:35 PST)
[AMBER] SHAKE problem Jonathan Church (Sun Dec 27 2020 - 21:26:32 PST)
- Re: [AMBER] SHAKE problem Bill Ross (Mon Dec 28 2020 - 00:08:04 PST)
  - Re: [AMBER] SHAKE problem Jonathan Church (Tue Dec 29 2020 - 08:58:48 PST)
[AMBER] Amber20 Installation Error Li,Haoxi (Mon Dec 28 2020 - 17:32:22 PST)
- Re: [AMBER] Amber20 Installation Error David A Case (Tue Dec 29 2020 - 06:47:10 PST)
- Re: [AMBER] Amber20 Installation Error David A Case (Wed Dec 30 2020 - 09:21:04 PST)
  - Re: [AMBER] Amber20 Installation Error Li,Haoxi (Wed Dec 30 2020 - 17:49:24 PST)
    - Re: [AMBER] Amber20 Installation Error David A Case (Thu Dec 31 2020 - 05:42:28 PST)
[AMBER] CMP-GMP Holly Freedman (Tue Dec 29 2020 - 14:31:59 PST)
- Re: [AMBER] CMP-GMP David A Case (Tue Dec 29 2020 - 18:26:54 PST)
  - Re: [AMBER] CMP-GMP Holly Freedman (Wed Dec 30 2020 - 07:48:22 PST)
    - Re: [AMBER] CMP-GMP David A Case (Wed Dec 30 2020 - 09:26:49 PST)
    - Re: [AMBER] CMP-GMP Holly Freedman (Wed Dec 30 2020 - 11:49:15 PST)
[AMBER] cremer MYRIAN TORRES RICO (Wed Dec 30 2020 - 04:48:16 PST)
- Re: [AMBER] cremer David A Case (Wed Dec 30 2020 - 06:10:29 PST)
  - Re: [AMBER] cremer MYRIAN TORRES RICO (Thu Dec 31 2020 - 02:46:25 PST)
    - Re: [AMBER] cremer Daniel Roe (Thu Dec 31 2020 - 06:10:00 PST)
    - Re: [AMBER] cremer MYRIAN TORRES RICO (Thu Dec 31 2020 - 06:32:28 PST)
    - Re: [AMBER] cremer David A Case (Thu Dec 31 2020 - 07:20:05 PST)
    - Re: [AMBER] cremer MYRIAN TORRES RICO (Thu Dec 31 2020 - 08:15:33 PST)
[AMBER] doubt frames simulation MYRIAN TORRES RICO (Thu Dec 31 2020 - 05:02:44 PST)
- Re: [AMBER] doubt frames simulation Daniel Roe (Thu Dec 31 2020 - 06:11:53 PST)
[AMBER] Fixed the problem of AMBER20 run with pmemd.cuda with CUDA11.1 and 3080 GPU card liu kai (Thu Dec 31 2020 - 05:34:05 PST)
- Re: [AMBER] Fixed the problem of AMBER20 run with pmemd.cuda with CUDA11.1 and 3080 GPU card Ross Walker (Thu Dec 31 2020 - 07:14:57 PST)
  - Re: [AMBER] Fixed the problem of AMBER20 run with pmemd.cuda with CUDA11.1 and 3080 GPU card Setyanto Md (Sun Jan 03 2021 - 23:47:14 PST)
- Re: [AMBER] Fixed the problem of AMBER20 run with pmemd.cuda with CUDA11.1 and 3080 GPU card David A Case (Thu Dec 31 2020 - 18:41:02 PST)
- Re: [AMBER] Fixed the problem of AMBER20 run with pmemd.cuda with CUDA11.1 and 3080 GPU card Mohd Farid Ismail (Fri Jan 01 2021 - 16:54:56 PST)
- Re: [AMBER] Fixed the problem of AMBER20 run with pmemd.cuda with CUDA11.1 and 3080 GPU card liu kai (Sat Jan 02 2021 - 18:35:20 PST)
[AMBER] Problem with cudaMalloc GpuBuffer Allocate failed out of memory assawin daducale (Fri Jan 01 2021 - 11:07:25 PST)
- Re: [AMBER] Problem with cudaMalloc GpuBuffer Allocate failed out of memory Elvis A F Martis (Fri Jan 01 2021 - 20:36:06 PST)
[AMBER] doubt frames simulation MYRIAN TORRES RICO (Sat Jan 02 2021 - 05:00:50 PST)
- Re: [AMBER] doubt frames simulation Carlos Simmerling (Sat Jan 02 2021 - 05:26:24 PST)
- Re: [AMBER] doubt frames simulation David A Case (Sat Jan 02 2021 - 05:55:59 PST)
  - Re: [AMBER] doubt frames simulation MYRIAN TORRES RICO (Sat Jan 02 2021 - 06:01:08 PST)
[AMBER] Problem with PB calculation CAVALLARO MATTIA (Sat Jan 02 2021 - 06:24:20 PST)
[AMBER] Generating LJ paramters of divalent copper ions angad sharma (Sat Jan 02 2021 - 10:15:43 PST)
- Re: [AMBER] Generating LJ paramters of divalent copper ions David A Case (Sun Jan 03 2021 - 06:09:27 PST)
[AMBER] do you know Gordon Richard Chalmers (Sun Jan 03 2021 - 04:57:50 PST)
- Re: [AMBER] do you know David A Case (Sun Jan 03 2021 - 06:16:11 PST)
[AMBER] error... MYRIAN TORRES RICO (Sun Jan 03 2021 - 09:19:00 PST)
- Re: [AMBER] error... Bill Ross (Sun Jan 03 2021 - 11:07:33 PST)
  - Re: [AMBER] error... MYRIAN TORRES RICO (Sun Jan 03 2021 - 11:43:56 PST)
    - Re: [AMBER] error... Bill Ross (Sun Jan 03 2021 - 13:14:18 PST)
- Re: [AMBER] error... Carlos Simmerling (Sun Jan 03 2021 - 13:29:47 PST)
  - Re: [AMBER] error... MYRIAN TORRES RICO (Mon Jan 04 2021 - 02:09:35 PST)
    - Re: [AMBER] error... Carlos Simmerling (Mon Jan 04 2021 - 05:38:24 PST)
[AMBER] SMD & MULTI_RMSD Fabian Glaser (Sun Jan 03 2021 - 09:47:21 PST)
- Re: [AMBER] SMD & MULTI_RMSD Feng Pan (Sun Jan 03 2021 - 12:50:54 PST)
  - Re: [AMBER] SMD & MULTI_RMSD Fabian Glaser (Sun Jan 03 2021 - 13:09:16 PST)
    - Re: [AMBER] SMD & MULTI_RMSD Feng Pan (Tue Jan 05 2021 - 06:43:15 PST)
    - Re: [AMBER] SMD & MULTI_RMSD Fabian Glaser (Mon Jan 11 2021 - 06:19:10 PST)
    - Re: [AMBER] SMD & MULTI_RMSD Feng Pan (Mon Jan 11 2021 - 12:11:07 PST)
[AMBER] Setting PME cutoff in Crystal Simulations Matthew Guberman-Pfeffer (Sun Jan 03 2021 - 12:37:09 PST)
- Re: [AMBER] Setting PME cutoff in Crystal Simulations David A Case (Mon Jan 04 2021 - 05:14:34 PST)
- Re: [AMBER] Setting PME cutoff in Crystal Simulations Matthew Guberman-Pfeffer (Tue Jan 05 2021 - 01:37:22 PST)
  - Re: [AMBER] Setting PME cutoff in Crystal Simulations David A Case (Tue Jan 05 2021 - 05:35:13 PST)
  - Re: [AMBER] Setting PME cutoff in Crystal Simulations Matthew Guberman-Pfeffer (Wed Jan 06 2021 - 00:33:05 PST)
    - Re: [AMBER] Setting PME cutoff in Crystal Simulations David A Case (Wed Jan 06 2021 - 06:22:13 PST)
- Re: [AMBER] Setting PME cutoff in Crystal Simulations Matthew Guberman-Pfeffer (Tue Jan 05 2021 - 19:03:59 PST)
[AMBER] How to apply GLYCAM Parameters Matthew Guberman-Pfeffer (Sun Jan 03 2021 - 12:45:07 PST)
[AMBER] Amber 20 installation, problems with the testing phase Beatriz Gomes Guimaraes (Mon Jan 04 2021 - 13:20:26 PST)
- Re: [AMBER] Amber 20 installation, problems with the testing phase David A Case (Tue Jan 05 2021 - 05:26:19 PST)
  - Re: [AMBER] Amber 20 installation, problems with the testing phase Beatriz Gomes Guimaraes (Tue Jan 05 2021 - 06:31:46 PST)
    - Re: [AMBER] Amber 20 installation, problems with the testing phase David A Case (Tue Jan 05 2021 - 19:37:14 PST)
    - Re: [AMBER] Amber 20 installation, problems with the testing phase Beatriz Gomes Guimaraes (Wed Jan 06 2021 - 08:17:11 PST)
    - Re: [AMBER] Amber 20 installation, problems with the testing phase Beatriz Gomes Guimaraes (Thu Jan 07 2021 - 05:21:44 PST)
    - Re: [AMBER] Amber 20 installation, problems with the testing phase David A Case (Thu Jan 07 2021 - 12:44:27 PST)
    - Re: [AMBER] Amber 20 installation, problems with the testing phase Beatriz Gomes Guimaraes (Thu Jan 07 2021 - 13:41:27 PST)
[AMBER] Error in the apr.py code - steered MD simulation Eduardo R. Almeida (Mon Jan 04 2021 - 19:29:23 PST)
[AMBER] cif to pdb Pinky Mazumder (Mon Jan 04 2021 - 20:19:22 PST)
- Re: [AMBER] cif to pdb David A Case (Tue Jan 05 2021 - 05:30:30 PST)
  - Re: [AMBER] cif to pdb Pinky Mazumder (Tue Jan 05 2021 - 23:07:49 PST)
- Re: [AMBER] cif to pdb Daniel Roe (Wed Jan 06 2021 - 02:18:54 PST)
[AMBER] Energy Evaluations Matthew Guberman-Pfeffer (Mon Jan 04 2021 - 20:51:42 PST)
- Re: [AMBER] Energy Evaluations Carlos Simmerling (Tue Jan 05 2021 - 04:37:36 PST)
- Re: [AMBER] Energy Evaluations Daniel Roe (Tue Jan 05 2021 - 08:14:15 PST)
[AMBER] tinker_to_amber Юлия Беляева (Tue Jan 05 2021 - 11:16:01 PST)
- Re: [AMBER] tinker_to_amber David A Case (Fri Jan 08 2021 - 06:57:54 PST)
[AMBER] NaN VDWAALS Error During Minimization Jatin Kashyap (Tue Jan 05 2021 - 16:55:17 PST)
- Re: [AMBER] NaN VDWAALS Error During Minimization David Cerutti (Tue Jan 05 2021 - 17:29:19 PST)
  - Re: [AMBER] NaN VDWAALS Error During Minimization Bill Ross (Tue Jan 05 2021 - 19:05:23 PST)
  - Re: [AMBER] NaN VDWAALS Error During Minimization Jatin Kashyap (Tue Jan 05 2021 - 19:18:47 PST)
    - Re: [AMBER] NaN VDWAALS Error During Minimization Bill Ross (Tue Jan 05 2021 - 19:45:56 PST)
    - Re: [AMBER] NaN VDWAALS Error During Minimization Jatin Kashyap (Tue Jan 05 2021 - 19:53:29 PST)
    - Re: [AMBER] NaN VDWAALS Error During Minimization Bill Ross (Tue Jan 05 2021 - 19:59:23 PST)
    - Re: [AMBER] NaN VDWAALS Error During Minimization Bill Ross (Tue Jan 05 2021 - 20:01:06 PST)
    - Re: [AMBER] NaN VDWAALS Error During Minimization Thomas Cheatham (Tue Jan 05 2021 - 20:33:17 PST)
    - Re: [AMBER] NaN VDWAALS Error During Minimization Thomas Cheatham (Tue Jan 05 2021 - 20:39:56 PST)
- Re: [AMBER] NaN VDWAALS Error During Minimization David A Case (Tue Jan 05 2021 - 19:44:39 PST)
  - Re: [AMBER] NaN VDWAALS Error During Minimization Jatin Kashyap (Tue Jan 05 2021 - 21:09:59 PST)
    - Re: [AMBER] NaN VDWAALS Error During Minimization Bill Ross (Tue Jan 05 2021 - 21:51:28 PST)
    - Re: [AMBER] NaN VDWAALS Error During Minimization Jatin Kashyap (Tue Jan 05 2021 - 22:28:52 PST)
    - Re: [AMBER] NaN VDWAALS Error During Minimization David Cerutti (Tue Jan 05 2021 - 22:36:39 PST)
    - Re: [AMBER] NaN VDWAALS Error During Minimization Bill Ross (Wed Jan 06 2021 - 00:48:17 PST)
    - Re: [AMBER] NaN VDWAALS Error During Minimization Jatin Kashyap (Thu Jan 07 2021 - 11:29:05 PST)
[AMBER] pytraj in python 3.9 Abdul-Rashid III Sampaco (Tue Jan 05 2021 - 20:54:53 PST)
- Re: [AMBER] pytraj in python 3.9 David A Case (Wed Jan 06 2021 - 06:29:39 PST)
  - Re: [AMBER] pytraj in python 3.9 Abdul-Rashid III Sampaco (Wed Jan 06 2021 - 19:53:50 PST)
[AMBER] Sander code doesn’t output trajectory files K Jan (Wed Jan 06 2021 - 04:58:23 PST)
- Re: [AMBER] Sander code doesn’t output trajectory files Carlos Simmerling (Wed Jan 06 2021 - 06:25:48 PST)
  - Re: [AMBER] Sander code doesn’t output trajectory files K Jan (Wed Jan 06 2021 - 06:57:16 PST)
    - Re: [AMBER] Sander code doesn’t output trajectory files Roitberg,Adrian E (Wed Jan 06 2021 - 07:00:44 PST)
    - Re: [AMBER] Sander code doesn’t output trajectory files K Jan (Wed Jan 06 2021 - 07:13:49 PST)
- Re: [AMBER] Sander code doesn’t output trajectory files David A Case (Wed Jan 06 2021 - 06:34:44 PST)
[AMBER] Fwd: copper RISM angad sharma (Wed Jan 06 2021 - 06:13:38 PST)
[AMBER] GB pairwise decomposition - Salt Bridge Tarsis (Wed Jan 06 2021 - 06:28:57 PST)
- Re: [AMBER] GB pairwise decomposition - Salt Bridge Carlos Simmerling (Wed Jan 06 2021 - 06:49:36 PST)
[AMBER] Bug in the Mol2 format: space converted into a new oxygen atom Mateusz Bieniek (Wed Jan 06 2021 - 06:40:28 PST)
- Re: [AMBER] Bug in the Mol2 format: space converted into a new oxygen atom David A Case (Fri Jan 08 2021 - 07:01:31 PST)
  - Re: [AMBER] Bug in the Mol2 format: space converted into a new oxygen atom liu junjun (Thu Feb 04 2021 - 12:22:25 PST)
  - Re: [AMBER] Bug in the Mol2 format: space converted into a new oxygen atom Junmei Wang (Mon Feb 08 2021 - 06:26:44 PST)
    - Re: [AMBER] Bug in the Mol2 format: space converted into a new oxygen atom David A Case (Mon Feb 22 2021 - 05:02:55 PST)
[AMBER] How does the xleap/teap recognize the H3O+ (hydronium) ions? Eduardo R. Almeida (Wed Jan 06 2021 - 15:15:55 PST)
- Re: [AMBER] How does the xleap/teap recognize the H3O+ (hydronium) ions? Bill Ross (Wed Jan 06 2021 - 17:06:34 PST)
  - Re: [AMBER] How does the xleap/teap recognize the H3O+ (hydronium) ions? Bill Ross (Wed Jan 06 2021 - 17:08:11 PST)
    - Re: [AMBER] How does the xleap/teap recognize the H3O+ (hydronium) ions? Eduardo R. Almeida (Wed Jan 06 2021 - 17:28:27 PST)
    - Re: [AMBER] How does the xleap/teap recognize the H3O+ (hydronium) ions? Eduardo R. Almeida (Wed Jan 06 2021 - 17:33:46 PST)
    - Re: [AMBER] How does the xleap/teap recognize the H3O+ (hydronium) ions? Bill Ross (Wed Jan 06 2021 - 18:03:59 PST)
    - Re: [AMBER] How does the xleap/teap recognize the H3O+ (hydronium) ions? Eduardo R. Almeida (Wed Jan 06 2021 - 18:18:58 PST)
    - Re: [AMBER] How does the xleap/teap recognize the H3O+ (hydronium) ions? Bill Ross (Wed Jan 06 2021 - 18:24:57 PST)
    - Re: [AMBER] How does the xleap/teap recognize the H3O+ (hydronium) ions? Eduardo R. Almeida (Wed Jan 06 2021 - 18:37:00 PST)
    - Re: [AMBER] How does the xleap/teap recognize the H3O+ (hydronium) ions? Bill Ross (Wed Jan 06 2021 - 18:56:01 PST)
    - Re: [AMBER] How does the xleap/teap recognize the H3O+ (hydronium) ions? Bill Ross (Wed Jan 06 2021 - 18:59:35 PST)
    - Re: [AMBER] How does the xleap/teap recognize the H3O+ (hydronium) ions? Eduardo R. Almeida (Wed Jan 06 2021 - 19:05:49 PST)
- Re: [AMBER] How does the xleap/teap recognize the H3O+ (hydronium) ions? Hector A. Baldoni (Wed Jan 06 2021 - 19:11:18 PST)
[AMBER] RMSD analysis K Jan (Thu Jan 07 2021 - 14:34:51 PST)
- Re: [AMBER] RMSD analysis Kenneth Huang (Thu Jan 07 2021 - 14:45:09 PST)
  - Re: [AMBER] RMSD analysis K Jan (Thu Jan 07 2021 - 15:26:14 PST)
    - Re: [AMBER] RMSD analysis Carlos Simmerling (Thu Jan 07 2021 - 17:55:01 PST)
- Re: [AMBER] RMSD analysis Daniel Roe (Fri Jan 08 2021 - 13:09:54 PST)
[AMBER] MD GPU Scaling Performance Jatin Kashyap (Thu Jan 07 2021 - 14:38:26 PST)
- Re: [AMBER] MD GPU Scaling Performance David A Case (Fri Jan 08 2021 - 06:47:42 PST)
[AMBER] CPPTRAJ error while Clustering Maghsoud, Yazdan (Fri Jan 08 2021 - 08:08:27 PST)
- Re: [AMBER] CPPTRAJ error while Clustering Daniel Roe (Fri Jan 08 2021 - 09:31:49 PST)
[AMBER] Error in xleap: water molecules Eduardo R. Almeida (Fri Jan 08 2021 - 15:39:20 PST)
- Re: [AMBER] Error in xleap: water molecules Bill Ross (Fri Jan 08 2021 - 20:43:00 PST)
- Re: [AMBER] Error in xleap: water molecules David A Case (Sat Jan 09 2021 - 05:51:19 PST)
  - Re: [AMBER] Error in xleap: water molecules Eduardo R. Almeida (Sat Jan 09 2021 - 06:42:19 PST)
    - Re: [AMBER] Error in xleap: water molecules Bill Ross (Sat Jan 09 2021 - 09:30:56 PST)
    - Re: [AMBER] Error in xleap: water molecules David A Case (Sat Jan 09 2021 - 13:10:50 PST)
    - Re: [AMBER] Error in xleap: water molecules Bill Ross (Sat Jan 09 2021 - 13:37:22 PST)
    - Re: [AMBER] Error in xleap: water molecules Eduardo R. Almeida (Sat Jan 09 2021 - 15:29:40 PST)
    - Re: [AMBER] Error in xleap: water molecules Bill Ross (Sat Jan 09 2021 - 15:31:41 PST)
    - Re: [AMBER] Error in xleap: water molecules Eduardo R. Almeida (Sat Jan 09 2021 - 15:44:17 PST)
    - Re: [AMBER] Error in xleap: water molecules Bill Ross (Sat Jan 09 2021 - 15:52:54 PST)
    - Re: [AMBER] Error in xleap: water molecules David A Case (Sat Jan 09 2021 - 18:25:13 PST)
    - Re: [AMBER] Error in xleap: water molecules Bill Ross (Sat Jan 09 2021 - 18:31:13 PST)
    - Re: [AMBER] Error in xleap: water molecules Eduardo R. Almeida (Sat Jan 09 2021 - 19:02:21 PST)
    - Re: [AMBER] Error in xleap: water molecules David A Case (Sun Jan 10 2021 - 07:45:24 PST)
    - Re: [AMBER] Error in xleap: water molecules Eduardo R. Almeida (Sun Jan 10 2021 - 11:13:36 PST)
[AMBER] how to pull group of atoms towards a fixed molecule using Steered molecular dynamics simulation Pinky Mazumder (Fri Jan 08 2021 - 17:11:43 PST)
[AMBER] How to apply shear loading on carbohydrates Pinky Mazumder (Fri Jan 08 2021 - 21:11:18 PST)
[AMBER] Domain distances using cpptraj Athena N (Fri Jan 08 2021 - 23:19:12 PST)
- [AMBER] Fwd: Domain distances using cpptraj Athena N (Sat Jan 09 2021 - 20:15:28 PST)
  - Re: [AMBER] Fwd: Domain distances using cpptraj David A Case (Sun Jan 10 2021 - 05:23:03 PST)
[AMBER] How to pull/push group of atoms Pinky Mazumder (Sat Jan 09 2021 - 21:06:06 PST)
[AMBER] Probmlems compiling under macOS Gustaf Olsson (Sun Jan 10 2021 - 00:13:00 PST)
- Re: [AMBER] Probmlems compiling under macOS David A Case (Sun Jan 10 2021 - 05:46:50 PST)
  - Re: [AMBER] Probmlems compiling under macOS Gustaf Olsson (Sun Jan 10 2021 - 09:24:07 PST)
    - Re: [AMBER] Probmlems compiling under macOS Gustaf Olsson (Sun Jan 10 2021 - 13:37:31 PST)
    - Re: [AMBER] Probmlems compiling under macOS David A Case (Mon Jan 11 2021 - 05:11:29 PST)
    - Re: [AMBER] Probmlems compiling under macOS Gustaf Olsson (Wed Jan 13 2021 - 22:32:01 PST)
    - Re: [AMBER] Probmlems compiling under macOS Gustaf Olsson (Mon Feb 08 2021 - 02:26:48 PST)
    - Re: [AMBER] Probmlems compiling under macOS David A Case (Mon Feb 08 2021 - 06:58:30 PST)
    - Re: [AMBER] Probmlems compiling under macOS Gustaf Olsson (Mon Feb 08 2021 - 23:50:07 PST)
    - Re: [AMBER] Probmlems compiling under macOS Gustaf Olsson (Tue Feb 09 2021 - 00:17:36 PST)
    - Re: [AMBER] Probmlems compiling under macOS David A Case (Tue Feb 09 2021 - 05:30:57 PST)
    - Re: [AMBER] Probmlems compiling under macOS Gustaf Olsson (Tue Feb 09 2021 - 07:42:17 PST)
    - Re: [AMBER] Probmlems compiling under macOS Gustaf Olsson (Wed Feb 10 2021 - 02:32:47 PST)
[AMBER] Error searching for compatible GPU Hongwei Tan (Sun Jan 10 2021 - 00:29:22 PST)
- Re: [AMBER] Error searching for compatible GPU David A Case (Sun Jan 10 2021 - 07:35:50 PST)
  - [AMBER] Amber GPU performance history David A Case (Sun Jan 10 2021 - 11:32:01 PST)
- Re: [AMBER] Error searching for compatible GPU Hongwei Tan (Sun Jan 10 2021 - 16:50:33 PST)
[AMBER] Issue about the generaton of rst files 辛志宏 (Sun Jan 10 2021 - 06:41:11 PST)
- Re: [AMBER] Issue about the generaton of rst files Daniel Roe (Mon Jan 11 2021 - 09:42:02 PST)
[AMBER] TI simulation blowing up with pmemd.CUDA Delwakkada Liyanage, Senal Dinuka (Sun Jan 10 2021 - 10:07:39 PST)
- Re: [AMBER] TI simulation blowing up with pmemd.CUDA David A Case (Sun Jan 10 2021 - 11:28:09 PST)
  - Re: [AMBER] TI simulation blowing up with pmemd.CUDA Delwakkada Liyanage, Senal Dinuka (Sun Jan 10 2021 - 12:08:21 PST)
    - Re: [AMBER] TI simulation blowing up with pmemd.CUDA David A Case (Mon Jan 11 2021 - 05:09:12 PST)
    - Re: [AMBER] TI simulation blowing up with pmemd.CUDA Debarati DasGupta (Mon Jan 11 2021 - 05:52:01 PST)
- Re: [AMBER] TI simulation blowing up with pmemd.CUDA Debarati DasGupta (Mon Jan 11 2021 - 07:27:22 PST)
- Re: [AMBER] TI simulation blowing up with pmemd.CUDA Debarati DasGupta (Mon Jan 11 2021 - 09:41:36 PST)
[AMBER] Preparation of input file for RAMD (Geng Dong) 东庚 (Sun Jan 10 2021 - 20:11:12 PST)
[AMBER] Lateral movement of membrane bound protein during MD simulation in Amber Biplab Ghosh (Sun Jan 10 2021 - 21:27:36 PST)
- Re: [AMBER] Lateral movement of membrane bound protein during MD simulation in Amber Stephan Schott (Mon Jan 11 2021 - 03:21:37 PST)
[AMBER] How to use AM1 for Ti atom in Amber? 孙天宇 (Sun Jan 10 2021 - 21:28:23 PST)
- Re: [AMBER] How to use AM1 for Ti atom in Amber? David A Case (Mon Jan 11 2021 - 05:32:54 PST)
[AMBER] backbone rmsd between mutant trajectories, comparing conformational space sampled Vaibhav Dixit (Sun Jan 10 2021 - 22:59:49 PST)
- Re: [AMBER] backbone rmsd between mutant trajectories, comparing conformational space sampled David A Case (Mon Jan 11 2021 - 05:18:40 PST)
  - Re: [AMBER] backbone rmsd between mutant trajectories, comparing conformational space sampled Vaibhav Dixit (Mon Jan 11 2021 - 22:52:25 PST)
    - Re: [AMBER] backbone rmsd between mutant trajectories, comparing conformational space sampled Hector A. Baldoni (Tue Jan 12 2021 - 08:44:05 PST)
[AMBER] Cpptraj v13 command is not working fixatomorder Ana Ziad (Sun Jan 10 2021 - 23:01:44 PST)
- Re: [AMBER] Cpptraj v13 command is not working fixatomorder Daniel Roe (Mon Jan 11 2021 - 09:43:55 PST)
[AMBER] Problem in running cmake Airy Sanjeev (Sun Jan 10 2021 - 23:17:00 PST)
- Re: [AMBER] Problem in running cmake David A Case (Mon Jan 11 2021 - 05:23:31 PST)
  - Re: [AMBER] Problem in running cmake Airy Sanjeev (Mon Jan 11 2021 - 19:01:15 PST)
[AMBER] error job MYRIAN TORRES RICO (Mon Jan 11 2021 - 03:09:58 PST)
- Re: [AMBER] error job David A Case (Mon Jan 11 2021 - 05:26:09 PST)
  - Re: [AMBER] error job MYRIAN TORRES RICO (Tue Jan 12 2021 - 01:02:25 PST)
    - Re: [AMBER] error job David A Case (Tue Jan 12 2021 - 05:25:58 PST)
    - Re: [AMBER] error job MYRIAN TORRES RICO (Tue Jan 12 2021 - 06:38:11 PST)
    - Re: [AMBER] error job Carlos Simmerling (Tue Jan 12 2021 - 06:51:34 PST)
    - Re: [AMBER] error job MYRIAN TORRES RICO (Tue Jan 12 2021 - 07:10:57 PST)
    - Re: [AMBER] error job Carlos Simmerling (Tue Jan 12 2021 - 07:41:44 PST)
    - Re: [AMBER] error job MYRIAN TORRES RICO (Tue Jan 12 2021 - 09:20:44 PST)
    - Re: [AMBER] error job Carlos Simmerling (Wed Jan 13 2021 - 04:40:21 PST)
    - Re: [AMBER] error job MYRIAN TORRES RICO (Thu Jan 14 2021 - 00:36:31 PST)
[AMBER] LEaP Error/questions. Sam Walsworth (Researcher) (Mon Jan 11 2021 - 03:45:14 PST)
- Re: [AMBER] LEaP Error/questions. David A Case (Mon Jan 11 2021 - 05:29:47 PST)
  - Re: [AMBER] LEaP Error/questions. Sam Walsworth (Researcher) (Mon Jan 11 2021 - 05:45:18 PST)
    - Re: [AMBER] LEaP Error/questions. David A Case (Mon Jan 11 2021 - 08:44:16 PST)
  - Re: [AMBER] LEaP Error/questions. Sam Walsworth (Researcher) (Mon Jan 11 2021 - 09:10:26 PST)
    - Re: [AMBER] LEaP Error/questions. Carlos Simmerling (Mon Jan 11 2021 - 09:29:29 PST)
    - Re: [AMBER] LEaP Error/questions. Maria Nagan (Mon Jan 11 2021 - 09:37:46 PST)
    - Re: [AMBER] LEaP Error/questions. Sam Walsworth (Researcher) (Mon Jan 11 2021 - 12:58:04 PST)
    - Re: [AMBER] LEaP Error/questions. Carlos Simmerling (Mon Jan 11 2021 - 14:09:33 PST)
    - Re: [AMBER] LEaP Error/questions. Sam Walsworth (Researcher) (Tue Jan 12 2021 - 04:18:08 PST)
    - Re: [AMBER] LEaP Error/questions. Carlos Simmerling (Tue Jan 12 2021 - 05:05:01 PST)
    - Re: [AMBER] LEaP Error/questions. Sam Walsworth (Researcher) (Tue Jan 12 2021 - 05:11:39 PST)
    - Re: [AMBER] LEaP Error/questions. David A Case (Tue Jan 12 2021 - 05:21:37 PST)
    - Re: [AMBER] LEaP Error/questions. Sam Walsworth (Researcher) (Wed Jan 13 2021 - 04:30:36 PST)
    - Re: [AMBER] LEaP Error/questions. Carlos Simmerling (Wed Jan 13 2021 - 04:37:09 PST)
    - Re: [AMBER] LEaP Error/questions. Sam Walsworth (Researcher) (Wed Jan 13 2021 - 05:27:55 PST)
    - Re: [AMBER] LEaP Error/questions. Daniel Roe (Wed Jan 13 2021 - 06:11:24 PST)
    - Re: [AMBER] LEaP Error/questions. Carlos Simmerling (Wed Jan 13 2021 - 06:13:08 PST)
    - Re: [AMBER] LEaP Error/questions. Sam Walsworth (Researcher) (Wed Jan 13 2021 - 06:38:33 PST)
    - Re: [AMBER] LEaP Error/questions. Carlos Simmerling (Wed Jan 13 2021 - 06:44:49 PST)
    - Re: [AMBER] LEaP Error/questions. Sam Walsworth (Researcher) (Wed Jan 13 2021 - 07:06:44 PST)
    - Re: [AMBER] LEaP Error/questions. David A Case (Wed Jan 13 2021 - 08:11:59 PST)
    - Re: [AMBER] LEaP Error/questions. Sam Walsworth (Researcher) (Wed Jan 13 2021 - 12:41:01 PST)
    - Re: [AMBER] LEaP Error/questions. David A Case (Thu Jan 14 2021 - 14:15:21 PST)
    - Re: [AMBER] LEaP Error/questions. Sam Walsworth (Researcher) (Fri Jan 15 2021 - 10:58:38 PST)
    - Re: [AMBER] LEaP Error/questions. David A Case (Fri Jan 15 2021 - 12:41:17 PST)
    - Re: [AMBER] LEaP Error/questions. Sam Walsworth (Researcher) (Fri Jan 15 2021 - 12:58:57 PST)
    - Re: [AMBER] LEaP Error/questions. David A Case (Tue Jan 12 2021 - 05:17:15 PST)
[AMBER] US or SMD for torsion angle steering? Fabian Glaser (Mon Jan 11 2021 - 06:31:08 PST)
- Re: [AMBER] US or SMD for torsion angle steering? Feng Pan (Tue Jan 12 2021 - 06:35:32 PST)
[AMBER] Pull group of atoms together Pinky Mazumder (Mon Jan 11 2021 - 10:34:11 PST)
- Re: [AMBER] Pull group of atoms together Carlos Simmerling (Mon Jan 11 2021 - 10:43:19 PST)
  - Re: [AMBER] Pull group of atoms together Pinky Mazumder (Tue Jan 12 2021 - 08:38:42 PST)
    - Re: [AMBER] Pull group of atoms together Carlos Simmerling (Tue Jan 12 2021 - 11:25:42 PST)
    - Re: [AMBER] Pull group of atoms together Pinky Mazumder (Tue Jan 12 2021 - 11:30:16 PST)
    - Re: [AMBER] Pull group of atoms together Carlos Simmerling (Tue Jan 12 2021 - 11:43:09 PST)
    - Re: [AMBER] Pull group of atoms together Pinky Mazumder (Tue Jan 12 2021 - 11:59:22 PST)
[AMBER] Spam purewater keyword Debarati DasGupta (Mon Jan 11 2021 - 12:49:02 PST)
[AMBER] Fwd: Creating a bond in leap Victoria E Hill (Mon Jan 11 2021 - 13:37:33 PST)
- Re: [AMBER] Fwd: Creating a bond in leap Kenneth Huang (Mon Jan 11 2021 - 14:03:23 PST)
[AMBER] Amber20 with PLUMED running slow, with GPU utilisation ~40% Amanda Buyan (Mon Jan 11 2021 - 19:24:58 PST)
- Re: [AMBER] Amber20 with PLUMED running slow, with GPU utilisation ~40% David A Case (Tue Jan 12 2021 - 09:51:06 PST)
  - Re: [AMBER] Amber20 with PLUMED running slow, with GPU utilisation ~40% Adrian Roitberg (Tue Jan 12 2021 - 09:55:56 PST)
    - Re: [AMBER] Amber20 with PLUMED running slow, with GPU utilisation ~40% Amanda Buyan (Tue Jan 12 2021 - 15:36:36 PST)
[AMBER] Issue about the generaton of rst files 辛志宏 (Tue Jan 12 2021 - 04:33:44 PST)
- Re: [AMBER] Issue about the generaton of rst files Daniel Roe (Tue Jan 12 2021 - 06:28:48 PST)
[AMBER] Problems when running make test.parallel Beatriz Gomes Guimaraes (Tue Jan 12 2021 - 06:35:36 PST)
- Re: [AMBER] Problems when running make test.parallel Daniel Roe (Tue Jan 12 2021 - 08:58:14 PST)
- Re: [AMBER] Problems when running make test.parallel Beatriz Gomes Guimaraes (Mon Jan 18 2021 - 10:53:18 PST)
[AMBER] abfQMMM with Terachem Eugen Hruska (Tue Jan 12 2021 - 10:21:06 PST)
[AMBER] Non-integer/zero charges from RESP fitting? Kenneth Huang (Tue Jan 12 2021 - 11:18:04 PST)
- Re: [AMBER] Non-integer/zero charges from RESP fitting? David A Case (Wed Jan 13 2021 - 05:15:17 PST)
- Re: [AMBER] Non-integer/zero charges from RESP fitting? Kenneth Huang (Wed Jan 13 2021 - 10:50:29 PST)
[AMBER] Python Error in MMPBSA.py, only for PBSA on final output Lennart Gundelach (Wed Jan 13 2021 - 01:43:07 PST)
- Re: [AMBER] Python Error in MMPBSA.py, only for PBSA on final output Ray Luo (Wed Jan 13 2021 - 09:10:46 PST)
  - Re: [AMBER] Python Error in MMPBSA.py, only for PBSA on final output Lennart Gundelach (Sat Jan 16 2021 - 02:14:54 PST)
    - Re: [AMBER] Python Error in MMPBSA.py, only for PBSA on final output Ray Luo (Sat Jan 16 2021 - 17:48:43 PST)
    - Re: [AMBER] Python Error in MMPBSA.py, only for PBSA on final output Lennart Gundelach (Fri Jan 22 2021 - 04:22:07 PST)
[AMBER] Errors whilst installing GPU Amber20 Victoria E Hill (Wed Jan 13 2021 - 03:58:43 PST)
- Re: [AMBER] Errors whilst installing GPU Amber20 David A Case (Wed Jan 13 2021 - 05:37:13 PST)
  - Re: [AMBER] Errors whilst installing GPU Amber20 Victoria E Hill (Wed Jan 13 2021 - 09:05:35 PST)
  - Re: [AMBER] Errors whilst installing GPU Amber20 tluchko (Wed Jan 13 2021 - 09:06:03 PST)
    - Re: [AMBER] Errors whilst installing GPU Amber20 Victoria E Hill (Wed Jan 13 2021 - 09:41:58 PST)
[AMBER] gaff/parm MYRIAN TORRES RICO (Thu Jan 14 2021 - 01:36:10 PST)
- Re: [AMBER] gaff/parm David A Case (Thu Jan 14 2021 - 05:34:07 PST)
  - Re: [AMBER] gaff/parm MYRIAN TORRES RICO (Thu Jan 14 2021 - 05:50:01 PST)
[AMBER] PROTEIN-DNA RMSD plots Syeda Amna Arshi (Thu Jan 14 2021 - 03:14:05 PST)
- Re: [AMBER] PROTEIN-DNA RMSD plots Carlos Simmerling (Thu Jan 14 2021 - 03:22:06 PST)
- Re: [AMBER] PROTEIN-DNA RMSD plots Dr. Anselm Horn (Thu Jan 14 2021 - 04:55:59 PST)
[AMBER] Error while clustering on CPPTRAJ dnlfr1994.gmail.com (Thu Jan 14 2021 - 05:03:45 PST)
- Re: [AMBER] Error while clustering on CPPTRAJ Daniel Roe (Thu Jan 14 2021 - 07:51:32 PST)
  - Re: [AMBER] Error while clustering on CPPTRAJ dnlfr1994.gmail.com (Thu Jan 14 2021 - 09:50:22 PST)
    - Re: [AMBER] Error while clustering on CPPTRAJ Daniel Roe (Thu Jan 14 2021 - 15:58:44 PST)
    - Re: [AMBER] Error while clustering on CPPTRAJ dnlfr1994.gmail.com (Tue Jan 19 2021 - 09:20:52 PST)
    - Re: [AMBER] Error while clustering on CPPTRAJ Daniel Roe (Tue Jan 19 2021 - 09:39:31 PST)
    - Re: [AMBER] Error while clustering on CPPTRAJ Daniel Fernández Remacha (Tue Jan 19 2021 - 09:50:24 PST)
    - Re: [AMBER] Error while clustering on CPPTRAJ Daniel Roe (Tue Jan 19 2021 - 10:03:31 PST)
[AMBER] Number of na, cl ions Женя Елизарова (Thu Jan 14 2021 - 08:10:11 PST)
- Re: [AMBER] Number of na, cl ions David A Case (Thu Jan 14 2021 - 14:08:49 PST)
[AMBER] DNA-ligand simulation Kehinde Idowu (Thu Jan 14 2021 - 16:33:20 PST)
- Re: [AMBER] DNA-ligand simulation Thomas Cheatham (Thu Jan 14 2021 - 16:41:40 PST)
[AMBER] Question of targeted molecular dynamics simulation 吴晓东 (Thu Jan 14 2021 - 18:37:16 PST)
- Re: [AMBER] Question of targeted molecular dynamics simulation Dr. Anselm Horn (Fri Jan 15 2021 - 09:14:18 PST)
[AMBER] Typo in update.13 for AmberTools20 Hashemi, Mohtadin (Fri Jan 15 2021 - 12:28:26 PST)
[AMBER] How to use GLYCAM_06j-1 in LAMMPS Pinky Mazumder (Fri Jan 15 2021 - 15:43:05 PST)
- Re: [AMBER] How to use GLYCAM_06j-1 in LAMMPS David A Case (Sat Jan 16 2021 - 06:44:04 PST)
  - Re: [AMBER] How to use GLYCAM_06j-1 in LAMMPS Pinky Mazumder (Sat Jan 16 2021 - 13:35:18 PST)
[AMBER] NonUniversalWarning: Modified off-diagonal LJ parameters detected Loki (Sat Jan 16 2021 - 03:54:54 PST)
- Re: [AMBER] NonUniversalWarning: Modified off-diagonal LJ parameters detected David A Case (Sat Jan 16 2021 - 06:45:31 PST)
- Re: [AMBER] NonUniversalWarning: Modified off-diagonal LJ parameters detected Loki (Sat Jan 16 2021 - 09:30:12 PST)
  - Re: [AMBER] NonUniversalWarning: Modified off-diagonal LJ parameters detected David A Case (Sat Jan 16 2021 - 11:22:39 PST)
[AMBER] Langevin thermostat different gamma_ln giving systematically different energies? Liao (Sat Jan 16 2021 - 17:44:16 PST)
- Re: [AMBER] Langevin thermostat different gamma_ln giving systematically different energies? Thomas Cheatham (Sat Jan 16 2021 - 18:23:48 PST)
[AMBER] How to apply Compressive loading on wood Pinky Mazumder (Sat Jan 16 2021 - 18:55:54 PST)
[AMBER] antechamber assigns DU as atom type for nitrogen nguerin (Sat Jan 16 2021 - 19:47:04 PST)
- Re: [AMBER] antechamber assigns DU as atom type for nitrogen David A Case (Sat Jan 23 2021 - 14:23:53 PST)
[AMBER] working with mmpbsa with protein and three ligands in same complex Sadaf Rani (Sun Jan 17 2021 - 02:36:31 PST)
- Re: [AMBER] working with mmpbsa with protein and three ligands in same complex David A Case (Sun Jan 17 2021 - 07:16:54 PST)
  - Re: [AMBER] working with mmpbsa with protein and three ligands in same complex Sadaf Rani (Tue Jan 19 2021 - 22:42:20 PST)
[AMBER] Distance of every c alpha in a protein to every other c alpha Jenny 148 (Sun Jan 17 2021 - 21:50:28 PST)
- Re: [AMBER] Distance of every c alpha in a protein to every other c alpha Daniel Roe (Tue Jan 19 2021 - 06:46:07 PST)
- [AMBER] Fwd: Distance of every c alpha in a protein to every other c alpha Jenny 148 (Mon Jan 25 2021 - 02:11:00 PST)
  - Re: [AMBER] Fwd: Distance of every c alpha in a protein to every other c alpha Daniel Roe (Mon Jan 25 2021 - 06:16:32 PST)
[AMBER] Reproducing Tutorial: Analysis of a nucleic acid simulation Jatin Kashyap (Mon Jan 18 2021 - 15:17:02 PST)
- Re: [AMBER] Reproducing Tutorial: Analysis of a nucleic acid simulation Carlos Simmerling (Mon Jan 18 2021 - 15:28:15 PST)
  - Re: [AMBER] Reproducing Tutorial: Analysis of a nucleic acid simulation Jatin Kashyap (Mon Jan 18 2021 - 15:32:45 PST)
    - Re: [AMBER] Reproducing Tutorial: Analysis of a nucleic acid simulation Carlos Simmerling (Mon Jan 18 2021 - 15:43:41 PST)
    - Re: [AMBER] Reproducing Tutorial: Analysis of a nucleic acid simulation Jatin Kashyap (Mon Jan 18 2021 - 15:47:58 PST)
    - Re: [AMBER] Reproducing Tutorial: Analysis of a nucleic acid simulation Carlos Simmerling (Mon Jan 18 2021 - 16:01:25 PST)
    - Re: [AMBER] Reproducing Tutorial: Analysis of a nucleic acid simulation Jatin Kashyap (Mon Jan 18 2021 - 16:06:35 PST)
    - Re: [AMBER] Reproducing Tutorial: Analysis of a nucleic acid simulation Roitberg,Adrian E (Mon Jan 18 2021 - 16:40:00 PST)
    - Re: [AMBER] Reproducing Tutorial: Analysis of a nucleic acid simulation Jatin Kashyap (Mon Jan 18 2021 - 16:48:50 PST)
    - Re: [AMBER] Reproducing Tutorial: Analysis of a nucleic acid simulation Carlos Simmerling (Mon Jan 18 2021 - 17:12:30 PST)
    - Re: [AMBER] Reproducing Tutorial: Analysis of a nucleic acid simulation Jatin Kashyap (Mon Jan 18 2021 - 17:40:11 PST)
    - Re: [AMBER] Reproducing Tutorial: Analysis of a nucleic acid simulation Carlos Simmerling (Mon Jan 18 2021 - 18:02:55 PST)
[AMBER] Extending DNA structure Airy Sanjeev (Mon Jan 18 2021 - 19:57:16 PST)
- Re: [AMBER] Extending DNA structure Vlad Cojocaru (Tue Jan 19 2021 - 01:39:58 PST)
  - Re: [AMBER] Extending DNA structure Airy Sanjeev (Tue Jan 19 2021 - 02:00:55 PST)
[AMBER] vlimit exceeded for step 0; vmax = 50.6241 Pinky Mazumder (Tue Jan 19 2021 - 13:50:09 PST)
[AMBER] Creating input files using tleap Nicy yadav (Tue Jan 19 2021 - 14:27:00 PST)
- Re: [AMBER] Creating input files using tleap David A Case (Wed Jan 20 2021 - 05:30:06 PST)
  - Re: [AMBER] Creating input files using tleap Nicy yadav (Wed Jan 20 2021 - 06:26:08 PST)
[AMBER] makedepend for sander Antoine MARION (Wed Jan 20 2021 - 03:26:06 PST)
- Re: [AMBER] makedepend for sander David A Case (Wed Jan 20 2021 - 05:09:43 PST)
  - Re: [AMBER] makedepend for sander Antoine MARION (Wed Jan 20 2021 - 06:14:04 PST)
[AMBER] combining crashed trajectories Ayesha Fatima (Wed Jan 20 2021 - 05:58:19 PST)
- Re: [AMBER] combining crashed trajectories Dr. Anselm Horn (Wed Jan 20 2021 - 09:25:43 PST)
- Re: [AMBER] combining crashed trajectories Daniel Roe (Fri Jan 22 2021 - 10:46:45 PST)
[AMBER] The long and winding STSM Luis Simon (Wed Jan 20 2021 - 07:56:33 PST)
- Re: [AMBER] The long and winding STSM Feng Pan (Fri Jan 29 2021 - 12:37:48 PST)
[AMBER] Major Cpptraj Update (GitHub) Daniel Roe (Wed Jan 20 2021 - 11:54:44 PST)
[AMBER] ZAFF force field Tabassum Khair Barbhuiya (Wed Jan 20 2021 - 17:09:11 PST)
- Re: [AMBER] ZAFF force field Pengfei Li (Fri Feb 26 2021 - 15:12:51 PST)
[AMBER] MMPBSA calculation cpptraj failed with ligand prmtop Sadaf Rani (Wed Jan 20 2021 - 21:13:09 PST)
- Re: [AMBER] MMPBSA calculation cpptraj failed with ligand prmtop Elvis A F Martis (Wed Jan 20 2021 - 23:52:57 PST)
  - Re: [AMBER] MMPBSA calculation cpptraj failed with ligand prmtop Sadaf Rani (Sun Jan 24 2021 - 20:47:03 PST)
    - Re: [AMBER] MMPBSA calculation cpptraj failed with ligand prmtop Sadaf Rani (Sun Jan 24 2021 - 21:03:10 PST)
[AMBER] Fwd: Error during amber16 installation spss4.iacs.res.in (Thu Jan 21 2021 - 02:29:46 PST)
- Re: [AMBER] Fwd: Error during amber16 installation David A Case (Thu Jan 21 2021 - 05:16:12 PST)
  - Re: [AMBER] Fwd: Error during amber16 installation spss4.iacs.res.in (Thu Jan 21 2021 - 20:59:09 PST)
    - Re: [AMBER] Fwd: Error during amber16 installation David A Case (Fri Jan 22 2021 - 07:17:02 PST)
[AMBER] question MYRIAN TORRES RICO (Thu Jan 21 2021 - 03:05:45 PST)
- Re: [AMBER] question David A Case (Thu Jan 21 2021 - 05:19:27 PST)
[AMBER] Cpptraj Stejskal, Lenka (Thu Jan 21 2021 - 07:14:43 PST)
- Re: [AMBER] Cpptraj Daniel Roe (Thu Jan 21 2021 - 07:19:48 PST)
  - Re: [AMBER] Cpptraj Daniel Roe (Fri Jan 22 2021 - 09:23:30 PST)
[AMBER] Nvidia RTX 3080/3090 Servers mish (Thu Jan 21 2021 - 18:48:54 PST)
- Re: [AMBER] Nvidia RTX 3080/3090 Servers Ross Walker (Fri Jan 22 2021 - 06:03:53 PST)
  - Re: [AMBER] Nvidia RTX 3080/3090 Servers mish (Fri Jan 22 2021 - 06:16:34 PST)
[AMBER] Energy minimization script raissa.conceicao.bol.com.br (Fri Jan 22 2021 - 05:45:00 PST)
- Re: [AMBER] Energy minimization script David A Case (Fri Jan 22 2021 - 07:22:15 PST)
  - Re: [AMBER] Energy minimization script raissa.conceicao.bol.com.br (Fri Jan 22 2021 - 12:14:00 PST)
[AMBER] How to extract restart file with velocity from a trajectory file? 辛志宏 (Fri Jan 22 2021 - 06:19:42 PST)
- Re: [AMBER] How to extract restart file with velocity from a trajectory file? Carlos Simmerling (Fri Jan 22 2021 - 09:32:11 PST)
[AMBER] Understanding File Format Specifications nguerin (Fri Jan 22 2021 - 12:48:45 PST)
- Re: [AMBER] Understanding File Format Specifications Thomas Cheatham (Fri Jan 22 2021 - 14:03:52 PST)
[AMBER] How to pull two group of atoms in two different direction? Pinky Mazumder (Sun Jan 24 2021 - 16:23:33 PST)
[AMBER] Running simulations richa anand (Sun Jan 24 2021 - 22:41:53 PST)
- Re: [AMBER] Running simulations David A Case (Tue Jan 26 2021 - 11:24:03 PST)
[AMBER] Amber 16/cpptraj diffusion command Pau Mayorga Delgado (Mon Jan 25 2021 - 00:37:48 PST)
- Re: [AMBER] Amber 16/cpptraj diffusion command Daniel Roe (Mon Jan 25 2021 - 06:11:36 PST)
[AMBER] DNA protein simulation protocol Airy Sanjeev (Mon Jan 25 2021 - 01:04:14 PST)
- Re: [AMBER] DNA protein simulation protocol David A Case (Mon Jan 25 2021 - 19:11:46 PST)
[AMBER] pdb4amber error Nicy yadav (Mon Jan 25 2021 - 08:24:33 PST)
- Re: [AMBER] pdb4amber error Scott Brozell (Tue Jan 26 2021 - 22:37:06 PST)
  - Re: [AMBER] pdb4amber error David A Case (Wed Jan 27 2021 - 05:14:14 PST)
[AMBER] overall and internal correlation function Mani Radh (Mon Jan 25 2021 - 09:48:12 PST)
[AMBER] OPC monovalent ion parameters Sebastian Oleksy (Mon Jan 25 2021 - 10:07:26 PST)
- Re: [AMBER] OPC monovalent ion parameters Carlos Simmerling (Mon Jan 25 2021 - 12:35:11 PST)
- Re: [AMBER] OPC monovalent ion parameters Cavender, Chapin (Sat Feb 13 2021 - 11:50:31 PST)
  - Re: [AMBER] OPC monovalent ion parameters Pengfei Li (Sat Feb 13 2021 - 15:58:03 PST)
    - Re: [AMBER] OPC monovalent ion parameters Thomas Cheatham (Sat Feb 13 2021 - 20:33:41 PST)
    - Re: [AMBER] OPC monovalent ion parameters Pengfei Li (Mon Feb 15 2021 - 08:54:28 PST)
    - Re: [AMBER] OPC monovalent ion parameters Matias Machado (Mon Feb 22 2021 - 11:16:46 PST)
    - Re: [AMBER] OPC monovalent ion parameters Pengfei Li (Fri Feb 26 2021 - 15:08:06 PST)
[AMBER] abmd ignores cv_min cv_max and resolution for colvar="TORSION" Luis Simon (Mon Jan 25 2021 - 13:03:43 PST)
- Re: [AMBER] abmd ignores cv_min cv_max and resolution for colvar="TORSION" Feng Pan (Fri Jan 29 2021 - 12:39:46 PST)
[AMBER] Help to generate prmtop and .crd files from a PDB trajectory Devlina Chakravarty (Mon Jan 25 2021 - 17:46:03 PST)
- Re: [AMBER] Help to generate prmtop and .crd files from a PDB trajectory Kenneth Huang (Tue Jan 26 2021 - 11:55:43 PST)
- Re: [AMBER] Help to generate prmtop and .crd files from a PDB trajectory Daniel Roe (Thu Jan 28 2021 - 07:03:28 PST)
[AMBER] PrmtopError: Complex natom != receptor natom + ligand natom Renato Araujo (Mon Jan 25 2021 - 17:49:58 PST)
- Re: [AMBER] PrmtopError: Complex natom != receptor natom + ligand natom David A Case (Mon Jan 25 2021 - 19:17:14 PST)
  - Re: [AMBER] PrmtopError: Complex natom != receptor natom + ligand natom Renato Araujo (Tue Jan 26 2021 - 08:56:11 PST)
    - Re: [AMBER] PrmtopError: Complex natom != receptor natom + ligand natom David A Case (Tue Jan 26 2021 - 11:19:55 PST)
[AMBER] how to get amber 18 tools Sadaf Rani (Wed Jan 27 2021 - 04:25:11 PST)
- Re: [AMBER] how to get amber 18 tools Carlos Simmerling (Wed Jan 27 2021 - 06:10:59 PST)
  - Re: [AMBER] how to get amber 18 tools Sadaf Rani (Wed Jan 27 2021 - 06:44:55 PST)
    - Re: [AMBER] how to get amber 18 tools David A Case (Wed Jan 27 2021 - 12:09:44 PST)
[AMBER] technical problems with installing amber20 Игорь Злотников (Wed Jan 27 2021 - 04:59:02 PST)
- Re: [AMBER] technical problems with installing amber20 David A Case (Wed Jan 27 2021 - 12:21:43 PST)
  - Re: [AMBER] technical problems with installing amber20 Игорь Злотников (Wed Jan 27 2021 - 12:29:34 PST)
    - Re: [AMBER] technical problems with installing amber20 David A Case (Thu Jan 28 2021 - 07:05:06 PST)
[AMBER] rotdif analysis in cpptraj Adeleh Mokhles Gerami (Wed Jan 27 2021 - 06:41:02 PST)
[AMBER] max pairlist cutoff must be less than unit cell max sphere radius! Pinky Mazumder (Wed Jan 27 2021 - 13:49:22 PST)
- Re: [AMBER] max pairlist cutoff must be less than unit cell max sphere radius! David A Case (Thu Jan 28 2021 - 07:07:32 PST)
  - Re: [AMBER] max pairlist cutoff must be less than unit cell max sphere radius! Pinky Mazumder (Thu Jan 28 2021 - 10:31:52 PST)
- Re: [AMBER] max pairlist cutoff must be less than unit cell max sphere radius! Pinky Mazumder (Mon Feb 01 2021 - 14:27:11 PST)
  - Re: [AMBER] max pairlist cutoff must be less than unit cell max sphere radius! Carlos Simmerling (Mon Feb 01 2021 - 15:27:34 PST)
[AMBER] How to fix the issue of generating restart file from a trajectory? 辛志宏 (Wed Jan 27 2021 - 20:00:04 PST)
- Re: [AMBER] How to fix the issue of generating restart file from a trajectory? Daniel Roe (Thu Jan 28 2021 - 07:10:41 PST)
[AMBER] Error in minimization Kehinde Idowu (Thu Jan 28 2021 - 13:06:05 PST)
- Re: [AMBER] Error in minimization Carlos Simmerling (Thu Jan 28 2021 - 13:51:06 PST)
[AMBER] Can we perform combined clustering with multiple prmtop files and mdcrd files? Debarati DasGupta (Fri Jan 29 2021 - 06:36:40 PST)
- Re: [AMBER] Can we perform combined clustering with multiple prmtop files and mdcrd files? Kenneth Huang (Fri Jan 29 2021 - 09:51:32 PST)
[AMBER] in chimera, which one should I use for carbohydrates Pinky Mazumder (Fri Jan 29 2021 - 07:38:28 PST)
- Re: [AMBER] in chimera, which one should I use for carbohydrates David A Case (Fri Jan 29 2021 - 09:32:23 PST)
[AMBER] Potential energy discrepancy in RXSGLD Charo del Genio (Fri Jan 29 2021 - 08:28:51 PST)
[AMBER] Suggestions on crossing energy barrier to break strong HBs Amit Sharma (Asstt. Prof., MCARS) (Fri Jan 29 2021 - 15:40:35 PST)
- Re: [AMBER] Suggestions on crossing energy barrier to break strong HBs David A Case (Fri Jan 29 2021 - 19:06:00 PST)
  - Re: [AMBER] Suggestions on crossing energy barrier to break strong HBs Amit Sharma (Asstt. Prof., MCARS) (Fri Jan 29 2021 - 22:27:43 PST)
    - Re: [AMBER] Suggestions on crossing energy barrier to break strong HBs Kenneth Huang (Sat Jan 30 2021 - 17:10:10 PST)
[AMBER] Bug when using RESPA in REMD runs Charo del Genio (Sat Jan 30 2021 - 03:23:41 PST)
- Re: [AMBER] Bug when using RESPA in REMD runs David A Case (Sat Jan 30 2021 - 07:01:26 PST)
  - Re: [AMBER] Bug when using RESPA in REMD runs Carlos Simmerling (Sat Jan 30 2021 - 07:08:30 PST)
    - Re: [AMBER] Bug when using RESPA in REMD runs Charo del Genio (Sat Jan 30 2021 - 07:51:18 PST)
- Re: [AMBER] Bug when using RESPA in REMD runs Brian Radak (Sat Jan 30 2021 - 07:01:45 PST)
[AMBER] Can't restart a RXSGLD run (possible bug) Charo del Genio (Sun Jan 31 2021 - 02:13:41 PST)
- [AMBER] Found bug in sander in restarting SGLD replica exchange runs Charo del Genio (Sun Jan 31 2021 - 04:35:28 PST)
  - Re: [AMBER] Found bug in sander in restarting SGLD replica exchange runs Carlos Simmerling (Tue Feb 02 2021 - 17:03:28 PST)
[AMBER] Non zero ligand warning Ayesha Fatima (Sun Jan 31 2021 - 05:10:51 PST)
- Re: [AMBER] Non zero ligand warning David A Case (Sun Jan 31 2021 - 06:24:59 PST)
  - Re: [AMBER] Non zero ligand warning Ayesha Fatima (Sun Jan 31 2021 - 08:12:55 PST)
    - Re: [AMBER] Non zero ligand warning Ayesha Fatima (Sun Jan 31 2021 - 08:41:24 PST)
  - Re: [AMBER] Non zero ligand warning Kenneth Huang (Sun Jan 31 2021 - 10:14:48 PST)
[AMBER] Patches to fix the replica exchange restart bug Charo del Genio (Sun Jan 31 2021 - 12:11:59 PST)
- [AMBER] Solution to the replica exchange SGLD restart bug Charo del Genio (Mon Feb 01 2021 - 13:40:41 PST)
[AMBER] how does tleap choose missing side chain conformations Vaibhav Dixit (Sun Jan 31 2021 - 19:51:51 PST)
- Re: [AMBER] how does tleap choose missing side chain conformations Carlos Simmerling (Mon Feb 01 2021 - 03:23:01 PST)
  - Re: [AMBER] how does tleap choose missing side chain conformations Vaibhav Dixit (Tue Feb 02 2021 - 03:07:48 PST)
[AMBER] configure_mpich error Nikolay N. Kuzmich (Mon Feb 01 2021 - 03:36:23 PST)
- Re: [AMBER] configure_mpich error David A Case (Mon Feb 01 2021 - 04:47:52 PST)
- Re: [AMBER] configure_mpich error Nikolay N. Kuzmich (Tue Feb 02 2021 - 08:29:49 PST)
[AMBER] erro free energy calculation Renato Araujo (Mon Feb 01 2021 - 03:56:21 PST)
- Re: [AMBER] erro free energy calculation David A Case (Mon Feb 01 2021 - 04:55:18 PST)
[AMBER] QM/MM in Amber Женя Елизарова (Tue Feb 02 2021 - 01:25:23 PST)
- Re: [AMBER] QM/MM in Amber Женя Елизарова (Tue Feb 02 2021 - 01:31:05 PST)
- Re: [AMBER] QM/MM in Amber David A Case (Tue Feb 02 2021 - 05:30:39 PST)
[AMBER] Hydrogen bond analysis tutorial Renato Araujo (Tue Feb 02 2021 - 11:13:29 PST)
- Re: [AMBER] Hydrogen bond analysis tutorial Maria Nagan (Tue Feb 02 2021 - 11:21:07 PST)
[AMBER] error while building Amber20 with Intel + CUDA Susan Chacko (Tue Feb 02 2021 - 12:20:43 PST)
- Re: [AMBER] error while building Amber20 with Intel + CUDA David A Case (Tue Feb 02 2021 - 13:27:40 PST)
  - Re: [AMBER] error while building Amber20 with Intel + CUDA Susan Chacko (Tue Feb 02 2021 - 13:33:46 PST)
[AMBER] Random seed for restart files that have velocities? Liao (Tue Feb 02 2021 - 18:15:57 PST)
- Re: [AMBER] Random seed for restart files that have velocities? Carlos Simmerling (Tue Feb 02 2021 - 18:42:50 PST)
  - Re: [AMBER] Random seed for restart files that have velocities? Liao (Tue Feb 02 2021 - 19:58:02 PST)
    - Re: [AMBER] Random seed for restart files that have velocities? David A Case (Wed Feb 03 2021 - 05:44:00 PST)
[AMBER] ModuleNotFoundError: No module named 'MMPBSA_mods' Ch Bilal (Wed Feb 03 2021 - 00:35:26 PST)
- Re: [AMBER] ModuleNotFoundError: No module named 'MMPBSA_mods' David A Case (Wed Feb 03 2021 - 05:47:56 PST)
[AMBER] Nudged Elastic Band solvent choice and initial heating problem 李明玉 (Wed Feb 03 2021 - 04:12:45 PST)
- Re: [AMBER] Nudged Elastic Band solvent choice and initial heating problem Carlos Simmerling (Wed Feb 03 2021 - 05:17:30 PST)
  - Re: [AMBER] Nudged Elastic Band solvent choice and initial heating problem 李明玉 (Wed Feb 03 2021 - 09:01:09 PST)
    - Re: [AMBER] Nudged Elastic Band solvent choice and initial heating problem Carlos Simmerling (Wed Feb 03 2021 - 09:17:26 PST)
- Re: [AMBER] Nudged Elastic Band solvent choice and initial heating problem David A Case (Wed Feb 03 2021 - 06:00:45 PST)
[AMBER] AMBER HREMD replica trajectory Richard Kullmann (Wed Feb 03 2021 - 06:34:11 PST)
- Re: [AMBER] AMBER HREMD replica trajectory Daniel Roe (Wed Feb 03 2021 - 06:46:39 PST)
- [AMBER] CPPTRAJ mindist comand Richard Kullmann (Wed Feb 24 2021 - 03:07:41 PST)
  - Re: [AMBER] CPPTRAJ mindist comand Daniel Roe (Wed Feb 24 2021 - 04:15:26 PST)
  - [AMBER] CPPTRAJ nativecontacts Richard Kullmann (Mon May 03 2021 - 07:28:36 PDT)
    - Re: [AMBER] CPPTRAJ nativecontacts Daniel Roe (Mon May 03 2021 - 08:48:13 PDT)
    - Re: [AMBER] CPPTRAJ nativecontacts Richard Kullmann (Mon May 10 2021 - 06:29:46 PDT)
    - Re: [AMBER] CPPTRAJ nativecontacts Daniel Roe (Tue May 11 2021 - 12:21:44 PDT)
- [AMBER] GB-HCP Example File and Setup Richard Kullmann (Wed Mar 24 2021 - 08:07:46 PDT)
[AMBER] GPU power usage drop for igb = 8 compared to igb = 2 Demian Riccardi (Wed Feb 03 2021 - 14:48:45 PST)
- Re: [AMBER] GPU power usage drop for igb = 8 compared to igb = 2 Carlos Simmerling (Wed Feb 03 2021 - 15:19:47 PST)
[AMBER] Prepare pbd file modified cyclodextrin Игорь Злотников (Thu Feb 04 2021 - 00:52:45 PST)
- [AMBER] Fwd: Prepare pbd file modified cyclodextrin Игорь Злотников (Sun Feb 14 2021 - 04:16:16 PST)
[AMBER] CUDE upgrade question and AMBER Seibold, Steve Allan (Thu Feb 04 2021 - 10:00:30 PST)
[AMBER] MMPBSA.py Error: Could not import Amber Python modules Vitor Rabelo (Thu Feb 04 2021 - 11:08:49 PST)
[AMBER] decompose running error Nisha Amarnath Jonniya (Thu Feb 04 2021 - 22:23:23 PST)
- Re: [AMBER] decompose running error David A Case (Fri Feb 05 2021 - 05:45:06 PST)
  - Re: [AMBER] decompose running error Nisha Amarnath Jonniya (Mon Feb 08 2021 - 21:25:41 PST)
    - Re: [AMBER] decompose running error Nisha Amarnath Jonniya (Mon Feb 08 2021 - 21:31:45 PST)
[AMBER] RAMD question (Xiaodong Wu) 吴晓东 (Fri Feb 05 2021 - 01:19:57 PST)
- Re: [AMBER] RAMD question (Xiaodong Wu) Carlos Simmerling (Fri Feb 05 2021 - 03:39:34 PST)
  - Re: [AMBER] RAMD question (Xiaodong Wu) Charles Lin (Fri Feb 05 2021 - 10:53:31 PST)
  - Re: [AMBER] RAMD question (Xiaodong Wu) Charles Lin (Fri Feb 05 2021 - 10:59:28 PST)
[AMBER] Prmtop missing resid and resname info Violeta Burns Casamayor (Fri Feb 05 2021 - 01:55:31 PST)
- Re: [AMBER] Prmtop missing resid and resname info Carlos Simmerling (Fri Feb 05 2021 - 03:38:44 PST)
- Re: [AMBER] Prmtop missing resid and resname info Kenneth Huang (Fri Feb 05 2021 - 07:21:00 PST)
Re: [AMBER] Fwd: unreadable *.mdcrd David A Case (Fri Feb 05 2021 - 05:51:40 PST)
- Re: [AMBER] Fwd: unreadable *.mdcrd Tomasz Miernik (Fri Feb 05 2021 - 14:07:04 PST)
- Re: [AMBER] Fwd: unreadable *.mdcrd Elvis A F Martis (Fri Feb 05 2021 - 17:01:30 PST)
[AMBER] curiosity about sander reading a traj being written by GPU code Vaibhav Dixit (Fri Feb 05 2021 - 08:39:10 PST)
- Re: [AMBER] curiosity about sander reading a traj being written by GPU code Vaibhav Dixit (Sat Feb 06 2021 - 05:15:31 PST)
- Re: [AMBER] curiosity about sander reading a traj being written by GPU code Vaibhav Dixit (Mon Feb 08 2021 - 20:39:57 PST)
  - Re: [AMBER] curiosity about sander reading a traj being written by GPU code Carlos Simmerling (Tue Feb 09 2021 - 03:35:27 PST)
    - Re: [AMBER] curiosity about sander reading a traj being written by GPU code Vaibhav Dixit (Tue Feb 09 2021 - 04:14:06 PST)
    - Re: [AMBER] curiosity about sander reading a traj being written by GPU code Adrian Roitberg (Tue Feb 09 2021 - 07:37:35 PST)
    - Re: [AMBER] curiosity about sander reading a traj being written by GPU code Kenneth Huang (Tue Feb 09 2021 - 08:15:35 PST)
    - Re: [AMBER] curiosity about sander reading a traj being written by GPU code Vaibhav Dixit (Wed Feb 10 2021 - 02:41:39 PST)
    - Re: [AMBER] curiosity about sander reading a traj being written by GPU code Vaibhav Dixit (Wed Feb 10 2021 - 02:51:53 PST)
[AMBER] External electric fields cannot be used when npt > 0 李明玉 (Fri Feb 05 2021 - 09:19:49 PST)
[AMBER] suggestion of a patch for building MPI version of MMPBSA.py Yoshitaka Moriwaki (Fri Feb 05 2021 - 09:43:17 PST)
- Re: [AMBER] suggestion of a patch for building MPI version of MMPBSA.py David A Case (Fri Feb 05 2021 - 11:53:12 PST)
  - Re: [AMBER] suggestion of a patch for building MPI version of MMPBSA.py Yoshitaka Moriwaki (Sat Feb 06 2021 - 02:18:28 PST)
    - Re: [AMBER] suggestion of a patch for building MPI version of MMPBSA.py David A Case (Sat Feb 06 2021 - 05:49:42 PST)
[AMBER] problem deriving implicit polarised charges charges with mdgx Luis Simon (Fri Feb 05 2021 - 13:10:59 PST)
- Re: [AMBER] problem deriving implicit polarised charges charges with mdgx Luis Simon (Sun Feb 07 2021 - 13:29:15 PST)
[AMBER] About changes in frcmod.parmbsc0 Alan (Sat Feb 06 2021 - 00:12:55 PST)
- Re: [AMBER] About changes in frcmod.parmbsc0 Thomas Cheatham (Sat Feb 06 2021 - 00:28:39 PST)
  - Re: [AMBER] About changes in frcmod.parmbsc0 David A Case (Sat Feb 06 2021 - 05:25:31 PST)
[AMBER] RAMD simulation (Xiaodong) 吴晓东 (Sat Feb 06 2021 - 23:00:28 PST)
[AMBER] Fix the dihedral angle during the simulation Rinsha Chk (Sun Feb 07 2021 - 01:06:16 PST)
- Re: [AMBER] Fix the dihedral angle during the simulation David A Case (Sun Feb 07 2021 - 05:46:06 PST)
  - Re: [AMBER] Fix the dihedral angle during the simulation Rinsha Chk (Sun Feb 07 2021 - 05:48:52 PST)
[AMBER] polarizable FF in amber18 or 20 Vaibhav Dixit (Sun Feb 07 2021 - 02:01:37 PST)
- Re: [AMBER] polarizable FF in amber18 or 20 David A Case (Sun Feb 07 2021 - 07:34:01 PST)
- Re: [AMBER] polarizable FF in amber18 or 20 Vaibhav Dixit (Thu Apr 29 2021 - 21:03:38 PDT)
  - Re: [AMBER] polarizable FF in amber18 or 20 Ray Luo (Sat May 01 2021 - 12:14:51 PDT)
    - Re: [AMBER] polarizable FF in amber18 or 20 Vaibhav Dixit (Sat May 01 2021 - 23:35:25 PDT)
    - Re: [AMBER] polarizable FF in amber18 or 20 Ray Luo (Mon May 03 2021 - 10:11:36 PDT)
    - Re: [AMBER] polarizable FF in amber18 or 20 Vaibhav Dixit (Mon May 03 2021 - 11:02:43 PDT)
[AMBER] CPPTRAJ cannot open RXSGLD trajectories out of the box Charo del Genio (Sun Feb 07 2021 - 05:59:33 PST)
- Re: [AMBER] CPPTRAJ cannot open RXSGLD trajectories out of the box Daniel Roe (Sun Feb 07 2021 - 06:38:11 PST)
[AMBER] multi source calls in tleap Alan (Sun Feb 07 2021 - 11:50:12 PST)
- Re: [AMBER] multi source calls in tleap David A Case (Mon Feb 08 2021 - 06:50:07 PST)
  - Re: [AMBER] multi source calls in tleap Matias Machado (Thu Feb 11 2021 - 05:52:23 PST)
    - Re: [AMBER] multi source calls in tleap Alan (Sun Feb 14 2021 - 23:45:30 PST)
    - Re: [AMBER] multi source calls in tleap Matias Machado (Mon Feb 22 2021 - 11:09:00 PST)
[AMBER] mdgx ipolQ charges of a charged residue Luis Simon (Mon Feb 08 2021 - 01:23:05 PST)
[AMBER] TI with igb. = 6 Holly Freedman (Mon Feb 08 2021 - 09:47:02 PST)
Re: [AMBER] CPPTRAJ - KMeans Value for K Piotr Fajer (Mon Feb 08 2021 - 10:15:33 PST)
- Re: [AMBER] CPPTRAJ - KMeans Value for K Christina Bergonzo (Tue Feb 09 2021 - 05:45:22 PST)
[AMBER] IEEE_OVERFLOW_FLAG Mudrovcic, Korana (Tue Feb 09 2021 - 06:22:56 PST)
- Re: [AMBER] IEEE_OVERFLOW_FLAG David A Case (Mon Feb 22 2021 - 04:56:33 PST)
  - Re: [AMBER] IEEE_OVERFLOW_FLAG Åke Sandgren (Mon Feb 22 2021 - 05:52:17 PST)
[AMBER] Preparation of i-Motif structures Sruthi Sudhakar (Tue Feb 09 2021 - 13:30:41 PST)
- Re: [AMBER] Preparation of i-Motif structures Petr Stadlbauer (Wed Feb 10 2021 - 09:34:15 PST)
  - Re: [AMBER] Preparation of i-Motif structures Sruthi Sudhakar (Sat Jun 19 2021 - 00:36:31 PDT)
    - Re: [AMBER] Preparation of i-Motif structures Petr Stadlbauer (Sat Jun 19 2021 - 02:58:20 PDT)
[AMBER] single strand RNA parameters Jorge Iulek (Wed Feb 10 2021 - 09:41:56 PST)
- Re: [AMBER] single strand RNA parameters Daniel Roe (Thu Feb 11 2021 - 06:28:49 PST)
  - Re: [AMBER] single strand RNA parameters Jiri Sponer (Thu Feb 11 2021 - 07:39:45 PST)
    - Re: [AMBER] single strand RNA parameters Jorge Iulek (Thu Feb 11 2021 - 08:41:54 PST)
    - Re: [AMBER] single strand RNA parameters Daniel Roe (Thu Feb 11 2021 - 10:08:41 PST)
    - Re: [AMBER] single strand RNA parameters Daniel Roe (Thu Feb 11 2021 - 12:38:25 PST)
    - Re: [AMBER] single strand RNA parameters Jorge Iulek (Sat Feb 13 2021 - 01:59:39 PST)
    - Re: [AMBER] single strand RNA parameters Jiri Sponer (Thu Feb 11 2021 - 10:59:27 PST)
    - Re: [AMBER] single strand RNA parameters Jorge Iulek (Sat Feb 13 2021 - 02:03:10 PST)
[AMBER] maximum no of atoms for simulation Pinky Mazumder (Wed Feb 10 2021 - 14:11:14 PST)
- Re: [AMBER] maximum no of atoms for simulation Adrian Roitberg (Wed Feb 10 2021 - 14:29:09 PST)
  - Re: [AMBER] maximum no of atoms for simulation Pinky Mazumder (Wed Feb 10 2021 - 15:01:44 PST)
[AMBER] Questions about loading FF02 and MMGBSA Matthew Guberman-Pfeffer (Wed Feb 10 2021 - 18:40:46 PST)
- Re: [AMBER] Questions about loading FF02 and MMGBSA David A Case (Thu Feb 11 2021 - 04:42:14 PST)
[AMBER] Parameters for Iron Oxide Matthew Guberman-Pfeffer (Thu Feb 11 2021 - 02:42:10 PST)
- Re: [AMBER] Parameters for Iron Oxide Maria Nagan (Fri Feb 12 2021 - 14:49:07 PST)
[AMBER] High value for force constant is acceptable? Rinsha Chk (Thu Feb 11 2021 - 03:50:58 PST)
- Re: [AMBER] High value for force constant is acceptable? David A Case (Thu Feb 18 2021 - 05:25:37 PST)
  - Re: [AMBER] High value for force constant is acceptable? Carlos Simmerling (Thu Feb 18 2021 - 05:39:02 PST)
    - Re: [AMBER] High value for force constant is acceptable? Rinsha Chk (Thu Feb 18 2021 - 22:52:37 PST)
  - Re: [AMBER] High value for force constant is acceptable? Karl Kirschner (Fri Feb 19 2021 - 10:39:29 PST)
[AMBER] leap hangs on dihedral in frcmod? Kenneth Huang (Thu Feb 11 2021 - 14:08:58 PST)
- Re: [AMBER] leap hangs on dihedral in frcmod? Matias Machado (Fri Feb 12 2021 - 04:13:31 PST)
  - Re: [AMBER] leap hangs on dihedral in frcmod? Kenneth Huang (Fri Feb 12 2021 - 14:09:22 PST)
[AMBER] Testing pmemd.cuda.MPI - how many failed file comparisons are innocuous? Nikolay N. Kuzmich (Fri Feb 12 2021 - 01:44:56 PST)
- Re: [AMBER] Testing pmemd.cuda.MPI - how many failed file comparisons are innocuous? David A Case (Fri Feb 12 2021 - 04:07:53 PST)
- Re: [AMBER] Testing pmemd.cuda.MPI - how many failed file comparisons are innocuous? Nikolay N. Kuzmich (Fri Feb 12 2021 - 08:57:35 PST)
[AMBER] Amber20 GPU plus PLUMED Domenico Marson (Fri Feb 12 2021 - 04:02:46 PST)
- Re: [AMBER] Amber20 GPU plus PLUMED David A Case (Thu Feb 18 2021 - 05:24:04 PST)
[AMBER] Fwd: MMPBSA Error Sadaf Rani (Fri Feb 12 2021 - 05:13:17 PST)
[AMBER] tLeap, Fatal: Atom does not have a type Alysia Mandato (Fri Feb 12 2021 - 11:08:52 PST)
- Re: [AMBER] tLeap, Fatal: Atom does not have a type Kenneth Huang (Fri Feb 12 2021 - 14:32:32 PST)
- Re: [AMBER] tLeap, Fatal: Atom does not have a type Maria Nagan (Fri Feb 12 2021 - 14:41:58 PST)
  - Re: [AMBER] tLeap, Fatal: Atom does not have a type Alysia Mandato (Mon Feb 15 2021 - 13:17:10 PST)
    - Re: [AMBER] tLeap, Fatal: Atom does not have a type Carlos Simmerling (Mon Feb 15 2021 - 13:23:31 PST)
    - Re: [AMBER] tLeap, Fatal: Atom does not have a type David A Case (Tue Feb 16 2021 - 05:13:40 PST)
- Re: [AMBER] tLeap, Fatal: Atom does not have a type raissa.conceicao.bol.com.br (Tue Feb 16 2021 - 03:40:18 PST)
[AMBER] Using divalent ions in LEaP Sam Walsworth (Researcher) (Fri Feb 12 2021 - 13:30:36 PST)
- Re: [AMBER] Using divalent ions in LEaP Maria Nagan (Fri Feb 12 2021 - 13:45:32 PST)
  - Re: [AMBER] Using divalent ions in LEaP Sam Walsworth (Researcher) (Fri Feb 12 2021 - 14:04:26 PST)
    - Re: [AMBER] Using divalent ions in LEaP Maria Nagan (Fri Feb 12 2021 - 14:14:44 PST)
- Re: [AMBER] Using divalent ions in LEaP Kenneth Huang (Fri Feb 12 2021 - 14:23:30 PST)
- Re: [AMBER] Using divalent ions in LEaP David A Case (Sat Feb 13 2021 - 06:10:55 PST)
[AMBER] Error while setting up constant pH MD simulations Yashraj Kulkarni (Sat Feb 13 2021 - 06:55:57 PST)
- Re: [AMBER] Error while setting up constant pH MD simulations Jason Swails (Fri Feb 26 2021 - 05:44:50 PST)
[AMBER] Disparities between dG solv from GB and PB Models mish (Sat Feb 13 2021 - 13:55:33 PST)
- Re: [AMBER] Disparities between dG solv from GB and PB Models Ray Luo (Sat Feb 13 2021 - 14:21:27 PST)
  - Re: [AMBER] Disparities between dG solv from GB and PB Models mish (Sat Feb 13 2021 - 15:23:24 PST)
[AMBER] Altering ligand positions in Xleap Sruthi Sudhakar (Tue Feb 16 2021 - 02:44:10 PST)
- Re: [AMBER] Altering ligand positions in Xleap David A Case (Tue Feb 16 2021 - 05:17:44 PST)
  - Re: [AMBER] Altering ligand positions in Xleap Gordon Richard Chalmers (Tue Feb 16 2021 - 05:20:46 PST)
[AMBER] Membrane protein-ligand simulation - application of multiple FF - compatibility and reliability Prasanth G, Research Scholar (Tue Feb 16 2021 - 09:49:09 PST)
- Re: [AMBER] Membrane protein-ligand simulation - application of multiple FF - compatibility and reliability Matias Machado (Mon Feb 22 2021 - 17:16:54 PST)
[AMBER] error with AMBER installation Mohammad Alaraby (Wed Feb 17 2021 - 04:50:46 PST)
- Re: [AMBER] error with AMBER installation David A Case (Wed Feb 17 2021 - 11:20:12 PST)
[AMBER] theoretical doubt about TI Gabriel Jara (Wed Feb 17 2021 - 05:54:14 PST)
Re: [AMBER] Help with installation David A Case (Thu Feb 18 2021 - 05:16:32 PST)
[AMBER] Making sense of tip3p.frcmod Paul, Austin (Thu Feb 18 2021 - 16:18:12 PST)
- Re: [AMBER] Making sense of tip3p.frcmod David A Case (Thu Feb 18 2021 - 18:24:39 PST)
[AMBER] GaMD output (gamd.log) file analysis jacob wick (Fri Feb 19 2021 - 01:08:20 PST)
- [AMBER] Fwd: GaMD output (gamd.log) file analysis jacob wick (Sun Feb 21 2021 - 00:51:31 PST)
[AMBER] query regarding heme forcefield parameters Patil Pranita Uttamrao (Fri Feb 19 2021 - 02:07:27 PST)
- Re: [AMBER] query regarding heme forcefield parameters David A Case (Fri Feb 19 2021 - 07:38:35 PST)
[AMBER] Thermodynamic integration for protein-protein interactions WW (Fri Feb 19 2021 - 06:35:25 PST)
- Re: [AMBER] Thermodynamic integration for protein-protein interactions Carlos Simmerling (Fri Feb 19 2021 - 07:30:49 PST)
- Re: [AMBER] Thermodynamic integration for protein-protein interactions David A Case (Fri Feb 19 2021 - 07:33:25 PST)
  - Re: [AMBER] Thermodynamic integration for protein-protein interactions neildancer.sina.com (Fri Feb 19 2021 - 08:02:29 PST)
    - Re: [AMBER] Thermodynamic integration for protein-protein interactions David A Case (Mon Feb 22 2021 - 04:54:33 PST)
    - Re: [AMBER] Thermodynamic integration for protein-protein interactions neildancer.sina.com (Mon Feb 22 2021 - 05:32:14 PST)
  - Re: [AMBER] Thermodynamic integration for protein-protein interactions WW (Thu Apr 08 2021 - 15:32:04 PDT)
    - Re: [AMBER] Thermodynamic integration for protein-protein interactions David A Case (Fri Apr 09 2021 - 05:12:18 PDT)
    - Re: [AMBER] Thermodynamic integration for protein-protein interactions WW (Sat Apr 10 2021 - 19:43:48 PDT)
    - Re: [AMBER] Thermodynamic integration for protein-protein interactions David A Case (Sat Apr 17 2021 - 13:30:46 PDT)
    - Re: [AMBER] Thermodynamic integration for protein-protein interactions WW (Sun Apr 18 2021 - 09:37:40 PDT)
[AMBER] tip3p water model in amber14 Swisher, Justin S (Fri Feb 19 2021 - 08:48:24 PST)
- Re: [AMBER] tip3p water model in amber14 Carlos Simmerling (Fri Feb 19 2021 - 09:33:45 PST)
  - Re: [AMBER] tip3p water model in amber14 Swisher, Justin S (Thu Feb 25 2021 - 10:36:55 PST)
    - Re: [AMBER] tip3p water model in amber14 David A Case (Thu Feb 25 2021 - 12:04:35 PST)
    - Re: [AMBER] tip3p water model in amber14 Swisher, Justin S (Thu Feb 25 2021 - 16:29:06 PST)
    - Re: [AMBER] tip3p water model in amber14 David A Case (Thu Feb 25 2021 - 17:54:45 PST)
    - Re: [AMBER] tip3p water model in amber14 Swisher, Justin S (Fri Feb 26 2021 - 08:59:07 PST)
    - Re: [AMBER] tip3p water model in amber14 David A Case (Fri Feb 26 2021 - 14:13:38 PST)
[AMBER] Interaction energy by MM-PBSA for a superantigen with important Zn(II) center SATYAJIT KHATUA (Fri Feb 19 2021 - 09:56:53 PST)
- Re: [AMBER] Interaction energy by MM-PBSA for a superantigen with important Zn(II) center David A Case (Sat Feb 20 2021 - 06:24:25 PST)
- Re: [AMBER] Interaction energy by MM-PBSA for a superantigen with important Zn(II) center SATYAJIT KHATUA (Tue Feb 23 2021 - 21:20:23 PST)
- Re: [AMBER] Interaction energy by MM-PBSA for a superantigen with important Zn(II) center SATYAJIT KHATUA (Fri Mar 05 2021 - 02:53:07 PST)
[AMBER] MAXPR error in sander sp job Vaibhav Dixit (Fri Feb 19 2021 - 20:06:57 PST)
- Re: [AMBER] MAXPR error in sander sp job Vaibhav Dixit (Sat Feb 20 2021 - 05:10:05 PST)
- Re: [AMBER] MAXPR error in sander sp job David A Case (Sat Feb 20 2021 - 06:16:08 PST)
  - Re: [AMBER] MAXPR error in sander sp job Vaibhav Dixit (Sat Feb 20 2021 - 06:49:52 PST)
    - Re: [AMBER] MAXPR error in sander sp job David A Case (Sat Feb 20 2021 - 14:09:26 PST)
    - Re: [AMBER] MAXPR error in sander sp job Vaibhav Dixit (Sat Feb 20 2021 - 15:31:38 PST)
    - Re: [AMBER] MAXPR error in sander sp job Carlos Simmerling (Sat Feb 20 2021 - 15:56:24 PST)
    - Re: [AMBER] MAXPR error in sander sp job Vaibhav Dixit (Sat Feb 20 2021 - 16:26:31 PST)
    - Re: [AMBER] MAXPR error in sander sp job Vaibhav Dixit (Sat Feb 20 2021 - 22:58:02 PST)
    - Re: [AMBER] MAXPR error in sander sp job Carlos Simmerling (Sun Feb 21 2021 - 04:08:13 PST)
    - Re: [AMBER] MAXPR error in sander sp job Vaibhav Dixit (Mon Feb 22 2021 - 02:36:40 PST)
    - Re: [AMBER] MAXPR error in sander sp job Carlos Simmerling (Mon Feb 22 2021 - 03:48:01 PST)
    - Re: [AMBER] MAXPR error in sander sp job Vaibhav Dixit (Mon Feb 22 2021 - 03:58:36 PST)
    - Re: [AMBER] MAXPR error in sander sp job David A Case (Mon Feb 22 2021 - 04:50:26 PST)
    - Re: [AMBER] MAXPR error in sander sp job Vaibhav Dixit (Mon Feb 22 2021 - 07:30:42 PST)
    - Re: [AMBER] MAXPR error in sander sp job David A Case (Mon Feb 22 2021 - 10:13:13 PST)
    - Re: [AMBER] MAXPR error in sander sp job Vaibhav Dixit (Mon Feb 22 2021 - 20:50:12 PST)
[AMBER] Stacking energy calculation Athena N (Sat Feb 20 2021 - 00:52:04 PST)
[AMBER] Why do trajectories get corrupted? Victoria E Hill (Sat Feb 20 2021 - 08:36:44 PST)
- Re: [AMBER] Why do trajectories get corrupted? Maria Nagan (Sat Feb 20 2021 - 09:09:34 PST)
  - Re: [AMBER] Why do trajectories get corrupted? Victoria E Hill (Sun Feb 21 2021 - 04:58:10 PST)
    - Re: [AMBER] Why do trajectories get corrupted? Carlos Simmerling (Sun Feb 21 2021 - 05:17:40 PST)
    - Re: [AMBER] Why do trajectories get corrupted? Victoria E Hill (Sun Feb 21 2021 - 05:36:06 PST)
    - Re: [AMBER] Why do trajectories get corrupted? Carlos Simmerling (Sun Feb 21 2021 - 05:51:19 PST)
    - Re: [AMBER] Why do trajectories get corrupted? Victoria E Hill (Sun Feb 21 2021 - 06:12:56 PST)
    - Re: [AMBER] Why do trajectories get corrupted? Carlos Simmerling (Sun Feb 21 2021 - 08:31:42 PST)
    - Re: [AMBER] Why do trajectories get corrupted? Daniel Roe (Tue Feb 23 2021 - 11:26:33 PST)
[AMBER] Sufficiently equilibrated or not Delwakkada Liyanage, Senal Dinuka (Sat Feb 20 2021 - 11:17:14 PST)
- Re: [AMBER] Sufficiently equilibrated or not Lachele Foley (Sat Feb 20 2021 - 11:41:24 PST)
  - Re: [AMBER] Sufficiently equilibrated or not Delwakkada Liyanage, Senal Dinuka (Sat Feb 20 2021 - 11:46:01 PST)
    - Re: [AMBER] Sufficiently equilibrated or not Lachele Foley (Sat Feb 20 2021 - 11:55:15 PST)
    - Re: [AMBER] Sufficiently equilibrated or not Delwakkada Liyanage, Senal Dinuka (Sat Feb 20 2021 - 11:58:31 PST)
    - Re: [AMBER] Sufficiently equilibrated or not Lachele Foley (Sat Feb 20 2021 - 13:30:56 PST)
    - Re: [AMBER] Sufficiently equilibrated or not Delwakkada Liyanage, Senal Dinuka (Sat Feb 20 2021 - 18:33:52 PST)
    - Re: [AMBER] Sufficiently equilibrated or not Gordon Richard Chalmers (Sat Feb 20 2021 - 22:24:29 PST)
    - Re: [AMBER] Sufficiently equilibrated or not Lachele Foley (Sat Feb 20 2021 - 23:04:17 PST)
    - Re: [AMBER] Sufficiently equilibrated or not Carlos Simmerling (Sun Feb 21 2021 - 05:58:27 PST)
    - Re: [AMBER] Sufficiently equilibrated or not Gordon Richard Chalmers (Sun Feb 21 2021 - 08:12:59 PST)
    - Re: [AMBER] Sufficiently equilibrated or not Carlos Simmerling (Sun Feb 21 2021 - 08:29:37 PST)
    - Re: [AMBER] Sufficiently equilibrated or not Gordon Richard Chalmers (Sun Feb 21 2021 - 09:00:45 PST)
    - Re: [AMBER] Sufficiently equilibrated or not Delwakkada Liyanage, Senal Dinuka (Mon Feb 22 2021 - 09:27:01 PST)
    - Re: [AMBER] Sufficiently equilibrated or not Carlos Simmerling (Mon Feb 22 2021 - 10:00:49 PST)
    - Re: [AMBER] Sufficiently equilibrated or not Brian Radak (Sun Feb 21 2021 - 08:29:07 PST)
- Re: [AMBER] Sufficiently equilibrated or not Carlos Simmerling (Sat Feb 20 2021 - 12:35:24 PST)
- Re: [AMBER] Sufficiently equilibrated or not Pengfei Li (Fri Feb 26 2021 - 15:31:15 PST)
[AMBER] case studies of MD based drug discovery Vaibhav Dixit (Sun Feb 21 2021 - 05:05:28 PST)
[AMBER] Odd number of electrons divyabharathi korlepara (Mon Feb 22 2021 - 05:57:27 PST)
- Re: [AMBER] Odd number of electrons David A Case (Mon Feb 22 2021 - 10:19:50 PST)
  - Re: [AMBER] Odd number of electrons divyabharathi korlepara (Tue Feb 23 2021 - 20:43:25 PST)
    - Re: [AMBER] Odd number of electrons Gustaf Olsson (Wed Feb 24 2021 - 00:08:47 PST)
[AMBER] Acpype error: Timed out process killed Shilpa Gupta (Mon Feb 22 2021 - 07:24:04 PST)
- Re: [AMBER] Acpype error: Timed out process killed David A Case (Mon Feb 22 2021 - 10:22:21 PST)
  - Re: [AMBER] Acpype error: Timed out process killed Alan (Mon Feb 22 2021 - 12:18:46 PST)
[AMBER] Regarding restarting of Gaussian Accelerated MD. Sruthi Sudhakar (Mon Feb 22 2021 - 20:39:04 PST)
[AMBER] Problem with pmemd.MPI Pranjal Bhuyan (Tue Feb 23 2021 - 02:36:56 PST)
- Re: [AMBER] Problem with pmemd.MPI David A Case (Tue Feb 23 2021 - 04:41:57 PST)
  - Re: [AMBER] Problem with pmemd.MPI Pranjal Bhuyan (Tue Feb 23 2021 - 21:45:21 PST)
    - Re: [AMBER] Problem with pmemd.MPI David A Case (Wed Feb 24 2021 - 04:24:52 PST)
[AMBER] Multiple Harmonic Restraints Li,Haoxi (Tue Feb 23 2021 - 08:44:27 PST)
- Re: [AMBER] Multiple Harmonic Restraints Thomas Gaillard (Tue Feb 23 2021 - 09:20:41 PST)
[AMBER] How to recompile AmberTools Matthew Guberman-Pfeffer (Tue Feb 23 2021 - 21:41:46 PST)
- Re: [AMBER] How to recompile AmberTools Gustaf Olsson (Wed Feb 24 2021 - 00:11:14 PST)
- Re: [AMBER] How to recompile AmberTools Matthew Guberman-Pfeffer (Wed Feb 24 2021 - 12:04:58 PST)
  - Re: [AMBER] How to recompile AmberTools David A Case (Wed Feb 24 2021 - 13:06:38 PST)
  - Re: [AMBER] How to recompile AmberTools Gustaf Olsson (Thu Feb 25 2021 - 00:02:54 PST)
[AMBER] MDGX charge fitting with some charges fixed or restrained Luis Simon (Wed Feb 24 2021 - 00:34:30 PST)
Re: [AMBER] [lsimon.usal.es: MDGX charge fitting with some charges fixed or restrained] David Cerutti (Wed Feb 24 2021 - 05:25:12 PST)
- Re: [AMBER] [lsimon.usal.es: MDGX charge fitting with some charges fixed or restrained] Luis Simon (Wed Feb 24 2021 - 09:20:24 PST)
[AMBER] Apply Lennar-Jones potential between small molecules Ming Tang (Wed Feb 24 2021 - 14:51:46 PST)
- Re: [AMBER] Apply Lennar-Jones potential between small molecules Carlos Simmerling (Thu Feb 25 2021 - 09:01:46 PST)
  - Re: [AMBER] Apply Lennar-Jones potential between small molecules Carlos Simmerling (Thu Feb 25 2021 - 09:15:54 PST)
    - Re: [AMBER] Apply Lennar-Jones potential between small molecules Ming Tang (Thu Feb 25 2021 - 13:17:00 PST)
    - Re: [AMBER] Apply Lennar-Jones potential between small molecules Carlos Simmerling (Thu Feb 25 2021 - 13:32:10 PST)
    - Re: [AMBER] Apply Lennar-Jones potential between small molecules Ming Tang (Thu Feb 25 2021 - 14:25:49 PST)
  - Re: [AMBER] Apply Lennar-Jones potential between small molecules Ming Tang (Mon Mar 15 2021 - 16:28:21 PDT)
    - Re: [AMBER] Apply Lennar-Jones potential between small molecules Carlos Simmerling (Tue Mar 16 2021 - 05:32:12 PDT)
    - Re: [AMBER] Apply Lennar-Jones potential between small molecules David A Case (Tue Mar 16 2021 - 05:55:43 PDT)
    - Re: [AMBER] Apply Lennar-Jones potential between small molecules Carlos Simmerling (Tue Mar 16 2021 - 06:41:38 PDT)
    - Re: [AMBER] Apply Lennar-Jones potential between small molecules Ming Tang (Wed Mar 17 2021 - 21:15:18 PDT)
    - Re: [AMBER] Apply Lennar-Jones potential between small molecules Carlos Simmerling (Thu Mar 18 2021 - 03:35:40 PDT)
    - Re: [AMBER] Apply Lennar-Jones potential between small molecules David A Case (Thu Mar 18 2021 - 07:51:06 PDT)
    - Re: [AMBER] Apply Lennar-Jones potential between small molecules A R (Fri Apr 09 2021 - 09:46:14 PDT)
    - Re: [AMBER] Apply Lennar-Jones potential between small molecules David A Case (Fri Apr 09 2021 - 18:14:05 PDT)
    - Re: [AMBER] Apply Lennar-Jones potential between small molecules A R (Sat Apr 10 2021 - 05:01:58 PDT)
    - Re: [AMBER] Apply Lennar-Jones potential between small molecules David A Case (Sun Apr 11 2021 - 06:16:03 PDT)
    - Re: [AMBER] Apply Lennar-Jones potential between small molecules Ming Tang (Thu Mar 18 2021 - 07:53:33 PDT)
    - Re: [AMBER] Apply Lennar-Jones potential between small molecules Carlos Simmerling (Thu Mar 18 2021 - 08:05:49 PDT)
    - Re: [AMBER] Apply Lennar-Jones potential between small molecules Ming Tang (Mon Mar 22 2021 - 21:31:19 PDT)
    - Re: [AMBER] Apply Lennar-Jones potential between small molecules Carlos Simmerling (Tue Mar 23 2021 - 03:35:23 PDT)
    - Re: [AMBER] Apply Lennar-Jones potential between small molecules Ming Tang (Tue Mar 23 2021 - 16:20:59 PDT)
    - Re: [AMBER] Apply Lennar-Jones potential between small molecules Daniel Roe (Wed Mar 24 2021 - 06:48:09 PDT)
    - Re: [AMBER] Apply Lennar-Jones potential between small molecules Ming Tang (Wed Mar 24 2021 - 15:55:41 PDT)
    - Re: [AMBER] Apply Lennar-Jones potential between small molecules Jaime Rubio Martinez (Wed Apr 28 2021 - 01:51:55 PDT)
Re: [AMBER] Calculating forces Daniel Roe (Thu Feb 25 2021 - 02:32:52 PST)
- Re: [AMBER] Calculating forces Click, Timothy Howard (Fri Feb 26 2021 - 07:27:20 PST)
[AMBER] AmberTools20 parallel test errors Alain Arsene (Thu Feb 25 2021 - 02:53:50 PST)
- Re: [AMBER] AmberTools20 parallel test errors David A Case (Thu Feb 25 2021 - 04:20:18 PST)
[AMBER] GPU TI PROBLEM Umut Çağan Uçar (Thu Feb 25 2021 - 05:36:25 PST)
- Re: [AMBER] GPU TI PROBLEM accuratefreeenergy.gmail.com (Thu Feb 25 2021 - 06:12:48 PST)
  - Re: [AMBER] GPU TI PROBLEM Umut Çağan Uçar (Fri Feb 26 2021 - 00:46:09 PST)
    - Re: [AMBER] GPU TI PROBLEM accuratefreeenergy.gmail.com (Fri Feb 26 2021 - 10:07:32 PST)
[AMBER] Amber18 + Ambertools20 Rafał Bachorz (Thu Feb 25 2021 - 06:04:39 PST)
- Re: [AMBER] Amber18 + Ambertools20 David A Case (Thu Feb 25 2021 - 08:49:15 PST)
[AMBER] MMPBSA, signal SIGSEGV failure Matthew Guberman-Pfeffer (Thu Feb 25 2021 - 08:11:29 PST)
- Re: [AMBER] MMPBSA, signal SIGSEGV failure Ray Luo (Thu Feb 25 2021 - 09:09:36 PST)
[AMBER] help with cpptraj error (segmentation fault) Cato, Lee (Thu Feb 25 2021 - 10:12:20 PST)
- Re: [AMBER] help with cpptraj error (segmentation fault) Daniel Roe (Thu Feb 25 2021 - 10:32:28 PST)
- Re: [AMBER] help with cpptraj error (segmentation fault) Daniel Roe (Tue Apr 13 2021 - 06:09:09 PDT)
[AMBER] Molecule volume in cpptraj? Gustavo Seabra (Thu Feb 25 2021 - 10:56:10 PST)
- Re: [AMBER] Molecule volume in cpptraj? Daniel Roe (Fri Feb 26 2021 - 06:44:45 PST)
  - Re: [AMBER] Molecule volume in cpptraj? Gustavo Seabra (Fri Feb 26 2021 - 13:01:02 PST)
[AMBER] Steered MD Pinky Mazumder (Thu Feb 25 2021 - 12:14:30 PST)
- Re: [AMBER] Steered MD Adrian Roitberg (Thu Feb 25 2021 - 12:22:18 PST)
  - Re: [AMBER] Steered MD Pinky Mazumder (Fri Feb 26 2021 - 07:43:20 PST)
    - Re: [AMBER] Steered MD Adrian Roitberg (Fri Feb 26 2021 - 08:14:12 PST)
    - Re: [AMBER] Steered MD Pinky Mazumder (Sat Feb 27 2021 - 06:29:17 PST)
    - Re: [AMBER] Steered MD Pinky Mazumder (Sat Feb 27 2021 - 06:37:50 PST)
- Re: [AMBER] Steered MD Carlos Simmerling (Thu Feb 25 2021 - 12:26:58 PST)
  - Re: [AMBER] Steered MD Pinky Mazumder (Thu Feb 25 2021 - 16:13:19 PST)
[AMBER] dimer shifts under NPT ensemble Qinghua Liao (Thu Feb 25 2021 - 16:04:23 PST)
- Re: [AMBER] dimer shifts under NPT ensemble David A Case (Thu Feb 25 2021 - 18:02:24 PST)
  - Re: [AMBER] dimer shifts under NPT ensemble Thomas Cheatham (Thu Feb 25 2021 - 19:44:07 PST)
    - Re: [AMBER] dimer shifts under NPT ensemble Qinghua Liao (Thu Feb 25 2021 - 23:59:59 PST)
    - Re: [AMBER] dimer shifts under NPT ensemble Thomas Gaillard (Fri Feb 26 2021 - 04:41:54 PST)
    - Re: [AMBER] dimer shifts under NPT ensemble Qinghua Liao (Fri Feb 26 2021 - 14:58:29 PST)
    - Re: [AMBER] dimer shifts under NPT ensemble Qinghua Liao (Fri Feb 26 2021 - 15:25:49 PST)
  - Re: [AMBER] dimer shifts under NPT ensemble Qinghua Liao (Thu Feb 25 2021 - 23:31:16 PST)
[AMBER] Calculating pairwise RMSD of two proteins Sadaf Rani (Fri Feb 26 2021 - 10:31:20 PST)
- Re: [AMBER] Calculating pairwise RMSD of two proteins Daniel Roe (Fri Feb 26 2021 - 12:36:12 PST)
[AMBER] cpptraj CMAP flag issue with charmm-gui parm7 files Wesley Michael Botello-Smith (Fri Feb 26 2021 - 13:40:53 PST)
- Re: [AMBER] cpptraj CMAP flag issue with charmm-gui parm7 files Daniel Roe (Fri Feb 26 2021 - 17:50:17 PST)
[AMBER] atom number difference in topology and simulated trajectory Ayesha Fatima (Sat Feb 27 2021 - 00:10:20 PST)
- Re: [AMBER] atom number difference in topology and simulated trajectory Elvis A F Martis (Sat Feb 27 2021 - 01:46:44 PST)
  - Re: [AMBER] atom number difference in topology and simulated trajectory Ayesha Fatima (Sat Feb 27 2021 - 02:38:36 PST)
    - Re: [AMBER] atom number difference in topology and simulated trajectory Elvis A F Martis (Sat Feb 27 2021 - 03:26:21 PST)
    - Re: [AMBER] atom number difference in topology and simulated trajectory Ayesha Fatima (Sat Feb 27 2021 - 22:56:56 PST)
    - Re: [AMBER] atom number difference in topology and simulated trajectory Elvis A F Martis (Sat Feb 27 2021 - 23:07:30 PST)
    - Re: [AMBER] atom number difference in topology and simulated trajectory Ayesha Fatima (Sun Feb 28 2021 - 01:38:34 PST)
    - Re: [AMBER] atom number difference in topology and simulated trajectory Elvis A F Martis (Sun Feb 28 2021 - 03:01:27 PST)
    - Re: [AMBER] atom number difference in topology and simulated trajectory Ayesha Fatima (Sun Feb 28 2021 - 08:39:55 PST)
    - Re: [AMBER] atom number difference in topology and simulated trajectory Elvis A F Martis (Sun Feb 28 2021 - 22:10:24 PST)
    - Re: [AMBER] atom number difference in topology and simulated trajectory Ayesha Fatima (Sun Mar 07 2021 - 08:50:12 PST)
    - Re: [AMBER] atom number difference in topology and simulated trajectory Elvis A F Martis (Sun Mar 07 2021 - 21:24:11 PST)
[AMBER] Amber-forcefield for QM/MM calculation Rinsha Chk (Mon Mar 01 2021 - 05:05:28 PST)
[AMBER] Superimpose mohamed marzouk (Mon Mar 01 2021 - 10:07:43 PST)
- Re: [AMBER] Superimpose Daniel Roe (Thu Mar 04 2021 - 11:06:11 PST)
  - Re: [AMBER] Superimpose mohamed marzouk (Sat Mar 27 2021 - 03:57:47 PDT)
[AMBER] Effect of different gamma_ln values Liao (Mon Mar 01 2021 - 12:29:29 PST)
- Re: [AMBER] Effect of different gamma_ln values Adrian Roitberg (Mon Mar 01 2021 - 15:42:50 PST)
[AMBER] positional and NMR distance restraints together Qinghua Liao (Mon Mar 01 2021 - 17:15:31 PST)
- Re: [AMBER] positional and NMR distance restraints together David A Case (Tue Mar 02 2021 - 06:13:25 PST)
[AMBER] use orca in amber wangjianing_mail (Tue Mar 02 2021 - 01:37:05 PST)
- Re: [AMBER] use orca in amber wangjianing_mail (Tue Mar 02 2021 - 02:31:31 PST)
- Re: [AMBER] use orca in amber James Kress (Tue Mar 02 2021 - 14:41:20 PST)
[AMBER] Free Energy Calculations using LIE and FEW Helena Damtoft Tjørnelund (Tue Mar 02 2021 - 02:21:27 PST)
[AMBER] Using DFT-D3(BJ) during QM/MM calculations Zhiyi Wu (Tue Mar 02 2021 - 02:22:02 PST)
- Re: [AMBER] Using DFT-D3(BJ) during QM/MM calculations Goetz, Andreas (Tue Mar 02 2021 - 12:05:27 PST)
  - Re: [AMBER] Using DFT-D3(BJ) during QM/MM calculations Zhiyi Wu (Tue Mar 02 2021 - 12:12:32 PST)
[AMBER] How to plot the Phi-Psi picture in Section 7 of “Tutorial 6.6 Nudged Elastic Band (NEB) simulations”? Li Dailin (Tue Mar 02 2021 - 20:10:01 PST)
- Re: [AMBER] How to plot the Phi-Psi picture in Section 7 of “Tutorial 6.6 Nudged Elastic Band (NEB) simulations”? Christina Bergonzo (Wed Mar 03 2021 - 06:17:30 PST)
  - [AMBER] 答复: How to plot the Phi-Psi picture in Section 7 of “Tutorial 6.6 Nudged Elastic Band (NEB) simulations”? Li Dailin (Fri Mar 05 2021 - 18:37:16 PST)
- Re: [AMBER] How to plot the Phi-Psi picture in Section 7 of “Tutorial 6.6 Nudged Elastic Band (NEB) simulations”? Carlos Simmerling (Wed Mar 03 2021 - 06:19:36 PST)
  - [AMBER] 答复: How to plot the Phi-Psi picture in Section 7 of “Tutorial 6.6 Nudged Elastic Band (NEB) simulations”? Li Dailin (Fri Mar 05 2021 - 18:38:33 PST)
[AMBER] MMPBSA/ Parmed error Jenny 148 (Tue Mar 02 2021 - 22:39:15 PST)
- Re: [AMBER] MMPBSA/ Parmed error David A Case (Wed Mar 03 2021 - 05:30:52 PST)
  - Re: [AMBER] MMPBSA/ Parmed error Jenny 148 (Wed Mar 03 2021 - 06:18:46 PST)
  - Re: [AMBER] MMPBSA/ Parmed error Sruthi Sudhakar (Wed Mar 03 2021 - 06:32:24 PST)
    - Re: [AMBER] MMPBSA/ Parmed error Hai Nguyen (Wed Mar 03 2021 - 18:18:53 PST)
    - Re: [AMBER] MMPBSA/ Parmed error Jenny 148 (Fri Mar 05 2021 - 23:02:56 PST)
    - Re: [AMBER] MMPBSA/ Parmed error David A Case (Sat Mar 06 2021 - 05:48:55 PST)
    - Re: [AMBER] MMPBSA/ Parmed error Jenny 148 (Mon Mar 08 2021 - 07:16:02 PST)
[AMBER] Simulation of optimized ligand without docking Ramanathan Rajesh (Wed Mar 03 2021 - 04:19:38 PST)
- Re: [AMBER] Simulation of optimized ligand without docking David A Case (Wed Mar 03 2021 - 05:37:09 PST)
[AMBER] Practical questions on NMR-refinment Gustavo Seabra (Wed Mar 03 2021 - 12:33:51 PST)
- Re: [AMBER] Practical questions on NMR-refinment David A Case (Wed Mar 03 2021 - 18:31:08 PST)
  - Re: [AMBER] Practical questions on NMR-refinment Gustavo Seabra (Thu Mar 04 2021 - 08:56:18 PST)
    - Re: [AMBER] Practical questions on NMR-refinment David A Case (Thu Mar 04 2021 - 13:20:27 PST)
[AMBER] makeDIST_RST Ming Tang (Wed Mar 03 2021 - 21:04:27 PST)
- Re: [AMBER] makeDIST_RST David A Case (Thu Mar 04 2021 - 05:41:04 PST)
- Re: [AMBER] makeDIST_RST Daniel Roe (Thu Mar 04 2021 - 08:17:50 PST)
  - Re: [AMBER] makeDIST_RST Ming Tang (Sat Mar 06 2021 - 18:20:58 PST)
    - Re: [AMBER] makeDIST_RST David A Case (Sun Mar 07 2021 - 05:06:17 PST)
    - Re: [AMBER] makeDIST_RST Ming Tang (Tue Mar 09 2021 - 14:51:09 PST)
    - Re: [AMBER] makeDIST_RST Daniel Roe (Tue Mar 09 2021 - 15:36:20 PST)
    - Re: [AMBER] makeDIST_RST Ming Tang (Wed Mar 10 2021 - 17:39:08 PST)
    - Re: [AMBER] makeDIST_RST David A Case (Tue Mar 09 2021 - 17:58:43 PST)
    - Re: [AMBER] makeDIST_RST Ming Tang (Sun Mar 14 2021 - 01:01:37 PST)
[AMBER] Problem Running E-REMD on GPUs Matthew Guberman-Pfeffer (Thu Mar 04 2021 - 19:13:20 PST)
Re: [AMBER] gcc9 aishen.free.fr (Thu Mar 04 2021 - 23:05:50 PST)
- Re: [AMBER] gcc9 Gustaf Olsson (Thu Mar 04 2021 - 23:44:45 PST)
Re: [AMBER] Parametrization of Virtual sites in Halogens David Cerutti (Fri Mar 05 2021 - 07:28:51 PST)
[AMBER] Pending deprecation of paramfit: Amber21 or Amber22? David Cerutti (Fri Mar 05 2021 - 08:01:22 PST)
[AMBER] Ambertools20 with amber18 Pinky Mazumder (Fri Mar 05 2021 - 10:32:17 PST)
- Re: [AMBER] Ambertools20 with amber18 David A Case (Fri Mar 05 2021 - 11:44:27 PST)
[AMBER] How to define COM for groups in ASMD Matthew Guberman-Pfeffer (Sat Mar 06 2021 - 00:12:38 PST)
- Re: [AMBER] How to define COM for groups in ASMD Kellon Belfon (Tue Mar 09 2021 - 18:37:38 PST)
[AMBER] Error when compiling AMBER20 fmying.xmu.edu.cn (Sun Mar 07 2021 - 22:38:32 PST)
- Re: [AMBER] Error when compiling AMBER20 David A Case (Mon Mar 08 2021 - 05:13:29 PST)
[AMBER] Is it possible to obtain vacuum charges (and only vacuum charges) with mdgx? Luis Simon (Mon Mar 08 2021 - 01:48:10 PST)
[AMBER] The issue regarding to list index out of range 辛志宏 (Mon Mar 08 2021 - 04:12:03 PST)
- Re: [AMBER] The issue regarding to list index out of range Mariano Curti (Mon Mar 08 2021 - 04:21:37 PST)
[AMBER] Generating library from cif file. sriram raghavan (Mon Mar 08 2021 - 07:24:10 PST)
- Re: [AMBER] Generating library from cif file. David A Case (Mon Mar 08 2021 - 08:31:40 PST)
[AMBER] Single Point QM/MM energy using Amber-Q-Chem interface Bowleg, Jerrano (Mon Mar 08 2021 - 07:55:54 PST)
- Re: [AMBER] Single Point QM/MM energy using Amber-Q-Chem interface Clorice Reinhardt (Mon Mar 08 2021 - 08:55:49 PST)
  - Re: [AMBER] Single Point QM/MM energy using Amber-Q-Chem interface Bowleg, Jerrano (Mon Mar 08 2021 - 09:56:48 PST)
    - Re: [AMBER] Single Point QM/MM energy using Amber-Q-Chem interface Clorice Reinhardt (Mon Mar 08 2021 - 13:53:08 PST)
[AMBER] Problem with AMBER20 compilation using Intel/20.4 compiler Samuel Mohan Dass, Premila (Mon Mar 08 2021 - 11:20:52 PST)
- Re: [AMBER] Problem with AMBER20 compilation using Intel/20.4 compiler Samuel Mohan Dass, Premila (Mon Mar 08 2021 - 11:25:09 PST)
- Re: [AMBER] Problem with AMBER20 compilation using Intel/20.4 compiler David A Case (Tue Mar 09 2021 - 09:15:56 PST)
  - Re: [AMBER] Problem with AMBER20 compilation using Intel/20.4 compiler Samuel Mohan Dass, Premila (Tue Mar 09 2021 - 09:23:34 PST)
- Re: [AMBER] Problem with AMBER20 compilation using Intel/20.4 compiler Shawn Brown (Wed Mar 24 2021 - 06:43:36 PDT)
  - Re: [AMBER] Problem with AMBER20 compilation using Intel/20.4 compiler David A Case (Wed Mar 24 2021 - 13:50:45 PDT)
    - Re: [AMBER] Problem with AMBER20 compilation using Intel/20.4 compiler Samuel Mohan Dass, Premila (Wed Mar 24 2021 - 14:10:22 PDT)
    - Re: [AMBER] Problem with AMBER20 compilation using Intel/20.4 compiler Shawn Brown (Thu Mar 25 2021 - 05:20:16 PDT)
Re: [AMBER] The issue regarding to list index out of range (???) 辛志宏 (Mon Mar 08 2021 - 16:07:57 PST)
[AMBER] Pair interaction energy Eduardo R. Almeida (Tue Mar 09 2021 - 06:53:50 PST)
- Re: [AMBER] Pair interaction energy Dr. Anselm Horn (Tue Mar 09 2021 - 11:50:42 PST)
  - Re: [AMBER] Pair interaction energy Eduardo R. Almeida (Tue Mar 09 2021 - 12:04:46 PST)
    - Re: [AMBER] Pair interaction energy Eduardo R. Almeida (Tue Mar 09 2021 - 14:33:43 PST)
    - Re: [AMBER] Pair interaction energy Dr. Anselm Horn (Wed Mar 10 2021 - 00:15:22 PST)
    - Re: [AMBER] Pair interaction energy Eduardo R. Almeida (Wed Mar 10 2021 - 05:23:41 PST)
[AMBER] Turning initial velocity off for continuous MD runs Aanshi Gandhi (Tue Mar 09 2021 - 09:35:24 PST)
- Re: [AMBER] Turning initial velocity off for continuous MD runs David A Case (Tue Mar 09 2021 - 13:12:03 PST)
[AMBER] LJ parameters LOZANO ORDOÑEZ, HECTOR (Wed Mar 10 2021 - 08:59:33 PST)
- Re: [AMBER] LJ parameters Luis Simon (Wed Mar 10 2021 - 09:14:57 PST)
  - Re: [AMBER] LJ parameters LOZANO ORDOÑEZ, HECTOR (Wed Mar 10 2021 - 09:48:51 PST)
- Re: [AMBER] LJ parameters Anthony Cruz-Balberdy (Wed Mar 10 2021 - 10:10:48 PST)
[AMBER] Problem with CG minimization in implicit solvent Alejandro Gil Ley (Wed Mar 10 2021 - 11:17:05 PST)
- Re: [AMBER] Problem with CG minimization in implicit solvent Adrian Roitberg (Thu Mar 11 2021 - 07:36:49 PST)
  - Re: [AMBER] Problem with CG minimization in implicit solvent David A Case (Thu Mar 11 2021 - 13:18:35 PST)
    - Re: [AMBER] Problem with CG minimization in implicit solvent Chris Neale (Thu Mar 11 2021 - 20:33:37 PST)
- Re: [AMBER] Problem with CG minimization in implicit solvent Alejandro Gil Ley (Thu Mar 11 2021 - 13:56:26 PST)
[AMBER] pmemd.cuda unstable with ff19SB+OPC and HMassRepartition Tucker Burgin (Wed Mar 10 2021 - 11:25:22 PST)
- Re: [AMBER] pmemd.cuda unstable with ff19SB+OPC and HMassRepartition Carlos Simmerling (Wed Mar 10 2021 - 12:52:30 PST)
- Re: [AMBER] pmemd.cuda unstable with ff19SB+OPC and HMassRepartition Gerald Monard (Thu Mar 11 2021 - 03:47:07 PST)
  - Re: [AMBER] pmemd.cuda unstable with ff19SB+OPC and HMassRepartition David A Case (Thu Mar 11 2021 - 05:48:30 PST)
- Re: [AMBER] pmemd.cuda unstable with ff19SB+OPC and HMassRepartition Tucker Burgin (Mon Mar 22 2021 - 08:10:42 PDT)
[AMBER] Secstruct error Kodituwakku,Dimuthu Nirmani (Wed Mar 10 2021 - 19:48:34 PST)
- Re: [AMBER] Secstruct error Daniel Roe (Sat Mar 13 2021 - 05:52:32 PST)
[AMBER] sander/orca/xtb ：Low parallel efficiency wangjianing_mail (Wed Mar 10 2021 - 20:12:58 PST)
- Re: [AMBER] sander/orca/xtb ：Low parallel efficiency Adrian Roitberg (Thu Mar 11 2021 - 06:11:30 PST)
[AMBER] GPU installation error amber18 Renato Araujo (Thu Mar 11 2021 - 04:53:14 PST)
- Re: [AMBER] GPU installation error amber18 David A Case (Thu Mar 11 2021 - 05:54:22 PST)
[AMBER] constant ph md Abhik Ghosh Moulick (Thu Mar 11 2021 - 08:00:46 PST)
- Re: [AMBER] constant ph md Adrian Roitberg (Thu Mar 11 2021 - 08:16:40 PST)
[AMBER] Why a target ion failed to move along the pathway in the simulated annealing version of Nudged Elastic Band (NEB) calculations? Li Dailin (Thu Mar 11 2021 - 17:55:57 PST)
- Re: [AMBER] Why a target ion failed to move along the pathway in the simulated annealing version of Nudged Elastic Band (NEB) calculations? Adrian Roitberg (Fri Mar 12 2021 - 12:20:54 PST)
  - [AMBER] 答复: Why a target ion failed to move along the pathway in the simulated annealing version of Nudged Elastic Band (NEB) calculations? Li Dailin (Fri Mar 12 2021 - 16:26:57 PST)
[AMBER] Error in tleap richa anand (Fri Mar 12 2021 - 02:04:28 PST)
[AMBER] Tleap Fatal error richa anand (Fri Mar 12 2021 - 03:09:37 PST)
- Re: [AMBER] Tleap Fatal error David A Case (Fri Mar 12 2021 - 04:54:30 PST)
- Re: [AMBER] Tleap Fatal error Kenneth Huang (Fri Mar 12 2021 - 22:16:12 PST)
[AMBER] Ligand moving out of active site after 250ns Sruthi Sudhakar (Fri Mar 12 2021 - 22:08:23 PST)
- Re: [AMBER] Ligand moving out of active site after 250ns Kenneth Huang (Sat Mar 13 2021 - 08:43:09 PST)
Re: [AMBER] AMBER Digest, Vol 3300, Issue 1 richa anand (Sat Mar 13 2021 - 00:29:36 PST)
[AMBER] Request for the sha256sum od amber20 Hector Martinez-Seara (Sat Mar 13 2021 - 02:43:07 PST)
[AMBER] Running MMPBSA on protein membrane system built using CHARMMGUI Chuck is Busy (Sat Mar 13 2021 - 09:51:09 PST)
- Re: [AMBER] Running MMPBSA on protein membrane system built using CHARMMGUI David A Case (Sat Mar 13 2021 - 14:08:06 PST)
  - Re: [AMBER] Running MMPBSA on protein membrane system built using CHARMMGUI Chuck is Busy (Sat Mar 13 2021 - 15:03:08 PST)
    - Re: [AMBER] Running MMPBSA on protein membrane system built using CHARMMGUI Ray Luo (Sat Mar 13 2021 - 15:31:44 PST)
    - Re: [AMBER] Running MMPBSA on protein membrane system built using CHARMMGUI Chuck is Busy (Sat Mar 13 2021 - 15:48:32 PST)
    - Re: [AMBER] Running MMPBSA on protein membrane system built using CHARMMGUI Ray Luo (Sat Mar 13 2021 - 18:33:34 PST)
    - Re: [AMBER] Running MMPBSA on protein membrane system built using CHARMMGUI David A Case (Sat Mar 13 2021 - 18:08:48 PST)
    - Re: [AMBER] Running MMPBSA on protein membrane system built using CHARMMGUI Chuck is Busy (Sat Mar 13 2021 - 19:11:04 PST)
[AMBER] AmberTools20 fails to compile with gcc10 (with workaround) Charo del Genio (Sat Mar 13 2021 - 12:06:20 PST)
- Re: [AMBER] AmberTools20 fails to compile with gcc10 (with workaround) aishen.free.fr (Sat Mar 13 2021 - 13:55:23 PST)
- Re: [AMBER] AmberTools20 fails to compile with gcc10 (with workaround) David A Case (Sat Mar 13 2021 - 14:03:57 PST)
- Re: [AMBER] AmberTools20 fails to compile with gcc10 (with workaround) David A Case (Sat Mar 13 2021 - 18:02:18 PST)
  - Re: [AMBER] AmberTools20 fails to compile with gcc10 (with workaround) Charo del Genio (Sun Mar 14 2021 - 07:41:06 PDT)
    - Re: [AMBER] AmberTools20 fails to compile with gcc10 (with workaround) David A Case (Sun Mar 14 2021 - 13:25:33 PDT)
    - Re: [AMBER] AmberTools20 fails to compile with gcc10 (with workaround) Carlos Simmerling (Sun Mar 14 2021 - 14:18:33 PDT)
    - Re: [AMBER] AmberTools20 fails to compile with gcc10 (with workaround) Charo del Genio (Mon Mar 15 2021 - 04:18:35 PDT)
[AMBER] Energy minimization problem richa anand (Sun Mar 14 2021 - 00:15:39 PST)
- Re: [AMBER] Energy minimization problem David A Case (Sun Mar 14 2021 - 05:56:48 PDT)
[AMBER] About the extract snapshop as input files from a trajectory files 辛志宏 (Sun Mar 14 2021 - 03:09:37 PDT)
[AMBER] Installation Ambertools20 Mac M1 (arm64) Mailing list (Sun Mar 14 2021 - 05:59:40 PDT)
- Re: [AMBER] Installation Ambertools20 Mac M1 (arm64) Gould, Ian R (Mon Mar 15 2021 - 01:12:52 PDT)
  - Re: [AMBER] Installation Ambertools20 Mac M1 (arm64) Mailing list (Mon Mar 15 2021 - 01:38:43 PDT)
    - Re: [AMBER] Installation Ambertools21 Mac M1 (arm64) Florian Nachon (Sat May 01 2021 - 05:49:43 PDT)
    - Re: [AMBER] Installation Ambertools21 Mac M1 (arm64) David A Case (Sat May 01 2021 - 09:51:00 PDT)
    - Re: [AMBER] Installation Ambertools21 Mac M1 (arm64) Yoshitaka Moriwaki (Sun May 02 2021 - 00:04:50 PDT)
    - Re: [AMBER] Installation Ambertools21 Mac M1 (arm64) Florian Nachon (Sun May 02 2021 - 04:38:41 PDT)
[AMBER] x=sequence aishen.free.fr (Mon Mar 15 2021 - 00:30:05 PDT)
- Re: [AMBER] x=sequence Christina Bergonzo (Mon Mar 15 2021 - 04:07:31 PDT)
  - Re: [AMBER] x=sequence aishen.free.fr (Mon Mar 15 2021 - 06:57:30 PDT)
[AMBER] hbond cpptraj Jon Uranga (Mon Mar 15 2021 - 06:47:17 PDT)
- Re: [AMBER] hbond cpptraj Clorice Reinhardt (Mon Mar 15 2021 - 15:27:27 PDT)
[AMBER] MCPB.py ZINC Mediated interactions parameterization Rana Rehan Khalid (Mon Mar 15 2021 - 14:56:17 PDT)
[AMBER] Visualizing NetCDF in VMD - ERROR Jatin Kashyap (Mon Mar 15 2021 - 21:23:07 PDT)
- Re: [AMBER] Visualizing NetCDF in VMD - ERROR Gustaf Olsson (Tue Mar 16 2021 - 01:00:38 PDT)
  - Re: [AMBER] Visualizing NetCDF in VMD - ERROR aishen.free.fr (Tue Mar 16 2021 - 01:49:59 PDT)
  - Re: [AMBER] Visualizing NetCDF in VMD - ERROR Jatin Kashyap (Tue Mar 16 2021 - 18:20:46 PDT)
    - Re: [AMBER] Visualizing NetCDF in VMD - ERROR Gustaf Olsson (Wed Mar 17 2021 - 00:51:29 PDT)
    - Re: [AMBER] Visualizing NetCDF in VMD - ERROR Hai Nguyen (Wed Mar 17 2021 - 09:47:40 PDT)
    - Re: [AMBER] Visualizing NetCDF in VMD - ERROR aishen.free.fr (Wed Mar 17 2021 - 14:13:13 PDT)
    - Re: [AMBER] Visualizing NetCDF in VMD - ERROR Hai Nguyen (Wed Mar 17 2021 - 20:47:15 PDT)
    - Re: [AMBER] Visualizing NetCDF in VMD - ERROR Jatin Kashyap (Wed Mar 17 2021 - 15:50:53 PDT)
    - Re: [AMBER] Visualizing NetCDF in VMD - ERROR Gustaf Olsson (Thu Mar 18 2021 - 02:02:29 PDT)
    - Re: [AMBER] Visualizing NetCDF in VMD - ERROR Daniel Roe (Wed Mar 17 2021 - 11:22:54 PDT)
    - Re: [AMBER] Visualizing NetCDF in VMD - ERROR Jatin Kashyap (Wed Mar 17 2021 - 13:54:09 PDT)
    - Re: [AMBER] Visualizing NetCDF in VMD - ERROR David A Case (Wed Mar 17 2021 - 18:09:57 PDT)
- Re: [AMBER] Visualizing NetCDF in VMD - ERROR ışılay öztürk (Tue Mar 16 2021 - 02:39:28 PDT)
  - Re: [AMBER] Visualizing NetCDF in VMD - ERROR Gustaf Olsson (Tue Mar 16 2021 - 02:50:11 PDT)
    - Re: [AMBER] Visualizing NetCDF in VMD - ERROR ışılay öztürk (Tue Mar 16 2021 - 03:00:09 PDT)
    - Re: [AMBER] Visualizing NetCDF in VMD - ERROR Gustaf Olsson (Tue Mar 16 2021 - 04:59:09 PDT)
    - Re: [AMBER] Visualizing NetCDF in VMD - ERROR ışılay öztürk (Tue Mar 16 2021 - 05:35:12 PDT)
[AMBER] Missing atom types for ligand with chlorine atoms Aliakbartehrani Zahra (Tue Mar 16 2021 - 00:23:38 PDT)
- Re: [AMBER] Missing atom types for ligand with chlorine atoms Juraj Dobias (Tue Mar 16 2021 - 01:27:05 PDT)
- Re: [AMBER] Missing atom types for ligand with chlorine atoms David A Case (Tue Mar 16 2021 - 06:03:08 PDT)
[AMBER] segmentation fault error richa anand (Tue Mar 16 2021 - 23:29:45 PDT)
- Re: [AMBER] segmentation fault error David A Case (Wed Mar 17 2021 - 06:58:54 PDT)
[AMBER] saving pdb and rst at specific frames in trajectory Sadaf Rani (Wed Mar 17 2021 - 06:23:17 PDT)
- Re: [AMBER] saving pdb and rst at specific frames in trajectory Gustaf Olsson (Wed Mar 17 2021 - 06:48:58 PDT)
  - Re: [AMBER] saving pdb and rst at specific frames in trajectory Sadaf Rani (Wed Mar 17 2021 - 07:09:53 PDT)
    - Re: [AMBER] saving pdb and rst at specific frames in trajectory Sadaf Rani (Thu Mar 18 2021 - 00:40:22 PDT)
    - Re: [AMBER] saving pdb and rst at specific frames in trajectory Gustaf Olsson (Thu Mar 18 2021 - 01:39:51 PDT)
    - Re: [AMBER] saving pdb and rst at specific frames in trajectory Gustaf Olsson (Thu Mar 18 2021 - 02:01:06 PDT)
- Re: [AMBER] saving pdb and rst at specific frames in trajectory Daniel Roe (Mon Mar 22 2021 - 07:43:42 PDT)
[AMBER] Unit of Electric Field Frequency Shakir Ali Siddiqui (Thu Mar 18 2021 - 04:05:13 PDT)
[AMBER] New In CPPTRAJ Daniel Roe (Thu Mar 18 2021 - 09:44:06 PDT)
- Re: [AMBER] New In CPPTRAJ Gustavo Seabra (Thu Mar 18 2021 - 16:52:51 PDT)
  - Re: [AMBER] New In CPPTRAJ aishen.free.fr (Fri Mar 19 2021 - 00:29:02 PDT)
- Re: [AMBER] New In CPPTRAJ An Ta (Fri Mar 19 2021 - 03:41:58 PDT)
- Re: [AMBER] New In CPPTRAJ Jatin Kashyap (Fri Mar 19 2021 - 03:46:35 PDT)
[AMBER] AMBER 18 Installation error Rituparna Roy (Fri Mar 19 2021 - 01:35:13 PDT)
- Re: [AMBER] AMBER 18 Installation error David A Case (Fri Mar 19 2021 - 06:56:18 PDT)
  - Re: [AMBER] AMBER 18 Installation error Rituparna Roy (Fri Mar 19 2021 - 07:29:44 PDT)
    - Re: [AMBER] AMBER 18 Installation error David A Case (Fri Mar 19 2021 - 17:52:37 PDT)
[AMBER] MMPBSA per residue decomposition - Calculation speed Jatin Kashyap (Fri Mar 19 2021 - 03:11:52 PDT)
- Re: [AMBER] MMPBSA per residue decomposition - Calculation speed David A Case (Fri Mar 19 2021 - 06:59:51 PDT)
  - Re: [AMBER] MMPBSA per residue decomposition - Calculation speed Jatin Kashyap (Tue Mar 30 2021 - 21:51:53 PDT)
    - Re: [AMBER] MMPBSA per residue decomposition - Calculation speed David A Case (Wed Mar 31 2021 - 05:23:17 PDT)
    - Re: [AMBER] MMPBSA per residue decomposition - Calculation speed Jatin Kashyap (Fri Apr 02 2021 - 13:23:43 PDT)
    - Re: [AMBER] MMPBSA per residue decomposition - Calculation speed Adrian Roitberg (Fri Apr 02 2021 - 13:30:46 PDT)
    - Re: [AMBER] MMPBSA per residue decomposition - Calculation speed Jatin Kashyap (Fri Apr 02 2021 - 13:43:13 PDT)
    - Re: [AMBER] MMPBSA per residue decomposition - Calculation speed Jatin Kashyap (Mon Apr 05 2021 - 15:33:24 PDT)
    - Re: [AMBER] MMPBSA per residue decomposition - Calculation speed Kashyap, Jatin (Wed Apr 07 2021 - 19:02:00 PDT)
    - Re: [AMBER] MMPBSA per residue decomposition - Calculation speed David A Case (Thu Apr 08 2021 - 05:17:48 PDT)
Re: [AMBER] New in CPPTRAJ Nikolay N. Kuzmich (Fri Mar 19 2021 - 12:35:57 PDT)
[AMBER] How to assess mutant-induced instability with MM-GBSA Matthew Guberman-Pfeffer (Fri Mar 19 2021 - 13:49:37 PDT)
- Re: [AMBER] How to assess mutant-induced instability with MM-GBSA David A Case (Sat Mar 20 2021 - 06:08:07 PDT)
[AMBER] Loading Topology & Trajectory Files Jatin Kashyap (Fri Mar 19 2021 - 14:24:41 PDT)
- Re: [AMBER] Loading Topology & Trajectory Files Daniel Roe (Mon Mar 22 2021 - 07:37:49 PDT)
  - Re: [AMBER] Loading Topology & Trajectory Files Gustaf Olsson (Tue Mar 23 2021 - 02:51:24 PDT)
    - Re: [AMBER] Loading Topology & Trajectory Files Daniel Roe (Wed Mar 24 2021 - 06:37:50 PDT)
    - Re: [AMBER] Loading Topology & Trajectory Files Gustaf Olsson (Wed Mar 24 2021 - 07:00:36 PDT)
[AMBER] Unknown PB option use_sav=0 Lennart Gundelach (Sat Mar 20 2021 - 01:07:50 PDT)
- Re: [AMBER] Unknown PB option use_sav=0 Ray Luo (Sun Mar 21 2021 - 17:04:37 PDT)
[AMBER] Solvating my box with specified number of water molecules 库米尔 (Sat Mar 20 2021 - 09:20:21 PDT)
- Re: [AMBER] Solvating my box with specified number of water molecules Matias Machado (Sun Mar 21 2021 - 08:08:00 PDT)
- Re: [AMBER] Solvating my box with specified number of water molecules Daniel Roe (Mon Mar 22 2021 - 07:22:32 PDT)
[AMBER] SIRAH CG Protein with Implicit Solvent Leung, Jeremy (Sat Mar 20 2021 - 10:09:31 PDT)
- Re: [AMBER] SIRAH CG Protein with Implicit Solvent Carlos Simmerling (Sun Mar 21 2021 - 07:00:45 PDT)
  - Re: [AMBER] SIRAH CG Protein with Implicit Solvent Matias Machado (Sun Mar 21 2021 - 07:55:38 PDT)
    - Re: [AMBER] SIRAH CG Protein with Implicit Solvent Leung, Jeremy (Mon Mar 22 2021 - 08:59:09 PDT)
[AMBER] 3D-RISM solvent placement with MoFT He, Amy (Sun Mar 21 2021 - 19:10:45 PDT)
- Re: [AMBER] 3D-RISM solvent placement with MoFT He, Amy (Mon Mar 22 2021 - 10:32:12 PDT)
- Re: [AMBER] 3D-RISM solvent placement with MoFT George M. Giambasu (Tue Mar 23 2021 - 18:31:53 PDT)
- Re: [AMBER] 3D-RISM solvent placement with MoFT He, Amy (Wed Mar 24 2021 - 21:59:06 PDT)
  - Re: [AMBER] 3D-RISM solvent placement with MoFT George Madalin Giambasu (Sun Mar 28 2021 - 18:42:25 PDT)
- Re: [AMBER] 3D-RISM solvent placement with MoFT He, Amy (Mon Mar 29 2021 - 22:16:06 PDT)
[AMBER] cpptraj killed MYRIAN TORRES RICO (Mon Mar 22 2021 - 02:37:51 PDT)
- Re: [AMBER] cpptraj killed Daniel Roe (Mon Mar 22 2021 - 07:25:50 PDT)
  - Re: [AMBER] cpptraj killed MYRIAN TORRES RICO (Mon Mar 22 2021 - 10:18:51 PDT)
    - Re: [AMBER] cpptraj killed Gustaf Olsson (Tue Mar 23 2021 - 00:45:34 PDT)
    - Re: [AMBER] cpptraj killed Mariano Curti (Tue Mar 23 2021 - 01:28:07 PDT)
[AMBER] Pmemd to run TI on protein mutations zz sheng (Mon Mar 22 2021 - 11:00:27 PDT)
- Re: [AMBER] Pmemd to run TI on protein mutations Carlos Simmerling (Mon Mar 22 2021 - 12:58:23 PDT)
  - Re: [AMBER] Pmemd to run TI on protein mutations zz sheng (Thu Mar 25 2021 - 07:09:38 PDT)
[AMBER] Seeking suggestions for breaking a covalent link between atoms Amit Sharma (Asstt. Prof., MCARS) (Tue Mar 23 2021 - 01:54:59 PDT)
- Re: [AMBER] Seeking suggestions for breaking a covalent link between atoms David A Case (Tue Mar 23 2021 - 06:40:29 PDT)
  - Re: [AMBER] Seeking suggestions for breaking a covalent link between atoms Amit Sharma (Asstt. Prof., MCARS) (Wed Mar 24 2021 - 07:28:11 PDT)
    - Re: [AMBER] Seeking suggestions for breaking a covalent link between atoms David A Case (Wed Mar 24 2021 - 08:17:49 PDT)
[AMBER] Benchmarks for new RTX3060 Игорь Злотников (Tue Mar 23 2021 - 10:43:23 PDT)
- Re: [AMBER] Benchmarks for new RTX3060 Игорь Злотников (Tue Mar 23 2021 - 10:52:15 PDT)
  - [AMBER] CpHMD with structurally different protonation states? Dr. Anselm Horn (Wed Mar 24 2021 - 04:58:04 PDT)
    - Re: [AMBER] CpHMD with structurally different protonation states? Cruzeiro, Vinicius (Wed Mar 24 2021 - 10:12:22 PDT)
    - [AMBER] MMPBSA errors A. Bakheit (Thu Mar 25 2021 - 03:15:11 PDT)
    - Re: [AMBER] MMPBSA errors David A Case (Thu Mar 25 2021 - 05:42:17 PDT)
    - Re: [AMBER] CpHMD with structurally different protonation states? Adrian Roitberg (Wed Mar 24 2021 - 10:22:59 PDT)
    - Re: [AMBER] CpHMD with structurally different protonation states? Dr. Anselm Horn (Thu Mar 25 2021 - 01:18:32 PDT)
    - [AMBER] Force field parameters for TYS ? Dr. Anselm Horn (Fri Mar 26 2021 - 11:44:11 PDT)
[AMBER] erro: cudaMemcpy GpuBuffer::Download failed an illegal memory access was encountered Renato Araujo (Wed Mar 24 2021 - 04:19:17 PDT)
- Re: [AMBER] erro: cudaMemcpy GpuBuffer::Download failed an illegal memory access was encountered David A Case (Wed Mar 24 2021 - 04:35:12 PDT)
  - Re: [AMBER] erro: cudaMemcpy GpuBuffer::Download failed an illegal memory access was encountered Renato Araujo (Wed Mar 24 2021 - 05:06:27 PDT)
  - Re: [AMBER] erro: cudaMemcpy GpuBuffer::Download failed an illegal memory access was encountered Renato Araujo (Wed Mar 24 2021 - 06:30:11 PDT)
    - Re: [AMBER] erro: cudaMemcpy GpuBuffer::Download failed an illegal memory access was encountered David A Case (Wed Mar 24 2021 - 08:07:13 PDT)
    - Re: [AMBER] erro: cudaMemcpy GpuBuffer::Download failed an illegal memory access was encountered Renato Araujo (Mon Mar 29 2021 - 05:47:19 PDT)
    - Re: [AMBER] erro: cudaMemcpy GpuBuffer::Download failed an illegal memory access was encountered David A Case (Mon Mar 29 2021 - 09:36:08 PDT)
    - Re: [AMBER] erro: cudaMemcpy GpuBuffer::Download failed an illegal memory access was encountered Renato Araujo (Mon Mar 29 2021 - 10:16:47 PDT)
    - Re: [AMBER] erro: cudaMemcpy GpuBuffer::Download failed an illegal memory access was encountered Song, Lin (Mon Mar 29 2021 - 10:37:33 PDT)
    - Re: [AMBER] erro: cudaMemcpy GpuBuffer::Download failed an illegal memory access was encountered Renato Araujo (Mon Mar 29 2021 - 10:42:07 PDT)
[AMBER] Discrepancy in pb binding energy (MMPBSA.py tutorial) Ali Saad Kusay (Wed Mar 24 2021 - 06:33:10 PDT)
[AMBER] Electric Field Gradient Mani Radh (Thu Mar 25 2021 - 04:24:42 PDT)
- Re: [AMBER] Electric Field Gradient David A Case (Thu Mar 25 2021 - 05:48:45 PDT)
- Re: [AMBER] Electric Field Gradient James Kress (Thu Mar 25 2021 - 09:23:29 PDT)
[AMBER] Addition of hydrogens - isoelectric point of protein Prasanth G, Research Scholar (Thu Mar 25 2021 - 12:11:49 PDT)
- Re: [AMBER] Addition of hydrogens - isoelectric point of protein Adrian Roitberg (Thu Mar 25 2021 - 12:14:21 PDT)
- Re: [AMBER] Addition of hydrogens - isoelectric point of protein Prasanth G, Research Scholar (Fri Mar 26 2021 - 18:25:39 PDT)
[AMBER] Selection of forcefield for protein-ligand simulations Prasanth G, Research Scholar (Thu Mar 25 2021 - 12:22:18 PDT)
- Re: [AMBER] Selection of forcefield for protein-ligand simulations Carlos Simmerling (Thu Mar 25 2021 - 12:49:54 PDT)
- [AMBER] Selection of forcefield for protein-ligand simulations Prasanth G, Research Scholar (Fri Mar 26 2021 - 17:24:26 PDT)
  - Re: [AMBER] Selection of forcefield for protein-ligand simulations Thomas Cheatham (Fri Mar 26 2021 - 17:52:47 PDT)
    - Re: [AMBER] Selection of forcefield for protein-ligand simulations Jaime Rubio Martinez (Sun Mar 28 2021 - 02:46:33 PDT)
[AMBER] Clustering based on predefined centroids Abhilash J (Thu Mar 25 2021 - 13:17:27 PDT)
- Re: [AMBER] Clustering based on predefined centroids Christina Bergonzo (Fri Mar 26 2021 - 05:35:23 PDT)
[AMBER] Problem with packmol-memgen when I try to installing Amber20 in GPU Dr. Gerardo Pérez Hernández (Fri Mar 26 2021 - 04:00:07 PDT)
- Re: [AMBER] Problem with packmol-memgen when I try to installing Amber20 in GPU David A Case (Fri Mar 26 2021 - 04:58:58 PDT)
- Re: [AMBER] Problem with packmol-memgen when I try to installing Amber20 in GPU Stephan Schott (Fri Mar 26 2021 - 05:21:12 PDT)
  - Re: [AMBER] Problem with packmol-memgen when I try to installing Amber20 in GPU Dr. Gerardo Pérez Hernández (Fri Mar 26 2021 - 13:10:09 PDT)
    - Re: [AMBER] Problem with packmol-memgen when I try to installing Amber20 in GPU David A Case (Fri Mar 26 2021 - 13:45:06 PDT)
[AMBER] Conversion of CHARMM optimized pdb to AMBER compatible pdb Cato, Lee (Fri Mar 26 2021 - 09:34:32 PDT)
- Re: [AMBER] Conversion of CHARMM optimized pdb to AMBER compatible pdb Carlos Simmerling (Fri Mar 26 2021 - 09:36:44 PDT)
- Re: [AMBER] Conversion of CHARMM optimized pdb to AMBER compatible pdb David A Case (Fri Mar 26 2021 - 13:34:39 PDT)
[AMBER] Distance tolerance for identifying common atoms in thermodynamics integration zz sheng (Fri Mar 26 2021 - 11:19:11 PDT)
- Re: [AMBER] Distance tolerance for identifying common atoms in thermodynamics integration David A Case (Fri Mar 26 2021 - 13:40:19 PDT)
  - Re: [AMBER] Distance tolerance for identifying common atoms in thermodynamics integration zz sheng (Fri Mar 26 2021 - 13:56:59 PDT)
    - Re: [AMBER] Distance tolerance for identifying common atoms in thermodynamics integration zz sheng (Mon Apr 05 2021 - 08:00:43 PDT)
[AMBER] Calculation halted on pmemd.cuda 库米尔 (Fri Mar 26 2021 - 17:10:06 PDT)
- Re: [AMBER] Calculation halted on pmemd.cuda Carlos Simmerling (Fri Mar 26 2021 - 18:32:29 PDT)
- Re: [AMBER] Calculation halted on pmemd.cuda 库米尔 (Sun Mar 28 2021 - 00:22:04 PDT)
  - Re: [AMBER] Calculation halted on pmemd.cuda Carlos Simmerling (Sun Mar 28 2021 - 04:25:19 PDT)
- Re: [AMBER] Calculation halted on pmemd.cuda David A Case (Sun Mar 28 2021 - 05:31:32 PDT)
- Re: [AMBER] Calculation halted on pmemd.cuda 库米尔 (Fri Apr 09 2021 - 09:44:04 PDT)
[AMBER] Using average frame for nmode entropy calculation? Liao (Sat Mar 27 2021 - 12:10:42 PDT)
- Re: [AMBER] Using average frame for nmode entropy calculation? David A Case (Sun Mar 28 2021 - 05:37:30 PDT)
  - Re: [AMBER] Using average frame for nmode entropy calculation? Liao (Sun Mar 28 2021 - 07:48:03 PDT)
    - [AMBER] Is it possible to create a deb for ubuntu or a pypi one ? aishen.free.fr (Sun Mar 28 2021 - 08:22:59 PDT)
    - Re: [AMBER] Is it possible to create a deb for ubuntu or a pypi one ? David A Case (Sun Mar 28 2021 - 14:06:07 PDT)
    - Re: [AMBER] Is it possible to create a deb for ubuntu or a pypi one ? Hrishikesh Dhondge (Mon Mar 29 2021 - 00:13:29 PDT)
    - Re: [AMBER] Is it possible to create a deb for ubuntu or a pypi one ? David A Case (Mon Mar 29 2021 - 05:28:53 PDT)
    - Re: [AMBER] Is it possible to create a deb for ubuntu or a pypi one ? aishen.free.fr (Mon Mar 29 2021 - 12:24:17 PDT)
    - [AMBER] about pytraj/cpptraj aishen (Mon Jun 07 2021 - 08:18:41 PDT)
    - Re: [AMBER] about pytraj/cpptraj David A Case (Mon Jun 07 2021 - 11:30:55 PDT)
    - Re: [AMBER] Using average frame for nmode entropy calculation? David A Case (Sun Mar 28 2021 - 13:43:20 PDT)
    - Re: [AMBER] Using average frame for nmode entropy calculation? Liao (Mon Mar 29 2021 - 11:05:42 PDT)
    - Re: [AMBER] Using average frame for nmode entropy calculation? Adrian Roitberg (Tue Mar 30 2021 - 09:20:37 PDT)
    - Re: [AMBER] Using average frame for nmode entropy calculation? Liao (Wed Mar 31 2021 - 20:07:49 PDT)
[AMBER] Unit of Electric field frequency Shakir Ali Siddiqui (Sun Mar 28 2021 - 12:03:21 PDT)
[AMBER] CHARMM Output - Empty Restraint File Aanshi Gandhi (Mon Mar 29 2021 - 08:46:46 PDT)
- Re: [AMBER] CHARMM Output - Empty Restraint File Carlos Simmerling (Mon Mar 29 2021 - 09:57:08 PDT)
  - Re: [AMBER] CHARMM Output - Empty Restraint File Aanshi Gandhi (Mon Mar 29 2021 - 10:29:52 PDT)
    - Re: [AMBER] CHARMM Output - Empty Restraint File Carlos Simmerling (Mon Mar 29 2021 - 11:25:48 PDT)
[AMBER] Calculating SASA using Surf and Molsurf Loo Kang (Mon Mar 29 2021 - 19:10:28 PDT)
[AMBER] Calculating displacement from PMF Pinky Mazumder (Tue Mar 30 2021 - 10:10:08 PDT)
- [AMBER] Great news! Adrian Roitberg (Thu Apr 01 2021 - 07:51:14 PDT)
  - Re: [AMBER] Great news! Ross Walker (Thu Apr 01 2021 - 08:05:58 PDT)
    - Re: [AMBER] Great news! andrea.cavalli.irb.usi.ch (Thu Apr 01 2021 - 08:10:23 PDT)
    - Re: [AMBER] Great news! Gordon Richard Chalmers (Thu Apr 01 2021 - 08:18:02 PDT)
    - Re: [AMBER] Great news! Karl Kirschner (Thu Apr 01 2021 - 08:26:09 PDT)
  - Re: [AMBER] Great news! James Kress (Thu Apr 01 2021 - 14:06:59 PDT)
    - Re: [AMBER] Great news! Piotr Fajer (Thu Apr 01 2021 - 14:08:58 PDT)
  - Re: [AMBER] Great news! Matias Machado (Fri Apr 02 2021 - 14:14:55 PDT)
[AMBER] Convert SIRAH coarse-grained model back to all-atomic pdb file format? Michael Shokhen (Tue Mar 30 2021 - 23:39:57 PDT)
- Re: [AMBER] Convert SIRAH coarse-grained model back to all-atomic pdb file format? Charo del Genio (Wed Mar 31 2021 - 00:39:45 PDT)
  - Re: [AMBER] Convert SIRAH coarse-grained model back to all-atomic pdb file format? Dr. Anselm Horn (Wed Mar 31 2021 - 01:08:58 PDT)
    - Re: [AMBER] Convert SIRAH coarse-grained model back to all-atomic pdb file format? Carlos Simmerling (Wed Mar 31 2021 - 04:00:48 PDT)
    - Re: [AMBER] Convert SIRAH coarse-grained model back to all-atomic pdb file format? Matias Machado (Wed Mar 31 2021 - 08:26:05 PDT)
[AMBER] Antechamber and mol2 file with .<TRIPOS>UNITY_ATOM_ATTR Alan (Wed Mar 31 2021 - 00:18:12 PDT)
- Re: [AMBER] Antechamber and mol2 file with .<TRIPOS>UNITY_ATOM_ATTR David A Case (Wed Mar 31 2021 - 05:45:28 PDT)
 - Re: [AMBER] Antechamber and mol2 file with .<TRIPOS>UNITY_ATOM_ATTR Scott Brozell (Fri Apr 16 2021 - 19:03:52 PDT)
 - Re: [AMBER] Antechamber and mol2 file with .<TRIPOS>UNITY_ATOM_ATTR Alan (Mon Apr 19 2021 - 03:40:47 PDT)
[AMBER] Calculating displacement from PMF Pinky Mazumder (Wed Mar 31 2021 - 06:58:49 PDT)
[AMBER] error while building non-GPU accelerated mpi version of amber Homeo Morphism (Thu Apr 01 2021 - 04:35:12 PDT)
- Re: [AMBER] error while building non-GPU accelerated mpi version of amber David A Case (Thu Apr 01 2021 - 06:08:38 PDT)
[AMBER] Questions about using the command "lie" Marko Sever (Thu Apr 01 2021 - 05:48:02 PDT)
[AMBER] example files for the hcp option for GB David A Case (Thu Apr 01 2021 - 06:30:49 PDT)
[AMBER] D-amino acid library gard nelson (Fri Apr 02 2021 - 11:14:50 PDT)
- Re: [AMBER] D-amino acid library Carlos Simmerling (Fri Apr 02 2021 - 11:47:56 PDT)
- Re: [AMBER] D-amino acid library gard nelson (Fri Apr 02 2021 - 13:26:30 PDT)
  - Re: [AMBER] D-amino acid library Carlos Simmerling (Fri Apr 02 2021 - 14:18:36 PDT)
[AMBER] Heat Output File Issue Swisher, Justin S (Fri Apr 02 2021 - 12:35:35 PDT)
- Re: [AMBER] Heat Output File Issue David A Case (Fri Apr 02 2021 - 17:34:49 PDT)
[AMBER] Protein dimension Samanta M (Sat Apr 03 2021 - 05:42:45 PDT)
- Re: [AMBER] Protein dimension Carlos Simmerling (Sat Apr 03 2021 - 06:11:28 PDT)
  - Re: [AMBER] Protein dimension Daniel Roe (Sun Apr 04 2021 - 07:11:25 PDT)
[AMBER] force field balance vs accuracy Brent Krueger (Mon Apr 05 2021 - 08:11:47 PDT)
- Re: [AMBER] force field balance vs accuracy Carlos Simmerling (Mon Apr 05 2021 - 08:31:33 PDT)
  - Re: [AMBER] force field balance vs accuracy Vaibhav Dixit (Mon Apr 05 2021 - 09:10:52 PDT)
[AMBER] Discrepancy in experimental and MMPBSA pattern of binding energy Manisha (Tue Apr 06 2021 - 07:55:56 PDT)
- Re: [AMBER] Discrepancy in experimental and MMPBSA pattern of binding energy Adrian Roitberg (Tue Apr 06 2021 - 08:54:22 PDT)
- Re: [AMBER] Discrepancy in experimental and MMPBSA pattern of binding energy Manisha (Tue Apr 06 2021 - 23:27:30 PDT)
- Re: [AMBER] Discrepancy in experimental and MMPBSA pattern of binding energy Manisha (Sun Apr 11 2021 - 22:50:16 PDT)
  - Re: [AMBER] Discrepancy in experimental and MMPBSA pattern of binding energy David A Case (Mon Apr 12 2021 - 05:59:49 PDT)
[AMBER] cleaning after installation Thomas Gaillard (Tue Apr 06 2021 - 08:23:44 PDT)
- Re: [AMBER] cleaning after installation David A Case (Tue Apr 06 2021 - 18:26:25 PDT)
Re: [AMBER] Discrepancy in experimental and MMPBSA pattern of Matthew Guberman-Pfeffer (Tue Apr 06 2021 - 12:06:43 PDT)
[AMBER] Add molecule to prmtop/inpcrd ? Gustavo Seabra (Tue Apr 06 2021 - 14:26:19 PDT)
- Re: [AMBER] Add molecule to prmtop/inpcrd ? Matias Machado (Wed Apr 07 2021 - 06:30:28 PDT)
- Re: [AMBER] Add molecule to prmtop/inpcrd ? Daniel Roe (Wed Apr 07 2021 - 07:31:42 PDT)
  - Re: [AMBER] Add molecule to prmtop/inpcrd ? Gustavo Seabra (Wed Apr 07 2021 - 12:29:17 PDT)
    - Re: [AMBER] Add molecule to prmtop/inpcrd ? David A Case (Wed Apr 07 2021 - 13:47:03 PDT)
[AMBER] Help for NETCDF Error :Input/Output error 余鸿艳 (Wed Apr 07 2021 - 04:51:19 PDT)
[AMBER] parmchk vs. parmchk2 for metal-ligand parameterization SARAH JEANNE LEFAVE (Wed Apr 07 2021 - 08:00:11 PDT)
[AMBER] Error using MCPB Maschietto, Federica (Wed Apr 07 2021 - 08:08:02 PDT)
[AMBER] Per residue free energy decomposition is not working ABDUL BASIT (Wed Apr 07 2021 - 08:42:10 PDT)
[AMBER] moving water away from a residue German P. Barletta (Wed Apr 07 2021 - 11:25:33 PDT)
[AMBER] molecular-dynamics docking: when everything docks to the receptor's site, how do you deal with it? Homeo Morphism (Thu Apr 08 2021 - 00:34:56 PDT)
- Re: [AMBER] molecular-dynamics docking: when everything docks to the receptor's site, how do you deal with it? David A Case (Thu Apr 08 2021 - 05:28:08 PDT)
[AMBER] Per residue free energy is not decomposed correctly Abdul Basit (Thu Apr 08 2021 - 10:03:52 PDT)
[AMBER] Erro installing AMBER18 with RTX3070 and CUDA 10.2 and NVIDIA 460.67 driver Giorgos Lambrinidis (Fri Apr 09 2021 - 04:09:23 PDT)
[AMBER] Error installing AMBER18 with RTX3070 and CUDA 10.2 and NVIDIA 460.67 driver Giorgos Lambrinidis (Fri Apr 09 2021 - 04:47:22 PDT)
- Re: [AMBER] Error installing AMBER18 with RTX3070 and CUDA 10.2 and NVIDIA 460.67 driver Ross Walker (Fri Apr 09 2021 - 06:14:09 PDT)
  - Re: [AMBER] Error installing AMBER18 with RTX3070 and CUDA 10.2 and NVIDIA 460.67 driver Giorgos Lambrinidis (Fri Apr 09 2021 - 09:03:24 PDT)
[AMBER] cpptraj atom definition bug found during RMSD/distance calculation? Liao (Fri Apr 09 2021 - 13:39:38 PDT)
- Re: [AMBER] cpptraj atom definition bug found during RMSD/distance calculation? Daniel Roe (Mon Apr 12 2021 - 06:26:52 PDT)
[AMBER] Questions about amber-adding counterions 马芳芳 (Sat Apr 10 2021 - 18:54:21 PDT)
- Re: [AMBER] Questions about amber-adding counterions Carlos Simmerling (Sun Apr 11 2021 - 03:56:48 PDT)
[AMBER] chromophore file. David Gae (Sat Apr 10 2021 - 23:44:22 PDT)
- Re: [AMBER] chromophore file. David A Case (Sun Apr 11 2021 - 06:22:21 PDT)
Re: [AMBER] Questions about amber-adding counterions (Carlos Simmerling) 马芳芳 (Sun Apr 11 2021 - 17:16:00 PDT)
- Re: [AMBER] Questions about amber-adding counterions (Carlos Simmerling) Carlos Simmerling (Mon Apr 12 2021 - 05:30:02 PDT)
- Re: [AMBER] Questions about amber-adding counterions (Carlos Simmerling) David A Case (Mon Apr 12 2021 - 05:49:35 PDT)
  - Re: [AMBER] Questions about amber-adding counterions (Carlos Simmerling) Carlos Simmerling (Mon Apr 12 2021 - 06:08:10 PDT)
[AMBER] Obtaining 3D structures from Reweighted PMF plots of accelerated MD Sruthi Sudhakar (Mon Apr 12 2021 - 03:33:48 PDT)
[AMBER] How to track oxygen molecules in MD Damiano Spadoni (Mon Apr 12 2021 - 09:51:01 PDT)
- Re: [AMBER] How to track oxygen molecules in MD Markowska (Mon Apr 12 2021 - 10:12:06 PDT)
- Re: [AMBER] How to track oxygen molecules in MD Daniel Roe (Tue Apr 13 2021 - 06:48:04 PDT)
  - Re: [AMBER] How to track oxygen molecules in MD Damiano Spadoni (Tue Apr 13 2021 - 07:17:16 PDT)
    - Re: [AMBER] How to track oxygen molecules in MD Damiano Spadoni (Wed Apr 14 2021 - 07:16:14 PDT)
    - Re: [AMBER] How to track oxygen molecules in MD Daniel Roe (Wed Apr 14 2021 - 07:48:05 PDT)
    - Re: [AMBER] How to track oxygen molecules in MD Markowska (Wed Apr 14 2021 - 08:27:13 PDT)
Re: [AMBER] Questions about amber-adding counterions (Carlos Simmerling and David A Case) 马芳芳 (Mon Apr 12 2021 - 19:13:55 PDT)
[AMBER] Problems when installing AMBER20 on CentOS 7: multiple definition of 'cifpin' 石谷沁 (Mon Apr 12 2021 - 20:48:20 PDT)
- Re: [AMBER] Problems when installing AMBER20 on CentOS 7: multiple definition of 'cifpin' David A Case (Tue Apr 13 2021 - 05:41:38 PDT)
[AMBER] 答复: Problems when installing AMBER20 on CentOS 7: multiple definition of 'cifpin' 石谷沁 (Mon Apr 12 2021 - 23:17:53 PDT)
- Re: [AMBER] 答复: Problems when installing AMBER20 on CentOS 7: multiple definition of 'cifpin' Tru Huynh (Tue Apr 13 2021 - 03:04:59 PDT)
- Re: [AMBER] 答复: Problems when installing AMBER20 on CentOS 7: multiple definition of 'cifpin' David A Case (Tue Apr 13 2021 - 05:44:52 PDT)
  - [AMBER] 答复: [ambermd.org代发]Re: 答复: Problems when installing AMBER20 on CentOS 7: multiple definition of 'cifpin' 石谷沁 (Tue Apr 13 2021 - 06:34:34 PDT)
    - Re: [AMBER] 答复: [ambermd.org代发]Re: 答复: Problems when installing AMBER20 on CentOS 7: multiple definition of 'cifpin' David A Case (Tue Apr 13 2021 - 08:33:49 PDT)
    - Re: [AMBER] 答复: [ambermd.org代发]Re: 答复: Problems when installing AMBER20 on CentOS 7: multiple definition of 'cifpin' Gerald Monard (Tue Apr 13 2021 - 15:49:43 PDT)
    - [AMBER] 答复: [ambermd.org代发]Re: 答复: [ambermd.org代发]Re: 答复: Problems when installing AMBER20 on CentOS 7: multiple definition of 'cifpin' 石谷沁 (Wed Apr 14 2021 - 03:22:35 PDT)
[AMBER] SMD analysing question (Xiaodong) 吴晓东 (Tue Apr 13 2021 - 18:26:04 PDT)
- Re: [AMBER] SMD analysing question (Xiaodong) Vishal Singh (Tue Apr 13 2021 - 19:23:07 PDT)
[AMBER] TI error on last window of calculations Rafał Madaj (Wed Apr 14 2021 - 01:35:43 PDT)
[AMBER] Nonstandard Residue Fernandez, Joseph P. (Wed Apr 14 2021 - 06:45:21 PDT)
- Re: [AMBER] Nonstandard Residue Lauren Raguette (Wed Apr 14 2021 - 08:24:26 PDT)
[AMBER] .rst file not produced during production run Roberts, Amy L2 (Wed Apr 14 2021 - 09:51:07 PDT)
- Re: [AMBER] .rst file not produced during production run Carlos Simmerling (Wed Apr 14 2021 - 10:02:06 PDT)
  - Re: [AMBER] .rst file not produced during production run Roberts, Amy L2 (Fri Apr 16 2021 - 12:04:57 PDT)
    - Re: [AMBER] .rst file not produced during production run David A Case (Fri Apr 16 2021 - 14:01:29 PDT)
    - Re: [AMBER] .rst file not produced during production run Roberts, Amy L2 (Wed Apr 21 2021 - 14:16:42 PDT)
[AMBER] Forcefield loading order and water parameters Reza Esmaeeli (Wed Apr 14 2021 - 10:24:26 PDT)
- Re: [AMBER] Forcefield loading order and water parameters Kellon Belfon (Wed Apr 14 2021 - 13:55:41 PDT)
- Re: [AMBER] Forcefield loading order and water parameters Gustaf Olsson (Thu Apr 15 2021 - 00:00:16 PDT)
[AMBER] "No module named pytraj" during make test step 石谷沁 (Wed Apr 14 2021 - 18:33:18 PDT)
- Re: [AMBER] "No module named pytraj" during make test step 石谷沁 (Thu Apr 15 2021 - 00:56:57 PDT)
- Re: [AMBER] "No module named pytraj" during make test step David A Case (Thu Apr 15 2021 - 05:22:43 PDT)
  - [AMBER] 答复: [ambermd.org代发]Re: "No module named pytraj" during make test step 石谷沁 (Thu Apr 15 2021 - 20:25:23 PDT)
    - Re: [AMBER] 答复: [ambermd.org代发]Re: "No module named pytraj" during make test step Hai Nguyen (Thu Apr 15 2021 - 21:40:25 PDT)
    - [AMBER] 答复: [ambermd.org代发]Re: 答复: [ambermd.org代发]Re: "No module named pytraj" during make test step 石谷沁 (Thu Apr 15 2021 - 22:55:45 PDT)
    - [AMBER] 答复: [ambermd.org代发]Re: 答复: [ambermd.org代发]Re: "No module named pytraj" during make test step 石谷沁 (Thu Apr 15 2021 - 23:27:01 PDT)
    - Re: [AMBER] 答复: [ambermd.org代发]Re: 答复: [ambermd.org代发]Re: "No module named pytraj" during make test step Hai Nguyen (Sat Apr 17 2021 - 22:14:43 PDT)
- Re: [AMBER] "No module named pytraj" during make test step Hai Nguyen (Thu Apr 15 2021 - 11:38:54 PDT)
  - [AMBER] 答复: [ambermd.org代发]Re: "No module named pytraj" during make test step 石谷沁 (Thu Apr 15 2021 - 20:02:47 PDT)
[AMBER] Cyclic Peptides: leap keeps adding missing atoms Tainah Dorina Marforio (Thu Apr 15 2021 - 03:34:07 PDT)
- Re: [AMBER] Cyclic Peptides: leap keeps adding missing atoms Dr. Anselm Horn (Thu Apr 15 2021 - 17:08:48 PDT)
  - [AMBER] R: Cyclic Peptides: leap keeps adding missing atoms Tainah Dorina Marforio (Mon Apr 19 2021 - 07:17:46 PDT)
[AMBER] Questions about Principle Component Analysis Li,Haoxi (Thu Apr 15 2021 - 11:56:50 PDT)
- Re: [AMBER] Questions about Principle Component Analysis Thomas Cheatham (Thu Apr 15 2021 - 13:17:00 PDT)
[AMBER] About REMD extracting temperature trajectory Ojet (Thu Apr 15 2021 - 19:32:57 PDT)
- Re: [AMBER] About REMD extracting temperature trajectory Daniel Roe (Fri Apr 16 2021 - 06:45:53 PDT)
[AMBER] 答复: [ambermd.org代发]Re: "No module named pytraj" during make test step 石谷沁 (Thu Apr 15 2021 - 20:31:59 PDT)
[AMBER] RMSIP waleed zalloum (Thu Apr 15 2021 - 21:01:28 PDT)
- Re: [AMBER] RMSIP Daniel Roe (Fri Apr 16 2021 - 06:50:07 PDT)
- Re: [AMBER] RMSIP Daniel Roe (Fri Apr 16 2021 - 12:08:31 PDT)
[AMBER] tleap solvate box problems Gabriel Titchiner (Fri Apr 16 2021 - 01:02:22 PDT)
- Re: [AMBER] tleap solvate box problems Daniel Roe (Fri Apr 16 2021 - 07:09:44 PDT)
[AMBER] halted quasi-harmonic MMPBSA calculation Vaibhav Dixit (Sat Apr 17 2021 - 08:35:44 PDT)
[AMBER] Umbrella sampling on Amber 18 vs Amber 20 Ramin Mehrani (Sat Apr 17 2021 - 08:59:56 PDT)
- Re: [AMBER] Umbrella sampling on Amber 18 vs Amber 20 David A Case (Sat Apr 17 2021 - 09:47:41 PDT)
  - Re: [AMBER] Umbrella sampling on Amber 18 vs Amber 20 Ramin Mehrani (Sat Apr 17 2021 - 10:20:32 PDT)
    - Re: [AMBER] Umbrella sampling on Amber 18 vs Amber 20 David A Case (Sat Apr 17 2021 - 13:27:54 PDT)
Re: [AMBER] AMBER Digest, Vol 3336, Issue 1 waleed zalloum (Sat Apr 17 2021 - 13:01:10 PDT)
- Re: [AMBER] AMBER Digest, Vol 3336, Issue 1 Daniel Roe (Fri Apr 23 2021 - 09:33:55 PDT)
[AMBER] Amber Experts A. Bakheit (Sun Apr 18 2021 - 03:52:40 PDT)
[AMBER] unusually high entropy values MMPBSA quasi-harmonic Vaibhav Dixit (Sun Apr 18 2021 - 10:20:59 PDT)
- Re: [AMBER] unusually high entropy values MMPBSA quasi-harmonic David A Case (Mon Apr 19 2021 - 06:18:08 PDT)
  - Re: [AMBER] unusually high entropy values MMPBSA quasi-harmonic Vaibhav Dixit (Mon Apr 19 2021 - 07:10:59 PDT)
    - Re: [AMBER] unusually high entropy values MMPBSA quasi-harmonic David A Case (Mon Apr 19 2021 - 11:38:59 PDT)
    - Re: [AMBER] unusually high entropy values MMPBSA quasi-harmonic Vaibhav Dixit (Tue Apr 20 2021 - 00:17:26 PDT)
    - Re: [AMBER] unusually high entropy values MMPBSA quasi-harmonic David A Case (Tue Apr 20 2021 - 04:58:48 PDT)
- Re: [AMBER] unusually high entropy values MMPBSA quasi-harmonic Adrian Roitberg (Mon Apr 19 2021 - 07:13:39 PDT)
  - Re: [AMBER] unusually high entropy values MMPBSA quasi-harmonic Vaibhav Dixit (Mon Apr 19 2021 - 07:19:04 PDT)
    - Re: [AMBER] unusually high entropy values MMPBSA quasi-harmonic Vaibhav Dixit (Mon Apr 19 2021 - 10:18:24 PDT)
[AMBER] Hack to install AmberTools20 on macOS Otto Sievert (Sun Apr 18 2021 - 18:45:36 PDT)
- Re: [AMBER] Hack to install AmberTools20 on macOS David A Case (Mon Apr 19 2021 - 06:27:13 PDT)
  - Re: [AMBER] Hack to install AmberTools20 on macOS Gustaf Olsson (Mon Apr 19 2021 - 23:44:36 PDT)
[AMBER] Distance restraints not working jacob wick (Mon Apr 19 2021 - 02:10:44 PDT)
- Re: [AMBER] Distance restraints not working David A Case (Tue Apr 20 2021 - 05:05:32 PDT)
  - Re: [AMBER] Distance restraints not working jacob wick (Thu Apr 22 2021 - 14:27:04 PDT)
[AMBER] 2.5 fs integration time step h_sahakyan.mb.sci.am (Mon Apr 19 2021 - 05:48:25 PDT)
- Re: [AMBER] 2.5 fs integration time step Carlos Simmerling (Mon Apr 19 2021 - 06:02:59 PDT)
[AMBER] amber manual - non-bonded terms Jutta Rogal (Mon Apr 19 2021 - 08:34:47 PDT)
[AMBER] Amber Tool Sangita Kachhap (Mon Apr 19 2021 - 09:54:59 PDT)
- Re: [AMBER] Amber Tool Carlos Simmerling (Mon Apr 19 2021 - 10:07:59 PDT)
  - Re: [AMBER] Amber Tool Sangita Kachhap (Mon Apr 19 2021 - 10:12:50 PDT)
[AMBER] 2.5 fs integration time step h_sahakyan.mb.sci.am (Mon Apr 19 2021 - 23:13:34 PDT)
- Re: [AMBER] 2.5 fs integration time step Carlos Simmerling (Tue Apr 20 2021 - 12:51:07 PDT)
[AMBER] Will AmberTool21 support gcc10? Gustaf Olsson (Tue Apr 20 2021 - 02:03:36 PDT)
- Re: [AMBER] Will AmberTool21 support gcc10? Daniel Roe (Wed Apr 21 2021 - 07:17:33 PDT)
  - Re: [AMBER] Will AmberTool21 support gcc10? Gustaf Olsson (Wed Apr 21 2021 - 23:34:17 PDT)
[AMBER] protein sticking out of solvation box causing instability Neville Bethel (Tue Apr 20 2021 - 10:34:53 PDT)
- Re: [AMBER] protein sticking out of solvation box causing instability Kenneth Huang (Tue Apr 20 2021 - 12:32:01 PDT)
- Re: [AMBER] protein sticking out of solvation box causing instability Neville Bethel (Wed Apr 21 2021 - 13:37:59 PDT)
  - Re: [AMBER] protein sticking out of solvation box causing instability Thomas Cheatham (Wed Apr 21 2021 - 19:52:49 PDT)
  - Re: [AMBER] protein sticking out of solvation box causing instability Daniel Roe (Thu Apr 22 2021 - 06:32:18 PDT)
[AMBER] running sander.MPI :forrtl: severe (174): SIGSEGV, segmentation fault occurred 周丽萍 (Wed Apr 21 2021 - 01:32:23 PDT)
- Re: [AMBER] running sander.MPI :forrtl: severe (174): SIGSEGV, segmentation fault occurred David A Case (Wed Apr 21 2021 - 05:13:52 PDT)
  - Re: [AMBER] running sander.MPI :forrtl: severe (174): SIGSEGV, segmentation fault occurred 周丽萍 (Wed Apr 21 2021 - 05:29:55 PDT)
    - Re: [AMBER] running sander.MPI :forrtl: severe (174): SIGSEGV, segmentation fault occurred David A Case (Wed Apr 21 2021 - 07:28:16 PDT)
    - Re: [AMBER] running sander.MPI :forrtl: severe (174): SIGSEGV, segmentation fault occurred 周丽萍 (Wed Apr 21 2021 - 22:13:02 PDT)
    - Re: [AMBER] running sander.MPI :forrtl: severe (174): SIGSEGV, segmentation fault occurred David A Case (Thu Apr 22 2021 - 05:35:32 PDT)
[AMBER] Error when using 1DRISM to generate .xvv organic solvent files Daniel Fowles (Wed Apr 21 2021 - 01:33:29 PDT)
[AMBER] Error in using ambpdb to convert rst to pdb Suchetana Gupta (Wed Apr 21 2021 - 07:41:23 PDT)
- Re: [AMBER] Error in using ambpdb to convert rst to pdb David A Case (Wed Apr 21 2021 - 08:37:36 PDT)
[AMBER] PatchingError: .patches/AmberTools20_Unapplied_Patches/update.13 failed to apply. No changes made from this patch David Ricardo Figueroa Blanco (Wed Apr 21 2021 - 15:20:47 PDT)
- Re: [AMBER] PatchingError: .patches/AmberTools20_Unapplied_Patches/update.13 failed to apply. No changes made from this patch David A Case (Thu Apr 22 2021 - 05:26:25 PDT)
[AMBER] Max relative errors questions in parallel and cuda.serial test 石谷沁 (Wed Apr 21 2021 - 19:50:16 PDT)
- Re: [AMBER] Max relative errors questions in parallel and cuda.serial test 石谷沁 (Wed Apr 21 2021 - 19:56:57 PDT)
  - Re: [AMBER] Max relative errors questions in parallel and cuda.serial test David A Case (Sat Apr 24 2021 - 06:32:15 PDT)
[AMBER] serial amber installation on wsl Ayesha Fatima (Thu Apr 22 2021 - 01:05:02 PDT)
- Re: [AMBER] serial amber installation on wsl David A Case (Thu Apr 22 2021 - 05:32:01 PDT)
  - Re: [AMBER] serial amber installation on wsl Ayesha Fatima (Fri Apr 23 2021 - 08:35:04 PDT)
[AMBER] error installing parallel amber Ayesha Fatima (Thu Apr 22 2021 - 01:51:29 PDT)
[AMBER] Problem with incomplete solvation with tleap Cato, Lee (Thu Apr 22 2021 - 07:43:46 PDT)
- Re: [AMBER] Problem with incomplete solvation with tleap Matias Machado (Thu Apr 22 2021 - 09:27:27 PDT)
- Re: [AMBER] Problem with incomplete solvation with tleap David A Case (Thu Apr 22 2021 - 11:48:05 PDT)
[AMBER] parmchk2 Alesadi, Amirhadi (Thu Apr 22 2021 - 20:26:23 PDT)
- Re: [AMBER] parmchk2 Thomas Cheatham (Thu Apr 22 2021 - 20:50:59 PDT)
[AMBER] Make the two ligands independent in one simulation 李明玉 (Fri Apr 23 2021 - 07:18:35 PDT)
- Re: [AMBER] Make the two ligands independent in one simulation 李明玉 (Fri Apr 23 2021 - 08:00:38 PDT)
- Re: [AMBER] Make the two ligands independent in one simulation James Kress (Fri Apr 23 2021 - 12:00:52 PDT)
  - Re: [AMBER] Make the two ligands independent in one simulation 李明玉 (Fri Apr 23 2021 - 19:47:05 PDT)
    - Re: [AMBER] Make the two ligands independent in one simulation Gustavo Seabra (Mon Apr 26 2021 - 11:51:29 PDT)
[AMBER] mmgbsa issue Ayesha Fatima (Fri Apr 23 2021 - 08:45:12 PDT)
- Re: [AMBER] mmgbsa issue David A Case (Fri Apr 23 2021 - 18:21:29 PDT)
  - Re: [AMBER] mmgbsa issue Ayesha Fatima (Sat Apr 24 2021 - 03:04:22 PDT)
[AMBER] mmgbsa error Ayesha Fatima (Fri Apr 23 2021 - 09:07:11 PDT)
[AMBER] Forcefield File and Adding My Own Polymer Unit Swisher, Justin S (Fri Apr 23 2021 - 12:00:47 PDT)
- Re: [AMBER] Forcefield File and Adding My Own Polymer Unit David A Case (Fri Apr 23 2021 - 18:19:28 PDT)
[AMBER] Questions about REMD extracting temperature trajectory Ojet (Fri Apr 23 2021 - 18:07:20 PDT)
- Re: [AMBER] Questions about REMD extracting temperature trajectory Charo del Genio (Sat Apr 24 2021 - 00:10:12 PDT)
[AMBER] WARNING: INCONSISTENCIES EXIST WITHIN INTERNAL POTENTIAL TERMS. THE VALIDITY OF THESE RESULTS ARE HIGHLY QUESTIONABLE 周丽萍 (Fri Apr 23 2021 - 20:28:24 PDT)
Re: [AMBER] [ambermd.org代发]Re: Max relative errors questions in parallel and cuda.serial test 石谷沁 (Sat Apr 24 2021 - 17:37:12 PDT)
- Re: [AMBER] [ambermd.org代发]Re: Max relative errors questions in parallel and cuda.serial test David A Case (Sun Apr 25 2021 - 05:03:54 PDT)
[AMBER] Regarding the forcefield parameters for cytochrome P450 heme group Patil Pranita Uttamrao (Sun Apr 25 2021 - 03:53:50 PDT)
Re: [AMBER] [ambermd.org代发]Re: [ambermd.org代发]Re: Max relative errors questions in parallel and cuda.serial test 石谷沁 (Sun Apr 25 2021 - 17:37:13 PDT)
[AMBER] TI free energy calculation issue after applying smoothstep in Amber20 zz sheng (Sun Apr 25 2021 - 20:32:38 PDT)
- Re: [AMBER] TI free energy calculation issue after applying smoothstep in Amber20 Abir Ganguly (Mon Apr 26 2021 - 05:19:01 PDT)
  - Re: [AMBER] TI free energy calculation issue after applying smoothstep in Amber20 zz sheng (Mon Apr 26 2021 - 07:44:14 PDT)
[AMBER] AMBER installation on multiple computers Ravi Abrol (Mon Apr 26 2021 - 01:12:22 PDT)
- Re: [AMBER] AMBER installation on multiple computers Gustaf Olsson (Mon Apr 26 2021 - 02:33:02 PDT)
[AMBER] AMBER/EVB Dusanka Golo (Mon Apr 26 2021 - 06:10:41 PDT)
- Re: [AMBER] AMBER/EVB David A Case (Thu May 20 2021 - 06:25:08 PDT)
[AMBER] MD Simulation of Ribosome including Protein & RNA Shirin Jamshidi (Mon Apr 26 2021 - 11:16:44 PDT)
- Re: [AMBER] MD Simulation of Ribosome including Protein & RNA Carlos Simmerling (Mon Apr 26 2021 - 11:46:01 PDT)
[AMBER] Covalent bonded inhibitors and mm-pb(gb)sa analys Hector A. Baldoni (Mon Apr 26 2021 - 12:58:23 PDT)
- Re: [AMBER] Covalent bonded inhibitors and mm-pb(gb)sa analys Carlos Simmerling (Mon Apr 26 2021 - 13:20:05 PDT)
[AMBER] Compile Amber20 with SGI/MPT 2.20 Gabriel Cretin (Tue Apr 27 2021 - 03:56:53 PDT)
- Re: [AMBER] Compile Amber20 with SGI/MPT 2.20 Gerald Monard (Tue Apr 27 2021 - 04:46:53 PDT)
  - Re: [AMBER] Compile Amber20 with SGI/MPT 2.20 Gabriel Cretin (Tue Apr 27 2021 - 06:32:54 PDT)
[AMBER] Citation for LEaP Robert Molt (Tue Apr 27 2021 - 16:52:43 PDT)
- Re: [AMBER] Citation for LEaP David A Case (Wed Apr 28 2021 - 04:50:52 PDT)
[AMBER] 答复: [ambermd.org代发]Re: Max relative errors questions in parallel and cuda.serial test 石谷沁 (Tue Apr 27 2021 - 17:54:26 PDT)
- Re: [AMBER] 答复: [ambermd.org代发]Re: Max relative errors questions in parallel and cuda.serial test David A Case (Wed Apr 28 2021 - 04:58:01 PDT)
  - [AMBER] 答复: [ambermd.org代发]Re: 答复: [ambermd.org代发]Re: Max relative errors questions in parallel and cuda.serial test 石谷沁 (Wed Apr 28 2021 - 17:57:46 PDT)
    - Re: [AMBER] 答复: [ambermd.org代发]Re: 答复: [ambermd.org代发]Re: Max relative errors questions in parallel and cuda.serial test David A Case (Thu Apr 29 2021 - 05:09:35 PDT)
[AMBER] Gaussian derived RESP charges and antechamber Gustaf Olsson (Wed Apr 28 2021 - 03:30:13 PDT)
- Re: [AMBER] Gaussian derived RESP charges and antechamber Hector A. Baldoni (Wed Apr 28 2021 - 05:30:24 PDT)
  - Re: [AMBER] Gaussian derived RESP charges and antechamber Gustaf Olsson (Wed Apr 28 2021 - 05:48:59 PDT)
    - Re: [AMBER] Gaussian derived RESP charges and antechamber Kenneth Huang (Wed Apr 28 2021 - 08:50:09 PDT)
[AMBER] Problems to install AmberTools20 Miguel Garavís (Wed Apr 28 2021 - 04:33:42 PDT)
- Re: [AMBER] Problems to install AmberTools20 David A Case (Wed Apr 28 2021 - 05:06:55 PDT)
  - Re: [AMBER] Problems to install AmberTools20 Miguel Garavís (Wed Apr 28 2021 - 05:14:49 PDT)
    - Re: [AMBER] Problems to install AmberTools20 David A Case (Wed Apr 28 2021 - 09:41:07 PDT)
    - Re: [AMBER] Problems to install AmberTools20 Miguel Garavís (Thu Apr 29 2021 - 03:43:12 PDT)
    - Re: [AMBER] Problems to install AmberTools20 David A Case (Thu Apr 29 2021 - 05:21:53 PDT)
[AMBER] Heating stages ntx = 1 or ntx=5 Jenny 148 (Wed Apr 28 2021 - 06:23:26 PDT)
[AMBER] CPPTRAJ configuration is failing Markus Metz (Wed Apr 28 2021 - 12:04:56 PDT)
- Re: [AMBER] CPPTRAJ configuration is failing David A Case (Wed Apr 28 2021 - 13:24:51 PDT)
[AMBER] Trouble Creating a pdb File Khong, Megan (Wed Apr 28 2021 - 14:14:36 PDT)
- Re: [AMBER] Trouble Creating a pdb File Gustaf Olsson (Wed Apr 28 2021 - 23:40:35 PDT)
[AMBER] Questions about REMD extracting temperature trajectory Ojet (Wed Apr 28 2021 - 23:26:12 PDT)
- Re: [AMBER] Questions about REMD extracting temperature trajectory Charo del Genio (Thu Apr 29 2021 - 01:45:46 PDT)
[AMBER] Adventures installing AMBER 20 in Centos 7 Azurmendi, Hugo (Thu Apr 29 2021 - 08:59:40 PDT)
- Re: [AMBER] Adventures installing AMBER 20 in Centos 7 David A Case (Thu Apr 29 2021 - 11:29:49 PDT)
  - Re: [AMBER] Adventures installing AMBER 20 in Centos 7 David A Case (Thu Apr 29 2021 - 12:48:16 PDT)
    - Re: [AMBER] [EXTERNAL] Re: Adventures installing AMBER 20 in Centos 7 Azurmendi, Hugo (Thu Apr 29 2021 - 13:01:46 PDT)
- Re: [AMBER] Adventures installing AMBER 20 in Centos 7 Gerald Monard (Thu Apr 29 2021 - 19:55:22 PDT)
  - Re: [AMBER] Adventures installing AMBER 20 in Centos 7 Kevin Keane (Thu Apr 29 2021 - 20:27:55 PDT)
[AMBER] cpptraj energy using 2 masks German P. Barletta (Thu Apr 29 2021 - 11:01:07 PDT)
- Re: [AMBER] cpptraj energy using 2 masks Daniel Roe (Fri Apr 30 2021 - 08:32:09 PDT)
- Re: [AMBER] cpptraj energy using 2 masks German P. Barletta (Fri Apr 30 2021 - 12:44:12 PDT)
[AMBER] FW: AMBER Digest, Vol 3348, Issue 1 Markus Metz (Thu Apr 29 2021 - 12:09:23 PDT)
[AMBER] trpcage benchmark: reduce 32x or dimerize ? Scott Brozell (Thu Apr 29 2021 - 18:26:12 PDT)
- Re: [AMBER] trpcage benchmark: reduce 32x or dimerize ? Carlos Simmerling (Fri Apr 30 2021 - 06:33:32 PDT)
  - Re: [AMBER] trpcage benchmark: reduce 32x or dimerize ? Scott Brozell (Tue May 04 2021 - 12:37:05 PDT)
[AMBER] Release of AmberTools21 David A Case (Thu Apr 29 2021 - 18:29:34 PDT)
- Re: [AMBER] Release of AmberTools21 aishen (Thu Apr 29 2021 - 22:56:22 PDT)
  - Re: [AMBER] Release of AmberTools21 aishen (Thu Apr 29 2021 - 23:15:45 PDT)
- Re: [AMBER] Release of AmberTools21 Gustaf Olsson (Fri Apr 30 2021 - 01:55:49 PDT)
  - Re: [AMBER] Release of AmberTools21 David A Case (Fri Apr 30 2021 - 05:26:27 PDT)
    - Re: [AMBER] Release of AmberTools21 Kshatresh Dutta Dubey (Sat May 01 2021 - 04:40:23 PDT)
- Re: [AMBER] Release of AmberTools21 Gustaf Olsson (Fri Apr 30 2021 - 06:23:18 PDT)
- Re: [AMBER] [EXTERNAL] Release of AmberTools21 Azurmendi, Hugo (Fri Apr 30 2021 - 13:33:05 PDT)
  - Re: [AMBER] [EXTERNAL] Release of AmberTools21 David A Case (Sat May 01 2021 - 05:25:01 PDT)
    - Re: [AMBER] [EXTERNAL] Release of AmberTools21 Gustaf Olsson (Thu May 06 2021 - 05:10:08 PDT)
    - Re: [AMBER] [EXTERNAL] Release of AmberTools21 David A Case (Thu May 06 2021 - 05:34:47 PDT)
    - Re: [AMBER] [EXTERNAL] Release of AmberTools21 Gustaf Olsson (Thu May 06 2021 - 05:51:29 PDT)
    - Re: [AMBER] [EXTERNAL] Release of AmberTools21 Gustaf Olsson (Thu May 06 2021 - 05:59:00 PDT)
    - Re: [AMBER] [EXTERNAL] Release of AmberTools21 Gustaf Olsson (Mon May 10 2021 - 03:54:50 PDT)
    - Re: [AMBER] [EXTERNAL] Release of AmberTools21 Gustaf Olsson (Mon May 10 2021 - 04:09:27 PDT)
    - Re: [AMBER] [EXTERNAL] Release of AmberTools21 Gustaf Olsson (Mon May 10 2021 - 06:00:47 PDT)
    - Re: [AMBER] [EXTERNAL] Release of AmberTools21 David A Case (Mon May 10 2021 - 06:06:59 PDT)
    - Re: [AMBER] [EXTERNAL] Release of AmberTools21 Gustaf Olsson (Mon May 10 2021 - 06:11:25 PDT)
    - Re: [AMBER] [EXTERNAL] Release of AmberTools21 Gustaf Olsson (Mon May 10 2021 - 07:41:18 PDT)
    - Re: [AMBER] [EXTERNAL] Release of AmberTools21 Gerald Monard (Tue May 11 2021 - 17:32:58 PDT)
    - Re: [AMBER] [EXTERNAL] Release of AmberTools21 Gustaf Olsson (Mon May 10 2021 - 07:41:35 PDT)
[AMBER] Troubleshooting long idle times in pmemd.MPI Kevin Keane (Thu Apr 29 2021 - 20:39:00 PDT)
- Re: [AMBER] Troubleshooting long idle times in pmemd.MPI David A Case (Sat May 01 2021 - 10:02:18 PDT)
  - Re: [AMBER] Troubleshooting long idle times in pmemd.MPI Kevin Keane (Sat May 01 2021 - 11:42:39 PDT)
    - Re: [AMBER] Troubleshooting long idle times in pmemd.MPI David A Case (Sun May 02 2021 - 05:30:29 PDT)
    - Re: [AMBER] Troubleshooting long idle times in pmemd.MPI Kevin Keane (Wed Jun 16 2021 - 21:45:31 PDT)
[AMBER] About cpptraj (v18) extracting temperature trajectory from REMD trajectory Ojet (Thu Apr 29 2021 - 21:02:49 PDT)
- Re: [AMBER] About cpptraj (v18) extracting temperature trajectory from REMD trajectory Daniel Roe (Fri Apr 30 2021 - 08:33:52 PDT)
[AMBER] installation of AmberTools 21 Qinghua Liao (Fri Apr 30 2021 - 07:54:17 PDT)
- Re: [AMBER] installation of AmberTools 21 David A Case (Fri Apr 30 2021 - 09:17:51 PDT)
  - Re: [AMBER] installation of AmberTools 21 Qinghua Liao (Fri Apr 30 2021 - 10:54:32 PDT)
    - Re: [AMBER] installation of AmberTools 21 David A Case (Fri Apr 30 2021 - 12:54:46 PDT)
    - Re: [AMBER] installation of AmberTools 21 Qinghua Liao (Fri Apr 30 2021 - 16:35:23 PDT)
    - Re: [AMBER] installation of AmberTools 21 David A Case (Sat May 01 2021 - 05:20:23 PDT)
    - Re: [AMBER] installation of AmberTools 21 Rudy Richardson (Sat May 01 2021 - 05:26:18 PDT)
    - Re: [AMBER] installation of AmberTools 21 David A Case (Sat May 01 2021 - 05:40:48 PDT)
    - Re: [AMBER] installation of AmberTools 21 Rudy Richardson (Sat May 01 2021 - 05:55:50 PDT)
    - Re: [AMBER] installation of AmberTools 21 Qinghua Liao (Sun May 02 2021 - 06:45:59 PDT)
[AMBER] converting gromacs topology to amber Ayesha Fatima (Sun May 02 2021 - 09:32:31 PDT)
- Re: [AMBER] converting gromacs topology to amber Daniel Roe (Mon May 03 2021 - 05:57:36 PDT)
  - Re: [AMBER] converting gromacs topology to amber Ayesha Fatima (Mon May 03 2021 - 06:30:12 PDT)
    - Re: [AMBER] converting gromacs topology to amber Daniel Roe (Mon May 03 2021 - 06:40:40 PDT)
    - Re: [AMBER] converting gromacs topology to amber Ayesha Fatima (Mon May 03 2021 - 06:49:23 PDT)
[AMBER] pmemd.cuda fails with "cudaMemcpyToSymbol: SetSim copy to cSim failed invalid device symbol" Laura SCALVINI (Mon May 03 2021 - 01:08:18 PDT)
- Re: [AMBER] pmemd.cuda fails with "cudaMemcpyToSymbol: SetSim copy to cSim failed invalid device symbol" David A Case (Mon May 03 2021 - 05:11:08 PDT)
[AMBER] atom-order problem with prmtop and cpptraj Vaibhav Dixit (Mon May 03 2021 - 01:16:13 PDT)
- Re: [AMBER] atom-order problem with prmtop and cpptraj Vaibhav Dixit (Mon May 03 2021 - 05:18:21 PDT)
  - Re: [AMBER] atom-order problem with prmtop and cpptraj Daniel Roe (Mon May 03 2021 - 05:47:16 PDT)
- Re: [AMBER] atom-order problem with prmtop and cpptraj David A Case (Mon May 03 2021 - 05:26:05 PDT)
  - Re: [AMBER] atom-order problem with prmtop and cpptraj Vaibhav Dixit (Mon May 03 2021 - 05:39:09 PDT)
[AMBER] Error due to faulty Connection atoms Guillem Vila I Julià (Mon May 03 2021 - 03:11:25 PDT)
- Re: [AMBER] Error due to faulty Connection atoms David A Case (Wed May 12 2021 - 06:11:24 PDT)
  - Re: [AMBER] Error due to faulty Connection atoms Guillem Vila I Julià (Wed May 19 2021 - 06:25:15 PDT)
[AMBER] Distance between nucleotides and amino acids Airy Sanjeev (Mon May 03 2021 - 03:19:47 PDT)
- Re: [AMBER] Distance between nucleotides and amino acids Daniel Roe (Mon May 03 2021 - 06:11:58 PDT)
[AMBER] MMPBSA calculation error Yogeshwaran Krishnan (Tue May 04 2021 - 05:09:25 PDT)
[AMBER] converting gromacs topology to amber Ayesha Fatima (Tue May 04 2021 - 15:04:26 PDT)
- Re: [AMBER] converting gromacs topology to amber David A Case (Wed May 05 2021 - 05:04:37 PDT)
[AMBER] N6-myristoyl lysine parameters Mark Fisher (Tue May 04 2021 - 19:02:39 PDT)
[AMBER] Query about AmberTools21 conda distribution Jan Brezovsky (Wed May 05 2021 - 00:52:31 PDT)
- Re: [AMBER] Query about AmberTools21 conda distribution David A Case (Sun May 09 2021 - 12:59:44 PDT)
[AMBER] guidance for microsecond long MD simulations Vaibhav Dixit (Wed May 05 2021 - 10:10:24 PDT)
- Re: [AMBER] guidance for microsecond long MD simulations David A Case (Wed May 05 2021 - 11:42:59 PDT)
[AMBER] Inconsistent results on TI with cpu vs gpu code Giorgos Lambrinidis (Wed May 05 2021 - 10:42:58 PDT)
[AMBER] Questions about QM/MM simulations 马芳芳 (Wed May 05 2021 - 18:55:39 PDT)
- Re: [AMBER] Questions about QM/MM simulations Goetz, Andreas (Wed May 05 2021 - 21:40:35 PDT)
[AMBER] AMBER20/AMBERTools21 Installation Errors when compiling mpich 石谷沁 (Thu May 06 2021 - 00:56:19 PDT)
- Re: [AMBER] AMBER20/AMBERTools21 Installation Errors when compiling mpich David A Case (Thu May 06 2021 - 05:14:09 PDT)
  - [AMBER] 答复: [ambermd.org代发]Re: AMBER20/AMBERTools21 Installation Errors when compiling mpich 石谷沁 (Thu May 06 2021 - 17:49:21 PDT)
    - Re: [AMBER] 答复: [ambermd.org代发]Re: AMBER20/AMBERTools21 Installation Errors when compiling mpich David A Case (Fri May 07 2021 - 05:14:07 PDT)
Re: [AMBER] [ambermd.org代发]Re: AMBER20/AMBERTools21 Installation Errors when compiling mpich 石谷沁 (Thu May 06 2021 - 06:40:12 PDT)
- Re: [AMBER] [ambermd.org代发]Re: AMBER20/AMBERTools21 Installation Errors when compiling mpich 石谷沁 (Fri May 07 2021 - 01:53:34 PDT)
[AMBER] Difficulty in doing umbrella sampling using LCOD method Soumyajit Karmakar (Thu May 06 2021 - 08:21:19 PDT)
[AMBER] differences in counterion position with water models and questions Vaibhav Dixit (Thu May 06 2021 - 23:07:13 PDT)
- Re: [AMBER] differences in counterion position with water models and questions Dr. Anselm Horn (Mon May 10 2021 - 05:37:52 PDT)
  - Re: [AMBER] differences in counterion position with water models and questions Vaibhav Dixit (Wed May 12 2021 - 09:20:40 PDT)
[AMBER] understanding DSSP outout Sadaf Rani (Thu May 06 2021 - 23:53:06 PDT)
- Re: [AMBER] understanding DSSP outout Daniel Roe (Fri May 14 2021 - 08:42:05 PDT)
Re: [AMBER] Questions about QM/MM simulations (Goetz, Andreas) 马芳芳 (Fri May 07 2021 - 01:48:21 PDT)
- Re: [AMBER] Questions about QM/MM simulations (Goetz, Andreas) Goetz, Andreas (Fri May 07 2021 - 12:05:34 PDT)
[AMBER] Amber20 CUDA.serial tests comparison failed with gb calculation: differences at e-01 level 石谷沁 (Fri May 07 2021 - 02:19:24 PDT)
- Re: [AMBER] Amber20 CUDA.serial tests comparison failed with gb calculation: differences at e-01 level David A Case (Fri May 07 2021 - 05:30:56 PDT)
  - [AMBER] 答复: [ambermd.org代发]Re: Amber20 CUDA.serial tests comparison failed with gb calculation: differences at e-01 level 石谷沁 (Fri May 07 2021 - 20:03:25 PDT)
[AMBER] Avoiding steric snafus with protein mutations in tleap? Tucker Burgin (Fri May 07 2021 - 08:36:52 PDT)
- Re: [AMBER] Avoiding steric snafus with protein mutations in tleap? Matias Machado (Sat May 08 2021 - 11:15:29 PDT)
[AMBER] Digest of issues installing AMBER21 in Centos 7 Azurmendi, Hugo (Sat May 08 2021 - 10:00:26 PDT)
- Re: [AMBER] Digest of issues installing AMBER21 in Centos 7 David A Case (Sun May 09 2021 - 05:46:51 PDT)
[AMBER] Query regarding density analysis ARITRA MITRA (Sun May 09 2021 - 08:12:40 PDT)
[AMBER] Inconsistent results on TI with cpu vs gpu code Giorgos Lambrinidis (Sun May 09 2021 - 09:19:12 PDT)
- Re: [AMBER] Inconsistent results on TI with cpu vs gpu code David A Case (Sun May 09 2021 - 12:56:04 PDT)
[AMBER] MBAR energies when using soft-core potential in pmemd TI Hosein Geraili Daronkola (Sun May 09 2021 - 15:15:01 PDT)
- Re: [AMBER] MBAR energies when using soft-core potential in pmemd TI David A Case (Mon May 10 2021 - 06:00:31 PDT)
  - Re: [AMBER] MBAR energies when using soft-core potential in pmemd TI Brian Radak (Mon May 10 2021 - 06:21:56 PDT)
[AMBER] Test Goetz, Andreas (Sun May 09 2021 - 18:03:14 PDT)
[AMBER] stacking interactions represented by force field equation? Martin Rosellen (Mon May 10 2021 - 07:31:31 PDT)
- Re: [AMBER] stacking interactions represented by force field equation? Carlos Simmerling (Mon May 10 2021 - 07:52:55 PDT)
  - Re: [AMBER] stacking interactions represented by force field equation? Jiri Sponer (Mon May 10 2021 - 09:02:38 PDT)
    - Re: [AMBER] stacking interactions represented by force field equation? Matias Machado (Tue May 11 2021 - 08:40:20 PDT)
    - Re: [AMBER] stacking interactions represented by force field equation? Jiri Sponer (Tue May 11 2021 - 10:04:20 PDT)
[AMBER] Keeping input protein hydrogens? Markus Metz (Mon May 10 2021 - 09:48:36 PDT)
- Re: [AMBER] Keeping input protein hydrogens? David A Case (Mon May 10 2021 - 13:58:28 PDT)
[AMBER] FEW MMGBSA calculation Yogeshwaran Krishnan (Tue May 11 2021 - 02:10:15 PDT)
[AMBER] solvent accessibility Cato, Lee (Tue May 11 2021 - 09:20:13 PDT)
- Re: [AMBER] solvent accessibility Daniel Roe (Fri May 14 2021 - 11:04:20 PDT)
  - Re: [AMBER] solvent accessibility David A Case (Fri May 14 2021 - 18:22:04 PDT)
- Re: [AMBER] solvent accessibility German P. Barletta (Sat May 15 2021 - 12:41:01 PDT)
  - Re: [AMBER] solvent accessibility David A Case (Sat May 15 2021 - 13:00:33 PDT)
[AMBER] Query regarding density analysis in CPPTRAJ. Raising this issue again. ARITRA MITRA (Tue May 11 2021 - 11:02:38 PDT)
- Re: [AMBER] Query regarding density analysis in CPPTRAJ. Raising this issue again. Daniel Roe (Tue May 11 2021 - 12:09:03 PDT)
  - Re: [AMBER] Query regarding density analysis in CPPTRAJ. Raising this issue again. ARITRA MITRA (Thu May 13 2021 - 07:34:06 PDT)
    - Re: [AMBER] Query regarding density analysis in CPPTRAJ. Raising this issue again. Daniel Roe (Thu May 13 2021 - 08:02:05 PDT)
    - Re: [AMBER] Query regarding density analysis in CPPTRAJ. Raising this issue again. ARITRA MITRA (Thu May 13 2021 - 08:06:14 PDT)
    - Re: [AMBER] Query regarding density analysis in CPPTRAJ. Raising this issue again. Daniel Roe (Thu May 13 2021 - 09:26:02 PDT)
[AMBER] Error Installing Amber20 on group's cluster Min Chiang Gary Ong (Tue May 11 2021 - 19:58:04 PDT)
- Re: [AMBER] Error Installing Amber20 on group's cluster David A Case (Wed May 12 2021 - 05:50:35 PDT)
  - Re: [AMBER] Error Installing Amber20 on group's cluster Min Chiang Gary Ong (Wed May 12 2021 - 08:11:17 PDT)
[AMBER] AMBER 18 citation endnote file Athena N (Tue May 11 2021 - 23:16:36 PDT)
[AMBER] MMPBSA.py and rms fit: Results depend on reference frame Lennart Gundelach (Wed May 12 2021 - 00:33:55 PDT)
- Re: [AMBER] MMPBSA.py and rms fit: Results depend on reference frame David A Case (Wed May 12 2021 - 06:00:55 PDT)
  - Re: [AMBER] MMPBSA.py and rms fit: Results depend on reference frame Lennart Gundelach (Thu May 27 2021 - 02:07:15 PDT)
[AMBER] Amber stuck on Control data for the run Victoria E Hill (Wed May 12 2021 - 03:11:49 PDT)
- Re: [AMBER] Amber stuck on Control data for the run David A Case (Wed May 12 2021 - 06:07:01 PDT)
- Re: [AMBER] Amber stuck on Control data for the run Daniel Roe (Wed May 12 2021 - 06:47:37 PDT)
- Re: [AMBER] Amber stuck on Control data for the run Matias Machado (Wed May 12 2021 - 07:00:41 PDT)
[AMBER] Effect of noisy force calculations Thomas Fox (Wed May 12 2021 - 06:49:48 PDT)
[AMBER] Mutate double stranded DNA? Gustavo Seabra (Wed May 12 2021 - 18:01:42 PDT)
- Re: [AMBER] Mutate double stranded DNA? Mariano Curti (Thu May 13 2021 - 00:29:18 PDT)
- Re: [AMBER] Mutate double stranded DNA? Carlos Simmerling (Thu May 13 2021 - 01:59:19 PDT)
  - Re: [AMBER] Mutate double stranded DNA? Vlad Cojocaru (Thu May 13 2021 - 03:45:46 PDT)
- Re: [AMBER] Mutate double stranded DNA? Gustavo Seabra (Thu May 13 2021 - 11:25:00 PDT)
  - Re: [AMBER] Mutate double stranded DNA? Vlad Cojocaru (Fri May 14 2021 - 09:03:41 PDT)
[AMBER] AmberTools21 cmake build H. Kawasaki (Wed May 12 2021 - 23:49:40 PDT)
- Re: [AMBER] AmberTools21 cmake build David A Case (Thu May 13 2021 - 05:56:02 PDT)
[AMBER] How to calculate the contribution to protein-protein aggregation from hydrophobic interactions ? 刘为 (Thu May 13 2021 - 06:05:05 PDT)
[AMBER] Selenomethionine force field parameters Rafał Madaj (Thu May 13 2021 - 10:50:25 PDT)
- Re: [AMBER] Selenomethionine force field parameters Kellon Belfon (Thu May 13 2021 - 17:14:55 PDT)
  - Re: [AMBER] Selenomethionine force field parameters David A Case (Thu May 13 2021 - 18:45:09 PDT)
    - Re: [AMBER] Selenomethionine force field parameters Kellon Belfon (Thu May 13 2021 - 20:35:25 PDT)
    - Re: [AMBER] Selenomethionine force field parameters Jeffrey Wagner (Fri May 14 2021 - 07:54:44 PDT)
    - Re: [AMBER] Selenomethionine force field parameters David A Case (Fri May 14 2021 - 09:01:17 PDT)
    - Re: [AMBER] Selenomethionine force field parameters Jeffrey Wagner (Fri May 14 2021 - 10:57:18 PDT)
    - Re: [AMBER] Selenomethionine force field parameters Kellon Belfon (Fri May 14 2021 - 11:57:44 PDT)
    - Re: [AMBER] Selenomethionine force field parameters Jeffrey Wagner (Fri May 14 2021 - 14:05:36 PDT)
  - Re: [AMBER] Selenomethionine force field parameters Rafał Madaj (Fri May 14 2021 - 23:58:26 PDT)
    - Re: [AMBER] Selenomethionine force field parameters Kellon Belfon (Sat May 15 2021 - 07:46:26 PDT)
    - Re: [AMBER] Selenomethionine force field parameters Kellon Belfon (Sat May 15 2021 - 14:23:31 PDT)
    - Re: [AMBER] Selenomethionine force field parameters Rafał Madaj (Sat May 15 2021 - 15:05:54 PDT)
    - Re: [AMBER] Selenomethionine force field parameters Kellon Belfon (Sat May 15 2021 - 15:26:18 PDT)
[AMBER] New In CPPTRAJ (May 2021) Daniel Roe (Thu May 13 2021 - 11:50:29 PDT)
- Re: [AMBER] New In CPPTRAJ (May 2021) xichen li (Fri May 14 2021 - 02:37:30 PDT)
  - Re: [AMBER] New In CPPTRAJ (May 2021) Daniel Roe (Fri May 14 2021 - 11:00:01 PDT)
[AMBER] Error running make install Rodrigo da Silva Bitzer (Thu May 13 2021 - 13:33:29 PDT)
- Re: [AMBER] Error running make install David A Case (Fri May 14 2021 - 05:33:57 PDT)
  - Re: [AMBER] Error running make install Rodrigo da Silva Bitzer (Fri May 14 2021 - 14:24:37 PDT)
[AMBER] CPPTRAJ nastruct not recognising G-U wobble base pairs Francis Acquah (Thu May 13 2021 - 15:48:36 PDT)
- Re: [AMBER] CPPTRAJ nastruct not recognising G-U wobble base pairs Daniel Roe (Fri May 14 2021 - 11:02:07 PDT)
[AMBER] Cpptraj segfaults on single REMD trajectories? Brian Radak (Fri May 14 2021 - 08:19:29 PDT)
- Re: [AMBER] Cpptraj segfaults on single REMD trajectories? Daniel Roe (Fri May 14 2021 - 08:32:20 PDT)
  - Re: [AMBER] Cpptraj segfaults on single REMD trajectories? Brian Radak (Fri May 14 2021 - 10:40:40 PDT)
    - Re: [AMBER] Cpptraj segfaults on single REMD trajectories? Daniel Roe (Fri May 14 2021 - 10:57:27 PDT)
[AMBER] Problem re. non-integer charge in glycoprotein RAJAS MALLENAHALLI RAO (Fri May 14 2021 - 09:24:07 PDT)
- Re: [AMBER] Problem re. non-integer charge in glycoprotein Dr. Anselm Horn (Mon May 17 2021 - 03:42:04 PDT)
- Re: [AMBER] Problem re. non-integer charge in glycoprotein RAJAS MALLENAHALLI RAO (Mon May 17 2021 - 05:23:36 PDT)
[AMBER] Multiple Dihedral Parameters Abdul Basit (Sun May 16 2021 - 09:51:03 PDT)
- Re: [AMBER] Multiple Dihedral Parameters David A Case (Sun May 16 2021 - 12:09:44 PDT)
[AMBER] MMGBSA using charmm36 force field-- positive value 周丽萍 (Sun May 16 2021 - 18:21:39 PDT)
[AMBER] Surprisingly Poor Performance of Quadro RTX5000 -- Any Ideas on Reasons... 石谷沁 (Sun May 16 2021 - 18:53:56 PDT)
[AMBER] Miniconda pkg install error H. Kawasaki (Mon May 17 2021 - 00:35:07 PDT)
- Re: [AMBER] Miniconda pkg install error David A Case (Mon May 17 2021 - 05:30:02 PDT)
[AMBER] Algorithm Details of Addions/Addions2 Robert Molt (Mon May 17 2021 - 09:12:37 PDT)
- Re: [AMBER] Algorithm Details of Addions/Addions2 David A Case (Thu May 20 2021 - 06:15:17 PDT)
[AMBER] CMake Error at cmake/jedbrown/FindFFTW.cmake:307 (add_library): Akinyemi Omoniyi (Tue May 18 2021 - 02:03:26 PDT)
- Re: [AMBER] CMake Error at cmake/jedbrown/FindFFTW.cmake:307 (add_library): David A Case (Tue May 18 2021 - 05:32:22 PDT)
  - Re: [AMBER] CMake Error at cmake/jedbrown/FindFFTW.cmake:307 (add_library): Akinyemi Omoniyi (Wed May 19 2021 - 21:46:31 PDT)
[AMBER] Combining GLYCAM and AMBER/GAFF Gustaf Olsson (Tue May 18 2021 - 06:25:30 PDT)
- Re: [AMBER] Combining GLYCAM and AMBER/GAFF David A Case (Thu May 20 2021 - 06:10:42 PDT)
  - Re: [AMBER] Combining GLYCAM and AMBER/GAFF Lachele Foley (Thu May 20 2021 - 19:32:21 PDT)
    - Re: [AMBER] Combining GLYCAM and AMBER/GAFF Gustaf Olsson (Thu May 20 2021 - 23:49:46 PDT)
[AMBER] Applying change to van der Waals for specific pairs of atom Smith, Richard (Tue May 18 2021 - 13:43:51 PDT)
- Re: [AMBER] Applying change to van der Waals for specific pairs of atom Song, Lin (Wed May 19 2021 - 15:03:55 PDT)
- Re: [AMBER] Applying change to van der Waals for specific pairs of atom David A Case (Thu May 20 2021 - 06:08:06 PDT)
[AMBER] Conformation search speed increase with Cartesian restraints Liao (Tue May 18 2021 - 20:41:58 PDT)
- Re: [AMBER] Conformation search speed increase with Cartesian restraints Charo del Genio (Wed May 19 2021 - 10:25:51 PDT)
  - Re: [AMBER] Conformation search speed increase with Cartesian restraints Liao (Wed May 19 2021 - 14:02:32 PDT)
    - Re: [AMBER] Conformation search speed increase with Cartesian restraints Charo del Genio (Thu May 20 2021 - 04:40:15 PDT)
[AMBER] Lite Hash Rate and pmemd.cuda Alessandro Contini (Wed May 19 2021 - 01:12:05 PDT)
[AMBER] How do I generate prmtop file for system containing more than 1 ligand? Min Chiang Gary Ong (Wed May 19 2021 - 06:24:13 PDT)
- Re: [AMBER] How do I generate prmtop file for system containing more than 1 ligand? Carlos Simmerling (Wed May 19 2021 - 09:19:40 PDT)
- Re: [AMBER] How do I generate prmtop file for system containing more than 1 ligand? David A Case (Wed May 19 2021 - 10:22:23 PDT)
[AMBER] Compiling Fortran on M1 chipset Joe Leonard (Wed May 19 2021 - 10:11:36 PDT)
[AMBER] Restraints and TI in absolute binding free energies Hans De Winter (Thu May 20 2021 - 03:39:25 PDT)
[AMBER] Covalent bonds across periodic boundaries supported yet/ever? Tucker Burgin (Thu May 20 2021 - 08:58:59 PDT)
- Re: [AMBER] Covalent bonds across periodic boundaries supported yet/ever? David A Case (Wed May 26 2021 - 06:08:31 PDT)
  - Re: [AMBER] Covalent bonds across periodic boundaries supported yet/ever? Matias Machado (Wed May 26 2021 - 13:14:38 PDT)
    - Re: [AMBER] Covalent bonds across periodic boundaries supported yet/ever? Thomas Cheatham (Wed May 26 2021 - 13:27:16 PDT)
[AMBER] AMberTools21 installation Neha Gandhi (Fri May 21 2021 - 23:40:34 PDT)
- Re: [AMBER] AMberTools21 installation Gustaf Olsson (Sun May 23 2021 - 23:33:58 PDT)
  - Re: [AMBER] AMberTools21 installation Neha Gandhi (Mon May 24 2021 - 02:39:55 PDT)
    - Re: [AMBER] AMberTools21 installation Gustaf Olsson (Mon May 24 2021 - 02:59:53 PDT)
    - Re: [AMBER] AMberTools21 installation David A Case (Wed May 26 2021 - 06:12:46 PDT)
[AMBER] Query about AmberTools21 conda distribution David A Case (Sat May 22 2021 - 05:08:08 PDT)
- Re: [AMBER] Query about AmberTools21 conda distribution Jan Brezovsky (Sat May 22 2021 - 08:09:21 PDT)
[AMBER] Clustering getting killed Sruthi Sudhakar (Sat May 22 2021 - 06:43:09 PDT)
- Re: [AMBER] Clustering getting killed Carlos Simmerling (Sat May 22 2021 - 08:18:49 PDT)
- Re: [AMBER] Clustering getting killed Daniel Roe (Sat May 22 2021 - 10:28:07 PDT)
  - Re: [AMBER] Clustering getting killed Daniel Roe (Sat May 22 2021 - 10:29:10 PDT)
[AMBER] distance matrix all atoms Fabian Glaser (Mon May 24 2021 - 06:59:58 PDT)
- Re: [AMBER] distance matrix all atoms Daniel Roe (Mon May 24 2021 - 08:36:02 PDT)
[AMBER] Residue-Ligand binding free energy calculations Rana Rehan Khalid (Mon May 24 2021 - 10:16:05 PDT)
- Re: [AMBER] Residue-Ligand binding free energy calculations Carlos Simmerling (Mon May 24 2021 - 10:20:36 PDT)
  - Re: [AMBER] Residue-Ligand binding free energy calculations Rana Rehan Khalid (Mon May 24 2021 - 10:26:13 PDT)
[AMBER] - Including ion type of interactions in free energy calculation Patil Pranita Uttamrao (Mon May 24 2021 - 22:34:20 PDT)
- Re: [AMBER] - Including ion type of interactions in free energy calculation David A Case (Wed May 26 2021 - 07:27:44 PDT)
[AMBER] - DFT method for heme QM calculation Patil Pranita Uttamrao (Tue May 25 2021 - 01:46:13 PDT)
- Re: [AMBER] - DFT method for heme QM calculation Dawid das (Tue May 25 2021 - 06:30:25 PDT)
[AMBER] Joining two molecules Gustaf Olsson (Tue May 25 2021 - 03:19:30 PDT)
- Re: [AMBER] Joining two molecules Daniel Roe (Tue May 25 2021 - 06:38:51 PDT)
  - Re: [AMBER] Joining two molecules Gustaf Olsson (Wed May 26 2021 - 00:48:40 PDT)
    - Re: [AMBER] Joining two molecules Gustaf Olsson (Wed May 26 2021 - 02:16:47 PDT)
    - Re: [AMBER] Joining two molecules Gustaf Olsson (Wed May 26 2021 - 05:44:56 PDT)
    - Re: [AMBER] Joining two molecules Daniel Roe (Wed May 26 2021 - 06:33:26 PDT)
    - Re: [AMBER] Joining two molecules Gustaf Olsson (Fri May 28 2021 - 01:44:19 PDT)
    - Re: [AMBER] Joining two molecules Daniel Roe (Fri May 28 2021 - 02:34:35 PDT)
    - Re: [AMBER] Joining two molecules Gustaf Olsson (Fri May 28 2021 - 02:47:27 PDT)
    - Re: [AMBER] Joining two molecules Daniel Roe (Fri May 28 2021 - 06:25:09 PDT)
    - Re: [AMBER] Joining two molecules Gustaf Olsson (Mon May 31 2021 - 00:37:12 PDT)
    - Re: [AMBER] Joining two molecules Gustaf Olsson (Mon May 31 2021 - 02:34:18 PDT)
- Re: [AMBER] Joining two molecules Dr. Anselm Horn (Tue May 25 2021 - 07:05:45 PDT)
  - Re: [AMBER] Joining two molecules Gustaf Olsson (Wed May 26 2021 - 00:49:31 PDT)
  - Re: [AMBER] Joining two molecules Gustaf Olsson (Wed May 26 2021 - 00:51:26 PDT)
[AMBER] kindly help with this mmpbsa.py.MPI error Gargi Bhattacharya (Tue May 25 2021 - 03:44:01 PDT)
- Re: [AMBER] kindly help with this mmpbsa.py.MPI error Daniel Roe (Tue May 25 2021 - 06:40:02 PDT)
[AMBER] test message David A Case (Tue May 25 2021 - 05:13:54 PDT)
Re: [AMBER] DFT method for heme QM calculationPranita, Matthew Guberman-Pfeffer (Tue May 25 2021 - 12:26:21 PDT)
- Re: [AMBER] DFT method for heme QM calculationPranita, Robert Molt (Tue May 25 2021 - 12:51:46 PDT)
[AMBER] Umbrella sampling Rana Rehan Khalid (Tue May 25 2021 - 15:00:35 PDT)
- Re: [AMBER] Umbrella sampling David A Case (Wed May 26 2021 - 06:26:59 PDT)
- Re: [AMBER] Umbrella sampling Thomas Cheatham (Wed May 26 2021 - 10:28:24 PDT)
[AMBER] ligand receptor dissociation study Rana Rehan Khalid (Wed May 26 2021 - 09:23:04 PDT)
- Re: [AMBER] ligand receptor dissociation study Song, Lin (Wed May 26 2021 - 09:39:04 PDT)
[AMBER] Umbrella Sampling error Rana Rehan Khalid (Wed May 26 2021 - 14:56:12 PDT)
[AMBER] Seek a solution for can't generate the mol2 files for the metal site residues Huimin Tian (Wed May 26 2021 - 18:33:33 PDT)
- Re: [AMBER] Seek a solution for can't generate the mol2 files for the metal site residues Daniel Roe (Thu May 27 2021 - 06:30:29 PDT)
[AMBER] MMGB/PBSA ligand with lone pair Katia Galentino (Thu May 27 2021 - 01:55:37 PDT)
- Re: [AMBER] MMGB/PBSA ligand with lone pair David A Case (Thu May 27 2021 - 07:12:34 PDT)
[AMBER] A bug in PMEMD which may cause aray (ti_dvdl_values) index out-of-boundary error Ye Mei (Thu May 27 2021 - 17:54:46 PDT)
[AMBER] Fortran runtime error: Ephraim Marondedze (Fri May 28 2021 - 01:13:48 PDT)
- Re: [AMBER] Fortran runtime error: David A Case (Fri May 28 2021 - 07:12:04 PDT)
  - Re: [AMBER] Fortran runtime error: Ephraim Marondedze (Fri May 28 2021 - 23:09:03 PDT)
[AMBER] Simulating dehydrated bilayers with a vacuum above and below Blake Armstrong (Fri May 28 2021 - 01:37:39 PDT)
[AMBER] Regarding the forcefield parameters for cytochrome P450 heme group Patil Pranita Uttamrao (Fri May 28 2021 - 12:39:00 PDT)
- Re: [AMBER] Regarding the forcefield parameters for cytochrome P450 heme group Vaibhav Dixit (Fri May 28 2021 - 22:21:01 PDT)
Re: [AMBER] MULTI_RMSD NFE-Error : Cannot read &colvar namelist! Feng Pan (Fri May 28 2021 - 22:07:57 PDT)
- Re: [AMBER] MULTI_RMSD NFE-Error : Cannot read &colvar namelist! Luis Simon (Sat May 29 2021 - 05:35:39 PDT)
  - Re: [AMBER] MULTI_RMSD NFE-Error : Cannot read &colvar namelist! Feng Pan (Sat May 29 2021 - 11:49:09 PDT)
[AMBER] Umbrella sampling (Protein Receptor--ligand) Rana Rehan Khalid (Sat May 29 2021 - 14:44:39 PDT)
- Re: [AMBER] Umbrella sampling (Protein Receptor--ligand) David A Case (Sun May 30 2021 - 17:31:59 PDT)
[AMBER] Error: Could not open file frcmod.ions1lm_126_hfe_opc: not found Akinyemi Omoniyi (Sat May 29 2021 - 21:39:39 PDT)
- Re: [AMBER] Error: Could not open file frcmod.ions1lm_126_hfe_opc: not found David A Case (Sun May 30 2021 - 05:05:08 PDT)
  - Re: [AMBER] Error: Could not open file frcmod.ions1lm_126_hfe_opc: not found Akinyemi Omoniyi (Sun May 30 2021 - 05:48:57 PDT)
  - Re: [AMBER] Error: Could not open file frcmod.ions1lm_126_hfe_opc: not found Pengfei Li (Wed Jun 09 2021 - 15:52:32 PDT)
[AMBER] APR- Umbrella sampling of Receptor- ligand complex Rana Rehan Khalid (Sun May 30 2021 - 12:38:54 PDT)
- Re: [AMBER] APR- Umbrella sampling of Receptor- ligand complex Niel Henriksen (Mon May 31 2021 - 20:37:49 PDT)
  - Re: [AMBER] APR- Umbrella sampling of Receptor- ligand complex Rana Rehan Khalid (Tue Jun 01 2021 - 09:48:07 PDT)
[AMBER] Error in pca analysis Sruthi Sudhakar (Mon May 31 2021 - 10:21:31 PDT)
- Re: [AMBER] Error in pca analysis Daniel Roe (Tue Jun 01 2021 - 06:03:11 PDT)
  - Re: [AMBER] Error in pca analysis Sruthi Sudhakar (Tue Jun 01 2021 - 06:51:52 PDT)
    - Re: [AMBER] Error in pca analysis Sruthi Sudhakar (Tue Jun 01 2021 - 12:22:59 PDT)
    - Re: [AMBER] Error in pca analysis Daniel Roe (Wed Jun 02 2021 - 11:02:18 PDT)
    - Re: [AMBER] Error in pca analysis Sruthi Sudhakar (Wed Jun 02 2021 - 11:28:57 PDT)
    - Re: [AMBER] Error in pca analysis Sruthi Sudhakar (Fri Jun 11 2021 - 23:41:41 PDT)
    - Re: [AMBER] Error in pca analysis Sruthi Sudhakar (Sat Jun 12 2021 - 14:16:10 PDT)
    - Re: [AMBER] Error in pca analysis Sruthi Sudhakar (Tue Jun 15 2021 - 20:57:22 PDT)
    - Re: [AMBER] Error in pca analysis Daniel Roe (Wed Jun 16 2021 - 06:18:39 PDT)
    - Re: [AMBER] Error in pca analysis Dr. Anselm Horn (Thu Jun 17 2021 - 02:21:40 PDT)
    - Re: [AMBER] Error in pca analysis Sruthi Sudhakar (Thu Jun 17 2021 - 04:22:36 PDT)
    - Re: [AMBER] Error in pca analysis Daniel Roe (Thu Jun 17 2021 - 08:06:12 PDT)
    - Re: [AMBER] Error in pca analysis Sruthi Sudhakar (Thu Jun 17 2021 - 09:06:40 PDT)
    - Re: [AMBER] Error in pca analysis Sruthi Sudhakar (Fri Jun 18 2021 - 23:12:37 PDT)
[AMBER] Identical results from thermodynamics integration runs zz sheng (Tue Jun 01 2021 - 08:43:55 PDT)
- Re: [AMBER] Identical results from thermodynamics integration runs Adrian Roitberg (Tue Jun 01 2021 - 09:06:16 PDT)
  - Re: [AMBER] Identical results from thermodynamics integration runs zz sheng (Tue Jun 01 2021 - 09:14:30 PDT)
[AMBER] radiopt=1 in not working in MMPBSA.py Abdul Basit (Tue Jun 01 2021 - 10:34:41 PDT)
- Re: [AMBER] radiopt=1 in not working in MMPBSA.py Ray Luo (Tue Jun 01 2021 - 11:57:31 PDT)
[AMBER] Nastruct reference file format Robert Molt (Tue Jun 01 2021 - 13:58:12 PDT)
[AMBER] A40 vs A5000 Fabian Glaser (Wed Jun 02 2021 - 05:45:55 PDT)
[AMBER] Running cpptraj in hpc Jenny 148 (Wed Jun 02 2021 - 08:27:13 PDT)
- Re: [AMBER] Running cpptraj in hpc Daniel Roe (Wed Jun 02 2021 - 10:48:40 PDT)
[AMBER] Regarding MMPBSA calculation Rinsha Chk (Wed Jun 02 2021 - 10:42:58 PDT)
- Re: [AMBER] Regarding MMPBSA calculation ABDUL BASIT (Wed Jun 02 2021 - 12:20:38 PDT)
[AMBER] position coordinate precision Lambach, Lauren (Wed Jun 02 2021 - 12:46:46 PDT)
- Re: [AMBER] position coordinate precision Daniel Roe (Wed Jun 02 2021 - 13:06:54 PDT)
  - Re: [AMBER] position coordinate precision Daniel Roe (Wed Jun 02 2021 - 13:09:50 PDT)
    - Re: [AMBER] position coordinate precision Lambach, Lauren (Wed Jun 02 2021 - 14:55:31 PDT)
- Re: [AMBER] position coordinate precision Carlos Simmerling (Wed Jun 02 2021 - 13:40:02 PDT)
[AMBER] gti_add_sc Holly Freedman (Thu Jun 03 2021 - 11:02:56 PDT)
Re: [AMBER] CMAP topology flag skipped Daniel Roe (Fri Jun 04 2021 - 06:20:35 PDT)
- Re: [AMBER] CMAP topology flag skipped Loki (Fri Jun 04 2021 - 07:57:13 PDT)
  - Re: [AMBER] CMAP topology flag skipped Daniel Roe (Fri Jun 11 2021 - 11:40:36 PDT)
- Re: [AMBER] CMAP topology flag skipped Loki (Thu Jun 10 2021 - 02:42:40 PDT)
[AMBER] Nastruct reference file format Robert Molt (Fri Jun 04 2021 - 08:42:27 PDT)
- Re: [AMBER] Nastruct reference file format Daniel Roe (Fri Jun 04 2021 - 10:30:57 PDT)
[AMBER] Query on Rmsd between clusters and population Athena N (Fri Jun 04 2021 - 10:00:06 PDT)
[AMBER] Adding several Helium atoms to a Lipid bilayer structure in AMBER Maghsoud, Yazdan (Fri Jun 04 2021 - 16:12:45 PDT)
- Re: [AMBER] Adding several Helium atoms to a Lipid bilayer structure in AMBER David A Case (Wed Jun 09 2021 - 06:08:40 PDT)
[AMBER] Program received signal SIGSEGV: Segmentation fault - invalid memory reference. Akinyemi Omoniyi (Sat Jun 05 2021 - 06:22:17 PDT)
- Re: [AMBER] Program received signal SIGSEGV: Segmentation fault - invalid memory reference. David A Case (Sat Jun 05 2021 - 09:28:39 PDT)
  - Re: [AMBER] Program received signal SIGSEGV: Segmentation fault - invalid memory reference. Akinyemi Omoniyi (Sat Jun 05 2021 - 15:15:00 PDT)
    - Re: [AMBER] Program received signal SIGSEGV: Segmentation fault - invalid memory reference. David A Case (Sun Jun 06 2021 - 05:18:44 PDT)
[AMBER] Possible impact of cryptomining limitations on new NVidia GPUs on pmemd performances Pietro Amodeo (Sun Jun 06 2021 - 01:28:40 PDT)
[AMBER] How to fix the numbering of amino acid that got shifted in topology file that created in amber Tleap priya murugan (Sun Jun 06 2021 - 21:11:34 PDT)
- Re: [AMBER] How to fix the numbering of amino acid that got shifted in topology file that created in amber Tleap Dr. Anselm Horn (Mon Jun 07 2021 - 00:42:34 PDT)
  - Re: [AMBER] How to fix the numbering of amino acid that got shifted in topology file that created in amber Tleap David A Case (Mon Jun 07 2021 - 04:46:50 PDT)
    - Re: [AMBER] How to fix the numbering of amino acid that got shifted in topology file that created in amber Tleap Daniel Roe (Mon Jun 07 2021 - 07:10:00 PDT)
    - [AMBER] Question about ff14SB parameters/atom types for TYR Dr. Anselm Horn (Tue Jun 08 2021 - 02:56:36 PDT)
    - Re: [AMBER] Question about ff14SB parameters/atom types for TYR Carlos Simmerling (Tue Jun 08 2021 - 11:19:30 PDT)
[AMBER] [MCPB.py]_KeyError: 'HZ2' sabrine kh (Mon Jun 07 2021 - 04:59:00 PDT)
- Re: [AMBER] [MCPB.py]_KeyError: 'HZ2' Pengfei Li (Tue Jun 08 2021 - 19:14:26 PDT)
[AMBER] What does the UVV file output for a LJ only system and why cant I recreate it? Daniel Fowles (Mon Jun 07 2021 - 04:59:26 PDT)
- Re: [AMBER] What does the UVV file output for a LJ only system and why cant I recreate it? David A Case (Wed Jun 09 2021 - 05:59:07 PDT)
[AMBER] [MCPB.py]_KeyError: 'HZ3' sabrine kh (Mon Jun 07 2021 - 05:03:25 PDT)
- Re: [AMBER] [MCPB.py]_KeyError: 'HZ3' Gustaf Olsson (Mon Jun 07 2021 - 05:26:57 PDT)
  - Re: [AMBER] [MCPB.py]_KeyError: 'HZ3' sabrine kh (Mon Jun 07 2021 - 08:40:48 PDT)
    - Re: [AMBER] [MCPB.py]_KeyError: 'HZ3' sabrine kh (Tue Jun 08 2021 - 06:16:42 PDT)
    - Re: [AMBER] [MCPB.py]_KeyError: 'HZ3' Gustaf Olsson (Tue Jun 08 2021 - 06:46:26 PDT)
[AMBER] knlskintest error when using HMR with 4fs Neville Bethel (Mon Jun 07 2021 - 09:48:53 PDT)
- Re: [AMBER] knlskintest error when using HMR with 4fs David A Case (Mon Jun 07 2021 - 11:47:40 PDT)
- Re: [AMBER] knlskintest error when using HMR with 4fs Neville Bethel (Thu Jun 10 2021 - 15:30:47 PDT)
[AMBER] NAB superimpose issue Mandar Kulkarni (Mon Jun 07 2021 - 14:52:04 PDT)
- Re: [AMBER] NAB superimpose issue David A Case (Tue Jun 08 2021 - 10:07:03 PDT)
  - Re: [AMBER] NAB superimpose issue Mandar Kulkarni (Thu Jun 10 2021 - 02:07:38 PDT)
    - Re: [AMBER] NAB superimpose issue David A Case (Thu Jun 10 2021 - 05:56:38 PDT)
    - Re: [AMBER] NAB superimpose issue Mandar Kulkarni (Thu Jun 10 2021 - 06:39:43 PDT)
    - Re: [AMBER] NAB superimpose issue Mandar Kulkarni (Thu Jun 10 2021 - 13:44:55 PDT)
    - Re: [AMBER] NAB superimpose issue David A Case (Fri Jun 11 2021 - 06:44:42 PDT)
    - Re: [AMBER] NAB superimpose issue Mandar Kulkarni (Sat Jun 12 2021 - 02:01:24 PDT)
[AMBER] Pressure tensor components in the GPU code. James Moraes de Almeida (Mon Jun 07 2021 - 15:06:23 PDT)
[AMBER] Error in calculating pair distribution function Umesh Roy (Mon Jun 07 2021 - 21:11:42 PDT)
[AMBER] Incomplete trajectory due to calculation halted error Razil Tahir (Tue Jun 08 2021 - 12:07:35 PDT)
- Re: [AMBER] Incomplete trajectory due to calculation halted error David A Case (Wed Jun 09 2021 - 05:48:59 PDT)
[AMBER] tleap error creating prmtop file Vaibhav Dixit (Wed Jun 09 2021 - 03:17:00 PDT)
- Re: [AMBER] tleap error creating prmtop file Carlos Simmerling (Wed Jun 09 2021 - 04:10:44 PDT)
[AMBER] Error in pdb4amber for AmberTools21 Bhattacharjee, Sinjini (Wed Jun 09 2021 - 06:26:09 PDT)
- Re: [AMBER] Error in pdb4amber for AmberTools21 David A Case (Wed Jun 09 2021 - 07:13:16 PDT)
[AMBER] Pressure tensor components in the GPU code. James Almeida (Wed Jun 09 2021 - 06:36:21 PDT)
[AMBER] pKa Calculation using PMEMD Monika Pareek (Wed Jun 09 2021 - 23:07:14 PDT)
- Re: [AMBER] pKa Calculation using PMEMD David A Case (Thu Jun 10 2021 - 05:06:47 PDT)
[AMBER] Some Problems by using NAB of AmberTools21 to model Circle-DNA 韩正威 (Thu Jun 10 2021 - 00:17:05 PDT)
- Re: [AMBER] Some Problems by using NAB of AmberTools21 to model Circle-DNA David A Case (Thu Jun 10 2021 - 05:44:54 PDT)
[AMBER] The code for modeling circular DNA is in the attachment 韩正威 (Thu Jun 10 2021 - 00:19:35 PDT)
[AMBER] TypeError: %c requires int or char Computational Chemistry (Thu Jun 10 2021 - 06:20:43 PDT)
- Re: [AMBER] TypeError: %c requires int or char David A Case (Thu Jun 10 2021 - 07:17:19 PDT)
- Re: [AMBER] TypeError: %c requires int or char Bhattacharjee, Sinjini (Thu Jun 10 2021 - 07:31:55 PDT)
[AMBER] an illegal memory access Reza Esmaeeli (Thu Jun 10 2021 - 07:12:48 PDT)
- Re: [AMBER] an illegal memory access David A Case (Thu Jun 10 2021 - 13:00:08 PDT)
[AMBER] To increase timesteps in MD simulations Syeda Amna Arshi (Thu Jun 10 2021 - 08:05:16 PDT)
- Re: [AMBER] To increase timesteps in MD simulations Carlos Simmerling (Thu Jun 10 2021 - 08:51:03 PDT)
[AMBER] Norleucine in ff99sb_ildn? Kenneth Huang (Thu Jun 10 2021 - 11:02:47 PDT)
- Re: [AMBER] Norleucine in ff99sb_ildn? David A Case (Thu Jun 10 2021 - 13:05:44 PDT)
[AMBER] how does amber calculate the water bridge fraction Ming Tang (Fri Jun 11 2021 - 02:47:02 PDT)
- Re: [AMBER] how does amber calculate the water bridge fraction Daniel Roe (Fri Jun 11 2021 - 10:48:18 PDT)
  - Re: [AMBER] how does amber calculate the water bridge fraction Ming Tang (Fri Jun 11 2021 - 16:27:16 PDT)
[AMBER] strange tleap error with bond command Vaibhav Dixit (Fri Jun 11 2021 - 23:01:45 PDT)
- Re: [AMBER] strange tleap error with bond command David A Case (Sun Jun 13 2021 - 18:37:14 PDT)
  - Re: [AMBER] strange tleap error with bond command Vaibhav Dixit (Sun Jun 13 2021 - 22:01:25 PDT)
[AMBER] query on principal component analysis trajectory Sruthi Sudhakar (Fri Jun 11 2021 - 23:53:33 PDT)
[AMBER] Problem of running a simulation in A100 GPU server. Jong Young Joung (Sun Jun 13 2021 - 06:36:48 PDT)
- Re: [AMBER] Problem of running a simulation in A100 GPU server. David A Case (Sun Jun 13 2021 - 18:47:17 PDT)
[AMBER] use QUICK for QM/MM simulation accelerated by gpu wangjianing_mail (Sun Jun 13 2021 - 08:23:40 PDT)
- Re: [AMBER] use QUICK for QM/MM simulation accelerated by gpu wangjianing_mail (Sun Jun 13 2021 - 09:07:34 PDT)
[AMBER] Which gpu should I select between tesla k80 and RTX30 series 东不拉 (Mon Jun 14 2021 - 06:34:06 PDT)
- Re: [AMBER] Which gpu should I select between tesla k80 and RTX30 series Adrian Roitberg (Mon Jun 14 2021 - 07:50:03 PDT)
  - Re: [AMBER] Which gpu should I select between tesla k80 and RTX30 series Ross Walker (Mon Jun 14 2021 - 09:27:53 PDT)
[AMBER] mmgbsa results raissa.conceicao.bol.com.br (Mon Jun 14 2021 - 12:50:33 PDT)
[AMBER] Amber20 5 times slower than Amber18? Yu Chen (Mon Jun 14 2021 - 14:08:12 PDT)
- Re: [AMBER] Amber20 5 times slower than Amber18? David A Case (Tue Jun 15 2021 - 06:02:19 PDT)
  - Re: [AMBER] Amber20 5 times slower than Amber18? Yu Chen (Tue Jun 15 2021 - 12:23:49 PDT)
[AMBER] Restart the crashed MD run in Amber18 Amir Zeb (Mon Jun 14 2021 - 23:42:47 PDT)
- Re: [AMBER] Restart the crashed MD run in Amber18 David A Case (Tue Jun 15 2021 - 06:05:14 PDT)
  - Re: [AMBER] Restart the crashed MD run in Amber18 Amir Zeb (Tue Jun 15 2021 - 18:03:07 PDT)
    - Re: [AMBER] Restart the crashed MD run in Amber18 David A Case (Wed Jun 16 2021 - 06:00:52 PDT)
    - Re: [AMBER] Restart the crashed MD run in Amber18 Amir Zeb (Thu Jun 17 2021 - 18:04:39 PDT)
    - Re: [AMBER] Restart the crashed MD run in Amber18 David A Case (Fri Jun 18 2021 - 05:10:10 PDT)
    - Re: [AMBER] Restart the crashed MD run in Amber18 Amir Zeb (Sun Jun 20 2021 - 17:54:47 PDT)
[AMBER] Fluctuation in GPU usage Aravind R (Tue Jun 15 2021 - 10:34:45 PDT)
- Re: [AMBER] Fluctuation in GPU usage Ross Walker (Tue Jun 15 2021 - 10:52:10 PDT)
[AMBER] Execution Trouble ankita mehta (Tue Jun 15 2021 - 20:04:29 PDT)
- Re: [AMBER] Execution Trouble David A Case (Wed Jun 16 2021 - 05:46:01 PDT)
  - Re: [AMBER] Execution Trouble ankita mehta (Thu Jun 17 2021 - 20:07:40 PDT)
    - Re: [AMBER] Execution Trouble David A Case (Fri Jun 18 2021 - 05:13:11 PDT)
[AMBER] issues in non-bonded and bonded force parameters Dr. Srinivasa B. Ramisetti (Wed Jun 16 2021 - 02:58:54 PDT)
[AMBER] cpptraj align using the same numbering Martin Rosellen (Wed Jun 16 2021 - 04:09:09 PDT)
- Re: [AMBER] cpptraj align using the same numbering David A Case (Wed Jun 16 2021 - 05:55:05 PDT)
  - Re: [AMBER] cpptraj align using the same numbering Daniel Roe (Wed Jun 16 2021 - 06:23:08 PDT)
    - Re: [AMBER] cpptraj align using the same numbering Martin Rosellen (Wed Jun 16 2021 - 09:05:42 PDT)
    - Re: [AMBER] cpptraj align using the same numbering Daniel Roe (Wed Jun 16 2021 - 12:15:34 PDT)
[AMBER] Can not locate tordef.lib file Souvik Dey (Wed Jun 16 2021 - 16:28:31 PDT)
[AMBER] Calculation of ligand restraints in TI Josiah Bones (Wed Jun 16 2021 - 18:13:46 PDT)
[AMBER] compilation error jamal kazazi (Wed Jun 16 2021 - 22:36:40 PDT)
[AMBER] issues with non-bonded and bonded force field parameterisation for Arsenic Dr. Srinivasa B. Ramisetti (Wed Jun 16 2021 - 22:45:06 PDT)
- Re: [AMBER] issues with non-bonded and bonded force field parameterisation for Arsenic Pengfei Li (Thu Jun 17 2021 - 15:21:59 PDT)
[AMBER] Amber20 installation, Amber.pip file broken Balogh Álex Kálmán (Thu Jun 17 2021 - 01:34:45 PDT)
- Re: [AMBER] Amber20 installation, Amber.pip file broken aishen (Thu Jun 17 2021 - 09:11:14 PDT)
  - Re: [AMBER] Amber20 installation, Amber.pip file broken jamal kazazi (Thu Jun 17 2021 - 09:55:05 PDT)
[AMBER] use QUICK for QM/MM simulation accelerated by gpu wangjianing_mail (Thu Jun 17 2021 - 03:37:40 PDT)
[AMBER] TI for inclusion complexes Eduardo R. Almeida (Thu Jun 17 2021 - 06:27:28 PDT)
[AMBER] issues with non-bonded and bonded force field parameterisation for Arsenic Srinivasa Ramisetti (Thu Jun 17 2021 - 07:52:26 PDT)
[AMBER] error with solvate.sh at remove command tleap Vaibhav Dixit (Thu Jun 17 2021 - 10:23:52 PDT)
- Re: [AMBER] error with solvate.sh at remove command tleap Vaibhav Dixit (Fri Jun 18 2021 - 02:07:45 PDT)
  - Re: [AMBER] error with solvate.sh at remove command tleap Daniel Roe (Sun Jun 20 2021 - 07:14:39 PDT)
- Re: [AMBER] error with solvate.sh at remove command tleap David A Case (Fri Jun 18 2021 - 05:02:21 PDT)
  - Re: [AMBER] error with solvate.sh at remove command tleap Vaibhav Dixit (Fri Jun 18 2021 - 06:12:37 PDT)
[AMBER] Fw: [josiah.bones.anu.edu.au: Calculation of ligand restraints in TI] Josiah Bones (Thu Jun 17 2021 - 15:08:33 PDT)
[AMBER] Absolute Binding Free Energy of Protein+Ligand Complex in AMBER20 - Boresch restraints, Smoothstep Josiah Bones (Thu Jun 17 2021 - 23:29:58 PDT)
- Re: [AMBER] Absolute Binding Free Energy of Protein+Ligand Complex in AMBER20 - Boresch restraints, Smoothstep Dickson, Callum (Fri Jun 18 2021 - 07:48:02 PDT)
[AMBER] install Amber20 GPU Centos 7 Sebastian Brickel (Fri Jun 18 2021 - 02:30:20 PDT)
- Re: [AMBER] install Amber20 GPU Centos 7 David A Case (Fri Jun 18 2021 - 05:22:30 PDT)
[AMBER] RMSD plot in ns Sadaf Rani (Sun Jun 20 2021 - 04:58:20 PDT)
- Re: [AMBER] RMSD plot in ns Reza Esmaeeli (Sun Jun 20 2021 - 05:10:06 PDT)
- Re: [AMBER] RMSD plot in ns Daniel Roe (Sun Jun 20 2021 - 07:22:25 PDT)
  - Re: [AMBER] RMSD plot in ns Dr. Anselm Horn (Mon Jun 21 2021 - 00:11:27 PDT)
[AMBER] Installation error AMBERTOOLS21 Mandar Kulkarni (Sun Jun 20 2021 - 05:22:22 PDT)

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